Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_pilon, whole genome shotgun sequence
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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 21
Found at i:3383378 original size:21 final size:21
Alignment explanation
Indices: 3383353--3383396 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3383343 AATTTAGTTA
3383353 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
3383374 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
3383395 AT
1 AT
3383397 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:3383397 original size:28 final size:28
Alignment explanation
Indices: 3383366--3383431 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
3383356 AGTTTGTTAG
3383366 TATAAATTATTAGTTTGTTAGTTTAAGT
1 TATAAATTATTAGTTTGTTAGTTTAAGT
*
3383394 TAT-ATTATATTAGTTTGTTAGTTTAAGT
1 TATAAAT-TATTAGTTTGTTAGTTTAAGT
*
3383422 TATATATTAT
1 TATAAATTAT
3383432 ATTATATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.91
29 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (28 bp):
TATAAATTATTAGTTTGTTAGTTTAAGT
Found at i:3383953 original size:10 final size:10
Alignment explanation
Indices: 3383938--3383971 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
3383928 AAATATTATT
3383938 TTTAAAATTA
1 TTTAAAATTA
3383948 TTTAAAATTA
1 TTTAAAATTA
3383958 TTTAAAATTA
1 TTTAAAATTA
3383968 TTTA
1 TTTA
3383972 GTGTTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTAAAATTA
Found at i:3384322 original size:15 final size:15
Alignment explanation
Indices: 3384252--3384327 Score: 70
Period size: 15 Copynumber: 5.3 Consensus size: 15
3384242 AGTAATCATG
*
3384252 ATTAAATCATATTATT
1 ATTAAATCAT-TAATT
*
3384268 ATTAAATCATTAAAT
1 ATTAAATCATTAATT
* *
3384283 ATCAAATCATT-A-G
1 ATTAAATCATTAATT
*
3384296 ATT-AAT-AATAATT
1 ATTAAATCATTAATT
3384309 ATTAAATCATTAATT
1 ATTAAATCATTAATT
3384324 ATTA
1 ATTA
3384328 TTAATATTAG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
11 2 0.04
12 4 0.08
13 5 0.10
14 4 0.08
15 23 0.48
16 10 0.21
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (15 bp):
ATTAAATCATTAATT
Found at i:3387311 original size:25 final size:25
Alignment explanation
Indices: 3387282--3387329 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
3387272 TGATATAACT
*
3387282 TGATTTAGTAATG-ATTTGATAATCA
1 TGATTTAATAATGAATTT-ATAATCA
3387307 TGATTTAATAATGAATTTATAAT
1 TGATTTAATAATGAATTTATAAT
3387330 TAAAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (25 bp):
TGATTTAATAATGAATTTATAATCA
Found at i:3387408 original size:49 final size:49
Alignment explanation
Indices: 3387290--3387562 Score: 374
Period size: 49 Copynumber: 5.6 Consensus size: 49
3387280 CTTGATTTAG
* * * * *
3387290 TAATGATTTGATAATCATGATT--TAATAATGAATTTATAATTAAAATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* * *
3387337 ATAATAATTAT-TTAGTAATGATTAGTAATAATAAAATTATTATTAATATT
1 -TAATGATT-TGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
3387387 TAATGATTTGTTAGTAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
*
3387436 TAATGATTT-AGTAGTAATGATTAGTAATAATAAAATTATTATTAATATT
1 TAATGATTTGA-TAGTAATGATTAGTAATAATGAAATTATTATTAATATT
* *
3387485 TAATGATTTGGTAGTAATGATTAGTAATAATGAAATTATTTTTAATATT
1 TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
3387534 TAATGATTTGATAGTAATGATTTAGTAAT
1 TAATGATTTGATAGTAATGA-TTAGTAAT
3387563 TATTAGTAAT
Statistics
Matches: 202, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
48 17 0.08
49 156 0.77
50 29 0.14
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (49 bp):
TAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:3387720 original size:26 final size:26
Alignment explanation
Indices: 3387686--3387803 Score: 141
Period size: 26 Copynumber: 4.5 Consensus size: 26
3387676 TATTATGATT
*
3387686 TAATAATGATTTAGTAATAATCGTTA
1 TAATAATGATTTAGTAATAATCATTA
* * *
3387712 TAATAATGATTTAATAATGAT-TTTAA
1 TAATAATGATTTAGTAATAATCATT-A
*
3387738 TATTTAATGATTT-GATAATAATCATTA
1 TA-ATAATGATTTAG-TAATAATCATTA
*
3387765 TAATAATGATTTAGTAATAATCATTC
1 TAATAATGATTTAGTAATAATCATTA
3387791 TAATAATGATTTA
1 TAATAATGATTTA
3387804 AATATTTAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
25 2 0.03
26 55 0.71
27 19 0.24
28 2 0.03
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (26 bp):
TAATAATGATTTAGTAATAATCATTA
Found at i:3387856 original size:26 final size:26
Alignment explanation
Indices: 3387826--3388090 Score: 277
Period size: 26 Copynumber: 10.6 Consensus size: 26
3387816 TTTGATGATT
*
3387826 TAATAATGATTTGATAATAATCATTA
1 TAATAATGATTTAATAATAATCATTA
* *
3387852 TAATAATGATTTAGTAATAATCATTC
1 TAATAATGATTTAATAATAATCATTA
*
3387878 TAAGAATGATTTAATAAT-A--ATT-
1 TAATAATGATTTAATAATAATCATTA
* * *
3387900 T--TAAT-ATTTAATGATTTGATGATT-
1 TAATAATGATTTAAT-A-ATAATCATTA
* *
3387924 TAGTAATGATTTGATAATAATCATTA
1 TAATAATGATTTAATAATAATCATTA
*
3387950 TAATAATGATTTAATAATAATCATTC
1 TAATAATGATTTAATAATAATCATTA
*
3387976 TAATAATGATTTAATAAT-A--ATGA
1 TAATAATGATTTAATAATAATCATTA
3387999 TAATAATGATTTAATAATAATCATTA
1 TAATAATGATTTAATAATAATCATTA
* *
3388025 TAATAATGATTTAATAGTAATGATT-
1 TAATAATGATTTAATAATAATCATTA
* * *
3388050 TAATAATGATTTAGTAATGAT-TTTA
1 TAATAATGATTTAATAATAATCATTA
3388075 TAATAATGATTTAATA
1 TAATAATGATTTAATA
3388091 CATTTAATAA
Statistics
Matches: 202, Mismatches: 24, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
19 7 0.03
20 4 0.02
21 1 0.00
22 2 0.01
23 23 0.11
24 7 0.03
25 41 0.20
26 111 0.55
27 6 0.03
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (26 bp):
TAATAATGATTTAATAATAATCATTA
Found at i:3387893 original size:49 final size:48
Alignment explanation
Indices: 3387683--3388090 Score: 196
Period size: 49 Copynumber: 8.4 Consensus size: 48
3387673 TAATATTATG
* * *
3387683 ATTTAATAATGATTTAGTAATAATCGTTATAATAATGATTTAATAATG
1 ATTTAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATC
*
3387731 ATTTTAATATTTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATC
1 A-TTT-A-A--TAATGATTTAATAATAATCATTATAATAATGA-TT--TAATAATC
* * *
3387787 ATTCTAATAATGA-TT--T-A-AAT-A-T-T--TAATGATTTGATGATTT
1 ATT-TAATAATGATTTAATAATAATCATTATAATAATGATTTAAT-AATC
* *
3387827 A-ATA---ATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATC
1 ATTTAATAATGATTTAATAATAATCATTATAATAATGA-TT--TAATAATC
* * * * * *
3387874 ATTCTAAGAATGATTTAATAATAAT-TTTAATATTTAATGATTTGATGATTT
1 ATT-TAATAATGATTTAATAATAATCATT-ATA-ATAATGATTTAAT-AATC
* * *
3387925 A-GTAATG---ATTTGATAATAATCATTATAATAATGATTTAATAATAATC
1 ATTTAATAATGATTTAATAATAATCATTATAATAATGA-TT--TAATAATC
*
3387972 ATTCTAATAATGATTTAATAAT-A--ATGATAATAATGATTTAATAATAATC
1 ATT-TAATAATGATTTAATAATAATCATTATAATAATGA-TT--TAATAATC
* * * *
3388021 ATTATAATAATGATTTAATAGTAATGATT-TAATAATGATTTAGTAATG
1 ATT-TAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATC
3388069 ATTTTATAATAATGATTTAATA
1 A--TT-TAATAATGATTTAATA
3388091 CATTTAATAA
Statistics
Matches: 279, Mismatches: 36, Indels: 88
0.69 0.09 0.22
Matches are distributed among these distances:
35 4 0.01
36 2 0.01
38 3 0.01
39 4 0.01
40 6 0.02
41 3 0.01
42 7 0.03
43 1 0.00
44 1 0.00
45 13 0.05
46 20 0.07
47 11 0.04
48 15 0.05
49 58 0.21
50 26 0.09
51 18 0.06
52 37 0.13
53 35 0.13
54 3 0.01
55 3 0.01
56 9 0.03
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (48 bp):
ATTTAATAATGATTTAATAATAATCATTATAATAATGATTTAATAATC
Found at i:3388304 original size:59 final size:56
Alignment explanation
Indices: 3388185--3388305 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 56
3388175 TCGAATTTAT
* * ** *
3388185 TAATGATTTTTAAATATTTAATGATTTGATACTAATGATTTAGTAATTATTATTAA
1 TAATGATTTTTAAATATTTAATGATTTGATACTAATGAATTACTAAAGATTACTAA
* *
3388241 TAATGATTTATTACTAATATTTAATTATTTGATACTAATGAATTACTAAAGATTACTAG
1 TAATGATTT-TTA--AATATTTAATGATTTGATACTAATGAATTACTAAAGATTACTAA
3388300 TAATGA
1 TAATGA
3388306 AATTATAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
56 9 0.16
57 3 0.05
59 43 0.78
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.46
Consensus pattern (56 bp):
TAATGATTTTTAAATATTTAATGATTTGATACTAATGAATTACTAAAGATTACTAA
Found at i:3388318 original size:59 final size:59
Alignment explanation
Indices: 3388197--3388318 Score: 147
Period size: 59 Copynumber: 2.1 Consensus size: 59
3388187 ATGATTTTTA
* * ** * * *
3388197 AATATTTAATGATTTGATACTAATGATTTAGTAATTATTATTAATAATGATTTATTACT
1 AATATTTAATGATTTGATACTAATGAATTACTAAAGATTACTAATAATGAATTATTAAT
* *
3388256 AATATTTAATTATTTGATACTAATGAATTACTAAAGATTACTAGTAATGAAATTA-TAAT
1 AATATTTAATGATTTGATACTAATGAATTACTAAAGATTACTAATAATG-AATTATTAAT
3388315 AATA
1 AATA
3388319 ATTTGATACT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 49 0.92
60 4 0.08
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.44
Consensus pattern (59 bp):
AATATTTAATGATTTGATACTAATGAATTACTAAAGATTACTAATAATGAATTATTAAT
Found at i:3390771 original size:45 final size:46
Alignment explanation
Indices: 3390716--3390803 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
3390706 CTTAACTATT
*
3390716 TAACTAAAACAAACTAATTAAATAATTTTT-TTATATAACTAACGAC
1 TAACTAAAACAAACTAATT-AATAATTTTTACTATATAACTAACGAC
*
3390762 TAAC-AAAACAAACTAATTAATTATTTTTAACTATATAACTAA
