Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold165.1
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: 1724686
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 30232 characters in sequence are not A, C, G, or T
File 4 of 8
Found at i:829679 original size:4 final size:4
Alignment explanation
Indices: 829670--829698 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
829660 ACGAGTGTGT
829670 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
829699 CATGACCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:829920 original size:9 final size:9
Alignment explanation
Indices: 829890--829965 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
829880 ATTCGAATAT
829890 ATATATAAA
1 ATATATAAA
*
829899 TTAT-TAAA
1 ATATATAAA
*
829907 AAATATATAA
1 ATATATA-AA
829917 A-ATAT-AA
1 ATATATAAA
* * *
829924 TTATTTTAA
1 ATATATAAA
*
829933 ATTTATAAA
1 ATATATAAA
829942 ATATATAAAA
1 ATATAT-AAA
829952 ATATATAAA
1 ATATATAAA
829961 ATATA
1 ATATA
829966 ATTATTAAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
7 2 0.04
8 9 0.17
9 29 0.56
10 12 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
ATATATAAA
Found at i:829979 original size:24 final size:24
Alignment explanation
Indices: 829892--829988 Score: 100
Period size: 24 Copynumber: 4.2 Consensus size: 24
829882 TCGAATATAT
*
829892 ATATAAATTATTAAAAAATATATAAA
1 ATAT-AATTATT-AAATATATATAAA
829918 ATATAATTATTTTAAAT-T-TATAAA
1 ATATAATTA--TTAAATATATATAAA
829942 ATAT-A-TA--AAA-ATATATAAA
1 ATATAATTATTAAATATATATAAA
829961 ATATAATTATTAAATATATATAAA
1 ATATAATTATTAAATATATATAAA
829985 ATAT
1 ATAT
829989 TGATTTGGTT
Statistics
Matches: 61, Mismatches: 1, Indels: 20
0.74 0.01 0.24
Matches are distributed among these distances:
18 4 0.07
19 10 0.16
20 1 0.02
21 2 0.03
22 2 0.03
23 4 0.07
24 23 0.38
25 6 0.10
26 7 0.11
27 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATAATTATTAAATATATATAAA
Found at i:829983 original size:43 final size:44
Alignment explanation
Indices: 829888--829989 Score: 149
Period size: 43 Copynumber: 2.4 Consensus size: 44
829878 ATATTCGAAT
*
829888 ATATATATAAATTATTAAAAAATATATAAAATATAATTATTTTAA
1 ATATATATAAAATATTAAAAAATATATAAAATATAATTA-TTTAA
829933 AT-T-TATAAAATA-TATAAAAATATATAAAATATAATTA-TTAA
1 ATATATATAAAATATTA-AAAAATATATAAAATATAATTATTTAA
829974 ATATATATAAAATATT
1 ATATATATAAAATATT
829990 GATTTGGTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
41 6 0.12
42 3 0.06
43 39 0.75
44 2 0.04
45 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (44 bp):
ATATATATAAAATATTAAAAAATATATAAAATATAATTATTTAA
Found at i:831251 original size:13 final size:14
Alignment explanation
Indices: 831227--831255 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
831217 TTAATGTTAG
831227 TTTAATTTTTAATT
1 TTTAATTTTTAATT
831241 TTTAA-TTTTAATT
1 TTTAATTTTTAATT
831254 TT
1 TT
831256 AAGACTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTAATTTTTAATT
Found at i:831257 original size:6 final size:7
Alignment explanation
Indices: 831227--831255 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
831217 TTAATGTTAG
831227 TTTAATT
1 TTTAATT
831234 TTTAATT
1 TTTAATT
831241 TTTAA-T
1 TTTAATT
831247 TTTAATT
1 TTTAATT
831254 TT
1 TT
831256 AAGACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTAATT
Found at i:831337 original size:19 final size:19
Alignment explanation
Indices: 831309--831348 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
831299 TTTTAAAAAA
*
831309 TTATGATTTT-TAATTATT
1 TTATGATTTTGTAATAATT
831327 TTATAGATTTTGTAATAATT
1 TTAT-GATTTTGTAATAATT
831347 TT
1 TT
831349 GAGCCTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 6 0.32
20 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TTATGATTTTGTAATAATT
Found at i:838608 original size:18 final size:18
Alignment explanation
Indices: 838580--838628 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
838570 TTATAATATT
838580 ATTTTTAAAATTTAAATAA
1 ATTTTT-AAATTTAAATAA
838599 ATTTTTAAATTTAAATAA
1 ATTTTTAAATTTAAATAA
838617 ATTTTTAAATTT
1 ATTTTTAAATTT
838629 TTAAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 24 0.80
19 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTTAAATTTAAATAA
Found at i:838609 original size:8 final size:8
Alignment explanation
Indices: 838596--838636 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
838586 AAAATTTAAA
838596 TAAATTTT
1 TAAATTTT
*
838604 TAAATTTAAA
1 TAAATTT--T
838614 TAAATTTT
1 TAAATTTT
838622 TAAATTTT
1 TAAATTTT
838630 TAAATTT
1 TAAATTT
838637 AAATATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 22 0.76
10 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TAAATTTT
Found at i:838627 original size:26 final size:27
Alignment explanation
Indices: 838596--838661 Score: 98
Period size: 26 Copynumber: 2.4 Consensus size: 27
838586 AAAATTTAAA
838596 TAAATTTTTAAATTTAAATA-AATTTT
1 TAAATTTTTAAATTTAAATATAATTTT
*
838622 TAAATTTTTAAATTTAAATATTATTTTT
1 TAAATTTTTAAATTTAAATA-TAATTTT
*
838650 TAAATTTATAAA
1 TAAATTTTTAAA
838662 ATATTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
26 20 0.56
28 16 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TAAATTTTTAAATTTAAATATAATTTT
Found at i:838632 original size:45 final size:44
Alignment explanation
Indices: 838580--838670 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 44
838570 TTATAATATT
*
838580 ATTTTTAAAATTTAAATA-AATTTTTAAATTTAAATAAATTTTTAA
1 ATTTTT-AAATTTAAATATAATTTTTAAATTTAAA-AAATATTTAA
* *
838625 ATTTTTAAATTTAAATATTATTTTTTAAATTTATAAAATATTTAA
1 ATTTTTAAATTTAAATA-TAATTTTTAAATTTAAAAAATATTTAA
838670 A
1 A
838671 AATATATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
44 11 0.27
45 16 0.39
46 14 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (44 bp):
ATTTTTAAATTTAAATATAATTTTTAAATTTAAAAAATATTTAA
Found at i:838666 original size:20 final size:20
Alignment explanation
Indices: 838569--838667 Score: 69
Period size: 20 Copynumber: 4.7 Consensus size: 20
838559 TTTGAAATGT
* *
838569 TTTATAATATTATTTTTAAAA
1 TTTA-AATAATATTTTTTAAA
838590 TTTAAATAA-A-TTTTTAAA
1 TTTAAATAATATTTTTTAAA
*
838608 TTTAAATAAATTTTTAAATTTTTAAA
1 TTTAAAT-AA----T-ATTTTTTAAA
*
838634 TTTAAATATTATTTTTTAAA
1 TTTAAATAATATTTTTTAAA
838654 TTTATAA-AATATTT
1 TTTA-AATAATATTT
838668 AAAAATATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 19
0.73 0.06 0.22
Matches are distributed among these distances:
18 14 0.22
19 3 0.05
20 23 0.36
21 7 0.11
25 2 0.03
26 15 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAAATAATATTTTTTAAA
Found at i:838800 original size:16 final size:16
Alignment explanation
Indices: 838767--838823 Score: 84
Period size: 15 Copynumber: 3.7 Consensus size: 16
838757 TTTTAAAAAA
838767 TTTAAA-TA-TAATTTT
1 TTTAAATTATTAA-TTT
838782 TTTAAATTATTAATTT
1 TTTAAATTATTAATTT
838798 TTTAAATTATTAA-TT
1 TTTAAATTATTAATTT
838813 TTTAAATTATT
1 TTTAAATTATT
838824 TTTAAAGATA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.47
16 18 0.45
17 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAATTATTAATTT
Found at i:838894 original size:14 final size:14
Alignment explanation
Indices: 838877--838944 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
838867 TAAAAAATAA
838877 ATTTTCTAATATAT
1 ATTTTCTAATATAT
*
838891 ATTTTCAAAT-TAT
1 ATTTTCTAATATAT
* * *
838904 TTTTTAATATATATAA
1 ATTTT-CTA-ATATAT
838920 ATTTTCTAATATAT
1 ATTTTCTAATATAT
838934 ATTTT-TAATAT
1 ATTTTCTAATAT
838945 TTTTTATCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 13 0.30
14 20 0.47
15 4 0.09
16 6 0.14
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTCTAATATAT
Found at i:838909 original size:41 final size:39
Alignment explanation
Indices: 838864--838960 Score: 122
Period size: 43 Copynumber: 2.4 Consensus size: 39
838854 ATATATAAAA
838864 TTTTAAAAAATAAATTTTCTAATATATATTTTCAAATTATT
1 TTTTAAAAAATAAATTTTCTAATATATATTTT-AAA-TATT
* *
838905 TTTTAATATATATAAATTTTCTAATATATATTTTTAATATT
1 TTTTAA-A-AAATAAATTTTCTAATATATATTTTAAATATT
**
838946 TTTTATCAAATAAAT
1 TTTTAAAAAATAAAT
838961 CATTTTTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 7 0.14
41 15 0.31
42 3 0.06
43 24 0.49
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (39 bp):
TTTTAAAAAATAAATTTTCTAATATATATTTTAAATATT
Found at i:838917 original size:29 final size:31
Alignment explanation
Indices: 838885--838944 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
838875 AAATTTTCTA
*
838885 ATATATATTTTCAAAT-TAT-TTTTTAATAT
1 ATATAAATTTTCAAATATATATTTTTAATAT
*
838914 ATATAAATTTTCTAATATATATTTTTAATAT
1 ATATAAATTTTCAAATATATATTTTTAATAT
838945 TTTTTATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 14 0.52
30 3 0.11
31 10 0.37
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (31 bp):
ATATAAATTTTCAAATATATATTTTTAATAT
Found at i:838993 original size:26 final size:26
Alignment explanation
Indices: 838942--839010 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 26
838932 ATATTTTTAA
*
838942 TATTTTTTATCAAATAAATCATTTTT
1 TATTTTTTATCAAATAAATCAATTTT
* *
838968 TATTTTTT-TCCAATCAATTCAATTTT
1 TATTTTTTATCAAAT-AAATCAATTTT
* * *
838994 CACTTTTTCT-AAATAAA
1 TATTTTTTATCAAATAAA
839011 ATATTATTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
25 7 0.21
26 26 0.76
27 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTTTTTATCAAATAAATCAATTTT
Found at i:839143 original size:112 final size:110
Alignment explanation
Indices: 839019--839218 Score: 285
Period size: 111 Copynumber: 1.8 Consensus size: 110
839009 AAATATTATT
* * *
839019 TTTTTAAATTTTAAATATAATTTAAAAAACGTTTGAATATCTATAAAAATATTTTTAAAAAATCA
1 TTTTTAAATTTTAAATAGAATTT-AAAAACGTTTGAATATATATAAAAATAATTTTAAAAAATCA
*
839084 TAA-TTTAATAAAAGTATATTTAAAATTTAAAAAACATAATTTTTTAC
65 TAATTTTAA-AAAAATA-ATTTAAAATTTAAAAAACATAATTTTTTAC
**** *
839131 TTTTTAAATTTTAAATAGAATTTAAATTTTTTTGAATATATTTAAAAATAATTTTAAAAAATCAT
