Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_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: 4987688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 20
Found at i:3500615 original size:22 final size:21
Alignment explanation
Indices: 3500574--3500613 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3500564 CTGTTGAACA
3500574 GGGGGGGAATCGGTACCCCTT
1 GGGGGGGAATCGGTACCCCTT
3500595 GGGGGGGAATCGGTACCCC
1 GGGGGGGAATCGGTACCCC
3500614 CTGAACATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.25, G:0.45, T:0.15
Consensus pattern (21 bp):
GGGGGGGAATCGGTACCCCTT
Found at i:3500672 original size:15 final size:15
Alignment explanation
Indices: 3500652--3500681 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3500642 AAACCTGCAG
3500652 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
3500667 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
3500682 CCTGGGGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:3500695 original size:20 final size:20
Alignment explanation
Indices: 3500667--3500707 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3500657 ATCTGTACCC
* *
3500667 GGGGTATCTGTACCCCCTGG
1 GGGGAATCTATACCCCCTGG
3500687 GGGGAATCTATACCCCCTGG
1 GGGGAATCTATACCCCCTGG
3500707 G
1 G
3500708 CAATCTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.29, G:0.34, T:0.22
Consensus pattern (20 bp):
GGGGAATCTATACCCCCTGG
Found at i:3500829 original size:29 final size:31
Alignment explanation
Indices: 3500797--3500856 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
3500787 AAACTTTGAA
3500797 TAAATTCAATT-AAGTCCAAAAA-CATTTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTTT
3500826 TAAATTCAATTCAAGTCCAAAAACCATTTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTTT
3500857 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTT
Found at i:3502160 original size:20 final size:20
Alignment explanation
Indices: 3502135--3502184 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3502125 TCTAAATCAT
3502135 TTTTCAAAATTTGATTTTGA
1 TTTTCAAAATTTGATTTTGA
3502155 TTTTCAAAATTTGATTTTGA
1 TTTTCAAAATTTGATTTTGA
3502175 TTTTCAAAAT
1 TTTTCAAAAT
3502185 CAACTTTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTTGATTTTGA
Found at i:3502192 original size:20 final size:19
Alignment explanation
Indices: 3502148--3502206 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
3502138 TCAAAATTTG
**
3502148 ATTTTGATTTTCAAAATTTG
1 ATTTTGATTTTCAAAA-TCA
3502168 ATTTTGATTTTCAAAATCA
1 ATTTTGATTTTCAAAATCA
*
3502187 ACTTTTG-CTTTCAAAATCA
1 A-TTTTGATTTTCAAAATCA
3502206 A
1 A
3502207 ATTATCTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 14 0.40
20 21 0.60
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (19 bp):
ATTTTGATTTTCAAAATCA
Found at i:3503544 original size:34 final size:32
Alignment explanation
Indices: 3503482--3503551 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3503472 CCTTACAAAC
* *
3503482 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
3503514 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
3503548 TCCC
1 TCCC
3503552 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:3503928 original size:19 final size:20
Alignment explanation
Indices: 3503891--3503932 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
3503881 TGTTGAACAG
3503891 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
3503911 GGGGGGAATCGGTACCCCCT
1 GGGGGGAATCGGTACCCCCT
3503931 GG
1 GG
3503933 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.29, G:0.43, T:0.14
Consensus pattern (20 bp):
GGGGGGAATCGGTACCCCCT
Found at i:3504146 original size:29 final size:31
Alignment explanation
Indices: 3504114--3504172 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 31
3504104 AAACTTTGAA
3504114 TAAATTCAATT-AAGTCCAAAAA-CATTTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTTT
3504143 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
3504173 GCCTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTT
Found at i:3508427 original size:2 final size:2
Alignment explanation
Indices: 3508420--3508462 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3508410 AAAAAGGGAA
3508420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3508462 A
1 A
3508463 AGCTGTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3510593 original size:8 final size:8
Alignment explanation
Indices: 3510580--3510633 Score: 63
Period size: 8 Copynumber: 6.8 Consensus size: 8
3510570 CCCAGTTTTT
3510580 ATATATAC
1 ATATATAC
3510588 ATATATAC
1 ATATATAC
* *
3510596 ATACATAA
1 ATATATAC
3510604 ATATATAC
1 ATATATAC
* *
3510612 ATACATAT
1 ATATATAC
*
3510620 ATATATAT
1 ATATATAC
3510628 ATATAT
1 ATATAT
3510634 TATTTTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:3510599 original size:12 final size:12
Alignment explanation
Indices: 3510579--3510633 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
3510569 ACCCAGTTTT
3510579 TATATATACATA
1 TATATATACATA
*
3510591 TATACATACATA
1 TATATATACATA
*
3510603 AATATATACATA
1 TATATATACATA
* *
3510615 CATATATATATA
1 TATATATACATA
3510627 TATATAT
1 TATATAT
3510634 TATTTTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (12 bp):
TATATATACATA
Found at i:3510623 original size:4 final size:4
Alignment explanation
Indices: 3510579--3510633 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
3510569 ACCCAGTTTT
* * * * * *
3510579 TATA TATA CATA TATA CATA CATA AATA TATA CATA CATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
3510627 TATA TAT
1 TATA TAT
3510634 TATTTTATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (4 bp):
TATA
Found at i:3510766 original size:39 final size:39
Alignment explanation
Indices: 3510653--3510771 Score: 138
Period size: 39 Copynumber: 3.1 Consensus size: 39
3510643 TTAAATGTTT
* * *
3510653 ATTTATAATTT-TCAAATTATTCCAC-TCTAACATTCTAA
1 ATTTTTAATTTCTTAAATTATTACACAT-TAACATTCTAA
*
3510691 ATTTTTAATTTCTTAAATT-TTACTACCA-TAATATTCTAA
1 ATTTTTAATTTCTTAAATTATTAC-A-CATTAACATTCTAA
*
3510730 ATTTTTAATTTCTTAAATTATTTCACATTAACATTCTAA
1 ATTTTTAATTTCTTAAATTATTACACATTAACATTCTAA
3510769 ATT
1 ATT
3510772 ATTTTTTAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
38 15 0.22
39 50 0.72
40 4 0.06
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (39 bp):
ATTTTTAATTTCTTAAATTATTACACATTAACATTCTAA
Found at i:3511584 original size:16 final size:19
Alignment explanation
Indices: 3511563--3511607 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 19
3511553 AAGAAATTTA
3511563 TTTTTATATTAG-TA-T-T
1 TTTTTATATTAGTTATTAT
*
3511579 TTTTTA-AATAGTTATTAT
1 TTTTTATATTAGTTATTAT
3511597 TTTTTATATTA
1 TTTTTATATTA
3511608 ATATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 1 0.04
18 7 0.30
19 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTTATATTAGTTATTAT
Found at i:3511604 original size:34 final size:34
Alignment explanation
Indices: 3511558--3511634 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 34
3511548 GTGGTAAGAA
* *
3511558 ATTTATTTTTATATTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTATATTAATATATTTATGTAAATA-TT
3511592 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTATATTAATATATTTATGTAAATATT
3511627 ATTTTTTT
1 ATTTTTTT
3511635 ATTAAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
34 22 0.58
35 9 0.24
36 7 0.18
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (34 bp):
ATTTTTTTTATATTAATATATTTATGTAAATATT
Found at i:3511659 original size:32 final size:30
Alignment explanation
Indices: 3511590--3511667 Score: 86
Period size: 32 Copynumber: 2.5 Consensus size: 30
3511580 TTTTAAATAG
3511590 TTATTATTTTTTATATTAATATATTTATGTAA
1 TTATTATTTTTT-TATTAATATATTTA-GTAA
*
3511622 ATATTATTTTTTTATTAAAATAATATTTA-TAA
1 TTATTATTTTTTTATT--AAT-ATATTTAGTAA
*
3511654 TTATTATTTATTTA
1 TTATTATTTTTTTA
3511668 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 4 0.10
32 26 0.65
33 3 0.08
34 7 0.17
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (30 bp):
TTATTATTTTTTTATTAATATATTTAGTAA
Found at i:3513172 original size:21 final size:21
Alignment explanation
Indices: 3513142--3513189 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3513132 GTAGGGGTAC
* *
3513142 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
3513163 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
3513184 ATGCCA
1 ATGCCA
3513190 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:3513219 original size:21 final size:21
Alignment explanation
Indices: 3513193--3513286 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
3513183 TATGCCATCT
* *
3513193 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
3513214 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
3513235 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
3513256 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
3513277 CCGCAGGGTT
1 CCGCAGGGTT
3513287 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:3517522 original size:20 final size:20
Alignment explanation
Indices: 3517497--3517534 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3517487 AAACATTGTT
*
3517497 TAATATACTAATTATATTAA
1 TAATATACTAAATATATTAA
3517517 TAATATACTAAATATATT
1 TAATATACTAAATATATT
3517535 TTTTTTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATACTAAATATATTAA
Found at i:3517720 original size:29 final size:32
Alignment explanation
Indices: 3517676--3517751 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 32
3517666 ATTCATCATG
* * *
3517676 TCAAATATTATTATAATA-TTG-AATTATTT-
1 TCAAATAATAATATAATATTTGTAATCATTTA
* *
3517705 TCAGATAATAATATAATATTTGTGATCATTTA
1 TCAAATAATAATATAATATTTGTAATCATTTA
3517737 TCAAATAATAATATA
1 TCAAATAATAATATA
3517752 TTCTAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 15 0.39
30 3 0.08
31 6 0.16
32 14 0.37
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (32 bp):
TCAAATAATAATATAATATTTGTAATCATTTA
Found at i:3520177 original size:142 final size:141
Alignment explanation
Indices: 3519899--3520185 Score: 466
Period size: 142 Copynumber: 2.0 Consensus size: 141
3519889 GATGCCTACC
* * **
3519899 ACAAGGCTGAGCTTCGCTTCCCTAATATGACAAACAAAGACGTACAGGTTCATGCTGTTTTGATG
1 ACAAGGCTAAGCTTCGCTTCCCTAATATGACAAACAAAGACGTACAGGTTCACGCTGTTTAAATG
* ** * *
3519964 CTAACTTGTCTCCAGATTTCCTGGGTCCATCAATATATAATGTTTGAAAAGAGGGTAATGCTTAG
66 CTAACTTGTCTCCACATTTCCTCAGTCCATCAATATATAATGCTTGAAAAGAGGATAATGCTTAG
*
3520029 CCTTGTCAATT
131 CATTGTCAATT
*
3520040 ACAAGGCTAAGCTTCGCTTCCCTAATATGACAAACAAAGACGTACAGGTTCGCGCTGTTTAAATG
1 ACAAGGCTAAGCTTCGCTTCCCTAATATGACAAACAAAGACGTACAGGTTCACGCTGTTTAAATG
3520105 CTTAACTTGTCTCCACATTTCCTCAGTCCATCAATATATAATGCTTGAAAAGAGGATAATGCTTA
66 C-TAACTTGTCTCCACATTTCCTCAGTCCATCAATATATAATGCTTGAAAAGAGGATAATGCTTA
3520170 GCATTGTCAATT
130 GCATTGTCAATT
3520182 ACAA
1 ACAA
3520186 TCAACATAAT
Statistics
Matches: 134, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
141 61 0.46
142 73 0.54
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (141 bp):
ACAAGGCTAAGCTTCGCTTCCCTAATATGACAAACAAAGACGTACAGGTTCACGCTGTTTAAATG
CTAACTTGTCTCCACATTTCCTCAGTCCATCAATATATAATGCTTGAAAAGAGGATAATGCTTAG
CATTGTCAATT
Found at i:3532854 original size:21 final size:21
Alignment explanation
Indices: 3532812--3532854 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3532802 TTTCTGGGCT
*
3532812 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
3532833 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
3532854 A
1 A
3532855 ACGAATATGA
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:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3533745 original size:4 final size:4
Alignment explanation
Indices: 3533736--3533764 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3533726 AAATGATGAC
3533736 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
