Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 62 of 120
Found at i:18405326 original size:30 final size:30
Alignment explanation
Indices: 18405287--18405373 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
18405277 TAGCAAAACA
*
18405287 CCCTCCACATTTTCAAGTGGTTGTAGGACAC
1 CCCT-CACATTTCCAAGTGGTTGTAGGACAC
*
18405318 CCCTCACATTTCCAAGTGGTTGTAAGACAC
1 CCCTCACATTTCCAAGTGGTTGTAGGACAC
*
18405348 CCC-CACATTTCCAAGTAGTTGTAGGA
1 CCCTCACATTTCCAAGTGGTTGTAGGA
18405374 TGATTTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.40
30 27 0.52
31 4 0.08
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (30 bp):
CCCTCACATTTCCAAGTGGTTGTAGGACAC
Found at i:18407724 original size:82 final size:79
Alignment explanation
Indices: 18407573--18407873 Score: 239
Period size: 82 Copynumber: 3.7 Consensus size: 79
18407563 AAAATCCAAT
* * * * * * **
18407573 AATAGAATATAATTTGTTAATCGGCGGGAATAAAT-TTCAAAATAGATTTAATCAACTTATTTTA
1 AATAGAATAAAATCTGTTAAACGACGGGAATAAATCCT-GAAATAGATTT-ATTTACTTATTTTA
18407637 TTTTGGAAACAAAATCA
64 -TTTGGAAACAAAATCA
*
18407654 AACTGGAATAAAATCTGTTAAACGACGGGAATAAATCCTGAAATAGATTTATTTACTTAATTATT
1 AA-TAGAATAAAATCTGTTAAACGACGGGAATAAATCCTGAAATAGATTTATTTACTT-ATT-TT
* *
18407719 ATTTGGTACCAAAATCCAA
63 ATTTGGAAACAAAAT-C-A
** * * * * *
18407738 ATATAGAATTGAATCTGTTCAACGACGGGAATAAGTCCCGAAACAAATTTATTTACTTATTCTCG
1 A-ATAGAATAAAATCTGTTAAACGACGGGAATAAATCCTGAAATAGATTTATTTACTTATT-T--
* * *
18407803 TTTTTGAAAATAAAATCA
62 TATTTGGAAACAAAATCA
* * *
18407821 AATAGAATAAAATCTATT-AACTGGCGAGAAATAAATCCTGAAATAGA-TTATTT
1 AATAGAATAAAATCTGTTAAAC-GACG-GGAATAAATCCTGAAATAGATTTATTT
18407874 TCCAATTTTA
Statistics
Matches: 175, Mismatches: 34, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
81 11 0.06
82 76 0.43
83 26 0.15
84 50 0.29
85 12 0.07
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (79 bp):
AATAGAATAAAATCTGTTAAACGACGGGAATAAATCCTGAAATAGATTTATTTACTTATTTTATT
TGGAAACAAAATCA
Found at i:18408057 original size:49 final size:50
Alignment explanation
Indices: 18408000--18408119 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 50
18407990 TTAGCGAACA
* *
18408000 TAAATAAATATAAATATTTATATTAAAA-CA-AGATCTTAATA-AAATTA-AT
1 TAAATAAATATTAATATTTATA-TAAAATCATAGAT-TTAA-ACAAATCACAT
*
18408049 TAAATAAATATTTATATTTATATAAAATCATTAGATTTAAACAAATCACAT
1 TAAATAAATATTAATATTTATATAAAATCA-TAGATTTAAACAAATCACAT
*
18408100 TAAATAAATATTCATATTTA
1 TAAATAAATATTAATATTTA
18408120 CTTAAAAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
48 5 0.08
49 23 0.37
50 9 0.15
51 25 0.40
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (50 bp):
TAAATAAATATTAATATTTATATAAAATCATAGATTTAAACAAATCACAT
Found at i:18409085 original size:2 final size:2
Alignment explanation
Indices: 18409078--18409111 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18409068 GCACAAACGC
18409078 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18409112 TCAATGATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18414061 original size:38 final size:39
Alignment explanation
Indices: 18413975--18414065 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 39
18413965 AAATTATCAG
* *
18413975 AATTGTTAAATATTTAAGAAAAAATAAAAATTCATATGA
1 AATTATTAAAAATTTAAGAAAAAATAAAAATTCATATGA
* *
18414014 ACTTA-TAAAAATTATAA-AAAAAATAAAAGTTC-TAAT-A
1 AATTATTAAAAATT-TAAGAAAAAATAAAAATTCAT-ATGA
18414051 AATTATTAAAAATTT
1 AATTATTAAAAATTT
18414066 TATAAAATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
37 7 0.16
38 31 0.70
39 6 0.14
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.34
Consensus pattern (39 bp):
AATTATTAAAAATTTAAGAAAAAATAAAAATTCATATGA
Found at i:18414768 original size:38 final size:37
Alignment explanation
Indices: 18414726--18414815 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 37
18414716 TTAATTAGAA
*
18414726 TTTTATATTTTTATAA-TATT-TATAAGTTTTCATAATTG
1 TTTTATATTTTTATAAGT-TTATATAAG-TTT-ATAATAG
* *
18414764 TTTTATAATTTTAATAAGTTTATATCAGTTTATAATAG
1 TTTTAT-ATTTTTATAAGTTTATATAAGTTTATAATAG
18414802 TTTTAATATTTTTA
1 TTTT-ATATTTTTA
18414816 ATATTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
38 22 0.50
39 16 0.36
40 6 0.14
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (37 bp):
TTTTATATTTTTATAAGTTTATATAAGTTTATAATAG
Found at i:18414855 original size:10 final size:9
Alignment explanation
Indices: 18414796--18414860 Score: 55
Period size: 9 Copynumber: 7.4 Consensus size: 9
18414786 TATCAGTTTA
*
18414796 TAATAGTTT
1 TAATATTTT
18414805 TAATATTTT
1 TAATATTTT
18414814 TAATATTTT
1 TAATATTTT
**
18414823 T--T-TGGT
1 TAATATTTT
*
18414829 GAATATTTT
1 TAATATTTT
18414838 TAATATTTT
1 TAATATTTT
*
18414847 TTATGATTTT
1 TAAT-ATTTT
18414857 TAAT
1 TAAT
18414861 CATGATTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
6 2 0.05
7 1 0.02
8 1 0.02
9 31 0.72
10 8 0.19
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (9 bp):
TAATATTTT
Found at i:18414869 original size:20 final size:19
Alignment explanation
Indices: 18414833--18414872 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
18414823 TTTGGTGAAT
**
18414833 ATTTTTAATATTTTTTATG
1 ATTTTTAATATGATTTATG
18414852 ATTTTTAATCATGATTTATG
1 ATTTTTAAT-ATGATTTATG
18414872 A
1 A
18414873 AAAAATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (19 bp):
ATTTTTAATATGATTTATG
Found at i:18415690 original size:19 final size:19
Alignment explanation
Indices: 18415667--18415730 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
18415657 GCATACAAAA
*
18415667 TGCATCCTGACACATAAAG
1 TGCATCCTGACACATGAAG
* * *
18415686 CGCATACT-AGCACACGAAG
1 TGCATCCTGA-CACATGAAG
*
18415705 TGCATCCTGGCACATGAAG
1 TGCATCCTGACACATGAAG
18415724 TGCATCC
1 TGCATCC
18415731 GTCATAATCT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
18 1 0.03
19 34 0.97
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.19
Consensus pattern (19 bp):
TGCATCCTGACACATGAAG
Found at i:18415691 original size:38 final size:38
Alignment explanation
Indices: 18415649--18415728 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
18415639 GACGTAACAT
* *
18415649 GCATACTGGCATACAAAATGCATCCTGACACATAAAGC
1 GCATACTAGCACACAAAATGCATCCTGACACATAAAGC
* * * * *
18415687 GCATACTAGCACACGAAGTGCATCCTGGCACATGAAGT
1 GCATACTAGCACACAAAATGCATCCTGACACATAAAGC
18415725 GCAT
1 GCAT
18415729 CCGTCATAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (38 bp):
GCATACTAGCACACAAAATGCATCCTGACACATAAAGC
Found at i:18419507 original size:13 final size:14
Alignment explanation
Indices: 18419484--18419515 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
18419474 ACTAACTTTT
18419484 AATTCAATAATTAA
1 AATTCAATAATTAA
18419498 AATT-AATAATTAA
1 AATTCAATAATTAA
18419511 AATTC
1 AATTC
18419516 CTCAATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTCAATAATTAA
Found at i:18422571 original size:17 final size:17
Alignment explanation
Indices: 18422531--18422564 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
18422521 TGATGAAGAT
18422531 GATGAGGAGAATGGCTC
1 GATGAGGAGAATGGCTC
18422548 GATGAGGAGAATGGCTC
1 GATGAGGAGAATGGCTC
18422565 AGAGAGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.41, T:0.18
Consensus pattern (17 bp):
GATGAGGAGAATGGCTC
Found at i:18425662 original size:23 final size:23
Alignment explanation
Indices: 18425588--18425778 Score: 132
Period size: 23 Copynumber: 8.5 Consensus size: 23
18425578 TAAACGGAAC
* * *
18425588 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
18425610 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
18425632 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
18425658 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
18425678 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
18425697 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
18425720 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
18425745 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
18425768 AATCAGAGAGC
1 AAACAGAGAGC
18425779 GCGCTAGTGT
Statistics
Matches: 132, Mismatches: 21, Indels: 31
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.08
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.02
22 18 0.14
23 58 0.44
24 2 0.02
25 29 0.22
26 8 0.06
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:18425728 original size:25 final size:23
Alignment explanation
Indices: 18425681--18425778 Score: 135
Period size: 23 Copynumber: 4.2 Consensus size: 23
18425671 ACAAAGTACT
*
18425681 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
18425704 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAT--CAGA
* *
18425729 GAGCACGAGAC-GTGCTAAACAGA
1 GAGCAC-ACACAGTGCTAATCAGA
18425752 GAGCACACACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
18425775 GAGC
1 GAGC
18425779 GCGCTAGTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
22 3 0.05
23 43 0.65
25 17 0.26
26 3 0.05
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.11
Consensus pattern (23 bp):
GAGCACACACAGTGCTAATCAGA
Found at i:18432077 original size:23 final size:23
Alignment explanation
Indices: 18432003--18432193 Score: 123
Period size: 23 Copynumber: 8.5 Consensus size: 23
18431993 TAAACGGAAC
* * *
18432003 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
18432025 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
18432047 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
**
18432073 AAACAGAGAATACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
18432096 -------GAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
18432112 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
18432135 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
18432160 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
18432183 AATCAGAGAGC
1 AAACAGAGAGC
18432194 GCGCTAGTGT
Statistics
Matches: 131, Mismatches: 22, Indels: 31
0.71 0.12 0.17
Matches are distributed among these distances:
16 13 0.10
22 18 0.14
23 61 0.47
24 2 0.02
25 29 0.22
26 8 0.06
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:18432111 original size:39 final size:39
Alignment explanation
Indices: 18432057--18432134 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
18432047 GGGCAACAGA
*
18432057 GAGCACACAAAGTGCTAAACAGAGAATACACAAAGTGCT
1 GAGCACACAAAGTGCTAAACAGAGAACACACAAAGTGCT
* * * *
18432096 GAGCACACGAAGTGCTAATCAGAGAGCACACACAGTGCT
1 GAGCACACAAAGTGCTAAACAGAGAACACACAAAGTGCT
