Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 189 of 310
Found at i:61595071 original size:100 final size:103
Alignment explanation
Indices: 61594882--61595131 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
61594872 ATTTGGGTAA
61594882 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
61594947 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
61594988 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
61595050 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
61595088 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
61595132 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:61603569 original size:26 final size:27
Alignment explanation
Indices: 61603529--61603579 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
61603519 TTCATATATT
*
61603529 TTATGTTTAAATATTT-TATTGAAGAA
1 TTATGTTTAAATATTTAAATTGAAGAA
*
61603555 TTATGTTTAATTATTTAAATTGAAG
1 TTATGTTTAAATATTTAAATTGAAG
61603580 TGGGATAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (27 bp):
TTATGTTTAAATATTTAAATTGAAGAA
Found at i:61603874 original size:3 final size:3
Alignment explanation
Indices: 61603866--61603913 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
61603856 TCTTCAAATC
61603866 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
61603914 GGCTTTAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:61613358 original size:50 final size:50
Alignment explanation
Indices: 61613284--61613462 Score: 166
Period size: 50 Copynumber: 3.4 Consensus size: 50
61613274 GAATAGGAAG
61613284 TAATAGATT-GAGTTATTAAGATTAATTAATTAAG-TTGGGTATTATGTAT
1 TAATAGATTAGAGTTATTAAGATTAATTAATT-AGTTTGGGTATTATGTAT
* * ** * *
61613333 TAATAGATTAGAGTTATTAAGATTAATTATTTTGAGTTATTAAGCAATTGGAATGGGAAG
1 TAATAGATTAGAGTTATTAAGATTAATTA-ATT-AG-T-TT-GGGTATT---AT--GTAT
*
61613393 TAATAGATTAGAGTTATTAAGATTAATTAATTAGTTTGGGTATTAGGTAT
1 TAATAGATTAGAGTTATTAAGATTAATTAATTAGTTTGGGTATTATGTAT
61613443 TAATAGATTAGA-TTAATTAA
1 TAATAGATTAGAGTT-ATTAA
61613463 TTTGGGTATT
Statistics
Matches: 104, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
49 11 0.11
50 38 0.37
51 4 0.04
52 1 0.01
54 2 0.02
55 8 0.08
56 2 0.02
57 1 0.01
58 4 0.04
59 2 0.02
60 31 0.30
ACGTcount: A:0.39, C:0.01, G:0.19, T:0.42
Consensus pattern (50 bp):
TAATAGATTAGAGTTATTAAGATTAATTAATTAGTTTGGGTATTATGTAT
Found at i:61613361 original size:27 final size:26
Alignment explanation
Indices: 61613284--61613376 Score: 76
Period size: 23 Copynumber: 3.8 Consensus size: 26
61613274 GAATAGGAAG
61613284 TAATAGATTGAGTTATTAAGATTAAT
1 TAATAGATTGAGTTATTAAGATTAAT
* *
61613310 TAATTA-AGTTG-GGTATTATG--T-AT
1 TAA-TAGA-TTGAGTTATTAAGATTAAT
61613333 TAATAGATTAGAGTTATTAAGATTAAT
1 TAATAGATT-GAGTTATTAAGATTAAT
*
61613360 T-AT--TTTGAGTTATTAAG
1 TAATAGATTGAGTTATTAAG
61613377 CAATTGGAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 19
0.69 0.06 0.24
Matches are distributed among these distances:
22 4 0.07
23 18 0.33
24 10 0.19
26 14 0.26
27 8 0.15
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (26 bp):
TAATAGATTGAGTTATTAAGATTAAT
Found at i:61613498 original size:40 final size:36
Alignment explanation
Indices: 61613412--61613489 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
61613402 AGAGTTATTA
*
61613412 AGATTA-ATTAATTAGTTTGGGTATTAGGTATTAAT
1 AGATTAGATTAATTAATTTGGGTATTAGGTATTAAT
*
61613447 AGATTAGATTAATTAATTTGGGTATTAGGTATTACT
1 AGATTAGATTAATTAATTTGGGTATTAGGTATTAAT
61613483 AGATTAG
1 AGATTAG
61613490 GGTTATTAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 6 0.15
36 34 0.85
ACGTcount: A:0.35, C:0.01, G:0.21, T:0.44
Consensus pattern (36 bp):
AGATTAGATTAATTAATTTGGGTATTAGGTATTAAT
Found at i:61613516 original size:23 final size:23
Alignment explanation
Indices: 61613452--61613523 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
61613442 TTAATAGATT
*
61613452 AGATTAATTAATTT-GGGTATTA
1 AGATTAATTAATTTAGGTTATTA
* *
61613474 GGTATT-ACTAGA-TTAGGGTTATTA
1 AG-ATTAATTA-ATTTA-GGTTATTA
61613498 AGATTAATTAATTTAGGTTATTA
1 AGATTAATTAATTTAGGTTATTA
61613521 AGA
1 AGA
61613524 AATTGGACTG
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 6 0.15
23 19 0.49
24 14 0.36
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.43
Consensus pattern (23 bp):
AGATTAATTAATTTAGGTTATTA
Found at i:61622206 original size:19 final size:20
Alignment explanation
Indices: 61622171--61622209 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61622161 TAGGGTTATG
61622171 AAAAGAAGAAGAGAGAATAA
1 AAAAGAAGAAGAGAGAATAA
*
61622191 AAAAGGAGAAGA-AGAATAA
1 AAAAGAAGAAGAGAGAATAA
61622210 GATAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.05
Consensus pattern (20 bp):
AAAAGAAGAAGAGAGAATAA
Found at i:61628285 original size:21 final size:21
Alignment explanation
Indices: 61628248--61628287 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61628238 TTATGTTGAT
*
61628248 TTATTTTTTTATGTATTTTAA
1 TTATTTTTATATGTATTTTAA
61628269 TTATTTTTCATAT-TATTTT
1 TTATTTTT-ATATGTATTTT
61628288 TATGTCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (21 bp):
TTATTTTTATATGTATTTTAA
Found at i:61628319 original size:31 final size:30
Alignment explanation
Indices: 61628249--61628321 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
61628239 TATGTTGATT
* *
61628249 TATTTTTTTATGTATTTTAATTATTTTTCA
1 TATTTTTTTATGTATTTTAATTATATTACA
61628279 TATTATTTTTATGTCATGTATTAATT-TATTACA
1 TATT-TTTTTATGT-AT-T-TTAATTATATTACA
61628312 -ATTTTTTTAT
1 TATTTTTTTAT
61628322 AATCATTGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
30 4 0.11
31 16 0.43
32 5 0.14
33 6 0.16
34 6 0.16
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (30 bp):
TATTTTTTTATGTATTTTAATTATATTACA
Found at i:61630997 original size:20 final size:19
Alignment explanation
Indices: 61630965--61631002 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
61630955 GAAAGGAAAC
*
61630965 AATGTCATCAATGTACAGA
1 AATGTCATAAATGTACAGA
61630984 AATGATCATAAATGTACAG
1 AATG-TCATAAATGTACAG
61631003 TGCAATGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (19 bp):
AATGTCATAAATGTACAGA
Found at i:61636137 original size:15 final size:16
Alignment explanation
Indices: 61636117--61636146 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61636107 TGCATGTTGG
61636117 AATATAAA-CTAGAAT
1 AATATAAATCTAGAAT
61636132 AATATAAATCTAGAA
1 AATATAAATCTAGAA
61636147 CTCAAACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (16 bp):
AATATAAATCTAGAAT
Found at i:61639603 original size:27 final size:28
Alignment explanation
Indices: 61639550--61639606 Score: 89
Period size: 27 Copynumber: 2.0 Consensus size: 28
61639540 TCCCCAATTC
*
61639550 TTCTCTTCAATTTTTTTTTTACTTTCCCT
1 TTCTCTTCAA-TTTTTTTTTACATTCCCT
61639579 TTCTCTTCAA-TTTTTTTTACATTCCCT
1 TTCTCTTCAATTTTTTTTTACATTCCCT
61639606 T
1 T
61639607 CCCTTTTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 17 0.63
29 10 0.37
ACGTcount: A:0.12, C:0.25, G:0.00, T:0.63
Consensus pattern (28 bp):
TTCTCTTCAATTTTTTTTTACATTCCCT
Found at i:61644345 original size:14 final size:13
Alignment explanation
Indices: 61644326--61644359 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
61644316 TAACATTTGC
61644326 AAAAAAGAACAAAA
1 AAAAAAGAA-AAAA
*
61644340 AAAAAAGAAAAGA
1 AAAAAAGAAAAAA
61644353 AAAAAAG
1 AAAAAAG
61644360 CTCACATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAA
Found at i:61644892 original size:13 final size:14
Alignment explanation
Indices: 61644865--61644897 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
61644855 GTTGTTTGAA
61644865 TTGGATTGAACCAT
1 TTGGATTGAACCAT
*
61644879 TTGG-TTGAATCAT
1 TTGGATTGAACCAT
61644892 TTGGAT
1 TTGGAT
61644898 CGAGAATCGA
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:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (14 bp):
TTGGATTGAACCAT
Found at i:61647432 original size:31 final size:34
Alignment explanation
Indices: 61647388--61647465 Score: 108
Period size: 32 Copynumber: 2.4 Consensus size: 34
61647378 TATAAAACTT
61647388 ATTTTATTGTTAATTTTGTTA-TATTTTAAAGAC
1 ATTTTATTGTTAATTTTGTTATTATTTTAAAGAC
*
61647421 ATTTT-TT-TTAATTTTGTTATTATTTTAGAGAC
1 ATTTTATTGTTAATTTTGTTATTATTTTAAAGAC
**
61647453 ATTTGCTTGTTAA
1 ATTTTATTGTTAA
