Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 55 of 138
Found at i:11383927 original size:35 final size:35
Alignment explanation
Indices: 11383846--11383928 Score: 123
Period size: 34 Copynumber: 2.4 Consensus size: 35
11383836 CCACAAGCCA
** * *
11383846 AAAATAAAGATGATTGGGATGAAGTTGCAAGTTAG
1 AAAATAAAGATGATTGGGATGAAACTACAAATTAG
11383881 -AAATAAAGATGATTGGGATGAAACTACAAATTAG
1 AAAATAAAGATGATTGGGATGAAACTACAAATTAG
11383915 AAAATAAAGATGAT
1 AAAATAAAGATGAT
11383929 CGGTGTCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 30 0.70
35 13 0.30
ACGTcount: A:0.49, C:0.04, G:0.23, T:0.24
Consensus pattern (35 bp):
AAAATAAAGATGATTGGGATGAAACTACAAATTAG
Found at i:11384662 original size:4 final size:4
Alignment explanation
Indices: 11384649--11384713 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
11384639 ATATTTATAA
* *
11384649 AAAT -AAT AAAT AAAT AATT AAGT AAAT AAAT AAAT AAATT AAA- AAATT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAA-T
* *
11384697 AAAA AAAT AAAA AAAT A
1 AAAT AAAT AAAT AAAT A
11384714 CTTGAAATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
3 6 0.12
4 37 0.74
5 7 0.14
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:11384677 original size:29 final size:29
Alignment explanation
Indices: 11384645--11384713 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
11384635 ATGTATATTT
* **
11384645 ATAAAAATAATAAA-TAAATAATTAAGTAA
1 ATAAAAA-AATAAATTAAAAAATTAAAAAA
*
11384674 ATAAATAAATAAATTAAAAAATTAAAAAA
1 ATAAAAAAATAAATTAAAAAATTAAAAAA
11384703 ATAAAAAAATA
1 ATAAAAAAATA
11384714 CTTGAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
28 6 0.18
29 28 0.82
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (29 bp):
ATAAAAAAATAAATTAAAAAATTAAAAAA
Found at i:11386113 original size:23 final size:22
Alignment explanation
Indices: 11386087--11386169 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 22
11386077 AAAAACTTAG
11386087 AGATTCACATCGAAAAATTTCAA
1 AGATTCACATC-AAAAATTTCAA
11386110 AGATTCACATTCAAAAACTTT-AA
1 AGATTCACA-TCAAAAA-TTTCAA
*
11386133 TA-TTTCACAATC-AAAATTTCAA
1 -AGATTCAC-ATCAAAAATTTCAA
*
11386155 AGATTCTCATCAAAA
1 AGATTCACATCAAAA
11386170 GGATTTTGGG
Statistics
Matches: 50, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
21 7 0.14
22 13 0.26
23 23 0.46
24 7 0.14
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.30
Consensus pattern (22 bp):
AGATTCACATCAAAAATTTCAA
Found at i:11386195 original size:45 final size:44
Alignment explanation
Indices: 11386006--11386310 Score: 211
Period size: 45 Copynumber: 6.6 Consensus size: 44
11385996 AGGTTCATAG
* * *
11386006 CCAAAATTCAAAGATTCTCAGTCGAAAAAAATTTTAGGGTTTCACATT
1 CCAAATTTCAAAGATTCTCATTC--AAAAAATTTT-GGGATTCACA-T
* ** * * * * *
11386054 CAAAAGGT-AAAGATTTTTATTCAAAAAACTTAGAGATTCACAT
1 CCAAATTTCAAAGATTCTCATTCAAAAAATTTTGGGATTCACAT
* * * ***
11386097 CGAAAAATTTCAAAGATTCACATTC-AAAAACTTTAATATTTCACAAT
1 C--CAAATTTCAAAGATTCTCATTCAAAAAATTTTGGGA-TTCAC-AT
* * *
11386144 CAAAATTTCAAAGATTCTCA-TCAAAAGGATTTTGGGATTCTCAT
1 CCAAATTTCAAAGATTCTCATTCAAAA-AATTTTGGGATTCACAT
*
11386188 CCGAAATTTCAAAGATTCTTATTCAAAAAATTTTGGGATTCACAT
1 CC-AAATTTCAAAGATTCTCATTCAAAAAATTTTGGGATTCACAT
* * *
11386233 CCAACATTTCAAAGATTCTCATTCAAAAAAAAAAATTATGGGATTTATAT
1 CCAA-ATTTCAAAGATTCTCATTC-----AAAAAATTTTGGGATTCACAT
*
11386283 CCAAAATTTCAAAGATTCTTATTCAAAA
1 CC-AAATTTCAAAGATTCTCATTCAAAA
11386311 GGTTTTTTTA
Statistics
Matches: 207, Mismatches: 34, Indels: 35
0.75 0.12 0.13
Matches are distributed among these distances:
43 2 0.01
44 15 0.07
45 104 0.50
46 27 0.13
47 14 0.07
48 5 0.02
50 38 0.18
51 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (44 bp):
CCAAATTTCAAAGATTCTCATTCAAAAAATTTTGGGATTCACAT
Found at i:11386292 original size:50 final size:50
Alignment explanation
Indices: 11386176--11386310 Score: 163
Period size: 50 Copynumber: 2.8 Consensus size: 50
11386166 AAAAGGATTT
* * * *
11386176 TGGGATTCTCATCCGAAATTTCAAAGATTCTTATTC-----AAAAAATTT
1 TGGGATTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAAAAAAATTA
*
11386221 TGGGATTCACATCCAACATTTCAAAGATTCTCATTCAAAAAAAAAAATTA
1 TGGGATTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAAAAAAATTA
* * *
11386271 TGGGATTTATATCCAAAATTTCAAAGATTCTTATTCAAAA
1 TGGGATTCACATCCAAAATTTCAAAGATTCTCATTCAAAA
11386311 GGTTTTTTTA
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
45 32 0.42
50 44 0.58
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.34
Consensus pattern (50 bp):
TGGGATTCACATCCAAAATTTCAAAGATTCTCATTCAAAAAAAAAAATTA
Found at i:11387673 original size:11 final size:11
Alignment explanation
Indices: 11387649--11387682 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
11387639 ATTTGCTTTC
11387649 TTTCTTTGTTTT
1 TTTCTTT-TTTT
11387661 TTTCTTTTTTT
1 TTTCTTTTTTT
11387672 TTTCTTTTTTT
1 TTTCTTTTTTT
11387683 CCTTTTCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:11390654 original size:16 final size:16
Alignment explanation
Indices: 11390633--11390669 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
11390623 AAAAAATTAT
* *
11390633 ATATATACAAAGAATA
1 ATATATACAAAAAACA
11390649 ATATATACAAAAAACA
1 ATATATACAAAAAACA
11390665 ATATA
1 ATATA
11390670 AAAGGTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.65, C:0.08, G:0.03, T:0.24
Consensus pattern (16 bp):
ATATATACAAAAAACA
Found at i:11391920 original size:18 final size:18
Alignment explanation
Indices: 11391899--11391955 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
11391889 TTATTTAAAC
11391899 ATAAAAATATATTAAA-AA
1 ATAAAAATATA-TAAATAA
*
11391917 ATAATAATATATAAATAA
1 ATAAAAATATATAAATAA
*
11391935 ATAAGTAAATAAATAAATAA
1 ATAA--AAATATATAAATAA
11391955 A
1 A
11391956 ATAGTTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 4 0.12
18 16 0.48
20 13 0.39
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
ATAAAAATATATAAATAA
Found at i:11391936 original size:4 final size:4
Alignment explanation
Indices: 11391911--11391955 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
11391901 AAAAATATAT
* *
11391911 TAAA -AAA T-AA T-AA TATA TAAA TAAA TAAG TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
11391956 ATAGTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
3 9 0.26
4 26 0.74
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (4 bp):
TAAA
Found at i:11391988 original size:24 final size:25
Alignment explanation
Indices: 11391942--11391989 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
11391932 TAAATAAGTA
* **
11391942 AATAAATAAATAAAATAGTTAAAAG
1 AATAAATAAAGAAAATACCTAAAAG
11391967 AATAAA-AAAGAAAATACCTAAAA
1 AATAAATAAAGAAAATACCTAAAA
11391990 TCAACTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.71, C:0.04, G:0.06, T:0.19
Consensus pattern (25 bp):
AATAAATAAAGAAAATACCTAAAAG
Found at i:11392669 original size:136 final size:137
Alignment explanation
Indices: 11392519--11392803 Score: 319
Period size: 136 Copynumber: 2.1 Consensus size: 137
11392509 TACAATCGAA
* *
11392519 ATGAAGTCACAAGTCAAGAATAAGAATGAATAGGAAAAAATCATAAACCAAAAATAAAGATGACC
1 ATGAAGTCACAAGTCAAGAACAAGAATGAACAGGAAAAAATCATAAACCAAAAATAAAGATGACC
* * * * *
11392584 AGGTA-GAAGCTGCAAGT-AAAAAATAGAGATGA-TTGAGA-CAAGCCGTAAATCAAAAAATAAA
66 ACG-ACAAAGCTACAAGTAAAAAAAAAGAGATGACTAG-GATCAAGCCGTAAAT-AAAAAATAAA
11392645 GATGACC-GAG
128 GATGACCAG-G
* * * * * * * *
11392655 ATGAAGTCACAAGTCAAGAACAAGGATGACCATGATAAAATCGTAAGCCAGAAATAAATATGACC
1 ATGAAGTCACAAGTCAAGAACAAGAATGAACAGGAAAAAATCATAAACCAAAAATAAAGATGACC
* * * *
11392720 ACGACAAAGCTACAAGTAAAAAAAAAGAGATGACTAGGATGAAGCCGTAAGTTAGAAATAAAGAT
66 ACGACAAAGCTACAAGTAAAAAAAAAGAGATGACTAGGATCAAGCCGTAAATAAAAAATAAAGAT
*
11392785 GATCAGG
131 GACCAGG
11392792 ATGAAGTCACAA
1 ATGAAGTCACAA
11392804 ATTGGAAAAT
Statistics
Matches: 124, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
135 1 0.01
136 67 0.54
137 43 0.35
138 13 0.10
ACGTcount: A:0.51, C:0.13, G:0.20, T:0.16
Consensus pattern (137 bp):
ATGAAGTCACAAGTCAAGAACAAGAATGAACAGGAAAAAATCATAAACCAAAAATAAAGATGACC
ACGACAAAGCTACAAGTAAAAAAAAAGAGATGACTAGGATCAAGCCGTAAATAAAAAATAAAGAT
GACCAGG
Found at i:11392820 original size:69 final size:67
Alignment explanation
Indices: 11392737--11392977 Score: 189
Period size: 69 Copynumber: 3.5 Consensus size: 67
11392727 AGCTACAAGT
* * * *
11392737 AAAAAAAAAGAGATGACTAGGATGAAGCCGTAAGTTAGAAATAAAGATGATCAGGATGAAGTCAC
1 AAAAAATAA-AGATGACTAGGATGAAGCCATAAGTTA-AAATAAAGATGATC-GGACGAAGCCAC
*
11392802 AAATT
63 AAATC
** * * * * * * * *
11392807 GGAAAATAAAGATGACCT-GAATGATGCCACAAGTCAAGAACAAGGATGATCGGGACAAAACCAC
1 AAAAAATAAAGATGA-CTAGGATGAAGCCATAAGTTAA-AATAAAGATGATC-GGACGAAGCCAC
*
11392871 -AAGC
63 AAATC
* * * ** *
11392875 CAAAAACAAAGATGACTATGATGAAATCGTAAGTTAAAAATAAAGATGATCGAGACGAAGCCACA
1 AAAAAATAAAGATGACTAGGATGAAGCCATAAGTT-AAAATAAAGATGATCG-GACGAAGCCACA
11392940 AATC
64 AATC
*
11392944 AAAAAATAAAGATGACTAGGACGAAGCCATAAGT
1 AAAAAATAAAGATGACTAGGATGAAGCCATAAGT
11392978 CAAGAACAAG
Statistics
Matches: 125, Mismatches: 40, Indels: 13
0.70 0.22 0.07
Matches are distributed among these distances:
67 3 0.02
68 44 0.35
69 70 0.56
70 8 0.06
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.16
Consensus pattern (67 bp):
AAAAAATAAAGATGACTAGGATGAAGCCATAAGTTAAAATAAAGATGATCGGACGAAGCCACAAA
TC
Found at i:11392880 original size:137 final size:137
Alignment explanation
Indices: 11392738--11392992 Score: 334
Period size: 137 Copynumber: 1.9 Consensus size: 137
11392728 GCTACAAGTA
* * * * *
11392738 AAAAAAAAGAGATGACTAGGATGAAGCCGTAAGTTAGAAATAAAGATGATC-AGGATGAAGTCAC
1 AAAAACAA-AGATGACTAGGATGAAACCGTAAGTTAAAAATAAAGATGATCGA-GACGAAGCCAC
*** * * *
11392802 AAATTGGAAAATAAAGATGACCT-GAATGATGCCACAAGTCAAGAACAAGGATGATCGGGACAAA
64 AAATCAAAAAATAAAGATGA-CTAGAACGAAGCCACAAGTCAAGAACAAGAATGATCGGGACAAA
11392866 ACCACAAGCC
128 ACCACAAGCC
* *
11392876 AAAAACAAAGATGACTATGATGAAATCGTAAGTTAAAAATAAAGATGATCGAGACGAAGCCACAA
1 AAAAACAAAGATGACTAGGATGAAACCGTAAGTTAAAAATAAAGATGATCGAGACGAAGCCACAA
* *
11392941 ATCAAAAAATAAAGATGACTAGGACGAAGCCATAAGTCAAGAACAAGAATGA
66 ATCAAAAAATAAAGATGACTAGAACGAAGCCACAAGTCAAGAACAAGAATGA
11392993 CTGGAATAAA
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
136 2 0.02
137 90 0.90
138 8 0.08
ACGTcount: A:0.50, C:0.14, G:0.21, T:0.15
Consensus pattern (137 bp):
AAAAACAAAGATGACTAGGATGAAACCGTAAGTTAAAAATAAAGATGATCGAGACGAAGCCACAA
