Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 395 of 438
Found at i:123091243 original size:21 final size:22
Alignment explanation
Indices: 123091212--123091269 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
123091202 GTTGAACCGA
* *
123091212 TTTAATAATTTTTTTTTAATTT
1 TTTAATAATTTTTTATGAATTT
123091234 TTTAA-AATTTTTTATGAA-TT
1 TTTAATAATTTTTTATGAATTT
*
123091254 TTTAATTAATTATTTA
1 TTTAA-TAATTTTTTA
123091270 ACTATTGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 7 0.23
21 11 0.35
22 13 0.42
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTAATAATTTTTTATGAATTT
Found at i:123092454 original size:22 final size:22
Alignment explanation
Indices: 123092409--123092451 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
123092399 ATTAAATCTC
*
123092409 TTAAAATCTTAAAAAATTTTAA
1 TTAAAATCTTAAAAAATTTAAA
*
123092431 TTAAAATCTT-CAAAATTTAAA
1 TTAAAATCTTAAAAAATTTAAA
123092452 ATTTCTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAATCTTAAAAAATTTAAA
Found at i:123092672 original size:21 final size:21
Alignment explanation
Indices: 123092646--123092701 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
123092636 AACAACGGTG
*
123092646 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
123092667 GCGGTGAGATTGGATATTGTA
1 GCGGTGAGATTAGATACTGTA
123092688 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
123092702 AACAATGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.38, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:123093352 original size:27 final size:28
Alignment explanation
Indices: 123093315--123093370 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
123093305 ATTTTATCAT
123093315 ATAAATTTAAAA-AATTAT-GAAAATGAC
1 ATAAATTTAAAATAATTATAG-AAATGAC
*
123093342 ATAACTTTAAAATTAATTATAGAAATGAC
1 ATAAATTTAAAA-TAATTATAGAAATGAC
123093371 CTTGTTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 11 0.44
29 13 0.52
30 1 0.04
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.32
Consensus pattern (28 bp):
ATAAATTTAAAATAATTATAGAAATGAC
Found at i:123099064 original size:45 final size:46
Alignment explanation
Indices: 123099015--123099108 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
123099005 TAATTTAAAA
123099015 TTTCAAGTTTGT-ATTAATTTAATTATAACAAATGTTTGACTTAAT
1 TTTCAAGTTTGTAATTAATTTAATTATAACAAATGTTTGACTTAAT
* *
123099060 TTTCAAGTTTGTAATTAATTTAGTTATAGCAAATGTTTGACTTAAT
1 TTTCAAGTTTGTAATTAATTTAATTATAACAAATGTTTGACTTAAT
123099106 TTT
1 TTT
123099109 ATTTGAAAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 12 0.26
46 34 0.74
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (46 bp):
TTTCAAGTTTGTAATTAATTTAATTATAACAAATGTTTGACTTAAT
Found at i:123102212 original size:68 final size:70
Alignment explanation
Indices: 123102140--123102337 Score: 294
Period size: 71 Copynumber: 2.8 Consensus size: 70
123102130 ACACCCTGTA
* * * *
123102140 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
123102202 ATAAAT
65 ATAAAT
*
123102208 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
123102273 ATAAAT
65 ATAAAT
*
123102279 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACG
123102338 AGACAAATCG
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 24 0.20
69 3 0.02
70 1 0.01
71 93 0.77
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:123102251 original size:41 final size:41
Alignment explanation
Indices: 123102206--123102323 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
123102196 TGAAAGATAA
123102206 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
123102247 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
123102277 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
123102318 ATGTAG
1 ATGTAG
123102324 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:123102263 original size:71 final size:71
Alignment explanation
Indices: 123102174--123102337 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
123102164 GAGATGTATC
123102174 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
123102239 AGGACA
66 AGGACA
123102245 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
123102310 AGGACA
66 AGGACA
123102316 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
123102338 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:123109829 original size:41 final size:41
Alignment explanation
Indices: 123109784--123109901 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
123109774 TGAAAGATAA
123109784 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
123109825 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
123109855 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
123109896 ATGTAG
1 ATGTAG
123109902 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:123109840 original size:71 final size:71
Alignment explanation
Indices: 123109752--123109915 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
123109742 GAGATGTATC
123109752 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
123109817 AGGACA
66 AGGACA
123109823 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
123109888 AGGACA
66 AGGACA
123109894 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
123109916 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:123112310 original size:11 final size:11
Alignment explanation
Indices: 123112294--123112320 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
123112284 TTCGTATGAT
123112294 AATTGTGGATA
1 AATTGTGGATA
123112305 AATTGTGGATA
1 AATTGTGGATA
123112316 AATTG
1 AATTG
123112321 CCTTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (11 bp):
AATTGTGGATA
Found at i:123119781 original size:15 final size:15
Alignment explanation
Indices: 123119763--123119792 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
123119753 TATAAAAGTG
123119763 TTTGATATATTAATA
1 TTTGATATATTAATA
123119778 TTTGATATATTAATA
1 TTTGATATATTAATA
123119793 AAAATTAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
TTTGATATATTAATA
Found at i:123120678 original size:2 final size:2
Alignment explanation
Indices: 123120673--123120704 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
123120663 TTCAACATTT
123120673 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
123120705 CATGATTTTC
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):
TA
Found at i:123120830 original size:23 final size:25
Alignment explanation
Indices: 123120802--123120853 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
123120792 ATTAATTGGA
*
123120802 TAAATTCTGAATAT-T-AAAAGTAT
1 TAAATTCTAAATATCTAAAAAGTAT
*
123120825 TAAATTTTAAATATCTAAAAAGTAT
1 TAAATTCTAAATATCTAAAAAGTAT
123120850 TAAA
1 TAAA
123120854 GATGGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.48
24 1 0.04
25 12 0.48
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (25 bp):
TAAATTCTAAATATCTAAAAAGTAT
Found at i:123128165 original size:28 final size:27
Alignment explanation
Indices: 123128104--123128171 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
123128094 CTAAATTCAA
* * *
123128104 ATTAAATAAGTTT-AAAATTATTTTTAT
1 ATTATATAA-TTTAAAAATTATATATAT
123128131 ATATATATAATTTAAAAATTATATATATT
1 AT-TATATAATTTAAAAATTATATATA-T
123128160 ATTATA-AATTTA
1 ATTATATAATTTA
123128172 TATTTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 11 0.31
28 21 0.60
29 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (27 bp):
ATTATATAATTTAAAAATTATATATAT
Found at i:123128173 original size:18 final size:17
Alignment explanation
Indices: 123128145--123128187 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
123128135 ATATAATTTA
123128145 AAAATTATATATATTATT
1 AAAATT-TATATATTATT
* *
123128163 ATAAATTTATATTTTAAT
1 A-AAATTTATATATTATT
123128181 AAAATTT
1 AAAATTT
123128188 GAAACCGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 11 0.50
19 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAATTTATATATTATT
Found at i:123129671 original size:6 final size:6
Alignment explanation
Indices: 123129660--123129701 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
123129650 CTGTCCATTG
123129660 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
