Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 36 of 199
Found at i:10211966 original size:27 final size:28
Alignment explanation
Indices: 10211847--10211968 Score: 160
Period size: 28 Copynumber: 4.4 Consensus size: 28
10211837 TATTGCACTG
* *
10211847 CACTGTTACTGTATTGGGCTAAGGCTCG
1 CACTGTTACTGTATTGGGCTAAGGCCCA
10211875 CACTGATT-CTGTATTGGGCTAAGGCCCA
1 CACTG-TTACTGTATTGGGCTAAGGCCCA
* *
10211903 CACTATTACTG-CTTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* *
10211930 TACTGTTACTGTATTAGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
10211958 CACTG-TACTGT
1 CACTGTTACTGT
10211969 CACTGAATAG
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
27 32 0.39
28 48 0.59
29 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:10217607 original size:94 final size:94
Alignment explanation
Indices: 10217502--10217677 Score: 289
Period size: 94 Copynumber: 1.9 Consensus size: 94
10217492 ACGAGATAAA
* *
10217502 AAAAGGATTTGATATATTCCTTATCAGATGAGGAGATAAAATTTAATTATTATTTAAAAGAGTTT
1 AAAAGGATTTGATATATTCCTTATCAGATAAGGAAATAAAATTTAATTATTATTTAAAAGAGTTT
10217567 TAGATAAAGAATAATTAAAATTCAAAAGC
66 TAGATAAAGAATAATTAAAATTCAAAAGC
* * * *
10217596 AAAAGGATTTGATATATTCCTTATCATATAAGTAAATAGAATTTAGTTATTATTTAAAAGAGTTT
1 AAAAGGATTTGATATATTCCTTATCAGATAAGGAAATAAAATTTAATTATTATTTAAAAGAGTTT
*
10217661 TAGATAAATAATAATTA
66 TAGATAAAGAATAATTA
10217678 TATTATTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
94 75 1.00
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (94 bp):
AAAAGGATTTGATATATTCCTTATCAGATAAGGAAATAAAATTTAATTATTATTTAAAAGAGTTT
TAGATAAAGAATAATTAAAATTCAAAAGC
Found at i:10217683 original size:35 final size:35
Alignment explanation
Indices: 10217643--10217711 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
10217633 AGAATTTAGT
10217643 TATTATTTAAAAGAGTTTTAGATAAATAATAATTA
1 TATTATTTAAAAGAGTTTTAGATAAATAATAATTA
* *
10217678 TATTATTTAAAATATTTTTAGATAAATAATAATT
1 TATTATTTAAAAGAGTTTTAGATAAATAATAATT
10217712 GAAATAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (35 bp):
TATTATTTAAAAGAGTTTTAGATAAATAATAATTA
Found at i:10217724 original size:38 final size:35
Alignment explanation
Indices: 10217647--10217725 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
10217637 TTTAGTTATT
**
10217647 ATTTAAAAGAGTTTTAGATAAATAATAATTATATT
1 ATTTAAAAGAGTTTTAGATAAATAATAATTATAGA
* *
10217682 ATTTAAAATATTTTTAGATAAATAATAATTGAAATAGA
1 ATTTAAAAGAGTTTTAGATAAATAATAATT---ATAGA
10217720 ATTTAA
1 ATTTAA
10217726 TTATCATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 28 0.76
38 9 0.24
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (35 bp):
ATTTAAAAGAGTTTTAGATAAATAATAATTATAGA
Found at i:10217740 original size:52 final size:50
Alignment explanation
Indices: 10217672--10217789 Score: 145
Period size: 52 Copynumber: 2.4 Consensus size: 50
10217662 AGATAAATAA
* *
10217672 TAATTATATTATTTAAAA-TATTTTTAGAT-AAATAATAATTGAAATAGAATT
1 TAATTATATTATTTAAAAGT-GTTTTAAATAAAAT-ATAATT-AAATAGAATT
10217723 TAATTATCATTATTTAAAAGTGTTTTAAATAAAATATAATTAAATAGAATT
1 TAATTAT-ATTATTTAAAAGTGTTTTAAATAAAATATAATTAAATAGAATT
*
10217774 TAAAT-TATTA-TTAAAA
1 TAATTATATTATTTAAAA
10217790 CGAGTTTTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
48 6 0.10
49 4 0.07
50 1 0.02
51 21 0.34
52 24 0.39
53 5 0.08
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (50 bp):
TAATTATATTATTTAAAAGTGTTTTAAATAAAATATAATTAAATAGAATT
Found at i:10218846 original size:16 final size:16
Alignment explanation
Indices: 10218820--10218873 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
10218810 TTTAGTTCGC
*
10218820 TGTATTGGAATAGAGG
1 TGTAATGGAATAGAGG
*
10218836 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
10218852 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
10218868 TGTAAT
1 TGTAAT
10218874 AGCAAATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.35, C:0.02, G:0.35, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:10222441 original size:16 final size:16
Alignment explanation
Indices: 10222420--10222451 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10222410 TCAAATCTAT
*
10222420 TTGAAGTGATTTAAAA
1 TTGAAGTGATGTAAAA
10222436 TTGAAGTGATGTAAAA
1 TTGAAGTGATGTAAAA
10222452 GGCATGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGAAGTGATGTAAAA
Found at i:10228027 original size:19 final size:19
Alignment explanation
Indices: 10228003--10228043 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
10227993 TCCAACCACT
10228003 TTGGTGGGTTCAATCGTCG
1 TTGGTGGGTTCAATCGTCG
10228022 TTGGTGGGTTCAATCGTCG
1 TTGGTGGGTTCAATCGTCG
10228041 TTG
1 TTG
10228044 AGGGTCTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.10, C:0.15, G:0.37, T:0.39
Consensus pattern (19 bp):
TTGGTGGGTTCAATCGTCG
Found at i:10231086 original size:16 final size:16
Alignment explanation
Indices: 10231065--10231096 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10231055 TCAACTCTAT
*
10231065 TTGAAGTGATTTAAAA
1 TTGAAGTGATGTAAAA
10231081 TTGAAGTGATGTAAAA
1 TTGAAGTGATGTAAAA
10231097 GGCATGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGAAGTGATGTAAAA
Found at i:10235591 original size:15 final size:16
Alignment explanation
Indices: 10235559--10235591 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
10235549 TCAAGATGGA
*
10235559 ATTTTGAATTCATTTG
1 ATTTTGAATTCATATG
10235575 ATTTTGAA-TCATATG
1 ATTTTGAATTCATATG
10235590 AT
1 AT
10235592 ACTTATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (16 bp):
ATTTTGAATTCATATG
Found at i:10239276 original size:34 final size:33
Alignment explanation
Indices: 10239238--10239303 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
10239228 ATAGAATTTA
*
10239238 GTTATT-ATTTAAAAGAGTTTTATATTAAATAATT
1 GTTATTAATTT-AAAGAGTTTTAGA-TAAATAATT
10239272 GTTATTAATTTAAAGAGTTTTAGATAAATAAT
1 GTTATTAATTTAAAGAGTTTTAGATAAATAAT
10239304 AATTAAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 8 0.27
34 18 0.60
35 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (33 bp):
GTTATTAATTTAAAGAGTTTTAGATAAATAATT
Found at i:10239332 original size:48 final size:48
Alignment explanation
Indices: 10239279--10239388 Score: 127
Period size: 47 Copynumber: 2.3 Consensus size: 48
10239269 ATTGTTATTA
* * * **
10239279 ATTT-AAAGAGTTTTAGATAAATA-ATAATTAAAACAGAATTTCATTAAT
1 ATTTAAAAGAGTTTTA-AAAAAAAGATAATTAAAA-AAAATTAAATTAAT
*
10239327 ATTTAAAAGAG-TTTAAAAAAAAGATAATTAAAAAAAATTAAATTATT
1 ATTTAAAAGAGTTTTAAAAAAAAGATAATTAAAAAAAATTAAATTAAT
10239374 ATTTAAAAGAGTTTT
1 ATTTAAAAGAGTTTT
10239389 TCAAATTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
47 26 0.49
48 21 0.40
49 6 0.11
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (48 bp):
ATTTAAAAGAGTTTTAAAAAAAAGATAATTAAAAAAAATTAAATTAAT
Found at i:10242086 original size:26 final size:27
Alignment explanation
Indices: 10242057--10242109 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
10242047 ATGATCGTAA
10242057 TTCCCCTAGAAGGTAAATGACT-ATTT
1 TTCCCCTAGAAGGTAAATGACTGATTT
* *
10242083 TTCCCCTCGAGGGTAAATGACTGATTT
1 TTCCCCTAGAAGGTAAATGACTGATTT
10242110 GTGCTATGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
TTCCCCTAGAAGGTAAATGACTGATTT
Found at i:10247690 original size:16 final size:16
Alignment explanation
Indices: 10247649--10247692 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
10247639 CAACCACATC
10247649 AGGTTCCATATGAGTA
1 AGGTTCCATATGAGTA
**
10247665 AGAG-AGCATATGAGTA
1 AG-GTTCCATATGAGTA
10247681 AGGTTCCATATG
1 AGGTTCCATATG
10247693 CTTCAATAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.27
Consensus pattern (16 bp):
AGGTTCCATATGAGTA
Found at i:10250016 original size:29 final size:29
Alignment explanation
Indices: 10249974--10250031 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
10249964 GGAAGTCATG
10249974 ATTCGACATAACCTCTCTGTGACTAACCC
1 ATTCGACATAACCTCTCTGTGACTAACCC
10250003 ATTCGACATAACCTCTCTGTGACTAACCC
1 ATTCGACATAACCTCTCTGTGACTAACCC
10250032 TTCATGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.34, G:0.10, T:0.28
Consensus pattern (29 bp):
ATTCGACATAACCTCTCTGTGACTAACCC
Found at i:10251573 original size:6 final size:6
Alignment explanation
Indices: 10251557--10251593 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
10251547 ACTAAAATGT
10251557 ATTAT- ATTATA ATTATA ATTAT- ATTATA ATGTATA AT
1 ATTATA ATTATA ATTATA ATTATA ATTATA AT-TATA AT
10251594 AGTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 13 0.45
7 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
ATTATA
Found at i:10251579 original size:17 final size:18
Alignment explanation
Indices: 10251557--10251593 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
10251547 ACTAAAATGT
10251557 ATTATATTATAAT-TATA