61647466 GTTGCATCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 12 0.30
32 17 0.43
33 7 0.17
34 4 0.10
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.59
Consensus pattern (34 bp):
ATTTTATTGTTAATTTTGTTATTATTTTAAAGAC
Found at i:61647554 original size:18 final size:18
Alignment explanation
Indices: 61647531--61647570 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
61647521 GAAATATTTA
*
61647531 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
61647549 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
61647567 TTTT
1 TTTT
61647571 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:61654133 original size:21 final size:21
Alignment explanation
Indices: 61654107--61654147 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61654097 AGACGAGCAA
* *
61654107 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
61654128 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
61654148 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:61659942 original size:81 final size:81
Alignment explanation
Indices: 61659848--61660089 Score: 376
Period size: 81 Copynumber: 3.0 Consensus size: 81
61659838 CTTCTAGAGG
* * * * * *
61659848 TGGTTCTGATTTATCTCCTCCTCGGAAGCGGAGGGTTAGGAATGACACACCCTCACCAGAAGCTT
1 TGGTACTGATTTATCTCCTCCTAGGAAACGGAGGGTTCGGAATGACACACCTTCACCAGAACCTT
61659913 TAGTAAACAGAGCAGA
66 TAGTAAACAGAGCAGA
*
61659929 TGGTACTGATTTATCTCCTCCTAGGAAACGTAGGGTTCGGAATGACACACCTTCACCAGAACCTT
1 TGGTACTGATTTATCTCCTCCTAGGAAACGGAGGGTTCGGAATGACACACCTTCACCAGAACCTT
* *
61659994 TAGTAAACCGAACAGA
66 TAGTAAACAGAGCAGA
*
61660010 TGGTACTGATTTATCTCCTCCAAGGAAACGGAGGGTTCGGAATGACACACCTTCACCAGAACCTT
1 TGGTACTGATTTATCTCCTCCTAGGAAACGGAGGGTTCGGAATGACACACCTTCACCAGAACCTT
* *
61660075 TAGCAAACAGGGCAG
66 TAGTAAACAGAGCAG
61660090 GTGCTGGTCT
Statistics
Matches: 146, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 146 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (81 bp):
TGGTACTGATTTATCTCCTCCTAGGAAACGGAGGGTTCGGAATGACACACCTTCACCAGAACCTT
TAGTAAACAGAGCAGA
Found at i:61670741 original size:9 final size:9
Alignment explanation
Indices: 61670717--61670753 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
61670707 TGAGTTTTCG
*
61670717 AATTCAAAT
1 AATTCGAAT
*
61670726 AACTCGAAT
1 AATTCGAAT
61670735 AATTCGAAT
1 AATTCGAAT
61670744 AATTCGAAT
1 AATTCGAAT
61670753 A
1 A
61670754 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:61671151 original size:19 final size:17
Alignment explanation
Indices: 61671105--61671165 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 17
61671095 CTCCCCCCTA
61671105 TTTACTTTCCCTCAAACT
1 TTTACTTTCCC-CAAACT
61671123 TTTA--TTCCCCAAAACTT
1 TTTACTTTCCCC-AAAC-T
61671140 TTTACTTTCCCCCTAAACT
1 TTTACTTT-CCCC-AAACT
61671159 TTTACTT
1 TTTACTT
61671166 CTCACCCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
15 1 0.03
16 9 0.24
17 5 0.14
18 4 0.11
19 10 0.27
20 8 0.22
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (17 bp):
TTTACTTTCCCCAAACT
Found at i:61671173 original size:20 final size:20
Alignment explanation
Indices: 61671134--61671173 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
61671124 TTATTCCCCA
*
61671134 AAACTTTTTACTTTCCCCCT
1 AAACTTTTTACTTTCACCCT
61671154 AAAC-TTTTACTTCTCACCCT
1 AAACTTTTTACTT-TCACCCT
61671174 TTACTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (20 bp):
AAACTTTTTACTTTCACCCT
Found at i:61671354 original size:9 final size:9
Alignment explanation
Indices: 61671340--61671368 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
61671330 AATTTCACAT
61671340 TTTATATTA
1 TTTATATTA
61671349 TTTATATTA
1 TTTATATTA
61671358 TTTATATTA
1 TTTATATTA
61671367 TT
1 TT
61671369 GAATTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:61672167 original size:82 final size:82
Alignment explanation
Indices: 61672030--61672193 Score: 247
Period size: 82 Copynumber: 2.0 Consensus size: 82
61672020 TTGACAAAAG
* * *
61672030 CTACTTAATTAAACTTTTATCCAATAAACTTGTCATATATGTATTATCTTCATAGGATATTCATG
1 CTACTTAATTAAACTTTTATCCAATAAACTTATCATATATGTATTACCCTCATAGGATATTCATG
*
61672095 ATCCGTTTAGGTTAAAT
66 ATCCCTTTAGGTTAAAT
* * * *
61672112 CTACTTAATTAAACTTTTATCCAATGAACTTATTATATGTGTGTTACCCTCATAGGATATTCATG
1 CTACTTAATTAAACTTTTATCCAATAAACTTATCATATATGTATTACCCTCATAGGATATTCATG
*
61672177 GTCCCTTTAGGTTAAAT
66 ATCCCTTTAGGTTAAAT
61672194 ATAACCCGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (82 bp):
CTACTTAATTAAACTTTTATCCAATAAACTTATCATATATGTATTACCCTCATAGGATATTCATG
ATCCCTTTAGGTTAAAT
Found at i:61676910 original size:22 final size:22
Alignment explanation
Indices: 61676882--61676930 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
61676872 TCGCAGAGTC
* *
61676882 TCATACTACCTGTAAAGGGTTT
1 TCATACTACCTATAAAGGGCTT
61676904 TCATACTACCTATAAAGGGCTT
1 TCATACTACCTATAAAGGGCTT
61676926 TCATA
1 TCATA
61676931 TACTAGTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (22 bp):
TCATACTACCTATAAAGGGCTT
Found at i:61680897 original size:19 final size:18
Alignment explanation
Indices: 61680869--61680905 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
61680859 ATGTAAAAAT
61680869 TATATATTTAAAATATAAA
1 TATATATTTAAAA-ATAAA
*
61680888 TATATGTTTAAAAATAAA
1 TATATATTTAAAAATAAA
61680906 ATACGACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TATATATTTAAAAATAAA
Found at i:61680907 original size:19 final size:18
Alignment explanation
Indices: 61680864--61680908 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
61680854 TTTACATGTA
61680864 AAAATTATATATTTAAAAT
1 AAAA-TATATATTTAAAAT
*
61680883 ATAAATATATGTTTAAAAAT
1 A-AAATATATATTT-AAAAT
61680903 AAAATA
1 AAAATA
61680909 CGACACTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATATATATTTAAAAT
Found at i:61681263 original size:12 final size:11
Alignment explanation
Indices: 61681240--61681270 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
61681230 AAATATTTAG
61681240 TTTTAGTTTTT
1 TTTTAGTTTTT
61681251 TTTTAGTTTTT
1 TTTTAGTTTTT
61681262 TTTTA-TTTT
1 TTTTAGTTTT
61681271 AAATTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.10, C:0.00, G:0.06, T:0.84
Consensus pattern (11 bp):
TTTTAGTTTTT
Found at i:61689502 original size:37 final size:37
Alignment explanation
Indices: 61689452--61689524 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
61689442 CATTCTAATC
61689452 AATCAATTGAAATTTGGAGTAAACCCATAGGGAAATG
1 AATCAATTGAAATTTGGAGTAAACCCATAGGGAAATG
* *
61689489 AATCAATTGAAATTTGTAGTAAATCCATAGGGAAAT
1 AATCAATTGAAATTTGGAGTAAACCCATAGGGAAAT
61689525 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (37 bp):
AATCAATTGAAATTTGGAGTAAACCCATAGGGAAATG
Found at i:61689933 original size:5 final size:5
Alignment explanation
Indices: 61689923--61689954 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
61689913 ATACTAACTC
61689923 TATAA TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TATAA TA
61689955 ATTCACCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:61697750 original size:26 final size:27
Alignment explanation
Indices: 61697721--61697801 Score: 69
Period size: 31 Copynumber: 2.9 Consensus size: 27
61697711 TAAATCAAAT
61697721 AAAAAAAGATTAGATACCAAATTAGG-
1 AAAAAAAGATTAGATACCAAATTAGGC
*
61697747 AAAAGGAGTTAAG-TTAAGGTACCAAATTAGGC
1 AAAA--A---AAGATT-AGATACCAAATTAGGC
*
61697779 AAAAAAA-ATTAAATACCAAATTA
1 AAAAAAAGATTAGATACCAAATTA
61697802 AGATAAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 16
0.70 0.05 0.25
Matches are distributed among these distances:
26 15 0.34
27 4 0.09
28 1 0.02
30 3 0.07
31 17 0.39
32 4 0.09
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.21
Consensus pattern (27 bp):
AAAAAAAGATTAGATACCAAATTAGGC
Found at i:61699089 original size:31 final size:30
Alignment explanation
Indices: 61699031--61699101 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 30
61699021 TTCGTCCTTC
* * *
61699031 TTTTTTT-GTTTTTAATATATGGTCCAATA
1 TTTTTTTACTTTTTAATAAATGGCCCAATA
61699060 TTTTTTTACTTTTTATATAAATGGCCCAATA
1 TTTTTTTACTTTTTA-ATAAATGGCCCAATA
* *
61699091 TGTTTATACTT
1 TTTTTTTACTT
61699102 CTTCTTCTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 7 0.20
30 6 0.17
31 22 0.63
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.56
Consensus pattern (30 bp):