ATCAAAAAATAAAGATGACTAGAACGAAGCCACAAGTCAAGAACAAGAATGATCGGGACAAAACC
ACAAGCC
Found at i:11393126 original size:35 final size:35
Alignment explanation
Indices: 11393079--11393159 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
11393069 AAGTTGCAAG
* *
11393079 TAAAAGAA-AAAGATAACTGAGAAGAAG-CTACAAA
1 TAAAAAAATAAAGATAACTAAGAAGAAGTC-ACAAA
**
11393113 TAAAAAAATAAAGATGGCTAAGAAGAAGTCACAAA
1 TAAAAAAATAAAGATAACTAAGAAGAAGTCACAAA
*
11393148 TCAAAAAATAAA
1 TAAAAAAATAAA
11393160 TATGATCAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
34 7 0.17
35 32 0.80
36 1 0.03
ACGTcount: A:0.63, C:0.09, G:0.15, T:0.14
Consensus pattern (35 bp):
TAAAAAAATAAAGATAACTAAGAAGAAGTCACAAA
Found at i:11393181 original size:35 final size:35
Alignment explanation
Indices: 11393098--11393186 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
11393088 AAGATAACTG
* *
11393098 AGAAGAAGCTACAAATAAAAAAATAAAGATGGCTA
1 AGAAGAAGCCACAAATCAAAAAATAAAGATGGCTA
* * *
11393133 AGAAGAAGTCACAAATCAAAAAATAAATAT-GATCA
1 AGAAGAAGCCACAAATCAAAAAATAAAGATGGCT-A
* *
11393168 AGATGAAGCCACAAGTCAA
1 AGAAGAAGCCACAAATCAA
11393187 GAACAATGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
34 2 0.04
35 43 0.96
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.15
Consensus pattern (35 bp):
AGAAGAAGCCACAAATCAAAAAATAAAGATGGCTA
Found at i:11394183 original size:18 final size:18
Alignment explanation
Indices: 11394162--11394200 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
11394152 TTTTCATTCA
11394162 TTTTTT-TCATTTTTTTCT
1 TTTTTTGTCA-TTTTTTCT
*
11394180 TTTTTTGTGATTTTTTCT
1 TTTTTTGTCATTTTTTCT
11394198 TTT
1 TTT
11394201 GTCTCTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.05, C:0.08, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTTTGTCATTTTTTCT
Found at i:11404753 original size:3 final size:3
Alignment explanation
Indices: 11404747--11404778 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11404737 TTGTTGTTAT
11404747 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
11404779 TTATTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:11404783 original size:3 final size:3
Alignment explanation
Indices: 11404777--11404806 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
11404767 CTACTACTAC
11404777 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11404807 AAAAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11405297 original size:29 final size:28
Alignment explanation
Indices: 11405243--11405300 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
11405233 TTTAATTACC
11405243 TTAATTTTTCTTTAAAAACATATTTTTA
1 TTAATTTTTCTTTAAAAACATATTTTTA
11405271 TTAATTTTTCTTTAAAAACATATTTTTA
1 TTAATTTTTCTTTAAAAACATATTTTTA
11405299 TT
1 TT
11405301 TTTAGTAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (28 bp):
TTAATTTTTCTTTAAAAACATATTTTTA
Found at i:11406285 original size:13 final size:13
Alignment explanation
Indices: 11406264--11406297 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
11406254 TCTTTTCTTA
*
11406264 TTTAATTTAATTC
1 TTTATTTTAATTC
11406277 TTTATTTTAATTC
1 TTTATTTTAATTC
11406290 TTTATTTT
1 TTTATTTT
11406298 TTATTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTTAATTC
Found at i:11407439 original size:16 final size:16
Alignment explanation
Indices: 11407408--11407441 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
11407398 AGATGATCCT
11407408 AAGCTTTCGCACAAAC
1 AAGCTTTCGCACAAAC
11407424 AAGCATTTCGCA-AAAC
1 AAGC-TTTCGCACAAAC
11407440 AA
1 AA
11407442 TAATAGTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18
Consensus pattern (16 bp):
AAGCTTTCGCACAAAC
Found at i:11408428 original size:19 final size:19
Alignment explanation
Indices: 11408404--11408446 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
11408394 TTTTATTTAG
*
11408404 GGTTTAGGATTTCACTTAA
1 GGTTTAGGATTACACTTAA
*
11408423 GGTTTAGGGTTACACTTAA
1 GGTTTAGGATTACACTTAA
*
11408442 TGTTT
1 GGTTT
11408447 CATTTTAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44
Consensus pattern (19 bp):
GGTTTAGGATTACACTTAA
Found at i:11410099 original size:19 final size:20
Alignment explanation
Indices: 11410075--11410112 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11410065 GTTCTGTCCA
11410075 TTTTTCCTTGCTT-TTTTCT
1 TTTTTCCTTGCTTCTTTTCT
*
11410094 TTTTTCTTTGCTTCTTTTC
1 TTTTTCCTTGCTTCTTTTC
11410113 CGTTTGGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTTCCTTGCTTCTTTTCT
Found at i:11410837 original size:8 final size:8
Alignment explanation
Indices: 11410824--11410889 Score: 54
Period size: 8 Copynumber: 8.9 Consensus size: 8
11410814 CCTTTACATT
11410824 TTTTATTA
1 TTTTATTA
11410832 TTTTATTA
1 TTTTATTA
11410840 TTTTA--A
1 TTTTATTA
11410846 TTTTATT-
1 TTTTATTA
*
11410853 GTTTATT-
1 TTTTATTA
11410860 TTATT-TT-
1 TT-TTATTA
*
11410867 TTTTAATA
1 TTTTATTA
*
11410875 TTTTAATA
1 TTTTATTA
11410883 TTTTATT
1 TTTTATT
11410890 TTTGTATGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
6 8 0.16
7 12 0.24
8 29 0.59
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (8 bp):
TTTTATTA
Found at i:11410842 original size:18 final size:18
Alignment explanation
Indices: 11410821--11410886 Score: 50
Period size: 18 Copynumber: 3.7 Consensus size: 18
11410811 TTTCCTTTAC
11410821 ATTTT-TTATTATTTTATT
1 ATTTTATTATT-TTTTATT
*
11410839 ATTTTA--ATTTTATTGTTT
1 ATTTTATTATTTT-TT-ATT
*
11410857 ATTTTATT-TTTTTTAAT
1 ATTTTATTATTTTTTATT
*
11410874 ATTTTAATATTTT
1 ATTTTATTATTTT
11410887 ATTTTTGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 2 0.05
17 13 0.34
18 19 0.50
19 4 0.11
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
ATTTTATTATTTTTTATT
Found at i:11410843 original size:17 final size:17
Alignment explanation
Indices: 11410824--11410886 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 17
11410814 CCTTTACATT
11410824 TTTTATTA-TTTTATTA
1 TTTTATTATTTTTATTA
11410840 TTTTAATT-TTATTGT-TTA
1 TTTT-ATTATT-TT-TATTA
* *
11410858 TTTTATTTTTTTTAATA
1 TTTTATTATTTTTATTA
*
11410875 TTTTAATATTTT
1 TTTTATTATTTT
11410887 ATTTTTGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.13
17 21 0.55
18 11 0.29
19 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTTATTATTTTTATTA
Found at i:11411396 original size:26 final size:26
Alignment explanation
Indices: 11411367--11411424 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
11411357 TTAAGAAATT
*
11411367 TTTTTTGTTTT-TTTTAGTATTTTTTA
1 TTTTTTCTTTTGTTTTAGT-TTTTTTA
*
11411393 TTTTTTCTTTTGTTTTTGTTTTTTTA
1 TTTTTTCTTTTGTTTTAGTTTTTTTA
11411419 TTTTTT
1 TTTTTT
11411425 TTTCCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 23 0.79
27 6 0.21
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.84
Consensus pattern (26 bp):
TTTTTTCTTTTGTTTTAGTTTTTTTA
Found at i:11411396 original size:27 final size:25
Alignment explanation
Indices: 11411364--11411427 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 25
11411354 TTCTTAAGAA
*
11411364 ATTTTTTTTGTTTTTTTTAGTATTTTTT
1 ATTTTTTTT-TTGTTTTT-GT-TTTTTT
11411392 ATTTTTTCTTTTGTTTTTGTTTTTTT
1 ATTTTTT-TTTTGTTTTTGTTTTTTT
11411418 ATTTTTTTTT
1 ATTTTTTTTT
11411428 CCTAAAACGA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
25 3 0.09
26 13 0.38
27 2 0.06
28 14 0.41
29 2 0.06
ACGTcount: A:0.08, C:0.02, G:0.06, T:0.84
Consensus pattern (25 bp):
ATTTTTTTTTTGTTTTTGTTTTTTT
Found at i:11411618 original size:32 final size:32
Alignment explanation
Indices: 11411577--11411660 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
11411567 TAGGTTTATA
* *
11411577 TGCCAATTAAACTAGACTTAAATTTTCATAGG
1 TGCCAATTAATCTAGGCTTAAATTTTCATAGG
11411609 TGCCAATTAATCTAGGCTTAAATTTTCATAGG
1 TGCCAATTAATCTAGGCTTAAATTTTCATAGG
*
11411641 TGTCAATTAATCTAGGCTTA
1 TGCCAATTAATCTAGGCTTA
11411661 CATGCCAGCT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (32 bp):
TGCCAATTAATCTAGGCTTAAATTTTCATAGG
Found at i:11411751 original size:33 final size:32
Alignment explanation
Indices: 11411663--11412019 Score: 213
Period size: 33 Copynumber: 11.0 Consensus size: 32
11411653 TAGGCTTACA
* *
11411663 TGCCAGCTAAA-T-TGCTTAAATTTTCATGGG
1 TGCCAGCTAAACTAGGCTTAAATTTTCATTGG
* * *
11411693 TGCCAGCTAAACTAAGTTTAAATTTTTATTGG
1 TGCCAGCTAAACTAGGCTTAAATTTTCATTGG
* *
11411725 TGCCAGTTAAACTAGGCTTTAAATTTTTATTGGG
1 TGCCAGCTAAACTAGGC-TTAAATTTTCATT-GG
* * ** *
11411759 TGCTAGATAATTTAAGCTTAAATTTTCATTGGG
1 TGCCAGCTAAACTAGGCTTAAATTTTCATT-GG
* * * *
11411792 TGTCTA-CTAAATTAGGCTTAAATTTTTATAGGG
1 TG-CCAGCTAAACTAGGCTTAAATTTTCAT-TGG
* *
11411825 TACCAGCTAAACTAGGCTTAAATTTTCATTGAA
1 TGCCAGCTAAACTAGGCTTAAATTTTCATTG-G
* * * * * *
11411858 TGCTAACTAGAC-CGCACTTAAAATTTT-GTTGAG
1 TGCCAGCTAAACTAG-GCTT-AAATTTTCATTG-G
* * * *
11411891 TGCTAGCTAAACTAGGCTGAAAGTTTCTTTGG
1 TGCCAGCTAAACTAGGCTTAAATTTTCATTGG
** * * *
11411923 TGCCAAATAATCTGGGCTTAAATTTTTCATTGA
1 TGCCAGCTAAACTAGGCTTAAA-TTTTCATTGG
* * * *
11411956 TGTCAACTAATCTAGGCTTAAATTTTCATTAGA
1 TGCCAGCTAAACTAGGCTTAAATTTTCATT-GG
** *
11411989 TGCTTGTTAAACTAGGCTTAAA-TTTCATTGG
1 TGCCAGCTAAACTAGGCTTAAATTTTCATTGG
11412020 GCGTTAGCTA
Statistics
Matches: 255, Mismatches: 58, Indels: 27
0.75 0.17 0.08
Matches are distributed among these distances:
30 11 0.04
31 2 0.01
32 70 0.27
33 147 0.58
34 25 0.10
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (32 bp):
TGCCAGCTAAACTAGGCTTAAATTTTCATTGG
Found at i:11411846 original size:99 final size:98
Alignment explanation
Indices: 11411676--11411855 Score: 247
Period size: 99 Copynumber: 1.8 Consensus size: 98
11411666 CAGCTAAATT
* * * *
11411676 GCTTAAATTTTCATGGGTGCCAGCTAAACTAAGTTTAAATTTTTATTGGTGCCAGTTAAACTAGG
1 GCTTAAATTTTCATGGGTGCCAGCTAAACTAAGCTTAAATTTTTATGGGTACCAGCTAAACTAGG
*
11411741 CTTTAAATTTTTATTGGGTGCTAGATAATTTAA
66 CTTTAAATTTTCATTGGGTGCTAGATAATTTAA
* * *
11411774 GCTTAAATTTTCATTGGGTGTCTA-CTAAATTAGGCTTAAATTTTTATAGGGTACCAGCTAAACT
1 GCTTAAATTTTCA-TGGGTG-CCAGCTAAACTAAGCTTAAATTTTTAT-GGGTACCAGCTAAACT
11411838 AGGC-TTAAATTTTCATTG
63 AGGCTTTAAATTTTCATTG
11411856 AATGCTAACT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
98 13 0.18
99 39 0.55
100 19 0.27
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (98 bp):
GCTTAAATTTTCATGGGTGCCAGCTAAACTAAGCTTAAATTTTTATGGGTACCAGCTAAACTAGG
CTTTAAATTTTCATTGGGTGCTAGATAATTTAA
Found at i:11412250 original size:22 final size:22
