Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 81 of 345
Found at i:22198984 original size:19 final size:18
Alignment explanation
Indices: 22198960--22199011 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
22198950 AAACAATTGA
*
22198960 TAAAGTACATTATAAATAT
1 TAAAGTAAATTATAAAT-T
* *
22198979 TAAAGTATATTTTAAATT
1 TAAAGTAAATTATAAATT
22198997 TAAA-TAAATTATAAA
1 TAAAGTAAATTATAAA
22199012 AATAATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 9 0.31
18 5 0.17
19 15 0.52
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAAGTAAATTATAAATT
Found at i:22206689 original size:6 final size:6
Alignment explanation
Indices: 22206680--22206719 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
22206670 TTTCTATTCC
22206680 TATTTT TA-TTT TATTTT TATTTT TATTTT TATTTT TATTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTT
22206720 ATCTTTTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TATTTT
Found at i:22206689 original size:12 final size:11
Alignment explanation
Indices: 22206660--22206719 Score: 66
Period size: 12 Copynumber: 5.2 Consensus size: 11
22206650 TGTCTTCTTG
*
22206660 TTTTATCTTAT
1 TTTTATTTTAT
* *
22206671 TTCTATTCCTAT
1 TTTTATT-TTAT
22206683 TTTTATTTTAT
1 TTTTATTTTAT
22206694 TTTTATTTTTAT
1 TTTTA-TTTTAT
22206706 TTTTATTTTTAT
1 TTTTA-TTTTAT
22206718 TT
1 TT
22206720 ATCTTTTATG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
11 13 0.31
12 29 0.69
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:22206712 original size:23 final size:23
Alignment explanation
Indices: 22206660--22206746 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
22206650 TGTCTTCTTG
* * **
22206660 TTTTATCTTATTTCTATTCCTAT
1 TTTTATTTTATTTTTATTTTTAT
22206683 TTTTATTTTATTTTTATTTTTAT
1 TTTTATTTTATTTTTATTTTTAT
*
22206706 TTTTATTTT-TATTTATCTTTTAT
1 TTTTATTTTATTTTTAT-TTTTAT
* *
22206729 GTTTCTTATTATCTTTTA
1 TTTTATT-TTAT-TTTTA
22206747 AAGACTTGTA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 6 0.12
23 39 0.75
24 2 0.04
25 1 0.02
26 4 0.08
ACGTcount: A:0.17, C:0.08, G:0.01, T:0.74
Consensus pattern (23 bp):
TTTTATTTTATTTTTATTTTTAT
Found at i:22206726 original size:11 final size:10
Alignment explanation
Indices: 22206660--22206728 Score: 61
Period size: 11 Copynumber: 6.6 Consensus size: 10
22206650 TGTCTTCTTG
22206660 TTTTATCTTAT
1 TTTTAT-TTAT
*
22206671 TTCTATTCCTAT
1 TTTTATT--TAT
22206683 TTTTATTTTAT
1 TTTTA-TTTAT
22206694 TTTTATTT-T
1 TTTTATTTAT
*
22206703 TATT-TTTAT
1 TTTTATTTAT
22206712 TTTTATTTAT
1 TTTTATTTAT
22206722 CTTTTAT
1 -TTTTAT
22206729 GTTTCTTATT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
8 3 0.06
9 8 0.17
10 9 0.19
11 19 0.40
12 7 0.15
13 2 0.04
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:22206726 original size:18 final size:18
Alignment explanation
Indices: 22206688--22206745 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
22206678 CCTATTTTTA
* *
22206688 TTTTATTTTTATTTTTAT
1 TTTTATTTTTATTTATCT
22206706 TTTTATTTTTATTTATCT
1 TTTTATTTTTATTTATCT
*
22206724 TTTATGTTTCTTA-TTATCT
1 TTT-TATTT-TTATTTATCT
22206743 TTT
1 TTT
22206746 AAAGACTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 19 0.54
19 13 0.37
20 3 0.09
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTATTTATCT
Found at i:22206740 original size:29 final size:29
Alignment explanation
Indices: 22206680--22206746 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
22206670 TTTCTATTCC
* *
22206680 TATTTTTATTTTATTTTTATTTTTATTTT
1 TATTTTTATTTTATTTTTATGTTTATTAT
*
22206709 TATTTTTA-TTTATCTTTTATGTTTCTTAT
1 TATTTTTATTTTAT-TTTTATGTTTATTAT
22206738 TATCTTTTA
1 TAT-TTTTA
22206747 AAGACTTGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 5 0.15
29 23 0.70
30 5 0.15
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.76
Consensus pattern (29 bp):
TATTTTTATTTTATTTTTATGTTTATTAT
Found at i:22210916 original size:15 final size:14
Alignment explanation
Indices: 22210898--22211110 Score: 58
Period size: 14 Copynumber: 15.2 Consensus size: 14
22210888 TTATTTTTCG
22210898 ATTATATATTATAT
1 ATTATATATTATAT
*
22210912 AATTATTTATTATAT
1 -ATTATATATTATAT
* *
22210927 ATTATTTATATTGTTT
1 ATTA--TATATTATAT
*
22210943 A-TATTTATTATAT
1 ATTATATATTATAT
* ** *
22210956 ATTACTTTTCACGAAAT
1 ATTA--TAT-ATTATAT
* *
22210973 ATTAT-TATTTTAC
1 ATTATATATTATAT
22210986 ATTAT-TATTTATAT
1 ATTATATA-TTATAT
22211000 ATTAT-TATTATTAT
1 ATTATATATTA-TAT
* *
22211014 ATT-TTTACTTGTAT
1 ATTATATA-TTATAT
*
22211028 AATATAT-TTAT-T
1 ATTATATATTATAT
22211040 AATTATATA-TATTAT
1 -ATTATATATTA-TAT
*
22211055 ATTAT-T-TT-TAC
1 ATTATATATTATAT
22211066 A-TATATACTT-TCAT
1 ATTATATA-TTAT-AT
*
22211080 ATTATATTATAAT-T
1 ATTATA-TATTATAT
*
22211094 ATTTTATATTATAT
1 ATTATATATTATAT
22211108 ATT
1 ATT
22211111 TTTTATCTAT
Statistics
Matches: 147, Mismatches: 27, Indels: 49
0.66 0.12 0.22
Matches are distributed among these distances:
10 3 0.02
11 4 0.03
12 1 0.01
13 42 0.29
14 49 0.33
15 26 0.18
16 14 0.10
17 8 0.05
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (14 bp):
ATTATATATTATAT
Found at i:22210923 original size:22 final size:23
Alignment explanation
Indices: 22210898--22210957 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 23
22210888 TTATTTTTCG
22210898 ATTATATATTATATA-ATTATTT
1 ATTATATATTATATATATTATTT
* *
22210920 ATTATATATTATTTATATTGTTT
1 ATTATATATTATATATATTATTT
*
22210943 A-TATTTATTATATAT
1 ATTATATATTATATAT
22210958 TACTTTTCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTATATATTATATATATTATTT
Found at i:22210938 original size:20 final size:20
Alignment explanation
Indices: 22210898--22211116 Score: 65
Period size: 20 Copynumber: 10.8 Consensus size: 20
22210888 TTATTTTTCG
*
22210898 ATTATATATTATATAATTATTT
1 ATTATATATTAT-TTA-TATTT
22210920 ATTATATATTATTTATATTGT
1 ATTATATATTATTTATATT-T
22210941 -TTATAT-TTATTATATATTACT
1 ATTATATATTATT-TATATT--T
* *
22210962 TTTCACGAAATATTA-TTAT-TTT
1 ATT----ATATATTATTTATATTT
*
22210984 A-CAT-TATTATTTATA--T
1 ATTATATATTATTTATATTT
*
22211000 ATTAT-TATTATTATATTTTT
1 ATTATATATTATT-TATATTT
* * *
22211020 ACTTGTATAATATATT-TATTA
1 A-TTATATATTAT-TTATATTT
22211041 ATTATATA-TATTATATTATTT
1 ATTATATATTATT-TA-TATTT
*
22211062 -TTACATATATACTTTCATATTAT
1 ATTATATAT-TA-TTT-ATATT-T
22211085 ATTATA-ATTATTT-TA--T
1 ATTATATATTATTTATATTT
*
22211101 ATTATATATTTTTTAT
1 ATTATATATTATTTAT
22211117 CTATATAATA
Statistics
Matches: 151, Mismatches: 17, Indels: 62
0.66 0.07 0.27
Matches are distributed among these distances:
16 14 0.09
17 20 0.13
18 5 0.03
19 11 0.07
20 30 0.20
21 18 0.12
22 30 0.20
23 7 0.05
24 6 0.04
25 3 0.02
26 4 0.03
27 3 0.02
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (20 bp):
ATTATATATTATTTATATTT
Found at i:22211058 original size:52 final size:51
Alignment explanation
Indices: 22210986--22211107 Score: 121
Period size: 52 Copynumber: 2.5 Consensus size: 51
22210976 ATTATTTTAC
* * *
22210986 ATTATT-ATT-TATATA-T-TATTATTATTATATTTTTACTTGT-ATAATAT
1 ATTATTAATTATATATATTATATTATTATTACATATATACTT-TCATAATAT
* *
22211033 ATTTATTAATTATATATATTATATTATTTTTACATATATACTTTCATATTAT
1 A-TTATTAATTATATATATTATATTATTATTACATATATACTTTCATAATAT
*
22211085 ATTA-TAATTATTTTATATTATAT
1 ATTATTAATTA-TATATATTATAT
22211108 ATTTTTTATC
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
47 1 0.02
48 5 0.08
49 3 0.05
50 12 0.19
51 16 0.26
52 25 0.40
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (51 bp):
ATTATTAATTATATATATTATATTATTATTACATATATACTTTCATAATAT
Found at i:22211102 original size:16 final size:16
Alignment explanation
Indices: 22211081--22211116 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
22211071 TACTTTCATA
22211081 TTATATTATA-ATTATT
1 TTATATTATATATT-TT
22211097 TTATATTATATATTTT
1 TTATATTATATATTTT
22211113 TTAT
1 TTAT
22211117 CTATATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTATATATTTT
Found at i:22211121 original size:15 final size:14
Alignment explanation
Indices: 22210971--22211123 Score: 70
Period size: 14 Copynumber: 10.7 Consensus size: 14
22210961 TTTTCACGAA
22210971 ATATTAT-TATTTT
1 ATATTATATATTTT
*
22210984 ACATTAT-TATTTAT
1 ATATTATATATTT-T
22210998 ATATTAT-TATTATT
1 ATATTATATATT-TT
* *
22211012 ATATT-TTTACTTGT
1 ATATTATATA-TTTT
*
22211026 ATAATATAT-TTATT
1 ATATTATATATT-TT
*
22211040 A-ATTATATATATT
1 ATATTATATATTTT
*
22211053 ATATTAT-T-TTTAC
1 ATATTATATATTT-T
* *
22211066 ATATATACTTTCATATT
1 ATAT-TA-TAT-ATTTT
22211083 ATATTATAATTATTTT
1 ATATTAT-A-TATTTT
22211099 ATATTATATATTTT
1 ATATTATATATTTT
*
22211113 TTATCTATATA
1 ATAT-TATATA
22211124 ATATTATCAT
Statistics
Matches: 108, Mismatches: 15, Indels: 32
0.70 0.10 0.21
Matches are distributed among these distances:
12 2 0.02
13 28 0.26
14 43 0.40
15 14 0.13
16 14 0.13
17 5 0.05
18 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (14 bp):
ATATTATATATTTT
Found at i:22211122 original size:36 final size:35
Alignment explanation
Indices: 22211042--22211130 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 35
22211032 TATTTATTAA
22211042 TTATATATATTATATTATTTTTACATATATACTTTC
1 TTAT-TATATTATATTATTTTTACATATATACTTTC
* * *
22211078 ATATTATATTATAATTATTTTATA-TTATATA-TTTT
1 TTATTATATTAT-ATTATTTT-TACATATATACTTTC
*
22211113 TTATCTATATAATATTAT
1 TTAT-TATATTATATTAT
22211131 CATTAAAGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
35 19 0.42
36 24 0.53
37 2 0.04
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (35 bp):
TTATTATATTATATTATTTTTACATATATACTTTC
Found at i:22211394 original size:18 final size:19
Alignment explanation
Indices: 22211373--22211418 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
22211363 TTCTAAACCA
22211373 ATATATTTTTTATT-TTAT
1 ATATATTTTTTATTCTTAT
* * *
22211391 ATATAATTATTATTCTTTT
1 ATATATTTTTTATTCTTAT
22211410 ATA-ATTTTT
1 ATATATTTTT
22211419 GTTATTATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATATTTTTTATTCTTAT
Found at i:22221710 original size:206 final size:206
Alignment explanation
Indices: 22221300--22221831 Score: 791
Period size: 206 Copynumber: 2.6 Consensus size: 206
22221290 GGGCTGTCAC
* * *
22221300 ATTTGGCAGCCTTGTGCTTACAAGGAGAAAATCGAAGACATAGCTGATTTGGCTTTCATGTGCTT
1 ATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTT
*
22221365 ACGTTGAAGCAAATCTAAGATGATTTGGCATCTGTGTATTGTCAGAGAACAAATCGAAGCCTGGC
66 ACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGCCTGGC
* * * * * * **
22221430 ATTCTCCACTTCGACAGAGGGCAGACACGTAGCAGATCTACCATTCAGATGTTTATACTGAAGTA
131 ATTCTCCACTTCAACAGAGAGCAGACACATAACAGATCTACCATTCAGATATTTACACTGAACAA
* *
22221495 GATCCAAGATG
196 GACCCAAGATA
* *
22221506 GTTTGGCATCCTTGTGCTTGCAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTT
1 ATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTT
* *
22221571 ACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAAAGAACAAATCGAAGTCTGGC
66 ACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGCCTGGC
* *
22221636 A-TCTCCATTTCAACGGAGAGCAGACACATAACAGATCTCACC-TTCAGATAATTT-CACTGAAA
131 ATTCTCCACTTCAACAGAGAGCAGACACATAACAGATCT-ACCATTCAGAT-ATTTACACTG-AA
22221698 CAAGACCCAAGATA
193 CAAGACCCAAGATA
* * *
22221712 ATTTGGCATTCTTGTGCTTACAAGGAACAAATTGAAGACATAGCTGATTTGGCTTTCACGTGCTT
1 ATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTT
* *
22221777 ACGATGAAGCAAATCTAAGATGATTTGGCATCTTTGTATTGTCAGAGAACAAATC
66 ACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATC
22221832 AAAAAAGCAG
Statistics
Matches: 295, Mismatches: 28, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
205 42 0.14
206 253 0.86
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (206 bp):
ATTTGGCATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGCTT
ACGTTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGCCTGGC
ATTCTCCACTTCAACAGAGAGCAGACACATAACAGATCTACCATTCAGATATTTACACTGAACAA
GACCCAAGATA
Found at i:22222043 original size:4 final size:4
Alignment explanation
Indices: 22222034--22222066 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
22222024 AACCGGGTCT
22222034 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
22222067 GTTTGTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:22223561 original size:20 final size:20
Alignment explanation
Indices: 22223538--22223678 Score: 82
Period size: 20 Copynumber: 7.0 Consensus size: 20
22223528 AATCTAACCC
*
22223538 TATATATTTATTTCTATTAT
1 TATATATTTATTTATATTAT
*
22223558 TATATATATAAATTTATTATTAT
1 TATATAT-T-TATTTA-TATTAT
22223581 TATTATTATTT-TTT-TATT-T
1 TA-TA-TATTTATTTATATTAT
* * *
22223600 T-TA-ACCTTATTTTTA-GAT
1 TATATA-TTTATTTATATTAT
*
22223618 TATATATTATATAATTATTTTAT
1 TATATATT-TAT--TTATATTAT
22223641 TATATA-TTATTTATATTAT
1 TATATATTTATTTATATTAT
22223660 TAT-TATTTATTATATATTA
1 TATATATTTATT-TATATTA
22223679 CTTTTCACGA
Statistics
Matches: 94, Mismatches: 10, Indels: 34
0.68 0.07 0.25
Matches are distributed among these distances:
15 1 0.01
16 2 0.02
17 5 0.05
18 6 0.06
19 21 0.22
20 22 0.23
21 4 0.04
22 11 0.12
23 16 0.17
24 3 0.03
25 3 0.03
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (20 bp):
TATATATTTATTTATATTAT
Found at i:22223577 original size:3 final size:3
Alignment explanation
Indices: 22223571--22223678 Score: 64
Period size: 3 Copynumber: 36.0 Consensus size: 3
22223561 ATATATAAAT
* * *** * *
22223571 TTA TTA TTA TTA TTA TTA TT- TTT TTA TTT TTA ACC TTA TTT TTA -GA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
22223617 TTA TATA TTA -TA TAA TTA TT- TTA TTA TATA TTA TT- TATA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA
22223662 TTA TTTA TTA TATA TTA
1 TTA -TTA TTA T-TA TTA
22223679 CTTTTCACGA
Statistics
Matches: 80, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
2 8 0.10
3 59 0.74
4 13 0.16
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:22223634 original size:15 final size:15
Alignment explanation
Indices: 22223616--22223873 Score: 119
Period size: 16 Copynumber: 16.8 Consensus size: 15
22223606 TTATTTTTAG
22223616 ATTA-TATATTATAT
1 ATTATTATATTATAT
*
22223630 AATTATTTTATTATAT
1 -ATTATTATATTATAT
22223646 ATTATTTATATTAT-T
1 ATTA-TTATATTATAT
22223661 ATTATT-TATTATAT
1 ATTATTATATTATAT
* ** *
22223675 ATTACTTTTCACGAAAT
1 ATTA-TTAT-ATTATAT
*
22223692 ATTATTAT-TT-TAC
1 ATTATTATATTATAT
22223705 ATTATTAT-TTATAT
1 ATTATTATATTATAT
22223719 ATTA-T-TATTATATT
1 ATTATTATATTATA-T
* * *
22223733 TTTACTTGTATAATAT
1 ATTA-TTATATTATAT
22223749 ATTTATTA-ATTATAT
1 A-TTATTATATTATAT
22223764 A-TATTATA-TAT-T
1 ATTATTATATTATAT
* *
22223776 ATTTTTACATATATACT
1 ATTATTATAT-TATA-T
*
22223793 TTCATATTATATTATA-
1 AT--TATTATATTATAT
22223809 ATTATTTTATATTATATT
1 ATTA--TTATATTATA-T
*
22223827 AATTTTATACTATTATAT
1 -ATTAT-TA-TATTATAT
* *
22223845 ATTTTTTTATCTATAT
1 ATTATTATAT-TATAT
22223861 ATTATTATCATTA
1 ATTATTAT-ATTA
22223874 AAGGTTTTAA
Statistics
Matches: 187, Mismatches: 26, Indels: 59
0.69 0.10 0.22
Matches are distributed among these distances:
12 3 0.02
13 36 0.19
14 20 0.11
15 28 0.15
16 50 0.27
17 27 0.14
18 7 0.04
19 16 0.09
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (15 bp):
ATTATTATATTATAT
Found at i:22223662 original size:27 final size:29
Alignment explanation
Indices: 22223624--22223847 Score: 97
Period size: 27 Copynumber: 7.9 Consensus size: 29
22223614 AGATTATATA
22223624 TTATATAATTA-T-TTTATTATATATTAT
1 TTATATAATTATTATTTATTATATATTAT
*
22223651 TTATATTATTATTATTTATTATATATTACT
1 TTATATAATTATTATTTATTATATATTA-T
* * * *
22223681 TT-TCACGAAATATTATTATTTTACATTATTAT
1 TTAT-A-TAATTATTATT-TATTATA-TATTAT
* *
22223713 TTATAT-ATTATTA-TTA-TAT-TTTTAC
1 TTATATAATTATTATTTATTATATATTAT
* *
22223738 TTGTATAATATATTTATTAATTATATA-TA-
1 TTATATAAT-TA-TTATTTATTATATATTAT
*
22223767 TTATAT-ATTATT-TTTA-CATATA-TACT
1 TTATATAATTATTATTTATTATATATTA-T
* *
22223793 TTCATATTA-TATTA-TAATTAT-T-TTAT
1 TT-ATATAATTATTATTTATTATATATTAT
*
22223819 ATTATATTAATT-TTATACTATTATATATT
1 -TTATA-TAATTATTAT-TTATTATATATT
22223848 TTTTTATCTA
Statistics
Matches: 146, Mismatches: 23, Indels: 52
0.66 0.10 0.24
Matches are distributed among these distances:
24 7 0.05
25 12 0.08
26 10 0.07
27 36 0.25
28 11 0.08
29 28 0.19
30 16 0.11
31 11 0.08
32 9 0.06
33 6 0.04
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (29 bp):
TTATATAATTATTATTTATTATATATTAT
Found at i:22223775 original size:54 final size:51
Alignment explanation
Indices: 22223705--22223825 Score: 129
Period size: 54 Copynumber: 2.3 Consensus size: 51
22223695 ATTATTTTAC
* * *
22223705 ATTATTAT-TTATATATTATTATTATATTTTTACTTGT-ATAATATATTTATTA
1 ATTATTATATTATATATTATTATTACATATATACTT-TCATAATATA-TTA-TA
* *
22223757 ATTATATATATTATATATTATTTTTACATATATACTTTCATATTATATTATA
1 ATTAT-TATATTATATATTATTATTACATATATACTTTCATAATATATTATA
22223809 ATTATTTTATATTATAT
1 ATTA--TTATATTATAT
22223826 TAATTTTATA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
52 11 0.19
53 17 0.29
54 31 0.53
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (51 bp):
ATTATTATATTATATATTATTATTACATATATACTTTCATAATATATTATA
Found at i:22223806 original size:111 final size:115
Alignment explanation
Indices: 22223646--22223850 Score: 248
Period size: 111 Copynumber: 1.8 Consensus size: 115
22223636 TTTATTATAT
* *
22223646 ATTATTTATATTATTATTATTTATTATATATTACTTTTCACGAAATA-T-T-ATTATTTTACA-T
1 ATTATATATATTATTATTATTTATTACATATTACTTTTCACGAAATATTATAATTATTTTACATT
*
22223707 -TATT-ATTTATATATTATTATTATATTTTTACTTGTATAATATATTTATTA
66 ATATTAATTT-TATACTATTA-TATATTTTTACTTGTATAATATATTTATTA
* * *
22223757 ATTATATATATTATATATTATTT-TTACATATATAC-TTTCA-TATTATATTATAATTATTTTAT
1 ATTATATATATTAT-TATTATTTATTACATAT-TACTTTTCACGA-AATATTATAATTATTTTAC
22223819 ATTATATTAATTTTATACTATTATATATTTTT
63 ATTATATTAATTTTATACTATTATATATTTTT
22223851 TTATCTATAT
Statistics
Matches: 79, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
110 1 0.01
111 28 0.35
112 12 0.15
113 1 0.01
114 10 0.13
115 10 0.13
116 13 0.16
117 4 0.05
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (115 bp):
ATTATATATATTATTATTATTTATTACATATTACTTTTCACGAAATATTATAATTATTTTACATT
ATATTAATTTTATACTATTATATATTTTTACTTGTATAATATATTTATTA
Found at i:22224041 original size:27 final size:27
Alignment explanation
Indices: 22224000--22224066 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 27
22223990 CATTAATTAC
* *
22224000 TTATTTTATAT-TATTCTA-AACTTATAT
1 TTATTATATATATATTATATAA-TTAT-T
22224027 TTA-TATATATATATTATATAATTATT
1 TTATTATATATATATTATATAATTATT
*
22224053 TTATTATAAATATA
1 TTATTATATATATA
22224067 AATTTCTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 10 0.29
27 22 0.65
28 2 0.06
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATTATATATATATTATATAATTATT
Found at i:22227776 original size:28 final size:30
Alignment explanation
Indices: 22227745--22227800 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
22227735 TATGTTAATT
22227745 AATTATAAAATATATT-ATTAT-TTATTCA
1 AATTATAAAATATATTAATTATATTATTCA
* **
22227773 AATTGTAATTTATATTAATTATATTATT
1 AATTATAAAATATATTAATTATATTATT
22227801 ATATTATGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 13 0.57
29 5 0.22
30 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
AATTATAAAATATATTAATTATATTATTCA
Found at i:22229106 original size:17 final size:17
Alignment explanation
Indices: 22229081--22229117 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
22229071 TTGTTGAAGA
*
22229081 ATCTATTTGGATTTTGC
1 ATCTATTTGGATTTTCC
*
22229098 ATCTGTTTGGATTTTCC
1 ATCTATTTGGATTTTCC
22229115 ATC
1 ATC
22229118 AGTCTGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.51
Consensus pattern (17 bp):
ATCTATTTGGATTTTCC
Found at i:22233526 original size:32 final size:32
Alignment explanation
Indices: 22233487--22233579 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
22233477 TTAGATATTG
*
22233487 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
22233519 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTGGATATTGAATTT
*
22233551 ATTATGTTTTAAACTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTGGATATTGAA
22233580 ATGATTGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTGGATATTGAATTT
Found at i:22234569 original size:29 final size:29
Alignment explanation
Indices: 22234530--22234587 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
22234520 TTTTAATGTG
22234530 GTGTAATATTAGTTATGCACTTGGACAAT
1 GTGTAATATTAGTTATGCACTTGGACAAT
*
22234559 GTGTAATATTAGTTATGCGCTTGGACAAT
1 GTGTAATATTAGTTATGCACTTGGACAAT
22234588 ATTGTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.38
Consensus pattern (29 bp):
GTGTAATATTAGTTATGCACTTGGACAAT
Found at i:22234771 original size:21 final size:17
Alignment explanation
Indices: 22234726--22234759 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
22234716 AATTACAAAA
22234726 TTTATTTAACTTTGGTT
1 TTTATTTAACTTTGGTT
22234743 TTTATTTAACTTTGGTT
1 TTTATTTAACTTTGGTT
22234760 GTTTTCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.06, G:0.12, T:0.65
Consensus pattern (17 bp):
TTTATTTAACTTTGGTT
Found at i:22234892 original size:18 final size:18
Alignment explanation
Indices: 22234871--22234913 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
22234861 AAAATTTAAA
22234871 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
22234889 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
22234907 ATGTAAA
1 ATATAAA
22234914 GACAGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:22235373 original size:46 final size:46
Alignment explanation
Indices: 22235306--22235409 Score: 172
Period size: 46 Copynumber: 2.3 Consensus size: 46
22235296 AGTGTCGTTT
*
22235306 TGGTGTGTTTGGGTGGTTTATTCCGGTGTGTTTGGGTGGATTATTC
1 TGGTGTGTTTGGGTGGTTTATTCCAGTGTGTTTGGGTGGATTATTC
* * *
22235352 TGGTGTGTTTGGGTGGTTTATTCTAGTGTGTTTGGTTGGATTATTT
1 TGGTGTGTTTGGGTGGTTTATTCCAGTGTGTTTGGGTGGATTATTC
22235398 TGGTGTGTTTGG
1 TGGTGTGTTTGG
22235410 TTAGAATCCG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.07, C:0.04, G:0.38, T:0.51
Consensus pattern (46 bp):
TGGTGTGTTTGGGTGGTTTATTCCAGTGTGTTTGGGTGGATTATTC
Found at i:22235411 original size:23 final size:23
Alignment explanation
Indices: 22235306--22235409 Score: 154
Period size: 23 Copynumber: 4.5 Consensus size: 23
22235296 AGTGTCGTTT
*
22235306 TGGTGTGTTTGGGTGGTTTATTC
1 TGGTGTGTTTGGGTGGATTATTC
*
22235329 CGGTGTGTTTGGGTGGATTATTC
1 TGGTGTGTTTGGGTGGATTATTC
*
22235352 TGGTGTGTTTGGGTGGTTTATTC
1 TGGTGTGTTTGGGTGGATTATTC
* * *
22235375 TAGTGTGTTTGGTTGGATTATTT
1 TGGTGTGTTTGGGTGGATTATTC
22235398 TGGTGTGTTTGG
1 TGGTGTGTTTGG
22235410 TTAGAATCCG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 72 1.00
ACGTcount: A:0.07, C:0.04, G:0.38, T:0.51
Consensus pattern (23 bp):
TGGTGTGTTTGGGTGGATTATTC
Found at i:22243269 original size:27 final size:26
Alignment explanation
Indices: 22243227--22243336 Score: 96
Period size: 26 Copynumber: 4.2 Consensus size: 26
22243217 AGGAAGCGTC
* *
22243227 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTACCAC-ATTATCTGAT
* *
22243254 CTGGTGGGTCTACCACATATAT-TGTT
1 CTGGTGGCTCTACCACAT-TATCTGAT
* *
22243280 CTGGTGGCTCTGCCACGATTATCTTAT
1 CTGGTGGCTCTACCAC-ATTATCTGAT
* * * *
22243307 CTGGTGACTCTATCACATTGTCTGTT
1 CTGGTGGCTCTACCACATTATCTGAT
22243333 CTGG
1 CTGG
22243337 CAGTCATGCT
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
26 33 0.50
27 33 0.50
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTACCACATTATCTGAT
Found at i:22243295 original size:26 final size:27
Alignment explanation
Indices: 22243227--22243317 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
22243217 AGGAAGCGTC
*
22243227 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* * *
22243254 CTGGTGGGTCTACCAC-ATATAT-TGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* *
22243280 CTGGTGGCTCTGCCACGATTATCTTAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
22243307 CTGGTGACTCT
1 CTGGTGGCTCT
22243318 ATCACATTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
26 22 0.42
27 30 0.58
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:22249438 original size:16 final size:15
Alignment explanation
Indices: 22249412--22249442 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
22249402 ACTAGATCGG
22249412 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
22249427 CAAAATGCCGAAAAGC
1 CAAAA-GCCGAAAAGC
22249443 TGATATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.26, G:0.19, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:22249874 original size:27 final size:26
Alignment explanation
Indices: 22249834--22249944 Score: 116
Period size: 27 Copynumber: 4.1 Consensus size: 26
22249824 AGGAAGTGTC
*
22249834 CTGGTGGCTATGCCACAATTATCTGATT
1 CTGGTGGCTCTGCCAC-ATTATCTG-TT
22249862 -TGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
* *
22249888 CTGGTGGCTCTGCCATGATTATCTATAT
1 CTGGTGGCTCTGCCA-CATTATCTGT-T
* * *
22249916 CTGGTGACTTTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
22249942 CTG
1 CTG
22249945 ACAGCCATGC
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
26 8 0.11
27 48 0.68
28 15 0.21
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.40
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:22249938 original size:54 final size:54
Alignment explanation
Indices: 22249834--22249944 Score: 136
Period size: 54 Copynumber: 2.1 Consensus size: 54
22249824 AGGAAGTGTC
*
22249834 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATTTGGTGACTCTGCCACATATATCTGTT
* ** * *
22249888 CTGGTGGCTCTGCCATGATTATCT-ATATCTGGTGACTTTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGAT-T-TGGTGACTCTGCCACATATATCTGTT
22249942 CTG
1 CTG
22249945 ACAGCCATGC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
53 2 0.04
54 33 0.67
55 14 0.29
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.40
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATTTGGTGACTCTGCCACATATATCTGTT
Found at i:22252805 original size:40 final size:40
Alignment explanation
Indices: 22252752--22252860 Score: 175
Period size: 40 Copynumber: 2.7 Consensus size: 40
22252742 ACTACTTGCT
*
22252752 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
* *
22252792 CAAATGCCTTCGGGACTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTAGCA
22252832 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
22252861 CATCCGAATA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
39 1 0.02
40 61 0.97
41 1 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
Found at i:22257686 original size:17 final size:16
Alignment explanation
Indices: 22257660--22257692 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
22257650 TCATCAAACG
22257660 GCATAAATCGGCCGGA
1 GCATAAATCGGCCGGA
22257676 GCATCAAATCGGCCGGA
1 GCAT-AAATCGGCCGGA
22257693 AAAGGAACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.30, C:0.27, G:0.30, T:0.12
Consensus pattern (16 bp):
GCATAAATCGGCCGGA
Found at i:22260744 original size:39 final size:39
Alignment explanation
Indices: 22260701--22260879 Score: 297
Period size: 39 Copynumber: 4.6 Consensus size: 39
22260691 ACTACTTGCT
*
22260701 CAAATGCCTTCGGGACTTAGCCCGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATATAGTAACTCGCA
22260740 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATATAGTAACTCGCA
*
22260780 CAAATGCCTTCGGGACTTAGCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATATAGTAACTCGCA
* *
22260819 CAAATGCCTTCGGGACTTAGCCCGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGATA-TAGTAACTCGCA
22260858 CAAATGCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
22260880 GGTTATCATC
Statistics
Matches: 133, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
38 1 0.01
39 95 0.71
40 37 0.28
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGATATAGTAACTCGCA
Found at i:22260799 original size:79 final size:78
Alignment explanation
Indices: 22260701--22260885 Score: 316
Period size: 79 Copynumber: 2.4 Consensus size: 78
22260691 ACTACTTGCT
* *
22260701 CAAATGCCTTCGGGACTTAGCCCGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAA
*
22260766 TATAGTAACTCGCA
66 T-TAGTAACTAGCA
*
22260780 CAAATGCCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAA
1 CAAATGCCTTCGGGACTTAGCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAA
*
22260845 TTAGTCACTAGCA
66 TTAGTAACTAGCA
22260858 CAAATGCCTTCGGGACTTAGCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCGGTTAT
22260886 CATCCGAATA
Statistics
Matches: 100, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
78 37 0.37
79 63 0.63
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.24
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGAA
TTAGTAACTAGCA
Found at i:22273270 original size:46 final size:46
Alignment explanation
Indices: 22273139--22273313 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
22273129 TGATATGTGT
* * ** *
22273139 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCC-ACATTACGAGA
1 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCTTGA-GACGAGA
* * * *
22273185 GCCAGTGTAAGACATGTTTGGAACATGCATCGGCATTGAGACGAGA
1 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCTTGAGACGAGA
** *
22273231 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCTTGAGATATACAA
1 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCTTGAGA-CGA-GA
*
22273279 GCTAGTGTAAGACTTGTCTT-GGACATGGCATCAGC
1 GCTAGTGTAAGACATGT-TTGGGACAT-GCATCAGC
22273314 TTGTTTAGTG
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
46 74 0.68
47 2 0.02
48 23 0.21
49 10 0.09
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTTTGGGACATGCATCAGCCTTGAGACGAGA
Found at i:22273384 original size:93 final size:98
Alignment explanation
Indices: 22273278--22273503 Score: 236
Period size: 98 Copynumber: 2.4 Consensus size: 98
22273268 GAGATATACA
* **
22273278 AGCTAGTGTAAGACTTGTCTTGG-ACATGGCATCAGCTT-G-T-T-T-AGTGTCAGTGTAAGACC
