Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 131 of 135
Found at i:40029220 original size:21 final size:19
Alignment explanation
Indices: 40029196--40029236 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
40029186 TATTTATTAT
40029196 TTATAAATTATTATAGGAAAA
1 TTATAAATTATTA-A-GAAAA
*
40029217 TTATTAATTATTAAGAAAA
1 TTATAAATTATTAAGAAAA
40029236 T
1 T
40029237 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
TTATAAATTATTAAGAAAA
Found at i:40034263 original size:15 final size:13
Alignment explanation
Indices: 40034231--40034255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40034221 GGACTTGATG
40034231 ATTTTAAAATATA
1 ATTTTAAAATATA
40034244 ATTTTAAAATAT
1 ATTTTAAAATAT
40034256 CAAATTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTAAAATATA
Found at i:40035459 original size:25 final size:25
Alignment explanation
Indices: 40035428--40035479 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40035418 GTTAACAGTA
40035428 TTAAAATTATTTTGTTAAATTCAGG
1 TTAAAATTATTTTGTTAAATTCAGG
40035453 TTAAAATTATTTTGTTAAATTCAGG
1 TTAAAATTATTTTGTTAAATTCAGG
40035478 TT
1 TT
40035480 CATTACAACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (25 bp):
TTAAAATTATTTTGTTAAATTCAGG
Found at i:40036826 original size:12 final size:12
Alignment explanation
Indices: 40036799--40036843 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
40036789 CACAAACAAG
**
40036799 CTCGTTTAAAAA
1 CTCGTTTATTAA
**
40036811 CTCGTTTATTGG
1 CTCGTTTATTAA
40036823 CTCGTTTATTAA
1 CTCGTTTATTAA
40036835 CTCGTTTAT
1 CTCGTTTAT
40036844 AGCTCATTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (12 bp):
CTCGTTTATTAA
Found at i:40036830 original size:24 final size:24
Alignment explanation
Indices: 40036798--40036843 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
40036788 TCACAAACAA
40036798 GCTCGTTTAAAAACTCGTTTATTG
1 GCTCGTTTAAAAACTCGTTTATTG
**
40036822 GCTCGTTTATTAACTCGTTTAT
1 GCTCGTTTAAAAACTCGTTTAT
40036844 AGCTCATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (24 bp):
GCTCGTTTAAAAACTCGTTTATTG
Found at i:40036853 original size:23 final size:24
Alignment explanation
Indices: 40036809--40036855 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
40036799 CTCGTTTAAA
* *
40036809 AACTCGTTTATTGGCTCGTTTATT
1 AACTCGTTTATTAGCTCATTTATT
40036833 AACTCGTTTA-TAGCTCATTTATT
1 AACTCGTTTATTAGCTCATTTATT
40036856 TATTAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (24 bp):
AACTCGTTTATTAGCTCATTTATT
Found at i:40037001 original size:11 final size:11
Alignment explanation
Indices: 40036985--40037048 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
40036975 TTCATGAACT
40036985 TGTTCGTTTAA
1 TGTTCGTTTAA
**
40036996 TGTTCGTGAACA
1 TGTTCGTTTA-A
*
40037008 TGTTCGATTAA
1 TGTTCGTTTAA
**
40037019 TGTTCGTGAACA
1 TGTTCGTTTA-A
*
40037031 TGTTCGATTAA
1 TGTTCGTTTAA
40037042 TGTTCGT
1 TGTTCGT
40037049 GAACATGTTT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
11 23 0.59
12 16 0.41
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (11 bp):
TGTTCGTTTAA
Found at i:40037005 original size:23 final size:23
Alignment explanation
Indices: 40036949--40037082 Score: 155
Period size: 23 Copynumber: 5.8 Consensus size: 23
40036939 TCATTAACAT
* *
40036949 TGTTTGTGAACTTGTTC-AGTTAAA
1 TGTTCGTGAACATGTTCGA-TT-AA
* * *
40036973 TGTTCATGAACTTGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
40036996 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
40037019 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
*
40037042 TGTTCGTGAACATGTTTGATTAA
1 TGTTCGTGAACATGTTCGATTAA
**
40037065 -GTTAAATGAACATGTTCG
1 TGTT-CGTGAACATGTTCG
40037083 TGAACATTAA
Statistics
Matches: 98, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
22 3 0.03
23 78 0.80
24 17 0.17
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.42
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:40037012 original size:12 final size:12
Alignment explanation
Indices: 40036944--40037057 Score: 69
Period size: 12 Copynumber: 9.7 Consensus size: 12
40036934 ATTATTCATT
*
40036944 AACATTGTTTGTG
1 AACA-TGTTCGTG
* *
40036957 AACTTGTTCAGTT
1 AACATGTTC-GTG
*
40036970 AA-ATGTTCATG
1 AACATGTTCGTG
* *
40036981 AACTTGTTCGTT
1 AACATGTTCGTG
*
40036993 TA-ATGTTCGTG
1 AACATGTTCGTG
40037004 AACATGTTCGAT-
1 AACATGTTCG-TG
*
40037016 TA-ATGTTCGTG
1 AACATGTTCGTG
40037027 AACATGTTCGAT-
1 AACATGTTCG-TG
*
40037039 TA-ATGTTCGTG
1 AACATGTTCGTG
40037050 AACATGTT
1 AACATGTT
40037058 TGATTAAGTT
Statistics
Matches: 75, Mismatches: 17, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
10 2 0.03
11 27 0.36
12 37 0.49
13 9 0.12
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (12 bp):
AACATGTTCGTG
Found at i:40041980 original size:13 final size:13
Alignment explanation
Indices: 40041962--40041986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40041952 CAAGATTGCT
40041962 ACCAAAATGGGAG
1 ACCAAAATGGGAG
40041975 ACCAAAATGGGA
1 ACCAAAATGGGA
40041987 CAAATGCTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.16, G:0.28, T:0.08
Consensus pattern (13 bp):
ACCAAAATGGGAG
Found at i:40042438 original size:39 final size:38
Alignment explanation
Indices: 40042382--40042483 Score: 132
Period size: 38 Copynumber: 2.7 Consensus size: 38
40042372 CATGTCACAT
* * *
40042382 GATCAAATTATAGTAAAGAGATTAAATTTGTAAAAAAAA
1 GATCAAATTATAATAAAGAGACTAAATTTAT-AAAAAAA
* * *
40042421 GGTCAAATTATAATAAAGAGACTAAATTTATGAAAAAC
1 GATCAAATTATAATAAAGAGACTAAATTTATAAAAAAA
*
40042459 GATAAAATTATAATAAAGAGACTAA
1 GATCAAATTATAATAAAGAGACTAA
40042484 TTTTTTTTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
38 28 0.51
39 27 0.49
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (38 bp):
GATCAAATTATAATAAAGAGACTAAATTTATAAAAAAA
Found at i:40042485 original size:18 final size:18
Alignment explanation
Indices: 40042426--40042485 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
40042416 AAAAAGGTCA
40042426 AATTATAATAAAGAGACT
1 AATTATAATAAAGAGACT
* *
40042444 AAATTTATGAA-AAACGATA-A
1 -AA-TTAT-AATAAA-GAGACT
40042464 AATTATAATAAAGAGACT
1 AATTATAATAAAGAGACT
40042482 AATT
1 AATT
40042486 TTTTTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 11
0.68 0.09 0.23
Matches are distributed among these distances:
17 5 0.16
18 11 0.34
19 4 0.12
20 7 0.22
21 5 0.16
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (18 bp):
AATTATAATAAAGAGACT
Found at i:40044949 original size:5 final size:5
Alignment explanation
Indices: 40044939--40044966 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40044929 CTATGTTCTC
40044939 CCTGT CCTGT CCTGT CCTGT CCTGT CCT
1 CCTGT CCTGT CCTGT CCTGT CCTGT CCT
40044967 TACCTAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.18, T:0.39
Consensus pattern (5 bp):
CCTGT
Found at i:40045789 original size:22 final size:22
Alignment explanation
Indices: 40045761--40045802 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
40045751 TTCAAATTGC
40045761 TTCCTTTTTCTTT-TTTTTTTCT
1 TTCCTTTTT-TTTCTTTTTTTCT
40045783 TTCCTTTTTTTTCTTTTTTT
1 TTCCTTTTTTTTCTTTTTTT
40045803 GAATAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTCCTTTTTTTTCTTTTTTTCT
Found at i:40048126 original size:47 final size:48
Alignment explanation
Indices: 40047980--40048131 Score: 144
Period size: 47 Copynumber: 3.3 Consensus size: 48
40047970 ATGCATAACC
*
40047980 TTGGCAACTAATTTAAGAACA--A-GA-G-GGGAACATTC-TTAATCAG
1 TTGGCAACTAATTTATGAACATGAGGATGAGGGAACA-TCATTAATCAG
*
40048023 TTGGCAACTAATTTATGAACATGAGGATGAGGGAACATCACTAATC-G
1 TTGGCAACTAATTTATGAACATGAGGATGAGGGAACATCATTAATCAG
* * * *
40048070 GTGGCAACTAATTT-TGAGCTTGAAGG-T-AGGGAAACATCGTTAATCAG
1 TTGGCAACTAATTTATGAACATG-AGGATGAGGG-AACATCATTAATCAG
*
40048117 TTGGAAACTAATTTA
1 TTGGCAACTAATTTA
40048132 GGATGACTTA
Statistics
Matches: 90, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
43 20 0.22
45 5 0.06
46 20 0.22
47 33 0.37
48 12 0.13
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (48 bp):
TTGGCAACTAATTTATGAACATGAGGATGAGGGAACATCATTAATCAG
Found at i:40063932 original size:12 final size:12
Alignment explanation
Indices: 40063908--40063943 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
40063898 TACTTTTACC
*
40063908 ATATATATTTAT
1 ATATATATGTAT
*
40063920 ATGTATATGTAT
1 ATATATATGTAT
40063932 ATATATATGTAT
1 ATATATATGTAT
40063944 GAGACAATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:40067027 original size:58 final size:59
Alignment explanation
Indices: 40066958--40067112 Score: 192
Period size: 58 Copynumber: 2.6 Consensus size: 59
40066948 AATTTTAATG
* *
40066958 ATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTAATAATATTTTTAACATA
* *
40067016 ATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
* *
40067074 ATTATTATTAAAATATGAA-TTAGTAAAAATTATAATATA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAAT-ATATA
40067113 TAATATTAGA
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
57 20 0.24
58 41 0.49
59 9 0.11
60 9 0.11
61 5 0.06
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
Found at i:40067106 original size:25 final size:24
Alignment explanation
Indices: 40067077--40067127 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
40067067 TAATATAATT
*
40067077 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
40067102 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
40067126 AT
1 AT
