Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 43 of 132
Found at i:11626062 original size:10 final size:10
Alignment explanation
Indices: 11626042--11626149 Score: 90
Period size: 10 Copynumber: 10.7 Consensus size: 10
11626032 TAAACTATCA
11626042 TAAACTGTGAT
1 TAAA-TGTGAT
*
11626053 TAAATATGAT
1 TAAATGTGAT
* *
11626063 TATATGTGAC
1 TAAATGTGAT
* *
11626073 TATATGTGGT
1 TAAATGTGAT
*
11626083 TATATGTGAT
1 TAAATGTGAT
*
11626093 TAAATATGAT
1 TAAATGTGAT
11626103 TAAATGTGAT
1 TAAATGTGAT
*
11626113 TATATGTGAT
1 TAAATGTGAT
**
11626123 TCTATGTGAT
1 TAAATGTGAT
** *
11626133 TATTTGTGGT
1 TAAATGTGAT
11626143 TAAATGT
1 TAAATGT
11626150 TACTATGGTT
Statistics
Matches: 80, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
10 76 0.95
11 4 0.05
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.45
Consensus pattern (10 bp):
TAAATGTGAT
Found at i:11626085 original size:20 final size:20
Alignment explanation
Indices: 11626047--11626140 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
11626037 TATCATAAAC
* *
11626047 TGTGATTAAATATGATTATA
1 TGTGATTATATGTGATTATA
* *
11626067 TGTGACTATATGTGGTTATA
1 TGTGATTATATGTGATTATA
* * *
11626087 TGTGATTAAATATGATTAAA
1 TGTGATTATATGTGATTATA
*
11626107 TGTGATTATATGTGATTCTA
1 TGTGATTATATGTGATTATA
*
11626127 TGTGATTATTTGTG
1 TGTGATTATATGTG
11626141 GTTAAATGTT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (20 bp):
TGTGATTATATGTGATTATA
Found at i:11626091 original size:40 final size:40
Alignment explanation
Indices: 11626047--11626134 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
11626037 TATCATAAAC
* *
11626047 TGTGATTAAATATGATTATATGTGACTATATGTGGTTATA
1 TGTGATTAAATATGATTAAATGTGACTATATGTGATTATA
* *
11626087 TGTGATTAAATATGATTAAATGTGATTATATGTGATTCTA
1 TGTGATTAAATATGATTAAATGTGACTATATGTGATTATA
11626127 TGTGATTA
1 TGTGATTA
11626135 TTTGTGGTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.45
Consensus pattern (40 bp):
TGTGATTAAATATGATTAAATGTGACTATATGTGATTATA
Found at i:11626093 original size:30 final size:30
Alignment explanation
Indices: 11626059--11626149 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
11626049 TGATTAAATA
*
11626059 TGATTATATGTGACTATATGTGGTTATATG
1 TGATTATATGTGATTATATGTGGTTATATG
* * * *
11626089 TGATTAAATATGATTAAATGTGATTATATG
1 TGATTATATGTGATTATATGTGGTTATATG
* * *
11626119 TGATTCTATGTGATTATTTGTGGTTAAATG
1 TGATTATATGTGATTATATGTGGTTATATG
11626149 T
1 T
11626150 TACTATGGTT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (30 bp):
TGATTATATGTGATTATATGTGGTTATATG
Found at i:11626168 original size:23 final size:23
Alignment explanation
Indices: 11626142--11626263 Score: 138
Period size: 23 Copynumber: 5.3 Consensus size: 23
11626132 TTATTTGTGG
* *
11626142 TTAAATGTTACTATGGTTTATGC
1 TTAAATGTTAATATGATTTATGC
11626165 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATATGATTTATGC
* *
11626188 TTAAATATTAATCTGATTTATGC
1 TTAAATGTTAATATGATTTATGC
* * * *
11626211 TTAAATATTAATGTGAATTATGT
1 TTAAATGTTAATATGATTTATGC
**
11626234 TTAAATGTTAAGGTGATTTATG-
1 TTAAATGTTAATATGATTTATGC
11626256 TGTAAATG
1 T-TAAATG
11626264 GACCCATGAA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
22 1 0.01
23 87 0.99
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TTAAATGTTAATATGATTTATGC
Found at i:11629228 original size:36 final size:36
Alignment explanation
Indices: 11629172--11629367 Score: 295
Period size: 36 Copynumber: 5.5 Consensus size: 36
11629162 GTGAAAGTGG
11629172 ATATGTGGG-ATGTTATTCATGCCATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
*
11629207 ATATGTGGGTATGTTATTCATGTCATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
* * * *
11629243 ATATATTGTTATGTTATTCATGTCATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
*
11629279 ATATGTGGGTATGTTATTCATGCTATGTGACAGTAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
* * * *
11629315 ATATGTGAGTATGTTATTCATGCCATGAGATAGAAA
1 ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
11629351 ATATGTGGGTATGTTAT
1 ATATGTGGGTATGTTAT
11629368 CCATTTTAGT
Statistics
Matches: 145, Mismatches: 15, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 9 0.06
36 136 0.94
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.39
Consensus pattern (36 bp):
ATATGTGGGTATGTTATTCATGCCATGTGACAGTAA
Found at i:11630946 original size:17 final size:17
Alignment explanation
Indices: 11630921--11631057 Score: 129
Period size: 17 Copynumber: 8.1 Consensus size: 17
11630911 TCATTTTGAG
11630921 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
* *
11630938 ATTTGTTTTAAGTTTAA
1 ATTTATTTTAAATTTAA
11630955 ATTTATTTTAAAATTTAA
1 ATTTATTTT-AAATTTAA
**
11630973 ATTTA-AATAAAGTTTAA
1 ATTTATTTTAAA-TTTAA
*
11630990 ATTTATTTTAAATTCAAA
1 ATTTATTTTAAATT-TAA
*
11631008 AGTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
* *
11631025 A-TTAATTTCAATTT--
1 ATTTATTTTAAATTTAA
*
11631039 ATTTGAATTTAAATTTAA
1 ATTT-ATTTTAAATTTAA
11631057 A
1 A
11631058 ATAAATAAGT
Statistics
Matches: 98, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
14 1 0.01
15 2 0.02
16 24 0.24
17 39 0.40
18 32 0.33
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:11630964 original size:11 final size:11
Alignment explanation
Indices: 11630950--11631003 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
11630940 TTGTTTTAAG
11630950 TTTAAATTTAT
1 TTTAAATTTAT
*
11630961 TTTAAAATTTAAA
1 TTT-AAATTT-AT
** *
11630974 TTTAAATAAAG
1 TTTAAATTTAT
11630985 TTTAAATTTAT
1 TTTAAATTTAT
11630996 TTTAAATT
1 TTTAAATT
11631004 CAAAAGTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
11 20 0.59
12 10 0.29
13 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:11630976 original size:35 final size:34
Alignment explanation
Indices: 11630921--11631032 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 34
11630911 TCATTTTGAG
*
11630921 ATTTATTTTAAATTTAAATTTGTTTTAAGTTTAA
1 ATTTATTTTAAATTTAAATTTATTTTAAGTTTAA
** *
11630955 ATTTATTTTAAAATTTAAATTTAAATAAAGTTTAA
1 ATTTATTTT-AAATTTAAATTTATTTTAAGTTTAA
* * *
11630990 ATTTATTTTAAATTCAAAAGTTATTTTAAATTTAA
1 ATTTATTTTAAATT-TAAATTTATTTTAAGTTTAA
*
11631025 ATTAATTT
1 ATTTATTT
11631033 CAATTTATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 14 0.22
35 51 0.78
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.54
Consensus pattern (34 bp):
ATTTATTTTAAATTTAAATTTATTTTAAGTTTAA
Found at i:11630990 original size:7 final size:6
Alignment explanation
Indices: 11630927--11631057 Score: 75
Period size: 6 Copynumber: 23.0 Consensus size: 6
11630917 TGAGATTTAT
** * *
11630927 TTTAAA TTTAAA TTT-GT TTTAAG TTTAAA TTT-AT TTTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* * * *
11630974 TTTAAA --TAAA GTTTAAA TTT-AT TTTAAA TTCAAAA GTT-AT TTTAAA
1 TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA
* *
11631020 TTTAAA -TT-AA TTTCAA TTT--A TTTGAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
11631058 ATAAATAAGT
Statistics
Matches: 96, Mismatches: 16, Indels: 26
0.70 0.12 0.19
Matches are distributed among these distances:
4 10 0.10
5 18 0.19
6 56 0.58
7 12 0.12
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:11631725 original size:3 final size:3
Alignment explanation
Indices: 11631711--11631787 Score: 77
Period size: 3 Copynumber: 25.3 Consensus size: 3
11631701 TATTAAATGC
* *
11631711 ATA ATGA ATA ATA ATA ATA A-A TATT CTCA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA -ATA AT-A ATA ATA ATA ATA ATA ATA
* *
11631758 ATA ATA ATA ATT TTA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11631788 AAAAGGAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
2 3 0.05
3 54 0.89
4 4 0.07
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:11631917 original size:27 final size:26
Alignment explanation
Indices: 11631886--11631944 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
11631876 AATCTGCAAA
11631886 AAAAACAAGCAAAGAACAG-TTTTTTTTT
1 AAAAA-AAG-AAA-AACAGTTTTTTTTTT
*
11631914 AAAAAAAGGAAAACAGTTTTTTTTTT
1 AAAAAAAGAAAAACAGTTTTTTTTTT
11631940 AAAAA
1 AAAAA
11631945 TGAGAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 5 0.17
26 16 0.55
27 3 0.10
28 5 0.17
ACGTcount: A:0.51, C:0.07, G:0.10, T:0.32
Consensus pattern (26 bp):
AAAAAAAGAAAAACAGTTTTTTTTTT
Found at i:11632944 original size:30 final size:30
Alignment explanation
Indices: 11632850--11633088 Score: 201
Period size: 30 Copynumber: 8.1 Consensus size: 30
11632840 CTTAGAAGGT
* * * *
11632850 CCTTGAACTTTCCAAAAATTATATTTTGAC
1 CCTTAAACTTTTCAAAAATTACATTTTAAC
*** * * *
11632880 CCCCGAACTTTCCAAAAATTATATTTTGAC
1 CCTTAAACTTTTCAAAAATTACATTTTAAC
*
11632910 CCTTAAACTTTTCAAAAATTACATTTTAAT
1 CCTTAAACTTTTCAAAAATTACATTTTAAC
11632940 CCTTAAACTTTTC-AAAATTACATTTTTAAC
1 CCTTAAACTTTTCAAAAATTACA-TTTTAAC
* *
11632970 CC-TAAAC-TCTCAAAAATTACATTTTTAC
1 CCTTAAACTTTTCAAAAATTACATTTTAAC
*
11632998 CCCTAAAC-TTTCAAAAA-TATCATTTTAA-
1 CCTTAAACTTTTCAAAAATTA-CATTTTAAC
* *
11633026 CCTCAAAC-TTTCTAAACATTAGCATTTT-AC
1 CCTTAAACTTTTC-AAAAATTA-CATTTTAAC
*
11633056 CCTCGAAACTTTT-AAAAATTAGCATTTT-AC
1 CCT-TAAACTTTTCAAAAATTA-CATTTTAAC
11633086 CCT
1 CCT
11633089 CGAACATCCA
Statistics
Matches: 180, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
28 23 0.13
29 48 0.27
30 102 0.57
31 4 0.02
32 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (30 bp):
CCTTAAACTTTTCAAAAATTACATTTTAAC
Found at i:11633089 original size:30 final size:29
Alignment explanation
Indices: 11632855--11633118 Score: 199
Period size: 30 Copynumber: 9.0 Consensus size: 29
11632845 AAGGTCCTTG
* *
11632855 AACTTTCCAAAAATTATATTTTGACCCCCG-
1 AACTTT-CAAAAATTACATTTT-ACCCTCGA
* *
11632885 AACTTTCCAAAAATTATATTTTGACCCT-TA
1 AACTTT-CAAAAATTACATTTT-ACCCTCGA
* *
11632915 AACTTTTCAAAAATTACATTTTAATCCT-TA
1 AAC-TTTCAAAAATTACATTTT-ACCCTCGA
11632945 AACTTTTC-AAAATTACATTTTTAACCCT--A
1 AAC-TTTCAAAAATTACA-TTTT-ACCCTCGA
* *
11632974 AACTCTCAAAAATTACATTTTTACCC-CTA
1 AACTTTCAAAAATTACA-TTTTACCCTCGA
*
11633003 AACTTTCAAAAA-TATCATTTTAACCTC-A
1 AACTTTCAAAAATTA-CATTTTACCCTCGA
*
11633031 AACTTTCTAAACATTAGCATTTTACCCTCGA
1 AACTTTC-AAAAATTA-CATTTTACCCTCGA
*
11633062 AACTTTTAAAAATTAGCATTTTACCCTCG-
1 AACTTTCAAAAATTA-CATTTTACCCTCGA
* *
11633091 AAC-ATCCAAAATTACCATTTTACCCTCG
1 AACTTTCAAAAATTA-CATTTTACCCTCG
11633119 GATGTCCAAA
Statistics
Matches: 205, Mismatches: 18, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
28 45 0.22
29 49 0.24
30 101 0.49
31 10 0.05
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (29 bp):
AACTTTCAAAAATTACATTTTACCCTCGA
Found at i:11633110 original size:28 final size:30
Alignment explanation
Indices: 11632953--11633118 Score: 134
Period size: 28 Copynumber: 5.7 Consensus size: 30
11632943 TAAACTTTTC
*
11632953 AAAATTA-CATTTTTAACCCT--AAACTCTCA
1 AAAATTAGCA-TTTT-ACCCTCGAAACTATCA
* *
11632982 AAAATTA-CATTTTTACCC-CTAAACTTTCA
1 AAAATTAGCA-TTTTACCCTCGAAACTATCA
* * *
11633011 AAAA-TATCATTTTAACCTC-AAACTTTCTA
1 AAAATTAGCATTTTACCCTCGAAACTATC-A
* * *
11633040 AACATTAGCATTTTACCCTCGAAACTTTTA
1 AAAATTAGCATTTTACCCTCGAAACTATCA
*
11633070 AAAATTAGCATTTTACCCTCG-AAC-ATCC
1 AAAATTAGCATTTTACCCTCGAAACTATCA
