Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 90 of 222
Found at i:28111521 original size:35 final size:35
Alignment explanation
Indices: 28111478--28111550 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
28111468 CATAACATCC
28111478 TCAGTTTA-TCTGACCAGTGTAGGGCACAACTATTG
1 TCAGTTTATTC-GACCAGTGTAGGGCACAACTATTG
*
28111513 TCAGTTTATTCGACCAGTGTAGGGCACAATTATTG
1 TCAGTTTATTCGACCAGTGTAGGGCACAACTATTG
28111548 TCA
1 TCA
28111551 ATATATTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 34 0.94
36 2 0.06
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (35 bp):
TCAGTTTATTCGACCAGTGTAGGGCACAACTATTG
Found at i:28122828 original size:37 final size:36
Alignment explanation
Indices: 28122770--28122884 Score: 167
Period size: 37 Copynumber: 3.1 Consensus size: 36
28122760 TTCCAACTAA
*
28122770 AACATGTCAATCGCTCGTAAGAGCTAATCCACCCGAT
1 AACATGTCAAT-GCTCATAAGAGCTAATCCACCCGAT
*
28122807 AACATGTCATATGCTCATAAGAGCTAATCCACCTGAT
1 AACATGTCA-ATGCTCATAAGAGCTAATCCACCCGAT
* *
28122844 AATATGCCAGATGCTCATAAGAGCTAATCCACCCGAT
1 AACATGTCA-ATGCTCATAAGAGCTAATCCACCCGAT
28122881 AACA
1 AACA
28122885 CGCCAGAACA
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
37 68 0.97
38 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.23
Consensus pattern (36 bp):
AACATGTCAATGCTCATAAGAGCTAATCCACCCGAT
Found at i:28124167 original size:25 final size:26
Alignment explanation
Indices: 28124139--28124198 Score: 95
Period size: 25 Copynumber: 2.3 Consensus size: 26
28124129 TTTTACTCCA
* *
28124139 GTAAATTTTTTATGATTTTA-CCTTG
1 GTAAAATTTTGATGATTTTACCCTTG
28124164 GTAAAATTTTGATGATTTTACCCTTG
1 GTAAAATTTTGATGATTTTACCCTTG
28124190 GTAAAATTT
1 GTAAAATTT
28124199 CGAAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 18 0.56
26 14 0.44
ACGTcount: A:0.28, C:0.08, G:0.13, T:0.50
Consensus pattern (26 bp):
GTAAAATTTTGATGATTTTACCCTTG
Found at i:28125788 original size:8 final size:8
Alignment explanation
Indices: 28125775--28125803 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
28125765 TGATTATGTT
28125775 ATTTTGTA
1 ATTTTGTA
28125783 ATTTTGTA
1 ATTTTGTA
28125791 ATTTTGTA
1 ATTTTGTA
28125799 ATTTT
1 ATTTT
28125804 TTGTATACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (8 bp):
ATTTTGTA
Found at i:28132801 original size:45 final size:44
Alignment explanation
Indices: 28132732--28132816 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
28132722 AAACCTTATT
* * *
28132732 CTATTAACCTCTAGTAGGGTATTTATCCTAAAAGTCTTACAGTC
1 CTATTAACCTCTAGTAGGGCATTTATACTAAAACTCTTACAGTC
*
28132776 CTATTAACCTTCTAGT-GGAGCATTTATACTAGAACTCTTAC
1 CTATTAACC-TCTAGTAGG-GCATTTATACTAAAACTCTTAC
28132817 TATTAACAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
44 11 0.31
45 24 0.69
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.36
Consensus pattern (44 bp):
CTATTAACCTCTAGTAGGGCATTTATACTAAAACTCTTACAGTC
Found at i:28133686 original size:15 final size:15
Alignment explanation
Indices: 28133668--28133698 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28133658 AAAATATTAA
28133668 ATTATAAAAATTTTC
1 ATTATAAAAATTTTC
*
28133683 ATTATGAAAATTTTC
1 ATTATAAAAATTTTC
28133698 A
1 A
28133699 ATGGGTTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (15 bp):
ATTATAAAAATTTTC
Found at i:28139082 original size:34 final size:35
Alignment explanation
Indices: 28139044--28139110 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28139034 CAGTAAAATG
*
28139044 TTTTCCGTAAAATGATTT-TTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTATTGAAAAATATTTTAC
* *
28139078 TTTTCTGTAAAATGATTTATTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTATTGAAAAATATTTT
28139111 CTGGCGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTATTGAAAAATATTTTAC
Found at i:28140474 original size:35 final size:36
Alignment explanation
Indices: 28140428--28140496 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
28140418 TGTCAATCAT
28140428 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
*
28140463 TTCAATATCCAACAAGGTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
28140497 TCTAACAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 28 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:28140494 original size:27 final size:28
Alignment explanation
Indices: 28140464--28140533 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
28140454 AATAATAAAT
*
28140464 TCAATATCCAACAAGGTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
28140491 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
28140519 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
28140534 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.20, G:0.04, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:28143644 original size:33 final size:33
Alignment explanation
Indices: 28143607--28143672 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
28143597 CAATCGTTAG
*
28143607 GGTGAGGAGAGTGAAAAGAGGAGCAGTGGAAAA
1 GGTGAAGAGAGTGAAAAGAGGAGCAGTGGAAAA
* * *
28143640 GGTGAAGAGAGTGAAGAGATGAGCTGTGGAAAA
1 GGTGAAGAGAGTGAAAAGAGGAGCAGTGGAAAA
28143673 TGTCTTACCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.03, G:0.44, T:0.12
Consensus pattern (33 bp):
GGTGAAGAGAGTGAAAAGAGGAGCAGTGGAAAA
Found at i:28144818 original size:13 final size:13
Alignment explanation
Indices: 28144802--28144854 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
28144792 TTTAAACCAA
28144802 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
28144815 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* * *
28144828 ACTTTTCCATAGT
1 ACTTTTCAAAAGC
28144841 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28144854 A
1 A
28144855 ATGAAGAACT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:28145022 original size:18 final size:18
Alignment explanation
Indices: 28144999--28145036 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28144989 ACCCTTGGAG
28144999 TAAAAAATTTATTTCAAA
1 TAAAAAATTTATTTCAAA
28145017 TAAAAAATTTATTTCAAA
1 TAAAAAATTTATTTCAAA
28145035 TA
1 TA
28145037 CATTCTACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAAATTTATTTCAAA
Found at i:28146142 original size:36 final size:36
Alignment explanation
Indices: 28146091--28146163 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
28146081 ACATCTCTCT
* *
28146091 AAAACACACAAGAAAGCACATAAGTGCTAACCCTAA
1 AAAACACACAAGAAAGAACAGAAGTGCTAACCCTAA
* * * *
28146127 AAAATACACCAGAAAGAACCGAAGTGCTAAGCCTAA
1 AAAACACACAAGAAAGAACAGAAGTGCTAACCCTAA
28146163 A
1 A
28146164 GGCATCAGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (36 bp):
AAAACACACAAGAAAGAACAGAAGTGCTAACCCTAA
Found at i:28148935 original size:46 final size:46
Alignment explanation
Indices: 28148870--28149085 Score: 265
Period size: 46 Copynumber: 4.7 Consensus size: 46
28148860 TGAATCATAG
* * * * *
28148870 TGCCTGGTTACCCGTTAGGGTTAAACCTACATGAATC-GAATGACAA
1 TGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCAG-ATAATAA
** * * *
28148916 TGCCTGGTCACCTATTAGGGTTGAACTTATACGAATCAGATAATAC
1 TGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCAGATAATAA
**
28148962 TGAATGGTCACCCGTTAGGGTTGAACCTACACGAATCAGATAATAA
1 TGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCAGATAATAA
* * *
28149008 TGCCTAGTCACTCGTTAGGGTTGAACCTACACGAAT-ACGATAATAG
1 TGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCA-GATAATAA
28149054 TGCCTGGTCACCCGTTAGGGTTGAACCTACAC
1 TGCCTGGTCACCCGTTAGGGTTGAACCTACAC
28149086 AACAATAGCC
Statistics
Matches: 144, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
45 1 0.01
46 142 0.99
47 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (46 bp):
TGCCTGGTCACCCGTTAGGGTTGAACCTACACGAATCAGATAATAA
Found at i:28157785 original size:16 final size:15
Alignment explanation
Indices: 28157744--28157790 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
28157734 TAATAAAATG
28157744 GATGAAAAGGTTATC
1 GATGAAAAGGTTATC
28157759 GATGAAAAGGTTATC
1 GATGAAAAGGTTATC
*
28157774 GATTAGAAAGGTTATC
1 GATGA-AAAGGTTATC
28157790 G
1 G
28157791 GTTGAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (15 bp):
GATGAAAAGGTTATC
Found at i:28159230 original size:20 final size:20
Alignment explanation
Indices: 28159205--28159242 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28159195 CCAAATCTTC
28159205 TTACTTT-CATTTGCATTTCA
1 TTACTTTCCA-TTGCATTTCA
28159225 TTACTTTCCATTGCATTT
1 TTACTTTCCATTGCATTT
28159243 ACTTTCTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.18, C:0.21, G:0.05, T:0.55
Consensus pattern (20 bp):
TTACTTTCCATTGCATTTCA
Found at i:28163474 original size:21 final size:21
Alignment explanation
Indices: 28163448--28163491 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
28163438 CCAATGTATC
28163448 ATTCTACCAATGAATACATCT
1 ATTCTACCAATGAATACATCT
*
28163469 ATTCTATCAATGAATACATCT
1 ATTCTACCAATGAATACATCT
28163490 AT
1 AT
28163492 GTCTCTTCTC
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:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (21 bp):
ATTCTACCAATGAATACATCT
Found at i:28164982 original size:21 final size:21
Alignment explanation
Indices: 28164956--28164996 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28164946 CAAACCCGAC
28164956 GAGTATCGATACTTTGTAAAT
1 GAGTATCGATACTTTGTAAAT
* *
28164977 GAGTATCGATATTTTTTAAA
1 GAGTATCGATACTTTGTAAA
28164997 AAGTATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (21 bp):
GAGTATCGATACTTTGTAAAT
Found at i:28165003 original size:20 final size:21
Alignment explanation
Indices: 28164957--28165008 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28164947 AAACCCGACG
* *
28164957 AGTATCGATACTTTGTAAATG
1 AGTATCGATATTTTGTAAATA
*
28164978 AGTATCGATATTTTTTAAA-A
1 AGTATCGATATTTTGTAAATA
*
28164998 AGTATCAATAT
1 AGTATCGATAT
28165009 AATATTATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (21 bp):
AGTATCGATATTTTGTAAATA
Found at i:28166717 original size:38 final size:37
Alignment explanation
Indices: 28166666--28166739 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 37
28166656 CAATACACCT
* *
28166666 GCACAAGCTTGCTAGGCACAAAGCCTGAATAACATCG
1 GCACAAGCCTGCTAGGCACAAAGCCCGAATAACATCG
* *
28166703 GCACAGAGCCTGCTAGGCACATAGCCCGAATAGCATC
1 GCACA-AGCCTGCTAGGCACAAAGCCCGAATAACATC
28166740 ATGTTTCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 5 0.16
38 27 0.84
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (37 bp):
GCACAAGCCTGCTAGGCACAAAGCCCGAATAACATCG
Found at i:28176515 original size:27 final size:28
Alignment explanation
Indices: 28176454--28176523 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 28
28176444 CTGTCCATAT
* *
28176454 AGACTATTCAATGTTTAATGTCCCGTCG
1 AGACTATCCCATGTTTAATGTCCCGTCG
* *
28176482 GGA-TATCCCATGTTTAATGTCCTGTC-
1 AGACTATCCCATGTTTAATGTCCCGTCG
*
28176508 AGACTATCTCATGTTT
1 AGACTATCCCATGTTT
28176524 TGTATCCGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
26 2 0.06
27 31 0.89
28 2 0.06
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (28 bp):
AGACTATCCCATGTTTAATGTCCCGTCG
Found at i:28179788 original size:38 final size:38
Alignment explanation
Indices: 28179746--28179959 Score: 225
Period size: 38 Copynumber: 5.6 Consensus size: 38
28179736 TCGGGCTCTA
* *
28179746 TGCCTAGCAGGCTTTGTGCTGGTGATATTCAGGCTATG
1 TGCCTAGCAGGCTTTGTGCCGGTGATATTCAGGCTTTG
* ** *
28179784 TGCCTAGTAGGCTTTGTGCCAATGATATTCGGGCTTTG
1 TGCCTAGCAGGCTTTGTGCCGGTGATATTCAGGCTTTG
* * *
28179822 TTCCTAGCAGACTTTGTGCCGGTGATATTCAGGTTTTG
