Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 178 of 210
Found at i:53076813 original size:51 final size:51
Alignment explanation
Indices: 53076686--53076852 Score: 280
Period size: 52 Copynumber: 3.2 Consensus size: 51
53076676 AAATTATTTA
53076686 TATTTAAAAAATCTCTATATTTTTAAAAAAAATAGTTTCTTTCTATATAAAT
1 TATTTAAAAAATCTCTATATTTTT-AAAAAAATAGTTTCTTTCTATATAAAT
53076738 TATTTAAAAAATCTCTATATTTTTTAAAAAAATAGTTTCTTTCTATATAAAT
1 TATTTAAAAAATCTCTATA-TTTTTAAAAAAATAGTTTCTTTCTATATAAAT
* * *
53076790 TATTTAAAAAATCTCTATATTTTTTAAAAAATAGTTACTTTATATATAAAT
1 TATTTAAAAAATCTCTATATTTTTAAAAAAATAGTTTCTTTCTATATAAAT
53076841 TATTTAATAAAA
1 TATTTAA-AAAA
53076853 ACATTTTTTA
Statistics
Matches: 110, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
51 36 0.33
52 69 0.63
53 5 0.05
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (51 bp):
TATTTAAAAAATCTCTATATTTTTAAAAAAATAGTTTCTTTCTATATAAAT
Found at i:53079450 original size:21 final size:21
Alignment explanation
Indices: 53079426--53079466 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
53079416 TTATGTGTTA
53079426 ACCTCTTGGAA-TACAGTGCAG
1 ACCT-TTGGAATTACAGTGCAG
53079447 ACCTTTGGAATTTACAGTGC
1 ACCTTTGGAA-TTACAGTGC
53079467 TATAGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
ACCTTTGGAATTACAGTGCAG
Found at i:53080697 original size:27 final size:27
Alignment explanation
Indices: 53080625--53080686 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
53080615 GGTCTAGTAA
*
53080625 TGGCGCCTCTCTATAAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
53080652 TGGCGCCTCTCTATGAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
53080679 TGGCGCCT
1 TGGCGCCT
53080687 ACCTGATAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.15, C:0.34, G:0.23, T:0.29
Consensus pattern (27 bp):
TGGCGCCTCTCTATGAGGCACCTTCAT
Found at i:53080790 original size:18 final size:18
Alignment explanation
Indices: 53080766--53080801 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
53080756 TAAAAAAATA
*
53080766 TAAAAAAATATT-TTATT
1 TAAAAAAAAATTATTATT
53080783 TAAAAAAAAATTATTATT
1 TAAAAAAAAATTATTATT
53080801 T
1 T
53080802 TTTTATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAAAAAAATTATTATT
Found at i:53085005 original size:4 final size:4
Alignment explanation
Indices: 53084998--53085041 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
53084988 TAGTATTAGA
* *
53084998 ATTT ATTT ATAT ATTTT ATTT ATTT ATTT ATAT ATTTT ATTT AT
1 ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT A-TTT ATTT AT
53085042 AATATATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
4 28 0.82
5 6 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:53085017 original size:13 final size:13
Alignment explanation
Indices: 53084999--53085086 Score: 54
Period size: 13 Copynumber: 7.5 Consensus size: 13
53084989 AGTATTAGAA
53084999 TTTATTTATATAT
1 TTTATTTATATAT
53085012 TTTA--T-T-TA-
1 TTTATTTATATAT
53085020 TTTATTTATATAT
1 TTTATTTATATAT
53085033 TTTATTTATA-A-
1 TTTATTTATATAT
* * *
53085044 TATATTAAAATAT
1 TTTATTTATATAT
*
53085057 TATA-TTA-ATA-
1 TTTATTTATATAT
53085067 -TTATTTATATAT
1 TTTATTTATATAT
53085079 TTCTATTT
1 TT-TATTT
53085087 CATTTGCATT
Statistics
Matches: 58, Mismatches: 5, Indels: 23
0.67 0.06 0.27
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 5 0.09
11 15 0.26
12 6 0.10
13 19 0.33
14 5 0.09
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATTTATATAT
Found at i:53085046 original size:16 final size:17
Alignment explanation
Indices: 53085016--53085049 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
53085006 ATATATTTTA
*
53085016 TTTATTTATTTATATAT
1 TTTATTTATTAATATAT
53085033 TTTATTTA-TAATATAT
1 TTTATTTATTAATATAT
53085049 T
1 T
53085050 AAAATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTATTAATATAT
Found at i:53085085 original size:17 final size:16
Alignment explanation
Indices: 53085000--53085085 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 16
53084990 GTATTAGAAT
53085000 TTATTTATATATTTTA
1 TTATTTATATATTTTA
*
53085016 TTTATTTATTTATATATT-
1 -TTATTTA--TATATTTTA
*
53085034 TTATTTATAATATATTA
1 TTATTTAT-ATATTTTA
** **
53085051 AAATATTATAT-TAATA
1 TTAT-TTATATATTTTA
53085067 TTATTTATATATTTCTA
1 TTATTTATATATTT-TA
53085084 TT
1 TT
53085086 TCATTTGCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
15 7 0.13
16 14 0.26
17 22 0.41
18 4 0.07
19 7 0.13
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTTATATATTTTA
Found at i:53088262 original size:17 final size:16
Alignment explanation
Indices: 53088240--53088273 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53088230 TTAATTAAGC
53088240 TTAGGTAATTATATTAA
1 TTAGGT-ATTATATTAA
*
53088257 TTAGGTTTTATATTAA
1 TTAGGTATTATATTAA
53088273 T
1 T
53088274 AATTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TTAGGTATTATATTAA
Found at i:53093957 original size:22 final size:20
Alignment explanation
Indices: 53093905--53093957 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
53093895 AAAATGTATG
53093905 AAATTATTAAATATTAAAAAA
1 AAATT-TTAAATATTAAAAAA
*
53093926 ACAA-TATAAATATTTTAAAAAA
1 A-AATTTTAAATA--TTAAAAAA
53093948 AAATTTTAAA
1 AAATTTTAAA
53093958 AATAATATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 6 0.23
21 4 0.15
22 16 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTTTAAATATTAAAAAA
Found at i:53095642 original size:456 final size:455
Alignment explanation
Indices: 53094785--53095682 Score: 1760
Period size: 456 Copynumber: 2.0 Consensus size: 455
53094775 AAGCTGAGTT
53094785 TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
1 TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
*
53094850 TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATTT
66 TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATCT
53094915 ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAATT
131 ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAATT
53094980 TTTTTTCCAAATTTCTTGATTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGTG
196 TTTTTTCCAAATTTCTTGATTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGTG
53095045 ACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAATC
261 ACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAATC
53095110 TCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAAA
326 TCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAAA
*
53095175 ATTTGTACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGCACAAAACTAATCC
391 ATTTATACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGCACAAAACTAATCC
53095240 TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
1 TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
53095305 TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATCT
66 TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATCT
53095370 ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAATT
131 ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAA-T
*
53095435 TTTTTTTCCAAATTTCTTGTTTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGT
195 TTTTTTTCCAAATTTCTTGATTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGT
53095500 GACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAAT
260 GACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAAT
53095565 CTCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAA
325 CTCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAA
53095630 AATTTATACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGC
390 AATTTATACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGC
53095683 TTAATCCATT
Statistics
Matches: 439, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
455 192 0.44
456 247 0.56
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (455 bp):
TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATCT
ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAATT
TTTTTTCCAAATTTCTTGATTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGTG
ACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAATC
TCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAAA
ATTTATACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGCACAAAACTAATCC
Found at i:53098839 original size:18 final size:17
Alignment explanation
Indices: 53098809--53098851 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
53098799 TTAATTATAT
53098809 TTAAATATA-ATAATTA
1 TTAAATATATATAATTA
53098825 TTAAATATATTATAATTA
1 TTAAATATA-TATAATTA
53098843 --AAATATATA
1 TTAAATATATA
53098852 ATTTAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.08
16 16 0.64
18 7 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATATATATAATTA
Found at i:53098933 original size:100 final size:99
Alignment explanation
Indices: 53098815--53099189 Score: 299
Period size: 100 Copynumber: 3.6 Consensus size: 99
53098805 ATATTTAAAT
*
53098815 ATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAAATTTATTCAA
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAAATTTATTCAA
53098880 ATTATAATATATGATATTATAAAATATAATTTAAC
66 ATTATAATATATGA-ATTATAAAATATAATTTAAC
* * *
53098915 ATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAATTTATTAATAATCAATAT
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATT-A-AAT--TTAT
** * * * *
53098980 TCTTA-TATAAATTTACTCAAATTATAATATATGATATTATA-
62 TCAAATTAT-AATATA-T-GAATTATAAAATATAAT-TTA-AC
* * * * * *
53099021 A-AA-TATAATTTAATATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAAT
1 ATAATTATTATTAAATAT-ATTATAATTAAA-ATA-TATAATT-TAATA-A-AA-TTATTAAATT
* * * *
53099084 TCTTAATAATTAATATTCTTATATGAATTTACTCAAATAAGATAATTTAAC
59 TATTCA-AATT-ATA---ATATATGAA-TTA-T--AA-AATATAATTTAAC
53099135 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAA
1 ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAA
53099190 TAATCAATAT
Statistics
Matches: 211, Mismatches: 34, Indels: 51
0.71 0.11 0.17
Matches are distributed among these distances:
100 50 0.24
101 1 0.00
102 3 0.01
103 3 0.01
104 22 0.10
105 27 0.13
106 8 0.04
107 10 0.05
108 5 0.02
109 11 0.05
110 8 0.04
111 9 0.04
112 8 0.04
113 8 0.04
114 9 0.04
115 18 0.09
116 11 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (99 bp):
ATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAAATTTATTCAA
ATTATAATATATGAATTATAAAATATAATTTAAC
Found at i:53098967 original size:44 final size:44
Alignment explanation
Indices: 53098880--53099077 Score: 135
Period size: 44 Copynumber: 4.8 Consensus size: 44
53098870 ATTTATTCAA
53098880 ATTATAATATATGATATTATAAAATATAATTTAACATAATTATT
1 ATTATAATATATGATATTATAAAATATAATTTAACATAATTATT
* * *
53098924 ATTA-AATATATTATAATTA-AAATATATGATTT-A-ATAAAT-TT
1 ATTATAATATATGAT-ATTATAAA-ATATAATTTAACATAATTATT
* * * *