1 ATTATATTATAATGTATA
10251574 ATTATATTATAATGTATA
1 ATTATATTATAATGTATA
10251592 AT
1 AT
10251594 AGTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTATATTATAATGTATA
Found at i:10256354 original size:43 final size:42
Alignment explanation
Indices: 10256306--10256420 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 42
10256296 CCCAAATATG
* * *
10256306 GTCTTACATGTAATCTCGTATCGATGCCAATAG-CCCAGCCATA
1 GTCTTACACG-AATCTCATATCGATGCCAAT-GTCCCAGACATA
* ** *
10256349 GTCTTACACAAAATAACATATCGATGCCAATGTCCCAGACATG
1 GTCTTACAC-GAATCTCATATCGATGCCAATGTCCCAGACATA
10256392 GTCTTACACGAAGTCTCATATCGATGCCA
1 GTCTTACACGAA-TCTCATATCGATGCCA
10256421 TATCACAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
42 3 0.05
43 56 0.95
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (42 bp):
GTCTTACACGAATCTCATATCGATGCCAATGTCCCAGACATA
Found at i:10262237 original size:21 final size:21
Alignment explanation
Indices: 10262213--10262253 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10262203 GTACCCCTAT
*
10262213 CACACGGGCGTGTCCCTCAGC
1 CACACAGGCGTGTCCCTCAGC
*
10262234 CACACAGGTGTGTCCCTCAG
1 CACACAGGCGTGTCCCTCAG
10262254 TTACATGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.39, G:0.27, T:0.17
Consensus pattern (21 bp):
CACACAGGCGTGTCCCTCAGC
Found at i:10281017 original size:27 final size:27
Alignment explanation
Indices: 10280959--10281044 Score: 129
Period size: 27 Copynumber: 3.2 Consensus size: 27
10280949 ATGGGGTCAA
10280959 TAAAATGACCGAAATA-CCCCAAAGGG
1 TAAAATGACCGAAATACCCCCAAAGGG
*
10280985 TGAAATGACCGAAATACCCCCAAAGGG
1 TAAAATGACCGAAATACCCCCAAAGGG
* * *
10281012 TTAAATGGCCGAAATACCCCCATAGGG
1 TAAAATGACCGAAATACCCCCAAAGGG
10281039 TAAAAT
1 TAAAAT
10281045 ATCTATTATA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
26 15 0.28
27 39 0.72
ACGTcount: A:0.42, C:0.23, G:0.20, T:0.15
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCCCAAAGGG
Found at i:10281415 original size:28 final size:28
Alignment explanation
Indices: 10281391--10281471 Score: 137
Period size: 28 Copynumber: 2.9 Consensus size: 28
10281381 TACCACATTG
10281391 TTACTGTAAT-GGGCTAAGGCCCACACTA
1 TTACTGT-ATCGGGCTAAGGCCCACACTA
10281419 TTACTGTATCGGGCTAAGGCCCACACTA
1 TTACTGTATCGGGCTAAGGCCCACACTA
*
10281447 TTACTGTATCGGGCTAGGGCCCACA
1 TTACTGTATCGGGCTAAGGCCCACA
10281472 TTGTACTATC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 2 0.04
28 49 0.96
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (28 bp):
TTACTGTATCGGGCTAAGGCCCACACTA
Found at i:10283058 original size:23 final size:24
Alignment explanation
Indices: 10283032--10283084 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
10283022 ATATACTACA
*
10283032 TTTTGAAGGCTTGATTTTA-CTTG
1 TTTTGAAGGCTTGATTATAGCTTG
* *
10283055 TTTTGGATGCTTGATTATAGCTTG
1 TTTTGAAGGCTTGATTATAGCTTG
10283079 TGTTTG
1 T-TTTG
10283085 TGTGCATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.64
24 5 0.20
25 4 0.16
ACGTcount: A:0.15, C:0.08, G:0.25, T:0.53
Consensus pattern (24 bp):
TTTTGAAGGCTTGATTATAGCTTG
Found at i:10283990 original size:20 final size:21
Alignment explanation
Indices: 10283957--10283995 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
10283947 TAGGATTAAT
10283957 AAAATAAAATAAATTAAAACA
1 AAAATAAAATAAATTAAAACA
*
10283978 AAAATTAAA-AAATTAAAA
1 AAAATAAAATAAATTAAAA
10283996 ATGAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAATAAAATAAATTAAAACA
Found at i:10284002 original size:21 final size:21
Alignment explanation
Indices: 10283957--10284013 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
10283947 TAGGATTAAT
*
10283957 AAAATAAAATAAATTAAAACA
1 AAAATAAAACAAATTAAAACA
*
10283978 AAAATTAAA-AAATTAAAA-A
1 AAAATAAAACAAATTAAAACA
*
10283997 TGAAAATGAAACAAATT
1 --AAAATAAAACAAATT
10284014 TTAAAATAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 9 0.29
21 16 0.52
22 5 0.16
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.21
Consensus pattern (21 bp):
AAAATAAAACAAATTAAAACA
Found at i:10292042 original size:56 final size:52
Alignment explanation
Indices: 10291874--10292071 Score: 251
Period size: 50 Copynumber: 3.8 Consensus size: 52
10291864 GATAATAACA
* *
10291874 TGCCAAAGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC-ATCTC-GG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCAGG
* * *
10291924 TGCTAACCCCATGTCCCAGACATGGTCTTACATGAGACCTCTCG-TCTCA-G
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCAGG
10291974 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC--GATCTC-AGG
** * *
10292029 ATGCCAATTCCATGTCCCAAACATGGTCTTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
10292072 TTACCCTAAT
Statistics
Matches: 128, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
50 83 0.65
52 1 0.01
53 4 0.03
54 1 0.01
55 1 0.01
56 38 0.30
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.25
Consensus pattern (52 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGATCTCAGG
Found at i:10306907 original size:62 final size:59
Alignment explanation
Indices: 10306838--10306954 Score: 171
Period size: 62 Copynumber: 1.9 Consensus size: 59
10306828 ACTGGTTATC
* * *
10306838 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTAATATAATAAAAT
1 TTAATATTAAATTTAATCTAATATTTATC-TG--GATAAATATTATATTAATATAATAAAAT
*
10306900 TTAATATTAAATTTAATCTAATATTTATCTGGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTGGATAAATATTATATTAATATAATA
10306955 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.43
61 2 0.04
62 27 0.53
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTGGATAAATATTATATTAATATAATAAAAT
Found at i:10314855 original size:54 final size:55
Alignment explanation
Indices: 10314772--10314876 Score: 160
Period size: 54 Copynumber: 1.9 Consensus size: 55
10314762 TCACACGGGT
*
10314772 GTGTGTCTAGACCGTATAACTCTATGACTTGTGTCACACAGG-TGTGTGCCTGGCC
1 GTGTGTCTAGACCGTATAACTCTATGACTTGGGTCACAC-GGTTGTGTGCCTGGCC
* *
10314827 GTGTG-CTAGACCGTGTAACTCTCTGACTTGGGTCACACGGTTGTGTGCCT
1 GTGTGTCTAGACCGTATAACTCTATGACTTGGGTCACACGGTTGTGTGCCT
10314877 AACCATGTGA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
53 2 0.04
54 39 0.85
55 5 0.11
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (55 bp):
GTGTGTCTAGACCGTATAACTCTATGACTTGGGTCACACGGTTGTGTGCCTGGCC
Found at i:10317369 original size:5 final size:6
Alignment explanation
Indices: 10317334--10317368 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10317324 ATTGCATATG
**
10317334 ATTTTT ATTTTT CCTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
10317369 AATCGTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:10317629 original size:19 final size:19
Alignment explanation
Indices: 10317605--10317644 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
10317595 TAATTACAAC
10317605 ATAATATAATTACACTTTT
1 ATAATATAATTACACTTTT
10317624 ATAATATAATTACACTTTT
1 ATAATATAATTACACTTTT
10317643 AT
1 AT
10317645 TCAATTAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATATAATTACACTTTT
Found at i:10320767 original size:16 final size:17
Alignment explanation
Indices: 10320741--10320779 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
10320731 CTGAATATGA
* *
10320741 TGAGTATTGGAAGGCAC
1 TGAGAATTGGAAGCCAC
10320758 -GAGAATTGGAAGCCAC
1 TGAGAATTGGAAGCCAC
10320774 TGAGAA
1 TGAGAA
10320780 CCTGAACAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (17 bp):
TGAGAATTGGAAGCCAC
Found at i:10322695 original size:16 final size:16
Alignment explanation
Indices: 10322674--10322704 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10322664 TAATGTGGTG
10322674 TATAAGGTGGTGTATA
1 TATAAGGTGGTGTATA
10322690 TATAAGGTGGTGTAT
1 TATAAGGTGGTGTAT
10322705 GAGTTTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (16 bp):
TATAAGGTGGTGTATA
Found at i:10331930 original size:17 final size:18
Alignment explanation
Indices: 10331896--10331930 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
10331886 CCATGATGTT
*
10331896 CGCCCGTGTGGGCCCACA
1 CGCCCGTGTGGACCCACA
10331914 CGCCCGTGT-GACCCACA
1 CGCCCGTGTGGACCCACA
10331931 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.14, C:0.46, G:0.29, T:0.11
Consensus pattern (18 bp):
CGCCCGTGTGGACCCACA
Found at i:10333886 original size:23 final size:24
Alignment explanation
Indices: 10333845--10333892 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
10333835 TGCCAATACT
10333845 TGGAACCAAAGTTTATTCGGTAAA
1 TGGAACCAAAGTTTATTCGGTAAA
*
10333869 TGGAATCAAA-TTTATTCGGTAAA
1 TGGAACCAAAGTTTATTCGGTAAA
10333892 T
1 T
10333893 AATAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (24 bp):
TGGAACCAAAGTTTATTCGGTAAA
Found at i:10333903 original size:19 final size:21
Alignment explanation
