Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 19 of 20
Found at i:3660762 original size:71 final size:71
Alignment explanation
Indices: 3660672--3660813 Score: 207
Period size: 71 Copynumber: 2.0 Consensus size: 71
3660662 TTGAGAATTT
* * * *
3660672 TAAAACAAATTTTTGTCTCGCTTGAGATAATTT-TTCTCAAAACAAATTTTGACTCGCTTGAGAC
1 TAAAACAAATTTTTATCTCGCTTGAGACAATTTCTT-TCAAAACAAATTTCGACTCACTTGAGAC
3660736 ATTTTTC
65 ATTTTTC
*
3660743 TAAAAGCAAA-TTTTATCTCGCTTGAGACAATTTCTTTCAAAACAAATTTCGTCTCACTTGAGAC
1 TAAAA-CAAATTTTTATCTCGCTTGAGACAATTTCTTTCAAAACAAATTTCGACTCACTTGAGAC
3660807 ATTTTTC
65 ATTTTTC
3660814 CTTTGAGACA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
71 58 0.91
72 6 0.09
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (71 bp):
TAAAACAAATTTTTATCTCGCTTGAGACAATTTCTTTCAAAACAAATTTCGACTCACTTGAGACA
TTTTTC
Found at i:3661029 original size:106 final size:105
Alignment explanation
Indices: 3660772--3661086 Score: 393
Period size: 106 Copynumber: 3.0 Consensus size: 105
3660762 GCTTGAGACA
* * * *
3660772 ATTTCTTTCAAAACAAATTTCGTCTCACTTGAGACATTTTTCCTTTGAGACACAAAATTTGAATT
1 ATTTTTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATT
*
3660837 TGTTTCACATTAAACAAAGTTGATCTCATTTGAGATCGGT
66 TGTTTCACATTAAACAAAGTTGATCTCACTTGAGATCGGT
* * * * *
3660877 -TTCTCTT-AAAACAAACTTCGTCTTGCTTGAGACATTTTTTTCCTTTGATATACAAATTTTGAA
1 ATTTTTTTCAAAACAAATTTCGTCTCGCTTGAGACA--TTTTTCCTTTGAGATACAAATTTTGAA
* * * * * *
3660940 CTTGATTCAC-TTGAAACAGAAATTAATCTCACTTGAGATTGTT
64 TTTGTTTCACATT-AAACA-AAGTTGATCTCACTTGAGATCGGT
* * *
3660983 ATTTTTTTCAAAACAAATTTTGTCTCGTTTGAGGCATTTTTCCTTTGAGATACAAATTTTGAATT
1 ATTTTTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATT
3661048 TGTTTTCACATTAAACAAAGTTGATCTCACTTGAGATCG
66 TG-TTTCACATTAAACAAAGTTGATCTCACTTGAGATCG
3661087 TTTTCTCAAA
Statistics
Matches: 173, Mismatches: 29, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
103 24 0.14
104 6 0.03
105 37 0.21
106 67 0.39
107 15 0.09
108 24 0.14
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (105 bp):
ATTTTTTTCAAAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATT
TGTTTCACATTAAACAAAGTTGATCTCACTTGAGATCGGT
Found at i:3661101 original size:36 final size:36
Alignment explanation
Indices: 3661060--3661162 Score: 95
Period size: 36 Copynumber: 2.8 Consensus size: 36
3661050 TTTTCACATT
**
3661060 AAACAAAGTTGATCTCACTTGAGATCGTTTTCTC-AA
1 AAACAAAGTTG-TCTCACTTGAGATCAATTTCTCTAA
** **
3661096 AAACAATTTTTTGTCTCGTTTGAGA-CAATTTCTCTAA
1 AAACAA--AGTTGTCTCACTTGAGATCAATTTCTCTAA
3661133 AAACAAATGTTGTCTCACTTGAGAT-AATTT
1 AAACAAA-GTTGTCTCACTTGAGATCAATTT
3661163 TCCAAATTAT
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
36 31 0.60
37 18 0.35
38 3 0.06
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.38
Consensus pattern (36 bp):
AAACAAAGTTGTCTCACTTGAGATCAATTTCTCTAA
Found at i:3661552 original size:30 final size:32
Alignment explanation
Indices: 3661513--3661591 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 32
3661503 TTTAAGACAA
*
3661513 TTTCTCTTAAAACAAA-C-ATCTTTGGGATTG
1 TTTCTCTTAAAACAAACCTATCTTTGAGATTG
* *
3661543 TTTCCCTTAAAACAAAACCTATCTTTGAGTTTG
1 TTTCTCTTAAAAC-AAACCTATCTTTGAGATTG
*
3661576 TTTCTCTTGAAACAAA
1 TTTCTCTTAAAACAAA
3661592 AGTCTATGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 12 0.29
31 3 0.07
32 4 0.10
33 22 0.54
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (32 bp):
TTTCTCTTAAAACAAACCTATCTTTGAGATTG
Found at i:3661577 original size:33 final size:31
Alignment explanation
Indices: 3661513--3661638 Score: 118
Period size: 29 Copynumber: 4.2 Consensus size: 31
3661503 TTTAAGACAA
*
3661513 TTTCTCTTAAAAC-AAACATCTTTGGGATTG
1 TTTCTCTTAAAACAAAACATCTTTGAGATTG
* *
3661543 TTTCCCTTAAAACAAAACCTATCTTTGAGTTTG
1 TTTCTCTTAAAACAAAA-C-ATCTTTGAGATTG
* * *
3661576 TTTCTCTTGAAACAAAA-GTCTATGAG-TTG
1 TTTCTCTTAAAACAAAACATCTTTGAGATTG
* * *
3661605 TTTCTTTTGAAATAAAA-ATCTTTGAG-TTG
1 TTTCTCTTAAAACAAAACATCTTTGAGATTG
3661634 TTTCT
1 TTTCT
3661639 TTTGAAAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
29 33 0.40
30 19 0.23
31 3 0.04
32 1 0.01
33 26 0.32
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (31 bp):
TTTCTCTTAAAACAAAACATCTTTGAGATTG
Found at i:3661607 original size:29 final size:29
Alignment explanation
Indices: 3661563--3661677 Score: 117
Period size: 29 Copynumber: 4.0 Consensus size: 29
3661553 AACAAAACCT
* *
3661563 ATCTTTGAGTTTGTTTCTCTTGAAACAAAA
1 ATCTATGAG-TTGTTTCTTTTGAAACAAAA
* *
3661593 GTCTATGAGTTGTTTCTTTTGAAATAAAA
1 ATCTATGAGTTGTTTCTTTTGAAACAAAA
*
3661622 ATCTTTGAGTTGTTTCTTTTG-AA-AAAA
1 ATCTATGAGTTGTTTCTTTTGAAACAAAA
* * * *
3661649 TTCTTTGAGTCTATTTCTTTTGAACCAAA
1 ATCTATGAGT-TGTTTCTTTTGAAACAAA
3661678 GTTTTGTTTC
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 13 0.18
28 12 0.16
29 38 0.52
30 10 0.14
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (29 bp):
ATCTATGAGTTGTTTCTTTTGAAACAAAA
Found at i:3661743 original size:29 final size:28
Alignment explanation
Indices: 3661711--3661777 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 28
3661701 TTGTGAAAAA
3661711 AAAACCTTTGAGTC-ATTTCTTTTGAAACC
1 AAAA-CTTTGAGTCTATTTCTTTTGAAA-C
3661740 AAAATCTTTGAGTCTATTTCTTTTGAAAC
1 AAAA-CTTTGAGTCTATTTCTTTTGAAAC
3661769 AAAACTTTG
1 AAAACTTTG
3661778 TCTCTCTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
28 5 0.14
29 18 0.50
30 13 0.36
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.40
Consensus pattern (28 bp):
AAAACTTTGAGTCTATTTCTTTTGAAAC
Found at i:3662416 original size:134 final size:134
Alignment explanation
Indices: 3662040--3662421 Score: 448
Period size: 134 Copynumber: 2.9 Consensus size: 134
3662030 AATCATTATC
*** * *
3662040 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAATTGTGTCATCTCCT-GACCATATCTCTTCA
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATC-CCTCGACCAGATCTCATCA
* * * *
3662104 TCATGTAGGAGTCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCATGTTATCA
65 TCACGTAGGAGCCGTGTCACCCATAGATAACCAGACGTCCTCATCACGTAGGAACCAAGTTATCA
3662169 CCTTA
130 CCTTA
* * * * *
3662174 CCTAAAGATGGCCAGAACTCTTCATCACGTATTAGCCGTGTCATCCCCCAACTAGATCTCATCAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCAGATCTCATCAT
* * * * * * *
3662239 CGCGTTGGAGCCATGTCAACCATAGATAACCAGCCTTCCTCATCGC-TAGGAACCAAGTTATCAC
66 CACGTAGGAGCCGTGTCACCCATAGATAACCAGACGTCCTCATCACGTAGGAACCAAGTTATCA-
3662303 CCTT-
130 CCTTA
* *
3662307 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCAGATTTCCTCA
1 CCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCAGATCTCATCA
* * * * *
3662372 TCACGTAGGAACCGTGTCACCCTTAGACAACCCAAAC-TCTTCATCACGTA
65 TCACGTAGGAGCCGTGTCACCCATAGATAA-CCAGACGTCCTCATCACGTA
3662422 TGAGAAGTGT
Statistics
Matches: 205, Mismatches: 38, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
133 31 0.15
134 168 0.82
135 6 0.03
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (134 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCAGATCTCATCAT
CACGTAGGAGCCGTGTCACCCATAGATAACCAGACGTCCTCATCACGTAGGAACCAAGTTATCAC
CTTA
Found at i:3662598 original size:3 final size:3
Alignment explanation
Indices: 3662587--3662616 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3662577 GGTCTTTTTT
3662587 TTA TATA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
3662617 TAACTTACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3664605 original size:10 final size:9
Alignment explanation
Indices: 3664581--3664614 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3664571 AAATCTGGAA
*
3664581 ACCGGTTTA
1 ACCGGTTTG
3664590 ACCGGTTTTG
1 ACCGG-TTTG
3664600 ACCGGTTTG
1 ACCGGTTTG
3664609 ACCGGT
1 ACCGGT
