Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 160 of 163
Found at i:45548924 original size:23 final size:22
Alignment explanation
Indices: 45548876--45548925 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
45548866 AAATTTAATT
45548876 TTTTAATTTTTATTTTCAAGAA
1 TTTTAATTTTTATTTTCAAGAA
*
45548898 -TTTAATTTATATATTTTTAA-AA
1 TTTTAATTT-T-TATTTTCAAGAA
45548920 TTTTAA
1 TTTTAA
45548926 AATTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 8 0.33
22 3 0.12
23 13 0.54
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTAATTTTTATTTTCAAGAA
Found at i:45549514 original size:29 final size:29
Alignment explanation
Indices: 45549481--45549537 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
45549471 AAAATTTAAA
*
45549481 TTAATTTGACCCTTTAAAAATAATAAAAT
1 TTAATTTAACCCTTTAAAAATAATAAAAT
* *
45549510 TTAATTTAATCCTTTAAAAATTATAAAA
1 TTAATTTAACCCTTTAAAAATAATAAAA
45549538 ATATAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (29 bp):
TTAATTTAACCCTTTAAAAATAATAAAAT
Found at i:45553550 original size:36 final size:36
Alignment explanation
Indices: 45553505--45553581 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
45553495 TTTGATTGAG
45553505 TTTTTATCTACTATGGGATTGTTGAGAAAATATATT
1 TTTTTATCTACTATGGGATTGTTGAGAAAATATATT
45553541 TTTTTATCTACTATGGGATTGTTGAGAAAATATATT
1 TTTTTATCTACTATGGGATTGTTGAGAAAATATATT
*
45553577 CTTTT
1 TTTTT
45553582 CCTGTGGTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (36 bp):
TTTTTATCTACTATGGGATTGTTGAGAAAATATATT
Found at i:45559466 original size:10 final size:9
Alignment explanation
Indices: 45559420--45559503 Score: 68
Period size: 9 Copynumber: 9.3 Consensus size: 9
45559410 CATGTGATTG
45559420 AAAATTATA
1 AAAATTATA
45559429 AAAA--ATA
1 AAAATTATA
*
45559436 AAAATCACTA
1 AAAATTA-TA
45559446 AAAATTATA
1 AAAATTATA
45559455 AAAATTATTA
1 AAAATTA-TA
**
45559465 AATTTTAATA
1 AAAATT-ATA
45559475 AAAA-TATA
1 AAAATTATA
45559483 AAAA-TATTA
1 AAAATTA-TA
*
45559492 AAATTTATA
1 AAAATTATA
45559501 AAA
1 AAA
45559504 TACATCAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
7 7 0.11
8 9 0.15
9 25 0.40
10 20 0.32
11 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTATA
Found at i:45559494 original size:37 final size:39
Alignment explanation
Indices: 45559432--45559504 Score: 98
Period size: 37 Copynumber: 1.9 Consensus size: 39
45559422 AATTATAAAA
*
45559432 AATAAAAATCACTAAAAATTATAAAAATTATTAAATTTT
1 AATAAAAATCACTAAAAATTATAAAAATTATAAAATTTT
*
45559471 AATAAAAAT-A-TAAAAA-TATTAAAATTTATAAAAT
1 AATAAAAATCACTAAAAATTA-TAAAAATTATAAAAT
45559505 ACATCAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 2 0.06
37 19 0.61
38 1 0.03
39 9 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (39 bp):
AATAAAAATCACTAAAAATTATAAAAATTATAAAATTTT
Found at i:45559513 original size:27 final size:28
Alignment explanation
Indices: 45559452--45559514 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
45559442 ACTAAAAATT
* *
45559452 ATAAAAATTATTAAATTTTAATAAAAAT
1 ATAAAAATTATTAAAATTTAATAAAAAC
45559480 ATAAAAA-TATTAAAATTT-ATAAAATAC
1 ATAAAAATTATTAAAATTTAATAAAA-AC
45559507 ATCAAAAA
1 AT-AAAAA
45559515 ATTTATTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 6 0.19
27 13 0.42
28 12 0.39
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAAAAATTATTAAAATTTAATAAAAAC
Found at i:45562638 original size:30 final size:30
Alignment explanation
Indices: 45562588--45562644 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
45562578 ATTTGGTGAC
*
45562588 AATTTTTTTAATTTAATATTTGAATTTAAT
1 AATTTTTTTAATTTAATATTTAAATTTAAT
**
45562618 AATTTTTTTAATTTGGTATTTAAATTT
1 AATTTTTTTAATTTAATATTTAAATTT
45562645 TATCGAGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.61
Consensus pattern (30 bp):
AATTTTTTTAATTTAATATTTAAATTTAAT
Found at i:45566505 original size:69 final size:69
Alignment explanation
Indices: 45566394--45566532 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
45566384 ATGTCCTTTG
*
45566394 TATTGAATGTGTTGATAGCAGTTTTGAGTTCGGTGATTGATTTAGCATGCTTCTCGACATCTTCT
1 TATTGAATGTGTTGATAGCAGTTTTGAGTTCGGTGAATGATTTAGCATGCTTCTCGACATCTTCT
45566459 TCAA
66 TCAA
*
45566463 TATTGAATGTGTTGATAGCAGTTTTGAGTTCTGTGAATGATTTAGCATGCTTCTCGACATCTTCT
1 TATTGAATGTGTTGATAGCAGTTTTGAGTTCGGTGAATGATTTAGCATGCTTCTCGACATCTTCT
45566528 TCAA
66 TCAA
45566532 T
1 T
45566533 TTGTTGGAAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.42
Consensus pattern (69 bp):
TATTGAATGTGTTGATAGCAGTTTTGAGTTCGGTGAATGATTTAGCATGCTTCTCGACATCTTCT
TCAA
Found at i:45567548 original size:6 final size:6
Alignment explanation
Indices: 45567537--45567593 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
45567527 ATTGTGACGC
** * ** *
45567537 TGATGG TGATGG CAATGG TGATGC TGATGG TGATGG CAATGG TGATGC
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
*
45567585 TGAAGG TGA
1 TGATGG TGA
45567594 CGCTGACGGC
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.23, C:0.07, G:0.42, T:0.28
Consensus pattern (6 bp):
TGATGG
Found at i:45567550 original size:24 final size:24
Alignment explanation
Indices: 45567518--45567593 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 24
45567508 GGTGGTGACT
* *
45567518 GTGATGGCAATTGTGACGCTGATG
1 GTGATGGCAATGGTGATGCTGATG
45567542 GTGATGGCAATGGTGATGCTGATG
1 GTGATGGCAATGGTGATGCTGATG
*
45567566 GTGATGGCAATGGTGATGCTGAAG
1 GTGATGGCAATGGTGATGCTGATG
45567590 GTGA
1 GTGA
45567594 CGCTGACGGC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.22, C:0.09, G:0.41, T:0.28
Consensus pattern (24 bp):
GTGATGGCAATGGTGATGCTGATG
Found at i:45567670 original size:18 final size:18
Alignment explanation
Indices: 45567621--45567675 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
45567611 ATGTTGATAG
45567621 TGGTGATGGCAATGGTGA
1 TGGTGATGGCAATGGTGA
* * *
45567639 CGGTGACGGGAATGGTGA
1 TGGTGATGGCAATGGTGA
*
45567657 TGGTGATGGCAATGTTGA
1 TGGTGATGGCAATGGTGA
45567675 T
1 T
45567676 TTTTCTGCAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.22, C:0.07, G:0.44, T:0.27
Consensus pattern (18 bp):
TGGTGATGGCAATGGTGA
Found at i:45569153 original size:18 final size:16
Alignment explanation
Indices: 45569130--45569163 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
45569120 ATCATCAATG
45569130 CTACAAATAAAAGTAAAA
1 CTACAAA-AAAA-TAAAA
45569148 CTACAAAAAAATAAAA
1 CTACAAAAAAATAAAA
45569164 AGAGAGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.71, C:0.12, G:0.03, T:0.15
Consensus pattern (16 bp):
CTACAAAAAAATAAAA
Found at i:45571962 original size:19 final size:19
Alignment explanation
Indices: 45571930--45571976 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 19
45571920 TTTTAAATTT
45571930 TTTATTTATATTTTAAAAATG
1 TTTATTT-TATTTTAAAAA-G
45571951 TTT-TTTTATTTTAAAAAG
1 TTTATTTTATTTTAAAAAG
45571969 TTTATTTT
1 TTTATTTT
45571977 TAAAGAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.16
19 15 0.60
20 3 0.12
21 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTATTTTATTTTAAAAAG
Found at i:45571976 original size:21 final size:20
Alignment explanation
Indices: 45571924--45571977 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
45571914 ATTAAATTTT
*
45571924 AAATTTTTTATTTATATTTTAA
1 AAATTTATT-TTT-TATTTTAA
*
45571946 AAATGT-TTTTTTATTTTAA
1 AAATTTATTTTTTATTTTAA
45571965 AAAGTTTATTTTT
1 AAA-TTTATTTTT
45571978 AAAGAGACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 11 0.39
20 5 0.18
21 7 0.25
22 5 0.18
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
AAATTTATTTTTTATTTTAA
Found at i:45572019 original size:20 final size:20
Alignment explanation
Indices: 45571994--45572031 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
45571984 ACTAAATTCT
45571994 TTAAATTAAAAATATAAAGA
1 TTAAATTAAAAATATAAAGA
**
45572014 TTAAATTTTAAATATAAA
1 TTAAATTAAAAATATAAA
45572032 AAAAACAACA
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:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
TTAAATTAAAAATATAAAGA
Found at i:45574158 original size:22 final size:22
Alignment explanation
Indices: 45574131--45574174 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
45574121 AAATTGAAAC
*
45574131 CTTGAATTTATTCATTAAATCT
1 CTTGAAATTATTCATTAAATCT
45574153 CTTGAAATTATTCATTAAATCT
1 CTTGAAATTATTCATTAAATCT
45574175 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.48
Consensus pattern (22 bp):
CTTGAAATTATTCATTAAATCT
Found at i:45576280 original size:20 final size:19
Alignment explanation
Indices: 45576250--45576297 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
45576240 TAACTTGAGA
* * *
45576250 TAAACAAAAGTGAAAGGAC
1 TAAATAAAAGTAAAAGAAC
45576269 TAAATTAAAAGTAAAAGAAC
1 TAAA-TAAAAGTAAAAGAAC
45576289 TAAATAAAA
1 TAAATAAAA
45576298 TATAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.65, C:0.06, G:0.12, T:0.17
Consensus pattern (19 bp):
TAAATAAAAGTAAAAGAAC
Found at i:45576303 original size:20 final size:20
Alignment explanation
