Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 7 of 32
Found at i:1096865 original size:23 final size:24
Alignment explanation
Indices: 1096705--1096930 Score: 164
Period size: 23 Copynumber: 9.8 Consensus size: 24
1096695 ATAATTATAT
1096705 AATATG-AATA-AATATAAAAATA
1 AATATGAAATATAATATAAAAATA
1096727 AA-AT-ATAATAT-ATATTAAAAAT-
1 AATATGA-AATATAATA-TAAAAATA
*
1096749 GATATG-AATATAATATAAAAATAA
1 AATATGAAATATAATATAAAAAT-A
*
1096773 AATATGATATAT-ATA-AAAAAT-
1 AATATGAAATATAATATAAAAATA
*
1096794 GATATG-AATATAATATAAAAATAA
1 AATATGAAATATAATATAAAAAT-A
*
1096818 AATATGATATAT-ATA-AAAAAT-
1 AATATGAAATATAATATAAAAATA
1096839 AATA-GAAATATAATATAAAAATA
1 AATATGAAATATAATATAAAAATA
* * * *
1096862 AATATTTAAAATTTTATATAAATTATA
1 AATA--TGAAATATAATATAAA-AATA
*
1096889 AATAT-AATTATAATATAATAAAT-
1 AATATGAAATATAATATAA-AAATA
*
1096912 TATAT-AAATATAATATAAA
1 AATATGAAATATAATATAAA
1096931 TATATAACGT
Statistics
Matches: 163, Mismatches: 18, Indels: 46
0.72 0.08 0.20
Matches are distributed among these distances:
20 10 0.06
21 17 0.10
22 35 0.21
23 44 0.27
24 28 0.17
25 10 0.06
26 12 0.07
27 7 0.04
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (24 bp):
AATATGAAATATAATATAAAAATA
Found at i:1096901 original size:90 final size:88
Alignment explanation
Indices: 1096706--1096924 Score: 230
Period size: 90 Copynumber: 2.4 Consensus size: 88
1096696 TAATTATATA
* * *
1096706 ATATGAATA-AATATAAAAATAAAATATAATATATATTAAAAATGATATGAATATAATATAAAAA
1 ATATAAATATAATATAAAAATAAAATAT-ATATATATAAAAAATAATATGAATATAATATAAAAA
* *
1096770 TAAAATATGATATATATAAAAAAT
65 TAAAATATAAAATATATAAAAAAT
*
1096794 GATATGAATATAATATAAAAATAAAATATGATATATATAAAAAATAATA-GAAATATAATATAAA
1 -ATATAAATATAATATAAAAATAAAATAT-ATATATATAAAAAATAATATG-AATATAATATAAA
* * *
1096858 AATAAATATTTAAAAT-TTTATATAAAT
63 AATAAA-ATATAAAATATATA-AAAAAT
* *
1096885 -TATAAATATAATTATAATATAATAAATTATATAAATATAA
1 ATATAAATATAA-TATAA-A-AATAAAATATATATATATAA
1096925 TATAAATATA
Statistics
Matches: 112, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
89 20 0.18
90 62 0.55
91 21 0.19
92 9 0.08
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (88 bp):
ATATAAATATAATATAAAAATAAAATATATATATATAAAAAATAATATGAATATAATATAAAAAT
AAAATATAAAATATATAAAAAAT
Found at i:1096912 original size:15 final size:13
Alignment explanation
Indices: 1096877--1096934 Score: 59
Period size: 13 Copynumber: 4.4 Consensus size: 13
1096867 TTAAAATTTT
1096877 ATATAAATTATAA
1 ATATAAATTATAA
1096890 ATAT-AATTATAA
1 ATATAAATTATAA
1096902 TATAATAAATTATATA
1 -AT-ATAAATTATA-A
1096918 A-ATATAA-TATAA
1 ATATA-AATTATAA
1096930 ATATA
1 ATATA
1096935 TAACGTAGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
12 10 0.26
13 16 0.41
14 4 0.10
15 8 0.21
16 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAAATTATAA
Found at i:1097683 original size:18 final size:18
Alignment explanation
Indices: 1097655--1097718 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 18
1097645 AATTTCATAT
1097655 AAATTATTATTTATTAATA
1 AAATTA-TATTTATTAATA
*
1097674 AAATTATATTT-TTATTA
1 AAATTATATTTATTAATA
* * *
1097691 AAATT-TAATTATAAAAA
1 AAATTATATTTATTAATA
1097708 TAAATTATATT
1 -AAATTATATT
1097719 ATTCTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
16 4 0.11
17 13 0.36
18 10 0.28
19 9 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTATATTTATTAATA
Found at i:1098221 original size:4 final size:4
Alignment explanation
Indices: 1098212--1098237 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1098202 TTCTGATCAA
1098212 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1098238 TGGCCCTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1098475 original size:8 final size:10
Alignment explanation
Indices: 1098434--1098489 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 10
1098424 TATAATTATA
1098434 TTTA-ATATT
1 TTTATATATT
*
1098443 TTAATTATATT
1 TTTA-TATATT
*
1098454 TATAATATATT
1 T-TTATATATT
1098465 TTTA-A-ATT
1 TTTATATATT
1098473 TTTATATATT
1 TTTATATATT
1098483 TTTATAT
1 TTTATAT
1098490 TCATCATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 7 0.17
9 5 0.12
10 12 0.30
11 13 0.32
12 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTATATATT
Found at i:1098488 original size:31 final size:30
Alignment explanation
Indices: 1098424--1098483 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1098414 ATAATAAGTA
1098424 TATAATTATATTTAATATTTTAATTATATT
1 TATAATTATATTTAATATTTTAATTATATT
* *
1098454 TATAATATATTTTTAA-ATTTTTA-TATATT
1 TATAAT-TATATTTAATATTTTAATTATATT
1098483 T
1 T
1098484 TTATATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 7 0.26
30 12 0.44
31 8 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TATAATTATATTTAATATTTTAATTATATT
Found at i:1099341 original size:16 final size:16
Alignment explanation
Indices: 1099320--1099386 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 16
1099310 GTAATTATTA
*
1099320 TTTTATTATTTTAATT
1 TTTTATTATTATAATT
**
1099336 TTTTATTATAATATTTGTT
1 TTTTATTAT--TA-TAATT
*
1099355 TTTATATTATTATAATA
1 TTT-TATTATTATAATT
1099372 TTTTATTATTATAAT
1 TTTTATTATTATAAT
1099387 ATATATAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
16 21 0.51
17 5 0.12
18 3 0.07
19 6 0.15
20 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.67
Consensus pattern (16 bp):
TTTTATTATTATAATT
Found at i:1099391 original size:23 final size:23
Alignment explanation
Indices: 1099339--1099395 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
1099329 TTTAATTTTT
*
1099339 TATTATAATATTTGTTTTTATAT
1 TATTATAATATTTGTTTTTATAA
1099362 TATTATAATATTT-TATTATTATAA
1 TATTATAATATTTGT-TT-TTATAA
1099386 TATATATAAT
1 TAT-TATAAT
1099396 TAAATACGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 1 0.03
23 15 0.50
24 8 0.27
25 6 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTATAATATTTGTTTTTATAA
Found at i:1101999 original size:2 final size:2
Alignment explanation
Indices: 1101992--1102026 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1101982 CAAAAACTAC
1101992 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 A
1102027 AAGAAGTTAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1103067 original size:16 final size:16
Alignment explanation
Indices: 1102995--1103070 Score: 66
Period size: 16 Copynumber: 4.7 Consensus size: 16
1102985 ATTTAAATTA
*
1102995 AAATTATTTTAAATTT
1 AAATTATTTTAGATTT
*
1103011 ATA-TATTTTTAGATTT
1 AAATTA-TTTTAGATTT
* * *
1103027 AAGTTTTTTTTGAGTTT
1 AAATTATTTTAGA-TTT
1103044 GAAA-TATTTTAGATTT
1 -AAATTATTTTAGATTT
1103060 AAATTATTTTA
1 AAATTATTTTA
1103071 AATACTGAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
15 5 0.11
16 28 0.61
17 11 0.24
18 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (16 bp):
AAATTATTTTAGATTT
Found at i:1103349 original size:14 final size:14
Alignment explanation
Indices: 1103330--1103381 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
1103320 ACTAAAATTT
1103330 TTAAAATATAAAAA
1 TTAAAATATAAAAA
*
1103344 TTAAAATATAAAAT
1 TTAAAATATAAAAA
*
1103358 TTAATAATATAAATA
1 TTAA-AATATAAAAA
1103373 TTAAAATAT
1 TTAAAATAT
1103382 TTTTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAATATAAAAA
Found at i:1103357 original size:21 final size:22
Alignment explanation
Indices: 1103330--1103381 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1103320 ACTAAAATTT
1103330 TTAAAATATAAAAAT-TAAA-A
1 TTAAAATATAAAAATATAAATA
* *
1103350 TATAAAATTTAATAATATAAATA
1 T-TAAAATATAAAAATATAAATA
1103373 TTAAAATAT
1 TTAAAATAT
1103382 TTTTTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 12 0.46
22 11 0.42
23 2 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAAATATAAAAATATAAATA
Found at i:1103381 original size:8 final size:8
Alignment explanation
Indices: 1103330--1103382 Score: 55
Period size: 7 Copynumber: 7.2 Consensus size: 8
