Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_pilon, 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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 17
Found at i:3479714 original size:36 final size:36
Alignment explanation
Indices: 3479670--3479761 Score: 166
Period size: 36 Copynumber: 2.6 Consensus size: 36
3479660 ATTTTTCTAC
3479670 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
3479706 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
* *
3479742 AAAAGTTCACAATGAGAAGA
1 AGAAGTTCATAATGAGAAGA
3479762 GCTTATTCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.18
Consensus pattern (36 bp):
AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
Found at i:3479725 original size:17 final size:17
Alignment explanation
Indices: 3479670--3479726 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
3479660 ATTTTTCTAC
3479670 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
3479687 AGAA-CTCATCTGAA-GAAGA
1 AGAAGTTCA--T-AATG-AGA
3479706 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
3479723 AGAA
1 AGAA
3479727 CTCATCTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 3 0.09
17 13 0.41
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:3479850 original size:16 final size:16
Alignment explanation
Indices: 3479831--3479886 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
3479821 CCAGAAAAGT
3479831 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
*
3479847 TCATCTGAA-GAAGAAGAAGT
1 TCA--T-AATG-AGAAGAA-C
3479867 TCATAATGAGAAGAAC
1 TCATAATGAGAAGAAC
3479883 TCAT
1 TCAT
3479887 CTGAAGAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 7 0.22
17 9 0.28
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.21
Consensus pattern (16 bp):
TCATAATGAGAAGAAC
Found at i:3479853 original size:155 final size:156
Alignment explanation
Indices: 3479672--3480040 Score: 695
Period size: 155 Copynumber: 2.3 Consensus size: 156
3479662 TTTTCTACAG
3479672 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAA
3479737 GAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGCAGA
66 GAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGCAGA
3479802 TATATTAGCATCAACCTTTCCAGA-A
131 TATATTAGCATCAACCTTTCCAGAGA
3479827 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAA
3479892 GAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGCAGA
66 GAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGCAGA
3479957 TATATTAGCATCAACCTTTCCAGAGA
131 TATATTAGCATCAACCTTTCCAGAGA
3479983 AAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGAACTCATCTG-A--AG-AAGAAGAAGTTCATAATGAGAAGA
3480041 GCTTATTCAA
Statistics
Matches: 209, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
155 154 0.74
156 28 0.13
157 1 0.00
159 2 0.01
160 24 0.11
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (156 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCTATCACAGAAGCAGA
TATATTAGCATCAACCTTTCCAGAGA
Found at i:3479874 original size:36 final size:35
Alignment explanation
Indices: 3479823--3479916 Score: 161
Period size: 36 Copynumber: 2.6 Consensus size: 35
3479813 CAACCTTTCC
3479823 AGAAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AGAAAAGTTCATAATGAGAAGAACTCATCTGAAGA
3479858 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AGAA-AAGTTCATAATGAGAAGAACTCATCTGAAGA
*
3479894 AGAAAAAGTTCACAATGAGAAGA
1 AG-AAAAGTTCATAATGAGAAGA
3479917 GCTTATTCAA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
35 4 0.07
36 50 0.89
37 2 0.04
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (35 bp):
AGAAAAGTTCATAATGAGAAGAACTCATCTGAAGA
Found at i:3480093 original size:124 final size:120
Alignment explanation
Indices: 3479863--3480139 Score: 355
Period size: 124 Copynumber: 2.3 Consensus size: 120
3479853 GAAGAAGAAG
3479863 AAGTTCATAATGAGAAGAACTCATCTG-A-AGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCA
* * * * * *
3479926 ACCTTTTGCATAATTCTATCACAGAAGCAGATATATTAGCATCAACCTTTCCAG-AGA
66 ACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACC---CCAGTAGA
* *
3479983 AAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATT
1 AAGTTCATAATGAGAAGAACTCATCTGAA-GAG-AAGAAAAAGTTCACAATGAGAAGAGCTTATT
* * * * * *
3480048 CAATCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCCCCAGTGGA
64 CAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACCCCAGTAGA
3480105 AAGTTCATAATGAGAAGAACTCATCTGAAGA-AAGA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGA
3480140 GAAGGATTTA
Statistics
Matches: 138, Mismatches: 14, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
119 4 0.03
120 27 0.20
121 7 0.05
122 31 0.22
123 2 0.01
124 67 0.49
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (120 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCA
ACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACATCAACCCCAGTAGA
Found at i:3480303 original size:3 final size:3
Alignment explanation
Indices: 3480295--3480335 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
3480285 ATTTATTTAT
*
3480295 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3480336 TAATATATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3485860 original size:36 final size:36
Alignment explanation
Indices: 3485808--3485879 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
3485798 TTACTTTCTG
*
3485808 TTTCAGATGCAACAGGATCCGAATCTAGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTAGTTCTTGGC
* *
3485844 TTTCAGAGGCATCAGGATCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTAGTTCTTGGC
3485880 GAATGCTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (36 bp):
TTTCAGAGGCAACAGGATCCGAATCTAGTTCTTGGC
Found at i:3487925 original size:18 final size:17
Alignment explanation
Indices: 3487898--3487946 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3487888 GATACCATGT
*
3487898 AGAAATCAGACTATAGAA
1 AGAAAACAGACTATAG-A
*
3487916 AGAAAACAGACTGTATAGT
1 AGAAAACAGAC--TATAGA
3487935 AGAAAACAGACT
1 AGAAAACAGACT
3487947 GTAAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.04
18 10 0.37
19 11 0.41
20 5 0.19
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.16
Consensus pattern (17 bp):
AGAAAACAGACTATAGA
Found at i:3489586 original size:35 final size:35
Alignment explanation
Indices: 3489540--3489611 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
3489530 CCAAAAAAGA
3489540 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
3489575 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
3489610 AG
1 AG
3489612 GGTTTTTAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:3490086 original size:2 final size:2
Alignment explanation
Indices: 3490079--3490109 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3490069 ATTTTATTAT
3490079 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3490110 TTCTTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3490288 original size:2 final size:2
Alignment explanation
Indices: 3490283--3490321 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3490273 CTTATAACTT
3490283 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3490322 TATTTTTCGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3490479 original size:41 final size:39
Alignment explanation
Indices: 3490434--3490510 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 39
3490424 AGGGCCCATT
* *
3490434 TTTTTGTTTTATTTCTAACTAAAGTCTCTCCCACTTTCCTA
1 TTTTTGTCTTATTTCTAACTAAAG-C-CCCCCACTTTCCTA
*
3490475 TTTTTGTCTTATTTCTGACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
3490511 GGTGAAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 10 0.30
40 1 0.03
41 22 0.67
ACGTcount: A:0.18, C:0.27, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTCCTA
Found at i:3494420 original size:11 final size:11
Alignment explanation
Indices: 3494404--3494429 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3494394 GGATTCTTTT
3494404 AATTCTTCAAG
1 AATTCTTCAAG
3494415 AATTCTTCAAG
1 AATTCTTCAAG
3494426 AATT
1 AATT
3494430 ATAGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (11 bp):
AATTCTTCAAG
Found at i:3495155 original size:16 final size:16
Alignment explanation
Indices: 3495134--3495190 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 16
3495124 AATCAAGAAC
3495134 AAAAAAGAAAAGAAGT
1 AAAAAAGAAAAGAAGT
* *
3495150 AAAAAAGAAAAAACAAGAAC
1 AAAAAAG--AAAAGAAG--T
3495170 AAAAAAGAAAAGAAGT
1 AAAAAAGAAAAGAAGT
3495186 AAAAA
1 AAAAA
3495191 TCAAAAGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 12 0.36
18 14 0.42
20 7 0.21
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.04
Consensus pattern (16 bp):
AAAAAAGAAAAGAAGT
Found at i:3495160 original size:21 final size:21
Alignment explanation
Indices: 3495136--3495183 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
3495126 TCAAGAACAA
*
3495136 AAAAGAA-AAGAAGTAAAAAAG
1 AAAAGAACAAGAA-CAAAAAAG
3495157 AAAA-AACAAGAACAAAAAAG
1 AAAAGAACAAGAACAAAAAAG
3495177 AAAAGAA
1 AAAAGAA
3495184 GTAAAAATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAGAACAAGAACAAAAAAG
Found at i:3495794 original size:25 final size:25
Alignment explanation
Indices: 3495760--3495814 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
3495750 ATGAAAGTTG
*
3495760 GGAGTCAGAGAACACTTCCAGTAGA
1 GGAGCCAGAGAACACTTCCAGTAGA
3495785 GGAGCCAGAGAACACTTCCAGTAGA