1 TTTTTAAATTTTAAATAGAATTTAAAAACGTTTGAATATATATAAAAATAATTTTAAAAAATCAT
839196 AATTTTAAAAAAATAATTTAAAA
66 AATTTTAAAAAAATAATTTAAAA
839219 AAATATATTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
110 8 0.10
111 43 0.55
112 27 0.35
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (110 bp):
TTTTTAAATTTTAAATAGAATTTAAAAACGTTTGAATATATATAAAAATAATTTTAAAAAATCAT
AATTTTAAAAAAATAATTTAAAATTTAAAAAACATAATTTTTTAC
Found at i:839192 original size:13 final size:14
Alignment explanation
Indices: 839174--839232 Score: 77
Period size: 14 Copynumber: 4.1 Consensus size: 14
839164 GAATATATTT
839174 AAAAATAATTTTAA
1 AAAAATAATTTTAA
839188 AAAATCATAATTTTAA
1 AAAA--ATAATTTTAA
839204 AAAAATAA-TTTAA
1 AAAAATAATTTTAA
839217 AAAAAT-ATATTTAA
1 AAAAATAAT-TTTAA
839231 AA
1 AA
839233 TTAAAAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.02
13 11 0.27
14 15 0.37
16 14 0.34
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAAATAATTTTAA
Found at i:839208 original size:17 final size:16
Alignment explanation
Indices: 839178--839222 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
839168 ATATTTAAAA
839178 ATAATTTTAAAAAATC
1 ATAATTTTAAAAAATC
839194 ATAATTTTAAAAAA--
1 ATAATTTTAAAAAATC
*
839208 ATAATTTAAAAAAAT
1 ATAATTTTAAAAAAT
839223 ATATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.48
16 14 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATTTTAAAAAATC
Found at i:839239 original size:21 final size:22
Alignment explanation
Indices: 839210--839269 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 22
839200 TTAAAAAAAT
*
839210 AATTTAAAAAAATATATTTA-A
1 AATTAAAAAAAATATATTTATA
*
839231 AATTAAAAAATATATATTTATA
1 AATTAAAAAAAATATATTTATA
839253 ATATTATAAAACAAATA
1 A-ATTA-AAAA-AAATA
839270 ATAAATTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 18 0.56
22 2 0.06
23 4 0.12
24 4 0.12
25 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTAAAAAAAATATATTTATA
Found at i:839258 original size:23 final size:22
Alignment explanation
Indices: 839208--839263 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 22
839198 TTTTAAAAAA
839208 ATAAT-TTAAAAAAATATATTT
1 ATAATATTAAAAAAATATATTT
839229 A-AA-ATTAAAAAATATATATTT
1 ATAATATTAAAAAA-ATATATTT
*
839250 ATAATATTATAAAA
1 ATAATATTAAAAAA
839264 CAAATAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
20 10 0.33
21 10 0.33
22 2 0.07
23 8 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATATTAAAAAAATATATTT
Found at i:839350 original size:31 final size:34
Alignment explanation
Indices: 839288--839350 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
839278 GAAAGGTCAT
* *
839288 ATATTTAAAAATAATTTATTTTAAATATTTTATA
1 ATATTAAAAAATAATTTATTTAAAATATTTTATA
839322 ATATTAAAAAATAA-TT-TTTAAAAT-TTTTA
1 ATATTAAAAAATAATTTATTTAAAATATTTTA
839351 AAAATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 5 0.19
32 7 0.26
33 2 0.07
34 13 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
ATATTAAAAAATAATTTATTTAAAATATTTTATA
Found at i:839352 original size:23 final size:23
Alignment explanation
Indices: 839321--839385 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
839311 AATATTTTAT
*
839321 AATA-TTAAAAAATAATTTTTAA
1 AATATTTAAAAAATAATTTATAA
*
839343 AAT-TTTTAAAAATAATATTATAA
1 AATATTTAAAAAATAAT-TTATAA
*
839366 AATATTTAAAATATACATTT
1 AATATTTAAAAAATA-ATTT
839386 CAGATTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 14 0.40
23 8 0.23
24 11 0.31
25 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATATTTAAAAAATAATTTATAA
Found at i:839353 original size:22 final size:22
Alignment explanation
Indices: 839321--839385 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
839311 AATATTTTAT
* *
839321 AATATTAAAAAATAATTTTTAA
1 AATATTTAAAAATAATTTATAA
*
839343 AATTTTTAAAAATAATATTATAA
1 AATATTTAAAAATAAT-TTATAA
839366 AATATTTAAAATATACATTT
1 AATATTTAAAA-ATA-ATTT
839386 CAGATTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.39
23 15 0.42
24 5 0.14
25 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATTTAAAAATAATTTATAA
Found at i:839429 original size:24 final size:25
Alignment explanation
Indices: 839402--839467 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
839392 TTATAAAATC
*
839402 AATAATAAACAAATAAATAAA-TAA
1 AATAATAAACAAATAAAAAAATTAA
*
839426 AATAA-AGGACAAATAAAAAAATTAA
1 AATAATA-AACAAATAAAAAAATTAA
* *
839451 AAT-GTAAATAAATAAAA
1 AATAATAAACAAATAAAA
839468 GAAAAACAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.03
24 26 0.76
25 7 0.21
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.20
Consensus pattern (25 bp):
AATAATAAACAAATAAAAAAATTAA
Found at i:845162 original size:7 final size:7
Alignment explanation
Indices: 845150--845190 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
845140 ATGTGAAGTT
845150 GTTTATG
1 GTTTATG
845157 GTTTATG
1 GTTTATG
845164 GTTTATG
1 GTTTATG
845171 GTTTATG
1 GTTTATG
*
845178 ATTTATG
1 GTTTATG
*
845185 ATTTAT
1 GTTTAT
845191 TAAACTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.59
Consensus pattern (7 bp):
GTTTATG
Found at i:853885 original size:45 final size:45
Alignment explanation
Indices: 853834--853928 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 45
853824 TACGTGATTC
* *
853834 TTTTTAT-ATT-TTTT-ATATTTTTTAAAGTATATATAATTTTTGGAA
1 TTTTTATAATTATTTTGA-ATTTTTGAAAAT-TAT-TAATTTTTGGAA
* *
853879 TTTTTATAATTATTTTGAATTTTTGAAAATTATTACTTTTTGTAA
1 TTTTTATAATTATTTTGAATTTTTGAAAATTATTAATTTTTGGAA
853924 TTTTT
1 TTTTT
853929 GTTGAGAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
45 22 0.51
46 6 0.14
47 14 0.33
48 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.63
Consensus pattern (45 bp):
TTTTTATAATTATTTTGAATTTTTGAAAATTATTAATTTTTGGAA
Found at i:853886 original size:18 final size:19
Alignment explanation
Indices: 853865--853912 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
853855 TTAAAGTATA
853865 TATAATT-TTTGGAATTTT
1 TATAATTATTTGGAATTTT
*
853883 TATAATTATTTTGAATTTT
1 TATAATTATTTGGAATTTT
*
853902 TGAAAATTATT
1 T-ATAATTATT
853913 ACTTTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 7 0.27
19 11 0.42
20 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TATAATTATTTGGAATTTT
Found at i:853894 original size:20 final size:20
Alignment explanation
Indices: 853871--853912 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
853861 TATATATAAT
*
853871 TTTTGGAATTTTT-ATAATTA
1 TTTT-GAATTTTTGAAAATTA
853891 TTTTGAATTTTTGAAAATTA
1 TTTTGAATTTTTGAAAATTA
853911 TT
1 TT
853913 ACTTTTTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (20 bp):
TTTTGAATTTTTGAAAATTA
Found at i:871462 original size:33 final size:33
Alignment explanation
Indices: 871401--871479 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
871391 CTCCTCCTCC
*
871401 TCCTCCTCTTCAT-CA--TCATCATCGTCATCT
1 TCCTCCTCTTCATCCACCTCATAATCGTCATCT
* * * *
871431 TCTTCTTCTTCCTCCACCTCATAATCTTCATCT
1 TCCTCCTCTTCATCCACCTCATAATCGTCATCT
871464 TCCTCCTCTTCATCCA
1 TCCTCCTCTTCATCCA
871480 ATACAATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
30 10 0.26
31 2 0.05
33 26 0.68
ACGTcount: A:0.15, C:0.42, G:0.01, T:0.42
Consensus pattern (33 bp):
TCCTCCTCTTCATCCACCTCATAATCGTCATCT
Found at i:879529 original size:31 final size:31
Alignment explanation
Indices: 879463--879530 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
879453 AGCCCCAATG
* * *
879463 TGAGAACAATTGCCTAGTTCAAGTCTGACTA
1 TGAGAACAATTGCCAAGTTCAAGGCTAACTA
* *
879494 TGAGAATAATTGTCAAGTTCAAGGGCTAACT-
1 TGAGAACAATTGCCAAGTTCAA-GGCTAACTA
879525 TGAGAA
1 TGAGAA
879531 AAAAAGTGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 25 0.81
32 6 0.19
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (31 bp):
TGAGAACAATTGCCAAGTTCAAGGCTAACTA
Found at i:889842 original size:11 final size:10
Alignment explanation
Indices: 889826--889877 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
889816 ATAAATACAT
889826 AAAAAAGTAAA
1 AAAAAAG-AAA
*
889837 AAAAAAGCAA
1 AAAAAAGAAA
*
889847 AAAATAGAAA
1 AAAAAAGAAA
*
889857 AAATAAATAAA
1 AAA-AAAGAAA
*
889868 AAAGAAGAAA
1 AAAAAAGAAA
889878 GGTTTAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 18 0.55
11 15 0.45
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.08
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:889869 original size:21 final size:21
Alignment explanation
Indices: 889812--889870 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 21
889802 CTAATAACCT
889812 AAAAATAAATACATAAAAAAGTA
1 AAAAATAAATA-A-AAAAAAGTA
* *
889835 AAAAA-AAAGCAAAAAATAG-A
1 AAAAATAAA-TAAAAAAAAGTA
889855 AAAAATAAATAAAAAA
1 AAAAATAAATAAAAAA
889871 GAAGAAAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 12 0.39
21 9 0.29
22 4 0.13
23 6 0.19
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAAATAAATAAAAAAAAGTA
Found at i:889876 original size:21 final size:20
Alignment explanation
Indices: 889812--889877 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
889802 CTAATAACCT
889812 AAAAATAAATACATAAAAAAGTA
1 AAAAATAAATA-A-AAAAAAG-A
* *
889835 AAAAA-AAAGCAAAAAATAGA
1 AAAAATAAA-TAAAAAAAAGA
889855 AAAAATAAATAAAAAAGAAGA
1 AAAAATAAATAAAAAA-AAGA
889876 AA
1 AA
889878 GGTTTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 12 0.33
21 14 0.39
22 4 0.11
23 6 0.17
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.11
Consensus pattern (20 bp):
AAAAATAAATAAAAAAAAGA
Found at i:905073 original size:2 final size:2
Alignment explanation
Indices: 905066--905093 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
905056 TGCTGCTTTA
905066 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
905094 TTGGTGGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:910478 original size:25 final size:25
Alignment explanation
Indices: 910450--910596 Score: 86
Period size: 25 Copynumber: 5.9 Consensus size: 25
910440 CTTCCAAGCC
*
910450 ATATAACGGGAAGCTCATGTGAGCT
