Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold214
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: 304316
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 3 of 4
Found at i:221859 original size:14 final size:15
Alignment explanation
Indices: 221840--221870 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
221830 TAATATTTTA
221840 AATTA-TTTAAATTT
1 AATTATTTTAAATTT
221854 AATTATTTTAAATTT
1 AATTATTTTAAATTT
221869 AA
1 AA
221871 ATCAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTATTTTAAATTT
Found at i:221865 original size:24 final size:22
Alignment explanation
Indices: 221823--221867 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
221813 TTCGAATCAT
221823 TTTAAATTAATATTTTAAATTA
1 TTTAAATTAATATTTTAAATTA
221845 TTTAAATTTAATTATTTTAAATT
1 TTTAAA-TTAA-TATTTTAAATT
221868 TAAATCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.29
23 4 0.19
24 11 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTAAATTAATATTTTAAATTA
Found at i:221866 original size:37 final size:39
Alignment explanation
Indices: 221795--221867 Score: 105
Period size: 37 Copynumber: 1.9 Consensus size: 39
221785 TAAAAAATAA
*
221795 ATTTTAATTTAATTTAAATTCGAATCATTTTAAATTAAT
1 ATTTTAAATTAATTTAAATTCGAATCATTTTAAATTAAT
* *
221834 ATTTTAAATT-ATTTAAATT-TAATTATTTTAAATT
1 ATTTTAAATTAATTTAAATTCGAATCATTTTAAATT
221868 TAAATCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 13 0.42
38 9 0.29
39 9 0.29
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (39 bp):
ATTTTAAATTAATTTAAATTCGAATCATTTTAAATTAAT
Found at i:221879 original size:24 final size:22
Alignment explanation
Indices: 221825--221879 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
221815 CGAATCATTT
**
221825 TAAATTAATATTTTAAATTATT
1 TAAATTAATATTTTAAATTAAA
221847 TAAATTTAATTATTTTAAATTTAAA
1 TAAA-TTAA-TATTTTAAA-TTAAA
*
221872 TCAATTAA
1 TAAATTAA
221880 AACTTGATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 13 0.48
25 6 0.22
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TAAATTAATATTTTAAATTAAA
Found at i:221971 original size:31 final size:29
Alignment explanation
Indices: 221912--221971 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
221902 AGGATTATTT
*
221912 TTTAATTTAGATTAAATAAATTTAAATTA
1 TTTAATTTAGATCAAATAAATTTAAATTA
221941 TTTATATTTATGATCAAATCAAA-TTAAATTA
1 TTTA-ATTTA-GATCAAAT-AAATTTAAATTA
221972 AATTTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 4 0.15
30 5 0.19
31 15 0.56
32 3 0.11
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (29 bp):
TTTAATTTAGATCAAATAAATTTAAATTA
Found at i:222385 original size:3 final size:3
Alignment explanation
Indices: 222377--222417 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
222367 GACCTTTAGG
222377 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
222418 CATTTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:222905 original size:18 final size:17
Alignment explanation
Indices: 222878--222918 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
222868 AATCAAATAC
*
222878 TATTTTCTATAATTTTT
1 TATTTTCTATAATTATT
222895 TATTCTTCTATAATTATT
1 TATT-TTCTATAATTATT
222913 TATTTT
1 TATTTT
222919 TAATTATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTCTATAATTATT
Found at i:223602 original size:28 final size:30
Alignment explanation
Indices: 223556--223629 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 30
223546 AAATATTTAA
*
223556 AAAAATATGATAA-ACTCAAAACATT-AT-T
1 AAAAATATAATAATA-TCAAAACATTAATAT
* *
223584 AAAAATATAATAATATCAATATATTAATAT
1 AAAAATATAATAATATCAAAACATTAATAT
* *
223614 CAAAATAAAATAATAT
1 AAAAATATAATAATAT
223630 ATCAAAATTG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 20 0.53
29 3 0.08
30 15 0.39
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.31
Consensus pattern (30 bp):
AAAAATATAATAATATCAAAACATTAATAT
Found at i:223606 original size:14 final size:14
Alignment explanation
Indices: 223587--223625 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
223577 CATTATTAAA
223587 AATATAATAATATC
1 AATATAATAATATC
*
223601 AATATATTAATATC
1 AATATAATAATATC
*
223615 AAAATAA-AATA
1 AATATAATAATA
223626 ATATATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
AATATAATAATATC
Found at i:224183 original size:7 final size:7
Alignment explanation
Indices: 224159--224201 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
224149 TATATACTTT
*
224159 TATTAAA
1 TATTTAA
224166 TATTTATA
1 TATTTA-A
224174 TATTTAA
1 TATTTAA
*
224181 TATTAAA
1 TATTTAA
*
224188 TATTTAT
1 TATTTAA
224195 TATTTAA
1 TATTTAA
224202 ATTCATTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TATTTAA
Found at i:224187 original size:22 final size:21
Alignment explanation
Indices: 224159--224201 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
224149 TATATACTTT
224159 TATTAAATATTTATATATTTAA
1 TATTAAATATTTAT-TATTTAA
224181 TATTAAATATTTATTATTTAA
1 TATTAAATATTTATTATTTAA
224202 ATTCATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTAAATATTTATTATTTAA
Found at i:224608 original size:16 final size:17
Alignment explanation
Indices: 224583--224623 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
224573 GTACATATAT
224583 TATT-TTTTAAAA-AAA
1 TATTATTTTAAAATAAA
224598 TATTATTTTAAAATAAA
1 TATTATTTTAAAATAAA
*
224615 -ATAATTTTA
1 TATTATTTTA
224624 TAAGTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 16 0.70
17 3 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTATTTTAAAATAAA
Found at i:224615 original size:18 final size:18
Alignment explanation
Indices: 224579--224617 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
224569 ATGAGTACAT
*
224579 ATATTATTTTTTAAAAAA
1 ATATTATTTTTAAAAAAA
224597 ATATTA-TTTTAAAATAAA
1 ATATTATTTTTAAAA-AAA
224615 ATA
1 ATA
224618 ATTTTATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATTATTTTTAAAAAAA
Found at i:225037 original size:16 final size:18
Alignment explanation
Indices: 225018--225050 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
225008 TCTATTTATT
225018 ATAA-TAATTTT-TCATA
1 ATAATTAATTTTATCATA
225034 ATAATTAATTTTATCAT
1 ATAATTAATTTTATCAT
225051 TACATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (18 bp):
ATAATTAATTTTATCATA
Found at i:225473 original size:22 final size:22
Alignment explanation
Indices: 225439--225480 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
225429 TTATTTTATC
225439 AAAAAATTAATTTTTAAATTGT
1 AAAAAATTAATTTTTAAATTGT
* * *
225461 AAAAATTTTATTTTTTAATT
1 AAAAAATTAATTTTTAAATT
225481 TCAACGAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AAAAAATTAATTTTTAAATTGT
Found at i:226849 original size:2 final size:2
Alignment explanation
Indices: 226842--226868 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
226832 AATCCTCTTT
226842 TA 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 TA T
226869 GATTGATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:227021 original size:8 final size:8
Alignment explanation
Indices: 227008--227040 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
226998 CTGGATCATA
227008 TTTTAAAT
1 TTTTAAAT
227016 TTTTAAAT
1 TTTTAAAT
*
227024 TTTT-ATT
1 TTTTAAAT
227031 TTTTAAAT
1 TTTTAAAT
227039 TT
1 TT
227041 AAATTGGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTAAAT
Found at i:227438 original size:15 final size:17
Alignment explanation
Indices: 227407--227439 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
227397 AAATCAATTG