18432135 AATAACAGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAACACACAAAGTGCT
Found at i:18432143 original size:25 final size:23
Alignment explanation
Indices: 18432096--18432193 Score: 128
Period size: 23 Copynumber: 4.2 Consensus size: 23
18432086 ACAAAGTGCT
18432096 GAGCACACGA-AGTGCTAATCAGA
1 GAGCACAC-ACAGTGCTAATCAGA
18432119 GAGCACACACAGTGCTAATAACAGA
1 GAGCACACACAGTGCTAAT--CAGA
* *
18432144 GAGCACGAGAC-GTGCTAAACAGA
1 GAGCAC-ACACAGTGCTAATCAGA
18432167 GAGCACACACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGA
18432190 GAGC
1 GAGC
18432194 GCGCTAGTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
22 4 0.06
23 42 0.64
25 17 0.26
26 3 0.05
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (23 bp):
GAGCACACACAGTGCTAATCAGA
Found at i:18446171 original size:38 final size:36
Alignment explanation
Indices: 18446111--18446185 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
18446101 ACCTTACAAT
* * * *
18446111 CTCCCTTAATATTTTTATCCAAAATCTTAAGATTGCAA
1 CTCCCTTAAGATTTCTA-CCCAAACCTTAAGATT-CAA
*
18446149 CTCCCTTAAGGTTTCTACCCAAACCTTAAGATTCAA
1 CTCCCTTAAGATTTCTACCCAAACCTTAAGATTCAA
18446185 C
1 C
18446186 CCTCTCAAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 4 0.12
37 14 0.44
38 14 0.44
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.35
Consensus pattern (36 bp):
CTCCCTTAAGATTTCTACCCAAACCTTAAGATTCAA
Found at i:18449097 original size:33 final size:33
Alignment explanation
Indices: 18449031--18449093 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
18449021 ATCTTTATGC
* *
18449031 CTTAAATTGAAAATGATTTTTATATAGGAGGAG
1 CTTAAATTCAAAATGATTTTTATATAAGAGGAG
18449064 CTTAAATTCAAAATG-TCTTTTAT-TAAGAGG
1 CTTAAATTCAAAATGAT-TTTTATATAAGAGG
18449094 GAGCAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 20 0.74
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (33 bp):
CTTAAATTCAAAATGATTTTTATATAAGAGGAG
Found at i:18452873 original size:14 final size:14
Alignment explanation
Indices: 18452853--18452914 Score: 79
Period size: 14 Copynumber: 4.3 Consensus size: 14
18452843 TGTATATATA
18452853 TATATATAAAAATG
1 TATATATAAAAATG
* * *
18452867 TAGATATAAGATTG
1 TATATATAAAAATG
18452881 TATATATATAAAATAG
1 TATATATA-AAAAT-G
18452897 TATATATAAAAATG
1 TATATATAAAAATG
18452911 TATA
1 TATA
18452915 AAATATATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
14 23 0.57
15 8 0.20
16 9 0.22
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (14 bp):
TATATATAAAAATG
Found at i:18452904 original size:30 final size:30
Alignment explanation
Indices: 18452824--18452914 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
18452814 ATATGTGTAA
* ** *
18452824 ATATAAAATAGTGTATATGTGTATATATATAT
1 ATATAAAATAGTATATATAAG-AT-TGTATAT
*
18452856 ATATAAAA-ATGTAGATATAAGATTGTATAT
1 ATATAAAATA-GTATATATAAGATTGTATAT
* *
18452886 ATATAAAATAGTATATATAAAAATGTATA
1 ATATAAAATAGTATATATAAGATTGTATA
18452915 AAATATATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
30 30 0.61
31 4 0.08
32 15 0.31
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (30 bp):
ATATAAAATAGTATATATAAGATTGTATAT
Found at i:18453158 original size:13 final size:13
Alignment explanation
Indices: 18453140--18453164 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18453130 GTAAAAATGG
18453140 TGGAAGGTGGGGT
1 TGGAAGGTGGGGT
18453153 TGGAAGGTGGGG
1 TGGAAGGTGGGG
18453165 ACCGAAAATA
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:0.16, C:0.00, G:0.64, T:0.20
Consensus pattern (13 bp):
TGGAAGGTGGGGT
Found at i:18463191 original size:17 final size:16
Alignment explanation
Indices: 18463149--18463191 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
18463139 TTTAACTTAT
*
18463149 TATTAATATTTTGATA
1 TATTAATATTTTAATA
* *
18463165 TATAAATATTTTAATG
1 TATTAATATTTTAATA
18463181 TAATTAATATT
1 T-ATTAATATT
18463192 AATTATAAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
TATTAATATTTTAATA
Found at i:18469791 original size:1 final size:1
Alignment explanation
Indices: 18469785--18469813 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
18469775 GCTACATAGT
18469785 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
18469814 TTTTAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:18470774 original size:21 final size:21
Alignment explanation
Indices: 18470728--18470781 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
18470718 CTTATGCTAG
18470728 CTCTACCGATACAAGTATGAT
1 CTCTACCGATACAAGTATGAT
*
18470749 TTCTACCGATACAAGT-TG-T
1 CTCTACCGATACAAGTATGAT
18470768 GCCTCTACCGATAC
1 --CTCTACCGATAC
18470782 TAGAAACTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 2 0.07
21 26 0.90
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (21 bp):
CTCTACCGATACAAGTATGAT
Found at i:18471242 original size:27 final size:27
Alignment explanation
Indices: 18471204--18471256 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
18471194 GCCATAAGAC
18471204 CGAGTGATGCAAAAACTACCGACAAAT
1 CGAGTGATGCAAAAACTACCGACAAAT
18471231 CGAGTGATGCAAAAACTACCGACAAA
1 CGAGTGATGCAAAAACTACCGACAAA
18471257 CTCTGCGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (27 bp):
CGAGTGATGCAAAAACTACCGACAAAT
Found at i:18474334 original size:21 final size:20
Alignment explanation
Indices: 18474310--18474372 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
18474300 TATAACAATG
18474310 TAAAAAATTCATAAAAGCTTA
1 TAAAAAATTCATAAAAG-TTA
* *
18474331 TAAAAAATTCAGAACAAGTTT
1 TAAAAAATTCATAA-AAGTTA
*
18474352 TAATAAATT-ATAAAA-TTA
1 TAAAAAATTCATAAAAGTTA
18474370 TAA
1 TAA
18474373 TTTTTTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 5 0.14
19 2 0.06
20 3 0.08
21 23 0.64
22 3 0.08
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAAAATTCATAAAAGTTA
Found at i:18476123 original size:3 final size:3
Alignment explanation
Indices: 18476115--18476143 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18476105 GACAAATACT
18476115 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18476144 TTGCTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:18476819 original size:4 final size:4
Alignment explanation
Indices: 18476734--18476776 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
18476724 AAATTTGAAG
*
18476734 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAA
18476777 GGAAGGAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 3 0.09
4 29 0.83
5 3 0.09
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:18477221 original size:20 final size:21
Alignment explanation
Indices: 18477180--18477222 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
18477170 TAATTTACTT
*
18477180 TAATTTAATTTTGTTAGTTAG
1 TAATTTAATTTTATTAGTTAG
*
18477201 TAATTTTATTTTATT-GTTAG
1 TAATTTAATTTTATTAGTTAG
18477221 TA
1 TA
18477223 GTAGTAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTATTAGTTAG
Found at i:18477815 original size:16 final size:15
Alignment explanation
Indices: 18477769--18477817 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
18477759 TAAACCTAAC
18477769 TAATTAATTACTAAAA
1 TAATTAATTAC-AAAA
18477785 T-A-TAATATA-AAAA
1 TAATTAAT-TACAAAA
18477798 TAATTAATTACCAAAA
1 TAATTAATTA-CAAAA
18477814 TAAT
1 TAAT
18477818 ATCCCCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.18
14 7 0.25
15 7 0.25
16 9 0.32
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATTAATTACAAAA
Found at i:18479195 original size:43 final size:43
Alignment explanation
Indices: 18479113--18479197 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 43
18479103 ATTAACATGT
* *
18479113 TAAATTATATTACTTGACTTGTGTTAATATGGTTGCATGTTAC
1 TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
* *
18479156 TAAATTATATTACTTTACTCT-TATTAGTAT-CTTGACATGTTA
1 TAAATTATATTACTTGACT-TGTATTAATATGCTTG-CATGTTA
18479198 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 3 0.08
43 32 0.89
44 1 0.03
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTTGTATTAATATGCTTGCATGTTAC
Found at i:18484439 original size:4 final size:4
Alignment explanation
Indices: 18484419--18484483 Score: 87
Period size: 4 Copynumber: 16.2 Consensus size: 4
18484409 AACACATTAC
* * *
18484419 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
18484467 CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT C
18484484 CCGTTTATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
3 3 0.06
4 48 0.89
5 3 0.06
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:18485489 original size:30 final size:31
Alignment explanation
Indices: 18485453--18485526 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
18485443 ATTAAAATTA
*
18485453 TTTAATAATTTTAT-TATTTCAAAAAATAAT
1 TTTAATAATTTTATATATTTAAAAAAATAAT
*
18485483 TTTAATAATTTTATATTTTTAAAAAAATAAT
1 TTTAATAATTTTATATATTTAAAAAAATAAT
18485514 TTTAATAATTTTA
1 TTTAATAATTTTA
18485527 AAATCATTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 14 0.34
31 27 0.66
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAATAATTTTATATATTTAAAAAAATAAT
Found at i:18485511 original size:22 final size:23
Alignment explanation
Indices: 18485486--18485529 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
18485476 AAATAATTTT
*
18485486 AATAATTTT-ATATTTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
18485508 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
18485530 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:18486278 original size:40 final size:40
Alignment explanation
Indices: 18486234--18486309 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
18486224 ATGGTAACTC
*
18486234 TAGTTTTACTTGCGTGTGCCACTAGGCCACCAAAGCACTT
1 TAGTTTTACTTGAGTGTGCCACTAGGCCACCAAAGCACTT
*
18486274 TAGTTTTACTTGAGTGTTCCACTAGGCCACCAAAGC
1 TAGTTTTACTTGAGTGTGCCACTAGGCCACCAAAGC
18486310 TTCAAGTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (40 bp):
TAGTTTTACTTGAGTGTGCCACTAGGCCACCAAAGCACTT
Found at i:18487295 original size:16 final size:16
Alignment explanation
Indices: 18487274--18487335 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 16
18487264 CGTTTGGTTC
18487274 GCTGTAATGGAATAAA
1 GCTGTAATGGAATAAA
* *
18487290 GCTGTAATGAAATAGA
1 GCTGTAATGGAATAAA
* * * *
18487306 GTTGTACTGTAATATA
1 GCTGTAATGGAATAAA
* *
18487322 GTTGTAATAGAATA
1 GCTGTAATGGAATA
18487336 GGGTTGTAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (16 bp):
GCTGTAATGGAATAAA
Found at i:18487579 original size:58 final size:56
Alignment explanation
Indices: 18487517--18487661 Score: 172
