Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008760.1 Hibiscus syriacus cultivar Beakdansim tig00111852_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 225222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11037 original size:19 final size:19
Alignment explanation
Indices: 11013--11054 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11003 GTTATTTTAG
* *
11013 TATATTTAAATTTTTATTT
1 TATATTTAAAGTTTGATTT
*
11032 TATATTTTAAGTTTGATTT
1 TATATTTAAAGTTTGATTT
11051 TATA
1 TATA
11055 CTTTTTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
TATATTTAAAGTTTGATTT
Found at i:13433 original size:51 final size:50
Alignment explanation
Indices: 13378--13476 Score: 110
Period size: 51 Copynumber: 2.0 Consensus size: 50
13368 CAATTAATAC
*
13378 ATACTCACA-CTGATATAAGTGAACAAAATAAAAAAAATGTAGCACTTAACA
1 ATACTCACATC-GATATAAGTGAACAAAAT-AAAAAAATGTAACACTTAACA
* * * * * *
13429 ATACTTACATCGTTGTAAGTGAATAAAGTAAAAAAGTGTAACACTTAA
1 ATACTCACATCGATATAAGTGAACAAAATAAAAAAATGTAACACTTAA
13477 TACGTACTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
50 17 0.43
51 22 0.55
52 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.25
Consensus pattern (50 bp):
ATACTCACATCGATATAAGTGAACAAAATAAAAAAATGTAACACTTAACA
Found at i:13698 original size:62 final size:62
Alignment explanation
Indices: 13581--13698 Score: 139
Period size: 62 Copynumber: 1.9 Consensus size: 62
13571 TTTCAAAGAA
* * * * *
13581 ATAAAAAATAAAAAAATAAAATATATATGAAGTTAATTGTGTACAAATTTTATTAAATATAT
1 ATAAAAAATAAAAAAAGAAAATATATATGAAGTTAATTATGTAAAAATATAATTAAATATAT
* * * *
13643 ATAAAATATAAATAATAGAAAAT-TATATTAAGTTATTTATGTAAAAATATAATTAA
1 ATAAAAAATAAA-AAAAGAAAATATATATGAAGTTAATTATGTAAAAATATAATTAA
13699 TTAGAAATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
62 38 0.83
63 8 0.17
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (62 bp):
ATAAAAAATAAAAAAAGAAAATATATATGAAGTTAATTATGTAAAAATATAATTAAATATAT
Found at i:13712 original size:12 final size:12
Alignment explanation
Indices: 13695--13724 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
13685 AAAAATATAA
13695 TTAATTAGAAAT
1 TTAATTAGAAAT
13707 TTAATTAGAAAT
1 TTAATTAGAAAT
13719 TTAATT
1 TTAATT
13725 TTTTAACGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TTAATTAGAAAT
Found at i:15916 original size:37 final size:37
Alignment explanation
Indices: 15840--15916 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
15830 TTTTTATATT
*
15840 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
15877 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
15914 TTT
1 TTT
15917 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:16153 original size:14 final size:14
Alignment explanation
Indices: 16136--16179 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
16126 TATTTAGTAT
16136 TTAAAATTTAATAC
1 TTAAAATTTAATAC
*
16150 TTAAAGTTTAATAC
1 TTAAAATTTAATAC
16164 TT-AAATTTATATAC
1 TTAAAATTTA-ATAC
16178 TT
1 TT
16180 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 6 0.22
14 21 0.78
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (14 bp):
TTAAAATTTAATAC
Found at i:17287 original size:14 final size:14
Alignment explanation
Indices: 17268--17294 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17258 CCTTCTCCAT
17268 AGATATTTGAAATA
1 AGATATTTGAAATA
17282 AGATATTTGAAAT
1 AGATATTTGAAAT
17295 CAAAGAGAAT
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:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
AGATATTTGAAATA
Found at i:22985 original size:34 final size:33
Alignment explanation
Indices: 22909--23015 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
22899 GTGGTAAGAA
* *
22909 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
22943 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
22978 A-TTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
23012 ATTT
1 ATTT
23016 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 1 0.02
33 11 0.18
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:22997 original size:36 final size:34
Alignment explanation
Indices: 22942--23020 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
22932 TTTAAATAGT
*
22942 TATTATTTTTTATATT--AAT-ATATTTATGTAAA
1 TATTATTTTTT-TATTAAAATAATATTTATATAAA
*
22974 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATTAAAATAATATTTATATAAA
*
23008 TATTATTTATTTA
1 TATTATTTTTTTA
23021 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 3 0.07
34 23 0.56
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTTATTAAAATAATATTTATATAAA
Found at i:24766 original size:21 final size:21
Alignment explanation
Indices: 24736--24783 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
24726 GCAGGGGTAC
* *
24736 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
24757 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
24778 ATGCCA
1 ATGCCA
24784 TCTCTGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:24815 original size:21 final size:21
Alignment explanation
Indices: 24789--24880 Score: 125
Period size: 21 Copynumber: 4.4 Consensus size: 21
24779 TGCCATCTCT
* *
24789 GCAGGGTTACATTCCGAGCCC
1 GCAGGGTTACATGCCTAGCCC
*
24810 GCAGGGTTACATTCCTAGCCC
1 GCAGGGTTACATGCCTAGCCC
24831 GCCA-GGTTACATGCCTAGCCC
1 G-CAGGGTTACATGCCTAGCCC
24852 GCCA-GGTTACATGCCTAGCCC
1 G-CAGGGTTACATGCCTAGCCC
24873 GCAGGGTT
1 GCAGGGTT
24881 TTATACCATA
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
GCAGGGTTACATGCCTAGCCC
Found at i:25459 original size:33 final size:34
Alignment explanation
Indices: 25400--25496 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 34
25390 AAATGTTTTT
25400 AAAATATAAATTATATTATTCGAAATTTAAAATA
1 AAAATATAAATTATATTATTCGAAATTTAAAATA
* * * *
25434 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATATAAATTATATTATTCGAAATTTAAAATA
*
25467 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATATAAATTATATTATTCGAAATTTAA
25497 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAATATAAATTATATTATTCGAAATTTAAAATA
Found at i:25503 original size:34 final size:33
Alignment explanation
Indices: 25398--25503 Score: 142
Period size: 34 Copynumber: 3.2 Consensus size: 33
25388 ATAAATGTTT
25398 TTAAAATATAAATTATATTATTCGAAATTTAAAA
1 TTAAAATATAAATTATATTATTCGAAATTT-AAA
* * *
25432 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATATAAATTATATTATTCGAAATTTAAA
*
25464 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATATAAATTATATTATTCGAAATTTAA-A
25499 TTAAA
1 TTAAA
25504 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.39
Consensus pattern (33 bp):
TTAAAATATAAATTATATTATTCGAAATTTAAA
Found at i:26063 original size:103 final size:103
Alignment explanation
Indices: 25884--26069 Score: 363
Period size: 103 Copynumber: 1.8 Consensus size: 103
25874 TTTAAGTTAT
*
25884 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
25949 GCGCCCCCGGGAACGCGCATGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCATGTACTGATATATCTAGTG
25987 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
26052 GCGCCCCCGGGAACGCGC
66 GCGCCCCCGGGAACGCGC
26070 CTTCACGTGA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 82 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (103 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCATGTACTGATATATCTAGTG
Found at i:26194 original size:126 final size:126
Alignment explanation
Indices: 25969--26464 Score: 976
Period size: 126 Copynumber: 3.9 Consensus size: 126