Indices: 10333853--10333904 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
10333843 CTTGGAACCA
10333853 AAGTTTATTCGGTAAATGGAAT
1 AAGTTTATTCGGTAAAT-GAAT
*
10333875 CAAATTTATTCGGTAAAT-AAT
1 -AAGTTTATTCGGTAAATGAAT
10333896 -AGTTTATTC
1 AAGTTTATTC
10333905 ATAATAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.30
21 3 0.11
23 16 0.59
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (21 bp):
AAGTTTATTCGGTAAATGAAT
Found at i:10333992 original size:9 final size:9
Alignment explanation
Indices: 10333978--10334003 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
10333968 TAATTAAATG
10333978 ATTAGTAAA
1 ATTAGTAAA
10333987 ATTAGTAAA
1 ATTAGTAAA
10333996 ATTAGTAA
1 ATTAGTAA
10334004 TATGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.35
Consensus pattern (9 bp):
ATTAGTAAA
Found at i:10334768 original size:22 final size:21
Alignment explanation
Indices: 10334735--10334775 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
10334725 AACTATATTT
10334735 CATGTTTAATT-AGTTAAAAA
1 CATGTTTAATTAAGTTAAAAA
10334755 CATGTCTTAAATTAAGTTAAA
1 CATGT-TT-AATTAAGTTAAA
10334776 TGTAATGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 4 0.22
23 7 0.39
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (21 bp):
CATGTTTAATTAAGTTAAAAA
Found at i:10335498 original size:85 final size:83
Alignment explanation
Indices: 10335355--10335612 Score: 329
Period size: 85 Copynumber: 3.1 Consensus size: 83
10335345 ACCACCGCTG
* * * *
10335355 ATTTGTAGTTACTGCCACATATTGTGGGTGCACAATATATTTGAAGTTTAAACAAACTGTCACTT
1 ATTTGCAGTTACTGCCAC-T-TTGTGGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTT
*
10335420 GGCTCATGATCGAACCACAT
64 GGTTCATGATCGAACCACAT
*
10335440 ATTTGCAGTTATTGCCACTTGTTGTGGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTT
1 ATTTGCAGTTACTGCCAC-T-TTGTGGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTT
10335505 GGTTCATGATCGAACCACAT
64 GGTTCATGATCGAACCACAT
* * * * **
10335525 ATTTGCAGTTACTGCTAC-TTGTGAGTGCACATCATATTTGTAGATTAAATAAACTACCACTTGG
1 ATTTGCAGTTACTGCCACTTTGTGGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTTGG
* * *
10335589 TTCGTAATTGAACCACACT
66 TTCATGATCGAACCACA-T
10335608 ATTTG
1 ATTTG
10335613 TAGATTAAAT
Statistics
Matches: 154, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
82 55 0.36
83 6 0.04
85 93 0.60
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (83 bp):
ATTTGCAGTTACTGCCACTTTGTGGGTGCACAACATATTTGTAGATTAAACAAACTGTCACTTGG
TTCATGATCGAACCACAT
Found at i:10335630 original size:48 final size:48
Alignment explanation
Indices: 10335559--10335669 Score: 213
Period size: 48 Copynumber: 2.3 Consensus size: 48
10335549 GTGCACATCA
10335559 TATTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACAC
1 TATTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACAC
10335607 TATTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACAC
1 TATTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACAC
*
10335655 TGTTTGTAGATTAAA
1 TATTTGTAGATTAAA
10335670 CTGTCACTCT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (48 bp):
TATTTGTAGATTAAATAAACTACCACTTGGTTCGTAATTGAACCACAC
Found at i:10336250 original size:28 final size:28
Alignment explanation
Indices: 10336219--10336327 Score: 119
Period size: 28 Copynumber: 3.9 Consensus size: 28
10336209 GTAATATTTG
* *
10336219 AAAAATAGGGGTAACATTGTGAAATCTA
1 AAAAATAGGGGTAAAATTGTAAAATCTA
* *
10336247 AAAAACTTGGGGTAAAATTGTAAAATCTT
1 AAAAA-TAGGGGTAAAATTGTAAAATCTA
* * * * *
10336276 GAAAATAAGGGAAAAACTATAAAATCTA
1 AAAAATAGGGGTAAAATTGTAAAATCTA
*
10336304 AAAAGTAGGGGTAAAATTGTAAAA
1 AAAAATAGGGGTAAAATTGTAAAA
10336328 CTTGAAAAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
28 40 0.63
29 23 0.37
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.24
Consensus pattern (28 bp):
AAAAATAGGGGTAAAATTGTAAAATCTA
Found at i:10336269 original size:57 final size:56
Alignment explanation
Indices: 10336175--10336340 Score: 156
Period size: 56 Copynumber: 2.9 Consensus size: 56
10336165 ATATTGGGTT
* * * ** * * *
10336175 AAAACTATAAAACCTAAAAAAATAAGGG-AAAGCTGTAATATTTGAAAAATAGGGGT
1 AAAACTATAAAATCT-AAAAACTAGGGGTAAAATTGTAAAATTTGAAAAATAAGGGA
* * * * *
10336231 AACATTGTGAAATCTAAAAAACTTGGGGTAAAATTGTAAAATCTTG-AAAATAAGGGA
1 AAAACTATAAAATCT-AAAAACTAGGGGTAAAATTGTAAAAT-TTGAAAAATAAGGGA
* *
10336288 AAAACTATAAAATCTAAAAAGTAGGGGTAAAATTGTAAAACTTGAAAAATAAG
1 AAAACTATAAAATCTAAAAACTAGGGGTAAAATTGTAAAATTTGAAAAATAAG
10336341 AGACACACAA
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
55 3 0.03
56 51 0.59
57 30 0.34
58 3 0.03
ACGTcount: A:0.52, C:0.07, G:0.17, T:0.23
Consensus pattern (56 bp):
AAAACTATAAAATCTAAAAACTAGGGGTAAAATTGTAAAATTTGAAAAATAAGGGA
Found at i:10336336 original size:29 final size:27
Alignment explanation
Indices: 10336216--10336338 Score: 97
Period size: 28 Copynumber: 4.4 Consensus size: 27
10336206 GCTGTAATAT
* *
10336216 TTGAAAAATAGGGGTAACATTGTGAAA
1 TTGAAAAATAGGGGTAAAATTGTAAAA
* *
10336243 TCTAAAAAACTTGGGGTAAAATTGTAAAA
1 T-TGAAAAA-TAGGGGTAAAATTGTAAAA
* * * *
10336272 TCTTG-AAAATAAGGGAAAAACTATAAAA
1 --TTGAAAAATAGGGGTAAAATTGTAAAA
10336300 TCT-AAAAAGTAGGGGTAAAATTGTAAAA
1 T-TGAAAAA-TAGGGGTAAAATTGTAAAA
10336328 CTTGAAAAATA
1 -TTGAAAAATA
10336339 AGAGACACAC
Statistics
Matches: 73, Mismatches: 14, Indels: 17
0.70 0.13 0.16
Matches are distributed among these distances:
26 1 0.01
27 6 0.08
28 38 0.52
29 26 0.36
30 1 0.01
31 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (27 bp):
TTGAAAAATAGGGGTAAAATTGTAAAA
Found at i:10340640 original size:38 final size:38
Alignment explanation
Indices: 10340596--10340669 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
10340586 TACCTACTAT
10340596 TACTGTTAAACCAAACACATGTTAAGCATGTCTACTGC
1 TACTGTTAAACCAAACACATGTTAAGCATGTCTACTGC
* ** *
10340634 TACTGTTGAACTGAATACATGTTAAGCATGTCTACT
1 TACTGTTAAACCAAACACATGTTAAGCATGTCTACT
10340670 ATTTTACATG
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:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (38 bp):
TACTGTTAAACCAAACACATGTTAAGCATGTCTACTGC
Found at i:10341732 original size:14 final size:14
Alignment explanation
Indices: 10341713--10341752 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
10341703 TTGATTACCA
10341713 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
10341727 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
10341741 GGAAAATGTTTT
1 GTAAAATGTTTT
10341753 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:10341761 original size:20 final size:20
Alignment explanation
Indices: 10341736--10341775 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10341726 CGTAAAATGA
*
10341736 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
10341756 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
10341776 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:10341765 original size:34 final size:35
Alignment explanation
Indices: 10341721--10341787 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
10341711 CAGTAAAATG
*
10341721 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
10341755 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
10341788 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:10341791 original size:14 final size:15
Alignment explanation
Indices: 10341715--10341791 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
10341705 GATTACCAGT
* *
10341715 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
10341729 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
10341743 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
10341763 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
10341778 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
10341792 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:10344604 original size:18 final size:18
Alignment explanation
Indices: 10344583--10344633 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
10344573 AGGAATGAAG
10344583 GAAGGGAGAAGAATGGAT
1 GAAGGGAGAAGAATGGAT
*** *
10344601 GAAGGGAGCTTACTGGAT
1 GAAGGGAGAAGAATGGAT
10344619 GAAGGGAGAAGAATG
1 GAAGGGAGAAGAATG
10344634 CCTGAGAGCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.43, T:0.14
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:10348047 original size:59 final size:59
Alignment explanation
Indices: 10347952--10348069 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 59
10347942 GGTTGAATGC
* *
10347952 ATACCTTCTGAAGCTAAAGAATGGCAAATAACGTTGTTGGTTGGATTCCTTTGGACGAT
1 ATACCTTCTGAAACTAAAGAATGGCAAATAACGTTGTTGGTTAGATTCCTTTGGACGAT
* *
10348011 ATACCTTCTGAAACTGAAGAATGGCAAATAATGTTGTTGGTTAGATTCCTTTGGACGAT
1 ATACCTTCTGAAACTAAAGAATGGCAAATAACGTTGTTGGTTAGATTCCTTTGGACGAT