1 AGCTAGTGTAAGACCTGTC-TGGTACATGGCATCAGCTTCGATGTATGAAAGTCAGTGTAAGACC
* *
22273337 TGTCTGGGACATGGCATCGATATCGATAGATGAG
65 TGTCTAGAACATGGCATCGATATCGATAGATGAG
* * *
22273371 AGCTAGTGTAAGACCTGTCTGGTATATGGCATCGGCTTCGATGTATGAAAGTTAGTGTAAGACCT
1 AGCTAGTGTAAGACCTGTCTGGTACATGGCATCAGCTTCGATGTATGAAAGTCAGTGTAAGACCT
* **
22273436 GTCTAGAACATGGCATCGACT-TTGAT-G-TGCT
66 GTCTAGAACATGGCATCGA-TATCGATAGATGAG
* * *
22273467 AGCCAGTGTAAGACCATGTCTGGGACATGGCGTCAGC
1 AGCTAGTGTAAGACC-TGTCTGGTACATGGCATCAGC
22273504 ATTTTATCCA
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
92 3 0.03
93 31 0.28
94 1 0.01
95 1 0.01
96 17 0.16
97 19 0.17
98 36 0.33
99 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.29
Consensus pattern (98 bp):
AGCTAGTGTAAGACCTGTCTGGTACATGGCATCAGCTTCGATGTATGAAAGTCAGTGTAAGACCT
GTCTAGAACATGGCATCGATATCGATAGATGAG
Found at i:22273386 original size:49 final size:47
Alignment explanation
Indices: 22273326--22273497 Score: 184
Period size: 49 Copynumber: 3.6 Consensus size: 47
22273316 GTTTAGTGTC
*
22273326 AGTGTAAGACCTGTCTGGGACATGGCATCGATATCGATAGATGAGAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGAT-TCGAT-GATGAAAGCT
* * * *
22273375 AGTGTAAGACCTGTCTGGTATATGGCATCGGCTTCGATGTATGAAAGTT
1 AGTGTAAGACCTGTCTGGGACATGGCATC-GATTCGATG-ATGAAAGCT
* * * ** *
22273424 AGTGTAAGACCTGTCTAGAACATGGCATCGACTTTGATG-TGCTAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGA-TTCGATGATGAAAGCT
22273471 AGTGTAAGACCATGTCTGGGACATGGC
1 AGTGTAAGACC-TGTCTGGGACATGGC
22273498 GTCAGCATTT
Statistics
Matches: 103, Mismatches: 16, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
47 15 0.15
48 15 0.15
49 71 0.69
50 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27
Consensus pattern (47 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGATTCGATGATGAAAGCT
Found at i:22284094 original size:192 final size:192
Alignment explanation
Indices: 22283767--22284153 Score: 738
Period size: 192 Copynumber: 2.0 Consensus size: 192
22283757 ATGAGAACAA
*
22283767 AGCCAACGAAAACAATCGGTGTTTATAACATCGATTCGGTCACTATGCTCTCTACTCAGGTAGAA
1 AGCCAACGAAAACAACCGGTGTTTATAACATCGATTCGGTCACTATGCTCTCTACTCAGGTAGAA
22283832 CTCTTGAATAAGAAAATTGATGGTTTTCTTAGTTCTTTATAGGTTCACCCAGTAATGCAATGCGA
66 CTCTTGAATAAGAAAATTGATGGTTTTCTTAGTTCTTTATAGGTTCACCCAGTAATGCAATGCGA
22283897 AGCAAGTGGAGGTGGATCAAGCAATTCAGAATATCAACCTTATGGCCATAACATAAATAACG
131 AGCAAGTGGAGGTGGATCAAGCAATTCAGAATATCAACCTTATGGCCATAACATAAATAACG
*
22283959 AGCCAACGAAAACAACCGGTGTTTATAACGTCGATTCGGTCACTATGCTCTCTACTCAGGTAGAA
1 AGCCAACGAAAACAACCGGTGTTTATAACATCGATTCGGTCACTATGCTCTCTACTCAGGTAGAA
22284024 CTCTTGAATAAGAAAATTGATGGTTTTCTTAGTTCTTTATAGGTTCACCCAGTAATGCAATGCGA
66 CTCTTGAATAAGAAAATTGATGGTTTTCTTAGTTCTTTATAGGTTCACCCAGTAATGCAATGCGA
**
22284089 AGCAAGTGGAGGTGGATCAAGCAATTCAGAATATCAACCTTATGGCCATAACATGGATAACG
131 AGCAAGTGGAGGTGGATCAAGCAATTCAGAATATCAACCTTATGGCCATAACATAAATAACG
22284151 AGC
1 AGC
22284154 AGTTAAATTA
Statistics
Matches: 191, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
192 191 1.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (192 bp):
AGCCAACGAAAACAACCGGTGTTTATAACATCGATTCGGTCACTATGCTCTCTACTCAGGTAGAA
CTCTTGAATAAGAAAATTGATGGTTTTCTTAGTTCTTTATAGGTTCACCCAGTAATGCAATGCGA
AGCAAGTGGAGGTGGATCAAGCAATTCAGAATATCAACCTTATGGCCATAACATAAATAACG
Found at i:22301082 original size:49 final size:47
Alignment explanation
Indices: 22300948--22301119 Score: 130
Period size: 49 Copynumber: 3.6 Consensus size: 47
22300938 GAGTGTCAGA
* * * ** * *
22300948 GTAAGAACTGTTTGGGACATGGCATCGACACCAATAGATGAGAGCCAGT
1 GTAAGACCTGTCTGGGACATGGCATCAACTTCGAT-G-TGATAGCCAGT
* *** ** *
22300997 GTAAGACCTGTCTAGGACACAACATCGGCTTCGATGT-ATAAAAGTCAGT
1 GTAAGACCTGTCTGGGACATGGCATCAACTTCGATGTGAT---AGCCAGT
* *
22301046 GTAAGACCTGTCTGGGACATGGCATCAACTTTGATGTGCTAGCCAGT
1 GTAAGACCTGTCTGGGACATGGCATCAACTTCGATGTGATAGCCAGT
*
22301093 GTAAGATCATGTCTGGGACATGGCATC
1 GTAAGA-CCTGTCTGGGACATGGCATC
22301120 GGCATTTTAT
Statistics
Matches: 96, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
46 1 0.01
47 13 0.14
48 20 0.21
49 61 0.64
50 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (47 bp):
GTAAGACCTGTCTGGGACATGGCATCAACTTCGATGTGATAGCCAGT
Found at i:22301762 original size:62 final size:62
Alignment explanation
Indices: 22301689--22301812 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
22301679 CACATTGTTT
22301689 TGGGAAAAATGAGTGGCTTATCATAGCTCTTTAGTCATTTTGTATAATGCCATGGATGGTGG
1 TGGGAAAAATGAGTGGCTTATCATAGCTCTTTAGTCATTTTGTATAATGCCATGGATGGTGG
*
22301751 TGGGAAAAATGAGTGGCTTGTCATAGCTCTTTAGTCATTTTGTATAATGCCATGGATGGTGG
1 TGGGAAAAATGAGTGGCTTATCATAGCTCTTTAGTCATTTTGTATAATGCCATGGATGGTGG
22301813 CTAATATTGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.35
Consensus pattern (62 bp):
TGGGAAAAATGAGTGGCTTATCATAGCTCTTTAGTCATTTTGTATAATGCCATGGATGGTGG
Found at i:22308052 original size:42 final size:42
Alignment explanation
Indices: 22308006--22308090 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
22307996 GTTCGATTTA
*
22308006 ATTAATTAGCACTAAGTGTGCGATACAATTATAGCCTCGGCT
1 ATTAACTAGCACTAAGTGTGCGATACAATTATAGCCTCGGCT
22308048 ATTAACTAGCACTAAGTGTGCGATACAATTATAGCCTCGGCT
1 ATTAACTAGCACTAAGTGTGCGATACAATTATAGCCTCGGCT
22308090 A
1 A
22308091 ATTATGTAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (42 bp):
ATTAACTAGCACTAAGTGTGCGATACAATTATAGCCTCGGCT
Found at i:22309967 original size:27 final size:27
Alignment explanation
Indices: 22309937--22310044 Score: 123
Period size: 27 Copynumber: 4.0 Consensus size: 27
22309927 AGCGTCCTGA
*
22309937 TGGCTATGCCACAATTATCTGATCTGG
1 TGGCTCTGCCACAATTATCTGATCTGG
22309964 TGGCTCTGCCACATATT-TCT-ATTCTGG
1 TGGCTCTGCCACA-ATTATCTGA-TCTGG
*
22309991 TGGCTCTGCCACGATTATCTGTATCTGG
1 TGGCTCTGCCACAATTATCTG-ATCTGG
* * *
22310019 TGACTCTGTCAC-ATTATCTGTTCTGG
1 TGGCTCTGCCACAATTATCTGATCTGG
22310045 CAACCATGCT
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
26 9 0.13
27 43 0.61
28 18 0.25
29 1 0.01
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (27 bp):
TGGCTCTGCCACAATTATCTGATCTGG
Found at i:22310043 original size:54 final size:54
Alignment explanation
Indices: 22309937--22310044 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
22309927 AGCGTCCTGA
* *
22309937 TGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTATTCTGG
1 TGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTATTCTGG
* * * *
22309991 TGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTATTCTGG
22310045 CAACCATGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 29 0.62
55 18 0.38
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (54 bp):
TGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTATTCTGG
Found at i:22316495 original size:22 final size:22
Alignment explanation
Indices: 22316456--22316498 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
22316446 ATCACTCTTC
* *
22316456 CTCTCCTTTTATTTTTCTTTTT
1 CTCTCCATTTATTATTCTTTTT
*
22316478 CTCTCCATTTGTTATTCTTTT
1 CTCTCCATTTATTATTCTTTT
22316499 CTTCTTCTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.67
Consensus pattern (22 bp):
CTCTCCATTTATTATTCTTTTT
Found at i:22317775 original size:27 final size:27
Alignment explanation
Indices: 22317735--22317846 Score: 129
Period size: 27 Copynumber: 4.1 Consensus size: 27
22317725 AGGAAGCGTC
*
22317735 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
22317762 CTGGTGGCTCTGCCACATATT-TCTGTT
1 CTGGTGGCTCTGCCACA-ATTATCTGAT
**
22317789 CTGGTGGCTCTGCCATGATTATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
* * *
22317817 CTGGTGACTCTGTCAC-ATTATCTGTT
1 CTGGTGGCTCTGCCACAATTATCTGAT
22317843 CTGG
1 CTGG
22317847 CAACCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.11
27 48 0.66
28 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:22317841 original size:54 final size:54
Alignment explanation
Indices: 22317735--22317846 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
22317725 AGGAAGCGTC
* *
22317735 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATTTCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* ** *
22317789 CTGGTGGCTCTGCCATGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
22317843 CTGG
1 CTGG
22317847 CAACCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:22324562 original size:20 final size:20
Alignment explanation
Indices: 22324534--22324574 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
22324524 TAAGTCCCGA
*
22324534 AGAGTATTCGTGCTAGTGAT
1 AGAGCATTCGTGCTAGTGAT
22324554 AGAGCATTCGTGCTAGTGAT
1 AGAGCATTCGTGCTAGTGAT
22324574 A
1 A
22324575 TATCCGGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (20 bp):
AGAGCATTCGTGCTAGTGAT
Found at i:22324587 original size:60 final size:60
Alignment explanation
Indices: 22324494--22324614 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
22324484 TAAGTCCTGA
* * *
22324494 AGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGTATTCGTGCTAGTGAT
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
22324554 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
22324614 A
1 A
22324615 TATCCGGGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (60 bp):
AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGAT
Found at i:22324609 original size:40 final size:40
Alignment explanation
Indices: 22324554--22324773 Score: 383
Period size: 40 Copynumber: 5.6 Consensus size: 40
22324544 TGCTAGTGAT
22324554 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
22324594 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
22324634 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
* *
22324674 AGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGA
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
22324714 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGT-CC-A
1 AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
* *
22324752 AGAGCATT-GTGCTGGTGTTATA
1 AGAGCATTCGTGCTAGTGATATA
22324774 GGCACTGTGT
