Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 19 of 28
Found at i:2845210 original size:20 final size:20
Alignment explanation
Indices: 2845151--2845219 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
2845141 TAATTTAATA
* *
2845151 AATTTAATTTAATTAAA-TTA
1 AATTTAAATTAA-TAAATTTT
* *
2845171 AATTTAAAATAAT--TTTTT
1 AATTTAAATTAATAAATTTT
2845189 AATTTAAATTAATAAATTTT
1 AATTTAAATTAATAAATTTT
2845209 AATTTAAATTA
1 AATTTAAATTA
2845220 TTAATTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
18 14 0.35
19 1 0.03
20 25 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTAAATTAATAAATTTT
Found at i:2845210 original size:33 final size:32
Alignment explanation
Indices: 2845153--2845290 Score: 92
Period size: 33 Copynumber: 4.3 Consensus size: 32
2845143 ATTTAATAAA
2845153 TTTAATTT-AATTAAATTAAATTTAAAATAATTT
1 TTTAATTTAAATT-AA-TAAATTTAAAATAATTT
** *
2845186 TTTAATTTAAATTAATAAATTTTAATTTAAATT
1 TTTAATTTAAATTAATAAA-TTTAAAATAATTT
* *
2845219 ATTAA-TT-AATTAATAAA---AAAATTATTAT
1 TTTAATTTAAATTAATAAATTTAAAATAATT-T
* * *
2845247 TTAAATTTTAAAAT-ATAAATATTAATATAATTT
1 TTTAA-TTTAAATTAATAAAT-TTAAAATAATTT
*
2845280 TTTATTTTAAA
1 TTTAATTTAAA
2845291 ATTTTTAATA
Statistics
Matches: 80, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
27 5 0.06
28 4 0.05
30 7 0.09
31 13 0.16
32 12 0.15
33 28 0.35
34 11 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTAATTTAAATTAATAAATTTAAAATAATTT
Found at i:2845227 original size:12 final size:12
Alignment explanation
Indices: 2845196--2845257 Score: 51
Period size: 12 Copynumber: 5.4 Consensus size: 12
2845186 TTTAATTTAA
2845196 ATTAA-TAAATT
1 ATTAATTAAATT
2845207 -TTAATTTAAATT
1 ATTAA-TTAAATT
2845219 ATTAATT-AATT
1 ATTAATTAAATT
* **
2845230 AATAAAAAAATT
1 ATTAATTAAATT
*
2845242 ATTATTTAAATT
1 ATTAATTAAATT
2845254 -TTAA
1 ATTAA
2845258 AATATAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
10 4 0.10
11 11 0.28
12 20 0.51
13 4 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTAAATT
Found at i:2845835 original size:21 final size:20
Alignment explanation
Indices: 2845802--2845868 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 20
2845792 GATATTAGTT
2845802 ATTATTT-AA-TTAATATAA
1 ATTATTTAAATTTAATATAA
*
2845820 TTTTATTTAAATTTAATTATAA
1 -ATTATTTAAATTTAA-TATAA
2845842 ATTATTTAAATATTAATATAAA
1 ATTATTTAAAT-TTAATAT-AA
2845864 ATTAT
1 ATTAT
2845869 ATTTTAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.15
20 2 0.05
21 17 0.41
22 16 0.39
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTATTTAAATTTAATATAA
Found at i:2845875 original size:18 final size:18
Alignment explanation
Indices: 2845854--2845912 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
2845844 TATTTAAATA
2845854 TTAATATAAAATTATATT
1 TTAATATAAAATTATATT
*
2845872 TTAATATTATAA-TATATT
1 TTAATA-TAAAATTATATT
*
2845890 TTAAATAATAAAATAAT-TT
1 TT-AAT-ATAAAATTATATT
2845909 TTAA
1 TTAA
2845913 ATTAAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
18 16 0.47
19 15 0.44
20 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATATAAAATTATATT
Found at i:2845904 original size:19 final size:19
Alignment explanation
Indices: 2845859--2845914 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2845849 AAATATTAAT
2845859 ATAAAATTATATTTT-AATA
1 ATAAAA-TATATTTTAAATA
* *
2845878 TTATAATATATTTTAAATA
1 ATAAAATATATTTTAAATA
2845897 ATAAAATA-ATTTTTAAAT
1 ATAAAATATA-TTTTAAAT
2845915 TAAATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.29
19 22 0.71
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAAAATATATTTTAAATA
Found at i:2845951 original size:28 final size:27
Alignment explanation
Indices: 2845896--2845951 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
2845886 TATTTTAAAT
2845896 AATAAAATAATTTTTAAATTAAATTTA
1 AATAAAATAATTTTTAAATTAAATTTA
*
2845923 AATAAAAT-TTTTTTATTAATTAAATTTA
1 AATAAAATAATTTTTA--AATTAAATTTA
2845951 A
1 A
2845952 TTTAATTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.23
27 8 0.31
28 12 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AATAAAATAATTTTTAAATTAAATTTA
Found at i:2846204 original size:12 final size:12
Alignment explanation
Indices: 2846179--2846216 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2846169 TTTGGGTTCG
2846179 AATTTTTATATTT
1 AATTTTTAT-TTT
2846192 AATTTTTATTTT
1 AATTTTTATTTT
*
2846204 AATATTT-TTTT
1 AATTTTTATTTT
2846215 AA
1 AA
2846217 AATTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 6 0.25
12 9 0.38
13 9 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
AATTTTTATTTT
Found at i:2846257 original size:22 final size:24
Alignment explanation
Indices: 2846224--2846274 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
2846214 TAAAATTATA
*
2846224 TATTTAATTTATGTAATATT-TTT
1 TATTTAATTTATATAATATTATTT
2846247 TATTT-ATTTATATAATATTAATTT
1 TATTTAATTTATATAATATT-ATTT
2846271 TATT
1 TATT
2846275 ACAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 13 0.52
23 5 0.20
24 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
TATTTAATTTATATAATATTATTT
Found at i:2846849 original size:27 final size:26
Alignment explanation
Indices: 2846787--2846867 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 26
2846777 GATTTTTATT
* *
2846787 ATATTTATGTATTTTATTATATTATAATA
1 ATATTTA-ATATTTTA-TAT-TTATAAAA
2846816 ATATTTAAAATATTTTATATTTATAAAA
1 ATATTT--AATATTTTATATTTATAAAA
2846844 AT-TTTAATATTTTAATAATTTATA
1 ATATTTAATATTTT-AT-ATTTATA
2846868 TTACATAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
25 8 0.17
26 2 0.04
27 10 0.22
28 9 0.20
29 9 0.20
30 7 0.15
31 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
ATATTTAATATTTTATATTTATAAAA
Found at i:2846853 original size:18 final size:18
Alignment explanation
Indices: 2846814--2846864 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
2846804 TATATTATAA
*
2846814 TAATATTTA-AAATATTT
1 TAATATTTATAAAAATTT
2846831 T-ATATTTATAAAAATTT
1 TAATATTTATAAAAATTT
*
2846848 TAATATTT-TAATAATTT
1 TAATATTTATAAAAATTT
2846865 ATATTACATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 7 0.23
17 17 0.57
18 6 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATTTATAAAAATTT
Found at i:2846887 original size:34 final size:34
Alignment explanation
Indices: 2846814--2846882 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 34
2846804 TATATTATAA
* *
2846814 TAATATTTAAAATATTTTATATTTATAAAAATTT
1 TAATATTTAAAATAATTTATATTTACAAAAATTT
* *
2846848 TAATATTT-TAATAATTTATA-TTACATAAATTT
1 TAATATTTAAAATAATTTATATTTACAAAAATTT
2846880 TAA
1 TAA
2846883 AATATGTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 13 0.42
33 10 0.32
34 8 0.26
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (34 bp):
TAATATTTAAAATAATTTATATTTACAAAAATTT
Found at i:2846957 original size:21 final size:21
Alignment explanation
Indices: 2846904--2846958 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
2846894 ATGTTATGTC
2846904 ATAT-TTTAAT-TGTTATATAT
1 ATATATTTAATAT-TTATATAT
* *
2846924 ATATATATCATATTTATATA-
1 ATATATTTAATATTTATATAT
2846944 ATTATATTTAATATT
1 A-TATATTTAATATT
2846959 ATCAAATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 5 0.18
21 22 0.79
22 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
ATATATTTAATATTTATATAT
Found at i:2847084 original size:21 final size:21
Alignment explanation
Indices: 2847051--2847090 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2847041 TATAAATATT
2847051 TATAATTAAATTTAAATAAAA
1 TATAATTAAATTTAAATAAAA
* *
2847072 TATATTTATATTTAAATAA
1 TATAATTAAATTTAAATAA
2847091 TAATTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAATTAAATTTAAATAAAA
Found at i:2848193 original size:7 final size:7
Alignment explanation
Indices: 2848181--2848220 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2848171 AACATCGAAT
2848181 AAATTTA
1 AAATTTA
2848188 AAATTT-
1 AAATTTA
2848194 AAATTTA
1 AAATTTA
*
2848201 AATTTTA
1 AAATTTA
*
2848208 ATATTTA
1 AAATTTA
2848215 AAATTT
1 AAATTT
2848221 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTA
Found at i:2848198 original size:13 final size:13
Alignment explanation
Indices: 2848180--2848220 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
2848170 TAACATCGAA
2848180 TAAATTTAAAATT
1 TAAATTTAAAATT
*
2848193 TAAATTTAAATTT
1 TAAATTTAAAATT
2848206 TAATATTTAAAATT
1 TAA-ATTTAAAATT
2848220 T
1 T
2848221 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:2849113 original size:23 final size:24
Alignment explanation
Indices: 2849087--2849137 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
2849077 TCACCAAATT
* *
2849087 TTTAAATAATAATA-ATTAATTAA
1 TTTAAATAAAAATATATTAATAAA
*
2849110 TTTAAATAAAAATATTTTAATAAA
1 TTTAAATAAAAATATATTAATAAA
2849134 TTTA
1 TTTA
2849138 TTTTAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 13 0.54
24 11 0.46
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAAATAAAAATATATTAATAAA
Found at i:2849891 original size:22 final size:22
Alignment explanation
Indices: 2849850--2849892 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2849840 TTTTTTAATT
*
2849850 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTAAAAAAATATA
2849872 TAAATTTAA-TAAAAATAATAT
1 TAAATTTAATTAAAAA-AATAT
2849893 TTTTATATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTAAAAAAATATA
Found at i:2851460 original size:21 final size:22
Alignment explanation
Indices: 2851417--2851460 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2851407 TTTTTTTTAT
** *
2851417 TTTTTATAATATAATGTATTTA
1 TTTTTATAATATAAAATAATTA
2851439 TTTTT-TAATATAAAATAATTA
1 TTTTTATAATATAAAATAATTA
2851460 T
1 T
2851461 ATAATAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTTTATAATATAAAATAATTA
Found at i:2851483 original size:15 final size:15
Alignment explanation
Indices: 2851451--2851498 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2851441 TTTTAATATA
*
2851451 AAATAATTATATAAT
1 AAATAAATATATAAT
**
2851466 AAATAAATATATTTT
1 AAATAAATATATAAT
*
2851481 AAATAAAATAAATAAT
1 AAAT-AAATATATAAT
2851497 AA
1 AA
2851499 TTTTAAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATAAATATATAAT
Found at i:2851492 original size:24 final size:22
Alignment explanation
Indices: 2851452--2851506 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
2851442 TTTAATATAA
*
2851452 AATAATTATATAAT-AAATAAAT
1 AATAATTTTA-AATAAAATAAAT
2851474 -AT-ATTTTAAATAAAATAAAT
1 AATAATTTTAAATAAAATAAAT
2851494 AATAATTTTAAAT
1 AATAATTTTAAAT
2851507 TTTAAATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 3 0.10
20 13 0.45
21 4 0.14
22 9 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATTTTAAATAAAATAAAT
Found at i:2851513 original size:24 final size:24
Alignment explanation
Indices: 2851463--2851506 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
2851453 ATAATTATAT
2851463 AATAAATAAATATATTTTAAATAA
1 AATAAATAAATATATTTTAAATAA
2851487 AATAAAT-AATA-ATTTTAAAT
1 AATAAATAAATATATTTTAAAT
2851507 TTTAAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 7 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAAATAAATATATTTTAAATAA
Found at i:2851940 original size:2 final size:2
Alignment explanation
Indices: 2851930--2852086 Score: 117
Period size: 2 Copynumber: 85.0 Consensus size: 2
2851920 AATGTTTTTT
*
2851930 TA TA T- TA TA TA TA TA TA TA T- TA TA T- TA TA TG T- 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
* * *
2851968 TA TA TA T- TA TG T- TA TA TA T- TA TC TA T- TA -A TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * ** *
2852005 TA TA TA AA CA GC TA TA TA TA TA -A TA -A TA TA TA TA TA GTG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
2852046 TA TA TA TA -A TA TA -A TA TA TA CA TA -A 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
2852085 TA
1 TA
2852087 AAAAAATAAT
Statistics
Matches: 124, Mismatches: 16, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
1 14 0.11
2 109 0.88
3 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2851965 original size:25 final size:26
Alignment explanation
Indices: 2851937--2852083 Score: 102
Period size: 25 Copynumber: 5.5 Consensus size: 26
2851927 TTTTATATTA
2851937 TATATATATATATTATAT-TATATGT
1 TATATATATATATTATATATATATGT
* *
2851962 TATATATATATATTATGT-TATATAT
1 TATATATATATATTATATATATATGT
* * * * *
2851987 TATCTATTAATATAAATATATATAAACAGC
1 TATATA-T-ATAT-ATTATATATATA-TGT
*
2852017 TATATATATA-ATAATATATATATAGT
1 TATATATATATATTATATATATAT-GT
* * **
2852043 GTATATATATAATATAATATATACATAA
1 -TATATATAT-ATATTATATATATATGT
2852071 TATATATATATAT
1 TATATATATATAT
2852084 ATAAAAAAAT
Statistics
Matches: 95, Mismatches: 18, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
25 28 0.29
26 15 0.16
27 22 0.23
28 9 0.09
29 16 0.17
30 5 0.05
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (26 bp):
TATATATATATATTATATATATATGT
Found at i:2851972 original size:27 final size:27
Alignment explanation
Indices: 2851934--2852085 Score: 91
Period size: 27 Copynumber: 5.6 Consensus size: 27
2851924 TTTTTTTATA
2851934 TTATATATATATATATTATATTATATG
1 TTATATATATATATATTATATTATATG
* *
2851961 -T-TATATATATATATTATGTTATATA
1 TTATATATATATATATTATATTATATG
* * * *
2851986 TTATCTAT-TAATATAAATATATATAAACAG
1 TTATATATAT-ATAT-ATTATAT-TATA-TG
* *
2852016 CTATATATATA-ATAATATA-TATATAG
1 TTATATATATATATATTATATTATAT-G
* * *
2852042 TGTATATATATA-ATATAATATATACATA
1 T-TATATATATATATATTATAT-TATATG
*
2852070 ATATATATATATATAT
1 TTATATATATATATAT
2852086 AAAAAAATAA
Statistics
Matches: 95, Mismatches: 18, Indels: 23
0.70 0.13 0.17
Matches are distributed among these distances:
25 22 0.23
26 7 0.07
27 34 0.36
28 15 0.16
29 9 0.09
30 7 0.07
31 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (27 bp):
TTATATATATATATATTATATTATATG
Found at i:2852095 original size:25 final size:27
Alignment explanation
Indices: 2851996--2852098 Score: 76
Period size: 27 Copynumber: 3.9 Consensus size: 27
2851986 TTATCTATTA
* *
2851996 ATATAA-AT-ATATATAAACAGCTATAT
1 ATATAATATAATATATAAATA-ATATAT
* *
2852022 ATAT-A-ATAATATATATATAGTGTATAT
1 ATATAATATAATATATAAATA--ATATAT
*
2852049 ATATAATATAATATATACATAATATAT
1 ATATAATATAATATATAAATAATATAT
2852076 ATATATATATAA-A-A-AAATAATAT
1 ATATA-ATATAATATATAAATAATAT
2852099 TTTGTTTATT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
25 11 0.17
26 14 0.22
27 20 0.31
28 7 0.11
29 13 0.20
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (27 bp):
ATATAATATAATATATAAATAATATAT
Found at i:2852264 original size:22 final size:22
Alignment explanation
Indices: 2852236--2852279 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2852226 ATTTTACCTC
*
2852236 AGATTTGATCACACTGTTGGAT
1 AGATTTGACCACACTGTTGGAT
2852258 AGATTTGACCACACTGTTGGAT
1 AGATTTGACCACACTGTTGGAT
2852280 TGTTTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (22 bp):
AGATTTGACCACACTGTTGGAT
Found at i:2852457 original size:25 final size:25
Alignment explanation
Indices: 2852415--2852464 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2852405 TAATTTTTTT
*
2852415 AAATTTTTTTAAAATTTTTAATTTA
1 AAATTTTTTTAAAATTTTAAATTTA
***
2852440 AAATTTTTTTATTTTTTTAAATTTA
1 AAATTTTTTTAAAATTTTAAATTTA
2852465 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
AAATTTTTTTAAAATTTTAAATTTA
Found at i:2852463 original size:10 final size:10
Alignment explanation
