Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold258
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: 5730937
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 24 of 25
Found at i:5548899 original size:55 final size:55
Alignment explanation
Indices: 5548833--5548946 Score: 201
Period size: 55 Copynumber: 2.1 Consensus size: 55
5548823 AGGGCATTGT
*
5548833 AATTCTCTTCCAATGTCCTAAGAATATAGCATGATTTTAGCTCAGTTTCGAACTC
1 AATTCTCTTCCAATGTCCTAAGAATATAGCATGATTTTAGCTCAGTTTCAAACTC
* *
5548888 AATTCTCTTCCACTGTCCTAAGAATATCGCATGATTTTAGCTCAGTTTCAAACTC
1 AATTCTCTTCCAATGTCCTAAGAATATAGCATGATTTTAGCTCAGTTTCAAACTC
5548943 AATT
1 AATT
5548947 TCATCAATGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (55 bp):
AATTCTCTTCCAATGTCCTAAGAATATAGCATGATTTTAGCTCAGTTTCAAACTC
Found at i:5555852 original size:25 final size:25
Alignment explanation
Indices: 5555801--5555861 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
5555791 ATTTTTTTAT
*
5555801 TAATATTTAATATAATTAATTAGAA
1 TAATATTTAATATAATTAAATAGAA
* *
5555826 TAATATTTATTATATTTATAATA-AA
1 TAATATTTAATATAATTA-AATAGAA
* *
5555851 TATTATATAAT
1 TAATATTTAAT
5555862 TAAAAATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
25 26 0.90
26 3 0.10
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TAATATTTAATATAATTAAATAGAA
Found at i:5557061 original size:2 final size:2
Alignment explanation
Indices: 5557054--5557079 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5557044 CAAAACCTTG
5557054 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
5557080 GGATTTATTT
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:5557517 original size:14 final size:14
Alignment explanation
Indices: 5557498--5557530 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5557488 ATTCCAAAAC
5557498 TATATAGTTTTTTA
1 TATATAGTTTTTTA
5557512 TATATA-TTTTTTA
1 TATATAGTTTTTTA
5557525 -ATATAG
1 TATATAG
5557531 AATGTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 7 0.39
14 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
TATATAGTTTTTTA
Found at i:5558864 original size:19 final size:18
Alignment explanation
Indices: 5558842--5558891 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
5558832 ACATTAAAAT
*
5558842 TTATTAATTTAATTATTAA
1 TTATTAATTTAA-TATCAA
5558861 TTATTATATTTAATATCAA
1 TTATTA-ATTTAATATCAA
*
5558880 ATATTAATTTAA
1 TTATTAATTTAA
5558892 ATAAAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 6 0.21
19 16 0.57
20 6 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATTAATTTAATATCAA
Found at i:5563428 original size:2 final size:2
Alignment explanation
Indices: 5563421--5563449 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5563411 AAAATCTTAT
5563421 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5563450 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5564462 original size:16 final size:16
Alignment explanation
Indices: 5564441--5564475 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5564431 ACTATCGATG
5564441 TTATTGACAAATATAA
1 TTATTGACAAATATAA
5564457 TTATTGACAAATATAA
1 TTATTGACAAATATAA
5564473 TTA
1 TTA
5564476 AAAGATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (16 bp):
TTATTGACAAATATAA
Found at i:5565029 original size:27 final size:28
Alignment explanation
Indices: 5564999--5565057 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
5564989 TTATTATTTA
*
5564999 AAATATTAAA-AATAATA-TTTCATAATT
1 AAATATTAAATAA-AATATTTTAATAATT
*
5565026 AAAT-TTAAATAAATTATTTTAATAATT
1 AAATATTAAATAAAATATTTTAATAATT
5565053 AAATA
1 AAATA
5565058 GTAATTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (28 bp):
AAATATTAAATAAAATATTTTAATAATT
Found at i:5567511 original size:13 final size:13
Alignment explanation
Indices: 5567495--5567522 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5567485 CTTTGTGCCT
5567495 GCATATCACAAGA
1 GCATATCACAAGA
5567508 GCATATCACAAGA
1 GCATATCACAAGA
5567521 GC
1 GC
5567523 CAGCTAAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.14
Consensus pattern (13 bp):
GCATATCACAAGA
Found at i:5569953 original size:2 final size:2
Alignment explanation
Indices: 5569946--5569981 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5569936 ATTAATGTGA
5569946 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
5569982 GAATGTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5573554 original size:22 final size:19
Alignment explanation
Indices: 5573504--5573556 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
5573494 AGTAATATTA
5573504 AATATATAATT-TTTATAT
1 AATATATAATTATTTATAT
* *
5573522 AATAAAAAATTATTTAATAT
1 AATATATAATTATTT-ATAT
5573542 ATATTATATAATTAT
1 A-A-TATATAATTAT
5573557 AAAATAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 9 0.33
19 3 0.11
20 5 0.19
21 1 0.04
22 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATATAATTATTTATAT
Found at i:5574163 original size:3 final size:3
Alignment explanation
Indices: 5574155--5574191 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5574145 AAGGACAGAG
5574155 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5574192 CGCCTATGGC
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:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5578794 original size:2 final size:2
Alignment explanation
Indices: 5578787--5578820 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5578777 TCATTAAACA
5578787 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
5578821 GTAACATATC
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:5583677 original size:2 final size:2
Alignment explanation
Indices: 5583666--5583717 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
5583656 GACATGCACA
5583666 AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
5583706 AA AG AG AG AG AG
1 AG AG AG AG AG AG
5583718 CGAGGAAGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5588097 original size:2 final size:2
Alignment explanation
Indices: 5588090--5588114 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5588080 ATCTTACATG
5588090 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 T
5588115 TTTAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5588657 original size:2 final size:2
Alignment explanation
Indices: 5588650--5588685 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5588640 ATGATGAATT
5588650 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
5588686 AGATTTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5590875 original size:9 final size:9
Alignment explanation
Indices: 5590863--5590930 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
5590853 TCATATTTTA
5590863 TAATTATAT
1 TAATTATAT
5590872 TAATTATA-
1 TAATTATAT
* *
5590880 TAAATATAA
1 TAATTATAT
5590889 T-ATATATTAT
1 TAAT-TA-TAT
* *
5590899 TAAATATAA
1 TAATTATAT
5590908 TATATTATAT
1 TA-ATTATAT
5590918 TAATTATACT
1 TAATTATA-T
5590928 TAA
1 TAA
5590931 ATAATATATT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
8 8 0.17
9 21 0.46
10 16 0.35
11 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (9 bp):
TAATTATAT
Found at i:5590887 original size:17 final size:18
Alignment explanation