1 TAACTAAAACAAACTAATTAATAATTTTT-ACTATATAACTAA
3390804 AATAATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 9 0.24
45 14 0.37
46 15 0.39
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.35
Consensus pattern (46 bp):
TAACTAAAACAAACTAATTAATAATTTTTACTATATAACTAACGAC
Found at i:3393484 original size:23 final size:24
Alignment explanation
Indices: 3393444--3393489 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
3393434 TTGTTTATAT
**
3393444 TTTATATTTTAATTTAAATAAATA
1 TTTATATTTTAAAATAAATAAATA
3393468 TTTAT-TTTTAAAATAAATAAAT
1 TTTATATTTTAAAATAAATAAAT
3393490 CCTCGAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTATATTTTAAAATAAATAAATA
Found at i:3394944 original size:22 final size:22
Alignment explanation
Indices: 3394913--3394954 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3394903 ATATATATAT
*
3394913 ATATATTAAAT-TATTTAAATAA
1 ATATAATAAATATA-TTAAATAA
3394935 ATATAATAAATATATTAAAT
1 ATATAATAAATATATTAAAT
3394955 TATAGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAATAAATATATTAAATAA
Found at i:3395029 original size:12 final size:13
Alignment explanation
Indices: 3394993--3395038 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
3394983 AAATGGGTTT
*
3394993 AATATTTTTATTTA
1 AATATTATT-TTTA
3395007 AACTA-TATTTTTA
1 AA-TATTATTTTTA
3395020 AA-ATTATTTTTA
1 AATATTATTTTTA
3395032 AATATTA
1 AATATTA
3395039 ATATATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
11 1 0.04
12 10 0.36
13 10 0.36
14 5 0.18
15 2 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
AATATTATTTTTA
Found at i:3395170 original size:26 final size:26
Alignment explanation
Indices: 3395122--3395180 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
3395112 TTATTTTTAT
3395122 AATTATTTTAAATAAAAATATA-T-A
1 AATTATTTTAAATAAAAATATATTAA
3395146 AATTATATTTAAA-ATAAAATAATATTAA
1 AATTAT-TTTAAATA-AAAAT-ATATTAA
3395174 AATTATT
1 AATTATT
3395181 AGAGAATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
24 7 0.23
25 11 0.37
26 3 0.10
27 2 0.07
28 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATTATTTTAAATAAAAATATATTAA
Found at i:3404442 original size:10 final size:10
Alignment explanation
Indices: 3404424--3404464 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
3404414 TTTCATTACA
3404424 TCAAATTCTC
1 TCAAATTCTC
*
3404434 TCAATTTCTC
1 TCAAATTCTC
*
3404444 TCAACTTCTC
1 TCAAATTCTC
*
3404454 TCAAATACTC
1 TCAAATTCTC
3404464 T
1 T
3404465 TATAATCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:3404538 original size:21 final size:20
Alignment explanation
Indices: 3404484--3404544 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
3404474 TGTCTAAGAT
3404484 ATATTTTATT-ATATT-TTTA
1 ATATTTTATTAAT-TTATTTA
3404503 ATATTTTGTATTTAATTTATTTA
1 ATA-TTT-TA-TTAATTTATTTA
3404526 ATATTTTACTTAA-TTATTT
1 ATATTTTA-TTAATTTATTT
3404545 TTTTGCATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
19 3 0.08
20 9 0.25
21 8 0.22
22 7 0.19
23 9 0.25
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
ATATTTTATTAATTTATTTA
Found at i:3406787 original size:26 final size:26
Alignment explanation
Indices: 3406732--3406791 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
3406722 ATTGATAGAT
* *
3406732 TTTTTTATTATATTTGTATTTAGTAC
1 TTTTTTATTATAGTTGTATTTAGGAC
*
3406758 -TTTTTATTATAGTTGT-TTATTGGAC
1 TTTTTTATTATAGTTGTATT-TAGGAC
3406783 TTTTTTATT
1 TTTTTTATT
3406792 GTAATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.07
25 19 0.66
26 8 0.28
ACGTcount: A:0.20, C:0.03, G:0.10, T:0.67
Consensus pattern (26 bp):
TTTTTTATTATAGTTGTATTTAGGAC
Found at i:3406898 original size:34 final size:34
Alignment explanation
Indices: 3406843--3406913 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
3406833 CGTTAATATG
3406843 GTTGGATTTATTTTAATTTATTTTG-TTAAATTT
1 GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
*
3406876 GTTGGACTTT-TTGTTAATTTATTTTGCTTAATTTT
1 GTTGGA-TTTATT-TTAATTTATTTTGCTTAAATTT
3406911 GTT
1 GTT
3406914 TATTACCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 8 0.24
34 16 0.47
35 10 0.29
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (34 bp):
GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
Found at i:3417001 original size:23 final size:24
Alignment explanation
Indices: 3416955--3417022 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 24
3416945 TTTTTACTTC
* *
3416955 AATATAAAATTTGTAATATTATAAT
1 AATATAAAATAT-AAATATTATAAT
3416980 -ATA-AAAAT-TAAAT-TTATAAT
1 AATATAAAATATAAATATTATAAT
*
3417000 AATATATAATATAAATATTATAA
1 AATATAAAATATAAATATTATAA
3417023 AGTATGACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 7 0.19
21 6 0.16
22 5 0.14
23 10 0.27
24 9 0.24
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
AATATAAAATATAAATATTATAAT
Found at i:3430701 original size:19 final size:20
Alignment explanation
Indices: 3430659--3430701 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3430649 AAATAAGATG
*
3430659 TTAAAAGAAAATAATAATAA
1 TTAAAAGAAAATAACAATAA
3430679 -TAAAAGAAAATAACAA-AA
1 TTAAAAGAAAATAACAATAA
3430697 TTAAA
1 TTAAA
3430702 GAGTAAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (20 bp):
TTAAAAGAAAATAACAATAA
Found at i:3430786 original size:18 final size:16
Alignment explanation
Indices: 3430763--3430823 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 16
3430753 GGATAAAACA
3430763 AATAAAAAAATGAAATTG
1 AATAAAAAAAT-AAA-TG
3430781 AATAAAATAAAATAAATG
1 AAT-AAA-AAAATAAATG
* *
3430799 AAGAAAAAAATATAT-
1 AATAAAAAAATAAATG
3430814 ATATAAAAAA
1 A-ATAAAAAA
3430824 GAATAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 1 0.03
16 15 0.41
17 3 0.08
18 7 0.19
19 6 0.16
20 5 0.14
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (16 bp):
AATAAAAAAATAAATG
Found at i:3430928 original size:26 final size:26
Alignment explanation
Indices: 3430899--3430953 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
3430889 TAATGAAAAT
* *
3430899 AAATAAATAGTATACAT-AAAATAATA
1 AAATAAAAAATATACATAAAAAT-ATA
*
3430925 AAATAAAAAATATATATAAAAATATA
1 AAATAAAAAATATACATAAAAATATA
3430951 AAA
1 AAA
3430954 ATGTATGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (26 bp):
AAATAAAAAATATACATAAAAATATA
Found at i:3431109 original size:25 final size:25
Alignment explanation
Indices: 3431081--3431128 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3431071 AAGTAAGAAT
3431081 ATATATATAGATAAAAAATAATATA
1 ATATATATAGATAAAAAATAATATA
* * *
3431106 ATATATATATATATATAATAATA
1 ATATATATAGATAAAAAATAATA
3431129 GGAAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
ATATATATAGATAAAAAATAATATA
Found at i:3431141 original size:36 final size:35
Alignment explanation
Indices: 3431079--3431146 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
3431069 TGAAGTAAGA
3431079 ATATATATATAGATAAAAAATAATATAATATATAT
1 ATATATATATAGATAAAAAATAATATAATATATAT
*
3431114 ATATATATAATA-ATAGGAAAATAATATAATATA
1 ATATATAT-ATAGATA-AAAAATAATATAATATA
3431147 ACGCAAAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (35 bp):
ATATATATATAGATAAAAAATAATATAATATATAT
Found at i:3431181 original size:10 final size:9
Alignment explanation
Indices: 3431168--3431205 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
3431158 AATGAAAAAA
3431168 AAATTATAAT
1 AAATTA-AAT
3431178 AAA-TAAAT
1 AAATTAAAT
3431186 AAATTAAAT
1 AAATTAAAT
3431195 ATAATTAAAT
1 A-AATTAAAT
3431205 A
1 A
3431206 TATATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 6 0.23
9 8 0.31
10 12 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTAAAT
Found at i:3431203 original size:19 final size:18
Alignment explanation
Indices: 3431168--3431205 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
3431158 AATGAAAAAA
3431168 AAATTATAATAAATAAAT
1 AAATTATAATAAATAAAT
3431186 AAATTA-AATATAATTAAAT
1 AAATTATAATA-AA-TAAAT
3431205 A
1 A
3431206 TATATATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTATAATAAATAAAT
Found at i:3431673 original size:37 final size:37
Alignment explanation
Indices: 3431624--3431728 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
3431614 GTGCTTGTGG
* * *
3431624 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
* * * *
3431661 ATTCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
3431698 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
3431729 GACGAAAAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:3432660 original size:106 final size:106
Alignment explanation
Indices: 3432476--3433431 Score: 1450
Period size: 106 Copynumber: 9.0 Consensus size: 106
3432466 GCATTGTTCC
* * * * *
3432476 GAGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
3432541 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3432582 GAGTCTAATATCCTTTGTTGTGAAGTTGAAATTGGCTCCGAAATTAGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3432647 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3432688 GAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
3432753 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
3432794 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
