Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 19 of 27
Found at i:3094000 original size:6 final size:6
Alignment explanation
Indices: 3093989--3094032 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
3093979 AACTTCATAT
* *
3093989 TTTTTA TTTTTA TTTTTTA TTTTTTA ATTTTA ATTTTA TTTTTA
1 TTTTTA TTTTTA -TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA
3094033 AATTATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 22 0.63
7 13 0.37
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:3094004 original size:13 final size:13
Alignment explanation
Indices: 3093986--3094031 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
3093976 AAAAACTTCA
3093986 TATTTTTTATTTT
1 TATTTTTTATTTT
3093999 TATTTTTTATTTT
1 TATTTTTTATTTT
* *
3094012 T-TAATTTTAATTT
1 TAT-TTTTTATTTT
3094025 TATTTTT
1 TATTTTT
3094032 AAATTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 1 0.04
13 26 0.93
14 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:3094026 original size:32 final size:32
Alignment explanation
Indices: 3093990--3094056 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
3093980 ACTTCATATT
** * * *
3093990 TTTTATTTTTATTTTTTATTTTTTAATTTTAA
1 TTTTATTTTTAAATTATATATTTTAATGTTAA
3094022 TTTTATTTTTAAATTATATATTTTAATGTTAA
1 TTTTATTTTTAAATTATATATTTTAATGTTAA
3094054 TTT
1 TTT
3094057 GCATTGTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (32 bp):
TTTTATTTTTAAATTATATATTTTAATGTTAA
Found at i:3094855 original size:3 final size:3
Alignment explanation
Indices: 3094847--3094883 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3094837 AAAGCATATT
3094847 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3094884 GAATTCGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3100200 original size:4 final size:4
Alignment explanation
Indices: 3100191--3100217 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3100181 GCAAAAGAAT
3100191 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
3100218 TATATATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:3101881 original size:20 final size:20
Alignment explanation
Indices: 3101852--3101936 Score: 70
Period size: 20 Copynumber: 4.4 Consensus size: 20
3101842 AATATTTATT
*
3101852 TTATTTTATTTTTTAAATTA
1 TTATTATATTTTTTAAATTA
* *
3101872 TTATTATATTTTTTAAAATG
1 TTATTATATTTTTTAAATTA
*
3101892 TT-TTATATATTTTTATATT-
1 TTATTATAT-TTTTTAAATTA
* * *
3101911 TTAATATATATTAT-AATTA
1 TTATTATATTTTTTAAATTA
3101930 -TATTATA
1 TTATTATA
3101937 ATTTATATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
18 9 0.17
19 11 0.21
20 32 0.62
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (20 bp):
TTATTATATTTTTTAAATTA
Found at i:3101938 original size:23 final size:23
Alignment explanation
Indices: 3101904--3101973 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
3101894 TTATATATTT
*
3101904 TTATATTTTAATATATATTATAA
1 TTATATTATAATATATATTATAA
*
3101927 TTATATTATAATTTATATTTATTAA
1 TTATATTATAATATATA-TTA-TAA
*
3101952 TAAT-TTATAATAT-TAATTATAA
1 TTATATTATAATATAT-ATTATAA
3101974 AATAATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 3 0.08
23 19 0.47
24 12 0.30
25 6 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATATTATAATATATATTATAA
Found at i:3101967 original size:16 final size:17
Alignment explanation
Indices: 3101900--3101968 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 17
3101890 TGTTTTATAT
* *
3101900 ATTTTTATATTTTAATA
1 ATTTATATATATTAATA
3101917 TATATTATAATTATATT-ATA
1 -AT-TTAT-A-TATATTAATA
*
3101937 ATTTATATTTATTAATA
1 ATTTATATATATTAATA
3101954 ATTTATA-ATATTAAT
1 ATTTATATATATTAAT
3101969 TATAAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 12 0.28
17 11 0.26
18 6 0.14
19 5 0.12
20 4 0.09
21 5 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTATATATATTAATA
Found at i:3101970 original size:20 final size:17
Alignment explanation
Indices: 3101903--3101960 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
3101893 TTTATATATT
3101903 TTTATA-TT-TTAATATA
1 TTTATATTTATTAATA-A
3101919 TATTATAATTATATT-ATAA
1 T-TTAT-ATT-TATTAATAA
3101938 TTTATATTTATTAATAA
1 TTTATATTTATTAATAA
3101955 TTTATA
1 TTTATA
3101961 ATATTAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 5 0.14
17 17 0.47
18 5 0.14
19 3 0.08
20 4 0.11
21 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATATTTATTAATAA
Found at i:3101972 original size:29 final size:27
Alignment explanation
Indices: 3101905--3101969 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
3101895 TATATATTTT
* *
3101905 TATATTTTAATATATATTATAATTATAT
1 TATAATTT-ATATATATTATAATTATAA
*
3101933 TATAATTTATATTTATTAATAATTTATAA
1 TATAATTTATATATATT-ATAA-TTATAA
3101962 TATTAATT
1 TA-TAATT
3101970 ATAAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 8 0.26
28 11 0.35
29 7 0.23
30 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TATAATTTATATATATTATAATTATAA
Found at i:3101973 original size:12 final size:13
Alignment explanation
Indices: 3101904--3101973 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 13
3101894 TTATATATTT
*
3101904 TTATATTTTAATA
1 TTATATTATAATA
3101917 -TATATTAT-A-A
1 TTATATTATAATA
3101927 TTATATTATAAT-
1 TTATATTATAATA
3101939 TTATATTTATTAATA
1 TTATA-TTA-TAATA
3101954 --AT-TTATAATA
1 TTATATTATAATA
3101964 TTA-ATTATAA
1 TTATATTATAA
3101974 AATAATTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 19
0.70 0.01 0.28
Matches are distributed among these distances:
10 6 0.13
11 12 0.26
12 20 0.43
13 5 0.11
14 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATTATAATA
Found at i:3102352 original size:23 final size:24
Alignment explanation
Indices: 3102314--3102370 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
3102304 GGAGGTTAAA
*
3102314 AAAATTTA-TAAATATTAAAT-TT
1 AAAATTAATTAAATATTAAATCTT
* *
3102336 TAAATTAATTAAATATTATATCTT
1 AAAATTAATTAAATATTAAATCTT
3102360 AAAATTAATTA
1 AAAATTAATTA
3102371 TATAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 6 0.21
23 11 0.38
24 12 0.41
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAATTAATTAAATATTAAATCTT
Found at i:3103212 original size:18 final size:18
Alignment explanation
Indices: 3103167--3103212 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
3103157 TAGTTAAGTA
* *
3103167 AAAATTTTATTTTAATAT
1 AAAATTTTTTTTTAAAAT
*
3103185 TAAATATTTTTTTTAAAAT
1 AAAAT-TTTTTTTTAAAAT
3103204 AAAATTTTT
1 AAAATTTTT
3103213 AATAATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AAAATTTTTTTTTAAAAT
Found at i:3103341 original size:36 final size:37
Alignment explanation
Indices: 3103269--3103345 Score: 86
Period size: 39 Copynumber: 2.1 Consensus size: 37
3103259 TATAAATATG
* ** *
3103269 ATAATAAATATTTTTTAAAATTAATTAAAATTTAATTTA
1 ATAAAAAATATTTTAAAAAATT-ATTAAAATATAA-TTA
3103308 ATAAAAAATATTTTAAAAAATT-TTAAAA-ATAATTA
1 ATAAAAAATATTTTAAAAAATTATTAAAATATAATTA
3103343 ATA
1 ATA
3103346 TTATTGTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
35 6 0.18
36 3 0.09
37 6 0.18
39 19 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (37 bp):
ATAAAAAATATTTTAAAAAATTATTAAAATATAATTA
Found at i:3103845 original size:23 final size:22
Alignment explanation
Indices: 3103794--3103845 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 22
