Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 130 of 199
Found at i:39368027 original size:19 final size:19
Alignment explanation
Indices: 39367959--39368035 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
39367949 ATCTGAATCC
* *
39367959 CGAACCTTGAACTTTAAACT
1 CGAAACTTGAAC-CTAAACT
* *
39367979 CGAATCTTGAACCTCGAACT
1 CGAAACTTGAACCT-AAACT
39367999 CG-AACTTGAACCTAAACT
1 CGAAACTTGAACCTAAACT
*
39368017 CGAAACCTGAACCATAAAC
1 CGAAACTTGAACC-TAAAC
39368036 CTCAAACTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.12
19 20 0.42
20 22 0.46
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.22
Consensus pattern (19 bp):
CGAAACTTGAACCTAAACT
Found at i:39368042 original size:20 final size:19
Alignment explanation
Indices: 39367973--39368035 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
39367963 CCTTGAACTT
* *
39367973 TAAACTCGAATCTTGAACC
1 TAAACTCGAAACCTGAACC
* *
39367992 TCGAACTCG-AACTTGAACC
1 T-AAACTCGAAACCTGAACC
39368011 TAAACTCGAAACCTGAACC
1 TAAACTCGAAACCTGAACC
39368030 ATAAAC
1 -TAAAC
39368036 CTCAAACTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 6 0.16
19 20 0.54
20 11 0.30
ACGTcount: A:0.40, C:0.29, G:0.11, T:0.21
Consensus pattern (19 bp):
TAAACTCGAAACCTGAACC
Found at i:39379995 original size:20 final size:20
Alignment explanation
Indices: 39379970--39380009 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
39379960 CGTAAAATGA
*
39379970 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
39379990 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
39380010 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:39379999 original size:34 final size:35
Alignment explanation
Indices: 39379955--39380021 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
39379945 AAGTAAAATA
*
39379955 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
39379989 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
39380022 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:39380025 original size:14 final size:15
Alignment explanation
Indices: 39379949--39380025 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
39379939 GATTGCAAGT
* *
39379949 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
39379963 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
39379977 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
39379997 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
39380012 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
39380026 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:39383736 original size:31 final size:29
Alignment explanation
Indices: 39383661--39383738 Score: 72
Period size: 31 Copynumber: 2.6 Consensus size: 29
39383651 TAATAAATAA
39383661 TTTTAA-AATTTTTTAAAAATTTAGTAAT
1 TTTTAAGAATTTTTTAAAAATTTAGTAAT
* *
39383689 TTGT-AGATATTCTTTTACCAAATTTAAG-AAT
1 TTTTAAGA-ATT-TTTTA-AAAATTT-AGTAAT
39383720 TTTTAAGAATTATTTTAAA
1 TTTTAAGAATT-TTTTAAA
39383739 GCTTTTCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
27 1 0.03
28 4 0.10
29 3 0.08
30 6 0.15
31 20 0.51
32 5 0.13
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (29 bp):
TTTTAAGAATTTTTTAAAAATTTAGTAAT
Found at i:39384425 original size:17 final size:17
Alignment explanation
Indices: 39384403--39384435 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
39384393 TTGTATAAAA
39384403 TTTATT-TTATTGTTAAT
1 TTTATTATTATT-TTAAT
39384420 TTTATTATTATTTTAA
1 TTTATTATTATTTTAA
39384436 AGACATTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
TTTATTATTATTTTAAT
Found at i:39384446 original size:30 final size:30
Alignment explanation
Indices: 39384412--39384474 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
39384402 ATTTATTTTA
39384412 TTGTTAATTTTATTATTATTTTAAAGACAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
* * *
39384442 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGACAT
39384472 TTG
1 TTG
39384475 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGACAT
Found at i:39384628 original size:12 final size:12
Alignment explanation
Indices: 39384598--39384631 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
39384588 TACATATTTT
39384598 AAAATT-ATATA
1 AAAATTAATATA
39384609 AAAA-TAATATA
1 AAAATTAATATA
39384620 AAAATTAATATA
1 AAAATTAATATA
39384632 GGCAGGTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 13 0.62
12 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:39385786 original size:66 final size:67
Alignment explanation
Indices: 39385711--39385853 Score: 234
Period size: 66 Copynumber: 2.1 Consensus size: 67
39385701 CATTTCTTTG
* *
39385711 CAAAATTTTAGTATTGTATTGAAATCATCATGGTAACTATATT-GAATCACCATCCATTTGCATT
1 CAAAATTTTAGTATTGTATTGAAATCACCATGATAACTATATTAGAATCACCATCCATTTGCATT
39385775 TA
66 TA
* * *
39385777 TAAAATTTTAGTATTGTATTGGAATCACCATGATAACTATATTAGAATCACCATTCATTTGCATT
1 CAAAATTTTAGTATTGTATTGAAATCACCATGATAACTATATTAGAATCACCATCCATTTGCATT
39385842 TA
66 TA
39385844 CAAAATTTTA
1 CAAAATTTTA
39385854 ATACTGTAAG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
66 39 0.56
67 31 0.44
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (67 bp):
CAAAATTTTAGTATTGTATTGAAATCACCATGATAACTATATTAGAATCACCATCCATTTGCATT
TA
Found at i:39388011 original size:27 final size:27
Alignment explanation
Indices: 39387970--39388095 Score: 137
Period size: 27 Copynumber: 4.7 Consensus size: 27
39387960 ATTTTAATAG
*
39387970 CCTTTGTGGCGAACTCTGAAAGGATGA
1 CCTTTATGGCGAACTCTGAAAGGATGA
* *
39387997 CCTTTATGGCAAACTCTGAAAGGATAA
1 CCTTTATGGCGAACTCTGAAAGGATGA
* * *
39388024 CCTTTATGGTGAACTCTAAAAGGATGG
1 CCTTTATGGCGAACTCTGAAAGGATGA
* * *
39388051 TCTTTATGGTGAACTCTGAAAGAAT-A
1 CCTTTATGGCGAACTCTGAAAGGATGA
* *
39388077 GCCTTTGTGGTGAACTCTG
1 -CCTTTATGGCGAACTCTG
39388096 TATTAACTGC
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
27 84 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (27 bp):
CCTTTATGGCGAACTCTGAAAGGATGA
Found at i:39388056 original size:54 final size:54
Alignment explanation
Indices: 39387965--39388094 Score: 170
Period size: 54 Copynumber: 2.4 Consensus size: 54
39387955 ATGGCATTTT
* * *
39387965 AATAGCCTTTGTGGCGAACTCTGAAAGGATGACCTTTATGGCAAACTCTGAAAG
1 AATAACCTTTGTGGTGAACTCTAAAAGGATGACCTTTATGGCAAACTCTGAAAG
* * ** **
39388019 GATAACCTTTATGGTGAACTCTAAAAGGATGGTCTTTATGGTGAACTCTGAAAG
1 AATAACCTTTGTGGTGAACTCTAAAAGGATGACCTTTATGGCAAACTCTGAAAG
*
39388073 AATAGCCTTTGTGGTGAACTCT
1 AATAACCTTTGTGGTGAACTCT
39388095 GTATTAACTG
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (54 bp):
AATAACCTTTGTGGTGAACTCTAAAAGGATGACCTTTATGGCAAACTCTGAAAG
Found at i:39391880 original size:23 final size:23
Alignment explanation
Indices: 39391849--39391914 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
39391839 ATACTCGGAT
39391849 TCCAACCAAACACACCAGAATGA
1 TCCAACCAAACACACCAGAATGA
*
39391872 TCCACCCAAACACACCAGAATGA
1 TCCAACCAAACACACCAGAATGA
*
39391895 TCCAACCAAACACACTAGAA
1 TCCAACCAAACACACCAGAA
39391915 CGACACCCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.47, C:0.36, G:0.08, T:0.09
Consensus pattern (23 bp):
TCCAACCAAACACACCAGAATGA
Found at i:39392068 original size:17 final size:17
Alignment explanation
Indices: 39392026--39392068 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
39392016 ATTTCAATTC
*
39392026 TCAATTCAATTTCACTT
1 TCAATTCAAATTCACTT
39392043 TC-ATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
39392060 TCAATTCAA
1 TCAATTCAA
39392069 CATACAATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:39392868 original size:16 final size:16
Alignment explanation
Indices: 39392849--39392881 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39392839 GAATGGTCTC
*
39392849 TGTTTCTTTTTTTCTT
1 TGTTTCTTTTATTCTT
39392865 TGTTTCTTTTATTCTT
1 TGTTTCTTTTATTCTT
39392881 T
1 T
39392882 TACTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.12, G:0.06, T:0.79
Consensus pattern (16 bp):
TGTTTCTTTTATTCTT
Found at i:39401034 original size:45 final size:45
Alignment explanation
Indices: 39400820--39401023 Score: 225
Period size: 44 Copynumber: 4.7 Consensus size: 45
39400810 ATATTGAACA
* * * *
39400820 ATGCCAACATCCCAGACGTGGTCTTACATGCT-ATCTC--ATATCG
1 ATGCCATCGTCCCAGACGTGGTCTTACACG-TAATCACATATATCG
39400863 ATGCCA-CTGTCCCAGACAG-GGTCTTACACG-AATCA-A-ATA-CG
1 ATGCCATC-GTCCCAGAC-GTGGTCTTACACGTAATCACATATATCG
*
39400904 ATGCCAAAT-G-CCCTAGACATGGTCTTACACGTAATCACATATATCG
1 ATGCC--ATCGTCCC-AGACGTGGTCTTACACGTAATCACATATATCG
39400950 AT-CCATCGTCCCAGACGTGGTCTTACACGTAATCACATATATCG
1 ATGCCATCGTCCCAGACGTGGTCTTACACGTAATCACATATATCG
39400994 ATGCCATCGTCCCAGACGTGGTCTTACACG
1 ATGCCATCGTCCCAGACGTGGTCTTACACG
39401024 AGAACACATA
Statistics
Matches: 140, Mismatches: 5, Indels: 30
0.80 0.03 0.17
Matches are distributed among these distances:
41 10 0.07
42 23 0.16
43 32 0.23
44 36 0.26
45 35 0.25
46 4 0.03
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (45 bp):
ATGCCATCGTCCCAGACGTGGTCTTACACGTAATCACATATATCG
Found at i:39403914 original size:43 final size:43
Alignment explanation
Indices: 39403853--39403957 Score: 156
Period size: 43 Copynumber: 2.4 Consensus size: 43
39403843 TGTCCCAGAC
* **
39403853 ATGGTCTTACATGGAAATCTCGTATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCCCAGCT
* *
39403897 ATGGTCTTACACAAAATCTCAAATCGATGCCAATAGCCTAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
39403940 ATGGTCTTACACGAAATC
1 ATGGTCTTACACGAAATC
39403958 AAACCTTGGA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
43 44 0.80
44 11 0.20
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:39404121 original size:31 final size:31
Alignment explanation
Indices: 39404075--39404281 Score: 249
Period size: 31 Copynumber: 6.7 Consensus size: 31
39404065 ATCCAATTCT
*
39404075 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
** * *
39404105 TGAATCAAATTTGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
39404136 CAAATC-AATTCGTCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
39404166 CAAATCAAATTCGGCATTGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
39404197 CAAATCAAATTCGACACTGTATATCTATA-A
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
39404227 AAAATTCAAATTTGGCAATGTATATCTATATA
1 CAAA-TCAAATTCGGCAATGTATATCCATATA
*
39404259 CAAATCAAATTCGGAAATGTATA
1 CAAATCAAATTCGGCAATGTATA
39404282 AAACATATAC
Statistics
Matches: 149, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
30 35 0.23
31 110 0.74
32 4 0.03
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:39404172 original size:61 final size:62
Alignment explanation
Indices: 39404075--39404281 Score: 267
Period size: 61 Copynumber: 3.4 Consensus size: 62
39404065 ATCCAATTCT
* **
39404075 CAAATC-AATTCGGCAATATATATCCATATATGAATCAAATTTGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATAAAAATCAAATTTGGCAATGTATATCTATATA
* * * * * *
39404136 CAAATC-AATTCGTCAATGTATATCCATATACAAATCAAATTCGGCATTGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATAAAAATCAAATTTGGCAATGTATATCTATATA
* * *
39404197 CAAATCAAATTCGACACTGTATATCTATA-AAAAATTCAAATTTGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATAAAAA-TCAAATTTGGCAATGTATATCTATATA
*
39404259 CAAATCAAATTCGGAAATGTATA
1 CAAATCAAATTCGGCAATGTATA
39404282 AAACATATAC
Statistics
Matches: 125, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
61 63 0.50
62 62 0.50
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (62 bp):
CAAATCAAATTCGGCAATGTATATCCATATAAAAATCAAATTTGGCAATGTATATCTATATA
Found at i:39404301 original size:93 final size:92