53098965 A-T-TAATA-ATCAATATTCTTATATA-AATTT-AC-TCAA--ATT
1 ATTATAATATAT-GATATTATAAAATATAATTTAACAT-AATTATT
*
53099003 A-TA--ATATATGATATTATAAAATATAATTTAATATAATTATT
1 ATTATAATATATGATATTATAAAATATAATTTAACATAATTATT
*
53099044 ATTA-AATATATTATAATTA-AAATATATAATTTAA
1 ATTATAATATATGAT-ATTATAAA-ATATAATTTAA
53099078 TAAAATTCTT
Statistics
Matches: 121, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
37 13 0.11
38 17 0.14
39 13 0.11
40 9 0.07
41 7 0.06
42 7 0.06
43 24 0.20
44 31 0.26
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (44 bp):
ATTATAATATATGATATTATAAAATATAATTTAACATAATTATT
Found at i:53099006 original size:120 final size:117
Alignment explanation
Indices: 53098863--53099283 Score: 450
Period size: 120 Copynumber: 3.7 Consensus size: 117
53098853 TTTAATAAAA
*
53098863 TTAT-TAAATTTATTCAAATTATAATATATGATATTATAAAATATAATTTAACATAATTATTATT
1 TTATATAAATTTACTCAAATTATAATATATGATATTATAAAATATAATTTAA-ATAATTATTATT
53098927 AAATATATTATAATTAAAATATATGATTTAATAAATTTATTAATAATCAATATTC
65 AAATATATTATAATTAAAATATAT-ATTTAATAAA-TTATTAATAATCAATATTC
53098982 TTATATAAATTTACTCAAATTATAATATATGATATTATAAAATATAATTTAATATAATTATTATT
1 TTATATAAATTTACTCAAATTATAATATATGATATTATAAAATATAATTTAA-ATAATTATTATT
* *
53099047 AAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTC
65 AAATATATTATAATTAAAATATAT-ATTTAAT-AAATTATTAATAATCAATATTC
* * ** * * *
53099102 TTATATGAATTTACTCAAA-TA-AGATA-AT-TTAACAT-AATTATTA-TTAAATATATTATAAT
1 TTATATAAATTTACTCAAATTATA-ATATATGATATTATAAAATATAATTTAAATA-ATTATTAT
*
53099161 TAAA-ATA-TATAA-T----T-TA-A--T-A-AAATTATTAATAATCAATATGC
64 TAAATATATTATAATTAAAATATATATTTAATAAATTATTAATAATCAATATTC
* * * * ** *
53099202 ATATATGAATTTATTAAAATTATAATATATGATGCTATAAAATATAATTTGAAATAATTAATATT
1 TTATATAAATTTACTCAAATTATAATATATGATATTATAAAATATAATTT-AAATAATTATTATT
*
53099267 AAATATATTTTAATTAA
65 AAATATATTATAATTAA
53099284 TATTAAATAA
Statistics
Matches: 259, Mismatches: 27, Indels: 41
0.79 0.08 0.13
Matches are distributed among these distances:
100 35 0.14
101 5 0.02
102 4 0.02
103 4 0.02
104 6 0.02
105 13 0.05
106 8 0.03
107 6 0.02
108 2 0.01
112 1 0.00
113 5 0.02
114 6 0.02
115 15 0.06
116 6 0.02
117 4 0.02
118 3 0.01
119 9 0.03
120 124 0.48
121 3 0.01
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (117 bp):
TTATATAAATTTACTCAAATTATAATATATGATATTATAAAATATAATTTAAATAATTATTATTA
AATATATTATAATTAAAATATATATTTAATAAATTATTAATAATCAATATTC
Found at i:53099053 original size:16 final size:17
Alignment explanation
Indices: 53099032--53099069 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
53099022 AATATAATTT
*
53099032 AATATAATTATTATT-A
1 AATATAATTATAATTAA
53099048 AATAT-ATTATAATTAA
1 AATATAATTATAATTAA
53099064 AATATA
1 AATATA
53099070 TAATTTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATAATTATAATTAA
Found at i:53099070 original size:16 final size:15
Alignment explanation
Indices: 53098802--53099079 Score: 103
Period size: 15 Copynumber: 18.9 Consensus size: 15
53098792 AAATAATTTA
*
53098802 ATTATATTTAAATAT
1 ATTATAATTAAATAT
* *
53098817 AATAATTATTAAATAT
1 -ATTATAATTAAATAT
53098833 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
53098847 A-TATAATTTAATA-
1 ATTATAATTAAATAT
* * *
53098860 A-AATTATTAAATTT
1 ATTATAATTAAATAT
53098874 ATTCA-AATTATAATAT
1 ATT-ATAATTA-AATAT
*
53098890 ATGAT-ATTATAA-A-
1 ATTATAATTA-AATAT
53098903 A-TATAATTTAACATA-
1 ATTATAA-TTAA-ATAT
*
53098918 ATTATTATTAAATAT
1 ATTATAATTAAATAT
53098933 ATTATAATTAAAATAT
1 ATTATAATT-AAATAT
* *
53098949 ATGATTTAA-TAAATTT
1 AT--TATAATTAAATAT
*
53098965 ATTAATAA-TCAATATT
1 ATT-ATAATTAAATA-T
* *
53098981 CTTAT-A-TAAATTT
1 ATTATAATTAAATAT
*
53098994 ACTCA-AATTATAATAT
1 A-TTATAATTA-AATAT
*
53099010 ATGAT-ATTATAA-A-
1 ATTATAATTA-AATAT
*
53099023 A-TATAATTTAATAT
1 ATTATAATTAAATAT
*
53099037 AATTATTATTAAATAT
1 -ATTATAATTAAATAT
53099053 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
53099067 A-TATAATTTAATA
1 ATTATAATTAAATA
53099080 AAATTCTTAA
Statistics
Matches: 199, Mismatches: 35, Indels: 58
0.68 0.12 0.20
Matches are distributed among these distances:
12 6 0.03
13 36 0.18
14 27 0.14
15 68 0.34
16 57 0.29
17 1 0.01
18 4 0.02
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:53099168 original size:16 final size:16
Alignment explanation
Indices: 53099125--53099170 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
53099115 CTCAAATAAG
*
53099125 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
53099141 ATTATT-AAATATATT
1 ATAATTAAAATATATT
53099156 ATAATTAAAATATAT
1 ATAATTAAAATATAT
53099171 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:53099177 original size:14 final size:15
Alignment explanation
Indices: 53099125--53099179 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
53099115 CTCAAATAAG
53099125 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
53099141 ATTATTAAATATATT
1 ATAATTAAATATATT
53099156 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
53099169 ATAATTTAATA
1 ATAATTAAATA
53099180 AAATTATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:53099194 original size:220 final size:220
Alignment explanation
Indices: 53098807--53099283 Score: 689
Period size: 220 Copynumber: 2.2 Consensus size: 220
53098797 ATTTAATTAT
*
53098807 ATTTAAATATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAAAT
1 ATTTAAATATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAAAT
* *
53098872 TTATTCAAATTATAATATATGATATTATAAAATATAATTTAACATAATTATTATTAAATATATTA
66 TAATTCAAATTAT-ATATATGATATTATAAAAGATAATTTAACATAATTATTATTAAATATATTA
* * * * *
53098937 TAATTAAAATATATGATTTAATAAATTTATTAATAATCAATATTCTTATATAAATTTACTCAAAT
130 TAATTAAAATATATAATTTAATAAAATTATTAATAATCAATATGCATATATAAATTTACTAAAAT
*
53099002 TATAATATATGATATTATAAAATATA
195 TATAATATATGATACTATAAAATATA
*
53099028 ATTT-AATATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTT-AA-
1 ATTTAAATATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAAAT
*
53099090 TAATT-AATATTCT-TATATGA-ATTTACTCAAATAAGATAATTTAACATAATTATTATTAAATA
66 TAATTCAA-ATTATATATATGATA-TTA-T--AA-AAGATAATTTAACATAATTATTATTAAATA
* *
53099152 TATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAATATGCATATATGAATTTATT
125 TATTATAATTAAAATATATAATTTAATAAAATTATTAATAATCAATATGCATATATAAATTTACT
*
53099217 AAAATTATAATATATGATGCTATAAAATATA
190 AAAATTATAATATATGATACTATAAAATATA
* * *
53099248 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAA
1 ATTTAAATATAATTATTATTAAATATATTATAATTAA
53099284 TATTAAATAA
Statistics
Matches: 233, Mismatches: 16, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
215 1 0.00
216 10 0.04
217 3 0.01
218 8 0.03
219 4 0.02
220 201 0.86
221 6 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (220 bp):
ATTTAAATATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAAAT
TAATTCAAATTATATATATGATATTATAAAAGATAATTTAACATAATTATTATTAAATATATTAT
AATTAAAATATATAATTTAATAAAATTATTAATAATCAATATGCATATATAAATTTACTAAAATT
ATAATATATGATACTATAAAATATA
Found at i:53099199 original size:100 final size:100
Alignment explanation
Indices: 53099025--53099214 Score: 335
Period size: 100 Copynumber: 1.9 Consensus size: 100
53099015 ATTATAAAAT
* *
53099025 ATAATTTAATATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA
1 ATAATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAA
* * *
53099090 TAATTAATATTCTTATATGAATTTACTCAAATAAG
66 TAATCAATATGCATATATGAATTTACTCAAATAAG
53099125 ATAATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAA
1 ATAATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAA
53099190 TAATCAATATGCATATATGAATTTA
66 TAATCAATATGCATATATGAATTTA
53099215 TTAAAATTAT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (100 bp):
ATAATTTAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAA
TAATCAATATGCATATATGAATTTACTCAAATAAG
Found at i:53100525 original size:137 final size:138
Alignment explanation
Indices: 53100276--53100546 Score: 438
Period size: 137 Copynumber: 2.0 Consensus size: 138
53100266 AACTTAAAAT
* * *
53100276 TGAAATCAATTATGGAATGCGTTACATTCAAAATAACAATAAACAAAATATGGATATAACACTAG
1 TGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACACTAA
** * *
53100341 CTACAAAAGTAATTTAACAATATCATGTGGTAACAAGTTCACCTGAAAGTG-AGATATGAAAGAT
66 CTACAAAAGTAATTTAACAATATCATGCAGTAACAAGTTCACATGAAAGTGCA-ATATGAAAGAC
53100405 ATGCCCAAA
130 ATGCCCAAA
* *
53100414 TGAAATCATTTATGGCATGAGTTACATTCAAAATAACAAT-AACAAAAGATGGATATAACACTAA
1 TGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACACTAA
53100478 CTACAAAAGTAATTTAACAATATCATGCAGTAACAAGTTCACATGAAAGTGCAATATGAAAGACA
66 CTACAAAAGTAATTTAACAATATCATGCAGTAACAAGTTCACATGAAAGTGCAATATGAAAGACA
53100543 TGCC
131 TGCC
53100547 ATTTTCTGAA
Statistics
Matches: 123, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
137 85 0.69
138 38 0.31
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (138 bp):
TGAAATCAATTATGGAATGAGTTACATTCAAAATAACAATAAACAAAAGATGGATATAACACTAA
CTACAAAAGTAATTTAACAATATCATGCAGTAACAAGTTCACATGAAAGTGCAATATGAAAGACA
TGCCCAAA
Found at i:53107013 original size:32 final size:31
Alignment explanation
Indices: 53106960--53107019 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
53106950 TAAAAAAAAG
* * *
53106960 TAAATTAACTAAAATTTAAAAATTAAAAGGT
1 TAAATTAACTAAAAATAAAAAATAAAAAGGT
*
53106991 TAAATTATTCTAAAAATAAAAAATAAAAA
1 TAAATTA-ACTAAAAATAAAAAATAAAAA
53107020 TAGTAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 7 0.29
32 17 0.71
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (31 bp):
TAAATTAACTAAAAATAAAAAATAAAAAGGT
Found at i:53116167 original size:50 final size:50
Alignment explanation
Indices: 53116109--53116211 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 50
53116099 AGTAGGATTG
* *
53116109 TTTCCGAACTACGTTAACAAACGATTGTGTGCAAATCTCTTCTTACCTTC
1 TTTCCGAACTACGTTAACAAACAATTGTGTGCAAATCTCTTCTTACCTAC
* *
53116159 TTTCCGAACTACGTTGACAAACAATTGTGTGCAAATCTTTTCTTACCTAC
1 TTTCCGAACTACGTTAACAAACAATTGTGTGCAAATCTCTTCTTACCTAC
53116209 TTT
1 TTT
53116212 GATTTTCGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (50 bp):
TTTCCGAACTACGTTAACAAACAATTGTGTGCAAATCTCTTCTTACCTAC
Found at i:53118933 original size:14 final size:14
Alignment explanation
Indices: 53118904--53118932 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
53118894 CAATATTTAC
53118904 TTATTTTGAAATTT
1 TTATTTTGAAATTT
53118918 TTATTTT-AAATTT
1 TTATTTTGAAATTT
53118931 TT
1 TT
53118933 TTCTCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTATTTTGAAATTT
Found at i:53128310 original size:18 final size:18
Alignment explanation
Indices: 53128273--53128341 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 18
53128263 GCGCATAGTT
* *
53128273 TTTATATAATGTACATACG
1 TTTATAT-ATATATATACG
*
