Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold109
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: 1855911
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.34
Warning! 69956 characters in sequence are not A, C, G, or T
File 8 of 13
Found at i:1022788 original size:15 final size:15
Alignment explanation
Indices: 1022768--1022819 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
1022758 AATTTTAAAA
1022768 ATTAAATATATTTAT
1 ATTAAATATATTTAT
1022783 ATTAAATATATATTTAT
1 ATT-AA-ATATATTTAT
* *
1022800 ATTTAATATTTTTAT
1 ATTAAATATATTTAT
1022815 ATTAA
1 ATTAA
1022820 TTAATATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 16 0.50
16 3 0.09
17 13 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTAAATATATTTAT
Found at i:1022808 original size:17 final size:17
Alignment explanation
Indices: 1022769--1022817 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
1022759 ATTTTAAAAA
1022769 TTAA-ATATATTTATAT
1 TTAATATATATTTATAT
*
1022785 TAAATATATATTTATAT
1 TTAATATATATTTATAT
1022802 TTAATAT-T-TTTATAT
1 TTAATATATATTTATAT
1022817 T
1 T
1022818 AATTAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 8 0.27
16 4 0.13
17 18 0.60
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATATATATTTATAT
Found at i:1026038 original size:35 final size:37
Alignment explanation
Indices: 1025971--1026063 Score: 97
Period size: 34 Copynumber: 2.6 Consensus size: 37
1025961 GAGACGTATC
*
1025971 AAATTTAAAAATTTATTTTATTATTTAAAATTAATAA
1 AAATTTAAAAATATATTTTATTATTTAAAATTAATAA
* * **
1026008 AAATTTTAAAATAT-TTTTATT-TTTATAATTAAATTT
1 AAATTTAAAAATATATTTTATTATTTAAAATT-AATAA
1026044 AAA--TAAAAATAT-TTTTATTA
1 AAATTTAAAAATATATTTTATTA
1026064 AATAAATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
34 15 0.31
35 8 0.17
36 13 0.27
37 12 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
AAATTTAAAAATATATTTTATTATTTAAAATTAATAA
Found at i:1026628 original size:17 final size:17
Alignment explanation
Indices: 1026606--1026648 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1026596 ATAAACTATT
1026606 ATATAAAATATA-ATATA
1 ATATAAAATATACATA-A
* *
1026623 ATATAAAAGATACGTAA
1 ATATAAAATATACATAA
1026640 ATATAAAAT
1 ATATAAAAT
1026649 TTTATATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (17 bp):
ATATAAAATATACATAA
Found at i:1026851 original size:33 final size:31
Alignment explanation
Indices: 1026790--1026858 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 31
1026780 TTAATTTTAA
*
1026790 ATTAAAATAATTATTTTAAAATATATTAAAT
1 ATTAAAATAATTATTTTAAAATAAATTAAAT
1026821 ATTAAAA-AATTATTTTAATAATTTAAATTAAAT
1 ATTAAAATAATTATTTTAA-AA--TAAATTAAAT
1026854 ATTAA
1 ATTAA
1026859 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.32
31 9 0.26
33 14 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
ATTAAAATAATTATTTTAAAATAAATTAAAT
Found at i:1028066 original size:35 final size:36
Alignment explanation
Indices: 1028000--1028070 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 36
1027990 TAAAAAATTA
1028000 AAAAATTATTTTTATATTTTATAATTAAATTTAAAT
1 AAAAATTATTTTTATATTTTATAATTAAATTTAAAT
*
1028036 AAAAA-TATTTTTA-ATTATTA-AATATTAATTTAAAT
1 AAAAATTATTTTTATATT-TTATAAT-TAAATTTAAAT
1028071 CAAATCGAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
34 6 0.19
35 21 0.66
36 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
AAAAATTATTTTTATATTTTATAATTAAATTTAAAT
Found at i:1028439 original size:30 final size:30
Alignment explanation
Indices: 1028378--1028462 Score: 91
Period size: 32 Copynumber: 2.8 Consensus size: 30
1028368 GATTTAATGT
*
1028378 TTAAATAAAT-TTTTAAATTTTATTTTAAA
1 TTAAATAAATATTTTAAATTTAATTTTAAA
* *
1028407 TTAAATAAATATTTTTAATTTAAATTTTAAT
1 TTAAATAAATATTTTAAATTT-AATTTTAAA
* *
1028438 TATAAATATATATTTAAAATATTAA
1 T-TAAATAAATATTTTAAAT-TTAA
1028463 AATATAAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
29 10 0.22
30 9 0.20
31 8 0.17
32 17 0.37
33 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TTAAATAAATATTTTAAATTTAATTTTAAA
Found at i:1028475 original size:22 final size:22
Alignment explanation
Indices: 1028436--1028478 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1028426 TTAAATTTTA
*
1028436 ATTATAAATATATATTTAAAAT
1 ATTATAAATATAAATTTAAAAT
1028458 ATTA-AAATATAAACTTTAAAA
1 ATTATAAATATAAA-TTTAAAA
1028479 GTTCATTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTATAAATATAAATTTAAAAT
Found at i:1029048 original size:42 final size:38
Alignment explanation
Indices: 1028996--1029106 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 38
1028986 TTATTTTTAA
*
1028996 TAATAAAAAATAACTTTTAAATGTTATTTAAAATATTACTTT
1 TAATAAAAAATAA--TTT-AAT-TAATTTAAAATATTACTTT
* *
1029038 TAATAAAAAATTTAATTTAATTAATTTAAATTATTATTTT
1 TAATAAAAAA--TAATTTAATTAATTTAAAATATTACTTT
*
1029078 TAATATAAAATAA-TTAA-TATATTTAAAAT
1 TAATAAAAAATAATTTAATTA-ATTTAAAAT
1029107 TTAAATATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
36 2 0.03
37 12 0.20
38 3 0.05
40 25 0.41
41 3 0.05
42 13 0.21
44 3 0.05
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (38 bp):
TAATAAAAAATAATTTAATTAATTTAAAATATTACTTT
Found at i:1029079 original size:40 final size:42
Alignment explanation
Indices: 1028971--1029089 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 42
1028961 GTTTTATTTT
* *
1028971 TTAATTTGAAATGATTTATTTTTAATAATAAAAAATAACTTTTAAA
1 TTAATTT-AAATTA-TTATTTTTAATAA-AAAATATAAC-TTTAAA
* * * *
1029017 TGTTATTTAAAATATTACTTTTAATAAAAAATTTAA-TTT-AA
1 T-TAATTTAAATTATTATTTTTAATAAAAAATATAACTTTAAA
*
1029058 TTAATTTAAATTATTATTTTTAATATAAAATA
1 TTAATTTAAATTATTATTTTTAATAAAAAATA
1029090 ATTAATATAT
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
40 26 0.43
41 3 0.05
42 3 0.05
44 7 0.11
45 12 0.20
46 5 0.08
47 5 0.08
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.49
Consensus pattern (42 bp):
TTAATTTAAATTATTATTTTTAATAAAAAATATAACTTTAAA
Found at i:1029570 original size:22 final size:22
Alignment explanation
Indices: 1029544--1029585 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1029534 TAATCAGATC
* *
1029544 TATTTGATTGATTTTTTAAATT
1 TATTTAATTGAATTTTTAAATT
*
1029566 TATTTAATTTAATTTTTAAA
1 TATTTAATTGAATTTTTAAA
1029586 ATGTTTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TATTTAATTGAATTTTTAAATT
Found at i:1030263 original size:23 final size:22
Alignment explanation
Indices: 1030235--1030277 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1030225 ATATTAAAAA
1030235 ATAT-TTTTTAT-ATTAATATTT
1 ATATATTTTTATAATTAA-ATTT
1030256 ATATATTTTTATAATTAAATTT
1 ATATATTTTTATAATTAAATTT
1030278 TTTGTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATATTTTTATAATTAAATTT
Found at i:1030587 original size:21 final size:20
Alignment explanation
Indices: 1030563--1030603 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1030553 ATTTTTTATT
*
1030563 TAAATATTATTATAAAATATA
1 TAAATATTAATAT-AAATATA
1030584 TAAATATTAATATAAATATA
1 TAAATATTAATATAAATATA
1030604 ATTTTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAATATTAATATAAATATA
Found at i:1030596 original size:12 final size:12
Alignment explanation
Indices: 1030563--1030602 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1030553 ATTTTTTATT
*
1030563 TAAATATTATTA
1 TAAATATTAATA
1030575 TAAA-A-T-ATA
1 TAAATATTAATA
1030584 TAAATATTAATA
1 TAAATATTAATA
1030596 TAAATAT
1 TAAATAT
1030603 AATTTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
9 6 0.25
10 2 0.08
11 2 0.08
12 14 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAATATTAATA
Found at i:1031412 original size:31 final size:33
Alignment explanation
Indices: 1031369--1031431 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
1031359 TGTTATATTT
1031369 TATATTTCATTTTT-TAATTTTATTT-TAAAAA
1 TATATTTCATTTTTATAATTTTATTTATAAAAA
1031400 TATATATT-ATTTTTATAATTTTATTTATAAAA
1 TATAT-TTCATTTTTATAATTTTATTTATAAAA
1031432 TTTAAAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 11 0.38
32 13 0.45
33 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (33 bp):
TATATTTCATTTTTATAATTTTATTTATAAAAA
Found at i:1031636 original size:26 final size:28
Alignment explanation
Indices: 1031607--1031660 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
1031597 ACTCGATTTG
* *
1031607 ATTAGTTTAATTTA-TTTAA-ATTAAAA
1 ATTAATTTAATTAATTTTAATATTAAAA
1031633 ATTAATTTAATTAATTTTAATATTAAAA
1 ATTAATTTAATTAATTTTAATATTAAAA
1031661 TTGATCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.50
27 5 0.21
28 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
ATTAATTTAATTAATTTTAATATTAAAA
Found at i:1031841 original size:22 final size:21
Alignment explanation
Indices: 1031810--1031869 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
1031800 TTAATTAAGT
* *
1031810 TTTTAGTTTAAATTTAGATGGG
1 TTTTAATTTAAATTTAAAT-GG
*
1031832 TTTTAATTTAGATTTAAATGG
1 TTTTAATTTAAATTTAAATGG
*
1031853 ATTTAAGTTTAAATTTA
1 TTTTAA-TTTAAATTTA
1031870 TATTTTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (21 bp):
TTTTAATTTAAATTTAAATGG
Found at i:1032940 original size:13 final size:12
Alignment explanation
Indices: 1032923--1032968 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
1032913 TATATAAAAA
1032923 ATAATTAAATTT
1 ATAATTAAATTT
1032935 AATAA-T-AATTT
1 -ATAATTAAATTT
1032946 AT-ATTAATATTT
1 ATAATTAA-ATTT
1032958 ATAATTAAATT
1 ATAATTAAATT
1032969 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
9 1 0.03
10 3 0.10
11 6 0.21
12 10 0.34
13 9 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAATTAAATTT
Found at i:1039165 original size:41 final size:41
Alignment explanation
Indices: 1039096--1039196 Score: 100
Period size: 41 Copynumber: 2.5 Consensus size: 41
1039086 TAATATAAAT
* *
1039096 AAAAATAAATAAAATATTATATATAATATAATATAATATTA
1 AAAAATAAATAAAATATTATAAAAAATATAATATAATATTA
* * *
1039137 AAAAATAAATATAAAT-TTTTAAAAAATATTATGTAATA-TA
1 AAAAATAAATA-AAATATTATAAAAAATATAATATAATATTA
** *
1039177 AATTATTAATAAAAT-TTATA
1 AAAAATAAATAAAATATTATA
1039197 TTAATATAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
39 8 0.16
40 10 0.20
41 28 0.56
42 4 0.08
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (41 bp):
AAAAATAAATAAAATATTATAAAAAATATAATATAATATTA