1 TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC TAATAC
123129702 GTGACATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
TAATAC
Found at i:123132943 original size:19 final size:19
Alignment explanation
Indices: 123132919--123132955 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
123132909 CGTTCATGTG
*
123132919 TTTTAACAATACTAGTGGT
1 TTTTAACAATACAAGTGGT
123132938 TTTTAACAATACAAGTGG
1 TTTTAACAATACAAGTGG
123132956 AAACATGCGT
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:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTTAACAATACAAGTGGT
Found at i:123137357 original size:20 final size:21
Alignment explanation
Indices: 123137322--123137360 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
123137312 TGAGGTAGTT
123137322 TTGAAATGGCAAAATATTAAA
1 TTGAAATGGCAAAATATTAAA
*
123137343 TTGAAAT-GTAAAATATTA
1 TTGAAATGGCAAAATATTA
123137361 CATGGAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (21 bp):
TTGAAATGGCAAAATATTAAA
Found at i:123142824 original size:108 final size:108
Alignment explanation
Indices: 123142635--123142860 Score: 434
Period size: 108 Copynumber: 2.1 Consensus size: 108
123142625 ACTTAGCGTG
*
123142635 TTAACAGTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAAACAT
1 TTAACATTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAAACAT
123142700 TGTGTGTTTCTCTCATTACTTTACTCCTTACTCTACTTTGAAT
66 TGTGTGTTTCTCTCATTACTTTACTCCTTACTCTACTTTGAAT
*
123142743 TTAACATTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAGACAT
1 TTAACATTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAAACAT
123142808 TGTGTGTTTCTCTCATTACTTTACTCCTTACTCTACTTTGAAT
66 TGTGTGTTTCTCTCATTACTTTACTCCTTACTCTACTTTGAAT
123142851 TTAACATTTA
1 TTAACATTTA
123142861 TGTTTGTTCC
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 116 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (108 bp):
TTAACATTTACGTGTTTAAGGGTGTTTGAATAGAACCATTGTGTTTGAATTGCGTTAACAAACAT
TGTGTGTTTCTCTCATTACTTTACTCCTTACTCTACTTTGAAT
Found at i:123147722 original size:69 final size:69
Alignment explanation
Indices: 123147607--123147745 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
123147597 TACACAATTA
*
123147607 TCATATGTGGGTGTCTAATTTCATAATGTATGATACTGTCAGTAGCTCTAATTTTATGGGTGAAT
1 TCATATGTGGGTGTCTAATTTCATAATGTATGATACTGTCAATAGCTCTAATTTTATGGGTGAAT
123147672 TTTT
66 TTTT
123147676 TCATATGTGGGTGTCTAATTTCATAATGTATGATACTGTCAATAGCTCTAATTTTATGGGTGAAT
1 TCATATGTGGGTGTCTAATTTCATAATGTATGATACTGTCAATAGCTCTAATTTTATGGGTGAAT
123147741 TTTT
66 TTTT
123147745 T
1 T
123147746 TCCGGTTTAC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.25, C:0.10, G:0.19, T:0.45
Consensus pattern (69 bp):
TCATATGTGGGTGTCTAATTTCATAATGTATGATACTGTCAATAGCTCTAATTTTATGGGTGAAT
TTTT
Found at i:123148986 original size:16 final size:16
Alignment explanation
Indices: 123148952--123148994 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
123148942 AGCAGTATAG
*
123148952 ATATATAAAATCAATA
1 ATATATAAAATCAAAA
123148968 ATATATAAAAT-ATAAA
1 ATATATAAAATCA-AAA
123148984 ATATAGTAAAA
1 ATATA-TAAAA
123148995 AGATACGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 18 0.75
17 5 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
ATATATAAAATCAAAA
Found at i:123149596 original size:8 final size:8
Alignment explanation
Indices: 123149579--123149640 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
123149569 TGTATTGGAA
*
123149579 TTTAATTT
1 TTTAAATT
123149587 TTTAAATT
1 TTTAAATT
123149595 TTTAAATT
1 TTTAAATT
**
123149603 TCAAAATT
1 TTTAAATT
123149611 CTGATTAAATT
1 -T--TTAAATT
*
123149622 ATTAAATT
1 TTTAAATT
*
123149630 TTTTAATT
1 TTTAAATT
123149638 TTT
1 TTT
123149641 TTTATTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
8 37 0.86
9 1 0.02
11 5 0.12
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (8 bp):
TTTAAATT
Found at i:123156978 original size:12 final size:12
Alignment explanation
Indices: 123156963--123156998 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
123156953 AAGAAAGGAG
123156963 AAGAGAAGAAAA
1 AAGAGAAGAAAA
*
123156975 AAGAGAAGGAAA
1 AAGAGAAGAAAA
*
123156987 AAGAAAAGAAAA
1 AAGAGAAGAAAA
123156999 GAGAAGGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAGAGAAGAAAA
Found at i:123157004 original size:22 final size:23
Alignment explanation
Indices: 123156952--123157005 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
123156942 AAATAAAGGG
*
123156952 AAAGA-AAGGAGAAGAGAAGAAA
1 AAAGAGAAGGAGAAAAGAAGAAA
123156974 AAAGAGAAGGA-AAAAGAA-AAGA
1 AAAGAGAAGGAGAAAAGAAGAA-A
123156996 AAAGAGAAGG
1 AAAGAGAAGG
123157006 TATAATTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 22 0.76
23 5 0.17
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (23 bp):
AAAGAGAAGGAGAAAAGAAGAAA
Found at i:123157125 original size:26 final size:26
Alignment explanation
Indices: 123157096--123157145 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
123157086 TTGTTGTTAG
* *
123157096 TTATTATTATTGTTAATACAAAACCC
1 TTATAATTATTGTTAATAAAAAACCC
*
123157122 TTATAATTATTGTTAGTAAAAAAC
1 TTATAATTATTGTTAATAAAAAAC
123157146 TATTATTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (26 bp):
TTATAATTATTGTTAATAAAAAACCC
Found at i:123157151 original size:26 final size:26
Alignment explanation
Indices: 123157096--123157151 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
123157086 TTGTTGTTAG
* * *
123157096 TTATTATTATTGTTAATACAAAACCC
1 TTATAATTATTGTTAATAAAAAACCA
* *
123157122 TTATAATTATTGTTAGTAAAAAACTA
1 TTATAATTATTGTTAATAAAAAACCA
123157148 TTAT
1 TTAT
123157152 TAGGATTGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (26 bp):
TTATAATTATTGTTAATAAAAAACCA
Found at i:123157196 original size:36 final size:37
Alignment explanation
Indices: 123157127--123157207 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 37
123157117 AACCCTTATA
* * *
123157127 ATTATTGTTAGTAAAAAACTATTATTAGGATTGTTGGTT
1 ATTATTGTTAGTAAAAAACCATAATT--GATTGTTAGTT
*
123157166 ATTATTGTTAGTAAAAAACCCTAATT-ATTGTTAGTT
1 ATTATTGTTAGTAAAAAACCATAATTGATTGTTAGTT
123157202 ATTATT
1 ATTATT
123157208 ATTGTTGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 15 0.39
39 23 0.61
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (37 bp):
ATTATTGTTAGTAAAAAACCATAATTGATTGTTAGTT
Found at i:123157207 original size:39 final size:37
Alignment explanation
Indices: 123157122--123157213 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 37
123157112 TACAAAACCC
*
123157122 TTATAATTATTGTTAGTAAAAAACTATTATTAGGATTG
1 TTATTATTATTGTTAGTAAAAAACTATTATTA-GATTG
*
123157160 TTGGTTATTATTGTTAGTAAAAAACCCTAATTATT-G-TTAG
1 TT-ATTATTATTGTTAGTAAAAAA--CT-ATTATTAGATT-G
123157200 TTATTATTATTGTT
1 TTATTATTATTGTT
123157214 GATTTATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
38 2 0.04
39 32 0.70
40 4 0.09
41 2 0.04
42 6 0.13
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (37 bp):
TTATTATTATTGTTAGTAAAAAACTATTATTAGATTG
Found at i:123157381 original size:21 final size:21
Alignment explanation
Indices: 123157355--123157398 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
123157345 AATAAAATAA
123157355 AATACCAAAATAGGTTGTTTG
1 AATACCAAAATAGGTTGTTTG
123157376 AATACCAAAATAGGTTGTTTG
1 AATACCAAAATAGGTTGTTTG
123157397 AA
1 AA
123157399 AGATTAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (21 bp):
AATACCAAAATAGGTTGTTTG
Found at i:123160238 original size:139 final size:139
Alignment explanation
Indices: 123160056--123160391 Score: 568
Period size: 139 Copynumber: 2.4 Consensus size: 139
123160046 TATTTCTAAA
* * *
123160056 ATTTTTAAAATTTTCGGATTCTA-TTTTTAAAATATACTATTTTCATATTTTATTTTTTTATCTT
1 ATTTCTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTATCTT
* * *
123160120 ATTTTAGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTTTAAATAACCCTGATTTTGTCCC
66 ATTTTAGTACATAATGTTTCAAATGTATTATTTTACTGTTTTTGAAATAACCCTGATTTTGTCCA
123160185 TTTCTTTGT
131 TTTCTTTGT
*
123160194 ATTTCTAAAATATTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTATCTT
1 ATTTCTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTATCTT
123160259 ATTTTAGTACATAATGTTTCAAATGTATTATTTTACTGTTTTTGAAATAACCCTGATTTTGTCCA