Period size: 56 Copynumber: 2.6 Consensus size: 56
18487507 TTTTAATAAG
*
18487517 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATATTTTAACAT
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTTTAA-AT
* * * *
18487574 AATTATTATTAAATACAATTTAAT--AAATGATATATAATTTAATAATATTTTTAAT
1 -ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTTTAAAT
* *
18487629 A-TA-TATTAAAATATAAATTAATAAAAATCATAA
1 ATTATTATT-AAATATAATTTAATAAAAATAATAA
18487662 TATATAATAT
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
52 4 0.05
53 14 0.19
54 1 0.01
55 9 0.12
56 25 0.33
58 22 0.29
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTTTAAAT
Found at i:18491547 original size:27 final size:25
Alignment explanation
Indices: 18491508--18491566 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 25
18491498 GGTGAAACCT
18491508 AAGG-AGAAGAAGGACAATGAGGAAGAG
1 AAGGAAGAAGAAGGACAAT---GAAGAG
*
18491535 AAGGAAGAA-AAGGATAATGAAGAG
1 AAGGAAGAAGAAGGACAATGAAGAG
18491559 AAGGAAGA
1 AAGGAAGA
18491567 TGCCTCGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 14 0.47
27 12 0.40
28 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.37, T:0.05
Consensus pattern (25 bp):
AAGGAAGAAGAAGGACAATGAAGAG
Found at i:18492601 original size:4 final size:4
Alignment explanation
Indices: 18492592--18492640 Score: 50
Period size: 4 Copynumber: 12.8 Consensus size: 4
18492582 ATTTATAAAA
* *
18492592 AAAG AAAG AAAG AAAG -AAG AAAG AGAA- AAAG -AAG AAAA AAAA AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG
18492638 AAA
1 AAA
18492641 TATATGTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 8 0.21
4 29 0.74
5 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:18492613 original size:15 final size:14
Alignment explanation
Indices: 18492588--18492640 Score: 67
Period size: 15 Copynumber: 3.9 Consensus size: 14
18492578 AGTCATTTAT
18492588 AAAAA-AAGAAAGA
1 AAAAAGAAGAAAGA
18492601 AAGAAAGAAGAAAGA
1 AA-AAAGAAGAAAGA
18492616 GAAAAAGAAGAAA-A
1 -AAAAAGAAGAAAGA
18492630 AAAAA-AAGAAA
1 AAAAAGAAGAAA
18492641 TATATGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.16
13 7 0.19
14 4 0.11
15 18 0.49
16 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGAAAGA
Found at i:18496440 original size:22 final size:22
Alignment explanation
Indices: 18496398--18496444 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
18496388 CTAAAATATG
18496398 AATTGAAAATTAAAATATATTTA
1 AATTGAAAATTAAAATATA-TTA
* *
18496421 AATTTAAAA-TAATATATATTA
1 AATTGAAAATTAAAATATATTA
18496442 AAT
1 AAT
18496445 CAATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 8 0.36
23 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTGAAAATTAAAATATATTA
Found at i:18497058 original size:14 final size:15
Alignment explanation
Indices: 18497030--18497058 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18497020 AAAAATTATC
18497030 AAATTCAATACCTAA
1 AAATTCAATACCTAA
18497045 AAATTCAA-ACCTAA
1 AAATTCAATACCTAA
18497059 TATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATTCAATACCTAA
Found at i:18512994 original size:27 final size:25
Alignment explanation
Indices: 18512948--18513010 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 25
18512938 GTCCCTGCAT
*
18512948 TTTTATTT-TATTTTAATTTAACCC
1 TTTTATTTATTTTTTAATTTAACCC
**
18512972 TTTATATTCTATTTTTTAATTTAGTCC
1 TTT-TATT-TATTTTTTAATTTAACCC
18512999 TTTTATTTATTT
1 TTTTATTTATTT
18513011 ATTTCAGTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
24 3 0.09
25 9 0.27
26 5 0.15
27 16 0.48
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.67
Consensus pattern (25 bp):
TTTTATTTATTTTTTAATTTAACCC
Found at i:18518289 original size:196 final size:192
Alignment explanation
Indices: 18517876--18518320 Score: 498
Period size: 192 Copynumber: 2.3 Consensus size: 192
18517866 TACCAGTACC
* * * ***
18517876 CGATGCTGCTCACACGAGCTGTCGAAGACTCGCAACATATGCGGTACCCCGGTCATCGATACAAT
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATCGATACAAT
* ** *
18517941 GTCTGTCTGTAAACTATCCCCTAACGATGCTACTCACACAAGCTGTTGAGAATATACATTCAAGC
66 ATCTGTCAATAAACTATCCCCTAACGATGCTACTCACACAAGCTGTCGAGAATATACATTCAAGC
* * * * *
18518006 ATAAATCCAGCCATCTTAGGGCCTATAATCTATTTTGGATTTCATATCTCTTTTTCAACTCA
131 ATAAATCCAACCATCGTAGGGCCTATAATCCATTTTGGATTTCATATCTCATTTCCAACTCA
* * * * * **
18518068 CGATGTTACTCACACGAGTTGTCGAGGACTCACAACATATGTGGTACCTTAACCATCGATACGGT
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATCGATACAAT
* * ** * *
18518133 ATCTGTGAATATAACTATTTCCCTAACGATGCTACTCACATGAGCTGTCGAGAATGTGCACTT-A
66 ATCTGTCAATA-AACTA-TCCCCTAACGATGCTACTCACACAAGCTGTCGAGAATATACA-TTCA
* * * * *
18518197 TGCATAAATCCTAACCATCGTAGGGTCTGTAATCCATTCTTGGA-TTCATTTCTCATTTCCTAGC
128 AGCATAAATCC-AACCATCGTAGGGCCTATAATCCATT-TTGGATTTCATATCTCATTTCC-AAC
18518261 TCA
190 TCA
* * *
18518264 CGATGCTACTCACACGAGCTGTCGAGGACTTGTAACATATGCGGTACCTCAGCCATC
1 CGATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATC
18518321 ACATCGGTTT
Statistics
Matches: 206, Mismatches: 41, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
192 59 0.29
193 5 0.02
194 47 0.23
195 36 0.17
196 59 0.29
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (192 bp):
CGATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCGGTACCTCAACCATCGATACAAT
ATCTGTCAATAAACTATCCCCTAACGATGCTACTCACACAAGCTGTCGAGAATATACATTCAAGC
ATAAATCCAACCATCGTAGGGCCTATAATCCATTTTGGATTTCATATCTCATTTCCAACTCA
Found at i:18526950 original size:23 final size:23
Alignment explanation
Indices: 18526924--18526970 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
18526914 ACCTTCATGC
18526924 ATGTCTAATATCAAGAGAAACTA
1 ATGTCTAATATCAAGAGAAACTA
18526947 ATGTCTAATATCAAGAGAAACTA
1 ATGTCTAATATCAAGAGAAACTA
18526970 A
1 A
18526971 CTTTTCATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (23 bp):
ATGTCTAATATCAAGAGAAACTA
Found at i:18539520 original size:52 final size:52
Alignment explanation
Indices: 18539377--18539523 Score: 188
Period size: 53 Copynumber: 2.8 Consensus size: 52
18539367 TGATGTCATT
* * * * **
18539377 GTGAGTAAATGAATCTTTTATGGGTTATGAGGTCCGATGACTAAGTTTCATC
1 GTGAGTATATGAATCCTTTATGGATTAAGAGGTCCGATGACTAAGTGACATC
*
18539429 GTGAGTATATGAAATCCTTTATGGATTTAA-AGGTACGATGACTAAGTGACATC
1 GTGAGTATATG-AATCCTTTATGGA-TTAAGAGGTCCGATGACTAAGTGACATC
* *
18539482 GTGAGTATATGGATCCTTTACGGATTAAGAGGTCCGATGACT
1 GTGAGTATATGAATCCTTTATGGATTAAGAGGTCCGATGACT
18539524 CTGTGTTATT
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
51 4 0.05
52 33 0.40
53 42 0.51
54 3 0.04
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.33
Consensus pattern (52 bp):
GTGAGTATATGAATCCTTTATGGATTAAGAGGTCCGATGACTAAGTGACATC
Found at i:18539538 original size:52 final size:52
Alignment explanation
Indices: 18539370--18539542 Score: 195
Period size: 52 Copynumber: 3.3 Consensus size: 52
18539360 GAGAGTCTGA
* * * * *
18539370 TGTCATTGTGAGTAAATGAATCTTTTATGGGTTATGAGGTCCGATGACTAAG
1 TGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGTCCGATGACTAAG
* *
18539422 TTTCATCGTGAGTATATGAAATCCTTTATGGATTTAA-AGGTACGATGACTAAG
1 TGTCATCGTGAGTATATG-AATCCTTTATGGA-TTAAGAGGTCCGATGACTAAG
* * * **
18539475 TGACATCGTGAGTATATGGATCCTTTACGGATTAAGAGGTCCGATGACTCTG
1 TGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGTCCGATGACTAAG
* *
18539527 TGTTATTGTGAGTATA
1 TGTCATCGTGAGTATA
18539543 CAAATCCCAC
Statistics
Matches: 101, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
51 4 0.04
52 52 0.51
53 42 0.42
54 3 0.03
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.36
Consensus pattern (52 bp):
TGTCATCGTGAGTATATGAATCCTTTATGGATTAAGAGGTCCGATGACTAAG
Found at i:18545977 original size:141 final size:141
Alignment explanation
Indices: 18545723--18546003 Score: 526
Period size: 141 Copynumber: 2.0 Consensus size: 141
18545713 TTGAGCTTGA
*
18545723 AATATAAGTCGACGTCAGTTCGAGGCCAAAAATTAGCTTGGCTTCTTAAGACGATTAAGGCTTTG
1 AATATAAGTCGACGTCAGATCGAGGCCAAAAATTAGCTTGGCTTCTTAAGACGATTAAGGCTTTG
* *
18545788 AGCATTAAGGTAAAGCCATATATGTGAATTGTATCCGTTTTATGTAAAGAAACTTGTTTTCTAGT
66 AGCATTAAGGCAAAGCCATAAATGTGAATTGTATCCGTTTTATGTAAAGAAACTTGTTTTCTAGT
18545853 AAAGTTATTCT
131 AAAGTTATTCT
*
18545864 AATATAAGTCGACGTCGGATCGAGGCCAAAAATTAGCTTGGCTTCTTAAGACGATTAAGGCTTTG
1 AATATAAGTCGACGTCAGATCGAGGCCAAAAATTAGCTTGGCTTCTTAAGACGATTAAGGCTTTG
18545929 AGCATTAAGGCAAAGCCATAAATGTGAATTGTATCCGTTTTATGTAAAGAAACTTGTTTTCTAGT
66 AGCATTAAGGCAAAGCCATAAATGTGAATTGTATCCGTTTTATGTAAAGAAACTTGTTTTCTAGT
18545994 AAAGTTATTC
131 AAAGTTATTC
18546004 CAATGGAATT
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
141 136 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (141 bp):
AATATAAGTCGACGTCAGATCGAGGCCAAAAATTAGCTTGGCTTCTTAAGACGATTAAGGCTTTG
AGCATTAAGGCAAAGCCATAAATGTGAATTGTATCCGTTTTATGTAAAGAAACTTGTTTTCTAGT
AAAGTTATTCT
Found at i:18546552 original size:61 final size:61
Alignment explanation
Indices: 18546428--18546619 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
18546418 CTTGTCACTA
* * * * *
18546428 ATAAAAAAAATTT-AAAATTTTTTGGTATTGACCATGGAATGGGT-GACACTCTCTTTTTTCAG
1 ATAAAAAAATTTTAAAAATTTTTT-GTGTTGACCATGCAAT-GGTCGACAC-CCCTTTTTACAG
* * *
18546490 ATAAAAAAATTTTAAAAATTTTTTGTGTTAATCATGCAATGGTCAACACCCCTTTTTACAG
1 ATAAAAAAATTTTAAAAATTTTTTGTGTTGACCATGCAATGGTCGACACCCCTTTTTACAG
* * * * ** *
18546551 ATAAAAAAATTTCAAAATTTTTTTATGTTGGCCATGCAAT-ACCGACACCCCCTTTTTATAG
1 ATAAAAAAATTTTAAAAATTTTTTGTGTTGACCATGCAATGGTCGACA-CCCCTTTTTACAG
18546612 ATAAAAAA
1 ATAAAAAA
18546620 TTTCAATTTT
Statistics
Matches: 109, Mismatches: 18, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
60 4 0.04
61 67 0.61
62 28 0.26
63 10 0.09
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (61 bp):
ATAAAAAAATTTTAAAAATTTTTTGTGTTGACCATGCAATGGTCGACACCCCTTTTTACAG
Found at i:18546640 original size:34 final size:34
Alignment explanation
Indices: 18546602--18546666 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
18546592 CCGACACCCC
*
18546602 CTTTTTA-TAGATAAAAAATTTCAATTTTTTTTGG
1 CTTTTTATTAGATAAAAAA-TTAAATTTTTTTTGG
* *
18546636 CTTTTTATTTGGTAAAAAATTAAATTTTTTT
1 CTTTTTATTAGATAAAAAATTAAATTTTTTT
18546667 GGTGTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 18 0.67
35 9 0.33
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (34 bp):
CTTTTTATTAGATAAAAAATTAAATTTTTTTTGG
Found at i:18547646 original size:19 final size:19
Alignment explanation
Indices: 18547600--18547646 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