3103784 AATATAAAAA
3103794 ATATA-TAATATAAAATTTTTT
1 ATATATTAATATAAAATTTTTT
* *
3103815 A-A-ATTAATGTAATATTTTATT
1 ATATATTAATATAAAATTTT-TT
3103836 ATATATTAAT
1 ATATATTAAT
3103846 TTTTTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.04
20 13 0.52
21 4 0.16
22 1 0.04
23 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
ATATATTAATATAAAATTTTTT
Found at i:3105267 original size:24 final size:24
Alignment explanation
Indices: 3105240--3105313 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 24
3105230 TAAATTAAAA
3105240 ATATATTTTATTTAAATATTTATT
1 ATATATTTTATTTAAATATTTATT
*
3105264 ATAT-TTACTATTTAAATA-TTATT
1 ATATATT-TTATTTAAATATTTATT
* * *
3105287 -TAAAATTTTAATTAAATTTATTATT
1 AT-ATATTTTATTTAAATAT-TTATT
3105312 AT
1 AT
3105314 GATGATTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
22 1 0.03
23 16 0.41
24 16 0.41
25 5 0.13
26 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (24 bp):
ATATATTTTATTTAAATATTTATT
Found at i:3111043 original size:22 final size:22
Alignment explanation
Indices: 3110999--3111080 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
3110989 TGTTTAAATT
* * *
3110999 TATTTATTTATTATTCATAAATA
1 TATTT-TTAATTATTTATTAATA
3111022 TATTTTTAATTATTTATTAATA
1 TATTTTTAATTATTTATTAATA
*
3111044 TATTACTTAA-TATTT-TTAA-A
1 TATT-TTTAATTATTTATTAATA
* *
3111064 TAATTTTATTTTATTTA
1 TATTTTTA-ATTATTTA
3111081 AATAAATTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.06
20 4 0.08
21 9 0.19
22 23 0.48
23 9 0.19
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTTTAATTATTTATTAATA
Found at i:3111750 original size:18 final size:18
Alignment explanation
Indices: 3111724--3111781 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 18
3111714 TTAGATTTTA
*
3111724 TTAACTTTTTATCAATTT
1 TTAAATTTTTATCAATTT
*
3111742 TTAAATTTTT-T-ATTTT
1 TTAAATTTTTATCAATTT
*
3111758 TTATAA-TTTTATCCAATTC
1 TTA-AATTTTTAT-CAATTT
3111777 TTAAA
1 TTAAA
3111782 AAATTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 11 0.34
17 4 0.12
18 11 0.34
19 6 0.19
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAATTTTTATCAATTT
Found at i:3117948 original size:47 final size:47
Alignment explanation
Indices: 3117897--3117992 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 47
3117887 GGACATGTTC
*
3117897 TTATGGTTTGTGGTACTTTAATTCTAATAATTCTAAGTTATTTGGGT
1 TTATGGTTTGTGGTACTTTAATTCTAACAATTCTAAGTTATTTGGGT
*
3117944 TTATGGTTTGTGGTACTTTAATTTTAACAATTCTAAGTTATTTGGGT
1 TTATGGTTTGTGGTACTTTAATTCTAACAATTCTAAGTTATTTGGGT
3117991 TT
1 TT
3117993 TCAGATAGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (47 bp):
TTATGGTTTGTGGTACTTTAATTCTAACAATTCTAAGTTATTTGGGT
Found at i:3126498 original size:3 final size:3
Alignment explanation
Indices: 3126490--3126522 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3126480 TAATTCCAAC
3126490 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3126523 TAAAGAGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3127077 original size:3 final size:3
Alignment explanation
Indices: 3127069--3127107 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3127059 TTCACACCAC
3127069 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3127108 ATGCTTCGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3127475 original size:13 final size:13
Alignment explanation
Indices: 3127444--3127488 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 13
3127434 TTAAAAGATA
3127444 AAAATTA-TTTTT
1 AAAATTATTTTTT
3127456 AATAATTATTTTTT
1 AA-AATTATTTTTT
3127470 AAAATTTTATTTTTT
1 AAAA--TTATTTTTT
3127485 AAAA
1 AAAA
3127489 ATTTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.07
13 7 0.24
14 7 0.24
15 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:3127479 original size:15 final size:16
Alignment explanation
Indices: 3127461--3127494 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3127451 TTTTTAATAA
3127461 TTATTTTTT-AAAATT
1 TTATTTTTTAAAAATT
3127476 TTATTTTTTAAAAATT
1 TTATTTTTTAAAAATT
3127492 TTA
1 TTA
3127495 AAAATAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTTTTTAAAAATT
Found at i:3129316 original size:23 final size:25
Alignment explanation
Indices: 3129266--3129316 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
3129256 CTCAGTCCAA
* * *
3129266 TAAAACATTTTTTTTATTTTAATAT
1 TAAAACATATTTTTAATTTAAATAT
3129291 TAAAA-ATATTTTTAATTTAAAT-T
1 TAAAACATATTTTTAATTTAAATAT
3129314 TAA
1 TAA
3129317 TTATAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TAAAACATATTTTTAATTTAAATAT
Found at i:3129578 original size:2 final size:2
Alignment explanation
Indices: 3129573--3129598 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3129563 AAAAATGACA
3129573 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
3129599 TTCATTCTTG
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:3129665 original size:2 final size:2
Alignment explanation
Indices: 3129658--3129697 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3129648 TTTTGGACAC
3129658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3129698 CCTCATTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3138714 original size:22 final size:22
Alignment explanation
Indices: 3138670--3138714 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3138660 GACTTTACAA
* *
3138670 ATATTTTCTAAAAAATATGAAT
1 ATATTTTCTAAAAAAAATAAAT
3138692 ATATTTTC-AGAAAAAAATAAAT
1 ATATTTTCTA-AAAAAAATAAAT
3138714 A
1 A
3138715 AAGATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (22 bp):
ATATTTTCTAAAAAAAATAAAT
Found at i:3139843 original size:12 final size:12
Alignment explanation
Indices: 3139828--3139853 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3139818 TTAAATACAT
3139828 AAAAAAATTAAA
1 AAAAAAATTAAA
3139840 AAAAAAATTAAA
1 AAAAAAATTAAA
3139852 AA
1 AA
3139854 TATATCCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAATTAAA
Found at i:3147517 original size:24 final size:24
Alignment explanation
Indices: 3147489--3147537 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3147479 AAAAGTAAAA
3147489 TCATTTGATGCAAAAGGCATATAT
1 TCATTTGATGCAAAAGGCATATAT
3147513 TCATTTGATGCAAAAGGCATATAT
1 TCATTTGATGCAAAAGGCATATAT
3147537 T
1 T
3147538 GTATAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (24 bp):
TCATTTGATGCAAAAGGCATATAT
Found at i:3151019 original size:18 final size:19
Alignment explanation
Indices: 3150983--3151020 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
3150973 CATATCATCA
3150983 ACAGTTGGCTTAGAACTTTC
1 ACAGTTGGC-TAGAACTTTC
*
3151003 ACAGTTGG-TAGAGCTTTC
1 ACAGTTGGCTAGAACTTTC
3151021 TGCTTGCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (19 bp):
ACAGTTGGCTAGAACTTTC
Found at i:3152431 original size:2 final size:2
Alignment explanation
Indices: 3152424--3152466 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3152414 TCTGGATCCA
3152424 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3152466 T
1 T
3152467 TTGCTTATCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3152924 original size:24 final size:24
Alignment explanation
Indices: 3152897--3152943 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3152887 ATTATATTTA
*
3152897 TTATTTAA-AAATATTATAAAAATG
1 TTATATAATAAATATT-TAAAAATG
3152921 TTATATAATAAATATTTAAAAAT
