Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008360.1 Hibiscus syriacus cultivar Beakdansim tig00111099_pilon, 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: 1563863
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:5432 original size:31 final size:32
Alignment explanation
Indices: 5375--5434 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
5365 AAATAAAAAT
*
5375 TAATTTGAAAGTGAGAGTGATTAAATTAAGAG
1 TAATTTGAAAGTGAGAGTAATTAAATTAAGAG
*
5407 TAATTTGAAAGTTA-AGTAATTAAATTAA
1 TAATTTGAAAGTGAGAGTAATTAAATTAA
5435 AAAAATAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.18, T:0.35
Consensus pattern (32 bp):
TAATTTGAAAGTGAGAGTAATTAAATTAAGAG
Found at i:26154 original size:95 final size:95
Alignment explanation
Indices: 26050--26224 Score: 296
Period size: 95 Copynumber: 1.8 Consensus size: 95
26040 TGTCGCTCGA
*
26050 GACTCTGATTTACGATTTATCGGTGATCTTTTAATAGTTTCATCATATTTTGTAGTTTGTTTGCC
1 GACTCTGATTTACGATTTATCGGTGATCTTTCAATAGTTTCATCATATTTTGTAGTTTGTTTGCC
26115 GATGCAGTCAAATTTATTCTCATGCTGCTC
66 GATGCAGTCAAATTTATTCTCATGCTGCTC
* * * *
26145 GACTCTGATTTACGATTTATCGGTGGTCTTTCAGTAGTTTCATCCTCTTTTGTAGTTTGTTTGCC
1 GACTCTGATTTACGATTTATCGGTGATCTTTCAATAGTTTCATCATATTTTGTAGTTTGTTTGCC
*
26210 GATGCAGTCATATTT
66 GATGCAGTCAAATTT
26225 GTTCGTATCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (95 bp):
GACTCTGATTTACGATTTATCGGTGATCTTTCAATAGTTTCATCATATTTTGTAGTTTGTTTGCC
GATGCAGTCAAATTTATTCTCATGCTGCTC
Found at i:26938 original size:2 final size:2
Alignment explanation
Indices: 26933--26967 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
26923 GTTTTTTTAA
26933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26968 CTTTGAGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33061 original size:16 final size:16
Alignment explanation
Indices: 33040--33073 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
33030 TTACTATTCA
*
33040 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
33056 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
33072 CG
1 CG
33074 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:39119 original size:29 final size:29
Alignment explanation
Indices: 39084--39165 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
39074 AAACTAAATT
* *
39084 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
39113 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
39142 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
39166 GTTATGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:43886 original size:29 final size:29
Alignment explanation
Indices: 43851--43932 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
43841 AAACTAAATT
* *
43851 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
43880 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
43909 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
43933 GTTATGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:48635 original size:63 final size:64
Alignment explanation
Indices: 48568--48692 Score: 182
Period size: 63 Copynumber: 1.9 Consensus size: 64
48558 CTCCGGAGCT
* *
48568 GGCGGCGGCAG-AAGTGGGTTTGGAGGAAGAACGGGCGGC-AGAAAGGGGGTTGGAGGAAGGACG
1 GGCGGCGGAAGAAAG-GGGGTTGGAGGAAGAACGGGCGGCGAGAAAGGGGGTTGGAGGAAGGACG
*
48631 GGCGGCGGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAG
1 GGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGC-G-AGAAAGGGGGTTGGAGGAAG
48693 AAAGGGGGTT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
63 32 0.58
64 3 0.05
66 20 0.36
ACGTcount: A:0.26, C:0.10, G:0.56, T:0.08
Consensus pattern (64 bp):
GGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGAGAAAGGGGGTTGGAGGAAGGACG
Found at i:48638 original size:33 final size:33
Alignment explanation
Indices: 48568--48692 Score: 186
Period size: 33 Copynumber: 3.9 Consensus size: 33
48558 CTCCGGAGCT
* * *
48568 GGCGGCGGCAG-AAGTGGGTTTGGAGGAAGAACG
1 GGCGGCGGAAGAAAG-GGGGTTGGAGGAAGGACG
48601 GGCGGC---AGAAAGGGGGTTGGAGGAAGGACG
1 GGCGGCGGAAGAAAGGGGGTTGGAGGAAGGACG
48631 GGCGGCGGAAGAAAGGGGGTTGGAGGAAGGACG
1 GGCGGCGGAAGAAAGGGGGTTGGAGGAAGGACG
48664 GGCGGCGGAAGAAAGGGGGTTGGAGGAAG
1 GGCGGCGGAAGAAAGGGGGTTGGAGGAAG
48693 AAAGGGGGTT
Statistics
Matches: 86, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
30 24 0.28
31 3 0.03
33 59 0.69
ACGTcount: A:0.26, C:0.10, G:0.56, T:0.08
Consensus pattern (33 bp):
GGCGGCGGAAGAAAGGGGGTTGGAGGAAGGACG
Found at i:48693 original size:18 final size:18
Alignment explanation
Indices: 48607--48712 Score: 89
Period size: 18 Copynumber: 6.2 Consensus size: 18
48597 AACGGGCGGC
48607 AGAAAGGGGGTTGGAGGA
1 AGAAAGGGGGTTGGAGGA
* * * *
48625 AG-GA-CGGG-CGGCGGA
1 AGAAAGGGGGTTGGAGGA
48640 AGAAAGGGGGTTGGAGGA
1 AGAAAGGGGGTTGGAGGA
* * * *
48658 AG-GA-CGGG-CGGCGGA
1 AGAAAGGGGGTTGGAGGA
48673 AGAAAGGGGGTTGGAGGA
1 AGAAAGGGGGTTGGAGGA
*
48691 AGAAAGGGGGTTGGGGGA
1 AGAAAGGGGGTTGGAGGA
48709 AGAA
1 AGAA
48713 CGGGCGGCGA
Statistics
Matches: 65, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
15 14 0.22
16 8 0.12
17 8 0.12
18 35 0.54
ACGTcount: A:0.30, C:0.06, G:0.57, T:0.08
Consensus pattern (18 bp):
AGAAAGGGGGTTGGAGGA
Found at i:48697 original size:51 final size:47
Alignment explanation
Indices: 48637--48741 Score: 156
Period size: 51 Copynumber: 2.1 Consensus size: 47
48627 GACGGGCGGC
*
48637 GGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCGGAAGAAAGGGGGTTGG
1 GGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGC-GAAG-AA-GGGGTTGG
*
48687 AGGAAGAAAGGGGGTTGGGGGAAGAACGGGCGGCGAAGAAGGGGTTGG
1 -GGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGAAGAAGGGGTTGG
48735 GGAAGAA
1 GGAAGAA
48742 CGGGCGGCGG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
47 7 0.13
48 8 0.15
49 2 0.04
50 4 0.08
51 31 0.60
ACGTcount: A:0.30, C:0.06, G:0.56, T:0.08
Consensus pattern (47 bp):
GGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGAAGAAGGGGTTGG
Found at i:48742 original size:29 final size:32
Alignment explanation
Indices: 48688--48774 Score: 108
Period size: 29 Copynumber: 2.8 Consensus size: 32
48678 GGGGGTTGGA
* *
48688 GGAAGAAAGGGGGTTGGGGGAAGAACGGGCGGC
1 GGAAG-AACGGGGTTCGGGGAAGAACGGGCGGC
48721 -GAAGAA-GGGGTT-GGGGAAGAACGGGCGGC
1 GGAAGAACGGGGTTCGGGGAAGAACGGGCGGC
*
48750 GGCAGAACGGGGTTCGGAGGAAGAA
1 GGAAGAACGGGGTTCGG-GGAAGAA
48775 AGGGGTTGGA
Statistics
Matches: 49, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
29 17 0.35
30 11 0.22
31 8 0.16
32 6 0.12
33 7 0.14
ACGTcount: A:0.29, C:0.10, G:0.54, T:0.07
Consensus pattern (32 bp):
GGAAGAACGGGGTTCGGGGAAGAACGGGCGGC
Found at i:48777 original size:80 final size:84
Alignment explanation
Indices: 48607--48798 Score: 281
Period size: 80 Copynumber: 2.4 Consensus size: 84
48597 AACGGGCGGC
* *
48607 AGAAAGGGGGTTGGAGGAAGGACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAGGACGGGCGGCGG
1 AGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGG
*
48672 AAGAAAGGGGGTTGGAGGA
66 AAGAAACGGGGTTGGAGGA
*
48691 AGAAAGGGGGTTGGGGGAAGAACGGGCGGC-GAAG-AA-GGGGTTGG-GGAAGAACGGGCGGCGG
1 AGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGG
*
48752 CAG-AACGGGGTTCGGAGGA
66 AAGAAACGGGGTT-GGAGGA
48771 AGAAA-GGGGTTGGAGGAAGAAC-GGCGGC
1 AGAAAGGGGGTTGGAGGAAGAACGGGCGGC
48799 AGAACAGGGT
Statistics
Matches: 101, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
78 6 0.06
79 24 0.24
80 29 0.29
81 8 0.08
82 2 0.02
83 4 0.04
84 28 0.28
ACGTcount: A:0.28, C:0.09, G:0.55, T:0.07
Consensus pattern (84 bp):
AGAAAGGGGGTTGGAGGAAGAACGGGCGGCGGAAGAAAGGGGGTTGGAGGAAGAACGGGCGGCGG
AAGAAACGGGGTTGGAGGA
Found at i:48779 original size:18 final size:18
Alignment explanation
Indices: 48637--48931 Score: 78
Period size: 18 Copynumber: 18.4 Consensus size: 18
48627 GACGGGCGGC
48637 GGAAGAAAGGGGGTT-GGA
1 GGAAGAAA-GGGGTTCGGA
* * *
48655 GGAAG-GACGGG--CGGC
1 GGAAGAAAGGGGTTCGGA
48670 GGAAGAAAGGGGGTT-GGA
1 GGAAGAAA-GGGGTTCGGA
*
48688 GGAAGAAAGGGGGTT-GGG
1 GGAAGAAA-GGGGTTCGGA
*
48706 GGAAG-AACGGG--CGG-
1 GGAAGAAAGGGGTTCGGA
*
48720 CGAAG-AAGGGGTT-GG-
1 GGAAGAAAGGGGTTCGGA
* *
48735 GGAAG-AACGGG--CGGC
