Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 176 of 206
Found at i:53600411 original size:44 final size:46
Alignment explanation
Indices: 53600344--53600436 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
53600334 TTATATCTCT
*
53600344 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
*
53600388 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTTTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
53600434 ATT
1 ATT
53600437 ACGCATCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 4 0.09
46 18 0.40
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
Found at i:53600439 original size:16 final size:16
Alignment explanation
Indices: 53600418--53600470 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
53600408 AGAATTACCT
*
53600418 ATTACGCCTTTATTCC
1 ATTACGCCTCTATTCC
*
53600434 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
* *
53600450 ATTACACCTCTATTCT
1 ATTACGCCTCTATTCC
53600466 ATTAC
1 ATTAC
53600471 AGCGAACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:53601606 original size:11 final size:11
Alignment explanation
Indices: 53601585--53601631 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
53601575 GTGTAGTTTG
53601585 TTTATTGTTATT
1 TTTA-TGTTATT
53601597 TTTATGTTATT
1 TTTATGTTATT
53601608 TTTAAT-TTATT
1 TTT-ATGTTATT
* *
53601619 TTAAAGTTATT
1 TTTATGTTATT
53601630 TT
1 TT
53601632 GTTAGCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 1 0.03
11 24 0.77
12 6 0.19
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.70
Consensus pattern (11 bp):
TTTATGTTATT
Found at i:53605787 original size:3 final size:3
Alignment explanation
Indices: 53605781--53605814 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
53605771 GTTATTTTTG
53605781 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
53605815 ACATATATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53605905 original size:29 final size:29
Alignment explanation
Indices: 53605849--53605906 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
53605839 ATTTTATAAT
* * *
53605849 AAATATATGTATATATTATAAATTTTTTA
1 AAATACATGTACATATTATAAATATTTTA
* *
53605878 AAATACATGTACATATTTTATATATTTTA
1 AAATACATGTACATATTATAAATATTTTA
53605907 TTATTATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (29 bp):
AAATACATGTACATATTATAAATATTTTA
Found at i:53605975 original size:18 final size:19
Alignment explanation
Indices: 53605947--53605984 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
53605937 ATAGTTTATA
*
53605947 TATATATACATTTACATTT
1 TATATATACATATACATTT
53605966 TATA-ATACATATACATTT
1 TATATATACATATACATTT
53605984 T
1 T
53605985 TCCATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATACATATACATTT
Found at i:53605979 original size:24 final size:25
Alignment explanation
Indices: 53605941--53606002 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
53605931 TTATATATAG
*
53605941 TTTAT-ATATATATACA-TTTACAT
1 TTTATAATACATATACATTTTACAT
*
53605964 TTTATAATACATATACATTTTTCCAT
1 TTTATAATACATATACA-TTTTACAT
*
53605990 TTTATAATTCATA
1 TTTATAATACATA
53606003 CATATTTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.15
24 10 0.30
26 18 0.55
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTATAATACATATACATTTTACAT
Found at i:53606009 original size:26 final size:26
Alignment explanation
Indices: 53605961--53606010 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
53605951 TATACATTTA
*
53605961 CATTTTATAATACATATACATTTTTC
1 CATTTTATAATACATACACATTTTTC
* *
53605987 CATTTTATAATTCATACATATTTT
1 CATTTTATAATACATACACATTTT
53606011 CACATACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (26 bp):
CATTTTATAATACATACACATTTTTC
Found at i:53609285 original size:10 final size:10
Alignment explanation
Indices: 53609270--53609343 Score: 58
Period size: 10 Copynumber: 6.7 Consensus size: 10
53609260 AGATTCAATG
53609270 CAAAAAAAAA
1 CAAAAAAAAA
53609280 CAAAAAAAAAA
1 C-AAAAAAAAA
53609291 CAAAAAAAGGAA
1 CAAAAAAA--AA
*
53609303 AAAAGAAGAACAA
1 CAAA-AA-AA-AA
*
53609316 AAAAACAAAAA
1 CAAAA-AAAAA
*
53609327 CAAAAAGAAA
1 CAAAAAAAAA
53609337 CAAAAAA
1 CAAAAAA
53609344 CCTCCACCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 18 0.34
11 16 0.30
12 8 0.15
13 9 0.17
14 2 0.04
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:53609285 original size:11 final size:12
Alignment explanation
Indices: 53609271--53609343 Score: 75
Period size: 11 Copynumber: 6.4 Consensus size: 12
53609261 GATTCAATGC
53609271 AAAAAA-AAACA
1 AAAAAAGAAACA
53609282 AAAAAA-AAACA
1 AAAAAAGAAACA
*
53609293 AAAAAAGGAA-A
1 AAAAAAGAAACA
*
53609304 AAAGAAG-AACA
1 AAAAAAGAAACA
*
53609315 AAAAAACAAA-A
1 AAAAAAGAAACA
53609326 ACAAAAAGAAACA
1 A-AAAAAGAAACA
53609339 AAAAA
1 AAAAA
53609344 CCTCCACCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
10 2 0.04
11 32 0.62
12 16 0.31
13 2 0.04
ACGTcount: A:0.85, C:0.08, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAACA
Found at i:53609850 original size:7 final size:7
Alignment explanation
Indices: 53609832--53609881 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
53609822 ATGATGTGAA
53609832 AAAAATG
1 AAAAATG
53609839 AAAAAATG
1 -AAAAATG
53609847 -AAAATG
1 AAAAATG
53609853 AAAAATG
1 AAAAATG
53609860 AAAAATGG
1 AAAAAT-G
53609868 AAAAA-G
1 AAAAATG
53609874 TAAAAATG
1 -AAAAATG
53609882 GAAAGGCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.18
7 17 0.45
8 14 0.37
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:53609850 original size:14 final size:13
Alignment explanation
Indices: 53609833--53609863 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
53609823 TGATGTGAAA
53609833 AAAATGAAAAAATG
1 AAAATG-AAAAATG
53609847 AAAATGAAAAATG
1 AAAATGAAAAATG
53609860 AAAA
1 AAAA
53609864 ATGGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:53611766 original size:18 final size:19
Alignment explanation
Indices: 53611734--53611771 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
53611724 ATAAAATGGA
* *
53611734 AAAATGTATATGTAT-TAT
1 AAAATGTAAACGTATATAT
53611752 AAAATGTAAACGTATATAT
1 AAAATGTAAACGTATATAT
53611771 A
1 A
53611772 TAAACTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37
Consensus pattern (19 bp):
AAAATGTAAACGTATATAT
Found at i:53611770 original size:26 final size:26
Alignment explanation
Indices: 53611708--53611757 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
53611698 TATGTATGTG
*
53611708 AAAATATGTATGAATTATAAAATGGA
1 AAAATATATATGAATTATAAAATGGA
* *
53611734 AAAATGTATATGTATTATAAAATG
1 AAAATATATATGAATTATAAAATG
53611758 TAAACGTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (26 bp):
AAAATATATATGAATTATAAAATGGA
Found at i:53611917 original size:3 final size:3
Alignment explanation
Indices: 53611909--53611942 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
53611899 ATGTATAAGT
53611909 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53611943 CAAAAATAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53613854 original size:48 final size:48
Alignment explanation
Indices: 53613792--53614011 Score: 170
Period size: 48 Copynumber: 4.6 Consensus size: 48
53613782 AATGTACTCT
* * *
53613792 AATGTATCTAATTTATATTACAAAGTTTGTTCCGCA-TTTTAATGTTGC
1 AATGAATCTAATTTAAATTACAAAGTTTGTTCC-AAGTTTTAATGTTGC
* *
53613840 AATTAATCTAATTTAAATTACAAACTTTGTTCCAAGTTTTAATGTTGC
1 AATGAATCTAATTTAAATTACAAAGTTTGTTCCAAGTTTTAATGTTGC
* *** *
53613888 AATGAATCTCAA-TTAAATTACAAAG-TTATTCTGTGTTTTAATGTTGT
1 AATGAATCT-AATTTAAATTACAAAGTTTGTTCCAAGTTTTAATGTTGC
* * * * *
53613935 GATGAAACCCAA-TTAAATAAATACAAAATTTG-TCTAAAG--TT--TGTTGC
1 AATG-AATCTAATTTAAAT---TACAAAGTTTGTTC-CAAGTTTTAATGTTGC
*
53613982 AATTAATCTAATTTAAATTACAAAGTTTGT
1 AATGAATCTAATTTAAATTACAAAGTTTGT
53614012 AATTTTGCAT
Statistics
Matches: 136, Mismatches: 26, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
44 10 0.07
46 5 0.04
47 42 0.31
48 64 0.47
49 4 0.03
50 8 0.06
51 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (48 bp):
AATGAATCTAATTTAAATTACAAAGTTTGTTCCAAGTTTTAATGTTGC
Found at i:53616039 original size:20 final size:22
Alignment explanation
Indices: 53616016--53616059 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
53616006 TTCAATCAAC
53616016 ATTTC-AATAAATCAAAAA-AA
1 ATTTCAAATAAATCAAAAACAA
53616036 ATTTCAAATAAATCAAAAACAA
1 ATTTCAAATAAATCAAAAACAA
53616058 AT
1 AT
53616060 AAAATTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.25
Consensus pattern (22 bp):
ATTTCAAATAAATCAAAAACAA
Found at i:53616333 original size:104 final size:103
Alignment explanation
Indices: 53616050--53616527 Score: 432
Period size: 104 Copynumber: 4.6 Consensus size: 103
53616040 CAAATAAATC
* * * * *
53616050 AAAAACAAATAAAATTACATT-ATAACAAATCACAATACACATTAAACTAAACAAATAATTTATA
1 AAAAA-AAAAAAAATTACATTAATAAAAAATCACACTA-A-ACTAAAC---ACAAACAATTTATA
53616114 ACCTAATCATAAATTACTAACAAAATAACTTTAAAATAA-TTTT
60 ACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTT
** * * * *
53616157 -AAAAAAATTATATT-CA-TAAAAAATCACAATAAATACTAAACTAAACACAAACAATTTATAAC
1 AAAAAAAAAAAAATTACATTAATAAA--A-AAT-CACACTAAACTAAACACAAACAATTTATAAC
53616219 CTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTT
62 CTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTT
53616261 AAAAACAAAAAAAATTACATTAATAAAAAATCACACTAAACTAAACACAAACAATTTA-ACACCT
1 AAAAA-AAAAAAAATTACATTAATAAAAAATCACACTAAACTAAACACAAACAATTTATA-ACCT
*
53616325 AATCATAAATTATTAA-AAAATAACTTTAAAATAACTTTTT
64 AATCATAAATTACTAACAAAATAACTTTAAAATAA-TTTTT
