Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold103
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: 2633873
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 16636 characters in sequence are not A, C, G, or T
File 6 of 21
Found at i:612696 original size:22 final size:22
Alignment explanation
Indices: 612670--612718 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
612660 GCCTTACACG
612670 TATATACGTG-ACTATATATACA
1 TATATACGTGTA-TATATATACA
* *
612692 TATATATGTGTATATATATATA
1 TATATACGTGTATATATATACA
612714 TATAT
1 TATAT
612719 GACCAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (22 bp):
TATATACGTGTATATATATACA
Found at i:612800 original size:17 final size:18
Alignment explanation
Indices: 612774--612819 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
612764 TATTGTATCT
*
612774 ATAAATTATAATTA-TTA
1 ATAAAATATAATTATTTA
612791 ATAAAATAT-ATTATTTA
1 ATAAAATATAATTATTTA
*
612808 ATATAATATAAT
1 ATAAAATATAAT
612820 GATAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.16
17 19 0.76
18 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAAATATAATTATTTA
Found at i:612931 original size:21 final size:20
Alignment explanation
Indices: 612914--612960 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
612904 AATTTTAATA
*
612914 TATTATTTTATATATTTATT
1 TATTATTTTATAAATTTATT
612934 TAATTATTTTATAAATTTATT
1 T-ATTATTTTATAAATTTATT
612955 TATTAT
1 TATTAT
612961 ATGGTATTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTATTTTATAAATTTATT
Found at i:616500 original size:2 final size:2
Alignment explanation
Indices: 616493--616518 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
616483 AAATAAAATG
616493 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
616519 TTTATCAAGA
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:619831 original size:1 final size:1
Alignment explanation
Indices: 619827--619851 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
619817 TTTTAGCAGG
619827 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
619852 CCAACCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:620703 original size:3 final size:3
Alignment explanation
Indices: 620695--620772 Score: 70
Period size: 3 Copynumber: 24.3 Consensus size: 3
620685 GCCTACCTTC
*
620695 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTGT TTA TTA TCTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA T-TA -TTA
620743 TCTA -TA TT- TATA TTTA TTA TTA TTTA TTA T
1 T-TA TTA TTA T-TA -TTA TTA TTA -TTA TTA T
620773 CTATCTATTT
Statistics
Matches: 64, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
2 3 0.05
3 46 0.72
4 13 0.20
5 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:620760 original size:10 final size:10
Alignment explanation
Indices: 620737--620813 Score: 50
Period size: 10 Copynumber: 7.5 Consensus size: 10
620727 GTTTATTATC
*
620737 TATTTATCTA
1 TATTTATATA
*
620747 TATTTATATT
1 TATTTATATA
*
620757 TA-TTATTATT
1 TATTTA-TATA
* *
620767 TATTATCTATC
1 TATT-TATATA
620778 TATTTATACT-
1 TATTTATA-TA
620788 TATTATATATA
1 TATT-TATATA
*
620799 TATATATATA
1 TATTTATATA
620809 TATTT
1 TATTT
620814 TAAATGACAT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
9 3 0.06
10 34 0.63
11 16 0.30
12 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTTATATA
Found at i:620769 original size:37 final size:37
Alignment explanation
Indices: 620719--620790 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
620709 ATTATTATTA
* * *
620719 TTATTATTGTTTATTATCTATTTATCTATATTTATAT
1 TTATTATTATTTATTATCTATCTATCTATACTTATAT
*
620756 TTATTATTATTTATTATCTATCTATTTATACTTAT
1 TTATTATTATTTATTATCTATCTATCTATACTTAT
620791 TATATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (37 bp):
TTATTATTATTTATTATCTATCTATCTATACTTATAT
Found at i:620806 original size:21 final size:21
Alignment explanation
Indices: 620750--620806 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
620740 TTATCTATAT
* *
620750 TTATATTTAT-TAT-TATTTA
1 TTATATATATATATATACTTA
* * *
620769 TTATCTATCTATTTATACTTA
1 TTATATATATATATATACTTA
620790 TTATATATATATATATA
1 TTATATATATATATATA
620807 TATATTTTAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 7 0.25
20 2 0.07
21 19 0.68
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATATATATATATACTTA
Found at i:620813 original size:31 final size:31
Alignment explanation
Indices: 620698--620813 Score: 93
Period size: 31 Copynumber: 3.9 Consensus size: 31
620688 TACCTTCTTA
620698 TTATTATTAT-TATTAT-TAT-TA-TTATTA-
1 TTATTATTATATATTATATATATATTTA-TAC
* * * *
620725 TTGTTTATTATCTATT-TATCTATATTTATAT
1 TT-ATTATTATATATTATATATATATTTATAC
* * *
620756 TTATTATTATTTATTATCTATCTATTTATAC
1 TTATTATTATATATTATATATATATTTATAC
620787 TTATTA-TATATATATATATATATATTT
1 TTATTATTATATAT-TATATATATATTT
620814 TAAATGACAT
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
27 2 0.03
28 8 0.11
29 6 0.09
30 21 0.30
31 33 0.47
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (31 bp):
TTATTATTATATATTATATATATATTTATAC
Found at i:621862 original size:23 final size:23
Alignment explanation
Indices: 621827--621871 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
621817 AAAAAATACA
* *
621827 TATTTATATTTTTTATTATTTAT
1 TATTCATAATTTTTATTATTTAT
621850 TATTCATAATTTTTATTATTTA
1 TATTCATAATTTTTATTATTTA
621872 AAATATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTCATAATTTTTATTATTTAT
Found at i:622950 original size:26 final size:27
Alignment explanation
Indices: 622899--622950 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
622889 ATTTAATATA
* *
622899 ATTTAACTTAAATTTATATGATTATTT
1 ATTTAACTTAAATTTATATAAATATTT
622926 ATTTAA-TTAAATATT-TATAAATATT
1 ATTTAACTTAAAT-TTATATAAATATT
622951 AAAAATCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
ATTTAACTTAAATTTATATAAATATTT
Found at i:623124 original size:19 final size:19
Alignment explanation
Indices: 623102--623153 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
623092 TTATTTGTAT
*
623102 TTTTTAATTTTAAATTTTA
1 TTTTTAATTTTAAATTATA
*
623121 TTTTTATTTTTAAATTATA
1 TTTTTAATTTTAAATTATA
*
623140 TATTTTAATGTTAA
1 T-TTTTAATTTTAA
623154 TTTGCATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTTAATTTTAAATTATA
Found at i:623128 original size:26 final size:26
Alignment explanation
Indices: 623090--623146 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
623080 ACTTTATATT
* *
623090 TTTTATTTGTATTTTTTAATTTTAAA
1 TTTTATTTGTATTTTTAAATTATAAA
* *
623116 TTTTATTTTTATTTTTAAATTATATA
1 TTTTATTTGTATTTTTAAATTATAAA
623142 TTTTA
1 TTTTA
623147 ATGTTAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TTTTATTTGTATTTTTAAATTATAAA
Found at i:623261 original size:6 final size:6
Alignment explanation
Indices: 623226--623276 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
623216 TTTTTTAGTC
*
623226 TTTTATA TTTTAA ATTTAGA TTTTAA TTTTAA TTTTTTAA TTTT-A TTTTAA
1 TTTTA-A TTTTAA TTTTA-A TTTTAA TTTTAA --TTTTAA TTTTAA TTTTAA
623277 AATAATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 5 0.13