Alignment explanation
Indices: 39404075--39404292 Score: 251
Period size: 92 Copynumber: 2.4 Consensus size: 92
39404065 ATCCAATTCT
* * ** ** * * * *
39404075 CAAATC-AATTCGGCAATATATATCCATATATGAATCAAATTTGGCAATGTATATCTATATACAA
1 CAAATCAAATTCGGAAATGTATAAACATATACAAATCAAATTCGACACTGTATATCTATATAAAA
*
39404139 ATCAATTCGTCAATGTATATCCATATA
66 ATCAATTCGGCAATGTATATCCATATA
* * *
39404166 CAAATCAAATTCGGCATTGTATAACCATATACAAATCAAATTCGACACTGTATATCTATA-AAAA
1 CAAATCAAATTCGGAAATGTATAAACATATACAAATCAAATTCGACACTGTATATCTATATAAAA
* *
39404230 ATTCAAATTTGGCAATGTATATCTATATA
66 A-TC-AATTCGGCAATGTATATCCATATA
39404259 CAAATCAAATTCGGAAATGTATAAAACATATACA
1 CAAATCAAATTCGGAAATGTAT-AAACATATACA
39404293 TTTCAATTCA
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
91 10 0.09
92 47 0.44
93 41 0.38
94 10 0.09
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.32
Consensus pattern (92 bp):
CAAATCAAATTCGGAAATGTATAAACATATACAAATCAAATTCGACACTGTATATCTATATAAAA
ATCAATTCGGCAATGTATATCCATATA
Found at i:39406409 original size:43 final size:42
Alignment explanation
Indices: 39406361--39406534 Score: 147
Period size: 43 Copynumber: 4.1 Consensus size: 42
39406351 GTGTGATTTC
*
39406361 GTGTAAGACCATGTCTGGGACATTGGCATTGATATGAGATTAT
1 GTGTAAGACCATGTCTGGGACATTGGCATCG-TATGAGATTAT
* *
39406404 GTGTAAGACCATGCCTGGGACATTGGTATCGTAT-ATGATT-T
1 GTGTAAGACCATGTCTGGGACATTGGCATCGTATGA-GATTAT
* * * * * *
39406445 CGTATAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATAAC
1 -GTGTAAGACCATGTCTGGGACATTGGCATCG-TATGAGATTAT
* * * * * *
39406489 ATGTAAGACCATATCTAGGATA-TGGCATTGTATGTGATATAT
1 GTGTAAGACCATGTCTGGGACATTGGCATCGTATGAGAT-TAT
39406531 GTGT
1 GTGT
39406535 TTTCGAGTAT
Statistics
Matches: 104, Mismatches: 21, Indels: 13
0.75 0.15 0.09
Matches are distributed among these distances:
41 10 0.10
42 44 0.42
43 50 0.48
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACATTGGCATCGTATGAGATTAT
Found at i:39406464 original size:42 final size:41
Alignment explanation
Indices: 39406354--39406481 Score: 159
Period size: 43 Copynumber: 3.0 Consensus size: 41
39406344 TCCCGAGGTG
*
39406354 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATTGATA
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATA
* *
39406395 TGAGATTAT-GTGTAAGACCATGCCTGGGACATTGGTATCGTATA
1 T--GATT-TCGTGTAAGACCATGTCTGGGACATTGGCATCG-ATA
* * *
39406439 TGATTTCGTATAAGACCCTGTCTGGGACAGTGGCATCGATA
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATA
39406480 TG
1 TG
39406482 TGATAACATG
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
41 7 0.09
42 30 0.41
43 32 0.43
44 5 0.07
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGATA
Found at i:39407970 original size:16 final size:16
Alignment explanation
Indices: 39407938--39407978 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
39407928 TTTACTTAAA
39407938 TATTTTA-CATACATT
1 TATTTTATCATACATT
*
39407953 TATTTTATCATCCATT
1 TATTTTATCATACATT
39407969 TATTTATATC
1 TATTT-TATC
39407979 TTTTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.30
16 12 0.52
17 4 0.17
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (16 bp):
TATTTTATCATACATT
Found at i:39408023 original size:3 final size:3
Alignment explanation
Indices: 39408003--39408050 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
39407993 CAAATTCTAG
* * * *
39408003 ATT ATTT ATT ATT CTT ATT ATT ATT AAT ATT ATC ATT ATC ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39408049 AT
1 AT
39408051 CCTTTTAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:39411502 original size:18 final size:19
Alignment explanation
Indices: 39411464--39411502 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
39411454 TGGTTCAAGC
*
39411464 TTTCAATCTCATATCTCAA
1 TTTCAATCTCACATCTCAA
*
39411483 TTTCAAT-TCACATTTCAA
1 TTTCAATCTCACATCTCAA
39411501 TT
1 TT
39411503 CATAATTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCACATCTCAA
Found at i:39411648 original size:23 final size:23
Alignment explanation
Indices: 39411621--39411685 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
39411611 ACGAATTCCT
*
39411621 ACCAAACACACCAGAATGATCCA
1 ACCAAACACACTAGAATGATCCA
*
39411644 CCCAAACACACTAGAATGATCCA
1 ACCAAACACACTAGAATGATCCA
39411667 ACCAAACACACTAGAATGA
1 ACCAAACACACTAGAATGA
39411686 CTCCCAGTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.48, C:0.32, G:0.09, T:0.11
Consensus pattern (23 bp):
ACCAAACACACTAGAATGATCCA
Found at i:39412652 original size:3 final size:3
Alignment explanation
Indices: 39412644--39412708 Score: 105
Period size: 3 Copynumber: 21.7 Consensus size: 3
39412634 ATGTATTAGT
39412644 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
*
39412690 TTA TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
39412709 TTTAATTCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.93
4 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39413100 original size:15 final size:15
Alignment explanation
Indices: 39413080--39413108 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39413070 TATAAAATTA
39413080 AATCATAAAAATCTT
1 AATCATAAAAATCTT
39413095 AATCATAAAAATCT
1 AATCATAAAAATCT
39413109 AATATTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCATAAAAATCTT
Found at i:39416494 original size:17 final size:18
Alignment explanation
Indices: 39416467--39416510 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
39416457 CCTTCATTTC
39416467 TTTCTTTTATTCTTTTA-G
1 TTTC-TTTATTCTTTTATG
39416485 TTTCTTTATTCTTTTATG
1 TTTCTTTATTCTTTTATG
*
39416503 TTTATTTA
1 TTTCTTTA
39416511 CTTTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.73
Consensus pattern (18 bp):
TTTCTTTATTCTTTTATG
Found at i:39416523 original size:23 final size:23
Alignment explanation
Indices: 39416480--39416523 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
39416470 CTTTTATTCT
**
39416480 TTTAGTTTCTTTATTCTTTTATG
1 TTTAGTTTCTTTATTAATTTATG
39416503 TTTA-TTTACTTTATTAATTTA
1 TTTAGTTT-CTTTATTAATTTA
39416524 ATAATAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (23 bp):
TTTAGTTTCTTTATTAATTTATG
Found at i:39426001 original size:37 final size:32
Alignment explanation
Indices: 39425926--39426003 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 32
39425916 ATTTTTTATT
* *
39425926 TAAT-ATTATTTTATTTTTAAAAAAATTTAAT
1 TAATAATTATTTTATTTTTAAAAAAATATAAA
39425957 TAATAATTATTTTATTTATATAAATAAAATGATAAA
1 TAATAATTATTTTATTT-T-TAAA-AAAAT-ATAAA
39425993 TAAGTAATTAT
1 TAA-TAATTAT
39426004 ATAATAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 4 0.10
32 12 0.31
33 1 0.03
34 4 0.10
35 5 0.13
36 6 0.15
37 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
TAATAATTATTTTATTTTTAAAAAAATATAAA
Found at i:39426119 original size:22 final size:22
Alignment explanation
Indices: 39426094--39426138 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39426084 AACATAACGA
39426094 TATATATAAAATAT-ATTTTTAT
1 TATATA-AAAATATAATTTTTAT
**
39426116 TATATAATTATATAATTTTTAT
1 TATATAAAAATATAATTTTTAT
39426138 T
1 T
39426139 TTTATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TATATAAAAATATAATTTTTAT
Found at i:39426127 original size:8 final size:8
Alignment explanation
Indices: 39426114--39426168 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
39426104 ATATATTTTT
39426114 ATTATATA
1 ATTATATA
39426122 ATTATATA
1 ATTATATA
*
39426130 ATT-T-TT
1 ATTATATA
*
39426136 ATT-T-TT
1 ATTATATA
39426142 ATTATATA
1 ATTATATA
*
39426150 ATTACATA
1 ATTATATA
39426158 ATTATATA
1 ATTATATA
39426166 ATT
1 ATT
39426169 TTTATTTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
6 10 0.24
7 2 0.05
8 29 0.71
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (8 bp):
ATTATATA
Found at i:39426127 original size:28 final size:28
Alignment explanation
Indices: 39426096--39426187 Score: 98
Period size: 28 Copynumber: 3.3 Consensus size: 28
39426086 CATAACGATA
39426096 TATATAAAATATATTTTTATTATATAAT
1 TATATAAAATATATTTTTATTATATAAT
** *
39426124 TATATAATTTTTATTTTTATTATATAAT
1 TATATAAAATATATTTTTATTATATAAT
* * *
39426152 TACATAATTATATAATTTTTATT-T-TATT
1 TATATAA-AATAT-ATTTTTATTATATAAT
39426180 TATATAAA
1 TATATAAA
39426188 TAAAAATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
28 40 0.75
29 4 0.08
30 9 0.17
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (28 bp):
TATATAAAATATATTTTTATTATATAAT
Found at i:39426159 original size:36 final size:36
Alignment explanation
Indices: 39426114--39426186 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 36
39426104 ATATATTTTT
*
39426114 ATTATATAATTATATAATTTTTATTTT-TATTATATA
1 ATTACATAATTATATAATTTTTATTTTAT-TTATATA
39426150 ATTACATAATTATATAATTTTTATTTTATTTATATA
1 ATTACATAATTATATAATTTTTATTTTATTTATATA
39426186 A
1 A
39426187 ATAAAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 34 0.97
37 1 0.03
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (36 bp):
ATTACATAATTATATAATTTTTATTTTATTTATATA
Found at i:39426248 original size:30 final size:30
Alignment explanation
Indices: 39426185--39426252 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 30
39426175 TTATTTATAT
**
39426185 AAATAAAAATTTATTAATTAAAAAACTTTA
1 AAATAAAAATTTATTAATTAAAAAACTAAA
*
39426215 AAATAATATATTTATTAATTAAAAAA-TAAA
1 AAATAA-AAATTTATTAATTAAAAAACTAAA
39426245 AAATAAAA
1 AAATAAAA
39426253 TAACATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 14 0.42
31 18 0.55
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (30 bp):
AAATAAAAATTTATTAATTAAAAAACTAAA
Found at i:39430177 original size:30 final size:29
Alignment explanation
Indices: 39430117--39430177 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
39430107 GGAGGGGAGG
* * **
39430117 GGAGTAAAAGTTTTAGGGGAAAGTGGAAA
1 GGAGTAAAAGTTTTAAGGAAAAGTAAAAA
39430146 GGAGTAAAAGTTTTGAAGGAAAAGTAAAAA
1 GGAGTAAAAGTTTT-AAGGAAAAGTAAAAA
39430176 GG
1 GG
39430178 TTTGAGAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (29 bp):
GGAGTAAAAGTTTTAAGGAAAAGTAAAAA
Found at i:39435690 original size:7 final size:7
Alignment explanation
Indices: 39435678--39435709 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
39435668 TTATCTGATC
39435678 AGTGACA
1 AGTGACA
39435685 AGTGACA
1 AGTGACA
39435692 AGTGACA
1 AGTGACA
*
39435699 AGTGATA
1 AGTGACA
39435706 AGTG
1 AGTG
39435710 GTAGCTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.31, T:0.19
Consensus pattern (7 bp):
AGTGACA
Found at i:39435728 original size:58 final size:58
Alignment explanation
Indices: 39435638--39435805 Score: 260
Period size: 58 Copynumber: 3.0 Consensus size: 58
39435628 CTGATCAATA
39435638 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
39435696 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG---A-T--C-AGTGACAAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
* * *
39435747 ACAAGTGATAAGTGGTAGCTTTAGCTACAGTTATTTGATCAGTGACAAGTGGCAAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
39435805 A
1 A
39435806 TAAATGTGAT
Statistics
Matches: 100, Mismatches: 3, Indels: 14
0.85 0.03 0.12
Matches are distributed among these distances:
51 46 0.46
52 1 0.01
54 2 0.02
55 2 0.02
57 1 0.01
58 48 0.48
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (58 bp):
ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGACAAGTG
Found at i:39435740 original size:51 final size:51
Alignment explanation
Indices: 39435685--39435808 Score: 221
Period size: 51 Copynumber: 2.4 Consensus size: 51
39435675 ATCAGTGACA
39435685 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