3664615 CACGACCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.15, C:0.24, G:0.29, T:0.32
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:3664654 original size:18 final size:18
Alignment explanation
Indices: 3664617--3664690 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 18
3664607 TGACCGGTCA
3664617 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
3664635 CGA----A-CTGTTGACC
1 CGACCCGACCCGTTGACC
3664648 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
* * *
3664666 TGACCTGACCCGTTGACA
1 CGACCCGACCCGTTGACC
3664684 CGACCCG
1 CGACCCG
3664691 TTGACCGTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
13 11 0.25
14 1 0.02
17 1 0.02
18 31 0.70
ACGTcount: A:0.19, C:0.43, G:0.23, T:0.15
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:3664665 original size:13 final size:13
Alignment explanation
Indices: 3664618--3664654 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3664608 GACCGGTCAC
3664618 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
3664631 GACCCGAACTGTT
1 GACCCGACCCGTT
3664644 GACCCGACCCG
1 GACCCGACCCG
3664655 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.43, G:0.24, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3664806 original size:29 final size:29
Alignment explanation
Indices: 3664733--3664800 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
3664723 ATTCGATTTT
*
3664733 GGTGCTATTTTGGGAATTAATTCAAAAAG
1 GGTGCTATTTTGGTAATTAATTCAAAAAG
* * *
3664762 GGTGTTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGTAATTAATTCAAAAAG
3664791 GGTGCTATTT
1 GGTGCTATTT
3664801 GTGTAAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTAATTCAAAAAG
Found at i:3665839 original size:42 final size:42
Alignment explanation
Indices: 3665727--3666059 Score: 438
Period size: 42 Copynumber: 7.8 Consensus size: 42
3665717 GATGTATTAT
* * *
3665727 CAGGTCCCTTTGCTATGTTCAAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTAC
*
3665769 CAGGTCCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTAC
3665812 CAGGTCCCTTTGCTGTGTGCGAA-GGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGTTTAC
*
3665854 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTAC
*
3665896 CAGGTCCATTTGCTGTGTGCGAA-GGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGTTTAC
*
3665938 CAGGTCCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCC-TTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTAC
* * * * * *
3665981 CAGGTCCCTTTGTTGTGTGCAATGATAAACCTTATAGTTTTC
1 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTAC
* * *
3666023 CTAGG-CTCCTCTGCTTTGTGCATAGGTTAAGCCTTAC
1 C-AGGTC-CCTTTGCTGTGTGCA-AGGGTAAGCCTTAC
3666060 TGGTGTATAG
Statistics
Matches: 259, Mismatches: 23, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
41 2 0.01
42 152 0.59
43 95 0.37
44 10 0.04
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (42 bp):
CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTAC
Found at i:3665998 original size:85 final size:85
Alignment explanation
Indices: 3665727--3666000 Score: 496
Period size: 85 Copynumber: 3.2 Consensus size: 85
3665717 GATGTATTAT
* * *
3665727 CAGGTCCCTTTGCTATGTTCAAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
3665792 GGGTAAGCCTTACAGTTTCC
66 GGGTAAGCCTTACAGTTTCC
3665812 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCC-TTTGCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
3665876 GGGTAAGCCTTACAGTTTCC
66 GGGTAAGCCTTACAGTTTCC
*
3665896 CAGGTCCATTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
3665961 GGGTAAGCCTTACAGTTTCC
66 GGGTAAGCCTTACAGTTTCC
*
3665981 CAGGTCCCTTTGTTGTGTGC
1 CAGGTCCCTTTGCTGTGTGC
3666001 AATGATAAAC
Statistics
Matches: 182, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
84 83 0.46
85 99 0.54
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.32
Consensus pattern (85 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
GGGTAAGCCTTACAGTTTCC
Found at i:3666014 original size:85 final size:84
Alignment explanation
Indices: 3665727--3666059 Score: 490
Period size: 85 Copynumber: 3.9 Consensus size: 84
3665717 GATGTATTAT
* * *
3665727 CAGGTCCCTTTGCTATGTTCAAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCC-TTTGCTGTGTGCAA
3665792 GGGTAAGCCTTACAGTTTCC
65 GGGTAAGCCTTACAGTTTCC
3665812 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
3665877 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
*
3665896 CAGGTCCATTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCC-TTTGCTGTGTGCAA
3665961 GGGTAAGCCTTACAGTTTCC
65 GGGTAAGCCTTACAGTTTCC
* * * * * * *
3665981 CAGGTCCCTTTGTTGTGTGC-AATGATAAACCTTATAGTTTTCCTAGG-CTCCTCTGCTTTGTGC
1 CAGGTCCCTTTGCTGTGTGCGAA-GGTAAGCCTTACAGTTTACC-AGGTC-CCTTTGCTGTGTGC
*
3666044 ATAGGTTAAGCCTTAC
63 A-AGGGTAAGCCTTAC
3666060 TGGTGTATAG
Statistics
Matches: 230, Mismatches: 13, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
84 85 0.37
85 127 0.55
86 18 0.08
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (84 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
GGTAAGCCTTACAGTTTCC
Found at i:3672155 original size:13 final size:13
Alignment explanation
Indices: 3672137--3672168 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3672127 GACCGGTCAC
*
3672137 GACCCGACCCGTT
1 GACCCGAACCGTT
3672150 GACCCGAACCGTT
1 GACCCGAACCGTT
3672163 GACCCG
1 GACCCG
3672169 TTGACCGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.44, G:0.25, T:0.12
Consensus pattern (13 bp):
GACCCGAACCGTT
Found at i:3672243 original size:29 final size:29
Alignment explanation
Indices: 3672211--3672278 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
3672201 ATTCGATTTT
3672211 GGTGCTATTTTCAG-AATTAAT-TCAAAAAG
1 GGTGCTATTTT-AGTAATT-ATCTCAAAAAG
* *
3672240 GGTGCTATTTTGGTAATTATCTTAAAAAG
1 GGTGCTATTTTAGTAATTATCTCAAAAAG
3672269 GGTGCTATTT
1 GGTGCTATTT
3672279 GTGTAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 3 0.09
29 32 0.91
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTAGTAATTATCTCAAAAAG
Found at i:3673263 original size:42 final size:41
Alignment explanation
Indices: 3673216--3673548 Score: 461
Period size: 42 Copynumber: 7.8 Consensus size: 41
3673206 GAAGTATTAT
*
3673216 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
3673258 CAGGTCCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCC-TTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
3673301 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
3673343 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
3673385 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
3673427 CAGGTCCCTTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCC-TTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
* * *
3673470 CAGGTCCCTTTGTTGTGTGCAAGGATAAACCTTACAGTTTTC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTTAC
* *
3673512 CTAGG-CTCCTCTGCTTTGTGCATAGGTTAAGCCTTAC
1 C-AGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
3673549 TGGTGTATAG
Statistics
Matches: 266, Mismatches: 14, Indels: 20
0.89 0.05 0.07
Matches are distributed among these distances:
41 4 0.02
42 156 0.59
43 94 0.35
44 12 0.05
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
Found at i:3673503 original size:85 final size:84
Alignment explanation
Indices: 3673216--3673548 Score: 535
Period size: 85 Copynumber: 3.9 Consensus size: 84
3673206 GAAGTATTAT
*
3673216 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCC-TTTGCTGTGTGCAA
3673281 GGGTAAGCCTTACAGTTTCC
65 GGGTAAGCCTTACAGTTTCC
3673301 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
3673366 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