1 TTATATAATAAATATTTAAAAAT
3152944 CAAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTATATAATAAATATTTAAAAATG
Found at i:3154046 original size:13 final size:14
Alignment explanation
Indices: 3154008--3154048 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
3153998 TTTTATTAAA
*
3154008 TTAATTATTTTATTT
1 TTAATTA-TTTAATT
3154023 TTAATTA-TTAATT
1 TTAATTATTTAATT
3154036 TT-ATTATTTAATT
1 TTAATTATTTAATT
3154049 AATAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 13 0.54
15 7 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTAATTATTTAATT
Found at i:3154397 original size:23 final size:22
Alignment explanation
Indices: 3154380--3154425 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3154370 TTTTAACTTC
3154380 TTTT-ATAT-ATTTTATTTAAT
1 TTTTGATATAATTTTATTTAAT
* *
3154400 TTTTGATATAATTTTAGTAAAT
1 TTTTGATATAATTTTATTTAAT
3154422 TTTT
1 TTTT
3154426 TTAATATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 14 0.64
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (22 bp):
TTTTGATATAATTTTATTTAAT
Found at i:3154429 original size:31 final size:31
Alignment explanation
Indices: 3154380--3154441 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
3154370 TTTTAACTTC
* *
3154380 TTTTATATATTTTATTTAATTTTTGATATAA
1 TTTTATAAATTTTATTTAATATTTGATATAA
3154411 TTTTAGTAAATTTT-TTTAATATTTGATATAA
1 TTTTA-TAAATTTTATTTAATATTTGATATAA
3154442 ATTCGATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 21 0.75
32 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (31 bp):
TTTTATAAATTTTATTTAATATTTGATATAA
Found at i:3154546 original size:21 final size:21
Alignment explanation
Indices: 3154433--3154548 Score: 62
Period size: 21 Copynumber: 5.5 Consensus size: 21
3154423 TTTTTAATAT
* * *
3154433 TTGATATAAATTCGATAACTA
1 TTGATATAATTTTGATAATTA
* **
3154454 TTGATATAATATTT-TTAATCC
1 TTGATATAAT-TTTGATAATTA
3154475 TTGATATAATTTT-AGTAAGTT-
1 TTGATATAATTTTGA-TAA-TTA
* * *
3154496 TTAACATAGTTTTGATAACTTA
1 TTGATATAATTTTGATAA-TTA
*
3154518 -T-ACGATAATTTTGATAATTA
1 TTGA-TATAATTTTGATAATTA
3154538 TTGATATAATT
1 TTGATATAATT
3154549 AATAATAATA
Statistics
Matches: 72, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
20 7 0.10
21 60 0.83
22 5 0.07
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.47
Consensus pattern (21 bp):
TTGATATAATTTTGATAATTA
Found at i:3155858 original size:29 final size:28
Alignment explanation
Indices: 3155814--3155872 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
3155804 TTTTTATTTA
* *
3155814 TTAAATTAATTATTAATATAATATTATT
1 TTAAAATAATTATTAAAATAATATTATT
* *
3155842 TTAAAATAATTTATTAAAATATTGTTATT
1 TTAAAATAA-TTATTAAAATAATATTATT
3155871 TT
1 TT
3155873 TATCTGCTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTAAAATAATTATTAAAATAATATTATT
Found at i:3156640 original size:24 final size:24
Alignment explanation
Indices: 3156576--3156661 Score: 81
Period size: 24 Copynumber: 3.6 Consensus size: 24
3156566 TCAAATGACA
* *
3156576 AAAAAATAATACAAACA-AGACAAG
1 AAAAAATAATACGAACACA-ACACG
3156600 AAAAACA-ACATAC--ACACAACACG
1 AAAAA-ATA-ATACGAACACAACACG
3156623 AAAAAATAATACGAACACAACACG
1 AAAAAATAATACGAACACAACACG
* *
3156647 AGAAAATAACACGAA
1 AAAAAATAATACGAA
3156662 ACTTAATTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
22 5 0.09
23 13 0.25
24 30 0.57
25 5 0.09
ACGTcount: A:0.65, C:0.20, G:0.08, T:0.07
Consensus pattern (24 bp):
AAAAAATAATACGAACACAACACG
Found at i:3156776 original size:23 final size:23
Alignment explanation
Indices: 3156747--3156798 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
3156737 GCTCATATTA
* * *
3156747 TTTTTATGTCATATTCGTGATAT
1 TTTTTATATCACATTCATGATAT
*
3156770 TTTTTATATCGCATTCATGATAT
1 TTTTTATATCACATTCATGATAT
3156793 TTTTTA
1 TTTTTA
3156799 GTGTTGTGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.58
Consensus pattern (23 bp):
TTTTTATATCACATTCATGATAT
Found at i:3159156 original size:18 final size:20
Alignment explanation
Indices: 3159116--3159167 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
3159106 ATATATTTTT
* *
3159116 TAAAAAATTCTTTAAATACA
1 TAAAAAAATCTTTAAATAAA
3159136 TAAAAAAAT-TTTAAA-AAA
1 TAAAAAAATCTTTAAATAAA
* *
3159154 TAAATATATCTTTA
1 TAAAAAAATCTTTA
3159168 TCAAAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 9 0.33
19 10 0.37
20 8 0.30
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAAAATCTTTAAATAAA
Found at i:3169410 original size:1 final size:1
Alignment explanation
Indices: 3169406--3169443 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
3169396 ATTTTTTCTC
3169406 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3169444 CCATTTTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3172350 original size:15 final size:16
Alignment explanation
Indices: 3172330--3172362 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3172320 ACTTTTTTTT
3172330 TTCAATTTGAATT-AA
1 TTCAATTTGAATTGAA
3172345 TTCAATTTGAATTGAA
1 TTCAATTTGAATTGAA
3172361 TT
1 TT
3172363 ATTAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (16 bp):
TTCAATTTGAATTGAA
Found at i:3176716 original size:15 final size:15
Alignment explanation
Indices: 3176696--3176738 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
3176686 TTCGTTGATG
3176696 TTTAATAATTTTAAT
1 TTTAATAATTTTAAT
*
3176711 TTTAATCATTTTAAT
1 TTTAATAATTTTAAT
3176726 TTTAATAATTTTA
1 TTTAATAATTTTA
3176739 TATAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTAATAATTTTAAT
Found at i:3176751 original size:24 final size:24
Alignment explanation
Indices: 3176707--3176755 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3176697 TTAATAATTT
* *
3176707 TAATTTTAATCATTTTAATTTTAA
1 TAATTTTAATAATTATAATTTTAA
*
3176731 TAATTTTATATAATTATATTTTTAA
1 TAATTTTA-ATAATTATAATTTTAA
3176756 AATATGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TAATTTTAATAATTATAATTTTAA
Found at i:3187907 original size:2 final size:2
Alignment explanation
Indices: 3187894--3187931 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3187884 AGTAAGAACA
*
3187894 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3187932 GGTTTACGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3188581 original size:18 final size:17
Alignment explanation
Indices: 3188544--3188582 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
3188534 TATAATTTAA
*
3188544 AATTTAAAATTTAATTT
1 AATTTAAAATTTAATAT
*
3188561 AATTTAAATATTTTATAT
1 AATTTAAA-ATTTAATAT
3188579 AATT
1 AATT
3188583 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTAAAATTTAATAT
Found at i:3188805 original size:29 final size:31
Alignment explanation
Indices: 3188766--3188843 Score: 79
Period size: 35 Copynumber: 2.5 Consensus size: 31
3188756 TACATGCATA
* *
3188766 AAATAATTAAAAAATAA-TATAATATAAT-T
1 AAATATTTAAAAAATAATTAAAATATAATAT
*
3188795 ATATATTTAAATTTTAAATAATTAAAATATAATAT
1 AAATATTTAAA----AAATAATTAAAATATAATAT
3188830 AAATATTTAAAAAA
1 AAATATTTAAAAAA
3188844 AATGTTACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
29 9 0.23
31 3 0.08
33 6 0.15
34 10 0.26
35 11 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATATTTAAAAAATAATTAAAATATAATAT
Found at i:3189072 original size:19 final size:20
Alignment explanation
Indices: 3189050--3189096 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