18547590 AAGAGAAAGC
18547600 GAAAAA-TAAAAGAAAAAA
1 GAAAAATTAAAAGAAAAAA
* *
18547618 GATAAGTTAAAAGAAAAATA
1 GAAAAATTAAAAGAAAAA-A
18547638 -AAAAATTAA
1 GAAAAATTAA
18547647 TTTATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.17
19 18 0.78
20 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (19 bp):
GAAAAATTAAAAGAAAAAA
Found at i:18548150 original size:58 final size:59
Alignment explanation
Indices: 18548050--18548168 Score: 145
Period size: 58 Copynumber: 2.0 Consensus size: 59
18548040 TAACAGAATC
* * *
18548050 AAGTGTATTTTAAGCAGTATCTGATTTTCCGCTGTAAACTCGATGGTTCTT-TGTAGTTT
1 AAGTGTATATTAAGCAGTATCTGATTTTCCGCTGTAAACTCGAGGGTT-TTATGGAGTTT
* * *
18548109 AAGTTTATATTAAGCAGTAT-TGATATTT-GGCTGTAGACTCGAGGGTTTTATGGAGTTT
1 AAGTGTATATTAAGCAGTATCTGAT-TTTCCGCTGTAAACTCGAGGGTTTTATGGAGTTT
18548167 AA
1 AA
18548169 CTAATTTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
57 2 0.04
58 29 0.56
59 21 0.40
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (59 bp):
AAGTGTATATTAAGCAGTATCTGATTTTCCGCTGTAAACTCGAGGGTTTTATGGAGTTT
Found at i:18551266 original size:24 final size:24
Alignment explanation
Indices: 18551239--18551286 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
18551229 TAAGAATATG
* *
18551239 AAAGATTAAAGAAGATGGAAGGTT
1 AAAGATCAAAGAAGATGAAAGGTT
* *
18551263 AAAGATCAAGGGAGATGAAAGGTT
1 AAAGATCAAAGAAGATGAAAGGTT
18551287 GAACATTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.31, T:0.19
Consensus pattern (24 bp):
AAAGATCAAAGAAGATGAAAGGTT
Found at i:18551395 original size:47 final size:47
Alignment explanation
Indices: 18551326--18551420 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
18551316 TCCCCTTTAG
*
18551326 ATGTTCATTGTATAAAAGATATGTCTCATTAAAAATCTTACTAAGAA
1 ATGTTCATTGTATAAAAGATATGTCTCATTAAAAATCTTACAAAGAA
18551373 ATGTTCATTGTATAAAAGATATGTCTCATTAAAAATCTTACAAAGAA
1 ATGTTCATTGTATAAAAGATATGTCTCATTAAAAATCTTACAAAGAA
18551420 A
1 A
18551421 AATCCTATGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (47 bp):
ATGTTCATTGTATAAAAGATATGTCTCATTAAAAATCTTACAAAGAA
Found at i:18555881 original size:59 final size:58
Alignment explanation
Indices: 18555722--18555947 Score: 311
Period size: 59 Copynumber: 3.9 Consensus size: 58
18555712 TCTGAGGGCA
18555722 AAAATGG-AATTTTGGTGAAAC-CGAGGTTAAAAAT-GAGATTTTGGAAAGTTCTG-GGGT
1 AAAATGGTAATTTTGGTGAAACTCG-GGTTAAAAATGGA-ATTTTGGAAAGTT-TGAGGGT
* *
18555779 AAAATGGTAATTTTGGTGAAATTCGGGTCAAAAATGGAATTTTGGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGGTGAAACTCGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
*
18555837 AAAATGGTAATTTTTGGTGAAACTAGGGTTAAAAATGGAATTTTGGAAAGTTT-AGGGGT
1 AAAATGGTAA-TTTTGGTGAAACTCGGGTTAAAAATGGAATTTTGGAAAGTTTGA-GGGT
*
18555896 AAAATGGTAATTTTTGGTGAAA-TCGGGGTTAAAAATAGAATTTTGGAAAGTT
1 AAAATGGTAA-TTTTGGTGAAACTC-GGGTTAAAAATGGAATTTTGGAAAGTT
18555948 CGGGACTAGA
Statistics
Matches: 155, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
57 9 0.06
58 51 0.33
59 95 0.61
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTGAAACTCGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGT
Found at i:18555950 original size:29 final size:29
Alignment explanation
Indices: 18555721--18555951 Score: 132
Period size: 29 Copynumber: 7.9 Consensus size: 29
18555711 CTCTGAGGGC
* *
18555721 AAAAATGGAATTTTGGTGAAA--CCGAGGTT
1 AAAAATGGAATTTT-G-GAAAGTTCGGGGTT
18555750 AAAAAT-GAGATTTTGGAAAGTTCTGGGG-T
1 AAAAATGGA-ATTTTGGAAAGTTC-GGGGTT
*
18555779 -AAAATGGTAATTTTGGTGAAA-TTC-GGGTC
1 AAAAATGG-AATTTT-G-GAAAGTTCGGGGTT
*
18555808 AAAAATGGAATTTTGGAAAGTTTGAGGG-T
1 AAAAATGGAATTTTGGAAAGTTCG-GGGTT
* *
18555837 -AAAATGGTAATTTTTGGTGAAA-CT-AGGGTT
1 AAAAATGG-AA-TTTT-G-GAAAGTTCGGGGTT
*
18555867 AAAAATGGAATTTTGGAAAGTTTAGGGG-T
1 AAAAATGGAATTTTGGAAAG-TTCGGGGTT
18555896 -AAAATGGTAATTTTTGGTGAAA--TCGGGGTT
1 AAAAATGG-AA-TTTT-G-GAAAGTTCGGGGTT
*
18555926 AAAAATAGAATTTTGGAAAGTTCGGG
1 AAAAATGGAATTTTGGAAAGTTCGGG
18555952 ACTAGAGAGC
Statistics
Matches: 161, Mismatches: 11, Indels: 60
0.69 0.05 0.26
Matches are distributed among these distances:
27 16 0.10
28 30 0.19
29 52 0.32
30 35 0.22
31 20 0.12
32 8 0.05
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (29 bp):
AAAAATGGAATTTTGGAAAGTTCGGGGTT
Found at i:18556589 original size:19 final size:19
Alignment explanation
Indices: 18556552--18556588 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18556542 AGGATCGTCC
*
18556552 CTTTTTTTTCTCTCTTTTT
1 CTTTTTATTCTCTCTTTTT
18556571 CTTTTTATTCT-TCTTTTT
1 CTTTTTATTCTCTCTTTTT
18556589 TAAACCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (19 bp):
CTTTTTATTCTCTCTTTTT
Found at i:18556957 original size:10 final size:10
Alignment explanation
Indices: 18556940--18556973 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
18556930 TTTTTTAAAA
18556940 TAATTATTAT
1 TAATTATTAT
*
18556950 TTATTATTAT
1 TAATTATTAT
*
18556960 TAATTAATAT
1 TAATTATTAT
18556970 TAAT
1 TAAT
18556974 GAGTTTGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TAATTATTAT
Found at i:18557762 original size:17 final size:17
Alignment explanation
Indices: 18557742--18557804 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
18557732 TTTTAAATGT
18557742 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
18557759 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
* **
18557775 ATTTAAAATTAATTCAA
1 ATTTAAATTTAAAACAA
*
18557792 ACTTAAA-TTAAAA
1 ATTTAAATTTAAAA
18557805 TCCAAGTTGG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 18 0.49
17 19 0.51
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:18557770 original size:33 final size:33
Alignment explanation
Indices: 18557733--18557805 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
18557723 TTCAAATTAT
** * *
18557733 TTTAAATGTATTTAAATTTAAAACAAATTTAAA
1 TTTAAATAAATTTAAAATTAAAACAAACTTAAA
**
18557766 TTTAAATAAATTTAAAATTAATTCAAACTTAAA
1 TTTAAATAAATTTAAAATTAAAACAAACTTAAA
*
18557799 TTAAAAT
1 TTTAAAT
18557806 CCAAGTTGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (33 bp):
TTTAAATAAATTTAAAATTAAAACAAACTTAAA
Found at i:18557788 original size:27 final size:27
Alignment explanation
Indices: 18557726--18557799 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
18557716 TTTAAGTTTC
* * **
18557726 AAATTATTTTAAATGTATTTAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
**
18557753 AAACAAATTTAAATTTAAATAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
* *
18557780 AAATTAATTCAAACTTAAAT
1 AAATTAATTTAAATTTAAAT
18557800 TAAAATCCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (27 bp):
AAATTAATTTAAATTTAAATAAATTTA
Found at i:18558476 original size:199 final size:200
Alignment explanation
Indices: 18558129--18558674 Score: 866
Period size: 199 Copynumber: 2.7 Consensus size: 200
18558119 TCTTCTTCCT
*
18558129 TGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGA-CTGCTTCTCAGTGTCTCATCTGGAAG
1 TGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACCTGC-TCTCAGTGTCTCATCAGGAAG
* * *
18558193 CTGGGTTCGAAGATTTGCTCATG-TTGAGCGCTGAGTTGGTGTTCTTCTCTGTATCTCATTAAGA
65 CTGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTGAGTTGGTGTTCTTCTCTGTATCTCATCAGGA
* * *
18558257 AGATGACCACCTCACTTGTTTTGATTCGCTTCTCTGGATTTCCTCAGGAAGACGAATCTGGTCCA
130 AGATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCA
18558322 CTTCTC
195 CTTCTC
* * *
18558328 TGTGTCTCATCAAGAAGCTAACCTTTTTATTGGTTCAACCTGCT-TCAGTGTCTCATCAGGAAGC
1 TGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTCTCAGTGTCTCATCAGGAAGC
* *
18558392 TGGGTTCGAAGATTTTCTCGTGTTTGAACGCTGAGTTGGTGTTCTTCTCTGTATCTCATCAGGAA
66 TGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTGAGTTGGTGTTCTTCTCTGTATCTCATCAGGAA
* * *
18558457 GATAACCGCCTCGCTTGTTTTGATTCGTTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTGCAC
131 GATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCAC
18558522 TTCTC
196 TTCTC
*
18558527 TGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTCTCAGTGTCTCATTAGGAAGC
1 TGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTCTCAGTGTCTCATCAGGAAGC
* ***
18558592 TGGGTTCGAAGATTTGCTCGTGTCTGAGCGCTGAGTT-ACATTCTTCTCTGTATCTCATCAGGAA
66 TGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTGAGTTGGTGTTCTTCTCTGTATCTCATCAGGAA
*
18558656 GATGATCGCCTCGCTTGTT
131 GATGACCGCCTCGCTTGTT
18558675 GAACTACTTC
Statistics
Matches: 317, Mismatches: 27, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
198 39 0.12
199 221 0.70
200 57 0.18
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (200 bp):
TGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGACCTGCTCTCAGTGTCTCATCAGGAAGC
TGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTGAGTTGGTGTTCTTCTCTGTATCTCATCAGGAA
GATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTCCTCAGGAAGACGAATCTGGTCCAC
TTCTC
Found at i:18570572 original size:59 final size:59
Alignment explanation
Indices: 18570418--18570815 Score: 540
Period size: 59 Copynumber: 6.8 Consensus size: 59
18570408 TTCGGGGGCA
* * * *
18570418 AAAATGG-AA-TTTTGTTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
18570475 AAAATGGTAA-TTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
18570533 AAAATGGTATTTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * * * *
18570592 AATATGGTACTTTTTGGT-AAAACTGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * * *
18570651 AAAATGGTAATTTTTGGTAAAATTGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* *
18570710 AAAATGGTAATTGTTGGTGAAACCGAGGTT-AAAATGGAATTTTGGAAAGTTTTA-GGGT
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAG-TTTAGGGGT
*
18570768 AAAATGGTAATTTTTGGTGAAA-CTAAGGTTAAAAATGGAATTTTGGAA
1 AAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTGGAA
18570816 TAAAACCAAA
Statistics
Matches: 308, Mismatches: 26, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
57 8 0.03
58 107 0.35
59 190 0.62
60 3 0.01
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:18570576 original size:117 final size:117
Alignment explanation
Indices: 18570418--18570815 Score: 538
Period size: 117 Copynumber: 3.4 Consensus size: 117
18570408 TTCGGGGGCA
* * * *
18570418 AAAATGG-AA-TTTTGTTAAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG
*
18570481 GTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
66 GTAATTTTGGTGAAAACGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * *
18570533 AAAATGGTATTTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTTAGGGGTAATATG
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG
* * * *
18570598 GTACTTTTTGGT-AAAACTGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGT
66 GTA-ATTTTGGTGAAAAC-GAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * * * *
18570651 AAAATGGTAATTTTTGGTAAAATTGGGGTTAAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATG
1 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG
*
18570716 GTAATTGTTGGTGAAACCGAGGTT-AAAATGGAATTTTGGAAAGTTTTA-GGGT
66 GTAATT-TTGGTGAAAACGAGGTTAAAAATGGAATTTTGGAAAG-TTTAGGGGT
*
18570768 AAAATGGTAATTTTTGGTGAAA-CTAAGGTTAAAAATGGAATTTTGGAA
1 AAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATGGAATTTTGGAA
18570816 TAAAACCAAA
Statistics
Matches: 245, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
115 7 0.03
116 1 0.00
117 121 0.49
118 112 0.46
119 4 0.02
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (117 bp):
AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATG
GTAATTTTGGTGAAAACGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:18570801 original size:30 final size:29
Alignment explanation
Indices: 18570709--18570811 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
18570699 AGTTTGGGGG
* **
18570709 TAAAATGGTAATTGTTGGTGAAACCGAGGT
1 TAAAATGG-AATTTTTGGTGAAACTAAGGT
* * *
18570739 TAAAATGGAA-TTTT-G-GAAAGTTTTAGGG
1 TAAAATGGAATTTTTGGTGAAA--CTAAGGT
18570767 TAAAATGGTAATTTTTGGTGAAACTAAGGT
1 TAAAATGG-AATTTTTGGTGAAACTAAGGT
18570797 TAAAAATGGAATTTT
1 T-AAAATGGAATTTT
18570812 GGAATAAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
26 4 0.07
27 1 0.02
28 14 0.24
29 4 0.07
30 23 0.40
31 8 0.14
32 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
TAAAATGGAATTTTTGGTGAAACTAAGGT
Found at i:18571885 original size:10 final size:10
Alignment explanation
Indices: 18571868--18571901 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
18571858 TTTTTTAAAA
18571868 TAATTATTAT
1 TAATTATTAT
*
18571878 TTATTATTAT
1 TAATTATTAT
*
18571888 TAATTAATAT
1 TAATTATTAT
18571898 TAAT
1 TAAT
18571902 GAGTTTGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TAATTATTAT
Found at i:18572689 original size:17 final size:17
Alignment explanation
Indices: 18572669--18572731 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
18572659 TTTTAAATGT
18572669 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
*
18572686 ATTTAAATTT-AAATAA
1 ATTTAAATTTAAAACAA
* **
18572702 ATTTAAAATTAATTCAA
1 ATTTAAATTTAAAACAA
*
18572719 ACTTAAA-TTAAAA
1 ATTTAAATTTAAAA
18572732 TCCAAGTTGG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 18 0.49
17 19 0.51
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:18572697 original size:33 final size:33
Alignment explanation
Indices: 18572660--18572732 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
18572650 TTCAAATTAT
** * *
18572660 TTTAAATGTATTTAAATTTAAAACAAATTTAAA
1 TTTAAATAAATTTAAAATTAAAACAAACTTAAA
**
18572693 TTTAAATAAATTTAAAATTAATTCAAACTTAAA
1 TTTAAATAAATTTAAAATTAAAACAAACTTAAA
*
18572726 TTAAAAT
1 TTTAAAT
18572733 CCAAGTTGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (33 bp):
TTTAAATAAATTTAAAATTAAAACAAACTTAAA
Found at i:18572715 original size:27 final size:27
Alignment explanation
Indices: 18572653--18572726 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
18572643 TTTAAGTTTC
* * **
18572653 AAATTATTTTAAATGTATTTAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
**
18572680 AAACAAATTTAAATTTAAATAAATTTA
1 AAATTAATTTAAATTTAAATAAATTTA
* *
18572707 AAATTAATTCAAACTTAAAT
1 AAATTAATTTAAATTTAAAT
18572727 TAAAATCCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (27 bp):
AAATTAATTTAAATTTAAATAAATTTA
Found at i:18573842 original size:17 final size:17
Alignment explanation
Indices: 18573807--18573848 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
18573797 GGAAAAAGTA
*
18573807 GTTATAAGAATATGAAAG
1 GTTA-AAGAAAATGAAAG
*
18573825 GTTAAAGAAAATGGAAG
1 GTTAAAGAAAATGAAAG
18573842 GTTAAAG
1 GTTAAAG
18573849 GTCAAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.26, T:0.24
Consensus pattern (17 bp):
GTTAAAGAAAATGAAAG
Found at i:18576023 original size:30 final size:30
Alignment explanation
Indices: 18575989--18576053 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
18575979 AATTATTTTA
* *
18575989 TTGTTAATTTTGTTATTATTTTAGACGCAT
1 TTGTTAATTTTGTTAATATTTTACACGCAT
*
18576019 TTGTTAATTTTGTTAATATTTTACAGGCAT
1 TTGTTAATTTTGTTAATATTTTACACGCAT
18576049 TTGTT
1 TTGTT
18576054 TGTTAAATTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.23, C:0.06, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTAATATTTTACACGCAT
Found at i:18577490 original size:47 final size:47
Alignment explanation
Indices: 18577425--18577548 Score: 144
Period size: 46 Copynumber: 2.7 Consensus size: 47
18577415 AATAACGCAA
* * *
18577425 ATAAACTGCCGATAATCAAAATTGTGGACAAGCCATCAAAATCGTAG
1 ATAAATTGCCAATAATCAAAATTGTGGACAAGCCATCAAAATCGGAG
* * * * *
18577472 ATATATTGCCAATAATCAAAATTAT-GACAAGCCATCACATTTGGAG
1 ATAAATTGCCAATAATCAAAATTGTGGACAAGCCATCAAAATCGGAG
*
18577518 ATAAATTGCCACATAATC-AAATTGTGAACAA
1 ATAAATTGCCA-ATAATCAAAATTGTGGACAA
18577549 TGTCACATTA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
46 33 0.52
47 31 0.48
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (47 bp):
ATAAATTGCCAATAATCAAAATTGTGGACAAGCCATCAAAATCGGAG
Found at i:18577540 original size:46 final size:47
Alignment explanation
Indices: 18577425--18577538 Score: 140
Period size: 47 Copynumber: 2.4 Consensus size: 47
18577415 AATAACGCAA
* * * *
18577425 ATAAACTGCCGATAATCAAAATTGTGGACAAGCCATCAAAATCGTAG
1 ATAAATTGCCAATAATCAAAATTATGGACAAGCCATCAAAATCGGAG
* * * *
18577472 ATATATTGCCAATAATCAAAATTAT-GACAAGCCATCACATTTGGAG
1 ATAAATTGCCAATAATCAAAATTATGGACAAGCCATCAAAATCGGAG
18577518 ATAAATTGCCACATAATCAAA
1 ATAAATTGCCA-ATAATCAAA
18577539 TTGTGAACAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
46 27 0.47
47 30 0.53
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (47 bp):
ATAAATTGCCAATAATCAAAATTATGGACAAGCCATCAAAATCGGAG
Found at i:18578674 original size:14 final size:14
Alignment explanation
Indices: 18578654--18578688 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
18578644 ATTTTTTTTA
18578654 ATATATATATACAT
1 ATATATATATACAT
*
18578668 ATTTATATATACAT
1 ATATATATATACAT
18578682 ATATATA
1 ATATATA
18578689 AATATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (14 bp):
ATATATATATACAT
Found at i:18579511 original size:29 final size:30
Alignment explanation
Indices: 18579465--18579665 Score: 117
Period size: 30 Copynumber: 6.7 Consensus size: 30
18579455 CTCAAAAAGT
*
18579465 CCCTAAACTTTCCAAAAA-TCACATTTTAA
1 CCCTAAACTTTCCAAAAATTCACATTATAA
* *
18579494 CCCTCAAACTTT-CTAAAATTTACATTATAA
1 CCCT-AAACTTTCCAAAAATTCACATTATAA
* * **
18579524 CCCTTAAACTCTCCAAAAATTTGA-ATT-TGG
1 CCC-TAAACTTTCCAAAAA-TTCACATTATAA
* * * * *
18579554 CCATGAACTTTACAAAAATTCAAATTAGAA
1 CCCTAAACTTTCCAAAAATTCACATTATAA
* * *
18579584 CCCTAAACTTTCC-AAAATTTACATTTTGAT
1 CCCTAAACTTTCCAAAAATTCACATTAT-AA
* * * * * *
18579614 CCCTTAGCTCTCTAAAAATTCAAATT-TGAC
1 CCCTAAACTTTCCAAAAATTCACATTAT-AA
*
18579644 CCCTAAACTTTCCAAAATTTCA
1 CCCTAAACTTTCCAAAAATTCA
18579666 TTTTAACCCC
Statistics
Matches: 127, Mismatches: 36, Indels: 17
0.71 0.20 0.09
Matches are distributed among these distances:
28 3 0.02
29 34 0.27
30 68 0.54
31 19 0.15
32 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.33
Consensus pattern (30 bp):
CCCTAAACTTTCCAAAAATTCACATTATAA
Found at i:18579661 original size:89 final size:89
Alignment explanation
Indices: 18579465--18579662 Score: 220
Period size: 89 Copynumber: 2.2 Consensus size: 89
18579455 CTCAAAAAGT
* * ** *
18579465 CCCTAAACTTTCCAAAAATCACATTTTAACCCTCAAACTTTCTAAAATTTACATTATAACCCTTA
1 CCCTAAACTTTCCAAAATTCAAATTAGAACCCTCAAACTTTCCAAAATTTACATTATAACCCTTA
** *
18579530 AACTCTCCAAAAATTTGAATTTGG
66 AACTCTCCAAAAATTCAAATTTGC
* * * * *
18579554 CCATGAACTTTACAAAAATTCAAATTAGAACCCT-AAACTTTCCAAAATTTACATTTTGATCCCT
1 CCCTAAACTTT-CCAAAATTCAAATTAGAACCCTCAAACTTTCCAAAATTTACATTAT-AACCCT
* *
18579618 T-AGCTCTCTAAAAATTCAAATTTGAC
64 TAAACTCTCCAAAAATTCAAATTTG-C
18579644 CCCTAAACTTTCCAAAATT
1 CCCTAAACTTTCCAAAATT
18579663 TCATTTTAAC
Statistics
Matches: 88, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
89 56 0.64
90 32 0.36
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.33
Consensus pattern (89 bp):
CCCTAAACTTTCCAAAATTCAAATTAGAACCCTCAAACTTTCCAAAATTTACATTATAACCCTTA
AACTCTCCAAAAATTCAAATTTGC
Found at i:18579929 original size:23 final size:24
Alignment explanation
Indices: 18579903--18579953 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
18579893 TTTTATCTCT
18579903 TTTAAAATTCCCTTT-TATTTT-TA
1 TTTAAAA-TCCCTTTATATTTTCTA
*
18579926 TTT-AAATCCTTTTATATTTTCTA
1 TTTAAAATCCCTTTATATTTTCTA
18579949 TTTAA
1 TTTAA
18579954 CCCTTCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.25
22 9 0.38
23 8 0.33
24 1 0.04
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTAAAATCCCTTTATATTTTCTA
Found at i:18579932 original size:22 final size:23
Alignment explanation
Indices: 18579911--18579953 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
18579901 CTTTTAAAAT
18579911 TCCCTTT-TATTTT-TATTTAAA
1 TCCCTTTATATTTTCTATTTAAA
*
18579932 TCCTTTTATATTTTCTATTTAA
1 TCCCTTTATATTTTCTATTTAA
18579954 CCCTTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.23, C:0.14, G:0.00, T:0.63
Consensus pattern (23 bp):
TCCCTTTATATTTTCTATTTAAA
Found at i:18582628 original size:26 final size:26
Alignment explanation
Indices: 18582413--18582635 Score: 201
Period size: 26 Copynumber: 8.8 Consensus size: 26
18582403 TTAGTAAATT
* * *
18582413 GCTCTTGCGAGCCAGTATAGTATATC
1 GCTCTTACGAGCCAATACAGTATATC
* * * *
18582439 GCTCTTATGAGCCAGTTCAATATATC
1 GCTCTTACGAGCCAATACAGTATATC
* *
18582465 GCTCTTACAAGCCAATACAATATAT-
1 GCTCTTACGAGCCAATACAGTATATC
* *
18582490 --TAC-T-C---CCAATACAGCATATA
1 GCT-CTTACGAGCCAATACAGTATATC
* * *
18582510 GCTCTTACAAGCCTATTCAGTATATC
1 GCTCTTACGAGCCAATACAGTATATC
* * *
18582536 ACTCTTACGAGCCAGTACAATATATC
1 GCTCTTACGAGCCAATACAGTATATC
* *
18582562 GCTCTTACGAGCTAATATAGTATATC
1 GCTCTTACGAGCCAATACAGTATATC
18582588 GCTCTTACGAGCCAATACAGTATATC
1 GCTCTTACGAGCCAATACAGTATATC
*
18582614 GCTCTTACGAGCCAATTCAGTA
1 GCTCTTACGAGCCAATACAGTA
18582636 ATTTCTTTAA
Statistics
Matches: 159, Mismatches: 29, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
