Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 177 of 193
Found at i:55228018 original size:24 final size:24
Alignment explanation
Indices: 55227986--55228043 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
55227976 AAGATTCTTT
55227986 ACTTTAGTCTCATCAGGCGTGCCA
1 ACTTTAGTCTCATCAGGCGTGCCA
55228010 ACTTTAGTCTCATCAGGCGTGCCA
1 ACTTTAGTCTCATCAGGCGTGCCA
55228034 ACTTTAGTCT
1 ACTTTAGTCT
55228044 TCATAATCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.33
Consensus pattern (24 bp):
ACTTTAGTCTCATCAGGCGTGCCA
Found at i:55231975 original size:12 final size:12
Alignment explanation
Indices: 55231958--55231982 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55231948 TGATGATGAT
55231958 GCTTTTGGTGAG
1 GCTTTTGGTGAG
55231970 GCTTTTGGTGAG
1 GCTTTTGGTGAG
55231982 G
1 G
55231983 ACATCTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.44, T:0.40
Consensus pattern (12 bp):
GCTTTTGGTGAG
Found at i:55232125 original size:15 final size:15
Alignment explanation
Indices: 55232105--55232134 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55232095 CTCTGGACAG
*
55232105 GATTCAGTTTCTGAA
1 GATTCAGGTTCTGAA
55232120 GATTCAGGTTCTGAA
1 GATTCAGGTTCTGAA
55232135 TGTTGATCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (15 bp):
GATTCAGGTTCTGAA
Found at i:55235009 original size:67 final size:67
Alignment explanation
Indices: 55234938--55235072 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
55234928 TACAAACAAT
*
55234938 ACAAACAGTAAAGATTCTTTACTTTAGTCTCATTAGGCGTGCCAACTTTAGTCTTCATAATCAGT
1 ACAAACAGTAAAGATTCTTTACTTTAGTCTCATCAGGCGTGCCAACTTTAGTCTTCATAATCAGT
55235003 AG
66 AG
55235005 ACAAACAGTAAAGATTCTTTACTTTAGTCTCATCAGGCGTGCCAACTTTAGTCTTCATAATCAGT
1 ACAAACAGTAAAGATTCTTTACTTTAGTCTCATCAGGCGTGCCAACTTTAGTCTTCATAATCAGT
55235070 AG
66 AG
55235072 A
1 A
55235073 GTTTGGGTCC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (67 bp):
ACAAACAGTAAAGATTCTTTACTTTAGTCTCATCAGGCGTGCCAACTTTAGTCTTCATAATCAGT
AG
Found at i:55235182 original size:18 final size:18
Alignment explanation
Indices: 55235161--55235195 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55235151 ATCTTCATCA
55235161 ATGTCTTCATCCTTATCC
1 ATGTCTTCATCCTTATCC
* *
55235179 ATGTTTTCATTCTTATC
1 ATGTCTTCATCCTTATC
55235196 TTGAGATCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.06, T:0.51
Consensus pattern (18 bp):
ATGTCTTCATCCTTATCC
Found at i:55243754 original size:82 final size:82
Alignment explanation
Indices: 55243617--55243786 Score: 322
Period size: 82 Copynumber: 2.1 Consensus size: 82
55243607 ATTTTTTTAC
*
55243617 ACAAATCCATTTTCGAGCCAAATATTTTTATTCAAATCCTCCAAAATTTTGGACAGACATTACCA
1 ACAAATCCATTTTCAAGCCAAATATTTTTATTCAAATCCTCCAAAATTTTGGACAGACATTACCA
*
55243682 AGTATCTCAACCCATGA
66 AGTATCCCAACCCATGA
55243699 ACAAATCCATTTTCAAGCCAAATATTTTTATTCAAATCCTCCAAAATTTTGGACAGACATTACCA
1 ACAAATCCATTTTCAAGCCAAATATTTTTATTCAAATCCTCCAAAATTTTGGACAGACATTACCA
55243764 AGTATCCCAACCCATGA
66 AGTATCCCAACCCATGA
55243781 ACAAAT
1 ACAAAT
55243787 TTACTTAAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.29
Consensus pattern (82 bp):
ACAAATCCATTTTCAAGCCAAATATTTTTATTCAAATCCTCCAAAATTTTGGACAGACATTACCA
AGTATCCCAACCCATGA
Found at i:55251055 original size:19 final size:19
Alignment explanation
Indices: 55251028--55251064 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55251018 ATGAATAATT
* *
55251028 TGGTTCAATTAAATTATGA
1 TGGTGCAATTAAAATATGA
55251047 TGGTGCAATTAAAATATG
1 TGGTGCAATTAAAATATG
55251065 GTAAAACTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (19 bp):
TGGTGCAATTAAAATATGA
Found at i:55251381 original size:45 final size:45
Alignment explanation
Indices: 55251312--55251404 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
55251302 TACATGCTAC
*
55251312 GTAACAATCAATTTAAACATATAAACAACTGATTCAAAAGAAACA
1 GTAACAATCAATTTAAACAGATAAACAACTGATTCAAAAGAAACA
* *
55251357 GTAACAATCGATTTAAACAGATAAACAATTGATTCAAAAGAAACA
1 GTAACAATCAATTTAAACAGATAAACAACTGATTCAAAAGAAACA
55251402 GTA
1 GTA
55251405 TTCTAACGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.54, C:0.14, G:0.10, T:0.23
Consensus pattern (45 bp):
GTAACAATCAATTTAAACAGATAAACAACTGATTCAAAAGAAACA
Found at i:55251385 original size:21 final size:19
Alignment explanation
Indices: 55251352--55251430 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 19
55251342 GATTCAAAAG
55251352 AAACAGTAACAATCGATTT
1 AAACAGTAACAATCGATTT
* *
55251371 AAACAGATAAACAATTGATTC
1 AAACAG-T-AACAATCGATTT
* *
55251392 AAA-AGAAACAGT--ATTCT
1 AAACAGTAACAATCGATT-T
55251409 -AAC-GTAACAATCGATTT
1 AAACAGTAACAATCGATTT
55251426 AAACA
1 AAACA
55251431 TATAAATTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
16 11 0.24
17 1 0.02
18 11 0.24
19 6 0.13
20 3 0.07
21 13 0.29
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (19 bp):
AAACAGTAACAATCGATTT
Found at i:55251422 original size:55 final size:55
Alignment explanation
Indices: 55251353--55251539 Score: 221
Period size: 55 Copynumber: 3.4 Consensus size: 55
55251343 ATTCAAAAGA
* * * *
55251353 AACAGTAACAATCGATTTAAACAGATAAACAATTGATTCAAAAGAAACAGTATTCT
1 AACA-TAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCT
* ** * *
55251409 AACGTAACAATCGATTTAAACATATAAATTATCGATTCAAAATAAGCAATATTCC
1 AACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCT
* * * * *
55251464 AACATGACAATTGATTTAAACATAAAAACAATCGATCCAAAAGGAGCAATATTCT
1 AACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCT
* *
55251519 AACATAACAATTGATTCAAAC
1 AACATAACAATCGATTTAAAC
55251540 CAAATTTGAC
Statistics
Matches: 110, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
55 107 0.97
56 3 0.03
ACGTcount: A:0.49, C:0.16, G:0.09, T:0.26
Consensus pattern (55 bp):
AACATAACAATCGATTTAAACATATAAACAATCGATTCAAAAGAAGCAATATTCT
Found at i:55252712 original size:14 final size:15
Alignment explanation
Indices: 55252685--55252731 Score: 51
Period size: 14 Copynumber: 3.0 Consensus size: 15
55252675 TTAAGGTTTA
*
55252685 AAAATTTTAATTAATT
1 AAAA-TTTATTTAATT
55252701 -AAATTTATTTAATT
1 AAAATTTATTTAATT
55252715 AAAAATTTATTCTAATT
1 -AAAATTTATT-TAATT
55252732 CCATTTGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.37
15 3 0.11
16 9 0.33
17 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
AAAATTTATTTAATT
Found at i:55253896 original size:116 final size:116
Alignment explanation
Indices: 55253692--55254039 Score: 678
Period size: 116 Copynumber: 3.0 Consensus size: 116
55253682 TAGACACGGT
*
55253692 GTCTCCCTTCTTTCAATCTTCCACCCACCTTCTTCATTGTCATTCTCGTTGATCAGTTGACAGAC
1 GTCTCCCTTCTTTCGATCTTCCACCCACCTTCTTCATTGTCATTCTCGTTGATCAGTTGACAGAC
55253757 TGACTTTGATACCTAATTATCATGTGGCATCATTGTTCTGTCCCTCAAAAA
66 TGACTTTGATACCTAATTATCATGTGGCATCATTGTTCTGTCCCTCAAAAA
55253808 GTCTCCCTTCTTTCGATCTTCCACCCACCTTCTTCATTGTCATTCTCGTTGATCAGTTGACAGAC
1 GTCTCCCTTCTTTCGATCTTCCACCCACCTTCTTCATTGTCATTCTCGTTGATCAGTTGACAGAC
55253873 TGACTTTGATACCTAATTATCATGTGGCATCATTGTTCTGTCCCTCAAAAA
66 TGACTTTGATACCTAATTATCATGTGGCATCATTGTTCTGTCCCTCAAAAA
55253924 GTCTCCCTTCTTTCGATCTTCCACCCACCTTCTTCATTGTCATTCTCGTTGATCAGTTGACAGAC
1 GTCTCCCTTCTTTCGATCTTCCACCCACCTTCTTCATTGTCATTCTCGTTGATCAGTTGACAGAC
*
55253989 CGACTTTGATACCTAATTATCATGTGGCATCATTGTTCTGTCCCTCAAAAA
66 TGACTTTGATACCTAATTATCATGTGGCATCATTGTTCTGTCCCTCAAAAA
55254040 TTCTGATCTT
Statistics
Matches: 230, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 230 1.00
ACGTcount: A:0.21, C:0.29, G:0.13, T:0.38
Consensus pattern (116 bp):
GTCTCCCTTCTTTCGATCTTCCACCCACCTTCTTCATTGTCATTCTCGTTGATCAGTTGACAGAC
TGACTTTGATACCTAATTATCATGTGGCATCATTGTTCTGTCCCTCAAAAA
Found at i:55258515 original size:18 final size:17
Alignment explanation
Indices: 55258479--55258518 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
55258469 TAATAAAAAT
55258479 ATAATTTTATTGTTTTA
1 ATAATTTTATTGTTTTA
55258496 ATAA-TTTATAT-TTTT-
1 ATAATTTTAT-TGTTTTA
55258511 ATAATTTT
1 ATAATTTT
55258519 TAAAAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
ATAATTTTATTGTTTTA
Found at i:55261011 original size:20 final size:21
Alignment explanation
Indices: 55260973--55261011 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
55260963 TGATGTGTAA
* *
55260973 ATTTTGTTCGAATTTTTTTCG
1 ATTTTGTTCCAATTATTTTCG
55260994 ATTTTG-TCCAATTATTTT
1 ATTTTGTTCCAATTATTTT
55261012 TATTTCTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.18, C:0.10, G:0.10, T:0.62
Consensus pattern (21 bp):
ATTTTGTTCCAATTATTTTCG
Found at i:55261011 original size:21 final size:21
Alignment explanation
Indices: 55260973--55261012 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55260963 TGATGTGTAA
*
55260973 ATTTTGTTCGAATTTTTTTCG
1 ATTTTGTTCCAATTTTTTTCG
55260994 ATTTTG-TCCAATTATTTTT
1 ATTTTGTTCCAATT-TTTTT
55261013 ATTTCTCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (21 bp):
ATTTTGTTCCAATTTTTTTCG
Found at i:55267022 original size:14 final size:15
Alignment explanation
Indices: 55267003--55267032 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
55266993 TATTTAACTT
55267003 TTGTTTTGGTT-TTG
1 TTGTTTTGGTTCTTG
55267017 TTGTTTTGGTTCTTG
1 TTGTTTTGGTTCTTG
55267032 T
1 T
55267033 GGTATTATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.00, C:0.03, G:0.27, T:0.70
Consensus pattern (15 bp):
TTGTTTTGGTTCTTG
Found at i:55268686 original size:61 final size:61
Alignment explanation
Indices: 55268615--55268888 Score: 248
Period size: 61 Copynumber: 4.3 Consensus size: 61
55268605 AAAAAAAAAA
* *
55268615 TTTATCAGATAAAAAAGGGGTGTCGGCCATGCAATGGCCAACACAAAAAAATTTGAATTTT
1 TTTATCAGATAAAAAAGGGGTGTCGGCCATGCAACGGCCAACACCAAAAAATTTGAATTTT
* *
55268676 TTTATTAGAT-AAAAAGGGGTGTTGGCCAGGGGTGTCGGCCATGCAACGGCCAACACCAAAAAAT
1 TTTATCAGATAAAAAAGGGGTGTCGGCCA------T-------GCAACGGCCAACACCAAAAAAT