6 17 0.45
7 10 0.26
8 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:623265 original size:14 final size:13
Alignment explanation
Indices: 623226--623274 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
623216 TTTTTTAGTC
*
623226 TTTTATATTTTAA
1 TTTTATTTTTTAA
* **
623239 ATTTAGATTTTAA
1 TTTTATTTTTTAA
623252 TTTTAATTTTTTAA
1 TTTT-ATTTTTTAA
623266 TTTTATTTT
1 TTTTATTTT
623275 AAAATAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTTAA
Found at i:623520 original size:18 final size:18
Alignment explanation
Indices: 623492--623527 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
623482 ATTTTAGATT
623492 TTTTATATTTAAGTTTTTA
1 TTTTATATTTAA-TTTTTA
623511 TTTT-TATTTAATTTTTA
1 TTTTATATTTAATTTTTA
623528 AATAGTGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTTATATTTAATTTTTA
Found at i:624172 original size:22 final size:24
Alignment explanation
Indices: 624129--624175 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
624119 TATTTATGTA
624129 TTTTTATAATTAAATTTAAATAATT
1 TTTTTATAATTAAA-TTAAATAATT
*
624154 TTTTTATTATTAAA-T-AATAATT
1 TTTTTATAATTAAATTAAATAATT
624176 AAAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
25 13 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTTATAATTAAATTAAATAATT
Found at i:625309 original size:20 final size:21
Alignment explanation
Indices: 625284--625322 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
625274 TTTGCATCGG
625284 ACACATA-TTTTTATTTTTCT
1 ACACATATTTTTTATTTTTCT
625304 ACACATATTTTTTATTTTT
1 ACACATATTTTTTATTTTT
625323 TTATCAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (21 bp):
ACACATATTTTTTATTTTTCT
Found at i:625844 original size:19 final size:20
Alignment explanation
Indices: 625816--625866 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
625806 ATATTTTATA
*
625816 ATTAAATTTAATTA-AAAAT
1 ATTAATTTTAATTATAAAAT
*
625835 ATTAATTTT-ATTATTAAAT
1 ATTAATTTTAATTATAAAAT
* *
625854 AATAATTTAAATT
1 ATTAATTTTAATT
625867 GATATGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.15
19 19 0.73
20 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTAATTTTAATTATAAAAT
Found at i:625847 original size:18 final size:19
Alignment explanation
Indices: 625820--625863 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
625810 TTTATAATTA
*
625820 AATTTAATTA-AAAATATT
1 AATTTAATTATAAAATAAT
* *
625838 AATTTTATTATTAAATAAT
1 AATTTAATTATAAAATAAT
625857 AATTTAA
1 AATTTAA
625864 ATTGATATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATTTAATTATAAAATAAT
Found at i:626170 original size:17 final size:18
Alignment explanation
Indices: 626133--626171 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
626123 TTTATAATAA
626133 AAATTATATTATTTAATT
1 AAATTATATTATTTAATT
626151 AAATTAATATT-TTT-ATT
1 AAATT-ATATTATTTAATT
626168 AAAT
1 AAAT
626172 ATTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAATTATATTATTTAATT
Found at i:626209 original size:20 final size:22
Alignment explanation
Indices: 626158--626214 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
626148 ATTAAATTAA
626158 TATTTTTATTAAATATTAAAAT
1 TATTTTTATTAAATATTAAAAT
** *
626180 TATTGATATTATAT-TTAAAAT
1 TATTTTTATTAAATATTAAAAT
626201 T-TTTTTATTAAATA
1 TATTTTTATTAAATA
626215 AGTTAATTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 9 0.32
21 8 0.29
22 11 0.39
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTTTTATTAAATATTAAAAT
Found at i:626959 original size:28 final size:28
Alignment explanation
Indices: 626887--626957 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 28
626877 CATAATTTAA
626887 AATTTTTTATTTAAATTAATTTATAAATT
1 AATTTTTTATTTAAA-TAATTTATAAATT
626916 AATTTTATTATTTTAAA-AATATTA-AAATAT
1 AATTTT-TTA-TTTAAATAAT-TTATAAAT-T
626946 AATTTTTATATT
1 AATTTTT-TATT
626958 AATATTTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
29 16 0.43
30 15 0.41
31 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTTTTTATTTAAATAATTTATAAATT
Found at i:628120 original size:28 final size:28
Alignment explanation
Indices: 628072--628126 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
628062 TATAGATCTG
* *
628072 ATAGTTTGAATATTTGTATTATGTTTAT
1 ATAGTTTGAATATTTGAATTATATTTAT
*
628100 ATAGTTTATAATATTT-AATTATATTTA
1 ATAGTTT-GAATATTTGAATTATATTTA
628127 AAGTATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (28 bp):
ATAGTTTGAATATTTGAATTATATTTAT
Found at i:628165 original size:18 final size:17
Alignment explanation
Indices: 628131--628185 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
628121 TATTTAAAGT
628131 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
628148 ATTTTGATATCTTA-AT-A
1 ATTTT-ATAT-TTATATAA
*
628165 A-TTCATA-TTATATAA
1 ATTTTATATTTATATAA
628180 ATTTTA
1 ATTTTA
628186 AAACATATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.10
14 2 0.06
15 5 0.16
16 5 0.16
17 7 0.23
18 6 0.19
19 3 0.10
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:628520 original size:16 final size:16
Alignment explanation
Indices: 628495--628538 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
628485 CTTTGAATTG
628495 AAAATAATTTAAA-AT
1 AAAATAATTTAAACAT
*
628510 CAAATTAATTTAAACAT
1 -AAAATAATTTAAACAT
628527 AAAATAATTTAA
1 AAAATAATTTAA
628539 TTTAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 23 0.92
17 2 0.08
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATAATTTAAACAT
Found at i:628894 original size:30 final size:30
Alignment explanation
Indices: 628850--628912 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
628840 TTTATTTTTG
* *
628850 TTTTATTAAATTTTACTACT-AAATTTTTAT
1 TTTTATTAAATTTTACCACTCAAA-ATTTAT
628880 TTTTGATT-AATTTTACCACTCAAAATTTAT
1 TTTT-ATTAAATTTTACCACTCAAAATTTAT
628910 TTT
1 TTT
628913 AAATGATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.57
Consensus pattern (30 bp):
TTTTATTAAATTTTACCACTCAAAATTTAT
Found at i:629208 original size:30 final size:31
Alignment explanation
Indices: 629169--629247 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
629159 AAATTTAAAC
*
629169 TAATCAAAAAT-AAAATCAAATAGA-AAATTT
1 TAATAAAAAATCAAAATCAAATA-ATAAATTT
* * *
629199 TAATTAAAAATCAAAGTTAAATAATAAATTT
1 TAATAAAAAATCAAAATCAAATAATAAATTT
*
629230 CAATAAAAAATTCAAAAT
1 TAATAAAAAA-TCAAAAT
629248 TTTTTTATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 11 0.28
31 23 0.57
32 6 0.15
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (31 bp):
TAATAAAAAATCAAAATCAAATAATAAATTT
Found at i:638281 original size:15 final size:15
Alignment explanation
Indices: 638261--638289 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
638251 ATAAAAAAAT
638261 TAAATATATTTATAA
1 TAAATATATTTATAA
638276 TAAATATATTTATA
1 TAAATATATTTATA
638290 TTAGATTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATATATTTATAA
Found at i:638573 original size:1 final size:1
Alignment explanation
Indices: 638567--638591 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
638557 TTACTCCCAG
638567 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