* *
39435736 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACAGTTATTTGATC
1 AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
*
39435787 AGTGACAAGTGGCAAGTGATAA
1 AGTGACAAGTGACAAGTGATAA
39435809 ATGTGATCCG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 70 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
Found at i:39442442 original size:14 final size:14
Alignment explanation
Indices: 39442423--39442450 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39442413 CAGGACACTC
39442423 GCAAAATTTTGGTG
1 GCAAAATTTTGGTG
39442437 GCAAAATTTTGGTG
1 GCAAAATTTTGGTG
39442451 AGCCTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
GCAAAATTTTGGTG
Found at i:39447121 original size:42 final size:43
Alignment explanation
Indices: 39447038--39447136 Score: 137
Period size: 42 Copynumber: 2.3 Consensus size: 43
39447028 TCCCAAACGT
* * *
39447038 GGTCTTACATGTAATCAAATAACGATGCCACTATCCTAGACAG
1 GGTCTTACACGTAATCAAATAACGATGCCAATATCCCAGACAG
* * *
39447081 GGTCTTACACGTAATCATAT-ACGATGCCAATGTCCCAGACAT
1 GGTCTTACACGTAATCAAATAACGATGCCAATATCCCAGACAG
39447123 GGTCTTACACGTAA
1 GGTCTTACACGTAA
39447137 ATCTCAAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
42 32 0.64
43 18 0.36
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (43 bp):
GGTCTTACACGTAATCAAATAACGATGCCAATATCCCAGACAG
Found at i:39447170 original size:44 final size:42
Alignment explanation
Indices: 39447015--39447176 Score: 150
Period size: 43 Copynumber: 3.8 Consensus size: 42
39447005 AAAAAGCTCG
* * * *
39447015 TACAATACCAACGTCCCAAACGTGGTCTTACATGTAATCAAA
1 TACAATGCCAACGTCCTAGACGTGGTCTTACACGTAATCAAA
* * *
39447057 TAACGATGCC-ACTATCCTAGACAG-GGTCTTACACGTAATCATA
1 T-ACAATGCCAAC-GTCCTAGAC-GTGGTCTTACACGTAATCAAA
* * * *
39447100 TACGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAA
1 TACAATGCCAACGTCCTAGACGTGGTCTTACACGT-AA--TCAAA
39447145 T-CAATGCCAACGTCCTAGACGTGGTCTTACAC
1 TACAATGCCAACGTCCTAGACGTGGTCTTACAC
39447177 AAAATCACAT
Statistics
Matches: 96, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
42 30 0.31
43 33 0.34
44 28 0.29
45 5 0.05
ACGTcount: A:0.33, C:0.27, G:0.15, T:0.25
Consensus pattern (42 bp):
TACAATGCCAACGTCCTAGACGTGGTCTTACACGTAATCAAA
Found at i:39451846 original size:32 final size:32
Alignment explanation
Indices: 39451810--39451874 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
39451800 TGTCTAATAA
39451810 TCTTCATGTTCCTGAGGCTAACCTAAATTTAT
1 TCTTCATGTTCCTGAGGCTAACCTAAATTTAT
39451842 TCTTCATGTTCCTGAGGCTAACCTAAATTTAT
1 TCTTCATGTTCCTGAGGCTAACCTAAATTTAT
39451874 T
1 T
39451875 GTTTGTTCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.42
Consensus pattern (32 bp):
TCTTCATGTTCCTGAGGCTAACCTAAATTTAT
Found at i:39456007 original size:18 final size:20
Alignment explanation
Indices: 39455984--39456025 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39455974 AAGTGCTTAA
*
39455984 ATATAATT-ATTAG-ATTTT
1 ATATAATTGATGAGTATTTT
39456002 ATATAATTGATGAGTATTTT
1 ATATAATTGATGAGTATTTT
39456022 ATAT
1 ATAT
39456026 TTGAGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.38
19 4 0.19
20 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
ATATAATTGATGAGTATTTT
Found at i:39458409 original size:20 final size:20
Alignment explanation
Indices: 39458372--39458412 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
39458362 ATTTAATGTC
39458372 ATTTTAACATTTTCATCCTA
1 ATTTTAACATTTTCATCCTA
39458392 ATTTTCAACATTTT-ATCCTA
1 ATTTT-AACATTTTCATCCTA
39458412 A
1 A
39458413 AAAAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTTAACATTTTCATCCTA
Found at i:39460637 original size:14 final size:15
Alignment explanation
Indices: 39460618--39460647 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39460608 ATTATTTAAC
39460618 TACTTTT-TTTATTT
1 TACTTTTATTTATTT
39460632 TACTTTTATTTATTT
1 TACTTTTATTTATTT
39460647 T
1 T
39460648 TAATTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (15 bp):
TACTTTTATTTATTT
Found at i:39461685 original size:84 final size:84
Alignment explanation
Indices: 39461597--39461754 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 84
39461587 TTTATTTTTA
* * * *
39461597 GGGGGCTAAAGTGTAATTTTATTATATATTAATTTATAATTTTATATTTATAAGAAGACTGAATT
1 GGGGGCTAAAGTGTAATTTCACTATATATTAATTTATAATTTTATATTTATAAGAAGACTAAAAT
*
39461662 GACAATTTTTCTTTTGGAG
66 GAAAATTTTTCTTTTGGAG
* * * *
39461681 GGGGGTTAAAGTGTAATTTCACTATGTATTAATTTATAATTTTCTATTTATAAGAGGACTAAAAT
1 GGGGGCTAAAGTGTAATTTCACTATATATTAATTTATAATTTTATATTTATAAGAAGACTAAAAT
39461746 GAAAATTTT
66 GAAAATTTT
39461755 CATTTTTGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
84 65 1.00
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (84 bp):
GGGGGCTAAAGTGTAATTTCACTATATATTAATTTATAATTTTATATTTATAAGAAGACTAAAAT
GAAAATTTTTCTTTTGGAG
Found at i:39476591 original size:13 final size:12
Alignment explanation
Indices: 39476554--39476677 Score: 72
Period size: 12 Copynumber: 9.9 Consensus size: 12
39476544 AAAAACTTAA
*
39476554 TGATTAAAAACT
1 TGATGAAAAACT
*
39476566 TGATGGAAAACT
1 TGATGAAAAACT
39476578 TGATGAAAAGACT
1 TGATGAAAA-ACT
*
39476591 TGATGAAAAGCT
1 TGATGAAAAACT
*
39476603 T-A-AAAAGAACT
1 TGATGAAA-AACT
**
39476614 TGATGCGAAACT
1 TGATGAAAAACT
* *
39476626 TAATAAAAAAACT
1 TGAT-GAAAAACT
*
39476639 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
39476654 TGATAAAAGAACT
1 TGATGAAA-AACT
*
39476667 TTATGAAAAAC
1 TGATGAAAAAC
39476678 ACTTGAAGAA
Statistics
Matches: 85, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
10 3 0.04
11 5 0.06
12 37 0.44
13 29 0.34
14 1 0.01
15 8 0.09
16 2 0.02
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:39476675 original size:25 final size:25
Alignment explanation
Indices: 39476554--39476677 Score: 103
Period size: 25 Copynumber: 5.0 Consensus size: 25
39476544 AAAAACTTAA
* *
39476554 TGATTAAA-AACTTGATGGAAAACT
1 TGATAAAAGAACTTGATGAAAAACT
*
39476578 TGATGAAAAG-ACTTGATGAAAAGCT
1 TGAT-AAAAGAACTTGATGAAAAACT
**
39476603 T-A-AAAAGAACTTGATGCGAAACT
1 TGATAAAAGAACTTGATGAAAAACT
* * *
39476626 TAATAAAAAAACTTGGTAATTAAAAACT
1 TGATAAAAGAACTT-G--ATGAAAAACT
*
39476654 TGATAAAAGAACTTTATGAAAAAC
1 TGATAAAAGAACTTGATGAAAAAC
39476678 ACTTGAAGAA
Statistics
Matches: 78, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
22 5 0.06
23 13 0.17
24 6 0.08
25 34 0.44
26 1 0.01
28 19 0.24
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (25 bp):
TGATAAAAGAACTTGATGAAAAACT
Found at i:39479259 original size:7 final size:7
Alignment explanation
Indices: 39479249--39479281 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
39479239 ACTATTTTCA
39479249 ATTTTTT
1 ATTTTTT
39479256 A-TTTTT
1 ATTTTTT
39479262 A-TTTTT
1 ATTTTTT
39479268 ATTTTTT
1 ATTTTTT
39479275 ATTTTTT
1 ATTTTTT
39479282 CTTTCTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.48
7 13 0.52
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:39479266 original size:5 final size:6
Alignment explanation
Indices: 39479251--39479280 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
39479241 TATTTTCAAT
39479251 TTTTTA TTTTTA TTTTTA TTTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTT
39479281 TCTTTCTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:39479267 original size:13 final size:12
Alignment explanation
Indices: 39479251--39479280 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
39479241 TATTTTCAAT
39479251 TTTTTATTTTTA
1 TTTTTATTTTTA
39479263 TTTTTATTTTTTA
1 TTTTTA-TTTTTA
39479276 TTTTT
1 TTTTT
39479281 TCTTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:39479296 original size:3 final size:3
Alignment explanation
Indices: 39479288--39479331 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
39479278 TTTTCTTTCT
* *
39479288 TTC TTC TTC TTT TTC TTC TTC TTT TTC TTTC TTTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC
39479332 AAAACCCTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 29 0.81
4 7 0.19
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:39479304 original size:12 final size:12
Alignment explanation
Indices: 39479287--39479331 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
39479277 TTTTTCTTTC
39479287 TTTCTTCTTCTT
1 TTTCTTCTTCTT
39479299 TTTCTTCTTCTT
1 TTTCTTCTTCTT
39479311 TTTC-T-TTCTT
1 TTTCTTCTTCTT
39479321 TCTTCTTCTTC
1 T-TTCTTCTTC
39479332 AAAACCCTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.20
11 4 0.13
12 17 0.57
13 3 0.10
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTCTTCTTCTT
Found at i:39479814 original size:30 final size:29
Alignment explanation
Indices: 39479679--39479854 Score: 147
Period size: 30 Copynumber: 6.0 Consensus size: 29
39479669 CAAACACTGC
* *
39479679 AAAAATTTTGGGGACAAAATATAATTTTGA
1 AAAAATTTAGGGGTCAAAATATAATTTT-A
* * * *
39479709 GAAAATTTAGGGGTCCAAATGTAATTTCA
1 AAAAATTTAGGGGTCAAAATATAATTTTA
* * * * * *
39479738 AAAAGTTGATGGGTCAAAATGTAAGTTAA
1 AAAAATTTAGGGGTCAAAATATAATTTTA
** *
39479767 AAAAAGTTTAGTTGTCAAAGTATAATTTTA
1 AAAAA-TTTAGGGGTCAAAATATAATTTTA
* *
39479797 GGAAAATTTAGGGGTCAAAATGA-AATTTCA
1 -AAAAATTTAGGGGTCAAAAT-ATAATTTTA
*
39479827 AAAAATTTAGGGGTCAAAATGTAATTTT
1 AAAAATTTAGGGGTCAAAATATAATTTT
39479855 TTATTTTTTG
Statistics
Matches: 112, Mismatches: 30, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
29 51 0.46
30 56 0.50
31 5 0.04
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (29 bp):
AAAAATTTAGGGGTCAAAATATAATTTTA
Found at i:39480543 original size:79 final size:77
Alignment explanation
Indices: 39480040--39481448 Score: 1421
Period size: 78 Copynumber: 18.2 Consensus size: 77
39480030 AAATAGAAAT
* * * * * *
39480040 AAAAATAGCTCGGCATGCGACCCGAAGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAA
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
* *
39480105 AACA-AAAATT-G
65 AACAGAAATTTAA
* * * *
39480116 AAAAATACCTCGGTATGTGGCCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTGAAA
1 AAAAATACCTCGGCATGT-GCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
*
39480181 AACAGAAATGTAA
65 AACAGAAATTTAA
* ***
39480194 CAAAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAAAAAA
1 -AAAAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
39480259 AACAGAAA-TT--
65 AACAGAAATTTAA
* * * *
39480269 AAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAA
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
* *
39480332 AA-ATAAAAATT-A
65 AACA-GAAATTTAA
** * * * **
39480344 AAAAATACCTCGGTGTGCGGCCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAA
1 AAAAATACCTCGGCATG-TGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT---TG
*
39480409 AAAAACAGAAATTAAA
62 AAAAACAGAAATTTAA
* *
39480425 AAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAA
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA
*
39480490 AAATAGAAATTTAA
64 AAACAGAAATTTAA
* * * * *
39480504 AAGAAATACCTCAGCATGTGTCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTAAAA
1 AA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-GAA
* *
39480569 AAATAGTAA-TT--
64 AAACAGAAATTTAA
* * * *
39480580 GAAAATACCTCTGC--GTGACCCGAGGCCCAACTCACCTCTCGCATTATGAGTTGATTTGTTTTG
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--T-TTTTG
*
39480643 AAAAAATAGAAA-TT-A
62 -AAAAACAGAAATTTAA
* *
39480658 AAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTTTGAA
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA
*
39480723 AAATAGAAATTTAA
64 AAACAGAAATTTAA
* * * * *
39480737 AAGAAATACCTAGGCATGTGTCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTCGAAA
1 AA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
39480802 ATA-A-AAA-TT--
65 A-ACAGAAATTTAA
* * * *
39480811 GAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTGA
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGA
*
39480874 AAAACAAAAATTTAA
63 AAAACAGAAATTTAA
* *
39480889 AAGAAATACATCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
1 AA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
39480954 AACAGAAATTTAA
65 AACAGAAATTTAA
* * * ***
39480967 AAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACTTATCGCAATATGAGTTGATTTAAAAAA
1 AA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
*
39481032 AATAGAAATTT--
65 AACAGAAATTTAA
* ** *
39481043 --AAATACCTCAGC--GTGACTTGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTT
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTT
*
39481104 GAGAAACAGAAATTTAA
61 GAAAAACAGAAATTTAA
* ** * * **
39481121 AAGAAATACCTCAGCATGTGTTCGAGGCTCAACTCACTTCTCGCAATATGACTTGATTTTAAAAA
1 AA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
39481186 AACAGAAATTT--
65 AACAGAAATTTAA
* * *
39481197 --AAATACCTCAGC--GTGACCCGAGGTTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGA
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGA
* *
39481258 AAAATAGAAATTAAA
63 AAAACAGAAATTTAA
*
39481273 AAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
*
39481338 AATAGAAATTTAAA
65 AACAGAAATTT-AA
*
39481352 AAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
1 AAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAA
39481417 AACAGAAATTTAA
65 AACAGAAATTTAA
39481430 AAGAAATACCTCGGCATGT
1 AA-AAATACCTCGGCATGT
39481449 ATCTCGCAAT
Statistics
Matches: 1130, Mismatches: 137, Indels: 129
0.81 0.10 0.09
Matches are distributed among these distances:
71 9 0.01
72 95 0.08
73 80 0.07
74 73 0.06
75 26 0.02
76 80 0.07
77 72 0.06
78 226 0.20
79 217 0.19
80 148 0.13
81 66 0.06
82 35 0.03
83 3 0.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (77 bp):
AAAAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA
ACAGAAATTTAA
Found at i:39480803 original size:154 final size:151
Alignment explanation
Indices: 39480028--39481448 Score: 1475
Period size: 154 Copynumber: 9.2 Consensus size: 151
39480018 TTTCTATTAA
* * * * *
39480028 AAAAATAGAAA-T--AAAAATAGCTCGGCATGCGACCCGAAGCTCAACTCACCTCTCGGATTATG
1 AAAAATAGAAATTAAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATG
* * * * * * *
39480090 AGTTGATCTTT-GAAAAACAAAAATTGAAAAATACCTCGGTATGTGGCCCAAGGCTCAACTCACT
65 AGTTGAT-TTTAAAAAAACAGAAATTTAAAAATACCTCGG-CTGTGACCCGAGGCTCAACTCACC
39480154 TCTCGCATTATGAGTTGATTTTTG
128 TCTCGCATTATGAGTTGATTTTTG
* *
39480178 AAAAACAGAAATGTAACAAAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATAT
1 AAAAATAGAAAT-TAA-AAAAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATAT
* *
39480243 GAGTTGATTTAAAAAAAACAGAAA-TTAAAAATACCTCAGC-GTGACCCGAGGCTCAACTCACCT
64 GAGTTGATTTTAAAAAAACAGAAATTTAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCT
* *
39480306 CTCGGATTATGAGTTGATCTTTG
129 CTCGCATTATGAGTTGATTTTTG
* ** * * *
39480329 AAAAAATAAAAATT-AAAAAATACCTCGGTGTGCGGCCCAAGGCTCAACTCACTTCTCGCAATAT
1 -AAAAATAGAAATTAAAAAAATACCTCGGCATG-TGCCCGAGGCTCAACTCACCTCTCGCAATAT
* *
39480393 GAGTTGATTTTAAAAAAAAAACAGAAATTAAAAAAAATACCTCGGCGTGTGACCTGAGGCTCAAC
64 GAGTTGATTTT---AAAAAAACAGAAATT--TAAAAATACCTCGGC-TGTGACCCGAGGCTCAAC
*
39480458 TCACCTCTCGCAATATGAGTTGATTTTTTG
123 TCACCTCTCGCATTATGAGTTGA-TTTTTG
* * * *
39480488 AAAAATAGAAATTTAAAAGAAATACCTCAGCATGTGTCTGAGGCTCAACTTACCTCTCGCAATAT
1 AAAAATAGAAA-TTAAAA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATAT
* * * * *
39480553 GAGTTGATTTTTAAAAAAATAGTAA-TTGAAAATACCTCTGC-GTGACCCGAGGCCCAACTCACC
64 GAGTTGA-TTTTAAAAAAACAGAAATTTAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACC
39480616 TCTCGCATTATGAGTTGATTTGTTTTG
128 TCTCGCATTATGAGTTGA--T-TTTTG
* *
39480643 AAAAAATAGAAATT-AAAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACATCTCGCAATAT
1 -AAAAATAGAAATTAAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATAT
** * * * *
39480707 GAGTTGATTTTTTGAAAAATAGAAATTTAAAAGAAATACCTAGGCATGTG-TCTGAGGCTCAACT
64 GAGTTGA-TTTTAAAAAAACAGAAATTT--AA-AAATACCTCGGC-TGTGACCCGAGGCTCAACT
* * *
39480771 CACCTCTTGCAATATGAGTTGATTTTCG
124 CACCTCTCGCATTATGAGTTGATTTTTG
* * * * *
39480799 -AAAATAAAAATT--GAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCACATTATG
1 AAAAATAGAAATTAAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATG
** * * *
39480859 AGTTGATTTTTTTGAAAAACAAAAATTTAAAAGAAATACATCGGCATGTG-TCCGAGGCTCAACT
65 AGTTGA--TTTTAAAAAAACAGAAATTT--AA-AAATACCTCGGC-TGTGACCCGAGGCTCAACT
*
39480923 CACCTCTCGCAATATGAGTTGATTTTTG
124 CACCTCTCGCATTATGAGTTGATTTTTG
* * * *
39480951 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGTGTCCGAGGCTCAACTCACTTATCGCAATAT
1 AAAAATAGAAA-TTAAAA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATAT
* * * **
39481016 GAGTTGATTTAAAAAAAATAGAAATTT--AAATACCTCAGC-GTGACTTGAGGCTCAACTCACCT
64 GAGTTGATTTTAAAAAAACAGAAATTTAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCT
39481078 CTCGCATTATGAGTTGATTTTTTTTTG
129 CTCGCATTATGAGTTGA----TTTTTG
* * * ** *
39481105 AGAAACAGAAATTTAAAAGAAATACCTCAGCATGTGTTCGAGGCTCAACTCACTTCTCGCAATAT
1 AAAAATAGAAA-TTAAAA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATAT
* * *
39481170 GACTTGATTTTAAAAAAACAGAAATTT--AAATACCTCAGC-GTGACCCGAGGTTCAACTCACCT
64 GAGTTGATTTTAAAAAAACAGAAATTTAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCT
39481232 CTCGCATTATGAGTTGATTTTTTTG
129 CTCGCATTATGAGTTGA--TTTTTG
*
39481257 AAAAATAGAAATTAAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATAT
1 AAAAATAGAAATT-AAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATAT
** *
39481322 GAGTTGATTTTTGAAAAATAGAAATTTAAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTC
64 GAGTTGATTTTAAAAAAACAGAAATTT---AAAAATACCTCGGC-TGTGACCCGAGGCTCAACTC
*
39481387 ACCTCTCGCAATATGAGTTGATTTTTG
125 ACCTCTCGCATTATGAGTTGATTTTTG
*
39481414 AAAAACAGAAATTTAAAAGAAATACCTCGGCATGT
1 AAAAATAGAAA-TTAAAA-AAATACCTCGGCATGT
39481449 ATCTCGCAAT
Statistics
Matches: 1091, Mismatches: 125, Indels: 102
0.83 0.09 0.08
Matches are distributed among these distances:
149 18 0.02
150 80 0.07
151 106 0.10
152 159 0.15
153 103 0.09
154 249 0.23
155 38 0.03
156 44 0.04
157 45 0.04
158 116 0.11
159 79 0.07
160 38 0.03
161 16 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (151 bp):
AAAAATAGAAATTAAAAAAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTAAAAAAACAGAAATTTAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCT
CGCATTATGAGTTGATTTTTG
Found at i:39480839 original size:384 final size:377
Alignment explanation
Indices: 39480058--39482028 Score: 1956
Period size: 384 Copynumber: 5.2 Consensus size: 377
39480048 CTCGGCATGC
* * * * * *
39480058 GACCCGAAGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAAACA-AAAATT-GAA-AA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
* * * * * *
39480120 ATACCTCGGTATGTGGCCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGATTTTTGAAAAACA
66 ATACCTCGGCATGT-GTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACA
*
39480185 GAAATGTAACAAAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
130 GAAAT-T---AAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
** * * *
39480249 A-TTTAAAAAAAACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGGAT
190 ATTTTTGAAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAA
* * ** * * *
39480313 TATGAGTTGA-TCTTTGAAAAAATAAAAATT-AAAAAATACCTCGGTGTGCGGCCCAAGGCTCAA
255 TATGAGTTGATTTTTTG-AAAAATAGAAATTAAAAAAATACCTCGGCATG-TGTCCGAGGCTCAA
* ** * *
39480376 CTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACAGAAATTAAAAAAAATACCTCGGCGT
318 CTCACCTCTCGCAATATGAGTTGATTTT--TGAAAATACA-AAATT--AAAAAATACCTCAGC--
39480441 GT
376 GT
* *
39480443 GACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAATAGAAATTTAAAAGA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTTAAAAGA
* * * *
39480508 AATACCTCAGCATGTGTCTGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTAAAAAAAT
65 AATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT-AAAAAAC
* * * * *
39480573 AGTAATTGAAAATACCTCTGC-GTGACCCGAGGCCCAACTCACCTCTCGCATTATGAGTTGATTT
129 AGAAATTAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--T
*
39480637 GTTTTGAAAAAATAGAAATTAAAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACATCTCGC
192 -TTTTGAAAAAATAGAAATT-AAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCTCGC
* *
39480702 AATATGAGTTGATTTTTTGAAAAATAGAAATTTAAAAGAAATACCTAGGCATGTGTCTGAGGCTC
253 AATATGAGTTGATTTTTTGAAAAATAGAAA-TTAAAA-AAATACCTCGGCATGTGTCCGAGGCTC
* * *
39480767 AACTCACCTCTTGCAATATGAGTTGATTTTCGAAAATA-AAAATT-GAAAATACCTCAGCGT
316 AACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATACAAAATTAAAAAATACCTCAGCGT
* * *
39480827 GACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTGAAAAACAAAAATTTAAAAG
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAG
* *
39480892 AAATACATCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC
64 AAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAAC
* * *
39480957 AGAAATTTAAAAGAAATACCTCGGCATGTG-TCCGAGGCTCAACTCACTTATCGCAATATGAGTT
129 AGAAA-TT--AA-AAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTT
** * **
39481021 GA-TTTAAAAAAAATAGAAATT-TAAATACCTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCA
189 GATTTTTGAAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCA
* * * * *
39481084 TTATGAGTTGATTTTTTTTTGAGAAACAGAAATTTAAAAGAAATACCTCAGCATGTGTTCGAGGC
254 ATATGAGTTGA---TTTTTTGAAAAATAGAAA-TTAAAA-AAATACCTCGGCATGTGTCCGAGGC
* * * * *
39481149 TCAACTCACTTCTCGCAATATGACTTGA-TTTTAAAAAAACAGAAATT--TAAATACCTCAGCGT
314 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAATACA-AAATTAAAAAATACCTCAGCGT
* * * *
39481211 GACCCGAGGTTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAA-TTAAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAG
* * *
39481275 AAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
64 AAATACCTCGGCATGTG-TCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAA
*
39481340 TAGAAATTTAAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
128 CAGAAA-TT---AAAAATACCTCGGC-TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
* * * * **
39481405 TGATTTTTG-AAAAACAGAAATTTAAAAGA----A--AT-ACCTC--GG--CATGT-A--TCTCG
188 TGATTTTTGAAAAAATAGAAATTAAAAATACCTCAGCGTGACC-CGAGGCTCAACTCACCTCTCG
** * * * *
39481455 CAATATGAGTTGA--TTTAAAAAAATAGAAATT--GAAAATACATCGGC--GTGACCCGAGGCTA
252 CAATATGAGTTGATTTTTTGAAAAATAGAAATTAAAAAAATACCTCGGCATGTG-TCCGAGGCTC
* * *
39481514 AACTCACCTATCGCATTATGAGTTGATTTTTTTTGAAAAATA-GAAATTAAAAAAAATACCTCGG
316 AACTCACCTCTCGCAATATGAGTTGA---TTTTTG-AAAATACAAAATT--AAAAAATACCTC--
* *
39481578 TGTGT
373 AGCGT
* *
39481583 GACTCGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
* *
39481648 ATACCTCGGCATGTGTCTGAGGCTTAACTCACCTCTCGCAATATGAGTTGA-TTTTAAAAAACAG
66 ATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAG
* * * * *
39481712 AAATTGAAAATAACTCAGC-GTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTT
131 AAATTAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*** *
39481776 -TTGAAATCAGAAATTAAAAAATACCTCGGCCTGTGACCCGAGGCTCAACTCACCTCTCGCAATA
196 GAAAAAAT-AGAAATT-AAAAATACCTCAG-C-GTGACCCGAGGCTCAACTCACCTCTCGCAATA
* *
39481840 TGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCCTGTGTCCGAGGCTCAACTC
257 TGAGTTGA-TTTTTTGAAAAATAGAAATTAAAAAAATACCTCGGCATGTGTCCGAGGCTCAACTC