227407 AAAAGAAAAATATAAAC
1 AAAAGAAAAATATAAAC
227424 AAAA-AAAAATA-AAAC
1 AAAAGAAAAATATAAAC
227439 A
1 A
227440 GTAACATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.82, C:0.06, G:0.03, T:0.09
Consensus pattern (17 bp):
AAAAGAAAAATATAAAC
Found at i:228893 original size:2 final size:2
Alignment explanation
Indices: 228886--228929 Score: 54
Period size: 2 Copynumber: 21.5 Consensus size: 2
228876 TATATTTGAG
*
228886 AT AT AT AT AT AT AT AT AT AT AT AT GAT -T AT GAT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT
228929 A
1 A
228930 ATTTTTTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
1 1 0.03
2 32 0.86
3 4 0.11
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:228947 original size:22 final size:21
Alignment explanation
Indices: 228917--228986 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 21
228907 TATGATTATG
228917 ATATATAAATATAATTTTTTAA
1 ATAT-TAAATATAATTTTTTAA
228939 ATATGTAAA-ATATATTTTTTAA
1 ATAT-TAAATATA-ATTTTTTAA
*
228961 AAATTAAATAT-ATTTATTATAA
1 ATATTAAATATAATTT-TT-TAA
228983 ATAT
1 ATAT
228987 ATATTTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
20 4 0.10
21 9 0.22
22 28 0.68
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
ATATTAAATATAATTTTTTAA
Found at i:228984 original size:20 final size:19
Alignment explanation
Indices: 228946--229011 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
228936 TAAATATGTA
* *
228946 AAATATATTTTTTAAAAATT
1 AAATATATTTATTATAAA-T
228966 AAATATATTTATTATAAAT
1 AAATATATTTATTATAAAT
228985 --ATATATTTA-TATATAAT
1 AAATATATTTATTATA-AAT
*
229002 AATTATATTT
1 AAATATATTT
229012 GAGTCTGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 4 0.10
17 12 0.30
19 8 0.20
20 16 0.40
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AAATATATTTATTATAAAT
Found at i:233028 original size:39 final size:39
Alignment explanation
Indices: 232974--233053 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
232964 CATGCTAATC
* *
232974 ATGGTTTCATAATTGTTGACGGCAGAGTAAATATAAAGA
1 ATGGTTTCATAATTGTTGAAGGCAGAGTAAATAAAAAGA
233013 ATGGTTTCATAATTGTTGAAGGCAGAGTAAATAAAAAGA
1 ATGGTTTCATAATTGTTGAAGGCAGAGTAAATAAAAAGA
233052 AT
1 AT
233054 TATCTTTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.30
Consensus pattern (39 bp):
ATGGTTTCATAATTGTTGAAGGCAGAGTAAATAAAAAGA
Found at i:234653 original size:11 final size:11
Alignment explanation
Indices: 234637--234703 Score: 56
Period size: 11 Copynumber: 6.5 Consensus size: 11
234627 TTGTAATTTG
234637 TATATTTATAT
1 TATATTTATAT
234648 TATATTTATA-
1 TATATTTATAT
234658 TAT-TTTA-A-
1 TATATTTATAT
*
234666 AATA-TTATAAT
1 TATATTTAT-AT
*
234677 TATATTTAAAT
1 TATATTTATAT
234688 TAT-TTTATATT
1 TATATTTATA-T
234699 TATAT
1 TATAT
234704 AGATTTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
8 6 0.13
9 4 0.09
10 9 0.20
11 22 0.49
12 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:234698 original size:45 final size:45
Alignment explanation
Indices: 234642--234732 Score: 132
Period size: 45 Copynumber: 2.0 Consensus size: 45
234632 ATTTGTATAT
234642 TTATATTATATTTATAT-ATTTTAAAATA-TTATAATTATATTTAAA
1 TTATATTATATTTATATAATTTTAAAATATTTATAATT-T-TTTAAA
*
234687 TTATTTTATATTTATATAGATTTTAAAATATTTATAATTTTTTAAA
1 TTATATTATATTTATATA-ATTTTAAAATATTTATAATTTTTTAAA
234733 ATAAATAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
45 16 0.38
46 6 0.14
47 12 0.29
48 8 0.19
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (45 bp):
TTATATTATATTTATATAATTTTAAAATATTTATAATTTTTTAAA
Found at i:234719 original size:20 final size:19
Alignment explanation
Indices: 234694--234735 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
234684 AAATTATTTT
234694 ATATTTATATAGATTTTAAA
1 ATATTTATA-AGATTTTAAA
**
234714 ATATTTATAATTTTTTAAA
1 ATATTTATAAGATTTTAAA
234733 ATA
1 ATA
234736 AATAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATATTTATAAGATTTTAAA
Found at i:234817 original size:31 final size:31
Alignment explanation
Indices: 234758--234817 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
234748 ATAATTTATA
*
234758 TTATATTAATTTTAAAAATATATTTATATCC
1 TTATATTAATTTTAAAAATATATATATATCC
**
234789 TTATATT-ATTTTAATTATATTATATATAT
1 TTATATTAATTTTAAAAATA-TATATATAT
234818 ATATATGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (31 bp):
TTATATTAATTTTAAAAATATATATATATCC
Found at i:234829 original size:36 final size:36
Alignment explanation
Indices: 234753--234842 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
234743 TAATAATAAT
* *
234753 TTATATTATATTAATTTTAAAAATATATTTATATCC
1 TTATATTATATTAATTATAAAAATATATATATATCC
* * * *
234789 TTATATTATTTTAATTATATTATATATATATATAT-G
1 TTATATTATATTAATTATA-AAAATATATATATATCC
234825 TTATATT-TATGTAATTAT
1 TTATATTATAT-TAATTAT
234843 TTTTTAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
35 2 0.04
36 31 0.69
37 12 0.27
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (36 bp):
TTATATTATATTAATTATAAAAATATATATATATCC
Found at i:235183 original size:71 final size:71
Alignment explanation
Indices: 235067--235257 Score: 321
Period size: 71 Copynumber: 2.7 Consensus size: 71
235057 TTGTAGTATT
* *
235067 AAAAATTATT-AATTAAATCATTCTATAATAATTTGTATAAATTGAATCTCTCTCTATTATTATG
1 AAAAATT-TTAAATTTAATCATTCTATAATAATTTGTATAAATTGAATCTCTCTCTATTATAATG
235131 TTCTATC
65 TTCTATC
235138 AAAAATTTTAAATTTAATCATTCTATAATAATTTGTATAAATTGAATCTCTCTCTATTATAATGT
1 AAAAATTTTAAATTTAATCATTCTATAATAATTTGTATAAATTGAATCTCTCTCTATTATAATGT
235203 TCTATC
66 TCTATC
* * *
235209 AAAAATTTTAAGTTTAACCATTCTATAATAATTTATATAAATTGAATCT
1 AAAAATTTTAAATTTAATCATTCTATAATAATTTGTATAAATTGAATCT
235258 TCAATTTTAT
Statistics
Matches: 114, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
70 2 0.02
71 112 0.98
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (71 bp):
AAAAATTTTAAATTTAATCATTCTATAATAATTTGTATAAATTGAATCTCTCTCTATTATAATGT
TCTATC
Found at i:236825 original size:13 final size:14
Alignment explanation
Indices: 236807--236843 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
236797 AATTTTTAAA
236807 TAAATTTACATT-T
1 TAAATTTACATTCT
*
236820 TAAATTTA-TTTCT
1 TAAATTTACATTCT
236833 TAAATTTACAT
1 TAAATTTACAT
236844 ACGTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
12 2 0.10
13 17 0.85
14 1 0.05
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAATTTACATTCT
Found at i:238844 original size:22 final size:21
Alignment explanation
Indices: 238790--238847 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
238780 TGTACATATA
238790 ATTTTGTTTATT-TTTAATGT
1 ATTTTGTTTATTATTTAATGT
238810 ATTCTTG---ACTTATTTAATTGT
1 ATT-TTGTTTA-TTATTTAA-TGT
238831 ATTTTGTTTATTATTTA
1 ATTTTGTTTATTATTTA
238848 TTATTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
18 1 0.03
19 2 0.06
20 11 0.35
21 9 0.29
22 7 0.23
23 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.09, T:0.66
Consensus pattern (21 bp):
ATTTTGTTTATTATTTAATGT
Found at i:238862 original size:15 final size:15
Alignment explanation
Indices: 238837--238880 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
238827 TTGTATTTTG
238837 TTTAT-TATTTATTA
1 TTTATATATTTATTA
238851 TTTATATATTTA-TA
1 TTTATATATTTATTA
*
238865 TTATATATCTTTATTA
1 TT-TATATATTTATTA
238881 CTATAAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 9 0.35
15 15 0.58
16 2 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATATATTTATTA
Found at i:239272 original size:18 final size:19
Alignment explanation