Statistics
Matches: 174, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
37 12 0.07
38 9 0.05
39 2 0.01
40 151 0.87
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
AGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGA
Found at i:22324645 original size:100 final size:100
Alignment explanation
Indices: 22324472--22324654 Score: 330
Period size: 100 Copynumber: 1.8 Consensus size: 100
22324462 ATTGAGAGTT
* * *
22324472 ATATATCCGGGCTAAGTCCTGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGA
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGA
*
22324537 GTATTCGTGCTAGTGATAGAGCATTCGTGCTAGTG
66 GCATTCGTGCTAGTGATAGAGCATTCGTGCTAGTG
22324572 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGA
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGA
22324637 GCATTCGTGCTAGTGATA
66 GCATTCGTGCTAGTGATA
22324655 TATCCGGGCT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (100 bp):
ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAAGA
GCATTCGTGCTAGTGATAGAGCATTCGTGCTAGTG
Found at i:22333122 original size:2 final size:2
Alignment explanation
Indices: 22333115--22333150 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22333105 TTGGATGTTG
22333115 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
22333151 TTGTTTTATA
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:22345211 original size:2 final size:2
Alignment explanation
Indices: 22345204--22345240 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
22345194 TATTCACAAC
*
22345204 TA TA TA TA TA TA TA TA TA TA CA 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
22345241 TTCATACTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22358696 original size:13 final size:13
Alignment explanation
Indices: 22358680--22358704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22358670 TTAAATCCGT
22358680 TAATTAGTTTAAA
1 TAATTAGTTTAAA
22358693 TAATTAGTTTAA
1 TAATTAGTTTAA
22358705 TGAACAAACC
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:22363708 original size:17 final size:16
Alignment explanation
Indices: 22363684--22363730 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
22363674 TTTAGTCTTA
22363684 TTTTATTTTTATTTTC
1 TTTTATTTTTATTTTC
22363700 TTTTGATTTTTATTTTC
1 TTTT-ATTTTTATTTTC
* *
22363717 ATTTCAATTTTATT
1 -TTTTATTTTTATT
22363731 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 4 0.15
17 20 0.74
18 3 0.11
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTTATTTTTATTTTC
Found at i:22368347 original size:46 final size:46
Alignment explanation
Indices: 22368235--22368481 Score: 171
Period size: 46 Copynumber: 5.3 Consensus size: 46
22368225 CCTAGACACA
* * * * *
22368235 GTCTTACACTAGCTCAT-ATCTCAA-GTCGATACCATGTCCCAGACAT
1 GTCTTACACTAGCT-ATCATCTCAAGGCCGAT-GCATATCTCAAACAT
* *
22368281 GGTCTTACACT-GACTATCATCTCGTA-GCTGATGCATATCTCAAACAT
1 -GTCTTACACTAG-CTATCATCTC-AAGGCCGATGCATATCTCAAACAT
* * *
22368328 GTCTTACACTAGCTTTCATCTCAAGGCCGTTGCATGTCTCAAACAT
1 GTCTTACACTAGCTATCATCTCAAGGCCGATGCATATCTCAAACAT
** * ** * *
22368374 GTCTTACACTAGCCCTCGTCTCAATACCGATGCCATGTCCCAAACAT
1 GTCTTACACTAGCTATCATCTCAAGGCCGATG-CATATCTCAAACAT
* * * * * * *
22368421 GGTCTTACACTGGCTCTCATAAT-ATGGCCGATGCATGTCCCAGACAT
1 -GTCTTACACTAGCTATCAT-CTCAAGGCCGATGCATATCTCAAACAT
22368468 GTCTTACACTAGCT
1 GTCTTACACTAGCT
22368482 CACACACAAA
Statistics
Matches: 164, Mismatches: 28, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
45 1 0.01
46 79 0.48
47 55 0.34
48 28 0.17
49 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (46 bp):
GTCTTACACTAGCTATCATCTCAAGGCCGATGCATATCTCAAACAT
Found at i:22370575 original size:25 final size:26
Alignment explanation
Indices: 22370522--22370575 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
22370512 TTTTAAGTCA
* **
22370522 TAAGTCATAATCCTAAGCTCTTAGTT
1 TAAGTCATAATCCTAAGCTCTAAACT
*
22370548 TAAGTC-TAATCCTAAGTTCTAAACT
1 TAAGTCATAATCCTAAGCTCTAAACT
22370573 TAA
1 TAA
22370576 ATTCTAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (26 bp):
TAAGTCATAATCCTAAGCTCTAAACT
Found at i:22372167 original size:144 final size:144
Alignment explanation
Indices: 22371958--22372249 Score: 496
Period size: 144 Copynumber: 2.0 Consensus size: 144
22371948 CTAGAAAACA
* *
22371958 TAAAAGAAAATTAATGAGAGGCATCCAAAAATAAAATAGAGAACAAGAAACATAAAAGTTGAAGT
1 TAAAAGAAAAGTAATGAGAGGCATCCAAAAACAAAATAGAGAACAAGAAACATAAAAGTTGAAGT
*
22372023 CTTTAACAGATTAAATTAAAAGAAATTGAAATACATTAAACAAAAAGGTTGAAAAGTCATTACAA
66 CTTTAACAGATTAAATTAAAAGAAACTGAAATACATTAAACAAAAAGGTTGAAAAGTCATTACAA
22372088 GCAAAGAAATAGAC
131 GCAAAGAAATAGAC
* *
22372102 TAAAAGAAAAGTAATGAG-GCGTATCCAACAACAAAATAGAGAACAAGAAACATAAAAGTTGAAG
1 TAAAAGAAAAGTAATGAGAG-GCATCCAAAAACAAAATAGAGAACAAGAAACATAAAAGTTGAAG
* *
22372166 TCTTTAACAGTTTAAATTAAAAGAAACTGAAATACATTAAACTAAAAGGTTGAAAAGTCATTACA
65 TCTTTAACAGATTAAATTAAAAGAAACTGAAATACATTAAACAAAAAGGTTGAAAAGTCATTACA
*
22372231 AGCAAAGAAATGGAC
130 AGCAAAGAAATAGAC
22372246 TAAA
1 TAAA
22372250 GGTCTAAATA
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
143 1 0.01
144 138 0.99
ACGTcount: A:0.55, C:0.10, G:0.15, T:0.20
Consensus pattern (144 bp):
TAAAAGAAAAGTAATGAGAGGCATCCAAAAACAAAATAGAGAACAAGAAACATAAAAGTTGAAGT
CTTTAACAGATTAAATTAAAAGAAACTGAAATACATTAAACAAAAAGGTTGAAAAGTCATTACAA
GCAAAGAAATAGAC
Found at i:22375006 original size:46 final size:45
Alignment explanation
Indices: 22374953--22375128 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 45
22374943 TATTTGGGCA
22374953 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
22374999 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
22375046 TCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
22375092 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
22375129 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.62
47 31 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:22375108 original size:93 final size:93
Alignment explanation
Indices: 22374949--22375120 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
22374939 AGGATATTTG
* * *
22374949 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
22375014 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
22375042 GGCATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
22375107 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
22375121 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:22380490 original size:46 final size:46
Alignment explanation
Indices: 22380437--22380611 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
22380427 TATTTGGGCA
22380437 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*** * *
22380483 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA--
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAATG
* *
22380530 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
22380576 CCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
22380612 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 16 0.15
46 53 0.49
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:22380592 original size:93 final size:92
Alignment explanation
Indices: 22380433--22380603 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 92
22380423 AGGATATTTG
* *
22380433 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
22380498 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGT-CGAGTTCGAGAGATGTAACTA
* *
22380526 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
22380591 TTGAGTCGAGTTC
66 TTGAGTCGAGTTC
22380604 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 7 0.09
93 67 0.91
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (92 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAG
TTGAGTCGAGTTCGAGAGATGTAACTA
Found at i:22383675 original size:178 final size:178
Alignment explanation
Indices: 22383376--22383741 Score: 565
Period size: 178 Copynumber: 2.1 Consensus size: 178
22383366 TTAAGAAAAT
*
22383376 GACTAAATTGTAAAGCTTAATTGTTAGTTTCGTATATTAGAGACCAAATTGAATAAAATGAAATA
1 GACTAAATTGTAAAGCTTAATTGTTAGTTTCGTATATTAGAGACCAAATTGAATAAAATGAAAAA
* * *
22383441 TTGTAATAAATTTTTTGTATGGATACAAAATAGAGGATCCCTAATGAGTTTTGGTGAAATCAGAT
66 TTGTAATAAATATTTGGTATGGATACAAAATAGAGGATCCCTAATGAGTTTTGGTGAAAACAGAT
*
22383506 TTTAATTCGAGGCTTTATATTGAAAGTTATGATTGTCCCGATTTTAGA
131 TTTAATTCGAGGCTTTAAATTGAAAGTTATGATTGTCCCGATTTTAGA
* *
22383554 GACTAAATTGTATAGCTTAATTGTTAGTTTCGTATATTAGGGACCAAATTGAATAAAAT-ACAAA
1 GACTAAATTGTAAAGCTTAATTGTTAGTTTCGTATATTAGAGACCAAATTGAATAAAATGA-AAA
* * * * * *
22383618 ATTTTCATAAATATTTGGTA-GAGATCCAAAATAGAGGGTTCCTAATGAGTTTTGGTGAAAAGAG
65 ATTGTAATAAATATTTGGTATG-GATACAAAATAGAGGATCCCTAATGAGTTTTGGTGAAAACAG
* *
22383682 ATTTTAATTCGAGGCTTTAAATTGAAAGTTATGTTTGTCCCGATTTTAGG
129 ATTTTAATTCGAGGCTTTAAATTGAAAGTTATGATTGTCCCGATTTTAGA
22383732 GACTAAATTG
1 GACTAAATTG
22383742 AGTAATTTGA
Statistics
Matches: 171, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
177 2 0.01
178 169 0.99
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (178 bp):
GACTAAATTGTAAAGCTTAATTGTTAGTTTCGTATATTAGAGACCAAATTGAATAAAATGAAAAA
TTGTAATAAATATTTGGTATGGATACAAAATAGAGGATCCCTAATGAGTTTTGGTGAAAACAGAT
TTTAATTCGAGGCTTTAAATTGAAAGTTATGATTGTCCCGATTTTAGA
Found at i:22385797 original size:2 final size:2
Alignment explanation
Indices: 22385790--22385825 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
22385780 TTTGAAAGGA
22385790 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
22385826 TTAAGATAGT
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:22388695 original size:30 final size:30
Alignment explanation
Indices: 22388661--22388718 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
22388651 CTAACTAAGT
22388661 CTTACTTTTCTAACTCAATTCATACTTTCA
1 CTTACTTTTCTAACTCAATTCATACTTTCA
22388691 CTTACTTTTCTAACTCAATTCATACTTT
1 CTTACTTTTCTAACTCAATTCATACTTT
22388719 ATTTCTACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (30 bp):
CTTACTTTTCTAACTCAATTCATACTTTCA
