Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 29 of 106
Found at i:5429635 original size:8 final size:8
Alignment explanation
Indices: 5429618--5429658 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
5429608 AACATTGTCA
5429618 TTTT-TTT
1 TTTTGTTT
5429625 TTTTGTTT
1 TTTTGTTT
5429633 TTTTGTTT
1 TTTTGTTT
5429641 TTTTGTTT
1 TTTTGTTT
5429649 TTTT-TTT
1 TTTTGTTT
5429656 TTT
1 TTT
5429659 AACCCAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 10 0.30
8 23 0.70
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (8 bp):
TTTTGTTT
Found at i:5429736 original size:43 final size:40
Alignment explanation
Indices: 5429668--5429804 Score: 156
Period size: 36 Copynumber: 3.4 Consensus size: 40
5429658 TAACCCAAAA
*
5429668 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACCTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTG-GAAA--TAAATT
*
5429711 GCTCCTCTAAACAGAGGCACTACGACTTTGG----AAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGGAAATAAATT
* * * *
5429747 GCTCCTCTAAACAAAAGCACCACGACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACAACGACTTTGGAAA-TAAATT
5429788 GCTCCTCTAAACAGAGG
1 GCTCCTCTAAACAGAGG
5429805 TAACGGAACT
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
36 32 0.40
41 20 0.25
42 1 0.01
43 28 0.35
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (40 bp):
GCTCCTCTAAACAGAGGCACAACGACTTTGGAAATAAATT
Found at i:5429816 original size:77 final size:78
Alignment explanation
Indices: 5429668--5429821 Score: 197
Period size: 77 Copynumber: 2.0 Consensus size: 78
5429658 TAACCCAAAA
* * *
5429668 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACCTAAATTGCTCCTCTAAACAGAGGCACTA
1 GCTCCTCTAAACAAAAGCACAACGACTTTGAGAAACCTAAATTGCTCCTCTAAACAGAGGCAC-A
5429733 CGACTTTGGAAATT
65 CGACTTTGGAAATT
* * * *
5429747 GCTCCTCTAAACAAAAGCACCACGACTTT-TGAAA-GTAAATTGCTCCTCTAAACAGAGGTA-AC
1 GCTCCTCTAAACAAAAGCACAACGACTTTGAGAAACCTAAATTGCTCCTCTAAACAGAGGCACAC
5429809 GGAACTTTGGAAA
66 -G-ACTTTGGAAA
5429822 AGTAAAATTG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
75 2 0.03
76 1 0.02
77 34 0.52
78 4 0.06
79 25 0.38
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (78 bp):
GCTCCTCTAAACAAAAGCACAACGACTTTGAGAAACCTAAATTGCTCCTCTAAACAGAGGCACAC
GACTTTGGAAATT
Found at i:5430866 original size:12 final size:11
Alignment explanation
Indices: 5430851--5430890 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
5430841 CACTTTTTCA
*
5430851 TTTTTTTCTCTT
1 TTTTTTTAT-TT
5430863 TTTTTTTATTAT
1 TTTTTTTATT-T
5430875 TTTTTTTATTT
1 TTTTTTTATTT
5430886 TTTTT
1 TTTTT
5430891 CAAACATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.07, C:0.05, G:0.00, T:0.88
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:5441085 original size:59 final size:60
Alignment explanation
Indices: 5440987--5441287 Score: 389
Period size: 59 Copynumber: 5.0 Consensus size: 60
5440977 CTTGTGTGGA
*
5440987 GAAAATTGATACTTTCAACTTTTCCCTAAAAA-ATATTTTTTTTGAAA-TTT-ATTTTTAAA
1 GAAAATTGATACTTTCAACTTTTCCC-AAAAATAT-TTTTTTTTGAAATTTTGATTTTTAAG
* ***
5441046 GAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTTGAAACTTTGATTTCCGAG
1 GAAAATTGATACTTTCAAC-TTTTCCCAAAAATATTTTTTTTTGAAATTTTGATTTTTAAG
* *
5441107 GAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTCTTTTGAAAATTT-ATTTTTAAG
1 GAAAATTGATACTTTCAACTTTTCC-CAAAAAT-ATTTTT-TTTTGAAATTTTGATTTTTAAG
* * *
5441169 GAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTCTAGAAATTTTGATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTCC-CAAAAATATTTTTTTTTGAAATTTTGATTTTTAAG
5441228 GAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTTTA
1 GAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTTT-GAAATTTTGATTTTTA
5441288 TTTAAAGAAA
Statistics
Matches: 213, Mismatches: 17, Indels: 21
0.85 0.07 0.08
Matches are distributed among these distances:
58 10 0.05
59 79 0.37
60 18 0.08
61 36 0.17
62 59 0.28
63 11 0.05
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.46
Consensus pattern (60 bp):
GAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTTGAAATTTTGATTTTTAAG
Found at i:5441333 original size:28 final size:27
Alignment explanation
Indices: 5441302--5441362 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
5441292 AAGAAAATAT
*
5441302 AATAAATAAAAATAAATA-AAAACAGAAA
1 AATAAAGAAAAATAAA-ACAAAA-AGAAA
* *
5441330 AATAAAGAAAAGTAAAACAAAAATAAA
1 AATAAAGAAAAATAAAACAAAAAGAAA
5441357 AATAAA
1 AATAAA
5441363 ATTAAGATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (27 bp):
AATAAAGAAAAATAAAACAAAAAGAAA
Found at i:5441363 original size:23 final size:22
Alignment explanation
Indices: 5441305--5441378 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
5441295 AAAATATAAT
5441305 AAATAAAAAT-AAATAAAAACAGAA
1 AAATAAAAATAAAAT-AAAAC--AA
* *
5441329 AAATAAAGA-AAAGTAAAACAA
1 AAATAAAAATAAAATAAAACAA
* *
5441350 AAATAAAAATAAAATTAAGATAA
1 AAATAAAAATAAAA-TAAAACAA
5441373 AAATAA
1 AAATAA
5441379 TATTAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
21 10 0.24
22 3 0.07
23 17 0.41
24 11 0.27
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (22 bp):
AAATAAAAATAAAATAAAACAA
Found at i:5441372 original size:17 final size:16
Alignment explanation
Indices: 5441300--5441389 Score: 63
Period size: 17 Copynumber: 5.3 Consensus size: 16
5441290 TAAAGAAAAT
*
5441300 ATAATAAATAAAAATAA
1 ATAA-AAATAAAATTAA
* *
5441317 ATAAAAACAGAAAAATAA
1 AT-AAAA-ATAAAATTAA
* * **
5441335 AGAAAAGTAAAACAAAA
1 ATAAAAATAAAA-TTAA
5441352 ATAAAAATAAAATTAA
1 ATAAAAATAAAATTAA
*
5441368 GATAAAAATAATATTAA
1 -ATAAAAATAAAATTAA
5441385 ATAAA
1 ATAAA
5441390 CCTAATCTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
16 11 0.19
17 36 0.61
18 12 0.20
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.19
Consensus pattern (16 bp):
ATAAAAATAAAATTAA
Found at i:5442310 original size:17 final size:17
Alignment explanation
Indices: 5442279--5442316 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
5442269 AGAAAAAAAA
5442279 ATAATGATAATAATCAG
1 ATAATGATAATAATCAG
5442296 ATAATCGATAA-AATCAG
1 ATAAT-GATAATAATCAG
5442313 ATAA
1 ATAA
5442317 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (17 bp):
ATAATGATAATAATCAG
Found at i:5442403 original size:19 final size:21
Alignment explanation
Indices: 5442379--5442434 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
5442369 GATAAAAACA
5442379 ATAATAAATAAAT-TATAA-T
1 ATAATAAATAAATATATAACT
5442398 ATAAT-AATAAATATATAACT
1 ATAATAAATAAATATATAACT
* *
5442418 ATATAAAAATACATATA
1 ATA-ATAAATAAATATA
5442435 CATATTAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 7 0.23
19 10 0.32
20 4 0.13
21 1 0.03
22 9 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAATAAATAAATATATAACT
Found at i:5442421 original size:22 final size:22
Alignment explanation
Indices: 5442378--5442434 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
5442368 AGATAAAAAC
* *
5442378 AATAATAAATAAATTATAATAT
1 AATAATAAATATATAATAATAT
5442400 AATAATAAATATATAACT-ATAT
1 AATAATAAATATATAA-TAATAT
* *
5442422 AAAAATACATATA
1 AATAATAAATATA
5442435 CATATTAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAATAAATATATAATAATAT
Found at i:5442492 original size:27 final size:27
Alignment explanation
Indices: 5442457--5442508 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
5442447 AAAGAAAAAA
*
5442457 AATAAATAA-AAATATACATATAATAAT
1 AATAAATAATAAA-ATACATAAAATAAT
5442484 AATAAATAATAAAATACATAAAATA
1 AATAAATAATAAAATACATAAAATA
5442509 CAAAAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (27 bp):
AATAAATAATAAAATACATAAAATAAT
Found at i:5442523 original size:9 final size:9
Alignment explanation
Indices: 5442510--5442540 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5442500 CATAAAATAC
5442510 AAAAGAAAA
1 AAAAGAAAA
*
5442519 GAAAGAAAA
1 AAAAGAAAA
5442528 AAAAGAAAA
1 AAAAGAAAA
5442537 AAAA
1 AAAA
5442541 TAATACAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:5442550 original size:18 final size:18
Alignment explanation
Indices: 5442505--5442556 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
5442495 AAATACATAA
*
5442505 AATACAAAAGAAAAGAAAG
1 AATAC-AAAGAAAAAAAAG
* * *
5442524 AAAAAAAAGAAAAAAAAT
1 AATACAAAGAAAAAAAAG
5442542 AATACAAAGTAAAAA
1 AATACAAAG-AAAAA
5442557 TTGTATTGGG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.79, C:0.04, G:0.10, T:0.08
Consensus pattern (18 bp):
AATACAAAGAAAAAAAAG
Found at i:5445152 original size:29 final size:29
Alignment explanation
Indices: 5445113--5445173 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
5445103 TTCAAGTACA
* *
5445113 TTATACTATTAATGAGTATCTCAGTAATC
1 TTATACCATTAATAAGTATCTCAGTAATC
5445142 TTATACCATTAATAAGTATCTCAGTAATC
1 TTATACCATTAATAAGTATCTCAGTAATC
5445171 TTA
1 TTA
5445174 CTGCTTTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (29 bp):
TTATACCATTAATAAGTATCTCAGTAATC
Found at i:5447004 original size:29 final size:29