1 GGAAGAAAGGGGTTCGGA
* *
48750 GGCAGAACGGGGTTCGGA
1 GGAAGAAAGGGGTTCGGA
48768 GGAAGAAAGGGGTT-GGA
1 GGAAGAAAGGGGTTCGGA
*
48785 GGAAG-AA-CGG--CGGCA
1 GGAAGAAAGGGGTTCGG-A
*
48800 -G-A-ACA-GGGTTCGGA
1 GGAAGAAAGGGGTTCGGA
48814 GGAA-AAAGGGGTT-GGA
1 GGAAGAAAGGGGTTCGGA
* *
48830 GGAAG-AACGGG--CGGC
1 GGAAGAAAGGGGTTCGGA
*
48845 GGCAGAAA--GG---GG-
1 GGAAGAAAGGGGTTCGGA
*
48857 GG-AGAACGGGGTTCGGA
1 GGAAGAAAGGGGTTCGGA
* *
48874 GGAAG-AATGGG--CGGC
1 GGAAGAAAGGGGTTCGGA
* *
48889 GGCAGAACGGGGTTCGGA
1 GGAAGAAAGGGGTTCGGA
48907 GGAAGAAAAGGGGTT-GGA
1 GGAAG-AAAGGGGTTCGGA
48925 GGAAGAA
1 GGAAGAA
48932 CGGGCGGCGG
Statistics
Matches: 207, Mismatches: 35, Indels: 71
0.66 0.11 0.23
Matches are distributed among these distances:
11 4 0.02
12 2 0.01
13 8 0.04
14 17 0.08
15 44 0.21
16 36 0.17
17 27 0.13
18 61 0.29
19 8 0.04
ACGTcount: A:0.30, C:0.09, G:0.53, T:0.08
Consensus pattern (18 bp):
GGAAGAAAGGGGTTCGGA
Found at i:48840 original size:95 final size:92
Alignment explanation
Indices: 48771--48946 Score: 270
Period size: 95 Copynumber: 1.9 Consensus size: 92
48761 GTTCGGAGGA
48771 AGAAAGGGGTT-GGAGGAAGAA-CGGCGGCAGAACAGGGTTCGGAGG-A-AAAAGGGGTTGGAGG
1 AGAAAGGGGTTCGGAGGAAGAAGCGGCGGCAGAACAGGGTTCGGAGGAAGAAAAGGGGTTGGAGG
48832 AAGAACGGGCGGCGGCAGAAAGGGGGG
66 AAGAACGGGCGGCGGCAGAAAGGGGGG
* *
48859 AGAACGGGGTTCGGAGGAAGAATGGGCGGCGGCAGAACGGGGTTCGGAGGAAGAAAAGGGGTTGG
1 AGAAAGGGGTTCGGAGGAAGAA---GCGGCGGCAGAACAGGGTTCGGAGGAAGAAAAGGGGTTGG
*
48924 AGGAAGAACGGGCGGCGGAAGAA
63 AGGAAGAACGGGCGGCGGCAGAA
48947 GCTGGTCCGG
Statistics
Matches: 78, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
88 10 0.13
89 10 0.13
93 23 0.29
94 1 0.01
95 34 0.44
ACGTcount: A:0.31, C:0.11, G:0.51, T:0.07
Consensus pattern (92 bp):
AGAAAGGGGTTCGGAGGAAGAAGCGGCGGCAGAACAGGGTTCGGAGGAAGAAAAGGGGTTGGAGG
AAGAACGGGCGGCGGCAGAAAGGGGGG
Found at i:51971 original size:39 final size:34
Alignment explanation
Indices: 51913--52103 Score: 102
Period size: 38 Copynumber: 5.2 Consensus size: 34
51903 CGAAAATATT
* **
51913 TATATTATATAGTTTTTTAAAATGTTCTTGAAAGCTTA
1 TATAATATATAG--TTTTAAAACATT-TTGAAAG-TTA
*
51951 TATACAATATATAAGTTTTAAAGCATTTTGAAAGTTA
1 TAT--AATATAT-AGTTTTAAAACATTTTGAAAGTTA
* *
51988 TATAATATATAGTTTT-GATCATTTTGAAA---A
1 TATAATATATAGTTTTAAAACATTTTGAAAGTTA
* * *
52018 TATAATGTATAGTTTTAAAAAAATATTTTTGGAAAATTTA
1 TATAATATATAGTTTT---AAAACA-TTTT-G-AAAGTTA
* *
52058 TATAATATATAGTTTAAAAAAACATTTTGGAAAACTTA
1 TATAATATATAGTTT--TAAAACATTTT-G-AAAGTTA
52096 TATAATAT
1 TATAATAT
52104 TTTTAAAAAC
Statistics
Matches: 124, Mismatches: 14, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
30 16 0.13
33 11 0.09
34 8 0.06
35 11 0.09
36 1 0.01
37 9 0.07
38 31 0.25
39 14 0.11
40 21 0.17
41 2 0.02
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (34 bp):
TATAATATATAGTTTTAAAACATTTTGAAAGTTA
Found at i:52062 original size:40 final size:38
Alignment explanation
Indices: 52017--52128 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 38
52007 CATTTTGAAA
* * *
52017 ATATAATGTATAGTTTTAAAAAAATATTTTTGGAAAATTT
1 ATATAATATATAG-TTTAAAAAAACA-TTTTGGAAAACTT
52057 ATATAATATATAGTTTAAAAAAACATTTTGGAAAACTT
1 ATATAATATATAGTTTAAAAAAACATTTTGGAAAACTT
** *
52095 ATATAATAT-T--TTTAAAAACTCATTTTTGAAAACT
1 ATATAATATATAGTTTAAAAAAACATTTTGGAAAACT
52129 ATCTTACCTC
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 21 0.32
37 1 0.02
38 21 0.32
39 11 0.17
40 12 0.18
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (38 bp):
ATATAATATATAGTTTAAAAAAACATTTTGGAAAACTT
Found at i:52086 original size:38 final size:40
Alignment explanation
Indices: 52017--52103 Score: 133
Period size: 38 Copynumber: 2.2 Consensus size: 40
52007 CATTTTGAAA
* * *
52017 ATATAATGTATAGTTTTAAAAAAATATTTTTGGAAAATTT
1 ATATAATATATAGTTTTAAAAAAACATTTTTGGAAAACTT
52057 ATATAATATATAG-TTTAAAAAAACA-TTTTGGAAAACTT
1 ATATAATATATAGTTTTAAAAAAACATTTTTGGAAAACTT
52095 ATATAATAT
1 ATATAATAT
52104 TTTTAAAAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 21 0.48
39 11 0.25
40 12 0.27
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.41
Consensus pattern (40 bp):
ATATAATATATAGTTTTAAAAAAACATTTTTGGAAAACTT
Found at i:52190 original size:7 final size:7
Alignment explanation
Indices: 52178--52228 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
52168 GACAGTCATT
52178 TTATATA
1 TTATATA
52185 TTATATA
1 TTATATA
* *
52192 GTCTATA
1 TTATATA
52199 TTATATA
1 TTATATA
52206 TTAT-TA
1 TTATATA
* *
52212 TTATTTT
1 TTATATA
52219 TTAT-TA
1 TTATATA
52225 TTAT
1 TTAT
52229 TTCATTTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
6 11 0.30
7 26 0.70
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (7 bp):
TTATATA
Found at i:52229 original size:13 final size:13
Alignment explanation
Indices: 52206--52230 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52196 ATATTATATA
52206 TTATTATTATTTT
1 TTATTATTATTTT
52219 TTATTATTATTT
1 TTATTATTATTT
52231 CATTTCATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTATTATTTT
Found at i:53509 original size:17 final size:16
Alignment explanation
Indices: 53467--53516 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
53457 TATTATTTTA
53467 TTTTTATTCAATTTGATCC
1 TTTTT-TTC-ATTT-ATCC
*
53486 TTTTTTTTATTTATCC
1 TTTTTTTCATTTATCC
53502 TTTGTTTTCATTTAT
1 TTT-TTTTCATTTAT
53517 TTTATTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.25
17 14 0.50
18 2 0.07
19 5 0.18
ACGTcount: A:0.16, C:0.12, G:0.04, T:0.68
Consensus pattern (16 bp):
TTTTTTTCATTTATCC
Found at i:53577 original size:4 final size:4
Alignment explanation
Indices: 53568--53643 Score: 52
Period size: 4 Copynumber: 19.5 Consensus size: 4
53558 CTCTTTAATC
* * *
53568 TTTA TTTA TTTA TTTA TTCTC TTTC TTTGA CTT- TTTA TTTA --TA TTTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA
* **
53615 TATA TTTA TTTA TTTA -ACA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
53644 GTTATTGTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
2 2 0.04
3 3 0.05
4 46 0.82
5 5 0.09
ACGTcount: A:0.24, C:0.07, G:0.01, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:53668 original size:14 final size:15
Alignment explanation
Indices: 53638--53670 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
53628 TTAACATTTA
53638 TTTATTGTTATTGTT
1 TTTATTGTTATTGTT
*
53653 TTTATT-TTATTTTT
1 TTTATTGTTATTGTT
53667 TTTA
1 TTTA
53671 CTAACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (15 bp):
TTTATTGTTATTGTT
Found at i:53747 original size:6 final size:6
Alignment explanation
Indices: 53736--53762 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
53726 AATCGAATAT
53736 TTTAAA TTTAAA TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT
53763 TCAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:65513 original size:31 final size:31
Alignment explanation
Indices: 65472--65549 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
65462 CAGTTACGTC
*
65472 GGGGACCATATTGCAAATGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
*
65503 GGGGATCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
* **
65534 AGGGACTGTATTGCAA
1 GGGGACCATATTGCAA
65550 GTTTTAAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (31 bp):
GGGGACCATATTGCAAACGGACTAAATGTTG
Found at i:74191 original size:11 final size:11
Alignment explanation
Indices: 74170--74200 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
74160 TATTTTTATT
74170 AAAAAATAAAAG
1 AAAAAA-AAAAG
74182 AAAAAAAAAAG
1 AAAAAAAAAAG
74193 AAAAAAAA
1 AAAAAAAA
74201 GAACCGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.90, C:0.00, G:0.06, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:75068 original size:2 final size:2
Alignment explanation
Indices: 75047--75110 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
75037 ACATAAGTGC
* * *
75047 AT AT AC AT AC AT AC 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
75089 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
75111 TTTACGAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:78585 original size:14 final size:13
Alignment explanation