10348070 GTTAATCCTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (59 bp):
ATACCTTCTGAAACTAAAGAATGGCAAATAACGTTGTTGGTTAGATTCCTTTGGACGAT
Found at i:10348413 original size:17 final size:17
Alignment explanation
Indices: 10348391--10348430 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
10348381 TCCACCAAGA
*
10348391 AATACTATTCGCCAGGC
1 AATACTATTAGCCAGGC
*
10348408 AATACTGTTAGCCAGGC
1 AATACTATTAGCCAGGC
*
10348425 TATACT
1 AATACT
10348431 TATACGCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (17 bp):
AATACTATTAGCCAGGC
Found at i:10350782 original size:14 final size:14
Alignment explanation
Indices: 10350763--10350790 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10350753 GTTTAAAGAT
10350763 GATTAAAAACTAAG
1 GATTAAAAACTAAG
10350777 GATTAAAAACTAAG
1 GATTAAAAACTAAG
10350791 TAAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
GATTAAAAACTAAG
Found at i:10360175 original size:12 final size:12
Alignment explanation
Indices: 10360137--10360175 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10360127 ACTTTCTTCT
*
10360137 TTACTTGCTCAC
1 TTACTTGCTTAC
*
10360149 TTACTTGTTTAC
1 TTACTTGCTTAC
*
10360161 TTACTTGCTTGC
1 TTACTTGCTTAC
10360173 TTA
1 TTA
10360176 AATAACTCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.10, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:10360520 original size:50 final size:50
Alignment explanation
Indices: 10360434--10360572 Score: 136
Period size: 50 Copynumber: 2.8 Consensus size: 50
10360424 TACTGCTAAT
* * ** * * *
10360434 GCCATATCCCA-AATATGGTCTTATATGAGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCACAA-ATGGTCTTATATGGGACCTCTCATATCGGTACCAAC
* * * *
10360484 GCCATGTCCTACACATGGTCTTATAGGGGACCTCTCATCTCGGTACCAAC
1 GCCATGTCCCACAAATGGTCTTATATGGGACCTCTCATATCGGTACCAAC
* * *
10360534 GCCATGTCCCAGAAATGGTCTTACATGGGACCTCCCATA
1 GCCATGTCCCACAAATGGTCTTATATGGGACCTCTCATA
10360573 GTCTTAGTGA
Statistics
Matches: 70, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
50 69 0.99
51 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCACAAATGGTCTTATATGGGACCTCTCATATCGGTACCAAC
Found at i:10364457 original size:13 final size:13
Alignment explanation
Indices: 10364422--10364458 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
10364412 GATATATTTG
10364422 TAATTTGAAAACT
1 TAATTTGAAAACT
*
10364435 TAGTTTGAAAACT
1 TAATTTGAAAACT
*
10364448 TAATTGGAAAA
1 TAATTTGAAAA
10364459 TTTGGAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (13 bp):
TAATTTGAAAACT
Found at i:10366342 original size:21 final size:22
Alignment explanation
Indices: 10366312--10366356 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
10366302 GAACAAATTG
*
10366312 TTGATTCTATTTCTTTTTTG-AT
1 TTGATTCTA-TTATTTTTTGTAT
10366334 TTGA-TCTATTATTTTTTGTAT
1 TTGATTCTATTATTTTTTGTAT
10366355 TT
1 TT
10366357 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 8 0.38
22 4 0.19
ACGTcount: A:0.16, C:0.07, G:0.09, T:0.69
Consensus pattern (22 bp):
TTGATTCTATTATTTTTTGTAT
Found at i:10370327 original size:21 final size:22
Alignment explanation
Indices: 10370290--10370334 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
10370280 AGAAAAAGAG
*
10370290 AAATACAAAAAAGAATAG-ATC
1 AAATACAAAAAAAAATAGAATC
10370311 AAAT-CAAAAAATAAATAGAATC
1 AAATACAAAAAA-AAATAGAATC
10370333 AA
1 AA
10370335 CAATTTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.69, C:0.09, G:0.07, T:0.16
Consensus pattern (22 bp):
AAATACAAAAAAAAATAGAATC
Found at i:10376477 original size:27 final size:27
Alignment explanation
Indices: 10376432--10376486 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
10376422 TGTTTTTCTA
*
10376432 CTATTGAAGATACAGATTCGTCGTATC
1 CTATTGAAGATACAAATTCGTCGTATC
* * *
10376459 CTATTGAAGATTCAAATTCTTTGTATC
1 CTATTGAAGATACAAATTCGTCGTATC
10376486 C
1 C
10376487 CATGTATGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (27 bp):
CTATTGAAGATACAAATTCGTCGTATC
Found at i:10379206 original size:21 final size:21
Alignment explanation
Indices: 10379171--10379216 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
10379161 CCTTGAATTC
*
10379171 CTCTATCAATTCAATT-TTTT
1 CTCTATCAATTCAATTCTTCT
*
10379191 CTCTATCCACTTCAATTCTTCT
1 CTCTAT-CAATTCAATTCTTCT
10379213 CTCT
1 CTCT
10379217 GATATCCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 9 0.41
22 7 0.32
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (21 bp):
CTCTATCAATTCAATTCTTCT
Found at i:10379212 original size:20 final size:20
Alignment explanation
Indices: 10379171--10379214 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10379161 CCTTGAATTC
*
10379171 CTCTATCAATTCAATTTTTT
1 CTCTATCAATTCAATTTCTT
*
10379191 CTCTATCCACTTCAA-TTCTT
1 CTCTAT-CAATTCAATTTCTT
10379211 CTCT
1 CTCT
10379215 CTGATATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (20 bp):
CTCTATCAATTCAATTTCTT
Found at i:10392412 original size:17 final size:17
Alignment explanation
Indices: 10392390--10392424 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10392380 TTGGCATCCA
10392390 TATGTTAATGAAAACCC
1 TATGTTAATGAAAACCC
*
10392407 TATGTTAATGACAACCC
1 TATGTTAATGAAAACCC
10392424 T
1 T
10392425 TTGTCAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (17 bp):
TATGTTAATGAAAACCC
Found at i:10395371 original size:49 final size:51
Alignment explanation
Indices: 10395149--10395482 Score: 280
Period size: 51 Copynumber: 6.7 Consensus size: 51
10395139 AAATAATGGC
* ** *
10395149 CACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGAA--A-GGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAATGG-AT-AATTATGAT
* * * * * ** *
10395199 CGCATGTGTAG---TATGTGTAGGCTACTATGCGTACCGGATAGTT-TCGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAATGGATAATTAT-GAT
* * * *
10395247 CACGCGTGTAGTACTATGTGCAGGCTACTATGTGTAATGGATATTTATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAATGGATAATTATGAT
* * * *
10395298 CACGTGAGTAGTAGTATGTACAGGCTACTACGTG-AATCGGA-AAGT-TGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAAT-GGATAATTATGAT
* * *
10395347 CATGTGTGTAGTACTATGTGCAGGCTACTACGTGTAATGGATATTTATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAATGGATAATTATGAT
* * *
10395398 CACGTGAGTAGTACTATGTGCAGGCTACTACGTG-AATTAGA-AAAT-TGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAA-TGGATAATTATGAT
* *
10395447 CATGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
10395483 TTGAATGATA
Statistics
Matches: 231, Mismatches: 39, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
45 1 0.00
46 2 0.01
47 24 0.10
48 10 0.04
49 70 0.30
50 24 0.10
51 99 0.43
52 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTAATGGATAATTATGAT
Found at i:10395497 original size:100 final size:100
Alignment explanation
Indices: 10395252--10395519 Score: 403
Period size: 100 Copynumber: 2.7 Consensus size: 100
10395242 TCGATCACGC
* *
10395252 GTGTAGTACTATGTGCAGGCTACTATGTGTAATGGATATTTATGGTCACGTGAGTAGTAGTATGT
1 GTGTAGTACTATGTGCAGGCTACTACGTGTAATGGATATTTATGGTCACGTGAGTAGTACTATGT
* * *
10395317 ACAGGCTACTACGTGAATCGGAAAGTTGATCATGT
66 GCAGGCTACTACGTGAATCAGAAAATTGATCATGT
10395352 GTGTAGTACTATGTGCAGGCTACTACGTGTAATGGATATTTATGGTCACGTGAGTAGTACTATGT
1 GTGTAGTACTATGTGCAGGCTACTACGTGTAATGGATATTTATGGTCACGTGAGTAGTACTATGT
*
10395417 GCAGGCTACTACGTGAATTAGAAAATTGATCATGT
66 GCAGGCTACTACGTGAATCAGAAAATTGATCATGT
* * * * * * *
10395452 GTGTAGTACTATGTGAAGGCTACTACGTGTATTGAATGA-TAATGGTTACTTGAGTGGTACTATG
1 GTGTAGTACTATGTGCAGGCTACTACGTGTAATGGAT-ATTTATGGTCACGTGAGTAGTACTATG
10395516 TGCA
65 TGCA
10395520 AACCACCGAA
Statistics
Matches: 154, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
100 153 0.99
101 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (100 bp):
GTGTAGTACTATGTGCAGGCTACTACGTGTAATGGATATTTATGGTCACGTGAGTAGTACTATGT
GCAGGCTACTACGTGAATCAGAAAATTGATCATGT
Found at i:10402554 original size:15 final size:16
Alignment explanation
Indices: 10402534--10402563 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10402524 TGGTGCCTTG
10402534 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
10402549 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
10402564 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:10404480 original size:86 final size:86
Alignment explanation
Indices: 10404334--10404497 Score: 229
Period size: 86 Copynumber: 1.9 Consensus size: 86
10404324 TCTGGAACAT
* * * **
10404334 TGGTGGTTCATCCACAAATTACTGACAAATATTATCAACAAATGTGTTTTGCATTTACAACAAGT
1 TGGTGGTTCATCCACAAATTACTGACAAATATTACCAACAAATATGTTGTGCATCCACAACAAGT
*
10404399 GGCAATTTATTTGCATATTAC
66 AGCAATTTATTTGCATATTAC
* * * *
10404420 TGGTGGTTCATCCACAAATTACTGACAACTTTTACCTACAGATATGTTGTGCATCCACAACAAGT
1 TGGTGGTTCATCCACAAATTACTGACAAATATTACCAACAAATATGTTGTGCATCCACAACAAGT
*
10404485 AGCATTTTATTTG