Alignment explanation
Indices: 5446916--5447015 Score: 98
Period size: 29 Copynumber: 3.4 Consensus size: 29
5446906 ATTTTCTCAT
*
5446916 TATTTTAACATT-AATATTAATTTAATAA
1 TATTTTAATATTAAATATTAATTTAATAA
* ** *
5446944 T-TCTTTAAATTTTTTATTTTAAGTTT-ATAA
1 TAT-TTT-AATATTAAATATTAA-TTTAATAA
5446974 TATTTTAATATTAAATATTAATTTAATAA
1 TATTTTAATATTAAATATTAATTTAATAA
*
5447003 TATTATAATATTA
1 TATTTTAATATTA
5447016 TTTGAATAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.02
28 7 0.12
29 31 0.54
30 14 0.25
31 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (29 bp):
TATTTTAATATTAAATATTAATTTAATAA
Found at i:5447010 original size:8 final size:8
Alignment explanation
Indices: 5446968--5447016 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
5446958 TATTTTAAGT
5446968 TTATAATA
1 TTATAATA
*
5446976 TTTTAATA
1 TTATAATA
5446984 TTA-AATA
1 TTATAATA
5446991 -T-TAAT-
1 TTATAATA
5446996 TTAATAATA
1 TT-ATAATA
5447005 TTATAATA
1 TTATAATA
5447013 TTAT
1 TTAT
5447017 TTGAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
6 5 0.15
7 4 0.12
8 23 0.68
9 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTATAATA
Found at i:5447011 original size:11 final size:10
Alignment explanation
Indices: 5446970--5447029 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
5446960 TTTTAAGTTT
5446970 ATAATATTT-
1 ATAATATTTA
*
5446979 -TAATATTAA
1 ATAATATTTA
*
5446988 ATATTAATTTA
1 ATAAT-ATTTA
5446999 ATAATATTATA
1 ATAATATT-TA
*
5447010 ATATTATTTGA
1 ATAATATTT-A
5447021 ATAATATTT
1 ATAATATTT
5447030 TGTATTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 7 0.17
10 7 0.17
11 26 0.65
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (10 bp):
ATAATATTTA
Found at i:5447015 original size:22 final size:21
Alignment explanation
Indices: 5446979--5447028 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 21
5446969 TATAATATTT
5446979 TAATATTAAATATTAATTT-AA
1 TAATATTAAATATT-ATTTGAA
5447000 TAATATTATAATATTATTTGAA
1 TAATATTA-AATATTATTTGAA
5447022 TAATATT
1 TAATATT
5447029 TTGTATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TAATATTAAATATTATTTGAA
Found at i:5447062 original size:50 final size:51
Alignment explanation
Indices: 5446970--5447068 Score: 137
Period size: 50 Copynumber: 2.0 Consensus size: 51
5446960 TTTTAAGTTT
* * *
5446970 ATAATATTTTAATATTAAATATTAATTTAATAATATTATAATATTATTTGA
1 ATAATATTTTAATATTAAATATTAATGTAATAAGATTATAATATAATTTGA
* * *
5447021 ATAATATTTT-GTATTAAATATTAATGTAATGAGATTTTAATATAATTT
1 ATAATATTTTAATATTAAATATTAATGTAATAAGATTATAATATAATTT
5447069 TAAATTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 32 0.76
51 10 0.24
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (51 bp):
ATAATATTTTAATATTAAATATTAATGTAATAAGATTATAATATAATTTGA
Found at i:5447087 original size:19 final size:19
Alignment explanation
Indices: 5447063--5447134 Score: 54
Period size: 25 Copynumber: 3.3 Consensus size: 19
5447053 GATTTTAATA
5447063 TAATTTTAAATTATTTATT
1 TAATTTTAAATTATTTATT
5447082 TAATTTATAATATTTTACTATTATT
1 TAATTT-TAA-A--TTA-T-TTATT
*
5447107 TAATTATTTAATTATTATAATT
1 TAATT-TTAAATTATT-T-ATT
5447129 TAATTT
1 TAATTT
5447135 AATTAATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
19 6 0.14
20 4 0.09
21 4 0.09
22 11 0.26
23 3 0.07
24 2 0.05
25 12 0.28
26 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATTTTAAATTATTTATT
Found at i:5447112 original size:8 final size:8
Alignment explanation
Indices: 5447101--5447139 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
5447091 ATATTTTACT
5447101 ATTATTTA
1 ATTATTTA
5447109 ATTATTTA
1 ATTATTTA
5447117 ATTATTATA
1 ATTATT-TA
5447126 ATTTAATTTA
1 A-TT-ATTTA
5447136 ATTA
1 ATTA
5447140 ATATAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 15 0.54
9 5 0.18
10 5 0.18
11 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTATTTA
Found at i:5447135 original size:19 final size:18
Alignment explanation
Indices: 5447101--5447152 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
5447091 ATATTTTACT
5447101 ATTATT-TAATT-ATTTA
1 ATTATTATAATTAATTTA
5447117 ATTATTATAATTTAATTTA
1 ATTATTATAA-TTAATTTA
*
5447136 ATTAATATAAATTAATT
1 ATTATTAT-AATTAATT
5447153 ATCTAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 6 0.19
17 3 0.10
18 2 0.06
19 18 0.58
20 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTATAATTAATTTA
Found at i:5448094 original size:31 final size:31
Alignment explanation
Indices: 5448052--5448112 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
5448042 TCTTTTTGAT
*
5448052 TATTATTATATAATAA-ATTAAGTAAATAAAG
1 TATTATCATATAATAAGATTAA-TAAATAAAG
5448083 TATTATCATATAATAAGATTAATAAATAAA
1 TATTATCATATAATAAGATTAATAAATAAA
5448113 TGTTATTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.38
Consensus pattern (31 bp):
TATTATCATATAATAAGATTAATAAATAAAG
Found at i:5448224 original size:17 final size:19
Alignment explanation
Indices: 5448191--5448229 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
5448181 AATTTTATAA
5448191 ATTAAATATTAAATTTTTT
1 ATTAAATATTAAATTTTTT
5448210 ATTAAATA-T-AATTTTTT
1 ATTAAATATTAAATTTTTT
5448227 ATT
1 ATT
5448230 TCTATGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
18 1 0.05
19 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTAAATATTAAATTTTTT
Found at i:5448259 original size:26 final size:28
Alignment explanation
Indices: 5448209--5448269 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
5448199 TTAAATTTTT
5448209 TATTAAATATAATTTTTTATTTCTATGG
1 TATTAAATATAATTTTTTATTTCTATGG
* *
5448237 TATTTAATATAA-TTTTTA-TTCTATTGC
1 TATTAAATATAATTTTTTATTTCTA-TGG
5448264 TATTAA
1 TATTAA
5448270 TAATTTGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.17
27 13 0.45
28 11 0.38
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (28 bp):
TATTAAATATAATTTTTTATTTCTATGG
Found at i:5448270 original size:26 final size:27
Alignment explanation
Indices: 5448209--5448271 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
5448199 TTAAATTTTT
*
5448209 TATTAAATATAATTTTTTATTTCTATGG
1 TATT-AATATAATTTTTTATTTCTATGC
5448237 TATTTAATATAA-TTTTTA-TTCTATTGC
1 TA-TTAATATAATTTTTTATTTCTA-TGC
5448264 TATTAATA
1 TATTAATA
5448272 ATTTGATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 11 0.34
27 10 0.31
28 9 0.28
29 2 0.06
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (27 bp):
TATTAATATAATTTTTTATTTCTATGC
Found at i:5448739 original size:12 final size:13
Alignment explanation
Indices: 5448722--5448751 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5448712 ATAAATTTAT
5448722 TATATTTTAA-AA
1 TATATTTTAATAA
5448734 TATATTTTAATAA
1 TATATTTTAATAA
5448747 TATAT
1 TATAT
5448752 ATATGAGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATTTTAATAA
Found at i:5449132 original size:71 final size:69
Alignment explanation
Indices: 5449046--5449194 Score: 187
Period size: 71 Copynumber: 2.1 Consensus size: 69
5449036 TTTTATACTA
* * *
5449046 TGATAATATTAATAAATATTAACAATTTAATTT-TGATTTTGCTATAATATAAGTAAAATTTGGT
1 TGATAATAATAATAAATAATAACAATTTAATTTAT-A-TTTGCTATAATATAAATAAAATTT-G-
5449110 ATA-CTTT
62 ATACCTTT
* * *
5449117 TGATAATAATGATAAATAATAACAATTTAATTTATATTTGTTATACTATAAATAAAATTTGATAC
1 TGATAATAATAATAAATAATAACAATTTAATTTATATTTGCTATAATATAAATAAAATTTGATAC
5449182 CTTT
66 CTTT
5449186 TGAT-ATAAT
1 TGATAATAAT
5449195 TTTGATTTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
68 8 0.11
69 9 0.13
70 21 0.30
71 31 0.44
72 1 0.01
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (69 bp):
TGATAATAATAATAAATAATAACAATTTAATTTATATTTGCTATAATATAAATAAAATTTGATAC
CTTT
Found at i:5449199 original size:11 final size:11
Alignment explanation
Indices: 5449183--5449248 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
5449173 ATTTGATACC
5449183 TTTTGATATAA
1 TTTTGATATAA
5449194 TTTTGATTTAATAA
1 TTTTGA--T-ATAA
*
5449208 CTTTTGATAAAA
1 -TTTTGATATAA
5449220 TTTT-A-ATAA
1 TTTTGATATAA
*
5449229 CTTTTGATACAA
1 -TTTTGATATAA
5449241 TTTTGATA
1 TTTTGATA
5449249 ACCGTCAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
9 3 0.07
10 5 0.11
11 19 0.42
12 6 0.13
13 2 0.04
14 4 0.09
15 6 0.13
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.52
Consensus pattern (11 bp):
TTTTGATATAA
Found at i:5449199 original size:21 final size:21
Alignment explanation
Indices: 5449168--5449324 Score: 84
Period size: 21 Copynumber: 7.1 Consensus size: 21
5449158 TATACTATAA
*
5449168 ATAAAA-TTTGATACCTTTTG
1 ATAAAATTTTGATAACTTTTG
*
5449188 ATATAATTTTGATTTAATAACTTTTG
1 ATAAAATTTTG-----ATAACTTTTG
*
5449214 ATAAAATTTTAATAACTTTTG
1 ATAAAATTTTGATAACTTTTG
* ** **
5449235 ATACAATTTTGATAACCGTCA
1 ATAAAATTTTGATAACTTTTG
** *
5449256 ATATTAGTTTGATAAC-TTTG
1 ATAAAATTTTGATAACTTTTG
* *
5449276 ATAATACAATTTTGATAATTTTTT
1 AT-A-A-AATTTTGATAACTTTTG
* *
5449300 ATAAAATTTTGGTAATCTCTTG
1 ATAAAATTTTGATAA-CTTTTG
5449322 ATA
1 ATA
5449325 TGGTTTTAAT
