Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 18 of 19
Found at i:2193781 original size:26 final size:26
Alignment explanation
Indices: 2193684--2193785 Score: 77
Period size: 26 Copynumber: 3.9 Consensus size: 26
2193674 TTACATAATA
*
2193684 TTAAAAAATAA-ATTAAATTATTTATATT
1 TTAAAAAATAATA-TAAA-TA-TAATATT
* * *
2193712 TT-AAAATTAAT-TAAAAATAAAATT
1 TTAAAAAATAATATAAATATAATATT
* *
2193736 ATTAAAAATTAATTAAAAATATAATATT
1 -TTAAAAAATAA-TATAAATATAATATT
2193764 TTAAAAAATAATATAAAT-TAAT
1 TTAAAAAATAATATAAATATAAT
2193786 TAATTAATTT
Statistics
Matches: 60, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
24 5 0.08
25 7 0.12
26 18 0.30
27 18 0.30
28 12 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TTAAAAAATAATATAAATATAATATT
Found at i:2194122 original size:26 final size:26
Alignment explanation
Indices: 2194093--2194175 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
2194083 TTGCTATTAT
2194093 TGTTATTGTTTATATTAAGTAATAGA
1 TGTTATTGTTTATATTAAGTAATAGA
* * * *
2194119 TGTTTATGGATTTATTATT-ACTATTA-T
1 TG-TTATTG-TTTA-TATTAAGTAATAGA
* * *
2194146 TGTTATTGTTTATTTTAAGAAATCGA
1 TGTTATTGTTTATATTAAGTAATAGA
2194172 TGTT
1 TGTT
2194176 TATGGATAGA
Statistics
Matches: 41, Mismatches: 11, Indels: 10
0.66 0.18 0.16
Matches are distributed among these distances:
24 3 0.07
25 7 0.17
26 11 0.27
27 7 0.17
28 9 0.22
29 4 0.10
ACGTcount: A:0.29, C:0.02, G:0.14, T:0.54
Consensus pattern (26 bp):
TGTTATTGTTTATATTAAGTAATAGA
Found at i:2194157 original size:53 final size:53
Alignment explanation
Indices: 2194079--2194182 Score: 172
Period size: 53 Copynumber: 2.0 Consensus size: 53
2194069 CATCTCTTTC
* *
2194079 ATTATTGCTATTATTGTTATTGTTTATATTAAGTAATAGATGTTTATGGATTT
1 ATTATTACTATTATTGTTATTGTTTATATTAAGAAATAGATGTTTATGGATTT
* *
2194132 ATTATTACTATTATTGTTATTGTTTATTTTAAGAAATCGATGTTTATGGAT
1 ATTATTACTATTATTGTTATTGTTTATATTAAGAAATAGATGTTTATGGAT
2194183 AGAATGTAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.54
Consensus pattern (53 bp):
ATTATTACTATTATTGTTATTGTTTATATTAAGAAATAGATGTTTATGGATTT
Found at i:2194291 original size:10 final size:11
Alignment explanation
Indices: 2194259--2194291 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2194249 TAAAATAATA
2194259 TTATAAATATT
1 TTATAAATATT
2194270 TTATAAATATT
1 TTATAAATATT
*
2194281 TT-TAAAAATT
1 TTATAAATATT
2194291 T
1 T
2194292 AAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATAAATATT
Found at i:2194314 original size:23 final size:22
Alignment explanation
Indices: 2194230--2194319 Score: 60
Period size: 23 Copynumber: 4.1 Consensus size: 22
2194220 AGATTGATTT
* *
2194230 TAAAATTTATTTTATTATTTAAA
1 TAAAATAT-TTTTAATATTTAAA
* * * *
2194253 -ATAATATTATAAATATTT-TA
1 TAAAATATTTTTAATATTTAAA
*
2194273 T-AAATATTTTTAAAAATTTAAA
1 TAAAATATTTTT-AATATTTAAA
*
2194295 TAAAATATATTTTATTATTTAAA
1 TAAAATAT-TTTTAATATTTAAA
2194318 TA
1 TA
2194320 GTAATTTGAA
Statistics
Matches: 49, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
20 8 0.16
21 14 0.29
22 7 0.14
23 16 0.33
24 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAAATATTTTTAATATTTAAA
Found at i:2195155 original size:12 final size:13
Alignment explanation
Indices: 2195132--2195167 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
2195122 ATAAAATTAA
*
2195132 AAATATAAAATAT
1 AAATAAAAAATAT
2195145 AAA-AAAAAATAT
1 AAATAAAAAATAT
2195157 AAATAAAAAAT
1 AAATAAAAAAT
2195168 TACTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAAAAAATAT
Found at i:2195785 original size:14 final size:15
Alignment explanation
Indices: 2195766--2195794 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2195756 AATTAAAAAA
2195766 ATTTAAATTT-TTTT
1 ATTTAAATTTATTTT
2195780 ATTTAAATTTATTTT
1 ATTTAAATTTATTTT
2195795 TGGTTTGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTAAATTTATTTT
Found at i:2196332 original size:12 final size:11
Alignment explanation
Indices: 2196286--2196333 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
2196276 TAAATTAAAT
2196286 ATTTAA-TTTA
1 ATTTAATTTTA
2196296 ATTTAA-TTTA
1 ATTTAATTTTA
*
2196306 ATTTGAATTTGA
1 ATTT-AATTTTA
2196318 ATTTAAGTTTTA
1 ATTTAA-TTTTA
2196330 ATTT
1 ATTT
2196334 TTTTTTGAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 14 0.42
11 4 0.12
12 15 0.45
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (11 bp):
ATTTAATTTTA
Found at i:2196334 original size:6 final size:5
Alignment explanation
Indices: 2196286--2196333 Score: 60
Period size: 5 Copynumber: 8.8 Consensus size: 5
2196276 TAAATTAAAT
2196286 ATTTA ATTTA ATTTA ATTTA ATTTGA ATTTGA ATTTA AGTTTTA ATTT
1 ATTTA ATTTA ATTTA ATTTA ATTT-A ATTT-A ATTTA A--TTTA ATTT
2196334 TTTTTTGAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 24 0.60
6 11 0.28
7 5 0.12
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (5 bp):
ATTTA
Found at i:2196684 original size:22 final size:21
Alignment explanation
Indices: 2196641--2196695 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
2196631 TGTTTTAATT
*
2196641 AATAAAAATATTTAAATTTAAA
1 AATAAAAA-ATTTAAATATAAA
*
2196663 AATAAAAAATTATTAATATAAA
1 AATAAAAAATT-TAAATATAAA
*
2196685 ATTAAATAAAT
1 AATAAA-AAAT
2196696 ACATTGTGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 21 0.75
23 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAAAAAATTTAAATATAAA
Found at i:2196847 original size:16 final size:16
Alignment explanation
Indices: 2196823--2196896 Score: 66
Period size: 16 Copynumber: 4.8 Consensus size: 16
2196813 ATAGAATTAG
*
2196823 ATATTATATATAAAA-A
1 ATATAATATA-AAAATA
2196839 ATATAATATAAAAATA
1 ATATAATATAAAAATA
*
2196855 ATATAATAT-AATATA
1 ATATAATATAAAAATA
* *
2196870 A-ATTATATTAAAATTA
1 ATATAATA-TAAAAATA
2196886 ATATAA-ATAAA
1 ATATAATATAAA
2196897 TTATTAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
14 5 0.10
15 15 0.31
16 25 0.52
17 3 0.06
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATAATATAAAAATA
Found at i:2196849 original size:14 final size:15
Alignment explanation
Indices: 2196830--2196896 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
2196820 TAGATATTAT
2196830 ATATAAAA-AATATA
1 ATATAAAATAATATA
2196844 ATATAAAAATAATATA
1 ATAT-AAAATAATATA
* *
2196860 ATATAATATAA-ATT
1 ATATAAAATAATATA
2196874 ATATTAAAATTAATATA
1 ATA-TAAAA-TAATATA
2196891 A-ATAAA
1 ATATAAA
2196897 TTATTAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
14 9 0.20
15 18 0.41
16 14 0.32
17 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATAAAATAATATA
Found at i:2196887 original size:21 final size:23
Alignment explanation
Indices: 2196836--2196923 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 23
2196826 TTATATATAA
*
2196836 AAAATATAATAT-AA-AAATAAT
1 AAAATATAATATAAATAAATATT
* *
2196857 ATAATATAATATAAAT-TATATT
1 AAAATATAATATAAATAAATATT
2196879 AAAAT-TAATATAAATAAATTATT
1 AAAATATAATATAAATAAA-TATT
* *
2196902 AAAAT-TTATATAAATATATATT
1 AAAATATAATATAAATAAATATT
2196924 TTTAAATATA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
21 21 0.38
22 15 0.27
23 20 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAATATAATATAAATAAATATT
Found at i:2196897 original size:14 final size:13
Alignment explanation
Indices: 2196825--2196899 Score: 55
Period size: 14 Copynumber: 5.3 Consensus size: 13
2196815 AGAATTAGAT
2196825 ATTATATATAAAAA
1 ATTA-ATATAAAAA
2196839 ATATAATATAAAAATA
1 AT-TAATAT-AAAA-A
2196855 ATATAATATAATATAA
1 AT-TAATATAA-A-AA
*
2196871 ATT-ATAT-TAAA
1 ATTAATATAAAAA
2196882 ATTAATATAAATAA
1 ATTAATATAAA-AA
2196896 ATTA
1 ATTA
2196900 TTAAAATTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
11 5 0.10
12 5 0.10
13 1 0.02
14 16 0.31
15 9 0.18
16 14 0.27