3189040 ATTGATTTTT
*
3189050 TTTTATTTTTTTC-ATCTTA
1 TTTTATTTTTTTCAATCTCA
3189069 TTTTA-TTTTTTCAATCTCA
1 TTTTATTTTTTTCAATCTCA
3189088 TTTT-TTTTT
1 TTTTATTTTT
3189097 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTATTTTTTTCAATCTCA
Found at i:3196189 original size:16 final size:17
Alignment explanation
Indices: 3196168--3196212 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
3196158 ATCTCATTTT
*
3196168 AAAAAAGCAAAAAA-AA
1 AAAAAAACAAAAAACAA
3196184 AAAAAAACAAAAAACAA
1 AAAAAAACAAAAAACAA
*
3196201 AACAACAACAAA
1 AA-AAAAACAAA
3196213 GGGGAAGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.52
17 4 0.16
18 8 0.32
ACGTcount: A:0.84, C:0.13, G:0.02, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAAAACAA
Found at i:3196203 original size:12 final size:12
Alignment explanation
Indices: 3196168--3196205 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3196158 ATCTCATTTT
3196168 AAAAAAGCAAAA-
1 AAAAAA-CAAAAC
*
3196180 AAAAAAAAAAAC
1 AAAAAACAAAAC
3196192 AAAAAACAAAAC
1 AAAAAACAAAAC
3196204 AA
1 AA
3196206 CAACAAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:3201088 original size:15 final size:16
Alignment explanation
Indices: 3201061--3201100 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
3201051 TAAATTACAA
3201061 AAAT-AAATGAAAA-AT
1 AAATAAAAT-AAAACAT
3201076 AAATAAAATAAAACAT
1 AAATAAAATAAAACAT
3201092 AAA-AAAATA
1 AAATAAAATA
3201101 TAATTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (16 bp):
AAATAAAATAAAACAT
Found at i:3201506 original size:10 final size:11
Alignment explanation
Indices: 3201491--3201540 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
3201481 TATTTTTATA
3201491 TTATAT-AAAT
1 TTATATAAAAT
3201501 TTATATAAAAAT
1 TTATAT-AAAAT
* *
3201513 TAATATAATAT
1 TTATATAAAAT
3201524 TTAT-TAATAAT
1 TTATATAA-AAT
3201535 TTATAT
1 TTATAT
3201541 TATATAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 9 0.28
11 13 0.41
12 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TTATATAAAAT
Found at i:3201518 original size:27 final size:26
Alignment explanation
Indices: 3201488--3201551 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 26
3201478 TATTATTTTT
3201488 ATATTATATAAATTTATATAAAAATTA
1 ATATTATATAAATTTAT-TAAAAATTA
* *
3201515 ATA-TA-AT--ATTTATTAATAATTT
1 ATATTATATAAATTTATTAAAAATTA
3201537 ATATTATATAAATTT
1 ATATTATATAAATTT
3201552 TAATATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
22 10 0.32
23 8 0.26
24 2 0.06
25 2 0.06
26 6 0.19
27 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATTATATAAATTTATTAAAAATTA
Found at i:3201538 original size:11 final size:12
Alignment explanation
Indices: 3201498--3201540 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
3201488 ATATTATATA
*
3201498 AATTTATATAAA
1 AATTTATATAAT
*
3201510 AATTAATATAAT
1 AATTTATATAAT
3201522 -ATTTAT-TAAT
1 AATTTATATAAT
3201532 AATTTATAT
1 AATTTATAT
3201541 TATATAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 4 0.15
11 11 0.42
12 11 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTTATATAAT
Found at i:3201544 original size:39 final size:36
Alignment explanation
Indices: 3201501--3201578 Score: 102
Period size: 39 Copynumber: 2.1 Consensus size: 36
3201491 TTATATAAAT
3201501 TTATATAAAAATTAATATAATATTTATTAATAATTTATA
1 TTATATAAAAATTAATATAATATTTA--AAT-ATTTATA
** *
3201540 TTATATAAATTTTAATATATTATTTAAATATTTATA
1 TTATATAAAAATTAATATAATATTTAAATATTTATA
3201576 TTA
1 TTA
3201579 AAATTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 10 0.28
37 3 0.08
39 23 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (36 bp):
TTATATAAAAATTAATATAATATTTAAATATTTATA
Found at i:3201553 original size:27 final size:26
Alignment explanation
Indices: 3201485--3201551 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 26
3201475 TATTATTATT
3201485 TTTATATTATATAAATTTATATAAAA
1 TTTATATTATATAAATTTATATAAAA
* *
3201511 ATTA-A-TATA-ATATTTAT-TAATAA
1 TTTATATTATATAAATTTATATAA-AA
3201534 TTTATATTATATAAATTT
1 TTTATATTATATAAATTT
3201552 TAATATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 3 0.09
23 12 0.36
24 5 0.15
25 5 0.15
26 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTATATTATATAAATTTATATAAAA
Found at i:3201560 original size:19 final size:20
Alignment explanation
Indices: 3201536--3201573 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3201526 ATTAATAATT
3201536 TATATTATATAAAT-TTTAA
1 TATATTATATAAATATTTAA
*
3201555 TATATTATTTAAATATTTA
1 TATATTATATAAATATTTA
3201574 TATTAAAATT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATTATATAAATATTTAA
Found at i:3201578 original size:49 final size:47
Alignment explanation
Indices: 3201461--3201583 Score: 124
Period size: 49 Copynumber: 2.5 Consensus size: 47
3201451 TAAATTTGAT
* * *
3201461 AATTTATATATTTATATTATTATTTTTATATTATATAAATTTATATAA
1 AATTTAAATATTTATATTAATA-ATTTATATTATATAAATTTATATAA
* *
3201509 AAATTAATATAATATT-TATTAATAATTTATATTATATAAATTTTAATATAT
1 AATTTAA-AT-AT-TTATATTAATAATTTATATTATATAAA-TTT-ATATAA
*
3201560 TATTTAAATATTTATATTAA-AATT
1 AATTTAAATATTTATATTAATAATT
3201584 AAAATGAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
48 11 0.18
49 25 0.40
50 14 0.23
51 12 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (47 bp):
AATTTAAATATTTATATTAATAATTTATATTATATAAATTTATATAA
Found at i:3206687 original size:22 final size:21
Alignment explanation
Indices: 3206618--3206687 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 21
3206608 GATTTAAAAT
3206618 ATAATATTTTTAATTTAATTTA
1 ATAATATTTTTAATTTAA-TTA
** *
3206640 ATTTTATTTTATTATTTAATTA
1 ATAATATTTT-TAATTTAATTA
3206662 ATAATATTTTTAATTTAATTA
1 ATAATATTTTTAATTTAATTA
3206683 CATAA
1 -ATAA
3206688 ATATATAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 10 0.25
22 23 0.57
23 7 0.17
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (21 bp):
ATAATATTTTTAATTTAATTA
Found at i:3207271 original size:19 final size:19
Alignment explanation
Indices: 3207242--3207291 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3207232 AGATATGAAT
* *
3207242 ATATTAATATAT-TAAAAT
1 ATATAAATATATATAAAAA
*
3207260 TTATAAAATATATATAAAAA
1 ATAT-AAATATATATAAAAA
3207280 ATATAAATATAT
1 ATATAAATATAT
3207292 GTATTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 3 0.12
19 15 0.58
20 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATATATATAAAAA
Found at i:3207274 original size:21 final size:22
Alignment explanation
Indices: 3207248--3207297 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
3207238 GAATATATTA
**
3207248 ATATATTAAAATTTATAAA-AT
1 ATATATTAAAAAATATAAATAT
3207269 ATATA-TAAAAAATATAAATAT
1 ATATATTAAAAAATATAAATAT
*
3207290 ATGTATTA
1 ATATATTA
3207298 TTAATATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.46
21 11 0.46
22 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATATATTAAAAAATATAAATAT
Found at i:3208336 original size:24 final size:24
Alignment explanation
Indices: 3208291--3208336 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
3208281 AACGTTGTTG
3208291 AAACAAAAAGTAATAATAATAATA
1 AAACAAAAAGTAATAATAATAATA
3208315 AAACATAAAA-TAA-AATATATAA
1 AAACA-AAAAGTAATAATA-ATAA
3208337 AATTATTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (24 bp):