Indices: 78534--78588 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 13
78524 ACTTCTAGAC
78534 TATTATTAA-ATT
1 TATTATTAAGATT
*
78546 ATATTAGGTTAATATT
1 -TATTA--TTAAGATT
78562 TATTATTAAGATT
1 TATTATTAAGATT
78575 TATTAATTAAGATT
1 TATT-ATTAAGATT
78589 AGATATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
13 16 0.43
14 9 0.24
15 9 0.24
16 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATTATTAAGATT
Found at i:83830 original size:22 final size:20
Alignment explanation
Indices: 83805--83852 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
83795 TATCATTAAC
*
83805 AATTTAACTATTTATCAATTTT
1 AATTTAACTATTGAT--ATTTT
* *
83827 AATTTTATTATTGATATTTT
1 AATTTAACTATTGATATTTT
83847 AATTTA
1 AATTTA
83853 GTTAATTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
AATTTAACTATTGATATTTT
Found at i:83892 original size:22 final size:22
Alignment explanation
Indices: 83845--83892 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
83835 TATTGATATT
*
83845 TTAATTTAGTTAATTTGATCAT
1 TTAATTTAGTTAATTTGATCAA
* *
83867 TTAA-TTATTTAATTATTATCAA
1 TTAATTTAGTTAATT-TGATCAA
83889 TTAA
1 TTAA
83893 GTCACTTACC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (22 bp):
TTAATTTAGTTAATTTGATCAA
Found at i:86248 original size:14 final size:14
Alignment explanation
Indices: 86231--86257 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
86221 TTTTTTTATT
86231 TTTTTTAAAATATA
1 TTTTTTAAAATATA
86245 TTTTTTAAAATAT
1 TTTTTTAAAATAT
86258 GCTTTTGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTTTTAAAATATA
Found at i:88886 original size:6 final size:6
Alignment explanation
Indices: 88875--88905 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
88865 TTTTCTAATT
88875 ATATTC ATATTC ATATTC ATATTC ATATTC A
1 ATATTC ATATTC ATATTC ATATTC ATATTC A
88906 AGATGTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTC
Found at i:89363 original size:25 final size:26
Alignment explanation
Indices: 89309--89360 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
89299 TATAAACATC
*
89309 AAATACAATAACTAATACTATTTATT
1 AAATAAAATAACTAATACTATTTATT
*
89335 -AATAAAATAA-TAATATTATTT-TT
1 AAATAAAATAACTAATACTATTTATT
89358 AAA
1 AAA
89361 ATACTAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 2 0.09
24 12 0.52
25 9 0.39
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (26 bp):
AAATAAAATAACTAATACTATTTATT
Found at i:89416 original size:25 final size:26
Alignment explanation
Indices: 89388--89443 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
89378 TTAATATTAT
* *
89388 TTATGTCAAT-ATTATTGTTAAAATA
1 TTATGTCAATAATTATTATAAAAATA
* *
89413 TTATGTCTATAATTTTTATAAAAATA
1 TTATGTCAATAATTATTATAAAAATA
89439 TTATG
1 TTATG
89444 ATTATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (26 bp):
TTATGTCAATAATTATTATAAAAATA
Found at i:89456 original size:26 final size:26
Alignment explanation
Indices: 89407--89457 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
89397 TATTATTGTT
*
89407 AAAATATTATGTCTATAATTTTTATA
1 AAAATATTATGTCTATAATATTTATA
*
89433 AAAATATTATGAT-TATTATATTTAT
1 AAAATATTATG-TCTATAATATTTAT
89458 TAAGTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (26 bp):
AAAATATTATGTCTATAATATTTATA
Found at i:89514 original size:42 final size:42
Alignment explanation
Indices: 89468--89548 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
89458 TAAGTAAAAT
* *
89468 TATTATAAAGTATATTAATTATTTATTAAAATAAGAATAATA
1 TATTATAAAGTATATTAATTACTTATCAAAATAAGAATAATA
* * *
89510 TATTATTAATTATATTAATTACTTATCAAAATAATAATA
1 TATTATAAAGTATATTAATTACTTATCAAAATAAGAATA
89549 TTATTAAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (42 bp):
TATTATAAAGTATATTAATTACTTATCAAAATAAGAATAATA
Found at i:90349 original size:59 final size:60
Alignment explanation
Indices: 90209--90352 Score: 166
Period size: 59 Copynumber: 2.4 Consensus size: 60
90199 AATCTTATTT
* * * * ** *
90209 TAAATTGATCCTTAAACTTTTGAATATTCCATTTTAATCCCTAAACTTTGACTTTCATTC
1 TAAATTGATCCTTAAACTTTTGAACATTCAATTTTAATACCTAAACTATGACACTCATAC
* *
90269 TAAATTAATCCTTAAAATTTTGAACATTCTAATTTT-ATACC-AAACTATGACACTCATAC
1 TAAATTGATCCTTAAACTTTTGAACATTC-AATTTTAATACCTAAACTATGACACTCATAC
* *
90328 TAAATTGATCATCAAACTTTTGAAC
1 TAAATTGATCCTTAAACTTTTGAAC
90353 CTTTTTCATC
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
59 35 0.50
60 30 0.43
61 5 0.07
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (60 bp):
TAAATTGATCCTTAAACTTTTGAACATTCAATTTTAATACCTAAACTATGACACTCATAC
Found at i:91422 original size:6 final size:6
Alignment explanation
Indices: 91411--91451 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
91401 GCACACCATG
91411 TCAATC TCAATC TCAATC TCAATC TCAATC TCAATC T-AATC
1 TCAATC TCAATC TCAATC TCAATC TCAATC TCAATC TCAATC
91452 GCTGTTTGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (6 bp):
TCAATC
Found at i:97782 original size:2 final size:2
Alignment explanation
Indices: 97775--97799 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
97765 CATAATCATA
97775 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
97800 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:97804 original size:2 final size:2
Alignment explanation
Indices: 97799--97832 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
97789 ACACACACAC
97799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
97833 GATAAAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104222 original size:16 final size:17
Alignment explanation
Indices: 104201--104233 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
104191 TTACTATTCA
104201 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
104217 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
104234 TGTCGGCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.36
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:115060 original size:9 final size:9
Alignment explanation
Indices: 115046--115073 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
115036 TATTAATATT
115046 TTAAAATAA
1 TTAAAATAA
115055 TTAAAATAA
1 TTAAAATAA
115064 TTAAAATAA
1 TTAAAATAA
115073 T
1 T
115074 ATATTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TTAAAATAA
Found at i:115109 original size:23 final size:23
Alignment explanation
Indices: 115055--115109 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
115045 TTTAAAATAA
* *
115055 TTAAAATAATTAAAATAATATATT
1 TTAAAAT-ATAAAAATAATAAATT
*
115079 TTATAATATAAAAATAA-AAATT
1 TTAAAATATAAAAATAATAAATT
115101 CTTAAAATA
1 -TTAAAATA
115110 ATAATTATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.15
23 16 0.62
24 6 0.23
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTAAAATATAAAAATAATAAATT
Found at i:115114 original size:3 final size:3
Alignment explanation
Indices: 115106--115175 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
115096 AAATTCTTAA
*
115106 AAT AAT AAT TAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
115153 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
115176 CTAGACTGGG
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:117967 original size:23 final size:23
Alignment explanation
Indices: 117936--117993 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
117926 TAAGCTACCA
*
117936 AAAGACAGAGAAAAACGAGCCAC
1 AAAGGCAGAGAAAAACGAGCCAC
* *** *
117959 AAAGGCAGAGATAAATTTGCCAT
1 AAAGGCAGAGAAAAACGAGCCAC
117982 AAAGGCAGAGAA
1 AAAGGCAGAGAA
117994 TATGTCACAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.52, C:0.16, G:0.24, T:0.09
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACGAGCCAC
Found at i:118171 original size:2 final size:2
Alignment explanation
Indices: 118164--118191 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
118154 AAAGAAGAAA
118164 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
118192 GGGAAGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:119132 original size:19 final size:18
Alignment explanation
Indices: 119107--119162 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
119097 ACCGATAAAT
119107 CGAACCGAACCAAAAAAC
1 CGAACCGAACCAAAAAAC
* *
119125 TTGAACCGTTA--AAAAAAC
1 -CGAACCG-AACCAAAAAAC
