Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 11 of 19
Found at i:1733166 original size:14 final size:15
Alignment explanation
Indices: 1733147--1733179 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1733137 AATAGTAATT
1733147 TAAATTT-AATTAAA
1 TAAATTTAAATTAAA
1733161 TAAATTTAAATTAAA
1 TAAATTTAAATTAAA
1733176 -AAAT
1 TAAAT
1733180 ATATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAATTTAAATTAAA
Found at i:1733166 original size:20 final size:21
Alignment explanation
Indices: 1733133--1733198 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 21
1733123 AATTTTTATT
1733133 ATTAAATAGTAATTTAAATTTA
1 ATTAAATA-TAATTTAAATTTA
1733155 ATTAAATA-AATTTAAA-TTA
1 ATTAAATATAATTTAAATTTA
*
1733174 A-AAAATATATATTTAAAATTTA
1 ATTAAATATA-ATTT-AAATTTA
1733196 ATT
1 ATT
1733199 TAACTCATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
18 5 0.14
19 5 0.14
20 12 0.32
21 3 0.08
22 12 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTAAATATAATTTAAATTTA
Found at i:1733174 original size:25 final size:25
Alignment explanation
Indices: 1733110--1733175 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
1733100 TTTTTATAAT
* * *
1733110 TAAATTTAAATAAAATTTTTATTAT
1 TAAATTTAAATTAAATTTTAATTAA
* *
1733135 TAAATAGTAATTTAAA-TTTAATTAAA
1 TAAAT-TTAAATTAAATTTTAATT-AA
1733161 TAAATTTAAATTAAA
1 TAAATTTAAATTAAA
1733176 AAATATATAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
25 19 0.59
26 13 0.41
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
TAAATTTAAATTAAATTTTAATTAA
Found at i:1733915 original size:34 final size:35
Alignment explanation
Indices: 1733855--1733944 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 35
1733845 TTATTCGAGT
* * * *
1733855 TTAATTAAATTTGATATTATTTTTTATT-ATTTAAA
1 TTAATTTAATTT-AAATTATTATTTATTGATTAAAA
1733890 TTAATTTAATTTAAATTATTATTTATTGATTAAAA
1 TTAATTTAATTTAAATTATTATTTATTGATTAAAA
*
1733925 TAATAATTTTTATTTAAATT
1 T--TAA-TTTAATTTAAATT
1733945 TAATTATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
34 13 0.28
35 18 0.39
37 3 0.07
38 12 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (35 bp):
TTAATTTAATTTAAATTATTATTTATTGATTAAAA
Found at i:1734235 original size:13 final size:15
Alignment explanation
Indices: 1734217--1734254 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
1734207 GTAAGATAAA
1734217 TATATTTA-ATTTTT
1 TATATTTATATTTTT
1734231 T-TA-TTATATTTTT
1 TATATTTATATTTTT
1734244 TATATTTATAT
1 TATATTTATAT
1734255 ATTATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 9 0.43
14 3 0.14
15 6 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATATTTATATTTTT
Found at i:1734250 original size:22 final size:22
Alignment explanation
Indices: 1734221--1734288 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
1734211 GATAAATATA
1734221 TTTA-ATTTTTTTATTATATTT
1 TTTATATTTTTTTATTATATTT
* *
1734242 TTTATATTTATATATTATATTT
1 TTTATATTTTTTTATTATATTT
1734264 TAATTAT-TTTTATATTATTATATTT
1 T--TTATATTTT-T-TTATTATATTT
1734289 ATGTCAATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
21 4 0.11
22 16 0.42
23 3 0.08
24 5 0.13
25 10 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTATATTTTTTTATTATATTT
Found at i:1734280 original size:11 final size:11
Alignment explanation
Indices: 1734225--1734282 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
1734215 AATATATTTA
*
1734225 ATTTTTTTATT
1 ATTTTTATATT
*
1734236 ATATTTTTTA-T
1 AT-TTTTATATT
*
1734247 ATTTATATATT
1 ATTTTTATATT
1734258 ATATTTTA-ATT
1 AT-TTTTATATT
1734269 ATTTTTATATT
1 ATTTTTATATT
1734280 ATT
1 ATT
1734283 ATATTTATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 10 0.25
11 19 0.47
12 11 0.28
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTTTATATT
Found at i:1734482 original size:15 final size:15
Alignment explanation
Indices: 1734464--1734502 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1734454 GTGTAAATTT
1734464 ATTTATTTTAAATAG
1 ATTTATTTTAAATAG
*
1734479 ATTTATTATTAAATTG
1 ATTTATT-TTAAATAG
*
1734495 AGTTATTT
1 ATTTATTT
1734503 ATTTGAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (15 bp):
ATTTATTTTAAATAG
Found at i:1734696 original size:20 final size:20
Alignment explanation
Indices: 1734649--1734703 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1734639 AATAATTAAA
1734649 AAATTAT-TTAAACTT--TT
1 AAATTATATTAAACTTAATT
*
1734666 AAATTAAATTAAACTTAATT
1 AAATTATATTAAACTTAATT
* *
1734686 TAATTATATTATACTTAA
1 AAATTATATTAAACTTAA
1734704 CTCGAGCTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 6 0.19
18 8 0.26
20 17 0.55
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATATTAAACTTAATT
Found at i:1737721 original size:31 final size:31
Alignment explanation
Indices: 1737680--1737744 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1737670 ATATGACACA
*
1737680 AAACCGAAATTTTATCACAAAACTAAAAGAG
1 AAACCGAAATTTCATCACAAAACTAAAAGAG
* *
1737711 AAACCTAAATTTCATCGCAAAACTAAAAGAG
1 AAACCGAAATTTCATCACAAAACTAAAAGAG
1737742 AAA
1 AAA
1737745 GAGCAAGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.17, G:0.09, T:0.18
Consensus pattern (31 bp):
AAACCGAAATTTCATCACAAAACTAAAAGAG
Found at i:1743537 original size:2 final size:2
Alignment explanation
Indices: 1743530--1743561 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1743520 ACAAATTGTA
1743530 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
1743562 TTGTTTTACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1745391 original size:20 final size:21
Alignment explanation
Indices: 1745355--1745394 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1745345 AAATAAAATT
1745355 AATTTAATTTAAAAATATAAA
1 AATTTAATTTAAAAATATAAA
*
1745376 AATTTTATTT-AAAATATAA
1 AATTTAATTTAAAAATATAA
1745395 CCTAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTAATTTAAAAATATAAA
Found at i:1745574 original size:5 final size:5
Alignment explanation
Indices: 1745566--1745623 Score: 52
Period size: 5 Copynumber: 12.2 Consensus size: 5
1745556 AGAGTAATTC
* * *
1745566 ATTTA ATTTA A-TAA ATTTA ATTTAA ATTT- -TTT- ATTTA AGTTA TTTTA
1 ATTTA ATTTA ATTTA ATTTA ATTT-A ATTTA ATTTA ATTTA ATTTA ATTTA
1745613 ATTTA ATTTA A
1 ATTTA ATTTA A
1745624 ATAATTATTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
3 3 0.07
4 6 0.14
5 29 0.67
6 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:1745638 original size:20 final size:18
Alignment explanation
Indices: 1745614--1745662 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 18
1745604 GTTATTTTAA
1745614 TTTAATTTAAATAATTATT
1 TTTAATTTAAATAA-TATT
* *
1745633 TATTAAATAAAATAATATT
1 T-TTAATTTAAATAATATT
1745652 TTT-ATTTAAAT
1 TTTAATTTAAAT
1745663 TTAATTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.24
18 2 0.08
19 6 0.24
20 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAATTTAAATAATATT
Found at i:1745698 original size:27 final size:29
Alignment explanation
Indices: 1745633--1745698 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 29
1745623 AATAATTATT
1745633 TATTAA-AT-AAAATAATATTTTTATTTAAA
1 TATTAATATAAAAATAATATTTTTA--TAAA
1745662 T-TTAATTATAAAAATAAT-TTTTTA-AAA
1 TATTAA-TATAAAAATAATATTTTTATAAA
1745689 TATTAATATA
1 TATTAATATA
1745699 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
27 8 0.24
28 8 0.24
29 1 0.03
30 8 0.24
31 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TATTAATATAAAAATAATATTTTTATAAA
Found at i:1745890 original size:20 final size:18
Alignment explanation
Indices: 1745867--1745911 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
1745857 AAATTTATTG
*
1745867 TATATGAATTTAATTTAAGT
1 TATATAAATTT-ATTTAA-T
1745887 TATATTAAATTTATTTAAT