1103320 ACTAAAATTT
1103330 TTAAAATA
1 TTAAAATA
1103338 -TAAAA-A
1 TTAAAATA
1103344 TTAAAATA
1 TTAAAATA
1103352 -TAAAAT-
1 TTAAAATA
1103358 TTAATAATA
1 TTAA-AATA
1103367 -T-AAATA
1 TTAAAATA
1103373 TTAAAATA
1 TTAAAATA
1103381 TT
1 TT
1103383 TTTTATTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
6 5 0.13
7 21 0.55
8 12 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
TTAAAATA
Found at i:1103694 original size:27 final size:28
Alignment explanation
Indices: 1103640--1103696 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 28
1103630 TTTATTCACC
1103640 CACTTTGATTTTATACATACATATATACATA
1 CACTTTGATTTTATACATAC--A-ATACATA
*
1103671 CACTTTGATTTTATACATGC-ATACAT
1 CACTTTGATTTTATACATACAATACAT
1103697 TCATTCATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
31 19 0.76
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (28 bp):
CACTTTGATTTTATACATACAATACATA
Found at i:1104252 original size:32 final size:33
Alignment explanation
Indices: 1104205--1104285 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 33
1104195 TTATATTTAA
* *
1104205 AATATTTTATATTTATATAAAATTT-AAATATT
1 AATAATTTATTTTTATATAAAATTTAAAATATT
1104237 AATAATTTA-TTTT-TATAAAATTTAAAATATT
1 AATAATTTATTTTTATATAAAATTTAAAATATT
*
1104268 TATATATTTATATTTTAT
1 AATA-ATTTAT-TTTTAT
1104286 TTATATTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 10 0.24
31 13 0.32
32 13 0.32
34 4 0.10
35 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (33 bp):
AATAATTTATTTTTATATAAAATTTAAAATATT
Found at i:1104254 original size:30 final size:32
Alignment explanation
Indices: 1104205--1104285 Score: 105
Period size: 32 Copynumber: 2.5 Consensus size: 32
1104195 TTATATTTAA
1104205 AATAT-TTTATATTTATATAAAATTT-AAATATT
1 AATATATTTAT-TTT-TATAAAATTTAAAATATT
1104237 AATA-ATTTATTTTTATAAAATTTAAAATATT
1 AATATATTTATTTTTATAAAATTTAAAATATT
*
1104268 TATATATTTATATTTTAT
1 AATATATTTAT-TTTTAT
1104286 TTATATTTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
30 10 0.23
31 13 0.30
32 15 0.34
33 6 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
AATATATTTATTTTTATAAAATTTAAAATATT
Found at i:1104279 original size:6 final size:6
Alignment explanation
Indices: 1104270--1104299 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1104260 AAAATATTTA
1104270 TATATT TATATT T-TATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT TATATT T
1104300 TTTATATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TATATT
Found at i:1104288 original size:11 final size:12
Alignment explanation
Indices: 1104270--1104299 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1104260 AAAATATTTA
1104270 TATATTTATATT
1 TATATTTATATT
1104282 T-TATTTATATT
1 TATATTTATATT
1104293 TATATTT
1 TATATTT
1104300 TTTATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATATTTATATT
Found at i:1104307 original size:17 final size:17
Alignment explanation
Indices: 1104266--1104307 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1104256 ATTTAAAATA
1104266 TTTATATATTTATATTT
1 TTTATATATTTATATTT
1104283 TATT-TATATTTATATTT
1 T-TTATATATTTATATTT
1104300 TTTATATA
1 TTTATATA
1104308 ATATAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTATATATTTATATTT
Found at i:1104462 original size:3 final size:3
Alignment explanation
Indices: 1104454--1104481 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1104444 CTTTGCTAAG
1104454 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1104482 TTCTTTTTAT
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):
TAT
Found at i:1104733 original size:27 final size:27
Alignment explanation
Indices: 1104701--1104759 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
1104691 ATAAATATTT
* *
1104701 AATAATAATAT-AAATT-AATAA-ATA
1 AATATTAATATAAAATTAAAAAATATA
*
1104725 AATATTAATTTAAAATTAAAAAATATA
1 AATATTAATATAAAATTAAAAAATATA
1104752 AATATTAA
1 AATATTAA
1104760 CTTTTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 9 0.31
25 5 0.17
26 4 0.14
27 11 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (27 bp):
AATATTAATATAAAATTAAAAAATATA
Found at i:1104748 original size:21 final size:23
Alignment explanation
Indices: 1104719--1104778 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
1104709 TATAAATTAA
1104719 TAAATAAATATTAAT-TTAA-AAT
1 TAAA-AAATATTAATATTAACAAT
* **
1104741 TAAAAAATATAAATATTAACTTT
1 TAAAAAATATTAATATTAACAAT
*
1104764 TAAAAAATTTTAATA
1 TAAAAAATATTAATA
1104779 GTTGTAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 9 0.29
22 8 0.26
23 14 0.45
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAAAAATATTAATATTAACAAT
Found at i:1104907 original size:18 final size:19
Alignment explanation
Indices: 1104875--1104917 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1104865 GTCTTCGGCT
1104875 TTAATAATAAAATATAAAA
1 TTAATAATAAAATATAAAA
* *
1104894 TTAA-AATAATATATAATA
1 TTAATAATAAAATATAAAA
1104912 TTAATA
1 TTAATA
1104918 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
TTAATAATAAAATATAAAA
Found at i:1104941 original size:27 final size:26
Alignment explanation
Indices: 1104894--1104947 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
1104884 AAATATAAAA
*
1104894 TTAAAATAATATATAATATTAATATT
1 TTAAAATAATATATAATATTAAAATT
*
1104920 TTAAAAT-TTATATAATCAATTAAAATT
1 TTAAAATAATATATAAT--ATTAAAATT
1104947 T
1 T
1104948 ATTATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 8 0.33
26 7 0.29
27 9 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TTAAAATAATATATAATATTAAAATT
Found at i:1104978 original size:17 final size:17
Alignment explanation
Indices: 1104921--1104980 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
1104911 ATTAATATTT
* *
1104921 TAAAATTTATATAATCAA
1 TAAAATTTTTAT-ATTAA
*
1104939 TTAAAATTTATTATTATT-T
1 -TAAAATTT-TTA-TATTAA
1104958 TAAAATTTTTATATTAA
1 TAAAATTTTTATATTAA
1104975 TAAAAT
1 TAAAAT
1104981 ATATAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.12
17 9 0.26
18 8 0.24
19 8 0.24
20 4 0.12
21 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAATTTTTATATTAA
Found at i:1106600 original size:13 final size:13
Alignment explanation
Indices: 1106582--1106612 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1106572 ATTAAAATTT
1106582 ATATTAAATAAAA
1 ATATTAAATAAAA
*
1106595 ATATTAAATATAA
1 ATATTAAATAAAA
1106608 ATATT
1 ATATT
1106613 TATAAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATTAAATAAAA
Found at i:1108830 original size:27 final size:27
Alignment explanation
Indices: 1108800--1108880 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
1108790 ATGAGTTTAA
1108800 AAAATATTAATATTTTATTTTATTATT
1 AAAATATTAATATTTTATTTTATTATT
*
1108827 AAAATA-T-ATATTTTATATTTTATAATT
1 AAAATATTAATA-TTT-TATTTTATTATT
*
1108854 -AAAT-TTAAT-TAATT-TTTTATTATT
1 AAAATATTAATAT-TTTATTTTATTATT
1108878 AAA
1 AAA
1108881 TAATAATTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
24 9 0.20
25 7 0.16
26 10 0.22
27 19 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
AAAATATTAATATTTTATTTTATTATT
Found at i:1108894 original size:27 final size:26
Alignment explanation
Indices: 1108817--1108891 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 26
1108807 TAATATTTTA
* *
1108817 TTTTATTATTAAA-ATATATATTTTATA
1 TTTTATTATTAAATA-ATA-ATTTAATT
* *
1108844 TTTTATAATTAAAT-TTAA-TTAATT
1 TTTTATTATTAAATAATAATTTAATT
1108868 TTTTATTATTAAATAATAATTTAA
1 TTTTATTATTAAATAATAATTTAA
1108892 ATTGAATTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
24 17 0.44
25 4 0.10
26 6 0.15
27 12 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTATTATTAAATAATAATTTAATT
Found at i:1110162 original size:30 final size:30
Alignment explanation
Indices: 1110125--1110257 Score: 162
Period size: 30 Copynumber: 4.5 Consensus size: 30
1110115 TTTTTCGGGC
* * *
1110125 CTATCGGTGCTCTTCCTTGGTTTGTCCCTG
1 CTATCGGTGCTTTTCCTCGGCTTGTCCCTG