3673385 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCC-TTTGCTGTGTGCAA
3673450 GGGTAAGCCTTACAGTTTCC
65 GGGTAAGCCTTACAGTTTCC
* * * * *
3673470 CAGGTCCCTTTGTTGTGTGC-AAGGATAAACCTTACAGTTTTCCTAGG-CTCCTCTGCTTTGTGC
1 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTTACC-AGGTC-CCTTTGCTGTGTGC
*
3673533 ATAGGTTAAGCCTTAC
63 A-AGGGTAAGCCTTAC
3673549 TGGTGTATAG
Statistics
Matches: 236, Mismatches: 7, Indels: 9
0.94 0.03 0.04
Matches are distributed among these distances:
84 88 0.37
85 130 0.55
86 18 0.08
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (84 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
GGTAAGCCTTACAGTTTCC
Found at i:3673505 original size:169 final size:171
Alignment explanation
Indices: 3673216--3673548 Score: 557
Period size: 169 Copynumber: 2.0 Consensus size: 171
3673206 GAAGTATTAT
*
3673216 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
*
3673281 GGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACC-A
66 GGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCGAAGGTAAACCTTACAGTTTACCTA
*
3673345 GG-TCCCTTTGCTGTGTGCA-AGGGTAAGCCTTACAGTTTCC
131 GGCT-CCTCTGCTGTGTGCATAGGGTAAGCCTTACAGTTTCC
3673385 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
* *
3673450 GGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGTTGTGTGC-AAGGATAAACCTTACAGTTTTCCT
66 GGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCGAAGG-TAAACCTTACAGTTTACCT
* *
3673514 AGGCTCCTCTGCTTTGTGCATAGGTTAAGCCTTAC
130 AGGCTCCTCTGCTGTGTGCATAGGGTAAGCCTTAC
3673549 TGGTGTATAG
Statistics
Matches: 153, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
168 4 0.03
169 119 0.78
170 16 0.10
171 14 0.09
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (171 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTTGCTGTGTGCAA
GGGTAAGCCTTACAGTTTCCCAGGTCCCTTTGCTGTGTGCGAAGGTAAACCTTACAGTTTACCTA
GGCTCCTCTGCTGTGTGCATAGGGTAAGCCTTACAGTTTCC
Found at i:3674087 original size:29 final size:27
Alignment explanation
Indices: 3674050--3674103 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
3674040 TTTCTATTTG
*
3674050 TTTCATTTTTAATATAATATTTGTTCATA
1 TTTCA-TTTTAAT-CAATATTTGTTCATA
* *
3674079 TTTCGTTTTAATCACTATTTGTTCA
1 TTTCATTTTAATCAATATTTGTTCA
3674104 CTAATATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 11 0.50
28 7 0.32
29 4 0.18
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (27 bp):
TTTCATTTTAATCAATATTTGTTCATA
Found at i:3680124 original size:19 final size:19
Alignment explanation
Indices: 3680097--3680194 Score: 115
Period size: 19 Copynumber: 5.1 Consensus size: 19
3680087 AATTCGCAAC
**
3680097 ACTGAATTTCAAATTTGCA
1 ACTGAATTTCAAATTCACA
* *
3680116 ACTGTATTTTAAATTCACA
1 ACTGAATTTCAAATTCACA
3680135 ACTGAATTTCAAATTCACA
1 ACTGAATTTCAAATTCACA
*
3680154 ACTGAATTTCAAATTCGCA
1 ACTGAATTTCAAATTCACA
* * *
3680173 ACTCGATTTTCGAATTCGCA
1 ACT-GAATTTCAAATTCACA
3680193 AC
1 AC
3680195 ACGAATTTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
19 53 0.77
20 16 0.23
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (19 bp):
ACTGAATTTCAAATTCACA
Found at i:3680211 original size:19 final size:20
Alignment explanation
Indices: 3679825--3680214 Score: 165
Period size: 20 Copynumber: 19.6 Consensus size: 20
3679815 AAATGACCAA
* * *
3679825 CAAATTCGCAACGCGAACTC
1 CAAATTCGCAACACGAATTT
* *
3679845 CAATTTCGCAAGC-C-AGTTT
1 CAAATTCGCAA-CACGAATTT
* *
3679864 CCAAATTCGCATCGCGAATTT
1 -CAAATTCGCAACACGAATTT
* *
3679885 GTAAA-TCGCAACACGGAA-GT
1 -CAAATTCGCAACAC-GAATTT
* *
3679905 CAAATTCGCAACGCG-ATAGT
1 CAAATTCGCAACACGAAT-TT
*
3679925 CAAATTCGCAACACTGAA-GT
1 CAAATTCGCAACAC-GAATTT
* *
3679945 CAAATTCGCAACGCGGATCTGT
1 CAAATTCGCAACACGAAT-T-T
*
3679967 -AAA-TCGCAACGCGAATCTGT
1 CAAATTCGCAACACGAAT-T-T
**
3679987 -AAA-TCGCAACGTGAATCTGT
1 CAAATTCGCAACACGAAT-T-T
*
3680007 -AAA-TCGCAACGCGAATCTGT
1 CAAATTCGCAACACGAAT-T-T
*
3680027 -AAA-TCGCAACACAGAA-GT
1 CAAATTCGCAACAC-GAATTT
**
3680045 CAAATTCGCAACAC-ATAAGT
1 CAAATTCGCAACACGA-ATTT
*
3680065 CAAATTCGCAACACAGAAGTT
1 CAAATTCGCAACAC-GAATTT
3680086 -AAATTCGCAACACTGAATTT
1 CAAATTCGCAACAC-GAATTT
* * *
3680106 CAAATTTGCAAC-TGTATTT
1 CAAATTCGCAACACGAATTT
* * *
3680125 TAAATTCACAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
3680144 CAAATTCACAAC-TGAATTT
1 CAAATTCGCAACACGAATTT
* *
3680163 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACACGAATTT
*
3680183 CGAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
3680203 -AATTTCGCAACA
1 CAAATTCGCAACA
3680215 GGTTTTAGTT
Statistics
Matches: 305, Mismatches: 43, Indels: 45
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.01
19 72 0.24
20 197 0.65
21 30 0.10
22 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:3681117 original size:24 final size:24
Alignment explanation
Indices: 3681059--3681105 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3681049 AGTCAGTATT
*
3681059 CAAAATTTGATCTTGGTCAATACC
1 CAAACTTTGATCTTGGTCAATACC
3681083 CAAACTTTGATCTTGGTCAATAC
1 CAAACTTTGATCTTGGTCAATAC
3681106 TCCGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (24 bp):
CAAACTTTGATCTTGGTCAATACC
Found at i:3683788 original size:21 final size:20
Alignment explanation
Indices: 3683692--3683789 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
3683682 GCAACGCTTA
*
3683692 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTAAC
* **** *
3683712 TATCGCAACACGAATTTGAC
1 TTTCGCGTTGCGAATTTAAC
* *
3683732 TTTCGTGATGCGAATTTAAC
1 TTTCGCGTTGCGAATTTAAC
* * *
3683752 TTTCGCGTTACAAATTTACC
1 TTTCGCGTTGCGAATTTAAC
*
3683772 TTTTTGCGTTGCGAATTT
1 -TTTCGCGTTGCGAATTT
3683790 GTACCTTTAA
Statistics
Matches: 58, Mismatches: 19, Indels: 1
0.74 0.24 0.01
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAC
Found at i:3683931 original size:14 final size:14
Alignment explanation
Indices: 3683912--3683948 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
3683902 ATAAAATTAA
3683912 ACAAATCAACTTTT
1 ACAAATCAACTTTT
3683926 ACAAATCAACTTTT
1 ACAAATCAACTTTT
3683940 ACAAATCAA
1 ACAAATCAA
3683949 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3683954 original size:81 final size:78
Alignment explanation
Indices: 3683845--3684002 Score: 255
Period size: 81 Copynumber: 2.0 Consensus size: 78
3683835 ATTTAAAGCA
3683845 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAAATAATTCTTATTTACACATA-AAAT
1 ACAAATCAACTTTTACAAATCAATTAAACAAGC--AAAAAATAATTCTTATTT-C-CATATAAAT
3683909 TAAACAAATCAACTTTT
62 TAAACAAATCAACTTTT
* *
3683926 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTTATCAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCATATAAATTAAA
3683991 CAAATCAACTTT
66 CAAATCAACTTT
3684003 CAATGTAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
77 3 0.04
78 20 0.27
79 18 0.24
81 33 0.45
ACGTcount: A:0.51, C:0.17, G:0.01, T:0.31
Consensus pattern (78 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCATATAAATTAAA
CAAATCAACTTTT
Found at i:3685411 original size:21 final size:21
Alignment explanation
Indices: 3685387--3685464 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
3685377 GAGTGACCCA
*
3685387 TTGAACGATGACAGGGGCCTC
1 TTGAACGATGACAGGAGCCTC
*
3685408 TTGAACGATGAAAGGAGCCTC
1 TTGAACGATGACAGGAGCCTC
* * * *
3685429 TTAAACGAT-AGGAGGCGTCTC
1 TTGAACGATGA-CAGGAGCCTC
3685450 TTGAACGATGACAGG
1 TTGAACGATGACAGG
3685465 TGAATCGGGC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 1 0.02
21 45 0.96
22 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (21 bp):
TTGAACGATGACAGGAGCCTC
Found at i:3685625 original size:4 final size:4
Alignment explanation
Indices: 3685604--3685641 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
3685594 GGGCCGCTGA
* *