66 ATTTTAGTACATAATGTTTCAAATGTATTATTTTACTGTTTTTGAAATAACCCTGATTTTGTCCA
*
123160324 TTTGTTTGT
131 TTTCTTTGT
*
123160333 A-TTCTTAAAATTTTCGGATTTTATTTTTTAAAATATATTATTTTCGTATTTTATTTTTT
1 ATTTC-TAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTT
123160392 ATACCATTTT
Statistics
Matches: 186, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
138 23 0.12
139 163 0.88
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.57
Consensus pattern (139 bp):
ATTTCTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCGTATTTTATTTTTTTATCTT
ATTTTAGTACATAATGTTTCAAATGTATTATTTTACTGTTTTTGAAATAACCCTGATTTTGTCCA
TTTCTTTGT
Found at i:123160445 original size:17 final size:16
Alignment explanation
Indices: 123160409--123160487 Score: 79
Period size: 16 Copynumber: 4.9 Consensus size: 16
123160399 TTTCGTATTT
*
123160409 TATTGTATTTTTTTCA
1 TATTTTATTTTTTTCA
*
123160425 TATTTTATTTCTTTTCC
1 TATTTTATTT-TTTTCA
123160442 TATTTTA-TTTTTTCA
1 TATTTTATTTTTTTCA
***
123160457 TGAAGATATTTTTTTCA
1 T-ATTTTATTTTTTTCA
*
123160474 TATTTTCTTTTTTT
1 TATTTTATTTTTTT
123160488 ATACTATTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
15 6 0.12
16 23 0.46
17 21 0.42
ACGTcount: A:0.18, C:0.09, G:0.04, T:0.70
Consensus pattern (16 bp):
TATTTTATTTTTTTCA
Found at i:123160834 original size:11 final size:11
Alignment explanation
Indices: 123160802--123160835 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
123160792 ATAAATTTAT
*
123160802 AAATTAAATCT
1 AAATTAAATCA
123160813 AAATTAAATCA
1 AAATTAAATCA
*
123160824 AAATCAAATCA
1 AAATTAAATCA
123160835 A
1 A
123160836 CAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (11 bp):
AAATTAAATCA
Found at i:123161134 original size:27 final size:27
Alignment explanation
Indices: 123161103--123161173 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
123161093 GTCTTGTCAA
*
123161103 GGTGCCGCCGGTGGCAGTGGCAACATC
1 GGTGCCGCCTGTGGCAGTGGCAACATC
** * * *
123161130 GGTGCTACCTCTGGCATTGGCACCATC
1 GGTGCCGCCTGTGGCAGTGGCAACATC
123161157 GGTGCCGCCTGTGGCAG
1 GGTGCCGCCTGTGGCAG
123161174 GCCCACTACC
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.20
Consensus pattern (27 bp):
GGTGCCGCCTGTGGCAGTGGCAACATC
Found at i:123172852 original size:42 final size:42
Alignment explanation
Indices: 123172805--123172887 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
123172795 AGATAGACAG
* * * ** *
123172805 TTTCTAGGCTTCTCATTTGGGAACTTGGTTGCAGAATGGGCC
1 TTTCTAGACTTCTCACTTGGAAACTTGACTGAAGAATGGGCC
123172847 TTTCTAGACTTCTCACTTGGAAACTTGACTGAAGAATGGGC
1 TTTCTAGACTTCTCACTTGGAAACTTGACTGAAGAATGGGC
123172888 AGGACAAAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (42 bp):
TTTCTAGACTTCTCACTTGGAAACTTGACTGAAGAATGGGCC
Found at i:123175388 original size:52 final size:55
Alignment explanation
Indices: 123175282--123175388 Score: 150
Period size: 57 Copynumber: 2.0 Consensus size: 55
123175272 GATAGTTACC
*
123175282 TATCCATATCAATGATTTGTTACTTTTATTTATTTATTTATTTATCAATGTTTTTTT
1 TATCCATATCAATGATCTGTTAC--TTATTTATTTATTTATTTATCAATGTTTTTTT
*
123175339 TATCCATATCACTGATCTGTTAC-T-TTT-TTTATTTATTTATCAAT-TTTTTT
1 TATCCATATCAATGATCTGTTACTTATTTATTTATTTATTTATCAATGTTTTTT
123175389 AAATCTAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
51 6 0.12
52 17 0.35
53 3 0.06
54 1 0.02
57 21 0.44
ACGTcount: A:0.23, C:0.11, G:0.05, T:0.61
Consensus pattern (55 bp):
TATCCATATCAATGATCTGTTACTTATTTATTTATTTATTTATCAATGTTTTTTT
Found at i:123175666 original size:8 final size:7
Alignment explanation
Indices: 123175648--123175840 Score: 104
Period size: 7 Copynumber: 27.0 Consensus size: 7
123175638 ACTAATTAAT
123175648 CTAAACC
1 CTAAACC
123175655 CTAAATCC
1 CTAAA-CC
*
123175663 CTAACCC
1 CTAAACC
*
123175670 CTAACCC
1 CTAAACC
*
123175677 CTAACCC
1 CTAAACC
123175684 CT-AACC
1 CTAAACC
123175690 CATAAACC
1 C-TAAACC
*
123175698 TTAAACC
1 CTAAACC
* *
123175705 ATAAAAC
1 CTAAACC
*
123175712 ATAAACC
1 CTAAACC
*
123175719 CTTAACC
1 CTAAACC
*
123175726 CTTAACC
1 CTAAACC
*
123175733 CTTAACC
1 CTAAACC
*
123175740 CTTAACC
1 CTAAACC
*
123175747 ATTAAACC
1 -CTAAACC
*
123175755 TTAAA-C
1 CTAAACC
*
123175761 CTCAACCC
1 CT-AAACC
*
123175769 CTTAAAAC
1 C-TAAACC
*
123175777 TTAAACC
1 CTAAACC
123175784 CT-AACC
1 CTAAACC
*
123175790 CTTAACC
1 CTAAACC
123175797 CATAAACC
1 C-TAAACC
*
123175805 ATAAACC
1 CTAAACC
*
123175812 CTAATCC
1 CTAAACC
*
123175819 ATAAACC
1 CTAAACC
*
123175826 CATAATCC
1 C-TAAACC
*
123175834 ATAAACC
1 CTAAACC
123175841 TTATAATAGT
Statistics
Matches: 149, Mismatches: 27, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
6 12 0.08
7 106 0.71
8 30 0.20
9 1 0.01
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:123175725 original size:50 final size:50
Alignment explanation
Indices: 123175665--123175809 Score: 141
Period size: 50 Copynumber: 2.9 Consensus size: 50
123175655 CTAAATCCCT
* *
123175665 AACCCCTAACCCCTAACCCCTAACCCATAAACCTTAAACCATAAAACAT-A
1 AACCCTTAACCCTTAACCCCTAACCC-TAAACCTTAAACCATAAAACATCA
* * * *
123175715 AACCCTTAACCCTTAACCCTTAACCCTTAACCATTAAACC-TTAAACCTCA
1 AACCCTTAACCCTTAACCCCTAACCCTAAACC-TTAAACCATAAAACATCA
* ** * * *
123175765 ACCCCTTAAAACTTAAACCCTAACCCTTAACCCATAAACCATAAA
1 AACCCTTAACCCTTAACCCCTAACCC-TAAACCTTAAACCATAAA
123175810 CCCTAATCCA
Statistics
Matches: 76, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
49 11 0.14
50 58 0.76
51 7 0.09
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (50 bp):
AACCCTTAACCCTTAACCCCTAACCCTAAACCTTAAACCATAAAACATCA
Found at i:123176978 original size:38 final size:39
Alignment explanation
Indices: 123176911--123177001 Score: 112
Period size: 38 Copynumber: 2.3 Consensus size: 39
123176901 GGTGTACATA
*
123176911 TAGCGACGTTTTTAAAAAAGCGCCACTAATACTCAATCTT
1 TAGCGGCGTTTTT-AAAAAGCGCCACTAATACTCAATCTT
* * *
123176951 TAGCGGCGTTTTT-AAAAGCGCCGCTAATGCTCATTCTT
1 TAGCGGCGTTTTTAAAAAGCGCCACTAATACTCAATCTT
* *
123176989 TAGTGGCATTTTT
1 TAGCGGCGTTTTT
123177002 CATTCAAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 33 0.73
40 12 0.27
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (39 bp):
TAGCGGCGTTTTTAAAAAGCGCCACTAATACTCAATCTT
Found at i:123180305 original size:19 final size:19
Alignment explanation
Indices: 123180253--123180297 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
123180243 TGCCTCTTTT
*
123180253 TGCATT-CATTTCATTCATC
1 TGCATTACATTTCA-TCATA
123180272 TGCATTACATTTCATCATA
1 TGCATTACATTTCATCATA
123180291 TGCATTA
1 TGCATTA
123180298 AGTTTCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (19 bp):
TGCATTACATTTCATCATA
Found at i:123188819 original size:2 final size:2
Alignment explanation
Indices: 123188812--123188852 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
123188802 TGGTAATTTC
123188812 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
123188853 TCATCGGTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:123189231 original size:20 final size:20
Alignment explanation
Indices: 123189208--123189273 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
123189198 CAGTAATAGT
*
123189208 AGTAATTTATTCATATCAAC
1 AGTAATTAATTCATATCAAC
* *
123189228 AGTAATTCATCCATATCAAC
1 AGTAATTAATTCATATCAAC
*
123189248 AGT-ATTAATTCATTTCAAC
1 AGTAATTAATTCATATCAAC
123189267 AGTAATT
1 AGTAATT
123189274 CATATGATCG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.40
20 24 0.60
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (20 bp):
AGTAATTAATTCATATCAAC
Found at i:123189267 original size:19 final size:19
Alignment explanation
Indices: 123189216--123189270 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
123189206 GTAGTAATTT
*
123189216 ATTCATATCAACAGTAATTC
1 ATTCATATCAACAGT-ATTA
*
123189236 ATCCATATCAACAGTATTA
1 ATTCATATCAACAGTATTA
*
123189255 ATTCATTTCAACAGTA
1 ATTCATATCAACAGTA
123189271 ATTCATATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (19 bp):
ATTCATATCAACAGTATTA
Found at i:123189465 original size:23 final size:23
Alignment explanation
Indices: 123189435--123189522 Score: 78
Period size: 23 Copynumber: 3.9 Consensus size: 23
123189425 TGATAAATAA
*
123189435 TAAGCTCTATTGAGCTGAAACGG
1 TAAGCTCTATCGAGCTGAAACGG