53128292 TTTTTAT-TATAGTATACG
1 TTTATATATATA-TATACG
53128310 TTTATATATATATATA--
1 TTTATATATATATATACG
*
53128326 TATATATATATATATA
1 TTTATATATATATATA
53128342 TATATATNNN
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
16 15 0.35
17 3 0.07
18 15 0.35
19 10 0.23
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTATATATATATATACG
Found at i:53128319 original size:2 final size:2
Alignment explanation
Indices: 53128312--53128348 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53128302 AGTATACGTT
53128312 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53128349 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53128484 original size:2 final size:2
Alignment explanation
Indices: 53128477--53128521 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
53128467 TATAGTTACT
*
53128477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53128519 TA T
1 TA T
53128522 TTTTTTCTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:53128726 original size:18 final size:18
Alignment explanation
Indices: 53128681--53128726 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
53128671 CACATGCACG
53128681 TTTTAAAATACACATGTT
1 TTTTAAAATACACATGTT
* *
53128699 TTTCAAAATACACATTTT
1 TTTTAAAATACACATGTT
*
53128717 TTTTATAATA
1 TTTTAAAATA
53128727 GATATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTTAAAATACACATGTT
Found at i:53130493 original size:31 final size:29
Alignment explanation
Indices: 53130458--53130529 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
53130448 CGGCTTAGTA
*
53130458 ACTAAAATGTTACAATACAATAACATAAGTG
1 ACTAAAATGTAACAATAC-A-AACATAAGTG
* * *
53130489 ACTAAAATGTAACATTTCAAATATAAGTG
1 ACTAAAATGTAACAATACAAACATAAGTG
53130518 ACTAAAATGTAA
1 ACTAAAATGTAA
53130530 TTTGAGGCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 21 0.57
30 1 0.03
31 15 0.41
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (29 bp):
ACTAAAATGTAACAATACAAACATAAGTG
Found at i:53139934 original size:61 final size:61
Alignment explanation
Indices: 53139864--53140054 Score: 205
Period size: 61 Copynumber: 3.2 Consensus size: 61
53139854 ATTTAATAAG
53139864 AATATATAATTTAATAAAATTCTTAATATTAAATATTTTTATATGAATTTATTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTTTTATATGAATTTATTAAAATCAT
* * * * * * * *
53139925 AATATATAATACT-ATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATT-TAATAAA
1 AATATATAAT-TTAATAAAATTCTTAATATT-AAAT-ATTTTTATATGAAT-TTATTAAAATCAT
* **
53139984 AATATATAATTTAATAAAATTCTTAAAATTAAATATTTTTATATGAATTTACAAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTTTTATATGAATTTATTAAAATCAT
53140045 AATATATAAT
1 AATATATAAT
53140055 ACTAAAAATA
Statistics
Matches: 101, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
58 3 0.03
59 32 0.32
60 22 0.22
61 41 0.41
62 3 0.03
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTTTTATATGAATTTATTAAAATCAT
Found at i:53139960 original size:120 final size:119
Alignment explanation
Indices: 53139829--53140211 Score: 558
Period size: 120 Copynumber: 3.3 Consensus size: 119
53139819 TTAATCATAT
* * * *
53139829 TTTAACATAATTATTATTAAATGTAATTTAATAAGAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
**
53139894 AAATATTTTTATATGAATTTATTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTA-AAAATATAA
53139949 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
53140014 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATAC--------T-A
66 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTAAAAATATAA
* *
53140059 ---AAAATAATTGTTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
* *
53140121 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTA-AAAATATAA
53140176 TTTTAAAA-AATTATTATTAAATATAATTTAATAAAA
1 -TTTAAAATAATTATTATTAAATATAATTTAATAAAA
53140212 TTCAATATAA
Statistics
Matches: 238, Mismatches: 11, Indels: 28
0.86 0.04 0.10
Matches are distributed among these distances:
107 101 0.42
110 1 0.00
111 1 0.00
116 1 0.00
117 1 0.00
120 129 0.54
121 4 0.02
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTAAAAATATAA
Found at i:53140075 original size:107 final size:108
Alignment explanation
Indices: 53139951--53140271 Score: 491
Period size: 107 Copynumber: 3.1 Consensus size: 108
53139941 AAATATAATT
*
53139951 TAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATTAA
1 TAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAA
* *
53140016 ATATTTTTATATGAATTTACAAAAATCATAATATATAATACTA
66 ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
*
53140059 -AAAATAATTGTTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAA
1 TAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAA
53140123 ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
66 ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
* * **
53140166 TAAAAT-ATAATT-TTAAA-A-AA-TTATTATTAA-ATATAATTTAATAAAATTC--AATA-TAA
1 TAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAA
*
53140222 TTATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
66 ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
53140265 TAAAATA
1 TAAAATA
53140272 TAATTTAAAA
Statistics
Matches: 201, Mismatches: 10, Indels: 12
0.90 0.04 0.05
Matches are distributed among these distances:
99 51 0.25
100 4 0.02
102 19 0.09
103 7 0.03
104 2 0.01
105 1 0.00
106 5 0.02
107 107 0.53
108 5 0.02
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (108 bp):
TAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAA
ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
Found at i:53142969 original size:100 final size:97
Alignment explanation
Indices: 53142840--53143145 Score: 362
Period size: 100 Copynumber: 3.0 Consensus size: 97
53142830 TTTTAAAATT
53142840 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAGTTTAATTTTATTAA
1 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-TTTAATTTTATTAA
53142905 ATTATATATTTTTATTAAATTATATTTAATAACA
65 ATTATATA-TTTTATTAAATTATATTTAATAACA
**
53142939 ACTATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATTTTAAGAA
1 A-TATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATTTTATTAA
* * * * * **
53143004 TTTTATTAAATTATATTTAATAATAATTATTTTA-AATT
65 -ATTA-TATATTTTA-TT-A-AATTA-TATTTAATAACA
53143042 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAAT
1 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAG-A-A--T-AT-TT---AAT
53143107 TTTATTAAATTATATATTTTATTAAATTATATTTAATAA
57 TTTATTAAATTATATATTTTATTAAATTATATTTAATAA
53143146 TAATTATGTT
Statistics
Matches: 174, Mismatches: 16, Indels: 27
0.80 0.07 0.12
Matches are distributed among these distances:
99 13 0.07
100 56 0.32
101 5 0.03
102 46 0.26
103 8 0.05
104 7 0.04
105 6 0.03
106 7 0.04
107 3 0.02
108 4 0.02
109 7 0.04
110 3 0.02
111 9 0.05
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (97 bp):
ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATTTTATTAAA
TTATATATTTTATTAAATTATATTTAATAACA
Found at i:53143019 original size:29 final size:26
Alignment explanation
Indices: 53142998--53143047 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
53142988 TATTTAATTT
53142998 TAAGAATT-TTATTAAATTATATTTAA
1 TAAGAATTATT-TTAAATTATATTTAA
*
53143024 TAATAATTATTTTAAATTATATTT
1 TAAGAATTATTTTAAATTATATTT
53143048 TATAGTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (26 bp):
TAAGAATTATTTTAAATTATATTTAA
Found at i:53143094 original size:47 final size:47
Alignment explanation
Indices: 53142840--53142992 Score: 157
Period size: 48 Copynumber: 3.1 Consensus size: 47
53142830 TTTTAAAATT
53142840 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGA
1 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGA
* * * * * * *
53142887 ATAGTTTA-A-TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAACA
1 ATATTTTATAGTATTA-TATATTAT-GA-TTTTAGTAAATT-CA--T-ATAAGA
53142939 ACTATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGA
1 A-TATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGA
53142987 ATATTT
1 ATATTT
53142993 AATTTTAAGA
Statistics
Matches: 82, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
45 4 0.05
46 8 0.10
47 13 0.16
48 17 0.21
49 2 0.02
51 2 0.02
52 17 0.21
53 7 0.09
54 8 0.10
55 4 0.05
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.51
Consensus pattern (47 bp):
ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGA
Found at i:53143125 original size:17 final size:17
Alignment explanation
Indices: 53143105--53143138 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53143095 AATATTAAGA
53143105 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53143122 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
53143139 TTAATAATAA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:53143163 original size:102 final size:102
Alignment explanation
Indices: 53142894--53143163 Score: 332
Period size: 102 Copynumber: 2.6 Consensus size: 102
53142884 AGAATAGTTT
* * *
53142894 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAACAACTATTTTATAGTATTATAT
1 AATTTTATTAAATTATATA-TTTTATTAAATTATATTTAATAATAATTATGTTA-A--A--ATAT
*
53142959 ATTATGATTTTAGTAAATTCATATAAGAATATTTAATTTTAAG
60 ATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* * * * **
53143002 AATTTTATTAAA-T-TATATTTAATAATAATTAT-TTTAAATTATATTTTATAG-TATTATATAT
1 AATTTTATTAAATTATATATTTTATTA-AATTATATTT-AATAATA-ATTAT-GTTAAAATATAT
53143063 TATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
62 TATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
53143104 AATTTTATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATA
1 AATTTTATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATA
53143164 ATTAAATTAT
Statistics
Matches: 138, Mismatches: 16, Indels: 22
0.78 0.09 0.12
Matches are distributed among these distances:
101 1 0.01
102 69 0.50
103 13 0.09
104 13 0.09
105 9 0.07
106 15 0.11
107 6 0.04
108 12 0.09
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (102 bp):
AATTTTATTAAATTATATATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATATTATG
ATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
Found at i:53143195 original size:37 final size:37
Alignment explanation
Indices: 53143127--53143202 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
53143117 TATATATTTT
*
53143127 ATTAAATTATATTTAATAATAATTATGTTAAAATATA
1 ATTAAATTATATTTAATAATAATTATATTAAAATATA
* *
53143164 ATTAAATTAT-TTATATTAATAATCT-TATTAAAATTTA
1 ATTAAATTATATT-TAATAATAAT-TATATTAAAATATA
53143201 AT
1 AT
53143203 AACAATAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 2 0.06
37 31 0.91
38 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTAAATTATATTTAATAATAATTATATTAAAATATA
Found at i:53144308 original size:4 final size:4
Alignment explanation
