Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 146 of 171
Found at i:44198928 original size:26 final size:26
Alignment explanation
Indices: 44198898--44198952 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
44198888 CGACAATGAA
44198898 AAAAATATCATAAAGAAAACGAAAAG
1 AAAAATATCATAAAGAAAACGAAAAG
*
44198924 AAAAATATCATAATGAAAACGAAAAG
1 AAAAATATCATAAAGAAAACGAAAAG
44198950 AAA
1 AAA
44198953 GAACACACAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.69, C:0.07, G:0.11, T:0.13
Consensus pattern (26 bp):
AAAAATATCATAAAGAAAACGAAAAG
Found at i:44205899 original size:22 final size:23
Alignment explanation
Indices: 44205856--44205906 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
44205846 TAAAACTTAC
44205856 ATATATGATTTTTTTATCAAAAT
1 ATATATGATTTTTTTATCAAAAT
*
44205879 GTATATGATTTTTTTAT-AAAAT
1 ATATATGATTTTTTTATCAAAAT
44205901 ATATAT
1 ATATAT
44205907 ATCATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (23 bp):
ATATATGATTTTTTTATCAAAAT
Found at i:44212712 original size:97 final size:97
Alignment explanation
Indices: 44212519--44212712 Score: 241
Period size: 97 Copynumber: 2.0 Consensus size: 97
44212509 AACCTTGGAA
* * *
44212519 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGACTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGACACAAATTTTCA
* * * *
44212584 GAATCAGAGATAAAGAAACATTGTCTTGATTT
66 AAATCAGAAATAAAGAAACATTGCCTCGATTT
* *
44212616 AAGGGTATTCGACTAT-TCTGATTTGAAGAAAAATCGCACCTAGTGAGTTAAGACACAAATTTTC
1 AAGGATATTCGACTATCTC-GATTTGAAGAAAAATCGCACCTAGTAAGTTAAGACACAAATTTTC
* *
44212680 AAAA-CTTGAAATAAA-AGAATATTGCCTCGATTT
65 AAAATC-AGAAATAAAGA-AACATTGCCTCGATTT
44212713 TAAAGGTTTC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
96 4 0.05
97 79 0.95
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (97 bp):
AAGGATATTCGACTATCTCGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGACACAAATTTTCA
AAATCAGAAATAAAGAAACATTGCCTCGATTT
Found at i:44213018 original size:29 final size:30
Alignment explanation
Indices: 44212978--44213321 Score: 184
Period size: 29 Copynumber: 11.8 Consensus size: 30
44212968 ACTCGGGGGC
**
44212978 AAAATGGTAATTTTT-GAAAGTTCAAGGTTA
1 AAAATGG-AATTTTTGGAAAGTTCGGGGTTA
* * * *
44213008 AAAATGGAATTTTTCGATA-TTCGAGGAT-
1 AAAATGGAATTTTTGGAAAGTTCGGGGTTA
* * **
44213036 GAAATGGTCATTTTTGGAAAGTTTTGGGTTA
1 AAAATGG-AATTTTTGGAAAGTTCGGGGTTA
* * *
44213067 AAAATGGAATTTTTAGACA-TCTAGGGG-T-
1 AAAATGGAATTTTTGGAAAGT-TCGGGGTTA
* **
44213095 AAAATGGTAATTTTTGGAAGGTTTAGGGTTA
1 AAAATGG-AATTTTTGGAAAGTTCGGGGTTA
** * * *
44213126 AAAATGGAATTTTTATACA-TCCGGGGGT-
1 AAAATGGAATTTTTGGAAAGTTCGGGGTTA
* * *
44213154 GAAATGGTAATTTTT-GAAAGGTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAA-GTTCGGGGTTA
*
44213185 AAAATGGAATTTTTAGACAA-TT-GGGG-T-
1 AAAATGGAATTTTTGGA-AAGTTCGGGGTTA
* *
44213212 AAAATGGTAATTTTTGGAAGGTTCGAGGTT-
1 AAAATGG-AATTTTTGGAAAGTTCGGGGTTA
* *
44213242 AAAAT-GAAATTTTGGAAAATTCGGGG-TA
1 AAAATGGAATTTTTGGAAAGTTCGGGGTTA
* * *
44213270 AAAATGTAA-TTTTGGAAAAGTTCGAGGTCA
1 AAAATGGAATTTTTGG-AAAGTTCGGGGTTA
*
44213300 AAAATGGAA-TTCTGGAAAGTTC
1 AAAATGGAATTTTTGGAAAGTTC
44213322 AAGGACGTCT
Statistics
Matches: 239, Mismatches: 52, Indels: 47
0.71 0.15 0.14
Matches are distributed among these distances:
27 9 0.04
28 59 0.25
29 76 0.32
30 72 0.30
31 21 0.09
32 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAAGTTCGGGGTTA
Found at i:44213072 original size:59 final size:58
Alignment explanation
Indices: 44212950--44213254 Score: 296
Period size: 59 Copynumber: 5.2 Consensus size: 58
44212940 GCCCGGGGGT
* * ** * *
44212950 AAAATGGTAA-TTTTAGACACTCGGGGGCAAAATGGTAATTTTTGAAAGTTCAAGGTTA
1 AAAATGG-AATTTTTAGACATTCGAGGGTGAAATGGTAATTTTTGAAAGTTTAGGGTTA
* * * * *
44213008 AAAATGGAATTTTTCGATATTCGAGGATGAAATGGTCATTTTTGGAAAGTTTTGGGTTA
1 AAAATGGAATTTTTAGACATTCGAGGGTGAAATGGTAATTTTT-GAAAGTTTAGGGTTA
* * *
44213067 AAAATGGAATTTTTAGACA-TCTAGGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTTA
1 AAAATGGAATTTTTAGACATTCGA-GGGTGAAATGGTAATTTTT-GAAAGTTTAGGGTTA
* * * * *
44213126 AAAATGGAATTTTTATACATCCGGGGGTGAAATGGTAATTTTTGAAAGGTTTGGGGTCA
1 AAAATGGAATTTTTAGACATTCGAGGGTGAAATGGTAATTTTTGAAA-GTTTAGGGTTA
* * * *
44213185 AAAATGGAATTTTTAGACAATT-G-GGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTT-
1 AAAATGGAATTTTTAGAC-ATTCGAGGGTGAAATGGTAATTTTTGAAAGTTTAG-GGTTA
*
44213242 AAAATGAAATTTT
1 AAAATGGAATTTT
44213255 GGAAAATTCG
Statistics
Matches: 205, Mismatches: 35, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
57 18 0.09
58 62 0.30
59 122 0.60
60 3 0.01
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (58 bp):
AAAATGGAATTTTTAGACATTCGAGGGTGAAATGGTAATTTTTGAAAGTTTAGGGTTA
Found at i:44213173 original size:117 final size:118
Alignment explanation
Indices: 44212950--44213254 Score: 388
Period size: 118 Copynumber: 2.6 Consensus size: 118
44212940 GCCCGGGGGT
* * *
44212950 AAAATGGTAA-TTTTAGACACTCGGGGGCAAAATGGTAATTTTT-GAAAGTTCAAGGTTAAAAAT
1 AAAATGG-AATTTTTAGACA-TCTGGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTTAAAAAT
* * * * * *
44213013 GGAATTTTTCGATATTCGAGGATGAAATGGTCATTTTTGGAAA-GTTTTGGGTTA
64 GGAATTTTTAGACATCCGAGGATGAAATGGTAATTTTTGGAAAGGTTTGGGGTCA
* *
44213067 AAAATGGAATTTTTAGACATCTAGGGGTAAAATGGTAATTTTTGGAAGGTTTAGGGTTAAAAATG
1 AAAATGGAATTTTTAGACATCT-GGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTTAAAAATG
* * *
44213132 GAATTTTTATACATCCGGGGGTGAAATGGTAATTTTT-GAAAGGTTTGGGGTCA
65 GAATTTTTAGACATCCGAGGATGAAATGGTAATTTTTGGAAAGGTTTGGGGTCA
*
44213185 AAAATGGAATTTTTAGACAAT-TGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTT-AAAATG
1 AAAATGGAATTTTTAGAC-ATCTGGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTTAAAAATG
*
44213248 AAATTTT
65 GAATTTT
44213255 GGAAAATTCG
Statistics
Matches: 165, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
116 16 0.10
117 71 0.43
118 76 0.46
119 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (118 bp):
AAAATGGAATTTTTAGACATCTGGGGTAAAATGGTAATTTTTGGAAGGTTCAAGGTTAAAAATGG
AATTTTTAGACATCCGAGGATGAAATGGTAATTTTTGGAAAGGTTTGGGGTCA
Found at i:44213264 original size:28 final size:28
Alignment explanation
Indices: 44213223--44213317 Score: 109
Period size: 28 Copynumber: 3.3 Consensus size: 28
44213213 AAATGGTAAT
** *
44213223 TTTTGGAAGGTTCGAGGTTAAAATGAAA
1 TTTTGGAAAATTCGAGGTAAAAATGAAA
* *
44213251 TTTTGGAAAATTCGGGGTAAAAATGTAA
1 TTTTGGAAAATTCGAGGTAAAAATGAAA
*
44213279 TTTTGGAAAAGTTCGAGGTCAAAAATGGAA
1 TTTTGGAAAA-TTCGAGGT-AAAAATGAAA
*
44213309 TTCTGGAAA
1 TTTTGGAAA
44213318 GTTCAAGGAC
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 33 0.58
29 7 0.12
30 17 0.30
ACGTcount: A:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (28 bp):
TTTTGGAAAATTCGAGGTAAAAATGAAA
Found at i:44213274 original size:58 final size:57
Alignment explanation
Indices: 44212973--44213310 Score: 233
Period size: 59 Copynumber: 5.8 Consensus size: 57
44212963 TAGACACTCG
* * * * *
44212973 GGGGCAAAATGGTAATTTTT-GAAAGTTCAAGGTTAAAAATGGAATTTTTCG-ATATTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAAT-GAAATTTT-GAAAATTC
* * * * * * * * *
44213030 GAGGATGAAATGGTCATTTTTGGAAAGTTTTG-GGTTAAAAATGGAATTTTTAGACATCTA
1 G-GGGTAAAATGGTAATTTTTGG-AAGGTTCGAGGTTAAAAATGAAATTTTGA-AAAT-TC
* * * * *
44213090 GGGGTAAAATGGTAATTTTTGGAAGGTT-TAGGGTTAAAAATGGAATTTTTATACATCC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGA-GGTTAAAAATGAAATTTTGA-AAATTC
* * * * * * *
44213148 GGGGGTGAAATGGTAATTTTTGAAAGGTTTGGGGTCAAAAATGGAATTTTTAGACAATT-
1 -GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAAT-GAAATTTT-GAAAATTC
44213207 GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTT-AAAATGAAATTTTGGAAAATTC
1 GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGAAATTTT-GAAAATTC
* * *
44213264 GGGGTAAAAAT-GTAA-TTTTGGAAAAGTTCGAGGTCAAAAATGGAATT
1 GGGGT-AAAATGGTAATTTTTGG-AAGGTTCGAGGTTAAAAATGAAATT
44213311 CTGGAAAGTT
Statistics
Matches: 222, Mismatches: 43, Indels: 31
0.75 0.15 0.10
Matches are distributed among these distances:
56 19 0.09
57 26 0.12
58 71 0.32
59 91 0.41
60 14 0.06
61 1 0.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.34
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGAAATTTTGAAAATTC
Found at i:44220086 original size:34 final size:34
Alignment explanation
Indices: 44220048--44220149 Score: 116
Period size: 34 Copynumber: 2.9 Consensus size: 34
44220038 AATACAAATG
*
44220048 CATATACAAAGCTTATCAAATACAGATGTA-ATTA
1 CATATACAAAGCTTATCAGATACAGATGTAGA-TA
* * * *
44220082 CATATATAGAGAGCTAATTAGATACAGGTGTAGATA
1 CATATACA-A-AGCTTATCAGATACAGATGTAGATA
*
44220118 CATATACAAAGCTTATCAGATACAGATATAGA
1 CATATACAAAGCTTATCAGATACAGATGTAGA
44220150 ATCCTACCCC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
34 26 0.47
35 2 0.04
36 26 0.47
37 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (34 bp):
CATATACAAAGCTTATCAGATACAGATGTAGATA
Found at i:44224899 original size:34 final size:34
Alignment explanation
Indices: 44224852--44224968 Score: 137
Period size: 34 Copynumber: 3.4 Consensus size: 34
44224842 TAACAAAGTA
** * * *
44224852 TATCAGAGGCAGATACAGATGCATATACAAAGCT
1 TATCAGATACAGATGCAGATACATATACAGAGCT
*
44224886 TATCAAATACAGATGCA-ATTACATATACAGAGCT
1 TATCAGATACAGATGCAGA-TACATATACAGAGCT
* * *
44224920 GATCAGATACAAATGTAGATACATATACAGAGCT
1 TATCAGATACAGATGCAGATACATATACAGAGCT
44224954 TATCAGATACAGATG
1 TATCAGATACAGATG
44224969 TAGAATCCTA
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
33 1 0.01
34 67 0.97
35 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (34 bp):
TATCAGATACAGATGCAGATACATATACAGAGCT
Found at i:44224965 original size:16 final size:16
Alignment explanation
Indices: 44224876--44224966 Score: 51
Period size: 16 Copynumber: 5.4 Consensus size: 16
44224866 ACAGATGCAT
* *
44224876 ATACAAAGCTTATCAA
1 ATACAGAGCTTATCAG
*
44224892 ATACAGATGCAATTA-CAT
1 ATACAGA-GC--TTATCAG
*
44224910 ATACAGAGCTGATCAG
1 ATACAGAGCTTATCAG
* * *
44224926 ATACAAATG-TAGATACAT
1 ATACAGA-GCT-TAT-CAG
44224944 ATACAGAGCTTATCAG
1 ATACAGAGCTTATCAG
44224960 ATACAGA
1 ATACAGA
44224967 TGTAGAATCC
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
15 2 0.03
16 24 0.41
17 11 0.19
18 18 0.31
19 3 0.05
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.24
Consensus pattern (16 bp):
ATACAGAGCTTATCAG
Found at i:44224970 original size:34 final size:34
Alignment explanation
Indices: 44224868--44224972 Score: 140
Period size: 34 Copynumber: 3.1 Consensus size: 34
44224858 AGGCAGATAC
* * * *
44224868 AGATGCATATACAAAGCTTATCAAATACAGATGC
1 AGATACATATACAGAGCTTATCAGATACAGATGT
* *
44224902 A-ATTACATATACAGAGCTGATCAGATACAAATGT
1 AGA-TACATATACAGAGCTTATCAGATACAGATGT
44224936 AGATACATATACAGAGCTTATCAGATACAGATGT
1 AGATACATATACAGAGCTTATCAGATACAGATGT
44224970 AGA
1 AGA
44224973 ATCCTACCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
33 1 0.02
34 59 0.97
35 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (34 bp):
AGATACATATACAGAGCTTATCAGATACAGATGT
Found at i:44225616 original size:42 final size:42
Alignment explanation
Indices: 44225529--44225618 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
44225519 GCCCGTGTGG
* ** * * *
44225529 CTCACACAGCTTGGCACATGCTTGTGTGGCTCATCTCAGTGC
1 CTCACACAGCTTGGCACACGCTCATGTGGCTCAACTCAATCC
*
44225571 CTCACACAGCTTGGCACACGAC-CATGTGGCTCAAGTCAATCC
1 CTCACACAGCTTGGCACACG-CTCATGTGGCTCAACTCAATCC
44225613 CTCACA
1 CTCACA
44225619 TGACCTGGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
42 39 0.98
43 1 0.03
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.23
Consensus pattern (42 bp):
CTCACACAGCTTGGCACACGCTCATGTGGCTCAACTCAATCC
Found at i:44230587 original size:24 final size:25
Alignment explanation
Indices: 44230540--44230589 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
44230530 CTAATAGGGG
* * *
44230540 AATTTACCCTTTGTTTTTTTAATAT
1 AATTTACCCATTGTCTTTTAAATAT
44230565 AATTTACCCATTG-CTTTTAAATAT
1 AATTTACCCATTGTCTTTTAAATAT
44230589 A
1 A
44230590 TGGATTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (25 bp):
AATTTACCCATTGTCTTTTAAATAT
Found at i:44243532 original size:21 final size:21
Alignment explanation
Indices: 44243506--44243551 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
44243496 TAATCACAAC
**
44243506 TTTATCAAAGGAATTCAGTTT
1 TTTATCAAACAAATTCAGTTT
*
44243527 TTTATCAACCAAATTCAGTTT
1 TTTATCAAACAAATTCAGTTT
44243548 TTTA
1 TTTA
44243552 GCTAGACTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTATCAAACAAATTCAGTTT
Found at i:44245709 original size:148 final size:149
Alignment explanation
Indices: 44245490--44245817 Score: 624
Period size: 149 Copynumber: 2.2 Consensus size: 149
44245480 CAGAATACAA
*
44245490 AAAGAAATGGAAGTTCG-TCTGCCTGGAAAATAAAAAGCACAAAGTAGAAATG-TTTTTTTTTTT
1 AAAGAAATGGAAGTT-GATCTGCCTGGAAAATAAAAAGCACAAAATAGAAATGTTTTTTTTTTTT
44245553 TTTTTTTTTATATTTTCTTTTAAGGAAATGGGAAATGAAAAAAGAAAGAAGAAAGTAGAAACCAA
65 TTTTTTTTTATATTTTCTTTTAAGGAAATGGGAAATGAAAAAAGAAAGAAGAAAGTAGAAACCAA
44245618 GGCTGAAGAGAAACCTTGAG
130 GGCTGAAGAGAAACCTTGAG
44245638 AAAGAAATGGAAGTTGATCTGCCTGGAAAATAAAAAGCACAAAATAGAAATGTTTTTTTTTTTTT
1 AAAGAAATGGAAGTTGATCTGCCTGGAAAATAAAAAGCACAAAATAGAAATGTTTTTTTTTTTTT