40067128 AATACAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:40071336 original size:153 final size:153
Alignment explanation
Indices: 40071058--40071360 Score: 597
Period size: 153 Copynumber: 2.0 Consensus size: 153
40071048 ATAAAATCAA
40071058 AATCTTATATAAAATTATACAAAATTAAAGTTCATGTACACCATAATTCTTGTATGGCTTTGGGA
1 AATCTTATATAAAATTATACAAAATTAAAGTTCATGTACACCATAATTCTTGTATGGCTTTGGGA
40071123 TTTAAGTGTTTTGAAAAAATGAACTCTATTGTCTTTTTTAGATGGTTAAAATATAACATAACTCC
66 TTTAAGTGTTTTGAAAAAATGAACTCTATTGTCTTTTTTAGATGGTTAAAATATAACATAACTCC
*
40071188 TTGTACTCTTCATAATTTTGTAT
131 TTGTACTCTTCATAAATTTGTAT
40071211 AATCTTATATAAAATTATACAAAATTAAAGTTCATGTACACCATAATTCTTGTATGGCTTTGGGA
1 AATCTTATATAAAATTATACAAAATTAAAGTTCATGTACACCATAATTCTTGTATGGCTTTGGGA
40071276 TTTAAGTGTTTTGAAAAAATGAACTCTATTGTCTTTTTTAGATGGTTAAAATATAACATAACTCC
66 TTTAAGTGTTTTGAAAAAATGAACTCTATTGTCTTTTTTAGATGGTTAAAATATAACATAACTCC
40071341 TTGTACTCTTCATAAATTTG
131 TTGTACTCTTCATAAATTTG
40071361 AAATTTATTT
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 149 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (153 bp):
AATCTTATATAAAATTATACAAAATTAAAGTTCATGTACACCATAATTCTTGTATGGCTTTGGGA
TTTAAGTGTTTTGAAAAAATGAACTCTATTGTCTTTTTTAGATGGTTAAAATATAACATAACTCC
TTGTACTCTTCATAAATTTGTAT
Found at i:40085221 original size:20 final size:21
Alignment explanation
Indices: 40085196--40085252 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
40085186 TATTTTTTAC
40085196 TATTTTAAATATAAA-AAATT
1 TATTTTAAATATAAACAAATT
*
40085216 TATTTTTATATAGTAAACAAATT
1 TA-TTTTAAATA-TAAACAAATT
* *
40085239 AATTATAAA-ATAAA
1 TATTTTAAATATAAA
40085253 TAAAATAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 6 0.20
21 9 0.30
22 9 0.30
23 6 0.20
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TATTTTAAATATAAACAAATT
Found at i:40086746 original size:23 final size:21
Alignment explanation
Indices: 40086699--40086748 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
40086689 TTGAGTGTTT
* *
40086699 TTGTTTTGTGCGTTTTTACTA
1 TTGTTTTGTGCATTTTTAATA
*
40086720 TTGTTTTGTTGTCATTTTTAATG
1 TTGTTTTG-TG-CATTTTTAATA
40086743 TTGTTT
1 TTGTTT
40086749 CGCTGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 2 0.08
23 14 0.58
ACGTcount: A:0.10, C:0.06, G:0.18, T:0.66
Consensus pattern (21 bp):
TTGTTTTGTGCATTTTTAATA
Found at i:40087543 original size:31 final size:31
Alignment explanation
Indices: 40087490--40087549 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
40087480 TTCAACCCTT
* *
40087490 AAAAATTGAAAACTTGTCATTAAGCCTTTCA
1 AAAAATTGAAAACTTGTAATTAAACCTTTCA
*
40087521 AAAAATTTGAAAA-TTTTAATTAAACCTTT
1 AAAAA-TTGAAAACTTGTAATTAAACCTTT
40087550 TAAATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.37
Consensus pattern (31 bp):
AAAAATTGAAAACTTGTAATTAAACCTTTCA
Found at i:40091530 original size:21 final size:21
Alignment explanation
Indices: 40091501--40091540 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
40091491 TTATCAAAAT
40091501 AAATCTAAAAATAAAAAACCAG
1 AAATCT-AAAATAAAAAACCAG
*
40091523 AAAT-TAAAATGAAAAACC
1 AAATCTAAAATAAAAAACC
40091541 GAGAGTCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 1 0.06
22 4 0.24
ACGTcount: A:0.68, C:0.12, G:0.05, T:0.15
Consensus pattern (21 bp):
AAATCTAAAATAAAAAACCAG
Found at i:40093109 original size:18 final size:18
Alignment explanation
Indices: 40093086--40093133 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
40093076 TGGTTAGTCA
40093086 TAAACCCAAAATTTATCC
1 TAAACCCAAAATTTATCC
*
40093104 TAAACCCCAAAA-TTATTC
1 TAAA-CCCAAAATTTATCC
40093122 -AAACCCAAAATT
1 TAAACCCAAAATT
40093134 AATCTTATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 7 0.26
17 4 0.15
18 9 0.33
19 7 0.26
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAACCCAAAATTTATCC
Found at i:40108892 original size:33 final size:32
Alignment explanation
Indices: 40108854--40108923 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
40108844 ATTATCGGGT
* *
40108854 CAAATTAAAAATAATT-AAAAGTATGAAAGAGAC
1 CAAATT-AAAACAATTAAAAAATATGAAAG-GAC
*
40108887 TAAATTAAAACAATTAAAAAATATGAAAGGAC
1 CAAATTAAAACAATTAAAAAATATGAAAGGAC
40108919 CAAAT
1 CAAAT
40108924 GCGCAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.21
Consensus pattern (32 bp):
CAAATTAAAACAATTAAAAAATATGAAAGGAC
Found at i:40109362 original size:33 final size:31
Alignment explanation
Indices: 40109299--40109363 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 31
40109289 TTTATTCCAT
*
40109299 CTTTTCATTTTCTTTCTTTTAAAACTAAACC
1 CTTTTCATTTTCTTTCTTTTAAAACCAAACC
* *
40109330 CTTTTCATTTTCTCTTTTTTTTTAAACCAAACC
1 CTTTTCA-TTT-TCTTTCTTTTAAAACCAAACC
40109363 C
1 C
40109364 AAATATGGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 7 0.24
32 3 0.10
33 19 0.66
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (31 bp):
CTTTTCATTTTCTTTCTTTTAAAACCAAACC
Found at i:40109924 original size:14 final size:15
Alignment explanation
Indices: 40109905--40109937 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40109895 TTTTTGGTCC
*
40109905 AATTTGG-CCTTTGT
1 AATTTGGACATTTGT
40109919 AATTTGGACATTTGT
1 AATTTGGACATTTGT
40109934 AATT
1 AATT
40109938 GAACATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (15 bp):
AATTTGGACATTTGT
Found at i:40110001 original size:17 final size:17
Alignment explanation
Indices: 40109955--40110036 Score: 94
Period size: 17 Copynumber: 4.8 Consensus size: 17
40109945 TTATTTAATT
*
40109955 TAAATTTTAAATATATAA
1 TAAA-TTTAAATTTATAA
40109973 TAAATTTAAATTTATAA
1 TAAATTTAAATTTATAA
40109990 TAAATTTAAATTT-TATA
1 TAAATTTAAATTTATA-A
* * * *
40110007 CAAACTTAAATTCAAAA
1 TAAATTTAAATTTATAA
40110024 TAAATTTAAATTT
1 TAAATTTAAATTT
40110037 TAAAACTAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
16 2 0.04
17 47 0.87
18 5 0.09
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:40110273 original size:20 final size:19
Alignment explanation
Indices: 40110244--40110285 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
40110234 TAAGTTAGGG
40110244 TAAAATTAAAAAAAAATTA
1 TAAAATTAAAAAAAAATTA
**
40110263 TAAAGATTAAAATTAAATTA
1 TAAA-ATTAAAAAAAAATTA
40110283 TAA
1 TAA
40110286 CTTTTACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAATTAAAAAAAAATTA
Found at i:40110787 original size:17 final size:17
Alignment explanation
Indices: 40110765--40110804 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
40110755 AAACTTAATT
40110765 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
40110782 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
40110799 TTTAAA
1 TTTAAA
40110805 ATTTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:40111532 original size:16 final size:14
Alignment explanation
Indices: 40111499--40111541 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
40111489 TAAATACATT
*
40111499 TTAAATAATAAGTA
1 TTAAATAATAAATA
40111513 TTAAATAATATTAATA
1 TTAAATAATA--AATA
40111529 TTAAATAA-AAATA
1 TTAAATAATAAATA
40111542 AAAGAAGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.15
14 10 0.38
15 1 0.04
16 11 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
TTAAATAATAAATA
Found at i:40112680 original size:116 final size:115
Alignment explanation
Indices: 40112527--40112862 Score: 368
Period size: 116 Copynumber: 2.9 Consensus size: 115
40112517 CCCTAACCTC
40112527 TCCAAAAATTACATTTTAACCCTAAACTTCTCAAAAATTACATTTTTACCCCCAAACTTCCAAGA
1 TCCAAAAATTACATTTTAACCCTAAACTT-TCAAAAATTACATTTTTACCCCCAAACTTCCAA-A
* **
40112592 AATCCCATTTTTACCCCTGAACTCCCAAAAATTACCATTTTACCC-CAAATG
64 AATCCCATTTTTACCCCTGAACTTCCAAAAATTACCATTTTACCCTCAAACA
* * *
40112643 TCCAAAAAGTACAATTTTGACCCTAAACTTTCAAAAATTACCA-TTTTACCCCCAAACTTCTTAA
1 TCCAAAAATTAC-ATTTTAACCCTAAACTTTCAAAAATTA-CATTTTTACCCCCAAACTTC-CAA
* * *
40112707 AAATACCATTTTTGA-CCCTAAACTTTCC-AAAATTACCATTTTACCCTCGAACA
63 AAATCCCATTTTT-ACCCCTGAAC-TTCCAAAAATTACCATTTTACCCTCAAACA
* ** * *
40112760 TCCAAAAATTACCATTTTTA-CCTCGGA-TGTCCAAAAATTACATTTTTA-CCCCAAATTTTCCA
1 TCCAAAAATTA-CATTTTAACCCT-AAACT-TTCAAAAATTACATTTTTACCCCCAAA-CTTCCA
40112822 AAAATCCCATTTTTACCCC-GAA-TATCCAAAAATTA-CATTTT
62 AAAATCCCATTTTTACCCCTGAACT-TCCAAAAATTACCATTTT
40112863 GCCCATGAGG
Statistics
Matches: 188, Mismatches: 18, Indels: 30
0.80 0.08 0.13
Matches are distributed among these distances:
113 1 0.01
114 9 0.05
115 10 0.05
116 105 0.56
117 62 0.33
118 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (115 bp):
TCCAAAAATTACATTTTAACCCTAAACTTTCAAAAATTACATTTTTACCCCCAAACTTCCAAAAA
TCCCATTTTTACCCCTGAACTTCCAAAAATTACCATTTTACCCTCAAACA
Found at i:40112783 original size:29 final size:29
Alignment explanation
Indices: 40112527--40112862 Score: 277
Period size: 29 Copynumber: 11.6 Consensus size: 29
40112517 CCCTAACCTC
* *
40112527 TCCAAAAATTA-CATTTTAACCCTAAACT
1 TCCAAAAATTACCATTTTTACCCCAAACT
40112555 TCTCAAAAATTA-CATTTTTACCCCCAAACT
1 TC-CAAAAATTACCATTTTTA-CCCCAAACT
* *
40112585 TCCAAGAAA-TCCCATTTTTACCCCTGAACT
1 TCCAA-AAATTACCATTTTTACCCC-AAACT
*
40112615 CCCAAAAATTACCA-TTTTACCCCAAA-T
1 TCCAAAAATTACCATTTTTACCCCAAACT
* * * *
40112642 GTCCAAAAAGTACAATTTTGACCCTAAACT
1 -TCCAAAAATTACCATTTTTACCCCAAACT
*
40112672 TTCAAAAATTACCA-TTTTACCCCCAAACT
1 TCCAAAAATTACCATTTTTA-CCCCAAACT
* *
40112701 TCTTAAAAA-TACCATTTTTGACCCTAAACTT
1 TC-CAAAAATTACCATTTTT-ACCCCAAAC-T
* *
40112732 TCC-AAAATTACCA-TTTTACCCTCGAACA
1 TCCAAAAATTACCATTTTTACCC-CAAACT
* **
40112760 TCCAAAAATTACCATTTTTACCTCGGA-T
1 TCCAAAAATTACCATTTTTACCCCAAACT
*
40112788 GTCCAAAAATTA-CATTTTTACCCCAAATTT
1 -TCCAAAAATTACCATTTTTACCCCAAA-CT