*
11633098 AAAATTACCATTTTACCCTCG
1 AAAATTAGCATTTTACCCTCG
11633119 GATGTCCAAA
Statistics
Matches: 119, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
28 42 0.35
29 36 0.30
30 34 0.29
31 7 0.06
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTAGCATTTTACCCTCGAAACTATCA
Found at i:11633112 original size:58 final size:55
Alignment explanation
Indices: 11632864--11633118 Score: 169
Period size: 58 Copynumber: 4.4 Consensus size: 55
11632854 GAACTTTCCA
* * * * * *
11632864 AAAATTATATTTTGACCCCCG-AACTTTCCAAAAATTATATTTTGACCCTTAAACTTTTCA
1 AAAATTACATTTT-ACCCTCGAAACTTT-TAAAAATTACATTTT-ACCCTCAAAC---TCC
* * *
11632924 AAAATTACATTTTAATCCT-TAAACTTTTCAAAATTACATTTTTAACCCT-AAACTCTC
1 AAAATTACATTTT-ACCCTCGAAACTTTTAAAAATTACA-TTTT-ACCCTCAAACTC-C
* * * *
11632981 AAAAATTACATTTTTACCC-CTAAACTTTCAAAAA-TATCATTTTAACCTCAAACTTTCT
1 -AAAATTACA-TTTTACCCTCGAAACTTTTAAAAATTA-CATTTTACCCTCAAAC--TCC
*
11633039 AAACATTAGCATTTTACCCTCGAAACTTTTAAAAATTAGCATTTTACCCTCGAACATCC
1 AAA-ATTA-CATTTTACCCTCGAAACTTTTAAAAATTA-CATTTTACCCTCAAAC-TCC
11633098 AAAATTACCATTTTACCCTCG
1 AAAATTA-CATTTTACCCTCG
11633119 GATGTCCAAA
Statistics
Matches: 158, Mismatches: 23, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
56 6 0.04
57 13 0.08
58 55 0.35
59 38 0.24
60 46 0.29
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (55 bp):
AAAATTACATTTTACCCTCGAAACTTTTAAAAATTACATTTTACCCTCAAACTCC
Found at i:11633126 original size:28 final size:28
Alignment explanation
Indices: 11633070--11633232 Score: 116
Period size: 28 Copynumber: 5.8 Consensus size: 28
11633060 GAAACTTTTA
* * **
11633070 AAAATTAGCATTTTACCCTCGAACATCC
1 AAAATTACCATTTTACCCTCGGATGTCC
11633098 AAAATTACCATTTTACCCTCGGATGTCC
1 AAAATTACCATTTTACCCTCGGATGTCC
* ** *
11633126 AAAAATTA-AATTTTTGACCCT-ATATTTTCC
1 -AAAATTACCA-TTTT-ACCCTCGGA-TGTCC
*
11633156 AAAAATTACCATTTTACCC-CGGGTGTCC
1 -AAAATTACCATTTTACCCTCGGATGTCC
* * ** * *
11633184 AAAATTATCGTTTTACTTTCGGGTGTAC
1 AAAATTACCATTTTACCCTCGGATGTCC
*
11633212 AAAATTACCATTTTGCCCTCG
1 AAAATTACCATTTTACCCTCG
11633233 AAAATCCAAA
Statistics
Matches: 105, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
27 14 0.13
28 53 0.50
29 16 0.15
30 21 0.20
31 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTCGGATGTCC
Found at i:11637618 original size:6 final size:6
Alignment explanation
Indices: 11637607--11637727 Score: 67
Period size: 6 Copynumber: 21.0 Consensus size: 6
11637597 TGAGATTTAT
** * *
11637607 TTTAAA TTTAAA TTT-GT TTTAAG TTTAAA TTT-AT TTTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* * * ** * *
11637654 TTTAAA -TGAAG TTTAAA TTT-AT TTTAAAA TCAAAA GTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
11637700 TTTAAA -TT-AA TTTGAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
11637728 ATAAATAAGT
Statistics
Matches: 84, Mismatches: 22, Indels: 18
0.68 0.18 0.15
Matches are distributed among these distances:
4 2 0.02
5 21 0.25
6 55 0.65
7 6 0.07
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:11637648 original size:12 final size:11
Alignment explanation
Indices: 11637630--11637681 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
11637620 TTGTTTTAAG
11637630 TTTAAATTTAT
1 TTTAAATTTAT
*
11637641 TTTAAAATTTAAA
1 TTT-AAATTT-AT
** *
11637654 TTTAAATGAAG
1 TTTAAATTTAT
11637665 TTTAAATTTAT
1 TTTAAATTTAT
11637676 TTTAAA
1 TTTAAA
11637682 ATCAAAAGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
11 18 0.56
12 10 0.31
13 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:11637656 original size:35 final size:34
Alignment explanation
Indices: 11637601--11637725 Score: 135
Period size: 35 Copynumber: 3.6 Consensus size: 34
11637591 TCATTTTGAG
*
11637601 ATTTATTTTAAATTTAAATTTGTTTTAAGTTTAA
1 ATTTATTTTAAATTTAAATTTATTTTAAGTTTAA
** *
11637635 ATTTATTTTAAAATTTAAATTTAAATGAAGTTTAA
1 ATTTATTTT-AAATTTAAATTTATTTTAAGTTTAA
** * *
11637670 ATTTATTTTAAAATCAAAAGTTATTTTAAATTTAA
1 ATTTATTTT-AAATTTAAATTTATTTTAAGTTTAA
* *
11637705 A-TTAATTTGAATTTAAATTTA
1 ATTTATTTTAAATTTAAATTTA
11637726 AAATAAATAA
Statistics
Matches: 74, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
33 9 0.12
34 15 0.20
35 50 0.68
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (34 bp):
ATTTATTTTAAATTTAAATTTATTTTAAGTTTAA
Found at i:11637726 original size:17 final size:17
Alignment explanation
Indices: 11637601--11637725 Score: 126
Period size: 17 Copynumber: 7.3 Consensus size: 17
11637591 TCATTTTGAG
11637601 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
* *
11637618 ATTTGTTTTAAGTTTAA
1 ATTTATTTTAAATTTAA
11637635 ATTTATTTTAAAATTTAA
1 ATTTATTTT-AAATTTAA
** * *
11637653 ATTTAAATGAAGTTTAA
1 ATTTATTTTAAATTTAA
**
11637670 ATTTATTTTAAAATCAAA
1 ATTTATTTT-AAATTTAA
*
11637688 AGTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
* *
11637705 A-TTAATTTGAATTTAA
1 ATTTATTTTAAATTTAA
11637721 ATTTA
1 ATTTA
11637726 AAATAAATAA
Statistics
Matches: 86, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
16 14 0.16
17 46 0.53
18 26 0.30
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:11638568 original size:36 final size:36
Alignment explanation
Indices: 11638508--11638619 Score: 136
Period size: 36 Copynumber: 3.1 Consensus size: 36
11638498 CGTTCAATCA
* * *
11638508 ATGTGACAGCAAATATGTGGGTATGTTATTCATGCC
1 ATGTAACAGAAAATATGTGAGTATGTTATTCATGCC
*
11638544 ATGTAACAGTAAATATGTGAGTATGTTATTCATGCC
1 ATGTAACAGAAAATATGTGAGTATGTTATTCATGCC
* * * *
11638580 ATG-AGATAGAAAATATGTAAATATGTTATTCATGTC
1 ATGTA-ACAGAAAATATGTGAGTATGTTATTCATGCC
11638616 ATGT
1 ATGT
11638620 GATAGTGAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
35 1 0.02
36 65 0.98
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.36
Consensus pattern (36 bp):
ATGTAACAGAAAATATGTGAGTATGTTATTCATGCC
Found at i:11638631 original size:36 final size:36
Alignment explanation
Indices: 11638529--11638631 Score: 134
Period size: 36 Copynumber: 2.9 Consensus size: 36
11638519 AATATGTGGG
* * * *
11638529 TATGTTATTCATGCCATGTAACAGTAAATATGTGAG
1 TATGTTATTCATGCCATGTGATAGTAAATATGTAAA
* *
11638565 TATGTTATTCATGCCATGAGATAGAAAATATGTAAA
1 TATGTTATTCATGCCATGTGATAGTAAATATGTAAA
* *
11638601 TATGTTATTCATGTCATGTGATAGTGAATAT
1 TATGTTATTCATGCCATGTGATAGTAAATAT
11638632 ATTATGCTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (36 bp):
TATGTTATTCATGCCATGTGATAGTAAATATGTAAA
Found at i:11639041 original size:10 final size:10
Alignment explanation
Indices: 11639026--11639137 Score: 125
Period size: 10 Copynumber: 11.2 Consensus size: 10
11639016 ATCATGAACC
11639026 GTGATTAAAT
1 GTGATTAAAT
*
11639036 GTGATTATAT
1 GTGATTAAAT
*
11639046 GTGGTTAAAT
1 GTGATTAAAT
* *
11639056 GTGACTATAT
1 GTGATTAAAT
*
11639066 GTGATTATAT
1 GTGATTAAAT
11639076 GTGATTAAAT
1 GTGATTAAAT
* * *
11639086 ATGACTATAT
1 GTGATTAAAT
11639096 GTGATTAAAT
1 GTGATTAAAT
11639106 GTGATTAAAT
1 GTGATTAAAT
**
11639116 GTGATTATTT
1 GTGATTAAAT
*
11639126 GTGGTTAAAT
1 GTGATTAAAT
11639136 GT
1 GT
11639138 TAGTATGACT
Statistics
Matches: 83, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 83 1.00
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (10 bp):
GTGATTAAAT
Found at i:11639070 original size:30 final size:30
Alignment explanation
Indices: 11639034--11639137 Score: 145
Period size: 30 Copynumber: 3.5 Consensus size: 30
11639024 CCGTGATTAA
* *
11639034 ATGTGATTATATGTGGTTAAATGTGACTAT
1 ATGTGATTAAATGTGATTAAATGTGACTAT
* *
11639064 ATGTGATTATATGTGATTAAATATGACTAT
1 ATGTGATTAAATGTGATTAAATGTGACTAT
*
11639094 ATGTGATTAAATGTGATTAAATGTGATTAT
1 ATGTGATTAAATGTGATTAAATGTGACTAT
* *
11639124 TTGTGGTTAAATGT
1 ATGTGATTAAATGT
11639138 TAGTATGACT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 67 1.00
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (30 bp):
ATGTGATTAAATGTGATTAAATGTGACTAT
Found at i:11639237 original size:23 final size:23
Alignment explanation
Indices: 11639130--11639251 Score: 129
Period size: 23 Copynumber: 5.3 Consensus size: 23
11639120 TTATTTGTGG
* * *
11639130 TTAAATGTTAGTATGACTTATGC
1 TTAAATGTTAATGTGATTTATGC
* * *
11639153 TTAAATGTTAATATGATTTGTAC
1 TTAAATGTTAATGTGATTTATGC
* *
11639176 TTGAATATTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
11639199 TTAAATATTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
* *
11639222 TTAAATGTTTAGGTGATTTATG-
1 TTAAATGTTAATGTGATTTATGC
11639244 TGTAAATG
1 T-TAAATG
11639252 GACCTATGAA
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
22 1 0.01
23 84 0.99
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (23 bp):
TTAAATGTTAATGTGATTTATGC
Found at i:11641035 original size:6 final size:6
Alignment explanation
Indices: 11641024--11641164 Score: 70
Period size: 6 Copynumber: 25.0 Consensus size: 6
11641014 TGAGATTTAT
** * * *
11641024 TTTAAA TTTAAA TTT-GT TTTAAG TTTAAA TTT-AT TTTAAAA TTTAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* * * * * *
11641071 TTTAAA -TCAAG TTTAAA TTT-AT TTTAAA TTCAAAA GTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA
* *
11641117 TTTAAA -TT-AA TTTCAA TTT--A TTTGAA TTTAAA TTT--A TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
11641159 TTTAAA
1 TTTAAA
11641165 ATAAATAAGT
Statistics
Matches: 100, Mismatches: 22, Indels: 26
0.68 0.15 0.18
Matches are distributed among these distances:
4 10 0.10
5 21 0.21
6 61 0.61
7 8 0.08
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:11641043 original size:17 final size:17
Alignment explanation
Indices: 11641018--11641129 Score: 116
Period size: 17 Copynumber: 6.5 Consensus size: 17
11641008 TCATTTTGAG
11641018 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
* *
11641035 ATTTGTTTTAAGTTTAA
1 ATTTATTTTAAATTTAA
11641052 ATTTATTTTAAAATTTAA
1 ATTTATTTT-AAATTTAA
* ** * *
11641070 TTTTAAATCAAGTTTAA
1 ATTTATTTTAAATTTAA
*
11641087 ATTTATTTTAAATTCAAA
1 ATTTATTTTAAATT-TAA
*
11641105 AGTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
*
11641122 ATTAATTT
1 ATTTATTT
11641130 CAATTTATTT
Statistics
Matches: 74, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
17 47 0.64
18 27 0.36
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:11641065 original size:12 final size:11
Alignment explanation
Indices: 11641047--11641100 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
11641037 TTGTTTTAAG
11641047 TTTAAATTTAT
1 TTTAAATTTAT
11641058 TTTAAAATTTAAT
1 TTT-AAATTT-AT
** *
11641071 TTTAAATCAAG
1 TTTAAATTTAT
11641082 TTTAAATTTAT
1 TTTAAATTTAT
11641093 TTTAAATT
1 TTTAAATT
11641101 CAAAAGTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 20 0.57
12 10 0.29
13 5 0.14
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:11641121 original size:35 final size:34
Alignment explanation
Indices: 11641018--11641129 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 34
11641008 TCATTTTGAG
*
11641018 ATTTATTTTAAATTTAAATTTGTTTTAAGTTTAA
1 ATTTATTTTAAATTTAAATTTATTTTAAGTTTAA
* ** *
11641052 ATTTATTTTAAAATTTAATTTTAAATCAAGTTTAA
1 ATTTATTTT-AAATTTAAATTTATTTTAAGTTTAA
* * *
11641087 ATTTATTTTAAATTCAAAAGTTATTTTAAATTTAA
1 ATTTATTTTAAATT-TAAATTTATTTTAAGTTTAA
*
11641122 ATTAATTT
1 ATTTATTT