1 TGCCTAGCAGGCTTTGTGCCGGTGATATTCAGGCTTTG
* * *
28179860 TACCTAGCAGGCTTTGTACCGGTGATATTCGGGCTCTT-
1 TGCCTAGCAGGCTTTGTGCCGGTGATATTCAGGCT-TTG
* * * *
28179898 TGCCTAGTAGGCTTTATGCTGGTGATATTC-GAGTTTTG
1 TGCCTAGCAGGCTTTGTGCCGGTGATATTCAG-GCTTTG
* * *
28179936 TGCCTAGTAGGCTTTATGCTGGTG
1 TGCCTAGCAGGCTTTGTGCCGGTG
28179960 TGTTATATCA
Statistics
Matches: 149, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
37 3 0.02
38 144 0.97
39 2 0.01
ACGTcount: A:0.15, C:0.18, G:0.29, T:0.37
Consensus pattern (38 bp):
TGCCTAGCAGGCTTTGTGCCGGTGATATTCAGGCTTTG
Found at i:28179866 original size:76 final size:75
Alignment explanation
Indices: 28179728--28179950 Score: 277
Period size: 76 Copynumber: 2.9 Consensus size: 75
28179718 ATAGAAACGT
* * * *
28179728 AATGTTATTCGGGCTCTATGCCTAGCAGGCTTTGTGCTGGTGATATTCAGGCTATGTGCCTAGTA
1 AATGATATTCGGGCT-TTTGCCTAGCAGGCTTTGTGCTGGTGATATTCAGGTTTTGTGCCTAGTA
*
28179793 GGCTTTGTGCC
65 GGCTTTGTACC
* * * * *
28179804 AATGATATTCGGGCTTTGTTCCTAGCAGACTTTGTGCCGGTGATATTCAGGTTTTGTACCTAGCA
1 AATGATATTCGGGCTTT-TGCCTAGCAGGCTTTGTGCTGGTGATATTCAGGTTTTGTGCCTAGTA
28179869 GGCTTTGTACC
65 GGCTTTGTACC
** * *
28179880 GGTGATATTCGGGCTCTTTGCCTAGTAGGCTTTATGCTGGTGATATTC-GAGTTTTGTGCCTAGT
1 AATGATATTCGGGCT-TTTGCCTAGCAGGCTTTGTGCTGGTGATATTCAG-GTTTTGTGCCTAGT
28179944 AGGCTTT
64 AGGCTTT
28179951 ATGCTGGTGT
Statistics
Matches: 125, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
75 2 0.02
76 121 0.97
77 2 0.02
ACGTcount: A:0.16, C:0.18, G:0.28, T:0.38
Consensus pattern (75 bp):
AATGATATTCGGGCTTTTGCCTAGCAGGCTTTGTGCTGGTGATATTCAGGTTTTGTGCCTAGTAG
GCTTTGTACC
Found at i:28183319 original size:8 final size:9
Alignment explanation
Indices: 28183297--28183333 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
28183287 AGACATTGAC
28183297 ATTTTTAAA
1 ATTTTTAAA
28183306 ATTTTTAAA
1 ATTTTTAAA
28183315 A-TTTTAAA
1 ATTTTTAAA
28183323 ATTTTTAAA
1 ATTTTTAAA
28183332 AT
1 AT
28183334 CATGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:28183321 original size:17 final size:17
Alignment explanation
Indices: 28183299--28183333 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
28183289 ACATTGACAT
28183299 TTTTAAAATTTTTAAAA
1 TTTTAAAATTTTTAAAA
28183316 TTTTAAAATTTTTAAAA
1 TTTTAAAATTTTTAAAA
28183333 T
1 T
28183334 CATGAAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTAAAATTTTTAAAA
Found at i:28192704 original size:24 final size:24
Alignment explanation
Indices: 28192649--28192764 Score: 119
Period size: 24 Copynumber: 4.8 Consensus size: 24
28192639 ATCTTCTTCT
*
28192649 TCTTCATCTTCACCTCCATCCAT-G
1 TCTTCATCTTCATCTCCA-CCATCG
* * *
28192673 TAC-CCATCTTCATCCCCACCATCA
1 T-CTTCATCTTCATCTCCACCATCG
* *
28192697 TCTTCATCTTGATCTCCACCGTCG
1 TCTTCATCTTCATCTCCACCATCG
* *
28192721 TCTTCATCTTGATCTCCACTATCG
1 TCTTCATCTTCATCTCCACCATCG
*
28192745 TCTCCATCTTCATCTCCACC
1 TCTTCATCTTCATCTCCACC
28192765 TTCAATTTTG
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
23 5 0.07
24 69 0.92
25 1 0.01
ACGTcount: A:0.17, C:0.42, G:0.05, T:0.35
Consensus pattern (24 bp):
TCTTCATCTTCATCTCCACCATCG
Found at i:28196330 original size:15 final size:15
Alignment explanation
Indices: 28196310--28196339 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28196300 CTTTTTCGGC
28196310 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
28196325 CGATTTGCTCTCTGT
1 CGATTTGCTCTCTGT
28196340 TTTACCCTCC
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:0.07, C:0.27, G:0.20, T:0.47
Consensus pattern (15 bp):
CGATTTGCTCTCTGT
Found at i:28199224 original size:59 final size:57
Alignment explanation
Indices: 28199158--28199346 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
28199148 ATTTTATTAA
28199158 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
28199217 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
28199278 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
28199337 ATCATATATT
1 ATCATATATT
28199347 ATTATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:28199255 original size:66 final size:64
Alignment explanation
Indices: 28199185--28199383 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
28199175 AAATATATTT
*
28199185 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
28199250 G
64 G
* * * * **
28199251 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAAG
* *
28199305 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAA
28199370 G
64 G
*
28199371 AATATTGATTATT
1 AATATTAATTATT
28199384 AAGAATTTTA
Statistics
Matches: 102, Mismatches: 17, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 9 0.09
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.26
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATTATTTGAGTAAATTCATATAAG
Found at i:28199277 original size:120 final size:120
Alignment explanation
Indices: 28199147--28199444 Score: 508
Period size: 120 Copynumber: 2.5 Consensus size: 120
28199137 AATTATTTTA
* * * *
28199147 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATATTT
28199211 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
28199267 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
* *
28199332 ATAGTATCATATATTATTATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
28199387 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
28199445 ATGATTAAAT
Statistics
Matches: 168, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
120 161 0.96
121 7 0.04
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:28199287 original size:61 final size:61
Alignment explanation
Indices: 28199220--28199407 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
28199210 TTATAGTATC
*
28199220 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * *
28199281 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATTATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
28199339 C
61 T
*
28199340 ATATATTATTATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
28199401 ATATATT
1 ATATATT
28199408 TTAATTATAA
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 17 0.18
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATTATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:28199307 original size:15 final size:15
Alignment explanation
Indices: 28199272--28199323 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28199262 TTAAGAATTT
*
28199272 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28199286 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28199300 TATTTAATAATAAT-
1 TATTTAATTATAATA
28199314 TATGTTAATT
1 TAT-TTAATT
28199324 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28199422 original size:16 final size:16
Alignment explanation
Indices: 28199401--28199442 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28199391 TTATTAAATT
*
28199401 ATATATTTTAATTATA
1 ATATATTTTAATAATA
28199417 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
28199432 AT-TATGTTTAA
1 ATATAT-TTTAA
28199443 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:28199427 original size:15 final size:15
Alignment explanation
Indices: 28199392--28199433 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28199382 TTAAGAATTT
*
28199392 TATTAAATTAT-ATA
1 TATTTAATTATAATA
28199406 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
28199420 TATTTAATAATAAT
1 TATTTAATTATAAT
28199434 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:28199643 original size:16 final size:16
Alignment explanation
Indices: 28199619--28199686 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
28199609 GATTTGCTAT
*
28199619 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
28199635 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
28199651 TACAACTCTAATCCAA
1 TACACCTCTAATCCAA
28199667 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28199683 TACA
1 TACA
28199687 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28200107 original size:16 final size:15
Alignment explanation
Indices: 28200075--28200109 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28200065 TAATATTTAC
*
28200075 TTTTTTCAATTATAA
1 TTTTTTCAATTAAAA
28200090 TTTTTTCAATTACAAA
1 TTTTTTCAATTA-AAA
28200106 TTTT
1 TTTT
28200110 ACAACTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTTTCAATTAAAA
Found at i:28204507 original size:16 final size:16
Alignment explanation
Indices: 28204486--28204519 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28204476 CCAATATCTA
* *
28204486 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
28204502 ATTATCACATTTACAC
1 ATTATCACATTTACAC
28204518 AT
1 AT
28204520 ATATATTCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:28210353 original size:37 final size:38
Alignment explanation
Indices: 28210312--28210387 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
28210302 TTGGAGGCAT
* **
28210312 CATGAC-ACAA-ATATCTATTGGTCCTTTGGGGTGACAC
1 CATGACGACAATAT-TCGATTGGTCCTTCAGGGTGACAC
*
28210349 CATGACGACACTATTCGATTGGTCCTTCAGGGTGACAC
1 CATGACGACAATATTCGATTGGTCCTTCAGGGTGACAC
28210387 C
1 C
28210388 TTGAAAGGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 6 0.18
38 25 0.76
39 2 0.06
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (38 bp):
CATGACGACAATATTCGATTGGTCCTTCAGGGTGACAC
Found at i:28212222 original size:15 final size:15
Alignment explanation
Indices: 28212202--28212230 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28212192 ATCCTTCACA
28212202 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
28212217 CACCGTGTTATCAA
1 CACCGTGTTATCAA
28212231 GCAATAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:28214911 original size:17 final size:17
Alignment explanation
Indices: 28214886--28214924 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
28214876 ATTAATCAAA
28214886 TTAACTAAATTAA-TTTC
1 TTAACTAAA-TAATTTTC
*
28214903 TTAATTAAATAATTTTC
1 TTAACTAAATAATTTTC
28214920 TTAAC
1 TTAAC
28214925 CCAATTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAACTAAATAATTTTC
Found at i:28219698 original size:13 final size:14
Alignment explanation
Indices: 28219676--28219725 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
28219666 GGATTCAATC
28219676 AATAAAAAAATCGA
1 AATAAAAAAATCGA
28219690 AATAAAAAAATC--
1 AATAAAAAAATCGA
*
28219702 AATCAAAAAAT-GAA
1 AATAAAAAAATCG-A
28219716 AATAAAAAAA
1 AATAAAAAAA
28219726 ATGAACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 10 0.32
14 21 0.68
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (14 bp):
AATAAAAAAATCGA
Found at i:28219709 original size:12 final size:12
Alignment explanation
Indices: 28219672--28219712 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
28219662 CTTCGGATTC
28219672 AATCAATAAAAA
1 AATCAATAAAAA
28219684 AATCGAAATAAAAA
1 AATC--AATAAAAA
*
28219698 AATCAATCAAAA
1 AATCAATAAAAA
28219710 AAT
1 AAT
28219713 GAAAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 14 0.54
14 12 0.46
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAATAAAAA
Found at i:28219728 original size:15 final size:16
Alignment explanation
Indices: 28219705--28219757 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
28219695 AAAAATCAAT
*
28219705 CAAAAAATGAAAATAA
1 CAAAAAATGAAAAAAA
28219721 -AAAAAATGAACAAAAA
1 CAAAAAATGAA-AAAAA
* *
28219737 CAAAAAAAGAAAAAAT
1 CAAAAAATGAAAAAAA
28219753 CAAAA
1 CAAAA
28219758 TCAAAATGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 10 0.31
16 13 0.41
17 9 0.28