Indices: 45576262--45576304 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
45576252 AACAAAAGTG
* *
45576262 AAAGGACTAAATTAAAAGTA
1 AAAGAACTAAATTAAAAATA
45576282 AAAGAACTAAA-TAAAATATA
1 AAAGAACTAAATTAAAA-ATA
45576302 AAA
1 AAA
45576305 AATTGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (20 bp):
AAAGAACTAAATTAAAAATA
Found at i:45577425 original size:19 final size:20
Alignment explanation
Indices: 45577388--45577425 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
45577378 TTATTAAATA
* *
45577388 TTAAAATAATATAATATAAT
1 TTAAAATAATAAAAAATAAT
45577408 TTAAAA-AATAAAAAATAA
1 TTAAAATAATAAAAAATAA
45577426 AGAATAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAAATAATAAAAAATAAT
Found at i:45577844 original size:20 final size:20
Alignment explanation
Indices: 45577821--45577891 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 20
45577811 AAAACGTATA
45577821 AAAAATAACATCTAAACAAC
1 AAAAATAACATCTAAACAAC
* *
45577841 AAAAATAACAACCAAAACAAC
1 AAAAATAAC-ATCTAAACAAC
*
45577862 AACAAAACAACAT-TAAAAACAAC
1 -A-AAAATAACATCT--AAACAAC
45577885 AAAAATA
1 AAAAATA
45577892 GCAACAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
20 9 0.22
21 14 0.35
22 3 0.08
23 14 0.35
ACGTcount: A:0.70, C:0.20, G:0.00, T:0.10
Consensus pattern (20 bp):
AAAAATAACATCTAAACAAC
Found at i:45577852 original size:12 final size:11
Alignment explanation
Indices: 45577834--45577936 Score: 68
Period size: 12 Copynumber: 9.0 Consensus size: 11
45577824 AATAACATCT
45577834 AAACAACAAAA
1 AAACAACAAAA
*
45577845 ATAACAAC--CA
1 A-AACAACAAAA
*
45577855 AAACAACAACA
1 AAACAACAAAA
*
45577866 AAACAACATTAA
1 AAACAACA-AAA
45577878 AAACAACAAAA
1 AAACAACAAAA
*
45577889 ATAGCAACAAAA
1 A-AACAACAAAA
* *
45577901 ACAATAGCAAAA
1 A-AACAACAAAA
45577913 ACAAC-ACAAAA
1 A-AACAACAAAA
45577924 ACAACAATCAAAA
1 A-AACAA-CAAAA
45577937 TAGTAAAAAG
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
11 24 0.32
12 37 0.50
13 5 0.07
ACGTcount: A:0.71, C:0.21, G:0.02, T:0.06
Consensus pattern (11 bp):
AAACAACAAAA
Found at i:45577891 original size:44 final size:44
Alignment explanation
Indices: 45577834--45577930 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
45577824 AATAACATCT
* *
45577834 AAACAACAAAAATAACAACCAAAACAACAAC-AAAACAACATTAA
1 AAACAACAAAAATAACAACAAAAACAACAACAAAAACAACA-CAA
* * *
45577878 AAACAACAAAAATAGCAACAAAAACAATAGCAAAAACAACACAA
1 AAACAACAAAAATAACAACAAAAACAACAACAAAAACAACACAA
45577922 AAACAACAA
1 AAACAACAA
45577931 TCAAAATAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 38 0.81
45 9 0.19
ACGTcount: A:0.71, C:0.22, G:0.02, T:0.05
Consensus pattern (44 bp):
AAACAACAAAAATAACAACAAAAACAACAACAAAAACAACACAA
Found at i:45577897 original size:15 final size:16
Alignment explanation
Indices: 45577879--45577935 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
45577869 CAACATTAAA
45577879 AACAACAAA-AATAGC
1 AACAACAAACAATAGC
45577894 AACAA-AAACAATAGC
1 AACAACAAACAATAGC
* * *
45577909 AAAAACAACACAAAAAC
1 AACAACAA-ACAATAGC
45577926 AACAATCAAA
1 AACAA-CAAA
45577936 ATAGTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 3 0.09
15 15 0.44
16 2 0.06
17 11 0.32
18 3 0.09
ACGTcount: A:0.70, C:0.21, G:0.04, T:0.05
Consensus pattern (16 bp):
AACAACAAACAATAGC
Found at i:45577945 original size:32 final size:33
Alignment explanation
Indices: 45577847--45577945 Score: 89
Period size: 32 Copynumber: 3.1 Consensus size: 33
45577837 CAACAAAAAT
* * * * *
45577847 AACAACCAAAACAACAAC-AAAACAACATTAAA
1 AACAACAAAAATAGCAACAAAAACAATAGTAAA
*
45577879 AACAACAAAAATAGCAACAAAAACAATAGCAAA
1 AACAACAAAAATAGCAACAAAAACAATAGTAAA
*
45577912 AACAACACAAAA-A-CAACAATCAA-AATAGTAAA
1 AACAACA-AAAATAGCAACAA-AAACAATAGTAAA
45577944 AA
1 AA
45577946 GAAACAACAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
32 31 0.55
33 21 0.38
34 4 0.07
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.07
Consensus pattern (33 bp):
AACAACAAAAATAGCAACAAAAACAATAGTAAA
Found at i:45577945 original size:56 final size:53
Alignment explanation
Indices: 45577838--45577977 Score: 129
Period size: 56 Copynumber: 2.6 Consensus size: 53
45577828 ACATCTAAAC
* * * *
45577838 AACAAAAATAACAACCAAAACAACA-ACAAAACAACATTAAAAACAACAAAAATAGC
1 AACAAAAA-AACAGCAAAAACAACACA-AAAACAACAATAAAAACAAC-AAAA-AGA
* * * **
45577894 AACAAAAACAATAGCAAAAACAACACAAAAACAACAATCAAAATAGTAAAAAGA
1 AACAAAAA-AACAGCAAAAACAACACAAAAACAACAATAAAAACAACAAAAAGA
* *
45577948 AACAACAAAACAGTAAAAACAACACAAAAA
1 AACAAAAAAACAGCAAAAACAACACAAAAA
45577978 TAGCAACCAG
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
53 20 0.29
54 9 0.13
55 4 0.06
56 36 0.51
57 1 0.01
ACGTcount: A:0.71, C:0.19, G:0.04, T:0.06
Consensus pattern (53 bp):
AACAAAAAAACAGCAAAAACAACACAAAAACAACAATAAAAACAACAAAAAGA
Found at i:45577974 original size:22 final size:22
Alignment explanation
Indices: 45577920--45577974 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
45577910 AAAACAACAC
* *
45577920 AAAAACAACA-ATCAAAATAGT
1 AAAAACAACACAACAAAACAGT
*
45577941 AAAAAGAA-ACAACAAAACAGT
1 AAAAACAACACAACAAAACAGT
45577962 AAAAACAACACAA
1 AAAAACAACACAA
45577975 AAATAGCAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.82
22 4 0.14
ACGTcount: A:0.71, C:0.16, G:0.05, T:0.07
Consensus pattern (22 bp):
AAAAACAACACAACAAAACAGT
Found at i:45578010 original size:53 final size:53
Alignment explanation
Indices: 45577909--45578012 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 53
45577899 AAACAATAGC
* *
45577909 AAAAACAACACAAAAACAACAATCAAAATAGTAAAAAGAAACAACAAAACAGT
1 AAAAACAACACAAAAACAACAACCAAAACAGTAAAAAGAAACAACAAAACAGT
* * * * *
45577962 AAAAACAACACAAAAATAGCAACCAGAACAGTTAAAAA-CAACACCAAAACA
1 AAAAACAACACAAAAACAACAACCAAAACAG-TAAAAAGAAACAACAAAACA
45578013 ACAATATTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 37 0.86
54 6 0.14
ACGTcount: A:0.67, C:0.20, G:0.06, T:0.07
Consensus pattern (53 bp):
AAAAACAACACAAAAACAACAACCAAAACAGTAAAAAGAAACAACAAAACAGT
Found at i:45589739 original size:197 final size:195
Alignment explanation
Indices: 45589379--45589973 Score: 678
Period size: 197 Copynumber: 3.0 Consensus size: 195
45589369 AAAAATCTTG
45589379 TGTGATGATCCCTTGCTGTCAATTTGTTAGTTGACATAGTGAATTTTGT-CCTATGTTACTCGGA
1 TGTG-TGATCCCTTGCTGTCAA-TTGTTAGTTGACATAGTGAATTTT-TCCCTATGTTACTCGGA
* * *
45589443 CT-TGGGTGTGAA-TATCAAATACGGGTTCGTATTTAACACGAGTATCGTTAGACTTTCCAAAGG
63 CTCT-GGTGT-AAGTGTCAAATACGGGTT-GTATTTAACACGAGTATCGTTAAACTTTTCAAAGG
* * *
45589506 TTTTCCATGTAATATACATATGTCAAACACGAGTGCTTCAAGAAAAATGAAGAACCTGAGTAACA
125 TTTTCCATGTAATATCCATATGTCAAACATGAGTGCTTCAAGAAAAATGAAGAACCTGAGCAACA
45589571 TAGCAT
190 TAGCAT
* * * **
45589577 TGTGTGATCGCTTGCTGTCAATTGTCAGTTGACATAGTTAATTTTTCCCTTACCTTACTCGGACT
1 TGTGTGATCCCTTGCTGTCAATTGTTAGTTGACATAGTGAATTTTTCCC-TATGTTACTCGGACT
* * * *
45589642 CTTGTGTAAGTGTCAAATATGGGTATGTATTTAATGA-GAGTATCGTTAAACTTTTCAAAGCTTT
65 CTGGTGTAAGTGTCAAATACGGGT-TGTATTTAA-CACGAGTATCGTTAAACTTTTCAAAGGTTT
* * ** ** *
45589706 TCCATTTAATATCCATGTGTCCGACATGAGTGCTTCAAGAAAAATGAAGAGTCTGAGCAACATAT
128 TCCATGTAATATCCATATGTCAAACATGAGTGCTTCAAGAAAAATGAAGAACCTGAGCAACATAG
45589771 CAT
193 CAT
* * * *
45589774 TGTGTGATCCCTAGCTGTCAATTGTTTGTTGACATAGTGAATTTTGCCCTATGTTACTTGGACTC
1 TGTGTGATCCCTTGCTGTCAATTGTTAGTTGACATAGTGAATTTTTCCCTATGTTACTCGGACTC
* * * * *
45589839 GGGTGTGAGTGTCAAATACAGGTGTGCATTTGACACGAGTATCGTTAGAATTTTCATTTTTCAAA
66 TGGTGTAAGTGTCAAATACGGGT-TGTATTTAACACGAGTATCGTTA-AA----C--TTTTCAAA
* * * *
45589904 GGTTTTCCATGTAATATCCATCTGTCAAACACTG-GTGCTTCAAGAAAAATGAAGAGCCCGAACA
123 GGTTTTCCATGTAATATCCATATGTCAAACA-TGAGTGCTTCAAGAAAAATGAAGAACCTGAGCA
45589968 ACATAG
187 ACATAG
45589974 ATTTTGCCTC
Statistics
Matches: 333, Mismatches: 49, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
195 2 0.01
196 75 0.23
197 180 0.54
198 7 0.02
201 1 0.00
203 66 0.20
204 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (195 bp):
TGTGTGATCCCTTGCTGTCAATTGTTAGTTGACATAGTGAATTTTTCCCTATGTTACTCGGACTC
TGGTGTAAGTGTCAAATACGGGTTGTATTTAACACGAGTATCGTTAAACTTTTCAAAGGTTTTCC
ATGTAATATCCATATGTCAAACATGAGTGCTTCAAGAAAAATGAAGAACCTGAGCAACATAGCAT
Found at i:45609362 original size:3 final size:3
Alignment explanation
Indices: 45609354--45609433 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
45609344 AAATTTCCCT
45609354 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
45609402 TTC TTC TTC TTC TTC TTC CTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
45609434 ATTATTATTA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:45618434 original size:14 final size:15
Alignment explanation
Indices: 45618404--45618437 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
45618394 TTTTAAAGAT
45618404 ATTTTGATTAAATAA
1 ATTTTGATTAAATAA
*
45618419 ATTTTG-TTATATAA
1 ATTTTGATTAAATAA
45618433 ATTTT
1 ATTTT
45618438 AAATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (15 bp):
ATTTTGATTAAATAA
Found at i:45618826 original size:30 final size:30
Alignment explanation
Indices: 45618746--45618826 Score: 73