Alignment explanation
Indices: 11412213--11412255 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11412203 CTTTACGTGT
*
11412213 CAGCTAATATGAACTTGTGTGC
1 CAGCTAATATGAACTTATGTGC
* *
11412235 CAGCTAATTTGGACTTATGTG
1 CAGCTAATATGAACTTATGTG
11412256 AAAAAGCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (22 bp):
CAGCTAATATGAACTTATGTGC
Found at i:11412799 original size:137 final size:138
Alignment explanation
Indices: 11412622--11412897 Score: 511
Period size: 137 Copynumber: 2.0 Consensus size: 138
11412612 GGGTTTCTCC
11412622 ACCTAAAGAGGATAAAAAGGTTTATAGTTTTTCATACAAGCTTATAGATGAAACAT-ATTTTTTT
1 ACCTAAAGAGGATAAAAAGGTTTATAGTTTTTCATACAAGCTTATAGATGAAACATAATTTTTTT
*
11412686 TAAAAACTATGAATCCTTTGAAAACTAAATATATTCAACAC-TTTCTTTAGTCTCCAAATGTGAT
66 T-AAAACTATGAATCCTTTGAAAACTAAACATATTCAACACTTTTCTTTAGTCTCCAAATGTGAT
11412750 ATTTTGATA
130 ATTTTGATA
*
11412759 ACCTAAAGGGGATAAAAAGGTTTATAGTTTTTCATACAAGCTTATAGATGAAACATAATTTTTTT
1 ACCTAAAGAGGATAAAAAGGTTTATAGTTTTTCATACAAGCTTATAGATGAAACATAATTTTTTT
11412824 TAAAACTATGAATCCTTTGAAAACTAAACATATTCAACACTTTTCTTTAGTCTCCAAATGTGATA
66 TAAAACTATGAATCCTTTGAAAACTAAACATATTCAACACTTTTCTTTAGTCTCCAAATGTGATA
11412889 TTTTGATA
131 TTTTGATA
11412897 A
1 A
11412898 ATGTCAAAGT
Statistics
Matches: 135, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
137 93 0.69
138 42 0.31
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (138 bp):
ACCTAAAGAGGATAAAAAGGTTTATAGTTTTTCATACAAGCTTATAGATGAAACATAATTTTTTT
TAAAACTATGAATCCTTTGAAAACTAAACATATTCAACACTTTTCTTTAGTCTCCAAATGTGATA
TTTTGATA
Found at i:11413509 original size:17 final size:18
Alignment explanation
Indices: 11413487--11413535 Score: 73
Period size: 17 Copynumber: 2.8 Consensus size: 18
11413477 CACCCATTCA
*
11413487 TTTTTTTTTTCTTTC-TT
1 TTTTTTTTTTCTTTCACT
11413504 TTTTTTTTTTCTTTCACT
1 TTTTTTTTTTCTTTCACT
*
11413522 TTTTCTTTTTCTTT
1 TTTTTTTTTTCTTT
11413536 TTCTCTTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTCTTTCACT
Found at i:11413529 original size:6 final size:6
Alignment explanation
Indices: 11413487--11413539 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
11413477 CACCCATTCA
**
11413487 TTTTT- TTTTTC TTTCTT- TTTTT- TTTTTC TTTCAC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTT-TTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
11413533 TTTTTC T
1 TTTTTC T
11413540 CTTTACCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
5 12 0.29
6 27 0.66
7 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:11413542 original size:26 final size:25
Alignment explanation
Indices: 11413498--11413558 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 25
11413488 TTTTTTTTTC
*
11413498 TTTCTTTTTTTTTTTTCTTT-CACTT
1 TTTCTTTTTTTTTTCTCTTTAC-CTT
11413523 TTTCTTTTTCTTTTTCTCTTTACCTT
1 TTTCTTTTT-TTTTTCTCTTTACCTT
11413549 TTT-TTTTTTT
1 TTTCTTTTTTT
11413559 CATTCTTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 2 0.06
25 14 0.42
26 16 0.48
27 1 0.03
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (25 bp):
TTTCTTTTTTTTTTCTCTTTACCTT
Found at i:11413575 original size:26 final size:24
Alignment explanation
Indices: 11413496--11413576 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 24
11413486 ATTTTTTTTT
*
11413496 TCTTTCTTTTTTTTTTTTCTTTCAC
1 TCTTT-TTTTTTTTTCTTCTTTCAC
*
11413521 T-TTTTCTTTTTCTTT-TTCTCTTTAC
1 TCTTTT-TTTTT-TTTCTTCT-TTCAC
11413546 -CTTTTTTTTTTTTCATTCTTTCAC
1 TCTTTTTTTTTTTTC-TTCTTTCAC
11413570 TACTTTT
1 T-CTTTT
11413577 CTTCCTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
23 4 0.09
24 21 0.46
25 16 0.35
26 5 0.11
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (24 bp):
TCTTTTTTTTTTTTCTTCTTTCAC
Found at i:11414078 original size:13 final size:13
Alignment explanation
Indices: 11414057--11414092 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
11414047 TTTCTTTGTC
*
11414057 CTTTCTTTTTTCT
1 CTTTTTTTTTTCT
11414070 CTTTTTTTTTTCT
1 CTTTTTTTTTTCT
11414083 -TTTTTTTTTT
1 CTTTTTTTTTT
11414093 ACATATCCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
CTTTTTTTTTTCT
Found at i:11414090 original size:11 final size:11
Alignment explanation
Indices: 11414057--11414091 Score: 52
Period size: 11 Copynumber: 3.0 Consensus size: 11
11414047 TTTCTTTGTC
11414057 CTTTCTTTTTTCT
1 CTTT-TTTTTT-T
11414070 CTTTTTTTTTT
1 CTTTTTTTTTT
11414081 CTTTTTTTTTT
1 CTTTTTTTTTT
11414092 TACATATCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.55
12 6 0.27
13 4 0.18
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:11418129 original size:25 final size:25
Alignment explanation
Indices: 11418101--11418153 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
11418091 AAACAAATAA
* *
11418101 ATAATAAAAATAACATAACA-ACCAT
1 ATAAT-AAAATAAAATAACAGAACAT
*
11418126 ATAATACAATAAAATAACAGAACAT
1 ATAATAAAATAAAATAACAGAACAT
11418151 ATA
1 ATA
11418154 CAGTGTCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.21
Consensus pattern (25 bp):
ATAATAAAATAAAATAACAGAACAT
Found at i:11427204 original size:27 final size:28
Alignment explanation
Indices: 11427174--11427233 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 28
11427164 ATAGTTAAGT
11427174 TAAAATATAAATAA-TAATTTTAAAAAA-
1 TAAAATATAAATAACTAA-TTTAAAAAAC
*
11427201 TAAAATGTAAATAACTTAATTTAAAAAAC
1 TAAAATATAAATAAC-TAATTTAAAAAAC
11427230 TAAA
1 TAAA
11427234 TTAATCTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 13 0.45
28 9 0.31
29 7 0.24
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (28 bp):
TAAAATATAAATAACTAATTTAAAAAAC
Found at i:11428121 original size:31 final size:31
Alignment explanation
Indices: 11428079--11428140 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
11428069 GTGGACTACA
* * *
11428079 CCTTTTTAAAAAGTAAAATCTTTAATTCAAT
1 CCTTTTCAAAAAGTAAAATCCTCAATTCAAT
11428110 CCTTTTCAAAAAGTAAAATCCTCAATTCAAT
1 CCTTTTCAAAAAGTAAAATCCTCAATTCAAT
11428141 ATTCCGTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (31 bp):
CCTTTTCAAAAAGTAAAATCCTCAATTCAAT
Found at i:11428215 original size:106 final size:105
Alignment explanation
Indices: 11428013--11428215 Score: 300
Period size: 106 Copynumber: 1.9 Consensus size: 105
11428003 CCCCTTTTTG
* * * * *
11428013 AAAAGCAAAATCTTCTATTCAATGTTTCGTGGATCAAAGATCATTTCTTTTTTAAGGTGGACTAC
1 AAAAGCAAAATCCTCAATTCAATATTCCGTGGATCAAAGATCATTTCTTTTTGAAGGTGGACTAC
*
11428078 ACCTTTTTAAAAAGTAAAATCTTTAATTCAATCCTTTTCA
66 ACCTTTTTAAAAAGTAAAATCTTCAATTCAATCCTTTTCA
* *
11428118 AAAAGTAAAATCCTCAATTCAATATTCCGTGGATCAATGATCATTT-TTTTTAAGAAGGTGGACT
1 AAAAGCAAAATCCTCAATTCAATATTCCGTGGATCAAAGATCATTTCTTTTT--GAAGGTGGACT
*
11428182 ACCCCTTTTTAAAAAGTAAAATCTTCAATTCAAT
64 ACACCTTTTTAAAAAGTAAAATCTTCAATTCAAT
11428216 GTTTGATGGA
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
104 5 0.06
105 40 0.46
106 42 0.48
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (105 bp):
AAAAGCAAAATCCTCAATTCAATATTCCGTGGATCAAAGATCATTTCTTTTTGAAGGTGGACTAC
ACCTTTTTAAAAAGTAAAATCTTCAATTCAATCCTTTTCA
Found at i:11428375 original size:16 final size:16
Alignment explanation
Indices: 11428354--11428391 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
11428344 AAAATCTTCA
11428354 ATTCAATGTTCTGTGG
1 ATTCAATGTTCTGTGG
*
11428370 ATTCAATGTTTTGTGG
1 ATTCAATGTTCTGTGG
11428386 A-TCAAT
1 ATTCAAT
11428392 CATGCTCACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.24, C:0.11, G:0.21, T:0.45
Consensus pattern (16 bp):
ATTCAATGTTCTGTGG
Found at i:11428444 original size:145 final size:146
Alignment explanation
Indices: 11428178--11428467 Score: 512
Period size: 145 Copynumber: 2.0 Consensus size: 146
11428168 TAAGAAGGTG
11428178 GACTACCCCTTTTTAAAAAGTAAAATCTTCAATTCAATGTTTGATGGATTCAATGTTTTGTGGAT
1 GACTACCCCTTTTTAAAAAGTAAAATCTTCAATTCAATGTTTGATGGATTCAATGTTTTGTGGAT
* * *
11428243 CAATCGTGCTCACTTGTGAGATCTTAAAGTTAAGATTGGGCCAGAGTCATTAGTCCTGGTTGGTT
66 CAATCATGCTCACTTGTGAGATCTTAAAATTAAGATTGGGCCAGAGTCATTAGTCCTGGGTGGTT
11428308 CGGTGGGAA-CTGCAT
131 CGGTGGGAACCTGCAT
11428323 GACTACCCCTTTTTAAAAAGTAAAATCTTCAATTCAATGTTCTG-TGGATTCAATGTTTTGTGGA
1 GACTACCCCTTTTTAAAAAGTAAAATCTTCAATTCAATGTT-TGATGGATTCAATGTTTTGTGGA
* *
11428387 TCAATCATGCTCACTTGTGAGATTTTAAAATTAAGATTGGGCCAGAGTCATTGGTCCTGGGTGGT
65 TCAATCATGCTCACTTGTGAGATCTTAAAATTAAGATTGGGCCAGAGTCATTAGTCCTGGGTGGT
11428452 TCGGTGGGAACCTGCA
130 TCGGTGGGAACCTGCA
11428468 CCATTGCTTA
Statistics
Matches: 138, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
145 131 0.95
146 7 0.05
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (146 bp):
GACTACCCCTTTTTAAAAAGTAAAATCTTCAATTCAATGTTTGATGGATTCAATGTTTTGTGGAT
CAATCATGCTCACTTGTGAGATCTTAAAATTAAGATTGGGCCAGAGTCATTAGTCCTGGGTGGTT
CGGTGGGAACCTGCAT
Found at i:11429047 original size:20 final size:18
Alignment explanation
Indices: 11429014--11429053 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
11429004 ACAAGATCTC
11429014 AAAATTTATTTTTAATTA
1 AAAATTTATTTTTAATTA
*
11429032 AAAATGTTAGTTTTTATTTA
1 AAAAT-TTA-TTTTTAATTA
11429052 AA
1 AA
11429054 TCCAATCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 3 0.16
20 11 0.58
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (18 bp):
AAAATTTATTTTTAATTA
Found at i:11432150 original size:46 final size:46
Alignment explanation
Indices: 11432100--11432467 Score: 364
Period size: 46 Copynumber: 8.1 Consensus size: 46
11432090 TTTTTTCAAG
* *
11432100 ATAAATTTAAAAACTTTTTTAAGAAAAGGAC-AAACAACTTTTAAAA
1 ATAAATTTAAAAACTCTTTTAAGAAAAGG-CTCAACAACTTTTAAAA
* * * * *
11432146 ATAAATTTAAAAGCTTTTTTAAGAAAAAGCTTAACAACTTTTGAAA
1 ATAAATTTAAAAACTCTTTTAAGAAAAGGCTCAACAACTTTTAAAA
* * * *
11432192 ATAAATTTTAAAGCTCCTTT-AGAAAAATGCTCAACAAC--TTAAAA
1 ATAAATTTAAAAACTCTTTTAAG-AAAAGGCTCAACAACTTTTAAAA
* *
11432236 A-AAA-TTAAAAACTCATTTAGGAAAAGGCTCAACAACTTTTAAAAA
1 ATAAATTTAAAAACTCTTTTAAGAAAAGGCTCAACAACTTTT-AAAA
* * * * * *
11432281 ATATATTTAAAAGCT-TATTTAGATAAAAGACTCAACATCTTTTGAAA
1 ATAAATTTAAAAACTCT-TTTA-AGAAAAGGCTCAACAACTTTTAAAA
* *
11432328 ATAAATTTAAAAACTCTTTTAA-AAAA-ACTCAATAACTTTT-AAA
1 ATAAATTTAAAAACTCTTTTAAGAAAAGGCTCAACAACTTTTAAAA
* * *
11432371 ATAATTTTAAAAACTCTTTTAATAAAAGGCTCAACAACTTTTGAAA
1 ATAAATTTAAAAACTCTTTTAAGAAAAGGCTCAACAACTTTTAAAA
* *
11432417 ATAAATTTAATAACTCCTTTAAGAAAAGGCAT-AACAAC-TTTAAAA
1 ATAAATTTAAAAACTCTTTTAAGAAAAGGC-TCAACAACTTTTAAAA
11432462 ATAAAT
1 ATAAAT
11432468 CCTGAAAAGG