123189458 TAAGCTCTATCGAGCT-AAACATGG
1 TAAGCTCTATCGAGCTGAAAC--GG
* *
123189482 --AGTTC-ATACGAGCTGAATCGG
1 TAAGCTCTAT-CGAGCTGAAACGG
123189503 TAAGCTCTAAT-GAGCTGAAA
1 TAAGCTCT-ATCGAGCTGAAA
123189523 ATAATAACCT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
21 4 0.08
22 14 0.27
23 30 0.58
24 2 0.04
25 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (23 bp):
TAAGCTCTATCGAGCTGAAACGG
Found at i:123189738 original size:2 final size:2
Alignment explanation
Indices: 123189731--123189766 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
123189721 ATTTCAAACC
123189731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
123189767 TCGATTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123191703 original size:44 final size:44
Alignment explanation
Indices: 123191488--123191713 Score: 138
Period size: 44 Copynumber: 5.1 Consensus size: 44
123191478 GAAATCAAGC
* * * **
123191488 CAAATCTTATCTCTCTGAAGATCCAGTGGAGCAGATTGAAGCCA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA
* * * *
123191532 CTAATCTTATGC-CCCTAAAGTTGCAGTGG-GACGGATTGAAATTATCA
1 CAAATCTTAT-CTCCCTGAAGTTGCAGTGGAG-CAGATTG-AAGT-T-A
** * **
123191579 TGGCAAATCTTATCTCCCTGAAGTTGCAAAGGAGCAGGTT--A-CCA
1 ---CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA
* * * * * * *
123191623 CAAATCTTTTCTTCCTAAAGATGTAATGGAGTAGATTGAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA
* *
123191667 CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA
123191711 CAA
1 CAA
123191714 GTCACAAATC
Statistics
Matches: 133, Mismatches: 36, Indels: 26
0.68 0.18 0.13
Matches are distributed among these distances:
41 29 0.22
43 2 0.02
44 68 0.51
45 3 0.02
47 2 0.02
49 1 0.01
50 27 0.20
51 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTTA
Found at i:123192913 original size:18 final size:18
Alignment explanation
Indices: 123192890--123192926 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
123192880 CCCACAGATC
123192890 GGCCAAAGAGGGGGTGGA
1 GGCCAAAGAGGGGGTGGA
123192908 GGCCAAAGAGGGGGTGGA
1 GGCCAAAGAGGGGGTGGA
123192926 G
1 G
123192927 AGAAAATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.11, G:0.57, T:0.05
Consensus pattern (18 bp):
GGCCAAAGAGGGGGTGGA
Found at i:123195682 original size:2 final size:2
Alignment explanation
Indices: 123195675--123195711 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
123195665 CTTTTCCAGT
123195675 TA TA TA TA TA 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 TA TA TA TA TA T
123195712 GTATTAATAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:123202008 original size:27 final size:29
Alignment explanation
Indices: 123201959--123202013 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
123201949 TTTTTTTTTT
* *
123201959 TTTCTTTATCATTTACTTCCTACTTAAAC
1 TTTCTTTATCATTTAATTACTACTTAAAC
123201988 TTTCTTT-T-ATTTAATTACTACTTAAA
1 TTTCTTTATCATTTAATTACTACTTAAA
123202014 TTTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.67
28 1 0.04
29 7 0.29
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTCTTTATCATTTAATTACTACTTAAAC
Found at i:123203579 original size:37 final size:36
Alignment explanation
Indices: 123203536--123203658 Score: 106
Period size: 37 Copynumber: 3.4 Consensus size: 36
123203526 TCACTTTTAG
*
123203536 TTTAATTTGGTAAACTAATATAAAGTAGTATCTAAAA
1 TTTAATTTGGTAAACTAATATAAAGTAATATCT-AAA
* ** * * * *
123203573 TTTAATTTGATTAAA--AATATTTAGTAACATTTTTAG
1 TTTAATTTG-GTAAACTAATATAAAGTAATA-TCTAAA
* *
123203609 TTTAATTTGGTAAACTAATACAAAGTAATTTCTAAA
1 TTTAATTTGGTAAACTAATATAAAGTAATATCTAAA
123203645 TATTAATTTGGTAA
1 T-TTAATTTGGTAA
123203659 GAAAATAATG
Statistics
Matches: 64, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
35 4 0.06
36 24 0.38
37 32 0.50
38 4 0.06
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (36 bp):
TTTAATTTGGTAAACTAATATAAAGTAATATCTAAA
Found at i:123203596 original size:73 final size:73
Alignment explanation
Indices: 123203518--123203654 Score: 213
Period size: 73 Copynumber: 1.9 Consensus size: 73
123203508 TTCATATTAA
* * *
123203518 ATTTAGTATCACTTTTAGTTTAATTTGGTAAACTAATATAAAGTAGTATCTAAA-ATTTAATTTG
1 ATTTAGTAACACTTTTAGTTTAATTTGGTAAACTAATACAAAGTAATATCTAAATA-TTAATTTG
123203582 ATTAAAAAT
65 ATTAAAAAT
* *
123203591 ATTTAGTAACATTTTTAGTTTAATTTGGTAAACTAATACAAAGTAATTTCTAAATATTAATTTG
1 ATTTAGTAACACTTTTAGTTTAATTTGGTAAACTAATACAAAGTAATATCTAAATATTAATTTG
123203655 GTAAGAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 57 0.98
74 1 0.02
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.45
Consensus pattern (73 bp):
ATTTAGTAACACTTTTAGTTTAATTTGGTAAACTAATACAAAGTAATATCTAAATATTAATTTGA
TTAAAAAT
Found at i:123207829 original size:31 final size:30
Alignment explanation
Indices: 123207763--123207829 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
123207753 TTAATGATAC
* *
123207763 ATAAACTAATTTAAAAACTTAAATATAATT
1 ATAAATTAATTTAAAAACTTAAATATAATG
* *
123207793 TTAAATTATATTTAAATAA-TTTAATATAATG
1 ATAAATTA-ATTTAAA-AACTTAAATATAATG
123207824 ATAAAT
1 ATAAAT
123207830 GTGTTGAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 6 0.20
31 22 0.73
32 2 0.07
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (30 bp):
ATAAATTAATTTAAAAACTTAAATATAATG
Found at i:123210685 original size:26 final size:26
Alignment explanation
Indices: 123210648--123210731 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
123210638 TGATACAAAT
* *
123210648 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
123210674 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
123210700 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
123210726 TGATAA
1 TGATAA
123210732 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:123212738 original size:136 final size:137
Alignment explanation
Indices: 123212493--123212778 Score: 529
Period size: 136 Copynumber: 2.1 Consensus size: 137
123212483 GAGTAGTCTC
123212493 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
123212558 TGTTATCTGAATAAGGGGCTAAGGCCCGGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
123212623 ACTGTTA
131 ACTGTTA
*
123212630 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
123212694 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
123212759 ACTGTTA
131 ACTGTTA
**
123212766 CCTGAATGGGCTT
1 CCCAAATGGGCTT
123212779 AAGCCCAATA
Statistics
Matches: 145, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 125 0.86
137 20 0.14
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:123213870 original size:2 final size:2
Alignment explanation
Indices: 123213863--123213888 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
123213853 TGAAAATGCA
123213863 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
123213889 CAACCATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123219174 original size:2 final size:2
Alignment explanation
Indices: 123219169--123219200 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
123219159 GAAACTAGGA
123219169 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
123219201 GATCATTAAA
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:123237563 original size:43 final size:43
Alignment explanation
Indices: 123237502--123237592 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
123237492 TGATATGGTT
** *
123237502 TTTAGCGGAGTTTATGGGGAAAGTGCTGCTAAAGATCATGTTC
1 TTTAGCGGAGTTTATGGGGAAAACGCCGCTAAAGATCATGTTC
* * *
123237545 TTTAGC-GACGTTTGTGGGGAAAACGCCGCTAAAGGTTATGTTC
1 TTTAGCGGA-GTTTATGGGGAAAACGCCGCTAAAGATCATGTTC
123237588 TTTAG
1 TTTAG
123237593 TGGCGCTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 2 0.05
43 39 0.95
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (43 bp):
TTTAGCGGAGTTTATGGGGAAAACGCCGCTAAAGATCATGTTC
Found at i:123250587 original size:17 final size:17
Alignment explanation
Indices: 123250565--123250599 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
123250555 AACAATTAAA
123250565 TAAATTGGAAATAAAAT
1 TAAATTGGAAATAAAAT
* *
123250582 TAAATTGGGAATTAAAT
1 TAAATTGGAAATAAAAT
123250599 T
1 T
123250600 CAGATTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (17 bp):
TAAATTGGAAATAAAAT