Period size: 30 Copynumber: 2.7 Consensus size: 30
45618736 TAGATCTTTG
45618746 TACTTTTAATAGATTT-AAAATTTAATCCTTA
1 TACTTTT--TAGATTTCAAAATTTAATCCTTA
*
45618777 TA-TTTTT--ATTTCTATAAATTTAGTCTCTT-
1 TACTTTTTAGATTTC-A-AAATTTAATC-CTTA
45618806 TACTTTTTAGATTTCAAAATT
1 TACTTTTTAGATTTCAAAATT
45618827 CAAGTCAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
26 4 0.10
28 2 0.05
29 11 0.26
30 17 0.40
31 3 0.07
32 5 0.12
ACGTcount: A:0.32, C:0.10, G:0.04, T:0.54
Consensus pattern (30 bp):
TACTTTTTAGATTTCAAAATTTAATCCTTA
Found at i:45620340 original size:30 final size:31
Alignment explanation
Indices: 45620267--45620342 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
45620257 TCTGTCCAAT
*
45620267 TTGGTA-TTCAAACTTGACACTTTTTTCTAAT
1 TTGGTACTT-AAACTTGACACTTTTTTCTAAG
* *
45620298 TTGATACCTAAACTTGACACTTTTTT-TAAG
1 TTGGTACTTAAACTTGACACTTTTTTCTAAG
45620328 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
45620343 TTTGAAATCC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 16 0.41
31 22 0.56
32 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.46
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACTTTTTTCTAAG
Found at i:45620340 original size:88 final size:89
Alignment explanation
Indices: 45620208--45620397 Score: 219
Period size: 88 Copynumber: 2.1 Consensus size: 89
45620198 TTAATATAAT
** * ***
45620208 ATTTAGTATTTAAACTTGACATTTTTCTTAATTTAGTACCTAAACTTTTT-CTGTCCAATTTGGT
1 ATTTAGTACCTAAACTTGACATTTTTCTTAAGTTAGTACCTAAACTTTTTGAAATCCAATTTGGT
45620272 A-TTCAAACTTGACACTTTTTTC-TA
66 ACTT-AAACTTGAC-CTTTTTTCTTA
* *
45620296 ATTT-GATACCTAAACTTGACACTTTTT-TTAAGTTGGTACTTAAACTTTTTGAAATCCAATTTG
1 ATTTAG-TACCTAAACTTGACA-TTTTTCTTAAGTTAGTACCTAAACTTTTTGAAATCCAATTTG
* *
45620359 GTACTTGAACTTGACTTTTTTTCTTA
64 GTACTTAAACTTGACCTTTTTTCTTA
45620385 ATTTAGTACCTAA
1 ATTTAGTACCTAA
45620398 TCTTTTTTAA
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
87 1 0.01
88 44 0.51
89 38 0.44
90 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.47
Consensus pattern (89 bp):
ATTTAGTACCTAAACTTGACATTTTTCTTAAGTTAGTACCTAAACTTTTTGAAATCCAATTTGGT
ACTTAAACTTGACCTTTTTTCTTA
Found at i:45621093 original size:13 final size:13
Alignment explanation
Indices: 45621075--45621101 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
45621065 AATGAAAATT
45621075 TCTAAATAGTAAC
1 TCTAAATAGTAAC
45621088 TCTAAATAGTAAC
1 TCTAAATAGTAAC
45621101 T
1 T
45621102 TTACCCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (13 bp):
TCTAAATAGTAAC
Found at i:45626972 original size:291 final size:291
Alignment explanation
Indices: 45626437--45627177 Score: 1257
Period size: 291 Copynumber: 2.5 Consensus size: 291
45626427 TCACAAGCTT
* * *
45626437 TGTTTAAGCTTTCTCTTTTATGTAAGTTCCTTTTTGTCTTGGGGACCCTCATTTCTTTTTTTTTT
1 TGTTAAAGCATTCTCTTTTATGTATGTTCCTTTTTGTCTTGGGGACCCTCATTTC-TTTTTTTTT
45626502 TCTTTCAATTTGGTACCTAATGACATATAAAACATCTCAGTTGCTTAAATTTTCTTCCTTTCAAG
65 TCTTTCAATTTGGTACCTAATGACATATAAAACATCTCAGTTGCTTAAATTTTCTTCCTTTCAAG
45626567 TTTCATGCAATTGCATCATACATTTTGCATTAGCAGTGAAATTTGTGGACATTTTTGTGTACTTA
130 TTTCATGCAATTGCATCATACATTTTGCATTAGCAGTGAAATTTGTGGACATTTTTGTGTACTTA
45626632 ATTGGCTATCAATATCATCATAAGCTTTTTCTTTAGGCAAAAGAGATTTTTTGTTGACAATTTTT
195 ATTGGCTATCAATATCATCATAAGCTTTTTCTTTAGGCAAAAGAGATTTTTTGTTGACAATTTTT
45626697 CCCCATTCCTTGCAAGCTTTGTCTAAGCTCAA
260 CCCCATTCCTTGCAAGCTTTGTCTAAGCTCAA
45626729 TGTTAAAGCATTCTCTTTTATGTATGTTCCTTTTTGTCTTGGGGACCCTCATTTCTTTTTTTTTT
1 TGTTAAAGCATTCTCTTTTATGTATGTTCCTTTTTGTCTTGGGGACCCTCATTTCTTTTTTTTTT
45626794 CTTTCAATTTGGTACCTAATGACATATAAAACATCTCAGTTGCTTAAATTTTCTTCCTTTCAAGT
66 CTTTCAATTTGGTACCTAATGACATATAAAACATCTCAGTTGCTTAAATTTTCTTCCTTTCAAGT
45626859 TTCATGCAATTGCATCATACATTTTGCATTAGCAGTGAAATTTGTGGACATTTTTGTGTACTTAA
131 TTCATGCAATTGCATCATACATTTTGCATTAGCAGTGAAATTTGTGGACATTTTTGTGTACTTAA
45626924 TTGGCTATCAATATCATCATAAGCTTTTTCTTTAGGCAAAAGAGATTTTTTGTTGACAATTTTTC
196 TTGGCTATCAATATCATCATAAGCTTTTTCTTTAGGCAAAAGAGATTTTTTGTTGACAATTTTTC
45626989 CCCATTCCTTGCAAGCTTTGTCTAAGCTCAA
261 CCCATTCCTTGCAAGCTTTGTCTAAGCTCAA
45627020 TGTTAAAGCATTCTCTTTTATGTATGTTCCTTTTTGTCTTGGGGACCCTCATTTAAAGATTGCTA
1 TGTTAAAGCATTCTCTTTTATGTATGTTCCTTTTTGTCTTGGGGACCCTCA--T-----TT-CT-
* * ** *
45627085 ATGATGGCTTATTTTTATTTCAATTTGGTACCTAATGGCATATAAAGTACCTCAGTTGCTTAAAT
57 -T--T---TT-TTTTTCTTTCAATTTGGTACCTAATGACATATAAAACATCTCAGTTGCTTAAAT
45627150 TTTCTTCCTTTCAAGTTTCATGCAATTG
115 TTTCTTCCTTTCAAGTTTCATGCAATTG
45627178 TGAAGTTTGC
Statistics
Matches: 425, Mismatches: 8, Indels: 17
0.94 0.02 0.04
Matches are distributed among these distances:
291 287 0.68
292 52 0.12
293 1 0.00
298 2 0.00
299 2 0.00
301 1 0.00
303 1 0.00
306 2 0.00
307 77 0.18
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.45
Consensus pattern (291 bp):
TGTTAAAGCATTCTCTTTTATGTATGTTCCTTTTTGTCTTGGGGACCCTCATTTCTTTTTTTTTT
CTTTCAATTTGGTACCTAATGACATATAAAACATCTCAGTTGCTTAAATTTTCTTCCTTTCAAGT
TTCATGCAATTGCATCATACATTTTGCATTAGCAGTGAAATTTGTGGACATTTTTGTGTACTTAA
TTGGCTATCAATATCATCATAAGCTTTTTCTTTAGGCAAAAGAGATTTTTTGTTGACAATTTTTC
CCCATTCCTTGCAAGCTTTGTCTAAGCTCAA
Found at i:45641661 original size:28 final size:28
Alignment explanation
Indices: 45641591--45641673 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 28
45641581 TCCGCCAATA
* *
45641591 TTATTTTTAATTT-TTTAA-AATTATAT
1 TTATTTTTTATTTATTTAATAATTTTAT
* *
45641617 TATGTTATTTTA-ATATTTAATAATTTTAT
1 T-TATT-TTTTATTTATTTAATAATTTTAT
* *
45641646 TTATTTTTTATTTATTGAATATTTTTAT
1 TTATTTTTTATTTATTTAATAATTTTAT
45641674 ATAGTATCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
26 1 0.02
27 9 0.20
28 26 0.59
29 8 0.18
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.66
Consensus pattern (28 bp):
TTATTTTTTATTTATTTAATAATTTTAT
Found at i:45651118 original size:108 final size:108
Alignment explanation
Indices: 45650978--45651211 Score: 387
Period size: 108 Copynumber: 2.2 Consensus size: 108
45650968 GAATTCAGAT
* *
45650978 TTCTAGAAAGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGTGATCAACTTCCTAGAGCGG
1 TTCTAGAAAGGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGGGATCAACTTCCTAGAGCGG
*
45651043 AATTAATGTCCACTCCTGATAAGGTCATTACTGCAAACCAAAC
66 AATTAATGTCCAATCCTGATAAGGTCATTACTGCAAACCAAAC
* *
45651086 TTCTAGAAGGGAATCAACTCCCACTTCCGGTGGGCTCGTTACTGGGGATCAACTTCCTAGAGCGG
1 TTCTAGAAAGGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGGGATCAACTTCCTAGAGCGG
*
45651151 AATTAATGTCCAATCCTGATAAGGTCATTACTGGAAACCAAAC
66 AATTAATGTCCAATCCTGATAAGGTCATTACTGCAAACCAAAC
***
45651194 TAAGAGAAAGGAATCAAC
1 TTCTAGAAAGGAATCAAC
45651212 CATAACCCCT
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 116 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (108 bp):
TTCTAGAAAGGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGGGATCAACTTCCTAGAGCGG
AATTAATGTCCAATCCTGATAAGGTCATTACTGCAAACCAAAC
Found at i:45651153 original size:54 final size:54
Alignment explanation
Indices: 45650987--45651153 Score: 155
Period size: 54 Copynumber: 3.1 Consensus size: 54
45650977 TTTCTAGAAA
* *
45650987 GGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGTGATCAACTTCCTAGAGC
1 GGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGAGATCAACTTCCTAGAGC
* * * * * * *
45651041 GGAATTAA-TGTCCAC-TCCTGATAAGG-TCATTACTGCAAACCAAACTT-CTAGAAG-
1 GGAATCAACT-CCCACTTCC-GGT-GGGCTCATTACTGGAGATC-AACTTCCTAG-AGC
* *
45651095 GGAATCAACTCCCACTTCCGGTGGGCTCGTTACTGGGGATCAACTTCCTAGAGC
1 GGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGAGATCAACTTCCTAGAGC
45651149 GGAAT
1 GGAAT
45651154 TAATGTCCAA
Statistics
Matches: 85, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
53 12 0.14
54 60 0.71
55 13 0.15
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (54 bp):
GGAATCAACTCCCACTTCCGGTGGGCTCATTACTGGAGATCAACTTCCTAGAGC
Found at i:45651182 original size:54 final size:54
Alignment explanation
Indices: 45651013--45651185 Score: 158
Period size: 54 Copynumber: 3.2 Consensus size: 54
45651003 TCTGGTGGGC
* *
45651013 TCATTACTGGTGATCAACTTCCTAGAGCGGAATTAATGTCCACTCCTGATAAGG
1 TCATTACTGGAGATCAACTTCCTAGAGCGGAATTAATGTCCAATCCTGATAAGG
* * * * * * * *
45651067 TCATTACTGCAAACCAAACTT-CTAGAAG-GGAATCAACT-CCCACTTCC-GGT-GGG
1 TCATTACTGGAGATC-AACTTCCTAG-AGCGGAATTAA-TGTCCA-ATCCTGATAAGG
* *
45651120 CTCGTTACTGGGGATCAACTTCCTAGAGCGGAATTAATGTCCAATCCTGATAAGG
1 -TCATTACTGGAGATCAACTTCCTAGAGCGGAATTAATGTCCAATCCTGATAAGG
45651175 TCATTACTGGA
1 TCATTACTGGA
45651186 AACCAAACTA
Statistics
Matches: 88, Mismatches: 21, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
53 13 0.15
54 62 0.70
55 13 0.15
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (54 bp):
TCATTACTGGAGATCAACTTCCTAGAGCGGAATTAATGTCCAATCCTGATAAGG
Found at i:45651236 original size:108 final size:108
Alignment explanation
Indices: 45650982--45651238 Score: 311
Period size: 108 Copynumber: 2.4 Consensus size: 108
45650972 TCAGATTTCT
* * * * * *
45650982 AGAAAGGAATCAACTCCCACTTCTGGTGGGCTCATTACTGGTGATCAACTTCCTAGAGCGGAATT