Statistics
Matches: 101, Mismatches: 25, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
20 8 0.08
21 53 0.52
22 7 0.07
23 10 0.10
24 5 0.05
26 18 0.18
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (21 bp):
ATAAAATTTTGATAACTTTTG
Found at i:5449784 original size:22 final size:22
Alignment explanation
Indices: 5449759--5449857 Score: 83
Period size: 22 Copynumber: 4.5 Consensus size: 22
5449749 AATAATTCAG
5449759 TACTAAGTTATAAATGATTTAT
1 TACTAAGTTATAAATGATTTAT
* ** *
5449781 TACTAAATTATTGATGATTTAC
1 TACTAAGTTATAAATGATTTAT
* * *
5449803 TACTACGTTACT-AATTATTAAT
1 TACTAAGTTA-TAAATGATTTAT
* *
5449825 TATTAAGTTATAACTGATTTAT
1 TACTAAGTTATAAATGATTTAT
* *
5449847 TATTAATTTAT
1 TACTAAGTTAT
5449858 CGATAATTTA
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
21 1 0.02
22 57 0.97
23 1 0.02
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (22 bp):
TACTAAGTTATAAATGATTTAT
Found at i:5449830 original size:88 final size:87
Alignment explanation
Indices: 5449656--5449819 Score: 202
Period size: 88 Copynumber: 1.9 Consensus size: 87
5449646 TTAATACTAT
* * *
5449656 TTTATCAATAATTTACTATAAGTTATAAATGATATATTATTAAATTATCAATTAATTACTACTAA
1 TTTATCAATAATTCACTATAAGTTATAAATGATATATTACTAAATTATCAATGAATTACTACTAA
* *
5449721 ATTAGTATTTAGGTACTATTAA
66 ATTACTAATTAGGTACTATTAA
* * * ** *
5449743 TTTATGAATAATTCAGTACTAAGTTATAAATGATTTATTACTAAATTATTGATGATTTACTACTA
1 TTTATCAATAATTCACTA-TAAGTTATAAATGATATATTACTAAATTATCAATGAATTACTACTA
**
5449808 CGTTACTAATTA
65 AATTACTAATTA
5449820 TTAATTATTA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
87 15 0.24
88 48 0.76
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (87 bp):
TTTATCAATAATTCACTATAAGTTATAAATGATATATTACTAAATTATCAATGAATTACTACTAA
ATTACTAATTAGGTACTATTAA
Found at i:5450174 original size:21 final size:21
Alignment explanation
Indices: 5450122--5450235 Score: 72
Period size: 21 Copynumber: 5.2 Consensus size: 21
5450112 ATTCATTACC
*
5450122 AAGTTATTCCTAATTTA-TATT
1 AAGTTA-TCATAATTTACTATT
**
5450143 AAACTACTCATAATTTACTATT
1 AAGTTA-TCATAATTTACTATT
* *
5450165 AAGTTATCATTGATTAACTATT
1 AAGTTATCA-TAATTTACTATT
* *
5450187 AAATT-TCGATGATTTACACTATT
1 AAGTTATC-ATAATTT--ACTATT
*
5450210 AAGTTAT-ATTAATTTACTTTT
1 AAGTTATCA-TAATTTACTATT
5450231 AAGTT
1 AAGTT
5450236 TTCAATGATT
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
21 33 0.45
22 24 0.33
23 15 0.21
24 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (21 bp):
AAGTTATCATAATTTACTATT
Found at i:5450244 original size:45 final size:45
Alignment explanation
Indices: 5450159--5450245 Score: 113
Period size: 45 Copynumber: 1.9 Consensus size: 45
5450149 CTCATAATTT
* *
5450159 ACTATTAAGTTATCATTGATTAACTATTAAATTTCGATGATTTAC
1 ACTATTAAGTTATCATTAATTAACTATTAAATTTCAATGATTTAC
* * *
5450204 ACTATTAAGTTAT-ATTAATTTACTTTTAAGTTTTCAATGATT
1 ACTATTAAGTTATCATTAATTAACTATTAA-ATTTCAATGATT
5450246 AACTACTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
44 13 0.36
45 23 0.64
ACGTcount: A:0.34, C:0.09, G:0.08, T:0.48
Consensus pattern (45 bp):
ACTATTAAGTTATCATTAATTAACTATTAAATTTCAATGATTTAC
Found at i:5450279 original size:66 final size:65
Alignment explanation
Indices: 5450153--5450282 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 65
5450143 AAACTACTCA
* * *
5450153 TAATTTACTATTAAGTTATCATTGATTAACTATTAAATTTCGATGATTTACACTATTAAGTTATA
1 TAATTTACTATTAAGTTATCAATGATTAACTACTAAATTTC-ATGATTTACACTACTAAGTTATA
5450218 T
65 T
* * *
5450219 TAATTTACTTTTAAGTTTTCAATGATTAACTACTAAATCATT-ATTGATTT-TACTACTAAGTTA
1 TAATTTACTATTAAGTTATCAATGATTAACTACTAAAT--TTCA-TGATTTACACTACTAAGTTA
5450282 T
63 T
5450283 TTATGATCTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
66 47 0.85
67 6 0.11
68 2 0.04
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (65 bp):
TAATTTACTATTAAGTTATCAATGATTAACTACTAAATTTCATGATTTACACTACTAAGTTATAT
Found at i:5450367 original size:22 final size:22
Alignment explanation
Indices: 5450341--5450411 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
5450331 TGACTTATTG
* *
5450341 TTAAGTTATCACTAATTTACTA
1 TTAAGTTATCAATGATTTACTA
* *
5450363 TTAAGTTATTAATGATTTATTA
1 TTAAGTTATCAATGATTTACTA
*
5450385 TTAAGTTATCAATGATTAACTA
1 TTAAGTTATCAATGATTTACTA
5450407 TTAAG
1 TTAAG
5450412 CTTTTATTTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.46
Consensus pattern (22 bp):
TTAAGTTATCAATGATTTACTA
Found at i:5450736 original size:22 final size:22
Alignment explanation
Indices: 5450711--5450818 Score: 92
Period size: 22 Copynumber: 5.0 Consensus size: 22
5450701 AAAATTAAGT
* **
5450711 TATCAGTGATTTACTGTTAAAC
1 TATCAATGATTTACTACTAAAC
*
5450733 TATCAATAATTTACTACTAAAC
1 TATCAATGATTTACTACTAAAC
* **
5450755 TATCAATGATTTATTACTAATT
1 TATCAATGATTTACTACTAAAC
* * * * *
5450777 TATGAATGATTTGCCATTAAAT
1 TATCAATGATTTACTACTAAAC
*
5450799 TATCAATGATTT-CTATTAAA
1 TATCAATGATTTACTACTAAA
5450819 TTATTGATAA
Statistics
Matches: 70, Mismatches: 16, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
21 7 0.10
22 63 0.90
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
TATCAATGATTTACTACTAAAC
Found at i:5451142 original size:21 final size:20
Alignment explanation
Indices: 5451085--5451144 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 20
5451075 AATTATACCA
5451085 ATTTATCATTAAATTATTTATG
1 ATTTAT-ATTAAATTA-TTATG
* * *
5451107 GTTCACTACTAAATTATTACTG
1 ATTTA-TATTAAATTATTA-TG
5451129 ATTTATATTAAATTAT
1 ATTTATATTAAATTAT
5451145 GTGTGACTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 13 0.43
22 16 0.53
23 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTTATATTAAATTATTATG
Found at i:5451288 original size:22 final size:21
Alignment explanation
Indices: 5451238--5451308 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
5451228 TTTTATGATA
*
5451238 ACTATTAAATTATAATTATTT
1 ACTACTAAATTATAATTATTT
* *
5451259 ATTACTAAATTATCATTAATTT
1 ACTACTAAATTATAATT-ATTT
* * * *
5451281 ACTGCTAAGTTATTTATAATTT
1 ACTACTAAATTA-TAATTATTT
5451303 ACTACT
1 ACTACT
5451309 GTCAATTAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 14 0.36
22 22 0.56
23 3 0.08
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (21 bp):
ACTACTAAATTATAATTATTT
Found at i:5451606 original size:21 final size:22
Alignment explanation
Indices: 5451514--5451617 Score: 77
Period size: 22 Copynumber: 4.8 Consensus size: 22
5451504 GGTATTATAC
* *
5451514 ATTTATTATTATA-TTATTACTA
1 ATTTACTATTA-AGTTATCACTA
** * * *
5451536 ATTTACTAAAAAGTTATTAATT
1 ATTTACTATTAAGTTATCACTA
* * * *
5451558 ATTAACTATTAAATTATCATTC
1 ATTTACTATTAAGTTATCACTA
5451580 ATTTACTATTAAGTT-TCACTA
1 ATTTACTATTAAGTTATCACTA
*
5451601 ATTTACTACTAAGTTAT
1 ATTTACTATTAAGTTAT
5451618 TGATAATTAT
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
21 19 0.30
22 44 0.70
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (22 bp):
ATTTACTATTAAGTTATCACTA
Found at i:5457280 original size:29 final size:29
Alignment explanation
Indices: 5457241--5457301 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
5457231 TTCAAGTACA
* *
5457241 TTATACTATTAATGAGTATCTCAGTAATC
1 TTATACCATTAATAAGTATCTCAGTAATC
5457270 TTATACCATTAATAAGTATCTCAGTAATC
1 TTATACCATTAATAAGTATCTCAGTAATC
5457299 TTA
1 TTA
5457302 CTGCTTTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (29 bp):
TTATACCATTAATAAGTATCTCAGTAATC
Found at i:5460101 original size:29 final size:28
Alignment explanation
Indices: 5460061--5460158 Score: 86
Period size: 28 Copynumber: 3.7 Consensus size: 28
5460051 ATTTTTTATT
5460061 TTAAGTTT-ATAATATTTTAATATTAAATA
1 TTAA-TTTAATAATATTTT-ATATTAAATA
5460090 TTAATTTAATAATA---T-TA-T-AATA
1 TTAATTTAATAATATTTTATATTAAATA
*
5460112 TT-ATTTGAATAATATTTTGTATTAAATA
1 TTAATTT-AATAATATTTTATATTAAATA
* *
5460140 TTAATTTAATGAGATTTTA
1 TTAATTTAATAATATTTTA
5460159 ATATAATTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
21 4 0.07
22 13 0.23
23 1 0.02
24 2 0.04
25 1 0.02
26 3 0.05
27 1 0.02
28 18 0.32
29 14 0.25
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (28 bp):
TTAATTTAATAATATTTTATATTAAATA
Found at i:5460109 original size:8 final size:8
Alignment explanation
Indices: 5460067--5460115 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
5460057 TATTTTAAGT
5460067 TTATAATA
1 TTATAATA
*
5460075 TTTTAATA
1 TTATAATA
5460083 TTA-AATA
1 TTATAATA
5460090 -T-TAAT-
1 TTATAATA
5460095 TTAATAATA
1 TT-ATAATA
5460104 TTATAATA
1 TTATAATA
5460112 TTAT
1 TTAT
5460116 TTGAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
6 5 0.15
7 4 0.12
8 23 0.68
9 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTATAATA
Found at i:5460110 original size:11 final size:10
Alignment explanation
Indices: 5460069--5460128 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 10
5460059 TTTTAAGTTT
5460069 ATAATATTT-
1 ATAATATTTA
*
5460078 -TAATATTAA
1 ATAATATTTA
*
5460087 ATATTAATTTA
1 ATAAT-ATTTA
5460098 ATAATATTATA
1 ATAATATT-TA