17 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTAATATAAAAA
Found at i:2196905 original size:23 final size:25
Alignment explanation
Indices: 2196858--2196917 Score: 88
Period size: 23 Copynumber: 2.4 Consensus size: 25
2196848 AAAAATAATA
2196858 TAATATAATATAAATTATATTAAAAT
1 TAATATAA-ATAAATTATATTAAAAT
2196884 TAATATAAATAAA-T-TATTAAAAT
1 TAATATAAATAAATTATATTAAAAT
*
2196907 TTATATAAATA
1 TAATATAAATA
2196918 TATATTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 19 0.58
24 1 0.03
25 5 0.15
26 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TAATATAAATAAATTATATTAAAAT
Found at i:2196934 original size:20 final size:21
Alignment explanation
Indices: 2196909--2196954 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2196899 ATTAAAATTT
2196909 ATATAAATAT-ATATTTTTAA
1 ATATAAATATAATATTTTTAA
*
2196929 ATATAATTATAATATTTTTAA
1 ATATAAATATAATATTTTTAA
2196950 ATATA
1 ATATA
2196955 CAAATTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATAAATATAATATTTTTAA
Found at i:2197464 original size:15 final size:14
Alignment explanation
Indices: 2197429--2197482 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
2197419 ATAAAAATAA
2197429 AATTATAAATTAAAT
1 AATTA-AAATTAAAT
2197444 AATTAAAATTAATAT
1 AATTAAAATTAA-AT
* *
2197459 ATTTAAATATAAAAT
1 AATTAAA-ATTAAAT
*
2197474 AAATAAAAT
1 AATTAAAAT
2197483 ATTAAATTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 9 0.27
15 20 0.61
16 4 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTAAAATTAAAT
Found at i:2197537 original size:19 final size:19
Alignment explanation
Indices: 2197515--2197583 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
2197505 AAAAAAAATT
2197515 AAATTATTTAATATTTAAA
1 AAATTATTTAATATTTAAA
* * *
2197534 AAATTAGTAAATAATTAAA
1 AAATTATTTAATATTTAAA
2197553 AAATTAAATTATAAT-TTTAAA
1 AAATT--ATT-TAATATTTAAA
2197574 ATAATTATTT
1 A-AATTATTT
2197584 TATTAATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 22 0.55
20 3 0.08
21 8 0.20
22 7 0.17
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (19 bp):
AAATTATTTAATATTTAAA
Found at i:2197612 original size:26 final size:25
Alignment explanation
Indices: 2197576--2197633 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
2197566 ATTTTAAAAT
*
2197576 AATTATTTTATTA-ATATATAAATAAA
1 AATTAATTTATTATATA-AT-AATAAA
2197602 AATTAATTTATTATATAATAATAAA
1 AATTAATTTATTATATAATAATAAA
*
2197627 ATTTAAT
1 AATTAAT
2197634 AAATATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 12 0.41
26 14 0.48
27 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTAATTTATTATATAATAATAAA
Found at i:2197624 original size:25 final size:26
Alignment explanation
Indices: 2197576--2197633 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
2197566 ATTTTAAAAT
*
2197576 AATTATTTTATTAATATATAAATAAA
1 AATTAATTTATTAATATATAAATAAA
2197602 AATTAATTTATT-ATATA-ATAATAAA
1 AATTAATTTATTAATATATA-AATAAA
*
2197627 ATTTAAT
1 AATTAAT
2197634 AAATATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 1 0.03
25 17 0.59
26 11 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTAATTTATTAATATATAAATAAA
Found at i:2198126 original size:9 final size:9
Alignment explanation
Indices: 2198089--2198154 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
2198079 GTATCAGTTA
*
2198089 TATTTTATT
1 TATTATATT
*
2198098 TATATATATCA
1 TAT-TATAT-T
*
2198109 TACTATATT
1 TATTATATT
2198118 TATTATATT
1 TATTATATT
*
2198127 TTTTAATATT
1 TATT-ATATT
* *
2198137 TATTAAACT
1 TATTATATT
2198146 TATTATATT
1 TATTATATT
2198155 CATATAATAT
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
9 24 0.56
10 17 0.40
11 2 0.05
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.61
Consensus pattern (9 bp):
TATTATATT
Found at i:2198135 original size:10 final size:10
Alignment explanation
Indices: 2198113--2198166 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
2198103 ATATCATACT
2198113 ATATTTATT-
1 ATATTTATTA
*
2198122 ATATTTTTTA
1 ATATTTATTA
2198132 ATATTTATTA
1 ATATTTATTA
*
2198142 A-ACTTATT-
1 ATATTTATTA
*
2198150 ATATTCATATA
1 ATATTTAT-TA
2198161 ATATTT
1 ATATTT
2198167 TTTATCATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 1 0.03
9 18 0.51
10 11 0.31
11 5 0.14
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTATTA
Found at i:2198402 original size:28 final size:27
Alignment explanation
Indices: 2198356--2198429 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
2198346 AATTTATATG
* * *
2198356 AATATAAAATATTTTAAATATAA-TTA
1 AATATAAAAAATTATAAATATAACATA
2198382 TAATATAAAAAATATATAAATATAACATA
1 -AATATAAAAAAT-TATAAATATAACATA
2198411 AATAT-AAAAATTATCAAAT
1 AATATAAAAAATTAT-AAAT
2198430 TACTTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.07
27 21 0.51
28 15 0.37
29 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (27 bp):
AATATAAAAAATTATAAATATAACATA
Found at i:2198403 original size:17 final size:19
Alignment explanation
Indices: 2198383--2198421 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2198373 ATATAATTAT
*
2198383 AATATAA-A-AAATATATA
1 AATATAACATAAATATAAA
2198400 AATATAACATAAATATAAA
1 AATATAACATAAATATAAA
2198419 AAT
1 AAT
2198422 TATCAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AATATAACATAAATATAAA
Found at i:2198420 original size:27 final size:27
Alignment explanation
Indices: 2198351--2198429 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 27
2198341 ATTAAAATTT
*
2198351 ATATGAATAT-AAAATATTTTAAATATAA
1 ATAT-AATATAAAAATA-TATAAATATAA
*
2198379 TTATAATATAAAAAATATATAAATATAA
1 ATATAATAT-AAAAATATATAAATATAA
2198407 CATA-AATATAAAAAT-TATCAAAT
1 -ATATAATATAAAAATATAT-AAAT
2198430 TACTTTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 3 0.07
27 15 0.34
28 18 0.41
29 8 0.18
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
ATATAATATAAAAATATATAAATATAA
Found at i:2201171 original size:25 final size:25
Alignment explanation
Indices: 2201096--2201173 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 25
2201086 ATAATTAATA
*
2201096 AAAATTTATCTTTTTAATT-TTTATATT
1 AAAA-TTAT-TTTTTAATTATTTA-AAT
* *
2201123 AATATATATTTTATAATTAAATTTAAAT
1 AAAAT-TATTTTTTAATT--ATTTAAAT
2201151 AAAATTATTTTTTAATTATTTAA
1 AAAATTATTTTTTAATTATTTAA
2201174 TATCTATTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
25 6 0.14
26 9 0.21
27 17 0.40
28 6 0.14
29 4 0.10
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (25 bp):
AAAATTATTTTTTAATTATTTAAAT
Found at i:2201408 original size:24 final size:24
Alignment explanation
Indices: 2201364--2201459 Score: 92
Period size: 24 Copynumber: 4.0 Consensus size: 24
2201354 AAATTTTATT
2201364 TTATTATTTAAAATAAT-ATTAAAA
1 TTATTATTT-AAATAATAATTAAAA
*
2201388 TTATT-TTTAAATTAATAATTATAA
1 TTATTATTTAAA-TAATAATTAAAA
* * * *
2201412 TTA-AATTTAAATAA-AAATATAT
1 TTATTATTTAAATAATAATTAAAA
2201434 TTAATTATTTAAATAATAATTAAAA
1 TT-ATTATTTAAATAATAATTAAAA
2201459 T
1 T
2201460 CGAATTAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
22 11 0.19
23 11 0.19
24 30 0.52
25 6 0.10
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATTATTTAAATAATAATTAAAA
Found at i:2201415 original size:18 final size:17
Alignment explanation
Indices: 2201381--2201423 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
2201371 TTAAAATAAT
**
2201381 ATTAAAATTATTTTTAA
1 ATTAAAATTATAATTAA
2201398 ATTAATAATTATAATTAA
1 ATTAA-AATTATAATTAA
*
2201416 ATTTAAAT
1 ATTAAAAT
2201424 AAAAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAAAATTATAATTAA
Found at i:2202421 original size:30 final size:30
Alignment explanation
Indices: 2202386--2202446 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
2202376 ATGTAGGTAA
*
2202386 TAAATTTTAAATT-TTATTAAATTAAATAAT