1 AGAAAGGAATCAACTCCAACTCCCGGAGGGATCATTACTGGGGATCAACTTCCTAGAGCGGAATT
* ***
45651047 AATGTCCACTCCTGATAAGGTCATTACTGCAAACCAAACTTCT
66 AATGTCCAATCCTGATAAGGTCATTACTGCAAACCAAACTAAG
* * * * * *
45651090 AGAAGGGAATCAACTCCCACTTCCGGTGGGCTCGTTACTGGGGATCAACTTCCTAGAGCGGAATT
1 AGAAAGGAATCAACTCCAACTCCCGGAGGGATCATTACTGGGGATCAACTTCCTAGAGCGGAATT
*
45651155 AATGTCCAATCCTGATAAGGTCATTACTGGAAACCAAACTAAG
66 AATGTCCAATCCTGATAAGGTCATTACTGCAAACCAAACTAAG
* *
45651198 AGAAAGGAATCAAC-CATAAC-CCCTGAGAGGATCATTACTGG
1 AGAAAGGAATCAACTC-CAACTCCCGGAG-GGATCATTACTGG
45651239 AAACCGAATT
Statistics
Matches: 130, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
107 5 0.04
108 125 0.96
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (108 bp):
AGAAAGGAATCAACTCCAACTCCCGGAGGGATCATTACTGGGGATCAACTTCCTAGAGCGGAATT
AATGTCCAATCCTGATAAGGTCATTACTGCAAACCAAACTAAG
Found at i:45657489 original size:155 final size:155
Alignment explanation
Indices: 45657207--45657494 Score: 441
Period size: 155 Copynumber: 1.9 Consensus size: 155
45657197 ACGTATGGTC
*
45657207 TTTATTAGTATTCCGACAAATCTTGACATCGCTGTGAATGATGTTTCACAACTTCAATTATTGTT
1 TTTATTAGTATTCCGACAAATCTTGACATCGCTGTGAATGATGTTTCACAACTTCAATGATTGTT
* * *
45657272 GGATGTATAAGCCTGTCCTAATGTTTGATAAGAACGACCTGAAGTTCGAATCCTGCAAAGGGTTT
66 AGATGTATAAGCCTGTCCTAACGTTTGATAAGAACGACCTGAAGTTCGAATCCCGCAAAGGGTTT
45657337 GCCGTTGTGGTGTTTCTGTACAGAG
131 GCCGTTGTGGTGTTTCTGTACAGAG
* ** * ** *
45657362 TTTATTAGTATTCCGACAATTCTTGATGTTGCTGTGAATGATGTTTCATGATTTCAATGATTGTT
1 TTTATTAGTATTCCGACAAATCTTGACATCGCTGTGAATGATGTTTCACAACTTCAATGATTGTT
** * *
45657427 AGATGTATAAGTTTGTCCTAACGTTTGATAAGAACGATCTGATGTTCGAATCCCGCAAAGGGTTT
66 AGATGTATAAGCCTGTCCTAACGTTTGATAAGAACGACCTGAAGTTCGAATCCCGCAAAGGGTTT
45657492 GCC
131 GCC
45657495 TTTTGCACTA
Statistics
Matches: 118, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
155 118 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.37
Consensus pattern (155 bp):
TTTATTAGTATTCCGACAAATCTTGACATCGCTGTGAATGATGTTTCACAACTTCAATGATTGTT
AGATGTATAAGCCTGTCCTAACGTTTGATAAGAACGACCTGAAGTTCGAATCCCGCAAAGGGTTT
GCCGTTGTGGTGTTTCTGTACAGAG
Found at i:45678888 original size:18 final size:18
Alignment explanation
Indices: 45678849--45678890 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45678839 TTCATGCTCC
*
45678849 GGTTCTGGTTCGGCTTCC
1 GGTTCTGGTTCGGCTTCA
* *
45678867 GGTTCTGGTTCTGTTTCA
1 GGTTCTGGTTCGGCTTCA
45678885 GGTTCT
1 GGTTCT
45678891 TGTATTAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.21, G:0.31, T:0.45
Consensus pattern (18 bp):
GGTTCTGGTTCGGCTTCA
Found at i:45687416 original size:18 final size:18
Alignment explanation
Indices: 45687393--45687428 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45687383 GCGGTAGAGG
45687393 AAGAAGAAGAAAGAAAGA
1 AAGAAGAAGAAAGAAAGA
* *
45687411 AAGAAGAGGAGAGAAAGA
1 AAGAAGAAGAAAGAAAGA
45687429 TCAATGGCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AAGAAGAAGAAAGAAAGA
Found at i:45688065 original size:23 final size:23
Alignment explanation
Indices: 45688039--45688082 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
45688029 TTTATTTCTT
45688039 TTAAAAAATAATAAAATTATAAA
1 TTAAAAAATAATAAAATTATAAA
* *
45688062 TTAATAAATGATAAAATTATA
1 TTAAAAAATAATAAAATTATA
45688083 TTTTGACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
TTAAAAAATAATAAAATTATAAA
Found at i:45703605 original size:22 final size:22
Alignment explanation
Indices: 45703562--45703605 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
45703552 TTAATAAAAA
*
45703562 AAATTATATTGGTGCTTTTTTT
1 AAATTATATTGGTGCTTATTTT
*
45703584 AAATTATTTTGGTTG-TTATTTT
1 AAATTATATTGG-TGCTTATTTT
45703606 TTGCTGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.61
Consensus pattern (22 bp):
AAATTATATTGGTGCTTATTTT
Found at i:45703623 original size:21 final size:22
Alignment explanation
Indices: 45703590--45703637 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
45703580 TTTTAAATTA
45703590 TTTTGGTTGTTATTTTTTGCTG
1 TTTTGGTTGTTATTTTTTGCTG
45703612 TTTTGG-TGTTATTTTTTGCTG
1 TTTTGGTTGTTATTTTTTGCTG
45703633 TTTTG
1 TTTTG
45703638 ATTGCTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.04, C:0.04, G:0.23, T:0.69
Consensus pattern (22 bp):
TTTTGGTTGTTATTTTTTGCTG
Found at i:45703642 original size:12 final size:12
Alignment explanation
Indices: 45703627--45703651 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45703617 GTGTTATTTT
45703627 TTGCTGTTTTGA
1 TTGCTGTTTTGA
45703639 TTGCTGTTTTGA
1 TTGCTGTTTTGA
45703651 T
1 T
45703652 ATTTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.24, T:0.60
Consensus pattern (12 bp):
TTGCTGTTTTGA
Found at i:45703643 original size:33 final size:32
Alignment explanation
Indices: 45703606--45703671 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
45703596 TTGTTATTTT
* * *
45703606 TTGCTGTTTTGGTGTTATTTTTTGCTGTTTTGA
1 TTGCTGTTTTGATATT-TTTTTTACTGTTTTGA
45703639 TTGCTGTTTTGATATTTTTTTTACTGTTTTGA
1 TTGCTGTTTTGATATTTTTTTTACTGTTTTGA
45703671 T
1 T
45703672 ATTGCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.09, C:0.06, G:0.20, T:0.65
Consensus pattern (32 bp):
TTGCTGTTTTGATATTTTTTTTACTGTTTTGA
Found at i:45703656 original size:20 final size:20
Alignment explanation
Indices: 45703633--45703674 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
45703623 TTTTTTGCTG
*
45703633 TTTTGATTGCTGTTTTGATA
1 TTTTGATTACTGTTTTGATA
**
45703653 TTTTTTTTACTGTTTTGATA
1 TTTTGATTACTGTTTTGATA
45703673 TT
1 TT
45703675 GCTATTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.67
Consensus pattern (20 bp):
TTTTGATTACTGTTTTGATA
Found at i:45703747 original size:12 final size:12
Alignment explanation
Indices: 45703732--45703756 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45703722 TTTTTGCTGC
45703732 TATTTTGATTGT
1 TATTTTGATTGT
45703744 TATTTTGATTGT
1 TATTTTGATTGT
45703756 T
1 T
45703757 TGGATGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TATTTTGATTGT
Found at i:45713086 original size:30 final size:31
Alignment explanation
Indices: 45713052--45713110 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
45713042 AACCTGGTGA
*
45713052 CTTAAATAAAAATTTT-GAATAGTTCAATGG
1 CTTAAATAAAAATTTTCGAATAATTCAATGG
* *
45713082 CTTAATTGAAAATTTTCGAATAATTCAAT
1 CTTAAATAAAAATTTTCGAATAATTCAAT
45713111 AACCAAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.39
Consensus pattern (31 bp):
CTTAAATAAAAATTTTCGAATAATTCAATGG
Found at i:45720041 original size:16 final size:16
Alignment explanation
Indices: 45720020--45720056 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
45720010 AACAAATTAT
**
45720020 TTGAATTGACTTAAAC
1 TTGAATTGACCAAAAC
45720036 TTGAATTGACCAAAAC
1 TTGAATTGACCAAAAC
45720052 TTGAA
1 TTGAA
45720057 AAATCAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (16 bp):
TTGAATTGACCAAAAC
Found at i:45723981 original size:17 final size:19
Alignment explanation
Indices: 45723955--45724004 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 19
45723945 TACTAATCCA
*
45723955 AAAAAAAAAATA-GAACT-
1 AAAAACAAAATATGAACTG
45723972 AAAAACAAAATATGAACTG
1 AAAAACAAAATATGAACTG
45723991 ATACAAACAAAATA
1 A-A-AAACAAAATA
45724005 AGAGTGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 11 0.39
18 5 0.18
19 1 0.04
20 1 0.04
21 10 0.36
ACGTcount: A:0.70, C:0.10, G:0.06, T:0.14
Consensus pattern (19 bp):
AAAAACAAAATATGAACTG
Found at i:45728333 original size:25 final size:24
Alignment explanation
Indices: 45728297--45728343 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
45728287 TTGTCAATTT
*
45728297 TTTTTAAAAAAATTGAATTTGAAC
1 TTTTCAAAAAAATTGAATTTGAAC
45728321 TTTTCAAACAAAATTGAATTTGA
1 TTTTCAAA-AAAATTGAATTTGA
45728344 CGATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (24 bp):
TTTTCAAAAAAATTGAATTTGAAC
Found at i:45734392 original size:6 final size:6
Alignment explanation
Indices: 45734378--45734412 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
45734368 AAGTCAATAG
*
45734378 GATGGA GATGAA GATGAA GATGAA GATGAA GATGA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATGA
45734413 TTTAAAGGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.37, T:0.17
Consensus pattern (6 bp):
GATGAA
Found at i:45744816 original size:18 final size:17
Alignment explanation
Indices: 45744762--45744816 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
45744752 AAATAATATT
* *
45744762 TAAAAATTATTTATTTAA
1 TAAAAATTA-TAAATTAA
45744780 TAAAAA-T-TAAATT-A
1 TAAAAATTATAAATTAA
45744794 TAAAAATTATAAAATTAA
1 TAAAAATTAT-AAATTAA
45744812 TAAAA
1 TAAAA
45744817 TATATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 7 0.23
15 5 0.16
16 1 0.03
17 6 0.19
18 12 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATTATAAATTAA
Found at i:45752222 original size:3 final size:3
Alignment explanation
Indices: 45752216--45752253 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
45752206 ATAATAATAA