Indices: 2852399--2852471 Score: 69
Period size: 10 Copynumber: 6.9 Consensus size: 10
2852389 TTTTCTTCCC
2852399 TTTTTATAATT
1 TTTTTA-AATT
2852410 TTTTTAAATT
1 TTTTTAAATT
2852420 TTTTTAAAATTT
1 TTTTT-AAA-TT
2852432 TTAATTTAAAATT
1 TT--TTT-AAATT
2852445 TTTTT--ATT
1 TTTTTAAATT
2852453 TTTTTAAATT
1 TTTTTAAATT
*
2852463 TATTTAAAT
1 TTTTTAAAT
2852472 AAATTATAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
8 8 0.15
10 20 0.36
11 12 0.22
12 4 0.07
13 4 0.07
14 7 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTTAAATT
Found at i:2857921 original size:28 final size:27
Alignment explanation
Indices: 2857879--2857944 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
2857869 AGCTTTCATA
** *
2857879 TTTGACAAATTCAAAAGAAACCACTATT
1 TTTGACAAACACAAAA-AAACCACAATT
* *
2857907 TTTGACAAACACAAAATAACTACAATT
1 TTTGACAAACACAAAAAAACCACAATT
*
2857934 TTTAACAAACA
1 TTTGACAAACA
2857945 AATAGGTGAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (27 bp):
TTTGACAAACACAAAAAAACCACAATT
Found at i:2858006 original size:23 final size:23
Alignment explanation
Indices: 2857980--2858026 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2857970 ACCACAATAC
2857980 TCATATGACAGAACCCCAAAAAT
1 TCATATGACAGAACCCCAAAAAT
2858003 TCATATGACAGAACCCCAAAAAT
1 TCATATGACAGAACCCCAAAAAT
2858026 T
1 T
2858027 AAGAAAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.19
Consensus pattern (23 bp):
TCATATGACAGAACCCCAAAAAT
Found at i:2859089 original size:22 final size:22
Alignment explanation
Indices: 2859005--2859138 Score: 66
Period size: 22 Copynumber: 6.0 Consensus size: 22
2858995 TCGTGAAAAA
2859005 AATTATATGATAAAA-ATAATAT
1 AATTATAT-ATAAAATATAATAT
* *
2859027 AAATATAT-TAAAAT-TTATAT
1 AATTATATATAAAATATAATAT
* *
2859047 AATT-TAAATTATTAATA-AATAT
1 AATTATATA-TA-AAATATAATAT
*
2859069 AATTTTATATAAAATATAATAT
1 AATTATATATAAAATATAATAT
* *
2859091 -TTTAAATATAATTAAAATATAAAAT
1 AATT--ATAT-A-TAAAATATAATAT
* *
2859116 AATT-TAAATATAATATAAATAT
1 AATTATATATAAAATAT-AATAT
2859138 A
1 A
2859139 TAAATTATTA
Statistics
Matches: 84, Mismatches: 15, Indels: 26
0.67 0.12 0.21
Matches are distributed among these distances:
19 2 0.02
20 13 0.15
21 15 0.18
22 31 0.37
23 8 0.10
24 1 0.01
25 12 0.14
26 2 0.02
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
AATTATATATAAAATATAATAT
Found at i:2859119 original size:16 final size:16
Alignment explanation
Indices: 2859093--2859133 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2859083 TATAATATTT
2859093 TAAATATAATTAAAATA
1 TAAA-ATAATTAAAATA
*
2859110 TAAAATAATTTAAATA
1 TAAAATAATTAAAATA
*
2859126 TAATATAA
1 TAAAATAA
2859134 ATATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATAATTAAAATA
Found at i:2859123 original size:27 final size:28
Alignment explanation
Indices: 2859075--2859142 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
2859065 ATATAATTTT
*
2859075 ATATAAAATAT--AATATTTTAAATATA
1 ATATAAAATATAAAATAATTTAAATATA
2859101 AT-TAAAATATAAAATAATTTAAATATA
1 ATATAAAATATAAAATAATTTAAATATA
2859128 ATATAAATATATAAA
1 ATATAAA-ATATAAA
2859143 TTATTAATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 8 0.22
26 2 0.05
27 16 0.43
28 4 0.11
29 7 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATATAAAATATAAAATAATTTAAATATA
Found at i:2859149 original size:27 final size:27
Alignment explanation
Indices: 2859015--2859149 Score: 95
Period size: 27 Copynumber: 5.1 Consensus size: 27
2859005 AATTATATGA
* *
2859015 TAAAAATAATATAAATATATTAA-AAT
1 TAAATATAATATAAATATATAAATAAT
* * * *
2859041 T-TATATAATTTAAAT-TATTAATAAA
1 TAAATATAATATAAATATATAAATAAT
* * *
2859066 TATAATTTTATATAAA-ATAT-AATATTT
1 TA-AATATAATATAAATATATAAATA-AT
2859093 TAAATATAAT-TAAA-ATATAAAATAATT
1 TAAATATAATATAAATATAT-AAATAA-T
*
2859120 TAAATATAATATAAATATATAAATTAT
1 TAAATATAATATAAATATATAAATAAT
2859147 TAA
1 TAA
2859150 TTTTATATAG
Statistics
Matches: 85, Mismatches: 14, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
24 6 0.07
25 22 0.26
26 11 0.13
27 33 0.39
28 9 0.11
29 4 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATATAATATAAATATATAAATAAT
Found at i:2859151 original size:32 final size:31
Alignment explanation
Indices: 2859051--2859152 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
2859041 TTATATAATT
**
2859051 TAAATTATTAA--TAAATATAATTTTATATA
1 TAAATTATTAATTTAAATATAATTAAATATA
* *
2859080 -AAATATAATATTTTAAATATAATTAAA-ATA
1 TAAAT-TATTAATTTAAATATAATTAAATATA
2859110 TAAA--A-TAATTTAAATATAATATAAATATA
1 TAAATTATTAATTTAAATATAAT-TAAATATA
2859139 TAAATTATTAATTT
1 TAAATTATTAATTT
2859153 TATATAGTAG
Statistics
Matches: 59, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
27 14 0.24
28 9 0.15
29 11 0.19
30 3 0.05
31 16 0.27
32 6 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
TAAATTATTAATTTAAATATAATTAAATATA
Found at i:2859371 original size:19 final size:19
Alignment explanation
Indices: 2859347--2859414 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
2859337 AAATTAAATT
2859347 AATTTTATGTATTTATATA
1 AATTTTATGTATTTATATA
* *
2859366 AATTTTTATATAATTTATATT
1 AA-TTTTATGT-ATTTATATA
* * * *
2859387 TATTTAATTTAATTAT-TA
1 AATTTTATGTATTTATATA
2859405 AATTTTATGT
1 AATTTTATGT
2859415 TATATTTACA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
18 8 0.22
19 7 0.19
20 13 0.35
21 9 0.24
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (19 bp):
AATTTTATGTATTTATATA
Found at i:2859854 original size:28 final size:26
Alignment explanation
Indices: 2859808--2859864 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 26
2859798 ATATTTTACG
2859808 ATTATATAAAATTTGATATGTTA-ATA
1 ATTATATAAAATTTGATAT-TTATATA
*
2859834 ATTATATAAATTTTAAGATATTTATATA
1 ATTATATAAAATTT--GATATTTATATA
2859862 ATT
1 ATT
2859865 TATTGTGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 13 0.48
27 3 0.11
28 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (26 bp):
ATTATATAAAATTTGATATTTATATA
Found at i:2862791 original size:15 final size:16
Alignment explanation
Indices: 2862760--2862794 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2862750 TCATTATTGT
*
2862760 ATATGAGTATAATTTA
1 ATATGAATATAATTTA
2862776 ATATGAATAT-ATTTA
1 ATATGAATATAATTTA
2862791 ATAT
1 ATAT
2862795 TTTTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (16 bp):
ATATGAATATAATTTA
Found at i:2862860 original size:26 final size:26
Alignment explanation
Indices: 2862823--2862874 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
2862813 TTTCATAAAT
*
2862823 TATATCTTATATA-TTATATTTAAAAA
1 TATATCTTATATAGATAT-TTTAAAAA
2862849 TATAT-TTGATATAGATATTTTAAAAA
1 TATATCTT-ATATAGATATTTTAAAAA
2862875 AAAATCGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 2 0.09
26 18 0.78
27 3 0.13
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (26 bp):
TATATCTTATATAGATATTTTAAAAA
Found at i:2866917 original size:21 final size:21
Alignment explanation
Indices: 2866891--2866937 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2866881 TGATTTGGTC
2866891 AATATTACTATTTAATAATAA
1 AATATTACTATTTAATAATAA
** *
2866912 AATATTTTTATTTAATTATAA
1 AATATTACTATTTAATAATAA
2866933 AATAT
1 AATAT
2866938 ATAAATATTA
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:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATTACTATTTAATAATAA
Found at i:2869804 original size:28 final size:28
Alignment explanation
Indices: 2869769--2869828 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
2869759 AGAAATTTCA
2869769 ATATTTTAAGTTGAATAGAATTGAGAGT
1 ATATTTTAAGTTGAATAGAATTGAGAGT
2869797 ATATTTTAAGTTGAATAGAATTGAGAGT
1 ATATTTTAAGTTGAATAGAATTGAGAGT
2869825 ATAT
1 ATAT
2869829 CGGTAGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (28 bp):