* *
40112818 TCCAAAAA-TCCCATTTTTACCCCGAA-T
1 TCCAAAAATTACCATTTTTACCCCAAACT
40112845 ATCCAAAAATTA-CATTTT
1 -TCCAAAAATTACCATTTT
40112863 GCCCATGAGG
Statistics
Matches: 251, Mismatches: 33, Indels: 48
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.01
28 53 0.21
29 129 0.51
30 63 0.25
31 4 0.02
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTTACCCCAAACT
Found at i:40112907 original size:57 final size:58
Alignment explanation
Indices: 40112527--40112923 Score: 206
Period size: 58 Copynumber: 6.9 Consensus size: 58
40112517 CCCTAACCTC
* **
40112527 TCCAAAAATTA-CATTTTAACCCTAAACT-TCTCAAAAATTACATTTTTACCCCCAAACT--
1 TCCAAAAATTACCATTTTTACCCCGAA-TGTC-CAAAAATTACATTTTTA-CCCCAAA-TGG
* *
40112585 TCCAAGAAA-TCCCATTTTTACCCCTGAACT-CCCAAAAATTACCA-TTTTACCCCAAAT-G
1 TCCAA-AAATTACCATTTTTACCCC-GAA-TGTCCAAAAATTA-CATTTTTACCCCAAATGG
* * * ** *
40112643 TCCAAAAAGTACAATTTTGACCCTAAACT-TTCAAAAATTACCA-TTTTACCCCCAAACT--
1 TCCAAAAATTACCATTTTTACCCCGAA-TGTCCAAAAATTA-CATTTTTA-CCCCAAA-TGG
* ** * * **
40112701 TCTTAAAAA-TACCATTTTTGACCCTAAACTTTCC-AAAATTACCA-TTTTACCCTCGAA-CA
1 TC-CAAAAATTACCATTTTT-ACCCCGAA-TGTCCAAAAATTA-CATTTTTACCC-CAAATGG
* * **
40112760 TCCAAAAATTACCATTTTTACCTCGGATGTCCAAAAATTACATTTTTACCCCAAATTT
1 TCCAAAAATTACCATTTTTACCCCGAATGTCCAAAAATTACATTTTTACCCCAAATGG
* * * *
40112818 TCCAAAAA-TCCCATTTTTACCCCGAATATCCAAAAATTACA-TTTT-GCCCATGA-GG
1 TCCAAAAATTACCATTTTTACCCCGAATGTCCAAAAATTACATTTTTACCCCA-AATGG
** **
40112873 TCCAAAAATTACCATTTTGCCCCCGAAGTGTCC-AAAATTACCGTTTTACCC
1 TCCAAAAATTACCATTTTTACCCCGAA-TGTCCAAAAATTACATTTTTACCC
40112924 TCGGGCATCA
Statistics
Matches: 276, Mismatches: 40, Indels: 46
0.76 0.11 0.13
Matches are distributed among these distances:
55 12 0.04
56 28 0.10
57 71 0.26
58 83 0.30
59 73 0.26
60 9 0.03
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (58 bp):
TCCAAAAATTACCATTTTTACCCCGAATGTCCAAAAATTACATTTTTACCCCAAATGG
Found at i:40118235 original size:22 final size:22
Alignment explanation
Indices: 40118210--40118252 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40118200 GTATCAATAT
40118210 AATAACGAAATGGA-AGCAAAAC
1 AATAACGAAAT-GACAGCAAAAC
40118232 AATAACGAAATGACAGCAAAA
1 AATAACGAAATGACAGCAAAA
40118253 TAGTATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.60, C:0.14, G:0.16, T:0.09
Consensus pattern (22 bp):
AATAACGAAATGACAGCAAAAC
Found at i:40118768 original size:22 final size:22
Alignment explanation
Indices: 40118692--40118755 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
40118682 AACAAAGCAC
* * *
40118692 AAAACCAGCAACCTC-TCTTGG
1 AAAACCAGCAGCATCTTCTTGA
**
40118713 AAAACCAATAGCATCTTCTTGA
1 AAAACCAGCAGCATCTTCTTGA
40118735 AAAACCAGCAGCATCTTCTTG
1 AAAACCAGCAGCATCTTCTTG
40118756 GAAAGCTAGC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
21 11 0.31
22 24 0.69
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.23
Consensus pattern (22 bp):
AAAACCAGCAGCATCTTCTTGA
Found at i:40119399 original size:21 final size:22
Alignment explanation
Indices: 40119368--40119409 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
40119358 AATATTTAAT
40119368 TTTTATATTTGGT-AGTTTTTTA
1 TTTTATATTT-GTAAGTTTTTTA
40119390 TTTTA-ATTTGTAAGTTTTTT
1 TTTTATATTTGTAAGTTTTTT
40119410 TCGTAGTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 12 0.63
22 5 0.26
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (22 bp):
TTTTATATTTGTAAGTTTTTTA
Found at i:40119763 original size:13 final size:13
Alignment explanation
Indices: 40119716--40119764 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
40119706 TTAACACTGC
*
40119716 TTTTAAGAAGTGA
1 TTTTAAAAAGTGA
*
40119729 TTTTAAAAAGTGC
1 TTTTAAAAAGTGA
**
40119742 TTTGGAAAAGTGA
1 TTTTAAAAAGTGA
40119755 TTTTAAAAAG
1 TTTTAAAAAG
40119765 ATTGGTTTAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (13 bp):
TTTTAAAAAGTGA
Found at i:40124754 original size:22 final size:22
Alignment explanation
Indices: 40124728--40124785 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
40124718 ATATTCAAAC
40124728 AATAATAATAAAATAGTAGCAA
1 AATAATAATAAAATAGTAGCAA
* ** *
40124750 TATAATAACGAAATAGTATCAA
1 AATAATAATAAAATAGTAGCAA
* *
40124772 AACAACAATAAAAT
1 AATAATAATAAAAT
40124786 GACAACAAAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (22 bp):
AATAATAATAAAATAGTAGCAA
Found at i:40130965 original size:22 final size:24
Alignment explanation
Indices: 40130926--40130974 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
40130916 AAAAATTAAC
40130926 TTATTTATTTTTACTTTT-AAGAGT
1 TTATTTATTTTTACTTTTCAAG-GT
40130950 TTATTT-TTTTTA-TTTTCAAGGT
1 TTATTTATTTTTACTTTTCAAGGT
40130972 TTA
1 TTA
40130975 AAATATAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.38
23 9 0.38
24 6 0.25
ACGTcount: A:0.22, C:0.04, G:0.08, T:0.65
Consensus pattern (24 bp):
TTATTTATTTTTACTTTTCAAGGT
Found at i:40143373 original size:381 final size:381
Alignment explanation
Indices: 40142670--40143807 Score: 1893
Period size: 381 Copynumber: 3.0 Consensus size: 381
40142660 AGAAAGCTTG
*
40142670 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATACATCTACTTGTGCAACTGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
* * *
40142735 GTACTTGTGAATAGATTATCAGAGGGAAACCAGAATCATCTCAATGCATTGAAGGGTAAGGATGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
*
40142800 ACAACTTGCAGAATCAGCGAAGGCAATCTTGAGTAAGGATGCTCTTTTGATCGACCAAGCTACCA
131 ACAACTTGCAGAATCAGCGGAGGCAATCTTGAGTAAGGATGCTCTTTTGATCGACCAAGCTACCA
40142865 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
* *
40142930 TGCACTGAACTTAGCCAGAGGCTTCTGAAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
261 TGCACTGAACTTCGCCAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
* *
40142995 TGAAGATATGGTGGAGAATGACATTTTGAAGTCACAGGAGGAGCTGTCTAATCTTA
326 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAAACTTA
40143051 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
* *
40143116 GTACTTATGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGTGTAAGGACGA
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
40143181 ACAACTTGCAGAATCAGCGGAGGCAATCTTGAGTAAGGATGCTCTTTTGATCGACCAAGCTACCA
131 ACAACTTGCAGAATCAGCGGAGGCAATCTTGAGTAAGGATGCTCTTTTGATCGACCAAGCTACCA
* *
40143246 TGATTGAAGAAGCAGAAACACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGATGCT
196 TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
*
40143311 TGCACTGAACTTCGCCAGAGGCTTCTGGAGGAGGAGCATCGTGCTGCTGCTATTGAACAAAAGCT
261 TGCACTGAACTTCGCCAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
* * *
40143376 TGAAGATATGGTCGAGAATGACTTTTTGAAGACACAGGAGGAGCTGTCTAAACTTG
326 TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAAACTTA
*
40143432 AGGACAGAATGAAGATGGCTGAAGATGACCTAAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
1 AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
* *
40143497 GTACTTGTGAATAGATTATCAGAGGCAAACCATCATCATCTCAGTGCATTGAAGGGTAAGGATTC
66 GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGA--C
* * *** * *
40143562 G--CAACTTGCTGAATCAGCAGAGATGATCTTGAGTAAGGATGCTCTTCTAATCGACCAAGCTAC
129 GAACAACTTGCAGAATCAGCGGAGGCAATCTTGAGTAAGGATGCTCTTTTGATCGACCAAGCTAC
* * *
40143625 CATGATTGAAGAAGCAGAAAAACATATTCGTTCCCTTGAAATTGAAGTTGCAAAGTCAGAGGAAG
194 CATGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAG
* * * ** * * * *
40143690 TTTGCACTGATCTCCGGAAAAGGCTTTTTGAGGAGGAGCAGCATGCTGCTGCTATTGAACAAAAG
259 CTTGCACTGAACTTCGCCAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAG
40143755 CTTGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAA
324 CTTGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAA
40143808 GCTAAGAACG
Statistics
Matches: 709, Mismatches: 46, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
381 707 1.00
383 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (381 bp):
AGGACAGAATGAAGATGGCTGAAGATGACCTGAGAAATGCATCTACTTGTGCAACTGTTGCTTTT
GTACTTGTGAATAGATTATCAGAGGCAAACCATAATCATCTCAATGCATTGAAGGGTAAGGACGA
ACAACTTGCAGAATCAGCGGAGGCAATCTTGAGTAAGGATGCTCTTTTGATCGACCAAGCTACCA
TGATTGAAGAAGCAGAAAAACATATTCATTCCCTTGAAACTGAAGTTGAAAAGTCAGAGGAAGCT
TGCACTGAACTTCGCCAGAGGCTTCTGGAGGAGGAGCAGCGTGCTGCTGCTATTGAACAAAAGCT
TGAAGATATGGTGGAGAATGACATTTTGAAGACACAGGAGGAGCTGTCTAAACTTA
Found at i:40146284 original size:222 final size:221
Alignment explanation
Indices: 40145896--40146459 Score: 860
Period size: 222 Copynumber: 2.5 Consensus size: 221
40145886 TTGTCCACTT
*
40145896 AGCTGACTCTGGGAAAAAGCTTACCAATGCTTATGCTGTC-CTTGATGGTTTAAAGAAAGAAATG
1 AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCAC-TGATGGTTTAAAGAAAGAAATG
* * *
40145960 ACTTTTACAAAATTAGATGCATGTTTGAAGGAGCAGCTATTGGTGGAGCGGGAAAGTGAGTTGTC
65 A-TTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTC
* * * * *
40146025 TTTTCTCCAAGAAAAAGTTGAAGAAGCACAGATTGAGTTAAGAATGTTGAAGAAAGAGAACTGTC
129 TTTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGTTAAGAAAGATGAAGAAAGAAAACTGTC
* *
40146090 TACTTCTCCAGGATTTGGATGAGAAGAA
194 TACTTCTCCAGAATTTGGACGAGAAGAA
* ** * *
40146118 AGCTGACTCTGGCAAAAAGCTTGTCAATGCCTATTCTGTCACTGATGGTTTAAAGAAAGAAATGA
1 AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCACTGATGGTTTAAAGAAAGAAATGA
*
40146183 TTTTCGCAAAATTAGATGCATGTTTGAAAGAGCACCTATTGGTGGAGCAGGAAAGTGAGTTGTCT
66 TTTT-GCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTCT
40146248 TTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGTTAAGAAAGATGAAGAAAGAAAACTGTCT
130 TTTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGTTAAGAAAGATGAAGAAAGAAAACTGTCT