AAACAAAAAGTAATAATAATAATA
Found at i:3208367 original size:21 final size:20
Alignment explanation
Indices: 3208327--3208391 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
3208317 ACATAAAATA
3208327 AAATAT-ATAAAATTATTAT
1 AAATATAATAAAATTATTAT
3208346 AAATATAATATAAA-TATGTAT
1 AAATATAATA-AAATTAT-TAT
* *
3208367 ACATATAA-AAATTTA-TAT
1 AAATATAATAAAATTATTAT
3208385 -AATATAA
1 AAATATAA
3208392 ATTATTAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 6 0.15
18 3 0.08
19 8 0.21
20 9 0.23
21 13 0.33
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
AAATATAATAAAATTATTAT
Found at i:3208386 original size:33 final size:32
Alignment explanation
Indices: 3208348--3208437 Score: 94
Period size: 33 Copynumber: 2.7 Consensus size: 32
3208338 ATTATTATAA
3208348 ATATAATATAAA-TATGTATACATATAAAAATTT
1 ATATAATATAAATTAT-TA-ACATATAAAAATTT
* * *
3208381 ATATAATATAAATTATTAATATATTAATATTT
1 ATATAATATAAATTATTAACATATAAAAATTT
3208413 ATATAAATATAATATT-TTAAACATA
1 ATAT-AATATAA-ATTATT-AACATA
3208438 ATTTATAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
32 15 0.31
33 23 0.47
34 11 0.22
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (32 bp):
ATATAATATAAATTATTAACATATAAAAATTT
Found at i:3208431 original size:18 final size:18
Alignment explanation
Indices: 3208364--3208431 Score: 56
Period size: 17 Copynumber: 4.0 Consensus size: 18
3208354 TATAAATATG
* * *
3208364 TATACATATAAAAATTTA
1 TATAAATATAATATTTTA
3208382 TAT-AATATAA-ATTATTA
1 TATAAATATAATATT-TTA
*
3208399 -ATATAT-TAATA-TTTA
1 TATAAATATAATATTTTA
3208414 TATAAATATAATATTTTA
1 TATAAATATAATATTTTA
3208432 AACATAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
15 3 0.08
16 13 0.32
17 17 0.43
18 7 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAAATATAATATTTTA
Found at i:3208433 original size:14 final size:15
Alignment explanation
Indices: 3208385--3208452 Score: 54
Period size: 14 Copynumber: 4.5 Consensus size: 15
3208375 AAATTTATAT
3208385 AATATAA-ATTATTA
1 AATATAATATTATTA
3208399 ATATATTAATATTTATATA
1 A-ATA-TAATA-TTAT-TA
3208418 AATATAATATT-TTA
1 AATATAATATTATTA
*
3208432 AACATAAT-TTA-TA
1 AATATAATATTATTA
3208445 ATATATAA
1 A-ATATAA
3208453 ATATAATACA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
13 5 0.11
14 15 0.33
15 4 0.09
16 5 0.11
17 6 0.13
18 7 0.16
19 3 0.07
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATAATATTATTA
Found at i:3209273 original size:2 final size:2
Alignment explanation
Indices: 3209266--3209299 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3209256 TTTGGTTCAG
*
3209266 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3209300 GACAAGTTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3212188 original size:17 final size:17
Alignment explanation
Indices: 3212166--3212201 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
3212156 TTGAGTTCCG
3212166 TTACTTGTTACGTGATT
1 TTACTTGTTACGTGATT
3212183 TTACTTGTTACGTGATT
1 TTACTTGTTACGTGATT
3212200 TT
1 TT
3212202 TTTGAGGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.56
Consensus pattern (17 bp):
TTACTTGTTACGTGATT
Found at i:3215889 original size:3 final size:3
Alignment explanation
Indices: 3215881--3215926 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3215871 GAAAAGGACC
3215881 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3215927 AAGTGCTGCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3220867 original size:87 final size:90
Alignment explanation
Indices: 3220713--3220890 Score: 245
Period size: 87 Copynumber: 2.0 Consensus size: 90
3220703 AACTCATTAC
*
3220713 GGTCGACAAAAAAACAGAACGAAAGAAAGAAAGATGACGGCACCCGGCAAGAAATCGGTAATTGT
1 GGTCGACAAAAAAACAGAACGAAAGAAAGAAAGACGACGG-ACCCGGCAAGAAATCGGTAATTGT
3220778 TAGGCACGTGTTTGCGGAAGATTTAG
65 TAGGCACGTGTTTGCGGAAGATTTAG
* * * * *
3220804 GGTCGGCAAAAAAACAGAACGAAAGAAAG-ACGACGAC-G-CCTGGTAAGAAATCGGTAGTTGTT
1 GGTCGACAAAAAAACAGAACGAAAGAAAGAAAGACGACGGACCCGGCAAGAAATCGGTAATTGTT
* * *
3220866 AGTCAGGTGTTTGCGGAAGGTTTAG
66 AGGCACGTGTTTGCGGAAGATTTAG
3220891 AGCGTGAGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
87 43 0.55
89 1 0.01
90 6 0.08
91 28 0.36
ACGTcount: A:0.37, C:0.15, G:0.30, T:0.18
Consensus pattern (90 bp):
GGTCGACAAAAAAACAGAACGAAAGAAAGAAAGACGACGGACCCGGCAAGAAATCGGTAATTGTT
AGGCACGTGTTTGCGGAAGATTTAG
Found at i:3221737 original size:41 final size:41
Alignment explanation
Indices: 3221680--3221761 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
3221670 AGTATCAGCT
3221680 TGAAACACCAATTTACCTTTAAGAGCTTCATCAGGTGCCAG
1 TGAAACACCAATTTACCTTTAAGAGCTTCATCAGGTGCCAG
*
3221721 TGAAACACCAATTTACCTTTGAGAGCTTCATCAGGTGCCAG
1 TGAAACACCAATTTACCTTTAAGAGCTTCATCAGGTGCCAG
3221762 CCAGCAGGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
TGAAACACCAATTTACCTTTAAGAGCTTCATCAGGTGCCAG
Found at i:3222482 original size:15 final size:15
Alignment explanation
Indices: 3222462--3222490 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3222452 TAACCATTTC
3222462 ACAAAAAAAAAAAAA
1 ACAAAAAAAAAAAAA
3222477 ACAAAAAAAAAAAA
1 ACAAAAAAAAAAAA
3222491 GCTCTCTGTC
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:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAAAAAAAAAAAA
Found at i:3222484 original size:13 final size:13
Alignment explanation
Indices: 3222466--3222490 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3222456 CATTTCACAA
3222466 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
3222479 AAAAAAAAAAAA
1 AAAAAAAAAAAA
3222491 GCTCTCTGTC
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:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:3229328 original size:3 final size:3
Alignment explanation
Indices: 3229320--3229360 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3229310 TCACATAACT
3229320 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3229361 GAGTTTATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3230014 original size:21 final size:21
Alignment explanation
Indices: 3229990--3230045 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
3229980 AAAATTATTA
3229990 ATTTATTAATAATTTTTTTTT
1 ATTTATTAATAATTTTTTTTT
* *
3230011 ATTTTTTAA-AATATATTTTTT
1 ATTTATTAATAAT-TTTTTTTT
3230032 A-TTA--AATAATTTTT
1 ATTTATTAATAATTTTT
3230046 GATGTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 5 0.17
19 3 0.10
20 5 0.17
21 16 0.55
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTATTAATAATTTTTTTTT
Found at i:3231142 original size:16 final size:15
Alignment explanation
Indices: 3231098--3231146 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
3231088 TTTAACTTAA
3231098 ATTTTA-AAAATATAT
1 ATTTTATAAAA-ATAT
3231113 ATTTT-T-AAAA-AT
1 ATTTTATAAAAATAT
3231125 ATTTTATAAAAGATAT
1 ATTTTATAAAA-ATAT
3231141 ATTTTA
1 ATTTTA
3231147 ATAATTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 7 0.24
13 2 0.07
14 6 0.21
15 6 0.21
16 8 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTTTATAAAAATAT
Found at i:3236061 original size:34 final size:34
Alignment explanation
Indices: 3236012--3236077 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
3236002 TATCTAGGGT
* *
3236012 TTTAAATTTTGTAAATAAGTATTAATTTTAGCTG
1 TTTAAATTTTATAAATAAGTATTAATCTTAGCTG
*