*
5460109 ATATTATTTGA
1 ATAATATTT-A
5460120 ATAATATTT
1 ATAATATTT
5460129 TGTATTAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 7 0.17
10 7 0.17
11 26 0.65
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (10 bp):
ATAATATTTA
Found at i:5460140 original size:50 final size:51
Alignment explanation
Indices: 5460069--5460167 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 51
5460059 TTTTAAGTTT
* *
5460069 ATAATATTTTAATATTAAATATTAATTTAATAATATTATAATATTATTTGA
1 ATAATATTTTAATATTAAATATTAATTTAATAAGATTATAATATAATTTGA
* * *
5460120 ATAATATTTT-GTATTAAATATTAATTTAATGAGATTTTAATATAATTT
1 ATAATATTTTAATATTAAATATTAATTTAATAAGATTATAATATAATTT
5460168 TAAATTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 33 0.77
51 10 0.23
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (51 bp):
ATAATATTTTAATATTAAATATTAATTTAATAAGATTATAATATAATTTGA
Found at i:5460213 original size:8 final size:8
Alignment explanation
Indices: 5460202--5460240 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
5460192 ATATTTTACT
5460202 ATTATTTA
1 ATTATTTA
5460210 ATTATTTA
1 ATTATTTA
5460218 ATTATTATA
1 ATTATT-TA
5460227 ATTTAATTTA
1 A-TT-ATTTA
5460237 ATTA
1 ATTA
5460241 ATATAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 15 0.54
9 5 0.18
10 5 0.18
11 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
ATTATTTA
Found at i:5460223 original size:27 final size:25
Alignment explanation
Indices: 5460174--5460250 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 25
5460164 ATTTTAAATT
*
5460174 ATTTATTTAATTTATATAATATTTTA
1 ATTTATTTAA-TTATATAATATTATA
* *
5460200 CTATTATTTAATTATTTAATTATTATA
1 AT-TTATTTAATTATATAA-TATTATA
5460227 ATTTAATTTAATTAATATAA-ATTA
1 ATTT-ATTTAATT-ATATAATATTA
5460251 ATTATCTGAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 14 0.33
27 23 0.55
28 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTATTTAATTATATAATATTATA
Found at i:5460235 original size:19 final size:18
Alignment explanation
Indices: 5460202--5460253 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
5460192 ATATTTTACT
5460202 ATTATT-TAATT-ATTTA
1 ATTATTATAATTAATTTA
5460218 ATTATTATAATTTAATTTA
1 ATTATTATAA-TTAATTTA
*
5460237 ATTAATATAAATTAATT
1 ATTATTAT-AATTAATT
5460254 ATCTGATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
16 6 0.19
17 3 0.10
18 2 0.06
19 18 0.58
20 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTATAATTAATTTA
Found at i:5460242 original size:14 final size:14
Alignment explanation
Indices: 5460205--5460254 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
5460195 TTTTACTATT
5460205 ATTTAATT-ATTTA
1 ATTTAATTAATTTA
*
5460218 A-TTATTATAATTTA
1 ATTTAAT-TAATTTA
*
5460232 ATTTAATTAATATA
1 ATTTAATTAATTTA
*
5460246 AATTAATTA
1 ATTTAATTA
5460255 TCTGATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 4 0.13
13 2 0.07
14 20 0.67
15 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTTAATTAATTTA
Found at i:5461289 original size:18 final size:18
Alignment explanation
Indices: 5461268--5461302 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5461258 GATTATTTAA
*
5461268 AATAATTTAATAATTTTT
1 AATAACTTAATAATTTTT
*
5461286 AATAACTTATTAATTTT
1 AATAACTTAATAATTTT
5461303 ATAAATGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAACTTAATAATTTTT
Found at i:5461843 original size:12 final size:13
Alignment explanation
Indices: 5461826--5461855 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5461816 ATAAATTTAT
5461826 TATATTTTAA-AA
1 TATATTTTAATAA
5461838 TATATTTTAATAA
1 TATATTTTAATAA
5461851 TATAT
1 TATAT
5461856 ATGAGGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATTTTAATAA
Found at i:5462225 original size:65 final size:65
Alignment explanation
Indices: 5462160--5462289 Score: 154
Period size: 70 Copynumber: 1.9 Consensus size: 65
5462150 AATATTAATA
*
5462160 AATATTAACAATTTAATTT-TGATTTTGCTATAATATAAGTAAAATTTGGTATACTTTTGATAAT
1 AATA-TAACAATTTAATTTAT-A-TTTGCTATAATATAAATAAAATTT-G-ATACTTTTGATAAT
5462224 AATGAT
61 AA-GAT
* *
5462230 AAATAATAACAATTTAATTTATATTTGTTATACTATAAATAAAATTTGATACTTTTGATA
1 -AAT-ATAACAATTTAATTTATATTTGCTATAATATAAATAAAATTTGATACTTTTGATA
5462290 TAATTTTGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
68 12 0.22
69 1 0.02
70 21 0.39
71 18 0.33
72 2 0.04
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (65 bp):
AATATAACAATTTAATTTATATTTGCTATAATATAAATAAAATTTGATACTTTTGATAATAAGAT
Found at i:5462298 original size:11 final size:11
Alignment explanation
Indices: 5462282--5462347 Score: 55
Period size: 11 Copynumber: 5.7 Consensus size: 11
5462272 AATTTGATAC
5462282 TTTTGATATAA
1 TTTTGATATAA
5462293 TTTTGATTTAATAA
1 TTTTGA--T-ATAA
*
5462307 CTTTTGATAAAA
1 -TTTTGATATAA
5462319 TTTT-A-ATAA
1 TTTTGATATAA
*
5462328 CTTTTGATACAA
1 -TTTTGATATAA
5462340 TTTTGATA
1 TTTTGATA
5462348 ACCGTCAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
9 3 0.07
10 5 0.11
11 19 0.42
12 6 0.13
13 2 0.04
14 4 0.09
15 6 0.13
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.52
Consensus pattern (11 bp):
TTTTGATATAA
Found at i:5462307 original size:68 final size:71
Alignment explanation
Indices: 5462146--5462293 Score: 198
Period size: 71 Copynumber: 2.1 Consensus size: 71
5462136 TTTTATACTA
* * * *
5462146 TGATAATATTAATAAATATTAACAATTTAATTTTGATTTTGCTATAATATAAGTAAAATTTGGTA
1 TGATAATAATGATAAATAATAACAATTTAATTTTGATTTTGCTATAATATAAATAAAATTTGGTA
5462211 TACTTT
66 TACTTT
* *
5462217 TGATAATAATGATAAATAATAACAATTTAA-TTT-ATATTTGTTATACTATAAATAAAATTT-G-
1 TGATAATAATGATAAATAATAACAATTTAATTTTGAT-TTTGCTATAATATAAATAAAATTTGGT
5462278 ATACTTT
65 ATACTTT
5462285 TGAT-ATAAT
1 TGATAATAAT
5462294 TTTGATTTAA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
67 5 0.07
68 11 0.16
69 3 0.04
70 24 0.34
71 27 0.39
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (71 bp):
TGATAATAATGATAAATAATAACAATTTAATTTTGATTTTGCTATAATATAAATAAAATTTGGTA
TACTTT
Found at i:5462323 original size:21 final size:21
Alignment explanation
Indices: 5462299--5462349 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
5462289 ATAATTTTGA
5462299 TTTAATAACTTTTGATAAAAT
1 TTTAATAACTTTTGATAAAAT
*
5462320 TTTAATAACTTTTGATACAAT
1 TTTAATAACTTTTGATAAAAT
*
5462341 TTTGATAAC
1 TTTAATAAC
5462350 CGTCAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
TTTAATAACTTTTGATAAAAT
Found at i:5462475 original size:22 final size:22
Alignment explanation
Indices: 5462428--5462481 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
5462418 TGATATGGTT
*
5462428 TTAATAACATTTTGGTAACTTA
1 TTAATAACATTTTGATAACTTA
*
5462450 -TAATATACTTTTTGATAA-TTA
1 TTAATA-ACATTTTGATAACTTA
5462471 TTAATAA-ATTT
1 TTAATAACATTT
5462482 GTATCATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 3 0.11
21 9 0.33
22 15 0.56
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (22 bp):
TTAATAACATTTTGATAACTTA
Found at i:5462871 original size:22 final size:22
Alignment explanation
Indices: 5462845--5462933 Score: 76
Period size: 22 Copynumber: 4.1 Consensus size: 22
5462835 GAATAATTCA
5462845 TACTAAGTTATAAATGATTTAT
1 TACTAAGTTATAAATGATTTAT
** *
5462867 TACTAA-TTATTGATGATTTAC
1 TACTAAGTTATAAATGATTTAT
* * *
5462888 TACTACGTTACT-AATTATTAAT
1 TACTAAGTTA-TAAATGATTTAT
*
5462910 TA-TAAAGTTATAACTGATTTAT
1 TACT-AAGTTATAAATGATTTAT
5462932 TA
1 TA
5462934 ATTAATTTTA
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
21 19 0.37
22 31 0.61
23 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (22 bp):
TACTAAGTTATAAATGATTTAT
Found at i:5462974 original size:66 final size:65
Alignment explanation
Indices: 5462849--5462975 Score: 150
Period size: 66 Copynumber: 1.9 Consensus size: 65
5462839 AATTCATACT
* * *
5462849 AAGTTATAAATGATTTATTACTAATTATTGATGATTTACTACTACGTTACTAATTATTAATTATA
1 AAGTTATAAATGATTTATTACTAATTATTGATGATTTACTACAAAGTTACTAATAATTAATTATA
* * * *
5462914 AAGTTATAACTGATTTATTAATTAATT-TT-ATCGTATTTACTACAAAGTTATTCATAATTAAT
1 AAGTTATAAATGATTTATT-ACTAATTATTGAT-G-ATTTACTACAAAGTTACTAATAATTAAT
5462976 AATTTAGACT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
64 2 0.04
65 21 0.40
66 29 0.56
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (65 bp):
AAGTTATAAATGATTTATTACTAATTATTGATGATTTACTACAAAGTTACTAATAATTAATTATA
Found at i:5463389 original size:22 final size:21
Alignment explanation
Indices: 5463341--5463401 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
5463331 TTAAGTTTCA
*
5463341 ATGATTAACTACTAAATCATT
1 ATGATTTACTACTAAATCATT
* *
5463362 ATTGATTTACTACTAAGTTATTT
1 A-TGATTTACTACTAAATCA-TT
* *
5463385 ATGATCTACAACTAAAT
1 ATGATTTACTACTAAAT
5463402 TTATCAAGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 1 0.03
22 28 0.88
23 3 0.09
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (21 bp):
ATGATTTACTACTAAATCATT
Found at i:5463487 original size:21 final size:22
Alignment explanation
Indices: 5463441--5463510 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
