Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold92
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: 2337674
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 499 characters in sequence are not A, C, G, or T
File 16 of 19
Found at i:1926435 original size:26 final size:25
Alignment explanation
Indices: 1926384--1926437 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1926374 AAAAATTAAA
* * * *
1926384 CTTATTTTAAAAATATGCCTTGACT
1 CTTAATTTAAAAACATGACTTAACT
1926409 CTTAATTTAAAAACATGAACTTAACT
1 CTTAATTTAAAAACATG-ACTTAACT
1926435 CTT
1 CTT
1926438 TTTATAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.41
Consensus pattern (25 bp):
CTTAATTTAAAAACATGACTTAACT
Found at i:1926566 original size:18 final size:18
Alignment explanation
Indices: 1926545--1926583 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1926535 AAGTTATTTT
1926545 AAAATTAAAATTTTTAAA
1 AAAATTAAAATTTTTAAA
*
1926563 AAAATTAAATTTTTTAAA
1 AAAATTAAAATTTTTAAA
1926581 AAA
1 AAA
1926584 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTAAAATTTTTAAA
Found at i:1926572 original size:17 final size:17
Alignment explanation
Indices: 1926545--1926607 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
1926535 AAGTTATTTT
1926545 AAAATTAAAATTTTTAAA
1 AAAATT-AAATTTTTAAA
*
1926563 AAAATTAAATTTTTTAA
1 AAAATTAAATTTTTAAA
*
1926580 AAAATT-ATTTTTTAAA
1 AAAATTAAATTTTTAAA
1926596 AATAATTTAAAT
1 AA-AA-TTAAAT
1926608 AAATCTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
16 10 0.26
17 18 0.47
18 8 0.21
19 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTAAATTTTTAAA
Found at i:1926912 original size:12 final size:11
Alignment explanation
Indices: 1926865--1926929 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
1926855 ATATGAATTA
1926865 AATTTAAATAT
1 AATTTAAATAT
1926876 AATATT-AATAT
1 AAT-TTAAATAT
* *
1926887 TATTTATAT-T
1 AATTTAAATAT
1926897 AATTTAAATAT
1 AATTTAAATAT
*
1926908 AAATTTTAAATTT
1 -AA-TTTAAATAT
*
1926921 TATTTAAAT
1 AATTTAAAT
1926930 TTATTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
10 10 0.23
11 20 0.47
12 5 0.12
13 8 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
AATTTAAATAT
Found at i:1926936 original size:34 final size:32
Alignment explanation
Indices: 1926860--1926936 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 32
1926850 ATTGAATATG
1926860 AATTAAATTTAAATATAATATTAATATTATTTA
1 AATT-AATTTAAATATAATATTAATATTATTTA
* * *
1926893 TATTAATTTAAATATAAATTTTAAATTTTATTTA
1 AATTAATTTAAATAT-AATATT-AATATTATTTA
*
1926927 AATTTATTTA
1 AATTAATTTA
1926937 TATTTAGCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 11 0.30
33 8 0.22
34 18 0.49
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
AATTAATTTAAATATAATATTAATATTATTTA
Found at i:1927000 original size:17 final size:18
Alignment explanation
Indices: 1926980--1927013 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1926970 ATCATTTATA
1926980 TTTTT-TTAAAATTTAAT
1 TTTTTATTAAAATTTAAT
*
1926997 TTTTTATTAAATTTTAA
1 TTTTTATTAAAATTTAA
1927014 AATTTAAATA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTATTAAAATTTAAT
Found at i:1927036 original size:26 final size:25
Alignment explanation
Indices: 1926983--1927037 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
1926973 ATTTATATTT
* * *
1926983 TTTTAAAATTTAATTTTTTATTAAA
1 TTTTAAAATTTAATATATTAATAAA
*
1927008 TTTTAAAATTTAAATATATTAATATA
1 TTTTAAAATTT-AATATATTAATAAA
1927034 TTTT
1 TTTT
1927038 TTAATGTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTTAAAATTTAATATATTAATAAA
Found at i:1927100 original size:19 final size:21
Alignment explanation
Indices: 1927078--1927124 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1927068 ATATTCTTTT
1927078 TATATTAAAAAT-T-AATTAA
1 TATATTAAAAATATAAATTAA
1927097 TATA-TAAAAATATAAAATTAA
1 TATATTAAAAATAT-AAATTAA
1927118 TATATTA
1 TATATTA
1927125 TATAATTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.29
19 5 0.21
21 10 0.42
22 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATTAAAAATATAAATTAA
Found at i:1927229 original size:19 final size:19
Alignment explanation
Indices: 1927195--1927235 Score: 50
Period size: 17 Copynumber: 2.2 Consensus size: 19
1927185 TTTAAACAAG
1927195 TTTATTTTTTTGTCTAA-A
1 TTTATTTTTTTGTCTAATA
1927213 TTTA-TTTTTTGATTCTAATA
1 TTTATTTTTTTG--TCTAATA
1927233 TTT
1 TTT
1927236 TTGTCAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 5 0.25
20 4 0.20
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTATTTTTTTGTCTAATA
Found at i:1927512 original size:15 final size:15
Alignment explanation
Indices: 1927492--1927535 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1927482 TATACACAAA
1927492 TATAAATTTTAAAAT
1 TATAAATTTTAAAAT
*
1927507 TATAAATATTTAATAT
1 TATAAAT-TTTAAAAT
* *
1927523 CAAAAATTTTAAA
1 TATAAATTTTAAA
1927536 TATCAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TATAAATTTTAAAAT
Found at i:1927529 original size:16 final size:16
Alignment explanation
Indices: 1927495--1927542 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1927485 ACACAAATAT
* *
1927495 AAATTTTAAA-ATTAT
1 AAATTTTAAATATCAA
1927510 AAATATTT-AATATCAA
1 AAAT-TTTAAATATCAA
1927526 AAATTTTAAATATCAA
1 AAATTTTAAATATCAA
1927542 A
1 A
1927543 TAAAAAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTTAAATATCAA
Found at i:1928010 original size:37 final size:37
Alignment explanation
Indices: 1927969--1928051 Score: 107
Period size: 37 Copynumber: 2.2 Consensus size: 37
1927959 ATATGTATAT
*
1927969 ATAATTAAA-ATTAATTAAAATTATA-TTATGTTAAATA
1 ATAATTAAATATT-ATTAAAATTATATTTATATTAAA-A
*
1928006 ATAATTAAATATTATTACAATTATATTTATATTAAAA
1 ATAATTAAATATTATTAAAATTATATTTATATTAAAA
1928043 ATAAATTAA
1 AT-AATTAA
1928052 TAAAATTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
37 23 0.56
38 18 0.44
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (37 bp):
ATAATTAAATATTATTAAAATTATATTTATATTAAAA
Found at i:1928344 original size:2 final size:2
Alignment explanation
Indices: 1928337--1928362 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1928327 GTAAACTGTA
1928337 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
1928363 TATTACCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1930689 original size:23 final size:23
Alignment explanation
Indices: 1930645--1930689 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1930635 ATTTCAATTC
* * * *
1930645 AAAAATAAATATATTTTTATATA
1 AAAAATAAAAATAATATCATATA
1930668 AAAAATAAAAATAATATCATAT
1 AAAAATAAAAATAATATCATAT
1930690 TTTGCTTTTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAAATAAAAATAATATCATATA
Found at i:1930773 original size:22 final size:21
Alignment explanation
Indices: 1930715--1930777 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 21
1930705 TAGAAAAAGT
*
1930715 TTTAATATGATATATGA-AT-
1 TTTAATATTATATATGATATA
*
1930734 TTTAATAATGTCTAATATGATATA
1 TTTAAT-AT-TAT-ATATGATATA
1930758 TTTAATA-TATATAT-ATATA
1 TTTAATATTATATATGATATA
1930777 T
1 T
1930778 CATTTTGTGC
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
19 12 0.33
20 6 0.17
21 3 0.08
22 6 0.17
23 3 0.08
24 6 0.17
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (21 bp):