45752216 TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45752254 GAAGATGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:45752708 original size:8 final size:9
Alignment explanation
Indices: 45752670--45752705 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
45752660 AAAATAAAAA
45752670 AAAATTATTT
1 AAAATT-TTT
*
45752680 AAATTTTTT
1 AAAATTTTT
45752689 AAAATTTTT
1 AAAATTTTT
45752698 AAAATTTT
1 AAAATTTT
45752706 AAATGAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 19 0.79
10 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AAAATTTTT
Found at i:45765869 original size:3 final size:3
Alignment explanation
Indices: 45765861--45765886 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45765851 AAGTACACCG
45765861 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
45765887 ATAAAAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45768587 original size:6 final size:6
Alignment explanation
Indices: 45768578--45768608 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
45768568 TTGGATTGGA
*
45768578 TCGAGA TCGAGT TCGAGT TCGAGT TCGAGT T
1 TCGAGT TCGAGT TCGAGT TCGAGT TCGAGT T
45768609 TGGTTTGGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.32
Consensus pattern (6 bp):
TCGAGT
Found at i:45774183 original size:19 final size:20
Alignment explanation
Indices: 45774137--45774177 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
45774127 TTCCTCCACC
45774137 AAAATTTAAATATATATTTAT
1 AAAA-TTAAATATATATTTAT
45774158 AAAATTAAA-ATATATGTTAT
1 AAAATTAAATATATAT-TTAT
45774178 CAATTATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 9 0.47
21 4 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AAAATTAAATATATATTTAT
Found at i:45775523 original size:28 final size:25
Alignment explanation
Indices: 45775492--45775557 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 25
45775482 AATTTTTGAG
45775492 AATTTTAATTAAATCTCTCTTTTTTTAA
1 AATTTTAATTAAAT-TC-CTTTTTTT-A
* *
45775520 AATTCTCATTAAATTCCTTTTTTTA
1 AATTTTAATTAAATTCCTTTTTTTA
*
45775545 AATATTAATTAAA
1 AATTTTAATTAAA
45775558 CCCATGGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
25 11 0.33
26 8 0.24
27 2 0.06
28 12 0.36
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (25 bp):
AATTTTAATTAAATTCCTTTTTTTA
Found at i:45775555 original size:25 final size:27
Alignment explanation
Indices: 45775495--45775557 Score: 78
Period size: 25 Copynumber: 2.4 Consensus size: 27
45775485 TTTTGAGAAT
45775495 TTTAATTAAATCTCTCTTTTTTTAAAA
1 TTTAATTAAATCTCTCTTTTTTTAAAA
*
45775522 TTCTCATTAAAT-TC-CTTTTTTT-AAA
1 TT-TAATTAAATCTCTCTTTTTTTAAAA
45775547 TATTAATTAAA
1 T-TTAATTAAA
45775558 CCCATGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 11 0.34
26 9 0.28
27 4 0.12
28 8 0.25
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTAATTAAATCTCTCTTTTTTTAAAA
Found at i:45779484 original size:17 final size:17
Alignment explanation
Indices: 45779449--45779483 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
45779439 TATCTTAAAC
45779449 AAGAAAAAGACAATGAA
1 AAGAAAAAGACAATGAA
45779466 AAGAAAAAGACAA-GAA
1 AAGAAAAAGACAATGAA
45779482 AA
1 AA
45779484 AAATTAGCAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.74, C:0.06, G:0.17, T:0.03
Consensus pattern (17 bp):
AAGAAAAAGACAATGAA
Found at i:45787190 original size:96 final size:97
Alignment explanation
Indices: 45787029--45787214 Score: 286
Period size: 96 Copynumber: 1.9 Consensus size: 97
45787019 TCATAAAAAT
* * * *
45787029 ATTAATTTAGGCAACTTTGTTAAATATGATTGATTGGATTTAGTATTATTTTTAGTAAAC-ATTT
1 ATTAATTCAAGCAACTTTATTAAATATGATTGATTGGATTTAGTATTATTTATAGTAAACTATTT
45787093 TTTTCTTAAATGATTTATTGAATAAACAATAA
66 TTTTCTTAAATGATTTATTGAATAAACAATAA
* * *
45787125 ATTAATTCAAGCAATTTTATTAAATATGATTGATTGGATTTAGTATT-TTTATAGTAAATGTTTT
1 ATTAATTCAAGCAACTTTATTAAATATGATTGATTGGATTTAGTATTATTTATAGTAAA-CTATT
45787189 TTTTTCTTAAATGATTTATTGAATAA
65 TTTTTCTTAAATGATTTATTGAATAA
45787215 CAAAGAAGCT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
95 10 0.12
96 43 0.53
97 28 0.35
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.49
Consensus pattern (97 bp):
ATTAATTCAAGCAACTTTATTAAATATGATTGATTGGATTTAGTATTATTTATAGTAAACTATTT
TTTTCTTAAATGATTTATTGAATAAACAATAA
Found at i:45804842 original size:15 final size:15
Alignment explanation
Indices: 45804824--45804858 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
45804814 AAAAATAATG
45804824 ATTTTCAAAACATCC
1 ATTTTCAAAACATCC
* *
45804839 ATTTTCAAAATATTC
1 ATTTTCAAAACATCC
45804854 ATTTT
1 ATTTT
45804859 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTTTCAAAACATCC
Found at i:45807119 original size:17 final size:17
Alignment explanation
Indices: 45807099--45807132 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
45807089 AAAAAAATTT
*
45807099 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
45807116 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
45807133 TTATTGTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:45809713 original size:27 final size:27
Alignment explanation
Indices: 45809663--45809718 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
45809653 CGATACCACC
* * *
45809663 ACAGTTCTCTATTCCTTTCAGCCCGTT
1 ACAGTACTCTATTCCTCTCAGCCCATT
45809690 ACAGTACTCTATTCCTCCTC-GCCCATT
1 ACAGTACTCTATTCCT-CTCAGCCCATT
45809717 AC
1 AC
45809719 CGCTGCAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.18, C:0.38, G:0.09, T:0.36
Consensus pattern (27 bp):
ACAGTACTCTATTCCTCTCAGCCCATT
Found at i:45809904 original size:6 final size:6
Alignment explanation
Indices: 45809893--45809939 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
45809883 TAGAATTAAA
*
45809893 TATGTT TATGTT TATGTT TATGTT TATGTT CT-TATT TATGTT TATGT
1 TATGTT TATGTT TATGTT TATGTT TATGTT -TATGTT TATGTT TATGT
45809940 ATATAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.17, C:0.02, G:0.15, T:0.66
Consensus pattern (6 bp):
TATGTT
Found at i:45810068 original size:26 final size:26
Alignment explanation
Indices: 45810013--45810088 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
45810003 GCTAAACCTC
**
45810013 ATTAAATAAATTCAAACATAAAAATT
1 ATTAAATAAATTCAAACATAAAAAGA
** *
45810039 ATTAAATAAATTCAAATTTAAACAGA
1 ATTAAATAAATTCAAACATAAAAAGA
* *
45810065 ATTAATTCCAAATTCAATCATAAA
1 ATTAAAT--AAATTCAAACATAAA
45810089 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
26 27 0.69
28 12 0.31
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.32
Consensus pattern (26 bp):
ATTAAATAAATTCAAACATAAAAAGA
Found at i:45812912 original size:27 final size:27
Alignment explanation
Indices: 45812857--45812911 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
45812847 ATTTTCTGCT
* * *
45812857 AACTTTCTGTTTCCTTTTCTTGTTCAA
1 AACTTTCTGCTTCCTTTCCTTCTTCAA
45812884 AACTTT-TGCTTCCTTTCCTTCTTCAA
1 AACTTTCTGCTTCCTTTCCTTCTTCAA
45812910 AA
1 AA
45812912 AATTGCTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.18, C:0.25, G:0.05, T:0.51
Consensus pattern (27 bp):
AACTTTCTGCTTCCTTTCCTTCTTCAA
Found at i:45824466 original size:24 final size:23
Alignment explanation
Indices: 45824439--45824484 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
45824429 AAAATATTTA
* *
45824439 TAAATATTAAATAATAAGATTAAT
1 TAAATATCAAAT-ATAAAATTAAT
*
45824463 TAAATCTCAAATATAAAATTAA
1 TAAATATCAAATATAAAATTAA
45824485 ACTTTGGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAATATCAAATATAAAATTAAT
Found at i:45837831 original size:50 final size:50
Alignment explanation
Indices: 45837777--45837931 Score: 118
Period size: 50 Copynumber: 3.1 Consensus size: 50
45837767 ATAAAAGGTC
45837777 TAAATCTAGTTTTAGTCCCTCTACTAAGCTAAAATTCGAAATTGAATCTT
1 TAAATCTAGTTTTAGTCCCTCTACTAAGCTAAAATTCGAAATTGAATCTT
* ** * *** * ** * ** ** *
45837827 TAAATCT-G--TTAATGGCTGCCTAGTTTTCAAAATATTATATATAAAAGGTC
1 TAAATCTAGTTTTAGTCCCT--CTACTAAGCTAAA-ATTCGAAATTGAATCTT
45837877 TAAATCTAGTTTTAGTCCCTCTACTAAGCTAAAATTCGAAATTGAATCTT
1 TAAATCTAGTTTTAGTCCCTCTACTAAGCTAAAATTCGAAATTGAATCTT
45837927 TAAAT
1 TAAAT
45837932 TAATTTGGCA
Statistics
Matches: 67, Mismatches: 32, Indels: 12
0.60 0.29 0.11
Matches are distributed among these distances:
47 6 0.09
49 9 0.13
50 37 0.55
51 9 0.13
53 6 0.09
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (50 bp):
TAAATCTAGTTTTAGTCCCTCTACTAAGCTAAAATTCGAAATTGAATCTT
Found at i:45837902 original size:100 final size:100
Alignment explanation
Indices: 45837729--45837931 Score: 406
Period size: 100 Copynumber: 2.0 Consensus size: 100
45837719 TTCTTGAAGG
45837729 AATCTGTTAATGGCTGCCTAGTTTTCAAAATATTATATATAAAAGGTCTAAATCTAGTTTTAGTC
1 AATCTGTTAATGGCTGCCTAGTTTTCAAAATATTATATATAAAAGGTCTAAATCTAGTTTTAGTC
45837794 CCTCTACTAAGCTAAAATTCGAAATTGAATCTTTA
66 CCTCTACTAAGCTAAAATTCGAAATTGAATCTTTA
45837829 AATCTGTTAATGGCTGCCTAGTTTTCAAAATATTATATATAAAAGGTCTAAATCTAGTTTTAGTC
1 AATCTGTTAATGGCTGCCTAGTTTTCAAAATATTATATATAAAAGGTCTAAATCTAGTTTTAGTC
45837894 CCTCTACTAAGCTAAAATTCGAAATTGAATCTTTA
66 CCTCTACTAAGCTAAAATTCGAAATTGAATCTTTA
45837929 AAT
1 AAT