638592 CCCTGAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:639273 original size:27 final size:26
Alignment explanation
Indices: 639205--639274 Score: 63
Period size: 29 Copynumber: 2.6 Consensus size: 26
639195 TTTTTTTATC
*
639205 TAAA-TTTATATATTTTATTTTATTA
1 TAAATTTTATATATTTTATTCTATTA
*
639230 TAATTATTTTAAGATATTTTATATCTA-TA
1 TAA--ATTTT-ATATATTTTAT-TCTATTA
639259 TAAATTTTGATATATT
1 TAAATTTT-ATATATT
639275 AATAATTCGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
25 3 0.08
27 12 0.33
28 3 0.08
29 15 0.42
30 3 0.08
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (26 bp):
TAAATTTTATATATTTTATTCTATTA
Found at i:640787 original size:2 final size:2
Alignment explanation
Indices: 640780--640805 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
640770 AAATGTTGAG
640780 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
640806 AAATATTTAA
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):
TA
Found at i:643351 original size:20 final size:21
Alignment explanation
Indices: 643315--643362 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
643305 ATAAGTTTTT
* *
643315 TTAATTTA-TATTGATTTAGA
1 TTAAATTACTATTGATTTAAA
643335 TTAAATTACTATT-ATTTAAA
1 TTAAATTACTATTGATTTAAA
*
643355 TTTAATTA
1 TTAAATTA
643363 TAAAATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (21 bp):
TTAAATTACTATTGATTTAAA
Found at i:643376 original size:22 final size:22
Alignment explanation
Indices: 643345--643392 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
643335 TTAAATTACT
*
643345 ATTATTTAAAT-TTAATTATAAA
1 ATTATATAAATATTAA-TATAAA
643367 ATTATATAAATATTAATATAAA
1 ATTATATAAATATTAATATAAA
643389 ATTA
1 ATTA
643393 ATTTTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTATATAAATATTAATATAAA
Found at i:644064 original size:20 final size:20
Alignment explanation
Indices: 644039--644076 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
644029 AATAAATATT
644039 AAATAT-TAATATTTTTTAAA
1 AAATATATAAT-TTTTTTAAA
644059 AAATATATAATTTTTTTA
1 AAATATATAATTTTTTTA
644077 TATATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATATATAATTTTTTTAAA
Found at i:645320 original size:16 final size:17
Alignment explanation
Indices: 645299--645332 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
645289 ATTTATGAAT
*
645299 TAAA-TTAAATTAAAAA
1 TAAATTTAAATAAAAAA
645315 TAAATTTAAATAAAAAA
1 TAAATTTAAATAAAAAA
645332 T
1 T
645333 TAAAAAAATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAATTTAAATAAAAAA
Found at i:645549 original size:24 final size:24
Alignment explanation
Indices: 645522--645569 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
645512 TTTTTTTCAC
* *
645522 TTTTTGTTTTTAATCTTGTCTTTG
1 TTTTTCTTTTTAATCGTGTCTTTG
*
645546 TTTTTCTTTTTTATCGTGTCTTTG
1 TTTTTCTTTTTAATCGTGTCTTTG
645570 GGTCAGCCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.06, C:0.10, G:0.12, T:0.71
Consensus pattern (24 bp):
TTTTTCTTTTTAATCGTGTCTTTG
Found at i:646325 original size:10 final size:10
Alignment explanation
Indices: 646283--646324 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
646273 TGTTGTATTC
646283 ATATTTT-AT
1 ATATTTTAAT
*
646292 ATATTTTATT
1 ATATTTTAAT
646302 ATATTTTAATT
1 ATATTTTAA-T
*
646313 ATTTTTTAAT
1 ATATTTTAAT
646323 AT
1 AT
646325 TATATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 7 0.25
10 12 0.43
11 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
ATATTTTAAT
Found at i:646333 original size:19 final size:19
Alignment explanation
Indices: 646278--646333 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
646268 ATTCATGTTG
*
646278 TATTCATATTTTATATATTT
1 TATT-ATATTTTATTTATTT
*
646298 TATTATATTTTAATTATTT
1 TATTATATTTTATTTATTT
*
646317 T-TTAATATTATATTTAT
1 TATT-ATATTTTATTTAT
646334 ATTGTATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 2 0.06
19 25 0.81
20 4 0.13
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TATTATATTTTATTTATTT
Found at i:646336 original size:11 final size:10
Alignment explanation
Indices: 646278--646320 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
646268 ATTCATGTTG
646278 TATTCATATTT
1 TATT-ATATTT
646289 TA-TATATTT
1 TATTATATTT
646298 TATTATATTT
1 TATTATATTT
*
646308 TAATTATTTTT
1 T-ATTATATTT
646319 TA
1 TA
646321 ATATTATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 8 0.28
10 10 0.34
11 11 0.38
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TATTATATTT
Found at i:646411 original size:16 final size:16
Alignment explanation
Indices: 646390--646421 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
646380 TATTCAGATA
646390 TGTCTTAATTTTGTAT
1 TGTCTTAATTTTGTAT
646406 TGTCTTAATTTTGTAT
1 TGTCTTAATTTTGTAT
646422 CACATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (16 bp):
TGTCTTAATTTTGTAT
Found at i:646574 original size:16 final size:17
Alignment explanation
Indices: 646555--646589 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
646545 TATCATGTTC
*
646555 ATATTATTTTTAAA-TT
1 ATATTATATTTAAAGTT
646571 ATATTATATTTAAAGTT
1 ATATTATATTTAAAGTT
646588 AT
1 AT
646590 TAAATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATATTATATTTAAAGTT
Found at i:646956 original size:3 final size:3
Alignment explanation
Indices: 646948--646976 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
646938 CCTTCTAGTC
646948 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
646977 TAAAACTTTG
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:647639 original size:20 final size:23
Alignment explanation
Indices: 647604--647649 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
647594 TAAAAAATTA
647604 AAAATAATTAATAA-TTATTTTT
1 AAAATAATTAATAATTTATTTTT
647626 AAAA-AATT-ATAATTTATTTTT
1 AAAATAATTAATAATTTATTTTT
647647 AAA
1 AAA
647650 TATATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.17
21 15 0.65
22 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATAATTAATAATTTATTTTT
Found at i:647757 original size:33 final size:33
Alignment explanation
Indices: 647711--647776 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
647701 AAAAAATTTA
647711 AAAAATGACATTTATCTTAAATATTATTAAATT
1 AAAAATGACATTTATCTTAAATATTATTAAATT
* *
647744 AAAAAT-ACTATTTATGTTTAATATTATTAAATT
1 AAAAATGAC-ATTTATCTTAAATATTATTAAATT
647777 CAAATTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (33 bp):
AAAAATGACATTTATCTTAAATATTATTAAATT
Found at i:650860 original size:23 final size:21
Alignment explanation
Indices: 650834--650900 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
650824 CCAAATAAAG
*
650834 TTTTGTAATTATAA-AATTTATA
1 TTTTTTAATTATAATAA--TATA
650856 TTTTTATAA-TATAATAATATA
1 TTTTT-TAATTATAATAATATA
* *
650877 TTTTTTAATAATAATTATA-A
1 TTTTTTAATTATAATAATATA
650897 TTTT
1 TTTT
650901 ATTTTATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 8 0.21
21 17 0.44
22 9 0.23
23 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
TTTTTTAATTATAATAATATA
Found at i:650878 original size:21 final size:21
Alignment explanation
Indices: 650852--650900 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