119143 CGAACCGAACCGAAAAAAC
1 CGAACCGAACC-AAAAAAC
119162 C
1 C
119163 AGTTTCGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 1 0.03
17 6 0.21
18 7 0.24
19 14 0.48
20 1 0.03
ACGTcount: A:0.52, C:0.29, G:0.12, T:0.07
Consensus pattern (18 bp):
CGAACCGAACCAAAAAAC
Found at i:120895 original size:23 final size:22
Alignment explanation
Indices: 120855--120897 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
120845 AAGAATATAA
* *
120855 TTATTTTTATTATGTTTTATGT
1 TTATTTTTATAATATTTTATGT
120877 TTATTTTTAATAATATTTTAT
1 TTATTTTT-ATAATATTTTAT
120898 AATGTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (22 bp):
TTATTTTTATAATATTTTATGT
Found at i:121320 original size:19 final size:19
Alignment explanation
Indices: 121296--121334 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
121286 AATAGTATCT
*
121296 TATATTA-ATTAATATATAA
1 TATATTATAATAA-ATATAA
121315 TATATTATAATAAATATAA
1 TATATTATAATAAATATAA
121334 T
1 T
121335 TCCATATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATATTATAATAAATATAA
Found at i:124555 original size:5 final size:5
Alignment explanation
Indices: 124545--124570 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
124535 TTAATGTTTC
124545 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
124571 ATATATGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:125066 original size:22 final size:21
Alignment explanation
Indices: 125038--125101 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 21
125028 CCGTTCAAAC
125038 TTCAAATTCATCTTTTAGTGAA
1 TTCAAATTCAT-TTTTAGTGAA
125060 TTCAAATTCATTTTTTTTTGAGTGAA
1 TTCAAATTCA----TTTTT-AGTGAA
125086 TTCAAATTCATTTTTA
1 TTCAAATTCATTTTTA
125102 ATTTATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
21 1 0.03
22 15 0.41
25 4 0.11
26 17 0.46
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.52
Consensus pattern (21 bp):
TTCAAATTCATTTTTAGTGAA
Found at i:125085 original size:26 final size:25
Alignment explanation
Indices: 125050--125100 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
125040 CAAATTCATC
125050 TTTTAGTGAATTCAAATTCATTTTT
1 TTTTAGTGAATTCAAATTCATTTTT
125075 TTTTGAGTGAATTCAAATTCATTTTT
1 TTTT-AGTGAATTCAAATTCATTTTT
125101 AATTTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (25 bp):
TTTTAGTGAATTCAAATTCATTTTT
Found at i:126925 original size:25 final size:25
Alignment explanation
Indices: 126891--126940 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
126881 TTTATGATAT
126891 ATTTCAATATGTTACATTAGTGGTA
1 ATTTCAATATGTTACATTAGTGGTA
126916 ATTTCAATATGTTACATTAGTGGTA
1 ATTTCAATATGTTACATTAGTGGTA
126941 TGTCTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (25 bp):
ATTTCAATATGTTACATTAGTGGTA
Found at i:138090 original size:16 final size:16
Alignment explanation
Indices: 138069--138105 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
138059 TAAGTCGAGG
*
138069 ATGCCGCCAGAAGAGA
1 ATGCCGCCAAAAGAGA
138085 ATGCCGCCAAAAGAGA
1 ATGCCGCCAAAAGAGA
138101 ATGCC
1 ATGCC
138106 TTATTAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.27, G:0.27, T:0.08
Consensus pattern (16 bp):
ATGCCGCCAAAAGAGA
Found at i:139312 original size:17 final size:17
Alignment explanation
Indices: 139286--139337 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
139276 ATTGTTCAAG
*
139286 AATAACTTAAAGAAATT
1 AATAATTTAAAGAAATT
**
139303 AATAATTTAAAGTTGATT
1 AATAATTTAAAG-AAATT
*
139321 AATAATTTAAACAAATT
1 AATAATTTAAAGAAATT
139338 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (17 bp):
AATAATTTAAAGAAATT
Found at i:139604 original size:12 final size:12
Alignment explanation
Indices: 139561--139605 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
139551 GATCACCACT
* *
139561 ACCATCACCACC
1 ACCATCATCATC
139573 ACCATCATCATC
1 ACCATCATCATC
*
139585 ACTATCATCATC
1 ACCATCATCATC
*
139597 ACCCTCATC
1 ACCATCATC
139606 TACATGGTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (12 bp):
ACCATCATCATC
Found at i:146196 original size:21 final size:22
Alignment explanation
Indices: 146172--146253 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
146162 TTGGTGCAGA
* *
146172 GGGAATCGATCCCCCCCATGA-
1 GGGAACCGATTCCCCCCATGAG
** *
146193 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCCATG-AG
146216 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGATTCCCCCCATGAG
* *
146237 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
146254 TGGGGTTCTG
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
21 32 0.64
22 1 0.02
23 17 0.34
ACGTcount: A:0.23, C:0.37, G:0.23, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCATGAG
Found at i:148230 original size:25 final size:28
Alignment explanation
Indices: 148201--148261 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 28
148191 ATATTTTGGA
*
148201 ATGTTTGAATTTGTGGAT-TGTGAA-TT
1 ATGTTTGAATTTATGGATGTGTGAACTT
*
148227 -TGTTTGGATTTATGGATGGTGTGAACTT
1 ATGTTTGAATTTATGGAT-GTGTGAACTT
148255 ATGTTTG
1 ATGTTTG
148262 GTGTGATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
25 15 0.52
27 6 0.21
28 2 0.07
29 6 0.21
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.49
Consensus pattern (28 bp):
ATGTTTGAATTTATGGATGTGTGAACTT
Found at i:148493 original size:13 final size:13
Alignment explanation
Indices: 148475--148518 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
148465 AAAGGGGGAG
148475 AAGTGTGTGTTTT
1 AAGTGTGTGTTTT
148488 AA--GTGTGTTTT
1 AAGTGTGTGTTTT
*
148499 ATGTGTGT-TTTT
1 AAGTGTGTGTTTT
148511 AAGTGTGT
1 AAGTGTGT
148519 TTTAAAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.37
12 11 0.41
13 6 0.22
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.55
Consensus pattern (13 bp):
AAGTGTGTGTTTT
Found at i:148503 original size:9 final size:11
Alignment explanation
Indices: 148479--148523 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
148469 GGGGAGAAGT
148479 GTGTGTTTTAA
1 GTGTGTTTTAA
*
148490 GTGTGTTTTAT
1 GTGTGTTTTAA
148501 GTGTGTTTTTAA
1 GTGTG-TTTTAA
148513 GTGTGTTTTAA
1 GTGTGTTTTAA
148524 AATGATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 21 0.68
12 10 0.32
ACGTcount: A:0.16, C:0.00, G:0.27, T:0.58
Consensus pattern (11 bp):
GTGTGTTTTAA
Found at i:148514 original size:23 final size:24
Alignment explanation
Indices: 148477--148522 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
148467 AGGGGGAGAA
148477 GTGTGTGTTTTAAGTGTGTTTTAT
1 GTGTGTGTTTTAAGTGTGTTTTAT
148501 GTGTGT-TTTTAAGTGTGTTTTA
1 GTGTGTGTTTTAAGTGTGTTTTA
148523 AAATGATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.13, C:0.00, G:0.28, T:0.59
Consensus pattern (24 bp):
GTGTGTGTTTTAAGTGTGTTTTAT
Found at i:150737 original size:4 final size:4
Alignment explanation
Indices: 150728--150872 Score: 98
Period size: 4 Copynumber: 34.8 Consensus size: 4
150718 ATATCCCTTC
* **
150728 AAAT AAAT AAAT AAAT AAATT CGAAA- CAAT AAAAT AAAT TCA- AAAT
1 AAAT AAAT AAAT AAAT AAA-T --AAAT AAAT -AAAT AAAT AAAT AAAT
* ** * *
150774 AAAT AAAT AAAT AAAC AAAT TCA- AAAT AAAT AAAT CCACCAT AAAT AAAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --A-AAT AAAT AAAT
* *
150824 AAAT TAAT CAAT AAAT AAAT AAAT AAAT CCAAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT AAAT AAAT AAA
150873 AATTACTGTC
Statistics
Matches: 110, Mismatches: 19, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
3 4 0.04
4 91 0.83
5 5 0.05
6 5 0.05
7 5 0.05
ACGTcount: A:0.68, C:0.08, G:0.01, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:150805 original size:42 final size:42
Alignment explanation
Indices: 150728--150872 Score: 141
Period size: 42 Copynumber: 3.4 Consensus size: 42
150718 ATATCCCTTC
*
150728 AAATAAATAAATAAATAAATTCGAAACAATAAAATAAATTCAAAAT
1 AAATAAATAAATAAACAAATTC--AA-AAT-AAATAAATTCAAAAT
* **
150774 AAATAAATAAATAAACAAATTCAAAATAAATAAATCCACCAT
1 AAATAAATAAATAAACAAATTCAAAATAAATAAATTCAAAAT
* * ** *
150816 AAATAAAAAAATTAATC-AATAAATAAATAAATAAA-TCCAAAT
1 AAATAAATAAA-TAAACAAATTCA-AAATAAATAAATTCAAAAT
150858 AAATAAATAAATAAA
1 AAATAAATAAATAAA
150873 AATTACTGTC
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