11641130 CAATTTATTT
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
34 14 0.22
35 49 0.78
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (34 bp):
ATTTATTTTAAATTTAAATTTATTTTAAGTTTAA
Found at i:11641144 original size:16 final size:16
Alignment explanation
Indices: 11641018--11641164 Score: 90
Period size: 17 Copynumber: 9.1 Consensus size: 16
11641008 TCATTTTGAG
11641018 ATTTATTTTAAATTTAA
1 ATTTA-TTTAAATTTAA
* *
11641035 ATTTGTTTTAAGTTTAA
1 ATTT-ATTTAAATTTAA
11641052 ATTTATTTTAAAATTTAA
1 ATTTA-TTT-AAATTTAA
* * * *
11641070 TTTTAAATCAAGTTTAA
1 ATTT-ATTTAAATTTAA
*
11641087 ATTTATTTTAAATTCAAA
1 ATTTA-TTTAAATT-TAA
*
11641105 AGTTATTTTAAATTT-A
1 ATTTA-TTTAAATTTAA
*
11641121 A---A-TT-AATTTCA
1 ATTTATTTAAATTTAA
*
11641132 ATTTATTTGAATTTAA
1 ATTTATTTAAATTTAA
11641148 ATTTATTTAAATTTAA
1 ATTTATTTAAATTTAA
11641164 A
1 A
11641165 ATAAATAAGT
Statistics
Matches: 101, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
10 5 0.05
11 4 0.04
13 1 0.01
14 1 0.01
15 2 0.02
16 25 0.25
17 36 0.36
18 26 0.26
19 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTATTTAAATTTAA
Found at i:11641852 original size:3 final size:3
Alignment explanation
Indices: 11641846--11641885 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
11641836 AAATATTCTC
**
11641846 AAT AAT AAT AAT AAT AAT AAT TTT AAT AAT AA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11641886 AAAAGGAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:11642983 original size:30 final size:30
Alignment explanation
Indices: 11642947--11643147 Score: 137
Period size: 30 Copynumber: 6.8 Consensus size: 30
11642937 GAAGGTCCTT
*
11642947 AAACTTTCCAAAAATTATATTTTTACCCTC
1 AAACTTTCCAAAAATTACATTTTTACCCTC
** * * *
11642977 AAACTTTTTATAAATTATATTTTAACCC-C
1 AAACTTTCCAAAAATTACATTTTTACCCTC
* *
11643006 TAAATTTTCTAAAAATTACA-TTTT-CCCTC
1 -AAACTTTCCAAAAATTACATTTTTACCCTC
* * *
11643035 GAATTTTCC-AAAATTACATTTTTACCCCC
1 AAACTTTCCAAAAATTACATTTTTACCCTC
** **
11643064 AAAC-TTCCAAAAACCATGTTTTTGACCC-C
1 AAACTTTCCAAAAATTACATTTTT-ACCCTC
* *
11643093 GAACTTTCCAAAAATTACCATTTTGA-CCTC
1 AAACTTTCCAAAAATTA-CATTTTTACCCTC
* *
11643123 AAATTTTTTCAAAAATTACCATTTT
1 AAA-CTTTCCAAAAATTA-CATTTT
11643148 ACCTTGGGTA
Statistics
Matches: 134, Mismatches: 27, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
27 9 0.07
28 18 0.13
29 27 0.20
30 57 0.43
31 23 0.17
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
AAACTTTCCAAAAATTACATTTTTACCCTC
Found at i:11643200 original size:29 final size:28
Alignment explanation
Indices: 11643158--11643236 Score: 113
Period size: 29 Copynumber: 2.8 Consensus size: 28
11643148 ACCTTGGGTA
11643158 TCCAAAATTACCATTTTGCCCCCAAAGTG
1 TCCAAAATTACCATTTTGCCCCCAAA-TG
* *
11643187 TCCAAAATTACCATTTTACCCCCAGATG
1 TCCAAAATTACCATTTTGCCCCCAAATG
*
11643215 TCCAAAAATTATCATTTTGCCC
1 TCC-AAAATTACCATTTTGCCC
11643237 TCGGGTATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 5 0.11
29 40 0.89
ACGTcount: A:0.32, C:0.30, G:0.08, T:0.30
Consensus pattern (28 bp):
TCCAAAATTACCATTTTGCCCCCAAATG
Found at i:11643223 original size:58 final size:58
Alignment explanation
Indices: 11643099--11643236 Score: 145
Period size: 58 Copynumber: 2.4 Consensus size: 58
11643089 CCCCGAACTT
* * * * *** *
11643099 TCCAAAAATTACCATTTTGACCTCAAATTTTTTCAAAAATTACCATTTTACCTTGGGTA
1 TCCAAAAATTACCATTTTGCCCCCAAA-TGTGTCAAAAATTACCATTTTACCCCAGATA
* *
11643158 TCC-AAAATTACCATTTTGCCCCCAAA-GTGTCCAAAATTACCATTTTACCCCCAGATG
1 TCCAAAAATTACCATTTTGCCCCCAAATGTGTCAAAAATTACCATTTTA-CCCCAGATA
*
11643215 TCCAAAAATTATCATTTTGCCC
1 TCCAAAAATTACCATTTTGCCC
11643237 TCGGGTATCC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
56 18 0.27
57 7 0.11
58 38 0.58
59 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTGCCCCCAAATGTGTCAAAAATTACCATTTTACCCCAGATA
Found at i:11643247 original size:29 final size:29
Alignment explanation
Indices: 11643132--11643253 Score: 106
Period size: 29 Copynumber: 4.3 Consensus size: 29
11643122 CAAATTTTTT
* ***
11643132 CAAAAATTACCATTTT-ACCTTGGGTATC
1 CAAAAATTACCATTTTGCCCCCAGGTATC
* *
11643160 C-AAAATTACCATTTTGCCCCCAAAGTGTC
1 CAAAAATTACCATTTTGCCCCC-AGGTATC
* * *
11643189 C-AAAATTACCATTTTACCCCCAGATGTC
1 CAAAAATTACCATTTTGCCCCCAGGTATC
* * *
11643217 CAAAAATTATCATTTTGCCCTCGGGTATC
1 CAAAAATTACCATTTTGCCCCCAGGTATC
11643246 CAAAAATT
1 CAAAAATT
11643254 GCATTTTTGA
Statistics
Matches: 76, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
27 14 0.18
28 9 0.12
29 53 0.70
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (29 bp):
CAAAAATTACCATTTTGCCCCCAGGTATC
Found at i:11648065 original size:22 final size:22
Alignment explanation
Indices: 11648024--11648065 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11648014 GATTATTCAA
*
11648024 ATAATAAAATTATATTTTTATT
1 ATAATAAAATTATAATTTTATT
11648046 ATAATAAAAATTA-AATTTTA
1 ATAAT-AAAATTATAATTTTA
11648066 ATTTTGACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATAAAATTATAATTTTATT
Found at i:11648787 original size:2 final size:2
Alignment explanation
Indices: 11648780--11648808 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
11648770 CTTATTTATT
11648780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11648809 GTGATTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11654409 original size:20 final size:20
Alignment explanation
Indices: 11654372--11654409 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11654362 AGAACAAAGC
*
11654372 TGAAGAAGACTTAGAAGATT
1 TGAAGAAGACTTACAAGATT
11654392 TGAAGAAGGA-TTACAAGA
1 TGAAGAA-GACTTACAAGA
11654410 AACTTCGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.21
Consensus pattern (20 bp):
TGAAGAAGACTTACAAGATT
Found at i:11664779 original size:49 final size:49
Alignment explanation
Indices: 11664699--11665251 Score: 404
Period size: 49 Copynumber: 11.3 Consensus size: 49
11664689 GAGGAAACAT
* * * * * *
11664699 CGAACCTTATACCTTAGAGATGTGAAAGGAAAGATTGAAGCCGCAATGA
1 CGAATCTTATACCTTAGAGATATGGAGGGAAAGATTGAAGCCGCAACGG
* * * * * *
11664748 TGATTCTTGTACCATAGAGATATGGAGGGAAAGGTTGAAGCCGCGACGG
1 CGAATCTTATACCTTAGAGATATGGAGGGAAAGATTGAAGCCGCAACGG
* * * * *
11664797 TGAACCTTATACCTTAGAGATAT-GATGCGAAATATTGAAGCAGCAACGG
1 CGAATCTTATACCTTAGAGATATGGA-GGGAAAGATTGAAGCCGCAACGG
* * * * * * * * *
11664846 CGAGTCTTGTACCATGGAGATATGGAAGGAAAGGTTAAAGCCGCGACAG
1 CGAATCTTATACCTTAGAGATATGGAGGGAAAGATTGAAGCCGCAACGG
* * * * *
11664895 CGAACCTTATACCTTAAAGATGT-GATGGGAAAGATTGAGGCCGCAACGA
1 CGAATCTTATACCTTAGAGATATGGA-GGGAAAGATTGAAGCCGCAACGG
* * * *
11664944 CGAATCTTATACCTTAAAAATATGGAGGGAAAGGTTGAAGCCGCGACGG
1 CGAATCTTATACCTTAGAGATATGGAGGGAAAGATTGAAGCCGCAACGG
* * * * *
11664993 CAAACCTTATACCTTAGAAATAT-TATGGGAAAGATTGAAGCCGCAATGG
1 CGAATCTTATACCTTAGAGATATGGA-GGGAAAGATTGAAGCCGCAACGG
* * * * *
11665042 CCAATC-TAGTACCATGGAAATAT-GATGGGAAAGATTGAAGCCGCAATGG
1 CGAATCTTA-TACCTTAGAGATATGGA-GGGAAAGATTGAAGCCGCAACGG
* ** * * * **
11665091 TGAATCTGGTACCATGGAGATATGGAGGGAAAGGTTGAAGCCGTGACGG
1 CGAATCTTATACCTTAGAGATATGGAGGGAAAGATTGAAGCCGCAACGG
* * * *
11665140 CGAACCTTATACCTTAGAGATGT-GATGGGAAAGATTAAAGCCGCAACAG
1 CGAATCTTATACCTTAGAGATATGGA-GGGAAAGATTGAAGCCGCAACGG
* * * *
11665189 TGAATCTTATA-CTCTA-AGGT-TGAAGAGGAGCAGATTGAAGCCGCAACGG
1 CGAATCTTATACCT-TAGAGATATGGAG-GGA-AAGATTGAAGCCGCAACGG
*
11665238 CGAATCTTACACCT
1 CGAATCTTATACCT
11665252 CAAAGTCGTA
Statistics
Matches: 392, Mismatches: 98, Indels: 27
0.76 0.19 0.05
Matches are distributed among these distances:
47 2 0.01
48 18 0.05
49 364 0.93
50 8 0.02
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (49 bp):
CGAATCTTATACCTTAGAGATATGGAGGGAAAGATTGAAGCCGCAACGG
Found at i:11664869 original size:98 final size:98
Alignment explanation
Indices: 11664699--11665085 Score: 461
Period size: 98 Copynumber: 3.9 Consensus size: 98
11664689 GAGGAAACAT
* ** * * *
11664699 CGAACCTTATACCTTAGAGATGTGAAAGGAAAGATTGAAGCCGCAATGATGATTCTTGTACCATA
1 CGAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATA
*
11664764 GAGATATGGAGGGAAAGGTTGAAGCCGCGACGG
66 GAAATATGGAGGGAAAGGTTGAAGCCGCGACGG
* * * * * * *
11664797 TGAACCTTATACCTTAGAGATATGATGCGAAATATTGAAGCAGCAACGGCGAGTCTTGTACCATG
1 CGAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATA
* * * *
11664862 GAGATATGGAAGGAAAGGTTAAAGCCGCGACAG
66 GAAATATGGAGGGAAAGGTTGAAGCCGCGACGG
* * * * *
11664895 CGAACCTTATACCTTAAAGATGTGATGGGAAAGATTGAGGCCGCAACGACGAATCTTATACCTTA
1 CGAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATA
*
11664960 AAAATATGGAGGGAAAGGTTGAAGCCGCGACGG
66 GAAATATGGAGGGAAAGGTTGAAGCCGCGACGG
* * * * * * * *
11664993 CAAACCTTATACCTTAGAAATATTATGGGAAAGATTGAAGCCGCAATGGCCAATCTAGTACCATG
1 CGAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATA
*
11665058 GAAATAT-GATGGGAAAGATTGAAGCCGC
66 GAAATATGGA-GGGAAAGGTTGAAGCCGC
11665086 AATGGTGAAT
Statistics
Matches: 241, Mismatches: 47, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
97 2 0.01
98 239 0.99
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.21
Consensus pattern (98 bp):
CGAACCTTATACCTTAGAGATATGATGGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATA
GAAATATGGAGGGAAAGGTTGAAGCCGCGACGG
Found at i:11665033 original size:196 final size:196
Alignment explanation
Indices: 11664699--11665065 Score: 527
Period size: 196 Copynumber: 1.9 Consensus size: 196
11664689 GAGGAAACAT
* * * * *
11664699 CGAACCTTATACCTTAGAGATGTGAAAGGAAAGATTGAAGCCGCAATGATGATTCTTGTACCATA
1 CGAACCTTATACCTTAAAGATGTGAAAGGAAAGATTGAAGCCGCAACGACGAATCTTATACCATA
* * ** *
11664764 GAGATATGGAGGGAAAGGTTGAAGCCGCGACGGTGAACCTTATACCTTAGAGATATGATGCGAAA
66 AAAATATGGAGGGAAAGGTTGAAGCCGCGACGGCAAACCTTATACCTTAGAAATATGATGCGAAA
* * * * *
11664829 TATTGAAGCAGCAACGGCGAGTCTTGTACCATGGAGATATGGAAGGAAAGGTTAAAGCCGCGACA
131 GATTGAAGCAGCAACGGCCAATCTAGTACCATGGAAATATGGAAGGAAAGGTTAAAGCCGCGACA
11664894 G
196 G
** * *
11664895 CGAACCTTATACCTTAAAGATGTGATGGGAAAGATTGAGGCCGCAACGACGAATCTTATACCTTA
1 CGAACCTTATACCTTAAAGATGTGAAAGGAAAGATTGAAGCCGCAACGACGAATCTTATACCATA
* *
11664960 AAAATATGGAGGGAAAGGTTGAAGCCGCGACGGCAAACCTTATACCTTAGAAATATTATGGGAAA
66 AAAATATGGAGGGAAAGGTTGAAGCCGCGACGGCAAACCTTATACCTTAGAAATATGATGCGAAA
* *
11665025 GATTGAAGCCGCAATGGCCAATCTAGTACCATGGAAATATG
131 GATTGAAGCAGCAACGGCCAATCTAGTACCATGGAAATATG
11665066 ATGGGAAAGA
Statistics
Matches: 148, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
196 148 1.00
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (196 bp):
CGAACCTTATACCTTAAAGATGTGAAAGGAAAGATTGAAGCCGCAACGACGAATCTTATACCATA
AAAATATGGAGGGAAAGGTTGAAGCCGCGACGGCAAACCTTATACCTTAGAAATATGATGCGAAA
GATTGAAGCAGCAACGGCCAATCTAGTACCATGGAAATATGGAAGGAAAGGTTAAAGCCGCGACA
G
Found at i:11665861 original size:60 final size:60
Alignment explanation
Indices: 11665765--11665885 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
11665755 AATGAAAATC
* * *
11665765 CTAAAACTCTATTCCCTTATCTATCGTCGCTGCCCTTCCTTCACCATGGCCACATCAACG
1 CTAAAACTCTATTCCCTTATCTACCGTCACTACCCTTCCTTCACCATGGCCACATCAACG
*
11665825 CTAAAAC-CTTATTCCCTTATCTACCGTCACTACCCTTCCTTCACTATGGCCACATCAACG
1 CTAAAACTC-TATTCCCTTATCTACCGTCACTACCCTTCCTTCACCATGGCCACATCAACG
11665885 C
1 C