3685604 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
3685642 TGCAGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:3688019 original size:22 final size:22
Alignment explanation
Indices: 3687992--3688042 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3687982 GATGGAGATA
3687992 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
**
3688014 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
3688036 GACGGAT
1 GACGGAT
3688043 GTCGCCGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:3688264 original size:20 final size:20
Alignment explanation
Indices: 3688202--3688488 Score: 181
Period size: 20 Copynumber: 14.3 Consensus size: 20
3688192 TAAACACGTT
* *
3688202 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTTGTG
* * * * *
3688222 TCGCAAATTTGACTATCGAG
1 TTGCGAATTTGACTTTTGTG
3688242 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
* * **
3688262 TTGCGAATCTGAAATTCAGTG
1 TTGCGAATTTG-ACTTTTGTG
* * *
3688283 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTTGTG
*
3688303 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTTGTG
*
3688323 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTTGTG
**
3688343 TTGCG-ATTT-ACTTATTCACG
1 TTGCGAATTTGACTT-TT-GTG
* * *
3688363 TTGTGATTTATAGA--TTTGCG
1 TTGCGAATT-T-GACTTTTGTG
* * *
3688383 TTGCGATTTATAGA--TTCGCG
1 TTGCGAATT-T-GACTTTTGTG
3688403 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTG
**
3688423 TTGCGAATTTGACTTCAGTG
1 TTGCGAATTTGACTTTTGTG
* * * *
3688443 TTGCAAATTTGACTATCGCG
1 TTGCGAATTTGACTTTTGTG
* *
3688463 TTACGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTTGTG
3688483 TTGCGA
1 TTGCGA
3688489 TTTACAAATT
Statistics
Matches: 210, Mismatches: 48, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
18 6 0.03
19 6 0.03
20 175 0.83
21 20 0.10
22 2 0.01
24 1 0.00
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (20 bp):
TTGCGAATTTGACTTTTGTG
Found at i:3688295 original size:61 final size:60
Alignment explanation
Indices: 3688227--3688348 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 60
3688217 TCGCGTCGCA
*
3688227 AATTTGACTATCGAGTTGCGAATTTGACTTTTGTGTTGCGAATCTGAAATTCAGTGTTGCG
1 AATTTGACTATCGAGTTGCGAATTTGACTTCTGTGTTGCGAATCTG-AATTCAGTGTTGCG
* * * *
3688288 AATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTCTGTGTTGCG
1 AATTTGACTATCGAGTTGCGAATTTGACTTCTGTGTTGCGAATCTGAATTCAGTGTTGCG
3688348 A
1 A
3688349 TTTACTTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 13 0.23
61 43 0.77
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.40
Consensus pattern (60 bp):
AATTTGACTATCGAGTTGCGAATTTGACTTCTGTGTTGCGAATCTGAATTCAGTGTTGCG
Found at i:3688346 original size:40 final size:40
Alignment explanation
Indices: 3688202--3688488 Score: 218
Period size: 40 Copynumber: 7.2 Consensus size: 40
3688192 TAAACACGTT
* * *
3688202 TTGCGAATTTGACTT-TCGCGTCGCAAATTTGACTATC-GAG
1 TTGCGAATTTGACTTCT-GCGTTGCGAATTTGACT-TCTGTG
* * * * *
3688242 TTGCGAATTTGACTTTTGTGTTGCGAATCTGAAATTCAGTG
1 TTGCGAATTTGACTTCTGCGTTGCGAATTTG-ACTTCTGTG
3688283 TTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACT-TCTGCGTTGCGAATTTGACTTCTGTG
* *
3688323 TTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACTTAT-TCACG
1 TTGCGAATTTGACTTCTGCGTTGCGAATTTGACTTCTGT---G
* * * *
3688363 TTGTGATTTATAGA-TT-TGCGTTGCGATTTATAGA-TTC-GCG
1 TTGCGAATT-T-GACTTCTGCGTTGCGAATT-T-GACTTCTGTG
* * *
3688403 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCAGTG
1 TTGCGAATTTGACTTCTGCGTTGCGAATTTGACTTCTGTG
* *
3688443 TTGCAAATTTGACTATC-GCGTTACGAATTTGACTTCTGTG
1 TTGCGAATTTGACT-TCTGCGTTGCGAATTTGACTTCTGTG
3688483 TTGCGA
1 TTGCGA
3688489 TTTACAAATT
Statistics
Matches: 197, Mismatches: 30, Indels: 40
0.74 0.11 0.15
Matches are distributed among these distances:
37 1 0.01
38 9 0.05
39 13 0.07
40 130 0.66
41 37 0.19
42 4 0.02
43 2 0.01
44 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (40 bp):
TTGCGAATTTGACTTCTGCGTTGCGAATTTGACTTCTGTG
Found at i:3688452 original size:140 final size:140
Alignment explanation
Indices: 3688280--3688554 Score: 401
Period size: 140 Copynumber: 2.0 Consensus size: 140
3688270 CTGAAATTCA
* * *
3688280 GTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT-TCTGTGTTGCGAATTTGACTTCTGTGT
1 GTGTTGCGAATTTGACTATCGCGTTGCAAATTTGACTATC-GCGTTACGAATTTGACTTCTGTGT
** * * * * *
3688344 TGCGATTTACTTATTCACGTTGTGATTTATAGATTTGCGTTGCGATTTATAGATTCGCGTTGCGA
65 TGCGATTTACAAATTCACGTTGCGATTAACAGATTCGCGTTGCGATTTACAGATTCGCGTTGCGA
3688409 ATTTGACTTTT
130 ATTTGACTTTT
*
3688420 GTGTTGCGAATTTGACT-TCAGTGTTGCAAATTTGACTATCGCGTTACGAATTTGACTTCTGTGT
1 GTGTTGCGAATTTGACTATC-GCGTTGCAAATTTGACTATCGCGTTACGAATTTGACTTCTGTGT
**
3688484 TGCGATTTACAAATTTGCGTTGCGATTAACAGATTCGCGTTGCGATTTACAGATTCGCGTTGCGA
65 TGCGATTTACAAATTCACGTTGCGATTAACAGATTCGCGTTGCGATTTACAGATTCGCGTTGCGA
3688549 ATTTGA
130 ATTTGA
3688555 AAACTGGGTT
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
139 2 0.02
140 116 0.97
141 2 0.02
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (140 bp):
GTGTTGCGAATTTGACTATCGCGTTGCAAATTTGACTATCGCGTTACGAATTTGACTTCTGTGTT
GCGATTTACAAATTCACGTTGCGATTAACAGATTCGCGTTGCGATTTACAGATTCGCGTTGCGAA
TTTGACTTTT
Found at i:3688486 original size:100 final size:97
Alignment explanation
Indices: 3688202--3688508 Score: 271
Period size: 100 Copynumber: 3.1 Consensus size: 97
3688192 TAAACACGTT
* * * * * * * *
3688202 TTGCGAATTTGACTTTCGCGTCGCAAATTTGACTATCGAGTTGCGAATTTGACTTTTGTGTTGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACT-TCGTGTTGC-AATTTGACTATCGCGTTGCG
* * *
3688267 AATCTGAAATTCAGTGTTGCGAATT-T-GACTATCGCG
64 AATTTG--ATTCTGTGTTGCGATTTATAGA-T-TCGCG
* * * *
3688303 TTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTCTGTGTTGCGATTT-ACTTATTCACGTTGT
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTC-GTGTTGCAATTTGAC-TA-TCGCGTTGC
* *
3688367 GATTTATAGATT-TGCGTTGCGATTTATAGATTCGCG
63 GAATT-T-GATTCTGTGTTGCGATTTATAGATTCGCG
*
3688403 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCAGTGTTGCAAATTTGACTATCGCGTTACG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTC-GTGTTGC-AATTTGACTATCGCGTTGCG
* * *
3688468 AATTTGACTTCTGTGTTGCGATTTACAAATTTGCG
64 AATTTGA-TTCTGTGTTGCGATTTATAGATTCGCG
3688503 TTGCGA
1 TTGCGA
3688509 TTAACAGATT
Statistics
Matches: 167, Mismatches: 28, Indels: 23
0.77 0.13 0.11
Matches are distributed among these distances:
98 2 0.01
99 5 0.03
100 100 0.60
101 54 0.32
102 5 0.03
103 1 0.01
ACGTcount: A:0.20, C:0.15, G:0.23, T:0.41
Consensus pattern (97 bp):
TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCGTGTTGCAATTTGACTATCGCGTTGCGAA
TTTGATTCTGTGTTGCGATTTATAGATTCGCG
Found at i:3688504 original size:40 final size:41
Alignment explanation
Indices: 3688402--3688504 Score: 97
Period size: 40 Copynumber: 2.6 Consensus size: 41
3688392 ATAGATTCGC
* * * *
3688402 GTTGCGAATTTGAC-TTTTGTGTTGCGAATTTGACTTCAGT
1 GTTGCAAATTTGACAATTTGCGTTACGAATTTGACTTCAGT
* * *
3688442 GTTGCAAATTTGACTA-TCGCGTTACGAATTTGACTTCTGT
1 GTTGCAAATTTGACAATTTGCGTTACGAATTTGACTTCAGT
*
3688482 GTTGC-GATTT-ACAAATTTGCGTT
1 GTTGCAAATTTGAC-AATTTGCGTT
3688505 GCGATTAACA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
38 2 0.04
39 5 0.10
40 44 0.86
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (41 bp):
GTTGCAAATTTGACAATTTGCGTTACGAATTTGACTTCAGT
Found at i:3688507 original size:20 final size:20
Alignment explanation
Indices: 3688482--3688548 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
3688472 TGACTTCTGT
* *
3688482 GTTGCGATTTACAAATTTGC
1 GTTGCGATTTACAGATTCGC
*
3688502 GTTGCGATTAACAGATTCGC
1 GTTGCGATTTACAGATTCGC
3688522 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
3688542 GTTGCGA