Found at i:1039176 original size:27 final size:28
Alignment explanation
Indices: 1039144--1039216 Score: 87
Period size: 27 Copynumber: 2.6 Consensus size: 28
1039134 TTAAAAAATA
1039144 AATATAAATTTTTAA-AAAATATTAT-GT
1 AATATAAATTTTTAATAAAAT-TTATAGT
* *
1039171 AATATAAATTATTAATAAAATTTATATT
1 AATATAAATTTTTAATAAAATTTATAGT
1039199 AATATAAAATATTTTAAT
1 AATAT-AAAT-TTTTAAT
1039217 TATAATTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 18 0.46
28 11 0.28
29 4 0.10
30 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (28 bp):
AATATAAATTTTTAATAAAATTTATAGT
Found at i:1039215 original size:15 final size:15
Alignment explanation
Indices: 1039159--1039221 Score: 51
Period size: 15 Copynumber: 4.1 Consensus size: 15
1039149 AAATTTTTAA
1039159 AAAATATTATGTAATAT
1 AAAATA-TAT-TAATAT
1039176 -AAAT-TATTAATA-
1 AAAATATATTAATAT
*
1039188 AAATTTATATTAATAT
1 AAA-ATATATTAATAT
*
1039204 AAAATATTTTAATTAT
1 AAAATATATTAA-TAT
1039220 AA
1 AA
1039222 TTATAATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
13 7 0.18
14 4 0.11
15 15 0.39
16 12 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
AAAATATATTAATAT
Found at i:1039247 original size:26 final size:26
Alignment explanation
Indices: 1039218--1039294 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 26
1039208 TATTTTAATT
*
1039218 ATAATTATAATTAAATTTATTTATAA
1 ATAATTAAAATTAAATTTATTTATAA
* *
1039244 ATAAATT-GAATTATAATTTA-TGATAA
1 AT-AATTAAAATTA-AATTTATTTATAA
*
1039270 ATATTTAAAATTTAAATTTAATTTA
1 ATAATTAAAA-TTAAATTT-ATTTA
1039295 ATTTAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
25 3 0.08
26 21 0.52
27 14 0.35
28 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
ATAATTAAAATTAAATTTATTTATAA
Found at i:1039417 original size:14 final size:14
Alignment explanation
Indices: 1039395--1039437 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1039385 ATATTATTTT
*
1039395 AATTGATTAAATTA
1 AATTTATTAAATTA
*
1039409 AATTTATTAAATAA
1 AATTTATTAAATTA
1039423 AATATTATCTAAATT
1 AAT-TTAT-TAAATT
1039438 TTTGAGCAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 15 0.62
15 4 0.17
16 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (14 bp):
AATTTATTAAATTA
Found at i:1039724 original size:15 final size:15
Alignment explanation
Indices: 1039704--1039753 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
1039694 AATTGTAAAA
1039704 ATTAAATATATTTAT
1 ATTAAATATATTTAT
1039719 ATTAAATAAATATTTAT
1 ATTAAAT--ATATTTAT
* * *
1039736 ATTTAAGATTTTTAT
1 ATTAAATATATTTAT
1039751 ATT
1 ATT
1039754 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 17 0.57
17 13 0.43
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTAAATATATTTAT
Found at i:1039724 original size:34 final size:35
Alignment explanation
Indices: 1039644--1039729 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 35
1039634 ATGTGTGATT
* * *
1039644 TTTATATTTAGTAAATATTTAAAAATAAAAATATAA
1 TTTATATTAAATAAAT-TGTAAAAATAAAAATATAA
* *
1039680 TTTTTATTAAAATAAATTGTAAAAAT-TAAATAT-A
1 TTTATATT-AAATAAATTGTAAAAATAAAAATATAA
1039714 TTTATATTAAATAAAT
1 TTTATATTAAATAAAT
1039730 ATTTATATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
33 8 0.19
34 8 0.19
35 6 0.14
36 15 0.35
37 6 0.14
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (35 bp):
TTTATATTAAATAAATTGTAAAAATAAAAATATAA
Found at i:1039927 original size:27 final size:25
Alignment explanation
Indices: 1039891--1039947 Score: 78
Period size: 27 Copynumber: 2.2 Consensus size: 25
1039881 TCGTTTATTA
1039891 ATATTTTTAAATATTTTATATAATAAT
1 ATATTTTTAAATATTTTA-ATAA-AAT
* *
1039918 TTATTTTTAAATTTTTTAATAAAAT
1 ATATTTTTAAATATTTTAATAAAAT
1039943 ATATT
1 ATATT
1039948 ATATACATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 7 0.26
26 4 0.15
27 16 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTTTTAAATATTTTAATAAAAT
Found at i:1040211 original size:18 final size:18
Alignment explanation
Indices: 1040185--1040232 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1040175 TTAAATTGGA
1040185 TTAATTTAAATTTATTTT
1 TTAATTTAAATTTATTTT
* **
1040203 TTAAATTAAATAAATTTT
1 TTAATTTAAATTTATTTT
1040221 TT-ATTTAAATTT
1 TTAATTTAAATTT
1040233 TAATTATAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATTTAAATTTATTTT
Found at i:1043258 original size:146 final size:144
Alignment explanation
Indices: 1043036--1043328 Score: 469
Period size: 146 Copynumber: 2.0 Consensus size: 144
1043026 TATGCAAGTA
* *
1043036 AGACTCCTCTTTGTCTCTATTAAAAAAAAATAATAAAGCTTTATTAATAAAGGTAAAATAAGTAG
1 AGACTCCTCTTTGTCTCTATTAAAAAAAAATAATAAAGCTTTATTAATAAAGGTAAAACAAATAG
* *
1043101 ATAGATATGAATTTAAATTGGAATCATAGATTTATTTTTAATTTTTTTGTATTTATTATAGTTTC
66 ATAGATATGAATTTAAATTGGAATCATAGATTCATTTTCAATTTTTTTGTATTTATTATAGTTTC
*
1043166 AAAATTATAATGGT
131 AAAATTATAATAGT
* * *
1043180 AGACTCCTCTTTGTCTCTATTAAAAAAAATAATAATATAGCTTTATTAATAAGGGTGAAACAAAT
1 AGACTCCTCTTTGTCTCTATT-AAAAAAA-AATAATAAAGCTTTATTAATAAAGGTAAAACAAAT
* * *
1043245 AGATAGATATGAATTTAAATTGTAATCATAGATTCATTTTCAATTTTTTTGTGTTTATTGTAGTT
64 AGATAGATATGAATTTAAATTGGAATCATAGATTCATTTTCAATTTTTTTGTATTTATTATAGTT
1043310 TCAAAATTATAATAGT
129 TCAAAATTATAATAGT
1043326 AGA
1 AGA
1043329 TTCATTTTTA
Statistics
Matches: 136, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
144 21 0.15
145 7 0.05
146 108 0.79
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (144 bp):
AGACTCCTCTTTGTCTCTATTAAAAAAAAATAATAAAGCTTTATTAATAAAGGTAAAACAAATAG
ATAGATATGAATTTAAATTGGAATCATAGATTCATTTTCAATTTTTTTGTATTTATTATAGTTTC
AAAATTATAATAGT
Found at i:1043831 original size:27 final size:28
Alignment explanation
Indices: 1043784--1043842 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
1043774 TTCCTTCAAA
1043784 CAAATATATATATGTAAAATAAAAATGAC
1 CAAATATATATA-GTAAAATAAAAATGAC
* *
1043813 CAAATATATATA-TATAATAGAAATGAC
1 CAAATATATATAGTAAAATAAAAATGAC
1043840 CAA
1 CAA
1043843 CAAATAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 16 0.57
29 12 0.43
ACGTcount: A:0.58, C:0.08, G:0.07, T:0.27
Consensus pattern (28 bp):
CAAATATATATAGTAAAATAAAAATGAC
Found at i:1043852 original size:27 final size:27
Alignment explanation
Indices: 1043791--1043863 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
1043781 AAACAAATAT
* * *
1043791 ATATATGTAAAATAAAAATGACCAAAT
1 ATATATATATAATAAAAATGACCAAAA
*
1043818 ATATATATATAATAGAAATGACCAACAA
1 ATATATATATAATAAAAATGACCAA-AA
* *
1043846 ATA-ATATTTCATAAAAAT
1 ATATATATATAATAAAAAT
1043864 AAAAAAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 34 0.89
28 4 0.11
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (27 bp):
ATATATATATAATAAAAATGACCAAAA
Found at i:1043852 original size:29 final size:30
Alignment explanation
Indices: 1043782--1043852 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 30
1043772 TTTTCCTTCA
1043782 AACAAATATATATATGTAAAATAAAAATGACC
1 AACAAATA-ATATA-GTAAAATAAAAATGACC
* * *
1043814 AA-ATAT-ATATA-TATAATAGAAATGACC
1 AACAAATAATATAGTAAAATAAAAATGACC
1043841 AACAAATAATAT
1 AACAAATAATAT
1043853 TTCATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
27 16 0.48
28 3 0.09
29 9 0.27
31 3 0.09
32 2 0.06
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (30 bp):
AACAAATAATATAGTAAAATAAAAATGACC
Found at i:1044927 original size:262 final size:262
Alignment explanation
Indices: 1044424--1045011 Score: 738
Period size: 262 Copynumber: 2.2 Consensus size: 262
1044414 TGCATATTGA
* * * *
1044424 AGATTACTATGTTATTTTATGCA-TTTAA-ATACGTTTAAGTCATTTTCTATGAATTAAAATTAT
1 AGATTATTATGTAATTTTATGCATTTTAAGAT-CATTTAAGTCATTTTCTATGATTTAAAATTAT
* * * * * *
1044487 TATATTATTTTATGCATTATAAAGATAGTGAAGTCATTTTTCATGATCTAAGAACTTCTTTTGTC
65 TATATCATTTCATGCATTATAAAGATAGTGAAGTCATATTCCACGATATAAGAACTTCTTTTGTC
** * *
1044552 ATTTCATGCATTTTAGAGATTTTTATGTCATCCCATTTATTTTTAGAGATTAATATATAATTTCA
130 ATTTCATGCATTTTAGAGATTTTTACATCATCCCATGTATTTTTAAAGATTAATATATAATTTCA
* * * *
1044617 TGCATCTTGGTTACTACTATACAATTTCATGGATTTTAGAGTTACTTTAGTCATTTTTCATGTTT
195 TGCATCTTAGTTACTACTATACAATTCCATGGATTTTAAAGTTACTTTAGTCAGTTTTCATGTTT
*
1044682 TAT
260 TAG
* *
1044685 AGATTATTATGTAATTTTACGCATTTTAAGATCATTTAAGTCATTGTCTATGATTTATAAATTAT
1 AGATTATTATGTAATTTTATGCATTTTAAGATCATTTAAGTCATTTTCTATGATTTA-AAATTAT
* * *** * * * * *
1044750 TTTATCATTTCATGCATTTTTGGGATATTGAAGTCATATTCCACGATAT-AGGATTTTTTTTGTT
65 TATATCATTTCATGCATTATAAAGATAGTGAAGTCATATTCCACGATATAAGAACTTCTTTTGTC
*
1044814 GTTTCATGCATTTTA-AGGATTTTTACATCATCCCATGTATTTTTAAAGATTAATATATAATTTC
130 ATTTCATGCATTTTAGA-GATTTTTACATCATCCCATGTATTTTTAAAGATTAATATATAATTTC
* * *
1044878 ATGCATCTTAGTTACTATTATGCAATTCCATGTATTTTAAAAG-TACTTTAGTCAGTTTTCATGT
194 ATGCATCTTAGTTACTACTATACAATTCCATGGATTTT-AAAGTTACTTTAGTCAGTTTTCATGT
1044942 TTTAG
258 TTTAG
* * *
1044947 AGATTATTATATAATTGTATGCATTTTAAGATTA-TTATAGTCATTTTCTATGATTTAAACATTA
1 AGATTATTATGTAATTTTATGCATTTTAAGATCATTTA-AGTCATTTTCTATGATTTAAA-ATTA
1045011 T
64 T
1045012 GATGCAAATT
Statistics
Matches: 280, Mismatches: 40, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
261 26 0.09
262 205 0.73
263 49 0.17
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.48
Consensus pattern (262 bp):
AGATTATTATGTAATTTTATGCATTTTAAGATCATTTAAGTCATTTTCTATGATTTAAAATTATT
ATATCATTTCATGCATTATAAAGATAGTGAAGTCATATTCCACGATATAAGAACTTCTTTTGTCA
TTTCATGCATTTTAGAGATTTTTACATCATCCCATGTATTTTTAAAGATTAATATATAATTTCAT
GCATCTTAGTTACTACTATACAATTCCATGGATTTTAAAGTTACTTTAGTCAGTTTTCATGTTTT
AG
Found at i:1045082 original size:262 final size:261
Alignment explanation
Indices: 1044515--1045082 Score: 648
Period size: 262 Copynumber: 2.2 Consensus size: 261
1044505 ATAAAGATAG
* * **
1044515 TGAAGTCATTTTTCATGATCTAAGAACTTCTTTTGTCATTTCATGCATTTTAGAGATTTTTATGT
1 TGAAGTCATTTTTCATGATATAAGAACTT-TTTTGTCGTTTCATGCATTTTAGAGATTTTTACAT
* * * *
1044580 CATCCCATTTATTTTTAGAGATTAATATATAATTTCATGCATCTTGGTTACTACTATACAATTTC
65 CATCCCATGTATTTTTAAAGATTAATATATAATTTCATGCATCTTAGTTACTACTATACAATTCC
* * * * *
1044645 ATGGATTTTAGAGTTACTTTAGTCATTTTTCATGTTTTATAGATTATTATGTAATTTTACGCATT
130 ATGGATTTTAAAGTTACTTTAGTCAGTTTTCATGTTTTAGAGATTATTATATAATTGTACGCATT
* * * **
1044710 TTAAGATCATTTAAGTCATTGTCTATGATTTATAAATTATTTTATCATTTCATGCATTTTTGGGA