ATATTTTAAGTTGAATAGAATTGAGAGT
Found at i:2874454 original size:20 final size:18
Alignment explanation
Indices: 2874424--2874477 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
2874414 ATCATTTGTG
2874424 TAATG-ATATTATATTAA
1 TAATGTATATTATATTAA
2874441 TATATAGTATATTAATAATTAA
1 TA-AT-GTATATT-AT-ATTAA
*
2874463 TAATTTATATTATAT
1 TAATGTATATTATAT
2874478 AAAATTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
17 2 0.06
18 4 0.13
19 3 0.10
20 11 0.35
21 4 0.13
22 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
TAATGTATATTATATTAA
Found at i:2878535 original size:2 final size:2
Alignment explanation
Indices: 2878530--2878585 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2878520 TTGAAAAAAT
2878530 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2878572 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
2878586 GCGAGGATAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2884621 original size:18 final size:19
Alignment explanation
Indices: 2884587--2884633 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
2884577 TTATTTACCG
2884587 TATTAAATATTTATTT-AA
1 TATTAAATATTTATTTAAA
*
2884605 TATTAAAT-TTATTTTTAAA
1 TATTAAATATT-TATTTAAA
2884624 TATTTAAATA
1 TA-TTAAATA
2884634 AATAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 2 0.08
18 12 0.50
19 4 0.17
20 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTAAATATTTATTTAAA
Found at i:2887367 original size:34 final size:34
Alignment explanation
Indices: 2887324--2887393 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
2887314 ACTCTAGTAG
* *
2887324 TTAGAGACTCACG-GATGCTTGACTGGGATGCATT
1 TTAGAGACTCA-GAAATGCTTGACTGAGATGCATT
2887358 TTAGAGACTCAGAAATGCTTGACTGAGATGCATT
1 TTAGAGACTCAGAAATGCTTGACTGAGATGCATT
2887392 TT
1 TT
2887394 TAGCTTCACG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 1 0.03
34 32 0.97
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (34 bp):
TTAGAGACTCAGAAATGCTTGACTGAGATGCATT
Found at i:2888166 original size:20 final size:19
Alignment explanation
Indices: 2888141--2888178 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2888131 ATATTATTTT
*
2888141 AAATATTATTTTTTAAATTA
1 AAATATTA-ATTTTAAATTA
2888161 AAATATTAATTTTAAATT
1 AAATATTAATTTTAAATT
2888179 TTAATCGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATTAATTTTAAATTA
Found at i:2889446 original size:21 final size:19
Alignment explanation
Indices: 2889408--2889460 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
2889398 ATCATATTTT
2889408 ATATTTTATTATATTAAAA
1 ATATTTTATTATATTAAAA
*
2889427 ATATTTTA-TAT-TTATATA
1 ATATTTTATTATATTA-AAA
*
2889445 A-ATTTTAATATATTAA
1 ATATTTTATTATATTAA
2889461 TAATTTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 9 0.30
18 10 0.33
19 11 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTTTATTATATTAAAA
Found at i:2889451 original size:17 final size:16
Alignment explanation
Indices: 2889429--2889476 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 16
2889419 TATTAAAAAT
2889429 ATTTTATATTTATATAA
1 ATTTTATATTTATAT-A
2889446 ATTTTAATATATTA-ATA
1 ATTTT-ATAT-TTATATA
2889463 ATTTATATATTTAT
1 ATTT-TATATTTAT
2889477 TATATTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.11
17 14 0.52
18 7 0.26
19 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTTATATTTATATA
Found at i:2889483 original size:17 final size:17
Alignment explanation
Indices: 2889390--2889514 Score: 63
Period size: 16 Copynumber: 7.5 Consensus size: 17
2889380 GATATATAAA
2889390 ATATTTATATCATATT-TT
1 ATATTTATAT-AT-TTATT
* **
2889408 ATATTTTATTATATTAAAA
1 ATA-TTTA-TATATTTATT
2889427 ATATTT-TATATTTATAT
1 ATATTTATATATTTAT-T
* *
2889444 AAATTT-TA-ATATATT
1 ATATTTATATATTTATT
2889459 AATAATTTATATATTTATT
1 -AT-ATTTATATATTTATT
2889478 ATATTTAGT-T-TTTATT
1 ATATTTA-TATATTTATT
2889494 ATATTT-TA-A-TTATT
1 ATATTTATATATTTATT
2889508 AT-TTTAT
1 ATATTTAT
2889515 TACTATCATC
Statistics
Matches: 85, Mismatches: 10, Indels: 28
0.69 0.08 0.23
Matches are distributed among these distances:
13 3 0.04
14 9 0.11
15 1 0.01
16 25 0.29
17 17 0.20
18 12 0.14
19 15 0.18
20 3 0.04
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (17 bp):
ATATTTATATATTTATT
Found at i:2889999 original size:19 final size:20
Alignment explanation
Indices: 2889951--2890001 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
2889941 ATAATATTTA
* *
2889951 TTAAATTTTAATTTTAATAT
1 TTAAATTATATTTTTAATAT
*
2889971 TTAAA-AATATTTTTAAT-T
1 TTAAATTATATTTTTAATAT
2889989 TTAAATTATATTT
1 TTAAATTATATTT
2890002 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.23
19 15 0.58
20 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAAATTATATTTTTAATAT
Found at i:2890002 original size:17 final size:19
Alignment explanation
Indices: 2889963--2890015 Score: 51
Period size: 17 Copynumber: 3.0 Consensus size: 19
2889953 AAATTTTAAT
*
2889963 TTTAATATTTAAAAATATT
1 TTTAATATTTAAAAATATA
*
2889982 TTTAAT-TTT-AAATTATA
1 TTTAATATTTAAAAATATA
*
2889999 TTTAA-AATT-AAAATATA
1 TTTAATATTTAAAAATATA
2890016 AATATAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 20 0.69
18 3 0.10
19 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAATATTTAAAAATATA
Found at i:2890049 original size:14 final size:14
Alignment explanation
Indices: 2890016--2890078 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
2890006 TTAAAATATA
*
2890016 AATATAACTACTTTT
1 AATATAA-TAATTTT
2890031 AATATAATAATTTT
1 AATATAATAATTTT
* *
2890045 GATATAATTATTTT
1 AATATAATAATTTT
*
2890059 AAAAATAAT-ATTTAT
1 -AATATAATAATTT-T
2890074 AATAT
1 AATAT
2890079 CTATAATGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 26 0.65
15 14 0.35
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (14 bp):
AATATAATAATTTT
Found at i:2890078 original size:29 final size:29
Alignment explanation
Indices: 2889992--2890078 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
2889982 TTTAATTTTA
* * *
2889992 AATTATATTTAAAATTAAAATATA-AATAT
1 AATTAT-TTTAAAAATAATATTTATAATAT
* * *
2890021 AACTACTTTT-AATATAATAATTT-TGATAT
1 AATTA-TTTTAAAAATAAT-ATTTATAATAT
2890050 AATTATTTTAAAAATAATATTTATAATAT
1 AATTATTTTAAAAATAATATTTATAATAT
2890079 CTATAATGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
28 13 0.30
29 30 0.68
30 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (29 bp):
AATTATTTTAAAAATAATATTTATAATAT
Found at i:2905608 original size:43 final size:42
Alignment explanation
Indices: 2905561--2905642 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 42
2905551 TTTTCGATTA
*
2905561 TTAAATA-TAAAAT-TATTTAAATCAAAATAATTAAATTAATTTT
1 TTAAATATTAAAATATATTT-AAT-AAAAT-ATAAAATTAATTTT
2905604 TTAAATATTTAAAATATATTTAATAAAATATAAAATTAA
1 TTAAATA-TTAAAATATATTTAATAAAATATAAAATTAA
2905643 ACTTAAACCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
43 16 0.46
44 5 0.14
45 9 0.26
46 5 0.14
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (42 bp):
TTAAATATTAAAATATATTTAATAAAATATAAAATTAATTTT
Found at i:2905639 original size:21 final size:20
Alignment explanation
Indices: 2905563--2905641 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 20
2905553 TTCGATTATT
2905563 AAATATAAAATTATTTAAATCA
1 AAATATAAAATTATTT-AAT-A
* **
2905585 AAATAATTAAATTAATTTTTTA
1 AAAT-ATAAAATT-ATTTAATA
*
2905607 AATATTTAAAATATATTTAATA
1 AA-ATATAAAAT-TATTTAATA
2905629 AAATATAAAATTA
1 AAATATAAAATTA
2905642 AACTTAAACC
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
20 2 0.04
21 8 0.18
22 20 0.44
23 11 0.24
24 4 0.09
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATATAAAATTATTTAATA
Found at i:2905703 original size:22 final size:22