Indices: 5590855--5590949 Score: 69
Period size: 17 Copynumber: 5.5 Consensus size: 18
5590845 TATATTTATC
* *
5590855 ATATTTTATAATTATATT
1 ATATTATATAAATATATT
5590873 A-ATTATATAAATATAATAT
1 ATATTATATAAATAT-AT-T
*
5590892 ATATTAT-TAAATATAAT
1 ATATTATATAAATATATT
5590909 ATATTATAT---TA-ATT
1 ATATTATATAAATATATT
*
5590923 ATACTTAAAT-AATATATT
1 ATA-TTATATAAATATATT
*
5590941 TTATTATAT
1 ATATTATAT
5590950 TTATAATTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
14 5 0.08
15 7 0.11
17 26 0.42
18 10 0.16
19 9 0.15
20 5 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATTATATAAATATATT
Found at i:5590895 original size:46 final size:46
Alignment explanation
Indices: 5590831--5590958 Score: 142
Period size: 46 Copynumber: 2.9 Consensus size: 46
5590821 TTTTAAAAAT
* *
5590831 TTAT-TAAATAT-GTATATATTTATCATATTTTATAATTATATTAA
1 TTATATAAATATAATATATATTTATTATATTTTATAATTATATTAA
* * *
5590875 TTATATAAATATAATATATA-TTATTAAATATAATATATTATATTAA
1 TTATATAAATATAATATATATTTATTATATTTTATA-ATTATATTAA
*
5590921 TTATACTTAA-ATAATATAT-TTTATTATA-TTTATAATTA
1 TTATA-TAAATATAATATATATTTATTATATTTTATAATTA
5590959 AAATTTTATA
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
44 8 0.11
45 22 0.31
46 37 0.53
47 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (46 bp):
TTATATAAATATAATATATATTTATTATATTTTATAATTATATTAA
Found at i:5590904 original size:19 final size:19
Alignment explanation
Indices: 5590874--5590925 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
5590864 AATTATATTA
5590874 ATTATATAAATATAATATAT
1 ATTAT-TAAATATAATATAT
5590894 ATTATTAAATATAATATAT
1 ATTATTAAATATAATATAT
*
5590913 -TATATTAATTATA
1 AT-TATTAAATATA
5590926 CTTAAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 24 0.80
20 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTATTAAATATAATATAT
Found at i:5590931 original size:29 final size:27
Alignment explanation
Indices: 5590896--5590976 Score: 76
Period size: 27 Copynumber: 2.9 Consensus size: 27
5590886 TAATATATAT
5590896 TATTAAATATAATATATTATATTAATTA
1 TATTAAA-ATAATATATTATATTAATTA
*
5590924 TACTT-AAATAATATATTTTATTATATTTA
1 TA-TTAAAATAATATATTATATTA-A-TTA
**
5590953 TAATTAAAATTTTATATT-TATTAA
1 T-ATTAAAATAATATATTATATTAA
5590977 ATATTAGATA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 15 0.33
28 6 0.13
29 13 0.29
30 11 0.24
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
TATTAAAATAATATATTATATTAATTA
Found at i:5590945 original size:27 final size:29
Alignment explanation
Indices: 5590844--5590960 Score: 87
Period size: 27 Copynumber: 3.9 Consensus size: 29
5590834 TTAAATATGT
* *
5590844 ATATATT-TATCATATTTTATAATTATATTA
1 ATATATTATATTATA-TTTATAATTA-AATA
* * * *
5590874 ATTATATAAATATAATATATATTATTAAATATA
1 A-TATAT-TATATTATATTTATAATT-AA-ATA
*
5590907 ATATATTATATTA-A-TTATACTTAAATA
1 ATATATTATATTATATTTATAATTAAATA
*
5590934 ATATATTTTATTATATTTATAATTAAA
1 ATATATTATATTATATTTATAATTAAA
5590961 ATTTTATATT
Statistics
Matches: 68, Mismatches: 12, Indels: 15
0.72 0.13 0.16
Matches are distributed among these distances:
27 15 0.22
28 3 0.04
29 15 0.22
30 2 0.03
31 10 0.15
32 13 0.19
33 10 0.15
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATATATTATATTATATTTATAATTAAATA
Found at i:5591467 original size:21 final size:21
Alignment explanation
Indices: 5591443--5591482 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5591433 AATTATAATG
* *
5591443 TTATTTTTTTAATTTATTTTT
1 TTATATTTTTAATATATTTTT
5591464 TTATATTTTTAATATATTT
1 TTATATTTTTAATATATTT
5591483 AAAAATACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATATTTTTAATATATTTTT
Found at i:5591471 original size:14 final size:13
Alignment explanation
Indices: 5591438--5591471 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5591428 TATAAAATTA
5591438 TAATGTTATTTTTT
1 TAAT-TTATTTTTT
5591452 TAATTTATTTTTT
1 TAATTTATTTTTT
5591465 TATATTT
1 TA-ATTT
5591472 TTAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TAATTTATTTTTT
Found at i:5591576 original size:22 final size:22
Alignment explanation
Indices: 5591536--5591577 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5591526 TTATTAAAAA
**
5591536 AATAAATAATTTCTTATAAATT
1 AATAAATAATTTCGCATAAATT
*
5591558 AATAATTAATTTCGCATAAA
1 AATAAATAATTTCGCATAAA
5591578 CATCATAAAA
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:0.50, C:0.07, G:0.02, T:0.40
Consensus pattern (22 bp):
AATAAATAATTTCGCATAAATT
Found at i:5591957 original size:21 final size:21
Alignment explanation
Indices: 5591932--5591976 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5591922 CAATAAGTAT
5591932 TTTAAT-TTATATATTATTAAA
1 TTTAATATTATA-ATTATTAAA
* *
5591953 TTTAATATTTTAATTATTATA
1 TTTAATATTATAATTATTAAA
5591974 TTT
1 TTT
5591977 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTAATATTATAATTATTAAA
Found at i:5591965 original size:29 final size:31
Alignment explanation
Indices: 5591924--5591990 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 31
5591914 TATAAATACA
5591924 ATAAGTATTTTAATT-TATATATTATT-AAATT
1 ATAA-TATTTTAATTAT-TATATTATTAAAATT
*
5591955 -TAATATTTTAATTATTATATTTTTAAAATT
1 ATAATATTTTAATTATTATATTATTAAAATT
5591985 ATAATA
1 ATAATA
5591991 AATAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 18 0.56
30 9 0.28
31 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (31 bp):
ATAATATTTTAATTATTATATTATTAAAATT
Found at i:5592141 original size:18 final size:18
Alignment explanation
Indices: 5592120--5592184 Score: 64
Period size: 18 Copynumber: 3.6 Consensus size: 18
5592110 ACATAATACA
5592120 TTAAT-ATTTTATTAATATT
1 TTAATAATTTT-TT-ATATT
*
5592139 TAAATAATTTTTTATATT
1 TTAATAATTTTTTATATT
*
5592157 TTAATCATTTTTTAT-TT
1 TTAATAATTTTTTATATT
5592174 GTT-ATAATTTT
1 -TTAATAATTTT
5592185 AAAAATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 9 0.22
18 20 0.50
19 6 0.15
20 5 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TTAATAATTTTTTATATT
Found at i:5592234 original size:21 final size:20
Alignment explanation
Indices: 5592196--5592233 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5592186 AAAATATAAA
*
5592196 ATTAAAAAATTAAATTTTAT
1 ATTAAAAAACTAAATTTTAT
5592216 ATTACAAAAACT-AATTTT
1 ATTA-AAAAACTAAATTTT
5592234 TTTTTACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTAAAAAACTAAATTTTAT
Found at i:5592296 original size:30 final size:28
Alignment explanation
Indices: 5592260--5592321 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
5592250 AAAATTACTA
* *
5592260 ATAAATTTTTACCATCAAATTTTATATAAT
1 ATAAATTATTA-CATCAAAATTTATA-AAT
* *
5592290 ATAAATTATTATATTAAAATTTATAAAT
1 ATAAATTATTACATCAAAATTTATAAAT
5592318 ATAA
1 ATAA
5592322 TATATTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.25
29 11 0.39
30 10 0.36
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (28 bp):
ATAAATTATTACATCAAAATTTATAAAT
Found at i:5592327 original size:28 final size:29
Alignment explanation
Indices: 5592280--5592349 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 29
5592270 ACCATCAAAT
5592280 TTTATATAATATAA-ATTATTAT-ATTAAAA
1 TTTATA-AATATAATATTATTATCA-TAAAA
*
5592309 TTTATAAATATAATA-TATTTTCATAAAA