195 TTAAGATCATTTAAGTCATTGTCTATGATTTATAAATTA-TTGATCAATTCACGCATTTTTGCCA
1044775 TAT
259 TAT
* * * * ** *
1044778 TGAAGTCATATTCCACGATATAGGATTTTTTTTGTTGTTTCATGCATTTTA-AGGATTTTTACAT
1 TGAAGTCATTTTTCATGATATAAGAACTTTTTTGTCGTTTCATGCATTTTAGA-GATTTTTACAT
* *
1044842 CATCCCATGTATTTTTAAAGATTAATATATAATTTCATGCATCTTAGTTACTATTATGCAATTCC
65 CATCCCATGTATTTTTAAAGATTAATATATAATTTCATGCATCTTAGTTACTACTATACAATTCC
* *
1044907 ATGTATTTTAAAAG-TACTTTAGTCAGTTTTCATGTTTTAGAGATTATTATATAATTGTATGCAT
130 ATGGATTTT-AAAGTTACTTTAGTCAGTTTTCATGTTTTAGAGATTATTATATAATTGTACGCAT
* * *
1044971 TTTAAGATTA-TTATAGTCATTTTCTATGATTTA-AACATTA-TGATGCAAATTCACGTATTTTC
194 TTTAAGATCATTTA-AGTCATTGTCTATGATTTATAA-ATTATTGAT-C-AATTCACGCA-TTT-
1045033 TTGCCAT-T
253 TTGCCATAT
* * * **
1045041 T-TAGTTATTTTTCATAACT-TAAGAACTTTTAAGTCGTTTCAT
1 TGAAGTCATTTTTCATGA-TATAAGAACTTTTTTGTCGTTTCAT
1045083 ATACTTTAAT
Statistics
Matches: 252, Mismatches: 44, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
260 3 0.01
261 7 0.03
262 206 0.82
263 31 0.12
264 5 0.02
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (261 bp):
TGAAGTCATTTTTCATGATATAAGAACTTTTTTGTCGTTTCATGCATTTTAGAGATTTTTACATC
ATCCCATGTATTTTTAAAGATTAATATATAATTTCATGCATCTTAGTTACTACTATACAATTCCA
TGGATTTTAAAGTTACTTTAGTCAGTTTTCATGTTTTAGAGATTATTATATAATTGTACGCATTT
TAAGATCATTTAAGTCATTGTCTATGATTTATAAATTATTGATCAATTCACGCATTTTTGCCATA
T
Found at i:1045254 original size:290 final size:290
Alignment explanation
Indices: 1044891--1045496 Score: 993
Period size: 290 Copynumber: 2.1 Consensus size: 290
1044881 CATCTTAGTT
*
1044891 ACTA-TTATGCAATTCCATGTATTTTAAAAGTACTTTAGTCAGTTTTCATGTTTTAGAGATTATT
1 ACTATTTATGCAATTTCATGTATTTTAAAAGTACTTTAGTCAGTTTTCATGTTTTAGAGATTATT
* **
1044955 ATATAATTGTATGCATTTTAAGATTATTATAGTCATTTTCTATGATTTAAACATTATGATGCAAA
66 ATATAATTGTATGCATTGTAAGATTATTATAGTCATTTTCTATGATGCAAACATTATGATGCAAA
* *
1045020 TTCACGTATTTTCTTGCCATTTTAGTTATTTTTCATAACTTAAGAACTTTTAAGTCGTTTCATAT
131 TTCACATATTTTCTTGCCATTTTAGTTATTTTTCATAACTTAAGAACTTTTAAGTCGTTTCATAC
*
1045085 ACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTAG
196 ACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTAA
*
1045150 GGTCATTCTAATAATTTACCATGATCTAGA
261 GGTCATTCTAATAATTTACCATGATCTAAA
*
1045180 ACTATTTATGCAATTTCATGTATTTTAAAGGTACTTTAGTCA-TATTTCATGTTTTAGAGATTAT
1 ACTATTTATGCAATTTCATGTATTTTAAAAGTACTTTAGTCAGT-TTTCATGTTTTAGAGATTAT
* * *
1045244 TATGTAATTGTATGCATTGTAAGATTATTTTAGTTATTTTCTATGATGCAAACATTATGATGCAA
65 TATATAATTGTATGCATTGTAAGATTATTATAGTCATTTTCTATGATGCAAACATTATGATGCAA
* *
1045309 ATTCACATATTTTCTTGCCATTTTAGTTATTTTTCATAATTTAAGAACTTTTAAGTCGTTTTATA
130 ATTCACATATTTTCTTGCCATTTTAGTTATTTTTCATAACTTAAGAACTTTTAAGTCGTTTCATA
* * ** *
1045374 CACTTTAATGTTATTTTAGTAAATTTTCATGATTTTGGACCGTTTATGCATTCTTATGTACTTTA
195 CACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTA
*
1045439 AGGTCATTCTAGTAATTTACCATGATCTAAA
260 AGGTCATTCTAATAATTTACCATGATCTAAA
1045470 ACTATTTATGCAATTTCAT-TCATTTTA
1 ACTATTTATGCAATTTCATGT-ATTTTA
1045497 GGATCGCTTT
Statistics
Matches: 294, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
289 6 0.02
290 288 0.98
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (290 bp):
ACTATTTATGCAATTTCATGTATTTTAAAAGTACTTTAGTCAGTTTTCATGTTTTAGAGATTATT
ATATAATTGTATGCATTGTAAGATTATTATAGTCATTTTCTATGATGCAAACATTATGATGCAAA
TTCACATATTTTCTTGCCATTTTAGTTATTTTTCATAACTTAAGAACTTTTAAGTCGTTTCATAC
ACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTAA
GGTCATTCTAATAATTTACCATGATCTAAA
Found at i:1045509 original size:290 final size:288
Alignment explanation
Indices: 1044891--1045580 Score: 978
Period size: 290 Copynumber: 2.4 Consensus size: 288
1044881 CATCTTAGTT
* *
1044891 ACTA-TTATGCAATTCCATGTATTTTAAAAGTACTTTAGTCAGTTTTCATGTTTTAGAGATTATT
1 ACTATTTATGCAATTTCATGTATTTT-AAGGTACTTTAGTCA-TTTTCATGTTTTAGAGATTATT
* * * * **
1044955 ATATAATTGTATGCATTTTAAGATTATTATAGTCATTTTCTATGATTTAAACATTATGATGCAAA
64 ATGTAATTGTATGCATTGTAAGATTATTTTAGTTATTTTCTATGATGCAAACATTATGATGCAAA
* *
1045020 TTCACGTATTTTCTTGCCATTTTAGTTATTTTTCATAACTTAAGAACTTTTAAGTCGTTTCATAT
129 TTCACATATTTTCTTGCCATTTTAGTTATTTTTCATAACTTAAGAACTTTTAAGTCGTTTCATAC
*
1045085 ACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTAG
194 ACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTAA
*
1045150 GGTCATTCTAATAATTTACCATGATCTAGA
259 GGTCATTCTAATAATTTACCATGATCTAAA
1045180 ACTATTTATGCAATTTCATGTATTTTAAAGGTACTTTAGTCATATTTCATGTTTTAGAGATTATT
1 ACTATTTATGCAATTTCATGTATTTT-AAGGTACTTTAGTCAT-TTTCATGTTTTAGAGATTATT
1045245 ATGTAATTGTATGCATTGTAAGATTATTTTAGTTATTTTCTATGATGCAAACATTATGATGCAAA
64 ATGTAATTGTATGCATTGTAAGATTATTTTAGTTATTTTCTATGATGCAAACATTATGATGCAAA
* *
1045310 TTCACATATTTTCTTGCCATTTTAGTTATTTTTCATAATTTAAGAACTTTTAAGTCGTTTTATAC
129 TTCACATATTTTCTTGCCATTTTAGTTATTTTTCATAACTTAAGAACTTTTAAGTCGTTTCATAC
* * ** *
1045375 ACTTTAATGTTATTTTAGTAAATTTTCATGATTTTGGACCGTTTATGCATTCTTATGTACTTTAA
194 ACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTAA
*
1045440 GGTCATTCTAGTAATTTACCATGATCTAAA
259 GGTCATTCTAATAATTTACCATGATCTAAA
* * * * *
1045470 ACTATTTATGCAATTTCAT-TCATTTT-AGGATCGCTTTAGTAATTTGTCATGTATTAGGGATTT
1 ACTATTTATGCAATTTCATGT-ATTTTAAGG-T-ACTTTAGTCATTT-TCATGTTTTAGAGATTA
* * * *
1045533 TTATGCAATTTTATG--TGTGTTAGAGTGA-TTTAGGTTATTTTCTATGAT
62 TTATGTAATTGTATGCAT-TGTAAGA-TTATTTTA-GTTATTTTCTATGAT
1045581 CTAAGGACTT
Statistics
Matches: 363, Mismatches: 29, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
288 4 0.01
289 19 0.05
290 340 0.94
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (288 bp):
ACTATTTATGCAATTTCATGTATTTTAAGGTACTTTAGTCATTTTCATGTTTTAGAGATTATTAT
GTAATTGTATGCATTGTAAGATTATTTTAGTTATTTTCTATGATGCAAACATTATGATGCAAATT
CACATATTTTCTTGCCATTTTAGTTATTTTTCATAACTTAAGAACTTTTAAGTCGTTTCATACAC
TTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTAAGG
TCATTCTAATAATTTACCATGATCTAAA
Found at i:1045631 original size:58 final size:58
Alignment explanation
Indices: 1045550--1045660 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
1045540 ATTTTATGTG
* * * *
1045550 TGTTAGAGTGATTTAGGTTATTTTCTATGATCTAAGGACTTCTATGTAATTTCGTATA
1 TGTTAGAGTCATTTAAGTCATTTTCTATGATCTAAGAACTTCTATGTAATTTCGTATA
* * * * *
1045608 TGTTGGAGTCATTTAAGTCATTTTTTATGCTTTAAGAACTTTTATGTAATTTC
1 TGTTAGAGTCATTTAAGTCATTTTCTATGATCTAAGAACTTCTATGTAATTTC
1045661 ATACATTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.49
Consensus pattern (58 bp):
TGTTAGAGTCATTTAAGTCATTTTCTATGATCTAAGAACTTCTATGTAATTTCGTATA
Found at i:1045644 original size:290 final size:288
Alignment explanation
Indices: 1044891--1045671 Score: 844
Period size: 290 Copynumber: 2.7 Consensus size: 288
1044881 CATCTTAGTT
* * * *
1044891 ACTA-TTATGCAATTCCATGTATTTTAAAAGTACTTTAGTCAGT-TTTCATGTTTTAGAGATTAT
1 ACTATTTATGCAATTTCATGTATTTT-AAGGTACTTTAGT-AATATTTCATGTATTAGAGATTAT
** * * * * **
1044954 TATATAATTGTATGCATTTTAAGATTATTATAGTCATTTTCTATGATTTAAACATTATGATGCAA
64 TATGCAATTGTATG-ATTGTAAGATGATTTTAGTTATTTTCTATGATGCAAACATTATGATGCAA
* * ** * * *
1045019 ATTCACGTATTTTCTTGCCATTTTAGTTATTTTTCATAACTTAAGAACTTTTAAGTCGTTTCATA
128 ATTCACATATGTTCGAGCCATTTAAGTCATTTTTCATAATTTAAGAACTTTTAAGTCGTTTCATA
*
1045084 TACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTA
193 CACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTA
* *
1045149 GGGTCATTCTAATAATTTACCATGATCTAGA
258 AGGTCATTCTAATAATTTACCATGATCTAAA
* *
1045180 ACTATTTATGCAATTTCATGTATTTTAAAGGTACTTTAGTCATATTTCATGTTTTAGAGATTATT
1 ACTATTTATGCAATTTCATGTATTTT-AAGGTACTTTAGTAATATTTCATGTATTAGAGATTATT
* *
1045245 ATGTAATTGTATGCATTGTAAGATTATTTTAGTTATTTTCTATGATGCAAACATTATGATGCAAA
65 ATGCAATTGTATG-ATTGTAAGATGATTTTAGTTATTTTCTATGATGCAAACATTATGATGCAAA
* ** * * *
1045310 TTCACATATTTTCTTGCCATTTTAGTTATTTTTCATAATTTAAGAACTTTTAAGTCGTTTTATAC
129 TTCACATATGTTCGAGCCATTTAAGTCATTTTTCATAATTTAAGAACTTTTAAGTCGTTTCATAC
* * ** *
1045375 ACTTTAATGTTATTTTAGTAAATTTTCATGATTTTGGACCGTTTATGCATTCTTATGTACTTTAA
194 ACTTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTAA
*
1045440 GGTCATTCTAGTAATTTACCATGATCTAAA
259 GGTCATTCTAATAATTTACCATGATCTAAA
* *
1045470 ACTATTTATGCAATTTCAT-TCATTTT-AGGATCGCTTTAGTAAT-TTGTCATGTATTAGGGATT
1 ACTATTTATGCAATTTCATGT-ATTTTAAGG-T-ACTTTAGTAATATT-TCATGTATTAGAGATT
* * * *
1045532 TTTATGCAATTTTATG-TGTGTTAGAGTGA-TTTAGGTTATTTTCTATGAT-CTAAGGAC-TTCT
62 ATTATGCAATTGTATGAT-TGTAAGA-TGATTTTA-GTTATTTTCTATGATGC-AA--ACATTAT
* * ** * * * ** * **
1045593 -ATGTAATTTCGTATATGTTGGAGTCATTTAAGTCATTTTTTATGCTTTAAGAACTTTTATGTAA
121 GATGCAAATTCACATATGTTCGAGCCATTTAAGTCATTTTTCATAATTTAAGAACTTTTAAGTCG
*
1045657 TTTCATACATTTTAA
186 TTTCATACACTTTAA
1045672 AAATATTTAA
Statistics
Matches: 429, Mismatches: 51, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
288 4 0.01
289 20 0.05
290 400 0.93
291 3 0.01
292 2 0.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (288 bp):
ACTATTTATGCAATTTCATGTATTTTAAGGTACTTTAGTAATATTTCATGTATTAGAGATTATTA
TGCAATTGTATGATTGTAAGATGATTTTAGTTATTTTCTATGATGCAAACATTATGATGCAAATT
CACATATGTTCGAGCCATTTAAGTCATTTTTCATAATTTAAGAACTTTTAAGTCGTTTCATACAC
TTTAATATCATTTTAGTAAATTTTCATGATTTAAGACCGTTTATGCATTCTCATGTACTTTAAGG
TCATTCTAATAATTTACCATGATCTAAA
Found at i:1046956 original size:16 final size:17
Alignment explanation
Indices: 1046920--1046959 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1046910 TAATATTGTC
*
1046920 ATTAAA-TTTACATTAA
1 ATTAAATTTTACATAAA
1046936 A-TAAATTTTACA-AAA
1 ATTAAATTTTACATAAA
1046951 ATTAAATTT
1 ATTAAATTT
1046960 ATTTTATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAAATTTTACATAAA
Found at i:1046960 original size:15 final size:16
Alignment explanation
Indices: 1046920--1046960 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1046910 TAATATTGTC
*
1046920 ATTAAATTTACATTAA
1 ATTAAATTTACATAAA
1046936 A-TAAATTTTACA-AAA
1 ATTAAA-TTTACATAAA
1046951 ATTAAATTTA
1 ATTAAATTTA
1046961 TTTTATGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAATTTACATAAA
Found at i:1049434 original size:149 final size:151
Alignment explanation
Indices: 1049162--1049440 Score: 327
Period size: 149 Copynumber: 1.9 Consensus size: 151
1049152 AGGATCATTG
* *
1049162 GGCACTTCTAAGTCAATGATAGACTTTACAGACCTTTTAGCATTTTTTCTCGAAACCTAGTCTTA
