Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
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: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 21 of 47
Found at i:3142317 original size:69 final size:70
Alignment explanation
Indices: 3142171--3142325 Score: 195
Period size: 69 Copynumber: 2.2 Consensus size: 70
3142161 TTCCTCCGAA
** **
3142171 GGGATACTCCAACCATGTTTTTTAAACTAATTGAAATTTAAATCTTATTTTGTCCAAATTATCAT
1 GGGATACTCCAACCCCGTTTTTTAAACTAATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
*
3142236 AGTTG
66 AGTCG
*** * * *
3142241 AAAATACTCCAACCCCG-TTTTTAAACTCATCAAAATTTAAGTCTTATTTTGTCGAAATTATCAT
1 GGGATACTCCAACCCCGTTTTTTAAACTAATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
*
3142305 TGTCG
66 AGTCG
3142310 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
3142326 ATTCCTCTAA
Statistics
Matches: 70, Mismatches: 15, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
69 58 0.83
70 12 0.17
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (70 bp):
GGGATACTCCAACCCCGTTTTTTAAACTAATCAAAATTTAAATCTTATTTTGTCCAAATTATCAT
AGTCG
Found at i:3142347 original size:27 final size:27
Alignment explanation
Indices: 3142309--3142382 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
3142299 TATCATTGTC
*
3142309 GGGGATACTCCAACCCCATTCCTCTAA
1 GGGGATATTCCAACCCCATTCCTCTAA
* *
3142336 GGGGATATTCCAATCCCATTCCTCTGA
1 GGGGATATTCCAACCCCATTCCTCTAA
* *
3142363 GGGTATATTCCAACCTCATT
1 GGGGATATTCCAACCCCATT
3142383 TTTCAATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.28
Consensus pattern (27 bp):
GGGGATATTCCAACCCCATTCCTCTAA
Found at i:3143770 original size:21 final size:22
Alignment explanation
Indices: 3143746--3143791 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
3143736 TGTATTTATG
3143746 TATGACAACTTACATATAT-TA
1 TATGACAACTTACATATATGTA
**
3143767 TATGACAACTTTGATATATGTA
1 TATGACAACTTACATATATGTA
3143789 TAT
1 TAT
3143792 ATATTTCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGACAACTTACATATATGTA
Found at i:3144086 original size:21 final size:21
Alignment explanation
Indices: 3144053--3144099 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
3144043 TAATAACGAG
**
3144053 TTTTTTTAGAAAAAGTGGATAAA
1 TTTTTTT--AAAAAGTAAATAAA
3144076 TTTTTTT-AAAAGTAAATAAA
1 TTTTTTTAAAAAGTAAATAAA
3144096 TTTT
1 TTTT
3144100 ATAAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 15 0.68
23 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (21 bp):
TTTTTTTAAAAAGTAAATAAA
Found at i:3144997 original size:25 final size:25
Alignment explanation
Indices: 3144969--3145179 Score: 97
Period size: 27 Copynumber: 8.5 Consensus size: 25
3144959 TTAGATTCGA
*
3144969 TAATAATTTATATATT-TATTTATAT
1 TAAT-ATTTATATATTATAATTATAT
* *
3144994 TAATTTTTTTATATTATAATTATAT
1 TAATATTTATATATTATAATTATAT
*
3145019 T-AT-TTTA-ATATTATAATTTTATT
1 TAATATTTATATATTATAATTATA-T
* * *
3145042 TAATATATTATATATTTTAA--AAAA
1 TAATAT-TTATATATTATAATTATAT
* *
3145066 TAATA-ATA-ATAATATATATTATA-
1 TAATATTTATATATTATA-ATTATAT
* *
3145089 TAAAATTTAATAAATTTATAATTTATAT
1 TAATATTT-ATATA-TTATAA-TTATAT
3145117 T-ATATTTAT-T-TTAT-ATTATATTT
1 TAATATTTATATATTATAATTATA--T
* * * *
3145140 TAATTATTTTTATATTATATTTAAAA
1 TAA-TATTTATATATTATAATTATAT
3145166 TAATAATTTATATA
1 TAAT-ATTTATATA
3145180 ATTTTTAATA
Statistics
Matches: 139, Mismatches: 24, Indels: 45
0.67 0.12 0.22
Matches are distributed among these distances:
21 11 0.08
22 17 0.12
23 15 0.11
24 22 0.16
25 23 0.17
26 20 0.14
27 26 0.19
28 5 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAATATTTATATATTATAATTATAT
Found at i:3145004 original size:14 final size:14
Alignment explanation
Indices: 3144974--3145032 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
3144964 TTCGATAATA
3144974 ATTTATA-T-ATTT
1 ATTTATATTAATTT
3144986 ATTTATATTAATTT
1 ATTTATATTAATTT
* *
3145000 TTTTATATTATAATT
1 ATTTATATTA-ATTT
*
3145015 ATATTATTTTAATATT
1 AT-TTATATTAAT-TT
3145031 AT
1 AT
3145033 AATTTTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
12 7 0.19
13 1 0.03
14 13 0.35
15 5 0.14
16 11 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTATATTAATTT
Found at i:3145020 original size:5 final size:5
Alignment explanation
Indices: 3144976--3145160 Score: 57
Period size: 5 Copynumber: 37.4 Consensus size: 5
3144966 CGATAATAAT
* * *
3144976 TTATA -TAT- TTAT- TTATA TTA-A TTTTT TTATA TTATAA TTATA TTATT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA
* * * * ** *
3145023 TTAATA TTATAA TTTTA TT-TA ATATA TTATA -TATT TTAAA AAATA ATA-A
1 TT-ATA TTAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * * * * *
3145072 TAATAA TATATA TTATA TAAAA TT-TA ATAAA TT-TA TAAT- TTATA TTATA
1 TTAT-A T-TATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* * *
3145121 TTTATT TTATA TTATA TTTTAA TTATTT TTATA TTATA TT
1 -TTATA TTATA TTATA TTAT-A TTA-TA TTATA TTATA TT
3145161 TAAAATAATA
Statistics
Matches: 128, Mismatches: 35, Indels: 34
0.65 0.18 0.17
Matches are distributed among these distances:
4 28 0.22
5 70 0.55
6 27 0.21
7 3 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:3145021 original size:16 final size:16
Alignment explanation
Indices: 3145002--3145158 Score: 62
Period size: 16 Copynumber: 9.9 Consensus size: 16
3144992 ATTAATTTTT
3145002 TTATATTATAATTAT-A
1 TTATATTAT-ATTATAA
*
3145018 TTATTTTAATATTATAA
1 TTATATT-ATATTATAA
* *
3145035 TTTTATT-TAATAT-A
1 TTATATTATATTATAA
*
3145049 TTATA-TATTTTA-AA
1 TTATATTATATTATAA
** * *
3145063 AAATAATA-ATAATAA
1 TTATATTATATTATAA
*
3145078 TATATATTATA-TAAAA
1 T-TATATTATATTATAA
* *
3145094 TT-TAATAAATTTATAA
1 TTATATTATA-TTATAA
*
3145110 TTTATATTATATT-TATT
1 -TTATATTATATTATA-A
*
3145127 TTATATTATATTTTAA
1 TTATATTATATTATAA
*
3145143 TTATTTTTATATTATA
1 TTA-TATTATATTATA
3145159 TTTAAAATAA
Statistics
Matches: 101, Mismatches: 25, Indels: 29
0.65 0.16 0.19
Matches are distributed among these distances:
13 1 0.01
14 19 0.19
15 10 0.10
16 41 0.41
17 25 0.25
18 5 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTATATTATAA
Found at i:3145029 original size:22 final size:21
Alignment explanation
Indices: 3144988--3145042 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
3144978 ATATATTTAT
*
3144988 TTAT-ATTA-ATTTTTTTATA
1 TTATAATTATATTTTTTAATA
3145007 TTATAATTATATTATTTTAATA
1 TTATAATTATATT-TTTTAATA
*
3145029 TTATAATTTTATTT
1 TTATAATTATATTT
3145043 AATATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.13
20 4 0.13
21 4 0.13
22 19 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATAATTATATTTTTTAATA
Found at i:3145084 original size:28 final size:27
Alignment explanation
Indices: 3145042--3145094 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
3145032 TAATTTTATT
* *
3145042 TAATATATTATATATTTTAAAAAATAA
1 TAATATAATATATATTATAAAAAATAA
*
3145069 TAATAATAATATATATTATATAAAAT
1 TAAT-ATAATATATATTATAAAAAAT
3145095 TTAATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TAATATAATATATATTATAAAAAATAA
Found at i:3145093 original size:30 final size:29
Alignment explanation
Indices: 3145042--3145121 Score: 74
Period size: 32 Copynumber: 2.7 Consensus size: 29
3145032 TAATTTTATT
*
3145042 TAATATATTATATATT-T-TAAAAAATAA
1 TAATATAATATATATTATATAAAAAATAA
**
3145069 TAATAATAATATATATTATATAAAATTTAA
1 TAAT-ATAATATATATTATATAAAAAATAA
*
3145099 TAAATTTATAATTTATATTATAT
1 T-AA--TATAATATATATTATAT
3145122 TTATTTTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 4 0.09
28 11 0.26
29 1 0.02
30 9 0.21
31 2 0.05
32 15 0.35
33 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
TAATATAATATATATTATATAAAAAATAA
Found at i:3145153 original size:22 final size:22
Alignment explanation
Indices: 3145111--3145196 Score: 79
Period size: 22 Copynumber: 4.0 Consensus size: 22
3145101 AATTTATAAT
* *
3145111 TTATATTATATTTA-TTTTATA
1 TTATATTTTAATTATTTTTATA
3145132 TTATATTTTAATTATTTTTATA
1 TTATATTTTAATTATTTTTATA
* * *
3145154 TTATATTTAAAATAATAATTTATA
1 TTATATTT-TAATTAT-TTTTATA
*
3145178 TAAT-TTTTAA-TATTTTTAT
1 TTATATTTTAATTATTTTTAT
3145197 TAATTAATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.09