TTTTTTTACTTTTTAATAAATGGCCCAATA
Found at i:61700292 original size:9 final size:9
Alignment explanation
Indices: 61700276--61700317 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
61700266 GAGTTAAACG
61700276 AATCGAGTT
1 AATCGAGTT
*
61700285 ATTCGAGTT
1 AATCGAGTT
61700294 AATCGAGTT
1 AATCGAGTT
*
61700303 AATCAAGTT
1 AATCGAGTT
*
61700312 ATTCGA
1 AATCGA
61700318 ATCAACTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (9 bp):
AATCGAGTT
Found at i:61700388 original size:9 final size:9
Alignment explanation
Indices: 61700371--61700407 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
61700361 TGCGTTTTCA
61700371 AATTCGAAT
1 AATTCGAAT
*
61700380 AACTCGAAT
1 AATTCGAAT
61700389 AATTCGAAT
1 AATTCGAAT
61700398 AATTCGAAT
1 AATTCGAAT
61700407 A
1 A
61700408 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:61700655 original size:30 final size:31
Alignment explanation
Indices: 61700621--61700680 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
61700611 AAACCTTTTA
*
61700621 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
61700651 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
61700681 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:61700948 original size:9 final size:9
Alignment explanation
Indices: 61700934--61700962 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
61700924 AATTTCACAT
61700934 TTTATATTA
1 TTTATATTA
61700943 TTTATATTA
1 TTTATATTA
61700952 TTTATATTA
1 TTTATATTA
61700961 TT
1 TT
61700963 GAATTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:61701343 original size:5 final size:5
Alignment explanation
Indices: 61701333--61701358 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
61701323 GAACAAATAT
61701333 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
61701359 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:61701458 original size:5 final size:5
Alignment explanation
Indices: 61701448--61701473 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
61701438 CTCGAAAATT
61701448 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
61701474 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:61705547 original size:11 final size:11
Alignment explanation
Indices: 61705531--61705556 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61705521 TCTAACAATA
61705531 TTTTTTATTTT
1 TTTTTTATTTT
61705542 TTTTTTATTTT
1 TTTTTTATTTT
61705553 TTTT
1 TTTT
61705557 AGAAAAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:61707738 original size:44 final size:43
Alignment explanation
Indices: 61707700--61708064 Score: 324
Period size: 44 Copynumber: 8.2 Consensus size: 43
61707690 AACTTTAGCA
*
61707700 AGATAAGATTTGTAGCTTCAATATGCTCCACTGCAACTTCAAGG
1 AGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTT-AAGG
* * *
61707744 AGATAAGATTTGTAGCTTCAATCCGTTCCACTGCAACTTCAGGG
1 AGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTT-AAGG
* * *
61707788 AGATAAGGTTTGT---TTTAATCTACTCCACTGCAACTTCAAGG
1 AGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTT-AAGG
* * *
61707829 AGATAAGATTTGTAGATTCAGTCTGCTCCACTGCAACTTCAGGG
1 AGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTT-AAGG
** *
61707873 AGATAAGATTTGTTGTTATAGCTTCAATCTGCTCTTCTGCAACTTTAGGG
1 AGATAAGA--T-TTG---TAGCTTCAATCTGCTCCACTGCAAC-TTAAGG
* *
61707923 AGATAAGGTTTGTAGCTGT-AATCTGTTCCACTGCAACTTCAAGG
1 AGATAAGATTTGTAGCT-TCAATCTGCTCCACTGCAACTT-AAGG
* * * * * *
61707967 AGATAAAATTTGTATCTTTAATCTGTTCCACTACAATTTCAAGG
1 AGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTT-AAGG
* * * * *
61708011 AGATAAGATTTGTAACTTTAATTTACTCCACTGCAACTTCAGGG
1 AGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTT-AAGG
*
61708055 AAATAAGATT
1 AGATAAGATT
61708065 CGCTATGGTA
Statistics
Matches: 270, Mismatches: 38, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
41 35 0.13
43 3 0.01
44 189 0.70
45 1 0.00
46 1 0.00
47 6 0.02
48 1 0.00
50 32 0.12
51 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (43 bp):
AGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTAAGG
Found at i:61707837 original size:85 final size:85
Alignment explanation
Indices: 61707725--61708064 Score: 358
Period size: 85 Copynumber: 3.9 Consensus size: 85
61707715 CTTCAATATG
* *
61707725 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCCGTTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAG
*
61707790 ATAAGGTTTGTTTTAATCTA
66 ATAAGATTTGTTTTAATCTA
* *
61707810 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGATTCAGTCTGCTCCACTGCAACTTCAGGGAG
1 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAG
*
61707875 ATAAGATTTGTTGTTATAGCTTCAA
66 ATAAGATTTGTT-TTA-A---TCTA
* * * * *
61707900 TCTGCTCTTCTGCAACTTTAGGGAGATAAGGTTTGTAGCTGT-AATCTGTTCCACTGCAACTTCA
1 -CT-C-C-ACTGCAACTTCAAGGAGATAAGATTTGTAGCT-TCAATCTGCTCCACTGCAACTTCA
* * *
61707964 AGGAGATAAAATTTGTATCTTTAATCTG
61 GGGAGATAAGATTTG--T-TTTAATCTA
* * * * * * * *
61707992 TTCCACTACAATTTCAAGGAGATAAGATTTGTAACTTTAATTTACTCCACTGCAACTTCAGGGAA
1 CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAG
61708057 ATAAGATT
66 ATAAGATT
61708065 CGCTATGGTA
Statistics
Matches: 210, Mismatches: 31, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
85 72 0.34
86 3 0.01
87 2 0.01
88 54 0.26
89 1 0.00
90 4 0.02
91 3 0.01
92 3 0.01
93 1 0.00
94 60 0.29
95 2 0.01
96 4 0.02
97 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (85 bp):
CTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAG
ATAAGATTTGTTTTAATCTA
Found at i:61708140 original size:182 final size:179
Alignment explanation
Indices: 61707716--61708160 Score: 454
Period size: 182 Copynumber: 2.5 Consensus size: 179
61707706 GATTTGTAGC
* * * * * *
61707716 TTCAATATGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCT-TCAATCCGTTCCACTGCAA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTCTATAGCTGT-AATCTGTTCCACTGCAA
* *
61707780 CTTCAGGGAGATAAGGTTTGTTTTAATCTACTCCACTGCAACTTCAAGGAGATAAGATTTGTAGA
65 CTTCAGGGAGATAAGATTTGTTTTAATCTACTCCACTACAACTTCAAGGAGATAAGATTTGTAGA
* * * * * * * *
61707845 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTTGTTATAGC
130 TTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTCGCTATGATAGA
** * * *
61707895 TTCAATCTGCTCTTCTGCAACTTTAGGGAGATAAGGTTTGTAGCTGTAATCTGTTCCACTGCAAC
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTCTATAGCTGTAATCTGTTCCACTGCAAC
* * ** *
61707960 TTCAAGGAGATAAAATTTGTATCTTTAATCTGTTCCACTACAATTTCAAGGAGATAAGATTTGTA
66 TTCAGGGAGATAAGATTTG--T-TTTAATCTACTCCACTACAACTTCAAGGAGATAAGATTTGTA
* * *
61708025 -ACTTTAATTTACTCCACTGCAACTTCAGGGAAATAAGATTCGCTATGGTAGA
128 GA-TTCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTCGCTATGATAGA
* * *
61708077 TTCAATCTG-TCCCACTGCGACTTCAGGG-G-TGTAGGATCTATAGCT-TAAATCT-TCTCTACT
1 TTCAATCTGCT-CCACTGCAACTTCAGGGAGAT-AAGG-TCTATAGCTGT-AATCTGT-TCCACT
*
61708137 GCAACTTTAGGGAGATAAGATTTG
61 GCAACTTCAGGGAGATAAGATTTG
61708161 CTATGGTGAT
Statistics
Matches: 220, Mismatches: 36, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
179 72 0.33
180 2 0.01
181 9 0.04
182 137 0.62
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (179 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTCTATAGCTGTAATCTGTTCCACTGCAAC
TTCAGGGAGATAAGATTTGTTTTAATCTACTCCACTACAACTTCAAGGAGATAAGATTTGTAGAT
TCAATCTACTCCACTGCAACTTCAGGGAAATAAGATTCGCTATGATAGA
Found at i:61711275 original size:18 final size:18
Alignment explanation
Indices: 61711252--61711292 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
61711242 TACAGTATCA
61711252 GTGGCTTATCTAGGCTAG
1 GTGGCTTATCTAGGCTAG
61711270 GTGGCTTATCTAGGCTAG
1 GTGGCTTATCTAGGCTAG
61711288 GTGGC
1 GTGGC
61711293 GTTAGTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.37, T:0.32
Consensus pattern (18 bp):
GTGGCTTATCTAGGCTAG
Found at i:61712665 original size:35 final size:35
Alignment explanation
Indices: 61712626--61712695 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
61712616 TAGATATATA
*
61712626 GGGAAAGTTCATCAGTTCCCATTTGACCTCTCCCC
1 GGGAAAGATCATCAGTTCCCATTTGACCTCTCCCC
61712661 GGGAAAGATCATCAGTTCCCATTTGACCTCTCCCC
1 GGGAAAGATCATCAGTTCCCATTTGACCTCTCCCC
61712696 CACTTAGTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.27
Consensus pattern (35 bp):