41 3 0.04
42 39 0.47
43 18 0.22
44 2 0.02
46 21 0.25
ACGTcount: A:0.68, C:0.08, G:0.01, T:0.23
Consensus pattern (42 bp):
AAATAAATAAATAAACAAATTCAAAATAAATAAATTCAAAAT
Found at i:157983 original size:28 final size:27
Alignment explanation
Indices: 157944--157996 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
157934 ATGACTTTCA
157944 ATACATATACAATGGGCCTTTAAATTG
1 ATACATATACAATGGGCCTTTAAATTG
157971 ATACAATATACAATGGGCCTTTAAAT
1 ATAC-ATATACAATGGGCCTTTAAAT
157997 CGTTTCAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (27 bp):
ATACATATACAATGGGCCTTTAAATTG
Found at i:161349 original size:19 final size:20
Alignment explanation
Indices: 161303--161350 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
161293 TTAAAATAAT
* *
161303 AATAAATTTAATATTTTTAA
1 AATAAATTTAATAATTTAAA
161323 AATAAATTTAA-AATTTAAA
1 AATAAATTTAATAATTTAAA
*
161342 AATTAATTT
1 AATAAATTT
161351 TATCGAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAAATTTAATAATTTAAA
Found at i:161831 original size:2 final size:2
Alignment explanation
Indices: 161826--161851 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
161816 TTTTTTAGAA
161826 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
161852 TAACGCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:165217 original size:17 final size:17
Alignment explanation
Indices: 165155--165225 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 17
165145 TGACAAATTT
*
165155 TAAAAAAAATATTTT-A
1 TAAAAAATATATTTTAA
* **
165171 TTAAAAAT-TATCATAA
1 TAAAAAATATATTTTAA
*
165187 -AAAATAATAAATTTTAA
1 TAAAA-AATATATTTTAA
*
165204 TAAAAAATATATTTTAT
1 TAAAAAATATATTTTAA
165221 TAAAA
1 TAAAA
165226 TTCGTAATTC
Statistics
Matches: 41, Mismatches: 10, Indels: 7
0.71 0.17 0.12
Matches are distributed among these distances:
15 7 0.17
16 10 0.24
17 20 0.49
18 4 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAATATATTTTAA
Found at i:166471 original size:16 final size:16
Alignment explanation
Indices: 166417--166472 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
166407 AAACTACGCA
166417 TTTAATATTTA-A-AT
1 TTTAATATTTATATAT
166431 TATT-AT-TTTAATATAT
1 T-TTAATATTT-ATATAT
166447 TTTAATATTTATAT-T
1 TTTAATATTTATATAT
166462 TTTAATTATTT
1 TTTAA-TATTT
166473 TAAAATCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.09
14 4 0.11
15 11 0.31
16 14 0.40
17 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTAATATTTATATAT
Found at i:169211 original size:227 final size:229
Alignment explanation
Indices: 168709--169244 Score: 909
Period size: 227 Copynumber: 2.4 Consensus size: 229
168699 GTTATATTGT
* *
168709 AAAGTATCTATCATTTTTATAAAAGTGTCTATACTTATTTCACTGT-GAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
168773 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
* *
168838 ATAATTTTGTGTGTAAATGAAATTATTAAATTAATATTATAGGTGGAAAACATGAAACACTATTA
131 ATAATTTTGTGTGTAAATAAAATTACTAAATTAATATTATAGGTGGAAAACATGAAACACTATTA
168903 AAAAAATTGAAACATAAATTACATAACTTTAAAA
196 AAAAAATTGAAACATAAATTACATAACTTTAAAA
*
168937 AAAGTATATATTATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
* *
169002 ATCTTTGGTTAATATTGTTAAATTTAAATTTTAAATAATATTTTATAAAATATC-AAATAATCAA
66 ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
* * *
169066 ATAATTTTTTGTGTAAATAAAATT-CTAAA-TAATATTGTCGGTGGAAAACATGAAACACTATTA
131 ATAATTTTGTGTGTAAATAAAATTACTAAATTAATATTATAGGTGGAAAACATGAAACACTATT-
169129 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
195 AAAAAAATTGAAACATAAATTACATAACTTTAAAA
* * *
169164 AAAGTATATATCATTTTTATAAAAGTGTCCATATTTATTTGACTGTGGAAAACATATTTATTATT
1 AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
*
169229 ATATTTGGTTAATATT
66 ATCTTTGGTTAATATT
169245 ATCGAAAGTA
Statistics
Matches: 291, Mismatches: 15, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
226 31 0.11
227 115 0.40
228 74 0.25
229 71 0.24
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (229 bp):
AAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAATATATTTATTATT
ATCTTTGGTTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAA
ATAATTTTGTGTGTAAATAAAATTACTAAATTAATATTATAGGTGGAAAACATGAAACACTATTA
AAAAAATTGAAACATAAATTACATAACTTTAAAA
Found at i:182928 original size:8 final size:8
Alignment explanation
Indices: 182915--182955 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
182905 CTCATTTTCA
182915 GAGAATTT
1 GAGAATTT
182923 GAGAATTT
1 GAGAATTT
*
182931 -AGAGTTT
1 GAGAATTT
*
182938 GGGAATTT
1 GAGAATTT
182946 GAGAATTT
1 GAGAATTT
182954 GA
1 GA
182956 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:183393 original size:127 final size:128
Alignment explanation
Indices: 183036--183513 Score: 861
Period size: 128 Copynumber: 3.7 Consensus size: 128
183026 ACTATACACA
* *
183036 TGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
183101 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
183164 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
183229 TTATATCACTCATGTCCCTCGGGGACACTAGAT-ATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTA-TTCATATCAGTACCTATTATTTCTCAGGGGACT
*
183292 TGAAGGCGCGTTCCC-GGGGAGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* *
183356 TTATGTCACTAATGTCCCTCGGGGACACTATTCATATCAGTACCAATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
183419 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
183484 TTATGTCACCCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
183514 GATATATCAG
Statistics
Matches: 335, Mismatches: 12, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
126 1 0.00
127 120 0.36
128 213 0.64
129 1 0.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:183508 original size:255 final size:256
Alignment explanation
Indices: 183036--183525 Score: 919
Period size: 255 Copynumber: 1.9 Consensus size: 256
183026 ACTATACACA
*
183036 TGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTA
1 TGAAGGCGCGTTCCCAGGGGAGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTA
* *
183101 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACTTG
66 TTATGTCACTAATGTCCCTCGGGGACACTATTCATATCAGTACCAATTATTTCTCAGGGGACTTG
183166 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
131 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
183231 ATATCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
196 ATATCACCCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
*
183292 TGAAGGCGCGTTCCC-GGGGAGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCAGGGGAGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTA
183356 TTATGTCACTAATGTCCCTCGGGGACACTATTCATATCAGTACCAATTATTTCTCAGGGGACTTG
66 TTATGTCACTAATGTCCCTCGGGGACACTATTCATATCAGTACCAATTATTTCTCAGGGGACTTG
183421 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
131 AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
183486 ATGTCACCCATGTCCCTCGGGGACACTAGATATATCAGTA
196 ATATCACCCATGTCCCTCGGGGACACTAGATATATCAGTA
183526 AATCAGGTAA
Statistics
Matches: 228, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
255 213 0.93
256 15 0.07
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (256 bp):
TGAAGGCGCGTTCCCAGGGGAGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTA
TTATGTCACTAATGTCCCTCGGGGACACTATTCATATCAGTACCAATTATTTCTCAGGGGACTTG
AAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
ATATCACCCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:183663 original size:23 final size:22
Alignment explanation
Indices: 183627--183669 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
183617 AAATTAGATA
*
183627 AAATGTGATGGATAAATTGAAT
1 AAATGTGAAGGATAAATTGAAT
*
183649 AAATGTGAAGTGATAAGTTGA
1 AAATGTGAAG-GATAAATTGA
183670 TTGTGACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.30
Consensus pattern (22 bp):
AAATGTGAAGGATAAATTGAAT
Found at i:184078 original size:17 final size:19
Alignment explanation
Indices: 184048--184094 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
184038 TAATAATTAT
* *
184048 ATAAATATTTTTTA-ATAA
1 ATAAATAATATTTACATAA
184066 A-AAATAATATTTACATAA
1 ATAAATAATATTTACATAA
*
184084 ATATATAATAT
1 ATAAATAATAT
