Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold196
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7488280
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 125249 characters in sequence are not A, C, G, or T
File 30 of 47
Found at i:4900518 original size:31 final size:31
Alignment explanation
Indices: 4900421--4900518 Score: 78
Period size: 31 Copynumber: 3.2 Consensus size: 31
4900411 TTAAATTAAG
4900421 TAAAAACTAAATTATTAAAAAA-ATATTTTGGA
1 TAAAAACTAAATTATTAAAAAATA-ATTTT-GA
* ** ***
4900453 T-AAAATTAAA-T-TTAAAAAATCCTTGAAA
1 TAAAAACTAAATTATTAAAAAATAATTTTGA
4900481 TTTAAAAACTAAATTATTAAAAAATAATTTTGA
1 --TAAAAACTAAATTATTAAAAAATAATTTTGA
4900514 TAAAA
1 TAAAA
4900519 TTAAATTTAA
Statistics
Matches: 48, Mismatches: 12, Indels: 13
0.66 0.16 0.18
Matches are distributed among these distances:
28 1 0.02
29 10 0.21
30 2 0.04
31 21 0.44
32 2 0.04
33 12 0.25
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (31 bp):
TAAAAACTAAATTATTAAAAAATAATTTTGA
Found at i:4900590 original size:74 final size:74
Alignment explanation
Indices: 4900501--4900658 Score: 255
Period size: 74 Copynumber: 2.1 Consensus size: 74
4900491 AAATTATTAA
*
4900501 AAAATAATTTTGATAAAATTAAATTTAAAAGATAATTAAAATATAAATATCATAAT-TTAACCTC
1 AAAATAATTTGGATAAAATTAAATTTAAAAGATAATTAAAATATAAATATCATAATATT-ACCTC
4900565 ATCATCAATT
65 ATCATCAATT
* * *
4900575 AAAATAATTTGGATAAAATTAAATTTAAGAGATAATTAAAATTTAAATATCATAATATTATCTCA
1 AAAATAATTTGGATAAAATTAAATTTAAAAGATAATTAAAATATAAATATCATAATATTACCTCA
4900640 TCATCAATT
66 TCATCAATT
*
4900649 AAAATGATTT
1 AAAATAATTT
4900659 TCTAACTTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
74 76 0.97
75 2 0.03
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.37
Consensus pattern (74 bp):
AAAATAATTTGGATAAAATTAAATTTAAAAGATAATTAAAATATAAATATCATAATATTACCTCA
TCATCAATT
Found at i:4900854 original size:6 final size:7
Alignment explanation
Indices: 4900839--4900863 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4900829 AAATCATATG
4900839 AAAATAA
1 AAAATAA
4900846 AAAATAA
1 AAAATAA
4900853 AAAATAA
1 AAAATAA
4900860 AAAA
1 AAAA
4900864 CCTTGTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:4901280 original size:25 final size:25
Alignment explanation
Indices: 4901219--4901265 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
4901209 TATTTTATAC
*
4901219 ATTTTCTATTTTTAGTTTTTGTTAT
1 ATTTTTTATTTTTAGTTTTTGTTAT
4901244 ATTTTTTATTTTTA-TTTTTGTT
1 ATTTTTTATTTTTAGTTTTTGTT
4901266 TCTTATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (25 bp):
ATTTTTTATTTTTAGTTTTTGTTAT
Found at i:4903267 original size:24 final size:25
Alignment explanation
Indices: 4903219--4903267 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
4903209 AAATAATCAA
4903219 AACTTATATGTTTATTATTTAGAGC
1 AACTTATATGTTTATTATTTAGAGC
*
4903244 AACTTAT-T-TTTCTTATCTTAGAGC
1 AACTTATATGTTTATTAT-TTAGAGC
4903268 TTCAATTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 8 0.36
25 7 0.32
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (25 bp):
AACTTATATGTTTATTATTTAGAGC
Found at i:4903941 original size:16 final size:15
Alignment explanation
Indices: 4903920--4903959 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4903910 ACGCTAAAGG
*
4903920 AGAAGATAAAAAAGAA
1 AGAAGA-AAAAAAAAA
4903936 AGAAGAAAAAAAAAA
1 AGAAGAAAAAAAAAA
4903951 AG-AGAAAAA
1 AGAAGAAAAA
4903960 CATTTTGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 10 0.43
16 6 0.26
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (15 bp):
AGAAGAAAAAAAAAA
Found at i:4905630 original size:23 final size:24
Alignment explanation
Indices: 4905596--4905649 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
4905586 CATATGAACT
* **
4905596 ATATAAAATTAA-AATTCATTTTA
1 ATATTAAATTAATAATAAATTTTA
*
4905619 TTATTAAATTAATAATAAATTTTA
1 ATATTAAATTAATAATAAATTTTA
4905643 ATATTAA
1 ATATTAA
4905650 TATTGAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATTAAATTAATAATAAATTTTA
Found at i:4905658 original size:19 final size:18
Alignment explanation
Indices: 4905622--4905667 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
4905612 CATTTTATTA
4905622 TTAAATTAATAATAAATT
1 TTAAATTAATAATAAATT
* *
4905640 TTAATATTAATATTGAATT
1 TTAA-ATTAATAATAAATT
*
4905659 TTTAATTAA
1 TTAAATTAA
4905668 CAACATATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
TTAAATTAATAATAAATT
Found at i:4911855 original size:16 final size:14
Alignment explanation
Indices: 4911836--4911877 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
4911826 GCTTTCTCAC
4911836 TTTATTTTCTTCTTAT
1 TTTATTTT-TT-TTAT
4911852 TTTATTTTTTTTAT
1 TTTATTTTTTTTAT
4911866 TTT-TTTATTTTT
1 TTTATTT-TTTTT
4911878 TTACTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.12
14 12 0.48
15 2 0.08
16 8 0.32
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTATTTTTTTTAT
Found at i:4911865 original size:9 final size:9
Alignment explanation
Indices: 4911851--4911879 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
4911841 TTTCTTCTTA
4911851 TTTTATTTT
1 TTTTATTTT
4911860 TTTTA-TTT
1 TTTTATTTT
4911868 TTTTATTTT
1 TTTTATTTT
4911877 TTT
1 TTT
4911880 ACTATTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTATTTT
Found at i:4911868 original size:8 final size:8
Alignment explanation
Indices: 4911836--4911880 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
4911826 GCTTTCTCAC
4911836 TTTATTTT
1 TTTATTTT
* * *
4911844 CTTCTTAT
1 TTTATTTT
4911852 TTTATTTTT
1 TTTA-TTTT
4911861 TTTATTTT
1 TTTATTTT
4911869 TTTATTTT
1 TTTATTTT
4911877 TTTA
1 TTTA
4911881 CTATTAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
8 23 0.77
9 7 0.23
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTATTTT
Found at i:4912175 original size:27 final size:27
Alignment explanation
Indices: 4912144--4912196 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
4912134 ACTGACTCGA
*
4912144 AAAAAATTTAAATAATTCATCAGCTTG
1 AAAAAATTCAAATAATTCATCAGCTTG
4912171 AAAAAATTCAAATAATTCATCAGCTT
1 AAAAAATTCAAATAATTCATCAGCTT
4912197 TTTTAGTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (27 bp):
AAAAAATTCAAATAATTCATCAGCTTG
Found at i:4918469 original size:2 final size:2
Alignment explanation
Indices: 4918462--4918502 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4918452 TTTTGTATCT
4918462 TA 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 TA T
4918503 TGTTAGAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4922973 original size:2 final size:2
Alignment explanation
Indices: 4922966--4923011 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4922956 TTAATTCTTC
4922966 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
4923008 AT AT
1 AT AT
4923012 TCAAATCCAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4923253 original size:5 final size:5
Alignment explanation
Indices: 4923243--4923273 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
4923233 CAGAAAATGC
*
4923243 ATTAT ATTAT ATGAT ATTAT ATTAT ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
4923274 GAGTTGTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (5 bp):
ATTAT
Found at i:4927185 original size:19 final size:19
Alignment explanation
Indices: 4927158--4927201 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4927148 ATTTACTCAG
* *
4927158 TTAAATCAATCTTTTTTAA
1 TTAATTCAATCTTATTTAA
*
4927177 TTAATTCAATCTTATTTAT
1 TTAATTCAATCTTATTTAA
4927196 TTAATT
1 TTAATT
4927202 TTTGAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATTCAATCTTATTTAA
Found at i:4927387 original size:24 final size:24
Alignment explanation
Indices: 4927341--4927388 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4927331 AATATAAATA
*
4927341 AAAATATATTTATATAATAATTTT
1 AAAATATATATATATAATAATTTT
*
4927365 AAAATATATAATATATCAT-ATTTT
1 AAAATATAT-ATATATAATAATTTT
4927389 CTGTGTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATATATAATAATTTT
Found at i:4927920 original size:66 final size:66
Alignment explanation
Indices: 4927846--4927973 Score: 195
Period size: 66 Copynumber: 1.9 Consensus size: 66
4927836 ATAATACATA
* ** * *
4927846 TTATTTTAAGATATGTTTAAAAATATATAT-TTGATATATCGTCCATTAATAATAATTATGCACT
1 TTATTTTAAGATATGTTTAAAAATATATATATT-ATATAACAACAATTAATAATAAATATGCACT
4927910 AT
65 AT
4927912 TTATTTTAAGATATGTTTAAAAATATATATATTATATAACAACAATTAATAATAAATATGCA
1 TTATTTTAAGATATGTTTAAAAATATATATATTATATAACAACAATTAATAATAAATATGCA
4927974 TTATCAATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 54 0.96
67 2 0.04
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (66 bp):
TTATTTTAAGATATGTTTAAAAATATATATATTATATAACAACAATTAATAATAAATATGCACTA
T
Found at i:4933507 original size:73 final size:73
Alignment explanation
Indices: 4933419--4933563 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 73
4933409 ATGGACATTA
* *
4933419 ACTAACCAAGAGATTTATTACAAAGCACATGATCAGAAGAACATACTTAACCAGAACACGAAGAA
1 ACTAACCAAGAGATTTAGTACAAAGCACATGATCAGAAGAACATACTTAACCAGAACACAAAGAA
4933484 GTGTCAAC
66 GTGTCAAC
*
4933492 ACTAACCAAGGGATTTAGTACAAAGCACATGATCAGAAGAACATACTTAACCAGAACACAAAGAA
1 ACTAACCAAGAGATTTAGTACAAAGCACATGATCAGAAGAACATACTTAACCAGAACACAAAGAA
4933557 GTGTCAA
66 GTGTCAA
4933564 TAGTTTCTGA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.17
Consensus pattern (73 bp):
ACTAACCAAGAGATTTAGTACAAAGCACATGATCAGAAGAACATACTTAACCAGAACACAAAGAA
GTGTCAAC
Found at i:4938255 original size:7 final size:7