TTTAATATTATATATGATATA
Found at i:1930775 original size:24 final size:21
Alignment explanation
Indices: 1930717--1930775 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 21
1930707 GAAAAAGTTT
1930717 TAATATGATATATGAATTTTAA
1 TAATAT-ATATATGAATTTTAA
* *
1930739 TAATGTCTAATATGATATATTTAA
1 TAATATAT-ATATGA-AT-TTTAA
1930763 TATATATATATAT
1 TA-ATATATATAT
1930776 ATCATTTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 1 0.03
22 11 0.38
23 2 0.07
24 11 0.38
25 4 0.14
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TAATATATATATGAATTTTAA
Found at i:1932693 original size:37 final size:36
Alignment explanation
Indices: 1932639--1932720 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 36
1932629 ATGTGTATAT
*
1932639 ATAATTAAAATTATTAAAATTATA-TTATGTTAAATA
1 ATAATTAAAATTATTAAAATTATATTTACGTTAAA-A
1932675 ATAATTAAATATTATTAAAATTATATTTACGTTAAAA
1 ATAATTAAA-ATTATTAAAATTATATTTACGTTAAAA
1932712 ATAAATTAA
1 AT-AATTAA
1932721 TAAAATGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
36 9 0.21
37 18 0.43
38 15 0.36
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (36 bp):
ATAATTAAAATTATTAAAATTATATTTACGTTAAAA
Found at i:1933601 original size:2 final size:2
Alignment explanation
Indices: 1933594--1933627 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1933584 GTAAACTGTA
1933594 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
1933628 TTTATTATCT
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:1938507 original size:41 final size:42
Alignment explanation
Indices: 1938411--1938508 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 42
1938401 TTTTTTTAAA
*
1938411 AAAT-AATTTAAAT-AAATTTAAATTATCTATTTATAAATAT
1 AAATAAATTTAAATAAAATTTAAATTATATATTTATAAATAT
* * * * *
1938451 TAATAAACTTGAATAAAATTTAAATTTTATATTT-TAAGT-T
1 AAATAAATTTAAATAAAATTTAAATTATATATTTATAAATAT
1938491 AAATTAAATTTAAATAAA
1 AAA-TAAATTTAAATAAA
1938509 TATAAATAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
40 6 0.13
41 23 0.50
42 17 0.37
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (42 bp):
AAATAAATTTAAATAAAATTTAAATTATATATTTATAAATAT
Found at i:1938793 original size:22 final size:22
Alignment explanation
Indices: 1938766--1938817 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
1938756 ATCACTTATC
1938766 ATTTTTAAATAAAATATAAT-TTT
1 ATTTTTAAA-AAAATA-AATATTT
*
1938789 ATTTTTTAAAAAATAAATATTT
1 ATTTTTAAAAAAATAAATATTT
1938811 ATTTTTA
1 ATTTTTA
1938818 CTTTTTCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 3 0.12
22 15 0.58
23 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTTAAAAAAATAAATATTT
Found at i:1939271 original size:9 final size:9
Alignment explanation
Indices: 1939257--1939287 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1939247 AATCAAATTT
1939257 AATATTTAA
1 AATATTTAA
1939266 AATATTTAA
1 AATATTTAA
*
1939275 AATATATAA
1 AATATTTAA
1939284 AATA
1 AATA
1939288 AAATATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
AATATTTAA
Found at i:1939387 original size:45 final size:45
Alignment explanation
Indices: 1939328--1939423 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 45
1939318 TAATACAAAC
**
1939328 TAAAAATCTATATAAACTTAAACACAAAATTAATTAAAACCCAAT
1 TAAAAATCTATATAAACTTAAACACAAAACCAATTAAAACCCAAT
* * * * *
1939373 TAAAAATTTATATAAACTTAAACCCAAACCCAATTAAAACTCATT
1 TAAAAATCTATATAAACTTAAACACAAAACCAATTAAAACCCAAT
1939418 TAAAAA
1 TAAAAA
1939424 AATTAACAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.56, C:0.17, G:0.00, T:0.27
Consensus pattern (45 bp):
TAAAAATCTATATAAACTTAAACACAAAACCAATTAAAACCCAAT
Found at i:1940479 original size:8 final size:8
Alignment explanation
Indices: 1940466--1940499 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
1940456 CATAAATATT
1940466 ATAAAAAA
1 ATAAAAAA
1940474 ATAAAAAA
1 ATAAAAAA
1940482 ATAAAGAAA
1 ATAAA-AAA
1940491 ATAAAAAA
1 ATAAAAAA
1940499 A
1 A
1940500 CTGAGAGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (8 bp):
ATAAAAAA
Found at i:1940491 original size:17 final size:16
Alignment explanation
Indices: 1940466--1940499 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
1940456 CATAAATATT
1940466 ATAAAAAAATAAAAAA
1 ATAAAAAAATAAAAAA
1940482 ATAAAGAAAATAAAAAA
1 ATAAA-AAAATAAAAAA
1940499 A
1 A
1940500 CTGAGAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (16 bp):
ATAAAAAAATAAAAAA
Found at i:1940823 original size:10 final size:10
Alignment explanation
Indices: 1940808--1940870 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
1940798 TAATTTTAAT
1940808 ATAAATAAAA
1 ATAAATAAAA
1940818 ATAAATAAAA
1 ATAAATAAAA
* * **
1940828 TTAATTTTAA
1 ATAAATAAAA
*
1940838 AT-AATTAAA
1 ATAAATAAAA
1940847 ATAAATAAAA
1 ATAAATAAAA
*
1940857 TCTAAATAAAA
1 -ATAAATAAAA
1940868 ATA
1 ATA
1940871 CTAAGACTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
9 7 0.17
10 25 0.61
11 9 0.22
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:1940847 original size:29 final size:31
Alignment explanation
Indices: 1940798--1940857 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1940788 AATAATTATA
1940798 TAATTTTAATATAAATAAAAATAAATAAAAT
1 TAATTTTAATATAAATAAAAATAAATAAAAT
*
1940829 TAATTTTAA-AT-AATTAAAATAAATAAAAT
1 TAATTTTAATATAAATAAAAATAAATAAAAT
1940858 CTAAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 17 0.61
30 2 0.07
31 9 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (31 bp):
TAATTTTAATATAAATAAAAATAAATAAAAT
Found at i:1942931 original size:19 final size:20
Alignment explanation
Indices: 1942909--1942956 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
1942899 ATATATTAAA
1942909 ATATTAAAAATTTAT-TTTT
1 ATATTAAAAATTTATATTTT
* *
1942928 ATATTAATATTTTATATTTT
1 ATATTAAAAATTTATATTTT
1942948 ATAATTAAA
1 AT-ATTAAA
1942957 TTTAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 13 0.54
20 6 0.25
21 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATTAAAAATTTATATTTT
Found at i:1942947 original size:21 final size:20
Alignment explanation
Indices: 1942919--1942959 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1942909 ATATTAAAAA
1942919 TTTAT-TTTTAT-ATTAATAT
1 TTTATATTTTATAATTAA-AT
1942938 TTTATATTTTATAATTAAAT
1 TTTATATTTTATAATTAAAT
1942958 TT
1 TT
1942960 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATATTTTATAATTAAAT
Found at i:1944769 original size:19 final size:18
Alignment explanation
Indices: 1944745--1944787 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1944735 TCAATCAAAC
*
1944745 TCAAATAAAATTTTAAATT
1 TCAAAT-AAATCTTAAATT
*
1944764 TCAAATCAATCTTAAATT
1 TCAAATAAATCTTAAATT
*
1944782 TAAAAT
1 TCAAAT
1944788 TCTTATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (18 bp):
TCAAATAAATCTTAAATT
Found at i:1946722 original size:16 final size:17
Alignment explanation
Indices: 1946697--1946729 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1946687 AAATAAAATA
1946697 AAAAATATTAATTAATT
1 AAAAATATTAATTAATT
1946714 AAAAA-ATTAATTAATT
1 AAAAATATTAATTAATT
1946730 TTGTATTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAATATTAATTAATT
Found at i:1951963 original size:33 final size:33
Alignment explanation