Found at i:22389174 original size:3 final size:3
Alignment explanation
Indices: 22389159--22389225 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
22389149 TCATATATAT
* * *
22389159 ATA ATA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA CATT ATA ATT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
22389205 ATA AT- ATA AT- ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
22389226 GTTTAATGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.89
4 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:22389390 original size:24 final size:23
Alignment explanation
Indices: 22389340--22389392 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 23
22389330 TTGTCTTCAT
22389340 TTTAATAATTTAATATAAAACTA
1 TTTAATAATTTAATATAAAACTA
*
22389363 --TAATAATTATAATA-AATATCTA
1 TTTAATAATT-TAATATAA-AACTA
22389385 TTTAATAA
1 TTTAATAA
22389393 CAAATACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 10 0.40
22 9 0.36
24 6 0.24
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAATAATTTAATATAAAACTA
Found at i:22394739 original size:3 final size:3
Alignment explanation
Indices: 22394733--22394767 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
22394723 TTCGTCGTCA
*
22394733 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG CTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
22394768 ATGATACGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.31, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:22401363 original size:19 final size:19
Alignment explanation
Indices: 22401339--22401378 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
22401329 GTCGGAAATA
*
22401339 GTTCAGGTATATTTAACAT
1 GTTCAGGTATAGTTAACAT
22401358 GTTCAGGTATAGTTAACAT
1 GTTCAGGTATAGTTAACAT
22401377 GT
1 GT
22401379 AAGGGTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (19 bp):
GTTCAGGTATAGTTAACAT
Found at i:22406621 original size:21 final size:21
Alignment explanation
Indices: 22406592--22406631 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22406582 ATGTGCGTTG
*
22406592 AGACATCAAGAACATATTTCA
1 AGACATCAAGAACAAATTTCA
*
22406613 AGACTTCAAGAACAAATTT
1 AGACATCAAGAACAAATTT
22406632 AAGTGATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.25
Consensus pattern (21 bp):
AGACATCAAGAACAAATTTCA
Found at i:22409387 original size:9 final size:9
Alignment explanation
Indices: 22409373--22409431 Score: 84
Period size: 9 Copynumber: 6.6 Consensus size: 9
22409363 ATAAGTATAA
22409373 AATTAACCG
1 AATTAACCG
*
22409382 AATTAATCG
1 AATTAACCG
22409391 AATTAACCG
1 AATTAACCG
22409400 AATT-ACCAG
1 AATTAACC-G
*
22409409 AATTAATCG
1 AATTAACCG
22409418 AATTAACCG
1 AATTAACCG
22409427 AATTA
1 AATTA
22409432 TTTGTATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
8 3 0.07
9 39 0.89
10 2 0.05
ACGTcount: A:0.46, C:0.17, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:22410181 original size:14 final size:15
Alignment explanation
Indices: 22410159--22410207 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
22410149 GTTTGATGTA
*
22410159 AAATATGATA-TATG
1 AAATTTGATATTATG
22410173 AAATTTGATATTAT-
1 AAATTTGATATTATG
22410187 AAATTT-ATAATTATG
1 AAATTTGAT-ATTATG
22410202 AAATTT
1 AAATTT
22410208 AAATTTAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 2 0.06
14 20 0.65
15 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (15 bp):
AAATTTGATATTATG
Found at i:22410207 original size:15 final size:15
Alignment explanation
Indices: 22410169--22410212 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
22410159 AAATATGATA
22410169 TATGAAATTTGAT-AT
1 TATGAAATTT-ATAAT
22410184 TAT-AAATTTATAAT
1 TATGAAATTTATAAT
22410198 TATGAAATTTA-AAT
1 TATGAAATTTATAAT
22410212 T
1 T
22410213 TAATCAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.07
14 15 0.56
15 10 0.37
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
TATGAAATTTATAAT
Found at i:22410496 original size:18 final size:18
Alignment explanation
Indices: 22410473--22410511 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
22410463 AGTTTTTTTT
22410473 TTATAAATA-ATAGATAGA
1 TTATAAATAGATAGATA-A
*
22410491 TTATAATTAGATAGATAA
1 TTATAAATAGATAGATAA
22410509 TTA
1 TTA
22410512 AGTTACCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (18 bp):
TTATAAATAGATAGATAA
Found at i:22411260 original size:12 final size:12
Alignment explanation
Indices: 22411243--22411291 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
22411233 TTTAATCATG
22411243 ATCTAGAATTTT
1 ATCTAGAATTTT
*
22411255 ATCTAGAA-TTA
1 ATCTAGAATTTT
22411266 AT-T-GAAACTTTT
1 ATCTAG-AA-TTTT
22411278 ATCTAGAATTTT
1 ATCTAGAATTTT
22411290 AT
1 AT
22411292 ATATCATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
9 1 0.03
10 3 0.10
11 4 0.13
12 18 0.60
13 3 0.10
14 1 0.03
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (12 bp):
ATCTAGAATTTT
Found at i:22416557 original size:12 final size:13
Alignment explanation
Indices: 22416540--22416582 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
22416530 AGCCACACTT
22416540 TTCTTTCTTT-TG
1 TTCTTTCTTTCTG
22416552 TTCTTTCTTTCTG
1 TTCTTTCTTTCTG
* *
22416565 TTC-CTCTTTCTC
1 TTCTTTCTTTCTG
22416577 TTCTTT
1 TTCTTT
22416583 GGTTTTACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.70
Consensus pattern (13 bp):
TTCTTTCTTTCTG
Found at i:22416560 original size:16 final size:16
Alignment explanation
Indices: 22416539--22416582 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
22416529 TAGCCACACT
**
22416539 TTTCTTTCTTTTGTTC
1 TTTCTTTCTTTTCCTC
*
22416555 TTTCTTTCTGTTCCTC
1 TTTCTTTCTTTTCCTC
22416571 TTTCTCTTCTTT
1 TTTCT-TTCTTT
22416583 GGTTTTACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.00, C:0.25, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTCTTTCTTTTCCTC
Found at i:22426177 original size:46 final size:46
Alignment explanation
Indices: 22426110--22426201 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
22426100 AAAAGGAAAT
*
22426110 TAAGTATATTCTTAGGGAATGTAAATTTAATTGCTGATCAATTGGC
1 TAAGTATATTCTTAGGGAATGTAAACTTAATTGCTGATCAATTGGC
22426156 TAAGTATATTCTTAGGGAATGTAAACTTAATTGCTGATCAATTGGC
1 TAAGTATATTCTTAGGGAATGTAAACTTAATTGCTGATCAATTGGC
22426202 AAAGATCAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (46 bp):
TAAGTATATTCTTAGGGAATGTAAACTTAATTGCTGATCAATTGGC
Found at i:22434077 original size:18 final size:18
Alignment explanation
Indices: 22434054--22434091 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
22434044 ACCATCTTCA
22434054 TCATCTCCATCTTCATCG
1 TCATCTCCATCTTCATCG
* *
22434072 TCATCTTCATCTTCGTCG
1 TCATCTCCATCTTCATCG
22434090 TC
1 TC
22434092 GCCTTGGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.37, G:0.08, T:0.42
Consensus pattern (18 bp):
TCATCTCCATCTTCATCG
Found at i:22436605 original size:307 final size:306
Alignment explanation
Indices: 22436191--22436768 Score: 732
Period size: 307 Copynumber: 1.9 Consensus size: 306
22436181 CCATGAGTTG
* * * *
22436191 TATATATATACTATTAATAAAACCCTTAACTAAGTTAGTATCATCCTCAACCGGGTCACCAACTC
1 TATATACACACTATTAATAAAACCCTTAACTAAGTTAATATCATCCTCAACCGAGTCACCAACTC
* * *
22436256 AGTTAGGAAGTTACGAGAATGTCCTTTCGTAATTAAAATAAGTAATATTATTCGAGGGCATTTTA
66 AGTTAAGAACTTACGAGAATGTCCTTTCGTAATTAAAATAAGTAATATTATTCGAGGACATTTTA
* * *
22436321 GCCTTGTCACTTTTAAAAAA-TCAATAAAAATATACAT-ATGATGATATTTGAACCCACACCAAT
131 GCCTTGTCACTTTAAAAAAAGTCAATAAAAACATACATAAT--TGATATTTAAACCCACACCAAT
**
22436384 TACATTTTTAAAACATATAATTTACCAC-TAATCTAAAGTTTTACTTTAATATTTTTATACATTT
194 TACATTAAT-AAACATATAATTTACCACTTAA-CTAAAGTTTTACTTTAATATTTTTATACATTT
22436448 AAATTTTATTATGCACACTCCATGAACTTTATCGGTTGTGTATTTGTATA
257 AAATTTTATTATGCACACTCCATGAACTTTATCGGTTGTGTATTTGTATA
* * * * *
22436498 TATATACACACTATTAATAAAACTCTTAACTGAGTTAATGTCATCCTCAACTGAGTCATCAACTC
1 TATATACACACTATTAATAAAACCCTTAACTAAGTTAATATCATCCTCAACCGAGTCACCAACTC
* * *
22436563 AGTTAAGAACTTATGAGAATGTCC-TTCTGTAATTAAAATAAGTAATATTATTTGAGGATATTTT
66 AGTTAAGAACTTACGAGAATGTCCTTTC-GTAATTAAAATAAGTAATATTATTCGAGGACATTTT
** * * * * * **
22436627 AGTTTTTTCACTTTAAAAAAAGTCAATTAAAACATGCATAATTGGTATTTAAACCTACGTCAATT
130 AGCCTTGTCACTTTAAAAAAAGTCAATAAAAACATACATAATTGATATTTAAACCCACACCAATT
** *** * * * * *
22436692 GTATTAATAATTTTTTAATTTACCACTTAACTAAAGTTTTATTTTGATATTTTTATATATTTTAA
195 ACATTAATAAACATATAATTTACCACTTAACTAAAGTTTTACTTTAATATTTTTATACATTTAAA
22436757 TTTTATTATGCA
260 TTTTATTATGCA
22436769 TGCTTTATTA
Statistics
Matches: 228, Mismatches: 39, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
306 60 0.26
307 152 0.67
308 14 0.06
309 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (306 bp):
TATATACACACTATTAATAAAACCCTTAACTAAGTTAATATCATCCTCAACCGAGTCACCAACTC
AGTTAAGAACTTACGAGAATGTCCTTTCGTAATTAAAATAAGTAATATTATTCGAGGACATTTTA
GCCTTGTCACTTTAAAAAAAGTCAATAAAAACATACATAATTGATATTTAAACCCACACCAATTA
CATTAATAAACATATAATTTACCACTTAACTAAAGTTTTACTTTAATATTTTTATACATTTAAAT
TTTATTATGCACACTCCATGAACTTTATCGGTTGTGTATTTGTATA
Found at i:22455186 original size:7 final size:7
Alignment explanation
Indices: 22455176--22455206 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
22455166 AGTTTTAATG
*
22455176 TTAGGGT
1 TTAGAGT
22455183 TTAGAGT
1 TTAGAGT
22455190 TTAGAGT
1 TTAGAGT
22455197 TTAGAGT
1 TTAGAGT
22455204 TTA
1 TTA
22455207 AGGTTTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (7 bp):
TTAGAGT
Found at i:22455193 original size:14 final size:14
Alignment explanation
Indices: 22455176--22455212 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
22455166 AGTTTTAATG
22455176 TTAGGGTTTAGAGT
1 TTAGGGTTTAGAGT
*
22455190 TTAGAGTTTAGAGT
1 TTAGGGTTTAGAGT
*
22455204 TTAAGGTTT
1 TTAGGGTTT
22455213 TAAGGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (14 bp):
TTAGGGTTTAGAGT
Found at i:22455205 original size:21 final size:21
Alignment explanation
Indices: 22455160--22455215 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
22455150 TTTTTGCTTG
*