** * * * * *
53616365 ----TTAAAAAATTTACATTCATAAAAAATCACAATAAACTAAGCTAAACACAGACAATATATAA
1 AAAAAAAAAAAAATTACATTAATAAAAAATCAC-----ACTAAACTAAACACAAACAATTTATAA
* *
53616426 CCTAAACATAAATTACTAACAAAATAACTTTAAAATGA-TTTT
61 CCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTT
*
53616468 AAAAAAATTAAAAAATTTA-A--AATCACAATAA--ACACTAAACTAAACACAAACAATTTATAA
1 AAAAAAA--AAAAAA-TTACATTAAT-A-AAAAATCACACTAAACTAAACACAAACAATTTATAA
53616528 TAATAATTAA
Statistics
Matches: 309, Mismatches: 34, Indels: 61
0.76 0.08 0.15
Matches are distributed among these distances:
99 25 0.08
102 24 0.08
103 76 0.25
104 97 0.31
105 33 0.11
106 19 0.06
107 11 0.04
108 11 0.04
109 10 0.03
110 3 0.01
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.28
Consensus pattern (103 bp):
AAAAAAAAAAAAATTACATTAATAAAAAATCACACTAAACTAAACACAAACAATTTATAACCTAA
TCATAAATTACTAACAAAATAACTTTAAAATAATTTTT
Found at i:53616444 original size:208 final size:206
Alignment explanation
Indices: 53616050--53616527 Score: 609
Period size: 208 Copynumber: 2.3 Consensus size: 206
53616040 CAAATAAATC
* * * * *
53616050 AAAAACAAATAAAATTACATT-ATAACAAATCACAATACACATTAAACTAAACAAATAATTTATA
1 AAAAACAAAAAAAATTACATTAATAAAAAATCACACTA-A-ACTAAAC---ACAAACAATTTATA
*
53616114 ACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTAAAAAAATTATATTCATAAAAA
61 ACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTTAAAAAAATTACATTCATAAAAA
* *
53616179 ATCACAATAAATACTAAACTAAACACAAACAATTTATAACCTAATCATAAATTACTAACAAAATA
126 ATCACAATAAATACTAAACTAAACACAAACAATATATAACCTAAACATAAATTACTAACAAAATA
53616244 ACTTTAAAATAATTTTT
191 ACTTTAAAATAA-TTTT
53616261 AAAAACAAAAAAAATTACATTAATAAAAAATCACACTAAACTAAACACAAACAATTTA-ACACCT
1 AAAAACAAAAAAAATTACATTAATAAAAAATCACACTAAACTAAACACAAACAATTTATA-ACCT
* *
53616325 AATCATAAATTATTAA-AAAATAACTTTAAAATAACTTTTTTTAAAAAATTTACATTCATAAAAA
65 AATCATAAATTACTAACAAAATAACTTTAAAATAA----TTTTAAAAAAATTACATTCATAAAAA
* *
53616389 ATCACAAT-AA-ACTAAGCTAAACACAGACAATATATAACCTAAACATAAATTACTAACAAAATA
126 ATCACAATAAATACTAAACTAAACACAAACAATATATAACCTAAACATAAATTACTAACAAAATA
*
53616452 ACTTTAAAATGATTTT
191 ACTTTAAAATAATTTT
*
53616468 AAAAA-AATTAAAAAATTTA-A--AATCACAATAA--ACACTAAACTAAACACAAACAATTTATA
1 AAAAACAA--AAAAAA-TTACATTAAT-A-AAAAATCACACTAAACTAAACACAAACAATTTATA
53616527 A
61 A
53616528 TAATAATTAA
Statistics
Matches: 241, Mismatches: 14, Indels: 29
0.85 0.05 0.10
Matches are distributed among these distances:
206 51 0.21
207 41 0.17
208 71 0.29
209 5 0.02
210 38 0.16
211 21 0.09
212 14 0.06
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.28
Consensus pattern (206 bp):
AAAAACAAAAAAAATTACATTAATAAAAAATCACACTAAACTAAACACAAACAATTTATAACCTA
ATCATAAATTACTAACAAAATAACTTTAAAATAATTTTAAAAAAATTACATTCATAAAAAATCAC
AATAAATACTAAACTAAACACAAACAATATATAACCTAAACATAAATTACTAACAAAATAACTTT
AAAATAATTTT
Found at i:53616601 original size:27 final size:29
Alignment explanation
Indices: 53616571--53616632 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
53616561 AAAACAACAT
*
53616571 AAAAAATA-AATAATCCCTTC-TATTTAA
1 AAAAAATATAATAATCCCTTCAAATTTAA
* *
53616598 AAAAAA-ATATTAATCCCTTCAAATTTTA
1 AAAAAATATAATAATCCCTTCAAATTTAA
53616626 AAAAAAT
1 AAAAAAT
53616633 TACAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 1 0.03
27 17 0.59
28 11 0.38
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAAAATATAATAATCCCTTCAAATTTAA
Found at i:53616603 original size:28 final size:28
Alignment explanation
Indices: 53616571--53616631 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
53616561 AAAACAACAT
*
53616571 AAAAAATAAATAATCCCTTC-TATTTAAA
1 AAAAAAT-AATAATCCCTTCAAATTTAAA
* *
53616599 AAAAAATATTAATCCCTTCAAATTTTAA
1 AAAAAATAATAATCCCTTCAAATTTAAA
53616627 AAAAA
1 AAAAA
53616632 TTACAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAAAATAATAATCCCTTCAAATTTAAA
Found at i:53616660 original size:4 final size:4
Alignment explanation
Indices: 53616653--53616700 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
53616643 CATACCTTCC
53616653 CTTT CTTT -TTT -TTT -TTT CTTT CTTT CTTCT CATTT CTTT CTTT -TTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT-T C-TTT CTTT CTTT CTTT
53616699 CT
1 CT
53616701 CCTTCTATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
3 12 0.30
4 22 0.55
5 4 0.10
6 2 0.05
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (4 bp):
CTTT
Found at i:53616690 original size:18 final size:18
Alignment explanation
Indices: 53616667--53616701 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53616657 CTTTTTTTTT
53616667 TTTCTTTCTTTCTTCTCA
1 TTTCTTTCTTTCTTCTCA
*
53616685 TTTCTTTCTTTTTTCTC
1 TTTCTTTCTTTCTTCTC
53616702 CTTCTATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTTCTTTCTTCTCA
Found at i:53620045 original size:3 final size:3
Alignment explanation
Indices: 53620037--53620063 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53620027 TTTGTTTTGT
53620037 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
53620064 ACATTTCGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:53633915 original size:6 final size:6
Alignment explanation
Indices: 53633904--53633928 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
53633894 AATAAATTTT
53633904 ATACCC ATACCC ATACCC ATACCC A
1 ATACCC ATACCC ATACCC ATACCC A
53633929 AGCCCAAATA
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:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
ATACCC
Found at i:53636247 original size:15 final size:16
Alignment explanation
Indices: 53636229--53636262 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
53636219 AAACCGAAAG
*
53636229 AAAG-AAGAAAAATAA
1 AAAGAAAGAAAAAGAA
53636244 AAAGAAAGAAAAAGAA
1 AAAGAAAGAAAAAGAA
53636260 AAA
1 AAA
53636263 AAAACCAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGAAAGAAAAAGAA
Found at i:53636264 original size:19 final size:19
Alignment explanation
Indices: 53636225--53636265 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
53636215 AAGAAAACCG
*
53636225 AAAGAAAGAAGAAAAATAA
1 AAAGAAAGAAGAAAAAAAA
53636244 AAAGAAAGAA-AAAGAAAAA
1 AAAGAAAGAAGAAA-AAAAA
53636263 AAA
1 AAA
53636266 ACCAAGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAGAAAGAAGAAAAAAAA
Found at i:53636277 original size:25 final size:23
Alignment explanation
Indices: 53636224--53636266 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
53636214 AAAGAAAACC
*
53636224 GAAAGAAAGAAGAAAAATAAAAA
1 GAAAGAAAGAAGAAAAAAAAAAA
53636247 GAAAGAAA-AAGAAAAAAAAA
1 GAAAGAAAGAAGAAAAAAAAA
53636267 CCAAGGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (23 bp):
GAAAGAAAGAAGAAAAAAAAAAA
Found at i:53645458 original size:16 final size:16
Alignment explanation
Indices: 53645437--53645470 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
53645427 TTTTAATTTT
53645437 TTAAAAAACAATAAAA
1 TTAAAAAACAATAAAA
*
53645453 TTAAAAAACTATAAAA
1 TTAAAAAACAATAAAA
53645469 TT
1 TT
53645471 TTTATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
TTAAAAAACAATAAAA
Found at i:53645721 original size:13 final size:13
Alignment explanation
Indices: 53645703--53645736 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
53645693 TTTTGTTGAG
*
53645703 AAGTGCTTTTAAA
1 AAGTGCTTTGAAA
*
53645716 AAGTGCTATGAAA
1 AAGTGCTTTGAAA
53645729 AAGTGCTT
1 AAGTGCTT
53645737 CACAAGTGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (13 bp):
AAGTGCTTTGAAA
Found at i:53646252 original size:3 final size:3
Alignment explanation
Indices: 53646244--53646273 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
53646234 TTGTTTGTTT
53646244 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
53646274 TATCATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:53648284 original size:35 final size:35
Alignment explanation
Indices: 53648161--53648284 Score: 97
Period size: 35 Copynumber: 3.5 Consensus size: 35
53648151 GTTATTGATT
* * *
53648161 GGTCCTTCGAGGCGACATCATGAC-GATGGTATATA
1 GGTCCTTCGAGGCGACACCGT-ACAAATGGTATATA
* * * ** * ** *
53648196 AGTCCTTCGGGGTGACACCGTGTAAACGGTGCACA
1 GGTCCTTCGAGGCGACACCGTACAAATGGTATATA
* **
53648231 GGTCCTACGAGGAAACACCGTACAAATGGTATATA
1 GGTCCTTCGAGGCGACACCGTACAAATGGTATATA
53648266 GGTCCTTCGAGGCGACACC
1 GGTCCTTCGAGGCGACACC
53648285 TCAAAAGGAG
Statistics
Matches: 62, Mismatches: 26, Indels: 2
0.69 0.29 0.02
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (35 bp):
GGTCCTTCGAGGCGACACCGTACAAATGGTATATA
Found at i:53651741 original size:23 final size:21
Alignment explanation
Indices: 53651702--53651749 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
53651692 TATTCAGCTC
* *
53651702 GAAACTCAAAATTTATATCATA
1 GAAACACAAAATATATAT-ATA
53651724 GAAACACATAAATATATATATA
1 GAAACACA-AAATATATATATA
53651746 -AAAC
1 GAAAC
53651750 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 4 0.17
22 10 0.43
23 9 0.39
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.27
Consensus pattern (21 bp):
GAAACACAAAATATATATATA
Found at i:53653962 original size:11 final size:11
Alignment explanation
Indices: 53653948--53653972 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53653938 AAATAAGGGA
53653948 TTATATATCGG
1 TTATATATCGG
53653959 TTATATATCGG
1 TTATATATCGG
53653970 TTA
1 TTA
53653973 CACGCTTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (11 bp):
TTATATATCGG
Found at i:53655304 original size:15 final size:15
Alignment explanation
Indices: 53655284--53655313 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