19 12 0.08
21 1 0.01
22 3 0.02
23 3 0.02
24 1 0.01
26 139 0.87
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (26 bp):
GCTCTTACGAGCCAATACAGTATATC
Found at i:18585660 original size:18 final size:16
Alignment explanation
Indices: 18585628--18585671 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
18585618 ATAGGATGAT
18585628 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
18585644 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
18585658 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
18585672 ACCTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:18594884 original size:10 final size:10
Alignment explanation
Indices: 18594869--18594893 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
18594859 AATTGTAAGG
18594869 CACATGTTAT
1 CACATGTTAT
18594879 CACATGTTAT
1 CACATGTTAT
18594889 CACAT
1 CACAT
18594894 CAATGTCAAA
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:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (10 bp):
CACATGTTAT
Found at i:18595167 original size:172 final size:172
Alignment explanation
Indices: 18594881--18595224 Score: 647
Period size: 172 Copynumber: 2.0 Consensus size: 172
18594871 CATGTTATCA
*
18594881 CATGTTATCACATCAATGTCAAATCCCTTTTTTCACCCTTTAATTTGAGATTATTCTTTTCTTTT
1 CATGTTATCACATCAATGTCAAATCCCTTTTTTCACCCTTTAATTTGAGATTAATCTTTTCTTTT
18594946 GGGGTATATTCAATCAATGAAAGACCTAGCAATTGGTTTACAATAGCTGAAAGTATCCCAGTGTG
66 GGGGTATATTCAATCAATGAAAGACCTAGCAATTGGTTTACAATAGCTGAAAGTATCCCAGTGTG
18595011 ACTTGAAATTCAGTTCTTGTTCAACCA-AGTTTCACTTCGAAG
131 ACTTGAAATTCAGTTCTTGTTCAA-CATAGTTTCACTTCGAAG
18595053 CATGTTATCACATCAATGTCAAATCCCTTTTTTCACCCTTTAATTTGAGATTAATC-TTTCTTTT
1 CATGTTATCACATCAATGTCAAATCCCTTTTTTCACCCTTTAATTTGAGATTAATCTTTTCTTTT
18595117 GGGGTATATTCAATCAATGAAAGACCCTAGCAATTGGTTTACAATAGCTGAAAGTATCCCAGTGT
66 GGGGTATATTCAATCAATGAAAGA-CCTAGCAATTGGTTTACAATAGCTGAAAGTATCCCAGTGT
18595182 GACTTGAAATTCAGTTCTTGTTCAACATAGTTTCACTTCGAAG
130 GACTTGAAATTCAGTTCTTGTTCAACATAGTTTCACTTCGAAG
18595225 ATCGATTTCG
Statistics
Matches: 169, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
171 34 0.20
172 135 0.80
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (172 bp):
CATGTTATCACATCAATGTCAAATCCCTTTTTTCACCCTTTAATTTGAGATTAATCTTTTCTTTT
GGGGTATATTCAATCAATGAAAGACCTAGCAATTGGTTTACAATAGCTGAAAGTATCCCAGTGTG
ACTTGAAATTCAGTTCTTGTTCAACATAGTTTCACTTCGAAG
Found at i:18596582 original size:21 final size:21
Alignment explanation
Indices: 18596558--18596600 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
18596548 CTTAAAACTC
18596558 TTTGATATTAAGTCAAAA-ACA
1 TTTGATA-TAAGTCAAAACACA
* *
18596579 TTTGTTATAAGTTAAAACACA
1 TTTGATATAAGTCAAAACACA
18596600 T
1 T
18596601 ATAAAACTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (21 bp):
TTTGATATAAGTCAAAACACA
Found at i:18597216 original size:14 final size:13
Alignment explanation
Indices: 18597197--18597236 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
18597187 AAATGAACTT
18597197 TTAACAATTTGAAA
1 TTAACAATTT-AAA
*
18597211 TTAACAATTTAAC
1 TTAACAATTTAAA
*
18597224 TTAACAATATAAA
1 TTAACAATTTAAA
18597237 CTTGTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (13 bp):
TTAACAATTTAAA
Found at i:18597229 original size:13 final size:14
Alignment explanation
Indices: 18597197--18597231 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
18597187 AAATGAACTT
18597197 TTAACAATTTGAAA
1 TTAACAATTTGAAA
*
18597211 TTAACAATTT-AAC
1 TTAACAATTTGAAA
18597224 TTAACAAT
1 TTAACAAT
18597232 ATAAACTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (14 bp):
TTAACAATTTGAAA
Found at i:18597410 original size:21 final size:21
Alignment explanation
Indices: 18597386--18597425 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18597376 TTACTTTAGA
18597386 GATTTCATTTAGAT-TTAAAGT
1 GATTTC-TTTAGATGTTAAAGT
*
18597407 GATTTCTTTTGATGTTAAA
1 GATTTCTTTAGATGTTAAA
18597426 ATATGTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (21 bp):
GATTTCTTTAGATGTTAAAGT
Found at i:18597483 original size:15 final size:15
Alignment explanation
Indices: 18597456--18597494 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
18597446 ATTAAAGTTT
*
18597456 TTAATATAATATTGGA
1 TTAATA-AATATTAGA
18597472 TTAATAAATATTAGA
1 TTAATAAATATTAGA
18597487 TGTAATAA
1 T-TAATAA
18597495 TGTAATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
TTAATAAATATTAGA
Found at i:18599360 original size:21 final size:20
Alignment explanation
Indices: 18599325--18599370 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
18599315 AAAATTACAA
**
18599325 AAAATATTTTTAAAAAGATTC
1 AAAATATTTACAAAAA-ATTC
*
18599346 AAAATATTTACAAAAATTTC
1 AAAATATTTACAAAAAATTC
18599366 AAAAT
1 AAAAT
18599371 TTATATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAATATTTACAAAAAATTC
Found at i:18599406 original size:45 final size:45
Alignment explanation
Indices: 18599312--18599421 Score: 115
Period size: 45 Copynumber: 2.5 Consensus size: 45
18599302 CTCTCTCACA
* *
18599312 ACAAAAATTAC-AAAA-A-ATATTTTTAAAAAGATTCAAAATATTT
1 ACAAAAATT-CTAAAATATATATTTTTAAAAAAATTCAAAAAATTT
*
18599355 ACAAAAATT-TCAAAATTTATATTTTTAAAAAAATT-AAAAGAAGTTT
1 ACAAAAATTCT-AAAATATATATTTTTAAAAAAATTCAAAA-AA-TTT
18599401 A-AAAAATTCTAAAATATATAT
1 ACAAAAATTCTAAAATATATAT
18599422 AAAAAAACTT
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
43 13 0.23
44 4 0.07
45 34 0.61
46 5 0.09
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (45 bp):
ACAAAAATTCTAAAATATATATTTTTAAAAAAATTCAAAAAATTT
Found at i:18601903 original size:31 final size:31
Alignment explanation
Indices: 18601867--18601942 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
18601857 TTTTTGGTTC
18601867 AATTTGATACTTAAACTTGACA-TTTTTTCTT
1 AATTTGATACTTAAACTTGACACTTTTTT-TT
*
18601898 AATTTGATACCTAAACTTGACACTTTTTTTT
1 AATTTGATACTTAAACTTGACACTTTTTTTT
* *
18601929 AAGTTGGTACTTAA
1 AATTTGATACTTAA
18601943 GCTTTTTGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 34 0.85
32 6 0.15
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.47
Consensus pattern (31 bp):
AATTTGATACTTAAACTTGACACTTTTTTTT
Found at i:18601949 original size:90 final size:90
Alignment explanation
Indices: 18601821--18601993 Score: 226
Period size: 90 Copynumber: 1.9 Consensus size: 90
18601811 TTAGTATTTG
* * ** *
18601821 AACTTGACACTTTTTCTTAATTTGGTAGTTAATTTTTTTTTGGTTC-AATTT-GATACTTAAACT
1 AACTTGACACTTTTTCTTAAGTTGGTACTTAA-GCTTTTTGGGTTCTAATTTAG-TACTTAAACT
18601884 TGAC-ATTTTTTCTTAATTTGATACCTA
64 TGACTATTTTTTC-TAATTTGATACCTA
* *
18601911 AACTTGACACTTTTTTTTAAGTTGGTACTTAAGCTTTTTGGGTTCTAATTTAGTACTTGAACTTG
1 AACTTGACACTTTTTCTTAAGTTGGTACTTAAGCTTTTTGGGTTCTAATTTAGTACTTAAACTTG
*
18601976 ACTCTTTTTTCTAATTTG
66 ACTATTTTTTCTAATTTG
18601994 GTACTTAATC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
89 10 0.14
90 54 0.75
91 8 0.11
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.51
Consensus pattern (90 bp):
AACTTGACACTTTTTCTTAAGTTGGTACTTAAGCTTTTTGGGTTCTAATTTAGTACTTAAACTTG
ACTATTTTTTCTAATTTGATACCTA
Found at i:18601960 original size:59 final size:59
Alignment explanation
Indices: 18601897--18602008 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
18601887 CATTTTTTCT
*
18601897 TAATTT-GATACCTAAACTTGACACTTTTTTTTAAGTTGGTACTTAAGCTTTTTGGGTTC
1 TAATTTAG-TACCTAAACTTGACACTTTTTTCTAAGTTGGTACTTAAGCTTTTTGGGTTC
* * * * *
18601956 TAATTTAGTACTTGAACTTGACTCTTTTTTCTAATTTGGTACTTAATCTTTTT
1 TAATTTAGTACCTAAACTTGACACTTTTTTCTAAGTTGGTACTTAAGCTTTTT
18602009 TTAATATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 45 0.98
60 1 0.02
ACGTcount: A:0.23, C:0.13, G:0.12, T:0.51
Consensus pattern (59 bp):
TAATTTAGTACCTAAACTTGACACTTTTTTCTAAGTTGGTACTTAAGCTTTTTGGGTTC
Found at i:18602220 original size:59 final size:57
Alignment explanation
Indices: 18602151--18602339 Score: 191
Period size: 60 Copynumber: 3.2 Consensus size: 57
18602141 TAATAAATTT
* * *
18602151 AGGTATCAAATTGAATCTAAAAAAACTTAGATACCAAATTAGGAAAAAATATTAAGTTC
1 AGGTACCAAATTG-ATCTAAAAAAATTTAGGTACCAAATTA-GAAAAAATATTAAGTTC
* * * *
18602210 AGGTACCAAATTTGATCCAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTC
1 AGGTACCAAA-TTGATCTAAAAAAA-TTTAGGTACCAAATT-AGAAAAAATATTAAGTTC
* * * *
18602270 AAGTACCAAATTGGGTCAATAAAAAAATTTAGGTACCAAATTA-AAAAAATATTAAATTA
1 AGGTACCAAATT-GATC--TAAAAAAATTTAGGTACCAAATTAGAAAAAATATTAAGTTC
*
18602329 AGATACCAAAT
1 AGGTACCAAAT
18602340 ATTATATTAA
Statistics
Matches: 107, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
59 41 0.38
60 43 0.40
61 16 0.15
62 7 0.07
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.26
Consensus pattern (57 bp):
AGGTACCAAATTGATCTAAAAAAATTTAGGTACCAAATTAGAAAAAATATTAAGTTC
Found at i:18603160 original size:17 final size:17
Alignment explanation
Indices: 18603138--18603210 Score: 58
Period size: 17 Copynumber: 4.1 Consensus size: 17
18603128 TATACAGTAG
18603138 TATCAAACAATTTCACA
1 TATCAAACAATTTCACA
*
18603155 TATCAATCAATTTAGCACAA
1 TATCAAACAATTT--CAC-A
* *
18603175 TGAT-AAACACTTTCGCA
1 T-ATCAAACAATTTCACA
* *
18603192 TATCAATCAATTTAACA
1 TATCAAACAATTTCACA
18603209 TA
1 TA
18603211 ATAACAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
16 2 0.05
17 25 0.58
18 2 0.05
19 3 0.07
20 9 0.21
21 2 0.05
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.32
Consensus pattern (17 bp):
TATCAAACAATTTCACA
Found at i:18603228 original size:37 final size:37
Alignment explanation
Indices: 18603153--18603240 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
18603143 AACAATTTCA
* * * *
18603153 CATATCAATCAATTTAGCACAATGATAAACACTTTCG
1 CATATCAATCAATTTAACACAATAACAAACACTCTCG
* * *
18603190 CATATCAATCAATTTAACATAATAACAAATAGTCTCG
1 CATATCAATCAATTTAACACAATAACAAACACTCTCG
*
18603227 CAAATCAATCAATT
1 CATATCAATCAATT
18603241 CAATACGTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (37 bp):
CATATCAATCAATTTAACACAATAACAAACACTCTCG
Found at i:18604794 original size:33 final size:32
Alignment explanation
Indices: 18604732--18604800 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
18604722 AAGAAAGATA
18604732 AATTCTATTAGGATTTGAAAAGGAGTAATTTG
1 AATTCTATTAGGATTTGAAAAGGAGTAATTTG
* *
18604764 AATTCTAGTTAGGAGTTT-AAAATGATTAATTTG
1 AATTCTA-TTAGGA-TTTGAAAAGGAGTAATTTG
18604797 AATT
1 AATT
18604801 TCAAATTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 7 0.21
33 23 0.70
34 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.19, T:0.41