Alignment explanation
Indices: 4938243--4938272 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
4938233 AATTTAATAC
4938243 TTTCTTT
1 TTTCTTT
4938250 TTTCTTT
1 TTTCTTT
4938257 TTTCTTT
1 TTTCTTT
4938264 TTT-TTT
1 TTTCTTT
4938270 TTT
1 TTT
4938273 GTGATCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTCTTT
Found at i:4943366 original size:31 final size:31
Alignment explanation
Indices: 4943323--4943385 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 31
4943313 ATCAACTGTT
*
4943323 GCCAGCCTAAATTTTG-AATTCAATTTGAAATA
1 GCCAGCCTAAA--TTGAAAATCAATTTGAAATA
4943355 GCCA-CCTAAATTGAAAATCAATTTGAAATA
1 GCCAGCCTAAATTGAAAATCAATTTGAAATA
4943385 G
1 G
4943386 GAAAGGCTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 3 0.10
30 16 0.55
31 6 0.21
32 4 0.14
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (31 bp):
GCCAGCCTAAATTGAAAATCAATTTGAAATA
Found at i:4943816 original size:44 final size:44
Alignment explanation
Indices: 4943754--4943878 Score: 214
Period size: 44 Copynumber: 2.8 Consensus size: 44
4943744 GGTGTTTTGT
* *
4943754 TTTATTTATTTTTTCGTGGATTGACATAGCCACCCAATTGCATA
1 TTTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATA
4943798 TTTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATA
1 TTTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATA
* *
4943842 TTTACTTATTTTTCCGTAGATTGGCATAGCCACCCAA
1 TTTATTTATTTTTCCGTGGATTGGCATAGCCACCCAA
4943879 ATTCTAACAA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 77 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (44 bp):
TTTATTTATTTTTCCGTGGATTGGCATAGCCACCCAATTGCATA
Found at i:4947372 original size:18 final size:18
Alignment explanation
Indices: 4947351--4947387 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4947341 CAAACACTTG
*
4947351 ATCATCATCAAATGCTTC
1 ATCATAATCAAATGCTTC
*
4947369 ATCATAATCAAATGTTTC
1 ATCATAATCAAATGCTTC
4947387 A
1 A
4947388 CATGTACAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (18 bp):
ATCATAATCAAATGCTTC
Found at i:4948049 original size:2 final size:2
Alignment explanation
Indices: 4948044--4948068 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4948034 ATTAGAAAAA
4948044 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
4948069 ATAGAGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4954114 original size:52 final size:52
Alignment explanation
Indices: 4954036--4954164 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
4954026 TGAAATATGA
*
4954036 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* *
4954088 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
4954140 AAATTTGCTTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
4954165 AAGATCATTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:4957041 original size:27 final size:27
Alignment explanation
Indices: 4957011--4957068 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
4957001 CAACAACTCC
*
4957011 GAGTTGCATTAGAAAGAGAGCAATATA
1 GAGTTGCATTAGAAAGAGAGCAACATA
4957038 GAGTTGCATTAGAAAGAGAGCAACATA
1 GAGTTGCATTAGAAAGAGAGCAACATA
4957065 GAGT
1 GAGT
4957069 GGCTCAGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.21
Consensus pattern (27 bp):
GAGTTGCATTAGAAAGAGAGCAACATA
Found at i:4964141 original size:21 final size:21
Alignment explanation
Indices: 4964117--4964163 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4964107 TTTGAAGCTG
4964117 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
4964137 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
4964158 ATTTTG
1 ATTTTG
4964164 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:4968025 original size:53 final size:53
Alignment explanation
Indices: 4967945--4968050 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
4967935 TTTGGCACCC
4967945 ATACTTCCTTAACAATTTTGCCTCTAAATTTATTTATTTTAGAGTTGCACGTG
1 ATACTTCCTTAACAATTTTGCCTCTAAATTTATTTATTTTAGAGTTGCACGTG
4967998 ATACTTCCTTAACAATTTTGCCTCTAAATTTATTTATTTTAGAGTTGCACGTG
1 ATACTTCCTTAACAATTTTGCCTCTAAATTTATTTATTTTAGAGTTGCACGTG
4968051 TGAAATGTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.45
Consensus pattern (53 bp):
ATACTTCCTTAACAATTTTGCCTCTAAATTTATTTATTTTAGAGTTGCACGTG
Found at i:4981311 original size:42 final size:43
Alignment explanation
Indices: 4981187--4981482 Score: 164
Period size: 42 Copynumber: 7.0 Consensus size: 43
4981177 TCAAGCCTGT
* * *
4981187 CTGTCGGCTTTTGACCCTAGAGACTTT-TCTA-CATTCAATCTGC
1 CTGTCGGC-TTTGACCCTAGAGACTTTCT-TACCTTTTAGTCTGC
* ** * * ** * **
4981230 ATGTCAACTTTGACCTTGGAGACTGCCTTATC-TCAAGTCTGC
1 CTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTTTAGTCTGC
* * *
4981272 TTGTCAGCTTTGA-CCTAGAAACTTTCTTACCTTTTAGTCTGC
1 CTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTTTAGTCTGC
* * * ** * *
4981314 CTGTTGGTTTTGACCCT-GAAGAC-TGCTT-CACTTAAAATCTAC
1 CTGTCGGCTTTGACCCTAG-AGACTTTCTTAC-CTTTTAGTCTGC
* * * * *
4981356 TTATCGGCTTTGACCCTAGAGACTTTCCTACC-TTTAATCTAC
1 CTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTTTAGTCTGC
* * * * *
4981398 CTGTCAGCTTTGACCTTTGAGACTTTCTTACC-CTCAGTCTGC
1 CTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTTTAGTCTGC
*
4981440 CTGTCGGCTTTGACCCTGGAGACTTT-TTCACCTTTTA-TCTGC
1 CTGTCGGCTTTGACCCTAGAGACTTTCTT-ACCTTTTAGTCTGC
4981482 C
1 C
4981483 CGTTTGCTTC
Statistics
Matches: 189, Mismatches: 53, Indels: 23
0.71 0.20 0.09
Matches are distributed among these distances:
41 15 0.08
42 153 0.81
43 20 0.11
44 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (43 bp):
CTGTCGGCTTTGACCCTAGAGACTTTCTTACCTTTTAGTCTGC
Found at i:4981447 original size:84 final size:84
Alignment explanation
Indices: 4981138--4981482 Score: 236
Period size: 84 Copynumber: 4.1 Consensus size: 84
4981128 CTTACCCCTC
* * * * * * * *
4981138 AATCTGCCTGTCGGCTTTGACCTTAGAGACTGCGTCA-TCTCAAGCCTGTCTGTCGGCTTTTGAC
1 AATCTGCCTGTCAGCTTTGACCTTTGAGACTTCCTTACCCTC-AGTCTGCCTGTCGGC-TTTGAC
* * *
4981202 CCTAGAGACTTTTCTACATTC
64 CCTAGAGACTTTCCTACCTTT
* * * * * * *
4981223 AATCTGCATGTCAACTTTGACCTTGGAGACTGCCTTA-TCTCAAGTCTGCTTGTCAGCTTTGA-C
1 AATCTGCCTGTCAGCTTTGACCTTTGAGACTTCCTTACCCTC-AGTCTGCCTGTCGGCTTTGACC
* *
4981286 CTAGAAACTTTCTTACCTTTT
65 CTAGAGACTTTCCTACC-TTT
* ** * * * * * * * * *
4981307 AGTCTGCCTGTTGGTTTTGACC-CTGAAGAC-TGCTT-CACTTAAAATCTACTTATCGGCTTTGA
1 AATCTGCCTGTCAGCTTTGACCTTTG-AGACTTCCTTAC-CCT-CAGTCTGCCTGTCGGCTTTGA
4981369 CCCTAGAGACTTTCCTACCTTT
63 CCCTAGAGACTTTCCTACCTTT
* *
4981391 AATCTACCTGTCAGCTTTGACCTTTGAGACTTTCTTACCCTCAGTCTGCCTGTCGGCTTTGACCC
1 AATCTGCCTGTCAGCTTTGACCTTTGAGACTTCCTTACCCTCAGTCTGCCTGTCGGCTTTGACCC
* *
4981456 TGGAGACTTT-TTCACCTTT
66 TAGAGACTTTCCT-ACCTTT
*
4981475 TATCTGCC
1 AATCTGCC
4981483 CGTTTGCTTC
Statistics
Matches: 199, Mismatches: 51, Indels: 21
0.73 0.19 0.08
Matches are distributed among these distances:
83 19 0.10
84 108 0.54
85 71 0.36
86 1 0.01
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.37
Consensus pattern (84 bp):
AATCTGCCTGTCAGCTTTGACCTTTGAGACTTCCTTACCCTCAGTCTGCCTGTCGGCTTTGACCC
TAGAGACTTTCCTACCTTT
Found at i:4982000 original size:11 final size:12
Alignment explanation
Indices: 4981982--4982027 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
4981972 TTTGACATTA
4981982 AAAATAAAAA-T
1 AAAATAAAAATT
*
4981993 ATAATAAAAATT
1 AAAATAAAAATT
4982005 AAAATAAAATAATT
1 AAAAT-AAA-AATT
4982019 -AAATAAAAA
1 AAAATAAAAA
4982028 ATATGTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
11 11 0.37
12 8 0.27
13 7 0.23
14 4 0.13
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:4982002 original size:17 final size:17
Alignment explanation
Indices: 4981980--4982027 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
4981970 TATTTGACAT
*
4981980 TAAAAATAAAAATATAA
1 TAAAAATAAAAATAAAA
*
4981997 TAAAAATTAAAATAAAA
1 TAAAAATAAAAATAAAA
4982014 TAATTAAATAAAAA
1 TAA--AAATAAAAA
4982028 ATATGTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 18 0.69
19 8 0.31
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAAAATAAAAATAAAA
Found at i:4982442 original size:12 final size:12
Alignment explanation
Indices: 4982425--4982466 Score: 66
Period size: 12 Copynumber: 3.3 Consensus size: 12
4982415 CAGCCGAGGT
4982425 GCAATGAAGAAA
1 GCAATGAAGAAA
4982437 GCAATGAAGCAAA
1 GCAATGAAG-AAA
4982450 TGCAATGAAGAAA
1 -GCAATGAAGAAA
4982463 GCAA
1 GCAA
4982467 ACGACAAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 13 0.46
13 6 0.21
14 9 0.32
ACGTcount: A:0.55, C:0.12, G:0.24, T:0.10
Consensus pattern (12 bp):
GCAATGAAGAAA
Found at i:4983010 original size:14 final size:12
Alignment explanation
Indices: 4982966--4983048 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 12
4982956 ATCGCAATAG
4982966 CAGAAACGAAAA
1 CAGAAACGAAAA
*
4982978 -A-AAAGGAAAA
1 CAGAAACGAAAA
*
4982988 -AGAATCGAAATA
1 CAGAAACGAAA-A
4983000 GCAGAAACGAAAA
1 -CAGAAACGAAAA
* *
4983013 AAGTAA-GAAAA
1 CAGAAACGAAAA
*
4983024 CAGAATCGAAATA
1 CAGAAACGAAA-A
4983037 GCAGAAAC-AAAA
1 -CAGAAACGAAAA
4983049 AAAAGAAAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
10 9 0.17
11 15 0.28
12 10 0.19
13 5 0.09
14 15 0.28
ACGTcount: A:0.65, C:0.11, G:0.18, T:0.06
Consensus pattern (12 bp):
CAGAAACGAAAA
Found at i:4983038 original size:37 final size:35
Alignment explanation
Indices: 4982954--4983058 Score: 153
Period size: 35 Copynumber: 3.0 Consensus size: 35
4982944 GAGAAGAGAG
*
4982954 GAATCGCAATAGCAGAAACGAAAAAA-AAGGAAAAA
1 GAATCGAAATAGCAGAAACGAAAAAAGAA-GAAAAA