1 GGAGCCAGAGAACACTTCCAGTAGA
3495810 GGAGC
1 GGAGC
3495815 ATGCAAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.31, T:0.13
Consensus pattern (25 bp):
GGAGCCAGAGAACACTTCCAGTAGA
Found at i:3496853 original size:36 final size:36
Alignment explanation
Indices: 3496749--3496872 Score: 140
Period size: 36 Copynumber: 3.4 Consensus size: 36
3496739 ACTCAAGATT
* * *
3496749 GTTTTTCTTAAAACAAATTTCGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * **
3496785 GTTTCTTTTGGAACTACGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
* *
3496822 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
3496858 ATTACTCTTGAAACA
1 GTTTCTCTTGAAACA
3496873 CAAAATCTTC
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
36 41 0.58
37 30 0.42
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:3497687 original size:106 final size:106
Alignment explanation
Indices: 3497535--3497960 Score: 699
Period size: 106 Copynumber: 4.0 Consensus size: 106
3497525 TCGCGCCACC
* *
3497535 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAACTTCTCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
*
3497600 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* *
3497641 CAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
* **
3497706 TTCAGAGCCAATTTCAACTTCACAGCGAAGGGCATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* *
3497747 CGAGACAGCACAAGTTCAACTTCACAACGGAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
*
3497812 TTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
* *
3497853 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGT
1 CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
* * * *
3497918 TCCATAACCAATTTCAACTTCACGGCGGAGGATATTGGACT
66 TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
3497959 CG
1 CG
3497961 GAACAATACA
Statistics
Matches: 297, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 297 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (106 bp):
CGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAAT
TTCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACT
Found at i:3498494 original size:35 final size:35
Alignment explanation
Indices: 3498438--3498514 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
3498428 ATGTAACCAA
*
3498438 AAAAAAGAGTTGGATTAGGACTCAAATACTAGTCT
1 AAAATAGAGTTGGATTAGGACTCAAATACTAGTCT
3498473 AAAATAGAGTTGGAATT-GGACTCAAATACTAGTCT
1 AAAATAGAGTTGG-ATTAGGACTCAAATACTAGTCT
3498508 AAAATAG
1 AAAATAG
3498515 GGTTTTTTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 37 0.93
36 3 0.08
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.26
Consensus pattern (35 bp):
AAAATAGAGTTGGATTAGGACTCAAATACTAGTCT
Found at i:3498915 original size:17 final size:18
Alignment explanation
Indices: 3498889--3498928 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3498879 ATTATATGGA
3498889 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
3498905 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
3498923 TATTAT
1 TATTAT
3498929 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:3499114 original size:2 final size:2
Alignment explanation
Indices: 3499109--3499134 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3499099 CCTATTATTA
3499109 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3499135 TCTTAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3499195 original size:2 final size:2
Alignment explanation
Indices: 3499190--3499291 Score: 65
Period size: 2 Copynumber: 53.5 Consensus size: 2
3499180 CTTATAACTT
* *
3499190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TT TA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
3499230 TT TCA TT TT TA T- TCA T- TA T- TA TA T- TA TT TT TA -A AA TA TA
1 TA T-A TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3499269 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
3499292 TATTATTTTC
Statistics
Matches: 81, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
1 7 0.09
2 72 0.89
3 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (2 bp):
TA
Found at i:3499308 original size:69 final size:69
Alignment explanation
Indices: 3499195--3499333 Score: 253
Period size: 69 Copynumber: 2.0 Consensus size: 69
3499185 AACTTTATAT
*
3499195 ATATATATATATATATATATATATTTATTTATTATTTTCATTTTTATTCATTATTATATTATTTT
1 ATATATATATATATATATATATATATATTTATTATTTTCATTTTTATTCATTATTATATTATTTT
3499260 TAAA
66 TAAA
3499264 ATATATATATATATATATATATATATA-TTATTATTTTCATTTTTTATTCATTATTATATTATTT
1 ATATATATATATATATATATATATATATTTATTATTTTCA-TTTTTATTCATTATTATATTATTT
3499328 TTAAA
65 TTAAA
3499333 A
1 A
3499334 AAAATCTTGT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
68 12 0.18
69 56 0.82
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (69 bp):
ATATATATATATATATATATATATATATTTATTATTTTCATTTTTATTCATTATTATATTATTTT
TAAA
Found at i:3499447 original size:40 final size:39
Alignment explanation
Indices: 3499404--3499478 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
3499394 AGGGCCCATT
* * * *
3499404 TTTTTATTTTATTTTTAACTAAAGTCTCCCACTTTCCTC
1 TTTTTATCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
* *
3499443 TTTTTGTCTTATTTCTGACTAAAGCCCCCCACTTTC
1 TTTTTATCTTATTTCTAACTAAAGCCCCCCACTTTC
3499479 GGTGAAGTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.19, C:0.27, G:0.05, T:0.49
Consensus pattern (39 bp):
TTTTTATCTTATTTCTAACTAAAGCCCCCCACTTTCCTC
Found at i:3499656 original size:9 final size:9
Alignment explanation
Indices: 3499625--3499710 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
3499615 ATTACTTTAC
3499625 TATTT-TTT
1 TATTTATTT
* *
3499633 TCTTTATCT
1 TATTTATTT
3499642 TATTTA-TT
1 TATTTATTT
3499650 TATTT-TATT
1 TATTTAT-TT
3499659 TATTTTATTT
1 TA-TTTATTT
*
3499669 T-TTTCTTT
1 TATTTATTT
*
3499677 TATTATATTC
1 TATT-TATTT
* *
3499687 TCTTTATCT
1 TATTTATTT
*
3499696 TATTTCTTT
1 TATTTATTT
3499705 TATTTA
1 TATTTA
3499711 CCTTGTTTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 13
0.68 0.17 0.15
Matches are distributed among these distances:
8 17 0.30
9 27 0.47
10 12 0.21
11 1 0.02
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.74
Consensus pattern (9 bp):
TATTTATTT
Found at i:3499660 original size:22 final size:21
Alignment explanation
Indices: 3499625--3499680 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3499615 ATTACTTTAC
*
3499625 TATTTTTTTCTTTATCTTATT
1 TATTTTTTTATTTATCTTATT
*
3499646 TATTTATTTTATTTATTTTATT
1 TATTT-TTTTATTTATCTTATT
*
3499668 TTTTTCTTTTATT
1 TATTT-TTTTATT
3499681 ATATTCTCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 5 0.17
22 25 0.83
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (21 bp):
TATTTTTTTATTTATCTTATT
Found at i:3499703 original size:13 final size:12
Alignment explanation
Indices: 3499625--3499710 Score: 64
Period size: 13 Copynumber: 6.5 Consensus size: 12
3499615 ATTACTTTAC
*
3499625 TATTTTTTTCTT
1 TATTTATTTCTT
*
3499637 TATCTTATTTATT
1 TAT-TTATTTCTT
*
3499650 TATTTTATTTATTT
1 TA-TTTATTT-CTT
*
3499664 TATTTTTTTCTTT
1 TATTTATTTC-TT
3499677 TATTATATTCTCTT
1 TATT-TATT-TCTT
3499691 TATCTTATTTCTTT
1 TAT-TTATTTC-TT
3499705 TATTTA
1 TATTTA
3499711 CCTTGTTTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
12 3 0.05
13 32 0.53
14 22 0.37
15 3 0.05
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTTATTTCTT
Found at i:3501936 original size:21 final size:21
Alignment explanation
Indices: 3501910--3501949 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3501900 TCTTTATTTT
**
3501910 ATAAAAATTTTATTCAGTTTG
1 ATAAAAATTCAATTCAGTTTG
3501931 ATAAAAATTCAATTCAGTT
1 ATAAAAATTCAATTCAGTT
3501950 GCAACTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (21 bp):
ATAAAAATTCAATTCAGTTTG
Found at i:3503069 original size:12 final size:12
Alignment explanation
Indices: 3503052--3503076 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3503042 CATTTAATTT
3503052 TTTTCTTATGTC
1 TTTTCTTATGTC
3503064 TTTTCTTATGTC
1 TTTTCTTATGTC
3503076 T
1 T
3503077 CGCCAATTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTCTTATGTC
Found at i:3506611 original size:16 final size:16
Alignment explanation
Indices: 3506590--3506624 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3506580 AATTAAAAAA
* *
3506590 ATAAAACTTATTAAAT
1 ATAAAACTAAATAAAT
3506606 ATAAAACTAAATAAAT
1 ATAAAACTAAATAAAT
3506622 ATA
1 ATA
3506625 CTTATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAAAACTAAATAAAT
Found at i:3507886 original size:21 final size:21
Alignment explanation
Indices: 3507861--3507918 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
3507851 TAAGTTTGCA
* *
3507861 CCGAAGTG-CCACATATTTCTC
1 CCGAAG-GACCACATAATTATC
3507882 CCGAAGGACCACATAATTATC
1 CCGAAGGACCACATAATTATC
3507903 CCGAAGGACCACATAA
1 CCGAAGGACCACATAA
3507919 AACCCTCGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.34, C:0.31, G:0.16, T:0.19
Consensus pattern (21 bp):
CCGAAGGACCACATAATTATC
Found at i:3508601 original size:22 final size:21
Alignment explanation
Indices: 3508573--3508643 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
3508563 ACCCTCACAA
*
3508573 TATCGATCCCATCCTTAACTGG
1 TATCGATCCC-TCCTTAACTAG
* * * *
3508595 TATCGATACCGCCCTCAC-AG
1 TATCGATCCCTCCTTAACTAG
3508615 TATCGATGCCCTCCTTAACTAG
1 TATCGAT-CCCTCCTTAACTAG
3508637 TATCGAT
1 TATCGAT