1 TATA-TAAATTTATTTAAT
1745906 TATATA
1 TATATA
1745912 TTAGTTCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 2 0.09
19 5 0.22
20 10 0.43
21 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
TATATAAATTTATTTAAT
Found at i:1745914 original size:21 final size:21
Alignment explanation
Indices: 1745873--1745910 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
1745863 ATTGTATATG
1745873 AATTTAATTTAAGTTATATTA
1 AATTTAATTTAAGTTATATTA
1745894 AATTT-ATTTAA-TTATAT
1 AATTTAATTTAAGTTATAT
1745911 ATTAGTTCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
AATTTAATTTAAGTTATATTA
Found at i:1746345 original size:40 final size:41
Alignment explanation
Indices: 1746268--1746345 Score: 99
Period size: 40 Copynumber: 1.9 Consensus size: 41
1746258 ATTCAAATTA
* *
1746268 TAAATTTTTAAATGTTAATTAATTATATATATTAATTGAGT
1 TAAATTTTTAAATGTTAATTAATCATATATATAAATTGAGT
1746309 TAAA-TTTTAAAT-TATAATTAATCATA-ATTATAAATTG
1 TAAATTTTTAAATGT-TAATTAATCATATA-TATAAATTG
1746346 TATAATAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
39 2 0.06
40 27 0.82
41 4 0.12
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (41 bp):
TAAATTTTTAAATGTTAATTAATCATATATATAAATTGAGT
Found at i:1746751 original size:23 final size:23
Alignment explanation
Indices: 1746703--1746752 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1746693 AATTAGTTAA
* * *
1746703 TATATTATTTATAATAATATTAT
1 TATATTAATTAAAATAATAATAT
1746726 TATATTAATTAAATATAATAAT-T
1 TATATTAATTAAA-ATAATAATAT
1746749 TATA
1 TATA
1746753 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TATATTAATTAAAATAATAATAT
Found at i:1747669 original size:15 final size:15
Alignment explanation
Indices: 1747640--1747677 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1747630 TAAATGATAT
*
1747640 TATTATTT-TTATTA
1 TATTATTTAATATTA
1747654 TATTATTTAATATTA
1 TATTATTTAATATTA
*
1747669 TATTTTTTA
1 TATTATTTA
1747678 CATTAATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTATTTAATATTA
Found at i:1750069 original size:2 final size:2
Alignment explanation
Indices: 1750062--1750090 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1750052 TATTGTTGGT
1750062 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1750091 TGGGTATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1750303 original size:19 final size:19
Alignment explanation
Indices: 1750276--1750335 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
1750266 TAGGTTTAGT
*
1750276 TTATTAAAATATAATAAAA
1 TTATAAAAATATAATAAAA
* * *
1750295 TTATAAAAAAATAAT-TAC
1 TTATAAAAATATAATAAAA
*
1750313 TATATAAAAATAAAATAAAA
1 T-TATAAAAATATAATAAAA
1750333 TTA
1 TTA
1750336 AAATTGAATA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
18 2 0.06
19 27 0.87
20 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TTATAAAAATATAATAAAA
Found at i:1750515 original size:21 final size:20
Alignment explanation
Indices: 1750489--1750548 Score: 57
Period size: 23 Copynumber: 2.8 Consensus size: 20
1750479 AATAATTATT
1750489 TAAAAATTTTATGAAATAAGA
1 TAAAAATTTTAT-AAATAAGA
* * *
1750510 TCAAAATTAATTATTATATGAGA
1 TAAAAATT--TTA-TAAATAAGA
1750533 TAAAAATTTTATAAAT
1 TAAAAATTTTATAAAT
1750549 TAAATTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
20 4 0.13
21 10 0.32
23 16 0.52
24 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (20 bp):
TAAAAATTTTATAAATAAGA
Found at i:1750975 original size:23 final size:23
Alignment explanation
Indices: 1750946--1750992 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1750936 TTTAATAATT
* *
1750946 TATATTATTGTATTATATTTTTA
1 TATATTATTATATTATAATTTTA
1750969 TATATTATTATATTATAATTTTA
1 TATATTATTATATTATAATTTTA
1750992 T
1 T
1750993 TTAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TATATTATTATATTATAATTTTA
Found at i:1750984 original size:15 final size:14
Alignment explanation
Indices: 1750966--1751057 Score: 59
Period size: 14 Copynumber: 6.4 Consensus size: 14
1750956 TATTATATTT
1750966 TTATATATTATTATA
1 TTATATATT-TTATA
1750981 TTATA-ATTTTAT-
1 TTATATATTTTATA
*
1750993 TTAAAATATTTTATA
1 TT-ATATATTTTATA
1751008 TTTATATAAATTTTA-A
1 -TTATAT--ATTTTATA
*
1751024 TTATAAGATTTT-TA
1 TTAT-ATATTTTATA
*
1751038 -AATATATATTTATA
1 TTATATAT-TTTATA
1751052 TTATAT
1 TTATAT
1751058 TATTATTACT
Statistics
Matches: 60, Mismatches: 6, Indels: 22
0.68 0.07 0.25
Matches are distributed among these distances:
12 5 0.08
13 11 0.18
14 18 0.30
15 16 0.27
16 4 0.07
17 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (14 bp):
TTATATATTTTATA
Found at i:1751009 original size:45 final size:45
Alignment explanation
Indices: 1750958--1751065 Score: 127
Period size: 43 Copynumber: 2.5 Consensus size: 45
1750948 TATTATTGTA
* **
1750958 TTATATTTTTATATATTATTATATTATAATTTTATTTAAA-ATAT-T
1 TTATATTTATATATATTATTA-ATTATAAGATT-TTTAAATATATAT
*
1751003 TTATATTTATATAAATT-TTAATTATAAGATTTTTAAATATATAT
1 TTATATTTATATATATTATTAATTATAAGATTTTTAAATATATAT
1751047 TTATA-TTATAT-TATTATTA
1 TTATATTTATATATATTATTA
1751066 CTTTATACTA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
42 9 0.16
43 22 0.40
44 9 0.16
45 15 0.27
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (45 bp):
TTATATTTATATATATTATTAATTATAAGATTTTTAAATATATAT
Found at i:1751046 original size:32 final size:32
Alignment explanation
Indices: 1750977--1751046 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
1750967 TATATATTAT
*
1750977 TATAT-TATAATTTTATTTAAAATATTTTATA
1 TATATATATAATTTTATTTAAAATATTTTAAA
* *
1751008 TTTATATA-AATTTTAATTATAAGAT-TTTTAAA
1 TATATATATAATTTT-ATT-TAAAATATTTTAAA
1751040 TATATAT
1 TATATAT
1751047 TTATATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
31 10 0.31
32 17 0.53
33 5 0.16
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
TATATATATAATTTTATTTAAAATATTTTAAA
Found at i:1751961 original size:36 final size:36
Alignment explanation
Indices: 1751911--1751984 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
1751901 TTAATTTTTT
** *
1751911 AAATAATTTTAATATAATATGATAAT-ATTATATAAA
1 AAATAATTAAAATATAATATGA-AATAAATATATAAA
*
1751947 AAATAATTAAAATATAATATTAAATAAATATATAAA
1 AAATAATTAAAATATAATATGAAATAAATATATAAA
1751983 AA
1 AA
1751985 TTTATATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 3 0.09
36 30 0.91
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (36 bp):
AAATAATTAAAATATAATATGAAATAAATATATAAA
Found at i:1751975 original size:25 final size:24
Alignment explanation
Indices: 1751934--1752012 Score: 83
Period size: 25 Copynumber: 3.3 Consensus size: 24
1751924 ATAATATGAT
1751934 AATATTATATAAA-AAATAATTAA
1 AATATTATATAAATAAATAATTAA
* *
1751957 AATATAATATTAAATAAATATATAAA
1 AATATTATA-TAAATAAATA-ATTAA
*
1751983 AAT-TTATATAATATAAATTA-TAA
1 AATATTATATAA-ATAAATAATTAA
1752006 AATATTA
1 AATATTA
1752013 AAAAATATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
23 13 0.28
24 11 0.24
25 15 0.33
26 7 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATATTATATAAATAAATAATTAA
Found at i:1751998 original size:17 final size:16
Alignment explanation
Indices: 1751976--1752036 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
1751966 TTAAATAAAT
1751976 ATATAAAAATTTATATA
1 ATATAAAAA-TTATATA
*
1751993 ATAT--AAATTATAAA
1 ATATAAAAATTATATA
*
1752007 ATATTAAAAAATATATAA
1 ATA-TAAAAATTATAT-A
1752025 ATATATAAAATT
1 ATATA-AAAATT
1752037 TTAAATTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.26
15 4 0.11
17 13 0.37
18 9 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATTATATA
Found at i:1752015 original size:32 final size:35
Alignment explanation
Indices: 1751921--1752029 Score: 104
Period size: 36 Copynumber: 3.2 Consensus size: 35
1751911 AAATAATTTT
* *