3432859 CCAGCGGTCCC-TCGTTGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3432899 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3432964 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGGGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3433005 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
3433070 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3433111 GAGTCCAATATCCTTCGCTGTGAAGTTCAATTTGGCTCTGAAATT-GGAAAGTTGCTTATTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACA
*
3433175 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3433217 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3433282 TCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
3433323 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTAGAAAATT-ATTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
3433387 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
3433428 GAGT
1 GAGT
3433432 GGCACGATAT
Statistics
Matches: 777, Mismatches: 70, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
105 151 0.19
106 621 0.80
107 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3433262 original size:423 final size:424
Alignment explanation
Indices: 3432476--3433431 Score: 1517
Period size: 423 Copynumber: 2.3 Consensus size: 424
3432466 GCATTGTTCC
* * * *
3432476 GAGTCCAATATCCTCCG-TCGTGAAGTTAAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* **
3432540 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTTGTTGTGA
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCATTGTGA
3432605 AGTTGAAATTGGCTCCGAAATTAGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
130 AGTTGAAATTGGCTCCGAAATTAGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
* * *
3432670 TTGAACTTGCGTTGTCTTGAGTCCAATATTCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGG
195 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTCAAATTGGCTCTGAAATTGG
* *
3432735 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
260 GAAATTGCTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
* * * *
3432800 AATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCG
325 AATATCCTTCGTTGTGAAGTTGAAATTAGATCTGAAATTGAGAAATTGTTTATTGACAACCAGCG
* *
3432865 GTCCC-TCGTTGTGAAGTTGAACTTGTGTTGTCTG
390 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
3432899 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
3432964 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGGGTTGTCTGGAGTCCAATATCCTTCATTGTGAA
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCATTGTGAA
* * *
3433029 GTTGAAATTGGCTCTGAAATT-GAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAG
131 GTTGAAATTGGCTCCGAAATTAG-GAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAG
*
3433093 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTCAATTTGGCTCTGAAATT-G
195 TTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTCAAATTGGCTCTGAAATTGG
*
3433157 GAAAGTTGCTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTC
260 GAAA-TTGCTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
* *
3433222 CAATATCCTTCGTTGTGAAGTTGAAATTAGATCTGAAATTGGGAAATTGTTTATTGACAATCAGC
324 CAATATCCTTCGTTGTGAAGTTGAAATTAGATCTGAAATTGAGAAATTGTTTATTGACAACCAGC
3433287 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
389 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
3433323 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTAGAAAATT-ATTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
3433387 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
3433432 GGCACGATAT
Statistics
Matches: 486, Mismatches: 43, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
422 6 0.01
423 404 0.83
424 76 0.16
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (424 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCATTGTGAA
GTTGAAATTGGCTCCGAAATTAGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTCAAATTGGCTCTGAAATTGGG
AAATTGCTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
ATATCCTTCGTTGTGAAGTTGAAATTAGATCTGAAATTGAGAAATTGTTTATTGACAACCAGCGG
TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:3434282 original size:22 final size:22
Alignment explanation
Indices: 3434256--3434332 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
3434246 TTATGTTTGG
3434256 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
3434278 TCAAAGGTTTGGCATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
3434300 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
3434322 TCAACGGTTTG
1 TCAAAGGTTTG
3434333 ATGGGGTAGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3434969 original size:16 final size:15
Alignment explanation
Indices: 3434950--3435008 Score: 57
Period size: 16 Copynumber: 3.7 Consensus size: 15
3434940 TTCTTTTTGA
3434950 TTTTTGTTCTTTCTTT
1 TTTTTGTT-TTTCTTT
3434966 TTTTTG-TTTTCTTCT
1 TTTTTGTTTTTCTT-T
*
3434981 TTTTTGCTTTTTTTCTT
1 TTTTTG-TTTTTCT-TT
*
3434998 TTTTTATTTTT
1 TTTTTGTTTTT
3435009 TTGCCCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 6 0.16
15 8 0.22
16 11 0.30
17 11 0.30
18 1 0.03
ACGTcount: A:0.02, C:0.10, G:0.05, T:0.83
Consensus pattern (15 bp):
TTTTTGTTTTTCTTT
Found at i:3434980 original size:17 final size:16
Alignment explanation
Indices: 3434950--3435002 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
3434940 TTCTTTTTGA
*
3434950 TTTTTGTTCTTTCTTT
1 TTTTTGTTTTTTCTTT
3434966 TTTTTGTTTTCTTCTTT
1 TTTTTGTTTT-TTCTTT
*
3434983 TTTGCT-TTTTTTCTTT
1 TTT-TTGTTTTTTCTTT
3434999 TTTT
1 TTTT
3435003 ATTTTTTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 18 0.56
17 13 0.41
18 1 0.03
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTGTTTTTTCTTT
Found at i:3435002 original size:8 final size:8
Alignment explanation
Indices: 3434959--3435010 Score: 61
Period size: 8 Copynumber: 6.4 Consensus size: 8
3434949 ATTTTTGTTC
3434959 TTTCTTTT
1 TTTCTTTT
3434967 TTT-TGTTT
1 TTTCT-TTT
3434975 TCTTCTTTT
1 T-TTCTTTT
*
3434984 TTGCTTTT
1 TTTCTTTT
3434992 TTTCTTTT
1 TTTCTTTT
*
3435000 TTTATTTT
1 TTTCTTTT
3435008 TTT
1 TTT
3435011 GCCCTTTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
7 1 0.03
8 30 0.79
9 6 0.16
10 1 0.03
ACGTcount: A:0.02, C:0.10, G:0.04, T:0.85
Consensus pattern (8 bp):
TTTCTTTT
Found at i:3439568 original size:19 final size:20
Alignment explanation
Indices: 3439526--3439568 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3439516 AAATAAGATG
*
3439526 TTAAAAGAAAATAATAATAA
1 TTAAAAGAAAATAACAATAA
3439546 -TAAAAGAAAATAACAA-AA
1 TTAAAAGAAAATAACAATAA
3439564 TTAAA
1 TTAAA
3439569 GAGTAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (20 bp):
TTAAAAGAAAATAACAATAA
Found at i:3439655 original size:20 final size:18
Alignment explanation
Indices: 3439630--3439677 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
3439620 GGATGAAACA
3439630 AATAAAAAAAAATGAAATTG
1 AATAAAAAAAAAT-AAA-TG
*
3439650 AATAAAATAAAATAAATG
1 AATAAAAAAAAATAAATG
*
3439668 AAGAAAAAAA
1 AATAAAAAAA
3439678 TATATATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 3 0.12
20 12 0.48
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (18 bp):
AATAAAAAAAAATAAATG
Found at i:3439785 original size:22 final size:19
Alignment explanation
Indices: 3439760--3439813 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 19
3439750 AAACATAATG
3439760 AAAATAAATAAATAGTATACA
1 AAAATAAA-AAATA-TATACA
*
3439781 TAAAATAAAAAATATATATA
1 -AAAATAAAAAATATATACA
3439801 AAAATATAAAAAT
1 AAAATA-AAAAAT
3439814 GTATGTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 6 0.20
20 11 0.37
21 5 0.17
22 8 0.27
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATAAAAAATATATACA
Found at i:3439788 original size:18 final size:18
Alignment explanation
Indices: 3439765--3439813 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
3439755 TAATGAAAAT
* *
3439765 AAATAAATAGTATACATA
1 AAATAAAAAATATACATA
*
3439783 AAATAAAAAATATATATAA
1 AAATAAAAAATATACAT-A
3439802 AAATATAAAAAT
1 AAATA-AAAAAT
3439814 GTATGTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 14 0.54
19 6 0.23
20 6 0.23
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATAAAAAATATACATA
Found at i:3439809 original size:21 final size:21
Alignment explanation
Indices: 3439760--3439812 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3439750 AAACATAATG
*
3439760 AAAATAAATAAATAGTATACAT
1 AAAATAAA-AAATAGTATACAA
*
3439782 AAAATAAAAAATA-TATATAA
1 AAAATAAAAAATAGTATACAA
3439802 AAATATAAAAA
1 AAA-ATAAAAA
3439813 TGTATGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 8 0.29
21 12 0.43
22 8 0.29
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (21 bp):
AAAATAAAAAATAGTATACAA
Found at i:3440105 original size:2 final size:2
Alignment explanation
Indices: 3440098--3440144 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3440088 AATAAATTAA
3440098 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
*
3440140 TT AT A
1 AT AT A
3440145 CATTGGTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3440587 original size:37 final size:37
Alignment explanation
Indices: 3440546--3440635 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
3440536 GGATCTTATC
* * * *
3440546 TTTAGGAGTTTAAATCATAGTAGAACTCTATTATATT
1 TTTAGGAGTTTGAATCATAATAAAACTCTATCATATT
* * *
3440583 TTTAGGAGTTTGAATCCTAATAAAATTTTATCATATT