* *
1110155 GTATCGGTGCTTTTTCTCGGCTTGTCCCTG
1 CTATCGGTGCTTTTCCTCGGCTTGTCCCTG
* *
1110185 CCATCAGTGCTTTT-CTCGGCTTGTCCCTG
1 CTATCGGTGCTTTTCCTCGGCTTGTCCCTG
* *
1110214 CCATCAGTGCTTTTCCGT-GGCTTGTCCCTG
1 CTATCGGTGCTTTTCC-TCGGCTTGTCCCTG
1110244 CTATCGGTGCTTTT
1 CTATCGGTGCTTTT
1110258 TTGGGGTTTG
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
29 29 0.32
30 61 0.67
31 1 0.01
ACGTcount: A:0.05, C:0.30, G:0.23, T:0.41
Consensus pattern (30 bp):
CTATCGGTGCTTTTCCTCGGCTTGTCCCTG
Found at i:1110224 original size:59 final size:59
Alignment explanation
Indices: 1110146--1110257 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
1110136 CTTCCTTGGT
** * *
1110146 TTGTCCCTGGTATCGGTGCTTTTTC-TCGGCTTGTCCCTGCCATCAGTGCTTTTCTCGGC
1 TTGTCCCTGCCATCAGTGCTTTTCCGT-GGCTTGTCCCTGCCATCAGTGCTTTTCTCGGC
* *
1110205 TTGTCCCTGCCATCAGTGCTTTTCCGTGGCTTGTCCCTGCTATCGGTGCTTTT
1 TTGTCCCTGCCATCAGTGCTTTTCCGTGGCTTGTCCCTGCCATCAGTGCTTTT
1110258 TTGGGGTTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.05, C:0.30, G:0.23, T:0.41
Consensus pattern (59 bp):
TTGTCCCTGCCATCAGTGCTTTTCCGTGGCTTGTCCCTGCCATCAGTGCTTTTCTCGGC
Found at i:1110269 original size:30 final size:29
Alignment explanation
Indices: 1110146--1110275 Score: 145
Period size: 30 Copynumber: 4.4 Consensus size: 29
1110136 CTTCCTTGGT
* *
1110146 TTGTCCCTGGTATCGGTGCTTTTTCTCGGC
1 TTGTCCCTGCTATCAGTGC-TTTTCTCGGC
*
1110176 TTGTCCCTGCCATCAGTGCTTTTCTCGGC
1 TTGTCCCTGCTATCAGTGCTTTTCTCGGC
*
1110205 TTGTCCCTGCCATCAGTGCTTTTC-CGTGGC
1 TTGTCCCTGCTATCAGTGCTTTTCTC--GGC
* * * *
1110235 TTGTCCCTGCTATCGGTGCTTTTTTGGGGT
1 TTGTCCCTGCTATCAGTGCTTTTCT-CGGC
1110265 TTGTCCCTGCT
1 TTGTCCCTGCT
1110276 GTCTATGCTC
Statistics
Matches: 88, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
28 1 0.01
29 34 0.39
30 53 0.60
ACGTcount: A:0.05, C:0.29, G:0.25, T:0.42
Consensus pattern (29 bp):
TTGTCCCTGCTATCAGTGCTTTTCTCGGC
Found at i:1110679 original size:2 final size:2
Alignment explanation
Indices: 1110672--1110706 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1110662 ACGTATACAT
1110672 AC AC AC 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 AC AC AC A
1110707 TATATATATT
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1111990 original size:31 final size:30
Alignment explanation
Indices: 1111899--1111990 Score: 84
Period size: 30 Copynumber: 3.0 Consensus size: 30
1111889 CAGGTACTTC
1111899 AACTAGTCAAAGTTCATTAAACATTTTTCTT
1 AACTAGTCAAAGTTCA-TAAACATTTTTCTT
* *
1111930 AACT-G--AACA-TGACATAAAAACTTTTTTCTT
1 AACTAGTCAA-AGT-TCAT--AAACATTTTTCTT
1111960 AACTAGTCAAAGTTCAGTAAACATTTTTCTT
1 AACTAGTCAAAGTTCA-TAAACATTTTTCTT
1111991 GACATATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
28 4 0.08
29 3 0.06
30 17 0.35
31 17 0.35
32 3 0.06
33 4 0.08
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (30 bp):
AACTAGTCAAAGTTCATAAACATTTTTCTT
Found at i:1112321 original size:2 final size:2
Alignment explanation
Indices: 1112316--1112343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1112306 ATGAGGGGGG
1112316 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1112344 ACCTTGTAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1113381 original size:20 final size:21
Alignment explanation
Indices: 1113345--1113383 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1113335 ACACTTTCAT
*
1113345 AAAAACATTTGTTTTGCTCTA
1 AAAAACATTTGTCTTGCTCTA
1113366 AAAAACATTT-TCTTGCTC
1 AAAAACATTTGTCTTGCTC
1113384 ATGCATGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (21 bp):
AAAAACATTTGTCTTGCTCTA
Found at i:1114722 original size:17 final size:17
Alignment explanation
Indices: 1114702--1114837 Score: 67
Period size: 17 Copynumber: 8.1 Consensus size: 17
1114692 ATAAAAATAT
1114702 AAATTAATAATATATTA
1 AAATTAATAATATATTA
* * *
1114719 AAATTTATAAAATATAA
1 AAATTAATAATATATTA
1114736 AATATTTAA-AATA-ATTA
1 AA-A-TTAATAATATATTA
*
1114753 TAA--AATAA-ATA-TA
1 AAATTAATAATATATTA
1114766 AATTATTAATAAATATATT-
1 AA--ATTAAT-AATATATTA
*
1114785 AAA--AA-CATATATTA
1 AAATTAATAATATATTA
*
1114799 TAAATTAATATTATATTA
1 -AAATTAATAATATATTA
*
1114817 AAATTTATATAATATTTTA
1 AAA-TTA-ATAATATATTA
1114836 AA
1 AA
1114838 TATAATTAAC
Statistics
Matches: 88, Mismatches: 13, Indels: 34
0.65 0.10 0.25
Matches are distributed among these distances:
13 13 0.15
14 3 0.03
15 6 0.07
16 1 0.01
17 29 0.33
18 16 0.18
19 19 0.22
20 1 0.01
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATTAATAATATATTA
Found at i:1114758 original size:11 final size:11
Alignment explanation
Indices: 1114731--1114807 Score: 54
Period size: 11 Copynumber: 7.0 Consensus size: 11
1114721 ATTTATAAAA
1114731 TATAAAAT-AT
1 TATAAAATAAT
1114741 T-TAAAATAAT
1 TATAAAATAAT
*
1114751 TATAAAATAAA
1 TATAAAATAAT
*
1114762 TAT-AAATTAT
1 TATAAAATAAT
1114772 TA-ATAAATATAT
1 TATA-AAATA-AT
*
1114784 TAAAAACATATAT
1 TATAAA-ATA-AT
*
1114797 TATAAATTAAT
1 TATAAAATAAT
1114808 ATTATATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
9 6 0.11
10 11 0.20
11 17 0.31
12 8 0.15
13 12 0.22
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (11 bp):
TATAAAATAAT
Found at i:1114764 original size:24 final size:26
Alignment explanation
Indices: 1114702--1114759 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
1114692 ATAAAAATAT
1114702 AAAT-TAATAATATATTAAAATTTATA
1 AAATATAA-AATATATTAAAATTTATA
1114728 AAATATAAAATAT-TTAAAATAATTATA
1 AAATATAAAATATATTAAAAT--TTATA
1114755 AAATA
1 AAATA
1114760 AATATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.24
26 9 0.31
27 13 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATATAAAATATATTAAAATTTATA
Found at i:1114766 original size:31 final size:32
Alignment explanation
Indices: 1114704--1114819 Score: 89
Period size: 31 Copynumber: 3.6 Consensus size: 32
1114694 AAAAATATAA
1114704 ATTAAT-AATATATTAAAATTTATAAAATATAAAAT
1 ATTAATAAATATATTAAAA---AT-AAATATAAAAT
* *
1114739 ATTTA-AAATA-ATTATAAAATAAATATAAATT
1 ATTAATAAATATATTA-AAAATAAATATAAAAT
* * *
1114770 ATTAATAAATATATTAAAAACATATATTATAA-
1 ATTAATAAATATATTAAAAATAAATA-TAAAAT
*
1114802 ATTAAT-ATTATATTAAAA
1 ATTAATAAATATATTAAAA
1114820 TTTATATAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
31 25 0.37
32 21 0.31
33 7 0.10
34 4 0.06
35 11 0.16
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (32 bp):
ATTAATAAATATATTAAAAATAAATATAAAAT
Found at i:1114809 original size:15 final size:15
Alignment explanation
Indices: 1114744--1114809 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
1114734 AAAATATTTA
1114744 AAATA-ATTATAAAAT
1 AAATATATTAT-AAAT
*
1114759 AAATATAAATTATTAAT
1 AAATAT--ATTATAAAT
1114776 AAATATATTA-AAA-
1 AAATATATTATAAAT
*
1114789 ACATATATTATAAAT
1 AAATATATTATAAAT
*
1114804 TAATAT
1 AAATAT
1114810 TATATTAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 9 0.22
14 5 0.12
15 13 0.32
17 9 0.22
18 5 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (15 bp):
AAATATATTATAAAT
Found at i:1114813 original size:18 final size:18
Alignment explanation
Indices: 1114792--1114843 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
1114782 ATTAAAAACA
1114792 TATATTATAAATTAATAT
1 TATATTATAAATTAATAT
*
1114810 TATATTA-AAATTTATAT
1 TATATTATAAATTAATAT
* *
1114827 AATATTTTAAATATAAT
1 TATATTATAAAT-TAAT
1114844 TAACATAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 14 0.50
18 11 0.39
19 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATATTATAAATTAATAT
Found at i:1115025 original size:65 final size:64
Alignment explanation
Indices: 1114951--1115080 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 64
1114941 TTATTTATTG
* * *
1114951 AACCTCGTAGATCCTGCGAATCATTCAATTAGGCCCCTTAACTTTTATTGTCTTGGACAAAATT
1 AACCTCGTAGAGCCTACAAATCATTCAATTAGGCCCCTTAACTTTTATTGTCTTGGACAAAATT
1115015 AACCGTCGTAGAGCCTACAAATCATTCAATTAGGCCCCTTAACTTTTATTGTCTTGGACAAAATT