Indices: 53144287--53144324 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
53144277 TCAAAATAAT
*
53144287 AATA AA-A AAGTA AGTA AATA AATA AATA AATA AATA AA
1 AATA AATA AA-TA AATA AATA AATA AATA AATA AATA AA
53144325 GAAAATGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.83
5 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:53144442 original size:51 final size:51
Alignment explanation
Indices: 53144357--53144491 Score: 141
Period size: 51 Copynumber: 2.6 Consensus size: 51
53144347 ATATAAAAAG
* * *
53144357 ATATATAAGTATGTACATATATGTATGTATATAAAAAT-TATAAAAAAATAT
1 ATATATAAGTATGTATATATAT-TATGAAAATAAAAATATATAAAAAAATAT
* * * *
53144408 ATATATAAGTATGTATATATATTCATGAAAATAAAAAATATGTATATAGATAT
1 ATATATAAGTATGTATATATATT-ATGAAAAT-AAAAATATATAAAAAAATAT
*
53144461 ATATAT-AGATATGTATATAAATTAT-AAAATA
1 ATATATAAG-TATGTATATATATTATGAAAATA
53144492 TAAGAAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
50 2 0.03
51 32 0.44
52 10 0.14
53 28 0.39
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (51 bp):
ATATATAAGTATGTATATATATTATGAAAATAAAAATATATAAAAAAATAT
Found at i:53144465 original size:12 final size:12
Alignment explanation
Indices: 53144445--53144479 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
53144435 AAAATAAAAA
53144445 ATATGTATATAG
1 ATATGTATATAG
*
53144457 ATATATATATAG
1 ATATGTATATAG
53144469 ATATGTATATA
1 ATATGTATATA
53144480 AATTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (12 bp):
ATATGTATATAG
Found at i:53144639 original size:35 final size:34
Alignment explanation
Indices: 53144599--53144691 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 34
53144589 AGAAGTATGT
*
53144599 ATATGTACATATATATATATAAATA-AGTTATAAAA
1 ATATGTACGTATATATATATAAATATA-TTAT-AAA
* * * *
53144634 ATATGTATGTGTATATGTATATATATATTATAAA
1 ATATGTACGTATATATATATAAATATATTATAAA
*
53144668 A-ATGTACGTATAATGTATATAAAT
1 ATATGTACGTAT-ATATATATAAAT
53144692 TATGAAGTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
33 8 0.17
34 13 0.28
35 24 0.52
36 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (34 bp):
ATATGTACGTATATATATATAAATATATTATAAA
Found at i:53145525 original size:11 final size:10
Alignment explanation
Indices: 53145500--53145533 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
53145490 TAATATTTCG
*
53145500 AAAAAAATAA
1 AAAAAAACAA
53145510 AAAAAAACAA
1 AAAAAAACAA
53145520 AGAAAAAACAA
1 A-AAAAAACAA
53145531 AAA
1 AAA
53145534 TAAGAAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:53146021 original size:16 final size:16
Alignment explanation
Indices: 53145996--53146033 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
53145986 TTGAATTACT
*
53145996 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
53146012 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
53146028 ATTACA
1 ATTACA
53146034 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:53152152 original size:16 final size:15
Alignment explanation
Indices: 53152118--53152169 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
53152108 ATATTTAAAA
*
53152118 ATTTT-AATTTTGA-
1 ATTTTAAATTTTTAT
53152131 ATTTTAAATTGTTTAT
1 ATTTTAAATT-TTTAT
53152147 ATTTTATAATTTTTAT
1 ATTTTA-AATTTTTAT
53152163 -TTTTAAA
1 ATTTTAAA
53152170 AAATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 8 0.24
16 11 0.32
17 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
ATTTTAAATTTTTAT
Found at i:53152196 original size:26 final size:24
Alignment explanation
Indices: 53152156--53152206 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
53152146 TATTTTATAA
*
53152156 TTTTTATTTTTAAAAAATATGATT
1 TTTTTATTTTTAAAAAATATAATT
53152180 TTTTTATATTTTAAAAAATTATAATT
1 TTTTTAT-TTTTAAAAAA-TATAATT
53152206 T
1 T
53152207 GAAAATTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.29
25 10 0.42
26 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTTTATTTTTAAAAAATATAATT
Found at i:53207734 original size:9 final size:9
Alignment explanation
Indices: 53207720--53207912 Score: 149
Period size: 9 Copynumber: 22.8 Consensus size: 9
53207710 AACTTATTTA
53207720 TTATGTAAG
1 TTATGTAAG
53207729 TTATGTAAG
1 TTATGTAAG
*
53207738 TTGTGTAAG
1 TTATGTAAG
53207747 TTATGTAAG
1 TTATGTAAG
*
53207756 CTATGTAAG
1 TTATGTAAG
*
53207765 TTGTGT-A-
1 TTATGTAAG
* *
53207772 TTATGAAAC
1 TTATGTAAG
53207781 TTATGTAAG
1 TTATGTAAG
*
53207790 TTATGT--C
1 TTATGTAAG
53207797 TTATGTAAG
1 TTATGTAAG
* *
53207806 TGATGTAAA
1 TTATGTAAG
*
53207815 ATATGT-A-
1 TTATGTAAG
53207822 TTATGTAAG
1 TTATGTAAG
*
53207831 TTATGTCAG
1 TTATGTAAG
*
53207840 TTGTGT-A-
1 TTATGTAAG
*
53207847 TTATGTAAA
1 TTATGTAAG
53207856 TTATGT-A-
1 TTATGTAAG
53207863 TTATGTAAG
1 TTATGTAAG
*
53207872 TTATGTAAT
1 TTATGTAAG
*
53207881 TTGTGT-A-
1 TTATGTAAG
*
53207888 TTATGTAAC
1 TTATGTAAG
* *
53207897 TTATTTAAT
1 TTATGTAAG
53207906 TTATGTA
1 TTATGTA
53207913 CGGTATGTGT
Statistics
Matches: 147, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
7 31 0.21
8 10 0.07
9 106 0.72
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:53207785 original size:25 final size:25
Alignment explanation
Indices: 53207718--53207862 Score: 139
Period size: 25 Copynumber: 5.7 Consensus size: 25
53207708 ATAACTTATT
*
53207718 TATTATGTAAGTTATGTAAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
53207743 TAAGTTATGTAAGCTATGTAAGTTGTG
1 T-A-TTATGAAAGTTATGTAAGTTGTG
* *
53207770 TATTATGAAACTTATGTAAGTTATG
1 TATTATGAAAGTTATGTAAGTTGTG
* * * ** *
53207795 TCTTATGTAAGTGATGTAAAATATG
1 TATTATGAAAGTTATGTAAGTTGTG
* *
53207820 TATTATGTAAGTTATGTCAGTTGTG
1 TATTATGAAAGTTATGTAAGTTGTG
53207845 TATTATGTAAA-TTATGTA
1 TATTATG-AAAGTTATGTA
53207863 TTATGTAAGT
Statistics
Matches: 98, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
25 71 0.72
26 4 0.04
27 23 0.23
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (25 bp):
TATTATGAAAGTTATGTAAGTTGTG
Found at i:53207799 original size:16 final size:16
Alignment explanation
Indices: 53207713--53207878 Score: 98
Period size: 16 Copynumber: 10.4 Consensus size: 16
53207703 TAGGAATAAC
*
53207713 TTATTTATTATGTAAG
1 TTATGTATTATGTAAG
*
53207729 TTATGTAAGTTGTGTAAG
1 TTATGT-A-TTATGTAAG
*
53207747 TTATGTAAGCTATGTAAG
1 TTATGT-A-TTATGTAAG
*
53207765 TTGTGTATTATG-AA-
1 TTATGTATTATGTAAG
*
53207779 --A---CTTATGTAAG
1 TTATGTATTATGTAAG
*
53207790 TTATGTCTTATGTAAG
1 TTATGTATTATGTAAG
* *
53207806 TGATGTAAAATATGT-A-
1 TTATGT--ATTATGTAAG
*
53207822 TTATGTAAGTTATGTCAG
1 TTATGT-A-TTATGTAAG
* *
53207840 TTGTGTATTATGTAAA
1 TTATGTATTATGTAAG
53207856 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
53207872 TTATGTA
1 TTATGTA
53207879 ATTTGTGTAT
Statistics
Matches: 118, Mismatches: 18, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
9 5 0.04
10 2 0.02
13 1 0.01
15 4 0.03
16 62 0.53
17 5 0.04
18 39 0.33
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.46
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:53207826 original size:41 final size:40
Alignment explanation
Indices: 53207781--53207895 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 40
53207771 ATTATGAAAC
53207781 TTATGTAAGTTATGTC-TTATGTAAGTGATGTAAAATATGTA
1 TTATGTAAGTTATGTCATTATGT-A-TGATGTAAAATATGTA
* * *
53207822 TTATGTAAGTTATGTCAGTTGTGTATTATGTAAATTATGTA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAAAATATGTA
* * *
53207863 TTATGTAAGTTATGTAATTTGTGTATTATGTAA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAA
53207896 CTTATTTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 61 0.91
42 1 0.01
43 5 0.07
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTCATTATGTATGATGTAAAATATGTA
Found at i:53207875 original size:25 final size:24
Alignment explanation
Indices: 53207719--53207912 Score: 99
Period size: 25 Copynumber: 7.7 Consensus size: 24
53207709 TAACTTATTT
* *
53207719 ATTATGTAAGTTATGTAAGTTGTGTA
1 ATTATGTAATTTATGT-A-TTATGTA
** *
53207745 AGTTATGTAAGCTATGTAAGTTGTGT-
1 A-TTATGTAATTTATGT-A-TTATGTA
* *
53207771 ATTATGAAACTTATGTAAGTTATGT-
1 ATTATGTAATTTATGT-A-TTATGTA
* * * *
53207796 CTTATGTAAGTGATGTAAAATATGT-
1 ATTATGTAATTTATGT--ATTATGTA
* *
53207821 ATTATGTAAGTTATGTCAGTTGTGT-
1 ATTATGTAATTTATGT-A-TTATGTA
*
53207846 ATTATGTAAATTATGTATTATGTA
1 ATTATGTAATTTATGTATTATGTA
*
53207870 AGTTATGTAATTTGTGTATTATGTA
1 A-TTATGTAATTTATGTATTATGTA
*
53207895 ACTTATTTAATTTATGTA
1 A-TTATGTAATTTATGTA
53207913 CGGTATGTGT
Statistics
Matches: 141, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.04
24 3 0.02
25 106 0.75
26 4 0.03
27 23 0.16
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (24 bp):
ATTATGTAATTTATGTATTATGTA
Found at i:53208114 original size:87 final size:88
Alignment explanation
Indices: 53208016--53208177 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 88
53208006 CTTAAAAATT
* *
53208016 TAATACTAATAAATTTAATATTTAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATA
1 TAATACTAATAAATTTAATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATA
53208081 -GGTTATATTAAAACAATATTTA
66 GGGTTATATTAAAACAATATTTA
53208103 TAATACTAATAAATTTAATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATA
1 TAATACTAATAAATTTAATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATA
53208168 GGGTTATATT
66 GGGTTATATT
53208178 NNNNNNNNNN
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
87 63 0.88
88 9 0.12
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (88 bp):
TAATACTAATAAATTTAATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATA
GGGTTATATTAAAACAATATTTA
Found at i:53208143 original size:18 final size:18
Alignment explanation
Indices: 53208083--53208143 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 18
53208073 ATTTTATAGG
53208083 TTAT-ATTAAAACAATAT
1 TTATAATTAAAACAATAT
* *
53208100 TTATAA-TACTAATAA-AT
1 TTATAATTA-AAACAATAT
53208117 TTA-ATATTAAAACAATAT
1 TTATA-ATTAAAACAATAT
53208135 TTATAATTA
1 TTATAATTA
53208144 TTTAGAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
16 1 0.03
17 16 0.47
18 16 0.47
19 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTATAATTAAAACAATAT
Found at i:53210097 original size:181 final size:185
Alignment explanation
Indices: 53209751--53210106 Score: 567
Period size: 195 Copynumber: 1.9 Consensus size: 185
53209741 TTTAATCCGA
53209751 ATAACCTTAACCGAATAGAAGAAACACTAAATAGAAGAAGTAGACGACTGCAAATGCGGGTTATA
1 ATAACCTTAACCGAATAGAAGAAACACTAAATAGAAGAAGTAGACGACTGCAAATGCGGGTTATA
*
53209816 GAGCGACCGCCGGAGTGGAGCCGACTGCAATGACAGGGGGGATTTGGGAATTTGGGGATTTAGGG
66 GAGCGACCGCCGGAGTGGAGCCGACTGCAACGACAGGGGGGATTTGGGAATTTGGGGA-TT----
53209881 AAATTAAATCGGGGAAACTGGGGGAATAGGAATTGGGGGAAAATGTGGGCTTAATCCGAAGAAAT
126 --ATT-AA-C-GGGAAACTGGGGGAATAGGAATTGGGGGAAAATGTGGGCTTAATCCGAAGAAAT
*