4982989 GAATCGAAATAGCAGAAACGAAAAAAGTAAGAAAACA
1 GAATCGAAATAGCAGAAACGAAAAAAG-AAGAAAA-A
4983026 GAATCGAAATAGCAGAAAC-AAAAAA-AAGAAAAA
1 GAATCGAAATAGCAGAAACGAAAAAAGAAGAAAAA
4983059 AAATAGAATC
Statistics
Matches: 66, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
33 1 0.02
34 7 0.11
35 25 0.38
36 11 0.17
37 22 0.33
ACGTcount: A:0.65, C:0.10, G:0.18, T:0.07
Consensus pattern (35 bp):
GAATCGAAATAGCAGAAACGAAAAAAGAAGAAAAA
Found at i:4984339 original size:38 final size:38
Alignment explanation
Indices: 4984293--4984368 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
4984283 AAATTTAAAA
*
4984293 AAATTCAACTTCCCTAAATTAATATTTTTTAAAAAATG
1 AAATTCAACTTCCCAAAATTAATATTTTTTAAAAAATG
4984331 AAATTCAACTTCCCAAAATTAATATTTTTTAAAAAATG
1 AAATTCAACTTCCCAAAATTAATATTTTTTAAAAAATG
4984369 TGATCGTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (38 bp):
AAATTCAACTTCCCAAAATTAATATTTTTTAAAAAATG
Found at i:4987812 original size:31 final size:31
Alignment explanation
Indices: 4987777--4987839 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
4987767 ATAAAACAAA
4987777 CTAAAAATGCCTAATCATCAGGGTCAAACCC
1 CTAAAAATGCCTAATCATCAGGGTCAAACCC
4987808 CTAAAAATGCCTAATCATCAGGGTCAAACCC
1 CTAAAAATGCCTAATCATCAGGGTCAAACCC
4987839 C
1 C
4987840 CCAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (31 bp):
CTAAAAATGCCTAATCATCAGGGTCAAACCC
Found at i:4988833 original size:174 final size:174
Alignment explanation
Indices: 4988543--4988894 Score: 704
Period size: 174 Copynumber: 2.0 Consensus size: 174
4988533 TAACCCAATT
4988543 TTCAAGTCTCATATATATAATATAGTGCTTATAATTTCAAATATCTTACTTGCATGTATCTAGCC
1 TTCAAGTCTCATATATATAATATAGTGCTTATAATTTCAAATATCTTACTTGCATGTATCTAGCC
4988608 AAAGGCCCAGGTCCTCTTGAGTTAATGCCTGAATCTTTAGAATTGGTTTACTAGTATGTTTACCA
66 AAAGGCCCAGGTCCTCTTGAGTTAATGCCTGAATCTTTAGAATTGGTTTACTAGTATGTTTACCA
4988673 AGTAATGTTGGCATAAATTTTAGCACTACACCACACATAACAAA
131 AGTAATGTTGGCATAAATTTTAGCACTACACCACACATAACAAA
4988717 TTCAAGTCTCATATATATAATATAGTGCTTATAATTTCAAATATCTTACTTGCATGTATCTAGCC
1 TTCAAGTCTCATATATATAATATAGTGCTTATAATTTCAAATATCTTACTTGCATGTATCTAGCC
4988782 AAAGGCCCAGGTCCTCTTGAGTTAATGCCTGAATCTTTAGAATTGGTTTACTAGTATGTTTACCA
66 AAAGGCCCAGGTCCTCTTGAGTTAATGCCTGAATCTTTAGAATTGGTTTACTAGTATGTTTACCA
4988847 AGTAATGTTGGCATAAATTTTAGCACTACACCACACATAACAAA
131 AGTAATGTTGGCATAAATTTTAGCACTACACCACACATAACAAA
4988891 TTCA
1 TTCA
4988895 TAAACAACTT
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 178 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (174 bp):
TTCAAGTCTCATATATATAATATAGTGCTTATAATTTCAAATATCTTACTTGCATGTATCTAGCC
AAAGGCCCAGGTCCTCTTGAGTTAATGCCTGAATCTTTAGAATTGGTTTACTAGTATGTTTACCA
AGTAATGTTGGCATAAATTTTAGCACTACACCACACATAACAAA
Found at i:4990137 original size:155 final size:153
Alignment explanation
Indices: 4989843--4990138 Score: 425
Period size: 155 Copynumber: 1.9 Consensus size: 153
4989833 TTGCAAGACA
* * *
4989843 AAGATTGGCTCAATAAGTAGAACCAGCAGACAGAAAAAATGTGCTGTAAAAAACTGAGAATTGTA
1 AAGATAGGCTCAATAAATAGAACCAGCAGACAGAAAAAATGTGCTGTAAAAAACTGAAAATTGTA
*
4989908 CACAACACTCACGTCTAAATATACTCAATATATTAAAACCAGAAATACTTAAAACACATTAAGCT
66 CACAACACTCACGTCTAAATATACTC-ATACATTAAAACCAGAAATACTTAAAACACATTAAGCT
4989973 TTGAGATGAAATCACCTTACCCCC
130 TTGAGATGAAATCACCTTACCCCC
*
4989997 AAGATAGGCTCAATAAATAGAACCAGCAGACAGAAAAGAAATGTGCTGTGAAAAACTGAAAATTG
1 AAGATAGGCTCAATAAATAGAACCAGCAGACAG-AAA-AAATGTGCTGTAAAAAACTGAAAATTG
* * * * * **
4990062 TACACAACAC-CAACTTAGTAAATATACTC-TACATTGAAACCTGTAATACTTAAAACATGTTAA
64 TACACAACACTC-ACGT-CTAAATATACTCATACATTAAAACCAGAAATACTTAAAACACATTAA
4990125 GCTTTGAGATGAAA
127 GCTTTGAGATGAAA
4990139 ATTGCCATAC
Statistics
Matches: 126, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
154 31 0.25
155 46 0.37
156 38 0.30
157 11 0.09
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (153 bp):
AAGATAGGCTCAATAAATAGAACCAGCAGACAGAAAAAATGTGCTGTAAAAAACTGAAAATTGTA
CACAACACTCACGTCTAAATATACTCATACATTAAAACCAGAAATACTTAAAACACATTAAGCTT
TGAGATGAAATCACCTTACCCCC
Found at i:4991691 original size:102 final size:102
Alignment explanation
Indices: 4991515--4991723 Score: 418
Period size: 102 Copynumber: 2.0 Consensus size: 102
4991505 AATTATAACC
4991515 AAAAGATTATAACGAAATTTCTGCTAATCCAAAAGATTTTCTGTCAAATACTTACTCTGCAATTG
1 AAAAGATTATAACGAAATTTCTGCTAATCCAAAAGATTTTCTGTCAAATACTTACTCTGCAATTG
4991580 AAAGGTTTCTTCAGCATGTGAGAGTCCCTAGCAGAAA
66 AAAGGTTTCTTCAGCATGTGAGAGTCCCTAGCAGAAA
4991617 AAAAGATTATAACGAAATTTCTGCTAATCCAAAAGATTTTCTGTCAAATACTTACTCTGCAATTG
1 AAAAGATTATAACGAAATTTCTGCTAATCCAAAAGATTTTCTGTCAAATACTTACTCTGCAATTG
4991682 AAAGGTTTCTTCAGCATGTGAGAGTCCCTAGCAGAAA
66 AAAGGTTTCTTCAGCATGTGAGAGTCCCTAGCAGAAA
4991719 AAAAG
1 AAAAG
4991724 GCCTATTAAA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 107 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (102 bp):
AAAAGATTATAACGAAATTTCTGCTAATCCAAAAGATTTTCTGTCAAATACTTACTCTGCAATTG
AAAGGTTTCTTCAGCATGTGAGAGTCCCTAGCAGAAA
Found at i:4991957 original size:85 final size:84
Alignment explanation
Indices: 4991810--4991975 Score: 305
Period size: 85 Copynumber: 2.0 Consensus size: 84
4991800 TAAGCCAGCA
*
4991810 TAAAAAGCAGCCTTCAAGGAAATAATTATTAGTAATAAATTTGAATCACTTCTAGCAACAATAAG
1 TAAAAAGCAGCCTTCAAGGAAATAATTATTACTAATAAATTTGAATCACTTCTAGCAACAATAAG
4991875 ACCTAAAAGAGTTTATTAG
66 ACCTAAAAGAGTTTATTAG
*
4991894 TAAACAAGCAGCCTTCAAGGAAATAATTATTACTAATAAATTTGAATCACTTCTAGTAACAATAA
1 TAAA-AAGCAGCCTTCAAGGAAATAATTATTACTAATAAATTTGAATCACTTCTAGCAACAATAA
4991959 GACCTAAAAGAGTTTAT
65 GACCTAAAAGAGTTTAT
4991976 ATCCAATTCG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
84 4 0.05
85 75 0.95
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (84 bp):
TAAAAAGCAGCCTTCAAGGAAATAATTATTACTAATAAATTTGAATCACTTCTAGCAACAATAAG
ACCTAAAAGAGTTTATTAG
Found at i:4994174 original size:2 final size:2
Alignment explanation
Indices: 4994169--4994200 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4994159 TATATATATA
4994169 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4994201 CATGTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4994322 original size:2 final size:2
Alignment explanation
Indices: 4994315--4994340 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4994305 TAAATGAGAA
4994315 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
4994341 GTGTGTGTGT
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:4994345 original size:2 final size:2
Alignment explanation
Indices: 4994340--4994371 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4994330 TATATATATA
*
4994340 TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
4994372 CATGTATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
TG
Found at i:4999044 original size:7 final size:7
Alignment explanation
Indices: 4999029--4999061 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
4999019 ATTGGAGCAG
4999029 AAAAA-T
1 AAAAATT
4999035 AAAAATT
1 AAAAATT
4999042 AAAAAATT
1 -AAAAATT
4999050 AAAAATT
1 AAAAATT
4999057 AAAAA
1 AAAAA
4999062 AAAAAAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 5 0.20
7 13 0.52
8 7 0.28
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAAATT
Found at i:4999069 original size:15 final size:15
Alignment explanation
Indices: 4999029--4999068 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
4999019 ATTGGAGCAG
4999029 AAAAATAAAAATTAA
1 AAAAATAAAAATTAA
*
4999044 AAAATTAAAAATTAA
1 AAAAATAAAAATTAA
4999059 AAAAA-AAAAA
1 AAAAATAAAAA
4999069 AGAATGGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAAATTAA
Found at i:5001058 original size:23 final size:23
Alignment explanation
Indices: 5001032--5001083 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
5001022 GGATGGATTC
5001032 GGTGCCATACCCTCGGCGGAGGA
1 GGTGCCATACCCTCGGCGGAGGA
*
5001055 GGTGCCATATCCTCGGCGGAGGA
1 GGTGCCATACCCTCGGCGGAGGA
5001078 GGTGCC
1 GGTGCC
5001084 TCCCGGCGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.15, C:0.29, G:0.40, T:0.15
Consensus pattern (23 bp):
GGTGCCATACCCTCGGCGGAGGA
Found at i:5002169 original size:17 final size:17
Alignment explanation
Indices: 5002147--5002189 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
5002137 TAAAAAAGTA
*
5002147 ATAATTTAACTATTTTT
1 ATAATTTAACTAATTTT
***
5002164 ATAATTTTTTTAATTTT
1 ATAATTTAACTAATTTT
5002181 ATAATTTAA
1 ATAATTTAA
5002190 AAGAAATTAA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTAACTAATTTT
Found at i:5003169 original size:30 final size:30
Alignment explanation
Indices: 5003133--5003190 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
5003123 CTTACAACAC
5003133 TATCTTTT-TAGGGCTAAGATAGAACCTCTT
1 TATCTTTTATA-GGCTAAGATAGAACCTCTT
*
5003163 TATCTTTTCATAGGTTAAGATAGAACCT
1 TATCTTTT-ATAGGCTAAGATAGAACCT
5003191 TTCTCCCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 15 0.60
32 2 0.08
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (30 bp):
TATCTTTTATAGGCTAAGATAGAACCTCTT
Found at i:5003218 original size:36 final size:32
Alignment explanation
Indices: 5003132--5003229 Score: 85
Period size: 36 Copynumber: 3.0 Consensus size: 32
5003122 CCTTACAACA
*
5003132 CTATCTTTTT--AGGGCTAAGATAGAACCTCT
1 CTATCTTTTTCAAAGGCTAAGATAGAACCTCT
* * *
5003162 TTATC-TTTTCATAGGTTAAGATAGAACCTTTCT
1 CTATCTTTTTCAAAGGCTAAGATAGAACC--TCT
* *
5003195 CCCTATCTTTTTCAAAGGCTAAGACAAAACCTCT
1 --CTATCTTTTTCAAAGGCTAAGATAGAACCTCT
5003229 C
1 C
5003230 AATCACTTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