11665886 CACGTCACTA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.23, C:0.39, G:0.08, T:0.30
Consensus pattern (60 bp):
CTAAAACTCTATTCCCTTATCTACCGTCACTACCCTTCCTTCACCATGGCCACATCAACG
Found at i:11667434 original size:23 final size:25
Alignment explanation
Indices: 11667390--11667435 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
11667380 AACTTGTGAA
* *
11667390 TTAAATATATATTTATTCAAATTTT
1 TTAAAAATATATTTAATCAAATTTT
11667415 TTAAAAATAT-TTTAAT-AAATT
1 TTAAAAATATATTTAATCAAATT
11667436 AATTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 5 0.26
25 9 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAAAAATATATTTAATCAAATTTT
Found at i:11670576 original size:8 final size:8
Alignment explanation
Indices: 11670565--11670589 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
11670555 AATTATAAAA
11670565 TAATTATT
1 TAATTATT
11670573 TAATTATT
1 TAATTATT
11670581 TAATTATT
1 TAATTATT
11670589 T
1 T
11670590 GTATTTAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATTATT
Found at i:11677436 original size:31 final size:31
Alignment explanation
Indices: 11677401--11677468 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
11677391 AAAATTAACA
* *
11677401 CAATGAAATAAATAGAAACTTTT-AAATAGTT
1 CAATGAAATAAATA-AAAATTTTCAAATAATT
** *
11677432 CAATGACTTAAATAAAAATTTTCGAATAATT
1 CAATGAAATAAATAAAAATTTTCAAATAATT
11677463 CAATGA
1 CAATGA
11677469 TCAAATTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (31 bp):
CAATGAAATAAATAAAAATTTTCAAATAATT
Found at i:11678435 original size:14 final size:14
Alignment explanation
Indices: 11678416--11678453 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
11678406 GCAAGAAAGG
11678416 GTAAATGATGGCAA
1 GTAAATGATGGCAA
*
11678430 GTAAATGATGACAA
1 GTAAATGATGGCAA
11678444 GTAAA-GATGG
1 GTAAATGATGG
11678454 AATAACTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21
Consensus pattern (14 bp):
GTAAATGATGGCAA
Found at i:11681899 original size:39 final size:38
Alignment explanation
Indices: 11681856--11681932 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 38
11681846 GTAGTTATTA
* *
11681856 ATATGGATGTAATTGAGATATATTATGTATATATAACAT
1 ATATGGATGTAATTGAGATAGATCATGTAT-TATAACAT
*
11681895 ATATGGATGTAATTGAGCTAGATCATGTATTATAACAT
1 ATATGGATGTAATTGAGATAGATCATGTATTATAACAT
11681933 TTAATTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 8 0.23
39 27 0.77
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (38 bp):
ATATGGATGTAATTGAGATAGATCATGTATTATAACAT
Found at i:11683090 original size:195 final size:195
Alignment explanation
Indices: 11682758--11683145 Score: 695
Period size: 195 Copynumber: 2.0 Consensus size: 195
11682748 TACCTTAGTT
* *
11682758 TTCATTCATCCTAATTTGCTACCTGAATTTGACTTCAATGTTCAATTTGGTACCTAAACCAAATG
1 TTCATTCATCCTAATTTGCTACCTGAATTTGACTTCAATGCTCAATTTGGCACCTAAACCAAATG
* * *
11682823 GCATCATGTGGTCCAATGAGTATTTGATGTCTAATCTAGTAAAAAAAAATATAGATGCTTAATTG
66 GCATCATGTGGTCCAACGAGTATTTGATGTCTAATCTAGTAAAAAAAAATATAGATACTTAACTG
11682888 GGACCAAAACATTCTCGGATACTAAATAGAACATTGAAGTCAAACTTGGATACTTGGGAAAAATA
131 GGACCAAAACATTCTCGGATACTAAATAGAACATTGAAGTCAAACTTGGATACTTGGGAAAAATA
*
11682953 TTCATTCATCCTAATTTGCTACCTGAGTTTGACTTCAATGCTCAATTTGGCACCTAAACCAAATG
1 TTCATTCATCCTAATTTGCTACCTGAATTTGACTTCAATGCTCAATTTGGCACCTAAACCAAATG
* *
11683018 GCATCATGTGGTCCAACGAGTATTTGATGTCTAGTCTAGTAAAAAAAATTATAGATACTTAACTG
66 GCATCATGTGGTCCAACGAGTATTTGATGTCTAATCTAGTAAAAAAAAATATAGATACTTAACTG
*
11683083 GGACCAAAACATTCTCGGATACTAAATAGAACATTGAAGTCAAACTTGGGTACTTGGGAAAAA
131 GGACCAAAACATTCTCGGATACTAAATAGAACATTGAAGTCAAACTTGGATACTTGGGAAAAA
11683146 AATTAGTATC
Statistics
Matches: 184, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
195 184 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (195 bp):
TTCATTCATCCTAATTTGCTACCTGAATTTGACTTCAATGCTCAATTTGGCACCTAAACCAAATG
GCATCATGTGGTCCAACGAGTATTTGATGTCTAATCTAGTAAAAAAAAATATAGATACTTAACTG
GGACCAAAACATTCTCGGATACTAAATAGAACATTGAAGTCAAACTTGGATACTTGGGAAAAATA
Found at i:11684474 original size:17 final size:17
Alignment explanation
Indices: 11684441--11684474 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
11684431 TTATTAAAAA
11684441 AATAAATTTTTACATTT
1 AATAAATTTTTACATTT
11684458 AATATAATTTTTA-ATTT
1 AATA-AATTTTTACATTT
11684475 CAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
AATAAATTTTTACATTT
Found at i:11686923 original size:15 final size:17
Alignment explanation
Indices: 11686898--11686929 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11686888 TTTTTTTAAA
11686898 TTAATAAGGCTA-AAAC
1 TTAATAAGGCTAGAAAC
11686914 TTAA-AAGGCTAGAAAC
1 TTAATAAGGCTAGAAAC
11686930 AAATTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (17 bp):
TTAATAAGGCTAGAAAC
Found at i:11687526 original size:59 final size:59
Alignment explanation
Indices: 11687448--11687559 Score: 179
Period size: 59 Copynumber: 1.9 Consensus size: 59
11687438 TAAAATATAA
*
11687448 AATTTGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGACTC
1 AATTCGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGACTC
* * * *
11687507 AATTCGGTACTTGGACTTGACATTTTTTCCTAATTTTGTACCTAAGCTTTTTT
1 AATTCGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTT
11687560 TAGATTCAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.46
Consensus pattern (59 bp):
AATTCGGTACTTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTGGACTC
Found at i:11687783 original size:59 final size:59
Alignment explanation
Indices: 11687720--11687832 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
11687710 ATTAATATTA
* *
11687720 AAAAAGATTAAGTACCAAATTAGAAAAAAGAGTCAAGTTCT-GGTATCAAATTAGACCCT
1 AAAAAGATTAAGTACCAAATTAAAAAAAAGAGTCAAGTT-TAGGTACCAAATTAGACCCT
* * *
11687779 AAAAAGTTTAAGTACCAACTTAAAAAAAAGTGTCAAGTTTAGGTACCAAATTAG
1 AAAAAGATTAAGTACCAAATTAAAAAAAAGAGTCAAGTTTAGGTACCAAATTAG
11687833 GAAAAAGTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 1 0.02
59 47 0.98
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (59 bp):
AAAAAGATTAAGTACCAAATTAAAAAAAAGAGTCAAGTTTAGGTACCAAATTAGACCCT
Found at i:11687818 original size:31 final size:31
Alignment explanation
Indices: 11687782--11687861 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
11687772 AGACCCTAAA
*
11687782 AAGTTTAAGTACCAACTTAAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
* **
11687813 AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
* *
11687844 AAATTTGAGTACCAAATT
1 AAGTTTAAGTACCAAATT
11687862 GGACTAAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAAAAAAAGTGTC
Found at i:11687903 original size:90 final size:90
Alignment explanation
Indices: 11687731--11687904 Score: 199
Period size: 90 Copynumber: 1.9 Consensus size: 90
11687721 AAAAGATTAA
* * ** * *
11687731 GTACCAAATTAGAAAAAAGAGTCAAGTTCTGGTATCAAATTAGACCCTAAAAAGTTTAAGTACCA
1 GTACCAAATTAGAAAAAAGAGTCAAATTCTGGTACCAAATTAGACCAAAAAAAATTTAAATACCA
*
11687796 ACTTAAAAAAAAGTGTCAAGTTTAG
66 AATTAAAAAAAAGTGTCAAGTTTAG
* * * * *
11687821 GTACCAAATTAGGAAAAAGTGTCAAATT-TGAGTACCAAATTGGACTAAAAAAAATTTAAATATC
1 GTACCAAATTAGAAAAAAGAGTCAAATTCTG-GTACCAAATTAGACCAAAAAAAATTTAAATACC
*
11687885 AAATTAGAAAATAA-TGTCAA
65 AAATTA-AAAAAAAGTGTCAA
11687905 ATTCAAATAC
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
89 2 0.03
90 61 0.88
91 6 0.09
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.26
Consensus pattern (90 bp):
GTACCAAATTAGAAAAAAGAGTCAAATTCTGGTACCAAATTAGACCAAAAAAAATTTAAATACCA
AATTAAAAAAAAGTGTCAAGTTTAG
Found at i:11690505 original size:83 final size:83
Alignment explanation
Indices: 11690353--11690506 Score: 236
Period size: 83 Copynumber: 1.9 Consensus size: 83
11690343 GTGAAAGAGT
* * * **
11690353 TTTTTTTGGGTTTTTCGACCATCGGAGACGGCGGTCAACGTCGTCGATGATCGGTGATCACGATG
1 TTTTTTTGGGTTTTCCGACCATCGGAGACGACGGTCAACATCGTCGATGATCGGTGATCACGACA
11690418 GAGGTGTGATGGCCTCCA
66 GAGGTGTGATGGCCTCCA
* * *
11690436 TTTTTTTGGGTTTTCCGACCATTGGAGACGACGGTCAACATCGTCGATGATCGGTGGTCATGACA
1 TTTTTTTGGGTTTTCCGACCATCGGAGACGACGGTCAACATCGTCGATGATCGGTGATCACGACA
11690501 GAGGTG
66 GAGGTG
11690507 CGACGACCTC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 63 1.00
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (83 bp):
TTTTTTTGGGTTTTCCGACCATCGGAGACGACGGTCAACATCGTCGATGATCGGTGATCACGACA
GAGGTGTGATGGCCTCCA
Found at i:11692838 original size:34 final size:34
Alignment explanation
Indices: 11692762--11692868 Score: 92
Period size: 34 Copynumber: 3.0 Consensus size: 34
11692752 TCTTTTTCCC
* *
11692762 TTTTTTATTTATTTTAT-ATTTTATTATTATTATTA
1 TTTTTTATTTATTTTGTCATTTTATT-TT-TTTTTA
* *
11692797 -CTATTATTTATTTTGTCATTTTATTTTTTTTTA
1 TTTTTTATTTATTTTGTCATTTTATTTTTTTTTA
11692830 TTTTTTATTAGTTATTTCTCGTCATTTCTATTTTTTTTT
1 TTTTTTA-T--TTATTT-T-GTCATTT-TATTTTTTTTT
11692869 GCTTCTTTCA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
33 5 0.09
34 19 0.33
35 9 0.16
37 6 0.10
38 1 0.02
39 7 0.12
40 11 0.19
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.73
Consensus pattern (34 bp):
TTTTTTATTTATTTTGTCATTTTATTTTTTTTTA
Found at i:11692959 original size:17 final size:17
Alignment explanation
Indices: 11692933--11692968 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
11692923 TATCATTTAA
*
11692933 TTATTTGATCTTTATTT
1 TTATTGGATCTTTATTT
11692950 TTATTGGATCTTTATTT
1 TTATTGGATCTTTATTT
11692967 TT
1 TT
11692969 TATATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.08, T:0.69
Consensus pattern (17 bp):
TTATTGGATCTTTATTT
Found at i:11692987 original size:25 final size:25
Alignment explanation
Indices: 11692943--11692995 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
11692933 TTATTTGATC
*
11692943 TTTATTTTTATTGGATCTTTA-TTT
1 TTTATTTTTATTGCATCTTTACTTT
11692967 TTTATATTTTATT-CATGCTTTACTTT
1 TTTAT-TTTTATTGCAT-CTTTACTTT
11692993 TTT
1 TTT
11692996 TTAATTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 7 0.28
25 12 0.48
26 6 0.24
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.70
Consensus pattern (25 bp):
TTTATTTTTATTGCATCTTTACTTT
Found at i:11693558 original size:7 final size:7
Alignment explanation
Indices: 11693543--11693572 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
11693533 CGATGAATGG
11693543 TTTTT-T
1 TTTTTAT
11693549 TTTTTAT
1 TTTTTAT
11693556 TTTTTAT
1 TTTTTAT
11693563 TTTTTAT
1 TTTTTAT
11693570 TTT
1 TTT
11693573 CGAGGACCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTAT
Found at i:11697673 original size:20 final size:20
Alignment explanation
Indices: 11697648--11697685 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11697638 GCCATTGTTT
*
11697648 AATGTTTGCCATTTTTAACC
1 AATGTTTGACATTTTTAACC
*
11697668 AATGTTTGATATTTTTAA
1 AATGTTTGACATTTTTAA
11697686 TTCATTGTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (20 bp):
AATGTTTGACATTTTTAACC
Found at i:11697673 original size:27 final size:27
Alignment explanation
Indices: 11697620--11697674 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
11697610 CCATTTTGAC
** *
11697620 TAATGTTTGCAATTGTTGGCCATTGTT
1 TAATGTTTGCAATTGTTAACCAATGTT
* *
11697647 TAATGTTTGCCATTTTTAACCAATGTT
1 TAATGTTTGCAATTGTTAACCAATGTT
11697674 T
1 T