22455160 GTTTAGAGTTTTAATGTTAGG
1 GTTTAGAGTTTTAATGTTAGA
22455181 GTTTAGAG-TTTAGA-GTTTAGA
1 GTTTAGAGTTTTA-ATG-TTAGA
22455202 GTTTA-AGGTTTTAA
1 GTTTAGA-GTTTTAA
22455216 GGATTTTAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
20 6 0.20
21 20 0.67
22 4 0.13
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (21 bp):
GTTTAGAGTTTTAATGTTAGA
Found at i:22458900 original size:30 final size:30
Alignment explanation
Indices: 22458865--22458927 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
22458855 ACTTATTTTA
22458865 TTGTTAATTTTATT-ATTATTTTAAAGGCAT
1 TTGTTAATTTT-TTAATTATTTTAAAGGCAT
*
22458895 TTGTTAATTTTTTAATTATTTTAGAGGCAT
1 TTGTTAATTTTTTAATTATTTTAAAGGCAT
22458925 TTG
1 TTG
22458928 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTTTAATTATTTTAAAGGCAT
Found at i:22459076 original size:12 final size:11
Alignment explanation
Indices: 22459049--22459082 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
22459039 TATATATATT
22459049 TAAAAATAATA
1 TAAAAATAATA
22459060 TAAAAATAATA
1 TAAAAATAATA
22459071 TAAAAATTAATA
1 TAAAAA-TAATA
22459083 CGGGCGGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:22459307 original size:9 final size:9
Alignment explanation
Indices: 22459284--22459313 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
22459274 ATTTATATTT
22459284 TATTAAAAA
1 TATTAAAAA
22459293 TA-TAAAAA
1 TATTAAAAA
22459301 TATTAAAAA
1 TATTAAAAA
22459310 TATT
1 TATT
22459314 GCCTTATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TATTAAAAA
Found at i:22459387 original size:55 final size:54
Alignment explanation
Indices: 22459279--22459400 Score: 147
Period size: 55 Copynumber: 2.2 Consensus size: 54
22459269 GCATTATTTA
* **** *
22459279 TATTTTATTAAAAATATAAAAATATTAAAAATATTGCCTTATTCAAAAGAACTTT
1 TATTTTATTAAAAATATAAAAATA-TAAAAAAATTAAAATATTAAAAAGAACTTT
*
22459334 TATTTTATTAAAAATATAAAAAGTA-AATAAAAATTAAAATATTAAAAATAACTTT
1 TATTTTATTAAAAATATAAAAA-TATAA-AAAAATTAAAATATTAAAAAGAACTTT
22459389 TATTTTATTAAA
1 TATTTTATTAAA
22459401 TAAAGCAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 2 0.03
55 54 0.93
56 2 0.03
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (54 bp):
TATTTTATTAAAAATATAAAAATATAAAAAAATTAAAATATTAAAAAGAACTTT
Found at i:22459956 original size:30 final size:30
Alignment explanation
Indices: 22459920--22459987 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
22459910 ATTGAAGTGT
22459920 TGGGCCCGGTGACTGTGTGGGCACTGTTGA
1 TGGGCCCGGTGACTGTGTGGGCACTGTTGA
* *
22459950 TGGGCCCGGTGATTGTGTGGGCATTGTTGA
1 TGGGCCCGGTGACTGTGTGGGCACTGTTGA
22459980 TGGGCCCG
1 TGGGCCCG
22459988 CGTCGTCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.09, C:0.19, G:0.44, T:0.28
Consensus pattern (30 bp):
TGGGCCCGGTGACTGTGTGGGCACTGTTGA
Found at i:22460492 original size:7 final size:7
Alignment explanation
Indices: 22460482--22460517 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
22460472 TTATATACAT
22460482 AATACTA
1 AATACTA
22460489 AATACTA
1 AATACTA
22460496 AATACTA
1 AATACTA
*
22460503 AATACGA
1 AATACTA
22460510 AATGACTA
1 AAT-ACTA
22460518 TTTTATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 23 0.88
8 3 0.12
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (7 bp):
AATACTA
Found at i:22461442 original size:26 final size:26
Alignment explanation
Indices: 22461400--22461499 Score: 81
Period size: 24 Copynumber: 4.1 Consensus size: 26
22461390 ACTATTATAA
*
22461400 AAAATTATA-AAAT-AAAAATTAATT
1 AAAATTACATAAATGAAAAATTAATT
22461424 AAAATTACATAAATGAAAAA--AATAT
1 AAAATTACATAAATGAAAAATTAAT-T
* * *
22461449 TAAA-TA-GT-ATTGAAAAATTAATT
1 AAAATTACATAAATGAAAAATTAATT
* *
22461472 AAAATTGCATAAATGAAAAAAT-ATT
1 AAAATTACATAAATGAAAAATTAATT
22461497 AAA
1 AAA
22461500 TAGTATTGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
22 8 0.14
23 5 0.08
24 17 0.29
25 15 0.25
26 14 0.24
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (26 bp):
AAAATTACATAAATGAAAAATTAATT
Found at i:22461465 original size:22 final size:22
Alignment explanation
Indices: 22461437--22461512 Score: 66
Period size: 22 Copynumber: 3.3 Consensus size: 22
22461427 ATTACATAAA
22461437 TGAAAAAAATATTAAATAGTAT
1 TGAAAAAAATATTAAATAGTAT
* * *
22461459 TGAAAAATTAAT-TAAAATTGCATAAA
1 TGAAAAA--AATATTAAATAG--T-AT
22461485 TG-AAAAAATATTAAATAGTAT
1 TGAAAAAAATATTAAATAGTAT
22461506 TGAAAAA
1 TGAAAAA
22461513 TTAAAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
21 3 0.07
22 12 0.29
23 9 0.22
24 9 0.22
25 5 0.12
26 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.09, T:0.30
Consensus pattern (22 bp):
TGAAAAAAATATTAAATAGTAT
Found at i:22461509 original size:47 final size:48
Alignment explanation
Indices: 22461413--22461516 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 48
22461403 ATTATAAAAT
22461413 AAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAGTATTG
1 AAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAGTATTG
*
22461461 AAAAATTAATTAAAATTGCATAAATG-AAAAAATATTAAATAGTATTG
1 AAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAGTATTG
22461508 AAAAATTAA
1 AAAAATTAA
22461517 AATAATCACT
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 30 0.55
48 25 0.45
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (48 bp):
AAAAATTAATTAAAATTACATAAATGAAAAAAATATTAAATAGTATTG
Found at i:22461696 original size:11 final size:11
Alignment explanation
Indices: 22461680--22461718 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
22461670 AGCTTTTAGA
22461680 AAATTTGAGAG
1 AAATTTGAGAG
22461691 AAATTTGAGAG
1 AAATTTGAGAG
22461702 -AATTATGAGAG
1 AAATT-TGAGAG
*
22461713 GAATTT
1 AAATTT
22461719 TGTGTGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 18 0.69
12 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.31
Consensus pattern (11 bp):
AAATTTGAGAG
Found at i:22465807 original size:93 final size:93
Alignment explanation
Indices: 22465695--22465959 Score: 478
Period size: 93 Copynumber: 2.8 Consensus size: 93
22465685 GCCCATAAGT
*
22465695 GAACTCGGACTCAACTCAACGAGCTCAGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
22465759 ACGAGATCGGATGCCTAGTTACATATCTC
65 ACGAGATCGGATGCCTAGTTACATATCTC
22465788 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
22465853 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGATCGGATGCCTAGTTACATATCTC
22465881 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
22465946 CGAGTTCGGATGCC
66 CGAGATCGGATGCC
22465960 CAAATATCCT
Statistics
Matches: 167, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 2 0.01
93 165 0.99
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGATCGGATGCCTAGTTACATATCTC
Found at i:22465955 original size:46 final size:45
Alignment explanation
Indices: 22465687--22465954 Score: 301
Period size: 46 Copynumber: 5.8 Consensus size: 45
22465677 TGTAACCTGC
*
22465687 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-GGCATTCGCAT
* *
22465733 CCATAAGTGAACTCGGACTCAACTCAACGAGATCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--T
* **
22465779 ACATATCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCAT
* *
22465826 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGC-A--T
* ***
22465872 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGG-CATTCGCAT
22465919 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
22465955 ATGCCCAAAT
Statistics
Matches: 186, Mismatches: 22, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
43 2 0.01
44 8 0.04
45 2 0.01
46 99 0.53
47 65 0.35
49 8 0.04
50 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATTCGCAT
Found at i:22467590 original size:31 final size:30
Alignment explanation
Indices: 22467544--22467655 Score: 133
Period size: 29 Copynumber: 3.7 Consensus size: 30
22467534 CTTTCACTTC
22467544 AACTTTTCCATATTTATACTTAT-CACACAA
1 AACTTTTCCATATTTATACTTATGC-CACAA
22467574 AACTTTTCGCATA-TT-TACTTATGCCACAA
1 AACTTTTC-CATATTTATACTTATGCCACAA
* *
22467603 AACTTTTCGCATATTTACAATTTATGCCAC-A
1 AACTTTTC-CATATTTA-TACTTATGCCACAA
*
22467634 AACTTTTCTATATTTATACTTA
1 AACTTTTCCATATTTATACTTA
22467656 GGTCTTGCTT
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
29 29 0.40
30 20 0.28
31 13 0.18
32 10 0.14
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (30 bp):
AACTTTTCCATATTTATACTTATGCCACAA
Found at i:22481453 original size:21 final size:21
Alignment explanation
Indices: 22481427--22481468 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
22481417 GATGCTCATA
22481427 CCTATTTATAAGTATATAATC
1 CCTATTTATAAGTATATAATC
22481448 CCTATTTATAAGTATATAATC
1 CCTATTTATAAGTATATAATC
22481469 ATCGTCTCTG
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:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (21 bp):
CCTATTTATAAGTATATAATC
Found at i:22482953 original size:3 final size:3
Alignment explanation
Indices: 22482945--22482981 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
22482935 GTTGAGGGTT
22482945 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
22482982 CTTGTGTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:22492311 original size:22 final size:21
Alignment explanation
Indices: 22492286--22492356 Score: 54
Period size: 23 Copynumber: 3.1 Consensus size: 21
22492276 ATATAAGTAT
22492286 ATATACACGAAATAGTATAAAA
1 ATATACACGAAATA-TATAAAA
* *
22492308 ATATATAAC-TAATAATATTAAAA
1 ATATA-CACGAAAT-ATA-TAAAA
*
22492331 TATATACATGATAATATATAAAA
1 -ATATACACGA-AATATATAAAA
22492354 ATA
1 ATA
22492357 ATAATATTAG
Statistics
Matches: 38, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
22 13 0.34
23 14 0.37
24 8 0.21
25 3 0.08
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (21 bp):
ATATACACGAAATATATAAAA
Found at i:22492388 original size:2 final size:2
Alignment explanation
Indices: 22492370--22492511 Score: 54
Period size: 2 Copynumber: 75.5 Consensus size: 2
22492360 ATATTAGAAA
* * * * *