** ** * * * *
39481905 ACCTCTCGCAATATGAGTCAATTTTTGAAAAATAGGAATTTAAAAAATACATCGGTATGT
321 ACCTCTCGCAATATGAGTTGATTTTTG-AAAATACAAAATTAAAAAATACCTCAG--CGT
* * * *
39481965 GACCCGAGGCTTAACTCACCTCTCGCAACATGTGTTGATTTTTGAGAAATACAGAAATTGAAAA
1 GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAA-ACAGAAATTTAAAA
39482029 ATATTTCTTG
Statistics
Matches: 1332, Mismatches: 175, Indels: 159
0.80 0.11 0.10
Matches are distributed among these distances:
362 3 0.00
363 75 0.06
364 17 0.01
365 17 0.01
366 5 0.00
367 6 0.00
368 19 0.01
369 14 0.01
370 58 0.04
371 22 0.02
372 37 0.03
373 19 0.01
374 3 0.00
375 3 0.00
376 3 0.00
377 3 0.00
378 3 0.00
379 2 0.00
380 20 0.02
381 36 0.03
382 55 0.04
383 75 0.06
384 305 0.23
385 209 0.16
386 60 0.05
387 9 0.01
388 66 0.05
389 74 0.06
390 4 0.00
391 52 0.04
392 7 0.01
393 39 0.03
394 12 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (377 bp):
GACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAA
ATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAAACAG
AAATTAAAAATACCTCGGCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
GAAAAAATAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAG
TTGATTTTTTGAAAAATAGAAATTAAAAAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTC
TCGCAATATGAGTTGATTTTTGAAAATACAAAATTAAAAAATACCTCAGCGT
Found at i:39480943 original size:231 final size:226
Alignment explanation
Indices: 39480061--39482029 Score: 2049
Period size: 231 Copynumber: 8.6 Consensus size: 226
39480051 GGCATGCGAC
* * * *
39480061 CCGAAGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAAACAAAAATTGAAAAATACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTG-AAAATAAAAATTG-AAAATACCT
* * * *
39480126 CGGTATGTGGCCCAAGGCTCAACTCACTTCTCGCATTATGAGTTGA--TTTTTGAAAAACAGAAA
63 CGG--CGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAA
* *
39480189 TGTAACAAAAATACCTCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTA
126 T-TAA-AAAAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
** *
39480254 AAAAAAACAGAAA-TT--AA-AAATACCTCAGC--GTGAC
189 TGAAAAACAGAAATTTAAAAGAAATACCT-AGCATGTG-T
* * *
39480288 CCGAGGCTCAACTCACCTCTCGGATTATGAGTTGATCTTTGAAAAAATAAAAATTAAAAAATACC
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT-TTTG--AAAATAAAAATT-GAAAATACC
* * * * * ****
39480353 TCGGTGTGCGGCCCAAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAAAAAAAACAGA
62 TCGGCGT--GACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTT-TTTGAAAAACAGA
* *
39480418 AATTAAAAAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
124 AATT-AAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T
*
39480483 TTTTGAAAAATAGAAATTTAAAAGAAATACCTCAGCATGTGT
186 TTTTGAAAAACAGAAATTTAAAAGAAATACCT-AGCATGTGT
* * * *
39480525 CTGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTAAAAAAATAGTAATTGAAAATACCT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAATAA-A--AATTGAAAATACCT
* * *
39480590 CTGCGTGACCCGAGGCCCAACTCACCTCTCGCATTATGAGTTGATTTGTTTTGAAAAAATAGAAA
63 CGGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTT-TTTTG-AAAAACAGAAA
* *
39480655 TT-AAAAAATACCTCAGCATGTGACCCGAGGCTCAACTCACATCTCGCAATATGAGTTGATTTTT
126 TTAAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
*
39480719 TGAAAAATAGAAATTTAAAAGAAATACCTAGGCATGTGT
189 TGAAAAACAGAAATTTAAAAGAAATACCTA-GCATGTGT
* * *
39480758 CTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTCGAAAATAAAAATTGAAAATACCTCA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT-GAAAATAAAAATTGAAAATACCTCG
* *
39480823 GCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTGAAAAACAAAAATTTA
65 GCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAA-TTA
* *
39480888 AAAGAAATACATCGGCATGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
129 AAA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
*
39480953 AAACAGAAATTTAAAAGAAATACCTCGGCATGTGT
193 AAACAGAAATTTAAAAGAAATACCT-AGCATGTGT
* * ** * *
39480988 CCGAGGCTCAACTCACTTATCGCAATATGAGTTGATTTAAAAAAAATAGAAATT-TAAATACCTC
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT--TGAAAATAAAAATTGAAAATACCTC
* ** *
39481052 AGCGTGACTTGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTTTGAGAAACAGAAAT
64 GGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTTGAAAAACAGAAA-
* ** * * *
39481117 TTAAAAGAAATACCTCAGCATGTGTTCGAGGCTCAACTCACTTCTCGCAATATGACTTGATTTTA
126 TTAAAA-AAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* *
39481182 AAAAAACAGAAATTT-----AAATACCTCAGC--GTGAC
190 GAAAAACAGAAATTTAAAAGAAATACCT-AGCATGTG-T
* * * *
39481214 CCGAGGTTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAAAAAT
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTG-AAAATAAAAATT---GAAAAT
* *
39481279 ACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAAATA
59 ACCTCGGC--GTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACA
*
39481342 GAAATTTAAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
122 GAAA-TT-AAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
39481407 ATTTTTGAAAAACAGAAATTTAAAAGAAATACCT--C--G-G-
184 ATTTTTGAAAAACAGAAATTTAAAAGAAATACCTAGCATGTGT
* ** * *
39481444 -C-A---T---GT-A--TCTCGCAATATGAGTTGATTTAAAAAAATAGAAATTGAAAATACATCG
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT-TGAAAATAAAAATTGAAAATACCTCG
* * *
39481498 GCGTGACCCGAGGCTAAACTCACCTATCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTA
65 GCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGA-TTTTTTTGAAAAACAGAAATT-
** * *
39481563 AAAAAAATACCTCGGTGTGTGACTCGAGGCTCAACTTACCTCTCGCAATATGAGTTGATTTTTGA
128 AAAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
*
39481628 AAAACAGAAATTTAAAAGAAATACCTCGGCATGTGT
192 AAAACAGAAATTTAAAAGAAATACCT-AGCATGTGT
* * * *
39481664 CTGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTT-AAAAAACAGAAATTGAAAATAACTC
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAATA-A-AAATTGAAAATACCTC
* * *
39481728 AGCGTGACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTG-AAATCAGAAATT-
64 GGCGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTA
*
39481791 AAAAAATACCTCGGCCTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG
129 AAAAAATACCTCGGCATGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTG
* *
39481856 AAAAACAGAAA-TTAAAA-AAATACCTCGGCCTGTGT
191 AAAAACAGAAATTTAAAAGAAATACCT-AGCATGTGT
** * * * *
39481891 CCGAGGCTCAACTCACCTCTCGCAATATGAGTCAATTTTTGAAAAATAGGAATTTAAAAAATACA
1 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTG-AAAATA-AAAATT-GAAAATACC
* * ** * ** *
39481956 TCGGTATGTGACCCGAGGCTTAACTCACCTCTCGCAACATGTGTTGATTTTTGAGAAATACAGAA
62 TCGG--CGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAA
*
39482021 ATTGAAAAA
125 ATTAAAAAA
39482030 TATTTCTTGG
Statistics
Matches: 1510, Mismatches: 149, Indels: 159
0.83 0.08 0.09
Matches are distributed among these distances:
211 37 0.02
213 103 0.07
214 17 0.01
216 16 0.01
218 1 0.00
219 18 0.01
221 1 0.00
222 2 0.00
225 5 0.00
226 34 0.02
227 152 0.10
228 85 0.06
229 50 0.03
230 206 0.14
231 282 0.19
232 173 0.11
233 147 0.10
234 90 0.06
235 16 0.01
236 36 0.02
237 36 0.02
238 3 0.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (226 bp):
CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAATAAAAATTGAAAATACCTCGG
CGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAA
AAAATACCTCGGCATGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
CAGAAATTTAAAAGAAATACCTAGCATGTGT
Found at i:39481815 original size:77 final size:77
Alignment explanation
Indices: 39481450--39482031 Score: 548
Period size: 78 Copynumber: 7.6 Consensus size: 77
39481440 TCGGCATGTA
**** * *
39481450 TCTCGCAATATGAGTTGA-TTTAAAAAAAT-AGAAATT-GAAAATACATCGG-C-GTGACCCGAG
1 TCTCGCAATATGAGTTGATTTTTTTGAAATCAGAAATTAAAAAATACCTCGGCCTGTGACCCGAG
*
39481510 GCTAAACTCACC
66 GCTCAACTCACC
* * **
39481522 TATCGCATTATGAGTTGATTTTTTTTGAAAAAT-AGAAATTAAAAAAAATACCTCGGTGTGTGAC
1 TCTCGCAATATGAGTTGA-TTTTTTTG--AAATCAGAAATT--AAAAAATACCTCGGCCTGTGAC
* *
39481586 TCGAGGCTCAACTTACC
61 CCGAGGCTCAACTCACC
* * *
39481603 TCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTG-TC
1 TCTCGCAATATGAGTTGATTTTTTTG-AAATCAGAAA-TT-AAA-AAATACCTCGGCCTGTGACC
* *
39481665 TGAGGCTTAACTCACC
62 CGAGGCTCAACTCACC
** * * * *
39481681 TCTCGCAATATGAGTTGA--TTTTAAAAAACAGAAATT-GAAAATAACTCAG-C-GTGACCCGAG
1 TCTCGCAATATGAGTTGATTTTTTTGAAATCAGAAATTAAAAAATACCTCGGCCTGTGACCCGAG
39481741 GCTCAACTCACC
66 GCTCAACTCACC
* *
39481753 TCTCACATTATGAGTTGATTTTTTTGAAATCAGAAATTAAAAAATACCTCGGCCTGTGACCCGAG
1 TCTCGCAATATGAGTTGATTTTTTTGAAATCAGAAATTAAAAAATACCTCGGCCTGTGACCCGAG
39481818 GCTCAACTCACC
66 GCTCAACTCACC
* *
39481830 TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCGGCCTGTG-TCCG
1 TCTCGCAATATGAGTTGATTTTTTTG-AAATCAGAAATT-AAAAAATACCTCGGCCTGTGACCCG
39481894 AGGCTCAACTCACC
64 AGGCTCAACTCACC
** *** * * **
39481908 TCTCGCAATATGAGTCAATTTTTGAAAAAT-AGGAATTTAAAAAATACATCGGTATGTGACCCGA
1 TCTCGCAATATGAGTTGATTTTTTTGAAATCA-GAAATTAAAAAATACCTCGGCCTGTGACCCGA
*
39481972 GGCTTAACTCACC
65 GGCTCAACTCACC
* * ** *
39481985 TCTCGCAACATGTGTTGATTTTTGAGAAATACAGAAATTGAAAAATA
1 TCTCGCAATATGAGTTGATTTTTTTGAAAT-CAGAAATTAAAAAATA
39482032 TTTCTTGGAG
Statistics
Matches: 424, Mismatches: 62, Indels: 42
0.80 0.12 0.08
Matches are distributed among these distances:
71 3 0.01
72 47 0.11
73 9 0.02
74 19 0.04
75 10 0.02
76 32 0.08
77 109 0.26
78 111 0.26
79 49 0.12
81 35 0.08
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (77 bp):
TCTCGCAATATGAGTTGATTTTTTTGAAATCAGAAATTAAAAAATACCTCGGCCTGTGACCCGAG
GCTCAACTCACC
Found at i:39481948 original size:155 final size:154
Alignment explanation
Indices: 39481450--39482029 Score: 646
Period size: 155 Copynumber: 3.8 Consensus size: 154
39481440 TCGGCATGTA
** * *
39481450 TCTCGCAATATGAGTTGA-TTTAAAAAAATA-GAAATT-GAAAATACATCGGC--GTGACCCGAG
1 TCTCGCAATATGAGTTGATTTTTGAAAAATAGGAATTTAAAAAATACATCGGCATGTGACCCGAG
* * * *
39481510 GCTAAACTCACCTATCGCATTATGAGTTGATTTTTTTTGAAAAATAGAAATTAAAAAAAATACCT
66 GCTTAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTGAAAAACAGAAATT-AAAAAAATACCT
* *
39481575 CGGTGTGTGACTCGAGGCTCAACTTACC
129 CGG-CTGTGAC-CGAGGCTCAACTCACC
* * * * *
39481603 TCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTTAAAAGAAATACCTCGGCATGTG-TCTG
1 TCTCGCAATATGAGTTGATTTTTGAAAAATAGGAATTT-AAA-AAATACATCGGCATGTGACCCG
* * *
39481667 AGGCTTAACTCACCTCTCGCAATATGAGTTGA---TTTTAAAAAACAGAAATT--GAAAATAACT
64 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCT
*
39481727 CAGC-GTGACCCGAGGCTCAACTCACC
129 CGGCTGTGA-CCGAGGCTCAACTCACC
* * *** * * *
39481753 TCTCACATTATGAGTTGATTTTTTTGAAATCA-GAAATTAAAAAATACCTCGGCCTGTGACCCGA
1 TCTCGCAATATGAGTTGATTTTTGAAAAAT-AGGAATTTAAAAAATACATCGGCATGTGACCCGA
*
39481817 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCTC
65 GGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCTC
*
39481882 GGCCTGTGTCCGAGGCTCAACTCACC
130 GG-CTGTGACCGAGGCTCAACTCACC
** *
39481908 TCTCGCAATATGAGTCAATTTTTGAAAAATAGGAATTTAAAAAATACATCGGTATGTGACCCGAG
1 TCTCGCAATATGAGTTGATTTTTGAAAAATAGGAATTTAAAAAATACATCGGCATGTGACCCGAG
* * ** * *
39481973 GCTTAACTCACCTCTCGCAACATGTGTTGATTTTTGAGAAATACAGAAATTGAAAAA
66 GCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAA
39482030 TATTTCTTGG
Statistics
Matches: 355, Mismatches: 54, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
148 16 0.05
149 36 0.10
150 47 0.13
151 2 0.01
152 27 0.08
153 18 0.05
154 20 0.06
155 140 0.39
156 3 0.01
157 1 0.00
158 11 0.03
159 31 0.09
160 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (154 bp):