1 AACC-TCGTAGAGCCTACAAATCATTCAATTAGGCCCCTTAACTTTTATTGTCTTGGACAAAATT
1115080 A
1 A
1115081 TTATTTTCAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 4 0.06
65 58 0.94
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (64 bp):
AACCTCGTAGAGCCTACAAATCATTCAATTAGGCCCCTTAACTTTTATTGTCTTGGACAAAATT
Found at i:1116067 original size:19 final size:19
Alignment explanation
Indices: 1116045--1116096 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1116035 TTATTAAAAA
1116045 TTTTAATATATTAATTAATT
1 TTTTAA-ATATTAATTAATT
* *
1116065 TTTACAAATTTTAATTAATT
1 TTT-TAAATATTAATTAATT
1116085 TTTTAAATATTA
1 TTTTAAATATTA
1116097 TATTTATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 18 0.67
21 2 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTAAATATTAATTAATT
Found at i:1116442 original size:13 final size:13
Alignment explanation
Indices: 1116424--1116449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1116414 CACGTTCTAC
1116424 AAATAAAATAAAA
1 AAATAAAATAAAA
1116437 AAATAAAATAAAA
1 AAATAAAATAAAA
1116450 TAAACGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:1116607 original size:14 final size:14
Alignment explanation
Indices: 1116588--1116635 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
1116578 TAATAATAAA
1116588 AAATATTTTTATAT
1 AAATATTTTTATAT
*
1116602 AAATATTTATA-AT
1 AAATATTTTTATAT
1116615 AAATATTTTATTATAT
1 AAATA-TTT-TTATAT
1116631 AAATA
1 AAATA
1116636 ATAATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 7 0.24
14 13 0.45
15 2 0.07
16 7 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AAATATTTTTATAT
Found at i:1116618 original size:13 final size:13
Alignment explanation
Indices: 1116583--1116622 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1116573 TAAAATAATA
*
1116583 ATAAAAAATATTT
1 ATAATAAATATTT
*
1116596 TTATATAAATATTT
1 ATA-ATAAATATTT
1116610 ATAATAAATATTT
1 ATAATAAATATTT
1116623 TATTATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATAATAAATATTT
Found at i:1116820 original size:17 final size:17
Alignment explanation
Indices: 1116765--1116822 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
1116755 TGATAAGTTG
*
1116765 ATATA-AATATAAAATA
1 ATATATAATATAATATA
* * *
1116781 AT-TAAAATATATTTTA
1 ATATATAATATAATATA
1116797 A-ATTATAATATAATATA
1 ATA-TATAATATAATATA
1116814 ATATATAAT
1 ATATATAAT
1116823 TATATTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
15 2 0.06
16 11 0.34
17 18 0.56
18 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATATAATATAATATA
Found at i:1116829 original size:28 final size:28
Alignment explanation
Indices: 1116768--1116851 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 28
1116758 TAAGTTGATA
* * *
1116768 TAAA-TATAAAATAAT-TAAAATATATTT
1 TAAATTATAATATAATATAATATATA-AT
1116795 TAAATTATAATATAATATAATATATAAT
1 TAAATTATAATATAATATAATATATAAT
* * *
1116823 TATATTAAAAT-TTATATAAGTATATAAT
1 TAAATTATAATATAATATAA-TATATAAT
1116851 T
1 T
1116852 TTTTAAATGT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
27 11 0.23
28 29 0.60
29 8 0.17
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
TAAATTATAATATAATATAATATATAAT
Found at i:1117053 original size:20 final size:20
Alignment explanation
Indices: 1117011--1117053 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1117001 TTAAAATGTT
*
1117011 TTTATTTATAAATTAATTCA
1 TTTATTTATAAATTAATACA
* *
1117031 TTTATTTCTAAATTAATAGA
1 TTTATTTATAAATTAATACA
1117051 TTT
1 TTT
1117054 TATATTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTATTTATAAATTAATACA
Found at i:1117226 original size:25 final size:25
Alignment explanation
Indices: 1117188--1117247 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
1117178 TCTCTTTCTT
1117188 GTTTTGTATT-GAGTTTAATTTTATA
1 GTTTTGT-TTCGAGTTTAATTTTATA
1117213 GTTTTGTTTCGAGTTTAATTTTATA
1 GTTTTGTTTCGAGTTTAATTTTATA
1117238 GTTTTGTTTC
1 GTTTTGTTTC
1117248 CTTTAGGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 2 0.06
25 32 0.94
ACGTcount: A:0.18, C:0.03, G:0.17, T:0.62
Consensus pattern (25 bp):
GTTTTGTTTCGAGTTTAATTTTATA
Found at i:1118642 original size:11 final size:12
Alignment explanation
Indices: 1118626--1118672 Score: 53
Period size: 11 Copynumber: 4.0 Consensus size: 12
1118616 TTGATATTCG
1118626 AATTTAATA-TT
1 AATTTAATATTT
1118637 AATTTATATATTT
1 AATTTA-ATATTT
*
1118650 AA-TTATTATTT
1 AATTTAATATTT
*
1118661 AATTTTATATTT
1 AATTTAATATTT
1118673 TATACATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 13 0.43
12 13 0.43
13 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTAATATTT
Found at i:1118795 original size:5 final size:5
Alignment explanation
Indices: 1118780--1118808 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
1118770 GTGTTCAAAT
1118780 TTAAA -TAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1118809 ATATATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TTAAA
Found at i:1119260 original size:14 final size:14
Alignment explanation
Indices: 1119241--1119303 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
1119231 AAATGATAAT
1119241 TAAATATAATTATA
1 TAAATATAATTATA
1119255 TAAATATAA-TATGAA
1 TAAATATAATTAT--A
1119270 TAAA-AT-ATT-TA
1 TAAATATAATTATA
1119281 -AAATATAATATAATA
1 TAAATATAAT-T-ATA
1119296 TAAATATA
1 TAAATATA
1119304 TTTTAAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
10 3 0.08
11 3 0.08
12 2 0.05
13 6 0.15
14 12 0.30
15 7 0.17
16 7 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
TAAATATAATTATA
Found at i:1119271 original size:11 final size:10
Alignment explanation
Indices: 1119243--1119407 Score: 51
Period size: 11 Copynumber: 16.7 Consensus size: 10
1119233 ATGATAATTA
1119243 AATATAAT-T
1 AATATAATAT
1119252 -ATATAAATAT
1 AATAT-AATAT
*
1119262 AATATGAATAA
1 AATAT-AATAT
* *
1119273 AATAT-TTAA
1 AATATAATAT
1119282 AATATAATAT
1 AATATAATAT
1119292 AATATAAATAT
1 AATAT-AATAT
* * *
1119303 ATTTTAAATTT
1 AATAT-AATAT
*
1119314 TATATAATAT
1 AATATAATAT
*
1119324 AA-ATTAT-T
1 AATATAATAT
* *
1119332 AATATATTAA
1 AATATAATAT
* * *
1119342 AATTTATTAA
1 AATATAATAT
*
1119352 AATATAAAAT
1 AATATAATAT
* *
1119362 -ATTTAAAAAT
1 AATAT-AATAT
*
1119372 AATTATTATAT
1 AA-TATAATAT
1119383 AA-A-AATA-
1 AATATAATAT
1119390 AATATAATAT
1 AATATAATAT
1119400 AAATATAA
1 -AATATAA
1119408 ATTTTTAAAA
Statistics
Matches: 115, Mismatches: 27, Indels: 26
0.68 0.16 0.15
Matches are distributed among these distances:
7 2 0.02
8 11 0.10
9 26 0.23
10 33 0.29
11 41 0.36
12 2 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (10 bp):
AATATAATAT
Found at i:1119271 original size:25 final size:24
Alignment explanation
Indices: 1119230--1119406 Score: 87
Period size: 25 Copynumber: 7.0 Consensus size: 24
1119220 CTCTTAATGC
*
1119230 TAAATGATAAT-TAAATATAATTATA
1 TAAAT-ATAATAT-AATATAAATATA
*
1119255 TAAATATAATATGAATA-AAATATT
1 TAAATATAATAT-AATATAAATATA
1119279 TAAAATATAATATAATATAAATATA
1 T-AAATATAATATAATATAAATATA
* *
1119304 TTTTAAATTTTATATAATATAAAT-TA
1 ---TAAATATAATATAATATAAATATA
* * *
1119330 TTAATATATTAAAATTTATTAAA-ATA
1 TAAATATAATATAA--TA-TAAATATA
* *
1119356 TAAAATATTTAA-A-AATAATTATTATA
1 T-AAATA--TAATATAAT-ATAAATATA
*
1119382 TAAAAATAAATATAATATAAATATA
1 TAAATAT-AATATAATATAAATATA
1119407 AATTTTTAAA
Statistics
Matches: 116, Mismatches: 18, Indels: 36
0.68 0.11 0.21
Matches are distributed among these distances:
23 10 0.09
24 17 0.15
25 44 0.38
26 17 0.15
27 24 0.21
28 2 0.02
29 2 0.02
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
TAAATATAATATAATATAAATATA
Found at i:1119276 original size:30 final size:27
Alignment explanation
Indices: 1119236--1119327 Score: 84
Period size: 27 Copynumber: 3.4 Consensus size: 27
1119226 ATGCTAAATG
1119236 ATAATTAAATATAATTATATAAATATAAT
1 ATAATTAAATATAATT-TA-AAATATAAT
1119265 ATGAA-TAAA-AT-ATTTAAAATATAAT
1 AT-AATTAAATATAATTTAAAATATAAT
* * *