1 TTTAGGAGTTTGAATCATAATAAAACTCTATCATATT
*
3440620 TTTAAGAGTTTGAATC
1 TTTAGGAGTTTGAATC
3440636 CTATTAGGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.44
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCATAATAAAACTCTATCATATT
Found at i:3442334 original size:24 final size:24
Alignment explanation
Indices: 3442268--3442337 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 24
3442258 TTACTTTTTT
*
3442268 TTATTTTATTCATTTGACTTTCTATTA
1 TTATTTTATT--TTTTA-TTTCTATTA
3442295 TTATTTTAATTTTTTATTTC-ATTA
1 TTATTTT-ATTTTTTATTTCTATTA
3442319 TTATTGTT-TTTGTTTATTT
1 TTATT-TTATTT-TTTATTT
3442338 TCTTTTTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 3 0.08
24 16 0.41
25 6 0.15
26 4 0.10
27 7 0.18
28 3 0.08
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (24 bp):
TTATTTTATTTTTTATTTCTATTA
Found at i:3445371 original size:6 final size:6
Alignment explanation
Indices: 3445360--3445384 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3445350 AAGATAAAAG
3445360 AAACAA AAACAA AAACAA AAACAA A
1 AAACAA AAACAA AAACAA AAACAA A
3445385 GGAAAAAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:3447246 original size:36 final size:37
Alignment explanation
Indices: 3447143--3447267 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 37
3447133 TTTGAGATTG
* *** *
3447143 TTCTCTCGAAACAAAGGGCTGTCTCTCTTGAGACTAAT
1 TTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGAC-AGT
* * *
3447181 TTACTC--AAAACAAAGTTTTGCCTCCCTTGAGACAGT
1 TT-CTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT
3447217 TTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAGT
1 TTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT
*
3447253 TTCCCTTGAAACAAA
1 TTCTCTTGAAACAAA
3447268 ATCTTTGAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
35 3 0.04
36 37 0.51
37 28 0.38
38 2 0.03
39 3 0.04
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (37 bp):
TTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGT
Found at i:3447381 original size:21 final size:21
Alignment explanation
Indices: 3447356--3447442 Score: 96
Period size: 21 Copynumber: 4.4 Consensus size: 21
3447346 TGAGACAGTT
3447356 TCTCTTGAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
*
3447377 TCTCTTCAAACAAATTTTGTC
1 TCTCTTGAAACAAATTTTGTC
* *
3447398 TCTCTTGAGAC--A-GTT-TC
1 TCTCTTGAAACAAATTTTGTC
3447415 -C-CTTGAAACAAAGTTTTGTC
1 TCTCTTGAAACAAA-TTTTGTC
3447435 TCTCTTGA
1 TCTCTTGA
3447443 GATAGTTTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 7 0.13
16 1 0.02
17 3 0.06
18 2 0.04
19 3 0.06
20 2 0.04
21 30 0.57
22 5 0.09
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.41
Consensus pattern (21 bp):
TCTCTTGAAACAAATTTTGTC
Found at i:3447381 original size:36 final size:36
Alignment explanation
Indices: 3447280--3447382 Score: 143
Period size: 37 Copynumber: 2.8 Consensus size: 36
3447270 CTTTGAATAT
* * *
3447280 GTTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
3447316 GTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
3447353 GTTTCTCTTGAAACAAATTTTGTCTCTCTT
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTT
3447383 CAAACAAATT
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 26 0.46
37 31 0.54
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.45
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:3447405 original size:94 final size:94
Alignment explanation
Indices: 3447285--3447461 Score: 282
Period size: 94 Copynumber: 1.9 Consensus size: 94
3447275 AATATGTTTT
* ** * *
3447285 TCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAG
1 TCTTCAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAG
3447350 ACAGTTTCTCTTGAAACAAATTTTGTCTC
66 ACAGTTTCTCTTGAAACAAATTTTGTCTC
* *
3447379 TCTTCAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAG
1 TCTTCAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAG
*
3447444 ATAGTTTCTCTTGAAACA
66 ACAGTTTCTCTTGAAACA
3447462 CCAACCTTTG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 75 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (94 bp):
TCTTCAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAG
ACAGTTTCTCTTGAAACAAATTTTGTCTC
Found at i:3447434 original size:37 final size:36
Alignment explanation
Indices: 3447384--3447461 Score: 129
Period size: 37 Copynumber: 2.1 Consensus size: 36
3447374 GTCTCTCTTC
3447384 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* *
3447420 AAACAAAGTTTTGTCTCTCTTGAGATAGTTTCTCTTG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
3447457 AAACA
1 AAACA
3447462 CCAACCTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 7 0.18
37 32 0.82
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:3447572 original size:33 final size:33
Alignment explanation
Indices: 3447514--3447634 Score: 154
Period size: 33 Copynumber: 3.6 Consensus size: 33
3447504 CCTGGAGACA
* *
3447514 GTTTCTCTTTAAGCACAAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACAC-AAAAAACCTTTGAAATC
* *
3447548 GTTTATCTTGAAACGCAAAAAACCTTTGAAATC
1 GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
*
3447581 GTTTCTCTTGAAACATAAAAAAAACCTTTGAAAAT-
1 GTTTCTCTTGAAAC--ACAAAAAACCTTTG-AAATC
3447616 GTTTCTCTTGAAACACAAA
1 GTTTCTCTTGAAACACAAA
3447635 GACCCTCGAG
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
33 34 0.45
34 12 0.16
35 26 0.34
36 4 0.05
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.31
Consensus pattern (33 bp):
GTTTCTCTTGAAACACAAAAAACCTTTGAAATC
Found at i:3447775 original size:85 final size:84
Alignment explanation
Indices: 3447627--3447956 Score: 378
Period size: 85 Copynumber: 3.9 Consensus size: 84
3447617 TTTCTCTTGA
* *
3447627 AACACAAAGACCCTCGAGTTCGACTACATTCAGCTTCGATGGAAAATCATTTGCAACATAGCTCA
1 AACA-AAAGACCTTCGAGTTCGACTACATTCAAC-TCGATGGAAAATCATTTGCAACATAGCTCA
3447692 AGGCAAGAAGGGCCATTTGCC
64 AGGCAAGAAGGGCCATTTGCC
3447713 AACAAAAGACCTTCGAGTTCGACTACATTCAACTTCGATGGAAAATCATTTGCAACATAGCTCAA
1 AACAAAAGACCTTCGAGTTCGACTACATTCAAC-TCGATGGAAAATCATTTGCAACATAGCTCAA
3447778 GGCAAGAAGGGCCATTTGCC
65 GGCAAGAAGGGCCATTTGCC
** * * * * * * * *
3447798 AACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG-TAGATAACTCAAG
1 AACAAAAGACCTTCGAGTTCGACTACATTCAACTCGATGGAAAATCATTTGCAACATAGCTCAAG
* * ** * *
3447862 GCTATAAGGGTTATCTGTC
66 GCAAGAAGGGCCATTTGCC
* * * * *
3447881 ATC-AAAGACCTTCGAGTTCGATTACATTCAACTCAGA-GGCAAATCAAATTTACAGCATAGCTC
1 AACAAAAGACCTTCGAGTTCGACTACATTCAACTC-GATGGAAAATC--ATTTGCAACATAGCTC
3447944 AAGGCAAGAAGGG
63 AAGGCAAGAAGGG
3447957 TTATCTGCTA
Statistics
Matches: 208, Mismatches: 32, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
82 34 0.16
83 26 0.12
84 18 0.09
85 126 0.61
86 4 0.02
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (84 bp):
AACAAAAGACCTTCGAGTTCGACTACATTCAACTCGATGGAAAATCATTTGCAACATAGCTCAAG
GCAAGAAGGGCCATTTGCC
Found at i:3449307 original size:24 final size:25
Alignment explanation
Indices: 3449257--3449322 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
3449247 TTACTTTTTT
* *
3449257 TTATTTTATTCATTTGACTTTCTATTA
1 TTATTTTATT-GTTTTA-TTTCTATTA
3449284 TTATTTTGATT-TTTTATTTC-ATTA
1 TTATTTT-ATTGTTTTATTTCTATTA
3449308 TTATTTTATTGTTTT
1 TTATTTTATTGTTTT
3449323 TGTTTATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
23 3 0.08
24 15 0.42
25 4 0.11
26 4 0.11
27 7 0.19
28 3 0.08
ACGTcount: A:0.20, C:0.06, G:0.05, T:0.70
Consensus pattern (25 bp):
TTATTTTATTGTTTTATTTCTATTA
Found at i:3449357 original size:26 final size:25
Alignment explanation
Indices: 3449328--3449389 Score: 90
Period size: 24 Copynumber: 2.4 Consensus size: 25
3449318 GTTTTTGTTT
*
3449328 ATTTTCTTTTTTTTTACTAACTTTTA
1 ATTTTC-TTGTTTTTACTAACTTTTA
3449354 ATTTTC-TGTTTTTACTAACTTTTA
1 ATTTTCTTGTTTTTACTAACTTTTA
3449378 ATTTTCTCTGTT
1 ATTTTCT-TGTT
3449390 ACCTATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
24 23 0.70
26 10 0.30
ACGTcount: A:0.18, C:0.13, G:0.03, T:0.66
Consensus pattern (25 bp):
ATTTTCTTGTTTTTACTAACTTTTA
Found at i:3449370 original size:24 final size:24
Alignment explanation
Indices: 3449338--3449384 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
3449328 ATTTTCTTTT
3449338 TTTTTACTAACTTTTAATTTTCTG
1 TTTTTACTAACTTTTAATTTTCTG
3449362 TTTTTACTAACTTTTAATTTTCT
1 TTTTTACTAACTTTTAATTTTCT
3449385 CTGTTACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTTTACTAACTTTTAATTTTCTG
Found at i:3451597 original size:151 final size:151
Alignment explanation
Indices: 3451262--3451711 Score: 731
Period size: 151 Copynumber: 3.0 Consensus size: 151
3451252 TATTACACAC
* * * *
3451262 TGCGGAATGCGACTATCGGATAGAGCAAAATCACAACTGATAATTTGATAAAATAAAAATGAAGA
1 TGCGGAATACGGCTATCGGATAGAGCAAAATCGCAACTGATAATTTGAGAAAATAAAAATGAAGA
* *
3451327 TAAAGAAGACACAAATTTTACGTGAAAACCCCCTAAATAACATAGGGTAAAAACCACGGGCAACG
66 TAAAGAAGACACAAATTTTACGTGAAAA-ACCCTAAATAATATAGGGTAAAAACCACGGGCAACG
3451392 GTAGAAGAATTTCACTAATTGT
130 GTAGAAGAATTTCACTAATTGT
* *
3451414 TGCGGAATACAGCTATCGGATAGAGTAAAATCGCAACTGATAATTTGAGAAAATAAAAATGAAGA
1 TGCGGAATACGGCTATCGGATAGAGCAAAATCGCAACTGATAATTTGAGAAAATAAAAATGAAGA
*
3451479 TAAAGAAGACACAAATTTTACGTGAAAAACCACTAAA-AATATATGGTAAAAACCACGGGCAACG