3508644 AATACCTTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
20 8 0.21
21 12 0.32
22 18 0.47
ACGTcount: A:0.24, C:0.32, G:0.14, T:0.30
Consensus pattern (21 bp):
TATCGATCCCTCCTTAACTAG
Found at i:3508603 original size:42 final size:42
Alignment explanation
Indices: 3508549--3508649 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
3508539 ATACCATCCC
3508549 CTGGTATCGATACTACCCTCACAATATCGAT-CCCATCCTTAA
1 CTGGTATCGATACTACCCTCACAATATCGATGCCC-TCCTTAA
** *
3508591 CTGGTATCGATACCGCCCTCACAGTATCGATGCCCTCCTTAA
1 CTGGTATCGATACTACCCTCACAATATCGATGCCCTCCTTAA
* *
3508633 CTAGTATCGATAATACC
1 CTGGTATCGATACTACC
3508650 TTTAAGAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 48 0.94
43 3 0.06
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.28
Consensus pattern (42 bp):
CTGGTATCGATACTACCCTCACAATATCGATGCCCTCCTTAA
Found at i:3510611 original size:26 final size:26
Alignment explanation
Indices: 3510580--3510633 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
3510570 AGCATAATCA
*
3510580 ACTACCTTCCCATCTTGCATTAAGAC
1 ACTACCTTCCCATATTGCATTAAGAC
*
3510606 ACTACCTTCTCATATTGCATTAAGAC
1 ACTACCTTCCCATATTGCATTAAGAC
3510632 AC
1 AC
3510634 ATCCCAAACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.31
Consensus pattern (26 bp):
ACTACCTTCCCATATTGCATTAAGAC
Found at i:3514097 original size:21 final size:21
Alignment explanation
Indices: 3514068--3514167 Score: 80
Period size: 21 Copynumber: 4.7 Consensus size: 21
3514058 AATTTGCGCC
*
3514068 GAAGTACCACATAATTGTCCT
1 GAAGGACCACATAATTGTCCT
*
3514089 GAAGGACCACATAGGTT-TGCACT
1 GAAGGACCACATA-ATTGT-C-CT
* * *
3514112 GAAGTG-CCACATATTTTTCCC
1 GAAG-GACCACATAATTGTCCT
*
3514133 GAATGACCACATAATTGT-CT
1 GAAGGACCACATAATTGTCCT
3514153 CGAAGGACCACATAA
1 -GAAGGACCACATAA
3514168 AACCCTCGAC
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
20 2 0.03
21 40 0.63
22 6 0.10
23 14 0.22
24 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (21 bp):
GAAGGACCACATAATTGTCCT
Found at i:3517172 original size:46 final size:46
Alignment explanation
Indices: 3517117--3517210 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
3517107 CTTGAAAAGG
*
3517117 AAAATAATTATTGAGGATTTTAAGATTTAATGAATAATGGAAAATA
1 AAAACAATTATTGAGGATTTTAAGATTTAATGAATAATGGAAAATA
*
3517163 AAAACAATTATTGAGGATTTTAAGATTTAATGAGTAATGGAAAATA
1 AAAACAATTATTGAGGATTTTAAGATTTAATGAATAATGGAAAATA
3517209 AA
1 AA
3517211 GATTGTTCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.50, C:0.01, G:0.16, T:0.33
Consensus pattern (46 bp):
AAAACAATTATTGAGGATTTTAAGATTTAATGAATAATGGAAAATA
Found at i:3520363 original size:32 final size:32
Alignment explanation
Indices: 3520327--3520473 Score: 124
Period size: 32 Copynumber: 4.6 Consensus size: 32
3520317 CACTGTTGCA
*
3520327 CATTATCTAAATGAAACACTTATACTACTGTG
1 CATTATCTAAATGCAACACTTATACTACTGTG
* *
3520359 CATTATCTAAATACAACA-TTA-A-TAATGATG
1 CATTATCTAAATGCAACACTTATACTACTG-TG
*
3520389 CACATTATCTAAATGCAACA-TTGATGCTGA-TGTG
1 --CATTATCTAAATGCAACACTT-ATACT-ACTGTG
* * * * * *
3520423 CATTATATGAATGCAACACTAACACTTCTTTG
1 CATTATCTAAATGCAACACTTATACTACTGTG
3520455 CATTATCTAAATGCAACAC
1 CATTATCTAAATGCAACAC
3520474 ACTTCTAGTA
Statistics
Matches: 92, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
29 4 0.04
30 3 0.03
31 3 0.03
32 74 0.80
33 2 0.02
34 2 0.02
35 3 0.03
36 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (32 bp):
CATTATCTAAATGCAACACTTATACTACTGTG
Found at i:3520409 original size:16 final size:16
Alignment explanation
Indices: 3520359--3520410 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
3520349 TACTACTGTG
*
3520359 CATTATCTAAATACAA
1 CATTATCTAAATGCAA
*
3520375 CATTA-ATAATGATGC-A
1 CATTATCTAA--ATGCAA
3520391 CATTATCTAAATGCAA
1 CATTATCTAAATGCAA
3520407 CATT
1 CATT
3520411 GATGCTGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
15 7 0.24
16 16 0.55
17 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (16 bp):
CATTATCTAAATGCAA
Found at i:3521488 original size:21 final size:21
Alignment explanation
Indices: 3521462--3521513 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3521452 CCCAATATTT
** *
3521462 GGTATGGATATTAGTTCATTC
1 GGTATGGATATTAACTCATCC
3521483 GGTATGGATATTAACTCATCC
1 GGTATGGATATTAACTCATCC
*
3521504 GATATGGATA
1 GGTATGGATA
3521514 CCAGCAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.37
Consensus pattern (21 bp):
GGTATGGATATTAACTCATCC
Found at i:3522771 original size:32 final size:31
Alignment explanation
Indices: 3522735--3522844 Score: 130
Period size: 32 Copynumber: 3.5 Consensus size: 31
3522725 ACTGCTATGT
*
3522735 ATTATATGAATGCGACCCTAACACTACTGTGC
1 ATTATATGAATGC-ACACTAACACTACTGTGC
* *
3522767 ATTATTTGAATGTCACACTAACACTATTGTGC
1 ATTATATGAATG-CACACTAACACTACTGTGC
* *
3522799 ATTATATGAAAGCAACACTGACACTACTGTGC
1 ATTATATGAATGC-ACACTAACACTACTGTGC
* *
3522831 ATTATCTAAATGCA
1 ATTATATGAATGCA
3522845 ACAAATTATT
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
31 2 0.03
32 63 0.95
33 1 0.02
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (31 bp):
ATTATATGAATGCACACTAACACTACTGTGC
Found at i:3523836 original size:21 final size:21
Alignment explanation
Indices: 3523798--3523852 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
3523788 CCAATCTTCA
** *
3523798 GTATGGATACCAGTTCATTCG
1 GTATGGATACCAACTCATCCG
* *
3523819 GTATAGATACCAACTCATCCT
1 GTATGGATACCAACTCATCCG
3523840 GTATGGATACCAA
1 GTATGGATACCAA
3523853 TGGTATCGAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (21 bp):
GTATGGATACCAACTCATCCG
Found at i:3524447 original size:10 final size:10
Alignment explanation
Indices: 3524432--3524457 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3524422 TGAAAAAATA
3524432 ATTTAATATT
1 ATTTAATATT
3524442 ATTTAATATT
1 ATTTAATATT
3524452 ATTTAA
1 ATTTAA
3524458 AAAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATTTAATATT
Found at i:3527043 original size:17 final size:17
Alignment explanation
Indices: 3527000--3527043 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
3526990 AAAAGGATAA
*
3527000 TAATAATAATAATAAAT
1 TAATAATAAAAATAAAT
* *
3527017 AAAAAATAAAAATAAAT
1 TAATAATAAAAATAAAT
*
3527034 TAATACTAAA
1 TAATAATAAA
3527044 TTAAAACCCA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (17 bp):
TAATAATAAAAATAAAT
Found at i:3546288 original size:20 final size:19
Alignment explanation
Indices: 3546265--3546323 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
3546255 AAGATATAGC
3546265 AAAAAGA-AGATAAAAAACAT
1 AAAAAGAGAGA-AAAAAA-AT
*
3546285 AAAAAGAGAGAAAAGAAAT
1 AAAAAGAGAGAAAAAAAAT
3546304 AAAGAAGAGAGAGAAAAAAA
1 AAA-AAGAGAGA-AAAAAAA
3546324 AGGTAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.15
20 20 0.59
21 9 0.26
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.05
Consensus pattern (19 bp):
AAAAAGAGAGAAAAAAAAT
Found at i:3548245 original size:54 final size:54
Alignment explanation
Indices: 3548157--3548610 Score: 527
Period size: 54 Copynumber: 8.4 Consensus size: 54
3548147 CCGAACAATA
* * **
3548157 TGATGTTTTCAAATGGATTTGGAAAGAAGCTAAGCCTAATAATCAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCT
* * * *
3548211 TGATGTTTTTAAATGGATTTTGAAGGAAGTTAAGCCTAATTTTCAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCT
* * * * * *
3548265 TGATGTATTCAAATGAATTTTGAAAGAAACTAAGCCGAATTTTTAGGAGTTTAT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCT
*
3548319 TGATGTTTT-AAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCT
** * * *
3548372 TGATGTTTAT-TTATGAAATTCT-AAAGGAGCTAAGCCTAATTTTCAAGGGTTTCT
1 TGATGTTT-TCAAATG-AATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCT
* * * * **
3548426 TGATGTCTTCAAATGAATTTTTAAAGAAGCTAAGCTTAATTTTTAGAAGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCT
* *
3548480 TGATGTTTTCAAATAAATTATTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATT-TTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCT
* * * *
3548535 TGATGATAGTTGCAAATGAATTTTGAAAAAAGCTAAACCTGATTTTCAGGGGTTTCT
1 TGATG-T--TTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCT
* *
3548592 TGATGTCTTCAAATTAATT
1 TGATGTTTTCAAATGAATT
3548611 GTTAGGATTT
Statistics
Matches: 338, Mismatches: 54, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
53 52 0.15
54 196 0.58
55 41 0.12
56 2 0.01
57 36 0.11
58 11 0.03
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (54 bp):
TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCT
Found at i:3548352 original size:161 final size:162
Alignment explanation
Indices: 3548157--3548610 Score: 590
Period size: 161 Copynumber: 2.8 Consensus size: 162
3548147 CCGAACAATA
* * **
3548157 TGATGTTTTCAAATGGATTTGGAAAGAAGCTAAGCCTAATAATCAGGGGTTTCTTGATGTTTTTA
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTTA
* * *
3548222 AATGGATTTTGAAGGAAGTTAAGCCTAATTTTCAGGGGTTTCTTGATGTATTCAAATGAATTTTG
66 AATGAATTTTGAAGGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTCAAATGAATTTTG
*
3548287 AAAGAAACTAAGCCGAATTTTTAGGAGTTTAT
131 AAAGAAACTAAGCCGAATTTTTAGAAGTTTAT
*
3548319 TGATGTTTT-AAATGAATTTTGAAAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTATT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTT-TT
* * * *
3548383 -TATGAAATTCTAAAGG-AGCTAAGCCTAATTTTCAAGGGTTTCTTGATGTCTTCAAATGAATTT
65 AAATG-AATTTTGAAGGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTCAAATGAATTT
* * ** *
3548446 TTAAAGAAGCTAAGCTTAATTTTTAGAAGTTTCT
129 TGAAAGAAACTAAGCCGAATTTTTAGAAGTTTAT
* *
3548480 TGATGTTTTCAAATAAATTATTGAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATAGT
1 TGATGTTTTCAAATGAATT-TTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATG-T--T
** ** * * *
3548545 TGCAAATGAATTTTGAAAAAAGCTAAACCTGATTTTCAGGGGTTTCTTGATGTCTTCAAATTAAT
62 TTTAAATGAATTTTGAAGGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTCAAATGAAT
3548610 T
127 T
3548611 GTTAGGATTT
Statistics
Matches: 251, Mismatches: 32, Indels: 14
0.85 0.11 0.05
Matches are distributed among these distances:
161 131 0.52
162 27 0.11
163 38 0.15
164 1 0.00
165 7 0.03
166 47 0.19
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (162 bp):
TGATGTTTTCAAATGAATTTTGAAAGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTTTTTA
AATGAATTTTGAAGGAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTCAAATGAATTTTG
AAAGAAACTAAGCCGAATTTTTAGAAGTTTAT
Found at i:3548672 original size:144 final size:144
Alignment explanation
Indices: 3548461--3548877 Score: 538
Period size: 144 Copynumber: 2.9 Consensus size: 144
3548451 GAAGCTAAGC
* *
3548461 TTAATTTTTAGAAGTTTCTTGATGTTTTCAAATAAATTATTGAAAGAAGCTAAGCCTAATTTTTA
1 TTAATTTTTAGGAGTTTCTTGATGTTTTCAAATAAATTATTGAAAGAAGCTAAGCCTTATTTTTA
* * * * *
3548526 GGGGTTTCTTGATGATAGTTGCAAATGAATTTTGAAAAAAGCTAAACCTGATTTTCAGGGGTTTC
66 GGGGTTTCTTGATGATAATTGCAAATGAATTTTAAAAAAATCTAAGCCTGATTTTTAGGGGTTTC
3548591 TTGATGTCTTCAAA
131 TTGATGTCTTCAAA
* * * *
3548605 TTAATTGTTAGGATTTTCTTGATGTTTTTAAATTAATTATTGAAAGAAGCTAA-CCTTAGTTTTT
1 TTAATTTTTAGGAGTTTCTTGATGTTTTCAAATAAATTATTGAAAGAAGCTAAGCCTTA-TTTTT
* * * * *
3548669 AGGGGTTTCTTGACGATAAATGCAAATGAATTTTCAAAAAATCTAAGCTTGATTTTTAGGGTTTT
65 AGGGGTTTCTTGATGATAATTGCAAATGAATTTTAAAAAAATCTAAGCCTGATTTTTAGGGGTTT
3548734 CTTGATGTCTTCAAA
130 CTTGATGTCTTCAAA
* * * * * * * *
3548749 TTAATTTTTAGGGGTTTCTAGATGTATCCAAATGAATT-TTTAAAGGAGCTAAGCCTGATTTTTA
1 TTAATTTTTAGGAGTTTCTTGATGTTTTCAAATAAATTATTGAAAGAAGCTAAGCCTTATTTTTA
* * *
3548813 GGGGTTTCTTGATG-T-CTT-CAAATGAATATTTAAAAAAATATAAGCCTAATTTTTAGGGGTTT
66 GGGGTTTCTTGATGATAATTGCAAATGAAT-TTTAAAAAAATCTAAGCCTGATTTTTAGGGGTTT
3548875 CTT
130 CTT
3548878 AATGATAATT
Statistics
Matches: 236, Mismatches: 34, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
140 9 0.04
141 33 0.14
142 1 0.00
143 35 0.15
144 158 0.67
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (144 bp):
TTAATTTTTAGGAGTTTCTTGATGTTTTCAAATAAATTATTGAAAGAAGCTAAGCCTTATTTTTA
GGGGTTTCTTGATGATAATTGCAAATGAATTTTAAAAAAATCTAAGCCTGATTTTTAGGGGTTTC
TTGATGTCTTCAAA
Found at i:3548756 original size:32 final size:32
Alignment explanation
Indices: 3548720--3548790 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
3548710 TCTAAGCTTG
* * * * *
3548720 ATTTTTAGGGTTTTCTTGATGTCTTCAAATTA
1 ATTTTTAGGGGTTTCTAGATGTATCCAAATGA
3548752 ATTTTTAGGGGTTTCTAGATGTATCCAAATGA
1 ATTTTTAGGGGTTTCTAGATGTATCCAAATGA
3548784 ATTTTTA
1 ATTTTTA
3548791 AAGGAGCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.49
Consensus pattern (32 bp):
ATTTTTAGGGGTTTCTAGATGTATCCAAATGA
Found at i:3548801 original size:86 final size:89
Alignment explanation
Indices: 3548664--3548844 Score: 242
Period size: 86 Copynumber: 2.1 Consensus size: 89
3548654 CTAACCTTAG
* * *
3548664 TTTTTAGGGGTTTCTTGACGATAAATGCAAATGAATTTTCAAAAAATCTAAGCTTGATTTTTAGG
1 TTTTTAGGGGTTTCTTGACGATAAATCCAAATGAATTTTCAAAAAAGCTAAGCCTGATTTTTAGG
* *
3548729 GTTTTCTTGATGTCTTCAAATTAA
66 GGTTTCTTGATGTCTTCAAATGAA
** * **
3548753 TTTTTAGGGGTTTC-T-A-GATGTATCCAAATGAATTTTTAAAGGAGCTAAGCCTGATTTTTAGG
1 TTTTTAGGGGTTTCTTGACGATAAATCCAAATGAATTTTCAAAAAAGCTAAGCCTGATTTTTAGG
3548815 GGTTTCTTGATGTCTTCAAATGAA
66 GGTTTCTTGATGTCTTCAAATGAA
*
3548839 TATTTA
1 TTTTTA
3548845 AAAAAATATA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
86 65 0.80
87 1 0.01
88 1 0.01
89 14 0.17
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (89 bp):
TTTTTAGGGGTTTCTTGACGATAAATCCAAATGAATTTTCAAAAAAGCTAAGCCTGATTTTTAGG
GGTTTCTTGATGTCTTCAAATGAA
Found at i:3548835 original size:54 final size:55
Alignment explanation
Indices: 3548750--3548877 Score: 168
Period size: 54 Copynumber: 2.3 Consensus size: 55
3548740 GTCTTCAAAT
* * ** *
3548750 TAATTTTTAGGGGTTTCTAGATGTATCCAAATGAAT-TTTTAAAGGAGCTAAGCC
1 TAATTTTTAGGGGTTTCTTGATGTATCCAAATGAATATTTAAAAAAAGATAAGCC
* * * *
3548804 TGATTTTTAGGGGTTTCTTGATGTCTTCAAATGAATATTTAAAAAAATATAAGCC
1 TAATTTTTAGGGGTTTCTTGATGTATCCAAATGAATATTTAAAAAAAGATAAGCC
3548859 TAATTTTTAGGGGTTTCTT
1 TAATTTTTAGGGGTTTCTT
3548878 AATGATAATT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 32 0.51
55 31 0.49
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.41
Consensus pattern (55 bp):
TAATTTTTAGGGGTTTCTTGATGTATCCAAATGAATATTTAAAAAAAGATAAGCC
Found at i:3549831 original size:37 final size:37
Alignment explanation
Indices: 3549776--3549889 Score: 117
Period size: 37 Copynumber: 3.1 Consensus size: 37
3549766 ACCTATTTCG
* *
3549776 AGAAATT-ATTT-TGTCATTCTTAAGATTGTTTCTCT
1 AGAAATTCATTTGAGTCATTCTTAGGATTGTTTCTCT
* *
3549811 AGAAATTCATTTGAGTCATTCTTAGGAATGTTTTTCT
1 AGAAATTCATTTGAGTCATTCTTAGGATTGTTTCTCT
* * * * *
3549848 AG-AATGTCGTTTGAATCCTTCTTAGGATTGTCTCCCT
1 AGAAAT-TCATTTGAGTCATTCTTAGGATTGTTTCTCT
3549885 AGAAA
1 AGAAA
3549890 CATTTTCAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
35 7 0.11
36 7 0.11
37 48 0.75
38 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (37 bp):
AGAAATTCATTTGAGTCATTCTTAGGATTGTTTCTCT
Found at i:3550837 original size:203 final size:205
Alignment explanation
Indices: 3550474--3551108 Score: 671
Period size: 203 Copynumber: 3.1 Consensus size: 205
3550464 CATTTCCAAT
*
3550474 GAAGAAGTTCATAATTAGAAGAACTTGTTCAACCTCAGCTTGATTCATCACATAAGGAGTTGAAT
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTCAGCTTGATTCATCACATAAGGAGTTGAAT
* ** * * *
3550539 CAATACCAGCACTTTTCTCGATTCCATAATATAAGAAGTTGGATCAACATCGTCTTTTCACTCGA
66 CAACACCAGCACTTGACTCGATTCCATAACATAAGAAGTTGGATCAACATCATCTTTTCACTCAA
* * * * * * *
3550604 TTCCATCATAGAATGAGGTGGATCAACATTTCCAATGGAATGGTTTGCAATGAGAAGAACTCGTC
131 ATCCATCACAAAAGGAGGTGGATCAACATTTCCAATGGAAGGGTTCGCAATGAGAAGAACTCATC
3550669 CGATGAGGGA
196 CGATGAGGGA
*
3550679 GAAGAATTTCATAATGAGAAGAACTTGTTCAACCTCAGCTTGATTCCATCACATAAGGAGTTAGA
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTCAGCTTGATT-CATCACATAAGGAGTT-GA
* * **
3550744 A-CAACACC-G-ACATTGACTC-A-TCCATAGCATAAGGAGTTGGATCAACATCATCTCTTT-GT
64 ATCAACACCAGCAC-TTGACTCGATTCCATAACATAAGAAGTTGGATCAACATCATCT-TTTCAC
* * *
3550803 TCAAATCCATCACAAAAGGAGGTGGATTAACATTTCCAATTGAAGGGTTCGTAATGAGAAGAACT
127 TCAAATCCATCACAAAAGGAGGTGGATCAACATTTCCAATGGAAGGGTTCGCAATGAGAAGAACT
3550868 CATCCGATGAGGGA
192 CATCCGATGAGGGA
* * * * *
3550882 GAAGAAGTTCATAATGAGAATAATTTGTTCAACCTCAGCTCGATTCATCACATAGGGAGTTGGAT
1 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTCAGCTTGATTCATCACATAAGGAGTTGAAT
* ** * * * * ** ** **
3550947 CAGCACCAGCACTTTTCTCGATTCCATCATATAAGAAGTTAGATCAGCATCGCCTTTTTGCTTGA
66 CAACACCAGCACTTGACTCGATTCCATAACATAAGAAGTTGGATCAACATCATCTTTTCACTCAA
* * * * * ** *
3551012 TTTCATCACAAAAGGAGGTCGATCAACA-TTGCAGTGGATA--GTTCATAATGTGAAGAACTCAT
131 ATCCATCACAAAAGGAGGTGGATCAACATTTCCAATGGA-AGGGTTCGCAATGAGAAGAACTCAT
* * *
3551074 TCGAGGA-GAA
195 CCGATGAGGGA
*
3551084 TGAAG-AGTTAATAATGAGAAGAACT
1 -GAAGAAGTTCATAATGAGAAGAACT
3551109 AATTCGAGGA
Statistics
Matches: 361, Mismatches: 57, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
201 2 0.01
202 40 0.11
203 173 0.48
204 19 0.05
205 102 0.28
206 22 0.06
207 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (205 bp):
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTCAGCTTGATTCATCACATAAGGAGTTGAAT
CAACACCAGCACTTGACTCGATTCCATAACATAAGAAGTTGGATCAACATCATCTTTTCACTCAA
ATCCATCACAAAAGGAGGTGGATCAACATTTCCAATGGAAGGGTTCGCAATGAGAAGAACTCATC
CGATGAGGGA
Found at i:3551107 original size:38 final size:38
Alignment explanation
Indices: 3551051--3551146 Score: 131
Period size: 38 Copynumber: 2.5 Consensus size: 38
3551041 TGCAGTGGAT
* * * *
3551051 AGTTCATAATGTGAAGAACTCATTCGAGGAGAATGAAG
1 AGTTAATAATGAGAAGAACTAATTCGAGGAGAATAAAG
*
3551089 AGTTAATAATGAGAAGAACTAATTCGAGGAGACTAAAG
1 AGTTAATAATGAGAAGAACTAATTCGAGGAGAATAAAG
3551127 AGTTCAA-AATGAGAAGAACT
1 AGTT-AATAATGAGAAGAACT
3551147 TGTAGCTCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
38 50 0.96
39 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.22
Consensus pattern (38 bp):
AGTTAATAATGAGAAGAACTAATTCGAGGAGAATAAAG
Found at i:3553162 original size:137 final size:136
Alignment explanation
Indices: 3552919--3553166 Score: 297
Period size: 137 Copynumber: 1.8 Consensus size: 136
3552909 TTATTTGGCC
* *
3552919 CTCTCTTATGCTCGAGGTTCCAAATTAATTATTCGATTCAACCATTGACTAAAATTAATTAGGAT
1 CTCTCTTATGCTCGAGGTTCCAAATTAATTATTCGATTCAA-CATTGACTAAAATCAATTAGGAG
* * *
3552984 TAATATTAGAGTCTCCATCTTACGCCTAATTTCACATTTAGTTCTTAAATTAGAAAAATTCTTAA
65 TAATATTAGAGCCTCCATCTTACGCCTAATTTCAAACTTAGTTCTTAAATTAGAAAAATTCTTAA
3553049 TTTGGTT
130 TTTGGTT
* * *
3553056 CTCTCTTTTGCTCGAGGTTCCAATTTAATTATTCGAATTGCATA-ATTGATTAAAATCAGA-TAG
1 CTCTCTTATGCTCGAGGTTCCAAATTAATTATTCG-ATT-CA-ACATTGACTAAAATCA-ATTAG
* * * **
3553119 G-GTAATGTTTAGAGCCTCCATTTTAGGTTTAATTT-AAACTTAGTTCTT
62 GAGTAAT-ATTAGAGCCTCCATCTTACGCCTAATTTCAAACTTAGTTCTT
3553167 TAATCTAGGA