Found at i:123262253 original size:17 final size:19
Alignment explanation
Indices: 123262231--123262269 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
123262221 AGATGAACAT
*
123262231 AAATA-TAAATTATT-TAA
1 AAATATTAAAGTATTGTAA
123262248 AAATATTAAAGTATTGTAA
1 AAATATTAAAGTATTGTAA
123262267 AAA
1 AAA
123262270 AAATCTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 8 0.42
19 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AAATATTAAAGTATTGTAA
Found at i:123262273 original size:22 final size:21
Alignment explanation
Indices: 123262246--123262291 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
123262236 TAAATTATTT
123262246 AAAAAT-ATTAAAGTATTGTAAA
1 AAAAATCATTAAA--ATTGTAAA
*
123262268 AAAAATCTTTAAAATTGTAAA
1 AAAAATCATTAAAATTGTAAA
123262289 AAA
1 AAA
123262292 TGGTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 11 0.50
22 6 0.27
23 5 0.23
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.30
Consensus pattern (21 bp):
AAAAATCATTAAAATTGTAAA
Found at i:123268190 original size:24 final size:23
Alignment explanation
Indices: 123268151--123268198 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
123268141 TATTATTTTT
*
123268151 ATATATTATACCATAATAAATTAA
1 ATATATTATAACATAA-AAATTAA
* *
123268175 ATATATTATAATATAAATATTAA
1 ATATATTATAACATAAAAATTAA
123268198 A
1 A
123268199 AAATATGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATATTATAACATAAAAATTAA
Found at i:123269592 original size:21 final size:21
Alignment explanation
Indices: 123269568--123269610 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
123269558 ACTTTTAAAA
* *
123269568 TAGTTACTTTTGTT-TACGTTT
1 TAGTCACTTATGTTATA-GTTT
123269589 TAGTCACTTATGTTATAGTTT
1 TAGTCACTTATGTTATAGTTT
123269610 T
1 T
123269611 GTAATATCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (21 bp):
TAGTCACTTATGTTATAGTTT
Found at i:123275412 original size:27 final size:28
Alignment explanation
Indices: 123275357--123275412 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
123275347 AGCATTTAGA
* *
123275357 GACTCCAATTGCATAGGATAAAAATCAT
1 GACTCCAATTGCATAAGATAAAAAACAT
123275385 GACT-CAATTGCA-AAGATAATAAAACAT
1 GACTCCAATTGCATAAGATAA-AAAACAT
123275412 G
1 G
123275413 TCCAACCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 15 0.60
28 4 0.16
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.23
Consensus pattern (28 bp):
GACTCCAATTGCATAAGATAAAAAACAT
Found at i:123278457 original size:2 final size:2
Alignment explanation
Indices: 123278452--123278479 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
123278442 AATTAATTAA
123278452 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
123278480 TTTCCAGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123282686 original size:25 final size:26
Alignment explanation
Indices: 123282658--123282712 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
123282648 AGTTATATAA
*
123282658 TATATGATTATATTAA-G-TTAAATTT
1 TATATGATTATAATAATGATT-AATTT
*
123282683 TATA-GATTTTAATAATGATTAATTT
1 TATATGATTATAATAATGATTAATTT
123282708 TATAT
1 TATAT
123282713 ATATATCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
24 9 0.36
25 14 0.56
26 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (26 bp):
TATATGATTATAATAATGATTAATTT
Found at i:123290931 original size:6 final size:6
Alignment explanation
Indices: 123290920--123290945 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
123290910 ATTAAGAACT
123290920 TAAATA TAAATA TAAATA TAAATA TA
1 TAAATA TAAATA TAAATA TAAATA TA
123290946 TATTATCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:123295706 original size:20 final size:20
Alignment explanation
Indices: 123295683--123295729 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
123295673 AAATTTTTAA
123295683 AAAATAATAAAAATTATTTT
1 AAAATAATAAAAATTATTTT
* * *
123295703 AAAAT-TTAACAATTTTTTT
1 AAAATAATAAAAATTATTTT
123295722 AAAA-AATA
1 AAAATAATA
123295730 TATCCAAGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATAATAAAAATTATTTT
Found at i:123306658 original size:13 final size:13
Alignment explanation
Indices: 123306640--123306682 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
123306630 AGCTACCCCT
123306640 TTTATTTTATTTA
1 TTTATTTTATTTA
123306653 TTTATTATTATTT-
1 TTTATT-TTATTTA
*
123306666 GTTATATTTATTTA
1 TTTAT-TTTATTTA
123306680 TTT
1 TTT
123306683 TTATTATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:123306673 original size:19 final size:19
Alignment explanation
Indices: 123306640--123306690 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
123306630 AGCTACCCCT
123306640 TTTA-TTTTATT-TATTTA
1 TTTATTTTTATTATATTTA
*
123306657 -TTATTATTTGTTATATTTA
1 TTTATT-TTTATTATATTTA
123306676 TTTATTTTTATTATA
1 TTTATTTTTATTATA
123306691 CTAATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 3 0.11
17 1 0.04
18 5 0.18
19 14 0.50
20 5 0.18
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTATTTTTATTATATTTA
Found at i:123306697 original size:23 final size:23
Alignment explanation
Indices: 123306647--123306697 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
123306637 CCTTTTATTT
**
123306647 TATTTATTTATTATTATTTGTTA
1 TATTTATTTATTATTATTTACTA
*
123306670 TATTTATTTATTTTTATTATACTA
1 TATTTATTTATTATTATT-TACTA
123306694 -ATTT
1 TATTT
123306698 TTCTTATACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTATTTATTATTATTTACTA
Found at i:123306764 original size:11 final size:12
Alignment explanation
Indices: 123306742--123306776 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
123306732 TCTACTATTT
123306742 CTATTATTTTTA
1 CTATTATTTTTA
*
123306754 GTATT-TTTTTA
1 CTATTATTTTTA
123306765 CTATTATTTTTA
1 CTATTATTTTTA
123306777 TTACAATTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (12 bp):
CTATTATTTTTA
Found at i:123319007 original size:13 final size:14
Alignment explanation
Indices: 123318984--123319012 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
123318974 TTAGAATAAG
123318984 TAGATAAATTTATT
1 TAGATAAATTTATT
123318998 TAGA-AAATTTATT
1 TAGATAAATTTATT
123319011 TA
1 TA
123319013 TTTTATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
TAGATAAATTTATT
Found at i:123323998 original size:21 final size:21
Alignment explanation
Indices: 123323965--123324004 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
123323955 AAAATTTAGG
* *
123323965 ATATTAAATTAATTAATTTCA
1 ATATTAAAGTAATGAATTTCA
*
123323986 ATATTACAGTAATGAATTT
1 ATATTAAAGTAATGAATTT
123324005 AGAAGGGATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
ATATTAAAGTAATGAATTTCA
Found at i:123325057 original size:9 final size:9
Alignment explanation
Indices: 123325045--123325070 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
123325035 GAAGAAGAGG
123325045 AGGAGGAGA
1 AGGAGGAGA
123325054 AGGAGGAGA
1 AGGAGGAGA
123325063 AGGAGGAG
1 AGGAGGAG
123325071 GAGAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (9 bp):
AGGAGGAGA
Found at i:123325057 original size:12 final size:12
Alignment explanation
Indices: 123325037--123325075 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
123325027 AAGAAAAAGA
123325037 AGAA-GAGGAGG
1 AGAAGGAGGAGG
* *
123325048 AGGAGAAGGAGG
1 AGAAGGAGGAGG
123325060 AGAAGGAGGAGG
1 AGAAGGAGGAGG
123325072 AGAA
1 AGAA
123325076 AAAATGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 3 0.13
12 20 0.87
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (12 bp):
AGAAGGAGGAGG
Found at i:123325757 original size:3 final size:3
Alignment explanation
Indices: 123325749--123325782 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
123325739 TTGACACATT
* *
123325749 TTC TTC TTC TTT TTC TTC TTC TTT TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
123325783 CTATTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (3 bp):
TTC
Found at i:123325762 original size:12 final size:12
Alignment explanation
Indices: 123325747--123325782 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
123325737 TCTTGACACA
123325747 TTTTCTTCTTCT
1 TTTTCTTCTTCT
123325759 TTTTCTTCTTCT
1 TTTTCTTCTTCT
123325771 TTTTCTTCTTCT
1 TTTTCTTCTTCT