650842 TTATAAAATT
650852 TATATTTTTATAAT-ATAATAA
1 TATATTTTT-TAATAATAATAA
*
650873 TATATTTTTTAATAATAATTA
1 TATATTTTTTAATAATAATAA
650894 TA-ATTTT
1 TATATTTT
650901 ATTTTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATTTTTTAATAATAATAA
Found at i:650905 original size:23 final size:23
Alignment explanation
Indices: 650839--650906 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 23
650829 TAAAGTTTTG
*
650839 TAATTATAAAATTTATATTTTTATAA
1 TAATTAT--AATTT-TATTTTAATAA
*
650865 T-ATAATAATATATT-TTTTAATAA
1 TAATTATAAT-T-TTATTTTAATAA
650888 TAATTATAATTTTATTTTA
1 TAATTATAATTTTATTTTA
650907 TTTATTGTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
22 2 0.06
23 18 0.51
24 9 0.26
25 5 0.14
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TAATTATAATTTTATTTTAATAA
Found at i:651536 original size:2 final size:2
Alignment explanation
Indices: 651529--651557 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
651519 CACATACATG
651529 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
651558 GTCTAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:651689 original size:28 final size:28
Alignment explanation
Indices: 651656--651709 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
651646 AATGAGTGTA
651656 GTGGGTGATACTGTCAAGTCTATGTATG
1 GTGGGTGATACTGTCAAGTCTATGTATG
*
651684 GTGGGTGATATTGTCAAGTCTATGTA
1 GTGGGTGATACTGTCAAGTCTATGTA
651710 GCAAAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.37
Consensus pattern (28 bp):
GTGGGTGATACTGTCAAGTCTATGTATG
Found at i:652747 original size:3 final size:3
Alignment explanation
Indices: 652739--652764 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
652729 AGTAAACAAT
652739 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
652765 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:652769 original size:3 final size:3
Alignment explanation
Indices: 652763--652806 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
652753 ATAATAATAA
652763 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
652807 ATAAAATAAC
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:654473 original size:22 final size:25
Alignment explanation
Indices: 654440--654493 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
654430 TATATATATT
654440 TATAT-AATTAA-TTA-ATTAA-AA
1 TATATAAATTAATTTATATTAATAA
*
654461 TATTTAAATTAATTTATATTAATAA
1 TATATAAATTAATTTATATTAATAA
654486 TATATAAA
1 TATATAAA
654494 AATAATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.15
22 6 0.22
23 3 0.11
24 5 0.19
25 9 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TATATAAATTAATTTATATTAATAA
Found at i:654712 original size:2 final size:2
Alignment explanation
Indices: 654705--654736 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
654695 TCTTAATTTC
654705 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
654737 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:655176 original size:2 final size:2
Alignment explanation
Indices: 655169--655201 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
655159 TAAAGCATTG
655169 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 T
655202 TAATTTATAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:656926 original size:21 final size:22
Alignment explanation
Indices: 656886--656927 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
656876 AATATTAAAA
656886 ATATTTTAATATTAAAATTTAT
1 ATATTTTAATATTAAAATTTAT
656908 ATATTTT-ATAATT-AAATTTA
1 ATATTTTAAT-ATTAAAATTTA
656928 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATATTTTAATATTAAAATTTAT
Found at i:657249 original size:84 final size:84
Alignment explanation
Indices: 657108--657264 Score: 262
Period size: 84 Copynumber: 1.9 Consensus size: 84
657098 TTCTTTAGAT
* *
657108 GTGAACATGGAAGCAGCCAGTGTTTACGTGTAATCCAGTTGAATGACATTCGAATGC-TCTTAAA
1 GTGAACATGAAAGAAGCCAGTGTTTACGTGTAATCCAGTTGAATGACATTCGAATGCTTC-TAAA
657172 GAGGACAATTCTATGTTTAC
65 GAGGACAATTCTATGTTTAC
*
657192 GTGAACATGAAAGAAGCCGGTGTTTACGTGTAATCCAGTTGAATGACATTCGAATGCTTCTAAAG
1 GTGAACATGAAAGAAGCCAGTGTTTACGTGTAATCCAGTTGAATGACATTCGAATGCTTCTAAAG
*
657257 AGGGCAAT
66 AGGACAAT
657265 CCCCAAAAAG
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
84 66 0.97
85 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (84 bp):
GTGAACATGAAAGAAGCCAGTGTTTACGTGTAATCCAGTTGAATGACATTCGAATGCTTCTAAAG
AGGACAATTCTATGTTTAC
Found at i:657817 original size:20 final size:18
Alignment explanation
Indices: 657776--657840 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
657766 TTAATATTTT
657776 TATATTATAAATTATTAA
1 TATATTATAAATTATTAA
*
657794 TATATTATAATTTATATAA
1 TATATTATAAATTAT-TAA
657813 -ATA-TATAATATT-TTAA
1 TATATTATAA-ATTATTAA
657829 TTATGATTATAA
1 -TAT-ATTATAA
657841 TATATAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
16 3 0.08
17 6 0.15
18 21 0.54
19 4 0.10
20 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TATATTATAAATTATTAA
Found at i:657821 original size:27 final size:26
Alignment explanation
Indices: 657754--657830 Score: 97
Period size: 25 Copynumber: 3.0 Consensus size: 26
657744 AAATAATATG
* *
657754 TATATAAATATATTAATATTTTTATA
1 TATATAAATATATTAATATTTTAATT
657780 T-TATAAAT-TATTAATATATTATAATT
1 TATATAAATATATTAATAT-TT-TAATT
657806 TATATAAATATA-TAATATTTTAATT
1 TATATAAATATATTAATATTTTAATT
657831 ATGATTATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
24 9 0.20
25 14 0.31
26 7 0.16
27 13 0.29
28 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TATATAAATATATTAATATTTTAATT
Found at i:657829 original size:35 final size:36
Alignment explanation
Indices: 657781--657850 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
657771 ATTTTTATAT
*
657781 TATAAATTATTAA-TAT-ATTATAATTTATATAAATA
1 TATAAATTATTAATTATGATTATAATATATA-AAATA
657816 TATAATATT-TTAATTATGATTATAATATATAAAAT
1 TATAA-ATTATTAATTATGATTATAATATATAAAAT
657851 TAAATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
35 9 0.29
36 10 0.32
37 12 0.39
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (36 bp):
TATAAATTATTAATTATGATTATAATATATAAAATA
Found at i:658036 original size:2 final size:2
Alignment explanation
Indices: 658029--658065 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
658019 GAATCTCTTT
658029 TA 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 TA T
658066 TAATTTTTCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:658139 original size:2 final size:2
Alignment explanation
Indices: 658122--658162 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
658112 TCCTCGGAAA
* * *
658122 AT AT AA AT AC AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
658163 AGTTGTGGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:658145 original size:14 final size:14
Alignment explanation
Indices: 658122--658158 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
658112 TCCTCGGAAA
*
658122 ATATAAATACATAT
1 ATATATATACATAT
658136 ATATATATACATAT
1 ATATATATACATAT
658150 ATATATATA
1 ATATATATA
658159 TATAAGTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATATATACATAT
Found at i:660304 original size:13 final size:11
Alignment explanation
Indices: 660276--660306 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
660266 AAATATTAAA
660276 ATATTATTTTT
1 ATATTATTTTT
660287 ATATTATTTTT
1 ATATTATTTTT
660298 ATA-TATTTT
1 ATATTATTTT
660307 ATAATTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:660378 original size:17 final size:17
Alignment explanation
Indices: 660340--660387 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
660330 TATTATTTAA
660340 TAAATATTTAATTTGATC
1 TAAA-ATTTAATTTGATC
* *
660358 T-AAATTTATATTTTATT
1 TAAAATTTA-ATTTGATC
660375 TAAAATTTAATTT
1 TAAAATTTAATTT
660388 ATATGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 13 0.50
18 8 0.31
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TAAAATTTAATTTGATC
Found at i:660714 original size:17 final size:18
Alignment explanation
Indices: 660688--660721 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
660678 GATTATAATT
*
660688 TAAAATTTTTTATTTAAA
1 TAAAATTTTTGATTTAAA
660706 TAAAA-TTTTGATTTAA
1 TAAAATTTTTGATTTAA
660722 TTTATGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TAAAATTTTTGATTTAAA
Found at i:660772 original size:19 final size:19
Alignment explanation
Indices: 660737--660794 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
660727 GAATTTATTT
*
660737 TATTATTTATT-TTTTAAAA
1 TATTATTT-TTATATTAAAA
660756 TATTATTTTTATATTAATAA
1 TATTATTTTTATATTAA-AA
660776 T-TTATATTTTATAATTAAA
1 TATTAT-TTTTAT-ATTAAA
660795 TTTAAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 2 0.06
19 17 0.50
20 10 0.29
21 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTATTTTTATATTAAAA
Found at i:660833 original size:26 final size:26
Alignment explanation
Indices: 660753--660834 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
660743 TTATTTTTTA
* * *
660753 AAATATTATT-TTTATATTAATAATTT
1 AAATTTTATTATTTA-AATAATAAATT
* * * *
660779 ATATTTTA-TAATTAAAT-TTAAATAA
1 AAATTTTATTATTTAAATAATAAAT-T
660804 AAATTTTATTATTTAAATAATAAATT
1 AAATTTTATTATTTAAATAATAAATT
660830 AAATT
1 AAATT
660835 AAATTAGATT
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
24 4 0.10
25 10 0.24
26 22 0.54
27 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
AAATTTTATTATTTAAATAATAAATT
Found at i:660835 original size:21 final size:20
Alignment explanation
Indices: 660794--660835 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
660784 TTATAATTAA
**
660794 ATTTAAATAAAAATTTTATT
1 ATTTAAATAAAAATTAAATT
660814 ATTTAAATAATAAATTAAATT
1 ATTTAAATAA-AAATTAAATT
660835 A
1 A
660836 AATTAGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAATAAAAATTAAATT
Found at i:661432 original size:20 final size:19
Alignment explanation
Indices: 661403--661446 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
661393 TAACGTGATT
* *
661403 ATTTTAATATTTTAGATAA
1 ATTTTAATATCTCAGATAA
661422 ATTTATAATATCTCAGATAA
1 ATTT-TAATATCTCAGATAA
661442 ATTTT
1 ATTTT
661447 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTTTAATATCTCAGATAA
Found at i:663073 original size:27 final size:27
Alignment explanation
Indices: 663037--663134 Score: 69
Period size: 32 Copynumber: 3.5 Consensus size: 27
663027 TATAATTATA
*
663037 TTTAAAATATT-TTATATTTATATAAAT
1 TTTAATATATTATTATATTTATAT-AAT
* *
663064 TTTGATATATTAATAACTTATATTATATTAAT
1 TTTAATATATT-ATTA--TAT-TTATA-TAAT
*
663096 TTTAATATATTCA-TATATTTATATTAT
1 TTTAATATATT-ATTATATTTATATAAT
663123 TTT--TATATTATT
1 TTTAATATATTATT
663135 TTTGATATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
24 1 0.02
25 7 0.12
27 15 0.26
28 5 0.09
29 5 0.09
31 4 0.07
32 19 0.33
33 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (27 bp):
TTTAATATATTATTATATTTATATAAT
Found at i:663097 original size:32 final size:33
Alignment explanation
Indices: 663048--663122 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 33
663038 TTAAAATATT
*
663048 TTATATTTATATAAATTTTGATATATTAATA-AC
1 TTATA-TTATATAAATTTTAATATATTAATATAC
* * *
663081 TTATATTATATTAATTTTAATATATTCATATAT
1 TTATATTATATAAATTTTAATATATTAATATAC
663114 TTATATTAT
1 TTATATTAT
663123 TTTTATATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
32 22 0.59
33 15 0.41
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (33 bp):
TTATATTATATAAATTTTAATATATTAATATAC
Found at i:663131 original size:39 final size:39
Alignment explanation
Indices: 663086--663175 Score: 114
Period size: 39 Copynumber: 2.3 Consensus size: 39
663076 ATAACTTATA
*
663086 TTATATTAATTTTAATA-TA-TTCATATATTTATATTATTT
1 TTATATTATTTTTAATATTATTTCATA-ATTTATATT-TTT
* *
663125 TTATATTATTTTTGATATTATTTCATAGTTTATATTTTT
1 TTATATTATTTTTAATATTATTTCATAATTTATATTTTT
663164 TTA-ATTATTTTT
1 TTATATTATTTTT
663176 TTATCATATC
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
38 9 0.20
39 21 0.46
40 10 0.22
41 6 0.13
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (39 bp):
TTATATTATTTTTAATATTATTTCATAATTTATATTTTT
Found at i:663142 original size:12 final size:11
Alignment explanation
Indices: 663113--663147 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
663103 TATTCATATA
663113 TTTATATTATT
1 TTTATATTATT
663124 TTTATATTATT
1 TTTATATTATT
663135 TTTGATATTATT
1 TTT-ATATTATT
663147 T
1 T
663148 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (11 bp):
TTTATATTATT
Found at i:663823 original size:25 final size:26
Alignment explanation
Indices: 663795--663871 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 26
663785 TTATATTTAT
663795 TTTAAATAATTAAATTTAAATAA-AA
1 TTTAAATAATTAAATTTAAATAATAA
* * * *
663820 TTT-ATTATTTTATTATTAAATAATAA
1 TTTAAATAATTAAAT-TTAAATAATAA
*
663846 TTTAAATCAAATTAAATTAAAATAAT
1 TTTAAAT--AATTAAATTTAAATAAT
663872 TTTATCTAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
24 7 0.18
25 11 0.29
26 5 0.13
27 2 0.05
28 8 0.21
29 5 0.13
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTAAATAATTAAATTTAAATAATAA
Found at i:663848 original size:37 final size:39
Alignment explanation
Indices: 663785--663858 Score: 109
Period size: 37 Copynumber: 1.9 Consensus size: 39
663775 ATACTTATAT
663785 TTATATTTATTTTAAATAATTAAATTTAAATAAAATTTA
1 TTATATTTATTTTAAATAATTAAATTTAAATAAAATTTA
*
663824 TTAT-TTTATTATTAAATAA-T-AATTTAAATCAAATT
1 TTATATTTATT-TTAAATAATTAAATTTAAATAAAATT
663859 AAATTAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
37 14 0.42
38 7 0.21
39 12 0.36
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (39 bp):
TTATATTTATTTTAAATAATTAAATTTAAATAAAATTTA
Found at i:665221 original size:11 final size:11
Alignment explanation
Indices: 665205--665241 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
665195 ATGTTATAAA
665205 AATTAAAAATT
1 AATTAAAAATT
665216 AATTAAAAATT
1 AATTAAAAATT
* *
665227 AAATAAAAATA
1 AATTAAAAATT
665238 AATT
1 AATT
665242 TTGATTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATTAAAAATT
Found at i:669784 original size:2 final size:2
Alignment explanation
Indices: 669743--669773 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
669733 CATAAAATTT