53209946 ATAACCTTAACCGAATAGAAGAAACACTGAATAGAAGAAGTAGACGACTGCAAATGCGGGTTATA
1 ATAACCTTAACCGAATAGAAGAAACACTAAATAGAAGAAGTAGACGACTGCAAATGCGGGTTATA
53210011 GAGCGACCGCCGGAGTGGAGCCGACTGCAACGACAGGGGGGATTTGGGAATTTGGGGA-T-TT-A
66 GAGCGACCGCCGGAGTGGAGCCGACTGCAACGACAGGGGGGATTTGGGAATTTGGGGATTATTAA
*
53210073 -GGGAAACTGGGGGAATAGGAATTGGGGGGAAATG
131 CGGGAAACTGGGGGAATAGGAATTGGGGGAAAATG
53210107 AAATCGGGGA
Statistics
Matches: 158, Mismatches: 3, Indels: 14
0.90 0.02 0.08
Matches are distributed among these distances:
181 33 0.21
184 1 0.01
186 2 0.01
193 1 0.01
195 121 0.77
ACGTcount: A:0.35, C:0.13, G:0.34, T:0.18
Consensus pattern (185 bp):
ATAACCTTAACCGAATAGAAGAAACACTAAATAGAAGAAGTAGACGACTGCAAATGCGGGTTATA
GAGCGACCGCCGGAGTGGAGCCGACTGCAACGACAGGGGGGATTTGGGAATTTGGGGATTATTAA
CGGGAAACTGGGGGAATAGGAATTGGGGGAAAATGTGGGCTTAATCCGAAGAAAT
Found at i:53210119 original size:24 final size:25
Alignment explanation
Indices: 53210090--53210144 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
53210080 TGGGGGAATA
53210090 GGAATT-GGGGGGAA-ATGAAATCGG
1 GGAATTGGGGGGGAATATGAAAT-GG
53210114 GGAATTGGGGGGGAATATGAAATGG
1 GGAATTGGGGGGGAATATGAAATGG
*
53210139 GAAATT
1 GGAATT
53210145 AGGGAATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 6 0.21
25 15 0.54
26 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.44, T:0.20
Consensus pattern (25 bp):
GGAATTGGGGGGGAATATGAAATGG
Found at i:53210710 original size:22 final size:22
Alignment explanation
Indices: 53210684--53210726 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
53210674 AAGTTTAACC
*
53210684 CGTAACCTTTATACTTTAAACT
1 CGTAACCTTTAAACTTTAAACT
53210706 CGTAACCTTTAAACTTTAAAC
1 CGTAACCTTTAAACTTTAAAC
53210727 CCTAAACTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (22 bp):
CGTAACCTTTAAACTTTAAACT
Found at i:53215919 original size:42 final size:42
Alignment explanation
Indices: 53215790--53216018 Score: 259
Period size: 42 Copynumber: 5.4 Consensus size: 42
53215780 ACGTCGCTAA
* * *
53215790 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATATT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTT
* * *
53215834 CTTTAGCGGCACTAAGGAAATAAACGCCGCTAAAGATCGTGTT
1 CTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGATCATGTT
*
53215877 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
*
53215919 CTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTT
* * *
53215962 CTATAGCGGTGCTT-GGTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAAGA-TCA-TGTT
53216004 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
53216019 TTTCACAAAC
Statistics
Matches: 162, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 80 0.49
43 70 0.43
44 11 0.07
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:53215944 original size:85 final size:86
Alignment explanation
Indices: 53215790--53216018 Score: 263
Period size: 85 Copynumber: 2.7 Consensus size: 86
53215780 ACGTCGCTAA
* * * *
53215790 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATATTCTTTAGCGGCACTAAGGAAAT
1 CTTTAGCGGCGCTTA-AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAT
**
53215855 AAACGCCGCT-AAAGATCGTGTT
65 AAACGCCGCTAAAAG-TAATGTT
*
53215877 CTTTAGCGGCGCTTATG-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGA-
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAA-AT
53215940 AAACGCCGCTAAAAGTAATGTT
65 AAACGCCGCTAAAAGTAATGTT
* * * **
53215962 CTATAGCGGTGCTT-GGTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
53216019 TTTCACAAAC
Statistics
Matches: 126, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
84 3 0.02
85 103 0.82
86 6 0.05
87 14 0.11
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (86 bp):
CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAATA
AACGCCGCTAAAAGTAATGTT
Found at i:53216220 original size:19 final size:19
Alignment explanation
Indices: 53216196--53216232 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
53216186 AATATTTCAA
53216196 ATTAAATGACTA-AAATAAT
1 ATTAAATGA-TATAAATAAT
53216215 ATTAAATGATATAAATAA
1 ATTAAATGATATAAATAA
53216233 AAGTGAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTAAATGATATAAATAAT
Found at i:53217644 original size:25 final size:25
Alignment explanation
Indices: 53217616--53217777 Score: 127
Period size: 25 Copynumber: 6.4 Consensus size: 25
53217606 ATAAAGTAAA
53217616 TATGAAAATTATGTAAGTTATTTAT
1 TATGAAAATTATGTAAGTTATTTAT
* *
53217641 TATGAAAATTATGTAAGTTGTGTAT
1 TATGAAAATTATGTAAGTTATTTAT
*
53217666 TATGAAAATTATGCTATG-TA---AGT
1 TATGAAAATTATG-TAAGTTATTTA-T
* * * * *
53217689 TATGTAAGTCATATAAGTTATGTAT
1 TATGAAAATTATGTAAGTTATTTAT
*
53217714 TAT-ATAAGTTATGTAAGTTATTTAT
1 TATGA-AAATTATGTAAGTTATTTAT
* * *
53217739 TATAAAAATTAAGTAAGTTATGTAATT
1 TATGAAAATTATGTAAGTTAT-TTA-T
53217766 TATGAATAATTA
1 TATGAA-AATTA
53217778 AAAAAATGTA
Statistics
Matches: 109, Mismatches: 17, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
22 4 0.04
23 12 0.11
25 75 0.69
26 7 0.06
27 6 0.06
28 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (25 bp):
TATGAAAATTATGTAAGTTATTTAT
Found at i:53217692 original size:9 final size:9
Alignment explanation
Indices: 53217680--53217821 Score: 95
Period size: 9 Copynumber: 16.7 Consensus size: 9
53217670 AAAATTATGC
53217680 TATGTAAGT
1 TATGTAAGT
53217689 TATGTAAGT
1 TATGTAAGT
* *
53217698 CATATAAGT
1 TATGTAAGT
53217707 TATGT-A-T
1 TATGTAAGT
*
53217714 TATATAAGT
1 TATGTAAGT
53217723 TATGTAAGT
1 TATGTAAGT
*
53217732 TAT-TTA-T
1 TATGTAAGT
** *
53217739 TATAAAAAT
1 TATGTAAGT
*
53217748 TAAGTAAGT
1 TATGTAAGT
*
53217757 TATGTAATT
1 TATGTAAGT
53217766 TATG-AA-T
1 TATGTAAGT
* **
53217773 AAT-TAAAAA
1 TATGT-AAGT
*
53217782 AATGTAAGT
1 TATGTAAGT
53217791 TATGTAAG-
1 TATGTAAGT
53217799 T-TGTAAGT
1 TATGTAAGT
53217807 TATGTAAGT
1 TATGTAAGT
53217816 TATGTA
1 TATGTA
53217822 TAATATTAAT
Statistics
Matches: 103, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
7 18 0.17
8 11 0.11
9 73 0.71
10 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (9 bp):
TATGTAAGT
Found at i:53217720 original size:16 final size:17
Alignment explanation
Indices: 53217684--53217728 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
53217674 TTATGCTATG
53217684 TAAGTTATGTAAGTCATA
1 TAAGTTATGT-AGTCATA
*
53217702 TAAGTTATGTA-TTATA
1 TAAGTTATGTAGTCATA
53217718 TAAGTTATGTA
1 TAAGTTATGTA
53217729 AGTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 15 0.58
17 1 0.04
18 10 0.38
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.44
Consensus pattern (17 bp):
TAAGTTATGTAGTCATA
Found at i:53217805 original size:16 final size:16
Alignment explanation
Indices: 53217784--53217816 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
53217774 ATTAAAAAAA
53217784 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
53217800 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
53217816 T
1 T
53217817 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:53217821 original size:34 final size:33
Alignment explanation
Indices: 53217680--53217821 Score: 101
Period size: 34 Copynumber: 4.2 Consensus size: 33
53217670 AAAATTATGC
53217680 TATGTAAGTTATGTAAGTCATATAAGTTATGT--AT
1 TATGTAAGTTATGTAAGT--TATAA-TTATGTAAAT
* * **
53217714 TATATAAGTTATGTAAGTTATTTATTATAAAAAT
1 TATGTAAGTTATGTAAGTTA-TAATTATGTAAAT
* * * *
53217748 TAAGTAAGTTATGTAATTTATGAATAAT-TAAAAA
1 TATGTAAGTTATGTAAGTTAT-AATTATGT-AAAT
* * *
53217782 AATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAGTTATAA-TTATGTAAAT
53217816 TATGTA
1 TATGTA
53217822 TAATATTAAT
Statistics
Matches: 82, Mismatches: 19, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
32 6 0.07
33 5 0.06
34 70 0.85
35 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.15, T:0.43
Consensus pattern (33 bp):
TATGTAAGTTATGTAAGTTATAATTATGTAAAT
Found at i:53217994 original size:9 final size:9
Alignment explanation
Indices: 53217980--53218199 Score: 128
Period size: 9 Copynumber: 24.6 Consensus size: 9
53217970 AATTAAAAAA
53217980 ATGTAAGTT
1 ATGTAAGTT
*
53217989 ATGTAAGGT
1 ATGTAAGTT
53217998 -TGTAAGTT
1 ATGTAAGTT
53218006 ATGTAAGTT
1 ATGTAAGTT
*
53218015 ATGTATA-AT
1 ATGTA-AGTT
53218024 AT-TAA-TT
1 ATGTAAGTT
53218031 AAT-TAAGTT
1 -ATGTAAGTT
*
53218040 ATGTAATTT
1 ATGTAAGTT
*
53218049 ATGTATA-AT
1 ATGTA-AGTT
53218058 AT-TAA-TT
1 ATGTAAGTT
53218065 AAT-TAAGTT
1 -ATGTAAGTT
*
53218074 ATGTAATTT
1 ATGTAAGTT
*
53218083 ATGTATAATATT
1 ATG--TAA-GTT
53218095 AATGTAAGTT
1 -ATGTAAGTT
*
53218105 ATGTAATTT
1 ATGTAAGTT
*
53218114 ATGTATAATATT
1 ATG--TAA-GTT
53218126 AATGTAAGTT
1 -ATGTAAGTT
53218136 ATGTAAG-T
1 ATGTAAGTT
53218144 -TGTAAGTT
1 ATGTAAGTT
53218152 ATGTAAGTT
1 ATGTAAGTT
*
53218161 ATGTATA-AT
1 ATGTA-AGTT
53218170 AT-TAA-TT
1 ATGTAAGTT
53218177 AAT-TAAGTT
1 -ATGTAAGTT
53218186 ATGTAAGTT
1 ATGTAAGTT
53218195 ATGTA
1 ATGTA
53218200 TAATACTAAT
Statistics
Matches: 173, Mismatches: 15, Indels: 46
0.74 0.06 0.20
Matches are distributed among these distances:
7 12 0.07
8 36 0.21
9 96 0.55
10 7 0.04
11 12 0.07
12 4 0.02
13 6 0.03
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:53218038 original size:34 final size:34
Alignment explanation
Indices: 53218000--53218209 Score: 219
Period size: 34 Copynumber: 5.9 Consensus size: 34
53217990 TGTAAGGTTG
53218000 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
*
53218034 TAAGTTATGTAATTTATGTATAATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
* *
53218068 TAAGTTATGTAATTTATGTATAATATTAA-T--G
1 TAAGTTATGTAAGTTATGTATAATATTAATTAAT
*
53218099 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTAT
1 TAAGTTATGTAAGTTATGTATAATATTAAT-T-A---AT
* *
53218138 GTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAAT
1 -TAAG-T-TATGTAA-----GTTATGTATAATATTAATTAAT
*
53218180 TAAGTTATGTAAGTTATGTATAATACTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAAT
53218210 GTAAGTTATG
Statistics
Matches: 151, Mismatches: 9, Indels: 32
0.79 0.05 0.17
Matches are distributed among these distances:
31 29 0.19
33 2 0.01
34 79 0.52
39 5 0.03
40 5 0.03
41 5 0.03
42 7 0.05
45 1 0.01
46 1 0.01
47 17 0.11
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (34 bp):
TAAGTTATGTAAGTTATGTATAATATTAATTAAT
Found at i:53218149 original size:16 final size:16
Alignment explanation
Indices: 53218128--53218160 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
53218118 ATAATATTAA
53218128 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
53218144 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
53218160 T
1 T
53218161 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:53218165 original size:65 final size:64
Alignment explanation
Indices: 53218000--53218154 Score: 184