1 TTTATAAATATAATATTATTATCATAAAA
5592337 -TTAT-AATATAATA
1 TTTATAAATATAATA
5592350 ACATAATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 9 0.24
27 4 0.11
28 17 0.45
29 8 0.21
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTATAAATATAATATTATTATCATAAAA
Found at i:5593358 original size:2 final size:2
Alignment explanation
Indices: 5593351--5593380 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5593341 CAAGAGGTTC
5593351 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5593381 GGCTGTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5596825 original size:15 final size:15
Alignment explanation
Indices: 5596805--5596835 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5596795 AAAATTTATT
*
5596805 AAATAATATTTTTAA
1 AAATAATAATTTTAA
5596820 AAATAATAATTTTAA
1 AAATAATAATTTTAA
5596835 A
1 A
5596836 TTTGAATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATAATAATTTTAA
Found at i:5597326 original size:2 final size:2
Alignment explanation
Indices: 5597321--5597345 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5597311 TAAAATTTTA
5597321 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 A
5597346 AAAGCATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5597941 original size:30 final size:31
Alignment explanation
Indices: 5597890--5597961 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
5597880 ATATTTAAAT
5597890 TTAATTATAAA-AATAAAAATAAAA-TTTTAA
1 TTAATT-TAAATAATAAAAATAAAATTTTTAA
*
5597920 TATCATTTAAATAAT-AAAATAAAATTTTTAA
1 T-TAATTTAAATAATAAAAATAAAATTTTTAA
5597951 TTAATTTAAAT
1 TTAATTTAAAT
5597962 CTGACTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
30 23 0.62
31 14 0.38
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (31 bp):
TTAATTTAAATAATAAAAATAAAATTTTTAA
Found at i:5606719 original size:21 final size:21
Alignment explanation
Indices: 5606693--5606736 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5606683 ATGTGATATA
*
5606693 AAAATATATA-ATTAATTAAAT
1 AAAATAAATATATT-ATTAAAT
5606714 AAAATAAATATATTATTAAAT
1 AAAATAAATATATTATTAAAT
5606735 AA
1 AA
5606737 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAATAAATATATTATTAAAT
Found at i:5606908 original size:34 final size:35
Alignment explanation
Indices: 5606870--5606943 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 35
5606860 TAATTATTTC
5606870 ATTTAATATGAT-AATATAATATGA-TTATATGTTT
1 ATTTAATATGATAAATATAATAT-ACTTATATGTTT
* * *
5606904 ATTT-ATATGGTAAATGTAATATACTTATATTTTT
1 ATTTAATATGATAAATATAATATACTTATATGTTT
*
5606938 ACTTAA
1 ATTTAA
5606944 ATAAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
33 7 0.21
34 25 0.76
35 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (35 bp):
ATTTAATATGATAAATATAATATACTTATATGTTT
Found at i:5613067 original size:2 final size:2
Alignment explanation
Indices: 5613060--5613090 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5613050 TTGTTTTAAG
5613060 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
5613091 CTTCATTATT
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:5615256 original size:22 final size:23
Alignment explanation
Indices: 5615224--5615266 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
5615214 GTCTTTCGTA
5615224 ATTTTTAAAAATATTT-TATTTTT
1 ATTTTTAAAAAT-TTTATATTTTT
5615247 ATTTTT-AAAATTTTATATTT
1 ATTTTTAAAAATTTTATATTT
5615267 ATTCATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 10 0.53
23 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTTAAAAATTTTATATTTTT
Found at i:5616224 original size:19 final size:19
Alignment explanation
Indices: 5616197--5616235 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
5616187 TATTTATATT
*
5616197 TAAAAATAACT-TTTAAAG
1 TAAAAATAAATGTTTAAAG
5616215 TAAAATATAAATGTTTAAAG
1 TAAAA-ATAAATGTTTAAAG
5616235 T
1 T
5616236 CATCAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (19 bp):
TAAAAATAAATGTTTAAAG
Found at i:5617334 original size:26 final size:26
Alignment explanation
Indices: 5617303--5617368 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
5617293 TTAATTTTTT
* *
5617303 TTAATATT-TATAAATATTTAATTAAA
1 TTAATATTACATAAAT-TTAAATTAAA
5617329 TTAATAATTACATAAATTTAAATTAAA
1 TTAAT-ATTACATAAATTTAAATTAAA
*
5617356 TT-ATATTAAATAA
1 TTAATATTACATAA
5617369 TTATTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 8 0.23
26 7 0.20
27 14 0.40
28 6 0.17
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAATATTACATAAATTTAAATTAAA
Found at i:5617492 original size:11 final size:11
Alignment explanation
Indices: 5617453--5617549 Score: 51
Period size: 11 Copynumber: 9.2 Consensus size: 11
5617443 AAATTATAAA
5617453 AATATAAA-AT
1 AATATAAATAT
* *
5617463 AAAATAAAACAT
1 AATAT-AAATAT
*
5617475 AAAATAAATAT
1 AATATAAATAT
5617486 AATATAAA-A-
1 AATATAAATAT
* *
5617495 AA-ATAATTAA
1 AATATAAATAT
* *
5617505 AACAT-AATGT
1 AATATAAATAT
* *
5617515 TATATAAAAAT
1 AATATAAATAT
*
5617526 AATATAAACAT
1 AATATAAATAT
*
5617537 AACATAAATAT
1 AATATAAATAT
5617548 AA
1 AA
5617550 AACGTATTTA
Statistics
Matches: 66, Mismatches: 15, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
8 4 0.06
9 3 0.05
10 12 0.18
11 40 0.61
12 7 0.11
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (11 bp):
AATATAAATAT
Found at i:5617511 original size:19 final size:19
Alignment explanation
Indices: 5617458--5617511 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
5617448 ATAAAAATAT
5617458 AAAATAAAATAAAACAT---
1 AAAAT-AAATAAAACATAAA
* *
5617475 AAAATAAATATAATATAAA
1 AAAATAAATAAAACATAAA
*
5617494 AAAATAATTAAAACATAA
1 AAAATAAATAAAACATAA
5617512 TGTTATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
16 9 0.31
17 5 0.17
19 15 0.52
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATAAATAAAACATAAA
Found at i:5617861 original size:20 final size:19
Alignment explanation
Indices: 5617833--5617871 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
5617823 TAAAATACTA
*
5617833 AATAAAAATAGCATGAATAT
1 AATAAAAATA-CATAAATAT
*
5617853 AATATAAATACATAAATAT
1 AATAAAAATACATAAATAT
5617872 GTCAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (19 bp):
AATAAAAATACATAAATAT
Found at i:5618109 original size:21 final size:22
Alignment explanation
Indices: 5618083--5618144 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
5618073 TACGATGATC
*
5618083 AAATTATG-TAAAAAATAAAAT
1 AAATTAAGATAAAAAATAAAAT
*
5618104 AAATTAAGATAAAATAT-AAAT
1 AAATTAAGATAAAAAATAAAAT
*
5618125 ACAACATAA-ATAAAAAATAA
1 A-AA-TTAAGATAAAAAATAA
5618145 TTAAAACACA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 12 0.36
22 17 0.52
23 4 0.12
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.24
Consensus pattern (22 bp):
AAATTAAGATAAAAAATAAAAT
Found at i:5618144 original size:11 final size:11
Alignment explanation
Indices: 5618091--5618173 Score: 51
Period size: 11 Copynumber: 7.4 Consensus size: 11
5618081 TCAAATTATG
5618091 TAAAAAATAAA
1 TAAAAAATAAA
* *
5618102 -ATAAATTAAGA
1 TAAAAAATAA-A
*
5618113 TAAAATATAAA
1 TAAAAAATAAA
* *
5618124 TACAACATAAA
1 TAAAAAATAAA
*
5618135 TAAAAAATAAT
1 TAAAAAATAAA
* *
5618146 TAAAACACAATA
1 TAAAAAATAA-A
*
5618158 CAAAAAATAATA