5463431 TGACTTATTG
* *
5463441 TTAAGTTATCACTAATTTACTA
1 TTAAGTTATCAATGATTTACTA
*
5463463 TTAAGTTATTAATGATTTA-TA
1 TTAAGTTATCAATGATTTACTA
*
5463484 TTAAGTTATCAATGATTAACTA
1 TTAAGTTATCAATGATTTACTA
5463506 TTAAG
1 TTAAG
5463511 CTTTTATTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 19 0.45
22 23 0.55
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.46
Consensus pattern (22 bp):
TTAAGTTATCAATGATTTACTA
Found at i:5463833 original size:22 final size:22
Alignment explanation
Indices: 5463808--5463915 Score: 92
Period size: 22 Copynumber: 5.0 Consensus size: 22
5463798 AAAATTAAGT
* **
5463808 TATCAGTGATTTACTGTTAAAC
1 TATCAATGATTTACTACTAAAC
*
5463830 TATCAATAATTTACTACTAAAC
1 TATCAATGATTTACTACTAAAC
* **
5463852 TATCAATGATTTATTACTAATT
1 TATCAATGATTTACTACTAAAC
* * * * *
5463874 TATGAATGATTTGCCATTAAAT
1 TATCAATGATTTACTACTAAAC
*
5463896 TATCAATGATTT-CTATTAAA
1 TATCAATGATTTACTACTAAA
5463916 TTATTGATAA
Statistics
Matches: 70, Mismatches: 16, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
21 7 0.10
22 63 0.90
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (22 bp):
TATCAATGATTTACTACTAAAC
Found at i:5464099 original size:22 final size:22
Alignment explanation
Indices: 5464019--5464100 Score: 55
Period size: 22 Copynumber: 3.9 Consensus size: 22
5464009 TAAATTACTG
* *
5464019 CTAAATTATCATTGATTTGTAA
1 CTAAATTATCAATGATTTATAA
* * * * *
5464041 TTAAATTATTAGTAATTTACTAT
1 CTAAATTATCAATGATTTA-TAA
*
5464064 C-AAGTTATC-A--ATTTATAA
1 CTAAATTATCAATGATTTATAA
5464082 CTAAATTATCAATGATTTA
1 CTAAATTATCAATGATTTA
5464101 CTATTATATT
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
18 3 0.07
19 12 0.28
20 1 0.02
22 25 0.58
23 2 0.05
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (22 bp):
CTAAATTATCAATGATTTATAA
Found at i:5464369 original size:22 final size:22
Alignment explanation
Indices: 5464344--5464410 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
5464334 GATTAACTAT
5464344 TAAATTATTAATTATTTATTAC
1 TAAATTATTAATTATTTATTAC
* * *
5464366 TAAATTA-TCATTAATTTACTGC
1 TAAATTATTAATT-ATTTATTAC
* * *
5464388 TAAGTTATTTATAATTTATTAC
1 TAAATTATTAATTATTTATTAC
5464410 T
1 T
5464411 GTCAATTAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
21 4 0.11
22 28 0.80
23 3 0.09
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (22 bp):
TAAATTATTAATTATTTATTAC
Found at i:5464708 original size:21 final size:22
Alignment explanation
Indices: 5464616--5464719 Score: 77
Period size: 22 Copynumber: 4.8 Consensus size: 22
5464606 GGTATTATAC
* *
5464616 ATTTATTATTATA-TTATTACTA
1 ATTTACTATTA-AGTTATCACTA
** * * *
5464638 ATTTACTAAAAAGTTATTAATT
1 ATTTACTATTAAGTTATCACTA
* * * *
5464660 ATTAACTATTAAATTATCATTC
1 ATTTACTATTAAGTTATCACTA
5464682 ATTTACTATTAAGTT-TCACTA
1 ATTTACTATTAAGTTATCACTA
*
5464703 ATTTACTACTAAGTTAT
1 ATTTACTATTAAGTTAT
5464720 TGATAATTAT
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
21 19 0.30
22 44 0.70
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (22 bp):
ATTTACTATTAAGTTATCACTA
Found at i:5470443 original size:29 final size:29
Alignment explanation
Indices: 5470404--5470464 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
5470394 TTCAAGTACA
* *
5470404 TTATACTATTAATGAGTATCTCAGTAATC
1 TTATACCATTAATAAGTATCTCAGTAATC
5470433 TTATACCATTAATAAGTATCTCAGTAATC
1 TTATACCATTAATAAGTATCTCAGTAATC
5470462 TTA
1 TTA
5470465 CTGCTTTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (29 bp):
TTATACCATTAATAAGTATCTCAGTAATC
Found at i:5471235 original size:2 final size:2
Alignment explanation
Indices: 5471228--5471257 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5471218 AGGGAATGCG
5471228 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
5471258 CAGTTTACAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5478967 original size:15 final size:15
Alignment explanation
Indices: 5478947--5478976 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5478937 GATAAGAGTT
*
5478947 AAATTTATTTTTTAA
1 AAATTTATATTTTAA
5478962 AAATTTATATTTTAA
1 AAATTTATATTTTAA
5478977 TAAAATAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AAATTTATATTTTAA
Found at i:5479176 original size:16 final size:16
Alignment explanation
Indices: 5479155--5479189 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5479145 AGCTAAAATT
*
5479155 ATTTTTATAAAAAGTG
1 ATTTTTAAAAAAAGTG
5479171 ATTTTTAAAAAAAGTG
1 ATTTTTAAAAAAAGTG
5479187 ATT
1 ATT
5479190 AATTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (16 bp):
ATTTTTAAAAAAAGTG
Found at i:5482306 original size:34 final size:35
Alignment explanation
Indices: 5482247--5482316 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
5482237 ATTATGGTAT
* *
5482247 TAAAAATAATATTATTAATATAATATATATTAATA
1 TAAAAATAATATTAATAATAAAATATATATTAATA
* *
5482282 TAAAATTAA-ATTAATAATAAAATATATATTTATA
1 TAAAAATAATATTAATAATAAAATATATATTAATA
5482316 T
1 T
5482317 CATGGATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 23 0.74
35 8 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (35 bp):
TAAAAATAATATTAATAATAAAATATATATTAATA
Found at i:5488401 original size:18 final size:18
Alignment explanation
Indices: 5488378--5488438 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
5488368 TCATCTTATT
5488378 TTTGTTATAAGCTTTTAC
1 TTTGTTATAAGCTTTTAC
**
5488396 TTTGTTATAA-AATTTA-
1 TTTGTTATAAGCTTTTAC
5488412 --TGTTATAAGCTTTTAC
1 TTTGTTATAAGCTTTTAC
5488428 TTTGTTATAAG
1 TTTGTTATAAG
5488439 TAAGAGTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 8 0.23
15 4 0.11
17 4 0.11
18 19 0.54
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTGTTATAAGCTTTTAC
Found at i:5488421 original size:32 final size:32
Alignment explanation
Indices: 5488375--5488437 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
5488365 TTGTCATCTT
*
5488375 ATTTTTGTTATAAGCTTTTACTTTGTTATAAA
1 ATTTATGTTATAAGCTTTTACTTTGTTATAAA
5488407 ATTTATGTTATAAGCTTTTACTTTGTTATAA
1 ATTTATGTTATAAGCTTTTACTTTGTTATAA
5488438 GTAAGAGTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.56
Consensus pattern (32 bp):
ATTTATGTTATAAGCTTTTACTTTGTTATAAA
Found at i:5489177 original size:41 final size:42
Alignment explanation
Indices: 5489119--5489203 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
5489109 AATATGCTTA
*
5489119 AATAATAGAAAACCCTAACTACAAATTGGAGCAACTAAGAAC
1 AATAATAGAAAACCCTAACTACAAATTGGACCAACTAAGAAC
* * * * *
5489161 AATAGTAG-AAACCCTAACTATAATTTTGACCAATTAAGAAC
1 AATAATAGAAAACCCTAACTACAAATTGGACCAACTAAGAAC
5489202 AA
1 AA
5489204 AAACAGAAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 30 0.81
42 7 0.19
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.21
Consensus pattern (42 bp):
AATAATAGAAAACCCTAACTACAAATTGGACCAACTAAGAAC
Found at i:5489243 original size:54 final size:56
Alignment explanation
Indices: 5489158--5489262 Score: 151
Period size: 54 Copynumber: 1.9 Consensus size: 56
5489148 AGCAACTAAG
* *
5489158 AACAATAGTAGAAACCCTAACTATAATTTTGACCAATTAAGAACAAAAACAGAAGC
1 AACAATAGTAGAAACCCTAAATATAAATTTGACCAATTAAGAACAAAAACAGAAGC
* * *
5489214 AACAATAG-A-AAACCTTAAATATAAATTTGAGCAATTAAGAACAACAACA
1 AACAATAGTAGAAACCCTAAATATAAATTTGACCAATTAAGAACAAAAACA
5489263 AAAAATCTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 35 0.80
55 1 0.02
56 8 0.18
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.20
Consensus pattern (56 bp):
AACAATAGTAGAAACCCTAAATATAAATTTGACCAATTAAGAACAAAAACAGAAGC
Found at i:5490207 original size:24 final size:24
Alignment explanation
Indices: 5490180--5490250 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 24
5490170 CAAATATCAC
5490180 ATAATAAAAATATGCCAAAATATT
1 ATAATAAAAATATGCCAAAATATT
*
5490204 ATAATAAAAATCAT-ACAAAA-A--
1 ATAATAAAAAT-ATGCCAAAATATT
*
5490225 ATGAA-AAAAATATGCAAAAATATT
1 AT-AATAAAAATATGCCAAAATATT
5490249 AT
1 AT
5490251 GCAAATAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 3 0.08
23 1 0.03
24 18 0.47
25 2 0.05
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.25
Consensus pattern (24 bp):
ATAATAAAAATATGCCAAAATATT
Found at i:5490410 original size:26 final size:27
Alignment explanation
Indices: 5490351--5490436 Score: 124
Period size: 26 Copynumber: 3.3 Consensus size: 27
5490341 ATTAATTATC
5490351 CATGC-AA-AAATATCATAATAAAAAT
1 CATGCAAATAAATATCATAATAAAAAT
* * *
5490376 CATGTAAATAAATATTATAA-AAACAT
1 CATGCAAATAAATATCATAATAAAAAT
5490402 CATGCAAATAAATATCATAATAAAAAT
1 CATGCAAATAAATATCATAATAAAAAT
5490429 CATGCAAA
1 CATGCAAA
5490437 CATATTATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.08
26 25 0.48
27 23 0.44
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.26
Consensus pattern (27 bp):
CATGCAAATAAATATCATAATAAAAAT
Found at i:5490425 original size:12 final size:12
Alignment explanation
Indices: 5490358--5490431 Score: 51
Period size: 12 Copynumber: 5.8 Consensus size: 12
5490348 ATCCATGCAA