1 GTTGCGA
3688549 ATTTGAAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:3688522 original size:60 final size:59
Alignment explanation
Indices: 3688362--3688524 Score: 136
Period size: 60 Copynumber: 2.7 Consensus size: 59
3688352 ACTTATTCAC
* * * * * *
3688362 GTTGTGATTTATAGATTTGCGTTGCGATTTATAGATTCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGATTTACA-ATTTGCGTTGCGATTAACAGATTCGCGTTACGAATTTGACTTCTGT
* * * * *
3688422 GTTGCGAATTTGAC--TTCAGTGTTGCAAATTTGAC-TA-TCGCGTTACGAATTTGACTTCTGT
1 GTTGCG-ATTT-ACAATT-TGCGTTGC-GA-TTAACAGATTCGCGTTACGAATTTGACTTCTGT
3688482 GTTGCGATTTACAAATTTGCGTTGCGATTAACAGATTCGCGTT
1 GTTGCGATTTAC-AATTTGCGTTGCGATTAACAGATTCGCGTT
3688525 GCGATTTACA
Statistics
Matches: 78, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
58 6 0.08
59 8 0.10
60 52 0.67
61 8 0.10
62 4 0.05
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (59 bp):
GTTGCGATTTACAATTTGCGTTGCGATTAACAGATTCGCGTTACGAATTTGACTTCTGT
Found at i:3688566 original size:140 final size:140
Alignment explanation
Indices: 3688282--3688593 Score: 387
Period size: 140 Copynumber: 2.2 Consensus size: 140
3688272 GAAATTCAGT
* * *
3688282 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTCTGTGTTGC
1 GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTTCTGCGTTACGAATTTGACTTCTGTGTTGC
** * * * * *
3688347 GATTTACTTATTCACGTTGTGATTTATAGATTTGCGTTGCGATTTATAGATTCGCGTTGCGAATT
66 GATTTACAAATTCACGTTGCGATTAACAGATTCGCGTTGCGATTTACAGATTCGCGTTGCGAATT
**** *
3688412 TGACTTTTGT
131 TGAAAACTGG
*
3688422 GTTGCGAATTTGACT-TCAGTGTTGCAAATTTGACTATC-GCGTTACGAATTTGACTTCTGTGTT
1 GTTGCGAATTTGACTATC-GCGTTGCAAATTTGACT-TCTGCGTTACGAATTTGACTTCTGTGTT
**
3688485 GCGATTTACAAATTTGCGTTGCGATTAACAGATTCGCGTTGCGATTTACAGATTCGCGTTGCGAA
64 GCGATTTACAAATTCACGTTGCGATTAACAGATTCGCGTTGCGATTTACAGATTCGCGTTGCGAA
3688550 TTTGAAAACTGG
129 TTTGAAAACTGG
* * *
3688562 GTTGCGAAATTGGAGT-TCGCGTTGCGAATTTG
1 GTTGCG-AATTTGACTATCGCGTTGCAAATTTG
3688594 TTGGTCATTT
Statistics
Matches: 147, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
139 2 0.01
140 134 0.91
141 11 0.07
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.40
Consensus pattern (140 bp):
GTTGCGAATTTGACTATCGCGTTGCAAATTTGACTTCTGCGTTACGAATTTGACTTCTGTGTTGC
GATTTACAAATTCACGTTGCGATTAACAGATTCGCGTTGCGATTTACAGATTCGCGTTGCGAATT
TGAAAACTGG
Found at i:3698085 original size:56 final size:56
Alignment explanation
Indices: 3698005--3698151 Score: 231
Period size: 56 Copynumber: 2.6 Consensus size: 56
3697995 CTACGGCTGA
* * * *
3698005 TATCTCTCTGTTTACAACAGTATAAAATAGCTGTGGAAAGAGGAAATTATGGCTGG
1 TATCTCTCTATTTACAGCAGTATAAAATAGCTATGGAAAGAGGAAATTATGACTGG
* *
3698061 TTTCTCTCTATTTACAGCAGTATAAAATAGCTATGGGAAGAGGAAATTATGACTGG
1 TATCTCTCTATTTACAGCAGTATAAAATAGCTATGGAAAGAGGAAATTATGACTGG
*
3698117 TATCTTTCTATTTACAGCAGTATAAAATAGCTATG
1 TATCTCTCTATTTACAGCAGTATAAAATAGCTATG
3698152 CAAGGAATTA
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 83 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (56 bp):
TATCTCTCTATTTACAGCAGTATAAAATAGCTATGGAAAGAGGAAATTATGACTGG
Found at i:3708535 original size:159 final size:162
Alignment explanation
Indices: 3708253--3708559 Score: 593
Period size: 159 Copynumber: 1.9 Consensus size: 162
3708243 ATGAGAATTA
3708253 CACACAAGCTTTCTATTTGCCTCCTTTAACCTAATATCAACCTTCAAGGGATTTGCATAACTACC
1 CACACAAGCTTTCTATTTGCCTCCTTTAACCTAATATCAACCTTCAAGGGATTTGCATAACTACC
3708318 GGGAAAACTAACAAAATAGAAATCATTGATGCTGGGAGCTGCTATACTCTTGAGAAGTAGTTCTA
66 GGGAAAACTAACAAAATAGAAATCATTGATGCTGGGAGCTGCTATACTCTTGAGAAGTAGTTCTA
3708383 CTGCTAAAATGAAATAGTGAAAATTTTGCAAT
131 CTGCTAAAATGAAATAGTGAAAATTTTGCAAT
3708415 CACA-AAGCTTTCTATTTGCCTCCTTTAACCTAATATCAACCTTCAA-GGATTTGCATAACTACC
1 CACACAAGCTTTCTATTTGCCTCCTTTAACCTAATATCAACCTTCAAGGGATTTGCATAACTACC
3708478 GGGAAAACTAACAAAATAG-AATCATTGATGCTGGGAGCTGCTATACTCTTGAGAAGTAGTTCTA
66 GGGAAAACTAACAAAATAGAAATCATTGATGCTGGGAGCTGCTATACTCTTGAGAAGTAGTTCTA
3708542 CTGCTAAAATGAAATAGT
131 CTGCTAAAATGAAATAGT
3708560 ATTTGGTTTT
Statistics
Matches: 145, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
159 63 0.43
160 36 0.25
161 42 0.29
162 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (162 bp):
CACACAAGCTTTCTATTTGCCTCCTTTAACCTAATATCAACCTTCAAGGGATTTGCATAACTACC
GGGAAAACTAACAAAATAGAAATCATTGATGCTGGGAGCTGCTATACTCTTGAGAAGTAGTTCTA
CTGCTAAAATGAAATAGTGAAAATTTTGCAAT
Found at i:3717553 original size:24 final size:24
Alignment explanation
Indices: 3717522--3717640 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
3717512 ACCAAAACAT
**
3717522 AAAT-CAGGTCAAGTATCTTATCA
1 AAATCCAGGTCAAGTATCAGATCA
3717545 AAATCCAGGTCAAGTATCAGATCA
1 AAATCCAGGTCAAGTATCAGATCA
* *
3717569 GAATCCAAGTCAAGTATCAGATCA
1 AAATCCAGGTCAAGTATCAGATCA
* * * *
3717593 TAATCCATGTCAAATATCATATCA
1 AAATCCAGGTCAAGTATCAGATCA
* *
3717617 GAATCCATGTCAAGTATCAGATCA
1 AAATCCAGGTCAAGTATCAGATCA
3717641 TAATTCAAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
23 4 0.05
24 80 0.95
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
AAATCCAGGTCAAGTATCAGATCA
Found at i:3717598 original size:48 final size:48
Alignment explanation
Indices: 3717529--3717644 Score: 169
Period size: 48 Copynumber: 2.4 Consensus size: 48
3717519 CATAAATCAG
** * *
3717529 GTCAAGTATCTTATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCATAATCCAGGTCAAATATCAGATCAGAATCCAA
* * *
3717577 GTCAAGTATCAGATCATAATCCATGTCAAATATCATATCAGAATCCAT
1 GTCAAGTATCAGATCATAATCCAGGTCAAATATCAGATCAGAATCCAA
3717625 GTCAAGTATCAGATCATAAT
1 GTCAAGTATCAGATCATAAT
3717645 TCAAATCGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.28
Consensus pattern (48 bp):
GTCAAGTATCAGATCATAATCCAGGTCAAATATCAGATCAGAATCCAA
Found at i:3717660 original size:72 final size:72
Alignment explanation
Indices: 3717529--3717662 Score: 180
Period size: 72 Copynumber: 1.9 Consensus size: 72
3717519 CATAAATCAG
* * * *
3717529 GTCAAGTATCTTATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAT
1 GTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGATCAT
3717594 AATCCAT
66 AATCCAT
* * * *
3717601 GTCAAATATCATATCAGAATCCATGTCAAGTATCAGATCATAATTCAAATCGAA-AATCAGAT
1 GTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATC-AAGAATCAGAT
3717663 AAAATATTCA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 51 0.96
73 2 0.04
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (72 bp):
GTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATCAAGAATCAGATCAT
AATCCAT
Found at i:3721329 original size:2 final size:2
Alignment explanation
Indices: 3721322--3721348 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3721312 TTTTTAAAAC
3721322 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3721349 CTCCCATCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3721586 original size:24 final size:24
Alignment explanation
Indices: 3721554--3721672 Score: 141
Period size: 24 Copynumber: 5.0 Consensus size: 24
3721544 ATCAAAACAT
*
3721554 AAAT-CAGGTCAAGTATCTTATCA
1 AAATCCAGGTCAAGTATCATATCA
*
3721577 AAATCTAGGTCAAGTATCATATCA
1 AAATCCAGGTCAAGTATCATATCA
* * *
3721601 TAATCCAAGTCAAGTATCAGATCA
1 AAATCCAGGTCAAGTATCATATCA
* * *
3721625 GAATCCATGTCAAATATCATATCA
1 AAATCCAGGTCAAGTATCATATCA
* *
3721649 AAATCCATGTCAAGTATCAGATCA
1 AAATCCAGGTCAAGTATCATATCA
3721673 GAATTCAAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
23 4 0.05
24 78 0.95
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (24 bp):
AAATCCAGGTCAAGTATCATATCA
Found at i:3721637 original size:48 final size:48
Alignment explanation
Indices: 3721561--3721676 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 48
3721551 CATAAATCAG