25959 GAACGCGCAT
25969 GTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCT
1 GTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCT
26034 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAG
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAG
26095 GTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCT
1 GTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCT
26160 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAG
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAG
26221 GTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCT
1 GTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCT
26286 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAG
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAG
*
26347 GTACTGATATATCTAATGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCT
1 GTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCT
26412 GACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
26465 CCGATTATAG
Statistics
Matches: 369, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
125 32 0.09
126 337 0.91
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.22
Consensus pattern (126 bp):
GTACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAG
Found at i:26545 original size:8 final size:8
Alignment explanation
Indices: 26532--26572 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
26522 TCACAATCTT
26532 TCAAATTC
1 TCAAATTC
26540 TCAAATTC
1 TCAAATTC
* *
26548 CCAAACTC
1 TCAAATTC
26556 T-AAATTC
1 TCAAATTC
26563 TCAAATTC
1 TCAAATTC
26571 TC
1 TC
26573 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:29597 original size:12 final size:13
Alignment explanation
Indices: 29564--29601 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
29554 AAATACATAA
29564 ATATATTTAATAT
1 ATATATTTAATAT
*
29577 ATTTATTTAATAT
1 ATATATTTAATAT
29590 A-ATATTTAATAT
1 ATATATTTAATAT
29602 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:31820 original size:31 final size:31
Alignment explanation
Indices: 31782--31842 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
31772 ATATAGTCAC
*
31782 TTTCGTTTTCATTTAATTAAGATATGATCAT
1 TTTCGTTTTCATTTAACTAAGATATGATCAT
* *
31813 TTTCGTTTTTATTTAACTAAGATGTGATCA
1 TTTCGTTTTCATTTAACTAAGATATGATCA
31843 CCACGGGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.51
Consensus pattern (31 bp):
TTTCGTTTTCATTTAACTAAGATATGATCAT
Found at i:34279 original size:5 final size:5
Alignment explanation
Indices: 34269--34293 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
34259 ATATATAACG
34269 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
34294 GTAACCTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:35607 original size:15 final size:15
Alignment explanation
Indices: 35569--35626 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
35559 AAAATTATTT
*
35569 AAATATTGAAAAGTT-
1 AAATATT-AAAAATTA
35584 AAATA-TAAAATATTA
1 AAATATTAAAA-ATTA
35599 AAA-ATTAAAAATTA
1 AAATATTAAAAATTA
* *
35613 AATTACTAAAAATT
1 AAATATTAAAAATT
35627 TGAATATACA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 4 0.11
14 10 0.28
15 22 0.61
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (15 bp):
AAATATTAAAAATTA
Found at i:37291 original size:60 final size:60
Alignment explanation
Indices: 37227--37343 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
37217 AAATGGTCCC
*
37227 TCAACTATAGTA-TATTGATTTATTAAG-TCCTTTGACTATTAAAAGTTATAAAATGGTTTT
1 TCAACTATAG-AGTATTGATTTATTAAGTTCC-TAGACTATTAAAAGTTATAAAATGGTTTT
* * * * *
37287 TCAACTATAGAGTGTTGCTTTGTTGAGTTCCTAGATTATTAAAAGTTATAAAATGGT
1 TCAACTATAGAGTATTGATTTATTAAGTTCCTAGACTATTAAAAGTTATAAAATGGT
37344 CACCGACTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 1 0.02
60 45 0.92
61 3 0.06
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (60 bp):
TCAACTATAGAGTATTGATTTATTAAGTTCCTAGACTATTAAAAGTTATAAAATGGTTTT
Found at i:41775 original size:18 final size:18
Alignment explanation
Indices: 41742--41779 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
41732 TACAACAATA
41742 AGTTAATGGTTAAATTGAT
1 AGTTAATGGTTAAATT-AT
*
41761 AGTTTATGG-TAAATTAT
1 AGTTAATGGTTAAATTAT
41778 AG
1 AG
41780 GCTTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.42
Consensus pattern (18 bp):
AGTTAATGGTTAAATTAT
Found at i:44968 original size:31 final size:31
Alignment explanation
Indices: 44914--44991 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
44904 CGATAACGTC
* **
44914 AGTGATGGATTTGTTA-GAATCAATAATGTT
1 AGTGATCGATTTGTTACGAATCAATAATAAT
44944 AGTGATCGATTTGTTACGAATCAATAATAAT
1 AGTGATCGATTTGTTACGAATCAATAATAAT
44975 AGTGA-CTGATTTGTTAC
1 AGTGATC-GATTTGTTAC
44992 TTTTAAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.37
31 27 0.63
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (31 bp):
AGTGATCGATTTGTTACGAATCAATAATAAT
Found at i:45936 original size:29 final size:29
Alignment explanation
Indices: 45904--45962 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
45894 AACGCATGAT
45904 TTTATATCAAGGATGGAATTTTAAAATCC
1 TTTATATCAAGGATGGAATTTTAAAATCC
45933 TTTATATCAAGGATGGAATTTTAAAATCC
1 TTTATATCAAGGATGGAATTTTAAAATCC
45962 T
1 T
45963 AGGCAAGGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (29 bp):
TTTATATCAAGGATGGAATTTTAAAATCC
Found at i:55067 original size:2 final size:2
Alignment explanation
Indices: 55062--55096 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
55052 TGCGTGTGTC
* *
55062 TA TA TA TT TA TT 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 TA TA TA TA T
55097 TAACAACATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:61986 original size:59 final size:57
Alignment explanation
Indices: 61923--62091 Score: 173
Period size: 58 Copynumber: 2.9 Consensus size: 57
61913 TAATTCTTAT
61923 ACTTTTG-AATATTCTAATTTCATCCCAAAACATGACTCTCATTCTAAATTAGTCATTGA
1 ACTTTTGAAAT-TTC-AATTTCATCCCAAAACATGAC-CTCATTCTAAATTAGTCATTGA
* * *
61982 ACTTTTGAACATTTCAATTTCAT-CTATAAAC-TAGAACTCATTCTAAATTAGTCCTTGA
1 ACTTTTGAA-ATTTCAATTTCATCCCA-AAACAT-GACCTCATTCTAAATTAGTCATTGA
* * **
62040 ATTTTTGAAATTTCAATTTCACTCTTCAAATTATGACCATCATTCTAAATTA
1 ACTTTTGAAATTTCAATTTCA-TC-CCAAAACATGACC-TCATTCTAAATTA
62092 ATCCCAATAC
Statistics
Matches: 92, Mismatches: 9, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
57 12 0.13
58 33 0.36
59 26 0.28
60 19 0.21
61 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (57 bp):
ACTTTTGAAATTTCAATTTCATCCCAAAACATGACCTCATTCTAAATTAGTCATTGA
Found at i:62040 original size:58 final size:59
Alignment explanation
Indices: 61960--62091 Score: 180
Period size: 58 Copynumber: 2.2 Consensus size: 59
61950 AAACATGACT
61960 CTCATTCTAAATTAGTCATTGAACTTTTGAACATTTCAATTTCA-TCTAT-AAACTA-GAA
1 CTCATTCTAAATTAGTCATTGAACTTTTGAA-ATTTCAATTTCACTCT-TCAAACTATGAA
* * * *
62018 CTCATTCTAAATTAGTCCTTGAATTTTTGAAATTTCAATTTCACTCTTCAAATTATGAC
1 CTCATTCTAAATTAGTCATTGAACTTTTGAAATTTCAATTTCACTCTTCAAACTATGAA
62077 CATCATTCTAAATTA
1 C-TCATTCTAAATTA
62092 ATCCCAATAC
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
57 13 0.20
58 37 0.56
59 3 0.05
60 13 0.20
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (59 bp):
CTCATTCTAAATTAGTCATTGAACTTTTGAAATTTCAATTTCACTCTTCAAACTATGAA
Found at i:62106 original size:60 final size:59
Alignment explanation
Indices: 61960--62108 Score: 139
Period size: 58 Copynumber: 2.5 Consensus size: 59
61950 AAACATGACT
* * **