1 GGCACTTCTAAGACAATGATAGACTTTACAGACCTTTTAGCATTTTTCCTCGAAACCTAGTCTTA
* * * *
1049227 TAAAATTACCATGTCCATTTCTACGCCGAAGGTATGAATTAAGAATGCATTTGTTTTTA-CTTTT
66 TAAAACTACCATGTCCATTTCTACGCCAAAGATATGAATTAAGAATACATTTGTTTTTATCTTTT
1049291 TCAAGTCTCTTAAGATCGTCA
131 TCAAGTCTCTTAAGATCGTCA
* ** * * *
1049312 GGCACTTCTAAGACGAT-AGTAGACTTTAGGGACTTTTTATCATTTTTCCT-GAAACTTAGTAC-
1 GGCACTTCTAAGACAATGA-TAGACTTTACAGACCTTTTAGCATTTTTCCTCGAAACCTAGT-CT
* * * **
1049374 TATAAAACTACCGA-GTCCGCTTT-TATGCCAAAGATATGAATTAGGAATATGTTTGTTTTTATC
64 TATAAAACTACC-ATGTCC-ATTTCTACGCCAAAGATATGAATTAAGAATACATTTGTTTTTATC
1049437 TTTT
127 TTTT
1049441 CTAAGTCCTT
Statistics
Matches: 107, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
149 56 0.52
150 51 0.48
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (151 bp):
GGCACTTCTAAGACAATGATAGACTTTACAGACCTTTTAGCATTTTTCCTCGAAACCTAGTCTTA
TAAAACTACCATGTCCATTTCTACGCCAAAGATATGAATTAAGAATACATTTGTTTTTATCTTTT
TCAAGTCTCTTAAGATCGTCA
Found at i:1053158 original size:18 final size:19
Alignment explanation
Indices: 1053137--1053172 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1053127 TTTTTTAAAT
1053137 ATATTAAAAAT-TTTATAA
1 ATATTAAAAATATTTATAA
*
1053155 ATATTAAATATATTTATA
1 ATATTAAAAATATTTATA
1053173 TTTAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATTAAAAATATTTATAA
Found at i:1054124 original size:23 final size:24
Alignment explanation
Indices: 1054082--1054130 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1054072 AATGTATTTT
1054082 TATTTAATATTATATTT-AAAATA
1 TATTTAATATTATATTTAAAAATA
1054105 TATTTAGATA-TA-ATTATAAAAATA
1 TATTTA-ATATTATATT-TAAAAATA
1054129 TA
1 TA
1054131 ATTTTTCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 3 0.13
23 9 0.39
24 11 0.48
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTTAATATTATATTTAAAAATA
Found at i:1055255 original size:24 final size:24
Alignment explanation
Indices: 1055228--1055274 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1055218 ATAAAACCAG
1055228 GGCATCCTCCTCCACTTCAACTAC
1 GGCATCCTCCTCCACTTCAACTAC
1055252 GGCATCCTCCTCCACTTCAACTA
1 GGCATCCTCCTCCACTTCAACTA
1055275 AGGTTCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.45, G:0.09, T:0.26
Consensus pattern (24 bp):
GGCATCCTCCTCCACTTCAACTAC
Found at i:1058171 original size:42 final size:44
Alignment explanation
Indices: 1058080--1058172 Score: 110
Period size: 42 Copynumber: 2.2 Consensus size: 44
1058070 GAACTCGATT
1058080 TAAAA-TTTTATATTATTATTTAAAATATTAATAAAAATTAAAAA
1 TAAAATTTTTATATTATTATTTAAAATA-TAATAAAAATTAAAAA
*
1058124 T---ATTTTTATATTA-TATTTATAACTA-AATAAAAA-TAAAAA
1 TAAAATTTTTATATTATTATTTA-AAATATAATAAAAATTAAAAA
1058163 TAAAATTTTT
1 TAAAATTTTT
1058173 TAAATAATAA
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
39 7 0.16
40 8 0.19
41 7 0.16
42 20 0.47
44 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (44 bp):
TAAAATTTTTATATTATTATTTAAAATATAATAAAAATTAAAAA
Found at i:1058194 original size:43 final size:46
Alignment explanation
Indices: 1058109--1058194 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 46
1058099 TTAAAATATT
* *
1058109 AATAAAAATTAAAAATATTTTTATATTATATTTATAACTAAATAAA
1 AATAAAAATTAAAAATATTTTTAAATAATATTTATAACTAAATAAA
*
1058155 AATAAAAA-T-AAAAT-TTTTTAAATAATAATTTA-AATTAAAT
1 AATAAAAATTAAAAATATTTTTAAATAAT-ATTTATAACTAAAT
1058195 TTATCATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 17 0.47
44 10 0.28
45 1 0.03
46 8 0.22
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (46 bp):
AATAAAAATTAAAAATATTTTTAAATAATATTTATAACTAAATAAA
Found at i:1058291 original size:30 final size:29
Alignment explanation
Indices: 1058255--1058371 Score: 105
Period size: 30 Copynumber: 3.9 Consensus size: 29
1058245 ATCAGATAAT
1058255 TTTAAATAATAA-AAATATATTTATGATATA
1 TTTAAAT-ATAATAAATATATTTAT-ATATA
* **
1058285 TTTAAATATAATTAATATA-AAATA-ATTAA
1 TTTAAATATAATAAATATATTTATATA-T-A
1058314 TTTAAATATAATATAAATATATTTATACTATA
1 TTTAAATAT-A-ATAAATATATTTATA-TATA
* *
1058346 TTTAAATCTAATTAATATATTTATAT
1 TTTAAATATAATAAATATATTTATAT
1058372 TTAAAATTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
27 1 0.01
28 2 0.03
29 17 0.24
30 28 0.39
31 9 0.13
32 12 0.17
33 1 0.01
34 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (29 bp):
TTTAAATATAATAAATATATTTATATATA
Found at i:1058302 original size:19 final size:19
Alignment explanation
Indices: 1058280--1058368 Score: 67
Period size: 21 Copynumber: 4.5 Consensus size: 19
1058270 TATATTTATG
1058280 ATATATTTAAATATAATTA
1 ATATATTTAAATATAATTA
1058299 ATATA---AAATAATTAATTTAA
1 ATATATTTAAAT-A-TAA-TT-A
* *
1058319 ATATAATATAAATATATTTA
1 ATAT-ATTTAAATATAATTA
*
1058339 TACTATATTTAAATCTAATTA
1 -A-TATATTTAAATATAATTA
1058360 ATATATTTA
1 ATATATTTA
1058369 TATTTAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
16 4 0.07
17 1 0.02
18 3 0.05
19 15 0.27
20 7 0.12
21 16 0.29
22 5 0.09
23 1 0.02
24 4 0.07
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATATTTAAATATAATTA
Found at i:1058302 original size:61 final size:61
Alignment explanation
Indices: 1058251--1058364 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
1058241 TTAAATCAGA
*
1058251 TAATTTTAA-ATAATAAAAATATATTTATGA-TATATTTAAATATAATTAATATAAAATAAT
1 TAATTTAAATATAATAAAAATATATTTAT-ACTATATTTAAATATAATTAATATAAAATAAT
* *
1058311 TAATTTAAATATAATATAAATATATTTATACTATATTTAAATCTAATTAATATA
1 TAATTTAAATATAATAAAAATATATTTATACTATATTTAAATATAATTAATATA
1058365 TTTATATTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
60 9 0.18
61 40 0.82
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (61 bp):
TAATTTAAATATAATAAAAATATATTTATACTATATTTAAATATAATTAATATAAAATAAT
Found at i:1058311 original size:14 final size:15
Alignment explanation
Indices: 1058287--1058325 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
1058277 ATGATATATT
1058287 TAAATATAATTAATA
1 TAAATATAATTAATA
*
1058302 TAAA-ATAATTAATT
1 TAAATATAATTAATA
1058316 TAAATATAAT
1 TAAATATAAT
1058326 ATAAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATATAATTAATA
Found at i:1058330 original size:11 final size:11
Alignment explanation
Indices: 1058287--1058334 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
1058277 ATGATATATT
1058287 TAAATATAAT-
1 TAAATATAATA
*
1058297 T-AATATAAAA
1 TAAATATAATA
*
1058307 T-AAT-TAATT
1 TAAATATAATA
1058316 TAAATATAATA
1 TAAATATAATA
1058327 TAAATATA
1 TAAATATA
1058335 TTTATACTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 11 0.35
10 8 0.26
11 12 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATATAATA
Found at i:1058459 original size:18 final size:19
Alignment explanation
Indices: 1058425--1058463 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
1058415 TGACACGAAT
1058425 AAAAACATAAAACTTAACA
1 AAAAACATAAAACTTAACA
1058444 AAAATACAT-AAA-TTAACA
1 AAAA-ACATAAAACTTAACA
1058462 AA
1 AA
1058464 TATATGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAACATAAAACTTAACA
Found at i:1058753 original size:20 final size:20
Alignment explanation
Indices: 1058719--1058781 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
1058709 TATTATAAAG
1058719 TAAA-TTTAAATAATTTAATT
1 TAAATTTTAAA-AATTTAATT
**
1058739 TTTATTTTAAAAATTGT-ATT
1 TAAATTTTAAAAATT-TAATT
*
1058759 TAAATTTTAAAAATATAATT
1 TAAATTTTAAAAATTTAATT
1058779 TAA
1 TAA
1058782 TTAAATTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.03
20 27 0.77
21 7 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TAAATTTTAAAAATTTAATT
Found at i:1059170 original size:24 final size:23
Alignment explanation
Indices: 1059134--1059199 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 23
1059124 AAATAAAAAA
**
1059134 TATATTATTTTAATTTATAAATAT
1 TATATTAAATTAATTTATAAAT-T
*
1059158 TATATTAAATTAAATTATATCAATT
1 TATATTAAATT-AATT-TATAAATT
* *
1059183 TAAATAAAATTAATTTA
1 TATATTAAATTAATTTA
1059200 AATCAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 2 0.06
24 13 0.37
25 14 0.40
26 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATTAAATTAATTTATAAATT
Found at i:1059176 original size:15 final size:15
Alignment explanation
Indices: 1059156--1059202 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1059146 ATTTATAAAT
*
1059156 ATTATATTAAATTAA
1 ATTATATTAATTTAA
*
1059171 ATTATATCAATTTAA
1 ATTATATTAATTTAA
* *
1059186 ATAAAATTAATTTAA
1 ATTATATTAATTTAA
1059201 AT
1 AT
1059203 CAAAATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTATATTAATTTAA
Found at i:1059213 original size:21 final size:20
Alignment explanation
Indices: 1059184--1059226 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1059174 ATATCAATTT
1059184 AAATAAAATTAATTTAAATCA
1 AAATAAAATTAA-TTAAATCA
* *
1059205 AAATTAAATTTATTAAATCA
1 AAATAAAATTAATTAAATCA
1059225 AA
1 AA
1059227 TAGACTCTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATAAAATTAATTAAATCA
Found at i:1059572 original size:21 final size:19
Alignment explanation
Indices: 1059530--1059593 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
1059520 ATTACATGAG
*
1059530 ATAAATATCACATAAAAAA
1 ATAAATATAACATAAAAAA
*
1059549 ATAATTATAACATAATATAAA
1 ATAAATATAACATAA-A-AAA
* *
1059570 ATATGATATAATATAAAAATA
1 ATA-AATATAACATAAAAA-A
1059591 ATA
1 ATA
1059594 TAATTATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 13 0.36
20 3 0.08
21 11 0.31
22 9 0.25
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
ATAAATATAACATAAAAAA
Found at i:1059610 original size:16 final size:16
Alignment explanation
Indices: 1059555--1059607 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 16
1059545 AAAAATAATT
*
1059555 ATAACATAATATAAAA
1 ATAATATAATATAAAA
*
1059571 TATGATATAATATAAAA
1 -ATAATATAATATAAAA
1059588 ATAATATAATTATAAAA
1 ATAATATAA-TATAAAA
1059605 ATA
1 ATA
1059608 TATTAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 8 0.25
17 24 0.75
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (16 bp):
ATAATATAATATAAAA
Found at i:1059623 original size:44 final size:46
Alignment explanation
Indices: 1059549--1059640 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 46
1059539 ACATAAAAAA
* *
1059549 ATAATTATAACATAATATAAAATATGATATAATATAAA-AA-TAAT
1 ATAATTATAAAATAATATAAAATATGATATAATACAAATAATTAAT
*