45837932 TAATTTGGCA
Statistics
Matches: 103, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 103 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (100 bp):
AATCTGTTAATGGCTGCCTAGTTTTCAAAATATTATATATAAAAGGTCTAAATCTAGTTTTAGTC
CCTCTACTAAGCTAAAATTCGAAATTGAATCTTTA
Found at i:45839857 original size:28 final size:28
Alignment explanation
Indices: 45839780--45839863 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 28
45839770 TAAACTTGGC
*
45839780 TTTGAATTT--TTTTTATTCAAATTAAAAT
1 TTTGAATTTAATTTTT-TTCACATT-AAAT
*
45839808 TTTGAACTTGATAATTATTTTCACATTAAAT
1 TTTGAA-TT--TAATTTTTTTCACATTAAAT
45839839 TTTGAATTTAATTTTTTTCACATTA
1 TTTGAATTTAATTTTTTTCACATTA
45839864 GGACTTAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
28 22 0.46
29 2 0.04
30 2 0.04
31 11 0.23
32 7 0.15
33 4 0.08
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (28 bp):
TTTGAATTTAATTTTTTTCACATTAAAT
Found at i:45843417 original size:15 final size:15
Alignment explanation
Indices: 45843397--45843427 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
45843387 AAACTTTACT
45843397 AAATAATATCCATAA
1 AAATAATATCCATAA
*
45843412 AAATAATATTCATAA
1 AAATAATATCCATAA
45843427 A
1 A
45843428 TCATAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAATATCCATAA
Found at i:45843679 original size:25 final size:26
Alignment explanation
Indices: 45843649--45843703 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
45843639 AATTGTATTT
*
45843649 AATTTTTTT-ATTTAAAAATTGAGTA
1 AATTTTTTTAATATAAAAATTGAGTA
*
45843674 AATTTTTTTAATATCAAAATTGAGTA
1 AATTTTTTTAATATAAAAATTGAGTA
45843700 AATT
1 AATT
45843704 AATCTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (26 bp):
AATTTTTTTAATATAAAAATTGAGTA
Found at i:45844186 original size:2 final size:2
Alignment explanation
Indices: 45844179--45844222 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
45844169 ATAAATAGGG
*
45844179 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45844221 AT
1 AT
45844223 GTATTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45846500 original size:119 final size:119
Alignment explanation
Indices: 45846289--45846518 Score: 352
Period size: 119 Copynumber: 1.9 Consensus size: 119
45846279 TCTTATAGTG
* * * * * *
45846289 TTAGTTGCTTGTAATTACTCTAGATATGTCGTATTTGAGTTGTGATAAAATCAATTATCAACATG
1 TTAGTTACTTATAATCACTCTAGATATGTCGTACTTGAGTTGTAACAAAATCAATTATCAACATG
* *
45846354 CTGTAATATTCTATTAATGTTGAGATTGAAGCCTTTATCGCGTCGATGGACGTA
66 CTGTAATATTCTATTAATGCTGAGATTGAAACCTTTATCGCGTCGATGGACGTA
* * * *
45846408 TTAGTTACTTATAATCACTTTAGATATGTCGTGCTTGATTTGTAACAAAATCAATTGTCAACATG
1 TTAGTTACTTATAATCACTCTAGATATGTCGTACTTGAGTTGTAACAAAATCAATTATCAACATG
45846473 CTGTAATATTCTATTAATGCTGAGATTGAAACCTTTATCGCGTCGA
66 CTGTAATATTCTATTAATGCTGAGATTGAAACCTTTATCGCGTCGA
45846519 CGAAGTTTAT
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
119 99 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (119 bp):
TTAGTTACTTATAATCACTCTAGATATGTCGTACTTGAGTTGTAACAAAATCAATTATCAACATG
CTGTAATATTCTATTAATGCTGAGATTGAAACCTTTATCGCGTCGATGGACGTA
Found at i:45872475 original size:1 final size:1
Alignment explanation
Indices: 45872469--45872503 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
45872459 TATAATAACC
45872469 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
45872504 CTTTGTAGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:45882684 original size:7 final size:7
Alignment explanation
Indices: 45882672--45882705 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
45882662 AAGGGTCTTC
45882672 TTTTCTA
1 TTTTCTA
45882679 TTTTCTA
1 TTTTCTA
45882686 TTTTCTA
1 TTTTCTA
45882693 TTTTCTA
1 TTTTCTA
45882700 TTTTCT
1 TTTTCT
45882706 TAGTCAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCTA
Found at i:45893687 original size:21 final size:20
Alignment explanation
Indices: 45893663--45893701 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
45893653 TTTTAAAAAT
45893663 TTAAATTAAATTTTATTTTTA
1 TTAAATTAAATTTT-TTTTTA
*
45893684 TTAATTTAAATTTTTTTT
1 TTAAATTAAATTTTTTTT
45893702 ATTTTAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTAAATTAAATTTTTTTTTA
Found at i:45907379 original size:31 final size:33
Alignment explanation
Indices: 45907321--45907394 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
45907311 TTTTTTTAAA
45907321 TATGTATAATTGAATCAAAATAAAAGTTTCGTG
1 TATGTATAATTGAATCAAAATAAAAGTTTCGTG
* ** *
45907354 TATGTAT-A-TGAATCACAATTCAAGTTTCATG
1 TATGTATAATTGAATCAAAATAAAAGTTTCGTG
45907385 --TGTATAATTG
1 TATGTATAATTG
45907395 CACCAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 5 0.14
30 1 0.03
31 21 0.60
32 1 0.03
33 7 0.20
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (33 bp):
TATGTATAATTGAATCAAAATAAAAGTTTCGTG
Found at i:45911887 original size:2 final size:2
Alignment explanation
Indices: 45911880--45911905 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45911870 CTGCAGTTGC
45911880 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
45911906 CACCTTTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45920429 original size:5 final size:5
Alignment explanation
Indices: 45920419--45920448 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
45920409 AGGTTTGTAA
45920419 GGATT GGATT GGATT GGATT GGATT GGATT
1 GGATT GGATT GGATT GGATT GGATT GGATT
45920449 AGTAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
GGATT
Found at i:45920736 original size:105 final size:105
Alignment explanation
Indices: 45920549--45920760 Score: 316
Period size: 105 Copynumber: 2.0 Consensus size: 105
45920539 TTTTGATTAT
* * * * *
45920549 CATAATCGATTTGGAGATTGGATTATCGGGTTCAATCATATTTTAGGTGTTTGCTCAGTCTTTGA
1 CATAATCGATTTGGAGAGTGGATTATCGAGTTAAATCATAATTTAGGTGTTTGCTCAGTCATTGA
* *
45920614 TCTTGAATTTTGGAGTATCTAGAATAGTTTACTCTTGTTA
66 TCTTGAACTTTGGAGTATCTAGAATAGCTTACTCTTGTTA
* * * *
45920654 CATAGTCGATTTGGAGAGTGGATTGTCGAGTTAAATTATAATTTAGGTGTTTGTTCAGTCATTGA
1 CATAATCGATTTGGAGAGTGGATTATCGAGTTAAATCATAATTTAGGTGTTTGCTCAGTCATTGA
*
45920719 TCTTGAACTTTGGAGTATCTAGGATAGCTTACTCTTGTTA
66 TCTTGAACTTTGGAGTATCTAGAATAGCTTACTCTTGTTA
45920759 CA
1 CA
45920761 AGAAAAGGAG
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 95 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (105 bp):
CATAATCGATTTGGAGAGTGGATTATCGAGTTAAATCATAATTTAGGTGTTTGCTCAGTCATTGA
TCTTGAACTTTGGAGTATCTAGAATAGCTTACTCTTGTTA
Found at i:45921160 original size:16 final size:17
Alignment explanation
Indices: 45921133--45921171 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
45921123 GTACAAATAA
45921133 AAAATGATTCAAAATTT
1 AAAATGATTCAAAATTT
* *
45921150 GAAATGA-TCAAATTTT
1 AAAATGATTCAAAATTT
45921166 AAAATG
1 AAAATG
45921172 GTTTAAACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.33
Consensus pattern (17 bp):
AAAATGATTCAAAATTT
Found at i:45936622 original size:3 final size:3
Alignment explanation
Indices: 45936614--45936670 Score: 98
Period size: 3 Copynumber: 19.0 Consensus size: 3
45936604 GATGAAGATT
45936614 GAA GAA GAA G-A GAA GAAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA GAA GAA GAA GAA GAA
45936659 GAA GAA GAA GAA
1 GAA GAA GAA GAA
45936671 TAAAGAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:45943338 original size:2 final size:2
Alignment explanation
Indices: 45943327--45943355 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
45943317 ACATTCTGTA
45943327 AT AT AT -T 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
45943356 GATTAGAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:45945637 original size:24 final size:22
Alignment explanation
Indices: 45945599--45945660 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 22
45945589 CGTGTAAAAA
* *
45945599 ATAAGATAAAATTAAATA-ATT
1 ATAAAATAAGATTAAATATATT
45945620 ATAAATATTAAGGATTAAA-ATATT
1 ATAAA-A-TAA-GATTAAATATATT
45945644 ATAAAATAAGATTAAAT
1 ATAAAATAAGATTAAAT
45945661 TAACGTAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
21 11 0.32
22 4 0.12
23 5 0.15
24 14 0.41
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (22 bp):
ATAAAATAAGATTAAATATATT
Found at i:45959816 original size:31 final size:31
Alignment explanation
Indices: 45959781--45959844 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
45959771 TTACAAAATG
* *
45959781 GTCACTGAACTATTTGAAAGTTTTTATTTAA
1 GTCACTGAACTATTCGAAAGTTTCTATTTAA
*
45959812 GTCACTGAGCTATTCGAAAGTTTCTATTTAA
1 GTCACTGAACTATTCGAAAGTTTCTATTTAA
45959843 GT
1 GT
45959845 AATTTGGCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (31 bp):
GTCACTGAACTATTCGAAAGTTTCTATTTAA
Found at i:45960826 original size:17 final size:17
Alignment explanation
Indices: 45960792--45960824 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45960782 CATTTACATC
*
45960792 TTTTAAAATTTATAAAA
1 TTTTAAAATATATAAAA
45960809 TTTTAAAATA-ATAAAA
1 TTTTAAAATATATAAAA
45960825 ATAAAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAAAATATATAAAA
Found at i:45963070 original size:59 final size:59