61960 CTCATTCTAAATTAGTCATTGA-ACTTTTGAACATTTCAATTTCATCTATAAACTAGAA
1 CTCATTCTAAATTAATCCTCAATACTTTTGAACATTTCAATTTCATCTATAAACTAGAA
* * * *
62018 CTCATTCTAAATTAGTCCTTGAAT--TTTTGAA-ATTTCAATTTCACTCT-TCAAATTATGAC
1 CTCATTCTAAATTAATCC-TCAATACTTTTGAACATTTCAATTTCA-TCTAT-AAACTA-GAA
62077 CATCATTCTAAATTAATCC-CAATACTTTTGAA
1 C-TCATTCTAAATTAATCCTCAATACTTTTGAA
62109 TCTTCCTAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
57 13 0.17
58 35 0.46
59 5 0.07
60 23 0.30
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (59 bp):
CTCATTCTAAATTAATCCTCAATACTTTTGAACATTTCAATTTCATCTATAAACTAGAA
Found at i:65457 original size:26 final size:25
Alignment explanation
Indices: 65425--65493 Score: 90
Period size: 22 Copynumber: 2.8 Consensus size: 25
65415 TAAATTATTT
65425 AAAATAAATCAATCCATACAATTAC
1 AAAATAAATCAATCCATACAATTAC
**
65450 AATAATAAATCAATCCAT---ATTTT
1 AA-AATAAATCAATCCATACAATTAC
65473 AAAATAAATCAATCCATACAA
1 AAAATAAATCAATCCATACAA
65494 ATAAATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 15 0.39
23 5 0.13
25 3 0.08
26 15 0.39
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (25 bp):
AAAATAAATCAATCCATACAATTAC
Found at i:65509 original size:32 final size:32
Alignment explanation
Indices: 65470--66017 Score: 479
Period size: 32 Copynumber: 19.4 Consensus size: 32
65460 CAATCCATAT
*
65470 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
65502 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
65534 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
65566 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
65598 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
65628 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
65646 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
65678 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
65700 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
65732 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
65754 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
65786 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
65816 --T--AATAAATCAATCC--A-T-AT------
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
65834 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
65866 TTTAAAATAAATTAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
65898 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
65920 TTTAAATTAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
65952 TTTAAAATAAATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
65974 TTTAAATTAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
66006 TTTAAAATAAAT
1 TTTAAAATAAAT
66018 TATTTTAAAA
Statistics
Matches: 430, Mismatches: 14, Indels: 144
0.73 0.02 0.24
Matches are distributed among these distances:
20 2 0.00
22 89 0.21
23 7 0.02
24 8 0.02
25 5 0.01
26 42 0.10
28 14 0.03
29 3 0.01
30 6 0.01
31 9 0.02
32 245 0.57
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:65675 original size:22 final size:23
Alignment explanation
Indices: 65600--65674 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
65590 ATAAATTATT
65600 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
65622 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
65648 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
65671 TAAA
1 TAAA
65675 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:65701 original size:54 final size:54
Alignment explanation
Indices: 65453--66017 Score: 617
Period size: 54 Copynumber: 10.1 Consensus size: 54
65443 CAATTACAAT
*
65453 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACAAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
65507 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * * * * *
65571 AATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAAT-C-CATACAACTA--CAA
1 AATAAATCAATCCATATT-TTAAA--A--T-AAATCAATCCATACTAATA-AATTATTTAA
65628 TAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 -AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
65683 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
65737 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* ** * * * *
65791 AATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCTAT
1 AATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--CT--AATAAAT-TATTTAA
* * *
65854 ACT-AATAAAT---TA-TTTAAAATAAATTAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
65903 AATAAATCAATTCATATTTTAAATTAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
65957 AATAAATCAATTCATATTTTAAATTAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
66011 AATAAAT
1 AATAAAT
66018 TATTTTAAAA
Statistics
Matches: 438, Mismatches: 37, Indels: 72
0.80 0.07 0.13
Matches are distributed among these distances:
49 6 0.01
50 13 0.03
52 11 0.03
53 8 0.02
54 246 0.56
55 12 0.03
56 2 0.00
57 11 0.03
58 39 0.09
59 7 0.02
60 14 0.03
62 14 0.03
63 8 0.02
64 47 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:65704 original size:22 final size:22
Alignment explanation
Indices: 65678--65720 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
65668 TAATAAATTA
*
65678 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
65700 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
65721 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:65729 original size:22 final size:22
Alignment explanation
Indices: 65680--65728 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
65670 ATAAATTATT
* **
65680 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
65702 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
65725 TAAA
1 TAAA
65729 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:65758 original size:22 final size:22
Alignment explanation
Indices: 65732--65774 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
65722 TAATAAATTA
65732 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
65754 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
65775 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:65783 original size:22 final size:22
Alignment explanation
Indices: 65734--65782 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
65724 ATAAATTATT
**
65734 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
65756 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
65779 TAAA
1 TAAA
65783 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:65783 original size:188 final size:194
Alignment explanation
Indices: 65502--65886 Score: 647
Period size: 188 Copynumber: 2.0 Consensus size: 194
65492 AAATAAATTA
65502 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCC--AC-AAT-AATTAT
*
65567 TTAAAATAAATCAATCCATATTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAAT
62 TTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAAT
*
65632 AAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCA
127 AAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCA
65697 TAT
192 TAT
65700 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-C-AT-A-T-TTTAA
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCACAATAATTATTTAA
*
65759 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAAT
66 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAAT
* *
65824 CAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATTAATCCATA
131 CAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
65887 CTAATAAATT
Statistics
Matches: 182, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