1059593 ATAATTATAAAA-ATATATTAAAAT-TTATATAATACAAATAATTAAT
1 ATAATTATAAAATA-ATA-TAAAATATGATATAATACAAATAATTAAT
1059639 AT
1 AT
1059641 TTTAAAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
43 1 0.02
44 26 0.63
45 8 0.20
46 6 0.15
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (46 bp):
ATAATTATAAAATAATATAAAATATGATATAATACAAATAATTAAT
Found at i:1060303 original size:20 final size:19
Alignment explanation
Indices: 1060275--1060323 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1060265 TATTAATATT
1060275 TATATATTTTATAATAAAAAA
1 TATA-ATTTTA-AATAAAAAA
* *
1060296 TATAATTTTAATTTAAAAA
1 TATAATTTTAAATAAAAAA
*
1060315 TATTATTTT
1 TATAATTTT
1060324 GAATTGGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 15 0.60
20 6 0.24
21 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATAATTTTAAATAAAAAA
Found at i:1060328 original size:20 final size:19
Alignment explanation
Indices: 1060291--1060328 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1060281 TTTTATAATA
1060291 AAAAATATAATTTTAATTT
1 AAAAATATAATTTTAATTT
*
1060310 AAAAATATTATTTTGAATT
1 AAAAATATAATTTT-AATT
1060329 GGGTTGAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAAAATATAATTTTAATTT
Found at i:1060677 original size:14 final size:15
Alignment explanation
Indices: 1060658--1060686 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1060648 ATTGACTTTT
1060658 TATATAA-AAAAATA
1 TATATAACAAAAATA
1060672 TATATAACAAAAATA
1 TATATAACAAAAATA
1060687 CAATTCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
TATATAACAAAAATA
Found at i:1061194 original size:28 final size:28
Alignment explanation
Indices: 1061162--1061218 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1061152 CGATGTCAAC
*
1061162 CCCATGTCATCATCTGTTCTTCCTCGGT
1 CCCATGTCATCATCTGTTCTTCCCCGGT
*
1061190 CCCATGTCATCATTTGTTCTTCCCCGGT
1 CCCATGTCATCATCTGTTCTTCCCCGGT
1061218 C
1 C
1061219 TGGTCTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.11, C:0.37, G:0.14, T:0.39
Consensus pattern (28 bp):
CCCATGTCATCATCTGTTCTTCCCCGGT
Found at i:1068456 original size:20 final size:20
Alignment explanation
Indices: 1068409--1068483 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
1068399 AAAAAGACAT
*
1068409 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1068428 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * * *
1068449 CATGTATCGGTATATTGAAA
1 AATGTATCGATACATTCATA
1068469 AATGTATCGATACAT
1 AATGTATCGATACAT
1068484 CAAGGTAAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1068477 original size:40 final size:39
Alignment explanation
Indices: 1068406--1068483 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1068396 GGTAAAAAGA
* *
1068406 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
1068445 CATACATGTATCGGTATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1068484 CAAGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1068936 original size:48 final size:48
Alignment explanation
Indices: 1068881--1068992 Score: 224
Period size: 48 Copynumber: 2.3 Consensus size: 48
1068871 ATTCAAAGCC
1068881 AGCGACATTGGGCTAAGGGAAAAGTGGACCAATGCGCTGATCAAGGCT
1 AGCGACATTGGGCTAAGGGAAAAGTGGACCAATGCGCTGATCAAGGCT
1068929 AGCGACATTGGGCTAAGGGAAAAGTGGACCAATGCGCTGATCAAGGCT
1 AGCGACATTGGGCTAAGGGAAAAGTGGACCAATGCGCTGATCAAGGCT
1068977 AGCGACATTGGGCTAA
1 AGCGACATTGGGCTAA
1068993 TAAAGGTGCC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.31, C:0.19, G:0.33, T:0.17
Consensus pattern (48 bp):
AGCGACATTGGGCTAAGGGAAAAGTGGACCAATGCGCTGATCAAGGCT
Found at i:1069243 original size:28 final size:28
Alignment explanation
Indices: 1069173--1069986 Score: 947
Period size: 28 Copynumber: 28.6 Consensus size: 28
1069163 TACTCACTTG
*
1069173 TGTGGGCTTT-AAAGGGGTGCCACTGACT
1 TGTGGGCTTTGAAA-GGATGCCACTGACT
1069201 TACGTGGGCTTTGAAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
**
1069231 CATGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
1069259 TGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1069286 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
** *
1069314 CATGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
1069341 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
1069369 CGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
1069397 TGCGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
*
1069429 GTGTGGGCTTTGAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
1069458 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1069486 CGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
1069514 TGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1069541 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
1069569 CGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
1069596 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
1069624 CGTGGGCTTTGAAAAGG-TGCCACTAATT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
1069652 TCGTGGGCTTTAAAAGGAGTGCCACTGACTT
1 T-GTGGGCTTTGAAAGGA-TGCCACTGAC-T
1069683 GTGTGGGCTTTGAAAGGGA-GCCACTGACT
1 -TGTGGGCTTTGAAA-GGATGCCACTGACT
1069712 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
1069740 TGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
1069768 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
1069796 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
** *
1069825 TGTGGGCTTTGAAAATAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
1069854 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
1069883 TGTGGGCTTTAAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
** *
1069912 TGTGGGCTTTGAAAATAGTACCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
1069941 TGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGA-TGCCACTGAC-T
1069971 TGTGGGCTTTGAAAGG
1 TGTGGGCTTTGAAAGG
1069987 GATGAACATT
Statistics
Matches: 699, Mismatches: 51, Indels: 70
0.85 0.06 0.09
Matches are distributed among these distances:
26 12 0.02
27 85 0.12
28 310 0.44
29 167 0.24
30 78 0.11
31 41 0.06
32 5 0.01
33 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:1069483 original size:172 final size:169
Alignment explanation
Indices: 1069124--1069986 Score: 1097
Period size: 172 Copynumber: 5.0 Consensus size: 169
1069114 GGCTTTGAAA
* * ** *
1069124 AAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAGTGTTACTCACTTGTGTGGGCTTT-AAAGG
1 AAAGGTGCCACTGACTC--GTGGGCTTTG-AAAGAGTGCCACTGAC-T-TGTGGGCTTTGAAA-G
* *
1069188 GGTGCCACTGACTTACGTGGGCTTTG-AAAGGATGCCACTGAC-TCATGGGCTTTGAAA-GAGTG
60 AGTGCCACTGAC-T-CGTGGGCTTTGAAAAGG-TGCCACTGACTTCGTGGGCTTTGAAAGGAGTG
*
1069250 CCACTGACTTGTGGGCTTTGAAA-GGTGCCACTGACTCGTGGGCTTTG
122 CCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1069297 AAAAGGTACCACTGACTCATGGGC-TTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGC
1 -AAAGGTGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGC
1069361 CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGCGTGGGCTTTGAAAGGAGTGCCACTGA
65 CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTT-CGTGGGCTTTGAAAGGAGTGCCACTGA
1069426 CTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
129 C-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
1069469 AAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG-GTGC
1 AAAGG-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGC
*
1069533 CACTGACTCGTGGGCTTTGAAAAGGTACCACTGAC-TCGTGGGC-TTGAAAGG-GTGCCACTGAC
65 CACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTCGTGGGCTTTGAAAGGAGTGCCACTGAC
* *
1069595 TTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTG
130 TTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * * *
1069635 AAAAGGTGCCACTAATTTCGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGG
1 -AAAGGTGCCACTGA-CTCGTGGGCTTTGAAA-GAGTGCCACTGAC-T-TGTGGGCTTTGAAAGA
* * * *
1069700 GAGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTT-GTGGGCTTCGCAAGG-GTGCCA
61 GTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACTGACTTCGTGGGCTTTGAAAGGAGTGCCA
*
1069762 CTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTTTG
125 CTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
1069807 AAAAGAGTGCCACTGACTTGTGGGCTTTGAAAATAGTGCCACTGATTTGTGGGCTTTGAAAAGAG
1 -AAAG-GTGCCACTGACTCGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAG
* * * ** *
1069872 TGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTGA-TTTGTGGGCTTTGAAAATAGTACCAC
62 TGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACTGACTTCGTGGGCTTTGAAAGGAGTGCCAC
1069936 TGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTTGTGGGCTTTG
126 TGACTTGTGGGCTTTGAAAGG-GTGCCACTGAC-TTGTGGGCTTTG
1069982 AAAGG
1 AAAGG
1069987 GATGAACATT
Statistics
Matches: 619, Mismatches: 43, Indels: 55
0.86 0.06 0.08
Matches are distributed among these distances:
166 66 0.11
167 27 0.04
168 59 0.10
169 26 0.04
170 50 0.08
171 88 0.14
172 189 0.31
173 73 0.12
174 29 0.05
175 12 0.02
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.28
Consensus pattern (169 bp):
AAAGGTGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCC
ACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTCGTGGGCTTTGAAAGGAGTGCCACTGACT
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:1069538 original size:227 final size:229
Alignment explanation
Indices: 1069096--1069984 Score: 1146
Period size: 227 Copynumber: 3.9 Consensus size: 229
1069086 TTAAAAAAAT
* *
1069096 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAG
1 GTGCCACTGA-CTTGTG--GGCTTTGAAAAGAG-TGCCACTGACTC--GTGGGCTTTGAAAAGAG
** * * * * * * *
1069160 TGTTACTCACTTGTGTGGGCTTT-AAAGGGGTGCCACTGACTTACGTGGGCTTTGAAAGGATGCC
60 TGCCACTGACTT-CGTGGGCTTTGAAAAGAGTGCCACTGACTT-TGTGGGCTTTAAAAGGGTGCC
** *
1069224 ACTGACTCATGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTTGAAAG-GTGCCACTGACTC
123 ACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTT
* *
1069287 GTGGGCTTTGAAAAGGTACCACTGACTCATGGGCTTGAAAGG
188 GTGGGCTTTGAAAAGGTGCCACTGACTCGTGGGCTTGAAAGG
1069329 GTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCAC
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCAC
* *
1069392 TGACTTGCGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGAC
66 TGACTT-CGTGGGCTTTGAAAAGAGTGCCACTGACTT-TGTGGGCTTTAAAAGGGTGCCACTGAC