Period size: 65 Copynumber: 2.3 Consensus size: 64
53217990 TGTAAGGTTG
* *
53218000 TAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATT
1 TAAGTAATGTAAGTTATG-ATAATATTAA-T--GTAAGTTATGTAATTTATGTATAATATTAATT
53218065 AAT
62 AAT
* *
53218068 TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATAATATTAATGTAA
1 TAAGTAATGTAAGTTATG-ATAATATTAATGTAAGTTATGTAATTTATGTATAATATTAAT-TAA
53218133 GT
64 -T
*
53218135 TATGTAAGTTGTAAGTTATG
1 TAAGTAA--TGTAAGTTATG
53218155 TAAGTTATGT
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
65 30 0.38
66 3 0.04
67 7 0.09
68 28 0.36
69 10 0.13
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.48
Consensus pattern (64 bp):
TAAGTAATGTAAGTTATGATAATATTAATGTAAGTTATGTAATTTATGTATAATATTAATTAAT
Found at i:53218214 original size:22 final size:21
Alignment explanation
Indices: 53218186--53218230 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
53218176 TAATTAAGTT
53218186 ATGTAAGTTATGTATAATACTA
1 ATGTAAGTTATGTATAATA-TA
*
53218208 ATGTAAGTTATGTATTATATA
1 ATGTAAGTTATGTATAATATA
53218229 AT
1 AT
53218231 AACAGCGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (21 bp):
ATGTAAGTTATGTATAATATA
Found at i:53220550 original size:24 final size:23
Alignment explanation
Indices: 53220495--53220551 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
53220485 TTCTAGAATT
*
53220495 GGGGGATTTTTGGGGGAAAATCG
1 GGGGGAATTTTGGGGGAAAATCG
* * * *
53220518 AGGGCAATTTTGGGGAGAAATTTG
1 GGGGGAATTTTGGGG-GAAAATCG
53220542 GGGGGAATTT
1 GGGGGAATTT
53220552 CAGCTAAGTG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.25, C:0.04, G:0.44, T:0.28
Consensus pattern (23 bp):
GGGGGAATTTTGGGGGAAAATCG
Found at i:53220914 original size:16 final size:16
Alignment explanation
Indices: 53220869--53220924 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
53220859 TAAATCTCAC
*
53220869 ATCTTTTATTTATT-T
1 ATCTTTTATTAATTGT
* *
53220884 ATTTATTTCTTAATTGT
1 ATCT-TTTATTAATTGT
53220901 ATCTTTTATTAATTGT
1 ATCTTTTATTAATTGT
53220917 ATCTTTTA
1 ATCTTTTA
53220925 ATTACTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 27 0.79
17 4 0.12
ACGTcount: A:0.23, C:0.07, G:0.04, T:0.66
Consensus pattern (16 bp):
ATCTTTTATTAATTGT
Found at i:53221628 original size:13 final size:14
Alignment explanation
Indices: 53221593--53221633 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
53221583 CAAACCCCTA
*
53221593 AAGT-CTAAACCGT
1 AAGTCCTAAACCAT
*
53221606 AAGTCATAAACCAT
1 AAGTCCTAAACCAT
53221620 AA-TCCTAAACCAT
1 AAGTCCTAAACCAT
53221633 A
1 A
53221634 TCTTTGGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 15 0.62
14 9 0.38
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (14 bp):
AAGTCCTAAACCAT
Found at i:53224162 original size:20 final size:20
Alignment explanation
Indices: 53224139--53224185 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
53224129 TATAATTTAC
*
53224139 ATAATATATA-TAAATAAAAT
1 ATAAAATATACTAAA-AAAAT
*
53224159 ATAAAATATACTACAAAAAT
1 ATAAAATATACTAAAAAAAT
53224179 ATAAAAT
1 ATAAAAT
53224186 GGGTTAGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAATATACTAAAAAAAT
Found at i:53226238 original size:126 final size:126
Alignment explanation
Indices: 53226034--53226286 Score: 411
Period size: 126 Copynumber: 2.0 Consensus size: 126
53226024 AACTAGTGTT
**
53226034 GGCATTGTGAATGCCGGCAACTATTAAAATATTATTTTTTTCTTTTTTATTTAAAATCATAGAAT
1 GGCATTGTGAATGCCAACAACTATTAAAATATTATTTTTTTCTTTTTTATTTAAAATCATAGAAT
53226099 ACTAGTATTTTTAAAGTGTATTT-AAAAAAAATACATATTGGTGCCGACGAACACAGTGCC
66 ACTAGTATTTTTAAAGTGTATTTGAAAAAAAATACATATTGGTGCCGACGAACACAGTGCC
* *
53226159 GGCATTGTGAATGCCAACACCTATTAAAATATTAATTTTTTTCTTTTTTATTTAAAATCCT-GAA
1 GGCATTGTGAATGCCAACAACTATTAAAATATT-ATTTTTTTCTTTTTTATTTAAAATCATAG-A
* * *
53226223 ATACTAGTATTTTTAAAGTGTATTTGAAAATAAATACATATTGGTGTCGGCGAACACAGTGCC
64 ATACTAGTATTTTTAAAGTGTATTTGAAAAAAAATACATATTGGTGCCGACGAACACAGTGCC
53226286 G
1 G
53226287 ACACAAAAAA
Statistics
Matches: 118, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
125 31 0.26
126 52 0.44
127 35 0.30
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (126 bp):
GGCATTGTGAATGCCAACAACTATTAAAATATTATTTTTTTCTTTTTTATTTAAAATCATAGAAT
ACTAGTATTTTTAAAGTGTATTTGAAAAAAAATACATATTGGTGCCGACGAACACAGTGCC
Found at i:53228215 original size:13 final size:13
Alignment explanation
Indices: 53228197--53228221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53228187 TAATTTATAT
53228197 GTGTGAAAATTTC
1 GTGTGAAAATTTC
53228210 GTGTGAAAATTT
1 GTGTGAAAATTT
53228222 TATCATTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:53232856 original size:42 final size:43
Alignment explanation
Indices: 53232755--53232912 Score: 133
Period size: 42 Copynumber: 3.7 Consensus size: 43
53232745 ATGTGATATT
** * * * *
53232755 GTGTAAGACTATGTCTGGGACGTTGGCATTGATT-TGAGATTTAC
1 GTGTAAGACCCTGTCTGGGACATTGGCATCG-TTAT-ATAATTAC
* * *
53232799 GTGTAAGATCATGTCTGGGACATTGGCGTCG-TATATAATTAC
1 GTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATAATTAC
* * * *
53232841 GTGTAAGACCCTGTCTGGGATAGTGGCATCGTTATTTGATTAC
1 GTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATAATTAC
* *
53232884 ATGTAAGACCAC-ATCTGGGACATTGGCAT
1 GTGTAAGACC-CTGTCTGGGACATTGGCAT
53232913 TGTACGAGCT
Statistics
Matches: 93, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
42 33 0.35
43 33 0.35
44 27 0.29
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (43 bp):
GTGTAAGACCCTGTCTGGGACATTGGCATCGTTATATAATTAC
Found at i:53232890 original size:43 final size:42
Alignment explanation
Indices: 53232755--53232912 Score: 131
Period size: 43 Copynumber: 3.7 Consensus size: 42
53232745 ATGTGATATT
* * *
53232755 GTGTAAGACTATGTCTGGGAC-GTTGGCATTG-ATTTGAGATTTAC
1 GTGTAAGACCATGTCTGGGACAG-TGGCATCGTATAT-A-A-TTAC
* * *
53232799 GTGTAAGATCATGTCTGGGACATTGGCGTCGTATATAATTAC
1 GTGTAAGACCATGTCTGGGACAGTGGCATCGTATATAATTAC
* * * *
53232841 GTGTAAGACCCTGTCTGGGATAGTGGCATCGTTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACAGTGGCATCG-TATATAATTAC
* ** *
53232884 ATGTAAGACCACATCTGGGACATTGGCAT
1 GTGTAAGACCATGTCTGGGACAGTGGCAT
53232913 TGTACGAGCT
Statistics
Matches: 92, Mismatches: 19, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
42 30 0.33
43 33 0.36
44 26 0.28
45 3 0.03
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACAGTGGCATCGTATATAATTAC
Found at i:53233123 original size:39 final size:40
Alignment explanation
Indices: 53233063--53233145 Score: 150
Period size: 39 Copynumber: 2.1 Consensus size: 40
53233053 AAGTATTATG
*
53233063 TATAACATGAAAAGATGAATTAATCATATAAATATGAGTA
1 TATAACATGAAAAAATGAATTAATCATATAAATATGAGTA
53233103 TATAACAT-AAAAAATGAATTAATCATATAAATATGAGTA
1 TATAACATGAAAAAATGAATTAATCATATAAATATGAGTA
53233142 TATA
1 TATA
53233146 TGCATGTGTA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 34 0.81
40 8 0.19
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (40 bp):
TATAACATGAAAAAATGAATTAATCATATAAATATGAGTA
Found at i:53233132 original size:20 final size:20
Alignment explanation
Indices: 53233072--53233133 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
53233062 GTATAACATG
*
53233072 AAAAGATGAATTAATCATAT
1 AAAAAATGAATTAATCATAT
* * * *
53233092 -AAATATG-AGTATATAACAT
1 AAAAAATGAATTA-ATCATAT
53233111 AAAAAATGAATTAATCATAT
1 AAAAAATGAATTAATCATAT
53233131 AAA
1 AAA
53233134 TATGAGTATA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
18 3 0.10
19 11 0.35
20 14 0.45
21 3 0.10
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAAAATGAATTAATCATAT
Found at i:53237929 original size:37 final size:32
Alignment explanation
Indices: 53237892--53237956 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
53237882 CAATGGTAAA
53237892 ATAAAATAAAAGTAAAACCCATATAGAATTAC
1 ATAAAATAAAAGTAAAACCCATATAGAATTAC
53237924 ATAAAATAAAAGTAAAACCCATATAGAATTAC
1 ATAAAATAAAAGTAAAACCCATATAGAATTAC
53237956 A
1 A
53237957 CTTCTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.60, C:0.12, G:0.06, T:0.22
Consensus pattern (32 bp):
ATAAAATAAAAGTAAAACCCATATAGAATTAC
Found at i:53238602 original size:24 final size:23
Alignment explanation
Indices: 53238544--53238603 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
53238534 CTATTTTCCA
*
53238544 TTATTT-AATATAAAGGTTTTTT
1 TTATTTAAATATAAAGGGTTTTT
*
53238566 TTA-TGAAATATATAAGGGGTTTTT
1 TTATTTAAATATA-AA-GGGTTTTT
53238590 TTATTTAACATATA
1 TTATTTAA-ATATA
53238604 TTTGTGTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 1 0.03
22 9 0.30
23 2 0.07
24 10 0.33
25 3 0.10
26 5 0.17
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.52
Consensus pattern (23 bp):
TTATTTAAATATAAAGGGTTTTT
Found at i:53240476 original size:7 final size:7
Alignment explanation
Indices: 53240466--53240498 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
53240456 CGTAACATGT
53240466 AACCCCA
1 AACCCCA
53240473 AACCCCA
1 AACCCCA
53240480 AACCCCA
1 AACCCCA
53240487 AACCCCA
1 AACCCCA
53240494 AACCC
1 AACCC
53240499 TTAACCCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.58, G:0.00, T:0.00
Consensus pattern (7 bp):
AACCCCA
Found at i:53240525 original size:21 final size:22
Alignment explanation
Indices: 53240480--53240552 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 22
53240470 CCAAACCCCA
53240480 AACCC-CAAACCCCA-AACCCTT-
1 AACCCTCAAA-CCCAGAA-CCTTG
**
53240501 AACCCTTGAACCC-GAACCTTG
1 AACCCTCAAACCCAGAACCTTG
*
53240522 AA-CCTCAAACCCATAACCTTG
1 AACCCTCAAACCCAGAACCTTG
53240543 AACCCT-AAAC
1 AACCCTCAAAC
53240553 TTCAATCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
20 12 0.29
21 25 0.60
22 5 0.12
ACGTcount: A:0.37, C:0.42, G:0.05, T:0.15
Consensus pattern (22 bp):
AACCCTCAAACCCAGAACCTTG
Found at i:53240566 original size:34 final size:35
Alignment explanation
Indices: 53240487--53240567 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
53240477 CCAAACCCCA
* * * *
53240487 AACCCCAAACCCTTAACCCTTGAACCCGAACCTTG
1 AACCTCAAACCCATAACCCTTGAACCCGAAACTTC
*
53240522 AACCTCAAACCCATAA-CCTTGAACCCTAAACTTC
1 AACCTCAAACCCATAACCCTTGAACCCGAAACTTC
* *
53240556 AATCTTAAACCC
1 AACCTCAAACCC
53240568 CCGAACCAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 25 0.64
35 14 0.36
ACGTcount: A:0.36, C:0.40, G:0.05, T:0.20
Consensus pattern (35 bp):
AACCTCAAACCCATAACCCTTGAACCCGAAACTTC
Found at i:53243705 original size:2 final size:2
Alignment explanation
Indices: 53243698--53243722 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53243688 TTAATAATCC
53243698 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
53243723 CATACTCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53246690 original size:20 final size:20
Alignment explanation