29 4 0.08
30 4 0.08
31 14 0.27
32 1 0.02
33 3 0.06
34 3 0.06
35 4 0.08
36 19 0.37
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (32 bp):
CTATCTTTTTCAAAGGCTAAGATAGAACCTCT
Found at i:5003722 original size:52 final size:52
Alignment explanation
Indices: 5003642--5003749 Score: 128
Period size: 52 Copynumber: 2.1 Consensus size: 52
5003632 ATGCATTTGA
* *
5003642 AATTCTAGCCGTTGGACTCAATATATCGATATAA-TTCATAATGTATCGATAC
1 AATTATAGCCGTTGGACTCAATATATCGATACAACTT-ATAATGTATCGATAC
* * * * * *
5003694 AATTATAGCTGTTGGGCTTAATGTATCGATACAACTTATCATGTATCGATAT
1 AATTATAGCCGTTGGACTCAATATATCGATACAACTTATAATGTATCGATAC
5003746 AATT
1 AATT
5003750 CAATTAAGGT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 45 0.96
53 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (52 bp):
AATTATAGCCGTTGGACTCAATATATCGATACAACTTATAATGTATCGATAC
Found at i:5004242 original size:13 final size:13
Alignment explanation
Indices: 5004224--5004248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5004214 AAATTGCACA
5004224 GTATCGATACATT
1 GTATCGATACATT
5004237 GTATCGATACAT
1 GTATCGATACAT
5004249 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:5004261 original size:20 final size:21
Alignment explanation
Indices: 5004236--5004288 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
5004226 ATCGATACAT
**
5004236 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAATAA
*
5004256 TGTATCGATACTTGAAAATAA
1 TGTATCGATACATGAAAATAA
5004277 TGTATCGATACA
1 TGTATCGATACA
5004289 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGAAAATAA
Found at i:5004358 original size:13 final size:13
Alignment explanation
Indices: 5004340--5004365 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5004330 GCACACAATA
5004340 TGTATCGATACAT
1 TGTATCGATACAT
5004353 TGTATCGATACAT
1 TGTATCGATACAT
5004366 CCTAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5010554 original size:13 final size:13
Alignment explanation
Indices: 5010532--5010569 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
5010522 CAGCATTCTC
*
5010532 TGTATCGATACAT
1 TGTATCGATACAG
*
5010545 TGTTTCGATACAG
1 TGTATCGATACAG
5010558 TGTATCGATACA
1 TGTATCGATACA
5010570 AGGGGATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:5010736 original size:20 final size:20
Alignment explanation
Indices: 5010701--5010741 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
5010691 CAAATTTCTT
5010701 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
5010723 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
5010742 AACAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:5012453 original size:22 final size:22
Alignment explanation
Indices: 5012427--5012471 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5012417 CGAAAGTGTT
*
5012427 AAATTATTTT-ACTAAGGGGGAG
1 AAATT-TTTTGACTAAGGGAGAG
*
5012449 AAATTTTTTGATTAAGGGAGAG
1 AAATTTTTTGACTAAGGGAGAG
5012471 A
1 A
5012472 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.38, C:0.02, G:0.27, T:0.33
Consensus pattern (22 bp):
AAATTTTTTGACTAAGGGAGAG
Found at i:5013044 original size:13 final size:13
Alignment explanation
Indices: 5013026--5013051 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5013016 CAAATACCTA
5013026 TGTATCGATACAT
1 TGTATCGATACAT
5013039 TGTATCGATACAT
1 TGTATCGATACAT
5013052 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5013064 original size:20 final size:21
Alignment explanation
Indices: 5013039--5013089 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
5013029 ATCGATACAT
**
5013039 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
5013059 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
5013080 TGTATCGATA
1 TGTATCGATA
5013090 TAGATCATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:5013161 original size:13 final size:13
Alignment explanation
Indices: 5013143--5013168 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5013133 ACACATAATA
5013143 TGTATCGATACAT
1 TGTATCGATACAT
5013156 TGTATCGATACAT
1 TGTATCGATACAT
5013169 CCTAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5013184 original size:33 final size:32
Alignment explanation
Indices: 5013123--5013190 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
5013113 GTAGCCAAAT
*
5013123 TTGTATCGATACACATAATATGTATCGATACA
1 TTGTATCGATACACATAAAATGTATCGATACA
*
5013155 TTGTATCGATACATCCTAAAATGTATCGATACA
1 TTGTATCGATACA-CATAAAATGTATCGATACA
5013188 TTG
1 TTG
5013191 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACACATAAAATGTATCGATACA
Found at i:5015991 original size:19 final size:20
Alignment explanation
Indices: 5015949--5016014 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 20
5015939 ATAAGTATCT
5015949 TTAATC-AT-AAATTTAATAG
1 TTAATCAATGAAA-TTAATAG
* *
5015968 CTAATCAATGTAAA-TAAT-T
1 TTAATCAATG-AAATTAATAG
5015987 TTAATC-ATGAAATTAATAG
1 TTAATCAATGAAATTAATAG
5016006 TTAATCAAT
1 TTAATCAAT
5016015 ACTAACAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
17 3 0.08
18 7 0.19
19 16 0.43
20 8 0.22
22 3 0.08
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (20 bp):
TTAATCAATGAAATTAATAG
Found at i:5017055 original size:19 final size:17
Alignment explanation
Indices: 5017031--5017086 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
5017021 TTTAAAATTC
5017031 ATATTTATCTCAATAAAT
1 ATATTTATCT-AATAAAT
5017049 AATATTTATCTAATAAAT
1 -ATATTTATCTAATAAAT
* *
5017067 ATAATTATCTAATAATT
1 ATATTTATCTAATAAAT
5017084 ATA
1 ATA
5017087 AGGTTAGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 18 0.51
18 7 0.20
19 10 0.29
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTTATCTAATAAAT
Found at i:5018984 original size:16 final size:17
Alignment explanation
Indices: 5018963--5018994 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5018953 AGATATTGCC
5018963 TTAATTT-TTTAAAATT
1 TTAATTTATTTAAAATT
5018979 TTAATTTATTTAAAAT
1 TTAATTTATTTAAAAT
5018995 ATAAATAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATTTATTTAAAATT
Found at i:5019362 original size:156 final size:156
Alignment explanation
Indices: 5019105--5019773 Score: 584
Period size: 156 Copynumber: 4.3 Consensus size: 156
5019095 GTTCTAATGC
** * * * ** *
5019105 AAAATTATTAAAATACCTTTAAGATATACCTTCGATGTGAAAGTATCTT-AGTAAACTCTAAAAG
1 AAAATTACGAAAATACCTCTAAGGTATACCTTTGACATGAAAGTATCTTGA-T-AACCCTAAAAG
* * **
5019169 ACTTAAAAATGATCATAAATGGGATGAACCTATCCTAAATACAC-ACTTTTGGCATAAAAGTATC
64 ACTTAAAAATGATCATAAATGAGATGAACCTATCCTAAATGCACAAC-TTTGGCATAAAAACATC
* *
5019233 CCGAAGACGACTTAAGACTTGCTTTTAAA
128 CCGAAGACGACCTAAGACTTGGTTTTAAA
* *
5019262 AAAATTACGAAAATACCTCTAAGGTATACCTTTGACATGAAAGTATCTTTATAACCCTAAAAAAC
1 AAAATTACGAAAATACCTCTAAGGTATACCTTTGACATGAAAGTATCTTGATAACCCTAAAAGAC
* *
5019327 TTAAAAATAATCATAAATGAGATGAACTTATCCTAAATGCACAACTTTGGCATAAAAACATCCC-
66 TTAAAAATGATCATAAATGAGATGAACCTATCCTAAATGCACAACTTTGGCATAAAAACATCCCG
* * *
5019391 AATGACGACCTAGGACTCGGTTCTAAA
131 AA-GACGACCTAAGACTTGGTTTTAAA
* * * ** * * ** **
5019418 AAAGTTATGAAAATGCC-CTTTGGGTATA-CTTTCA-ATGGGAAAGTATCTTGGTAACCGGAATG
1 AAAATTACGAAAATACCTC-TAAGGTATACCTTTGACAT--GAAAGTATCTTGATAACCCTAAAA
* * * *
5019480 GACACT-AAAATGATCATAAATGAGATGAAACTATCCTAAATGCACATCTTTGGCGTAAAAACAT
63 GAC-TTAAAAATGATCATAAATGAGATGAACCTATCCTAAATGCACAACTTTGGCATAAAAACAT
* ** * *
5019544 CCTGGTGATGACCTAAGACTTGGTTTTAGA
127 CCCGAAGACGACCTAAGACTTGGTTTTAAA
* * ** * * * *
5019574 AAAATTACGAAAATTCC-CTTGAGGTATACCTTTGATGTGAAAGTATCTCGGTAACCTTAATAGA
1 AAAATTACGAAAATACCTC-TAAGGTATACCTTTGACATGAAAGTATCTTGATAACCCTAAAAGA
*** * * * ** * *
5019638 CACCAAAATGATCATAAGTGGGATGAACCTATCCTGAATGCACAACTTCAGCATAAAAGCATCCT
65 CTTAAAAATGATCATAAATGAGATGAACCTATCCTAAATGCACAACTTTGGCATAAAAACATCCC
** * * *
5019703 GGTGACAATCTAAGACTTGGTTTT-AG
130 GAAGACGACCTAAGACTTGGTTTTAAA
* * *
5019729 AAAATTACAAAAATACCTCT-TGGTATATCTTTGACATGAAAGTAT
1 AAAATTACGAAAATACCTCTAAGGTATACCTTTGACATGAAAGTAT
5019774 TCGATGGCCC
Statistics
Matches: 420, Mismatches: 80, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
154 23 0.05
155 24 0.06
156 320 0.76
157 51 0.12
158 2 0.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (156 bp):
AAAATTACGAAAATACCTCTAAGGTATACCTTTGACATGAAAGTATCTTGATAACCCTAAAAGAC
TTAAAAATGATCATAAATGAGATGAACCTATCCTAAATGCACAACTTTGGCATAAAAACATCCCG
AAGACGACCTAAGACTTGGTTTTAAA
Found at i:5021297 original size:33 final size:33
Alignment explanation
Indices: 5021253--5021317 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
5021243 CACACCTAGA
*
5021253 TGTATCGATACAAATTGCTAAGTATCGATACAT
1 TGTATCCATACAAATTGCTAAGTATCGATACAT
**
5021286 TGTATCCATACAAATTGCTTTGTATCGATACA
1 TGTATCCATACAAATTGCTAAGTATCGATACA
5021318 CTATGAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCCATACAAATTGCTAAGTATCGATACAT
Found at i:5021948 original size:34 final size:34
Alignment explanation
Indices: 5021837--5021948 Score: 118
Period size: 34 Copynumber: 3.3 Consensus size: 34
5021827 AGAGTGATTG
* * *
5021837 GAAGGTTCTTTCTTAGCCTTTAAAAAAGATAGGGA
1 GAAGGTTCTATCTTAGCCTGT-GAAAAGATAGGGA
* * * * *
5021872 AAATGTTCTATCTTAGCTTGTGAAAAAATAAGGA
1 GAAGGTTCTATCTTAGCCTGTGAAAAGATAGGGA
*
5021906 -AGATGTTCTATCTTAGCCTGTGAAAAGATAGGGA
1 GA-AGGTTCTATCTTAGCCTGTGAAAAGATAGGGA
5021940 GAAGGTTCT
1 GAAGGTTCT
5021949 GTTAGGATTT
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
33 1 0.02
34 45 0.71
35 17 0.27
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (34 bp):