184095 AAAATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 6 0.25
19 8 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAATAATATTTACATAA
Found at i:184131 original size:34 final size:34
Alignment explanation
Indices: 184068--184134 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
184058 TTTAATAAAA
* *
184068 AATAATATTTACATAAATATATAATATAAAATAT
1 AATAATATTTACATAAAAATATAACATAAAATAT
184102 AATAACTATTTA-A-AAAAATACTAACATAAAATA
1 AATAA-TATTTACATAAAAATA-TAACATAAAATA
184135 AATTTCTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 6 0.21
34 17 0.59
35 6 0.21
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (34 bp):
AATAATATTTACATAAAAATATAACATAAAATAT
Found at i:184985 original size:30 final size:30
Alignment explanation
Indices: 184946--185017 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
184936 TTTATGTACT
* *
184946 TAAAATATTTTTTT-GTCAAAATAAATACC
1 TAAACTATTTTTTTAATCAAAATAAATACC
* **
184975 TAAAGTTATTTTTTTAATCAAAATAGGTACC
1 TAAA-CTATTTTTTTAATCAAAATAAATACC
185006 TAAACTATTTTT
1 TAAACTATTTTT
185018 AAGGCTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.11
30 16 0.44
31 16 0.44
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (30 bp):
TAAACTATTTTTTTAATCAAAATAAATACC
Found at i:186847 original size:32 final size:32
Alignment explanation
Indices: 186783--186847 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
186773 GTGAATGAGC
* *
186783 TTCTGCTTTTGCTTGTATATTTTATAAGGAGT
1 TTCTGCTTTTGCTTATATATTTTATAACGAGT
* *
186815 TTCTGCTTTTGCTTATGTATTTTATATCGAGT
1 TTCTGCTTTTGCTTATATATTTTATAACGAGT
186847 T
1 T
186848 GTCAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.55
Consensus pattern (32 bp):
TTCTGCTTTTGCTTATATATTTTATAACGAGT
Found at i:190257 original size:13 final size:13
Alignment explanation
Indices: 190239--190264 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
190229 GTTCACATTG
190239 ATTGACATGAACT
1 ATTGACATGAACT
190252 ATTGACATGAACT
1 ATTGACATGAACT
190265 GGGTAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATTGACATGAACT
Found at i:191593 original size:19 final size:20
Alignment explanation
Indices: 191569--191660 Score: 62
Period size: 20 Copynumber: 4.6 Consensus size: 20
191559 AAATGACCAA
*
191569 CAAATTCGCAACGCGATCT-
1 CAAATTCGCAACGCGAACTC
* *
191588 CAAATTCGTAACGTGAACTC
1 CAAATTCGCAACGCGAACTC
* ** *
191608 CAATTTCGCAAC-ATAAGTTC
1 CAAATTCGCAACGCGAA-CTC
* **
191628 CAAAATCGCAACGCGGTCTTC
1 CAAATTCGCAACGCGAAC-TC
191649 CAAATTCGCAAC
1 CAAATTCGCAAC
191661 ACAAATAGGT
Statistics
Matches: 53, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
19 18 0.34
20 22 0.42
21 13 0.25
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACGCGAACTC
Found at i:191682 original size:20 final size:20
Alignment explanation
Indices: 191657--191703 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
191647 TCCAAATTCG
191657 CAACACAAATAGGTAAATCC
1 CAACACAAATAGGTAAATCC
* * *
191677 CAACACGAATATGTAAATCG
1 CAACACAAATAGGTAAATCC
191697 CAACACA
1 CAACACA
191704 GAAGTCAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.26, G:0.11, T:0.15
Consensus pattern (20 bp):
CAACACAAATAGGTAAATCC
Found at i:191905 original size:20 final size:20
Alignment explanation
Indices: 191880--191951 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
191870 GGAGAATTCG
191880 CGTTGCGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* **
191900 CGTTGCGATTTACCTATTCG
1 CGTTGCGATTTACATATTAT
* * *
191920 CATTGTGAATTACATATTAT
1 CGTTGCGATTTACATATTAT
191940 CGTTGCGATTTA
1 CGTTGCGATTTA
191952 ACTATTCGCA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:191933 original size:40 final size:40
Alignment explanation
Indices: 191875--191967 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
191865 AATTTGGAGA
* * * *
191875 ATTCGCGTTGCGATTTACATATTATCGTTGCGATTTACCT
1 ATTCGCATTGTGAATTACATATTATCGTTGCGATTTAACT
191915 ATTCGCATTGTGAATTACATATTATCGTTGCGATTTAACT
1 ATTCGCATTGTGAATTACATATTATCGTTGCGATTTAACT
191955 ATTCGCATTGTGA
1 ATTCGCATTGTGA
191968 TTTAACTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (40 bp):
ATTCGCATTGTGAATTACATATTATCGTTGCGATTTAACT
Found at i:191969 original size:20 final size:20
Alignment explanation
Indices: 191906--191984 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
191896 TTATCGTTGC
*
191906 GATTTACCTATTCGCATTGT
1 GATTTAACTATTCGCATTGT
* ** * *
191926 GAATT-ACATATTATCGTTGC
1 GATTTAAC-TATTCGCATTGT
191946 GATTTAACTATTCGCATTGT
1 GATTTAACTATTCGCATTGT
*
191966 GATTTAACTATTCACATTG
1 GATTTAACTATTCGCATTG
191985 CGAATTTGAC
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.93
21 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
GATTTAACTATTCGCATTGT
Found at i:192287 original size:105 final size:105
Alignment explanation
Indices: 192156--192367 Score: 354
Period size: 105 Copynumber: 2.0 Consensus size: 105
192146 AAAATCGCAA
*
192156 TGCGAATTTCATTTTCGCAATGCTAATTACCTATATCGGTAATTAGCATTGCGAAATTCGAGTTG
1 TGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCATTGCGAAATTCGAGTTG
192221 CAAATTTGGAGAATTCGAGTAT-CGATTTACATATTATCGT
66 CAAATTTGGAGAATTCGAGT-TGCGATTTACATATTATCGT
* *
192261 TGCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTG
1 TGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCATTGCGAAATTCGAGTTG
* * *
192326 CAAATTTGGAGAATTTGCGTTGTGATTTACATATTATCGT
66 CAAATTTGGAGAATTCGAGTTGCGATTTACATATTATCGT
192366 TG
1 TG
192368 TGATTTACCT
Statistics
Matches: 100, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
104 1 0.01
105 99 0.99
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (105 bp):
TGCGAATTTCATTTTCGCAACGCTAATTACCTATATCGGTAATTAGCATTGCGAAATTCGAGTTG
CAAATTTGGAGAATTCGAGTTGCGATTTACATATTATCGT
Found at i:192368 original size:20 final size:20
Alignment explanation
Indices: 192342--192390 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
192332 TGGAGAATTT
192342 GCGTTGTGATTTACATATTA
1 GCGTTGTGATTTACATATTA
* * *
192362 TCGTTGTGATTTACCTATTC
1 GCGTTGTGATTTACATATTA
192382 GCGTTGTGA
1 GCGTTGTGA
192391 ATTTGACTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.45
Consensus pattern (20 bp):
GCGTTGTGATTTACATATTA
Found at i:193194 original size:15 final size:15
Alignment explanation
Indices: 193168--193203 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
193158 ATAAGGAGTT
*
193168 GAAGAGGGAGAAGGA
1 GAAGAAGGAGAAGGA
*
193183 GGAGAAGGAGAAGGA
1 GAAGAAGGAGAAGGA
193198 GAAGAA
1 GAAGAA
193204 CGAGGAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAGAAGGA
Found at i:203636 original size:23 final size:23
Alignment explanation
Indices: 203593--203644 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
203583 AAAACTCAAG
203593 AAAAGAAAAGAAAATACATAATA-T
1 AAAA-AAAAGAAAATACATAA-AGT
203617 AAAAAAAAGAAAATGA-ATAAAGT
1 AAAAAAAAGAAAAT-ACATAAAGT
203640 AAAAA
1 AAAAA
203645 TAAAAGACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 1 0.04
23 20 0.77
24 5 0.19
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.13
Consensus pattern (23 bp):
AAAAAAAAGAAAATACATAAAGT
Found at i:209718 original size:24 final size:24
Alignment explanation
Indices: 209691--209745 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
209681 CTGCATGTAC
*
209691 TCTCACACAC-CCACTTAACAGTAA
1 TCTCACACACTCC-CTTAACAGCAA
209715 TCTCACACACTCCCTTAACAGCAA
1 TCTCACACACTCCCTTAACAGCAA
*
209739 CCTCACA
1 TCTCACA
209746 TATTATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.35, C:0.42, G:0.04, T:0.20
Consensus pattern (24 bp):
TCTCACACACTCCCTTAACAGCAA
Found at i:209939 original size:28 final size:28
Alignment explanation
Indices: 209855--209956 Score: 91
Period size: 28 Copynumber: 3.5 Consensus size: 28
209845 TTTCATTTAA
*
209855 ATACCTAAAGTATTTTTTGCTCAAAATA-
1 ATACTTAAAGTATTTTTTG-TCAAAATAG
*
209883 ACTA-TATAAAGTTATATTTTTAGTTAAAATAG
1 A-TACT-TAAAG-TAT-TTTTT-GTCAAAATAG
*
209915 ATACTTAAAGTATTTTATGTCAAAATAG
1 ATACTTAAAGTATTTTTTGTCAAAATAG
* *
209943 GTACTTAAACTATT
1 ATACTTAAAGTATT
209957 CAAACATTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
28 22 0.36
29 11 0.18
30 6 0.10
31 19 0.31