Statistics
Matches: 272, Mismatches: 35, Indels: 31
0.80 0.10 0.09
Matches are distributed among these distances:
42 25 0.09
43 28 0.10
44 24 0.09
45 36 0.13
46 108 0.40
47 33 0.12
48 18 0.07
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.32
Consensus pattern (46 bp):
ATAAATTTAAAAACTCTTTTAAGAAAAGGCTCAACAACTTTTAAAA
Found at i:11432418 original size:89 final size:90
Alignment explanation
Indices: 11432100--11432465 Score: 322
Period size: 89 Copynumber: 4.0 Consensus size: 90
11432090 TTTTTTCAAG
* * * * * * *
11432100 ATAAATTTAAAAACTTTTTTA-AGAAAAGGAC-AAACAACTTTTAAAAATAAATTTAAAAGCTTT
1 ATAATTTTAAAAACTCTTTTAGATAAAAGG-CTCAACAACTTTTGAAAATAAATTTAAAAACTCT
*
11432163 TTTAAGAAAAAGCTTAACAACTTTTGAAA
65 TTTAA-AAAAA-CTCAACAACTTTT-AAA
* * * * *
11432192 ATAAATTTT-AAAGCTCCTTTAGA-AAAATGCTCAACAAC--TT-AAAA-AAAATTAAAAACTCA
1 AT-AATTTTAAAAACTCTTTTAGATAAAAGGCTCAACAACTTTTGAAAATAAATTTAAAAACTCT
**
11432251 TTTAGGAAAAGGCTCAACAACTTTTAAA
65 TTTA--AAAAAACTCAACAACTTTTAAA
* * * *
11432279 AAATATATTTAAAAGCT-TATTTAGATAAAAGACTCAACATCTTTTGAAAATAAATTTAAAAACT
1 ATA-AT-TTTAAAAACTCT-TTTAGATAAAAGGCTCAACAACTTTTGAAAATAAATTTAAAAACT
*
11432343 CTTTTAAAAAAACTCAATAACTTTTAAA
63 CTTTTAAAAAAACTCAACAACTTTTAAA
* *
11432371 ATAATTTTAAAAACTCTTTTA-ATAAAAGGCTCAACAACTTTTGAAAATAAATTTAATAACTCCT
1 ATAATTTTAAAAACTCTTTTAGATAAAAGGCTCAACAACTTTTGAAAATAAATTTAAAAACTCTT
* *
11432435 TTAAGAAAAGGCAT-AACAACTTTAAAA
66 TTAA-AAAA-AC-TCAACAACTTTTAAA
11432462 ATAA
1 ATAA
11432466 ATCCTGAAAA
Statistics
Matches: 224, Mismatches: 32, Indels: 37
0.76 0.11 0.13
Matches are distributed among these distances:
86 1 0.00
87 6 0.03
88 30 0.13
89 62 0.28
90 32 0.14
91 20 0.09
92 46 0.21
93 10 0.04
94 17 0.08
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.32
Consensus pattern (90 bp):
ATAATTTTAAAAACTCTTTTAGATAAAAGGCTCAACAACTTTTGAAAATAAATTTAAAAACTCTT
TTAAAAAAACTCAACAACTTTTAAA
Found at i:11432870 original size:33 final size:32
Alignment explanation
Indices: 11432784--11432870 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
11432774 TTGGTGCCTG
*
11432784 CTAAACTGAGCTTAAATCTCATTCTATTGACAA
1 CTAAACTG-GCTTAAATCTCATTCTAGTGACAA
* * *
11432817 CTAAACTGACTTAAACCTCATTCTAGTGCCAA
1 CTAAACTGGCTTAAATCTCATTCTAGTGACAA
*
11432849 CTAAACTAGGCTTAAGTCTCAT
1 CTAAACT-GGCTTAAATCTCAT
11432871 CTTTTTTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
32 27 0.59
33 19 0.41
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (32 bp):
CTAAACTGGCTTAAATCTCATTCTAGTGACAA
Found at i:11433146 original size:15 final size:17
Alignment explanation
Indices: 11433107--11433150 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 17
11433097 TTTCCCCCTT
11433107 TTTTCT-TTATTTTCAC
1 TTTTCTCTTATTTTCAC
*
11433123 TTTTTTCTTA-TTTCA-
1 TTTTCTCTTATTTTCAC
11433138 TTTTCTCTT-TTTT
1 TTTTCTCTTATTTT
11433151 TTCAAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 11 0.46
16 10 0.42
17 3 0.12
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTCTTATTTTCAC
Found at i:11436108 original size:15 final size:15
Alignment explanation
Indices: 11436063--11436120 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
11436053 CATTTTTTTC
*
11436063 CTTTTATTTTTC-TT
1 CTTTTTTTTTTCTTT
*
11436077 CTTTTCTTTGGTTCTTT
1 CTTTT-TTT-TTTCTTT
11436094 CTTTTTTTTTTCTTT
1 CTTTTTTTTTTCTTT
* *
11436109 CATTTTCTTTTC
1 CTTTTTTTTTTC
11436121 CATTTCTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.14
15 18 0.50
16 6 0.17
17 7 0.19
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.76
Consensus pattern (15 bp):
CTTTTTTTTTTCTTT
Found at i:11445493 original size:19 final size:19
Alignment explanation
Indices: 11445452--11445491 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
11445442 TTGCTTCTAA
*
11445452 TTGTTTTTGTTGGTTGTCT
1 TTGTTTTTGTTGGTTATCT
11445471 TTGTTTTTGTTGTGTTATCT
1 TTGTTTTTGTTG-GTTATCT
11445491 T
1 T
11445492 GTAGATTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.03, C:0.05, G:0.23, T:0.70
Consensus pattern (19 bp):
TTGTTTTTGTTGGTTATCT
Found at i:11445988 original size:13 final size:14
Alignment explanation
Indices: 11445961--11445998 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
11445951 CAAAAAATTA
11445961 AAATAAATCAAAAT
1 AAATAAATCAAAAT
11445975 AAATAAAT-AAAAT
1 AAATAAATCAAAAT
* *
11445988 ATATAATTCAA
1 AAATAAATCAA
11445999 TTTATGTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATAAATCAAAAT
Found at i:11446087 original size:18 final size:19
Alignment explanation
Indices: 11446061--11446102 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
11446051 GTCAATTAAT
* *
11446061 AATTCAAATAT-CCAAAAG
1 AATTTAAATATCCCAAAAA
11446079 AATTTAAATATCCCAAAAA
1 AATTTAAATATCCCAAAAA
11446098 AATTT
1 AATTT
11446103 TATCTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (19 bp):
AATTTAAATATCCCAAAAA
Found at i:11446410 original size:22 final size:22
Alignment explanation
Indices: 11446385--11446426 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
11446375 ACAGCCATGT
*
11446385 AAGTAAAAATGCCACATCAAAA
1 AAGTAAAAATACCACATCAAAA
* *
11446407 AAGTTAAAATACCATATCAA
1 AAGTAAAAATACCACATCAA
11446427 GTTCAGACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.17, G:0.07, T:0.19
Consensus pattern (22 bp):
AAGTAAAAATACCACATCAAAA
Found at i:11448816 original size:14 final size:14
Alignment explanation
Indices: 11448775--11448821 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
11448765 AATTAATCAA
* *
11448775 AAAAATTAAAATAA
1 AAAAATTAAATTAC
11448789 AATAAATT-AATTAC
1 AA-AAATTAAATTAC
11448803 AAAAATTAAATTAC
1 AAAAATTAAATTAC
11448817 AAAAA
1 AAAAA
11448822 AAAAAGCAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 5 0.17
14 19 0.66
15 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATTAAATTAC
Found at i:11454183 original size:66 final size:62
Alignment explanation
Indices: 11454050--11454244 Score: 162
Period size: 66 Copynumber: 3.0 Consensus size: 62
11454040 ACTATTGGCT
* * * *
11454050 TACAAAAAATTTGGAAGGGATTATTGAAGGTGTTTTTTGCCAAAAACACCTTTAATAATAGA
1 TACAAAAAATTTTGAAGGGATTATTAAAGGTGTTTTTTGCCAAAAACACCTTCAATAATACA
* ** *
11454112 TACAAAAAATTTTGAAGGGGATTATTAAAGGCTTTTGTTTTTT-CCATAAATGCCTTCAATAATC
1 TACAAAAAATTTTGAA-GGGATTATTAAAGG----TGTTTTTTGCCAAAAACACCTTCAATAATA
11454176 CA
61 CA
* * * * *
11454178 TACAAAAAATTTTGTTGAAGGGATTA-TATAAGGCG-TTTTTGACAAAAAATACCTTTAATAATC
1 TACAAAAAA--TT-TTGAAGGGATTATTA-AAGGTGTTTTTTG-CCAAAAACACCTTCAATAATA
11454241 CA
61 CA
11454243 TA
1 TA
11454245 AATTATTCAA
Statistics
Matches: 109, Mismatches: 13, Indels: 19
0.77 0.09 0.13
Matches are distributed among these distances:
62 15 0.14
63 18 0.17
64 1 0.01
65 21 0.19
66 26 0.24
67 10 0.09
68 13 0.12
69 5 0.05
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (62 bp):
TACAAAAAATTTTGAAGGGATTATTAAAGGTGTTTTTTGCCAAAAACACCTTCAATAATACA
Found at i:11454569 original size:12 final size:14
Alignment explanation
Indices: 11454540--11454566 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11454530 TTTTTCTATG
11454540 TTCATATAAATATA
1 TTCATATAAATATA
11454554 TTCATATAAATAT
1 TTCATATAAATAT
11454567 TCAATTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TTCATATAAATATA
Found at i:11454904 original size:24 final size:25
Alignment explanation
Indices: 11454863--11454909 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
11454853 TCATATAAGT
*
11454863 TGCCAATTGATATAAAACAAATATA
1 TGCCAATTAATATAAAACAAATATA
* *
11454888 TGCCAA-TAATATTAAACCAATA
1 TGCCAATTAATATAAAACAAATA
11454910 CCTCAATCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (25 bp):
TGCCAATTAATATAAAACAAATATA
Found at i:11458712 original size:171 final size:172
Alignment explanation
Indices: 11458424--11458737 Score: 404
Period size: 171 Copynumber: 1.8 Consensus size: 172
11458414 AAAAAACACG
* * * * * * *
11458424 AATTATTGAAGGCGTTTTTGGCCAAAAATACCTTCAATAACCCCATTCAATATTTTGTTATGGAT
1 AATTATTCAAGGCATTTTTAGCCAAAAACACCTTCAATAACCCCATTCAATATTTTGTAAAGAAT
* *
11458489 TATTCAAAGCATTTTCTAGGCAAAAACACCTTCAATAATATCCTGATAAAAATTGAAAGG-GATT
66 TATTCAAAGCATTTTCTAGGCAAAAACACCTTCAATAATACCCTGATAAAAATT-AAAGGACATT
11458553 ATTCAAGG-ATTTTTTGGCCATAAATGCCTTGAATAATGCACA
130 ATTCAAGGCATTTTTTGGCCATAAATGCCTTGAATAATGCACA
* * * *
11458595 AATTATTCAAGGCATTTTTAGCCACAAACCCCTTCAATAACCCTATTCATTATTTTGTAAAGAAT
1 AATTATTCAAGGCATTTTTAGCCAAAAACACCTTCAATAACCCCATTCAATATTTTGTAAAGAAT
* * *
11458660 TATTCAAGGTATTTTCTA-GCTAAAAACGCCTTCAATAAT-CCCATCG-TAAAAATTAAAGGACA
66 TATTCAAAGCATTTTCTAGGC-AAAAACACCTTCAATAATACCC-T-GATAAAAATTAAAGGACA
*
11458722 TTATTGAAGGCATTTT
128 TTATTCAAGGCATTTT
11458738 ATGGGAAAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
170 9 0.07
171 106 0.88
172 6 0.05
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (172 bp):
AATTATTCAAGGCATTTTTAGCCAAAAACACCTTCAATAACCCCATTCAATATTTTGTAAAGAAT
TATTCAAAGCATTTTCTAGGCAAAAACACCTTCAATAATACCCTGATAAAAATTAAAGGACATTA
TTCAAGGCATTTTTTGGCCATAAATGCCTTGAATAATGCACA
Found at i:11459018 original size:247 final size:246
Alignment explanation
Indices: 11458603--11459118 Score: 690
Period size: 247 Copynumber: 2.1 Consensus size: 246
11458593 CAAATTATTC
* * * * *
11458603 AAGGCATTTTTAGCCACAAACCCCTTCAATAACCCTATTCATTATTTTGTAAAGAATTATTCAAG
1 AAGGCATTTTTGGCCAAAAAACCCTTCAATAACCCCATTCAATATTTTGTAAAGAATTATTCAAG
*
11458668 GTATTTTCTAGCTAAAAACGCCTTCAATAATCCCATCGTAAAAATTAAAGGACATTATTGAAGGC
66 GTATTTTCTAGCTAAAAACGCCTTCAACAATCCCATCGTAAAAATTAAAGGA-ATTATTGAAGGC
* * *
11458733 ATTTTATGGGAAAAAATACCTTGAATATTTG-AAAAAAA-AATGCTGGGATTATTGAAGGTGTTT
130 ATTTTATGAGAAAAAATACCTTGAATATTCGAAAAAAAAGAATGCTGGGATTATTGAAGGTATTT
*
11458796 TTGATAG-AAAATG-CTTTAATAATC-CGCAATGAATGAATAAATCATGGGTTATAT
195 TTGATAGAAAAATGCCTTCAATAATCTC-C----AATGAATAAATCATGGGTTATAT
* *
11458850 AAGGCATTTTTGGCCAAAAAAGCCTTCAATAACCCCATTCAATATTTTGT-AAGAGATTATTGAA
1 AAGGCATTTTTGGCCAAAAAACCCTTCAATAACCCCATTCAATATTTTGTAAAGA-ATTATTCAA
* * * *
11458914 GG-AGTTTTCTGGCTAAAAATGCCTTTAACAATCCCATTGTAAAAATTGAAAGCG-ATTATTGAA
65 GGTA-TTTTCTAGCTAAAAACGCCTTCAACAATCCCATCGTAAAAATT-AAAG-GAATTATTGAA
*
11458977 GGCATTTTCTGAGAAAAAA-ACCTTGAATATTCGTAAAAAAAAAGAATGCTGGGATTATTGAAGG
127 GGCATTTTATGAGAAAAAATACCTTGAATATTCG--AAAAAAAAGAATGCTGGGATTATTGAAGG
* *
11459041 TATTTTTTATAGAAAAATGCCTTCAGTAATCTCCAATGAATAAATCATGGGTTATAT
190 TATTTTTGATAGAAAAATGCCTTCAATAATCTCCAATGAATAAATCATGGGTTATAT