44245703 TTTTTTTTATATTTTCTTTTAAGGAAATGGGAAATGAAAAAAGAAAGAAGAAAGTAGAAACCAAG
66 TTTTTTTTATATTTTCTTTTAAGGAAATGGGAAATGAAAAAAGAAAGAAGAAAGTAGAAACCAAG
44245768 GCTGAAGAGAAACCTTGAG
131 GCTGAAGAGAAACCTTGAG
44245787 AAAGAAATGGAAGTTGATCTGCCTGGAAAAT
1 AAAGAAATGGAAGTTGATCTGCCTGGAAAAT
44245818 TCAACTACTG
Statistics
Matches: 177, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
147 1 0.01
148 49 0.28
149 127 0.72
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.29
Consensus pattern (149 bp):
AAAGAAATGGAAGTTGATCTGCCTGGAAAATAAAAAGCACAAAATAGAAATGTTTTTTTTTTTTT
TTTTTTTTATATTTTCTTTTAAGGAAATGGGAAATGAAAAAAGAAAGAAGAAAGTAGAAACCAAG
GCTGAAGAGAAACCTTGAG
Found at i:44246959 original size:25 final size:27
Alignment explanation
Indices: 44246904--44246960 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
44246894 TAACAAATGC
*
44246904 TTATTTTTGTAATTAATTTATTTTCCA
1 TTATTTTTGTAATTAATTTATTTTACA
* *
44246931 -TATTTTT-TAATTAA-TTGTTTTATA
1 TTATTTTTGTAATTAATTTATTTTACA
44246955 TTATTT
1 TTATTT
44246961 GGGAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 7 0.27
25 12 0.46
26 7 0.27
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (27 bp):
TTATTTTTGTAATTAATTTATTTTACA
Found at i:44248828 original size:59 final size:58
Alignment explanation
Indices: 44248513--44248945 Score: 482
Period size: 59 Copynumber: 7.4 Consensus size: 58
44248503 TTGAATTGTA
* * * ** *
44248513 CAAAAATTACA-TTTTGACCCTAAACTTTCTAAAAAATA-CATTTT--CCCTAAATTTC
1 CAAAAATTCCATTTTTGACCC-GAACTTTCTAAAAATTACCATTTTACCCCCGAACTTC
* * * *
44248568 TAAAAATTCCATTTTTGACCCCAATTTTTCTAAAAATTACCATTTTACCCCCGAACTCC
1 CAAAAATTCCATTTTTGACCCGAA-CTTTCTAAAAATTACCATTTTACCCCCGAACTTC
** * *
44248627 CAAAAATTCCA-TTTTGACCCGATTTTTCCATAAATTACCATTTTACCCCCGAACTTC
1 CAAAAATTCCATTTTTGACCCGAACTTTCTAAAAATTACCATTTTACCCCCGAACTTC
* * *
44248684 CAAAAATTCCATTTTTGACCCCAATTTTTTCAAAAATTACCATTTTACCCCCTGAACTTC
1 CAAAAATTCCATTTTTGACCCGAACTTTCT-AAAAATTACCATTTTACCCCC-GAACTTC
* *
44248744 CAAAAATTCCATTTTTGACCTTGAACTTTCTAAAAATTACCATTTTACCCTCGAACTTC
1 CAAAAATTCCATTTTTGACC-CGAACTTTCTAAAAATTACCATTTTACCCCCGAACTTC
* * * *
44248803 CAAAAATTCCATTTTTGATCCTGAACTTCCTAAAAATTACCATTTTACCCCTGTACTTC
1 CAAAAATTCCATTTTTGA-CCCGAACTTTCTAAAAATTACCATTTTACCCCCGAACTTC
* * *
44248862 CAAAAATTCCTTTTTTTGACCCCGAA-TTTCTTAAAATTACCATTTTACCCTCGAACTTC
1 CAAAAATTCC-ATTTTTGA-CCCGAACTTTCTAAAAATTACCATTTTACCCCCGAACTTC
* * *
44248921 TAAAGATTCTATTTTTGACCTCGAA
1 CAAAAATTCCATTTTTGACC-CGAA
44248946 GTGTCCAAAA
Statistics
Matches: 325, Mismatches: 41, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
55 11 0.03
56 21 0.06
57 50 0.15
58 35 0.11
59 141 0.43
60 61 0.19
61 6 0.02
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (58 bp):
CAAAAATTCCATTTTTGACCCGAACTTTCTAAAAATTACCATTTTACCCCCGAACTTC
Found at i:44248861 original size:30 final size:29
Alignment explanation
Indices: 44248599--44248920 Score: 240
Period size: 30 Copynumber: 11.0 Consensus size: 29
44248589 CAATTTTTCT
* *
44248599 AAAAATTACCATTTTACCCCCGAACTCCC
1 AAAAATTACCATTTTACCCCTGAACTTCC
**
44248628 AAAAATT-CCATTTTGA-CCC-GATTTTTCC
1 AAAAATTACCATTTT-ACCCCTGA-ACTTCC
* *
44248656 ATAAATTACCATTTTACCCCCGAACTTCC
1 AAAAATTACCATTTTACCCCTGAACTTCC
* *
44248685 AAAAATT-CCATTTTTGACCCC--AATTTTTTC
1 AAAAATTACCA-TTTT-ACCCCTGAA--CTTCC
44248715 AAAAATTACCATTTTACCCCCTGAACTTCC
1 AAAAATTACCATTTTA-CCCCTGAACTTCC
* *
44248745 AAAAATT-CCATTTTTGA-CCTTGAACTTTCT
1 AAAAATTACCA-TTTT-ACCCCTGAAC-TTCC
44248775 AAAAATTACCATTTTA-CCCTCGAACTTCC
1 AAAAATTACCATTTTACCCCT-GAACTTCC
*
44248804 AAAAATT-CCATTTTTGA-TCCTGAACTTCC
1 AAAAATTACCA-TTTT-ACCCCTGAACTTCC
*
44248833 TAAAAATTACCATTTTACCCCTGTACTTCC
1 -AAAAATTACCATTTTACCCCTGAACTTCC
* * *
44248863 AAAAATT-CCTTTTTTTGACCCC-GAATTTCT
1 AAAAATTACC--ATTTT-ACCCCTGAACTTCC
*
44248893 TAAAATTACCATTTTA-CCCTCGAACTTC
1 AAAAATTACCATTTTACCCCT-GAACTTC
44248921 TAAAGATTCT
Statistics
Matches: 239, Mismatches: 25, Indels: 58
0.74 0.08 0.18
Matches are distributed among these distances:
27 5 0.02
28 31 0.13
29 87 0.36
30 97 0.41
31 17 0.07
32 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCCTGAACTTCC
Found at i:44248916 original size:29 final size:30
Alignment explanation
Indices: 44248514--44248945 Score: 231
Period size: 29 Copynumber: 14.8 Consensus size: 30
44248504 TGAATTGTAC
*
44248514 AAAAATTA-CATTTTGACCCT-AAACTTTCT
1 AAAAATTACCATTTTGACCCTCGAA-TTTCT
* *
44248543 AAAAAATA-CATTTT--CCCT-AAATTTCT
1 AAAAATTACCATTTTGACCCTCGAATTTCT
44248569 AAAAATT-CCATTTTTGACCC-C-AATTTTTCT
1 AAAAATTACCA-TTTTGACCCTCGAA--TTTCT
* * * *
44248599 AAAAATTACCATTTT-ACCCCCGAACTCCC
1 AAAAATTACCATTTTGACCCTCGAATTTCT
* *
44248628 AAAAATT-CCATTTTGA-CC-CGATTTTTCC
1 AAAAATTACCATTTTGACCCTCGA-ATTTCT
* * * *
44248656 ATAAATTACCATTTT-ACCCCCGAACTTCC
1 AAAAATTACCATTTTGACCCTCGAATTTCT
*
44248685 AAAAATT-CCATTTTTGACCC-C-AATTTTTT
1 AAAAATTACCA-TTTTGACCCTCGAA-TTTCT
* * *
44248714 CAAAAATTACCATTTT-ACCCCCTGAACTTCC
1 -AAAAATTACCATTTTGACCCTC-GAATTTCT
*
44248745 AAAAATT-CCATTTTTGA-CCTTGAACTTTCT
1 AAAAATTACCA-TTTTGACCCTCGAA-TTTCT
* *
44248775 AAAAATTACCATTTT-ACCCTCGAACTTCC
1 AAAAATTACCATTTTGACCCTCGAATTTCT
* *
44248804 AAAAATT-CCATTTTTGATCCT-GAACTTCCT
1 AAAAATTACCA-TTTTGACCCTCGAA-TTTCT
* * *
44248834 AAAAATTACCATTTT-ACCC-CTGTACTTCC
1 AAAAATTACCATTTTGACCCTC-GAATTTCT
*
44248863 AAAAATT-CCTTTTTTTGACCC-CGAATTTCT
1 AAAAATTACC--ATTTTGACCCTCGAATTTCT
* *
44248893 TAAAATTACCATTTT-ACCCTCGAACTTCT
1 AAAAATTACCATTTTGACCCTCGAATTTCT
* *
44248922 AAAGATT-CTATTTTTGA-CCTCGAA
1 AAAAATTACCA-TTTTGACCCTCGAA
44248946 GTGTCCAAAA
Statistics
Matches: 318, Mismatches: 44, Indels: 82
0.72 0.10 0.18
Matches are distributed among these distances:
26 13 0.04
27 14 0.04
28 37 0.12
29 124 0.39
30 104 0.33
31 24 0.08
32 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAAATTACCATTTTGACCCTCGAATTTCT
Found at i:44258131 original size:22 final size:21
Alignment explanation
Indices: 44258103--44258159 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
44258093 CCTCTCACTT
44258103 TTCTTTCTCATTTTTTTCTC-A
1 TTCTTTCTCATTTTTTTC-CAA
*
44258124 TTCCTTTCTTATTTCTTTTCCAA
1 TT-CTTTCTCATTT-TTTTCCAA
44258147 TTCTTTCTC-TTTT
1 TTCTTTCTCATTTT
44258160 AATCACTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
20 1 0.03
21 5 0.16
22 17 0.55
23 8 0.26
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.67
Consensus pattern (21 bp):
TTCTTTCTCATTTTTTTCCAA
Found at i:44258141 original size:11 final size:11
Alignment explanation
Indices: 44258102--44258155 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
44258092 GCCTCTCACT
44258102 TTTCTTTCTCA
1 TTTCTTTCTCA
*
44258113 TTTTTTTCTCA
1 TTTCTTTCTCA
* *
44258124 TTCCTTTCTTA
1 TTTCTTTCTCA
44258135 TTTCTTT-TCCA
1 TTTCTTTCT-CA
*
44258146 ATTCTTTCTC
1 TTTCTTTCTC
44258156 TTTTAATCAC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
10 1 0.03
11 32 0.94
12 1 0.03
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTCTTTCTCA
Found at i:44259787 original size:3 final size:3
Alignment explanation
Indices: 44259766--44259811 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
44259756 TATGATATTC
*
44259766 TAT T-T TAT TATT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44259811 T
1 T
44259812 TTGGAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:44260918 original size:49 final size:49
Alignment explanation
Indices: 44260838--44261553 Score: 446
Period size: 49 Copynumber: 14.7 Consensus size: 49
44260828 ACCATGTAGA
* * * * *
44260838 CATGGAGGGAAAGATTTAAGTCGCAACGGTGAACCTTTTACCTTAGAAG
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * * *
44260887 CATGAAGGGAAAGATTTAAGCCGCAATGGTGAATCC-AGTACC-AAGAAG
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCGAA-CCTTGTACCTCAGAAG
* * ** * *
44260935 ATATGGAGGGAAAGGCTTAAGTCGTAACGGCGAACCTTGTACCTCAGAAG
1 -CATGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* *
44260985 CATGAAGGGAAAGATTTAAG-CTGCAATGCCGAATCC-AGTA-C-CATGAAG
1 CATGAAGGGAAAGATTTAAGTC-GCAATGGCGAA-CCTTGTACCTCA-GAAG
* * *
44261033 ATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
1 -CATGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * *
44261083 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCC-AGTACCAC-GAAG
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCGAA-CCTTGTACCTCAGAAG
* * * * * * *
44261131 -ATATAGAGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTATCTCAG-GG
1 CAT-GA-AGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
** ** * * * *
44261180 ACATGAAGGGAAAGATTTAAGTCATAACAGCGAATCTAGTACCAC-TAAG
1 -CATGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * *
44261229 ATATGGAGGGAAAGA--T--GTCACAATGGCGAACCTTGTACCTCAGAAG
1 -CATGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * * * * *
44261275 CATAAAAGGGAAAGATTTAAG-CTGCGACGACGAATCC-AGTACCAC-GAAG
1 CAT-GAAGGGAAAGATTTAAGTC-GCAATGGCGAA-CCTTGTACCTCAGAAG
** * ** * *
44261324 ACACAAAGGGAAAGGTTTAAGTCGCAATGGAAAACCTTATACCTTAGAAG
1 -CATGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * * * * * *
44261374 CACGAAGGTAAAGGTTTAAGCCGTAATGGCGAGCCTTATACCTCAGAAG
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * * * * * *
44261423 CATAAAGGGAAAGATTTAAGCCGTAACGGCGAATCTAGTACCAC-GAAG
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
** * * *
44261471 ACACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCGGAAG
1 -CA-TGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
* * * *
44261522 CATGAA-AGAAAAATTTAAGCCGCAACGGCGAA
1 CATGAAGGGAAAGATTTAAGTCGCAATGGCGAA
44261554 TTTAGTACCA
Statistics
Matches: 513, Mismatches: 119, Indels: 71
0.73 0.17 0.10
Matches are distributed among these distances:
45 21 0.04
46 12 0.02
47 5 0.01
48 50 0.10
49 340 0.66
50 75 0.15
51 10 0.02
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (49 bp):
CATGAAGGGAAAGATTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG
Found at i:44260993 original size:98 final size:98
Alignment explanation
Indices: 44260824--44261405 Score: 661
Period size: 98 Copynumber: 6.0 Consensus size: 98
44260814 CTACAGGTCT
* * * * * * *
44260824 CAGTACCATGTAGACATGGAGGGAAAGATTTAAGTCGCAACGGTGAACCTTTTACCTTAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* *
44260889 TGAAGGGAAAGATTTAAGCCGCAATGGTGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * *
44260922 CAGTACCAAGAAGATATGGAGGGAAAGGCTTAAGTCGTAACGGCGAACCTTGTACCTCAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* * *
44260987 TGAAGGGAAAGATTTAAGCTGCAATGCCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* *
44261020 CAGTACCATGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
*
44261085 TGAAGGGAAAGATTTAAGTCGCAACGGCGAATC
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
44261118 CAGTACCACGAAGATATAGAGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTATCTCAG-GGAC
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-C
* ** *
44261182 ATGAAGGGAAAGATTTAAGTCATAACAGCGAATC
65 ATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* * * * *
44261216 TAGTACCACTAAGATATGGAGGGAAA-G---ATGTCACAATGGCGAACCTTGTACCTCAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* * * *
44261277 TAAAAGGGAAAGATTTAAGCTGCGACGACGAATC
66 T-GAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* *** * ** * *
44261311 CAGTACCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGAAAACCTTATACCTTAGAAGCA
1 CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
* * * * *
44261376 CGAAGGTAAAGGTTTAAGCCGTAATGGCGA
66 TGAAGGGAAAGATTTAAGCCGCAACGGCGA
44261406 GCCTTATACC
Statistics
Matches: 408, Mismatches: 69, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
94 26 0.06
95 45 0.11
96 1 0.00
97 2 0.00
98 306 0.75
99 28 0.07
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (98 bp):
CAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA
TGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
Found at i:44261093 original size:147 final size:148
Alignment explanation
Indices: 44260883--44261553 Score: 550
Period size: 147 Copynumber: 4.6 Consensus size: 148
44260873 TTTTACCTTA
* * * * * * * *
44260883 GAAG-CATGAAGGGAAAGATTTAAGCCGCAATGGTGAATCC-AGTACC-AAGAAGATATGGAGGG
1 GAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAA-CCTTGTACCTCAGAAG-CATGAAGGG
* * *
44260945 AAAGGCTTAAGTCGTAACGGCGAACCTTGTACCTCAGAAGCAT-GAAGGGAAAGATTTAAGCTGC
64 AAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAAAAGGGAAAGATTTAAGCTGC
* * *
44261009 AATGCCGAATCCAGTACCAT
129 AACGACGAATCCAGTACCAC
* **
44261029 GAAGATATGGAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAA
1 GAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAA
* * * * *
44261094 AGATTTAAGTCGCAACGGCGAATCC-AGTACCAC-GAAG-ATATAGAGGGAAAGGTTTAAG-TCG
66 AGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGAAGCATA-AAAGGGAAAGATTTAAGCT-G
* *
44261155 CAACGAC-AAACCTTGTATCTCA-
128 CAACGACGAATCC-AGTA-C-CAC
* * * ** ** * * * * * *
44261177 G-GGACATGAAGGGAAAGATTTAAGTCATAACAGCGAATCTAGTACCAC-TAAGATATGGAGGGA
1 GAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAG-CATGAAGGGA
* * * *
44261240 AA-G---ATGTCACAATGGCGAACCTTGTACCTCAGAAGCATAAAAGGGAAAGATTTAAGCTGCG
65 AAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAAAAGGGAAAGATTTAAGCTGCA
