Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, 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: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 93 of 109
Found at i:18654906 original size:22 final size:22
Alignment explanation
Indices: 18654880--18654923 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18654870 TGTATATTTA
* *
18654880 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
18654902 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
18654924 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:18664155 original size:19 final size:20
Alignment explanation
Indices: 18664131--18664174 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
18664121 TAATTTTATA
18664131 TTTATA-TTAAAAATAATAT
1 TTTATATTTAAAAATAATAT
18664150 TTTATATTTAAAAATAATAT
1 TTTATATTTAAAAATAATAT
18664170 TTTAT
1 TTTAT
18664175 TAATTTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTATATTTAAAAATAATAT
Found at i:18668906 original size:27 final size:26
Alignment explanation
Indices: 18668866--18668925 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
18668856 TATTTGATAC
* *
18668866 ATAAAATTATAATAAGA-TATAATAAA
1 ATAATATTATAATAAAATTA-AATAAA
*
18668892 ATAATATTATGAATAAAATTAAATTAA
1 ATAATATTAT-AATAAAATTAAATAAA
18668919 ATAATAT
1 ATAATAT
18668926 CATCATATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 9 0.31
27 18 0.62
28 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (26 bp):
ATAATATTATAATAAAATTAAATAAA
Found at i:18669771 original size:21 final size:19
Alignment explanation
Indices: 18669747--18669792 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
18669737 TTTACATATA
18669747 TTTAATAAATTAATTTTTTAT
1 TTTAAT-AATTAA-TTTTTAT
18669768 TTTAATAATATAATTTTTAT
1 TTTAATAAT-TAATTTTTAT
18669788 TTTAA
1 TTTAA
18669793 ATTAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTAATAATTAATTTTTAT
Found at i:18669784 original size:20 final size:21
Alignment explanation
Indices: 18669747--18669801 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
18669737 TTTACATATA
18669747 TTTAATAAATTAATTTTTTAT
1 TTTAATAAATTAATTTTTTAT
18669768 TTTAAT-AATATAA-TTTTTAT
1 TTTAATAAAT-TAATTTTTTAT
*
18669788 TTTAAATTAATTAA
1 TTT-AATAAATTAA
18669802 AATTAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 13 0.42
21 15 0.48
22 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAATAAATTAATTTTTTAT
Found at i:18671855 original size:17 final size:17
Alignment explanation
Indices: 18671835--18671876 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
18671825 TGAATTAATT
18671835 TATATATAATTCACATA
1 TATATATAATTCACATA
* *
18671852 TATATATAATTTATATA
1 TATATATAATTCACATA
18671869 TATATATA
1 TATATATA
18671877 TGAATTCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATATAATTCACATA
Found at i:18671867 original size:15 final size:15
Alignment explanation
Indices: 18671791--18671874 Score: 57
Period size: 17 Copynumber: 5.5 Consensus size: 15
18671781 TTTAATAAAG
18671791 TATATATAATTT-TA
1 TATATATAATTTATA
* *
18671805 T-T-TTTAATTTTTA
1 TATATATAATTTATA
* * *
18671818 TATACTTTGAATTAATT
1 TATA-TAT-AATTTATA
*
18671835 TATATATAATTCACATA
1 TATATATAATT--TATA
18671852 TATATATAATTTATA
1 TATATATAATTTATA
18671867 TATATATA
1 TATATATA
18671875 TATGAATTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
12 7 0.13
13 4 0.07
14 2 0.04
15 15 0.27
16 5 0.09
17 22 0.40
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (15 bp):
TATATATAATTTATA
Found at i:18688972 original size:52 final size:51
Alignment explanation
Indices: 18688905--18689061 Score: 170
Period size: 52 Copynumber: 3.0 Consensus size: 51
18688895 TATAATCATA
* * * * *
18688905 CAAATTTACCCATTAAGAATCACTCTCCTCTTAGAATTCTTCTTTTGTAAGT
1 CAAACTTACCTATTAAGAATCTCT-TTCTCTTAGAATTCTTCTTTTGCAAGT
* ** * * * *
18688957 CAAATTTGTCTATTAAGAATCTTTTTTCTTTTAAAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATC-TCTTTCTCTTAGAATTCTTCTTTTGCAAGT
*
18689009 CAAACTTACCTATTAAGAATCTCATTTCTCTTAGAATTCTTTTTTTGCAAGT
1 CAAACTTACCTATTAAGAATCTC-TTTCTCTTAGAATTCTTCTTTTGCAAGT
18689061 C
1 C
18689062 TTCTTGTCCA
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
51 1 0.01
52 83 0.98
53 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.08, T:0.45
Consensus pattern (51 bp):
CAAACTTACCTATTAAGAATCTCTTTCTCTTAGAATTCTTCTTTTGCAAGT
Found at i:18689443 original size:50 final size:50
Alignment explanation
Indices: 18689381--18689494 Score: 138
Period size: 50 Copynumber: 2.3 Consensus size: 50
18689371 CCCAAATCTT
* **
18689381 GAACCTTCAGCTCTTCCCACGTCTTGAAACTTTGACTATTCTCACGTTTC
1 GAACCTTCAGCTCTTCCCACATCTTGAAACTTCAACTATTCTCACGTTTC
* * * * * *
18689431 TAACCTTTAGCTCTTTCCACATTTTGAATCTTCAACTCTTCTCACGTTTC
1 GAACCTTCAGCTCTTCCCACATCTTGAAACTTCAACTATTCTCACGTTTC
*
18689481 GAACCTTCAACTCT
1 GAACCTTCAGCTCT
18689495 GACACCACTT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.21, C:0.32, G:0.09, T:0.39
Consensus pattern (50 bp):
GAACCTTCAGCTCTTCCCACATCTTGAAACTTCAACTATTCTCACGTTTC
Found at i:18689488 original size:25 final size:25
Alignment explanation
Indices: 18689381--18689494 Score: 88
Period size: 25 Copynumber: 4.6 Consensus size: 25
18689371 CCCAAATCTT
* *
18689381 GAACCTTCAGCTCTTCCCACGTCTT-
1 GAACCTTCAACTCTTCTCACGT-TTC
* ** *
18689406 GAAACTTTGACTATTCTCACGTTTC
1 GAACCTTCAACTCTTCTCACGTTTC
* * * * *
18689431 TAACCTTTAGCTCTT-TCCACATTTT
1 GAACCTTCAACTCTTCT-CACGTTTC
*
18689456 GAATCTTCAACTCTTCTCACGTTTC
1 GAACCTTCAACTCTTCTCACGTTTC
18689481 GAACCTTCAACTCT
1 GAACCTTCAACTCT
18689495 GACACCACTT
Statistics
Matches: 66, Mismatches: 20, Indels: 6
0.72 0.22 0.07
Matches are distributed among these distances:
24 3 0.05
25 62 0.94
26 1 0.02
ACGTcount: A:0.21, C:0.32, G:0.09, T:0.39
Consensus pattern (25 bp):
GAACCTTCAACTCTTCTCACGTTTC
Found at i:18691936 original size:71 final size:71
Alignment explanation
Indices: 18691840--18691979 Score: 244
Period size: 71 Copynumber: 2.0 Consensus size: 71
18691830 TTCACATCGG
* *
18691840 TAAGGTGACTCATATACTCATATCTGACTCATTAGTATAAAAACAACGTAAGTATAAAAACAAAA
1 TAAGGTGACTCATAGACTCATATCTGACTCATTAGTATAAAAACAACATAAGTATAAAAACAAAA
18691905 TTTCGA
66 TTTCGA
* *
18691911 TAAGGTGACTCATAGACTCATATCTGACTCATTAGTATAAATACAACATAAGTATAAAAACAAAT
1 TAAGGTGACTCATAGACTCATATCTGACTCATTAGTATAAAAACAACATAAGTATAAAAACAAAA
18691976 TTTC
66 TTTC
18691980 TTCTCAATCT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (71 bp):
TAAGGTGACTCATAGACTCATATCTGACTCATTAGTATAAAAACAACATAAGTATAAAAACAAAA
TTTCGA
Found at i:18692351 original size:19 final size:19
Alignment explanation
Indices: 18692327--18692390 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
18692317 GGGTTAATTG
*
18692327 TTAAAGTTCAAGTTTCGTA
1 TTAAAGCTCAAGTTTCGTA
* *
18692346 TTAAAGCTCGAA-TTTTGTG
1 TTAAAGCTC-AAGTTTCGTA
*
18692365 TTAAAGCTCATGTTTCGTA
1 TTAAAGCTCAAGTTTCGTA
18692384 TTAAAGC
1 TTAAAGC
18692391 ACAAAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
18 1 0.03
19 34 0.92
20 2 0.05
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (19 bp):
TTAAAGCTCAAGTTTCGTA
Found at i:18694170 original size:23 final size:22
Alignment explanation
Indices: 18694140--18694183 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
18694130 AATGCATATA
18694140 TTTTAAAAAATAGAAAAATTAAT
1 TTTTAAAAAATA-AAAAATTAAT
*
18694163 TTTTAAAAAATAATAAATTAA
1 TTTTAAAAAATAAAAAATTAA
18694184 GGAAAGTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTTAAAAAATAAAAAATTAAT
Found at i:18694236 original size:33 final size:32
Alignment explanation
Indices: 18694199--18694262 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
18694189 GTGTGTATGG
18694199 AAAAAATATTAAAAAAATAAT-TAATAAATGAT
1 AAAAAATA-TAAAAAAATAATATAATAAATGAT
*
18694231 AAAAAATATAAAAAATTAATAATAATAAATGA
1 AAAAAATATAAAAAAATAAT-ATAATAAATGA
18694263 ACATCTCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 11 0.38
32 8 0.28
33 10 0.34
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (32 bp):
AAAAAATATAAAAAAATAATATAATAAATGAT
Found at i:18694255 original size:23 final size:23
Alignment explanation
Indices: 18694202--18694260 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
18694192 TGTATGGAAA
* **
18694202 AAATATTAAAAAA-ATAATTAAT
1 AAATAATAAAAAATATAAAAAAT
*
18694224 AAATGATAAAAAATATAAAAAAT
1 AAATAATAAAAAATATAAAAAAT
* *
18694247 TAATAATAATAAAT
1 AAATAATAAAAAAT
18694261 GAACATCTCT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
AAATAATAAAAAATATAAAAAAT
Found at i:18694717 original size:13 final size:13
Alignment explanation
Indices: 18694695--18694724 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18694685 GTATTTGGAT
18694695 ATTTAGAAAAAAA
1 ATTTAGAAAAAAA
*
18694708 ATTTATAAAAAAA
1 ATTTAGAAAAAAA
18694721 ATTT
1 ATTT
18694725 CATTGCTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