* *
40146313 GCTTCTCCAGAATTTGGACGAGAAGGA
195 ACTTCTCCAGAATTTGGACGAGAAGAA
* * * * *
40146340 AGCAGACACTGGAAAAAATCTTACCAATGCTTATGCTGTCATTGATGGTTTAAAGAAAGAAATAA
1 AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCACTGATGGTTTAAAGAAAGAAATGA
*
40146405 TTTTTGCAAAAGTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAG
66 -TTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAG
40146460 GATATCAAAG
Statistics
Matches: 309, Mismatches: 30, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
221 4 0.01
222 300 0.97
223 5 0.02
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.27
Consensus pattern (221 bp):
AGCTGACTCTGGAAAAAAGCTTACCAATGCTTATGCTGTCACTGATGGTTTAAAGAAAGAAATGA
TTTTGCAAAATTAGATGCATGTTTGAAAGAGCAGCTATTGGTGGAGCAGGAAAGTGAGTTGTCTT
TTCTACAAGAAAAAGTTGAAGAAGCACAAATTGAGTTAAGAAAGATGAAGAAAGAAAACTGTCTA
CTTCTCCAGAATTTGGACGAGAAGAA
Found at i:40149393 original size:29 final size:29
Alignment explanation
Indices: 40149336--40149393 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
40149326 TCCTGTGGAT
* * *
40149336 TGGATCAATTTAGTCCCTCTATTATTAAA
1 TGGATCAATTTAGTCCCTATACTAGTAAA
* *
40149365 TGGATCAATTTAGTCCCTATGCTGGTAAA
1 TGGATCAATTTAGTCCCTATACTAGTAAA
40149394 AAGAATCAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (29 bp):
TGGATCAATTTAGTCCCTATACTAGTAAA
Found at i:40175339 original size:66 final size:66
Alignment explanation
Indices: 40175224--40175416 Score: 269
Period size: 66 Copynumber: 2.9 Consensus size: 66
40175214 CGATGACAAC
* * *
40175224 GATTCTGCATCCATGAATGCTGAAAGTGCAAAGGGAGAAGTGAAAGAAGAGGAAAAGGAAGAAGA
1 GATTCTGAATCCTTGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGAAGA
40175289 T
66 T
* * * * *
40175290 GTTTCTGTATCCTTGAATGCTGAAACTGCGAAGGGAGAAGAGAACGAAGAGGAAAAGGAAGAAGA
1 GATTCTGAATCCTTGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGAAGA
40175355 T
66 T
* * * * *
40175356 GATTCTGAATCTTTAAATGCTGAAAGTTCAAAAGAAGAAGAGAAAGAAGAGGAAAAGGAAG
1 GATTCTGAATCCTTGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAG
40175417 GGGAGCAGGA
Statistics
Matches: 110, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 110 1.00
ACGTcount: A:0.44, C:0.09, G:0.30, T:0.17
Consensus pattern (66 bp):
GATTCTGAATCCTTGAATGCTGAAAGTGCAAAGGGAGAAGAGAAAGAAGAGGAAAAGGAAGAAGA
T
Found at i:40184904 original size:12 final size:11
Alignment explanation
Indices: 40184883--40184909 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40184873 ATTATTTTCA
40184883 TTTTCATTTTT
1 TTTTCATTTTT
40184894 TTTTCATTTTT
1 TTTTCATTTTT
40184905 TTTTC
1 TTTTC
40184910 TTGTCTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCATTTTT
Found at i:40188439 original size:22 final size:22
Alignment explanation
Indices: 40188396--40188444 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
40188386 TACCTTAGTT
**
40188396 TACAAAAATTAAGAAAGTAATA
1 TACAAAAATTAAGAAAAAAATA
40188418 TACAAAATATT-AGAAAAAAATA
1 TACAAAA-ATTAAGAAAAAAATA
*
40188440 AACAA
1 TACAA
40188445 TTTAACAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.20
Consensus pattern (22 bp):
TACAAAAATTAAGAAAAAAATA
Found at i:40196242 original size:30 final size:28
Alignment explanation
Indices: 40196208--40196276 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
40196198 ACAATTGAAT
40196208 TTAAATTTTAAAATCTAAAAAATAGAAAGA
1 TTAAATTTTAAAA-CT-AAAAATAGAAAGA
* * * *
40196238 TTAAATTTTTATAACTGAAAATATAAGGA
1 TTAAA-TTTTAAAACTAAAAATAGAAAGA
40196267 TTAAATTTTA
1 TTAAATTTTA
40196277 CTTTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 5 0.15
29 15 0.44
30 7 0.21
31 7 0.21
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (28 bp):
TTAAATTTTAAAACTAAAAATAGAAAGA
Found at i:40208524 original size:2 final size:2
Alignment explanation
Indices: 40208511--40208544 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
40208501 TCCTTCTCTG
40208511 TA TA TA -A T- 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
40208545 ATTATTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40208669 original size:3 final size:3
Alignment explanation
Indices: 40208661--40208704 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
40208651 TTAAGTGTTT
** *
40208661 TTC TTC TTC TTC TTC TTC TT- TTC TTC TAG ATC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
40208705 CTTTACAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.05, C:0.30, G:0.02, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:40208684 original size:20 final size:21
Alignment explanation
Indices: 40208659--40208703 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
40208649 TATTAAGTGT
40208659 TTTTCTTCT-TCTTCTTCTTC
1 TTTTCTTCTATCTTCTTCTTC
40208679 TTTTCTTCTAGATCTTCTTCTTC
1 TTTTCTTCT--ATCTTCTTCTTC
40208702 TT
1 TT
40208704 CCTTTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
23 13 0.59
ACGTcount: A:0.04, C:0.27, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTCTTCTATCTTCTTCTTC
Found at i:40209534 original size:18 final size:18
Alignment explanation
Indices: 40209511--40209545 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40209501 ATGTATATAT
*
40209511 ATATATATACATACATAC
1 ATATATATACAGACATAC
40209529 ATATATATACAGACATA
1 ATATATATACAGACATA
40209546 TTAGGTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.31
Consensus pattern (18 bp):
ATATATATACAGACATAC
Found at i:40209538 original size:14 final size:14
Alignment explanation
Indices: 40209498--40209546 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
40209488 ACCACAAATT
* *
40209498 TACATGTATATATA
1 TACATATATATACA
* *
40209512 TATATATACATACA
1 TACATATATATACA
40209526 TACATATATATACA
1 TACATATATATACA
*
40209540 GACATAT
1 TACATAT
40209547 TAGGTCTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (14 bp):
TACATATATATACA
Found at i:40210165 original size:205 final size:205
Alignment explanation
Indices: 40209848--40210567 Score: 1098
Period size: 205 Copynumber: 3.5 Consensus size: 205
40209838 GACTCAGCCG
* *
40209848 AAAAAAACAAATGGTCTGTGTTGTAGTTGATTGCAAACCATTATCCGGGTTTGGTACCATTCATT
1 AAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCATTATCCGGGTTTGGTACCATTCATT
*
40209913 CGTATGATAAAAGTGTGTGTGTTTTTGGTAGTCGAGGTGTCTGTTTATTCTAGGAAATAAAGGAC
66 CATATGATAAAAGTGTGTGTGTTTTTGGTAGTCGAGGTGTCTGTTTATTCTAGGAAATAAAGGAC
* *
40209978 GTTGTTGTGATAATTATAGCCTGTTAACTAATATGGTGTTTTCTTTTACCAGCTTGTACTTACGG
131 GTTGTTGTGATAATTATAGCCTGTTAACTAATACGGTGTTTTCTTTTACTAGCTTGTACTTACGG
*
40210043 CTTAACCCAA
196 CTTAACCAAA
* *
40210053 AAAAAAACAAATGGTTTGTGTTGTAGTTTATTGCAAATCATTATCTGGGTTTGGTACCATTCATT
1 AAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCATTATCCGGGTTTGGTACCATTCATT
* * * *
40210118 CGTATGATAAAAGTGTTTGTGTTTTTGGTAGTTGAGGTGTCTGTTTATTGTAGGAAATAAAGGAC
66 CATATGATAAAAGTGTGTGTGTTTTTGGTAGTCGAGGTGTCTGTTTATTCTAGGAAATAAAGGAC
* * *
40210183 GTTGTTGTGATAATTATAGCCGGTTAACTAATACGGTGTTTTCTTTTACTGGCTTGTACTTACAG
131 GTTGTTGTGATAATTATAGCCTGTTAACTAATACGGTGTTTTCTTTTACTAGCTTGTACTTACGG
40210248 CTTAACCAAAA
196 CTTAACC-AAA
* * ** **
40210259 AAAAAAACAAATGGTTTATGTTGTAGTTGACTGCAAATTGTTATCCGGGTTTGGTACCGGTCATT
1 AAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCATTATCCGGGTTTGGTACCATTCATT
* * *
40210324 TATATGATAAAAGTGTTTGTGTTTTTGGTAGTCGAGGTGTCGGTTTATTCTAGGAAATAAAGGAC
66 CATATGATAAAAGTGTGTGTGTTTTTGGTAGTCGAGGTGTCTGTTTATTCTAGGAAATAAAGGAC
* * * * *
40210389 GCTATTGTGATAATTATAGCCTGGTAACTAATACGGTGTTTTCTTTTACTAACTTGTACTTATGG
131 GTTGTTGTGATAATTATAGCCTGTTAACTAATACGGTGTTTTCTTTTACTAGCTTGTACTTACGG
*
40210454 CTTAACAAAA
196 CTTAACCAAA
* * * * *
40210464 AAAAAAAAAAATGGTTTGCGTTGTAGTTTATTGCAAATCGTTATCCGGGTTTGGTACCGTTCATT
1 AAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCATTATCCGGGTTTGGTACCATTCATT
*
40210529 CATATGATAAAAGTGTGTGTGTTTTTTGCTAGTCGAGGT
66 CATATGATAAAAGTGTGTGTG-TTTTTGGTAGTCGAGGT
40210568 ATCCATTTAG
Statistics
Matches: 468, Mismatches: 45, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
205 270 0.58
206 198 0.42
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (205 bp):
AAAAAAACAAATGGTTTGTGTTGTAGTTGATTGCAAATCATTATCCGGGTTTGGTACCATTCATT
CATATGATAAAAGTGTGTGTGTTTTTGGTAGTCGAGGTGTCTGTTTATTCTAGGAAATAAAGGAC
GTTGTTGTGATAATTATAGCCTGTTAACTAATACGGTGTTTTCTTTTACTAGCTTGTACTTACGG
CTTAACCAAA
Found at i:40217956 original size:5 final size:5
Alignment explanation
Indices: 40217946--40217979 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
40217936 GAAAGCAAAA
40217946 GCAAG GCAAG GCAAG GCAAG GCAAG GCAAG GCAA
1 GCAAG GCAAG GCAAG GCAAG GCAAG GCAAG GCAA
40217980 CACAGGCAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.21, G:0.38, T:0.00
Consensus pattern (5 bp):
GCAAG
Found at i:40219699 original size:22 final size:24
Alignment explanation
Indices: 40219647--40219712 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 24
40219637 AAGAAGTAGC
*
40219647 GAGGAAAGAA-AGGAGAGAAGCGA
1 GAGGGAAGAAGAGGAGAGAAGCGA
* *
40219670 GAGTGAAGAAGAGGAGAGGAGC-A
1 GAGGGAAGAAGAGGAGAGAAGCGA
* *
40219693 G-GGGAAGAAGATGAAAGAAG
1 GAGGGAAGAAGAGGAGAGAAG
40219713 AGAAGATGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
22 15 0.43
23 10 0.29
24 10 0.29
ACGTcount: A:0.48, C:0.03, G:0.45, T:0.03
Consensus pattern (24 bp):
GAGGGAAGAAGAGGAGAGAAGCGA
Found at i:40219744 original size:18 final size:18
Alignment explanation
Indices: 40219722--40219778 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
40219712 GAGAAGATGG
40219722 AGAAGAAGG-GGAAGGAGA