GAAGGTTCTATCTTAGCCTGTGAAAAGATAGGGA
Found at i:5022254 original size:20 final size:20
Alignment explanation
Indices: 5022229--5022299 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
5022219 ACCCTGAAAA
5022229 GTATCGATACACATTTAAAT
1 GTATCGATACACATTTAAAT
* *
5022249 GTATCGATACAGATTGTATA-
1 GTATCGATACACATT-TAAAT
**
5022269 GTATCGATACACA-CAAATAT
1 GTATCGATACACATTTAA-AT
5022289 GTATCGATACA
1 GTATCGATACA
5022300 GGACATTGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 37 0.88
21 3 0.07
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (20 bp):
GTATCGATACACATTTAAAT
Found at i:5022352 original size:53 final size:53
Alignment explanation
Indices: 5022269--5022405 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
5022259 AGATTGTATA
5022269 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
* *
5022323 GTATCGATACACACAATATGTATCGATACAGGTCATTGGTAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
* *
5022376 GTATCAATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
5022406 TTGGAAGTAG
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 65 0.82
54 14 0.18
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:5022468 original size:9 final size:10
Alignment explanation
Indices: 5022429--5022467 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5022419 AATCTCATTT
5022429 TCACTGTTCA
1 TCACTGTTCA
*
5022439 TCACTATTCA
1 TCACTGTTCA
*
5022449 TTACTGTTCA
1 TCACTGTTCA
5022459 -CACTGTTCA
1 TCACTGTTCA
5022468 CGTATCACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.23, C:0.28, G:0.08, T:0.41
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:5026071 original size:20 final size:20
Alignment explanation
Indices: 5026046--5026083 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5026036 TGGATTTTTC
5026046 CAAAATGTATCGATACATTG
1 CAAAATGTATCGATACATTG
*
5026066 CAAAATGTATTGATACAT
1 CAAAATGTATCGATACAT
5026084 CTAAGTTTTT
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:0.13, T:0.32
Consensus pattern (20 bp):
CAAAATGTATCGATACATTG
Found at i:5026117 original size:13 final size:13
Alignment explanation
Indices: 5026099--5026123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5026089 TTTTTCAAAT
5026099 TGTATCGATACAC
1 TGTATCGATACAC
5026112 TGTATCGATACA
1 TGTATCGATACA
5026124 TGAAAATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:5029126 original size:13 final size:14
Alignment explanation
Indices: 5029104--5029142 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
5029094 ATTATGCCTA
*
5029104 GTATCAATACAT-T
1 GTATCGATACATGT
5029117 GTATCGATACATGT
1 GTATCGATACATGT
5029131 GTATCGATACAT
1 GTATCGATACAT
5029143 ACTCAATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (14 bp):
GTATCGATACATGT
Found at i:5029318 original size:19 final size:20
Alignment explanation
Indices: 5029294--5029331 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5029284 TTAATTTCAA
5029294 ATGAA-TGTATCGATACATT
1 ATGAATTGTATCGATACATT
5029313 ATGAATTGTATCGATACAT
1 ATGAATTGTATCGATACAT
5029332 AGTAATGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (20 bp):
ATGAATTGTATCGATACATT
Found at i:5036260 original size:79 final size:79
Alignment explanation
Indices: 5035952--5036259 Score: 298
Period size: 79 Copynumber: 3.9 Consensus size: 79
5035942 TGGAGATAAC
* * *
5035952 AACAGGGCTGGAGTATCCGCGATTATGAAAAATCGATATTTTGGAAATAAAATCAGGGTTGGAGT
1 AACAGGGTTGGAGTATCCACGATTATGAAAAATCGATGTTTTGGAAATAAAATCAGGGTTGGAGT
*
5036017 ATCCCCTCGGAAAT
66 ATCCCCTCGAAAAT
* ** * * * *
5036031 AACAAGGTTGGAGTATCCTTGATTAT-AGAAAATTGATGTTTTGAAAATAAAATCGGGGTTAGAG
1 AACAGGGTTGGAGTATCCACGATTATGA-AAAATCGATGTTTTGGAAATAAAATCAGGGTTGGAG
* * *
5036095 TTTCTCCTCAAAAAT
65 TATCCCCTCGAAAAT
* * * * * **** *
5036110 AAC-GGGATTAGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATATGGCCGGGGTTGGAG
1 AACAGGG-TTGGAGTATCCACGATTATGAAAAATCGATGTTTTGGAAATAAAATCAGGGTTGGAG
5036174 TATCCCCGT-GAAAAT
65 TATCCCC-TCGAAAAT
* * * * * *
5036189 AACAGGGTTGGAGTATCCACGATTATGAGAAATTGGTGTTTTGGAAATAAAATTAGAGTTTGAGT
1 AACAGGGTTGGAGTATCCACGATTATGAAAAATCGATGTTTTGGAAATAAAATCAGGGTTGGAGT
5036254 ATCCCC
66 ATCCCC
5036260 GATTGTGAAA
Statistics
Matches: 178, Mismatches: 46, Indels: 10
0.76 0.20 0.04
Matches are distributed among these distances:
78 3 0.02
79 170 0.96
80 5 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (79 bp):
AACAGGGTTGGAGTATCCACGATTATGAAAAATCGATGTTTTGGAAATAAAATCAGGGTTGGAGT
ATCCCCTCGAAAAT
Found at i:5036263 original size:51 final size:51
Alignment explanation
Indices: 5036195--5036310 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 51
5036185 AAATAACAGG
* * * * * *
5036195 GTTGGAGTATCCACGATTATGAGAAATTGGTGTTTTGGAAATAAAATTAGA
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAATCAGA
* * * *
5036246 GTTTGAGTATCCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAATCAGA
5036297 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
5036311 TCGAAAATAA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATTAGTATTTTAGAAATAAAATCAGA
Found at i:5036392 original size:108 final size:107
Alignment explanation
Indices: 5036256--5036525 Score: 328
Period size: 108 Copynumber: 2.5 Consensus size: 107
5036246 GTTTGAGTAT
* *
5036256 CCCCGATTGTGAAAAATTAGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAA
1 CCCCAATTATGAAAAATTAGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAA
* * * *
5036321 -TGGGATTGGAGTAT-CCCGATTACATAATGGGGTTGGAATAC
66 CAGGG-TTGGAGTATCCCCGATGAAATAACGGGGTTGGAATAC
* * * * ** *
5036362 CCCCGATTATGAAAAAAATCAATATTTTAGATATAAAGCCAGGGTTGGAGTATCCCCTCGAAAAT
1 CCCCAATTATG--AAAAATTAGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAAT
* *
5036427 AACAGGGTTGGAGTATCCCCGATGAAATAACGGGGTTGGAGTAT
64 AACAGGGTTGGAGTATCCCCGATGAAATAACGGGGTTGGAATAC
* * * *
5036471 CCCCAATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 CCCCAATTATGAAAAATTAGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
5036526 GATTGTGGTA
Statistics
Matches: 136, Mismatches: 24, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
106 10 0.07
107 34 0.25
108 57 0.42
109 35 0.26
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (107 bp):
CCCCAATTATGAAAAATTAGTATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAA
CAGGGTTGGAGTATCCCCGATGAAATAACGGGGTTGGAATAC
Found at i:5036441 original size:28 final size:28
Alignment explanation
Indices: 5036401--5036474 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
5036391 GATATAAAGC
5036401 CAGGGTTGGAGTATCCCCTCGA-AAATAA
1 CAGGGTTGGAGTATCCCC-CGAGAAATAA
5036429 CAGGGTTGGAGTAT-CCCCGATGAAATAA
1 CAGGGTTGGAGTATCCCCCGA-GAAATAA
*
5036457 CGGGGTTGGAGTATCCCC
1 CAGGGTTGGAGTATCCCC
5036475 AATTATGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 3 0.07
27 3 0.07
28 33 0.79
29 3 0.07
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.22
Consensus pattern (28 bp):
CAGGGTTGGAGTATCCCCCGAGAAATAA
Found at i:5036553 original size:51 final size:51
Alignment explanation
Indices: 5036461--5036604 Score: 153
Period size: 51 Copynumber: 2.8 Consensus size: 51
5036451 AAATAACGGG
* * * * * *
5036461 GTTGGAGTATCCCCAATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGATGCTTTAGAAATAAAATCAGA
* **
5036512 GTTGGAGTATCCCCGATTGTGGTAAATCGATGCTTTAGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGATGCTTTAGAAATAAAATCAGA
* * * ** *
5036563 GTTTGAGTATCCTCGATTAAGAAAAATTAATGTTTTAGAAAT
1 GTTGGAGTATCCCCGATTATGAAAAATCGATGCTTTAGAAAT
5036605 GGAACCGAGA
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGAAAAATCGATGCTTTAGAAATAAAATCAGA
Found at i:5038999 original size:20 final size:20
Alignment explanation
Indices: 5038974--5039028 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
5038964 GTAAACCCTG
*
5038974 AATGTATCAATACAATGAAC
1 AATGTATCGATACAATGAAC
*
5038994 AATGTATCGATATAATGAAC
1 AATGTATCGATACAATGAAC
5039014 AATGTATCGATACAA
1 AATGTATCGATACAA
5039029 ATTGTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:5039797 original size:41 final size:42
Alignment explanation
Indices: 5039736--5039876 Score: 151
Period size: 41 Copynumber: 3.3 Consensus size: 42
5039726 CTTTTTGTGG
*
5039736 AAAAAGGAAAACGAAA-TACGTCCTGCTCTTTGAGGACAAA-A
1 AAAAAGGAAAA-TAAAGTACGTCCTGCTCTTTGAGGACAAAGA
* *
5039777 AAAAAGGAAAATAAAGTACGTCCTGCTCTTTGAGAACTAGAAGG
1 AAAAAGGAAAATAAAGTACGTCCTGCTCTTTGAGGAC-A-AAGA
* * * *
5039821 GAAAAGAGAGAAATGAAGTGCATCCTGCTCTTTGAGGACAAAGGA
1 AAAAAG-GA-AAATAAAGTACGTCCTGCTCTTTGAGGACAAA-GA
5039866 AAAAAGGAAAA
1 AAAAAGGAAAA
5039877 AGCGTCCTGC
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
40 3 0.04
41 31 0.37
42 1 0.01
43 5 0.06
44 9 0.11
45 9 0.11
46 25 0.30
ACGTcount: A:0.46, C:0.13, G:0.23, T:0.17
Consensus pattern (42 bp):
AAAAAGGAAAATAAAGTACGTCCTGCTCTTTGAGGACAAAGA
Found at i:5039908 original size:37 final size:37
Alignment explanation
Indices: 5039854--5039925 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
5039844 CCTGCTCTTT
5039854 GAGGACAAAGGAAAAAAGGAAAAAGCGTCCTGCTCAA
1 GAGGACAAAGGAAAAAAGGAAAAAGCGTCCTGCTCAA
* * *
5039891 GAGGGCAAAGGAGAAAAGGAAAAGGCGTCCTGCTC
1 GAGGACAAAGGAAAAAAGGAAAAAGCGTCCTGCTC
5039926 TTTGAGGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.43, C:0.17, G:0.32, T:0.08
Consensus pattern (37 bp):
GAGGACAAAGGAAAAAAGGAAAAAGCGTCCTGCTCAA
Found at i:5039977 original size:61 final size:61
Alignment explanation
Indices: 5039904--5040238 Score: 431
Period size: 61 Copynumber: 5.6 Consensus size: 61