Indices: 53246644--53246682 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
53246634 AAACTACTCT
*
53246644 TTTTTTTACTATTTTCTTGC
1 TTTTTTTACTATTTTATTGC
*
53246664 TTTTTTTACTGTTTTATTG
1 TTTTTTTACTATTTTATTG
53246683 TTATTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.72
Consensus pattern (20 bp):
TTTTTTTACTATTTTATTGC
Found at i:53247778 original size:42 final size:42
Alignment explanation
Indices: 53247719--53247804 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
53247709 AGGAAAAATA
*
53247719 GTACTACATCGTGTATTTACTCCTCCTCAGGGCACATCACAT
1 GTACTACATCGTGTATTTACTCCCCCTCAGGGCACATCACAT
*
53247761 GTACTACATCGTGTATTTACTCCCCCTCAGGGCATATCACAT
1 GTACTACATCGTGTATTTACTCCCCCTCAGGGCACATCACAT
53247803 GT
1 GT
53247805 TATCTTATAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.31
Consensus pattern (42 bp):
GTACTACATCGTGTATTTACTCCCCCTCAGGGCACATCACAT
Found at i:53254263 original size:2 final size:2
Alignment explanation
Indices: 53254256--53254285 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53254246 GTAGGGACGT
53254256 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
53254286 TGGGACACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:53260996 original size:43 final size:43
Alignment explanation
Indices: 53260935--53261019 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
53260925 ATATCCAAGC
*
53260935 CAAGGGTGGCAACAATAGTTTAATTATATCGAGTGACCATAGT
1 CAAGGATGGCAACAATAGTTTAATTATATCGAGTGACCATAGT
* * *
53260978 CAAGGATGGCGACAATAGTTTAATTATATTGCGTGACCATAG
1 CAAGGATGGCAACAATAGTTTAATTATATCGAGTGACCATAG
53261020 GATAGACAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (43 bp):
CAAGGATGGCAACAATAGTTTAATTATATCGAGTGACCATAGT
Found at i:53273637 original size:12 final size:12
Alignment explanation
Indices: 53273614--53273648 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
53273604 GAACTTTCTT
53273614 TTTTTAATATATA
1 TTTTTAA-ATATA
53273627 TTTTTAAATATA
1 TTTTTAAATATA
53273639 TTTATTAAAT
1 TTT-TTAAAT
53273649 TACATTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTAAATATA
Found at i:53274711 original size:22 final size:22
Alignment explanation
Indices: 53274653--53274711 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
53274643 CATTTATATC
*
53274653 ATAATTTCCAAAATTTAAATTT
1 ATAATTTCCATAATTTAAATTT
** * *
53274675 ATAA-ACCCCTGAATTTTAATTT
1 ATAATTTCCAT-AATTTAAATTT
53274697 ATAATTTCCATAATT
1 ATAATTTCCATAATT
53274712 AAGCCACCAA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
21 2 0.07
22 22 0.81
23 3 0.11
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAATTTCCATAATTTAAATTT
Found at i:53279778 original size:20 final size:21
Alignment explanation
Indices: 53279753--53279840 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 21
53279743 GAATATTTAC
*
53279753 AATAATGCATAATAAAA-TAA
1 AATAATACATAATAAAAGTAA
*
53279773 AATAATACATGATAAAAGCATTACAA
1 AATAATACATAATAAAAG---T--AA
53279799 AATAATACATAATAAAA-TAA
1 AATAATACATAATAAAAGTAA
** *
53279819 AATAATGTAAAATAAAAGTAA
1 AATAATACATAATAAAAGTAA
53279840 A
1 A
53279841 TAAATAGATA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 31 0.56
21 4 0.07
22 1 0.02
24 1 0.02
26 18 0.33
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (21 bp):
AATAATACATAATAAAAGTAA
Found at i:53280735 original size:12 final size:12
Alignment explanation
Indices: 53280718--53280742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53280708 TTCAATCACC
53280718 TTTCAATATTTT
1 TTTCAATATTTT
53280730 TTTCAATATTTT
1 TTTCAATATTTT
53280742 T
1 T
53280743 CTTTGTACTG
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCAATATTTT
Found at i:53281400 original size:16 final size:17
Alignment explanation
Indices: 53281374--53281409 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
53281364 GTATATATAC
*
53281374 ATACTTCTATACTTTAT
1 ATACTTCTATAATTTAT
53281391 ATACTT-TATAATTTAT
1 ATACTTCTATAATTTAT
53281407 ATA
1 ATA
53281410 TACGTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (17 bp):
ATACTTCTATAATTTAT
Found at i:53281427 original size:23 final size:23
Alignment explanation
Indices: 53281401--53281473 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
53281391 ATACTTTATA
53281401 ATTTATATATACGTTATACATAT
1 ATTTATATATACGTTATACATAT
*
53281424 ATTTTTATAATA--TATATACATAT
1 ATTTATAT-ATACGT-TATACATAT
* *
53281447 A--TACATATACG-TGTACATAT
1 ATTTATATATACGTTATACATAT
*
53281467 TTTTATA
1 ATTTATA
53281474 ACTTATTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 13
0.67 0.11 0.23
Matches are distributed among these distances:
20 11 0.29
21 3 0.08
22 4 0.11
23 17 0.45
24 3 0.08
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (23 bp):
ATTTATATATACGTTATACATAT
Found at i:53281498 original size:43 final size:43
Alignment explanation
Indices: 53281404--53281549 Score: 107
Period size: 47 Copynumber: 3.2 Consensus size: 43
53281394 CTTTATAATT
53281404 TATATATACGTTATACATATATTTTTATAATATATATACATATA
1 TATATATACGTTATACA-ATATTTTTATAATATATATACATATA
* * *
53281448 TACATATACG-TGTAC-ATATTTTTATAACTTATTTATATATATGTATA
1 TATATATACGTTATACAATATTTTTATAA--TA--TATATACA--TATA
* * * * *
53281495 TATACATACTTATATATTCTATATATTTTATAATTTATATACATATC
1 TATATATACGT-TATA--CAATAT-TTTTATAATATATATACATATA
53281542 TATATATA
1 TATATATA
53281550 TACATCTATA
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
41 12 0.15
43 6 0.08
44 9 0.11
45 7 0.09
47 21 0.27
49 10 0.13
51 2 0.03
52 4 0.05
53 8 0.10
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (43 bp):
TATATATACGTTATACAATATTTTTATAATATATATACATATA
Found at i:53281551 original size:53 final size:50
Alignment explanation
Indices: 53281463--53281561 Score: 126
Period size: 53 Copynumber: 1.9 Consensus size: 50
53281453 ATACGTGTAC
* * *
53281463 ATATTTTTATAACTTATTTATATATATGTATATATACATACTTATATATTCT
1 ATATTTTTATAACTTATATACATATATATATATATACAT-C-TATATATTCT
* *
53281515 ATATATTTTATAATTTATATACATATCTATATATATACATCTATATA
1 ATAT-TTTTATAACTTATATACATATATATATATATACATCTATATA
53281562 CATTTTTTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 6 0.15
52 5 0.12
53 30 0.73
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (50 bp):
ATATTTTTATAACTTATATACATATATATATATATACATCTATATATTCT
Found at i:53281841 original size:18 final size:20
Alignment explanation
Indices: 53281814--53281860 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
53281804 TTCATTTATT
*
53281814 TATTTATTTATATGTC-CA-
1 TATTTTTTTATATGTCTCAG
53281832 TATTTTTTTA-ATGTCTCAG
1 TATTTTTTTATATGTCTCAG
53281851 T-TTTTTTTAT
1 TATTTTTTTAT
53281861 TTACTTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 5 0.20
18 19 0.76
19 1 0.04
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (20 bp):
TATTTTTTTATATGTCTCAG
Found at i:53281954 original size:21 final size:20
Alignment explanation
Indices: 53281923--53281967 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
53281913 TTGCTCATAT
*
53281923 TATTTTTATTCATATTAT-CA
1 TATTTTTATTC-CATTATGCA
53281943 TATTTATTATTCCATTATGCA
1 TATTT-TTATTCCATTATGCA
53281964 TATT
1 TATT
53281968 AACACCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTTTATTCCATTATGCA
Found at i:53282239 original size:107 final size:107
Alignment explanation
Indices: 53281995--53282325 Score: 443
Period size: 107 Copynumber: 3.1 Consensus size: 107
53281985 AAGGAAAATT
*
53281995 TTTCTAAA-TAAGGCAATGTTTTGCGTTTGGAAGTTCGAGAAAACGTGCCCTAATGTGCTGGGTT
1 TTTC-AAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
** * *
53282059 TCGATTTTTTTTGTTCGACCAAATAGCCAAATATCCTTTTAAAA
65 TCGA-TTTTTCCGTCCGACCAAATAGCCAAATATCATTTTAAAA
* * * * *
53282103 TTTTAAAGTAAGGAAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAATGTGCTAGGTTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
53282168 CGATTTTTCCGTCCGACCATATAGCCAAATATCATTTTAAAA
66 CGATTTTTCCGTCCGACCAAATAGCCAAATATCATTTTAAAA
*
53282210 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATATGCTGGGTTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* ** * * * *
53282275 CGATTTCT-CGT-TTAGCCAAATAGCCAAATACCCTCTTAAAG
66 CGATTTTTCCGTCCGA-CCAAATAGCCAAATATCATTTTAAAA
53282316 TTTCAAAGTA
1 TTTCAAAGTA
53282326 TGGGTTTTGG
Statistics
Matches: 196, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
105 1 0.01
106 34 0.17
107 103 0.53
108 58 0.30
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (107 bp):
TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCCGTCCGACCAAATAGCCAAATATCATTTTAAAA
Found at i:53285846 original size:33 final size:33
Alignment explanation
Indices: 53285808--53286064 Score: 210
Period size: 33 Copynumber: 7.8 Consensus size: 33
53285798 GGAGTAGAAA
* * *
53285808 CTGATGGGGTGGGTTATGTTGAAGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * *** *
53285841 TTGATGGGGAGGGTGATGTTGAAGGAAAATGAA-
1 CTGATGGGGAGGGTGATGTAGAAGGGGTA-CAAG
* **
53285874 ATGATGATGAGGGTGATGTAGAAGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * * * * *
53285907 TTGATAGGAAGGGTGATGTTGAAGGAGTAGAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
** ** *
53285940 CTGATATGGAAAGTGATGTAGAAGAGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * * *
53285973 CTGATGAGGTGGGTAATGTAGATGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * *
53286006 CTGTTGGGGAAGGTGATGTAGAAGGGGTACAAA
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* *
53286039 CTGTTGGGGAGGGTGATGTTGAAGGG
1 CTGATGGGGAGGGTGATGTAGAAGGG
53286065 TAGAAGGTGA
Statistics
Matches: 173, Mismatches: 49, Indels: 4
0.77 0.22 0.02
Matches are distributed among these distances:
32 2 0.01
33 169 0.98
34 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.43, T:0.24
Consensus pattern (33 bp):
CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
Found at i:53285928 original size:99 final size:98
Alignment explanation
Indices: 53285818--53286063 Score: 237
Period size: 99 Copynumber: 2.5 Consensus size: 98
53285808 CTGATGGGGT
* * *
53285818 GGGTTATGTTGAAGGGGTACAAGTTGATGGGGAGGGTGATGTTGAAGG-AAAATGAAATGATGAT
1 GGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGGTAAAA-G--ATGATGAG
* *
53285882 GAGGGTGATGTAGAAGGGGTACAAGTTGAT-AGGAA
63 GAGGGTAATGTAGAAGGGGTACAAGCTGATGAGGAA
* * ** ** * * *
53285917 GGGTGATGTTGAAGGAGTAGAAGCTGATATGGAAAGTGATGTAGAAGAGGTACAAGCTGATGAGG
1 GGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTG-A-AGGTAAAAGATGATGAGG
* * * *
53285982 TGGGTAATGTAGATGGGGTACAAGCTGTTGGGGAA
64 AGGGTAATGTAGAAGGGGTACAAGCTGATGAGGAA
* * *
53286017 -GGTGATGTAGAAGGGGTACAAACTGTTGGGGAGGGTGATGTTGAAGG
1 GGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGG
53286064 GTAGAAGGTG
Statistics
Matches: 115, Mismatches: 28, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
97 3 0.03
98 1 0.01
99 99 0.86
100 5 0.04