21 14 0.26
22 17 0.32
23 8 0.15
24 9 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATATTTTAATTATTTTTATA
Found at i:3145211 original size:45 final size:46
Alignment explanation
Indices: 3145126--3145231 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 46
3145116 TTATATTTAT
* **
3145126 TTTATATTATATTTTAATTATTTTTATATTATATTTAAAATAATAA
1 TTTATATAATATTTTAATTATTTTTATATTATATAAAAAATAATAA
*
3145172 TTTATATAAT-TTTTAA-TATTTTTATTAATTA-ATAAAAAATAATTA
1 TTTATATAATATTTTAATTATTTTTA-T-ATTATATAAAAAATAATAA
* *
3145217 TTAAT-TAATAATTTA
1 TTTATATAATATTTTA
3145232 TATAATAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 12 0.24
45 26 0.51
46 13 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (46 bp):
TTTATATAATATTTTAATTATTTTTATATTATATAAAAAATAATAA
Found at i:3145242 original size:19 final size:19
Alignment explanation
Indices: 3145166--3145251 Score: 61
Period size: 19 Copynumber: 4.6 Consensus size: 19
3145156 ATATTTAAAA
**
3145166 TAATAATTTATATAATTTT
1 TAATAATTTATATAATAAT
*
3145185 TAAT-ATTT-T-TATTAAT
1 TAATAATTTATATAATAAT
*** *
3145201 TAATAAAAAATAATTATTAAT
1 TAATAATTTAT-A-TAATAAT
3145222 TAATAATTTATATAATAAT
1 TAATAATTTATATAATAAT
*
3145241 TAATTATTTAT
1 TAATAATTTAT
3145252 TAACTAACGA
Statistics
Matches: 51, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
16 8 0.16
17 2 0.04
18 5 0.10
19 20 0.39
20 1 0.02
21 15 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAATTTATATAATAAT
Found at i:3146490 original size:3 final size:3
Alignment explanation
Indices: 3146484--3146512 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3146474 GTTTTTTTCT
3146484 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3146513 TTTTTTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3147064 original size:27 final size:27
Alignment explanation
Indices: 3147012--3147064 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
3147002 AAAAAATATA
*
3147012 ATAATTTTTATTTAATTTTTTGATTTC
1 ATAATTTTTATTTAATTTTTTCATTTC
3147039 ATAA-TTTTATTTAATTTTATTCATTT
1 ATAATTTTTATTTAATTTT-TTCATTT
3147065 TTATAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (27 bp):
ATAATTTTTATTTAATTTTTTCATTTC
Found at i:3147498 original size:3 final size:3
Alignment explanation
Indices: 3147492--3147527 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
3147482 AATAATAATA
*
3147492 ATT ATT ATT ATT ATT ATA ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3147528 ATAATAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:3147529 original size:18 final size:18
Alignment explanation
Indices: 3147489--3147523 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3147479 AATAATAATA
3147489 ATAATTATTATTATTATT
1 ATAATTATTATTATTATT
3147507 ATAATTATTATTATTAT
1 ATAATTATTATTATTAT
3147524 ATTAATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATAATTATTATTATTATT
Found at i:3147892 original size:36 final size:36
Alignment explanation
Indices: 3147839--3147926 Score: 108
Period size: 36 Copynumber: 2.5 Consensus size: 36
3147829 ATATTTGAGA
*
3147839 TTAAAA-AAATTTTATTATGTTATATT-AACATAGTT
1 TTAAAATAATTTTTATTATGTTATATTCAA-ATAGTT
* * *
3147874 TTAATATAATTTTTATTATGTTTTATTCAAATATTT
1 TTAAAATAATTTTTATTATGTTATATTCAAATAGTT
*
3147910 TTAAAATACTTTTTATT
1 TTAAAATAATTTTTATT
3147927 TAAAATTGTA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 5 0.11
36 38 0.84
37 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (36 bp):
TTAAAATAATTTTTATTATGTTATATTCAAATAGTT
Found at i:3150091 original size:63 final size:63
Alignment explanation
Indices: 3149983--3150113 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
3149973 ATATGTTGTT
3149983 TTTCCAAGACCTGCATGTTATTTGGTTTTAGCTAAACAATGCTTCTTGTCTGTGTGTTTAACA
1 TTTCCAAGACCTGCATGTTATTTGGTTTTAGCTAAACAATGCTTCTTGTCTGTGTGTTTAACA
* *
3150046 TTTCGAAGACCTGCATGTTATTTGGTTTTAGCTAAACAATTCTTCTTGTCTGTGTGTTTAACA
1 TTTCCAAGACCTGCATGTTATTTGGTTTTAGCTAAACAATGCTTCTTGTCTGTGTGTTTAACA
3150109 TTTCC
1 TTTCC
3150114 TGGTGATTCT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.44
Consensus pattern (63 bp):
TTTCCAAGACCTGCATGTTATTTGGTTTTAGCTAAACAATGCTTCTTGTCTGTGTGTTTAACA
Found at i:3152181 original size:7 final size:7
Alignment explanation
Indices: 3152166--3152215 Score: 91
Period size: 7 Copynumber: 7.1 Consensus size: 7
3152156 TTTAGAACAG
3152166 CATCAGC
1 CATCAGC
*
3152173 CATCGGC
1 CATCAGC
3152180 CATCAGC
1 CATCAGC
3152187 CATCAGC
1 CATCAGC
3152194 CATCAGC
1 CATCAGC
3152201 CATCAGC
1 CATCAGC
3152208 CATCAGC
1 CATCAGC
3152215 C
1 C
3152216 TTAGGGAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.26, C:0.44, G:0.16, T:0.14
Consensus pattern (7 bp):
CATCAGC
Found at i:3160151 original size:2 final size:2
Alignment explanation
Indices: 3160144--3160179 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3160134 TGTAGACAAC
3160144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3160180 CCTGTTTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3161671 original size:21 final size:21
Alignment explanation
Indices: 3161646--3161694 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3161636 AAAACAATAA
*
3161646 TAGTGATGAGATTAATTATTG
1 TAGTGATGAGATTAAGTATTG
* *
3161667 TAGTGGTGGGATTAAGTATTG
1 TAGTGATGAGATTAAGTATTG
*
3161688 TAATGAT
1 TAGTGAT
3161695 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.41
Consensus pattern (21 bp):
TAGTGATGAGATTAAGTATTG
Found at i:3161851 original size:14 final size:15
Alignment explanation
Indices: 3161802--3161851 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
3161792 ATGTGCATAT
*
3161802 ATATATATATAATAA
1 ATATATAAATAATAA
*
3161817 ATAATTTAAATAATAA
1 AT-ATATAAATAATAA
3161833 A-ATATAAATAA-AA
1 ATATATAAATAATAA
3161846 ATATAT
1 ATATAT
3161852 TTATGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 3 0.10
14 13 0.43
15 2 0.07
16 12 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATATAAATAATAA
Found at i:3161885 original size:21 final size:24
Alignment explanation
Indices: 3161861--3161913 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 24
3161851 TTTATGTTAA
3161861 ATAAAAATTAA-AAATT-TT-ATT
1 ATAAAAATTAATAAATTATTAATT
3161882 ATAAAAA--AATAAATTATTAATT
1 ATAAAAATTAATAAATTATTAATT
*
3161904 ATTAAAATTA
1 ATAAAAATTA
3161914 TATTGACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 2 0.08
20 5 0.19
21 9 0.35
22 9 0.35
24 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAAAAATTAATAAATTATTAATT
Found at i:3161994 original size:65 final size:61
Alignment explanation
Indices: 3161822--3162040 Score: 165
Period size: 65 Copynumber: 3.5 Consensus size: 61
3161812 AATAAATAAT
* * *
3161822 TTAAATAATAAAATATAAA-TAAAAATATATTTATGTTAAATAAAAATTAAAAATTTTATTA
1 TTAAATAATAAAATATAAATTAAAATTATATTTATATTAAA-AAAAATTAAAAATTATATTA
* * * * * *** *
3161883 TAAAAAAATAAATTATTAATTATTAAAATTATATTGACAACCAAAAAAATTACTAAATTATACTT
1 TTAAATAATAAAATA-TAA--ATTAAAATTATATTTATATTAAAAAAAATTA-AAAATTATA-TT
3161948 ACA
61 --A
* *
3161951 TTAAATAATAAAATATAAATTAAAATTATGTTTATATTAAAAAATTATT-AAAATTATATTA
1 TTAAATAATAAAATATAAATTAAAATTATATTTATATTAAAAAA-AATTAAAAATTATATTA
* * *
3162012 TATAAA-AATCAATTATTAAAATAAAATTA
1 T-TAAATAATAAAATA-TAAATTAAAATTA
3162041 AAAATAATAA
Statistics
Matches: 121, Mismatches: 26, Indels: 21
0.72 0.15 0.12
Matches are distributed among these distances:
61 21 0.17
62 19 0.16
63 2 0.02
64 17 0.14
65 41 0.34
66 5 0.04
67 3 0.02
68 13 0.11
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (61 bp):
TTAAATAATAAAATATAAATTAAAATTATATTTATATTAAAAAAAATTAAAAATTATATTA
Found at i:3162003 original size:28 final size:28
Alignment explanation
Indices: 3161969--3162033 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
3161959 TAAAATATAA
* *
3161969 ATTAAAATTATGTTTATATTAAAA-AATT
1 ATTAAAATTAT-ATTATATAAAAACAATT
3161997 ATTAAAATTATATTATATAAAAATCAATT
1 ATTAAAATTATATTATATAAAAA-CAATT
3162026 ATTAAAAT
1 ATTAAAAT
3162034 AAAATTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 10 0.30
28 11 0.33
29 12 0.36
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (28 bp):