Indices: 1951919--1951983 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1951909 CACATGCAGA
* *
1951919 TGTATCGATACA-AGTTGTAATGTATCGATACAT
1 TGTATCAATACACA-TTGCAATGTATCGATACAT
1951952 TGTATCAATACACATTGCAATGTATCGATACA
1 TGTATCAATACACATTGCAATGTATCGATACA
1951984 CTATGGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCAATACACATTGCAATGTATCGATACAT
Found at i:1952591 original size:34 final size:34
Alignment explanation
Indices: 1952552--1952660 Score: 114
Period size: 34 Copynumber: 3.2 Consensus size: 34
1952542 TATAATTCTT
*
1952552 AAGATAATTAAGAGGTTCTATCTAAACCTTCAAA
1 AAGATAATTAAGAGGTTCTATCTAAGCCTTCAAA
* * *
1952586 AAGAT-AGTATAGAGGTTCTATCTTAGGCTTCAAA
1 AAGATAATTA-AGAGGTTCTATCTAAGCCTTCAAA
* * **
1952620 AAGATAGTGT-TGAGGTTCTATCTAAGCCTTTGAA
1 AAGATAAT-TAAGAGGTTCTATCTAAGCCTTCAAA
1952654 AAGATAA
1 AAGATAA
1952661 AGTTGTAAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
33 3 0.05
34 56 0.93
36 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (34 bp):
AAGATAATTAAGAGGTTCTATCTAAGCCTTCAAA
Found at i:1954602 original size:17 final size:17
Alignment explanation
Indices: 1954572--1954605 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1954562 TCATATGAAA
* *
1954572 TTTTGTTCATATTTTTG
1 TTTTGATCAAATTTTTG
1954589 TTTTGATCAAATTTTTG
1 TTTTGATCAAATTTTTG
1954606 GTGATAATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTTGATCAAATTTTTG
Found at i:1954790 original size:19 final size:20
Alignment explanation
Indices: 1954766--1954805 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1954756 CTTTGATTGA
1954766 TCTTGTATTTTATG-TTAAT
1 TCTTGTATTTTATGCTTAAT
* *
1954785 TCTTGTGTTTTGTGCTTAAT
1 TCTTGTATTTTATGCTTAAT
1954805 T
1 T
1954806 GTTCCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.62
Consensus pattern (20 bp):
TCTTGTATTTTATGCTTAAT
Found at i:1956868 original size:25 final size:26
Alignment explanation
Indices: 1956830--1956879 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1956820 CATTGGGAAA
*
1956830 AAAAAAGGGAGAGAGAAAATTTATAG
1 AAAAAAGGGAGAGACAAAATTTATAG
*
1956856 AAAAAAGGG-GAGACAAAGTTTATA
1 AAAAAAGGGAGAGACAAAATTTATA
1956880 AATTCGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.56, C:0.02, G:0.26, T:0.16
Consensus pattern (26 bp):
AAAAAAGGGAGAGACAAAATTTATAG
Found at i:1958185 original size:34 final size:34
Alignment explanation
Indices: 1958147--1958245 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 34
1958137 AAGATGATTA
*
1958147 AGAGGTTCTATCTAAGCCTTTGAAAAGATTGTGT
1 AGAGGTTCTATCTAAGCCTTTGAAAAGATAGTGT
* * **
1958181 AGAGGTTCTATATTAGCCTTCAAAAAGATAGTGT
1 AGAGGTTCTATCTAAGCCTTTGAAAAGATAGTGT
** * * *
1958215 TTAAGTTTTATCTAAGTCTTTGAAAAGATAG
1 AGAGGTTCTATCTAAGCCTTTGAAAAGATAG
1958246 AGTTGTAAAG
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.36
Consensus pattern (34 bp):
AGAGGTTCTATCTAAGCCTTTGAAAAGATAGTGT
Found at i:1959929 original size:11 final size:11
Alignment explanation
Indices: 1959913--1959949 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
1959903 TAGCAGATTT
1959913 TTTTTCTTTTC
1 TTTTTCTTTTC
1959924 TTTTTCTTTT-
1 TTTTTCTTTTC
*
1959934 TTTTTTTTTTC
1 TTTTTCTTTTC
1959945 TTTTT
1 TTTTT
1959950 TGAGGGCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:1959936 original size:21 final size:21
Alignment explanation
Indices: 1959910--1959949 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1959900 TCTTAGCAGA
1959910 TTTTTTTTCTTTTCTTTTTCT
1 TTTTTTTTCTTTTCTTTTTCT
*
1959931 TTTTTTTTTTTTTCTTTTT
1 TTTTTTTTCTTTTCTTTTT
1959950 TGAGGGCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (21 bp):
TTTTTTTTCTTTTCTTTTTCT
Found at i:1959937 original size:15 final size:15
Alignment explanation
Indices: 1959910--1959950 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1959900 TCTTAGCAGA
*
1959910 TTTTT-TTTCTTTTC
1 TTTTTCTTTTTTTTC
*
1959924 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTC
1959939 TTTTTCTTTTTT
1 TTTTTCTTTTTT
1959951 GAGGGCCGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.21
15 19 0.79
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTCTTTTTTTTC
Found at i:1960079 original size:24 final size:25
Alignment explanation
Indices: 1960052--1960104 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
1960042 TTAAAGTTTA
*
1960052 AATTATTTAATAA-TTATATAAA-AT
1 AATTATTT-ATAATTTAAATAAATAT
*
1960076 AATT-TTTTTAATTTAAATAAATAT
1 AATTATTTATAATTTAAATAAATAT
1960100 AATTA
1 AATTA
1960105 AAATTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 3 0.12
23 11 0.46
24 10 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTATTTATAATTTAAATAAATAT
Found at i:1960518 original size:21 final size:21
Alignment explanation
Indices: 1960477--1960518 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1960467 TAACTTAGTT
**
1960477 TATTGATATATATATTTAAAA
1 TATTGATATATATATACAAAA
*
1960498 TATTGATATATTTATACAAAA
1 TATTGATATATATATACAAAA
1960519 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (21 bp):
TATTGATATATATATACAAAA
Found at i:1960524 original size:23 final size:22
Alignment explanation
Indices: 1960476--1960524 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
1960466 TTAACTTAGT
**
1960476 TTATTGATATATATATTTAAAA
1 TTATTGATATATATATCAAAAA
*
1960498 -TATTGATATATTTATACAAAAA
1 TTATTGATATATATAT-CAAAAA
1960520 TTATT
1 TTATT
1960525 TTTAAAGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 14 0.64
22 4 0.18
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (22 bp):
TTATTGATATATATATCAAAAA
Found at i:1962424 original size:14 final size:13
Alignment explanation
Indices: 1962414--1962450 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1962404 ATTTTAAATA
1962414 TAATTTTTTAATT
1 TAATTTTTTAATT
*
1962427 TAAATTATTTAATT
1 T-AATTTTTTAATT
1962441 TAATTTTTTA
1 TAATTTTTTA
1962451 TTAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TAATTTTTTAATT
Found at i:1962477 original size:34 final size:34
Alignment explanation
Indices: 1962428--1962495 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
1962418 TTTTTAATTT
** *
1962428 AAATTATTTAATTTAATTTTTTATTAAAAATAAA
1 AAATTATTTAATTTAAAATTTAATTAAAAATAAA
*
1962462 AAATATATTT-ATTTAAAATTTAATTAAAATTAAA
1 AAAT-TATTTAATTTAAAATTTAATTAAAAATAAA
1962496 TATATTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 24 0.83
35 5 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (34 bp):
AAATTATTTAATTTAAAATTTAATTAAAAATAAA
Found at i:1962831 original size:18 final size:18
Alignment explanation
Indices: 1962817--1962863 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1962807 TTAAAATTAT
1962817 ATTTAAAAAATAAATATA
1 ATTTAAAAAATAAATATA
*
1962835 ATTTTAAAAATTAAA-ATA
1 A-TTTAAAAAATAAATATA
* *
1962853 AATAAAAAAAT
1 ATTTAAAAAAT
1962864 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.29
18 5 0.21
19 12 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTTAAAAAATAAATATA
Found at i:1962840 original size:19 final size:18
Alignment explanation
Indices: 1962808--1962853 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1962798 TATTATCTCT
*
1962808 TAAAATTATATTTAAAAAA
1 TAAAATAAT-TTTAAAAAA
*
1962827 TAAATATAATTTTAAAAAT
1 TAAA-ATAATTTTAAAAAA
1962846 TAAAATAA
1 TAAAATAA