53655274 AAATAGGATC
53655284 ATATTAGGAGAATGA
1 ATATTAGGAGAATGA
53655299 ATATTAGGAGAATGA
1 ATATTAGGAGAATGA
53655314 TGTAACACAC
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:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (15 bp):
ATATTAGGAGAATGA
Found at i:53658034 original size:18 final size:18
Alignment explanation
Indices: 53658011--53658061 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
53658001 GCTTAAATTA
53658011 AATACCCAAACCCAATAC
1 AATACCCAAACCCAATAC
* * *
53658029 AATACCTAAACCCGATTC
1 AATACCCAAACCCAATAC
53658047 AA-AGCCCAAACCCAA
1 AATA-CCCAAACCCAA
53658062 CTCATCCCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.47, C:0.37, G:0.04, T:0.12
Consensus pattern (18 bp):
AATACCCAAACCCAATAC
Found at i:53663387 original size:53 final size:53
Alignment explanation
Indices: 53663329--53663475 Score: 242
Period size: 53 Copynumber: 2.8 Consensus size: 53
53663319 AAAAAGAATG
* * *
53663329 GACCAAAGTGAAAACCTGCAAAGGGCACTTTGATTCCTAAAAAAAAAGGGAGA
1 GACCAAAGTGAAAACCCGCAAAGGGCGCTTTGATTCCTAAAAAAAAAAGGAGA
53663382 GACCAAAGTGAAAACCCGCAAAGGGCGCTTTGATTCCTAAAAAAAAAAGGAGA
1 GACCAAAGTGAAAACCCGCAAAGGGCGCTTTGATTCCTAAAAAAAAAAGGAGA
* *
53663435 GACCAAAGTGAAGACCCGCAAAGGGCGCTTTGAGT-CTAAAA
1 GACCAAAGTGAAAACCCGCAAAGGGCGCTTTGATTCCTAAAA
53663476 TAATAATAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
52 6 0.07
53 83 0.93
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (53 bp):
GACCAAAGTGAAAACCCGCAAAGGGCGCTTTGATTCCTAAAAAAAAAAGGAGA
Found at i:53664859 original size:44 final size:44
Alignment explanation
Indices: 53664789--53665169 Score: 188
Period size: 44 Copynumber: 8.8 Consensus size: 44
53664779 TGAAGATGGC
* * * *
53664789 AGATCGTATATCCCTGAAGTTACAGTGGAGTAGATTAAAGCCAAT
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAA-ACAAT
* ** *
53664834 A-ATCCTATCTCCCTGAAGATGCAGTGGAGCGGATTAAAATAAT
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACAAT
* * ** * *
53664877 AGATCTTATCTCTCTGAAGTTGCAGCAGAGTAGATT---GCATT
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACAAT
* * * * * * * ** **
53664918 AGGTCTTATCTCCTTGAGGTTGTAGTGGAGCAGACTGAGTA-AGC
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGA-TTAAAACAAT
* * * ** * * ****
53664962 AGGTCTTATC-CCCTTGAAGTTACAGTGGAACAGACTGAAGATGGC
1 AGATCCTATCTCCC-TGAAGTTGCAGTGGAGTAGA-TTAAAACAAT
* * *
53665007 AGATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTAAAGCCAAT
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAA-ACAAT
*
53665052 A-ATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAATAAT
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACAAT
* * * * * ** *
53665095 TGATCTTATCTCTCTGAAGTTGCAATAGAGTAGA-T--CGCATT
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACAAT
* * *
53665136 AGGTCTTATCTCCCTGAGGTTGCAGTGGAGTAGA
1 AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGA
53665170 CTGAGTAAAC
Statistics
Matches: 257, Mismatches: 69, Indels: 24
0.73 0.20 0.07
Matches are distributed among these distances:
41 58 0.23
42 1 0.00
43 10 0.04
44 156 0.61
45 29 0.11
46 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (44 bp):
AGATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAACAAT
Found at i:53665127 original size:218 final size:217
Alignment explanation
Indices: 53664746--53665239 Score: 772
Period size: 218 Copynumber: 2.3 Consensus size: 217
53664736 AAATCACAAA
* * *
53664746 GTCTTATCCCCCTAAAGTTGCAGTGGGGCAGACTGAAGATGGCAGATCGTATATCCCTGAAGTTA
1 GTCTTAT-CCCCTAAAGTTGCAGTGGGGCAGACTGAAGATGGCAGATCTTATCTCCCTAAAGTTA
*
53664811 CAGTGGAGTAGATTAAAGCCAATAATCCTATCTCCCTGAAGATGCAGTGGAGCGGATTAAAATAA
65 CAGTGGAGTAGATTAAAGCCAATAATCCTATCTCCCTGAAGATGCAGTGGAGCAGATTAAAATAA
* * * *
53664876 TAGATCTTATCTCTCTGAAGTTGCAGCAGAGTAGATTGCATTAGGTCTTATCTCCTTGAGGTTGT
130 TAGATCTTATCTCTCTGAAGTTGCAACAGAGTAGATCGCATTAGGTCTTATCTCCCTGAGGTTGC
*
53664941 AGTGGAGCAGACTGAGTAAGCAG
195 AGTGGAGCAGACTGAGTAAACAG
* * ** *
53664964 GTCTTATCCCCTTGAAGTTACAGTGGAACAGACTGAAGATGGCAGATCTTATCTCCCTAAAGTTG
1 GTCTTATCCCC-TAAAGTTGCAGTGGGGCAGACTGAAGATGGCAGATCTTATCTCCCTAAAGTTA
* *
53665029 CAGTGGAGTAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAATAA
65 CAGTGGAGTAGATTAAAGCCAATAATCCTATCTCCCTGAAGATGCAGTGGAGCAGATTAAAATAA
* *
53665094 TTGATCTTATCTCTCTGAAGTTGCAATAGAGTAGATCGCATTAGGTCTTATCTCCCTGAGGTTGC
130 TAGATCTTATCTCTCTGAAGTTGCAACAGAGTAGATCGCATTAGGTCTTATCTCCCTGAGGTTGC
*
53665159 AGTGGAGTAGACTGAGTAAACAG
195 AGTGGAGCAGACTGAGTAAACAG
* *
53665182 GTCTTATCCTCCTAAAGTTGCAGTGGGGCAGACTAAAGATGGCAGGTCTTATCTCCCT
1 GTCTTATCC-CCTAAAGTTGCAGTGGGGCAGACTGAAGATGGCAGATCTTATCTCCCT
53665240 GAGCGGCAGT
Statistics
Matches: 249, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
217 4 0.02
218 243 0.98
219 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (217 bp):
GTCTTATCCCCTAAAGTTGCAGTGGGGCAGACTGAAGATGGCAGATCTTATCTCCCTAAAGTTAC
AGTGGAGTAGATTAAAGCCAATAATCCTATCTCCCTGAAGATGCAGTGGAGCAGATTAAAATAAT
AGATCTTATCTCTCTGAAGTTGCAACAGAGTAGATCGCATTAGGTCTTATCTCCCTGAGGTTGCA
GTGGAGCAGACTGAGTAAACAG
Found at i:53665423 original size:44 final size:43
Alignment explanation
Indices: 53665370--53665828 Score: 263
Period size: 44 Copynumber: 10.7 Consensus size: 43
53665360 TCACATTCAG
*
53665370 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAATAGAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATA-AAGAAACCAA
* * * * *
53665414 TCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ATCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCA-AATAAAGA-AACCAA
* * * * * * *
53665458 TCTTATCTCTCTGAAGTTGCAGTAGAGCAAAT--CGCATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATAAAGAAACCAA
* * * *
53665499 TCTTATCT-CCTGGAAGTTGCAATGGAGCAGACAGAAGAAACCAG
1 TCTTATCTCCCT-GAAGTTGCAGTGGAGCAAATA-AAGAAACCAA
* * ** * *
53665543 TCCTATCTCCCTGAAGTTGCTGTGGAGCGGATTAA-AACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATAAAGAAAC-CA-A
* * * * * * * *
53665587 ACTTATCTCTCTGAAGTTGCAGTAGAGCAGAT--CGCATCCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATAAAGAAACCAA
* * * * *
53665628 TCTTATCGCCTTGAAGTTGCAGTGGAGCAGACAGAAGAAAACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATA-AAGAAACCAA
* * * * * *
53665672 TCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAA-ACCACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC-AAATAAAGA-AACCAA
** * * * * * *
53665716 TCTTATCTTTCTGAAGTTGTAGTAGAGCAAAT--CGCATCCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATAAAGAAACCAA
* *
53665757 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATA-AAGAAACCAA
* *
53665801 TCCTATCTCCCTGAAGTTACAGTGGAGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC
53665829 GGATCAAAAT
Statistics
Matches: 303, Mismatches: 92, Indels: 40
0.70 0.21 0.09
Matches are distributed among these distances:
40 2 0.01
41 80 0.26
42 5 0.02
43 12 0.04
44 197 0.65
45 7 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAAATAAAGAAACCAA
Found at i:53665592 original size:129 final size:129
Alignment explanation
Indices: 53665352--53665873 Score: 760
Period size: 129 Copynumber: 4.0 Consensus size: 129
53665342 TAGGTAAAAA
* * * * * *
53665352 AGAGCAGATCACATTCAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAAATAGAAGAAACCAATCC
1 AGAGCAAATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
* *
53665417 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGT
66 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGT
* * *
53665481 AGAGCAAATCGCATCTAGTCTTATCT-CCTGGAAGTTGCAATGGAGCAGACAGAAGAAACCAGTC
1 AGAGCAAATCGCATCCAGTCTTATCTCCCT-GAAGTTGCAGTGGAGCAGACAGAAGAAACCAATC
* *
53665545 CTATCTCCCTGAAGTTGCTGTGGAGCGGATTAAAACCACAGAA-CTTATCTCTCTGAAGTTGCAG
65 CTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACA-AATCTTATCTCTCTGAAGTTGCAG
53665609 T
129 T
* * * *
53665610 AGAGCAGATCGCATCCAGTCTTATCGCCTTGAAGTTGCAGTGGAGCAGACAGAAGAAAACAATCC
1 AGAGCAAATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
* * * *
53665675 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAAATCTTATCTTTCTGAAGTTGTAGT
66 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGT
53665739 AGAGCAAATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
1 AGAGCAAATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
* ** *** *
53665804 TATCTCCCTGAAGTTACAGTGGAGCGGATCAAAATGATGGATCTCATCTCTCTGAAGTTGCAGT
66 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGT
53665868 AGAGCA
1 AGAGCA
53665874 GATCATATCA
Statistics
Matches: 350, Mismatches: 39, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
128 5 0.01
129 341 0.97
130 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (129 bp):
AGAGCAAATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAACCAATCC
TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAGT
Found at i:53665808 original size:85 final size:85
Alignment explanation
Indices: 53665370--53665828 Score: 279
Period size: 85 Copynumber: 5.3 Consensus size: 85
53665360 TCACATTCAG
* * * * * *
53665370 TCTTATCTCCCTGAAGTTGTAGTGGAGCAAATAGAAGAAACCAATCCTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAAT---AGAATCCAGTCTTATCTCCCTGAAGTTGCA
* * *
53665435 GTGGAGCAGATTA-AA-ATCACAAA
63 GTGGAGCAGA-CAGAAGA-AACCAA
* * * * *
53665458 TCTTATCTCTCTGAAGTTGCAGTAGAGCAAATCGCATCTAGTCTTATCT-CCTGGAAGTTGCAAT
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATAGAATCCAGTCTTATCTCCCT-GAAGTTGCAGT
*
53665522 GGAGCAGACAGAAGAAACCAG
65 GGAGCAGACAGAAGAAACCAA
* * * * * * * * *