101 4 0.03
102 3 0.03
ACGTcount: A:0.30, C:0.04, G:0.42, T:0.24
Consensus pattern (98 bp):
GGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGGTAAAAGATGATGAGGAG
GGTAATGTAGAAGGGGTACAAGCTGATGAGGAA
Found at i:53285956 original size:66 final size:66
Alignment explanation
Indices: 53285787--53286070 Score: 234
Period size: 66 Copynumber: 4.3 Consensus size: 66
53285777 GCTGGGAAGA
** * ** ** * * * *
53285787 GTGATGTTGGTGGAGTAGAAACTGATGGGGTGGGTTATGTTGAAGGGGTACAAGTTGATGGGGAG
1 GTGATGTTGAAGGAGTAGAAGCTGATATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAGGGAG
53285852 G
66 G
** * * * *
53285853 GTGATGTTGAAGGAAAATGAA-ATGATGAT-GAGGGTGATGTAGAAGGGGTACAAGTTGATAGGA
1 GTGATGTTGAAGGAGTA-GAAGCTGAT-ATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAGGG
53285916 AGG
64 AGG
* * *
53285919 GTGATGTTGAAGGAGTAGAAGCTGATATGGAAAGTGATGTAGAAGAGGTACAAGCTGAT-GAGGT
1 GTGATGTTGAAGGAGTAGAAGCTGATATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAG-GGA
53285983 GG
65 GG
* * * * * * ** * * *
53285985 GTAATGTAGATGGGGTACAAGCTGTTGGGGAAGGTGATGTAGAAGGGGTACAAACTGTTGGGGAG
1 GTGATGTTGAAGGAGTAGAAGCTGATATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAGGGAG
53286050 G
66 G
53286051 GTGATGTTGAAGG-GTAGAAG
1 GTGATGTTGAAGGAGTAGAAG
53286071 GTGACGAGGA
Statistics
Matches: 174, Mismatches: 38, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
65 12 0.07
66 158 0.91
67 4 0.02
ACGTcount: A:0.30, C:0.04, G:0.43, T:0.24
Consensus pattern (66 bp):
GTGATGTTGAAGGAGTAGAAGCTGATATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAGGGAG
G
Found at i:53291030 original size:22 final size:22
Alignment explanation
Indices: 53291000--53291042 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
53290990 ACAGCAGAAC
* *
53291000 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
53291022 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
53291043 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:53291188 original size:43 final size:42
Alignment explanation
Indices: 53291132--53291469 Score: 378
Period size: 42 Copynumber: 8.0 Consensus size: 42
53291122 GCGCTTACAT
53291132 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* *
53291174 AAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTAT
1 -AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
** * * *
53291217 AAAAATGCGTCGCTAAAGATCATGTTCTTTAGTGGCGCTTAC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * ** *
53291259 AAATAAACGCCGCTAAAGAACATAATCTTTAGCAGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* *
53291301 AAATAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTAGG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-G
* *
53291344 AAAAAAACGCCGCTAAAGTTCATGTTCTTTAGCGGCGCTTTTG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAG
** * * *
53291387 AGGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTT-G
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAG
**
53291428 TTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 -AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
53291470 TTTCACAAAT
Statistics
Matches: 251, Mismatches: 38, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.01
42 139 0.55
43 108 0.43
44 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:53291435 original size:85 final size:84
Alignment explanation
Indices: 53291134--53291468 Score: 360
Period size: 85 Copynumber: 4.0 Consensus size: 84
53291124 GCTTACATAA
*
53291134 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGTAAAAAAACGCCGCTAAAGATCATG
* *
53291199 TTCTTTAGCGGCGGTTAT-
66 TTCTTTAGCGGCGCTTTTG
* * * * *
53291217 AAAAATGCGTCGCTAAAGATCATGTTCTTTAGTGGCGCTTA-CAAATAAACGCCGCTAAAGAACA
1 AAAAA--CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGTAAAAAAACGCCGCTAAAGATCA
** * *
53291281 TAATCTTTAGCAGCGC-TTAG
64 TGTTCTTTAGCGGCGCTTTTG
* * *
53291301 AAATAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAGTTCA
1 -AA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGTAAAAAAACGCCGCTAAAGATCA
53291366 TGTTCTTTAGCGGCGCTTTTG
64 TGTTCTTTAGCGGCGCTTTTG
* * * **
53291387 AGGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTT-GTTCAAAAACGCCGCTAAA-AGT
1 A--AAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAGTAAAAAAACGCCGCTAAAGA-T
53291449 -AGTGTTCTTTAGCGGCGCTT
62 CA-TGTTCTTTAGCGGCGCTT
53291469 ATTTCACAAA
Statistics
Matches: 211, Mismatches: 29, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
83 6 0.03
84 64 0.30
85 103 0.49
86 37 0.18
87 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (84 bp):
AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGTAAAAAAACGCCGCTAAAGATCATG
TTCTTTAGCGGCGCTTTTG
Found at i:53291489 original size:18 final size:18
Alignment explanation
Indices: 53291466--53291503 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
53291456 TTTAGCGGCG
53291466 CTTATTTCACAAATGCCA
1 CTTATTTCACAAATGCCA
53291484 CTTATTTCACAAATGCCA
1 CTTATTTCACAAATGCCA
53291502 CT
1 CT
53291504 GTTTTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (18 bp):
CTTATTTCACAAATGCCA
Found at i:53342204 original size:7 final size:7
Alignment explanation
Indices: 53342192--53342231 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
53342182 CAACTAATCG
53342192 TATTAAT
1 TATTAAT
53342199 TATT-A-
1 TATTAAT
53342204 -ATTAAT
1 TATTAAT
53342210 TATTAAT
1 TATTAAT
53342217 TATTAAT
1 TATTAAT
*
53342224 TAATAAT
1 TATTAAT
53342231 T
1 T
53342232 CTGGCACGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
4 3 0.10
5 1 0.03
6 1 0.03
7 24 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
TATTAAT
Found at i:53342209 original size:11 final size:11
Alignment explanation
Indices: 53342193--53342231 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
53342183 AACTAATCGT
53342193 ATTAATTATTA
1 ATTAATTATTA
53342204 ATTAATTATTA
1 ATTAATTATTA
53342215 ATT-ATTAATTA
1 ATTAATT-ATTA
53342226 A-TAATT
1 ATTAATT
53342232 CTGGCACGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 22 0.85
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATTAATTATTA
Found at i:53342215 original size:18 final size:18
Alignment explanation
Indices: 53342192--53342227 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53342182 CAACTAATCG
53342192 TATTAATTATTAATTAAT
1 TATTAATTATTAATTAAT
53342210 TATTAATTATTAATTAAT
1 TATTAATTATTAATTAAT
53342228 AATTCTGGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTAATTATTAATTAAT
Found at i:53342271 original size:16 final size:16
Alignment explanation
Indices: 53342251--53342303 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
53342241 TTGGTTCGCT
*
53342251 GTAATGGAATAGAGGT
1 GTAATGGAATAGAGGC
*
53342267 GTAATGAAATAGAGGC
1 GTAATGGAATAGAGGC
*
53342283 GTAATGGAATACAGGC
1 GTAATGGAATAGAGGC
53342299 GTAAT
1 GTAAT
53342304 AGGTAATCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.40, C:0.06, G:0.32, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:53351387 original size:15 final size:16
Alignment explanation
Indices: 53351357--53351389 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53351347 GAATCAAGGG
53351357 ATTTTATTTGATTTTT
1 ATTTTATTTGATTTTT
*
53351373 ATTTT-TTTTATTTTT
1 ATTTTATTTGATTTTT
53351388 AT
1 AT
53351390 CGTTATTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
ATTTTATTTGATTTTT
Found at i:53352174 original size:26 final size:25
Alignment explanation
Indices: 53352145--53352223 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 25
53352135 GTTCATTCAC
53352145 ATGCATTTTTCTTATATAATATATAT
1 ATGCATTTTT-TTATATAATATATAT
* *
53352171 ATGCATTTCTTTTATATAGTAT-TCAC
1 ATGCATTT-TTTTATATAATATAT-AT
53352197 AT--ATTGTTTTTTATATAATATATAT
1 ATGCA-T-TTTTTTATATAATATATAT
53352222 AT
1 AT
53352224 ATATATATGC
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
24 1 0.02
25 17 0.39
26 24 0.55
27 2 0.05
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (25 bp):
ATGCATTTTTTTATATAATATATAT
Found at i:53352549 original size:15 final size:16
Alignment explanation
Indices: 53352526--53352571 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
53352516 TTCCTTTATT
* *
53352526 TTATCTTTT-TATCCC
1 TTATATTTTATATACC
53352541 TTATATTTTTATATACC
1 TTATA-TTTTATATACC
53352558 TTATATTTTATATA
1 TTATATTTTATATA
53352572 TACGTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 4 0.15
16 13 0.48
17 10 0.37
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATATTTTATATACC
Found at i:53352561 original size:17 final size:18
Alignment explanation
Indices: 53352539--53352574 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
53352529 TCTTTTTATC
53352539 CCTTATATTTT-TATATA
1 CCTTATATTTTATATATA
53352556 CCTTATATTTTATATATA
1 CCTTATATTTTATATATA
53352574 C
1 C
53352575 GTATTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (18 bp):
CCTTATATTTTATATATA
Found at i:53354542 original size:15 final size:15
Alignment explanation
Indices: 53354522--53354571 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
53354512 TGTAGTTGAA
53354522 GATGACGACGACAAC
1 GATGACGACGACAAC
* *
53354537 GATGACGACGACGAT
1 GATGACGACGACAAC
* *
53354552 GATGACGATGACAAG
1 GATGACGACGACAAC
53354567 GATGA
1 GATGA
53354572 AGATGATGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.32, T:0.12
Consensus pattern (15 bp):
GATGACGACGACAAC
Found at i:53358018 original size:25 final size:27
Alignment explanation
Indices: 53357985--53358038 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
53357975 AGTTTTATTA
*
53357985 ATAGTTATATAATATAATATTATA-GT
1 ATAGTTATATAATATAATACTATATGT
*
53358011 ATAG-TATATAATGTAATACTATATGT
1 ATAGTTATATAATATAATACTATATGT
53358037 AT
1 AT
53358039 TAATAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 17 0.68
26 8 0.32
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (27 bp):
ATAGTTATATAATATAATACTATATGT
Found at i:53358033 original size:20 final size:21
Alignment explanation
Indices: 53357996--53358043 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
53357986 TAGTTATATA
* *
53357996 ATATAATATTATAGTATA-GT
1 ATATAATATAATACTATATGT
*
53358016 ATATAATGTAATACTATATGT
1 ATATAATATAATACTATATGT
53358037 AT-TAATA
1 ATATAATA
53358044 GTTATGTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (21 bp):
ATATAATATAATACTATATGT
Found at i:53359292 original size:29 final size:29
Alignment explanation
Indices: 53359251--53359309 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
53359241 GAATGTAAAC
*
53359251 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAAAACACTACA
53359280 TATATTTTTTATTTTTAAAAAACACTACA
1 TATATTTTTTATTTTTAAAAAACACTACA
53359309 T
1 T
53359310 TTAAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAAAACACTACA
Done.