Alignment explanation
Indices: 45962991--45963232 Score: 299
Period size: 59 Copynumber: 4.1 Consensus size: 59
45962981 ATTTTTGACT
* *
45962991 TTCGAGGGTAAAAAT-GTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAG
1 TTCGGGGGT-AAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
* * * *
45963050 TTCGGGGGCAAAATGGTAATTTTTGGAGAAATCGAGGTCAAAAATGGGATTTTGGAAGG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
* * * *
45963109 TT-TGGGGTAAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
* ** * * * *
45963167 TTCGGGGGTAAAGTGGTAATTTTTTATGAAATCGGGGTTATAAATGGAATTTTAGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
*
45963226 TTTGGGG
1 TTCGGGG
45963233 ACTAGAGAGC
Statistics
Matches: 159, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
58 57 0.36
59 102 0.64
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAG
Found at i:45963102 original size:30 final size:30
Alignment explanation
Indices: 45962992--45963160 Score: 111
Period size: 29 Copynumber: 5.7 Consensus size: 30
45962982 TTTTTGACTT
* *
45962992 TCGAGGGT-AAAAATGTAATTTTTGGTGAAA
1 TCGA-GGTCAAAAATGGAATTTTTGGAGAAA
* *
45963022 TCGGGGTCAAAAATGGAA-TTTTGGA-AAGT
1 TCGAGGTCAAAAATGGAATTTTTGGAGAA-A
* *
45963051 TCGGGGGC-AAAATGGTAATTTTTGGAGAAA
1 TCGAGGTCAAAAATGG-AATTTTTGGAGAAA
* **
45963081 TCGAGGTCAAAAATGGGA-TTTTGGA-AGGT
1 TCGAGGTCAAAAATGGAATTTTTGGAGA-AA
* * * *
45963110 TTGGGGT--AAAATGGTAATTTTGGGTGAAA
1 TCGAGGTCAAAAATGG-AATTTTTGGAGAAA
*
45963139 TCGAGGTTAAAAATGGAATTTT
1 TCGAGGTCAAAAATGGAATTTT
45963161 GGAAGGTTCG
Statistics
Matches: 107, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
27 7 0.07
28 11 0.10
29 40 0.37
30 33 0.31
31 16 0.15
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.31
Consensus pattern (30 bp):
TCGAGGTCAAAAATGGAATTTTTGGAGAAA
Found at i:45963161 original size:30 final size:30
Alignment explanation
Indices: 45962992--45963162 Score: 115
Period size: 30 Copynumber: 5.8 Consensus size: 30
45962982 TTTTTGACTT
* * *
45962992 TCGAGGGTAAAAATGTAATTTTTGGTGAAA
1 TCGAGGGTAAAAATGGAATTTTGGGAGAAA
*
45963022 TCG-GGGTCAAAAATGGAATTTT-GGA-AAGT
1 TCGAGGGT-AAAAATGGAATTTTGGGAGAA-A
** *
45963051 TCG-GGGGCAAAATGGTAATTTTTGGAGAAA
1 TCGAGGGTAAAAATGG-AATTTTGGGAGAAA
* * **
45963081 TCGA-GGTCAAAAATGGGATTTTGGAAG-GT
1 TCGAGGGT-AAAAATGGAATTTTGGGAGAAA
* *
45963110 TTG-GGGT-AAAATGGTAATTTTGGGTGAAA
1 TCGAGGGTAAAAATGG-AATTTTGGGAGAAA
*
45963139 TCGAGGTTAAAAATGGAATTTTGG
1 TCGAGGGTAAAAATGGAATTTTGG
45963163 AAGGTTCGGG
Statistics
Matches: 108, Mismatches: 21, Indels: 24
0.71 0.14 0.16
Matches are distributed among these distances:
27 7 0.06
28 17 0.16
29 25 0.23
30 43 0.40
31 16 0.15
ACGTcount: A:0.33, C:0.05, G:0.32, T:0.30
Consensus pattern (30 bp):
TCGAGGGTAAAAATGGAATTTTGGGAGAAA
Found at i:45963187 original size:29 final size:29
Alignment explanation
Indices: 45963031--45963189 Score: 96
Period size: 29 Copynumber: 5.5 Consensus size: 29
45963021 ATCGGGGTCA
* *
45963031 AAAATGG-AATTTTGGAAAGTTCGGGGGC
1 AAAATGGTAATTTTGGAAGGTTCGGGGGT
** *
45963059 AAAATGGTAATTTTTGG-AGAAATC-GAGGT
1 AAAATGGTAA-TTTTGGAAG-GTTCGGGGGT
* *
45963088 CAAAAATGG-GATTTTGGAAGGTT-TGGGGT
1 --AAAATGGTAATTTTGGAAGGTTCGGGGGT
** ** * *
45963117 AAAATGGTAATTTTGGGTGAAATCGAGGTT
1 AAAATGGTAATTTTGGAAG-GTTCGGGGGT
45963147 AAAAATGG-AATTTTGGAAGGTTCGGGGGT
1 -AAAATGGTAATTTTGGAAGGTTCGGGGGT
*
45963176 AAAGTGGTAATTTT
1 AAAATGGTAATTTT
45963190 TTATGAAATC
Statistics
Matches: 95, Mismatches: 24, Indels: 23
0.67 0.17 0.16
Matches are distributed among these distances:
27 7 0.07
28 21 0.22
29 30 0.32
30 23 0.24
31 14 0.15
ACGTcount: A:0.33, C:0.04, G:0.33, T:0.31
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAGGTTCGGGGGT
Found at i:45963187 original size:117 final size:117
Alignment explanation
Indices: 45962996--45963232 Score: 325
Period size: 117 Copynumber: 2.0 Consensus size: 117
45962986 TGACTTTCGA
* *
45962996 GGGTAAAAATGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAAGTTCGGGGGCAA
1 GGGTAAAAATGTAATTTTGGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGGGGGCAA
* * *
45963061 AATGGTAATTTTTGGA-GAAATCGAGGTCAAAAATGGGATTTTGGAAGGTTTG
66 AATGGTAATTTTT-GATGAAATCGAGGTCAAAAATGGAATTTTAGAAAGTTTG
* * *
45963113 GGGT-AAAATGGTAATTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAGGTTCGGGGGTA
1 GGGTAAAAAT-GTAATTTTGGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGGGGGCA
* * * * *
45963177 AAGTGGTAATTTTTTATGAAATCGGGGTTATAAATGGAATTTTAGAAAGTTTG
65 AAATGGTAATTTTTGATGAAATCGAGGTCAAAAATGGAATTTTAGAAAGTTTG
45963230 GGG
1 GGG
45963233 ACTAGAGAGC
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
116 6 0.06
117 99 0.94
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (117 bp):
GGGTAAAAATGTAATTTTGGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGGGGGCAA
AATGGTAATTTTTGATGAAATCGAGGTCAAAAATGGAATTTTAGAAAGTTTG
Found at i:45965123 original size:18 final size:18
Alignment explanation
Indices: 45965100--45965183 Score: 77
Period size: 18 Copynumber: 4.7 Consensus size: 18
45965090 ATTGGGTTTC
*
45965100 AATTTATAA-TAATTTTTA
1 AATTTAAAATTAA-TTTTA
*
45965118 AATTTAAAA-TAAATTTA
1 AATTTAAAATTAATTTTA
*
45965135 AACTT-AAATTAAATTTT-
1 AATTTAAAATT-AATTTTA
45965152 AATTTAAAGATTAATTTTA
1 AATTTAAA-ATTAATTTTA
*
45965171 AATTTAAATTTAA
1 AATTTAAAATTAA
45965184 AATAAATCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
16 3 0.05
17 13 0.24
18 28 0.51
19 11 0.20
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
AATTTAAAATTAATTTTA
Found at i:45965125 original size:6 final size:6
Alignment explanation
Indices: 45965114--45965229 Score: 91
Period size: 6 Copynumber: 20.0 Consensus size: 6
45965104 TATAATAATT
* * *
45965114 TTTAAA TTTAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTTAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
45965160 GATTAAT TTTAAA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA -TAAAA
1 -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
45965207 TTT-AA TCTTAAA -ATAAA TTTAAA
1 TTTAAA T-TTAAA TTTAAA TTTAAA
45965230 AAAGTCCGAT
Statistics
Matches: 86, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
5 24 0.28
6 56 0.65
7 6 0.07
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:45965136 original size:17 final size:17
Alignment explanation
Indices: 45965100--45965229 Score: 93
Period size: 17 Copynumber: 7.1 Consensus size: 17
45965090 ATTGGGTTTC
* *
45965100 AATTTATAATAATTTTTA
1 AATTTAAAATAA-ATTTA
45965118 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* * *
45965135 AACTTAAATTAAATTTT
1 AATTTAAAATAAATTTA
45965152 AATTTAAAGATTAATTTTAAATTTA
1 AATTT--A-A--AA---TAAATTTA
*
45965177 AATTTAAAATAAATCTA
1 AATTTAAAATAAATTTA
45965194 AATTT-AAATAAAATTT-
1 AATTTAAAAT-AAATTTA
45965210 AATCTTAAAATAAATTTA
1 AAT-TTAAAATAAATTTA
45965228 AA
1 AA
45965230 AAAGTCCGAT
Statistics
Matches: 90, Mismatches: 10, Indels: 24
0.73 0.08 0.19
Matches are distributed among these distances:
16 7 0.08
17 47 0.52
18 17 0.19
19 1 0.01
20 3 0.03
22 2 0.02
23 1 0.01
25 12 0.13
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:45965144 original size:12 final size:12
Alignment explanation
Indices: 45965114--45965229 Score: 91
Period size: 11 Copynumber: 10.0 Consensus size: 12
45965104 TATAATAATT
45965114 TTTAAATTTAAA
1 TTTAAATTTAAA
*
45965126 -ATAAATTTAAA
1 TTTAAATTTAAA
*
45965137 CTTAAA-TTAAA
1 TTTAAATTTAAA
*
45965148 TTTTAATTTAAA
1 TTTAAATTTAAA
* *
45965160 GATTAATTTTAAA
1 -TTTAAATTTAAA
45965173 TTTAAATTTAAA
1 TTTAAATTTAAA
* *
45965185 -ATAAATCTAAA
1 TTTAAATTTAAA
*
45965196 TTTAAA-TAAAA
1 TTTAAATTTAAA
45965207 TTT-AATCTTAAA
1 TTTAAAT-TTAAA
*
45965219 -ATAAATTTAAA
1 TTTAAATTTAAA
45965230 AAAGTCCGAT
Statistics
Matches: 81, Mismatches: 16, Indels: 15
0.72 0.14 0.13
Matches are distributed among these distances:
10 2 0.02
11 40 0.49
12 30 0.37
13 9 0.11
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:45965179 original size:59 final size:58
Alignment explanation
Indices: 45965114--45965226 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 58
45965104 TATAATAATT
* * *
45965114 TTTAAATTTAAAATAAATTTAAACTTAAATTAAATTTTAAT-TTAAAGATTAATTTTAAA
1 TTTAAATTTAAAATAAATCTAAACTTAAA-TAAAATTTAATCTTAAA-ATAAATTTTAAA
*
45965173 TTTAAATTTAAAATAAATCTAAATTTAAATAAAATTTAATCTTAAAATAAATTT
1 TTTAAATTTAAAATAAATCTAAACTTAAATAAAATTTAATCTTAAAATAAATTT
45965227 AAAAAAGTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 17 0.35
59 32 0.65
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (58 bp):
TTTAAATTTAAAATAAATCTAAACTTAAATAAAATTTAATCTTAAAATAAATTTTAAA
Found at i:45973457 original size:60 final size:60
Alignment explanation
Indices: 45973386--45973624 Score: 292
Period size: 60 Copynumber: 4.0 Consensus size: 60
45973376 ATTTAGAGTT
45973386 TGTATTATAGACAACGAGAAACACTTAATTAGATAAAATTTTCAAAAG-AAAAGAAATGTA
1 TGTATTATAGACAACGAGAAACACTTAATTAGATAAAATTTTCAAAAGAAAAAGAAAT-TA
* * * *
45973446 TGCATTATAGACAAC-AGGAAACACTTGATTAGATAAATTTTTCAAAAGAAAAAGAAAAATA