66 TAAAGAAGACACAAATTTTACGTGAAAAACC-CTAAATAATATAGGGTAAAAACCACGGGCAACG
3451543 GTAGAAGAATTTCACTAATTGT
130 GTAGAAGAATTTCACTAATTGT
* *
3451565 TGCGGAATACGGCTATCGGACAGAGCAAAATCGCAACTGATAATTTGAGAAGATAAAAATGAAGA
1 TGCGGAATACGGCTATCGGATAGAGCAAAATCGCAACTGATAATTTGAGAAAATAAAAATGAAGA
* * *
3451630 TAAAGAAGACACAAATTTTATGTGGAAAACCCTTAAATAATATAGGGTAAAAACCACGAGCAACG
66 TAAAGAAGACACAAATTTTACGTGAAAAACCC-TAAATAATATAGGGTAAAAACCACGGGCAACG
*
3451695 GTAGAATAATTTCACTA
130 GTAGAAGAATTTCACTA
3451712 TGAGAAAATA
Statistics
Matches: 277, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
150 1 0.00
151 143 0.52
152 133 0.48
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.21
Consensus pattern (151 bp):
TGCGGAATACGGCTATCGGATAGAGCAAAATCGCAACTGATAATTTGAGAAAATAAAAATGAAGA
TAAAGAAGACACAAATTTTACGTGAAAAACCCTAAATAATATAGGGTAAAAACCACGGGCAACGG
TAGAAGAATTTCACTAATTGT
Found at i:3451773 original size:34 final size:34
Alignment explanation
Indices: 3451728--3451795 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
3451718 AATAAGAATT
*
3451728 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
3451763 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAAT
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAAT
3451796 TCTCAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 24 0.80
35 4 0.13
36 2 0.07
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:3453494 original size:35 final size:35
Alignment explanation
Indices: 3453401--3453496 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
3453391 AACATAGTCA
*
3453401 TCAATTACATTCTAAACCCCAAAATCCAAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATGCT
* * *
3453436 TCAATCATATTCTAAACCTCAAATTCCAAAATGCT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATGCT
* **
3453471 TCAATTACATGCCCAACCCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
3453497 ATAATCCATT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.40, C:0.30, G:0.03, T:0.27
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATGCT
Found at i:3453926 original size:142 final size:144
Alignment explanation
Indices: 3453658--3453946 Score: 440
Period size: 142 Copynumber: 2.0 Consensus size: 144
3453648 AAATACTCAA
*
3453658 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATAAAGTC
** * *
3453723 GAATTGAATTGAATTTTTGAGTTTATGTTTAAATTTAATAATAAATATTTATCATATTATAATA-
66 --A--GAATTGAATTTTCAAGTTTATGTTTAAATTTAATAATAAATATTTATAATACTATAATAT
3453787 TATTTTGATTCTAATTTAG
127 TA-TTTGATTCTAATTTAG
*
3453806 TTCAGTTTATAAAATATTTGACTCGAAA-TTTTTCGATTTGAGTTTATAAAATTTAAATAAAGTC
1 TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATAAAGTC
* *
3453870 -GAATTGAATTTTCAAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATT
66 AGAATTGAATTTTCAAGTTTATGTTTAAATTTAATAATAAATATTTATAATACTATAATATTATT
3453934 TGATTCTAATTTA
131 TGATTCTAATTTA
3453947 AATAGTTTTT
Statistics
Matches: 132, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
142 68 0.52
143 2 0.02
147 35 0.27
148 27 0.20
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (144 bp):
TTCAGTTTATAAAATAGTTGACTCGAAATTTTTTCGATTTGAGTTTATAAAATTTAAATAAAGTC
AGAATTGAATTTTCAAGTTTATGTTTAAATTTAATAATAAATATTTATAATACTATAATATTATT
TGATTCTAATTTAG
Found at i:3454031 original size:24 final size:24
Alignment explanation
Indices: 3454004--3454055 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
3453994 TATGTGATAT
3454004 ACATATATCATACAGAGTCAAGGG
1 ACATATATCATACAGAGTCAAGGG
*
3454028 ACATATATCATACAGAGTCGAGGG
1 ACATATATCATACAGAGTCAAGGG
3454052 ACAT
1 ACAT
3454056 GACTCAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (24 bp):
ACATATATCATACAGAGTCAAGGG
Found at i:3457162 original size:20 final size:20
Alignment explanation
Indices: 3457129--3457167 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3457119 CATATATCTT
*
3457129 TTATTTTCAGAAGGGACACC
1 TTATTTTCAGAAGGCACACC
* *
3457149 TTATTTTGATAAGGCACAC
1 TTATTTTCAGAAGGCACAC
3457168 GTCCCTATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (20 bp):
TTATTTTCAGAAGGCACACC
Found at i:3465811 original size:10 final size:10
Alignment explanation
Indices: 3465798--3465833 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
3465788 CGTTCGGTAA
3465798 TATGTTCGTT
1 TATGTTCGTT
3465808 TATGTTCGTT
1 TATGTTCGTT
*
3465818 TATGTTCATT
1 TATGTTCGTT
3465828 TATGTT
1 TATGTT
3465834 TAGCCCAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.14, C:0.08, G:0.17, T:0.61
Consensus pattern (10 bp):
TATGTTCGTT
Found at i:3466072 original size:34 final size:34
Alignment explanation
Indices: 3466032--3466096 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
3466022 CATTTATTGT
* * *
3466032 GTTCGTTTACATTCGTTTGTTTGTGTTCGTTAAC
1 GTTCGTTTACATCCATTTGTTTATGTTCGTTAAC
3466066 GTTCGTTTACATCCATTTGTTTATGTTCGTT
1 GTTCGTTTACATCCATTTGTTTATGTTCGTT
3466097 CATTTGTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.54
Consensus pattern (34 bp):
GTTCGTTTACATCCATTTGTTTATGTTCGTTAAC
Found at i:3466111 original size:24 final size:24
Alignment explanation
Indices: 3466000--3466113 Score: 81
Period size: 24 Copynumber: 4.8 Consensus size: 24
3465990 AAAATCTATT
* *
3466000 TTCATTTATGTTCGTTTATGTTCA
1 TTCATTTGTGTTCGTTTATGTTCG
* **
3466024 TTTA-TTGTGTTCGTTTACATTCG
1 TTCATTTGTGTTCGTTTATGTTCG
** * *
3466047 TTTGTTTGTGTTCGTTAACGTTCG
1 TTCATTTGTGTTCGTTTATGTTCG
***
3466071 TTTACATCCAT-TT-GTTTATGTTCG
1 -TT-CATTTGTGTTCGTTTATGTTCG
3466095 TTCATTTGTGTTCGTTTAT
1 TTCATTTGTGTTCGTTTAT
3466114 CATTTAAATG
Statistics
Matches: 67, Mismatches: 18, Indels: 10
0.71 0.19 0.11
Matches are distributed among these distances:
22 4 0.06
23 22 0.33
24 35 0.52
25 4 0.06
26 2 0.03
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (24 bp):
TTCATTTGTGTTCGTTTATGTTCG
Found at i:3468470 original size:24 final size:21
Alignment explanation
Indices: 3468424--3468473 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
3468414 ATATGTATTT
3468424 TAATAATTTTTAATTATTTAA
1 TAATAATTTTTAATTATTTAA
*
3468445 TAATAAATATTTTAA-TATTTTA
1 TAAT-AAT-TTTTAATTATTTAA
3468467 -AATAATT
1 TAATAATT
3468474 ATTCAATCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.04
20 3 0.12
21 7 0.27
22 9 0.35
23 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TAATAATTTTTAATTATTTAA
Found at i:3472799 original size:92 final size:93
Alignment explanation
Indices: 3472633--3472817 Score: 255
Period size: 92 Copynumber: 2.0 Consensus size: 93
3472623 AGAATTCAAT
* * *
3472633 CAATCACTACATGGTTTAAAGTTAAAAGCAATATGAGCATGAAAACTTAAAAGGCACAAAAATAT
1 CAATCACTACATGGTTTAAAGATAAAAGAAATAAGAGCATGAAAACTTAAAAGGCACAAAAATAT
** *
3472698 ACATGAACAGGCTTTGGAAGATGTATGA
66 ACACCAACAGACTTTGGAAGATGTATGA
* * ** * *
3472726 CAATCATTACATGGTTTAAAGAT-ACAGAAATAAGAGCATGAAAACTTACGAGGCACGAAAATCT
1 CAATCACTACATGGTTTAAAGATAAAAGAAATAAGAGCATGAAAACTTAAAAGGCACAAAAATAT
3472790 ACACCAACAGACTTTGGAAGATGTATGA
66 ACACCAACAGACTTTGGAAGATGTATGA
3472818 AACTGCGAGA
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
92 59 0.74
93 21 0.26
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (93 bp):
CAATCACTACATGGTTTAAAGATAAAAGAAATAAGAGCATGAAAACTTAAAAGGCACAAAAATAT
ACACCAACAGACTTTGGAAGATGTATGA
Found at i:3487102 original size:2 final size:2
Alignment explanation
Indices: 3487089--3487121 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
3487079 TAAAATTATT
3487089 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
3487122 ATTTAACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3487279 original size:29 final size:28
Alignment explanation
Indices: 3487210--3487279 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
3487200 GGACTTCAAT
*
3487210 TTTCAAATTTAAAAAGTAAAAGATTAAA
1 TTTCAAATATAAAAAGTAAAAGATTAAA
* * *
3487238 TTT-ATGAAAATAAAAAGTAGAAAGATTGAG
1 TTTCA--AATATAAAAAGTA-AAAGATTAAA
3487268 TTTCAAATATAA
1 TTTCAAATATAA
3487280 GAAAAGGAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
27 1 0.03
28 3 0.09
29 17 0.52
30 11 0.33
31 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.11, T:0.31
Consensus pattern (28 bp):
TTTCAAATATAAAAAGTAAAAGATTAAA
Found at i:3489433 original size:20 final size:20
Alignment explanation
Indices: 3489388--3489445 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
3489378 GCATGGGTAG
3489388 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
3489412 TGTATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
3489432 TGCATCGATGCACT
1 TGCATCGATGCACT
3489446 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:3490424 original size:2 final size:2
Alignment explanation
Indices: 3490417--3490497 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
3490407 ATACGTTGAT
3490417 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3490459 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3490498 GAAAGGTGCA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3496083 original size:64 final size:64
Alignment explanation
Indices: 3496030--3496192 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 64
3496020 CGGTGCACCA
*
3496030 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
3496094 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* * *
3496159 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