53665543 TCCTATCTCCCTGAAGTTGCTGTGGAGCGGATTAAAACCACAGAACTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGC-AAATAGAATC-CAG-TCTTATCTCCCTGAAGTTGCA
* * * *
53665608 GT--AG-AG-CAGATCGCATCCAG
63 GTGGAGCAGACAGA-AGAAACCAA
* * * * ** * * *
53665628 TCTTATCGCCTTGAAGTTGCAGTGGAGCAGACAGAAGAAAACAATCCTATCTCCCTAAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCA-A-A-TAGAATCCAGTCTTATCTCCCTGAAGTTGCA
* * * *
53665693 GTGGAGCGGATTA-AA-ACCACAAA
63 GTGGAGCAGA-CAGAAGA-AACCAA
** * * *
53665716 TCTTATCTTTCTGAAGTTGTAGTAGAGCAAATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATAGAATCCAGTCTTATCTCCCTGAAGTTGCAGTG
53665781 GAGCAGACAGAAGAAACCAA
66 GAGCAGACAGAAGAAACCAA
* * *
53665801 TCCTATCTCCCTGAAGTTACAGTGGAGC
1 TCTTATCTCCCTGAAGTTGCAGTAGAGC
53665829 GGATCAAAAT
Statistics
Matches: 273, Mismatches: 79, Indels: 41
0.69 0.20 0.10
Matches are distributed among these distances:
84 9 0.03
85 169 0.62
86 11 0.04
87 8 0.03
88 72 0.26
89 3 0.01
90 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (85 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAAATAGAATCCAGTCTTATCTCCCTGAAGTTGCAGTG
GAGCAGACAGAAGAAACCAA
Found at i:53671199 original size:10 final size:10
Alignment explanation
Indices: 53671157--53671199 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
53671147 GAAAATAGTC
*
53671157 AAAATTAATC
1 AAAATTAATT
53671167 AAAATTAACTAT
1 AAAATTAA-T-T
53671179 AAAATTAATT
1 AAAATTAATT
*
53671189 AAAATTTATT
1 AAAATTAATT
53671199 A
1 A
53671200 TGTTCATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 19 0.66
11 2 0.07
12 8 0.28
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATTAATT
Found at i:53672768 original size:27 final size:28
Alignment explanation
Indices: 53672738--53672806 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 28
53672728 AGTTGATAAA
53672738 AATTAATATATAAA-TTAT-AAATTATAT
1 AATTAATATATAAAGTTATCAAATTAT-T
53672765 AATT-ATATATTAAAGTTTATCAAATTATT
1 AATTAATATA-TAAAG-TTATCAAATTATT
53672794 AA-TAATAT-TAAAG
1 AATTAATATATAAAG
53672807 ATATTTATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
26 5 0.14
27 13 0.35
28 1 0.03
29 11 0.30
30 7 0.19
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (28 bp):
AATTAATATATAAAGTTATCAAATTATT
Found at i:53672770 original size:15 final size:16
Alignment explanation
Indices: 53672744--53672776 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
53672734 TAAAAATTAA
53672744 TATATAAATTATAAAT
1 TATATAAATTATAAAT
*
53672760 TATAT-AATTATATAT
1 TATATAAATTATAAAT
53672775 TA
1 TA
53672777 AAGTTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATAAATTATAAAT
Found at i:53676580 original size:62 final size:62
Alignment explanation
Indices: 53676483--53676607 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
53676473 TAGAATTATA
* * *
53676483 AAGTCAGCAGGAAAGATAAACTTATCTACATGTACCAATACGTTCTCGATTTATCCTTTTGG
1 AAGTCAGCAGGAAAGATAAACTTACCTACATGTACCAATACGTCCTCGATTTATCCTTCTGG
* *
53676545 AAGTCAGCAGGAAGGATAAACTTACCTACATGTACCAATACGTCCTCGATTTTTCCTTCTGG
1 AAGTCAGCAGGAAAGATAAACTTACCTACATGTACCAATACGTCCTCGATTTATCCTTCTGG
53676607 A
1 A
53676608 TGTGCTAAGG
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (62 bp):
AAGTCAGCAGGAAAGATAAACTTACCTACATGTACCAATACGTCCTCGATTTATCCTTCTGG
Found at i:53679474 original size:23 final size:23
Alignment explanation
Indices: 53679448--53679496 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
53679438 ACGATTTAAT
53679448 AATTAATTCATTAGTTATCTAAA
1 AATTAATTCATTAGTTATCTAAA
53679471 AATTAATTCATTAGTTATCTAAA
1 AATTAATTCATTAGTTATCTAAA
53679494 AAT
1 AAT
53679497 AATAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (23 bp):
AATTAATTCATTAGTTATCTAAA
Found at i:53684032 original size:25 final size:23
Alignment explanation
Indices: 53683990--53684040 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
53683980 ATTAATTTTA
*
53683990 ATTAAATAAAATATTAATAAATAT
1 ATTAAATAAAATAATAATAAA-AT
*
53684014 ATTATAATGAAATAATAATAAAAT
1 ATTA-AATAAAATAATAATAAAAT
53684038 ATT
1 ATT
53684041 CAACCAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTAAATAAAATAATAATAAAAT
Found at i:53685342 original size:23 final size:22
Alignment explanation
Indices: 53685306--53685348 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
53685296 TGAATAATAT
*
53685306 TAATAAATAAAAATTATAATTA
1 TAATAAATAAAAATGATAATTA
53685328 TAATAATATAAAAATGATAAT
1 TAATAA-ATAAAAATGATAAT
53685349 AACCAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
TAATAAATAAAAATGATAATTA
Found at i:53686409 original size:18 final size:19
Alignment explanation
Indices: 53686381--53686418 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
53686371 TTCTTTATAT
53686381 ATTATTTATAATTTTTTAA
1 ATTATTTATAATTTTTTAA
53686400 ATTA-TTATAATTTTTTAA
1 ATTATTTATAATTTTTTAA
53686418 A
1 A
53686419 ATATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTATTTATAATTTTTTAA
Found at i:53686420 original size:19 final size:19
Alignment explanation
Indices: 53686355--53686420 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
53686345 TTTCGAAAAG
*
53686355 TTTTAAAATT-TTA-ACTT
1 TTTTAAAATTATTATAATT
*
53686372 TCTTTATATATTATTTATAATT
1 T-TTTA-AAATTA-TTATAATT
53686394 TTTT-AAATTATTATAATT
1 TTTTAAAATTATTATAATT
53686412 TTTTAAAAT
1 TTTTAAAAT
53686421 ATAAATTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.03
18 16 0.40
19 13 0.32
21 6 0.15
22 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAAAATTATTATAATT
Found at i:53686456 original size:19 final size:19
Alignment explanation
Indices: 53686425--53686475 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
53686415 TAAAATATAA
*
53686425 ATTTTGAAATTTTTATAAAT
1 ATTTTG-AATTTTTACAAAT
* *
53686445 ATTTTGAATTTTAACAATT
1 ATTTTGAATTTTTACAAAT
53686464 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
53686476 TTTTTGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 5 0.19
19 16 0.59
20 6 0.22
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (19 bp):
ATTTTGAATTTTTACAAAT
Found at i:53692720 original size:23 final size:24
Alignment explanation
Indices: 53692687--53692736 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
53692677 TTTTTTTTTC
53692687 TTCTAAATTTA-ATCTAAAATAATT
1 TTCTAAATTTATAT-TAAAATAATT
*
53692711 TTCT-AATTTATATTAAAATAGTT
1 TTCTAAATTTATATTAAAATAATT
53692734 TTC
1 TTC
53692737 CTCTAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (24 bp):
TTCTAAATTTATATTAAAATAATT
Found at i:53697506 original size:4 final size:4
Alignment explanation
Indices: 53697499--53697530 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
53697489 AATCTTATAT
*
53697499 ATAC ATAC ATGC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
53697531 CATCTCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:53699185 original size:24 final size:27
Alignment explanation
Indices: 53699142--53699191 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 27
53699132 TACATCGATC
53699142 CATTCACATTATAAATAACA-TAATAA
1 CATTCACATTATAAATAACATTAATAA
53699168 CATTCA-ATT-TAAATAACATTAATA
1 CATTCACATTATAAATAACATTAATA
53699192 CGATAATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.39
25 8 0.35
26 6 0.26
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (27 bp):
CATTCACATTATAAATAACATTAATAA
Found at i:53706727 original size:14 final size:14
Alignment explanation
Indices: 53706710--53706739 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
53706700 AACATTTCTC
53706710 AACATAACTTTCAA
1 AACATAACTTTCAA
*
53706724 AACATAACTTTTAA
1 AACATAACTTTCAA
53706738 AA
1 AA
53706740 TCTTCCAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (14 bp):
AACATAACTTTCAA
Found at i:53708435 original size:14 final size:14
Alignment explanation
Indices: 53708411--53708461 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
53708401 ACAACGAAGT
*
53708411 AAAAGAAAGAAAGG
1 AAAAAAAAGAAAGG
*
53708425 GAAAAAAAGAAAGG
1 AAAAAAAAGAAAGG
53708439 AAAAGAAAAG--AGG
1 AAAA-AAAAGAAAGG
*
53708452 AAAAAGAAGA
1 AAAAAAAAGA
53708462 GAAACGAACG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 4 0.13
13 7 0.23
14 15 0.48
15 5 0.16
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAGG
Found at i:53709913 original size:12 final size:12
Alignment explanation
Indices: 53709896--53709946 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
53709886 AATTATAAAA
53709896 TTATATTAATAT
1 TTATATTAATAT
53709908 TTATATTAA-AT
1 TTATATTAATAT
* *
53709919 ATTAAATATAATAA
1 -TTATAT-TAATAT
*
53709933 TTATATTAAAAT
1 TTATATTAATAT
53709945 TT
1 TT
53709947 TAAATATCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 2 0.06
12 20 0.65
13 8 0.26
14 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTATATTAATAT
Found at i:53709930 original size:25 final size:26
Alignment explanation
Indices: 53709902--53709987 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 26
53709892 AAAATTATAT
*
53709902 TAATATTTATATT-AAATATTAAATA
1 TAATAATTATATTAAAATATTAAATA
*
53709927 TAATAATTATATTAAAATTTTAAATA
1 TAATAATTATATTAAAATATTAAATA
*
53709953 TCACTAATAATATATTAAAATA-T-AATA
1 T-AATAAT--TATATTAAAATATTAAATA
*
53709980 TAGTAATT
1 TAATAATT
53709988 TATACCTCTA
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
24 1 0.02
25 12 0.23
26 17 0.33
27 10 0.19
28 1 0.02
29 11 0.21
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (26 bp):
TAATAATTATATTAAAATATTAAATA
Found at i:53711416 original size:73 final size:73
Alignment explanation
Indices: 53711297--53711445 Score: 298
Period size: 73 Copynumber: 2.0 Consensus size: 73