ACGTcount: A:0.79, C:0.08, G:0.06, T:0.08
Consensus pattern (16 bp):
CAAAAAATGAAAAAAA
Found at i:28219736 original size:26 final size:26
Alignment explanation
Indices: 28219672--28219725 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
28219662 CTTCGGATTC
*
28219672 AATCAATAAAAAAATCGAAATAAAAA
1 AATCAATCAAAAAATCGAAATAAAAA
28219698 AATCAATCAAAAAAT-GAAAATAAAAA
1 AATCAATCAAAAAATCG-AAATAAAAA
28219724 AA
1 AA
28219726 ATGAACAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (26 bp):
AATCAATCAAAAAATCGAAATAAAAA
Found at i:28219743 original size:26 final size:27
Alignment explanation
Indices: 28219672--28219755 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 27
28219662 CTTCGGATTC
* **
28219672 AATCAATAAAAAAATCGAAAT-AAAAA
1 AATCAATCAAAAAATAAAAATAAAAAA
*
28219698 AATCAATCAAAAAATGAAAATAAAAAA
1 AATCAATCAAAAAATAAAAATAAAAAA
* *
28219725 AATGAA-CAAAAACA-AAAAA-AGAAAA
1 AATCAATCAAAAA-ATAAAAATAAAAAA
28219750 AATCAA
1 AATCAA
28219756 AATCAAAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
25 10 0.20
26 28 0.57
27 11 0.22
ACGTcount: A:0.75, C:0.08, G:0.05, T:0.12
Consensus pattern (27 bp):
AATCAATCAAAAAATAAAAATAAAAAA
Found at i:28219802 original size:12 final size:13
Alignment explanation
Indices: 28219787--28219821 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
28219777 GAGAATGATA
*
28219787 AAAATAAAAAA-G
1 AAAAGAAAAAAGG
28219799 AAAAGAAAAAAGG
1 AAAAGAAAAAAGG
28219812 AAAAGAAAAA
1 AAAAGAAAAA
28219822 GGAGAGTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAAAGG
Found at i:28222084 original size:88 final size:88
Alignment explanation
Indices: 28221918--28222087 Score: 202
Period size: 88 Copynumber: 1.9 Consensus size: 88
28221908 AACAGATCAG
* *
28221918 TGAAGATAGCAGATCTTGCCTTCCTACACTGACAGCGAAGCAGATCGAGAACACTAGCCCTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTACACTGACAGCGAAGCAGATCGAGAACACTAACCCTACCT
**
28221983 CCCTCGGTTGCAGTGGAGCAGGT
66 CCCTCGGCAGCAGTGGAGCAGGT
* * **
28222006 TGAAGATAGCAGATCTTGCCTTCCTGCA-TGGACAGCGAAGTAGATCGAAGATAC-C-AATTCTA
1 TGAAGATAGCAGATCTTGCCTTCCTACACT-GACAGCGAAGCAGATCG-AGA-ACACTAACCCTA
* *
28222068 TCTCCCTGGGCAGCAGTGGA
63 CCTCCCTCGGCAGCAGTGGA
28222088 ATAGATTGAA
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
87 1 0.01
88 62 0.90
89 4 0.06
90 2 0.03
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTACACTGACAGCGAAGCAGATCGAGAACACTAACCCTACCT
CCCTCGGCAGCAGTGGAGCAGGT
Found at i:28222099 original size:43 final size:44
Alignment explanation
Indices: 28222046--28222161 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 44
28222036 GACAGCGAAG
* *
28222046 TAGATCGAAGA-TACCAATTCTATCTCCCTGGGCAGCAGTGGAA
1 TAGATTGAAGATTACCAATCCTATCTCCCTGGGCAGCAGTGGAA
*** * *
28222089 TAGATTGAAGATTGTGAGTCCTATCTCCCTGGTCAGCAGTGGAA
1 TAGATTGAAGATTACCAATCCTATCTCCCTGGGCAGCAGTGGAA
* *
28222133 TAGGTTGAA-ATTA-CAGATCTTATCTCCCT
1 TAGATTGAAGATTACCA-ATCCTATCTCCCT
28222162 AACCAGTAGT
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 1 0.02
43 24 0.41
44 34 0.58
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (44 bp):
TAGATTGAAGATTACCAATCCTATCTCCCTGGGCAGCAGTGGAA
Found at i:28222325 original size:131 final size:131
Alignment explanation
Indices: 28222105--28222725 Score: 951
Period size: 131 Copynumber: 4.7 Consensus size: 131
28222095 GAAGATTGTG
*
28222105 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT-GAAATTACAGATCTTATCTCCCTAACCAGT
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGT
* ** *
28222169 AGTGGAGTAGATCGAAGACAACGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAT
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAC
28222234 A
131 A
*
28222235 AGTCCTATCTCCCTGGTCAGCACTGGAATAGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGT
* * * * *
28222300 AGTGGAGCAAATCAAAGATGGCGAATCTTATCTCCCCCAGGAGTAGGGAAGCAGATTTAAGCAAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAC
28222365 A
131 A
* * * *
28222366 A-ACTCTATCTCCCTGGACAGCAGTGGAATAGGTT-GAAGATTATAGACCTTATCTCCCTAAGCA
1 AGTC-CTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAA-ATTACAGATCTTATCTCCCTAAGCA
* * * *
28222429 GTAGTAGAGCAGATCGAAGACGGCAAATCTTATCGTCCCTAGGAGTAGGGAAGCAGATTTAAGCC
64 GTAGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCC
28222494 ACA
129 ACA
** * *
28222497 AGTATTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTAAAGATCTCATCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGT
*
28222562 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCTAGGAGTAGGGAAGCAGATTTAAGCCAC
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAC
28222627 A
131 A
*
28222628 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTGCAGATCTTATCTCCCTAAGCAGT
1 AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGT
* * *
28222693 AGTGGAGCAGATCGAAAATGGCAAATCTTATCT
66 AGTGGAGCAGATCGAAGACGGCGAATCTTATCT
28222726 CCCTGAGGTT
Statistics
Matches: 443, Mismatches: 43, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
130 37 0.08
131 403 0.91
132 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.25
Consensus pattern (131 bp):
AGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGAAGACGGCGAATCTTATCTTCCCCAGGAGTAGGGAAGCAGATTTAAGCCAC
A
Found at i:28222721 original size:44 final size:43
Alignment explanation
Indices: 28222413--28222729 Score: 130
Period size: 44 Copynumber: 7.3 Consensus size: 43
28222403 GATTATAGAC
* * *
28222413 CTTATCTCCCTAAGCAGTAGTAGAGCAGATCGAAGACGGCAAAT
1 CTTATCTCCCT-AGCAGTAGTGGAGCAGATCGAAAATGGCAAAT
* ** *
28222457 CTTATCGTCCCTAGGAGTAG-GGAAGCAGAT--TTAA-GCCACAAGT
1 CTTATC-TCCCTAGCAGTAGTGG-AGCAGATCGAAAATGGCA-AA-T
* * * ** * * * **
28222500 ATTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAAT-TAAAGAT
1 CTTATCTCCCTAG-CAGTAGTGGAGCAGATCGAAAATGGCAA-AT
* * * *
28222544 CTCATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAAT
1 CTTATCTCCCT-AGCAGTAGTGGAGCAGATCGAAAATGGCAAAT
* ** *
28222588 CTTATCTTCCCTAGGAGTAG-GGAAGCAGAT--TTAA-GCCACAAGT
1 CTTATC-TCCCTAGCAGTAGTGG-AGCAGATCGAAAATGGCA-AA-T
* * * ** * * * * *
28222631 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATTGCAGAT
1 CTTATCTCCCTAG-CAGTAGTGGAGCAGATCGAAAATGGCAAAT
28222675 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAAATGGCAAAT
1 CTTATCTCCCT-AGCAGTAGTGGAGCAGATCGAAAATGGCAAAT
28222719 CTTATCTCCCT
1 CTTATCTCCCT
28222730 GAGGTTGCAG
Statistics
Matches: 191, Mismatches: 60, Indels: 44
0.65 0.20 0.15
Matches are distributed among these distances:
41 5 0.03
42 18 0.09
43 31 0.16
44 115 0.60
45 20 0.10
46 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (43 bp):
CTTATCTCCCTAGCAGTAGTGGAGCAGATCGAAAATGGCAAAT
Found at i:28222895 original size:44 final size:44
Alignment explanation
Indices: 28222843--28223143 Score: 150
Period size: 44 Copynumber: 6.9 Consensus size: 44
28222833 TAGATCGCAT
*
28222843 CAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAG
1 CAGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAG
* * *
28222887 CAGGTCTTATC-CCTCTGAAGTTGCAGTGGGGCAGACTGAAG-ATGG
1 CAGGTCTTATCTCC-CTGAGGTTGCAGTGGAGCAGACTG-AGTA-AG
* * * * * ** * * **
28222932 CAGATTTTACCTCCCTGAGATTACAGTGGAATACATTGAAGCCA-
1 CAGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTG-AGTAAG
* * * * * * * * *
28222976 CTA-ATCCTATCTCCTTGAGGTTGTAGCGGAACAGATTAAAATAA-
1 C-AGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACT-GAGTAAG
* * ** * * * * * *
28223020 AAGATCTTATCTTTCTGAAGTTGCAGTAGAGTAGA-T-CG-CAT
1 CAGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAG
*
28223061 CAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAG
1 CAGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAG
* * *
28223105 CAGGTTTTATCCCCCTGAGGTTGCAGTGGGGCAGACTGA
1 CAGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGA
28223144 AGATGACAGA
Statistics
Matches: 185, Mismatches: 60, Indels: 24
0.69 0.22 0.09
Matches are distributed among these distances:
40 1 0.01
41 27 0.15
42 1 0.01
43 5 0.03
44 118 0.64
45 31 0.17
46 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (44 bp):
CAGGTCTTATCTCCCTGAGGTTGCAGTGGAGCAGACTGAGTAAG
Found at i:28222983 original size:218 final size:218
Alignment explanation
Indices: 28222693--28223533 Score: 1215
Period size: 218 Copynumber: 3.9 Consensus size: 218
28222683 CCTAAGCAGT
* * * * * * ** *
28222693 AGTGGAGCAGA-TCGAAAATGGCAAATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCC
1 AGTGGGGCAGACT-GAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAGCC
* * ** *
28222757 -CATAATCCTATATCCCTTAAGTTGCAGTGGAGCAGATAAAAATAATGGATCTTATCTATCTGAA
65 AC-TAATCCTATCTCCCTTAAGTTGCAGTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAA
28222821 GTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAA
129 GTTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAA
*
28222886 GCAGGTCTTATCCCTCTGAAGTTGC
194 GCAGGTCTTATCCCCCTGAAGTTGC
*
28222911 AGTGGGGCAGACTGAAGATGGCAGATTTTACCTCCCTGAGATTACAGTGGAATACATTGAAGCCA
1 AGTGGGGCAGACTGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAGCCA
* * * * *
28222976 CTAATCCTATCT-CCTTGAGGTTGTAGCGGAACAGATTAAAATAAAAGATCTTATCTTTCTGAAG
66 CTAATCCTATCTCCCTT-AAGTTGCAGTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAG
28223040 TTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAG
130 TTGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAG
* *
28223105 CAGGTTTTATCCCCCTGAGGTTGC
195 CAGGTCTTATCCCCCTGAAGTTGC
* * *
28223129 AGTGGGGCAGACTGAAGATGACAGATTTTACCTCCCTGAGGTTATAGTGGAGTACATTGAAGCCA
1 AGTGGGGCAGACTGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAGCCA
* * * *
28223194 CTAATCCTATCTCCCTGAGGTTGCAG-CG-GCGGATTAAAATAAAAGATCTTATCTCTCTGAAGT
66 CTAATCCTATCTCCCTTAAGTTGCAGTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGT
* *
28223257 TGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCAGAGCAAACTGAGTAAGC
131 TGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGC
* *
28223322 AAGTCTTATCCCCCTAAAGTTGC
196 AGGTCTTATCCCCCTGAAGTTGC
* * * *
28223345 AGTGGGGTAGACAGAAGATGGCGGATTTTACCTCCCTGAGGTTATAGTGGAATACATTGAAGCCA
1 AGTGGGGCAGACTGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAGCCA
* * * *
28223410 CTAATCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAATAAAAGATCTTATCTCTCTAAAGT
66 CTAATCCTATCTCCCTTAAGTTGCAGTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGT
* * *
28223475 TGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGA
131 TGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGA
28223534 AGATGGCGAA
Statistics
Matches: 565, Mismatches: 52, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
216 198 0.35
217 6 0.01
218 356 0.63
219 5 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (218 bp):
AGTGGGGCAGACTGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAATACATTGAAGCCA
CTAATCCTATCTCCCTTAAGTTGCAGTGGAGCAGATTAAAATAAAAGATCTTATCTCTCTGAAGT
TGCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGC
AGGTCTTATCCCCCTGAAGTTGC
Found at i:28223282 original size:434 final size:436
Alignment explanation
Indices: 28222724--28223533 Score: 1266
Period size: 434 Copynumber: 1.9 Consensus size: 436
28222714 CAAATCTTAT
* * * *
28222724 CTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCCATAATCCTATATCCCTTAAGTTGCAGTGGAG
1 CTCCCTGAGGTTACAGTGGAGCACATTGAAGCCCATAATCCTATATCCCTGAAGTTGCAGTCGAG
**
28222789 CAGATAAAAATAATGGATCTTATCTATCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATC
66 CAGATAAAAATAAAAGATCTTATCTATCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATC
* * * * *
28222854 TCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAGGTCTTATCCCTCTGAAGTTGCAGTGGGGC
131 TCCCTGAGGTTGCAGCAGAGCAAACTGAGTAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGGC
*
28222919 AGACTGAAGATGGCAGATTTTACCTCCCTGAGATTACAGTGGAATACATTGAAGCCACTAATCCT
196 AGACAGAAGATGGCAGATTTTACCTCCCTGAGATTACAGTGGAATACATTGAAGCCACTAATCCT
* * * * * * *
28222984 ATCTCCTTGAGGTTGTAGCGGAACAGATTAAAATAAAAGATCTTATCTTTCTGAAGTTGCAGTAG
261 ATCTCCCTAAAGTTGCAGCAGAACAGATTAAAATAAAAGATCTTATCTCTCTAAAGTTGCAGTAG
*
28223049 AGTAGATCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAGGTTTTA
326 AGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGTAAGCAGGTTTTA
28223114 TCCCCCTGAGGTTGCAGTGGGGCAGACTGAAGATGACAGATTTTAC
391 TCCCCCTGAGGTTGCAGTGGGGCAGACTGAAGATGACAGATTTTAC
* * * *
28223160 CTCCCTGAGGTTATAGTGGAGTACATTGAAG-CCACTAATCCTATCTCCCTGAGGTTGCAG-CG-
1 CTCCCTGAGGTTACAGTGGAGCACATTGAAGCCCA-TAATCCTATATCCCTGAAGTTGCAGTCGA
* * *
28223222 GCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTAT
65 GCAGATAAAAATAAAAGATCTTATCTATCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTAT
28223287 CTCCCTGAGGTTGCAGCAGAGCAAACTGAGTAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGG
130 CTCCCTGAGGTTGCAGCAGAGCAAACTGAGTAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGG
* * * *
28223352 TAGACAGAAGATGGCGGATTTTACCTCCCTGAGGTTATAGTGGAATACATTGAAGCCACTAATCC
195 CAGACAGAAGATGGCAGATTTTACCTCCCTGAGATTACAGTGGAATACATTGAAGCCACTAATCC
* * *
28223417 TATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAATAAAAGATCTTATCTCTCTAAAGTTGCAGTA
260 TATCTCCCTAAAGTTGCAGCAGAACAGATTAAAATAAAAGATCTTATCTCTCTAAAGTTGCAGTA
* *
28223482 GAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGA
325 GAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGA
28223534 AGATGGCGAA
Statistics
Matches: 337, Mismatches: 36, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
434 284 0.84
435 4 0.01
436 49 0.15
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (436 bp):
CTCCCTGAGGTTACAGTGGAGCACATTGAAGCCCATAATCCTATATCCCTGAAGTTGCAGTCGAG
CAGATAAAAATAAAAGATCTTATCTATCTGAAGTTGCAGTAGAGTAGATCGCATCAGGTCTTATC
TCCCTGAGGTTGCAGCAGAGCAAACTGAGTAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGGC
AGACAGAAGATGGCAGATTTTACCTCCCTGAGATTACAGTGGAATACATTGAAGCCACTAATCCT
ATCTCCCTAAAGTTGCAGCAGAACAGATTAAAATAAAAGATCTTATCTCTCTAAAGTTGCAGTAG
AGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGTAAGCAGGTTTTA
TCCCCCTGAGGTTGCAGTGGGGCAGACTGAAGATGACAGATTTTAC
Found at i:28223426 original size:89 final size:88
Alignment explanation
Indices: 28223328--28223612 Score: 238
Period size: 89 Copynumber: 3.2 Consensus size: 88
28223318 AAGCAAGTCT
* * *
28223328 TATCCCCCTAAAGTTGCAGTGGGGTAGACAGAAGATGGCGGATTTTACCTCCCTGAGGTTATAGT
1 TATCTCCCTAAAGTTGCAGTGGGGCAGACAGAAGATGGCGGATTTTACCTCCCT-AGGTTACAGT
*
28223393 GGAATACATTGAAGCCACTAATCC
65 GGAGTACATTGAAGCCACTAATCC
* * * * **** * * * * *
28223417 TATCTCCCTAAAGTTGCAGTAGAGCGGATTA-AA-ATAAAAGATCTTATCTCTCTAAAGTTGCAG
1 TATCTCCCTAAAGTTGCAGTGGGGCAGA-CAGAAGATGGCGGATTTTACCTCCCT-AGGTTACAG
* * * * * ** *
28223480 TAGAGTAGATCGCA-TCA--GGTCT
64 TGGAGTACATTGAAGCCACTAATCC
* * *
28223502 TATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAATTTTACCTCCCTAGGGTTACAGT
1 TATCTCCCTAAAGTTGCAGTGGGGCAGACAGAAGATGGCGGATTTTACCTCCCTA-GGTTACAGT
28223567 GGAGTACATTGAAGCCACTAATCC
65 GGAGTACATTGAAGCCACTAATCC
*
28223591 TATCTCCCTGAAGTTGCAGTGG
1 TATCTCCCTAAAGTTGCAGTGG
28223613 AGCGGATTAA
Statistics
Matches: 139, Mismatches: 50, Indels: 14
0.68 0.25 0.07
Matches are distributed among these distances:
85 29 0.21
86 28 0.20
87 4 0.03
88 28 0.20
89 49 0.35
90 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (88 bp):
TATCTCCCTAAAGTTGCAGTGGGGCAGACAGAAGATGGCGGATTTTACCTCCCTAGGTTACAGTG
GAGTACATTGAAGCCACTAATCC
Found at i:28223705 original size:174 final size:174
Alignment explanation
Indices: 28223324--28223707 Score: 617
Period size: 174 Copynumber: 2.2 Consensus size: 174
28223314 GAGTAAGCAA
* * * * *
28223324 GTCTTATCCCCCTAAAGTTGCAGTGGGGTAGACAGAAGATGGCGGATTTTACCTCCCTGAGGTTA
1 GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAATTTTACCTCCCTGAGGTTA
*
28223389 TAGTGGAATACATTGAAGCCACTAATCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAATAA
66 CAGTGGAATACATTGAAGCCACTAATCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAATAA
28223454 AAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCGCATCAG
131 AAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCGCATCAG
28223498 GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAATTTTACCTCCCT-AGGGTT
1 GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAATTTTACCTCCCTGA-GGTT
* * *
28223562 ACAGTGGAGTACATTGAAGCCACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATA
65 ACAGTGGAATACATTGAAGCCACTAATCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAATA
* * *
28223627 AAAGATCTTATCTCTCTGAAGTTGCATTAGAGTAGCTCGCATCAG
130 AAAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCGCATCAG
* * *
28223672 GTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGA
1 GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGA
28223708 GAAAACAAGT
Statistics
Matches: 194, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
173 1 0.01
174 193 0.99
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (174 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCGAATTTTACCTCCCTGAGGTTA
CAGTGGAATACATTGAAGCCACTAATCCTATCTCCCTAAAGTTGCAGTAGAGCGGATTAAAATAA
AAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCGCATCAG
Found at i:28223797 original size:174 final size:174
Alignment explanation
Indices: 28223412--28223797 Score: 372
Period size: 174 Copynumber: 2.2 Consensus size: 174
28223402 TGAAGCCACT
** ***
28223412 AATCCTATCTCCCTAAAGTTGCAGT-AGAGCGGATTAAAATAAAAGATCTTATCTCTCTAAAGTT
1 AATCCTATCTCCCCGAAGTTGCAGTGA-AAAAGATTAAAATAAAAGATCTTATCTCTCTAAAGTT
* * ***
28223476 GCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGC
65 GCAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGAAAAC
* * * * * * * *
28223541 GAATTTTACCTCCCTAGGGTTACAGTGGAGTACATTGAAGCCACT
130 GAATCTTACCCCCCTAGAGTTACAGTGGAGCACAATGAAACAACG
* * *** *
28223586 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATAAAAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCCGAAGTTGCAGTGAAAAAGATTAAAATAAAAGATCTTATCTCTCTAAAGTTG
* * *
28223651 CATTAGAGTAGCTCGCATCAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTG-AGAAAAC-
66 CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGAAAACG
* * *
28223714 AAGTCTTACCCCCCT-GAAGTTACAGTGGGGCAGAATGAGAATAACG
131 AA-TCTTACCCCCCTAG-AGTTACAGTGGAGCACAATGA-AACAACG
* *
28223760 AAT-CT-TGCTTCCCCGACA-TTGTAGTTAAAAAGATTAAA
1 AATCCTAT-C-TCCCCGA-AGTTGCAGTGAAAAAGATTAAA
28223798 GCTACAACGG
Statistics
Matches: 176, Mismatches: 29, Indels: 14
0.80 0.13 0.06
Matches are distributed among these distances:
172 4 0.02
173 33 0.19
174 138 0.78
175 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (174 bp):
AATCCTATCTCCCCGAAGTTGCAGTGAAAAAGATTAAAATAAAAGATCTTATCTCTCTAAAGTTG
CAGTAGAGTAGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAAGAAAACG
AATCTTACCCCCCTAGAGTTACAGTGGAGCACAATGAAACAACG
Found at i:28223848 original size:50 final size:50
Alignment explanation
Indices: 28223790--28223971 Score: 186
Period size: 50 Copynumber: 3.7 Consensus size: 50
28223780 GTAGTTAAAA
* * **
28223790 AGATTAAAGCTACAACGGTAAATCTTACTTTGCAGGCAGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGCAAATCTTACTTCCCAGGCAGTGCAGTGGAAC
* * * * ** *
28223840 AGATTAAAGCCACAACGGCAAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGCAAATCTTACTTCCCAGGCAGTGCAGTGGAAC
* * ** *
28223890 AAATTAAAGCTACAACGGTGAATCTTACTTCCCAGGCGGTGCAGTGG-AC
1 AGATTAAAGCCACAACGGCAAATCTTACTTCCCAGGCAGTGCAGTGGAAC
* * *
28223939 ATATTAAAGCCACAACGACAAATCTTGCTTCCC
1 AGATTAAAGCCACAACGGCAAATCTTACTTCCC
28223972 CTGCGGTTAA
Statistics
Matches: 103, Mismatches: 29, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
49 28 0.27
50 75 0.73
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGCAAATCTTACTTCCCAGGCAGTGCAGTGGAAC
Found at i:28223887 original size:100 final size:99
Alignment explanation
Indices: 28223760--28223972 Score: 345
Period size: 100 Copynumber: 2.1 Consensus size: 99
28223750 GAGAATAACG
* * **
28223760 AATCTTGCTTCCCCGACATTGTAGTTAAAAAGATTAAAGCTACAACGGTAAATCTTACTTTGCAG
1 AATCTTGCTTCCCCGACATTGCAGTTAAAAAAATTAAAGCTACAACGGTAAATCTTACTTCCCAG
*
28223825 GCAGTGCAGTGGAACAGATTAAAGCCACAACGGCA
66 GCAGTGCAGTGG-ACAGATTAAAGCCACAACGACA
*
28223860 AATCTTGCTTCCCCGACATTGCAGTTAAAAAAATTAAAGCTACAACGGTGAATCTTACTTCCCAG
1 AATCTTGCTTCCCCGACATTGCAGTTAAAAAAATTAAAGCTACAACGGTAAATCTTACTTCCCAG
* *
28223925 GCGGTGCAGTGGACATATTAAAGCCACAACGACA
66 GCAGTGCAGTGGACAGATTAAAGCCACAACGACA
28223959 AATCTTGCTTCCCC
1 AATCTTGCTTCCCC
28223973 TGCGGTTAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
99 34 0.32
100 71 0.68
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (99 bp):
AATCTTGCTTCCCCGACATTGCAGTTAAAAAAATTAAAGCTACAACGGTAAATCTTACTTCCCAG
GCAGTGCAGTGGACAGATTAAAGCCACAACGACA
Found at i:28224269 original size:22 final size:23
Alignment explanation
Indices: 28224244--28224292 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
28224234 TGCCCGGCCC
*
28224244 AAATCAGAAATAAAT-AAACAAA
1 AAATCAGAAAAAAATAAAACAAA
* *
28224266 AAATTATAAAAAAATAAAAACAAA
1 AAATCAGAAAAAAAT-AAAACAAA
28224290 AAA
1 AAA
28224293 CAAATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 12 0.55
24 10 0.45
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (23 bp):
AAATCAGAAAAAAATAAAACAAA
Found at i:28224824 original size:21 final size:23
Alignment explanation
Indices: 28224800--28224842 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28224790 GCTCTCCCCA
28224800 GCCACG-C-ACACCTCCGTACAT
1 GCCACGTCTACACCTCCGTACAT
*
28224821 GCCACGTCTGCACCTCCGTACA
1 GCCACGTCTACACCTCCGTACA
28224843 CACCACATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.21, C:0.47, G:0.16, T:0.16
Consensus pattern (23 bp):
GCCACGTCTACACCTCCGTACAT
Found at i:28224937 original size:208 final size:208
Alignment explanation
Indices: 28224579--28224996 Score: 809
Period size: 208 Copynumber: 2.0 Consensus size: 208
28224569 GACCTCCAGC
* *
28224579 ACCGCTCTCCCCAGCCACGCACACCTCCGTACATGCCACGTCTGCGCCTCCGTACACACCACGTC
1 ACCGCTCTCCCCAGCCACGCACACCTCCGTACATGCCACGTCTGCACCTCCGTACACACCACATC
28224644 CCTCGCCGTACGCCGTACCTGCAAATAGAGCCAAACAACGCAGCAGAAAGGAGAAAAATTGTATT
66 CCTCGCCGTACGCCGTACCTGCAAATAGAGCCAAACAACGCAGCAGAAAGGAGAAAAATTGTATT
28224709 TCATTTTTTGATGTTGTTTTATCTTTATTTTTTCCAGCCTATAAAACAAAAGGCTAAAACTTTGT
131 TCATTTTTTGATGTTGTTTTATCTTTATTTTTTCCAGCCTATAAAACAAAAGGCTAAAACTTTGT
28224774 AATTTTTTTACGG
196 AATTTTTTTACGG
28224787 ACCGCTCTCCCCAGCCACGCACACCTCCGTACATGCCACGTCTGCACCTCCGTACACACCACATC
1 ACCGCTCTCCCCAGCCACGCACACCTCCGTACATGCCACGTCTGCACCTCCGTACACACCACATC
*
28224852 CCTCGCCGTACGTCGTACCTGCAAATAGAGCCAAACAACGCAGCAGAAAGGAGAAAAATTGTATT
66 CCTCGCCGTACGCCGTACCTGCAAATAGAGCCAAACAACGCAGCAGAAAGGAGAAAAATTGTATT
28224917 TCATTTTTTGATGTTGTTTTATCTTTATTTTTTCCAGCCTATAAAACAAAAGGCTAAAACTTTGT
131 TCATTTTTTGATGTTGTTTTATCTTTATTTTTTCCAGCCTATAAAACAAAAGGCTAAAACTTTGT
28224982 AATTTTTTTACGG
196 AATTTTTTTACGG
28224995 AC
1 AC
28224997 ACTCATTCAA
Statistics
Matches: 207, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
208 207 1.00
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (208 bp):