Alignment explanation
Indices: 2905651--2905708 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
2905641 AAACTTAAAC
2905651 CTATCTAAACCTAAACTAAAAAT
1 CTATCTAAA-CTAAACTAAAAAT
* *
2905674 CTAT-TAAACTTAAGTAAAAA-
1 CTATCTAAACTAAACTAAAAAT
2905694 CTCATCTAAACTAAA
1 CT-ATCTAAACTAAA
2905709 AGCCTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 2 0.07
21 12 0.40
22 12 0.40
23 4 0.13
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.28
Consensus pattern (22 bp):
CTATCTAAACTAAACTAAAAAT
Found at i:2907601 original size:103 final size:104
Alignment explanation
Indices: 2907369--2907658 Score: 325
Period size: 103 Copynumber: 2.7 Consensus size: 104
2907359 AGGTTAAAAT
* * **
2907369 GGTAAACTTGA-AGTAAACATAGATGCTGGCTTATTAACATGAAGCGGACTTTGAGCTAATGCTA
1 GGTAAACTT-ACACTAAACATAGATGCTGGCTGATTAACATGAA-TAG-CTTTGAGCTAATGCTA
* * *
2907433 CATTGTTCTTATTTTTTATTTTTCTTAAAGTAACTCTTTTCGA
63 -ATTGTTCTTATTTTTCATATTTCTTAAAGTAACTCTTTTCAA
* * * *
2907476 GGTAGACTTGCATTAAACATAGATGCTGGCTGATTAACATCAATAGCTTTGAGCTAATGCT-A-T
1 GGTAAACTTACACTAAACATAGATGCTGGCTGATTAACATGAATAGCTTTGAGCTAATGCTAATT
* * *
2907539 GTTCTTGTTTTTCATATTTCTTAAAAGTACCTGTTTTCAA
66 GTTCTTATTTTTCATATTTCTT-AAAGTAACTCTTTTCAA
* *
2907579 GGTAAACTTACACTAAACATAGATGCTGGCTGATTAACATGAATAGGGCTTTGATCTAATGTTAC
1 GGTAAACTTACACTAAACATAGATGCTGGCTGATTAACATGAATA--GCTTTGAGCTAATGCTA-
* *
2907644 GTTGTTGTTATTTTT
63 ATTGTTCTTATTTTT
2907659 TATTTTTTTA
Statistics
Matches: 154, Mismatches: 22, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
102 20 0.13
103 56 0.36
105 29 0.19
106 1 0.01
107 37 0.24
108 11 0.07
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.40
Consensus pattern (104 bp):
GGTAAACTTACACTAAACATAGATGCTGGCTGATTAACATGAATAGCTTTGAGCTAATGCTAATT
GTTCTTATTTTTCATATTTCTTAAAGTAACTCTTTTCAA
Found at i:2908603 original size:24 final size:24
Alignment explanation
Indices: 2908532--2908608 Score: 57
Period size: 24 Copynumber: 3.0 Consensus size: 24
2908522 TATCTAAGTT
* *
2908532 TATATATTTTTT-AAATATTTATA
1 TATAAATTTTTTAAAATATTTAAA
*
2908555 TTTAATATTTATGTTATATATATATTTAAA
1 TATAA-ATTT-T-TTA-A-A-ATATTTAAA
*
2908585 TATAAATTTTTTAAAATATATAAA
1 TATAAATTTTTTAAAATATTTAAA
2908609 AAATAAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
23 3 0.07
24 12 0.29
25 2 0.05
26 3 0.07
27 3 0.07
28 2 0.05
29 5 0.12
30 12 0.29
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (24 bp):
TATAAATTTTTTAAAATATTTAAA
Found at i:2910877 original size:24 final size:24
Alignment explanation
Indices: 2910850--2910914 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
2910840 AATAGAGGAA
* *
2910850 GAGGAGGAAGTGGAAGTGGAAGTT
1 GAGGAGGAGGTGGAAGAGGAAGTT
* * *
2910874 GAGGAAGAGGTAGAAGAGGAGGTT
1 GAGGAGGAGGTGGAAGAGGAAGTT
*
2910898 GAAGAGGAGGTGGAAGA
1 GAGGAGGAGGTGGAAGA
2910915 AGAGGACGAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.12
Consensus pattern (24 bp):
GAGGAGGAGGTGGAAGAGGAAGTT
Found at i:2910901 original size:12 final size:12
Alignment explanation
Indices: 2910880--2910919 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2910870 AGTTGAGGAA
2910880 GAGGTAGAAGAG
1 GAGGTAGAAGAG
*
2910892 GAGGTTGAAGAG
1 GAGGTAGAAGAG
* *
2910904 GAGGTGGAAGAA
1 GAGGTAGAAGAG
2910916 GAGG
1 GAGG
2910920 ACGAGAATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.53, T:0.10
Consensus pattern (12 bp):
GAGGTAGAAGAG
Found at i:2917036 original size:133 final size:134
Alignment explanation
Indices: 2916722--2917045 Score: 384
Period size: 134 Copynumber: 2.4 Consensus size: 134
2916712 TTTTTCCTCT
* * * * * *
2916722 CTTATAATTCCATCCGACAAATGAATTGCTTCCATCTTCCATGGACTTTAAC-TCACCTTCCACT
1 CTTACAATTCCATCCAACAAATGAATTACTCCCATCTTCCATGGACTCT-ACTTCATCTTCCACT
* ** ****
2916786 AGCATCAGACCAAATAGATATCCAATTCTCTATTAAAATTGTCCGACCAACCAGTTTGGTTCTTT
65 AGCATCAAACCAAATAGATATCCAATTCTCTATTAAAACCGTCCGACCAACCAGTCCCCTTCTTT
* *
2916851 CATCA
130 AAGCA
* * *
2916856 CTTACAATTTCATCCAATAAAGGAATTACTCCCATCTTCCATGGACTCTACTTCATCTTCCACTA
1 CTTACAATTCCATCCAACAAATGAATTACTCCCATCTTCCATGGACTCTACTTCATCTTCCACTA
* * * **** *
2916921 GCATCAAACCAAATATATCTCCAATTCTCTATT-AAACCGTTCGACCAGTTGGTCCCCTTTTTTA
66 GCATCAAACCAAATAGATATCCAATTCTCTATTAAAACCGTCCGACCAACCAGTCCCCTTCTTTA
2916985 AGCA
131 AGCA
2916989 CTTACAATTCCATCCAACAAATGAATTACTCCCATCTTCCATGGACTC-ACTTCATCT
1 CTTACAATTCCATCCAACAAATGAATTACTCCCATCTTCCATGGACTCTACTTCATCT
2917046 GTTCATCTTC
Statistics
Matches: 160, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
132 9 0.06
133 68 0.43
134 83 0.52
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (134 bp):
CTTACAATTCCATCCAACAAATGAATTACTCCCATCTTCCATGGACTCTACTTCATCTTCCACTA
GCATCAAACCAAATAGATATCCAATTCTCTATTAAAACCGTCCGACCAACCAGTCCCCTTCTTTA
AGCA
Found at i:2921071 original size:24 final size:24
Alignment explanation
Indices: 2921044--2921109 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 24
2921034 TAATTTATTT
2921044 TATTTAAATTTAATTATAAAAAT-A
1 TATTTAAATTTAA-TATAAAAATAA
*
2921068 TA-TT-AATATTAATATAAAATTAA
1 TATTTAAAT-TTAATATAAAAATAA
2921091 TATTTAATATTTTAATATA
1 TATTTAA-A-TTTAATATA
2921110 TTTTAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
22 11 0.31
23 9 0.26
24 4 0.11
25 1 0.03
26 9 0.26
27 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATTTAAATTTAATATAAAAATAA
Found at i:2925681 original size:15 final size:16
Alignment explanation
Indices: 2925654--2925691 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2925644 TTTCTTTACT
2925654 TTTATTTACTTTTATC
1 TTTATTTACTTTTATC
*
2925670 TTTATTTA-TTTTTTC
1 TTTATTTACTTTTATC
*
2925685 TTAATTT
1 TTTATTT
2925692 TGAAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTACTTTTATC
Found at i:2926519 original size:14 final size:14
Alignment explanation
Indices: 2926500--2926528 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2926490 ACCATGGCAC
2926500 TTTTTTTTT-AATT
1 TTTTTTTTTAAATT
2926513 TTTTTTTTTAAATT
1 TTTTTTTTTAAATT
2926527 TT
1 TT
2926529 AACAAATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTTTAAATT
Found at i:2926968 original size:19 final size:20
Alignment explanation
Indices: 2926923--2926970 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2926913 AAAATTTTAA
2926923 TTTATTATT-TAAAATTTATT
1 TTTA-TATTATAAAATTTATT
**
2926943 TAAATATTATAAAA-TTATT
1 TTTATATTATAAAATTTATT
2926962 TTTATATTA
1 TTTATATTA
2926971 ATATTTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTATATTATAAAATTTATT
Found at i:2926978 original size:26 final size:26
Alignment explanation
Indices: 2926937--2927016 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 26
2926927 TTATTTAAAA
2926937 TTTAT-TTAA-ATATTATAAAATTATT
1 TTTATATTAATAT-TTATAAAATTATT
*
2926962 TTTATATTAATATTTAT-ATATT-TT
1 TTTATATTAATATTTATAAAATTATT
* * ** *
2926986 TTTAAATAAATATAAATAAAAATATT
1 TTTATATTAATATTTATAAAATTATT
2927012 TTTAT
1 TTTAT
2927017 TATTTAAACA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
24 15 0.35
25 12 0.28
26 14 0.33
27 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTATATTAATATTTATAAAATTATT
Found at i:2927513 original size:19 final size:19
Alignment explanation
Indices: 2927489--2927537 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
2927479 TATATATATA
*
2927489 TATATAATTAAATTATTTT
1 TATATAATTAAATAATTTT
* *
2927508 TATATATTTATATAATTTT
1 TATATAATTAAATAATTTT
*
2927527 TATGTAATTAA
1 TATATAATTAA
2927538 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TATATAATTAAATAATTTT
Found at i:2929925 original size:15 final size:16
Alignment explanation
Indices: 2929905--2929934 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2929895 TTGACTTTGG
2929905 AATTATATT-ACTTAC