Indices: 239233--239269 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
239223 TCCAATGAAA
*
239233 ATTTTTATTGAAAAAGATT
1 ATTTTTAATGAAAAAGATT
239252 ATTTTTAATGAAAAAGAT
1 ATTTTTAATGAAAAAGAT
239270 ATTGCTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (19 bp):
ATTTTTAATGAAAAAGATT
Found at i:239278 original size:18 final size:19
Alignment explanation
Indices: 239241--239278 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
239231 AAATTTTTAT
**
239241 TGAAAAAGATTATTTTTAA
1 TGAAAAAGATTATTGCTAA
239260 TGAAAAAGA-TATTGCTAA
1 TGAAAAAGATTATTGCTAA
239278 T
1 T
239279 AGTAATACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.37
Consensus pattern (19 bp):
TGAAAAAGATTATTGCTAA
Found at i:240666 original size:11 final size:11
Alignment explanation
Indices: 240652--240685 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
240642 AGAATTTATC
240652 TTATTTTATAA
1 TTATTTTATAA
*
240663 TTATTTGATAA
1 TTATTTTATAA
240674 TTATATTTATAA
1 TTAT-TTTATAA
240686 AATAAACTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
TTATTTTATAA
Found at i:242376 original size:50 final size:50
Alignment explanation
Indices: 242317--242478 Score: 234
Period size: 50 Copynumber: 3.2 Consensus size: 50
242307 AGTTGCTTAG
* * * *
242317 AGTCAACAATTACGACCACCTCTTTTTATTGTTAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTTGATTATTAAAGGTTGGTGAAGAAT
* * * *
242367 AGTCAACAATTACGGTCATCTCTCTCGATTATCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTTGATTATTAAAGGTTGGTGAAGAAT
* *
242417 AGTCAACAATTATGGCCACCTCTCTTGATTATTAAAGGTTGGTGAAAAAT
1 AGTCAACAATTACGGCCACCTCTCTTGATTATTAAAGGTTGGTGAAGAAT
242467 AGTCAACAATTA
1 AGTCAACAATTA
242479 GTTTTGGTGG
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 98 1.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTTGATTATTAAAGGTTGGTGAAGAAT
Found at i:246999 original size:50 final size:48
Alignment explanation
Indices: 246893--247038 Score: 156
Period size: 50 Copynumber: 3.0 Consensus size: 48
246883 AGTTGCTTAG
* * *
246893 AGTCAACAATTACGGCCACCTCTCTCTATTGTC-AAGG---TGAAGAAT
1 AGTCAACAATTAC-GCTATCTCTCTCGATTGTCAAAGGTTATGAAGAAT
*
246938 AGTCAATAATTACGACTATCTCTCTCGATTGTCAAAGGTTAATGAAGAAT
1 AGTCAACAATTACG-CTATCTCTCTCGATTGTCAAAGGTT-ATGAAGAAT
* * *
246988 AGTCAACAATTACGGTCATCTCTCTCGATTGTCAAAGATTGATAAAGAAT
1 AGTCAACAATTACGCT-ATCTCTCTCGATTGTCAAAGGTT-ATGAAGAAT
247038 A
1 A
247039 ATTAATAATT
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
44 1 0.01
45 27 0.32
46 4 0.05
49 1 0.01
50 52 0.61
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (48 bp):
AGTCAACAATTACGCTATCTCTCTCGATTGTCAAAGGTTATGAAGAAT
Found at i:247049 original size:50 final size:50
Alignment explanation
Indices: 246932--247049 Score: 157
Period size: 50 Copynumber: 2.4 Consensus size: 50
246922 TGTCAAGGTG
* *
246932 AAGAATAGTCAATAATTACGACTATCTCTCTCGATTGTCAAAGGTTAATG
1 AAGAATAGTCAATAATTACGACTATCTCTCTCGATTGTCAAAGATTAATA
* * *
246982 AAGAATAGTCAACAATTACG-GTCATCTCTCTCGATTGTCAAAGATTGATA
1 AAGAATAGTCAATAATTACGACT-ATCTCTCTCGATTGTCAAAGATTAATA
* *
247032 AAGAATAATTAATAATTA
1 AAGAATAGTCAATAATTA
247050 ATTTTGGTAG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
49 1 0.02
50 58 0.98
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (50 bp):
AAGAATAGTCAATAATTACGACTATCTCTCTCGATTGTCAAAGATTAATA
Found at i:249435 original size:9 final size:9
Alignment explanation
Indices: 249421--249458 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
249411 TTATATATTT
249421 AAAATAATA
1 AAAATAATA
249430 AAAAT-ATA
1 AAAATAATA
249438 AAAATACA-A
1 AAAATA-ATA
249447 AAAATAATA
1 AAAATAATA
249456 AAA
1 AAA
249459 TTATTTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 9 0.35
9 16 0.62
10 1 0.04
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (9 bp):
AAAATAATA
Found at i:250315 original size:12 final size:13
Alignment explanation
Indices: 250289--250317 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
250279 TAAAAAAAAA
250289 TTAAATTTTAAAT
1 TTAAATTTTAAAT
250302 TTAAA-TTTAAAT
1 TTAAATTTTAAAT
250314 TTAA
1 TTAA
250318 CATAGTTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTAAATTTTAAAT
Found at i:250479 original size:24 final size:24
Alignment explanation
Indices: 250452--250497 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
250442 AAAATATTTC
*
250452 AAATCAATTCAAAATAAATAAAAA
1 AAATCAAGTCAAAATAAATAAAAA
* *
250476 AAATTAAGTCAAACTAAATAAA
1 AAATCAAGTCAAAATAAATAAA
250498 TAACTTAATC
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:0.67, C:0.09, G:0.02, T:0.22
Consensus pattern (24 bp):
AAATCAAGTCAAAATAAATAAAAA
Found at i:253659 original size:16 final size:16
Alignment explanation
Indices: 253634--253719 Score: 82
Period size: 16 Copynumber: 5.4 Consensus size: 16
253624 TCTAATATCG
*
253634 AAAATGATTTAAACTC
1 AAAATAATTTAAACTC
253650 AAAATAATTTAAACTC
1 AAAATAATTTAAACTC
* * * *
253666 AAAATGATTTGAATTT
1 AAAATAATTTAAACTC
* * *
253682 AAAATGATTTAAAATT
1 AAAATAATTTAAACTC
* *
253698 AAAATAATCTAAACTA
1 AAAATAATTTAAACTC
253714 AAAATA
1 AAAATA
253720 CACAAAAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (16 bp):
AAAATAATTTAAACTC
Found at i:253670 original size:32 final size:32
Alignment explanation
Indices: 253634--253719 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
253624 TCTAATATCG
* *
253634 AAAATGATTTAAACTCAAAATAATTTAAACTC
1 AAAATGATTTAAACTAAAAATAATTTAAAATC
* * * * *
253666 AAAATGATTTGAATTTAAAATGATTTAAAATT
1 AAAATGATTTAAACTAAAAATAATTTAAAATC
* *
253698 AAAATAATCTAAACTAAAAATA
1 AAAATGATTTAAACTAAAAATA
253720 CACAAAAATT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (32 bp):
AAAATGATTTAAACTAAAAATAATTTAAAATC
Found at i:254319 original size:3 final size:3
Alignment explanation
Indices: 254311--254366 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
254301 CAATCCATGC
*
254311 ATT ATT ATT ATT A-T ATT -TAT ATT ATT TTT ATT -TT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
254353 ATTT ATT A-T ATT AT
1 A-TT ATT ATT ATT AT
254367 AATTTTTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
2 9 0.20
3 32 0.73
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:254335 original size:14 final size:14
Alignment explanation
Indices: 254316--254367 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
254306 CATGCATTAT
254316 TATTATTATATTTA
1 TATTATTATATTTA
*
254330 TATTATTTTTATTT-
1 TATTA-TTATATTTA
254344 TATTATTATATTTA
1 TATTATTATATTTA
254358 T-TATATTATA
1 TAT-TATTATA
254368 ATTTTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 8 0.24
14 18 0.55
15 7 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTATTATATTTA
Found at i:254335 original size:17 final size:17
Alignment explanation
Indices: 254313--254366 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
254303 ATCCATGCAT
254313 TATTATTATTATATTTA
1 TATTATTATTATATTTA
254330 TATTATT-TT-TATTT-
1 TATTATTATTATATTTA
*
254344 TATTATTA-TATTTATTA
1 TATTATTATTATAT-TTA
254361 TATTAT
1 TATTAT
254367 AATTTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
14 8 0.25
15 7 0.22
16 4 0.12
17 13 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATTATTATATTTA
Found at i:254336 original size:20 final size:22
Alignment explanation
Indices: 254311--254367 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
254301 CAATCCATGC
254311 ATTATTATTATTATA-T-TTAT
1 ATTATTATTATTATATTATTAT
* *
254331 ATTATTTTTATTTTATTATTAT
1 ATTATTATTATTATATTATTAT
254353 ATTTATTA-TATTATA