1962854 ATAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 16 0.67
20 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATAATTTTAAAAAA
Found at i:1966875 original size:14 final size:15
Alignment explanation
Indices: 1966858--1966895 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1966848 TACAATTTTT
1966858 AAAATATAT-AAATA
1 AAAATATATAAAATA
1966872 AAAATA-ATAAAATA
1 AAAATATATAAAATA
1966886 ATAAATATAT
1 A-AAATATAT
1966896 GACATCTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 12 0.57
15 5 0.24
16 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATATATAAAATA
Found at i:1968058 original size:19 final size:20
Alignment explanation
Indices: 1968014--1968067 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1968004 TGCTAGTTTT
***
1968014 ATGTATCGATACAATTGTGT
1 ATGTATCGATACAATTGAAC
1968034 ATGTATCGATACAATT-AAC
1 ATGTATCGATACAATTGAAC
1968053 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1968068 GTATCGATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAC
Found at i:1968109 original size:20 final size:20
Alignment explanation
Indices: 1968086--1968139 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1968076 GCAAAGCATA
1968086 ATGTATCAATACATCTGGAT
1 ATGTATCAATACATCTGGAT
1968106 ATGTATCAATACATCTGGAT
1 ATGTATCAATACATCTGGAT
*
1968126 ATGTATCGATACAT
1 ATGTATCAATACAT
1968140 ATAAGGATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCAATACATCTGGAT
Found at i:1975565 original size:20 final size:20
Alignment explanation
Indices: 1975540--1975593 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1975530 GTTTGAGACA
**
1975540 ATGTATCGATACAAT-TCGTT
1 ATGTATCGATACAATAT-GCC
1975560 ATGTATCGATACAATATGCC
1 ATGTATCGATACAATATGCC
1975580 ATGTATCGATACAA
1 ATGTATCGATACAA
1975594 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATATGCC
Found at i:1976649 original size:24 final size:23
Alignment explanation
Indices: 1976599--1976651 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
1976589 ACATAAATTT
**
1976599 TAAAATTATAAATATTTAATATC
1 TAAAATTATAAATATTTAATAAA
1976622 TAAAATTATTAAATA-TTAAGTAAA
1 TAAAATTA-TAAATATTTAA-TAAA
1976646 TAAAAT
1 TAAAAT
1976652 AAATATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TAAAATTATAAATATTTAATAAA
Found at i:1977646 original size:17 final size:18
Alignment explanation
Indices: 1977617--1977677 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 18
1977607 TTTTTATTTA
*
1977617 AATTTAATT-ATAAAAAT
1 AATTTATTTAATAAAAAT
*
1977634 AATTT-TTTAATAAGAAT
1 AATTTATTTAATAAAAAT
* *
1977651 CATTTATTTAA-AAAGAT
1 AATTTATTTAATAAAAAT
1977668 AATTTGATTT
1 AATTT-ATTT
1977678 TTGAAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
16 2 0.06
17 24 0.69
18 9 0.26
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
AATTTATTTAATAAAAAT
Found at i:1977783 original size:2 final size:2
Alignment explanation
Indices: 1977776--1977802 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1977766 GACAAATCTC
1977776 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1977803 AAATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1977849 original size:43 final size:43
Alignment explanation
Indices: 1977781--1977868 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
1977771 ATCTCATATA
* *
1977781 TATATATATATATATATATATAAAATAAAATATGGTGCATGCT
1 TATATATATATATATATATAAAAAATAAAATATGGTACATGCT
*
1977824 TATATATATATATATCTATAAAAAATAAAATATGGTACATGCT
1 TATATATATATATATATATAAAAAATAAAATATGGTACATGCT
1977867 TA
1 TA
1977869 CCTAGTAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.39
Consensus pattern (43 bp):
TATATATATATATATATATAAAAAATAAAATATGGTACATGCT
Found at i:1978166 original size:3 final size:3
Alignment explanation
Indices: 1978158--1978183 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1978148 TTTAAGTAAT
1978158 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1978184 TTCGATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1981715 original size:24 final size:24
Alignment explanation
Indices: 1981662--1981719 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
1981652 TTTCTTCCCC
*
1981662 CTTCAATGCTTGTTGTTTTTCCTT
1 CTTCAATGCTTGTTGTTTGTCCTT
1981686 CTTCAATGCTTGTTG-TTGT-CTT
1 CTTCAATGCTTGTTGTTTGTCCTT
1981708 CTGGTCAATGCT
1 CT--TCAATGCT
1981720 GCTATCGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 5 0.16
23 3 0.10
24 23 0.74
ACGTcount: A:0.10, C:0.21, G:0.17, T:0.52
Consensus pattern (24 bp):
CTTCAATGCTTGTTGTTTGTCCTT
Found at i:1981829 original size:42 final size:42
Alignment explanation
Indices: 1981782--1981888 Score: 121
Period size: 42 Copynumber: 2.5 Consensus size: 42
1981772 TTTTTCCTTG
*
1981782 ATTTTTTTTGTTTTGATTTCTTTGATTTTTTATTTTTTTAA-A
1 ATTTTTTTT-TTTTGATTTCTTTGATTTTTTAATTTTTTAATA
*
1981824 ATTTTTTGATTTCTTTGA-TT-TTTGATTTTTTAATTTTTTAATT
1 ATTTTTT--TTT-TTTGATTTCTTTGATTTTTTAATTTTTTAATA
1981867 ATTTTTTTAATTTTTGATTTCT
1 ATTTTTTT--TTTTTGATTTCT
1981889 ACTCATTATT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
41 1 0.02
42 32 0.58
43 14 0.25
44 8 0.15
ACGTcount: A:0.18, C:0.03, G:0.07, T:0.73
Consensus pattern (42 bp):
ATTTTTTTTTTTTGATTTCTTTGATTTTTTAATTTTTTAATA
Found at i:1981862 original size:51 final size:51
Alignment explanation
Indices: 1981792--1981888 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
1981782 ATTTTTTTTG
* *
1981792 TTTTGATTTCTTTGATTTTTTATT-TTTTTAAAATTTTTTGATTTCTTTGAT
1 TTTTGATTTCTTTAATTTTTAATTATTTTTAAAA-TTTTTGATTTCTTTGAT
**
1981843 TTTTGATTT-TTTAATTTTTTAATTATTTTTTTAATTTTTGATTTCT
1 TTTTGATTTCTTTAA-TTTTTAATTATTTTTAAAATTTTTGATTTCT
1981889 ACTCATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 4 0.10
51 29 0.73
52 7 0.17
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (51 bp):
TTTTGATTTCTTTAATTTTTAATTATTTTTAAAATTTTTGATTTCTTTGAT
Found at i:1981881 original size:8 final size:8
Alignment explanation
Indices: 1981779--1981862 Score: 68
Period size: 8 Copynumber: 10.2 Consensus size: 8
1981769 TCTTTTTTCC
1981779 TTGATTTT
1 TTGATTTT
1981787 TT--TTGTT
1 TTGATT-TT
1981794 TTGATTTCT
1 TTGATTT-T
1981803 TTGATTTT
1 TTGATTTT
1981811 TT-ATTTTT
1 TTGA-TTTT
*
1981819 TTAAAATTTT
1 TT--GATTTT
1981829 TTGATTTCT
1 TTGATTT-T
1981838 TTGA-TTT
1 TTGATTTT
1981845 TTGATTTT
1 TTGATTTT
*
1981853 TTAATTTT
1 TTGATTTT
1981861 TT
1 TT
1981863 AATTATTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
6 2 0.03
7 10 0.16
8 30 0.47
9 15 0.23
10 6 0.09
11 1 0.02
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.74
Consensus pattern (8 bp):
TTGATTTT
Found at i:1983119 original size:23 final size:23
Alignment explanation
Indices: 1983071--1983115 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1983061 CTGGTTGAAT
*
1983071 GATAAATAATTATAAGTGACAAA
1 GATAAATAATTATAAGTAACAAA
*
1983094 GATATATAATT-TAAGTAACAAA
1 GATAAATAATTATAAGTAACAAA
1983116 AGATTCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.56, C:0.04, G:0.11, T:0.29
Consensus pattern (23 bp):
GATAAATAATTATAAGTAACAAA
Found at i:1983820 original size:25 final size:25
Alignment explanation
Indices: 1983771--1983817 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1983761 AAATATCAAG
1983771 TAAATAAAATAAATATAAATATATT
1 TAAATAAAATAAATATAAATATATT