5039894 GGCAAAGGAG
*
5039904 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTATGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTT
* * * ** * *
5039965 AAAAGGAGAAGGCGTCTTGCTTTTTGAGGACT-GAAGGTGCCACTAGCTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
*
5040025 AAAAGGAAAAGGCGTCCTGCTTTTTGAGGACTAGAAAAT-CTCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGC-CACCAACTTGTGTGGGCTTT
* * *
5040086 GAAAGGCGAAA-GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAAGG-AAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
5040147 -----G-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
* * *
5040202 AAAAGGAAAAGGCATCCTGTTCCTTGAGGACTA-AAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAA
5040239 GTGAAAGGAG
Statistics
Matches: 241, Mismatches: 22, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
54 3 0.01
55 49 0.20
56 1 0.00
60 56 0.23
61 128 0.53
62 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (61 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:5040036 original size:121 final size:122
Alignment explanation
Indices: 5039904--5040238 Score: 447
Period size: 116 Copynumber: 2.8 Consensus size: 122
5039894 GGCAAAGGAG
*
5039904 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACT-GAAAAGTGCCACCAACTTGTATGGGCTTTAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTAAA
* * * ** * *
5039968 AGGAGAAGGCGTCTTGCTTTTTGAGGACT-GAAGGTGCCACTAGCTTGTGTGGGCTTT
65 AGGAGAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
* *
5040025 AAAAGGAAAAGGCGTCCTGCTTTTTGAGGACTAGAAAAT-CTCACCAACTTGTGTGGGCTTTGAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGC-CACCAACTTGTGTGGGCTTTAAA
* *
5040089 AGGCGAAAGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
65 AGGAGAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
5040147 -----G-AAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAA
1 AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAA
* * *
5040206 GGAAAAGGCATCCTGTTCCTTGAGGACTA-AAAA
66 GGAGAAGGCATCCTGCTCTTTGAGGACTAGAAAA
5040239 GTGAAAGGAG
Statistics
Matches: 191, Mismatches: 19, Indels: 14
0.85 0.08 0.06
Matches are distributed among these distances:
115 4 0.02
116 78 0.41
117 2 0.01
120 1 0.01
121 77 0.40
122 29 0.15
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (122 bp):
AAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAA
GGAGAAGGCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT
Found at i:5040314 original size:277 final size:278
Alignment explanation
Indices: 5039966--5040496 Score: 700
Period size: 277 Copynumber: 1.9 Consensus size: 278
5039956 ATGGGCTTTA
* * * * * *
5039966 AAAGGAGAAGGCGTCTTGCTTTTTGAGGACTGAAGGTGCCACTAGCTTGTGTGGGCTTTAAAAGG
1 AAAGGAGAAGGCGTCTTACTCTTTGAGGACGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
* * *
5040031 AAAAGGCGTCCTGCTTTTTGAGGACTAGAAA-A-TCTCACCAACTTGTGTGGGCTTT-GAAAGGC
66 AAAAGGCGTCCTGCTCTTTGAGGACTA-AAAGATTC-CACCAACTTGTGTGGGCTTTAAAAAAG-
*
5040093 GAAA-GCATCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-G-AAAGGCG
128 AAAAGGCATCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAGAAAAGGCG
** *
5040155 TCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCATCC
192 TCCTGCTCTTTGAGGACTA-AAAATGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCC
5040219 TGTTCCTTGAGGACTAAAAAGTG
256 TGTTCCTTGAGGACTAAAAAGTG
5040242 AAAGGAG-AGAGCGTCTTACTCTTTGAGGACAGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
1 AAAGGAGAAG-GCGTCTTACTCTTTGAGGAC-GGAAAGTGCCACCAACTTGTGTGGGCTTTAAAA
*
5040306 GGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGGTTCCACCAACTTGTGTGGGCTTTAAAAAAGA
64 GGAAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATTCCACCAACTTGTGTGGGCTTTAAAAAAGA
** ** *
5040371 AAAGGTGTCCTGCTCTTTGAGGACTGAAGGTGCCACTAACTTGTGTGGGCTTTGAAAAGAAAAAG
129 AAAGGCATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT----AG-AAAAG
* **
5040436 GTGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAG
189 GCGTCCTGCTCTTTGAGGACTAAAAATGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAG
5040497 ACTTCCTACT
Statistics
Matches: 219, Mismatches: 22, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
275 2 0.01
276 28 0.13
277 105 0.48
278 25 0.11
282 1 0.00
283 23 0.11
284 35 0.16
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (278 bp):
AAAGGAGAAGGCGTCTTACTCTTTGAGGACGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGG
AAAAGGCGTCCTGCTCTTTGAGGACTAAAAGATTCCACCAACTTGTGTGGGCTTTAAAAAAGAAA
AGGCATCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAGAAAAGGCGTCCT
GCTCTTTGAGGACTAAAAATGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGGCATCCTGTTC
CTTGAGGACTAAAAAGTG
Found at i:5040362 original size:161 final size:156
Alignment explanation
Indices: 5040105--5040395 Score: 417
Period size: 161 Copynumber: 1.8 Consensus size: 156
5040095 AAGCATCCTG
5040105 CTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
1 CTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
* *
5040170 ACTAGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCATCCTGTTCCTTGAGGACT
66 ACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCCTGCTCCTTGAGGACT
5040234 AAAAAGTGAAAGGAGAGAGCGTCTTA
131 AAAAAGTGAAAGGAGAGAGCGTCTTA
*
5040260 CTCTTTGAGGAC-AGGAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTC
1 CTCTTTGAGGACTA-GAAAATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCCTGCTC
* * ** *
5040324 TTTGAGGACTA-AAAGGTTCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGTGTCCTGCTCTT
59 TTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCCTGCTCCT
5040388 TGAGGACT
123 TGAGGACT
5040396 GAAGGTGCCA
Statistics
Matches: 119, Mismatches: 8, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
154 1 0.01
155 39 0.33
160 4 0.03
161 48 0.40
162 27 0.23
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (156 bp):
CTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGG
ACTAGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAAGAAAAGGCATCCTGCTCCTTGAGGACT
AAAAAGTGAAAGGAGAGAGCGTCTTA
Found at i:5040557 original size:63 final size:62
Alignment explanation
Indices: 5040260--5040586 Score: 459
Period size: 61 Copynumber: 5.3 Consensus size: 62
5040250 GAGCGTCTTA
* * *
5040260 CTCTTTGAGGAC-AGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGAAAAGGCGTCCTG
1 CTCTTTGAGGACTA-GAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCCTG
* * *
5040321 CTCTTTGAGGACTAAAAGGTTCCACCAACTTGTGTGGGCTTT-AAAAAAGAAAAGGTGTCCTG
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGA-AAAAGGTGTCCTG
*
5040383 CTCTTTGAGGACT-GAAGGTGCCACTAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCCTG
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCCTG
** * *
5040444 CTCTTTGAGGACTA-AAGGTGCCACCAACTCATGTGGGCTTTGAAAAGAAAAAGACT-TCCTA
1 CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG-GTGTCCTG
*
5040505 CTCTTTGAGGACTAGAAGGGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGTGTCCTG
1 CTCTTTGAGGACTAGAA-GGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCCTG
*
5040568 CTCTTTGAGGACTAAAAGG
1 CTCTTTGAGGACTAGAAGG
5040587 GCTAAAAAGA
Statistics
Matches: 239, Mismatches: 19, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
61 146 0.61
62 37 0.15
63 56 0.23
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (62 bp):
CTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGGTGTCCTG
Found at i:5048239 original size:19 final size:20
Alignment explanation
Indices: 5048211--5048262 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
5048201 TCGATACAAC
*
5048211 GTATCAATACATGCTC-ATT
1 GTATCGATACATGCTCAATT
*
5048230 GTATCGATACATACTCAATT
1 GTATCGATACATGCTCAATT
5048250 GTATCGATACATG
1 GTATCGATACATG
5048263 AAACTGGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (20 bp):
GTATCGATACATGCTCAATT
Found at i:5048333 original size:33 final size:33
Alignment explanation
Indices: 5048291--5048357 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
5048281 CTAAGTGAAA
*
5048291 TGTATCAATACATG-GGACAATGTATCGATACAT
1 TGTATCAATACATGAAGA-AATGTATCGATACAT
*
5048324 TGTATCAATACATGAAGAATTGTATCGATACAT
1 TGTATCAATACATGAAGAAATGTATCGATACAT
5048357 T
1 T
5048358 ATGCCCAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (33 bp):
TGTATCAATACATGAAGAAATGTATCGATACAT
Found at i:5049131 original size:21 final size:22
Alignment explanation
Indices: 5049105--5049160 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 22
5049095 GCTTACAGAC
**
5049105 TGTATCGATACATGTTTA-AAT
1 TGTATCGATACATGTCAAGAAT
5049126 TGTATCGATACA--TCAAGAAT
1 TGTATCGATACATGTCAAGAAT
5049146 TGTATCGATACATGT
1 TGTATCGATACATGT
5049161 GACCCAACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 2 0.07
20 15 0.50
21 12 0.40
22 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (22 bp):
TGTATCGATACATGTCAAGAAT
Found at i:5049658 original size:34 final size:34
Alignment explanation
Indices: 5049577--5049678 Score: 107
Period size: 34 Copynumber: 3.0 Consensus size: 34
5049567 ATAGTGATTG
* *
5049577 AGAGGTTCTATCTTAGCTTTTGAAAAAGATAAGGA
1 AGAGGTTCTATCTTAGCTTATG-AAAAGATAGGGA
* * *
5049612 AGATGTTGTATCTTAGCCTATGAAAAGATAGGG-
1 AGAGGTTCTATCTTAGCTTATGAAAAGATAGGGA
* * *
5049645 AGAAGGTTTTATCTTAGCTTGTTAAAAGATAGGG
1 AG-AGGTTCTATCTTAGCTTATGAAAAGATAGGG
5049679 TTATAAGGTT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
33 2 0.04
34 36 0.64
35 18 0.32