44261301 ACGACGAATCCAGTACCAC
130 ACGACGAATCCAGTACCAC
* ** * * * *
44261320 GAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGAAAACCTTATACCTTAGAAGCACGAAGGTAA
1 GAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAA
* * * * * * *
44261385 AGGTTTAAGCCGTAATGGCGAGCCTTATACCTCAGAAGCAT-AAAGGGAAAGATTTAAGCCGTAA
66 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAAAAGGGAAAGATTTAAGCTGCAA
* *
44261449 CGGCGAATCTAGTACCAC
131 CGACGAATCCAGTACCAC
* * * *
44261467 GAAGACACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCGGAAGCATGAA-AGA
1 GAAGACA-TAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGA
** *
44261531 AAAATTTAAGCCGCAACGGCGAA
65 AAGGTTTAAGTCGCAACGGCGAA
44261554 TTTAGTACCA
Statistics
Matches: 411, Mismatches: 90, Indels: 47
0.75 0.16 0.09
Matches are distributed among these distances:
142 4 0.01
143 21 0.05
144 69 0.17
145 14 0.03
146 18 0.04
147 198 0.48
148 85 0.21
149 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (148 bp):
GAAGACATAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTACCTCAGAAGCATGAAGGGAA
AGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATAAAAGGGAAAGATTTAAGCTGCAA
CGACGAATCCAGTACCAC
Found at i:44261501 original size:99 final size:98
Alignment explanation
Indices: 44261378--44261563 Score: 275
Period size: 99 Copynumber: 1.9 Consensus size: 98
44261368 TAGAAGCACG
* * * *
44261378 AAGGTAAAGGTTTAAGCCGTAATGGCGAGCCTTATACCTCAGAAGCAT-AAAGGGAAAGATTTAA
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCAGAAGCATGAAA--GAAAAATTTAA
*
44261442 GCCGTAACGGCGAATCTAGTACCACGAAGACACAA
64 GCCGCAACGGCGAATCTAGTACCACGAAGACACAA
* *
44261477 AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCGGAAGCATGAAAGAAAAATTTAAGC
1 AAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCAGAAGCATGAAAGAAAAATTTAAGC
*
44261542 CGCAACGGCGAATTTAGTACCA
66 CGCAACGGCGAATCTAGTACCA
44261564 TGCAGATTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
98 32 0.41
99 43 0.55
100 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (98 bp):
AAGGGAAAGGTTTAAGCCGCAATGGCGAACCTTATACCTCAGAAGCATGAAAGAAAAATTTAAGC
CGCAACGGCGAATCTAGTACCACGAAGACACAA
Found at i:44262007 original size:11 final size:11
Alignment explanation
Indices: 44261977--44262056 Score: 52
Period size: 12 Copynumber: 6.7 Consensus size: 11
44261967 ACTTTTGATT
* *
44261977 TTAAATTTATA
1 TTAATTTTAAA
*
44261988 TTAAGTTTAAA
1 TTAATTTTAAA
*
44261999 TTGATTTTAAA
1 TTAATTTTAAA
44262010 TTAATTTTTAAAAA
1 TTAA-TTTT--AAA
*
44262024 TTTAAATTTAAA
1 -TTAATTTTAAA
*
44262036 TTTATTTTTAAA
1 -TTAATTTTAAA
44262048 TTTAATTTT
1 -TTAATTTT
44262057 TGTTTAAATT
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
11 21 0.38
12 25 0.45
14 6 0.11
15 4 0.07
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (11 bp):
TTAATTTTAAA
Found at i:44262020 original size:12 final size:12
Alignment explanation
Indices: 44261993--44262057 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
44261983 TTATATTAAG
*
44261993 TTTAAATTGA-T
1 TTTAAATTAATT
44262004 TTTAAATTAATT
1 TTTAAATTAATT
*
44262016 TTTAAAAATTTAA-A
1 TTT--AAA-TTAATT
*
44262030 TTTAAATTTATT
1 TTTAAATTAATT
44262042 TTTAAATTTAATT
1 TTTAAA-TTAATT
44262055 TTT
1 TTT
44262058 GTTTAAATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
11 12 0.28
12 13 0.30
13 8 0.19
14 6 0.14
15 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTTAAATTAATT
Found at i:44262047 original size:18 final size:17
Alignment explanation
Indices: 44262024--44262067 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
44262014 TTTTTAAAAA
44262024 TTTAAATTTAAATTTATT-
1 TTTAAATTT-AATTT-TTG
44262042 TTTAAATTTAATTTTTG
1 TTTAAATTTAATTTTTG
44262059 TTTAAATTT
1 TTTAAATTT
44262068 GAAACGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.08
17 14 0.56
18 9 0.36
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTAAATTTAATTTTTG
Found at i:44262344 original size:18 final size:19
Alignment explanation
Indices: 44262317--44262361 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
44262307 CATGCTGCCA
* *
44262317 CGTCAGCATCAACAGCC-C
1 CGTCACCATCAACAACCAC
*
44262335 CGTCACCATCATCAACCAC
1 CGTCACCATCAACAACCAC
44262354 CGTCACCA
1 CGTCACCA
44262362 GCAAGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.29, C:0.47, G:0.11, T:0.13
Consensus pattern (19 bp):
CGTCACCATCAACAACCAC
Found at i:44264029 original size:29 final size:28
Alignment explanation
Indices: 44263995--44264398 Score: 177
Period size: 29 Copynumber: 13.9 Consensus size: 28
44263985 TAAACTGTCT
*
44263995 AAAAATTACATTTTGAGCTCGAACTTTCC
1 AAAAATTACATTTT-ACCTCGAACTTTCC
*
44264024 AAAAATTACATTTTAGCC-C-AAATTTCC
1 AAAAATTACATTTTA-CCTCGAACTTTCC
* *
44264051 AAAAATTCCATTTTAGCC-C-AATTTTTCC
1 AAAAATTACATTTTA-CCTCGAA-CTTTCC
*
44264079 AAAAATTACCATTTTACCTCGAAC-TCCC
1 AAAAATTA-CATTTTACCTCGAACTTTCC
* * *
44264107 AAAAAATCCATTTTGACCTC-AATTTTTCC
1 AAAAATTACATTTT-ACCTCGAA-CTTTCC
* *
44264136 AAAAATTACCATTTTACCCCCGAAC-TTCA
1 AAAAATTA-CATTTTA-CCTCGAACTTTCC
* * * *
44264165 AAAAATTCCATTTTTGACGT-TAATTTTTCC
1 AAAAATTACA-TTTT-ACCTCGAA-CTTTCC
*
44264195 AAAAATTACCATTTTACCCCTTGAAC-TTCC
1 AAAAATTA-CATTTTA--CCTCGAACTTTCC
* *
44264225 AAAAATTCCATTATTGACCTCGAACTTTCT
1 AAAAATTACATT-TT-ACCTCGAACTTTCC
* * *
44264255 AAAAATTACCGTTTTCCCCCGAAC-TTCC
1 AAAAATTA-CATTTTACCTCGAACTTTCC
* * * * * *
44264283 AAAGATTTCATTGTTGATCCT-AAAATATCT
1 AAAAATTACATT-TT-A-CCTCGAACTTTCC
* *
44264313 AAAAATTACCATTTTACCCCCATAC-TTCC
1 AAAAATTA-CATTTTACCTCGA-ACTTTCC
* * *
44264342 AAAAATTCCATTTTTGACC-CTAAATTTCC
1 AAAAATTACA-TTTT-ACCTCGAACTTTCC
*
44264371 TAGAAATTACCATTTTACCCTCGAACTT
1 -AAAAATTA-CATTTTA-CCTCGAACTT
44264399 CTAAAGATTC
Statistics
Matches: 281, Mismatches: 57, Indels: 72
0.69 0.14 0.18
Matches are distributed among these distances:
27 38 0.14
28 50 0.18
29 91 0.32
30 79 0.28
31 21 0.07
32 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.35
Consensus pattern (28 bp):
AAAAATTACATTTTACCTCGAACTTTCC
Found at i:44264209 original size:59 final size:59
Alignment explanation
Indices: 44264019--44264419 Score: 410
Period size: 59 Copynumber: 6.9 Consensus size: 59
44264009 GAGCTCGAAC
* * * *
44264019 TTTCCAAAAATTA-CATTTTA-GCCCAAATTTCCAAAAATTCCATTTTAG-CCC-AATT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCTAATT
* * *
44264074 TTTCCAAAAATTACCATTTTA-CCTCGAACTCCCAAAAAATCCA-TTTTGA-CCTCAATT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCT-AATT
* **
44264131 TTTCCAAAAATTACCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTGACGTTAATT
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCTAATT
* * * *
44264190 TTTCCAAAAATTACCATTTTACCCCTTGAACTTCCAAAAATTCCATTATTGACCTCGAA-C
1 TTTCCAAAAATTACCATTTTACCCC-CGAACTTCCAAAAATTCCATTTTTGACC-CTAATT
* * * * * * **
44264250 TTTCTAAAAATTACCGTTTT-CCCCCGAACTTCCAAAGATTTCATTGTTGATCCTAAAA
1 TTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCTAATT
* * *
44264308 TATCTAAAAATTACCATTTTACCCCC-ATACTTCCAAAAATTCCATTTTTGACCCTAA-A
1 TTTCCAAAAATTACCATTTTACCCCCGA-ACTTCCAAAAATTCCATTTTTGACCCTAATT
* * * * *
44264366 TTTCCTAGAAATTACCATTTTACCCTCGAACTTCTAAAGATTCTATTTTTGACC
1 TTTCC-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACC
44264420 TCGAAGTGTC
Statistics
Matches: 290, Mismatches: 42, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
55 19 0.07
56 23 0.08
57 28 0.10
58 64 0.22
59 110 0.38
60 44 0.15
61 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (59 bp):
TTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCTAATT
Found at i:44264278 original size:118 final size:116
Alignment explanation
Indices: 44263995--44264420 Score: 454
Period size: 118 Copynumber: 3.7 Consensus size: 116
44263985 TAAACTGTCT
* * * * *
44263995 AAAAATTACATTTTGAGCTCGAACTTTCCAAAAATTA-CATTTTA-GCCCAAATTTCCAAAAATT
1 AAAAATTCCATTTTGACCTCGAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATT
* * * *
44264058 CCATTTTAG-CCCAATTTTTCCAAAAATTACCATTTTACCTC-GAACTCCC
66 CCATTTTTGACCTAATTTTTCCAAAAATTACCATTTTACCCCTGAACTTCC
* * *
44264107 AAAAAATCCATTTTGACCTC-AATTTTTCCAAAAATTACCATTTTACCCCCGAACTTCAAAAAAT
1 AAAAATTCCATTTTGACCTCGAA-CTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT
*
44264171 TCCATTTTTGACGTTAATTTTTCCAAAAATTACCATTTTACCCCTTGAACTTCC
65 TCCATTTTTGAC-CTAATTTTTCCAAAAATTACCATTTTACCCC-TGAACTTCC
* * *
44264225 AAAAATTCCATTATTGACCTCGAACTTTCTAAAAATTACCGTTTT-CCCCCGAACTTCCAAAGAT
1 AAAAATTCCATT-TTGACCTCGAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAAT
* * ** * * *
44264289 TTCATTGTTGATCCTAAAATATCTAAAAATTACCATTTTACCCC-CATACTTCC
65 TCCATTTTTGA-CCTAATTTTTCCAAAAATTACCATTTTACCCCTGA-ACTTCC
* * * * * *
44264342 AAAAATTCCATTTTTGACC-CTAAATTTCCTAGAAATTACCATTTTACCCTCGAACTTCTAAAGA
1 AAAAATTCCA-TTTTGACCTCGAACTTTCC-AAAAATTACCATTTTACCCCCGAACTTCCAAAAA
*
44264406 TTCTATTTTTGACCT
64 TTCCATTTTTGACCT
44264421 CGAAGTGTCA
Statistics
Matches: 263, Mismatches: 37, Indels: 23
0.81 0.11 0.07
Matches are distributed among these distances:
111 2 0.01
112 30 0.11
113 7 0.03
114 23 0.09
115 1 0.00
116 36 0.14
117 38 0.14
118 97 0.37
119 27 0.10
120 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (116 bp):
AAAAATTCCATTTTGACCTCGAACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATT
CCATTTTTGACCTAATTTTTCCAAAAATTACCATTTTACCCCTGAACTTCC
Found at i:44268204 original size:41 final size:41
Alignment explanation
Indices: 44268156--44268397 Score: 227
Period size: 41 Copynumber: 5.9 Consensus size: 41
44268146 GAAAAACATT
* * * *
44268156 GCTAATGCTCTTACTTTTAGCGGCGCTGT-TTAATAAACGTC
1 GCTAATGCTCTGACCTTTAGCGGCGCT-TACTAATAAACGCC
* *
44268197 GCTAATGCTCTGACCTTTAGCGGCACTTACTCATAAACGCC
1 GCTAATGCTCTGACCTTTAGCGGCGCTTACTAATAAACGCC
* * * * * *
44268238 GCTAATTCTCTGATCTTTAGCAGCGCTT-TTCCATAAACACC
1 GCTAATGCTCTGACCTTTAGCGGCGCTTACT-AATAAACGCC
* * * * *
44268279 GCTAATGCACTAACCTTTAGCGGCGCTTCCTAAAAAACGTC
1 GCTAATGCTCTGACCTTTAGCGGCGCTTACTAATAAACGCC
* * *
44268320 GCTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAACGCT
1 GCTAATGCTCTGACCTTTAGCGGCGCTTACTAATAAACGCC
* * * * *
44268361 GCTAATGATTTGACCTTTAGCGGTGCTTCCTCATAAA
1 GCTAATGCTCTGACCTTTAGCGGCGCTTACTAATAAA
44268398 TGTTGCTATT
Statistics
Matches: 167, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
40 2 0.01
41 164 0.98
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (41 bp):
GCTAATGCTCTGACCTTTAGCGGCGCTTACTAATAAACGCC
Found at i:44268257 original size:82 final size:80
Alignment explanation
Indices: 44268156--44268397 Score: 268
Period size: 82 Copynumber: 3.0 Consensus size: 80
44268146 GAAAAACATT
* * *
44268156 GCTAATGCTCTTACTTTTAGCGGCGCTGTTTAATAAACGTCGCTAATGCTCTGACCTTTAGCGGC
1 GCTAATGCTCTGACCTTTAGCGGCGCT-TTTCATAAACG-CGCTAATGCTCTGACCTTTAGCGGC
* *
44268221 ACTTACTCATAAACGCC
64 GCTTCCTCATAAACGCC
* * * * * *
44268238 GCTAATTCTCTGATCTTTAGCAGCGCTTTTCCATAAACACCGCTAATGCACTAACCTTTAGCGGC
1 GCTAATGCTCTGACCTTTAGCGGCGCTTTT-CATAAAC-GCGCTAATGCTCTGACCTTTAGCGGC
* * *
44268303 GCTTCCTAAAAAACGTC
64 GCTTCCTCATAAACGCC
* * * *
44268320 GCTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAACGCTGCTAATGATTTGACCTTTAGCGGT
1 GCTAATGCTCTGACCTTTAGCGGCGCTT-TTCATAAACGC-GCTAATGCTCTGACCTTTAGCGGC
44268385 GCTTCCTCATAAA
64 GCTTCCTCATAAA
44268398 TGTTGCTATT
Statistics
Matches: 130, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
81 4 0.03
82 125 0.96
83 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (80 bp):
GCTAATGCTCTGACCTTTAGCGGCGCTTTTCATAAACGCGCTAATGCTCTGACCTTTAGCGGCGC
TTCCTCATAAACGCC
Found at i:44268379 original size:123 final size:123
Alignment explanation
Indices: 44268156--44268381 Score: 328
Period size: 123 Copynumber: 1.8 Consensus size: 123
44268146 GAAAAACATT
* * * * *
44268156 GCTAATGCTCTTACTTTTAGCGGCGCTGTTTAATAAACGTCGCTAATGCTCTGACCTTTAGCGGC
1 GCTAATGCACTAACCTTTAGCGGCGCTGTCTAAAAAACGTCGCTAATGCTCTGACCTTTAGCGGC
** *
44268221 ACTTACTCATAAACGCCGCTAATTCTCTGATCTTTAGCAGCGCTTTTCCATAAACACC
66 ACTTACTCATAAACGCCGCTAATGATCTGACCTTTAGCAGCGCTTTTCCATAAACACC
44268279 GCTAATGCACTAACCTTTAGCGGCGCT-TCCTAAAAAACGTCGCTAATGCTCTGACCTTTAGCGG
1 GCTAATGCACTAACCTTTAGCGGCGCTGT-CTAAAAAACGTCGCTAATGCTCTGACCTTTAGCGG
* * * *
44268343 CGCTTCCTCATAAACGCTGCTAATGATTTGACCTTTAGC
65 CACTTACTCATAAACGCCGCTAATGATCTGACCTTTAGC
44268382 GGTGCTTCCT
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
122 1 0.01
123 89 0.99
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (123 bp):
GCTAATGCACTAACCTTTAGCGGCGCTGTCTAAAAAACGTCGCTAATGCTCTGACCTTTAGCGGC
ACTTACTCATAAACGCCGCTAATGATCTGACCTTTAGCAGCGCTTTTCCATAAACACC
Found at i:44275572 original size:162 final size:162
Alignment explanation
Indices: 44275316--44275875 Score: 757
Period size: 162 Copynumber: 3.5 Consensus size: 162
44275306 GGGTTATAAG
* * ** * *
44275316 TTCCAATTTCGAGCAACTCTTTATCTTCAAAGTATGCAATTGCCCAAGAGGATTAGCAGCAGACC
1 TTCCAATTGCAAGCAACTCTTTATCTTCAAAGTATGCAATTGCCCAAGACTATTAGCAACAGACA
*
44275381 GTGAGAAGAGATACTTTAAATTATCGCATTTTTCAACTTTTACTTCCCTTAAACTTTGGAGGCTT
66 GTGGGAAGAGATACTTTAAATTATCGCATTTTTCAACTTTTACTTCCCTTAAACTTTGGAGGCTT
*
44275446 ATGTATGGCATTTGTGGGTCTTGGATTATGTC
131 AAGTATGGCATTTGTGGGTCTTGGATTATGTC
* *
44275478 TTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATGCAATTGTCCAAGACTATTAGCAACAGACA