** * * * *
3721561 GTCAAGTATCTTATCAAAATCTAGGTCAAGTATCATATCATAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGGTCAAATATCATATCAAAATCCAA
* *
3721609 GTCAAGTATCAGATCAGAATCCATGTCAAATATCATATCAAAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAAATATCATATCAAAATCCAA
3721657 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
3721677 TCAAATAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 60 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAAATATCATATCAAAATCCAA
Found at i:3721692 original size:72 final size:72
Alignment explanation
Indices: 3721561--3721694 Score: 169
Period size: 72 Copynumber: 1.9 Consensus size: 72
3721551 CATAAATCAG
* * * * * * * **
3721561 GTCAAGTATCTTATCAAAATCTAGGTCAAGTATCATATCATAATCCAAGTCAAGTATCAGATCAG
1 GTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATAAAAAATCAGATCAG
3721626 AATCCAT
66 AATCCAT
* *
3721633 GTCAAATATCATATCAAAATCCATGTCAAGTATCAGATCAGAATTCAAATAAAAAATCAGAT
1 GTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATAAAAAATCAGAT
3721695 AAAATATTCA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
72 51 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.28
Consensus pattern (72 bp):
GTCAAATATCATATCAAAATCCAGGTCAAGTATCAGATCAGAATCCAAATAAAAAATCAGATCAG
AATCCAT
Found at i:3726982 original size:124 final size:123
Alignment explanation
Indices: 3726749--3726996 Score: 406
Period size: 124 Copynumber: 2.0 Consensus size: 123
3726739 AAGAGGTTAA
* *
3726749 AATTGGGTTAGTAATATGACAATAATTGTTTAGTATTTTAGTGCTAAATTGGTGGGTTAATCAAA
1 AATTGGGTTAGTAATATAACAATAATTGTTTAGTATTTTAGGGCTAAATTGGTGGGTTAATCAAA
* * * *
3726814 CCAACGTGAGTGGCCATTCCATCTAGGTATGGGGTATTGTGTTTCTACATAAGGGTTT
66 CCAACGCGAGTAGCCATTCCATCTAGGTATGGGGTAGTGTGTTTCTACATAAAGGTTT
3726872 AATTGGGTTAGTAATATAACAATAATTGTTTAGTATTTTAGGGCTAATATTGGTGGGTTAATCAA
1 AATTGGGTTAGTAATATAACAATAATTGTTTAGTATTTTAGGGCTAA-ATTGGTGGGTTAATCAA
* * *
3726937 ACCCACGCGAGTAGCTATTTCATCTAGGTATGGGGTAGTGTGTTTCTACATAAAGGTTT
65 ACCAACGCGAGTAGCCATTCCATCTAGGTATGGGGTAGTGTGTTTCTACATAAAGGTTT
3726996 A
1 A
3726997 TTGATATAAG
Statistics
Matches: 115, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
123 45 0.39
124 70 0.61
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (123 bp):
AATTGGGTTAGTAATATAACAATAATTGTTTAGTATTTTAGGGCTAAATTGGTGGGTTAATCAAA
CCAACGCGAGTAGCCATTCCATCTAGGTATGGGGTAGTGTGTTTCTACATAAAGGTTT
Found at i:3732688 original size:9 final size:9
Alignment explanation
Indices: 3732674--3732698 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3732664 ACAACTTCAT
3732674 TTTTTTTTC
1 TTTTTTTTC
3732683 TTTTTTTTC
1 TTTTTTTTC
3732692 TTTTTTT
1 TTTTTTT
3732699 ACGAAGTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:3733771 original size:14 final size:14
Alignment explanation
Indices: 3733752--3733779 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3733742 TATGTTCTAG
3733752 CTCAACTGGCAGGT
1 CTCAACTGGCAGGT
3733766 CTCAACTGGCAGGT
1 CTCAACTGGCAGGT
3733780 GGCAGGCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (14 bp):
CTCAACTGGCAGGT
Found at i:3737527 original size:49 final size:49
Alignment explanation
Indices: 3737455--3737554 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
3737445 TGGTTCCTCC
3737455 CAAGTTTCTCTCGAACACTAAGAATGTGATACCTAGACATTCTCTCAAA
1 CAAGTTTCTCTCGAACACTAAGAATGTGATACCTAGACATTCTCTCAAA
*
3737504 CAAGTTTCTCTCGAACACTAAGAATGTGATACCTAGACATTCTCTTAAA
1 CAAGTTTCTCTCGAACACTAAGAATGTGATACCTAGACATTCTCTCAAA
3737553 CA
1 CA
3737555 CTAAGTAATC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (49 bp):
CAAGTTTCTCTCGAACACTAAGAATGTGATACCTAGACATTCTCTCAAA
Found at i:3738435 original size:20 final size:20
Alignment explanation
Indices: 3738406--3738444 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3738396 ATTTCACCAC
*
3738406 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
3738426 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
3738445 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:3741683 original size:2 final size:2
Alignment explanation
Indices: 3741676--3741708 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3741666 ATACCTAACA
3741676 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3741709 GTACACAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3742970 original size:125 final size:125
Alignment explanation
Indices: 3742827--3743070 Score: 373
Period size: 125 Copynumber: 2.0 Consensus size: 125
3742817 ATTGGGGCAG
*
3742827 GACTGAACCCACATCATGTTGAGATGACAAGATTCGGACCAATG-AGGCATTAAGAATGAGCCTT
1 GACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAA-GAAGGCATTAAGAATGAGCCTT
* * * *
3742891 ATAATTTGAGGTATTGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATGTTGAGGCGC
65 ACAAATTGAGGTATTGGGGCATTTCGAAGACCCGTACCAGTATAAGATAATGTTGAGGCGC
* * *
3742952 GACTGAACCCACATCATGTTGAGATGACAAGGTTCAGACCAAGAAGGCATTGAGCATGAGCCTTA
1 GACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGCATTAAGAATGAGCCTTA
* * *
3743017 CAAATTGAGGTGTTGGGGTATTTCGAAGACCCGTACTAGTATAAGATAATGTTG
66 CAAATTGAGGTATTGGGGCATTTCGAAGACCCGTACCAGTATAAGATAATGTTG
3743071 GGGCACTAGT
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 1 0.01
125 106 0.99
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (125 bp):
GACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAAGAAGGCATTAAGAATGAGCCTTA
CAAATTGAGGTATTGGGGCATTTCGAAGACCCGTACCAGTATAAGATAATGTTGAGGCGC
Found at i:3744057 original size:102 final size:102
Alignment explanation
Indices: 3743881--3744074 Score: 343
Period size: 102 Copynumber: 1.9 Consensus size: 102
3743871 GACAAAAAAC
* *
3743881 AAAGACCATAAGATGATTGGGCAAATCTCCAAGAGTAGTAAGCTGCTACACTGATATATGAGTAA
1 AAAGACCACAAGATGATTGGGCAAATCTCCAAGAGTAGTAAACTGCTACACTGATATATGAGTAA
3743946 ACCATATAGAAGAACAATCAAGAGAAAGAGAGAAAGA
66 ACCATATAGAAGAACAATCAAGAGAAAGAGAGAAAGA
* *
3743983 AAAGACCACAAGATGATTGGGCAGATCTCCAAGAGTAGTAAACTGCTACACTGATATCTGAGTAA
1 AAAGACCACAAGATGATTGGGCAAATCTCCAAGAGTAGTAAACTGCTACACTGATATATGAGTAA
*
3744048 ACCATATAGAAGAACAATGAAGAGAAA
66 ACCATATAGAAGAACAATCAAGAGAAA
3744075 TAAGACTAGT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 87 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (102 bp):
AAAGACCACAAGATGATTGGGCAAATCTCCAAGAGTAGTAAACTGCTACACTGATATATGAGTAA
ACCATATAGAAGAACAATCAAGAGAAAGAGAGAAAGA
Found at i:3744675 original size:151 final size:151
Alignment explanation
Indices: 3744394--3744803 Score: 633
Period size: 151 Copynumber: 2.7 Consensus size: 151
3744384 AAAAAATGAA
* * *
3744394 ATGAGAAACGTTTCTCATTCAACTTTGAAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTA
1 ATGAGAAAGGTTTCTCATTCAAATTTGAAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTTTTA
* **
3744459 CCTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCAGGATG
66 CCTAGTAAAATATTTCCAAAATTTATAAGTCCTTTGGGCCATCCATAAGACCTTCAGGCAGGATG
3744524 TTTTCACATGACTATCAAAAT
131 TTTTCACATGACTATCAAAAT
*
3744545 ATGAGAAAGGTTTCTCATTCAAATTTGAAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTTTTA
1 ATGAGAAAGGTTTCTCATTCAAATTTGAAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTTTTA
* *
3744610 CCTAGTAAAATATTTCCAAAATTAATAAGTCCTTTGGGCCATCCATAAGACCTTCAGGCATGATG
66 CCTAGTAAAATATTTCCAAAATTTATAAGTCCTTTGGGCCATCCATAAGACCTTCAGGCAGGATG
* * *
3744675 TTTTCACATGTCTTTCGAAAT
131 TTTTCACATGACTATCAAAAT
* * * *
3744696 ATGAGAAAGGGTTCTCATATTAAATCTG-AAATTTAAAATTTTTGAAAAGTAAGAAAGGTTTTTT
1 ATGAGAAAGGTTTCTCAT-TCAAATTTGAAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTTTT
* **
3744760 ACCTAGTAAACTATTTTTAAAATTTATAAGTCCTTTGGGCCATC
65 ACCTAGTAAAATATTTCCAAAATTTATAAGTCCTTTGGGCCATC
3744804 AGTAACTCTT
Statistics
Matches: 237, Mismatches: 21, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