*
1983796 TAAA-AAAATACA-ATAAAT-TATT
1 TAAATAAAATAAATATAAATATATT
1983818 ATTAATTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 6 0.29
24 7 0.33
25 4 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
TAAATAAAATAAATATAAATATATT
Found at i:1984522 original size:14 final size:14
Alignment explanation
Indices: 1984487--1984528 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1984477 TTAATATTAA
*
1984487 AATATTTTTAAAATT
1 AATATTTTT-ATATT
*
1984502 TAT-TTTTTATATT
1 AATATTTTTATATT
1984515 AATATTTTTATATT
1 AATATTTTTATATT
1984529 TTATAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 6 0.26
14 15 0.65
15 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:1984524 original size:21 final size:21
Alignment explanation
Indices: 1984500--1984542 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1984490 ATTTTTAAAA
*
1984500 TTTATTTTTTAT-ATTAATATT
1 TTTATATTTTATAATTAA-ATT
1984521 TTTATATTTTATAATTAAATT
1 TTTATATTTTATAATTAAATT
1984542 T
1 T
1984543 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATATTTTATAATTAAATT
Found at i:1984822 original size:18 final size:17
Alignment explanation
Indices: 1984772--1984822 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
1984762 ACTTAATTAT
*
1984772 AAAA-ATAATTTTTTTA
1 AAAAGATAATTTATTTA
*
1984788 AAAAGAATCATTTATTTA
1 AAAAG-ATAATTTATTTA
1984806 AAAAGATAATTTGATTT
1 AAAAGATAATTT-ATTT
1984823 TTGAAAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 4 0.14
17 6 0.21
18 19 0.66
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (17 bp):
AAAAGATAATTTATTTA
Found at i:1984928 original size:2 final size:2
Alignment explanation
Indices: 1984921--1984949 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1984911 GACAAATCTC
1984921 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 A
1984950 AATAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1987455 original size:22 final size:21
Alignment explanation
Indices: 1987421--1987469 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1987411 TAAAATATTT
1987421 TTAAATTT-TAT-TTTTAT-A
1 TTAAATTTATATATTTTATAA
1987439 TTAATATTTATATATTTTATAA
1 TTAA-ATTTATATATTTTATAA
1987461 TTAAATTTA
1 TTAAATTTA
1987470 AATAAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.15
19 4 0.15
20 3 0.11
21 11 0.41
22 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAAATTTATATATTTTATAA
Found at i:1988459 original size:19 final size:19
Alignment explanation
Indices: 1988437--1988476 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1988427 AATTATAAAT
*
1988437 ATAAAATTATATAAATATA
1 ATAAAAATATATAAATATA
* *
1988456 ATAAAAATATTTAAATTTA
1 ATAAAAATATATAAATATA
1988475 AT
1 AT
1988477 TTATTATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAAAATATATAAATATA
Found at i:1990387 original size:15 final size:16
Alignment explanation
Indices: 1990356--1990405 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1990346 AAAAATAATT
*
1990356 AAAATATAATATAATAA
1 AAAATATAAT-TTATAA
1990373 AAAATAT-ATTTATAA
1 AAAATATAATTTATAA
* *
1990388 ATATTATAATTTATAA
1 AAAATATAATTTATAA
1990404 AA
1 AA
1990406 TATAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 10 0.36
16 11 0.39
17 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATATAATTTATAA
Found at i:1990395 original size:27 final size:25
Alignment explanation
Indices: 1990343--1990397 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
1990333 AAAATAAAAT
1990343 ATAAAAAATAATTAAAATATAATATA
1 ATAAAAAATAATTAAAATAT-ATATA
1990369 ATAAAAAATATATTTATAAATAT-TATA
1 ATAAAAAATA-A-TTA-AAATATATATA
1990396 AT
1 AT
1990398 TTATAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 10 0.38
27 7 0.27
28 3 0.12
29 6 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATAAAAAATAATTAAAATATATATA
Found at i:1990414 original size:16 final size:16
Alignment explanation
Indices: 1990335--1990416 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
1990325 ATCACATAAA
*
1990335 AATAAAATATAAAAAAT
1 AATAAAATAT-AAAATT
*
1990352 AATTAAAATATAATA-T
1 AA-TAAAATATAAAATT
* *
1990368 AATAAAAAAT-ATATT
1 AATAAAATATAAAATT
* *
1990383 TAT-AAATATTATAATT
1 AATAAAATA-TAAAATT
*
1990399 TATAAAATATAAAATT
1 AATAAAATATAAAATT
1990415 AA
1 AA
1990417 ATATTATTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
14 7 0.13
15 11 0.21
16 16 0.31
17 10 0.19
18 8 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAAATATAAAATT
Found at i:1991087 original size:14 final size:14
Alignment explanation
Indices: 1991061--1991095 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1991051 CACTAATTAA
*
1991061 TTAATAAAAATATT
1 TTAATATAAATATT
*
1991075 TTTATATAAATATT
1 TTAATATAAATATT
1991089 TTAATAT
1 TTAATAT
1991096 TTTATATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATATAAATATT
Found at i:1991714 original size:16 final size:16
Alignment explanation
Indices: 1991693--1991723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1991683 AAAGTGAATT
1991693 ATAAATATAAAATTAC
1 ATAAATATAAAATTAC
*
1991709 ATAAATATAATATTA
1 ATAAATATAAAATTA
1991724 TACTCAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATAAATATAAAATTAC
Found at i:1992087 original size:11 final size:11
Alignment explanation
Indices: 1992068--1992123 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
1992058 AATATTATCA
*
1992068 AATAAAAAAAT
1 AATATAAAAAT
1992079 AATATAAAAAT
1 AATATAAAAAT
1992090 AAT-T---AA-
1 AATATAAAAAT
*
1992096 AATATAATAA-
1 AATATAAAAAT
1992106 AATATAAAAAT
1 AATATAAAAAT
1992117 AATATAA
1 AATATAA
1992124 TTATAACGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 3 0.08
7 3 0.08
10 12 0.32
11 20 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:1992093 original size:38 final size:38
Alignment explanation
Indices: 1992050--1992123 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
1992040 AAATTATTTG
* * *
1992050 ATAATTTAAATATTATCAAATAAAAAAATAATATAAAA
1 ATAATTAAAATATAATAAAATAAAAAAATAATATAAAA
*
1992088 ATAATTAAAATATAATAAAATATAAAAATAATATAA
1 ATAATTAAAATATAATAAAATAAAAAAATAATATAA
1992124 TTATAACGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (38 bp):
ATAATTAAAATATAATAAAATAAAAAAATAATATAAAA
Found at i:1992170 original size:20 final size:20
Alignment explanation
Indices: 1992117--1992170 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
1992107 ATATAAAAAT
**
1992117 AATATAATTATAACGTATATA
1 AATA-AATTATAATTTATATA
1992138 AATAAATTATAATTTATATAA
1 AATAAATTATAATTTATAT-A
1992159 AATAAA-TATAAT
1 AATAAATTATAAT
1992171 ATAAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
AATAAATTATAATTTATATA
Found at i:1992175 original size:11 final size:11
Alignment explanation
Indices: 1992077--1992175 Score: 57
Period size: 11 Copynumber: 8.9 Consensus size: 11
1992067 AAATAAAAAA
*
1992077 ATAATATAAAA
1 ATAATATAAAT
1992088 ATAAT-TAAAAT
1 ATAATAT-AAAT
1992099 ATAATA-AAAT
1 ATAATATAAAT
*
1992109 ATAA-AAATAAT
1 ATAATATA-AAT
1992120 ATAATTATAACGTAT
1 ATAA-TATAA---AT
1992135 ATAA-ATAAATT
1 ATAATATAAA-T
*
1992146 ATAAT-T-TAT
1 ATAATATAAAT
*
1992155 ATAAAATAAAT
1 ATAATATAAAT
1992166 ATAATATAAA
1 ATAATATAAA
1992176 ATTAAATATT
Statistics
Matches: 69, Mismatches: 6, Indels: 26
0.68 0.06 0.26