5490358 AAATATCATAAT
1 AAATATCATAAT
*
5490370 AAAAATCATGTAAAT
1 AAATATCA--T-AAT
*
5490385 AAATATTATAA-
1 AAATATCATAAT
*
5490396 AAACATCATGCAAAT
1 AAATATCAT---AAT
5490411 AAATATCATAAT
1 AAATATCATAAT
*
5490423 AAAAATCAT
1 AAATATCAT
5490432 GCAAACATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
11 7 0.15
12 20 0.42
13 1 0.02
14 3 0.06
15 17 0.35
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.28
Consensus pattern (12 bp):
AAATATCATAAT
Found at i:5491902 original size:17 final size:17
Alignment explanation
Indices: 5491873--5491916 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
5491863 AAAATTGAAT
5491873 ATAATAA-ATAATAAAA
1 ATAATAATATAATAAAA
*
5491889 ACTAA-AATATAATAATA
1 A-TAATAATATAATAAAA
5491906 ATAATAATATA
1 ATAATAATATA
5491917 TAATTTTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAATATAATAAAA
Found at i:5492397 original size:9 final size:9
Alignment explanation
Indices: 5492365--5492397 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
5492355 AACAGGTGGT
5492365 AAAAAATATA
1 AAAAAAT-TA
5492375 AAAAAATT-
1 AAAAAATTA
5492383 AAAAAATTA
1 AAAAAATTA
5492392 AAAAAA
1 AAAAAA
5492398 AAGTGGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 7 0.32
10 7 0.32
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAAAATTA
Found at i:5492398 original size:18 final size:18
Alignment explanation
Indices: 5492364--5492397 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
5492354 CAACAGGTGG
5492364 TAAAAAATATAAAAAAAT
1 TAAAAAATATAAAAAAAT
5492382 TAAAAAAT-TAAAAAAA
1 TAAAAAATATAAAAAAA
5492398 AAGTGGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
TAAAAAATATAAAAAAAT
Found at i:5495390 original size:21 final size:22
Alignment explanation
Indices: 5495365--5495408 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5495355 CATGTTATTC
*
5495365 ATTCATAC-TATGGTTTATTTA
1 ATTCATACTTATGCTTTATTTA
5495386 ATTCATACTTATGCTTTATTTA
1 ATTCATACTTATGCTTTATTTA
5495408 A
1 A
5495409 ATTACATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (22 bp):
ATTCATACTTATGCTTTATTTA
Found at i:5495833 original size:18 final size:18
Alignment explanation
Indices: 5495810--5495846 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5495800 TCTCACCCTA
**
5495810 TTCTTTTTTTCTTTTCTT
1 TTCTTTTTTGATTTTCTT
5495828 TTCTTTTTTGATTTTCTT
1 TTCTTTTTTGATTTTCTT
5495846 T
1 T
5495847 ATGTTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (18 bp):
TTCTTTTTTGATTTTCTT
Found at i:5498122 original size:20 final size:22
Alignment explanation
Indices: 5498082--5498122 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5498072 GGTAACCTAA
5498082 GTTTTAATTTTCTTAGTTATTT
1 GTTTTAATTTTCTTAGTTATTT
5498104 GTTTTAATTTT-TT-GTTATT
1 GTTTTAATTTTCTTAGTTATT
5498123 AGGACAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 2 0.11
22 11 0.58
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (22 bp):
GTTTTAATTTTCTTAGTTATTT
Found at i:5503725 original size:93 final size:92
Alignment explanation
Indices: 5503624--5503899 Score: 213
Period size: 93 Copynumber: 3.1 Consensus size: 92
5503614 ATAACTATCC
5503624 ATCAGTATAAGTATGCTATATACTGACACTTACCTATATTGACGATCAAATTATATAAGTAAAAA
1 ATCAGTATAAGTATG-TATATACTGACACTTACCTATATTGACGATCAAATTATATAAGTAAAAA
5503689 GTATCTATACTGATGAATTTTTGTTACT
65 GTATCTATACTGATGAATTTTTGTTACT
* * * * *** *
5503717 ATCAGTAT-AGACAGTGTCTATAC-CA-AC--A-C--T-TTGTACAATCATCGT-TATAGGTAAA
1 ATCAGTATAAG-TA-TGTATATACTGACACTTACCTATATTG-ACGATCAAATTATATAAGTAAA
*** * * * ***
5503772 TTTTTTCT-GAC-GGT-ATATAAATGTT--T
63 AAGTATCTATACTGATGA-ATTTTTGTTACT
* * *
5503798 GTCAGTATAAGTATATTATATACTGACACTTACCTATATTGACGGTCAAATTATATAAGTAAAAA
1 ATCAGTATAAGTAT-GTATATACTGACACTTACCTATATTGACGATCAAATTATATAAGTAAAAA
5503863 GTATCTATACTGATGAATTTTTGTTACT
65 GTATCTATACTGATGAATTTTTGTTACT
5503891 ATCAGTATA
1 ATCAGTATA
5503900 GACAGTGTCT
Statistics
Matches: 125, Mismatches: 38, Indels: 40
0.62 0.19 0.20
Matches are distributed among these distances:
80 1 0.01
81 15 0.12
82 4 0.03
83 10 0.08
84 2 0.02
85 17 0.14
86 9 0.07
88 8 0.06
89 17 0.14
90 2 0.02
91 10 0.08
92 4 0.03
93 24 0.19
94 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (92 bp):
ATCAGTATAAGTATGTATATACTGACACTTACCTATATTGACGATCAAATTATATAAGTAAAAAG
TATCTATACTGATGAATTTTTGTTACT
Found at i:5503822 original size:174 final size:173
Alignment explanation
Indices: 5503561--5503999 Score: 707
Period size: 174 Copynumber: 2.5 Consensus size: 173
5503551 TATATCATAC
* * * * ** * * * * ***
5503561 CTATACCAGCACTTTATACAACCATCGGTATAAATAAACTTTTCTGATGGTATATAACTATCCAT
1 CTATACCAACACTTTGTACAATCATCGTTATAGGTAAATTTTTCTGACGGTATATAAATGTTTGT
**
5503626 CAGTATAAGTATGCTATATACTGACACTTACCTATATTGACGATCAAATTATATAAGTAAAAAGT
66 CAGTATAAGTATATTATATACTGACACTTACCTATATTGACGATCAAATTATATAAGTAAAAAGT
5503691 ATCTATACTGATGAATTTTTGTTACTATCAGTATAGACAGTGT
131 ATCTATACTGATGAATTTTTGTTACTATCAGTATAGACAGTGT
5503734 CTATACCAACACTTTGTACAATCATCGTTATAGGTAAATTTTTTCTGACGGTATATAAATGTTTG
1 CTATACCAACACTTTGTACAATCATCGTTATAGGTAAA-TTTTTCTGACGGTATATAAATGTTTG
*
5503799 TCAGTATAAGTATATTATATACTGACACTTACCTATATTGACGGTCAAATTATATAAGTAAAAAG
65 TCAGTATAAGTATATTATATACTGACACTTACCTATATTGACGATCAAATTATATAAGTAAAAAG
5503864 TATCTATACTGATGAATTTTTGTTACTATCAGTATAGACAGTGT
130 TATCTATACTGATGAATTTTTGTTACTATCAGTATAGACAGTGT
*
5503908 CTATACCAACACTTTGTACAATTATCGTTATAGGTAAACTTTTTCTGACGGTATATAAATGTTTG
1 CTATACCAACACTTTGTACAATCATCGTTATAGGTAAA-TTTTTCTGACGGTATATAAATGTTTG
5503973 TCAGTATAAGTATATTATATACTGACA
65 TCAGTATAAGTATATTATATACTGACA
5504000 GTTATAACAC
Statistics
Matches: 247, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
173 32 0.13
174 215 0.87
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (173 bp):
CTATACCAACACTTTGTACAATCATCGTTATAGGTAAATTTTTCTGACGGTATATAAATGTTTGT
CAGTATAAGTATATTATATACTGACACTTACCTATATTGACGATCAAATTATATAAGTAAAAAGT
ATCTATACTGATGAATTTTTGTTACTATCAGTATAGACAGTGT
Found at i:5503985 original size:87 final size:87
Alignment explanation
Indices: 5503720--5503986 Score: 199
Period size: 87 Copynumber: 3.1 Consensus size: 87
5503710 TGTTACTATC
*
5503720 AGTATAGACAGTGTCTATACCAACACTTTGTACAATCATCGTTATAGGTAAATTTTTTCTGACGG
1 AGTATAGACAGTGTCTATACCAACACTTTGTACAATCATCGTTATAGGTAAAATTTTTCTGACGG
5503785 TATATAAATGTTTGTCAGTATA
66 TATATAAATGTTTGTCAGTATA
* * * * ** ** *** * ** *
5503807 AGTATATTATA-T-ACTGACACTTAC-CTATAT-TGACGGTCAAATTATATAAGTAAAAAGTATC
1 AGTATA-GACAGTGTCT-ATACCAACACT-T-TGT-ACAATCATCGT-TATAGGTAAAATTTTTC
* * * * *
5503868 T-A---TACTGATGAATTTTTGTTACTATC
60 TGACGGTA-T-ATAAATGTTTGTCAGTATA
* *
5503894 AGTATAGACAGTGTCTATACCAACACTTTGTACAATTATCGTTATAGGTAAACTTTTTCTGACGG
1 AGTATAGACAGTGTCTATACCAACACTTTGTACAATCATCGTTATAGGTAAAATTTTTCTGACGG
5503959 TATATAAATGTTTGTCAGTATA
66 TATATAAATGTTTGTCAGTATA
5503981 AGTATA
1 AGTATA
5503987 TTATATACTG
Statistics
Matches: 121, Mismatches: 43, Indels: 32
0.62 0.22 0.16
Matches are distributed among these distances:
85 15 0.12
86 14 0.12
87 62 0.51
88 15 0.12
89 15 0.12
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (87 bp):
AGTATAGACAGTGTCTATACCAACACTTTGTACAATCATCGTTATAGGTAAAATTTTTCTGACGG
TATATAAATGTTTGTCAGTATA
Found at i:5505263 original size:15 final size:16
Alignment explanation
Indices: 5505239--5505270 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5505229 TAAAAAAATA
5505239 TTATTAAAAACATTTT
1 TTATTAAAAACATTTT
5505255 TTATTAAAAACATTTT
1 TTATTAAAAACATTTT
5505271 AAATAATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TTATTAAAAACATTTT
Found at i:5505263 original size:60 final size:60
Alignment explanation
Indices: 5505141--5505288 Score: 165
Period size: 60 Copynumber: 2.5 Consensus size: 60
5505131 TTTTTTATAA
** ** * **
5505141 AAAAACATCATAAATAAT-TTAAAAAAATAAAATGAGATTATTGAATGCATTTTTTGAAT
1 AAAAACATTTTAAATAATCTTAAAAAAATAAAAAAAGATTATTAAAAACATTTTTTGAAT
* * *
5505200 AAAAACGTTTTAAATAATCTTAAAAGAAATAAAAAAATATTATTAAAAACATTTTTT-ATT
1 AAAAACATTTTAAATAATCTTAAAA-AAATAAAAAAAGATTATTAAAAACATTTTTTGAAT
*
5505260 AAAAACATTTTAAATAATCTCAATAAAAA
1 AAAAACATTTTAAATAATCTTAA-AAAAA
5505289 CTTAAATTCT
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
59 15 0.20
60 32 0.43
61 27 0.36
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (60 bp):
AAAAACATTTTAAATAATCTTAAAAAAATAAAAAAAGATTATTAAAAACATTTTTTGAAT
Found at i:5507508 original size:24 final size:24
Alignment explanation
Indices: 5507468--5507516 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
5507458 AAATCATATC
* *
5507468 ATATTATGATTATAAATA-AATTA
1 ATATTATAATTAAAAATATAATTA
5507491 ATATTAATAATTAAAAATATAATTA
1 ATATT-ATAATTAAAAATATAATTA
5507516 A
1 A
5507517 AAAAAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 11 0.50
25 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
ATATTATAATTAAAAATATAATTA
Found at i:5508058 original size:8 final size:8
Alignment explanation
Indices: 5508045--5508077 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