1119290 ATAATATAAATAT-ATTTTAAATTTTAT
1 ATAAT-TAAATATAATTTAAAATATAAT
1119317 ATAATATAAAT
1 ATAAT-TAAAT
1119328 TATTAATATA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
24 2 0.04
25 11 0.20
26 6 0.11
27 27 0.48
28 2 0.04
29 6 0.11
30 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (27 bp):
ATAATTAAATATAATTTAAAATATAAT
Found at i:1119288 original size:16 final size:16
Alignment explanation
Indices: 1119269--1119373 Score: 63
Period size: 17 Copynumber: 6.2 Consensus size: 16
1119259 TATAATATGA
1119269 ATAAAATATTTAAAAT
1 ATAAAATATTTAAAAT
* *
1119285 ATAATATAATATAAATAT
1 ATAAAAT-ATTTAAA-AT
*
1119303 ATTTTAAAT-TTTATATAAT
1 A--TAAAATATTTA-A-AAT
* *
1119322 ATAAATTA-TTAATAT
1 ATAAAATATTTAAAAT
*
1119337 ATTAAAATTTATTAAAAT
1 A-TAAAATAT-TTAAAAT
1119355 ATAAAATATTTAAAA-
1 ATAAAATATTTAAAAT
1119370 ATAA
1 ATAA
1119374 TTATTATATA
Statistics
Matches: 67, Mismatches: 12, Indels: 21
0.67 0.12 0.21
Matches are distributed among these distances:
15 7 0.10
16 18 0.27
17 20 0.30
18 13 0.19
19 4 0.06
20 5 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAAATATTTAAAAT
Found at i:1119318 original size:27 final size:27
Alignment explanation
Indices: 1119236--1119417 Score: 111
Period size: 26 Copynumber: 6.8 Consensus size: 27
1119226 ATGCTAAATG
1119236 ATAAT-TAAATATAATTATATAAATATAAT
1 ATAATATAAATAT-ATT-TA-AAATATAAT
*
1119265 ATGA-ATAAA-ATATTTAAAATATAAT
1 ATAATATAAATATATTTAAAATATAAT
1119290 ATAATATAAATATATTTTAAATTTTATATAAT
1 ATAATATAAATATA-TTTAAA----ATATAAT
* * *
1119322 ATAAATTATTAATATA-TTAAAATTTATT
1 AT-AA-TATAAATATATTTAAAATATAAT
*
1119350 AAAATATAAA-ATATTTAAAA-ATAATT
1 ATAATATAAATATATTTAAAATATAA-T
*
1119376 ATTATATAAA-A-A--T-AAATATAAT
1 ATAATATAAATATATTTAAAATATAAT
1119398 ATAAATATAAAT-T-TTTAAAA
1 AT-AATATAAATATATTTAAAA
1119418 AAATATTAAA
Statistics
Matches: 122, Mismatches: 12, Indels: 41
0.70 0.07 0.23
Matches are distributed among these distances:
22 6 0.05
23 12 0.10
25 19 0.16
26 31 0.25
27 8 0.07
28 14 0.11
29 7 0.06
32 14 0.11
33 2 0.02
34 9 0.07
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.42
Consensus pattern (27 bp):
ATAATATAAATATATTTAAAATATAAT
Found at i:1119342 original size:32 final size:32
Alignment explanation
Indices: 1119283--1119364 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 32
1119273 AATATTTAAA
* *
1119283 ATATAATAT-AATATAAATATATTTTAAATTTT
1 ATATAATATAAATATTAATATA-TTTAAAATTT
1119315 ATATAATATAAATTATTAATATA-TTAAAATTT
1 ATATAATATAAA-TATTAATATATTTAAAATTT
*
1119347 ATTAAAATATAAAATATT
1 A-TATAATAT-AAATATT
1119365 TAAAAATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 18 0.42
33 13 0.30
34 12 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATATAATATAAATATTAATATATTTAAAATTT
Found at i:1119385 original size:17 final size:17
Alignment explanation
Indices: 1119365--1119409 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1119355 ATAAAATATT
* *
1119365 TAAAAATAATTATTATA
1 TAAAAATAAATATAATA
1119382 TAAAAATAAATATAATA
1 TAAAAATAAATATAATA
*
1119399 TAAATATAAAT
1 TAAAAATAAAT
1119410 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATAAATATAATA
Found at i:1119490 original size:23 final size:23
Alignment explanation
Indices: 1119418--1119491 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
1119408 ATTTTTAAAA
* *
1119418 AAATATTAAAAAAATATTTTTATT
1 AAAT-TTAAATAAATTTTTTTATT
* * *
1119442 AATATTT--ATATATTATTATAATT
1 AA-ATTTAAATAAATT-TTTTTATT
1119465 AAATTTAAATAAATTTTTTTATT
1 AAATTTAAATAAATTTTTTTATT
1119488 AAAT
1 AAAT
1119492 AAATAATAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
22 8 0.21
23 18 0.47
24 10 0.26
25 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTAAATAAATTTTTTTATT
Found at i:1121815 original size:222 final size:216
Alignment explanation
Indices: 1121392--1121823 Score: 587
Period size: 217 Copynumber: 2.0 Consensus size: 216
1121382 GTTTTGCCAG
* * * * *
1121392 TTCCCAGTGAACATCTAAACATCCTTACTTTAGCAACACATATTTCATCAAAATTTCTTTATTTG
1 TTCCCAGTGAACATCTAAACATCATTACTTTAGCAACACACATTTCATCAAAAGTTCATAATTTG
* * * ** * *
1121457 ACAACAGAGTATGAGGGTCACAAAGAATATATTTAAATCATCGTGAATGAGATCTGTAAAAAGAA
66 ACAACAGAATATCAGGGTCACAAAGAATATATGTAAATCAAAGTGAACGAGATCCGTAAAAAGAA
1121522 TGGCAACTCGAGATCCTCATACTAGCAAAAAATCAGAAAACAACAATATCTGAGAATGATTTTGC
131 TGGCAACTCGAGATCCTCATACTAGCAAAAAATCAGAAAACAACAATATCTGAGAATGATTTTGC
*
1121587 CTGATACAAATTTCTTGCTCT
196 CTGATACAAACTTCTTGCTCT
* * *
1121608 TTCCCAGTGAATATCTAAATATCATTACTTTAGCAACACACATTTCATTCAAAAGTTGATAATTT
1 TTCCCAGTGAACATCTAAACATCATTACTTTAGCAACACACATTTCA-TCAAAAGTTCATAATTT
* * * * * *
1121673 GACGACAGAATATCAGTGTCACAAAGAATTTATGTAAATCAAAGTGAACGGGATCCGTATACAGA
65 GACAACAGAATATCAGGGTCACAAAGAATATATGTAAATCAAAGTGAACGAGATCCGTAAAAAGA
*
1121738 ATGGACATCAACTTGAGA-CCTCCATACTAGCAAAAATATCAGAAAACAACAATATCTGAGAATG
130 ATGG----CAACTCGAGATCCT-CATACTAGCAAAAA-ATCAGAAAACAACAATATCTGAGAATG
1121802 ATTTTGCCTGATACAAACTTCT
189 ATTTTGCCTGATACAAACTTCT
1121824 CATCTATGCT
Statistics
Matches: 186, Mismatches: 23, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
216 43 0.23
217 69 0.37
220 3 0.02
221 23 0.12
222 48 0.26
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.29
Consensus pattern (216 bp):
TTCCCAGTGAACATCTAAACATCATTACTTTAGCAACACACATTTCATCAAAAGTTCATAATTTG
ACAACAGAATATCAGGGTCACAAAGAATATATGTAAATCAAAGTGAACGAGATCCGTAAAAAGAA
TGGCAACTCGAGATCCTCATACTAGCAAAAAATCAGAAAACAACAATATCTGAGAATGATTTTGC
CTGATACAAACTTCTTGCTCT
Found at i:1122814 original size:38 final size:38
Alignment explanation
Indices: 1122763--1122841 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
1122753 GTGAGCTTCC
*
1122763 TGATGTTTGGTTCGAAGCAGTCGTCAAAGGGCTAACGA
1 TGATGTTTGGTTCGAAGCAGCCGTCAAAGGGCTAACGA
1122801 TGATGTTTGGTTCGAAGCAGCCGTCAAAGGGCTAACGA
1 TGATGTTTGGTTCGAAGCAGCCGTCAAAGGGCTAACGA
1122839 TGA
1 TGA
1122842 AAGGCGCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (38 bp):
TGATGTTTGGTTCGAAGCAGCCGTCAAAGGGCTAACGA
Found at i:1125677 original size:37 final size:37
Alignment explanation
Indices: 1125622--1125695 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1125612 TGACAATAGA
* *
1125622 GAGAGGTGGTCGTAATTGTTGACGATTCTTCACCAAC
1 GAGAGGTGGCCATAATTGTTGACGATTCTTCACCAAC
*
1125659 GAGAGGTGGCCATTATTGTTGACGATTCTTCACCAAC
1 GAGAGGTGGCCATAATTGTTGACGATTCTTCACCAAC
1125696 CTTTGACAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (37 bp):
GAGAGGTGGCCATAATTGTTGACGATTCTTCACCAAC
Found at i:1125734 original size:50 final size:50
Alignment explanation
Indices: 1125659--1125754 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
1125649 CTTCACCAAC
*
1125659 GAGAGGTGGCCATTATTGTTGACGATTCTTCACCAACCTTTGACAATAAA
1 GAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAAA
* * * *
1125709 GAGAGGTGGTCATAATTGTTGACGATTCTTTATCAATCTTTGACAA
1 GAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACCTTTGACAA
1125755 ATGTGGCCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (50 bp):
GAGAGGTGGCCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAAA
Found at i:1130201 original size:50 final size:50
Alignment explanation
Indices: 1130126--1130307 Score: 283
Period size: 50 Copynumber: 3.6 Consensus size: 50
1130116 AGTTGTTACC
* * * * * *
1130126 ATTGTTGACTATCCTTCATCAACCTTTGATAATAGAGAGAGGTGGTCGTA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
* *
1130176 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTTGCCATT
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
*
1130226 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGACCATA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
1130276 ATTGTTGACGATTCTTCACCAACCTTTGACAA
1 ATTGTTGACGATTCTTCACCAACCTTTGACAA
1130308 ATGTGACTAT
Statistics
Matches: 121, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 121 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (50 bp):
ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATA
Found at i:1134826 original size:35 final size:35
Alignment explanation
Indices: 1134780--1134850 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
1134770 CTGGAATATC
1134780 AAATGTGCTAAACTTATTCTCTCGGGGTTATTCTT
1 AAATGTGCTAAACTTATTCTCTCGGGGTTATTCTT
*
1134815 AAATGTGCTAAACTTATTCTCTTGGGGTTATTCTT
1 AAATGTGCTAAACTTATTCTCTCGGGGTTATTCTT
1134850 A
1 A
1134851 CTGTGTCAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (35 bp):
AAATGTGCTAAACTTATTCTCTCGGGGTTATTCTT
Found at i:1139879 original size:17 final size:18
Alignment explanation
Indices: 1139859--1139892 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1139849 AAAAAATAAA
1139859 ATTTATG-TTATATTAAT
1 ATTTATGATTATATTAAT
*
1139876 ATTTATGATTTTATTAA
1 ATTTATGATTATATTAA
1139893 AATAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (18 bp):
ATTTATGATTATATTAAT
Found at i:1141092 original size:7 final size:7
Alignment explanation
Indices: 1141082--1141111 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1141072 TTTTTTAAAT
1141082 TATTTAA
1 TATTTAA
1141089 TATTTAA
1 TATTTAA
1141096 TATTT-A
1 TATTTAA
1141102 TATTTAA
1 TATTTAA
1141109 TAT
1 TAT
1141112 GTTTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TATTTAA
Found at i:1141104 original size:13 final size:14
Alignment explanation
Indices: 1141082--1141111 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1141072 TTTTTTAAAT
1141082 TATTTAATATTTAA
1 TATTTAATATTTAA
1141096 TATTT-ATATTTAA
1 TATTTAATATTTAA
1141109 TAT
1 TAT
1141112 GTTTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTTAATATTTAA
Found at i:1141180 original size:10 final size:10
Alignment explanation
Indices: 1141145--1141185 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1141135 TATAATTTTT
1141145 TTAAAAAATA
1 TTAAAAAATA
*
1141155 TTATAAATATA
1 TTA-AAAAATA
*
1141166 TTAAAAAAAA
1 TTAAAAAATA
1141176 TTAAAAAATA
1 TTAAAAAATA
1141186 AATATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:1147547 original size:17 final size:18
Alignment explanation
Indices: 1147527--1147560 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1147517 TATTTTTGAG
1147527 ATTAT-AAAAAAATTATA
1 ATTATCAAAAAAATTATA
*
1147544 ATTATCAAAAATATTAT
1 ATTATCAAAAAAATTAT
1147561 TTGAGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTATCAAAAAAATTATA
Found at i:1148304 original size:13 final size:13
Alignment explanation
Indices: 1148286--1148312 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1148276 ACATTATGCT
1148286 TTGTATCGATACA
1 TTGTATCGATACA
1148299 TTGTATCGATACA
1 TTGTATCGATACA
1148312 T
1 T
1148313 GCTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1148342 original size:20 final size:19
Alignment explanation
Indices: 1148296--1148352 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1148286 TTGTATCGAT
1148296 ACATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
* *
1148315 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGC
*
1148334 ACAATTGTATCAATACATG
1 AC-ATTGTATCGATACATG
1148353 AGATTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1148420 original size:13 final size:13
Alignment explanation
Indices: 1148402--1148426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1148392 CATGGGATAA
1148402 TGTATCGATACAC
1 TGTATCGATACAC
1148415 TGTATCGATACA
1 TGTATCGATACA
1148427 TGAGGAAATT
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1148424 original size:33 final size:34
Alignment explanation
Indices: 1148382--1148447 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 34
1148372 TATTACTATT
1148382 TGTATCGATACATG-GGATAA-TGTATCGATACAC
1 TGTATCGATACATGAGGA-AATTGTATCGATACAC
1148415 TGTATCGATACATGAGGAAATTGTATCGATACA
1 TGTATCGATACATGAGGAAATTGTATCGATACA
1148448 TTGCTTGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 16 0.52
34 15 0.48
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (34 bp):
TGTATCGATACATGAGGAAATTGTATCGATACAC
Found at i:1149324 original size:24 final size:22
Alignment explanation
Indices: 1149297--1149350 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1149287 AAAAATTAAA
1149297 AATTAAAATATAATTTTTTAATTT
1 AATTAAAAT-TAATTTTTT-ATTT
* *
1149321 AATTAAGATTTATTTTTTATTT
1 AATTAAAATTAATTTTTTATTT
*
1149343 TATTAAAA
1 AATTAAAA
1149351 ACTAATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 10 0.38
23 8 0.31
24 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
AATTAAAATTAATTTTTTATTT
Found at i:1149757 original size:8 final size:8
Alignment explanation
Indices: 1149739--1149775 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
1149729 ATCTATATAT
1149739 AAAATTT-
1 AAAATTTA
1149746 AAAATTTAA
1 AAAATTT-A
1149755 AAAATTTA
1 AAAATTTA
1149763 AAAATTTA
1 AAAATTTA
1149771 AAAAT
1 AAAAT
1149776 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.25
8 14 0.50
9 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATTTA
Found at i:1149768 original size:17 final size:16
Alignment explanation
Indices: 1149739--1149785 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
1149729 ATCTATATAT
1149739 AAAATTTAAAATTTAA
1 AAAATTTAAAATTTAA
1149755 AAAATTTAAAAATTTAA
1 AAAATTT-AAAATTTAA
1149772 AAATATTTTAAAAT
1 AAA-A-TTTAAAAT
1149786 ATTTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.25
17 12 0.43
18 6 0.21
19 3 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTTAAAATTTAA
Found at i:1149779 original size:10 final size:9
Alignment explanation
Indices: 1149746--1149789 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
1149736 TATAAAATTT
1149746 AAAATTTAA
1 AAAATTTAA
1149755 AAAATTT-A
1 AAAATTTAA
1149763 AAAATTTAA
1 AAAATTTAA
1149772 AAATATTTTAA
1 AAA-A-TTTAA
*
1149783 AATATTT
1 AAAATTT
1149790 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
8 8 0.26
9 14 0.45
10 2 0.06
11 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTAA
Found at i:1150406 original size:7 final size:7
Alignment explanation
Indices: 1150396--1150423 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1150386 TTGAATATTT
1150396 ATAAATA
1 ATAAATA
1150403 ATAAATA
1 ATAAATA
1150410 ATAAATA
1 ATAAATA
1150417 ATAAATA
1 ATAAATA
1150424 TTTAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
ATAAATA
Found at i:1150848 original size:20 final size:20
Alignment explanation
Indices: 1150825--1150863 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1150815 TTTAAACTGA
1150825 TAAAAAATAAAAAAATCATT
1 TAAAAAATAAAAAAATCATT
** *
1150845 TAAAACCTAAAAAGATCAT
1 TAAAAAATAAAAAAATCAT
1150864 AAAAGCTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (20 bp):
TAAAAAATAAAAAAATCATT
Found at i:1150929 original size:8 final size:8
Alignment explanation
Indices: 1150916--1150940 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1150906 TGTTATTAAA
1150916 TTTAAATT
1 TTTAAATT
1150924 TTTAAATT
1 TTTAAATT
1150932 TTTAAATT
1 TTTAAATT
1150940 T
1 T
1150941 ACATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTAAATT
Found at i:1150985 original size:17 final size:17
Alignment explanation
Indices: 1150943--1150995 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
1150933 TTAAATTTAC
*
1150943 ATTAAAAATCATACTAATT
1 ATTAAAAAT-ATA-TTATT
*
1150962 AATTAAATATATATTATT
1 -ATTAAAAATATATTATT
*
1150980 ATTAAAAATTTATTAT
1 ATTAAAAATATATTAT
1150996 ATTTAATACT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 14 0.48
18 4 0.14
19 3 0.10
20 8 0.28
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAAAAATATATTATT
Found at i:1163335 original size:13 final size:13
Alignment explanation
Indices: 1163313--1163351 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1163303 TAATGAAAAA
1163313 TAAATTTAATTTT
1 TAAATTTAATTTT
**
1163326 TATGTTTAA-TTT
1 TAAATTTAATTTT
1163338 TAAATTTAATTTT
1 TAAATTTAATTTT
1163351 T
1 T