55268740 TTGAATTTT
53 TTGAATTTT
* * * * * ** *
55268749 TTTATCTGAT-AAAAAGGTGGTGTCTGCCATGCAATGGCGAACACTAAAAACCTTGATTTTT
1 TTTATCAGATAAAAAAGG-GGTGTCGGCCATGCAACGGCCAACACCAAAAAATTTGAATTTT
** *
55268810 TTTATCAGATAAAAATTGTGTGTCGGCCAATGC-ACGGCCAACACCAAAAAATTTGAACTTTT
1 TTTATCAGATAAAAAAGGGGTGTCGGCC-ATGCAACGGCCAACACCAAAAAATTTGAA-TTTT
55268872 TTTATCAGATAAAAAAG
1 TTTATCAGATAAAAAAG
55268889 CATGGTCGAC
Statistics
Matches: 169, Mismatches: 27, Indels: 33
0.74 0.12 0.14
Matches are distributed among these distances:
60 17 0.10
61 69 0.41
62 28 0.17
66 1 0.01
68 1 0.01
73 44 0.26
74 9 0.05
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (61 bp):
TTTATCAGATAAAAAAGGGGTGTCGGCCATGCAACGGCCAACACCAAAAAATTTGAATTTT
Found at i:55268748 original size:73 final size:74
Alignment explanation
Indices: 55268630--55268771 Score: 243
Period size: 73 Copynumber: 1.9 Consensus size: 74
55268620 CAGATAAAAA
*
55268630 AGGGGTGTCGGCCATGCAATGGCCAACACAAAAAAATTTGAATTTTTTTAT-TAGATAAAAAGG-
1 AGGGGTGTCGGCCATGCAACGGCCAACACAAAAAAATTTGAATTTTTTTATCT-GATAAAAAGGT
55268693 GGTGTTGGCC
65 GGTGTTGGCC
*
55268703 AGGGGTGTCGGCCATGCAACGGCCAACACCAAAAAATTTGAATTTTTTTATCTGATAAAAAGGTG
1 AGGGGTGTCGGCCATGCAACGGCCAACACAAAAAAATTTGAATTTTTTTATCTGATAAAAAGGTG
55268768 GTGT
66 GTGT
55268772 CTGCCATGCA
Statistics
Matches: 65, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
73 59 0.91
74 6 0.09
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (74 bp):
AGGGGTGTCGGCCATGCAACGGCCAACACAAAAAAATTTGAATTTTTTTATCTGATAAAAAGGTG
GTGTTGGCC
Found at i:55269287 original size:12 final size:12
Alignment explanation
Indices: 55269270--55269294 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55269260 TTAGAAGGGC
55269270 TAGTTAATTTTT
1 TAGTTAATTTTT
55269282 TAGTTAATTTTT
1 TAGTTAATTTTT
55269294 T
1 T
55269295 TTATCATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TAGTTAATTTTT
Found at i:55274443 original size:23 final size:23
Alignment explanation
Indices: 55274391--55274441 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
55274381 TAAAAGTAAA
*
55274391 AATTATTAAAAATATATTTTTAT
1 AATTTTTAAAAATATATTTTTAT
55274414 AATTTTTAAAAATA-A-TTTTAT
1 AATTTTTAAAAATATATTTTTAT
55274435 AATTTTT
1 AATTTTT
55274442 TTTATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 13 0.48
22 1 0.04
23 13 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTTTAAAAATATATTTTTAT
Found at i:55276064 original size:36 final size:37
Alignment explanation
Indices: 55275989--55276056 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
55275979 TTTGTCCAAA
*
55275989 TATATAAAATATGTTTTATATAAAGTATATAAAAATG
1 TATATAAAATATGTTTTATATAAAGTATAAAAAAATG
55276026 TATA-AAAATA-GATTTTATA-AAA-TATAAAAAA
1 TATATAAAATATG-TTTTATATAAAGTATAAAAAA
55276057 TTATGTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 8 0.28
35 4 0.14
36 13 0.45
37 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (37 bp):
TATATAAAATATGTTTTATATAAAGTATAAAAAAATG
Found at i:55276789 original size:55 final size:55
Alignment explanation
Indices: 55276630--55276790 Score: 187
Period size: 55 Copynumber: 2.9 Consensus size: 55
55276620 TAATTTTTAA
* * * * * *
55276630 AAAATATTGCTTCTTTTGAATCGATTATTTTTATGTTTAAATTGATTGTCATGTT
1 AAAATATTACTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATATT
** * * *
55276685 AAAATACAACTTCCTTTGAATCGATTGTTTACATGTTTAAATCAATTGTTATATT
1 AAAATATTACTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATATT
** * *
55276740 GGAATATTACTTTTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTA
1 AAAATATTACTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTA
55276791 CGTAGCACAT
Statistics
Matches: 86, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 86 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (55 bp):
AAAATATTACTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTGTTATATT
Found at i:55282870 original size:7 final size:6
Alignment explanation
Indices: 55282848--55282933 Score: 69
Period size: 6 Copynumber: 15.0 Consensus size: 6
55282838 GGGCTCAATA
* *
55282848 AAATTT AAATTT --ATTT GAAATTT AAATTT -ATTTT AAGTTT AAATTT
1 AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT
*
55282894 --ATTT GAAATTT AAATTT --ATTAT AAATTT AAGTTT AAATTT
1 AAATTT -AAATTT AAATTT AAATT-T AAATTT AAATTT AAATTT
55282934 GTTTAAATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
4 11 0.17
5 5 0.08
6 38 0.58
7 11 0.17
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:55282870 original size:11 final size:10
Alignment explanation
Indices: 55282850--55282942 Score: 59
Period size: 10 Copynumber: 8.9 Consensus size: 10
55282840 GCTCAATAAA
55282850 ATTTAAATTT
1 ATTTAAATTT
55282860 ATTTGAAATTT
1 ATTT-AAATTT
*
55282871 AAATTT-ATTTT
1 --ATTTAAATTT
55282882 AAGTTTAAATTT
1 -A-TTTAAATTT
*
55282894 ATTTGAA---
1 ATTTAAATTT
55282901 ATTTAAATTT
1 ATTTAAATTT
55282911 ATTATAAATTT
1 ATT-TAAATTT
55282922 AAGTTTAAATTT
1 -A-TTTAAATTT
*
55282934 GTTTAAATT
1 ATTTAAATT
55282943 AATAATATCC
Statistics
Matches: 67, Mismatches: 5, Indels: 22
0.71 0.05 0.23
Matches are distributed among these distances:
7 6 0.09
10 22 0.33
11 21 0.31
12 12 0.18
13 6 0.09
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:55282870 original size:17 final size:17
Alignment explanation
Indices: 55282848--55282928 Score: 119
Period size: 17 Copynumber: 4.8 Consensus size: 17
55282838 GGGCTCAATA
55282848 AAATTTAAATTTATTTG
1 AAATTTAAATTTATTTG
*
55282865 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTG
*
55282882 AAGTTTAAATTTATTTG
1 AAATTTAAATTTATTTG
55282899 AAATTTAAATTTATTAT-
1 AAATTTAAATTTATT-TG
*
55282916 AAATTTAAGTTTA
1 AAATTTAAATTTA
55282929 AATTTGTTTA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
17 57 0.98
18 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTG
Found at i:55282894 original size:34 final size:34
Alignment explanation
Indices: 55282848--55282928 Score: 135
Period size: 34 Copynumber: 2.4 Consensus size: 34
55282838 GGGCTCAATA
*
55282848 AAATTTAAATTTATTTGAAATTTAAATTTATTTT
1 AAATTTAAATTTATTTGAAATTTAAATTTATTAT
*
55282882 AAGTTTAAATTTATTTGAAATTTAAATTTATTAT
1 AAATTTAAATTTATTTGAAATTTAAATTTATTAT
*
55282916 AAATTTAAGTTTA
1 AAATTTAAATTTA
55282929 AATTTGTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (34 bp):
AAATTTAAATTTATTTGAAATTTAAATTTATTAT
Found at i:55284716 original size:99 final size:99
Alignment explanation
Indices: 55284537--55284754 Score: 355
Period size: 99 Copynumber: 2.2 Consensus size: 99
55284527 CCGCGAATCG
*
55284537 ATGAGGCACTGGGTGCCAAATTACTTCGGTTTAACCGATGAGACACTGGGTGTCACTTGCATTAT
1 ATGAGGCACTGGGTGCCAAATTACTTCGGTTTAACCGATGAGACAATGGGTGTCACTTGCATTAT
* * *
55284602 AGCGTTGGGCACGACTATTATTTCGGTTTATCCA
66 AGCGCTGGGCACGACTATTACTTCAGTTTATCCA
55284636 ATGAGGCACTGGGTGCCAAATTACTTCGGTTTAACCGATGAGACAATGGGTGTCACTTGCATTAT
1 ATGAGGCACTGGGTGCCAAATTACTTCGGTTTAACCGATGAGACAATGGGTGTCACTTGCATTAT
** **
55284701 AGCGCTGGGTGCGACTATTACTTCAGTTTATCTG
66 AGCGCTGGGCACGACTATTACTTCAGTTTATCCA
*
55284735 ATGAGGCATTGGGTGCCAAA
1 ATGAGGCACTGGGTGCCAAA
55284755 CTAGTGTGTT
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 110 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (99 bp):
ATGAGGCACTGGGTGCCAAATTACTTCGGTTTAACCGATGAGACAATGGGTGTCACTTGCATTAT
AGCGCTGGGCACGACTATTACTTCAGTTTATCCA
Found at i:55287700 original size:30 final size:28
Alignment explanation
Indices: 55287651--55287918 Score: 200
Period size: 30 Copynumber: 9.1 Consensus size: 28
55287641 CTCAAAAGGT
* *
55287651 CCCTGAACTATCCAAAAATTATATTTTGAC
1 CCCTAAACT-TCCAAAAATTACATTTT-AC
* *
55287681 CCCTAAACTTCATAAAAATTACATTTTAA
1 CCCTAAACTTC-CAAAAATTACATTTTAC
*
55287710 CCCTAAACTTTCTAAAAATTACATTATTA-
1 CCCTAAAC-TTCCAAAAATTACATT-TTAC
*
55287739 CCCTCAAACTTCCAAAAATTACCATTTTGC
1 CCCT-AAACTTCCAAAAATTA-CATTTTAC
*
55287769 CCTTAAACTTTCCAAAAA-TAGCATTTTTAC
1 CCCTAAAC-TTCCAAAAATTA-CA-TTTTAC
* *
55287799 CCCTAAATTTCCAAAAATTGTCATTTTAC
1 CCCTAAACTTCCAAAAATT-ACATTTTAC
** *
55287828 CCCCGAACTTCTAAAAATT-CTATTTTTAAC
1 CCCTAAACTTCCAAAAATTAC-A-TTTT-AC
* * ** *
55287858 CTCGAATTTTCCAAAAATTACCATTTAAC
1 CCCTAAACTTCCAAAAATTA-CATTTTAC
*
55287887 CCCTAAACTTCACAAAAATTATATTTTTAC
1 CCCTAAACTTC-CAAAAATTACA-TTTTAC
55287917 CC
1 CC
55287919 TCGAACTTTT
Statistics
Matches: 192, Mismatches: 29, Indels: 34
0.75 0.11 0.13
Matches are distributed among these distances:
27 1 0.01
28 1 0.01
29 93 0.48
30 95 0.49
31 1 0.01
32 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCTAAACTTCCAAAAATTACATTTTAC
Found at i:55287765 original size:59 final size:58
Alignment explanation
Indices: 55287664--55288110 Score: 226
Period size: 59 Copynumber: 7.6 Consensus size: 58
55287654 TGAACTATCC
* *
55287664 AAAAATTATATTTTGACCC-CTAAACTTCATAAAAATTA-CATTTTAACCCTAAACTTTCT
1 AAAAATTACATTTT-ACCCTC-AAACTTC-CAAAAATTACCATTTTAACCCTAAACTTTCT
* *
55287723 AAAAATTACATTATTACCCTCAAACTTCCAAAAATTACCATTTT-GCCCTTAAACTTTCC
1 AAAAATTACATT-TTACCCTCAAACTTCCAAAAATTACCATTTTAACCC-TAAACTTTCT
* ** * **
55287782 AAAAA-TAGCATTTTTACCC-CTAAATTTCCAAAAATTGTCATTTTACCCCCGAAC-TTCT
1 AAAAATTA-CA-TTTTACCCTC-AAACTTCCAAAAATTACCATTTTAACCCTAAACTTTCT
* ** *
55287840 AAAAATT-CTATTTTTAACCTCGAATTTTCCAAAAATTACCA-TTTAACCCCTAAAC-TTCAC
1 AAAAATTAC-A-TTTTACCCTC-AAACTTCCAAAAATTACCATTTTAA-CCCTAAACTTTC-T
* * * * * * * *
55287900 AAAAATTATATTTTTACCCTCGAACTTTTCAAAAATTATGC-TTTTACCCCTGATC-ATCT
1 AAAAATTACA-TTTTACCCTCAAAC-TTCCAAAAATTA-CCATTTTAACCCTAAACTTTCT
* * * * *
55287959 AAAAAATACCATTTTACCCTCGAA-TGTCTAAAAATT-GCATTTTTTACCCTAAACTTT-T
1 AAAAATTA-CATTTTACCCTCAAACT-TCCAAAAATTACCA-TTTTAACCCTAAACTTTCT
* ** * * * * *
55288017 CAAAAATTACAATTTTGCCC-CCGAGTATCCAAAAAGTATCATTTTACCCCTGAAA-TGTCT
1 -AAAAATTAC-ATTTTACCCTCAAACT-TCCAAAAATTACCATTTTAACCCT-AAACTTTCT
* *