1 TTCCAATTGCAAGCAACTCTTTATCTTCAAAGTATGCAATTGCCCAAGACTATTAGCAACAGACA
* *
44275543 GTGGGAAGAGATACTTTAAATTGTCGCATTTTTCAACTTTTACTTCCCATAAACTTTGGAGGCTT
66 GTGGGAAGAGATACTTTAAATTATCGCATTTTTCAACTTTTACTTCCCTTAAACTTTGGAGGCTT
* *
44275608 ACGTATGGCACTTGTGGG-CTTTGGATTATGTC
131 AAGTATGGCATTTGTGGGTC-TTGGATTATGTC
* *
44275640 TTCCAATTGCAAGCAACTCTTTATCTCCAAAGTATGCAATTGCCCAAGACCATTAGCAACAGACA
1 TTCCAATTGCAAGCAACTCTTTATCTTCAAAGTATGCAATTGCCCAAGACTATTAGCAACAGACA
** * * * * * *
44275705 GACGAAAGAGATGCTTCAAATTATCGCATTTTTCAACTTTTACATCCTTTAAACTTTGGAGTCTT
66 GTGGGAAGAGATACTTTAAATTATCGCATTTTTCAACTTTTACTTCCCTTAAACTTTGGAGGCTT
* *
44275770 AAGT-TCGGC-TCTTGTGAGTCTTGGATTATTTC
131 AAGTAT-GGCAT-TTGTGGGTCTTGGATTATGTC
* * * * ** * *
44275802 TACCAATTGCAAGCAGCTCTTTATTTTCAAAGTATGCAATTTCCCAAGGTTGTTAGCAACAGATA
1 TTCCAATTGCAAGCAACTCTTTATCTTCAAAGTATGCAATTGCCCAAGACTATTAGCAACAGACA
*
44275867 TTGGGAAGA
66 GTGGGAAGA
44275876 TATATTTCAA
Statistics
Matches: 351, Mismatches: 43, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
161 2 0.01
162 348 0.99
163 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (162 bp):
TTCCAATTGCAAGCAACTCTTTATCTTCAAAGTATGCAATTGCCCAAGACTATTAGCAACAGACA
GTGGGAAGAGATACTTTAAATTATCGCATTTTTCAACTTTTACTTCCCTTAAACTTTGGAGGCTT
AAGTATGGCATTTGTGGGTCTTGGATTATGTC
Found at i:44279735 original size:21 final size:20
Alignment explanation
Indices: 44279682--44279742 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
44279672 TTTATTTAAT
* *
44279682 TTTTTTAAATTTAAAAAATA
1 TTTTTTATATTTTAAAAATA
*
44279702 TTTTTTATATTTTTAAAATA
1 TTTTTTATATTTTAAAAATA
*
44279722 TTTTTTCATTTTTTAAAAATA
1 TTTTTT-ATATTTTAAAAATA
44279743 ATTCTTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTATATTTTAAAAATA
Found at i:44294117 original size:21 final size:22
Alignment explanation
Indices: 44294093--44294136 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
44294083 GTGATCTGGG
*
44294093 AAAAAATAAAAATAAA-AGAAA
1 AAAAAATAAAAAGAAATAGAAA
*
44294114 AAAAAATTAAAAGAAATAGAAA
1 AAAAAATAAAAAGAAATAGAAA
44294136 A
1 A
44294137 TAGGAGTGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (22 bp):
AAAAAATAAAAAGAAATAGAAA
Found at i:44294119 original size:16 final size:17
Alignment explanation
Indices: 44294094--44294129 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
44294084 TGATCTGGGA
44294094 AAAAATAAAAATAAAAG
1 AAAAATAAAAATAAAAG
*
44294111 AAAAA-AAAATTAAAAG
1 AAAAATAAAAATAAAAG
44294127 AAA
1 AAA
44294130 TAGAAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAATAAAAATAAAAG
Found at i:44301567 original size:12 final size:12
Alignment explanation
Indices: 44301546--44301574 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
44301536 GAGATGAAGG
44301546 TTTT-GGAGTGT
1 TTTTGGGAGTGT
44301557 TTTTGGGAGTGT
1 TTTTGGGAGTGT
44301569 TTTTGG
1 TTTTGG
44301575 ATGCACGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.07, C:0.00, G:0.38, T:0.55
Consensus pattern (12 bp):
TTTTGGGAGTGT
Found at i:44315558 original size:16 final size:17
Alignment explanation
Indices: 44315537--44315575 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
44315527 CTTTTTTTAG
44315537 TTTTTTATA-TATTGAT-
1 TTTTTTATATTATT-ATA
44315553 TTTTTTATATTATTATA
1 TTTTTTATATTATTATA
44315570 TTTTTT
1 TTTTTT
44315576 GTCAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTATATTATTATA
Found at i:44315902 original size:22 final size:22
Alignment explanation
Indices: 44315861--44315908 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
44315851 ATTAAAATAC
*
44315861 ATATTTTTATATTAATATTTAT
1 ATATTTTTATATTAATATTTAA
*
44315883 ATATTTTTATAATTCA-ATTTAA
1 ATATTTTTAT-ATTAATATTTAA
44315905 ATAT
1 ATAT
44315909 AATATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTATATTAATATTTAA
Found at i:44316169 original size:1 final size:1
Alignment explanation
Indices: 44316165--44316193 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
44316155 TTTTGTCTTG
44316165 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
44316194 GAAATCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:44318901 original size:162 final size:162
Alignment explanation
Indices: 44318678--44318985 Score: 492
Period size: 162 Copynumber: 1.9 Consensus size: 162
44318668 TCAAAGTTTC
*
44318678 CAATTGCCCAAGACTATTAGCAACACACATTGGAAAAAGATATTTCAAATTATTGCATTCTGCAA
1 CAATTGCCCAAGACTATTAGCAACACACATTGGAAAAAGATATTTCAAATTATAGCATTCTGCAA
* *
44318743 CTTGTACTTCCCTTAAGCATTGGAAGCTTATGCTTGATACTTG-TGGATCTTGAATTATTTCTTT
66 CTTGTACTTCCCTTAAGAATTGGAAGCTTATGCTTGATACTTGTTGG-TCTTGAATTATTTCTTC
44318807 CAATCCAAAGCACCTCTTTATTTTCAGAGCTTG
130 CAATCCAAAGCACCTCTTTATTTTCAGAGCTTG
* * * * *
44318840 CAATTGCCCAAGGCTATTAGCAACACACATTGGGAAGAGATATTTCAATTTATAGCATTCTGTAA
1 CAATTGCCCAAGACTATTAGCAACACACATTGGAAAAAGATATTTCAAATTATAGCATTCTGCAA
* * * *
44318905 CTTGTACTTCCCTTACGAATTGGAAGCTTATGTTTGGTACTTGTTGGTCTTGGATTATTTCTTCC
66 CTTGTACTTCCCTTAAGAATTGGAAGCTTATGCTTGATACTTGTTGGTCTTGAATTATTTCTTCC
44318970 AATCCAAAGCACCTCT
131 AATCCAAAGCACCTCT
44318986 CTATCTTTAG
Statistics
Matches: 133, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
162 130 0.98
163 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (162 bp):
CAATTGCCCAAGACTATTAGCAACACACATTGGAAAAAGATATTTCAAATTATAGCATTCTGCAA
CTTGTACTTCCCTTAAGAATTGGAAGCTTATGCTTGATACTTGTTGGTCTTGAATTATTTCTTCC
AATCCAAAGCACCTCTTTATTTTCAGAGCTTG
Found at i:44325014 original size:42 final size:42
Alignment explanation
Indices: 44324955--44325037 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
44324945 GAATCCTTCA
44324955 ATTGAATTTTTGTTATTTTTGTCCCAATCCCTTTCTTTGTAG
1 ATTGAATTTTTGTTATTTTTGTCCCAATCCCTTTCTTTGTAG
44324997 ATTGAATTTTTGTTATTTTTGTCCCAATCCCTTTCTTTGTA
1 ATTGAATTTTTGTTATTTTTGTCCCAATCCCTTTCTTTGTA
44325038 TATCTGCGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (42 bp):
ATTGAATTTTTGTTATTTTTGTCCCAATCCCTTTCTTTGTAG
Found at i:44326900 original size:45 final size:44
Alignment explanation
Indices: 44326853--44327002 Score: 196
Period size: 43 Copynumber: 3.4 Consensus size: 44
44326843 GTAATGAACA
* *
44326853 TTTGCGGCTATTTTTGTTTGAGTAAATGTCGCATATGTGTGCACAT
1 TTTGCTGCTGTTTTTG-TTGAGTAAATGTCGCA-ATGTGTGCACAT
*
44326899 TTTGCTGCTGTTTTTATTGAGTAAATGTCGC-ATGTGTGCACAT
1 TTTGCTGCTGTTTTTGTTGAGTAAATGTCGCAATGTGTGCACAT
* *
44326942 TTTGTTGCTGTTTTTGTTGAGTAAAATGCCGCAAATGTGTGCACA-
1 TTTGCTGCTGTTTTTGTTGAGT-AAATGTCGC-AATGTGTGCACAT
*
44326987 TTTGCTGCTGCTTTTG
1 TTTGCTGCTGTTTTTG
44327003 GATGAGTTTA
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
43 32 0.34
44 8 0.09
45 29 0.31
46 24 0.26
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (44 bp):
TTTGCTGCTGTTTTTGTTGAGTAAATGTCGCAATGTGTGCACAT
Found at i:44334686 original size:25 final size:24
Alignment explanation
Indices: 44334622--44334687 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 24
44334612 ATGGGAGTAA
*
44334622 CATCTGATTATGTATCTAAAATTG
1 CATCTGATTTTGTATCTAAAATTG
44334646 CATCTGATTTTGTATCTAAAATTGG
1 CATCTGATTTTGTATCTAAAATT-G
*
44334671 CATTTGTATTTT-TATCT
1 CATCTG-ATTTTGTATCT
44334688 GTTTGGTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 22 0.58
25 11 0.29
26 5 0.13
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (24 bp):
CATCTGATTTTGTATCTAAAATTG
Found at i:44336967 original size:18 final size:19
Alignment explanation
Indices: 44336938--44336983 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
44336928 TTATATAAAT
*
44336938 TTTTCTATTTTTTTAAATAA
1 TTTT-TATTTTTTAAAATAA
44336958 TTTTTATTTTTTAAAATAA
1 TTTTTATTTTTTAAAATAA
44336977 TTTTTAT
1 TTTTTAT
44336984 AAAATTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTATTTTTTAAAATAA
Found at i:44348280 original size:18 final size:18
Alignment explanation
Indices: 44348254--44348288 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44348244 CACATTAAGT
*
44348254 AACATAATTAAGTCATTC
1 AACACAATTAAGTCATTC
*
44348272 AACACAATTTAGTCATT
1 AACACAATTAAGTCATT
44348289 TTAGGGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (18 bp):
AACACAATTAAGTCATTC
Found at i:44358537 original size:40 final size:40
Alignment explanation
Indices: 44358430--44358543 Score: 165
Period size: 40 Copynumber: 2.9 Consensus size: 40
44358420 TTTGGATAGA
* * * * *
44358430 AAACGCCGCAAAAGATAAATCAATAGCAACGTTTTTTCAT
1 AAACGCCACAAAAGGTAAAGCAATAGCGACGTTTTTCCAT
*
44358470 AAACACCACAAAAGGTAAAGCAATAGCGACGTTTTTCCAT
1 AAACGCCACAAAAGGTAAAGCAATAGCGACGTTTTTCCAT
*
44358510 AAACGCCACAAAAGGTAAAGCAATAGCGGCGTTT
1 AAACGCCACAAAAGGTAAAGCAATAGCGACGTTT
44358544 ATAGAAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (40 bp):
AAACGCCACAAAAGGTAAAGCAATAGCGACGTTTTTCCAT
Found at i:44358613 original size:41 final size:41
Alignment explanation
Indices: 44358555--44358696 Score: 187
Period size: 41 Copynumber: 3.5 Consensus size: 41
44358545 TAGAAAAAAT
* *
44358555 GCCGCTAAATGTTAGAGCATTAGTGGCGCTTATGGGAAAGC
1 GCCGCTAAAGGTTAGAGCATTAGCGGCGCTTATGGGAAAGC
* *
44358596 ACCGCTAAAGATTAGAGCATTAGCGGCGCTTATGGGAAAGC
1 GCCGCTAAAGGTTAGAGCATTAGCGGCGCTTATGGGAAAGC
* * * * *
44358637 GTCGCTAAAGGTCAGAGCATTAGCGACGATTATGGGGAAAAC
1 GCCGCTAAAGGTTAGAGCATTAGCGGCGCTTAT-GGGAAAGC
44358679 GCCGCTAAAGGTTA-AGCA
1 GCCGCTAAAGGTTAGAGCA
44358697 AACGTTGCTA
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 68 0.78
42 19 0.22
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.20
Consensus pattern (41 bp):
GCCGCTAAAGGTTAGAGCATTAGCGGCGCTTATGGGAAAGC
Found at i:44358688 original size:42 final size:41
Alignment explanation
Indices: 44358510--44358696 Score: 180
Period size: 41 Copynumber: 4.6 Consensus size: 41
44358500 GTTTTTCCAT
* * * * * **
44358510 AAACGCCACAAAAGG-TAAAGCAATAGCGGCGTTTATAGAAA
1 AAACGCCGCTAAAGGTTAGAGCATTAGCGGCGCTTAT-GGGA
* * *
44358551 AAATGCCGCTAAATGTTAGAGCATTAGTGGCGCTTATGGGA
1 AAACGCCGCTAAAGGTTAGAGCATTAGCGGCGCTTATGGGA
* * *
44358592 AAGCACCGCTAAAGATTAGAGCATTAGCGGCGCTTATGGGA
1 AAACGCCGCTAAAGGTTAGAGCATTAGCGGCGCTTATGGGA
* * * * *
44358633 AAGCGTCGCTAAAGGTCAGAGCATTAGCGACGATTATGGGGA
1 AAACGCCGCTAAAGGTTAGAGCATTAGCGGCGCTTAT-GGGA
44358675 AAACGCCGCTAAAGGTTA-AGCA
1 AAACGCCGCTAAAGGTTAGAGCA
44358697 AACGTTGCTA
Statistics
Matches: 119, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 83 0.70
42 36 0.30
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (41 bp):
AAACGCCGCTAAAGGTTAGAGCATTAGCGGCGCTTATGGGA
Found at i:44359179 original size:42 final size:42
Alignment explanation
Indices: 44359036--44359233 Score: 207
Period size: 42 Copynumber: 4.7 Consensus size: 42
44359026 CATGCATCAT
* * * * ** * *
44359036 CTAAAGAACATGATCTTTAGCGGCGTTTGTGAGGGAAGTGCCA
1 CTAAAGACCATGTTCTATAGCGGCGTTTATG-GAAAAGCGCCG
* * * *
44359079 CTAAAGACCATGTTCTTTAGCGGCGTTTGTGTGGAAAGTGCCG
1 CTAAAGACCATGTTCTATAGCGGCGTTTATG-GAAAAGCGCCG
* **
44359122 CTAAAGATCATGTTCTATAGCGGCGTTTATGGAAAAGCATCG
1 CTAAAGACCATGTTCTATAGCGGCGTTTATGGAAAAGCGCCG
* * *
44359164 CTAAAGACCATGTTCTATAGCGACATTTATGGAAAAGCGCCA
1 CTAAAGACCATGTTCTATAGCGGCGTTTATGGAAAAGCGCCG
*
44359206 CTAAAGACCATGTTCTATATCGGCGTTT
1 CTAAAGACCATGTTCTATAGCGGCGTTT
44359234 TCCTCATAAA
Statistics
Matches: 134, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 68 0.51
43 66 0.49
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (42 bp):
CTAAAGACCATGTTCTATAGCGGCGTTTATGGAAAAGCGCCG
Found at i:44363237 original size:23 final size:23
Alignment explanation
Indices: 44363209--44363271 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
44363199 TAAAACTTAC
* *
44363209 ATATATGATTTTTTTATCAAAAT
1 ATATATGATTTTTTTATAAAAAA
*
44363232 ATATATGATTTTTATATAAAAAA
1 ATATATGATTTTTTTATAAAAAA
44363255 ATATAT-ATTATTTTTAT
1 ATATATGATT-TTTTTAT
44363272 TAATTTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 3 0.09
23 32 0.91
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (23 bp):
ATATATGATTTTTTTATAAAAAA
Found at i:44363255 original size:25 final size:24
Alignment explanation
Indices: 44363209--44363274 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 24
44363199 TAAAACTTAC
**
44363209 ATATATGATTTTT-TTATCAAAAT
1 ATATATGATTTTTATTAAAAAAAT
44363232 ATATATGATTTTTATATAAAAAAAT
1 ATATATGATTTTTAT-TAAAAAAAT
*
44363257 ATATATTATTTTTATTAA
1 ATATATGATTTTTATTAA
44363275 TTTATTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 13 0.34
24 4 0.11
25 21 0.55
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (24 bp):
ATATATGATTTTTATTAAAAAAAT
Found at i:44364333 original size:25 final size:24
Alignment explanation
Indices: 44364286--44364333 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
44364276 ATAATTATAA
*
44364286 ATAAAAAAAGACATTTAATTACTT
1 ATAAAAAAAGACATTTAAATACTT
44364310 ATAAAAATAAGA-ATTCTAAATACT
1 ATAAAAA-AAGACATT-TAAATACT
44364334 ATTACCCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.31
Consensus pattern (24 bp):
ATAAAAAAAGACATTTAAATACTT
Found at i:44371017 original size:20 final size:18
Alignment explanation
Indices: 44370969--44371017 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
44370959 TTGTTTTTGT
44370969 TTTTTATTTCATTAATTC
1 TTTTTATTTCATTAATTC
* *
44370987 TTTTTCTTTTCACTTATTTTC
1 TTTTT-ATTTCA-TTA-ATTC
44371008 TTTTTATTTC
1 TTTTTATTTC
44371018 TTCTGGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 5 0.20