ATTAAAATTATATTATATAAAAACAATT
Found at i:3163192 original size:25 final size:26
Alignment explanation
Indices: 3163135--3163195 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
3163125 TTAAATATTA
**
3163135 ATGTGAATTTTGATTAATATATATTTT
1 ATGT-AATTTTGATTAATATATATGAT
*
3163162 AT-TAATTTTGATTACT-TATATGAT
1 ATGTAATTTTGATTAATATATATGAT
3163186 ATGTAATTTT
1 ATGTAATTTT
3163196 ATGTTCAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 8 0.27
25 19 0.63
26 1 0.03
27 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (26 bp):
ATGTAATTTTGATTAATATATATGAT
Found at i:3163256 original size:2 final size:2
Alignment explanation
Indices: 3163251--3163293 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3163241 ATATATATAT
3163251 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3163293 A
1 A
3163294 TATGCAACCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3163931 original size:17 final size:18
Alignment explanation
Indices: 3163895--3163932 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3163885 AGAATGTTTG
*
3163895 TTTTCTGTTTATTTTCCT
1 TTTTCTGTTTAATTTCCT
3163913 TTTTCTGTTTAATTT-CT
1 TTTTCTGTTTAATTTCCT
3163930 TTT
1 TTT
3163933 AGCTTTGCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.08, C:0.13, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTCTGTTTAATTTCCT
Found at i:3171874 original size:20 final size:21
Alignment explanation
Indices: 3171846--3171885 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3171836 TCGGATTCGA
3171846 TATACATG-TAAAGTTTTAAT
1 TATACATGATAAAGTTTTAAT
*
3171866 TATATATGTATAAAGTTTTA
1 TATACATG-ATAAAGTTTTA
3171886 TCATGACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (21 bp):
TATACATGATAAAGTTTTAAT
Found at i:3172813 original size:2 final size:2
Alignment explanation
Indices: 3172806--3172839 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3172796 GGAAAACAAA
3172806 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3172840 TAAAATAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3173336 original size:20 final size:20
Alignment explanation
Indices: 3173303--3173342 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3173293 TTCATAAATT
** *
3173303 TATTTATTTTTATATTTTTA
1 TATTTATTCATATAATTTTA
3173323 TATTTATTCATATAATTTTA
1 TATTTATTCATATAATTTTA
3173343 CATAAATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TATTTATTCATATAATTTTA
Found at i:3176878 original size:22 final size:23
Alignment explanation
Indices: 3176847--3176891 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
3176837 TTCTTAGCTA
3176847 AAAAATAGAAAAGAAAAAGAAAG
1 AAAAATAGAAAAGAAAAAGAAAG
*
3176870 AAAAA-AGAAAAGAAAAATAAAG
1 AAAAATAGAAAAGAAAAAGAAAG
3176892 CTATTTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (23 bp):
AAAAATAGAAAAGAAAAAGAAAG
Found at i:3180725 original size:146 final size:145
Alignment explanation
Indices: 3180431--3180704 Score: 347
Period size: 146 Copynumber: 1.9 Consensus size: 145
3180421 CTACGCCTAA
* * **
3180431 TATGTATCCTCAGCATAGAAGCGACTCGGTGACAAATTAGGACTTGATTTTAGAAAAATCATGAA
1 TATGTACCCTCAGCATAGAAACGACTCGGTGACAAATTAGGACTTGATTTTAGAAAAATCACAAA
* * * * *
3180496 AATGCCCCTATGAGTATACCTTCGACATGAAAGTATCTCAGTAACCTTAAAAGACTTAAACAGGA
66 AAAGCCCCTATGAGGATACCTTCGACATGAAAGTATCCCAATAACCTTAAAAGACTTAAAAAGGA
*
3180561 AAAATGAACCTACGCC
131 AAAATGAA-CTACACC
* * *
3180577 TATGTACCCTCGGCATAGAAACGACTCGGTGACAAATTAGGACTTGGTTTTAGAAAAATTACAAA
1 TATGTACCCTCAGCATAGAAACGACTCGGTGACAAATTAGGACTTGATTTTAGAAAAATCACAAA
* * * * *
3180642 AAAGCCCTTAT-AGGATACCTTTGAC-TTATAAGT-TCCCAATACCCTTAAAGGACTTAAAAAGG
66 AAAGCCCCTATGAGGATACCTTCGACATGA-AAGTATCCCAATAACCTTAAAAGACTTAAAAAGG
3180704 A
130 A
3180705 TTATAGATGG
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
144 27 0.25
145 16 0.15
146 67 0.61
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (145 bp):
TATGTACCCTCAGCATAGAAACGACTCGGTGACAAATTAGGACTTGATTTTAGAAAAATCACAAA
AAAGCCCCTATGAGGATACCTTCGACATGAAAGTATCCCAATAACCTTAAAAGACTTAAAAAGGA
AAAATGAACTACACC
Found at i:3182911 original size:163 final size:161
Alignment explanation
Indices: 3182722--3183338 Score: 512
Period size: 163 Copynumber: 3.6 Consensus size: 161
3182712 GAATTTTAAG
* * *
3182722 AAAAAAATGAAGAATTCATAAAAATAAATGAATTTTTAAAAACTAATTTAATATGAATTAGATGA
1 AAAAAAATGAAAAATTCATGAAAATAAATGAATTTTTAAAAACTAATTTAATATGAATTAAATGA
* *
3182787 TGATATTTGATAAATTTTAAAAATTATAAACCAAGAAAAATCCTCTCGAAAACGTTTACGGAGTA
66 TGATATTTGATAAATTTTAAAAATTA-AAACTAAGAAAAATCC-CTCGAAAACATTTACGGAGTA
3182852 GAAAACTCTTTATTTT-GAAAATAAAAAAATTTC
129 GAAAACTCTTTATTTTAGAAAA-AAAAAAATTTC
* * *
3182885 AAAAAAATGAAAAATTCATGAAAATAAATGAATTTTTAAAAACTGATTTAACATGAGTTAAATGA
1 AAAAAAATGAAAAATTCATGAAAATAAATGAATTTTTAAAAACTAATTTAATATGAATTAAATGA
* * * * **
3182950 TGATATTTGATAAATTTTAAAAATTAAAAATAAAAAACAATCCCCCCAAAAACATTTATAGAGTA
66 TGATATTTGATAAATTTTAAAAATTAAAACTAAGAAA-AAT-CCCTCGAAAACATTTACGGAGTA
*
3183015 GAAAACATTTATAAAGTAGAAAACTCCGTGTTTCA-AAAACAAGAAAAATTTC
129 GAAAAC-TCT-T----T-----A-----T-TTT-AGAAAA-AA-AAAAATTTC
**
3183067 AAGGAAAAATGAAAAATTCATGAAAATAAATGAATTTCTTAAAAA-TAATTTAATATG-ATCTAA
1 AAAAAAA--TGAAAAATTCATGAAAATAAATGAATTT-TTAAAAACTAATTTAATATGAAT-TAA
* *
3183130 ATGATAATATTTGATAAATTTTAAAAATTAAAAACTAAGAAAAATCCCTTCGAAAATATTTACGG
62 ATGATGATATTTGATAAATTTTAAAAATT-AAAACTAAGAAAAATCCC-TCGAAAACATTTACGG
** * * *
3183195 AGTAGAAAACTCCGTATTTTAGAAACAAGAAGAATTTTA
125 AGTAGAAAACTCTTTATTTTAGAAA-AA-AAAAAATTTC
* * * * * * * * *
3183234 AAGAAAAATAAAAAATTAATG-AAATAAAAGGAATTTTTCAAAATTGATTTCAT-GGTAATTAAG
1 AA-AAAAATGAAAAATTCATGAAAAT-AAATGAATTTTTAAAAACTAATTTAATATG-AATTAAA
* *
3183297 CGATGATATTT-AAAGAATTTT-AAAATTAAAAACTAGAGAAAA
63 TGATGATATTTGATA-AATTTTAAAAATT-AAAACTA-AGAAAA
3183339 TTACACCAAA
Statistics
Matches: 368, Mismatches: 48, Indels: 73
0.75 0.10 0.15
Matches are distributed among these distances:
162 8 0.02
163 110 0.30
164 4 0.01
165 28 0.08
166 52 0.14
167 17 0.05
168 6 0.02
169 1 0.00
173 1 0.00
174 1 0.00
178 1 0.00
179 1 0.00
180 3 0.01
181 6 0.02
182 14 0.04
183 5 0.01
184 93 0.25
185 17 0.05
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (161 bp):
AAAAAAATGAAAAATTCATGAAAATAAATGAATTTTTAAAAACTAATTTAATATGAATTAAATGA
TGATATTTGATAAATTTTAAAAATTAAAACTAAGAAAAATCCCTCGAAAACATTTACGGAGTAGA
AAACTCTTTATTTTAGAAAAAAAAAAATTTC
Found at i:3183021 original size:18 final size:18
Alignment explanation
Indices: 3182998--3183038 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
3182988 AATCCCCCCA
*
3182998 AAAACATTTATAGAGTAG
1 AAAACATTTATAAAGTAG
3183016 AAAACATTTATAAAGTAG
1 AAAACATTTATAAAGTAG
3183034 AAAAC
1 AAAAC
3183039 TCCGTGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.24
Consensus pattern (18 bp):
AAAACATTTATAAAGTAG
Found at i:3183318 original size:166 final size:166
Alignment explanation
Indices: 3183029--3183338 Score: 378
Period size: 166 Copynumber: 1.9 Consensus size: 166
3183019 ACATTTATAA
* * * *
3183029 AGTAGAAAACTCCGTGTTTCAAAAACAAGAAAAATTTCAAGGAAAAATGAAAAATTCATGAAAAT
1 AGTAGAAAACTCCGTATTTCAAAAACAAGAAAAATTTCAAAGAAAAATAAAAAATTAATGAAAAT
* * * *
3183094 AAATGAATTTCTTAAAAATAATTTAATATGATCTAAATGATAATATTTGATAAATTTTAAAAATT
66 AAAGGAATTTCTTAAAAATAATTTAATATAATCTAAACGATAATATTTGAAAAATTTT-AAAATT
3183159 AAAAACTA-AGAAAAATCCCTTCGAAAATATTTACGG
130 AAAAACTAGAGAAAAATCCCTTCGAAAATATTTACGG
* * * *
3183195 AGTAGAAAACTCCGTATTTTAGAAACAAGAAGAATTTTAAAGAAAAATAAAAAATTAATG-AAAT
1 AGTAGAAAACTCCGTATTTCAAAAACAAGAAAAATTTCAAAGAAAAATAAAAAATTAATGAAAAT
* * * * * *
3183259 AAAAGGAATTT-TTCAAAATTGATTTCATGGTAAT-TAAGCGATGATATTT-AAAGAATTTTAAA
66 -AAAGGAATTTCTT-AAAAATAATTTAAT-ATAATCTAAACGATAATATTTGAAA-AATTTTAAA
3183321 ATTAAAAACTAGAGAAAA
127 ATTAAAAACTAGAGAAAA
3183339 TTACACCAAA
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
165 22 0.18
166 96 0.79
167 3 0.02
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.29
Consensus pattern (166 bp):
AGTAGAAAACTCCGTATTTCAAAAACAAGAAAAATTTCAAAGAAAAATAAAAAATTAATGAAAAT
AAAGGAATTTCTTAAAAATAATTTAATATAATCTAAACGATAATATTTGAAAAATTTTAAAATTA
AAAACTAGAGAAAAATCCCTTCGAAAATATTTACGG