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
137 48 0.52
138 41 0.44
139 3 0.03
140 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (136 bp):
CTCTCTTATGCTCGAGGTTCCAAATTAATTATTCGATTCAACATTGACTAAAATCAATTAGGAGT
AATATTAGAGCCTCCATCTTACGCCTAATTTCAAACTTAGTTCTTAAATTAGAAAAATTCTTAAT
TTGGTT
Found at i:3556388 original size:18 final size:18
Alignment explanation
Indices: 3556365--3556408 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
3556355 TGACACGGTT
3556365 CAAGTATCGTAAAGTGAG
1 CAAGTATCGTAAAGTGAG
3556383 CAAGTATCGTAAAGTGAG
1 CAAGTATCGTAAAGTGAG
3556401 CAAGTATC
1 CAAGTATC
3556409 ACTATAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (18 bp):
CAAGTATCGTAAAGTGAG
Found at i:3557395 original size:2 final size:2
Alignment explanation
Indices: 3557390--3557435 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
3557380 ATATTAAGTT
*
3557390 TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3557432 TA TA
1 TA TA
3557436 AGATTTGATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3559060 original size:2 final size:2
Alignment explanation
Indices: 3559053--3559091 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3559043 TGTTAGATTT
3559053 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3559092 TAAATTTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3562417 original size:23 final size:24
Alignment explanation
Indices: 3562391--3562435 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3562381 ATGAACTTAG
*
3562391 AAATTT-AAGGGTGCAAAATTATA
1 AAATTTCAAGGGTACAAAATTATA
*
3562414 AAATTTCAGGGGTACAAAATTA
1 AAATTTCAAGGGTACAAAATTA
3562436 GATCATCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.29
Consensus pattern (24 bp):
AAATTTCAAGGGTACAAAATTATA
Found at i:3567028 original size:60 final size:60
Alignment explanation
Indices: 3566920--3567033 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 60
3566910 TCAGATGATC
* * * * *
3566920 ATTTTATAACTTTTAATAGTCGATGGACTCAATAAAGCATCACTCTATAGTCGAAGGTTT
1 ATTTTACAACTTTTAATAGTCAATGGACTCAACAAAACATCACTCTATAATCGAAGGTTT
* *
3566980 ATTTTACAACTTTTAATAGTCAA-GTGATTCAACAAAATATCA-TCCTATAATCGA
1 ATTTTACAACTTTTAATAGTCAATG-GACTCAACAAAACATCACT-CTATAATCGA
3567034 GTGATCATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
59 2 0.04
60 43 0.96
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (60 bp):
ATTTTACAACTTTTAATAGTCAATGGACTCAACAAAACATCACTCTATAATCGAAGGTTT
Found at i:3567270 original size:21 final size:21
Alignment explanation
Indices: 3567246--3567297 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
3567236 AAATTATTTT
*
3567246 AAATTTCAATTTTTTTTAAAA
1 AAATTTCAATTTTGTTTAAAA
* *
3567267 AAATTGTAAATTTTGTTTAACA
1 AAATT-TCAATTTTGTTTAAAA
3567289 AAA-TTCAAT
1 AAATTTCAAT
3567298 GACTTAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.15
21 6 0.23
22 16 0.62
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
AAATTTCAATTTTGTTTAAAA
Found at i:3570783 original size:20 final size:21
Alignment explanation
Indices: 3570729--3570791 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
3570719 GATTCCCCTG
3570729 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
3570753 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
3570773 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
3570792 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:3577228 original size:74 final size:73
Alignment explanation
Indices: 3577092--3577232 Score: 176
Period size: 74 Copynumber: 1.9 Consensus size: 73
3577082 GGCACGTGGA
* * ** * *
3577092 TACCTTAAAATTTAATTTTTCTTCGATTAATTATTTATTTTATTAGTGATATACATCTTGAAATT
1 TACCCTAAAATTTAAATTTTCTTCGATTAATTATTTATTTTAGGAGTGATATACACCCTGAAATT
3577157 TTTATACT
66 TTTATACT
* * *
3577165 TACCCTAAAATTTTAAATTTTCTTCGATTAATTATTTATTTTACGGATTG-TGTCCACCCTGAAA
1 TACCCTAAAA-TTTAAATTTTCTTCGATTAATTATTTATTTTA-GGAGTGATATACACCCTGAAA
3577229 TTTT
64 TTTT
3577233 ATTTTTACCT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
73 9 0.16
74 45 0.79
75 3 0.05
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (73 bp):
TACCCTAAAATTTAAATTTTCTTCGATTAATTATTTATTTTAGGAGTGATATACACCCTGAAATT
TTTATACT
Found at i:3578404 original size:13 final size:13
Alignment explanation
Indices: 3578386--3578413 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3578376 GAAATATATT
3578386 TGTATATCACATA
1 TGTATATCACATA
3578399 TGTATATCACATA
1 TGTATATCACATA
3578412 TG
1 TG
3578414 AAAAAATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (13 bp):
TGTATATCACATA
Found at i:3580198 original size:20 final size:19
Alignment explanation
Indices: 3580159--3580210 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3580149 TTTCTTTGAT
3580159 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
3580178 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
3580198 ATTTATAAAATAA
1 A-TTAAAAAATAA
3580211 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:3580311 original size:120 final size:120
Alignment explanation
Indices: 3580068--3580302 Score: 282
Period size: 120 Copynumber: 2.0 Consensus size: 120
3580058 AATATATATT
* * * * *
3580068 AATTTATATAT-ATTTAT-AAATAAAATATTTATTTATTTAGAAATATCATAAAAGGACTTCTAG
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCGAG
* * * *
3580131 GTGCCTTAAGACAGTTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAAC
66 GTACCTTAAGACAGTCCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
*
3580186 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCGA
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCGA
* ** * **
3580251 GTTATTTTAAGACTG-CCCTTTC-TTAATATTGGAAAATAAATAAAT-ATTAAAA
65 GGTACCTTAAGACAGTCCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAA
3580303 TAGGATTAAA
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 17 0.17
119 26 0.27
120 38 0.39
121 17 0.17
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCGAG
GTACCTTAAGACAGTCCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:3580401 original size:3 final size:3
Alignment explanation
Indices: 3580393--3580428 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3580383 TTTATGGTTA
*
3580393 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3580429 TAAAAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3581776 original size:3 final size:3
Alignment explanation
Indices: 3581759--3581811 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
3581749 TTTGGGCATG
* *
3581759 TAA TAA -AA TTAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA TGA TAAA
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
3581806 TAA TAA
1 TAA TAA
3581812 AAAACCAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
2 2 0.05
3 33 0.79
4 7 0.17
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3581783 original size:19 final size:18
Alignment explanation
Indices: 3581759--3581799 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
3581749 TTTGGGCATG
3581759 TAATAAAATTAATAATAAA
1 TAATAAAATTAATAAT-AA
*
3581778 TAATAATATTAATAATAA
1 TAATAAAATTAATAATAA
3581796 TAAT
1 TAAT
3581800 GATAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAAAATTAATAATAA
Found at i:3582527 original size:20 final size:20
Alignment explanation
Indices: 3582504--3582560 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
3582494 GTTGAACAAA
*
3582504 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTAC
* * *
3582524 TTCTTCTTCA-GATG-ACGAG
1 TTCTTC-TCATTATGAACTAC
3582543 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
3582561 CTACTTGGCA
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
18 3 0.11
19 11 0.39
20 11 0.39
21 3 0.11
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.46
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTAC
Found at i:3582718 original size:113 final size:113
Alignment explanation
Indices: 3582154--3583274 Score: 1547
Period size: 113 Copynumber: 10.0 Consensus size: 113
3582144 ATAGAGTTAT
* *
3582154 GCAAAAGGTTGAACAAGCTCTTTTCATTAT-AA--GCTTCTT-CTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* * * * **
3582215 ATTATGACCTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * * **
3582263 ACAAAAAGTTAAACAAATTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A--AGTTCTT
* * * * * * * *
3582324 CTCATCATGAACTCTACT-TGGCAATGTTGATCCATCAAATGATGAATTTAA
63 CTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
** * * *
3582375 ATAAAAGGTTGAACAAACTCTTCTCATTATGAGCTTATTCTT-CTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* * * **
3582439 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* * **
3582487 ACAAAAAGTTGAACAAATTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A--AGTTCTT
* * * * * * *
3582548 CTCATTATGAACTCTACT-TGGCAATGTTGATCCATCAAATGATGAATTTAA
63 CTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
** * *
3582599 ATAAAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
3582664 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
3582712 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
3582777 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
3582825 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
3582890 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
*
3582938 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
3583003 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