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.32
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCTTATGAAAAGATAGGGA
Found at i:5050428 original size:14 final size:14
Alignment explanation
Indices: 5050392--5050430 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5050382 AAATTTTCTT
5050392 TTACTTTTTTATTA
1 TTACTTTTTTATTA
* *
5050406 TTATTTTTTTGTTA
1 TTACTTTTTTATTA
*
5050420 TTACGTTTTTA
1 TTACTTTTTTA
5050431 ATTTGATTTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (14 bp):
TTACTTTTTTATTA
Found at i:5053693 original size:2 final size:2
Alignment explanation
Indices: 5053688--5053721 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5053678 TACAACATAG
5053688 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
5053722 CTGCATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5054006 original size:23 final size:23
Alignment explanation
Indices: 5053980--5054029 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5053970 CAAAAACTCT
*
5053980 TTTTAACTCTCC-TTTTTTTTAAC
1 TTTT-ACTCTCCAATTTTTTTAAC
* *
5054003 TTTTTCTTTCCAATTTTTTTAAC
1 TTTTACTCTCCAATTTTTTTAAC
5054026 TTTT
1 TTTT
5054030 TCAAAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTACTCTCCAATTTTTTTAAC
Found at i:5055228 original size:13 final size:13
Alignment explanation
Indices: 5055210--5055235 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5055200 ACACACAGTA
5055210 TGTATCGATACAT
1 TGTATCGATACAT
5055223 TGTATCGATACAT
1 TGTATCGATACAT
5055236 CATAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5055251 original size:33 final size:32
Alignment explanation
Indices: 5055190--5055257 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
5055180 GTAGCCAAAC
**
5055190 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
5055222 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
5055255 TTG
1 TTG
5055258 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:5061392 original size:13 final size:13
Alignment explanation
Indices: 5061373--5061411 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
5061363 ATAGCATTCT
5061373 CTGTATCGATACA
1 CTGTATCGATACA
* *
5061386 TTGTATCAATACA
1 CTGTATCGATACA
5061399 CTGTATCGATACA
1 CTGTATCGATACA
5061412 AAGGGATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (13 bp):
CTGTATCGATACA
Found at i:5061578 original size:20 final size:20
Alignment explanation
Indices: 5061543--5061583 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
5061533 CAAAATTCTT
5061543 GTTTTTCACTTCAAAATACATC
1 GTTTTTCAC-TCAAAAT-CATC
5061565 GTTTTTCA-TCAAAATCATC
1 GTTTTTCACTCAAAATCATC
5061584 AACAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 7 0.37
22 8 0.42
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (20 bp):
GTTTTTCACTCAAAATCATC
Found at i:5063909 original size:21 final size:20
Alignment explanation
Indices: 5063861--5063916 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5063851 ATACACATTT
**
5063861 AAATGTATCGATACATGACC
1 AAATGTATCGATACATGAAA
*
5063881 AAATGTATCGATACTTGAAA
1 AAATGTATCGATACATGAAA
5063901 AAGATGTATCGATACA
1 AA-ATGTATCGATACA
5063917 AGTCATTGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
AAATGTATCGATACATGAAA
Found at i:5063986 original size:13 final size:13
Alignment explanation
Indices: 5063968--5063993 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5063958 ACACACAGTA
5063968 TGTATCGATACAT
1 TGTATCGATACAT
5063981 TGTATCGATACAT
1 TGTATCGATACAT
5063994 CATAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5064009 original size:33 final size:32
Alignment explanation
Indices: 5063948--5064015 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
5063938 ATAGCCAAAC
**
5063948 TTGTATCGATACACACAGTATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
5063980 TTGTATCGATACATCATAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
5064013 TTG
1 TTG
5064016 GCTTGTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:5066148 original size:166 final size:166
Alignment explanation
Indices: 5065743--5066485 Score: 811
Period size: 165 Copynumber: 4.5 Consensus size: 166
5065733 TGTTTTCAAC
* * *
5065743 AGGATTTTTCTAGGTTTTTAATTCTTAAAATTCATCAAATATTATTATTTAATTCATATTAAATT
1 AGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATT
* * * * * * **
5065808 ATTTTTTAAAAATTTATTGATATTCATGAGTTTTTCATTTTTTCTTTGAAA-AATCTCTATTTTT
66 AGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTCATTTTTTCCTTGAAATTTTC-CTATTTTT
* * **
5065872 GAAATATAGAGTTTTTTACTCCAT-AATTTTTTTCAG
130 GAAAAATAGAGTTTTCTACTCCATAAATTTTTTTGGG
* * * *
5065908 AGGATTTTTCTTAGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAATTCATGTTAAATC
1 AGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATT
* * * ** *
5065973 AATTTTCAAAAATTCATTCATTTTTATGAGTTTTTCTTTTTTTCCTTGAAATTTTTTTATTTTTA
66 AGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTCATTTTTTCCTTGAAATTTTCCTATTTTTG
* *
5066038 AAAAATAGAGTTTTCTACTCCATAAATGGTTTTGGGG
131 AAAAATAGAGTTTTCTACTCCATAAAT-TTTTTTGGG
* * * *
5066075 TGGA-TTTTCTTGGTTTTTAACTTTTAAAATTCATCAAATATTATTATTTATTTTATAGTAAATT
1 AGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATT
* * *
5066139 AGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTAAATTTGTTTCCTTAAAATTCTCCTATTTT
66 AGTTTTCAAAAATTCATTCATTTTCATGAGTTTTT-CATTT-TTTCCTTGAAATTTTCCTATTTT
*
5066204 T--AAAATACGAAGTTTTCTACTCCGTAAATTTTTTTGGG
129 TGAAAAATA-G-AGTTTTCTACTCCATAAATTTTTTTGGG
** * * ** *
5066242 AAAATTTTTCTTCGTTTTTAATTTTTAAAATTCATAAAATATTATTATTTATTTTTTATTAGATC
1 AGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAAT-
*
5066307 T-GTTTTC-AAAA---ATTCA--TTC---A-TTTTTCATTTTTT-CTTGAAATTTTCCTAGTTTT
65 TAGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTCATTTTTTCCTTGAAATTTTCCTATTTTT
* *** **
5066360 GAAAAATCGAGTTTTCTACTTTGTAAATATTTTCAGGG
130 GAAAAATAGAGTTTTCTACTCCATAAAT-TTTTTTGGG
* * * *
5066398 -CGATTTTTCTTGGCTTTTGATTTTTAAAATTCATAAAATATTATTATTTATTTCATATTAAATT
1 AGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATT
5066462 AGTTTTCAAAAATTCATTCATTTT
66 AGTTTTCAAAAATTCATTCATTTT
5066486 TCATTTTTTC
Statistics
Matches: 490, Mismatches: 69, Indels: 42
0.82 0.11 0.07
Matches are distributed among these distances:
154 1 0.00
155 95 0.19
156 15 0.03
157 9 0.02
158 5 0.01
159 6 0.01
161 2 0.00
162 3 0.01
164 5 0.01
165 131 0.27
166 96 0.20
167 24 0.05
168 97 0.20
169 1 0.00
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.52
Consensus pattern (166 bp):
AGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAAATT
AGTTTTCAAAAATTCATTCATTTTCATGAGTTTTTCATTTTTTCCTTGAAATTTTCCTATTTTTG
AAAAATAGAGTTTTCTACTCCATAAATTTTTTTGGG
Found at i:5066407 original size:155 final size:156
Alignment explanation
Indices: 5066214--5066548 Score: 462
Period size: 155 Copynumber: 2.2 Consensus size: 156
5066204 TAAAATACGA
** ** *
5066214 AGTTTTCTACTCCGTAAAT-TTTTTTGGGAAAATTTTTCTTCGTTTTTAATTTTTAAAATTCATA
1 AGTTTTCTACTCCGTAAATATTTTCAGGG-CGATTTTTCTTCGCTTTTAATTTTTAAAATTCATA
** *
5066278 AAATATTATTATTTATTTTTTATTAGATCT-GTTTTCAAAAATTCATTCATTTTTCATTTTTTC-
65 AAATATTATTATTTATTTCATATTAAAT-TAGTTTTCAAAAATTCATTCATTTTTCATTTTTTCT
* * * *
5066341 TTGAAATTTTCCTAGTTTTGAAAAA-TCG
129 TTGAAATCTCCCTA-TTTTCAAAAAGCCG
** * *
5066369 AGTTTTCTACTTTGTAAATATTTTCAGGGCGATTTTTCTTGGCTTTTGATTTTTAAAATTCATAA
1 AGTTTTCTACTCCGTAAATATTTTCAGGGCGATTTTTCTTCGCTTTTAATTTTTAAAATTCATAA
5066434 AATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTTCATTTTTTCTTT
66 AATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTTCATTTTTTCTTT
5066499 GAAATCTCCCTATTTTCAAAAAGCCG
131 GAAATCTCCCTATTTTCAAAAAGCCG
*
5066525 AGTTTTCTTCTCCGTAAATATTTT
1 AGTTTTCTACTCCGTAAATATTTT
5066549 GGTAGGATTT
Statistics
Matches: 157, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
154 1 0.01
155 114 0.73
156 42 0.27
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (156 bp):
AGTTTTCTACTCCGTAAATATTTTCAGGGCGATTTTTCTTCGCTTTTAATTTTTAAAATTCATAA
AATATTATTATTTATTTCATATTAAATTAGTTTTCAAAAATTCATTCATTTTTCATTTTTTCTTT
GAAATCTCCCTATTTTCAAAAAGCCG
Found at i:5066558 original size:155 final size:153
Alignment explanation
Indices: 5066214--5066597 Score: 461
Period size: 155 Copynumber: 2.5 Consensus size: 153
5066204 TAAAATACGA
* ** *
5066214 AGTTTTCTACTCCGTAAATTTTTTTGGGAAAATTTTTCTTCGTTTTTAATTTTTAAAATTCATAA
1 AGTTTTCTACTCCGTAAA-TATTTT-GGAGGATTTTTCTTCGCTTTTAATTTTTAAAATTCATAA
** *
5066279 AATATTATTATTTATTTTTTATTAGATCTGTTTTCAAAAATTCATTCATTTTTCATTTTTTCTTG
64 AATATTATTATTTATTTCATATTAAATCTGTTTTCAAAAATTCATTCATTTTTCATTTTTTCTTG
* * * *
5066344 AAATTTTCCTAGTTTTGAAAAATCG
129 AAATCTCCCTAGTTTTCAAAAACCG
** * *
5066369 AGTTTTCTACTTTGTAAATATTTTCAGG-GCGATTTTTCTTGGCTTTTGATTTTTAAAATTCATA
1 AGTTTTCTACTCCGTAAATATTTT--GGAG-GATTTTTCTTCGCTTTTAATTTTTAAAATTCATA
5066433 AAATATTATTATTTATTTCATATTAAAT-TAGTTTTCAAAAATTCATTCATTTTTCATTTTTTCT
63 AAATATTATTATTTATTTCATATTAAATCT-GTTTTCAAAAATTCATTCATTTTTCATTTTTTC-
5066497 TTGAAATCTCCCTA-TTTTCAAAAAGCCG
126 TTGAAATCTCCCTAGTTTTCAAAAA-CCG
* * * * **
5066525 AGTTTTCTTCTCCGTAAATATTTTGGTAGGATTTTT-ATCGATTTAAAATTTTTAAAATTCATCC
1 AGTTTTCTACTCCGTAAATATTTTGG-AGGATTTTTCTTCGCTTT-TAATTTTTAAAATTCATAA
5066589 AATATTATT
64 AATATTATT
5066598 GTTAAACTCC
Statistics
Matches: 195, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
154 13 0.07
155 146 0.75
156 36 0.18
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.51
Consensus pattern (153 bp):
AGTTTTCTACTCCGTAAATATTTTGGAGGATTTTTCTTCGCTTTTAATTTTTAAAATTCATAAAA