1163352 TATGATTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (13 bp):
TAAATTTAATTTT
Found at i:1163360 original size:26 final size:26
Alignment explanation
Indices: 1163313--1163380 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
1163303 TAATGAAAAA
* *
1163313 TAAATTTAA-TTTTTATGTTTAATTT
1 TAAATTTAATTTTTTATGATTAAATT
1163338 TAAATTTAATTTTTTATGATTAAATT
1 TAAATTTAATTTTTTATGATTAAATT
*
1163364 TAAATTAAAATTTTTTA
1 TAAATT-TAATTTTTTA
1163381 GTACAAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 9 0.24
26 20 0.53
27 9 0.24
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (26 bp):
TAAATTTAATTTTTTATGATTAAATT
Found at i:1163464 original size:33 final size:32
Alignment explanation
Indices: 1163427--1163490 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1163417 AATTGAATAT
* *
1163427 TTAAATTTAATTTATTTTTTAATAATAATTAAA
1 TTAAATTAAATTTATATTTTAA-AATAATTAAA
*
1163460 TTAAATTAAATTTATATTTTAAAATATTTAA
1 TTAAATTAAATTTATATTTTAAAATAATTAA
1163491 CTTTATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTAAATTAAATTTATATTTTAAAATAATTAAA
Found at i:1166620 original size:21 final size:21
Alignment explanation
Indices: 1166586--1166626 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1166576 AATTTTTATT
1166586 TAAATTTAATTATAAAATAAA
1 TAAATTTAATTATAAAATAAA
1166607 TAAATATTAA-TATAAAATAA
1 TAAAT-TTAATTATAAAATAA
1166627 TATTTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATTTAATTATAAAATAAA
Found at i:1166637 original size:19 final size:18
Alignment explanation
Indices: 1166604--1166664 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
1166594 ATTATAAAAT
*
1166604 AAATAA-ATATTAATATA
1 AAATAATATTTTAATATA
*
1166621 AAATAATATTTTTAATATTT
1 AAATAATA-TTTTAATA-TA
1166641 AAAT-ATATTTTAGATAATA
1 AAATAATATTTTA-AT-ATA
1166660 AAATA
1 AAATA
1166665 GATTGTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
17 6 0.17
18 6 0.17
19 17 0.49
20 6 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATAATATTTTAATATA
Found at i:1166818 original size:19 final size:20
Alignment explanation
Indices: 1166794--1166839 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1166784 GTTAATTAAA
1166794 ATATTAAAAATT-TATTTTT
1 ATATTAAAAATTATATTTTT
* *
1166813 ATATTAATATTTATATTTTT
1 ATATTAAAAATTATATTTTT
1166833 A-ATTAAA
1 ATATTAAA
1166840 TTATTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTAAAAATTATATTTTT
Found at i:1168009 original size:11 final size:11
Alignment explanation
Indices: 1167995--1168019 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1167985 TTTTTTTATA
1167995 TATTTAAAAAT
1 TATTTAAAAAT
1168006 TATTTAAAAAT
1 TATTTAAAAAT
1168017 TAT
1 TAT
1168020 AATTTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TATTTAAAAAT
Found at i:1170877 original size:11 final size:11
Alignment explanation
Indices: 1170848--1170877 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
1170838 GATTTATTTA
1170848 AATTAAAAATT
1 AATTAAAAATT
1170859 AATATAAAAATT
1 AAT-TAAAAATT
1170871 AATTAAA
1 AATTAAA
1170878 TGGATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTAAAAATT
Found at i:1171000 original size:18 final size:20
Alignment explanation
Indices: 1170953--1171002 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
1170943 TAAATATATG
*
1170953 TTATTAAATATATTTTAAATA
1 TTATTTAAT-TATTTTAAATA
1170974 TTAATTTAATTATTTT-AAT-
1 TT-ATTTAATTATTTTAAATA
1170993 TTATTTAATT
1 TTATTTAATT
1171003 TTATATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.30
19 2 0.07
20 3 0.11
21 8 0.30
22 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTTAATTATTTTAAATA
Found at i:1171009 original size:22 final size:21
Alignment explanation
Indices: 1170961--1171020 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
1170951 TGTTATTAAA
1170961 TATATTTTAA-ATATTAATTT
1 TATATTTTAATATATTAATTT
* *
1170981 AATTATTTTAATTTATTTAATTT
1 TA-TATTTTAATATA-TTAATTT
1171004 TATATTTTAATA-ATTAA
1 TATATTTTAATATATTAA
1171021 AAATCGATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 5 0.15
21 9 0.27
22 11 0.33
23 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTTTAATATATTAATTT
Found at i:1171678 original size:21 final size:20
Alignment explanation
Indices: 1171646--1171684 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1171636 TATTATTATT
1171646 TAAATTTAAATATAAAATATA
1 TAAATTTAAATA-AAAATATA
1171667 TAAATATT-AATAAAAATA
1 TAAAT-TTAAATAAAAATA
1171685 ATTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 9 0.53
22 2 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAATTTAAATAAAAATATA
Found at i:1172898 original size:17 final size:17
Alignment explanation
Indices: 1172875--1172913 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1172865 CGAGATTAAA
*
1172875 ATATTATAATATTTTAT
1 ATATTATAATAATTTAT
* *
1172892 TTATTATATTAATTTAT
1 ATATTATAATAATTTAT
1172909 ATATT
1 ATATT
1172914 TTTAAAATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATATTATAATAATTTAT
Found at i:1173146 original size:22 final size:20
Alignment explanation
Indices: 1173121--1173161 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
1173111 ATAAAATAAA
1173121 AATTTTAAATTAAACTAAATTC
1 AATTTTAAA-TAAA-TAAATTC
1173143 AATTTTAAATAAATAAATT
1 AATTTTAAATAAATAAATT
1173162 TTTTAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 4 0.21
22 9 0.47
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTTAAATAAATAAATTC
Found at i:1173450 original size:12 final size:12
Alignment explanation
Indices: 1173433--1173457 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1173423 AACTAAGACT
1173433 TATTAAAAATAA
1 TATTAAAAATAA
1173445 TATTAAAAATAA
1 TATTAAAAATAA
1173457 T
1 T
1173458 TACATGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TATTAAAAATAA
Found at i:1173643 original size:18 final size:18
Alignment explanation
Indices: 1173620--1173654 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1173610 TAATTTTAAA
*
1173620 TTAAATTTATTTAAAAAT
1 TTAAATATATTTAAAAAT
1173638 TTAAATATATTTAAAAA
1 TTAAATATATTTAAAAA
1173655 ATATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAATATATTTAAAAAT
Found at i:1179284 original size:6 final size:6
Alignment explanation
Indices: 1179269--1179314 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
1179259 CATCTCTCAT
* * * *
1179269 ATATAC ATATAT ATATAT ATATAG ATATAG ATATAA ATATAG ATAT
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATAT
1179315 GTACATAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (6 bp):
ATATAG
Found at i:1179290 original size:18 final size:18
Alignment explanation
Indices: 1179267--1179314 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1179257 AGCATCTCTC
* *
1179267 ATATATACATATATATAT
1 ATATATAGATATAGATAT
1179285 ATATATAGATATAGATAT
1 ATATATAGATATAGATAT
*
1179303 AAATATAGATAT
1 ATATATAGATAT
1179315 GTACATAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (18 bp):
ATATATAGATATAGATAT
Found at i:1179811 original size:3 final size:3
Alignment explanation
Indices: 1179803--1179838 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1179793 AATATGCAAT
1179803 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1179839 ATCTTAGACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1180181 original size:33 final size:33
Alignment explanation
Indices: 1180109--1180193 Score: 84
Period size: 33 Copynumber: 2.6 Consensus size: 33
1180099 ATCGATTTAA
1180109 ATTAA-TATTTAATAATAAAAAATTATAAAATAT
1 ATTAATTA-TTAATAATAAAAAATTATAAAATAT
* ** *
1180142 AATAATTATTAAT-ATAAAAAAGTTATAATTTTT
1 ATTAATTATTAATAATAAAAAA-TTATAAAATAT
* *
1180175 ATTAATTATGAAAAATAAA
1 ATTAATTATTAATAATAAA
1180194 TATAAATAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
32 8 0.19
33 27 0.64
34 7 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (33 bp):
ATTAATTATTAATAATAAAAAATTATAAAATAT
Found at i:1180197 original size:29 final size:26