22492370 AT AT AT GT AC AT A- AT AT AT AT AT AT AT AT AA AA AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
22492411 AT A- AT AT AGT AT -T A- AA AT AT AA AA AT AT A- AT AT -T AA AA
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
22492449 AT AT AT AT A- AT AT AT AT A- AA AT AT AT AC AC A- AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
22492489 -T AA AT AT AT AT AC AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
22492512 CTTGTTAGAG
Statistics
Matches: 108, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
1 11 0.10
2 93 0.86
3 4 0.04
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (2 bp):
AT
Found at i:22492495 original size:34 final size:33
Alignment explanation
Indices: 22492391--22492512 Score: 126
Period size: 34 Copynumber: 3.6 Consensus size: 33
22492381 TAATATATAT
22492391 ATATATATAAAAATATATACATAATATAGTATTAA
1 ATATATAT-AAAATATATACA-AATATAGTATTAA
* *
22492426 A-ATATA-AAAATATAATATTAAAAATA-TA-TATA
1 ATATATATAAAATAT-ATA-CAAATATAGTATTA-A
22492458 ATATATATAAAATATATACACAATATAGTATTAA
1 ATATATATAAAATATATACA-AATATAGTATTAA
22492492 ATATATATACATAATATATAC
1 ATATATATA-A-AATATATAC
22492513 TTGTTAGAGA
Statistics
Matches: 73, Mismatches: 4, Indels: 19
0.76 0.04 0.20
Matches are distributed among these distances:
31 2 0.03
32 12 0.16
33 21 0.29
34 25 0.34
35 4 0.05
36 9 0.12
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (33 bp):
ATATATATAAAATATATACAAATATAGTATTAA
Found at i:22495362 original size:15 final size:15
Alignment explanation
Indices: 22495342--22495373 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
22495332 TGTATGATTG
22495342 AATAAGCATAGTAGT
1 AATAAGCATAGTAGT
22495357 AATAAGCATAGTAGT
1 AATAAGCATAGTAGT
22495372 AA
1 AA
22495374 GGCTATATCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATAAGCATAGTAGT
Found at i:22496899 original size:17 final size:19
Alignment explanation
Indices: 22496879--22496916 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
22496869 ATATAAATAG
*
22496879 ATAAATG-ATA-AAATAAA
1 ATAAATGTATATAAAAAAA
22496896 ATAAATGTATATAAAAAAA
1 ATAAATGTATATAAAAAAA
22496915 AT
1 AT
22496917 TAGGTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 3 0.17
19 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (19 bp):
ATAAATGTATATAAAAAAA
Found at i:22498542 original size:21 final size:23
Alignment explanation
Indices: 22498495--22498548 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
22498485 CATTAAAGAT
**
22498495 AAAATAATATATAAAACTTTTTA
1 AAAATAATATATAAAACTAATTA
*
22498518 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
22498539 AAAAT-ATATA
1 AAAATAATATA
22498549 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:22498601 original size:25 final size:25
Alignment explanation
Indices: 22498486--22498651 Score: 74
Period size: 24 Copynumber: 6.6 Consensus size: 25
22498476 ATTAGTATCC
*
22498486 ATTAAAGATAAAATAATATATAAAACT
1 ATTAAA-AT-AAATAATATATAAAAAT
**
22498513 -TTTTAA-AAATAATATATAAACAAT
1 ATTAAAATAAATAATATATAAA-AAT
* * * *
22498537 -TCAAAATATATAATGTGTAAAAA-
1 ATTAAAATAAATAATATATAAAAAT
* *
22498560 AGGTTTAAAATACATAATATATGAAAAT
1 A---TTAAAATAAATAATATATAAAAAT
* *
22498588 ATTAAAGTAAATAATGTATAAAAAT
1 ATTAAAATAAATAATATATAAAAAT
* * ** * *
22498613 -TTGAAATGAGCATTAAATAAAAA-
1 ATTAAAATAAATAATATATAAAAAT
*
22498636 GTTAAAATAAATAATA
1 ATTAAAATAAATAATA
22498652 ACAAAAAATG
Statistics
Matches: 100, Mismatches: 31, Indels: 19
0.67 0.21 0.13
Matches are distributed among these distances:
23 14 0.14
24 32 0.32
25 32 0.32
26 3 0.03
27 18 0.18
28 1 0.01
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.31
Consensus pattern (25 bp):
ATTAAAATAAATAATATATAAAAAT
Found at i:22498776 original size:14 final size:14
Alignment explanation
Indices: 22498757--22498857 Score: 61
Period size: 14 Copynumber: 7.3 Consensus size: 14
22498747 TATAAATAGA
22498757 AATAGAAATATAAT
1 AATAGAAATATAAT
22498771 AATAGAAATATAAT
1 AATAGAAATATAAT
22498785 AGAT--AAATA-AA-
1 A-ATAGAAATATAAT
22498796 AATTAGATAA-ATAAT
1 AA-TAGA-AATATAAT
* * *
22498811 AATAGTATTAGAAT
1 AATAGAAATATAAT
* *
22498825 AACA-AAATAAATAT
1 AATAGAAATATA-AT
*
22498839 AAATAGAAACATAAT
1 -AATAGAAATATAAT
22498854 AATA
1 AATA
22498858 ATAGCAATAA
Statistics
Matches: 66, Mismatches: 10, Indels: 22
0.67 0.10 0.22
Matches are distributed among these distances:
10 1 0.02
11 2 0.03
12 2 0.03
13 12 0.18
14 35 0.53
15 9 0.14
16 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (14 bp):
AATAGAAATATAAT
Found at i:22498795 original size:43 final size:41
Alignment explanation
Indices: 22498720--22498857 Score: 106
Period size: 40 Copynumber: 3.3 Consensus size: 41
22498710 ATGTATAAGA
* *
22498720 AAAATAATAAT-GAAA-ATAATATTAGTATATAAATAGAAATAG
1 AAAATAATAATAGAAATATAATA--ACTAAATAAATA-AAATAG
*
22498762 AAATATAATAATAGAAATATAATAGA-TAAAT-AA-AAATTAG
1 AAA-ATAATAATAGAAATATAATA-ACTAAATAAATAAAATAG
* * * *
22498802 ATAAATAATAATAGTATTAGAATAACAAAATAAATATAAATAG
1 A-AAATAATAATAGAAATATAATAACTAAATAAATA-AAATAG
22498845 AAACATAATAATA
1 AAA-ATAATAATA
22498858 ATAGCAATAA
Statistics
Matches: 79, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
39 1 0.01
40 27 0.34
41 5 0.06
42 8 0.10
43 27 0.34
44 5 0.06
45 6 0.08
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (41 bp):
AAAATAATAATAGAAATATAATAACTAAATAAATAAAATAG
Found at i:22502007 original size:18 final size:20
Alignment explanation
Indices: 22501967--22502010 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
22501957 GTGGCCGGAG
22501967 CTCCCCCTCCCCTCTCTTCT
1 CTCCCCCTCCCCTCTCTTCT
*
22501987 CTCCCCGCT-CCCTCTTTTCT
1 CTCCCC-CTCCCCTCTCTTCT
22502007 CTCC
1 CTCC
22502011 TTCCCCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.00, C:0.61, G:0.02, T:0.36
Consensus pattern (20 bp):
CTCCCCCTCCCCTCTCTTCT
Found at i:22502515 original size:12 final size:11
Alignment explanation
Indices: 22502472--22502511 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
22502462 ATTTTTTTAC
22502472 ATATTATTAAT
1 ATATTATTAAT
*
22502483 ATTATTATTAGT
1 A-TATTATTAAT
*
22502495 ATTTTATTAAT
1 ATATTATTAAT
22502506 ATATTA
1 ATATTA
22502512 ATTATTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
ATATTATTAAT
Found at i:22502597 original size:13 final size:14
Alignment explanation
Indices: 22502573--22502603 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
22502563 ATCATTATTA
22502573 ATATTAATATATGT
1 ATATTAATATATGT
22502587 ATATT-ATATATGT
1 ATATTAATATATGT
22502600 ATAT
1 ATAT
22502604 ATTCGTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (14 bp):
ATATTAATATATGT
Found at i:22502823 original size:12 final size:12
Alignment explanation
Indices: 22502802--22502886 Score: 58
Period size: 12 Copynumber: 7.4 Consensus size: 12
22502792 TTCTTAATAT
22502802 TATATT-TTATA
1 TATATTATTATA
22502813 TATATTATTATA
1 TATATTATTATA
22502825 TATATT-TTA-A
1 TATATTATTATA
*
22502835 TATCATTAGTCATA
1 TAT-ATTA-TTATA
* *
22502849 T-TCTTCTT-T-
1 TATATTATTATA
*
22502858 TATACTATTATA
1 TATATTATTATA
22502870 TATA-TATATATA
1 TATATTAT-TATA
22502882 TATAT
1 TATAT
22502887 CTAATATTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
9 1 0.02
10 9 0.16
11 17 0.30
12 25 0.44
13 3 0.05
14 2 0.04
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.56
Consensus pattern (12 bp):
TATATTATTATA
Found at i:22515589 original size:71 final size:71
Alignment explanation
Indices: 22515468--22515599 Score: 201
Period size: 71 Copynumber: 1.9 Consensus size: 71
22515458 GTTTTCCAAG
* * *
22515468 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATGTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATGTAT
22515533 GTTTCA
66 GTTTCA
* * * *
22515539 AAAATCAACTCGTATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAAT
22515600 TTCTGCTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 54 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATGTAT
GTTTCA
Found at i:22515648 original size:160 final size:160
Alignment explanation
Indices: 22515377--22515934 Score: 1046
Period size: 160 Copynumber: 3.5 Consensus size: 160
22515367 TTGTTTTTTC
*
22515377 CAAAAATCAACTCATATTGCGAGAAGTGAGTAGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
22515442 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
22515507 GACACGTTGAGGTAATTTCAATGTATGTTT
131 GACACGTTGAGGTAATTTCAATGTATGTTT
*
22515537 CAAAAATCAACTCGTATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
22515602 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATGTTGCGAGAGGTGAGTTGAGCCTCAA
66 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
22515667 GACACGTTGAGGTAATTTCAATGTATGTTT
131 GACACGTTGAGGTAATTTCAATGTATGTTT
*
22515697 CAAAAATCAACTCGTATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
22515762 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
*
22515827 GACACGTTGAGGTAATTTCAATTTATGTTT
131 GACACGTTGAGGTAATTTCAATGTATGTTT
22515857 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
22515922 TTG-TGTTTTAATT
66 CTGCT-TTTTAATT
22515935 TCAACTCATA
Statistics
Matches: 390, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
159 1 0.00
160 389 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (160 bp):
CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
GACACGTTGAGGTAATTTCAATGTATGTTT
Found at i:22515749 original size:71 final size:71
Alignment explanation
Indices: 22515628--22515759 Score: 192
Period size: 71 Copynumber: 1.9 Consensus size: 71
22515618 GTTTTCCAAG
* * * *
22515628 AAAATCAGCTCATGTTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATGTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATGTAT
22515693 GTTTCA
66 GTTTCA
* * * *
22515699 AAAATCAACTCGTATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAAT
22515760 TTCTGCTTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 53 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.28
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATGTAT
GTTTCA
Done.