55288077 -AAAATTACCGTTTTACCCTCAAACATCCAAAAAT
1 AAAAATTA-CATTTTACCCTCAAACTTCCAAAAAT
55288111 CGCATTTCTG
Statistics
Matches: 299, Mismatches: 59, Indels: 61
0.71 0.14 0.15
Matches are distributed among these distances:
56 2 0.01
57 2 0.01
58 79 0.26
59 159 0.53
60 52 0.17
61 5 0.02
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAAATTACATTTTACCCTCAAACTTCCAAAAATTACCATTTTAACCCTAAACTTTCT
Found at i:55287926 original size:30 final size:29
Alignment explanation
Indices: 55287656--55288110 Score: 188
Period size: 29 Copynumber: 15.4 Consensus size: 29
55287646 AAGGTCCCTG
* *
55287656 AACTATCCAAAAATTATATTTTGACCC-CTA
1 AACT-TCCAAAAATTACATTTTTACCCTC-A
* *
55287686 AACTTCATAAAAATTACATTTTAACCCT-A
1 AACTTC-CAAAAATTACATTTTTACCCTCA
* *
55287715 AACTTTCTAAAAATTACATTATTACCCTCA
1 AAC-TTCCAAAAATTACATTTTTACCCTCA
* *
55287745 AACTTCCAAAAATTACCA-TTTTGCCCTTA
1 AACTTCCAAAAATTA-CATTTTTACCCTCA
55287774 AACTTTCCAAAAA-TAGCATTTTTACCC-CTA
1 AAC-TTCCAAAAATTA-CATTTTTACCCTC-A
* * * *
55287804 AATTTCCAAAAATTGTCA-TTTTACCCCCG
1 AACTTCCAAAAATT-ACATTTTTACCCTCA
* *
55287833 AACTTCTAAAAATT-CTATTTTTAACCTCGA
1 AACTTCCAAAAATTAC-ATTTTTACCCTC-A
** *
55287863 ATTTTCCAAAAATTACCA-TTTAACCC-CTA
1 AACTTCCAAAAATTA-CATTTTTACCCTC-A
* *
55287892 AACTTCACAAAAATTATATTTTTACCCTCG
1 AACTTC-CAAAAATTACATTTTTACCCTCA
* *** *
55287922 AACTTTTCAAAAATTATGCTTTTACCC-CTG
1 AAC-TTCCAAAAATTACATTTTTACCCTC-A
* * * * *
55287952 ATCATCTAAAAAATACCA-TTTTACCCTCG
1 AACTTCCAAAAATTA-CATTTTTACCCTCA
* *
55287981 AA-TGTCTAAAAATTGCATTTTTTACCCT-A
1 AACT-TCCAAAAATTACA-TTTTTACCCTCA
* * * *
55288010 AACTTTTCAAAAATTACAATTTTGCCC-CC
1 AAC-TTCCAAAAATTACATTTTTACCCTCA
* * * *
55288039 GAGTATCCAAAAAGTATCA-TTTTACCCCTGA
1 AACT-TCCAAAAATTA-CATTTTTA-CCCTCA
* **
55288070 AA-TGT-CTAAAATTACCGTTTTACCCTCA
1 AACT-TCCAAAAATTACATTTTTACCCTCA
*
55288098 AACATCCAAAAAT
1 AACTTCCAAAAAT
55288111 CGCATTTCTG
Statistics
Matches: 322, Mismatches: 67, Indels: 73
0.70 0.15 0.16
Matches are distributed among these distances:
27 1 0.00
28 13 0.04
29 164 0.51
30 137 0.43
31 6 0.02
32 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (29 bp):
AACTTCCAAAAATTACATTTTTACCCTCA
Found at i:55288051 original size:88 final size:90
Alignment explanation
Indices: 55287694--55288080 Score: 225
Period size: 88 Copynumber: 4.4 Consensus size: 90
55287684 TAAACTTCAT
* * * * * *
55287694 AAAAATTA-CATTTTAACCCT-AAACTTTCTAAAAATTACA-TTATTACCCTCAAAC-TTCCAAA
1 AAAAAATACCATTTTACCCCTGAAA-TGTCTAAAAATTGCATTTTTTACCCTCAAACTTTTCAAA
* * *** * *
55287755 AATTACCATTTTGCCCTTAAACTTTCC
65 AATTACAATTTTACCCCCGATC-ATCC
* * * * * *
55287782 -AAAAATAGCATTTTTACCCCT-AAATTTCCAAAAATTGTCA--TTTTACCCCCGAACTTCT-AA
1 AAAAAATACCA-TTTTACCCCTGAAATGTCTAAAAATTG-CATTTTTTACCCTCAAACTTTTCAA
* * * **
55287842 AAATT-CTATTTTTAACCTCGAATTTTCC
64 AAATTAC-AATTTTACCCCCG-ATCATCC
* * * *
55287870 AAAAATTACCATTTAACCCCT-AAACT-TCACAAAAATT--ATATTTTTACCCTCGAACTTTTCA
1 AAAAAATACCATTTTACCCCTGAAA-TGTC-TAAAAATTGCAT-TTTTTACCCTCAAACTTTTCA
*** * *
55287931 AAAATTATGCTTTTACCCCTGATCATCT
63 AAAATTACAATTTTACCCCCGATCATCC
55287959 AAAAAATACCATTTTA-CCCTCG-AATGTCTAAAAATTGCATTTTTTACCCT-AAACTTTTCAAA
1 AAAAAATACCATTTTACCCCT-GAAATGTCTAAAAATTGCATTTTTTACCCTCAAACTTTTCAAA
*
55288021 AATTACAATTTTGCCCCCGAGT-ATCC
65 AATTACAATTTTACCCCCGA-TCATCC
* *
55288047 AAAAAGTATCATTTTACCCCTGAAATGTCTAAAA
1 AAAAAATACCATTTTACCCCTGAAATGTCTAAAA
55288081 TTACCGTTTT
Statistics
Matches: 234, Mismatches: 43, Indels: 43
0.73 0.13 0.13
Matches are distributed among these distances:
86 1 0.00
87 7 0.03
88 112 0.48
89 97 0.41
90 17 0.07
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (90 bp):
AAAAAATACCATTTTACCCCTGAAATGTCTAAAAATTGCATTTTTTACCCTCAAACTTTTCAAAA
ATTACAATTTTACCCCCGATCATCC
Found at i:55290423 original size:21 final size:20
Alignment explanation
Indices: 55290395--55290444 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 20
55290385 CCTCTGCTTC
55290395 CCTCGCTTCTCTCGTTGCTG
1 CCTCGCTTCTCTCGTTGCTG
55290415 CCTCTGCTTCTCTCGTTGCTG
1 CCTC-GCTTCTCTCGTTGCTG
55290436 CCTCCGCTT
1 CCT-CGCTT
55290445 TAAGTTGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.14
21 23 0.82
22 1 0.04
ACGTcount: A:0.00, C:0.42, G:0.18, T:0.40
Consensus pattern (20 bp):
CCTCGCTTCTCTCGTTGCTG
Found at i:55290668 original size:27 final size:27
Alignment explanation
Indices: 55290591--55290660 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
55290581 GCTTAGAGGA
*
55290591 AAGCACCGCTAATGACCTGACCCTCAT
1 AAGCACCGCTAATGACCTGACCTTCAT
55290618 AAGCACCGCTAATGACCTGACCTTCAT
1 AAGCACCGCTAATGACCTGACCTTCAT
*
55290645 AAGCGCCGCTAATGAC
1 AAGCACCGCTAATGAC
55290661 TTAACCTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (27 bp):
AAGCACCGCTAATGACCTGACCTTCAT
Found at i:55290709 original size:41 final size:40
Alignment explanation
Indices: 55290645--55291016 Score: 323
Period size: 41 Copynumber: 8.9 Consensus size: 40
55290635 TGACCTTCAT
* * *
55290645 AAGCGCCGCTAATGACTTAACCTTTAGTGGCGCTTAGAGGA
1 AAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTTAG-GGA
* *
55290686 AAGCGCTGCTAATGACCTGACCTTTAGCGGCGCTTAGGTAA
1 AAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTTAGG-GA
*** *
55290727 AAGCATGGCTAATGACCTGACCTTTAGCGGTGCTGGT-GGGA
1 AAGCGCCGCTAATGACCTGACCTTTAGCGGCGCT--TAGGGA
* * * *
55290768 AAGTGCCGCTAATGACATGACCTTTAGCTGTGCTTAGGGGA
1 AAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTTA-GGGA
** ** *
55290809 AAGCATCGCTAATGACCTGACCTTTAGCAACGCTTAGGTAA
1 AAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTTAGG-GA
* *
55290850 AAGCGCCGCTAATGACCTAACCTTTAGCGGTGCTTAGGGGA
1 AAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTTA-GGGA
* * *
55290891 AAACGCCACTAATGACTTGACCTTTAGCGGCGCTTAGGGGA
1 AAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTTA-GGGA
*
55290932 AAGGGCCGCTAATGACCTGATCTTTCTGACCTTTAGCGGCGCTTAGGGGA
1 AAGCGCCGCT-A--A--TGA-C---CTGACCTTTAGCGGCGCTTA-GGGA
* * * *
55290982 AAGTGTCGCTAATAACCTGAACTTTAGCGGCGCTT
1 AAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTT
55291017 TACTTTACCT
Statistics
Matches: 271, Mismatches: 44, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
39 1 0.00
40 3 0.01
41 219 0.81
42 5 0.02
43 1 0.00
44 2 0.01
45 2 0.01
46 3 0.01
47 2 0.01
49 1 0.00
50 32 0.12
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
AAGCGCCGCTAATGACCTGACCTTTAGCGGCGCTTAGGGA
Found at i:55290873 original size:123 final size:122
Alignment explanation
Indices: 55290648--55290956 Score: 388
Period size: 123 Copynumber: 2.5 Consensus size: 122
55290638 CCTTCATAAG
* * *
55290648 CGCCGCTAATGACTTAACCTTTAG-TGGCGCTTAGAGGAAAGCGCTGCTAATGACCTGACCTTTA
1 CGCCGCTAATGACTTGACCTTTAGCT-GCGCTTAGGGGAAAGC-CCGCTAATGACCTGACCTTTA
** ** * * *
55290712 GCGGCGCTTAGGTAAAAGCATGGCTAATGACCTGACCTTTAGCGGTGC-TGGTGGGAAAG
64 GCAACGCTTAGGTAAAAGCACCGCTAATGACCTAACCTTTAGCGGTGCTTAG-GGGAAAA
* * * *
55290771 TGCCGCTAATGACATGACCTTTAGCTGTGCTTAGGGGAAAGCATCGCTAATGACCTGACCTTTAG
1 CGCCGCTAATGACTTGACCTTTAGCTGCGCTTAGGGGAAAGC-CCGCTAATGACCTGACCTTTAG
*
55290836 CAACGCTTAGGTAAAAGCGCCGCTAATGACCTAACCTTTAGCGGTGCTTAGGGGAAAA
65 CAACGCTTAGGTAAAAGCACCGCTAATGACCTAACCTTTAGCGGTGCTTAGGGGAAAA
* * * *
55290894 CGCCACTAATGACTTGACCTTTAGCGGCGCTTAGGGGAAAGGGCCGCTAATGACCTGATCTTT
1 CGCCGCTAATGACTTGACCTTTAGCTGCGCTTAGGGGAAA-GCCCGCTAATGACCTGACCTTT
55290957 CTGACCTTTA
Statistics
Matches: 159, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
123 155 0.97
124 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (122 bp):
CGCCGCTAATGACTTGACCTTTAGCTGCGCTTAGGGGAAAGCCCGCTAATGACCTGACCTTTAGC
AACGCTTAGGTAAAAGCACCGCTAATGACCTAACCTTTAGCGGTGCTTAGGGGAAAA
Found at i:55290983 original size:50 final size:50
Alignment explanation
Indices: 55290908--55291006 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
55290898 ACTAATGACT
* *
55290908 TGACCTTTAGCGGCGCTTAGGGGAAAGGGCCGCTAATGACCTGATCTTTC
1 TGACCTTTAGCGGCGCTTAGGGGAAAGGGCCGCTAATAACCTGAACTTTC
* *
55290958 TGACCTTTAGCGGCGCTTAGGGGAAAGTGTCGCTAATAACCTGAACTTT
1 TGACCTTTAGCGGCGCTTAGGGGAAAGGGCCGCTAATAACCTGAACTTT
55291007 AGCGGCGCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (50 bp):
TGACCTTTAGCGGCGCTTAGGGGAAAGGGCCGCTAATAACCTGAACTTTC
Found at i:55291028 original size:22 final size:21
Alignment explanation
Indices: 55291003--55291043 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
55290993 ATAACCTGAA
55291003 CTTTAGCGGCGCTTTACTTTAC
1 CTTTAGCGGCG-TTTACTTTAC
* *
55291025 CTTTTGCGGCGTTTTCTTT
1 CTTTAGCGGCGTTTACTTT
55291044 CCAAACGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.07, C:0.24, G:0.20, T:0.49
Consensus pattern (21 bp):
CTTTAGCGGCGTTTACTTTAC
Found at i:55291381 original size:41 final size:40
Alignment explanation
Indices: 55291284--55291543 Score: 249
Period size: 41 Copynumber: 6.4 Consensus size: 40
55291274 CTAGTGAAAA
* * *
55291284 AGGGAAAAGCGCCGCTAATGACCTGACCTTTAGCGGTGCTT
1 AGGGGAAAGCGCCGCTAATGACCTGACCTTTAG-TGCGCTT
* * * *
55291325 -GTGGG---GTGCTGCTAATGACATGACATTTAGTGGCGCTT
1 AG-GGGAAAGCGCCGCTAATGACCTGACCTTTAGT-GCGCTT
*
55291363 AGGGGAAAGCGTCGCTAATGACCTGACCTTTAGTTGCGCTT
1 AGGGGAAAGCGCCGCTAATGACCTGACCTTTAG-TGCGCTT
*** * *
55291404 AGATAAAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTT
1 AGGGGAAAGCGCCGCTAATGACCTGACCTTTAG-TGCGCTT
* * * *
55291445 AGGGGAAAGGGTCGCTAATGACCTAACCTTTAGCTGCACTT
1 AGGGGAAAGCGCCGCTAATGACCTGACCTTTAG-TGCGCTT
*
55291486 ATGGGAAAGCGCCGCTAATGACCTGACCTTTAGCTGCGCTT
1 AGGGGAAAGCGCCGCTAATGACCTGACCTTTAG-TGCGCTT
* *
55291527 AGTGTAAAGCGCCGCTA
1 AGGGGAAAGCGCCGCTA
55291544 TTGCTTTACC
Statistics
Matches: 178, Mismatches: 34, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
38 29 0.16
39 1 0.01
40 1 0.01
41 146 0.82
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