3496193 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 39 0.46
65 46 0.54
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:3496164 original size:19 final size:19
Alignment explanation
Indices: 3496140--3496190 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3496130 GAAAATATTC
3496140 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
3496159 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
3496178 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
3496191 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:3497208 original size:21 final size:21
Alignment explanation
Indices: 3497174--3497217 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3497164 CAGGAGCTGG
3497174 AGGAGGAGCACGAGAAGAACT
1 AGGAGGAGCACGAGAAGAACT
* *
3497195 AGGAGTAGCTCGAGAAGAACT
1 AGGAGGAGCACGAGAAGAACT
3497216 AG
1 AG
3497218 CTCCCGGAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.14, G:0.36, T:0.09
Consensus pattern (21 bp):
AGGAGGAGCACGAGAAGAACT
Found at i:3498073 original size:21 final size:21
Alignment explanation
Indices: 3498017--3498080 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
3498007 TCAATAATCC
* *
3498017 ATTAGGA-GCTTGAGGATCAGG
1 ATTAGGATG-TTGAGGAACGGG
* **
3498038 ATTAGGTTGAGGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
3498059 ATTAGGATGTTGAGGAACGGG
1 ATTAGGATGTTGAGGAACGGG
3498080 A
1 A
3498081 GGACGGTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.42, T:0.22
Consensus pattern (21 bp):
ATTAGGATGTTGAGGAACGGG
Found at i:3502694 original size:22 final size:21
Alignment explanation
Indices: 3502652--3502691 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3502642 GAGTTTGTTT
*
3502652 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3502673 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3502692 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3504769 original size:19 final size:19
Alignment explanation
Indices: 3504745--3504795 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
3504735 GAAAATATTC
3504745 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
3504764 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
3504783 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
3504796 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:3504771 original size:65 final size:65
Alignment explanation
Indices: 3504620--3504797 Score: 216
Period size: 64 Copynumber: 2.8 Consensus size: 65
3504610 GAACACTTGA
*** * *
3504620 TGCATCGATGCACCAAGTGTGCATTGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGG
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGG
** * **
3504684 TGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGA
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-
3504748 G
65 G
* * *
3504749 TGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
3504798 CAATTAATTC
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 48 0.50
65 48 0.50
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGG
Found at i:3504837 original size:65 final size:65
Alignment explanation
Indices: 3504647--3504846 Score: 200
Period size: 65 Copynumber: 3.1 Consensus size: 65
3504637 TGTGCATTGA
* ** *
3504647 TGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTTG-TGCATC
1 TGCATGAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-TGATGCATC
*
3504709 GA
64 GG
* *
3504711 TGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--GAGTGCATC
1 TGCATGAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA-TGCATC
3504774 GG
64 GG
* *
3504776 TGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGACTGATGCAT
1 TGCATGAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGACTGATGCAT
3504838 CGG
63 CGG
3504841 TGCATG
1 TGCATG
3504847 CCTTTGAATA
Statistics
Matches: 116, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 43 0.37
65 60 0.52
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (65 bp):
TGCATGAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGATGCATCGG
Found at i:3511634 original size:2 final size:2
Alignment explanation
Indices: 3511627--3511657 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
3511617 ATGTGATTGC
3511627 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
3511658 GATTTGGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3512070 original size:23 final size:23
Alignment explanation
Indices: 3512002--3512070 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
3511992 ACATATTATA
*
3512002 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
3512025 CGGTA-TTATGGTGCAATTCTACG
1 TGGCACTT-CGGTGCATTTCTACG
*
3512048 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
3512071 AGCTGTGGTG
Statistics
Matches: 34, Mismatches: 10, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
22 2 0.06
23 30 0.88
24 2 0.06
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.36
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:3512922 original size:28 final size:27
Alignment explanation
Indices: 3512868--3512959 Score: 159
Period size: 27 Copynumber: 3.4 Consensus size: 27
3512858 TTTGTTCAGG
3512868 TCGGGTCGGG-TTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
3512894 TCGGGTCGGGTTTTTATAAGTGTGATAT
1 TCGGGTCGGGTTTTT-TAAGTGTGATAT
*
3512922 TCGGGTTGGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
3512949 TCGGGTCGGGT
1 TCGGGTCGGGT
3512960 CGGGTCGGGG
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
26 10 0.16
27 26 0.42
28 26 0.42
ACGTcount: A:0.14, C:0.08, G:0.36, T:0.42
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:3521789 original size:37 final size:37
Alignment explanation
Indices: 3521731--3521802 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
3521721 GGATGGAGAA
* *
3521731 AGTTTAGTTCTTTTCTTTCTTTGTCTAATATGTGTAT
1 AGTTTAGTTCTTCTCTCTCTTTGTCTAATATGTGTAT
* *
3521768 AGTTTTGTTCTTCTCTCTCTTTGTCTAATTTGTGT
1 AGTTTAGTTCTTCTCTCTCTTTGTCTAATATGTGT
3521803 GTGCTTTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.12, C:0.14, G:0.14, T:0.60
Consensus pattern (37 bp):
AGTTTAGTTCTTCTCTCTCTTTGTCTAATATGTGTAT
Found at i:3526090 original size:48 final size:47
Alignment explanation
Indices: 3526015--3526109 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 47
3526005 CGGGAGCATC
*
3526015 GCCGTTTTAGAAGGCAACAAATGGAGGAAATCGCTCAAGCTTTGATA
1 GCCGTTTTAGAAGGCAACAAATAGAGGAAATCGCTCAAGCTTTGATA
*
3526062 GCCGTTTTAGCAAGGCAACAAATAGAGGAAATCGCTCGAGCTTTGATA
1 GCCGTTTTAG-AAGGCAACAAATAGAGGAAATCGCTCAAGCTTTGATA
3526110 TCCAGTGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 10 0.22
48 35 0.78
ACGTcount: A:0.34, C:0.18, G:0.25, T:0.23
Consensus pattern (47 bp):
GCCGTTTTAGAAGGCAACAAATAGAGGAAATCGCTCAAGCTTTGATA
Found at i:3528509 original size:30 final size:30
Alignment explanation
Indices: 3528473--3528539 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
3528463 CCCGAAGGAC
* *
3528473 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
3528503 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
*
3528533 CTGTCCA
1 CTATCCA
3528540 TTGGTCCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.19
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:3528570 original size:31 final size:31
Alignment explanation
Indices: 3528532--3528655 Score: 128
Period size: 31 Copynumber: 4.0 Consensus size: 31
3528522 ATCCTCGGCA
*
3528532 ACTGTCCAT-TGGTCCCGAAGAACCTAGGTAT
1 ACTGTCCATAT-GTCCCGAAGAACATAGGTAT
* **
3528563 ACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAT
*
3528594 ACTATCCATATGTCCCGAA-AGACATAGGTAATT
1 ACTGTCCATATGTCCCGAAGA-ACATAGGT-A-T
* *
3528627 A-TGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTCCCGAAGAACATAGGTA
3528656 AACCCTCAAC
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
30 1 0.01
31 49 0.64
32 24 0.31
33 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (31 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAT
Found at i:3533012 original size:20 final size:21
Alignment explanation
Indices: 3532987--3533038 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3532977 TTTTCCCAAT
*
3532987 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
3533007 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3533028 TCGCAATGCGA
1 TCGCAATGCGA
3533039 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3533052 original size:20 final size:20
Alignment explanation
Indices: 3533027--3533161 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
3533017 AATTGGGAAA
3533027 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
3533047 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
3533067 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
3533088 ATCGCAACGAGATATTGACT
1 ATCGCAATGCGATACTGACT
* * *
3533108 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
3533128 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
3533148 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
3533162 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 65 0.68
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:3533071 original size:61 final size:61
Alignment explanation