1 ATATAACGGGAAGCTCATGAGAGCT
** * *
910475 ATATAATAGGAAGCTCTTGCGAGCT
1 ATATAACGGGAAGCTCATGAGAGCT
* * *
910500 A-ATTATCGGAAAGCTCAT-ACGAGCC
1 ATA-TAACGGGAAGCTCATGA-GAGCT
* * *
910525 ATA-AATGGGAAGCTCAAGAGAGCC
1 ATATAACGGGAAGCTCATGAGAGCT
* * *
910549 AT-TAATCAGGAAGCTCGTGAGAGTT
1 ATATAA-CGGGAAGCTCATGAGAGCT
* * *
910574 AAATATCGGGAAGCTCGTGAGAG
1 ATATAACGGGAAGCTCATGAGAG
910597 TTAAATATCG
Statistics
Matches: 91, Mismatches: 24, Indels: 14
0.71 0.19 0.11
Matches are distributed among these distances:
24 20 0.22
25 68 0.75
26 3 0.03
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (25 bp):
ATATAACGGGAAGCTCATGAGAGCT
Found at i:910560 original size:74 final size:75
Alignment explanation
Indices: 910446--910589 Score: 184
Period size: 74 Copynumber: 1.9 Consensus size: 75
910436 AGCTCTTCCA
* * * * * *
910446 AGCCATATAACGGGAAGCTCATGTGAGCTATATAATAGGAAGCTCTTGCGAGCTAATTATCGGAA
1 AGCCATATAACGGGAAGCTCAAGAGAGCCATATAATAGGAAGCTCGTGAGAGCTAAATATCGGAA
910511 AGCTCATACG
66 AGCTCATACG
* * *
910521 AGCCATA-AATGGGAAGCTCAAGAGAGCCAT-TAATCAGGAAGCTCGTGAGAGTTAAATATCGGG
1 AGCCATATAACGGGAAGCTCAAGAGAGCCATATAAT-AGGAAGCTCGTGAGAGCTAAATATCGGA
910584 AAGCTC
65 AAGCTC
910590 GTGAGAGTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
73 4 0.07
74 48 0.81
75 7 0.12
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.22
Consensus pattern (75 bp):
AGCCATATAACGGGAAGCTCAAGAGAGCCATATAATAGGAAGCTCGTGAGAGCTAAATATCGGAA
AGCTCATACG
Found at i:910597 original size:25 final size:25
Alignment explanation
Indices: 910557--910606 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
910547 CCATTAATCA
910557 GGAAGCTCGTGAGAGTTAAATATCG
1 GGAAGCTCGTGAGAGTTAAATATCG
910582 GGAAGCTCGTGAGAGTTAAATATCG
1 GGAAGCTCGTGAGAGTTAAATATCG
910607 AGACGCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (25 bp):
GGAAGCTCGTGAGAGTTAAATATCG
Found at i:910621 original size:25 final size:25
Alignment explanation
Indices: 910558--910621 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
910548 CATTAATCAG
* * *
910558 GAAGCTCGTGAGAGTTAAATATCGG
1 GAAGCTCATAAGAGTTAAATATCGA
* *
910583 GAAGCTCGTGAGAGTTAAATATCGA
1 GAAGCTCATAAGAGTTAAATATCGA
* *
910608 GACGCTTATAAGAG
1 GAAGCTCATAAGAG
910622 CTGTGGCGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.23
Consensus pattern (25 bp):
GAAGCTCATAAGAGTTAAATATCGA
Found at i:912401 original size:24 final size:25
Alignment explanation
Indices: 912373--912441 Score: 88
Period size: 24 Copynumber: 2.8 Consensus size: 25
912363 AGCCCATATT
**
912373 AAATATATATTTAATATATGTA-AA
1 AAATATATATTTAATATATAAATAA
* *
912397 AAATATATATTTGAT-TAAAAATAA
1 AAATATATATTTAATATATAAATAA
912421 AAATATATATTTAATATATAA
1 AAATATATATTTAATATATAA
912442 TTCGGGCCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 3 0.08
24 30 0.81
25 4 0.11
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (25 bp):
AAATATATATTTAATATATAAATAA
Found at i:922082 original size:59 final size:59
Alignment explanation
Indices: 921990--922165 Score: 352
Period size: 59 Copynumber: 3.0 Consensus size: 59
921980 ACGAGTGAAT
921990 AGAAATTTAGATCTACATTAGATCTTACTTGAATCGCCTCATCTATTCTCCTGATGAGA
1 AGAAATTTAGATCTACATTAGATCTTACTTGAATCGCCTCATCTATTCTCCTGATGAGA
922049 AGAAATTTAGATCTACATTAGATCTTACTTGAATCGCCTCATCTATTCTCCTGATGAGA
1 AGAAATTTAGATCTACATTAGATCTTACTTGAATCGCCTCATCTATTCTCCTGATGAGA
922108 AGAAATTTAGATCTACATTAGATCTTACTTGAATCGCCTCATCTATTCTCCTGATGAG
1 AGAAATTTAGATCTACATTAGATCTTACTTGAATCGCCTCATCTATTCTCCTGATGAG
922166 TAAGTTTAGT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 117 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (59 bp):
AGAAATTTAGATCTACATTAGATCTTACTTGAATCGCCTCATCTATTCTCCTGATGAGA
Found at i:924041 original size:18 final size:18
Alignment explanation
Indices: 923992--924044 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 18
923982 CTTTAGATTT
* *
923992 TTTTAAAATTTTTAT-AT
1 TTTTAAAAATTTTATAAA
**
924009 TTTTAAAAA-AATATAAA
1 TTTTAAAAATTTTATAAA
924026 TTTTAAAAATTTTATAAA
1 TTTTAAAAATTTTATAAA
924044 T
1 T
924045 ATTTTAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 3 0.11
17 18 0.64
18 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAAATTTTATAAA
Found at i:927927 original size:191 final size:185
Alignment explanation
Indices: 927587--927967 Score: 559
Period size: 191 Copynumber: 2.0 Consensus size: 185
927577 AGCTAATCTG
927587 TTCAGATTTCAATCTAACTCAAACATTTAAAGTCTTTTGATTAACTTGAATAAAAAATATTTTAT
1 TTCAGATTTCAATCTAACTCAAACA--TAAAG-CTTTTGATTAACTTGAATAAAAAATATTTTAT
927652 CTGATTTATCAAAAAGACTATCAATTTAAAAAAAAAAAGATTAATTTTTTGTTGAGGGCTTTTTA
63 CTGATTTATCAAAAAGACTATCAATTTAAAAAAAAAAAGATTAATTTTTTGTTGAGGGCTTTTTA
** **
927717 TTATTTTCTTTTTCATTCTTTTTCCTCTCTTTGTGGTCCCTTTCACTTCTTCTCTCCA
128 TTATTTTCTTTTTCATTCTTTTTCCTCTCTTTGCCGTCCCTTTCACTTCCCCTCTCCA
*
927775 TTCAGATTTCAATTTAACTCAAACA-AAA-CATTTTGATTAACTTGAATAAAAAAATATTTTATC
1 TTCAGATTTCAATCTAACTCAAACATAAAGC-TTTTGATTAACTTGAAT-AAAAAATATTTTATC
* ****
927838 TGATTTATCAAGAAGACTATCAATTTTTTTTAAAAAAAGATTAAACTAAATTTTTGTTGAGGGCT
64 TGATTTATCAAAAAGACTATCAA-TTTAAAAAAAAAAAGATT-AA-T---TTTTTGTTGAGGGCT
927903 TTTTATTATTTTCTTTTTCATTCTTTTTCCTCTCTTTGCCGTCCCTTTCACTTCCCCTCTCCA
123 TTTTATTATTTTCTTTTTCATTCTTTTTCCTCTCTTTGCCGTCCCTTTCACTTCCCCTCTCCA
927966 TT
1 TT
927968 TCTCTCCTTT
Statistics
Matches: 175, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
183 1 0.01
184 17 0.10
185 40 0.23
186 14 0.08
187 2 0.01
188 25 0.14
191 76 0.43
ACGTcount: A:0.30, C:0.17, G:0.08, T:0.45
Consensus pattern (185 bp):
TTCAGATTTCAATCTAACTCAAACATAAAGCTTTTGATTAACTTGAATAAAAAATATTTTATCTG
ATTTATCAAAAAGACTATCAATTTAAAAAAAAAAAGATTAATTTTTTGTTGAGGGCTTTTTATTA
TTTTCTTTTTCATTCTTTTTCCTCTCTTTGCCGTCCCTTTCACTTCCCCTCTCCA
Found at i:931917 original size:21 final size:21
Alignment explanation
Indices: 931888--931932 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
931878 GACATGGTCG
*
931888 TGTGGCTGCTCCACACGCCCA
1 TGTGACTGCTCCACACGCCCA
* * *
931909 TGTGACTGCTTCGCATGCCCA
1 TGTGACTGCTCCACACGCCCA
931930 TGT
1 TGT
931933 ACGTAAGCCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.36, G:0.24, T:0.27
Consensus pattern (21 bp):
TGTGACTGCTCCACACGCCCA
Found at i:931971 original size:126 final size:126
Alignment explanation
Indices: 931741--931976 Score: 346
Period size: 126 Copynumber: 1.9 Consensus size: 126
931731 AGTCCAAACT
* * *
931741 GTGTCGCTCTTGACATGGCCGTGTGGCTACTCCACACGCCCGTGTGATTGCTTCACATGCCCGTG
1 GTGTCGCTCTTGACATGGCCGTGTGGCTACTCCACACGCCCATGTGACTGCTTCACATGCCCATG
* * *
931806 TACATAAATCGTGTAACTCACTATGCCCGTGTAATATAAAGTCACGCGACCGTGTCGCATC
66 TACATAAACCGTGTAACTCACTATGCCCATGTAATATAAAATCACGCGACCGTGTCGCATC
* * * *
931867 GTGTGGCTCTTGACATGGTCGTGTGGCTGCTCCACACGCCCATGTGACTGCTTCGCATGCCCATG
1 GTGTCGCTCTTGACATGGCCGTGTGGCTACTCCACACGCCCATGTGACTGCTTCACATGCCCATG
* * * *
931932 TACGTAAGCCGTGTAACTCATTGTGCCCATGTAATATAAAATCAC
66 TACATAAACCGTGTAACTCACTATGCCCATGTAATATAAAATCAC
931977 AAGGTCATGT
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
126 96 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (126 bp):
GTGTCGCTCTTGACATGGCCGTGTGGCTACTCCACACGCCCATGTGACTGCTTCACATGCCCATG
TACATAAACCGTGTAACTCACTATGCCCATGTAATATAAAATCACGCGACCGTGTCGCATC
Found at i:934701 original size:26 final size:27
Alignment explanation
Indices: 934649--934703 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
934639 AATAAATGTT
* * *
934649 TTTTTAAAATAATTTTTTTATTTTTTA
1 TTTTTAAAACAATTTTTTTAGTGTTTA
*
934676 TTTTTAAAACAA-TTTTTTGGTGTTTA
1 TTTTTAAAACAATTTTTTTAGTGTTTA
934702 TT
1 TT
934704 AAAAAAATGG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TTTTTAAAACAATTTTTTTAGTGTTTA
Found at i:935015 original size:6 final size:6
Alignment explanation
Indices: 935004--935029 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
934994 TGAAGGAAGA
935004 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
935030 GAGGAGTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:944185 original size:11 final size:11
Alignment explanation
Indices: 944059--944125 Score: 55
Period size: 11 Copynumber: 6.2 Consensus size: 11
944049 TTAAAAAAGA
944059 TTGTTATTATT
1 TTGTTATTATT
* *
944070 TTTTTATTGTT
1 TTGTTATTATT
* *
944081 TT-TCATTGTT
1 TTGTTATTATT
* *
944091 TTGCTATAATT
1 TTGTTATTATT
*
944102 TTGTTATTATA
1 TTGTTATTATT
*
944113 TTGTTACTATT
1 TTGTTATTATT
944124 TT
1 TT
944126 TATTGTTATT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
10 9 0.21
11 34 0.79
ACGTcount: A:0.18, C:0.04, G:0.09, T:0.69
Consensus pattern (11 bp):
TTGTTATTATT
Found at i:946457 original size:29 final size:30
Alignment explanation
Indices: 946398--946455 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
946388 TCCGAGCCTT
*
946398 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
946428 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
946456 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:946685 original size:13 final size:13
Alignment explanation
Indices: 946667--946698 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
946657 TTTCCAGCAA
946667 TTATGAATTTATT
1 TTATGAATTTATT
946680 TTATGAATTTATT
1 TTATGAATTTATT
*
946693 TGATGA
1 TTATGA
946699 TGATCCAAGC
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:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:946906 original size:50 final size:50
Alignment explanation
Indices: 946793--947034 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
946783 ATTTGGGTAA
* * *
946793 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
946849 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
946899 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
946949 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
946999 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
947035 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:946982 original size:100 final size:103
Alignment explanation