Matches are distributed among these distances:
9 6 0.09
10 13 0.19
11 37 0.54
12 1 0.01
13 6 0.09
15 6 0.09
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:1992987 original size:15 final size:13
Alignment explanation
Indices: 1992958--1992982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1992948 ATTAAGTCAA
1992958 AAAAAATTTAAAT
1 AAAAAATTTAAAT
1992971 AAAAAATTTAAA
1 AAAAAATTTAAA
1992983 AATAATTCGA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAAATTTAAAT
Found at i:1994677 original size:15 final size:15
Alignment explanation
Indices: 1994659--1994715 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
1994649 TGTATTCATA
1994659 TTATATTTATATATT
1 TTATATTTATATATT
** *
1994674 TTAT-CGTATCATA-A
1 TTATATTTAT-ATATT
*
1994688 TTATATTTAAATATT
1 TTATATTTATATATT
1994703 TTATATTTATATA
1 TTATATTTATATA
1994716 AATTTTGATA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (15 bp):
TTATATTTATATATT
Found at i:1994744 original size:34 final size:34
Alignment explanation
Indices: 1994690--1994795 Score: 103
Period size: 34 Copynumber: 3.1 Consensus size: 34
1994680 TATCATAATT
* *
1994690 ATATTTAAATATTTTATATTTATATAA-ATTTTG
1 ATATTTTAATATTTTATATTTATATAATATTTTA
1994723 ATATTTTAATATCTATT-TATTTATATAATATTTTA
1 ATATTTTAATAT-T-TTATATTTATATAATATTTTA
* * * *
1994758 ATTATTTT-TTATGTCATATTTATGTAATA-TTTA
1 A-TATTTTAATATTTTATATTTATATAATATTTTA
1994791 ATATT
1 ATATT
1994796 ATTGAGTTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 4 0.06
33 17 0.27
34 24 0.39
35 11 0.18
36 6 0.10
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (34 bp):
ATATTTTAATATTTTATATTTATATAATATTTTA
Found at i:1994764 original size:20 final size:19
Alignment explanation
Indices: 1994685--1994765 Score: 52
Period size: 17 Copynumber: 4.5 Consensus size: 19
1994675 TATCGTATCA
1994685 TAATTATATTTA-AATATTT
1 TAATTAT-TTTATAATATTT
1994704 T-A-TATTTATATAA-ATTT
1 TAATTATTT-TATAATATTT
* *
1994721 TGA-TA-TTT-TAATA-TC
1 TAATTATTTTATAATATTT
*
1994736 TATTTATTTATATAATATTT
1 TAATTATTT-TATAATATTT
1994756 TAATTATTTT
1 TAATTATTTT
1994766 TTATGTCATA
Statistics
Matches: 48, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
15 5 0.10
16 6 0.12
17 14 0.29
18 7 0.15
19 7 0.15
20 9 0.19
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (19 bp):
TAATTATTTTATAATATTT
Found at i:1995564 original size:18 final size:20
Alignment explanation
Indices: 1995518--1995564 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 20
1995508 ATTAAAATAT
1995518 ATATATTATTATTTAATATTA
1 ATAT-TTATTATTTAATATTA
* *
1995539 AAAATTATT-TTT-ATATTA
1 ATATTTATTATTTAATATTA
1995557 ATATTTAT
1 ATATTTAT
1995565 GATTAAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 12 0.55
19 3 0.14
20 5 0.23
21 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTATTATTTAATATTA
Found at i:1995746 original size:21 final size:21
Alignment explanation
Indices: 1995717--1995764 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1995707 ATGGCATAAA
* * *
1995717 AAATAAAAATATTTTATATAT
1 AAATTAAAATATCTAATATAT
1995738 AAATTAAAATATCTAATATAT
1 AAATTAAAATATCTAATATAT
1995759 AAATTA
1 AAATTA
1995765 TCTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTAAAATATCTAATATAT
Found at i:1996011 original size:32 final size:32
Alignment explanation
Indices: 1995974--1996070 Score: 92
Period size: 32 Copynumber: 3.0 Consensus size: 32
1995964 AATTAATTAA
1995974 ATTTAAATTATTATTTAAATAATAAAATATTT
1 ATTTAAATTATTATTTAAATAATAAAATATTT
* *
1996006 ATTTAAATT-TAATTATAAA-ATATATAAATATTA
1 ATTTAAATTATTATT-TAAATA-ATA-AAATATTT
* * *
1996039 ATATAAATTATT-TTTTAATAATTAATATATTT
1 ATTTAAATTATTATTTAAATAA-TAAAATATTT
1996071 TAAATAATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
31 5 0.10
32 26 0.50
33 20 0.38
34 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTTAAATTATTATTTAAATAATAAAATATTT
Found at i:1996035 original size:33 final size:33
Alignment explanation
Indices: 1995973--1996047 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
1995963 AAATTAATTA
*
1995973 AATTTAAA-TTATTATTTAAATAATAAAATATT
1 AATTTAAATTTATTATTAAAATAATAAAATATT
*
1996005 TATTTAAATTTAATTA-TAAAAT-ATATAAATATT
1 AATTTAAATTT-ATTATTAAAATAATA-AAATATT
*
1996038 AATATAAATT
1 AATTTAAATT
1996048 ATTTTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 10 0.28
33 22 0.61
34 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (33 bp):
AATTTAAATTTATTATTAAAATAATAAAATATT
Found at i:1996256 original size:3 final size:3
Alignment explanation
Indices: 1996243--1996272 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1996233 AAGCGAGTAA
*
1996243 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1996273 TTAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1998121 original size:2 final size:2
Alignment explanation
Indices: 1998114--1998138 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1998104 ATGGGTGGGG
1998114 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1998139 CATAGATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2000409 original size:20 final size:20
Alignment explanation
Indices: 2000367--2000406 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2000357 AAAATTAACA
2000367 ATTATTATATTTAATATAAT
1 ATTATTATATTTAATATAAT
*
2000387 ATTATTAT-TTTGA-ATAAT
1 ATTATTATATTTAATATAAT
2000405 AT
1 AT
2000407 ATTTACTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTATTATATTTAATATAAT
Found at i:2000578 original size:14 final size:15
Alignment explanation
Indices: 2000546--2000578 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
2000536 TTTTTTTTAA
2000546 AAATTATATTTAATT
1 AAATTATATTTAATT
2000561 -AATTAT-TTTAATT
1 AAATTATATTTAATT
2000574 AAATT
1 AAATT
2000579 TTAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTATATTTAATT
Found at i:2000865 original size:13 final size:14
Alignment explanation
Indices: 2000847--2000875 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2000837 AAAGATGAAT
2000847 AAAATAA-TAAATA
1 AAAATAAGTAAATA
2000860 AAAATAAGTAAATA
1 AAAATAAGTAAATA
2000874 AA
1 AA
2000876 TAAATGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AAAATAAGTAAATA
Found at i:2001037 original size:19 final size:20
Alignment explanation
Indices: 2001005--2001042 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2000995 AATTATTTTA
2001005 AAGATAAAAAT-AAATAATT
1 AAGATAAAAATAAAATAATT
**
2001024 AAGATAAATTTAAAATAAT
1 AAGATAAAAATAAAATAAT
2001043 AACACTCAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAGATAAAAATAAAATAATT
Found at i:2001364 original size:30 final size:31
Alignment explanation
Indices: 2001297--2001417 Score: 129
Period size: 30 Copynumber: 3.8 Consensus size: 31
2001287 CATTTATAAG
* *
2001297 TTAATTTCAAATTGAATTTTTTAATTATATCAA
1 TTAATTTTAAATTAAATTTTTTAA-T-TATCAA
*
2001330 TTAATTTTAAATTAAATTTTTTAATCAT-AA
1 TTAATTTTAAATTAAATTTTTTAATTATCAA
* *
2001360 TTAATTTTAAATTAAAATTTTTAATTATGAA
1 TTAATTTTAAATTAAATTTTTTAATTATCAA
* *
2001391 TCAA-TTTAATTTAAATTTAATTTAATT
1 TTAATTTTAAATTAAATTT--TTTAATT
2001418 CATGGAAAGG
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
30 40 0.52
31 7 0.09
32 8 0.10
33 22 0.29
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (31 bp):