11459098 AAGGCATTTTTGGCCAAAAAA
1 AAGGCATTTTTGGCCAAAAAA
11459119 AATCTTGAAT
Statistics
Matches: 239, Mismatches: 19, Indels: 21
0.86 0.07 0.08
Matches are distributed among these distances:
246 18 0.08
247 118 0.49
248 48 0.20
249 8 0.03
250 30 0.13
251 6 0.03
252 10 0.04
253 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (246 bp):
AAGGCATTTTTGGCCAAAAAACCCTTCAATAACCCCATTCAATATTTTGTAAAGAATTATTCAAG
GTATTTTCTAGCTAAAAACGCCTTCAACAATCCCATCGTAAAAATTAAAGGAATTATTGAAGGCA
TTTTATGAGAAAAAATACCTTGAATATTCGAAAAAAAAGAATGCTGGGATTATTGAAGGTATTTT
TGATAGAAAAATGCCTTCAATAATCTCCAATGAATAAATCATGGGTTATAT
Found at i:11467458 original size:55 final size:55
Alignment explanation
Indices: 11467348--11467473 Score: 162
Period size: 55 Copynumber: 2.3 Consensus size: 55
11467338 TGAAACATAT
* * **
11467348 AAGTCTATACTGACAATCTCTAACCATCGATAAAGGTAAGAAAATTAAAGTATAC
1 AAGTCTATACTGACAGTCTCTAACCATCGATAAAGATAAGAAAATTAAAAAATAC
* * * * *
11467403 AATTTTATACTGACAGTCTCTAACCATTGGTATAGATAAGAAAATTAAAAAATAC
1 AAGTCTATACTGACAGTCTCTAACCATCGATAAAGATAAGAAAATTAAAAAATAC
*
11467458 AAGTCTATACTAACAG
1 AAGTCTATACTGACAG
11467474 ATGCTAAGCA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (55 bp):
AAGTCTATACTGACAGTCTCTAACCATCGATAAAGATAAGAAAATTAAAAAATAC
Found at i:11467491 original size:55 final size:55
Alignment explanation
Indices: 11467348--11467501 Score: 132
Period size: 55 Copynumber: 2.8 Consensus size: 55
11467338 TGAAACATAT
* * * * * * **
11467348 AAGTCTATACTGACAATCTCTAACCA-TCGATAAAGGTAAGAAAATTAAAGTATAC
1 AAGTCTATACTAACAGTCGCTAACCATTAG-TATAGATAAGAAAATTAAAAAATAC
* * * * *
11467403 AATTTTATACTGACAGTCTCTAACCATTGGTATAGATAAGAAAATTAAAAAATAC
1 AAGTCTATACTAACAGTCGCTAACCATTAGTATAGATAAGAAAATTAAAAAATAC
* * *
11467458 AAGTCTATACTAACAGAT-GCTAAGCATTAGTATAGGTAAAAAAA
1 AAGTCTATACTAACAG-TCGCTAACCATTAGTATAGATAAGAAAA
11467502 AATTACAAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
55 78 0.96
56 3 0.04
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (55 bp):
AAGTCTATACTAACAGTCGCTAACCATTAGTATAGATAAGAAAATTAAAAAATAC
Found at i:11468952 original size:16 final size:16
Alignment explanation
Indices: 11468927--11468959 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
11468917 AATTGACTGA
*
11468927 TAAGGTTCAATTTAAT
1 TAAGGCTCAATTTAAT
11468943 TAAGGCTCAATTTAAT
1 TAAGGCTCAATTTAAT
11468959 T
1 T
11468960 GGAAGTCTTA
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:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (16 bp):
TAAGGCTCAATTTAAT
Found at i:11472754 original size:52 final size:51
Alignment explanation
Indices: 11472697--11472810 Score: 122
Period size: 52 Copynumber: 2.2 Consensus size: 51
11472687 AATCGTAATT
* *
11472697 GAGAGATTTTTGAAATTTAATTCCAAAATCAATTGGCATTAAAAATGAT-GT
1 GAGAGATTTTTGAAATTTAATTCCAAAATCAATTGACATT-AAAATGATAGC
* * ** * * *
11472748 GTAGAGATTATCGGGATTTAATTCCATAATCCATTTACATTAAAATGATAGC
1 G-AGAGATTTTTGAAATTTAATTCCAAAATCAATTGACATTAAAATGATAGC
11472800 GAGAGATTTTT
1 GAGAGATTTTT
11472811 TATATTTGAT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
51 17 0.34
52 33 0.66
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (51 bp):
GAGAGATTTTTGAAATTTAATTCCAAAATCAATTGACATTAAAATGATAGC
Found at i:11474167 original size:53 final size:53
Alignment explanation
Indices: 11474109--11474299 Score: 170
Period size: 53 Copynumber: 3.5 Consensus size: 53
11474099 CTAATTGTTC
*
11474109 CACCATTTGGGCCAAATTAGAAATATTTTCTTTTTCAAAATTT-TAAAATTTTT
1 CACCATTTGGGCCAATTTAGAAATATTTTCTTTTTCAAAATTTCT-AAATTTTT
* * ***
11474162 CACCATTTGAGCCTATTTAGAAATTCATTTTATTTCTCTTTTTTTTAATTTCTAAATTTTT
1 CACCATTTGGGCCAATTTAG-AA---A---TATTT-TCTTTTTCAAAATTTCTAAATTTTT
* * *
11474223 CACAATTTGGGTCAATTTAGAAATATATTT-TTTTTCAGAATTTCTAAATTTTT
1 CACCATTTGGGCCAATTTAGAAATAT-TTTCTTTTTCAAAATTTCTAAATTTTT
* **
11474276 CACCATTTTGGCTTATTTAGAAAT
1 CACCATTTGGGCCAATTTAGAAAT
11474300 TCTTTTTATT
Statistics
Matches: 110, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
53 56 0.51
54 6 0.05
55 2 0.02
57 2 0.02
60 7 0.06
61 36 0.33
62 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (53 bp):
CACCATTTGGGCCAATTTAGAAATATTTTCTTTTTCAAAATTTCTAAATTTTT
Found at i:11474212 original size:61 final size:59
Alignment explanation
Indices: 11474154--11474319 Score: 175
Period size: 53 Copynumber: 2.9 Consensus size: 59
11474144 CAAAATTTTA
*
11474154 AAATTTTTCACCATTTGAGCCTATTTAGAAATTCATTTTATTTCTCTTTTTTTTAATTTCT
1 AAATTTTTCACCATTTG-GCCTATTTAGAAATTCATTTTATTTCT-TTTTTTTGAATTTCT
* * * **
11474215 AAATTTTTCACAATTTGGGTCAATTTAGAAA-T-A---TA-TT-TTTTTTCAGAATTTCT
1 AAATTTTTCACCATTT-GGCCTATTTAGAAATTCATTTTATTTCTTTTTTTTGAATTTCT
* *
11474268 AAATTTTTCACCATTTTGGCTTATTTAGAAATTCTTTTTATTTCTTTTTTTT
1 AAATTTTTCACCA-TTTGGCCTATTTAGAAATTCATTTTATTTCTTTTTTTT
11474320 CGGAAAGAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
53 35 0.42
54 5 0.06
55 2 0.02
56 2 0.02
58 2 0.02
59 3 0.04
60 7 0.08
61 26 0.31
62 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (59 bp):
AAATTTTTCACCATTTGGCCTATTTAGAAATTCATTTTATTTCTTTTTTTTGAATTTCT
Found at i:11474298 original size:114 final size:113
Alignment explanation
Indices: 11474113--11474319 Score: 312
Period size: 114 Copynumber: 1.8 Consensus size: 113
11474103 TTGTTCCACC
11474113 ATTTGGGCCAAATTAGAAATATTTTCTTTTTCAAAATTTTAAAATTTTTCACCATTTGAGCCTAT
1 ATTTGGGCCAAATTAGAAATATTTTCTTTTTCAAAATTTTAAAATTTTTCACCATTTGAGCCTAT
11474178 TTAGAAATTCATTTTATTTCTCTTTTTTTTAATTTCTAAATTTTTCACA
66 TTAGAAATTCATTTTATTTCT-TTTTTTTTAATTTCTAAATTTTTCACA
* * * *
11474227 ATTTGGGTCAATTTAGAAATATATTT-TTTTTCAGAATTTCT-AAATTTTTCACCATTTTG-GCT
1 ATTTGGGCCAAATTAGAAATAT-TTTCTTTTTCAAAATTT-TAAAATTTTTCACCA-TTTGAGCC
*
11474289 TATTTAGAAATTCTTTTTATTTCTTTTTTTT
63 TATTTAGAAATTCATTTTATTTCTTTTTTTT
11474320 CGGAAAGAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
113 7 0.08
114 70 0.82
115 8 0.09
ACGTcount: A:0.28, C:0.12, G:0.07, T:0.54
Consensus pattern (113 bp):
ATTTGGGCCAAATTAGAAATATTTTCTTTTTCAAAATTTTAAAATTTTTCACCATTTGAGCCTAT
TTAGAAATTCATTTTATTTCTTTTTTTTTAATTTCTAAATTTTTCACA
Found at i:11474701 original size:190 final size:190
Alignment explanation
Indices: 11474340--11474701 Score: 455
Period size: 190 Copynumber: 1.9 Consensus size: 190
11474330 ATAATATGAC
* * * *
11474340 AATTATTTTTATTTAAATTTTATTTAAATTATTCCACCATTTGGGACAAATTTAAAGAAAATTTC
1 AATTATTGTTATTGAAACTTTATCTAAATTATTCCACCATTTGGGACAAATTTAAAGAAAATTTC
* * *
11474405 TCACCTAGAGATTTCTTAGAAAATTTACCATTTGAAATTTCTAAAAATCTCATCCTTAGATAATT
66 ACACCTAGAAATTTCTTAGAAAATTTACCATTTGAAATTTCTAAAAATCTCATCATTAGATAATT
* * * *
11474470 GTCAAATATTTTCAACCCAAATTTTTATTTTTTATTTTTTTTTGTTAGAAAATAAATATT
131 ATCAAATATTCTCAAACCAAATTTTTATTTTATATTTTTTTTTGTTAGAAAATAAATATT
*
11474530 AATTATTGTTATTGAAACTTTATCTAAATTATTCTACCATTTGGGACAAATTTAGACA-AAAATT
1 AATTATTGTTATTGAAACTTTATCTAAATTATTCCACCATTTGGGACAAATTTA-A-AGAAAATT
* *
11474594 TCACACCTAGAAATTT-TATAG-AAATTTACCATTTGAAATTTCTATAAAT-TCCATCATTGGAT
64 TCACACCTAGAAATTTCT-TAGAAAATTTACCATTTGAAATTTCTAAAAATCT-CATCATTAGAT
** ****
11474656 AATTAAT-ATTTATTCTCAAATTTTATTTTATATTTTATATTTTTTT
127 AATT-ATCAAATATTCTCAAACCAAATTTT-TATTTTATATTTTTTT
11474702 CTAAATTTAA
Statistics
Matches: 146, Mismatches: 20, Indels: 11
0.82 0.11 0.06
Matches are distributed among these distances:
189 1 0.01
190 104 0.71
191 40 0.27
192 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.46
Consensus pattern (190 bp):
AATTATTGTTATTGAAACTTTATCTAAATTATTCCACCATTTGGGACAAATTTAAAGAAAATTTC
ACACCTAGAAATTTCTTAGAAAATTTACCATTTGAAATTTCTAAAAATCTCATCATTAGATAATT
ATCAAATATTCTCAAACCAAATTTTTATTTTATATTTTTTTTTGTTAGAAAATAAATATT
Found at i:11475240 original size:12 final size:12
Alignment explanation
Indices: 11475219--11475251 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11475209 AATGGTGTTG
*
11475219 AAAAAA-TCACT
1 AAAAAATTCACC
11475230 AAAAAATTCACC
1 AAAAAATTCACC
11475242 AAAAAATTCA
1 AAAAAATTCA
11475252 ATGAAAACTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAATTCACC
Found at i:11478312 original size:18 final size:18
Alignment explanation
Indices: 11478285--11478326 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
11478275 GGAAAATGAT
11478285 GAAAAAAAAAAAAGAAG-G
1 GAAAAAAAAAAAA-AAGAG
*
11478303 GAAAACAAAAAAAAAGAG
1 GAAAAAAAAAAAAAAGAG
11478321 GAAAAA
1 GAAAAA
11478327 TTGATAGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (18 bp):
GAAAAAAAAAAAAAAGAG
Found at i:11478326 original size:19 final size:20
Alignment explanation
Indices: 11478289--11478326 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
11478279 AATGATGAAA
*
11478289 AAAAAAAAAGAAGGGAAAAC
1 AAAAAAAAAGAAGGAAAAAC
11478309 AAAAAAAAAG-AGGAAAAA
1 AAAAAAAAAGAAGGAAAAA
11478327 TTGATAGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGAAGGAAAAAC
Found at i:11478641 original size:15 final size:15
Alignment explanation
Indices: 11478607--11478657 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
11478597 AAATGTGTGC
11478607 AAAAAAAAAAG--CA
1 AAAAAAAAAAGTACA
*
11478620 AACAAAAAAAGGTA-A
1 AA-AAAAAAAAGTACA
*
11478635 AAAAAAAAAATTACA
1 AAAAAAAAAAGTACA
11478650 AAAAAAAA
1 AAAAAAAA
11478658 GAGCAAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.06
14 17 0.55
15 12 0.39
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (15 bp):
AAAAAAAAAAGTACA
Found at i:11480453 original size:60 final size:60
Alignment explanation
Indices: 11480356--11480480 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 60
11480346 TATAAACTTT
* *
11480356 ATTTTTTTAACTTGCAATTCAATCTCGGTCACTTATTTCAATCTCAGCTCAGTCCAGATC
1 ATTTTTTTAACTTGCAATTCAATCTCGGTCACCTATTTCAATCTCAGCTCAATCCAGATC
* * ** *
11480416 ATTTTTTCTGACTTGC-ATTCAATCTTGGTCACCTATTTTGATCTCGGCTCAATCCAGATC
1 ATTTTTT-TAACTTGCAATTCAATCTCGGTCACCTATTTCAATCTCAGCTCAATCCAGATC
11480476 ATTTT
1 ATTTT
11480481 ATTTCCTGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 50 0.88
61 7 0.12
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (60 bp):
ATTTTTTTAACTTGCAATTCAATCTCGGTCACCTATTTCAATCTCAGCTCAATCCAGATC
Found at i:11480791 original size:50 final size:51
Alignment explanation
Indices: 11480696--11480827 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 51
11480686 AATTTTTTAG
* * ** * *
11480696 ATTTAATTCTAGAATCAATTGGCATTAAAAATGATATGGAGAGATTGTCAGA
1 ATTTAATTCCAAAATCAATTCACATT-AAAATAATAGGGAGAGATTGTCAGA