ATTTAGAAAAAAA
Found at i:18696696 original size:3 final size:3
Alignment explanation
Indices: 18696688--18696731 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
18696678 GTTTTCCTTG
18696688 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18696732 CTCTTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:18698521 original size:14 final size:14
Alignment explanation
Indices: 18698502--18698530 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
18698492 AAAGGCTATT
18698502 AGGATTTTTCAGGA
1 AGGATTTTTCAGGA
18698516 AGGATTTTTCAGGA
1 AGGATTTTTCAGGA
18698530 A
1 A
18698531 CAACAAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.07, G:0.28, T:0.34
Consensus pattern (14 bp):
AGGATTTTTCAGGA
Found at i:18706755 original size:23 final size:21
Alignment explanation
Indices: 18706712--18706764 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 21
18706702 GTACTTTGCT
*
18706712 TAAAAAAGAAACAAAGAAAAA
1 TAAAAAAAAAACAAAGAAAAA
18706733 TGAAGAAAAAAAACAAA-ATAAAA
1 T-AA-AAAAAAAACAAAGA-AAAA
18706756 TAAAAAAAA
1 TAAAAAAAA
18706765 CTAAGAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 7 0.25
22 5 0.18
23 16 0.57
ACGTcount: A:0.81, C:0.04, G:0.08, T:0.08
Consensus pattern (21 bp):
TAAAAAAAAAACAAAGAAAAA
Found at i:18707814 original size:48 final size:48
Alignment explanation
Indices: 18707753--18708015 Score: 255
Period size: 48 Copynumber: 5.4 Consensus size: 48
18707743 CATTTCAAAC
* *
18707753 AAGATTTTTAAAGTTT-AATAGCCTTTGTTTATAAGGAGTCATTTCTAAT
1 AAGATTTTTAAAGTTTCAA-AGCCTTTATTTATAAGGAGCCATTT-TAAT
* * * * * *
18707802 -AGATTTTTAAAGTTTCAAAACATCTATTTATAAAGAGCTATTTTGAGT
1 AAGATTTTTAAAGTTTCAAAGCCTTTATTTATAAGGAGCCATTTT-AAT
* * * * *
18707850 GAGA-TTTTAAAATTTCAAAGCCTCTGTTTATAAGGAGCCATTTTAAGC
1 AAGATTTTTAAAGTTTCAAAGCCTTTATTTATAAGGAGCCATTTTAA-T
* *
18707898 AAGATTTTTAAAGTTTCAAAG-CTCTTATTTATGAGGAGCCATTTCAAT
1 AAGATTTTTAAAGTTTCAAAGCCT-TTATTTATAAGGAGCCATTTTAAT
* * * *
18707946 AAAATTTTTAAAGTTTTAAAGTCTTTATTTATATGGAGCCAATTTTAGAT
1 AAGATTTTTAAAGTTTCAAAGCCTTTATTTATAAGGAGCC-ATTTTA-AT
*
18707996 AAGATTTTTAAATTTTCAAA
1 AAGATTTTTAAAGTTTCAAA
18708016 AAGTCCATTT
Statistics
Matches: 174, Mismatches: 31, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
47 2 0.01
48 107 0.61
49 46 0.26
50 19 0.11
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (48 bp):
AAGATTTTTAAAGTTTCAAAGCCTTTATTTATAAGGAGCCATTTTAAT
Found at i:18707956 original size:97 final size:95
Alignment explanation
Indices: 18707743--18708016 Score: 268
Period size: 97 Copynumber: 2.8 Consensus size: 95
18707733 TATCACGAAT
* *
18707743 CATTTCAA-ACAAGATTTTTAAAGTTTAATAGCCTTTGTTTATAAGGAGTCATTTCTAA-TAGAT
1 CATTTCAATA-AA-ATTTTTAAAGTTTAA-AGCCTTTGTTTATAAGGAGCCATTT-TAAGAAGAT
18707806 TTTTAAAGTTTCAAAACATCTATTTATAAAGAGC
62 TTTTAAAGTTTCAAAACATCTATTTATAAAGAGC
* * * * * * *
18707840 TATTTTGAGTGAGA-TTTTAAAATTTCAAAGCCTCTGTTTATAAGGAGCCATTTTAAGCAAGATT
1 CA-TTTCAATAAAATTTTTAAAGTTT-AAAGCCTTTGTTTATAAGGAGCCATTTTAAG-AAGATT
* * *
18707904 TTTAAAGTTTCAAAGC-TCTTATTTATGAGGAGC
63 TTTAAAGTTTCAAAACATC-TATTTATAAAGAGC
* * * *
18707937 CATTTCAATAAAATTTTTAAAGTTTTAAAGTCTTTATTTATATGGAGCCAATTTTAGATAAGATT
1 CATTTCAATAAAATTTTTAAAG-TTTAAAGCCTTTGTTTATAAGGAGCC-ATTTTA-AGAAGATT
*
18708002 TTTAAATTTTCAAAA
63 TTTAAAGTTTCAAAA
18708017 AGTCCATTTA
Statistics
Matches: 142, Mismatches: 25, Indels: 19
0.76 0.13 0.10
Matches are distributed among these distances:
95 3 0.02
96 42 0.30
97 63 0.44
98 33 0.23
99 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (95 bp):
CATTTCAATAAAATTTTTAAAGTTTAAAGCCTTTGTTTATAAGGAGCCATTTTAAGAAGATTTTT
AAAGTTTCAAAACATCTATTTATAAAGAGC
Found at i:18710355 original size:17 final size:17
Alignment explanation
Indices: 18710333--18710366 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
18710323 AGTGTGCAAG
* *
18710333 GAAAAATATTAAAAAAT
1 GAAAAAAATAAAAAAAT
18710350 GAAAAAAATAAAAAAAT
1 GAAAAAAATAAAAAAAT
18710367 AAATGATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
GAAAAAAATAAAAAAAT
Found at i:18714261 original size:18 final size:18
Alignment explanation
Indices: 18714238--18714272 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
18714228 CGATAACCAC
18714238 ACTATTACCAAATATCAG
1 ACTATTACCAAATATCAG
18714256 ACTATTACCAAATATCA
1 ACTATTACCAAATATCA
18714273 AAATCCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (18 bp):
ACTATTACCAAATATCAG
Found at i:18714590 original size:30 final size:30
Alignment explanation
Indices: 18714556--18714617 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
18714546 ACATAAAATA
* *
18714556 TTAAAGGCTTATTTGGATTTAAATTAAAGG
1 TTAAAAGCTTATTTGGATTAAAATTAAAGG
* *
18714586 TTAAAAGCTTATTTGTATTAAAATTCAAGG
1 TTAAAAGCTTATTTGGATTAAAATTAAAGG
18714616 TT
1 TT
18714618 GATGACTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (30 bp):
TTAAAAGCTTATTTGGATTAAAATTAAAGG
Found at i:18718073 original size:21 final size:21
Alignment explanation
Indices: 18718015--18718075 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 21
18718005 AAATAAAATA
18718015 AAAAAACAATGAAAGAAAAACCCT
1 AAAAAA-AATG-AA-AAAAACCCT
*
18718039 AAAATAGAAA--AAAAAAAGCCT
1 AAAA-A-AAATGAAAAAAACCCT
18718060 AAAAAAAATGAAAAAA
1 AAAAAAAATGAAAAAA
18718076 CCCATTGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
19 3 0.09
20 1 0.03
21 18 0.56
22 2 0.06
24 4 0.12
25 3 0.09
26 1 0.03
ACGTcount: A:0.74, C:0.10, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAAAAAATGAAAAAAACCCT
Found at i:18723247 original size:2 final size:2
Alignment explanation
Indices: 18723240--18723270 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
18723230 TTTCAAAATC
18723240 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18723271 TGATTAGGTT
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):
AT
Found at i:18724467 original size:16 final size:15
Alignment explanation
Indices: 18724430--18724459 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18724420 ACATTAATCT
18724430 TTTTTATTTCTTTTC
1 TTTTTATTTCTTTTC
18724445 TTTTTATTT-TTTTC
1 TTTTTATTTCTTTTC
18724459 T
1 T
18724460 CATTTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTTCTTTTC
Found at i:18724657 original size:6 final size:6
Alignment explanation
Indices: 18724646--18724671 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
18724636 TGATGGCTCT
18724646 TCCCTC TCCCTC TCCCTC TCCCTC TC
1 TCCCTC TCCCTC TCCCTC TCCCTC TC
18724672 AGCCCACAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
TCCCTC
Found at i:18727343 original size:13 final size:14
Alignment explanation
Indices: 18727307--18727343 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18727297 TTTGAAAAAA
*
18727307 TTTT-GATATATAT
1 TTTTAGATAAATAT
18727320 TTTTAGATAAATAT
1 TTTTAGATAAATAT
18727334 TTTTAG-TAAA
1 TTTTAGATAAA
18727344 AATGTTACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (14 bp):
TTTTAGATAAATAT
Found at i:18727414 original size:12 final size:12
Alignment explanation
Indices: 18727397--18727422 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18727387 TTAAATTATA
18727397 AATAATTTTTTT
1 AATAATTTTTTT
18727409 AATAATTTTTTT
1 AATAATTTTTTT
18727421 AA
1 AA
18727423 CATATTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATAATTTTTTT
Found at i:18727721 original size:22 final size:21
Alignment explanation
Indices: 18727696--18727739 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
18727686 ATATAATTTT
* *
18727696 AATTATAATGAAACAATTGTAA
1 AATTATAAT-AAAAAATTATAA
18727718 AATTATAATAAAAAATTATAA
1 AATTATAATAAAAAATTATAA
18727739 A
1 A
18727740 TGAAATACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (21 bp):
AATTATAATAAAAAATTATAA
Found at i:18729858 original size:21 final size:22
Alignment explanation
Indices: 18729833--18729885 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
18729823 ATCCAAATTA
18729833 ATAAAATATTTA-TTTTTAAAT
1 ATAAAATATTTATTTTTTAAAT
18729854 ATAAAATA-TTATTTTTTAAAT
1 ATAAAATATTTATTTTTTAAAT
18729875 AT-AAATATTTA
1 ATAAAATATTTA
18729886 AATATATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.27
21 22 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAAAATATTTATTTTTTAAAT
Found at i:18738001 original size:14 final size:15
Alignment explanation
Indices: 18737979--18738012 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
18737969 AATAAAATAT
*
18737979 TATTTTTAATATAAA
1 TATTTTAAATATAAA
18737994 TATTTTAAAATATAAA
1 TATTTT-AAATATAAA
18738010 TAT
1 TAT
18738013 AAAATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTTAAATATAAA
Found at i:18739329 original size:23 final size:23
Alignment explanation
Indices: 18739305--18739355 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
18739295 TTAAAATATA
18739305 TTTATTTTGTTATAATTTATTTAT
1 TTTA-TTTGTTATAATTTATTTAT