Indices: 946793--947042 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
946783 ATTTGGGTAA
946793 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
946858 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
946899 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
946961 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
946999 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
947043 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:960070 original size:133 final size:133
Alignment explanation
Indices: 959894--960144 Score: 380
Period size: 133 Copynumber: 1.9 Consensus size: 133
959884 AAAAATTGGA
* * *
959894 ATTAGCGGCGTTTTCTGAGAAACGCTGGTAACGATAACGAATTTGAGGAAAAAATTT-GAGCAAA
1 ATTAGCGGCGTTTTCAGAGAAACGCCGGTAAAGATAACGAATTTGAGGAAAAAATTTGGA-CAAA
* * * *
959958 ACAG-TACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCATTTTAAAAAACACCGGAAAAG
65 AC-GCTACCGTTTTATTGCTTCATTTTATTTCCTTAGTGGCGCATTGTAAAAAACACCGGAAAAG
960022 AATGC
129 AATGC
* * *
960027 ATTAGCGGCGTTTTCAGGGAAACGCCGGTAAAGATATCTAATTTGAGGAAAAAATTTGGACAAAA
1 ATTAGCGGCGTTTTCAGAGAAACGCCGGTAAAGATAACGAATTTGAGGAAAAAATTTGGACAAAA
960092 CGCTACCGTTTTATTGCTTCATTTTATTTCCTTAGTGGCGCATTGTAAAAAAC
66 CGCTACCGTTTTATTGCTTCATTTTATTTCCTTAGTGGCGCATTGTAAAAAAC
960145 GCCGCAAATA
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
132 1 0.01
133 103 0.97
134 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (133 bp):
ATTAGCGGCGTTTTCAGAGAAACGCCGGTAAAGATAACGAATTTGAGGAAAAAATTTGGACAAAA
CGCTACCGTTTTATTGCTTCATTTTATTTCCTTAGTGGCGCATTGTAAAAAACACCGGAAAAGAA
TGC
Found at i:960202 original size:43 final size:43
Alignment explanation
Indices: 960145--960229 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
960135 TGTAAAAAAC
960145 GCCGCAAATATTGGGATATAGTGGCGTTATTGGAGAAACGCCT
1 GCCGCAAATATTGGGATATAGTGGCGTTATTGGAGAAACGCCT
960188 GCCGCAAATATTGGGATATAGTGGCGTTATTGGAGAAACGCC
1 GCCGCAAATATTGGGATATAGTGGCGTTATTGGAGAAACGCC
960230 GGTAAAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.16, G:0.31, T:0.25
Consensus pattern (43 bp):
GCCGCAAATATTGGGATATAGTGGCGTTATTGGAGAAACGCCT
Found at i:960700 original size:20 final size:20
Alignment explanation
Indices: 960675--960729 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
960665 TTTGTGTTCT
960675 GGGCTTAGAGTTTAGGTTTA
1 GGGCTTAGAGTTTAGGTTTA
* * *
960695 GGGCTTGGAGATTGAGTTTTA
1 GGGCTTAGAG-TTTAGGTTTA
* *
960716 AGGTTTAGAGTTTA
1 GGGCTTAGAGTTTA
960730 CATTTCAGCG
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.22, C:0.04, G:0.35, T:0.40
Consensus pattern (20 bp):
GGGCTTAGAGTTTAGGTTTA
Found at i:963026 original size:27 final size:27
Alignment explanation
Indices: 962996--963051 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
962986 AGATTGGGTT
962996 TTGTCGTATTTTTAATTTTGATTTTGC
1 TTGTCGTATTTTTAATTTTGATTTTGC
963023 TTGTCGTATTTTTAATTTTGATTTTGC
1 TTGTCGTATTTTTAATTTTGATTTTGC
963050 TT
1 TT
963052 TCTTATTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.14, C:0.07, G:0.14, T:0.64
Consensus pattern (27 bp):
TTGTCGTATTTTTAATTTTGATTTTGC
Found at i:964555 original size:13 final size:13
Alignment explanation
Indices: 964534--964566 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
964524 TGTTTTAATA
*
964534 TCTATATAAGTTT
1 TCTAAATAAGTTT
964547 TCTAAATAAGTTT
1 TCTAAATAAGTTT
964560 TCTAAAT
1 TCTAAAT
964567 TTATTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.48
Consensus pattern (13 bp):
TCTAAATAAGTTT
Found at i:964597 original size:15 final size:15
Alignment explanation
Indices: 964562--964600 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
964552 ATAAGTTTTC
*
964562 TAAATTTATTTGTAT
1 TAAATTTATTAGTAT
964577 TAAAATTTATTAGTAT
1 T-AAATTTATTAGTAT
964593 TAAATTTA
1 TAAATTTA
964601 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TAAATTTATTAGTAT
Found at i:964643 original size:62 final size:62
Alignment explanation
Indices: 964543--964662 Score: 143
Period size: 62 Copynumber: 1.9 Consensus size: 62
964533 ATCTATATAA
* *** * * *
964543 GTTTTCTAAATAAGTTTTCTAAATTTATTTGTATTAAAATTTAT-TAGTATTAAATTTACTTC
1 GTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATATATGT-GTATTAAATTTACTTC
* *
964605 GTTTTCTAAATAAGTGTTCTAAATTTGGGAGAAATAAAATATATGTGTATTAAGTTTA
1 GTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATATATGTGTATTAAATTTA
964663 TAAGTTTCTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
62 47 0.98
63 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (62 bp):
GTTTTCTAAATAAGTGTTCTAAATTTAGGAGAAATAAAATATATGTGTATTAAATTTACTTC
Found at i:964844 original size:21 final size:21
Alignment explanation
Indices: 964818--964896 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
964808 TGTTATAATA
*
964818 CATAACTTGTATATAAGCTTG
1 CATAACTTATATATAAGCTTG
*
964839 CATAACTTATATTTAAGCTTG
1 CATAACTTATATATAAGCTTG
* * *
964860 CATAACTTACATAATAA-TTTA
1 CATAACTTATAT-ATAAGCTTG
964881 CATAACTTATATATAA
1 CATAACTTATATATAA
964897 TAGCATAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 4 0.08
21 43 0.86
22 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (21 bp):
CATAACTTATATATAAGCTTG
Found at i:964855 original size:116 final size:116
Alignment explanation
Indices: 964723--964963 Score: 448
Period size: 116 Copynumber: 2.1 Consensus size: 116
964713 TTATATAATA
964723 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACA-A
1 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
964787 CATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
66 -ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
* *
964839 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACATAACTTATATATAATAGCATA
1 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
964904 ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
66 ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
964955 CATAACTTA
1 CATAACTTA
964964 CATAAATTAA
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
116 121 0.99
117 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (116 bp):
CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
Found at i:964991 original size:27 final size:27
Alignment explanation
Indices: 964946--965552 Score: 962
Period size: 27 Copynumber: 21.7 Consensus size: 27
964936 TAACTTGTAT
*
964946 ATAAGCTTGCATAACTTACATAAATTAA
1 ATAA-CTTACATAACTTACATAAATTAA
*
964974 ATAACTTACACAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965001 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965028 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965055 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
*
965082 ATAACTTGCATAACTTACATAAACTTGCATAA
1 ATAACTTACATAACTTACATAAA--T---TAA
*
965114 ATTAAATAACTTACATAACTTACATAAATTAA
1 A-T--A-AC-TTACATAACTTACATAAATTAA
965146 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965173 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965200 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965227 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965254 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965281 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965308 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965335 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965362 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965389 ATAACTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
965416 ATAACTTACATAACTTACATAAATTACATAAATTAA
1 ATAACTTACAT-A---AC-----TTACATAAATTAA
*
965452 ATAACTTACATAACTTACATAACTTAA
1 ATAACTTACATAACTTACATAAATTAA
*
965479 ATAATTTACATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
*
965506 ATAACTTGCATAACTTACATAAATTAA
1 ATAACTTACATAACTTACATAAATTAA
*
965533 ATTACTTACATAACTTACAT
1 ATAACTTACATAACTTACAT
965553 TATACATAAC
Statistics
Matches: 546, Mismatches: 14, Indels: 39
0.91 0.02 0.07
Matches are distributed among these distances:
27 479 0.88
28 6 0.01
29 2 0.00
31 3 0.01
32 10 0.02
33 1 0.00
35 3 0.01
36 25 0.05
37 17 0.03
ACGTcount: A:0.51, C:0.15, G:0.01, T:0.33
Consensus pattern (27 bp):
ATAACTTACATAACTTACATAAATTAA
Found at i:965550 original size:9 final size:9
Alignment explanation
Indices: 964932--965670 Score: 793
Period size: 9 Copynumber: 82.8 Consensus size: 9
964922 TATGTTATAA
964932 TACATAACTT
1 TACATAAC-T
*
964942 GTATATAAGCT
1 -TACATAA-CT
*
964953 TGCATAACT
1 TACATAACT
*
964962 TACATAAAT
1 TACATAACT
*
964971 TAAATAACT
1 TACATAACT
*
964980 TACACAACT
1 TACATAACT
*
964989 TACATAAAT
1 TACATAACT
*
964998 TAAATAACT
1 TACATAACT
965007 TACATAACT
1 TACATAACT
*
965016 TACATAAAT
1 TACATAACT
*
965025 TAAATAACT
1 TACATAACT
965034 TACATAACT
1 TACATAACT
*
965043 TACATAAAT
1 TACATAACT
*
965052 TAAATAACT
1 TACATAACT
965061 TACATAACT
1 TACATAACT
*
965070 TACATAAAT
1 TACATAACT
*
965079 TAAATAACT
1 TACATAACT
*
965088 TGCATAACT
1 TACATAACT
965097 TACATAAACT
1 TACAT-AACT
* *
965107 TGCATAAAT
1 TACATAACT
*
965116 TAAATAACT
1 TACATAACT
965125 TACATAACT
1 TACATAACT
*
965134 TACATAAAT
1 TACATAACT
*
965143 TAAATAACT
1 TACATAACT
965152 TACATAACT
1 TACATAACT
*
965161 TACATAAAT
1 TACATAACT
*
965170 TAAATAACT
1 TACATAACT
965179 TACATAACT
1 TACATAACT
*
965188 TACATAAAT
1 TACATAACT
*
965197 TAAATAACT
1 TACATAACT
965206 TACATAACT
1 TACATAACT
*
965215 TACATAAAT
1 TACATAACT
*
965224 TAAATAACT
1 TACATAACT
965233 TACATAACT
1 TACATAACT
*
965242 TACATAAAT
1 TACATAACT
*
965251 TAAATAACT
1 TACATAACT
965260 TACATAACT
1 TACATAACT
*
965269 TACATAAAT
1 TACATAACT
*
965278 TAAATAACT
1 TACATAACT
965287 TACATAACT
1 TACATAACT
*
965296 TACATAAAT
1 TACATAACT
*
965305 TAAATAACT
1 TACATAACT
965314 TACATAACT
1 TACATAACT
*
965323 TACATAAAT
1 TACATAACT
*
965332 TAAATAACT
1 TACATAACT
965341 TACATAACT
1 TACATAACT
*
965350 TACATAAAT
1 TACATAACT
*
965359 TAAATAACT
1 TACATAACT
965368 TACATAACT
1 TACATAACT
*
965377 TACATAAAT
1 TACATAACT
*
965386 TAAATAACT