3236046 TTTAGATTTTATAAATAAGTATTAATCTTAGC
1 TTTAAATTTTATAAATAAGTATTAATCTTAGC
3236078 CGTCTATTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (34 bp):
TTTAAATTTTATAAATAAGTATTAATCTTAGCTG
Found at i:3236289 original size:18 final size:19
Alignment explanation
Indices: 3236268--3236312 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
3236258 TTTAAATTTT
3236268 TAAAAATTAA-TTTAAATA
1 TAAAAATTAATTTTAAATA
* *
3236286 TAAAAAATAATTTTTAAATT
1 TAAAAATTAA-TTTTAAATA
3236306 TAAAAAT
1 TAAAAAT
3236313 GATGTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAATTAATTTTAAATA
Found at i:3242557 original size:3 final size:3
Alignment explanation
Indices: 3242549--3242575 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3242539 AGAACGTCCC
3242549 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3242576 GCTAATTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3243994 original size:2 final size:2
Alignment explanation
Indices: 3243987--3244018 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3243977 CCAATGCAAC
3243987 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3244019 GCTTTTCTGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3244205 original size:2 final size:2
Alignment explanation
Indices: 3244200--3244226 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3244190 CTGAAAAAAA
3244200 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3244227 ATTAAATGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3244637 original size:27 final size:26
Alignment explanation
Indices: 3244607--3244665 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
3244597 ATTTATATTA
*
3244607 TATATAAATTTTAATATATTAATA-AAT
1 TATATAAATATTAAT-T-TTAATACAAT
*
3244634 TATAT-AATATTAATTTTAATACATT
1 TATATAAATATTAATTTTAATACAAT
3244659 TATATAA
1 TATATAA
3244666 TCTTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 6 0.21
25 8 0.29
26 9 0.32
27 5 0.18
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
TATATAAATATTAATTTTAATACAAT
Found at i:3244682 original size:25 final size:25
Alignment explanation
Indices: 3244607--3244676 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
3244597 ATTTATATTA
* *
3244607 TATATAAATTTTAATATATTAATA-AAT
1 TATAT-AATATTAAT-T-TTAATACATT
3244634 TATATAATATTAATTTTAATACATT
1 TATATAATATTAATTTTAATACATT
* *
3244659 TATATAATCTTATTTTTA
1 TATATAATATTAATTTTA
3244677 TAACATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
24 6 0.16
25 19 0.50
26 8 0.21
27 5 0.13
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATAATATTAATTTTAATACATT
Found at i:3244910 original size:23 final size:22
Alignment explanation
Indices: 3244884--3244969 Score: 75
Period size: 19 Copynumber: 4.3 Consensus size: 22
3244874 TCATATGCTG
3244884 TTATATTTAAATTATATTATATA
1 TTATA-TTAAATTATATTATATA
*
3244907 TTATA-TAAATT-T-TAATATA
1 TTATATTAAATTATATTATATA
3244926 TTA-A-TAAATT-TATTATATA
1 TTATATTAAATTATATTATATA
3244945 -TATATT-AA-TATATT-TATA
1 TTATATTAAATTATATTATATA
*
3244963 TAATATT
1 TTATATT
3244970 TTAATTATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 14
0.76 0.04 0.19
Matches are distributed among these distances:
18 15 0.27
19 27 0.49
20 2 0.04
21 6 0.11
23 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTATATTAAATTATATTATATA
Found at i:3244937 original size:17 final size:19
Alignment explanation
Indices: 3244902--3244978 Score: 71
Period size: 18 Copynumber: 4.4 Consensus size: 19
3244892 AAATTATATT
3244902 ATATATTATATAAATTTTA
1 ATATATTATATAAATTTTA
3244921 ATATATTA-ATAAA-TTT-
1 ATATATTATATAAATTTTA
*
3244937 AT-TA-TATAT--ATATTA
1 ATATATTATATAAATTTTA
3244952 ATATATTTATATAATATTTTA
1 ATATA-TTATATAA-ATTTTA
3244973 AT-TATT
1 ATATATT
3244979 TTTATGTAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
13 1 0.02
14 4 0.09
15 6 0.13
16 4 0.09
17 3 0.06
18 10 0.21
19 10 0.21
20 2 0.04
21 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATATTATATAAATTTTA
Found at i:3245450 original size:2 final size:2
Alignment explanation
Indices: 3245443--3245469 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3245433 TTTATTCTAT
3245443 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3245470 GACCCACAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3251892 original size:37 final size:37
Alignment explanation
Indices: 3251815--3251885 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
3251805 GTTTATCATT
* ** *
3251815 TTAATTTCAGATCAATTAGGTTTAACACTCATATTAA
1 TTAATTTCAAATCAATTAAATTTAACACTCAAATTAA
* *
3251852 TTAATTTCAAATCAATTAAATTTAATACTTAAAT
1 TTAATTTCAAATCAATTAAATTTAACACTCAAAT
3251886 ATATTAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (37 bp):
TTAATTTCAAATCAATTAAATTTAACACTCAAATTAA
Found at i:3252008 original size:27 final size:27
Alignment explanation
Indices: 3251978--3252031 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3251968 TAACATCGAA
*
3251978 TTTAAATTTAAAT-AAATTAATTAAATT
1 TTTAAATTCAAATAAAATTAA-TAAATT
3252005 TTTAAATTCAAATCAAAATTAATAAAT
1 TTTAAATTCAAAT-AAAATTAATAAAT
3252032 CTAAATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 12 0.50
28 5 0.21
29 7 0.29
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (27 bp):
TTTAAATTCAAATAAAATTAATAAATT
Found at i:3253582 original size:2 final size:2
Alignment explanation
Indices: 3253575--3253618 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3253565 TATTCATTCC
3253575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3253617 AT
1 AT
3253619 GTTAGGAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3254199 original size:2 final size:2
Alignment explanation
Indices: 3254192--3254217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3254182 TAGATTGTTC
3254192 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
3254218 TTTAGTTTCA
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:3258484 original size:23 final size:20
Alignment explanation
Indices: 3258460--3258524 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 20
3258450 TAAAATTTTA
3258460 AAAAATATATAATATTTATATT
1 AAAAATAT-TAATA-TTATATT
3258482 AAAAATATTACATCAATTATATTT
1 AAAAATATTA-AT--ATTATA-TT
3258506 AAAAATATT-ATATTATATT
1 AAAAATATTAATATTATATT
3258525 TTTTATATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
19 2 0.05
20 6 0.15
21 2 0.05
22 12 0.31
23 5 0.13
24 12 0.31
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAAATATTAATATTATATT
Found at i:3258529 original size:23 final size:24
Alignment explanation
Indices: 3258456--3258529 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
3258446 ACATTAAAAT
3258456 TTTAAAAA-A-TATATAATATTTA
1 TTTAAAAATATTATATAATATTTA
* *
3258478 TATTAAAAATATTACATCAAT-TATA
1 T-TTAAAAATATTATAT-AATATTTA
*
3258503 TTTAAAAATATTATATTATATTT-
1 TTTAAAAATATTATATAATATTTA
3258526 TTTA
1 TTTA
3258530 TATTATTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.02
23 13 0.31
24 17 0.40
25 8 0.19
26 3 0.07
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (24 bp):
TTTAAAAATATTATATAATATTTA
Found at i:3258543 original size:11 final size:10
Alignment explanation
Indices: 3258510--3258551 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
3258500 ATATTTAAAA
*
3258510 ATATTATATT
1 ATATTATTTT
3258520 ATATT-TTTT
1 ATATTATTTT
3258529 ATATTATTTT