*
18739329 TTTATTTGTTATATTTTATTTAT
1 TTTATTTGTTATAATTTATTTAT
18739352 TTTA
1 TTTA
18739356 ATATTATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTATTTGTTATAATTTATTTAT
Found at i:18739362 original size:22 final size:23
Alignment explanation
Indices: 18739314--18739392 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
18739304 ATTTATTTTG
* * *
18739314 TTATAATTTATTTATTTTATTTG
1 TTATATTTTATTTATTTTATATA
18739337 TTATATTTTATTTATTTTA-ATA
1 TTATATTTTATTTATTTTATATA
* * *
18739359 TTATATCTTA-TTATTATATCTA
1 TTATATTTTATTTATTTTATATA
18739381 TTTATATATTTA
1 -TTATAT-TTTA
18739393 GTATAGTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 7 0.15
22 12 0.26
23 24 0.52
24 3 0.07
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (23 bp):
TTATATTTTATTTATTTTATATA
Found at i:18742399 original size:2 final size:2
Alignment explanation
Indices: 18742394--18742418 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18742384 TGTGTGTGTC
18742394 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18742419 CCTCTTAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18744060 original size:24 final size:25
Alignment explanation
Indices: 18744004--18744057 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
18743994 AAATAATAAT
* *
18744004 AAAAATTACTGTAGTTACGATTAAA
1 AAAAATTACTATAATTACGATTAAA
* *
18744029 AAAAATTATTATAATTATGATTAAA
1 AAAAATTACTATAATTACGATTAAA
18744054 AAAA
1 AAAA
18744058 TTAATGATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (25 bp):
AAAAATTACTATAATTACGATTAAA
Found at i:18744067 original size:25 final size:26
Alignment explanation
Indices: 18744004--18744067 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 26
18743994 AAATAATAAT
* *
18744004 AAAAATTACTG-TAGTTACGATTAAA
1 AAAAATTAATGATAATTACGATTAAA
* *
18744029 AAAAATT-ATTATAATTATGATT-AA
1 AAAAATTAATGATAATTACGATTAAA
18744053 AAAAATTAATGATAA
1 AAAAATTAATGATAA
18744068 ATTTATGTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (26 bp):
AAAAATTAATGATAATTACGATTAAA
Found at i:18744070 original size:26 final size:25
Alignment explanation
Indices: 18744022--18744078 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 25
18744012 CTGTAGTTAC
*
18744022 GATTAAAAAAAATTATTATAA-TTAT
1 GATT-AAAAAAATTATGATAATTTAT
18744047 GATTAAAAAAATTAATGATAAATTTAT
1 GATTAAAAAAATT-ATGAT-AATTTAT
18744074 G-TTAA
1 GATTAA
18744079 TTTGATCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 9 0.32
25 8 0.29
26 6 0.21
27 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (25 bp):
GATTAAAAAAATTATGATAATTTAT
Found at i:18744639 original size:21 final size:21
Alignment explanation
Indices: 18744614--18744704 Score: 65
Period size: 21 Copynumber: 4.1 Consensus size: 21
18744604 ATAAATAAAA
18744614 TTTGATAACTTTTTATACAAT
1 TTTGATAACTTTTTATACAAT
** * * *
18744635 TTTGATTTCGATTGTTTTTGATAAA
1 TTTGATAAC--TT-TTTAT-ACAAT
* *
18744660 TTTGATGACTTTTAATACAAT
1 TTTGATAACTTTTTATACAAT
* *
18744681 TTTGATAAATTTTGATACAAT
1 TTTGATAACTTTTTATACAAT
18744702 TTT
1 TTT
18744705 AGTAACATTT
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
21 31 0.60
22 3 0.06
23 4 0.08
24 4 0.08
25 10 0.19
ACGTcount: A:0.31, C:0.07, G:0.10, T:0.53
Consensus pattern (21 bp):
TTTGATAACTTTTTATACAAT
Found at i:18744693 original size:10 final size:10
Alignment explanation
Indices: 18744650--18744704 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
18744640 TTTCGATTGT
18744650 TTTTGATAAA
1 TTTTGATAAA
* *
18744660 -TTTGATGAC
1 TTTTGATAAA
*
18744669 TTTTAATACAA
1 TTTTGATA-AA
18744680 TTTTGATAAA
1 TTTTGATAAA
18744690 TTTTGATACAA
1 TTTTGATA-AA
18744701 TTTT
1 TTTT
18744705 AGTAACATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
9 7 0.19
10 15 0.42
11 14 0.39
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (10 bp):
TTTTGATAAA
Found at i:18744718 original size:21 final size:21
Alignment explanation
Indices: 18744650--18744704 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
18744640 TTTCGATTGT
* *
18744650 TTTTGATA-AA-TTTGATGAC
1 TTTTGATACAATTTTGATAAA
*
18744669 TTTTAATACAATTTTGATAAA
1 TTTTGATACAATTTTGATAAA
18744690 TTTTGATACAATTTT
1 TTTTGATACAATTTT
18744705 AGTAACATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 7 0.23
20 2 0.07
21 21 0.70
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTTGATACAATTTTGATAAA
Found at i:18744808 original size:22 final size:21
Alignment explanation
Indices: 18744783--18744833 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
18744773 TCTTTGACAA
18744783 AATTTTGATAATTTTTT-TATGT
1 AATTTTGATAATTTTTTGTA--T
*
18744805 AATTTTGGTAATTTTTTGTAT
1 AATTTTGATAATTTTTTGTAT
18744826 AATTTTGA
1 AATTTTGA
18744834 GAACTTATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (21 bp):
AATTTTGATAATTTTTTGTAT
Found at i:18744821 original size:21 final size:22
Alignment explanation
Indices: 18744783--18744833 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
18744773 TCTTTGACAA
*
18744783 AATTTTGATAATTTTTTTATGT
1 AATTTTGATAATTTTTTTATAT
* *
18744805 AATTTTGGTAA-TTTTTTGTAT
1 AATTTTGATAATTTTTTTATAT
18744826 AATTTTGA
1 AATTTTGA
18744834 GAACTTATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (22 bp):
AATTTTGATAATTTTTTTATAT
Found at i:18745155 original size:22 final size:22
Alignment explanation
Indices: 18745130--18745215 Score: 73
Period size: 22 Copynumber: 3.9 Consensus size: 22
18745120 ATGATTGACA
18745130 ATTAAATTATCATTGATTTATT
1 ATTAAATTATCATTGATTTATT
* * * **
18745152 ATTATATTATTAGTGATTTACA
1 ATTAAATTATCATTGATTTATT
* ** *
18745174 ATTGAGCTATCAATGATTTATT
1 ATTAAATTATCATTGATTTATT
* *
18745196 ACTAAATTATCATTAATTTA
1 ATTAAATTATCATTGATTTA
18745216 CTACTAGTTT
Statistics
Matches: 45, Mismatches: 19, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTAAATTATCATTGATTTATT
Found at i:18745220 original size:22 final size:22
Alignment explanation
Indices: 18745181--18745259 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 22
18745171 ACAATTGAGC
* *
18745181 TATCAATGATTTATTACTAAAT
1 TATCAATAATTTACTACTAAAT
* **
18745203 TATCATTAATTTACTACTAGTT
1 TATCAATAATTTACTACTAAAT
* * *
18745225 TATTAATGATTTACTACAAAAT
1 TATCAATAATTTACTACTAAAT
**
18745247 TATTGATAATTTA
1 TATCAATAATTTA
18745260 TTTACTTATT
Statistics
Matches: 44, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.39, C:0.09, G:0.05, T:0.47
Consensus pattern (22 bp):
TATCAATAATTTACTACTAAAT
Found at i:18745373 original size:22 final size:22
Alignment explanation
Indices: 18745348--18745432 Score: 89
Period size: 22 Copynumber: 3.9 Consensus size: 22
18745338 TGATTAACTA
*
18745348 ATTTATTACTAAATTATTACTG
1 ATTTATTACTAAATTATTAGTG
** *
18745370 ATTTAGAACTAAGTTATTAGTG
1 ATTTATTACTAAATTATTAGTG
**
18745392 ATTTATTACTATTTTATTAGTG
1 ATTTATTACTAAATTATTAGTG
* * *
18745414 ATTTACTACTGAACTATTA
1 ATTTATTACTAAATTATTA
18745433 ATAATTCACT
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.48
Consensus pattern (22 bp):
ATTTATTACTAAATTATTAGTG
Found at i:18745380 original size:33 final size:32
Alignment explanation
Indices: 18745343--18745405 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
18745333 ATCAATGATT
*
18745343 AACTAATTTATTACTAAATTATTACTGATTTAG
1 AACTAAGTTATTACTAAATTATTACT-ATTTAG
* * *
18745376 AACTAAGTTATTAGTGATTTATTACTATTT
1 AACTAAGTTATTACTAAATTATTACTATTT
18745406 TATTAGTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 4 0.15
33 22 0.85
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.48
Consensus pattern (32 bp):
AACTAAGTTATTACTAAATTATTACTATTTAG
Found at i:18745432 original size:44 final size:44
Alignment explanation
Indices: 18745348--18745432 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
18745338 TGATTAACTA
* *
18745348 ATTTATTACTAAATTATTACTGATTTAGAACTAAGTTATTAGTG
1 ATTTATTACTAAATTATTACTGATTTACAACTAAGCTATTAGTG
** * *
18745392 ATTTATTACTATTTTATTAGTGATTTACTACTGAA-CTATTA
1 ATTTATTACTAAATTATTACTGATTTACAACT-AAGCTATTA
18745433 ATAATTCACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 32 0.94
45 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.48
Consensus pattern (44 bp):
ATTTATTACTAAATTATTACTGATTTACAACTAAGCTATTAGTG
Found at i:18745505 original size:22 final size:22
Alignment explanation
Indices: 18745458--18745511 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
18745448 ATCGTCAATA
* *
18745458 ATTTACTATTATATTATTATGC
1 ATTTATTATTATATTATCATGC
18745480 ATTTATTATTATATTATCATTG-
1 ATTTATTATTATATTATCA-TGC
18745502 ATTTATTATT
1 ATTTATTATT
18745512 TAGTTTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (22 bp):
ATTTATTATTATATTATCATGC
Found at i:18745659 original size:44 final size:43
Alignment explanation
Indices: 18745578--18745867 Score: 132
Period size: 44 Copynumber: 6.7 Consensus size: 43
18745568 ATTTACTACC
* * *