ACCGCTCTCCCCAGCCACGCACACCTCCGTACATGCCACGTCTGCACCTCCGTACACACCACATC
CCTCGCCGTACGCCGTACCTGCAAATAGAGCCAAACAACGCAGCAGAAAGGAGAAAAATTGTATT
TCATTTTTTGATGTTGTTTTATCTTTATTTTTTCCAGCCTATAAAACAAAAGGCTAAAACTTTGT
AATTTTTTTACGG
Found at i:28229318 original size:25 final size:25
Alignment explanation
Indices: 28229290--28229363 Score: 103
Period size: 25 Copynumber: 3.0 Consensus size: 25
28229280 TCCAGCTCTT
*
28229290 ATGAGCTTCCCGTTATTCAGCTTGC
1 ATGAGCTTCCCGTTATTCAGCTCGC
*
28229315 ATGAGCTTCCCGTTATTCAACTCGC
1 ATGAGCTTCCCGTTATTCAGCTCGC
* * *
28229340 ATGAGCTTTCTGTTATTTAGCTCG
1 ATGAGCTTCCCGTTATTCAGCTCG
28229364 GAGAAGCTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.38
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATTCAGCTCGC
Found at i:28230418 original size:13 final size:13
Alignment explanation
Indices: 28230400--28230432 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
28230390 AGCACACGGG
*
28230400 CATGTGGCTTGGC
1 CATGTGGCTAGGC
28230413 CATGT-GCTAGGC
1 CATGTGGCTAGGC
28230425 CATGTGGC
1 CATGTGGC
28230433 CCAAGTCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.12, C:0.24, G:0.36, T:0.27
Consensus pattern (13 bp):
CATGTGGCTAGGC
Found at i:28236275 original size:36 final size:37
Alignment explanation
Indices: 28236211--28236284 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
28236201 GAACAAACAA
* *
28236211 TTTTAATTAAATTAAATTATTTATATATA-AAAATAT
1 TTTTAATTAAATTAAATTATTAAAATATATAAAATAT
* *
28236247 TTTTAATTAAATTTTAATTA-TAAAATATATGAAATAT
1 TTTTAATTAAA-TTAAATTATTAAAATATATAAAATAT
28236284 T
1 T
28236285 AGTGTAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 18 0.56
37 14 0.44
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (37 bp):
TTTTAATTAAATTAAATTATTAAAATATATAAAATAT
Found at i:28244994 original size:9 final size:9
Alignment explanation
Indices: 28244980--28245022 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
28244970 TGATTTTTCG
28244980 AATTCGAAT
1 AATTCGAAT
28244989 AATTCG---
1 AATTCGAAT
28244995 AATTCGAAT
1 AATTCGAAT
28245004 AATTCGAAT
1 AATTCGAAT
28245013 AATTCGAAT
1 AATTCGAAT
28245022 A
1 A
28245023 TCAAACTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.19
9 25 0.81
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28244996 original size:15 final size:15
Alignment explanation
Indices: 28244976--28245012 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
28244966 GAGTTGATTT
28244976 TTCGAATTCGAATAA
1 TTCGAATTCGAATAA
28244991 TTCGAATTCGAATAA
1 TTCGAATTCGAATAA
28245006 TTCGAAT
1 TTCGAAT
28245013 AATTCGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (15 bp):
TTCGAATTCGAATAA
Found at i:28245099 original size:21 final size:21
Alignment explanation
Indices: 28245058--28245100 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28245048 ACTCCAAACT
* *
28245058 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
28245079 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
28245100 C
1 C
28245101 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:28247292 original size:22 final size:23
Alignment explanation
Indices: 28247247--28247292 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
28247237 TTTGATAATA
28247247 TGTTTTGATATAACAAATTAAAG
1 TGTTTTGATATAACAAATTAAAG
*
28247270 TGTTCTTGA-ATAA-AAGTTAAAG
1 TGTT-TTGATATAACAAATTAAAG
28247292 T
1 T
28247293 TGAACAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.39
Consensus pattern (23 bp):
TGTTTTGATATAACAAATTAAAG
Found at i:28247544 original size:20 final size:21
Alignment explanation
Indices: 28247505--28247546 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28247495 TATTGATTTA
* *
28247505 CAAAAATTATTGATACCTTTT
1 CAAAAAGTATCGATACCTTTT
*
28247526 CAAAAAGTATCGATACTTTTT
1 CAAAAAGTATCGATACCTTTT
28247547 ACTAGGTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (21 bp):
CAAAAAGTATCGATACCTTTT
Found at i:28250531 original size:33 final size:32
Alignment explanation
Indices: 28250494--28250556 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 32
28250484 TTATTAGCTT
*
28250494 TAAATTGAAAATGAATTTTATATAGGGGGAGCC
1 TAAATTGAAAATGAATTTTAT-TAAGGGGAGCC
*
28250527 TAAATTGAAGATGAATTTTATTAAGGGGAG
1 TAAATTGAAAATGAATTTTATTAAGGGGAG
28250557 AAATTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (32 bp):
TAAATTGAAAATGAATTTTATTAAGGGGAGCC
Found at i:28250682 original size:22 final size:24
Alignment explanation
Indices: 28250639--28250682 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
28250629 TAATAATAAG
28250639 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
28250663 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
28250683 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:28251531 original size:27 final size:25
Alignment explanation
Indices: 28251501--28251550 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
28251491 TTTTAGTTTA
*
28251501 ATAAGATAATAATAAATAAAAAAATAT
1 ATAAAATAA-AATAAA-AAAAAAATAT
*
28251528 ATAAAATAAAATAAAAACAAAAT
1 ATAAAATAAAATAAAAAAAAAAT
28251551 TGTGATTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 6 0.29
27 8 0.38
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (25 bp):
ATAAAATAAAATAAAAAAAAAATAT
Found at i:28254095 original size:21 final size:20
Alignment explanation
Indices: 28254071--28254121 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
28254061 ACTGAGTTAA
*
28254071 AAGAGTTGAAAGCAGTTTTTC
1 AAGAGTTGAAA-CAGTTTTGC
*
28254092 AAGAGTTGGAAATAGTTTTGC
1 AAGAGTT-GAAACAGTTTTGC
28254113 AAGAGTTGA
1 AAGAGTTGA
28254122 CTGATAGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 21 0.78
22 4 0.15
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (20 bp):
AAGAGTTGAAACAGTTTTGC
Found at i:28271979 original size:22 final size:23
Alignment explanation
Indices: 28271953--28271995 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
28271943 TATCACCTTT
28271953 TTACCT-A-TTTACAAAATTACCC
1 TTACCTAACTTTA-AAAATTACCC
28271975 TTACCTAACTTTAAAAATTAC
1 TTACCTAACTTTAAAAATTAC
28271996 TCAATTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (23 bp):
TTACCTAACTTTAAAAATTACCC
Found at i:28276260 original size:33 final size:33
Alignment explanation
Indices: 28276213--28276279 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
28276203 AAATATTTTG
* *
28276213 AAAAAAACAAGAAATTCGAAAAGAAATTCAAAA
1 AAAAAAACAAGAAATTCAAAAAAAAATTCAAAA
* * *
28276246 AAAAAAAGAGGAAATTCAAAAAAAAATTTAAAA
1 AAAAAAACAAGAAATTCAAAAAAAAATTCAAAA
28276279 A
1 A
28276280 GAGTGAAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.13
Consensus pattern (33 bp):
AAAAAAACAAGAAATTCAAAAAAAAATTCAAAA
Found at i:28277294 original size:13 final size:12
Alignment explanation
Indices: 28277276--28277327 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 12
28277266 TGTGAGCAAG
28277276 AAAAGAACATTGA
1 AAAAGAA-ATTGA
28277289 AAAAGAAATTG-
1 AAAAGAAATTGA
28277300 -AAAGAAATTG-
1 AAAAGAAATTGA
*
28277310 -AAGGAAA-TGA
1 AAAAGAAATTGA
28277320 AAAAGAAA
1 AAAAGAAA
28277328 AAAAAAGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 16 0.46
11 6 0.17
12 4 0.11
13 7 0.20
ACGTcount: A:0.65, C:0.02, G:0.19, T:0.13
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:28281915 original size:29 final size:30
Alignment explanation
Indices: 28281878--28281936 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
28281868 GAATTGGATC
*
28281878 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAAATTCATGTATAAAATTGCACA
* *
28281908 AAAT-AAAAATTCATGTTTACAATTGCACA
1 AAATCAAAAATTCATGTATAAAATTGCACA
28281937 TTAAACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.31
Consensus pattern (30 bp):
AAATCAAAAATTCATGTATAAAATTGCACA
Found at i:28282281 original size:60 final size:60
Alignment explanation
Indices: 28282188--28282309 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
28282178 AAGTTAAAAC
28282188 TTTCCACAACCTGTGTACCAAATAATTATCCTAAAAACAATGATATTTAATGAAATGAAA
1 TTTCCACAACCTGTGTACCAAATAATTATCCTAAAAACAATGATATTTAATGAAATGAAA
28282248 TTTCCACAACCTGTGTACCAAATAATTATCCTAAAAACAATGATATTTAATGAAATGAAA
1 TTTCCACAACCTGTGTACCAAATAATTATCCTAAAAACAATGATATTTAATGAAATGAAA
28282308 TT
1 TT
28282310 ATGATTGAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.31
Consensus pattern (60 bp):
TTTCCACAACCTGTGTACCAAATAATTATCCTAAAAACAATGATATTTAATGAAATGAAA
Found at i:28284181 original size:114 final size:114
Alignment explanation
Indices: 28284027--28284817 Score: 1357
Period size: 114 Copynumber: 6.9 Consensus size: 114
28284017 ATAGCGGCAG
* * *
28284027 TAGCAGCGTTTGTTTGTAAGCGCCGCAAACAATATTAAACAAAACGCAGCGTACAAGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
28284092 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
* *
28284141 TAGCGGTGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGTAGCGTACAAGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
*
28284206 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGTATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
* *
28284255 TAGCGGCATTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAGGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
* *
28284320 ATAGTAGAATTGGTGGCGTTTCTGTCAAAACGCCGCTGAAGTGTATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
* * *
28284369 TAGCGGCATTTGTTTGTAAGCGCCGCAAAAAATGTTAAAGAAAACGCAGCGTACAGGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
* *
28284434 ATAGTAGAATTGGTGGCGTTTCTGTCAAAACGCCGCTAAAGTGGATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
* *
28284483 TAGCAGCGTTTGCTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
* *
28284548 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATAAA
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
28284597 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
1 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
* * *
28284662 ATAGTTGAATTTGTGGCGTTTCTGTAAAAATGCCGCTGAAGTGGATCAT
66 ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
*
28284711 TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAAATGTTAAACAAAACGCAGCGTACAAAATTGAGG
1 TAGCGGCGTTTGTTTGTAAGCGCCGC-AAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGG
*
28284776 TATAGTAGAATTGGTGGCGTTTCTATAAAAACGCCGCTGAAG
65 TATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAG
28284818 CACATTATTA
Statistics
Matches: 641, Mismatches: 35, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
114 566 0.88
115 75 0.12
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (114 bp):
TAGCGGCGTTTGTTTGTAAGCGCCGCAAAAAATGTTAAACAAAACGCAGCGTACAAGATTGAGGT
ATAGTAGAATTGGTGGCGTTTCTGTAAAAACGCCGCTGAAGTGGATCAT
Found at i:28285610 original size:25 final size:26
Alignment explanation
Indices: 28285576--28285627 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
28285566 TTGTTTGTGG
*
28285576 TTTACGGGTTTAATATTTATGGTTAA
1 TTTACGGGTTTAAGATTTATGGTTAA
28285602 TTTA-GGGTTTAAGATTTATGGTTAA
1 TTTACGGGTTTAAGATTTATGGTTAA
28285627 T
1 T
28285628 GTTTACGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.27, C:0.02, G:0.21, T:0.50
Consensus pattern (26 bp):
TTTACGGGTTTAAGATTTATGGTTAA
Found at i:28286657 original size:17 final size:19
Alignment explanation
Indices: 28286637--28286677 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
28286627 CTGTCATCTC
28286637 CCCCAAATCCCTAA-A-TT
1 CCCCAAATCCCTAACAGTT
*
28286654 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAACAGTT
28286673 CCCCA
1 CCCCA
28286678 TACCCGACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 13 0.65