11697675 GATATTTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (27 bp):
TAATGTTTGCAATTGTTAACCAATGTT
Found at i:11700954 original size:16 final size:16
Alignment explanation
Indices: 11700929--11700968 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
11700919 TTACAATACC
* *
11700929 CATTTTTTTATTTTAT
1 CATTTATTTATTTCAT
11700945 CATTTATTTATTTCAT
1 CATTTATTTATTTCAT
11700961 -ATTTATTT
1 CATTTATTT
11700969 TTATTTCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (16 bp):
CATTTATTTATTTCAT
Found at i:11700973 original size:17 final size:17
Alignment explanation
Indices: 11700933--11700987 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
11700923 AATACCCATT
*
11700933 TTTTTATTTTATCATTTA
1 TTTTTATTTCAT-ATTTA
11700951 --TTTATTTCATATTTA
1 TTTTTATTTCATATTTA
*
11700966 TTTTTATTTCATGTTTA
1 TTTTTATTTCATATTTA
11700983 CTTTT
1 -TTTT
11700988 GTTTATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 5 0.16
16 9 0.28
17 14 0.44
18 4 0.12
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTTATTTCATATTTA
Found at i:11701312 original size:23 final size:23
Alignment explanation
Indices: 11701269--11701313 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11701259 TTATTTTCAT
* * *
11701269 TATTTCTTTATTTTCTTTAATTG
1 TATTTATTTATTTTATCTAATTG
11701292 TATTTATTTATTTTATCTAATT
1 TATTTATTTATTTTATCTAATT
11701314 CATATAAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTATTTATTTTATCTAATTG
Found at i:11705920 original size:13 final size:13
Alignment explanation
Indices: 11705902--11705936 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
11705892 GTGTGAAAAT
11705902 TAAATTATTAAGA
1 TAAATTATTAAGA
* *
11705915 TAAATTAGTAAGT
1 TAAATTATTAAGA
11705928 TAAATTATT
1 TAAATTATT
11705937 GCGATTATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (13 bp):
TAAATTATTAAGA
Found at i:11713518 original size:21 final size:20
Alignment explanation
Indices: 11713488--11713527 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
11713478 AAGTGAAAAG
*
11713488 AACAAAAAGAAATGAGTAAA
1 AACAAAAAGAAAAGAGTAAA
11713508 AACACAAAAGAAAAGAGTAA
1 AACA-AAAAGAAAAGAGTAA
11713528 GAAAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.07
Consensus pattern (20 bp):
AACAAAAAGAAAAGAGTAAA
Found at i:11715301 original size:17 final size:17
Alignment explanation
Indices: 11715272--11715304 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11715262 AAACTTTGCT
11715272 TTTATTTTCTATTTTAG
1 TTTATTTTCTATTTTAG
11715289 TTTATCTTT-TATTTTA
1 TTTAT-TTTCTATTTTA
11715305 CGCCTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (17 bp):
TTTATTTTCTATTTTAG
Found at i:11737302 original size:21 final size:21
Alignment explanation
Indices: 11737253--11737307 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
11737243 ACCAGCATAC
*
11737253 TCAGATGCATCCACACCAAAA
1 TCAGATGCAGCCACACCAAAA
* * *
11737274 CCATATGCAGCCACACCAGAA
1 TCAGATGCAGCCACACCAAAA
11737295 TCAGATGCAGCCA
1 TCAGATGCAGCCA
11737308 TAACTCTTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.35, G:0.15, T:0.13
Consensus pattern (21 bp):
TCAGATGCAGCCACACCAAAA
Found at i:11744560 original size:17 final size:17
Alignment explanation
Indices: 11744538--11744571 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11744528 TGTTAGTAAG
* *
11744538 CATTGTCGTTACATTTT
1 CATTGTCATCACATTTT
11744555 CATTGTCATCACATTTT
1 CATTGTCATCACATTTT
11744572 AGAGTTAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.09, T:0.50
Consensus pattern (17 bp):
CATTGTCATCACATTTT
Found at i:11757595 original size:21 final size:20
Alignment explanation
Indices: 11757571--11757613 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
11757561 CCGCTCCAAG
* *
11757571 GATAAGAAGCGCAGGAAGGAA
1 GATAAGAAGAGAAGGAA-GAA
11757592 GATAAGAAGAGAAGGAAGAA
1 GATAAGAAGAGAAGGAAGAA
11757612 GA
1 GA
11757614 ATCACCATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.53, C:0.05, G:0.37, T:0.05
Consensus pattern (20 bp):
GATAAGAAGAGAAGGAAGAA
Found at i:11760566 original size:23 final size:25
Alignment explanation
Indices: 11760535--11760583 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
11760525 TTATGTCCCA
11760535 CTTCATCTCACC-CCCTTATTTCTC
1 CTTCATCTCACCACCCTTATTTCTC
* *
11760559 CTTC-TCTCACCATCCTTTTTTCTC
1 CTTCATCTCACCACCCTTATTTCTC
11760583 C
1 C
11760584 CTTTTAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.10, C:0.45, G:0.00, T:0.45
Consensus pattern (25 bp):
CTTCATCTCACCACCCTTATTTCTC
Found at i:11763173 original size:17 final size:16
Alignment explanation
Indices: 11763151--11763195 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
11763141 TGGCTATATA
11763151 TTTCTTTTCTTTTCTCT
1 TTTCTTTTCTTTTCT-T
11763168 TTTCTTCTTC-TTTCTT
1 TTTCTT-TTCTTTTCTT
11763184 TTTC-TTTCTTTT
1 TTTCTTTTCTTTT
11763196 TGTGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 4 0.15
16 5 0.19
17 11 0.42
18 3 0.12
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTCTTTTCTTTTCTT
Found at i:11763194 original size:10 final size:11
Alignment explanation
Indices: 11763151--11763196 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
11763141 TGGCTATATA
11763151 TTTCTTTTCTT
1 TTTCTTTTCTT
11763162 TTCTCTTTTCTT
1 TT-TCTTTTCTT
*
11763174 CTTC-TTTCTT
1 TTTCTTTTCTT
11763184 TTTC-TTTCTT
1 TTTCTTTTCTT
11763194 TTT
1 TTT
11763197 GTGATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 18 0.56
11 4 0.12
12 10 0.31
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:11763819 original size:18 final size:16
Alignment explanation
Indices: 11763794--11763835 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
11763784 ACTAACAAGA
*
11763794 AAAATGCAGTGACAAAT
1 AAAATGCAATGAC-AAT
11763811 AACAATGCAATGACAAT
1 AA-AATGCAATGACAAT
11763828 AAAATGCA
1 AAAATGCA
11763836 TGCAACTACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 7 0.30
18 10 0.43
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (16 bp):
AAAATGCAATGACAAT
Found at i:11779414 original size:13 final size:13
Alignment explanation
Indices: 11779396--11779421 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11779386 CGCTGACACT
11779396 TATCGCATTGTTG
1 TATCGCATTGTTG
11779409 TATCGCATTGTTG
1 TATCGCATTGTTG
11779422 AACAAAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (13 bp):
TATCGCATTGTTG
Found at i:11790752 original size:19 final size:20
Alignment explanation
Indices: 11790717--11790755 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
11790707 ACCCAAATCA
11790717 TGTGAATAAATAAAAATTAGT
1 TGTGAATAAAT-AAAATTAGT
11790738 TGTGAATAAAT-AAATTAG
1 TGTGAATAAATAAAATTAG
11790756 ACTTGGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
TGTGAATAAATAAAATTAGT
Found at i:11796909 original size:10 final size:10
Alignment explanation
Indices: 11796894--11796918 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11796884 CTATTGTGTC
11796894 ACACTTAGGA
1 ACACTTAGGA
11796904 ACACTTAGGA
1 ACACTTAGGA
11796914 ACACT
1 ACACT
11796919 CCTCGTCAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (10 bp):
ACACTTAGGA
Found at i:11799715 original size:13 final size:13
Alignment explanation
Indices: 11799697--11799721 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11799687 CATATTTTAT
11799697 CATTTTTAGCATG
1 CATTTTTAGCATG
11799710 CATTTTTAGCAT
1 CATTTTTAGCAT
11799722 TTTTAGCTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:11807021 original size:20 final size:19
Alignment explanation
Indices: 11806987--11807025 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
11806977 CACACTCGTT
* *
11806987 GAAGAAATAAGAAAAGAGGA
1 GAAGAAAGAA-AAAAAAGGA
11807007 GAAGAAAGAAAAAAAAGGA
1 GAAGAAAGAAAAAAAAGGA
11807026 AGACACTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (19 bp):
GAAGAAAGAAAAAAAAGGA
Found at i:11808723 original size:42 final size:41
Alignment explanation
Indices: 11808664--11808862 Score: 265
Period size: 42 Copynumber: 4.7 Consensus size: 41
11808654 TATAGGATAG
* * *
11808664 GGTCTTTAGCGGCGCTTTCCCATAACCGCCGCTAAAGAACAT
1 GGTCTTTAGCGGCGCTTTCCCACAAACGCCGGT-AAGAACAT
**
11808706 GGTCTTTAGCGGCGCTTTTTGCACAAACGCCGGTAAGAACAT
1 GGTCTTTAGCGGCGC-TTTCCCACAAACGCCGGTAAGAACAT
*
11808748 GGTCTTTAGCGGCGATTTTCCCACAAACGCCGGTAAGAACAT
1 GGTCTTTAGCGGCG-CTTTCCCACAAACGCCGGTAAGAACAT
11808790 GGTCTTTAGCGGCGCTTTCCCACAAACG-CGGATAAAGAACAT
1 GGTCTTTAGCGGCGCTTTCCCACAAACGCCGG-T-AAGAACAT
* *
11808832 GGTCTTTAGAGGCACTTTTCCCACAAACGCC
1 GGTCTTTAGCGGCGC-TTTCCCACAAACGCC
11808863 ACTAACAATA
Statistics
Matches: 140, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
40 3 0.02
41 14 0.10
42 96 0.69
43 26 0.19
44 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (41 bp):
GGTCTTTAGCGGCGCTTTCCCACAAACGCCGGTAAGAACAT
Found at i:11816165 original size:41 final size:41
Alignment explanation
Indices: 11816108--11816469 Score: 402
Period size: 41 Copynumber: 8.8 Consensus size: 41
11816098 TAGCGGCATT
* * * *
11816108 TTTCACATAAGTGCCGCTAATGCTCTGACCTTTAGCGGAGC
1 TTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * *
11816149 TTTCCCATAAGCGCCGCTATTGCTCTTACCTTTAGTGGCAC
1 TTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * * *
11816190 TTGCCAATAAGTGCCGCTATTGCTCTGACCTTTAGCGGTGC
1 TTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
** *
11816231 TTTCTTATAAGCGCCGCTATTGCTTTGACCTTTAGCGGCGC
1 TTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
** *
11816272 TTGGCCATAAACGCCGCTATTGCTCTGACCTTTAGCGGCGC
1 TTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * * * *
11816313 TTGTGCCCAAAAGCGCCGCTATTACTCTGACATTTAGTGGAGC
1 TT-T-CCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * * *
11816356 TTGCCCATAACCGCCGCTATTGCTCTTACCTTTAGCAGCGC
1 TTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * *
11816397 TTGCCCATAAGCGCCGCTATTGCTCTAACCTTTAGTGGCGC
1 TTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
* * * *
11816438 ATTCCCATAAGCACCACAATTGCTCT-ACCTTT
1 TTTCCCATAAGCGCCGCTATTGCTCTGACCTTT
11816470 TGTGATGTTT
Statistics
Matches: 267, Mismatches: 52, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
40 6 0.02
41 228 0.85
43 33 0.12
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.31
Consensus pattern (41 bp):
TTTCCCATAAGCGCCGCTATTGCTCTGACCTTTAGCGGCGC
Found at i:11816409 original size:166 final size:164
Alignment explanation
Indices: 11816120--11816437 Score: 440
Period size: 166 Copynumber: 1.9 Consensus size: 164
11816110 TCACATAAGT
* * * *
11816120 GCCGCTAATGCTCTGACCTTTAGCGGAGCTTTCCCATAAGCGCCGCTATTGCTCTTACCTTTAGT
1 GCCGCTAATGCTCTGACCTTTAGCGGAGCTTTCCCAAAAGCGCCGCTATTACTCTGACATTTAGT
** * * * **
11816185 GGCACTTGCCAATAAGTGCCGCTATTGCTCTGACCTTTAGCGGTGCTTTCTTATAAGCGCCGCTA
66 GGCACTTGCCAATAACCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCGCCGCTA
* *
11816250 TTGCTTTGACCTTTAGCGGCGCTTGGCCATAAAC
131 TTGCTCTAACCTTTAGCGGCGCTTGGCCATAAAC
* *
11816284 GCCGCTATTGCTCTGACCTTTAGCGGCGCTTGTGCCCAAAAGCGCCGCTATTACTCTGACATTTA
1 GCCGCTAATGCTCTGACCTTTAGCGGAGCTT-T-CCCAAAAGCGCCGCTATTACTCTGACATTTA
* *
11816349 GTGG-AGCTTGCCCATAACCGCCGCTATTGCTCTTACCTTTAGCAGCGCTTGCCCATAAGCGCCG