1 TAAATTTT-AATTATTAATAAATTAAATAAT
* *
2202416 TAAATTTTTATTATTAATAAATTAAGTAAT
1 TAAATTTTAATTATTAATAAATTAAATAAT
2202446 T
1 T
2202447 TAAGTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 3 0.11
30 24 0.89
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
TAAATTTTAATTATTAATAAATTAAATAAT
Found at i:2202431 original size:22 final size:22
Alignment explanation
Indices: 2202383--2202440 Score: 57
Period size: 22 Copynumber: 2.5 Consensus size: 22
2202373 TTTATGTAGG
2202383 TAATAAATTTTAAATTTTATTAAAT
1 TAATAAA--TTAAATTTTATT-AAT
2202408 TAA-ATAATTAAATTTTTATT-AT
1 TAATA-AATTAAA-TTTTATTAAT
2202430 TAATAAATTAA
1 TAATAAATTAA
2202441 GTAATTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
22 11 0.37
23 6 0.20
24 8 0.27
25 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATAAATTAAATTTTATTAAT
Found at i:2203164 original size:9 final size:10
Alignment explanation
Indices: 2203150--2203182 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
2203140 AAATAATATG
2203150 ATATAAA-AA
1 ATATAAATAA
2203159 ATATAAATATA
1 ATATAAATA-A
2203170 ATATAAATAA
1 ATATAAATAA
2203180 ATA
1 ATA
2203183 AATATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.32
10 5 0.23
11 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
ATATAAATAA
Found at i:2203167 original size:20 final size:19
Alignment explanation
Indices: 2203134--2203188 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
2203124 TTTAATCTTG
*
2203134 ATAAAAAAAT-AATATGAT
1 ATAAAAAAATAAATATAAT
2203152 ATAAAAAATATAAATATAAT
1 ATAAAAAA-ATAAATATAAT
*
2203172 ATAAATAAATAAATATA
1 ATAAAAAAATAAATATA
2203189 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 8 0.24
19 11 0.33
20 14 0.42
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAAAAATAAATATAAT
Found at i:2203176 original size:38 final size:38
Alignment explanation
Indices: 2203134--2203208 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
2203124 TTTAATCTTG
2203134 ATAAAAAAAT-AATATGATATAAAAAATATA-AATATAAT
1 ATAAAAAAATAAATAT-AT-TAAAAAATATATAATATAAT
* **
2203172 ATAAATAAATAAATATATTAAAATTTATATAATATAA
1 ATAAAAAAATAAATATATTAAAAAATATATAATATAA
2203209 ATTAGTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 9 0.28
38 18 0.56
39 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (38 bp):
ATAAAAAAATAAATATATTAAAAAATATATAATATAAT
Found at i:2203207 original size:33 final size:33
Alignment explanation
Indices: 2203165--2203240 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
2203155 AAAAATATAA
*
2203165 ATATAATATAAATAAATAA-ATATATTAAAATTT
1 ATATAATATAAATAAATAACATATAAT-AAATTT
* * *
2203198 ATATAATATAAATTAGTAACATATAATAATTTT
1 ATATAATATAAATAAATAACATATAATAAATTT
2203231 ATA-AATATAA
1 ATATAATATAA
2203241 TATTTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 7 0.18
33 25 0.66
34 6 0.16
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (33 bp):
ATATAATATAAATAAATAACATATAATAAATTT
Found at i:2203249 original size:14 final size:14
Alignment explanation
Indices: 2203223--2203256 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
2203213 GTAACATATA
2203223 ATAATTTTATAAAT
1 ATAATTTTATAAAT
2203237 ATAATATTT-TAAAT
1 ATAAT-TTTATAAAT
2203251 ATAATT
1 ATAATT
2203257 ATAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 15 0.79
15 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATTTTATAAAT
Found at i:2207921 original size:41 final size:42
Alignment explanation
Indices: 2207870--2207950 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 42
2207860 AATATATTGT
2207870 ATTTATAAAAAT-T-TTAATATATTAATAATTTATATTATATAA
1 ATTTATAAAAATATATTAATATATT-AT-ATTTATATTATATAA
* *
2207912 ATTT-TAAAAATATATTTATATATTATATTTTTATTATAT
1 ATTTATAAAAATATATTAATATATTATATTTATATTATAT
2207951 TATACGTGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 19 0.54
42 7 0.20
43 9 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (42 bp):
ATTTATAAAAATATATTAATATATTATATTTATATTATATAA
Found at i:2207948 original size:11 final size:13
Alignment explanation
Indices: 2207922--2207988 Score: 52
Period size: 14 Copynumber: 5.2 Consensus size: 13
2207912 ATTTTAAAAA
2207922 TATATTTATATAT
1 TATATTTATATAT
2207935 TATATTT-T-TAT
1 TATATTTATATAT
*
2207946 TATA-TTATACGTGT
1 TATATTTATA--TAT
*
2207960 CATATTTATATAAT
1 TATATTTATAT-AT
*
2207974 CATATTTA-ATAT
1 TATATTTATATAT
2207986 TAT
1 TAT
2207989 CAAGTTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
10 2 0.05
11 8 0.18
12 5 0.11
13 10 0.23
14 14 0.32
15 5 0.11
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (13 bp):
TATATTTATATAT
Found at i:2208193 original size:4 final size:4
Alignment explanation
Indices: 2208184--2208217 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2208174 TAATACATGT
2208184 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
2208218 AAATATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2208482 original size:4 final size:4
Alignment explanation
Indices: 2208473--2208506 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2208463 TAATACATGT
2208473 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
2208507 AAATATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2208502 original size:289 final size:290
Alignment explanation
Indices: 2208032--2208615 Score: 1143
Period size: 289 Copynumber: 2.0 Consensus size: 290
2208022 TTTCCATTCC
2208032 TTATACAAAAAATGTACGAGAGCTTCAATTTTTTTTTACGGAATAGCAAATATCAAATGCTTAAA
1 TTATACAAAAAATGTACGAGAGCTTCAATTTTTTTTTACGGAATAGCAAATATCAAATGCTTAAA
2208097 ATCATTAATTACTAAAAGGTAACCATCCCATGCATTGGTGGTGGAAATAAAAAAGCTTCAAAAGC
66 ATCATTAATTACTAAAAGGTAACCATCCCATGCATTGGTGGTGGAAATAAAAAAGCTTCAAAAGC
2208162 AGCTTCATAGGATAATACATGTTTTATTTATTTATTTATTTATTTATTTATTTATTAAATATATT
131 AGCTTCATAGGATAATACATGTTTTATTTATTTATTTATTTATTTATTTATTTATTAAATATATT
2208227 TTATAAGACACATATCATTTAATTAATTTA-TTATGAAGTTTTTTTTATTATCAGTATATGAAAT
196 TTATAAGACACATATCATTTAATTAATTTATTTATGAAGTTTTTTTTATTATCAGTATATGAAAT
2208291 AATTATTCATTAATAAATAATAATTCTAAA
261 AATTATTCATTAATAAATAATAATTCTAAA
*
2208321 TTATACAAAAAATGTATGAGAGCTTCAATTTTTTTTTACGGAATAGCAAATATCAAATGCTTAAA
1 TTATACAAAAAATGTACGAGAGCTTCAATTTTTTTTTACGGAATAGCAAATATCAAATGCTTAAA
*
2208386 ATCATTTATTACTAAAAGGTAACCATCCCATGCATTGGTGGTGGAAATAAAAAAGCTTCAAAAGC
66 ATCATTAATTACTAAAAGGTAACCATCCCATGCATTGGTGGTGGAAATAAAAAAGCTTCAAAAGC
2208451 AGCTTCATAGGATAATACATGTTTTATTTATTTATTTATTTATTTATTTATTTATTAAATATATT
131 AGCTTCATAGGATAATACATGTTTTATTTATTTATTTATTTATTTATTTATTTATTAAATATATT
2208516 TTATAAGACACATATCATTTAATTAATTTATTTATGAAGTTTTTTTTATTATCAGTATATGAAAT
196 TTATAAGACACATATCATTTAATTAATTTATTTATGAAGTTTTTTTTATTATCAGTATATGAAAT
2208581 AATTATTCATTAATAAATAATAATTCTAAA
261 AATTATTCATTAATAAATAATAATTCTAAA
2208611 TTATA
1 TTATA
2208616 TTTGTCGCGA
Statistics
Matches: 292, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
289 223 0.76
290 69 0.24
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (290 bp):
TTATACAAAAAATGTACGAGAGCTTCAATTTTTTTTTACGGAATAGCAAATATCAAATGCTTAAA
ATCATTAATTACTAAAAGGTAACCATCCCATGCATTGGTGGTGGAAATAAAAAAGCTTCAAAAGC
AGCTTCATAGGATAATACATGTTTTATTTATTTATTTATTTATTTATTTATTTATTAAATATATT
TTATAAGACACATATCATTTAATTAATTTATTTATGAAGTTTTTTTTATTATCAGTATATGAAAT
AATTATTCATTAATAAATAATAATTCTAAA
Found at i:2214173 original size:17 final size:18
Alignment explanation
Indices: 2214097--2214175 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 18
2214087 TCAAAATTTA
*
2214097 TAAA-ATATAAATATTTT
1 TAAATATATAAATATATT
* *
2214114 TAAATATAATTTTAATAT-TA
1 TAAATAT-A--TAAATATATT
*
2214134 TAAATATATAAATATGATA
1 TAAATATATAAATAT-ATT
2214153 TAAATATATAAAT-TATT
1 TAAATATATAAATATATT
2214170 TAAATA
1 TAAATA