66 AGCAATTTATTTG
10404498 TCAATGTTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 67 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (86 bp):
TGGTGGTTCATCCACAAATTACTGACAAATATTACCAACAAATATGTTGTGCATCCACAACAAGT
AGCAATTTATTTGCATATTAC
Found at i:10415269 original size:138 final size:138
Alignment explanation
Indices: 10415108--10415605 Score: 703
Period size: 138 Copynumber: 3.6 Consensus size: 138
10415098 ATGTAGTATT
* * *
10415108 AATTAATTAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGATACGAAAATTAA
1 AATTTATTAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAA
* * *
10415173 TATTCTTTTGGAAATAATATAATTAATATATGAATTTTATTCATACAAAATGTTAATTTTATATA
66 TATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTTTATATA
*
10415238 TTTTACCG
131 TTTTACTG
* * *
10415246 AATTTATTAATATAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGGAAATTAA
1 AATTTATTAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAA
* *
10415311 TATTCTTTTGAAAAAAGAATATAATT-ATATATAAATTTGATTCATACAAAATATTAATTTTATA
66 TATTCTTTTG--GAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTTTATA
10415375 TATTTTACTG
129 TATTTTACTG
* * * *
10415385 AATTTATTAATATAAATAGTTATATTAATTAATTTCT-GTCAAATTATAAAAAACATGAAAGTTA
1 AATTTATTAATATAAACAGTTATATTAATTAATTT-TGGTCAAAATATAAAAGACATGAAAATTA
* * *
10415449 ATATTCTTTTGGAAAGAATATAATAAATATATGAATTTGATTCATGCAAAATATTAATTGTATAT
65 ATATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTTTATAT
*
10415514 ATTTTATTG
130 ATTTTACTG
* ** * * *
10415523 AATTTATTAATATAAACAGTTATATTAATTTATTTCAGTCAAAGTATAAAATATATGAAAATTAA
1 AATTTATTAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAA
**
10415588 TATTCTTTTCTAAAGAAT
66 TATTCTTTTGGAAAGAAT
10415606 TTTTTTTTTC
Statistics
Matches: 321, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
137 12 0.04
138 186 0.58
139 110 0.34
140 13 0.04
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (138 bp):
AATTTATTAATATAAACAGTTATATTAATTAATTTTGGTCAAAATATAAAAGACATGAAAATTAA
TATTCTTTTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTTTATATA
TTTTACTG
Found at i:10417007 original size:17 final size:15
Alignment explanation
Indices: 10416985--10417019 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 15
10416975 AATAAAAACT
10416985 AAAAATTAACTAAGTAA
1 AAAAATTAA--AAGTAA
10417002 AAAAATTAAAAGTAA
1 AAAAATTAAAAGTAA
10417017 AAA
1 AAA
10417020 TTCTAATGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (15 bp):
AAAAATTAAAAGTAA
Found at i:10432515 original size:12 final size:12
Alignment explanation
Indices: 10432498--10432536 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10432488 ATGAGTTATT
10432498 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
10432510 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
10432522 TAAGTGAGTAAG
1 TAAGTAAGCAAG
10432534 TAA
1 TAA
10432537 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:10434560 original size:4 final size:4
Alignment explanation
Indices: 10434551--10434593 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
10434541 ATGAGTTATT
* * *
10434551 TAAG TAAG TAAG TAAG TAAG TAAA CAAG TAAG TTAG TAAG TAA
1 TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAA
10434594 AGAAGCGAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.02, G:0.21, T:0.26
Consensus pattern (4 bp):
TAAG
Found at i:10434581 original size:20 final size:20
Alignment explanation
Indices: 10434556--10434594 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10434546 TTATTTAAGT
10434556 AAGTAAGTAAGTAAGTAAAC
1 AAGTAAGTAAGTAAGTAAAC
*
10434576 AAGTAAGTTAGTAAGTAAA
1 AAGTAAGTAAGTAAGTAAA
10434595 GAAGCGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.21, T:0.23
Consensus pattern (20 bp):
AAGTAAGTAAGTAAGTAAAC
Found at i:10435946 original size:4 final size:4
Alignment explanation
Indices: 10435937--10435975 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
10435927 GTGAGTTGTT
* * *
10435937 TAAG TAAG TAAG TAAG TAAA CAAG TAAG TGAG TAAG TAA
1 TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAAG TAA
10435976 AGAAGCGAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (4 bp):
TAAG
Found at i:10435963 original size:20 final size:20
Alignment explanation
Indices: 10435938--10435976 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10435928 TGAGTTGTTT
10435938 AAGTAAGTAAGTAAGTAAAC
1 AAGTAAGTAAGTAAGTAAAC
*
10435958 AAGTAAGTGAGTAAGTAAA
1 AAGTAAGTAAGTAAGTAAA
10435977 GAAGCGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.03, G:0.23, T:0.21
Consensus pattern (20 bp):
AAGTAAGTAAGTAAGTAAAC
Found at i:10437226 original size:12 final size:12
Alignment explanation
Indices: 10437209--10437247 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10437199 ATGAGTTATT
10437209 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
10437221 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
10437233 TAAGTGAGTAAG
1 TAAGTAAGCAAG
10437245 TAA
1 TAA
10437248 AGAAGCTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:10437802 original size:12 final size:12
Alignment explanation
Indices: 10437785--10437823 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
10437775 ATGAGTTATT
10437785 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
10437797 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
10437809 TAAGTGAGTAAG
1 TAAGTAAGCAAG
10437821 TAA
1 TAA
10437824 AGAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:10440785 original size:12 final size:12
Alignment explanation
Indices: 10440768--10440818 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
10440758 ATGAGTTATT
10440768 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
10440780 TAAGTAAACAAG
1 TAAGTAAGCAAG
*
10440792 TAAGTGAA-TAAG
1 TAAGT-AAGCAAG
* *
10440804 TAAATAAGCGAG
1 TAAGTAAGCAAG
10440816 TAA
1 TAA
10440819 AGATTCTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 2 0.06
12 28 0.88
13 2 0.06
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.20
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:10444938 original size:12 final size:12
Alignment explanation
Indices: 10444921--10444971 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
10444911 ATGAGTTATT
10444921 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
10444933 TAAGTAAACAAG
1 TAAGTAAGCAAG
*
10444945 TAAGTGAA-TAAG
1 TAAGT-AAGCAAG
* *
10444957 TAAATAAGCGAG
1 TAAGTAAGCAAG
10444969 TAA
1 TAA
10444972 AGATTCTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
11 2 0.06
12 28 0.88
13 2 0.06
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.20
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:10448697 original size:51 final size:51
Alignment explanation
Indices: 10448621--10448723 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
10448611 AGTGAACTTG
*
10448621 TACCAAATATAATTACCTGAAAAAGAGAAAAGAAAATCATGGACAGTTGGA
1 TACCAAATATAACTACCTGAAAAAGAGAAAAGAAAATCATGGACAGTTGGA
* ** **
10448672 TACCAGATATAACTACCTGAAAAAGAGGGAAGAAAATCATGGATTGTTGGA
1 TACCAAATATAACTACCTGAAAAAGAGAAAAGAAAATCATGGACAGTTGGA
10448723 T
1 T
10448724 TTACTCTAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.47, C:0.12, G:0.20, T:0.21
Consensus pattern (51 bp):
TACCAAATATAACTACCTGAAAAAGAGAAAAGAAAATCATGGACAGTTGGA
Found at i:10458512 original size:21 final size:21
Alignment explanation
Indices: 10458465--10458515 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
10458455 CATCTCCCCA
*
10458465 ATTAGACTTAATAGGTGACAT
1 ATTAGTCTTAATAGGTGACAT
10458486 ATTAGTCTTAATAGGTGACAT
1 ATTAGTCTTAATAGGTGACAT
10458507 ATTAGTCTT
1 ATTAGTCTT
10458516 TCAATCGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (21 bp):
ATTAGTCTTAATAGGTGACAT
Found at i:10461580 original size:2 final size:2
Alignment explanation
Indices: 10461575--10461616 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
10461565 ATATATATAT
*
10461575 AG AG AG AG AG AG AG AC 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
10461617 CACGTAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10466171 original size:21 final size:21
Alignment explanation
Indices: 10466128--10466174 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
10466118 GCGGCGGTTA
* *
10466128 TGGTTCCTCCGACGGGGATTT
1 TGGTTCCTCCGAAGGGCATTT
10466149 TGGTTCCTCCGATAGGGCA-TT
1 TGGTTCCTCCGA-AGGGCATTT
10466170 TGGTT
1 TGGTT
10466175 TTCGGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.11, C:0.21, G:0.32, T:0.36
Consensus pattern (21 bp):
TGGTTCCTCCGAAGGGCATTT
Found at i:10467116 original size:7 final size:7
Alignment explanation
Indices: 10467106--10467131 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
10467096 TTATATACAT
10467106 AATACTA
1 AATACTA
10467113 AATACTA