3583051 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
3583116 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
* *
3583164 GCAAAAGGTTGAACAAGCTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* * *
3583229 ATTATGAACTTTCTCTGGAAATGTTGATCCAT--TGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
3583275 ATCTTTGCTA
Statistics
Matches: 934, Mismatches: 60, Indels: 34
0.91 0.06 0.03
Matches are distributed among these distances:
109 57 0.06
110 4 0.00
111 16 0.02
112 231 0.25
113 592 0.63
114 1 0.00
115 22 0.02
116 11 0.01
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
Found at i:3584747 original size:11 final size:9
Alignment explanation
Indices: 3584725--3584781 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 9
3584715 CTTGACCCCC
3584725 TCTTTTTCTT
1 TCTTTTT-TT
3584735 TCTTTTCCTTT
1 TCTTTT--TTT
*
3584746 TCTTCTTTT
1 TCTTTTTTT
*
3584755 T-TTTTTCT
1 TCTTTTTTT
3584763 T-TTTTTTT
1 TCTTTTTTT
3584771 TCTTTTTTT
1 TCTTTTTTT
3584780 TC
1 TC
3584782 AAGCATAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
8 13 0.32
9 13 0.32
10 6 0.15
11 7 0.17
12 1 0.03
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:3584753 original size:14 final size:11
Alignment explanation
Indices: 3584727--3584780 Score: 72
Period size: 11 Copynumber: 4.6 Consensus size: 11
3584717 TGACCCCCTC
*
3584727 TTTTTCTTTCT
1 TTTTTTTTTCT
3584738 TTTCCTTTTCTTCT
1 TTT--TTTT-TTCT
3584752 TTTTTTTTTCT
1 TTTTTTTTTCT
3584763 TTTTTTTTTCT
1 TTTTTTTTTCT
3584774 TTTTTTT
1 TTTTTTT
3584781 CAAGCATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
11 25 0.64
12 4 0.10
13 3 0.08
14 7 0.18
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:3584761 original size:25 final size:22
Alignment explanation
Indices: 3584727--3584780 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 22
3584717 TGACCCCCTC
*
3584727 TTTTTCTTTCTTTTCCTTTTCTTCT
1 TTTTTTTTTCTTTT--TTTT-TTCT
3584752 TTTTTTTTTCTTTTTTTTTTCT
1 TTTTTTTTTCTTTTTTTTTTCT
3584774 TTTTTTT
1 TTTTTTT
3584781 CAAGCATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 11 0.39
23 4 0.14
25 13 0.46
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTTTTTTTCTTTTTTTTTTCT
Found at i:3584766 original size:20 final size:20
Alignment explanation
Indices: 3584730--3584781 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3584720 CCCCCTCTTT
*
3584730 TTCTTTCTTTTCCTTTTCTTC
1 TTCTTTTTTTTCCTTTT-TTC
* *
3584751 TT-TTTTTTTTCTTTTTTTT
1 TTCTTTTTTTTCCTTTTTTC
3584770 TTCTTTTTTTTC
1 TTCTTTTTTTTC
3584782 AAGCATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 21 0.78
21 2 0.07
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (20 bp):
TTCTTTTTTTTCCTTTTTTC
Found at i:3595401 original size:25 final size:26
Alignment explanation
Indices: 3595373--3595439 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
3595363 TTAATACATG
*
3595373 AATAAAATAA-ATAAATAAAAAT-ATT
1 AATAAAATAATATAAA-AAAAATAAGT
*
3595398 AATAAAATAATATAAAAATAATAAGT
1 AATAAAATAATATAAAAAAAATAAGT
*
3595424 AATAAAA-AATTTAAAA
1 AATAAAATAATATAAAA
3595440 GATAAGAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 23 0.62
26 14 0.38
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (26 bp):
AATAAAATAATATAAAAAAAATAAGT
Found at i:3595403 original size:12 final size:12
Alignment explanation
Indices: 3595376--3595421 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
3595366 ATACATGAAT
3595376 AAAATAAATAAATA
1 AAAAT-AAT-AATA
*
3595390 AAAATATTAAT-
1 AAAATAATAATA
3595401 AAAATAAT-ATA
1 AAAATAATAATA
3595412 AAAATAATAA
1 AAAATAATAA
3595422 GTAATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 2 0.07
11 15 0.54
12 4 0.14
13 2 0.07
14 5 0.18
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAATAATAATA
Found at i:3595417 original size:16 final size:17
Alignment explanation
Indices: 3595386--3595433 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
3595376 AAAATAAATA
*
3595386 AATAAAAATATTAATAAAAT
1 AATAAAAA-A-TAAT-AAGT
3595406 AATATAAAAATAATAAGT
1 AATA-AAAAATAATAAGT
3595424 AATAAAAAAT
1 AATAAAAAAT
3595434 TTAAAAGATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 6 0.23
18 7 0.27
19 4 0.15
20 5 0.19
21 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (17 bp):
AATAAAAAATAATAAGT
Found at i:3595899 original size:45 final size:48
Alignment explanation
Indices: 3595848--3595938 Score: 118
Period size: 48 Copynumber: 1.9 Consensus size: 48
3595838 TAAATTGTCT
*
3595848 CTATTA-TTAGAAATTA-AA-AATTAAAAATATAT-TTAATTTATAATC
1 CTATTATTTA-AAATTATAATAATGAAAAATATATATTAATTTATAATC
*
3595893 CTATTATTTTAAAATTATAATTATGAAAAATATATATTAATTTATA
1 CTATTA-TTTAAAATTATAATAATGAAAAATATATATTAATTTATA
3595939 TATATTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
45 6 0.15
46 6 0.15
47 5 0.13
48 12 0.31
49 10 0.26
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (48 bp):
CTATTATTTAAAATTATAATAATGAAAAATATATATTAATTTATAATC
Found at i:3596061 original size:20 final size:19
Alignment explanation
Indices: 3596022--3596073 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3596012 TTTCTTTGAT
3596022 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
3596041 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
3596061 ATTTATAAAATAA
1 A-TTAAAAAATAA
3596074 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:3596174 original size:120 final size:119
Alignment explanation
Indices: 3595935--3596165 Score: 283
Period size: 120 Copynumber: 1.9 Consensus size: 119
3595925 TATATTAATT
* * *
3595935 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAAGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAAGTACCT
* *
3596000 TAAGACAGCTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGACA-CTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACAATTAA
* *
3596055 TATATA-ATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATC-CAGTTA
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCTAAG-TA
** **
3596118 TTTTAAGACTA-TCCTTTC-TTAATATTGGAAAATAAATAAAT-ATTAAAA
63 CCTTAAGAC-ACTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAA
3596166 TAGGATTAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
118 7 0.07
119 26 0.27
120 48 0.50
121 14 0.15
122 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (119 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAAGTACCT
TAAGACACTCCTTTCTTTAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:3596263 original size:3 final size:3
Alignment explanation
Indices: 3596255--3596284 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3596245 TTTATGGTTA
*
3596255 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3596285 TAAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3597621 original size:3 final size:3
Alignment explanation
Indices: 3597604--3597663 Score: 68
Period size: 3 Copynumber: 19.0 Consensus size: 3
3597594 TTTGGGCATG
*
3597604 TAA TAA -AA TTAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
3597651 TAA TAAA TAA TAA
1 TAA T-AA TAA TAA
3597664 AAAACCAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 2 0.04
3 37 0.74
4 11 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3597626 original size:7 final size:7
Alignment explanation
Indices: 3597614--3597664 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
3597604 TAATAAAATT
3597614 AATAATA
1 AATAATA
3597621 AATAATA
1 AATAATA
3597628 ATATTAAT-
1 A-A-TAATA
3597636 AATAAT-
1 AATAATA
3597642 AATAA-A
1 AATAATA
3597648 TAATAATA
1 -AATAATA
3597656 AATAATA
1 AATAATA
3597663 AA
1 AA
3597665 AAACCAAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
6 9 0.23
7 23 0.59
8 3 0.08
9 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AATAATA
Found at i:3597628 original size:10 final size:10
Alignment explanation
Indices: 3597604--3597663 Score: 69
Period size: 10 Copynumber: 6.6 Consensus size: 10
3597594 TTTGGGCATG
*
3597604 TAATAA-AAT
1 TAATAATAAA
3597613 TAATAATAAA
1 TAATAATAAA
3597623 TAATAAT--A
1 TAATAATAAA
3597631 T--TAAT-AA
1 TAATAATAAA
3597638 TAATAATAAA
1 TAATAATAAA
3597648 TAATAATAAA
1 TAATAATAAA
3597658 TAATAA
1 TAATAA
3597664 AAAACCAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
6 4 0.09
7 2 0.04
8 2 0.04
9 10 0.22
10 27 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TAATAATAAA
Found at i:3597628 original size:19 final size:19
Alignment explanation
Indices: 3597604--3597665 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
3597594 TTTGGGCATG
3597604 TAATAAAATTAATAATAAA
1 TAATAAAATTAATAATAAA
*
3597623 TAATAATATTAATAAT-AA
1 TAATAAAATTAATAATAAA
3597641 TAAT-AAA-TAATAATAAA
1 TAATAAAATTAATAATAAA
3597658 TAATAAAA
1 TAATAAAA
3597666 AACCAAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.18
17 8 0.21
18 9 0.23
19 15 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAATAAAATTAATAATAAA
Found at i:3598686 original size:25 final size:27
Alignment explanation
Indices: 3598651--3598701 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
3598641 TTTATTTATA
*
3598651 TTATATTATTTT-TAT-TATATATATC
1 TTATATAATTTTATATATATATATATC
3598676 TTATATAATTTTATATATATATATAT
1 TTATATAATTTTATATATATATATAT
3598702 GTATAGATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
26 3 0.13
27 9 0.39
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
TTATATAATTTTATATATATATATATC