Consensus pattern (32 bp):
AATTCTATTAGGATTTGAAAAGGAGTAATTTG
Found at i:18605659 original size:18 final size:19
Alignment explanation
Indices: 18605637--18605685 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
18605627 TTCTACTTTC
18605637 AAGGGTTCGCATACTTAT-
1 AAGGGTTCGCATACTTATA
* * *
18605655 TAGGGTTCACAGACTTATA
1 AAGGGTTCGCATACTTATA
18605674 AAGGG-TCGCATA
1 AAGGGTTCGCATA
18605686 TATAAGTACT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (19 bp):
AAGGGTTCGCATACTTATA
Found at i:18609032 original size:15 final size:15
Alignment explanation
Indices: 18609009--18609042 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
18608999 CAAGAATTTT
18609009 TAAAGTGCAAGAAAA
1 TAAAGTGCAAGAAAA
* *
18609024 TAAATTGCAAGAAAG
1 TAAAGTGCAAGAAAA
18609039 TAAA
1 TAAA
18609043 CTGGTAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (15 bp):
TAAAGTGCAAGAAAA
Found at i:18610379 original size:175 final size:175
Alignment explanation
Indices: 18610088--18610438 Score: 684
Period size: 175 Copynumber: 2.0 Consensus size: 175
18610078 CGAGGCTAAG
*
18610088 AATGCGTAAAAGATTACTCTTTTCGAGAGTTATCACACCCCCAAACTTGAGTTGTTGCTTGTCTT
1 AATGCGTAAAAGATTACTCTTTTCGAGAGTTATCACACCCCCAAACTTGAGTTGTTACTTGTCTT
18610153 CAAGCAAAAATGCATGAATGCATGAAAGCTTTGTCATGGCATCATTGAGAAATCAAAAGTCTTAC
66 CAAGCAAAAATGCATGAATGCATGAAAGCTTTGTCATGGCATCATTGAGAAATCAAAAGTCTTAC
18610218 AAAGCATACCTTAGTATTTCCATTCTTAGAATATCTCATAAATCT
131 AAAGCATACCTTAGTATTTCCATTCTTAGAATATCTCATAAATCT
18610263 AATGCGTAAAAGATTACTCTTTTCGAGAGTTATCACACCCCCAAACTTGAGTTGTTACTTGTCTT
1 AATGCGTAAAAGATTACTCTTTTCGAGAGTTATCACACCCCCAAACTTGAGTTGTTACTTGTCTT
18610328 CAAGCAAAAATGCATGAATGCATGAAAGCTTTGTCATGGCATCATTGAGAAATCAAAAGTCTTAC
66 CAAGCAAAAATGCATGAATGCATGAAAGCTTTGTCATGGCATCATTGAGAAATCAAAAGTCTTAC
*
18610393 AGAGCATACCTTAGTATTTCCATTCTTAGAATATCTCATAAATCT
131 AAAGCATACCTTAGTATTTCCATTCTTAGAATATCTCATAAATCT
18610438 A
1 A
18610439 GAAACATAAC
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 174 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (175 bp):
AATGCGTAAAAGATTACTCTTTTCGAGAGTTATCACACCCCCAAACTTGAGTTGTTACTTGTCTT
CAAGCAAAAATGCATGAATGCATGAAAGCTTTGTCATGGCATCATTGAGAAATCAAAAGTCTTAC
AAAGCATACCTTAGTATTTCCATTCTTAGAATATCTCATAAATCT
Found at i:18611428 original size:11 final size:13
Alignment explanation
Indices: 18611408--18611444 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
18611398 TAATGGCGTC
*
18611408 TTCTCCTTCTCTT
1 TTCTCTTTCTCTT
18611421 TT-T-TTTCTCTT
1 TTCTCTTTCTCTT
18611432 TTCTCTTTCTCTT
1 TTCTCTTTCTCTT
18611445 CCTCTTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 9 0.43
12 2 0.10
13 10 0.48
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTCTCTTTCTCTT
Found at i:18618803 original size:23 final size:23
Alignment explanation
Indices: 18618776--18620115 Score: 1623
Period size: 23 Copynumber: 58.3 Consensus size: 23
18618766 ACATACTCAC
18618776 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18618799 TTTAATCATAAATCACAGTAATA
1 TTTAAGCACAAATCACATTAATA
18618822 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18618845 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18618868 TTTGAGCACAAATAATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18618891 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18618914 TTTGA-CAACAAATCATATTAATA
1 TTTAAGC-ACAAATCACATTAATA
*
18618937 TTTAAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18618960 TTTGAGAACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * * *
18618983 TTTAAGAATAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619006 TTTAAGGATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619029 TTTAAGCACAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619052 TTTGAGCACAAATCAGATTAATA
1 TTTAAGCACAAATCACATTAATA
18619075 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619098 TTTAAGCACAAATTATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18619121 TTTGAGTACAAATCAGATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18619144 TTTAAGTAC-ATTCCACATTATTA
1 TTTAAGCACAAAT-CACATTAATA
* * *
18619167 TTTGAGAACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
** * *
18619190 TTTAATAACAAATAAAATTAATA
1 TTTAAGCACAAATCACATTAATA
18619213 TTTAAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619236 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619259 TTTAAGCACAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619282 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619305 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619328 TTTAAGCAGAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18619351 CTTAATCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619374 CTTAAGCACAAATCACATTACTA
1 TTTAAGCACAAATCACATTAATA
* *
18619397 TTTAATCATAAATCAGC-TTAATA
1 TTTAAGCACAAATCA-CATTAATA
* * *
18619420 TTTAAGCATAAATTACATTCATA
1 TTTAAGCACAAATCACATTAATA
* *
18619443 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619466 TTTAAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619489 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619512 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619535 TTTAAGCACAAATCGCATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18619558 TTTAAGCATAAATCATATTAA-C
1 TTTAAGCACAAATCACATTAATA
*
18619580 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619603 TTTAAGCACAAATTACATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619626 TTTGAGCACAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619649 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619672 TTTAAGCAGAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18619695 CTTAATCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619718 CTTAAGCACAAATCACATTACTA
1 TTTAAGCACAAATCACATTAATA
* *
18619741 TTTAATCATAAATCAGC-TTAATA
1 TTTAAGCACAAATCA-CATTAATA
* * *
18619764 TTTAAGCATAAATTACATTCATA
1 TTTAAGCACAAATCACATTAATA
* *
18619787 TTTGAGCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619810 TTTAAGCACAAATCATATT-ATCA
1 TTTAAGCACAAATCACATTAAT-A
* *
18619833 TTTAAGCATAAATCACAATAATA
1 TTTAAGCACAAATCACATTAATA
*
18619856 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619879 TTTAAGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
*
18619902 TTTAAGCACAAATCGCATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18619925 TTTAAGCATAAATCATATTAA-C
1 TTTAAGCACAAATCACATTAATA
* *
18619947 TTTAAGCATAAATCACAATAATA
1 TTTAAGCACAAATCACATTAATA
*
18619970 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* *
18619993 TTTAAGCACAAATCATATTAACA
1 TTTAAGCACAAATCACATTAATA
* * * *
18620016 TTTAAGTATAAATTACAATAATA
1 TTTAAGCACAAATCACATTAATA
*
18620039 TTTAAGCATAAATCACATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18620062 TTTAGGCATAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
* * *
18620085 TTTGACCACAAATCATATTAATA
1 TTTAAGCACAAATCACATTAATA
18620108 TTTAAGCA
1 TTTAAGCA
18620116 TAGATATAAG
Statistics
Matches: 1146, Mismatches: 159, Indels: 24
0.86 0.12 0.02
Matches are distributed among these distances:
22 46 0.04
23 1094 0.95
24 6 0.01
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (23 bp):
TTTAAGCACAAATCACATTAATA
Found at i:18622349 original size:6 final size:6
Alignment explanation
Indices: 18622338--18622363 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
18622328 GGTTTTCTCC
18622338 AAAATG AAAATG AAAATG AAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AA
18622364 GAAATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:18626553 original size:13 final size:13
Alignment explanation
Indices: 18626535--18626569 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
18626525 AGAGTTTCTG
18626535 GGAGAAAATTTGA
1 GGAGAAAATTTGA
*
18626548 GGAGAAAGTTTGA
1 GGAGAAAATTTGA
*
18626561 AGAGAAAAT
1 GGAGAAAAT
18626570 ATGATTACCA
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:0.31, T:0.20
Consensus pattern (13 bp):
GGAGAAAATTTGA
Found at i:18627845 original size:10 final size:10
Alignment explanation
Indices: 18627830--18627866 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
18627820 CATAAGGTTA
18627830 ATTAATTATG
1 ATTAATTATG
18627840 ATTAATTATG
1 ATTAATTATG
*
18627850 -TTAATTTTG
1 ATTAATTATG
18627859 ATTAATTA
1 ATTAATTA
18627867 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (10 bp):
ATTAATTATG
Found at i:18629231 original size:36 final size:37
Alignment explanation
Indices: 18629189--18629266 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 37
18629179 ATGGAATACA
* * *
18629189 ATAAAATGTTTATTATATTTATTTGT-GTTTTTT-AAT
1 ATAAAATATGTATTATATTTA-TGGTAGTTTTTTAAAT
18629225 ATAAAATATGTATTATATTTATGGTAGTTTTTTAAAT
1 ATAAAATATGTATTATATTTATGGTAGTTTTTTAAAT
18629262 ATAAA
1 ATAAA
18629267 TACTTTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 3 0.08
36 26 0.70
37 8 0.22
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (37 bp):
ATAAAATATGTATTATATTTATGGTAGTTTTTTAAAT
Found at i:18629357 original size:16 final size:14
Alignment explanation
Indices: 18629326--18629369 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
18629316 TTTGTGTATT
18629326 ATATTTTTAAAAAA
1 ATATTTTTAAAAAA
18629340 ATATTTTTAAATAAAA
1 ATATTTTT-AA-AAAA
* *
18629356 ATAATCTTAAAAAA
1 ATATTTTTAAAAAA
18629370 TAAAATATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 12 0.46
15 4 0.15
16 10 0.38
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATTTTTAAAAAA
Found at i:18631360 original size:58 final size:58
Alignment explanation
Indices: 18631251--18631404 Score: 179
Period size: 58 Copynumber: 2.6 Consensus size: 58
18631241 AGGAAAAAAA
* * *
18631251 ACACCCCT-TTTAATCTGATAAAAAATATCAAATTTTTGGATGTTGGTCATGCAATG-GCG
1 ACACCCCTATTT-ATCAGAT-AAAAA-ATCAAATTTTTGGATGTTGGCCATGCAATGACCG
* * *
18631310 ACACCCACTTTTTGTCAGATAAAAAAGTCAATTTTTTGG-TGTTGGCCATGCAATGACCG
1 ACACCC-CTATTTATCAGATAAAAAA-TCAAATTTTTGGATGTTGGCCATGCAATGACCG
*
18631369 ACACCCCTATTTATCTGATAAAAAATCAAATTTTTG
1 ACACCCCTATTTATCAGATAAAAAATCAAATTTTTG
18631405 CATGGCCGAC
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
57 10 0.12
58 32 0.39
59 30 0.37
60 7 0.09
61 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (58 bp):
ACACCCCTATTTATCAGATAAAAAATCAAATTTTTGGATGTTGGCCATGCAATGACCG
Found at i:18631511 original size:61 final size:60
Alignment explanation
Indices: 18631405--18631658 Score: 203
Period size: 60 Copynumber: 4.2 Consensus size: 60