1 AATACTA
10467120 AATACTA
1 AATACTA
10467127 AATAC
1 AATAC
10467132 CAATGACTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:10467336 original size:20 final size:20
Alignment explanation
Indices: 10467299--10467336 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
10467289 ATTATTTTTA
*
10467299 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
10467319 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
10467337 TACCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:10469687 original size:20 final size:20
Alignment explanation
Indices: 10469644--10469833 Score: 71
Period size: 20 Copynumber: 9.8 Consensus size: 20
10469634 TAAAAATAAT
* *
10469644 AAAAATTAT-TAAATTTTAA
1 AAAAATTATAAAAATTGTAA
10469663 TAAAAATTATAAAAATTGT-A
1 -AAAAATTATAAAAATTGTAA
10469683 AAAAATATATAAAAAATTGT-A
1 AAAAAT-TAT-AAAAATTGTAA
** * *
10469704 AAATTTTATAAAAA-T-CAT
1 AAAAATTATAAAAATTGTAA
* *
10469722 AAAAATTAT-AAAA-TATAT
1 AAAAATTATAAAAATTGTAA
* * * *
10469740 AGAAATATAGAAAAAAT-TAT
1 AAAAAT-TATAAAAATTGTAA
* *
10469760 AAAACTT-TATAAATTCGTAA
1 AAAAATTATAAAAATT-GTAA
* * *
10469780 GAATATTATAAAAA-AGTAA
1 AAAAATTATAAAAATTGTAA
* *
10469799 AGAAA-TAT-AAAATTCGCAA
1 AAAAATTATAAAAATT-GTAA
10469818 AAAAATTATAAAAATT
1 AAAAATTATAAAAATT
10469834 ATCATACCAA
Statistics
Matches: 127, Mismatches: 28, Indels: 29
0.69 0.15 0.16
Matches are distributed among these distances:
17 9 0.07
18 23 0.18
19 27 0.21
20 36 0.28
21 32 0.25
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAAATTATAAAAATTGTAA
Found at i:10469698 original size:21 final size:19
Alignment explanation
Indices: 10469664--10469734 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 19
10469654 AAATTTTAAT
10469664 AAAAATTATAAAAATTGTA
1 AAAAATTATAAAAATTGTA
10469683 AAAAATATATAAAAAATTGTA
1 AAAAAT-TAT-AAAAATTGTA
** **
10469704 AAATTTTATAAAAATCAT-
1 AAAAATTATAAAAATTGTA
10469722 AAAAATTATAAAA
1 AAAAATTATAAAA
10469735 TATATAGAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 11 0.25
19 13 0.30
20 6 0.14
21 14 0.32
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (19 bp):
AAAAATTATAAAAATTGTA
Found at i:10469705 original size:10 final size:10
Alignment explanation
Indices: 10469664--10469763 Score: 75
Period size: 10 Copynumber: 10.3 Consensus size: 10
10469654 AAATTTTAAT
10469664 AAAAATTAT-
1 AAAAATTATA
*
10469673 AAAAATTGTA
1 AAAAATTATA
10469683 AAAAATATATA
1 AAAAAT-TATA
*
10469694 AAAAATTGTA
1 AAAAATTATA
**
10469704 AAATTTTAT-
1 AAAAATTATA
*
10469713 AAAAATCAT-
1 AAAAATTATA
10469722 AAAAATTATA
1 AAAAATTATA
*
10469732 AAATA-TAT-
1 AAAAATTATA
* *
10469740 AGAAATATAGA
1 AAAAAT-TATA
10469751 AAAAATTATA
1 AAAAATTATA
10469761 AAA
1 AAA
10469764 CTTTATAAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
8 3 0.04
9 25 0.36
10 27 0.39
11 14 0.20
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:10469717 original size:49 final size:49
Alignment explanation
Indices: 10469619--10469740 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 49
10469609 GACATGTGCC
* *
10469619 AAAAATGATAAAAA--AT-AAAAATA-ATAAAAATTATTAAATTTTAAT
1 AAAAATCATAAAAATTATAAAAAATATATAAAAATTATAAAATTTTAAT
* * *
10469664 AAAAATTATAAAAATTGTAAAAAATATATAAAAAATTGTAAAATTTT-AT
1 AAAAATCATAAAAATTATAAAAAATATAT-AAAAATTATAAAATTTTAAT
*
10469713 AAAAATCATAAAAATTATAAAATATATA
1 AAAAATCATAAAAATTATAAAAAATATA
10469741 GAAATATAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
45 13 0.20
47 1 0.02
48 7 0.11
49 29 0.45
50 15 0.23
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (49 bp):
AAAAATCATAAAAATTATAAAAAATATATAAAAATTATAAAATTTTAAT
Found at i:10469745 original size:18 final size:18
Alignment explanation
Indices: 10469619--10469734 Score: 74
Period size: 19 Copynumber: 6.2 Consensus size: 18
10469609 GACATGTGCC
*
10469619 AAAAATGATAAAAA--AT
1 AAAAATCATAAAAATTAT
*
10469635 AAAAATAATAAAAATTATT
1 AAAAATCATAAAAATTA-T
** *
10469654 AAATTTTAATAAAAATTAT
1 AAA-AATCATAAAAATTAT
**
10469673 AAAAATTGTAAAAAATATAT
1 AAAAATCAT-AAAAAT-TAT
** *
10469693 AAAAAATTGTAAAATTTTAT
1 -AAAAATCATAAAA-ATTAT
10469713 AAAAATCATAAAAATTAT
1 AAAAATCATAAAAATTAT
10469731 AAAA
1 AAAA
10469735 TATATAGAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 14
0.76 0.10 0.13
Matches are distributed among these distances:
16 13 0.16
18 11 0.14
19 25 0.31
20 22 0.27
21 10 0.12
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAATCATAAAAATTAT
Found at i:10469757 original size:49 final size:50
Alignment explanation
Indices: 10469654--10469754 Score: 127
Period size: 49 Copynumber: 2.1 Consensus size: 50
10469644 AAAAATTATT
* * *
10469654 AAATTTTAATAAAAATTATAAAAATTGTAAAAAATATATAAAAAATTGTA
1 AAATTTTAATAAAAATCATAAAAATTGTAAAAAATATATAAAAAATAGAA
* *
10469704 AAATTTT-ATAAAAATCATAAAAA-T-TATAAAATATATAGAAATATAGAA
1 AAATTTTAATAAAAATCATAAAAATTGTAAAAAATATATA-AAAAATAGAA
10469752 AAA
1 AAA
10469755 ATTATAAAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
47 12 0.27
48 11 0.24
49 15 0.33
50 7 0.16
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (50 bp):
AAATTTTAATAAAAATCATAAAAATTGTAAAAAATATATAAAAAATAGAA
Found at i:10470060 original size:9 final size:9
Alignment explanation
Indices: 10470036--10470155 Score: 57
Period size: 9 Copynumber: 12.7 Consensus size: 9
10470026 AAATTTTACC
10470036 ATTTTTATA
1 ATTTTTATA
* *
10470045 TTATTTTATG
1 AT-TTTTATA
10470055 ATTTTTATA
1 ATTTTTATA
*
10470064 ATTTTTTTTCTA
1 A---TTTTTATA
10470076 ATTTTTAATA
1 ATTTTT-ATA
*
10470086 TGTTTTTAT-
1 -ATTTTTATA
10470095 ATTTTTATTAA
1 ATTTTTA-T-A
* *
10470106 AATTTAATA
1 ATTTTTATA
10470115 ATTTTTATA
1 ATTTTTATA
** *
10470124 ACCTTTATTG
1 ATTTTTA-TA
10470134 ATTTTTAT-
1 ATTTTTATA
10470142 -TTTTTATA
1 ATTTTTATA
10470150 ATTTTT
1 ATTTTT
10470156 TACTACATGT
Statistics
Matches: 82, Mismatches: 17, Indels: 24
0.67 0.14 0.20
Matches are distributed among these distances:
7 7 0.09
8 6 0.07
9 33 0.40
10 18 0.22
11 10 0.12
12 8 0.10
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (9 bp):
ATTTTTATA
Found at i:10470070 original size:19 final size:19
Alignment explanation
Indices: 10469990--10470070 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
10469980 TTAAAGGGCA
*
10469990 TTTTTATGCA-TTTTATACT
1 TTTTTATG-ATTTTTATAAT
* *
10470009 TTTTTATGACTTTTATAAA
1 TTTTTATGATTTTTATAAT
* **
10470028 ATTTTACCATTTTTAT-AT
1 TTTTTATGATTTTTATAAT
10470046 TATTTTATGATTTTTATAAT
1 T-TTTTATGATTTTTATAAT
10470066 TTTTT
1 TTTTT
10470071 TTCTAATTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
18 2 0.04
19 44 0.90
20 3 0.06
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTTATGATTTTTATAAT
Found at i:10472949 original size:24 final size:26
Alignment explanation
Indices: 10472900--10472950 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 26
10472890 AATTAATTTT
10472900 TAGTGAAGATAGGTCGGAACTGTTAAA
1 TAGTGAAGATAGG-CGGAACTGTTAAA
10472927 TAGTGAA-ATAGG-GGAAACT-TTAAA
1 TAGTGAAGATAGGCGG-AACTGTTAAA
10472951 GAATAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.30
25 4 0.17
26 5 0.22
27 7 0.30
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.25
Consensus pattern (26 bp):
TAGTGAAGATAGGCGGAACTGTTAAA
Found at i:10473799 original size:21 final size:21
Alignment explanation
Indices: 10473773--10473840 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
10473763 TTGTTTTGAG
10473773 TACTGAATTGAATTGTGAAGT
1 TACTGAATTGAATTGTGAAGT
* *
10473794 TACTGAA-T--ATTGTTATGT
1 TACTGAATTGAATTGTGAAGT
* *
10473812 GTACTGCATTGAATTGTGAAAT
1 -TACTGAATTGAATTGTGAAGT
*
10473834 TATTGAA
1 TACTGAA
10473841 GTAATGAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 2 0.06
21 12 0.34
22 7 0.20
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (21 bp):
TACTGAATTGAATTGTGAAGT
Found at i:10473804 original size:40 final size:40
Alignment explanation
Indices: 10473737--10473840 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
10473727 AGACTGACAT
* * * *
10473737 TGAACTGAATTATGGAA-TACTGAATATTGTTTTGAGTAC
1 TGAATTGAATTGTGAAATTACTGAATATTGTTATGAGTAC
* *
10473776 TGAATTGAATTGTGAAGTTACTGAATATTGTTATGTGTAC
1 TGAATTGAATTGTGAAATTACTGAATATTGTTATGAGTAC
* *
10473816 TGCATTGAATTGTGAAATTATTGAA
1 TGAATTGAATTGTGAAATTACTGAA
10473841 GTAATGAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
39 13 0.24
40 42 0.76
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (40 bp):
TGAATTGAATTGTGAAATTACTGAATATTGTTATGAGTAC
Found at i:10474112 original size:45 final size:45
Alignment explanation
Indices: 10474045--10474131 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
10474035 CCGACTACTT
* * *
10474045 TTACTGTTACTGATTTGACACTTTGTGTATCGAATACTATTAATC
1 TTACTATTACCGATTCGACACTTTGTGTATCGAATACTATTAATC
*
10474090 TTACTATTACCGATTCGACACTTTGTGTGTCGAATACTATTA