GGGAAAGATCATCAGTTCCCATTTGACCTCTCCCC
Found at i:61715984 original size:19 final size:20
Alignment explanation
Indices: 61715946--61715990 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
61715936 AGGGCCTTTT
*
61715946 ATGAAATTTAATGCATATG-
1 ATGAAATGTAATGCATATGA
61715965 ATGAAATGTAATGC-TAATGA
1 ATGAAATGTAATGCAT-ATGA
61715985 ATGAAA
1 ATGAAA
61715991 AATGAATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 16 0.70
20 6 0.26
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (20 bp):
ATGAAATGTAATGCATATGA
Found at i:61719768 original size:23 final size:22
Alignment explanation
Indices: 61719717--61719768 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
61719707 ATGAAACAAC
*
61719717 TTTAATAATAAATTGATGATGA
1 TTTAATAATAAATTGATAATGA
*
61719739 TAATAATAAT-AATGTCGATAATGA
1 T-TTAATAATAAAT-T-GATAATGA
61719763 TTTAAT
1 TTTAAT
61719769 TAATGAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
22 4 0.17
23 12 0.50
24 8 0.33
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.40
Consensus pattern (22 bp):
TTTAATAATAAATTGATAATGA
Found at i:61742225 original size:80 final size:80
Alignment explanation
Indices: 61742126--61742282 Score: 278
Period size: 80 Copynumber: 2.0 Consensus size: 80
61742116 TCTCAAGTCC
* * *
61742126 CCATAAAAACATGATATTCAATCAAAGAAAACAAAGTTTATAAAATTAACACAAATTTTAAAGTT
1 CCATAAAAACATGACATTCAATCAAAGAAAACAAAGTTTATAAAATAAACACAAATATTAAAGTT
61742191 TTACAAGTAAGAGCT
66 TTACAAGTAAGAGCT
*
61742206 CCATAAAAACATGACATTCAATCAAAGATAACAAAGTTTATAAAATAAACACAAATATTAAAGTT
1 CCATAAAAACATGACATTCAATCAAAGAAAACAAAGTTTATAAAATAAACACAAATATTAAAGTT
61742271 TTACAAGTAAGA
66 TTACAAGTAAGA
61742283 CAATTGGAGG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (80 bp):
CCATAAAAACATGACATTCAATCAAAGAAAACAAAGTTTATAAAATAAACACAAATATTAAAGTT
TTACAAGTAAGAGCT
Found at i:61747202 original size:7 final size:7
Alignment explanation
Indices: 61747180--61747241 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
61747170 AACCCAATCT
61747180 TTATTT-
1 TTATTTA
61747186 TTATTT-
1 TTATTTA
61747192 TTATTTA
1 TTATTTA
*
61747199 TTATTTTCCT
1 TTA-TTT--A
61747209 TTATTT-
1 TTATTTA
61747215 TCT-TTTA
1 T-TATTTA
61747222 TTATTTA
1 TTATTTA
61747229 TTATTTA
1 TTATTTA
61747236 TTATTT
1 TTATTT
61747242 TATTTTATTT
Statistics
Matches: 48, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
6 17 0.35
7 22 0.46
8 3 0.06
9 3 0.06
10 3 0.06
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (7 bp):
TTATTTA
Found at i:61747228 original size:30 final size:29
Alignment explanation
Indices: 61747178--61747234 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
61747168 GCAACCCAAT
61747178 CTTTATTTTTATTTTTATTTATTATTTTC
1 CTTTATTTTTATTTTTATTTATTATTTTC
61747207 CTTTATTTTCT-TTTATTATTTATTATTT
1 CTTTATTTT-TATTT-TTATTTATTATTT
61747235 ATTATTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (29 bp):
CTTTATTTTTATTTTTATTTATTATTTTC
Found at i:61747481 original size:42 final size:42
Alignment explanation
Indices: 61747396--61747478 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
61747386 TGTCATATCT
** **
61747396 CTGCAGCCAAACAGTCCTATTCAGCCTTAAAATCCCCAAAAC
1 CTGCAGCCAAACACCCCTATTCAGCAATAAAATCCCCAAAAC
* *
61747438 CTGCAGCCAAACACCCCTTTTCAGCAAATAAAACCCCCAAA
1 CTGCAGCCAAACACCCCTATTCAGC-AATAAAATCCCCAAA
61747479 CCTTACATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 22 0.65
43 12 0.35
ACGTcount: A:0.37, C:0.37, G:0.08, T:0.17
Consensus pattern (42 bp):
CTGCAGCCAAACACCCCTATTCAGCAATAAAATCCCCAAAAC
Found at i:61747638 original size:46 final size:46
Alignment explanation
Indices: 61747580--61747671 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
61747570 CCGAAGCTGA
* *
61747580 ACCGTCGTTGCCACGTCACCCACCCCGTCTCCACCTCTTGCCGTTT
1 ACCGCCGTTGCCACGTCACCCACCCCGTCTCCACCTCTTACCGTTT
*
61747626 ACCGCCGTTGCCATGTCACCCACCCCGTCTCCACCTCTTACCGTTT
1 ACCGCCGTTGCCACGTCACCCACCCCGTCTCCACCTCTTACCGTTT
61747672 CGCCATCTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.12, C:0.48, G:0.14, T:0.26
Consensus pattern (46 bp):
ACCGCCGTTGCCACGTCACCCACCCCGTCTCCACCTCTTACCGTTT
Found at i:61748456 original size:118 final size:118
Alignment explanation
Indices: 61748248--61748478 Score: 372
Period size: 118 Copynumber: 2.0 Consensus size: 118
61748238 TGTTTTCCAT
* * *
61748248 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAATCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
61748313 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
61748366 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
* ****
61748431 CTACTTTGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
61748479 ACCGGAAATA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 103 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:61748618 original size:11 final size:11
Alignment explanation
Indices: 61748604--61748641 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
61748594 AATAAAATTT
61748604 AAAAAAAGAAA
1 AAAAAAAGAAA
61748615 AAAAAAAGAAA
1 AAAAAAAGAAA
61748626 AAAAAGAAGAAA
1 AAAAA-AAGAAA
61748638 AAAA
1 AAAA
61748642 TAAGTACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:61748621 original size:12 final size:12
Alignment explanation
Indices: 61748604--61748641 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
61748594 AATAAAATTT
61748604 AAAAAAAG-AAA
1 AAAAAAAGAAAA
61748615 AAAAAAAGAAAA
1 AAAAAAAGAAAA
*
61748627 AAAAGAAGAAAA
1 AAAAAAAGAAAA
61748639 AAA
1 AAA
61748642 TAAGTACTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:61760628 original size:23 final size:23
Alignment explanation
Indices: 61760596--61760639 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
61760586 ACTACCATTT
61760596 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
61760619 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
61760640 ATAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:61760632 original size:13 final size:11
Alignment explanation
Indices: 61760600--61760642 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
61760590 CCATTTTCTA
*
61760600 AATAAAATAAT
1 AATAAAATATT
61760611 AAT-AAATATCT
1 AATAAAATAT-T
61760622 AAGTAAAATATT
1 AA-TAAAATATT
61760634 AATAAAATA
1 AATAAAATA
61760643 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:61762197 original size:57 final size:57
Alignment explanation
Indices: 61762124--61762241 Score: 218
Period size: 57 Copynumber: 2.1 Consensus size: 57
61762114 CATTGCAGTA
*
61762124 ACAAACTATGATTTACCTTGCTATGATGCTCGACTGTAATTCTCAAATCCATGGCCG
1 ACAAACTATGATTTACCTTGCTACGATGCTCGACTGTAATTCTCAAATCCATGGCCG
*
61762181 ACAAACTATGATTTACCTTGCTACGATGCTCGACTGTAATTCTCGAATCCATGGCCG
1 ACAAACTATGATTTACCTTGCTACGATGCTCGACTGTAATTCTCAAATCCATGGCCG
61762238 ACAA
1 ACAA
61762242 CTAATGCCAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (57 bp):
ACAAACTATGATTTACCTTGCTACGATGCTCGACTGTAATTCTCAAATCCATGGCCG
Found at i:61764764 original size:20 final size:20
Alignment explanation
Indices: 61764739--61764779 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
61764729 TAAATCATCT
61764739 ACTTGGTTGTGGCTTTAAGG
1 ACTTGGTTGTGGCTTTAAGG
61764759 ACTTGGTTGTGGCTTTAAGG
1 ACTTGGTTGTGGCTTTAAGG
61764779 A
1 A
61764780 TTTTATGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.10, G:0.34, T:0.39
Consensus pattern (20 bp):
ACTTGGTTGTGGCTTTAAGG
Found at i:61769571 original size:12 final size:12
Alignment explanation
Indices: 61769554--61769601 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
61769544 TGTCATTAAC
61769554 ATATAAAACCAA
1 ATATAAAACCAA
*
61769566 ATATAAAACTTTAA
1 ATATAAAAC--CAA
61769580 CATATAAAACCAA
1 -ATATAAAACCAA
61769593 ATATAAAAC
1 ATATAAAAC
61769602 TTTACTCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 18 0.58
13 2 0.06
14 2 0.06
15 9 0.29
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (12 bp):
ATATAAAACCAA
Found at i:61769580 original size:27 final size:27
Alignment explanation
Indices: 61769549--61769605 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
61769539 CAATATGTCA
61769549 TTAACATATAAAACCAAATATAAAACT
1 TTAACATATAAAACCAAATATAAAACT
61769576 TTAACATATAAAACCAAATATAAAACT
1 TTAACATATAAAACCAAATATAAAACT
61769603 TTA
1 TTA