18745578 AAGTTATTATTAATTTA-TATTAAATTATCT-ATTATTTATTATT
1 AAGTTATCATT-ATTTACTATTAAGTTAT-TGATAATTTATTATT
* *
18745621 AAGTTATCACTTATTAACTATTAAGTTATTGATAATTTACTATT
1 AAGTTATCA-TTATTTACTATTAAGTTATTGATAATTTATTATT
* * ** * *
18745665 AAGTTAT--TGATTTACTTTTAAGTT-TCCAATAATTAATAATT
1 AAGTTATCATTATTTACTATTAAGTTAT-TGATAATTTATTATT
* * * *
18745706 AAATTGTCATTGATTTACTACTAAGTTATTTATAATTTATT-TCT
1 AAGTTATCATT-ATTTACTATTAAGTTATTGATAATTTATTAT-T
* * * * * *
18745750 GAGTTTGTCAATTAATTACCATTAA---ACTGAAACTAATTTACTATT
1 AAG-TTATC-ATTATTTACTATTAAGTTATTG--A-TAATTTATTATT
* * *
18745795 AAGTTATCACTAATTTACTATTAAATTATT-ATTAATTTATTACT
1 AAGTTATCA-TTATTTACTATTAAGTTATTGA-TAATTTATTATT
* * * *
18745839 AATTTATCAATTATTAAATACTAAGTTAT
1 AAGTTATC-ATTATTTACTATTAAGTTAT
18745868 CACTTATTTT
Statistics
Matches: 182, Mismatches: 45, Indels: 39
0.68 0.17 0.15
Matches are distributed among these distances:
40 1 0.01
41 29 0.16
42 2 0.01
43 16 0.09
44 101 0.55
45 27 0.15
46 4 0.02
47 2 0.01
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (43 bp):
AAGTTATCATTATTTACTATTAAGTTATTGATAATTTATTATT
Found at i:18745672 original size:22 final size:21
Alignment explanation
Indices: 18745563--18745688 Score: 96
Period size: 22 Copynumber: 6.0 Consensus size: 21
18745553 GTTACATTAT
* **
18745563 TTATGATTTACTACCAAGTTA
1 TTATAATTTACTATTAAGTTA
*
18745584 TTATTAATTTA-TATTAAATTA
1 TTA-TAATTTACTATTAAGTTA
* *
18745605 TCTATTATTTATTATTAAGTTA
1 T-TATAATTTACTATTAAGTTA
* * *
18745627 TCACTTATTAACTATTAAGTTA
1 TTA-TAATTTACTATTAAGTTA
18745649 TTGATAATTTACTATTAAGTTA
1 TT-ATAATTTACTATTAAGTTA
* *
18745671 -T-TGATTTACTTTTAAGTT
1 TTATAATTTACTATTAAGTT
18745689 TCCAATAATT
Statistics
Matches: 86, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
19 15 0.17
21 19 0.22
22 51 0.59
23 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.06, T:0.52
Consensus pattern (21 bp):
TTATAATTTACTATTAAGTTA
Found at i:18745795 original size:22 final size:23
Alignment explanation
Indices: 18745765--18745819 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
18745755 TGTCAATTAA
*
18745765 TTACCATTAAACTGA-AACTAAT
1 TTACTATTAAACTGATAACTAAT
* * *
18745787 TTACTATT-AAGTTATCACTAAT
1 TTACTATTAAACTGATAACTAAT
18745809 TTACTATTAAA
1 TTACTATTAAA
18745820 TTATTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 21 0.78
23 2 0.07
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (23 bp):
TTACTATTAAACTGATAACTAAT
Found at i:18745823 original size:22 final size:22
Alignment explanation
Indices: 18745781--18745847 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
18745771 TTAAACTGAA
*
18745781 ACTAATTTACTATTAAGTTATC
1 ACTAATTTACTATTAAATTATC
*
18745803 ACTAATTTACTATTAAATTATT
1 ACTAATTTACTATTAAATTATC
* * * *
18745825 ATTAATTTATTACTAATTTATC
1 ACTAATTTACTATTAAATTATC
18745847 A
1 A
18745848 ATTATTAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (22 bp):
ACTAATTTACTATTAAATTATC
Found at i:18745841 original size:11 final size:11
Alignment explanation
Indices: 18745781--18745845 Score: 58
Period size: 11 Copynumber: 5.9 Consensus size: 11
18745771 TTAAACTGAA
*
18745781 ACTAATTTACT
1 ACTAATTTATT
* * *
18745792 ATTAAGTTATC
1 ACTAATTTATT
*
18745803 ACTAATTTACT
1 ACTAATTTATT
* *
18745814 ATTAAATTATT
1 ACTAATTTATT
*
18745825 ATTAATTTATT
1 ACTAATTTATT
18745836 ACTAATTTAT
1 ACTAATTTAT
18745846 CAATTATTAA
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 41 1.00
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (11 bp):
ACTAATTTATT
Found at i:18746845 original size:153 final size:152
Alignment explanation
Indices: 18746567--18746859 Score: 550
Period size: 153 Copynumber: 1.9 Consensus size: 152
18746557 AAAAAGAAAC
*
18746567 AAAAAAGACTTGTAACATTTTTTAGAAGGCTAGAAAGTTAATTTGTTTTTTAAATTTACATGAGT
1 AAAAAAGACTTGTAACATTTTTTAGAAAGCTAGAAAGTTAATTTGTTTTTTAAATTTACATGAGT
18746632 GTGACCTAATATTTAATATTTGTGACAAATGGGTTTGTGAATAATAATGTGGGTGCAATAAATAT
66 GTGACCTAATATTTAATATTTGTGACAAATGGGTTTGTGAATAATAATGTGGGTGCAATAAATAT
18746697 ATAAATAATAGTGTCGACAAAA
131 ATAAATAATAGTGTCGACAAAA
*
18746719 AAAAAAGGACTTGTAACATTTTTTGGAAAGCTAGAAAGTTAATTTGTTTTTTAAATTTACATGAG
1 AAAAAA-GACTTGTAACATTTTTTAGAAAGCTAGAAAGTTAATTTGTTTTTTAAATTTACATGAG
*
18746784 TGTGACTTAATATTTAATATTTGTGACAAATGGGTTTGTGAATAATAATGTGGGTGCAATAAATA
65 TGTGACCTAATATTTAATATTTGTGACAAATGGGTTTGTGAATAATAATGTGGGTGCAATAAATA
18746849 TATAAATAATA
130 TATAAATAATA
18746860 ATGTGATTTT
Statistics
Matches: 137, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
152 6 0.04
153 131 0.96
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (152 bp):
AAAAAAGACTTGTAACATTTTTTAGAAAGCTAGAAAGTTAATTTGTTTTTTAAATTTACATGAGT
GTGACCTAATATTTAATATTTGTGACAAATGGGTTTGTGAATAATAATGTGGGTGCAATAAATAT
ATAAATAATAGTGTCGACAAAA
Found at i:18747240 original size:22 final size:22
Alignment explanation
Indices: 18747211--18747850 Score: 167
Period size: 22 Copynumber: 28.7 Consensus size: 22
18747201 CAAAGCCGTC
*
18747211 AATGATTTA-TTTATAAATTATT
1 AATGATTTACTAT-TAAATTATT
* * *
18747233 AATAATTTACTATTAATTTATA
1 AATGATTTACTATTAAATTATT
* *
18747255 AATGATTTACCATTAAATTATG
1 AATGATTTACTATTAAATTATT
*
18747277 AATGATTTTATTATTAAATTATT
1 AATGA-TTTACTATTAAATTATT
*
18747300 GATGATTTACTA-TAAATATATT
1 AATGATTTACTATTAAAT-TATT
* *
18747322 AATGATTTATTA-TAAAGTTA-A
1 AATGATTTACTATTAAA-TTATT
* * * *
18747343 AATTGATTTACGACTAATTTATC
1 AA-TGATTTACTATTAAATTATT
* * *
18747366 AATAATTTACTA-CAAAGTTATC
1 AATGATTTACTATTAAA-TTATT
* * * *
18747388 AATGATTAACTAATT-TACTACTA
1 AATGATTTACT-ATTAAATTA-TT
* * *
18747411 AATTATATCACCGATTTACAATTAAATT
1 AATGAT-TTA-CTA-TTA-AATT--ATT
* * **
18747439 ATTAGTAATTTATTATTACGTTATT
1 A--A-TGATTTACTATTAAATTATT
* *
18747464 AATTATTTACTATTAAGTTA-T
1 AATGATTTACTATTAAATTATT
* * *
18747485 CA-G-TTTATTATTAAGTTATT
1 AATGATTTACTATTAAATTATT
*
18747505 AATAATTTACTATTAAATTATT
1 AATGATTTACTATTAAATTATT
* **
18747527 ATTGATTTACTATTTTATTATT
1 AATGATTTACTATTAAATTATT
* * ** *
18747549 ATAT-ATTTACAACTACGTTATC
1 A-ATGATTTACTATTAAATTATT
* * * * *
18747571 ATTAATTTATTATTTAATTTTT
1 AATGATTTACTATTAAATTATT
* * * *
18747593 GATTATTTATTATAAAATTATT
1 AATGATTTACTATTAAATTATT
* * *
18747615 -ATCGATTTATTACTAAATTATC
1 AAT-GATTTACTATTAAATTATT
* * * * * * *
18747637 CATAATTCATTATCAAGTTATC
1 AATGATTTACTATTAAATTATT
* * *
18747659 ACTCATTCA-TATTAAATTATCT
1 AATGATTTACTATTAAATTAT-T
* * *
18747681 -ATGGTTTACTATTAAGTTATC
1 AATGATTTACTATTAAATTATT
* * * *
18747702 ACTAATTAACTTTTAAATTATCAAT
1 AATGATTTACTATTAAATTAT---T
* * *
18747727 AATTTAATTACTATTAACTTA-T
1 AA-TGATTTACTATTAAATTATT
* * * *
18747749 ACTGATTTATTTTTAAATTTTT
1 AATGATTTACTATTAAATTATT
* *
18747771 AATGATTAATTATTAAATTATT
1 AATGATTTACTATTAAATTATT
* * * *
18747793 AAT-AATTACTACTAATTTATC
1 AATGATTTACTATTAAATTATT
* * *
18747814 ATTAATTTACTACTAAATTATT
1 AATGATTTACTATTAAATTATT
*
18747836 TATGATTTACTATTA
1 AATGATTTACTATTA
18747851 TTAATTAATT
Statistics
Matches: 444, Mismatches: 137, Indels: 74
0.68 0.21 0.11
Matches are distributed among these distances:
19 14 0.03
20 2 0.00
21 53 0.12
22 296 0.67
23 38 0.09
24 3 0.01
25 8 0.02
26 13 0.03
27 4 0.01
28 5 0.01
29 2 0.00
30 3 0.01
31 3 0.01
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.49
Consensus pattern (22 bp):
AATGATTTACTATTAAATTATT
Found at i:18747466 original size:19 final size:19
Alignment explanation
Indices: 18747444--18747507 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
18747434 AAATTATTAG
*
18747444 TAATTTATTATTACGTTAT
1 TAATTTATTATTAAGTTAT
*
18747463 TAATTATTTACTATTAAGTTAT
1 T-A--ATTTATTATTAAGTTAT
* *
18747485 CAGTTTATTATTAAGTTAT
1 TAATTTATTATTAAGTTAT
18747504 TAAT
1 TAAT
18747508 AATTTACTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
19 18 0.51
20 1 0.03
21 1 0.03
22 15 0.43
ACGTcount: A:0.34, C:0.05, G:0.06, T:0.55
Consensus pattern (19 bp):
TAATTTATTATTAAGTTAT
Found at i:18747503 original size:11 final size:11
Alignment explanation
Indices: 18747431--18747529 Score: 53
Period size: 11 Copynumber: 9.3 Consensus size: 11
18747421 CCGATTTACA
*
18747431 ATTAAATTATT
1 ATTAAGTTATT
* *
18747442 AGTAATTTATT
1 ATTAAGTTATT
*
18747453 ATTACGTTATT
1 ATTAAGTTATT
* *
18747464 AATT-ATTTACT
1 -ATTAAGTTATT
*
18747475 ATTAAGTTATC
1 ATTAAGTTATT
*
18747486 AGT---TTATT
1 ATTAAGTTATT
18747494 ATTAAGTTATT
1 ATTAAGTTATT
* * *
18747505 AATAATTTACT
1 ATTAAGTTATT
*
18747516 ATTAAATTATT
1 ATTAAGTTATT
18747527 ATT
1 ATT
18747530 GATTTACTAT
Statistics
Matches: 63, Mismatches: 20, Indels: 10
0.68 0.22 0.11
Matches are distributed among these distances:
8 6 0.10
10 3 0.05
11 51 0.81
12 3 0.05
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (11 bp):
ATTAAGTTATT
Found at i:18747504 original size:41 final size:41
Alignment explanation
Indices: 18747424--18747525 Score: 132
Period size: 41 Copynumber: 2.4 Consensus size: 41