Found at i:3188761 original size:206 final size:206
Alignment explanation
Indices: 3188397--3188768 Score: 485
Period size: 206 Copynumber: 1.8 Consensus size: 206
3188387 CATTTATTCC
** * *
3188397 TATGTATCATTATTACATAGGTGATGATGAATGAACATTGTAGCTAATGTTTGTACTTTACACCC
1 TATGTATCATTATTACATAGGTGATGATGAACAAACATTATAGCCAATGTTTGTACTTTACACCC
* * * * * * *
3188462 TATAAGCCATCATATGCCTTAATAAATTGCCTTGGCATGCCATTATGCTGTCCGATGGATAGCTA
66 TATAAGCCATCATAAGCCCTAATAAATTACCTTGGCATGCCATTATGCCGTCCAATGGACAACTA
* *
3188527 ATACTCGTTGTTTCCTTAAGCAATAGCAAATGAATGCTCTCATGTATTATCCTATTTAAGGCCCC
131 ATACTCATCGTTTCCTTAAGCAATAGCAAATGAATGCTCTCATGTATTATCCTATTTAAGGCCCC
3188592 ATATCTTCGTT
196 ATATCTTCGTT
* ** * * *
3188603 TATGTATCATTGTTATGTAGGTGATGATGAACAAACATTATCGCCAATGTTTGTACTTTACATCT
1 TATGTATCATTATTACATAGGTGATGATGAACAAACATTATAGCCAATGTTTGTACTTTACACCC
* * * *
3188668 TGTAAGGCATCATAAGCCCTAATAAGTTACC-TGGACATGCCGTTATGCCGTCCAATGGACAACT
66 TATAAGCCATCATAAGCCCTAATAAATTACCTTGG-CATGCCATTATGCCGTCCAATGGACAACT
* * **
3188732 AATGCTCATCGTTTCCTTAGGTGATAGCAAATGAATG
130 AATACTCATCGTTTCCTTAAGCAATAGCAAATGAATG
3188769 TTATCACCTA
Statistics
Matches: 138, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
205 3 0.02
206 135 0.98
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (206 bp):
TATGTATCATTATTACATAGGTGATGATGAACAAACATTATAGCCAATGTTTGTACTTTACACCC
TATAAGCCATCATAAGCCCTAATAAATTACCTTGGCATGCCATTATGCCGTCCAATGGACAACTA
ATACTCATCGTTTCCTTAAGCAATAGCAAATGAATGCTCTCATGTATTATCCTATTTAAGGCCCC
ATATCTTCGTT
Found at i:3190445 original size:34 final size:35
Alignment explanation
Indices: 3190407--3190473 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3190397 CCTTACAACA
3190407 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
3190441 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
3190474 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:3190949 original size:13 final size:13
Alignment explanation
Indices: 3190931--3190956 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3190921 CAATTTTTTG
3190931 TGTATCGATACAT
1 TGTATCGATACAT
3190944 TGTATCGATACAT
1 TGTATCGATACAT
3190957 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3191041 original size:20 final size:20
Alignment explanation
Indices: 3191016--3191088 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3191006 CATCCTTTTT
3191016 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3191036 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
3191057 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3191077 ATGTATCGATAC
1 ATGTATCGATAC
3191089 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3191061 original size:21 final size:21
Alignment explanation
Indices: 3190995--3191071 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
3190985 CTGCCAAGAA
*
3190995 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
3191016 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
3191036 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
3191057 ATGTATCGATACATT
1 ATGTATCGATACATT
3191072 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:3191061 original size:41 final size:41
Alignment explanation
Indices: 3190995--3191088 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
3190985 CTGCCAAGAA
3190995 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
3191036 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
3191077 ATGTATCGATAC
1 ATGTATCGATAC
3191089 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:3191695 original size:48 final size:48
Alignment explanation
Indices: 3191640--3191735 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
3191630 AAATTTTACG
3191640 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
*
3191688 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTTTCTCCT
1 AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
3191736 TTATCTCCCC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (48 bp):
AATTTGTACATTCTCCCCCTTAATAAGGTAATTCACGCATTCTCTCCT
Found at i:3195025 original size:21 final size:21
Alignment explanation
Indices: 3195001--3195042 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3194991 ATCCATTTCT
* *
3195001 TCATTTTCATCAACCTCTTGA
1 TCATCTTCATCAACATCTTGA
*
3195022 TCATCTTCATCATCATCTTGA
1 TCATCTTCATCAACATCTTGA
3195043 ACGATTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.43
Consensus pattern (21 bp):
TCATCTTCATCAACATCTTGA
Found at i:3196173 original size:34 final size:35
Alignment explanation
Indices: 3196135--3196201 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
3196125 CCTTACAACA
3196135 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
3196169 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
3196202 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:3196677 original size:13 final size:13
Alignment explanation
Indices: 3196659--3196684 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3196649 CAATTTTTTG
3196659 TGTATCGATACAT
1 TGTATCGATACAT
3196672 TGTATCGATACAT
1 TGTATCGATACAT
3196685 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3196769 original size:20 final size:20
Alignment explanation
Indices: 3196744--3196816 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3196734 CATCCTTTTT
3196744 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
3196764 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
3196785 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3196805 ATGTATCGATAC
1 ATGTATCGATAC
3196817 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3196789 original size:21 final size:21
Alignment explanation
Indices: 3196723--3196799 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
3196713 CTGCCAAGAA
*
3196723 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
3196744 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
3196764 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
3196785 ATGTATCGATACATT
1 ATGTATCGATACATT
3196800 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:3196789 original size:41 final size:41
Alignment explanation
Indices: 3196723--3196816 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
3196713 CTGCCAAGAA
3196723 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
3196764 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
3196805 ATGTATCGATAC
1 ATGTATCGATAC
3196817 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:3197359 original size:94 final size:94
Alignment explanation
Indices: 3197198--3197480 Score: 408
Period size: 94 Copynumber: 3.0 Consensus size: 94
3197188 AGCCATTTTC
* * *
3197198 AGCCTTTGCTCATTAACCCAATGTCTGGTTTGAGCATGTTTTGTCACACCAGAATTCATGCTAGA
1 AGCCTTTGCTCATTAACCCAATGTCTGGTTTGAACATGTTTTGTCACACTAGAATTCATGCCAGA
*
3197263 TTCACAGCTCAAATTTCTAATCAGATTTG
66 TTCACAGCTCAAATTTCTGATCAGATTTG
* *
3197292 AGCCTTTGCTCATTAACCCTATGTCTGGTTTGAACATATTTTGTCACACTAGAATTCATGCCAGA
1 AGCCTTTGCTCATTAACCCAATGTCTGGTTTGAACATGTTTTGTCACACTAGAATTCATGCCAGA
* *
3197357 TTCACAGCTTAAATTTTTGATCAGATTTG
66 TTCACAGCTCAAATTTCTGATCAGATTTG
* * * * *
3197386 AACCTTTGCTCATTGAGCCAATGTCTAGTTTGAACATGTTTTGTCACA-TTGAAATTCATGCC-G
1 AGCCTTTGCTCATTAACCCAATGTCTGGTTTGAACATGTTTTGTCACACTAG-AATTCATGCCAG
*
3197449 AATTCATAGCTCAAATTTCTGATCAGATTTG
65 -ATTCACAGCTCAAATTTCTGATCAGATTTG
3197480 A
1 A
3197481 ATCAAATGTA
Statistics
Matches: 169, Mismatches: 18, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
93 3 0.02
94 166 0.98
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (94 bp):
AGCCTTTGCTCATTAACCCAATGTCTGGTTTGAACATGTTTTGTCACACTAGAATTCATGCCAGA
TTCACAGCTCAAATTTCTGATCAGATTTG
Found at i:3211448 original size:21 final size:22
Alignment explanation
Indices: 3211424--3211472 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
3211414 ACAAATCGAA
3211424 AAAAAATATA-TAAAAAA-TGTC
1 AAAAAAT-TACTAAAAAATTGTC
3211445 -AAAAATTACTAAAAAATTGTC
1 AAAAAATTACTAAAAAATTGTC
3211466 AACAAAA
1 AA-AAAA
3211473 GAAAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 2 0.08
20 13 0.54
21 4 0.17
22 1 0.04
23 4 0.17
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAAAATTACTAAAAAATTGTC
Found at i:3211450 original size:20 final size:21
Alignment explanation
Indices: 3211425--3211467 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
3211415 CAAATCGAAA
3211425 AAAAATATA-TAAAAAA-TGTC
1 AAAAAT-TACTAAAAAATTGTC
3211445 AAAAATTACTAAAAAATTGTC
1 AAAAATTACTAAAAAATTGTC
3211466 AA
1 AA
3211468 CAAAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.62
21 6 0.29
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAAATTACTAAAAAATTGTC
Found at i:3211764 original size:19 final size:19
Alignment explanation
Indices: 3211740--3211777 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3211730 GATAAAGTGT
3211740 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
3211759 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
3211778 ATTTAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
TTGAAAAAAAAAAAAAAAA
Found at i:3211768 original size:20 final size:20
Alignment explanation
Indices: 3211743--3211780 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3211733 AAAGTGTTTG
3211743 AAAAAAAAAAAAAAAATTGA
1 AAAAAAAAAAAAAAAATTGA
3211763 AAAAAAAAAAAAAAAATT
1 AAAAAAAAAAAAAAAATT
3211781 TAAATGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.11
Consensus pattern (20 bp):
AAAAAAAAAAAAAAAATTGA
Found at i:3211807 original size:21 final size:21
Alignment explanation
Indices: 3211783--3211839 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3211773 AAAAAATTTA
3211783 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3211804 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3211825 AATGTATCGATACAT
1 AATGTATCGATACAT
3211840 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3211919 original size:19 final size:19
Alignment explanation
Indices: 3211895--3211962 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3211885 AATTCAACAA
3211895 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3211914 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3211929 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3211946 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3211963 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3211934 original size:13 final size:13
Alignment explanation
Indices: 3211916--3211940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3211906 ACATAAGTTT
3211916 TGTATCGATACAA
1 TGTATCGATACAA
3211929 TGTATCGATACA
1 TGTATCGATACA
3211941 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3211938 original size:32 final size:32
Alignment explanation
Indices: 3211897--3211959 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3211887 TTCAACAATT
*
3211897 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3211929 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3211960 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3212020 original size:13 final size:13
Alignment explanation
Indices: 3212002--3212027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3211992 CATTTTTCTG
3212002 TGTATCGATACAT
1 TGTATCGATACAT
3212015 TGTATCGATACAT
1 TGTATCGATACAT
3212028 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3212024 original size:33 final size:33
Alignment explanation
Indices: 3211982--3212048 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3211972 GCCAAGGAAA
***
3211982 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3212015 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3212048 T
1 T
3212049 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3214565 original size:28 final size:27
Alignment explanation
Indices: 3214498--3214570 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
3214488 CTTCACAATC
* *
3214498 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
3214525 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
3214553 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3214571 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:3214615 original size:51 final size:51
Alignment explanation
Indices: 3214553--3214723 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
3214543 TTATTTCTGA
* * *
3214553 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * * *
3214604 GGGGATACTCCAACCCGGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
3214657 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
3214709 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3214724 TCGTTATTTC
Statistics
Matches: 95, Mismatches: 22, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
51 35 0.37
52 18 0.19
53 31 0.33
54 11 0.12
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:3214742 original size:28 final size:28
Alignment explanation
Indices: 3214706--3214787 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
3214696 ATTTTTCACA
*
3214706 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3214734 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3214762 --CGAAGGAACACTCCAACCTCGTTATT
1 ATCG--GGGATACTCCAACCTCGTTATT
3214788 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 2 0.04
28 43 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:3216985 original size:21 final size:21
Alignment explanation
Indices: 3216961--3217002 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3216951 GTTGGACACC
* *
3216961 TAGTACAATCATGTCAATCCT
1 TAGTACAATAATCTCAATCCT
*
3216982 TAGTAGAATAATCTCAATCCT
1 TAGTACAATAATCTCAATCCT
3217003 CCAAATCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (21 bp):
TAGTACAATAATCTCAATCCT
Found at i:3217219 original size:29 final size:29
Alignment explanation
Indices: 3217163--3217219 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
3217153 AACAAAAGGC
***
3217163 CACAAGTCAATGGCACCCTTTTCGAAGCT
1 CACAAGTCAATGGCACCCTTTAAAAAGCT
* *
3217192 CACAAGTTAGTGGCACCCTTTAAAAAGC
1 CACAAGTCAATGGCACCCTTTAAAAAGC
3217220 CCGCACGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (29 bp):
CACAAGTCAATGGCACCCTTTAAAAAGCT
Found at i:3217469 original size:82 final size:82
Alignment explanation
Indices: 3217275--3217639 Score: 360
Period size: 82 Copynumber: 4.5 Consensus size: 82
3217265 TCTCCTTTTG
* * * * * * ** * * *
3217275 AGCCCAATGTCACTGGCCTTGAATTAGCATATTGGCATCTTGCTTTAAGTAATGCAGCATCTATC
1 AGCCCAATGTCAGTGGCCATGAATCAACACATTGGCACCTTGCCCTAAGTCATGCGGCATCCATC
* * *
3217340 TAAATC--TTCCTCTCA
66 TAAATCTTTTTCACTAA
* * * * * **
3217355 AGCCCAATGT-TGCTAGCCTTGAATCAACACATTAGCACCTTGCCCTAAGTCATGCGACATCTGT
1 AGCCCAATGTCAG-TGGCCATGAATCAACACATTGGCACCTTGCCCTAAGTCATGCGGCATCCAT
3217419 CTAAATCTTTTTCACTAA
65 CTAAATCTTTTTCACTAA
* * ** *
3217437 AGCCCAATGTCAGTAGCAATGAATCAACACATTGGCATATTGCTCTAAGTCATGCGGCATCCATC
1 AGCCCAATGTCAGTGGCCATGAATCAACACATTGGCACCTTGCCCTAAGTCATGCGGCATCCATC
*
3217502 TAAATCTTTTTCATTAA
66 TAAATCTTTTTCACTAA
* * * * * * *
3217519 AGCCCAAT-ACCGATGGCCATGAATTAACACATTGGCACCTTGTCCTAAGTTATACGGTATCCAT
1 AGCCCAATGTCAG-TGGCCATGAATCAACACATTGGCACCTTGCCCTAAGTCATGCGGCATCCAT
3217583 CTAAATCTTTTTCACTAA
65 CTAAATCTTTTTCACTAA
* *
3217601 AGCCCAATGTCACTGGCCATGAATCAATACATTGGCACC
1 AGCCCAATGTCAGTGGCCATGAATCAACACATTGGCACC
3217640 CTTATCATTT
Statistics
Matches: 233, Mismatches: 46, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
80 56 0.24
81 2 0.01
82 173 0.74
83 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (82 bp):
AGCCCAATGTCAGTGGCCATGAATCAACACATTGGCACCTTGCCCTAAGTCATGCGGCATCCATC
TAAATCTTTTTCACTAA
Found at i:3217687 original size:51 final size:52
Alignment explanation
Indices: 3217632--3217730 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 52
3217622 AATCAATACA
*
3217632 TTGGCACCCTTATCAT-TTTAAGTCCAATGAT-GTTGGCCTTAGATCAGCACT
1 TTGGCACCCTTATCATCTTTAAGTCCAATG-TCGCTGGCCTTAGATCAGCACT
* *
3217683 TTGGCACCTTTATCATCTTTAAGTCCAATGTCGCTGGCCTTGGATCAG
1 TTGGCACCCTTATCATCTTTAAGTCCAATGTCGCTGGCCTTAGATCAG
3217731 TTATAGGCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 16 0.37
52 27 0.63
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (52 bp):
TTGGCACCCTTATCATCTTTAAGTCCAATGTCGCTGGCCTTAGATCAGCACT
Found at i:3217813 original size:52 final size:52
Alignment explanation