188 128 0.70
189 1 0.01
190 1 0.01
192 2 0.01
194 1 0.01
197 1 0.01
198 48 0.26
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (194 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCACAATAATTATTTAA
AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAAT
CAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:65838 original size:80 final size:83
Alignment explanation
Indices: 65700--65972 Score: 385
Period size: 86 Copynumber: 3.3 Consensus size: 83
65690 CAATTCATAT
65700 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAA
65765 TCAATTCATACTAATAAATTA
63 TCAATTCATACTAATAAATTA
*
65786 TTTAAAATAAATCAATCCATAC-AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATC
1 TTTAAAATAAATCAATCCATACTAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATC
65847 AA-TCTATACTAATAAATTA
65 AATTC-ATACTAATAAATTA
* * *
65866 TTTAAAATAAATTAATCCATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAATTAAA
1 TTTAAAATAAATCAATCCATACTAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAA
*
65931 TCAATCCATACTAATAAATTA
63 TCAATTCATACTAATAAATTA
*
65952 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
65973 TTTTAAATTA
Statistics
Matches: 169, Mismatches: 8, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
79 2 0.01
80 70 0.41
81 2 0.01
82 2 0.01
84 2 0.01
85 2 0.01
86 88 0.52
87 1 0.01
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (83 bp):
TTTAAAATAAATCAATCCATACTAATAAATATTAAATAAATCAATCCATATTTTAAAATAAATCA
ATTCATACTAATAAATTA
Found at i:65876 original size:14 final size:14
Alignment explanation
Indices: 65857--65909 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
65847 AATCTATACT
65857 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
65871 AATAAATTAATCCATACT
1 AATAAATT-AT--TTA-A
65889 AATAAATTATTTAA
1 AATAAATTATTTAA
65903 AATAAAT
1 AATAAAT
65910 CAATTCATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 15 0.48
15 4 0.13
17 4 0.13
18 8 0.26
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:65885 original size:220 final size:223
Alignment explanation
Indices: 65372--66017 Score: 835
Period size: 220 Copynumber: 2.9 Consensus size: 223
65362 AAATTATTTA
* *
65372 AAATAAATCAGTCTATATTTTAAAATAAATCAAT-TCATACTAATAAATTATTTAAAATAAATCA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCA
* * *
65436 ATCCATAC-----AATTA--CAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATACAA
65 ATCCATACTAATAAATTATTTAA-AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTA
65494 ATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACTAA
129 ATAAATTATTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATACTAA
*
65559 TAAATTATTTAAAATAAATCAATCCATATTAATAAATTATTT
184 TAAATTATTTAAAATAAATCAATCCATATCAATAAA-TA-TT
*** * * * *
65601 AAAATAAATCAATCCATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-TTTAAAATAAATC
1 -AAATAAATCAATCCATA-TTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATC
65659 AATCCATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTA
64 AATCCATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTA
*
65724 ATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTT
129 ATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTT
*
65789 AAAATAAATCAATCCATA-CAACTACA-A-T
194 AAAATAAATCAATCCATATCAA-TAAATATT
*
65817 -AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATTAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAA
*
65881 TCCATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAATTAAATCAATCCATACTAAT
66 TCCATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAAT
* *
65946 AAATTATTTAAAATAAATCAATTCATATTTTAAATTAAATCAATCCATACTAATAAATTATTTAA
131 AAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
66011 AATAAAT
196 AATAAAT
66018 TATTTTAAAA
Statistics
Matches: 372, Mismatches: 27, Indels: 44
0.84 0.06 0.10
Matches are distributed among these distances:
213 5 0.01
214 25 0.07
215 1 0.00
216 3 0.01
218 2 0.01
219 3 0.01
220 202 0.54
221 1 0.00
222 1 0.00
224 24 0.06
225 1 0.00
226 2 0.01
228 2 0.01
229 7 0.02
230 86 0.23
231 7 0.02
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.35
Consensus pattern (223 bp):
AAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAA
TCCATACTAATAAATTATTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAAT
AAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
AATAAATCAATCCATATCAATAAATATT
Found at i:65923 original size:22 final size:22
Alignment explanation
Indices: 65898--65940 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
65888 TAATAAATTA
*
65898 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
*
65920 TTTAAATTAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
65941 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:65978 original size:22 final size:22
Alignment explanation
Indices: 65952--66054 Score: 80
Period size: 22 Copynumber: 4.5 Consensus size: 22
65942 TAATAAATTA
*
65952 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
*
65974 TTTAAATTAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
65997 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
66021 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
66043 TTTATAATAAAT
1 TTTAAAATAAAT
66055 TATTTTATAA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
22 33 0.55
23 13 0.22
24 12 0.20
25 2 0.03
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:66026 original size:15 final size:15
Alignment explanation
Indices: 65997--66112 Score: 94
Period size: 15 Copynumber: 7.5 Consensus size: 15
65987 AATCCATACT
65997 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
66011 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
66026 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
66048 AATAAATTATTTTAT
1 AATAAATTATTTTAA
66063 AAT-AATT-TTTTAA
1 AATAAATTATTTTAA
* *
66076 AATAAATTTTTTTAT
1 AATAAATTATTTTAA
* *
66091 AATAATTTTTTTTAA
1 AATAAATTATTTTAA
66106 AATAAAT
1 AATAAAT
66113 AACCTTATTA
Statistics
Matches: 86, Mismatches: 6, Indels: 19
0.77 0.05 0.17
Matches are distributed among these distances:
13 8 0.09
14 17 0.20
15 43 0.50
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
22 10 0.12
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:66034 original size:69 final size:65
Alignment explanation
Indices: 65943--66095 Score: 184
Period size: 69 Copynumber: 2.3 Consensus size: 65
65933 AATCCATACT
*
65943 AATAAATTA-TTTAAAATAAATCAATTCATATTTTA-AATTAAATCAATCCATACTAATAAATTA
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAA-TAAAT-AAT-CATA-TAAT-AATTA
66006 TTTAA
61 TTTAA
* ** *
66011 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTATAATAATTTTTTAA
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATAATCATATAATAATTATTTAA
* *
66076 AATAAATTTTTTTATAATAA
1 AATAAATTATTTTAAAATAA
66096 TTTTTTTTAA
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
65 27 0.36
66 4 0.05
67 2 0.03
68 11 0.14
69 30 0.39
70 2 0.03
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (65 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATAATCATATAATAATTATTTAA
Found at i:66079 original size:28 final size:29
Alignment explanation
Indices: 66042--66112 Score: 108
Period size: 28 Copynumber: 2.4 Consensus size: 29
66032 TCAATCCATA
*
66042 TTTTATAATAAATTATTTTATAATAA-TT
1 TTTTAAAATAAATTATTTTATAATAATTT
*
66070 TTTTAAAATAAATTTTTTTATAATAATTTT
1 TTTTAAAATAAATTATTTTATAATAA-TTT
66100 TTTTAAAATAAAT