1 ATATTATTTT
3258539 CATATTTATTTT
1 -ATA-TTATTTT
3258551 A
1 A
3258552 AGTATTGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
9 8 0.29
10 9 0.32
11 4 0.14
12 7 0.25
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
ATATTATTTT
Found at i:3261655 original size:2 final size:2
Alignment explanation
Indices: 3261648--3261688 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3261638 TGGACACGCA
3261648 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3261689 AGGTTTCGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3263554 original size:23 final size:25
Alignment explanation
Indices: 3263519--3263568 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
3263509 CAATGTAATA
* * *
3263519 AAAAATGATTTGATATGAT-TATTT
1 AAAAATGAATTGAAATAATATATTT
3263543 AAAAAT-AATTGAAATAATATATTT
1 AAAAATGAATTGAAATAATATATTT
3263567 AA
1 AA
3263569 TATTATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (25 bp):
AAAAATGAATTGAAATAATATATTT
Found at i:3265167 original size:24 final size:23
Alignment explanation
Indices: 3265127--3265171 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
3265117 ATAGTTTTAT
3265127 ATATTTTTAATTAATATTTAATA
1 ATATTTTTAATTAATATTTAATA
3265150 ATATTATTT-ATTATATATTTAA
1 ATATT-TTTAATTA-ATATTTAA
3265172 ATTTTCATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATATTTTTAATTAATATTTAATA
Found at i:3267149 original size:51 final size:51
Alignment explanation
Indices: 3267073--3267174 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
3267063 AAATATTACA
*
3267073 TTAATTGAATTAATATTCTATATGTCCCATTGAATCTTATTTAGAAAGTTT
1 TTAATTAAATTAATATTCTATATGTCCCATTGAATCTTATTTAGAAAGTTT
3267124 TTAATTAAATTAATATTCTATATGTCCCATTGAATCTTATTTAGAAAGTTT
1 TTAATTAAATTAATATTCTATATGTCCCATTGAATCTTATTTAGAAAGTTT
3267175 GAGGTTAGTG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.47
Consensus pattern (51 bp):
TTAATTAAATTAATATTCTATATGTCCCATTGAATCTTATTTAGAAAGTTT
Found at i:3268804 original size:2 final size:2
Alignment explanation
Indices: 3268797--3268839 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3268787 TAGAGGTAAA
*
3268797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3268839 A
1 A
3268840 AATCTTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3270083 original size:38 final size:39
Alignment explanation
Indices: 3270032--3270110 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
3270022 AAACTTTCTC
3270032 TTGTTCAAATTGCATA-TTGATAATCACAGCAAAATAGA
1 TTGTTCAAATTGCATATTTGATAATCACAGCAAAATAGA
*
3270070 TTGTTCAAATTGCATATTTGATAATCACGGCAAAATAGA
1 TTGTTCAAATTGCATATTTGATAATCACAGCAAAATAGA
3270109 TT
1 TT
3270111 CCAACTACAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 16 0.41
39 23 0.59
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (39 bp):
TTGTTCAAATTGCATATTTGATAATCACAGCAAAATAGA
Found at i:3278320 original size:2 final size:2
Alignment explanation
Indices: 3278313--3278347 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3278303 GGGTGAGTTT
3278313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3278348 GAAATATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3278493 original size:6 final size:6
Alignment explanation
Indices: 3278482--3278507 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3278472 TTTAATATTA
3278482 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
3278508 CATAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:3279403 original size:18 final size:18
Alignment explanation
Indices: 3279380--3279424 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3279370 GATCAACTGA
*
3279380 TTAATTAATTTAATAAAT
1 TTAATTAATTAAATAAAT
3279398 TTAATTAATTAAATAAAT
1 TTAATTAATTAAATAAAT
*
3279416 TAAATTAAT
1 TTAATTAAT
3279425 AATTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAATTAAATAAAT
Found at i:3282073 original size:16 final size:16
Alignment explanation
Indices: 3282052--3282091 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3282042 TTATTTAATT
3282052 TATTTTAAATTTAAAA
1 TATTTTAAATTTAAAA
* *
3282068 TTTTTTGAATTTAAAA
1 TATTTTAAATTTAAAA
3282084 TATTTTAA
1 TATTTTAA
3282092 GATATATATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATTTTAAATTTAAAA
Found at i:3282182 original size:3 final size:3
Alignment explanation
Indices: 3282174--3282206 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
3282164 AAATAAATTG
*
3282174 TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3282207 AGTAAGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3283247 original size:11 final size:11
Alignment explanation
Indices: 3283233--3283303 Score: 56
Period size: 11 Copynumber: 6.3 Consensus size: 11
3283223 CATAATTATT
3283233 TAATAAAAATA
1 TAATAAAAATA
3283244 TAATTTAAAAA-A
1 TAA--TAAAAATA
*
3283256 TAATTAAAATA
1 TAATAAAAATA
3283267 TGACATAAAAA-A
1 T-A-ATAAAAATA
**
3283279 TAATATTAATA
1 TAATAAAAATA
*
3283290 TAATATAAATA
1 TAATAAAAATA
3283301 TAA
1 TAA
3283304 AAACGTATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
10 10 0.20
11 20 0.41
12 7 0.14
13 12 0.24
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (11 bp):
TAATAAAAATA
Found at i:3283264 original size:23 final size:23
Alignment explanation
Indices: 3283233--3283298 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
3283223 CATAATTATT
**
3283233 TAATAAAAATATAATTTAAAAAA
1 TAATAAAAATATAACATAAAAAA
* *
3283256 TAATTAAAATATGACATAAAAAA
1 TAATAAAAATATAACATAAAAAA
** *
3283279 TAATATTAATATAATATAAA
1 TAATAAAAATATAACATAAA
3283299 TATAAAAACG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
TAATAAAAATATAACATAAAAAA
Found at i:3283631 original size:28 final size:29
Alignment explanation
Indices: 3283575--3283631 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
3283565 CTTTTTTTAA
* *
3283575 TTAACAAAGATTTATTAATAATTATTTAT
1 TTAACAAAGATTTATTAATAATAAATTAT
3283604 TTAA-AAA-ATTTATTAAATAATAAATTAT
1 TTAACAAAGATTTATT-AATAATAAATTAT
3283632 AATAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.28
28 14 0.56
29 4 0.16
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
TTAACAAAGATTTATTAATAATAAATTAT
Found at i:3284062 original size:2 final size:2
Alignment explanation
Indices: 3284055--3284088 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3284045 TTGCTTTGAG
3284055 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3284089 GTGTGTGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3284345 original size:2 final size:2
Alignment explanation
Indices: 3284338--3284365 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3284328 TGAACACCAA
3284338 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3284366 TAATTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3285442 original size:19 final size:22
Alignment explanation
Indices: 3285418--3285468 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
3285408 GCTCAAAATA
*
3285418 AATTTTT-TATTTTT-T-TTAT
1 AATTTTTAAATTTTTATATTAT
3285437 AATTTTTAAATTTTTATATTAT
1 AATTTTTAAATTTTTATATTAT
3285459 AATTTTTAAA
1 AATTTTTAAA
3285469 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 7 0.25
20 6 0.21
21 1 0.04
22 14 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
AATTTTTAAATTTTTATATTAT
Found at i:3287800 original size:475 final size:477