* * ** *
11480748 ATTTAATTCCATAATC-ATTCACATTAAAATAATAGGGAGAGATTTTTGGG
1 ATTTAATTCCAAAATCAATTCACATTAAAATAATAGGGAGAGATTGTCAGA
* *
11480798 ATTTAATTTCAAAATCAATTCTCATTAAAA
1 ATTTAATTCCAAAATCAATTCACATTAAAA
11480828 AGAAAATCAA
Statistics
Matches: 66, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
50 33 0.50
51 19 0.29
52 14 0.21
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (51 bp):
ATTTAATTCCAAAATCAATTCACATTAAAATAATAGGGAGAGATTGTCAGA
Found at i:11481390 original size:25 final size:23
Alignment explanation
Indices: 11481337--11481391 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
11481327 TTCTGTTTTG
*
11481337 ATTTTATTTTTCTTATTTTGTTT
1 ATTTTATTTCTCTTATTTTGTTT
11481360 ATTTTTATTTACTCTTATTATT-TCTT
1 A-TTTTATTT-CTCTTATT-TTGT-TT
11481386 ATTTTA
1 ATTTTA
11481392 AGTTGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 1 0.04
24 8 0.30
25 13 0.48
26 5 0.19
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTTATTTCTCTTATTTTGTTT
Found at i:11482430 original size:63 final size:62
Alignment explanation
Indices: 11482362--11482484 Score: 210
Period size: 63 Copynumber: 2.0 Consensus size: 62
11482352 ATAGATATAT
*
11482362 ATATATGGATCCATTAATAACCGAATAAGTGTTATACATTTGTTGATATTTAGATCAAAATGG
1 ATATATGGATCCATTAATAACCGAATAAGTGTTATACA-TTATTGATATTTAGATCAAAATGG
* *
11482425 ATATATGGATCCATTAATAACGGTATAAGTGTTATACATTATTGATATTTAGATCAAAAT
1 ATATATGGATCCATTAATAACCGAATAAGTGTTATACATTATTGATATTTAGATCAAAAT
11482485 AGCTAAGTGT
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
62 21 0.37
63 36 0.63
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (62 bp):
ATATATGGATCCATTAATAACCGAATAAGTGTTATACATTATTGATATTTAGATCAAAATGG
Found at i:11486544 original size:19 final size:20
Alignment explanation
Indices: 11486503--11486553 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
11486493 TATAAATGAC
11486503 AATTAATAAAATT-AAAATAT
1 AATT-ATAAAATTAAAAATAT
11486523 AATTATAAAATTAAAAAT-T
1 AATTATAAAATTAAAAATAT
*
11486542 AA-TATTAAATTA
1 AATTATAAAATTA
11486554 TAATACACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.31
19 11 0.38
20 9 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTATAAAATTAAAAATAT
Found at i:11487015 original size:7 final size:8
Alignment explanation
Indices: 11486987--11487014 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
11486977 TCGAATATTA
11486987 TTTTTAAT
1 TTTTTAAT
11486995 TTTTTAAT
1 TTTTTAAT
11487003 TTTTTAAT
1 TTTTTAAT
11487011 TTTT
1 TTTT
11487015 ATATGTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTAAT
Found at i:11487082 original size:18 final size:19
Alignment explanation
Indices: 11487051--11487091 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
11487041 ATTTTTATTT
* *
11487051 TATAAAAATTTAAAATATA
1 TATAAAAATCTAAAAAATA
11487070 TATAAAAA-CTAAAAAATA
1 TATAAAAATCTAAAAAATA
11487088 TATA
1 TATA
11487092 TTTGATTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
TATAAAAATCTAAAAAATA
Found at i:11487747 original size:16 final size:16
Alignment explanation
Indices: 11487722--11487755 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
11487712 AATCAAATAA
11487722 TAAATATA-TTTAAAT
1 TAAATATATTTTAAAT
11487737 TAAATTATATTTTAAAT
1 TAAA-TATATTTTAAAT
11487754 TA
1 TA
11487756 TTAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATATATTTTAAAT
Found at i:11499623 original size:17 final size:16
Alignment explanation
Indices: 11499601--11499657 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
11499591 ACTTTTAATT
11499601 CTTGTTTAATTATTTTA
1 CTTGTTT-ATTATTTTA
*
11499618 CTTGTTTGTT-TTACTT-
1 CTTGTTTATTATT--TTA
11499634 CTTGTTTGATTATTTTA
1 CTTGTTT-ATTATTTTA
11499651 CTTGTTT
1 CTTGTTT
11499658 TCATGTTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
15 2 0.06
16 11 0.33
17 18 0.55
18 2 0.06
ACGTcount: A:0.14, C:0.09, G:0.11, T:0.67
Consensus pattern (16 bp):
CTTGTTTATTATTTTA
Found at i:11499630 original size:33 final size:33
Alignment explanation
Indices: 11499593--11499657 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
11499583 ATCTACTTAC
11499593 TTTTAATTCTTGTTTAATTATTTTACTTGTTTG
1 TTTTAATTCTTGTTTAATTATTTTACTTGTTTG
* *
11499626 TTTTACTTCTTGTTTGATTATTTTACTTGTTT
1 TTTTAATTCTTGTTTAATTATTTTACTTGTTT
11499658 TCATGTTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.15, C:0.08, G:0.09, T:0.68
Consensus pattern (33 bp):
TTTTAATTCTTGTTTAATTATTTTACTTGTTTG
Found at i:11501171 original size:13 final size:13
Alignment explanation
Indices: 11501153--11501198 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
11501143 GAGGAAAATT
*
11501153 AATAATTATTGTA
1 AATAATTATTATA
*
11501166 AATAATAATTATA
1 AATAATTATTATA
*
11501179 AAAATATTATTATA
1 AATA-ATTATTATA
11501193 AATAAT
1 AATAAT
11501199 AAAATTATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
AATAATTATTATA
Found at i:11507715 original size:25 final size:25
Alignment explanation
Indices: 11507687--11507738 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
11507677 AGAGAGTTCT
*
11507687 GATTAGCCATTAAGTTGACTTTTTG
1 GATTAGCCATTAAGTTGACATTTTG
11507712 GATTAGCCATTAAGTTGACATTTTG
1 GATTAGCCATTAAGTTGACATTTTG
11507737 GA
1 GA
11507739 ATAGGACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (25 bp):
GATTAGCCATTAAGTTGACATTTTG
Found at i:11510006 original size:21 final size:21
Alignment explanation
Indices: 11509980--11510021 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11509970 TATGTACCAC
**
11509980 CACAACAACATTTTTCTTCAT
1 CACAACAACATTCCTCTTCAT
*
11510001 CACAACACCATTCCTCTTCAT
1 CACAACAACATTCCTCTTCAT
11510022 ATCACTTTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (21 bp):
CACAACAACATTCCTCTTCAT
Found at i:11511401 original size:17 final size:17
Alignment explanation
Indices: 11511379--11511411 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11511369 ATTCATATAG
11511379 TTTCTTTGTGTTGTAGT
1 TTTCTTTGTGTTGTAGT
*
11511396 TTTCTTTGTTTTGTAG
1 TTTCTTTGTGTTGTAG
11511412 GTCAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.67
Consensus pattern (17 bp):
TTTCTTTGTGTTGTAGT
Found at i:11512711 original size:62 final size:61
Alignment explanation
Indices: 11512389--11512962 Score: 170
Period size: 63 Copynumber: 9.2 Consensus size: 61
11512379 AGCCTAACAC
* * ** **
11512389 ACCTTGAGTAATCCCCTTCAATTTTTTTG--GGGATTATTCAAAGTGTTTTTTTGCCAAAAAAT
1 ACCTTGAATAATCCCTTTCAA-TTTTTTGAAGGGATTATTC-AAG-GCATTTTTGATAAAAAAT
* *** * * * *
11512451 -CCTTAAATAAT-CCTTT-AATAAAAATTGAAAGGGATTATTCGAGGCATTTCTAACAAAAAAAT
1 ACCTTGAATAATCCCTTTCAAT--TTTTTG-AAGGGATTATTCAAGGCATTTTTGA-TAAAAAAT
* * * * * *
11512513 ATCTTGAATAATCCCTTTTAATTTTTGTGAAGAGATTATTCAAGGCATTTTTGGTCAGAAATT
1 ACCTTGAATAATCCCTTTCAATTTTT-TGAAGGGATTATTCAAGGCATTTTTGAT-AAAAAAT
* * * **** * * * * *
11512576 ACTTTGAATAATCTCTTACAAAAAATTGATTGGGGTTATT-GAGAGTATTTTTTGACAAAAAAT
1 ACCTTGAATAATCCCTTTCAATTTTTTGA-AGGGATTATTCAAG-GCA-TTTTTGATAAAAAAT
* ** *
11512639 ACCTTCAATAATTTCTTTCAATTTTTATGAAGGGATTATTCAAGGTATTTTTGATAAAAAAT
1 ACCTTGAATAATCCCTTTCAATTTTT-TGAAGGGATTATTCAAGGCATTTTTGATAAAAAAT
* **** * * *** * *
11512701 ACCTTGAATAATTCCTTT-ATAAAAATTGAAGGGGCTTTTTCATTACATTTTTGGCT-AGAAAT
1 ACCTTGAATAATCCCTTTCA-ATTTTTTGAA-GGGATTATTCAAGGCATTTTT-GATAAAAAAT
* ** ** * *
11512763 ACCTTGAATAA-CCCATTCAATTTTTTGTAAATGATTATTCAAGGTGTTTTCTGGCT-AAAAAC
1 ACCTTGAATAATCCCTTTCAATTTTTTG-AAGGGATTATTCAAGGCATTTT-T-GATAAAAAAT
*** * * * * ** *
11512825 ACCTTGAATAATCCCCTTAT-AAAAATTGGATGGGATTATTAAAGGCGTTTTTGGCCAACAAAT
1 ACCTTGAATAAT-CCCTT-TCAATTTTTTGAAGGGATTATTCAAGGCATTTTT-GATAAAAAAT
* * *
11512888 ACCTTAAATAA--CCTTAATCAATTTTTTTGTAAGAGATTA-TCAAGGCGATTTCT-AGTAAAAA
1 ACCTTGAATAATCCCTT--TCAA-TTTTTTG-AAGGGATTATTCAAGGC-ATTTTTGA-TAAAAA
11512949 AT
60 AT
*
11512951 ATCTTGAATAAT
1 ACCTTGAATAAT
11512963 GCAAAAAAAA
Statistics
Matches: 364, Mismatches: 115, Indels: 64
0.67 0.21 0.12
Matches are distributed among these distances:
58 1 0.00
59 2 0.01
60 11 0.03
61 40 0.11
62 106 0.29
63 162 0.45
64 38 0.10
65 4 0.01
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (61 bp):
ACCTTGAATAATCCCTTTCAATTTTTTGAAGGGATTATTCAAGGCATTTTTGATAAAAAAT
Found at i:11512725 original size:126 final size:124
Alignment explanation
Indices: 11512328--11512998 Score: 334
Period size: 124 Copynumber: 5.4 Consensus size: 124
11512318 TTTGGCCAAA
* * ** * * ** * *
11512328 ACCTTGAATAATCCCTTACAAAAATTG-AAGAGGATTATTTAAGCCATTTCTAGC-CTAACACAC
1 ACCTTGAATAATCCTTTAAAAAAATTGAAAG-GGATTATTCGAGGCATTTCTAACAAAAAAATAC
* * * * * **
11512391 CTTGAGTAATCCCCTTCAATTTTTTTG--GGGATTATTCAAAGTGTTTTTTTGCCAAAAAAT
65 CTTCAATAATCCCTTTCAATTTTTATGAAGGGATTATTC-AAG-GTATTTTTGATAAAAAAT
* *
11512451 -CCTTAAATAATCCTTTAATAAAAATTGAAAGGGATTATTCGAGGCATTTCTAACAAAAAAATAT
1 ACCTTGAATAATCCTTTAA-AAAAATTGAAAGGGATTATTCGAGGCATTTCTAACAAAAAAATAC
* * * * * * * *
11512515 CTTGAATAATCCCTTTTAATTTTTGTGAAGAGATTATTCAAGGCATTTTTGGTCAGAAATT
65 CTTCAATAATCCCTTTCAATTTTTATGAAGGGATTATTCAAGGTATTTTTGAT-AAAAAAT
* ** * * * *
11512576 ACTTTGAATAAT-CTCTTACAAAAAATTGATTGGGGTTATT-GAGAGTATTTTTTGAC-AAAAAA
1 ACCTTGAATAATCCT-TTA-AAAAAATTGAAAGGGATTATTCGAG-GCA-TTTCTAACAAAAAAA
**
11512638 TACCTTCAATAATTTCTTTCAATTTTTATGAAGGGATTATTCAAGGTATTTTTGATAAAAAAT
62 TACCTTCAATAATCCCTTTCAATTTTTATGAAGGGATTATTCAAGGTATTTTTGATAAAAAAT
* * * * ** * ** * *
11512701 ACCTTGAATAATTCCTTTATAAAAATTGAAGGGGCTTTTTC-ATTACATTTTTGGC-TAGAAATA
1 ACCTTGAATAA-TCCTTTAAAAAAATTGAAAGGGATTATTCGA-GGCATTTCTAACAAAAAAATA
* * ** * * *
11512764 CCTTGAATAA-CCCATTCAATTTTT-TGTAAATGATTATTCAAGGTGTTTTCTGGCT-AAAAAC
64 CCTTCAATAATCCCTTTCAATTTTTATG-AAGGGATTATTCAAGGTATTTT-T-GATAAAAAAT
* * * * ** * * ** * *
11512825 ACCTTGAATAATCCCCTTATAAAAATTGGATGGGATTATTAAAGGCGTTTTTGGCCAACAAATAC
1 ACCTTGAATAAT-CCTTTAAAAAAATTGAAAGGGATTATTCGAGGCATTTCTAACAAAAAAATAC
* * * * *
11512890 CTTAAATAA--CCTTAATCAATTTTTTTGTAAGAGATTA-TCAAGGCGATTTCT-AGTAAAAAAT
65 CTTCAATAATCCCTT--TCAATTTTTATG-AAGGGATTATTCAAGG-TATTTTTGA-TAAAAAAT
* * ** * * *
11512951 ATCTTGAATAATGC-AAAAAAAAATGGAAGGGGATTATTCAAGGCATTT
1 ACCTTGAATAATCCTTTAAAAAAATTGAAAGGGATTATTCGAGGCATTT
11512999 TTGGCCAGAA
Statistics
Matches: 428, Mismatches: 93, Indels: 53
0.75 0.16 0.09
Matches are distributed among these distances:
122 17 0.04
123 58 0.14
124 136 0.32
125 66 0.15
126 129 0.30
127 22 0.05
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (124 bp):