Indices: 3533024--3533155 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
3533014 GCGAATTGGG
* * * * *
3533024 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
3533085 AAAATCGCAACGAGATATTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
3533146 ATAATCGCAA
1 AAAATCGCAA
3533156 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3533357 original size:22 final size:22
Alignment explanation
Indices: 3533329--3533372 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3533319 CACTCTCTCA
3533329 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
**
3533351 CCCATCTCCGGTGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
3533373 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:3533689 original size:20 final size:20
Alignment explanation
Indices: 3533635--3533693 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3533625 GCGATTCTCT
**
3533635 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
3533655 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
3533675 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
3533694 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:3535032 original size:18 final size:18
Alignment explanation
Indices: 3535011--3535055 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
3535001 TCCACTTCGG
*
3535011 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
3535029 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
3535047 GAGCCATCA
1 GAGCCATCA
3535056 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:3535561 original size:20 final size:20
Alignment explanation
Indices: 3535536--3535581 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3535526 TAGTTTACTT
*
3535536 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
3535556 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
3535576 TCGCAA
1 TCGCAA
3535582 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:3535590 original size:19 final size:20
Alignment explanation
Indices: 3535547--3535602 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
3535537 CGCAACATGA
3535547 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
3535567 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
3535586 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
3535603 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:3535629 original size:19 final size:19
Alignment explanation
Indices: 3535575--3535671 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
3535565 GGAAATGGCT
3535575 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3535594 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
3535608 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3535627 ATCGCAAT--G--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
3535641 ATTGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3535660 GTCGCAATGCGA
1 ATCGCAATGCGA
3535672 TTTGTGTTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 20 0.33
15 2 0.03
16 3 0.05
17 3 0.05
18 2 0.03
19 31 0.51
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3535667 original size:33 final size:33
Alignment explanation
Indices: 3535575--3535668 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
3535565 GGAAATGGCT
*
3535575 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
3535608 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
* *
3535641 ATTGCAATGCGAAATGAAAGTCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
3535669 CGATTTGTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:3535702 original size:14 final size:14
Alignment explanation
Indices: 3535683--3535772 Score: 72
Period size: 14 Copynumber: 5.8 Consensus size: 14
3535673 TTGTGTTTCG
3535683 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3535697 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
3535713 CGCATTACGATTTTGT
1 CG--TTGCGATTTTGT
*
3535729 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
3535746 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
3535762 CGTTGCGATTT
1 CGTTGCGATTT
3535773 GCATTTCGCA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 25 0.41
15 3 0.05
16 12 0.20
17 4 0.07
18 11 0.18
19 6 0.10
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3535747 original size:33 final size:33
Alignment explanation
Indices: 3535678--3535789 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
3535668 GCGATTTGTG
*
3535678 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
3535710 TTTCGCATTACGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
3535743 TTTCGCATTGCGATTTTGTCGTTGCGATTTGCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
3535776 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
3535790 AGCCATTTCC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 25 0.33
33 50 0.67
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:3535808 original size:20 final size:19
Alignment explanation
Indices: 3535774--3535829 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
3535764 TTGCGATTTG
*
3535774 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3535793 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
3535813 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
3535830 TTTAAGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3537726 original size:14 final size:14
Alignment explanation
Indices: 3537692--3537730 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3537682 TTGATTGTTT
3537692 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
3537706 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
3537720 TGTTGATTTGT
1 AATTGATTTGT
3537731 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:3537891 original size:19 final size:19
Alignment explanation
Indices: 3537867--3537934 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
3537857 ATCGCAACGA
3537867 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3537886 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
3537905 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
3537919 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
3537935 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:3537978 original size:20 final size:20
Alignment explanation
Indices: 3537961--3538050 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
3537951 CGATTTTCTA
3537961 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
3537981 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
3538001 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
3538021 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
3538041 GTTGCGATAG
1 GTTGCGATAG
3538051 TCAAATGAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
19 3 0.05
20 52 0.90
21 3 0.05
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:3538591 original size:12 final size:12
Alignment explanation
Indices: 3538572--3538605 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3538562 CTCTCCGGCG
3538572 ACATCCGTTCCT
1 ACATCCGTTCCT
*
3538584 ATATCCGTTCCT
1 ACATCCGTTCCT
3538596 ACATCC-TTCC
1 ACATCCGTTCC
3538606 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:3539187 original size:24 final size:24
Alignment explanation
Indices: 3539160--3539213 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3539150 GTATTCGAAA
* *
3539160 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGACAATACCCGGAC
* *
3539184 TTTGATATTGGACAATACTCGGAT
1 TTTGATATTGGACAATACCCGGAC
3539208 TTTGAT
1 TTTGAT
3539214 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGACAATACCCGGAC
Found at i:3539405 original size:12 final size:12
Alignment explanation
Indices: 3539388--3539424 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
3539378 ATATAATCCT
3539388 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3539400 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3539412 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3539424 G
1 G
3539425 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3541640 original size:19 final size:19
Alignment explanation
Indices: 3541618--3541761 Score: 111
Period size: 19 Copynumber: 8.4 Consensus size: 19
3541608 GGAAATTACT
3541618 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3541637 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3541656 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
3541670 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
3541689 ATCTCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
3541703 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
3541722 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
3541736 ATCGCAATGCGAGATGAAA
1 ATCGCAATGCGAAATGAAA
3541755 ATCGCAA
1 ATCGCAA
3541762 CCCGAATTTA
Statistics
Matches: 96, Mismatches: 14, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
14 26 0.27
15 7 0.07
16 2 0.02
17 2 0.02
18 7 0.07
19 52 0.54
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3541680 original size:33 final size:33
Alignment explanation
Indices: 3541638--3541770 Score: 198
Period size: 33 Copynumber: 4.0 Consensus size: 33
3541628 GAAATGAAAA
3541638 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
3541671 TCGCAATGCGAAATGAAAATCTCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