151 230 0.97
152 7 0.03
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (151 bp):
ATGAGAAAGGTTTCTCATTCAAATTTGAAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTTTTA
CCTAGTAAAATATTTCCAAAATTTATAAGTCCTTTGGGCCATCCATAAGACCTTCAGGCAGGATG
TTTTCACATGACTATCAAAAT
Found at i:3745086 original size:233 final size:233
Alignment explanation
Indices: 3744634--3745209 Score: 769
Period size: 233 Copynumber: 2.5 Consensus size: 233
3744624 TCCAAAATTA
** * * * *
3744634 ATAAGTCCTTTGGGCCATCCATAAGACCTTCAGGCATGATGTTTTCACATGTCTTTCGAAATATG
1 ATAAGTCCTTCAGGCCATCCATAAGACCTTTAGACAAGATGTTTTCACATGTCTTTTGAAATATG
* * * * *
3744699 AGAAAGGGTTCTCATATTAAATCTGAAATTTAAAATTTTTGAAAAGTAAGAAAGGTTTTTTACCT
66 AGAAAGGTTTCTCATATTAAATCTAAAATTTGAAA-TTTTGAAAAGTAAGAAAAGTTTCTTACCT
* ** * *
3744764 AGTAAACTATTTTTAAAATTTATAAGTCCTTTGGGCCATCAGTAACTCTTTCAAGCATGATGCTC
130 AGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAACTCTTTCAAGCATGATACTC
3744829 AAATCCTTCGGGTCATTTGTAAGCCTTTCGAGCAAGATG
195 AAATCCTTCGGGTCATTTGTAAGCCTTTCGAGCAAGATG
* * *
3744868 ATAAGTCCTTCAGGCCATCCATAAGACTTTTATACAGGATGTTTTCACATGTCTTTTGAAATATG
1 ATAAGTCCTTCAGGCCATCCATAAGACCTTTAGACAAGATGTTTTCACATGTCTTTTGAAATATG
*
3744933 AGAAAGGTTTCTCATATTAAATCTAAAAATTGAAATTTTGAAAAGTAAGAAAAGTTTCTTACCTA
66 AGAAAGGTTTCTCATATTAAATCTAAAATTTGAAATTTTGAAAAGTAAGAAAAGTTTCTTACCTA
* * * * *
3744998 GTAAAATATTTCCCAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATATTTA
131 GTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAACTCTTTCAAGCATGATACTCA
* *
3745063 AATCTTTTGGGTCATTTGTAAGCCTTTCGAGCAAGATG
196 AATCCTTCGGGTCATTTGTAAGCCTTTCGAGCAAGATG
* * * * * * *
3745101 GTAAGTCTTTCATGCCATCCATAAGACCTTTGGACAAGATTTTTTTCACATGTC-TATCAAACTA
1 ATAAGTCCTTCAGGCCATCCATAAGACCTTTAGACAAGA-TGTTTTCACATGTCTTTTGAAA-TA
* ** *
3745165 TAAGAAAGGTTTCTCAT-TTAAATCTTCAATTTGAAATTTTAAAAA
64 TGAGAAAGGTTTCTCATATTAAATCTAAAATTTGAAATTTTGAAAA
3745210 ATATGATATT
Statistics
Matches: 299, Mismatches: 41, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
233 180 0.60
234 119 0.40
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (233 bp):
ATAAGTCCTTCAGGCCATCCATAAGACCTTTAGACAAGATGTTTTCACATGTCTTTTGAAATATG
AGAAAGGTTTCTCATATTAAATCTAAAATTTGAAATTTTGAAAAGTAAGAAAAGTTTCTTACCTA
GTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAACTCTTTCAAGCATGATACTCA
AATCCTTCGGGTCATTTGTAAGCCTTTCGAGCAAGATG
Found at i:3745415 original size:115 final size:115
Alignment explanation
Indices: 3745213--3745423 Score: 359
Period size: 115 Copynumber: 1.8 Consensus size: 115
3745203 TTAAAAAATA
*
3745213 TGATATTCCCTTCAGAAGAAGAAGAACAGATCCCTCTTTTCCAAGGTTTGATATTCCCTGAGTGA
1 TGATATTCCCTTCAGAAGAAGAAGAACAGATCCCTCTTTTCCAAGGTTTGATATTCCCAGAGTGA
3745278 CAGCAGAACAAATATGCCCTAATTCAATGGATCACATCTATTTCCAGATC
66 CAGCAGAACAAATATGCCCTAATTCAATGGATCACATCTATTTCCAGATC
** * *
3745328 TGATATTCCCTTCAGAAGAAGCGGAATAGATTCCTCTTTTCCAAGGTTTGATATTCCCAGAGTGA
1 TGATATTCCCTTCAGAAGAAGAAGAACAGATCCCTCTTTTCCAAGGTTTGATATTCCCAGAGTGA
* *
3745393 CAGCGGAACAAATCTGCCCTAATTCAATGGA
66 CAGCAGAACAAATATGCCCTAATTCAATGGA
3745424 ACAAATCTGC
Statistics
Matches: 89, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
115 89 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (115 bp):
TGATATTCCCTTCAGAAGAAGAAGAACAGATCCCTCTTTTCCAAGGTTTGATATTCCCAGAGTGA
CAGCAGAACAAATATGCCCTAATTCAATGGATCACATCTATTTCCAGATC
Found at i:3745455 original size:24 final size:24
Alignment explanation
Indices: 3745397--3745447 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3745387 GAGTGACAGC
3745397 GGAACAAATCTGCCCTAATTCAAT
1 GGAACAAATCTGCCCTAATTCAAT
3745421 GGAACAAATCTGCCCTAATTCAAT
1 GGAACAAATCTGCCCTAATTCAAT
3745445 GGA
1 GGA
3745448 TCACATCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.24
Consensus pattern (24 bp):
GGAACAAATCTGCCCTAATTCAAT
Found at i:3745521 original size:48 final size:48
Alignment explanation
Indices: 3745453--3745785 Score: 429
Period size: 48 Copynumber: 6.9 Consensus size: 48
3745443 ATGGATCACA
* *
3745453 TCTCTT-T-CAAGATCTGATATTCCCTTCAGAGTAAGCGAAACATGTC
1 TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTC
* *
3745499 TCTCTTCTCCAAGATTTTATATTCCCTTCAGAGTAAGCGGAATATGTC
1 TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTC
* *
3745547 TCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGAGGAACATGCCTC
1 TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACATG--TC
* * * * *
3745597 TCAACTTC-CCCAGATTTGATATTCCCTTCAGAGTAAGTGGAATAGGTC
1 TC-TCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTC
* * * *
3745645 TCTCTTCTCAAAGATTTGATATTCCCTTCAGTGTAAGAGGAACAAGTC
1 TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTC
* * *
3745693 TCTTTTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGCAGAACATGTC
1 TC-TCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTC
* *
3745742 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACA
1 TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACA
3745786 AGTATGCCCC
Statistics
Matches: 249, Mismatches: 31, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
46 6 0.02
47 5 0.02
48 156 0.63
49 41 0.16
50 37 0.15
51 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (48 bp):
TCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGCGGAACATGTC
Found at i:3745652 original size:98 final size:96
Alignment explanation
Indices: 3745453--3745785 Score: 447
Period size: 98 Copynumber: 3.5 Consensus size: 96
3745443 ATGGATCACA
* * *
3745453 TCTCTT-TC-AAGATCTGATATTCCCTTCAGAGTAAGCGAAACATG-TCTCTCTTCTCCAAGATT
1 TCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGAGGAACATGCTCTCTCTTC-CCAAGATT
*
3745515 TTATATTCCCTTCAGAGTAAGCGGAATATGTC
65 TGATATTCCCTTCAGAGTAAGCGGAATATGTC
* *
3745547 TCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGAGGAACATGCCTCTCAACTTCCCCAGAT
1 TCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGAGGAACATG-CTCTC-TCTTCCCAAGAT
* *
3745612 TTGATATTCCCTTCAGAGTAAGTGGAATAGGTC
64 TTGATATTCCCTTCAGAGTAAGCGGAATATGTC
* * * * *
3745645 TCTCTTCTCAAAGATTTGATATTCCCTTCAGTGTAAGAGGAACAAGTCTCTTTTTTTCCAAGATT
1 TCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGAGGAACATG-CTCTCTCTTCCCAAGATT
* *
3745710 TGATATTCCCTTCAGAGTAAGCAGAACATGTC
65 TGATATTCCCTTCAGAGTAAGCGGAATATGTC
* * *
3745742 TCTCTTTTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACA
1 TCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGAGGAACA
3745786 AGTATGCCCC
Statistics
Matches: 210, Mismatches: 24, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
94 6 0.03
95 2 0.01
96 33 0.16
97 77 0.37
98 88 0.42
99 4 0.02
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (96 bp):
TCTCTTCTCAAAGATTTGATATTCCCTTCAGAGTAAGAGGAACATGCTCTCTCTTCCCAAGATTT
GATATTCCCTTCAGAGTAAGCGGAATATGTC
Found at i:3746378 original size:14 final size:14
Alignment explanation
Indices: 3746359--3746392 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3746349 TTACGTACCG
3746359 TAATCCACTAAACC
1 TAATCCACTAAACC
*
3746373 TAATCCACTAAACT
1 TAATCCACTAAACC
3746387 TAATCC
1 TAATCC
3746393 TTTCAACCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.26
Consensus pattern (14 bp):
TAATCCACTAAACC
Found at i:3747009 original size:124 final size:123
Alignment explanation
Indices: 3746779--3747026 Score: 379
Period size: 124 Copynumber: 2.0 Consensus size: 123
3746769 AAGAGGTTAA
* *
3746779 AATTGGGTTAGTATTATGACAATAATTGTTTAGTATTTTAGTGCTAAATTGGTGGGTTAATCAAA
1 AATTGGGTTAGTAATATAACAATAATTGTTTAGTATTTTAGTGCTAAATTGGTGGGTTAATCAAA
* * * * * *
3746844 CCCACGTGAGTGGCCATTCCATCTAGGTATGGGGTATTGTGTTTTTACATAAGGGTTT
66 CCCACGTGAGTAGCCATTCCATATAGGGATGGGGTAGTGTGTTTCTACATAAAGGTTT
*
3746902 AATTGGGTTAGTAATATAACAATAATTGTTTAGTATTTTATTGCTAAAATTGGTGGGTTAATCAA