TATTATTATTTATTTCATATTAAATCTGTTTTCAAAAATTCATTCATTTTTCATTTTTTCTTGAA
ATCTCCCTAGTTTTCAAAAACCG
Found at i:5066982 original size:10 final size:10
Alignment explanation
Indices: 5066967--5067026 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 10
5066957 TCAGCAAAAA
5066967 AAAAAAAGAG
1 AAAAAAAGAG
5066977 AAAAAAAGAAAAG
1 AAAAAAAG---AG
5066990 AAAAAAAAGAG
1 -AAAAAAAGAG
*
5067001 AAAAAAATAAG
1 AAAAAAA-GAG
*
5067012 AAAAATAG-G
1 AAAAAAAGAG
5067021 AAAAAA
1 AAAAAA
5067027 TAGTTAGGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
9 6 0.15
10 15 0.37
11 10 0.24
13 2 0.05
14 8 0.20
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:5066982 original size:11 final size:11
Alignment explanation
Indices: 5066966--5067016 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
5066956 CTCAGCAAAA
5066966 AAAAAAAAGAG
1 AAAAAAAAGAG
*
5066977 AAAAAAAGAAAAG
1 -AAAAAA-AAGAG
5066990 AAAAAAAAGAG
1 AAAAAAAAGAG
5067001 AAAAAAATA-AG
1 AAAAAAA-AGAG
5067012 AAAAA
1 AAAAA
5067017 TAGGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 18 0.51
12 13 0.37
13 4 0.11
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:5066982 original size:15 final size:14
Alignment explanation
Indices: 5066962--5066997 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
5066952 GAAACTCAGC
5066962 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
*
5066976 GAAAAAAAGAAAAGA
1 -AAAAAAAAAAAAGA
5066991 AAAAAAA
1 AAAAAAA
5066998 GAGAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:5066993 original size:22 final size:21
Alignment explanation
Indices: 5066962--5067026 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
5066952 GAAACTCAGC
5066962 AAAAAA-AAAAAAGAGAAAAA
1 AAAAAAGAAAAAAGAGAAAAA
*
5066982 AAGAAAAGAAAAAAAAGAGAAAA
1 AA-AAAAGAAAAAAGAGA-AAAA
*
5067005 AAATAAGAAAAATAG-GAAAAA
1 AAAAAAGAAAAA-AGAGAAAAA
5067026 A
1 A
5067027 TAGTTAGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.05
21 9 0.24
22 20 0.53
23 7 0.18
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (21 bp):
AAAAAAGAAAAAAGAGAAAAA
Found at i:5066993 original size:24 final size:23
Alignment explanation
Indices: 5066962--5067016 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
5066952 GAAACTCAGC
5066962 AAAAAAAAAAAAGAGAAAAAAAG
1 AAAAAAAAAAAAGAGAAAAAAAG
*
5066985 AAAAGAAAAAAAAGAGAAAAAAAT
1 AAAA-AAAAAAAAGAGAAAAAAAG
*
5067009 AAGAAAAA
1 AAAAAAAA
5067017 TAGGAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAAAAGAGAAAAAAAG
Found at i:5068012 original size:143 final size:139
Alignment explanation
Indices: 5067783--5068122 Score: 448
Period size: 143 Copynumber: 2.4 Consensus size: 139
5067773 AAGGCTTTTG
* *
5067783 ATATTTCTATGGATATTCGTAGGGGTATAAAAGTCTTTAAAACTTTTCGTATCTTTTCGAGTCTC
1 ATATTCCTATGG-TTTTCGTAGGGGTATAAAA-TCTTTAAAACTTTTCGTATCTTTTCGAGTCTC
* **
5067848 CATTACGGTACAAAATAAATTTTCTTAAAAATTAAAAAATTAAATAAAAATTGTTATCTTAATTT
64 CATTAAGGTACAAAATAAATTTT-TTAAAAATTAAAAAATTAAATAAAAATAATTATCTTAATTT
*
5067913 TTCAAAATTTTT
128 TTCAAAATTTCT
* *
5067925 AATATTCTTATGGTTTTCCGTAGGGGTATAGAAATCTTTAAAACTTTTCATATCTTTTCG-GTTC
1 -ATATTCCTATGGTTTT-CGTAGGGGTATA-AAATCTTTAAAACTTTTCGTATCTTTTCGAG-TC
* * ** * *
5067989 TCCATTAAGGTACGAAATGAATTTTTTGGAAATTAAAAATTTAAATAAAAATAATTGTCTTAATT
62 TCCATTAAGGTACAAAATAAATTTTTTAAAAATTAAAAAATTAAATAAAAATAATTATCTTAATT
* *
5068054 TTTTAAGATTTCT
127 TTTCAAAATTTCT
*
5068067 ATATTCCTATGGTTTTCGTAGGGGTATAAAAATTTTTAAAACTTTTCGTATCTTTT
1 ATATTCCTATGGTTTTCGTAGGGGTAT-AAAATCTTTAAAACTTTTCGTATCTTTT
5068123 TGGGTTTCTA
Statistics
Matches: 174, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
140 36 0.21
141 16 0.09
142 48 0.28
143 71 0.41
144 3 0.02
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (139 bp):
ATATTCCTATGGTTTTCGTAGGGGTATAAAATCTTTAAAACTTTTCGTATCTTTTCGAGTCTCCA
TTAAGGTACAAAATAAATTTTTTAAAAATTAAAAAATTAAATAAAAATAATTATCTTAATTTTTC
AAAATTTCT
Found at i:5070092 original size:13 final size:13
Alignment explanation
Indices: 5070074--5070098 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5070064 CATAGGACAT
5070074 TGTATCGATACAA
1 TGTATCGATACAA
5070087 TGTATCGATACA
1 TGTATCGATACA
5070099 TGGTAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5070111 original size:33 final size:33
Alignment explanation
Indices: 5070054--5070118 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
5070044 TATCACTGTT
* *
5070054 TGTATCGATACATAGGACATTGTATCGATACAA
1 TGTATCGATACATAGGAAAATGTATCGATACAA
*
5070087 TGTATCGATACAT-GGTAAAATGTATTGATACA
1 TGTATCGATACATAGG-AAAATGTATCGATACA
5070119 TTATGCCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 26 0.93
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATAGGAAAATGTATCGATACAA
Found at i:5071094 original size:20 final size:21
Alignment explanation
Indices: 5071043--5071096 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
5071033 TTTTACAATT
*
5071043 TGTATCGATACAAACAATAAA
1 TGTATCGATACATACAATAAA
** * *
5071064 TGTATTAATACATA-AGTGAA
1 TGTATCGATACATACAATAAA
5071084 TGTATCGATACAT
1 TGTATCGATACAT
5071097 GCCTCAAATG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (21 bp):
TGTATCGATACATACAATAAA
Found at i:5073865 original size:10 final size:9
Alignment explanation
Indices: 5073850--5073945 Score: 59
Period size: 10 Copynumber: 9.9 Consensus size: 9
5073840 TTTTCCAAAA
5073850 TTTTTTTCT
1 TTTTTTTCT
*
5073859 TTCTTTTCAT
1 TTTTTTTC-T
5073869 TTTTTTTCTT
1 TTTTTTTC-T
5073879 TTTTTTTCT
1 TTTTTTTCT
5073888 AATTTTTTTAC-
1 --TTTTTTT-CT
*
5073899 TTTTTTACT
1 TTTTTTTCT
*
5073908 TTTCTTTTTT
1 TTT-TTTTCT
*
5073918 TTTCTTTTAAT
1 TTT-TTTT-CT
**
5073929 TTTTTCACT
1 TTTTTTTCT
5073938 TTTTTTTC
1 TTTTTTTC
5073946 AAAGCAAATA
Statistics
Matches: 68, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
8 1 0.01
9 24 0.35
10 31 0.46
11 11 0.16
12 1 0.01
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:5073874 original size:9 final size:8
Alignment explanation
Indices: 5073850--5073925 Score: 50
Period size: 8 Copynumber: 9.5 Consensus size: 8
5073840 TTTTCCAAAA
5073850 TTTTTTTC
1 TTTTTTTC
5073858 TTTCTTTTC
1 TTT-TTTTC
5073867 ATTTTTTTTC
1 --TTTTTTTC
5073877 TTTTTTT-
1 TTTTTTTC
* **
5073884 TTCTAAT-
1 TTTTTTTC
*
5073891 TTTTTTAC
1 TTTTTTTC
*
5073899 TTTTTTAC
1 TTTTTTTC
*
5073907 TTTTCTT-
1 TTTTTTTC
5073914 TTTTTTTC
1 TTTTTTTC
5073922 TTTT
1 TTTT
5073926 AATTTTTTCA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
7 13 0.25
8 27 0.51
9 5 0.09
10 5 0.09
11 3 0.06
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:5073933 original size:16 final size:15
Alignment explanation
Indices: 5073851--5073944 Score: 52
Period size: 15 Copynumber: 6.3 Consensus size: 15
5073841 TTTCCAAAAT
*
5073851 TTTTTTCTTTCTTTTCA
1 TTTTTT-TTACTTTT-A
5073868 TTTTTTTT-C-TTT-
1 TTTTTTTTACTTTTA
* * *
5073880 TTTTTTCTAATTTTT
1 TTTTTTTTACTTTTA
*
5073895 TTACTTTTTTACTTTTC
1 TT--TTTTTTACTTTTA
*
5073912 TTTTTTTTTCTTTTA
1 TTTTTTTTACTTTTA
* *
5073927 ATTTTTTCACTTTT-
1 TTTTTTTTACTTTTA
5073941 TTTT
1 TTTT
5073945 CAAAGCAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
12 7 0.11
14 9 0.15
15 25 0.41
16 2 0.03
17 18 0.30
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTTTACTTTTA
Found at i:5074987 original size:41 final size:41
Alignment explanation
Indices: 5074916--5075068 Score: 177
Period size: 41 Copynumber: 3.8 Consensus size: 41
5074906 AATTTAAATT
* *
5074916 AGAA-CTCTTATTTGATAAGGCGTGGACACGTTAAGAAAAC
1 AGAAGCTCTCATTTGATAAGGCGTGGGCACGTTAAGAAAAC
* * *
5074956 AGAAGCTTTCATTTGGTAAGGTGTGGGCACGTTAAAGAAATA-
1 AGAAGCTCTCATTTGATAAGGCGTGGGCACGTT-AAGAAA-AC
* *
5074998 A-AAGCTCTCATTTGATAAGACATGGGCACGTTAAGAAAAC
1 AGAAGCTCTCATTTGATAAGGCGTGGGCACGTTAAGAAAAC
* * *
5075038 AGAAACTCTAATTTGATAAAGCGTGGGCACG
1 AGAAGCTCTCATTTGATAAGGCGTGGGCACG
5075069 CTCTATGAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
39 1 0.01
40 11 0.12
41 73 0.78
42 7 0.08
43 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (41 bp):
AGAAGCTCTCATTTGATAAGGCGTGGGCACGTTAAGAAAAC
Found at i:5076719 original size:20 final size:20
Alignment explanation
Indices: 5076694--5076767 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
5076684 CTGCCAATCT
5076694 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
5076714 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
**
5076734 CATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGTC
*
5076753 CATGTATTGATACAA
1 CATGTATCGATACAA
5076768 AGCATAATGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 16 0.31
20 35 0.69
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:5079305 original size:13 final size:13
Alignment explanation
Indices: 5079287--5079311 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5079277 AATAGTACCC
5079287 AATGTATCGATAT
1 AATGTATCGATAT
5079300 AATGTATCGATA
1 AATGTATCGATA
5079312 CAAGGAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:5083156 original size:32 final size:33
Alignment explanation
Indices: 5083115--5083182 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
5083105 GTAGCCAAAC
*
5083115 TTGTATCGATACA-CA-AAGTACGTATCGATACA
1 TTGTATCGATACACCATAA-AACGTATCGATACA
*
5083147 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAACGTATCGATACA
5083180 TTG
1 TTG
5083183 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 13 0.41
33 17 0.53
34 2 0.06
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAACGTATCGATACA
Done.