Indices: 3217649--3217878 Score: 193
Period size: 52 Copynumber: 4.4 Consensus size: 52
3217639 CCTTATCATT
* * * * * * * *
3217649 TTAAGTCCAATGAT-GTTGGCCTTAGATCAGCACTTTGGCACCTTTATCATCT
1 TTAAGACCAATG-TCGTTGGCCTTAGATCAACACATTAGCAACTTTGTCAGCC
* * * *** *
3217701 TTAAGTCCAATGTCGCTGGCCTTGGATC-AGTTA-TAGGCAACTTTGT-TGCC
1 TTAAGACCAATGTCGTTGGCCTTAGATCAACACATTA-GCAACTTTGTCAGCC
*
3217751 TCTAAGACCAATGTTGTTGGCCTTAGATCAACACATTAGCAACTTTGTCA-CAC
1 T-TAAGACCAATGTCGTTGGCCTTAGATCAACACATTAGCAACTTTGTCAGC-C
* *
3217804 TTAAGACCAATGTCGTTGGCCTTCGATCAACACATTGGCAACTTTGT-AGCCC
1 TTAAGACCAATGTCGTTGGCCTTAGATCAACACATTAGCAACTTTGTCAG-CC
* *
3217856 TTAAGACCAATATCATTGGCCTT
1 TTAAGACCAATGTCGTTGGCCTT
3217879 GAATTAGCAT
Statistics
Matches: 143, Mismatches: 26, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
50 3 0.02
51 33 0.23
52 102 0.71
53 5 0.03
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (52 bp):
TTAAGACCAATGTCGTTGGCCTTAGATCAACACATTAGCAACTTTGTCAGCC
Found at i:3219101 original size:94 final size:93
Alignment explanation
Indices: 3218932--3219177 Score: 303
Period size: 94 Copynumber: 2.6 Consensus size: 93
3218922 AGCCATTTTC
* *
3218932 AGCCTTTACTCATTGACCAAATGTCTGGTTTGAACATGTTTTGTCACACCAGAATTCATGCAAGA
1 AGCCTTTGCTCATTGACCTAATGTCTGGTTTGAACATGTTTTGTCACACCA-AATTCATGCAAGA
* *
3218997 TTCAGAGCTTAAATTTCTAATCAGATTTG
65 TTCACAGCTTAAATTTCTAATCAGATTTA
* * **
3219026 AGCTTTTGCTCATTAACCTAATGTCTGGTTTGAACATGTTTTGTCACACCGAAATTCATGTTAGA
1 AGCCTTTGCTCATTGACCTAATGTCTGGTTTGAACATGTTTTGTCACACC-AAATTCATGCAAGA
* * * **
3219091 TTTACAGCTTAAATTTTTGATTGGATTTA
65 TTCACAGCTTAAATTTCTAATCAGATTTA
* * ** *
3219120 AGCCTTTGCTTATTGACCTAATATCTAATTTAAACATGTTTTGTCACACCAAAATTCA
1 AGCCTTTGCTCATTGACCTAATGTCTGGTTTGAACATGTTTTGTCACACC-AAATTCA
3219178 CAGCTCAAAT
Statistics
Matches: 130, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
94 129 0.99
95 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (93 bp):
AGCCTTTGCTCATTGACCTAATGTCTGGTTTGAACATGTTTTGTCACACCAAATTCATGCAAGAT
TCACAGCTTAAATTTCTAATCAGATTTA
Found at i:3221521 original size:27 final size:27
Alignment explanation
Indices: 3221464--3221523 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
3221454 TATCCACGAG
*
3221464 GATACTCCAACCCCATCTTTCCAAAGG
1 GATACTCCAACCCCATCTTTCCAAAGA
* *
3221491 GATACTCTAACCCTATCTTTCCGAAA-A
1 GATACTCCAACCCCATCTTTCC-AAAGA
3221518 GATACT
1 GATACT
3221524 TTAATCTTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.32, C:0.32, G:0.10, T:0.27
Consensus pattern (27 bp):
GATACTCCAACCCCATCTTTCCAAAGA
Found at i:3224309 original size:13 final size:13
Alignment explanation
Indices: 3224291--3224316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3224281 TACAGCAAGT
3224291 ATGTATCGATACA
1 ATGTATCGATACA
3224304 ATGTATCGATACA
1 ATGTATCGATACA
3224317 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3226558 original size:21 final size:21
Alignment explanation
Indices: 3226525--3226569 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3226515 TTGCAAGTTG
*
3226525 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
3226547 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
3226567 AAA
1 AAA
3226570 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:3230489 original size:20 final size:21
Alignment explanation
Indices: 3230420--3230497 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 21
3230410 AATGTCCAAA
*
3230420 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
3230440 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
3230465 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
3230485 TTGTATCGATACA
1 ATGTATCGATACA
3230498 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 30 0.64
24 3 0.06
25 14 0.30
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:3230504 original size:13 final size:13
Alignment explanation
Indices: 3230486--3230549 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
3230476 CATTTTTCTT
3230486 TGTATCGATACAA
1 TGTATCGATACAA
*
3230499 TGTATCGATACAC
1 TGTATCGATACAA
3230512 TGTATCGATACAA
1 TGTATCGATACAA
*
3230525 TGTATCGATACAC
1 TGTATCGATACAA
3230538 TGTATCGATACA
1 TGTATCGATACA
3230550 GGGTGATTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3230522 original size:26 final size:26
Alignment explanation
Indices: 3230486--3230549 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
3230476 CATTTTTCTT
3230486 TGTATCGATACAATGTATCGATACAC
1 TGTATCGATACAATGTATCGATACAC
3230512 TGTATCGATACAATGTATCGATACAC
1 TGTATCGATACAATGTATCGATACAC
3230538 TGTATCGATACA
1 TGTATCGATACA
3230550 GGGTGATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (26 bp):
TGTATCGATACAATGTATCGATACAC
Found at i:3233110 original size:13 final size:13
Alignment explanation
Indices: 3233092--3233117 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3233082 TACAGCAAGT
3233092 ATGTATCGATACA
1 ATGTATCGATACA
3233105 ATGTATCGATACA
1 ATGTATCGATACA
3233118 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3237310 original size:9 final size:9
Alignment explanation
Indices: 3237292--3237325 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3237282 TCAATCGTCA
3237292 AAGATGATG
1 AAGATGATG
*
3237301 AAGATAATG
1 AAGATGATG
*
3237310 ATGATGATG
1 AAGATGATG
3237319 AAGATGA
1 AAGATGA
3237326 AATTGACTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (9 bp):
AAGATGATG
Found at i:3239920 original size:13 final size:13
Alignment explanation
Indices: 3239887--3239923 Score: 60
Period size: 11 Copynumber: 3.0 Consensus size: 13
3239877 CACACCCAGA
3239887 TGTATCGATACAT
1 TGTATCGATACAT
3239900 TG--TCGATACAT
1 TGTATCGATACAT
3239911 TGTATCGATACAT
1 TGTATCGATACAT
3239924 GTTAATTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 11 0.50
13 11 0.50
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3239933 original size:19 final size:20
Alignment explanation
Indices: 3239909--3239962 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
3239899 TTGTCGATAC
**
3239909 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
*
3239928 ATTGTATCAATACATGGACA
1 ATTGTATCGATACATGGACA
3239948 ATTGTATCGATACAT
1 ATTGTATCGATACAT
3239963 AAGATTGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:3243292 original size:13 final size:13
Alignment explanation
Indices: 3243274--3243304 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3243264 ACAATTCATC
3243274 ATGTATCGATACA
1 ATGTATCGATACA
3243287 ATGTATCGATACA
1 ATGTATCGATACA
*
3243300 TTGTA
1 ATGTA
3243305 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3243292 original size:33 final size:33
Alignment explanation
Indices: 3243254--3243320 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
3243244 GTTACAAGCT
*
3243254 ATGTATCGATACAATT-CATCATGTATCGATACA
1 ATGTATCGATAC-ATTGCACCATGTATCGATACA
*
3243287 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGCACCATGTATCGATACA
3243320 A
1 A
3243321 ACAATGGAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACATTGCACCATGTATCGATACA
Found at i:3243394 original size:19 final size:19
Alignment explanation
Indices: 3243349--3243403 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
3243339 CTGCCAATCT
**
3243349 CATGTATCGATACAATTGT
1 CATGTATCGATACAATTAA
3243368 CAATGTATCGATACAATTAA
1 C-ATGTATCGATACAATTAA
3243388 CATGTATCGATACAAT
1 CATGTATCGATACAAT
3243404 GTATCGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATTAA
Found at i:3243407 original size:13 final size:13
Alignment explanation
Indices: 3243389--3243415 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3243379 TACAATTAAC
3243389 ATGTATCGATACA
1 ATGTATCGATACA
3243402 ATGTATCGATACA
1 ATGTATCGATACA
3243415 A
1 A
3243416 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3245713 original size:20 final size:23
Alignment explanation
Indices: 3245688--3245734 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
3245678 TTCTATTGAT
3245688 GATTTTG-A-TGAAAAA-TGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
3245708 GATTTTGAAGTGAAAAAGTGAAA
1 GATTTTGAAGTGAAAAAGTGAAA
3245731 -ATTT
1 GATTT