1 TACATAACT
965395 TACATAACT
1 TACATAACT
*
965404 TACATAAAT
1 TACATAACT
*
965413 TAAATAACT
1 TACATAACT
965422 TACATAACT
1 TACATAACT
*
965431 TACATAAAT
1 TACATAACT
*
965440 TACATAAAT
1 TACATAACT
*
965449 TAAATAACT
1 TACATAACT
965458 TACATAACT
1 TACATAACT
965467 TACATAACT
1 TACATAACT
* *
965476 TAAATAATT
1 TACATAACT
965485 TACATAACT
1 TACATAACT
*
965494 TACATAAAT
1 TACATAACT
*
965503 TAAATAACT
1 TACATAACT
*
965512 TGCATAACT
1 TACATAACT
*
965521 TACATAAAT
1 TACATAACT
* *
965530 TAAATTACT
1 TACATAACT
965539 TACATAACT
1 TACATAACT
*
965548 TACATTA--
1 TACATAACT
965555 TACATAACCT
1 TACATAA-CT
*
965565 T-CTTAACT
1 TACATAACT
*
965573 TACATTA--
1 TACATAACT
*
965580 TACACAACT
1 TACATAACT
*
965589 CACATAA-T
1 TACATAACT
* *
965597 T--ATTATT
1 TACATAACT
*
965604 ATACACAACT
1 -TACATAACT
*
965614 TACATTACT
1 TACATAACT
965623 TACAGT-ACT
1 TACA-TAACT
965632 TACATAA--
1 TACATAACT
965639 TACATAA--
1 TACATAACT
965646 TACATAACT
1 TACATAACT
965655 TACATAACT
1 TACATAACT
965664 TACATAA
1 TACATAA
965671 TACATAAAAA
Statistics
Matches: 598, Mismatches: 114, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
6 3 0.01
7 26 0.04
8 6 0.01
9 537 0.90
10 18 0.03
11 7 0.01
12 1 0.00
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.34
Consensus pattern (9 bp):
TACATAACT
Found at i:965644 original size:7 final size:7
Alignment explanation
Indices: 965632--965677 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
965622 TTACAGTACT
965632 TACATAA
1 TACATAA
965639 TACATAA
1 TACATAA
965646 TACATAA
1 TACATAA
965653 CTTACATAA
1 --TACATAA
965662 CTTACATAA
1 --TACATAA
965671 TACATAA
1 TACATAA
965678 AAATATATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 21 0.57
9 16 0.43
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.30
Consensus pattern (7 bp):
TACATAA
Found at i:971207 original size:21 final size:21
Alignment explanation
Indices: 971181--971227 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
971171 CTACAACTTA
* *
971181 AAGCAGATGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
*
971202 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
971223 AAGCA
1 AAGCA
971228 AAGGTTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.19, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:971671 original size:42 final size:42
Alignment explanation
Indices: 971613--971773 Score: 200
Period size: 42 Copynumber: 3.8 Consensus size: 42
971603 GTTTTTGTAC
* * * *
971613 AAAAGCGCCGCTAAAGAACATGTTCTTTAGTGGCACTTAATA
1 AAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAATA
* * *
971655 AAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTT-ATA
1 AAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAATA
*
971696 TAAAAACGCTGCTAAAGAACATGTTCTTCAGCGGCGCTTAGA-A
1 -AAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTA-ATA
* *
971739 AAAAACGCCGCTAAAGACCATGTTCTTCAGTGGCG
1 AAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCG
971774 TTTTTCTCAA
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.03
42 99 0.95
43 1 0.01
44 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTCAGCGGCGCTTAATA
Found at i:971794 original size:84 final size:84
Alignment explanation
Indices: 971597--971804 Score: 247
Period size: 84 Copynumber: 2.5 Consensus size: 84
971587 TCCCTAAAAT
* * *
971597 AGTGGCGTTTTTGTACAAAAGCGCCGCTAAAGAACATGTTCTTTAGTGGCACTTAATAAAAAACG
1 AGTGGCGTTTTTAT-C-AAAGCGCCGCTAAAGAACATGTTCTTCAGCGGCACTTAATAAAAAACG
* *
971662 CCACTAAAGATCATGTTCTTT
64 CCACTAAAGACCATGTTCTTC
* * * * * * *
971683 AGCGGCGCTTATATAAAAACGCTGCTAAAGAACATGTTCTTCAGCGGCGCTTAGA-AAAAAACGC
1 AGTGGCGTTTTTATCAAAGCGCCGCTAAAGAACATGTTCTTCAGCGGCACTTA-ATAAAAAACGC
*
971747 CGCTAAAGACCATGTTCTTC
65 CACTAAAGACCATGTTCTTC
* *
971767 AGTGGCGTTTTTCTCAAAGCACCGCTAAAGAACATGTT
1 AGTGGCGTTTTTATCAAAGCGCCGCTAAAGAACATGTT
971805 TTTTTTATAA
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
84 89 0.89
85 1 0.01
86 10 0.10
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (84 bp):
AGTGGCGTTTTTATCAAAGCGCCGCTAAAGAACATGTTCTTCAGCGGCACTTAATAAAAAACGCC
ACTAAAGACCATGTTCTTC
Found at i:976085 original size:13 final size:13
Alignment explanation
Indices: 976067--976093 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
976057 ATGTACTGAT
976067 TATTATATATATA
1 TATTATATATATA
976080 TATTATATATATA
1 TATTATATATATA
976093 T
1 T
976094 GTAATCAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATATATATA
Found at i:992081 original size:3 final size:3
Alignment explanation
Indices: 992073--992118 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
992063 ATAAAGAAGG
*
992073 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
992119 GGATTAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:992837 original size:6 final size:5
Alignment explanation
Indices: 992798--992830 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
992788 TTTATAGTCG
*
992798 AAAAT GAAA- AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
992831 ATCAAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 22 0.88
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:995704 original size:21 final size:21
Alignment explanation
Indices: 995678--995721 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
995668 TTGGAAGTAT
995678 TTTTCAACAATAGCTTTAAAC
1 TTTTCAACAATAGCTTTAAAC
995699 TTTTCAACAATAGCTTTAAAC
1 TTTTCAACAATAGCTTTAAAC
995720 TT
1 TT
995722 AGGAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (21 bp):
TTTTCAACAATAGCTTTAAAC
Found at i:995731 original size:21 final size:21
Alignment explanation
Indices: 995686--995731 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
995676 ATTTTTCAAC
** *
995686 AATAGCTTTAAACTTTTCAAC
1 AATAGCTTTAAACTTAGCAAA
*
995707 AATAGCTTTAAACTTAGGAAA
1 AATAGCTTTAAACTTAGCAAA
995728 AATA
1 AATA
995732 TTAGAAACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.33
Consensus pattern (21 bp):
AATAGCTTTAAACTTAGCAAA
Found at i:999303 original size:18 final size:18
Alignment explanation
Indices: 999280--999323 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
999270 ATTGGGTTTA
*
999280 GGGTTTAGGTTTAGATTC
1 GGGTTTAGGTATAGATTC
*
999298 GGGTTTGGGTATAGATTC
1 GGGTTTAGGTATAGATTC
999316 GGGTTTAG
1 GGGTTTAG
999324 TTAATGGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.05, G:0.39, T:0.41
Consensus pattern (18 bp):
GGGTTTAGGTATAGATTC
Found at i:1001215 original size:7 final size:7
Alignment explanation
Indices: 1001203--1001228 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1001193 TAGTCGATTG
1001203 GTATTTA
1 GTATTTA
1001210 GTATTTA
1 GTATTTA
1001217 GTATTTA
1 GTATTTA
1001224 GTATT
1 GTATT
1001229 ATGTAATAAC
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:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:1001905 original size:18 final size:18
Alignment explanation
Indices: 1001878--1001917 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1001868 CAGGTGCGTT
*
1001878 TCCTAGCCCTTATATGTA
1 TCCTAACCCTTATATGTA
1001896 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
1001914 TCCT
1 TCCT
1001918 TTTCCAAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.07, T:0.40
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:1002213 original size:18 final size:18
Alignment explanation
Indices: 1002172--1002213 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1002162 AGATGCCGTA
*
1002172 CCGGAAGAACAACCGCCG
1 CCGGAACAACAACCGCCG
**
1002190 GAGGAACAACAACCGCCG
1 CCGGAACAACAACCGCCG
1002208 CCGGAA
1 CCGGAA
1002214 GCTAGAGAAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.36, G:0.29, T:0.00
Consensus pattern (18 bp):
CCGGAACAACAACCGCCG
Found at i:1002370 original size:25 final size:25
Alignment explanation
Indices: 1002339--1002515 Score: 215
Period size: 25 Copynumber: 7.3 Consensus size: 25
1002329 TATTTTGATA
1002339 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
* *** *
1002364 TTTTTTGA-GT--TATTTTA-ATA-
1 TTATTTGATGTAATAAAATAGAAAT
*
1002384 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAAT
*
1002409 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAAT
*
1002434 TTATTTAATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
*
1002459 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAAT
1002484 TTATTTGATGTAAT-AAATAGAAAAT
1 TTATTTGATGTAATAAAATAG-AAAT
1002509 TT-TTTGA
1 TTATTTGA
1002516 GTTATTTTGA
Statistics
Matches: 130, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
20 7 0.05
21 4 0.03
22 4 0.03
23 4 0.03
24 14 0.11
25 97 0.75
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAAT
Found at i:1002378 original size:45 final size:47
Alignment explanation
Indices: 1002328--1002543 Score: 196
Period size: 50 Copynumber: 4.6 Consensus size: 47
1002318 AATATTTTGA
*
1002328 ATATTTTGATATTATTTGATGTAATAAAATAGAAATTTTTTTGA-GT
1 ATATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGATGT
* *
1002374 -TATTTTAATATTATTTGATGTAATAAAATAGAAGTTTATTTGATGT
1 ATATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGATGT
** * *
1002420 AATAAAATAGA-AGTTTATTTAATGTAATAAAATAGAAATTTATTTGATGT
1 -AT-ATTTTGATA--TTATTTGATGTAATAAAATAGAAATTTATTTGATGT
** *
1002470 AATAAAATAGA-AGTTTATTTGATGTAAT-AAATAGAAAATTT-TTTGA-GT
1 -AT-ATTTTGATA--TTATTTGATGTAATAAAATAG-AAATTTATTTGATGT
*
1002518 -TATTTTGATATTATTCGATGTAATAA
1 ATATTTTGATATTATTTGATGTAATAA
1002544 CATGAGCTTA
Statistics
Matches: 147, Mismatches: 14, Indels: 19
0.82 0.08 0.11
Matches are distributed among these distances:
44 13 0.09
45 45 0.31
46 4 0.03
48 4 0.03
49 14 0.10
50 67 0.46
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (47 bp):
ATATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGATGT
Found at i:1006039 original size:122 final size:125
Alignment explanation
Indices: 1005724--1006068 Score: 518
Period size: 127 Copynumber: 2.8 Consensus size: 125
1005714 AAACATGCTG
* * *