19 5 0.20
20 7 0.28
21 8 0.32
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATTTCATTAATTC
Found at i:44374714 original size:162 final size:160
Alignment explanation
Indices: 44374284--44374789 Score: 624
Period size: 162 Copynumber: 3.1 Consensus size: 160
44374274 AACAGCTCCA
* * *
44374284 TATCTTCAGAGTTTGCAGTTGCCCAAGACTATTAGCAGCACACGTTGGGAAGAGATACTTCAAAT
1 TATCTTCAGAGTTCGCAATTGCCCAAGACTATTAGCAACACACGTTGGGAAGAGATACTTCAAAT
* * * *
44374349 TATTGCATTCTGTAACTTCTACTTTCCATAGCTCTTGGAAGCTTATGTTTGACACTCT-TGAGTT
66 TATTGCATTC-GTAACTTCTACTTTCCATAGC-CTTGAAAGCTTATGTTTGATA-TTTGTGAGTC
44374413 TTGGATTATTTCTTCCATACCAAAGCA-C-CTC
128 TTGGATTATTTCTTCCATACCAAAGCACCTCTC
* * * * *
44374444 TATCTTCAGAGTTCGCAATTTCCCAAGATTACTAGCGACACACGTTGGGAAGAGATACTTCAAAC
1 TATCTTCAGAGTTCGCAATTGCCCAAGACTATTAGCAACACACGTTGGGAAGAGATACTTCAAAT
* * * *
44374509 TATTGCATTTTGTAACTTCTACTTTCCATAGCCCTTAAAAGCTTATGTTTGATTTTTGTGGGTCT
66 TATTGCA-TTCGTAACTTCTACTTTCCATAG-CCTTGAAAGCTTATGTTTGATATTTGTGAGTCT
* *
44374574 TGAATTATTTCTTTCA-ATCCAAAGCACCTCTC
129 TGGATTATTTCTTCCATA-CCAAAGCACCTCTC
* * ** ** *
44374606 TATCTTCAAAGTTCGCAATCGCCCAAGACTATTAGCAACACACACTGAAAAGAGATATTTCAAAT
1 TATCTTCAGAGTTCGCAATTGCCCAAGACTATTAGCAACACACGTTGGGAAGAGATACTTCAAAT
* * * * *
44374671 TATTGCATTCGATAACTTGTACTTCCCTTAAGCATTGAAAGCTTATGTTTGATACTTGTGAGTCT
66 TATTGCATTCG-TAACTTCTACTTTCCAT-AGCCTTGAAAGCTTATGTTTGATATTTGTGAGTCT
44374736 TGGATTATTTCTTCCATACCAAAGCACCTCTC
129 TGGATTATTTCTTCCATACCAAAGCACCTCTC
*
44374768 TATCTTCAGTGTTCGCAGATTG
1 TATCTTCAGAGTTCGCA-ATTG
44374790 GCCGCCTTGA
Statistics
Matches: 292, Mismatches: 44, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
159 3 0.01
160 128 0.44
161 7 0.02
162 148 0.51
163 6 0.02
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (160 bp):
TATCTTCAGAGTTCGCAATTGCCCAAGACTATTAGCAACACACGTTGGGAAGAGATACTTCAAAT
TATTGCATTCGTAACTTCTACTTTCCATAGCCTTGAAAGCTTATGTTTGATATTTGTGAGTCTTG
GATTATTTCTTCCATACCAAAGCACCTCTC
Found at i:44376363 original size:162 final size:162
Alignment explanation
Indices: 44376046--44376584 Score: 956
Period size: 162 Copynumber: 3.3 Consensus size: 162
44376036 CCATTTGCTT
* * *
44376046 GCAATTCTTTATCTT-TAGAGTATGCAATTGCCCAAGGCCATTAGCAACGGACATTGGAAAGAGA
1 GCAATTCTTTATCTTCAAG-GTATGCAATTGCCCAAGGCTATTAGCAACAGACATTGGAAAGAGA
*
44376110 AACCTCAAATTATTGCATT-TTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCAC
65 AGCCTCAAATTATTGCATTCTTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCAC
44376174 TTGTGAGTCTTGGATTATGCCTTCCAAGCTGAA
130 TTGTGAGTCTTGGATTATGCCTTCCAAGCTGAA
* *
44376207 GCAATTCTTTAACTTCAAGGTATGCAACTGCCCAAGGCTATTAGCAACAGACATTGGAAAGAGAA
1 GCAATTCTTTATCTTCAAGGTATGCAATTGCCCAAGGCTATTAGCAACAGACATTGGAAAGAGAA
* *
44376272 GCCTCAAATTATTGCATTCTTCAACTTCTATTTCCCTTAAACTTTTGAGGCTTATGTATGGCAAT
66 GCCTCAAATTATTGCATTCTTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCACT
44376337 TGTGAGTCTTGGATTATGCCTTCCAAGCTGAA
131 TGTGAGTCTTGGATTATGCCTTCCAAGCTGAA
44376369 GCAATTCTTTATCTTCAAGGTATGCAATTGCCCAAGGCTATTAGCAACAGACATTGGAAAGAGAA
1 GCAATTCTTTATCTTCAAGGTATGCAATTGCCCAAGGCTATTAGCAACAGACATTGGAAAGAGAA
44376434 GCCTCAAATTATTGCATTCTTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCACT
66 GCCTCAAATTATTGCATTCTTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCACT
**
44376499 TGTGAGTCTTGGATTATGCCTTCCAAGCTCCA
131 TGTGAGTCTTGGATTATGCCTTCCAAGCTGAA
*
44376531 TCAATTCTTTATCTTCAAGGTATGCAATTGCCCAAGGCTATTAGCAACAGACAT
1 GCAATTCTTTATCTTCAAGGTATGCAATTGCCCAAGGCTATTAGCAACAGACAT
44376585 CGGGAAGATA
Statistics
Matches: 361, Mismatches: 15, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
161 74 0.20
162 287 0.80
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (162 bp):
GCAATTCTTTATCTTCAAGGTATGCAATTGCCCAAGGCTATTAGCAACAGACATTGGAAAGAGAA
GCCTCAAATTATTGCATTCTTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCACT
TGTGAGTCTTGGATTATGCCTTCCAAGCTGAA
Found at i:44376648 original size:324 final size:322
Alignment explanation
Indices: 44376046--44376649 Score: 867
Period size: 324 Copynumber: 1.9 Consensus size: 322
44376036 CCATTTGCTT
* *
44376046 GCAATTCTTTATCTTTAGAGTATGCAATTGCCCAAGGCCATTAGCAACGGACATTGGAAAGAGAA
1 GCAATTCTTTATCTTAAGAGTATGCAATTGCCCAAGGCCATTAGCAACAGACATTGGAAAGAGAA
44376111 ACCTCAAATTATTGCATTTTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCACTT
66 ACCTCAAATTATTGCATTTTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCACTT
*
44376176 GTGAGTCTTGGATTATGCCTTCCAAGCTGAAGCAATTCTTTAACTTCAAGGTATGCAACTGCCCA
131 GTGAGTCTTGGATTATGCCTTCCAAGCTCAAGCAATTCTTTAACTTCAAGGTATGCAACTGCCCA
* * ** ** * * * **
44376241 AGGCTATTAGCAACAGACATTGGAAAGAGAAGCCTCAAATTATTGCATTCTTCAACTTCTATTTC
196 AGGCTATTAGCAACAGACATCGGAAAGAGAAGCCTAAAAAAACGGAACTCTTCAACTTCAAAAT-
*
44376306 CCTTAAACTTTTGAGGCTTATGTATGGCAATTGTGAGTCTTGGATTATGCCTTCCAAGCTGAA
260 CCTTAAACTTTGGAGGCTTATGTATGGCAATTGTGAGTCTTGGATTATGCCTTCCAAGCTGAA
*
44376369 GCAATTCTTTATCTTCAAG-GTATGCAATTGCCCAAGGCTATTAGCAACAGACATTGGAAAGAGA
1 GCAATTCTTTATCTT-AAGAGTATGCAATTGCCCAAGGCCATTAGCAACAGACATTGGAAAGAGA
*
44376433 AGCCTCAAATTATTGCATTCTTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCAC
65 AACCTCAAATTATTGCATT-TTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCAC
* * * *
44376498 TTGTGAGTCTTGGATTATGCCTTCCAAGCTCCATCAATTCTTTATCTTCAAGGTATGCAATTGCC
129 TTGTGAGTCTTGGATTATGCCTTCCAAGCTCAAGCAATTCTTTAACTTCAAGGTATGCAACTGCC
* * * *
44376563 CAAGGCTATTAGCAACAGACATCGGGAAGATATATTG-C-AAAAAAACGGAACTC-TCTATTTCA
194 CAAGGCTATTAGCAACAGACATCGGAAAGAGA-A--GCCTAAAAAAACGGAACTCTTCAACTTCA
*
44376625 ACAAT-CTTCAGACTTTGGAGGCTTA
256 A-AATCCTT-AAACTTTGGAGGCTTA
44376650 AATGACAACT
Statistics
Matches: 248, Mismatches: 26, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
323 79 0.32
324 157 0.63
325 10 0.04
326 1 0.00
327 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (322 bp):
GCAATTCTTTATCTTAAGAGTATGCAATTGCCCAAGGCCATTAGCAACAGACATTGGAAAGAGAA
ACCTCAAATTATTGCATTTTCAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGTATGGCACTT
GTGAGTCTTGGATTATGCCTTCCAAGCTCAAGCAATTCTTTAACTTCAAGGTATGCAACTGCCCA
AGGCTATTAGCAACAGACATCGGAAAGAGAAGCCTAAAAAAACGGAACTCTTCAACTTCAAAATC
CTTAAACTTTGGAGGCTTATGTATGGCAATTGTGAGTCTTGGATTATGCCTTCCAAGCTGAA
Found at i:44386279 original size:10 final size:9
Alignment explanation
Indices: 44386252--44386278 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
44386242 TCTATTCGAT
44386252 TTGAAAAAA
1 TTGAAAAAA
44386261 TTGAAAAAA
1 TTGAAAAAA
44386270 TTGAAAAAA
1 TTGAAAAAA
44386279 AAACTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (9 bp):
TTGAAAAAA
Found at i:44386707 original size:97 final size:96
Alignment explanation
Indices: 44386532--44386728 Score: 308
Period size: 97 Copynumber: 2.0 Consensus size: 96
44386522 GATTGTGAAA
* *
44386532 ATAAAAAATTCCAAAGAGTCTTTTAACTCTGAAATTTGCTTCAAGAAAAACATAAAAAGATGACA
1 ATAAAAAATTCCAAAGAGTCTTTTAACTCTG-AATTTGCCTCAAGAAAAACATAAAAAAATGACA
44386597 TCAAATCATATATAAGTTTAATTTACGTATAT
65 TCAAATCATATATAAGTTTAATTTACGTATAT
44386629 ATAAAAAA-TCCAAAGAGTCTTTTAACTCTG-ATTTGCCTCAAGAAAAACATAAAAAAAAAATGA
1 ATAAAAAATTCCAAAGAGTCTTTTAACTCTGAATTTGCCTCAAGAAAAACAT---AAAAAAATGA
* *
44386692 CATCAGATCATATATAAGTTTAATTTATGTATAT
63 CATCAAATCATATATAAGTTTAATTTACGTATAT
44386726 ATA
1 ATA
44386729 GACATGACTA
Statistics
Matches: 93, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
94 19 0.20
96 22 0.24
97 52 0.56
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (96 bp):
ATAAAAAATTCCAAAGAGTCTTTTAACTCTGAATTTGCCTCAAGAAAAACATAAAAAAATGACAT
CAAATCATATATAAGTTTAATTTACGTATAT
Found at i:44390127 original size:162 final size:162
Alignment explanation
Indices: 44389899--44390418 Score: 765
Period size: 162 Copynumber: 3.2 Consensus size: 162
44389889 TCCTCAAAGC
* * * * * * *
44389899 TCCCAGTTGCCCAAGATTATTAGCAACTCACGTTGGTAAGAGATACTCCAAATTACTGCATTCTG
1 TCCCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGATACTTCAAATTATTGCATTCTG
* ** * *
44389964 TAACTTGTA-TTATCTTTAGGCAC-TGAAAGCTTATGTTTGACACTTGTGGGTTTTGAATTATTT
66 TAACTTCTACTT-TCCATA-GCCCTTGGAAGCTTATGTTTGACACTTGTGGGTTTTGAATTATTT
* * *
44390027 CTTCCAATCCAAAACACGTCTCTATCTTTAGAGT
129 CTTCCAATCCAAAGCACCTCTCTATCTTCAGAGT
* * *
44390061 TCCCAATTGCCCAAGACTATTAACAACACACATCGGGAAGAGATACTTCAAATTATTACATTCTG
1 TCCCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGATACTTCAAATTATTGCATTCTG
*
44390126 TAACTTCTACTTTCCGTAGCCCTTGGAAGCTTATGTTTGACACTTGTGGGTTTTGAATTATTTCT
66 TAACTTCTACTTTCCATAGCCCTTGGAAGCTTATGTTTGACACTTGTGGGTTTTGAATTATTTCT
44390191 TCCAATCCAAAGCACCTCTCTATCTTCAGAGT
131 TCCAATCCAAAGCACCTCTCTATCTTCAGAGT
* * * * *
44390223 TCGCAACTGCCCAAGACTATTAGCAACACACATTGGGAAGAGATATTTCAAATTATTGTATTCAG
1 TCCCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGATACTTCAAATTATTGCATTCTG
*
44390288 TAACTTCTACTTTCCATAACCCTTGGAAGCTTATGTTTGACACTTGTGGGTTTTGAATTATTTCT
66 TAACTTCTACTTTCCATAGCCCTTGGAAGCTTATGTTTGACACTTGTGGGTTTTGAATTATTTCT
*
44390353 TCCAACCCAAAGCACCTCTCTATCTTCAGAGT
131 TCCAATCCAAAGCACCTCTCTATCTTCAGAGT
*
44390385 TCTCAATTGCCCAAGACTATTAGCAACACACATT
1 TCCCAATTGCCCAAGACTATTAGCAACACACATT
44390419 TTCAGGTTAG
Statistics
Matches: 325, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
161 3 0.01
162 320 0.98
163 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (162 bp):
TCCCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGATACTTCAAATTATTGCATTCTG
TAACTTCTACTTTCCATAGCCCTTGGAAGCTTATGTTTGACACTTGTGGGTTTTGAATTATTTCT
TCCAATCCAAAGCACCTCTCTATCTTCAGAGT
Found at i:44397277 original size:21 final size:21
Alignment explanation
Indices: 44397251--44397296 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
44397241 TAATCACAAC
* *
44397251 TTTATCAAACGAATTCAGTTT
1 TTTATCAAACAAATTCAGCTT
*
44397272 TTTATCAACCAAATTCAGCTT
1 TTTATCAAACAAATTCAGCTT
44397293 TTTA
1 TTTA
44397297 GCTAGACTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (21 bp):
TTTATCAAACAAATTCAGCTT
Found at i:44398501 original size:22 final size:24
Alignment explanation
Indices: 44398474--44398532 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
44398464 TAAAACTTAC
*
44398474 ATATATGATTTTT-TAT-CAAAAT
1 ATATATGATTTTTGTATAAAAAAT
44398496 ATATATGATTTTTGTATAAAAAAT
1 ATATATGATTTTTGTATAAAAAAT
*
44398520 ATATATTATTTTT
1 ATATATGATTTTT
44398533 ACTAATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 13 0.39
23 3 0.09
24 17 0.52
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (24 bp):
ATATATGATTTTTGTATAAAAAAT
Found at i:44406441 original size:59 final size:57
Alignment explanation
Indices: 44406321--44406809 Score: 374
Period size: 59 Copynumber: 8.4 Consensus size: 57
44406311 CCCTAAACTA
* * * * * *
44406321 TCCAAAAATTACATTTTGACCCT-AAACTTTCTAAAAATTACATTTTACCCCTAAATT
1 TCCAAAAATTCCATTTTGACCCTCGAAC-TTCCAAAAATTCCATTTTACCCCGATATT
* ** * *
44406378 TCCAAAAATTCCATTTTTGACAC-CGATTTTTCCAAAAATTACCGTTTTACCCCGATTTT
1 TCCAAAAATTCCA-TTTTGACCCTCGA-ACTTCCAAAAATT-CCATTTTACCCCGATATT
* * * ** *
44406437 TCCAAAATTTACCATTTT-ACCCCACGAACTCCCAAAAATTCCATTTTTGACCTTGATTTT
1 TCCAAAAATT-CCATTTTGA-CCCTCGAACTTCCAAAAATTCCA-TTTT-ACCCCGATATT
*
44406497 TCCAAAAATTACCATTTT-ACCCTCGAACTTCCAAAAATTCCATTTTTGACCCC-AGTTTT
1 TCCAAAAATT-CCATTTTGACCCTCGAACTTCCAAAAATTCCA-TTTT-ACCCCGA-TATT
* ** * * *
44406556 TCCAAAAATTACATTTT-AGGCTCGAACTCCCAAAAATTCCATTTTTAACCTCG-TTTT
1 TCCAAAAATTCCATTTTGACCCTCGAACTTCCAAAAATTCCA-TTTT-ACCCCGATATT
*
44406613 TCCAAAAATTACCATTTT-ACCCTCGAACTTCCAAAAATTCCATTTTACCCCTTGA-ACT
1 TCCAAAAATT-CCATTTTGACCCTCGAACTTCCAAAAATTCCATTTTACCCC--GATATT
* * * *
44406671 TCCAAAAATTCCATTTTGACCC-CAAACTTTCTAAAAATTACCATTTTACCCTTGA-ACT
1 TCCAAAAATTCCATTTTGACCCTCGAAC-TTCCAAAAATT-CCATTTTACCC-CGATATT
* *
44406729 TCCAAAAATTCCATTTTTGA-CCTCGAATTTCCCAAAAATTACCATTTTACCCTCGA-ACT
1 TCCAAAAATTCCA-TTTTGACCCTCGAACTT-CCAAAAATT-CCATTTTACCC-CGATATT
*
44406788 TCCAAAGATTCCATTTTTGACC
1 TCCAAAAATTCCA-TTTTGACC
44406810 TTGAAGTGTC
Statistics
Matches: 364, Mismatches: 45, Indels: 43
0.81 0.10 0.10
Matches are distributed among these distances:
56 4 0.01
57 41 0.11
58 134 0.37
59 151 0.41
60 34 0.09
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (57 bp):
TCCAAAAATTCCATTTTGACCCTCGAACTTCCAAAAATTCCATTTTACCCCGATATT
Found at i:44406805 original size:29 final size:28
Alignment explanation
Indices: 44406316--44406804 Score: 355
Period size: 29 Copynumber: 16.8 Consensus size: 28
44406306 GAGGTCCCTA
* *
44406316 AACTATCCAAAAATTACATTTTGACCCT-A
1 AACT-TCCAAAAATTCCATTTT-ACCCTCG
* * *
44406345 AACTTTCTAAAAATTACATTTTACCC-CTA
1 AAC-TTCCAAAAATTCCATTTTACCCTC-G
* *
44406374 AATTTCCAAAAATTCCATTTTTGACAC-CG
1 AACTTCCAAAAATTCCA-TTTT-ACCCTCG
** *
44406403 ATTTTTCCAAAAATTACCGTTTTACCC-CG
1 A-ACTTCCAAAAATT-CCATTTTACCCTCG
** * *
44406432 ATTTTTCCAAAATTTACCATTTTACCCCACG
1 A-ACTTCCAAAAATT-CCATTTTA-CCCTCG
* *
44406463 AACTCCCAAAAATTCCATTTTTGA-CCTTG
1 AACTTCCAAAAATTCCA-TTTT-ACCCTCG
**
44406492 ATTTTTCCAAAAATTACCATTTTACCCTCG
1 A-ACTTCCAAAAATT-CCATTTTACCCTCG
44406522 AACTTCCAAAAATTCCATTTTTGACCC-CAG
1 AACTTCCAAAAATTCCA-TTTT-ACCCTC-G
*** * **
44406552 TTTTTCCAAAAATTACATTTTAGGCTCG
1 AACTTCCAAAAATTCCATTTTACCCTCG
* *
44406580 AACTCCCAAAAATTCCATTTTTAACCTCG
1 AACTTCCAAAAATTCCA-TTTTACCCTCG