Found at i:3598765 original size:17 final size:18
Alignment explanation
Indices: 3598740--3598805 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
3598730 GCTATGTATA
3598740 TATATTTTTTCTTAATAT
1 TATATTTTTTCTTAATAT
* **
3598758 TATATTTTATACGTTTTTAT
1 TATATTTT-TTC-TTAATAT
3598778 ATATATTTTTTCTTAATAT
1 -TATATTTTTTCTTAATAT
*
3598797 TCTATTTTT
1 TATATTTTT
3598806 GTTTTTATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
18 16 0.42
19 7 0.18
20 7 0.18
21 8 0.21
ACGTcount: A:0.26, C:0.06, G:0.02, T:0.67
Consensus pattern (18 bp):
TATATTTTTTCTTAATAT
Found at i:3598847 original size:27 final size:25
Alignment explanation
Indices: 3598807--3598863 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
3598797 TCTATTTTTG
3598807 TTTTTATTTATTTATATATATTATA
1 TTTTTATTTATTTATATATATTATA
* * *
3598832 TTTTTACTTTATTTTATTTATTTTCTA
1 TTTTTA-TTTA-TTTATATATATTATA
3598859 TTTTT
1 TTTTT
3598864 TTCTTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 6 0.22
26 4 0.15
27 17 0.63
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTTATTTATTTATATATATTATA
Found at i:3599062 original size:6 final size:6
Alignment explanation
Indices: 3599051--3599088 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
3599041 TAACATTTTA
*
3599051 TTTATT TTTATT TTTATT TTTATT TGTT-TT GTTATT TT
1 TTTATT TTTATT TTTATT TTTATT T-TTATT TTTATT TT
3599089 CCATTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 2 0.07
6 24 0.86
7 2 0.07
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:3599102 original size:25 final size:24
Alignment explanation
Indices: 3599046--3599105 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
3599036 TTTTTTAACA
* *
3599046 TTTTATTT-ATTT-TTATTTTTAT
1 TTTTATTTGTTTTGTTATTTTCAT
3599068 TTTTATTTGTTTTGTTATTTTCCAT
1 TTTTATTTGTTTTGTTATTTT-CAT
3599093 TTTT-TCTTGTTTT
1 TTTTAT-TTGTTTT
3599106 ATTTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 8 0.25
23 3 0.09
24 8 0.25
25 13 0.41
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (24 bp):
TTTTATTTGTTTTGTTATTTTCAT
Found at i:3602239 original size:13 final size:12
Alignment explanation
Indices: 3602203--3602254 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 12
3602193 CAATCAGAAC
3602203 AAAAAGAGAAAA
1 AAAAAGAGAAAA
3602215 AAAGCAATGAGAAAA
1 AAA--AA-GAGAAAA
3602230 TAAAAAGAGAAAA
1 -AAAAAGAGAAAA
3602243 AACAAAG-GAAAA
1 AA-AAAGAGAAAA
3602255 TTGAAGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 10 0.29
13 11 0.31
14 4 0.11
15 7 0.20
16 3 0.09
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:3603972 original size:37 final size:38
Alignment explanation
Indices: 3603917--3603991 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
3603907 GAAGATTTTA
* * *
3603917 TCTCGCTTGAGATAGTTTCCCTTGAAACA-AAATATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
*
3603954 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTG
1 TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
3603992 AAAACATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (38 bp):
TCTCCCTTGAGACAGTTTCCCTTGAAACATAAACATTG
Found at i:3604065 original size:37 final size:37
Alignment explanation
Indices: 3603998--3604084 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 37
3603988 ATTGAAAACA
* ** *
3603998 TTTCCCTTGAAAC-GAATTTTGTCTTTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3604034 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
*
3604071 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
3604085 TAAACATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 13 0.29
37 32 0.71
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:3604087 original size:102 final size:102
Alignment explanation
Indices: 3603917--3604183 Score: 446
Period size: 102 Copynumber: 2.6 Consensus size: 102
3603907 GAAGATTTTA
* *
3603917 TCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
* *
3603982 ATAAACATTGAAAACATTTCCCTTGAAACGAATTTTG
66 ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
*
3604019 TCTTTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
*
3604084 ATAAACATTGAAAACATTTCCCTTGAAATAAATTTCG
66 ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
* * *
3604121 TCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAA
3604184 TAAATTTTAT
Statistics
Matches: 155, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 33 0.21
102 122 0.79
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (102 bp):
TCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
ATAAACATTGAAAACATTTCCCTTGAAACAAATTTCG
Found at i:3604147 original size:36 final size:36
Alignment explanation
Indices: 3604100--3604360 Score: 252
Period size: 36 Copynumber: 7.4 Consensus size: 36
3604090 ATTGAAAACA
*
3604100 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
3604136 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* **
3604172 TTTCCCTTGAAATAAATTTTATCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
3604208 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
*** * * *
3604237 TTTTATTTGAAA-AATTTTCATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * *
3604272 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
3604309 TTTCTCTTGAAACAAATTTCTTCTCTCTTAAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
3604345 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
3604361 ATCTTTGAAT
Statistics
Matches: 186, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
28 4 0.02
29 14 0.08
30 2 0.01
31 1 0.01
33 1 0.01
34 1 0.01
35 14 0.08
36 119 0.64
37 30 0.16
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:3604293 original size:137 final size:136
Alignment explanation
Indices: 3603998--3604423 Score: 464
Period size: 137 Copynumber: 3.1 Consensus size: 136
3603988 ATTGAAAACA
* * * *
3603998 TTTCCCTTGAAACGAATTTTGTCTTTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-AAAATTTT-TCTCTCT
* * * * * *
3604063 TGAGACAGTTTCTCTTGAAACATAAACA-TTGAAAACATTTCCCTTGAAATAAATTTCGTCTCTC
64 TGAGACAGTTTCCCTTGAAACA-AAATATTTGAATACATTTCACTTGAAATAAATTTCATCTCCC
3604127 TTGAGACAG
128 TTGAGACAG
*
3604136 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTATCTCTCTT
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAATTTT-TCTCTCTT
* ** * * *
3604201 GAGACAGTTTCCCTTGAAACAAATTATTTGAATATGTTTTATTTGAAA-AATTTTCATCTCCCTT
65 GAGACAGTTTCCCTTGAAACAAAATATTTGAATACATTTCACTTGAAATAAATTTCATCTCCCTT
3604265 GAGACAG
130 GAGACAG
** * * * *
3604272 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCTTCTCTCT
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAATTT-TTCTCTCT
* * ** * * * * *
3604337 TAAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTAAAACAAAATTT-TTCTCCC
64 TGAGACAGTTTCCCTTGAAACAAAATATTTGAATACATTTCACTTGAAA-TAAATTTCATCTCCC
3604401 TTGAGACAG
128 TTGAGACAG
3604410 -TTCCTCTTGAAACA
1 TTTCC-CTTGAAACA
3604424 CAAAATCTTC
Statistics
Matches: 243, Mismatches: 39, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
136 33 0.14
137 138 0.57
138 67 0.28
139 5 0.02
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (136 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAATTTTTCTCTCTTG
AGACAGTTTCCCTTGAAACAAAATATTTGAATACATTTCACTTGAAATAAATTTCATCTCCCTTG
AGACAG
Found at i:3604422 original size:65 final size:67
Alignment explanation
Indices: 3604318--3604480 Score: 208
Period size: 67 Copynumber: 2.4 Consensus size: 67
3604308 GTTTCTCTTG
* * **
3604318 AAAC-AAATTTCTTCTCTCTTAAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCC
1 AAACAAAATTT-TTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCC
3604380 CTA
65 CTA
3604383 AAACAAAATTTTTCTCCCTTGAGACAG-TTCCTCTTGAAACACAAAATCTTCAAATTTATTTCCC
1 AAACAAAATTTTTCTCCCTTGAGACAGTTTCC-CTTGAAACACAAAATCTTCAAATTTATTTCCC
*
3604447 TTA
65 CTA
* *
3604450 AAACAAAATTTTGTTTCCCTTGAGACCGTTT
1 AAACAAAATTTT-TCTCCCTTGAGACAGTTT
3604481 TCATGAAACA
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
64 4 0.05
65 22 0.26
66 8 0.09
67 36 0.42
68 13 0.15
69 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (67 bp):
AAACAAAATTTTTCTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:3604454 original size:67 final size:67
Alignment explanation
Indices: 3604309--3604501 Score: 207
Period size: 67 Copynumber: 2.9 Consensus size: 67
3604299 CTTGAGACAG
* * * * **
3604309 TTTCTCTTGAAAC-AAATTTCTTCTCTCTTAAGACAGTTTCC-CTTG-AA-ACAAAATCTTTGAA
1 TTTCCCTTAAAACAAAATTT-TTCTCCCTTGAGACAG-TTCCTCTTGAAACACAAAATCTTCAAA
3604370 TTTA
64 TTTA
*
3604374 TTTCCCCTAAAACAAAATTTTTCTCCCTTGAGACAGTTCCTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAAATTTTTCTCCCTTGAGACAGTTCCTCTTGAAACACAAAATCTTCAAATT
3604439 TA
66 TA
* * * *
3604441 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACCGTT-TTCATGAAACAACAAATATCTT
1 TTTCCCTTAAAACAAAATTTT-TCTCCCTTGAGACAGTTCCTCTTGAAAC-ACAAA-ATCTT
3604502 TGAGATCGTT
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
64 4 0.04
65 28 0.26
66 8 0.07
67 44 0.40
68 20 0.18
69 5 0.05
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (67 bp):
TTTCCCTTAAAACAAAATTTTTCTCCCTTGAGACAGTTCCTCTTGAAACACAAAATCTTCAAATT
TA
Found at i:3606747 original size:14 final size:14
Alignment explanation
Indices: 3606721--3606789 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
3606711 ATATTCCTCT
3606721 TTTAT-TTAT-TTA
1 TTTATATTATATTA
3606733 TTTATATTATATTA