1 A-TTATTATTATTATA
254368 ATTTTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 13 0.43
21 1 0.03
22 11 0.37
23 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTATTATTATTATATTATTAT
Found at i:254371 original size:28 final size:29
Alignment explanation
Indices: 254315--254385 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 29
254305 CCATGCATTA
* *
254315 TTATTATTATATTTA-TATTATTTTTATT
1 TTATTATTATATTTATTATTATTATAATT
254343 TTATTATTATATTTATTA-TATTATAATT
1 TTATTATTATATTTATTATTATTATAATT
* *
254371 TT-TAAATATATTTAT
1 TTATTATTATATTTAT
254386 GAGTTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 11 0.29
28 25 0.66
29 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTATTATTATATTTATTATTATTATAATT
Found at i:254374 original size:17 final size:17
Alignment explanation
Indices: 254318--254374 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
254308 TGCATTATTA
254318 TTATTATATTTATATTATTT
1 TTATTATA-TTATA--ATTT
* * *
254338 TTATTTTATTATTATAT
1 TTATTATATTATAATTT
254355 TTATTATATTATAATTT
1 TTATTATATTATAATTT
254372 TTA
1 TTA
254375 AATATATTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 20 0.65
19 4 0.13
20 7 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTATATTATAATTT
Found at i:254382 original size:18 final size:18
Alignment explanation
Indices: 254357--254408 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
254347 TATTATATTT
254357 ATTATATTATAATTTTTAA
1 ATTATATTAT-ATTTTTAA
*
254376 A-TATATT-TATGAGTTTAA
1 ATTATATTATAT--TTTTAA
254394 ATTATATTATATTTT
1 ATTATATTATATTTT
254409 AATATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 9
0.71 0.05 0.24
Matches are distributed among these distances:
16 2 0.07
17 1 0.04
18 14 0.52
19 7 0.26
20 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (18 bp):
ATTATATTATATTTTTAA
Found at i:254438 original size:37 final size:36
Alignment explanation
Indices: 254319--254438 Score: 82
Period size: 37 Copynumber: 3.1 Consensus size: 36
254309 GCATTATTAT
* * * *
254319 TATTATATTTATATTATTTTTATT-TTATTATTATATT
1 TATTATATTT-TAATATTTTAATTATT-TTTTTATATA
* *
254356 TATTATATTATAAT-TTTTAAATATATTTATGAGTTTAAATTA
1 TATTATATTTTAATATTTT-AAT-TATTT-T---TTTATA-TA
254398 TATTATATTTTAATATTTTAATTATTTTTTTATATCA
1 TATTATATTTTAATATTTTAATTATTTTTTTATAT-A
254435 TATT
1 TATT
254439 TAATATTACT
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
35 4 0.06
36 6 0.09
37 21 0.32
38 3 0.05
40 1 0.02
41 9 0.14
42 17 0.26
43 4 0.06
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (36 bp):
TATTATATTTTAATATTTTAATTATTTTTTTATATA
Found at i:257704 original size:2 final size:2
Alignment explanation
Indices: 257697--257739 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
257687 GATCAGTCAC
257697 AG AG AG AG AG AG AG 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 AG AG AG AG AG AG AG
257739 A
1 A
257740 ATGTTAACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:258924 original size:2 final size:2
Alignment explanation
Indices: 258917--258942 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
258907 ATAGATAGAT
258917 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
258943 GGAATGCACA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:266917 original size:13 final size:13
Alignment explanation
Indices: 266901--266958 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
266891 TATATTTAAA
266901 TATTTAAATTTAT
1 TATTTAAATTTAT
*
266914 TATTTAAATTT-G
1 TATTTAAATTTAT
* *
266926 TATAGTAAATTTGAA
1 TAT-TTAAATTT-AT
*
266941 TATTTAATTTTAT
1 TATTTAAATTTAT
266954 TATTT
1 TATTT
266959 TTTATTTGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
12 3 0.08
13 24 0.67
14 6 0.17
15 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (13 bp):
TATTTAAATTTAT
Found at i:268578 original size:21 final size:21
Alignment explanation
Indices: 268535--268579 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
268525 GATGAAATAA
* *
268535 TTAATATAAGTTATAATATTT
1 TTAATATAACTTATAATAATT
**
268556 TTAATATAACTTATTTTAATT
1 TTAATATAACTTATAATAATT
268577 TTA
1 TTA
268580 TACCAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTAATATAACTTATAATAATT
Found at i:269078 original size:46 final size:45
Alignment explanation
Indices: 269009--269104 Score: 102
Period size: 46 Copynumber: 2.1 Consensus size: 45
268999 ATATTCGTAT
* ** * * *
269009 TTAAACTAATTAAAATTGGTTATTGCTAGTACAACTGAATATATA
1 TTAAACCAATTAAAATTAATTATTACTAATACAACTAAATATATA
* * *
269054 CTTAAACCAATTGAAATTAATTATTATTAATACAATTAAATATATA
1 -TTAAACCAATTAAAATTAATTATTACTAATACAACTAAATATATA
269100 TTAAA
1 TTAAA
269105 TTCATTTTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
45 5 0.12
46 36 0.88
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (45 bp):
TTAAACCAATTAAAATTAATTATTACTAATACAACTAAATATATA
Found at i:269247 original size:46 final size:46
Alignment explanation
Indices: 269118--269253 Score: 164
Period size: 46 Copynumber: 3.0 Consensus size: 46
269108 ATTTTTAGAC
* * ** * *
269118 TAATTAAAATTTATCAATAAGCGTACAATTGAATATACACTTAAAT
1 TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTAAAG
**
269164 TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTCGAG
1 TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTAAAG
* ** *
269210 TAATTAAAATTAATCATTATTTTTACAATTGAATATATAATTAA
1 TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTAA
269254 TGTTACTACA
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (46 bp):
TAATTAAAATTAATCATTAATAGTACAATTGAATATATACTTAAAG
Found at i:270263 original size:30 final size:29
Alignment explanation
Indices: 270194--270274 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
270184 TGAAATTGCA
270194 AAATGATCTTAGTTCATAAAAAATAACCT
1 AAATGATCTTAGTTCATAAAAAATAACCT
* * *
270223 AAATAATCTTAGATT-ATGAAAAATAACTT
1 AAATGATCTTAG-TTCATAAAAAATAACCT
*
270252 AAATGATTCTTACATTCATAAAA
1 AAATGA-TCTTA-GTTCATAAAA
270275 GTTACATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
29 28 0.67
30 9 0.21
31 5 0.12
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATGATCTTAGTTCATAAAAAATAACCT
Found at i:270351 original size:29 final size:30
Alignment explanation
Indices: 270289--270399 Score: 97
Period size: 29 Copynumber: 3.8 Consensus size: 30
270279 CATAAAGTCT
* **
270289 CTAAAATA-ATGCAAATTACA-AAAATGATT
1 CTAAAATATATG-AAATTACATAAAATAACC
* *
270318 TTAAAATATATGAAATTACATAAAA-ATCC
1 CTAAAATATATGAAATTACATAAAATAACC
*
270347 CTAAAATATGAT-AAATT-CTTAAAATAACC
1 CTAAAATAT-ATGAAATTACATAAAATAACC
* *
270376 TTAAAATATATGAAATTATATAAA
1 CTAAAATATATGAAATTACATAAA
270400 GCCCTTAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
28 8 0.12
29 44 0.68
30 13 0.20
ACGTcount: A:0.55, C:0.09, G:0.05, T:0.32
Consensus pattern (30 bp):
CTAAAATATATGAAATTACATAAAATAACC
Found at i:270351 original size:58 final size:58
Alignment explanation
Indices: 270276--270399 Score: 137
Period size: 58 Copynumber: 2.2 Consensus size: 58
270266 TTCATAAAAG
* * * **
270276 TTACAT-AAAGTCTCTAAAATAATG-CAAATTAC-AAAAATGATTTTAAAATATATGAAA
1 TTACATAAAAATCCCTAAAAT-ATGACAAATT-CTAAAAATAACCTTAAAATATATGAAA
* *
270333 TTACATAAAAATCCCTAAAATATGATAAATTCTTAAAATAACCTTAAAATATATGAAA
1 TTACATAAAAATCCCTAAAATATGACAAATTCTAAAAATAACCTTAAAATATATGAAA
*
270391 TTATATAAA
1 TTACATAAA
270400 GCCCTTAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
57 10 0.18
58 46 0.82
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.32
Consensus pattern (58 bp):