AGGGGAAAGCGCCGCTAATGACCTGACCTTTAGTGCGCTT
Found at i:55291450 original size:82 final size:82
Alignment explanation
Indices: 55291335--55291543 Score: 276
Period size: 82 Copynumber: 2.5 Consensus size: 82
55291325 GTGGGGTGCT
* * * * *
55291335 GCTAATGACATGACATTTAGTGGCGCTTAGGGGAAAGCGTCGCTAATGACCTGACCTTTAGTTGC
1 GCTAATGACCTGACCTTTAGCGGCGCTTAGGGGAAAGCGTCGCTAATGACCTAACCTTTAGCTGC
* *
55291400 GCTTA-GATAAAAGCGCC
66 ACTTATG-GAAAAGCGCC
* *
55291417 GCTAATGACCTAACCTTTAGCGGCGCTTAGGGGAAAGGGTCGCTAATGACCTAACCTTTAGCTGC
1 GCTAATGACCTGACCTTTAGCGGCGCTTAGGGGAAAGCGTCGCTAATGACCTAACCTTTAGCTGC
*
55291482 ACTTATGGGAAAGCGCC
66 ACTTATGGAAAAGCGCC
* * * *
55291499 GCTAATGACCTGACCTTTAGCTGCGCTTAGTGTAAAGCGCCGCTA
1 GCTAATGACCTGACCTTTAGCGGCGCTTAGGGGAAAGCGTCGCTA
55291544 TTGCTTTACC
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
82 109 0.99
83 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (82 bp):
GCTAATGACCTGACCTTTAGCGGCGCTTAGGGGAAAGCGTCGCTAATGACCTAACCTTTAGCTGC
ACTTATGGAAAAGCGCC
Found at i:55291505 original size:123 final size:120
Alignment explanation
Indices: 55291287--55291543 Score: 324
Period size: 123 Copynumber: 2.1 Consensus size: 120
55291277 GTGAAAAAGG
* * * *
55291287 GAAAAGCGCCGCTAATGACCTGACCTTTAGCGGTGCTTGTGGGGTGCTGCTAATGACATGACATT
1 GAAAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTGGGGGGTGCTGCTAATGACATAACATT
* * *
55291352 TAGTGGCGCTTAGGGGAAAGCGTCGCTAATGACCTGACCTTTAGTTGCGCTTAGAT
66 TAGTGGCACTTAGGGGAAAGCGCCGCTAATGACCTGACCTTTAGCTGCGCTTAG-T
*
55291408 -AAAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTAGGGGAAAGG-G-TCGCTAATGACCTA
1 GAAAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTT-GGGG---GGTGCT-GCTAATGACATA
* *
55291470 ACCTTTAGCT-GCACTTATGGGAAAGCGCCGCTAATGACCTGACCTTTAGCTGCGCTTAGT
61 ACATTTAG-TGGCACTTAGGGGAAAGCGCCGCTAATGACCTGACCTTTAGCTGCGCTTAGT
*
55291530 GTAAAGCGCCGCTA
1 GAAAAGCGCCGCTA
55291544 TTGCTTTACC
Statistics
Matches: 118, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
120 35 0.30
121 3 0.03
122 2 0.02
123 75 0.64
124 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (120 bp):
GAAAAGCGCCGCTAATGACCTAACCTTTAGCGGCGCTTGGGGGGTGCTGCTAATGACATAACATT
TAGTGGCACTTAGGGGAAAGCGCCGCTAATGACCTGACCTTTAGCTGCGCTTAGT
Found at i:55301608 original size:24 final size:24
Alignment explanation
Indices: 55301580--55301662 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
55301570 TAGAGTAATA
* *
55301580 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAATTCAAACAAATAAAC
*
55301604 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTCAAACAAATAAAC
* * *
55301628 AGAATTTAATTCAAATAATTAAAC
1 AGAGTTTAATTCAAACAAATAAAC
55301652 AGAGTTTAATT
1 AGAGTTTAATT
55301663 GAAAGATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.29
Consensus pattern (24 bp):
AGAGTTTAATTCAAACAAATAAAC
Found at i:55303622 original size:24 final size:24
Alignment explanation
Indices: 55303593--55303643 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
55303583 AGTTTGATTC
*
55303593 AAACAAATAAACAGAATTTAATTG
1 AAACAAATAAACAGAATTTAACTG
* *
55303617 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAATTTAACTG
55303641 AAA
1 AAA
55303644 GATTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:55304904 original size:21 final size:23
Alignment explanation
Indices: 55304878--55304921 Score: 74
Period size: 21 Copynumber: 2.0 Consensus size: 23
55304868 AATATGTTTG
55304878 TTTATTT-ATTAAAA-AAATTAA
1 TTTATTTAATTAAAATAAATTAA
55304899 TTTATTTAATTAAAATAAATTAA
1 TTTATTTAATTAAAATAAATTAA
55304922 AAATATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 7 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTTATTTAATTAAAATAAATTAA
Found at i:55305355 original size:14 final size:16
Alignment explanation
Indices: 55305325--55305356 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55305315 ATAAGAATTT
55305325 AAATATGACTAATAGA
1 AAATATGACTAATAGA
55305341 AAATATGA-T-ATAGA
1 AAATATGACTAATAGA
55305355 AA
1 AA
55305357 TGGATTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.59, C:0.03, G:0.12, T:0.25
Consensus pattern (16 bp):
AAATATGACTAATAGA
Found at i:55310621 original size:16 final size:17
Alignment explanation
Indices: 55310594--55310626 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
55310584 TAATTTTTAA
*
55310594 AAAAATATATAATACAT
1 AAAAATATATAAAACAT
55310611 AAAAATA-ATAAAACAT
1 AAAAATATATAAAACAT
55310627 TCAAATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAATATATAAAACAT
Found at i:55310850 original size:16 final size:17
Alignment explanation
Indices: 55310826--55310860 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
55310816 AGTAAAATAA
55310826 TAAAAAAATAAT-TTTT
1 TAAAAAAATAATATTTT
*
55310842 TAAATAAATAATATTTT
1 TAAAAAAATAATATTTT
55310859 TA
1 TA
55310861 TCTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAAAATAATATTTT
Found at i:55311898 original size:21 final size:21
Alignment explanation
Indices: 55311859--55311898 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55311849 ATTTTTCAAG
*
55311859 TTTTAGATTATTTATTTTACC
1 TTTTAGATTATTTAATTTACC
55311880 TTTTA-ATTATTTCAATTTA
1 TTTTAGATTATTT-AATTTA
55311899 AAGGTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTAGATTATTTAATTTACC
Found at i:55330742 original size:50 final size:48
Alignment explanation
Indices: 55330679--55330784 Score: 142
Period size: 50 Copynumber: 2.2 Consensus size: 48
55330669 ATAAATATTA
55330679 TAAATAAATATTTATATTTATGTAAAAA-ATCATATCTAAACAAAACAAAT
1 TAAATAAATATTTATATTTATGTAAAAACATCATAT-TAAA-AAAAC-AAT
* * **
55330729 TAAATAAATATTTATGTTTATTTAAAAACATCATATTTGAAAAACAAT
1 TAAATAAATATTTATATTTATGTAAAAACATCATATTAAAAAAACAAT
55330777 TAAATAAA
1 TAAATAAA
55330785 CAAGATCTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
48 11 0.22
49 5 0.10
50 28 0.55
51 7 0.14
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.36
Consensus pattern (48 bp):
TAAATAAATATTTATATTTATGTAAAAACATCATATTAAAAAAACAAT
Found at i:55332447 original size:18 final size:16
Alignment explanation
Indices: 55332406--55332448 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
55332396 ATAAATTATG
*
55332406 ATATTTTTTAGTTTTT
1 ATATTTTTTAGTTTTC
*
55332422 ATGATTTTCTAAGTTTTC
1 AT-ATTTT-TTAGTTTTC
55332440 ATATTTTTT
1 ATATTTTTT
55332449 TGGGGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
16 3 0.14
17 10 0.45
18 9 0.41
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (16 bp):
ATATTTTTTAGTTTTC
Found at i:55333938 original size:21 final size:21
Alignment explanation
Indices: 55333903--55333948 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
55333893 ACAGTTGAAA
*
55333903 TCAACCGATTTGTTTCCTGTAC
1 TCAACCGACTTGTTT-CTGTAC
*
55333925 TCAACCG-CTTGTTTCTTTAC
1 TCAACCGACTTGTTTCTGTAC
55333945 TCAA
1 TCAA
55333949 ATGTCTCCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 6 0.27
22 7 0.32
ACGTcount: A:0.20, C:0.28, G:0.11, T:0.41
Consensus pattern (21 bp):
TCAACCGACTTGTTTCTGTAC
Found at i:55342263 original size:228 final size:228
Alignment explanation
Indices: 55341849--55342532 Score: 713
Period size: 228 Copynumber: 3.0 Consensus size: 228
55341839 AACTTAGAAA
* * * * * * * *
55341849 CCACCACGAAGACGCAAGACAAGGTGGAGAGTGGATTCCTTCTGAATATTGTAATCAGCCAAAGT
1 CCACCACGAAGACGCAAGACCAGATGGAGAGTCGACTCCTTCTGGATGTTGTAATCGGCCAAGGT
** * * ** * * * * * *
55341914 CCTCCCATCTTCCAATTGTTTCCCAGCGAAA-ATCAACCTTTGCTGATCTGGTGGAATCCCTTCT
66 CCGACCATCCTCGAGCTGTTTCCCGGC-AAAGATGAGCCTTTGCTGGTCTGGTGGGATCCCTTCC
* * * * * * *
55341978 TTGTCCTGAATCTTCGCCTTAACATTGTCGATCGTATCGGAGCTCTCCACCTCCAAAGTTATGGT
130 TTGTCTTGGATCTTGGCCTTAACGTTGTCGATCGTGTCGGAGCTCTCGACTTCCAAAGTTATGGT
*
55342043 TTTCCCAGTCAACGTCTTGACGAAAATCTGCATC
195 CTTCCCAGTCAACGTCTTGACGAAAATCTGCATC
* * * *
55342077 CCACCACGAAGCCTCAATACCAGATGGAGGGTCGACTCCTTCTGGATGTTGTAATCGGCCAAGGT
1 CCACCACGAAGACGCAAGACCAGATGGAGAGTCGACTCCTTCTGGATGTTGTAATCGGCCAAGGT
* * * *
55342142 GCGACCGTCCTCGAGTTGTTTCCCGGCAAAGATGAGCCTTTGCTGGTCTGGTGGGATGCCTTCCT
66 CCGACCATCCTCGAGCTGTTTCCCGGCAAAGATGAGCCTTTGCTGGTCTGGTGGGATCCCTTCCT
* * * *
55342207 TGTCTTGGATCTTGGCCTTGACGTTGTCGATGGTGTCAGAGCTTTCGACTTCCAAAGTTATGGTC
131 TGTCTTGGATCTTGGCCTTAACGTTGTCGATCGTGTCGGAGCTCTCGACTTCCAAAGTTATGGTC
* * ** * * *
55342272 TTGCCGGTCAGGGTTTTGACGAAGATCTGCATG
196 TTCCCAGTCAACGTCTTGACGAAAATCTGCATC
* * * * *
55342305 CCACCACGTAGACGGAGGACGAGATGGAGAGTGGACTCCTTCTGGATGTTGTAATCGGCCAAGGT
1 CCACCACGAAGACGCAAGACCAGATGGAGAGTCGACTCCTTCTGGATGTTGTAATCGGCCAAGGT
* * * * * * *
55342370 CCGGCCATCTTCGAGCTGTTTTCCGGCGAAGATGAGACGTTGTTGGTCTGGTGGGATCCCTTCCT
66 CCGACCATCCTCGAGCTGTTTCCCGGCAAAGATGAGCCTTTGCTGGTCTGGTGGGATCCCTTCCT
* * * ** *
55342435 TGTCTTGGATTTTGGCCTTAACGTTGTCGATCGTGTCGGAACTCTCGACTTCGAGGGTGATGGTC
131 TGTCTTGGATCTTGGCCTTAACGTTGTCGATCGTGTCGGAGCTCTCGACTTCCAAAGTTATGGTC
* * ** * *
55342500 TTGCCGGTCAGGGTCTTAACGAAGATCTGCATC
196 TTCCCAGTCAACGTCTTGACGAAAATCTGCATC
55342533 TTGATTGGAC
Statistics
Matches: 377, Mismatches: 78, Indels: 2
0.82 0.17 0.00
Matches are distributed among these distances:
227 3 0.01
228 374 0.99
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (228 bp):
CCACCACGAAGACGCAAGACCAGATGGAGAGTCGACTCCTTCTGGATGTTGTAATCGGCCAAGGT
CCGACCATCCTCGAGCTGTTTCCCGGCAAAGATGAGCCTTTGCTGGTCTGGTGGGATCCCTTCCT
TGTCTTGGATCTTGGCCTTAACGTTGTCGATCGTGTCGGAGCTCTCGACTTCCAAAGTTATGGTC
TTCCCAGTCAACGTCTTGACGAAAATCTGCATC
Found at i:55344483 original size:18 final size:18
Alignment explanation
Indices: 55344460--55344495 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55344450 TTATAGAGCA
*
55344460 AATGTACAATCTATTTAT
1 AATGTACAAACTATTTAT
*
55344478 AATGTATAAACTATTTAT
1 AATGTACAAACTATTTAT
55344496 TATCTATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (18 bp):
AATGTACAAACTATTTAT