53711287 GAAATAAATC
53711297 GAGGAATCCACGGACAGTGCGACGACTTTGGCATTCGCTAAAGATATATGATCCCCAGATGGTCT
1 GAGGAATCCACGGACAGTGCGACGACTTTGGCATTCGCTAAAGATATATGATCCCCAGATGGTCT
53711362 TCTCTATG
66 TCTCTATG
53711370 GAGGAATCCACGGACAGTGCGACGACTTTGGCATTCGCTAAAGATATATGATCCCCAGATGGTCT
1 GAGGAATCCACGGACAGTGCGACGACTTTGGCATTCGCTAAAGATATATGATCCCCAGATGGTCT
53711435 TCTCTATG
66 TCTCTATG
53711443 GAG
1 GAG
53711446 ACAGATTAGT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (73 bp):
GAGGAATCCACGGACAGTGCGACGACTTTGGCATTCGCTAAAGATATATGATCCCCAGATGGTCT
TCTCTATG
Found at i:53713993 original size:16 final size:16
Alignment explanation
Indices: 53713969--53714020 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
53713959 TTTGGTTCGC
53713969 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
53713985 TGTACTGGATTAGAGG
1 TGTATTGGATTAGAGG
53714001 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
53714017 TGTA
1 TGTA
53714021 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.25, C:0.02, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:53714084 original size:44 final size:45
Alignment explanation
Indices: 53714001--53714091 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
53713991 GGATTAGAGG
* * *
53714001 TGTATTGGATTAGAGGTGTAATAGCTAATCTACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
**
53714046 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
53714090 TG
1 TG
53714092 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 20 0.49
45 21 0.51
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.38
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCTACTGTTTGGTTGAA
Found at i:53714106 original size:39 final size:43
Alignment explanation
Indices: 53714001--53714114 Score: 128
Period size: 45 Copynumber: 2.7 Consensus size: 43
53713991 GGATTAGAGG
* *
53714001 TGTATTGGATTAGAGGTGTAATAGCTAATCTACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCTAATCTACTGTTTGGTT--A
* **
53714046 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCTAATCTACTGTTTGGTTA
53714086 TG-AATGGAATAGAGGTGTAATAGCATAAT
1 TGTAATGGAATAGAGGTGTAATAGC-TAAT
53714115 GGAAAAAACT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
39 20 0.33
40 2 0.03
41 4 0.07
43 1 0.02
44 13 0.21
45 21 0.34
ACGTcount: A:0.31, C:0.05, G:0.28, T:0.36
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCTAATCTACTGTTTGGTTA
Found at i:53714277 original size:18 final size:17
Alignment explanation
Indices: 53714256--53714290 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53714246 TTATTATTAA
*
53714256 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53714274 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53714291 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53714397 original size:18 final size:17
Alignment explanation
Indices: 53714376--53714410 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53714366 ATATTATGAA
*
53714376 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
53714394 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
53714411 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:53716034 original size:67 final size:69
Alignment explanation
Indices: 53715948--53716078 Score: 194
Period size: 67 Copynumber: 1.9 Consensus size: 69
53715938 TTACTGCAAC
* * *
53715948 ATATTAAAATTAGAACACACTATCAAAGAGTTGAAGTTGC-AATTACACTTTATAAAAAAAATTA
1 ATATTAAAATTAGAACACACTATCAAAGAATTGAAGATGCAAATTAAACTTTATAAAAAAAATTA
53716012 AACA
66 AACA
* * *
53716016 ATATT-AATTTAGAACACACTATCAAAGAATTGAAGATGCAAATTAAATTTTATAAAAATAATT
1 ATATTAAAATTAGAACACACTATCAAAGAATTGAAGATGCAAATTAAACTTTATAAAAAAAATT
53716079 GAGAGACAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 31 0.55
68 25 0.45
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (69 bp):
ATATTAAAATTAGAACACACTATCAAAGAATTGAAGATGCAAATTAAACTTTATAAAAAAAATTA
AACA
Found at i:53722503 original size:20 final size:20
Alignment explanation
Indices: 53722478--53722515 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53722468 TTAACTTAAT
*
53722478 AAACCTTATTTTGATTAAAC
1 AAACCTTATTTTAATTAAAC
53722498 AAACCTTATTTTAATTAA
1 AAACCTTATTTTAATTAA
53722516 TCTAATGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (20 bp):
AAACCTTATTTTAATTAAAC
Found at i:53724083 original size:42 final size:41
Alignment explanation
Indices: 53724021--53724160 Score: 169
Period size: 42 Copynumber: 3.4 Consensus size: 41
53724011 TTATGTTTAA
* * *
53724021 CTCTTATGAGCTTCTATTTAACTCATACAAGTTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTTAACTC-TACGAGTTTCTGTTCAG
*
53724063 CTCTTACGAGCTTCTGTTTAACTCTTATGAGTTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTTAACTC-TACGAGTTTCTGTTCAG
* * * *
53724105 CTCTTACGAGCTTCTGTTCAGCT-TTCGAGCTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTTAACTCTACGAGTTTCTGTTCAG
53724145 CT-TT-CGAGCTTCTGTT
1 CTCTTACGAGCTTCTGTT
53724161 AATGATGTAC
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
38 12 0.14
39 2 0.02
40 16 0.18
42 58 0.66
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (41 bp):
CTCTTACGAGCTTCTGTTTAACTCTACGAGTTTCTGTTCAG
Found at i:53724120 original size:63 final size:61
Alignment explanation
Indices: 53724014--53724141 Score: 175
Period size: 63 Copynumber: 2.1 Consensus size: 61
53724004 TTTTACTTTA
* *
53724014 TGTTTAACTCTTATGAGCTTCTATTTAACTCATACAAGTTTCTGTTCAGCTCTTACGAGCTTC
1 TGTTTAACTCTTATGAGCTTCTATTCAACTCATACAAGCTTCTGTTCAGCT-TT-CGAGCTTC
* * * * *
53724077 TGTTTAACTCTTATGAGTTTCTGTTCAGCTCTTACGAGCTTCTGTTCAGCTTTCGAGCTTC
1 TGTTTAACTCTTATGAGCTTCTATTCAACTCATACAAGCTTCTGTTCAGCTTTCGAGCTTC
53724138 TGTT
1 TGTT
53724142 CAGCTTTCGA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 12 0.21
62 2 0.03
63 44 0.76
ACGTcount: A:0.18, C:0.22, G:0.16, T:0.45
Consensus pattern (61 bp):
TGTTTAACTCTTATGAGCTTCTATTCAACTCATACAAGCTTCTGTTCAGCTTTCGAGCTTC
Found at i:53724135 original size:19 final size:21
Alignment explanation
Indices: 53724021--53724160 Score: 153
Period size: 21 Copynumber: 6.9 Consensus size: 21
53724011 TTATGTTTAA
* * * *
53724021 CTCTTATGAGCTTCTATTTAA
1 CTCTTACGAGCTTCTGTTCAG
* * *
53724042 CTCATACAAGTTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTCAG
* *
53724063 CTCTTACGAGCTTCTGTTTAA
1 CTCTTACGAGCTTCTGTTCAG
* *
53724084 CTCTTATGAGTTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTCAG
53724105 CTCTTACGAGCTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTCAG
53724126 CT-TT-CGAGCTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTCAG
53724145 CT-TT-CGAGCTTCTGTT
1 CTCTTACGAGCTTCTGTT
53724161 AATGATGTAC
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
19 31 0.31
20 2 0.02
21 68 0.67
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (21 bp):
CTCTTACGAGCTTCTGTTCAG
Found at i:53727619 original size:90 final size:90
Alignment explanation
Indices: 53727466--53727655 Score: 371
Period size: 90 Copynumber: 2.1 Consensus size: 90
53727456 CTCACCCTGC
*
53727466 AGTTGCTGCTTTGAATCTTGATACGAGCTGATTTGAATGTTGTTATACTTTCTCAATATTGTTCC
1 AGTTGCTGCTTTAAATCTTGATACGAGCTGATTTGAATGTTGTTATACTTTCTCAATATTGTTCC
53727531 AAGTTCGAGATATTTTCTCTAAAGT
66 AAGTTCGAGATATTTTCTCTAAAGT
53727556 AGTTGCTGCTTTAAATCTTGATACGAGCTGATTTGAATGTTGTTATACTTTCTCAATATTGTTCC
1 AGTTGCTGCTTTAAATCTTGATACGAGCTGATTTGAATGTTGTTATACTTTCTCAATATTGTTCC
53727621 AAGTTCGAGATATTTTCTCTAAAGT
66 AAGTTCGAGATATTTTCTCTAAAGT
53727646 AGTTGCTGCT
1 AGTTGCTGCT
53727656 GCACCTTGCC
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 99 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (90 bp):
AGTTGCTGCTTTAAATCTTGATACGAGCTGATTTGAATGTTGTTATACTTTCTCAATATTGTTCC
AAGTTCGAGATATTTTCTCTAAAGT
Found at i:53729823 original size:32 final size:32
Alignment explanation
Indices: 53729782--53729848 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
53729772 TGAATTACTA
* *
53729782 ATTACAACTCTATTTCATTACAACTTTATTCC
1 ATTACAACTCTATTCCATTACAACATTATTCC
*
53729814 ATTACAACTCTATTCCATTACAACATTATTTC
1 ATTACAACTCTATTCCATTACAACATTATTCC
53729846 ATT
1 ATT
53729849 CCAATGAACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (32 bp):
ATTACAACTCTATTCCATTACAACATTATTCC
Found at i:53729848 original size:16 final size:16
Alignment explanation
Indices: 53729782--53729837 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
53729772 TGAATTACTA
*
53729782 ATTACAACTCTATTTC
1 ATTACAACTCTATTCC
*
53729798 ATTACAACTTTATTCC
1 ATTACAACTCTATTCC
53729814 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
53729830 ATTACAAC
1 ATTACAAC
53729838 ATTATTTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.34, C:0.27, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:53730585 original size:15 final size:15
Alignment explanation
Indices: 53730565--53730595 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
53730555 AATACTGTTT
53730565 ATTTTTATTCATTTG
1 ATTTTTATTCATTTG
*
53730580 ATTTTTATTTATTTG
1 ATTTTTATTCATTTG
53730595 A
1 A
53730596 GAGAACTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (15 bp):
ATTTTTATTCATTTG
Found at i:53730738 original size:24 final size:22
Alignment explanation
Indices: 53730686--53730742 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
53730676 TATTCTACAA
53730686 AATTTAAATTAGATAACTTATT
1 AATTTAAATTAGATAACTTATT
* * *
53730708 ATTTTTAAATTATTATAGCTTAATT
1 A-ATTTAAATTA-GATAACTT-ATT
53730733 AATTTAAATT
1 AATTTAAATT
53730743 TATAATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.04
23 9 0.32
24 14 0.50