ACCTTGAATAATCCTTTAAAAAAATTGAAAGGGATTATTCGAGGCATTTCTAACAAAAAAATACC
TTCAATAATCCCTTTCAATTTTTATGAAGGGATTATTCAAGGTATTTTTGATAAAAAAT
Found at i:11512876 original size:124 final size:122
Alignment explanation
Indices: 11512328--11513019 Score: 356
Period size: 126 Copynumber: 5.6 Consensus size: 122
11512318 TTTGGCCAAA
* * * * * * * * * *
11512328 ACCTTGAATAATCCCTTACAAAAATTGAAGAGGATTATTTAAGCCATTTCTAGCCTA-ACACACC
1 ACCTTGAATAATCCCTTATAAAAATTGGAGGGGATTATTCAAGGCATTT-TTGGCAAGAAATACC
* * *** * * *
11512392 TTGAGTAATCC-CCTTCAATTTTTT-TGGGGATTATTCAAAGTGTTTTTTTGCCAAAAAAT
65 TTGAATAA-CCTCATTCAATTTTTTGTAAAGATTATTCAAGGTG-TTTTCTG-TAAAAAAT
* * * * * * ** * *
11512451 -CCTTAAATAATCCTTTAATAAAAATTGAAAGGGATTATTCGAGGCATTTCTAACAAAAAAATAT
1 ACCTTGAATAATCCCTT-ATAAAAATTGGAGGGGATTATTCAAGGCATTTTTGGC-AAGAAATAC
* * ** * *
11512515 CTTGAATAATCC-CTTTTAA-TTTTTGTGAAGAGATTATTCAAGGCATTTT-TGGTCAGAAATT
64 CTTGAATAA-CCTCATTCAATTTTTTGT-AA-AGATTATTCAAGGTGTTTTCT-GT-AAAAAAT
* * * * * * *
11512576 ACTTTGAATAATCTCTTACAAAAAATT-GATTGGGG-TTATT-GAGAGTATTTTTTGACAAAAAA
1 ACCTTGAATAATCCCTTA-TAAAAATTGGA--GGGGATTATTCAAG-GCA-TTTTTGGCAAGAAA
* ** * * *
11512638 TACCTTCAATAATTTCTTTCAATTTTTATG-AAGGGATTATTCAAGGTATTTT-TGATAAAAAAT
61 TACCTTGAATAACCTCATTCAATTTTT-TGTAA-AGATTATTCAAGGTGTTTTCTG-TAAAAAAT
* * * * *** *
11512701 ACCTTGAATAATTCCTTTATAAAAATTGAAGGGGCTTTTTCATTACATTTTTGGCTAGAAATACC
1 ACCTTGAATAA-TCCCTTATAAAAATTGGAGGGGATTATTCAAGGCATTTTTGGCAAGAAATACC
*
11512766 TTGAATAACC-CATTCAATTTTTTGTAAATGATTATTCAAGGTGTTTTCTGGCT-AAAAAC
65 TTGAATAACCTCATTCAATTTTTTGTAAA-GATTATTCAAGGTGTTTTCT-G-TAAAAAAT
* * * *
11512825 ACCTTGAATAATCCCCTTATAAAAATTGGATGGGATTATTAAAGGCGTTTTTGGCCAACAAATAC
1 ACCTTGAATAAT-CCCTTATAAAAATTGGAGGGGATTATTCAAGGCATTTTTGG-CAAGAAATAC
* * * * *
11512890 CTTAAATAACCTTAATCAATTTTTTTGTAAGAGATTA-TCAAGGCGATTTCTAGTAAAAAAT
64 CTTGAATAACCTCATTCAA-TTTTTTGTAA-AGATTATTCAAGGTGTTTTCT-GTAAAAAAT
* * * * * * *
11512951 ATCTTGAATAAT-GC-AAAAAAAAATGGAAGGGGATTATTCAAGGCATTTTTGGCCAGAAACACC
1 ACCTTGAATAATCCCTTATAAAAATTGG-AGGGGATTATTCAAGGCATTTTTGGCAAGAAATACC
11513014 TTGAAT
65 TTGAAT
11513020 TATCCTTTTT
Statistics
Matches: 436, Mismatches: 100, Indels: 66
0.72 0.17 0.11
Matches are distributed among these distances:
122 17 0.04
123 85 0.19
124 118 0.27
125 64 0.15
126 121 0.28
127 28 0.06
128 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (122 bp):
ACCTTGAATAATCCCTTATAAAAATTGGAGGGGATTATTCAAGGCATTTTTGGCAAGAAATACCT
TGAATAACCTCATTCAATTTTTTGTAAAGATTATTCAAGGTGTTTTCTGTAAAAAAT
Found at i:11513195 original size:62 final size:62
Alignment explanation
Indices: 11513129--11513297 Score: 189
Period size: 61 Copynumber: 2.7 Consensus size: 62
11513119 ATTTTTGCCA
* * *
11513129 AAAAATACATTGAATAATCCCTTACAAAAAATTGAATGGGGTTATGCAAGGTGTTTCTGACC
1 AAAAATACCTTGAATAATCCCTTACAAAAAATTGAATAGGATTATGCAAGGTGTTTCTGACC
* *** ** * * *
11513191 AAAAATACCTTGAATAATTCCCTT--ATATTTTTTTATAGGATTATTCAAGGTGTTTTTGCCC
1 AAAAATACCTTGAATAA-TCCCTTACAAAAAATTGAATAGGATTATGCAAGGTGTTTCTGACC
*
11513252 AAAAACTGCCTTGAATAATCCCTTACAAAAAATTGAATAGGATTAT
1 AAAAA-TACCTTGAATAATCCCTTACAAAAAATTGAATAGGATTAT
11513298 TCAATGTATT
Statistics
Matches: 84, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
61 37 0.44
62 27 0.32
63 20 0.24
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (62 bp):
AAAAATACCTTGAATAATCCCTTACAAAAAATTGAATAGGATTATGCAAGGTGTTTCTGACC
Found at i:11520519 original size:42 final size:42
Alignment explanation
Indices: 11520451--11520743 Score: 184
Period size: 42 Copynumber: 6.9 Consensus size: 42
11520441 AGAATAGTTT
* * *
11520451 TTAAATAATAATCATTTAAGGCATTTCTTCAACCCAAATGCC
1 TTAAATGATCATCATTTAAGGCATTTCTTCAACCAAAATGCC
* * * * ***
11520493 TTGAATGATCATCATTTAAGGTATTTCTTTAGCCTAAAATTTAT
1 TTAAATGATCATCATTTAAGGCATTTCTTCAACC-AAAA-TGCC
* * * * * *
11520537 TTGAATGATGATTTATTAAAGGCATTT-TTTAGGA-AAAAATGCC
1 TTAAATGATCA-TCATTTAAGGCATTTCTTCA--ACCAAAATGCC
* ** *
11520580 TTAAATGATCATCATTGAAGGCATTT-TT-AAAGAAAACGCC
1 TTAAATGATCATCATTTAAGGCATTTCTTCAACCAAAATGCC
* * * *
11520620 TTAAATTATCAACATTTAAGGCATTTTTTGAGA--AGAAATGCC
1 TTAAATGATCATCATTTAAGGCATTTCTTCA-ACCA-AAATGCC
* * * **
11520662 TTAAATAATGATCATTTAAGGCATTTTTTCAACCCGAATGCC
1 TTAAATGATCATCATTTAAGGCATTTCTTCAACCAAAATGCC
* * *
11520704 TTGAATGATCATCATGTAAGGTATTTCTTCAACCCAAAAT
1 TTAAATGATCATCATTTAAGGCATTTCTTCAA-CCAAAAT
11520744 TTATTTGGGT
Statistics
Matches: 195, Mismatches: 43, Indels: 25
0.74 0.16 0.10
Matches are distributed among these distances:
39 1 0.01
40 30 0.15
41 5 0.03
42 109 0.56
43 19 0.10
44 19 0.10
45 12 0.06
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (42 bp):
TTAAATGATCATCATTTAAGGCATTTCTTCAACCAAAATGCC
Found at i:11521258 original size:42 final size:42
Alignment explanation
Indices: 11521212--11521298 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
11521202 TTTTGATAAG
*
11521212 AAACACC-TAAATTAATGATCATTTAAGGCATTTCTTCAACCC
1 AAACACCTTAAA-TAATCATCATTTAAGGCATTTCTTCAACCC
* *
11521254 AAACACCTTAAATGATCATCATTTAAGGCATTTCTTCAGCCC
1 AAACACCTTAAATAATCATCATTTAAGGCATTTCTTCAACCC
11521296 AAA
1 AAA
11521299 ATTTATTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 37 0.90
43 4 0.10
ACGTcount: A:0.38, C:0.24, G:0.08, T:0.30
Consensus pattern (42 bp):
AAACACCTTAAATAATCATCATTTAAGGCATTTCTTCAACCC
Found at i:11521833 original size:39 final size:38
Alignment explanation
Indices: 11521760--11521833 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
11521750 AGAAAAAGAA
* *
11521760 AAAAACCCAAAAAGAAAAAAAAAAATAATAAAGTGCTG
1 AAAAACCCAAAAAGAAAAAAAAAAAAAAGAAAGTGCTG
*
11521798 AAAAAGCCAAAAA-AAAAAAAAAAAGAAAGAGAAGTG
1 AAAAACCCAAAAAGAAAAAAAAAAA-AAAGA-AAGTG
11521834 GACAAAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 11 0.35
38 15 0.48
39 5 0.16
ACGTcount: A:0.72, C:0.08, G:0.14, T:0.07
Consensus pattern (38 bp):
AAAAACCCAAAAAGAAAAAAAAAAAAAAGAAAGTGCTG
Found at i:11523648 original size:21 final size:21
Alignment explanation
Indices: 11523622--11523664 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11523612 TGTTGAGCTA
* * *
11523622 ATTTTTCTTTTAATTTTTGTG
1 ATTTTTCTATTAAATCTTGTG
11523643 ATTTTTCTATTAAATCTTGTG
1 ATTTTTCTATTAAATCTTGTG
11523664 A
1 A
11523665 AAAACTTGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (21 bp):
ATTTTTCTATTAAATCTTGTG
Found at i:11525049 original size:21 final size:22
Alignment explanation
Indices: 11525025--11525065 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11525015 TAAAAGCCAC
*
11525025 AACTAAA-ACAAAAGCCAAAAA
1 AACTAAAGACAAAAACCAAAAA
11525046 AACTAAAGACAAAAACCAAA
1 AACTAAAGACAAAAACCAAA
11525066 GCTTGAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.71, C:0.20, G:0.05, T:0.05
Consensus pattern (22 bp):
AACTAAAGACAAAAACCAAAAA
Found at i:11525468 original size:20 final size:21
Alignment explanation
Indices: 11525439--11525479 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11525429 ATGAGATAAA
*
11525439 AAATAAC-AAAATAAAGAAGG
1 AAATAACAAAAAAAAAGAAGG
*
11525459 AAATAGCAAAAAAAAAGAAGG
1 AAATAACAAAAAAAAAGAAGG
11525480 GCGATGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.71, C:0.05, G:0.17, T:0.07
Consensus pattern (21 bp):
AAATAACAAAAAAAAAGAAGG
Found at i:11527329 original size:14 final size:14
Alignment explanation
Indices: 11527294--11527335 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
11527284 GAGGTGCATT
*
11527294 TTTTTTC-CTTTTC
1 TTTTTTCTCTTCTC
11527307 TTGTCTTTCTCTTCTC
1 TT-T-TTTCTCTTCTC
11527323 TTTTTTCTCTTCT
1 TTTTTTCTCTTCT
11527336 TTTCCTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 2 0.08
14 11 0.44
15 5 0.20
16 7 0.28
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTTCTCTTCTC
Found at i:11528429 original size:13 final size:13
Alignment explanation
Indices: 11528385--11528434 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
11528375 ATCTTAAACC
*
11528385 AAAACCCTAAGGTT
1 AAAACCCTAA-ATT
*
11528399 AAAACCCTAAATC
1 AAAACCCTAAATT
* *
11528412 GAAACCTTAAATT
1 AAAACCCTAAATT
11528425 AAAACCCTAA
1 AAAACCCTAA
11528435 CCTCATCTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.20
Consensus pattern (13 bp):
AAAACCCTAAATT
Found at i:11530599 original size:18 final size:17
Alignment explanation
Indices: 11530578--11530623 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
11530568 ATTTCCTTTT
*
11530578 TTATTTAAATTTCTATG
1 TTATTTAAATTACTATG
*
11530595 CTTATTTTAATTACTATG
1 -TTATTTAAATTACTATG
*
11530613 TAATTTAAATT
1 TTATTTAAATT
11530624 CTCATACTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (17 bp):
TTATTTAAATTACTATG
Found at i:11531010 original size:13 final size:13
Alignment explanation
Indices: 11530992--11531064 Score: 83
Period size: 13 Copynumber: 5.6 Consensus size: 13
11530982 CAAATTAGTG
11530992 AAACCCTAAAATA
1 AAACCCTAAAATA
*
11531005 AAACCCTAAAACA
1 AAACCCTAAAATA
11531018 AAACCCTAAAATA
1 AAACCCTAAAATA
* * *
11531031 AAATCCTAGAATG
1 AAACCCTAAAATA
* * *
11531044 AAATCCTGAAATG
1 AAACCCTAAAATA
11531057 AAACCCTA
1 AAACCCTA
11531065 GACCCTGTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.55, C:0.23, G:0.05, T:0.16
Consensus pattern (13 bp):
AAACCCTAAAATA
Found at i:11531166 original size:26 final size:26
Alignment explanation
Indices: 11531137--11531193 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
11531127 TAAAACCTTG
*
11531137 AAACCCAAAATGCACTCAAAACCCCA
1 AAACCCAAAATCCACTCAAAACCCCA
*
11531163 AAACCCAAAATCCACTTAAAACCCCA
1 AAACCCAAAATCCACTCAAAACCCCA
11531189 AAACC
1 AAACC
11531194 ATCATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.51, C:0.39, G:0.02, T:0.09
Consensus pattern (26 bp):
AAACCCAAAATCCACTCAAAACCCCA
Found at i:11536296 original size:23 final size:23
Alignment explanation
Indices: 11536269--11536316 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
11536259 AGAAAATGAG
*
11536269 ATGTTTAGAAGATATACTTGGAC
1 ATGTTTAGAAGATATACTTAGAC
11536292 ATGTTTAGAAGATATACTTAGAC
1 ATGTTTAGAAGATATACTTAGAC
11536315 AT
1 AT
11536317 TGAAGTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (23 bp):
ATGTTTAGAAGATATACTTAGAC
Found at i:11542360 original size:11 final size:10
Alignment explanation
Indices: 11542333--11542359 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
11542323 GCAAAAATAT
11542333 AAAAAAAGTA
1 AAAAAAAGTA
11542343 AAAAAAAGTA
1 AAAAAAAGTA
11542353 AAAAAAA
1 AAAAAAA