18 1 0.05
19 6 0.30
ACGTcount: A:0.29, C:0.46, G:0.02, T:0.22
Consensus pattern (19 bp):
CCCCAAATCCCTAACAGTT
Found at i:28288506 original size:9 final size:9
Alignment explanation
Indices: 28288465--28288698 Score: 204
Period size: 9 Copynumber: 25.8 Consensus size: 9
28288455 TACAAGATTA
*
28288465 TACATAAAT
1 TACATAACT
* *
28288474 TAAATTACT
1 TACATAACT
28288483 TACATAACT
1 TACATAACT
*
28288492 TGA-ATAAAT
1 T-ACATAACT
* *
28288501 TAAATAAGT
1 TACATAACT
28288510 TACATAACT
1 TACATAACT
*
28288519 TACATAACC
1 TACATAACT
*
28288528 TACATAAAT
1 TACATAACT
*
28288537 TAAATAACT
1 TACATAACT
28288546 TACATAACT
1 TACATAACT
*
28288555 TACATAAAT
1 TACATAACT
*
28288564 TA-AGTAACC
1 TACA-TAACT
*
28288573 TACATAACA
1 TACATAACT
28288582 TACATAAACT
1 TACAT-AACT
* *
28288592 TGCATAAAT
1 TACATAACT
*
28288601 TAAATAACT
1 TACATAACT
*
28288610 TACATAACC
1 TACATAACT
*
28288619 TACATAAAT
1 TACATAACT
*
28288628 TAAATAACT
1 TACATAACT
*
28288637 TCCATAACT
1 TACATAACT
*
28288646 TACATAAAT
1 TACATAACT
28288655 TA-AGTAACT
1 TACA-TAACT
*
28288664 TACATAACA
1 TACATAACT
28288673 TACATAAACT
1 TACAT-AACT
*
28288683 TGCATAACT
1 TACATAACT
28288692 TACATAA
1 TACATAA
28288699 AAATATATCA
Statistics
Matches: 177, Mismatches: 40, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
8 3 0.02
9 157 0.89
10 17 0.10
ACGTcount: A:0.50, C:0.17, G:0.03, T:0.31
Consensus pattern (9 bp):
TACATAACT
Found at i:28288600 original size:37 final size:37
Alignment explanation
Indices: 28288540--28288652 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 37
28288530 CATAAATTAA
* *
28288540 ATAACTTACAT-AACTTACATAAATTAAGTAACCTAC
1 ATAACATACATAAACTTACATAAATTAAATAACCTAC
* *
28288576 ATAACATACATAAACTTGCATAAATTAAATAACTTAC
1 ATAACATACATAAACTTACATAAATTAAATAACCTAC
* * * ** *
28288613 ATAACCTACATAAA-TTAAATAACTTCCATAACTTAC
1 ATAACATACATAAACTTACATAAATTAAATAACCTAC
28288649 ATAA
1 ATAA
28288653 ATTAAGTAAC
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
36 31 0.47
37 35 0.53
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.30
Consensus pattern (37 bp):
ATAACATACATAAACTTACATAAATTAAATAACCTAC
Found at i:28288719 original size:91 final size:91
Alignment explanation
Indices: 28288520--28288719 Score: 276
Period size: 91 Copynumber: 2.2 Consensus size: 91
28288510 TACATAACTT
* *
28288520 ACATAACCTACATAAATTAAATAACTTACATAACTTACATAAATTAAGTAACCTACATAACATAC
1 ACATAACATACACAAATTAAATAACTTACATAACTTACATAAATTAAGTAACCTACATAACATAC
**
28288585 ATAAACTTGCATAAATTAAATAACTT
66 ATAAACTTGCATAAATTAAATAACAA
* * * *
28288611 ACATAACCTACATAAATTAAATAACTTCCATAACTTACATAAATTAAGTAACTTACATAACATAC
1 ACATAACATACACAAATTAAATAACTTACATAACTTACATAAATTAAGTAACCTACATAACATAC
* *
28288676 ATAAACTTGCATAACTTACATAA-AA
66 ATAAACTTGCATAAATTAAATAACAA
* *
28288701 ATATATCATATCACAAATT
1 ACATAACATA-CACAAATT
28288720 TTTGTAATTC
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
90 7 0.07
91 91 0.93
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (91 bp):
ACATAACATACACAAATTAAATAACTTACATAACTTACATAAATTAAGTAACCTACATAACATAC
ATAAACTTGCATAAATTAAATAACAA
Found at i:28294547 original size:43 final size:42
Alignment explanation
Indices: 28294457--28294619 Score: 274
Period size: 42 Copynumber: 3.9 Consensus size: 42
28294447 GTATAAAAAT
28294457 GCCGCTACAA-AACATGGTCTTTAGAGGCGTTTTTTTCTAAGC
1 GCCGCTA-AAGAACATGGTCTTTAGAGGCGTTTTTTTCTAAGC
* *
28294499 GCCGCTAAAGAATATGGTCTTTAGCGGCGTTTTTTTTCTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGAGGCG-TTTTTTTCTAAGC
28294542 GCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCTAAGC
1 GCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCTAAGC
*
28294584 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
1 GCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTT
28294620 TTGTAAACGC
Statistics
Matches: 114, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
41 2 0.02
42 72 0.63
43 40 0.35
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
GCCGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCTAAGC
Found at i:28294556 original size:85 final size:85
Alignment explanation
Indices: 28294457--28294620 Score: 303
Period size: 85 Copynumber: 1.9 Consensus size: 85
28294447 GTATAAAAAT
*
28294457 GCCGCTACAAAACATGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAATATGGTCTTTA
1 GCCGCTACAAAACATGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTA
28294522 GCGGCGTTTTTTTTCTAAGC
66 GCGGCGTTTTTTTTCTAAGC
28294542 GCCGCTA-AAGAACATGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTT
1 GCCGCTACAA-AACATGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTT
28294606 AGCGGCGTTTTTTTT
65 AGCGGCGTTTTTTTT
28294621 TGTAAACGCT
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
84 2 0.03
85 75 0.97
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (85 bp):
GCCGCTACAAAACATGGTCTTTAGAGGCGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTA
GCGGCGTTTTTTTTCTAAGC
Found at i:28294740 original size:22 final size:22
Alignment explanation
Indices: 28294709--28294752 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28294699 TAGTGGCGTT
* *
28294709 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAGACCTA
28294731 AAAAAACGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAGACCTA
28294753 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAGACCTA
Found at i:28294860 original size:14 final size:14
Alignment explanation
Indices: 28294837--28294871 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28294827 TTTGAATTTA
28294837 TTTTTAAAAAATATT
1 TTTTTAAAAAA-ATT
28294852 TTTTTAAAAAAATT
1 TTTTTAAAAAAATT
*
28294866 TATTTA
1 TTTTTA
28294872 TAGCATGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTTTAAAAAAATT
Found at i:28300493 original size:41 final size:41
Alignment explanation
Indices: 28300435--28300625 Score: 328
Period size: 41 Copynumber: 4.6 Consensus size: 41
28300425 CTTAATTTAA
* *
28300435 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28300477 CAGATCACCGACACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28300518 CAGATCACCGGCACTTATCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28300559 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACTTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28300600 CAGATCACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
28300626 ATGTATAGTC
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
41 138 0.97
42 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:28308229 original size:41 final size:40
Alignment explanation
Indices: 28308171--28308357 Score: 297
Period size: 41 Copynumber: 4.7 Consensus size: 40
28308161 CTTAATTTAA
*
28308171 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGG-TTATAACCTGATT
*
28308213 CAGATCACCGACACTTAG-CTGCTAGGTTATAACCTGA-T
1 CAGATCACCGGCACTTAGCCTGCTAGGTTATAACCTGATT
*
28308251 CAGATCACCGGCACTTATCCTGCTAGGTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTATAACCTGATT
28308291 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGG-TTATAACCTGATT
*
28308332 CAGATCATCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
28308358 ACGTATAGTC
Statistics
Matches: 136, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
38 17 0.12
39 29 0.21
40 35 0.26
41 51 0.38
42 4 0.03
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (40 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTATAACCTGATT
Found at i:28315989 original size:41 final size:41
Alignment explanation
Indices: 28315931--28316120 Score: 328
Period size: 41 Copynumber: 4.6 Consensus size: 41
28315921 CTTAATTTAA
* *
28315931 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28315973 CAGATCACCGACACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28316014 CAGATCACCGGCACTTATCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28316055 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28316096 CAGATCACCGGCACTTAG-CTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
28316121 ACGTATAGTC
Statistics
Matches: 142, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
40 7 0.05
41 131 0.92
42 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:28323754 original size:41 final size:41
Alignment explanation
Indices: 28323696--28323885 Score: 328
Period size: 41 Copynumber: 4.6 Consensus size: 41
28323686 CTTAATTTAA
* *
28323696 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28323738 CAGATCACCGACACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28323779 CAGATCACCGGCACTTATCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28323820 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28323861 CAGATCACCGGCACTTAG-CTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
28323886 ACGTATAGTC
Statistics
Matches: 142, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
40 7 0.05
41 131 0.92
42 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:28331400 original size:37 final size:36
Alignment explanation
Indices: 28331333--28331501 Score: 181
Period size: 38 Copynumber: 4.6 Consensus size: 36
28331323 TATAATTTAA
*
28331333 CAGATTCACGGCACTTAGCTGCTA-GCTTATAGCTGATT
1 CAGA-TCAC-GCACTTAGCTGCTAGGTTTATA-CTGATT
28331371 CAGATCACG-ACTTAGCCTGCTAGGTTTATAACTGATT
1 CAGATCACGCACTTAG-CTGCTAGGTTTAT-ACTGATT
* *
28331408 CA-ATCACGCA-TTACCTGCTAGG-TTATAAT-A-T
1 CAGATCACGCACTTAGCTGCTAGGTTTATACTGATT
28331439 CAGATCACCGCACTTAGCTGCTAGGTTTATACCTGATT
1 CAGATCA-CGCACTTAGCTGCTAGGTTTATA-CTGATT
28331477 CAGATCACGGCACTTAGTCTGCTAG
1 CAGATCAC-GCACTTAG-CTGCTAG
28331502 ACGTATGTCT
Statistics
Matches: 113, Mismatches: 5, Indels: 25
0.79 0.03 0.17
Matches are distributed among these distances:
31 3 0.03
32 5 0.04
33 6 0.05
34 15 0.13
35 19 0.17
36 17 0.15
37 20 0.18
38 21 0.19
39 7 0.06
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (36 bp):
CAGATCACGCACTTAGCTGCTAGGTTTATACTGATT
Found at i:28332037 original size:12 final size:14
Alignment explanation
Indices: 28332019--28332050 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
28332009 ATTCATCCAA
28332019 CTTATAC-AAATAT
1 CTTATACAAAATAT
28332032 -TTATACAAAATAT
1 CTTATACAAAATAT
28332045 CTTATA
1 CTTATA
28332051 TAATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 6 0.35
14 5 0.29
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTATACAAAATAT
Found at i:28339102 original size:41 final size:41
Alignment explanation
Indices: 28339044--28339234 Score: 337
Period size: 41 Copynumber: 4.6 Consensus size: 41
28339034 CTTAATTTAA
* *
28339044 CAGATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28339086 CAGATCACCGACACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
*
28339127 CAGATCACCGGCACTTATCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28339168 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
28339209 CAGATCACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
28339235 ACATATAGTC
Statistics
Matches: 143, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 139 0.97
42 4 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:28341157 original size:90 final size:90
Alignment explanation
Indices: 28341004--28341187 Score: 332
Period size: 90 Copynumber: 2.0 Consensus size: 90
28340994 TTACGCGATT
*
28341004 TAATCCTTTTATTTAATCAGACACTCAAACGACGAAATTAAAACATGAAAATTTCATAAAATTAA
1 TAATCCTTTTATTTAATCAGACACTCAAACGACGAAATTAAAACACGAAAATTTCATAAAATTAA
28341069 ATTCACACATAATAAACACACAAAA