25 4 0.14
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.51
Consensus pattern (22 bp):
AATTTAAATTAGATAACTTATT
Found at i:53733650 original size:37 final size:37
Alignment explanation
Indices: 53733596--53733669 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
53733586 ATTCTACCGA
*
53733596 TTTCTATTAAAATAAGAGAGAATTTTTATTTTCACCC
1 TTTCTATTAAAAGAAGAGAGAATTTTTATTTTCACCC
53733633 TTTCTATTAAAAGAAGAGAGAATTTTTATTTTCACCC
1 TTTCTATTAAAAGAAGAGAGAATTTTTATTTTCACCC
53733670 CAAAAGTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (37 bp):
TTTCTATTAAAAGAAGAGAGAATTTTTATTTTCACCC
Found at i:53734711 original size:18 final size:18
Alignment explanation
Indices: 53734660--53734701 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
53734650 TTGGTAAGTA
53734660 TAATTTAGTTCTTTTTTG
1 TAATTTAGTTCTTTTTTG
53734678 TAATTTAGTTCTTTTTTG
1 TAATTTAGTTCTTTTTTG
53734696 TAATTT
1 TAATTT
53734702 TTATGTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.19, C:0.05, G:0.10, T:0.67
Consensus pattern (18 bp):
TAATTTAGTTCTTTTTTG
Found at i:53736152 original size:33 final size:33
Alignment explanation
Indices: 53736115--53736180 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
53736105 GTAAATTAAG
53736115 TTAAATTTCATATGGACTTACTAAGTATTTGAT
1 TTAAATTTCATATGGACTTACTAAGTATTTGAT
53736148 TTAAATTTCATATGGACTTACTAAGTATTTGAT
1 TTAAATTTCATATGGACTTACTAAGTATTTGAT
53736181 ATACTTACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (33 bp):
TTAAATTTCATATGGACTTACTAAGTATTTGAT
Found at i:53738701 original size:29 final size:29
Alignment explanation
Indices: 53738661--53738741 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
53738651 TCCACCTTGA
* *
53738661 CACGAATTCTCAATAAACAAGTTTTTCAT
1 CACGAACTCTCAATGAACAAGTTTTTCAT
**
53738690 CGTGAACTCTCAATGAACAAGTTTTTCAT
1 CACGAACTCTCAATGAACAAGTTTTTCAT
53738719 CACGAACTCTCAATGAACAAGTT
1 CACGAACTCTCAATGAACAAGTT
53738742 CTCCACCTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (29 bp):
CACGAACTCTCAATGAACAAGTTTTTCAT
Found at i:53739553 original size:13 final size:13
Alignment explanation
Indices: 53739535--53739566 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
53739525 GGCTTAACAT
53739535 TCTGCATATTGAA
1 TCTGCATATTGAA
53739548 TCTGCATATTGAA
1 TCTGCATATTGAA
53739561 TCTGCA
1 TCTGCA
53739567 AAGAACTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (13 bp):
TCTGCATATTGAA
Found at i:53746204 original size:69 final size:69
Alignment explanation
Indices: 53746093--53746221 Score: 231
Period size: 69 Copynumber: 1.9 Consensus size: 69
53746083 AATTCTAACA
*
53746093 GTTGTTATATCAAAATATTACAAAATCAAAGTTAATGATTTGGAATCGAAAATAAAAGAATTCTT
1 GTTGTTATATCAAAATATTACAAAATCAAAGTTAACGATTTGGAATCGAAAATAAAAGAATTCTT
53746158 AAAT
66 AAAT
* *
53746162 GTTGTTATATCAAAATGTTACAAAATCAAAGTTAACGATTTGGAATTGAAAATAAAAGAA
1 GTTGTTATATCAAAATATTACAAAATCAAAGTTAACGATTTGGAATCGAAAATAAAAGAA
53746222 AGAAAAAGGT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 57 1.00
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (69 bp):
GTTGTTATATCAAAATATTACAAAATCAAAGTTAACGATTTGGAATCGAAAATAAAAGAATTCTT
AAAT
Found at i:53746633 original size:16 final size:17
Alignment explanation
Indices: 53746612--53746657 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
53746602 AATCATTAAG
53746612 AAAATT-TTAAAGAGAT
1 AAAATTATTAAAGAGAT
*
53746628 AAAATTAGTTTAAGAGAT
1 AAAATTA-TTAAAGAGAT
*
53746646 AAAAGTATTAAA
1 AAAATTATTAAA
53746658 TTGAGTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 6 0.24
17 4 0.16
18 15 0.60
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (17 bp):
AAAATTATTAAAGAGAT
Found at i:53752296 original size:3 final size:3
Alignment explanation
Indices: 53752288--53752316 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53752278 AACAAAAATA
53752288 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53752317 ACAATTCCAT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53755189 original size:10 final size:10
Alignment explanation
Indices: 53755161--53755190 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
53755151 AGTGCAGAGA
53755161 AAAACTAAAG
1 AAAACTAAAG
53755171 AAAACCTAAAG
1 AAAA-CTAAAG
53755182 AAAACTAAA
1 AAAACTAAA
53755191 CCTAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.13, G:0.07, T:0.10
Consensus pattern (10 bp):
AAAACTAAAG
Found at i:53757578 original size:25 final size:25
Alignment explanation
Indices: 53757550--53757619 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 25
53757540 TGGCTCTTAT
53757550 GAGCTTCCTGATTAATGGCTCTCTG
1 GAGCTTCCTGATTAATGGCTCTCTG
** * * *
53757575 GAGCTTTTTGA-TATTGGCTCGCTT
1 GAGCTTCCTGATTAATGGCTCTCTG
*
53757599 GAACTTCCTGATT-ATGGCTCT
1 GAGCTTCCTGATTAATGGCTCT
53757620 TATGAGTTTC
Statistics
Matches: 34, Mismatches: 10, Indels: 3
0.72 0.21 0.06
Matches are distributed among these distances:
24 24 0.71
25 10 0.29
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (25 bp):
GAGCTTCCTGATTAATGGCTCTCTG
Found at i:53757690 original size:25 final size:26
Alignment explanation
Indices: 53757662--53757731 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
53757652 TTCTCATTAC
53757662 ATGGCTCACATGAGCTTCCC-GTTAT
1 ATGGCTCACATGAGCTTCCCAGTTAT
* * * *
53757687 ATGGCTCAAAAGAGCTACCCATTTAT
1 ATGGCTCACATGAGCTTCCCAGTTAT
53757713 AT-GCTCACATGAGCATTCC
1 ATGGCTCACATGAGC-TTCC
53757732 TGAATATGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 27 0.75
26 9 0.25
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (26 bp):
ATGGCTCACATGAGCTTCCCAGTTAT
Found at i:53760519 original size:23 final size:23
Alignment explanation
Indices: 53760483--53760528 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
53760473 AGACTTAAAG
53760483 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
53760506 TGTAATA-CCTCGAAAATTACTAC
1 TGTAATATCC-CGAAAATTACTAC
53760529 AATAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:53766536 original size:25 final size:25
Alignment explanation
Indices: 53766477--53766538 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
53766467 CATTTGTGGA
* *
53766477 TCTTATGAGCTTTTTATTAATTGGC
1 TCTTATGAGCTTTTGATTAACTGGC
***
53766502 TCTCCGGAGCTTTTCGA-TAACTGGC
1 TCTTATGAGCTTTT-GATTAACTGGC
53766527 TCTTATGAGCTT
1 TCTTATGAGCTT
53766539 CCTAATTAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (25 bp):
TCTTATGAGCTTTTGATTAACTGGC
Found at i:53766690 original size:25 final size:25
Alignment explanation
Indices: 53766640--53766714 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
53766630 GGAGTTTCTT
*
53766640 GTTACATGGCTCACATGAGCTTCCC
1 GTTACATGGCTCACAAGAGCTTCCC
53766665 GTTACATGGCTCGA-AAGAG-TTACCC
1 GTTACATGGCTC-ACAAGAGCTT-CCC
* *
53766690 GCTTATAT-GCTCACATGAGCATTCC
1 G-TTACATGGCTCACAAGAGC-TTCC
53766715 TAAATATGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
24 3 0.07
25 28 0.68
26 8 0.20
27 2 0.05
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (25 bp):
GTTACATGGCTCACAAGAGCTTCCC
Found at i:53769493 original size:16 final size:16
Alignment explanation
Indices: 53769456--53769495 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
53769446 TTGATAAAAT
* *
53769456 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
53769472 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
53769488 TAAAATTA
1 TAAAATTA
53769496 TCAATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:53769523 original size:16 final size:15
Alignment explanation
Indices: 53769498--53769528 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
53769488 TAAAATTATC
53769498 AATTTATTAATTGTT
1 AATTTATTAATTGTT
53769513 AATTGTATTAATTGTT
1 AATT-TATTAATTGTT
53769529 GTAACAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (15 bp):
AATTTATTAATTGTT
Found at i:53769589 original size:16 final size:16
Alignment explanation
Indices: 53769565--53769603 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
53769555 AAAATTATCA
* *
53769565 AATTATTAATTGTATT
1 AATTGTTAATTGTAAT
53769581 AATTGTTAATTGTAAT
1 AATTGTTAATTGTAAT
53769597 AATTGTT
1 AATTGTT
53769604 GTAACAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (16 bp):
AATTGTTAATTGTAAT
Found at i:53769589 original size:75 final size:74
Alignment explanation
Indices: 53769490--53769633 Score: 234
Period size: 75 Copynumber: 1.9 Consensus size: 74
53769480 ATTGTTAGTA
*
53769490 AAATTATCAATTTATTAATTGTTAATTGTATTAATTGTTGTAACAAAATCTAACAGTTGATTAGT
1 AAATTATCAATTTATTAATTGTTAATTGTAATAATTGTTGTAACAAAATCTAACAGTTGATTAGT
53769555 AAAATTATC
66 AAAATTATC
* ***
53769564 AAATTATTAATTGTATTAATTGTTAATTGTAATAATTGTTGTAACAAAATCTAATTTTTGATTAG
1 AAATTATCAATT-TATTAATTGTTAATTGTAATAATTGTTGTAACAAAATCTAACAGTTGATTAG
53769629 TAAAA
65 TAAAA
53769634 CAAACCTGAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
74 11 0.17
75 53 0.83
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (74 bp):
AAATTATCAATTTATTAATTGTTAATTGTAATAATTGTTGTAACAAAATCTAACAGTTGATTAGT
AAAATTATC
Found at i:53779874 original size:132 final size:132
Alignment explanation
Indices: 53779637--53780271 Score: 664
Period size: 132 Copynumber: 4.8 Consensus size: 132
53779627 TTTTATGAGT
* * * * * * *
53779637 AATTTTATTTGAGTTAGCTGATCTTAGATCGTAACTCTGAACAGCTTATTGATTTAATATCGCAG
1 AATTTTATTTGAGTTAGCTGATCTCATATCGCAACTCTGAACAACTCATTGATTTAAGATCGCAA
* * *
53779702 CTGATATTGTTAAGGCTCGCTGATTTAAGATCGCAACCTAAGTTCATTCGATTT-AGAATCATGA
66 CTGATATTGTTAAAGTTCGCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAAG-ATCATGA