1 TAAAAAATAA-A
5618170 TAAA
1 TAAA
5618174 CATGATACGA
Statistics
Matches: 52, Mismatches: 17, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
10 7 0.13
11 27 0.52
12 18 0.35
ACGTcount: A:0.71, C:0.06, G:0.01, T:0.22
Consensus pattern (11 bp):
TAAAAAATAAA
Found at i:5618152 original size:22 final size:23
Alignment explanation
Indices: 5618112--5618173 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
5618102 ATAAATTAAG
* * * *
5618112 ATAAAATATAAATACAACATAA-
1 ATAAAAAATAATTAAAACACAAT
5618134 ATAAAAAATAATTAAAACACAAT
1 ATAAAAAATAATTAAAACACAAT
*
5618157 ACAAAAAATAATATAAA
1 ATAAAAAATAAT-TAAA
5618174 CATGATACGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 18 0.55
23 11 0.33
24 4 0.12
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (23 bp):
ATAAAAAATAATTAAAACACAAT
Found at i:5618481 original size:20 final size:21
Alignment explanation
Indices: 5618438--5618483 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
5618428 ATCTCCTTCC
**
5618438 TTTTCTTTTCTTTTTTTCTCT
1 TTTTCTTTTCTTTTCATCTCT
5618459 TTTTC-TTTCTTTTCATCT-T
1 TTTTCTTTTCTTTTCATCTCT
5618478 TTTTCT
1 TTTTCT
5618484 CTCCCTGCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTCTTTTCATCTCT
Found at i:5619229 original size:35 final size:35
Alignment explanation
Indices: 5619176--5619244 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 35
5619166 GATAATCCGT
*
5619176 AAATATTTTATTATATT-AAAATTATATTAATTTTA
1 AAATATTTTATTAAATTAAAAATTATA-TAATTTTA
5619211 AAAT-TTTTAATTAAATTAAAAAATTATATAATTT
1 AAATATTTT-ATTAAATT-AAAAATTATATAATTT
5619245 GATAGTGAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 4 0.13
35 11 0.37
36 6 0.20
37 9 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
AAATATTTTATTAAATTAAAAATTATATAATTTTA
Found at i:5619948 original size:22 final size:23
Alignment explanation
Indices: 5619900--5619949 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
5619890 ATTAAAAATT
*
5619900 AAAATTTTCATAATTTTTATATA
1 AAAATTTTCATAATTTTTATACA
5619923 AAAATTTT-ATAATTTTTATACA
1 AAAATTTTCATAATTTTTATACA
5619945 AAAAT
1 AAAAT
5619950 AATTATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATTTTCATAATTTTTATACA
Found at i:5621116 original size:28 final size:28
Alignment explanation
Indices: 5621046--5621114 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
5621036 AATAACTTAT
*
5621046 AAATATAAATGTAAA-TTTGATTTTTTTC
1 AAAT-TAAATGTAAATTTTAATTTTTTTC
5621074 AAATTAAATGTAAATTTTAATTTTTTT-
1 AAATTAAATGTAAATTTTAATTTTTTTC
*
5621101 GAATTAAATGTAAA
1 AAATTAAATGTAAA
5621115 ATATTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.48
Consensus pattern (28 bp):
AAATTAAATGTAAATTTTAATTTTTTTC
Found at i:5628902 original size:2 final size:2
Alignment explanation
Indices: 5628895--5628936 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5628885 AATGAAGCAA
5628895 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
5628937 TCTGAATGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5630672 original size:18 final size:18
Alignment explanation
Indices: 5630659--5630706 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
5630649 TTAATTTAAT
5630659 TTAAATTATAAATTATAA
1 TTAAATTATAAATTATAA
5630677 TTATAATTAT-AATTATAA
1 TTA-AATTATAAATTATAA
5630695 TTAAATT-TAAAT
1 TTAAATTATAAAT
5630707 AAAAATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 1 0.04
17 7 0.25
18 14 0.50
19 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATTATAAATTATAA
Found at i:5630686 original size:12 final size:12
Alignment explanation
Indices: 5630650--5630737 Score: 69
Period size: 12 Copynumber: 7.5 Consensus size: 12
5630640 TATTTAATCT
5630650 TAATT-TAATT-
1 TAATTATAATTA
5630660 TAAATTATAAATTA
1 T-AATTAT-AATTA
5630674 TAATTATAATTA
1 TAATTATAATTA
5630686 TAATTATAATTA
1 TAATTATAATTA
*
5630698 -AATT-TAAATA
1 TAATTATAATTA
* *
5630708 AAAATATTAATTA
1 TAATTA-TAATTA
*
5630721 -AATAATAATTA
1 TAATTATAATTA
*
5630732 AAATTA
1 TAATTA
5630738 ATTAAAATTA
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.09
11 17 0.27
12 25 0.39
13 15 0.23
14 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATTATAATTA
Found at i:5630738 original size:6 final size:6
Alignment explanation
Indices: 5630656--5630752 Score: 53
Period size: 6 Copynumber: 16.7 Consensus size: 6
5630646 ATCTTAATTT
* * * * * *
5630656 AATTTA AATTATA AATTAT AATTAT AATTAT AATTAT AATT-A AATTTA
1 AATTAA AATTA-A AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA
* *
5630704 AA-TAA AAATATT AATT-A AA-TAA TAATTAA AATT-- AATTAA AATTAA
1 AATTAA AATTA-A AATTAA AATTAA -AATTAA AATTAA AATTAA AATTAA
5630749 AATT
1 AATT
5630753 TTTTATAATC
Statistics
Matches: 75, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
4 5 0.07
5 11 0.15
6 47 0.63
7 12 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTAA
Found at i:5630741 original size:10 final size:10
Alignment explanation
Indices: 5630713--5630748 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
5630703 AAATAAAAAT
5630713 ATTAATTAAA
1 ATTAATTAAA
*
5630723 TAATAATTAAA
1 -ATTAATTAAA
5630734 ATTAATTAAA
1 ATTAATTAAA
5630744 ATTAA
1 ATTAA
5630749 AATTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTAATTAAA
Found at i:5630826 original size:28 final size:27
Alignment explanation
Indices: 5630778--5630835 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
5630768 CACCGTGAGC
5630778 AATAATATTTTTTTAAATAAA-TAAAA
1 AATAATATTTTTTTAAATAAATTAAAA
* *
5630804 AATATTATTATTTTTATTATAAATTAAAA
1 AATAATATT-TTTTTA-AATAAATTAAAA
5630833 AAT
1 AAT
5630836 TTTAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 8 0.30
27 6 0.22
28 5 0.19
29 8 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AATAATATTTTTTTAAATAAATTAAAA
Found at i:5631464 original size:17 final size:16
Alignment explanation
Indices: 5631444--5631503 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
5631434 AATATATAAT
*
5631444 TATTAAATAGTTATATC
1 TATTAAATA-ATATATC
5631461 TATTTAAATAATATATC
1 TA-TTAAATAATATATC
5631478 TATTTTAAA-AATAT-T-
1 TA--TTAAATAATATATC
5631493 TATTAAATAAT
1 TATTAAATAAT
5631504 GTAAAGATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
13 5 0.13
14 3 0.08
15 2 0.05
16 1 0.03
17 15 0.38
18 13 0.33
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (16 bp):
TATTAAATAATATATC
Found at i:5631491 original size:15 final size:17
Alignment explanation
Indices: 5631455--5631503 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
5631445 ATTAAATAGT
5631455 TATATCTATTTAAATAA
1 TATATCTATTTAAATAA
5631472 TATATCTATTTTAAA-AA
1 TATATCTA-TTTAAATAA
5631489 TAT-T-TA-TTAAATAA
1 TATATCTATTTAAATAA
5631503 T
1 T
5631504 GTAAAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.17
14 3 0.10
15 2 0.07
16 1 0.03
17 13 0.43
18 6 0.20
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATCTATTTAAATAA
Found at i:5631519 original size:73 final size:75
Alignment explanation
Indices: 5631371--5631520 Score: 173
Period size: 73 Copynumber: 2.0 Consensus size: 75
5631361 TTAATTTATT
* **
5631371 TTAAGATAATTATATTTATTTAAATCGTAATATATATTTAAATAGATATTATTAAATAATAAAAA