TTAATTTTAAATTAAATTTTTTAATTATCAA
Found at i:2001372 original size:63 final size:65
Alignment explanation
Indices: 2001292--2001413 Score: 169
Period size: 63 Copynumber: 1.9 Consensus size: 65
2001282 ATCATCATTT
* *
2001292 ATAAGTTAATTTCAAATTGAATTTTTTAATTAT-ATCAA-TTAATTTTAAATTAAATTTTTTAAT
1 ATAAGTTAATTTCAAATTAAAATTTTTAATTATAATCAATTTAA-TTTAAATTAAATTTTTTAAT
2001355 C
65 C
* *
2001356 ATAA-TTAATTTTAAATTAAAATTTTTAATTATGAATCAATTTAATTTAAATTTAATTT
1 ATAAGTTAATTTCAAATTAAAATTTTTAATTAT-AATCAATTTAATTTAAATTAAATTT
2001414 AATTCATGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
63 25 0.49
64 4 0.08
65 18 0.35
66 4 0.08
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (65 bp):
ATAAGTTAATTTCAAATTAAAATTTTTAATTATAATCAATTTAATTTAAATTAAATTTTTTAATC
Found at i:2001684 original size:34 final size:34
Alignment explanation
Indices: 2001615--2001685 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
2001605 TGGCAATTCA
* *
2001615 TTTAATTTGATTTAATTAAATTTAAATTTTTTAT
1 TTTAATTTGATTTAATTAAATTTAAATATTATAT
* *
2001649 TTTAATTTTATTTAAGTTAATTTTAAA-ATTATAT
1 TTTAATTTGATTTAA-TTAAATTTAAATATTATAT
2001683 TTT
1 TTT
2001686 TATATTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 22 0.69
35 10 0.31
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (34 bp):
TTTAATTTGATTTAATTAAATTTAAATATTATAT
Found at i:2001711 original size:21 final size:20
Alignment explanation
Indices: 2001665--2001711 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2001655 TTTATTTAAG
* *
2001665 TTAATTTTAAAATTATATTT
1 TTAATATTAAAAATATATTT
2001685 TT-ATATTAAATAATATATTT
1 TTAATATTAAA-AATATATTT
2001705 TTAATAT
1 TTAATAT
2001712 ATTTTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATATTAAAAATATATTT
Found at i:2002123 original size:18 final size:18
Alignment explanation
Indices: 2002085--2002123 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2002075 GTTACTAGAT
*
2002085 TTTGATTTTTTTAATTTA
1 TTTGATTTTTTTAATTAA
2002103 TTTGA-TTTTTTAATCTAA
1 TTTGATTTTTTTAAT-TAA
2002121 TTT
1 TTT
2002124 TTAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTGATTTTTTTAATTAA
Found at i:2002189 original size:14 final size:15
Alignment explanation
Indices: 2002167--2002203 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
2002157 ATTAATAATA
2002167 ATTTATTATATTTTT
1 ATTTATTATATTTTT
2002182 ATTT-TTATATTTTT
1 ATTTATTATATTTTT
2002196 AATTTATT
1 -ATTTATT
2002204 TGATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 10 0.50
15 8 0.40
16 2 0.10
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTATTATATTTTT
Found at i:2003778 original size:22 final size:22
Alignment explanation
Indices: 2003753--2003810 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 22
2003743 ATTTAGTCAT
2003753 ATTTAAAATAATATATATATAA
1 ATTTAAAATAATATATATATAA
2003775 ATTT--AAT-ATAT-TATATAA
1 ATTTAAAATAATATATATATAA
2003793 ATTTTAAAATAATCATAT
1 A-TTTAAAATAAT-ATAT
2003811 TTTTATGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
18 8 0.27
19 7 0.23
20 3 0.10
21 3 0.10
22 6 0.20
23 2 0.07
24 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTAAAATAATATATATATAA
Found at i:2003810 original size:20 final size:21
Alignment explanation
Indices: 2003753--2003810 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
2003743 ATTTAGTCAT
2003753 ATTTAAAATAATATATATATAA
1 ATTTAAAATAAT-TATATATAA
*
2003775 ATTTAATAT-ATTATATA-AA
1 ATTTAAAATAATTATATATAA
* *
2003794 TTTTAAAATAATCATAT
1 ATTTAAAATAATTATAT
2003811 TTTTATGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 9 0.29
20 12 0.39
21 2 0.06
22 8 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTAAAATAATTATATATAA
Found at i:2003865 original size:20 final size:19
Alignment explanation
Indices: 2003826--2003879 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
2003816 TGTTATATTC
* *
2003826 ATATTTTTTATATCATTTT
1 ATATTTTTTTTATAATTTT
2003845 ATATTTTATTTTATAATTTT
1 ATATTTT-TTTTATAATTTT
2003865 ATAATTTTCTTTTAT
1 AT-ATTTT-TTTTAT
2003880 TGTTTAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 7 0.23
20 12 0.40
21 11 0.37
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.69
Consensus pattern (19 bp):
ATATTTTTTTTATAATTTT
Found at i:2003877 original size:21 final size:21
Alignment explanation
Indices: 2003831--2003879 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2003821 TATTCATATT
2003831 TTTTATATCATTTTATATTTTA
1 TTTTATA-CATTTTATATTTTA
*
2003853 TTTTATA-ATTTTATAATTTTC
1 TTTTATACATTTTAT-ATTTTA
2003874 TTTTAT
1 TTTTAT
2003880 TGTTTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 7 0.28
21 11 0.44
22 7 0.28
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATACATTTTATATTTTA
Found at i:2008651 original size:22 final size:22
Alignment explanation
Indices: 2008619--2008664 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
2008609 ATGTGTCTAA
* *
2008619 CACGAGAGTGTTTAATTTTTTC
1 CACGAGAGTGTTCAATATTTTC
*
2008641 CACGAGTGTGTTCAATATTTTC
1 CACGAGAGTGTTCAATATTTTC
2008663 CA
1 CA
2008665 AAATTTCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (22 bp):
CACGAGAGTGTTCAATATTTTC
Found at i:2010313 original size:20 final size:19
Alignment explanation
Indices: 2010265--2010313 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2010255 TTATTCATTG
* *
2010265 TATTTAATTTATTTAAAAT
1 TATTTTATTTATTTAAAAA
*
2010284 TATATATATTTATTTAAAAAA
1 TAT-TTTATTTATTT-AAAAA
2010305 TATTTTATT
1 TATTTTATT
2010314 AATATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.12
20 14 0.58
21 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTATTTATTTAAAAA
Found at i:2011282 original size:20 final size:18
Alignment explanation
Indices: 2011257--2011327 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 18
2011247 AAATCCTTGT
*
2011257 ATGTATCGATACACATCCA
1 ATGTATCGATACA-ATACA
*
2011276 GATGTATCGATACATTATACT
1 -ATGTATCGATACA--ATACA
* *
2011297 TTGTATCGATACAATTCA
1 ATGTATCGATACAATACA
2011315 ATGTATCGATACA
1 ATGTATCGATACA
2011328 TTATATCGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.35
20 25 0.58
21 3 0.07
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (18 bp):
ATGTATCGATACAATACA
Found at i:2011326 original size:38 final size:40
Alignment explanation
Indices: 2011258--2011332 Score: 127
Period size: 38 Copynumber: 1.9 Consensus size: 40
2011248 AATCCTTGTA
2011258 TGTATCGATACACATCCAGATGTATCGATACATTATACTT
1 TGTATCGATACACATCCAGATGTATCGATACATTATACTT
*
2011298 TGTATCGATACA-ATTCA-ATGTATCGATACATTATA
1 TGTATCGATACACATCCAGATGTATCGATACATTATA
2011333 TCGATACATG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 18 0.53
39 4 0.12
40 12 0.35
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (40 bp):
TGTATCGATACACATCCAGATGTATCGATACATTATACTT
Found at i:2011353 original size:32 final size:33
Alignment explanation
Indices: 2011300--2011375 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 33
2011290 TTATACTTTG
2011300 TATCGATACA--ATTCAATGTATCGATACATTA
1 TATCGATACATGATTCAATGTATCGATACATTA
*
2011331 TATCGATACATGA-TCAATGTATCGATACATTG
1 TATCGATACATGATTCAATGTATCGATACATTA
2011363 TATCGATACATGA
1 TATCGATACATGA
2011376 AACTAACCGT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