1005724 CTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCATAAATTATTCTCAAATAGCATCCTGCTAG
1 CTGTAGCAAAAGCGCGTCCACGAGGGCTCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
1005789 AAGCGATTTTATACTATTTGCTCAGAAACGTGAAAAAAAAAACTTATTTCATCCATGACCTA
66 AAGCGATTTTATACTATTTGCTCAGAAACGT--AAAAAAAAACTTATTTCATCCATGACCTA
* * *
1005851 CTGTAGCAAAAACGCGTCCACGAGGG-TGCGATTTCACAAATTCGTCTCAAATAGCATCCTGTTA
1 CTGTAGCAAAAGCGCGTCCACGAGGGCT-CGATTTCACAAATTCTTCTCAAATAGCATCCTGCTA
* *
1005915 GAAGTGATTTTATACTATTTGCTCAGAAACGT-CAAAAAAA-TTATTTCATCCATGACCTA
65 GAAGCGATTTTATACTATTTGCTCAGAAACGTAAAAAAAAACTTATTTCATCCATGACCTA
* * *
1005974 CT-TAGCGAAAGCGCGTCCTCGAGGGCTCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTAG
1 CTGTAGCAAAAGCGCGTCCACGAGGGCTCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
* *
1006038 AAGCGATTTTATACTATTTGATCAAAAACGT
66 AAGCGATTTTATACTATTTGCTCAGAAACGT
1006069 TAACTCGAAA
Statistics
Matches: 199, Mismatches: 17, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
122 82 0.41
123 22 0.11
124 7 0.04
127 88 0.44
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (125 bp):
CTGTAGCAAAAGCGCGTCCACGAGGGCTCGATTTCACAAATTCTTCTCAAATAGCATCCTGCTAG
AAGCGATTTTATACTATTTGCTCAGAAACGTAAAAAAAAACTTATTTCATCCATGACCTA
Found at i:1009339 original size:20 final size:21
Alignment explanation
Indices: 1009308--1009360 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1009298 ATAATTACGT
1009308 TTATTTTCTTTAAATTAA-GAG
1 TTATTTT-TTTAAATTAATGAG
* *
1009329 TTATTTTTTTAACTTAATGAT
1 TTATTTTTTTAAATTAATGAG
*
1009350 TTATTTATTTA
1 TTATTTTTTTA
1009361 TTTTTCACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (21 bp):
TTATTTTTTTAAATTAATGAG
Found at i:1014649 original size:108 final size:108
Alignment explanation
Indices: 1014460--1014825 Score: 732
Period size: 108 Copynumber: 3.4 Consensus size: 108
1014450 ATTTAACAGT
1014460 TAAATTAACAAATTTTAGTAATGTAAGGACTTAATTGATATAATCTTTTTTGAGAGAAAATATCG
1 TAAATTAACAAATTTTAGTAATGTAAGGACTTAATTGATATAATCTTTTTTGAGAGAAAATATCG
1014525 AGCACCTCTTGAATTAATAATAAAAATAAACCAAACACAGAGG
66 AGCACCTCTTGAATTAATAATAAAAATAAACCAAACACAGAGG
1014568 TAAATTAACAAATTTTAGTAATGTAAGGACTTAATTGATATAATCTTTTTTGAGAGAAAATATCG
1 TAAATTAACAAATTTTAGTAATGTAAGGACTTAATTGATATAATCTTTTTTGAGAGAAAATATCG
1014633 AGCACCTCTTGAATTAATAATAAAAATAAACCAAACACAGAGG
66 AGCACCTCTTGAATTAATAATAAAAATAAACCAAACACAGAGG
1014676 TAAATTAACAAATTTTAGTAATGTAAGGACTTAATTGATATAATCTTTTTTGAGAGAAAATATCG
1 TAAATTAACAAATTTTAGTAATGTAAGGACTTAATTGATATAATCTTTTTTGAGAGAAAATATCG
1014741 AGCACCTCTTGAATTAATAATAAAAATAAACCAAACACAGAGG
66 AGCACCTCTTGAATTAATAATAAAAATAAACCAAACACAGAGG
1014784 TAAATTAACAAATTTTAGTAATGTAAGGACTTAATTGATATA
1 TAAATTAACAAATTTTAGTAATGTAAGGACTTAATTGATATA
1014826 GTTTTAGTAG
Statistics
Matches: 258, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 258 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31
Consensus pattern (108 bp):
TAAATTAACAAATTTTAGTAATGTAAGGACTTAATTGATATAATCTTTTTTGAGAGAAAATATCG
AGCACCTCTTGAATTAATAATAAAAATAAACCAAACACAGAGG
Found at i:1017660 original size:16 final size:16
Alignment explanation
Indices: 1017639--1017706 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
1017629 TTTGGTTCGC
1017639 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
1017655 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
1017671 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1017687 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
1017703 TGTA
1 TGTA
1017707 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:1017970 original size:18 final size:19
Alignment explanation
Indices: 1017937--1017976 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1017927 CATAATTATT
1017937 ATTAAATAATTTTAATAAA
1 ATTAAATAATTTTAATAAA
*
1017956 ATTATATAA-TTTAATAAA
1 ATTAAATAATTTTAATAAA
1017974 ATT
1 ATT
1017977 CTTAATAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTAAATAATTTTAATAAA
Found at i:1018082 original size:18 final size:17
Alignment explanation
Indices: 1018059--1018095 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1018049 AATTATTATT
1018059 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
1018075 AAATATATGATTTAATA
1 AAATATATGATTTAATA
1018092 AAAT
1 AAAT
1018096 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:1018093 original size:59 final size:57
Alignment explanation
Indices: 1017922--1018096 Score: 142
Period size: 59 Copynumber: 3.0 Consensus size: 57
1017912 TTAATCATAT
* *
1017922 TTTAACATAATTATTATTAAATA-ATTTTAA-TAAAATTATATAATTTAATAAAATTC
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAA-TATATGATTTAATAAAATTA
* * * * ** * * *
1017978 TTAATAATCA-ATATTCTTATATGAATTTACTCAAATCATAATATATGATACT-ATAAAATATAA
1 TT--TAA-CATA-ATTATTAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAAT-T-A
1018041 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1018097 TAAAATAATT
Statistics
Matches: 87, Mismatches: 20, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
56 2 0.02
58 6 0.07
59 37 0.43
60 13 0.15
61 22 0.25
62 5 0.06
63 2 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.45
Consensus pattern (57 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTA
Found at i:1018166 original size:26 final size:28
Alignment explanation
Indices: 1018137--1018197 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
1018127 CATGAATTTG
*
1018137 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
1018163 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
1018191 TAAAATT
1 TATAATT
1018198 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:1018195 original size:47 final size:46
Alignment explanation
Indices: 1018144--1018287 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
1018134 TTGTATAATT
1018144 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
1018191 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
1018235 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
1018282 TAAAAT
1 TAAAAT
1018288 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:1018207 original size:91 final size:90
Alignment explanation
Indices: 1018112--1018319 Score: 317
Period size: 91 Copynumber: 2.3 Consensus size: 90
1018102 TAATTATAAC
* * * * *
1018112 TAATAAATTATCTTACATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
1018177 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
1018203 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
1018268 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
1018294 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
1018320 CTAAAATCAA
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
91 86 0.80
92 21 0.20
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:1018279 original size:44 final size:43
Alignment explanation
Indices: 1018137--1018279 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
1018127 CATGAATTTG
* *
1018137 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
1018181 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
1018228 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
1018272 TATAATTT
1 TATAATTT
1018280 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:1018294 original size:47 final size:47
Alignment explanation
Indices: 1018162--1018300 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
1018152 TTATTATTAC
* *
1018162 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
1018209 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
1018253 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1018300 A
1 A
1018301 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:1021826 original size:24 final size:24
Alignment explanation
Indices: 1021799--1021847 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1021789 AATAAAAGTT
*
1021799 ATAAAAAT-TATTAAACTTTAATAA
1 ATAAAAATAT-TTAAAATTTAATAA
*
1021823 ATAAAAATATTTAAAATTTACTAA
1 ATAAAAATATTTAAAATTTAATAA
1021847 A
1 A
1021848 CATGAGAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAAAATATTTAAAATTTAATAA
Found at i:1022235 original size:19 final size:19
Alignment explanation
Indices: 1022193--1022240 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
1022183 ATTTCTATAT
*
1022193 ATTTTATAATGTTTTACGA
1 ATTTTATAATATTTTACGA
* * *
1022212 TTTTTATAATATTTTTCTA
1 ATTTTATAATATTTTACGA
1022231 ATTTT-TAATA
1 ATTTTATAATA
1022241 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (19 bp):
ATTTTATAATATTTTACGA
Found at i:1022291 original size:19 final size:19
Alignment explanation
Indices: 1022262--1022307 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1022252 TTTCTTATAT
1022262 TTTTTATTAAAATTTAATAA
1 TTTTTA-TAAAATTTAATAA
* * *
1022282 TTTTTATAAATTTTATTGA
1 TTTTTATAAAATTTAATAA
1022301 TTTTTAT
1 TTTTTAT
1022308 TTTTTATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTATAAAATTTAATAA
Found at i:1023990 original size:3 final size:3
Alignment explanation
Indices: 1023959--1024109 Score: 91
Period size: 3 Copynumber: 52.3 Consensus size: 3
1023949 ATTACTCTTG
* * * * *
1023959 TTA TTA ATA TTA TT- TT- TTA CTA -TA ATA TTA TTA TTA TCA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * *
1024004 ATA TTA GCA TTT TTA TT- TTA TTA TTA -TA GTCA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
** * * * *
1024047 TTA CAA TTA TTA TAA GTA TTA TTA TTA TTA CTA ATA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1024094 TTA TTA CTA TTA TTA T
1 TTA TTA TTA TTA TTA T
1024110 CCATTGTTAT
Statistics
Matches: 110, Mismatches: 31, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
2 14 0.13
3 95 0.86
4 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:1024097 original size:23 final size:23
Alignment explanation
Indices: 1024016--1024109 Score: 100
Period size: 23 Copynumber: 4.0 Consensus size: 23
1024006 ATTAGCATTT
*
1024016 TTATTTTATTATTA-TAGTCATTA
1 TTATTTTATTATTACTA-TTATTA