TCTCGCAATATGAGTTGATTTTTGAAAAATAGGAATTTAAAAAATACATCGGCATGTGACCCGAG
GCTTAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAAATACCTCG
GCTGTGACCGAGGCTCAACTCACC
Found at i:39482893 original size:8 final size:8
Alignment explanation
Indices: 39482882--39482925 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
39482872 TTTTTTCTCT
39482882 TTTTTTTG
1 TTTTTTTG
39482890 TTTTTTTG
1 TTTTTTTG
39482898 TTTTTTT-
1 TTTTTTTG
*
39482905 TGTTTTTG
1 TTTTTTTG
39482913 TTTTTTTG
1 TTTTTTTG
39482921 TTTTT
1 TTTTT
39482926 AGGCATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 6 0.18
8 27 0.82
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTTTG
Found at i:39482918 original size:17 final size:17
Alignment explanation
Indices: 39482862--39482925 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
39482852 TCATCTTGAT
* *
39482862 TTTTTTCTTCTTTTTTCTC
1 TTTTTT-TTGTTTTTT-TG
39482881 TTTTTTTTGTTTTTTTG
1 TTTTTTTTGTTTTTTTG
39482898 TTTTTTTTG--TTTTTG
1 TTTTTTTTGTTTTTTTG
39482913 -TTTTTTTGTTTTT
1 TTTTTTTTGTTTTT
39482926 AGGCATAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 8 0.20
15 6 0.15
16 3 0.07
17 10 0.24
18 8 0.20
19 6 0.15
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.86
Consensus pattern (17 bp):
TTTTTTTTGTTTTTTTG
Found at i:39482925 original size:9 final size:9
Alignment explanation
Indices: 39482862--39482924 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
39482852 TCATCTTGAT
*
39482862 TTTTTTCTTC
1 TTTTTT-TTG
* *
39482872 TTTTTTCTC
1 TTTTTTTTG
39482881 TTTTTTTTG
1 TTTTTTTTG
39482890 -TTTTTTTG
1 TTTTTTTTG
39482898 TTTTTTTTG
1 TTTTTTTTG
39482907 TTTTTGTTT-
1 TTTTT-TTTG
39482916 TTTTGTTTT
1 TTTT-TTTT
39482925 TAGGCATAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
8 8 0.17
9 29 0.62
10 10 0.21
ACGTcount: A:0.00, C:0.06, G:0.08, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:39489000 original size:20 final size:20
Alignment explanation
Indices: 39488975--39489074 Score: 88
Period size: 20 Copynumber: 5.2 Consensus size: 20
39488965 GATTCGATTG
39488975 AAACACGAGAATTTTTTTTA
1 AAACACGAGAATTTTTTTTA
*
39488995 AAACACGAGAA----TTTTG
1 AAACACGAGAATTTTTTTTA
* *
39489011 AAACACAATAATTTTTTTTAA
1 AAACACGAGAATTTTTTTT-A
*
39489032 AAACACG-GAA-ATTTTTT-
1 AAACACGAGAATTTTTTTTA
*
39489049 AAACACAAGAATTTTTTTTTA
1 AAACACGAGAA-TTTTTTTTA
39489070 AAACA
1 AAACA
39489075 AATTTTTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
16 13 0.21
17 6 0.10
18 3 0.05
19 6 0.10
20 23 0.37
21 11 0.18
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (20 bp):
AAACACGAGAATTTTTTTTA
Found at i:39489012 original size:36 final size:37
Alignment explanation
Indices: 39488972--39489074 Score: 138
Period size: 38 Copynumber: 2.8 Consensus size: 37
39488962 CGTGATTCGA
*
39488972 TTGAAACACGAGAATTTTTTTTAAAACAC-GAGAA-TT
1 TTGAAACACAAGAATTTTTTTTAAAACACGGA-AATTT
*
39489008 TTGAAACACAATAATTTTTTTTAAAAACACGGAAATTT
1 TTGAAACACAAGAATTTTTTTT-AAAACACGGAAATTT
*
39489046 TTTAAACACAAGAATTTTTTTTTAAAACA
1 TTGAAACACAAGAA-TTTTTTTTAAAACA
39489075 AATTTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
36 20 0.34
37 9 0.15
38 22 0.37
39 8 0.14
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.37
Consensus pattern (37 bp):
TTGAAACACAAGAATTTTTTTTAAAACACGGAAATTT
Found at i:39489028 original size:19 final size:18
Alignment explanation
Indices: 39488975--39489066 Score: 71
Period size: 19 Copynumber: 5.0 Consensus size: 18
39488965 GATTCGATTG
*
39488975 AAACACGAGAATTTTTTTT
1 AAACACAAGAA-TTTTTTT
* *
39488994 AAAACACGAGAA--TTTTG
1 -AAACACAAGAATTTTTTT
*
39489011 AAACACAATAATTTTTTTT
1 AAACACAAGAA-TTTTTTT
* * *
39489030 AAAAACACGGAAATTTTTT
1 AAACACA-AGAATTTTTTT
39489049 AAACACAAGAATTTTTTT
1 AAACACAAGAATTTTTTT
39489067 TTAAAACAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 9 0.16
17 4 0.07
18 9 0.16
19 22 0.39
20 13 0.23
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (18 bp):
AAACACAAGAATTTTTTT
Found at i:39489053 original size:38 final size:36
Alignment explanation
Indices: 39488972--39489074 Score: 136
Period size: 36 Copynumber: 2.8 Consensus size: 36
39488962 CGTGATTCGA
*
39488972 TTGAAACACGAGAATTTTTTTTAAAACACGAGAATT
1 TTGAAACACAAGAATTTTTTTTAAAACACGAGAATT
*
39489008 TTGAAACACAATAATTTTTTTTAAAAACACG-GAAATTT
1 TTGAAACACAAGAATTTTTTTT-AAAACACGAG-AA-TT
*
39489046 TTTAAACACAAGAATTTTTTTTTAAAACA
1 TTGAAACACAAGAA-TTTTTTTTAAAACA
39489075 AATTTTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
36 21 0.36
37 10 0.17
38 20 0.34
39 8 0.14
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.37
Consensus pattern (36 bp):
TTGAAACACAAGAATTTTTTTTAAAACACGAGAATT
Found at i:39489078 original size:17 final size:20
Alignment explanation
Indices: 39488975--39489084 Score: 69
Period size: 19 Copynumber: 6.0 Consensus size: 20
39488965 GATTCGATTG
* *
39488975 AAACACGAGAATTTTTTTTA
1 AAACACAAGAATTTTTTTTT
* *
39488995 AAACACGAGAA----TTTTG
1 AAACACAAGAATTTTTTTTT
*
39489011 AAACACAATAA-TTTTTTTT
1 AAACACAAGAATTTTTTTTT
* * *
39489030 AAAAACACGGAA--ATTTTTT
1 AAACACA-AGAATTTTTTTTT
39489049 AAACACAAGAATTTTTTTTT
1 AAACACAAGAATTTTTTTTT
39489069 AAA-AC-A-AATTTTTTTT
1 AAACACAAGAATTTTTTTT
39489085 GATAAATTAC
Statistics
Matches: 73, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
16 13 0.18
17 10 0.14
18 4 0.05
19 24 0.33
20 22 0.30
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (20 bp):
AAACACAAGAATTTTTTTTT
Found at i:39489766 original size:7 final size:7
Alignment explanation
Indices: 39489754--39489831 Score: 50
Period size: 7 Copynumber: 10.3 Consensus size: 7
39489744 ATTTTCAAAT
*
39489754 TTTTTTA
1 TTTTTTC
39489761 TTTTTT-
1 TTTTTTC
39489767 TATTTTTC
1 T-TTTTTC
39489775 TTTTTTC
1 TTTTTTC
39489782 TTTTTTTTC
1 --TTTTTTC
*
39489791 TTTCTTC
1 TTTTTTC
39489798 TTCTTCTTC
1 TT-TT-TTC
39489807 TTCTTCTTC
1 TT-TT-TTC
*
39489816 TTCTTTC
1 TTTTTTC
*
39489823 TTTCTTC
1 TTTTTTC
39489830 TT
1 TT
39489832 CTTCAAAACC
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
6 1 0.02
7 35 0.58
8 3 0.05
9 21 0.35
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:39489780 original size:16 final size:17
Alignment explanation
Indices: 39489752--39489799 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
39489742 CTATTTTCAA
39489752 ATTTTT-TTATTTT-TTT
1 ATTTTTCTT-TTTTCTTT
39489768 ATTTTTCTTTTTTCTTT
1 ATTTTTCTTTTTTCTTT
*
39489785 -TTTTTCTTTCTTCTT
1 ATTTTTCTTTTTTCTT
39489800 CTTCTTCTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 24 0.83
17 5 0.17
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.83
Consensus pattern (17 bp):
ATTTTTCTTTTTTCTTT
Found at i:39489785 original size:6 final size:6
Alignment explanation
Indices: 39489763--39489831 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
39489753 TTTTTTTATT
* * * *
39489763 TTTTTA TTTTTC TTTTT- TCTTT- TTTTTC TTTCTTC TTCTTC TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT-TTC TTTTTC TTTTTC
*
39489810 TTCTTC TTCTTTC TTTCTTC TT
1 TTTTTC TT-TTTC TTT-TTC TT
39489832 CTTCAAAACC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
5 8 0.15
6 31 0.57
7 15 0.28
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:39489798 original size:3 final size:3
Alignment explanation
Indices: 39489792--39489835 Score: 70
Period size: 3 Copynumber: 14.0 Consensus size: 3
39489782 TTTTTTTTCT
39489792 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTTC TTTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC -TTC TTC TTC TTC
39489836 AAAACCCTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.82
4 7 0.17
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:39490245 original size:29 final size:29
Alignment explanation
Indices: 39490182--39490317 Score: 125
Period size: 30 Copynumber: 4.7 Consensus size: 29
39490172 CAAAAATTCT
* *
39490182 GGGGCCAAAATATAATTTTGAGAAAA-TTTA
1 GGGGTCAAAATGTAATTTT-A-AAAAGTTTA
* *
39490212 GGGGTCTAAATGTAATTTTTAAAAGTTTA
1 GGGGTCAAAATGTAATTTTAAAAAGTTTA
* *
39490241 TGGGTCAAAATGTAA-CTTAAAAAGTTTA
1 GGGGTCAAAATGTAATTTTAAAAAGTTTA
* **
39490269 GGAGTCAAAATAAAATTTTAGGAAAA-TTTA
1 GGGGTCAAAATGTAATTTTA--AAAAGTTTA
*
39490299 GGGGTCAAAATGCAATTTT
1 GGGGTCAAAATGTAATTTT
39490318 TTATTTTTTT
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
28 26 0.30
29 20 0.23
30 36 0.42
31 4 0.05
ACGTcount: A:0.41, C:0.06, G:0.20, T:0.33
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTAAAAAGTTTA
Found at i:39490275 original size:28 final size:28
Alignment explanation
Indices: 39490204--39490310 Score: 85
Period size: 28 Copynumber: 3.7 Consensus size: 28
39490194 TAATTTTGAG
* * *
39490204 AAAA-TTTAGGGGTCTAAATGTAATTTTT
1 AAAAGTTTA-GGGTCAAAATGTAATCTTA
39490232 AAAAGTTTATGGGTCAAAATGTAA-CTTA
1 AAAAGTTTA-GGGTCAAAATGTAATCTTA
** *
39490260 AAAAGTTTAGGAGTCAAAATAAAATTTTA
1 AAAAGTTTAGG-GTCAAAATGTAATCTTA
39490289 GGAAAA-TTTAGGGGTCAAAATG
1 --AAAAGTTTA-GGGTCAAAATG
39490311 CAATTTTTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.03
28 25 0.38
29 20 0.31
30 12 0.18
31 6 0.09
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.33
Consensus pattern (28 bp):
AAAAGTTTAGGGTCAAAATGTAATCTTA
Found at i:39496362 original size:37 final size:37
Alignment explanation
Indices: 39496321--39496402 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
39496311 AAATATTTAT
* *
39496321 TAATCAATGTTCAAACTTTGAACATGCTTTATTAAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
*
39496358 TAATCAATGTTAAAACTTTGAACATGCTTTAATGAAC
1 TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
39496395 TAATCAAT
1 TAATCAAT
39496403 ATATTTATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (37 bp):
TAATCAATGTTAAAACTTTGAACATGCTTTAATAAAC
Found at i:39496481 original size:32 final size:33
Alignment explanation
Indices: 39496445--39496519 Score: 134
Period size: 32 Copynumber: 2.3 Consensus size: 33
39496435 TTAAAGCTTG
*
39496445 AATTATACATATACCAACAATTAATTTTA-GTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
39496477 AATTATACATACACCAACAATTAATTTTAGGTC
1 AATTATACATACACCAACAATTAATTTTAGGTC
39496510 AATTATACAT
1 AATTATACAT
39496520 GCTTTATAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 28 0.68
33 13 0.32
ACGTcount: A:0.44, C:0.16, G:0.04, T:0.36
Consensus pattern (33 bp):
AATTATACATACACCAACAATTAATTTTAGGTC
Found at i:39499904 original size:16 final size:16
Alignment explanation
Indices: 39499883--39499918 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
39499873 GATTTGCTAT
*
39499883 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
39499899 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39499915 TACA
1 TACA
39499919 GCGAATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:39500445 original size:5 final size:5
Alignment explanation
Indices: 39500435--39500470 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
39500425 AGCAACCATC
39500435 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
39500471 CATAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:39500758 original size:28 final size:28
Alignment explanation
Indices: 39500703--39500769 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
39500693 AATTATGTAC
* *
39500703 ATATATATAAAAATTTATAGACGTATAT
1 ATATATATAAAAATGTATAGACGGATAT
*
39500731 ATATATTATAAAAATGTAT-GATGGATAT
1 ATATA-TATAAAAATGTATAGACGGATAT
39500759 AGGTATATATA
1 A--TATATATA
39500770 TGTATGTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 13 0.39
29 16 0.48
30 4 0.12
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.39