3533765 ATGGTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:3534050 original size:30 final size:30
Alignment explanation
Indices: 3534016--3534298 Score: 539
Period size: 30 Copynumber: 9.4 Consensus size: 30
3534006 GGTTCTTCGG
*
3534016 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3534046 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3534076 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3534106 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3534136 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3534166 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3534196 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3534226 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
3534256 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
3534286 GACCTTTGGATAG
1 GACCTCTGGATAG
3534299 GTCCTTCGAA
Statistics
Matches: 250, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 250 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:3537671 original size:21 final size:21
Alignment explanation
Indices: 3537629--3537671 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3537619 TTTCTGGGCT
* *
3537629 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
3537650 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
3537671 A
1 A
3537672 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:3538561 original size:4 final size:4
Alignment explanation
Indices: 3538552--3538576 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3538542 AAATGATGAC
3538552 ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT A
3538577 ATGGTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:3538816 original size:31 final size:31
Alignment explanation
Indices: 3538767--3538842 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
3538757 GTCTTTCGAG
* * * *
3538767 ACATATGGACAATATACCTATGTTCTAAGGA
1 ACATATGGATAGTTTACCTAGGTTCTAAGGA
** *
3538798 ACATATGGATAGTTTACCTAGGTTCTTCGGG
1 ACATATGGATAGTTTACCTAGGTTCTAAGGA
*
3538829 ACCTATGGATAGTT
1 ACATATGGATAGTT
3538843 ACCGAGGATC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (31 bp):
ACATATGGATAGTTTACCTAGGTTCTAAGGA
Found at i:3538862 original size:30 final size:30
Alignment explanation
Indices: 3538828--3539110 Score: 512
Period size: 30 Copynumber: 9.4 Consensus size: 30
3538818 GGTTCTTCGG
*
3538828 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3538858 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
3538888 GACCTCTGGATAGTTATCGAGGATCTTTGT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3538918 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
3538948 GACCTCTGGATAGTTATCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3538978 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3539008 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
3539038 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
3539068 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
3539098 GACCTTTGGATAG
1 GACCTCTGGATAG
3539111 GTCCTTCGGA
Statistics
Matches: 244, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 244 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:3542551 original size:20 final size:20
Alignment explanation
Indices: 3542526--3542591 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
3542516 TCTGGACAAG
3542526 CAGTATCGATACTGTTCTTA
1 CAGTATCGATACTGTTCTTA
* *
3542546 CAGTATCGATAC--CTCATGAA
1 CAGTATCGATACTGTTC-T-TA
*
3542566 CAGTACCGATACTGTTCTTA
1 CAGTATCGATACTGTTCTTA
3542586 CAGTAT
1 CAGTAT
3542592 ATATACCTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 30 0.83
21 1 0.03
22 2 0.06
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (20 bp):
CAGTATCGATACTGTTCTTA
Found at i:3542581 original size:40 final size:40
Alignment explanation
Indices: 3542526--3542622 Score: 158
Period size: 40 Copynumber: 2.4 Consensus size: 40
3542516 TCTGGACAAG
* *
3542526 CAGTATCGATACTGTTCTTACAGTATCGATACCTCATGAA
1 CAGTAACGATACTGTTCTTACAGTATAGATACCTCATGAA
* *
3542566 CAGTACCGATACTGTTCTTACAGTATATATACCTCATGAA
1 CAGTAACGATACTGTTCTTACAGTATAGATACCTCATGAA
3542606 CAGTAACGATACTGTTC
1 CAGTAACGATACTGTTC
3542623 ATATGGTATT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (40 bp):
CAGTAACGATACTGTTCTTACAGTATAGATACCTCATGAA
Found at i:3542617 original size:20 final size:20
Alignment explanation
Indices: 3542545--3542617 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
3542535 TACTGTTCTT
*
3542545 ACAGTATCGATACCTCATGA
1 ACAGTAACGATACCTCATGA
* * *
3542565 ACAGTACCGATACTGTTC-T-T
1 ACAGTAACGATAC--CTCATGA
*
3542585 ACAGTATA-TATACCTCATGA
1 ACAGTA-ACGATACCTCATGA
3542605 ACAGTAACGATAC
1 ACAGTAACGATAC
3542618 TGTTCATATG
Statistics
Matches: 39, Mismatches: 8, Indels: 12
0.66 0.14 0.20
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 32 0.82
21 1 0.03
22 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (20 bp):
ACAGTAACGATACCTCATGA
Found at i:3546636 original size:110 final size:112
Alignment explanation
Indices: 3546448--3546659 Score: 320
Period size: 110 Copynumber: 1.9 Consensus size: 112
3546438 ACAATCTGGG
* * *
3546448 CACCTAAAATGATAACGTTGAAAACGTTAGACACCTACTTTTAACGAGAAATTCTTTAGACATCT
1 CACCTAAAATGATAACGTTGAAAACATTAGACACCTACTTTTAACGAGAAATTCTTTAGACACCC
*
3546513 AAAGTTAACTTTGAATATAATATGGACACTTAATTTTACAACCTAGA
66 AAAGTTAACTTTGAATATAATATGAACACTTAATTTTACAACCTAGA
* * *
3546560 CACCTAAAATGATAACGTTGAAAACATTA-A-ACTTACTTTTAACGAGAACTTGTTTAGACACCC
1 CACCTAAAATGATAACGTTGAAAACATTAGACACCTACTTTTAACGAGAAATTCTTTAGACACCC
* * *
3546623 AAAGTTAATTTTGAATATAATTTGAACACTTATTTTT
66 AAAGTTAACTTTGAATATAATATGAACACTTAATTTT
3546660 TACATTAACA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
110 61 0.68
111 1 0.01
112 28 0.31
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (112 bp):
CACCTAAAATGATAACGTTGAAAACATTAGACACCTACTTTTAACGAGAAATTCTTTAGACACCC
AAAGTTAACTTTGAATATAATATGAACACTTAATTTTACAACCTAGA
Found at i:3550253 original size:102 final size:102
Alignment explanation
Indices: 3550071--3550266 Score: 313
Period size: 102 Copynumber: 1.9 Consensus size: 102
3550061 TACATAATCT
* * * *
3550071 TTTTAGTTGAAAATGGTAAATTTGAATGATATTTAAATTTTGATCCTCATATTTTGTGTGCATCG
1 TTTTAGTTGAAAATGGTAAATTTAAATGATATTTAAATTTTGATCCTCATATTTTATGTGCACCA
3550136 CATCATACATATTTTATTTATTAGTTGTATGTCATCC
66 CATCATACATATTTTATTTATTAGTTGTATGTCATCC
* * *
3550173 TTTTAGTTGAAAATGGTAAATTTAAATGATATTTAAATTTTGATCCTTATGTTTTATTTGCACCA
1 TTTTAGTTGAAAATGGTAAATTTAAATGATATTTAAATTTTGATCCTCATATTTTATGTGCACCA
3550238 CATCATACA-ACTTTTATTTATTAGTTGTA
66 CATCATACATA-TTTTATTTATTAGTTGTA
3550267 CTAATGTGTG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 1 0.01
102 85 0.99
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (102 bp):
TTTTAGTTGAAAATGGTAAATTTAAATGATATTTAAATTTTGATCCTCATATTTTATGTGCACCA
CATCATACATATTTTATTTATTAGTTGTATGTCATCC
Found at i:3561705 original size:9 final size:9
Alignment explanation
Indices: 3561691--3561748 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
3561681 ACTTTGCCTG
3561691 AAGAAAAAA
1 AAGAAAAAA
3561700 AAGAAAAAA
1 AAGAAAAAA
* *
3561709 AGGAAAAGA
1 AAGAAAAAA
*
3561718 AAGAGGAAAA
1 AAGA-AAAAA
**
3561728 AAGATGAAA
1 AAGAAAAAA
3561737 AAGAAAATAA
1 AAGAAAA-AA
3561747 AA
1 AA
3561749 ATAAATAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
9 27 0.71
10 11 0.29
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:3577266 original size:36 final size:36
Alignment explanation
Indices: 3577180--3577294 Score: 119
Period size: 36 Copynumber: 3.2 Consensus size: 36
3577170 AATAGATTTT
3577180 AAACCATAACACATTACATTAA-AGAGATAAAAAC-AC
1 AAACC-TAACACATTACATTAAGA-AGATAAAAACAAC
* *
3577216 AAAACGATGA-ACATTACATTAAGAAGATAAAAACAAC
1 -AAAC-CTAACACATTACATTAAGAAGATAAAAACAAC
* * * *
3577253 AAACCTAACACATTACGTTAAGGACATAAATACAAC
1 AAACCTAACACATTACATTAAGAAGATAAAAACAAC
3577289 AAACCT
1 AAACCT
3577295 TATACACACC
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
35 2 0.03
36 55 0.83
37 9 0.14
ACGTcount: A:0.56, C:0.19, G:0.08, T:0.17
Consensus pattern (36 bp):
AAACCTAACACATTACATTAAGAAGATAAAAACAAC
Found at i:3578201 original size:142 final size:142
Alignment explanation
Indices: 3577936--3578205 Score: 387
Period size: 142 Copynumber: 1.9 Consensus size: 142
3577926 AATGTTTTTG
* * * *
3577936 AAATGGAGTGATATATCACTGAAAAATTTATGAAGTGAAATTATTGGGCATTGAAAAGTTTCTAT
1 AAATGAAGTGATATATCACTGAAAAATTTATAAAGTGAAATTATTGGGAACTGAAAAGTTTCTAT
* * * **
3578001 AATTGTGCATTAAATGGTTTATGAGAAATGGACATTTTTGTGAAATGGAGTGGCATATCACTATT
66 AATTGTGCATTAAATGGTCTATGAGAAATGGACATTTTTCTGAAATGAAGTAACATATCACTATT
3578066 AAAAAGTTTCTA
131 AAAAAGTTTCTA
* ** *
3578078 AAATGAAGTGATATATCAGTGAAAGGTTTATAAAGTGAAGTTATTGGGAACTGAAAAGTTTCTAT
1 AAATGAAGTGATATATCACTGAAAAATTTATAAAGTGAAATTATTGGGAACTGAAAAGTTTCTAT
* ** *
3578143 CATTGTGCATTAAATGGTCTATGAGAAATGGATGTTTTTCTGAAATGAAGTAATATATCACTA
66 AATTGTGCATTAAATGGTCTATGAGAAATGGACATTTTTCTGAAATGAAGTAACATATCACTA
3578206 AAAAGTTTCT
Statistics
Matches: 111, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
142 111 1.00
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (142 bp):
AAATGAAGTGATATATCACTGAAAAATTTATAAAGTGAAATTATTGGGAACTGAAAAGTTTCTAT
AATTGTGCATTAAATGGTCTATGAGAAATGGACATTTTTCTGAAATGAAGTAACATATCACTATT
AAAAAGTTTCTA
Found at i:3578229 original size:107 final size:107
Alignment explanation
Indices: 3578072--3578328 Score: 320
Period size: 107 Copynumber: 2.4 Consensus size: 107
3578062 TATTAAAAAG
* * * * * *
3578072 TTTCTAAAATGAAGTGATATATCAGTGAAAGGTTTATAAAGTGAAGTTATTGGGA-ACTGAAAAG
1 TTTCTAAAATGAAGTGATATATCACTAAAAAGTTTCTGAAGTGAAATTATT-GGACACTGAAAAG
*
3578136 TTTCTATCATTGTGCATTAAATGGTCTATGAGAAATGGA-TGTT
65 TTTCTATCATTGTGAATTAAATGGTCTAT-AGAAATGGACTGTT
* *
3578179 TTTCTGAAATGAAGTAATATATCACTAAAAAGTTTCTGAAGTGAAATTATTGGACACTGAAAAGT
1 TTTCTAAAATGAAGTGATATATCACTAAAAAGTTTCTGAAGTGAAATTATTGGACACTGAAAAGT
* * * *
3578244 TTTTGTCATTTTGAATTAAATGGTCTATAGAAATGGACTTTT
66 TTCTATCATTGTGAATTAAATGGTCTATAGAAATGGACTGTT
* *
3578286 TTTTTTAAATGAAGTGATATATCACTACTGAAAAGTTTCTGAA
1 TTTCTAAAATGAAGTGATATATCACTA---AAAAGTTTCTGAA
3578329 ATAAAGTGAC
Statistics
Matches: 129, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
106 12 0.09
107 104 0.81
110 13 0.10
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (107 bp):
TTTCTAAAATGAAGTGATATATCACTAAAAAGTTTCTGAAGTGAAATTATTGGACACTGAAAAGT
TTCTATCATTGTGAATTAAATGGTCTATAGAAATGGACTGTT
Found at i:3578365 original size:107 final size:106
Alignment explanation
Indices: 3578127--3578365 Score: 247
Period size: 107 Copynumber: 2.2 Consensus size: 106
3578117 GTTATTGGGA
* *
3578127 ACTGAAAAGTTTCTATCAT-TGTGCATTAAATGGTCTATGAGAAATGGATGTTTTTCTGAAATGA
1 ACTGAAAAGTTTCT-GCATAT-TGAATTAAATGGTCTATGAGAAATGGATGTTTTTCTGAAATGA
* * *
3578191 AGTAATATATCACTAAAAAGTTTCTGAAGTGAAATTATTGGAC
64 AGTAATATATCACTAAAAAGTTTCTGAAATGAAATGAATGGAC
* * * * *
3578234 ACTGAAAAGTTTTTGTCATTTTGAATTAAATGGTCTAT-AGAAATGGACTTTTTTTTTTAAATGA
1 ACTGAAAAGTTTCTG-CATATTGAATTAAATGGTCTATGAGAAATGGA-TGTTTTTCTGAAATGA
* *
3578298 AGTGATATATCACTACTGAAAAGTTTCTGAAAT-AAAGTGACAT-GTC
64 AGTAATATATCACTA---AAAAGTTTCTGAAATGAAA-TGA-ATGGAC
3578344 ACTGAAAAGTTTCTG-A-ATTGAA
1 ACTGAAAAGTTTCTGCATATTGAA
3578366 GTTATTGGCC
Statistics
Matches: 111, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
106 9 0.08
107 64 0.58
108 2 0.02
109 3 0.03
110 32 0.29
111 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (106 bp):
ACTGAAAAGTTTCTGCATATTGAATTAAATGGTCTATGAGAAATGGATGTTTTTCTGAAATGAAG
TAATATATCACTAAAAAGTTTCTGAAATGAAATGAATGGAC
Found at i:3599299 original size:19 final size:21
Alignment explanation
Indices: 3599277--3599323 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
3599267 ATGGTATTGG
3599277 TACCATA-ATAG-AGTATCAA
1 TACCATACATAGTAGTATCAA
*
3599296 TACCATATCATAGTAGTATCGA