TTACATAAAAATCCCTAAAATATGACAAATTCTAAAAATAACCTTAAAATATATGAAA
Found at i:270543 original size:29 final size:28
Alignment explanation
Indices: 270453--270543 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 28
270443 TAAAATTGCA
* * *
270453 TAATAATTTGTAAAACATAGAAAATGAT
1 TAATAATTTTTAAATCATAAAAAATGAT
*
270481 TAA-AATTATCTTAAAATACATGAAATAAT-A-
1 TAATAATT-T-TT-AAAT-CAT-AAAAAATGAT
270511 TAATAATTTTTAAATCATAAAAAATGACT
1 TAATAATTTTTAAATCATAAAAAATGA-T
270540 TAAT
1 TAAT
270544 TATACTAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
26 6 0.12
27 8 0.16
28 8 0.16
29 7 0.14
30 7 0.14
31 8 0.16
32 5 0.10
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (28 bp):
TAATAATTTTTAAATCATAAAAAATGAT
Found at i:270756 original size:12 final size:12
Alignment explanation
Indices: 270739--270777 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
270729 AAACTTTCTC
270739 TTTTTTCTTTAT
1 TTTTTTCTTTAT
270751 TTTTTTCTCTT-T
1 TTTTTTCT-TTAT
270763 TTTTTTC-TTAT
1 TTTTTTCTTTAT
270774 TTTT
1 TTTT
270778 CTTTTATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 5 0.20
12 16 0.64
13 2 0.08
ACGTcount: A:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTCTTTAT
Found at i:270759 original size:21 final size:21
Alignment explanation
Indices: 270733--270779 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
270723 TTGAAGAAAC
270733 TTTCTCTTTTTTCTTTATT-TT
1 TTTCTCTTTTTT-TTTATTATT
*
270754 TTTCTCTTTTTTTTTCTTATT
1 TTTCTCTTTTTTTTTATTATT
270775 TTTCT
1 TTTCT
270780 TTTATGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTCTCTTTTTTTTTATTATT
Found at i:270761 original size:14 final size:12
Alignment explanation
Indices: 270739--270782 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
270729 AAACTTTCTC
*
270739 TTTTTTCTTTAT
1 TTTTTTCTTTTT
*
270751 TTTTTTCTCTTT
1 TTTTTTCTTTTT
270763 TTTTTTCTTATTT
1 TTTTTTCTT-TTT
270776 TTCTTTT
1 TT-TTTT
270783 ATGGTTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 18 0.67
13 5 0.19
14 4 0.15
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:272767 original size:20 final size:19
Alignment explanation
Indices: 272742--272786 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
272732 TAAAATCAAT
*
272742 TTTTTATTAATTTAATATAA
1 TTTTTATTAATTAAAT-TAA
*
272762 TTTTTATTGATTAAATTAA
1 TTTTTATTAATTAAATTAA
272781 TTTTTA
1 TTTTTA
272787 CTAAGTTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTATTAATTAAATTAA
Found at i:273227 original size:12 final size:12
Alignment explanation
Indices: 273210--273239 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
273200 CATGGAAGAT
*
273210 TTATTTATTTAC
1 TTATTTATTTAA
273222 TTATTTATTTAA
1 TTATTTATTTAA
273234 TTATTT
1 TTATTT
273240 TTGTATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATTTATTTAA
Found at i:274168 original size:17 final size:16
Alignment explanation
Indices: 274148--274215 Score: 91
Period size: 16 Copynumber: 4.2 Consensus size: 16
274138 AAAAAATATT
*
274148 AATAATTTAAACTCGAA
1 AATAATTTAAACT-TAA
*
274165 AATAATTTAAATTTAA
1 AATAATTTAAACTTAA
*
274181 AATAATCTAAACTTAA
1 AATAATTTAAACTTAA
*
274197 AATTATTTAAACTTAA
1 AATAATTTAAACTTAA
274213 AAT
1 AAT
274216 GAATCGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
16 33 0.73
17 12 0.27
ACGTcount: A:0.54, C:0.07, G:0.01, T:0.37
Consensus pattern (16 bp):
AATAATTTAAACTTAA
Found at i:274184 original size:16 final size:16
Alignment explanation
Indices: 274148--274263 Score: 81
Period size: 16 Copynumber: 7.2 Consensus size: 16
274138 AAAAAATATT
**
274148 AATAATTTAAACTCGAA
1 AATAATTTAAA-TTTAA
274165 AATAATTTAAATTTAA
1 AATAATTTAAATTTAA
* *
274181 AATAATCTAAACTTAA
1 AATAATTTAAATTTAA
* *
274197 AATTATTTAAACTTAA
1 AATAATTTAAATTTAA
** *
274213 AATGAA-TCGAATCTAA
1 AAT-AATTTAAATTTAA
* **
274229 AATGATTTAAATTCGA
1 AATAATTTAAATTTAA
* *
274245 AATAATCTAAATCTAA
1 AATAATTTAAATTTAA
274261 AAT
1 AAT
274264 TATTCGAACC
Statistics
Matches: 75, Mismatches: 22, Indels: 5
0.74 0.22 0.05
Matches are distributed among these distances:
15 1 0.01
16 62 0.83
17 12 0.16
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.34
Consensus pattern (16 bp):
AATAATTTAAATTTAA
Found at i:274205 original size:32 final size:33
Alignment explanation
Indices: 274148--274267 Score: 131
Period size: 32 Copynumber: 3.7 Consensus size: 33
274138 AAAAAATATT
* * *
274148 AATAATTTAAACTCGAAAATAATTTAAATTTAA
1 AATAATCTAAACTCTAAAATTATTTAAATTTAA
*
274181 AATAATCTAAACT-TAAAATTATTTAAACTTAA
1 AATAATCTAAACTCTAAAATTATTTAAATTTAA
* * **
274213 AATGAATC-GAA-TCTAAAATGATTTAAATTCGA
1 AAT-AATCTAAACTCTAAAATTATTTAAATTTAA
274245 AATAATCTAAA-TCTAAAATTATT
1 AATAATCTAAACTCTAAAATTATT
274268 CGAACCTATA
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
31 5 0.07
32 52 0.71
33 16 0.22
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (33 bp):
AATAATCTAAACTCTAAAATTATTTAAATTTAA
Found at i:274262 original size:48 final size:46
Alignment explanation
Indices: 274210--274309 Score: 110
Period size: 48 Copynumber: 2.1 Consensus size: 46
274200 TATTTAAACT
* * *
274210 TAAAATGAATCGAATCTAAAATGATTTAAATTCGAAATAATCTAAATC
1 TAAAATGAATCGAACCTAAAATGA-TTAAACTCGAAA-AATCTAAATA
* * * * *
274258 TAAAATTATTCGAACCTATAATTATTAAACTCGATAAATCTAAATA
1 TAAAATGAATCGAACCTAAAATGATTAAACTCGAAAAATCTAAATA
274304 TAAAAT
1 TAAAAT
274310 TTAATTGATT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 15 0.34
47 10 0.23
48 19 0.43
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (46 bp):
TAAAATGAATCGAACCTAAAATGATTAAACTCGAAAAATCTAAATA
Found at i:274467 original size:23 final size:24
Alignment explanation
Indices: 274407--274467 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
274397 CTTAAATTGT
274407 TTAATCTTAAAATTACTCAAATTAAA
1 TTAA-CTTAAAA-TACTCAAATTAAA
** * *
274433 AAAAATTCAAATA-TCAAATTAAA
1 TTAACTTAAAATACTCAAATTAAA
274456 TTAACTTAAAAT
1 TTAACTTAAAAT
274468 TAAAATAATT
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
23 18 0.67
24 2 0.07
25 5 0.19
26 2 0.07
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (24 bp):
TTAACTTAAAATACTCAAATTAAA
Found at i:274469 original size:16 final size:16
Alignment explanation
Indices: 274448--274484 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
274438 TTCAAATATC
*
274448 AAATTAAATTAACTTA
1 AAATTAAAATAACTTA
*
274464 AAATTAAAATAATTTA
1 AAATTAAAATAACTTA
274480 AAATT
1 AAATT
274485 TTAAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAAAATAACTTA
Found at i:279586 original size:14 final size:15
Alignment explanation
Indices: 279567--279600 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
279557 ATATTAATAT
279567 ATTTT-AAAAATAAA
1 ATTTTAAAAAATAAA
*
279581 ATTTTAAAAAATAAT
1 ATTTTAAAAAATAAA
279596 ATTTT
1 ATTTT
279601 TATTATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTTAAAAAATAAA
Found at i:280741 original size:147 final size:147
Alignment explanation
Indices: 280477--280773 Score: 544
Period size: 147 Copynumber: 2.0 Consensus size: 147
280467 AGAATGTGGC
280477 CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTATTT
1 CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTATTT
280542 TAATATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAAATTAGGAATTTTTTTTTTGTTCATA
66 TAATATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAAATTAGGAATTTTTTTTTTGTTCATA
280607 AGATTAGGAAATTAAAT
131 AGATTAGGAAATTAAAT
280624 CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTATTT
1 CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTATTT
* *
280689 T-A-ATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAGATTAGGAATTTTTTTTTTTTGTTTA
66 TAATATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAAATTAGGAA--TTTTTTTTTTGTTCA
280752 TAAGATTAGGAAATTAAAT
129 TAAGATTAGGAAATTAAAT
280771 CTT
1 CTT
280774 CATTTTTTTT
Statistics
Matches: 146, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
145 43 0.29
146 1 0.01
147 102 0.70
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (147 bp):
CTTTTTCTCAAATCAAAGCAAAAGTAAAAACTATCCACCAAATATTTATCTTTAAAATTTTATTT
TAATATATATAATAAATAGGCTTCAAAAAGGAAGAAAAAAATTAGGAATTTTTTTTTTGTTCATA
AGATTAGGAAATTAAAT
Found at i:281414 original size:16 final size:16
Alignment explanation
Indices: 281371--281421 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
281361 TTTAAATTAT
*
281371 ATTAAATTAAATTTTA
1 ATTAAAATAAATTTTA
*
281387 A-TAAAAT-TATTTTA
1 ATTAAAATAAATTTTA
*
281401 ATTAAAATAGATTTTA
1 ATTAAAATAAATTTTA
*
281417 TTTAA
1 ATTAA
281422 TTTAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.24
15 11 0.38
16 11 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
ATTAAAATAAATTTTA
Found at i:281441 original size:15 final size:18
Alignment explanation
Indices: 281412--281449 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
281402 TTAAAATAGA
281412 TTTTATTTAATTTAAT-T
1 TTTTATTTAATTTAATAT
281429 TTTTATTT-A-TTAATAT
1 TTTTATTTAATTTAATAT
281445 TTTTA
1 TTTTA
281450 AATTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 8 0.40
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTAATTTAATAT
Found at i:281455 original size:22 final size:21
Alignment explanation
Indices: 281430--281495 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 21
281420 AATTTAATTT
281430 TTTATTTATTAATATTTTTAAA
1 TTTA-TTATTAATATTTTTAAA
* * *
281452 TTTAATTA-TAAAATATATAAA
1 TTT-ATTATTAATATTTTTAAA
* *
281473 TATTAATATAAATATTTTTAAA
1 T-TTATTATTAATATTTTTAAA
281495 T
1 T
281496 GATAAATAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
21 14 0.42
22 18 0.55
23 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATTATTAATATTTTTAAA
Found at i:281502 original size:17 final size:18
Alignment explanation
Indices: 281468--281513 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
281458 TATAAAATAT
*
281468 ATAAATATT-AAT-ATAA
1 ATAAATTTTAAATGATAA
*
281484 AT-ATTTTTAAATGATAA
1 ATAAATTTTAAATGATAA
281501 ATAAATTTTAAAT
1 ATAAATTTTAAAT
281514 AAAAGATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 5 0.21
17 6 0.25
18 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAAATTTTAAATGATAA
Found at i:281511 original size:18 final size:17
Alignment explanation
Indices: 281455--281514 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 17
281445 TTTTAAATTT
* *
281455 AATTATAAA-ATATATA
1 AATTTTAAATATAAATA
*
281471 AATATT-AATATAAAT-
1 AATTTTAAATATAAATA
*
281486 ATTTTTAAATGATAAATA
1 AATTTTAAAT-ATAAATA
281504 AATTTTAAATA
1 AATTTTAAATA
281515 AAAGATATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
15 6 0.18
16 12 0.35
17 7 0.21
18 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTTAAATATAAATA
Found at i:281828 original size:6 final size:6
Alignment explanation
Indices: 281815--281875 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
281805 AATTTGTGTG
* * * * *
281815 TATATA TATGTA TATATA TATATA TATATA GATATA GATAGA TAGATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
281863 TGTATG TATATA T
1 TATATA TATATA T
281876 CAGATTCCAC
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:281828 original size:10 final size:10
Alignment explanation
Indices: 281813--281873 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
281803 TAAATTTGTG
281813 TGTATATATA
1 TGTATATATA
281823 TGTATATATA
1 TGTATATATA
*
281833 TATATATATA
1 TGTATATATA
*
281843 TAG-ATATAGA
1 T-GTATATATA
*
281853 TAG-ATAGATA
1 T-GTATATATA
*
281863 TGTATGTATA
1 TGTATATATA
281873 T
1 T
281874 ATCAGATTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 1 0.02
10 41 0.98
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (10 bp):
TGTATATATA
Found at i:281832 original size:4 final size:4
Alignment explanation
Indices: 281815--281875 Score: 59
Period size: 4 Copynumber: 15.2 Consensus size: 4
281805 AATTTGTGTG
* * * * *
281815 TATA TATA TGTA TATA TATA TATA TATA TAGA TATA GATA GATA GATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
281863 TGTA TGTA TATA T
1 TATA TATA TATA T
281876 CAGATTCCAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:282375 original size:19 final size:20
Alignment explanation
Indices: 282348--282402 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
282338 AAATTGCTTT
282348 TTTCTTTTCATAATTAA-GA
1 TTTCTTTTCATAATTAAGGA
* * *
282367 TTTCATTTCATTATTAAGGG
1 TTTCTTTTCATAATTAAGGA
282387 TTT-TTTTCATAATTAA
1 TTTCTTTTCATAATTAA
282403 AATTACCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.55
Consensus pattern (20 bp):
TTTCTTTTCATAATTAAGGA
Found at i:285162 original size:2 final size:2
Alignment explanation
Indices: 285155--285191 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
285145 TTAATGCAAC
285155 AT 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 AT A
285192 ATTTTGTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:285224 original size:13 final size:14
Alignment explanation
Indices: 285206--285253 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
285196 TGTTCAAATA
285206 AATAATTT-ATTTT
1 AATAATTTAATTTT
285219 AATAATTTAATTTT
1 AATAATTTAATTTT
* **
285233 AAT-TTTTAATTAA
1 AATAATTTAATTTT
285246 AATAATTT
1 AATAATTT
285254 TTTATTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATAATTTAATTTT
Found at i:285253 original size:16 final size:16
Alignment explanation
Indices: 285232--285265 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
285222 AATTTAATTT
285232 TAATTTTTAATTAAAA
1 TAATTTTTAATTAAAA
* *
285248 TAATTTTTTATTATAA
1 TAATTTTTAATTAAAA
285264 TA
1 TA
285266 TGTCGAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATTTTTAATTAAAA
Found at i:285812 original size:22 final size:22
Alignment explanation
Indices: 285787--285828 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
285777 TAAAAAAATT
285787 TTAAAATATTTT-TATATTAATA
1 TTAAAATATTTTATA-ATTAATA
*
285809 TTAATATATTTTATAATTAA
1 TTAAAATATTTTATAATTAA
285829 ATAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTAAAATATTTTATAATTAATA
Found at i:285835 original size:21 final size:20
Alignment explanation
Indices: 285790--285835 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
285780 AAAAATTTTA
285790 AAATATTTTTATATTAATAT
1 AAATATTTTTATATTAATAT
*
285810 TAATATATTTTATAATTAA-AT
1 AAATAT-TTTTAT-ATTAATAT
285831 AAATA
1 AAATA
285836 AAAATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATATTTTTATATTAATAT
Found at i:286445 original size:7 final size:8
Alignment explanation
Indices: 286423--286449 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
286413 TAAATTTAAT
286423 TATAAAAA
1 TATAAAAA
286431 TATAAAAA
1 TATAAAAA
286439 TATAAAAA
1 TATAAAAA
286447 TAT
1 TAT
286450 TTTTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
TATAAAAA
Found at i:286480 original size:18 final size:18
Alignment explanation
Indices: 286438--286481 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
286428 AAATATAAAA
286438 ATATAAAAATATTTTTAT
1 ATATAAAAATATTTTTAT
* *
286456 ATTTAAATATATTTTTA-