1 TGTATTATAGACAACGA-GAAACACTTAATTAGATAAAATTTTCAAAAGAAAAAG-AAATTA
** * *
45973507 CATATTATAGACAACGAGAAACACTTATTTAGATAAATTTTTC--AA-AAAAA-AAATTA
1 TGTATTATAGACAACGAGAAACACTTAATTAGATAAAATTTTCAAAAGAAAAAGAAATTA
* * ** *
45973563 TGTATTATAGACAACGAGAACCATTTGTTTAGATAAAATTTTCAAAAGAAAAAGAAAATA
1 TGTATTATAGACAACGAGAAACACTTAATTAGATAAAATTTTCAAAAGAAAAAGAAATTA
45973623 TG
1 TG
45973625 AATATCACCA
Statistics
Matches: 154, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
56 42 0.27
58 7 0.05
59 8 0.05
60 50 0.32
61 43 0.28
62 4 0.03
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.28
Consensus pattern (60 bp):
TGTATTATAGACAACGAGAAACACTTAATTAGATAAAATTTTCAAAAGAAAAAGAAATTA
Found at i:45973580 original size:56 final size:57
Alignment explanation
Indices: 45973386--45973615 Score: 259
Period size: 56 Copynumber: 3.9 Consensus size: 57
45973376 ATTTAGAGTT
*
45973386 TGTATTATAGACAACGAGAAACACTTAATTAGATAAAATTTTCAAAAGAAAAGAAATGTA
1 TGTATTATAGACAACGAGAAACACTTATTTAGATAAAATTTTCAAAA-AAAA-AAAT-TA
* * *
45973446 TGCATTATAGACAAC-AGGAAACACTTGA-TTAGATAAATTTTTCAAAAGAAAAAGAAAAATA
1 TGTATTATAGACAACGA-GAAACACTT-ATTTAGATAAAATTTTC--AA-AAAAA-AAAATTA
** *
45973507 CATATTATAGACAACGAGAAACACTTATTTAGATAAATTTTTC-AAAAAAAAAATTA
1 TGTATTATAGACAACGAGAAACACTTATTTAGATAAAATTTTCAAAAAAAAAAATTA
* * * *
45973563 TGTATTATAGACAACGAGAACCATTTGTTTAGATAAAATTTTCAAAAGAAAAA
1 TGTATTATAGACAACGAGAAACACTTATTTAGATAAAATTTTCAAAAAAAAAA
45973616 GAAAATATGA
Statistics
Matches: 147, Mismatches: 14, Indels: 21
0.81 0.08 0.12
Matches are distributed among these distances:
56 43 0.29
57 13 0.09
58 1 0.01
59 1 0.01
60 38 0.26
61 39 0.27
62 9 0.06
63 3 0.02
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.28
Consensus pattern (57 bp):
TGTATTATAGACAACGAGAAACACTTATTTAGATAAAATTTTCAAAAAAAAAAATTA
Found at i:45990683 original size:21 final size:21
Alignment explanation
Indices: 45990641--45990684 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
45990631 ATTAACAAAT
* *
45990641 AAAAAAGAGAAATCAAAAAGG
1 AAAAAAAAGAAAACAAAAAGG
* *
45990662 AAAAAAAAGAAAAGAAAGAGG
1 AAAAAAAAGAAAACAAAAAGG
45990683 AA
1 AA
45990685 CCCCCGATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGAAAACAAAAAGG
Found at i:45996129 original size:4 final size:4
Alignment explanation
Indices: 45996120--45996146 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
45996110 GTCAGACTAA
45996120 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
45996147 GATTTCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:46013197 original size:21 final size:21
Alignment explanation
Indices: 46013163--46013204 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
46013153 TTTTTCAAAA
* *
46013163 ATTAGACTAGTGATTGAATTG
1 ATTAGACTACTGATTCAATTG
*
46013184 ATTAGGCTACTGATTCAATTG
1 ATTAGACTACTGATTCAATTG
46013205 GTCTGGACGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (21 bp):
ATTAGACTACTGATTCAATTG
Found at i:46022859 original size:14 final size:15
Alignment explanation
Indices: 46022830--46022862 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
46022820 AATAAATGAC
*
46022830 TAAATTATATAAAAT
1 TAAAATATATAAAAT
46022845 TAAAATATA-AAAAT
1 TAAAATATATAAAAT
46022859 TAAA
1 TAAA
46022863 TCTTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATATATAAAAT
Found at i:46025903 original size:17 final size:16
Alignment explanation
Indices: 46025865--46025910 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
46025855 TCATCTCTTG
46025865 AAAAATTAAAATATTA
1 AAAAATTAAAATATTA
*
46025881 ATAAAATCTAAACATATAA
1 A-AAAAT-TAAA-ATATTA
46025900 AAAAATTAAAA
1 AAAAATTAAAA
46025911 AATATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.08
17 9 0.35
18 9 0.35
19 6 0.23
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATTAAAATATTA
Found at i:46025908 original size:27 final size:25
Alignment explanation
Indices: 46025872--46025922 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
46025862 TTGAAAAATT
* *
46025872 AAAATATTAATAAAATCTAAACATATA
1 AAAAAATTAA-AAAATATAAA-ATATA
46025899 AAAAAATTAAAAAATATAAAATAT
1 AAAAAATTAAAAAATATAAAATAT
46025923 CTTTTACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 9 0.41
27 9 0.41
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAAAATTAAAAAATATAAAATATA
Found at i:46025915 original size:18 final size:18
Alignment explanation
Indices: 46025865--46025919 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
46025855 TCATCTCTTG
*
46025865 AAAAATTAAAATAT-TAA
1 AAAAATTAAAAAATATAA
* *
46025882 TAAAATCT-AAACATATAA
1 AAAAAT-TAAAAAATATAA
46025900 AAAAATTAAAAAATATAA
1 AAAAATTAAAAAATATAA
46025918 AA
1 AA
46025920 TATCTTTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAATTAAAAAATATAA
Found at i:46036829 original size:16 final size:16
Alignment explanation
Indices: 46036810--46036843 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
46036800 TTTTCTTGAG
46036810 AACAACTAATATTTAA
1 AACAACTAATATTTAA
*
46036826 AACAACTATTATTTAA
1 AACAACTAATATTTAA
46036842 AA
1 AA
46036844 TAATTAACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (16 bp):
AACAACTAATATTTAA
Found at i:46053693 original size:24 final size:24
Alignment explanation
Indices: 46053640--46053693 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
46053630 TTTTTAATTA
46053640 ATAAAATAATTAATTAATTAAAACT
1 ATAAAATAATTAA-TAATTAAAACT
46053665 A-AAAATAATTAA-ACATATAAAA-T
1 ATAAAATAATTAATA-AT-TAAAACT
46053688 ATAAAA
1 ATAAAA
46053694 AAAAAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
22 1 0.04
23 4 0.15
24 20 0.77
25 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
ATAAAATAATTAATAATTAAAACT
Found at i:46055408 original size:22 final size:21
Alignment explanation
Indices: 46055359--46055426 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 21
46055349 ATTTTAAAAA
* *
46055359 ATTATAAAATATTTATTGAATT
1 ATTAAAAAAT-TTTATTAAATT
46055381 ATTTAAAAAATTTTATTCAAATT
1 A-TTAAAAAATTTTATT-AAATT
*
46055404 ATTAAATTAAATTTTTTTAAATT
1 ATTAAA--AAATTTTATTAAATT
46055427 TAATAGATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 12 0.31
23 18 0.46
24 9 0.23
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
ATTAAAAAATTTTATTAAATT
Found at i:46056102 original size:15 final size:16
Alignment explanation
Indices: 46056082--46056111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46056072 GATGTATTCA
46056082 TGGG-TTGGATCGAGT
1 TGGGTTTGGATCGAGT
46056097 TGGGTTTGGATCGAG
1 TGGGTTTGGATCGAG
46056112 CTTAAGTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.07, G:0.47, T:0.33
Consensus pattern (16 bp):
TGGGTTTGGATCGAGT
Found at i:46062660 original size:14 final size:14
Alignment explanation
Indices: 46062639--46062718 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
46062629 TTAAATTTAC
46062639 AATTTAATCTCTAT
1 AATTTAATCTCTAT
* * *
46062653 ATTTTAATTTCAAAT
1 AATTTAATCTC-TAT
46062668 AATTTAATCTCTAT
1 AATTTAATCTCTAT
* * *
46062682 ATTTTAATTTCAAAT
1 AATTTAATCTC-TAT
*
46062697 AATTTAATCTCTTT
1 AATTTAATCTCTAT
*
46062711 AAATTAAT
1 AATTTAAT
46062719 TAATCATGTT
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
14 28 0.56
15 22 0.44
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTAATCTCTAT
Found at i:46062675 original size:15 final size:15
Alignment explanation
Indices: 46062655--46062704 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
46062645 ATCTCTATAT
46062655 TTTAATTTCAAATAA
1 TTTAATTTCAAATAA
* * *
46062670 TTTAATCTC-TATAT
1 TTTAATTTCAAATAA
46062684 TTTAATTTCAAATAA
1 TTTAATTTCAAATAA
46062699 TTTAAT
1 TTTAAT
46062705 CTCTTTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAATTTCAAATAA
Found at i:46062719 original size:29 final size:29
Alignment explanation
Indices: 46062639--46062708 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
46062629 TTAAATTTAC
46062639 AATTTAATCTCTATATTTTAATTTCAAAT
1 AATTTAATCTCTATATTTTAATTTCAAAT
46062668 AATTTAATCTCTATATTTTAATTTCAAAT
1 AATTTAATCTCTATATTTTAATTTCAAAT
46062697 AATTTAATCTCT
1 AATTTAATCTCT
46062709 TTAAATTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (29 bp):
AATTTAATCTCTATATTTTAATTTCAAAT
Found at i:46064009 original size:12 final size:12
Alignment explanation
Indices: 46063992--46064016 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46063982 GTCTCTAAAA
46063992 AAATAAATATAT
1 AAATAAATATAT
46064004 AAATAAATATAT
1 AAATAAATATAT
46064016 A
1 A
46064017 GTAAAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAAATATAT
Found at i:46081648 original size:22 final size:22
Alignment explanation
Indices: 46081623--46081673 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
46081613 TTTATTGTTG
*
46081623 TTTTATTACGATTTTGTTATCA
1 TTTTATTACGATGTTGTTATCA
* * *
46081645 TTTTACTACTATGTTGTTATTA
1 TTTTATTACGATGTTGTTATCA
46081667 TTTTATT
1 TTTTATT
46081674 GTTAATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.63
Consensus pattern (22 bp):
TTTTATTACGATGTTGTTATCA
Done.