61769606 CTCCCACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (27 bp):
TTAACATATAAAACCAAATATAAAACT
Found at i:61786138 original size:21 final size:22
Alignment explanation
Indices: 61786109--61786155 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
61786099 CAGAAGGAGT
*
61786109 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
61786131 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
61786152 GAGT
1 GAGT
61786156 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:61789348 original size:21 final size:22
Alignment explanation
Indices: 61789319--61789365 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
61789309 TAGAAGGAGT
*
61789319 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
61789341 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
61789362 GAGT
1 GAGT
61789366 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:61790648 original size:27 final size:27
Alignment explanation
Indices: 61790610--61790664 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
61790600 ATATTAACAG
61790610 CACAACCTTAAATTCTAACAGTTTAGT
1 CACAACCTTAAATTCTAACAGTTTAGT
*
61790637 CACAGCCTTAAATTCTAACAGTTTAGT
1 CACAACCTTAAATTCTAACAGTTTAGT
61790664 C
1 C
61790665 GGTATCAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.33
Consensus pattern (27 bp):
CACAACCTTAAATTCTAACAGTTTAGT
Found at i:61791459 original size:6 final size:6
Alignment explanation
Indices: 61791448--61791478 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
61791438 GTCAAGGATG
61791448 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
1 GGGGAA GGGGAA GGGGAA GGGGAA GGGGAA G
61791479 CAGAAAATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:61792006 original size:17 final size:16
Alignment explanation
Indices: 61791983--61792025 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
61791973 CTATTAGTAG
*
61791983 TTTTTTATATTCATAT
1 TTTTTTATATTCATAA
*
61791999 TATTTTTATA-ACATAA
1 T-TTTTTATATTCATAA
61792015 TTTTTTATATT
1 TTTTTTATATT
61792026 TTTTTTGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 8 0.36
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTTATATTCATAA
Found at i:61793336 original size:22 final size:22
Alignment explanation
Indices: 61793300--61793343 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
61793290 CAGAAAAATG
61793300 TTAACAATATTTTAAAAGTTTAA
1 TTAACAATATTTTAAAA-TTTAA
*
61793323 TTAA-AATGTTTTAAAATTTAA
1 TTAACAATATTTTAAAATTTAA
61793344 ATCATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
TTAACAATATTTTAAAATTTAA
Found at i:61797174 original size:89 final size:85
Alignment explanation
Indices: 61797048--61797229 Score: 226
Period size: 89 Copynumber: 2.1 Consensus size: 85
61797038 AAAATTAGAG
* * * *
61797048 GGTCTTATTGATGTATTTTGAAATTTCAAGTACCCAATTGAGTGCA-AAAAAAAGTAGGGTCATA
1 GGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGA--ACATAAAAAAAG--GGG-CATA
*
61797112 ATTGCTTTTTTTGAAAATA-TTTGAA
61 ATTGCATTTTTTGAAAA-AGTTTGAA
* *
61797137 GGTCTTTTTGATGCATTTTGAAAGTTCAAGTATCCAATTGAACATAAAAAAAGGGGCTTAATTGC
1 GGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAACATAAAAAAAGGGGCATAATTGC
61797202 ATTTTTTGAAAAAGTTTGAA
66 ATTTTTTGAAAAAGTTTGAA
61797222 GG-CTTTTT
1 GGTCTTTTT
61797230 ACACCCTTAA
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
84 7 0.08
85 27 0.32
86 3 0.04
87 2 0.02
88 8 0.10
89 37 0.44
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (85 bp):
GGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAACATAAAAAAAGGGGCATAATTGC
ATTTTTTGAAAAAGTTTGAA
Found at i:61797275 original size:22 final size:23
Alignment explanation
Indices: 61797249--61797306 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
61797239 AGCCTATATA
61797249 TTATAAAAAATAATAT-ATTTAT
1 TTATAAAAAATAATATAATTTAT
* **
61797271 TTATAAAAAGTGTTATAATTTAT
1 TTATAAAAAATAATATAATTTAT
*
61797294 TTATAAGAAATAA
1 TTATAAAAAATAA
61797307 AGTTTCTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 13 0.46
23 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TTATAAAAAATAATATAATTTAT
Found at i:61805284 original size:13 final size:13
Alignment explanation
Indices: 61805262--61805294 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
61805252 AAGGGTTTGT
61805262 TTAT-TAAACTAA
1 TTATCTAAACTAA
61805274 TTATCTAAACTAA
1 TTATCTAAACTAA
*
61805287 TTAACTAA
1 TTATCTAA
61805295 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:61814685 original size:15 final size:15
Alignment explanation
Indices: 61814667--61814699 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
61814657 TCGTGGTGAT
61814667 ATTGTTGTGAGCAAA
1 ATTGTTGTGAGCAAA
61814682 ATTGTTGTGAGCAAA
1 ATTGTTGTGAGCAAA
61814697 ATT
1 ATT
61814700 AGTACTCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (15 bp):
ATTGTTGTGAGCAAA
Found at i:61817136 original size:16 final size:17
Alignment explanation
Indices: 61817105--61817139 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
61817095 TTGAAACAGC
61817105 TTAAATAAATAATTAAA
1 TTAAATAAATAATTAAA
*
61817122 TTAATTAAA-AATTAAA
1 TTAAATAAATAATTAAA
61817138 TT
1 TT
61817140 GGACATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATAAATAATTAAA
Found at i:61820037 original size:21 final size:23
Alignment explanation
Indices: 61820013--61820067 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
61820003 ATAAAAATGT
*
61820013 ATTTTAAATATTATTT-GATA-A
1 ATTTTAAATATTATTTAGAAATA
61820034 ATTTTAAAT-TT-TTTAGAAATA
1 ATTTTAAATATTATTTAGAAATA
*
61820055 ATTTTAAAAATTA
1 ATTTTAAATATTA
61820068 ATAATTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 5 0.18
21 18 0.64
22 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
ATTTTAAATATTATTTAGAAATA
Found at i:61834863 original size:77 final size:77
Alignment explanation
Indices: 61834726--61834873 Score: 226
Period size: 77 Copynumber: 1.9 Consensus size: 77
61834716 ACCCTACCCT
* * *
61834726 TTTAGTTAATATCATTGTACATTTCTACTTAACTCTAATTTCAACCAAACTTGACTCAATCCTTG
1 TTTAGTTAATATCATGGTACATTTCTACTTAACTCTAATTTCAACCAAACTGGACACAATCCTTG
61834791 TTGGAACTATCC
66 TTGGAACTATCC
* * *
61834803 TTTAGTTAATATCATGGTACATTTGTACTTGACTCTAATTTCAACTAAA-TCGGACACAATCCTT
1 TTTAGTTAATATCATGGTACATTTCTACTTAACTCTAATTTCAACCAAACT-GGACACAATCCTT
61834867 GTTGGAA
65 GTTGGAA
61834874 TTAGGGAATG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
76 1 0.02
77 63 0.98
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (77 bp):
TTTAGTTAATATCATGGTACATTTCTACTTAACTCTAATTTCAACCAAACTGGACACAATCCTTG
TTGGAACTATCC
Found at i:61841929 original size:21 final size:21
Alignment explanation
Indices: 61841886--61841943 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
61841876 CGAATATGCC
* *
61841886 AACAGAAGCTC--AAAAGCTG
1 AACAGAAGCTCGTAAGAGTTG
*
61841905 AACAGAAGCTTGTAAGAGTTG
1 AACAGAAGCTCGTAAGAGTTG
61841926 AACAGAAGCTCGTAAGAG
1 AACAGAAGCTCGTAAGAG
61841944 CTGATTCACC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.30
21 23 0.70
ACGTcount: A:0.43, C:0.16, G:0.26, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGTTG
Found at i:61845922 original size:11 final size:11
Alignment explanation
Indices: 61845908--61845945 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
61845898 TTTTTCATTT
61845908 TTTTACTATTA
1 TTTTACTATTA
*
61845919 TTTTCCTATTA
1 TTTTACTATTA
*
61845930 TATTACTATTA
1 TTTTACTATTA
61845941 TTTTA
1 TTTTA
61845946 TTGTTATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTACTATTA
Found at i:61856571 original size:25 final size:25
Alignment explanation
Indices: 61856543--61856598 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
61856533 CAAAAAAACC
* * *
61856543 TATATATATAATATATTTAAATTAT
1 TATATAGATAATATATTCAAATAAT
* *
61856568 TATAAAGATATTATATTCAAATAAT
1 TATATAGATAATATATTCAAATAAT
*
61856593 TTTATA
1 TATATA
61856599 CACATACGTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
TATATAGATAATATATTCAAATAAT
Found at i:61869688 original size:19 final size:19
Alignment explanation
Indices: 61869655--61869693 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
61869645 TTGAAAACAA
*
61869655 AATAACATGATTTTT-TTT
1 AATAACATAATTTTTATTT
61869673 AATAATCATAATTTTTATTT
1 AATAA-CATAATTTTTATTT
61869693 A
1 A
61869694 TTCAGCAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (19 bp):