***
44406609 TTTTTCCAAAAATTACCATTTTACCCTCG
1 AACTTCCAAAAATT-CCATTTTACCCTCG
*
44406638 AACTTCCAAAAATTCCATTTTACCCCTTG
1 AACTTCCAAAAATTCCATTTTA-CCCTCG
*
44406667 AACTTCCAAAAATTCCATTTTGACCC-CA
1 AACTTCCAAAAATTCCATTTT-ACCCTCG
* *
44406695 AACTTTCTAAAAATTACCATTTTACCCTTG
1 AAC-TTCCAAAAATT-CCATTTTACCCTCG
44406725 AACTTCCAAAAATTCCATTTTTGA-CCTCG
1 AACTTCCAAAAATTCCA-TTTT-ACCCTCG
*
44406754 AATTTCCCAAAAATTACCATTTTACCCTCG
1 AACTT-CCAAAAATT-CCATTTTACCCTCG
*
44406784 AACTTCCAAAGATTCCATTTT
1 AACTTCCAAAAATTCCATTTT
44406805 TGACCTTGAA
Statistics
Matches: 375, Mismatches: 55, Indels: 61
0.76 0.11 0.12
Matches are distributed among these distances:
28 55 0.15
29 197 0.53
30 111 0.30
31 12 0.03
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.36
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTACCCTCG
Found at i:44417964 original size:22 final size:22
Alignment explanation
Indices: 44417907--44417964 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
44417897 CCCTAAAGCC
*
44417907 TCTCACTTTTCTTTCTCATTTT
1 TCTCTCTTTTCTTTCTCATTTT
* ** *
44417929 TCTCTCATCCCTTTCTTATTTCT
1 TCTCTCTTTTCTTTCTCATTT-T
44417952 T-TCTCTTTTCTTT
1 TCTCTCTTTTCTTT
44417965 TCCAACTCTT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (22 bp):
TCTCTCTTTTCTTTCTCATTTT
Found at i:44418535 original size:7 final size:7
Alignment explanation
Indices: 44418525--44418572 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
44418515 ACCATTAATT
44418525 GTTGACC
1 GTTGACC
*
44418532 GTTGACA
1 GTTGACC
44418539 GTTGACC
1 GTTGACC
* *
44418546 GTTAACT
1 GTTGACC
*
44418553 GTTTACC
1 GTTGACC
*
44418560 ATTGACC
1 GTTGACC
44418567 GTTGAC
1 GTTGAC
44418573 TTTTTCGAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (7 bp):
GTTGACC
Found at i:44418537 original size:28 final size:28
Alignment explanation
Indices: 44418501--44418572 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
44418491 TCGGCCGTTA
*
44418501 ACCATTGACCATTGACCATTAATTGTTG
1 ACCATTGACCATTGACCATTAACTGTTG
* * *
44418529 ACCGTTGA-CAGTTGACCGTTAACTGTTT
1 ACCATTGACCA-TTGACCATTAACTGTTG
*
44418557 ACCATTGACCGTTGAC
1 ACCATTGACCATTGAC
44418573 TTTTTCGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 2 0.06
28 33 0.92
29 1 0.03
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (28 bp):
ACCATTGACCATTGACCATTAACTGTTG
Found at i:44419638 original size:9 final size:9
Alignment explanation
Indices: 44419614--44419648 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
44419604 TATTCTATTT
44419614 TATTATTTAC
1 TATTA-TTAC
*
44419624 TATTATTAT
1 TATTATTAC
44419633 TATTATTAC
1 TATTATTAC
44419642 TATTATT
1 TATTATT
44419649 TTGATTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTATTAC
Found at i:44425050 original size:22 final size:22
Alignment explanation
Indices: 44425020--44425091 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
44425010 AAGCCTCTCA
44425020 CTTTT-CTTTCTCATT-TTTCT
1 CTTTTCCTTTCTCATTCTTTCT
*
44425040 CTTATTCCTTTCTTATTCCTTTCT
1 CTT-TTCCTTTCTCATT-CTTTCT
*
44425064 CTTTTCTTTTC-CAATTCTTTCT
1 CTTTTCCTTTCTC-ATTCTTTCT
44425086 CTTTTC
1 CTTTTC
44425092 TTCAAATCCG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
22 21 0.48
23 10 0.23
24 8 0.18
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.65
Consensus pattern (22 bp):
CTTTTCCTTTCTCATTCTTTCT
Found at i:44425051 original size:13 final size:13
Alignment explanation
Indices: 44425035--44425066 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
44425025 CTTTCTCATT
44425035 TTTCTCTTATTCC
1 TTTCTCTTATTCC
44425048 -TT-TCTTATTCC
1 TTTCTCTTATTCC
44425059 TTTCTCTT
1 TTTCTCTT
44425067 TTCTTTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 9 0.53
12 4 0.24
13 4 0.24
ACGTcount: A:0.06, C:0.28, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTCTCTTATTCC
Found at i:44425645 original size:14 final size:14
Alignment explanation
Indices: 44425628--44425665 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
44425618 ATCGTTAACC
44425628 GTTGACCGTTGACT
1 GTTGACCGTTGACT
* *
44425642 GTTGATCATTGACT
1 GTTGACCGTTGACT
44425656 -TTGACCGTTG
1 GTTGACCGTTG
44425666 GCTTTTTCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (14 bp):
GTTGACCGTTGACT
Found at i:44426725 original size:3 final size:3
Alignment explanation
Indices: 44426704--44426743 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
44426694 TATGATATTC
*
44426704 TAT T-T TAT TATT TAC TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
44426744 TTGGAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:44427829 original size:49 final size:49
Alignment explanation
Indices: 44427762--44428579 Score: 612
Period size: 49 Copynumber: 16.7 Consensus size: 49
44427752 ACCACGCAGA
* * * *
44427762 CATGGAGGGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTTAGAAG
1 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * *
44427811 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCC-GGTA-C-CATGAAG
1 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCTCA-GAAG
* * * *
44427859 ATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAG
1 -CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * * * *
44427909 CATGAAGGGAAAGATTTAAGCCACAATGGCGAATCC-AGTACCAC-GAAG
1 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGAAG
* *
44427957 ATATTG-AGGGAAAGATTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAG
1 -CA-TGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * * *
44428007 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCAC-GAAAA
1 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAG-AAG
* * * * * *
44428056 TATGGAGGGAAATG-TTTATGTCGCAATGGCAAACCTTGTACCTCAAAAG
1 CATGAAGGGAAA-GATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * * *
44428105 CATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCC-AGTACCAC-GAAG
1 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGAAG
* * * * * *
44428153 ATATGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTATCTTAG-GG
1 -CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * * * * *
44428202 ACATGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTATCACA-AAG
1 -CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * * * *
44428251 ATATGGAGGGAAAGGTTTAAGTTGCAACGGCAAACCTTGTACCTCAGAAG
1 -CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * * * * *
44428301 CATAAAAGGGAAAGATTTAAGCCGCGACAGCGAATCC-AG--CATCACGAAG
1 CAT-GAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCTCA-GAAG
** * * * * * *
44428350 ACACAAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTATACCTCGGAAT
1 -CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * * *
44428400 CATGAAGGGAAAGGTTTAAGTCGTAATGGCGAACCTTATACCTCAGAAG
1 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * *
44428449 CATAAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTA-C-CATGAAG
1 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTTGTACCTCA-GAAG
** * * * *
44428497 ACACAAAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTATACCTCGGAAG
1 -CA-TGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
* * *
44428548 CATGAAAGGAAA-ATTTAAGCCACAACGGCGAA
1 CATGAAGGGAAAGATTTAAGTCGCAACGGCGAA
44428580 TTTATTACCA
Statistics
Matches: 598, Mismatches: 135, Indels: 73
0.74 0.17 0.09
Matches are distributed among these distances:
47 3 0.01
48 49 0.08
49 450 0.75
50 83 0.14
51 12 0.02
52 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (49 bp):
CATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG
Found at i:44427919 original size:98 final size:98
Alignment explanation
Indices: 44427749--44428419 Score: 885
Period size: 98 Copynumber: 6.8 Consensus size: 98
44427739 TACAGGTCTT
* * * *
44427749 AGTACCACGCAGACATGGAGGGAAAGGTTTAAGTCGTAACGGCGAACCTTGTACCTTAGAAGCAT
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCAT
*
44427814 GAAGGGAAAGATTTAAGCCGCAACGACGAATCC
66 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * *
44427847 GGTACCATGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCAT
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCAT
* *
44427912 GAAGGGAAAGATTTAAGCCACAATGGCGAATCC
66 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * *
44427945 AGTACCACGAAGATATTGAGGGAAAGATTTAAGTCGCAACGGTGAACCTTGTACCTCAGAAGCAT
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCAT
* *
44428010 GAAGGGAAAGATTTAAGTCGCAACGGCGAATCT
66 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * * * * *
44428043 AGTACCACGAAAATATGGAGGGAAATGTTTATGTCGCAATGGCAAACCTTGTACCTCAAAAGCAT
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCAT
*
44428108 GAAGGGAAAGATTTAAGCCGCAACGGTGAATCC
66 GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * * * *
44428141 AGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTTGTATCTTAG-GGACA
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-CA
* *
44428205 TGAAGGGAAAGATTTAAGCCGCAACGGTGAATCT
65 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * * *
44428239 AGTATCACAAAGATATGGAGGGAAAGGTTTAAGTTGCAACGGCAAACCTTGTACCTCAGAAGCAT
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCAT
* * *
44428304 AAAAGGGAAAGATTTAAGCCGCGACAGCGAATCC
66 -GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
* * * *** * * * * *
44428338 AGCATCACGAAGACACAAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTATACCTCGGAATCAT
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCAT
*
44428403 GAAGGGAAAGGTTTAAG
66 GAAGGGAAAGATTTAAG
44428420 TCGTAATGGC
Statistics
Matches: 501, Mismatches: 69, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
97 1 0.00
98 417 0.83
99 83 0.17
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (98 bp):
AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCAT
GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC
Found at i:44429051 original size:23 final size:22
Alignment explanation
Indices: 44429022--44429070 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
44429012 TTTTTAAAAG
*
44429022 ATTTAAATTTACTTTAATTTTAA
1 ATTTAAATTT-CTTTAAATTTAA
*
44429045 ATTTAAATTTTTTTAAATTTAA
1 ATTTAAATTTCTTTAAATTTAA
44429067 ATTT
1 ATTT
44429071 TGTTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTAAATTTCTTTAAATTTAA
Found at i:44429065 original size:6 final size:6
Alignment explanation
Indices: 44429022--44429070 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
44429012 TTTTTAAAAG
* * *
44429022 ATTTAA ATTT-A CTTTAA TTTTAA ATTTAA ATTT-- TTTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
44429067 ATTT
1 ATTT
44429071 TGTTTAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
4 3 0.09
5 4 0.11
6 28 0.80
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (6 bp):
ATTTAA
Found at i:44429078 original size:17 final size:16
Alignment explanation
Indices: 44429039--44429081 Score: 77
Period size: 16 Copynumber: 2.6 Consensus size: 16
44429029 TTTACTTTAA
44429039 TTTTAAATTTAAATTT
1 TTTTAAATTTAAATTT
44429055 TTTTAAATTTAAATTT
1 TTTTAAATTTAAATTT
44429071 TGTTTAAATTT
1 T-TTTAAATTT
44429082 GAAACGGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTAAATTTAAATTT
Found at i:44430155 original size:41 final size:41
Alignment explanation
Indices: 44430053--44430309 Score: 257
Period size: 41 Copynumber: 6.3 Consensus size: 41
44430043 TTTTATGCAT
* * * * * * *
44430053 GCCGCTAATTCTTTGATCTTTAGCGACGCTTACTCATAAAT
1 GCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTAATAAAC
* * * *
44430094 GCC-CTAATGCTCTAATCTTTAGTGGCGCTTTCCT-ATAAAT
1 GCCGCTAATGCTCTGACCTTTAGCGGCGC-TTCCTAATAAAC
* * *
44430134 GTCGCTAATGCTCTGACCTTTAGCGGTGCTTCCTAAAAAAC
1 GCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTAATAAAC
* * * *
44430175 GTCGCTAATGCTTTGACCTTTAGCGACGCTTCCTAAAAAAC
1 GCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTAATAAAC
* * *
44430216 ACCGTTAATGCTCTGACCTTTAGCGGCGCTTCCTCATAAAC
1 GCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTAATAAAC
* * * *
44430257 GCCGCTAATGCTTTGACCTTTAGCGGTGCTTCTTCATAAAC
1 GCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTAATAAAC
*
44430298 GCCGCTATTGCT
1 GCCGCTAATGCT
44430310 TAACCATTTG
Statistics
Matches: 184, Mismatches: 29, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
40 33 0.18
41 151 0.82
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.33
Consensus pattern (41 bp):
GCCGCTAATGCTCTGACCTTTAGCGGCGCTTCCTAATAAAC
Found at i:44430298 original size:123 final size:122
Alignment explanation
Indices: 44430053--44430310 Score: 320
Period size: 123 Copynumber: 2.1 Consensus size: 122
44430043 TTTTATGCAT
* * * * ** * *
44430053 GCCGCTAATTCTTTGATCTTTAGCGACGCTTACTCATAAATGCCCTAATGCTCTAATCTTTAGTG
1 GCCGCTAATGCTTTGACCTTTAGCGACGCTTACTAAAAAACACCCTAATGCTCTAACCTTTAGCG
* *
44430118 GCGCTTTCCTATAAATGTCGCTAATGCTCTGACCTTTAGCGGTGCTTCCTAAAAAAC
66 GCGCTTTCCTATAAACGCCGCTAATGCTCTGACCTTTAGCGGTGCTTCCTAAAAAAC
* * * *
44430175 GTCGCTAATGCTTTGACCTTTAGCGACGCTTCCTAAAAAACACCGTTAATGCTCTGACCTTTAGC
1 GCCGCTAATGCTTTGACCTTTAGCGACGCTTACTAAAAAACACC-CTAATGCTCTAACCTTTAGC
* * * *
44430240 GGCGC-TTCCTCATAAACGCCGCTAATGCTTTGACCTTTAGCGGTGCTTCTTCATAAAC
65 GGCGCTTTCCT-ATAAACGCCGCTAATGCTCTGACCTTTAGCGGTGCTTCCTAAAAAAC
*
44430298 GCCGCTATTGCTT
1 GCCGCTAATGCTT