1 TACCATA-CATAGTAGTATCAA
3599318 TACCAT
1 TACCAT
3599324 GATGGATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
21 4 0.17
22 13 0.54
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (21 bp):
TACCATACATAGTAGTATCAA
Found at i:3599924 original size:81 final size:81
Alignment explanation
Indices: 3599831--3602484 Score: 2778
Period size: 81 Copynumber: 32.8 Consensus size: 81
3599821 ATGGTCTAAA
* * ** * * *
3599831 TAAAAGATTAAATGGCCTAGCTGTACATTTGGGAGAAAGGTACCAATTATGCAAATTAAATGAAC
1 TAAAAGA-TAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAC
*
3599896 GGTTAAAGACAGTTGAG
65 GGTTAAAGACCGTTGAG
* * * **
3599913 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTAAATCATGCAAGTTAGATGAATA
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
**
3599978 GTTAAAGATAGTTGAG
66 GTTAAAGACCGTTGAG
* * * *
3599994 TAAAAGAGAAATGGCCTAGCTGTGCATTTGGTAGAAAAGTGTCAATTATG-TCAGTTAGATGAAT
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCT-AGTTAGATGAAC
*
3600058 GGTTAAAGACTGTTGAG
65 GGTTAAAGACCGTTGAG
* * * * *
3600075 TAAAATATAAATGGACTAGTTGTGCATTTGTCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
** * *
3600140 GTGTCAATTA-TGTCG-G
66 GT-T-AAAGACCGTTGAG
* ** * * * *
3600156 T--AAGATGAATGGAATAGTTGTGCATTTGGCAGAAAGGTGTCAATTATG-TCGGTAAGATGAAT
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCT-AGTTAGATGAAC
3600218 GGTTAAAGACCGTTGAG
65 GGTTAAAGACCGTTGAG
** * * * **
3600235 TAAAAGATAAATGGAATAGATGTGCATTTGGCAGAAATGTATCAATTATGCTAGTTAGATGAATT
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
*
3600300 GTTAAAGAACGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * * * *
3600316 TAAAACATAAATGGCCTAGCTTTGTATTTGGCAGAAA-GTTTGCAATTATGTTATTTAAATGAAT
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGT-CAATTATGCTAGTTAGATGAAC
* * *
3600380 GTTTAAAGACGGTTTAG
65 GGTTAAAGACCGTTGAG
* * * * *
3600397 TAAAAGATAAATGGCATAGCTATTCATTTGGCCGAAAGGTGTCAATTATG-TCAGTAAGATGAAC
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCT-AGTTAGATGAAC
*
3600461 GGTTAAAAACCGTTGAG
65 GGTTAAAGACCGTTGAG
* * * * * **
3600478 TAAAAGATAAATGGCATAGCTGTGCATTTGGCAGAAAGGTGTCACTTAT-ATAAGTAAGTTGATT
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCT-AGTTAGATGAAC
* * *
3600542 AGTGAAAGATCGTTGAG
65 GGTTAAAGACCGTTGAG
* * ** * *
3600559 TAAAAGAT-AATGTCATAGAAGTACATTTGGCAGAAAGGTATCAATTATGCTAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
*
3600623 GTTAAAGACCATTGAG
66 GTTAAAGACCGTTGAG
* * * * *
3600639 TAAAAGGTAAATGGCCTCGCTGTGCATTTGGCAGAAA-GTTTGCAATTATGTTAGTTAGATGAAT
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGT-CAATTATGCTAGTTAGATGAAC
*
3600703 GGTTAACGACCGTTGAG
65 GGTTAAAGACCGTTGAG
* * * *
3600720 TAAAAGATAAATGGCCTAGCTGTGCATTTGGTAGAAAGGTGTCAATTATG-TCAGTAAAATGAAT
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCT-AGTTAGATGAAC
3600784 GGTTAAA-AGCCGTTGAG
65 GGTTAAAGA-CCGTTGAG
*** * * * * *
3600801 TAAAAGATAAATGTTATAGATGTTCATTTGGCAAAAAGGTGTCAATTATGCCAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
* *
3600866 ATTAAAGACTGTTGAG
66 GTTAAAGACCGTTGAG
* * * * *
3600882 TAAAAGATAAATGGTCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGTTAGTAAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
* **
3600947 GTTAAATATTGTTGAG
66 GTTAAAGACCGTTGAG
* * ** *
3600963 TAAAA-ACTAAATGGCATAGATGTGCATTTGGCAGAAAGGCATCAATTATGCTAGTTAGATAAAC
1 TAAAAGA-TAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAC
*
3601027 GGTTAAAGACTGTTGAG
65 GGTTAAAGACCGTTGAG
* * * * * *
3601044 TAAAAGATAAATGGCCTAGCTATGCATTTGGTAGAAAGTTCG-CAACTATGATAGTTAGGTGAAC
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGT-GTCAATTATGCTAGTTAGATGAAC
*
3601108 GATTAAAGACCGTTGAG
65 GGTTAAAGACCGTTGAG
** * * *
3601125 TAAAAGATAAATGGAATAGTTGTGCATTTGGCAGAAAGGTGTAAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
* *
3601190 GTTAAAAATCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * *
3601206 TAAAAGATTAATGACCTAGTTGTGCATTCGGTAGAAAGGTGTCAATTATGCTAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
* ** *
3601271 ATTAAAGACTTTTGAA
66 GTTAAAGACCGTTGAG
* * * * * *
3601287 TAAAAGATAAATGGCCTAGTTGTGCATTTGGCAGAAAGATGTCAATTATACCAGTTAAATGAACA
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
* ** *
3601352 ATTAAAGATTGTTAAG
66 GTTAAAGACCGTTGAG
* * * * * * *
3601368 TAAAAGATAAATAGCCTAGATGTGCATTTGACATAAAGATGTCAATTATGCCAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
3601433 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* ** ** *
3601449 TAAAAGATAAATGGCCTCGCAATGCATTTGGCAGAAATATGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
*
3601514 GTTAAAGAGCGTTGAG
66 GTTAAAGACCGTTGAG
** * * * * *
3601530 TAAAAGATAAATGGTGTAGTTGTGCATTTGGCATAAAGGAGTTAAATATGCTAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
* *
3601595 ATTAAAGACTGTTGAG
66 GTTAAAGACCGTTGAG
* * *
3601611 CAAAAGATAAATGGCCTAGCTGTGCATTTGGCGGAAAGATGTCAATTATGCTAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
*
3601676 GTTAAAAACCGTTGAG
66 GTTAAAGACCGTTGAG
** * * * * *
3601692 TAAAAGATAAAAAGCCCAACTGTGCTTTTGGCATAAATGTGTCAATTATGCTAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
3601757 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
*
3601773 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGAGTCAATTATG-TCAGTTAGATGAAC
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCT-AGTTAGATGAAC
* **
3601837 GATTAATA-ATTGTTGAG
65 GGTTAA-AGACCGTTGAG
* *
3601854 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCTGAAAGGTGTCAATTATGCTAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
*
3601919 GTTAAAGATCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * * *
3601935 TAAAAGATAAACGACCTAGCTATGCATTTAGCATAAAGGTATCAATTATGAC-AATTAGATGAAC
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATG-CTAGTTAGATGAAC
* * *
3601999 GTTTACAGATCGTTGAG
65 GGTTAAAGACCGTTGAG
* * * *
3602016 TAAAAGATAAATGGACCTAGCTATGCATTTGGTAGAAAGGTGTCAATTATACCAG-TAGATGAAC
1 TAAAAGATAAATGG-CCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAAC
* ** *
3602080 GATTACTGATCGTTGAG
65 GGTTAAAGACCGTTGAG
* * * * * * * * **
3602097 TAAAAAAGAAATGGCTTAGTTATGCATTTGGCAAAAATGTTTCAATTATGCTAACTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
* *
3602162 GTTAAACATCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * * * *
3602178 TAAAAGATAAATGACATAGTTGTGCATTTTGCAAAAAATGTGTCAATTATACCAGTTAGATGAAC
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGC-AGAAAGGTGTCAATTATGCTAGTTAGATGAAC
*
3602243 GGTTAAAGACCGTTGAT
65 GGTTAAAGACCGTTGAG
* * * * *
3602260 TAAAAGATAAATGGCCTAACTGTGCATTTGGCAGAAATGTGTCATTTATGCCAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
*
3602325 GTTAAATACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * *
3602341 TAAAAGCTAAATGGTCTAGTTCTGCATTTGGTAGAAAGGTGGCAATTATGCTAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
3602406 GTTAAAGATCC-TTGAG
66 GTTAAAGA-CCGTTGAG
* * * * *
3602422 -AAGAAGATAAATGGCCTAGATGTGCATTCGGTA-TAAGAGTGTCAATTATGCAAGTTAGATGAA
1 TAA-AAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAG-GTGTCAATTATGCTAGTTAGATGAA
3602485 AAGTTAATTG
Statistics
Matches: 2157, Mismatches: 377, Indels: 77
0.83 0.14 0.03
Matches are distributed among these distances:
77 3 0.00
78 4 0.00
79 57 0.03
80 111 0.05
81 1853 0.86
82 126 0.06
83 3 0.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (81 bp):
TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCTAGTTAGATGAACG
GTTAAAGACCGTTGAG
Found at i:3600161 original size:27 final size:27
Alignment explanation
Indices: 3600112--3600164 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
3600102 TTGTCAGAAA
*
3600112 GGTGTCAATTATGCCAGTTAGATGAAC
1 GGTGTCAATTATGCCAGTAAGATGAAC
* *
3600139 GGTGTCAATTATGTCGGTAAGATGAA
1 GGTGTCAATTATGCCAGTAAGATGAA
3600165 TGGAATAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.30
Consensus pattern (27 bp):
GGTGTCAATTATGCCAGTAAGATGAAC
Found at i:3607458 original size:81 final size:81
Alignment explanation
Indices: 3607350--3607612 Score: 382
Period size: 81 Copynumber: 3.2 Consensus size: 81
3607340 ATGGTCTAAA
* * *
3607350 TAAAAGATTAAATGACCTAGTTTTGCATTTGGCATAAAGGTGTCAATTATGCTAGTTAGATGAAT
1 TAAAAGA-TAAATGACCTAGTTATGCATTTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAAT
*
3607415 GGTTAAAGACCGTTAAG
65 GGTTAAAGACTGTTAAG
* *
3607432 TAAAAGATAAATGGCCTAGTTATGCATTTGGTAGAAATGTGTCAATTATGCTAGTTAGATGAATG
1 TAAAAGATAAATGACCTAGTTATGCATTTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAATG
* * * *
3607497 ATTAAAGGCTGATCAG
66 GTTAAAGACTGTTAAG
* *
3607513 TAAAAGATAAATGACCTAGCTATGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAATG
1 TAAAAGATAAATGACCTAGTTATGCATTTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAATG
* *
3607578 GTTAAAGACTATTGAG
66 GTTAAAGACTGTTAAG
*
3607594 TAAAAGATAAATGGCCTAG
1 TAAAAGATAAATGACCTAG
3607613 CAGCAATCAT
Statistics
Matches: 161, Mismatches: 20, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
81 154 0.96
82 7 0.04
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (81 bp):
TAAAAGATAAATGACCTAGTTATGCATTTGGCAGAAATGTGTCAATTATGCTAGTTAGATGAATG
GTTAAAGACTGTTAAG
Found at i:3615387 original size:54 final size:54
Alignment explanation
Indices: 3615328--3615786 Score: 692
Period size: 54 Copynumber: 8.5 Consensus size: 54
3615318 TTCTGTGGTT
* *
3615328 TTGCACACGTAGTGCAAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
*
3615382 TTGCACACATAGTGTCAATAC-AGAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAGG
* * *
3615436 TTGCACACATAGTGTCAATACGGAAATTCAT-AACTTGTTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* * *
3615489 TTGCACACATGGTTCCAATACGAAAATTCATAAACTTGTTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
* * *
3615543 TTGCACACATAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTATTAGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
*
3615597 TTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
3615651 TTGCACACATAGTGCCAATAC-AGAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAGG
* *
3615705 TTACACACATAGTGTCAATAC-AGAAATTCATAAACTTATTATGAATTTCTTAGG
1 TTGCACACATAGTGCCAATACGA-AAATTCATAAACTTATTATGAATTTCTTAGG
* **
3615759 TTTCACACATAGAACCAATACGGAAAAT
1 TTGCACACATAGTGCCAATAC-GAAAAT
3615787 GAAACACATA
Statistics
Matches: 375, Mismatches: 24, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
53 49 0.13
54 321 0.86
55 4 0.01
56 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGG
Found at i:3616762 original size:23 final size:23
Alignment explanation
Indices: 3616732--3616782 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
3616722 TTAAGGTTTC
3616732 AAAACCAACCCAAAAACAAAAGG
1 AAAACCAACCCAAAAACAAAAGG
3616755 AAAACCAACCCAAAAACAAAAGG
1 AAAACCAACCCAAAAACAAAAGG
3616778 AAAAC
1 AAAAC
3616783 AAACATTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.67, C:0.25, G:0.08, T:0.00
Consensus pattern (23 bp):
AAAACCAACCCAAAAACAAAAGG
Found at i:3621559 original size:112 final size:111
Alignment explanation
Indices: 3621324--3621530 Score: 269
Period size: 112 Copynumber: 1.9 Consensus size: 111
3621314 CTCACATCAT
* *
3621324 TATGAATATC-ATGGGTGGAACCTTTTATACCGAAAATGCATCGTTATGCATTAAGCAAAATCGA
1 TATGAATA-CAATGGGTGGAACCTTTTATACCGAAAATGCACCGTTATGCATTAAGAAAAATCGA
* * ** *
3621388 TCGATAACTTTCATACACGAAGTATGTCGAAATGGTAATTCACCTAA
65 TCGATAACTATCATACACGAAGTATGTCAAAATGACAATTAACCTAA
* * *
3621435 TTATGAATACAATGGGTGGCACCTTTTATGCCGAAAATGCACCGTTATGCATTAA-AAAAATTGA
1 -TATGAATACAATGGGTGGAACCTTTTATACCGAAAATGCACCGTTATGCATTAAGAAAAATCGA
3621499 TCGAT-ACTATCATACA-GAAAGTATGTCAAAAT
65 TCGATAACTATCATACACG-AAGTATGTCAAAAT
3621531 ACACCTATAA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
109 1 0.01
110 23 0.27
111 13 0.15
112 49 0.57
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (111 bp):
TATGAATACAATGGGTGGAACCTTTTATACCGAAAATGCACCGTTATGCATTAAGAAAAATCGAT