1 AATTATATTAACTTAC
2929920 AATTATATTAACTTA
1 AATTATATTAACTTA
2929935 TCTTTGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTATATTAACTTAC
Found at i:2931834 original size:33 final size:32
Alignment explanation
Indices: 2931797--2931896 Score: 80
Period size: 34 Copynumber: 3.0 Consensus size: 32
2931787 AAAAATTATT
*
2931797 TATAATTATT-ATAT-TTAAGATATTATATATTTA
1 TATAATT-TTAATATATTAA-AAATT-TATATTTA
*
2931830 TATAAATTTTAATATATTAAAAATTTATTTTTA
1 TAT-AATTTTAATATATTAAAAATTTATATTTA
* * *
2931863 TATAAATTTTTAATAAATTAATAGTTT-TATTTA
1 TAT-AA-TTTTAATATATTAAAAATTTATATTTA
2931896 T
1 T
2931897 TAAGTATTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
33 24 0.42
34 29 0.51
35 4 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (32 bp):
TATAATTTTAATATATTAAAAATTTATATTTA
Found at i:2932970 original size:25 final size:23
Alignment explanation
Indices: 2932915--2932971 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
2932905 TGTATATATG
2932915 TTAAATTTATATAATTTATTTTA
1 TTAAATTTATATAATTTATTTTA
*
2932938 TTATAATTATATTTAATTT-TTTTAA
1 TTA-AATT-TATATAATTTATTTT-A
2932963 TTTAAATTT
1 -TTAAATTT
2932972 TAATATATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 3 0.10
24 9 0.31
25 14 0.48
26 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTAAATTTATATAATTTATTTTA
Found at i:2933014 original size:19 final size:19
Alignment explanation
Indices: 2932984--2933028 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2932974 ATATATTGAT
2932984 ATATTT-TATA-TTATATAA
1 ATATTTATATATTTATAT-A
*
2933002 ATATTTATATATTTATATT
1 ATATTTATATATTTATATA
2933021 ATATTTAT
1 ATATTTAT
2933029 GTTAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 12 0.50
20 6 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTTATATATTTATATA
Found at i:2933015 original size:8 final size:8
Alignment explanation
Indices: 2932945--2933019 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 8
2932935 TTATTATAAT
2932945 TATATTTA
1 TATATTTA
* *
2932953 -ATTTTTT
1 TATATTTA
2932960 TA-ATTTA
1 TATATTTA
*
2932967 AAT-TTTAA
1 TATATTT-A
*
2932975 TATATTGA
1 TATATTTA
2932983 TATATTT-
1 TATATTTA
2932990 TATATTATA
1 TATATT-TA
2932999 TAAATATTTA
1 T--ATATTTA
2933009 TATATTTA
1 TATATTTA
2933017 TAT
1 TAT
2933020 TATATTTATG
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
7 18 0.35
8 22 0.43
9 3 0.06
10 3 0.06
11 5 0.10
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (8 bp):
TATATTTA
Found at i:2933620 original size:10 final size:10
Alignment explanation
Indices: 2933597--2933659 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
2933587 ATTTGATAAA
* *
2933597 ATATAAAAAA
1 ATATAAATAT
2933607 ATATAAATAT
1 ATATAAATAT
2933617 ATATAATATGAAT
1 ATATAA-AT--AT
2933630 ATATAAATAT
1 ATATAAATAT
2933640 AT-TAAAT-T
1 ATATAAATAT
*
2933648 TTATAAA-AT
1 ATATAAATAT
2933657 ATA
1 ATA
2933660 AATTTTAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
8 2 0.05
9 12 0.27
10 18 0.41
11 2 0.05
12 2 0.05
13 8 0.18
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
ATATAAATAT
Found at i:2933672 original size:15 final size:15
Alignment explanation
Indices: 2933642--2933683 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
2933632 ATAAATATAT
2933642 TAAATTTTATAAAATA
1 TAAATTTTA-AAAATA
2933658 TAAATTTTAAAAATA
1 TAAATTTTAAAAATA
2933673 TAAATTTTAAA
1 TAAATTTTAAA
2933684 TATAATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAATTTTAAAAATA
Found at i:2933686 original size:13 final size:14
Alignment explanation
Indices: 2933604--2933688 Score: 64
Period size: 15 Copynumber: 5.6 Consensus size: 14
2933594 AAAATATAAA
*
2933604 AAAATATAAATATAT
1 AAAATATAAAT-TTT
* * *
2933619 ATAATATGAATATAT
1 AAAATATAAAT-TTT
2933634 AAATATATTAAATTTTAT
1 AAA-ATA-TAAA-TTT-T
2933652 AAAATATAAATTTT
1 AAAATATAAATTTT
2933666 AAAAATATAAATTTT
1 -AAAATATAAATTTT
2933681 -AAATATAA
1 AAAATATAA
2933689 TATAAATACA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
13 8 0.13
14 1 0.02
15 32 0.53
16 7 0.12
17 7 0.12
18 5 0.08
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (14 bp):
AAAATATAAATTTT
Found at i:2933695 original size:33 final size:33
Alignment explanation
Indices: 2933595--2933696 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
2933585 AAATTTGATA
* *
2933595 AAATATAAAAAAATA-TAAA-TATATATAATAT
1 AAATATATAAAAATATTAAATTTTATATAATAT
* * *
2933626 GAATATATAAATATATTAAATTTTATAAAATAT
1 AAATATATAAAAATATTAAATTTTATATAATAT
*
2933659 AAAT-TTTAAAAATA-TAAATTTTAAATATAATAT
1 AAATATATAAAAATATTAAATTTT--ATATAATAT
2933692 AAATA
1 AAATA
2933697 CAAAAATTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
31 20 0.35
32 12 0.21
33 25 0.44
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (33 bp):
AAATATATAAAAATATTAAATTTTATATAATAT
Found at i:2933969 original size:2 final size:2
Alignment explanation
Indices: 2933964--2933991 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2933954 ATTTTTTTAA
2933964 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
2933992 TGCTGGATAA
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:2934195 original size:2 final size:2
Alignment explanation
Indices: 2934188--2934220 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2934178 ATGGGTAGAA
*
2934188 AT AT AT AT AT AT AG AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2934221 CCTCACTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2937341 original size:20 final size:21
Alignment explanation
Indices: 2937311--2937349 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2937301 TTGTAAATTC
*
2937311 AAAATATTATTTTTTATTATT
1 AAAATATTATTTTATATTATT
2937332 AAAA-ATTATTTTATATTA
1 AAAATATTATTTTATATTA
2937350 ATATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAAATATTATTTTATATTATT
Found at i:2937364 original size:21 final size:21
Alignment explanation
Indices: 2937338--2937380 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
2937328 TATTAAAAAT
2937338 TATTTTAT-ATTAATATTTAAA
1 TATTTTATAATTAA-ATTTAAA
2937359 TATTTTATAATTAAATTTAAA
1 TATTTTATAATTAAATTTAAA
2937380 T
1 T
2937381 TAAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTATAATTAAATTTAAA
Found at i:2937408 original size:29 final size:27
Alignment explanation
Indices: 2937356--2937413 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
2937346 ATTAATATTT
*
2937356 AAATATTTTATAATTAAATTTAAATTA
1 AAATATTTTATAATTAAATATAAATTA
2937383 AAATATTTTTATTAATT-AATAATAAATTA
1 AAATA-TTTTA-TAATTAAAT-ATAAATTA
2937412 AA
1 AA
2937414 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 5 0.19
28 8 0.30
29 14 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATATTTTATAATTAAATATAAATTA
Found at i:2937409 original size:50 final size:50
Alignment explanation
Indices: 2937329--2937439 Score: 113
Period size: 51 Copynumber: 2.2 Consensus size: 50
2937319 ATTTTTTATT
* **
2937329 ATTAAAA-ATTATTTTATATTAATATTTAAA-TATTTTATAATTAAATTTAA
1 ATTAAAATATTATTTTATATTAATATATAAATTAAATTA-AATTAAA-TTAA
*
2937379 ATTAAAATATTTTTATTA-ATTAATA-ATAAATTAAATTAAATTAAATTAA
1 ATTAAAATATTATT-TTATATTAATATATAAATTAAATTAAATTAAATTAA
2937428 ATTTTAAAATAT
1 A--TTAAAATAT
2937440 CATATTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
49 5 0.10
50 18 0.35
51 26 0.50
52 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (50 bp):
ATTAAAATATTATTTTATATTAATATATAAATTAAATTAAATTAAATTAA
Found at i:2937415 original size:5 final size:5
Alignment explanation
Indices: 2937405--2937430 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2937395 TAATTAATAA
2937405 TAAAT TAAAT TAAAT TAAAT TAAAT T
1 TAAAT TAAAT TAAAT TAAAT TAAAT T