1 AGAAGAAGGAGG-AGGAGA
* *
40219740 TGAAGTAGGAGGAGGAGA
1 AGAAGAAGGAGGAGGAGA
*
40219758 AGAAGAAGAAGG-GGA-A
1 AGAAGAAGGAGGAGGAGA
40219774 AGAAG
1 AGAAG
40219779 GGAAGTGGTG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 6 0.18
17 3 0.09
18 22 0.67
19 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.47, T:0.04
Consensus pattern (18 bp):
AGAAGAAGGAGGAGGAGA
Found at i:40220302 original size:31 final size:31
Alignment explanation
Indices: 40220267--40220332 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
40220257 TTAAAAAATG
40220267 GTCACTAAATTATTTAAAAAATTTTATTTAA
1 GTCACTAAATTATTTAAAAAATTTTATTTAA
* **
40220298 GTCACTAAATTATTTGAAAGTTTTTATTTAA
1 GTCACTAAATTATTTAAAAAATTTTATTTAA
40220329 GTCA
1 GTCA
40220333 TTGCATTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (31 bp):
GTCACTAAATTATTTAAAAAATTTTATTTAA
Found at i:40227171 original size:123 final size:123
Alignment explanation
Indices: 40226952--40227352 Score: 482
Period size: 123 Copynumber: 3.3 Consensus size: 123
40226942 TCGTGTAATG
* * * **
40226952 CAACTCATGAGCCGAAACCGGTCCTCTCCTCCTCGAATTAGAAACTGAACTAATACTCTCGGTAG
1 CAACTCGTGAGCCGAAACCGATCCTCTCCTCCTCGAATTAGAAACCGAACCGATACTCTCGGTAG
* * * * *
40227017 ATCGGAAGCTTGCACTTTTCACATCATCCGATTCTTTCCTAGACAAAAC-GACACAATT
66 ACCGAAAGCTTGCATTTTTCACATCCTCCGATTCTTTCCTATACAAAACAG-CACAATT
* * * **
40227075 CAACTCGGGAACCGAAACCAATCCTCTCCT-CTTTAATCTAGAAACCGAACCGATACTCTCGGTA
1 CAACTCGTGAGCCGAAACCGATCCTCTCCTCCTCGAAT-TAGAAACCGAACCGATACTCTCGGTA
* * **
40227139 GACCGAAAGCTTGCATTTTTCACATCCTCCGATTCTTTCCTATACAAGACATCATGATT
65 GACCGAAAGCTTGCATTTTTCACATCCTCCGATTCTTTCCTATACAAAACAGCACAATT
* * * * **
40227198 CAACTCGTGAGCCGAAATCGATCTTCTCCTCCTCGAGTTAGAAACCAAACCGATACTCTCACTAG
1 CAACTCGTGAGCCGAAACCGATCCTCTCCTCCTCGAATTAGAAACCGAACCGATACTCTCGGTAG
* * * *
40227263 ACCGAAAGCTTCCATTTTTTACAGCCTCCGGTTCTTTCCTATACAAAACAGCACAATT
66 ACCGAAAGCTTGCATTTTTCACATCCTCCGATTCTTTCCTATACAAAACAGCACAATT
* * *
40227321 CAACTCGTGAGCCGAATCTGGTCCTCTCCTCC
1 CAACTCGTGAGCCGAAACCGATCCTCTCCTCC
40227353 CGATACTCTC
Statistics
Matches: 232, Mismatches: 43, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
122 5 0.02
123 223 0.96
124 4 0.02
ACGTcount: A:0.28, C:0.31, G:0.14, T:0.27
Consensus pattern (123 bp):
CAACTCGTGAGCCGAAACCGATCCTCTCCTCCTCGAATTAGAAACCGAACCGATACTCTCGGTAG
ACCGAAAGCTTGCATTTTTCACATCCTCCGATTCTTTCCTATACAAAACAGCACAATT
Found at i:40227431 original size:105 final size:104
Alignment explanation
Indices: 40227247--40227574 Score: 325
Period size: 117 Copynumber: 3.0 Consensus size: 104
40227237 AGAAACCAAA
** * * * *
40227247 CCGATACTCTCACTAGACCGAAAGCTTCCATTTTTTACAGCCTCCGGTTCTTTCCTATACAAAAC
1 CCGATACTCTCGGTAGACCGAAAGCTTGCATTTTTCACATCCTCCGGTTCTTTCCCATACAAAAC
*
40227312 AGCACAATTCAACTCGTGAGCCGAATCTGGTCCTCTCCTC
66 AGCACAATTCAACTCGTGAGCCGAAAC-GGTCCTCTCCTC
* * *
40227352 CCGATACTCTCGGTAGACCG-AAGACTTGCATTCTTCACATCCTCCGATTCTTTCCCATGCAAAA
1 CCGATACTCTCGGTAGACCGAAAG-CTTGCATTTTTCACATCCTCCGGTTCTTTCCCATACAAAA
* * * * * *
40227416 CATCATAATTGAACTCGAGAGCCGGAAGCAGTCCTCTCCTCCTAGAC
65 CAGCACAATTCAACTCGTGAGCC-GAAACGGT-C-CT-CTCCT---C
* *
40227463 ACCGAACCAATACTCTCGGTAGATCGAAAGCTTGCATTTTTCACATACTCCGGTTCTTTCCCATA
1 -CCG-----ATACTCTCGGTAGACCGAAAGCTTGCATTTTTCACATCCTCCGGTTCTTTCCCATA
* *
40227528 CAAATCAGCACAATTCAACTCGTGAGCCGAAACCGGTCCGCTCCTC
60 CAAAACAGCACAATTCAACTCGTGAGCCGAAA-CGGTCCTCTCCTC
40227574 C
1 C
40227575 TCGAGCTCAA
Statistics
Matches: 179, Mismatches: 28, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
104 3 0.02
105 72 0.40
106 5 0.03
107 2 0.01
108 5 0.03
110 1 0.01
111 2 0.01
112 3 0.02
114 5 0.03
115 1 0.01
116 4 0.02
117 73 0.41
118 3 0.02
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (104 bp):
CCGATACTCTCGGTAGACCGAAAGCTTGCATTTTTCACATCCTCCGGTTCTTTCCCATACAAAAC
AGCACAATTCAACTCGTGAGCCGAAACGGTCCTCTCCTC
Found at i:40227555 original size:222 final size:225
Alignment explanation
Indices: 40227124--40227574 Score: 597
Period size: 222 Copynumber: 2.0 Consensus size: 225
40227114 AGAAACCGAA
* * *
40227124 CCGATACTCTCGGTAGACCGAAAGCTTGCATTTTTCACATCCTCCGATTCTTTCCTATACAAGAC
1 CCGATACTCTCGGTAGACCGAAAGCTTGCATTCTTCACATCCTCCGATTCTTTCCCATACAAAAC
* * * * *
40227189 ATCATGATTCAACTCGTGAGCCGAAATCGATCTTCTCCTCCTCGAGTTAGAAACCAAACCGATAC
66 ATCATAATTCAACTCGAGAGCCGAAAGCGATC-TCTCCTCCTC--GCTAGAAACCAAACCAATAC
* * *
40227254 TCTCACTAGACCGAAAGCTTCCATTTTTTACAGCCTCCGGTTCTTTCCTATACAAAACAGCACAA
128 TCTCACTAGACCGAAAGCTTCCATTTTTCACAGACTCCGGTTCTTTCCCATACAAAACAGCACAA
* * *
40227319 TTCAACTCGTGAGCCGAATCTGGTCCTCTCCTC
193 TTCAACTCGTGAGCCGAAACCGGTCCGCTCCTC
*
40227352 CCGATACTCTCGGTAGACCG-AAGACTTGCATTCTTCACATCCTCCGATTCTTTCCCATGCAAAA
1 CCGATACTCTCGGTAGACCGAAAG-CTTGCATTCTTCACATCCTCCGATTCTTTCCCATACAAAA
* * * *
40227416 CATCATAATTGAACTCGAGAGCCGGAAGC-AGTC-CT-CTCCTC-CTAGACACCGAACCAATACT
65 CATCATAATTCAACTCGAGAGCCGAAAGCGA-TCTCTCCTCCTCGCTAGAAACCAAACCAATACT
** * * * *
40227477 CTCGGTAGATCGAAAGCTTGCATTTTTCACATACTCCGGTTCTTTCCCATACAAATCAGCACAAT
129 CTCACTAGACCGAAAGCTTCCATTTTTCACAGACTCCGGTTCTTTCCCATACAAAACAGCACAAT
40227542 TCAACTCGTGAGCCGAAACCGGTCCGCTCCTC
194 TCAACTCGTGAGCCGAAACCGGTCCGCTCCTC
40227574 C
1 C
40227575 TCGAGCTCAA
Statistics
Matches: 196, Mismatches: 25, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
222 102 0.52
225 6 0.03
226 2 0.01
227 4 0.02
228 82 0.42
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (225 bp):
CCGATACTCTCGGTAGACCGAAAGCTTGCATTCTTCACATCCTCCGATTCTTTCCCATACAAAAC
ATCATAATTCAACTCGAGAGCCGAAAGCGATCTCTCCTCCTCGCTAGAAACCAAACCAATACTCT
CACTAGACCGAAAGCTTCCATTTTTCACAGACTCCGGTTCTTTCCCATACAAAACAGCACAATTC
AACTCGTGAGCCGAAACCGGTCCGCTCCTC
Found at i:40232798 original size:13 final size:13
Alignment explanation
Indices: 40232780--40232807 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40232770 CGGCAGTTAC
40232780 GACGGAAAAAACG
1 GACGGAAAAAACG
40232793 GACGGAAAAAACG
1 GACGGAAAAAACG
40232806 GA
1 GA
40232808 TGAAATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.32, T:0.00
Consensus pattern (13 bp):
GACGGAAAAAACG
Found at i:40236042 original size:91 final size:91
Alignment explanation
Indices: 40235905--40236085 Score: 208
Period size: 91 Copynumber: 2.0 Consensus size: 91
40235895 CGGAAAGTTT
* * **
40235905 AAAAAATATTTTTTCTACCCATACTCAAACTCAAATGTCCGGAAAAT-ATAATATAATAAAT-AA
1 AAAAAATATTTTTACAACCCATACTCAAACTCAAATGTCCCAAAAATGA-AATATAATAAATAAA
* *
40235968 TAATTTTTACAATTATTCTAGAAAATA
65 TAATTTGTACAATTATCCTAGAAAATA
* *
40235995 AAAAAATATTTTTACAACATCATACTCAAA-TCAAA-GTGCACCAAAAATGAAATATAATTAATA
1 AAAAAATATTTTTACAAC-CCATACTCAAACTCAAATGT-C-CCAAAAATGAAATATAATAAATA
* *
40236058 AATAATTTGTACATTTATCCTTGAAAAT
63 AATAATTTGTACAATTATCCTAGAAAAT
40236086 TTAAGAAATA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
89 2 0.03
90 22 0.29
91 27 0.36
92 25 0.33
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (91 bp):
AAAAAATATTTTTACAACCCATACTCAAACTCAAATGTCCCAAAAATGAAATATAATAAATAAAT
AATTTGTACAATTATCCTAGAAAATA
Found at i:40243310 original size:43 final size:43
Alignment explanation
Indices: 40243249--40243335 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
40243239 TTCAAAGTGT
* *
40243249 CACATGTTGCTTTCTTACTGGTTTCGTATTTCTTACAGTTCAA
1 CACATGTTGCTTTCTTACTGGTTTCATACTTCTTACAGTTCAA
*
40243292 CACATGTTGCTTTCTTACTGGTTTCATACTTCTTATAGTTCAA
1 CACATGTTGCTTTCTTACTGGTTTCATACTTCTTACAGTTCAA
40243335 C
1 C
40243336 TAGTCATATG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.46
Consensus pattern (43 bp):
CACATGTTGCTTTCTTACTGGTTTCATACTTCTTACAGTTCAA
Found at i:40245163 original size:2 final size:2
Alignment explanation
Indices: 40245158--40245184 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40245148 ACATACATAT
40245158 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
40245185 TGAAGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40246729 original size:30 final size:30
Alignment explanation
Indices: 40246695--40246769 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 30
40246685 TTTTGAAAAT
* *
40246695 TTTTAATTTTTCAAAAAAAATCATTATGCC
1 TTTTAATTTTTCAAAAAAAATAATTAAGCC
* *
40246725 TTTTAATTTTT-AAAAAAATTAATTAAGTC
1 TTTTAATTTTTCAAAAAAAATAATTAAGCC
*
40246754 TTAT-ATTTTTCAAAAA
1 TTTTAATTTTTCAAAAA
40246770 TTCTCATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.15
29 22 0.56
30 11 0.28
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTTAATTTTTCAAAAAAAATAATTAAGCC
Found at i:40247179 original size:20 final size:19
Alignment explanation
Indices: 40247154--40247213 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 19
40247144 CACACTATGA
40247154 ATCCTAAACCTTAAACTCAG
1 ATCCTAAA-CTTAAACTCAG
40247174 ATCCTAAACTTCAAACCTC-G
1 ATCCTAAACTT-AAA-CTCAG
*
40247194 AACCTCAAATCTTAAACTCA
1 ATCCT-AAA-CTTAAACTCA
40247214 AAATCTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
19 3 0.09
20 19 0.56
21 9 0.26
22 3 0.09
ACGTcount: A:0.40, C:0.32, G:0.03, T:0.25
Consensus pattern (19 bp):
ATCCTAAACTTAAACTCAG
Found at i:40259654 original size:111 final size:111
Alignment explanation
Indices: 40259460--40259675 Score: 423
Period size: 111 Copynumber: 1.9 Consensus size: 111
40259450 TATCCTTAGC
40259460 TGAACTTCGTTGTGATTACTGTTCAATTTGAATCGGATATGAAAAAAAATATATATATCAAAATT
1 TGAACTTCGTTGTGATTACTGTTCAATTTGAATCGGATATGAAAAAAAATATATATATCAAAATT
40259525 ATACATTAACTTTCATCTAATTTGCAATGTCATATATGAGGATAGA
66 ATACATTAACTTTCATCTAATTTGCAATGTCATATATGAGGATAGA
*