CGATAACTATCATACACGAAGTATGTCAAAATGACAATTAACCTAA
Found at i:3624978 original size:23 final size:23
Alignment explanation
Indices: 3624927--3625016 Score: 130
Period size: 23 Copynumber: 4.0 Consensus size: 23
3624917 AGAACCCCCT
* * *
3624927 AGGGGGTATTGATTCCCC-T-AC
1 AGGGGGAATTGGTTCCCCTTCAA
3624948 AGGGGGAATTGGTTCCCCTTCAA
1 AGGGGGAATTGGTTCCCCTTCAA
*
3624971 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATTGGTTCCCCTTCAA
3624994 AGGGGGAATTGGTTCCCCTTCAA
1 AGGGGGAATTGGTTCCCCTTCAA
3625017 GAAGGTATCG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 16 0.26
22 1 0.02
23 45 0.73
ACGTcount: A:0.21, C:0.23, G:0.30, T:0.26
Consensus pattern (23 bp):
AGGGGGAATTGGTTCCCCTTCAA
Found at i:3628600 original size:24 final size:24
Alignment explanation
Indices: 3628571--3628622 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3628561 GAATTTTCTC
*
3628571 CTTTTTAAAAACGTTTTGATCCAA
1 CTTTTTAAAAACATTTTGATCCAA
* *
3628595 CTTTTTCAAATCATTTTGATCCAA
1 CTTTTTAAAAACATTTTGATCCAA
3628619 CTTT
1 CTTT
3628623 ATCAAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (24 bp):
CTTTTTAAAAACATTTTGATCCAA
Found at i:3632346 original size:42 final size:42
Alignment explanation
Indices: 3632294--3632405 Score: 188
Period size: 42 Copynumber: 2.6 Consensus size: 42
3632284 AGATAAAAAA
* *
3632294 ATAAGAATAAAATAATAAAATATAAATTATTTTAAATGGGAG
1 ATAAGGATAAAATAATAAAATATAAATTATTTTAAATGGAAG
*
3632336 ATAAGGATAAAATAATAAAACATAAATTATTTTAAATGGAAG
1 ATAAGGATAAAATAATAAAATATAAATTATTTTAAATGGAAG
3632378 ATAAGGATAAAATAATAAAATAATAAAT
1 ATAAGGATAAAATAATAAAAT-ATAAAT
3632406 AATAATTATA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 59 0.91
43 6 0.09
ACGTcount: A:0.60, C:0.01, G:0.11, T:0.29
Consensus pattern (42 bp):
ATAAGGATAAAATAATAAAATATAAATTATTTTAAATGGAAG
Found at i:3632496 original size:13 final size:13
Alignment explanation
Indices: 3632474--3632511 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
3632464 ATAATGAGAT
*
3632474 AAAAATTAAATTA
1 AAAAAATAAATTA
3632487 AAAAAATAAA-TA
1 AAAAAATAAATTA
3632499 AATAAAATAAATT
1 AA-AAAATAAATT
3632512 GAGATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 4 0.18
13 17 0.77
14 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAATAAATTA
Found at i:3633269 original size:20 final size:22
Alignment explanation
Indices: 3633214--3633264 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3633204 TAGCCTTCAA
* * *
3633214 AATCCTAAAACAAGGTAAATAT
1 AATCCTAAAATAAAGAAAATAT
3633236 AATCCTAAAATAAAGAAAATA-
1 AATCCTAAAATAAAGAAAATAT
3633257 AATCCTAA
1 AATCCTAA
3633265 TTAAAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 8 0.31
22 18 0.69
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.22
Consensus pattern (22 bp):
AATCCTAAAATAAAGAAAATAT
Found at i:3633388 original size:92 final size:93
Alignment explanation
Indices: 3633255--3633443 Score: 344
Period size: 92 Copynumber: 2.0 Consensus size: 93
3633245 ATAAAGAAAA
* * *
3633255 TAAATCCTAATTAAAATACTTAAAACTATTTTAACTAAAATACCTAAAACAAAGATAAGATAAAA
1 TAAATCCAAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAGATAAAA
3633320 TATAATATAATATTT-AAAATAATATCC
66 TATAATATAATATTTAAAAATAATATCC
3633347 TAAATCCAAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAGATAAAA
1 TAAATCCAAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAGATAAAA
3633412 TATAATATAATATTTAAAAATAATATCC
66 TATAATATAATATTTAAAAATAATATCC
3633440 TAAA
1 TAAA
3633444 ACATGAGTTT
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
92 77 0.83
93 16 0.17
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.30
Consensus pattern (93 bp):
TAAATCCAAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAAGATAAAA
TATAATATAATATTTAAAAATAATATCC
Found at i:3633716 original size:18 final size:18
Alignment explanation
Indices: 3633695--3633733 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3633685 TCGAAACGAA
* *
3633695 CAAATAAGCCACATAAAC
1 CAAATAAACCACAGAAAC
3633713 CAAATAAACCACAGAAAC
1 CAAATAAACCACAGAAAC
3633731 CAA
1 CAA
3633734 TGATTATGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.28, G:0.05, T:0.08
Consensus pattern (18 bp):
CAAATAAACCACAGAAAC
Found at i:3645634 original size:15 final size:15
Alignment explanation
Indices: 3645610--3645644 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3645600 GAGCACCTGG
3645610 GCTAGATTTGTGGAA
1 GCTAGATTTGTGGAA
*
3645625 GCTAGCTTTGTGGAA
1 GCTAGATTTGTGGAA
3645640 GCTAG
1 GCTAG
3645645 TCTTATGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.31
Consensus pattern (15 bp):
GCTAGATTTGTGGAA
Found at i:3649884 original size:20 final size:20
Alignment explanation
Indices: 3649855--3649893 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3649845 ATTTCACCAC
*
3649855 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
3649875 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
3649894 TATGGGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3652995 original size:10 final size:11
Alignment explanation
Indices: 3652973--3653001 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
3652963 TCTTCTGGTC
3652973 ATAAATCAAAA
1 ATAAATCAAAA
3652984 ATAAAT-AAAA
1 ATAAATCAAAA
3652994 ATAAATCA
1 ATAAATCA
3653002 GTATTTGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (11 bp):
ATAAATCAAAA
Found at i:3653278 original size:6 final size:6
Alignment explanation
Indices: 3653269--3653294 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3653259 TAATAATTAT
3653269 AAGATA AAGATA AAGATA AAGATA AA
1 AAGATA AAGATA AAGATA AAGATA AA
3653295 AATGGGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAGATA
Found at i:3655013 original size:54 final size:54
Alignment explanation
Indices: 3654839--3655000 Score: 256
Period size: 54 Copynumber: 3.0 Consensus size: 54
3654829 CATACGTAGA
3654839 GCCAATACA-GAAATTCATAAACTTATTATGAATTTCTTAGGTTGCA-AACATAGT
1 GCCAATA-AGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACAA-ATAGT
*
3654893 GCCAATAAGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGT
1 GCCAATAAGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACAAATAGT
* * *
3654947 GCTAATACGGAAATTTATAAACTTATTATGAATTTCTTAGGTTGCACAAATAGT
1 GCCAATAAGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACAAATAGT
3655001 ACGAATATGG
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
53 1 0.01
54 99 0.98
55 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (54 bp):
GCCAATAAGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACAAATAGT
Found at i:3662214 original size:12 final size:12
Alignment explanation
Indices: 3662199--3662246 Score: 71
Period size: 12 Copynumber: 3.9 Consensus size: 12
3662189 CCAAAAATTA
3662199 AAATAAAATAAT
1 AAATAAAATAAT
3662211 AAATAAAATAAACT
1 AAATAAAAT-AA-T
3662225 AAAT-AAATAAT
1 AAATAAAATAAT
3662236 AAATAAAATAA
1 AAATAAAATAA
3662247 AATGAAACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.15
12 17 0.52
13 6 0.18
14 5 0.15
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:3662230 original size:21 final size:20
Alignment explanation
Indices: 3662199--3662247 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3662189 CCAAAAATTA
3662199 AAATAAAAT-AATAAAT-A-
1 AAATAAAATAAATAAATAAT
*
3662216 AAATAAACTAAATAAATAAT
1 AAATAAAATAAATAAATAAT
3662236 AAATAAAATAAA
1 AAATAAAATAAA
3662248 ATGAAACGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 8 0.30
18 7 0.26
19 1 0.04
20 11 0.41
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
AAATAAAATAAATAAATAAT
Found at i:3662238 original size:16 final size:16
Alignment explanation
Indices: 3662197--3662249 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
3662187 GACCAAAAAT
3662197 TAAAATAAAATAATAAA
1 TAAAAT-AAATAATAAA
3662214 TAAAATAAACTAAATAAA
1 TAAAATAAA-T-AATAAA
3662232 T--AATAAAT-A-AAA
1 TAAAATAAATAATAAA
3662244 TAAAAT
1 TAAAAT
3662250 GAAACGCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
12 4 0.12
13 1 0.03
14 3 0.09
15 1 0.03
16 9 0.28
17 7 0.22
18 7 0.22
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (16 bp):
TAAAATAAATAATAAA
Found at i:3662238 original size:25 final size:26
Alignment explanation
Indices: 3662199--3662247 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
3662189 CCAAAAATTA
3662199 AAATAAAATAATAAATAAAATAAACT
1 AAATAAAATAATAAATAAAATAAACT
3662225 AAAT-AAATAATAAATAAAATAAA
1 AAATAAAATAATAAATAAAATAAA
3662248 ATGAAACGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (26 bp):
AAATAAAATAATAAATAAAATAAACT
Found at i:3668429 original size:20 final size:20
Alignment explanation
Indices: 3668404--3668463 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
3668394 TTTTTGTGCA
*
3668404 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
3668424 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
3668445 GAAGGGGAACCGAT-CCCCC
1 G-A-GGGAACCGATACCCCC
3668464 CCCACAGGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.47
21 2 0.06
22 6 0.18
23 10 0.29
ACGTcount: A:0.25, C:0.33, G:0.27, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:3672089 original size:37 final size:37
Alignment explanation
Indices: 3671992--3672152 Score: 202
Period size: 37 Copynumber: 4.3 Consensus size: 37
3671982 TAATTTCTTA
* * *
3671992 AAAACTATATACTATATAAAATTTC-AAAATGTTTTC
1 AAAACTATATATTATATATATTTTCAAAAATGTTTTC
*
3672028 AAAATTATATATTATATAATTATTTTCAAAAATGTTTTC
1 AAAACTATATATTATAT-A-TATTTTCAAAAATGTTTTC
* *
3672067 AAAATTATATATTATATATATTTTCAAAAACGTTTTC
1 AAAACTATATATTATATATATTTTCAAAAATGTTTTC
*
3672104 AAAACTATACA--ATATATATTTTCCAAAAATCGTTTTC
1 AAAACTATATATTATATATATTTT-CAAAAAT-GTTTTC
3672141 AAAACTATATAT
1 AAAACTATATAT
3672153 ATTTTTTAAA
Statistics
Matches: 110, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
35 11 0.10
36 21 0.19
37 44 0.40
38 6 0.05
39 28 0.25
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.42
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTCAAAAATGTTTTC
Found at i:3672223 original size:37 final size:35
Alignment explanation
Indices: 3672115--3672223 Score: 102
Period size: 35 Copynumber: 3.2 Consensus size: 35
3672105 AAACTATACA
** *
3672115 ATATATATTTTCCAAAAAT-CGTTTTC--AAAACT
1 ATATATATTTTTTAAAAATCCATTTTCTAAAAACT
* * *
3672147 ATATATATTTTTTAAAAATCGATTTTTTAAAAAGT
1 ATATATATTTTTTAAAAATCCATTTTCTAAAAACT
*
3672182 ATATATTATATGTTT-AAAA-CCATTTTCTAAAAACT
1 ATATA-TAT-TTTTTAAAAATCCATTTTCTAAAAACT
3672217 ATATATA
1 ATATATA
3672224 AAAATTATAC
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
32 17 0.27
33 4 0.06
34 2 0.03
35 28 0.45
36 7 0.11
37 4 0.06
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (35 bp):
ATATATATTTTTTAAAAATCCATTTTCTAAAAACT
Found at i:3672574 original size:85 final size:85
Alignment explanation
Indices: 3672464--3672870 Score: 526
Period size: 85 Copynumber: 4.8 Consensus size: 85
3672454 CGCTATCGTC
* * *
3672464 GAGCTGAATGGAATCGAACTTGAAGGTTTTTGTTGACAGATAACCCTTCTCGTCTTGAGCTATGT
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGC
*
3672529 TGTAAATTGGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * * ** ** * *
3672549 GAGCTGAATGGAATCAAAATCGAAGGTTTTTGTTGACATATAAACCTTCTCACCTTGAGATATGT
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGC
3672614 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * * * **
3672634 GAGCTAAATAGAATCAAACTCGAAGTTTTTTGTTGACAGATAGCCCTTCTCGTCCCGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGC
* *
3672699 TATAAATTTGATATACCCTT
66 TGTAAATTTGATATGCCCTT
* ** * * * * *
3672719 AAATTGAATGTAATCGAACTCGAAGGTTTTTGTAGACATATAGCTCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGC
3672784 TGTAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * *
3672804 GAGCTGAATGTAATCGAACTTGAAGGTTTTTGTTGACAGATAGCCCTTCTCGTCGTGAGCTATGC
1 GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGC
3672869 TG
66 TG
3672871 CAAACAGTTT
Statistics
Matches: 273, Mismatches: 49, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
85 273 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGGAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGC
TGTAAATTTGATATGCCCTT
Found at i:3674364 original size:99 final size:99
Alignment explanation
Indices: 3674255--3674533 Score: 416
Period size: 99 Copynumber: 2.8 Consensus size: 99
3674245 TCATTGTCTA
* * *
3674255 GCTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCACTTGCTCTAGAGGGACAACTCAAGC
1 GCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGC
3674320 TTTATTGTATAAATATTATAATCACCTTTATCAG
66 TTTATTGTATAAATATTATAATCACCTTTATCAG
* *
3674354 GCTAGCTGAATCTTATCCATAAAGCCAGAGCGTTTAACCAATTGCTCTAGAGTGG-TAACTCAAG
1 GCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAG-GGACAACTCAAG
* *
3674418 TTTTATTGTATAGATATTATAATCACCTTTATCAG
65 CTTTATTGTATAAATATTATAATCACCTTTATCAG
* * * * * *
3674453 GCTAGCTGAATCTTATCTATAAAGTCAGGGCGTTTAAACAATTGCTCTAGAGAGACAGCTCAGGC
1 GCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGC
*
3674518 TTTATTGTATACATAT
66 TTTATTGTATAAATAT
3674534 AATATTATAA
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
98 1 0.01
99 158 0.98
100 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (99 bp):
GCTAGCTGAATCTTATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGC
TTTATTGTATAAATATTATAATCACCTTTATCAG
Found at i:3679923 original size:2 final size:2
Alignment explanation
Indices: 3679916--3679955 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3679906 ATCATCATAA
3679916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3679956 TTTTTTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3680075 original size:36 final size:36
Alignment explanation
Indices: 3680018--3680197 Score: 140
Period size: 36 Copynumber: 5.0 Consensus size: 36
3680008 TTATATTATT
* * * *
3680018 TTTTAAAAACTATACACTATATTAATTTGC-AAAATG
1 TTTTCAAAACTATATATTATA-TAATTTTCAAAAATG
*
3680054 TTTTCAAAACTATATATTATATATTTATTTTCAAAAA-A
1 TTTTCAAAACTATATATTATATA---ATTTTCAAAAATG
** * *
3680092 AATTCAAAATTATATATTATATATATTTTCAAAAACG
1 TTTTCAAAACTATATATTATATA-ATTTTCAAAAATG
* *
3680129 TTTTCAAAACTATATAATATAT-ATTTTCCAAAAATCT
1 TTTTCAAAACTATATATTATATAATTTT-CAAAAAT-G
*
3680166 TTTTCAAAA-T-TATA-TAAAT-ATTTTCAAAAATG
1 TTTTCAAAACTATATATTATATAATTTTCAAAAATG
3680198 CGAATTTTAA
Statistics
Matches: 120, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
33 7 0.06
34 9 0.08
35 11 0.09
36 37 0.31
37 27 0.22
38 25 0.21
39 4 0.03
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (36 bp):
TTTTCAAAACTATATATTATATAATTTTCAAAAATG
Found at i:3680089 original size:38 final size:38
Alignment explanation
Indices: 3680035--3680154 Score: 145
Period size: 38 Copynumber: 3.2 Consensus size: 38
3680025 AACTATACAC
* * *
3680035 TATATTAATTTGCAAAATGTTTTCAAAACTATATATTA
1 TATATTTATTTTCAAAAAGTTTTCAAAACTATATATTA
*** *
3680073 TATATTTATTTTCAAAAAAAATTCAAAATTATATATTA
1 TATATTTATTTTCAAAAAGTTTTCAAAACTATATATTA
*
3680111 TATA--TATTTTCAAAAACGTTTTCAAAACTATATAATA
1 TATATTTATTTTCAAAAA-GTTTTCAAAACTATATATTA
3680148 TATATTT
1 TATATTT
3680155 TCCAAAAATC
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
36 12 0.18
37 19 0.28
38 35 0.52
39 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATTTATTTTCAAAAAGTTTTCAAAACTATATATTA
Found at i:3680143 original size:35 final size:35
Alignment explanation
Indices: 3680048--3680251 Score: 125
Period size: 35 Copynumber: 5.6 Consensus size: 35
3680038 ATTAATTTGC
*
3680048 AAAATGTTTTCAAAACTATATATTATATATTTATTTTCA
1 AAAACGTTTTCAAAAC--TATATTATATA--TATTTTCA
*** *
3680087 AAAA-AAATTCAAAATTATATATTATATATATTTTCA
1 AAAACGTTTTCAAAA--CTATATTATATATATTTTCA
*
3680123 AAAACGTTTTCAAAACTATATAATATATATTTTCCA
1 AAAACGTTTTCAAAACTATATTATATATATTTT-CA
* *
3680159 AAAATCTTTTTCAAAA-T-TA-TATAAATATTTTCA
1 AAAA-CGTTTTCAAAACTATATTATATATATTTTCA
* *
3680192 AAAATGCGAATTTTAAAAAGTATA-TAT-TATATGTTT-A
1 AAAA--CG--TTTTCAAAACTATATTATATATAT-TTTCA
*
3680229 AAACCGTTTTCTAAAAACTATAT
1 AAAACGTTTTC--AAAACTATAT
3680252 ATAAAAATTA
Statistics
Matches: 132, Mismatches: 19, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
33 10 0.08
34 11 0.08
35 28 0.21
36 27 0.20
37 26 0.20
38 26 0.20
39 4 0.03
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (35 bp):
AAAACGTTTTCAAAACTATATTATATATATTTTCA
Found at i:3680378 original size:32 final size:33
Alignment explanation
Indices: 3680354--3680414 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
3680344 ATATGCACGT
3680354 ATAT-GATTTATTCAAAT-AAGAAATATGACAA
1 ATATGGATTTATTCAAATGAAGAAATATGACAA
*
3680385 ATATGGATTTATTCAAATGAGGAAATATGA
1 ATATGGATTTATTCAAATGAAGAAATATGA
3680415 ATTTATCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 4 0.15
32 13 0.48
33 10 0.37
ACGTcount: A:0.48, C:0.05, G:0.15, T:0.33
Consensus pattern (33 bp):
ATATGGATTTATTCAAATGAAGAAATATGACAA
Found at i:3681630 original size:87 final size:82
Alignment explanation
Indices: 3681440--3681688 Score: 277
Period size: 87 Copynumber: 3.0 Consensus size: 82
3681430 TAAAAAATAT
* ** * *
3681440 GGGGAAATGGAAAAATCGTAATATCAAT-AAGCCCGCTTGATGCTAATAAAAAATTATAAAGAAA
1 GGGGAAATGGAAAAATCGTGATATCAATCAAG-TTGCTTGATACTAACAAAAAATTATAAAGAAA
3681504 TATAGTTTCAGAAATTAG
65 TATAGTTTCAGAAATTAG
* * * *
3681522 GGAAGAAATGAAAAAATCGTGATATCAATCAAGTTGCTTGATATTAACAAGAAAATTATATATAT
1 GG-GGAAATGGAAAAATCGTGATATCAATCAAGTTGCTTGATACTAACAA-AAAATTATA-A-AG
*
3681587 ATATATATAGTTTTA-AAGATTAG
62 A-A-ATATAGTTTCAGAA-ATTAG
* *
3681610 GGGGAAATGGAAAAATCGTGATATCAATCAACTTGTTTGATACTAACAATAAAATTATAAAGAAA
1 GGGGAAATGGAAAAATCGTGATATCAATCAAGTTGCTTGATACTAACAA-AAAATTATAAAGAAA
* *
3681675 TTTAGTTTTAGAAA
65 TATAGTTTCAGAAA
3681689 GGCTTAATAC
Statistics
Matches: 140, Mismatches: 18, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
82 2 0.01
83 46 0.33
84 15 0.11
85 3 0.02
86 3 0.02
87 54 0.39
88 17 0.12
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (82 bp):
GGGGAAATGGAAAAATCGTGATATCAATCAAGTTGCTTGATACTAACAAAAAATTATAAAGAAAT
ATAGTTTCAGAAATTAG
Found at i:3690482 original size:46 final size:45
Alignment explanation
Indices: 3690393--3690557 Score: 233
Period size: 45 Copynumber: 3.7 Consensus size: 45
3690383 TACAACTTTC
* * *
3690393 TTACCAATATACATATCATATATCCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATATATTCCATAAGCTCGTAAGCTTATT
*
3690438 TTACCAATATACTTACCATATATTTCCATAAGCTCATAAGCTTATT
1 TTACCAATATACTTACCATATA-TTCCATAAGCTCGTAAGCTTATT
* * *
3690484 TTACCAATATACTTATCATTTAATCCATAAGCTCGTAAGCTTATT
1 TTACCAATATACTTACCATATATTCCATAAGCTCGTAAGCTTATT
* *
3690529 TTACCAATACACTTGCCAT-TATTCCATAA
1 TTACCAATATACTTACCATATATTCCATAA
3690558 CCATATACCA
Statistics
Matches: 107, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
44 9 0.08
45 57 0.53
46 41 0.38
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (45 bp):
TTACCAATATACTTACCATATATTCCATAAGCTCGTAAGCTTATT
Found at i:3690579 original size:20 final size:20
Alignment explanation
Indices: 3690554--3690596 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3690544 CCATTATTCC
* * *
3690554 ATAACCATATACCATAGGCA
1 ATAACCATAAACAATAGACA
3690574 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGACA
3690594 ATA
1 ATA
3690597 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:3693181 original size:20 final size:20
Alignment explanation
Indices: 3693155--3693205 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
3693145 TACTGATGTG
3693155 GGTATCGATACTATGAGGAA
1 GGTATCGATACTATGAGGAA
*
3693175 TGTATCGATACTATGAGGAA
1 GGTATCGATACTATGAGGAA
3693195 GGTATCGATAC
1 GGTATCGATAC
3693206 CATGGATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (20 bp):
GGTATCGATACTATGAGGAA
Found at i:3693708 original size:54 final size:54
Alignment explanation
Indices: 3693624--3693966 Score: 436
Period size: 54 Copynumber: 6.4 Consensus size: 54
3693614 CTATGTGTAC
* * ** * *
3693624 TATAGGTACTAAATGTGCAACCCATGGAATTCATCATATGTTGATCAACGACTG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * * *
3693678 TATAGGCACTAAGTGTGCAACCCACAGAATTCTTAATATGTTTATGAATGATCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * *
3693732 TATAAGCACTAAGTGTACAACCCACAAAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
3693786 TATAGGCACTAAGTGTGCAACCCACATAATTCATCATATGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* *
3693840 TATAGGTACTAAGTGTGCAACCCACAGAATTCATCATATGTTTATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
* * * *
3693894 TATAGGCACTAAGTGTGCAACCCAC-GAAATTCATAATATGTTTATGAATGATCG
1 TATAGGCACTAAGTGTGCAACCCACAG-AATTCATCATATGTTGATGAACGACCG
* * *
3693948 TATCGACACTATGTGTGCA
1 TATAGGCACTAAGTGTGCA
3693967 TCTTAAAGAA
Statistics
Matches: 254, Mismatches: 34, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 253 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAGAATTCATCATATGTTGATGAACGACCG
Found at i:3696111 original size:12 final size:12
Alignment explanation
Indices: 3696094--3696119 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3696084 TTGTTGTGCT
3696094 TGCTCCTCGGGC
1 TGCTCCTCGGGC
3696106 TGCTCCTCGGGC
1 TGCTCCTCGGGC
3696118 TG
1 TG
3696120 TTCAGGCTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.38, G:0.35, T:0.27
Consensus pattern (12 bp):
TGCTCCTCGGGC
Found at i:3699494 original size:21 final size:21
Alignment explanation
Indices: 3699468--3699524 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
3699458 ATCATCGAAA
3699468 ACAACATGTATAGACTCTTCT
1 ACAACATGTATAGACTCTTCT
3699489 ACAACATGTATAGACTCTTCT
1 ACAACATGTATAGACTCTTCT
3699510 ACAACATGT-TAGACT
1 ACAACATGTATAGACT
3699525 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.17
21 30 0.83
ACGTcount: A:0.35, C:0.23, G:0.11, T:0.32
Consensus pattern (21 bp):
ACAACATGTATAGACTCTTCT
Found at i:3701104 original size:22 final size:21
Alignment explanation
Indices: 3701062--3701101 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3701052 GAATTTATTT
*
3701062 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
3701083 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
3701102 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:3705692 original size:15 final size:15
Alignment explanation
Indices: 3705672--3705706 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3705662 CCTGTTTCTT
3705672 TGGCTTCGTATCGAA
1 TGGCTTCGTATCGAA
3705687 TGGCTTCGTATCGAA
1 TGGCTTCGTATCGAA
3705702 TGGCT
1 TGGCT
3705707 CCAATAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (15 bp):
TGGCTTCGTATCGAA
Found at i:3709291 original size:18 final size:19
Alignment explanation
Indices: 3709268--3709315 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
3709258 GATACAATTA
* *
3709268 GTATCGATAC-TGATGTAG
1 GTATCGATACATGAGGAAG
3709286 GTATCGATACTATGAGGAAG
1 GTATCGATAC-ATGAGGAAG
3709306 GTATCGATAC
1 GTATCGATAC
3709316 CATGGATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.29
Consensus pattern (19 bp):
GTATCGATACATGAGGAAG
Found at i:3709831 original size:54 final size:54
Alignment explanation
Indices: 3709737--3710023 Score: 371
Period size: 54 Copynumber: 5.3 Consensus size: 54
3709727 CTATGTGTAC
* * * *
3709737 TATAGTCACTATGTGTGCAACCCACATAATTCGTCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
* * * *
3709791 TATATGAACTAAGTGTGCAACCCACAAAATTCACCATATGTTGATAAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
* * * *
3709845 TATAGGCACTAAGTGTGCAACCCAAAAAATTCATCATATGTTTATGAATGATCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
*
3709899 TATAGGCACTAAGTGTGTAACCCA-AAGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACAA-AATTCATCATATGTTGATGAACGACCG
* * *
3709953 TATAGGCACTAAGTGTGCAACCCACATAATTCAT-ACTATGTTTATGAACTACCG
1 TATAGGCACTAAGTGTGCAACCCACAAAATTCATCA-TATGTTGATGAACGACCG
* * *
3710007 TATCGACACTATGTGTG