66 ATTCACACATAATAAACACACAAAA
* *
28341094 TAATCCTTTTATTTAATCGGACACTCAAACGACGAAATTAAAACACGAAAATTTCATACAATTAA
1 TAATCCTTTTATTTAATCAGACACTCAAACGACGAAATTAAAACACGAAAATTTCATAAAATTAA
*
28341159 ATTCACACATAGTAAACACACAAAA
66 ATTCACACATAATAAACACACAAAA
28341184 TAAT
1 TAAT
28341188 ATTAAAATAT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.27
Consensus pattern (90 bp):
TAATCCTTTTATTTAATCAGACACTCAAACGACGAAATTAAAACACGAAAATTTCATAAAATTAA
ATTCACACATAATAAACACACAAAA
Found at i:28342994 original size:14 final size:14
Alignment explanation
Indices: 28342975--28343004 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28342965 TCCCATGTGT
*
28342975 TTGAAAATGAATTC
1 TTGAAAAAGAATTC
28342989 TTGAAAAAGAATTC
1 TTGAAAAAGAATTC
28343003 TT
1 TT
28343005 TTGGTCAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (14 bp):
TTGAAAAAGAATTC
Found at i:28343621 original size:41 final size:43
Alignment explanation
Indices: 28343561--28343644 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
28343551 TATATTTTTT
*
28343561 TATATTGTTTCAAGCTTTTTT-TTTA-ATTTTTAATTAATAAA
1 TATATTGTTTCAAGCTTTTTTATTCATATTTTTAATTAATAAA
*
28343602 TATATTGTTTTCAA-TTTTTTTAATTCATATTTTTAATTAATAA
1 TATATTG-TTTCAAGCTTTTTT-ATTCATATTTTTAATTAATAA
28343645 CTCTTTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
41 13 0.35
42 6 0.16
43 3 0.08
44 15 0.41
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (43 bp):
TATATTGTTTCAAGCTTTTTTATTCATATTTTTAATTAATAAA
Found at i:28344324 original size:26 final size:26
Alignment explanation
Indices: 28344293--28344343 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
28344283 TTTGTATGTG
28344293 TATTTGAAATATTTCACATATAAAAA
1 TATTTGAAATATTTCACATATAAAAA
*
28344319 TATTTGAAATATTTTACATATAAAA
1 TATTTGAAATATTTCACATATAAAA
28344344 TAATAATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (26 bp):
TATTTGAAATATTTCACATATAAAAA
Found at i:28348701 original size:34 final size:38
Alignment explanation
Indices: 28348631--28348701 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 38
28348621 TACAGATGTC
* *
28348631 TAGGATTATAAGTTATCTTCAAGGTTTCAATTTAGGGA
1 TAGGATTATAAGTTATCTTCAAGGTTTAAATCTAGGGA
28348669 TAGGATTATAAG-T-T-TT-AAGGTTTAAATCTAGGG
1 TAGGATTATAAGTTATCTTCAAGGTTTAAATCTAGGG
28348702 GTAGTTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 15 0.48
35 2 0.06
36 1 0.03
37 1 0.03
38 12 0.39
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (38 bp):
TAGGATTATAAGTTATCTTCAAGGTTTAAATCTAGGGA
Found at i:28350214 original size:649 final size:649
Alignment explanation
Indices: 28348977--28350272 Score: 2565
Period size: 649 Copynumber: 2.0 Consensus size: 649
28348967 GGTCAAGGAA
28348977 GAGAAAATCAGAGTTAAGAAACATAATTGGCTGTGATACAATGTGTGAATAAAGATTTTTGTGTG
1 GAGAAAATCAGAGTTAAGAAACATAATTGGCTGTGATACAATGTGTGAATAAAGATTTTTGTGTG
28349042 CATTATATGTTAGTCTGTGATAGGAACTAGTGAGAGCCCAAATGGAGAGATTCTTGAAGGTGCCC
66 CATTATATGTTAGTCTGTGATAGGAACTAGTGAGAGCCCAAATGGAGAGATTCTTGAAGGTGCCC
28349107 AAAACTTGTTTAACTTACTGGAAGATAGTCTTGTTGGTGAATTTCATTTTGGTGAGGAAGAAAAC
131 AAAACTTGTTTAACTTACTGGAAGATAGTCTTGTTGGTGAATTTCATTTTGGTGAGGAAGAAAAC
28349172 CCTTCACGGTGCTGGTCTTGCAAATTGTGCAATACAAGGTTGATTGGAGGAGTGGTTGGTGCATG
196 CCTTCACGGTGCTGGTCTTGCAAATTGTGCAATACAAGGTTGATTGGAGGAGTGGTTGGTGCATG
28349237 CCCTTGAAATAAATGGGGGCAGAATTAAGACTCAGGTTGATTTTCATTGTAAGATGCATGTAGAA
261 CCCTTGAAATAAATGGGGGCAGAATTAAGACTCAGGTTGATTTTCATTGTAAGATGCATGTAGAA
*
28349302 GATTACCTGGATTGGGAAGCTAGTTTGGAGACTTATTTTGAGTTGAAACCTATAGTGGAGGCTAG
326 GATTACCTGGATTGGGAAGCTAGTTTGGAGAATTATTTTGAGTTGAAACCTATAGTGGAGGCTAG
28349367 GAAACTACTGTTTGTGAAACTAAAATTGAAAGGCACTGCGTTCCAATGGTGGAAGAGAGTTGAAG
391 GAAACTACTGTTTGTGAAACTAAAATTGAAAGGCACTGCGTTCCAATGGTGGAAGAGAGTTGAAG
28349432 AGCAACATGCATGTGTCACGATCTGCGCATGAAACATGCCCATGTAAGCCCAAAATCAGCACATG
456 AGCAACATGCATGTGTCACGATCTGCGCATGAAACATGCCCATGTAAGCCCAAAATCAGCACATG
*
28349497 GGAACCACACTGAAGCGAAATTGCACAAGCAGTTCCTACCAGCTGATTATGCAATAGAGTTTTTT
521 GGAACCACACTGAAGCGAAATTGCACAAGCAATTCCTACCAGCTGATTATGCAATAGAGTTTTTT
28349562 GAGAAGCTCCACTCATTAAGGCAGAAGGGATTGTCTGTGTACATTTCTTAACTTAACAATTTGT
586 GAGAAGCTCCACTCATTAAGGCAGAAGGGATTGTCTGTGTACATTTCTTAACTTAACAATTTGT
28349626 GAGAAAATCAGAGTTAAGAAACATAATTGGCTGTGATACAATGTGTGAATAAAGATTTTTGTGTG
1 GAGAAAATCAGAGTTAAGAAACATAATTGGCTGTGATACAATGTGTGAATAAAGATTTTTGTGTG
28349691 CATTATATGTTAGTCTGTGATAGGAACTAGTGAGAGCCCAAATGGAGAGATTCTTGAAGGTGCCC
66 CATTATATGTTAGTCTGTGATAGGAACTAGTGAGAGCCCAAATGGAGAGATTCTTGAAGGTGCCC
28349756 AAAACTTGTTTAACTTACTGGAAGATAGTCTTGTTGGTGAATTTCATTTTGGTGAGGAAGAAAAC
131 AAAACTTGTTTAACTTACTGGAAGATAGTCTTGTTGGTGAATTTCATTTTGGTGAGGAAGAAAAC
28349821 CCTTCACGGTGCTGGTCTTGCAAATTGTGCAATACAAGGTTGATTGGAGGAGTGGTTGGTGCATG
196 CCTTCACGGTGCTGGTCTTGCAAATTGTGCAATACAAGGTTGATTGGAGGAGTGGTTGGTGCATG
28349886 CCCTTGAAATAAATGGGGGCAGAATTAAGACTCAGGTTGATTTTCATTGTAAGATGCATGTAGAA
261 CCCTTGAAATAAATGGGGGCAGAATTAAGACTCAGGTTGATTTTCATTGTAAGATGCATGTAGAA
28349951 GATTACCTGGATTGGGAAGCTAGTTTGGAGAATTATTTTGAGTTGAAACCTATAGTGGAGGCTAG
326 GATTACCTGGATTGGGAAGCTAGTTTGGAGAATTATTTTGAGTTGAAACCTATAGTGGAGGCTAG
28350016 GAAACTACTGTTTGTGAAACTAAAATTGAAAGGCACTGCGTTCCAATGGTGGAAGAGAGTTGAAG
391 GAAACTACTGTTTGTGAAACTAAAATTGAAAGGCACTGCGTTCCAATGGTGGAAGAGAGTTGAAG
*
28350081 AGCAACATGCATGTGTCACGATCTGCGCATGAAACATGCCCATGTAAGCCCAAAATCAGCATATG
456 AGCAACATGCATGTGTCACGATCTGCGCATGAAACATGCCCATGTAAGCCCAAAATCAGCACATG
28350146 GGAACCACACTGAAGCGAAATTGCACAAGCAATTCCTACCAGCTGATTATGCAATAGAGTTTTTT
521 GGAACCACACTGAAGCGAAATTGCACAAGCAATTCCTACCAGCTGATTATGCAATAGAGTTTTTT
28350211 GAGAAGCTCCACTCATTAAGGCAGAAGGGATTGTCTGTGTACATTTCTTAACTTAACAATTT
586 GAGAAGCTCCACTCATTAAGGCAGAAGGGATTGTCTGTGTACATTTCTTAACTTAACAATTT
28350273 CCCTATTTGA
Statistics
Matches: 644, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
649 644 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (649 bp):
GAGAAAATCAGAGTTAAGAAACATAATTGGCTGTGATACAATGTGTGAATAAAGATTTTTGTGTG
CATTATATGTTAGTCTGTGATAGGAACTAGTGAGAGCCCAAATGGAGAGATTCTTGAAGGTGCCC
AAAACTTGTTTAACTTACTGGAAGATAGTCTTGTTGGTGAATTTCATTTTGGTGAGGAAGAAAAC
CCTTCACGGTGCTGGTCTTGCAAATTGTGCAATACAAGGTTGATTGGAGGAGTGGTTGGTGCATG
CCCTTGAAATAAATGGGGGCAGAATTAAGACTCAGGTTGATTTTCATTGTAAGATGCATGTAGAA
GATTACCTGGATTGGGAAGCTAGTTTGGAGAATTATTTTGAGTTGAAACCTATAGTGGAGGCTAG
GAAACTACTGTTTGTGAAACTAAAATTGAAAGGCACTGCGTTCCAATGGTGGAAGAGAGTTGAAG
AGCAACATGCATGTGTCACGATCTGCGCATGAAACATGCCCATGTAAGCCCAAAATCAGCACATG
GGAACCACACTGAAGCGAAATTGCACAAGCAATTCCTACCAGCTGATTATGCAATAGAGTTTTTT
GAGAAGCTCCACTCATTAAGGCAGAAGGGATTGTCTGTGTACATTTCTTAACTTAACAATTTGT
Found at i:28361864 original size:135 final size:137
Alignment explanation
Indices: 28361605--28361885 Score: 458
Period size: 135 Copynumber: 2.1 Consensus size: 137
28361595 GAGAACATAG
* *
28361605 ATATAATTAATATATGAATTTGATTAATACAAAATATTAATTGTATATATTTTATCGAATTTATT
1 ATATAATTAATATATGAATTTGATTAATACAAAATA-TAATTGTATATATTTTACCAAATTTATT
*
28361670 AATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATCAATATTCTTT
65 AATATAAACAAGTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATCAATATTCTTT
*
28361735 TGGAAAGA
130 TGGAAAAA
*
28361743 ATATAATTAATATATGAATTTGATTCATACAAAATA-AATTGTATATATTTTACCAAATTTATTA
1 ATATAATTAATATATGAATTTGATTAATACAAAATATAATTGTATATATTTTACCAAATTTATTA
* * *
28361807 ATATAAA-TAGTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTT
66 ATATAAACAAGTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATCAATATTCTTTT
28361871 GGAAAAA
131 GGAAAAA
*
28361878 AAATAATT
1 ATATAATT
28361886 TATTTTCTAA
Statistics
Matches: 134, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
135 66 0.49
136 33 0.25
138 35 0.26
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (137 bp):
ATATAATTAATATATGAATTTGATTAATACAAAATATAATTGTATATATTTTACCAAATTTATTA
ATATAAACAAGTATATTAATTAATTTCGGTCAAAATATAAAAGACATGAAAATCAATATTCTTTT
GGAAAAA
Found at i:28362205 original size:288 final size:287
Alignment explanation
Indices: 28361835--28362405 Score: 989
Period size: 288 Copynumber: 2.0 Consensus size: 287
28361825 TTAATTTCGG
28361835 TCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAAAAAATAATTTATTTTCTAACTTT
1 TCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAAAAAATAATTTATTTTCTAACTTT
28361900 CCATTTGCCTTCTCCATTAATAAAGGAATAATCCCGGTTTTCCTTTTTAATATGTGATATCAAAG
66 CCATTTGCCTTCTCCATTAATAAAGGAATAATCCCGGTTTTCCTTTTTAATATGTGATATCAAAG
* *
28361965 AGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGTTACCAACTTAATAATTTAAAAGGTCTAG
131 AGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGCTACCAACTTAATAATTTAAAAGGTCTAA
* *
28362030 CAACTGTTTTTAATTCTCTTTGAAAAGTTCAAAAGAAAGTGGTTGTTCGTTTTTAACTGGGTGGA
196 CAACTGTTTTTAATTCTCTTTAAAAAGTTCAAAAGAAAGTGGTTGTTCGTTTTTAACGGGGTGGA
*
28362095 CTATGTAAAGGCCGAGACATTTTATTT
261 CTACGTAAAGGCCGAGACATTTTATTT
* * * *
28362122 TCAAAATTATAAAAGGCATGGAAATTAATATTCTTTTGGAAAGAATATAATTTCTTTTCTAACTT
1 TCAAAA-TATAAAAGACATGGAAATTAATATTCTTTTGGAAAAAAAATAATTTATTTTCTAACTT
*
28362187 TCCATTTGCCTTCTCCATTAATAAAGGAATAGTCCCGGTTTTCCTTTTTAATATGTGATATCAAA
65 TCCATTTGCCTTCTCCATTAATAAAGGAATAATCCCGGTTTTCCTTTTTAATATGTGATATCAAA
28362252 GAGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGCTACCAACTTAATAATTTAAAAGGTCTA
130 GAGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGCTACCAACTTAATAATTTAAAAGGTCTA
* * * *
28362317 ACAATTGTTTTTAATTCTCTTTAAAAATTTCAAAATAAAGTGGTTGTTTGTTTTTAACGGGGTGG
195 ACAACTGTTTTTAATTCTCTTTAAAAAGTTCAAAAGAAAGTGGTTGTTCGTTTTTAACGGGGTGG
* *
28362382 ACTACGTAGAGGCTGAGACATTTT
260 ACTACGTAAAGGCCGAGACATTTT
28362406 CGTTGTGGCT
Statistics
Matches: 267, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
287 6 0.02
288 261 0.98
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (287 bp):
TCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAAAAAATAATTTATTTTCTAACTTT
CCATTTGCCTTCTCCATTAATAAAGGAATAATCCCGGTTTTCCTTTTTAATATGTGATATCAAAG
AGGATAAAAGGATGATAGTCCCTTAGTGTGTTAATGCTACCAACTTAATAATTTAAAAGGTCTAA
CAACTGTTTTTAATTCTCTTTAAAAAGTTCAAAAGAAAGTGGTTGTTCGTTTTTAACGGGGTGGA
CTACGTAAAGGCCGAGACATTTTATTT
Found at i:28365202 original size:75 final size:75
Alignment explanation
Indices: 28365069--28365213 Score: 209
Period size: 75 Copynumber: 1.9 Consensus size: 75
28365059 ATGGAAAGCA
* ** * * *
28365069 ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCCCTTTGCATTCTTTATTAATAAGG
1 ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCCATCAGCATTATCTATTAATAAGA
28365134 GAATAATCCT
66 GAATAATCCT
* * *
28365144 ATATTCTTTTGGAAAGAATATATTTGATTTTTCTAACTTTCCATCAGCCTTATCTATTAATAAGA
1 ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCCATCAGCATTATCTATTAATAAGA
28365209 GAATA
66 GAATA
28365214 TTTTTGGTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (75 bp):
ATATTCTTTTGGAAAGAATATAATTCATTTTTCTAACTTTCCATCAGCATTATCTATTAATAAGA
GAATAATCCT
Found at i:28366464 original size:51 final size:53
Alignment explanation
Indices: 28366344--28366528 Score: 181
Period size: 51 Copynumber: 3.6 Consensus size: 53
28366334 AAAGTGCTGG
* *** *
28366344 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTAC--CAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACATCAGATAGTGAT-GA
* * * *
28366394 TCGCATGTGTAGTACTATGTGGAGGCTACTATGCGTAC-T-GGATAGCT-TTGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACATCAGATAG-TGATGA
* * *
28366445 TCACGTGTGTAGTACTATGTGCAGGCTACTA--CGTGCATCAGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACATCAGATAGTGATGA
28366496 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
28366529 TGAACCGGTA