32 3 0.05
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (28 bp):
ATACTTAAAGTATTTTTTGTCAAAATAG
Found at i:214642 original size:20 final size:20
Alignment explanation
Indices: 214619--214656 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
214609 ATTATTATTT
214619 TATTAA-TATAATTAAAATAA
1 TATTAATTA-AATTAAAATAA
214639 TATTAATTAAATTAAAAT
1 TATTAATTAAATTAAAAT
214657 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATTAATTAAATTAAAATAA
Found at i:218667 original size:158 final size:158
Alignment explanation
Indices: 218379--218694 Score: 616
Period size: 158 Copynumber: 2.0 Consensus size: 158
218369 GCCACTAGTG
218379 CCGTCCCGCTGGTAAAGATGCTGTGTCATCCAGGACCTGTCTCGTCATTGGCATTCCATCCCAAT
1 CCGTCCCGCTGGTAAAGATGCTGTGTCATCCAGGACCTGTCTCGTCATTGGCATTCCATCCCAAT
218444 GGCCATGTCATGGCTACATCTGGGAGAGAAAATAAAATCAAGATTTGGGACTTGAGGAAGTTGAG
66 GGCCATGTCATGGCTACATCTGGGAGAGAAAATAAAATCAAGATTTGGGACTTGAGGAAGTTGAG
218509 GTTATCCAATCATTGCCATGCCATGCAA
131 GTTATCCAATCATTGCCATGCCATGCAA
218537 CCGTCCCGCTGGTAAAGATGCTGTGTCATCCAGGACCTGTCTCGTCATTGGCATTCCATCCCAAT
1 CCGTCCCGCTGGTAAAGATGCTGTGTCATCCAGGACCTGTCTCGTCATTGGCATTCCATCCCAAT
218602 GGCCATGTCATGGCTACATCTGGGAGAGAAAATAAAATCAAGA-TTGGGACTTGAGGAAGTTTGA
66 GGCCATGTCATGGCTACATCTGGGAGAGAAAATAAAATCAAGATTTGGGACTTGAGGAAG-TTGA
218666 GGTTATCCAATCATTGCCATGCCATGCAA
130 GGTTATCCAATCATTGCCATGCCATGCAA
218695 ACCTTGAATT
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
157 16 0.10
158 141 0.90
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (158 bp):
CCGTCCCGCTGGTAAAGATGCTGTGTCATCCAGGACCTGTCTCGTCATTGGCATTCCATCCCAAT
GGCCATGTCATGGCTACATCTGGGAGAGAAAATAAAATCAAGATTTGGGACTTGAGGAAGTTGAG
GTTATCCAATCATTGCCATGCCATGCAA
Found at i:220106 original size:12 final size:12
Alignment explanation
Indices: 220089--220119 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
220079 ATGAGACTCG
220089 TATAAATGAGTT
1 TATAAATGAGTT
220101 TATAAATGAGTT
1 TATAAATGAGTT
*
220113 GATAAAT
1 TATAAAT
220120 AAGATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (12 bp):
TATAAATGAGTT
Found at i:220207 original size:9 final size:9
Alignment explanation
Indices: 220195--220235 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
220185 TTCATATTCA
220195 TTTATTTAT
1 TTTATTTAT
220204 TTTATTTAT
1 TTTATTTAT
*
220213 TTTATTAAT
1 TTTATTTAT
*
220222 ATTTATTTAA
1 -TTTATTTAT
220232 TTTA
1 TTTA
220236 ATATATGAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTATTTAT
Found at i:221795 original size:43 final size:44
Alignment explanation
Indices: 221717--221831 Score: 115
Period size: 43 Copynumber: 2.6 Consensus size: 44
221707 GTCGATGATT
* ***
221717 TTCTCGTATTATGATCGTGTTTTTGCCGTCATCGTCATCG-CTG
1 TTCTCGTATTATGATCGTGTTCTTGTTATCATCGTCATCGTCTG
** * * *
221760 TTCTCGTATTATGATCGTGTTCTTGTTATTGTCGTCGTCGTTTTT
1 TTCTCGTATTATGATCGTGTTCTTGTTATCATCGTCATCG-TCTG
* *
221805 TTCTTGTATTATGATCGTGTTGTTGTT
1 TTCTCGTATTATGATCGTGTTCTTGTT
221832 GTTTTGCTTG
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 33 0.56
45 26 0.44
ACGTcount: A:0.10, C:0.17, G:0.21, T:0.52
Consensus pattern (44 bp):
TTCTCGTATTATGATCGTGTTCTTGTTATCATCGTCATCGTCTG
Found at i:223295 original size:37 final size:37
Alignment explanation
Indices: 223219--223295 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
223209 TTTTTATATT
*
223219 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
223256 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
223293 TTT
1 TTT
223296 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:224663 original size:135 final size:135
Alignment explanation
Indices: 224413--224681 Score: 376
Period size: 135 Copynumber: 2.0 Consensus size: 135
224403 GATCAGCATG
*
224413 TGTTCGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAATCAGCCGCTGCT
1 TGTTCGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCAGCCGCTGCT
* * ** *
224478 CTTTTTTTAGACTCAAAGCCTTTGTATAGAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCT
66 CGTTTTTCAGAAGCAAAGCCTTTGTATAGAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCA
224543 CTTCA
131 CTTCA
* * * * * * * **
224548 TGTTTGATACTGAAGATGTTCAAGACGGCAAGAGATGGTCCTCTCAGCCACAACCATCTTCTGCT
1 TGTTCGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCAGCCGCTGCT
* * *
224613 CGTTTTTCAGAAGCGAAGCCTTTGTATAGAACTTCATCATATCCCTAGCAGCAACCAGATCCTCA
66 CGTTTTTCAGAAGCAAAGCCTTTGTATAGAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCA
224678 CTTC
131 CTTC
224682 TGAAGGGAAC
Statistics
Matches: 116, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
135 116 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (135 bp):
TGTTCGATACAGAAGATGCTCAAGAAGGCAAGAGATGGTCCTCACAACCACAACCAGCCGCTGCT
CGTTTTTCAGAAGCAAAGCCTTTGTATAGAACTTCATCATATCCCCAGCAGCAACCAGAGCCTCA
CTTCA
Found at i:226784 original size:33 final size:33
Alignment explanation
Indices: 226745--226810 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
226735 CTCTTCACCC
226745 CCTTCCCCTTTTTTTCCTTCCCTAAAATACGGG
1 CCTTCCCCTTTTTTTCCTTCCCTAAAATACGGG
226778 CCTTCCCCTTTTTTTCCTTCCCTAAAATACGGG
1 CCTTCCCCTTTTTTTCCTTCCCTAAAATACGGG
226811 GAATTTGATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.15, C:0.36, G:0.09, T:0.39
Consensus pattern (33 bp):
CCTTCCCCTTTTTTTCCTTCCCTAAAATACGGG
Found at i:227427 original size:6 final size:7
Alignment explanation
Indices: 227410--227439 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
227400 CTCTCTTTTC
*
227410 TTTTTCA
1 TTTTTAA
227417 TTTTTAA
1 TTTTTAA
227424 TTTTTAA
1 TTTTTAA
227431 TTTTTAA
1 TTTTTAA
227438 TT
1 TT
227440 GTTTGGTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTAA
Found at i:232487 original size:21 final size:21
Alignment explanation
Indices: 232458--232497 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
232448 GGCATAAAAT
*
232458 ATATCAAAAAGTATAGTTTAG
1 ATATCAAAAAGTAAAGTTTAG
* *
232479 ATATTAAAACGTAAAGTTT
1 ATATCAAAAAGTAAAGTTT
232498 CAATGATGTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.35
Consensus pattern (21 bp):
ATATCAAAAAGTAAAGTTTAG
Found at i:235965 original size:2 final size:2
Alignment explanation
Indices: 235954--235984 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
235944 GTTAGAACTT
235954 TA TA -A 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
235985 CTTTGAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:241972 original size:14 final size:14
Alignment explanation
Indices: 241953--241979 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
241943 GTTAGGGTGA
241953 TTTTTTAATGAGGT
1 TTTTTTAATGAGGT
241967 TTTTTTAATGAGG
1 TTTTTTAATGAGG
241980 CCCCGTGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (14 bp):
TTTTTTAATGAGGT
Found at i:242086 original size:30 final size:30
Alignment explanation
Indices: 242050--242110 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
242040 AACCCCAACT
242050 GTTCGAAAACCCGCGAGAGAGAGAGAGAGA
1 GTTCGAAAACCCGCGAGAGAGAGAGAGAGA
242080 GTTCGAAAACCCGCGAGAGAGAGAGAGAGA
1 GTTCGAAAACCCGCGAGAGAGAGAGAGAGA
242110 G
1 G
242111 AGAGTCTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.38, T:0.07
Consensus pattern (30 bp):
GTTCGAAAACCCGCGAGAGAGAGAGAGAGA
Found at i:244163 original size:14 final size:14
Alignment explanation
Indices: 244146--244176 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
244136 CTTTCTCCCT
244146 TTCAGACTCTCTCA
1 TTCAGACTCTCTCA
244160 TTCAGACTCTCTCA
1 TTCAGACTCTCTCA
244174 TTC
1 TTC
244177 TTCTCATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.35, G:0.06, T:0.39
Consensus pattern (14 bp):
TTCAGACTCTCTCA
Found at i:245992 original size:39 final size:39
Alignment explanation
Indices: 245947--246026 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
245937 AATTATATCA
245947 TTTTAATATAAAAAAACTAATAAATATATTTTTATTAAT
1 TTTTAATATAAAAAAACTAATAAATATATTTTTATTAAT
*
245986 TTTTAATATAAAGAAACTAATAAATATATTTTTATTAAT
1 TTTTAATATAAAAAAACTAATAAATATATTTTTATTAAT
246025 TT
1 TT
246027 ATGTTAATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (39 bp):
TTTTAATATAAAAAAACTAATAAATATATTTTTATTAAT