*
3541704 TCGCAATGCGAAATGAAAATCGCAACGAGGGAA--
1 TCGCAATGCGAAATGAAAATCGCAAC--GCGAATT
* *
3541737 TCGCAATGCGAGATGAAAATCGCAACCCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
3541770 T
1 T
3541771 AATTTCGCGT
Statistics
Matches: 90, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
31 3 0.03
33 83 0.92
35 4 0.04
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCGAATT
Found at i:3541945 original size:14 final size:14
Alignment explanation
Indices: 3541926--3541962 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3541916 CATCAATTAA
3541926 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3541940 ACAAATCACCTTTT
1 ACAAATCAACTTTT
3541954 ACAAATCAA
1 ACAAATCAA
3541963 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3543835 original size:91 final size:90
Alignment explanation
Indices: 3543659--3543843 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
3543649 ATTTCAAACT
*
3543659 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
*
3543724 AGAATTGGTAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
3543752 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
3543816 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
3543843 T
1 T
3543844 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:3545403 original size:14 final size:14
Alignment explanation
Indices: 3545384--3545439 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
3545374 GGAAATGACT
3545384 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
3545398 ATCGCAACGCAAAATGA
1 ATCGCAACG--AGA-GA
3545415 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
3545431 ATCGCAACG
1 ATCGCAACG
3545440 CAAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 4 0.11
19 9 0.26
ACGTcount: A:0.41, C:0.25, G:0.23, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:3545418 original size:33 final size:33
Alignment explanation
Indices: 3545360--3545458 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
3545350 ACGAGATAAT
* *
3545360 GAGAATCGCAATGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-AAAATGACTATCGCAACGA
3545394 GAGAATCGCAACGCAAAATGACTATCGCAACGA
1 GAGAATCGCAACGCAAAATGACTATCGCAACGA
**
3545427 GAGAATCGCAACGCAAAATGAAAATCGCAACG
1 GAGAATCGCAACGCAAAATGACTATCGCAACG
3545459 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 48 0.79
34 13 0.21
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCAAAATGACTATCGCAACGA
Found at i:3545455 original size:52 final size:52
Alignment explanation
Indices: 3545397--3545508 Score: 188
Period size: 52 Copynumber: 2.2 Consensus size: 52
3545387 GCAACGAGAG
**
3545397 AATCGCAACGCAAAATGACTATCGCAACGAGAGAATCGCAACGCAAAATGAA
1 AATCGCAACGCAAAATGAAAATCGCAACGAGAGAATCGCAACGCAAAATGAA
* *
3545449 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGCAAAATGAAAATCGCAACGAGAGAATCGCAACGCAAAATGAA
3545501 AATCGCAA
1 AATCGCAA
3545509 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (52 bp):
AATCGCAACGCAAAATGAAAATCGCAACGAGAGAATCGCAACGCAAAATGAA
Found at i:3545475 original size:33 final size:33
Alignment explanation
Indices: 3545438--3545508 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
3545428 AGAATCGCAA
3545438 CGCAA-AATGAAAATCGCAACGCGAAATGAAAAT
1 CGCAACAA-GAAAATCGCAACGCGAAATGAAAAT
* *
3545471 CGCAACGAGAGAATCGCAACGCGAAATGAAAAT
1 CGCAACAAGAAAATCGCAACGCGAAATGAAAAT
3545504 CGCAA
1 CGCAA
3545509 TGCGATTTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 34 0.97
34 1 0.03
ACGTcount: A:0.48, C:0.21, G:0.21, T:0.10
Consensus pattern (33 bp):
CGCAACAAGAAAATCGCAACGCGAAATGAAAAT
Found at i:3545513 original size:19 final size:19
Alignment explanation
Indices: 3545335--3545513 Score: 118
Period size: 19 Copynumber: 10.1 Consensus size: 19
3545325 TCTTTTGGTT
*
3545335 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
3545354 GATAATGAGAATCGCAATGC
1 GA-AATGAAAATCGCAACGC
**
3545374 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
3545392 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* **
3545408 AAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3545425 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3545441 AAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
3545460 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
3545477 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3545493 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
3545512 GA
1 GA
3545514 TTTTGGTTTC
Statistics
Matches: 124, Mismatches: 19, Indels: 34
0.70 0.11 0.19
Matches are distributed among these distances:
14 28 0.23
15 3 0.02
16 4 0.03
17 4 0.03
18 4 0.03
19 53 0.43
20 26 0.21
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3545542 original size:19 final size:19
Alignment explanation
Indices: 3545509--3545553 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3545499 AAAATCGCAA
*
3545509 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
3545528 TGCGATTTTTATTTCGTGT
1 TGCGATTTTGATTTCGCGT
3545547 TGCGATT
1 TGCGATT
3545554 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.13, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:3546150 original size:20 final size:20
Alignment explanation
Indices: 3546109--3546180 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3546099 GCTATGTAAA
* *
3546109 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
3546129 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
3546149 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
3546170 TCGCATTGCGA
1 TCGCATTGCGA
3546181 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.07
20 29 0.66
21 12 0.27
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:3546194 original size:21 final size:21
Alignment explanation
Indices: 3546170--3546242 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
3546160 TTTTCCTAAT
* *
3546170 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
3546191 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTACGAAAA
*
3546211 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTACGAAAA
* *
3546232 TTGCATTGCGA
1 TCGCAATGCGA
3546243 TAGTCAGTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTACGAAAA
Found at i:3546345 original size:21 final size:22
Alignment explanation
Indices: 3546296--3546345 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
3546286 TACTTATTCA
3546296 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGGGAAAATCG
**
3546317 CAACGCGAAATT-GGAAAATCG
1 CATTGCGAAATTGGGAAAATCG
3546338 CATTGCGA
1 CATTGCGA
3546346 TAGTCATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGGGAAAATCG
Found at i:3548666 original size:21 final size:21
Alignment explanation
Indices: 3548551--3548666 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
3548541 GCGAAATAAA
**
3548551 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
3548571 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
3548591 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
3548612 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
3548632 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
3548654 AATCGCAACGCGA
1 AATCGCAACGCGA
3548667 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:3548679 original size:20 final size:20
Alignment explanation
Indices: 3548654--3548825 Score: 256
Period size: 20 Copynumber: 8.6 Consensus size: 20
3548644 GATTTTCCAG
* ** *
3548654 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3548674 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3548694 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3548714 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3548734 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3548754 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3548774 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3548794 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
3548814 AATCGCAACGCG
1 AATCGCAACGCG
3548826 ATTTTTAAAG
Statistics
Matches: 139, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
19 1 0.01
20 136 0.98
21 2 0.01
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3549245 original size:33 final size:33
Alignment explanation
Indices: 3549206--3549276 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3549196 TTCACTTAGA
3549206 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
3549239 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
3549272 TTTCA
1 TTTCA
3549277 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:3549382 original size:21 final size:20
Alignment explanation
Indices: 3549356--3549462 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
3549346 TGCAGAAGAG
3549356 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
3549377 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
3549397 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGA-AAATGAAAA
3549419 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
3549433 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
3549452 TCGCAACGAGA
1 TCGCAACGAGA
3549463 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 26 0.37
22 9 0.13
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Done.