AATAACATAATTTTTATTT
Found at i:61871935 original size:19 final size:20
Alignment explanation
Indices: 61871908--61871959 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
61871898 AGATGAAATG
*
61871908 TAAACATTTAATTAAAT-TT
1 TAAAAATTTAATTAAATATT
61871927 TAAAAATTTTAA--AAATATT
1 TAAAAA-TTTAATTAAATATT
61871946 TAAAAATTATAATT
1 TAAAAATT-TAATT
61871960 TTTATACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 6 0.22
19 16 0.59
20 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAAAATTTAATTAAATATT
Found at i:61871941 original size:10 final size:9
Alignment explanation
Indices: 61871921--61871953 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
61871911 ACATTTAATT
61871921 AAATTTTAA
1 AAATTTTAA
61871930 AAATTTTAA
1 AAATTTTAA
61871939 AAATATTTAA
1 AAAT-TTTAA
61871949 AAATT
1 AAATT
61871954 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATTTTAA
Found at i:61871964 original size:9 final size:9
Alignment explanation
Indices: 61871952--61871991 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
61871942 TATTTAAAAA
61871952 TTATAATTT
1 TTATAATTT
*
61871961 TTATACTTT
1 TTATAATTT
61871970 TTAATAATTT
1 TT-ATAATTT
*
61871980 TAATAATTT
1 TTATAATTT
61871989 TTA
1 TTA
61871992 GTTTTTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (9 bp):
TTATAATTT
Found at i:61871972 original size:25 final size:25
Alignment explanation
Indices: 61871944--61872002 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
61871934 TTTAAAAATA
61871944 TTTAAAAATTATAAT-TTTTATACTT
1 TTTAAAAATTATAATATTTT-TACTT
* * *
61871969 TTTAATAATTTTAATAATTTTTAGTT
1 TTTAAAAATTATAAT-ATTTTTACTT
61871995 TTTAAAAA
1 TTTAAAAA
61872003 ATAACCTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 13 0.46
26 11 0.39
27 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTAAAAATTATAATATTTTTACTT
Found at i:61871978 original size:19 final size:19
Alignment explanation
Indices: 61871954--61871991 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
61871944 TTTAAAAATT
* *
61871954 ATAATTTTTATACTTTTTA
1 ATAATTTTAATAATTTTTA
61871973 ATAATTTTAATAATTTTTA
1 ATAATTTTAATAATTTTTA
61871992 GTTTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
ATAATTTTAATAATTTTTA
Found at i:61872029 original size:8 final size:9
Alignment explanation
Indices: 61872009--61872042 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
61871999 AAAAATAACC
*
61872009 TTTTAAATT
1 TTTTAAAAT
61872018 TTTTAAAAT
1 TTTTAAAAT
61872027 TTTT-AAAT
1 TTTTAAAAT
61872035 TTTTAAAA
1 TTTTAAAA
61872043 AGTAACTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:61872043 original size:18 final size:18
Alignment explanation
Indices: 61871919--61872043 Score: 71
Period size: 18 Copynumber: 6.8 Consensus size: 18
61871909 AAACATTTAA
61871919 TTAAA-TTTTAAAAATTT
1 TTAAATTTTTAAAAATTT
* *
61871936 TAAAAATATTTAAAAA-TT
1 T-TAAATTTTTAAAAATTT
* * *
61871954 AT-AATTTTT-ATACTTT
1 TTAAATTTTTAAAAATTT
* *
61871970 TTAATAATTTTAATAATTT
1 TTAA-ATTTTTAAAAATTT
*
61871989 TT-AGTTTTTAAAAAATAACCTT
1 TTAAATTTTT-AAAAAT----TT
*
61872011 TTAAATTTTTTAAAATTT
1 TTAAATTTTTAAAAATTT
61872029 TTAAATTTTTAAAAA
1 TTAAATTTTTAAAAA
61872044 GTAACTAAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 23
0.67 0.13 0.19
Matches are distributed among these distances:
15 2 0.03
16 9 0.11
17 6 0.08
18 32 0.40
19 16 0.20
22 9 0.11
23 6 0.08
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (18 bp):
TTAAATTTTTAAAAATTT
Found at i:61872162 original size:15 final size:16
Alignment explanation
Indices: 61872142--61872176 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
61872132 TAAGGTGATT
*
61872142 TAAT-AAAAATTAAAA
1 TAATAAAAAAATAAAA
61872157 TAATAAAAAAATAAAA
1 TAATAAAAAAATAAAA
61872173 TAAT
1 TAAT
61872177 TTTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
TAATAAAAAAATAAAA
Found at i:61873389 original size:21 final size:19
Alignment explanation
Indices: 61873342--61873394 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
61873332 AAATTGAAAA
61873342 TTTTTAA-TTAAAGTATTT
1 TTTTTAATTTAAAGTATTT
*
61873360 TTTTATAATTTAAATTAATTT
1 TTTT-TAATTTAAAGT-ATTT
61873381 TATTTTAATTTAAA
1 T-TTTTAATTTAAA
61873395 AGTGTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 4 0.13
19 3 0.10
20 6 0.20
21 14 0.47
22 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTTAATTTAAAGTATTT
Found at i:61875199 original size:12 final size:12
Alignment explanation
Indices: 61875182--61875206 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61875172 AAAAACAAAA
61875182 ACCTTGTTGATC
1 ACCTTGTTGATC
61875194 ACCTTGTTGATC
1 ACCTTGTTGATC
61875206 A
1 A
61875207 GCCTATCATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (12 bp):
ACCTTGTTGATC
Found at i:61877072 original size:23 final size:22
Alignment explanation
Indices: 61877045--61877090 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
61877035 AGAAAAAATG
61877045 AGAGAGA-TTCGAATACAAGAAAA
1 AGAGAGACTTC-AATACAA-AAAA
61877068 AGAGAGACTTTCAATACAAAAAA
1 AGAGAGAC-TTCAATACAAAAAA
61877091 TACAAGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 11 0.52
24 7 0.33
25 3 0.14
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (22 bp):
AGAGAGACTTCAATACAAAAAA
Found at i:61877072 original size:25 final size:24
Alignment explanation
Indices: 61877037--61877090 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
61877027 TTTTTTTGAG
*
61877037 AAAAAATGAGAGAGATTCGAATACA
1 AAAAAATGAGAGACATTC-AATACA
*
61877062 AGAAAAA-GAGAGACTTTCAATACA
1 A-AAAAATGAGAGACATTCAATACA
61877086 AAAAA
1 AAAAA
61877091 TACAAGAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 7 0.27
25 10 0.38
26 5 0.19
ACGTcount: A:0.59, C:0.09, G:0.17, T:0.15
Consensus pattern (24 bp):
AAAAAATGAGAGACATTCAATACA
Found at i:61877382 original size:3 final size:3
Alignment explanation
Indices: 61877364--61877727 Score: 65
Period size: 3 Copynumber: 121.3 Consensus size: 3
61877354 GGGGAGAGTG
* * *
61877364 TTA TTT TTA ATA TTA TTA TTA TTA TTA TTA TTA CTT- TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
* * * * * * *
61877409 TT- CTA TATA CTA TTA CTG TT- TTCT TTA TTA TTA TTA TTA GTA GTAA
1 TTA TTA T-TA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA -TTA
* * * * * *
61877455 CGTA ATA GTA TTT TTA TTA CTT- TTA CCTTT TTA TTA CTA TTA TTA TTAA
1 -TTA TTA TTA TTA TTA TTA -TTA TTA --TTA TTA TTA TTA TTA TTA TT-A
** * * * * *
61877504 TCTA CAA TTA TTA TTT TTA TCA ATA -TA GTA TTA TT- TTC TT- TT-
1 T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** *
61877546 TTT TTA -TA TTG TTA TTA TTA TTA GCA CGTA -TA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * * * *
61877590 TTA TTA TTA TTA TTT TCTA TTA TCA TTA ATA TGTA GT- TTG TT- TT-
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* ** * * * * *
61877634 TTA TTA TTA TTA TTT TTA ACA CTA TTA TCA TCA TTA -TA CTAA CTTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA
* * ** * *
61877680 TTT TTA ATA TTA TTA CCA TTA -TA TTA TTA TTA CTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
61877727 T
1 T
61877728 CCGTCCTATT
Statistics
Matches: 259, Mismatches: 76, Indels: 52
0.67 0.20 0.13
Matches are distributed among these distances:
2 28 0.11
3 206 0.80
4 22 0.08
5 3 0.01
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:61878017 original size:125 final size:123
Alignment explanation
Indices: 61877888--61878138 Score: 290
Period size: 121 Copynumber: 2.0 Consensus size: 123
61877878 ATTTTTCAAG
* * *
61877888 TAAAGGCAATATTCGGTATTTAGAAATTCGAGAAATCGTGTCTTAATGTACTGAGTTTCGGTTTT
1 TAAAGGCAATATTCCGTATTTAGAAATTCGAGAAATCGTG-C---ACGTACTGAGTTTCGATTTT
** * *
61877953 TTGTTTGATCTAAGTAACCGATTATCC-TTTT-AAATTAAAATACATGAGTTTTAAATAAAA
62 TCATTTGATCTAAATAACCGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATAAAA
* * * * * *
61878013 TAAAGGTAATATTCCGTATTTAGAAATTTGAGTAGTCGTGCCCGTACTGGGTTTCGATTTTTCAT
1 TAAAGGCAATATTCCGTATTTAGAAATTCGAGAAATCGTGCACGTACTGAGTTTCGATTTTTCAT
** * *
61878078 TTGATCTAAATATTCGAATATCCTTTTTTAAAATTTAAATACATGAGTTTTAAATGAAA
66 TTGATCTAAATAACCGAATATCC-TTTTTAAAATTAAAATACATGAGTTTTAAATAAAA
61878137 TA
1 TA
61878139 GAGGGCAAGC
Statistics
Matches: 106, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