18747414 TATATCACCG
* * * *
18747424 ATTTACAATTAAATTATTAGTAATTTATTATTACGTTATTAATT
1 ATTTACTATTAAATTATCAG---TTTATTATTAAGTTATTAATA
*
18747468 ATTTACTATTAAGTTATCAGTTTATTATTAAGTTATTAATA
1 ATTTACTATTAAATTATCAGTTTATTATTAAGTTATTAATA
18747509 ATTTACTATTAAATTAT
1 ATTTACTATTAAATTAT
18747526 TATTGATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 35 0.67
44 17 0.33
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (41 bp):
ATTTACTATTAAATTATCAGTTTATTATTAAGTTATTAATA
Found at i:18747581 original size:85 final size:85
Alignment explanation
Indices: 18747424--18747582 Score: 187
Period size: 85 Copynumber: 1.9 Consensus size: 85
18747414 TATATCACCG
* * * *
18747424 ATTTACAATTAAATTATTAGTAATTTATTATTACGTTATTAATTATTTACTATTAAGTTATCAGT
1 ATTTACAATTAAATTATTAGTAATTTACTATTACATTATTAATTATTTACAACTAAGTTATCAGT
*
18747489 TTATTATTAAGTTATTAATA
66 TAATTATTAAGTTATTAATA
* * * ** *
18747509 ATTTACTATTAAATTATTATTGATTTACTATTTTATTATT-ATATATTTACAACTACGTTATCA-
1 ATTTACAATTAAATTATTAGTAATTTACTATTACATTATTAAT-TATTTACAACTAAGTTATCAG
18747572 TTAATTTATTA
65 TTAA-TTATTA
18747583 TTTAATTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
84 5 0.08
85 56 0.92
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.53
Consensus pattern (85 bp):
ATTTACAATTAAATTATTAGTAATTTACTATTACATTATTAATTATTTACAACTAAGTTATCAGT
TAATTATTAAGTTATTAATA
Found at i:18747675 original size:43 final size:44
Alignment explanation
Indices: 18747628--18747730 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 44
18747618 GATTTATTAC
* * * *
18747628 TAAATTATCCATAATTCATTATCAAGTTATCACTCATTCA-TAT
1 TAAATTATCAATAATTCACTATCAAGTTATCACTAATTAACTAT
* ** * * *
18747671 TAAATTATCTATGGTTTACTATTAAGTTATCACTAATTAACTTT
1 TAAATTATCAATAATTCACTATCAAGTTATCACTAATTAACTAT
18747715 TAAATTATCAATAATT
1 TAAATTATCAATAATT
18747731 TAATTACTAT
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
43 32 0.68
44 15 0.32
ACGTcount: A:0.38, C:0.14, G:0.04, T:0.45
Consensus pattern (44 bp):
TAAATTATCAATAATTCACTATCAAGTTATCACTAATTAACTAT
Found at i:18747863 original size:14 final size:14
Alignment explanation
Indices: 18747846--18747897 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
18747836 TATGATTTAC
18747846 TATTATTAATTAAT
1 TATTATTAATTAAT
18747860 TATTATTAAACTT-AT
1 TATTATT-AA-TTAAT
* *
18747875 TACTATCAATTAAT
1 TATTATTAATTAAT
18747889 TATTATTAA
1 TATTATTAA
18747898 ACGAAAATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 2 0.06
14 18 0.58
15 9 0.29
16 2 0.06
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTATTAATTAAT
Found at i:18747909 original size:26 final size:29
Alignment explanation
Indices: 18747853--18747912 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
18747843 TACTATTATT
* * *
18747853 AATTAATTATTATTAAACTTATTACTATC
1 AATTAATTATTATTAAACTGATAAATATC
18747882 AATTAATTATTATTAAAC-GA-AAAT-TC
1 AATTAATTATTATTAAACTGATAAATATC
18747908 AATTA
1 AATTA
18747913 CTATTAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.25
27 2 0.07
28 1 0.04
29 18 0.64
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (29 bp):
AATTAATTATTATTAAACTGATAAATATC
Found at i:18748009 original size:44 final size:44
Alignment explanation
Indices: 18747781--18748057 Score: 154
Period size: 44 Copynumber: 6.3 Consensus size: 44
18747771 AATGATTAAT
* * * *
18747781 TATTAAATTATTAA-TAATTACTACTAATTTATCATTAATTTAC
1 TATTAAGTTATTAATTAATTACTATTAAATTATCATTCATTTAC
* * * * * * *
18747824 TACTAAATTATTTATGATTTACTATTATTAATTAATTATT-ATTAAAC
1 TATTAAGTTATTAATTAATTACTATTA--AATT-ATCATTCATT-TAC
* * * ** ** *
18747871 TTATT-A-CTATCAATTAATTATTATTAAACGAAAATTCAATTAC
1 -TATTAAGTTATTAATTAATTACTATTAAATTATCATTCATTTAC
* * * * * *
18747914 TATTAAGTTGTT-ATTAATTTACTATTAAGTTATCACTGAGTTAT
1 TATTAAGTTATTAATTAA-TTACTATTAAATTATCATTCATTTAC
* *
18747958 TACTAAGTTATTAATT-ATTAACTACTAAATTATCATTCATTTAC
1 TATTAAGTTATTAATTAATT-ACTATTAAATTATCATTCATTTAC
* * * *
18748002 TATTAAGTTATCACTTAATTAGTATTAAATTATCCA-TGATTTAC
1 TATTAAGTTATTAATTAATTACTATTAAATTAT-CATTCATTTAC
18748046 TATTAAGTTATT
1 TATTAAGTTATT
18748058 GATGATTACT
Statistics
Matches: 171, Mismatches: 49, Indels: 27
0.69 0.20 0.11
Matches are distributed among these distances:
42 4 0.02
43 26 0.15
44 102 0.60
45 8 0.05
46 20 0.12
47 8 0.05
48 3 0.02
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (44 bp):
TATTAAGTTATTAATTAATTACTATTAAATTATCATTCATTTAC
Found at i:18748013 original size:22 final size:21
Alignment explanation
Indices: 18747910--18748056 Score: 114
Period size: 22 Copynumber: 6.7 Consensus size: 21
18747900 GAAAATTCAA
* *
18747910 TTACTATTAAGTTGTTATTAAT
1 TTACTATTAAGTTATCATT-AT
* *
18747932 TTACTATTAAGTTATCACTGAG
1 TTACTATTAAGTTATCA-TTAT
* * *
18747954 TTATTACTAAGTTATTAATTAT
1 TTACTATTAAGTTA-TCATTAT
* * *
18747976 TAACTACTAAATTATCATTCAT
1 TTACTATTAAGTTATCATT-AT
*
18747998 TTACTATTAAGTTATCACTTAA
1 TTACTATTAAGTTATCA-TTAT
* * *
18748020 TTAGTATTAAATTATCCATGAT
1 TTACTATTAAGTTAT-CATTAT
18748042 TTACTATTAAGTTAT
1 TTACTATTAAGTTAT
18748057 TGATGATTAC
Statistics
Matches: 97, Mismatches: 23, Indels: 10
0.75 0.18 0.08
Matches are distributed among these distances:
21 4 0.04
22 86 0.89
23 7 0.07
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (21 bp):
TTACTATTAAGTTATCATTAT
Found at i:18748068 original size:21 final size:21
Alignment explanation
Indices: 18747998--18748069 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
18747988 TATCATTCAT
* * *
18747998 TTACTATTAAGTTATCACTTAA
1 TTACTATTAAATTATC-CATGA
*
18748020 TTAGTATTAAATTATCCATGA
1 TTACTATTAAATTATCCATGA
* **
18748041 TTTACTATTAAGTTATTGATGA
1 -TTACTATTAAATTATCCATGA
18748063 TTACTAT
1 TTACTAT
18748070 CGATTATGCT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 10 0.24
22 31 0.76
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (21 bp):
TTACTATTAAATTATCCATGA
Found at i:18748349 original size:32 final size:32
Alignment explanation
Indices: 18748313--18748378 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
18748303 TAATAAATTA
18748313 AAATCATAACTTTTATACTAATAAATATATAC
1 AAATCATAACTTTTATACTAATAAATATATAC
18748345 AAATCATAACTTTTATACTAATAAATATATAC
1 AAATCATAACTTTTATACTAATAAATATATAC
18748377 AA
1 AA
18748379 TATATTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
AAATCATAACTTTTATACTAATAAATATATAC
Found at i:18752506 original size:22 final size:22
Alignment explanation
Indices: 18752481--18752551 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
18752471 ATTATTAGAG
* *
18752481 ATTTATTATTAAGTTATTAATA
1 ATTTATTATTAAATTATCAATA
* *
18752503 ATTTATTACTAAATTATCAATG
1 ATTTATTATTAAATTATCAATA
* * *
18752525 ATTTACTATTAATTTATGAATA
1 ATTTATTATTAAATTATCAATA
18752547 ATTTA
1 ATTTA
18752552 CTACCAAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
ATTTATTATTAAATTATCAATA
Found at i:18752519 original size:44 final size:44
Alignment explanation
Indices: 18752480--18752576 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
18752470 TATTATTAGA
* *
18752480 GATTTATTATTAAGTTATTAATAATTTATTACTAAATTATCAAT
1 GATTTACTATTAAGTTATGAATAATTTATTACTAAATTATCAAT
* * * * *
18752524 GATTTACTATTAATTTATGAATAATTTACTACCAAATTGTTAAT
1 GATTTACTATTAAGTTATGAATAATTTATTACTAAATTATCAAT
18752568 GATTTACTA
1 GATTTACTA
18752577 AGTTATTGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.39, C:0.07, G:0.06, T:0.47
Consensus pattern (44 bp):
GATTTACTATTAAGTTATGAATAATTTATTACTAAATTATCAAT
Found at i:18752530 original size:19 final size:19
Alignment explanation
Indices: 18752508--18752592 Score: 62
Period size: 22 Copynumber: 4.2 Consensus size: 19
18752498 TAATAATTTA
*
18752508 TTACTAAATTATCAATGAT
1 TTACTAAATTATTAATGAT
* *
18752527 TTACTATTAATTTATGAATAAT
1 TTACTA--AA-TTATTAATGAT
*
18752549 TTACTACCAAATTGTTAATGAT
1 TTACT---AAATTATTAATGAT
* *
18752571 TTACTAAGTTATTGATGAT
1 TTACTAAATTATTAATGAT
18752590 TTA
1 TTA
18752593 TTATAAAGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
19 20 0.38
21 2 0.04
22 27 0.52
23 2 0.04
25 1 0.02
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (19 bp):
TTACTAAATTATTAATGAT
Found at i:18752548 original size:11 final size:11
Alignment explanation
Indices: 18752481--18752551 Score: 61
Period size: 11 Copynumber: 6.5 Consensus size: 11
18752471 ATTATTAGAG
*
18752481 ATTTATTATTA
1 ATTTATTAATA
*
18752492 AGTTATTAATA
1 ATTTATTAATA
*
18752503 ATTTATTACTA
1 ATTTATTAATA
* * *
18752514 AATTATCAATG
1 ATTTATTAATA
* *
18752525 ATTTACTATTA
1 ATTTATTAATA
*
18752536 ATTTATGAATA
1 ATTTATTAATA
18752547 ATTTA
1 ATTTA
18752552 CTACCAAATT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
11 44 1.00
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (11 bp):
ATTTATTAATA
Found at i:18752572 original size:22 final size:22
Alignment explanation
Indices: 18752494--18752576 Score: 85