64 GTGGCA-CTTGCCAATAACCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCGCCG
*
11816413 CTATTGCTCTAACCTTTAGTGGCGC
128 CTATTGCTCTAACCTTTAGCGGCGC
11816438 ATTCCCATAA
Statistics
Matches: 133, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
164 29 0.22
165 2 0.02
166 102 0.77
ACGTcount: A:0.18, C:0.30, G:0.22, T:0.30
Consensus pattern (164 bp):
GCCGCTAATGCTCTGACCTTTAGCGGAGCTTTCCCAAAAGCGCCGCTATTACTCTGACATTTAGT
GGCACTTGCCAATAACCGCCGCTATTGCTCTGACCTTTAGCAGCGCTTGCCCATAAGCGCCGCTA
TTGCTCTAACCTTTAGCGGCGCTTGGCCATAAAC
Found at i:11827043 original size:10 final size:10
Alignment explanation
Indices: 11827030--11827072 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
11827020 ACATATATAT
11827030 TTTTTTGTTC
1 TTTTTTGTTC
*
11827040 TTTTTTCTT-
1 TTTTTTGTTC
11827049 TTTTTTGTTC
1 TTTTTTGTTC
11827059 TTTTTCT-TTC
1 TTTTT-TGTTC
11827069 TTTT
1 TTTT
11827073 ATGTGACTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 8 0.28
10 20 0.69
11 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.84
Consensus pattern (10 bp):
TTTTTTGTTC
Found at i:11827053 original size:19 final size:18
Alignment explanation
Indices: 11827029--11827072 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
11827019 TACATATATA
11827029 TTTTTTTGTTCTTTTTTCT
1 TTTTTTTGTTC-TTTTTCT
11827048 TTTTTTTGTTCTTTTTCT
1 TTTTTTTGTTCTTTTTCT
*
11827066 TTCTTTT
1 TTTTTTT
11827073 ATGTGACTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTTTGTTCTTTTTCT
Found at i:11827633 original size:17 final size:17
Alignment explanation
Indices: 11827593--11827641 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
11827583 ATGATATATG
*
11827593 AAAATGCAATGACAATG
1 AAAATGCAATGACAATA
* * *
11827610 TAGATGCAGTGACAATA
1 AAAATGCAATGACAATA
11827627 AAAATGCAATGACAA
1 AAAATGCAATGACAA
11827642 AGGAAATGTG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATA
Found at i:11827648 original size:17 final size:17
Alignment explanation
Indices: 11827592--11827649 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
11827582 AATGATATAT
*
11827592 GAAAATGCAATGACAAT
1 GAAAATGCAATGACAAA
* * *
11827609 GTAGATGCAGTGACAATA
1 GAAAATGCAATGACAA-A
11827627 -AAAATGCAATGACAAA
1 GAAAATGCAATGACAAA
*
11827643 GGAAATG
1 GAAAATG
11827650 TGGTGACACT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 1 0.03
17 30 0.97
ACGTcount: A:0.50, C:0.10, G:0.22, T:0.17
Consensus pattern (17 bp):
GAAAATGCAATGACAAA
Found at i:11851305 original size:24 final size:24
Alignment explanation
Indices: 11851246--11851306 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
11851236 GAGTAATAAG
* * **
11851246 AGTTTGACTCAAACAAATAAACGG
1 AGTTTAACTGAAACAAATAAACAA
*
11851270 AGTTTAATTGAAACAAATAAACAA
1 AGTTTAACTGAAACAAATAAACAA
11851294 AGTTTAACTGAAA
1 AGTTTAACTGAAA
11851307 GATTATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:11882215 original size:11 final size:11
Alignment explanation
Indices: 11882199--11882223 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11882189 TTTATTTTAC
11882199 TATTTTTATTT
1 TATTTTTATTT
11882210 TATTTTTATTT
1 TATTTTTATTT
11882221 TAT
1 TAT
11882224 CTTAATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:11882723 original size:102 final size:102
Alignment explanation
Indices: 11882547--11882751 Score: 392
Period size: 102 Copynumber: 2.0 Consensus size: 102
11882537 AGGACGACAC
*
11882547 ACATAAAAAATACGTGTTCCTGTAATACAAGTGCTCATGTTGCTTTATTCATATGATATTTCCTG
1 ACATAAAAAATACGTGTTCCTGTAATACAAGTGCTCACGTTGCTTTATTCATATGATATTTCCTG
11882612 CATATTATGTTGCTAGTTTTTGGTTTGTAGTGGATGT
66 CATATTATGTTGCTAGTTTTTGGTTTGTAGTGGATGT
*
11882649 ACATAACAAATACGTGTTCCTGTAATACAAGTGCTCACGTTGCTTTATTCATATGATATTTCCTG
1 ACATAAAAAATACGTGTTCCTGTAATACAAGTGCTCACGTTGCTTTATTCATATGATATTTCCTG
11882714 CATATTATGTTGCTAGTTTTTGGTTTGTAGTGGATGT
66 CATATTATGTTGCTAGTTTTTGGTTTGTAGTGGATGT
11882751 A
1 A
11882752 ATAGTACATT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (102 bp):
ACATAAAAAATACGTGTTCCTGTAATACAAGTGCTCACGTTGCTTTATTCATATGATATTTCCTG
CATATTATGTTGCTAGTTTTTGGTTTGTAGTGGATGT
Found at i:11887715 original size:23 final size:23
Alignment explanation
Indices: 11887688--11887749 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
11887678 TTGGAATTAT
*
11887688 TATGCGAAAATATGGAAATATGC
1 TATGCGAAAATATGCAAATATGC
11887711 TATGCGAAAATATGCAAATATGC
1 TATGCGAAAATATGCAAATATGC
* *
11887734 AATGCGAAAAAATGCA
1 TATGCGAAAATATGCA
11887750 TGTATGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (23 bp):
TATGCGAAAATATGCAAATATGC
Found at i:11887768 original size:23 final size:23
Alignment explanation
Indices: 11887706--11887773 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
11887696 AATATGGAAA
* * * **
11887706 TATGCTATGCGAAAATATGCAAA
1 TATGCAATGCGAAAAAAGGCATG
*
11887729 TATGCAATGCGAAAAAATGCATG
1 TATGCAATGCGAAAAAAGGCATG
*
11887752 TATGTAATGC-AAGAAAAGGCAT
1 TATGCAATGCGAA-AAAAGGCAT
11887774 TGATTTTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.05
23 36 0.95
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (23 bp):
TATGCAATGCGAAAAAAGGCATG
Found at i:11891460 original size:30 final size:30
Alignment explanation
Indices: 11891416--11891896 Score: 99
Period size: 29 Copynumber: 16.5 Consensus size: 30
11891406 TGCCAGGGGC
11891416 AAAATGGTAATTTTTAGGA-AGTTCGAGGTTA
1 AAAATGGTAATTTTT-GGACA-TTCGAGGTTA
*
11891447 AAAATGG-AATTTTTGGACATTCGGGGTT-
1 AAAATGGTAATTTTTGGACATTCGAGGTTA
* *
11891475 AAAATGCTAA-TTTTGGA-A----AGTTTA
1 AAAATGGTAATTTTTGGACATTCGAGGTTA
* ** *
11891499 GGAAATGG-AATTTTTGGA-AGTTTAAGGGT-
1 -AAAATGGTAATTTTTGGACA-TTCGAGGTTA
* * * *
11891528 AAAATGGTAATTTTAGGAAAGTAT-GGGGTCA
1 AAAATGGTAATTTTTGGACA-T-TCGAGGTTA
* * * * **
11891559 AAAAT--AAAATTTTGGATATTTGAGCAT-
1 AAAATGGTAATTTTTGGACATTCGAGGTTA
* * * *
11891586 AAAATGGTAATTTTTGGAAAGTTTGGGGTCA
1 AAAATGGTAATTTTTGGACA-TTCGAGGTTA
* * *
11891617 AAAATGG-AATTTTTGGA-AGTCTAAGGGT-
1 AAAATGGTAATTTTTGGACATTC-GAGGTTA
* * * *
11891645 AAAATGGTAATATTTGGGCAGTTTG-GAGTCA
1 AAAATGGTAATTTTTGGACA-TTCGAG-GTTA
* *
11891676 AAAATGG-AATTTTTAGACATTCGAGGGT-
1 AAAATGGTAATTTTTGGACATTCGAGGTTA
* * * * *
11891704 AAAATGGTAATTTTGGGAAAGTTTGGGGTCA
1 AAAATGGTAATTTTTGGACA-TTCGAGGTTA
* * * * *
11891735 AAAATAG-ATTTTTTGGA-AGTTTGGGGGT-
1 AAAATGGTAATTTTTGGACA-TTCGAGGTTA
* *
11891763 AAAATGGTAATTTTTGGGA-AGTT-TAGGGTGA
1 AAAATGGTAATTTTT-GGACA-TTCGA-GGTTA
* * * *
11891794 AAAATGG-AAGTTTTGGACATTTGGGGGT-
1 AAAATGGTAATTTTTGGACATTCGAGGTTA
* * * * * *
11891822 AGAATGGTAATTATGGGAAAGTTCGGGGTGAA
1 AAAATGGTAATTTTTGGACA-TTCGAGGT-TA
* *
11891854 AAAATAG-AATTTTTGGAAATTCGAGG-T-
1 AAAATGGTAATTTTTGGACATTCGAGGTTA
11891881 AAAATGGTAATTTTTG
1 AAAATGGTAATTTTTG
11891897 TGAAGTTCGA
Statistics
Matches: 324, Mismatches: 86, Indels: 83
0.66 0.17 0.17
Matches are distributed among these distances:
23 3 0.01
24 2 0.01
25 13 0.04
27 13 0.04
28 57 0.18
29 96 0.30
30 84 0.26
31 51 0.16
32 5 0.02
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGACATTCGAGGTTA
Found at i:11891469 original size:29 final size:31
Alignment explanation
Indices: 11891416--11891907 Score: 104
Period size: 30 Copynumber: 16.9 Consensus size: 31
11891406 TGCCAGGGGC
11891416 AAAATGGTAATTTTTAGGAAGTTCGAGGTTA
1 AAAATGGTAATTTTTAGGAAGTTCGAGGTTA
*
11891447 AAAATGG-AATTTTT-GGACA-TTCGGGGTT-
1 AAAATGGTAATTTTTAGGA-AGTTCGAGGTTA
* *
11891475 AAAATGCTAA-TTTT-GGAAAGTT-TAGG---
1 AAAATGGTAATTTTTAGG-AAGTTCGAGGTTA
** *
11891501 -AAATGG-AATTTTT-GGAAGTTTAAGGGT-
1 AAAATGGTAATTTTTAGGAAGTTCGAGGTTA
* *
11891528 AAAATGGTAA-TTTTAGGAAAGTAT-GGGGTCA
1 AAAATGGTAATTTTTAGG-AAGT-TCGAGGTTA
* * * **
11891559 AAAAT--AAAATTTT-GGATA-TTTGAGCAT-
1 AAAATGGTAATTTTTAGGA-AGTTCGAGGTTA
* * *
11891586 AAAATGGTAATTTTT-GGAAAGTTTGGGGTCA
1 AAAATGGTAATTTTTAGG-AAGTTCGAGGTTA
* *
11891617 AAAATGG-AATTTTT-GGAAG-TCTAAGGGT-
1 AAAATGGTAATTTTTAGGAAGTTC-GAGGTTA
* * * * *
11891645 AAAATGGTAATATTTGGGCAGTTTG-GAGTCA
1 AAAATGGTAATTTTTAGGAAGTTCGAG-GTTA
*
11891676 AAAATGG-AATTTTTA-GACA-TTCGAGGGT-
1 AAAATGGTAATTTTTAGGA-AGTTCGAGGTTA
* * * *
11891704 AAAATGGTAA-TTTTGGGAAAGTTTGGGGTCA
1 AAAATGGTAATTTTTAGG-AAGTTCGAGGTTA
* * * * *
11891735 AAAATAG--ATTTTTTGGAAGTTTGGGGGT-
1 AAAATGGTAATTTTTAGGAAGTTCGAGGTTA
* * *
11891763 AAAATGGTAATTTTTGGGAAGTT-TAGGGTGA
1 AAAATGGTAATTTTTAGGAAGTTCGA-GGTTA
* * * *
11891794 AAAATGG-AAGTTTT-GGACA-TTTGGGGGT-
1 AAAATGGTAATTTTTAGGA-AGTTCGAGGTTA
* * * * *
11891822 AGAATGGTAA-TTATGGGAAAGTTCGGGGTGAA
1 AAAATGGTAATTTTTAGG-AAGTTCGAGGT-TA
* *
11891854 AAAATAG-AATTTTT-GGAAATTCGAGG-T-
1 AAAATGGTAATTTTTAGGAAGTTCGAGGTTA
11891881 AAAATGGTAATTTTT-GTGAAGTTCGAG
1 AAAATGGTAATTTTTAG-GAAGTTCGAG
11891908 TGCAATAATG
Statistics
Matches: 339, Mismatches: 71, Indels: 104
0.66 0.14 0.20
Matches are distributed among these distances:
24 7 0.02
25 14 0.04
27 12 0.04
28 71 0.21
29 87 0.26
30 95 0.28
31 45 0.13
32 8 0.02
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (31 bp):
AAAATGGTAATTTTTAGGAAGTTCGAGGTTA
Found at i:11891487 original size:59 final size:57
Alignment explanation
Indices: 11891411--11891973 Score: 354
Period size: 59 Copynumber: 9.7 Consensus size: 57
11891401 TTCGATGCCA
* * *
11891411 GGGGCAAAATGGTAATTTTTAGG-AAGTTCGAGGTTAAAAATGGAATTTTTGGACATTC
1 GGGGTAAAATGGTAATTTTTGGGAAAGTT-GAGGTCAAAAATGGAATTTTTGGA-ATTC
* * *
11891469 GGGGTTAAAATGCTAA-TTTT-GGAAAGTTTAGG----AAATGGAATTTTTGGAAGTTTA
1 GGGG-TAAAATGGTAATTTTTGGGAAAGTTGAGGTCAAAAATGGAATTTTTGGAA--TTC
* * * * * *
11891523 AGGGTAAAATGGTAA-TTTTAGGAAAGTATGGGGTCAAAAAT-AAAATTTTGGATATTT
1 GGGGTAAAATGGTAATTTTTGGGAAAGT-TGAGGTCAAAAATGGAATTTTTGGA-ATTC
** * *
11891580 GAGCATAAAATGGTAATTTTT-GGAAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTCTA
1 G-GGGTAAAATGGTAATTTTTGGGAAAG-TTGAGGTCAAAAATGGAATTTTTGGAA-T-TC
* * * *
11891640 AGGGTAAAATGGTAATATTTGGG-CAGTTTG-GAGTCAAAAATGGAATTTTTAGACATTC
1 GGGGTAAAATGGTAATTTTTGGGAAAG-TTGAG-GTCAAAAATGGAATTTTTGGA-ATTC
* * * *
11891698 GAGGGTAAAATGGTAA-TTTTGGGAAAGTTTGGGGTCAAAAATAGATTTTTTGGAAGTTTG
1 G-GGGTAAAATGGTAATTTTTGGGAAAG-TTGAGGTCAAAAATGGAATTTTTGGAA--TTC
* * * *
11891758 GGGGTAAAATGGTAATTTTTGGG-AAGTTTAGGGTGAAAAATGGAAGTTTTGGACATTTG
1 GGGGTAAAATGGTAATTTTTGGGAAAGTTGA-GGTCAAAAATGGAATTTTTGGA-A-TTC
* * * * *
11891817 GGGGTAGAATGGTAA-TTATGGGAAAGTTCGGGGTGAAAAAATAGAATTTTTGGAAATTC
1 GGGGTAAAATGGTAATTTTTGGGAAAGTT-GAGGT-CAAAAATGGAATTTTTGG-AATTC
* * * * *
11891876 GAGGTAAAATGGTAATTTTTGTG-AAGTTCGA-GTGCAATAATGTAAATTTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTTGGGAAAGTT-GAGGT-CAAAAATGGAATTTTTGG-AA-TTC
* * *
11891935 AGGGTCAAAAT-ATAATTTTT-GGAAAGTTTAAGGTCAAAA
1 GGGGT-AAAATGGTAATTTTTGGGAAAG-TTGAGGTCAAAA
11891974 TATGATTTTT
Statistics
Matches: 406, Mismatches: 61, Indels: 75
0.75 0.11 0.14
Matches are distributed among these distances:
52 1 0.00
53 30 0.07
54 12 0.03
55 3 0.01
57 7 0.02
58 91 0.22
59 215 0.53
60 46 0.11
61 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTGGGAAAGTTGAGGTCAAAAATGGAATTTTTGGAATTC
Found at i:11891511 original size:24 final size:28
Alignment explanation
Indices: 11891475--11891549 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 28
11891465 ATTCGGGGTT
*
11891475 AAAATGCTAATTTTGGAAAGTTT-A-GG