669743 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 T
669774 TCTTCATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:669957 original size:7 final size:7
Alignment explanation
Indices: 669945--669994 Score: 55
Period size: 7 Copynumber: 6.7 Consensus size: 7
669935 ATATAGGTTT
669945 TATTTAA
1 TATTTAA
669952 TATTTAA
1 TATTTAA
669959 TAAATTTAA
1 T--ATTTAA
*
669968 AATTTAA
1 TATTTAA
*
669975 AATTTAA
1 TATTTAA
669982 TATTTATA
1 TATTTA-A
669990 TATTT
1 TATTT
669995 GTAAAATGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
7 26 0.68
8 6 0.16
9 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TATTTAA
Found at i:670554 original size:27 final size:27
Alignment explanation
Indices: 670527--670624 Score: 74
Period size: 31 Copynumber: 3.4 Consensus size: 27
670517 ATTTAATTTA
670527 AATATATAAAAATTTTAAAATCAATTAAT
1 AATATATAAAAATTTTAAAAT-AATT-AT
* * *
670556 ATAAATTATTAAAATATTAAAATTAA-TAT
1 A-ATA-TATAAAAATTTTAAAA-TAATTAT
*
670585 AA-ATATAAAATTTATTAAATATAATTAT
1 AATATATAAAAATT-TTAAA-ATAATTAT
670613 AATATAATAAAA
1 AATAT-ATAAAA
670625 TATATAAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
26 7 0.13
27 9 0.16
28 7 0.13
29 6 0.11
30 9 0.16
31 16 0.29
32 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (27 bp):
AATATATAAAAATTTTAAAATAATTAT
Found at i:670561 original size:32 final size:31
Alignment explanation
Indices: 670519--670593 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 31
670509 TATAAAAAAT
* *
670519 TTAATTTAAATATATAAAAATTTTAAAATCAA
1 TTAATATAAAT-TATAAAAATATTAAAATCAA
* *
670551 TTAATATAAATTATTAAAATATTAAAATTAA
1 TTAATATAAATTATAAAAATATTAAAATCAA
670582 TATAAATATAAA
1 T-T-AATATAAA
670594 ATTTATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 18 0.49
32 11 0.30
33 8 0.22
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
TTAATATAAATTATAAAAATATTAAAATCAA
Found at i:670580 original size:17 final size:17
Alignment explanation
Indices: 670558--670632 Score: 62
Period size: 17 Copynumber: 4.1 Consensus size: 17
670548 CAATTAATAT
*
670558 AAATTATTAAAATATTA
1 AAATTAATAAAATATTA
670575 AAATTAATATAAATA-TA
1 AAATTAATA-AAATATTA
*
670592 AAATTTATTAAATATAATTA
1 AAA-TTAATAAA-AT-ATTA
*
670612 TAATATAATAAAATATATA
1 AAAT-TAATAAAATAT-TA
670631 AA
1 AA
670633 TATCATATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
17 15 0.33
18 14 0.30
19 7 0.15
20 10 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATTAATAAAATATTA
Found at i:673941 original size:105 final size:104
Alignment explanation
Indices: 673759--673967 Score: 373
Period size: 105 Copynumber: 2.0 Consensus size: 104
673749 ATAAACTGTC
*
673759 AATGTTAACTTGAACCTTGTATATTGTAGTTGACAACCTTCCCTCACGGTTTATATTGGCCCCTG
1 AATGTTAACTTGAACCTTGTATATTGTAGTTGACAACCTTCCCTCACAGTTTATATTGGCCCCTG
*
673824 AATTCTAACTAGTTCCCAACAACTAACTGAATCAATTCAG
66 AATTCTAACTAGTTCCCAACAACCAACT-AATCAATTCAG
* *
673864 AATGTTAACTTGAACCTTGTATATTGTAGTTGACAACCTTCCCTCACAGTTTATATTTGCCCTTG
1 AATGTTAACTTGAACCTTGTATATTGTAGTTGACAACCTTCCCTCACAGTTTATATTGGCCCCTG
673929 AATTCTAACTAGTTCCCAACAACCAACTAATCAATTCAG
66 AATTCTAACTAGTTCCCAACAACCAACTAATCAATTCAG
673968 CAAAATAACT
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
104 11 0.11
105 89 0.89
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (104 bp):
AATGTTAACTTGAACCTTGTATATTGTAGTTGACAACCTTCCCTCACAGTTTATATTGGCCCCTG
AATTCTAACTAGTTCCCAACAACCAACTAATCAATTCAG
Found at i:674624 original size:20 final size:22
Alignment explanation
Indices: 674589--674631 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
674579 ATTATTTTAA
*
674589 ATTTAAATTATATTTTATATTT
1 ATTTAAATTATATTTTAAATTT
674611 ATTTAAA-T-TATTTTAAATTT
1 ATTTAAATTATATTTTAAATTT
674631 A
1 A
674632 AACGATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 1 0.05
22 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTAAATTATATTTTAAATTT
Found at i:674632 original size:16 final size:16
Alignment explanation
Indices: 674573--674633 Score: 59
Period size: 16 Copynumber: 3.4 Consensus size: 16
674563 AGTTAAAATT
*
674573 ATTTTAATTATTTTAA
1 ATTTAAATTATTTTAA
674589 ATTTAAATTATATTTTATA
1 ATTTAAA-T-TATTTTA-A
674608 TTTATTTAAATTATTTTAA
1 ---ATTTAAATTATTTTAA
674627 ATTTAAA
1 ATTTAAA
674634 CGATTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
16 13 0.34
17 1 0.03
18 7 0.18
19 2 0.05
20 7 0.18
21 1 0.03
22 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:675469 original size:33 final size:34
Alignment explanation
Indices: 675389--675470 Score: 85
Period size: 33 Copynumber: 2.4 Consensus size: 34
675379 TATTATTATT
675389 AATTAATATATTTAAAAAATTATATTTAATAATAGA
1 AATTAATATA-TT-AAAAATTATATTTAATAATAGA
* * * * *
675425 AATTAAAATATTAAATATTATA-TTAATATTTGC
1 AATTAATATATTAAAAATTATATTTAATAATAGA
*
675458 ATTTAATATATTA
1 AATTAATATATTA
675471 TTATTTCACA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
33 19 0.49
34 9 0.23
35 2 0.05
36 9 0.23
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45
Consensus pattern (34 bp):
AATTAATATATTAAAAATTATATTTAATAATAGA
Found at i:675560 original size:17 final size:16
Alignment explanation
Indices: 675538--675572 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
675528 GAGTTTGAAA
*
675538 ATAAATTATTTATATAT
1 ATAAATTATCTA-ATAT
675555 ATAAATTATCTAATAT
1 ATAAATTATCTAATAT
675571 AT
1 AT
675573 TTTCTCTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAATTATCTAATAT
Found at i:684274 original size:16 final size:16
Alignment explanation
Indices: 684253--684286 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
684243 AAACATAAAA
684253 ATTATTAATATCTTAT
1 ATTATTAATATCTTAT
*
684269 ATTATTAGTATCTTAT
1 ATTATTAATATCTTAT
684285 AT
1 AT
684287 AAAATGGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTATTAATATCTTAT
Found at i:684916 original size:18 final size:18
Alignment explanation
Indices: 684893--684928 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
684883 TTTATCAATA
684893 TTTGAACTAAAAAATTTG
1 TTTGAACTAAAAAATTTG
* *
684911 TTTGAATTAAAGAATTTG
1 TTTGAACTAAAAAATTTG
684929 AATCCTCTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.42
Consensus pattern (18 bp):
TTTGAACTAAAAAATTTG
Found at i:685423 original size:2 final size:2
Alignment explanation
Indices: 685401--685441 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
685391 TAACTACTAG
* * *
685401 TA TA TC TA TA CA TA CA 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 TA TA TA T
685442 TACAGCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:690078 original size:21 final size:21
Alignment explanation
Indices: 690036--690074 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
690026 TATTTTTATT
690036 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
690057 TAAATATTAA-TA-AAAATA
1 TAAAT-TTAATTATAAAATA
690075 ATATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:692007 original size:18 final size:19
Alignment explanation
Indices: 691984--692020 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
691974 TAATAAATAA
691984 AAATATATA-ATATTAATT