Period size: 22 Copynumber: 3.8 Consensus size: 22
18752484 TATTATTAAG
*
18752494 TTATTAATAATTTATTACTAAA
1 TTATTAATAATTTACTACTAAA
* * * *
18752516 TTATCAATGATTTACTATTAAT
1 TTATTAATAATTTACTACTAAA
* *
18752538 TTATGAATAATTTACTACCAAA
1 TTATTAATAATTTACTACTAAA
* *
18752560 TTGTTAATGATTTACTA
1 TTATTAATAATTTACTA
18752577 AGTTATTGAT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (22 bp):
TTATTAATAATTTACTACTAAA
Found at i:18753106 original size:30 final size:30
Alignment explanation
Indices: 18753070--18753143 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
18753060 AAATTGTAAG
*
18753070 TTTTTAAAATTTAGTGACCAAAATAAAAAT
1 TTTTTAAAATTTAGTAACCAAAATAAAAAT
* ** *
18753100 TTTTTAAAAATTAAGTAACCAAAATTTATAT
1 TTTTT-AAAATTTAGTAACCAAAATAAAAAT
*
18753131 TTTTAAAAATTTA
1 TTTTTAAAATTTA
18753144 CAAATGCCAC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (30 bp):
TTTTTAAAATTTAGTAACCAAAATAAAAAT
Found at i:18756985 original size:16 final size:16
Alignment explanation
Indices: 18756961--18757000 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
18756951 GTCCAATATG
*
18756961 AACTATTTGACCTTAA
1 AACTTTTTGACCTTAA
*
18756977 AACTTTTTGGCCTTAA
1 AACTTTTTGACCTTAA
*
18756993 AAGTTTTT
1 AACTTTTT
18757001 CACACTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (16 bp):
AACTTTTTGACCTTAA
Found at i:18776575 original size:2 final size:2
Alignment explanation
Indices: 18776568--18776601 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18776558 TTCTTATTTT
18776568 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
18776602 AGCAATGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18780676 original size:7 final size:7
Alignment explanation
Indices: 18780664--18780714 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
18780654 CACTTATATG
18780664 TAAAAAT
1 TAAAAAT
18780671 TAAAAA-
1 TAAAAAT
18780677 TAAAAAT
1 TAAAAAT
* *
18780684 TATATAT
1 TAAAAAT
*
18780691 GCAAAAAT
1 -TAAAAAT
18780699 TAAAAAT
1 TAAAAAT
18780706 T-AAAAT
1 TAAAAAT
18780712 TAA
1 TAA
18780715 GTTTAGTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
6 12 0.34
7 19 0.54
8 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (7 bp):
TAAAAAT
Found at i:18780682 original size:13 final size:13
Alignment explanation
Indices: 18780664--18780714 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
18780654 CACTTATATG
18780664 TAAAAATTAAAAA
1 TAAAAATTAAAAA
* *
18780677 TAAAAATTATATA
1 TAAAAATTAAAAA
18780690 TGCAAAAATTAAAAA
1 T--AAAAATTAAAAA
*
18780705 TTAAAATTAA
1 TAAAAATTAA
18780715 GTTTAGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 20 0.65
15 11 0.35
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (13 bp):
TAAAAATTAAAAA
Found at i:18780689 original size:28 final size:28
Alignment explanation
Indices: 18780658--18780713 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
18780648 TTAATTCACT
*
18780658 TATATGTAAAAATTAAAAATAAAAATTA
1 TATATGCAAAAATTAAAAATAAAAATTA
*
18780686 TATATGCAAAAATTAAAAATTAAAATTA
1 TATATGCAAAAATTAAAAATAAAAATTA
18780714 AGTTTAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (28 bp):
TATATGCAAAAATTAAAAATAAAAATTA
Found at i:18781878 original size:18 final size:17
Alignment explanation
Indices: 18781855--18781888 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18781845 AAATACTTAC
18781855 ATAATATAATATTTTATA
1 ATAATA-AATATTTTATA
*
18781873 ATAATAAATTTTTTAT
1 ATAATAAATATTTTAT
18781889 CTCAAGATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATAATAAATATTTTATA
Found at i:18782217 original size:9 final size:9
Alignment explanation
Indices: 18782190--18782223 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
18782180 GCTAAATTTT
18782190 TTTTATATA
1 TTTTATATA
18782199 TTATTAATATA
1 TT-TT-ATATA
18782210 TTTTATATA
1 TTTTATATA
18782219 TTTTA
1 TTTTA
18782224 AGAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 12 0.52
10 4 0.17
11 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTATATA
Found at i:18782857 original size:2 final size:2
Alignment explanation
Indices: 18782846--18782874 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18782836 CGTATATTTC
18782846 AT AT -T 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
18782875 GATGTTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:18786618 original size:34 final size:34
Alignment explanation
Indices: 18786570--18786644 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
18786560 AAAGGAGGCC
18786570 AATGCCTAACGGGAATTAGGGAAGGGGAATTTGCA
1 AATG-CTAACGGGAATTAGGGAAGGGGAATTTGCA
*
18786605 AATGCTAAGGGGAATTAGGGAAGGGGAATTTGCA
1 AATGCTAACGGGAATTAGGGAAGGGGAATTTGCA
18786639 AATGCT
1 AATGCT
18786645 TAGAATCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
34 35 0.90
35 4 0.10
ACGTcount: A:0.35, C:0.09, G:0.35, T:0.21
Consensus pattern (34 bp):
AATGCTAACGGGAATTAGGGAAGGGGAATTTGCA
Found at i:18788644 original size:12 final size:12
Alignment explanation
Indices: 18788629--18788662 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
18788619 TATCTCATTA
18788629 TATATCATATAT
1 TATATCATATAT
18788641 TATATCATATAT
1 TATATCATATAT
* *
18788653 AATATTATAT
1 TATATCATAT
18788663 TACAACATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATCATATAT
Found at i:18788772 original size:24 final size:25
Alignment explanation
Indices: 18788725--18788772 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
18788715 ATGATACATA
* *
18788725 AAATAATAATAAATAATTATATTAT
1 AAATAATAATAAATAATCAAATTAT
*
18788750 AAATTATAA-AAATAATCAAATTA
1 AAATAATAATAAATAATCAAATTA
18788773 AAAAAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATAATAATAAATAATCAAATTAT
Found at i:18788908 original size:19 final size:19
Alignment explanation
Indices: 18788863--18788911 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
18788853 TATTTTTTAT
*
18788863 TTTATTTAATATTATTCAAA
1 TTTATTTAA-AATATTCAAA
**
18788883 TCCATTTAAAATATTCAAA
1 TTTATTTAAAATATTCAAA
18788902 TTTATTTAAA
1 TTTATTTAAA
18788912 TTGATAAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTATTTAAAATATTCAAA
Found at i:18800538 original size:16 final size:17
Alignment explanation
Indices: 18800510--18800541 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18800500 TGTGAAAATC
18800510 TTAAAAATAATATATTT
1 TTAAAAATAATATATTT
18800527 TTAAAAAT-ATATATT
1 TTAAAAATAATATATT
18800542 AATTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAAAATAATATATTT
Found at i:18801855 original size:13 final size:13
Alignment explanation
Indices: 18801837--18801875 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
18801827 CCCTTATTGT
18801837 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
18801850 GAAAAAAAAAAAA
1 GAAAAAAAAAAAA
* *
18801863 -AAAGAAACAAAA
1 GAAAAAAAAAAAA
18801875 G
1 G
18801876 GATAGTGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAAAA
Found at i:18801859 original size:16 final size:17
Alignment explanation
Indices: 18801838--18801874 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
18801828 CCTTATTGTG
18801838 AAAAAAAAAAAAGAAA-
1 AAAAAAAAAAAAGAAAC
18801854 AAAAAAAAAAAAGAAAC
1 AAAAAAAAAAAAGAAAC
18801871 AAAA
1 AAAA
18801875 GGATAGTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.92, C:0.03, G:0.05, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAGAAAC
Found at i:18809506 original size:24 final size:24
Alignment explanation
Indices: 18809479--18809524 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
18809469 ATATTATTTC
18809479 AACAATTTTTAATTGGTAATTTTT
1 AACAATTTTTAATTGGTAATTTTT
* * *
18809503 AACATTTTTTTATTGTTAATTT
1 AACAATTTTTAATTGGTAATTT
18809525 GATTATAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (24 bp):
AACAATTTTTAATTGGTAATTTTT
Found at i:18816358 original size:240 final size:237
Alignment explanation
Indices: 18815865--18816430 Score: 544
Period size: 240 Copynumber: 2.4 Consensus size: 237
18815855 ACTACATTAC
* ** * * * * *
18815865 TTTTTATTGTAATATAGTAATTGAGTGCTTTATAACAAACAATTGA-AAATTTAAAACAACTAAA
1 TTTTTATTATAACGTAGTAATTGAATGCGTTA-AAAAAACAATT-ACAAAGTTAAAACAACTACA
* * * * * * * * *
18815929 ATGAAACATTGCATTAA-TTTTTTTGAAAATTCAGTAATTAAGTGCG-T---AAAAAAATTATAT
64 ATAAAATATTACATTAAGTTTTATT-ATAATGCAGTAATTGATTGTGTTACAAAAAAAATTATAT
* * * * * *
18815989 TTTAAAAACAATTACAATCATATACTACGTTAATTTTTATTATAATGCAGTAATTGAATACATAA
128 TTTAAAAACAACTAAAATCAAATACTACGTGAAATTTTATTATAATGAAGTAATTGAATACATAA
* * *
18816054 AAAAATTTGATAATTTAAAACAATTATAATCAAATAATGCATTGA
193 AAAAAATTGACAATTTAAAACAATTATAATCAAATAATGAATTGA
* * *
18816099 TTTTTATTATAAGGTAGTAATTGAATGCGTTAAAATAACAATTAACAAAGTT-AAACAATTACAA
1 TTTTTATTATAACGTAGTAATTGAATGCGTTAAAAAAACAATT-ACAAAGTTAAAACAACTACAA
* *
18816163 TAAAATATTGCATTAATTTTTATTATAATGCAGTAATTGATTGTGTTACAAAAAATAATTATATT
65 TAAAATATTACATTAAGTTTTATTATAATGCAGTAATTGATTGTGTTACAAAAAA-AATTATATT