*
1069457 TTGTGGGCTTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
129 TTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGC
*
1069521 TTTG-AAAGGTGCCACTGACTCGTGGGCTTTGAAAAG
194 TTTGAAAAGGTGCCACTGACTCGTGGGC-TTGAAAGG
* * * *
1069557 GTACCACTGACTCGTGGGC-TTG-AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCAC
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCAC
*
1069619 TGAC-TCGTGGGCTTTGAAAAG-GTGCCACT-AATTTCGTGGGCTTTAAAAGGAGTGCCACTGAC
66 TGACTTCGTGGGCTTTGAAAAGAGTGCCACTGACTTT-GTGGGCTTTAAAAGG-GTGCCACTGAC
*
1069681 TTGTGTGGGCTTTGAAAGG-GAGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGG
129 -T-TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGG
* * * *
1069745 GCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCGAAAGG
192 GCTTTGAAAAGGTGCCACTGACTCGTGGGCTT-GAAAGG
* *
1069784 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAATAGTGCCAC
1 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCAC
* * *
1069849 TGA-TTTGTGGGCTTTGAAAAGAGTGCCACTGAC-TTGTGGGCTTTAAAAAGAGTGCCACTGATT
66 TGACTTCGTGGGCTTTGAAAAGAGTGCCACTGACTTTGTGGGCTTT-AAAAGGGTGCCACTGACT
** *
1069912 TGTGGGCTTTGAAAATAGTACCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTTGTGGG
130 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC-TTGTGGG
1069977 CTTTGAAA
193 CTTTGAAA
1069985 GGGATGAACA
Statistics
Matches: 589, Mismatches: 44, Indels: 48
0.86 0.06 0.07
Matches are distributed among these distances:
222 1 0.00
223 17 0.03
224 19 0.03
225 16 0.03
226 90 0.15
227 200 0.34
228 65 0.11
229 63 0.11
230 67 0.11
231 35 0.06
232 1 0.00
233 14 0.02
234 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (229 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCAC
TGACTTCGTGGGCTTTGAAAAGAGTGCCACTGACTTTGTGGGCTTTAAAAGGGTGCCACTGACTT
GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTT
TGAAAAGGTGCCACTGACTCGTGGGCTTGAAAGG
Found at i:1069582 original size:255 final size:253
Alignment explanation
Indices: 1069143--1069986 Score: 1293
Period size: 255 Copynumber: 3.3 Consensus size: 253
1069133 ACTGACACAT
** *
1069143 GTGGGCTTTGAAAAGAGTGTTACTCACTTGTGTGGGCTTT-AAAGGGGTGCCACTGACTTACGTG
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAA-GGGTGCCACTGACTT--GTG
*
1069207 GGCTTTGAAAGGATGCCACTGACTCATGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAA
63 GGCTTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAA
*
1069272 AGGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCATGGGCTTGAAAGGGTGCCACT
128 AGGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACT
1069337 GACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGC
193 GACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGA-TT-C
*
1069400 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1069465 TTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
66 TTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
1069530 TGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGAC
131 TGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGAC
*
1069595 TTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAATTTC
196 TTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGA-TTC
*
1069654 GTGGGCTTT-AAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGAGCCACTGACTTGTGGG
1 GTGGGCTTTGAAAA-GAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGG
* * * * *
1069718 CTTTGAAA-GAGTGCCACTGACTTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCGAAA
65 CTTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
* * * **
1069782 GGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAATAGTGCC
129 -GGTGCCACTGACTCGTGGGCTTTGAAAAG-GTACCACTGACTCGTGGGC-TTG-AAAGGGTGCC
* * *
1069847 ACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTGATT
190 ACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACTGATT
*
1069912 T
253 C
* *
1069913 GTGGGCTTTGAAAATAGTACCACTGAC-T-TGTGGGCTTTGAAAGGAGTGCCACTGACTTTGTGG
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGG-GTGCCACTGAC-TTGTGG
1069976 GCTTTGAAAGG
64 GCTTTGAAAGG
1069987 GATGAACATT
Statistics
Matches: 546, Mismatches: 28, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
253 5 0.01
254 115 0.21
255 218 0.40
256 17 0.03
257 70 0.13
258 39 0.07
259 68 0.12
260 14 0.03
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (253 bp):
GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
TTTGAAAGGATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG
TGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGAC
TTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGATTC
Found at i:1071219 original size:1 final size:1
Alignment explanation
Indices: 1071215--1071275 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
1071205 TTTTTTGCTA
* * * * * * *
1071215 TTTTTTTCTTTTTTTTGTTTTTTTGTTTTGTTTTTGTTTTGTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1071276 GGGTGTAAAG
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:1071235 original size:16 final size:15
Alignment explanation
Indices: 1071216--1071275 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 15
1071206 TTTTTGCTAT
1071216 TTTTTTCTTTTTTTTG
1 TTTTTT-TTTTTTTTG
1071232 TTTTTTTGTTTTGTTTTTG
1 --TTTTT-TTTT-TTTTTG
1071251 TTTTGTTTTTTTTTTG
1 TTTT-TTTTTTTTTTG
1071267 TTTTTTTTT
1 TTTTTTTTT
1071276 GGGTGTAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.13
16 10 0.26
17 8 0.21
18 9 0.23
19 7 0.18
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:1071237 original size:11 final size:11
Alignment explanation
Indices: 1071205--1071275 Score: 81
Period size: 11 Copynumber: 6.5 Consensus size: 11
1071195 GACCCTTCTA
* *
1071205 TTTTTTGCTAT
1 TTTTTTGTTTT
*
1071216 TTTTTTCTTTT
1 TTTTTTGTTTT
1071227 TTTTGTT-TTTT
1 TTTT-TTGTTTT
*
1071238 TGTTTTGTTTT
1 TTTTTTGTTTT
*
1071249 TGTTTTGTTTT
1 TTTTTTGTTTT
1071260 TTTTTTGTTTT
1 TTTTTTGTTTT
1071271 TTTTT
1 TTTTT
1071276 GGGTGTAAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
10 2 0.04
11 49 0.92
12 2 0.04
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:1084332 original size:22 final size:21
Alignment explanation
Indices: 1084287--1084340 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
1084277 TGGACATGTT
*
1084287 AAAAATGTATGAAACATAATA
1 AAAAATGCATGAAACATAATA
1084308 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAAT-A
1084330 AAAAATGCATG
1 AAAAATGCATG
1084341 GTCAAAGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.20
Consensus pattern (21 bp):
AAAAATGCATGAAACATAATA
Found at i:1085300 original size:20 final size:20
Alignment explanation
Indices: 1085253--1085327 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1085243 AAAAAGACAT
*
1085253 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1085272 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1085293 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1085313 AATGTATCGATACAT
1 AATGTATCGATACAT
1085328 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1085321 original size:40 final size:39
Alignment explanation
Indices: 1085250--1085327 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1085240 GGTAAAAAGA
* *
1085250 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1085289 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1085328 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1085868 original size:43 final size:43
Alignment explanation
Indices: 1085803--1085889 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
1085793 GGGGTATTAG
*
1085803 AATATCTTGCATTGTCAACATATCTTTAATTATAATCATCATC
1 AATATCTTGCATTGTCAACATATCTTTAATTATAATCAACATC
*
1085846 AATATCTTGCATTGTCAGCATATCTTTAATTATAATCAACATC
1 AATATCTTGCATTGTCAACATATCTTTAATTATAATCAACATC
1085889 A
1 A
1085890 TATTGATAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.40
Consensus pattern (43 bp):
AATATCTTGCATTGTCAACATATCTTTAATTATAATCAACATC
Found at i:1087353 original size:9 final size:9
Alignment explanation
Indices: 1087326--1087355 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1087316 TCAAAGTTGT
1087326 GATTATTAA
1 GATTATTAA
*
1087335 AATTATTAA
1 GATTATTAA
1087344 GATTATTAA
1 GATTATTAA
1087353 GAT
1 GAT
1087356 AATCGTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (9 bp):
GATTATTAA
Found at i:1091533 original size:71 final size:71
Alignment explanation
Indices: 1091417--1091559 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
1091407 AAGGGGGGGG
1091417 GGGGGGGGGGGGGGAGGCATCAATATAGACATCTAACACTATTGTTTCTTATTTTCATTTTGTTT
1 GGGGGGGGGGGGGGAGGCATCAATATAGACATCTAACACTATTGTTTCTTATTTTCATTTTGTTT
1091482 ATGGAA
66 ATGGAA
1091488 GGGGGGGGGGGGGGAGGCATCAATATAGACATCTAACACTATTGTTTCTTATTTTCATTTTGTTT
1 GGGGGGGGGGGGGGAGGCATCAATATAGACATCTAACACTATTGTTTCTTATTTTCATTTTGTTT
1091553 ATGGAA
66 ATGGAA
1091559 G
1 G
1091560 ATACCATTAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.24, C:0.11, G:0.30, T:0.35
Consensus pattern (71 bp):
GGGGGGGGGGGGGGAGGCATCAATATAGACATCTAACACTATTGTTTCTTATTTTCATTTTGTTT
ATGGAA
Found at i:1092019 original size:21 final size:21
Alignment explanation
Indices: 1091981--1092020 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1091971 AAAAATATAA
* * *
1091981 TAATAAATTATTTTTTAAAAT
1 TAATAAAATAATTATTAAAAT
1092002 TAATAAAATAATTATTAAA
1 TAATAAAATAATTATTAAA
1092021 TACAAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATAAAATAATTATTAAAAT
Found at i:1092985 original size:2 final size:2
Alignment explanation
Indices: 1092978--1093031 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1092968 ATGGCACTTT
1092978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1093020 TA TA TA AA TA TA
1 TA TA TA TA TA TA
1093032 ATTTATTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1094579 original size:30 final size:30
Alignment explanation
Indices: 1094538--1094601 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1094528 AATTAACATG
* * *
1094538 AGTGATTTAATTTGTTAATAATAAAAATTT
1 AGTGATATAATTTGATAAAAATAAAAATTT
1094568 AGTGATATAATTTGATAAAAATAAAAATTT
1 AGTGATATAATTTGATAAAAATAAAAATTT
1094598 -GTGA
1 AGTGA
1094602 CTCACATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (30 bp):