Found at i:55344503 original size:18 final size:18
Alignment explanation
Indices: 55344470--55344504 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55344460 AATGTACAAT
*
55344470 CTATTTATAATGTATAAA
1 CTATTTATAATCTATAAA
*
55344488 CTATTTATTATCTATAA
1 CTATTTATAATCTATAA
55344505 TCTACATATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.49
Consensus pattern (18 bp):
CTATTTATAATCTATAAA
Found at i:55346240 original size:46 final size:46
Alignment explanation
Indices: 55346172--55346265 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 46
55346162 CACTACCTGT
* *
55346172 TTATGCACTTCGGGGCTGTCTCGTTACACGCTTTGACGTGGTCCCG
1 TTATGCACTTCGGGGCTATCTCGTTACACGCTTCGACGTGGTCCCG
* * * * * *
55346218 TTATGTACTTCGGTGTTATCTCGTTACATGCTTCGATGTTGTCCCG
1 TTATGCACTTCGGGGCTATCTCGTTACACGCTTCGACGTGGTCCCG
55346264 TT
1 TT
55346266 CTATTGCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.39
Consensus pattern (46 bp):
TTATGCACTTCGGGGCTATCTCGTTACACGCTTCGACGTGGTCCCG
Found at i:55346265 original size:23 final size:23
Alignment explanation
Indices: 55346188--55346265 Score: 57
Period size: 23 Copynumber: 3.4 Consensus size: 23
55346178 ACTTCGGGGC
* * * *
55346188 TGTCTCGTTACACGCTTTGACGT
1 TGTCCCGTTACATGCTTCGATGT
* ** * *
55346211 GGTCCCGTTATGTACTTCGGTGT
1 TGTCCCGTTACATGCTTCGATGT
* *
55346234 TATCTCGTTACATGCTTCGATGT
1 TGTCCCGTTACATGCTTCGATGT
55346257 TGTCCCGTT
1 TGTCCCGTT
55346266 CTATTGCATA
Statistics
Matches: 37, Mismatches: 18, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.41
Consensus pattern (23 bp):
TGTCCCGTTACATGCTTCGATGT
Found at i:55347505 original size:53 final size:52
Alignment explanation
Indices: 55347466--55347584 Score: 150
Period size: 53 Copynumber: 2.2 Consensus size: 52
55347456 AAATTGAAAT
55347466 AAATAAGTGAAAAAATTCAAGTAAACAATGATAACACAACAAGATTATAATAAAA
1 AAATAAGT--AAAAATTCAAGTAAACAATGATAACACAACAAGA-TATAATAAAA
* * *
55347521 AAATAAGTAAAAATTCATGTAAACAATAATAACACAATAAGATTATAA-AAAA
1 AAATAAGTAAAAATTCAAGTAAACAATGATAACACAACAAGA-TATAATAAAA
* *
55347573 ACATAAGCAAAA
1 AAATAAGTAAAA
55347585 GTTTAAAATA
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
52 14 0.24
53 37 0.63
55 8 0.14
ACGTcount: A:0.63, C:0.09, G:0.08, T:0.20
Consensus pattern (52 bp):
AAATAAGTAAAAATTCAAGTAAACAATGATAACACAACAAGATATAATAAAA
Found at i:55360071 original size:24 final size:25
Alignment explanation
Indices: 55360039--55360091 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 25
55360029 AACATAAAAG
*
55360039 AAAAAATTAAATTGCT-TAAAAGAA
1 AAAAAATTAAATTGCTCAAAAAGAA
55360063 AAAAAATTAAATTGCTCAAAAAGAA
1 AAAAAATTAAATTGCTCAAAAAGAA
55360088 AAAA
1 AAAA
55360092 TATGGGGACC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.66, C:0.06, G:0.08, T:0.21
Consensus pattern (25 bp):
AAAAAATTAAATTGCTCAAAAAGAA
Found at i:55367387 original size:23 final size:25
Alignment explanation
Indices: 55367360--55367411 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
55367350 AAGCTATTTA
*
55367360 ATTTAAAAT-TTTAAT-AAAAAATC
1 ATTTAAAATATTAAATCAAAAAATC
* *
55367383 ATTTAGAATATTAAATCAAAAAATT
1 ATTTAAAATATTAAATCAAAAAATC
55367408 ATTT
1 ATTT
55367412 TTTAGAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.33
24 5 0.21
25 11 0.46
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTTAAAATATTAAATCAAAAAATC
Found at i:55369063 original size:19 final size:20
Alignment explanation
Indices: 55369036--55369078 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
55369026 AATATTTTTT
*
55369036 TTTCTTTTC-TCTTCTACAG
1 TTTCGTTTCTTCTTCTACAG
* *
55369055 TTTCGTTTCTTCTTTTATAG
1 TTTCGTTTCTTCTTCTACAG
55369075 TTTC
1 TTTC
55369079 CAATCAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.09, C:0.21, G:0.07, T:0.63
Consensus pattern (20 bp):
TTTCGTTTCTTCTTCTACAG
Found at i:55369155 original size:3 final size:3
Alignment explanation
Indices: 55369141--55369177 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
55369131 CAATTTTGTC
* *
55369141 TCT TCT TAT TCT TCT TCA TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
55369178 TCGACCTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.05, C:0.30, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:55370633 original size:13 final size:14
Alignment explanation
Indices: 55370614--55370646 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
55370604 ATGAAGGTTA
55370614 ATTAAATTTTATTT
1 ATTAAATTTTATTT
55370628 -TTAAATTTTATTT
1 ATTAAATTTTATTT
55370641 ATTAAA
1 ATTAAA
55370647 GTGTGAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTAAATTTTATTT
Found at i:55375521 original size:15 final size:15
Alignment explanation
Indices: 55375501--55375531 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
55375491 GAAGATAAAT
55375501 TTAACGTTCATTATA
1 TTAACGTTCATTATA
55375516 TTAACGTTCATTATA
1 TTAACGTTCATTATA
55375531 T
1 T
55375532 AAAAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.06, T:0.48
Consensus pattern (15 bp):
TTAACGTTCATTATA
Found at i:55383719 original size:21 final size:21
Alignment explanation
Indices: 55383664--55383719 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
55383654 GCAATGGAGC
*
55383664 AAGTCTCGAGACTTGGCTCAA
1 AAGTCTCGAGACTTAGCTCAA
* * *
55383685 AAGTATTGATACTTAGCTCAA
1 AAGTCTCGAGACTTAGCTCAA
55383706 AAGTCTCGAGACTT
1 AAGTCTCGAGACTT
55383720 TGTCCTTTGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (21 bp):
AAGTCTCGAGACTTAGCTCAA
Found at i:55386067 original size:40 final size:40
Alignment explanation
Indices: 55386023--55386109 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
55386013 ATTTTAAAGT
*
55386023 TTATAAAAAGTATTAGAAATTAATT-AAAAATCATAAAATC
1 TTATAAAAAGTA-TAAAAATTAATTAAAAAATCATAAAATC
** *
55386063 TTATAAAATTTATAAAAATTAATTAAAAAATCATAAAATG
1 TTATAAAAAGTATAAAAATTAATTAAAAAATCATAAAATC
55386103 TTATAAA
1 TTATAAA
55386110 TTTTAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 11 0.26
40 31 0.74
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (40 bp):
TTATAAAAAGTATAAAAATTAATTAAAAAATCATAAAATC
Found at i:55388381 original size:22 final size:22
Alignment explanation
Indices: 55388351--55388411 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
55388341 CTCTCCAATA
55388351 TTTACAAATTTTATCAATAAAC
1 TTTACAAATTTTATCAATAAAC
* * *
55388373 TTTA-AAAATTTAACCATAAAC
1 TTTACAAATTTTATCAATAAAC
*
55388394 TTTACAAATTTTGTCAAT
1 TTTACAAATTTTATCAAT
55388412 TTAATCTTGA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.41
Consensus pattern (22 bp):
TTTACAAATTTTATCAATAAAC
Found at i:55388879 original size:27 final size:27
Alignment explanation
Indices: 55388851--55388904 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
55388841 ATCTAGACAA
*
55388851 TTATAAAAATTTCAAAAAAATTAATAAT
1 TTATAAAAAATT-AAAAAAATTAATAAT
*
55388879 TTATAAAAAATTATAAAAATTAATAA
1 TTATAAAAAATTAAAAAAATTAATAA
55388905 AAATGCGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
TTATAAAAAATTAAAAAAATTAATAAT
Found at i:55388899 original size:20 final size:20
Alignment explanation
Indices: 55388849--55388907 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
55388839 AAATCTAGAC
55388849 AATTATAAAAATTTCA-AAAA
1 AATTATAAAAATTT-ATAAAA
*
55388869 AA-T-TAATAATTTATAAAA
1 AATTATAAAAATTTATAAAA
*
55388887 AATTATAAAAATTAATAAAA
1 AATTATAAAAATTTATAAAA
55388907 A
1 A
55388908 TGCGAAAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 1 0.03
18 14 0.42
19 2 0.06
20 16 0.48
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTATAAAAATTTATAAAA
Found at i:55388908 original size:10 final size:9
Alignment explanation
Indices: 55388849--55388908 Score: 50
Period size: 10 Copynumber: 6.3 Consensus size: 9
55388839 AAATCTAGAC
55388849 AATTATAAA
1 AATTATAAA
*
55388858 AATTTCAAAAA
1 AA-TT-ATAAA
*
55388869 AATTA-ATA
1 AATTATAAA
*
55388877 ATTTATAAAA
1 AATTAT-AAA
55388887 AATTATAAA
1 AATTATAAA
55388896 AATTAATAAA
1 AATT-ATAAA
55388906 AAT
1 AAT
55388909 GCGAAAGAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 6 0.15
9 10 0.24
10 19 0.46
11 6 0.15
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (9 bp):
AATTATAAA
Found at i:55389127 original size:19 final size:20
Alignment explanation
Indices: 55389103--55389145 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
55389093 ATATTTAAAA
55389103 TTAAT-ATTTTTAGTAAT-TT
1 TTAATAATTTTTA-TAATATT
55389122 TTAATAATTTTTATAATATT
1 TTAATAATTTTTATAATATT
55389142 TTAA
1 TTAA
55389146 AAAATTATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTAATAATTTTTATAATATT
Found at i:55389505 original size:20 final size:20
Alignment explanation
Indices: 55389476--55389513 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55389466 CCTTGAATTG
* *
55389476 TTTTATTTATTAAATTATCA
1 TTTTACTTATAAAATTATCA
55389496 TTTTACTTATAAAATTAT
1 TTTTACTTATAAAATTAT
55389514 TAGTTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTACTTATAAAATTATCA
Found at i:55389611 original size:20 final size:20
Alignment explanation
Indices: 55389566--55389615 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
55389556 TTAATTAAAA
*
55389566 ATAT-TTTTTATAATTTTGT
1 ATATATTTTTATAAATTTGT
*
55389585 ATCTATTTTTATAAAATTT-T
1 ATATATTTTTAT-AAATTTGT
55389605 ATATATTTTTA
1 ATATATTTTTA
55389616 CCCAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 3 0.12
20 18 0.69
21 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
ATATATTTTTATAAATTTGT
Found at i:55389614 original size:10 final size:10
Alignment explanation
Indices: 55389566--55389615 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
55389556 TTAATTAAAA
55389566 ATAT-TTTTT
1 ATATATTTTT
55389575 ATA-ATTTTGT
1 ATATATTTT-T
*
55389585 ATCTATTTTT
1 ATATATTTTT
* *
55389595 ATAAAATTTT
1 ATATATTTTT
55389605 ATATATTTTT
1 ATATATTTTT
55389615 A