Alignment explanation
Indices: 3286907--3287847 Score: 1814
Period size: 475 Copynumber: 2.0 Consensus size: 477
3286897 AATTTGAAAG
3286907 CAAAGAATTTCTCAGTTTTAAAAAGTCATAAATGGTGCAAATGATTTAACGAACTCCTCTATCTT
1 CAAAGAATTTCTCAGTTTTAAAAAGTCATAAATGGTGCAAATGATTTAACGAACTCCTCTATCTT
*
3286972 GTTTCAAAACTTAAAAATTTAAAAAGGTTTTTAGAGCCCAACAACCAATTTATGCTCAAGATCCC
66 GTTTCAAAACTTAAAAATTTAAAAAGGTTTTTAGAGCCCAACAACCAATATATGCTCAAGATCCC
3287037 TTTCCTATTAAAAAGGGTTTTCATTTGCGCCATCGTTCAATTTCACTGGCAAACACGATTGTGTG
131 TTTCC--TTAAAAAGGGTTTTCATTTGCGCCATCGTTCAATTTCACTGGCAAACACGATTGTGTG
3287102 AAAGAAAGGATTTCCCAGTTTCCCAGTTCCCGAAACAGAGGAAGGGAAGATGGAGGAGAAGAGCA
194 AAAGAAAGGATTTCCCAGTTTCCCAGTTCCCGAAACAGAGGAAGGGAAGATGGAGGAGAAGAGCA
3287167 AAGTCCTGATATTAGGAGCAACGGGAAGATTAGGTTTCCATTTAGCCAAATTCAGCCTCCAATTC
259 AAGTCCTGATATTAGGAGCAACGGGAAGATTAGGTTTCCATTTAGCCAAATTCAGCCTCCAATTC
3287232 GGTCACCCCACTGTTATTCTTATCAGAGATTCCTGTTATACTGACCCCAACAAAGTTCAAAAACT
324 GGTCACCCCACTGTTATTCTTATCAGAGATTCCTGTTATACTGACCCCAACAAAGTTCAAAAACT
*
3287297 CAACTTTCTCTCCAATGCTGGTGCCATTCCCCTCAAGGTTACTTCTTTTGATC-TTTTTTTTTTT
389 CAACTTTCTCTCCAATGCTGGTGCCATTCCCCTCAAGGTTACTTCTTTTCATCTTTTTTTTTTTT
3287361 TTCGACTTCTTTTCGACTTCTTAT
454 TTCGACTTCTTTTCGACTTCTTAT
*
3287385 CAAAGAATTTCTCAGTTTTAAAGAGTCATAAATGGTGCAAATGATTTAACGAACTCCTCTATCTT
1 CAAAGAATTTCTCAGTTTTAAAAAGTCATAAATGGTGCAAATGATTTAACGAACTCCTCTATCTT
3287450 GTTTCAAAACTTAAAAATTTAAAAAGGTTTTTAGAGCCCAACAACCAATATATGCTCAAGATCCC
66 GTTTCAAAACTTAAAAATTTAAAAAGGTTTTTAGAGCCCAACAACCAATATATGCTCAAGATCCC
3287515 TTTCC-TAAAAAGGGTTTTCATTTGCGCCATCGTTCAATTTCACTGGCAAACACGATTGTGTGAA
131 TTTCCTTAAAAAGGGTTTTCATTTGCGCCATCGTTCAATTTCACTGGCAAACACGATTGTGTGAA
*
3287579 AGAAAGGGTTTCCCAGTTTCCCAGTTCCCGAAACAGAGGAAGGGAAGATGGAGGAGAAGAGCAAA
196 AGAAAGGATTTCCCAGTTTCCCAGTTCCCGAAACAGAGGAAGGGAAGATGGAGGAGAAGAGCAAA
3287644 GTCCTGATATTAGGAGCAACGGGAAGATTAGGTTTCCATTTAGCCAAATTCAGCCTCCAATTCGG
261 GTCCTGATATTAGGAGCAACGGGAAGATTAGGTTTCCATTTAGCCAAATTCAGCCTCCAATTCGG
3287709 TCACCCCACTGTTATTCTTATCAGAGATTCCTGTTATACTGACCCCAACAAAGTTCAAAAACTCA
326 TCACCCCACTGTTATTCTTATCAGAGATTCCTGTTATACTGACCCCAACAAAGTTCAAAAACTCA
3287774 ACTTTCTCTCCAATGCTGGTGCCATTCCCCTCAAGGTTACTTCTTTTCATCTTTTTTTTTTTTTT
391 ACTTTCTCTCCAATGCTGGTGCCATTCCCCTCAAGGTTACTTCTTTTCATCTTTTTTTTTTTTTT
3287839 CGACTTCTT
456 CGACTTCTT
3287848 ATTTATGATT
Statistics
Matches: 458, Mismatches: 4, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
475 303 0.66
476 22 0.05
478 133 0.29
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (477 bp):
CAAAGAATTTCTCAGTTTTAAAAAGTCATAAATGGTGCAAATGATTTAACGAACTCCTCTATCTT
GTTTCAAAACTTAAAAATTTAAAAAGGTTTTTAGAGCCCAACAACCAATATATGCTCAAGATCCC
TTTCCTTAAAAAGGGTTTTCATTTGCGCCATCGTTCAATTTCACTGGCAAACACGATTGTGTGAA
AGAAAGGATTTCCCAGTTTCCCAGTTCCCGAAACAGAGGAAGGGAAGATGGAGGAGAAGAGCAAA
GTCCTGATATTAGGAGCAACGGGAAGATTAGGTTTCCATTTAGCCAAATTCAGCCTCCAATTCGG
TCACCCCACTGTTATTCTTATCAGAGATTCCTGTTATACTGACCCCAACAAAGTTCAAAAACTCA
ACTTTCTCTCCAATGCTGGTGCCATTCCCCTCAAGGTTACTTCTTTTCATCTTTTTTTTTTTTTT
CGACTTCTTTTCGACTTCTTAT
Found at i:3298142 original size:19 final size:20
Alignment explanation
Indices: 3298120--3298161 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3298110 TTATCTACCA
3298120 TGAA-AATTAAAAAAAAAAT
1 TGAATAATTAAAAAAAAAAT
* *
3298139 TGAATGATTAAAAAAAAAGT
1 TGAATAATTAAAAAAAAAAT
3298159 TGA
1 TGA
3298162 GATCTTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TGAATAATTAAAAAAAAAAT
Found at i:3298170 original size:21 final size:20
Alignment explanation
Indices: 3298125--3298176 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3298115 TACCATGAAA
*
3298125 ATTAAAAAAAAAATTGAATG
1 ATTAAAAAAAAAATTGAATC
*
3298145 ATTAAAAAAAAAGTTGAGATC
1 ATTAAAAAAAAAATTGA-ATC
*
3298166 TTTAAGAAAAA
1 ATTAA-AAAAA
3298177 TCAATATAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 16 0.59
21 6 0.22
22 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.25
Consensus pattern (20 bp):
ATTAAAAAAAAAATTGAATC
Found at i:3298888 original size:24 final size:26
Alignment explanation
Indices: 3298828--3298891 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 26
3298818 TTCTTATGTG
* *
3298828 AATTCATAAAATATTTAAATATTTATT
1 AATTTATAAAA-ATATAAATATTTATT
3298855 AA-TTAT-AAAATATAAAT-TTT-TT
1 AATTTATAAAAATATAAATATTTATT
3298877 AATTTATAAAAATAT
1 AATTTATAAAAATAT
3298892 TTTAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 7 0.21
24 14 0.42
25 3 0.09
26 3 0.09
27 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTTATAAAAATATAAATATTTATT
Found at i:3299888 original size:22 final size:23
Alignment explanation
Indices: 3299843--3299892 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
3299833 ATTAATTTAG
*
3299843 TTAATATATTTAGGAAAATAAATT
1 TTAAAATATTTA-GAAAATAAATT
*
3299867 TTAAAATATTTA-AAAATTAATT
1 TTAAAATATTTAGAAAATAAATT
3299889 TTAA
1 TTAA
3299893 TATTAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.54
24 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TTAAAATATTTAGAAAATAAATT
Found at i:3299957 original size:19 final size:19
Alignment explanation
Indices: 3299916--3299958 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3299906 AAATAATTAA
*
3299916 TAAAAATATATATTTAATT
1 TAAAAATATATATTTAATG
*
3299935 TAAAAATATGAT-TTTTATG
1 TAAAAATAT-ATATTTAATG
3299954 TAAAA
1 TAAAA
3299959 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
TAAAAATATATATTTAATG
Found at i:3300237 original size:3 final size:3
Alignment explanation
Indices: 3300229--3300256 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3300219 TATGAAAATT
3300229 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3300257 GATGTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3304792 original size:23 final size:21
Alignment explanation
Indices: 3304758--3304806 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
3304748 AATAAAAAAT
* *
3304758 ATTATAAATATTTAATTTTAA
1 ATTATAAATATTAAATATTAA
3304779 ATTATAAATTTATTAAATATTAA
1 ATTATAAA--TATTAAATATTAA
*
3304802 TTTAT
1 ATTAT
3304807 TACACAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 8 0.35
23 15 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTATAAATATTAAATATTAA
Found at i:3304805 original size:15 final size:15
Alignment explanation
Indices: 3304762--3304808 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
3304752 AAAAATATTA
3304762 TAAATATTTAA-TT-T
1 TAAATA-TTAATTTAT
*
3304776 TAAATTATAAATTTAT
1 TAAA-TATTAATTTAT
3304792 TAAATATTAATTTAT
1 TAAATATTAATTTAT
3304807 TA
1 TA
3304809 CACAAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 7 0.25
15 16 0.57
16 5 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAAATATTAATTTAT
Found at i:3318753 original size:21 final size:25
Alignment explanation
Indices: 3318714--3318785 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 25
3318704 ATTTTTTTTA
*
3318714 TTATTAATATTTATAATTAAT-AT-T
1 TTATT-ATATGTATAATTAATAATAT
3318738 TTATTATA-GT-TAATTATAATAATAT
1 TTATTATATGTATAA-T-TAATAATAT
3318763 TTATTATATGTATAATT-ATAATA
1 TTATTATATGTATAATTAATAATA
3318786 AATATGATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
21 3 0.07
22 2 0.05
23 7 0.17
24 13 0.32
25 10 0.24
26 3 0.07
27 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
TTATTATATGTATAATTAATAATAT
Done.