AGTGATATAATTTGATAAAAATAAAAATTT
Found at i:1095261 original size:20 final size:19
Alignment explanation
Indices: 1095223--1095261 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1095213 CTATAAATAG
*
1095223 AAGCTCCCTCCTCCATCTC
1 AAGCTCCCTCATCCATCTC
*
1095242 AAGCATCCCTCATCCTTCTC
1 AAGC-TCCCTCATCCATCTC
1095262 TTGTATCCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.49, G:0.05, T:0.28
Consensus pattern (19 bp):
AAGCTCCCTCATCCATCTC
Found at i:1099823 original size:20 final size:20
Alignment explanation
Indices: 1099798--1099846 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
1099788 AAATAGAGGC
1099798 TCCCTCTTCCATCTCAAGCA
1 TCCCTCTTCCATCTCAAGCA
* * ** *
1099818 TCCCTCATCCTTCTCTTGTA
1 TCCCTCTTCCATCTCAAGCA
1099838 TCCCTCTTC
1 TCCCTCTTC
1099847 AATTCTTTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.12, C:0.45, G:0.04, T:0.39
Consensus pattern (20 bp):
TCCCTCTTCCATCTCAAGCA
Found at i:1100694 original size:31 final size:34
Alignment explanation
Indices: 1100639--1100704 Score: 111
Period size: 31 Copynumber: 2.0 Consensus size: 34
1100629 AAAAAATATA
1100639 TATATATATATATATAAAATATTAAGAAAAAGGC
1 TATATATATATATATAAAATATTAAGAAAAAGGC
1100673 TATATA-ATATATAT-AAA-ATTAAGAAAAAGGC
1 TATATATATATATATAAAATATTAAGAAAAAGGC
1100704 T
1 T
1100705 GGCAGTCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 15 0.47
32 3 0.09
33 8 0.25
34 6 0.19
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (34 bp):
TATATATATATATATAAAATATTAAGAAAAAGGC
Found at i:1100939 original size:6 final size:6
Alignment explanation
Indices: 1100928--1100992 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
1100918 CATATAAGTC
* * *
1100928 ATATAA ATATAA ATATAA ATAT-A TTATAA ATTATTAA ATAT-A TTAAAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA A-TA-TAA ATATAA ATATAA
* *
1100976 ATTTTA ATATAA ATATA
1 ATATAA ATATAA ATATA
1100993 TACATGTCAT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
5 7 0.16
6 30 0.67
7 4 0.09
8 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
ATATAA
Found at i:1100957 original size:17 final size:18
Alignment explanation
Indices: 1100935--1100986 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
1100925 GTCATATAAA
1100935 TATAAATA-TAAATATAT
1 TATAAATATTAAATATAT
1100952 TATAAATTATTAAATATAT
1 TATAAA-TATTAAATATAT
* *
1100971 TAAAAAT-TTTAATATA
1 TATAAATATTAAATATA
1100987 AATATATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 14 0.45
18 3 0.10
19 14 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAATATTAAATATAT
Found at i:1100967 original size:19 final size:19
Alignment explanation
Indices: 1100935--1100986 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1100925 GTCATATAAA
1100935 TATAAA-TA-TAAATATAT
1 TATAAATTATTAAATATAT
1100952 TATAAATTATTAAATATAT
1 TATAAATTATTAAATATAT
*
1100971 TAAAAATT-TT-AATATA
1 TATAAATTATTAAATATA
1100987 AATATATACA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 12 0.38
18 4 0.12
19 16 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAAATTATTAAATATAT
Found at i:1101100 original size:12 final size:11
Alignment explanation
Indices: 1101007--1101101 Score: 51
Period size: 12 Copynumber: 8.9 Consensus size: 11
1100997 TGTCATATTA
1101007 ATTAT-TTTAT
1 ATTATATTTAT
*
1101017 -TTATATTTAA
1 ATTATATTTAT
*
1101027 ATGTAT-TTTGAA
1 AT-TATATTT-AT
1101039 ATGTATA-TTAT
1 AT-TATATTTAT
*
1101050 ATTAT-TTTTT
1 ATTATATTTAT
*
1101060 ATTA-A-ATAT
1 ATTATATTTAT
1101069 ATTATATTTAT
1 ATTATATTTAT
*
1101080 ATAATATTTCAT
1 ATTATATTT-AT
*
1101092 GTTATATTTA
1 ATTATATTTA
1101102 AAATTATTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
9 10 0.15
10 15 0.23
11 19 0.29
12 22 0.33
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:1101405 original size:2 final size:2
Alignment explanation
Indices: 1101356--1101386 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1101346 CTTTGAATCT
1101356 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
1101387 CAATTTTTAA
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:1104799 original size:25 final size:26
Alignment explanation
Indices: 1104744--1104807 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
1104734 AATAACATCT
*
1104744 TGTTAAAATATAAAAAAAATTCACAA
1 TGTTAAAATATAAAAAAAATTCAAAA
* * *
1104770 T-TTAAAATA-AGAAAAGATTTAAAA
1 TGTTAAAATATAAAAAAAATTCAAAA
*
1104794 TGTTAAAATTTAAA
1 TGTTAAAATATAAA
1104808 TTTTAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
24 12 0.40
25 15 0.50
26 3 0.10
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (26 bp):
TGTTAAAATATAAAAAAAATTCAAAA
Found at i:1106494 original size:18 final size:16
Alignment explanation
Indices: 1106459--1106489 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1106449 TTTAATTTTA
*
1106459 TAAATTTTTTTATAAT
1 TAAATTTTTTTAAAAT
1106475 TAAATTTTTTTAAAA
1 TAAATTTTTTTAAAA
1106490 AATTATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TAAATTTTTTTAAAAT
Found at i:1107020 original size:2 final size:2
Alignment explanation
Indices: 1107013--1107040 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1107003 TCTTCACCTC
1107013 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
1107041 TGGTTCCATT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1109680 original size:20 final size:20
Alignment explanation
Indices: 1109655--1109694 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1109645 TTATGGCCTT
1109655 GATGTTTTAATGTGATGATA
1 GATGTTTTAATGTGATGATA
1109675 GATGTTTTAATGTGATGATA
1 GATGTTTTAATGTGATGATA
1109695 ACAGTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.45
Consensus pattern (20 bp):
GATGTTTTAATGTGATGATA
Found at i:1111895 original size:2 final size:2
Alignment explanation
Indices: 1111890--1111920 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1111880 ATCTATTGAA
1111890 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1111921 GTAGATATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1113391 original size:7 final size:6
Alignment explanation
Indices: 1113349--1113431 Score: 52
Period size: 6 Copynumber: 13.7 Consensus size: 6
1113339 AATTTTTTTC
1113349 AAAAAT AAAAGAT AACAAA- AGAAAAT -AAAAT AAAAACT AAAAAT --AAAT
1 AAAAAT AAAA-AT AA-AAAT A-AAAAT AAAAAT AAAAA-T AAAAAT AAAAAT
*
1113397 AAAAATT AAGAAA- AAAGAA- AAAAAT TAAAAT AAAA
1 AAAAA-T AA-AAAT AAA-AAT AAAAAT AAAAAT AAAA
1113432 TGGATATGAC
Statistics
Matches: 63, Mismatches: 2, Indels: 24
0.71 0.02 0.27
Matches are distributed among these distances:
4 4 0.06
5 8 0.13
6 31 0.49
7 15 0.24
8 5 0.08
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:1113417 original size:17 final size:16
Alignment explanation
Indices: 1113370--1113418 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1113360 ATAACAAAAG
1113370 AAAATAAAATAAAAACT
1 AAAA-AAAATAAAAACT
*
1113387 AAAAATAAATAAAAATT
1 AAAAA-AAATAAAAACT
*
1113404 AAGAAAAAAGAAAAA
1 AA-AAAAAATAAAAA
1113419 AATTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.86
18 3 0.11
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (16 bp):
AAAAAAAATAAAAACT
Found at i:1113935 original size:16 final size:16
Alignment explanation
Indices: 1113884--1113936 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
1113874 CAAATAACTC
*
1113884 AAAATAATTTAAACTT
1 AAAATAATTTAAAATT
1113900 AAAATAATTT-AAATT
1 AAAATAATTTAAAATT
1113915 AAAAATAATTTAAAATT
1 -AAAATAATTTAAAATT
1113932 AAAAT
1 AAAAT
1113937 CAATCCAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.12
16 25 0.74
17 5 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATAATTTAAAATT
Found at i:1115350 original size:2 final size:2
Alignment explanation
Indices: 1115343--1115401 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1115333 ATCATCGATA
* *
1115343 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT TT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1115384 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1115402 GACACAATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1167570 original size:13 final size:13
Alignment explanation
Indices: 1167552--1167577 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1167542 ACAAAGATCG
1167552 ATGTATCGATACA
1 ATGTATCGATACA
1167565 ATGTATCGATACA
1 ATGTATCGATACA
1167578 TTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1167588 original size:21 final size:21
Alignment explanation
Indices: 1167564--1167625 Score: 124
Period size: 21 Copynumber: 3.0 Consensus size: 21
1167554 GTATCGATAC
1167564 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1167585 AATGTATCGATACATTTCCTT
1 AATGTATCGATACATTTCCTT
1167606 AATGTATCGATACATTTCCT
1 AATGTATCGATACATTTCCT
1167626 GGGCAGTAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (21 bp):
AATGTATCGATACATTTCCTT
Found at i:1167677 original size:30 final size:31
Alignment explanation
Indices: 1167638--1167711 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 31
1167628 GCAGTAGCTT
* *
1167638 TGTAGCGATACTTTGTATCGATACAAC-TTA
1 TGTATCGATACATTGTATCGATACAACATTA
*
1167668 TGTATCGATACATTGTATCGATACAACATTTT
1 TGTATCGATACATTGTATCGATACAACA-TTA
1167700 TGTATCGATACA
1 TGTATCGATACA
1167712 AATCGTTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 25 0.64
32 14 0.36
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (31 bp):
TGTATCGATACATTGTATCGATACAACATTA
Found at i:1167686 original size:13 final size:13
Alignment explanation
Indices: 1167637--1167692 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 13
1167627 GGCAGTAGCT
* *
1167637 TTGTAGCGATACT
1 TTGTATCGATACA
1167650 TTGTATCGATACAA
1 TTGTATCGATAC-A
1167664 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1167680 TTGTATCGATACA
1 TTGTATCGATACA
1167693 ACATTTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
13 23 0.62
14 1 0.03
16 2 0.05
17 11 0.30
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1167867 original size:17 final size:17
Alignment explanation
Indices: 1167845--1167878 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1167835 TAGCCCGGAC
*
1167845 AAAATGAGGTGTCTACA
1 AAAATGAGATGTCTACA
1167862 AAAATGAGATGTCTACA
1 AAAATGAGATGTCTACA