2214176 ATTAAATTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
17 18 0.35
18 3 0.06
19 17 0.33
20 8 0.15
21 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (18 bp):
TAAATATATAAATATATT
Found at i:2214718 original size:2 final size:2
Alignment explanation
Indices: 2214711--2214744 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2214701 TTATATTCAA
*
2214711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2214745 GAAGAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2215179 original size:16 final size:16
Alignment explanation
Indices: 2215160--2215214 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
2215150 ATATATATCT
2215160 TAAAATTTATATAATA
1 TAAAATTTATATAATA
*
2215176 T-AAATTTTTA-ATATA
1 TAAAATTTATATA-ATA
*
2215191 TTAAAATTTAAATAAATA
1 -TAAAATTTATAT-AATA
2215209 TAAAAT
1 TAAAAT
2215215 ATCTTAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
14 1 0.03
15 11 0.35
16 2 0.06
17 13 0.42
18 3 0.10
19 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:2215189 original size:18 final size:18
Alignment explanation
Indices: 2215160--2215233 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 18
2215150 ATATATATCT
2215160 TAAAATTT--ATATAATA
1 TAAAATTTAAATATAATA
* *
2215176 TAAATTTTTAATAT-AT-
1 TAAAATTTAAATATAATA
2215192 TAAAATTTAAATA-AATA
1 TAAAATTTAAATATAATA
2215209 TAAAATATCTTAAATATAATTA
1 T-AAA-AT-TTAAATATAA-TA
2215231 TAA
1 TAA
2215234 TATAATAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
16 20 0.43
17 3 0.07
18 7 0.15
19 2 0.04
20 7 0.15
21 4 0.09
22 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAATTTAAATATAATA
Found at i:2215702 original size:14 final size:13
Alignment explanation
Indices: 2215677--2215725 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
2215667 TTTTAAATGT
2215677 TAAATAAAAATAA
1 TAAATAAAAATAA
2215690 TAAATATAAAATAA
1 TAAATA-AAAATAA
* *
2215704 AAAATTACAAAAAAA
1 TAAA-TA-AAAATAA
2215719 TAAATAA
1 TAAATAA
2215726 TTTATAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 7 0.23
14 12 0.40
15 11 0.37
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAATAAAAATAA
Found at i:2216465 original size:16 final size:17
Alignment explanation
Indices: 2216432--2216473 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2216422 TACTTAAATG
2216432 ATTTTTTAATATTATTA
1 ATTTTTTAATATTATTA
* *
2216449 ATTTTTTTAT-TTGTTA
1 ATTTTTTAATATTATTA
*
2216465 ATATTTTAA
1 ATTTTTTAA
2216474 AATAGTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
ATTTTTTAATATTATTA
Found at i:2222391 original size:2 final size:2
Alignment explanation
Indices: 2222384--2222417 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2222374 ATTGAGAATC
2222384 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2222418 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2222422 original size:2 final size:2
Alignment explanation
Indices: 2222417--2222449 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2222407 ATATATATAT
2222417 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 A
2222450 TTGAGGGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2223120 original size:30 final size:28
Alignment explanation
Indices: 2223058--2223145 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 28
2223048 ATTTAACTTG
* *
2223058 ATATTTTGTGTAT-TTATATTATTTTTAA
1 ATATTTTAT-TATATTATATTATTTTAAA
2223086 ATATTTTATTATATTATAATTATATTTAAA
1 ATATTTTATTATATTAT-ATTAT-TTTAAA
* *
2223116 ATA--TT-TTATATTATATTAATTTAAT
1 ATATTTTATTATATTATATTATTTTAAA
2223141 ATATT
1 ATATT
2223146 AATAAAACAT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
25 8 0.16
26 4 0.08
27 12 0.24
28 14 0.27
29 5 0.10
30 8 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
ATATTTTATTATATTATATTATTTTAAA
Found at i:2223137 original size:25 final size:27
Alignment explanation
Indices: 2223071--2223146 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 27
2223061 TTTTGTGTAT
* *
2223071 TTATATTATTTTTAAATATTTTATTATA
1 TTATATTATATTTAAA-ATATTATTATA
2223099 TTATAATTATATTTAAAATATT-TTATA
1 TTAT-ATTATATTTAAAATATTATTATA
*
2223126 TTATATTA-ATTTAATATATTA
1 TTATATTATATTTAAAATATTA
2223147 ATAAAACATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
25 11 0.26
26 4 0.09
27 9 0.21
28 8 0.19
29 11 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATATTATATTTAAAATATTATTATA
Found at i:2225867 original size:2 final size:2
Alignment explanation
Indices: 2225860--2225896 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2225850 CTCCTTTCAT
2225860 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2225897 TTCCATGTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2228510 original size:26 final size:27
Alignment explanation
Indices: 2228476--2228547 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
2228466 AAAAGTCACA
* *
2228476 TTTTGTATTTGTCAAAAATGGTAGTTCC
1 TTTT-TATTTGTAAAAAATGGGAGTTCC
* *
2228504 -TTTTATTTATAAAAAATGGGGGTTCC
1 TTTTTATTTGTAAAAAATGGGAGTTCC
*
2228530 TTTTTGTTTGTAAAAAAT
1 TTTTTATTTGTAAAAAAT
2228548 AGTGGCTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 19 0.51
27 18 0.49
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (27 bp):
TTTTTATTTGTAAAAAATGGGAGTTCC
Found at i:2228534 original size:27 final size:26
Alignment explanation
Indices: 2228489--2228547 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
2228479 TGTATTTGTC
*
2228489 AAAAATGGTAGTTCCTTTTATTTATA
1 AAAAATGGGAGTTCCTTTTATTTATA
* * *
2228515 AAAAATGGGGGTTCCTTTTTGTTTGTA
1 AAAAATGGGAGTTCC-TTTTATTTATA
2228542 AAAAAT
1 AAAAAT
2228548 AGTGGCTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (26 bp):
AAAAATGGGAGTTCCTTTTATTTATA
Found at i:2233423 original size:2 final size:2
Alignment explanation
Indices: 2233416--2233453 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2233406 ATGCATGTAC
2233416 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2233454 GCATTGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2234389 original size:27 final size:26
Alignment explanation
Indices: 2234332--2234389 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
2234322 TATATTCATA
** *
2234332 ATAAAAATATATTAAATATAAATATT
1 ATAAAAATATAAAAAATATAAATATC
* *
2234358 TTAAAAATAATAAAAAATTTAAATATC
1 ATAAAAAT-ATAAAAAATATAAATATC
2234385 ATAAA
1 ATAAA
2234390 TTGTAATAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (26 bp):
ATAAAAATATAAAAAATATAAATATC
Found at i:2239131 original size:22 final size:22
Alignment explanation
Indices: 2239098--2239156 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
2239088 ATTTATATCA
*
2239098 TAATA-TTAATAAATAAATATAT
1 TAATATTTTATAAATAAAT-TAT
2239120 TAA-ATTTTATAAAAATAAATTAT
1 TAATATTTTAT--AAATAAATTAT
2239143 TAATATTTTA-AAAT
1 TAATATTTTATAAAT
2239157 TTATATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
21 5 0.16
22 7 0.22
23 6 0.19
24 14 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATATTTTATAAATAAATTAT
Found at i:2239739 original size:16 final size:16
Alignment explanation
Indices: 2239690--2239749 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 16
2239680 TTTATTAATT
*
2239690 ATAAATAATAAATATAA
1 ATAAA-AATAAATTTAA
*
2239707 ATAATATAATATAAATTACA
1 ATAA-A-AATA-AATTTA-A
2239727 ATAAAAATAAATTTAA
1 ATAAAAATAAATTTAA
2239743 ATAAAAA
1 ATAAAAA
2239750 ATTAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.22
17 9 0.24
18 10 0.27
19 5 0.14
20 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAATAAATTTAA
Found at i:2240633 original size:23 final size:21
Alignment explanation
Indices: 2240606--2240657 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
2240596 TATTTCACTA
2240606 TTTATAATAATATTAAATATTAT