1 TATAGGCACTAAGTGTG
3710024 GATCTCAAAG
Statistics
Matches: 203, Mismatches: 27, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
53 3 0.01
54 199 0.98
55 1 0.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGATGAACGACCG
Found at i:3713218 original size:17 final size:18
Alignment explanation
Indices: 3713184--3713218 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3713174 AGCTACTTTT
3713184 AGTATCGATACTCAAGGG
1 AGTATCGATACTCAAGGG
3713202 AGTATCGATAC-CAAGGG
1 AGTATCGATACTCAAGGG
3713219 TAAAGTACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (18 bp):
AGTATCGATACTCAAGGG
Found at i:3714581 original size:34 final size:34
Alignment explanation
Indices: 3714538--3714603 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
3714528 GGATAAAATT
*
3714538 TTGAAGTATTCTATAATCTACTGTGCATTTAGTA
1 TTGAAGTATTCTAGAATCTACTGTGCATTTAGTA
* **
3714572 TTGAAGTATTCTAGAATTTGTTGTGCATTTAG
1 TTGAAGTATTCTAGAATCTACTGTGCATTTAG
3714604 ATGAGGTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (34 bp):
TTGAAGTATTCTAGAATCTACTGTGCATTTAGTA
Found at i:3714625 original size:32 final size:34
Alignment explanation
Indices: 3714559--3714628 Score: 90
Period size: 32 Copynumber: 2.1 Consensus size: 34
3714549 TATAATCTAC
*
3714559 TGTGCATTTAGTATTGAAGTATTCTAGAATTTGT
1 TGTGCATTTAGTATTGAAGTATTCTAGAAGTTGT
* * *
3714593 TGTGCATTTAG-A-TGAGGTTTTTTAGAAGTTGT
1 TGTGCATTTAGTATTGAAGTATTCTAGAAGTTGT
3714625 TGTG
1 TGTG
3714629 TGTCTAGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 20 0.62
33 1 0.03
34 11 0.34
ACGTcount: A:0.23, C:0.04, G:0.26, T:0.47
Consensus pattern (34 bp):
TGTGCATTTAGTATTGAAGTATTCTAGAAGTTGT
Found at i:3718786 original size:34 final size:34
Alignment explanation
Indices: 3718743--3718844 Score: 186
Period size: 34 Copynumber: 3.0 Consensus size: 34
3718733 GTAGGGAGAA
* *
3718743 TATTGAAGTATTCTAGAATCTGATGTGCATTTAG
1 TATTGAAGTATTCTGGTATCTGATGTGCATTTAG
3718777 TATTGAAGTATTCTGGTATCTGATGTGCATTTAG
1 TATTGAAGTATTCTGGTATCTGATGTGCATTTAG
3718811 TATTGAAGTATTCTGGTATCTGATGTGCATTTAG
1 TATTGAAGTATTCTGGTATCTGATGTGCATTTAG
3718845 ATGAGATTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (34 bp):
TATTGAAGTATTCTGGTATCTGATGTGCATTTAG
Found at i:3721931 original size:21 final size:21
Alignment explanation
Indices: 3721905--3722004 Score: 112
Period size: 21 Copynumber: 4.7 Consensus size: 21
3721895 AGTCCATCAA
3721905 AGTGCATCCATGCACCTCTGC
1 AGTGCATCCATGCACCTCTGC
* *
3721926 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCTCTGC
*
3721947 AGTGCATCCATGCACCTGCTAC
1 AGTGCATCCATGCACCT-CTGC
* * * *
3721969 TTGTGCATCGATGCACC-ATGT
1 -AGTGCATCCATGCACCTCTGC
3721990 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3722005 TTCATTTCGA
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
20 13 0.20
21 36 0.55
22 2 0.03
23 14 0.22
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCACCTCTGC
Found at i:3722003 original size:43 final size:42
Alignment explanation
Indices: 3721905--3722004 Score: 139
Period size: 43 Copynumber: 2.4 Consensus size: 42
3721895 AGTCCATCAA
* *
3721905 AGTGCATCCATGCACCTCTGCAGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCTCTACAGTGCATCCATGCACCCATGT
* *
3721947 AGTGCATCCATGCACCTGCTACTTGTGCATCGATGCA-CCATGT
1 AGTGCATCCATGCACCT-CTAC-AGTGCATCCATGCACCCATGT
3721990 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3722005 TTCATTTCGA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
42 17 0.33
43 23 0.44
44 12 0.23
ACGTcount: A:0.21, C:0.34, G:0.20, T:0.25
Consensus pattern (42 bp):
AGTGCATCCATGCACCTCTACAGTGCATCCATGCACCCATGT
Found at i:3722049 original size:20 final size:20
Alignment explanation
Indices: 3722024--3722078 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
3722014 AATGCAATTA
*
3722024 GTGCATCGATGCACCCTACT
1 GTGCATCCATGCACCCTACT
*
3722044 GTGCATCCATGCACCCTGCT
1 GTGCATCCATGCACCCTACT
3722064 GTGCATCCATGCACC
1 GTGCATCCATGCACC
3722079 AAGGCTGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.18, C:0.38, G:0.20, T:0.24
Consensus pattern (20 bp):
GTGCATCCATGCACCCTACT
Found at i:3725200 original size:21 final size:21
Alignment explanation
Indices: 3725176--3725220 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3725166 TTTCAAACAA
3725176 TTTGGTAACAATTGATATCAT
1 TTTGGTAACAATTGATATCAT
* * *
3725197 TTTGTTAACAATTGGTATCTT
1 TTTGGTAACAATTGATATCAT
3725218 TTT
1 TTT
3725221 CATTAAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (21 bp):
TTTGGTAACAATTGATATCAT
Found at i:3725478 original size:21 final size:20
Alignment explanation
Indices: 3725454--3725550 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 20
3725444 AGTGCATCCA
3725454 TGCATCCATGCATCCCTGCAG
1 TGCATCCATGCA-CCCTGCAG
3725475 TGCATCCATGCACCCCTGCAG
1 TGCATCCATGCA-CCCTGCAG
*
3725496 TGAATCCATGCA-CCTGCCACTAG
1 TGCATCCATGCACCCTG---C-AG
* * *
3725519 TGCATCGATGCACCATGTAG
1 TGCATCCATGCACCCTGCAG
3725539 TGCATCCATGCA
1 TGCATCCATGCA
3725551 ATCCATTTCG
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
19 4 0.06
20 13 0.20
21 31 0.48
22 1 0.02
23 12 0.19
24 3 0.05
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (20 bp):
TGCATCCATGCACCCTGCAG
Found at i:3726558 original size:33 final size:34
Alignment explanation
Indices: 3726509--3726573 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
3726499 CACATGTTCA
3726509 AAGTTTGCCCACCAACCAAGATGAAATTTCCAAT
1 AAGTTTGCCCACCAACCAAGATGAAATTTCCAAT
3726543 AAGTTTG-CCACCAACCAAGATGAAATTTCCA
1 AAGTTTGCCCACCAACCAAGATGAAATTTCCA
3726574 TCTTGCCAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.23
Consensus pattern (34 bp):
AAGTTTGCCCACCAACCAAGATGAAATTTCCAAT
Found at i:3726579 original size:29 final size:31
Alignment explanation
Indices: 3726517--3726581 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
3726507 CAAAGTTTGC
*
3726517 CCACCAACCAAGATGAAATTTCCAATAAGTTTG
1 CCACCAACCAAGATGAAATTTCCAAT-A-CTTG
3726550 CCACCAACCAAGATGAAATTTCC-AT-CTTG
1 CCACCAACCAAGATGAAATTTCCAATACTTG
3726579 CCA
1 CCA
3726582 ACTTAATTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 6 0.19
32 2 0.06
33 23 0.74
ACGTcount: A:0.37, C:0.29, G:0.11, T:0.23
Consensus pattern (31 bp):
CCACCAACCAAGATGAAATTTCCAATACTTG
Found at i:3731300 original size:38 final size:36
Alignment explanation
Indices: 3731187--3731300 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 36
3731177 TCAAATATGG
*
3731187 AATTCCCATATTCAAAGTTTGGCCACCTACCAAA-GA
1 AATTCCCATGTTCAAAGTTTGGCCACC-ACCAAATGA
* * *
3731223 ATTTTCCAATGTGT-ACAAG-TTAGCCACCA--AATATGA
1 A-ATTCCCATGT-TCA-AAGTTTGGCCACCACCAA-ATGA
3731259 AATTCCCATGTTCAAAGTTTGGCCACCAACCAAGATGA
1 AATTCCCATGTTCAAAGTTTGGCCACC-ACCAA-ATGA
3731297 AATT
1 AATT
3731301 TTTAACTTGC
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
34 6 0.10
35 18 0.30
36 6 0.10
37 16 0.27
38 14 0.23
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (36 bp):
AATTCCCATGTTCAAAGTTTGGCCACCACCAAATGA
Found at i:3732030 original size:25 final size:25
Alignment explanation
Indices: 3731993--3732042 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3731983 GCTGCCAATG
3731993 CTCATCTTCACCAACTAGAATATTA
1 CTCATCTTCACCAACTAGAATATTA
*
3732018 CTCATCTTTACCAACTAGAATATTA
1 CTCATCTTCACCAACTAGAATATTA
3732043 AACAACTACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (25 bp):
CTCATCTTCACCAACTAGAATATTA
Found at i:3737520 original size:75 final size:74
Alignment explanation
Indices: 3737426--3737619 Score: 232
Period size: 74 Copynumber: 2.6 Consensus size: 74
3737416 CATAAATAAA
* * *
3737426 GTCAAATATCAAGACTCAAACCATAATATTAAGTTTAGAACAGTAAAATCCATAA-ACAAACCAC
1 GTCAAATTTCAAGACTCAAACCATAATATTAAGTCTAGAACAATAAAAT-CATAATA-AAACCA-
*
3737490 T-TTATTAAAAT
63 TAATATTAAAAT
* * * * *
3737501 GTCAAATTTCAAGATTCAAACCACAATATTAACTCTAGAATAATAAAATCATAATAAAATCATAA
1 GTCAAATTTCAAGACTCAAACCATAATATTAAGTCTAGAACAATAAAATCATAATAAAACCATAA
*
3737566 TATTAAAGT
66 TATTAAAAT
*
3737575 GTCAAATCTT-AAGACTCAAACCATAATATTAAGTCTAGAAAAATA
1 GTCAAAT-TTCAAGACTCAAACCATAATATTAAGTCTAGAACAATA
3737620 TTAAACCCAA
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
73 1 0.01
74 56 0.55
75 45 0.44
ACGTcount: A:0.50, C:0.15, G:0.07, T:0.28
Consensus pattern (74 bp):
GTCAAATTTCAAGACTCAAACCATAATATTAAGTCTAGAACAATAAAATCATAATAAAACCATAA
TATTAAAAT
Found at i:3737556 original size:11 final size:11
Alignment explanation
Indices: 3737540--3737567 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3737530 TAACTCTAGA
3737540 ATAATAAAATC
1 ATAATAAAATC
3737551 ATAATAAAATC
1 ATAATAAAATC
3737562 ATAATA
1 ATAATA
3737568 TTAAAGTGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (11 bp):
ATAATAAAATC
Found at i:3751614 original size:21 final size:21
Alignment explanation
Indices: 3751584--3751623 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3751574 TATCAAAAGT
3751584 AGTACCGATACTCC-CTATATG
1 AGTACCGATAC-CCTCTATATG
*
3751605 AGTACTGATACCCTCTATA
1 AGTACCGATACCCTCTATA
3751624 CTAGGCAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (21 bp):
AGTACCGATACCCTCTATATG
Found at i:3757937 original size:20 final size:20
Alignment explanation
Indices: 3757912--3757984 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
3757902 CCCTTCAAGG
3757912 AGTATCGATACTCGAGATCC
1 AGTATCGATACTCGAGATCC
* *
3757932 AGTATCGATACTAGTGATCC
1 AGTATCGATACTCGAGATCC
* *
3757952 ATTATCGATACTCGGGATCC
1 AGTATCGATACTCGAGATCC
*
3757972 AATATCGATACTC
1 AGTATCGATACTC
3757985 AGAGGGTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTCGAGATCC
Found at i:3760239 original size:21 final size:21
Alignment explanation
Indices: 3760215--3760264 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
3760205 TCAAACAAAC
*
3760215 TTGAATGATTGAATTCAAGGG
1 TTGAATGATTAAATTCAAGGG
3760236 TTGAATGATTAAATTCAAGGG
1 TTGAATGATTAAATTCAAGGG
3760257 TTGAATGA
1 TTGAATGA
3760265 AGTCTGATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (21 bp):
TTGAATGATTAAATTCAAGGG
Found at i:3763515 original size:23 final size:23
Alignment explanation
Indices: 3763489--3763556 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
3763479 TACAATAACA
3763489 TATTAGGTAGCGCTTATATAATG
1 TATTAGGTAGCGCTTATATAATG
*
3763512 TATTAGGTAACGCTTATATAATG
1 TATTAGGTAGCGCTTATATAATG
*
3763535 TAATAGGTAGCGCTTATATAAT
1 TATTAGGTAGCGCTTATATAAT
3763557 AAAATAGGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (23 bp):
TATTAGGTAGCGCTTATATAATG
Found at i:3764084 original size:200 final size:197
Alignment explanation
Indices: 3763640--3764164 Score: 592
Period size: 200 Copynumber: 2.6 Consensus size: 197
3763630 AGCGCATATA
* * *
3763640 TTGACCTATTTTCTAAGT-AAACCGGTATATTTATATC-GATAACATTGCAAATTTACCTATTAC
1 TTGACCTATTTTCTAA-TAAAACCGGTATATTTATACCAG-TTACATTGTAAATTTACCTATTAC
* * * * *
3763703 ATTATAAATATCGGTTTCAATGTTTTTTGGATCGATACAATTT--TAAATGTATCTATACTTTAT
64 ATTATAATTATCGGTTTCAATG-TTTTGGGATCGATAC-TTTTAATAAATGTATCAACACTTTAT
* * *
3763766 GCATGCACCTCGTTGGGCATTCATTCTAGAAAAAAGTATCAACAGAAACTTAAAAAGTGTCGATA
127 GCATGCACCCCGTTGGGCATTCATTATAGAAAAAAGTATCAACACAAACTTAAAAAGTGTCGATA
3763831 CATTAT
192 CATTAT
* * * * * * *
3763837 TTAGATCTATTTTCTCATAAAACCGATATATTTCTATCGAG-TACATTGTAAATTTATCTATCAC
1 TT-GACCTATTTTCTAATAAAACCGGTATATTTATA-CCAGTTACATTGTAAATTTACCTATTAC
*
3763901 ATTGTAATTATCGGTTTCAATGTTTGTGGGATCGATACTTTTAATAAATGTATCAACACTTTATG
64 ATTATAATTATCGGTTTCAATGTTT-TGGGATCGATACTTTTAATAAATGTATCAACACTTTATG
* * * * * * * **
3763966 CGTGCACCCCGTTTGGTATTCATTATGGACGAAAAGTATCGACACAAATTTAAATGGTGTCGATA
128 CATGCACCCCGTTGGGCATTCATTATAGA-AAAAAGTATCAACACAAACTTAAAAAGTGTCGATA
*
3764031 CTTTAT
192 CATTAT
* * *
3764037 GTTGACCTATTGTCTTATAAAACTGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACA
1 -TTGACCTATTTTCTAATAAAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACA
* * * * *
3764102 TTATAATCATTGGTTTCGATGTTATTGGGATCGATACTTTTAATAAATGTATCGACACATTAT