31 10 0.24
32 31 0.74
33 1 0.02
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (33 bp):
TATCGATACATGATTCAATGTATCGATACATTA
Found at i:2011445 original size:20 final size:20
Alignment explanation
Indices: 2011403--2011456 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
2011393 CTACTACTAT
* *
2011403 TTGTATCGATACATGACACA
1 TTGTATCGATACATGAAAAA
2011423 TTGTATCGATACAT-AAATAA
1 TTGTATCGATACATGAAA-AA
*
2011443 TTGTATTGATACAT
1 TTGTATCGATACAT
2011457 TGTCCCAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGAAAAA
Found at i:2016192 original size:16 final size:16
Alignment explanation
Indices: 2016168--2016198 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2016158 AAAGGCTTTT
*
2016168 AAAATTTTTAATAGAA
1 AAAAGTTTTAATAGAA
2016184 AAAAGTTTTAATAGA
1 AAAAGTTTTAATAGA
2016199 GGAAATATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAAGTTTTAATAGAA
Found at i:2020115 original size:20 final size:19
Alignment explanation
Indices: 2020090--2020194 Score: 82
Period size: 20 Copynumber: 5.7 Consensus size: 19
2020080 AAACCCTTGT
2020090 ATGTATCGATACA-CATCCA
1 ATGTATCGATACATCAT-CA
* *
2020109 GATGTATTGATACATGATCA
1 -ATGTATCGATACATCATCA
2020129 ATGTATCGAT--A-CAT--
1 ATGTATCGATACATCATCA
*
2020143 -TGTATCGATACATGATCA
1 ATGTATCGATACATCATCA
2020161 ATGTATCGATACATGCA-CA
1 ATGTATCGATACAT-CATCA
*
2020180 ATTATATCGATACAT
1 A-TGTATCGATACAT
2020195 GAAATTGGCA
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
13 9 0.13
15 1 0.01
16 4 0.06
17 1 0.01
19 25 0.36
20 27 0.39
21 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACATCATCA
Found at i:2020134 original size:19 final size:19
Alignment explanation
Indices: 2020090--2020196 Score: 95
Period size: 19 Copynumber: 5.8 Consensus size: 19
2020080 AAACCCTTGT
*
2020090 ATGTATCGATACA-CATCCA
1 ATGTATCGATACATGAT-CA
*
2020109 GATGTATTGATACATGATCA
1 -ATGTATCGATACATGATCA
2020129 ATGTATCGATAC---AT--
1 ATGTATCGATACATGATCA
2020143 -TGTATCGATACATGATCA
1 ATGTATCGATACATGATCA
2020161 ATGTATCGATACATGCA-CA
1 ATGTATCGATACATG-ATCA
*
2020180 ATTATATCGATACATGA
1 A-TGTATCGATACATGA
2020197 AATTGGCAGT
Statistics
Matches: 74, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
13 11 0.15
16 4 0.05
19 29 0.39
20 28 0.38
21 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (19 bp):
ATGTATCGATACATGATCA
Found at i:2020148 original size:13 final size:13
Alignment explanation
Indices: 2020130--2020155 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2020120 ACATGATCAA
2020130 TGTATCGATACAT
1 TGTATCGATACAT
2020143 TGTATCGATACAT
1 TGTATCGATACAT
2020156 GATCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2020153 original size:32 final size:32
Alignment explanation
Indices: 2020111--2020174 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
2020101 CACATCCAGA
*
2020111 TGTATTGATACATGATCAATGTATCGATACAT
1 TGTATCGATACATGATCAATGTATCGATACAT
2020143 TGTATCGATACATGATCAATGTATCGATACAT
1 TGTATCGATACATGATCAATGTATCGATACAT
2020175 GCACAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATGATCAATGTATCGATACAT
Found at i:2020249 original size:20 final size:20
Alignment explanation
Indices: 2020224--2020277 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2020214 CTACCACCAT
* *
2020224 TTGTATCGATACATGGCA-CA
1 TTGTATCGATACAT-GAATAA
2020244 TTGTATCGATACATGAATAA
1 TTGTATCGATACATGAATAA
2020264 TTGTATCGATACAT
1 TTGTATCGATACAT
2020278 TGTCCCAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGAATAA
Found at i:2021498 original size:27 final size:27
Alignment explanation
Indices: 2021452--2021521 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
2021442 ATTGAAAAAC
* * *
2021452 GGGGTTAAAGTATCCCCTCGGAAGAAT
1 GGGGTTAGAGTGTCCTCTCGGAAGAAT
*
2021479 GGGGTTGGAGTGTCCTCTCGGAAGAAT
1 GGGGTTAGAGTGTCCTCTCGGAAGAAT
2021506 GGGGTTAGAGTGTCCT
1 GGGGTTAGAGTGTCCT
2021522 TGATAATGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.21, C:0.16, G:0.37, T:0.26
Consensus pattern (27 bp):
GGGGTTAGAGTGTCCTCTCGGAAGAAT
Found at i:2021944 original size:11 final size:10
Alignment explanation
Indices: 2021924--2021958 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
2021914 ATGAGGATCG
2021924 ATTTAAAAAT
1 ATTTAAAAAT
2021934 ATTTCAAAAAT
1 ATTT-AAAAAT
*
2021945 ATCTAAAAAT
1 ATTTAAAAAT
2021955 ATTT
1 ATTT
2021959 TTCTTAGTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTTAAAAAT
Found at i:2023846 original size:20 final size:20
Alignment explanation
Indices: 2023818--2023874 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
2023808 GTAAAAAGAC
2023818 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
2023838 AGAACGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
2023858 AGAATGTATCGATACAT
1 AGAATGTATCGATACAT
2023875 CTAGGAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.28
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:2024221 original size:18 final size:18
Alignment explanation
Indices: 2024198--2024232 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2024188 CTTGGGCGAT
2024198 AGTAATACTAGGATGGGA
1 AGTAATACTAGGATGGGA
2024216 AGTAATACTAGGATGGG
1 AGTAATACTAGGATGGG
2024233 TAACCTCTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.06, G:0.34, T:0.23
Consensus pattern (18 bp):
AGTAATACTAGGATGGGA
Found at i:2025142 original size:14 final size:14
Alignment explanation
Indices: 2025123--2025159 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2025113 TTTATTTTTA
*
2025123 ATTATATAATATAT
1 ATTATATAATATAC
*
2025137 ATTATATAATTTAC
1 ATTATATAATATAC
2025151 ATTATATAA
1 ATTATATAA
2025160 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATATAATATAC
Found at i:2029879 original size:2 final size:2
Alignment explanation
Indices: 2029872--2029900 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2029862 AATATTGTTG
2029872 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
2029901 TTTACTTATG
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:2029988 original size:28 final size:27
Alignment explanation
Indices: 2029936--2030025 Score: 103
Period size: 28 Copynumber: 3.3 Consensus size: 27
2029926 AATTAATTTG
* *
2029936 TATTTATTATATAAT-ACCAAA-TATA
1 TATTTATTATAAAATAACAAAATTATA
2029961 TATTTATTATAAAATAACAAAACTTATA
1 TATTTATTATAAAATAACAAAA-TTATA
* * *
2029989 TATTTTTTATACAATAATAAAATTTATA
1 TATTTATTATAAAATAACAAAA-TTATA
2030017 TATTTATTA
1 TATTTATTA
2030026 AATTATTATA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
25 14 0.25
26 5 0.09
28 36 0.65
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.47
Consensus pattern (27 bp):
TATTTATTATAAAATAACAAAATTATA
Found at i:2030655 original size:18 final size:18
Alignment explanation
Indices: 2030634--2030680 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 18
2030624 ATAAAAATTA
2030634 AAATTAAAATAATAATAT
1 AAATTAAAATAATAATAT
2030652 AAA-T-AAATAA-AA-AT
1 AAATTAAAATAATAATAT
*
2030666 ATATTAAAA-AATAAT
1 AAATTAAAATAATAAT
2030681 TTAATAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 9
0.71 0.03 0.26
Matches are distributed among these distances:
14 4 0.17
15 5 0.21
16 11 0.46
17 1 0.04
18 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATTAAAATAATAATAT
Done.