1 TTTATAATAATATT-AATA-TAT
* *
2240629 TTTATATTAATATTTATATAT
1 TTTATAATAATATTAATATAT
2240650 TTTATAAT
1 TTTATAAT
2240658 TAAATTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTATAATAATATTAATATAT
Found at i:2240652 original size:21 final size:22
Alignment explanation
Indices: 2240606--2240665 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
2240596 TATTTCACTA
* *
2240606 TTTATAATAATATTAAATATTAT
1 TTTATATTAATATT-TATATTAT
2240629 TTTATATTAATATTTATA-TAT
1 TTTATATTAATATTTATATTAT
2240650 TTTATAATTAA-ATTTA
1 TTTAT-ATTAATATTTA
2240666 AATAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.38
22 8 0.24
23 13 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATATTAATATTTATATTAT
Found at i:2242431 original size:19 final size:18
Alignment explanation
Indices: 2242407--2242442 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2242397 TTTATATTTA
2242407 AAAATTTAATAAAAAATAT
1 AAAA-TTAATAAAAAATAT
*
2242426 AAAATTATTAAAAAATA
1 AAAATTAATAAAAAATA
2242443 AGTAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATTAATAAAAAATAT
Found at i:2244643 original size:18 final size:17
Alignment explanation
Indices: 2244611--2244644 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2244601 AGTTTGATCT
*
2244611 CAAGTTGATAAGACAAC
1 CAAGTGGATAAGACAAC
2244628 CAAGTGGATCAAGACAA
1 CAAGTGGAT-AAGACAA
2244645 TTAACTCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (17 bp):
CAAGTGGATAAGACAAC
Found at i:2250188 original size:10 final size:10
Alignment explanation
Indices: 2250175--2250215 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
2250165 ATTTTATGAA
2250175 TTTTTAAAAT
1 TTTTTAAAAT
*
2250185 TTTTTAATTAT
1 TTTTTAA-AAT
2250196 TTTTTAAAATT
1 TTTTTAAAA-T
2250207 TTTTTAAAA
1 TTTTTAAAA
2250216 ATATTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:2251494 original size:157 final size:156
Alignment explanation
Indices: 2251214--2251495 Score: 429
Period size: 157 Copynumber: 1.8 Consensus size: 156
2251204 CCTCGAAGTC
* * *
2251214 TTGATTTTATTTTTTATTTCTGTTTACTCATTTATCATATTTTCCCCCAACATGTGATATTAACA
1 TTGATTTTATTTTTTATTTCTATTTACTCATCTACCATATTTTCCCCCAACATGTGATATTAACA
* * * *
2251279 AATTTTTGTAATAATTGCAGCTCGTTACATAATGTCAATAACGTTCATAATTGTAACATAATGTC
66 AATTTTTGTAACAATTACAGCTCGTTACATAATGTCAATAACATTCATAATTGCAACATAATGTC
2251344 AATAACATACATAATGGTTCGAAATT
131 AATAACATACATAATGGTTCGAAATT
* * * *
2251370 TTGATTTTATTTTTTATTTTTATTTACTCATCTACCATATTTTTTCTCTAACATGTGATATTAAC
1 TTGATTTTATTTTTTATTTCTATTTACTCATCTACCATA-TTTTCCCCCAACATGTGATATTAAC
* * *
2251435 AAATTTTTGTAACAATTACATCTTGTTACATAATGTCAGTAACATTCATAATTGCAACATA
65 AAATTTTTGTAACAATTACAGCTCGTTACATAATGTCAATAACATTCATAATTGCAACATA
2251496 GTGACTGTAT
Statistics
Matches: 111, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
156 35 0.32
157 76 0.68
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (156 bp):
TTGATTTTATTTTTTATTTCTATTTACTCATCTACCATATTTTCCCCCAACATGTGATATTAACA
AATTTTTGTAACAATTACAGCTCGTTACATAATGTCAATAACATTCATAATTGCAACATAATGTC
AATAACATACATAATGGTTCGAAATT
Found at i:2251675 original size:24 final size:24
Alignment explanation
Indices: 2251648--2251703 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
2251638 CCCTTTCTAT
2251648 AAGCATGATTAGCTTAATTGCTCC
1 AAGCATGATTAGCTTAATTGCTCC
2251672 AAGCATGATTAGCTTAATTGCTCC
1 AAGCATGATTAGCTTAATTGCTCC
2251696 AAGCATGA
1 AAGCATGA
2251704 AATATTTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (24 bp):
AAGCATGATTAGCTTAATTGCTCC
Found at i:2253871 original size:22 final size:22
Alignment explanation
Indices: 2253846--2253887 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2253836 AATATTTATC
2253846 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
2253868 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
2253888 ATTTTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:2254162 original size:22 final size:22
Alignment explanation
Indices: 2254137--2254218 Score: 57
Period size: 22 Copynumber: 3.8 Consensus size: 22
2254127 AATCTAAATT
2254137 ATTATTTAATAATAAAAATTTA
1 ATTATTTAATAATAAAAATTTA
** *
2254159 ATTATAAAAT-ATATAAATATTA
1 ATTATTTAATAATAAAAAT-TTA
2254181 A-TA--TAA-AATAAAAATTTTA
1 ATTATTTAATAATAAAAA-TTTA
*
2254200 TATTATTTAAATAGTAAAA
1 -ATTATTT-AATAATAAAA
2254219 TAAGCCAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
19 11 0.24
20 2 0.04
21 11 0.24
22 12 0.27
23 1 0.02
24 2 0.04
25 6 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
ATTATTTAATAATAAAAATTTA
Found at i:2256100 original size:15 final size:15
Alignment explanation
Indices: 2256080--2256115 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2256070 TAAGGATTTC
2256080 TTTATACTAAAAA-AA
1 TTTATA-TAAAAATAA
2256095 TTTATATAAAAATAA
1 TTTATATAAAAATAA
2256110 TTTATA
1 TTTATA
2256116 ATTTAACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTATATAAAAATAA
Found at i:2257968 original size:8 final size:8
Alignment explanation
Indices: 2257955--2258041 Score: 58
Period size: 8 Copynumber: 11.0 Consensus size: 8
2257945 TCGATTATTA
2257955 AATTTTAT
1 AATTTTAT
2257963 AATTTTAT
1 AATTTTAT
*
2257971 CTATTTTA-
1 -AATTTTAT
*
2257979 AACTATTA-
1 AA-TTTTAT
2257987 AATTTTA-
1 AATTTTAT
2257994 AATTTTAT
1 AATTTTAT
*
2258002 GATTTTATT
1 AATTTTA-T
*
2258011 TATTTTA-
1 AATTTTAT
2258018 AATTATTA-
1 AATT-TTAT
*
2258026 AATCTTAT
1 AATTTTAT
2258034 AATTTTAT
1 AATTTTAT
2258042 CAAAAAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
7 18 0.28
8 33 0.52
9 13 0.20
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (8 bp):
AATTTTAT
Found at i:2257997 original size:39 final size:39
Alignment explanation
Indices: 2257952--2258041 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 39
2257942 TCTTCGATTA
*
2257952 TTAAATTTTATAATTTTATCTATTTTAAACTATTAAATT
1 TTAAATTTTATAATTTTATCTATTTTAAACTATTAAATC
* * *
2257991 TTAAATTTTATGATTTTATTTATTTTAAATTATTAAATC
1 TTAAATTTTATAATTTTATCTATTTTAAACTATTAAATC
2258030 TTATAATTTTAT
1 TTA-AATTTTAT
2258042 CAAAAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 38 0.83
40 8 0.17
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (39 bp):
TTAAATTTTATAATTTTATCTATTTTAAACTATTAAATC
Found at i:2258006 original size:15 final size:15
Alignment explanation
Indices: 2257955--2258040 Score: 59
Period size: 15 Copynumber: 5.5 Consensus size: 15
2257945 TCGATTATTA
2257955 AATTTTATAATTTTAT
1 AATTTTA-AATTTTAT
* *
2257971 CTATTTTAAACTATTA-
1 -AATTTTAAA-TTTTAT
2257987 AATTTTAAATTTTAT
1 AATTTTAAATTTTAT
* *
2258002 GATTTTATTTATTTTA-
1 AATTTTA--AATTTTAT
*
2258018 AATTATTAAATCTTAT
1 AATT-TTAAATTTTAT
2258034 AATTTTA
1 AATTTTA
2258041 TCAAAAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
14 4 0.07
15 22 0.41
16 9 0.17
17 19 0.35
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (15 bp):
AATTTTAAATTTTAT
Found at i:2259785 original size:2 final size:2
Alignment explanation
Indices: 2259778--2259825 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2259768 ATGACTAAAC
2259778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2259820 AT AT AT
1 AT AT AT
2259826 GAATCTGATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2262306 original size:36 final size:36
Alignment explanation
Indices: 2262259--2262332 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
2262249 TATGTCCGAC
2262259 ATTAAGACTCGAGTTTGAATAATATTGAAATGATAA
1 ATTAAGACTCGAGTTTGAATAATATTGAAATGATAA
2262295 ATTAAGACTCGAGTTTGAATAATATTGAAATGATAA
1 ATTAAGACTCGAGTTTGAATAATATTGAAATGATAA
2262331 AT
1 AT
2262333 GAAGTCTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (36 bp):
ATTAAGACTCGAGTTTGAATAATATTGAAATGATAA
Found at i:2264590 original size:2 final size:2
Alignment explanation