3245735 GTGGAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 1 0.04
22 11 0.46
23 5 0.21
ACGTcount: A:0.47, C:0.00, G:0.21, T:0.32
Consensus pattern (23 bp):
GATTTTGAAGTGAAAAAGTGAAA
Found at i:3251957 original size:33 final size:32
Alignment explanation
Indices: 3251920--3251983 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
3251910 ACAAGCTATA
3251920 TATCGATACAATTCAT-CATGTATCAATACAACG
1 TATCGATAC-ATT-ATACATGTATCAATACAACG
*
3251953 TATCGATACATTATACCATGTATCGATACAA
1 TATCGATACATTATA-CATGTATCAATACAA
3251984 ACAGTGAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 2 0.07
32 3 0.11
33 23 0.82
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (32 bp):
TATCGATACATTATACATGTATCAATACAACG
Found at i:3251968 original size:20 final size:20
Alignment explanation
Indices: 3251945--3251982 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3251935 TCATGTATCA
3251945 ATACAACGTATCGATACATT
1 ATACAACGTATCGATACATT
* *
3251965 ATACCATGTATCGATACA
1 ATACAACGTATCGATACA
3251983 AACAGTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (20 bp):
ATACAACGTATCGATACATT
Found at i:3252071 original size:13 final size:13
Alignment explanation
Indices: 3252053--3252078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3252043 ACAATTAACT
3252053 TGTATTGATACAA
1 TGTATTGATACAA
3252066 TGTATTGATACAA
1 TGTATTGATACAA
3252079 AGCATAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATTGATACAA
Found at i:3254735 original size:31 final size:31
Alignment explanation
Indices: 3254695--3254767 Score: 128
Period size: 31 Copynumber: 2.3 Consensus size: 31
3254685 TTTTGGGACT
3254695 TCAAGTAAAGCAAACAAAAGACGAGATCTTCA
1 TCAA-TAAAGCAAACAAAAGACGAGATCTTCA
3254727 TCAATAAAGCAAACAAAAGACGAGATCTTCA
1 TCAATAAAGCAAACAAAAGACGAGATCTTCA
*
3254758 TCAATCAAGC
1 TCAATAAAGC
3254768 GAAATATACT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 36 0.90
32 4 0.10
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (31 bp):
TCAATAAAGCAAACAAAAGACGAGATCTTCA
Found at i:3255969 original size:13 final size:13
Alignment explanation
Indices: 3255951--3256037 Score: 129
Period size: 13 Copynumber: 6.7 Consensus size: 13
3255941 ACAATATTCT
3255951 TCGATACATTGTA
1 TCGATACATTGTA
*
3255964 TCGATACACTGTA
1 TCGATACATTGTA
*
3255977 TCGATATATTGTA
1 TCGATACATTGTA
*
3255990 TCGATACACTGTA
1 TCGATACATTGTA
*
3256003 TCGATATATTGTA
1 TCGATACATTGTA
*
3256016 TCGATACACTGTA
1 TCGATACATTGTA
3256029 TCGATACAT
1 TCGATACAT
3256038 AGGGTACTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 64 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (13 bp):
TCGATACATTGTA
Found at i:3255987 original size:26 final size:26
Alignment explanation
Indices: 3255951--3256034 Score: 159
Period size: 26 Copynumber: 3.2 Consensus size: 26
3255941 ACAATATTCT
*
3255951 TCGATACATTGTATCGATACACTGTA
1 TCGATATATTGTATCGATACACTGTA
3255977 TCGATATATTGTATCGATACACTGTA
1 TCGATATATTGTATCGATACACTGTA
3256003 TCGATATATTGTATCGATACACTGTA
1 TCGATATATTGTATCGATACACTGTA
3256029 TCGATA
1 TCGATA
3256035 CATAGGGTAC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (26 bp):
TCGATATATTGTATCGATACACTGTA
Found at i:3258541 original size:19 final size:20
Alignment explanation
Indices: 3258517--3258569 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3258507 ACATTATGAT
**
3258517 TTGTATCGATACAT-GTTAA
1 TTGTATCGATACATGGACAA
3258536 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
3258556 TTGTATCGATACAT
1 TTGTATCGATACAT
3258570 AAGATTGGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:3258637 original size:13 final size:13
Alignment explanation
Indices: 3258619--3258644 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3258609 CATGGTCTAA
3258619 TGTATCGATACAT
1 TGTATCGATACAT
3258632 TGTATCGATACAT
1 TGTATCGATACAT
3258645 GATGAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3258656 original size:33 final size:33
Alignment explanation
Indices: 3258598--3258666 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3258588 CTACCACTGT
* *
3258598 TTGTATCGATACATGGTCTAATGTATCGATACA
1 TTGTATCGATACATGATCGAATGTATCGATACA
* *
3258631 TTGTATCGATACATGAT-GAATTGTATTGATATA
1 TTGTATCGATACATGATCGAA-TGTATCGATACA
3258664 TTG
1 TTG
3258667 CTTGTAACGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (33 bp):
TTGTATCGATACATGATCGAATGTATCGATACA
Found at i:3261626 original size:20 final size:21
Alignment explanation
Indices: 3261601--3261639 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
3261591 ATTTTTCAAA
3261601 ATGTATCGATACAT-TGAATG
1 ATGTATCGATACATCTGAATG
3261621 ATGTATCGATACATCTGAA
1 ATGTATCGATACATCTGAA
3261640 AAAACTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATCTGAATG
Found at i:3263473 original size:13 final size:13
Alignment explanation
Indices: 3263455--3263480 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3263445 CAATTTTTTG
3263455 TGTATCGATACAT
1 TGTATCGATACAT
3263468 TGTATCGATACAT
1 TGTATCGATACAT
3263481 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3263545 original size:21 final size:21
Alignment explanation
Indices: 3263519--3263594 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
3263509 CTGCCAAGAA
*
3263519 ATGTATCGATACATATTTTTT
1 ATGTATCGATACATATTTTTC
****
3263540 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATATTTTTC
3263560 ATGTATCGATACATCA-TTTTC
1 ATGTATCGATACAT-ATTTTTC
3263581 ATGTATCGATACAT
1 ATGTATCGATACAT
3263595 TGCAACATGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATATTTTTC
Found at i:3263565 original size:20 final size:20
Alignment explanation
Indices: 3263540--3263612 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
3263530 CATATTTTTT
3263540 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*
3263560 ATGTATCGATACA-T-CATTTTC
1 ATGTATCGATACATTGCA---AC
3263581 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3263601 ATGTATCGATAC
1 ATGTATCGATAC
3263613 TTTGAATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 26 0.57
21 14 0.30
22 1 0.02
23 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3263585 original size:41 final size:41
Alignment explanation
Indices: 3263519--3263612 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
3263509 CTGCCAAGAA
*
3263519 ATGTATCGATACATATTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
3263560 ATGTATCGATACATCA-TTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAT-ATTTTTCATGTATCGATACATTGCAAC
3263601 ATGTATCGATAC
1 ATGTATCGATAC
3263613 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 50 0.98
42 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
Found at i:3266082 original size:13 final size:13
Alignment explanation
Indices: 3266064--3266101 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3266054 ATAATCACCC
3266064 TGTATCGATACAG
1 TGTATCGATACAG
*
3266077 TGTATCGATACAT
1 TGTATCGATACAG
3266090 TGTATCGATACA
1 TGTATCGATACA
3266102 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3266115 original size:20 final size:20
Alignment explanation
Indices: 3266090--3266166 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
3266080 ATCGATACAT
3266090 TGTATCGATACAAAGAAAAA
1 TGTATCGATACAAAGAAAAA
* *
3266110 TGTATCGATACATAGAATTTCCAGA
1 TGTATCGATACAAAGAA-----AAA
*
3266135 TGTATCGATACACAA-AAACA
1 TGTATCGATACA-AAGAAAAA
3266155 TGTATCGATACA
1 TGTATCGATACA
3266167 TTTTGGACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 30 0.64
25 16 0.34
26 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (20 bp):
TGTATCGATACAAAGAAAAA
Found at i:3270045 original size:21 final size:21
Alignment explanation
Indices: 3270016--3270060 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3270006 AAGTTTTCAT
*
3270016 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3270036 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3270058 TTT
1 TTT
3270061 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3272296 original size:13 final size:13
Alignment explanation
Indices: 3272278--3272303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3272268 CAATTTTTTG