1 AAATATATATATATTAATT
*
692002 AAATATATATATTTTAATT
1 AAATATATATATATTAATT
692021 TTTTTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATATATATATATTAATT
Found at i:692733 original size:18 final size:18
Alignment explanation
Indices: 692710--692766 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 18
692700 AATTTTGAAG
*
692710 TATTCATATATTATGTCA
1 TATTCATATATTATATCA
*
692728 TATTCATATAATCATATCA
1 TATTCATAT-ATTATATCA
*
692747 TATTTAATATTATTATATCA
1 TA-TTCATA-TATTATATCA
692767 ACATAATAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.28
19 9 0.28
20 13 0.41
21 1 0.03
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.49
Consensus pattern (18 bp):
TATTCATATATTATATCA
Found at i:693317 original size:18 final size:18
Alignment explanation
Indices: 693289--693333 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
693279 TATCAAATAT
*
693289 ATAAATATTAATA-AAAA
1 ATAAATTTTAATAGAAAA
*
693306 ATAATATTTTAATAGTAAA
1 ATAA-ATTTTAATAGAAAA
693325 ATAAATTTT
1 ATAAATTTT
693334 TGAATTCATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAAATTTTAATAGAAAA
Found at i:694569 original size:21 final size:22
Alignment explanation
Indices: 694515--694570 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 22
694505 AATTGATTAA
* *
694515 AATAAAATTTAATA-GATTTTT
1 AATAAAATTTTATATTATTTTT
694536 AATAAAA---TATATTA-TTTT
1 AATAAAATTTTATATTATTTTT
694554 AATAAAATTTTATATTA
1 AATAAAATTTTATATTA
694571 ATATAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 14 0.48
19 1 0.03
21 14 0.48
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATAAAATTTTATATTATTTTT
Found at i:694571 original size:16 final size:18
Alignment explanation
Indices: 694534--694573 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
694524 TAATAGATTT
*
694534 TTAATAAAATATATTATT
1 TTAATAAAATATATTATA
694552 TTAATAAAAT-T-TTATA
1 TTAATAAAATATATTATA
694568 TTAATA
1 TTAATA
694574 TAAAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 1 0.05
18 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATAAAATATATTATA
Found at i:694866 original size:5 final size:5
Alignment explanation
Indices: 694842--694912 Score: 58
Period size: 5 Copynumber: 14.2 Consensus size: 5
694832 GATAATATTA
* * *
694842 AATAT AAT-T -ATAT AAATAT AATAT -ATAT AAAAT AATTAA AAAAT AATAT
1 AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT
*
694891 GATAT AATAT AATAT AAATAT A
1 AATAT AATAT AATAT -AATAT A
694913 TATTTTAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
3 2 0.04
4 6 0.12
5 32 0.62
6 12 0.23
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:694897 original size:10 final size:10
Alignment explanation
Indices: 694842--694912 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 10
694832 GATAATATTA
694842 AATATAAT-T
1 AATATAATAT
694851 -ATATAAATAT
1 AATAT-AATAT
694861 AATAT-ATAT
1 AATATAATAT
* *
694870 AAAATAATTAA
1 AATATAA-TAT
*
694881 AAAATAATAT
1 AATATAATAT
*
694891 GATATAATAT
1 AATATAATAT
694901 AATATAAATAT
1 AATAT-AATAT
694912 A
1 A
694913 TATTTTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
8 4 0.08
9 11 0.22
10 16 0.32
11 19 0.38
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (10 bp):
AATATAATAT
Found at i:694915 original size:20 final size:20
Alignment explanation
Indices: 694833--695007 Score: 75
Period size: 20 Copynumber: 8.8 Consensus size: 20
694823 TAATCATATG
*
694833 ATAATATTAAATATA-ATTAT
1 ATAATA-TAAATATATATAAT
*
694853 ATAA-ATATAATATATATAAA
1 ATAATATA-AATATATATAAT
* *
694873 ATAAT-TAAAAAATAATATGAT
1 ATAATAT-AAATAT-ATATAAT
*
694894 ATAATAT-AATATAAAT-AT
1 ATAATATAAATATATATAAT
* * *
694912 ATATTTTAAAATTTATATAAT
1 ATAATAT-AAATATATATAAT
* *
694933 ATAAGTTATTAATATATCAAAAT
1 ATAA--TATAAATATAT-ATAAT
*
694956 -TTATATAAATATA-A-AAT
1 ATAATATAAATATATATAAT
*
694973 AT--TTTAAATATGATTATAAT
1 ATAATATAAATAT-A-TATAAT
694993 ATAATA-AAATATATA
1 ATAATATAAATATATA
695008 AATTATTAAA
Statistics
Matches: 116, Mismatches: 20, Indels: 39
0.66 0.11 0.22
Matches are distributed among these distances:
16 8 0.07
17 4 0.03
18 11 0.09
19 13 0.11
20 42 0.36
21 22 0.19
22 10 0.09
23 6 0.05
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.41
Consensus pattern (20 bp):
ATAATATAAATATATATAAT
Found at i:696930 original size:18 final size:18
Alignment explanation
Indices: 696866--696923 Score: 65
Period size: 17 Copynumber: 3.5 Consensus size: 18
696856 TTGTATTTTT
696866 TTATT-AATT-ATATAAA
1 TTATTAAATTAATATAAA
696882 -TA-TAAATTTAATATAAA
1 TTATTAAA-TTAATATAAA
696899 TTATTAAATTAATA-AAA
1 TTATTAAATTAATATAAA
696916 TT-TTAAAT
1 TTATTAAAT
696924 ATAAATACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.03
15 4 0.11
16 8 0.22
17 12 0.32
18 8 0.22
19 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATTAAATTAATATAAA
Found at i:697131 original size:3 final size:3
Alignment explanation
Indices: 697123--697217 Score: 142
Period size: 3 Copynumber: 32.3 Consensus size: 3
697113 AAATTATCTC
*
697123 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
697170 TAGA -CA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
697214 TAA T
1 TAA T
697218 TATTATTATT
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.05
3 79 0.94
4 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:697222 original size:3 final size:3
Alignment explanation
Indices: 697216--697244 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
697206 AATAATAATA
697216 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
697245 ATGTAACATG
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:698661 original size:13 final size:13
Alignment explanation
Indices: 698643--698667 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
698633 TTTCACTATA
698643 TATCGATATAATG
1 TATCGATATAATG
698656 TATCGATATAAT
1 TATCGATATAAT
698668 ATCCCATGTA
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:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
TATCGATATAATG
Found at i:699412 original size:20 final size:20
Alignment explanation
Indices: 699389--699449 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
699379 ATATATAAAA
*
699389 CTCCCCTTTAATAAAATTTT
1 CTCCCCTTTAATAAAAATTT
*
699409 CTCCCCCTTAATAAAAATTT
1 CTCCCCTTTAATAAAAATTT
* *
699429 -TCCCCTTTTA-AAAAATAT
1 CTCCCCTTTAATAAAAATTT
699447 CTC
1 CTC
699450 TCCTCTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 7 0.20
19 10 0.29
20 18 0.51
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (20 bp):
CTCCCCTTTAATAAAAATTT
Found at i:707575 original size:20 final size:20
Alignment explanation
Indices: 707550--707587 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
707540 TACTGCTAGT
707550 TTCATGTATCGATACAATTC
1 TTCATGTATCGATACAATTC
707570 TTCATGTATCGATACAAT
1 TTCATGTATCGATACAAT
707588 GAACATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACAATTC
Found at i:707596 original size:19 final size:20
Alignment explanation
Indices: 707552--707603 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
707542 CTGCTAGTTT
**
707552 CATGTATCGATACAATTCTT