1 TTAAGATAATTATATCTATTTAAATAATAATATATATTTAAATAGATATTATTAAATAATAAAAA
*
5631436 TATATAATTA
66 GATATAATTA
* * **
5631446 TTAA-ATAGTTATATCTATTTAAATAAT-ATATCTATTTTAAA-A-ATATTTATTAAATAATGTA
1 TTAAGATAATTATATCTATTTAAATAATAATATATA-TTTAAATAGATA-TTATTAAATAATAAA
*
5631507 AAGATATGATTA
64 AAGATATAATTA
5631519 TT
1 TT
5631521 CATGATAAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
72 3 0.05
73 32 0.50
74 25 0.39
75 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (75 bp):
TTAAGATAATTATATCTATTTAAATAATAATATATATTTAAATAGATATTATTAAATAATAAAAA
GATATAATTA
Found at i:5634108 original size:13 final size:14
Alignment explanation
Indices: 5634090--5634123 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5634080 GTATTTGATG
5634090 AAATAAATATT-AA
1 AAATAAATATTAAA
*
5634103 AAATAAATTTTAAA
1 AAATAAATATTAAA
5634117 AAATAAA
1 AAATAAA
5634124 ACGCTCTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAAATATTAAA
Found at i:5634210 original size:18 final size:19
Alignment explanation
Indices: 5634187--5634229 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
5634177 GTCGGCAAAA
*
5634187 ATTATT-AAATTATATTTT
1 ATTATTAAAAATATATTTT
5634205 ATTATTTAAAAATATATTTT
1 ATTA-TTAAAAATATATTTT
*
5634225 TTTAT
1 ATTAT
5634230 ATTTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 3 0.14
20 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATTAAAAATATATTTT
Found at i:5634281 original size:3 final size:3
Alignment explanation
Indices: 5634273--5634303 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5634263 TTAAATCACC
5634273 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5634304 TAACATAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5634411 original size:10 final size:10
Alignment explanation
Indices: 5634396--5634424 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
5634386 ACATCGAACA
5634396 TATATATATG
1 TATATATATG
5634406 TATATATATG
1 TATATATATG
5634416 TATATATAT
1 TATATATAT
5634425 AATTAATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TATATATATG
Found at i:5634818 original size:11 final size:11
Alignment explanation
Indices: 5634794--5634833 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
5634784 TTGAATATTA
5634794 TTATATATTATTT
1 TTATATA-T-TTT
5634807 TTATATATTTT
1 TTATATATTTT
*
5634818 TTAAATATTTT
1 TTATATATTTT
5634829 TTATA
1 TTATA
5634834 AATATTATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 17 0.68
12 1 0.04
13 7 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATATTTT
Found at i:5634839 original size:13 final size:12
Alignment explanation
Indices: 5634798--5634839 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
5634788 ATATTATTAT
*
5634798 ATATTATTTTTAT
1 ATATT-TTTTTAA
5634811 ATA-TTTTTTAA
1 ATATTTTTTTAA
5634822 ATATTTTTTATAA
1 ATATTTTTT-TAA
5634835 ATATT
1 ATATT
5634840 ATGTTATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 9 0.35
12 6 0.23
13 11 0.42
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATATTTTTTTAA
Found at i:5634944 original size:11 final size:11
Alignment explanation
Indices: 5634928--5634957 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5634918 TTTTGATTCG
5634928 TATATTTATAT
1 TATATTTATAT
5634939 TATATTTATAT
1 TATATTTATAT
5634950 TAT-TTTAT
1 TATATTTAT
5634958 GTTACGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATATTTATAT
Found at i:5635293 original size:19 final size:19
Alignment explanation
Indices: 5635266--5635320 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
5635256 TTTGGTTTGT
* * *
5635266 AAAGGGAGAGAAAGAAGGA
1 AAAGAGAGAGAAAAAAAGA
5635285 AAAGAGAGAGAAAAAAAGA
1 AAAGAGAGAGAAAAAAAGA
* *
5635304 AAAAAAAGAGAAAAAAA
1 AAAGAGAGAGAAAAAAA
5635321 CGATAGAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (19 bp):
AAAGAGAGAGAAAAAAAGA
Found at i:5635307 original size:9 final size:10
Alignment explanation
Indices: 5635291--5635320 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
5635281 AGGAAAAGAG
5635291 AGAGAAAAAA
1 AGAGAAAAAA
5635301 AGA-AAAAAA
1 AGAGAAAAAA
5635310 AGAGAAAAAA
1 AGAGAAAAAA
5635320 A
1 A
5635321 CGATAGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (10 bp):
AGAGAAAAAA
Found at i:5635654 original size:17 final size:17
Alignment explanation
Indices: 5635634--5635686 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
5635624 GTATTTTATT
5635634 TTTATA-TATATGTTGAA
1 TTTATATTATAT-TTGAA
*
5635651 TTTATATTATATTTCAA
1 TTTATATTATATTTGAA
*
5635668 TTCATATTATATTTTGAA
1 TTTATATTATA-TTTGAA
5635686 T
1 T
5635687 AACTAATCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 20 0.65
18 11 0.35
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.57
Consensus pattern (17 bp):
TTTATATTATATTTGAA
Found at i:5636277 original size:18 final size:18
Alignment explanation
Indices: 5636250--5636287 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5636240 TTTATATAAA
*
5636250 TATTTATATATTAATAATT
1 TATTTATATATAAAT-ATT
5636269 TATTT-TATATAAATATT
1 TATTTATATATAAATATT
5636286 TA
1 TA
5636288 CATGTTCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTTATATATAAATATT
Found at i:5636357 original size:39 final size:40
Alignment explanation
Indices: 5636304--5636402 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 40
5636294 CGTGTATTCC
* *
5636304 TATTATA-TTCATATTATTTTTATGTCATAT-TATATTTTA
1 TATTATATTTTATATTATTTTTATGTCATATCT-TAATTTA
* * * *
5636343 -ATTATTTTTTATATTATGTATGTGTCATATCTTAATTTA
1 TATTATATTTTATATTATTTTTATGTCATATCTTAATTTA
*
5636382 TCTTATATTTTATA-TATTTTT
1 TATTATATTTTATATTATTTTT
5636403 TTATATGATT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
38 5 0.11
39 30 0.64
40 12 0.26
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (40 bp):
TATTATATTTTATATTATTTTTATGTCATATCTTAATTTA
Found at i:5636461 original size:28 final size:29
Alignment explanation
Indices: 5636423--5636481 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
5636413 AAATTTCTCT
*
5636423 TAAATTTATTT-ATTAAATATTTT-TAAA
1 TAAATTTATTTAATTAAAAATTTTATAAA
5636450 TAAATTTTATTTAATTAAAAATTTTATAAA
1 TAAA-TTTATTTAATTAAAAATTTTATAAA
5636480 TA
1 TA
5636482 TTAAAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 4 0.14
28 7 0.25
29 11 0.39
30 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TAAATTTATTTAATTAAAAATTTTATAAA
Found at i:5636583 original size:25 final size:23
Alignment explanation
Indices: 5636525--5636583 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
5636515 ATTTAAATAT
*
5636525 ATTTAAATATTTTAATAATTTATA
1 ATTTAAAT-TTTTAACAATTTATA
*
5636549 TTTTACAATTTTTAACATATTTATAA
1 ATTTA-AATTTTTAACA-ATTTAT-A
5636575 ATTTAAATT
1 ATTTAAATT
5636584 ATATTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 11 0.38
25 13 0.45
26 5 0.17
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTAAATTTTTAACAATTTATA
Found at i:5637437 original size:4 final size:4
Alignment explanation
Indices: 5637428--5637452 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5637418 ATCCAACTTT
5637428 ACAA ACAA ACAA ACAA ACAA ACAA A
1 ACAA ACAA ACAA ACAA ACAA ACAA A
5637453 AAAGGAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:5643027 original size:2 final size:2