1751921 AATATAATATGATAAT-ATTATATAAAAAATA-ATTAA
1 AATATAATATTA-AATAAATATATAAAAAATATA-T-A
*
1751957 AATATAATATTAAATAAATATAT-AAAAATTTATA
1 AATATAATATTAAATAAATATATAAAAAATATATA
*
1751991 TAATATAA-ATTATA-AAATAT-TAAAAAATATATA
1 -AATATAATATTAAATAAATATATAAAAAATATATA
1752024 AATATA
1 AATATA
1752030 TAAAATTTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
32 7 0.11
33 16 0.25
34 6 0.09
35 17 0.27
36 18 0.28
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (35 bp):
AATATAATATTAAATAAATATATAAAAAATATATA
Found at i:1752033 original size:51 final size:45
Alignment explanation
Indices: 1751970--1752074 Score: 120
Period size: 45 Copynumber: 2.2 Consensus size: 45
1751960 ATAATATTAA
1751970 ATAAATATATAAAAATTTATATAATATAAATTATAAAATATTAAAAAATAT
1 ATAAATATAT-AAAATTT-TA-AAT-TAAATTATAAAATA--AAAAAATAT
* * *
1752021 ATAAATATATAAAATTTTAAATTCAATTATAACATAAAAAATTAT
1 ATAAATATATAAAATTTTAAATTAAATTATAAAATAAAAAAATAT
*
1752066 ACAAATATA
1 ATAAATATA
1752075 ATATTTATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
45 16 0.32
47 12 0.24
48 3 0.06
49 2 0.04
50 7 0.14
51 10 0.20
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (45 bp):
ATAAATATATAAAATTTTAAATTAAATTATAAAATAAAAAAATAT
Found at i:1752268 original size:23 final size:23
Alignment explanation
Indices: 1752218--1752261 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
1752208 ATTATAACGA
1752218 TAAAATT--AATTATTATAAAAG
1 TAAAATTAAAATTATTATAAAAG
1752239 TAAAATTAAAATTATTAATAAAA
1 TAAAATTAAAATTATT-ATAAAA
1752262 TATAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
23 7 0.35
24 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAAATTAAAATTATTATAAAAG
Found at i:1752456 original size:29 final size:29
Alignment explanation
Indices: 1752398--1752458 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
1752388 AATATGTATT
*
1752398 AAATTTATATTTATATTAAATAATAATTA
1 AAATTTATATTTATATTAAAAAATAATTA
* *
1752427 AAATTT-TATTTATTTTAAAAAAGTATTTA
1 AAATTTATATTTATATTAAAAAA-TAATTA
1752456 AAA
1 AAA
1752459 ATAAATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
AAATTTATATTTATATTAAAAAATAATTA
Found at i:1752777 original size:24 final size:24
Alignment explanation
Indices: 1752750--1752830 Score: 94
Period size: 24 Copynumber: 3.3 Consensus size: 24
1752740 AATGTACCCT
1752750 AAATATAACATAATTTTAAATATA
1 AAATATAACATAATTTTAAATATA
*
1752774 AAATATAACATAA--ATAAATGATTA
1 AAATATAACATAATTTTAAAT-A-TA
*
1752798 AAATATAATATAAATTTATAAATATA
1 AAATATAACAT-AATTT-TAAATATA
1752824 AAATATA
1 AAATATA
1752831 TATAATATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
22 5 0.10
23 1 0.02
24 25 0.52
25 2 0.04
26 9 0.19
27 1 0.02
28 5 0.10
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (24 bp):
AAATATAACATAATTTTAAATATA
Found at i:1752793 original size:50 final size:50
Alignment explanation
Indices: 1752733--1752830 Score: 121
Period size: 50 Copynumber: 2.0 Consensus size: 50
1752723 CAAAATTTCA
1752733 ATAAAAAAATGTACCCT-AAATATAACAT-AATTT-TAAATATAAAATATAAC
1 ATAAAAAAATG-A--CTAAAATATAACATAAATTTATAAATATAAAATATAAC
* * *
1752783 ATAAATAAATGATTAAAATATAATATAAATTTATAAATATAAAATATA
1 ATAAAAAAATGACTAAAATATAACATAAATTTATAAATATAAAATATA
1752831 TATAATATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
47 1 0.02
48 10 0.24
49 6 0.14
50 25 0.60
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (50 bp):
ATAAAAAAATGACTAAAATATAACATAAATTTATAAATATAAAATATAAC
Found at i:1752817 original size:13 final size:13
Alignment explanation
Indices: 1752801--1752852 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 13
1752791 ATGATTAAAA
1752801 TATAATATAAATT
1 TATAATATAAATT
1752814 TATAAATATAAAATAT
1 TAT-AATAT-AAAT-T
1752830 ATATAATATAAA-T
1 -TATAATATAAATT
1752843 TATTAATATA
1 TA-TAATATA
1752853 TTAAAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.06
13 11 0.32
14 5 0.15
15 7 0.21
16 6 0.18
17 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATAATATAAATT
Found at i:1752835 original size:11 final size:11
Alignment explanation
Indices: 1752769--1752927 Score: 57
Period size: 11 Copynumber: 14.1 Consensus size: 11
1752759 ATAATTTTAA
1752769 ATATAAAATAT
1 ATATAAAATAT
* *
1752780 A-ACATAAATAA
1 ATATA-AAATAT
1752791 ATGATTAAAATAT
1 AT-A-TAAAATAT
*
1752804 AATATAAATTTATAA
1 -ATATAAA---ATAT
1752819 ATATAAAATAT
1 ATATAAAATAT
* *
1752830 ATATAATATAA
1 ATATAAAATAT
*
1752841 AT-TATTAATAT
1 ATATA-AAATAT
1752852 AT-TAAAAT-T
1 ATATAAAATAT
1752861 -TATAAAA-AT
1 ATATAAAATAT
1752870 ATATAAAATATT
1 ATATAAAATA-T
* * *
1752882 AAATATTATTAT
1 ATATA-AAATAT
1752894 AATATAAAA-AT
1 -ATATAAAATAT
1752905 A-ATATAAATAT
1 ATATA-AAATAT
1752916 -TATATAAATAT
1 ATATA-AAATAT
1752927 A
1 A
1752928 AAATATCAGA
Statistics
Matches: 110, Mismatches: 18, Indels: 39
0.66 0.11 0.23
Matches are distributed among these distances:
8 1 0.01
9 10 0.09
10 18 0.16
11 43 0.39
12 11 0.10
13 14 0.13
14 10 0.09
15 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (11 bp):
ATATAAAATAT
Found at i:1752880 original size:27 final size:27
Alignment explanation
Indices: 1752789--1752930 Score: 101
Period size: 27 Copynumber: 5.1 Consensus size: 27
1752779 TAACATAAAT
* * * *
1752789 AAATGATTAAAATATAATATAAATTTAT
1 AAAT-ATTAAAATATTATAAAAATATAA
*
1752817 AAATA-TAAAATATATATAATATAAATTATTA
1 AAATATTAAAATAT-TAT-A-A-AAA-TATAA
*
1752848 ATATATTAAAAT-TTATAAAAATATATA
1 AAATATTAAAATATTATAAAAATATA-A
* *
1752875 AAATATT-AAATATTATTATAATATAA
1 AAATATTAAAATATTATAAAAATATAA
* *
1752901 AAATAATATAAATATTATATAAATATAA
1 AAATATTA-AAATATTATAAAAATATAA
1752929 AA
1 AA
1752931 TATCAGATAT
Statistics
Matches: 90, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
26 22 0.24
27 24 0.27
28 24 0.27
29 1 0.01
30 6 0.07
31 7 0.08
32 6 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.39
Consensus pattern (27 bp):
AAATATTAAAATATTATAAAAATATAA
Found at i:1752933 original size:35 final size:35
Alignment explanation
Indices: 1752796--1752933 Score: 114
Period size: 35 Copynumber: 4.0 Consensus size: 35
1752786 AATAAATGAT
1752796 TAAAATATAATAT-AA-ATT-TATAAATATAAAATA
1 TAAAA-ATAATATAAATATTATATAAATATAAAATA
* *
1752829 T--ATATAATATAAATTATTA-ATATAT-TAAAATTTA
1 TAAAAATAATATAAA-TATTATATAAATATAAAA--TA
* * *
1752863 TAAAAAT-ATATAAAATATTAAAT-ATTATTATAATA
1 TAAAAATAATAT-AAATATTATATAAATA-TAAAATA
1752898 TAAAAATAATATAAATATTATATAAATATAAAATA
1 TAAAAATAATATAAATATTATATAAATATAAAATA
1752933 T
1 T
1752934 CAGATATAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
30 7 0.09
31 3 0.04
32 5 0.06
33 9 0.11
34 3 0.04
35 36 0.44
36 15 0.18
37 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (35 bp):
TAAAAATAATATAAATATTATATAAATATAAAATA
Found at i:1753297 original size:31 final size:33
Alignment explanation
Indices: 1753223--1753293 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 33
1753213 AATATTTACA
* *
1753223 ATATATTTAATTTAAATAAAAAGTAGCAATTAT
1 ATATATTTAATTTAAATAAAAAGCAACAATTAT
1753256 ATATAATTTAATTTAAATAAAAAGCAACAATTAT
1 ATAT-ATTTAATTTAAATAAAAAGCAACAATTAT
1753290 ATAT
1 ATAT
1753294 TTAAAACTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 4 0.11
34 31 0.89
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (33 bp):
ATATATTTAATTTAAATAAAAAGCAACAATTAT
Found at i:1755274 original size:2 final size:2
Alignment explanation
Indices: 1755267--1755316 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1755257 GAACCTTCTA
1755267 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
1755309 AT AT AT AT
1 AT AT AT AT
1755317 TTAATTAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1756038 original size:19 final size:20
Alignment explanation