1 CATGTATCGATACAATTCAA
*
707572 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTCAA
707591 CATGTATCGATAC
1 CATGTATCGATAC
707604 TTTATATCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTCAA
Found at i:707617 original size:32 final size:33
Alignment explanation
Indices: 707576--707638 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
707566 ATTCTTCATG
* *
707576 TATCGATACAATG-AACATGTATCGATACTTTA
1 TATCGATACAAAGCAACATATATCGATACTTTA
*
707608 TATCGATACAAAGCAATATATATCGATACTT
1 TATCGATACAAAGCAACATATATCGATACTT
707639 CTGGGCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (33 bp):
TATCGATACAAAGCAACATATATCGATACTTTA
Found at i:708915 original size:15 final size:16
Alignment explanation
Indices: 708895--708927 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
708885 CCTGAACATG
708895 AAAAAACC-CAAACCC
1 AAAAAACCTCAAACCC
708910 AAAAAACCTCAAACCC
1 AAAAAACCTCAAACCC
708926 AA
1 AA
708928 GACTGACTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.61, C:0.36, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAAAACCTCAAACCC
Found at i:709031 original size:15 final size:16
Alignment explanation
Indices: 709011--709043 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
709001 CCTGAACATG
709011 AAAAAACC-CAAACCC
1 AAAAAACCTCAAACCC
709026 AAAAAACCTCAAACCC
1 AAAAAACCTCAAACCC
709042 AA
1 AA
709044 GACTGACTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.61, C:0.36, G:0.00, T:0.03
Consensus pattern (16 bp):
AAAAAACCTCAAACCC
Found at i:709043 original size:116 final size:116
Alignment explanation
Indices: 708834--709062 Score: 433
Period size: 116 Copynumber: 2.0 Consensus size: 116
708824 TAAACTCGAA
708834 AAACCCAAATCCAAAATGGCCTGAACTCAAAATAGCTTGAAACCCAAAGAACCTGAACATGAAAA
1 AAACCCAAATCCAAAATGGCCTGAACTCAAAATAGCTTGAAACCCAAAGAACCTGAACATGAAAA
708899 AACCCAAACCCAAAAAACCTCAAACCCAAGACTGACTCGAACT-GAACATG
66 AACCCAAACCCAAAAAACCTCAAACCCAAGACTGACTCGAACTCGAACATG
*
708949 AAACCTCAAATCCAAAATGGCTTGAACTCAAAATAGCTTGAAACCCAAAGAACCTGAACATGAAA
1 AAACC-CAAATCCAAAATGGCCTGAACTCAAAATAGCTTGAAACCCAAAGAACCTGAACATGAAA
709014 AAACCCAAACCCAAAAAACCTCAAACCCAAGACTGACTCGAACTCGAAC
65 AAACCCAAACCCAAAAAACCTCAAACCCAAGACTGACTCGAACTCGAAC
709063 TCGAATTTAA
Statistics
Matches: 111, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
115 5 0.05
116 102 0.92
117 4 0.04
ACGTcount: A:0.48, C:0.29, G:0.11, T:0.13
Consensus pattern (116 bp):
AAACCCAAATCCAAAATGGCCTGAACTCAAAATAGCTTGAAACCCAAAGAACCTGAACATGAAAA
AACCCAAACCCAAAAAACCTCAAACCCAAGACTGACTCGAACTCGAACATG
Found at i:709235 original size:22 final size:22
Alignment explanation
Indices: 709210--709263 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
709200 ATATATGATA
709210 AAATAATAAT-TTATCAAAAAAT
1 AAATAAT-ATCTTATCAAAAAAT
* * *
709232 AAATTATATCTTATTAAAAAGT
1 AAATAATATCTTATCAAAAAAT
*
709254 AAATTATATC
1 AAATAATATC
709264 ATGAGCTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATAATATCTTATCAAAAAAT
Found at i:710542 original size:20 final size:19
Alignment explanation
Indices: 710490--710545 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
710480 TTAAAAATTA
*
710490 ATTTTATATAACAAAT-TA-
1 ATTTTATA-AATAAATATAG
*
710508 ATTTTATATATAAATATAG
1 ATTTTATAAATAAATATAG
710527 ATTTTAATAAATAAATATA
1 ATTTT-ATAAATAAATATA
710546 TTGAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.16
18 10 0.31
19 5 0.16
20 12 0.38
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTTTATAAATAAATATAG
Found at i:710734 original size:16 final size:16
Alignment explanation
Indices: 710715--710752 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
710705 GAAAAAACCT
*
710715 GAACTCGAAAAGGCTC
1 GAACTCGAAAAAGCTC
*
710731 GAACTCGAAAAATCTC
1 GAACTCGAAAAAGCTC
710747 GAACTC
1 GAACTC
710753 AAATAGGCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.26, G:0.18, T:0.16
Consensus pattern (16 bp):
GAACTCGAAAAAGCTC
Found at i:714371 original size:30 final size:30
Alignment explanation
Indices: 714314--714372 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
714304 GCGGGATTTG
* * ** *
714314 TATATCATTTAATTTTGTACGATAATTTAA
1 TATATAATTTAATATTGTAAAAAAATTTAA
714344 TATATAATTTAATATTGTAAAAAAATTTA
1 TATATAATTTAATATTGTAAAAAAATTTA
714373 CCATTAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (30 bp):
TATATAATTTAATATTGTAAAAAAATTTAA
Found at i:714631 original size:21 final size:22
Alignment explanation
Indices: 714607--714654 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
714597 TGTGATAAAA
*
714607 ATAAA-TTTTAAATATTTAATC
1 ATAAATTTTTAAATATTAAATC
* *
714628 ATAAATTTTTATATATTAAATT
1 ATAAATTTTTAAATATTAAATC
714650 ATAAA
1 ATAAA
714655 AAATAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTTTTAAATATTAAATC
Found at i:714808 original size:12 final size:13
Alignment explanation
Indices: 714791--714823 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
714781 AAAAATTTTA
*
714791 AAAATTTATTA-T
1 AAAATTTATAATT
714803 AAAATTTATAATT
1 AAAATTTATAATT
714816 AAAATTTA
1 AAAATTTA
714824 ATTTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAAATTTATAATT
Found at i:715856 original size:16 final size:16
Alignment explanation
Indices: 715837--715884 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
715827 GTTTTTTAGT
715837 TTTTAAATTTAAATTA
1 TTTTAAATTTAAATTA
* * **
715853 TTTTGAGTTCGAATTA
1 TTTTAAATTTAAATTA
715869 TTTTAAATTTGAAATT
1 TTTTAAATTT-AAATT
715885 TTAATTTTTT
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
16 19 0.83
17 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.54
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:716792 original size:109 final size:110
Alignment explanation
Indices: 716575--716781 Score: 281
Period size: 109 Copynumber: 1.9 Consensus size: 110
716565 TAATCAACAT
* * * * *
716575 TCATGAAAATGAAGAAGTTCAAACATATTTATAAGGGTGAAATGGATACGAATAAAGCAATTTCT
1 TCATGAAAATGAAGAAGTTCAAACATATTTACAAGAGTGAAATAGACACGAATAAAGCAATTCCT
* *
716640 GTCTTACCTCGCTTAATTATCATCTCTATTATTGAAGAGATTACG
66 GTCTTACCTCACTCAATTATCATCTCTATTATTGAAGAGATTACG
* * * **
716685 TCATGGAAATGAAGAATTTC-AACATATTTACAAGAGTGTAATAGACGTGAATAAAGCAATTCCT
1 TCATGAAAATGAAGAAGTTCAAACATATTTACAAGAGTGAAATAGACACGAATAAAGCAATTCCT
* *
716749 GTCTTACTTCACTCAATTATCATCTTTATTATT
66 GTCTTACCTCACTCAATTATCATCTCTATTATT
716782 ATTGTGATTA
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
109 65 0.78
110 18 0.22
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (110 bp):
TCATGAAAATGAAGAAGTTCAAACATATTTACAAGAGTGAAATAGACACGAATAAAGCAATTCCT
GTCTTACCTCACTCAATTATCATCTCTATTATTGAAGAGATTACG
Found at i:716908 original size:16 final size:16
Alignment explanation
Indices: 716871--716914 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
716861 TTTTTTAACA
716871 TTAAA-ATTTTA-ATT
1 TTAAATATTTTATATT
**
716885 TTTTATATTTTATATT
1 TTAAATATTTTATATT
716901 TTAAATATTTTATA
1 TTAAATATTTTATA
716915 ATTAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 3 0.12
15 6 0.25
16 15 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAAATATTTTATATT
Done.