1 ATATAAAAATATTTTTAT
286473 ATAATAAAA
1 AT-ATAAAA
286482 TAAGCTTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATAAAAATATTTTTAT
Found at i:286482 original size:19 final size:18
Alignment explanation
Indices: 286440--286483 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
286430 ATATAAAAAT
286440 ATAAAA-ATATTTTTATA
1 ATAAAATATATTTTTATA
* *
286457 TTTAAATATATTTTTAATA
1 ATAAAATATATTTTT-ATA
286476 ATAAAATA
1 ATAAAATA
286484 AGCTTTTAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 4 0.19
18 8 0.38
19 9 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATAAAATATATTTTTATA
Found at i:286697 original size:21 final size:21
Alignment explanation
Indices: 286648--286685 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
286638 TTTGTCTAAC
286648 TTAAAAT-A-ATATTTTTAAA
1 TTAAAATAATATATTTTTAAA
286667 TTAAAATAATATATTTTTA
1 TTAAAATAATATATTTTTA
286686 TTTAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAAATAATATATTTTTAAA
Found at i:288784 original size:16 final size:18
Alignment explanation
Indices: 288762--288809 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 18
288752 AGCTTGGAAG
288762 ATTATTTTTTATTTT-TT
1 ATTATTTTTTATTTTATT
*
288779 -TTATTTATTATTTTTATT
1 ATTATTTTTTA-TTTTATT
288797 ATTATTTTTTATT
1 ATTATTTTTTATT
288810 CATCAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.35
17 4 0.15
18 4 0.15
19 9 0.35
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
ATTATTTTTTATTTTATT
Found at i:288787 original size:13 final size:13
Alignment explanation
Indices: 288769--288809 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
288759 AAGATTATTT
288769 TTTATTTTTTTTA
1 TTTATTTTTTTTA
*
288782 TTTATTATTTTTA
1 TTTATTTTTTTTA
288795 -TTATTATTTTTTA
1 TTTATT-TTTTTTA
288808 TT
1 TT
288810 CATCAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.21
13 18 0.75
14 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTTTTTA
Found at i:289342 original size:14 final size:14
Alignment explanation
Indices: 289322--289407 Score: 58
Period size: 14 Copynumber: 6.4 Consensus size: 14
289312 ATATTATGAC
289322 ATATT-TATTAAAT
1 ATATTATATTAAAT
*
289335 ATATTTTATT--A-
1 ATATTATATTAAAT
*
289346 ATCTTAT-TTAAAT
1 ATATTATATTAAAT
*
289359 ATACTATATTAAAT
1 ATATTATATTAAAT
* **
289373 TTATTATATTATTTTT
1 ATATTATATTA--AAT
289389 ATATT-TATTAAAT
1 ATATTATATTAAAT
289402 ATATTA
1 ATATTA
289408 AATTTATATC
Statistics
Matches: 54, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
10 2 0.04
11 5 0.09
12 2 0.04
13 16 0.30
14 19 0.35
15 5 0.09
16 5 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
ATATTATATTAAAT
Found at i:289406 original size:24 final size:24
Alignment explanation
Indices: 289322--289407 Score: 78
Period size: 24 Copynumber: 3.8 Consensus size: 24
289312 ATATTATGAC
289322 ATATTTATTAAATATATT-TTATT
1 ATATTTATTAAATATATTATTATT
*
289345 A-ATCTTATTTAAATATACTA-TATT
1 ATAT-TTA-TTAAATATATTATTATT
* *
289369 AAATTTA-T---TATATTATTTTT
1 ATATTTATTAAATATATTATTATT
289389 ATATTTATTAAATATATTA
1 ATATTTATTAAATATATTA
289408 AATTTATATC
Statistics
Matches: 50, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
19 6 0.12
20 9 0.18
21 1 0.02
22 3 0.06
23 4 0.08
24 25 0.50
25 2 0.04
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
ATATTTATTAAATATATTATTATT
Found at i:290605 original size:25 final size:26
Alignment explanation
Indices: 290559--290613 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 26
290549 AAAATATAAC
* *
290559 TTTTTATAATATTTAATGATTAAAATT
1 TTTTTATAATATTAAATAATT-AAATT
*
290586 TTTTTATAA-A-TAAATAATTATATT
1 TTTTTATAATATTAAATAATTAAATT
290610 TTTT
1 TTTT
290614 AATTTACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 8 0.32
25 7 0.28
26 1 0.04
27 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTTATAATATTAAATAATTAAATT
Found at i:290964 original size:13 final size:14
Alignment explanation
Indices: 290936--290962 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
290926 CAATATTTTG
290936 TAAATTTTTTTAAA
1 TAAATTTTTTTAAA
290950 TAAATTTTTTTAA
1 TAAATTTTTTTAA
290963 TATATGGTAT
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):
TAAATTTTTTTAAA
Found at i:291768 original size:16 final size:16
Alignment explanation
Indices: 291749--291789 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
291739 TAAATTGATT
291749 TAATTTTAAAATTCAA
1 TAATTTTAAAATTCAA
291765 TAA-TTT-AAATTCAA
1 TAATTTTAAAATTCAA
*
291779 AATATTTTAAA
1 TA-ATTTTAAA
291790 TCTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 9 0.43
15 4 0.19
16 6 0.29
17 2 0.10
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTTTAAAATTCAA
Found at i:291796 original size:15 final size:16
Alignment explanation
Indices: 291763--291805 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
291753 TTTAAAATTC
291763 AATAATTTAAATTCAA
1 AATAATTTAAATTCAA
* *
291779 AATATTTTAAA-TCTA
1 AATAATTTAAATTCAA
*
291794 AATAATTCAAAT
1 AATAATTTAAAT
291806 ATTAAATACA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATTTAAATTCAA
Found at i:291818 original size:38 final size:38
Alignment explanation
Indices: 291769--291843 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
291759 ATTCAATAAT
* * * *
291769 TTAAATTCAAAATATTTTAAATCTAAATAATTCAAATA
1 TTAAATACAAAATAATATAAATCTAAACAATTCAAATA
* *
291807 TTAAATACAAAATAATATAAATTTAAACAATTTAAAT
1 TTAAATACAAAATAATATAAATCTAAACAATTCAAAT
291844 TTATTCTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (38 bp):
TTAAATACAAAATAATATAAATCTAAACAATTCAAATA
Found at i:292539 original size:2 final size:2
Alignment explanation
Indices: 292534--292564 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
292524 ATAGTGTGTG
*
292534 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
292565 CAGATTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:292932 original size:32 final size:32
Alignment explanation
Indices: 292859--292932 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
292849 AATATTTTTA
* * * *
292859 TTTAAATTTATTTATAAAAGTATTTTTAAATT
1 TTTAAATTAATTTATAAAAATATATTTAAACT
**
292891 TTTTTATTAATTTATAAATAATA-ATTTAAACT
1 TTTAAATTAATTTATAAA-AATATATTTAAACT
292923 TTTAAATTAA
1 TTTAAATTAA
292933 ACTTTATTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
32 30 0.91
33 3 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (32 bp):
TTTAAATTAATTTATAAAAATATATTTAAACT
Found at i:294559 original size:22 final size:22
Alignment explanation
Indices: 294533--294588 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
294523 TTATTGATTA
294533 TAATATTAAAATATTTT-TATAT
1 TAATATTAAAATATTTTATA-AT
* *
294555 TAATATTTATATATTTTATAAT
1 TAATATTAAAATATTTTATAAT
*
294577 TAA-ATAAAAATA
1 TAATATTAAAATA
294589 AAAATATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 6 0.21
22 20 0.71
23 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATTAAAATATTTTATAAT
Found at i:295313 original size:13 final size:14
Alignment explanation
Indices: 295295--295342 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
295285 TGTTTCAATA
295295 AATAATTT-ATTTT
1 AATAATTTAATTTT
295308 AATAATTTAATTTT
1 AATAATTTAATTTT
* **
295322 AAT-TTTTAATTAA
1 AATAATTTAATTTT
295335 AATAATTT
1 AATAATTT
295343 TTTGTTATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATAATTTAATTTT
Found at i:295318 original size:18 final size:19
Alignment explanation
Indices: 295276--295321 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
295266 CAAAATATAT