65 TTATAATTATCGGTTTCAATGTT-TTGGGATCGATACTTTTAATAAATGTATCAACACTTTAT
3764165 ATTCTGGAAA
Statistics
Matches: 273, Mismatches: 44, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
197 9 0.03
198 77 0.28
199 45 0.16
200 139 0.51
201 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (197 bp):
TTGACCTATTTTCTAATAAAACCGGTATATTTATACCAGTTACATTGTAAATTTACCTATTACAT
TATAATTATCGGTTTCAATGTTTTGGGATCGATACTTTTAATAAATGTATCAACACTTTATGCAT
GCACCCCGTTGGGCATTCATTATAGAAAAAAGTATCAACACAAACTTAAAAAGTGTCGATACATT
AT
Found at i:3764315 original size:177 final size:178
Alignment explanation
Indices: 3763999--3764336 Score: 468
Period size: 177 Copynumber: 1.9 Consensus size: 178
3763989 TATGGACGAA
* ** * * * *
3763999 AAGTATCGACACAAATTTAAATGGTGTCGATACTTTATGTTGACCTATTGTCTTATAAAACTGGT
1 AAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATATTGTCTAATAAAACCGGT
*
3764064 ATATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATCATTGGTTTCGATGTTATTG
66 ATATTTATACCAGTTACATTGTAAATTCACCTATTACATTATAATCATTGGTTTCGATGTTATTG
3764129 GGATCGATACTTTTA-ATAAATGTATCGACACATTATATTCTGGAAAAT
131 GGATCGATACTTTTAGA-AAATGTATCGACACATTATATTCTGGAAAAT
* * * *
3764177 AAGTATTGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATGTTTTCTAAT-TAACCGGT
1 AAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATATTGTCTAATAAAACCGGT
* * * * *
3764241 ATATTTATATCGGTTACATTGTTAGTTCACCTATTACATTATAATTATTGGTTTCGATGTT-TCT
66 ATATTTATACCAGTTACATTGTAAATTCACCTATTACATTATAATCATTGGTTTCGATGTTAT-T
3764305 GAGG-TCGATACTTTTAGAAAATGTATCGACAC
130 G-GGATCGATACTTTTAGAAAATGTATCGACAC
3764337 CTATTCAGCT
Statistics
Matches: 140, Mismatches: 17, Indels: 7
0.85 0.10 0.04
Matches are distributed among these distances:
176 1 0.01
177 89 0.64
178 50 0.36
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (178 bp):
AAGTATCGACACAAATTCAAAAAGTGTCGATACATTATGTTGACATATTGTCTAATAAAACCGGT
ATATTTATACCAGTTACATTGTAAATTCACCTATTACATTATAATCATTGGTTTCGATGTTATTG
GGATCGATACTTTTAGAAAATGTATCGACACATTATATTCTGGAAAAT
Found at i:3765217 original size:19 final size:19
Alignment explanation
Indices: 3765193--3765241 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
3765183 TTACATTCAC
3765193 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
* *
3765212 ATACAACATTATAAATCTT
1 ATACAAAATTATAAATCGT
*
3765231 ATAAAAAATTA
1 ATACAAAATTA
3765242 ACCCTACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:3766770 original size:200 final size:200
Alignment explanation
Indices: 3766396--3767344 Score: 932
Period size: 200 Copynumber: 4.8 Consensus size: 200
3766386 GCGTAATTTA
* * * * * *
3766396 AAAACGTATCGACACAAAT-TTAAAAGTATCAATACATTATGTTAACCTATTTTCTCATAAAACC
1 AAAATGTATCAACACAAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACC
* * * *
3766460 GGTATATTTATAACGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCGATGTTT
66 GGTATACTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTT
* *
3766525 TTTGGATCGATACTTTTTATAAATGTATTGAAACTTTATGCGTGCACCCCGTTTTGT-ATTCATT
131 TTTGGATCGATACTTTTTAAAAATGTATCGAAACTTTATGCGTGCACCCCGTTTT-TCATTCATT
*
3766589 CTAGAG
195 CTAGAC
* *
3766595 AAAATGTATCAACACAAATCTAAAAAGTGTCGATACATTATGTTCATCTATTTTCTCATAAAACT
1 AAAATGTATCAACACAAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACC
*
3766660 GGTATACTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTTGATG-TT
66 GGTATACTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTT
*
3766724 TTTGAGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCCGTTTTTCATTCATT
131 TTTG-GATCGATACTTTTTAAAAATGTATCGAAACTTTATGCGTGCACCCCGTTTTTCATTCATT
*
3766789 CTGGAC
195 CTAGAC
* *
3766795 AAAATGTATCCACACTAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACC
1 AAAATGTATCAACACAAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACC
* * *
3766860 GATATAGTTATACCGGTTAC-------A--T---TA-TA-A-T-T-A-T-CA-GTTTCGATGTTT
66 GGTATACTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTT
** * * ** *
3766905 TTGAGATCGATACTTTTTAAAAATGTATCGACACTTTATGTGTGCACCCCGTTTGGCATTCATTA
131 TTTGGATCGATACTTTTTAAAAATGTATCGAAACTTTATGCGTGCACCCCGTTTTTCATTCATTC
*
3766970 TGGAC
196 TAGAC
* * * * *
3766975 AAAATATATCGACACAAATTTAAACAGTGTTGATACATTATGTAT-ACCTATTTTCTCATAAAAC
1 AAAATGTATCAACACAAATCTAAAAAGTGTCGATACATTATGT-TCACCTATTTTCTCATAAAAC
* * * * * *
3767039 CGATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCAATATT
65 CGGTATACTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTT
* * * * * * * * * *** *
3767104 TTTTAGATCGATACAATTTT--AAATGTATCGACACTTTTATACTTGAAGCTCATTGAGCA--AA
130 TTTTGGATCGATAC-TTTTTAAAAATGTATCGAAAC-TTTATGCGTGCACCCCGTTTTTCATTCA
** *
3767165 GGCTCAAAC
193 TTCT-AGAC
* * * * * * *
3767174 AAAAAGTATCGACACAAATTTAAAAGGTGTCGATACTTTATGCTT-ACCTATTTTCTCGTAAAAT
1 AAAATGTATCAACACAAATCTAAAAAGTGTCGATACATTATG-TTCACCTATTTTCTCATAAAAC
* * * * * * * *
3767238 TGATATATTTATACTGGTCACATTCTAAATTTACCTATTACATTATAAGTT-TCGGTTTTGATGT
65 CGGTATACTTATACCGGTTACATTGTAAATTTACCTATTACATTATAA-TTATAGGTTTCGATGT
* *
3767302 TTTTTGGATCGATGCTTTTTTAAAAATGTATCGACACTTTATG
129 TTTTTGGATCGATAC-TTTTTAAAAATGTATCGAAACTTTATG
3767345 GGAAACTTTA
Statistics
Matches: 638, Mismatches: 80, Indels: 63
0.82 0.10 0.08
Matches are distributed among these distances:
180 146 0.23
181 6 0.01
182 1 0.00
183 1 0.00
184 1 0.00
185 1 0.00
186 1 0.00
187 3 0.00
188 2 0.00
189 1 0.00
191 1 0.00
192 2 0.00
193 3 0.00
194 1 0.00
195 1 0.00
196 1 0.00
197 1 0.00
198 3 0.00
199 165 0.26
200 279 0.44
201 18 0.03
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (200 bp):
AAAATGTATCAACACAAATCTAAAAAGTGTCGATACATTATGTTCACCTATTTTCTCATAAAACC
GGTATACTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAGGTTTCGATGTTT
TTTGGATCGATACTTTTTAAAAATGTATCGAAACTTTATGCGTGCACCCCGTTTTTCATTCATTC
TAGAC
Found at i:3767012 original size:180 final size:180
Alignment explanation
Indices: 3766696--3767062 Score: 594
Period size: 180 Copynumber: 2.0 Consensus size: 180
3766686 AATTTACCTA
*
3766696 TTACATTATAATTATAGGTTTTGATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACACTT
1 TTACATTATAATTATAGGTTTCGATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACACTT
** * * *
3766761 TATGCGTGCACCCCGTTTTTCATTCATTCTGGACAAAATGTATCCACACTAATCTAAAAAGTGTC
66 TATGCGTGCACCCCGTTTGGCATTCATTATGGACAAAATATATCCACACAAATCTAAAAAGTGTC
3766826 GATACATTATGT-TCACCTATTTTCTCATAAAACCGATATAGTTATACCGG
131 GATACATTATGTAT-ACCTATTTTCTCATAAAACCGATATAGTTATACCGG
3766876 TTACATTATAATTATCA-GTTTCGATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACACT
1 TTACATTATAATTAT-AGGTTTCGATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACACT
* * * *
3766940 TTATGTGTGCACCCCGTTTGGCATTCATTATGGACAAAATATATCGACACAAATTTAAACAGTGT
65 TTATGCGTGCACCCCGTTTGGCATTCATTATGGACAAAATATATCCACACAAATCTAAAAAGTGT
* *
3767005 TGATACATTATGTATACCTATTTTCTCATAAAACCGATATATTTATACCGG
130 CGATACATTATGTATACCTATTTTCTCATAAAACCGATATAGTTATACCGG
3767056 TTACATT
1 TTACATT
3767063 GTAAATTTAC
Statistics
Matches: 173, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
180 171 0.99
181 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (180 bp):
TTACATTATAATTATAGGTTTCGATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACACTT
TATGCGTGCACCCCGTTTGGCATTCATTATGGACAAAATATATCCACACAAATCTAAAAAGTGTC
GATACATTATGTATACCTATTTTCTCATAAAACCGATATAGTTATACCGG
Found at i:3767224 original size:199 final size:200
Alignment explanation
Indices: 3766973--3767341 Score: 530
Period size: 199 Copynumber: 1.8 Consensus size: 200
3766963 TTCATTATGG
*
3766973 ACAAAATATATCGACACAAATTTAAACAGTGTTGATACATTATGTATACCTATTTTCTCATAAAA
1 ACAAAATATATCGACACAAATTTAAACAGTGTCGATACATTATGTATACCTATTTTCTCATAAAA
* * *
3767038 CCGATATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTTTCGGTTTCAATAT
66 CCGATATATTTATACCGGTCACATTCTAAATTTACCTATTACATTATAAGTTTCGGTTTCAATAT
3767103 TTTTTAGATCGATACAATTTT-AAATGTATCGACACTTTTATACTTGAAGCTCATTGAGCAAAGG
131 TTTTTAGATCGATACAATTTTAAAATGTATCGACACTTTTATACTTGAAGCTCATTGAGCAAAGG
3767167 CTCAA
196 CTCAA
* *
3767172 ACAAAA-AGTATCGACACAAATTTAAA-AGGTGTCGATACTTTATGCT-TACCTATTTTCTCGTA
1 ACAAAATA-TATCGACACAAATTTAAACA-GTGTCGATACATTATG-TATACCTATTTTCTCATA
** * **
3767234 AAATTGATATATTTATACTGGTCACATTCTAAATTTACCTATTACATTATAAGTTTCGGTTTTGA
63 AAACCGATATATTTATACCGGTCACATTCTAAATTTACCTATTACATTATAAGTTTCGGTTTCAA
* * * **
3767299 TGTTTTTTGGATCGATGCTTTTTTAAAAATGTATCGACACTTT
128 TATTTTTTAGATCGATACAATTTT-AAAATGTATCGACACTTT
3767342 ATGGGAAACT
Statistics
Matches: 149, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
198 2 0.01
199 129 0.87
200 1 0.01
201 17 0.11
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (200 bp):
ACAAAATATATCGACACAAATTTAAACAGTGTCGATACATTATGTATACCTATTTTCTCATAAAA
CCGATATATTTATACCGGTCACATTCTAAATTTACCTATTACATTATAAGTTTCGGTTTCAATAT
TTTTTAGATCGATACAATTTTAAAATGTATCGACACTTTTATACTTGAAGCTCATTGAGCAAAGG
CTCAA
Found at i:3767602 original size:18 final size:18
Alignment explanation
Indices: 3767579--3767615 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3767569 CGAAATTTAT
3767579 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
3767597 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
3767615 A
1 A
3767616 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:3768939 original size:6 final size:6
Alignment explanation
Indices: 3768932--3768965 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3768922 GTTTGGATCA
* *
3768932 TCATCA TCATCT TCATCG TCATCT TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
3768966 TGACCTCTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.21, C:0.32, G:0.03, T:0.44
Consensus pattern (6 bp):
TCATCT
Found at i:3771132 original size:200 final size:200
Alignment explanation
Indices: 3770440--3771990 Score: 1898
Period size: 200 Copynumber: 7.8 Consensus size: 200
3770430 TTTTAAAATG
* * * * * * * *
3770440 GTATCAACACAAATTT-AACAATTGTCGATACTTTATGCT-GACTTATTTTCTCCTAAAACCGGT
1 GTATCGACACAAATTTCAA-AAGTGTCGATACATTATG-TAGACCTATTCTCACATAAAACCGAT
* ** * * * *
3770503 ATATTTATATCGGTTACATTGGAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTG
64 ATATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTG
* * * * *
3770568 GGATCGACAC-TTTTAAAAATGTATTGACACTTAATGGGTGCACCCTTTT-GGCATTTC-TTCTG
129 GGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCA-TTCATTCTG
3770630 GACAAAAA
193 GACAAAAA
* * * * ** * * *
3770638 CTATCTACATAAATTCCTGAAGTGTCGATACATTTTCTAGACCTATTCTCACATAAAACCGGTAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGATAT
* *
3770703 ATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATGATGGGTTTCGTTGTTTCTGG
66 ATTTATACCGGTTACATT-ATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* *
3770767 GATCGATACTTTTTATAAATATATCGACACTTTATGCGTGCACCATTTTTTTGGGCATTCATTCT
130 GATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCA---TTTTGGGCATTCATTCT
3770832 GGACAAAATA
192 GGACAAAA-A
* * * * *
3770842 -TATTGACACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCAAATAAAACCGGTAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGATAT
* * * * * *
3770906 ATTTATACCAGTTACATTAAAAAATTACCTATTACATTATAATTATCGGTTTCAATATCTCTGGG
66 ATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * * *
3770971 ATCGACACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCATTTTAGGCATTCATTCTGAAC
131 ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC
3771036 AAAAA
196 AAAAA
* * *
3771041 GTATCGACACCAATTTCAAATGTGTCGATACATTATGTAGACCTATTATCACATAAAACCGATAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGATAT
* * *
3771106 ATTTATACTGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGGG
66 ATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * * *
3771171 ATCGATA-ATTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGCATTCCTTCTGGAC
131 ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC
*
3771235 AAACA