123325783 CTATTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTCTTCTTCT
Found at i:123327476 original size:2 final size:2
Alignment explanation
Indices: 123327464--123327501 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
123327454 CATGAAAGAG
*
123327464 TA TA TA CA 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
123327502 ATGTTCAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:123331950 original size:40 final size:40
Alignment explanation
Indices: 123331903--123331979 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
123331893 ACACCATGTG
*
123331903 GGGATAAAATCGACCCACCCAGCTCTACACACCAAGTATA
1 GGGATAAAATCGACCCACCCAGCCCTACACACCAAGTATA
*
123331943 GGGATAAAATCGACCCATCCAGCCCTACACACCAAGT
1 GGGATAAAATCGACCCACCCAGCCCTACACACCAAGT
123331980 GGTACTGTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.34, G:0.16, T:0.14
Consensus pattern (40 bp):
GGGATAAAATCGACCCACCCAGCCCTACACACCAAGTATA
Found at i:123339249 original size:13 final size:13
Alignment explanation
Indices: 123339231--123339255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
123339221 GGGCTCACAC
123339231 GCCCGTGTGGCCT
1 GCCCGTGTGGCCT
123339244 GCCCGTGTGGCC
1 GCCCGTGTGGCC
123339256 CACACGGCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.40, G:0.40, T:0.20
Consensus pattern (13 bp):
GCCCGTGTGGCCT
Found at i:123339654 original size:56 final size:56
Alignment explanation
Indices: 123339587--123339697 Score: 177
Period size: 56 Copynumber: 2.0 Consensus size: 56
123339577 ATCTTCTTAT
* * *
123339587 CTTCGACGAAAAACGGTGTTTTCTTGCTGTTTAAAACCCTGATTAATGATCCACAC
1 CTTCGACGAAAAACAGTGTTTCCTTGCTGTTTAAAACCCCGATTAATGATCCACAC
* *
123339643 CTTCGATGAAAAACAGTGTTTCCTTGCTGTTTAGAACCCCGATTAATGATCCACA
1 CTTCGACGAAAAACAGTGTTTCCTTGCTGTTTAAAACCCCGATTAATGATCCACA
123339698 GATCATTGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (56 bp):
CTTCGACGAAAAACAGTGTTTCCTTGCTGTTTAAAACCCCGATTAATGATCCACAC
Found at i:123341044 original size:21 final size:21
Alignment explanation
Indices: 123340987--123341117 Score: 86
Period size: 21 Copynumber: 5.9 Consensus size: 21
123340977 TAAAGCTATC
*
123340987 ACCCACCAATCACAACCAATTAT
1 ACCCTCCAA-CACAACCAATT-T
* *
123341010 AGCCT-CAGAAACAACCAATTT
1 ACCCTCCA-ACACAACCAATTT
*
123341031 ACCCTCCAACACAACC-ATGT
1 ACCCTCCAACACAACCAATTT
* *
123341051 ATCCTCCAAACACAACCAAATAT
1 ACCCTCC-AACACAACC-AATTT
*
123341074 ACCCTTCAAACACAACCATATATAT
1 ACCC-TCCAACACAACCA-AT-T-T
*
123341099 AACCTCCAAACACAACCAA
1 ACCCTCC-AACACAACCAA
123341118 GTATACCCAC
Statistics
Matches: 85, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
20 9 0.11
21 21 0.25
22 15 0.18
23 21 0.25
24 5 0.06
25 14 0.16
ACGTcount: A:0.44, C:0.37, G:0.02, T:0.17
Consensus pattern (21 bp):
ACCCTCCAACACAACCAATTT
Found at i:123341087 original size:23 final size:23
Alignment explanation
Indices: 123340997--123341152 Score: 110
Period size: 23 Copynumber: 7.0 Consensus size: 23
123340987 ACCCACCAAT
* *
123340997 CACAACCAATTATAGCC-TCAGAA
1 CACAACCAAATATACCCTTCA-AA
* *
123341020 -ACAACC-AATTTACCC-TCCAA
1 CACAACCAAATATACCCTTCAAA
* * *
123341040 CACAACC--ATGTATCCTCCAAA
1 CACAACCAAATATACCCTTCAAA
123341061 CACAACCAAATATACCCTTCAAA
1 CACAACCAAATATACCCTTCAAA
* *
123341084 CACAACCATATATATAACCTCCAAA
1 CACAACCA-A-ATATACCCTTCAAA
* **
123341109 CACAACCAAGTATACCCACCAAA
1 CACAACCAAATATACCCTTCAAA
* *
123341132 TACAA-CTAATATACCCTTCAA
1 CACAACCAAATATACCCTTCAA
123341153 TATATCCACT
Statistics
Matches: 106, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
20 8 0.08
21 24 0.23
22 18 0.17
23 34 0.32
24 2 0.02
25 20 0.19
ACGTcount: A:0.44, C:0.35, G:0.03, T:0.19
Consensus pattern (23 bp):
CACAACCAAATATACCCTTCAAA
Found at i:123353968 original size:16 final size:16
Alignment explanation
Indices: 123353918--123353970 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 16
123353908 CCTAAAATTA
123353918 TTAATTC-TAATTATT
1 TTAATTCTTAATTATT
* * *
123353933 TTAATATTTTATTTA-A
1 TTAAT-TCTTAATTATT
123353949 TTAATTCTTAATTATT
1 TTAATTCTTAATTATT
123353965 TTAATT
1 TTAATT
123353971 ATCTAATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 12 0.41
16 12 0.41
17 5 0.17
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAATTCTTAATTATT
Found at i:123353977 original size:24 final size:23
Alignment explanation
Indices: 123353925--123353971 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
123353915 TTATTAATTC
*
123353925 TAATT-ATT-TTAATATTTTATT
1 TAATTAATTCTTAATATTTTAAT
123353946 TAATTAATTCTTAATTATTTTAAT
1 TAATTAATTCTTAA-TATTTTAAT
123353970 TA
1 TA
123353972 TCTAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 5 0.23
22 3 0.14
23 4 0.18
24 10 0.45
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TAATTAATTCTTAATATTTTAAT
Found at i:123358474 original size:13 final size:14
Alignment explanation
Indices: 123358451--123358483 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
123358441 TTTATTTTAT
*
123358451 TAAAATTAAATAAA
1 TAAAATCAAATAAA
123358465 -AAAATCAAATAAA
1 TAAAATCAAATAAA
123358478 TAAAAT
1 TAAAAT
123358484 ATATAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAATCAAATAAA
Found at i:123362893 original size:19 final size:20
Alignment explanation
Indices: 123362864--123362904 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
123362854 ATAAAATATA
123362864 AAAATATATAGAATTTTATT
1 AAAATATATAGAATTTTATT
*
123362884 AAAA-ATATAGAATTTTTTT
1 AAAATATATAGAATTTTATT
123362903 AA
1 AA
123362905 TTTATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAATATATAGAATTTTATT
Found at i:123363103 original size:19 final size:19
Alignment explanation
Indices: 123363081--123363132 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
123363071 ATCTAATATT
**
123363081 TATTAAAAAATTTGGAAAA
1 TATTAAAAAATTTAAAAAA
*
123363100 TATTAAAAATTTTAAAAAA
1 TATTAAAAAATTTAAAAAA
*
123363119 TATAAAAAAATTTA
1 TATTAAAAAATTTA
123363133 TTAAAAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
TATTAAAAAATTTAAAAAA
Found at i:123363138 original size:21 final size:20
Alignment explanation
Indices: 123363104--123363146 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
123363094 GGAAAATATT
123363104 AAAAATTTTAAAAAATATAA
1 AAAAATTTTAAAAAATATAA
* *
123363124 AAAAATTTATTAAAAGTATAA
1 AAAAATTT-TAAAAAATATAA
123363145 AA
1 AA
123363147 GCCTAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAATTTTAAAAAATATAA
Found at i:123364966 original size:16 final size:16
Alignment explanation
Indices: 123364945--123365004 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
123364935 TGAGAAAACC
123364945 AAAAAGAAAAAGAAAG
1 AAAAAGAAAAAGAAAG
*
123364961 AAAAAGAAAAAGAAGG
1 AAAAAGAAAAAGAAAG
* *
123364977 AAGAAGAAGAAG-AAG
1 AAAAAGAAAAAGAAAG
123364992 AAGAAAAGAAAAA
1 -A-AAAAGAAAAA
123365005 CTAACGTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 2 0.06
16 26 0.72
17 8 0.22
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAG
Found at i:123364984 original size:3 final size:3
Alignment explanation
Indices: 123364948--123365001 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
123364938 GAAAACCAAA
* * *
123364948 AAG AAA AAG AAAG AAA AAG AAA AAG AAGG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG -AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG
123364995 AA- AAG AA
1 AAG AAG AA
123365002 AAACTAACGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:123364986 original size:19 final size:19
Alignment explanation
Indices: 123364945--123365004 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
123364935 TGAGAAAACC
123364945 AAAAAGAAAAAG-A--AAG
1 AAAAAGAAAAAGAAGGAAG
123364961 AAAAAGAAAAAGAAGGAAG
1 AAAAAGAAAAAGAAGGAAG
* * *
123364980 AAGAAGAAGAAGAAGAAAAG
1 AAAAAGAAAAAGAAG-GAAG
123365000 AAAAA
1 AAAAA
123365005 CTAACGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 12 0.33
17 1 0.03
19 16 0.44
20 7 0.19
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAGAAGGAAG
Found at i:123365988 original size:31 final size:29
Alignment explanation
Indices: 123365944--123366037 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 29
123365934 ACAAATTAAA
*
123365944 TTTTTTTATAATTTTAACAT-TTTTTCTAAT