Alignment explanation
Indices: 5643020--5643047 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5643010 ATTTCGTTTG
5643020 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
5643048 CACGCTCTAA
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):
TA
Found at i:5645408 original size:2 final size:2
Alignment explanation
Indices: 5645403--5645460 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
5645393 TTTTCAAACA
5645403 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5645445 AG AG AG AG AG AG -G AG A
1 AG AG AG AG AG AG AG AG A
5645461 AGAAGAAAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5645745 original size:26 final size:24
Alignment explanation
Indices: 5645708--5645763 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 24
5645698 AGAATAGTAA
5645708 TTAAAATATTATTATATTATTTTT
1 TTAAAATATTATTATATTATTTTT
* *
5645732 TTAAAGATAATTATTATTTTTTTTTT
1 TTAAA-AT-ATTATTATATTATTTTT
5645758 TTAAAA
1 TTAAAA
5645764 AAAAATTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 5 0.18
25 3 0.11
26 20 0.71
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTAAAATATTATTATATTATTTTT
Found at i:5648182 original size:13 final size:15
Alignment explanation
Indices: 5648157--5648192 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
5648147 ATATAATATT
5648157 TTAAATATATAAAAA
1 TTAAATATATAAAAA
5648172 -TAAAT-TATAAAAA
1 TTAAATATATAAAAA
5648185 TTAAATAT
1 TTAAATAT
5648193 GTTAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.42
14 10 0.53
15 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAATATATAAAAA
Found at i:5651059 original size:21 final size:20
Alignment explanation
Indices: 5651035--5651086 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
5651025 AAACAAAATG
* *
5651035 AAAAGCAAAAAATAAATAATT
1 AAAAGCAAAAAACAAAT-AGT
* *
5651056 AAAAACAAGAAACAAATAGT
1 AAAAGCAAAAAACAAATAGT
5651076 AAGAAGCAAAA
1 AA-AAGCAAAA
5651087 TTTAACCAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.71, C:0.08, G:0.10, T:0.12
Consensus pattern (20 bp):
AAAAGCAAAAAACAAATAGT
Found at i:5652359 original size:22 final size:21
Alignment explanation
Indices: 5652318--5652360 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5652308 AATTATTTTT
*
5652318 AATAAAAATATTTCAATTTAA
1 AATAAAAATATTACAATTTAA
*
5652339 AATAAAAATAATTACATTTTAA
1 AATAAAAAT-ATTACAATTTAA
5652361 TTATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AATAAAAATATTACAATTTAA
Found at i:5652649 original size:17 final size:17
Alignment explanation
Indices: 5652627--5652703 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 17
5652617 GTATATTTTA
5652627 TATAAA-TATAATAATAT
1 TATAAATTATAAT-ATAT
*
5652644 TATAAATTTTAATATAT
1 TATAAATTATAATATAT
*
5652661 TATTAATTTATATTATATAT
1 TA-TAAATTATA--ATATAT
* *
5652681 TAAAATATTTATATTATAT
1 TATAA-A-TTATAATATAT
5652700 TATA
1 TATA
5652704 TTAATTATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
17 12 0.26
18 12 0.26
19 10 0.21
20 8 0.17
21 5 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAATTATAATATAT
Found at i:5652711 original size:19 final size:21
Alignment explanation
Indices: 5652661--5652711 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 21
5652651 TTTAATATAT
5652661 TATTAATTTATATTATATATTA
1 TATTAA-TTATATTATATATTA
* * *
5652683 AAATATTTATA-T-TATATTA
1 TATTAATTATATTATATATTA
5652702 TATTAATTAT
1 TATTAATTAT
5652712 TTTTTTATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
19 14 0.61
20 1 0.04
21 5 0.22
22 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATTATATTATATATTA
Found at i:5653013 original size:17 final size:18
Alignment explanation
Indices: 5652991--5653026 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
5652981 TATTATTATC
5652991 ATATAAATATATAT-AAT
1 ATATAAATATATATGAAT
5653008 ATATAAATATATATGAAT
1 ATATAAATATATATGAAT
5653026 A
1 A
5653027 AAGTACCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (18 bp):
ATATAAATATATATGAAT
Found at i:5655133 original size:28 final size:27
Alignment explanation
Indices: 5655067--5655159 Score: 82
Period size: 28 Copynumber: 3.4 Consensus size: 27
5655057 TTCAAAAATT
* *
5655067 TATTTTATTATTTATTGTAT-TATAATA
1 TATTTTATAATTTATTTTATAT-TAATA
* *
5655094 TTTTTTAAAATTTATTTTTATATTAATA
1 TATTTTATAATTTA-TTTTATATTAATA
* * * *
5655122 TATTTTATAATTAAATTTA-AATAAAA
1 TATTTTATAATTTATTTTATATTAATA
5655148 TATTTTATAATT
1 TATTTTATAATT
5655160 AAATAATCAA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
26 17 0.31
27 15 0.28
28 21 0.39
29 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (27 bp):
TATTTTATAATTTATTTTATATTAATA
Found at i:5656748 original size:45 final size:45
Alignment explanation
Indices: 5656670--5656758 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
5656660 AGATTTGAAT
*
5656670 TAATATTTAATAAAAAATATTTTTTAAAATTTAATTATAAAATAG
1 TAATATTTAATAAAAAATATTTTTTAAAATTTAAATATAAAATAG
* * *
5656715 TAATA-TTAATATAAAAT-TATTTTTAATATTTTAAATATATAATA
1 TAATATTTAATAAAAAATAT-TTTTTAA-AATTTAAATATAAAATA
5656759 CTTTGTATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
43 1 0.03
44 18 0.47
45 19 0.50
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (45 bp):
TAATATTTAATAAAAAATATTTTTTAAAATTTAAATATAAAATAG
Found at i:5659599 original size:26 final size:28
Alignment explanation
Indices: 5659563--5659621 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
5659553 AACCATAATC
5659563 AAATTATAAAAAT-ATTATAATTTTTTA
1 AAATTATAAAAATAATTATAATTTTTTA
* *
5659590 AAATT-TAAAAATAATTTTATTTTTTTA
1 AAATTATAAAAATAATTATAATTTTTTA
5659617 AAATT
1 AAATT
5659622 CAATACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AAATTATAAAAATAATTATAATTTTTTA
Found at i:5659768 original size:21 final size:19
Alignment explanation
Indices: 5659742--5659791 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
5659732 TTAAATTTAT
5659742 TATTAATTCAATTATATAATA
1 TATTAATT-AATTAT-TAATA
**
5659763 TATTAATTTTTTATTAATA
1 TATTAATTAATTATTAATA
5659782 TATTATATTA
1 TATTA-ATTA
5659792 TTTTTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 10 0.40
20 7 0.28
21 8 0.32
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTAATTAATTATTAATA
Found at i:5660028 original size:23 final size:24
Alignment explanation
Indices: 5659992--5660036 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
5659982 CATAAAATTT
*
5659992 TAAATAATAATTAATTAATTTAAA
1 TAAATAATAATTAATAAATTTAAA
*
5660016 TAAA-AATATTTAATAAATTTA
1 TAAATAATAATTAATAAATTTA
5660037 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAATAATAATTAATAAATTTAAA
Found at i:5660064 original size:27 final size:28
Alignment explanation
Indices: 5659993--5660064 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 28
5659983 ATAAAATTTT
*
5659993 AAATA-ATAATT-AATTAATTTAAATAA
1 AAATATATAATTAAATTATTTTAAATAA
* *
5660019 AAATATTTAA-TAAATTTATTTTAAA-AT
1 AAATATATAATTAAA-TTATTTTAAATAA
*
5660046 TAATATATAATTAAATTAT
1 AAATATATAATTAAATTAT
5660065 ATAACATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 6 0.16
27 18 0.49
28 13 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATATATAATTAAATTATTTTAAATAA
Found at i:5660107 original size:25 final size:26