3272278 TGTATCGATACAT
1 TGTATCGATACAT
3272291 TGTATCGATACAT
1 TGTATCGATACAT
3272304 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3272368 original size:21 final size:21
Alignment explanation
Indices: 3272342--3272417 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
3272332 CTGCCAAGAA
*
3272342 ATGTATCGATACATATTTTTT
1 ATGTATCGATACATATTTTTC
****
3272363 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATATTTTTC
3272383 ATGTATCGATACATCA-TTTTC
1 ATGTATCGATACAT-ATTTTTC
3272404 ATGTATCGATACAT
1 ATGTATCGATACAT
3272418 TGCAACATGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATATTTTTC
Found at i:3272388 original size:20 final size:20
Alignment explanation
Indices: 3272363--3272435 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
3272353 CATATTTTTT
3272363 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
*
3272383 ATGTATCGATACA-T-CATTTTC
1 ATGTATCGATACATTGCA---AC
3272404 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
3272424 ATGTATCGATAC
1 ATGTATCGATAC
3272436 TTTGAATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 26 0.57
21 14 0.30
22 1 0.02
23 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:3272408 original size:41 final size:41
Alignment explanation
Indices: 3272342--3272435 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
3272332 CTGCCAAGAA
*
3272342 ATGTATCGATACATATTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
3272383 ATGTATCGATACATCA-TTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAT-ATTTTTCATGTATCGATACATTGCAAC
3272424 ATGTATCGATAC
1 ATGTATCGATAC
3272436 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 50 0.98
42 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATATTTTTCATGTATCGATACATTGCAAC
Found at i:3273577 original size:30 final size:30
Alignment explanation
Indices: 3273542--3273598 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
3273532 GAACTTTTTG
3273542 AAAATAAAATTTGGCATTTAACAAAGGTCA
1 AAAATAAAATTTGGCATTTAACAAAGGTCA
* *
3273572 AAAATAAATTTTGGCATTTGACAAAGG
1 AAAATAAAATTTGGCATTTAACAAAGG
3273599 GGGAGAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (30 bp):
AAAATAAAATTTGGCATTTAACAAAGGTCA
Found at i:3276657 original size:15 final size:15
Alignment explanation
Indices: 3276637--3276666 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3276627 GAGTAAAAGG
3276637 TTAATTTATTACTTT
1 TTAATTTATTACTTT
3276652 TTAATTTATTACTTT
1 TTAATTTATTACTTT
3276667 CTCAATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTAATTTATTACTTT
Found at i:3282631 original size:7 final size:7
Alignment explanation
Indices: 3282621--3282655 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
3282611 AATTTTGAGT
3282621 CTGGTGA
1 CTGGTGA
3282628 CTGGTGA
1 CTGGTGA
3282635 CTGGTGA
1 CTGGTGA
3282642 CTGGTGA
1 CTGGTGA
3282649 CTGGTGA
1 CTGGTGA
3282656 TGTGAGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.43, T:0.29
Consensus pattern (7 bp):
CTGGTGA
Found at i:3282796 original size:22 final size:23
Alignment explanation
Indices: 3282739--3282795 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
3282729 GAGTTTATTT
3282739 ATTTATTTTTTTATAAAAAAATA
1 ATTTATTTTTTTATAAAAAAATA
3282762 ATTTATTTTTTTATAAAAAAATA
1 ATTTATTTTTTTATAAAAAAATA
3282785 ATTTATTTTTT
1 ATTTATTTTTT
3282796 ACCTTTGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATTTATTTTTTTATAAAAAAATA
Found at i:3284893 original size:16 final size:16
Alignment explanation
Indices: 3284764--3284888 Score: 103
Period size: 16 Copynumber: 7.7 Consensus size: 16
3284754 ATACTATTTA
*
3284764 TTAAAATTAATTTAAAC
1 TTAAAA-TAATTTAAAT
*
3284781 TCAAAATAA-TTATAAT
1 TTAAAATAATTTA-AAT
* *
3284797 TTAAAA-AAATCATAA-
1 TTAAAATAATTTA-AAT
3284812 TTAAAATAATTTAAAT
1 TTAAAATAATTTAAAT
* *
3284828 TAAAAATAATTTAAAC
1 TTAAAATAATTTAAAT
* * *
3284844 ATAACATAAACTTAAAT
1 TTAAAAT-AATTTAAAT
3284861 TTAAAATAATTTAAAT
1 TTAAAATAATTTAAAT
3284877 TTAAAAATAATT
1 TT-AAAATAATT
3284889 CAATTCAAAT
Statistics
Matches: 86, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
15 13 0.15
16 47 0.55
17 26 0.30
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAATAATTTAAAT
Found at i:3285358 original size:16 final size:15
Alignment explanation
Indices: 3285337--3285416 Score: 74
Period size: 16 Copynumber: 5.1 Consensus size: 15
3285327 ATTTATTAAA
3285337 AAAATAGAATTATAAT
1 AAAATA-AATTATAAT
3285353 AAAAT-AATTATTATAT
1 AAAATAAATTA-TA-AT
*
3285369 AAAAATAAATTAAAAT
1 -AAAATAAATTATAAT
* *
3285385 AAAAATAAAATAAAAT
1 -AAAATAAATTATAAT
3285401 AAAAT-AATTATAAT
1 AAAATAAATTATAAT
3285415 AA
1 AA
3285417 TAATTTAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 14 0.25
15 7 0.12
16 24 0.43
17 6 0.11
18 5 0.09
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (15 bp):
AAAATAAATTATAAT
Found at i:3285386 original size:32 final size:31
Alignment explanation
Indices: 3285329--3285388 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
3285319 TATATTTGAT
*
3285329 TTATTAAAAAAATAGAATTATAATAAAATAA
1 TTATTAAAAAAATAGAATTAAAATAAAATAA
3285360 TTATTATATAAAAATA-AATTAAAATAAAA
1 TTATTA-A-AAAAATAGAATTAAAATAAAA
3285389 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 6 0.23
32 13 0.50
33 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (31 bp):
TTATTAAAAAAATAGAATTAAAATAAAATAA
Found at i:3285387 original size:5 final size:5
Alignment explanation
Indices: 3285370--3285407 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
3285360 TTATTATATA
*
3285370 AAAAT AAATT AAAAT AAAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AA
3285408 TTATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:3286573 original size:128 final size:128
Alignment explanation
Indices: 3286338--3286576 Score: 293
Period size: 128 Copynumber: 1.9 Consensus size: 128
3286328 TCAAGGTTTA
* * * * * *
3286338 TTATGATTATATATTTAATTTAATTAAAATTTTTAATGTATTATTAATTGATTTTAGATTAAATG
1 TTATGATCATATATTTAATCTAATTAAAATTTTTAACGTATCATCAATTGATTTTAAATTAAATG
* * * * * **
3286403 TTTTAAAGTTAAGTTTAATTTCTTTTTTGAGGTTATCTCATTTTTTTTAAGTGTCAAATTTGT
66 ATTTAAAGTTAAATTTAATTTCTTCTTTGAGATCATAACATTTTTTTTAAGTGTCAAATTTGT
* *
3286466 TTATGATCATATATTTAATCTAATTAAATTTTTTTACGTATCATCAATTGATTTTAAATTAAATG
1 TTATGATCATATATTTAATCTAATTAAAATTTTTAACGTATCATCAATTGATTTTAAATTAAAT-
* *
3286531 GATTTATAGTTAAATTTCATTTTCTTCTTT-AGATCA-AACATTTTTT
65 GATTTAAAGTTAAATTT-AATTTCTTCTTTGAGATCATAACATTTTTT
3286577 ATGAGAGCCC
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
128 64 0.70
129 18 0.20
130 10 0.11
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.54
Consensus pattern (128 bp):
TTATGATCATATATTTAATCTAATTAAAATTTTTAACGTATCATCAATTGATTTTAAATTAAATG
ATTTAAAGTTAAATTTAATTTCTTCTTTGAGATCATAACATTTTTTTTAAGTGTCAAATTTGT
Found at i:3291290 original size:2 final size:2
Alignment explanation
Indices: 3291283--3291326 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3291273 AGACCTGCAA
3291283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3291325 AT
1 AT
3291327 GTACATGCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3294836 original size:3 final size:3
Alignment explanation
Indices: 3294828--3294864 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3294818 TACCACAGAG
3294828 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
3294865 AAGTGCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3295884 original size:14 final size:15
Alignment explanation
Indices: 3295854--3295885 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3295844 AATGATCGAA
3295854 AAAATTAAATAAATT
1 AAAATTAAATAAATT
3295869 AAAATTAAAT-AATT
1 AAAATTAAATAAATT
3295883 AAA
1 AAA
3295886 GTCCGGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATTAAATAAATT
Found at i:3296039 original size:3 final size:3
Alignment explanation
Indices: 3296033--3296079 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
3296023 TTTTTTTTTT
* *
3296033 TTA TTA TTA TTA TTA TTA TTG TTA TTG TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3296080 GAAATATGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Done.