2937431 TTAAAATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:2942352 original size:13 final size:13
Alignment explanation
Indices: 2942336--2942360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2942326 TAAAATAAAC
2942336 AAAGAAAAGAAGA
1 AAAGAAAAGAAGA
2942349 AAAGAAAAGAAG
1 AAAGAAAAGAAG
2942361 TGTACATACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAAAGAAGA
Found at i:2943222 original size:18 final size:17
Alignment explanation
Indices: 2943161--2943230 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 17
2943151 AAAGATTAAA
*
2943161 TTAAAT-TAAATTATTAT
1 TTAAATATAAA-TATAAT
* *
2943178 TTAAATAATAAAAATTATT
1 TTAAAT-ATAAATA-TAAT
*
2943197 TTATATATAAATATAAT
1 TTAAATATAAATATAAT
*
2943214 TATAAATATTAATATAA
1 T-TAAATATAAATATAA
2943231 AAATATTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
17 10 0.24
18 20 0.49
19 11 0.27
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATATAAATATAAT
Found at i:2945539 original size:2 final size:2
Alignment explanation
Indices: 2945532--2945570 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2945522 ACCTCATGAT
2945532 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2945571 TTAATAAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2947040 original size:2 final size:2
Alignment explanation
Indices: 2947033--2947059 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2947023 GTCACCAATT
2947033 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 T
2947060 GATGTCTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2952756 original size:18 final size:16
Alignment explanation
Indices: 2952742--2952775 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
2952732 CTTTCTCGTC
2952742 TTCTTCTCCTCTCTCT
1 TTCTTCTCCTCTCTCT
2952758 TTCTCTCTCTCTCTCTCT
1 TTCT-TCTC-CTCTCTCT
2952776 CTGTGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCTTCTCCTCTCTCT
Found at i:2956158 original size:2 final size:2
Alignment explanation
Indices: 2956153--2956178 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2956143 AAAAAAGTTG
2956153 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
2956179 TATGAAGAGA
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:2958910 original size:16 final size:18
Alignment explanation
Indices: 2958863--2958912 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
2958853 AAATAAGTGA
2958863 AAAAAAAGAATAAACGACG
1 AAAAAAAGAA-AAACGACG
* *
2958882 AAAAAAATAAAAAGGAC-
1 AAAAAAAGAAAAACGACG
*
2958899 AAAAAAAAAAAAAC
1 AAAAAAAGAAAAAC
2958913 ACACTCTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 12 0.44
18 6 0.22
19 9 0.33
ACGTcount: A:0.78, C:0.08, G:0.10, T:0.04
Consensus pattern (18 bp):
AAAAAAAGAAAAACGACG
Found at i:2959215 original size:32 final size:34
Alignment explanation
Indices: 2959170--2959240 Score: 83
Period size: 33 Copynumber: 2.1 Consensus size: 34
2959160 AATTAAATTT
* ** *
2959170 TATTTGTTTAATTTATTAATTTTA-AAAAATTAA
1 TATTTGTTAAATTTATTAATAATATAAAAATAAA
*
2959203 TATTT-TTAAATTTTTTAATAATATAAAAATAAA
1 TATTTGTTAAATTTATTAATAATATAAAAATAAA
2959236 TATTT
1 TATTT
2959241 ATTTTTATGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (34 bp):
TATTTGTTAAATTTATTAATAATATAAAAATAAA
Found at i:2961057 original size:3 final size:3
Alignment explanation
Indices: 2961049--2961077 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2961039 TGGCCAATCT
2961049 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2961078 TTTGCAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2961296 original size:18 final size:18
Alignment explanation
Indices: 2961275--2961309 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2961265 TGTTACCTGA
* *
2961275 TGTGAGGTTGTCCACCTT
1 TGTGAGGCTGTCAACCTT
2961293 TGTGAGGCTGTCAACCT
1 TGTGAGGCTGTCAACCT
2961310 GTAGCCTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.23, G:0.29, T:0.34
Consensus pattern (18 bp):
TGTGAGGCTGTCAACCTT
Found at i:2964022 original size:2 final size:2
Alignment explanation
Indices: 2964015--2964049 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2964005 AAAATTTGTG
2964015 TA TA TA 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
2964050 TTATCCTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2966169 original size:12 final size:12
Alignment explanation
Indices: 2966154--2966185 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2966144 ACATGTGTGC
*
2966154 ATACATATTTTT
1 ATACATATTTTA
2966166 ATACATATTTTA
1 ATACATATTTTA
2966178 ATACATAT
1 ATACATAT
2966186 AATATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (12 bp):
ATACATATTTTA
Found at i:2966807 original size:15 final size:14
Alignment explanation
Indices: 2966771--2966821 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
2966761 ATATATAATT
2966771 AATAATATTAATAA
1 AATAATATTAATAA
*
2966785 AGTAATATTAATTAA
1 AATAATATTAA-TAA
*
2966800 AATGATATTAATAA
1 AATAATATTAATAA
*
2966814 AAAAATAT
1 AATAATAT
2966822 AATTAGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (14 bp):
AATAATATTAATAA
Found at i:2967120 original size:28 final size:27
Alignment explanation
Indices: 2967083--2967144 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
2967073 GTAAAAGTAC
2967083 AAAATTTATATAAATTAAAAATT-AAATT
1 AAAA-TTATATAAATT-AAAATTAAAATT
**
2967111 ATAAATTATATTTATTAAAATTAAAATT
1 A-AAATTATATAAATTAAAATTAAAATT
2967139 AAAATT
1 AAAATT
2967145 GTAGTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
27 11 0.37
28 16 0.53
29 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAAATTATATAAATTAAAATTAAAATT
Found at i:2967143 original size:27 final size:30
Alignment explanation
Indices: 2967100--2967158 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
2967090 ATATAAATTA
2967100 AAAATTAAATTATAAA-T-TA-TATTTATT
1 AAAATTAAATTATAAATTGTAGTATTTATT
2967127 AAAATTAAAATTA-AAATTGTAGTATTTATT
1 AAAATT-AAATTATAAATTGTAGTATTTATT
2967157 AA
1 AA
2967159 TAAATTATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
27 9 0.32
28 7 0.25
29 2 0.07
30 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (30 bp):
AAAATTAAATTATAAATTGTAGTATTTATT
Found at i:2967216 original size:3 final size:3
Alignment explanation
Indices: 2967208--2967251 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2967198 AAAAGAAATT
2967208 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2967252 TGCCTTGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2967958 original size:15 final size:16
Alignment explanation
Indices: 2967940--2967969 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2967930 AAAATACAAT
2967940 AAAAAAA-GGAAAAAA
1 AAAAAAAGGGAAAAAA
2967955 AAAAAAAGGGAAAAA
1 AAAAAAAGGGAAAAA
2967970 CCCATGTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAGGGAAAAAA
Found at i:2968817 original size:25 final size:25
Alignment explanation
Indices: 2968778--2968853 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
2968768 TCAGTTTAAA
*
2968778 TAAAATTAATTTTAATATAAATTTT-T
1 TAAAA-TAATATTAAT-TAAATTTTAT
2968804 TAAAATAATATTAATTTAAATTATTAT
1 TAAAATAATATTAA-TTAAATT-TTAT
* *
2968831 TTAAATAATA-AAATTAAATTTTA
1 TAAAATAATATTAATTAAATTTTA
2968854 AATTAAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
24 3 0.07
25 21 0.48
26 10 0.23
27 10 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAAATAATATTAATTAAATTTTAT
Found at i:2968834 original size:12 final size:13
Alignment explanation
Indices: 2968812--2968863 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 13
2968802 TTTAAAATAA
2968812 TATTAATTTAAAT
1 TATTAATTTAAAT
2968825 TATT-ATTTAAAT
1 TATTAATTTAAAT
* * *
2968837 AATAAAATTAAAT
1 TATTAATTTAAAT
*
2968850 T-TTAAATTAAAT
1 TATTAATTTAAAT
2968862 TA