** * *
1024039 TTATTTTATTACAATTATTATAA
1 TTATTTTATTATTACTATTATTA
* *
1024062 GTATTATTATTATTACTAATATTA
1 TTATT-TTATTATTACTATTATTA
1024086 TTATTTTATTATTACTATTATTA
1 TTATTTTATTATTACTATTATTA
1024109 T
1 T
1024110 CCATTGTTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
23 38 0.67
24 19 0.33
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (23 bp):
TTATTTTATTATTACTATTATTA
Found at i:1024105 original size:47 final size:46
Alignment explanation
Indices: 1024017--1024106 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 46
1024007 TTAGCATTTT
* *
1024017 TATTTTATTATTATAGTCATTATTATTTTATTACAATTATTATAAG
1 TATTTTATTATTATAATCATTATTATTTTATTACAACTATTATAAG
**
1024063 TATTATTATTATTACTAAT-ATTATTATTTTATTATTACTATTAT
1 TATT-TTATTATTA-TAATCATTATTATTTTATTACAACTATTAT
1024107 TATCCATTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 4 0.11
47 31 0.82
48 3 0.08
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.59
Consensus pattern (46 bp):
TATTTTATTATTATAATCATTATTATTTTATTACAACTATTATAAG
Found at i:1024218 original size:3 final size:3
Alignment explanation
Indices: 1024210--1024243 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1024200 TTTTTGTTAC
1024210 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1024244 ACTTTCATGT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1024292 original size:27 final size:25
Alignment explanation
Indices: 1024234--1024289 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
1024224 ATTATTATTA
*
1024234 TTATTATTATACTTTCATGTTTACT
1 TTATTATTATACTTCCATGTTTACT
*
1024259 TTATTATATATACATTCCATTTTTA-T
1 TTATTAT-TATAC-TTCCATGTTTACT
1024285 TTATT
1 TTATT
1024290 TATTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 7 0.26
26 11 0.41
27 9 0.33
ACGTcount: A:0.27, C:0.11, G:0.02, T:0.61
Consensus pattern (25 bp):
TTATTATTATACTTCCATGTTTACT
Found at i:1025236 original size:19 final size:18
Alignment explanation
Indices: 1025199--1025242 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1025189 TTCGTTGCAT
1025199 TTCATTTTTATAGTTTGC
1 TTCATTTTTATAGTTTGC
1025217 TTCATTTTGCTATA-TTTGC
1 TTCATTTT--TATAGTTTGC
*
1025236 TTTATTT
1 TTCATTT
1025243 GTTCAAGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.16, C:0.11, G:0.09, T:0.64
Consensus pattern (18 bp):
TTCATTTTTATAGTTTGC
Found at i:1026927 original size:106 final size:105
Alignment explanation
Indices: 1026742--1027039 Score: 425
Period size: 106 Copynumber: 2.8 Consensus size: 105
1026732 AAAATTCAAG
* *
1026742 AGGATATTTGGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCAAA
1 AGGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAA
* * *
1026807 TTTCCAAACGCAAAACATTACCTTATTTTGTAATTTTTGAA
66 TTTCCAAACGCAAAACATTACCTTATTTT-AAAATTTTAAA
* *
1026848 AGGATATTTAGCTATTTGGTTGAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAA
1 AGGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAA
** *
1026913 TTTCCAAATACAAAACATTGCCTTATTTTAAAATTTTAAA
66 TTTCCAAACGCAAAACATTACCTTATTTTAAAATTTTAAA
* * * *
1026953 AGGATATTAAGCCATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGCACG-TTCCTC
*
1027018 GAATTTCTAAACGCAAAACATT
63 GAATTTCCAAACGCAAAACATT
1027040 GCCTCAATTA
Statistics
Matches: 171, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
105 33 0.19
106 87 0.51
107 27 0.16
108 24 0.14
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (105 bp):
AGGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAA
TTTCCAAACGCAAAACATTACCTTATTTTAAAATTTTAAA
Found at i:1029370 original size:44 final size:44
Alignment explanation
Indices: 1029316--1029472 Score: 174
Period size: 44 Copynumber: 3.6 Consensus size: 44
1029306 GCTTTGGTCT
1029316 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGACTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGACTTTAATCC
* * * * ** * *
1029360 GCTCTACTGCAACTTCAGAGAGACAGGAT-TGGTTTCTTCT-GTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATCT-GTGACTT-TAATCC
* **
1029404 GCTCCACTGTAACTTCAGGGAGATAAGATCTGTGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGACTTTAATCC
*
1029448 TCTCCACTGCAACTTCAGGGAGATA
1 GCTCCACTGCAACTTCAGGGAGATA
1029473 GGATTGGCTT
Statistics
Matches: 89, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
43 2 0.02
44 85 0.96
45 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATCTGTGACTTTAATCC
Found at i:1029424 original size:88 final size:88
Alignment explanation
Indices: 1029312--1029492 Score: 283
Period size: 88 Copynumber: 2.1 Consensus size: 88
1029302 CATGGCTTTG
*
1029312 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGACTTTAATCCGCTCTACTGCAACTTCA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGACTTTAATCCGCTCCACTGCAACTTCA
1029377 GAGAGACAGGATTGG-TTTCTTCT
66 GAGAGACAGGATTGGCTTT-TTCT
* ** *
1029400 GTCTGCTCCACTGTAACTTCAGGGAGATAAGATCTGTGGTTTTAATCCTCTCCACTGCAACTTCA
1 GTCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGACTTTAATCCGCTCCACTGCAACTTCA
* *
1029465 GGGAGATAGGATTGGCTTTTTCT
66 GAGAGACAGGATTGGCTTTTTCT
1029488 GTCTG
1 GTCTG
1029493 TTTAACGTCG
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
88 82 0.96
89 3 0.04
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (88 bp):
GTCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTGACTTTAATCCGCTCCACTGCAACTTCA
GAGAGACAGGATTGGCTTTTTCT
Found at i:1029586 original size:50 final size:49
Alignment explanation
Indices: 1029532--1029811 Score: 199
Period size: 50 Copynumber: 5.7 Consensus size: 49
1029522 TGCATCGCCT
* * *
1029532 GGGAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTGAGTTGCAATGTCG
1 GGGAAGTAAGATTCGCCATTGTAGCTTCAATCTTTTCA-TTGCAATGTCA
* * * * * * *
1029582 GGGAAATAAGATTCACCATTGTGGCTTCAATCTGTTCCACTGCAAAGTTA
1 GGGAAGTAAGATTCGCCATTGTAGCTTCAATCT-TTTCATTGCAATGTCA
* * ** * *
1029632 GGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATATCA
1 GGGAAGTAAGATTCGCCATTGTAGCTTCAATC-TTTTCATTGCAATGTCA
* * ** * *
1029682 TGGAAGTAAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGC-ATCG-C-
1 GGGAAGTAAGATTCGCCATTGTAGCTTCAATCT-TTTCATTGCAAT-GTCA
** * * * * * *
1029730 CTGAAATAAGATTTGCCGTTGTGGCCTCAATCTTTTGATTGCAATGTCA
1 GGGAAGTAAGATTCGCCATTGTAGCTTCAATCTTTTCATTGCAATGTCA
*
1029779 GGGATA-TGAGATTCGCCATTGTAGCTTCAATCT
1 GGGA-AGTAAGATTCGCCATTGTAGCTTCAATCT
1029812 GTTCCACTGT
Statistics
Matches: 177, Mismatches: 45, Indels: 17
0.74 0.19 0.07
Matches are distributed among these distances:
47 7 0.04
48 28 0.16
49 28 0.16
50 110 0.62
51 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (49 bp):
GGGAAGTAAGATTCGCCATTGTAGCTTCAATCTTTTCATTGCAATGTCA
Found at i:1029760 original size:48 final size:48
Alignment explanation
Indices: 1029699--1029859 Score: 137
Period size: 48 Copynumber: 3.3 Consensus size: 48
1029689 AAGATCCGCT
*
1029699 GTTGTAGCTTCAATCTGTTCCACTGCATCGCCTGAAATAAGATTTGCC
1 GTTGTAGCCTCAATCTGTTCCACTGCATCGCCTGAAATAAGATTTGCC
* ** * ** * * *
1029747 GTTGTGGCCTCAATCT-TTTGATTGCAAT-GTCAGGGATATGAGATTCGCC
1 GTTGTAGCCTCAATCTGTTCCACTGC-ATCG-C-CTGAAATAAGATTTGCC
* * * * *
1029796 ATTGTAGCTTCAATCTGTTCCACTGTACCGCTTGAAATAAGATTTGCC
1 GTTGTAGCCTCAATCTGTTCCACTGCATCGCCTGAAATAAGATTTGCC
*
1029844 GTTGTGGCCTCAATCT
1 GTTGTAGCCTCAATCT
1029860 TTTCAATTGC
Statistics
Matches: 82, Mismatches: 26, Indels: 10
0.69 0.22 0.08
Matches are distributed among these distances:
47 7 0.09
48 42 0.51
49 27 0.33
50 6 0.07
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (48 bp):
GTTGTAGCCTCAATCTGTTCCACTGCATCGCCTGAAATAAGATTTGCC
Found at i:1029809 original size:97 final size:97
Alignment explanation
Indices: 1029502--1029871 Score: 395
Period size: 100 Copynumber: 3.8 Consensus size: 97
1029492 GTTTAACGTC
* * * *
1029502 GTAGCTTCAATCTGTTCCGCTGCATCGCCTGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCT-GGAAATAAGATTCGCCGTTGTGGCCTCAATCTTT
* * *
1029567 TGAGTTGCAATGTCGGGGAAATAAGATTCACCATT
65 T-AATTGCAATGTCAGGG-AATAAGATTCGCCATT
* ** * * * * *
1029602 GTGGCTTCAATCTGTTCCACTGCAAAG-TTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCT-GGAAA-TAAGATTCGCCGTTGTGGCCTCAATC-T
* * * **
1029666 TTTAATTGCAATATCATGGAAGTAAGATCCGCTGTT
63 TTTAATTGCAATGTCAGGGAA-TAAGATTCGCCATT
*
1029702 GTAGCTTCAATCTGTTCCACTGCATCGCCT-GAAATAAGATTTGCCGTTGTGGCCTCAATCTTTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTT
* *
1029766 GATTGCAATGTCAGGGATATGAGATTCGCCATT
66 AATTGCAATGTCAGGGA-ATAAGATTCGCCATT
* * * *
1029799 GTAGCTTCAATCTGTTCCACTGTACCG-CTTGAAATAAGATTTGCCGTTGTGGCCTCAATCTTTT
1 GTAGCTTCAATCTGTTCCACTGCATCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTT
1029863 CAATTGCAA
66 -AATTGCAA
1029872 ACTATGGTTA
Statistics
Matches: 225, Mismatches: 38, Indels: 16
0.81 0.14 0.06
Matches are distributed among these distances:
96 2 0.01
97 87 0.39
98 29 0.13
99 11 0.05
100 91 0.40
101 5 0.02
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (97 bp):
GTAGCTTCAATCTGTTCCACTGCATCGCCTGGAAATAAGATTCGCCGTTGTGGCCTCAATCTTTT
AATTGCAATGTCAGGGAATAAGATTCGCCATT
Found at i:1037513 original size:18 final size:18
Alignment explanation
Indices: 1037490--1037525 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1037480 GCAATACAAT
1037490 TCGATCGGGTGTTATATC
1 TCGATCGGGTGTTATATC
1037508 TCGATCGGGTGTTATATC
1 TCGATCGGGTGTTATATC
1037526 CATCACGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (18 bp):
TCGATCGGGTGTTATATC
Found at i:1041427 original size:109 final size:108
Alignment explanation
Indices: 1041238--1041566 Score: 471
Period size: 109 Copynumber: 3.0 Consensus size: 108
1041228 TGGATTAAGA
* * * *
1041238 TTTAAGAGGATATTCGGCTATTTGGTCCAACGAG-AAATCGAAACCCAGCACATTAGGGCACGTT
1 TTTAAAAGGATATTTGGCAATTTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTT
*
1041302 TTCTCGAATTTTCAAACGCAAAACATTGCCTTATTTTGAAATT
66 TTCTCGAATTTTCAAACGCAAAACATTGCCTTATTTTGAAAAT
* * *
1041345 TTTAAAAGGATATTTGGCAATTTGATCGGACGAGAAAAATCGAAACCCAGCACATTAGGGCACAT