1 TTTTAAAATAAAT
66113 AACCTTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 24 0.62
30 15 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TTTTAAAATAAATTATTTTATAATAATTT
Found at i:77386 original size:19 final size:19
Alignment explanation
Indices: 77362--77404 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
77352 TGAACCGGCT
77362 GTTCAAACCGGTTTTGCAG
1 GTTCAAACCGGTTTTGCAG
77381 GTTCAAACCGGTTTTGCAG
1 GTTCAAACCGGTTTTGCAG
*
77400 ATTCA
1 GTTCA
77405 CCTCGGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (19 bp):
GTTCAAACCGGTTTTGCAG
Found at i:78834 original size:15 final size:15
Alignment explanation
Indices: 78813--78862 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
78803 CTAACACATC
78813 CGAATAACACATATT
1 CGAATAACACATATT
* * *
78828 GGAATAACATATATC
1 CGAATAACACATATT
78843 CGAATAACACATATT
1 CGAATAACACATATT
*
78858 TGAAT
1 CGAAT
78863 TCTGATATGA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (15 bp):
CGAATAACACATATT
Found at i:84562 original size:21 final size:20
Alignment explanation
Indices: 84538--84584 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
84528 TAATTTGTTG
*
84538 ATTAATTCAAAATTATATTTT
1 ATTAATTCAAAATT-TATTTA
84559 ATTAA-TCAAAATTTATTTA
1 ATTAATTCAAAATTTATTTA
84578 ATTAATT
1 ATTAATT
84585 ATTGAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 9 0.38
21 5 0.21
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAATTCAAAATTTATTTA
Found at i:84639 original size:5 final size:5
Alignment explanation
Indices: 84625--84676 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
84615 TGATTAATTT
* * **
84625 TTTAA ATTAA TTTAA TTTTAA -ATAA TTTAA TTTAA AATAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA -TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
84675 TT
1 TT
84677 ATTCGATCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
4 3 0.08
5 29 0.78
6 5 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
TTTAA
Found at i:84673 original size:15 final size:15
Alignment explanation
Indices: 84625--84674 Score: 82
Period size: 15 Copynumber: 3.3 Consensus size: 15
84615 TGATTAATTT
*
84625 TTTAAATTAATTTAA
1 TTTAAAATAATTTAA
*
84640 TTTTAAATAATTTAA
1 TTTAAAATAATTTAA
84655 TTTAAAATAATTTAA
1 TTTAAAATAATTTAA
84670 TTTAA
1 TTTAA
84675 TTATTCGATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAAAATAATTTAA
Found at i:86065 original size:20 final size:19
Alignment explanation
Indices: 86042--86088 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
86032 CATTAATTAC
86042 TCTTTTTTTTTTTCAATTCA
1 TCTTTTTTTTTTT-AATTCA
86062 TCTTTTATTTTTTTAATTCA
1 TCTTTT-TTTTTTTAATTCA
86082 TCTTTTT
1 TCTTTTT
86089 AACTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.04
20 18 0.69
21 7 0.27
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (19 bp):
TCTTTTTTTTTTTAATTCA
Found at i:88689 original size:18 final size:19
Alignment explanation
Indices: 88666--88705 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
88656 ATAAAAAATT
88666 TAATAAAATAAT-ATTATA
1 TAATAAAATAATCATTATA
*
88684 TAATAAAATAATCATTTTA
1 TAATAAAATAATCATTATA
88703 TAA
1 TAA
88706 CTTTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATAAAATAATCATTATA
Found at i:88693 original size:15 final size:15
Alignment explanation
Indices: 88645--88693 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
88635 ATTATTTTAT
88645 AAAT-TTTAATAATA
1 AAATATTTAATAATA
*
88659 AAAAATTTAATAA-A
1 AAATATTTAATAATA
88673 ATAATA-TTATATAATA
1 A-AATATTTA-ATAATA
88689 AAATA
1 AAATA
88694 ATCATTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
14 8 0.28
15 19 0.66
16 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATATTTAATAATA
Found at i:104171 original size:163 final size:162
Alignment explanation
Indices: 103901--104225 Score: 641
Period size: 163 Copynumber: 2.0 Consensus size: 162
103891 TTGAATACGA
103901 GAACTATCCATTAGAGAGAAATCTTTCCAGAAATCTTCATTCTGAGGTATACTAAAGGATGTCTT
1 GAACTATCCATTAGAGAGAAATCTTTCCAGAAATCTTCATTCTGAGGTATACTAAAGGATGTCTT
103966 TGCCTGTATCCTCGTGGTCTGAGGGGTCATCAGAATCAGAGTCAAGTAACTGAAATCTTCGAATA
66 TGCCTGTATCCTCGTGGTCTGAGGGGTCATCAGAATCAGAGTCAAGTAACTGAAATCTTCGAATA
104031 GGACTGATAGTTTAACTTTGGAAATGTCAACCC
131 GGACTGATAG-TTAACTTTGGAAATGTCAACCC
104064 GAACTATCCATTAGAGAGAAATCTTTCCAGAAATCTTCATTCTGAGGTATACTAAAGGATGTCTT
1 GAACTATCCATTAGAGAGAAATCTTTCCAGAAATCTTCATTCTGAGGTATACTAAAGGATGTCTT
104129 TGCCTGTATCCTCGTGGTCTGAGGGGTCATCAGAATCAGAGTCAAGTAACTGAAATCTTCGAATA
66 TGCCTGTATCCTCGTGGTCTGAGGGGTCATCAGAATCAGAGTCAAGTAACTGAAATCTTCGAATA
104194 GGACTGATAGTTAACTTTGGAAATGTCAACCC
131 GGACTGATAGTTAACTTTGGAAATGTCAACCC
104226 ATCACGTCTT
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
162 22 0.14
163 140 0.86
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (162 bp):
GAACTATCCATTAGAGAGAAATCTTTCCAGAAATCTTCATTCTGAGGTATACTAAAGGATGTCTT
TGCCTGTATCCTCGTGGTCTGAGGGGTCATCAGAATCAGAGTCAAGTAACTGAAATCTTCGAATA
GGACTGATAGTTAACTTTGGAAATGTCAACCC
Found at i:108352 original size:19 final size:20
Alignment explanation
Indices: 108318--108355 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
108308 ATAAGGTACA
108318 AAAATAATAGAAATATTATG
1 AAAATAATAGAAATATTATG
*
108338 AAAATATTA-AAATATTAT
1 AAAATAATAGAAATATTAT
108356 TATAATACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATAATAGAAATATTATG
Found at i:108536 original size:3 final size:3
Alignment explanation
Indices: 108528--108553 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
108518 AAGAATGGAA
108528 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
108554 GGGAAAACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:115259 original size:29 final size:29
Alignment explanation
Indices: 115226--115285 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
115216 TCCGTATCTC
115226 GATTCTGATTTAAACTTGAAAACAGGTGA
1 GATTCTGATTTAAACTTGAAAACAGGTGA
*
115255 GATTCTGCTTTAAACTTGAAAACAGGTGA
1 GATTCTGATTTAAACTTGAAAACAGGTGA
115284 GA
1 GA
115286 GAAAATGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.30
Consensus pattern (29 bp):
GATTCTGATTTAAACTTGAAAACAGGTGA
Found at i:116144 original size:2 final size:2
Alignment explanation
Indices: 116137--116162 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
116127 TTACAGAGCC
116137 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
116163 AAGAACCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:121300 original size:6 final size:6
Alignment explanation
Indices: 121289--121316 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
121279 AAGACAGAGT
121289 GAAAGA GAAAGA GAAAGA GAAAGA GAAA
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAA
121317 TGGGTTGCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:121300 original size:18 final size:18
Alignment explanation
Indices: 121277--121316 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
121267 GCCTGGGAAG
* *
121277 GAAAGACAGAGTGAAAGA
1 GAAAGACAAAGAGAAAGA
*
121295 GAAAGAGAAAGAGAAAGA
1 GAAAGACAAAGAGAAAGA
121313 GAAA
1 GAAA
121317 TGGGTTGCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.33, T:0.03
Consensus pattern (18 bp):
GAAAGACAAAGAGAAAGA
Found at i:121633 original size:31 final size:29
Alignment explanation
Indices: 121580--121680 Score: 96
Period size: 31 Copynumber: 3.4 Consensus size: 29
121570 TTCATTTAAG
*
121580 TACCTAAAGTATTTTTTTGTCAAAATAAA
1 TACCTAAAGTATTTTTTGGTCAAAATAAA
**
121609 TACCTAAAGTCATATTTTTGGTCAAAATAGG