Statistics
Matches: 109, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
49 4 0.04
50 36 0.33
51 67 0.61
52 1 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (53 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACATCAGATAGTGATGA
Found at i:28366464 original size:101 final size:102
Alignment explanation
Indices: 28366344--28366528 Score: 302
Period size: 101 Copynumber: 1.8 Consensus size: 102
28366334 AAAGTGCTGG
* *
28366344 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGCACCAGATAGTGAT-GGTCACATGTGTAGT
*
28366407 ACTATGTGGAGGCTACTATGCGTACTGGATAGCTTTGA
65 ACTATGTGCAGGCTACTATGCGTACTGGATAGCTTTGA
* *
28366445 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGCATCAGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGCACCAGATAGTGATGGTCACATGTGTAGTA
28366510 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
28366529 TGAACCGGTA
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
101 39 0.51
102 34 0.44
103 4 0.05
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACATGCACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACTGGATAGCTTTGA
Found at i:28366567 original size:101 final size:100
Alignment explanation
Indices: 28366346--28366536 Score: 258
Period size: 102 Copynumber: 1.9 Consensus size: 100
28366336 AGTGCTGGTC
* *
28366346 ACGTGTGTAGTACTATGTGCAGGCTACTACATGTACCAGAATGATAGGTCGCATGTGTAGTACTA
1 ACGTGTGTA-TACTATGTGCAGGCTACTACATGCACCAGAATGATAGGTCACATGTGTAGTACTA
* * * *
28366411 TGTGGAGGCTACTATGCGTACTGGATAGCTTTGATC
65 TGTGCAGGCTACTATGCGAACCGGATAGCTTTGATA
* *
28366447 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGCATCAGATAGTGAT-GGTCACATGTGTAGTAC
1 ACGTGTGTA-TACTATGTGCAGGCTACTACATGCACCAGA-A-TGATAGGTCACATGTGTAGTAC
*
28366511 TATGTGCAGGCTACTATGTGAACCGG
63 TATGTGCAGGCTACTATGCGAACCGG
28366537 TATCATTAAT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 37 0.46
102 39 0.49
103 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (100 bp):
ACGTGTGTATACTATGTGCAGGCTACTACATGCACCAGAATGATAGGTCACATGTGTAGTACTAT
GTGCAGGCTACTATGCGAACCGGATAGCTTTGATA
Found at i:28366775 original size:16 final size:16
Alignment explanation
Indices: 28366754--28366785 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28366744 TGATTGAAAG
*
28366754 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
28366770 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
28366786 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:28373283 original size:16 final size:16
Alignment explanation
Indices: 28373262--28373330 Score: 129
Period size: 16 Copynumber: 4.3 Consensus size: 16
28373252 TTTGGTTCGC
28373262 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28373278 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28373294 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
28373310 AGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28373326 TGTAT
1 TGTAT
28373331 AGCAAATCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28373585 original size:18 final size:17
Alignment explanation
Indices: 28373564--28373598 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28373554 TTATTATTAA
*
28373564 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28373582 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28373599 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28373664 original size:157 final size:157
Alignment explanation
Indices: 28373455--28373767 Score: 563
Period size: 157 Copynumber: 2.0 Consensus size: 157
28373445 ATACCCTTAG
* * *
28373455 CATAAATTTGTTTTGGTAAATGATTATTGTTTTTGTTATTTAAATTTTAATAAGATTATTATTAT
1 CATAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATAT
* *
28373520 CAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
66 CAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATA
28373585 TAATTTAATAAAATTCTTAATAATTAC
131 TAATTTAATAAAATTCTTAATAATTAC
*
28373612 CATAAATTTATTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATAT
1 CATAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATAT
28373677 CAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATA
66 CAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATA
*
28373742 TAATTTAATAAAGTTCTTAATAATTA
131 TAATTTAATAAAATTCTTAATAATTA
28373768 ATATTCTTAT
Statistics
Matches: 149, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 149 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (157 bp):
CATAAATTTATTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATAT
CAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATA
TAATTTAATAAAATTCTTAATAATTAC
Found at i:28373738 original size:16 final size:16
Alignment explanation
Indices: 28373701--28373742 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28373691 TTAATCATAT
*
28373701 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28373717 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28373732 TTAAAATATAT
1 TTAAAATATAT
28373743 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28373749 original size:14 final size:15
Alignment explanation
Indices: 28373710--28373751 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28373700 TTTAAACATA
*
28373710 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28373725 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28373739 A-TATAATTTAATA
1 ATTATAATTAAATA
28373752 AAGTTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28373764 original size:82 final size:81
Alignment explanation
Indices: 28373521--28373770 Score: 213
Period size: 76 Copynumber: 3.1 Consensus size: 81
28373511 TATTATTATC
* *
28373521 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
28373586 AATTTAATAAAATTCTT
66 AATTTAAT-AAATTCTT
* * * * *
28373603 AATAATTACCATAAATTT-AT--T-TTGGT-AA-ATTATTATTGTT--AT-TGTTAT--TTAAAT
1 AATAA-TA-AAT-AATTTAATCATATT--TAAACATAATTATTATTAAATATATTATAATTAAAA
* * *
28373657 TTTAATAAGATT-ATTAATATC--
61 TAT-ATAA-TTTAATAAAT-TCTT
28373678 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
28373743 AATTTAATAAAGTTCTT
66 AATTTAATAAA-TTCTT
*
28373760 AATAATTAATA
1 AATAATAAATA
28373771 TTCTTATATG
Statistics
Matches: 126, Mismatches: 19, Indels: 46
0.66 0.10 0.24
Matches are distributed among these distances:
72 5 0.04
73 4 0.03
74 3 0.02
75 8 0.06
76 22 0.17
77 8 0.06
78 8 0.06
79 9 0.07
80 10 0.08
81 20 0.16
82 18 0.14
83 3 0.02
84 4 0.03
85 4 0.03
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (81 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
AATTTAATAAATTCTT
Found at i:28373851 original size:157 final size:158
Alignment explanation
Indices: 28373502--28373852 Score: 366
Period size: 157 Copynumber: 2.2 Consensus size: 158
28373492 ATTTAAATTT
* *
28373502 TAATAAGATTATTATTATCAATAAT-AA-ATATTTTAATCATATTTAAACATAATTATTATTAAA
1 TAATAAGATAATTAATATCAATAATAAATATATTTTAATCATATTTAAACATAATTATTATTAAA
* *
28373565 TATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTACCATAAATTTATTTTGGTA
66 TATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTA-CATAAATTTATTATGGTA
* * ** * * * * *
28373630 AATTATTATTGTTATTGTTATTTAAATTT
130 AATTATAAATCATAATGATATTGAAACTA
*
28373659 TAATAAGATTATTAATATCAATAATAAATA-A-TTTAATCATATTTAAACATAATTATTATTAAA
1 TAATAAGATAATTAATATCAATAATAAATATATTTTAATCATATTTAAACATAATTATTATTAAA
* *
28373722 TATATTATAATTAAAATATATAATTTAATAAAGTTCTTAATAATTA-AT-ATTCTTA-TAT-G-A
66 TATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTACATAAAT-TTATTATGGTA
* *
28373782 ATTTACTCAAATCATAAT-ATA-TGATACTA
130 AATTA-T-AAATCATAATGATATTGAAACTA
* *
28373811 TAA-AAGATAATTTGAAATAATTAATATTAAATATATTTTAAT
1 TAATAAGATAA-TT--AAT-ATCAATAATAAATATATTTTAAT
28373853 TAAAATATAT
Statistics
Matches: 164, Mismatches: 19, Indels: 22
0.80 0.09 0.11
Matches are distributed among these distances:
151 6 0.04
152 14 0.09
153 4 0.02
154 12 0.07
155 17 0.10
156 1 0.01
157 106 0.65
158 3 0.02
159 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (158 bp):
TAATAAGATAATTAATATCAATAATAAATATATTTTAATCATATTTAAACATAATTATTATTAAA
TATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTACATAAATTTATTATGGTAA
ATTATAAATCATAATGATATTGAAACTA
Found at i:28376862 original size:51 final size:51
Alignment explanation
Indices: 28376781--28376894 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 51
28376771 TATACCATCT
* * * **
28376781 AGAAACACACCTAGGCATTGAGTGCCAAGCCTGTAGGCTACACATCCCTCC
1 AGAAACACACCTGGGCATTGAATGCAAAGCCCATAGGCTACACATCCCTCC
*
28376832 AGAAACACACCTGGGCATTGAATGCAAAGCCCATAGGCTACACATCTCTCC
1 AGAAACACACCTGGGCATTGAATGCAAAGCCCATAGGCTACACATCCCTCC
28376883 A-AAACACACCTG
1 AGAAACACACCTG
28376895 AATCTCCATA
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 11 0.19
51 46 0.81
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.17
Consensus pattern (51 bp):
AGAAACACACCTGGGCATTGAATGCAAAGCCCATAGGCTACACATCCCTCC
Found at i:28384275 original size:16 final size:16
Alignment explanation
Indices: 28384250--28384285 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
28384240 AGCAAGAAAA
28384250 ACAA-AACCCATGTTC
1 ACAATAACCCATGTTC
28384265 ACAATAACCCATGTTC
1 ACAATAACCCATGTTC
28384281 ACAAT
1 ACAAT
28384286 TTGACTATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.42, C:0.31, G:0.06, T:0.22
Consensus pattern (16 bp):
ACAATAACCCATGTTC
Found at i:28410478 original size:13 final size:13
Alignment explanation
Indices: 28410447--28410586 Score: 63
Period size: 13 Copynumber: 10.5 Consensus size: 13
28410437 TATCTTTTTC
*
28410447 CATATAACCAGTT
1 CATATAACCATTT
* *
28410460 CGTATAACTATTT
1 CATATAACCATTT
*
28410473 CATAT-ATCATTTTT
1 CATATAACCA--TTT
28410487 CATATAACCGATTT
1 CATATAACC-ATTT
*
28410501 -GTATAACCATTT
1 CATATAACCATTT
* ***
28410513 TATATATTTATTT
1 CATATAACCATTT
*
28410526 CTATATAACCAATT
1 C-ATATAACCATTT
*
28410540 CATAT-ATCATTTTTT
1 CATATAACCA---TTT
* *
28410555 TAGATAACCGATTT
1 CATATAACC-ATTT
28410569 -ATATAACCATTT
1 CATATAACCATTT
28410581 CATATA
1 CATATA
28410587 TTTATTTTCA
Statistics
Matches: 92, Mismatches: 23, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
12 13 0.14
13 45 0.49
14 23 0.25
15 7 0.08
16 3 0.03
17 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (13 bp):
CATATAACCATTT
Found at i:28410491 original size:40 final size:39
Alignment explanation
Indices: 28410427--28410545 Score: 134
Period size: 40 Copynumber: 3.0 Consensus size: 39
28410417 ATCCAGTGTT
28410427 CCATTTTATATATCTTTTTCCATATAACCAGTTCGTATAA
1 CCATTTTATATATCTTTTT-CATATAACCAGTTCGTATAA
* * *
28410467 CTATTTCATATATCATTTTTCATATAACC-GATTTGTATAA
1 CCATTTTATATATC-TTTTTCATATAACCAG-TTCGTATAA
* *
28410507 CCATTTTATATAT-TTATTTCTATATAACCAATTCATATA
1 CCATTTTATATATCTT-TTTC-ATATAACCAGTTCGTATA
28410546 TCATTTTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 54 0.82
41 5 0.08
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (39 bp):
CCATTTTATATATCTTTTTCATATAACCAGTTCGTATAA
Found at i:28410563 original size:28 final size:29
Alignment explanation
Indices: 28410513--28410573 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
28410503 ATAACCATTT
*
28410513 TATATATTTATTTCTATATAACCAATTCA
1 TATATATTTATTTCTAGATAACCAATTCA
* *
28410542 TATATCATTT-TTT-TAGATAACCGATTTA
1 TATAT-ATTTATTTCTAGATAACCAATTCA
28410570 TATA
1 TATA
28410574 ACCATTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 16 0.57
29 8 0.29
30 4 0.14
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.49
Consensus pattern (29 bp):
TATATATTTATTTCTAGATAACCAATTCA
Done.