1 TTTAAAAGGATATTTGGCAATTTGGTCGAACGAG-AAAATCGAAACCCAGCACATTAGGGCACGT
* *
1041410 TTTCTCGAATTTCCAAACGCAAAACATTGTCTTATTTTGAAAAT
65 TTTCTCGAATTTTCAAACGCAAAACATTGCCTTATTTTGAAAAT
* * * *
1041454 TTTAAAAGGATATTTGGCCATTTGGTCGAATGAGAGAAATCAAAACCCAGCATATTAGGGCACGT
1 TTTAAAAGGATATTTGGCAATTTGGTCGAACGAGA-AAATCGAAACCCAGCACATTAGGGCACGT
* * *
1041519 TTTCTCGAATTTTCAAACGCAAAATATTGCCTTACTTAGAAAAAT
65 TTTCTCGAATTTTCAAACGCAAAACATTGCCTTATTTTG-AAAAT
1041564 TTT
1 TTT
1041567 CCTTTTTGAA
Statistics
Matches: 196, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
107 28 0.14
108 1 0.01
109 159 0.81
110 8 0.04
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (108 bp):
TTTAAAAGGATATTTGGCAATTTGGTCGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTT
TTCTCGAATTTTCAAACGCAAAACATTGCCTTATTTTGAAAAT
Found at i:1041619 original size:20 final size:20
Alignment explanation
Indices: 1041594--1041631 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1041584 GTTAATATGC
1041594 ATAATG-GAATAATAAACATG
1 ATAATGTGAATAA-AAACATG
1041614 ATAATGTGAATAAAAACA
1 ATAATGTGAATAAAAACA
1041632 ATATGAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.58, C:0.05, G:0.13, T:0.24
Consensus pattern (20 bp):
ATAATGTGAATAAAAACATG
Found at i:1043175 original size:23 final size:23
Alignment explanation
Indices: 1043132--1043176 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1043122 ATCACCTTTT
*
1043132 AAACTGTTTTTTTTATTTTCTTG
1 AAACTGTTTTTTTTATGTTCTTG
*
1043155 AAACTGTTTTTTTTGTGTTCTT
1 AAACTGTTTTTTTTATGTTCTT
1043177 TTTCCAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (23 bp):
AAACTGTTTTTTTTATGTTCTTG
Found at i:1044729 original size:43 final size:42
Alignment explanation
Indices: 1044664--1044981 Score: 438
Period size: 43 Copynumber: 7.4 Consensus size: 42
1044654 GCGTCGCTAA
* * *
1044664 CTTTAGCGGTGTTTTCCCCACAAACGCCGCTATAGATCATGAC
1 CTTTAGCGGCGTTTT-TCCACAAACGCCGCTATAGACCATGAC
*
1044707 CTTTAGCGGCATTTTTCACACAAACGCCGCTATAGACCATGAC
1 CTTTAGCGGCGTTTTTC-CACAAACGCCGCTATAGACCATGAC
*
1044750 CTTTAGCGGCGTTTTTCCTACAAACGCCGTTATAGACCATGAC
1 CTTTAGCGGCGTTTTTCC-ACAAACGCCGCTATAGACCATGAC
*
1044793 CTTTAGCGGCGTTTTTCCTATAAACGCCGCTATAGACCATGAC
1 CTTTAGCGGCGTTTTTCC-ACAAACGCCGCTATAGACCATGAC
*
1044836 CTTTAGCGGCGCTTTTTCCACAAACGCCACTATAGACCATGAC
1 CTTTAGCGGCG-TTTTTCCACAAACGCCGCTATAGACCATGAC
* *
1044879 CTTTAGCGGCACTTTTTCCTACAAACGCCGCTAAAGACCATGAC
1 CTTTAGCGGC-GTTTTTCC-ACAAACGCCGCTATAGACCATGAC
* * * *
1044923 CTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAGGCCTTGAC
1 CTTTAGCGGCG-TTTTTCCACAAACGCCGCTATAGACCATGAC
*
1044966 CTTTAGCGGCATTTTT
1 CTTTAGCGGCGTTTTT
1044982 TTTAAAACGC
Statistics
Matches: 250, Mismatches: 19, Indels: 13
0.89 0.07 0.05
Matches are distributed among these distances:
42 6 0.02
43 199 0.80
44 45 0.18
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTCCACAAACGCCGCTATAGACCATGAC
Found at i:1045026 original size:130 final size:130
Alignment explanation
Indices: 1044664--1044982 Score: 374
Period size: 130 Copynumber: 2.5 Consensus size: 130
1044654 GCGTCGCTAA
* * * * *
1044664 CTTTAGCGGTGTTTTCCCCACAAACGCCGCTATAGATCATGACCTTTAGCGGCA-TTTTTCACAC
1 CTTTAGCGGCGTTTTACCTACAAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTC-CAC
* ** *** * *
1044728 AAACGCCGCTATAGACCATGACCTTT-AGCGGCGTTTTTCCTACAAACGCCGTTATAGACCATGA
65 AAACGCCACTATAGACCATGACCTTTAAAAGAAATTTTTCCTACAAACGCCGCTAAAGACCATGA
1044792 C
130 C
* * * *
1044793 CTTTAGCGGCGTTTTTCCTATAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTTCCACA
1 CTTTAGCGGCGTTTTACCTACAAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTCCACA
*** * *
1044858 AACGCCACTATAGACCATGACCTTTAGCGGCACTTTTTCCTACAAACGCCGCTAAAGACCATGAC
66 AACGCCACTATAGACCATGACCTTTAAAAGAAATTTTTCCTACAAACGCCGCTAAAGACCATGAC
* * *
1044923 CTTTAGCGGCGCTTTTACC-ACAAACGCCGCTAAAGGCCTTGACCTTTAGCGGCATTTTTT
1 CTTTAGCGGCG-TTTTACCTACAAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTT
1044983 TTAAAACGCC
Statistics
Matches: 165, Mismatches: 22, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
129 76 0.46
130 83 0.50
131 6 0.04
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (130 bp):
CTTTAGCGGCGTTTTACCTACAAACGCCGCTAAAGACCATGACCTTTAGCGGCACTTTTTCCACA
AACGCCACTATAGACCATGACCTTTAAAAGAAATTTTTCCTACAAACGCCGCTAAAGACCATGAC
Found at i:1045212 original size:19 final size:20
Alignment explanation
Indices: 1045178--1045216 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1045168 TACAAAAATG
1045178 TTAAAAGTTAAAAATGATAA
1 TTAAAAGTTAAAAATGATAA
*
1045198 TTAAAAG-TCAAAATGATAA
1 TTAAAAGTTAAAAATGATAA
1045217 AAATATTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (20 bp):
TTAAAAGTTAAAAATGATAA
Found at i:1050831 original size:16 final size:17
Alignment explanation
Indices: 1050810--1050956 Score: 119
Period size: 16 Copynumber: 8.8 Consensus size: 17
1050800 ATTAAGTAAA
1050810 TTATGTAAGTTATGT-G
1 TTATGTAAGTTATGTAG
*
1050826 TTATGTAAGATATGTAAG
1 TTATGTAAGTTATGT-AG
**
1050844 -T-TGTATTTTATGTAAG
1 TTATGTAAGTTATGT-AG
*
1050860 TTCTGT-A-TTATGTATG
1 TTATGTAAGTTATGTA-G
*
1050876 TTATGTAAGTTGTGTAG
1 TTATGTAAGTTATGTAG
* *
1050893 -AATGTAAGCTATGTAAG
1 TTATGTAAGTTATGT-AG
**
1050910 TTATGTAAGTGGTGTA-
1 TTATGTAAGTTATGTAG
1050926 TTATGTAAGTTATGTAAG
1 TTATGTAAGTTATGT-AG
1050944 TTATGTAAGTTAT
1 TTATGTAAGTTAT
1050957 TATGTAAGTT
Statistics
Matches: 104, Mismatches: 16, Indels: 20
0.74 0.11 0.14
Matches are distributed among these distances:
15 1 0.01
16 62 0.60
17 8 0.08
18 33 0.32
ACGTcount: A:0.29, C:0.01, G:0.23, T:0.46
Consensus pattern (17 bp):
TTATGTAAGTTATGTAG
Found at i:1050858 original size:41 final size:41
Alignment explanation
Indices: 1050810--1050888 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
1050800 ATTAAGTAAA
*
1050810 TTATGTAAGTTATGTGTTATGTAAGATATGTAAGTTGTATT
1 TTATGTAAGTTATGTATTATGTAAGATATGTAAGTTGTATT
* * *
1050851 TTATGTAAGTTCTGTATTATGTATGTTATGTAAGTTGT
1 TTATGTAAGTTATGTATTATGTAAGATATGTAAGTTGT
1050889 GTAGAATGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.27, C:0.01, G:0.22, T:0.51
Consensus pattern (41 bp):
TTATGTAAGTTATGTATTATGTAAGATATGTAAGTTGTATT
Found at i:1050898 original size:41 final size:41
Alignment explanation
Indices: 1050812--1050918 Score: 115
Period size: 41 Copynumber: 2.6 Consensus size: 41
1050802 TAAGTAAATT
* ***
1050812 ATGTAAGTTATGTGTTATGTAAGATATGTAAGTTGTATTTT
1 ATGTAAGTTATGTATTATGTAAGATATGTAAGTTGTATAGA
* * * *
1050853 ATGTAAGTTCTGTATTATGTATGTTATGTAAGTTGTGTAGA
1 ATGTAAGTTATGTATTATGTAAGATATGTAAGTTGTATAGA
*
1050894 ATGTAAGCTATGTAAGTTATGTAAG
1 ATGTAAGTTATGT-A-TTATGTAAG
1050919 TGGTGTATTA
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
41 44 0.83
42 1 0.02
43 8 0.15
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.45
Consensus pattern (41 bp):
ATGTAAGTTATGTATTATGTAAGATATGTAAGTTGTATAGA
Found at i:1050906 original size:34 final size:34
Alignment explanation
Indices: 1050868--1050954 Score: 129
Period size: 34 Copynumber: 2.6 Consensus size: 34
1050858 AGTTCTGTAT
*
1050868 TATGTATGTTATGTAAGTTGTGTAGAATGTAAGC
1 TATGTAAGTTATGTAAGTTGTGTAGAATGTAAGC
* ** *
1050902 TATGTAAGTTATGTAAGTGGTGTATTATGTAAGT
1 TATGTAAGTTATGTAAGTTGTGTAGAATGTAAGC
1050936 TATGTAAGTTATGTAAGTT
1 TATGTAAGTTATGTAAGTT
1050955 ATTATGTAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.30, C:0.01, G:0.25, T:0.44
Consensus pattern (34 bp):
TATGTAAGTTATGTAAGTTGTGTAGAATGTAAGC
Found at i:1050950 original size:25 final size:25
Alignment explanation
Indices: 1050798--1050969 Score: 126
Period size: 25 Copynumber: 7.0 Consensus size: 25
1050788 ATATATTTAC
* *
1050798 GTATTAAGTAAATTATGTAAGTTAT
1 GTATTATGTAAGTTATGTAAGTTAT
* * *
1050823 GTGTTATGTAAGATATGTAAGTTGT
1 GTATTATGTAAGTTATGTAAGTTAT
* * *
1050848 ATTTTATGTAAGTTCTGT-A-TTAT
1 GTATTATGTAAGTTATGTAAGTTAT
* *
1050871 GTATGTTATGTAAGTTGTGT-AG-AAT
1 GTA--TTATGTAAGTTATGTAAGTTAT
* **
1050896 GTAAGCTATGTAAGTTATGTAAGTGGT
1 GT-A-TTATGTAAGTTATGTAAGTTAT
1050923 GTATTATGTAAGTTATGTAAGTTAT
1 GTATTATGTAAGTTATGTAAGTTAT
*
1050948 GTA--A-GTTA-TTATGTAAGTTAT
1 GTATTATGTAAGTTATGTAAGTTAT
1050969 G
1 G
1050970 CAAGCTTATA
Statistics
Matches: 119, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
21 14 0.12
22 3 0.03
23 5 0.04
24 1 0.01
25 89 0.75
26 4 0.03
27 3 0.03
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (25 bp):
GTATTATGTAAGTTATGTAAGTTAT
Found at i:1050961 original size:12 final size:12
Alignment explanation
Indices: 1050944--1050968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1050934 GTTATGTAAG
1050944 TTATGTAAGTTA
1 TTATGTAAGTTA
1050956 TTATGTAAGTTA
1 TTATGTAAGTTA
1050968 T
1 T
1050969 GCAAGCTTAT
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:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:1050961 original size:21 final size:21
Alignment explanation
Indices: 1050935--1051157 Score: 115
Period size: 21 Copynumber: 10.5 Consensus size: 21
1050925 ATTATGTAAG
1050935 TTATGTAAGTTATGTAAGTTA
1 TTATGTAAGTTATGTAAGTTA
*
1050956 TTATGTAAGTTATGCAAGCTTA
1 TTATGTAAGTTATGTAAG-TTA
*
1050978 -TATATAAGTTATGT-A-TTA
1 TTATGTAAGTTATGTAAGTTA
* ** *
1050996 TAACATCAAGTATTATGTAATTTA
1 TTATGT-AAG--TTATGTAAGTTA
* * *
1051020 TTATGTTA-TTATAT-A-TAA
1 TTATGTAAGTTATGTAAGTTA
* *
1051038 GTTATGTAAGTTAT-TATGTAA
1 -TTATGTAAGTTATGTAAGTTA
* *
1051059 GTTATGCAAGCTTATATATAAGTTA
1 -TTATGTAAG--T-TATGTAAGTTA
1051084 TGTAT-TAAGTTATGTAAGTTA
1 T-TATGTAAGTTATGTAAGTTA
*
1051105 TTATGTAAGTTATGCAAGCTTA
1 TTATGTAAGTTATGTAAG-TTA
* * *
1051127 -TATATAAGTTAT-TATGTAA
1 TTATGTAAGTTATGTAAGTTA
1051146 GTTATGTAAGTT
1 -TTATGTAAGTT
1051158 TATAACATTT
Statistics
Matches: 158, Mismatches: 24, Indels: 40
0.71 0.11 0.18
Matches are distributed among these distances:
18 5 0.03
19 14 0.09
20 18 0.11
21 84 0.53
22 13 0.08
23 3 0.02
24 13 0.08
25 8 0.05
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (21 bp):
TTATGTAAGTTATGTAAGTTA
Done.