1 TA
2968864 ATCAAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTAATTTAAAT
Found at i:2969074 original size:17 final size:16
Alignment explanation
Indices: 2969033--2969104 Score: 54
Period size: 17 Copynumber: 4.3 Consensus size: 16
2969023 TTATGTTTTT
*
2969033 ATTATATTTAAATAAATT
1 ATTA-ATTTAAATAAA-A
* *
2969051 TTTATTTTAAATAAAA
1 ATTAATTTAAATAAAA
**
2969067 ATTAATTTATCTTAAAA
1 ATTAATTTA-AATAAAA
* *
2969084 ATTTATTTAAATATAA
1 ATTAATTTAAATAAAA
2969100 ATTAA
1 ATTAA
2969105 AAATTTAAAA
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
16 15 0.37
17 23 0.56
18 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTAATTTAAATAAAA
Found at i:2969169 original size:29 final size:29
Alignment explanation
Indices: 2969078--2969210 Score: 119
Period size: 30 Copynumber: 4.6 Consensus size: 29
2969068 TTAATTTATC
2969078 TTAAAAATTTATTTAAATATAAATTAAAAA
1 TTAAAAATTTATTT-AATATAAATTAAAAA
* * * * * *
2969108 TTTAAAACTTATTAAAAAATATATTAAATA
1 TTAAAAATTTATT-TAATATAAATTAAAAA
*
2969138 TTAAAAATTTATTTAATGTAAATTAAAAA
1 TTAAAAATTTATTTAATATAAATTAAAAA
** *
2969167 TTAAGTATCTATTTAA-ATATAA-TAAAAA
1 TTAAAAATTTATTTAATATA-AATTAAAAA
2969195 -TATAAAATTTATTTAA
1 TTA-AAAATTTATTTAA
2969211 ATACAAAATT
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
27 2 0.03
28 18 0.22
29 26 0.32
30 34 0.43
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
TTAAAAATTTATTTAATATAAATTAAAAA
Found at i:2969212 original size:17 final size:16
Alignment explanation
Indices: 2969192--2969225 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2969182 AATATAATAA
*
2969192 AAATATAAAATTTATTT
1 AAATACAAAATTT-TTT
2969209 AAATACAAAATTTTTT
1 AAATACAAAATTTTTT
2969225 A
1 A
2969226 TTATTTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATACAAAATTTTTT
Found at i:2969220 original size:59 final size:60
Alignment explanation
Indices: 2969078--2969213 Score: 158
Period size: 59 Copynumber: 2.3 Consensus size: 60
2969068 TTAATTTATC
*
2969078 TTAAAAATTTATTTAAATATAAATTAAAAATTTAAAACTTATTAAAAAATATATTAAATA
1 TTAAAAATTTATTTAAATATAAATTAAAAATTTAAAACTTATTAAAAAATATATAAAATA
* * * *
2969138 TTAAAAATTTATTT-AATGTAAATTAAAAA-TTAAGTA-TCTATTTAAATATA-ATAAAA-A
1 TTAAAAATTTATTTAAATATAAATTAAAAATTTAA-AACT-TATTAAAAAATATATAAAATA
2969195 -TATAAAATTTATTTAAATA
1 TTA-AAAATTTATTTAAATA
2969214 CAAAATTTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
56 2 0.03
57 12 0.18
58 13 0.20
59 25 0.38
60 14 0.21
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (60 bp):
TTAAAAATTTATTTAAATATAAATTAAAAATTTAAAACTTATTAAAAAATATATAAAATA
Found at i:2979927 original size:18 final size:20
Alignment explanation
Indices: 2979911--2979951 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2979901 TCGTTAAATA
2979911 TAAATATATTTAAAAATTAT
1 TAAATATATTTAAAAATTAT
**
2979931 TTTATATATTTAAAAAATTAT
1 TAAATATATTT-AAAAATTAT
2979952 ATTTATTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAATATATTTAAAAATTAT
Found at i:2979939 original size:20 final size:22
Alignment explanation
Indices: 2979914--2979957 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
2979904 TTAAATATAA
2979914 ATATATTT-AAAAATTAT-TTT
1 ATATATTTAAAAAATTATATTT
2979934 ATATATTTAAAAAATTATATTT
1 ATATATTTAAAAAATTATATTT
2979956 AT
1 AT
2979958 TCATGCTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATATTTAAAAAATTATATTT
Found at i:2980482 original size:4 final size:4
Alignment explanation
Indices: 2980473--2980497 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2980463 ATTCCATGGA
2980473 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
2980498 AGCATGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:2982293 original size:6 final size:6
Alignment explanation
Indices: 2982284--2982312 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2982274 GTTAATCTGC
2982284 CCTTGT CCTTGT CCTTGT CCTTGT CCTTG
1 CCTTGT CCTTGT CCTTGT CCTTGT CCTTG
2982313 CTGCACTCTA
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:0.00, C:0.34, G:0.17, T:0.48
Consensus pattern (6 bp):
CCTTGT
Found at i:2982839 original size:2 final size:2
Alignment explanation
Indices: 2982832--2982870 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2982822 AAGAAAGTGG
2982832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2982871 GAAAATCACT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2983157 original size:17 final size:17
Alignment explanation
Indices: 2983135--2983177 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2983125 AAGTTAATGC
2983135 AATAATTGAGAAAATAA
1 AATAATTGAGAAAATAA
* * *
2983152 AATAATAGATAAGATAA
1 AATAATTGAGAAAATAA
2983169 AATATATTG
1 AATA-ATTG
2983178 GCTAGTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (17 bp):
AATAATTGAGAAAATAA
Found at i:2983658 original size:17 final size:18
Alignment explanation
Indices: 2983626--2983659 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2983616 TTAAATAAAT
2983626 TATAAAAAATAAAATTAA
1 TATAAAAAATAAAATTAA
*
2983644 TATAAATAA-AAAATTA
1 TATAAAAAATAAAATTA
2983660 TTAATTAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TATAAAAAATAAAATTAA
Found at i:2985964 original size:21 final size:23
Alignment explanation
Indices: 2985936--2985991 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 23
2985926 ATCTAATATG
2985936 ATAT-ATATTATTAAATATT-T-
1 ATATAATATTATTAAATATTGTA
* *
2985956 ATTTAATATTA-AAAATATTGTA
1 ATATAATATTATTAAATATTGTA
2985978 ATATAA-ATTATTAA
1 ATATAATATTATTAA
2985992 TATAATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 10 0.36
21 11 0.39
22 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATAATATTATTAAATATTGTA
Found at i:2986596 original size:15 final size:15
Alignment explanation
Indices: 2986572--2986601 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2986562 TTTATTTTTT
*
2986572 ATATATAATATATTA
1 ATATAAAATATATTA
2986587 ATATAAAATATATTA
1 ATATAAAATATATTA
2986602 CTTATATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATAAAATATATTA
Found at i:2990911 original size:3 final size:3
Alignment explanation
Indices: 2990905--2990933 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2990895 AAGCAATTAC
2990905 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2990934 AAAAGCAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2991499 original size:35 final size:35
Alignment explanation
Indices: 2991425--2991500 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
2991415 AGATTATTAT
**
2991425 TTAAATAATAAAATAATTATTTTAATATAATATTT
1 TTAAATAATAAAATAATTATTTTAATATAATATAA
*
2991460 TTAAATAATAAAATAATT-TTTTTATATCAA-ATAAA
1 TTAAATAATAAAATAATTATTTTAATAT-AATAT-AA
2991495 TTAAAT
1 TTAAAT
2991501 CAAAATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (35 bp):
TTAAATAATAAAATAATTATTTTAATATAATATAA
Found at i:2992059 original size:16 final size:16
Alignment explanation
Indices: 2992038--2992068 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2992028 TAATTAATTA
*
2992038 ATTTATTTTTTTATTT
1 ATTTATTTTTATATTT
2992054 ATTTATTTTTATATT
1 ATTTATTTTTATATT
2992069 GCTAAATGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTATTTTTATATTT
Found at i:2996585 original size:14 final size:14
Alignment explanation
Indices: 2996566--2996617 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
2996556 AATAATATTT
2996566 TAAATAAAAATATA
1 TAAATAAAAATATA
*
2996580 TAAATATAAATA-A
1 TAAATAAAAATATA
**
2996593 TAAA-ATATTATATA
1 TAAATA-AAAATATA
2996607 TAAATAAAAAT
1 TAAATAAAAAT
2996618 GTTTGCTTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
12 1 0.03
13 8 0.28
14 19 0.66
15 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATAAAAATATA
Done.