44430311 AACCATTTGT
Statistics
Matches: 114, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
122 41 0.36
123 73 0.64
ACGTcount: A:0.22, C:0.27, G:0.17, T:0.33
Consensus pattern (122 bp):
GCCGCTAATGCTTTGACCTTTAGCGACGCTTACTAAAAAACACCCTAATGCTCTAACCTTTAGCG
GCGCTTTCCTATAAACGCCGCTAATGCTCTGACCTTTAGCGGTGCTTCCTAAAAAAC
Found at i:44431146 original size:9 final size:9
Alignment explanation
Indices: 44431132--44431158 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
44431122 ACTAAAGATT
44431132 CACTCAAAG
1 CACTCAAAG
44431141 CACTCAAAG
1 CACTCAAAG
44431150 CACTCAAAG
1 CACTCAAAG
44431159 TGTTTAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.33, G:0.11, T:0.11
Consensus pattern (9 bp):
CACTCAAAG
Found at i:44439100 original size:162 final size:162
Alignment explanation
Indices: 44438887--44439259 Score: 518
Period size: 162 Copynumber: 2.3 Consensus size: 162
44438877 ACTTCTGGTC
* ***
44438887 CTTGAATTATTTCTTGCAATTGGGAA-CACCTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACT
1 CTTGAATTATTTCTTCCAA-TCCAAAGCACCTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACT
*
44438951 ATTAG-CAACACACATTGGGAAGAGATATATCAAATTATTGCAACCTGAAACTTGTAGTTCCCTT
65 ATTAGAC-ACACACATTGGGAAGAGATATATCAAATTATTGCAACCTGAAACTTGTACTTCCCTT
*
44439015 AAGCATTGGAAGCCTATGTTTG-TAACTTGTGGGT
129 AAGCATTGGAAGCCTATGTTTGAT-ACTTGTGGAT
* * * *
44439049 GTTGGATTATTTCTTCCAATCCAAAGCACCTATCTATCTTCAGAGTTTGCAATTGCCCAAGGCTA
1 CTTGAATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTA
* * * ** *
44439114 TTAGACGCAGACATTGGGAAGAGATATTTCAAATTATTGCATTCTGTAACTTGTACTTCCCTTAA
66 TTAGACACACACATTGGGAAGAGATATATCAAATTATTGCAACCTGAAACTTGTACTTCCCTTAA
*
44439179 GCATTGGAAGCTTATGTTTGATACTTGTGGAT
131 GCATTGGAAGCCTATGTTTGATACTTGTGGAT
* * *
44439211 CTTGAATTATTTCTTCCAATCCGAAGCACTTCTCTATCTTCAGCGTTTG
1 CTTGAATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTCAGAGTTTG
44439260 TAAATTGGGC
Statistics
Matches: 185, Mismatches: 23, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
161 3 0.02
162 180 0.97
163 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (162 bp):
CTTGAATTATTTCTTCCAATCCAAAGCACCTCTCTATCTTCAGAGTTTGCAATTGCCCAAGACTA
TTAGACACACACATTGGGAAGAGATATATCAAATTATTGCAACCTGAAACTTGTACTTCCCTTAA
GCATTGGAAGCCTATGTTTGATACTTGTGGAT
Found at i:44440485 original size:162 final size:162
Alignment explanation
Indices: 44439887--44440473 Score: 809
Period size: 162 Copynumber: 3.6 Consensus size: 162
44439877 AACATATGTT
*** *
44439887 TGGCACTTGTGGGTCTTGGATTATAAGTTCCAATTTCGAGCAACTCTTTATCTTCAAAGTATGCA
1 TGGCACTTGTGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATGCA
** * * *
44439952 ATTGCCCAAGAGGATTAGCAACAGACCGTGAGAAGAGATACTTTAAATTACCGCATTTTTCAACT
66 ATTGCCCAAGACTATTAGCAACAGACAGTGGGAAGAGATACTTTAAATTATCGCATTTTTCAACT
*
44440017 TTTACTTCCCTTAAACTTTGGAGGCTTATGTA
131 TTTACTTCCCTTAAACTTTGGAGGCTTAAGTA
* *
44440049 TGGCATTTGCGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATGCA
1 TGGCACTTGTGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATGCA
*
44440114 ATTGTCCAAGACTATTAGCAACAGACAGTGGGAAGAGATACTTTAAATTATCGCATTTTTCAACT
66 ATTGCCCAAGACTATTAGCAACAGACAGTGGGAAGAGATACTTTAAATTATCGCATTTTTCAACT
* * *
44440179 TTTACTTCCCATAAACTTTGCAGGCTTACGTA
131 TTTACTTCCCTTAAACTTTGGAGGCTTAAGTA
* *
44440211 TGGCACTTGTGCG-CTTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTCCAAAGTATGC
1 TGGCACTTGTGGGTC-TTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATGC
* ** * *
44440275 AATTGCCCAAGACCATTAGCAACAGACAGACGGAAGAGATGCTTCAAATTATCGCATTTTTCAAC
65 AATTGCCCAAGACTATTAGCAACAGACAGTGGGAAGAGATACTTTAAATTATCGCATTTTTCAAC
* * * *
44440340 TTTTACATCCTTTAAACATTGGAGTCTTAAGT-
130 TTTTACTTCCCTTAAACTTTGGAGGCTTAAGTA
* * * * *
44440372 TCGGCACTTGTGAGTCTTGGATTATTTCTTCCAATTGCAAGCAGCTCTTTATTTTCAAAGTATGC
1 T-GGCACTTGTGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATGC
* ** * *
44440437 AATTTCCCAAGGTTATTAGCAACAGATATTGGGAAGA
65 AATTGCCCAAGACTATTAGCAACAGACAGTGGGAAGA
44440474 TATATTTCAA
Statistics
Matches: 376, Mismatches: 46, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
161 2 0.01
162 373 0.99
163 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (162 bp):
TGGCACTTGTGGGTCTTGGATTATGTCTTCCAATTGCGAGCAACTCTTTATCTTCAAAGTATGCA
ATTGCCCAAGACTATTAGCAACAGACAGTGGGAAGAGATACTTTAAATTATCGCATTTTTCAACT
TTTACTTCCCTTAAACTTTGGAGGCTTAAGTA
Found at i:44444364 original size:10 final size:10
Alignment explanation
Indices: 44444351--44444387 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
44444341 AATTTAAAAA
44444351 ATATTTTTAT
1 ATATTTTTAT
44444361 ATATTTTTA-
1 ATATTTTTAT
*
44444370 ATATTTTTTT
1 ATATTTTTAT
44444380 AT-TTTTTA
1 ATATTTTTA
44444388 AAAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 13 0.54
10 11 0.46
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
ATATTTTTAT
Found at i:44444372 original size:19 final size:18
Alignment explanation
Indices: 44444350--44444388 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
44444340 AAATTTAAAA
44444350 AATATTTTTATATATTTTT
1 AATATTTTTATAT-TTTTT
*
44444369 AATATTTTTTTATTTTTT
1 AATATTTTTATATTTTTT
44444387 AA
1 AA
44444389 AAAATAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
AATATTTTTATATTTTTT
Found at i:44447540 original size:21 final size:21
Alignment explanation
Indices: 44447515--44447564 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
44447505 GAATTTCAGC
*
44447515 AGCAATCTATAGATTTCCAAA
1 AGCAAACTATAGATTTCCAAA
* * *
44447536 AGCAAACTGTGGATTTTCAAA
1 AGCAAACTATAGATTTCCAAA
*
44447557 AGAAAACT
1 AGCAAACT
44447565 GAGGCATCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (21 bp):
AGCAAACTATAGATTTCCAAA
Found at i:44447565 original size:21 final size:21
Alignment explanation
Indices: 44447526--44447565 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44447516 GCAATCTATA
*
44447526 GATTTCCAAAAGCAAACTGTG
1 GATTTCCAAAAGAAAACTGTG
*
44447547 GATTTTCAAAAGAAAACTG
1 GATTTCCAAAAGAAAACTG
44447566 AGGCATCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
GATTTCCAAAAGAAAACTGTG
Found at i:44451614 original size:6 final size:6
Alignment explanation
Indices: 44451603--44451628 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
44451593 GGCAACTCAA
44451603 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
44451629 TTATTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:44451650 original size:18 final size:17
Alignment explanation
Indices: 44451608--44451665 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
44451598 CTCAATTATT
44451608 TTTATTTTTATTT-T-TA
1 TTTA-TTTTATTTATCTA
*
44451624 TTT-TTTTATTTCTCTA
1 TTTATTTTATTTATCTA
*
44451640 TCTTATTTTATTTATTTA
1 T-TTATTTTATTTATCTA
44451658 TTTATTTT
1 TTTATTTT
44451666 TGTCCAGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 8 0.22
15 1 0.03
16 6 0.17
17 9 0.25
18 12 0.33
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTATTTATCTA
Found at i:44452478 original size:105 final size:105
Alignment explanation
Indices: 44452356--44452548 Score: 277
Period size: 105 Copynumber: 1.8 Consensus size: 105
44452346 ATGTGTTAGA
*
44452356 CTGAGTAACCGGGATGGAGTGCTT-GGTTGTCACTTCACTTT-GCGTCAAAAGGGCTAATGCATT
1 CTGAGTAACCGGGATGGAGTGCTTAGG-TGTCACTTCA-TTTCGCGTCAAAAGGGCCAATGCATT
*
44452419 C-TACAA-AAAAAAAGAGAAGAAAAATATTGAGAGCATGTTGGG
64 CTTA-AAGAAAAAAAAAGAA-AAAAATATTGAGAGCATGTTGGG
* * *
44452461 CTGAGTAACCGGGATGGAGTGCTTAGGTGTCATTTCATTTCGCGTCAAAAGGTCCAATGTATTCT
1 CTGAGTAACCGGGATGGAGTGCTTAGGTGTCACTTCATTTCGCGTCAAAAGGGCCAATGCATTCT
44452526 TAAAGAAAAAAAAAGAAAAAAAT
66 TAAAGAAAAAAAAAGAAAAAAAT
44452549 TGACAAAATA
Statistics
Matches: 79, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
104 3 0.04
105 61 0.77
106 15 0.19
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.25
Consensus pattern (105 bp):
CTGAGTAACCGGGATGGAGTGCTTAGGTGTCACTTCATTTCGCGTCAAAAGGGCCAATGCATTCT
TAAAGAAAAAAAAAGAAAAAAATATTGAGAGCATGTTGGG
Found at i:44453130 original size:19 final size:19
Alignment explanation
Indices: 44453108--44453152 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
44453098 TTATATTAGA
44453108 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
44453127 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
44453146 ATTTAAT
1 ATTTAAT
44453153 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:44453171 original size:14 final size:14
Alignment explanation
Indices: 44453152--44453181 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
44453142 TTGTATTTAA
44453152 TTTATATTTATCTT
1 TTTATATTTATCTT
44453166 TTTATATTTATCTT
1 TTTATATTTATCTT
44453180 TT
1 TT
44453182 AGAGTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:44453973 original size:15 final size:16
Alignment explanation
Indices: 44453953--44453982 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44453943 CTTCCCTATT
44453953 TTCTA-TTTCTTTTAG
1 TTCTATTTTCTTTTAG
44453968 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
44453983 TTTTTAATTC
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:0.13, C:0.13, G:0.03, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAG
Found at i:44453987 original size:22 final size:22
Alignment explanation
Indices: 44453948--44454008 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
44453938 TTCGACTTCC
* *
44453948 CTATTTTCTATTT-CTTTTAGTT
1 CTATTTTCT-TTTATTTTTAATT
44453970 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTATTTTTAATT
*
44453992 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTATTTTT
44454009 CCTTAGATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.49
22 18 0.51
ACGTcount: A:0.13, C:0.11, G:0.03, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTATTTTTAATT
Found at i:44459946 original size:18 final size:18
Alignment explanation
Indices: 44459923--44459961 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
44459913 AAAATTTGAC
*
44459923 AAAAAAT-ATAATAATATA
1 AAAAAATCAAAAT-ATATA
44459941 AAAAAATCAAAATATATA
1 AAAAAATCAAAATATATA
44459959 AAA
1 AAA
44459962 TTAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAATCAAAATATATA
Found at i:44459946 original size:30 final size:30
Alignment explanation
Indices: 44459885--44459947 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
44459875 ATGACATCAT
**
44459885 AATTTGAAAAAAATTATAAAAATATTTAAA
1 AATTTGAAAAAAATTATAAAAATATAAAAA
*
44459915 AATTTGACAAAAAA-TATAATAATATAAAAA
1 AATTTGA-AAAAAATTATAAAAATATAAAAA
44459945 AAT
1 AAT
44459948 CAAAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (30 bp):
AATTTGAAAAAAATTATAAAAATATAAAAA
Found at i:44459956 original size:24 final size:24
Alignment explanation
Indices: 44459922--44459970 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
44459912 AAAAATTTGA
*
44459922 CAAAAAATATAATAATATAAAAAAAT
1 CAAAATATATAA-AAT-TAAAAAAAT
44459948 CAAAATATATAAAATTAAAAAAA
1 CAAAATATATAAAATTAAAAAAA
44459971 AGTTCAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 3 0.14
26 11 0.50
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.22
Consensus pattern (24 bp):
CAAAATATATAAAATTAAAAAAAT
Found at i:44459957 original size:26 final size:24
Alignment explanation
Indices: 44459922--44459987 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 24
44459912 AAAAATTTGA
44459922 CAAAAAATATAATAATATAAAAAAAT
1 CAAAAAATATAA-AAT-TAAAAAAAT
*
44459948 CAAAATATATAAAATTAAAAAAAAGTT
1 CAAAAAATATAAAATT-AAAAAAA--T
44459975 CAAAAAATATAAA
1 CAAAAAATATAAA
44459988 TAAAATCTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 1 0.03
25 10 0.29
26 11 0.31
27 13 0.37
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.23
Consensus pattern (24 bp):
CAAAAAATATAAAATTAAAAAAAT
Found at i:44459988 original size:26 final size:23
Alignment explanation
Indices: 44459922--44459992 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 23
44459912 AAAAATTTGA
44459922 CAAAAAATATAATAATATAAAAAAAT
1 CAAAAAATAT-A-AATA-AAAAAAAT
*
44459948 CAAAATATATAAAATTAAAAAAAAGTT
1 CAAAAAATAT-AAA-TAAAAAAAA--T
44459975 CAAAAAATATAAATAAAA
1 CAAAAAATATAAATAAAA
44459993 TCTAAATCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 14 0.35
26 16 0.40
27 10 0.25
ACGTcount: A:0.72, C:0.04, G:0.01, T:0.23
Consensus pattern (23 bp):
CAAAAAATATAAATAAAAAAAAT
Found at i:44466710 original size:105 final size:105
Alignment explanation
Indices: 44466524--44466719 Score: 281
Period size: 105 Copynumber: 1.9 Consensus size: 105
44466514 ACGAAAAATA
*
44466524 AATAAATTAGGAGTGTATTAGGTTGAGTAACAGGGATGGAGTACTTGAGTTGTCATTCCATTTTG
1 AATAAATTAGGAGTGTATTAGGTTGAGTAACAGGGATGGAGTACTTGAGTTGTCATTCCATTTCG
* *
44466589 CTTCAAAAGAGTCAATATATTCTTAAGTAAAAATGATGAT
66 CTTAAAAAGAGCCAATATATTCTTAAGTAAAAATGATGAT
* * * *
44466629 AATAAATT-GAGAGTGTGTTAGGTTGAGTAACCGGGATGG-GATGCTTGGGTTGTCATTCCATTT
1 AATAAATTAG-GAGTGTATTAGGTTGAGTAACAGGGATGGAG-TACTTGAGTTGTCATTCCATTT
44466692 CGCGTTAAAAAG-GCCAATATATTCTTAA
64 CGC-TTAAAAAGAGCCAATATATTCTTAA
44466720 ACAAAAGAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
104 2 0.02
105 72 0.89
106 7 0.09
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.34
Consensus pattern (105 bp):
AATAAATTAGGAGTGTATTAGGTTGAGTAACAGGGATGGAGTACTTGAGTTGTCATTCCATTTCG
CTTAAAAAGAGCCAATATATTCTTAAGTAAAAATGATGAT