121 37 0.35
123 4 0.04
124 30 0.28
125 35 0.33
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (123 bp):
TAAAGGCAATATTCCGTATTTAGAAATTCGAGAAATCGTGCACGTACTGAGTTTCGATTTTTCAT
TTGATCTAAATAACCGAATATCCTTTTTAAAATTAAAATACATGAGTTTTAAATAAAA
Found at i:61882028 original size:20 final size:20
Alignment explanation
Indices: 61881977--61882026 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
61881967 AATGGCCTCC
* *
61881977 TTTTTCTTTTTCTTCTTTGT
1 TTTTTTTTTTTGTTCTTTGT
61881997 TTTTTTTTTTTGTT-TTTGT
1 TTTTTTTTTTTGTTCTTTGT
61882016 TTTTTTTTTTT
1 TTTTTTTTTTT
61882027 TGGTATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (20 bp):
TTTTTTTTTTTGTTCTTTGT
Found at i:61882057 original size:1 final size:1
Alignment explanation
Indices: 61882051--61882091 Score: 64
Period size: 1 Copynumber: 41.0 Consensus size: 1
61882041 CATAAATAGA
* *
61882051 TTTTTTTTTTTTTTTTTTTTTGTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
61882092 GGTATTATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (1 bp):
T
Found at i:61882082 original size:20 final size:20
Alignment explanation
Indices: 61882053--61882092 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
61882043 TAAATAGATT
*
61882053 TTTTTTTTTTTTTTTTTTTG
1 TTTTTGTTTTTTTTTTTTTG
61882073 TTTTTGTTTTTTTTTTTTTG
1 TTTTTGTTTTTTTTTTTTTG
61882093 GTATTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (20 bp):
TTTTTGTTTTTTTTTTTTTG
Found at i:61882088 original size:64 final size:64
Alignment explanation
Indices: 61881996--61882117 Score: 244
Period size: 64 Copynumber: 1.9 Consensus size: 64
61881986 TTCTTCTTTG
61881996 TTTTTTTTTTTTGTTTTTGTTTTTTTTTTTTTGGTATTATAAAGTCATAAATAGATTTTTTTTT
1 TTTTTTTTTTTTGTTTTTGTTTTTTTTTTTTTGGTATTATAAAGTCATAAATAGATTTTTTTTT
61882060 TTTTTTTTTTTTGTTTTTGTTTTTTTTTTTTTGGTATTATAAAGTCATAAATAGATTT
1 TTTTTTTTTTTTGTTTTTGTTTTTTTTTTTTTGGTATTATAAAGTCATAAATAGATTT
61882118 CAAATCTGAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.18, C:0.02, G:0.10, T:0.70
Consensus pattern (64 bp):
TTTTTTTTTTTTGTTTTTGTTTTTTTTTTTTTGGTATTATAAAGTCATAAATAGATTTTTTTTT
Found at i:61886667 original size:16 final size:16
Alignment explanation
Indices: 61886646--61886677 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
61886636 AAACAAATTT
*
61886646 ATTATATTTTATAAAA
1 ATTATAATTTATAAAA
61886662 ATTATAATTTATAAAA
1 ATTATAATTTATAAAA
61886678 TTTGCAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTATAATTTATAAAA
Found at i:61887951 original size:20 final size:21
Alignment explanation
Indices: 61887928--61887972 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
61887918 AACTTCTAAA
61887928 TTAAACCCATTAAAATCAC-T
1 TTAAACCCATTAAAATCACAT
61887948 TTAAACCCATTAAAATCACAT
1 TTAAACCCATTAAAATCACAT
61887969 TTAA
1 TTAA
61887973 CATTTAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAACCCATTAAAATCACAT
Found at i:61904550 original size:17 final size:18
Alignment explanation
Indices: 61904522--61904555 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
61904512 TATTCTCTAT
61904522 TTTAATTTTCACAATTTA
1 TTTAATTTTCACAATTTA
61904540 TTTAA-TTTCACAATTT
1 TTTAATTTTCACAATTT
61904556 CAATCAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATTTTCACAATTTA
Found at i:61906664 original size:26 final size:25
Alignment explanation
Indices: 61906613--61906664 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
61906603 ATTTTGTTAA
* * *
61906613 TTATTAAAAATAAATTTATGATATT
1 TTATAAAAAATAAATTTATAAAATT
61906638 TTATAAAAAATATAATTTATAAAATT
1 TTATAAAAAATA-AATTTATAAAATT
61906664 T
1 T
61906665 GCAACCAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TTATAAAAAATAAATTTATAAAATT
Found at i:61907944 original size:20 final size:21
Alignment explanation
Indices: 61907921--61907965 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
61907911 AACTTCTAAA
61907921 TTAAACCCATTAAAATCAC-T
1 TTAAACCCATTAAAATCACAT
61907941 TTAAACCCATTAAAATCACAT
1 TTAAACCCATTAAAATCACAT
61907962 TTAA
1 TTAA
61907966 CATTTAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAACCCATTAAAATCACAT
Found at i:61911292 original size:23 final size:25
Alignment explanation
Indices: 61911266--61911312 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
61911256 TATCATTCAT
*
61911266 TTCATTATAT-CA-ATATTTTATGG
1 TTCATCATATCCATATATTTTATGG
*
61911289 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
61911313 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGG
Found at i:61911633 original size:46 final size:46
Alignment explanation
Indices: 61911573--61911694 Score: 183
Period size: 46 Copynumber: 2.7 Consensus size: 46
61911563 TTTGACGTGA
* * * *
61911573 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTC-TTTTCATGTCACGT
*
61911619 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCATGTCACGT
61911665 TGCCATGGTATCTTTCAACCATGGTCTTAC
1 TGCCATGGTATCTTTCAACCATGGTCTTAC
61911695 ACATCTCATA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
45 5 0.07
46 64 0.93
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.43
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCTTTTCATGTCACGT
Found at i:61911955 original size:46 final size:46
Alignment explanation
Indices: 61911895--61912022 Score: 173
Period size: 38 Copynumber: 3.0 Consensus size: 46
61911885 TTTGACGTGA
* * *
61911895 TGCCATAGTGTCTTTCAACTATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
61911941 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--AT-AGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
61911979 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
61912023 AGAGCACACT
Statistics
Matches: 71, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
38 32 0.45
39 2 0.03
40 3 0.04
41 1 0.01
43 1 0.01
44 3 0.04
45 2 0.03
46 27 0.38
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:61911969 original size:322 final size:314
Alignment explanation
Indices: 61911384--61912019 Score: 1130
Period size: 322 Copynumber: 2.0 Consensus size: 314
61911374 ACTTATTTCG
61911384 TTTATCCATTTTCATAATTATTTCATAAAACGCTTTTGTACATATATTTTCATATGACCAGTTCT
1 TTTATCCATTTTCATAATTATTTCATAAAACGCTTTTGTACATATATTTTCATATGACCAGTTCT
61911449 TGTAAATATTTCACACAACCATTTCATATAACCATTCGTCATCTGATACATTTTACCTGAATATC
66 TGTAAATATTTCACACAACCATTTCATATAACCATTCGTCATCTGATACATTTTACCTGAATATC
61911514 AATTGTTCAACAGATGTTATAGCGTCTCCCATCCATGGTCTTATTTATCTTTGACGTGATGCCAT
131 AATTGTTCAACAGATGTTATAGCGTCTCCCATCCATGGTCTTATTTATCTTTGACGTGATGCCAT
* * *
61911579 AGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGT
196 AGTGTCTTTCAACTATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAACCATGGT
*
61911644 CTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATAT
261 CTTA--C---ACA--T-ACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATAT
61911706 TTTATCCATTTTCATAATTATTTCATAAAACGCTTTTGTACATATATTTTCATATGACCAGTTCT
1 TTTATCCATTTTCATAATTATTTCATAAAACGCTTTTGTACATATATTTTCATATGACCAGTTCT
61911771 TGTAAATATTTCACACAACCATTTCATATAACCATTCGTCATCTGATACATTTTACCTGAATATC
66 TGTAAATATTTCACACAACCATTTCATATAACCATTCGTCATCTGATACATTTTACCTGAATATC
61911836 AATTGTTCAACAGATGTTATAGCGTCTCCCATCCATGGTCTTATTTATCTTTGACGTGATGCCAT
131 AATTGTTCAACAGATGTTATAGCGTCTCCCATCCATGGTCTTATTTATCTTTGACGTGATGCCAT
61911901 AGTGTCTTTCAACTATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATCTTTCAACCATGG
196 AGTGTCTTTCAACTATGGTCTTACACATTTTC-TATCAGGTTGCCATGGTATCTTTCAACCATGG
* *
61911965 TCTTACACATAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
260 TCTTACACATACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATAT
61912020 CAGAGAGCAC
Statistics
Matches: 307, Mismatches: 6, Indels: 10
0.95 0.02 0.03
Matches are distributed among these distances:
314 43 0.14
315 1 0.00
317 2 0.01
320 1 0.00
321 4 0.01
322 256 0.83
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.41
Consensus pattern (314 bp):
TTTATCCATTTTCATAATTATTTCATAAAACGCTTTTGTACATATATTTTCATATGACCAGTTCT
TGTAAATATTTCACACAACCATTTCATATAACCATTCGTCATCTGATACATTTTACCTGAATATC
AATTGTTCAACAGATGTTATAGCGTCTCCCATCCATGGTCTTATTTATCTTTGACGTGATGCCAT
AGTGTCTTTCAACTATGGTCTTACACATTTTCTATCAGGTTGCCATGGTATCTTTCAACCATGGT
CTTACACATACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATAT
Found at i:61916069 original size:20 final size:21
Alignment explanation
Indices: 61916046--61916090 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
61916036 AACTTCTAAA
61916046 TTAAA-CCTATTAAAATCAC-T
1 TTAAATCC-ATTAAAATCACAT
61916066 TTAAATCCATTAAAATCACAT
1 TTAAATCCATTAAAATCACAT
61916087 TTAA
1 TTAA
61916091 CGTTTAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.36
Consensus pattern (21 bp):
TTAAATCCATTAAAATCACAT
Found at i:61923324 original size:26 final size:26
Alignment explanation
Indices: 61923295--61923344 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
61923285 TCAAACATGC
*
61923295 ATTTAGGTCAATTTA-GTCCTAGGGAT
1 ATTTAGGT-AATTTATCTCCTAGGGAT
*
61923321 ATTTCGGTAATTTATCTCCTAGGG
1 ATTTAGGTAATTTATCTCCTAGGG
61923345 GTAAAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGGGAT
Found at i:61924868 original size:26 final size:25
Alignment explanation
Indices: 61924832--61924915 Score: 123
Period size: 26 Copynumber: 3.2 Consensus size: 25
61924822 CATGAAATTC
61924832 TTATCATGAAACATTTATCTAACCCA
1 TTATCATGAAACATTTA-CTAACCCA
61924858 TTATCATGAAACATTTACTTAACCCA
1 TTATCATGAAACATTTAC-TAACCCA
* *
61924884 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTA-CTAACCCA
61924910 TTATCA
1 TTATCA
61924916 ATTTGTACCA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
25 1 0.02
26 52 0.96
27 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.36
Consensus pattern (25 bp):
TTATCATGAAACATTTACTAACCCA
Found at i:61929145 original size:8 final size:8
Alignment explanation
Indices: 61929134--61929173 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
61929124 TGTTTTATTA
61929134 TATTATAT
1 TATTATAT
*
61929142 TATTATCT
1 TATTATAT
*
61929150 TCTTATAT
1 TATTATAT
*
61929158 TAATATAT
1 TATTATAT
61929166 TATTATAT
1 TATTATAT
61929174 CATATACTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (8 bp):
TATTATAT
Found at i:61929184 original size:24 final size:25
Alignment explanation
Indices: 61929137--61929189 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
61929127 TTTATTATAT
* *
61929137 TATATTATTATCTTCTTATATTAA-
1 TATATTATTATCATCATATATTAAG
61929161 TATATTATTAT-ATCATATACTTAAG
1 TATATTATTATCATCATATA-TTAAG
61929186 TATA
1 TATA
61929190 AAGTATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.24
24 15 0.60
25 4 0.16
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.53
Consensus pattern (25 bp):
TATATTATTATCATCATATATTAAG
Found at i:61930729 original size:31 final size:31
Alignment explanation
Indices: 61930691--61930752 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
61930681 CATTAACTAC
61930691 GGTCAAATAAAATGTCGATTATTGCTAATTG
1 GGTCAAATAAAATGTCGATTATTGCTAATTG
61930722 GGTCAAATAAAATGTCGATTATTGCTAATTG
1 GGTCAAATAAAATGTCGATTATTGCTAATTG
61930753 ATTCATCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (31 bp):
GGTCAAATAAAATGTCGATTATTGCTAATTG
Found at i:61933760 original size:27 final size:27
Alignment explanation
Indices: 61933722--61933778 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
61933712 CAAGAAGATG
61933722 TGATAAGGGGTTGATCATTATTGAATC
1 TGATAAGGGGTTGATCATTATTGAATC
61933749 TGATAAGGGGTTGATCATTATTGAATC
1 TGATAAGGGGTTGATCATTATTGAATC
61933776 TGA
1 TGA
61933779 CTCTAGCTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (27 bp):
TGATAAGGGGTTGATCATTATTGAATC
Found at i:61936328 original size:17 final size:17
Alignment explanation
Indices: 61936283--61936328 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
61936273 AGAGAAATTC
61936283 ATTTATTTTTATATAAAAT
1 ATTT-TTTTT-TATAAAAT
* *
61936302 AATTTGTTTTATAAAAT
1 ATTTTTTTTTATAAAAT
61936319 ATTTTTTTTT
1 ATTTTTTTTT
61936329 GAAAAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 16 0.70
18 4 0.17
19 3 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
ATTTTTTTTTATAAAAT
Found at i:61937078 original size:2 final size:2
Alignment explanation
Indices: 61937071--61937118 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
61937061 GTGAGTGAGT
61937071 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
61937112 GG GA GA G
1 GA GA GA G
61937119 GGAGGGAGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:61937123 original size:10 final size:10
Alignment explanation
Indices: 61937077--61937149 Score: 51
Period size: 10 Copynumber: 7.3 Consensus size: 10
61937067 GAGTGAGAGA
* *
61937077 GAGAGAGAGA
1 GAGAGGGAGG
* *
61937087 GAGAGAGAGA
1 GAGAGGGAGG
*
61937097 GAGAGAGAGAG
1 GAGAGGGAG-G
*
61937108 AAGAGGGAGAG
1 GAGAGGGAG-G
61937119 G-GAGGGAGG
1 GAGAGGGAGG
*
61937128 GGGAGGG-GG
1 GAGAGGGAGG
61937137 GAGAGGGAGG
1 GAGAGGGAGG
61937147 GAG
1 GAG
61937150 GAACAAAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
9 10 0.18
10 36 0.65
11 9 0.16
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (10 bp):
GAGAGGGAGG
Found at i:61937144 original size:13 final size:14
Alignment explanation
Indices: 61937116--61937150 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
61937106 AGAAGAGGGA
*
61937116 GAGGGAGGGAGGGG
1 GAGGGAGGGAGAGG
61937130 GAGGG-GGGAGAGG
1 GAGGGAGGGAGAGG
61937143 GAGGGAGG
1 GAGGGAGG
61937151 AACAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (14 bp):
GAGGGAGGGAGAGG
Found at i:61941318 original size:30 final size:30
Alignment explanation
Indices: 61941235--61941320 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
61941225 TAGGTACTTC
* *
61941235 CACACGGGTGATCCACACGCCCGCGTGTGC
1 CACACGGGTGATCCACACGCCCGTGTGTGA
* *
61941265 CACATGGGTGATCCACATGCCCGTGTGTGA
1 CACACGGGTGATCCACACGCCCGTGTGTGA
61941295 CACACGGGTAGAT-CACACGCCCGTGT
1 CACACGGGT-GATCCACACGCCCGTGT
61941321 ATCATGGCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
30 46 0.94
31 3 0.06
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.17
Consensus pattern (30 bp):
CACACGGGTGATCCACACGCCCGTGTGTGA
Found at i:61943402 original size:23 final size:23
Alignment explanation
Indices: 61943354--61943417 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
61943344 ATATATTCAA
61943354 ATTATGTTTTATTCTATA-ACGTTT
1 ATTAT-TTTTATTCTATATACG-TT
61943378 ATTATTTTTATTCTATATTAC-TT
1 ATTATTTTTATTCTATA-TACGTT
*
61943401 ATTATTTTT-TTATATAT
1 ATTATTTTTATTCTATAT
61943418 GTTATGTATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 1 0.03
22 6 0.16
23 23 0.62
24 5 0.14
25 2 0.05
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (23 bp):
ATTATTTTTATTCTATATACGTT
Found at i:61945218 original size:53 final size:54
Alignment explanation
Indices: 61945150--61945357 Score: 233
Period size: 53 Copynumber: 3.9 Consensus size: 54
61945140 TTTCCTTTTT
* * *
61945150 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * * ** *
61945203 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGTCTTATA
1 GAACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCC-TTGCCTTATA
** * *
61945257 GTAACTTATTAATACCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
1 G-AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* *
61945312 GAACTTATCAATGCCATG-CATTGGCATGGTCTTACATGATATCCTT
1 GAACTTACCAATGCCATGTC-TTGACATGGTCTTACATGATATCCTT
61945358 ATGTTACCAA
Statistics
Matches: 129, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
52 2 0.02
53 44 0.34
54 40 0.31
55 41 0.32
56 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (54 bp):
GAACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATA
Found at i:61946888 original size:28 final size:27
Alignment explanation
Indices: 61946845--61946903 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 27
61946835 TTAAAAAAAA
*
61946845 CTTATTTCTCTTTTGAGTGTCAATATT
1 CTTATTTCTCTCTTGAGTGTCAATATT
61946872 CTTAGTTTCTCTCTTGAGTGTCAATATT
1 CTTA-TTTCTCTCTTGAGTGTCAATATT
61946900 CTTA
1 CTTA
61946904 CCTTTCGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.53
Consensus pattern (27 bp):
CTTATTTCTCTCTTGAGTGTCAATATT
Found at i:61952574 original size:21 final size:21
Alignment explanation
Indices: 61952549--61952590 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
61952539 ACAGAAGAGA
61952549 AAGTAAAAATCATCAGAGATT
1 AAGTAAAAATCATCAGAGATT
61952570 AAGTAAAAATCATCAGAGATT
1 AAGTAAAAATCATCAGAGATT
61952591 GCTTGAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (21 bp):
AAGTAAAAATCATCAGAGATT
Done.