Indices: 1756000--1756063 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 20
1755990 ATTTCATCAA
*
1756000 TTATAATTTTTTTTAAAATT
1 TTATAATTTTTATTAAAATT
*
1756020 TTAT-ATTTTTATTATAATT
1 TTATAATTTTTATTAAAATT
** * *
1756039 AAATATATATTTATAAAAATT
1 TTATA-ATTTTTATTAAAATT
1756060 TTAT
1 TTAT
1756064 TATATTAATA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 15 0.45
20 4 0.12
21 14 0.42
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATAATTTTTATTAAAATT
Found at i:1756085 original size:32 final size:31
Alignment explanation
Indices: 1756049--1756110 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
1756039 AAATATATAT
*
1756049 TTATAAAAATTTTATTATATTAATAATTAATA
1 TTATAAAAATTTAATTATATTAAT-ATTAATA
* *
1756081 TTATATAAATTTAATTATATTTATATTAAT
1 TTATAAAAATTTAATTATATTAATATTAAT
1756111 TTTTGTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TTATAAAAATTTAATTATATTAATATTAATA
Found at i:1756095 original size:20 final size:20
Alignment explanation
Indices: 1756072--1756112 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1756062 ATTATATTAA
1756072 TAATTA-ATATTATATAAATT
1 TAATTATAT-TTATATAAATT
*
1756092 TAATTATATTTATATTAATT
1 TAATTATATTTATATAAATT
1756112 T
1 T
1756113 TTGTATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTATATTTATATAAATT
Found at i:1758757 original size:35 final size:35
Alignment explanation
Indices: 1758702--1758772 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
1758692 TACGGTCCTA
*
1758702 TGAACCTTGACCGAATATGCTGTTTTG-CAATACTG
1 TGAACCTTGACCGAAAATGCTGTTTTGTC-ATACTG
*
1758737 TGAACCTTGACTGAAAATGCTGTTTTGTCATACTG
1 TGAACCTTGACCGAAAATGCTGTTTTGTCATACTG
1758772 T
1 T
1758773 AAATACGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 32 0.97
36 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (35 bp):
TGAACCTTGACCGAAAATGCTGTTTTGTCATACTG
Found at i:1759564 original size:28 final size:28
Alignment explanation
Indices: 1759532--1759587 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
1759522 GAAGCAACGT
*
1759532 AGCATCTTAAACTCGAGTTTAAGAAAAA
1 AGCATCTCAAACTCGAGTTTAAGAAAAA
*
1759560 AGCATCTCAAACTTGAGTTTAAGAAAAA
1 AGCATCTCAAACTCGAGTTTAAGAAAAA
1759588 GAAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (28 bp):
AGCATCTCAAACTCGAGTTTAAGAAAAA
Found at i:1760707 original size:26 final size:26
Alignment explanation
Indices: 1760677--1760727 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1760667 GCACATTATT
1760677 TATAAATATT-TTAAAAAATAAAAAAA
1 TATAAAT-TTATTAAAAAATAAAAAAA
* *
1760703 TATAAATTTATTATAATATAAAAAA
1 TATAAATTTATTAAAAAATAAAAAA
1760728 TAAACGTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
TATAAATTTATTAAAAAATAAAAAAA
Found at i:1761009 original size:6 final size:6
Alignment explanation
Indices: 1761000--1761081 Score: 52
Period size: 6 Copynumber: 14.3 Consensus size: 6
1760990 TTTTAATATT
1761000 ATTTAA ATTT-- ATTTAA ATTT-A ATTT-A ATTTAAA ATTTAA ATTT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA
* * * *
1761043 ATTTAT ATTTATA AATAAA TATTTAA AATT-A ATTTAA AT
1 ATTTAA ATTTA-A ATTTAA -ATTTAA ATTTAA ATTTAA AT
1761082 AGAAACTTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
4 8 0.13
5 14 0.23
6 26 0.43
7 12 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:1761011 original size:10 final size:10
Alignment explanation
Indices: 1760998--1761054 Score: 62
Period size: 10 Copynumber: 5.4 Consensus size: 10
1760988 AATTTTAATA
1760998 TTATTTAAAT
1 TTATTTAAAT
1761008 TTATTTAAAT
1 TTATTTAAAT
1761018 TTAATTT-AAT
1 TT-ATTTAAAT
1761028 TTAAAATTTAAAT
1 TT---ATTTAAAT
*
1761041 TTATTTATAT
1 TTATTTAAAT
1761051 TTAT
1 TTAT
1761055 AAATAAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 28 0.67
11 4 0.10
12 5 0.12
13 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTATTTAAAT
Found at i:1761040 original size:23 final size:23
Alignment explanation
Indices: 1761010--1761080 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 23
1761000 ATTTAAATTT
1761010 ATTTAAATTTAATTTAATTTAAA
1 ATTTAAATTTAATTTAATTTAAA
1761033 ATTTAAATTT-ATTTATATTTATAA
1 ATTTAAATTTAATTTA-ATTTA-AA
* *
1761057 A-TAAATATTTAAAATTAATTTAAA
1 ATTTAA-ATTT-AATTTAATTTAAA
1761081 TAGAAACTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 5 0.12
23 18 0.44
24 9 0.22
25 5 0.12
26 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTAAATTTAATTTAATTTAAA
Found at i:1762870 original size:2 final size:2
Alignment explanation
Indices: 1762863--1762900 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1762853 ATAAAGAAAT
*
1762863 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA AA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1762901 TGTATATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1768391 original size:11 final size:11
Alignment explanation
Indices: 1768375--1768408 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1768365 ACTATATGTC
1768375 ATATTTAATTA
1 ATATTTAATTA
*
1768386 ATATTTAATTT
1 ATATTTAATTA
*
1768397 ATTTTTAATTA
1 ATATTTAATTA
1768408 A
1 A
1768409 ATTATCCCGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATATTTAATTA
Found at i:1768828 original size:23 final size:23
Alignment explanation
Indices: 1768798--1768842 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1768788 TATGATAAGA
* *
1768798 AAAAAATAATTAAAATATAACAT
1 AAAAAATAATAAAAACATAACAT
1768821 AAAAAATAATAAAAACATAACA
1 AAAAAATAATAAAAACATAACA
1768843 CAAATGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (23 bp):
AAAAAATAATAAAAACATAACAT
Found at i:1780056 original size:2 final size:2
Alignment explanation
Indices: 1780049--1780082 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1780039 CTGGTTTTAC
1780049 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
1780083 TAATTTTTTC
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:1782338 original size:25 final size:24
Alignment explanation
Indices: 1782303--1782359 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
1782293 ATCTTGCTGC
1782303 TGATTTTTTATTCC-TTTGATAGGT
1 TGATTTTTTA-TCCGTTTGATAGGT
*
1782327 TGATTATTTTATCCGTTTGATTGGT
1 TGATT-TTTTATCCGTTTGATAGGT
1782352 TCGATTTT
1 T-GATTTT
1782360 AAGATTTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 8 0.28
25 17 0.59
26 4 0.14
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.58
Consensus pattern (24 bp):
TGATTTTTTATCCGTTTGATAGGT
Found at i:1782517 original size:27 final size:29
Alignment explanation
Indices: 1782486--1782541 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1782476 TAAAATTTTA
1782486 AAAAATAAAT-TAT-TTATATTATTATAT
1 AAAAATAAATGTATATTATATTATTATAT
* *
1782513 AAAAATAATTGTATATTATATTTTTATAT
1 AAAAATAAATGTATATTATATTATTATAT
1782542 TATAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 9 0.36
28 3 0.12
29 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
AAAAATAAATGTATATTATATTATTATAT
Found at i:1783056 original size:4 final size:4
Alignment explanation
Indices: 1783047--1783090 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
1783037 AAACAATTCC
* * * *
1783047 TATA TATA TAAA TACA TATA TATA TATA TACA TATA CATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
1783091 CACAACGTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (4 bp):
TATA
Found at i:1783067 original size:14 final size:14
Alignment explanation
Indices: 1783048--1783092 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1783038 AACAATTCCT
1783048 ATATATATAAATAC
1 ATATATATAAATAC
1783062 ATATATATATATATAC
1 ATATATATA-A-ATAC
* *
1783078 ATATACATATATAC
1 ATATATATAAATAC
1783092 A
1 A
1783093 CAACGTGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 14 0.52
15 1 0.04
16 12 0.44