Consensus pattern (28 bp):
ATATATATAAAAATGTATAGACGGATAT
Found at i:39502616 original size:49 final size:49
Alignment explanation
Indices: 39502563--39502693 Score: 217
Period size: 49 Copynumber: 2.7 Consensus size: 49
39502553 ATTTAGCTTT
* * *
39502563 AATTTGTTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCCGGTCTTC
1 AATTTGCTCCACTGCAACTTCAGGGAGATAAAATTTGTAGCCGGTCTTC
* *
39502612 AATTTGCTCCACTACAACTTCAGGGAGATAAAATTTGTAGTCGGTCTTC
1 AATTTGCTCCACTGCAACTTCAGGGAGATAAAATTTGTAGCCGGTCTTC
39502661 AATTTGCTCCACTGCAACTTCAGGGAGATAAAA
1 AATTTGCTCCACTGCAACTTCAGGGAGATAAAA
39502694 CTTATGGCTC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 76 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (49 bp):
AATTTGCTCCACTGCAACTTCAGGGAGATAAAATTTGTAGCCGGTCTTC
Found at i:39513080 original size:22 final size:22
Alignment explanation
Indices: 39513052--39513095 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
39513042 AGGGAAATAC
39513052 TTGTATGTGCTCCTCTAAAGAT
1 TTGTATGTGCTCCTCTAAAGAT
39513074 TTGTATGTGCTCCTCTAAAGAT
1 TTGTATGTGCTCCTCTAAAGAT
39513096 CGAGCAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (22 bp):
TTGTATGTGCTCCTCTAAAGAT
Found at i:39516144 original size:35 final size:33
Alignment explanation
Indices: 39516082--39516158 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 33
39516072 TATATGAAAA
39516082 TTATAAAATAAAAAATATAAGTATGTATATATAT
1 TTATAAAATAAAAAATAT-AGTATGTATATATAT
*
39516116 TTATATAAATAAAAAATAT-GTACGTGTATGTATAT
1 TTATA-AAATAAAAAATATAGTA--TGTATATATAT
39516151 TTATAAAA
1 TTATAAAA
39516159 GGGATACATG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
33 3 0.08
34 8 0.21
35 28 0.72
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (33 bp):
TTATAAAATAAAAAATATAGTATGTATATATAT
Found at i:39516403 original size:32 final size:34
Alignment explanation
Indices: 39516341--39516414 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 34
39516331 AATTATGTAC
* * *
39516341 ATATATA-TATAAACATTTATAGACGTATATA-T
1 ATATATATTATAAAAATGTATAGACGGATATAGT
*
39516373 ATATATATTATAAAAATGTAT-GATGGATATAGGT
1 ATATATATTATAAAAATGTATAGACGGATATA-GT
39516407 ATATATAT
1 ATATATAT
39516415 GTATGTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
32 15 0.43
33 11 0.31
34 9 0.26
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (34 bp):
ATATATATTATAAAAATGTATAGACGGATATAGT
Found at i:39517391 original size:6 final size:6
Alignment explanation
Indices: 39517371--39517410 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
39517361 AAAAGGGTTC
*
39517371 AAAAAG AAAAGAT AAAAAT AAAAAT AAAAAT -AAAAT AAAA
1 AAAAAT AAAA-AT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
39517411 TAAGATAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (6 bp):
AAAAAT
Found at i:39517397 original size:12 final size:12
Alignment explanation
Indices: 39517371--39517410 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
39517361 AAAAGGGTTC
*
39517371 AAAAAGAAAAGAT
1 AAAAATAAAA-AT
39517384 AAAAATAAAAAT
1 AAAAATAAAAAT
39517396 AAAAAT-AAAAT
1 AAAAATAAAAAT
39517407 AAAA
1 AAAA
39517411 TAAGATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 9 0.35
12 8 0.31
13 9 0.35
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:39518321 original size:13 final size:13
Alignment explanation
Indices: 39518303--39518327 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39518293 TCTGTATTAA
39518303 ATTTTTTTATATT
1 ATTTTTTTATATT
39518316 ATTTTTTTATAT
1 ATTTTTTTATAT
39518328 ACATATAAAG
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTTTTATATT
Found at i:39519091 original size:37 final size:37
Alignment explanation
Indices: 39519036--39519116 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
39519026 GTATAAATAT
* **
39519036 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTTAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
*
39519073 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
39519110 ATTGATT
1 ATTGATT
39519117 TAAAACAACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.42
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
Found at i:39521625 original size:16 final size:16
Alignment explanation
Indices: 39521604--39521639 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
39521594 ACTAATTCGC
39521604 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39521620 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39521636 TGTA
1 TGTA
39521640 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:39521892 original size:16 final size:16
Alignment explanation
Indices: 39521855--39521896 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39521845 TTAATCATAT
*
39521855 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
39521871 TT-AAATATATTATAA
1 TTAAAATATATTATAA
39521886 TTAAAATATAT
1 TTAAAATATAT
39521897 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:39521903 original size:14 final size:15
Alignment explanation
Indices: 39521864--39521905 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39521854 TTTAAACATA
*
39521864 ATTATTATTAAATAT
1 ATTATAATTAAATAT
39521879 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
39521893 A-TATAATTTAATA
1 ATTATAATTAAATA
39521906 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:39522023 original size:14 final size:15
Alignment explanation
Indices: 39521974--39522025 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
39521964 ATAAAATATA
39521974 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
39521989 TATTAAATATATTAT
1 AATTAAATATATTAT
39522004 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
39522017 AATTTAATA
1 AATTAAATA
39522026 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:39522073 original size:120 final size:121
Alignment explanation
Indices: 39521853--39522150 Score: 487
Period size: 120 Copynumber: 2.5 Consensus size: 121
39521843 TTTTAATCAT
*
39521853 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
39521918 ATTAATATTCTTATATGAATTTACTCCAATAATAATATATGATACTATAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATAATAATAAATGATACTAT-AAATGA-AA
39521975 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
39522038 ATTAATATTCTTATATGAATTTACTCAAATCATAATAAATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATAATAATAAATGATACTATAAATGAAA
* * *
39522094 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
39522151 TAAAATAATT
Statistics
Matches: 167, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
119 7 0.04
120 155 0.93
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATAATAATAAATGATACTATAAATGAAA
Found at i:39527799 original size:33 final size:33
Alignment explanation
Indices: 39527760--39527835 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
39527750 ATTATAAAGC
*
39527760 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
39527793 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
39527826 ATGTATAATT
1 ATGTATAATT
39527836 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:39527933 original size:37 final size:37
Alignment explanation
Indices: 39527878--39527959 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
39527868 GTATAAATAT
* *
39527878 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
*
39527915 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
39527952 ATTGATTA
1 ATTGATTA
39527960 ATAAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
Found at i:39531149 original size:5 final size:5
Alignment explanation
Indices: 39531109--39531134 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
39531099 GCAAATCGGC
39531109 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
39531135 TCGAATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:39533947 original size:82 final size:82
Alignment explanation
Indices: 39533840--39533994 Score: 238
Period size: 82 Copynumber: 1.9 Consensus size: 82
39533830 TTATTTTTAG
* * * *
39533840 GGGGCTAAAGTGTAATTTTATTATATATTAATTTATAATTTTATATTTATAAGAAGACTGAATTG
1 GGGGCTAAAGTGTAATTTCACTATATATTAATTTATAATTTTATATTTATAAGAAGACTAAAATG
*
39533905 ACAATTTTTCTTTTGGA
66 AAAATTTTTCTTTTGGA
* * *
39533922 GGGGTTAAAGTGTAATTTCACTATATATTAATTTATAATTTTCTATTTATAAGAGGACTAAAATG
1 GGGGCTAAAGTGTAATTTCACTATATATTAATTTATAATTTTATATTTATAAGAAGACTAAAATG
39533987 AAAATTTT
66 AAAATTTT
39533995 CATTTTTGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (82 bp):
GGGGCTAAAGTGTAATTTCACTATATATTAATTTATAATTTTATATTTATAAGAAGACTAAAATG
AAAATTTTTCTTTTGGA
Found at i:39536300 original size:26 final size:26
Alignment explanation
Indices: 39536271--39536321 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
39536261 TTACTATTAC
* *
39536271 TATTATTATTTTTCCTTTTT-TTATTT
1 TATTATT-TATTTACTTTTTATTATTT
39536297 TATTATTTATTTACTTTTTATTATT
1 TATTATTTATTTACTTTTTATTATT
39536322 ACCATATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (26 bp):
TATTATTTATTTACTTTTTATTATTT
Found at i:39536432 original size:18 final size:19
Alignment explanation
Indices: 39536409--39536449 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
39536399 TTTAAATTCA
39536409 TTTATTTTAT-TATATCAT
1 TTTATTTTATCTATATCAT
*
39536427 TTTA-TTTATCTATATCCT
1 TTTATTTTATCTATATCAT
39536445 TTTAT
1 TTTAT
39536450 ATAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTATTTTATCTATATCAT
Found at i:39537033 original size:27 final size:22
Alignment explanation
Indices: 39536980--39537024 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
39536970 ATAAAGTGTG
39536980 AATTATTTTTATTTTATTAACA
1 AATTATTTTTATTTTATTAACA
39537002 AATTATTTTTATTTTATTAACA
1 AATTATTTTTATTTTATTAACA
39537024 A
1 A
39537025 GTGTCATTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTATTTTTATTTTATTAACA
Found at i:39538871 original size:46 final size:46
Alignment explanation
Indices: 39538768--39539020 Score: 433
Period size: 46 Copynumber: 5.6 Consensus size: 46
39538758 TACGTATGAT
* *
39538768 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
39538811 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
39538857 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
39538903 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
39538949 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
39538995 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
39539021 ATTACTCAAA
Statistics
Matches: 201, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
43 10 0.05
44 5 0.02
45 28 0.14
46 158 0.79
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:39544583 original size:3 final size:3
Alignment explanation
Indices: 39544575--39544634 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
39544565 ATATGTATAG
*
39544575 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39544623 TAA TAA TAA TAA
1 TAA TAA TAA TAA
39544635 AATCATAGCA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39549599 original size:44 final size:44
Alignment explanation
Indices: 39549536--39549624 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
39549526 GTTTTCACTA
39549536 TAGTTTCCATCTATTTGATTGGCAGAGTATAATTATATCATAAT
1 TAGTTTCCATCTATTTGATTGGCAGAGTATAATTATATCATAAT
39549580 TAGTTTCCATCTATTTGATTGGCAGAGTATAATTATATCATAAT
1 TAGTTTCCATCTATTTGATTGGCAGAGTATAATTATATCATAAT
39549624 T
1 T
39549625 CTCATCATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (44 bp):
TAGTTTCCATCTATTTGATTGGCAGAGTATAATTATATCATAAT
Found at i:39551024 original size:30 final size:33
Alignment explanation