1 TTACTATTACCGATTCGACACTTTGTGTATCGAATACTATTA
10474132 CTGTTATCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (45 bp):
TTACTATTACCGATTCGACACTTTGTGTATCGAATACTATTAATC
Found at i:10474145 original size:39 final size:39
Alignment explanation
Indices: 10474040--10474281 Score: 153
Period size: 39 Copynumber: 6.1 Consensus size: 39
10474030 ATATGCCGAC
* * *
10474040 TACTTTTACTGTTA-CTGATTTGACACTTTGTGTATCGAA
1 TACTATTACTGTTATC-GATTCGACACTTTGTGTGTCGAA
10474079 TACTATTAATCT-TACTATTACCGATTCGACACTTTGTGTGTCGAA
1 TACTATT-A-CTGT--TA-T--CGATTCGACACTTTGTGTGTCGAA
* *
10474124 TACTATTACTGTTATCAATTCGGCACTTTGTGTGTCGAA
1 TACTATTACTGTTATCGATTCGACACTTTGTGTGTCGAA
* * *
10474163 TATTGTTACCGTTATTGTTACCGATTC-AGCACTTTGTGTGTCG--
1 TA---CTA---TTACTGTTATCGATTCGA-CACTTTGTGTGTCGAA
* *
10474206 -A--A-TACTGTTATTGATTCGGCACTTTGTGTGTCGAA
1 TACTATTACTGTTATCGATTCGACACTTTGTGTGTCGAA
* * *
10474241 TACTGTTACTATTA-CTGATTCGTCACTTTGTGTGTCGAA
1 TACTATTACTGTTATC-GATTCGACACTTTGTGTGTCGAA
10474280 TA
1 TA
10474282 TTGTTACCGT
Statistics
Matches: 161, Mismatches: 18, Indels: 48
0.71 0.08 0.21
Matches are distributed among these distances:
33 26 0.16
36 1 0.01
37 1 0.01
39 61 0.38
40 2 0.01
41 3 0.02
42 7 0.04
43 2 0.01
44 2 0.01
45 55 0.34
46 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (39 bp):
TACTATTACTGTTATCGATTCGACACTTTGTGTGTCGAA
Found at i:10474222 original size:33 final size:33
Alignment explanation
Indices: 10474185--10474248 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
10474175 TATTGTTACC
10474185 GATTCAGCACTTTGTGTGTCGAATACTGTTATT
1 GATTCAGCACTTTGTGTGTCGAATACTGTTATT
*
10474218 GATTCGGCACTTTGTGTGTCGAATACTGTTA
1 GATTCAGCACTTTGTGTGTCGAATACTGTTA
10474249 CTATTACTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (33 bp):
GATTCAGCACTTTGTGTGTCGAATACTGTTATT
Found at i:10474262 original size:117 final size:116
Alignment explanation
Indices: 10474101--10474334 Score: 344
Period size: 117 Copynumber: 2.0 Consensus size: 116
10474091 TACTATTACC
*
10474101 GATTCGACACTTTGTGTGTCGAATACTATTACTGTTATCAATTCGGCACTTTGTGTGTCGAATAT
1 GATTCGACACTTTGTGTGTCGAATACTATTACTATTATCAATTCGGCACTTTGTGTGTCGAATAT
* * *
10474166 TGTTACCGTTATTGTTACCGATTCAGCACTTTGTGTGTCGAATACTGTTATT
66 TGTTACCG-TACTGTTACAGATTCAGCACTTTGTGTGTCAAATACTGTTATT
* * * *
10474218 GATTCGGCACTTTGTGTGTCGAATACTGTTACTATTA-CTGATTCGTCACTTTGTGTGTCGAATA
1 GATTCGACACTTTGTGTGTCGAATACTATTACTATTATC-AATTCGGCACTTTGTGTGTCGAATA
** *
10474282 TTGTTACCGTACTGTTACAGATTTGGCACTTTGTGTGTTAAATACTGTTATT
65 TTGTTACCGTACTGTTACAGATTCAGCACTTTGTGTGTCAAATACTGTTATT
10474334 G
1 G
10474335 TTACTGTTAC
Statistics
Matches: 105, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
116 39 0.37
117 66 0.63
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (116 bp):
GATTCGACACTTTGTGTGTCGAATACTATTACTATTATCAATTCGGCACTTTGTGTGTCGAATAT
TGTTACCGTACTGTTACAGATTCAGCACTTTGTGTGTCAAATACTGTTATT
Found at i:10474287 original size:39 final size:39
Alignment explanation
Indices: 10474090--10474340 Score: 201
Period size: 39 Copynumber: 6.3 Consensus size: 39
10474080 ACTATTAATC
* * *
10474090 TTACTATTACCGATTCGACACTTTGTGTGTCGAATACTA
1 TTACTATTACTGATTCGGCACTTTGTGTGTCGAATACTG
* * *
10474129 TTACTGTTA-TCAATTCGGCACTTTGTGTGTCGAATATTG
1 TTACTATTACT-GATTCGGCACTTTGTGTGTCGAATACTG
* *
10474168 TTACCGTTATTGTTACCGATTCAGCACTTTGTGTGTCGAATACTG
1 TTA-C--TA---TTACTGATTCGGCACTTTGTGTGTCGAATACTG
10474213 -T--TA-T--TGATTCGGCACTTTGTGTGTCGAATACTG
1 TTACTATTACTGATTCGGCACTTTGTGTGTCGAATACTG
* *
10474246 TTACTATTACTGATTCGTCACTTTGTGTGTCGAATATTG
1 TTACTATTACTGATTCGGCACTTTGTGTGTCGAATACTG
* * **
10474285 TTACCGTACTGTTACAGATTTGGCACTTTGTGTGTTAAATACTG
1 TTA-C-TA---TTACTGATTCGGCACTTTGTGTGTCGAATACTG
* *
10474329 TTATTGTTACTG
1 TTACTATTACTG
10474341 TTACTTACTG
Statistics
Matches: 169, Mismatches: 24, Indels: 38
0.73 0.10 0.16
Matches are distributed among these distances:
33 27 0.16
34 1 0.01
35 1 0.01
36 2 0.01
37 1 0.01
39 72 0.43
40 2 0.01
41 2 0.01
42 2 0.01
44 31 0.18
45 28 0.17
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.43
Consensus pattern (39 bp):
TTACTATTACTGATTCGGCACTTTGTGTGTCGAATACTG
Found at i:10474343 original size:22 final size:23
Alignment explanation
Indices: 10474317--10474359 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
10474307 GCACTTTGTG
10474317 TGTTAAATACTG-TTATTGTTAC
1 TGTTAAATACTGATTATTGTTAC
**
10474339 TGTTACTTACTGATTATTGTT
1 TGTTAAATACTGATTATTGTT
10474360 TAGGTACTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.53
Consensus pattern (23 bp):
TGTTAAATACTGATTATTGTTAC
Found at i:10478968 original size:13 final size:13
Alignment explanation
Indices: 10478952--10478981 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
10478942 TCCATAAATC
10478952 CACAACATATTTT
1 CACAACATATTTT
*
10478965 CACAATATATTTT
1 CACAACATATTTT
10478978 CACA
1 CACA
10478982 TATAAATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (13 bp):
CACAACATATTTT
Found at i:10487369 original size:20 final size:20
Alignment explanation
Indices: 10487344--10487383 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10487334 AATATTTTCC
*
10487344 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
10487364 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
10487384 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:10487389 original size:34 final size:35
Alignment explanation
Indices: 10487332--10487398 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
10487322 CAAACAGCAG
*
10487332 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
10487367 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
10487399 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:10487390 original size:14 final size:14
Alignment explanation
Indices: 10487367--10487406 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
10487357 ACAGAAAAGT
*
10487367 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
10487381 AAATCATTTTACGG
1 AAAACATTTTACAG
10487395 AAAACATTTTAC
1 AAAACATTTTAC
10487407 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:10487822 original size:25 final size:25
Alignment explanation
Indices: 10487794--10487843 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
10487784 CCACCATCTT
10487794 TTAAATTGACTAAATTTTCATTTAA
1 TTAAATTGACTAAATTTTCATTTAA
10487819 TTAAATTGACTAAATTTTCATTTAA
1 TTAAATTGACTAAATTTTCATTTAA
10487844 AGTCTTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (25 bp):
TTAAATTGACTAAATTTTCATTTAA
Found at i:10488943 original size:11 final size:11
Alignment explanation
Indices: 10488929--10488984 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
10488919 ATATCCAAAT
*
10488929 AATAACTATAA
1 AATAACAATAA
* *
10488940 AATAATAGTAA
1 AATAACAATAA
*
10488951 AATAACAACAA
1 AATAACAATAA
*
10488962 AATAAC-ATCA
1 AATAACAATAA
10488972 AATAACAATAA
1 AATAACAATAA
10488983 AA
1 AA
10488985 AAGAGTGTCG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
10 8 0.23
11 27 0.77
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.20
Consensus pattern (11 bp):
AATAACAATAA
Found at i:10488954 original size:22 final size:21
Alignment explanation
Indices: 10488929--10488984 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
10488919 ATATCCAAAT
* *
10488929 AATAACTATAAAATAATAGTAA
1 AATAACAATAAAATAACA-TAA
* *
10488951 AATAACAACAAAATAACATCA
1 AATAACAATAAAATAACATAA
10488972 AATAACAATAAAA
1 AATAACAATAAAA
10488985 AAGAGTGTCG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.68, C:0.11, G:0.02, T:0.20
Consensus pattern (21 bp):
AATAACAATAAAATAACATAA
Found at i:10490408 original size:15 final size:17
Alignment explanation
Indices: 10490378--10490410 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
10490368 TGTTAGCACT
10490378 TAAAATATATTATATAG
1 TAAAATATATTATATAG
10490395 TAAAATA-ATATATATA
1 TAAAATATAT-TATATA
10490411 CAAAAAATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAAATATATTATATAG
Found at i:10490452 original size:3 final size:3
Alignment explanation
Indices: 10490444--10490501 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
10490434 AACTAATACA
* * * * * * *
10490444 AAT AAT AAT ACT AAT AAT TAT AGT AAC ATT AAT AAT AAT AAC AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
10490492 AAT AAT AAT A
1 AAT AAT AAT A
10490502 GTTAAGTAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10490456 original size:18 final size:18
Alignment explanation
Indices: 10490425--10490459 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
10490415 AAATGTAAAT
10490425 AAATATATAAACTAATAC
1 AAATATATAAACTAATAC
10490443 AAATA-ATAATACTAATA
1 AAATATATAA-ACTAATA
10490460 ATTATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATATAAACTAATAC
Found at i:10490476 original size:18 final size:18
Alignment explanation
Indices: 10490455--10490503 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
10490445 ATAATAATAC
* *
10490455 TAATAATTATAGTAACAT
1 TAATAATAATAGTAACAA
**
10490473 TAATAATAATAACAACAA
1 TAATAATAATAGTAACAA
10490491 TAATAATAATAGT
1 TAATAATAATAGT
10490504 TAAGTAATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (18 bp):
TAATAATAATAGTAACAA
Found at i:10490485 original size:15 final size:15
Alignment explanation
Indices: 10490444--10490499 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
10490434 AACTAATACA
10490444 AATAATAAT-ACTAAT
1 AATAATAATAAC-AAT
* * *
10490459 AATTATAGTAACATT
1 AATAATAATAACAAT
*
10490474 AATAATAATAACAAC
1 AATAATAATAACAAT
10490489 AATAATAATAA
1 AATAATAATAA
10490500 TAGTTAAGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
15 31 0.94
16 2 0.06
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:10496217 original size:18 final size:18
Alignment explanation
Indices: 10496178--10496220 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
10496168 ACGAGAGTTT
*
10496178 AAAAAATATATTAAAACT
1 AAAAAATATATTAAAACA
*
10496196 AAAAAATA-AGTTTAAACA
1 AAAAAATATA-TTAAAACA
10496214 AAAAAAT
1 AAAAAAT
10496221 TTAAGTTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (18 bp):
AAAAAATATATTAAAACA
Found at i:10497968 original size:16 final size:16
Alignment explanation
Indices: 10497931--10497972 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
10497921 TTAATCATAT
*
10497931 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
10497947 TT-AAATATATTATAA
1 TTAAAATATATTATAA
10497962 TTAAAATATAT
1 TTAAAATATAT
10497973 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:10497979 original size:14 final size:15
Alignment explanation
Indices: 10497940--10497981 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
10497930 TTTAAACATA
*
10497940 ATTATTATTAAATAT
1 ATTATAATTAAATAT
10497955 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
10497969 A-TATAATTTAATA
1 ATTATAATTAAATA
10497982 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:10498073 original size:120 final size:121
Alignment explanation
Indices: 10497929--10498223 Score: 513
Period size: 120 Copynumber: 2.5 Consensus size: 121
10497919 ATTTAATCAT
* * *
10497929 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAAAA
10497994 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
10498050 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAAAA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAAAA
*
10498114 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
66 ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
* * *
10498170 ATTTGAA-GTAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAA
1 ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAA
10498224 TTTAAAATAA
Statistics
Matches: 167, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
120 161 0.96
121 6 0.04
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (121 bp):
ATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAAAA
ATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
Found at i:10498092 original size:18 final size:17
Alignment explanation
Indices: 10498069--10498105 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
10498059 AATTATTATT
10498069 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
10498085 AAATATATGATTTAATA
1 AAATATATGATTTAATA
10498102 AAAT
1 AAAT
10498106 TCTTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:10498094 original size:59 final size:58
Alignment explanation
Indices: 10498027--10498215 Score: 165
Period size: 59 Copynumber: 3.2 Consensus size: 58
10498017 CTCAAATCAT
10498027 AATATATGATACTATAAAAGATAATTTAACATAATTATTATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAAGATAATTTAA-ATAATTATTATTAAATATATTTTAATTAA
* * ** *
10498086 AATATATGAT--T-TAATAA-A-ATTCTTAAA-AATTAATATTCTTATATGAATTTACTCAAATC
1 AATATATGATACTATAA-AAGATAAT-TTAAATAATTATTATT-AAATAT--ATTT--T--AATT
*
10498145 AT
57 AA
* *
10498147 AATATATGATACTATAAAAGATAATTTGAAGTAATTAATATTAAATATATTTTAATTAA
1 AATATATGATACTATAAAAGATAATTT-AAATAATTATTATTAAATATATTTTAATTAA
10498206 AATATATGAT
1 AATATATGAT
10498216 TTAATAAATT
Statistics
Matches: 102, Mismatches: 12, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
54 9 0.09
55 7 0.07
56 8 0.08
57 7 0.07
59 25 0.25
61 15 0.15
63 7 0.07
64 6 0.06
65 8 0.08
66 10 0.10
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (58 bp):
AATATATGATACTATAAAAGATAATTTAAATAATTATTATTAAATATATTTTAATTAA
Found at i:10498276 original size:47 final size:46
Alignment explanation
Indices: 10498208--10498374 Score: 143
Period size: 47 Copynumber: 3.7 Consensus size: 46
10498198 TTAATTAAAA
10498208 TATATG-ATTTAATA-AATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATACAATTTAAAATAATTATAA-TAATAAATTTTCT
* * **
10498254 TATATGAATTTTTACAATTTAAAATAATTATTATTACATATAA-TTTAA
1 TATATGAATTTATACAATTTAAAATAATTA-TAATA-ATA-AATTTTCT
* * * *
10498302 TA-AT-AA--TATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAATTTATACAATTT-AAAATAATT-ATAATAATAAATTTTCT
10498345 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATACAATTTAAAATAATTA
10498375 ATATTAAATA
Statistics
Matches: 93, Mismatches: 15, Indels: 26
0.69 0.11 0.19
Matches are distributed among these distances:
42 2 0.02
43 8 0.09
44 17 0.18
45 5 0.05
46 13 0.14
47 36 0.39
48 10 0.11
49 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATACAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:10498317 original size:91 final size:91
Alignment explanation
Indices: 10498241--10498446 Score: 340
Period size: 91 Copynumber: 2.3 Consensus size: 91
10498231 TAATTATAAC
* * * *
10498241 TAATAAATTTTCTTATATGAATTTTTACAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAAATTAATAAT
*
10498306 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
10498332 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAAATTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAAATTAATAAT
*
10498397 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
10498423 TAATAAAATGTTCTTATATGAATT
1 TAAT-AAATTTTCTTATATGAATT
10498447 AACTAAAATC
Statistics
Matches: 107, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
91 89 0.83
92 18 0.17
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAAATTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:10498408 original size:44 final size:43
Alignment explanation
Indices: 10498269--10498408 Score: 102
Period size: 44 Copynumber: 3.1 Consensus size: 43
10498259 GAATTTTTAC
* * *
10498269 AATTTAAAATAATTATTATTACATATAATTTAATAATAATATAT
1 AATTTAAAATAATTAATATTAAATATAAATTAATAAT-ATATAT
** * * *** * *
10498313 AATTTCATAAAATTCTTGATAATAAAT-TTTCTTATATGAATTTATAC
1 AA-TT--TAAAATAATTAATATTAAATATAAATTA-AT-AATATATAT
10498360 AATTTAAAATAATTAATATTAAATATAAATTAATAATGATATAT
1 AATTTAAAATAATTAATATTAAATATAAATTAATAAT-ATATAT
10498404 AATTT
1 AATTT
10498409 CATAAAATTC
Statistics
Matches: 69, Mismatches: 20, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
43 3 0.04
44 29 0.42
45 6 0.09
46 6 0.09
47 22 0.32
48 3 0.04
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (43 bp):
AATTTAAAATAATTAATATTAAATATAAATTAATAATATATAT
Found at i:10498423 original size:47 final size:47
Alignment explanation
Indices: 10498291--10498429 Score: 126
Period size: 47 Copynumber: 3.0 Consensus size: 47
10498281 TTATTATTAC
* * *
10498291 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAAATTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
*** * * ** *
10498338 AT-TTTCTT-AT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAAATTAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
10498382 ATATAAATTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAAATTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
10498429 A
1 A
10498430 ATGTTCTTAT
Statistics
Matches: 67, Mismatches: 18, Indels: 14
0.68 0.18 0.14
Matches are distributed among these distances:
44 18 0.27
45 14 0.21
46 14 0.21
47 21 0.31
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (47 bp):
ATATAAATTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:10499714 original size:15 final size:16
Alignment explanation
Indices: 10499693--10499738 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
10499683 ATTGACAACA
10499693 TCAAAACAGAACACAT
1 TCAAAACAGAACACAT
10499709 TC-AAACA-AGACACA-
1 TCAAAACAGA-ACACAT
10499723 TCAAAACAGAACACAT
1 TCAAAACAGAACACAT
10499739 GCCTACCAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.12
15 20 0.77
16 3 0.12
ACGTcount: A:0.57, C:0.26, G:0.07, T:0.11
Consensus pattern (16 bp):
TCAAAACAGAACACAT
Done.