40259571 TGAACTTCGTTGTGATTACTGTTCAATTTGAATCGGATATGAAAAAATATATATATATCAAAATT
1 TGAACTTCGTTGTGATTACTGTTCAATTTGAATCGGATATGAAAAAAAATATATATATCAAAATT
40259636 ATACATTAACTTTCATCTAATTTGCAATGTCATATATGAG
66 ATACATTAACTTTCATCTAATTTGCAATGTCATATATGAG
40259676 TTTTAATTTT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (111 bp):
TGAACTTCGTTGTGATTACTGTTCAATTTGAATCGGATATGAAAAAAAATATATATATCAAAATT
ATACATTAACTTTCATCTAATTTGCAATGTCATATATGAGGATAGA
Found at i:40259847 original size:31 final size:31
Alignment explanation
Indices: 40259812--40259904 Score: 75
Period size: 31 Copynumber: 3.1 Consensus size: 31
40259802 TTTTAAATGC
40259812 ATATAATTGAATTAAAATTAAAATTTTATGT
1 ATATAATTGAATTAAAATTAAAATTTTATGT
* ** * * *
40259843 ATAT-ATATGAATCACGATTTAAGTTTTAGGT
1 ATATAAT-TGAATTAAAATTAAAATTTTATGT
* * *
40259874 GTATAATTGTATT-AAA-TCAAATTTTATGT
1 ATATAATTGAATTAAAATTAAAATTTTATGT
40259903 AT
1 AT
40259905 CAAATTACAC
Statistics
Matches: 45, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
29 11 0.24
30 3 0.07
31 29 0.64
32 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (31 bp):
ATATAATTGAATTAAAATTAAAATTTTATGT
Found at i:40270994 original size:30 final size:30
Alignment explanation
Indices: 40270927--40271000 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
40270917 CCCCTCAAAA
* *
40270927 TTTTAAAAGTTCTAATTAAGCCTTCCATAAG
1 TTTTAAAAGTTTTAATTAAACCTTCCAT-AG
* *
40270958 TTTTAAAAATTTTAATTAAACCTTCCGAT-T
1 TTTTAAAAGTTTTAATTAAACCTTCC-ATAG
40270988 TTTTAAAAGTTTT
1 TTTTAAAAGTTTT
40271001 CTCATCAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 12 0.32
31 23 0.62
32 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (30 bp):
TTTTAAAAGTTTTAATTAAACCTTCCATAG
Found at i:40280457 original size:17 final size:17
Alignment explanation
Indices: 40280425--40280459 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40280415 GTAATTTATG
* *
40280425 ATTTATGTTGAGTTTTA
1 ATTTATGTTAAATTTTA
40280442 ATTTATGTTAAATTTTA
1 ATTTATGTTAAATTTTA
40280459 A
1 A
40280460 GTTTTGAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (17 bp):
ATTTATGTTAAATTTTA
Found at i:40287373 original size:58 final size:58
Alignment explanation
Indices: 40287283--40287399 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
40287273 ATACGGGGAA
40287283 AGCACGGCTAAGGATGAAGAATGGACCAGTGGTGTGGATTCTTATCTGCCACGTGGCG
1 AGCACGGCTAAGGATGAAGAATGGACCAGTGGTGTGGATTCTTATCTGCCACGTGGCG
40287341 AGCACGGCTAAGGATGAAGAATGGACCAGTGGTGTGGATTCTTATCTGCCACGTGGCG
1 AGCACGGCTAAGGATGAAGAATGGACCAGTGGTGTGGATTCTTATCTGCCACGTGGCG
40287399 A
1 A
40287400 ATTATAATTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.22
Consensus pattern (58 bp):
AGCACGGCTAAGGATGAAGAATGGACCAGTGGTGTGGATTCTTATCTGCCACGTGGCG
Found at i:40302002 original size:32 final size:34
Alignment explanation
Indices: 40301941--40302003 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
40301931 GAGAATTGAA
40301941 ATTGTATAAAATATTAAGGTAAATTATATTTAAG
1 ATTGTATAAAATATTAAGGTAAATTATATTTAAG
*
40301975 ATTGT-TAAATTATT-A-GTAAATTTATATTT
1 ATTGTATAAAATATTAAGGTAAA-TTATATTT
40302004 TCGTCTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 5 0.19
32 9 0.33
33 8 0.30
34 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (34 bp):
ATTGTATAAAATATTAAGGTAAATTATATTTAAG
Found at i:40311080 original size:14 final size:14
Alignment explanation
Indices: 40311061--40311088 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40311051 ATCCATTTTT
40311061 TTATTAAAAATTCA
1 TTATTAAAAATTCA
40311075 TTATTAAAAATTCA
1 TTATTAAAAATTCA
40311089 ATTCATTTCT
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTATTAAAAATTCA
Found at i:40324261 original size:21 final size:18
Alignment explanation
Indices: 40324218--40324264 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
40324208 TATTACTAAA
40324218 TTGAT-ATTTAAAAATAT
1 TTGATAATTTAAAAATAT
40324235 TT-ATAATTTAAAAATAAGTT
1 TTGATAATTTAAAAAT-A--T
40324255 TTGATAATTT
1 TTGATAATTT
40324265 TAATAACTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.08
17 12 0.48
18 1 0.04
20 3 0.12
21 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
TTGATAATTTAAAAATAT
Found at i:40328571 original size:20 final size:22
Alignment explanation
Indices: 40328546--40328596 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
40328536 GATAAGTCGA
40328546 ATTAATTAGATC-ATTGA-TTT
1 ATTAATTAGATCGATTGATTTT
* *
40328566 ATTAATTCGATCGATTTATTTT
1 ATTAATTAGATCGATTGATTTT
40328588 ATTTAATTA
1 A-TTAATTA
40328597 AATAAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.44
21 4 0.16
22 4 0.16
23 6 0.24
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (22 bp):
ATTAATTAGATCGATTGATTTT
Found at i:40334804 original size:13 final size:14
Alignment explanation
Indices: 40334778--40334809 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
40334768 GATGTGAACT
40334778 TAAT-TAAATGTTA
1 TAATATAAATGTTA
40334791 TAATATAAAT-TTA
1 TAATATAAATGTTA
40334804 TAATAT
1 TAATAT
40334810 GACGAGGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TAATATAAATGTTA
Found at i:40353882 original size:23 final size:22
Alignment explanation
Indices: 40353838--40353881 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40353828 TAATAATCGT
40353838 TTATTTTTAATCTGTTTTAAAA
1 TTATTTTTAATCTGTTTTAAAA
*
40353860 TTATTTATTAAT-TTTTTTAAAA
1 TTATTT-TTAATCTGTTTTAAAA
40353882 AAAAACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTATTTTTAATCTGTTTTAAAA
Found at i:40354446 original size:63 final size:63
Alignment explanation
Indices: 40354371--40354510 Score: 280
Period size: 63 Copynumber: 2.2 Consensus size: 63
40354361 AAATAATAAT
40354371 AATAGAAATATATTAAGAGAACAAATAATATTAAAATAATTACTAAATTTATACTTTTTTAAA
1 AATAGAAATATATTAAGAGAACAAATAATATTAAAATAATTACTAAATTTATACTTTTTTAAA
40354434 AATAGAAATATATTAAGAGAACAAATAATATTAAAATAATTACTAAATTTATACTTTTTTAAA
1 AATAGAAATATATTAAGAGAACAAATAATATTAAAATAATTACTAAATTTATACTTTTTTAAA
40354497 AATAGAAATATATT
1 AATAGAAATATATT
40354511 TCCAAATTTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 77 1.00
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.36
Consensus pattern (63 bp):
AATAGAAATATATTAAGAGAACAAATAATATTAAAATAATTACTAAATTTATACTTTTTTAAA
Found at i:40355086 original size:17 final size:17
Alignment explanation
Indices: 40355064--40355102 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
40355054 CGGCACTCGA
*
40355064 CAGAGACAAAACAGAGG
1 CAGAGACAAAACAGAAG
40355081 CAGAGACAAAACAGAAG
1 CAGAGACAAAACAGAAG
40355098 CAGAG
1 CAGAG
40355103 CAACGATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.54, C:0.18, G:0.28, T:0.00
Consensus pattern (17 bp):
CAGAGACAAAACAGAAG
Found at i:40359522 original size:22 final size:22
Alignment explanation
Indices: 40359497--40359538 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40359487 TGTTATATTA
40359497 TATTAATTACTCATTAATTACT
1 TATTAATTACTCATTAATTACT
* * *
40359519 TATTACTTATTCCTTAATTA
1 TATTAATTACTCATTAATTA
40359539 TAGATTAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTAATTACTCATTAATTACT
Found at i:40374904 original size:6 final size:6
Alignment explanation
Indices: 40374893--40374917 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40374883 TATGTGGACC
40374893 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
40374918 TTGACACAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:40376653 original size:2 final size:2
Alignment explanation
Indices: 40376567--40376634 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
40376557 AAAAAAATCA
40376567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40376609 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
40376635 TAAATTCTAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40376912 original size:26 final size:26
Alignment explanation
Indices: 40376877--40376930 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
40376867 TAACTCAAAC
* *
40376877 AATTTCACTCGATTCGACTCAACTTG
1 AATTTCACTCCACTCGACTCAACTTG
* * *
40376903 AATTTTACTCCACTCGATTCAATTTG
1 AATTTCACTCCACTCGACTCAACTTG
40376929 AA
1 AA
40376931 AAAAATTCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.37
Consensus pattern (26 bp):
AATTTCACTCCACTCGACTCAACTTG
Found at i:40383548 original size:26 final size:26
Alignment explanation
Indices: 40383518--40383572 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
40383508 TGGACGATTT
40383518 AAAGAGTAAATTAATTTTT-TTATTAA
1 AAAGA-TAAATTAATTTTTATTATTAA
** *
40383544 AAAGATTCATTTATTTTTATTATTAA
1 AAAGATAAATTAATTTTTATTATTAA
40383570 AAA
1 AAA
40383573 TTTACGCGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (26 bp):
AAAGATAAATTAATTTTTATTATTAA
Found at i:40393237 original size:28 final size:27
Alignment explanation
Indices: 40393205--40393286 Score: 73
Period size: 28 Copynumber: 3.1 Consensus size: 27
40393195 TTTTATTTTA
40393205 TTTATTTAAAAAATAGATAAATTAAATT
1 TTTATTTAAAAAATAG-TAAATTAAATT
* ** **
40393233 TTTATTT----AATCGTATTTTATTTT
1 TTTATTTAAAAAATAGTAAATTAAATT
40393256 TTTATTTAAAAAATAGGTAAATTAAATT
1 TTTATTTAAAAAATA-GTAAATTAAATT
40393284 TTT
1 TTT
40393287 GTACATTAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
23 14 0.36
24 4 0.10
27 3 0.08
28 18 0.46
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.52
Consensus pattern (27 bp):
TTTATTTAAAAAATAGTAAATTAAATT
Found at i:40410625 original size:32 final size:32
Alignment explanation
Indices: 40410559--40410626 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