1 A
55389616 CCCAAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
9 7 0.22
10 20 0.62
11 5 0.16
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (10 bp):
ATATATTTTT
Found at i:55393107 original size:17 final size:17
Alignment explanation
Indices: 55393085--55393120 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55393075 CGAAATGATG
55393085 CAAATTTAAAATTAATC
1 CAAATTTAAAATTAATC
*
55393102 CAAATTTAAAATTACTC
1 CAAATTTAAAATTAATC
55393119 CA
1 CA
55393121 CTTGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (17 bp):
CAAATTTAAAATTAATC
Found at i:55393215 original size:2 final size:2
Alignment explanation
Indices: 55393210--55393236 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55393200 TCATAGTGTG
55393210 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 T
55393237 GATGAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55402703 original size:29 final size:30
Alignment explanation
Indices: 55402671--55402732 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 30
55402661 GTTTCACGTG
*
55402671 TATAATTACAC-TAAATTAAAATTCATATA
1 TATAATTACACATAAATCAAAATTCATATA
55402700 TATAATTACACATTAAATCAAAATTCATATA
1 TATAATTACACA-TAAATCAAAATTCATATA
55402731 TA
1 TA
55402733 ATTTTGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 11 0.37
31 19 0.63
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (30 bp):
TATAATTACACATAAATCAAAATTCATATA
Found at i:55402733 original size:29 final size:28
Alignment explanation
Indices: 55402671--55402735 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 28
55402661 GTTTCACGTG
*
55402671 TATAATTACACTAAATTAAAATTCATATA
1 TATAATTACACTAAATCAAAATTCA-ATA
55402700 TATAATTACACATTAAATCAAAATTC-ATA
1 TATAATTACAC--TAAATCAAAATTCAATA
55402729 TATAATT
1 TATAATT
55402736 TTGAGATTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 21 0.64
31 12 0.36
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (28 bp):
TATAATTACACTAAATCAAAATTCAATA
Found at i:55405379 original size:58 final size:58
Alignment explanation
Indices: 55405197--55405544 Score: 400
Period size: 58 Copynumber: 6.0 Consensus size: 58
55405187 AAAGAAACGA
* * **** *
55405197 TGAAATCGGGGTTAAAAATGGGACTTTT-GGATACCCGGGGGCAAAATGGTAATTTTGG
1 TGAAATCGAGGTTAAAAAT-GGAATTTTAGGAGGTTCGGGGGTAAAATGGTAATTTTGG
*
55405255 TGAAATCGGGGTTTAAAAATGGAATTTTTA--AGGCTTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGAGG-TTAAAAATGGAA-TTTTAGGAGG-TTCGGGGGTAAAATGGTAA-TTTTGG
*
55405315 TGAAATCAAGGTTAAAAATGGAATTTTAGGAGGTTCGGGGGTAAAATGGTAATTTTGG
1 TGAAATCGAGGTTAAAAATGGAATTTTAGGAGGTTCGGGGGTAAAATGGTAATTTTGG
* * *
55405373 TGAAATCGAGGTT-AAAATGGAATTTTGGGAAGTTCGAGGGTAAAATGGTAATTTTTGG
1 TGAAATCGAGGTTAAAAATGGAATTTTAGGAGGTTCGGGGGTAAAATGGTAA-TTTTGG
* * * * *
55405431 TGAAATCGAGGTCAAAAATGGAATTTTAGGAAGTTTGGGGGTGAAATGGTAATTTTAG
1 TGAAATCGAGGTTAAAAATGGAATTTTAGGAGGTTCGGGGGTAAAATGGTAATTTTGG
* * ** *
55405489 TGAAATC-AGGGTTTAAAATAGAATTTTAAAAGGTTCGAGGGTAAAATGGTAATTTT
1 TGAAATCGA-GGTTAAAAATGGAATTTTAGGAGGTTCGGGGGTAAAATGGTAATTTT
55405545 AGGAAGTTTC
Statistics
Matches: 253, Mismatches: 27, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
57 36 0.14
58 106 0.42
59 93 0.37
60 18 0.07
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (58 bp):
TGAAATCGAGGTTAAAAATGGAATTTTAGGAGGTTCGGGGGTAAAATGGTAATTTTGG
Found at i:55405448 original size:116 final size:116
Alignment explanation
Indices: 55405232--55405544 Score: 443
Period size: 116 Copynumber: 2.7 Consensus size: 116
55405222 TTTGGATACC
* * * *
55405232 CGGGGGCAAAATGGTAATTTTGGTGAAATCGGGGTTTAAAAATGGAATTTTTAAGGCTTCGGGGG
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTT-AAAATGGAATTTTAAAGG-TTCGAGGG
* *
55405297 TAAAATGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGAATTTTAGGAGGTT
64 TAAAATGGTAATTTTTGGTGAAATCAAGGTCAAAAATGGAATTTTAGGAAGTT
*
55405350 CGGGGGTAAAATGGTAATTTTGGTGAAATCGAGG-TTAAAATGGAATTTTGGGAA-GTTCGAGGG
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTTAAAATGGAATTTT--AAAGGTTCGAGGG
*
55405413 TAAAATGGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTAGGAAGTT
64 TAAAATGGTAATTTTTGGTGAAATCAAGGTCAAAAATGGAATTTTAGGAAGTT
* * * *
55405466 TGGGGGTGAAATGGTAATTTTAGTGAAATC-AGGGTTTAAAATAGAATTTTAAAAGGTTCGAGGG
1 CGGGGGTAAAATGGTAATTTTGGTGAAATCGA-GGTTTAAAATGGAATTTT-AAAGGTTCGAGGG
55405530 TAAAATGGTAATTTT
64 TAAAATGGTAATTTT
55405545 AGGAAGTTTC
Statistics
Matches: 177, Mismatches: 13, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
115 1 0.01
116 101 0.57
117 41 0.23
118 34 0.19
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (116 bp):
CGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTTAAAATGGAATTTTAAAGGTTCGAGGGTA
AAATGGTAATTTTTGGTGAAATCAAGGTCAAAAATGGAATTTTAGGAAGTT
Found at i:55405500 original size:28 final size:28
Alignment explanation
Indices: 55405294--55405546 Score: 114
Period size: 29 Copynumber: 8.7 Consensus size: 28
55405284 AAGGCTTCGG
*
55405294 GGGTAAAATGGTAATTTTTGGTGAAATCAA
1 GGGTAAAATGGTAA-TTTTAGTGAAATC-A
* ** *
55405324 GGTTAAAAATGG-AATTTTAG-GAGGTTCGG
1 GGGT-AAAATGGTAATTTTAGTGA-AATC-A
*
55405353 GGGTAAAATGGTAATTTTGGTGAAATCGA
1 GGGTAAAATGGTAATTTTAGTGAAATC-A
* * *
55405382 GGTTAAAATGG-AATTTT-GGGAAGTTCGA
1 GGGTAAAATGGTAATTTTAGTGAA-ATC-A
*
55405410 GGGTAAAATGGTAATTTTTGGTGAAATC-
1 GGGTAAAATGGTAA-TTTTAGTGAAATCA
* **
55405438 GAGGTCAAAAATGG-AATTTTAG-GAAGTTTGG
1 G-GGT--AAAATGGTAATTTTAGTGAA--ATCA
*
55405469 GGGTGAAATGGTAATTTTAGTGAAATCA
1 GGGTAAAATGGTAATTTTAGTGAAATCA
*
55405497 GGGTTTAAAATAG-AATTTTA---AAAGGTTCGA
1 GGG--TAAAATGGTAATTTTAGTGAAA---TC-A
55405527 GGGTAAAATGGTAATTTTAG
1 GGGTAAAATGGTAATTTTAG
55405547 GAAGTTTCGG
Statistics
Matches: 172, Mismatches: 27, Indels: 48
0.70 0.11 0.19
Matches are distributed among these distances:
26 3 0.02
27 4 0.02
28 50 0.29
29 64 0.37
30 32 0.19
31 19 0.11
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTAGTGAAATCA
Found at i:55405542 original size:29 final size:28
Alignment explanation
Indices: 55405502--55405572 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
55405492 AATCAGGGTT
55405502 TAAAATAG-AATTTTA-AAAGGTTCGAGGG
1 TAAAAT-GTAATTTTAGAAAGGTTCG-GGG
* *
55405530 TAAAATGGTAATTTTAGGAAGTTTCGGGG
1 TAAAAT-GTAATTTTAGAAAGGTTCGGGG
55405559 TCAAAATGTAATTT
1 T-AAAATGTAATTT
55405573 CTGGACTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.19
29 18 0.49
30 12 0.32
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (28 bp):
TAAAATGTAATTTTAGAAAGGTTCGGGG
Found at i:55407112 original size:17 final size:17
Alignment explanation
Indices: 55407090--55407165 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
55407080 AATTTAATTT
*
55407090 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* **
55407107 TAAATTTAAATTTTATG
1 TAAATTTAAATTTAAAA
* *
55407124 CAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
55407141 TAAATCT-AATTTAAAA
1 TAAATTTAAATTTAAAA
55407157 CTAAATTTA
1 -TAAATTTA
55407166 TGTCATTGGG
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 8 0.18
17 36 0.82
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:55407163 original size:34 final size:35
Alignment explanation
Indices: 55407090--55407165 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
55407080 AATTTAATTT
* * * * **
55407090 TAAATTTAAATTTATAATAAATTTAAATTTTATGC
1 TAAATTTAAATTCAAAATAAATCTAAATTTAAAAC
55407125 -AAATTTAAATTCAAAATAAATCT-AATTTAAAAC
1 TAAATTTAAATTCAAAATAAATCTAAATTTAAAAC
55407158 TAAATTTA
1 TAAATTTA
55407166 TGTCATTGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 7 0.21
34 27 0.79
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAATTTAAATTCAAAATAAATCTAAATTTAAAAC
Found at i:55408866 original size:25 final size:22
Alignment explanation
Indices: 55408822--55409020 Score: 133
Period size: 23 Copynumber: 8.8 Consensus size: 22
55408812 ACACTAGCGC
* *
55408822 GCTCTCTGATTAGAACTGTGTGT
1 GCTCTCTGTTTAGCACT-TGTGT
*
55408845 GCTCTCTGTTCAGCACTGTGTGT
1 GCTCTCTGTTTAGCACT-TGTGT
*
55408868 GCTCTTTGTTTAGCACGTCT-TGT
1 GCTCTCTGTTTAGCAC-T-TGTGT
55408891 GCTCTCTGTCATTAGCACTTCGTGT
1 GCTCTCTGT--TTAGCACTT-GTGT
*
55408916 GCTCTCTGATTAGCACTT-TGT
1 GCTCTCTGTTTAGCACTTGTGT
* *
55408937 G-TGCTCAG--TA-C-TTTGTGT
1 GCT-CTCTGTTTAGCACTTGTGT
*
55408955 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCAC-TTGTGT
* *
55408978 GCTCTCTGTTACCCAGCACTTATGT
1 GCTCTCTGTT---TAGCACTTGTGT
* *
55409003 GCTCTTTGTTTAGTACTT
1 GCTCTCTGTTTAGCACTT
55409021 CGGTACTCTC
Statistics
Matches: 141, Mismatches: 19, Indels: 33
0.73 0.10 0.17
Matches are distributed among these distances:
17 2 0.01
18 8 0.06
19 3 0.02
20 3 0.02
21 9 0.06
22 6 0.04
23 70 0.50
24 3 0.02
25 32 0.23
26 5 0.04
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (22 bp):
GCTCTCTGTTTAGCACTTGTGT
Found at i:55408940 original size:48 final size:46
Alignment explanation
Indices: 55408822--55408942 Score: 138
Period size: 48 Copynumber: 2.6 Consensus size: 46
55408812 ACACTAGCGC
* *
55408822 GCTCTCTGATTAGAACTGTGTGTGCTCTCTGTTCAGCACTGTGTGT
1 GCTCTCTGATTAGCACTCTGTGTGCTCTCTGTTCAGCACTGTGTGT
* * *
55408868 GCTCTTTGTTTAGCACGTCT-TGTGCTCTCTGTCATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCAC-TCTGTGTGCTCTCTGT--TCAGCACTGT-GTGT
*
55408916 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTCTGTGTGCTC
55408943 AGTACTTTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
46 25 0.40
47 5 0.08
48 32 0.52
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.41
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTCTGTGTGCTCTCTGTTCAGCACTGTGTGT
Found at i:55408971 original size:39 final size:39
Alignment explanation
Indices: 55408907--55408981 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
55408897 TGTCATTAGC
*
55408907 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