1 TTTTTTTATAATTTTAA-ATATCTTTCT-AT
*
123365974 TTTTTTTCTAAATTTTAAATATCTTTCTA-
1 TTTTTTTAT-AATTTTAAATATCTTTCTAT
*
123366003 TTTTTTTATAATTTTGAATAT-TTT-TAT
1 TTTTTTTATAATTTTAAATATCTTTCTAT
123366030 TTTCTTTT
1 TTT-TTTT
123366038 CTGGATTTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
26 2 0.04
27 6 0.11
28 15 0.27
29 8 0.14
30 11 0.20
31 14 0.25
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.68
Consensus pattern (29 bp):
TTTTTTTATAATTTTAAATATCTTTCTAT
Found at i:123368758 original size:17 final size:16
Alignment explanation
Indices: 123368722--123368760 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
123368712 CAAAGGATTC
* *
123368722 ATTATTCATTTTTTAT
1 ATTATTAATTTTTTAA
123368738 ATTATTAATTATTTTAA
1 ATTATTAATT-TTTTAA
123368755 ATTATT
1 ATTATT
123368761 TTAGGGTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTATTAATTTTTTAA
Found at i:123369173 original size:23 final size:22
Alignment explanation
Indices: 123369147--123369189 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
123369137 AATTTCTTCT
123369147 TTTTCGTATTATTCATTTTAACC
1 TTTTCGTATTA-TCATTTTAACC
**
123369170 TTTTTTTATTATCATTTTAA
1 TTTTCGTATTATCATTTTAA
123369190 ACTTGTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.23, C:0.12, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTCGTATTATCATTTTAACC
Found at i:123369207 original size:21 final size:21
Alignment explanation
Indices: 123369158--123369207 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
123369148 TTTCGTATTA
* * **
123369158 TTCATTTTAACCTTTTTTTAT
1 TTCATTTTAAACTTGTTACAT
123369179 TATCATTTTAAACTTGTTACAT
1 T-TCATTTTAAACTTGTTACAT
123369201 TTCATTT
1 TTCATTT
123369208 GCGTTAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.02, T:0.60
Consensus pattern (21 bp):
TTCATTTTAAACTTGTTACAT
Found at i:123374897 original size:21 final size:21
Alignment explanation
Indices: 123374859--123374898 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
123374849 ACTACTCAAG
*
123374859 AGAAGCCGATTGATCCATCTC
1 AGAAGCCGATTCATCCATCTC
123374880 AGAAGCCGGATTCA-CCATC
1 AGAAGCC-GATTCATCCATC
123374899 AAGACTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAAGCCGATTCATCCATCTC
Found at i:123386981 original size:26 final size:26
Alignment explanation
Indices: 123386949--123387052 Score: 145
Period size: 26 Copynumber: 4.0 Consensus size: 26
123386939 TGAAATGCCC
*
123386949 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
123386975 ATTATGGAATATTTTCCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
123387001 ATCATAGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
123387027 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
123387053 GTCAATTTGT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 67 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:123390482 original size:31 final size:31
Alignment explanation
Indices: 123390414--123390473 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
123390404 CTTATTCATG
*
123390414 GATTACCCAACCACGATGACCTACCACCCCA
1 GATTGCCCAACCACGATGACCTACCACCCCA
* * *
123390445 GATTGCCCAACGACGATGGCTTACCACCC
1 GATTGCCCAACCACGATGACCTACCACCC
123390474 TGAATTGCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.28, C:0.42, G:0.15, T:0.15
Consensus pattern (31 bp):
GATTGCCCAACCACGATGACCTACCACCCCA
Found at i:123393487 original size:82 final size:82
Alignment explanation
Indices: 123393382--123393547 Score: 314
Period size: 82 Copynumber: 2.0 Consensus size: 82
123393372 TAAAATCTGC
123393382 TTATATATGGAAACTTATCTTATTGATTTGATTCCAATAAATCTGATTAAAATTTTAAATCAAAT
1 TTATATATGGAAACTTATCTTATTGATTTGATTCCAATAAATCTGATTAAAATTTTAAATCAAAT
123393447 TGAGTTAATGGTAGATT
66 TGAGTTAATGGTAGATT
*
123393464 TTATATATGGAAACTTATCTTATTGATTTGATTCCAATAAATCTGATTAAAATTTTATATCAAAT
1 TTATATATGGAAACTTATCTTATTGATTTGATTCCAATAAATCTGATTAAAATTTTAAATCAAAT
*
123393529 TGATTTAATGGTAGATT
66 TGAGTTAATGGTAGATT
123393546 TT
1 TT
123393548 GTGTATTTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (82 bp):
TTATATATGGAAACTTATCTTATTGATTTGATTCCAATAAATCTGATTAAAATTTTAAATCAAAT
TGAGTTAATGGTAGATT
Found at i:123395096 original size:17 final size:17
Alignment explanation
Indices: 123395074--123395114 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
123395064 ATGTGGTCGC
123395074 CCGTGTGCGAGACACGA
1 CCGTGTGCGAGACACGA
123395091 CCGTGTGCGAGACACGA
1 CCGTGTGCGAGACACGA
123395108 CCGTGTG
1 CCGTGTG
123395115 GTGGCCACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.37, T:0.15
Consensus pattern (17 bp):
CCGTGTGCGAGACACGA
Found at i:123396468 original size:2 final size:2
Alignment explanation
Indices: 123396461--123396490 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
123396451 ACCTATAACC
123396461 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
123396491 AATAATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123400395 original size:35 final size:35
Alignment explanation
Indices: 123400349--123400419 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
123400339 TTATCTTCAG
*
123400349 AGTTTGTTTCGTATAGATCATGTAATATTCCTTAC
1 AGTTTGGTTCGTATAGATCATGTAATATTCCTTAC
123400384 AGTTTGGTTCGTATAGATCATGTAATATTCCTTAC
1 AGTTTGGTTCGTATAGATCATGTAATATTCCTTAC
123400419 A
1 A
123400420 CTTATCTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (35 bp):
AGTTTGGTTCGTATAGATCATGTAATATTCCTTAC
Found at i:123403108 original size:91 final size:93
Alignment explanation
Indices: 123402951--123403135 Score: 248
Period size: 91 Copynumber: 2.0 Consensus size: 93
123402941 TTTAAAAACT
* * * *
123402951 AAAATATATTTAACATAATGATAAATATAAAAATTATATTTTTTCATTATATAATTATTAATTTA
1 AAAATATATTTAACATAATGATAAATATAAAAATTATATTATATAATTACATAATTATTAATTTA
* *
123403016 TTTATATAAATAAAGGAGTTATTAATTA
66 TTTATATAAATAAAAGAGTAATTAATTA
* * * * * *
123403044 AAAATATTTTTAACATAAT-A-ATATATAAATATTTTATTATATAATTACATATTTATTATTTTA
1 AAAATATATTTAACATAATGATAAATATAAAAATTATATTATATAATTACATAATTATTAATTTA
123403107 TTTATATAAATAAAAGAGTAATTAATTA
66 TTTATATAAATAAAAGAGTAATTAATTA
123403135 A
1 A
123403136 TATGTTGAGT
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
91 61 0.76
92 1 0.01
93 18 0.22
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (93 bp):
AAAATATATTTAACATAATGATAAATATAAAAATTATATTATATAATTACATAATTATTAATTTA
TTTATATAAATAAAAGAGTAATTAATTA
Found at i:123404557 original size:53 final size:52
Alignment explanation
Indices: 123404410--123404610 Score: 202
Period size: 52 Copynumber: 4.0 Consensus size: 52
123404400 TGACAGAAAA
* *
123404410 GATGTGATATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTAC
1 GATGTGATATGTGATTCCGTATAAGACCATAACTGGGCTATGGCATCGGTAC
* * **
123404462 AATGTGAT-T-CGAGTTCCCGTATAAGACCATAACTGGGCTATGGCATCGGTGT
1 GATGTGATATGTGA-TT-CCGTATAAGACCATAACTGGGCTATGGCATCGGTAC
* *
123404514 GATGTGATAATGTGATTCCGTATAAGACCATATCTGGGATATGGCATCGGT--
1 GATGTGAT-ATGTGATTCCGTATAAGACCATAACTGGGCTATGGCATCGGTAC
* ** * *
123404565 -ATGT--TATGTGA-TCCGTGTAAGACCATGGCAGGGCTATGGCTTCGGT
1 GATGTGATATGTGATTCCGTATAAGACCATAACTGGGCTATGGCATCGGT
123404611 GAGTGATGTG
Statistics
Matches: 128, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
46 29 0.23
47 6 0.05
48 1 0.01
50 5 0.04
51 3 0.02
52 47 0.37
53 32 0.25
54 3 0.02
55 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (52 bp):
GATGTGATATGTGATTCCGTATAAGACCATAACTGGGCTATGGCATCGGTAC
Found at i:123404620 original size:46 final size:47
Alignment explanation
Indices: 123404418--123404620 Score: 151
Period size: 46 Copynumber: 4.1 Consensus size: 47
123404408 AAGATGTGAT
* * *
123404418 ATGTGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTG
1 ATGTGATTCCGTATAAGACCATAGCAGGGATATGGCATCGGT---ATGTG
* * *
123404468 AT-TCGAGTTCCCGTATAAGACCATAACTGGGCTATGGCATCGGTGTGATGTG
1 ATGT-GA-TT-CCGTATAAGACCATAGCAGGGATATGGCATC-G-GT-ATGTG
* * *
123404520 ATAATGTGATTCCGTATAAGACCATATCTGGGATATGGCATCGGTATGTT
1 ---ATGTGATTCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTG
* * * *
123404570 ATGTGA-TCCGTGTAAGACCATGGCAGGGCTATGGCTTCGGTGA-GTG
1 ATGTGATTCCGTATAAGACCATAGCAGGGATATGGCATCGGT-ATGTG
123404616 ATGTG
1 ATGTG
123404621 TGACAATGTG