* * **
18816228 TTAAAAATAACTAAAATCAAATATTACG-GAAATTTTATTATAATGAAGTAATTGACA-ATGTTA
129 TTAAAAACAACTAAAATCAAATACTACGTGAAATTTTATTATAATGAAGTAATTGA-ATA-CATA
*
18816291 AAATAACAATTGACAATTTAAAACAATTATAATCAAAT-ATTAAGTT-A
192 AAA-AA-AATTGACAATTTAAAACAATTATAATCAAATAATGAA-TTGA
* * * * ***
18816338 -TTTTATTATATAACGTAGTAATTGATTGTGTTAAAAAAATAATTATATTTTTAAAACAACTACA
1 TTTTTA-T-TATAACGTAGTAATTGAATGCGTTAAAAAAACAATTACAAAGTTAAAACAACTACA
*
18816402 ATCAAATATTACATTAAGTTTTATTATAA
64 ATAAAATATTACATTAAGTTTTATTATAA
18816431 CATAGTAACT
Statistics
Matches: 271, Mismatches: 46, Indels: 24
0.79 0.13 0.07
Matches are distributed among these distances:
233 50 0.18
234 39 0.14
237 30 0.11
238 43 0.16
239 11 0.04
240 98 0.36
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.38
Consensus pattern (237 bp):
TTTTTATTATAACGTAGTAATTGAATGCGTTAAAAAAACAATTACAAAGTTAAAACAACTACAAT
AAAATATTACATTAAGTTTTATTATAATGCAGTAATTGATTGTGTTACAAAAAAAATTATATTTT
AAAAACAACTAAAATCAAATACTACGTGAAATTTTATTATAATGAAGTAATTGAATACATAAAAA
AAATTGACAATTTAAAACAATTATAATCAAATAATGAATTGA
Found at i:18816426 original size:160 final size:160
Alignment explanation
Indices: 18816018--18816430 Score: 434
Period size: 160 Copynumber: 2.6 Consensus size: 160
18816008 ATATACTACG
* * *** * *
18816018 TTAATTTTTATTATAATGCAGTAATTGAAT-ACATA-AAAAAAT--TTGATA-ATTTAAAACAAT
1 TTAATTTTTATTATAACGCAGTAATTGATTGTGTTACAAAAAATAATT-ATATTTTTAAAACAAC
* * * * * *
18816078 TATAATCAAATAATGCATTGATTTTTATTATAAGGTAGTAATTGAATGCGTTAAAATAACAATTA
65 TAAAATCAAATATTACATTAAATTTTATTATAAGGAAGTAATTGAAT-CGTTAAAATAACAATTA
*
18816143 ACAAAGTTAAACAATTACAATAAAATATTGCA
129 ACAAAGTTAAACAATTACAATAAAATATTGAA
* * *
18816175 TTAATTTTTATTATAATGCAGTAATTGATTGTGTTACAAAAAATAATTATATTTTAAAAATAACT
1 TTAATTTTTATTATAACGCAGTAATTGATTGTGTTACAAAAAATAATTATATTTTTAAAACAACT
** * *
18816240 AAAATCAAATATTAC-GGAAATTTTATTATAATGAAGTAATTGACAAT-GTTAAAATAACAATTG
66 AAAATCAAATATTACATTAAATTTTATTATAAGGAAGTAATTG--AATCGTTAAAATAACAATTA
* * *
18816303 AC-AATTTAAAACAATTATAATCAAATATT-AA
129 ACAAAGTT-AAACAATTACAATAAAATATTGAA
* *
18816334 GTTATTTTATTA-TATAACGTAGTAATTGATTGTGTTA-AAAAAATAATTATATTTTTAAAACAA
1 -TTAATTT-TTATTATAACGCAGTAATTGATTGTGTTACAAAAAATAATTATATTTTTAAAACAA
* *
18816397 CTACAATCAAATATTACATTAAGTTTTATTATAA
64 CTAAAATCAAATATTACATTAAATTTTATTATAA
18816431 CATAGTAACT
Statistics
Matches: 214, Mismatches: 31, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
157 29 0.14
158 2 0.01
159 52 0.24
160 102 0.48
161 26 0.12
162 3 0.01
ACGTcount: A:0.47, C:0.07, G:0.08, T:0.38
Consensus pattern (160 bp):
TTAATTTTTATTATAACGCAGTAATTGATTGTGTTACAAAAAATAATTATATTTTTAAAACAACT
AAAATCAAATATTACATTAAATTTTATTATAAGGAAGTAATTGAATCGTTAAAATAACAATTAAC
AAAGTTAAACAATTACAATAAAATATTGAA
Found at i:18816431 original size:80 final size:81
Alignment explanation
Indices: 18815851--18816430 Score: 389
Period size: 80 Copynumber: 7.3 Consensus size: 81
18815841 TAATTAGGTA
* * * * * * * *
18815851 AAATACTACATTACTTTTTATTGTAATATAGTAATTGAGTGCT-TTATAACAAACAATTGA-AAA
1 AAATATTACATTAATTTTTATTATAATGTAGTAATTGAATG-TGTTA-AAAAAATAATTGATATA
* * *
18815914 TTTAAAACAACTAAAATG
64 TTTAAAACAATTACAATC
* * * *
18815932 AAACATTGCATTAATTTTT-TTGAAAAT-TCAGTAATT-AA-GTGCGT--AAAAA-AATT-ATAT
1 AAATATTACATTAATTTTTATT-ATAATGT-AGTAATTGAATGTG-TTAAAAAAATAATTGATAT
18815989 -TTTAAAAACAATTACAATC
63 ATTT-AAAACAATTACAATC
* * * * ***
18816008 ATATACTACGTTAATTTTTATTATAATGCAGTAATTGAAT-ACATAAAAAAAT--TTGATA-ATT
1 AAATATTACATTAATTTTTATTATAATGTAGTAATTGAATGTGTTAAAAAAATAATTGATATATT
*
18816069 TAAAACAATTATAATC
66 TAAAACAATTACAATC
* * * * * * * * * * *
18816085 AAATAATGCATTGATTTTTATTATAAGGTAGTAATTGAATGCGTTAAAATAACAATTAACAAAGT
1 AAATATTACATTAATTTTTATTATAATGTAGTAATTGAATGTGTTAAAAAAATAATTGATATATT
*
18816150 T-AAACAATTACAATA
66 TAAAACAATTACAATC
* * *
18816165 AAATATTGCATTAATTTTTATTATAATGCAGTAATTGATTGTGTTACAAAAAATAATT-ATAT-T
1 AAATATTACATTAATTTTTATTATAATGTAGTAATTGAATGTGTTA-AAAAAATAATTGATATAT
* * *
18816228 TTAAAAATAACTAAAATC
65 TT-AAAACAATTACAATC
** * * * * * *
18816246 AAATATTAC-GGAAATTTTATTATAATGAAGTAATTGACA-ATGTTAAAATAACAATTGACA-AT
1 AAATATTACATTAATTTTTATTATAATGTAGTAATTGA-ATGTGTTAAAAAAATAATTGATATAT
*
18816308 TTAAAACAATTATAATC
65 TTAAAACAATTACAATC
* * * *
18816325 AAATATTA-AGTTATTTTATTA-TATAACGTAGTAATTGATTGTGTTAAAAAAATAATT-ATATT
1 AAATATTACA-TTAATTT-TTATTATAATGTAGTAATTGAATGTGTTAAAAAAATAATTGATATA
*
18816387 TTTAAAACAACTACAATC
64 TTTAAAACAATTACAATC
*
18816405 AAATATTACATTAAGTTTTATTATAA
1 AAATATTACATTAATTTTTATTATAA
18816431 CATAGTAACT
Statistics
Matches: 382, Mismatches: 85, Indels: 65
0.72 0.16 0.12
Matches are distributed among these distances:
75 4 0.01
76 43 0.11
77 57 0.15
78 19 0.05
79 37 0.10
80 163 0.43
81 59 0.15
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (81 bp):
AAATATTACATTAATTTTTATTATAATGTAGTAATTGAATGTGTTAAAAAAATAATTGATATATT
TAAAACAATTACAATC
Found at i:18817854 original size:16 final size:15
Alignment explanation
Indices: 18817816--18817856 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
18817806 TCACGTGATA
*
18817816 AATTTTTTTAAAAAT
1 AATTTTATTAAAAAT
18817831 AATTTTATTAAAAAT
1 AATTTTATTAAAAAT
*
18817846 ATTTATTATTA
1 AATT-TTATTA
18817857 TTATAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTTATTAAAAAT
Found at i:18820536 original size:40 final size:41
Alignment explanation
Indices: 18820468--18820550 Score: 150
Period size: 40 Copynumber: 2.0 Consensus size: 41
18820458 ATGGTGCTGA
*
18820468 TATACATGCTGAATTGAATTATGGACAACATACATGGATTT
1 TATACATGCTGAATTGAATTAAGGACAACATACATGGATTT
18820509 TATACATGCTGAA-TGAATTAAGGACAACATACATGGATTT
1 TATACATGCTGAATTGAATTAAGGACAACATACATGGATTT
18820549 TA
1 TA
18820551 CATACTGTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 28 0.68
41 13 0.32
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.33
Consensus pattern (41 bp):
TATACATGCTGAATTGAATTAAGGACAACATACATGGATTT
Found at i:18824927 original size:16 final size:16
Alignment explanation
Indices: 18824906--18824936 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18824896 ACATCCATAT
18824906 TTTATATATCTATTTA
1 TTTATATATCTATTTA
*
18824922 TTTATATATGTATTT
1 TTTATATATCTATTT
18824937 TAATAAACAA
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:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (16 bp):
TTTATATATCTATTTA
Found at i:18824986 original size:23 final size:24
Alignment explanation
Indices: 18824955--18825004 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
18824945 AAAATTTTTA
18824955 TTAAATAAT-ATAAATT-AT-TATT
1 TTAAATAATCA-AAATTAATATATT
18824977 TTAAATTAATCAAAATTAATATATT
1 TTAAA-TAATCAAAATTAATATATT
18825002 TTA
1 TTA
18825005 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.21
23 9 0.38
24 3 0.12
25 7 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAATAATCAAAATTAATATATT
Found at i:18825019 original size:25 final size:25
Alignment explanation
Indices: 18824991--18825050 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 25
18824981 ATTAATCAAA
18824991 ATTAATATAT-TTTATTAAAAAATAT
1 ATTAATATATATTTA-TAAAAAATAT
18825016 ATTAATATATATTTATAAAAAAT-T
1 ATTAATATATATTTATAAAAAATAT
18825040 ATCTAA-ATATA
1 AT-TAATATATA
18825051 CAATATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
24 8 0.24
25 21 0.64
26 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTAATATATATTTATAAAAAATAT
Found at i:18842031 original size:19 final size:21
Alignment explanation
Indices: 18841981--18842052 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 21
18841971 TGTATTAAAT
* *
18841981 ATTTAAATTAAAT-ATATATG
1 ATTTTAATTAAATAATTTATG
*
18842001 ATTTT-GTATAAATAATTT-T-
1 ATTTTAAT-TAAATAATTTATG
*
18842020 ATTTTAATTAAA-ATTTTATG
1 ATTTTAATTAAATAATTTATG
18842040 ATTTTAATTAAAT
1 ATTTTAATTAAAT
18842053 CACATGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
18 4 0.10
19 11 0.27
20 23 0.56
21 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (21 bp):
ATTTTAATTAAATAATTTATG
Found at i:18846067 original size:18 final size:18
Alignment explanation
Indices: 18846034--18846068 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18846024 TATCCGAATC
**
18846034 CGATCCCGAATTCGACTT
1 CGATCCCGAACCCGACTT
18846052 CGATCCCGAACCCGACT
1 CGATCCCGAACCCGACT
18846069 ACAGAGCCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.40, G:0.17, T:0.20
Consensus pattern (18 bp):
CGATCCCGAACCCGACTT
Found at i:18854639 original size:57 final size:57
Alignment explanation
Indices: 18854575--18854688 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
18854565 GAAAAGTTTG
*
18854575 AATATCTTCCATATTTACTTTAAATGAGCTCACAATAGAAGAGCTCATATTTGCATC
1 AATATCTTCCATATTTACTTTAAATGAGCTCACAATAGAAGAGCTCAGATTTGCATC
* *
18854632 AATATCTTCTATATTTGCTTTAAATGAGCTCACAATAGAAGAGCTCAGATTTGCATC