53779766 ACA
130 ACA
* * *
53779769 AATTTTATTTGAGTTAGCTGATCTCATATTGCAACTCTGAACAACTCGTTGATTTAAGATCACAA
1 AATTTTATTTGAGTTAGCTGATCTCATATCGCAACTCTGAACAACTCATTGATTTAAGATCGCAA
* * * * *
53779834 TTGATATTGTTAAAGTTCACTGATTTAATATCGTAACCTAAGTTCATTTGATTTAAGATCGTGAA
66 CTGATATTGTTAAAGTTCGCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAAGATCATGAA
53779899 CA
131 CA
* * * ** * *
53779901 AATTTTATTTGAGTTAGTTGATTTCATATCACAACTCCAAACAGCTCACTGATTTAAGATCGCAA
1 AATTTTATTTGAGTTAGCTGATCTCATATCGCAACTCTGAACAACTCATTGATTTAAGATCGCAA
* * * ** * * *
53779966 ATGATATTGTTAATGTTTGCTGATTTAATATAACAACCTAAGTTCATTCAATTTAAAATCGTGAA
66 CTGATATTGTTAAAGTTCGCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAAGATCATGAA
53780031 CA
131 CA
* ** *
53780033 AATTTTATTTGAATTAGCTGATCTCGGATAGCAACT-TCGAACAACTCATTGATTTAAGATCGCA
1 AATTTTATTTGAGTTAGCTGATCTCATATCGCAACTCT-GAACAACTCATTGATTTAAGATCGCA
* * * * * * * * * *
53780097 ATTGATATTATTAAGGCTCGTTGATTTAAGATCACAAAACTAATTTCATTCGATTTAAGATTATG
65 ACTGATATTGTTAAAGTTCGCTGATTTAATATCGC-AACCTAAGTTCATTCGATTTAAGATCATG
53780162 AACA
129 AACA
* * * * * * ** *
53780166 AATTTTATTTAAGTTAGTTGATCTCATATCGCAACTATGAACAACTCTTTGGTTTAAAATTACAG
1 AATTTTATTTGAGTTAGCTGATCTCATATCGCAACTCTGAACAACTCATTGATTTAAGATCGCAA
* * * * *
53780231 CTAATATTGTTAATA-TTAGCTAATTTAATGTCGTAACCTAA
66 CTGATATTGTTAA-AGTTCGCTGATTTAATATCGCAACCTAA
53780272 CTCCAATTAA
Statistics
Matches: 410, Mismatches: 88, Indels: 10
0.81 0.17 0.02
Matches are distributed among these distances:
132 308 0.75
133 101 0.25
134 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (132 bp):
AATTTTATTTGAGTTAGCTGATCTCATATCGCAACTCTGAACAACTCATTGATTTAAGATCGCAA
CTGATATTGTTAAAGTTCGCTGATTTAATATCGCAACCTAAGTTCATTCGATTTAAGATCATGAA
CA
Found at i:53786330 original size:21 final size:23
Alignment explanation
Indices: 53786287--53786331 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
53786277 AACTGACATG
53786287 TAAATAATACATGTTAGAAATCA
1 TAAATAATACATGTTAGAAATCA
53786310 TAAA-AATACATGTTA-AAATCA
1 TAAATAATACATGTTAGAAATCA
53786331 T
1 T
53786332 GTTTTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.31
Consensus pattern (23 bp):
TAAATAATACATGTTAGAAATCA
Found at i:53795399 original size:10 final size:10
Alignment explanation
Indices: 53795367--53795391 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53795357 CTCTTAATTT
53795367 AATTCTAAAA
1 AATTCTAAAA
53795377 AATTCTAAAA
1 AATTCTAAAA
53795387 AATTC
1 AATTC
53795392 AAAGAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (10 bp):
AATTCTAAAA
Found at i:53805011 original size:46 final size:45
Alignment explanation
Indices: 53804944--53805306 Score: 379
Period size: 46 Copynumber: 8.6 Consensus size: 45
53804934 TTTGAGTACT
* *
53804944 TCTGATCAAGAGATAAAGTGATAAGTTGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAG-TGTAGCTTTAGCTACACTTA
53804990 TCTGATCAAGTGACAAAGTGATAA--GTA-C--T-G---CACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGCTTTAGCTACACTTA
*
53805026 TCTGATCAAGAGACAAAGTGATAAGTTGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAG-TGTAGCTTTAGCTACACTTA
*
53805072 TCTGATCAAGTGAAAAAGTGATAA--GT-GC--T-G---CACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGCTTTAGCTACACTTA
*
53805108 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGT-GTAGCTTTAGCTACACTTA
* *
53805154 ACTGATCAAGTGAAAAAGTGAT-A----AG---T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGTAGCTTTAGCTACACTTA
*
53805190 TCTGATCAGGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGT-GTAGCTTTAGCTACACTTA
*
53805236 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGT-GTAGCTTTAGCTACACTTA
* *
53805282 TCTAATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
53805307 ATCATGTGTA
Statistics
Matches: 270, Mismatches: 17, Indels: 63
0.77 0.05 0.18
Matches are distributed among these distances:
36 86 0.32
37 2 0.01
39 7 0.03
40 7 0.03
42 7 0.03
43 8 0.03
44 11 0.04
45 7 0.03
46 135 0.50
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGTAGCTTTAGCTACACTTA
Found at i:53805081 original size:82 final size:82
Alignment explanation
Indices: 53804944--53805262 Score: 548
Period size: 82 Copynumber: 3.9 Consensus size: 82
53804934 TTTGAGTACT
* * *
53804944 TCTGATCAAGAGATAAAGTGATAAGTTGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
53805009 GATAAGTACTGCACTTA
66 GATAAGTGCTGCACTTA
*
53805026 TCTGATCAAGAGACAAAGTGATAAGTTGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
53805091 GATAAGTGCTGCACTTA
66 GATAAGTGCTGCACTTA
*
53805108 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTAACTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
53805173 GATAAGTGCTACACTTA
66 GATAAGTGCTGCACTTA
* * *
53805190 TCTGATCAGGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
53805255 GATAAGTG
66 GATAAGTG
53805263 GTAGCCTTAG
Statistics
Matches: 227, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 227 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTGCACTTA
Found at i:53805172 original size:128 final size:123
Alignment explanation
Indices: 53805062--53805306 Score: 315
Period size: 128 Copynumber: 2.0 Consensus size: 123
53805052 TGTAGCTTTA
53805062 GCTACACTTATCTGATCAAGTGAAAAAGTGATAA-GT-GC-T-G-CACTTATCTGATCAAGAGAC
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGGTAGCTTAGACACTTATCTGATCAAGAGAC
* *
53805122 AAAGTGATAAGTGGTAGCTTTAGCTACACTTAACTGATCAAGTGAAAAAGTGATAAGT
66 AAAGTGATAAGTGGTAGCCTTAGCTACACTTAACTGATCAAGAGAAAAAGTGATAAGT
* *
53805180 GCTACACTTATCTGATCAGGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAA--GGTAGC-TTAG--ACACTTATCTGATCAA
* * * * *
53805245 GTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTAATC-AG-GGACAAGTGATAAGT
61 GAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTAACTGATCAAGAGAAAAAGTGATAAGT
53805306 G
1 G
53805307 ATCATGTGTA
Statistics
Matches: 109, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
118 32 0.29
121 2 0.02
122 2 0.02
124 1 0.01
125 1 0.01
126 14 0.13
127 2 0.02
128 55 0.50
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (123 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGGTAGCTTAGACACTTATCTGATCAAGAGAC
AAAGTGATAAGTGGTAGCCTTAGCTACACTTAACTGATCAAGAGAAAAAGTGATAAGT
Found at i:53811119 original size:26 final size:28
Alignment explanation
Indices: 53811061--53811122 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 28
53811051 AATTGAACCA
*
53811061 TCCATCAAAATACAAACATCAATAAAGTG
1 TCCATCAAAATACAAACA-CAATAAACTG
*
53811090 TCCATCAAAATAC-AACA-ATTAAACTG
1 TCCATCAAAATACAAACACAATAAACTG
53811116 TCCATCA
1 TCCATCA
53811123 TCAAAATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 14 0.45
28 4 0.13
29 13 0.42
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.23
Consensus pattern (28 bp):
TCCATCAAAATACAAACACAATAAACTG
Found at i:53811673 original size:24 final size:24
Alignment explanation
Indices: 53811628--53811673 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
53811618 CAACAGTTTG
* *
53811628 AGAATGAGCTGGTGGAGCATGATC
1 AGAAGGAGCTGGTGGAACATGATC
*
53811652 AGAAGGAGCTGGTGGAATATGA
1 AGAAGGAGCTGGTGGAACATGA
53811674 GTTGTTGGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.39, T:0.20
Consensus pattern (24 bp):
AGAAGGAGCTGGTGGAACATGATC
Found at i:53821506 original size:26 final size:26
Alignment explanation
Indices: 53821459--53821529 Score: 108
Period size: 26 Copynumber: 2.8 Consensus size: 26
53821449 GCCAATATCG
53821459 GGAAGCTC-CGAAGAGCCATTAATCA
1 GGAAGCTCACGAAGAGCCATTAATCA
* * *
53821484 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCACGAAGAGCCATTAATCA
53821510 GGAAGCTCACGAAGAGCCAT
1 GGAAGCTCACGAAGAGCCAT
53821530 ATAACGGGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
25 8 0.20
26 32 0.80
ACGTcount: A:0.35, C:0.24, G:0.25, T:0.15
Consensus pattern (26 bp):
GGAAGCTCACGAAGAGCCATTAATCA
Found at i:53821537 original size:26 final size:26
Alignment explanation
Indices: 53821331--53821544 Score: 105
Period size: 24 Copynumber: 8.6 Consensus size: 26
53821321 ATCCGGGCTT
* *
53821331 TATAACGAGAAGCTCATG-AGAGCCA
1 TATAACGGGAAGCTCACGAAGAGCCA
* * *
53821356 TATTTA--GGAAGCTCA-TACGAGCCA
1 TA-TAACGGGAAGCTCACGAAGAGCCA
* * *
53821380 -ATAATGGGTAGCTC-TGAAGAGCCA
1 TATAACGGGAAGCTCACGAAGAGCCA
* **
53821404 T-TAACGAGAAGCTCTGGATAGA--CA
1 TATAACGGGAAGCTCACGA-AGAGCCA
* * * * *
53821428 TATATCGGGTAGTTCAAG-CGAGCCA
1 TATAACGGGAAGCTCACGAAGAGCCA
*
53821453 -ATATCGGGAAGCTC-CGAAGAGCCA
1 TATAACGGGAAGCTCACGAAGAGCCA
* *
53821477 T-TAATCAGGAAGCTCACAAAGAGCC-
1 TATAA-CGGGAAGCTCACGAAGAGCCA
*
53821502 TTTAATCGGGAAGCTCACGAAGAGCCA
1 TATAA-CGGGAAGCTCACGAAGAGCCA
*
53821529 TATAACGGGATGCTCA
1 TATAACGGGAAGCTCA
53821545 TAAGAGCTGC
Statistics
Matches: 142, Mismatches: 30, Indels: 33
0.69 0.15 0.16
Matches are distributed among these distances:
22 2 0.01
23 4 0.03
24 61 0.43
25 26 0.18
26 45 0.32
27 4 0.03
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (26 bp):
TATAACGGGAAGCTCACGAAGAGCCA
Found at i:53821627 original size:25 final size:25
Alignment explanation
Indices: 53821599--53821672 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
53821589 TCGGGTTGCT
53821599 GCAAAGAGCTATTAACGGGAAGCTC
1 GCAAAGAGCTATTAACGGGAAGCTC
* *
53821624 GC-AAGAACCATATAACGGGAAGCTC
1 GCAAAGAGCTAT-TAACGGGAAGCTC
* * * *
53821649 G-AGAGGGCTAATAACGGGATGCTC
1 GCAAAGAGCTATTAACGGGAAGCTC
53821673 TTTCAAGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
24 19 0.49
25 20 0.51
ACGTcount: A:0.35, C:0.20, G:0.30, T:0.15