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATATATAAATAC
Found at i:1783071 original size:6 final size:6
Alignment explanation
Indices: 1783047--1783090 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
1783037 AAACAATTCC
* * * *
1783047 TATATA TATAAA TACATA TATATA TATATA CATATA CATATA TA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TA
1783091 CACAACGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (6 bp):
TATATA
Found at i:1783089 original size:16 final size:16
Alignment explanation
Indices: 1783047--1783090 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
1783037 AAACAATTCC
*
1783047 TATATATATAAATACA
1 TATATATATATATACA
1783063 TATATATATATATACA
1 TATATATATATATACA
*
1783079 TATACATATATA
1 TATATATATATA
1783091 CACAACGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATATATATATACA
Found at i:1785688 original size:69 final size:69
Alignment explanation
Indices: 1785577--1785707 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 69
1785567 TTATCGTCAC
* *
1785577 TCATAACAGATAACATCACTAGACCGACAAAGAACAGATATAACAATCC-TGCTGAAATGACATC
1 TCATAACAGATAACATCACTACACCGACAAAGAACAGATATAACAA-CCTTGCCGAAATGACATC
1785641 ATCGT
65 ATCGT
* * *
1785646 TCATAACAGATAATATCACTACACTGACAAAGAGA-AGATATAATAACCTTGCCGAAATGACA
1 TCATAACAGATAACATCACTACACCGACAAAGA-ACAGATATAACAACCTTGCCGAAATGACA
1785708 CAACCGAAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 2 0.04
69 52 0.95
70 1 0.02
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (69 bp):
TCATAACAGATAACATCACTACACCGACAAAGAACAGATATAACAACCTTGCCGAAATGACATCA
TCGT
Found at i:1790700 original size:2 final size:2
Alignment explanation
Indices: 1790693--1790739 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1790683 ATTAAAATAA
1790693 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
1790735 AG AG A
1 AG AG A
1790740 AACGAGGGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1793907 original size:11 final size:12
Alignment explanation
Indices: 1793871--1793904 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1793861 TGGGAAATTT
1793871 TTTTTTTCATAA
1 TTTTTTTCATAA
*
1793883 TTTATTT-ATAA
1 TTTTTTTCATAA
1793894 TTTTTTTCATA
1 TTTTTTTCATA
1793905 TTTAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTTTCATAA
Found at i:1794055 original size:25 final size:26
Alignment explanation
Indices: 1794008--1794085 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 26
1793998 ATAAAAATTA
*
1794008 TAAATTAT-TAAAATT-ATAT-TAAT
1 TAAATTATATAATATTAATATATAAT
*
1794031 TAAATT-TAATAATTTTAA-ATATAA-
1 TAAATTAT-ATAATATTAATATATAAT
1794055 TATAATTATATAATATTAATATATAAT
1 TA-AATTATATAATATTAATATATAAT
1794082 TAAA
1 TAAA
1794086 GATAATATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
22 1 0.02
23 6 0.14
24 9 0.20
25 17 0.39
26 9 0.20
27 2 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAATTATATAATATTAATATATAAT
Found at i:1794061 original size:17 final size:17
Alignment explanation
Indices: 1794039--1794096 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
1794029 ATTAAATTTA
1794039 ATAATTTTAAATATAAT
1 ATAATTTTAAATATAAT
*
1794056 ATAATTATATAATATTAAT
1 ATAATTTTA-AATA-TAAT
* *
1794075 AT-ATAATTAAAGATAAT
1 ATAAT-TTTAAATATAAT
1794092 ATAAT
1 ATAAT
1794097 ATAAAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 14 0.42
18 11 0.33
19 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATAATTTTAAATATAAT
Found at i:1794067 original size:13 final size:13
Alignment explanation
Indices: 1794049--1794100 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
1794039 ATAATTTTAA
1794049 ATATAATATAATT
1 ATATAATATAATT
1794062 ATATAATATTAA-T
1 ATATAATA-TAATT
* *
1794075 ATATAATTAAAGATA
1 ATATAA-TATA-ATT
1794090 ATATAATATAA
1 ATATAATATAA
1794101 AAATAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 17 0.53
14 9 0.28
15 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATAATATAATT
Found at i:1794093 original size:28 final size:28
Alignment explanation
Indices: 1794062--1794132 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
1794052 TAATATAATT
* * *
1794062 ATATAATATTAATATATAATTAAAGATA
1 ATATAATATAAATATATAAATAAACATA
*
1794090 ATATAATATAAAAATA-AAATAAACATA
1 ATATAATATAAATATATAAATAAACATA
*
1794117 ATACAA-ATAAATATAT
1 ATATAATATAAATATAT
1794133 TAAAATTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
26 8 0.22
27 14 0.39
28 14 0.39
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (28 bp):
ATATAATATAAATATATAAATAAACATA
Found at i:1794186 original size:11 final size:11
Alignment explanation
Indices: 1794092--1794203 Score: 61
Period size: 11 Copynumber: 9.7 Consensus size: 11
1794082 TAAAGATAAT
1794092 ATAATATAAAA
1 ATAATATAAAA
* *
1794103 ATAAAATAAAC
1 ATAATATAAAA
*
1794114 ATAATACAAATA
1 ATAATATAAA-A
1794126 A-ATATATTAAAA
1 ATA-ATA-TAAAA
* *
1794138 TTTATGTATTAAAA
1 -ATA-ATA-TAAAA
1794152 AT-A-ATAAAA
1 ATAATATAAAA
1794161 AT-ATGATAAAA
1 ATAAT-ATAAAA
1794172 ATAATATAAAA
1 ATAATATAAAA
*
1794183 ATAATATTAATAC
1 ATAATA-TAA-AA
1794196 ATAATATA
1 ATAATATA
1794204 TCAAAAACTC
Statistics
Matches: 80, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
9 8 0.10
10 1 0.01
11 38 0.47
12 12 0.15
13 11 0.14
14 10 0.12
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:1794944 original size:20 final size:19
Alignment explanation
Indices: 1794857--1794967 Score: 81
Period size: 20 Copynumber: 5.8 Consensus size: 19
1794847 ATTATTTAAA
*
1794857 ATTAAA-AATATT-ATTAT
1 ATTAAATAATTTTAATTAT
* *
1794874 ATT-AATATTTTTAATTAA
1 ATTAAATAATTTTAATTAT
1794892 ATTTAAATAACTTTTTAATT-T
1 A-TTAAATAA--TTTTAATTAT
1794913 ATCT-AATAATTTTAATTAT
1 AT-TAAATAATTTTAATTAT
*
1794932 ATTAAATTAATTTAAATT-T
1 ATTAAA-TAATTTTAATTAT
1794951 AATTAAATAATATTTAA
1 -ATTAAATAAT-TTTAA
1794968 ACTCAATTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
16 2 0.03
17 7 0.09
18 14 0.19
19 12 0.16
20 30 0.40
21 2 0.03
22 8 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTAAATAATTTTAATTAT
Found at i:1795278 original size:39 final size:37
Alignment explanation
Indices: 1795235--1795347 Score: 106
Period size: 39 Copynumber: 3.0 Consensus size: 37
1795225 TAATAAATAA
*
1795235 TAAAAATATTAAAATTAAAATAAATAAATTTATATATTT
1 TAAAAATA-TAAAATT-AAATAAATAAATATATATATTT
* * * *
1795274 TAAAATAAATAAATATTAATTAAATATATATATATTTTT
1 TAAAA-ATATAAA-ATTAAATAAATAAATATATATATTT
*
1795313 TAAAAA-ATAATAATTATATAAATAAATA-AT-TATTT
1 TAAAAATATAA-AATTAAATAAATAAATATATATATTT
1795348 AATAAAATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
35 4 0.06
36 2 0.03
37 17 0.27
38 2 0.03
39 32 0.52
40 5 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (37 bp):
TAAAAATATAAAATTAAATAAATAAATATATATATTT
Found at i:1795296 original size:20 final size:20
Alignment explanation
Indices: 1795219--1795297 Score: 63
Period size: 24 Copynumber: 3.7 Consensus size: 20
1795209 AATATATTTA
*
1795219 AAATATTAA-T-AAATAATAA
1 AAATATTAATTAAAATAA-AT
1795238 AAATATTAAAATTAAAATAAAT
1 AAATATT--AATTAAAATAAAT
*
1795260 AAATTTATATATTTTAAAATAAAT
1 AAA--TAT-TA-ATTAAAATAAAT
1795284 AAATATTAATTAAA
1 AAATATTAATTAAA
1795298 TATATATATA
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
19 7 0.14
20 5 0.10
21 4 0.08
22 8 0.16
23 7 0.14
24 17 0.35
25 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATATTAATTAAAATAAAT
Found at i:1795315 original size:19 final size:19
Alignment explanation
Indices: 1795255--1795340 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
1795245 AAAATTAAAA
*
1795255 TAAATAAATTTATATATTTT
1 TAAATAAATATATAT-TTTT
* * **
1795275 AAAATAAATAAATATTAAT
1 TAAATAAATATATATTTTT
*
1795294 TAAATATATATATATTTTT
1 TAAATAAATATATATTTTT
* *