40410549 ATATCGATTG
** * *
40410559 TGAAGAATGGACACTACAAATGGTATTTTGGT
1 TGAAGAATGGACACTACAAATAATACTTTAGT
*
40410591 TGAAGAATGGACAGTACAAATAATACTTTAGT
1 TGAAGAATGGACACTACAAATAATACTTTAGT
40410623 TGAA
1 TGAA
40410627 TTCAAATAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (32 bp):
TGAAGAATGGACACTACAAATAATACTTTAGT
Found at i:40414567 original size:18 final size:18
Alignment explanation
Indices: 40414530--40414568 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40414520 AATATATTTA
*
40414530 AATATCTCATAATAATAT
1 AATATCTCATAATAAAAT
40414548 AATATCTCTATAA-AAAAT
1 AATATCTC-ATAATAAAAT
40414566 AAT
1 AAT
40414569 TTTGTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (18 bp):
AATATCTCATAATAAAAT
Found at i:40417491 original size:17 final size:17
Alignment explanation
Indices: 40417469--40417501 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40417459 CGTAATCTCA
40417469 CTCTGTTTTGTCTCTGC
1 CTCTGTTTTGTCTCTGC
40417486 CTCTGTTTTGTCTCTG
1 CTCTGTTTTGTCTCTG
40417502 TCGAGTGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.18, T:0.55
Consensus pattern (17 bp):
CTCTGTTTTGTCTCTGC
Found at i:40425297 original size:29 final size:31
Alignment explanation
Indices: 40425263--40425335 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
40425253 ATGGGGACTA
*
40425263 GATCAAATTAGTCCCTC-TATTATT-AAAAG
1 GATCAAATTAGTCCCTCATAATATTAAAAAG
*
40425292 GATCAATTTAGT-CCTCATAATATTAAAAAG
1 GATCAAATTAGTCCCTCATAATATTAAAAAG
* *
40425322 AATCAAATAAGTCC
1 GATCAAATTAGTCC
40425336 AAATTGTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 4 0.11
29 17 0.47
30 14 0.39
31 1 0.03
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
GATCAAATTAGTCCCTCATAATATTAAAAAG
Found at i:40430280 original size:30 final size:30
Alignment explanation
Indices: 40430235--40430306 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
40430225 AATAACCTAT
* * * *
40430235 AATTTTATAATTTTTAGAGGATT-AAATTAA
1 AATTTTATCACTTTTA-AAGATTCAAAATAA
*
40430265 AATTTTATCACTTTTAAAGATTCAAAATAT
1 AATTTTATCACTTTTAAAGATTCAAAATAA
40430295 AATTTTATCACT
1 AATTTTATCACT
40430307 ATTATTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 5 0.14
30 31 0.86
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.46
Consensus pattern (30 bp):
AATTTTATCACTTTTAAAGATTCAAAATAA
Found at i:40440051 original size:14 final size:14
Alignment explanation
Indices: 40440034--40440075 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
40440024 ATTTTAAATT
* *
40440034 TAAATATTATATAA
1 TAAATAATATAAAA
40440048 TAAATAATATAAAA
1 TAAATAATATAAAA
40440062 TAAATAATATAAAA
1 TAAATAATATAAAA
40440076 AATCAATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATAATATAAAA
Found at i:40440802 original size:19 final size:20
Alignment explanation
Indices: 40440778--40440830 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 20
40440768 TAAAATTTGA
40440778 TTTTTAAATATTTTATAA-T
1 TTTTTAAATATTTTATAATT
*
40440797 TTTTT--ACATTTTATAATT
1 TTTTTAAATATTTTATAATT
*
40440815 TCTTTTAAATTTTTTA
1 T-TTTTAAATATTTTA
40440831 ATGCTAGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
17 10 0.37
18 2 0.07
19 9 0.33
21 6 0.22
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTAAATATTTTATAATT
Found at i:40440832 original size:19 final size:18
Alignment explanation
Indices: 40440778--40440832 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
40440768 TAAAATTTGA
40440778 TTTTTAAATATTTTATAA-T
1 TTTTTAAAT-TTTT-TAATT
* *
40440797 TTTTTACATTTTATAATT
1 TTTTTAAATTTTTTAATT
40440815 TCTTTTAAATTTTTTAAT
1 T-TTTTAAATTTTTTAAT
40440833 GCTAGGGACA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.10
18 5 0.17
19 22 0.73
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTAAATTTTTTAATT
Found at i:40451745 original size:6 final size:6
Alignment explanation
Indices: 40451736--40451789 Score: 72
Period size: 6 Copynumber: 9.0 Consensus size: 6
40451726 ATAAAGATAA
* * *
40451736 TGTATG TGTATG TGTATG TGTATG TGTATG CGTATG TATATG TATATG
1 TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG TGTATG
*
40451784 TATATG
1 TGTATG
40451790 GCCCACATAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.48
Consensus pattern (6 bp):
TGTATG
Found at i:40452029 original size:33 final size:31
Alignment explanation
Indices: 40451974--40452053 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 31
40451964 ATGTTGTTAA
40451974 TAAA-TTTAAAATTT-ATTCTTTATATTTTTT
1 TAAATTTTAAAATTTAATTCTTTAT-TTTTTT
40452004 T-AATTTTAGAAATTTAATTCTTTTATTTTTTT
1 TAAATTTTA-AAATTTAATTC-TTTATTTTTTT
40452036 TCAAATTTTAAAATTTAA
1 T-AAATTTTAAAATTTAA
40452054 GTTCAAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
29 2 0.05
30 5 0.11
31 6 0.14
32 11 0.25
33 13 0.30
34 7 0.16
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (31 bp):
TAAATTTTAAAATTTAATTCTTTATTTTTTT
Found at i:40465680 original size:31 final size:30
Alignment explanation
Indices: 40465617--40465681 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
40465607 TAGCGATTCA
40465617 TTTTACTGTTTAGAAAAAATAAAGAATATT
1 TTTTACTGTTTAGAAAAAATAAAGAATATT
*
40465647 TTTTACTGTTTAGAAAGCAATAAA-AATATT
1 TTTTACTGTTTAGAAA-AAATAAAGAATATT
40465677 TTTTA
1 TTTTA
40465682 TTTAAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 27 0.82
31 6 0.18
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (30 bp):
TTTTACTGTTTAGAAAAAATAAAGAATATT
Found at i:40470255 original size:47 final size:47
Alignment explanation
Indices: 40470201--40470294 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
40470191 ACATAATAAC
* *
40470201 TTTAAATATTTTTATCGAGTCTTAATTTGAATGACATTAATATTATT
1 TTTAAATATTTTGATCGAGTCTTAATTTGAATAACATTAATATTATT
* *
40470248 TTTAAATATTTTGATCGAGTCTTAATTTGATTAACATTAGTATTATT
1 TTTAAATATTTTGATCGAGTCTTAATTTGAATAACATTAATATTATT
40470295 GTCAATGCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (47 bp):
TTTAAATATTTTGATCGAGTCTTAATTTGAATAACATTAATATTATT
Found at i:40471878 original size:12 final size:13
Alignment explanation
Indices: 40471855--40471883 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
40471845 AGTTGGAAAC
40471855 CATACAATACATA
1 CATACAATACATA
40471868 CATAC-ATACATA
1 CATACAATACATA
40471880 CATA
1 CATA
40471884 TATGGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
CATACAATACATA
Found at i:40486254 original size:20 final size:20
Alignment explanation
Indices: 40486229--40486266 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40486219 TGGCTAAGTT
*
40486229 GTTTCCACCATTGTTGAATG
1 GTTTCCACCATCGTTGAATG
*
40486249 GTTTCCGCCATCGTTGAA
1 GTTTCCACCATCGTTGAA
40486267 GCTTTTCAAG
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:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (20 bp):
GTTTCCACCATCGTTGAATG
Found at i:40492417 original size:25 final size:24
Alignment explanation
Indices: 40492375--40492426 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
40492365 TGCTAATATC
*
40492375 ATATAAATCATTACATAAATATTAA
1 ATATAAATCATTACATAAA-AGTAA
*
40492400 ATATAAATTAGTTA-ATAAAAGTAA
1 ATATAAATCA-TTACATAAAAGTAA
40492424 ATA
1 ATA
40492427 AATAACAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 14 0.58
26 3 0.12
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (24 bp):
ATATAAATCATTACATAAAAGTAA
Found at i:40492839 original size:18 final size:18
Alignment explanation
Indices: 40492816--40492854 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
40492806 AAAAATCAAA
*
40492816 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
40492834 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
40492852 TTT
1 TTT
40492855 GTCCCATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Found at i:40493895 original size:18 final size:18
Alignment explanation
Indices: 40493868--40493916 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 18
40493858 TTCTTTTTTT
40493868 TTAT-TTATAAAATATTA
1 TTATATTATAAAATATTA
40493885 TTATATTAT--AATATTA
1 TTATATTATAAAATATTA
*
40493901 TTA-ATAATTAAAATAT
1 TTATATTA-TAAAATAT
40493917 CTTTTTGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 4 0.15
18 9 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATATTATAAAATATTA
Found at i:40506214 original size:16 final size:16
Alignment explanation
Indices: 40506193--40506248 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
40506183 GATATAAAAT
40506193 ATAAAAATAAAAATTA
1 ATAAAAATAAAAATTA
* **
40506209 ATAAAATTAAATTTTA
1 ATAAAAATAAAAATTA
*
40506225 ATAAAAATATAAAAATA
1 ATAAAAATA-AAAATTA
*
40506242 ATTAAAA
1 ATAAAAA
40506249 CTTTATTAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
16 21 0.68
17 10 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAAAAATAAAAATTA
Found at i:40510291 original size:13 final size:13
Alignment explanation
Indices: 40510273--40510300 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40510263 GATAGATGAC
40510273 TGTTTACCCGATA
1 TGTTTACCCGATA
40510286 TGTTTACCCGATA
1 TGTTTACCCGATA
40510299 TG
1 TG
40510301 ATTGAACCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTTTACCCGATA
Found at i:40515927 original size:2 final size:2
Alignment explanation
Indices: 40515920--40515959 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40515910 TTATTTTAAT
40515920 TA TA TA TA TA 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 TA TA
40515960 AATCATCAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40517294 original size:51 final size:52
Alignment explanation