18631395 CAAATTTTTG
* *** ** * *
18631405 CATGGCCGACACCCTCTTTTTTCAGATAAAATTTTTTTAAATTTTTTTATGTTGGTCATGG
1 CATGACCGACACCCT-TTTTTTCAGATAAAAAAATTCAAAATTTTTTGATGTTGGTCATGC
* *
18631466 CATGATCGACACCCTTTTTTTCAAATAAAAAAATTCAAAATTTTTTGATGTTGGTCATGC
1 CATGACCGACACCCTTTTTTTCAGATAAAAAAATTCAAAATTTTTTGATGTTGGTCATGC
* * ** * * * *
18631526 CATGGCCGACACCCCTTTTCGCAGATAAAAAAATTTCAAAAATTTTTGGTGTCGGCCATGC
1 CATGACCGACACCCTTTTTTTCAGATAAAAAAA-TTCAAAATTTTTTGATGTTGGTCATGC
* * * *
18631587 CATGGCCGACACTCCCTTTTATTT--GGT-AAAAAATT--AAATTTTTTAAGTGTTGGTCATGT
1 CATGACCGACA--CCCTTTT-TTTCAGATAAAAAAATTCAAAATTTTTTGA-TGTTGGTCATGC
* *
18631646 AATGGCCGACACC
1 CATGACCGACACC
18631659 AATTTCTCCT
Statistics
Matches: 157, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
57 2 0.01
58 8 0.05
59 19 0.12
60 66 0.42
61 53 0.34
62 2 0.01
63 6 0.04
64 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (60 bp):
CATGACCGACACCCTTTTTTTCAGATAAAAAAATTCAAAATTTTTTGATGTTGGTCATGC
Found at i:18631605 original size:62 final size:60
Alignment explanation
Indices: 18631472--18631606 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 60
18631462 ATGGCATGAT
* ** * * * *
18631472 CGACACCCTTTTTTTCAAATAAAAAAATTCAAAATTTTTTGATGTTGGTCATGCCATGGC
1 CGACACCCCTTTTCGCAGATAAAAAAATTCAAAAATTTTTGATGTCGGCCATGCCATGGC
*
18631532 CGACACCCCTTTTCGCAGATAAAAAAATTTCAAAAATTTTTGGTGTCGGCCATGCCATGGC
1 CGACACCCCTTTTCGCAGATAAAAAAA-TTCAAAAATTTTTGATGTCGGCCATGCCATGGC
18631593 CGACACTCCCTTTT
1 CGACAC-CCCTTTT
18631607 ATTTGGTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
60 23 0.35
61 35 0.54
62 7 0.11
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (60 bp):
CGACACCCCTTTTCGCAGATAAAAAAATTCAAAAATTTTTGATGTCGGCCATGCCATGGC
Found at i:18632488 original size:17 final size:17
Alignment explanation
Indices: 18632468--18632522 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
18632458 AAAAAATAAT
18632468 AATTAGAATATACAGGA
1 AATTAGAATATACAGGA
*
18632485 AATTAGAA-A-ATA--A
1 AATTAGAATATACAGGA
*
18632498 AATTAAAATATACAGGA
1 AATTAGAATATACAGGA
18632515 AATTAGAA
1 AATTAGAA
18632523 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.27
14 1 0.03
15 4 0.13
16 1 0.03
17 16 0.53
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.24
Consensus pattern (17 bp):
AATTAGAATATACAGGA
Found at i:18632508 original size:30 final size:30
Alignment explanation
Indices: 18632460--18632565 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
18632450 AAATTTTAAA
*
18632460 AAAATAATAATTAGAATATACAGGAAATTAG
1 AAAATAA-AATTAAAATATACAGGAAATTAG
18632491 AAAATAAAATTAAAATATACAGGAAATTAG
1 AAAATAAAATTAAAATATACAGGAAATTAG
* * * * * *
18632521 AAATTAAATTTAAAATAAAAACGAAATTAC
1 AAAATAAAATTAAAATATACAGGAAATTAG
* *
18632551 AAATTAAATTTAAAA
1 AAAATAAAATTAAAA
18632566 AGTAAACGAA
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
30 61 0.90
31 7 0.10
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (30 bp):
AAAATAAAATTAAAATATACAGGAAATTAG
Found at i:18634713 original size:18 final size:19
Alignment explanation
Indices: 18634670--18634714 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
18634660 CTCTCTTAGG
*
18634670 GTTAAGGTTTTTTAATTTT
1 GTTAAGGTTTATTAATTTT
18634689 GTT-AGGTTTATTAATTTT
1 GTTAAGGTTTATTAATTTT
18634707 -TTAAGGTT
1 GTTAAGGTT
18634715 AGGGTTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 19 0.79
19 3 0.12
ACGTcount: A:0.22, C:0.00, G:0.18, T:0.60
Consensus pattern (19 bp):
GTTAAGGTTTATTAATTTT
Found at i:18637584 original size:21 final size:21
Alignment explanation
Indices: 18637560--18637602 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18637550 AAATGTATTA
*
18637560 AATGATTAAATTACATGATTT
1 AATGAGTAAATTACATGATTT
**
18637581 AATGAGTAAATTGGATGATTT
1 AATGAGTAAATTACATGATTT
18637602 A
1 A
18637603 TTTTGATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.02, G:0.16, T:0.40
Consensus pattern (21 bp):
AATGAGTAAATTACATGATTT
Found at i:18637885 original size:36 final size:36
Alignment explanation
Indices: 18637802--18638073 Score: 258
Period size: 36 Copynumber: 7.6 Consensus size: 36
18637792 TCGATGGAGA
* * * * *
18637802 GCTTACGTCTTGGTTAGAGTGTAATACTATGTGAGT
1 GCTTACGTCTCGGTTAGAGCGTAATGCTATGTAATT
* * ** * *
18637838 GCATACATCTCGGTTAGAATGTATTGCTGTGTAATT
1 GCTTACGTCTCGGTTAGAGCGTAATGCTATGTAATT
* **
18637874 GCTTACGTCTCGGTTAGAGCGTAATGCTAAGGGATT
1 GCTTACGTCTCGGTTAGAGCGTAATGCTATGTAATT
* * * *
18637910 TCTTACGTCTCGATTAGAGTGTAATGCTATGTGATT
1 GCTTACGTCTCGGTTAGAGCGTAATGCTATGTAATT
* * *
18637946 GCATACGTCTCGGTTAGAACGTATTGCTATGTAATT
1 GCTTACGTCTCGGTTAGAGCGTAATGCTATGTAATT
* *
18637982 GCTTACGTCTCGGTTAGAGCGTAATGCTAAG-AGAGT
1 GCTTACGTCTCGGTTAGAGCGTAATGCTATGTA-ATT
* * * *
18638018 GCTTACGTCTCGGTTAGAGCGCAATGCTAAGTGACT
1 GCTTACGTCTCGGTTAGAGCGTAATGCTATGTAATT
* * *
18638054 ACTTATGTCTCAGTTAGAGC
1 GCTTACGTCTCGGTTAGAGC
18638074 TTAAGGCCAT
Statistics
Matches: 193, Mismatches: 41, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
35 1 0.01
36 192 0.99
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.35
Consensus pattern (36 bp):
GCTTACGTCTCGGTTAGAGCGTAATGCTATGTAATT
Found at i:18637992 original size:108 final size:108
Alignment explanation
Indices: 18637802--18638051 Score: 383
Period size: 108 Copynumber: 2.3 Consensus size: 108
18637792 TCGATGGAGA
* * * *
18637802 GCTTACGTCTTGGTTAGAGTGTAATACTATGTGAGTGCATACATCTCGGTTAGAATGTATTGCTG
1 GCTTACGTCTCGGTTAGAGTGTAATGCTATGTGAGTGCATACATCTCGGTTAGAACGTATTGCTA
* *
18637867 TGTAATTGCTTACGTCTCGGTTAGAGCGTAATGCTAAGGGATT
66 TGTAATTGCTTACGTCTCGGTTAGAGCGTAATGCTAAGAGAGT
* * * *
18637910 TCTTACGTCTCGATTAGAGTGTAATGCTATGTGATTGCATACGTCTCGGTTAGAACGTATTGCTA
1 GCTTACGTCTCGGTTAGAGTGTAATGCTATGTGAGTGCATACATCTCGGTTAGAACGTATTGCTA
18637975 TGTAATTGCTTACGTCTCGGTTAGAGCGTAATGCTAAGAGAGT
66 TGTAATTGCTTACGTCTCGGTTAGAGCGTAATGCTAAGAGAGT
* * *
18638018 GCTTACGTCTCGGTTAGAGCGCAATGCTAAGTGA
1 GCTTACGTCTCGGTTAGAGTGTAATGCTATGTGA
18638052 CTACTTATGT
Statistics
Matches: 127, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 127 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (108 bp):
GCTTACGTCTCGGTTAGAGTGTAATGCTATGTGAGTGCATACATCTCGGTTAGAACGTATTGCTA
TGTAATTGCTTACGTCTCGGTTAGAGCGTAATGCTAAGAGAGT
Found at i:18639497 original size:44 final size:44
Alignment explanation
Indices: 18639448--18639571 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 44
18639438 GATTGTATCT
* * *
18639448 TATTTCATATTGGTGCATATCTTACATCATATCATAGCACATTA
1 TATTTCATAATGGAGCATATCTTACAACATATCATAGCACATTA
* * *
18639492 TATTTCATAAT-GACGCATATATTATAACATATCATAGCATATTA
1 TATTTCATAATGGA-GCATATCTTACAACATATCATAGCACATTA
* ** * *
18639536 GATTTCATACCGGAGCATATCTTATAACATAGCATA
1 TATTTCATAATGGAGCATATCTTACAACATATCATA
18639572 TCCTACCCGC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 64 0.96
45 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (44 bp):
TATTTCATAATGGAGCATATCTTACAACATATCATAGCACATTA
Found at i:18639877 original size:41 final size:40
Alignment explanation
Indices: 18639779--18640028 Score: 376
Period size: 41 Copynumber: 6.1 Consensus size: 40
18639769 CACAAAAACT
* *
18639779 AGAGCAATAGCGGCGCTTATAGAAAAGCGCCGCTAAAAGT-
1 AGAGCAATAGCGGCGCTTAT-GGAAAGCGCCGCTAAAGGTC
*
18639819 GGAGCAATAGCGGCGCTTATGGTAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGG-AAAGCGCCGCTAAAGGTC
18639860 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGG-AAAGCGCCGCTAAAGGTC
* *
18639901 AGATCAATAGCGGCGCTTATGAGCAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATG-GAAAGCGCCGCTAAAGGTC
*
18639942 AGAGCAATAGTGGCGCTTATGAGAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATG-GAAAGCGCCGCTAAAGGTC
*
18639983 AGAGCAATAGCGGCGCTTATGGTCAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGG-AAAGCGCCGCTAAAGGTC
18640024 AGAGC
1 AGAGC
18640029 TAAAGGTCAG
Statistics
Matches: 194, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
39 1 0.01
40 36 0.19
41 156 0.80
42 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (40 bp):
AGAGCAATAGCGGCGCTTATGGAAAGCGCCGCTAAAGGTC
Found at i:18639982 original size:123 final size:124
Alignment explanation
Indices: 18639783--18640281 Score: 582
Period size: 123 Copynumber: 4.0 Consensus size: 124
18639773 AAAACTAGAG
* * *
18639783 CAATAGCGGCGCTTAT-AGAAAAGCGCCGCTAAAAGT-GGAGCAATAGCGGCGCTTATGGTAAAG
1 CAATAGCGGCGCTTATGAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAG
18639846 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTCAGAT
66 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTCAGAT
* *
18639905 CAATAGCGGCGCTTATGAG-CAAGCGCCGCTAAAGGTCAGAGCAATAGTGGCGCTTAT-GAGAAA
1 CAATAGCGGCGCTTATGAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGA-AAA
**
18639968 GCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGTCAAGCGCCGCTAAAGGTCAGAGCTAAA
65 GCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGG--AAAAG-CGC-------C---GCTAAA
18640033 GGTCAGAT
117 GGTCAGAT
* ** *
18640041 CAATAGCGGCGCTTATGAG-AAAGCACCGCTAAAGGTCAGATTAATAGCGGCGCTTAT-GAGCAA
1 CAATAGCGGCGCTTATGAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGA-AAA
* * ** *
18640104 GCGCCGCTAAAAGTCGGAGCAATAGCGGCGCTTATGGTCAAGCGCCGCTAAAGGTCAGAG
65 GCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTCAGAT
** * *
18640164 CAATAGCGGCGCTTATG-GTCAAGCGCCGCTAAAGGTCAGACCAATAGCGGCACTTATGGAAAAG
1 CAATAGCGGCGCTTATGAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAG
* * * *
18640228 CGCCGCTAAATGTCATAGCAATAGCGGCGCTTAT-GAGCAAGCGCCGTTAAAGGT
66 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGA-AAAGCGCCGCTAAAGGT
18640282 TAAAGCAGAA
Statistics
Matches: 327, Mismatches: 31, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
122 34 0.10
123 173 0.53
124 2 0.01
125 3 0.01
126 4 0.01
133 4 0.01
134 1 0.00
136 106 0.32
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.17
Consensus pattern (124 bp):
CAATAGCGGCGCTTATGAGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAG
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTCAGAT
Found at i:18640032 original size:13 final size:13
Alignment explanation
Indices: 18640014--18640039 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18640004 GTCAAGCGCC
18640014 GCTAAAGGTCAGA
1 GCTAAAGGTCAGA
18640027 GCTAAAGGTCAGA
1 GCTAAAGGTCAGA
18640040 TCAATAGCGG
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:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (13 bp):
GCTAAAGGTCAGA
Done.