Statistics
Matches: 130, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
46 36 0.28
47 7 0.05
49 1 0.01
50 7 0.05
51 4 0.03
52 36 0.28
53 30 0.23
54 4 0.03
55 4 0.03
56 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (47 bp):
ATGTGATTCCGTATAAGACCATAGCAGGGATATGGCATCGGTATGTG
Found at i:123410258 original size:20 final size:20
Alignment explanation
Indices: 123410233--123410274 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
123410223 CAGTGAAAAT
123410233 ATTAGTAAAAGTGTTATGGC
1 ATTAGTAAAAGTGTTATGGC
123410253 ATTAGTAAAAGTGTTATGGC
1 ATTAGTAAAAGTGTTATGGC
123410273 AT
1 AT
123410275 CGACATGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.36
Consensus pattern (20 bp):
ATTAGTAAAAGTGTTATGGC
Found at i:123411318 original size:52 final size:53
Alignment explanation
Indices: 123411249--123411403 Score: 179
Period size: 52 Copynumber: 3.0 Consensus size: 53
123411239 GACGGAAAAG
* *
123411249 ATGTGATATG-TGCTTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
1 ATGTGATAAGATGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
** * * ***
123411301 ATGTGATTCGA-GTTTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTGTG
1 ATGTGATAAGATGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
* * * *
123411353 ATGTGATAATATGATTCCATATAAGACCATATCTGGGATATGGCATCGGTA
1 ATGTGATAAGATGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTA
123411404 TGTTATGTGA
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
52 52 0.61
53 33 0.39
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (53 bp):
ATGTGATAAGATGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACA
Found at i:123411441 original size:46 final size:52
Alignment explanation
Indices: 123411262--123411442 Score: 151
Period size: 52 Copynumber: 3.6 Consensus size: 52
123411252 TGATATGTGC
* * *** *** *
123411262 TTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATTCGA-GT
1 TTCCATATAAGACCATAGCTGGGCTATGGCATCAGTGTGATGT-ATAATATGA
*
123411314 TTCCGTATAAGACCATAGCTGGGCTATGGCATCAGTGTGATGTGATAATATGA
1 TTCCATATAAGACCATAGCTGGGCTATGGCATCAGTGTGATGT-ATAATATGA
* * *
123411367 TTCCATATAAGACCATATCTGGGATATGGCATC-G-GT-ATGT-T-ATGTGA
1 TTCCATATAAGACCATAGCTGGGCTATGGCATCAGTGTGATGTATAATATGA
* * *
123411414 -TCCATGTAAGACCATGGCAGGGCTATGGC
1 TTCCATATAAGACCATAGCTGGGCTATGGC
123411443 TTTGGTGTGT
Statistics
Matches: 111, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 24 0.22
47 5 0.05
48 1 0.01
50 4 0.04
51 2 0.02
52 44 0.40
53 31 0.28
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (52 bp):
TTCCATATAAGACCATAGCTGGGCTATGGCATCAGTGTGATGTATAATATGA
Found at i:123416082 original size:16 final size:15
Alignment explanation
Indices: 123416058--123416087 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
123416048 TTCAAAAATT
*
123416058 TTTTTTTTTTGAGTG
1 TTTTTGTTTTGAGTG
123416073 TTTTTGTTTTGAGTG
1 TTTTTGTTTTGAGTG
123416088 ATGAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (15 bp):
TTTTTGTTTTGAGTG
Found at i:123423956 original size:31 final size:30
Alignment explanation
Indices: 123423917--123423976 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
123423907 ACATGTACTA
123423917 TTTTTTATCAGTTTGGTCAT-TATACTTTAC
1 TTTTTTATCAGTTTGG-CATCTATACTTTAC
*
123423947 TTTTGTTATCAGTTTGGCCTCTATACTTTA
1 TTTT-TTATCAGTTTGGCATCTATACTTTA
123423977 ATTATGCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.22
31 21 0.78
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.55
Consensus pattern (30 bp):
TTTTTTATCAGTTTGGCATCTATACTTTAC
Found at i:123424082 original size:9 final size:9
Alignment explanation
Indices: 123424052--123424092 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
123424042 TCAAATTCAC
123424052 TTAAAAAT-
1 TTAAAAATA
*
123424060 TTAAAAAGCA
1 TTAAAAA-TA
123424070 -TAAAAATA
1 TTAAAAATA
123424078 TTAAAAATA
1 TTAAAAATA
123424087 TTAAAA
1 TTAAAA
123424093 TTTCAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 8 0.29
9 20 0.71
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
TTAAAAATA
Found at i:123424091 original size:18 final size:18
Alignment explanation
Indices: 123424052--123424101 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
123424042 TCAAATTCAC
123424052 TTAAAAATTTAAAAAGCA
1 TTAAAAATTTAAAAAGCA
*
123424070 -TAAAAATATTAAAAA-TA
1 TTAAAAAT-TTAAAAAGCA
123424087 TT-AAAATTTCAAAAA
1 TTAAAAATTT-AAAAA
123424102 AAATCATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 2 0.07
17 18 0.64
18 8 0.29
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (18 bp):
TTAAAAATTTAAAAAGCA
Found at i:123424123 original size:20 final size:20
Alignment explanation
Indices: 123424079--123424124 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
123424069 ATAAAAATAT
123424079 TAAAAATATTAAAATTTCAA
1 TAAAAATATTAAAATTTCAA
* *
123424099 AAAAAATCA-TAAAATTTCTA
1 TAAAAAT-ATTAAAATTTCAA
123424119 TAAAAA
1 TAAAAA
123424125 ACCCAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAAAATATTAAAATTTCAA
Found at i:123424365 original size:21 final size:21
Alignment explanation
Indices: 123424340--123424409 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
123424330 CATAAAAATG
*
123424340 TAAAAGAATTCGTAAAATTTC
1 TAAAAGAATTCATAAAATTTC
* *
123424361 TAAAAGAATACCATAAAATTCTT
1 TAAAAGAAT-TCATAAAATT-TC
*
123424384 TAAAA-AATTCATAAAAAATTC
1 TAAAAGAATTCAT-AAAATTTC
123424405 TAAAA
1 TAAAA
123424410 TTTTATAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
21 18 0.45
22 16 0.40
23 6 0.15
ACGTcount: A:0.56, C:0.10, G:0.04, T:0.30
Consensus pattern (21 bp):
TAAAAGAATTCATAAAATTTC
Found at i:123428094 original size:4 final size:4
Alignment explanation
Indices: 123428087--123428111 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
123428077 TAAACAAATG
123428087 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
123428112 GTGAGCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:123428679 original size:47 final size:46
Alignment explanation
Indices: 123428627--123428722 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 46
123428617 AATTTAGCGC
* *
123428627 TTCAAT-ATTT-ATAAATTCTATTAATTTGATTTTAATTTTTAAAAAAA
1 TTCAATAATTTAAT-AATT-TATTAATTTAATCTTAA-TTTTAAAAAAA
*
123428674 TTCAATAAATTTAATCATTTATTAATTTAATCTTAATTTTAAAAAAA
1 TTCAAT-AATTTAATAATTTATTAATTTAATCTTAATTTTAAAAAAA
123428721 TT
1 TT
123428723 AAGAATAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
47 19 0.44
48 15 0.35
49 7 0.16
50 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (46 bp):
TTCAATAATTTAATAATTTATTAATTTAATCTTAATTTTAAAAAAA
Found at i:123429268 original size:10 final size:10
Alignment explanation
Indices: 123429223--123429265 Score: 63
Period size: 9 Copynumber: 4.5 Consensus size: 10
123429213 ATAATACATC
123429223 AAATACATTA
1 AAATACATTA
123429233 AAA-ACATTA
1 AAATACATTA
123429242 AAA-ACATTA
1 AAATACATTA
*
123429251 AAATAAATTA
1 AAATACATTA
123429261 AAATA
1 AAATA
123429266 AATATTTTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 18 0.58
10 13 0.42
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (10 bp):
AAATACATTA
Found at i:123431132 original size:58 final size:58
Alignment explanation
Indices: 123431023--123431133 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
123431013 GTACACGGTA
* * * * * *
123431023 AAGGTATATGGCATAAGACCATGGATGAAAGACGCCATGGCGACAATATATAAAGTAT
1 AAGGTAAATGACATAAGACCATAGATGAAAGACGCCATGACAACAAGATATAAAGTAT
** *
123431081 AAGGTAAATGACATAAGACCATAGATGAAAGACGCTTTGACAACTAGATATAA
1 AAGGTAAATGACATAAGACCATAGATGAAAGACGCCATGACAACAAGATATAA
123431134 TGAGTAAGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.21
Consensus pattern (58 bp):
AAGGTAAATGACATAAGACCATAGATGAAAGACGCCATGACAACAAGATATAAAGTAT
Found at i:123433006 original size:26 final size:26
Alignment explanation
Indices: 123432957--123433006 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
123432947 GCTTTTAAAG
**
123432957 AAATATAAAAAATAAAATTTATAATA
1 AAATATAAAAAATAAAATAAATAATA
* *
123432983 AAATTTAAAAAATCAAATAAATAA
1 AAATATAAAAAATAAAATAAATAA
123433007 ATTTTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (26 bp):
AAATATAAAAAATAAAATAAATAATA
Done.