Indices: 2264583--2264618 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2264573 AAAAATACTC
*
2264583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2264619 GAAGCATGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2265330 original size:19 final size:19
Alignment explanation
Indices: 2265308--2265359 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
2265298 AATCGATCAA
*
2265308 AATTAATTAAATTTGATTT
1 AATTAATTAAATTTGAATT
* * *
2265327 AATTTATTTAATTTTAATT
1 AATTAATTAAATTTGAATT
* *
2265346 AAGTAATTCAATTT
1 AATTAATTAAATTT
2265360 TAATATACTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
AATTAATTAAATTTGAATT
Found at i:2274246 original size:16 final size:17
Alignment explanation
Indices: 2274214--2274246 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2274204 TGATCAATTT
*
2274214 AATTTATTTAGATTAAA
1 AATTAATTTAGATTAAA
2274231 AATTAATTTA-ATTAAA
1 AATTAATTTAGATTAAA
2274247 TTTAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AATTAATTTAGATTAAA
Found at i:2274256 original size:21 final size:21
Alignment explanation
Indices: 2274212--2274257 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2274202 TTTGATCAAT
* *
2274212 TTAATTTATTTAGATTAAAAA
1 TTAATTTAATTAAATTAAAAA
* *
2274233 TTAATTTAATTAAATTTAATA
1 TTAATTTAATTAAATTAAAAA
2274254 TTAA
1 TTAA
2274258 AATTGATTGA
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:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TTAATTTAATTAAATTAAAAA
Found at i:2274391 original size:22 final size:22
Alignment explanation
Indices: 2274365--2274430 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
2274355 TTTTATTTTT
*
2274365 TTTAGATAAATTTAAGTTTAAA
1 TTTAGATAGATTTAAGTTTAAA
*
2274387 TTTAGATAGGCTTT-AGTTTAAA
1 TTTAGATA-GATTTAAGTTTAAA
* **
2274409 TTTATATAGGCTTAAGTTTAAA
1 TTTAGATAGATTTAAGTTTAAA
2274431 ATTATATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 3 0.08
22 31 0.84
23 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.14, T:0.45
Consensus pattern (22 bp):
TTTAGATAGATTTAAGTTTAAA
Found at i:2274435 original size:22 final size:22
Alignment explanation
Indices: 2274376--2274437 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
2274366 TTAGATAAAT
*
2274376 TTAAGTTTAAATTTAGATAGGC
1 TTAAGTTTAAATTTATATAGGC
*
2274398 TTTAGTTTAAATTTATATAGGC
1 TTAAGTTTAAATTTATATAGGC
*
2274420 TTAAGTTTAAAATTATAT
1 TTAAGTTTAAATTTATAT
2274438 TTTATTAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.37, C:0.03, G:0.13, T:0.47
Consensus pattern (22 bp):
TTAAGTTTAAATTTATATAGGC
Found at i:2275830 original size:19 final size:19
Alignment explanation
Indices: 2275790--2275859 Score: 78
Period size: 19 Copynumber: 3.8 Consensus size: 19
2275780 TGACATTTTA
2275790 AATA-AAATA-TAAAAAA-
1 AATATAAATATTAAAAAAT
2275806 AA-ATAAATATTAAAAAAT
1 AATATAAATATTAAAAAAT
2275824 AATATAAATATTATAAAAAT
1 AATATAAATATTA-AAAAAT
*
2275844 -ATACAAATATATAAAA
1 AATATAAATAT-TAAAA
2275860 TATATGCAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
15 1 0.02
16 7 0.15
17 7 0.15
18 2 0.04
19 22 0.47
20 8 0.17
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (19 bp):
AATATAAATATTAAAAAAT
Found at i:2275922 original size:14 final size:14
Alignment explanation
Indices: 2275898--2275937 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
2275888 AAAATTTTTA
2275898 TTAATATATAATATT
1 TTAA-ATATAATATT
2275913 TTAAATATAATATT
1 TTAAATATAATATT
*
2275927 TATTAATATAA
1 T-TAAATATAA
2275938 AATACTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATATAATATT
Found at i:2276169 original size:20 final size:19
Alignment explanation
Indices: 2276128--2276172 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2276118 CACCTAAAAA
* * *
2276128 TAATTAAATTTAATTTTTT
1 TAATTAAAATAAATTTTAT
2276147 TAATTAAAATAAATATTTAT
1 TAATTAAAATAAAT-TTTAT
2276167 TAATTA
1 TAATTA
2276173 GTTTTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATTAAAATAAATTTTAT
Found at i:2276350 original size:16 final size:16
Alignment explanation
Indices: 2276313--2276347 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2276303 AATATAAAAA
*
2276313 TAATTTTTTTAATATT
1 TAATTTTTTTAATAAT
2276329 TAATTTTTTTAAATAAT
1 TAATTTTTTT-AATAAT
2276346 TA
1 TA
2276348 TTTAAATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTTTTAATAAT
Found at i:2285620 original size:14 final size:14
Alignment explanation
Indices: 2285601--2285633 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2285591 TTGATTTTAC
2285601 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
2285615 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
2285629 AAAAA
1 AAAAA
2285634 TTCATTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:2286210 original size:21 final size:23
Alignment explanation
Indices: 2286175--2286228 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 23
2286165 AAGTTACTGA
2286175 ATTTAATAATAATA-TTTTTAAAT
1 ATTTAAT-ATAATATTTTTTAAAT
2286198 ATTTAAT-TAATATTTTTTAAAT
1 ATTTAATATAATATTTTTTAAAT
2286220 ATTT-ATATA
1 ATTTAATATA
2286229 CTTATTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
21 7 0.24
22 15 0.52
23 7 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAATATAATATTTTTTAAAT
Found at i:2286264 original size:6 final size:7
Alignment explanation
Indices: 2286249--2286294 Score: 67
Period size: 7 Copynumber: 6.4 Consensus size: 7
2286239 TGATATTTAA
2286249 AAATTTT
1 AAATTTT
2286256 AAA-TTT
1 AAATTTT
2286262 AAATTTT
1 AAATTTT
2286269 AAATTTT
1 AAATTTT
2286276 AAATATTT
1 AAAT-TTT
2286284 ATAATTTT
1 A-AATTTT
2286292 AAA
1 AAA
2286295 ATGTATATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.17
7 19 0.53
8 8 0.22
9 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:2286267 original size:13 final size:13
Alignment explanation
Indices: 2286249--2286290 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
2286239 TGATATTTAA
2286249 AAATTTTAAATTT
1 AAATTTTAAATTT
2286262 AAATTTTAAATTTT
1 AAATTTTAAA-TTT
2286276 AAATATTTATAATTT
1 AAAT-TTTA-AATTT
2286291 TAAAATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 10 0.38
14 7 0.27
15 7 0.27
16 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AAATTTTAAATTT
Found at i:2286731 original size:19 final size:18
Alignment explanation
Indices: 2286692--2286734 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2286682 TTTGTAAATA
2286692 TTTAATAAAAATATATAT
1 TTTAATAAAAATATATAT
*
2286710 TTTATTAAATAATATGAT-T
1 TTTAATAAA-AATAT-ATAT
2286729 TTTAAT
1 TTTAAT
2286735 GTAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 8 0.38
19 11 0.52
20 2 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTAATAAAAATATATAT
Found at i:2286969 original size:20 final size:23
Alignment explanation
Indices: 2286944--2287000 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
2286934 TAATTTAATT
2286944 AAATAATTATAA-A-T-ATTAAA
1 AAATAATTATAATATTAATTAAA
2286964 AAATAATTATAATATTAATTAAA
1 AAATAATTATAATATTAATTAAA
*
2286987 AAATAAATATAATA
1 AAATAATTATAATA
2287001 AACAAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 12 0.36
21 1 0.03
22 1 0.03
23 19 0.58
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
AAATAATTATAATATTAATTAAA
Found at i:2286999 original size:17 final size:18
Alignment explanation
Indices: 2286952--2287009 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 18
2286942 TTAAATAATT
* *
2286952 ATAAATATTAAAAAATAA
1 ATAAATATTAATAAACAA
*
2286970 TTATAATATTAATTAAA-AA
1 ATA-AATATTAA-TAAACAA
2286989 ATAAATA-TAATAAACAA
1 ATAAATATTAATAAACAA
2287006 ATAA
1 ATAA
2287010 TAAATATGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 4 0.12
17 9 0.26
18 6 0.18
19 12 0.35