1167879 TAACTGATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (17 bp):
AAAATGAGATGTCTACA
Found at i:1169278 original size:22 final size:23
Alignment explanation
Indices: 1169250--1169295 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
1169240 GGGAATTTCA
1169250 TGAAAA-TTTGAGAAAAAAT-GTC
1 TGAAAATTTTGA-AAAAAATCGTC
1169272 TGAAAATTTTGAAAAAAATCGTC
1 TGAAAATTTTGAAAAAAATCGTC
1169295 T
1 T
1169296 AGAGGGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.48, C:0.07, G:0.15, T:0.30
Consensus pattern (23 bp):
TGAAAATTTTGAAAAAAATCGTC
Found at i:1174165 original size:28 final size:28
Alignment explanation
Indices: 1174121--1174190 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
1174111 TCTGAGTTAA
* *
1174121 AACCCACATTAGTTAGCACCCAAGTCA-
1 AACCCATATTAGCTAGCACCCAAGTCAG
* * *
1174148 AAGCCCATGTTAGCTAGCATCTAAGTCAG
1 AA-CCCATATTAGCTAGCACCCAAGTCAG
1174177 AACCCATATTAGCT
1 AACCCATATTAGCT
1174191 GGCATTTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (28 bp):
AACCCATATTAGCTAGCACCCAAGTCAG
Found at i:1174169 original size:56 final size:55
Alignment explanation
Indices: 1174109--1174267 Score: 158
Period size: 56 Copynumber: 2.8 Consensus size: 55
1174099 TGTTAGGGCA
* * *
1174109 CATCTGAGTTAAAACCCACATTAGTTAGCACCCAAGTCAAAGCCCATGTTAGCTAG
1 CATCTGAGTCAAAACCCACATTAGTT-GCACACAAGTCAAAGCCCATGATAGCTAG
* * * * *** *
1174165 CATCTAAGTCAGAACCCATATTAGCTGGCATTTGAA-TCAAAGCCCATGATAGCTGG
1 CATCTGAGTCAAAACCCACATTAG-TTGCA-CACAAGTCAAAGCCCATGATAGCTAG
* *
1174221 CATCTGAGTCAAAGCCTACATTAGTTGACACACAAGTCAAAGCCCAT
1 CATCTGAGTCAAAACCCACATTAGTTG-CACACAAGTCAAAGCCCAT
1174268 ATTAATTGCC
Statistics
Matches: 80, Mismatches: 19, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
55 4 0.05
56 73 0.91
57 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (55 bp):
CATCTGAGTCAAAACCCACATTAGTTGCACACAAGTCAAAGCCCATGATAGCTAG
Found at i:1174195 original size:28 final size:28
Alignment explanation
Indices: 1174142--1174306 Score: 115
Period size: 28 Copynumber: 5.9 Consensus size: 28
1174132 GTTAGCACCC
* *
1174142 AAGTCAAAGCCCATGTTAGCTAGCATCT
1 AAGTCAAAGCCCATATTAGCTGGCATCT
*
1174170 AAGTCAGAA-CCCATATTAGCTGGCATTT
1 AAGTCA-AAGCCCATATTAGCTGGCATCT
1174198 GAA-TCAAAGCCCATGA-TAGCTGGCATCT
1 -AAGTCAAAGCCCAT-ATTAGCTGGCATCT
* * * * * *
1174226 GAGTCAAAGCCTACATTAGTTGACA-CAC
1 AAGTCAAAGCCCATATTAGCTGGCATC-T
** * *
1174254 AAGTCAAAGCCCATATTAATTGCCATTTT
1 AAGTCAAAGCCCATATTAGCTGGCA-TCT
* *
1174283 AA-TCAAAGCCCACATTAGTTGGCA
1 AAGTCAAAGCCCATATTAGCTGGCA
1174307 CCCCAGTTAA
Statistics
Matches: 108, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.05
28 96 0.89
29 7 0.06
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (28 bp):
AAGTCAAAGCCCATATTAGCTGGCATCT
Found at i:1174225 original size:112 final size:110
Alignment explanation
Indices: 1173984--1174300 Score: 297
Period size: 112 Copynumber: 2.8 Consensus size: 110
1173974 TAAGTTGAAT
* * * *
1173984 CCCATGGTAGCTGGCATTTAAGTTAAAACCCACATTAGTTG-ACACATGAGTCAAAGCCTATATT
1 CCCATGATAGCTGGCATCTGAGTTAAAACCCACATTAGTTGCACACA--AGTCAAAGCCCATATT
* * * * *
1174048 AATTGCATCTAGGTTAAAGCCCATATTAGCTAGTGCTTGAGTTAAAG
64 AATAGCATCTAAGTCAAAGCCCATATTAGCTAGTGCTTGAATCAAAG
* * * *
1174095 CCTATGTTAG--GGCACATCTGAGTTAAAACCCACATTAGTTAGCACCCAAGTCAAAGCCCATGT
1 CCCATGATAGCTGG--CATCTGAGTTAAAACCCACATTAGTT-GCACACAAGTCAAAGCCCATAT
*
1174158 TAGCTAGCATCTAAGTCAGAA-CCCATATTAGCT-G-GCATTTGAATCAAAG
63 TA-ATAGCATCTAAGTCA-AAGCCCATATTAGCTAGTGC--TTGAATCAAAG
* * *
1174207 CCCATGATAGCTGGCATCTGAGTCAAAGCCTACATTAGTTGACACACAAGTCAAAGCCCATATTA
1 CCCATGATAGCTGGCATCTGAGTTAAAACCCACATTAGTTG-CACACAAGTCAAAGCCCATATTA
* * *
1174272 ATTGCCATTTTAA-TCAAAGCCCACATTAG
65 ATAG-CA-TCTAAGTCAAAGCCCATATTAG
1174301 TTGGCACCCC
Statistics
Matches: 168, Mismatches: 24, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
109 2 0.01
110 2 0.01
111 53 0.32
112 99 0.59
113 10 0.06
114 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (110 bp):
CCCATGATAGCTGGCATCTGAGTTAAAACCCACATTAGTTGCACACAAGTCAAAGCCCATATTAA
TAGCATCTAAGTCAAAGCCCATATTAGCTAGTGCTTGAATCAAAG
Found at i:1176884 original size:16 final size:17
Alignment explanation
Indices: 1176852--1176885 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1176842 TAAAAAATTA
*
1176852 CTAAAATTGTTTTCATG
1 CTAAAATTGTATTCATG
1176869 CTAAAATT-TATTCATG
1 CTAAAATTGTATTCATG
1176885 C
1 C
1176886 ATGGCTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (17 bp):
CTAAAATTGTATTCATG
Found at i:1178685 original size:20 final size:20
Alignment explanation
Indices: 1178660--1178699 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1178650 TTAAGCACAG
1178660 TATATTTAAAAAAAGAATTC
1 TATATTTAAAAAAAGAATTC
*
1178680 TATATTTGAAAAAAGAATTC
1 TATATTTAAAAAAAGAATTC
1178700 CATTAAGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (20 bp):
TATATTTAAAAAAAGAATTC
Found at i:1179925 original size:21 final size:21
Alignment explanation
Indices: 1179901--1179998 Score: 146
Period size: 21 Copynumber: 4.7 Consensus size: 21
1179891 ATTTTATCCA
1179901 AATGTATCGATACATTTGAAG
1 AATGTATCGATACATTTGAAG
1179922 AATGTATCGATACATTTGAAG
1 AATGTATCGATACATTTGAAG
**
1179943 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGAAG
1179964 AATGTATCGATACATTCT-ACA-
1 AATGTATCGATACATT-TGA-AG
1179985 AATGTATCGATACA
1 AATGTATCGATACA
1179999 GGGTCCCAAC
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
21 70 0.99
22 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (21 bp):
AATGTATCGATACATTTGAAG
Found at i:1180058 original size:19 final size:17
Alignment explanation
Indices: 1180034--1180162 Score: 102
Period size: 19 Copynumber: 7.8 Consensus size: 17
1180024 AATTCAACAA
1180034 TTTGTATCGATACATAAG
1 TTTGTATCGATACA-AAG
1180052 TTTTGTATCGATAC-AA-
1 -TTTGTATCGATACAAAG
1180068 --TGTATCGATACACAAG
1 TTTGTATCGATACA-AAG
1180084 TATTGTATCGATAC-AA-
1 T-TTGTATCGATACAAAG
1180100 --TGTATCGATACACAAG
1 TTTGTATCGATACA-AAG
1180116 TATTGTATCGATAC-AA-
1 T-TTGTATCGATACAAAG
1180132 --TGTATCGATACACAAG
1 TTTGTATCGATACA-AAG
1180148 TATTGTATCGATACA
1 T-TTGTATCGATACA
1180163 TAATTAGCTA
Statistics
Matches: 92, Mismatches: 0, Indels: 36
0.72 0.00 0.28
Matches are distributed among these distances:
13 33 0.36
15 6 0.07
17 6 0.07
19 47 0.51
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (17 bp):
TTTGTATCGATACAAAG
Found at i:1180073 original size:13 final size:13
Alignment explanation
Indices: 1180055--1180143 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
1180045 ACATAAGTTT
1180055 TGTATCGATACAA
1 TGTATCGATACAA
1180068 TGTATCGATACACAAGTA
1 TGTATCGAT--AC-A--A
1180086 TTGTATCGATACAA
1 -TGTATCGATACAA
1180100 TGTATCGATACACAAGTA
1 TGTATCGAT--AC-A--A
1180118 TTGTATCGATACAA
1 -TGTATCGATACAA
1180132 TGTATCGATACA
1 TGTATCGATACA
1180144 CAAGTATTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 30 0.47
14 2 0.03
15 4 0.06
16 4 0.06
17 4 0.06
18 2 0.03
19 18 0.28
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1180077 original size:32 final size:32
Alignment explanation
Indices: 1180036--1180162 Score: 236
Period size: 32 Copynumber: 4.0 Consensus size: 32
1180026 TTCAACAATT
* *
1180036 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACACAAGTATTGTATCGATACAA
1180068 TGTATCGATACACAAGTATTGTATCGATACAA
1 TGTATCGATACACAAGTATTGTATCGATACAA
1180100 TGTATCGATACACAAGTATTGTATCGATACAA
1 TGTATCGATACACAAGTATTGTATCGATACAA
1180132 TGTATCGATACACAAGTATTGTATCGATACA
1 TGTATCGATACACAAGTATTGTATCGATACA
1180163 TAATTAGCTA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 93 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (32 bp):
TGTATCGATACACAAGTATTGTATCGATACAA
Found at i:1180223 original size:13 final size:13
Alignment explanation
Indices: 1180205--1180230 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1180195 CATTTTTCTG
1180205 TGTATCGATACAT
1 TGTATCGATACAT
1180218 TGTATCGATACAT
1 TGTATCGATACAT
1180231 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1180227 original size:33 final size:33
Alignment explanation
Indices: 1180185--1180251 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1180175 GCCAAGGAAA
***
1180185 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1180218 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1180251 T
1 T
1180252 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1181991 original size:24 final size:24
Alignment explanation
Indices: 1181941--1181991 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1181931 TAAACTTGTC
* *
1181941 AAGATTTAAATCTTATTTTTTCTT
1 AAGATTTAAATCTTATTTTTGCCT
1181965 AAGATTTAAATCTTATTTTTGCCT
1 AAGATTTAAATCTTATTTTTGCCT
1181989 AAG
1 AAG
1181992 TTATTGTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (24 bp):
AAGATTTAAATCTTATTTTTGCCT
Found at i:1182971 original size:27 final size:27
Alignment explanation
Indices: 1182914--1182983 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
1182904 CTTCACAATC
**
1182914 GGGGATACTCCAACCCAGTTAATCATC
1 GGGGATACTCCAACCCAGTTAATCAGA
* *
1182941 GGGGATACTCCAACCC-GTTATTTCCGA
1 GGGGATACTCCAACCCAGTTA-ATCAGA
*
1182968 GGGGACACTCCAACCC
1 GGGGATACTCCAACCC
1182984 CAGCTTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.11
27 33 0.89
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.20
Consensus pattern (27 bp):
GGGGATACTCCAACCCAGTTAATCAGA
Found at i:1184727 original size:21 final size:21
Alignment explanation
Indices: 1184684--1184728 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1184674 CATCTTTGTC
* ***
1184684 TAAATGTATCGATACATTTCT
1 TAAATATATCGATACAAGGCT
1184705 TAAATATATCGATACAAGGCT
1 TAAATATATCGATACAAGGCT
1184726 TAA
1 TAA
1184729 CAGTCAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (21 bp):
TAAATATATCGATACAAGGCT
Found at i:1184822 original size:21 final size:21
Alignment explanation
Indices: 1184775--1184830 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1184765 TGCAAACAGT
*
1184775 AAATGTATCGATACATAAGTG
1 AAATGTATCGATACATAACTG
**
1184796 -AATGTATCGATACATGCCTG
1 AAATGTATCGATACATAACTG
1184816 AAATGTATCGATACA
1 AAATGTATCGATACA
1184831 AAACCACTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
AAATGTATCGATACATAACTG
Done.