1 TTTATATTATATTA
*
3606747 TTTTTATTATATATA
1 TTTATATTATAT-TA
*
3606762 TCTTATATCATATTA
1 T-TTATATTATATTA
*
3606777 TATATATATATAT
1 TTTATAT-TATAT
3606790 ATATATATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
12 5 0.11
13 4 0.09
14 19 0.40
15 10 0.21
16 9 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTATATTATATTA
Found at i:3606761 original size:2 final size:2
Alignment explanation
Indices: 3606754--3606797 Score: 56
Period size: 2 Copynumber: 22.5 Consensus size: 2
3606744 TTATTTTTAT
*
3606754 TA TA TA TA TC T- TA TA TCA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
3606795 TA T
1 TA T
3606798 GTATGTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3606774 original size:16 final size:15
Alignment explanation
Indices: 3606731--3606795 Score: 69
Period size: 16 Copynumber: 4.2 Consensus size: 15
3606721 TTTATTTATT
3606731 TATTTATATTATAT-
1 TATTTATATTATATA
*
3606745 TATTTTTATTATATA
1 TATTTATATTATATA
*
3606760 TATCTTATATCATATTA
1 TAT-TTATATTATA-TA
*
3606777 TATATATATATATATA
1 TATTTATAT-TATATA
3606793 TAT
1 TAT
3606796 ATGTATGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
14 13 0.31
15 3 0.07
16 18 0.43
17 8 0.19
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTATATTATATA
Found at i:3606806 original size:12 final size:12
Alignment explanation
Indices: 3606754--3606813 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
3606744 TTATTTTTAT
*
3606754 TATATATATCT-
1 TATATATATGTA
3606765 TATATCATAT-TA
1 TATAT-ATATGTA
*
3606777 TATATATATATA
1 TATATATATGTA
3606789 TATATATATGTA
1 TATATATATGTA
* *
3606801 TGTATAAATGTA
1 TATATATATGTA
3606813 T
1 T
3606814 TAATTTTTGT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
11 10 0.23
12 33 0.77
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (12 bp):
TATATATATGTA
Found at i:3606878 original size:36 final size:33
Alignment explanation
Indices: 3606838--3606940 Score: 93
Period size: 36 Copynumber: 3.0 Consensus size: 33
3606828 TTGCTATGTA
3606838 TATATATTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATTTTTCTTAATATTATATTTT-T--GTTTT
*
3606874 TATATATATATTTCCTTAATATTCTATTTTTGTTTT
1 TATATAT-T-TTT-CTTAATATTATATTTTTGTTTT
* * * *
3606910 TATTTATTTAT-AT-ATATTATATTTTTATTTT
1 TATATATTTTTCTTAATATTATATTTTTGTTTT
3606941 ATTTTTTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
31 16 0.28
32 1 0.02
34 2 0.03
35 1 0.02
36 18 0.31
37 1 0.02
38 4 0.07
39 15 0.26
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (33 bp):
TATATATTTTTCTTAATATTATATTTTTGTTTT
Found at i:3606944 original size:42 final size:42
Alignment explanation
Indices: 3606893--3607028 Score: 109
Period size: 42 Copynumber: 3.1 Consensus size: 42
3606883 ATTTCCTTAA
*
3606893 TATTCTATTTTTGTTTTTATTTATTTATATATATTATATTTT
1 TATTTTATTTTTGTTTTTATTTATTTATATATATTATATTTT
* * *
3606935 TATTTTATTTTT-TTTTCTATTTTTTTCTTAATATCATGTATATCTT
1 TATTTTATTTTTGTTTT-TATTTATTT-AT-ATAT-AT-TATATTTT
* *
3606981 TATTTT-TTACTTG-TTTTACTTAGTATTATATAT-TTATTATTTT
1 TATTTTATT-TTTGTTTTTATTTA-T-TTATATATATTA-TATTTT
3607024 TATTT
1 TATTT
3607029 GTTTTAGTAA
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
41 4 0.05
42 21 0.28
43 12 0.16
44 4 0.05
45 12 0.16
46 20 0.27
47 2 0.03
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (42 bp):
TATTTTATTTTTGTTTTTATTTATTTATATATATTATATTTT
Found at i:3609561 original size:37 final size:36
Alignment explanation
Indices: 3609511--3609588 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
3609501 TAGTCACTTG
* *
3609511 TTTAATTTTTTTAATTCATTACTATTTAGCCCCTAAT
1 TTTAATTTATTTAATTCATTACAATTTAG-CCCTAAT
* * *
3609548 TTTAATTTATTTAATTTATTTCAATTTAGCCCTTAT
1 TTTAATTTATTTAATTCATTACAATTTAGCCCTAAT
3609584 TTTAA
1 TTTAA
3609589 ATCATTTCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 11 0.31
37 25 0.69
ACGTcount: A:0.28, C:0.13, G:0.03, T:0.56
Consensus pattern (36 bp):
TTTAATTTATTTAATTCATTACAATTTAGCCCTAAT
Found at i:3614094 original size:12 final size:12
Alignment explanation
Indices: 3614073--3614199 Score: 82
Period size: 12 Copynumber: 10.6 Consensus size: 12
3614063 TTTATCTGAT
3614073 TTCTGATTTGAA
1 TTCTGATTTGAA
* *
3614085 TTCTGTTTTGAT
1 TTCTGATTTGAA
3614097 TTCTGATTTGAA
1 TTCTGATTTGAA
* * *
3614109 TTATGTTTTGAT
1 TTCTGATTTGAA
*
3614121 TTCTGATATGAA
1 TTCTGATTTGAA
*
3614133 TTCTG-TTCTGAT
1 TTCTGATT-TGAA
* *
3614145 TTCTGATCTGGA
1 TTCTGATTTGAA
3614157 TTCTG-TTCT-AA
1 TTCTGATT-TGAA
* *
3614168 TATATGATCTGAA
1 T-TCTGATTTGAA
*
3614181 TTCT-ATTTTGAT
1 TTCTGA-TTTGAA
3614193 TTCTGAT
1 TTCTGAT
3614200 ATGTCCATTT
Statistics
Matches: 84, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
11 5 0.06
12 73 0.87
13 6 0.07
ACGTcount: A:0.20, C:0.10, G:0.16, T:0.54
Consensus pattern (12 bp):
TTCTGATTTGAA
Found at i:3614101 original size:24 final size:24
Alignment explanation
Indices: 3614069--3614199 Score: 163
Period size: 24 Copynumber: 5.5 Consensus size: 24
3614059 ATGTTTTATC
*
3614069 TGATTTCTGATTTGAATTCTGTTT
1 TGATTTCTGATCTGAATTCTGTTT
* *
3614093 TGATTTCTGATTTGAATTATGTTT
1 TGATTTCTGATCTGAATTCTGTTT
* *
3614117 TGATTTCTGATATGAATTCTGTTC
1 TGATTTCTGATCTGAATTCTGTTT
* *
3614141 TGATTTCTGATCTGGATTCTGTTC
1 TGATTTCTGATCTGAATTCTGTTT
* * * *
3614165 TAATATATGATCTGAATTCTATTT
1 TGATTTCTGATCTGAATTCTGTTT
3614189 TGATTTCTGAT
1 TGATTTCTGAT
3614200 ATGTCCATTT
Statistics
Matches: 92, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 92 1.00
ACGTcount: A:0.21, C:0.10, G:0.16, T:0.53
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTCTGTTT
Found at i:3615637 original size:38 final size:38
Alignment explanation
Indices: 3615581--3615676 Score: 149
Period size: 38 Copynumber: 2.5 Consensus size: 38
3615571 ACCAGTGGAC
* * *
3615581 AGTTCATAATGAGAAGAACTCATTCGAGGATATTAAAG
1 AGTTAATAATGAGAAGAACTCATTCGAGGAGAGTAAAG
3615619 AGTTAATAATGAGAAGAACTCATTCGAGGAGAGTAAAG
1 AGTTAATAATGAGAAGAACTCATTCGAGGAGAGTAAAG
3615657 AGTTCAA-AATGAGAAGAACT
1 AGTT-AATAATGAGAAGAACT
3615677 TATAGCTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 52 0.96
39 2 0.04
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (38 bp):
AGTTAATAATGAGAAGAACTCATTCGAGGAGAGTAAAG
Found at i:3618515 original size:28 final size:29
Alignment explanation
Indices: 3618484--3618553 Score: 119
Period size: 28 Copynumber: 2.5 Consensus size: 29
3618474 TCTTTCATTG
3618484 TTCT-TTTTACTTTTTTAGTTAGTTTCCC
1 TTCTATTTTACTTTTTTAGTTAGTTTCCC
3618512 TTCTATTTT-CTTTTTTAGTTAGTTTCCC
1 TTCTATTTTACTTTTTTAGTTAGTTTCCC
3618540 TTCTATTTTA-TTTT
1 TTCTATTTTACTTTT
3618554 CCTCTCCCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
28 36 0.90
29 4 0.10
ACGTcount: A:0.11, C:0.16, G:0.06, T:0.67
Consensus pattern (29 bp):
TTCTATTTTACTTTTTTAGTTAGTTTCCC
Found at i:3622930 original size:18 final size:19
Alignment explanation
Indices: 3622893--3622932 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3622883 ATTTATAAAC
*
3622893 TAAACTAATATGAATGAAA
1 TAAAATAATATGAATGAAA
*
3622912 TAAAATAATAT-AGTGAAA
1 TAAAATAATATGAATGAAA
3622930 TAA
1 TAA
3622933 CTAGTATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.60, C:0.03, G:0.10, T:0.28
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:3624736 original size:3 final size:3
Alignment explanation
Indices: 3624730--3624755 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3624720 ATACTACTAC
3624730 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
3624756 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3626294 original size:137 final size:136
Alignment explanation
Indices: 3626043--3626347 Score: 298
Period size: 138 Copynumber: 2.2 Consensus size: 136
3626033 GATTTTTTTG
* *
3626043 ATTTGGCCCTCGCTTATGCTCGAGGTTCCAAATTAATTATTTGATTCAACCATTGACTAAAATTA
1 ATTTGGCCCTCGCTTATGCTCGAGGTTCCAAATTAATTATTCGATTCAA-CATTGACTAAAATGA
* * *
3626108 ATTAGGATTAATATTAGAGCCTCCATCTTAAGCCTAATTTCACATTTAGTCATTAAATTAGGAAA
65 ATTAGGAGTAATATTAGAGCCTCCATCTTAAGCCTAATTTCAAACTTAGTCATTAAATTAGGAAA
3626173 ATTCTTA
130 ATTCTTA
* * ** *
3626180 ATTTGGTCCTCGCTTTTGCTCGAGGTTCCAGTTTAATTATTCGAATTGCATA-ATTGATTAAAAT
1 ATTTGGCCCTCGCTTATGCTCGAGGTTCCAAATTAATTATTCG-ATT-CA-ACATTGACTAAAAT
* * * ** *
3626244 CGGA-TAGG-GTAATATTTAGAGCCTCCATTTTATGTTTAATTT-AAACTTAGTTC-TTTAATCT
63 -GAATTAGGAGTAATA-TTAGAGCCTCCATCTTAAGCCTAATTTCAAACTTAG-TCATTAAAT-T
* **
3626305 AGGAGAATT-TCCG
124 AGGAAAATTCT-TA
* *
3626318 ATTTGGCCTTCGCTTATGCTTGAGGTTCCA
1 ATTTGGCCCTCGCTTATGCTCGAGGTTCCA
3626348 TTTTTGTTGT
Statistics
Matches: 137, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
137 55 0.40
138 78 0.57
139 3 0.02
140 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (136 bp):
ATTTGGCCCTCGCTTATGCTCGAGGTTCCAAATTAATTATTCGATTCAACATTGACTAAAATGAA
TTAGGAGTAATATTAGAGCCTCCATCTTAAGCCTAATTTCAAACTTAGTCATTAAATTAGGAAAA
TTCTTA
Found at i:3628389 original size:41 final size:41
Alignment explanation
Indices: 3628344--3628425 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
3628334 CGAATCGGGT
3628344 TGGGTGAAGGATGTAAAATTTTTGGATCGGTCGGGTTGGCC
1 TGGGTGAAGGATGTAAAATTTTTGGATCGGTCGGGTTGGCC
3628385 TGGGTGAAGGATGTAAAATTTTTGGATCGGTCGGGTTGGCC
1 TGGGTGAAGGATGTAAAATTTTTGGATCGGTCGGGTTGGCC
3628426 GAAACCCGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.20, C:0.10, G:0.39, T:0.32
Consensus pattern (41 bp):
TGGGTGAAGGATGTAAAATTTTTGGATCGGTCGGGTTGGCC
Done.