11542360 AAAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (10 bp):
AAAAAAAGTA
Found at i:11542369 original size:20 final size:19
Alignment explanation
Indices: 11542332--11542375 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
11542322 AGCAAAAATA
**
11542332 TAAAAAAAGTAAAAAAAAG
1 TAAAAAAAAAAAAAAAAAG
11542351 TAAAAAAAAAAAAAGAAAAG
1 TAAAAAAAAAAAAA-AAAAG
*
11542371 GAAAA
1 TAAAA
11542376 TGAATGCCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (19 bp):
TAAAAAAAAAAAAAAAAAG
Found at i:11542744 original size:16 final size:16
Alignment explanation
Indices: 11542723--11542818 Score: 63
Period size: 16 Copynumber: 5.8 Consensus size: 16
11542713 ACTAATGGAT
11542723 AGAAAAAAATGAAAAA
1 AGAAAAAAATGAAAAA
*
11542739 AGAAAAAATATG--AGA
1 AGAAAAAA-ATGAAAAA
*
11542754 AGTAAAAAATG-AAAA
1 AGAAAAAAATGAAAAA
* *
11542769 GGTTAAAAAATGAAAAA
1 AG-AAAAAAATGAAAAA
**
11542786 ATGAAAAAAAAAATAAAA
1 A-GAAAAAAATGA-AAAA
11542804 AGAAGAGAAAATGAA
1 AGAA-A-AAAATGAA
11542819 TACTCAAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
14 3 0.05
15 12 0.19
16 17 0.27
17 17 0.27
18 8 0.13
19 5 0.08
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (16 bp):
AGAAAAAAATGAAAAA
Found at i:11542795 original size:9 final size:8
Alignment explanation
Indices: 11542726--11542794 Score: 54
Period size: 8 Copynumber: 8.8 Consensus size: 8
11542716 AATGGATAGA
11542726 AAAAAATG
1 AAAAAATG
11542734 AAAAAA-G
1 AAAAAATG
11542741 AAAAAAT-
1 AAAAAATG
* *
11542748 ATGAGAA-G
1 A-AAAAATG
11542756 TAAAAAATG
1 -AAAAAATG
** *
11542765 AAAAGGTT
1 AAAAAATG
11542773 AAAAAATG
1 AAAAAATG
11542781 AAAAAATG
1 AAAAAATG
11542789 AAAAAA
1 AAAAAA
11542795 AAAATAAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
7 8 0.17
8 36 0.78
9 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.13
Consensus pattern (8 bp):
AAAAAATG
Found at i:11542814 original size:20 final size:20
Alignment explanation
Indices: 11542773--11542814 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
11542763 TGAAAAGGTT
*
11542773 AAAAAATGAAAAAATGAAAA
1 AAAAAATGAAAAAAAGAAAA
11542793 AAAAAAT-AAAAAGAAGAGAAA
1 AAAAAATGAAAAA-AAGA-AAA
11542814 A
1 A
11542815 TGAATACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 5 0.26
20 10 0.53
21 4 0.21
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAAAATGAAAAAAAGAAAA
Found at i:11543539 original size:79 final size:79
Alignment explanation
Indices: 11543405--11543614 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 79
11543395 CAAATGATGA
** * * * * * *
11543405 GGATCAATGGATGGAATTCATTTTG-GAATGGCTAGTACTGAGAAGCCTGTTAATGGTGATCAAG
1 GGATCAATGGACAGAATTCATTATGAGAAT-GCTAATGCTAAAAAGCCTGTGAATGGTGATCAAG
11543469 TGATAAACATAATGT
65 TGATAAACATAATGT
11543484 GGATCAGA-GGACAGAATTCATTAT-AGAATGCTTAATGCTAAAAAGCCTGTGAATGGTGATCAA
1 GGATCA-ATGGACAGAATTCATTATGAGAATGC-TAATGCTAAAAAGCCTGTGAATGGTGATCAA
*
11543547 GTGATGAACATAATGT
64 GTGATAAACATAATGT
* * * * * *
11543563 GGATCAATTGATAGAATTTATTCTGAGATTGCTAATGCTAAGAAGCCTGTGA
1 GGATCAATGGACAGAATTCATTATGAGAATGCTAATGCTAAAAAGCCTGTGA
11543615 TTAAATGATA
Statistics
Matches: 111, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 101 0.91
80 7 0.06
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.30
Consensus pattern (79 bp):
GGATCAATGGACAGAATTCATTATGAGAATGCTAATGCTAAAAAGCCTGTGAATGGTGATCAAGT
GATAAACATAATGT
Found at i:11544561 original size:41 final size:41
Alignment explanation
Indices: 11544488--11544997 Score: 413
Period size: 41 Copynumber: 12.1 Consensus size: 41
11544478 GATTATCGAA
* * *
11544488 GAGC-TTTTTTTTTTCAAAAGTTGTGGTGCCTCTATTTAGAG
1 GAGCATTTTATTTTTC-AAAGTTGTTGAGCCTCTATTTAGAG
* *
11544529 GAGCATTTTACTTTTCAAAGTTGTAGTA-CCTCTATTTAGAG
1 GAGCATTTTATTTTTCAAAGTTGTTG-AGCCTCTATTTAGAG
** * * *
11544570 GAATATTTTATTTTTCAAAGTTG-TGATGCTTCTGTTAAGAG
1 GAGCATTTTATTTTTCAAAGTTGTTGA-GCCTCTATTTAGAG
* ** * *
11544611 GAGCTTAATTTATTTTTCGAAAAGTCATTGAGCCTTTATTTAGAA
1 GAGC--ATTTTATTTTTC--AAAGTTGTTGAGCCTCTATTTAGAG
* * ** * *
11544656 GAGCCTTATTTATTTTTCAAACTCATTAAGCCTCTGTTTAGAG
1 GAG-CAT-TTTATTTTTCAAAGTTGTTGAGCCTCTATTTAGAG
* *
11544699 GAGCCTTTTATTTTTCAAAGTTGTTGAGCCTTTGA-TTAGAG
1 GAGCATTTTATTTTTCAAAGTTGTTGAGCCTCT-ATTTAGAG
* * *
11544740 GAGCCTTTTATTTTTCAAAGTCGTTGTGCCTCTATTTAGAG
1 GAGCATTTTATTTTTCAAAGTTGTTGAGCCTCTATTTAGAG
* * *
11544781 GAGTC-TATTTATTTTTCAAAGTCGTTGAGCCTTTGTTTAGAG
1 GAG-CAT-TTTATTTTTCAAAGTTGTTGAGCCTCTATTTAGAG
* * *
11544823 GAGCTTTTTATTTTTCAAAGTTGTTAAGTCTCTATTTAGAG
1 GAGCATTTTATTTTTCAAAGTTGTTGAGCCTCTATTTAGAG
* ** *
11544864 GAGCCTTTTATTTTTATCAAAGTTGTTGAGCCTCTGCTTAGAT
1 GAGCATTTTA-TTTT-TCAAAGTTGTTGAGCCTCTATTTAGAG
*
11544907 GAGCATTGTTTATTTTCCAAAGTTGTTGAGCCTCTGA-TTAGAG
1 GAGCA-T-TTTATTTTTCAAAGTTGTTGAGCCTCT-ATTTAGAG
* * *
11544950 GAGCTTTATTTATTTTTTCCAAAAGTTG-TGAACTTCTATTTAGAG
1 GAGC-AT-TTTA-TTTTT-C-AAAGTTGTTGAGCCTCTATTTAGAG
11544995 GAG
1 GAG
11544998 TCAGAGTCAA
Statistics
Matches: 382, Mismatches: 61, Indels: 48
0.78 0.12 0.10
Matches are distributed among these distances:
39 1 0.00
40 2 0.01
41 166 0.43
42 52 0.14
43 92 0.24
44 10 0.03
45 48 0.13
46 11 0.03
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (41 bp):
GAGCATTTTATTTTTCAAAGTTGTTGAGCCTCTATTTAGAG
Found at i:11545143 original size:16 final size:16
Alignment explanation
Indices: 11545122--11545158 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
11545112 TTTTACTAAT
*
11545122 AAAAAAATAAAAATTA
1 AAAAAAATAAAAAATA
11545138 AAAAAAATAAAAAATA
1 AAAAAAATAAAAAATA
11545154 AAAAA
1 AAAAA
11545159 GCTGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAAAATAAAAAATA
Found at i:11557933 original size:23 final size:23
Alignment explanation
Indices: 11557907--11557952 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
11557897 CATTTCCTTC
11557907 TTTTTTTTTCTTTTTGT-TGTTGG
1 TTTTTTTTT-TTTTTGTATGTTGG
*
11557930 TTTTTTTTTTTTTTTTATGTTGG
1 TTTTTTTTTTTTTTGTATGTTGG
11557953 CAATGGTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.80
Consensus pattern (23 bp):
TTTTTTTTTTTTTTGTATGTTGG
Found at i:11559980 original size:3 final size:3
Alignment explanation
Indices: 11559974--11559998 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
11559964 AATTATTATG
11559974 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
11559999 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:11560918 original size:19 final size:19
Alignment explanation
Indices: 11560896--11560937 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
11560886 TAGGTTTTCC
*
11560896 TTTTTTCATTTTATTTTTA
1 TTTTTTCATTTCATTTTTA
11560915 TTTTTTCATTTCATTTTTA
1 TTTTTTCATTTCATTTTTA
11560934 TTTT
1 TTTT
11560938 ACTTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTCATTTCATTTTTA
Found at i:11560968 original size:11 final size:11
Alignment explanation
Indices: 11560954--11560989 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
11560944 TTTTAACCCA
11560954 TTTTATTTATT
1 TTTTATTTATT
11560965 TTTTATTTATT
1 TTTTATTTATT
*
11560976 TATTA-TTATT
1 TTTTATTTATT
11560986 TTTT
1 TTTT
11560990 TAAAAAAGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:11560976 original size:20 final size:20
Alignment explanation
Indices: 11560930--11560989 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
11560920 TCATTTCATT
* *
11560930 TTTATTTTACTTATTTTTAA
1 TTTATTTTATTTATTTTTTA
***
11560950 CCCATTTTATTTATTTTTTA
1 TTTATTTTATTTATTTTTTA
11560970 TTTA-TTTATTATTATTTTTT
1 TTTATTTTA-T-TTATTTTTT
11560990 TAAAAAAGGG
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
19 4 0.13
20 17 0.57
21 9 0.30
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTTTATTTATTTTTTA
Found at i:11561147 original size:19 final size:20
Alignment explanation
Indices: 11561117--11561174 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
11561107 TTTTCAGAAT
11561117 AATAATAAAAAAATCTTTTC-
1 AATAA-AAAAAAATCTTTTCA
* *
11561137 AATAAAAAAAAGTCCTTTCA
1 AATAAAAAAAAATCTTTTCA
* *
11561157 AATAAACAAAAATATTTT
1 AATAAAAAAAAATCTTTT
11561175 TTTAGGATTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 12 0.39
20 19 0.61
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAAAAAAATCTTTTCA
Found at i:11572811 original size:119 final size:119
Alignment explanation
Indices: 11572667--11572886 Score: 334
Period size: 119 Copynumber: 1.8 Consensus size: 119
11572657 GTTTCGTCTC
* *
11572667 GATCATTTCTTATGATTCATGGTTTCGTCCCGATCATTTATTTTTAACCTTGACTCGATCTTGGT
1 GATCATTTCTTATGATTCATGGTTTCATCCCGATCATTTATTTTTAACCTCGACTCGATCTTGGT
* * * *
11572732 CACTT-TATTTTGACTCATGGTTTTGTCTCAATCACTTGGTCTTGGCTCAGTCCA
66 CA-TTCCATCTTGACTCATAGTTTAGTCTCAATCACTTGGTCTTGGCTCAGTCCA
* * *
11572786 GATCATTTCTTATGATTCATGGTTTCATCCTGGTCATTTATTTTTTACCTCGACTCGATCTTGGT
1 GATCATTTCTTATGATTCATGGTTTCATCCCGATCATTTATTTTTAACCTCGACTCGATCTTGGT
*
11572851 CATTCCATCTTGACTCATAGTTTAGTCTCGATCACT
66 CATTCCATCTTGACTCATAGTTTAGTCTCAATCACT
11572887 CGATCTTAGT
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
118 2 0.02
119 88 0.98
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (119 bp):
GATCATTTCTTATGATTCATGGTTTCATCCCGATCATTTATTTTTAACCTCGACTCGATCTTGGT
CATTCCATCTTGACTCATAGTTTAGTCTCAATCACTTGGTCTTGGCTCAGTCCA
Found at i:11572901 original size:119 final size:119
Alignment explanation
Indices: 11572667--11572912 Score: 332
Period size: 119 Copynumber: 2.1 Consensus size: 119
11572657 GTTTCGTCTC
* *
11572667 GATCATTTCTTATGATTCATGGTTTCGTCCCGATCATTTATTTTTAACCTTGACTCGATCTTGGT
1 GATCATTTCTTATGATTCATGGTTTCATCCCGATCATTTATTTTTAACCTCGACTCGATCTTGGT
* * * * * * *
11572732 CACTTTATTTTGACTCATGGTTTTGTCTCAATCACTTGGTCTTGGCTCAGTCCA
66 CACTTCATCTTGACTCATAGTTTAGTCTCAATCACTCGATCTTAGCTCAGTCCA
* * *
11572786 GATCATTTCTTATGATTCATGGTTTCATCCTGGTCATTTATTTTTTACCTCGACTCGATCTTGGT
1 GATCATTTCTTATGATTCATGGTTTCATCCCGATCATTTATTTTTAACCTCGACTCGATCTTGGT
* * *
11572851 CA-TTCCATCTTGACTCATAGTTTAGTCTCGATCACTCGATCTTAGTTCAGTCTA
66 CACTT-CATCTTGACTCATAGTTTAGTCTCAATCACTCGATCTTAGCTCAGTCCA
*
11572905 GGTCATTT
1 GATCATTT
11572913 TTCAGATTTG
Statistics
Matches: 110, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
118 2 0.02
119 108 0.98
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.44
Consensus pattern (119 bp):
GATCATTTCTTATGATTCATGGTTTCATCCCGATCATTTATTTTTAACCTCGACTCGATCTTGGT
CACTTCATCTTGACTCATAGTTTAGTCTCAATCACTCGATCTTAGCTCAGTCCA
Done.