20 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAATATTAATAAACAA
Found at i:2287008 original size:40 final size:38
Alignment explanation
Indices: 2286934--2287037 Score: 95
Period size: 40 Copynumber: 2.6 Consensus size: 38
2286924 TTAAACTGAT
2286934 TAATTTAATTAAATAATTATAAATATTAAAAAATAATTA
1 TAATTTAATTAAATAA-TATAAATATTAAAAAATAATTA
2286973 TAATATTAATTAAA-AA-ATAAATATAATAAACAAATAATAAATA
1 TAAT-TTAATTAAATAATATAAATAT--TAAA-AAATAAT---TA
* *
2287016 TGTATTTAATTTAATAATATAA
1 T-AATTTAATTAAATAATATAA
2287038 TTTTTAATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
37 8 0.15
39 10 0.19
40 16 0.30
43 11 0.21
44 4 0.08
45 4 0.08
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (38 bp):
TAATTTAATTAAATAATATAAATATTAAAAAATAATTA
Found at i:2287730 original size:24 final size:24
Alignment explanation
Indices: 2287703--2287766 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 24
2287693 AGAATATAAT
2287703 AAATATAATATGAAA-A-AATAATTA
1 AAATATAATAT-AAATATAAT-ATTA
*
2287727 AAATATGATATAAATATAATATTA
1 AAATATAATATAAATATAATATTA
*
2287751 AAAAATTAA-ATAAATA
1 AAATA-TAATATAAATA
2287767 AAAAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 3 0.09
24 26 0.76
25 5 0.15
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (24 bp):
AAATATAATATAAATATAATATTA
Found at i:2287745 original size:35 final size:33
Alignment explanation
Indices: 2287689--2287779 Score: 101
Period size: 35 Copynumber: 2.6 Consensus size: 33
2287679 GCCTGTCGGA
*
2287689 AATTAGAATATAATAAATATAATATGAAAAAAT
1 AATTAAAATATAATAAATATAATATGAAAAAAT
*
2287722 AATTAAAATATGATATAAATATAATATTAAAAAATT
1 AATTAAAATAT-A-ATAAATATAATATGAAAAAA-T
* * *
2287758 AAATAAATAAAAAATAAATATA
1 AATTAAA-ATATAATAAATATA
2287780 TGAATATGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 10 0.20
34 1 0.02
35 28 0.57
36 8 0.16
37 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (33 bp):
AATTAAAATATAATAAATATAATATGAAAAAAT
Found at i:2288021 original size:9 final size:9
Alignment explanation
Indices: 2288007--2288036 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2287997 TTGAATTCTC
2288007 ATTAAAAAT
1 ATTAAAAAT
2288016 ATT-AAAAT
1 ATTAAAAAT
2288024 ATTAAAAAT
1 ATTAAAAAT
2288033 ATTA
1 ATTA
2288037 TTATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:2288617 original size:24 final size:24
Alignment explanation
Indices: 2288545--2288630 Score: 70
Period size: 24 Copynumber: 3.5 Consensus size: 24
2288535 AAATTTTATA
*
2288545 ATATTAAATATGATTTTTAATATAAT
1 ATATTAAA-AT-ATTTATAATATAAT
* *
2288571 ACATATAAAAT-TATTA-AAAATAAT
1 ATAT-TAAAATAT-TTATAATATAAT
2288595 ATATTAAAATATTTATAATATAA-
1 ATATTAAAATATTTATAATATAAT
*
2288618 ATTATTAATATAT
1 A-TATTAAAATAT
2288631 CAAAATTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
23 10 0.20
24 28 0.57
25 2 0.04
26 5 0.10
27 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (24 bp):
ATATTAAAATATTTATAATATAAT
Found at i:2288658 original size:30 final size:29
Alignment explanation
Indices: 2288607--2288688 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
2288597 ATTAAAATAT
* *
2288607 TTATAATATAA-ATTATTAATATATCAAAA
1 TTATAATAAAATATTATAAATATAT-AAAA
* *
2288636 TTA-ATATAAAATATTATAAATATAATTATA
1 TTATA-ATAAAATATTATAAATAT-ATAAAA
2288666 TTATAATAAAATA-TATAAATATA
1 TTATAATAAAATATTATAAATATA
2288689 ATATTAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
28 2 0.04
29 17 0.38
30 23 0.51
31 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (29 bp):
TTATAATAAAATATTATAAATATATAAAA
Found at i:2288688 original size:23 final size:24
Alignment explanation
Indices: 2288575--2288699 Score: 68
Period size: 24 Copynumber: 5.2 Consensus size: 24
2288565 TATAATACAT
*
2288575 ATAAAAT-TATTAAAAATAATA-TA
1 ATAAAATATA-TAAATATAATATTA
* *
2288598 TTAAAATATTTATAATATAA-ATTA
1 ATAAAATATATA-AATATAATATTA
* *
2288622 TTAATATATCA-AAAT-TAATA-TA
1 ATAAAATAT-ATAAATATAATATTA
*
2288644 A-AATAT-TATAAATATAATTATATTATA
1 ATAAAATATATAAATAT-A--ATA-T-TA
2288671 ATAAAATATATAAATATAATATTA
1 ATAAAATATATAAATATAATATTA
2288695 ATAAA
1 ATAAA
2288700 TAGATTACTA
Statistics
Matches: 80, Mismatches: 7, Indels: 29
0.69 0.06 0.25
Matches are distributed among these distances:
19 1 0.01
20 5 0.06
21 6 0.08
22 6 0.08
23 13 0.16
24 28 0.35
25 1 0.01
26 3 0.04
27 3 0.04
28 5 0.06
29 9 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAAAATATATAAATATAATATTA
Found at i:2288698 original size:27 final size:27
Alignment explanation
Indices: 2288602--2288698 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 27
2288592 AATATATTAA
*
2288602 AATATTTATAATATAAAT-TATTAATATAT
1 AATATTAATAATA-AAATATA-TAA-ATAT
*
2288631 CAAAATTAAT-ATAAAATATTATAAATAT
1 -AATATTAATAATAAAATA-TATAAATAT
*
2288659 AATTATATTATAATAAAATATATAAATAT
1 AA-TAT-TAATAATAAAATATATAAATAT
2288688 AATATTAATAA
1 AATATTAATAA
2288699 ATAGATTACT
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
27 7 0.12
28 13 0.23
29 20 0.35
30 17 0.30
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (27 bp):
AATATTAATAATAAAATATATAAATAT
Found at i:2288701 original size:23 final size:23
Alignment explanation
Indices: 2288638--2288699 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
2288628 TATCAAAATT
* * *
2288638 AATATAAAATATTATAA-ATATA
1 AATATAATATAATAAAATATATA
* *
2288660 ATTATATTATAATAAAATATATA
1 AATATAATATAATAAAATATATA
2288683 AATATAATATTAATAAA
1 AATATAATA-TAATAAA
2288700 TAGATTACTA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 12 0.39
23 12 0.39
24 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AATATAATATAATAAAATATATA
Found at i:2289181 original size:22 final size:22
Alignment explanation
Indices: 2289139--2289185 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2289129 TTTAAGAAAT
2289139 ATTTAATATATTTAATATTTAA
1 ATTTAATATATTTAATATTTAA
* *
2289161 ATTTAA-ATTTTTATATTTTTAA
1 ATTTAATATATTTA-ATATTTAA
2289183 ATT
1 ATT
2289186 GTAACCGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTAATATATTTAATATTTAA
Found at i:2289557 original size:2 final size:2
Alignment explanation
Indices: 2289550--2289577 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2289540 CAATAAAGTA
2289550 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
2289578 TGGCACACAA
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:2292996 original size:15 final size:14
Alignment explanation
Indices: 2292976--2293023 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
2292966 AAATAAAATT
2292976 AAATAATTATTATA
1 AAATAATTATTATA
2292990 CAAATAATGTATT-TA
1 -AAATAAT-TATTATA
*
2293005 AAATAATAATTATA
1 AAATAATTATTATA
2293019 TAAAT
1 -AAAT
2293024 CATTTGTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 3 0.10
14 9 0.31
15 13 0.45
16 4 0.14
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (14 bp):
AAATAATTATTATA
Found at i:2293391 original size:3 final size:3
Alignment explanation
Indices: 2293383--2293423 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2293373 AACAAGATTG
2293383 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2293424 CATATTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2293692 original size:12 final size:12
Alignment explanation
Indices: 2293675--2293715 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
2293665 GATCGTATCA
2293675 TTTTATTTTATT
1 TTTTATTTTATT
*
2293687 TTTTATATTATT
1 TTTTATTTTATT
*
2293699 TTATATTTTAATT
1 TTTTATTTT-ATT
2293712 TTTT
1 TTTT
2293716 TCTTATTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 18 0.75
13 6 0.25
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:2293894 original size:3 final size:3
Alignment explanation
Indices: 2293886--2293924 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2293876 AGGTATATTC