1 AAAATGGTAATTTTGGAAAGTTTAAGGG
11891501 -AAATGG-AATTTTTGG-AAGTTTAAGGG
1 AAAATGGTAA-TTTTGGAAAGTTTAAGGG
11891527 TAAAATGGTAATTTTAGGAAAGT
1 -AAAATGGTAATTTT-GGAAAGT
11891550 ATGGGGTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
24 8 0.20
25 12 0.30
26 2 0.05
28 10 0.25
29 4 0.10
30 4 0.10
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (28 bp):
AAAATGGTAATTTTGGAAAGTTTAAGGG
Found at i:11891753 original size:118 final size:118
Alignment explanation
Indices: 11891416--11891973 Score: 541
Period size: 118 Copynumber: 4.8 Consensus size: 118
11891406 TGCCAGGGGC
* * * *
11891416 AAAATGGTAATTTTTAGGAAG-TTCGAGGTTAAAAATGGAATTTTTGGACATTCG-GGGTTAAAA
1 AAAATGGTAATTTTTGGGAAGTTTGGA-GTCAAAAATGGAAATTTTGGACATTCGAGGG-TAAAA
* * *
11891479 TGCTAATTTT-GGAAAGTTT-AGG----AAATGGAATTTTTGGAAGTTTAAGGGT
64 TGGTAATTTTGGGAAAGTTTGGGGTCAAAAATAGAATTTTTGGAAGTTTAAGGGT
* * * * * * * **
11891528 AAAATGGTAATTTTAGGAAAGTATGGGGTCAAAAAT-AAAATTTTGGATATTTGAGCATAAAATG
1 AAAATGGTAATTTTTGGGAAGTTTGGAGTCAAAAATGGAAATTTTGGACATTCGAGGGTAAAATG
* * *
11891592 GTAATTTTTGGAAAGTTTGGGGTCAAAAATGGAATTTTTGGAAGTCTAAGGGT
66 GTAATTTTGGGAAAGTTTGGGGTCAAAAATAGAATTTTTGGAAGTTTAAGGGT
* * * *
11891645 AAAATGGTAATATTTGGGCAGTTTGGAGTCAAAAATGGAATTTTTAGACATTCGAGGGTAAAATG
1 AAAATGGTAATTTTTGGGAAGTTTGGAGTCAAAAATGGAAATTTTGGACATTCGAGGGTAAAATG
* **
11891710 GTAATTTTGGGAAAGTTTGGGGTCAAAAATAGATTTTTTGGAAGTTTGGGGGT
66 GTAATTTTGGGAAAGTTTGGGGTCAAAAATAGAATTTTTGGAAGTTTAAGGGT
* * * * *
11891763 AAAATGGTAATTTTTGGGAAGTTTAGG-GTGAAAAATGGAAGTTTTGGACATTTGGGGGTAGAAT
1 AAAATGGTAATTTTTGGGAAGTTT-GGAGTCAAAAATGGAAATTTTGGACATTCGAGGGTAAAAT
* * * * **
11891827 GGTAATTATGGGAAAGTTCGGGGTGAAAAAATAGAATTTTTGGAAATTCGA-GGT
65 GGTAATTTTGGGAAAGTTTGGGGT-CAAAAATAGAATTTTTGGAAGTTTAAGGGT
* * * * *
11891881 AAAATGGTAATTTTTGTGAAG-TTCGAGTGCAATAATGTAAATTTTGGAAAGTTC-AGGGTCAAA
1 AAAATGGTAATTTTTGGGAAGTTTGGAGT-CAAAAATGGAAATTTTGGACA-TTCGAGGGT-AAA
* * **
11891944 AT-ATAATTTTTGGAAAGTTTAAGGTCAAAA
63 ATGGTAATTTTGGGAAAGTTTGGGGTCAAAA
11891974 TATGATTTTT
Statistics
Matches: 364, Mismatches: 67, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
111 27 0.07
112 36 0.10
113 4 0.01
116 1 0.00
117 64 0.18
118 203 0.56
119 29 0.08
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (118 bp):
AAAATGGTAATTTTTGGGAAGTTTGGAGTCAAAAATGGAAATTTTGGACATTCGAGGGTAAAATG
GTAATTTTGGGAAAGTTTGGGGTCAAAAATAGAATTTTTGGAAGTTTAAGGGT
Found at i:11891956 original size:29 final size:29
Alignment explanation
Indices: 11891854--11891993 Score: 110
Period size: 29 Copynumber: 4.8 Consensus size: 29
11891844 TCGGGGTGAA
*
11891854 AAAATAGAATTTTTGGAAA-TTC-GAGGT-
1 AAAATATAATTTTTGGAAAGTTCAG-GGTC
* *
11891881 AAAATGGTAATTTTTGTG-AAGTTC-GAGTGC
1 AAAAT-ATAATTTTTG-GAAAGTTCAGGGT-C
* *
11891911 AATAATGTAAATTTTGGAAAGTTCAGGGTC
1 AA-AATATAATTTTTGGAAAGTTCAGGGTC
* *
11891941 AAAATATAATTTTTGGAAAGTTTAAGGTC
1 AAAATATAATTTTTGGAAAGTTCAGGGTC
* * *
11891970 AAAATATGATTTTTAGACAGTTCA
1 AAAATATAATTTTTGGAAAGTTCA
11891994 AGGACCTTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
27 5 0.05
28 12 0.13
29 49 0.53
30 20 0.22
31 6 0.07
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.36
Consensus pattern (29 bp):
AAAATATAATTTTTGGAAAGTTCAGGGTC
Found at i:11893108 original size:3 final size:3
Alignment explanation
Indices: 11893100--11893186 Score: 102
Period size: 3 Copynumber: 28.7 Consensus size: 3
11893090 GACTGCCTTT
* *
11893100 TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** * *
11893148 TTA CTA TTA AGA ATA GTA TTA TTA TTA TTGA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TT
11893187 GATTCTATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:11893369 original size:6 final size:6
Alignment explanation
Indices: 11893342--11893411 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
11893332 GACTTTGTTT
* * *
11893342 ATTTAA ATTTAGA A--TAA TTTTAA ATTTAA ATATAA ATTTAA A-ATAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
11893388 ATTT-A ATCTTAA A-ATAA ATTTAA A
1 ATTTAA AT-TTAA ATTTAA ATTTAA A
11893412 ATGGATTTAG
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
4 1 0.02
5 13 0.27
6 31 0.63
7 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:11893378 original size:29 final size:28
Alignment explanation
Indices: 11893345--11893413 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 28
11893335 TTTGTTTATT
* *
11893345 TAAATTTAGAATAATTTTAAAT-TTAAATA
1 TAAATTTAAAATAAATTT-AATCTTAAA-A
11893374 TAAATTTAAAATAAATTTAATCTTAAAA
1 TAAATTTAAAATAAATTTAATCTTAAAA
11893402 TAAATTTAAAAT
1 TAAATTTAAAAT
11893414 GGATTTAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 16 0.43
29 21 0.57
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (28 bp):
TAAATTTAAAATAAATTTAATCTTAAAA
Found at i:11893381 original size:18 final size:17
Alignment explanation
Indices: 11893342--11893411 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
11893332 GACTTTGTTT
*
11893342 ATTTAAATTTAGAATAA
1 ATTTAAATTTAAAATAA
*
11893359 TTTTAAATTT-AAAT--
1 ATTTAAATTTAAAATAA
11893373 A--TAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
11893388 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
11893405 ATTTAAA
1 ATTTAAA
11893412 ATGGATTTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
12 7 0.16
13 4 0.09
15 1 0.02
16 6 0.14
17 23 0.53
18 2 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:11893413 original size:11 final size:12
Alignment explanation
Indices: 11893362--11893393 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
11893352 AGAATAATTT
11893362 TAAATTTAAATA
1 TAAATTTAAATA
11893374 TAAATTTAAA-A
1 TAAATTTAAATA
11893385 TAAATTTAA
1 TAAATTTAA
11893394 TCTTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:11904592 original size:23 final size:23
Alignment explanation
Indices: 11904562--11904623 Score: 106
Period size: 23 Copynumber: 2.7 Consensus size: 23
11904552 TTAGAATTAT
11904562 TATGCGAAAATATGCAAATATGC
1 TATGCGAAAATATGCAAATATGC
11904585 TATGCGAAAATATGCAAATATGC
1 TATGCGAAAATATGCAAATATGC
* *
11904608 AATGCGAAAAAATGCA
1 TATGCGAAAATATGCA
11904624 TGTATGTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.23
Consensus pattern (23 bp):
TATGCGAAAATATGCAAATATGC
Found at i:11904634 original size:23 final size:23
Alignment explanation
Indices: 11904563--11904635 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
11904553 TAGAATTATT
11904563 ATGCGAAAATATGCAAATATGCT-
1 ATGCGAAAATATGCAAATATG-TA
*
11904586 ATGCGAAAATATGCAAATATGCA
1 ATGCGAAAATATGCAAATATGTA
* **
11904609 ATGCGAAAAAATGCATGTATGTA
1 ATGCGAAAATATGCAAATATGTA
11904632 ATGC
1 ATGC
11904636 AAGAAAAGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (23 bp):
ATGCGAAAATATGCAAATATGTA
Found at i:11904642 original size:23 final size:23
Alignment explanation
Indices: 11904580--11904647 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
11904570 AATATGCAAA
* * * **
11904580 TATGCTATGCGAAAATATGCAAA
1 TATGCAATGCGAAAAAAGGCATG
*
11904603 TATGCAATGCGAAAAAATGCATG
1 TATGCAATGCGAAAAAAGGCATG
*
11904626 TATGTAATGC-AAGAAAAGGCAT
1 TATGCAATGCGAA-AAAAGGCAT
11904648 TGATTTTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.05
23 36 0.95
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (23 bp):
TATGCAATGCGAAAAAAGGCATG
Found at i:11908602 original size:28 final size:29
Alignment explanation
Indices: 11908541--11909035 Score: 222
Period size: 29 Copynumber: 16.9 Consensus size: 29
11908531 TGCCAAGGGC
*
11908541 AAAATGGTAATTTTTAGGAAGTTCGA-GGTCA
1 AAAATGG-AATTTTT-GAAAGTTCGAGGGT-A
*
11908572 AAAATGGAATTTTTGACA-TTCGAGGGT-
1 AAAATGGAATTTTTGAAAGTTCGAGGGTA
* *
11908599 AAAATGGTAATTTTGGGAAAGTT-TAGGGTTA
1 AAAATGG-AATTTT-TGAAAGTTCGAGGG-TA
** **
11908630 AAAATGGAATTTTTGGTAGTTTAAGGGT-
1 AAAATGGAATTTTTGAAAGTTCGAGGGTA
*
11908658 AAAATGGTAATTTTGGGAAAGTAT-G-GGGTCA
1 AAAATGG-AATTTT-TGAAAGT-TCGAGGGT-A
** * * *
11908689 AAAATAAAATTTTTGGATGTTCGGGGGT-
1 AAAATGGAATTTTTGAAAGTTCGAGGGTA
* * * ** *
11908717 AAAATGCTAATTTTGGGAAGTTTTAGGTTA
1 AAAATG-GAATTTTTGAAAGTTCGAGGGTA
* * *
11908747 AAAA-AGAATTTTTGGAAG-CCTGAGGGTA
1 AAAATGGAATTTTTGAAAGTTC-GAGGGTA
* * *
11908775 AAATTGTAATTTTGGGAAAGTTCGA-GGTCA
1 AAAATGGAATTTT-TGAAAGTTCGAGGGT-A
* * * *
11908805 AAAATAGAAATTTTGAAAGTTTGGGGGT-
1 AAAATGGAATTTTTGAAAGTTCGAGGGTA
*
11908833 AAAATGGTAATTTTTGGGAAGTTC-AGGGTGA
1 AAAATGG-AATTTTT-GAAAGTTCGAGGGT-A
*
11908864 AAAATGGAATTTTTGGACA-TTCG-GGGT-
1 AAAATGGAATTTTT-GAAAGTTCGAGGGTA
* *
11908891 AAAATGGTAATTTTGGGAAGTTCG-GGGTTA
1 AAAATGG-AATTTTTGAAAGTTCGAGGG-TA
*
11908921 AAAATGGAATTTTTGGAAA-TTC-AAGGT-
1 AAAATGGAATTTTT-GAAAGTTCGAGGGTA
* * *
11908948 AAAATGGTAATTTTTGTGAAGCTCGAGGGCA
1 AAAATGG-AATTTTTG-AAAGTTCGAGGGTA
* * * * *
11908979 ATAATGTAAATTTTGGAAAGTTCAAGGGTC
1 AAAATG-GAATTTTTGAAAGTTCGAGGGTA
*
11909009 AAAATGTAATTTTTGAAAAGTT-GAGGG
1 AAAATGGAATTTTTG-AAAGTTCGAGGG
11909036 GTCAAAATAT
Statistics
Matches: 349, Mismatches: 75, Indels: 82
0.69 0.15 0.16
Matches are distributed among these distances:
27 24 0.07
28 72 0.21
29 107 0.31
30 106 0.30
31 40 0.11
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGAAAGTTCGAGGGTA
Found at i:11908605 original size:58 final size:58
Alignment explanation
Indices: 11908536--11909021 Score: 434
Period size: 59 Copynumber: 8.3 Consensus size: 58
11908526 TTCGATGCCA
* * *
11908536 AGGGCAAAATGGTAATTTTTAGGAAGTTCGAGGTCAAAAATGGAATTTTT-GACATTCG
1 AGGGTAAAATGGTAA-TTTTGGGAAGTTCGAGGTCAAAAATGGAATTTTTGGAAATTCG
* * * * **
11908594 AGGGTAAAATGGTAATTTTGGGAAAGTT-TAGGGTTAAAAATGGAATTTTTGGTAGTTTA
1 AGGGTAAAATGGTAATTTTGGG-AAGTTCGA-GGTCAAAAATGGAATTTTTGGAAATTCG
* ** **
11908653 AGGGTAAAATGGTAATTTTGGGAAAGTAT-GGGGTCAAAAATAAAATTTTTGGATGTTCG
1 AGGGTAAAATGGTAATTTTGGG-AAGT-TCGAGGTCAAAAATGGAATTTTTGGAAATTCG
* * ** * * **
11908712 GGGGTAAAATGCTAATTTTGGGAAGTTTTAGGTTAAAAA-AGAATTTTTGG-AAGCCTG
1 AGGGTAAAATGGTAATTTTGGGAAGTTCGAGGTCAAAAATGGAATTTTTGGAAATTC-G
* * * *
11908769 AGGGTAAAATTGTAATTTTGGGAAAGTTCGAGGTCAAAAATAGAAATTTT-GAAAGTTTG
1 AGGGTAAAATGGTAATTTTGGG-AAGTTCGAGGTCAAAAATGGAATTTTTGGAAA-TTCG
* * *
11908828 GGGGTAAAATGGTAATTTTTGGGAAGTTC-AGGGTGAAAAATGGAATTTTTGGACATTCG
1 AGGGTAAAATGGTAA-TTTTGGGAAGTTCGA-GGTCAAAAATGGAATTTTTGGAAATTCG
* *
11908887 -GGGTAAAATGGTAATTTTGGGAAGTTCGGGGTTAAAAATGGAATTTTTGGAAATTC-
1 AGGGTAAAATGGTAATTTTGGGAAGTTCGAGGTCAAAAATGGAATTTTTGGAAATTCG
* * * * * * * *
11908943 AAGGTAAAATGGTAATTTTTGTGAAGCTCGAGGGCAATAATGTAAATTTTGGAAAGTTCA
1 AGGGTAAAATGGTAA-TTTTGGGAAGTTCGAGGTCAAAAATGGAATTTTTGGAAA-TTCG
11909003 AGGGTCAAAAT-GTAATTTT
1 AGGGT-AAAATGGTAATTTT
11909022 TGAAAAGTTG
Statistics
Matches: 351, Mismatches: 58, Indels: 37
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.00
57 89 0.25
58 110 0.31
59 127 0.36
60 19 0.05
61 5 0.01
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (58 bp):
AGGGTAAAATGGTAATTTTGGGAAGTTCGAGGTCAAAAATGGAATTTTTGGAAATTCG
Found at i:11908792 original size:116 final size:117
Alignment explanation
Indices: 11908536--11908961 Score: 469
Period size: 116 Copynumber: 3.7 Consensus size: 117
11908526 TTCGATGCCA
* * * ** *
11908536 AGGGCAAAATGGTAATTTTTAGG-AAGTTCGAGGTCAAAAATGGAATTTTT-GACA-TTCGAGGG