55408946 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
55408982 TCTGTTACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:55410483 original size:18 final size:18
Alignment explanation
Indices: 55410460--55410499 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
55410450 TTGAAATTTG
* *
55410460 TAATTCTAATAATTTGAA
1 TAATTCCAATAACTTGAA
55410478 TAATTCCAATAACTTGAA
1 TAATTCCAATAACTTGAA
55410496 TAAT
1 TAAT
55410500 AAATTGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (18 bp):
TAATTCCAATAACTTGAA
Found at i:55421736 original size:18 final size:18
Alignment explanation
Indices: 55421713--55421749 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55421703 ACAATTCATA
55421713 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
55421731 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
55421749 T
1 T
55421750 TGATCACAAA
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:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:55421901 original size:15 final size:15
Alignment explanation
Indices: 55421869--55421908 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
55421859 TATAATTAAC
55421869 CACATA-ATATTTCA
1 CACATATATATTTCA
* *
55421883 CACATATATTTTTCT
1 CACATATATATTTCA
55421898 CACATATATAT
1 CACATATATAT
55421909 ATCATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (15 bp):
CACATATATATTTCA
Found at i:55442786 original size:10 final size:10
Alignment explanation
Indices: 55442771--55442797 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55442761 GAAAATGACC
55442771 AAGCAAGGTA
1 AAGCAAGGTA
55442781 AAGCAAGGTA
1 AAGCAAGGTA
55442791 AAGCAAG
1 AAGCAAG
55442798 CACAGAACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.11, G:0.30, T:0.07
Consensus pattern (10 bp):
AAGCAAGGTA
Found at i:55457787 original size:13 final size:13
Alignment explanation
Indices: 55457769--55457794 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55457759 CCTAACTTAT
55457769 GTTAGATGTGGGG
1 GTTAGATGTGGGG
55457782 GTTAGATGTGGGG
1 GTTAGATGTGGGG
55457795 ATGAATAAAT
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:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (13 bp):
GTTAGATGTGGGG
Found at i:55462585 original size:15 final size:15
Alignment explanation
Indices: 55462532--55462577 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
55462522 ATATGATCAA
* *
55462532 ATTAATTAATTTTAC
1 ATTAATTAATATTAT
*
55462547 ATTAATATACTATTAT
1 ATTAAT-TAATATTAT
55462563 ATTAATTAATATTAT
1 ATTAATTAATATTAT
55462578 TTTTATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTAATTAATATTAT
Found at i:55473649 original size:175 final size:175
Alignment explanation
Indices: 55473358--55473711 Score: 699
Period size: 175 Copynumber: 2.0 Consensus size: 175
55473348 TGCATGTTAC
*
55473358 TGGCTGGATTGCATTATGATATATCTCCTAATATCTTTGTCTATGATTTTCTTTATTGAAGTTTC
1 TGGCTGGATTGCATTATGATATATCTCCTAATATCTTTGTCTATGATTTTCTTTACTGAAGTTTC
55473423 TGATTTACGATTTGTTGGATGGAGCACATTGGTTTAATTTTGGATCTGCTTATTACTTCTTTGGC
66 TGATTTACGATTTGTTGGATGGAGCACATTGGTTTAATTTTGGATCTGCTTATTACTTCTTTGGC
55473488 TGCATATGTTCAAGCTACTTTTTTTTATATGCTCATGAAAGTTTG
131 TGCATATGTTCAAGCTACTTTTTTTTATATGCTCATGAAAGTTTG
55473533 TGGCTGGATTGCATTATGATATATCTCCTAATATCTTTGTCTATGATTTTCTTTACTGAAGTTTC
1 TGGCTGGATTGCATTATGATATATCTCCTAATATCTTTGTCTATGATTTTCTTTACTGAAGTTTC
55473598 TGATTTACGATTTGTTGGATGGAGCACATTGGTTTAATTTTGGATCTGCTTATTACTTCTTTGGC
66 TGATTTACGATTTGTTGGATGGAGCACATTGGTTTAATTTTGGATCTGCTTATTACTTCTTTGGC
55473663 TGCATATGTTCAAGCTACTTTTTTTTATATGCTCATGAAAGTTTG
131 TGCATATGTTCAAGCTACTTTTTTTTATATGCTCATGAAAGTTTG
55473708 TGGC
1 TGGC
55473712 CCCATAATCT
Statistics
Matches: 178, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 178 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.47
Consensus pattern (175 bp):
TGGCTGGATTGCATTATGATATATCTCCTAATATCTTTGTCTATGATTTTCTTTACTGAAGTTTC
TGATTTACGATTTGTTGGATGGAGCACATTGGTTTAATTTTGGATCTGCTTATTACTTCTTTGGC
TGCATATGTTCAAGCTACTTTTTTTTATATGCTCATGAAAGTTTG
Found at i:55481855 original size:11 final size:13
Alignment explanation
Indices: 55481836--55481870 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
55481826 CTATGGCAAC
*
55481836 GCACACACACCTT
1 GCACACACACATT
55481849 GCACACACACATT
1 GCACACACACATT
55481862 GCACACACA
1 GCACACACA
55481871 GGTGCTCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.43, G:0.09, T:0.11
Consensus pattern (13 bp):
GCACACACACATT
Found at i:55482149 original size:4 final size:4
Alignment explanation
Indices: 55482140--55482170 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
55482130 CGATATTCTA
55482140 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
55482171 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:55482362 original size:13 final size:13
Alignment explanation
Indices: 55482344--55482368 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55482334 ATAATGTACT
55482344 ACTATTATATATA
1 ACTATTATATATA
55482357 ACTATTATATAT
1 ACTATTATATAT
55482369 TATAAATTAT
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:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (13 bp):
ACTATTATATATA
Found at i:55485205 original size:2 final size:2
Alignment explanation
Indices: 55485198--55485223 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55485188 CTATTTTTGA
55485198 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
55485224 TTGAAAAAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55486449 original size:18 final size:18
Alignment explanation
Indices: 55486417--55486460 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
55486407 TTATAATTTT
55486417 TATTGTTTAGATTTTT-AA
1 TATT-TTTAGATTTTTGAA
55486435 TATTTTTAGATTTTTTGAA
1 TATTTTTAGA-TTTTTGAA
55486454 -ATTTTTA
1 TATTTTTA
55486461 TATATTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
18 16 0.67
19 2 0.08
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (18 bp):
TATTTTTAGATTTTTGAA
Found at i:55506950 original size:218 final size:218
Alignment explanation
Indices: 55506571--55507013 Score: 832
Period size: 218 Copynumber: 2.0 Consensus size: 218
55506561 TTACAAAAAG
55506571 AAATTTAAAGCATTCAACTTTCATAGAGGAAAATAATGCATCATGCAAGATCTACTCAAATAATC
1 AAATTTAAAGCATTCAACTTTCATAGAGGAAAATAATGCATCATGCAAGATCTACTCAAATAATC
55506636 AAACACCAAAAAAATACATGCCAAAGCAAGAAGCTCCTTTTTTACCATTTTTCAAAGAGTATGAA
66 AAACACCAAAAAAATACATGCCAAAGCAAGAAGCTCCTTTTTTACCATTTTTCAAAGAGTATGAA
* *
55506701 CTCAAATAAGCAAAATTTTTAATTGGAAATTCTTAAGCAAAACCTGTATATGATCTGAACAAAAA
131 CTCAAATAAGCAAAATTTTTAATTAGAAATTCTTAAGCAAAACCTCTATATGATCTGAACAAAAA
55506766 AAATTAGTAGATGAATCTGAAGA
196 AAATTAGTAGATGAATCTGAAGA
55506789 AAATTTAAAGCATTCAACTTTCATAGAGGAAAATAATGCATCATGCAAGATCTACTCAAATAATC
1 AAATTTAAAGCATTCAACTTTCATAGAGGAAAATAATGCATCATGCAAGATCTACTCAAATAATC
55506854 AAACACCAAAAAAATACATGCCAAAGCAAGAAGCTCCTTTTTTACCATTTTTCAAAGAGTATGAA
66 AAACACCAAAAAAATACATGCCAAAGCAAGAAGCTCCTTTTTTACCATTTTTCAAAGAGTATGAA
* * *
55506919 CTCAAATAAGCAAAATTTTTAATTAGAAATTCTTAAGCAACACCTCTATATGATTTGAACAAAGA
131 CTCAAATAAGCAAAATTTTTAATTAGAAATTCTTAAGCAAAACCTCTATATGATCTGAACAAAAA
*
55506984 AATTTAGTAGATGAATCTGAAGA
196 AAATTAGTAGATGAATCTGAAGA
55507007 AAATTTA
1 AAATTTA
55507014 CTAGCTTGTT
Statistics
Matches: 219, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
218 219 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.28
Consensus pattern (218 bp):
AAATTTAAAGCATTCAACTTTCATAGAGGAAAATAATGCATCATGCAAGATCTACTCAAATAATC
AAACACCAAAAAAATACATGCCAAAGCAAGAAGCTCCTTTTTTACCATTTTTCAAAGAGTATGAA
CTCAAATAAGCAAAATTTTTAATTAGAAATTCTTAAGCAAAACCTCTATATGATCTGAACAAAAA
AAATTAGTAGATGAATCTGAAGA
Found at i:55519578 original size:13 final size:13
Alignment explanation
Indices: 55519560--55519622 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
55519550 CTTAAACCAA
55519560 ACTTTTCAAAAGT
1 ACTTTTCAAAAGT
*
55519573 ACTTTTCAAAATT
1 ACTTTTCAAAAGT
* * * *
55519586 ATTTTTCTAACGC
1 ACTTTTCAAAAGT
55519599 ACTTTT-AAAAGT
1 ACTTTTCAAAAGT
*
55519611 ACTTCTCAAAAG
1 ACTTTTCAAAAG
55519623 CAATGTTAAA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
12 8 0.21
13 30 0.79
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (13 bp):
ACTTTTCAAAAGT
Found at i:55520017 original size:14 final size:14
Alignment explanation
Indices: 55519998--55520024 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55519988 ATATAGATTT
55519998 AATAGAGATGAAAA
1 AATAGAGATGAAAA
55520012 AATAGAGATGAAA
1 AATAGAGATGAAA
55520025 TTATTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (14 bp):
AATAGAGATGAAAA
Found at i:55520807 original size:29 final size:29
Alignment explanation
Indices: 55520756--55520814 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
55520746 AATTTTTTAA
*
55520756 AATTTTAAAAATTAAAAAACATTTAAATT
1 AATTTTAAAAATTAAAAAACATTAAAATT
*
55520785 AATTTTAAAAAATT-AAAATCATTAAAATT
1 AATTTT-AAAAATTAAAAAACATTAAAATT
55520814 A
1 A
55520815 TTAAACAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (29 bp):
AATTTTAAAAATTAAAAAACATTAAAATT
Found at i:55520809 original size:39 final size:37
Alignment explanation
Indices: 55520737--55520811 Score: 89
Period size: 37 Copynumber: 1.9 Consensus size: 37
55520727 GACACATCAT
**
55520737 CATTTAATTAATTTTTTAAAATTTTAAAAATTAAAAAA
1 CATTTAATTAA-TTTTTAAAAAATTAAAAATTAAAAAA
55520775 CATTTAAATTAA-TTTTAAAAAATTAAAATCATTAAAA
1 CATTT-AATTAATTTTTAAAAAATTAAAA--ATTAAAA
55520812 TTATTAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 14 0.44
38 5 0.16
39 13 0.41
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (37 bp):
CATTTAATTAATTTTTAAAAAATTAAAAATTAAAAAA
Found at i:55520842 original size:11 final size:11
Alignment explanation
Indices: 55520826--55520859 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