Alignment explanation
Indices: 1180135--1180220 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
1180125 AAAAAATTAT
1180135 AAAATATAATAATTATTAATATAAAA
1 AAAATATAATAATTATTAATATAAAA
** **
1180161 AAGTTATAATTTTTATTAATTATGAAAA
1 AAAATATAATAATTATTAA-TAT-AAAA
1180189 ATAAATATAAATAA-T-TTAA-ATAAAA
1 A-AAATAT-AATAATTATTAATATAAAA
1180214 TAAAATA
1 -AAAATA
1180221 AATTTATTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
25 9 0.19
26 18 0.38
27 3 0.06
28 9 0.19
29 5 0.11
30 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
AAAATATAATAATTATTAATATAAAA
Found at i:1180219 original size:19 final size:20
Alignment explanation
Indices: 1180187--1180226 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1180177 TAATTATGAA
1180187 AAATAAATATAAAT-AATTT
1 AAATAAATATAAATAAATTT
1180206 AAATAAA-ATAAAATAAATTT
1 AAATAAATAT-AAATAAATTT
1180226 A
1 A
1180227 TTCAAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 11 0.58
20 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAAATATAAATAAATTT
Found at i:1180233 original size:24 final size:24
Alignment explanation
Indices: 1180186--1180233 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1180176 TTAATTATGA
*
1180186 AAAATAAATATAAATAATTTAAAT
1 AAAATAAATATAAATAATTCAAAT
*
1180210 AAAATAAA-ATAAATTTATTCAAAT
1 AAAATAAATATAAA-TAATTCAAAT
1180234 CTAAACGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAATAAATATAAATAATTCAAAT
Found at i:1182034 original size:2 final size:2
Alignment explanation
Indices: 1182027--1182064 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1182017 CAAAGGCACT
1182027 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1182065 AAGCAGCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1182494 original size:13 final size:15
Alignment explanation
Indices: 1182463--1182493 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1182453 TTTTTTTAAA
1182463 ATAACATATATATAT
1 ATAACATATATATAT
*
1182478 ATAACATAAATATAT
1 ATAACATATATATAT
1182493 A
1 A
1182494 AATATTTAAA
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:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAACATATATATAT
Found at i:1182853 original size:20 final size:21
Alignment explanation
Indices: 1182818--1182859 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1182808 ATTATTTTTT
*
1182818 ATATTATATATTTTTATTTAAA
1 ATATTATATA-TTTTATATAAA
1182840 ATATTATATA-TTTATATAAA
1 ATATTATATATTTTATATAAA
1182860 TTTTTATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
22 10 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATATTATATATTTTATATAAA
Found at i:1182866 original size:20 final size:20
Alignment explanation
Indices: 1182818--1182878 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1182808 ATTATTTTTT
*
1182818 ATATTATATATTTTTATTTAAA
1 ATATTATATA--TTTATATAAA
1182840 ATATTATATATTTATATAAA
1 ATATTATATATTTATATAAA
* * * *
1182860 TTTTTATACATTAATATAA
1 ATATTATATATTTATATAA
1182879 TTTATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 24 0.71
22 10 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTATATATTTATATAAA
Found at i:1182898 original size:33 final size:30
Alignment explanation
Indices: 1182815--1182921 Score: 85
Period size: 33 Copynumber: 3.3 Consensus size: 30
1182805 AAAATTATTT
*
1182815 TTTATATTATAT--ATTTT-TATTTAAAATA
1 TTTATATTATATAAATTTTATAATT-AAATA
1182843 TTATATATTTATATAAATTTTTATACATTAATATAA
1 TT-TATA-TTATATAAA-TTTTATA-ATTAA-AT-A
*
1182879 TTTATATTATATAAATTTTAATTTATTAAATTA
1 TTTATATTATATAAATTTT-A-TAATTAAA-TA
1182912 TTTATATTAT
1 TTTATATTAT
1182922 TTTTTTTATA
Statistics
Matches: 65, Mismatches: 2, Indels: 19
0.76 0.02 0.22
Matches are distributed among these distances:
28 2 0.03
29 4 0.06
30 6 0.09
32 1 0.02
33 20 0.31
34 20 0.31
35 9 0.14
36 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTATATTATATAAATTTTATAATTAAATA
Found at i:1182929 original size:14 final size:15
Alignment explanation
Indices: 1182912--1182940 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1182902 TATTAAATTA
1182912 TTTATATTAT-TTTT
1 TTTATATTATATTTT
1182926 TTTATATTATATTTT
1 TTTATATTATATTTT
1182941 ATTTTTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATATTATATTTT
Found at i:1183432 original size:26 final size:26
Alignment explanation
Indices: 1183380--1183433 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1183370 TTAAATATTG
*
1183380 ATAAAATTTAACTTAACCTGAATTTA
1 ATAAAATTTAACTTAACATGAATTTA
* *
1183406 ATAAAATTTAATTTTACAT-AATCTTA
1 ATAAAATTTAACTTAACATGAAT-TTA
1183432 AT
1 AT
1183434 CATTAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 3 0.12
26 21 0.88
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
ATAAAATTTAACTTAACATGAATTTA
Found at i:1183612 original size:29 final size:30
Alignment explanation
Indices: 1183558--1183615 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1183548 TCAAATCATG
*
1183558 TTAATTTTTATATATTTTTATTTTTTTACT
1 TTAATTTTTATATATTTTTATGTTTTTACT
1183588 TTAATTTTT-T-TATTTATTATGTTTTTAC
1 TTAATTTTTATATATTT-TTATGTTTTTAC
1183616 ATAATAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.19
29 12 0.46
30 9 0.35
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.72
Consensus pattern (30 bp):
TTAATTTTTATATATTTTTATGTTTTTACT
Found at i:1185264 original size:20 final size:21
Alignment explanation
Indices: 1185227--1185271 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1185217 TATTGTTAAG
*
1185227 ATTTTTTAAATATATAAA-AT
1 ATTTTTTAAAAATATAAATAT
1185247 ATTTTTTAAAAA-ATTAAATAT
1 ATTTTTTAAAAATA-TAAATAT
1185268 ATTT
1 ATTT
1185272 ATTTCGAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 15 0.68
21 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTTTAAAAATATAAATAT
Found at i:1188477 original size:9 final size:8
Alignment explanation
Indices: 1188452--1188524 Score: 55
Period size: 7 Copynumber: 9.2 Consensus size: 8
1188442 ACCGACAAAA
1188452 ATATTTAAT
1 ATATTT-AT
1188461 ATATTTAT
1 ATATTTAT
1188469 CATATTTAT
1 -ATATTTAT
* *
1188478 AT-GTAAT
1 ATATTTAT
1188485 AT-TTTAT
1 ATATTTAT
1188492 ATATTT-T
1 ATATTTAT
*
1188499 ATAATTA-
1 ATATTTAT
1188506 ATATTATAT
1 ATATT-TAT
*
1188515 TTATTTAT
1 ATATTTAT
1188523 AT
1 AT
1188525 TTATATAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
7 20 0.39
8 13 0.25
9 18 0.35
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (8 bp):
ATATTTAT
Found at i:1188499 original size:23 final size:21
Alignment explanation
Indices: 1188461--1188530 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 21
1188451 AATATTTAAT
1188461 ATATT-TATCATATTTATATGTA
1 ATATTATAT-ATATTTATAT-TA
*
1188483 ATATTTTATATATTTTATAATTA
1 ATATTATATATA-TTTAT-ATTA
* *
1188506 ATATTATATTTATTTATATTT
1 ATATTATATATATTTATATTA
1188527 ATAT
1 ATAT
1188531 AAAATATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.17
22 13 0.31
23 20 0.48
24 2 0.05
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (21 bp):
ATATTATATATATTTATATTA
Found at i:1188536 original size:28 final size:27
Alignment explanation
Indices: 1188481--1188542 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
1188471 TATTTATATG
1188481 TAATATTTTATATATTTTATAATTAATA
1 TAATATTTTATATATTTTATAA-TAATA
* *
1188509 TTATATTTATTTATATTTATATAA-AATA
1 TAATATTT-TATATATTT-TATAATAATA
1188537 TAATAT
1 TAATAT
1188543 ATATATACAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 16 0.55
29 8 0.28
30 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TAATATTTTATATATTTTATAATAATA
Found at i:1188807 original size:17 final size:17
Alignment explanation
Indices: 1188773--1188805 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1188763 AAAATTAATT
1188773 TTTTATTTAAATTTAAA
1 TTTTATTTAAATTTAAA
1188790 TTTTATTT-AATTTAAA
1 TTTTATTTAAATTTAAA
1188806 ATAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATTTAAATTTAAA
Done.