1 TACCTAAAGT-AT-TTTTTGGTCAAAATAAA
* ** **
121640 TACCCAAAGTATTTCAT-GTCAAAATAGG
1 TACCTAAAGTATTTTTTGGTCAAAATAAA
*
121668 TACCTAAACTATT
1 TACCTAAAGTATT
121681 CAAACTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
28 22 0.35
29 13 0.21
30 4 0.06
31 23 0.37
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.36
Consensus pattern (29 bp):
TACCTAAAGTATTTTTTGGTCAAAATAAA
Found at i:122023 original size:15 final size:17
Alignment explanation
Indices: 121989--122027 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
121979 TCCTAAACAT
121989 ATTTTAAAATTGGATACA
1 ATTTT-AAATTGGATACA
122007 ATTTTAAATT-G-TACA
1 ATTTTAAATTGGATACA
122022 ATTTTA
1 ATTTTA
122028 TTCCCCCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.48
16 1 0.05
17 5 0.24
18 5 0.24
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (17 bp):
ATTTTAAATTGGATACA
Found at i:137842 original size:17 final size:17
Alignment explanation
Indices: 137816--137871 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 17
137806 AAAATATAAC
137816 ATAAATAAATAATAAATT
1 ATAAA-AAATAATAAATT
137834 ATAAAAAATAATATGAA-T
1 ATAAAAAATAATA--AATT
*
137852 ATAAAAATATAATTAATT
1 ATAAAAA-ATAATAAATT
137870 AT
1 AT
137872 TTTATAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 10 0.30
18 16 0.48
19 7 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
ATAAAAAATAATAAATT
Found at i:137856 original size:32 final size:31
Alignment explanation
Indices: 137804--137866 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
137794 TATTATTTAT
137804 TAAAAATATAACATAAATAAATAATA-AATTA
1 TAAAAATATAACATAAATAAA-AATATAATTA
*
137835 TAAAAA-ATAATATGAATATAAAAATATAATTA
1 TAAAAATATAACAT-AA-ATAAAAATATAATTA
137867 ATTATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 6 0.21
31 12 0.43
32 10 0.36
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (31 bp):
TAAAAATATAACATAAATAAAAATATAATTA
Found at i:138177 original size:23 final size:24
Alignment explanation
Indices: 138132--138179 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
138122 GTTTCAAACT
138132 AATTATTTTCCATTAAAAAAATTA
1 AATTATTTTCCATTAAAAAAATTA
*
138156 AATTCTTTTCCATT-AAAAAATTA
1 AATTATTTTCCATTAAAAAAATTA
138179 A
1 A
138180 CAGTCATCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (24 bp):
AATTATTTTCCATTAAAAAAATTA
Found at i:138673 original size:21 final size:21
Alignment explanation
Indices: 138626--138665 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
138616 ATCGATATTT
*
138626 TTTATTATCTTTTTATTTTTA
1 TTTATTATCATTTTATTTTTA
*
138647 TATATTAT-ATTTTATTTTT
1 TTTATTATCATTTTATTTTT
138666 CTCTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTATCATTTTATTTTTA
Found at i:139275 original size:21 final size:22
Alignment explanation
Indices: 139221--139275 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
139211 ATAACTTTAA
*
139221 CTTTATGACACATTTTTTTTGG
1 CTTTATGACACATTTTCTTTGG
* *
139243 CTTTA-GTCACACTTTTCTTTGT
1 CTTTATGACACA-TTTTCTTTGG
139265 CTTTATGACAC
1 CTTTATGACAC
139276 GTTTACGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 5 0.19
22 18 0.67
23 4 0.15
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (22 bp):
CTTTATGACACATTTTCTTTGG
Found at i:145295 original size:31 final size:31
Alignment explanation
Indices: 145257--145332 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
145247 GGGGAAATGA
* *
145257 TCCCTAACGTTATCGGTCCATTCGATTTTAG
1 TCCCTAACGTTATCGATCCATTCGATTTAAG
* * *
145288 TCCCTAACATTATCGATTCGTTCGATTTAAG
1 TCCCTAACGTTATCGATCCATTCGATTTAAG
145319 TCCCTCAATCGTTA
1 TCCCT-AA-CGTTA
145333 ACTCCAATTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 31 0.84
32 2 0.05
33 4 0.11
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.38
Consensus pattern (31 bp):
TCCCTAACGTTATCGATCCATTCGATTTAAG
Found at i:151439 original size:31 final size:32
Alignment explanation
Indices: 151403--151467 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
151393 TCTCAAAAAA
*
151403 TCGGG-TAGGGTGGAAGG-TGTATATTTTTAGG
1 TCGGGTTAGGGTGG-AGGATGTATAATTTTAGG
* *
151434 TCGGGTTCGGGTGGAGGATGTATAATTTTCGG
1 TCGGGTTAGGGTGGAGGATGTATAATTTTAGG
151466 TC
1 TC
151468 AGGCTGATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 8 0.28
32 21 0.72
ACGTcount: A:0.17, C:0.08, G:0.40, T:0.35
Consensus pattern (32 bp):
TCGGGTTAGGGTGGAGGATGTATAATTTTAGG
Found at i:152059 original size:24 final size:24
Alignment explanation
Indices: 152022--152070 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
152012 GATACATTGA
*
152022 ACAATGTGTATGCAATGATCCCCC
1 ACAATATGTATGCAATGATCCCCC
* *
152046 ACAATATGTGTGCACTGATCCCCC
1 ACAATATGTATGCAATGATCCCCC
152070 A
1 A
152071 TGTGCTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (24 bp):
ACAATATGTATGCAATGATCCCCC
Found at i:152133 original size:27 final size:27
Alignment explanation
Indices: 152095--152146 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
152085 GATAGATGTG
152095 TCATATAATTCGTTGCCACGGTTCGGT
1 TCATATAATTCGTTGCCACGGTTCGGT
*
152122 TCATATAATTCGTTGTCACGGTTCG
1 TCATATAATTCGTTGCCACGGTTCG
152147 AGTCAATCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (27 bp):
TCATATAATTCGTTGCCACGGTTCGGT
Found at i:166408 original size:13 final size:13
Alignment explanation
Indices: 166355--166430 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 13
166345 TTATATTTTA
166355 AAATATAAATTAT
1 AAATATAAATTAT
* **
166368 CAATGTATAAAAAAT
1 -AA-ATATAAATTAT
166383 AAATATAAATTAT
1 AAATATAAATTAT
* *
166396 AAATATTATTTATT
1 AAATATAAATTA-T
166410 ATAA-ATAAA-T-T
1 A-AATATAAATTAT
166421 AAATATAAAT
1 AAATATAAAT
166431 AACTGAATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
10 2 0.04
11 7 0.15
13 19 0.40
14 9 0.19
15 10 0.21
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (13 bp):
AAATATAAATTAT
Found at i:169105 original size:29 final size:29
Alignment explanation
Indices: 169058--169131 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
169048 TAAATAATTG
* * *
169058 AATACTTTAGGTACCTATTTTGAC-CAAAA
1 AATATTTTAGGTACTTA-TTTGACAAAAAA
*
169087 ACTATTTTAGGTACTTATTTGACAAAAAA
1 AATATTTTAGGTACTTATTTGACAAAAAA
*
169116 AATATTTTAAGTACTT
1 AATATTTTAGGTACTT
169132 GAATGAAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 6 0.16
29 32 0.84
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.39
Consensus pattern (29 bp):
AATATTTTAGGTACTTATTTGACAAAAAA
Found at i:176377 original size:58 final size:59
Alignment explanation
Indices: 176265--176395 Score: 140
Period size: 58 Copynumber: 2.2 Consensus size: 59
176255 TTTACGAATG
* * ** * * * *
176265 AAATGGAAAGATTCAAAAGTTTGGGGGTCAATTTAGAATGAAGGTCATACTTTGGGGA-
1 AAATTGAAATATTCAAAAGTTTGGGACTCAATTTACAATGAAAGTCATAATTTGGCGAT
*
176323 AAATTGAAATATTCAAAAGTTTGAGGACT-AATTTACAATGAAAGTGATAATTTGGCGATT
1 AAATTGAAATATTCAAAAGTTTG-GGACTCAATTTACAATGAAAGTCATAATTTGGCGA-T
*
176383 AAATTAAAATATT
1 AAATTGAAATATT
176396 GAAGTATAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
58 45 0.75
59 3 0.05
60 12 0.20
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.31
Consensus pattern (59 bp):
AAATTGAAATATTCAAAAGTTTGGGACTCAATTTACAATGAAAGTCATAATTTGGCGAT
Found at i:176847 original size:60 final size:60
Alignment explanation
Indices: 176743--176879 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 60
176733 TGACTCTGGA
* * * ** * *
176743 GATGAAATGGAAAGATTCAAAAGTTTGGAGACCGGTTTAGAATGAATGCCATAGTTTGGC