Indices: 40517239--40517347 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
40517229 CATAAACATG
* *
40517239 CATGATACATGAATGACAAATGTGCCG-TATCATGTATGTGTTTCCGATAGA
1 CATGATACATGAATGACAAATGTGCCGTTATCATGTACGTGATTCCGATAGA
* * **
40517290 CATGATATATGAATGATAAATGTGTTGTTATCATGTACGTGATTCCGATAGA
1 CATGATACATGAATGACAAATGTGCCGTTATCATGTACGTGATTCCGATAGA
40517342 CATGAT
1 CATGAT
40517348 TAAAACATTG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 23 0.45
52 28 0.55
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (52 bp):
CATGATACATGAATGACAAATGTGCCGTTATCATGTACGTGATTCCGATAGA
Found at i:40518823 original size:26 final size:28
Alignment explanation
Indices: 40518792--40518848 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
40518782 ATAACCAAAT
*
40518792 CAAATTGAATCAAA-TTT-AAATTCAGA
1 CAAATTAAATCAAATTTTCAAATTCAGA
*
40518818 CAAATTAAATCAAATTTTCAAATTCGGA
1 CAAATTAAATCAAATTTTCAAATTCAGA
40518846 CAA
1 CAA
40518849 GAAATAACAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 13 0.48
27 3 0.11
28 11 0.41
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.30
Consensus pattern (28 bp):
CAAATTAAATCAAATTTTCAAATTCAGA
Found at i:40528657 original size:18 final size:20
Alignment explanation
Indices: 40528634--40528676 Score: 65
Period size: 18 Copynumber: 2.3 Consensus size: 20
40528624 TGTCACATCA
40528634 ATAAAAAA-ATT-AAAAATT
1 ATAAAAAATATTCAAAAATT
40528652 ATAAAAAATATTCAAAAATT
1 ATAAAAAATATTCAAAAATT
40528672 A-AAAA
1 ATAAAA
40528677 TTAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.35
19 7 0.30
20 8 0.35
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (20 bp):
ATAAAAAATATTCAAAAATT
Found at i:40528682 original size:6 final size:7
Alignment explanation
Indices: 40528638--40528683 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
40528628 ACATCAATAA
40528638 AAAAATT
1 AAAAATT
40528645 AAAAATT
1 AAAAATT
*
40528652 ATAAA--
1 AAAAATT
*
40528657 AAATATT
1 AAAAATT
40528664 CAAAAATT
1 -AAAAATT
40528672 AAAAATT
1 AAAAATT
40528679 AAAAA
1 AAAAA
40528684 AACATGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
5 3 0.09
7 23 0.72
8 6 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:40538449 original size:4 final size:4
Alignment explanation
Indices: 40538440--40538472 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
40538430 ATCTCCAAGG
40538440 TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA T
40538473 GGGCATGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:40551803 original size:21 final size:22
Alignment explanation
Indices: 40551777--40551831 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
40551767 AAAACTCTAT
40551777 TATTTTGCTATTGTTTT-CTCAC
1 TATTTTGCTATTGTTTTGCT-AC
40551799 T-TTTTG-TCATTGTTTTGCTAC
1 TATTTTGCT-ATTGTTTTGCTAC
*
40551820 TATTTTACTATT
1 TATTTTGCTATT
40551832 TTTGTTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 10 0.36
23 1 0.04
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.62
Consensus pattern (22 bp):
TATTTTGCTATTGTTTTGCTAC
Found at i:40555128 original size:85 final size:85
Alignment explanation
Indices: 40554911--40555131 Score: 282
Period size: 85 Copynumber: 2.6 Consensus size: 85
40554901 GATGTTAGAT
* * * * * **
40554911 TAGGAGAAAAGGGTTGTTGGAAATGTCGAGATTCGAATCTTGAACTCACTGAAAGTTGTGTATGA
1 TAGGAGAAAGGGGTTGTTGTAAATGTCGAGATTCGAATCTTGAACTTACTAAAAGATGAATATGA
*
40554976 AACATTGGTTTTGGTTGAAA
66 AACATTGGTTATGGTTGAAA
* * *
40554996 T-GAGAGAAAGGGATTGCTGTAAATGTCGAGATTCGAATCTTGGACTTACTAAAAGATGAATATG
1 TAG-GAGAAAGGGGTTGTTGTAAATGTCGAGATTCGAATCTTGAACTTACTAAAAGATGAATATG
40555060 AAACATTGGTTATGGTTGAAA
65 AAACATTGGTTATGGTTGAAA
* * * **
40555081 TAGGAGAAAGGGGTTGTTGTAAATGTCAAAATTCGGATCCCGAACTTACTA
1 TAGGAGAAAGGGGTTGTTGTAAATGTCGAGATTCGAATCTTGAACTTACTA
40555132 TCTAATTATT
Statistics
Matches: 115, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
84 1 0.01
85 113 0.98
86 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.30
Consensus pattern (85 bp):
TAGGAGAAAGGGGTTGTTGTAAATGTCGAGATTCGAATCTTGAACTTACTAAAAGATGAATATGA
AACATTGGTTATGGTTGAAA
Found at i:40557654 original size:4 final size:4
Alignment explanation
Indices: 40557645--40557822 Score: 132
Period size: 4 Copynumber: 45.2 Consensus size: 4
40557635 ACACCTACAC
* * * * ** *
40557645 CATA CATA CACA CACTA CACA CATA CATA CATC CACA CACG CATG CATA
1 CATA CATA CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
40557694 CATA CATA CATG CATG CATG CATA C--A CATA CATA CACA CATG CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
40557740 CATA TATA GATG CATA CATA CATA CATA CATA CATA CAT- -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
40557786 CATG CATG CATG CATGA -ATA CATA CATA CATA CATA C
1 CATA CATA CATA CAT-A CATA CATA CATA CATA CATA C
40557823 GAACCCGAAA
Statistics
Matches: 144, Mismatches: 23, Indels: 14
0.80 0.13 0.08
Matches are distributed among these distances:
2 4 0.03
3 1 0.01
4 136 0.94
5 3 0.02
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (4 bp):
CATA
Found at i:40557659 original size:21 final size:21
Alignment explanation
Indices: 40557610--40557675 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
40557600 ACTAAGAAGG
40557610 TACATACACACACGTACACAC-
1 TACATACACACAC-TACACACA
40557631 --C-TACACAC-CTACAC-CA
1 TACATACACACACTACACACA
40557647 TACATACACACACTACACACA
1 TACATACACACACTACACACA
40557668 TACATACA
1 TACATACA
40557676 TCCACACACG
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
15 1 0.03
16 5 0.13
17 1 0.03
18 8 0.21
19 8 0.21
20 6 0.15
21 10 0.26
ACGTcount: A:0.44, C:0.39, G:0.02, T:0.15
Consensus pattern (21 bp):
TACATACACACACTACACACA
Found at i:40557739 original size:50 final size:50
Alignment explanation
Indices: 40557646--40557822 Score: 176
Period size: 50 Copynumber: 3.4 Consensus size: 50
40557636 CACCTACACC
* * * *
40557646 ATACATACACACACTACACACATACATACATCCACACACGCATGCATACATA
1 ATACATACATACA-TACATACA-ACATACATACACACATGCATGCATACATA
* * * *
40557698 CATACATGCATGCATGCATAC-ACATACATACACACATGCATGCATATATA
1 -ATACATACATACATACATACAACATACATACACACATGCATGCATACATA
* * *
40557748 GATGCATACATACATACATACATACATACATATACATACATGCATGCATGCATGA
1 -ATACATACATACATACATACA-ACATAC--ATACACACATGCATGCATACAT-A
40557803 ATACATACATACATACATAC
1 ATACATACATACATACATAC
40557823 GAACCCGAAA
Statistics
Matches: 102, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
50 42 0.41
52 11 0.11
53 10 0.10
54 38 0.37
55 1 0.01
ACGTcount: A:0.43, C:0.27, G:0.07, T:0.23
Consensus pattern (50 bp):
ATACATACATACATACATACAACATACATACACACATGCATGCATACATA
Found at i:40557762 original size:58 final size:58
Alignment explanation
Indices: 40557690--40557822 Score: 178
Period size: 58 Copynumber: 2.3 Consensus size: 58
40557680 CACACGCATG
* * *
40557690 CATACATACATACATGCATGCATGCATACACATACATACACACATGCATGCAT-ATATA
1 CATACATACATACATACATACATACATACACATACATACACACATGCATGCATGA-ATA
* * * **
40557748 GATGCATACATACATACATACATACATACATATACATACATGCATGCATGCATGAATA
1 CATACATACATACATACATACATACATACACATACATACACACATGCATGCATGAATA
40557806 CATACATACATACATAC
1 CATACATACATACATAC
40557823 GAACCCGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 63 0.98
59 1 0.02
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (58 bp):
CATACATACATACATACATACATACATACACATACATACACACATGCATGCATGAATA
Found at i:40557810 original size:54 final size:54
Alignment explanation
Indices: 40557645--40557822 Score: 173
Period size: 58 Copynumber: 3.2 Consensus size: 54
40557635 ACACCTACAC
* * ** * *
40557645 CATACATACACACACTAC--ACACATACATACATCCACACACGCATGCATACATA
1 CATACATACATACA-TACATACACATACATACATACATGCATGCATGAATACATA
* * * *
40557698 CATACATGCATGCATGCATACACATACATACACACATGCATGCAT-ATATAGATGCATA
1 CATACATACATACATACATACACATACATACATACATGCATGCATGA-AT--A--CATA
* *
40557756 CATACATACATACATACATACATATACATACATGCATGCATGCATGAATACATA
1 CATACATACATACATACATACACATACATACATACATGCATGCATGAATACATA
40557810 CATACATACATAC
1 CATACATACATAC
40557823 GAACCCGAAA
Statistics
Matches: 101, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
52 2 0.02
53 11 0.11
54 40 0.40
56 2 0.02
58 45 0.45
59 1 0.01
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (54 bp):
CATACATACATACATACATACACATACATACATACATGCATGCATGAATACATA
Found at i:40558625 original size:16 final size:17
Alignment explanation
Indices: 40558590--40558627 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40558580 AAAATTTTCG
40558590 ATTTTAGATTTCAAATC
1 ATTTTAGATTTCAAATC
* *
40558607 ATTTTAGGTTT-ATATC
1 ATTTTAGATTTCAAATC
40558623 ATTTT
1 ATTTT
40558628 GAATTGGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (17 bp):
ATTTTAGATTTCAAATC
Found at i:40561051 original size:10 final size:10
Alignment explanation
Indices: 40561036--40561063 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40561026 ACAATCAAAC
40561036 AAAAGGAAAA
1 AAAAGGAAAA
40561046 AAAAGGAAAA
1 AAAAGGAAAA
40561056 AAAAGGAA
1 AAAAGGAA
40561064 CTCTAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (10 bp):
AAAAGGAAAA
Found at i:40564968 original size:25 final size:26
Alignment explanation
Indices: 40564920--40564970 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
40564910 TCATTCATGA
*
40564920 GAATAAAATATATTTTATTGTCAATT
1 GAATAAAATATATTTTATTATCAATT
40564946 GAATAAAATATA-TTTATTATCAATT
1 GAATAAAATATATTTTATTATCAATT
40564971 ATTTACCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (26 bp):
GAATAAAATATATTTTATTATCAATT
Done.