295276 ATTTAATTTTGTTTCAATA
1 ATTTAATTTTGTTTCAATA
*
295295 A-ATAATTTAT-TTT-AATA
1 ATTTAATTT-TGTTTCAATA
295312 ATTTAATTTT
1 ATTTAATTTT
295322 AATTTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
ATTTAATTTTGTTTCAATA
Found at i:295897 original size:21 final size:23
Alignment explanation
Indices: 295873--295917 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
295863 TAATAAAAAA
295873 ATTAAAATATTTTA-TATT-AAT
1 ATTAAAATATTTTATTATTGAAT
*
295894 ATTAATATATTTTATTATTGAAT
1 ATTAAAATATTTTATTATTGAAT
295917 A
1 A
295918 ATAATTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 4 0.19
23 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTAAAATATTTTATTATTGAAT
Found at i:296297 original size:16 final size:16
Alignment explanation
Indices: 296264--296330 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
296254 CCCAATCCCA
* *
296264 AATCCGAAATAACTTG
1 AATCCGAAATGACCTG
** *
296280 AATTTGAAATGATCTG
1 AATCCGAAATGACCTG
296296 AATCCGAAATGACCTG
1 AATCCGAAATGACCTG
*
296312 AA-CTCGAAATTACCTG
1 AATC-CGAAATGACCTG
296328 AAT
1 AAT
296331 AATTAACCTG
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
15 1 0.03
16 39 0.98
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (16 bp):
AATCCGAAATGACCTG
Found at i:296321 original size:32 final size:32
Alignment explanation
Indices: 296264--296330 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
296254 CCCAATCCCA
* * * *
296264 AATCCGAAATAACTTGAATTTGAAATGATCTG
1 AATCCGAAATAACCTGAACTCGAAATGACCTG
* *
296296 AATCCGAAATGACCTGAACTCGAAATTACCTG
1 AATCCGAAATAACCTGAACTCGAAATGACCTG
296328 AAT
1 AAT
296331 AATTAACCTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (32 bp):
AATCCGAAATAACCTGAACTCGAAATGACCTG
Found at i:297418 original size:16 final size:16
Alignment explanation
Indices: 297380--297410 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
297370 CCCGATTGAT
*
297380 TCGAACCCGAAATAAC
1 TCGAACTCGAAATAAC
297396 TCGAACTCGAAATAA
1 TCGAACTCGAAATAA
297411 TCCGAACTTA
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:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (16 bp):
TCGAACTCGAAATAAC
Found at i:297439 original size:32 final size:32
Alignment explanation
Indices: 297367--297486 Score: 91
Period size: 32 Copynumber: 3.8 Consensus size: 32
297357 TCCGAGTGTT
* * * * *
297367 AAACCCG-ATTGATTCGAACCCGAAATAACTC
1 AAACCCGAAATGATCCGAATCCAAAATGACTC
* * * * *
297398 GAACTCGAAATAATCCGAA-CTTAAAATGATTC
1 AAACCCGAAATGATCCGAATC-CAAAATGACTC
* *
297430 AAACCCGAAATGATCTGAATCCAAAGTGACTC
1 AAACCCGAAATGATCCGAATCCAAAATGACTC
* *
297462 AAACCCGAAATGATCCAAACCCAAA
1 AAACCCGAAATGATCCGAATCCAAA
297487 TGATGCGAAC
Statistics
Matches: 67, Mismatches: 19, Indels: 5
0.74 0.21 0.05
Matches are distributed among these distances:
31 6 0.09
32 60 0.90
33 1 0.01
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.18
Consensus pattern (32 bp):
AAACCCGAAATGATCCGAATCCAAAATGACTC
Found at i:297489 original size:15 final size:16
Alignment explanation
Indices: 297421--297490 Score: 65
Period size: 16 Copynumber: 4.4 Consensus size: 16
297411 TCCGAACTTA
*
297421 AAATGATTCAAACCCG
1 AAATGATCCAAACCCG
** *
297437 AAATGATCTGAATCC-
1 AAATGATCCAAACCCG
297452 AAAGTGA-CTCAAACCCG
1 AAA-TGATC-CAAACCCG
297469 AAATGATCCAAACCC-
1 AAATGATCCAAACCCG
297484 AAATGAT
1 AAATGAT
297491 GCGAACTCGA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
15 11 0.26
16 28 0.65
17 4 0.09
ACGTcount: A:0.44, C:0.24, G:0.13, T:0.19
Consensus pattern (16 bp):
AAATGATCCAAACCCG
Found at i:299033 original size:19 final size:20
Alignment explanation
Indices: 298995--299033 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
298985 AATATGATGG
*
298995 GATAAAATCTAAAACGTTAA
1 GATAAAATCAAAAACGTTAA
*
299015 GATAAAATGAAAAAC-TTAA
1 GATAAAATCAAAAACGTTAA
299034 TCAAAAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (20 bp):
GATAAAATCAAAAACGTTAA
Found at i:299261 original size:22 final size:22
Alignment explanation
Indices: 299236--299277 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
299226 CTCAAAATAT
*
299236 GATTTTTAGATTT-TTAAATTGA
1 GATTTTGA-ATTTATTAAATTGA
299258 GATTTTGAATTTATTAAATT
1 GATTTTGAATTTATTAAATT
299278 TTAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (22 bp):
GATTTTGAATTTATTAAATTGA
Found at i:300064 original size:32 final size:31
Alignment explanation
Indices: 299994--300074 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
299984 ATGATATATA
**
299994 AAATTATTA-ATAATAT-AATAAAAATATTTT
1 AAATT-TTATATAATATAAATAAAAATATAAT
* *
300024 AAAATTTATATAATATAAATAATTAATATAAT
1 AAATTTTATATAATATAAATAA-AAATATAAT
*
300056 AAATTTTATAAAATATAAA
1 AAATTTTATATAATATAAA
300075 ATACTAATAC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
29 3 0.07
30 11 0.26
31 5 0.12
32 23 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
AAATTTTATATAATATAAATAAAAATATAAT
Found at i:300083 original size:32 final size:32
Alignment explanation
Indices: 300023--300083 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
300013 AAAAATATTT
* *
300023 TAAAATTTATATAATATAAATAATTAATATAA
1 TAAAATTTATAAAATATAAATAACTAATATAA
*
300055 TAAATTTTATAAAATATAAA-ATACTAATA
1 TAAAATTTATAAAATATAAATA-ACTAATA
300084 CAAATCGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.04
32 24 0.96
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAATTTATAAAATATAAATAACTAATATAA
Found at i:300691 original size:23 final size:23
Alignment explanation
Indices: 300655--300699 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
300645 ATATACATCG
300655 TAAATATATTTATTAATTTTATT
1 TAAATATATTTATTAATTTTATT
*
300678 TAAAT-TATTATATTATTTTTAT
1 TAAATATATT-TATTAATTTTAT
300700 ATTATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TAAATATATTTATTAATTTTATT
Found at i:300703 original size:19 final size:18
Alignment explanation
Indices: 300659--300707 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
300649 ACATCGTAAA
300659 TATATTTATTAATTTTATT
1 TATA-TTATTAATTTTATT
*
300678 TAAATTATTATATTATT-TT
1 TATATTATTA-ATT-TTATT
300697 TATATTATTAA
1 TATATTATTAA
300708 ATATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.27
19 17 0.65
20 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATATTATTAATTTTATT
Found at i:301332 original size:10 final size:10
Alignment explanation
Indices: 301317--301342 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
301307 TCATGACTTA
301317 TATTTATAAT
1 TATTTATAAT
301327 TATTTATAAT
1 TATTTATAAT
301337 TATTTA
1 TATTTA
301343 ATTCATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TATTTATAAT
Found at i:303535 original size:18 final size:18
Alignment explanation
Indices: 303499--303550 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 18
303489 TAAATATTCG
* **
303499 TAAAATCAAAATATCAAT
1 TAAAATAAAAATAAAAAT
* *
303517 TTAATTAAAAATAAAAAT
1 TAAAATAAAAATAAAAAT
*
303535 TAAAATAAAATTAAAA
1 TAAAATAAAAATAAAA
303551 TAAAAAATTA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAATAAAAATAAAAAT
Found at i:303546 original size:11 final size:11
Alignment explanation
Indices: 303519--303555 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
303509 ATATCAATTT
303519 AATTAAAAATAAA
1 AATT-AAAAT-AA
303532 AATTAAAATAA
1 AATTAAAATAA
303543 AATTAAAATAA
1 AATTAAAATAA
303554 AA
1 AA
303556 AATTACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 15 0.62
12 5 0.21
13 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AATTAAAATAA
Done.