1 GATGAAATTGAAATATTCAAAAGTTTAGAGACCAATTTAAAATGAAAGCCATAGTTTGGC
* * *
176803 GATGAAATTGAAATATTCAAAAGTTTA-AGGACTAATTTAAAATGAAAGTCATAGTTTGGT
1 GATGAAATTGAAATATTCAAAAGTTTAGA-GACCAATTTAAAATGAAAGCCATAGTTTGGC
176863 GATGAAATTGAAATATT
1 GATGAAATTGAAATATT
176880 TAATGATTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
59 1 0.02
60 65 0.98
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.31
Consensus pattern (60 bp):
GATGAAATTGAAATATTCAAAAGTTTAGAGACCAATTTAAAATGAAAGCCATAGTTTGGC
Found at i:181278 original size:29 final size:30
Alignment explanation
Indices: 181221--181277 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
181211 TCAGCTATAA
*
181221 TAATAAATACAATTTAAAGATAGATTTTAT
1 TAATAAATACAATTTAAAGAAAGATTTTAT
181251 TAATAAATACAA-TTAAAGAGAAGATTT
1 TAATAAATACAATTTAAAGA-AAGATTT
181278 AGTATTTACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.35
Consensus pattern (30 bp):
TAATAAATACAATTTAAAGAAAGATTTTAT
Found at i:184684 original size:340 final size:340
Alignment explanation
Indices: 184064--184732 Score: 1266
Period size: 340 Copynumber: 2.0 Consensus size: 340
184054 TACTCAAATC
*
184064 AATTAAAGAAAATATAAATCCTAAAATTATTTGAAAAGAAAAAACTCTTCTCAAATATAACCCAA
1 AATTAAAGAAAATATAAATACTAAAATTATTTGAAAAGAAAAAACTCTTCTCAAATATAACCCAA
*
184129 TTAATTTTATGTTCGTTTGTTTACGTTCGTTCATTTGTGTTTGTTTATCATTTAAATGAACGAAC
66 TTAATTTTATGTTCGTTTGTTTACGTTCGTTCATTTGTGTTTATTTATCATTTAAATGAACGAAC
*
184194 ACGAACAAGCTAAATTTCTTAATGAATGAACACGAACAATAAATTTGTTCGTTTAGTTGTTTGTG
131 ACGAACAAGCTAAATTTCTTAATGAATGAACACGAACAAGAAATTTGTTCGTTTAGTTGTTTGTG
*
184259 TTCGTTCGATTAAAGTTAAACGAACGAACATGATTACATCATTGTTCATGCTCGTTCTCGATCCA
196 TTCGTTCGATTAAAGTTAAACGAACGAACATGAATACATCATTGTTCATGCTCGTTCTCGATCCA
184324 AGAAAACAGTAAAAGGAAGCATTATTTTTACGGAATTAGCAATGAAATTAGTAGCAAAACTTATA
261 AGAAAACAGTAAAAGGAAGCATTATTTTTACGGAATTAGCAATGAAATTAGTAGCAAAACTTATA
184389 GAAGGAAGATGCTAT
326 GAAGGAAGATGCTAT
184404 AATTAAAGAAAATATAAATACTAAAATTATTTGAAAAGAAAAAACTCTTCTCAAATATAACCCAA
1 AATTAAAGAAAATATAAATACTAAAATTATTTGAAAAGAAAAAACTCTTCTCAAATATAACCCAA
184469 TTAATTTTATGTTCGTTTGTTTACGTTCGTTCATTTGTGTTTATTTATCATTTAAATGAACGAAC
66 TTAATTTTATGTTCGTTTGTTTACGTTCGTTCATTTGTGTTTATTTATCATTTAAATGAACGAAC
*
184534 ACGAACAATCTAAATTTCTTAATGAATGAACACGAACAAGAAATTTGTTCGTTTAGTTGTTTGTG
131 ACGAACAAGCTAAATTTCTTAATGAATGAACACGAACAAGAAATTTGTTCGTTTAGTTGTTTGTG
* *
184599 TTCGTTCGATTAAAGTTAAACGAATGAACATGAATACATCCTTGTTCATGCTCGTTCTCGATCCA
196 TTCGTTCGATTAAAGTTAAACGAACGAACATGAATACATCATTGTTCATGCTCGTTCTCGATCCA
*
184664 AGAAAACAGTAAAAGGAAGCATTATTTTTACTGAATTAGCAATGAAATTAGTAGCAAAACTTATA
261 AGAAAACAGTAAAAGGAAGCATTATTTTTACGGAATTAGCAATGAAATTAGTAGCAAAACTTATA
184729 GAAG
326 GAAG
184733 ATGCTATAGC
Statistics
Matches: 321, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
340 321 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (340 bp):
AATTAAAGAAAATATAAATACTAAAATTATTTGAAAAGAAAAAACTCTTCTCAAATATAACCCAA
TTAATTTTATGTTCGTTTGTTTACGTTCGTTCATTTGTGTTTATTTATCATTTAAATGAACGAAC
ACGAACAAGCTAAATTTCTTAATGAATGAACACGAACAAGAAATTTGTTCGTTTAGTTGTTTGTG
TTCGTTCGATTAAAGTTAAACGAACGAACATGAATACATCATTGTTCATGCTCGTTCTCGATCCA
AGAAAACAGTAAAAGGAAGCATTATTTTTACGGAATTAGCAATGAAATTAGTAGCAAAACTTATA
GAAGGAAGATGCTAT
Found at i:189045 original size:173 final size:173
Alignment explanation
Indices: 188756--189259 Score: 990
Period size: 173 Copynumber: 2.9 Consensus size: 173
188746 TATCCAAGCC
* *
188756 TTGTCTCAATTGTTAGCAAGACGAGACACATATAAGACAATAGCCAGGAAGATCTGTTATCTGGT
1 TTGTCTCAAATGTTAGCAAGACGAGACACATATAAGACAATAGCCAGGAAGATCTGATATCTGGT
188821 TACCTAGAGTCCCAAATATTAGGTGAAAAGGGAAAATAGTACTTAAAACAATGTTGAATTTGTAT
66 TACCTAGAGTCCCAAATATTAGGTGAAAAGGGAAAATAGTACTTAAAACAATGTTGAATTTGTAT
188886 CCAGGCAAAAACTAAGCTCAAAACAGATATAAGACAATTGAAT
131 CCAGGCAAAAACTAAGCTCAAAACAGATATAAGACAATTGAAT
188929 TTGTCTCAAATGTTAGCAAGACGAGACACATATAAGACAATAGCCAGGAAGATCTGATATCTGGT
1 TTGTCTCAAATGTTAGCAAGACGAGACACATATAAGACAATAGCCAGGAAGATCTGATATCTGGT
188994 TACCTAGAGTCCCAAATATTAGGTGAAAAGGGAAAATAGTACTTAAAACAATGTTGAATTTGTAT
66 TACCTAGAGTCCCAAATATTAGGTGAAAAGGGAAAATAGTACTTAAAACAATGTTGAATTTGTAT
189059 CCAGGCAAAAACTAAGCTCAAAACAGATATAAGACAATTGAAT
131 CCAGGCAAAAACTAAGCTCAAAACAGATATAAGACAATTGAAT
189102 TTGTCTCAAATGTTAGCAAGACGAGACACATATAAGACAATAGCCAGGAAGATCTGATATCTGGT
1 TTGTCTCAAATGTTAGCAAGACGAGACACATATAAGACAATAGCCAGGAAGATCTGATATCTGGT
189167 TACCTAGAGTCCCAAATATTAGGTGAAAAGGGAAAATAGTACTTAAAACAATGTTGAATTTGTAT
66 TACCTAGAGTCCCAAATATTAGGTGAAAAGGGAAAATAGTACTTAAAACAATGTTGAATTTGTAT
189232 CCAGGCAAAAACTAAGCTCAAAACAGAT
131 CCAGGCAAAAACTAAGCTCAAAACAGAT
189260 GGGAAGACAT
Statistics
Matches: 329, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 329 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (173 bp):
TTGTCTCAAATGTTAGCAAGACGAGACACATATAAGACAATAGCCAGGAAGATCTGATATCTGGT
TACCTAGAGTCCCAAATATTAGGTGAAAAGGGAAAATAGTACTTAAAACAATGTTGAATTTGTAT
CCAGGCAAAAACTAAGCTCAAAACAGATATAAGACAATTGAAT
Found at i:194079 original size:61 final size:61
Alignment explanation
Indices: 193953--194068 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
193943 TTTAGCACAC
* * * *
193953 CATCCCATTAGACTAACTGTAAAATTTAAATCTTTGACCTCAATTAAGGAATCTAAAACCT
1 CATCCCATTAGACTAACTGCAAAATTCAAATCTATGACCTCAATTAAAGAATCTAAAACCT
* * **
194014 CATCCCATTAGACTAACTGCGAGATTCAAATCTATGACCTCGGTTAAAGAATCTA
1 CATCCCATTAGACTAACTGCAAAATTCAAATCTATGACCTCAATTAAAGAATCTA
194069 GTATCTCATC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.29
Consensus pattern (61 bp):
CATCCCATTAGACTAACTGCAAAATTCAAATCTATGACCTCAATTAAAGAATCTAAAACCT
Found at i:195043 original size:23 final size:25
Alignment explanation
Indices: 195017--195066 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
195007 CCATGAAGTA
195017 TTAAAC-TTTT-CCCACTTTGCCCC
1 TTAAACATTTTCCCCACTTTGCCCC
* *
195040 TT-AACATTTTCCCCATTTTGTCCC
1 TTAAACATTTTCCCCACTTTGCCCC
195064 TTA
1 TTA
195067 CAATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 3 0.14
23 6 0.27
24 13 0.59
ACGTcount: A:0.18, C:0.34, G:0.04, T:0.44
Consensus pattern (25 bp):
TTAAACATTTTCCCCACTTTGCCCC
Found at i:201187 original size:2 final size:2
Alignment explanation
Indices: 201180--201226 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
201170 TTTATATCTT
201180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
201222 TA TA T
1 TA TA T
201227 CAATCAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:204363 original size:31 final size:31
Alignment explanation
Indices: 204299--204373 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
204289 TTTTTTGAAA
*
204299 TTTAGGTATTAAAATGAATCAAATTTGGAAG
1 TTTAGGTATTAAAATGAATCAAAATTGGAAG
*
204330 TTTAGGTATTAAAAT-AGATTAAAATT-GATAG
1 TTTAGGTATTAAAATGA-ATCAAAATTGGA-AG
*
204361 TTTAGGTACTAAA
1 TTTAGGTATTAAA
204374 TGCGTTAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 36 0.92
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.37
Consensus pattern (31 bp):
TTTAGGTATTAAAATGAATCAAAATTGGAAG
Found at i:204925 original size:16 final size:16
Alignment explanation
Indices: 204906--204947 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
204896 AAAATCATCA
*
204906 TGAAGCGAAATTAACC
1 TGAACCGAAATTAACC
204922 TGAACCGAAATTAACC
1 TGAACCGAAATTAACC
* *
204938 CGAATCGAAA
1 TGAACCGAAA
204948 GAAACCCGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (16 bp):
TGAACCGAAATTAACC
Found at i:204947 original size:32 final size:32
Alignment explanation