5508035 CTTCAAAATT
*
5508045 TTTTTTTC
1 TTTTCTTC
5508053 TTTT-TTC
1 TTTTCTTC
5508060 TTTTCTTC
1 TTTTCTTC
5508068 TTTTCTTC
1 TTTTCTTC
5508076 TT
1 TT
5508078 CCTTTGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTCTTC
Found at i:5508082 original size:20 final size:21
Alignment explanation
Indices: 5508048--5508087 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5508038 CAAAATTTTT
* *
5508048 TTTTCTTTTTTCTTT-TCTTC
1 TTTTCTTCTTCCTTTGTCTTC
5508068 TTTTCTTCTTCCTTTGTCTT
1 TTTTCTTCTTCCTTTGTCTT
5508088 GTGTATATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTCTTCTTCCTTTGTCTTC
Found at i:5511922 original size:123 final size:123
Alignment explanation
Indices: 5511776--5512014 Score: 401
Period size: 124 Copynumber: 1.9 Consensus size: 123
5511766 ATCACATAAT
* *
5511776 TATTATTATTTTTTTTTTCTAGAATCAACCTTTTTA-GAATGTTAATAAAA-ATATATTAGTTTT
1 TATTACTATTTTTTTTTGCTAGAATCAACCTTTTTATG-ATGTTAATAAAATATATATTAGTTTT
* *
5511839 TAGCAGTTATATATACATATATTAATTTATGACAGAATGAGGCTTCTATGTCAAGCGAG
65 TAGCACTTATATATACATATATTAATTTATGACAGAATAAGGCTTCTATGTCAAGCGAG
5511898 TATTACTATTTTGTTTTTGCTAGAATCAACCTTTTTATGATGTTAATAAAATATATATTAGTTTT
1 TATTACTATTTT-TTTTTGCTAGAATCAACCTTTTTATGATGTTAATAAAATATATATTAGTTTT
*
5511963 TAGCACTTATATATACATATATTAATTTATGACAGAATAAGGTTTCTATGTC
65 TAGCACTTATATATACATATATTAATTTATGACAGAATAAGGCTTCTATGTC
5512015 CAAGTCTAAT
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
122 11 0.10
123 35 0.32
124 63 0.58
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (123 bp):
TATTACTATTTTTTTTTGCTAGAATCAACCTTTTTATGATGTTAATAAAATATATATTAGTTTTT
AGCACTTATATATACATATATTAATTTATGACAGAATAAGGCTTCTATGTCAAGCGAG
Found at i:5513387 original size:2 final size:2
Alignment explanation
Indices: 5513375--5513411 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
5513365 TACAATGTCT
5513375 TA TA CTA TA TA 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 TA TA TA TA TA
5513412 GTAAGAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5513750 original size:2 final size:2
Alignment explanation
Indices: 5513743--5513767 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5513733 TTGACCTATG
5513743 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5513768 CCATCTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5537692 original size:30 final size:31
Alignment explanation
Indices: 5537658--5537744 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
5537648 TATTTATCAG
*
5537658 TTGAATACTTAAACATCTATTCTCACT-CAA
1 TTGAATACTTAAACATCTATTTTCACTCCAA
* * * *
5537688 TTGAATTCATAAATATCTATTTTTACTCCAA
1 TTGAATACTTAAACATCTATTTTCACTCCAA
* * *
5537719 TTTAATCCTTAAACATCAATTTTCAC
1 TTGAATACTTAAACATCTATTTTCAC
5537745 CTCAGTTATG
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 22 0.49
31 23 0.51
ACGTcount: A:0.36, C:0.21, G:0.02, T:0.41
Consensus pattern (31 bp):
TTGAATACTTAAACATCTATTTTCACTCCAA
Found at i:5546047 original size:21 final size:20
Alignment explanation
Indices: 5546017--5546055 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5546007 CGTTTTATTC
*
5546017 TTTTATATTTATGACATTTCT
1 TTTTAAATTTA-GACATTTCT
5546038 TTTTAAATTTAGACATTT
1 TTTTAAATTTAGACATTT
5546056 TTGGCTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTAAATTTAGACATTTCT
Found at i:5550756 original size:3 final size:3
Alignment explanation
Indices: 5550750--5550823 Score: 52
Period size: 3 Copynumber: 25.3 Consensus size: 3
5550740 AATAACATGC
* *
5550750 AAT AAT AAT -AT AAT ACAT CAT GCAAT AAT AAT -AT AAT AAAT CAT AA-
1 AAT AAT AAT AAT AAT A-AT AAT --AAT AAT AAT AAT AAT -AAT AAT AAT
5550796 AAT AAT -AT AAT AAT -AT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5550824 TAAATTATCA
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
2 12 0.21
3 38 0.67
4 5 0.09
5 2 0.04
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5550764 original size:8 final size:8
Alignment explanation
Indices: 5550751--5550823 Score: 69
Period size: 8 Copynumber: 8.8 Consensus size: 8
5550741 ATAACATGCA
5550751 ATAATAAT
1 ATAATAAT
5550759 ATAATACAT
1 ATAATA-AT
5550768 CATGCAATAAT
1 -AT--AATAAT
5550779 A-ATATAAT
1 ATA-ATAAT
*
5550787 A-AATCAT
1 ATAATAAT
*
5550794 AAAATAAT
1 ATAATAAT
5550802 ATAATAAT
1 ATAATAAT
5550810 ATAATAAT
1 ATAATAAT
5550818 ATAATA
1 ATAATA
5550824 TAAATTATCA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
7 6 0.11
8 39 0.70
9 2 0.04
10 3 0.05
11 2 0.04
12 4 0.07
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.33
Consensus pattern (8 bp):
ATAATAAT
Found at i:5550773 original size:23 final size:22
Alignment explanation
Indices: 5550738--5550848 Score: 105
Period size: 23 Copynumber: 5.2 Consensus size: 22
5550728 CACAATGCAA
5550738 ATAATAA-CATGCAATAATAAT
1 ATAATAATCATGCAATAATAAT
5550759 ATAATACATCATGCAATAATAAT
1 ATAATA-ATCATGCAATAATAAT
5550782 ATAATAAATCAT--AA-AATAAT
1 ATAAT-AATCATGCAATAATAAT
5550802 ATAATAAT-AT--AATAATATAAT
1 ATAATAATCATGCAAT-A-ATAAT
*
5550823 ATAAATTATCATGCAAT--TAAT
1 AT-AATAATCATGCAATAATAAT
5550844 ATAAT
1 ATAAT
5550849 CATGCAATTA
Statistics
Matches: 79, Mismatches: 1, Indels: 21
0.78 0.01 0.21
Matches are distributed among these distances:
18 4 0.05
19 3 0.04
20 15 0.19
21 21 0.27
22 6 0.08
23 26 0.33
24 1 0.01
25 3 0.04
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (22 bp):
ATAATAATCATGCAATAATAAT
Found at i:5550787 original size:5 final size:5
Alignment explanation
Indices: 5550777--5550826 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
5550767 TCATGCAATA
*
5550777 ATAAT ATAAT A-AAT CATAAA ATAAT ATAAT A-ATAT AATAAT ATAAT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATA-AT -ATAAT ATAAT
5550823 ATAA
1 ATAA
5550827 ATTATCATGC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
4 4 0.11
5 28 0.74
6 5 0.13
7 1 0.03
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:5550978 original size:12 final size:13
Alignment explanation
Indices: 5550960--5550995 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
5550950 ATAAATACTA
5550960 CATATAAAAAAAT
1 CATATAAAAAAAT
5550973 -ATATAAAAAAAT
1 CATATAAAAAAAT
*
5550985 CAAATAAAAAA
1 CATATAAAAAA
5550996 TAAAAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (13 bp):
CATATAAAAAAAT
Found at i:5551002 original size:18 final size:19
Alignment explanation
Indices: 5550979--5551014 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
5550969 AAATATATAA
5550979 AAAAATCAAATAA-AAAAT
1 AAAAATCAAATAACAAAAT
5550997 AAAAATCAAATAACAAAA
1 AAAAATCAAATAACAAAA
5551015 AAAGTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (19 bp):
AAAAATCAAATAACAAAAT
Found at i:5552328 original size:43 final size:43
Alignment explanation
Indices: 5552240--5552376 Score: 168
Period size: 43 Copynumber: 3.2 Consensus size: 43
5552230 AAATGAATTA
* * * *
5552240 AGAAATGGGCT-CTTCTAAACAAAGGCTCAACAACTATAAACTG
1 AGAAATGGGCTCCTT-TAAACAGAGGCTAAACAACTTTAAAATG
* * *
5552283 AGATATGGGCTCCTTTAAACAGAGGTTAAAAAACTTTAAAATG
1 AGAAATGGGCTCCTTTAAACAGAGGCTAAACAACTTTAAAATG
* *
5552326 AGAAATGGGCTCATTTAAAGAGAGGCTAAACAACTTTAAAATG
1 AGAAATGGGCTCCTTTAAACAGAGGCTAAACAACTTTAAAATG
*
5552369 AAAAATGG
1 AGAAATGG
5552377 CTGGGACTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 77 0.96
44 3 0.04
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (43 bp):
AGAAATGGGCTCCTTTAAACAGAGGCTAAACAACTTTAAAATG
Found at i:5552591 original size:63 final size:63
Alignment explanation
Indices: 5552420--5552591 Score: 143
Period size: 63 Copynumber: 2.7 Consensus size: 63
5552410 GGACTTAGTT
* * * * * * *
5552420 AAGGTTAGAAATAAGTGATTGGAACTAAATCATAAGTCAAAATAATAAATAACTTGGATTGAGTC
1 AAGGTTA-AAATAAGTGATTGGGACTGAACCATAAGTTAAAA-AAGAAATAACCTAGATTGAGTC
* * * * * * *
5552485 GAGGTCAAAAGTAAGTGACTAGGATTGAACTGCA-AGGTT-AAAAAGAAA-GACCTAGATTGAGT
1 AAGGTTAAAA-TAAGTGATTGGGACTGAAC--CATAAGTTAAAAAAGAAATAACCTAGATTGAGT
5552547 C
63 C
5552548 AAGGTTGAAAATAAGTGATTGGGACTGAACCATAAGTTAAAAAA
1 AAGGTT-AAAATAAGTGATTGGGACTGAACCATAAGTTAAAAAA
5552592 ATAAATTATC
Statistics
Matches: 81, Mismatches: 20, Indels: 14
0.70 0.17 0.12
Matches are distributed among these distances:
61 2 0.02
62 4 0.05
63 37 0.46
64 12 0.15
65 21 0.26
66 3 0.04
67 2 0.02
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.24
Consensus pattern (63 bp):
AAGGTTAAAATAAGTGATTGGGACTGAACCATAAGTTAAAAAAGAAATAACCTAGATTGAGTC
Found at i:5553049 original size:33 final size:32
Alignment explanation
Indices: 5552975--5553090 Score: 117
Period size: 33 Copynumber: 3.5 Consensus size: 32
5552965 TCGTAAAAGT
* * *
5552975 TTCAGAATCACAAGAATGAAAATTTGCAAGAC
1 TTCAGATTCACAAGAATGAAGATTTGCAAGAA
* *
5553007 TTCAGATTCACAAGAATGGAAGATTTACAGGAA
1 TTCAGATTCACAAGAAT-GAAGATTTGCAAGAA
* *
5553040 TTCAGATTCATAAGAAATTCAAG-TTTGCAAGAGA
1 TTCAGATTCACAAG-AA-TGAAGATTTGCAAGA-A
*
5553074 TTCAAATTCACAAGAAT
1 TTCAGATTCACAAGAAT
5553091 TTCAAAGATT
Statistics