1 AATATCTTCCATATTTACTTTAAATGAGCTCACAATAGAAGAGCTCAGATTTGCATC
18854689 TATCACATGC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (57 bp):
AATATCTTCCATATTTACTTTAAATGAGCTCACAATAGAAGAGCTCAGATTTGCATC
Found at i:18862459 original size:21 final size:20
Alignment explanation
Indices: 18862435--18862479 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
18862425 AATCATTCGA
*
18862435 AATCAAATCAATTTAAAATT
1 AATCAAATCAAATTAAAATT
* *
18862455 GAATCAATTCAAATTCAAATT
1 -AATCAAATCAAATTAAAATT
18862476 AATC
1 AATC
18862480 GAATTCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.33
Consensus pattern (20 bp):
AATCAAATCAAATTAAAATT
Found at i:18864349 original size:14 final size:15
Alignment explanation
Indices: 18864319--18864360 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
18864309 AATAATACTA
18864319 TAAAAGAATTAAATTT
1 TAAAA-AATTAAATTT
18864335 TAAAAAATT-AATTT
1 TAAAAAATTAAATTT
*
18864349 TAAAAAAATAAA
1 TAAAAAATTAAA
18864361 CATGATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
15 6 0.25
16 5 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
TAAAAAATTAAATTT
Found at i:18866980 original size:17 final size:18
Alignment explanation
Indices: 18866948--18866981 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18866938 ATTATAAATT
18866948 ATAAATTTAAAATAAAAA
1 ATAAATTTAAAATAAAAA
*
18866966 ATAAA-TTATAATAAAA
1 ATAAATTTAAAATAAAA
18866982 TTTTGAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAATTTAAAATAAAAA
Found at i:18868680 original size:26 final size:26
Alignment explanation
Indices: 18868644--18868701 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
18868634 CCAGCTTTTA
18868644 ATTCAATTAAATAAA-CATATAAAAAT
1 ATTCAATTAAATAAAGCATA-AAAAAT
* *
18868670 ATTCATTTAAATAAATGGATAAAAAAT
1 ATTCAATTAAATAAA-GCATAAAAAAT
18868697 ATTCA
1 ATTCA
18868702 GTTATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 14 0.50
27 11 0.39
28 3 0.11
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (26 bp):
ATTCAATTAAATAAAGCATAAAAAAT
Found at i:18871279 original size:12 final size:12
Alignment explanation
Indices: 18871262--18871288 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
18871252 AATTTTTTAT
18871262 AAGGGATTATTC
1 AAGGGATTATTC
18871274 AAGGGATTATTC
1 AAGGGATTATTC
18871286 AAG
1 AAG
18871289 TATTTTTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (12 bp):
AAGGGATTATTC
Found at i:18872577 original size:24 final size:24
Alignment explanation
Indices: 18872537--18872583 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
18872527 AAACCATATC
* *
18872537 ATATTATGATTATAAATA-AATTA
1 ATATTATAATTAAAAATATAATTA
18872560 ATATTAATAATTAAAAATATAATT
1 ATATT-ATAATTAAAAATATAATT
18872584 CAAAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATTATAATTAAAAATATAATTA
Found at i:18874190 original size:22 final size:24
Alignment explanation
Indices: 18874165--18874211 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
18874155 TATATATAAT
18874165 TATTT-TTTAATTTT-TAATTATA
1 TATTTATTTAATTTTATAATTATA
*
18874187 TATTTATTTAATTTTATATTTATA
1 TATTTATTTAATTTTATAATTATA
18874211 T
1 T
18874212 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 9 0.41
24 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTTATTTAATTTTATAATTATA
Found at i:18874198 original size:16 final size:16
Alignment explanation
Indices: 18874177--18874214 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
18874167 TTTTTTAATT
18874177 TTTAATTATATATTTA
1 TTTAATTATATATTTA
*
18874193 TTTAATTTTATATTTA
1 TTTAATTATATATTTA
18874209 TATTAA
1 T-TTAA
18874215 AAAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAATTATATATTTA
Found at i:18874253 original size:20 final size:19
Alignment explanation
Indices: 18874205--18874247 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
18874195 TAATTTTATA
*
18874205 TTTATATTAAAAAATAATAT
1 TTTATATT-TAAAATAATAT
18874225 TTTATATTTAAAA-AATAT
1 TTTATATTTAAAATAATAT
18874243 TTTAT
1 TTTAT
18874248 TAATTTCAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 4 0.18
20 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTATATTTAAAATAATAT
Found at i:18883553 original size:1 final size:1
Alignment explanation
Indices: 18883549--18883578 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
18883539 TTTCGTCCCC
*
18883549 TTTTTTTTTTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
18883579 CAGTTTCGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:18887120 original size:15 final size:15
Alignment explanation
Indices: 18887076--18887120 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
18887066 AATATAATTA
* *
18887076 AAATTTTTTTAAAAA
1 AAATTTTATTAAAAT
18887091 AAATTTATATT-AAAT
1 AAATTT-TATTAAAAT
18887106 AAATTTTATTAAAAT
1 AAATTTTATTAAAAT
18887121 TAATATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 4 0.15
15 19 0.73
16 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATTTTATTAAAAT
Found at i:18887476 original size:16 final size:16
Alignment explanation
Indices: 18887455--18887485 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18887445 CTGTCACTTT
*
18887455 TTTTTTTGCTTTTTTA
1 TTTTTTTCCTTTTTTA
18887471 TTTTTTTCCTTTTTT
1 TTTTTTTCCTTTTTT
18887486 GTAAATTTTT
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:0.03, C:0.10, G:0.03, T:0.84
Consensus pattern (16 bp):
TTTTTTTCCTTTTTTA
Found at i:18887704 original size:21 final size:21
Alignment explanation
Indices: 18887678--18887744 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
18887668 ATGTCAGTTA
*
18887678 TTTTTTTAATCTATTT-TTTCT
1 TTTTTTTAATC-ATTTATTTAT
18887699 TTTTTTT-ATCATTTATTTAT
1 TTTTTTTAATCATTTATTTAT
*
18887719 TTTATTTTAAAT-ATTTATATAT
1 TTT-TTTT-AATCATTTATTTAT
18887741 TTTT
1 TTTT
18887745 ATAATATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 4 0.10
20 10 0.25
21 12 0.30
22 12 0.30
23 2 0.05
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTTTAATCATTTATTTAT
Found at i:18887721 original size:20 final size:20
Alignment explanation
Indices: 18887675--18887727 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
18887665 TCTATGTCAG
*
18887675 TTATTTTTTTAATCTATTTT
1 TTATTTTTTTTATCTATTTT
*
18887695 TTCTTTTTTTTATC-ATTTAT
1 TTATTTTTTTTATCTATTT-T
18887715 TTATTTTATTTTA
1 TTATTTT-TTTTA
18887728 AATATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.14
20 19 0.68
21 5 0.18
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (20 bp):
TTATTTTTTTTATCTATTTT
Found at i:18887966 original size:17 final size:18
Alignment explanation
Indices: 18887933--18887974 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
18887923 ATATACATAA
*
18887933 AATATGATAAGATAAGAT
1 AATATTATAAGATAAGAT
18887951 AATATTATAA-ATAAGAT
1 AATATTATAAGATAAGAT
*
18887968 TATATTA
1 AATATTA
18887975 AATAATATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (18 bp):
AATATTATAAGATAAGAT
Found at i:18888080 original size:16 final size:18
Alignment explanation
Indices: 18888061--18888097 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
18888051 AATTATTTTT
18888061 TTTAAATT-TT-ATATAA
1 TTTAAATTATTAATATAA
18888077 TTTAAATTATTAATATAA
1 TTTAAATTATTAATATAA
18888095 TTT
1 TTT
18888098 TTAAGAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
18 9 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTAAATTATTAATATAA
Found at i:18888343 original size:26 final size:26
Alignment explanation
Indices: 18888309--18888358 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
18888299 CTTATATATA
* *
18888309 TTATATTAATAAATTTATTTTTTATC
1 TTATATTAATAAATTAATATTTTATC
*
18888335 TTATTTTAATAAATTAATATTTTA
1 TTATATTAATAAATTAATATTTTA
18888359 AATTTAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATATTAATAAATTAATATTTTATC
Found at i:18898528 original size:19 final size:18
Alignment explanation
Indices: 18898493--18898529 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
18898483 AATATTTTAA
18898493 AAAATTTATAAAAATAAT
1 AAAATTTATAAAAATAAT
*
18898511 AAAATAT-TAAAAAT-AT
1 AAAATTTATAAAAATAAT
18898527 AAA
1 AAA
18898530 GAAAATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 7 0.39
18 6 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATTTATAAAAATAAT
Found at i:18904747 original size:27 final size:27
Alignment explanation
Indices: 18904717--18904799 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
18904707 AATAAATATT
* *
18904717 ATATTA-ATTAATAGATTTATATTTTAA
1 ATATTATATTAA-AAATTTATAATTTAA
*
18904744 ATATTATATTAAAAATTTTTAATTTAA
1 ATATTATATTAAAAATTTATAATTTAA
* * *
18904771 ATATCACATTAAATATTTCATAATTTAA
1 ATATTATATTAAAAATTT-ATAATTTAA
18904799 A
1 A
18904800 GTTTATTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
27 33 0.70
28 14 0.30
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (27 bp):
ATATTATATTAAAAATTTATAATTTAA
Done.