Alignment explanation
Indices: 5660079--5660133 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
5660069 CATATATTTA
5660079 AATT-AAAATAAAATTTAATAATAA-T
1 AATTAAAAAT-AAATTTAATAATAATT
* *
5660104 AATTAAAAATAATTTTAATATTAATT
1 AATTAAAAATAAATTTAATAATAATT
5660130 AATT
1 AATT
5660134 TTTATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTAAAAATAAATTTAATAATAATT
Found at i:5660170 original size:15 final size:17
Alignment explanation
Indices: 5660139--5660172 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
5660129 TAATTTTTAT
5660139 TATTTTATAATTAAAAA
1 TATTTTATAATTAAAAA
5660156 TATTTTA-AA-TAAAAA
1 TATTTTATAATTAAAAA
5660171 TA
1 TA
5660173 ATAAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTTATAATTAAAAA
Found at i:5660191 original size:17 final size:16
Alignment explanation
Indices: 5660147--5660196 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
5660137 ATTATTTTAT
* **
5660147 AATTAAAAATATTTTA
1 AATTAAAAATAATAAA
5660163 AA-TAAAAATAATAAA
1 AATTAAAAATAATAAA
5660178 AATTAAAAATTAATAAA
1 AATTAAAAA-TAATAAA
5660195 AA
1 AA
5660197 ATATATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 12 0.41
16 8 0.28
17 9 0.31
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AATTAAAAATAATAAA
Found at i:5665737 original size:13 final size:13
Alignment explanation
Indices: 5665719--5665745 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5665709 AGGAGCGTTT
5665719 TCCTAGTTTCTAG
1 TCCTAGTTTCTAG
5665732 TCCTAGTTTCTAG
1 TCCTAGTTTCTAG
5665745 T
1 T
5665746 TGAAGTAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.48
Consensus pattern (13 bp):
TCCTAGTTTCTAG
Found at i:5666205 original size:97 final size:97
Alignment explanation
Indices: 5666038--5666233 Score: 356
Period size: 97 Copynumber: 2.0 Consensus size: 97
5666028 CATTTATATT
* *
5666038 TTTATATGTAATTAAGTGTTAAAATATAAATATATAAAAAAACTAATATAAGTATATAATATAAC
1 TTTATATATAATTAAGTGTTAAAATATAAATATATAAAAAAACTAATATAAGTACATAATATAAC
*
5666103 CTGAAACAACAGGGGCGGCTGGTAATGTATGG
66 ATGAAACAACAGGGGCGGCTGGTAATGTATGG
*
5666135 TTTATATATAATTAAGTGTTAAAATATAAATATATAAAAAAATTAATATAAGTACATAATATAAC
1 TTTATATATAATTAAGTGTTAAAATATAAATATATAAAAAAACTAATATAAGTACATAATATAAC
5666200 ATGAAACAACAGGGGCGGCTGGTAATGTATGG
66 ATGAAACAACAGGGGCGGCTGGTAATGTATGG
5666232 TT
1 TT
5666234 GGCCCCCAAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.32
Consensus pattern (97 bp):
TTTATATATAATTAAGTGTTAAAATATAAATATATAAAAAAACTAATATAAGTACATAATATAAC
ATGAAACAACAGGGGCGGCTGGTAATGTATGG
Found at i:5666469 original size:16 final size:16
Alignment explanation
Indices: 5666450--5666500 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
5666440 AATAAATATA
5666450 TTATATATTTATTTAT
1 TTATATATTTATTTAT
*
5666466 TTATATATTTTTTTAT
1 TTATATATTTATTTAT
*
5666482 TTATTAAATTTAATTTAT
1 TTA-TATATTT-ATTTAT
5666500 T
1 T
5666501 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 18 0.60
17 6 0.20
18 6 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATATATTTATTTAT
Found at i:5671325 original size:23 final size:22
Alignment explanation
Indices: 5671282--5671323 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5671272 TTTTATAAAA
5671282 TATTTAATAATTAAAAAATATT
1 TATTTAATAATTAAAAAATATT
*
5671304 TATTT-ATAATTATAAAATAT
1 TATTTAATAATTAAAAAATAT
5671324 ATAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTTAATAATTAAAAAATATT
Found at i:5671497 original size:18 final size:19
Alignment explanation
Indices: 5671466--5671505 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5671456 TTGGTTATGA
5671466 TAAAATTTATAATT-TTAT
1 TAAAATTTATAATTATTAT
5671484 TAAAGATTTA-AATTATTAT
1 TAAA-ATTTATAATTATTAT
5671503 TAA
1 TAA
5671506 TTTTATTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TAAAATTTATAATTATTAT
Found at i:5679683 original size:16 final size:15
Alignment explanation
Indices: 5679662--5679717 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 15
5679652 ATCAATCTCG
5679662 GATTCAAACTTTTTC
1 GATTCAAACTTTTTC
5679677 AGATTCAAACTTTTTC
1 -GATTCAAACTTTTTC
5679693 GATTTCAAA-TTATTTC
1 GA-TTCAAACTT-TTTC
5679709 GAATTCAAA
1 G-ATTCAAA
5679718 TAATTTTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.11
16 32 0.86
17 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (15 bp):
GATTCAAACTTTTTC
Found at i:5679718 original size:16 final size:16
Alignment explanation
Indices: 5679679--5679735 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
5679669 ACTTTTTCAG
5679679 ATTCAAACTT-TTTCGA
1 ATTCAAA-TTATTTCGA
*
5679695 TTTCAAATTATTTCGA
1 ATTCAAATTATTTCGA
* **
5679711 ATTCAAATAATTTTAA
1 ATTCAAATTATTTCGA
5679727 ATTCAAATT
1 ATTCAAATT
5679736 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 2 0.06
16 32 0.94
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.46
Consensus pattern (16 bp):
ATTCAAATTATTTCGA
Found at i:5680025 original size:2 final size:2
Alignment explanation
Indices: 5680018--5680042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5680008 TTGATTGCAC
5680018 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 A
5680043 CCTGTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5684357 original size:27 final size:26
Alignment explanation
Indices: 5684300--5684358 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
5684290 TATTAAAAGT
** * *
5684300 TTAATATTTTTAAATAAAATTTTAATT
1 TTAA-ATTTTTAAATAAAAAATAAATA
5684327 TTAAATTTTATAAATAAAAAATAAATA
1 TTAAATTTT-TAAATAAAAAATAAATA
5684354 TTAAA
1 TTAAA
5684359 CTTGTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TTAAATTTTTAAATAAAAAATAAATA
Found at i:5684612 original size:18 final size:17
Alignment explanation
Indices: 5684583--5684624 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
5684573 TATTAAAATT
*
5684583 AAAATTATAAATTTATG
1 AAAATAATAAATTTATG
*
5684600 AAATATAATAAATTTTTG
1 AAA-ATAATAAATTTATG
5684618 AAAATAA
1 AAAATAA
5684625 ATATATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
AAAATAATAAATTTATG
Found at i:5684681 original size:28 final size:29
Alignment explanation
Indices: 5684636--5684732 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 29
5684626 TATATGATTT
*
5684636 AAATTAATTAAATTTTAAATTTTAAAAAA
1 AAATTAATTAAATATTAAATTTTAAAAAA
* * *
5684665 AAATT-ATTAAATATTAATTTTTAAATAT
1 AAATTAATTAAATATTAAATTTTAAAAAA
**
5684693 AAA-T-A-TATAA-ATT-AATTTTTTAAAA
1 AAATTAATTA-AATATTAAATTTTAAAAAA
5684718 AAATTAATTAAATAT
1 AAATTAATTAAATAT
5684733 AAGTTTTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
25 10 0.19
26 6 0.11
27 7 0.13
28 26 0.48
29 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATTAATTAAATATTAAATTTTAAAAAA
Found at i:5684740 original size:28 final size:26
Alignment explanation
Indices: 5684661--5684741 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 26
5684651 TAAATTTTAA
5684661 AAAAAAATTATTAAATATTAA-TTTTT
1 AAAAAAATTATTAAATA-TAATTTTTT
5684687 AAATATAAA-TATATAAAT-TAATTTTTT
1 AAA-A-AAATTAT-TAAATATAATTTTTT
5684714 AAAAAAATTAATTAAATATAAGTTTTTT
1 AAAAAAATT-ATTAAATATAA-TTTTTT
5684742 TCCTTGGTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
25 3 0.06
26 13 0.28
27 17 0.36
28 14 0.30