2293886 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2293925 AAAGAAAAGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2294870 original size:21 final size:19
Alignment explanation
Indices: 2294846--2294891 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
2294836 ATATATTAAA
*
2294846 TATATATATGTAAAAATATAT
1 TATATATAT-TAAAAA-AAAT
2294867 TATATATATTAAAAAAAAT
1 TATATATATTAAAAAAAAT
2294886 TATATA
1 TATATA
2294892 CTAAAATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 9 0.38
20 6 0.25
21 9 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TATATATATTAAAAAAAAT
Found at i:2295246 original size:40 final size:40
Alignment explanation
Indices: 2295191--2295282 Score: 157
Period size: 40 Copynumber: 2.3 Consensus size: 40
2295181 AGACATTTCT
2295191 TTGAGAAAACAATTGCATGCTCAAAAGGATATTAATTTAA
1 TTGAGAAAACAATTGCATGCTCAAAAGGATATTAATTTAA
* * *
2295231 TTGAGAAAATAATTGCATGCTTAAAAGGATATTAATTTAC
1 TTGAGAAAACAATTGCATGCTCAAAAGGATATTAATTTAA
2295271 TTGAGAAAACAA
1 TTGAGAAAACAA
2295283 AATAATTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.46, C:0.09, G:0.15, T:0.30
Consensus pattern (40 bp):
TTGAGAAAACAATTGCATGCTCAAAAGGATATTAATTTAA
Found at i:2297617 original size:20 final size:20
Alignment explanation
Indices: 2297580--2297635 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
2297570 TAAAAAAATT
*
2297580 ATAAAAATTAT-T-TTTAT-
1 ATAAAATTTATATATTTATA
2297597 ATAAATATTTATATATTTATA
1 ATAAA-ATTTATATATTTATA
* *
2297618 ATTAAATTTATATTTTTA
1 ATAAAATTTATATATTTA
2297636 ATTATTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 5 0.16
18 5 0.16
19 1 0.03
20 17 0.53
21 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAAAATTTATATATTTATA
Found at i:2298065 original size:12 final size:12
Alignment explanation
Indices: 2298042--2298075 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2298032 CATACACATC
2298042 AAAATGAAAAAAT
1 AAAAT-AAAAAAT
2298055 AAAATAAAAAAT
1 AAAATAAAAAAT
*
2298067 AAAAGAAAA
1 AAAATAAAA
2298076 TTGTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:2298858 original size:22 final size:22
Alignment explanation
Indices: 2298833--2298874 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2298823 TTTATAATAT
2298833 TATTTATAT-ATTAATATTTATA
1 TATTTATATAATTAA-ATTTATA
*
2298855 TATTTTTATAATTAAATTTA
1 TATTTATATAATTAAATTTA
2298875 AATAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTATATAATTAAATTTATA
Found at i:2303521 original size:21 final size:21
Alignment explanation
Indices: 2303455--2303522 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
2303445 TCAAGAACTC
2303455 TTAAGAATATGTTCATAAACGTATA
1 TTAA-AATATGTTCATAAA--TA-A
* * **
2303480 ATCAAATATGTTCATGGATAA
1 TTAAAATATGTTCATAAATAA
*
2303501 TTAAAATTTGTTCATAAATAA
1 TTAAAATATGTTCATAAATAA
2303522 T
1 T
2303523 AAATAAATAA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
21 18 0.53
22 2 0.06
24 12 0.35
25 2 0.06
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.38
Consensus pattern (21 bp):
TTAAAATATGTTCATAAATAA
Found at i:2304051 original size:3 final size:3
Alignment explanation
Indices: 2304043--2304079 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2304033 TCAAAAGCAT
2304043 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2304080 ATGTTTAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2305991 original size:13 final size:13
Alignment explanation
Indices: 2305973--2305997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2305963 AATATTAGAC
2305973 ATGATATAATTAT
1 ATGATATAATTAT
2305986 ATGATATAATTA
1 ATGATATAATTA
2305998 CGATATAAAA
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
ATGATATAATTAT
Found at i:2306145 original size:11 final size:10
Alignment explanation
Indices: 2306093--2306166 Score: 61
Period size: 9 Copynumber: 7.9 Consensus size: 10
2306083 TAAGAAATAA
*
2306093 AAATTTATAT
1 AAATATATAT
2306103 AAAT-T-T-T
1 AAATATATAT
*
2306110 AAATAT-TTT
1 AAATATATAT
2306119 AAATATA-AT
1 AAATATATAT
* *
2306128 TATTATATAT
1 AAATATATAT
2306138 AAA-ATATAT
1 AAATATATAT
2306147 AAATATGATAT
1 AAATAT-ATAT
2306158 AAATATATA
1 AAATATATA
2306167 AATTATCAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
7 5 0.09
8 3 0.06
9 23 0.43
10 12 0.23
11 10 0.19
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (10 bp):
AAATATATAT
Found at i:2307011 original size:2 final size:2
Alignment explanation
Indices: 2307004--2307041 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2306994 CACTTGATGA
2307004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2307042 TAAGCATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2311782 original size:14 final size:15
Alignment explanation
Indices: 2311730--2311784 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
2311720 AAAATAATTT
* *
2311730 TAAAAAATTAAATTTA
1 TAAATAATTAAA-ATA
*
2311746 TAAAT-ATTTAAATA
1 TAAATAATTAAAATA
2311760 TAAATTAATTAAAAT-
1 TAAA-TAATTAAAATA
2311775 TAAATAATTA
1 TAAATAATTA
2311785 TTATATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 12 0.36
15 10 0.30
16 11 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TAAATAATTAAAATA
Found at i:2312296 original size:17 final size:17
Alignment explanation
Indices: 2312249--2312296 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2312239 TTAATTAATT
2312249 TTAATTTAATTTAAAATC
1 TTAATTTAA-TTAAAATC
* * * *
2312267 TTAATTGATTTAAAGTG
1 TTAATTTAATTAAAATC
2312284 TTAATTTAATTAA
1 TTAATTTAATTAA
2312297 TTAATTTGAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (17 bp):
TTAATTTAATTAAAATC
Found at i:2312994 original size:29 final size:30
Alignment explanation
Indices: 2312960--2313024 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
2312950 AAATATTAAA
* *
2312960 TATATTTTATCAAATTTATTAT-ATTATTT
1 TATATTTTATCAAATTAATTATAATTATAT
* *
2312989 TATA-TTTATTAAATTAATTTTAATTATAT
1 TATATTTTATCAAATTAATTATAATTATAT
2313018 TATATTT
1 TATATTT
2313025 AAAATTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 14 0.47
29 14 0.47
30 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TATATTTTATCAAATTAATTATAATTATAT
Found at i:2312995 original size:19 final size:19
Alignment explanation
Indices: 2312972--2313023 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
2312962 TATTTTATCA
2312972 AATTTATTATATT-ATTTT
1 AATTTATTATATTAATTTT
*
2312990 ATATTTATTAAATTAATTTT
1 A-ATTTATTATATTAATTTT
2313010 AATTATATTATATT
1 AATT-TATTATATT
2313024 TAAAATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 1 0.03
19 14 0.48
20 14 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTATTATATTAATTTT
Found at i:2313025 original size:29 final size:28
Alignment explanation
Indices: 2312952--2313025 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
2312942 TATAATATAA
* *
2312952 ATATTA-AATATATTTTATCAAATTTATT
1 ATATTATATTATA-TTTATCAAATTAATT
* *
2312980 ATATTATTTTATATTTATTAAATTAATT
1 ATATTATATTATATTTATCAAATTAATT
*
2313008 TTAATTATATTATATTTA
1 AT-ATTATATTATATTTA
2313026 AAATTATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 20 0.53
29 18 0.47
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
ATATTATATTATATTTATCAAATTAATT
Found at i:2313185 original size:16 final size:16
Alignment explanation
Indices: 2313160--2313203 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
2313150 ATTTTGACTA
* *
2313160 TTTATATATATATTTT
1 TTTATTTATAAATTTT
2313176 TTTATTTATAAATTTT
1 TTTATTTATAAATTTT
*
2313192 TATATGTTATAA
1 TTTAT-TTATAA
2313204 TAATATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 18 0.75
17 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTATTTATAAATTTT
Done.