1795313 TAAA-AAATA-ATAATTATA
1 TAAATAAATATAT-ATTTTT
1795331 TAAATAAATA
1 TAAATAAATA
1795341 ATTATTTAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
17 2 0.04
18 12 0.24
19 25 0.49
20 12 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATAAATATATATTTTT
Found at i:1795335 original size:37 final size:38
Alignment explanation
Indices: 1795253--1795347 Score: 101
Period size: 37 Copynumber: 2.6 Consensus size: 38
1795243 TTAAAATTAA
*
1795253 AATAAATAAATTTATATATTTTAAAATAAATAAATATT
1 AATAAATAAATATATATATTTTAAAATAAATAAATATT
* *
1795291 AATTAAATATATATATAT-TTTTTAAA-AAAT-AATAATT
1 AA-TAAATAAATATATATATTTTAAAATAAATAAAT-ATT
1795328 ATATAAATAAATA-AT-TATTT
1 A-ATAAATAAATATATATATTT
1795348 AATAAAATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
35 1 0.02
36 8 0.16
37 17 0.35
38 10 0.20
39 13 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (38 bp):
AATAAATAAATATATATATTTTAAAATAAATAAATATT
Found at i:1795352 original size:19 final size:19
Alignment explanation
Indices: 1795253--1795353 Score: 61
Period size: 19 Copynumber: 5.3 Consensus size: 19
1795243 TTAAAATTAA
*
1795253 AATAAATAAATTTATATATTT
1 AATAAATAAA-TAAT-TATTT
* *
1795274 TA-AAATAAATAAATA-TT
1 AATAAATAAATAATTATTT
*
1795291 AATTAAATATATATATATTTTTT
1 AA-TAAATA-A-ATA-ATTATTT
*
1795314 AAAAAAT-AATAATTA--T
1 AATAAATAAATAATTATTT
1795330 -ATAAATAAATAATTATTT
1 AATAAATAAATAATTATTT
1795348 AATAAA
1 AATAAA
1795354 ATTTTAATCC
Statistics
Matches: 61, Mismatches: 9, Indels: 22
0.66 0.10 0.24
Matches are distributed among these distances:
15 5 0.08
16 9 0.15
17 3 0.05
18 6 0.10
19 15 0.25
20 9 0.15
21 4 0.07
22 6 0.10
23 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAAATAAATAATTATTT
Found at i:1795670 original size:14 final size:13
Alignment explanation
Indices: 1795653--1795700 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 13
1795643 ATTTTGAAAG
*
1795653 TAAATTTTTTTATT
1 TAAATTTATTT-TT
1795667 TAAATTTATTTTT
1 TAAATTTATTTTT
1795680 TAAATATAATATTTTT
1 TAAAT-T--TATTTTT
1795696 TAAAT
1 TAAAT
1795701 CCTTTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 7 0.23
14 11 0.37
16 12 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAAATTTATTTTT
Found at i:1798420 original size:26 final size:26
Alignment explanation
Indices: 1798357--1798412 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
1798347 ATGTATCACA
1798357 AAGTAGATAATTAATTCTAAAATTCT
1 AAGTAGATAATTAATTCTAAAATTCT
* *
1798383 ATGTAGATAATTAATTTTAAAATTCT
1 AAGTAGATAATTAATTCTAAAATTCT
1798409 AAGT
1 AAGT
1798413 GTTAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (26 bp):
AAGTAGATAATTAATTCTAAAATTCT
Found at i:1798484 original size:2 final size:2
Alignment explanation
Indices: 1798477--1798504 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1798467 TATTTATTGA
1798477 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
1798505 TTTGTAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1799624 original size:16 final size:16
Alignment explanation
Indices: 1799603--1799645 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1799593 TAATAAAATA
1799603 TATATTTTAAATATTT
1 TATATTTTAAATATTT
*
1799619 TATATTATATAA-ATTT
1 TATATTTTA-AATATTT
1799635 TA-ATTTTAAAT
1 TATATTTTAAAT
1799646 TGAATCGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 2 0.09
15 5 0.22
16 14 0.61
17 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATTTTAAATATTT
Found at i:1800794 original size:20 final size:20
Alignment explanation
Indices: 1800771--1800808 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1800761 TTAAATTTTG
1800771 AATTTAAATTAAATTTTTAA
1 AATTTAAATTAAATTTTTAA
1800791 AATTTAAATTAAATTTTT
1 AATTTAAATTAAATTTTT
1800809 TATTTAACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATTTAAATTAAATTTTTAA
Found at i:1801811 original size:21 final size:23
Alignment explanation
Indices: 1801777--1801819 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1801767 TAAATTTAAA
*
1801777 TAAAAATATGTTA-TTTAAATTT
1 TAAAAATATATTATTTTAAATTT
1801799 TAAAAA-ATATTATTTTAAATT
1 TAAAAATATATTATTTTAAATT
1801820 ATAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAATATATTATTTTAAATTT
Found at i:1802943 original size:19 final size:19
Alignment explanation
Indices: 1802921--1802969 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1802911 TATAATTAAA
1802921 TTAAATAAAATATATTATT
1 TTAAATAAAATATATTATT
*
1802940 TTAATTTAAAA-ATATTATT
1 TTAA-ATAAAATATATTATT
*
1802959 TTAAATCAAAT
1 TTAAATAAAAT
1802970 TAATTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 4 0.16
19 16 0.64
20 5 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAATAAAATATATTATT
Found at i:1804238 original size:12 final size:14
Alignment explanation
Indices: 1804229--1804290 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
1804219 TCCGTTTATA
1804229 TTATTTTTTATAAT
1 TTATTTTTTATAAT
*
1804243 TTATTTTTTAAAAAT
1 TTATTTTTT-ATAAT
* *
1804258 ATATATTTTTAAAAT
1 TTAT-TTTTTATAAT
* *
1804273 TTAGTCTTTATTAAT
1 TTATTTTTTA-TAAT
1804288 TTA
1 TTA
1804291 ATAATTTATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
14 14 0.36
15 20 0.51
16 5 0.13
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (14 bp):
TTATTTTTTATAAT
Found at i:1804246 original size:14 final size:14
Alignment explanation
Indices: 1804229--1804275 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
1804219 TCCGTTTATA
*
1804229 TTATTTTTTATAAT
1 TTATTTTTTAAAAT
1804243 TTATTTTTTAAAAAT
1 TTATTTTTT-AAAAT
*
1804258 ATATATTTTTAAAAT
1 TTAT-TTTTTAAAAT
1804273 TTA
1 TTA
1804276 GTCTTTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 9 0.32
15 14 0.50
16 5 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTTTTAAAAT
Found at i:1805425 original size:254 final size:254
Alignment explanation
Indices: 1804971--1805483 Score: 900
Period size: 254 Copynumber: 2.0 Consensus size: 254
1804961 AAAATTTTTT
* *
1804971 ATAACCAAAAATCGCATGAGTTTGAACTCCGATCCGAATTGTTTATACCATTATATGTACTAACC
1 ATAAACAAAAATCGCATGAGTTTGAACTCCGATCCGAATTGTTTATACCATTATATATACTAACC
*
1805036 TGACTTCAAGCTGAAACCCTTTTTAATGCATCTCTCTTCTTTAGATAAAGCAACGTGAAGTTATC
66 TGACTTCAAGCTGAAACCCTTTTTAATGCATCTCTCTTCTTTAGATAAAGCAAAGTGAAGTTATC
* *
1805101 CAGAAATTGATGACGATGATCAGGGCTATCTGTAAATTTCTTAACCCTGAGACATTGAGTGCAGA
131 CAGAAATTGATGACGATGATCAGGGCTATCTGAAAATTTCTTAACCCTGAGACATTGAGTGCAAA
1805166 GGCAATAATTCCGCTGGCACCTGTCGAAGCAATGGATGCAACAAAAGTAAATACCTGTG
196 GGCAATAATTCCGCTGGCACCTGTCGAAGCAATGGATGCAACAAAAGTAAATACCTGTG
* * *
1805225 ATAAACAAAAATCGCATTAGTTTGAACTCCGATCCGAATTTTTTCTACCATTATATATACTAACC
1 ATAAACAAAAATCGCATGAGTTTGAACTCCGATCCGAATTGTTTATACCATTATATATACTAACC
* * * *
1805290 TGACTTGAAGCTGAAGCCCTTTTTAATGCATCTCTCTTCTTTAGATCAAGCAAAGTGATGTTATC
66 TGACTTCAAGCTGAAACCCTTTTTAATGCATCTCTCTTCTTTAGATAAAGCAAAGTGAAGTTATC
*
1805355 CAGAAATTGATGACGATGATCAGGGCTATCTGAAAATTTCTTAGCCCTGAGACATTGAGTGCAAA
131 CAGAAATTGATGACGATGATCAGGGCTATCTGAAAATTTCTTAACCCTGAGACATTGAGTGCAAA
*
1805420 GGCAATAATTCCGCTGGCACCTGTCGAAGCAATGGATGCAACAAAAGTAAATACCTTTG
196 GGCAATAATTCCGCTGGCACCTGTCGAAGCAATGGATGCAACAAAAGTAAATACCTGTG
1805479 ATAAA
1 ATAAA
1805484 GCGGTCGCAA
Statistics
Matches: 245, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
254 245 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (254 bp):
ATAAACAAAAATCGCATGAGTTTGAACTCCGATCCGAATTGTTTATACCATTATATATACTAACC
TGACTTCAAGCTGAAACCCTTTTTAATGCATCTCTCTTCTTTAGATAAAGCAAAGTGAAGTTATC
CAGAAATTGATGACGATGATCAGGGCTATCTGAAAATTTCTTAACCCTGAGACATTGAGTGCAAA
GGCAATAATTCCGCTGGCACCTGTCGAAGCAATGGATGCAACAAAAGTAAATACCTGTG
Found at i:1809507 original size:17 final size:20
Alignment explanation