55520816 TAAACAATAT
55520826 ATATTTTTAAA
1 ATATTTTTAAA
*
55520837 ATATTTTTAAT
1 ATATTTTTAAA
55520848 A-ATTTTTAAA
1 ATATTTTTAAA
55520858 AT
1 AT
55520860 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATATTTTTAAA
Found at i:55521010 original size:17 final size:19
Alignment explanation
Indices: 55520971--55521012 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
55520961 AATATAAATT
*
55520971 TAAAAATTAAAATAGATAA
1 TAAAAATTAAAATAGAAAA
55520990 -AAAAATT-AAATA-AAAA
1 TAAAAATTAAAATAGAAAA
55521006 TAAAAAT
1 TAAAAAT
55521013 ATATTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 3 0.14
17 11 0.52
18 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (19 bp):
TAAAAATTAAAATAGAAAA
Found at i:55528877 original size:4 final size:4
Alignment explanation
Indices: 55528868--55528946 Score: 131
Period size: 4 Copynumber: 19.8 Consensus size: 4
55528858 AATATGCCAT
* * *
55528868 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGCA TGCA TGCA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
55528916 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGT
55528947 TGCTTTAAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 73 1.00
ACGTcount: A:0.24, C:0.04, G:0.25, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:55535003 original size:2 final size:2
Alignment explanation
Indices: 55534996--55535022 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55534986 TAGATGATAA
55534996 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
55535023 ACAAACCTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55540380 original size:21 final size:21
Alignment explanation
Indices: 55540354--55540395 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
55540344 TAAATCTTAA
* *
55540354 AAAAAATCTATTTAACTAATT
1 AAAAAATATATATAACTAATT
55540375 AAAAAATATATATAACTAATT
1 AAAAAATATATATAACTAATT
55540396 TAACCTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (21 bp):
AAAAAATATATATAACTAATT
Found at i:55545712 original size:134 final size:132
Alignment explanation
Indices: 55545471--55545736 Score: 480
Period size: 134 Copynumber: 2.0 Consensus size: 132
55545461 ATCTCAACAT
55545471 AACTTTTCTTCTTTTTGTTCTCTACTCATATGGTGATTGAAACAATTGCATGTCTCCATGCTTTG
1 AACTTTTCTTCTTTTTGTTCTCTACTCATATGGTGATTGAAACAATTGCATGTCTCCATGCTTTG
*
55545536 AAGATTGCAGTAGATTTGGGTCATCAAAATGTCATATTAGAAGAAGATGCTTTCATTATAATCAA
66 AAGATTGCAGTAGATATGGG--ATCAAAATGTCATATTAGAAGAAGATGCTTTCATTATAATCAA
55545601 TAAA
129 TAAA
* *
55545605 AACTTTTCTTCTTTTTGTTCTCTACTCATATGGTGATTGAAGCCATTGCATGTCTCCATGCTTTG
1 AACTTTTCTTCTTTTTGTTCTCTACTCATATGGTGATTGAAACAATTGCATGTCTCCATGCTTTG
55545670 AAGATTGCAGTAGATATGGG-TCAAAATGTCATATTAGAAGAAGATGCTTTCATTATAATCAATA
66 AAGATTGCAGTAGATATGGGATCAAAATGTCATATTAGAAGAAGATGCTTTCATTATAATCAATA
55545734 AA
131 AA
55545736 A
1 A
55545737 TGTGCTAGTC
Statistics
Matches: 129, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
131 47 0.36
134 82 0.64
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (132 bp):
AACTTTTCTTCTTTTTGTTCTCTACTCATATGGTGATTGAAACAATTGCATGTCTCCATGCTTTG
AAGATTGCAGTAGATATGGGATCAAAATGTCATATTAGAAGAAGATGCTTTCATTATAATCAATA
AA
Found at i:55551344 original size:20 final size:23
Alignment explanation
Indices: 55551303--55551359 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 23
55551293 TTTCCATCCC
55551303 TAAACCCTTAAAAA-TAATAACCT
1 TAAA-CCTTAAAAACTAATAACCT
55551326 T-AACCTTAAAAACT-A-AACCT
1 TAAACCTTAAAAACTAATAACCT
*
55551346 TAAACTTTAAAAAC
1 TAAACCTTAAAAAC
55551360 CTTAGCCCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 6 0.19
21 21 0.68
22 3 0.10
23 1 0.03
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAACCTTAAAAACTAATAACCT
Found at i:55552317 original size:30 final size:31
Alignment explanation
Indices: 55552252--55552318 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
55552242 TTTAGTACTC
* * *
55552252 AAACTTGACACTTTTTCCTAATTTGGTATTT
1 AAACTTGACACTTTTTCCTAAGTTGGCACTT
*
55552283 AAACTTGACACTTTTT-TTAAGTTGGCACTT
1 AAACTTGACACTTTTTCCTAAGTTGGCACTT
55552313 AAACTT
1 AAACTT
55552319 TTTGGGATCC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.45
Consensus pattern (31 bp):
AAACTTGACACTTTTTCCTAAGTTGGCACTT
Found at i:55562264 original size:159 final size:156
Alignment explanation
Indices: 55561970--55562269 Score: 420
Period size: 159 Copynumber: 1.9 Consensus size: 156
55561960 ACTTGGTTGA
*
55561970 ACTTTATAGGATGTAGTGACACTTCCTTTTATGAAGCATAGTCTAGATGCTTGTTTGTCATTGTG
1 ACTTTATAGGATGTAGTGACACTTCCTTTTATGAAGCATACTCTAGATGCTTGTTTGTCATTGTG
* * * * * *
55562035 AGATGCCAAAAAATTATGTTACTTGGGAGGATTGTTATATCAAGACTCCTGCTTGGTTATATTAG
66 AGATGCCAAAAAATGATGTAACTTAGGAGAATTGTTATATAAAGACACCTGCTTGGTTATATTAG
55562100 AAAAAAATCAGTTTCATATCAAGACG
131 AAAAAAATCAGTTTCATATCAAGACG
* * * * ** *
55562126 ACTTTCTAGGATGCTAGTGCCACTTCTTTTTGTGAATTATACTCTAGATGTTTGTTTCTGTCATT
1 ACTTTATAGGATG-TAGTGACACTTCCTTTTATGAAGCATACTCTAGATGCTTG-TT-TGTCATT
* *
55562191 GTGAGATGCCAAAACATGATGTAATTTAGGAGAATTGTTATATAAAAGACACCTGCTTGGTTATA
63 GTGAGATGCCAAAAAATGATGTAACTTAGGAGAATTGTTATAT-AAAGACACCTGCTTGGTTATA
55562256 TTAGAAAAAAATCA
127 TTAGAAAAAAATCA
55562270 TAGTGCTCAG
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
156 12 0.10
157 33 0.27
158 2 0.02
159 44 0.35
160 33 0.27
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (156 bp):
ACTTTATAGGATGTAGTGACACTTCCTTTTATGAAGCATACTCTAGATGCTTGTTTGTCATTGTG
AGATGCCAAAAAATGATGTAACTTAGGAGAATTGTTATATAAAGACACCTGCTTGGTTATATTAG
AAAAAAATCAGTTTCATATCAAGACG
Found at i:55564328 original size:15 final size:15
Alignment explanation
Indices: 55564304--55564347 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
55564294 TTCAGATGAT
*
55564304 ACAGCAGCAGCAGCA
1 ACAGCAGCAGCAACA
* *
55564319 ACAACAGCAGCAACC
1 ACAGCAGCAGCAACA
55564334 ACAGCAGCAGCAAC
1 ACAGCAGCAGCAAC
55564348 GGCAGCAGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.43, C:0.36, G:0.20, T:0.00
Consensus pattern (15 bp):
ACAGCAGCAGCAACA
Found at i:55564355 original size:12 final size:12
Alignment explanation
Indices: 55564311--55564354 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
55564301 GATACAGCAG
55564311 CAGCAGCAACAA
1 CAGCAGCAACAA
*
55564323 CAGCAGCAACCA
1 CAGCAGCAACAA
*
55564335 CAGCAGCAGCAA
1 CAGCAGCAACAA
*
55564347 CGGCAGCA
1 CAGCAGCA
55564355 GGCACAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.41, C:0.36, G:0.23, T:0.00
Consensus pattern (12 bp):
CAGCAGCAACAA
Found at i:55564887 original size:18 final size:18
Alignment explanation
Indices: 55564848--55564891 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
55564838 GACCCAGCAA
*
55564848 CAGCAACAGTTGCAACTG
1 CAGCAACAGTTGCAAATG
*
55564866 CAGCAGCAGTTGCAGAAT-
1 CAGCAACAGTTGCA-AATG
55564884 CAGCAACA
1 CAGCAACA
55564892 ACAGCAACAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (18 bp):
CAGCAACAGTTGCAAATG
Found at i:55578569 original size:45 final size:45
Alignment explanation
Indices: 55578518--55578635 Score: 134
Period size: 44 Copynumber: 2.6 Consensus size: 45
55578508 GTTATCGTGT
*
55578518 CAAAAACACTTATAAAACTTAGAGCTCGCCAATGTGAGGAT-CTCG
1 CAAAAACACTTATAAAACTTAGAGCTCGCCAATATGAGG-TGCTCG
* ** *
55578563 CAAAAACTCTTAT-TCA-TATAGAGCTCGCCAATATGATGTGCTCG
1 CAAAAACACTTATAAAACT-TAGAGCTCGCCAATATGAGGTGCTCG
* *
55578607 CAAAAGCACTTATAAAACATAGAGCTCGC
1 CAAAAACACTTATAAAACTTAGAGCTCGC
55578636 ACAGCATGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
43 2 0.03
44 34 0.58
45 23 0.39
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (45 bp):
CAAAAACACTTATAAAACTTAGAGCTCGCCAATATGAGGTGCTCG
Found at i:55580362 original size:16 final size:16
Alignment explanation
Indices: 55580341--55580373 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55580331 AGCGAACTCG
55580341 CGTATTCGAGATCATC
1 CGTATTCGAGATCATC
55580357 CGTATTCGAGATCATC
1 CGTATTCGAGATCATC
55580373 C
1 C
55580374 TTGTTCCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.30
Consensus pattern (16 bp):
CGTATTCGAGATCATC
Found at i:55583579 original size:14 final size:14
Alignment explanation
Indices: 55583562--55583591 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55583552 TTTAAACTCT
*
55583562 AAAAGATAAATCTA
1 AAAAGATAAATATA
55583576 AAAAGATAAATATA
1 AAAAGATAAATATA
55583590 AA
1 AA
55583592 TTAAATATAA
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:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAGATAAATATA
Found at i:55587167 original size:6 final size:6
Alignment explanation
Indices: 55587156--55587217 Score: 124
Period size: 6 Copynumber: 10.3 Consensus size: 6
55587146 ATCGATGTAT
55587156 CTGCTC CTGCTC CTGCTC CTGCTC CTGCTC CTGCTC CTGCTC CTGCTC
1 CTGCTC CTGCTC CTGCTC CTGCTC CTGCTC CTGCTC CTGCTC CTGCTC
55587204 CTGCTC CTGCTC CT
1 CTGCTC CTGCTC CT
55587218 ACTGGCTGGG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.16, T:0.34
Consensus pattern (6 bp):
CTGCTC
Found at i:55588598 original size:21 final size:20
Alignment explanation
Indices: 55588560--55588598 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55588550 CTATTTAAAT
*
55588560 AATTTATATATTTTAAATTA
1 AATTTATATATTTGAAATTA
*
55588580 AATTTTTATCATTTGAAAT
1 AATTTATAT-ATTTGAAAT
55588599 GTTAAAGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTTATATATTTGAAATTA
Found at i:55588807 original size:18 final size:19
Alignment explanation
Indices: 55588778--55588813 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
55588768 ATTTCTCCTA
55588778 TTTATGTTTTTCCCTTTTT
1 TTTATGTTTTTCCCTTTTT
*
55588797 TTTAT-TTTTTCTCTTTT
1 TTTATGTTTTTCCCTTTT
55588814 GCTTTGCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.06, C:0.14, G:0.03, T:0.78
Consensus pattern (19 bp):
TTTATGTTTTTCCCTTTTT
Done.