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (26 bp):
AAAAAAATTATTAAATATAATTTTTT
Found at i:5688429 original size:2 final size:2
Alignment explanation
Indices: 5688422--5688455 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5688412 AGTAAAAGAA
5688422 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5688456 GAGGGGAAAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5689043 original size:14 final size:14
Alignment explanation
Indices: 5689018--5689064 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
5689008 ATAATTAATT
5689018 ATAAAAATATTGATA
1 ATAAAAA-ATTGATA
5689033 ATAAAAAATTGA-A
1 ATAAAAAATTGATA
* *
5689046 ATTAAAAAAATAATA
1 A-TAAAAAATTGATA
5689061 ATAA
1 ATAA
5689065 TGTTACACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.07
14 17 0.61
15 9 0.32
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (14 bp):
ATAAAAAATTGATA
Found at i:5689977 original size:39 final size:37
Alignment explanation
Indices: 5689904--5689992 Score: 101
Period size: 39 Copynumber: 2.4 Consensus size: 37
5689894 GTAGTTAATG
* *
5689904 ATATAAATATAAAAATATAATTAATATATATTTTTAA
1 ATATAAAAATAAAAATATAATTAAAATATATTTTTAA
*
5689941 ATATAAAAATAAAATTATTAAATATAAAATAT-TTTTTAA
1 ATATAAAAATAAAAATA-T-AAT-TAAAATATATTTTTAA
5689980 A-ATAATAAATAAA
1 ATATAA-AAATAAA
5689993 TAATTTTAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
37 15 0.33
38 5 0.11
39 18 0.40
40 7 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (37 bp):
ATATAAAAATAAAAATATAATTAAAATATATTTTTAA
Found at i:5693632 original size:2 final size:2
Alignment explanation
Indices: 5693625--5693660 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5693615 GGAAATTAAA
5693625 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
5693661 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5694700 original size:22 final size:22
Alignment explanation
Indices: 5694675--5694716 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5694665 TTATTGCAAT
5694675 TAAAA-AAAATTAAAATATAATA
1 TAAAATAAAA-TAAAATATAATA
*
5694697 TAAAATATAATAAAATATAA
1 TAAAATAAAATAAAATATAA
5694717 AAATAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAAATAAAATATAATA
Found at i:5694702 original size:12 final size:11
Alignment explanation
Indices: 5694685--5694728 Score: 56
Period size: 10 Copynumber: 4.0 Consensus size: 11
5694675 TAAAAAAAAT
5694685 TAAAATATAATA
1 TAAAATATAA-A
5694697 TAAAATAT-AA
1 TAAAATATAAA
5694707 TAAAATATAAA
1 TAAAATATAAA
5694718 -AATAATATAAA
1 TAA-AATATAAA
5694729 AATATTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 11 0.37
11 11 0.37
12 8 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAAATATAAA
Found at i:5694722 original size:28 final size:27
Alignment explanation
Indices: 5694680--5694737 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
5694670 GCAATTAAAA
5694680 AAAATTAAAATATAATATAAAATATAAT
1 AAAATTAAAATATAATATAAAA-ATAAT
*
5694708 AAAATATAAAA-ATAATATAAAAATATT
1 AAAAT-TAAAATATAATATAAAAATAAT
5694735 AAA
1 AAA
5694738 TTTTATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 7 0.25
28 16 0.57
29 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATTAAAATATAATATAAAAATAAT
Found at i:5694726 original size:11 final size:11
Alignment explanation
Indices: 5694700--5694732 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5694690 TATAATATAA
*
5694700 AATATAATAA-
1 AATATAAAAAT
5694710 AATATAAAAAT
1 AATATAAAAAT
5694721 AATATAAAAAT
1 AATATAAAAAT
5694732 A
1 A
5694733 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:5695347 original size:8 final size:8
Alignment explanation
Indices: 5695329--5695363 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
5695319 CTTTTTTACT
5695329 TTTACTATA
1 TTTA-TATA
*
5695338 TTTATTTA
1 TTTATATA
5695346 TTTATATA
1 TTTATATA
5695354 TTTATATA
1 TTTATATA
5695362 TT
1 TT
5695364 CCATATACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 20 0.83
9 4 0.17
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (8 bp):
TTTATATA
Found at i:5696504 original size:15 final size:16
Alignment explanation
Indices: 5696484--5696536 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
5696474 AAATAATTTA
5696484 AATATAATATAT-TAT
1 AATATAATATATATAT
5696499 AATATATATATATATAT
1 AATATA-ATATATATAT
5696516 ATGATATAA-ATATATA-
1 A--ATATAATATATATAT
5696532 AATAT
1 AATAT
5696537 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 7 0.21
17 11 0.32
18 1 0.03
19 5 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AATATAATATATATAT
Found at i:5696505 original size:2 final size:2
Alignment explanation
Indices: 5696485--5696536 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
5696475 AATAATTTAA
*
5696485 AT AT A- AT AT AT -T AT A- AT AT AT AT AT AT AT AT AT GAT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
*
5696525 AT AT AT AA AT AT
1 AT AT AT AT AT AT
5696537 TTTAAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 3 0.07
2 37 0.88
3 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5696522 original size:19 final size:19
Alignment explanation
Indices: 5696485--5696536 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
5696475 AATAATTTAA
5696485 ATATA-ATATAT-TATAAT
1 ATATATATATATATATAAT
*
5696502 ATATATATATATATATGAT
1 ATATATATATATATATAAT
* *
5696521 ATAAATATATAAATAT
1 ATATATATATATATAT
5696537 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 5 0.17
18 6 0.20
19 19 0.63
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATATATATATATATATAAT
Found at i:5696557 original size:31 final size:33
Alignment explanation
Indices: 5696519--5696592 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 33
5696509 TATATATATG
5696519 ATATAAATATATAAATATT-TTAAAAT-TTAT-A
1 ATATAAATATATAAAT-TTATTAAAATGTTATAA
* *
5696550 ATATAAAT-TATTAATTTATTAAATTGTTATAA
1 ATATAAATATATAAATTTATTAAAATGTTATAA
5696582 ATATAAA-ATAT
1 ATATAAATATAT
5696593 TTTTAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
29 2 0.05
30 12 0.32
31 12 0.32
32 11 0.30
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (33 bp):
ATATAAATATATAAATTTATTAAAATGTTATAA
Found at i:5696600 original size:26 final size:25
Alignment explanation
Indices: 5696520--5696613 Score: 66
Period size: 26 Copynumber: 3.4 Consensus size: 25
5696510 ATATATATGA
* *
5696520 TATAAATATATAAATATTTTAAAATT
1 TATAAATATA-AAATATTTTTAATTT
5696546 TAT-AATATAAATTATTAATTTATTAAATTGT
1 TATAAATATAAA--A-T-ATTT-TT-AATT-T
5696577 TATAAATATAAAATATTTTTAATTAAT
1 TATAAATATAAAATATTTTTAATT--T
5696604 TA-AAATATAA
1 TATAAATATAA
5696614 TAAAATATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
24 2 0.04
25 6 0.11
26 16 0.29
27 6 0.11
28 8 0.14
29 2 0.04
30 4 0.07
31 4 0.07
32 8 0.14
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (25 bp):
TATAAATATAAAATATTTTTAATTT
Found at i:5699887 original size:14 final size:14
Alignment explanation
Indices: 5699868--5699894 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5699858 ATGAAGAAAT
5699868 ATAAATTTTAAAAA
1 ATAAATTTTAAAAA
5699882 ATAAATTTTAAAA
1 ATAAATTTTAAAA
5699895 TTTTAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAAATTTTAAAAA
Done.