1 AGGGTAAAATGGTAA-TTTTGGGAAAGTTCGGGGTCAAAAATAAAATTTTTGGA-AGTTCGGGGG
* * *
11908598 TAAAATGGTAATTTTGGGAAAGTTTAGGGTTAAAAATGGAATTTTTGGTAGTTTA
64 TAAAATGGTAATTTTGGG-AAGTTTAGGGTTAAAAATGGAATTTTTGGAAGTCTG
*
11908653 AGGGTAAAATGGTAATTTTGGGAAAGTAT-GGGGTCAAAAATAAAATTTTTGGATGTTCGGGGGT
1 AGGGTAAAATGGTAATTTTGGGAAAGT-TCGGGGTCAAAAATAAAATTTTTGGAAGTTCGGGGGT
* * *
11908717 AAAATGCTAATTTTGGGAAGTTTTA-GGTTAAAAA-AGAATTTTTGGAAGCCTG
65 AAAATGGTAATTTTGGGAAG-TTTAGGGTTAAAAATGGAATTTTTGGAAGTCTG
* * * *
11908769 AGGGTAAAATTGTAATTTTGGGAAAGTTCGAGGTCAAAAATAGAAA-TTTTGAAAGTTTGGGGGT
1 AGGGTAAAATGGTAATTTTGGGAAAGTTCGGGGTCAAAAATA-AAATTTTTGGAAGTTCGGGGGT
* * *
11908833 AAAATGGTAATTTTTGGGAAGTTCAGGGTGAAAAATGGAATTTTTGGACATTC-G
65 AAAATGGTAA-TTTTGGGAAGTTTAGGGTTAAAAATGGAATTTTTGGA-AGTCTG
* ** * **
11908887 -GGGTAAAATGGTAATTTTGGG-AAGTTCGGGGTTAAAAATGGAATTTTTGGAAATTC-AAGGTA
1 AGGGTAAAATGGTAATTTTGGGAAAGTTCGGGGTCAAAAATAAAATTTTTGGAAGTTCGGGGGTA
11908949 AAATGGTAATTTT
66 AAATGGTAATTTT
11908962 TGTGAAGCTC
Statistics
Matches: 263, Mismatches: 34, Indels: 27
0.81 0.10 0.08
Matches are distributed among these distances:
114 4 0.02
115 16 0.06
116 109 0.41
117 89 0.34
118 43 0.16
119 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (117 bp):
AGGGTAAAATGGTAATTTTGGGAAAGTTCGGGGTCAAAAATAAAATTTTTGGAAGTTCGGGGGTA
AAATGGTAATTTTGGGAAGTTTAGGGTTAAAAATGGAATTTTTGGAAGTCTG
Found at i:11909000 original size:175 final size:175
Alignment explanation
Indices: 11908541--11909023 Score: 518
Period size: 175 Copynumber: 2.7 Consensus size: 175
11908531 TGCCAAGGGC
* * *
11908541 AAAATGGTAATTTTTAGGAAGTTCGAGGTCAAAAATGGAATTTTT-GACATTCGAGGGTAAAATG
1 AAAATGGTAA-TTTTGGGAAGTTCGAGGTTAAAAATGGAATTTTTGGAAATTC-AGGGTAAAATG
** * * *
11908605 GTAATTTTGGGAAAGTTTAGGGTTAAAAATGGAATTTTTGG-TAGTTTAAGGGTAAAATGGTAA-
64 GTAATTTTGGGAAAGTCGAGGG-CAAAAAT-GAAATTTTGGAAAGTTTAAGGGTAAAATGGTAAT
* **
11908668 TTTTGGGAAAGTATGGGGTCAAAAATAAAATTTTTGGATGTTCGGGGGT
127 TTTTGGGAAAGTATAGGGTCAAAAATAAAATTTTTGGACATTCGGGGGT
* ** * ** * *
11908717 AAAATGCTAATTTTGGGAAGTTTTAGGTTAAAAA-AGAATTTTTGGAAGCCTGAGGGTAAAATTG
1 AAAATGGTAATTTTGGGAAGTTCGAGGTTAAAAATGGAATTTTTGGAA-ATTCAGGGTAAAATGG
* **
11908781 TAATTTTGGGAAAGTTCGAGGTCAAAAATAGAAATTTT-GAAAGTTTGGGGGTAAAATGGTAATT
65 TAATTTTGGGAAAG-TCGAGGGCAAAAAT-GAAATTTTGGAAAGTTTAAGGGTAAAATGGTAATT
* **
11908845 TTTGGG-AAGT-TCAGGGTGAAAAATGGAATTTTTGGACATTC-GGGGT
128 TTTGGGAAAGTAT-AGGGTCAAAAATAAAATTTTTGGACATTCGGGGGT
* *
11908891 AAAATGGTAATTTTGGGAAGTTCGGGGTTAAAAATGGAATTTTTGGAAATTCAAGGTAAAATGGT
1 AAAATGGTAATTTTGGGAAGTTCGAGGTTAAAAATGGAATTTTTGGAAATTCAGGGTAAAATGGT
* * *
11908956 AATTTTTGTG-AAGCTCGAGGGCAATAATGTAAATTTTGGAAAGTTCAAGGGTCAAAAT-GTAAT
66 AA-TTTTGGGAAAG-TCGAGGGCAAAAATG-AAATTTTGGAAAGTTTAAGGGT-AAAATGGTAAT
11909019 TTTTG
127 TTTTG
11909024 AAAAGTTGAG
Statistics
Matches: 253, Mismatches: 43, Indels: 23
0.79 0.13 0.07
Matches are distributed among these distances:
173 1 0.00
174 81 0.32
175 145 0.57
176 26 0.10
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.34
Consensus pattern (175 bp):
AAAATGGTAATTTTGGGAAGTTCGAGGTTAAAAATGGAATTTTTGGAAATTCAGGGTAAAATGGT
AATTTTGGGAAAGTCGAGGGCAAAAATGAAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTT
GGGAAAGTATAGGGTCAAAAATAAAATTTTTGGACATTCGGGGGT
Found at i:11909035 original size:29 final size:28
Alignment explanation
Indices: 11908536--11909035 Score: 210
Period size: 30 Copynumber: 17.1 Consensus size: 28
11908526 TTCGATGCCA
*
11908536 AGGGCAAAATGGTAATTTTTAGG-AAGTTCG
1 AGGGTAAAAT-GTAATTTTT-GGAAAGTT-G
* *
11908566 A-GGTCAAAAATGGAATTTTT-GACA-TTCG
1 AGGGT--AAAATGTAATTTTTGGAAAGTT-G
* *
11908594 AGGGTAAAATGGTAATTTTGGGAAAGTTT
1 AGGGTAAAAT-GTAATTTTTGGAAAGTTG
* * *
11908623 AGGGTTAAAAATGGAATTTTTGG-TAGTTTA
1 AGGG-T-AAAATGTAATTTTTGGAAAG-TTG
*
11908653 AGGGTAAAATGGTAATTTTGGGAAAGTATG
1 AGGGTAAAAT-GTAATTTTTGGAAAGT-TG
** *
11908683 -GGGTCAAAAATAAAATTTTTGG-ATGTTCG
1 AGGGT--AAAATGTAATTTTTGGAAAGTT-G
* * *
11908712 GGGGTAAAATGCTAA-TTTTGGGAAGTTTT
1 AGGGTAAAATG-TAATTTTTGGAAAG-TTG
* * *
11908741 AGGTTAAAAAAG-AATTTTTGG-AAGCCTG
1 AGGGT-AAAATGTAATTTTTGGAAAG-TTG
*
11908769 AGGGTAAAATTGTAATTTTGGGAAAGTTCG
1 AGGGTAAAA-TGTAATTTTTGGAAAGTT-G
*
11908799 A-GGTCAAAAATAG-AAATTTT-GAAAGTTTG
1 AGGGT--AAAAT-GTAATTTTTGGAAAG-TTG
* * *
11908828 GGGGTAAAATGGTAATTTTTGGGAAGTTC
1 AGGGTAAAAT-GTAATTTTTGGAAAGTTG
* *
11908857 AGGGTGAAAAATGGAATTTTTGGACA-TTCG
1 AGGGT--AAAATGTAATTTTTGGAAAGTT-G
*
11908887 -GGGTAAAATGGTAA-TTTTGGGAAGTTCG
1 AGGGTAAAAT-GTAATTTTTGGAAAGTT-G
* *
11908915 -GGGTTAAAAATGGAATTTTTGGAAA-TTC
1 AGGG-T-AAAATGTAATTTTTGGAAAGTTG
* *
11908943 AAGGTAAAATGGTAATTTTTGTG-AAGCTCG
1 AGGGTAAAAT-GTAATTTTTG-GAAAG-TTG
* * *
11908973 AGGGCAATAATGTAAATTTTGGAAAGTTCA
1 AGGGTAA-AATGTAATTTTTGGAAAGTT-G
*
11909003 AGGGTCAAAATGTAATTTTTGAAAAGTTG
1 AGGGT-AAAATGTAATTTTTGGAAAGTTG
11909032 AGGG
1 AGGG
11909036 GTCAAAATAT
Statistics
Matches: 356, Mismatches: 64, Indels: 101
0.68 0.12 0.19
Matches are distributed among these distances:
27 26 0.07
28 69 0.19
29 98 0.28
30 133 0.37
31 30 0.08
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (28 bp):
AGGGTAAAATGTAATTTTTGGAAAGTTG
Found at i:11909051 original size:29 final size:29
Alignment explanation
Indices: 11908987--11909065 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
11908977 CAATAATGTA
* *
11908987 AATTTTGGAAAGTTCAAGGGTCAAAATGT
1 AATTTTGAAAAGTTCAAGGGTCAAAATAT
* *
11909016 AATTTTTGAAAAGTTGAGGGGTCAAAATAT
1 AA-TTTTGAAAAGTTCAAGGGTCAAAATAT
* *
11909046 GATTTTTAAACAGTTCAAGG
1 AATTTTGAAA-AGTTCAAGG
11909066 ACCTTTTAGG
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 9 0.22
30 31 0.77
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (29 bp):
AATTTTGAAAAGTTCAAGGGTCAAAATAT
Found at i:11913631 original size:11 final size:11
Alignment explanation
Indices: 11913615--11913648 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
11913605 GATCGGGCCC
11913615 TTTTAAATTTA
1 TTTTAAATTTA
11913626 TTTTAAATTTGA
1 TTTTAAATTT-A
*
11913638 ATTTAAATTTA
1 TTTTAAATTTA
11913649 AATTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:11913640 original size:6 final size:6
Alignment explanation
Indices: 11913616--11913668 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
11913606 ATCGGGCCCT
* * *
11913616 TTTAAA TTT-AT TTTAAA TTTGAA TTTAAA TTTAAA TTT-AT TTTCAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
11913663 TTTAAA
1 TTTAAA
11913669 AAAAAAAAGC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 8 0.21
6 26 0.68
7 4 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:11915019 original size:30 final size:29
Alignment explanation
Indices: 11914961--11915071 Score: 134
Period size: 29 Copynumber: 3.8 Consensus size: 29
11914951 CATCGAAACA
* * *
11914961 TCTAAAATTTACATTTGTACCCCTAAAAT
1 TCTAAAAATTACATTTTTACCCCGAAAAT
11914990 TCTAAAAATTACATTTTTACCCCCGAAAA-
1 TCTAAAAATTACATTTTTA-CCCCGAAAAT
** *
11915019 TCTAAAAATCCCATTTTTGACCCCGAAACT
1 TCTAAAAATTACATTTTT-ACCCCGAAAAT
*
11915049 TCCAAAAATTACATTTTTACCCC
1 TCTAAAAATTACATTTTTACCCC
11915072 CGAACTTCCA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
29 46 0.66
30 24 0.34
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (29 bp):
TCTAAAAATTACATTTTTACCCCGAAAAT
Found at i:11915073 original size:30 final size:29
Alignment explanation
Indices: 11914954--11915093 Score: 133
Period size: 29 Copynumber: 4.8 Consensus size: 29
11914944 ATTTTGGCAT
* * *
11914954 CGAAACATCTAAAATTTACATTTGTACCC
1 CGAAACTTCTAAAAATTACATTTTTACCC
* *
11914983 CTAAAATTCTAAAAATTACATTTTTACCCC
1 CGAAACTTCTAAAAATTACATTTTTA-CCC
* **
11915013 CGAAA-ATCTAAAAATCCCATTTTTGACCC
1 CGAAACTTCTAAAAATTACATTTTT-ACCC
*
11915042 CGAAACTTCCAAAAATTACATTTTTACCCC
1 CGAAACTTCTAAAAATTACATTTTTA-CCC
* *
11915072 CG-AACTTC-CAAAATTCCATTTT
1 CGAAACTTCTAAAAATTACATTTT
11915094 GGACCTCAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
28 12 0.13
29 52 0.57
30 28 0.30
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.32
Consensus pattern (29 bp):
CGAAACTTCTAAAAATTACATTTTTACCC
Found at i:11915106 original size:29 final size:29
Alignment explanation
Indices: 11914974--11915107 Score: 87
Period size: 29 Copynumber: 4.6 Consensus size: 29
11914964 AAAATTTACA
* *
11914974 TTTGTACCCCTAAAA-TTCTAAAAATTACAT
1 TTTG-ACCCC-AAAACTTCCAAAAATTCCAT
* * *
11915004 TTTTACCCCCGAAAA--TCTAAAAATCCCATT
1 TTTGA-CCCC-AAAACTTCCAAAAATTCCA-T
* *
11915034 TTTGACCCCGAAACTTCCAAAAATTACAT
1 TTTGACCCCAAAACTTCCAAAAATTCCAT
* **
11915063 TTTTACCCCCGAACTTCC-AAAATTCCAT
1 TTTGACCCCAAAACTTCCAAAAATTCCAT
*
11915091 TTTGGACCTCAAAACTT
1 TTT-GACCCCAAAACTT
11915108 TAAAATTACC
Statistics
Matches: 82, Mismatches: 17, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
28 15 0.18
29 41 0.50
30 26 0.32
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (29 bp):
TTTGACCCCAAAACTTCCAAAAATTCCAT
Found at i:11915182 original size:59 final size:57
Alignment explanation
Indices: 11915109--11915239 Score: 147
Period size: 59 Copynumber: 2.2 Consensus size: 57
11915099 TCAAAACTTT
* * * *
11915109 AAAATTACCGTTTTACTCTCGAATGTCCAAAAAATCCATTTTTGATCCC-GATTTTTCC
1 AAAATTACCATTTTACCCTCGAATGTCCAAAAAAT-CATTTTT-AACCCAAATTTTTCC
* * **
11915167 AATAATTACCATTTTACCCTTGAATGTCTAAAATGTCATTTTTAACCCAAAATTTTTCC
1 AA-AATTACCATTTTACCCTCGAATGTCCAAAAAATCATTTTTAACCC-AAATTTTTCC
11915226 AAAATTACCATTTT
1 AAAATTACCATTTT
11915240 GCCTCTGAGA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
57 4 0.06
58 21 0.34
59 37 0.60
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (57 bp):
AAAATTACCATTTTACCCTCGAATGTCCAAAAAATCATTTTTAACCCAAATTTTTCC
Found at i:11915287 original size:29 final size:29
Alignment explanation
Indices: 11915226--11915305 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 29
11915216 AAATTTTTCC
* * * *
11915226 AAAATTACCATTTTGCCTCTGAGAGTCCC
1 AAAATTACCATTTTACCCCCGAGAGTCCA
11915255 AAAATTACCATTTTACCCCCGAGTA-TCCA
1 AAAATTACCATTTTACCCCCGAG-AGTCCA
* *
11915284 AAAAGT-CTCATTTTAACCCCGA
1 AAAATTAC-CATTTTACCCCCGA
11915306 TTGGATCGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.02
29 41 0.95
30 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.29
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAGAGTCCA
Found at i:11921381 original size:49 final size:49
Alignment explanation
Indices: 11921282--11921445 Score: 168
Period size: 49 Copynumber: 3.3 Consensus size: 49
11921272 TGTACCTCAG
* * * ** *
11921282 AGACACGACGGGAAAGATGTAAAGCCGTAACGGCGGATCCAGTACCACGA
1 AGACATGAAGGGAAAGATCT-AAGCCGCGACAGCGGATCCAGTACCACGA
* * *
11921332 AGACATGAAGGGAAAGATCTAAGCCGCGA-TGACGGACCCAGTACTACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCGACAG-CGGATCCAGTACCACGA
* * * *
11921381 AGACAGGAAGAGAAAGATCTAAGCTGCGACAGCAGATCCAGTACCACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCGACAGCGGATCCAGTACCACGA
**
11921430 AGATTTGAAGGGAAAG
1 AGACATGAAGGGAAAG
11921446 GTTTAATTCG
Statistics
Matches: 93, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
48 1 0.01
49 74 0.80
50 18 0.19
ACGTcount: A:0.38, C:0.21, G:0.29, T:0.12
Consensus pattern (49 bp):
AGACATGAAGGGAAAGATCTAAGCCGCGACAGCGGATCCAGTACCACGA
Done.