196 AAAAA
* * * *
3771240 GTATCGACACAAATTCCAAAAGTGTCGATACATTATGTACACTTATTCTCTCATAAAACC-AGTA
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGA-TA
* * * * *
3771304 TAGTTATACCGGTTACATTTTAAATTTACCTATTACATTATAATTATGGGTTTCAATGTTTCTGA
65 TATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
** * * * *
3771369 GATAAATACCTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTATGGA
130 GATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGA
3771434 CAAAAA
195 CAAAAA
* * * *
3771440 GTATCGACGCCAATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAA-CTAGTA
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGA-TA
*** * *
3771504 TATTTATGTTGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCTGG
65 TATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGG
* * * *
3771569 GATCGACACTTTTAAAAAATGTATCGACACTTTATGGGTGCA-CA-------CATTCCTTCTGGA
130 GATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGA
3771626 CAAACAA
195 CAAA-AA
* * * *
3771633 -TATCGACACAAATTCCAGAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGATAT
* * * * * *
3771697 ATTTATACTGGTTACATTGTAAATTTACCTATTATATTATAATTATAGGCTTCGATGTTTCTGGG
66 ATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
* * *
3771762 ATCGATACTTTTTATAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGAC
131 ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC
3771827 AAAAA
196 AAAAA
* * * * *
3771832 GTATCGACACCAATTTCAAAAGTGTCGATGCATTATGTAGACCTATTCTAACATAAATCTGATAT
1 GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGATAT
* *
3771897 ATTTATACCGGTTATATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
66 ATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
*
3771962 ATCGATACTTTTTATAAATGTATCGACAC
131 ATCGATACTTTTTAAAAATGTATCGACAC
3771991 ATCTGCTTAC
Statistics
Matches: 1157, Mismatches: 170, Indels: 50
0.84 0.12 0.04
Matches are distributed among these distances:
192 160 0.14
193 5 0.00
197 1 0.00
198 112 0.10
199 207 0.18
200 498 0.43
202 8 0.01
203 165 0.14
204 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (200 bp):
GTATCGACACAAATTTCAAAAGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGATAT
ATTTATACCGGTTACATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTCTGGG
ATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATTTTGGGCATTCATTCTGGAC
AAAAA
Found at i:3771358 original size:399 final size:399
Alignment explanation
Indices: 3770441--3771990 Score: 2045
Period size: 392 Copynumber: 3.9 Consensus size: 399
3770431 TTTAAAATGG
* * * * * * *
3770441 TATCAACACAAATTTAACAATTGTCGATACTTTATGCT-GACTTATTTTCTCCTAAAACCGGTAT
1 TATCGACACAAATTCAA-AAGTGTCGATACATTATG-TAGACCTATTCTCTCATAAAACCGGTAT
* * * *
3770505 ATTTATATCGGTTACATTGGAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGG
64 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAATATTTCTGGG
* * * * *
3770570 ATCGACAC-TTTTAAAAATGTATTGACACTTAATGGGTGCACCCTTTT-GGCATTTC-TTCTGGA
129 ATCGACACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCA-TTCATTCTGGA
* * ** * * * *
3770632 CAAAAACTATCTACATAAATTCCTGAA-GTGTCGATACATTTTCTAGACCTATTCTCACATAAAA
193 CAAAAAGTATCGACACCAATTTC-AAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAA
* * *
3770696 CCGGTATATTTATACCGGTTACATTGA-AAAATTACCTATTACATTATAATGATGGGTTTCGTTG
257 CCGATATATTTATACCGGTTACATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGATG
* * * * *
3770760 TTTCTGGGATCGATACTTTTTATAAATATATCGACACTTTATGCGTGCACCATTTTTTTGGGCAT
321 TCTCTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACC---CTTTTGGGCAT
*
3770825 TCATTCTGGACAAA-ATA
383 TCCTTCTGGACAAACA-A
* * **
3770842 TATTGACACAAAATTAAAAAGTGTCGATACATTATGTAGACCTATTCTCAAATAAAACCGGTATA
1 TATCGACAC-AAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
* ** * *
3770907 TTTATACCAGTTACATTAAAAAATTACCTATTACATTATAATTATCGGTTTCAATATCTCTGGGA
65 TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAATATTTCTGGGA
* *
3770972 TCGACACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCATTTTAGGCATTCATTCTGAACA
130 TCGACACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACA
*
3771037 AAAAGTATCGACACCAATTTCAAATGTGTCGATACATTATGTAGACCTATTATCACATAAAACCG
195 AAAAGTATCGACACCAATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCG
*
3771102 ATATATTTATACTGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTC
260 ATATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTC
*
3771167 TGGGATCGATA-ATTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGCATTCCTTCT
325 TGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGCATTCCTTCT
*
3771231 GGACAAACAG
390 GGACAAACAA
* * *
3771241 TATCGACACAAATTCCAAAAGTGTCGATACATTATGTACACTTATTCTCTCATAAAACCAGTATA
1 TATCGACACAAATT-CAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
* * * * *
3771306 GTTATACCGGTTACATTTTAAATTTACCTATTACATTATAATTATGGGTTTCAATGTTTCTGAGA
65 TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAATATTTCTGGGA
** * * * *
3771371 TAAATACCTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTATGGACA
130 TCGACACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACA
* *
3771436 AAAAGTATCGACGCCAATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAA-CT
195 AAAAGTATCGACACCAATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCG
***
3771500 AGTATATTTATGTTGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCT
260 A-TATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCT
* * * *
3771565 CTGGGATCGACACTTTTAAAAAATGTATCGACACTTTATGGGTGCA--C------ACATTCCTTC
324 CTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGCATTCCTTC
3771622 TGGACAAACAA
389 TGGACAAACAA
*
3771633 TATCGACACAAATTCCAGAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAATT-CAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
* * * * * *
3771698 TTTATACTGGTTACATTGTAAATTTACCTATTATATTATAATTATAGGCTTCGATGTTTCTGGGA
65 TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAATATTTCTGGGA
* * *
3771763 TCGATACTTTTTATAAATGTATCAACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACA
130 TCGACACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACA
* * * * *
3771828 AAAAGTATCGACACCAATTTCAAAAGTGTCGATGCATTATGTAGACCTATTCTAACATAAATCTG
195 AAAAGTATCGACACCAATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCG
* * * *
3771893 ATATATTTATACCGGTTATATTATAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
260 ATATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTC
*
3771958 TGGGATCGATACTTTTTATAAATGTATCGACAC
325 TGGGATCGATACTTTTTAAAAATGTATCGACAC
3771991 ATCTGCTTAC
Statistics
Matches: 1023, Mismatches: 114, Indels: 33
0.87 0.10 0.03
Matches are distributed among these distances:
392 341 0.33
393 1 0.00
398 8 0.01
399 320 0.31
400 32 0.03
401 109 0.11
402 78 0.08
403 134 0.13
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (399 bp):
TATCGACACAAATTCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATAT
TTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAATATTTCTGGGAT
CGACACTTTTTAAAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATTCTGGACAA
AAAGTATCGACACCAATTTCAAATGTGTCGATACATTATGTAGACCTATTCTCACATAAAACCGA
TATATTTATACCGGTTACATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTCTCT
GGGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGCATTCCTTCTG
GACAAACAA
Found at i:3772031 original size:15 final size:15
Alignment explanation
Indices: 3772007--3772045 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
3771997 TTACCTATTT
* *
3772007 TTTGGAAACTTTATG
1 TTTGGGAACTTTACG
3772022 TTTGGGAACTTTACG
1 TTTGGGAACTTTACG
3772037 TTTGGGAAC
1 TTTGGGAAC
3772046 CATACTGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (15 bp):
TTTGGGAACTTTACG
Found at i:3773966 original size:18 final size:18
Alignment explanation
Indices: 3773943--3773999 Score: 105
Period size: 18 Copynumber: 3.2 Consensus size: 18
3773933 TCCTCCTCAT
3773943 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
3773961 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
3773979 TTCCTCCATCTTTTTTTC
1 TTCCTCCATCTTTTCTTC
3773997 TTC
1 TTC
3774000 ATATTTTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.05, C:0.37, G:0.00, T:0.58
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:3774216 original size:33 final size:33
Alignment explanation
Indices: 3774179--3774245 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
3774169 CCATCTTAAG
* * *
3774179 TTCACCCCTCAACACCTTAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAAATTCATTCACCAC
3774212 TTCACCCCTCAACACCTCAAATTCATTCACCAC
1 TTCACCCCTCAACACCTCAAATTCATTCACCAC
3774245 T
1 T
3774246 CCATCTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.45, G:0.00, T:0.28
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAAATTCATTCACCAC
Found at i:3774304 original size:21 final size:21
Alignment explanation
Indices: 3774279--3774322 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3774269 CCCCTTATGC
3774279 CTCTCAAGTGTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
*
3774300 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTCTCTTCGACT
3774321 CT
1 CT
3774323 TGATTATCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.34, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTCTCTTCGACT
Found at i:3777035 original size:112 final size:112
Alignment explanation
Indices: 3776838--3777074 Score: 314
Period size: 112 Copynumber: 2.1 Consensus size: 112
3776828 ATACTTATAT
** *
3776838 TAAAGTATCGACACTTTCAATATATCCGGTCGCTCTATATCGGTTTTGTCCTTTAGAGACCGTTT
1 TAAAGTATCGACACTTTCAATATATCCGGTCAATCTATATCGGTTTTGTCCTTTAGAGACCGGTT
* * * *
3776903 TTGTCATATTTTTACTTGTTATATCGTTGTAGATCAATACATTGTTA
66 TTATCATATTTTTACATGTTATATCGATATAGATCAATACATTGTTA
* * * *
3776950 TAAAGTATCGACACTTTCAATATATCCGG-CAATGCTTTATCGGTTTTGTCTTTTCGAGATCGGT
1 TAAAGTATCGACACTTTCAATATATCCGGTCAAT-CTATATCGGTTTTGTCCTTTAGAGACCGGT
* * * *
3777014 TTTATCATATTTTTACATGTTATATTGATATGGATCGATACATTTTTA
65 TTTATCATATTTTTACATGTTATATCGATATAGATCAATACATTGTTA
*
3777062 TAAAGTAACGACA
1 TAAAGTATCGACA
3777075 TAAACCGACA
Statistics
Matches: 108, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
111 2 0.02
112 106 0.98
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.43
Consensus pattern (112 bp):
TAAAGTATCGACACTTTCAATATATCCGGTCAATCTATATCGGTTTTGTCCTTTAGAGACCGGTT
TTATCATATTTTTACATGTTATATCGATATAGATCAATACATTGTTA
Found at i:3778426 original size:44 final size:44
Alignment explanation
Indices: 3778372--3778459 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
3778362 ATTTTATTTG
*
3778372 AGATTGAAATGGAGGTGATTTGGGGTTTGAATTTGCCATATATC
1 AGATTGAAATGGAGGTGATTTGGGCTTTGAATTTGCCATATATC
* *
3778416 AGATTTAAATGGAGGTTATTTGGGCTTTGAATTTGCCATATATC
1 AGATTGAAATGGAGGTGATTTGGGCTTTGAATTTGCCATATATC
3778460 GAGAGACGTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.39
Consensus pattern (44 bp):
AGATTGAAATGGAGGTGATTTGGGCTTTGAATTTGCCATATATC
Found at i:3784000 original size:41 final size:41
Alignment explanation
Indices: 3783955--3784047 Score: 132
Period size: 41 Copynumber: 2.3 Consensus size: 41
3783945 TCAGCAGGGA
* * * *
3783955 GTATCGATACTGTTTATATGGTATCGATACCATAGGGATTG
1 GTATCGATACTGTTTATACGATATCAATACCACAGGGATTG
* *
3783996 GTATCGATATTGTTTATACGATATCAATACCACATGGATTG
1 GTATCGATACTGTTTATACGATATCAATACCACAGGGATTG
3784037 GTATCGATACT
1 GTATCGATACT
3784048 AAGGGTTCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (41 bp):
GTATCGATACTGTTTATACGATATCAATACCACAGGGATTG
Found at i:3792464 original size:23 final size:23
Alignment explanation
Indices: 3792437--3792482 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3792427 TGCTAGGTTG
3792437 ATAAAGAGGAATCATTGGTTTCT
1 ATAAAGAGGAATCATTGGTTTCT
3792460 ATAAAGAGGAATCATTGGTTTCT
1 ATAAAGAGGAATCATTGGTTTCT
3792483 TTGGAGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (23 bp):
ATAAAGAGGAATCATTGGTTTCT
Done.