Found at i:248734 original size:21 final size:21
Alignment explanation
Indices: 248700--248743 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
248690 AATATGAGAC
*
248700 TGAAGAAACTACAAGAAAAAG
1 TGAAGAAACAACAAGAAAAAG
*
248721 TGAAGGAACAACAAGAAAAAG
1 TGAAGAAACAACAAGAAAAAG
248742 TG
1 TG
248744 GGAGAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.59, C:0.09, G:0.23, T:0.09
Consensus pattern (21 bp):
TGAAGAAACAACAAGAAAAAG
Found at i:254618 original size:19 final size:20
Alignment explanation
Indices: 254596--254637 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
254586 ATTAGCAACG
254596 TACATGTGAGAT-TTTTTTT
1 TACATGTGAGATATTTTTTT
*
254615 TACATGTGATATATTTTTTT
1 TACATGTGAGATATTTTTTT
254635 TAC
1 TAC
254638 TTTAACAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57
Consensus pattern (20 bp):
TACATGTGAGATATTTTTTT
Found at i:263972 original size:17 final size:18
Alignment explanation
Indices: 263943--263978 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
263933 ATTCGAAATC
263943 ATTTAATAAATCCTTAAT
1 ATTTAATAAATCCTTAAT
263961 ATTTAA-AAATCCTTAAT
1 ATTTAATAAATCCTTAAT
263978 A
1 A
263979 AAAAAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAATAAATCCTTAAT
Found at i:264778 original size:17 final size:17
Alignment explanation
Indices: 264756--264794 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
264746 ACTGGTAGAG
264756 ATTTTAAATTCTTTTAT
1 ATTTTAAATTCTTTTAT
*
264773 ATTTT-AATTTTTTTAT
1 ATTTTAAATTCTTTTAT
264789 ATTTTA
1 ATTTTA
264795 TATTAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTAAATTCTTTTAT
Found at i:275045 original size:20 final size:20
Alignment explanation
Indices: 274997--275047 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
274987 CGATTATCTC
** *
274997 GTTGCGATAGTCATTTTTGT
1 GTTGCGATTTTCATTTTCGT
275017 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTCATTTTCGT
275037 GTTGCGATTTT
1 GTTGCGATTTT
275048 AAGTTTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:275054 original size:20 final size:20
Alignment explanation
Indices: 275015--275054 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
275005 AGTCATTTTT
* *
275015 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTTAAGTTTC
275035 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
275055 ATAAACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (20 bp):
GTGTTGCGATTTTAAGTTTC
Found at i:277066 original size:16 final size:16
Alignment explanation
Indices: 277045--277075 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
277035 GCGAATTTAG
*
277045 TTTCGCGTTGCGATTT
1 TTTCGCATTGCGATTT
277061 TTTCGCATTGCGATT
1 TTTCGCATTGCGATT
277076 ATCTTGTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (16 bp):
TTTCGCATTGCGATTT
Found at i:277106 original size:20 final size:20
Alignment explanation
Indices: 277081--277128 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
277071 CGATTATCTT
*
277081 GTTGCGATATTCAAATTCGC
1 GTTGCGATAGTCAAATTCGC
**
277101 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCAAATTCGC
277121 GTTGCGAT
1 GTTGCGAT
277129 TTTAAGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGTCAAATTCGC
Found at i:277755 original size:21 final size:21
Alignment explanation
Indices: 277638--277777 Score: 104
Period size: 21 Copynumber: 6.7 Consensus size: 21
277628 GACTCACCTG
* *
277638 TCATCGTTCAAGAGGCCTCTC
1 TCATCATTCAAGAGGCCCCTC
*
277659 -CTATCATTCAAGAGGCCTCTC
1 TC-ATCATTCAAGAGGCCCCTC
* * *
277680 -CTATCGTTCAATAGGCCCCTA
1 TC-ATCATTCAAGAGGCCCCTC
** **
277701 TCATCCCTCAAGAGTACCCTC
1 TCATCATTCAAGAGGCCCCTC
*
277722 TCATCATTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTC
* * *
277743 TCATCGTTGAAGAGGTCCCTC
1 TCATCATTCAAGAGGCCCCTC
* *
277764 CCACCATTCAAGAG
1 TCATCATTCAAGAG
277778 CCCGATTCAC
Statistics
Matches: 93, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
20 1 0.01
21 91 0.98
22 1 0.01
ACGTcount: A:0.24, C:0.34, G:0.16, T:0.26
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Found at i:279180 original size:14 final size:14
Alignment explanation
Indices: 279161--279197 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
279151 GCTTGTTTAA
279161 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
279175 TTGATTTCTAAAAG
1 TTGATTTGTAAAAG
279189 TTGATTTGT
1 TTGATTTGT
279198 TTAATTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:279354 original size:20 final size:20
Alignment explanation
Indices: 279317--279394 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
279307 AGGTACACTT
* *
279317 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGTCAAAA
* * *
279337 TTGCAATGCAAAAGTCAAAA
1 TCGCAACGCGAAAGTCAAAA
*
279357 TCGCAACGCGAAAGCCAAAA
1 TCGCAACGCGAAAGTCAAAA
279377 TCGCAACGCGAAAGTCAA
1 TCGCAACGCGAAAGTCAA
279395 TTCGCATTGC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAA
Found at i:279458 original size:20 final size:20
Alignment explanation
Indices: 279433--279509 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
279423 ACGATTTTCT
*
279433 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
279453 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
* *
279473 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
* *
279493 CGTTACGATATTCAAAT
1 CGTTGCGATAGTCAAAT
279510 GAATGTGTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:279489 original size:40 final size:40
Alignment explanation
Indices: 279434--279509 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
279424 CGATTTTCTC
*
279434 GTTGCGATAGTCAAATTCCCGTTGCGATAATCAAATTCAT
1 GTTGCGATAGTCAAATTCCCGTTACGATAATCAAATTCAT
* *
279474 GTTGCGATAGTCAAATTCGCGTTACGATATTCAAAT
1 GTTGCGATAGTCAAATTCCCGTTACGATAATCAAAT
279510 GAATGTGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (40 bp):
GTTGCGATAGTCAAATTCCCGTTACGATAATCAAATTCAT
Found at i:279732 original size:140 final size:140
Alignment explanation
Indices: 279480--279762 Score: 503
Period size: 140 Copynumber: 2.0 Consensus size: 140
279470 TCATGTTGCG
*
279480 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGACAGCAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGACAACAACTGAACAGATCA
*
279545 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTATACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
279610 AATACACATA
131 AATACACATA
* * * *
279620 ATAGTCAAATTCGTGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAATAGATCA
1 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGACAACAACTGAACAGATCA
*
279685 TAGCAATGTTCAAACTCAAGTTACTAATACATGCTTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
279750 AATACACATA
131 AATACACATA
279760 ATA
1 ATA
279763 CAACGTTTGC
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 136 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGACAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:279850 original size:12 final size:12
Alignment explanation
Indices: 279820--279850 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
279810 AAGCCGGTTG
*
279820 TGATTGAGATTT
1 TGATTGCGATTT
279832 TGATTGCGATTT
1 TGATTGCGATTT
279844 TGATTGC
1 TGATTGC
279851 CTTTTTCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.06, G:0.26, T:0.48
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:282140 original size:24 final size:24
Alignment explanation
Indices: 282107--282159 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
282097 TGAAACATCT
282107 TCAAAATCCGAGTATTGACCAAGA
1 TCAAAATCCGAGTATTGACCAAGA
* *
282131 TCAAAGTCCGGGTATTGACCAAGA
1 TCAAAATCCGAGTATTGACCAAGA
282155 TCAAA
1 TCAAA
282160 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
TCAAAATCCGAGTATTGACCAAGA
Found at i:282173 original size:24 final size:24
Alignment explanation
Indices: 282107--282173 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 24
282097 TGAAACATCT
* * *
282107 TCAAAATCCGAGTATTGACCAAGA
1 TCAAAGTCCGAATACTGACCAAGA
** *
282131 TCAAAGTCCGGGTATTGACCAAGA
1 TCAAAGTCCGAATACTGACCAAGA
* *
282155 TCAAATTTCGAATACTGAC
1 TCAAAGTCCGAATACTGAC
282174 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
TCAAAGTCCGAATACTGACCAAGA
Done.