Indices: 204918--204978 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
204908 AAGCGAAATT
* **
204918 AACCTGAACCGAAATTAACCCGAATCGAAAGA
1 AACCCGAACCGAAAGGAACCCGAATCGAAAGA
*
204950 AACCCGACCCGAAAGGAACCCGAATCGAA
1 AACCCGAACCGAAAGGAACCCGAATCGAA
204979 TCTAACCCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.44, C:0.30, G:0.18, T:0.08
Consensus pattern (32 bp):
AACCCGAACCGAAAGGAACCCGAATCGAAAGA
Found at i:204953 original size:16 final size:16
Alignment explanation
Indices: 204934--204978 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
204924 AACCGAAATT
204934 AACCCGAATCGAAAGA
1 AACCCGAATCGAAAGA
** *
204950 AACCCGACCCGAAAGG
1 AACCCGAATCGAAAGA
204966 AACCCGAATCGAA
1 AACCCGAATCGAA
204979 TCTAACCCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.44, C:0.31, G:0.20, T:0.04
Consensus pattern (16 bp):
AACCCGAATCGAAAGA
Found at i:204986 original size:32 final size:32
Alignment explanation
Indices: 204934--205002 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
204924 AACCGAAATT
* * *
204934 AACCCGAATCGAAAGAAACCCGACCCGAAAGG
1 AACCCGAATCGAAACAAACCCGACCCAAAAGC
* *
204966 AACCCGAATCGAATCTAACCCGACCCAAAAGC
1 AACCCGAATCGAAACAAACCCGACCCAAAAGC
204998 AACCC
1 AACCC
205003 AAACAAATTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.36, G:0.16, T:0.06
Consensus pattern (32 bp):
AACCCGAATCGAAACAAACCCGACCCAAAAGC
Found at i:205082 original size:18 final size:17
Alignment explanation
Indices: 205061--205110 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
205051 AATATTGAAT
205061 TAATTTAAATAAAATTGA
1 TAATTTAAATAAAATT-A
*
205079 TAATTT-ATTAAATATTA
1 TAATTTAAATAAA-ATTA
205096 T-ATTTATAATAAAAT
1 TAATTTA-AATAAAAT
205111 AATAGTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
16 4 0.15
17 9 0.33
18 14 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TAATTTAAATAAAATTA
Found at i:205280 original size:42 final size:42
Alignment explanation
Indices: 205204--205311 Score: 191
Period size: 42 Copynumber: 2.6 Consensus size: 42
205194 TTGTTATAAA
205204 AATATTAGATTTATAAT-AAAATAATAGAAAACAAAGAAAAT
1 AATATTAGATTTATAATAAAAATAATAGAAAACAAAGAAAAT
*
205245 AATATTAGATTTATAATAAAAATAATAGAAAACAAATAAAAT
1 AATATTAGATTTATAATAAAAATAATAGAAAACAAAGAAAAT
205287 AATATTAGATTTATAATAAATAATA
1 AATATTAGATTTATAATAAA-AATA
205312 TAAAGTTTCC
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
41 17 0.27
42 43 0.67
43 4 0.06
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (42 bp):
AATATTAGATTTATAATAAAAATAATAGAAAACAAAGAAAAT
Found at i:205287 original size:19 final size:19
Alignment explanation
Indices: 205218--205290 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
205208 TTAGATTTAT
205218 AATAAAATAATAGAAAACA
1 AATAAAATAATAGAAAACA
* * ***
205237 AAGAAAATAATATTAGATTTA
1 AATAAAATAATA-GA-AAACA
205258 TAATAAAAATAATAGAAAACA
1 -AAT-AAAATAATAGAAAACA
205279 AATAAAATAATA
1 AATAAAATAATA
205291 TTAGATTTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
19 20 0.50
20 4 0.10
21 4 0.10
22 3 0.08
23 9 0.22
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.23
Consensus pattern (19 bp):
AATAAAATAATAGAAAACA
Found at i:205732 original size:32 final size:33
Alignment explanation
Indices: 205685--205766 Score: 105
Period size: 32 Copynumber: 2.5 Consensus size: 33
205675 ATTAAACTAG
** *
205685 TAACCGATCCAATATTGACCCGA-CCCAAAATC
1 TAACCGATCTGATATTGACCCGATCCAAAAATC
*
205717 TAACCGATCTGATATTAACCCGATCCAAAAATC
1 TAACCGATCTGATATTGACCCGATCCAAAAATC
*
205750 -AACCGATTTGATATTGA
1 TAACCGATCTGATATTGA
205767 TCTGAACCGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 35 0.81
33 8 0.19
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (33 bp):
TAACCGATCTGATATTGACCCGATCCAAAAATC
Found at i:206016 original size:33 final size:33
Alignment explanation
Indices: 205979--206042 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
205969 TTTATAACGC
*
205979 CGTTAGTGAAAAGCGGTTGAGCAACTAAAAAGG
1 CGTTAGTGAAAAACGGTTGAGCAACTAAAAAGG
206012 CGTTAGTGAAAAACGGTTGAGCAACTAAAAA
1 CGTTAGTGAAAAACGGTTGAGCAACTAAAAA
206043 TCTAATGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (33 bp):
CGTTAGTGAAAAACGGTTGAGCAACTAAAAAGG
Found at i:209886 original size:2 final size:2
Alignment explanation
Indices: 209879--209910 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
209869 ATAATTTTAC
209879 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
209911 TAAGTTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:215694 original size:39 final size:39
Alignment explanation
Indices: 215636--215891 Score: 377
Period size: 39 Copynumber: 6.5 Consensus size: 39
215626 GATTCACTCT
* *
215636 CTGCTCCAGAGAAGCCGAACCCACCCGCAGATGACGGAT
1 CTGCTCCAGAGAAGCCGAACCCGCCCGCAGATGACGGAG
** *
215675 CTAATCCAGAGAAGCCGAACCCGCCCGTAGATGACGGAG
1 CTGCTCCAGAGAAGCCGAACCCGCCCGCAGATGACGGAG
* * *
215714 CTTCTTCAGAGAAGACGAACCCGCCCGCAGATGACGGAG
1 CTGCTCCAGAGAAGCCGAACCCGCCCGCAGATGACGGAG
* *
215753 CTGCTACAGAGAAGCCGAACCCACCCCGCAGATGACGGAG
1 CTGCTCCAGAGAAGCCGAACCC-GCCCGCAGATGACGGAG
* *
215793 CTACTTCAGAGAAGCCGAACCCGCCCGCAGATGACGGAG
1 CTGCTCCAGAGAAGCCGAACCCGCCCGCAGATGACGGAG
* *
215832 CTGCTACAGAGAAGACGAACCCGCCCGCAGATGACGGAG
1 CTGCTCCAGAGAAGCCGAACCCGCCCGCAGATGACGGAG
215871 CTGCTCCAGAGAAGCCGAACC
1 CTGCTCCAGAGAAGCCGAACC
215892 ATCCGCCGAG
Statistics
Matches: 194, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
39 158 0.81
40 36 0.19
ACGTcount: A:0.29, C:0.33, G:0.28, T:0.10
Consensus pattern (39 bp):
CTGCTCCAGAGAAGCCGAACCCGCCCGCAGATGACGGAG
Found at i:215843 original size:118 final size:117
Alignment explanation
Indices: 215636--215891 Score: 440
Period size: 118 Copynumber: 2.2 Consensus size: 117
215626 GATTCACTCT
*
215636 CTGCTCCAGAGAAGCCGAACCCACCCGCAGATGACGGATCTAATCCAGAGAAGCCGAACCCGCCC
1 CTGCTCCAGAGAAGCCGAACCCACCCGCAGATGACGGAGCTAATCCAGAGAAGCCGAACCCGCCC
* * *
215701 GTAGATGACGGAGCTTCTTCAGAGAAGACGAACCCGCCCGCAGATGACGGAG
66 GCAGATGACGGAGCTGCTACAGAGAAGACGAACCCGCCCGCAGATGACGGAG
* * *
215753 CTGCTACAGAGAAGCCGAACCCACCCCGCAGATGACGGAGCTACTTCAGAGAAGCCGAACCCGCC
1 CTGCTCCAGAGAAGCCGAACCCA-CCCGCAGATGACGGAGCTAATCCAGAGAAGCCGAACCCGCC
215818 CGCAGATGACGGAGCTGCTACAGAGAAGACGAACCCGCCCGCAGATGACGGAG
65 CGCAGATGACGGAGCTGCTACAGAGAAGACGAACCCGCCCGCAGATGACGGAG
215871 CTGCTCCAGAGAAGCCGAACC
1 CTGCTCCAGAGAAGCCGAACC
215892 ATCCGCCGAG
Statistics
Matches: 130, Mismatches: 8, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
117 22 0.17
118 108 0.83
ACGTcount: A:0.29, C:0.33, G:0.28, T:0.10
Consensus pattern (117 bp):
CTGCTCCAGAGAAGCCGAACCCACCCGCAGATGACGGAGCTAATCCAGAGAAGCCGAACCCGCCC
GCAGATGACGGAGCTGCTACAGAGAAGACGAACCCGCCCGCAGATGACGGAG
Found at i:221750 original size:21 final size:21
Alignment explanation
Indices: 221723--221763 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
221713 GGATTATTAT
*
221723 TAAATTTTAAA-AATTATAAA
1 TAAAATTTAAACAATTATAAA
*
221743 TAAAATTTAAACAGTTATAAA
1 TAAAATTTAAACAATTATAAA
221764 ATTATCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAAATTTAAACAATTATAAA
Found at i:221821 original size:25 final size:25
Alignment explanation
Indices: 221792--221841 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
221782 GAATTTTTAC
*
221792 AAAATAGTCATTAAATTTATCATAT
1 AAAATAGTAATTAAATTTATCATAT
* * *
221817 AAAATATTAATTTAATTTATTATAT
1 AAAATAGTAATTAAATTTATCATAT
221842 TTCTTACAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
AAAATAGTAATTAAATTTATCATAT
Done.