Found at i:44477925 original size:22 final size:24
Alignment explanation
Indices: 44477882--44477925 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
44477872 TGATAATATG
44477882 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
44477906 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
44477926 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:44478167 original size:20 final size:21
Alignment explanation
Indices: 44478129--44478170 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
44478119 AAACAATGAC
*
44478129 AAAAAGTATCGATACCTTTTT
1 AAAAAGTATCAATACCTTTTT
*
44478150 AAAAAGTTTCAATA-CTTTTT
1 AAAAAGTATCAATACCTTTTT
44478170 A
1 A
44478171 CCAGGTACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (21 bp):
AAAAAGTATCAATACCTTTTT
Found at i:44479168 original size:116 final size:116
Alignment explanation
Indices: 44479035--44479265 Score: 408
Period size: 116 Copynumber: 2.0 Consensus size: 116
44479025 TTGTGGTATA
* *
44479035 TTTTGTATTTTTTTTACTAAAAGAATGGCATCAATGTCAATTTCACAAGTTTTAGTGAGATTAGT
1 TTTTGTATTTTTTTTACTAAAAGAATGGCATCAAAGTAAATTTCACAAGTTTTAGTGAGATTAGT
* *
44479100 TTTGAAAGAAGATCTTCACCTGCATGGAACTCGATTCGAAGGTATTACTAT
66 TTTGAAAGAAGATCTTCACCTACACGGAACTCGATTCGAAGGTATTACTAT
*
44479151 TTTTTTATTTTTTTTACTAAAAGAATGGCATCAAAGTAAATTTCACAAGTTTTAGTGAGATTAGT
1 TTTTGTATTTTTTTTACTAAAAGAATGGCATCAAAGTAAATTTCACAAGTTTTAGTGAGATTAGT
*
44479216 TTTGAAAGAAGATCTTCACCTACACGGAGCTCGATTCGAAGGTATTACTA
66 TTTGAAAGAAGATCTTCACCTACACGGAACTCGATTCGAAGGTATTACTA
44479266 ATTTGGTCCT
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 109 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (116 bp):
TTTTGTATTTTTTTTACTAAAAGAATGGCATCAAAGTAAATTTCACAAGTTTTAGTGAGATTAGT
TTTGAAAGAAGATCTTCACCTACACGGAACTCGATTCGAAGGTATTACTAT
Found at i:44480719 original size:43 final size:43
Alignment explanation
Indices: 44480617--44480719 Score: 134
Period size: 43 Copynumber: 2.4 Consensus size: 43
44480607 CACACGGATT
* * *
44480617 GGGCACACGGGCGTGTATCAGACCGTGTGTGCATACTGTTTTG
1 GGGCACACGGGCGTGTGTCAGACCATGTGTACATACTGTTTTG
* * *
44480660 GGGCACACGAGCGTGTGTCAGACCATGTGTATATATTGTTTTG
1 GGGCACACGGGCGTGTGTCAGACCATGTGTACATACTGTTTTG
* *
44480703 GGGCAAACGGGTGTGTG
1 GGGCACACGGGCGTGTG
44480720 CCAAACTGTG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.18, C:0.17, G:0.36, T:0.28
Consensus pattern (43 bp):
GGGCACACGGGCGTGTGTCAGACCATGTGTACATACTGTTTTG
Found at i:44480730 original size:41 final size:43
Alignment explanation
Indices: 44480653--44480732 Score: 101
Period size: 43 Copynumber: 1.9 Consensus size: 43
44480643 GTGTGCATAC
* * *
44480653 TGTTTTGGGGCACACGAGCGTGTGTCAGACCATGTGTATATAT
1 TGTTTTGGGGCAAACGAGCGTGTGCCAGAACATGTGTATATAT
* *
44480696 TGTTTTGGGGCAAACGGGTGTGTGCCA-AAC-TGTGTAT
1 TGTTTTGGGGCAAACGAGCGTGTGCCAGAACATGTGTAT
44480733 GCATACTATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
41 7 0.22
42 2 0.06
43 23 0.72
ACGTcount: A:0.20, C:0.15, G:0.33, T:0.33
Consensus pattern (43 bp):
TGTTTTGGGGCAAACGAGCGTGTGCCAGAACATGTGTATATAT
Found at i:44495169 original size:23 final size:24
Alignment explanation
Indices: 44495141--44495200 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
44495131 TAAAACTTGC
* *
44495141 ATATATGATTTTTTTAT-CAAAAT
1 ATATATGATTTTTGTATAAAAAAT
44495164 ATATATGATTTTTGTATAAAAAAT
1 ATATATGATTTTTGTATAAAAAAT
*
44495188 ATATATTATTTTT
1 ATATATGATTTTT
44495201 ATTAATTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (24 bp):
ATATATGATTTTTGTATAAAAAAT
Found at i:44495984 original size:25 final size:23
Alignment explanation
Indices: 44495956--44496001 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
44495946 TAATTTCCAA
*
44495956 AAATTCAAATTTTTATAAAAATTCC
1 AAATT-AAA-TTTTAAAAAAATTCC
*
44495981 AAATTTAATTTTAAAAAAATT
1 AAATTAAATTTTAAAAAAATT
44496002 TAAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 2 0.11
25 5 0.26
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATTAAATTTTAAAAAAATTCC
Found at i:44499638 original size:58 final size:58
Alignment explanation
Indices: 44499478--44499638 Score: 175
Period size: 58 Copynumber: 2.8 Consensus size: 58
44499468 TAAAATTTTT
* * * * *
44499478 TACTTAAATTTGACATTTTTTCTTAATTTGGTACCTAAATTTTTT-TGCTCCAATTTAG
1 TACTCAAACTTGACACTTTTTCTTAATTTGGTA-CTTAATTTTTTAGGCTCCAATTTAG
* * * * *
44499536 TACTCAAACTTGGCACTTTTT-TTAAGTTGGTACTTCAACTTTTTAGGGTCCAATTTGG
1 TACTCAAACTTGACACTTTTTCTTAATTTGGTACTT-AATTTTTTAGGCTCCAATTTAG
*
44499594 TAC-CTAAACTTGACTCTTTTTCTTAATTTGGTACTTAATTTTTTA
1 TACTC-AAACTTGACACTTTTTCTTAATTTGGTACTTAATTTTTTA
44499639 ATATTATTTC
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
56 2 0.02
57 18 0.21
58 52 0.61
59 13 0.15
ACGTcount: A:0.24, C:0.16, G:0.11, T:0.49
Consensus pattern (58 bp):
TACTCAAACTTGACACTTTTTCTTAATTTGGTACTTAATTTTTTAGGCTCCAATTTAG
Found at i:44499839 original size:31 final size:30
Alignment explanation
Indices: 44499804--44499967 Score: 149
Period size: 31 Copynumber: 5.4 Consensus size: 30
44499794 TAAAAAAAGC
44499804 TTAGGTACCAAATTAGGAAAAAATGCCAAGT
1 TTAGGTACCAAATTAGGAAAAAATG-CAAGT
* *
44499835 TTAGGTACCAAATTGGGTTCAAAAA---AAGT
1 TTAGGTACCAAATTAGG--AAAAAATGCAAGT
* *
44499864 TTAGGTACCAAATTAAGAAAAAGTGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAATG-CAAGT
**
44499895 TTAGGTACCAAATTAAGTCAAAAA--CAAGT
1 TTAGGTACCAAATT-AGGAAAAAATGCAAGT
* *
44499924 TTAGGTACCAAATTAAGAAAAAGTGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAATG-CAAGT
* *
44499955 TCAAGTACCAAAT
1 TTAGGTACCAAAT
44499968 GTTATATTAA
Statistics
Matches: 107, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
27 4 0.04
28 5 0.05
29 38 0.36
31 50 0.47
32 5 0.05
33 5 0.05
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (30 bp):
TTAGGTACCAAATTAGGAAAAAATGCAAGT
Found at i:44499873 original size:29 final size:29
Alignment explanation
Indices: 44499795--44499940 Score: 140
Period size: 29 Copynumber: 4.9 Consensus size: 29
44499785 AATTGAATCT
* **
44499795 AAAAA-AAGCTTAGGTACCAAATT-AGGA
1 AAAAACAAGTTTAGGTACCAAATTAAGTC
**
44499822 AAAAATGCCAAGTTTAGGTACCAAATTGGGTTC
1 AAAAA---CAAGTTTAGGTACCAAATTAAG-TC
44499855 AAAAA-AAGTTTAGGTACCAAATTAAG--
1 AAAAACAAGTTTAGGTACCAAATTAAGTC
44499881 AAAAAGTGTCAAGTTTAGGTACCAAATTAAGTC
1 AAAAA----CAAGTTTAGGTACCAAATTAAGTC
44499914 AAAAACAAGTTTAGGTACCAAATTAAG
1 AAAAACAAGTTTAGGTACCAAATTAAG
44499941 AAAAAGTGTC
Statistics
Matches: 100, Mismatches: 6, Indels: 24
0.77 0.05 0.18
Matches are distributed among these distances:
26 5 0.05
27 5 0.05
29 41 0.41
31 38 0.38
32 1 0.01
33 10 0.10
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (29 bp):
AAAAACAAGTTTAGGTACCAAATTAAGTC
Found at i:44499877 original size:60 final size:59
Alignment explanation
Indices: 44499795--44499967 Score: 256
Period size: 60 Copynumber: 2.9 Consensus size: 59
44499785 AATTGAATCT
* * * * **
44499795 AAAAAAAGCTTAGGTACCAAATTAGGAAAAAATGCCAAGTTTAGGTACCAAATTGGGTTC
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTTAGGTACCAAATTAAG-TC
44499855 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTTAGGTACCAAATTAAGTC
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTTAGGTACCAAATTAAGTC
* *
44499914 AAAAACAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTACCAAAT
1 AAAAA-AAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTTAGGTACCAAAT
44499968 GTTATATTAA
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 7 0.07
60 97 0.93
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTTAGGTACCAAATTAAGTC
Found at i:44500626 original size:71 final size:71
Alignment explanation
Indices: 44500382--44500738 Score: 449
Period size: 71 Copynumber: 5.1 Consensus size: 71
44500372 CTTGGATTCA
* * *
44500382 TTTCACATTTA-AGTGACTCACGATGCTGTA-AGGAATTCGTAACAGATGCAAGATCTC-ACCAT
1 TTTCAC-TTTACAGTGACTCACGATGCTGTAGA-GAATCCGCAACAAATGCAAGATCTCAACCAT
*
44500444 CGGACCAA
64 CGGACCAT
* * * *
44500452 TTTCACATTTA-AGTGACTCACGATGCTGTAGAGAAACCGCAACAAATGTAAGATCTTAGCCATC
1 TTTCAC-TTTACAGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATC
44500516 GGACCA-
65 GGACCAT
* *
44500522 GTTCACTTTACAGTGACTCACGATGCTGTAGAGAATTCGCAACAAATGC-AGAATCTCAACCATC
1 TTTCACTTTACAGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAG-ATCTCAACCATC
44500586 GGACCAT
65 GGACCAT
* * * *
44500593 TTTCACTTTACAGTGACTCACAATGCTGTAGAGAATCCACAAAAAATGCAAGATCTCAGCCATC-
1 TTTCACTTTACAGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCG
*
44500657 GAGCTAT
66 GA-CCAT
* * * *
44500664 TTTCACTTTACAGTGACTCATGATGCTATAGAGAATCCGTAACAAATGCAGGATCTCAACCATCG
1 TTTCACTTTACAGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCG
44500729 GACCAT
66 GACCAT
44500735 TTTC
1 TTTC
44500739 CATCTTTGGC
Statistics
Matches: 250, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
69 6 0.02
70 107 0.43
71 133 0.53
72 4 0.02
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (71 bp):
TTTCACTTTACAGTGACTCACGATGCTGTAGAGAATCCGCAACAAATGCAAGATCTCAACCATCG
GACCAT
Found at i:44500732 original size:142 final size:141
Alignment explanation
Indices: 44500380--44500738 Score: 494
Period size: 142 Copynumber: 2.5 Consensus size: 141
44500370 TTCTTGGATT
* *
44500380 CATTTCACATTTA-AGTGACTCACGATGCTGTA-AGGAATTCGTAACAGATGCAAGATCTC-ACC
1 CATTTCAC-TTTACAGTGACTCACGATGCTGTAGA-GAATTCGTAACAAATGCAGGATCTCAACC
* * * * *
44500442 ATCGGACCAATTTCACATTTAAGTGACTCACGATGCTGTAGAGAAACCGCAACAAATGTAAGATC
64 ATCGGACCATTTTCACATTTAAGTGACTCACAATGCTGTAGAGAAACCACAAAAAATGCAAGATC
*
44500507 TTAGCCATCGGAC
129 TCAGCCATCGGAC
* * *
44500520 CAGTTCACTTTACAGTGACTCACGATGCTGTAGAGAATTCGCAACAAATGCAGAATCTCAACCAT
1 CATTTCACTTTACAGTGACTCACGATGCTGTAGAGAATTCGTAACAAATGCAGGATCTCAACCAT
*
44500585 CGGACCATTTTCAC-TTTACAGTGACTCACAATGCTGTAGAGAATCCACAAAAAATGCAAGATCT
66 CGGACCATTTTCACATTTA-AGTGACTCACAATGCTGTAGAGAAACCACAAAAAATGCAAGATCT
44500649 CAGCCATC-GAGC
130 CAGCCATCGGA-C
* * * *
44500661 TATTTTCACTTTACAGTGACTCATGATGCTATAGAGAATCCGTAACAAATGCAGGATCTCAACCA
1 CA-TTTCACTTTACAGTGACTCACGATGCTGTAGAGAATTCGTAACAAATGCAGGATCTCAACCA
44500726 TCGGACCATTTTC
65 TCGGACCATTTTC
44500739 CATCTTTGGC
Statistics
Matches: 194, Mismatches: 19, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
139 4 0.02
140 53 0.27
141 68 0.35
142 69 0.36
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (141 bp):
CATTTCACTTTACAGTGACTCACGATGCTGTAGAGAATTCGTAACAAATGCAGGATCTCAACCAT
CGGACCATTTTCACATTTAAGTGACTCACAATGCTGTAGAGAAACCACAAAAAATGCAAGATCTC
AGCCATCGGAC
Found at i:44501172 original size:26 final size:26
Alignment explanation
Indices: 44501141--44501194 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
44501131 TTTCCAACTT
44501141 GCCGAATGTTTAAAAACATTCCTACA
1 GCCGAATGTTTAAAAACATTCCTACA
*
44501167 GCCGAATGTTTAAAAGCATTCCTACA
1 GCCGAATGTTTAAAAACATTCCTACA
44501193 GC
1 GC
44501195 TCATTTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (26 bp):
GCCGAATGTTTAAAAACATTCCTACA
Found at i:44505352 original size:29 final size:29
Alignment explanation
Indices: 44505293--44505512 Score: 150
Period size: 29 Copynumber: 7.5 Consensus size: 29
44505283 TCGAGGGTAG
* * *
44505293 AATGGTAATTTTTGGACACTCGGGGGCAAA
1 AATGGTAATTTTTGGACATTC-AGGGTAAA
* *
44505323 AAT-GTGATTTTTGGGCATTCAGTGGT-AA
1 AATGGTAATTTTTGGACATTCAG-GGTAAA
* *
44505351 AATGGTAATTTTTGAAAAGTTCAGGGTCAAA
1 AATGGTAATTTTTGGACA-TTCAGGGT-AAA
*
44505382 AAT-GTAATTTTTGGACATCCAAGGGT-AA
1 AATGGTAATTTTTGGACATTC-AGGGTAAA
*
44505410 AATGGTAATTTTTGGATATTCAGGGGT-AA
1 AATGGTAATTTTTGGACATTCA-GGGTAAA
* * *
44505439 AATGGTAATTTTT-CAAAGTTTTAGGGTTAAA
1 AATGGTAATTTTTGGACA--TTCAGGG-TAAA
* **
44505470 AATGG-AATTTTTGCACATTTTGGGGCT-AA
1 AATGGTAATTTTTGGACA-TTCAGGG-TAAA
44505499 AATGGTAATTTTTG
1 AATGGTAATTTTTG
44505513 AAAGTTTTGG
Statistics
Matches: 156, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
28 14 0.09
29 75 0.48
30 52 0.33
31 15 0.10
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (29 bp):
AATGGTAATTTTTGGACATTCAGGGTAAA
Found at i:44505389 original size:30 final size:30
Alignment explanation
Indices: 44505293--44505561 Score: 144
Period size: 29 Copynumber: 9.0 Consensus size: 30
44505283 TCGAGGGTAG
* * * * *
44505293 AATGGTAATTTTTGGACACTCGGGGGCAAA
1 AATGGTAATTTTTGAAAATTCAGGGTCAAA
* ***
44505323 AAT-GTGATTTTTGGGCATTCAGTGGT--AA
1 AATGGTAATTTTTGAAAATTCAG-GGTCAAA
44505351 AATGGTAATTTTTGAAAAGTTCAGGGTCAAA
1 AATGGTAATTTTTGAAAA-TTCAGGGTCAAA
* * *
44505382 AAT-GTAATTTTTGGACATCCAAGGGT--AA
1 AATGGTAATTTTTGAAAATTC-AGGGTCAAA
* *
44505410 AATGGTAATTTTTGGATATTCAGGGGT--AA
1 AATGGTAATTTTTGAAAATTCA-GGGTCAAA
* * * *
44505439 AATGGTAATTTTTCAAAGTTTTAGGGTTAAA
1 AATGGTAATTTTTGAAA-ATTCAGGGTCAAA
* * ** * *
44505470 AATGG-AATTTTTGCACATTTTGGGGCTAA
1 AATGGTAATTTTTGAAAATTCAGGGTCAAA
* **
44505499 AATGGTAATTTTTGAAAGTTTTGGAGTCAAA
1 AATGGTAATTTTTGAAAATTCAGG-GTCAAA
*
44505530 AAT-GAAATTTTTGAAAACTTCAAGGGTCAAA
1 AATGGTAATTTTTGAAAA-TTC-AGGGTCAAA
44505561 A
1 A
44505562 TATGATTTAT
Statistics
Matches: 188, Mismatches: 36, Indels: 29
0.74 0.14 0.11
Matches are distributed among these distances:
28 11 0.06
29 82 0.44
30 65 0.35
31 28 0.15
32 2 0.01
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.35
Consensus pattern (30 bp):
AATGGTAATTTTTGAAAATTCAGGGTCAAA
Done.