Matches: 69, Mismatches: 11, Indels: 8
0.78 0.12 0.09
Matches are distributed among these distances:
32 17 0.25
33 33 0.48
34 18 0.26
35 1 0.01
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (32 bp):
TTCAGATTCACAAGAATGAAGATTTGCAAGAA
Found at i:5553087 original size:17 final size:17
Alignment explanation
Indices: 5553038--5553096 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
5553028 GATTTACAGG
* *
5553038 AATTCAGATTCATAAGA
1 AATTCAAATTCACAAGA
* **
5553055 AATTCAAGTTTGCAAGA
1 AATTCAAATTCACAAGA
*
5553072 GATTCAAATTCACAAGA
1 AATTCAAATTCACAAGA
*
5553089 ATTTCAAA
1 AATTCAAA
5553097 GATTCGCAAA
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.29
Consensus pattern (17 bp):
AATTCAAATTCACAAGA
Found at i:5553284 original size:45 final size:45
Alignment explanation
Indices: 5553207--5553324 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 45
5553197 AAGTTCATAG
* * * *
5553207 CCAAAA-TTTAAATATTCTCATTTAAAGAATTTTGGGATTCACAT
1 CCAAAAGTTCAAAAATTCTCATTCAAAAAATTTTGGGATTCACAT
* * *
5553251 CTAGAGGTTCAAAAATTCTCATTCAAAAAATTTTGGGATTCACAT
1 CCAAAAGTTCAAAAATTCTCATTCAAAAAATTTTGGGATTCACAT
* * *
5553296 CCAAAATTTCAAAGATTCTCATTCTAAAA
1 CCAAAAGTTCAAAAATTCTCATTCAAAAA
5553325 GCTCCATATT
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
44 3 0.05
45 57 0.95
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (45 bp):
CCAAAAGTTCAAAAATTCTCATTCAAAAAATTTTGGGATTCACAT
Found at i:5558403 original size:23 final size:23
Alignment explanation
Indices: 5558365--5558428 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
5558355 TATCATGCAA
5558365 ATAATA-A-CATGAAATAATAAT
1 ATAATATATCATGAAATAATAAT
* *
5558386 ATAATGTATCATGCAATAATAAT
1 ATAATATATCATGAAATAATAAT
*
5558409 ATAATATATCATAAAATAAT
1 ATAATATATCATGAAATAAT
5558429 GTAATAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 5 0.14
22 1 0.03
23 30 0.83
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.33
Consensus pattern (23 bp):
ATAATATATCATGAAATAATAAT
Found at i:5558428 original size:20 final size:22
Alignment explanation
Indices: 5558377--5558434 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
5558367 AATAACATGA
*
5558377 AATAATAATATAATGTATCATGC
1 AATAATAATATAATATATCAT-C
5558400 AATAATAATATAATATATCAT-
1 AATAATAATATAATATATCATC
*
5558421 AA-AATAATGTAATA
1 AATAATAATATAATA
5558435 ATATAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 11 0.33
21 2 0.06
23 20 0.61
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (22 bp):
AATAATAATATAATATATCATC
Found at i:5558435 original size:23 final size:25
Alignment explanation
Indices: 5558409--5558470 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 25
5558399 CAATAATAAT
5558409 ATAATAT-ATCATAAA-ATAATGTA
1 ATAATATAATCATAAATATAATGTA
*
5558432 ATAATATAAT-ATAAATTATCATGTA
1 ATAATATAATCATAAA-TATAATGTA
5558457 ATAAATATAATCAT
1 AT-AATATAATCAT
5558471 GCAATTATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 12 0.36
24 2 0.06
25 9 0.27
26 8 0.24
27 2 0.06
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (25 bp):
ATAATATAATCATAAATATAATGTA
Found at i:5558608 original size:20 final size:20
Alignment explanation
Indices: 5558567--5558612 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
5558557 TCATGCAATT
* *
5558567 AAATAAATACTAAAATATAA
1 AAATAAATACTAAAAAACAA
5558587 AAATAATATA-TAAAAAAC-A
1 AAATAA-ATACTAAAAAACAA
5558606 AAATAAA
1 AAATAAA
5558613 AAAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.04
19 7 0.30
20 12 0.52
21 3 0.13
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (20 bp):
AAATAAATACTAAAAAACAA
Found at i:5558614 original size:13 final size:13
Alignment explanation
Indices: 5558577--5558625 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
5558567 AAATAAATAC
*
5558577 TAAAATATAAAAA
1 TAAAATAAAAAAA
*
5558590 TAATATATAAAAAA
1 TAAAATA-AAAAAA
*
5558604 CAAAATAAAAAAA
1 TAAAATAAAAAAA
5558617 TAAAA-AAAA
1 TAAAATAAAA
5558626 GTAAAAATCA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 4 0.13
13 16 0.53
14 10 0.33
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (13 bp):
TAAAATAAAAAAA
Found at i:5558838 original size:14 final size:14
Alignment explanation
Indices: 5558819--5558846 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5558809 TTCATCAAAC
5558819 TTGAAGAAGAAAAA
1 TTGAAGAAGAAAAA
5558833 TTGAAGAAGAAAAA
1 TTGAAGAAGAAAAA
5558847 GAGAACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.14
Consensus pattern (14 bp):
TTGAAGAAGAAAAA
Found at i:5558997 original size:71 final size:69
Alignment explanation
Indices: 5558848--5559004 Score: 167
Period size: 71 Copynumber: 2.2 Consensus size: 69
5558838 GAAGAAAAAG
* *
5558848 AGAACAAAAACAAAAAAAAATACTGCAGCAAACAGAACAGAAACCAGAGAAAAATACTACAGCAG
1 AGAACAGAAACCAAAAAAAATACTGCAGCAAACAGAACAGAAACCAGAGAAAAATACTACAGCAG
*
5558913 AAGC
66 AAAC
* * ** *
5558917 AGAATAGAAACCAGAAAAAAATATTGCAGCAGAAACAGAGTAGAAACCA-A-AAAATATACTGTC
1 AGAACAGAAACCA-AAAAAAATACTGCAGC--AAACAGAACAGAAACCAGAGAAAA-ATACT-AC
5558980 -GCAGAAAC
61 AGCAGAAAC
*
5558988 ATAACAGAAACCAAAAA
1 AGAACAGAAACCAAAAA
5559005 TTATACTACA
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
69 10 0.14
70 23 0.32
71 24 0.33
72 16 0.22
ACGTcount: A:0.59, C:0.17, G:0.15, T:0.09
Consensus pattern (69 bp):
AGAACAGAAACCAAAAAAAATACTGCAGCAAACAGAACAGAAACCAGAGAAAAATACTACAGCAG
AAAC
Found at i:5559021 original size:35 final size:36
Alignment explanation
Indices: 5558848--5559021 Score: 153
Period size: 36 Copynumber: 5.0 Consensus size: 36
5558838 GAAGAAAAAG
* * *
5558848 AGAACA-AAAACAAAAAAAAATACTGCAGC--AAAC
1 AGAACAGAAACCAGAAAAAAATACTACAGCAGAAAC
* *
5558881 AGAACAGAAACCAGAGAAAAATACTACAGCAGAAGC
1 AGAACAGAAACCAGAAAAAAATACTACAGCAGAAAC
* * *
5558917 AGAATAGAAACCAGAAAAAAATATTGCAGCAGAAAC
1 AGAACAGAAACCAGAAAAAAATACTACAGCAGAAAC
** * *
5558953 AGAGTAGAAACCA-AAAAATATACTGTC-GCAGAAAC
1 AGAACAGAAACCAGAAAAAAATACT-ACAGCAGAAAC
* ** *
5558988 ATAACAGAAACCA-AAAATTATACTACAGTAGAAA
1 AGAACAGAAACCAGAAAAAAATACTACAGCAGAAA
5559022 TTGGAAAGCA
Statistics
Matches: 116, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
33 6 0.05
34 20 0.17
35 43 0.37
36 47 0.41
ACGTcount: A:0.58, C:0.17, G:0.14, T:0.11
Consensus pattern (36 bp):
AGAACAGAAACCAGAAAAAAATACTACAGCAGAAAC
Found at i:5559676 original size:3 final size:3
Alignment explanation
Indices: 5559668--5559720 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
5559658 CCTTTTTTAC
* * * *
5559668 ATT ATT ATT ATT ATT ATT AGT ATT ATC ATT ATT TTT ATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5559716 ATT AT
1 ATT AT
5559721 AGGATTATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5560249 original size:14 final size:14
Alignment explanation
Indices: 5560232--5560291 Score: 86
Period size: 14 Copynumber: 4.4 Consensus size: 14
5560222 TCAAAATCCT
*
5560232 AAATTGAATCCCTA
1 AAATTGAAGCCCTA
*
5560246 AAATTGAAGCCTTA
1 AAATTGAAGCCCTA
5560260 AAATTGAAGCCCT-
1 AAATTGAAGCCCTA
*
5560273 AAATTGAAACCCTA
1 AAATTGAAGCCCTA
5560287 AAATT
1 AAATT
5560292 AAAATCTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.29
14 29 0.71
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (14 bp):
AAATTGAAGCCCTA
Found at i:5560249 original size:41 final size:41
Alignment explanation
Indices: 5560203--5560327 Score: 110
Period size: 41 Copynumber: 3.1 Consensus size: 41
5560193 TTAAATTCCT
* * *
5560203 TAAAATTAAAACCCTAAAGTCAAAATCCTAAATTGAATCCC
1 TAAAATTAAAACCCTAAAATCAAAACCCTAAATTGAAACCC
* * * ** *
5560244 TAAAATTGAAGCCTTAAAATTGAAGCCCTAAATTGAAACCC
1 TAAAATTAAAACCCTAAAATCAAAACCCTAAATTGAAACCC
* * ** *
5560285 TAAAATTAAAA-TCTTAAATTTACACCCTAAA-TGAAACCC
1 TAAAATTAAAACCCTAAAATCAAAACCCTAAATTGAAACCC
5560324 TAAA
1 TAAA
5560328 TCCAAACTTA
Statistics
Matches: 67, Mismatches: 17, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 12 0.18
40 14 0.21
41 41 0.61
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (41 bp):
TAAAATTAAAACCCTAAAATCAAAACCCTAAATTGAAACCC
Found at i:5560272 original size:28 final size:27
Alignment explanation
Indices: 5560232--5560291 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
5560222 TCAAAATCCT
* * *
5560232 AAATTGAATCCCTAAAATTGAAGCCTTA
1 AAATTGAAGCCCT-AAATTGAAACCCTA
5560260 AAATTGAAGCCCTAAATTGAAACCCTA
1 AAATTGAAGCCCTAAATTGAAACCCTA
5560287 AAATT
1 AAATT
5560292 AAAATCTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 17 0.59
28 12 0.41
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (27 bp):
AAATTGAAGCCCTAAATTGAAACCCTA
Found at i:5565473 original size:20 final size:20
Alignment explanation
Indices: 5565440--5565480 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5565430 CAAAATCATC
** *
5565440 TAAGAATTTTCAAGAGTCTT
1 TAAGAATTACCAAGAATCTT
5565460 TAAGAATTACCAAGAATCTT
1 TAAGAATTACCAAGAATCTT
5565480 T
1 T
5565481 CTTTTCTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (20 bp):
TAAGAATTACCAAGAATCTT
Done.