Indices: 1809472--1809511 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
1809462 AATTTAAAAC
1809472 AAAAAATATTAAAATTTTAA
1 AAAAAATATTAAAATTTTAA
1809492 AAAAAATA-T-AAA-TTTAA
1 AAAAAATATTAAAATTTTAA
1809509 AAA
1 AAA
1809512 GAGATAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.40
18 3 0.15
19 1 0.05
20 8 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATATTAAAATTTTAA
Found at i:1809508 original size:25 final size:25
Alignment explanation
Indices: 1809443--1809510 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
1809433 AATTTAAATG
*
1809443 AAAAAAT-TAAACTTAAAATAATTTA
1 AAAAAATATAAATTTAAAAT-ATTTA
*
1809468 AAACAA-A-AAATATTAAAAT-TTTAA
1 AAAAAATATAAAT-TTAAAATATTT-A
1809492 AAAAAATATAAATTTAAAA
1 AAAAAATATAAATTTAAAA
1809511 AGAGATAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
23 3 0.09
24 9 0.26
25 19 0.54
26 4 0.11
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAAATATAAATTTAAAATATTTA
Found at i:1810391 original size:31 final size:32
Alignment explanation
Indices: 1810356--1810433 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 32
1810346 GACTGTTACA
* * *
1810356 ATTTTTAATTT-TTTAGAGATAATTATTAATT
1 ATTTTTAATTTCTTTAGAAATAATTATAAATC
*
1810387 ATTTTTAATTTTTCTTTTGAAATAATTATAAATC
1 ATTTTTAA--TTTCTTTAGAAATAATTATAAATC
1810421 ATTTTTAATTTCT
1 ATTTTTAATTTCT
1810434 CTATATTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 8 0.20
32 5 0.12
33 3 0.08
34 24 0.60
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (32 bp):
ATTTTTAATTTCTTTAGAAATAATTATAAATC
Found at i:1810526 original size:26 final size:26
Alignment explanation
Indices: 1810463--1810518 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
1810453 GTGTATCACA
1810463 AAGTAGATAATTAATTCTAAAATTCT
1 AAGTAGATAATTAATTCTAAAATTCT
*
1810489 AAGTAGATAATTAATTTTAAAATTCT
1 AAGTAGATAATTAATTCTAAAATTCT
1810515 AAGT
1 AAGT
1810519 GTTAAATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.39
Consensus pattern (26 bp):
AAGTAGATAATTAATTCTAAAATTCT
Found at i:1810751 original size:13 final size:14
Alignment explanation
Indices: 1810726--1810754 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1810716 ATTAAAATAC
1810726 ATTAAATAGTTTTA
1 ATTAAATAGTTTTA
1810740 ATTAAA-AGTTTTA
1 ATTAAATAGTTTTA
1810753 AT
1 AT
1810755 ATTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATTAAATAGTTTTA
Found at i:1812994 original size:18 final size:16
Alignment explanation
Indices: 1812967--1813000 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
1812957 TTTTTTACTC
1812967 AAAATATTTTTAATTAT
1 AAAATA-TTTTAATTAT
1812984 AAAATTATTTTAATTAT
1 AAAA-TATTTTAATTAT
1813001 TTTAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATTTTAATTAT
Found at i:1813000 original size:9 final size:9
Alignment explanation
Indices: 1812986--1813010 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1812976 TTAATTATAA
1812986 AATTATTTT
1 AATTATTTT
1812995 AATTATTTT
1 AATTATTTT
1813004 AATTATT
1 AATTATT
1813011 ATCAAGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
AATTATTTT
Found at i:1815952 original size:18 final size:18
Alignment explanation
Indices: 1815929--1815964 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1815919 AACAAAAAAT
*
1815929 ATATTATTTTAATTTAAA
1 ATATTATTTTAAATTAAA
1815947 ATATTATTTTAAATTAAA
1 ATATTATTTTAAATTAAA
1815965 TCAATTTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATTTTAAATTAAA
Found at i:1820582 original size:21 final size:22
Alignment explanation
Indices: 1820544--1820589 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1820534 ATCTGTTGAA
* **
1820544 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1820565 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1820587 ACT
1 ACT
1820590 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1823206 original size:26 final size:26
Alignment explanation
Indices: 1823177--1823235 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
1823167 CAATTTTTAT
*
1823177 AAATAAAAATAACCACCATATTTGAC
1 AAATAAAAAAAACCACCATATTTGAC
* *
1823203 AAATACAAAAAAAATCACTATATTTGAC
1 AAAT--AAAAAAAACCACCATATTTGAC
1823231 AAATA
1 AAATA
1823236 CAAAGGATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 5 0.18
28 23 0.82
ACGTcount: A:0.58, C:0.15, G:0.03, T:0.24
Consensus pattern (26 bp):
AAATAAAAAAAACCACCATATTTGAC
Found at i:1823314 original size:22 final size:22
Alignment explanation
Indices: 1823289--1823331 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1823279 GGATAGCCAT
1823289 CCACCACAGCTACAATATAAAA
1 CCACCACAGCTACAATATAAAA
1823311 CCACCACAGCTACAATATAAA
1 CCACCACAGCTACAATATAAA
1823332 CACCGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.33, G:0.05, T:0.14
Consensus pattern (22 bp):
CCACCACAGCTACAATATAAAA
Found at i:1823457 original size:39 final size:36
Alignment explanation
Indices: 1823380--1823451 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
1823370 AATGACGTAC
1823380 GCAATTATTTAGACAACGGCAGCAGCAACAAGACCA
1 GCAATTATTTAGACAACGGCAGCAGCAACAAGACCA
* **
1823416 GCAATTATTTGGGTAACGGCAGCAGCAACAAGACCA
1 GCAATTATTTAGACAACGGCAGCAGCAACAAGACCA
1823452 ACAGCAGTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (36 bp):
GCAATTATTTAGACAACGGCAGCAGCAACAAGACCA
Found at i:1823842 original size:33 final size:32
Alignment explanation
Indices: 1823796--1823859 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1823786 GTAAATTTGA
*
1823796 TTTATTTAAATTTATTTATATAATAAAAATATT
1 TTTATTTAAATTTAATTATA-AATAAAAATATT
*
1823829 TTTATTTATATTTAATTATAAATAAAAATAT
1 TTTATTTAAATTTAATTATAAATAAAAATAT
1823860 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 11 0.38
33 18 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TTTATTTAAATTTAATTATAAATAAAAATATT
Found at i:1825022 original size:28 final size:29
Alignment explanation
Indices: 1824977--1825046 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
1824967 AGTCACGAAT
1824977 AAAATAATTAAAATATAATATGAT-ATAA
1 AAAATAATTAAAATATAATATGATAATAA
1825005 AAAATAATATAAAA-ATAATATGATAAT-A
1 AAAATAAT-TAAAATATAATATGATAATAA
*
1825033 AAAATATTTAAAAT
1 AAAATAATTAAAAT
1825047 TTATATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
27 5 0.13
28 26 0.68
29 7 0.18
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATAATTAAAATATAATATGATAATAA
Found at i:1825033 original size:17 final size:16
Alignment explanation
Indices: 1824985--1825038 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
1824975 ATAAAATAAT
1824985 TAAAATATAATATGATA
1 TAAAA-ATAATATGATA
1825002 T-AAAA-AATA--ATA
1 TAAAAATAATATGATA
1825014 TAAAAATAATATGATAA
1 TAAAAATAATATGAT-A
1825031 TAAAAATA
1 TAAAAATA
1825039 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.12
13 4 0.12
14 8 0.25
15 1 0.03
16 5 0.16
17 10 0.31
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (16 bp):
TAAAAATAATATGATA
Found at i:1825391 original size:16 final size:17
Alignment explanation
Indices: 1825347--1825392 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
1825337 TTGATTTATT
1825347 TATTAAA-AATTTTAAA
1 TATTAAATAATTTTAAA
1825363 TATTTTAAAATAATTTT-AA
1 TA--TT-AAATAATTTTAAA
1825382 TATTAAATAAT
1 TATTAAATAAT
1825393 AAATAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 2 0.08
19 7 0.27
20 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTAAATAATTTTAAA
Found at i:1826192 original size:24 final size:24
Alignment explanation
Indices: 1826160--1826215 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
1826150 GGAGCAGTAG
1826160 CCGCTTTCTTCTTCTTTTCCTGCT
1 CCGCTTTCTTCTTCTTTTCCTGCT
1826184 CCGCTTTCTTCTTCTTTTCCTGCT
1 CCGCTTTCTTCTTCTTTTCCTGCT
1826208 CCGCTTTC
1 CCGCTTTC