Indices: 39550988--39551059 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 33
39550978 TAGTTTTTTT
*
39550988 TTATTATATTG-TTAATACTGTT-TATT-TATA
1 TTATTATATTGTTTAATACTATTATATTATATA
* *
39551018 TTATTAT-TAGTTTAATATTATTATATTATATA
1 TTATTATATTGTTTAATACTATTATATTATATA
39551050 TTATTATATT
1 TTATTATATT
39551060 TACTTATATG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 2 0.06
30 16 0.47
31 4 0.12
32 11 0.32
33 1 0.03
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (33 bp):
TTATTATATTGTTTAATACTATTATATTATATA
Found at i:39551043 original size:8 final size:8
Alignment explanation
Indices: 39551013--39551059 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
39551003 TACTGTTTAT
39551013 TTATATTA
1 TTATATTA
39551021 TTATTAGTT-
1 TTA-TA-TTA
*
39551030 TAATATTA
1 TTATATTA
39551038 TTATATTA
1 TTATATTA
39551046 -TATATTA
1 TTATATTA
39551053 TTATATT
1 TTATATT
39551060 TACTTATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
7 9 0.27
8 18 0.55
9 4 0.12
10 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (8 bp):
TTATATTA
Found at i:39551059 original size:15 final size:14
Alignment explanation
Indices: 39551009--39551056 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
39550999 TTAATACTGT
39551009 TTATTTATATTATTA
1 TTATTTATA-TATTA
39551024 TTAGTTTA-ATATTA
1 TTA-TTTATATATTA
39551038 TTATATTATATATTA
1 TTAT-TTATATATTA
39551053 TTAT
1 TTAT
39551057 ATTTACTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 1 0.03
14 11 0.37
15 14 0.47
16 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATTTATATATTA
Found at i:39555061 original size:24 final size:24
Alignment explanation
Indices: 39555029--39555086 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
39555019 TTCCAGAAAG
39555029 AAATGCAGGATCAACTTCAGCAGC
1 AAATGCAGGATCAACTTCAGCAGC
*
39555053 AAATGCAGGATCAACTTCAGTAGC
1 AAATGCAGGATCAACTTCAGCAGC
*
39555077 AAATGTAGGA
1 AAATGCAGGA
39555087 GCAGCTCGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (24 bp):
AAATGCAGGATCAACTTCAGCAGC
Found at i:39558531 original size:13 final size:14
Alignment explanation
Indices: 39558511--39558543 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
39558501 TTTTTCGTAT
39558511 GTATTTTTGAGCCA
1 GTATTTTTGAGCCA
39558525 GTATTTTTGAGCCA
1 GTATTTTTGAGCCA
39558539 GTATT
1 GTATT
39558544 CTTTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (14 bp):
GTATTTTTGAGCCA
Found at i:39558608 original size:23 final size:24
Alignment explanation
Indices: 39558563--39558616 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
39558553 TTTTTTCGAG
* * *
39558563 TAATTATTCTTTTTTTCTTTTTC-
1 TAATCATTCTTTTATTCTATTTCA
39558586 TACATCATTCTTTTATTC-ATTTCA
1 TA-ATCATTCTTTTATTCTATTTCA
39558610 TAATCAT
1 TAATCAT
39558617 ATTTTGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (24 bp):
TAATCATTCTTTTATTCTATTTCA
Found at i:39563676 original size:50 final size:50
Alignment explanation
Indices: 39563621--39563913 Score: 208
Period size: 50 Copynumber: 5.9 Consensus size: 50
39563611 TTGGCATTAC
** *
39563621 AGTGGAACGGATTGAAGCCACAACGGTGAATCTTGTTTCCCTGGCAGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGGCAGTGT
* * * * * * * * * *
39563671 TGTGGAATAGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTGC
1 AGTGGAAAAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGGCAGTGT
** * * ** *
39563721 AGTTAAAAATATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGGCAGTGT
* * * * * * * * *
39563771 AGTGGAACAGATTGAAGCTACGACGGCGGATCTAGTTTCCCCGACATTGC
1 AGTGGAAAAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGGCAGTGT
* ** * *** * *
39563821 AATTTAAAAGATTGAAGCCACAACGACGAATCTTACCTCTCTGGCGGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGGCAGTGT
* * * *
39563871 AGTGGAATAGATTGAAGTCACGACGGTGAATCTTGTTTCCCTG
1 AGTGGAAAAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTG
39563914 ACATTGCAGT
Statistics
Matches: 172, Mismatches: 71, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
50 172 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (50 bp):
AGTGGAAAAGATTGAAGCCACAACGGCGAATCTTGTTTCCCTGGCAGTGT
Found at i:39563754 original size:100 final size:99
Alignment explanation
Indices: 39563631--39563937 Score: 418
Period size: 100 Copynumber: 3.1 Consensus size: 99
39563621 AGTGGAACGG
* ** * *
39563631 ATTGAAGCCACAACGGTGAATCTTGTTTCCCTGGCAGTGTTGTGGAATAGATTGAAGCTACGACG
1 ATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGACG
*
39563696 GCGGATCTGGTTTCCCCGACATTGCAGTTAAAAA
66 GCGGATCTAGTTTCCCCGACATTGCAGTTAAAAA
* *
39563730 TATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGAC
1 -ATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
* *
39563795 GGCGGATCTAGTTTCCCCGACATTGCAATTTAAAAG
65 GGCGGATCTAGTTTCCCCGACATTGC-AGTTAAAAA
* * *
39563831 ATTGAAGCCACAACGACGAATCTTACCTCTCTGGCGGTGTAGTGGAATAGATTGAAG-TCACGAC
1 ATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCT-ACGAC
* * * *
39563895 GGTGAATCTTGTTTCCCTGACATTGCAGTTAAACAA
65 GGCGGATCTAGTTTCCCCGACATTGCAGTTAAA-AA
39563931 ATTGAAG
1 ATTGAAG
39563938 TAAATAATTC
Statistics
Matches: 183, Mismatches: 21, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
99 7 0.04
100 169 0.92
101 7 0.04
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (99 bp):
ATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGACG
GCGGATCTAGTTTCCCCGACATTGCAGTTAAAAA
Found at i:39564161 original size:82 final size:82
Alignment explanation
Indices: 39563979--39564144 Score: 235
Period size: 82 Copynumber: 2.0 Consensus size: 82
39563969 GAGCGGATCA
* * * * *
39563979 AAATGATAGATCTCATCTCTCTAATGTTGCAATAGAGCAGATTGTATCAGACTCATCTTTAAAAT
1 AAATGACAGATCTTATCTCTCTAATGTTGCAATAGAGCAGATCGCATCAAACTCATCTTTAAAAT
**
39564044 TGCAGTGGAATAAGTTG
66 TGCAGCAGAATAAGTTG
* *
39564061 AAATGACAGATCTTATCTCTCTGAA-GTTGCAATAGAGCAGATCGCATCAAACTTATTTTTAAAA
1 AAATGACAGATCTTATCTCTCT-AATGTTGCAATAGAGCAGATCGCATCAAACTCATCTTTAAAA
39564125 TTGCAGCAGAATAAGTTG
65 TTGCAGCAGAATAAGTTG
39564143 AA
1 AA
39564145 GCTACAAGTC
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 72 0.97
83 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (82 bp):
AAATGACAGATCTTATCTCTCTAATGTTGCAATAGAGCAGATCGCATCAAACTCATCTTTAAAAT
TGCAGCAGAATAAGTTG
Found at i:39564173 original size:82 final size:82
Alignment explanation
Indices: 39563979--39564173 Score: 214
Period size: 82 Copynumber: 2.4 Consensus size: 82
39563969 GAGCGGATCA
* * * ** * * *
39563979 AAATGATAGATCTCATCTCTCTAATGTTGCAATAGAGCAGATTGTATCAGACTCATCTTTAAAAT
1 AAATGACAGATCTTATCTCCCTAAAATTGCAATAGAGCAGATCGCATCAAACTCATCTTTAAAAT
**
39564044 TGCAGTGGAATAAGTTG
66 TGCAGCAGAATAAGTTG
* * * * *
39564061 AAATGACAGATCTTATCTCTCTGAAGTTGCAATAGAGCAGATCGCATCAAACTTATTTTTAAAAT
1 AAATGACAGATCTTATCTCCCTAAAATTGCAATAGAGCAGATCGCATCAAACTCATCTTTAAAAT
39564126 TGCAGCAGAATAAGTTG
66 TGCAGCAGAATAAGTTG
*
39564143 AAGCT-ACA-AGTCTTATCTCCCTAAAATTGCA
1 AA-ATGACAGA-TCTTATCTCCCTAAAATTGCA
39564174 GTGGAACAGA
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
81 1 0.01
82 94 0.98
83 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (82 bp):
AAATGACAGATCTTATCTCCCTAAAATTGCAATAGAGCAGATCGCATCAAACTCATCTTTAAAAT
TGCAGCAGAATAAGTTG
Found at i:39564641 original size:30 final size:32
Alignment explanation
Indices: 39564616--39564675 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
39564606 TATTATATTG
*
39564616 TTAATACTGTT-TATT-TATATTATTATTAGT
1 TTAATACTATTATATTATATATTATTATTAGT
*
39564646 TTAATATTATTATATTATATATTATTATTA
1 TTAATACTATTATATTATATATTATTATTA
39564676 TATTTACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 9 0.35
31 4 0.15
32 13 0.50
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (32 bp):
TTAATACTATTATATTATATATTATTATTAGT
Found at i:39564669 original size:15 final size:14
Alignment explanation
Indices: 39564626--39564678 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
39564616 TTAATACTGT
39564626 TTATTTATATTATTA
1 TTATTTATA-TATTA
39564641 TTAGTTTA-ATATTA
1 TTA-TTTATATATTA
39564655 TTATATTATATATTA
1 TTAT-TTATATATTA
39564670 TTA-TTATAT
1 TTATTTATAT
39564679 TTACTTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.20
14 11 0.31
15 13 0.37
16 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATTTATATATTA
Found at i:39578464 original size:30 final size:32
Alignment explanation
Indices: 39578439--39578498 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
39578429 TATTATATTG
*
39578439 TTAATACTGTT-TATT-TATATTATTATTAGT
1 TTAATACTATTATATTATATATTATTATTAGT
*
39578469 TTAATATTATTATATTATATATTATTATTA
1 TTAATACTATTATATTATATATTATTATTA
39578499 TATTTACTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 9 0.35
31 4 0.15
32 13 0.50
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (32 bp):
TTAATACTATTATATTATATATTATTATTAGT
Found at i:39578492 original size:15 final size:14
Alignment explanation
Indices: 39578449--39578501 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
39578439 TTAATACTGT
39578449 TTATTTATATTATTA
1 TTATTTATA-TATTA
39578464 TTAGTTTA-ATATTA
1 TTA-TTTATATATTA
39578478 TTATATTATATATTA
1 TTAT-TTATATATTA
39578493 TTA-TTATAT
1 TTATTTATAT
39578502 TTACTTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
13 7 0.20
14 11 0.31
15 13 0.37
16 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTATTTATATATTA
Found at i:39582863 original size:44 final size:44
Alignment explanation
Indices: 39582812--39583002 Score: 198
Period size: 44 Copynumber: 4.4 Consensus size: 44
39582802 GATTTGCTCT
39582812 CTGCAACTTCAGAGAGATAAGATCTGTGATTTCAATCCGCTCCA
1 CTGCAACTTCAGAGAGATAAGATCTGTGATTTCAATCCGCTCCA
* * * *
39582856 CTGCAACTTCAG-GAAGATAGGATTACCG-G-TTTTAATCTGCTCCA
1 CTGCAACTTCAGAG-AGATAAGA-T-CTGTGATTTCAATCCGCTCCA
* * * * *
39582900 CTGCAACTTCAGGGAGATAAGAT-T-AGA-TGCAATCTGCT-CT
1 CTGCAACTTCAGAGAGATAAGATCTGTGATTTCAATCCGCTCCA
* *
39582940 CTGCAATTTCAGAGAGATAAGATCTGTGATTTCAATCCGCTCTA
1 CTGCAACTTCAGAGAGATAAGATCTGTGATTTCAATCCGCTCCA
*
39582984 CTGCAACTTCAGGGAGATA
1 CTGCAACTTCAGAGAGATA
39583003 GGATTACCGG
Statistics
Matches: 119, Mismatches: 18, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
40 22 0.18
41 11 0.09
42 2 0.02
43 11 0.09
44 68 0.57
45 3 0.03
46 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (44 bp):
CTGCAACTTCAGAGAGATAAGATCTGTGATTTCAATCCGCTCCA
Found at i:39583006 original size:128 final size:129
Alignment explanation
Indices: 39582762--39583029 Score: 439
Period size: 128 Copynumber: 2.1 Consensus size: 129
39582752 GCTATCTTAG
* *
39582762 TCTGCTCCACTGCAATCTTCAGGGAAATAAGACTAGATACGATTTGCTCTCTGCAACTTCAGAGA
1 TCTGCTCCACTGCAATCTTCAGGGAAATAAGACTAGATACAATCTGCTCTCTGCAACTTCAGAGA
*
39582827 GATAAGATCTGTGATTTCAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTACCGGTTTTAA
66 GATAAGATCTGTGATTTCAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTACCGGCTTTAA
* * * *
39582891 TCTGCTCCACTGCAA-CTTCAGGGAGATAAGATTAGATGCAATCTGCTCTCTGCAATTTCAGAGA
1 TCTGCTCCACTGCAATCTTCAGGGAAATAAGACTAGATACAATCTGCTCTCTGCAACTTCAGAGA
* *
39582955 GATAAGATCTGTGATTTCAATCCGCTCTACTGCAACTTCAGGGAGATAGGATTACCGGCTTTAA
66 GATAAGATCTGTGATTTCAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTACCGGCTTTAA
*
39583019 TATGCTCCACT
1 TCTGCTCCACT
39583030 TCAGGGAGAT
Statistics
Matches: 129, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
128 114 0.88
129 15 0.12
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (129 bp):
TCTGCTCCACTGCAATCTTCAGGGAAATAAGACTAGATACAATCTGCTCTCTGCAACTTCAGAGA
GATAAGATCTGTGATTTCAATCCGCTCCACTGCAACTTCAGGAAGATAGGATTACCGGCTTTAA
Done.