Consensus pattern (25 bp):
GCAAAGAGCTATTAACGGGAAGCTC
Found at i:53821629 original size:24 final size:23
Alignment explanation
Indices: 53821602--53821672 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 23
53821592 GGTTGCTGCA
53821602 AAGAGCTATTAACGGGAAGCTCG
1 AAGAGCTATTAACGGGAAGCTCG
* *
53821625 CAAGAACCATATAACGGGAAGCTCG
1 -AAGAGCTAT-TAACGGGAAGCTCG
* * *
53821650 AGAGGGCTAATAACGGGATGCTC
1 A-AGAGCTATTAACGGGAAGCTC
53821673 TTTCAAGTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 20 0.53
25 18 0.47
ACGTcount: A:0.35, C:0.20, G:0.30, T:0.15
Consensus pattern (23 bp):
AAGAGCTATTAACGGGAAGCTCG
Found at i:53824456 original size:24 final size:24
Alignment explanation
Indices: 53824429--53824477 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
53824419 CTTTTGGAGA
53824429 GTTGAAAAGGTTTAGAGAAATTTG
1 GTTGAAAAGGTTTAGAGAAATTTG
*
53824453 GTTGAAAAGGTTTAGAGAATTTTG
1 GTTGAAAAGGTTTAGAGAAATTTG
53824477 G
1 G
53824478 GTGGGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (24 bp):
GTTGAAAAGGTTTAGAGAAATTTG
Found at i:53826255 original size:21 final size:19
Alignment explanation
Indices: 53826208--53826255 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
53826198 TTAATTGGTA
*
53826208 TTATATACATATAATATAG
1 TTATATATATATAATATAG
53826227 TT-TAATATATATATATATAAG
1 TTAT-ATATATATA-ATAT-AG
53826248 TTATATAT
1 TTATATAT
53826256 TATGATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
19 10 0.42
20 4 0.17
21 8 0.33
22 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (19 bp):
TTATATATATATAATATAG
Found at i:53826328 original size:15 final size:15
Alignment explanation
Indices: 53826295--53826329 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
53826285 TAAAGGTTAT
* *
53826295 AATAATAAAAGTAAT
1 AATAATAAAAGAAAG
53826310 AATAATAAAAGAAAG
1 AATAATAAAAGAAAG
53826325 AATAA
1 AATAA
53826330 AGAAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (15 bp):
AATAATAAAAGAAAG
Found at i:53827494 original size:20 final size:20
Alignment explanation
Indices: 53827455--53827494 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
53827445 TGAATGGTAT
*
53827455 GGTATGTGAATTGGAAATGA
1 GGTATGTGAATTGAAAATGA
53827475 GGTA-GTGAATTGAAATATGA
1 GGTATGTGAATTGAAA-ATGA
53827495 AAAATGAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.30
Consensus pattern (20 bp):
GGTATGTGAATTGAAAATGA
Found at i:53842928 original size:12 final size:12
Alignment explanation
Indices: 53842913--53842957 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
53842903 ATAAAGATCA
*
53842913 AGATTAAGATGG
1 AGATGAAGATGG
* *
53842925 AGATGGAGGTGG
1 AGATGAAGATGG
*
53842937 AGGTGAAGATGG
1 AGATGAAGATGG
53842949 AGATGAAGA
1 AGATGAAGA
53842958 AGATGAGGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.44, T:0.18
Consensus pattern (12 bp):
AGATGAAGATGG
Found at i:53843257 original size:73 final size:75
Alignment explanation
Indices: 53843174--53843444 Score: 265
Period size: 75 Copynumber: 3.7 Consensus size: 75
53843164 AAGTTTTTCT
* *
53843174 ATTGTATTTTACATCAAT-A-ATATACTTATTTACAATCTACGAAAAAAATTAAAAATTATTTTT
1 ATTGTATTTTACATCAATAATATATACTTATTTACAATCTACGAAAAAAATTAAAAATTGTTTAT
*
53843237 ATTATATTCG
66 ATTGTATTCG
* *
53843247 ATTGTTTTTTATATCAATAATATATACTTATTTACAATCTACG-AAAAAATTAAAAAAATTGTTT
1 ATTGTATTTTACATCAATAATATATACTTATTTACAATCTACGAAAAAAATT--AAAAATTGTTT
*
53843311 GTATTGTATT-G
64 ATATTGTATTCG
*** *
53843322 TATCACATGTCTT-C-TCAAT-A-ATATGCTTATTTACAATCTACGAAAAATGAA--AAAAATTG
1 -ATTGTAT-T-TTACATCAATAATATATACTTATTTACAATCTACGAAAAA--AATTAAAAATTG
* * *
53843381 TTTACATTGTTTTCT
61 TTTATATTGTATTCG
* * *
53843396 ATTGTATTTTACATCAATAATATATACTTTTTTACAATTTACCAAAAAA
1 ATTGTATTTTACATCAATAATATATACTTATTTACAATCTACGAAAAAA
53843445 TGAGAAGCAA
Statistics
Matches: 161, Mismatches: 22, Indels: 30
0.76 0.10 0.14
Matches are distributed among these distances:
71 2 0.01
72 2 0.01
73 44 0.27
74 31 0.19
75 51 0.32
76 26 0.16
77 3 0.02
78 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (75 bp):
ATTGTATTTTACATCAATAATATATACTTATTTACAATCTACGAAAAAAATTAAAAATTGTTTAT
ATTGTATTCG
Found at i:53843303 original size:75 final size:73
Alignment explanation
Indices: 53843174--53843445 Score: 266
Period size: 73 Copynumber: 3.7 Consensus size: 73
53843164 AAGTTTTTCT
* *
53843174 ATTGTATTTTACATCAATAATATACTTATTTACAATCTACGAAAAAAATT-AAAAATTATTTTTA
1 ATTGTATTTTACATCAATAATATACTTATTTACAATCTACG-AAAAAATTAAAAAATTGTTTATA
*
53843238 TTATATTCG
65 TTGTATTCG
* * *
53843247 ATTGTTTTTTATATCAATAATATATACTTATTTACAATCTACGAAAAAATTAAAAAAATTGTTTG
1 ATTGTATTTTACATCAAT-A-ATATACTTATTTACAATCTACGAAAAAATT-AAAAAATTGTTTA
53843312 TATTGTATT-G
63 TATTGTATTCG
*** * *
53843322 TATCACATGTCTT-C-TCAATAATATGCTTATTTACAATCTACG-AAAAATGAAAAAAATTGTTT
1 -ATTGTAT-T-TTACATCAATAATATACTTATTTACAATCTACGAAAAAAT-TAAAAAATTGTTT
* * *
53843384 ACATTGTTTTCT
62 ATATTGTATTCG
* * *
53843396 ATTGTATTTTACATCAATAATATATACTTTTTTACAATTTACCAAAAAAT
1 ATTGTATTTTACATCAAT-A-ATATACTTATTTACAATCTACGAAAAAAT
53843446 GAGAAGCAAT
Statistics
Matches: 162, Mismatches: 23, Indels: 25
0.77 0.11 0.12
Matches are distributed among these distances:
71 2 0.01
72 2 0.01
73 50 0.31
74 31 0.19
75 42 0.26
76 32 0.20
77 1 0.01
78 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (73 bp):
ATTGTATTTTACATCAATAATATACTTATTTACAATCTACGAAAAAATTAAAAAATTGTTTATAT
TGTATTCG
Found at i:53849463 original size:23 final size:23
Alignment explanation
Indices: 53849433--53849479 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
53849423 AGTAATTGCA
53849433 AATTATTAGAACGATACTTCTAG
1 AATTATTAGAACGATACTTCTAG
53849456 AATTATTAGAACGATACTTCTAG
1 AATTATTAGAACGATACTTCTAG
53849479 A
1 A
53849480 CATAATTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (23 bp):
AATTATTAGAACGATACTTCTAG
Found at i:53856742 original size:41 final size:41
Alignment explanation
Indices: 53856637--53856749 Score: 136
Period size: 41 Copynumber: 2.8 Consensus size: 41
53856627 TAAGTTCAAG
* *
53856637 CTTTATGCCTCGCAGGCTTTATGCCGGTGAATTATATCAGG
1 CTTTATGCCTCGCAGGCTTTGTGCCGGTGAATTATATCAGA
* * * *
53856678 CTTTAAGCCTCGCAGGCTCTGTGCCTGTGAATTATATTAGA
1 CTTTATGCCTCGCAGGCTTTGTGCCGGTGAATTATATCAGA
* * * *
53856719 CTTTATGTCTAGCAGGGTTTGTGCTGGTGAA
1 CTTTATGCCTCGCAGGCTTTGTGCCGGTGAA
53856750 ATGTATCGGG
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (41 bp):
CTTTATGCCTCGCAGGCTTTGTGCCGGTGAATTATATCAGA
Found at i:53864041 original size:41 final size:41
Alignment explanation
Indices: 53863996--53864152 Score: 197
Period size: 41 Copynumber: 3.8 Consensus size: 41
53863986 TTTTGTAAGT
*
53863996 TCAGGCTTTATGCCTCGCAGGCTTTATGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
* * * *
53864037 TCAGGCTTTAAGCCTAGCAGGCTCTGTGCCTGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
* ** * * *
53864078 TCAGACTTTATTTCTAGCAGGCTTTGTGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
* *
53864119 TCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG
53864153 TTTTATACAA
Statistics
Matches: 97, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
Found at i:53865242 original size:2 final size:2
Alignment explanation
Indices: 53865235--53865260 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53865225 ATGTGCTTAA
53865235 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
53865261 GAGGAAANNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53870701 original size:32 final size:33
Alignment explanation
Indices: 53870665--53870749 Score: 93
Period size: 32 Copynumber: 2.6 Consensus size: 33
53870655 AACTTTTTAG
* * *
53870665 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
53870697 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTTACAGCAAATCTACCAAACACCA
* *
53870729 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
53870750 GTTTTACAGA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
32 37 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACACCA
Found at i:53870788 original size:14 final size:14
Alignment explanation
Indices: 53870765--53870804 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53870755 ACAGAAAAGT
*
53870765 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
53870779 AAATCATTTTACGG
1 AAAACATTTTACAG
53870793 AAAACATTTTAC
1 AAAACATTTTAC
53870805 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:53870789 original size:34 final size:35
Alignment explanation
Indices: 53870730--53870796 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
53870720 CAAACACCAG
* *
53870730 AAAATATTTTCCAGTAAATCGTTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
53870765 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
53870797 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:53874613 original size:49 final size:49
Alignment explanation
Indices: 53874498--53874642 Score: 157
Period size: 49 Copynumber: 3.0 Consensus size: 49
53874488 ATTACATTGC
* * * *
53874498 AACTCGGGCTCCCAATTCATAGTGGTTATACGGTCACAGGTTCAAGTAT
1 AACTCAGGCTCCCAATTGATAGTGGTTATGCGGTCATAGGTTCAAGTAT
* * *
53874547 AACT-AGGGCTTCTAATTGATGGTGGTTATGCGGTCATAGGTTCAAGTAT
1 AACTCA-GGCTCCCAATTGATAGTGGTTATGCGGTCATAGGTTCAAGTAT
* * * * * *
53874596 AACTCAGGCCCCCAATTGACAGTGATTTTGCTGTCATGGGTTCAAGT
1 AACTCAGGCTCCCAATTGATAGTGGTTATGCGGTCATAGGTTCAAGT
53874643 TTCATGCCAC
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
49 77 0.99
50 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (49 bp):
AACTCAGGCTCCCAATTGATAGTGGTTATGCGGTCATAGGTTCAAGTAT
Done.