1826216 AATGCCTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.00, C:0.39, G:0.09, T:0.52
Consensus pattern (24 bp):
CCGCTTTCTTCTTCTTTTCCTGCT
Found at i:1828613 original size:22 final size:23
Alignment explanation
Indices: 1828579--1828637 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
1828569 TTTTATTTAA
*
1828579 TTTAAAAAATAAA-TAAATATTT
1 TTTAAAAATTAAACTAAATATTT
* *
1828601 TTTAAATATTAAAACTATATATTT
1 TTTAAAAATT-AAACTAAATATTT
*
1828625 TATAAAAATTAAA
1 TTTAAAAATTAAA
1828638 AAAAAATGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 8 0.27
23 6 0.20
24 16 0.53
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTAAAAATTAAACTAAATATTT
Found at i:1829523 original size:18 final size:18
Alignment explanation
Indices: 1829500--1829539 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1829490 TTTAATTCGT
* *
1829500 AATAATATTTATCATTAA
1 AATAATAATTATCATAAA
*
1829518 AATAATAATTATTATAAA
1 AATAATAATTATCATAAA
1829536 AATA
1 AATA
1829540 TCTGGTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATAATTATCATAAA
Found at i:1829661 original size:2 final size:2
Alignment explanation
Indices: 1829654--1829692 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1829644 TAACCTAATC
1829654 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1829693 TACCAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1830075 original size:6 final size:6
Alignment explanation
Indices: 1830064--1830126 Score: 53
Period size: 6 Copynumber: 10.5 Consensus size: 6
1830054 ATTTTGTATC
*
1830064 TTTAAA TTTAAA TTTTAAA TTTTAAA TTTAAA -TAAAA TTT--- TTTAAAAA
1 TTTAAA TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTT--AAA
1830112 TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
1830127 TTTATTTGAC
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 3 0.06
5 4 0.08
6 25 0.52
7 13 0.27
8 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:1830082 original size:7 final size:7
Alignment explanation
Indices: 1830064--1830096 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1830054 ATTTTGTATC
1830064 TTTAAA-
1 TTTAAAT
1830070 TTTAAAT
1 TTTAAAT
1830077 TTTAAAT
1 TTTAAAT
1830084 TTTAAA-
1 TTTAAAT
1830090 TTTAAAT
1 TTTAAAT
1830097 AAAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TTTAAAT
Found at i:1830082 original size:13 final size:13
Alignment explanation
Indices: 1830064--1830127 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
1830054 ATTTTGTATC
1830064 TTTAAATTTAAAT
1 TTTAAATTTAAAT
1830077 TTTAAATTTTAAA-
1 TTTAAA-TTTAAAT
*
1830090 TTTAAA-TAAAAT
1 TTTAAATTTAAAT
* *
1830102 TTT---TTAAAAA
1 TTTAAATTTAAAT
1830112 TTTAAATTTAAAT
1 TTTAAATTTAAAT
1830125 TTT
1 TTT
1830128 TTATTTGACA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 8 0.20
11 4 0.10
12 3 0.07
13 20 0.49
14 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTAAATTTAAAT
Found at i:1830115 original size:22 final size:23
Alignment explanation
Indices: 1830087--1830130 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1830077 TTTAAATTTT
1830087 AAATTTAAA-TAAAATTTTTTAA
1 AAATTTAAATTAAAATTTTTTAA
*
1830109 AAATTTAAATTTAAATTTTTTA
1 AAATTTAAATTAAAATTTTTTA
1830131 TTTGACATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATTTAAATTAAAATTTTTTAA
Found at i:1830627 original size:31 final size:32
Alignment explanation
Indices: 1830584--1830643 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
1830574 AGTTATAAAA
*
1830584 AAAATTATAAATATATTAAATTT-TTTTTAAG
1 AAAACTATAAATATATTAAATTTATTTTTAAG
* *
1830615 AAAACTATAAATATGTTAATTTTATTTTT
1 AAAACTATAAATATATTAAATTTATTTTT
1830644 TATGTAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (32 bp):
AAAACTATAAATATATTAAATTTATTTTTAAG
Found at i:1830849 original size:16 final size:16
Alignment explanation
Indices: 1830817--1830847 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1830807 GCTTTGCTTC
1830817 ATTTATTTATTATTTT
1 ATTTATTTATTATTTT
1830833 ATTTATTT-TTATTTT
1 ATTTATTTATTATTTT
1830848 TAAACCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTATTTATTATTTT
Found at i:1831354 original size:19 final size:20
Alignment explanation
Indices: 1831319--1831359 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1831309 GAATTAATTT
1831319 ATTAAAATTAAAATAAT-AA
1 ATTAAAATTAAAATAATCAA
**
1831338 ATTAAAATTAATCTAATCAA
1 ATTAAAATTAAAATAATCAA
1831358 AT
1 AT
1831360 CAATGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
ATTAAAATTAAAATAATCAA
Found at i:1832802 original size:2 final size:2
Alignment explanation
Indices: 1832795--1832826 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1832785 TCTTAACTTA
1832795 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
1832827 TGTCAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1834233 original size:2 final size:2
Alignment explanation
Indices: 1834226--1834269 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
1834216 AACGTAAAAT
* *
1834226 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1834268 TA
1 TA
1834270 AGATTTAGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1834818 original size:15 final size:15
Alignment explanation
Indices: 1834795--1834824 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1834785 AAATGCATAA
1834795 AAAAATTAATTAATT
1 AAAAATTAATTAATT
*
1834810 AAAACTTAATTAATT
1 AAAAATTAATTAATT
1834825 TGTAATGTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAATTAATTAATT
Found at i:1835873 original size:15 final size:15
Alignment explanation
Indices: 1835848--1835888 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1835838 TACATATTTT
*
1835848 AATCATATTTATAAA
1 AATCTTATTTATAAA
*
1835863 AATTTTATTTATAAA
1 AATCTTATTTATAAA
1835878 AATCTTATTTA
1 AATCTTATTTA
1835889 ATTTAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
AATCTTATTTATAAA
Found at i:1836425 original size:13 final size:15
Alignment explanation
Indices: 1836391--1836426 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1836381 GATAAATATA
1836391 AATATATAAAAAAAT
1 AATATATAAAAAAAT
*
1836406 AATATATAAAAAAAC
1 AATATATAAAAAAAT
1836421 AATATA
1 AATATA
1836427 CTTATCTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
AATATATAAAAAAAT
Found at i:1837544 original size:15 final size:14
Alignment explanation
Indices: 1837519--1837555 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
1837509 CTTTAAAAAA
1837519 TTTATTTTAAATTT
1 TTTATTTTAAATTT
1837533 TTTATATTTAAATTT
1 TTTAT-TTTAAATTT
*
1837548 TTAATTTT
1 TTTATTTT
1837556 TATTTAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTTAAATTT
Found at i:1837561 original size:19 final size:19
Alignment explanation
Indices: 1837532--1837569 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
1837522 ATTTTAAATT
1837532 TTTTATATTTAAATTTTTAA
1 TTTTATATTT-AATTTTTAA
1837552 TTTT-TATTTAATTTTTAA
1 TTTTATATTTAATTTTTAA
1837570 ATAATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATATTTAATTTTTAA
Found at i:1838136 original size:71 final size:71
Alignment explanation
Indices: 1837999--1838136 Score: 159
Period size: 71 Copynumber: 1.9 Consensus size: 71
1837989 ATAATAGTTG
** * ** **
1837999 TGCATTGTTCACATAATGGTGCACGTAATTATTTGGGCAACAGCAGCAACAACAGCAACAGGAGC
1 TGCATTGTTCACATAATGACGCACGCAATTATTTGAACAACAGCAGCAACAACAGCAACAACAGC
1838064 AGCGGT
66 AGCGGT
* * * * * *
1838070 TGCATTGTTCACGTAATGACGCATGCAATTATTTGAACAATAGTAGCAACAACAGGAGCAACAGC
1 TGCATTGTTCACATAATGACGCACGCAATTATTTGAACAACAGCAGCAACAACAGCAACAACAGC
1838135 AG
66 AG
1838137 TCGAAGAACA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
71 54 1.00
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (71 bp):
TGCATTGTTCACATAATGACGCACGCAATTATTTGAACAACAGCAGCAACAACAGCAACAACAGC
AGCGGT
Done.