1 AATTGGGTTAGTAATATAACAATAATTGTTTAGTATTTTAGTGCT-AAATTGGTGGGTTAATCAA
* * *
3746967 ATCCACGTGAGTAGCTATTTCATATAGGGATGGGGTAGTGTGTTTCTACATAAAGGTTT
65 ACCCACGTGAGTAGCCATTCCATATAGGGATGGGGTAGTGTGTTTCTACATAAAGGTTT
3747026 A
1 A
3747027 TTGATGTAAG
Statistics
Matches: 112, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
123 42 0.38
124 70 0.62
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (123 bp):
AATTGGGTTAGTAATATAACAATAATTGTTTAGTATTTTAGTGCTAAATTGGTGGGTTAATCAAA
CCCACGTGAGTAGCCATTCCATATAGGGATGGGGTAGTGTGTTTCTACATAAAGGTTT
Found at i:3750217 original size:2 final size:2
Alignment explanation
Indices: 3750212--3750237 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3750202 TATTATATTT
3750212 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
3750238 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3750242 original size:2 final size:2
Alignment explanation
Indices: 3750237--3750294 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
3750227 ACACACACAC
3750237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3750279 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3750295 TAAATTATAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3750822 original size:29 final size:29
Alignment explanation
Indices: 3750780--3750839 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
3750770 CGAGCTAGGG
*
3750780 GTAGGTCGCCATGCCTTCCAGGCGACCTT
1 GTAGGTCGCCATGCCCTCCAGGCGACCTT
* *
3750809 GTAGGTTGCCATGCCCTCCGGGCGACCTT
1 GTAGGTCGCCATGCCCTCCAGGCGACCTT
3750838 GT
1 GT
3750840 GTCCTTGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.12, C:0.33, G:0.30, T:0.25
Consensus pattern (29 bp):
GTAGGTCGCCATGCCCTCCAGGCGACCTT
Found at i:3751437 original size:21 final size:21
Alignment explanation
Indices: 3751408--3751451 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3751398 AATTTAGTTA
*
3751408 ATTAGTTTGTTAGTATAAATT
1 ATTAATTTGTTAGTATAAATT
* *
3751429 ATTAATTTGTTAGTTTAAGTT
1 ATTAATTTGTTAGTATAAATT
3751450 AT
1 AT
3751452 ATTATATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (21 bp):
ATTAATTTGTTAGTATAAATT
Found at i:3751459 original size:28 final size:28
Alignment explanation
Indices: 3751428--3751481 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
3751418 TAGTATAAAT
3751428 TATTAATTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
* *
3751456 TATTAGTTTGTTAGTTTATGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
3751482 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:3751891 original size:14 final size:14
Alignment explanation
Indices: 3751872--3751898 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3751862 GTAATTTATT
3751872 ATTTTTTGTTGTTC
1 ATTTTTTGTTGTTC
3751886 ATTTTTTGTTGTT
1 ATTTTTTGTTGTT
3751899 GTGTATGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
ATTTTTTGTTGTTC
Found at i:3752022 original size:16 final size:16
Alignment explanation
Indices: 3751967--3752024 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
3751957 ATTTATTCCC
*
3751967 GTTTAAAAAATATTGT
1 GTTTAAAAAATATTTT
* *
3751983 GTATAAAAATATTTAGTGTT
1 GTTTAAAAA-A--TA-TTTT
3752003 GTTTAAAAAATATTTT
1 GTTTAAAAAATATTTT
3752019 GTTTAA
1 GTTTAA
3752025 TTTATATTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 17 0.52
17 3 0.09
19 3 0.09
20 10 0.30
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (16 bp):
GTTTAAAAAATATTTT
Found at i:3755243 original size:21 final size:21
Alignment explanation
Indices: 3755216--3755303 Score: 58
Period size: 21 Copynumber: 4.3 Consensus size: 21
3755206 TTTGATAGTA
3755216 ATGATTAGTAATAATGAAATT
1 ATGATTAGTAATAATGAAATT
* * *
3755237 ATTATTAATATTTAATG--ATT
1 ATGATTAGTA-ATAATGAAATT
* ** * *
3755257 -TGA-TAGTAATGATTTAGTA
1 ATGATTAGTAATAATGAAATT
3755276 ATGATTAGTAATAATGAAATT
1 ATGATTAGTAATAATGAAATT
*
3755297 ATTATTA
1 ATGATTA
3755304 ATATTTAATG
Statistics
Matches: 46, Mismatches: 16, Indels: 10
0.64 0.22 0.14
Matches are distributed among these distances:
17 3 0.07
18 4 0.09
19 3 0.07
20 6 0.13
21 25 0.54
22 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.44
Consensus pattern (21 bp):
ATGATTAGTAATAATGAAATT
Found at i:3755244 original size:49 final size:49
Alignment explanation
Indices: 3755162--3755330 Score: 221
Period size: 49 Copynumber: 3.2 Consensus size: 49
3755152 AATAATTATT
* *
3755162 TAGTCATGAGTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
3755211 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTT-A--A--TGAT--T--TGA
3755269 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
1 --TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
3755320 TAGTAATGATT
1 TAGTAATGATT
3755331 TGGTAATGAT
Statistics
Matches: 107, Mismatches: 2, Indels: 22
0.82 0.02 0.17
Matches are distributed among these distances:
49 48 0.45
50 1 0.01
51 3 0.03
52 1 0.01
53 1 0.01
54 4 0.04
55 4 0.04
56 1 0.01
57 1 0.01
58 3 0.03
59 1 0.01
60 39 0.36
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGA
Found at i:3755255 original size:35 final size:35
Alignment explanation
Indices: 3755214--3755316 Score: 100
Period size: 35 Copynumber: 3.2 Consensus size: 35
3755204 GATTTGATAG
3755214 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
* * * *
3755249 TAATGATT--TGAT-A-G---TAATGATT--TA-G
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
3755274 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
3755309 TAATGATT
1 TAATGATT
3755317 TGATAGTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
25 8 0.16
26 2 0.04
27 3 0.06
28 7 0.14
29 1 0.02
31 1 0.02
32 7 0.14
33 3 0.06
34 2 0.04
35 16 0.32
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.46
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:3755279 original size:60 final size:60
Alignment explanation
Indices: 3755211--3755358 Score: 278
Period size: 60 Copynumber: 2.5 Consensus size: 60
3755201 AATGATTTGA
3755211 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
3755271 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
* *
3755331 TGGTAATGATTAGTAATCATGAAATTAT
1 TAGTAATGATTAGTAATAATGAAATTAT
3755359 AAAAATGATT
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 86 1.00
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (60 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATT
Found at i:3755743 original size:49 final size:49
Alignment explanation
Indices: 3755623--3755799 Score: 202
Period size: 49 Copynumber: 3.6 Consensus size: 49
3755613 TTGATTTAGC
* * ** *
3755623 AATGATTTGATAATCATGATT--TAATAATGATTTTA-TATTTAAAATTAT
1 AATGATTTGATAGTAATGATTAGTAATAATGAAATTATTA-TTAATATT-T
*
3755671 AAT-ATTT-ATTTAGTCATGATTAGTAATAATGAAATTATTATTAATATTT
1 AATGATTTGA--TAGTAATGATTAGTAATAATGAAATTATTATTAATATTT
*
3755720 AATGATTTGATAGTAATGATTAGTAATAATAAAATTATTATTAATATTT
1 AATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTT
*
3755769 AATGAATTGATAGTAATGATTTAGTAATAAT
1 AATGATTTGATAGTAATGA-TTAGTAATAAT
3755800 CATTATAATA
Statistics
Matches: 114, Mismatches: 7, Indels: 14
0.84 0.05 0.10
Matches are distributed among these distances:
46 1 0.01
47 4 0.04
48 13 0.11
49 59 0.52
50 34 0.30
51 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (49 bp):
AATGATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATATTT
Found at i:3755799 original size:14 final size:14
Alignment explanation
Indices: 3755782--3755847 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 14
3755772 GAATTGATAG
3755782 TAATGATTTAGTAA
1 TAATGATTTAGTAA
*
3755796 TAATCA-TTA-TAA
1 TAATGATTTAGTAA
3755808 TAATGATTT-GATAA
1 TAATGATTTAG-TAA
3755822 TAATGA-TT--TAA
1 TAATGATTTAGTAA
3755833 TAATGATTTAGTAA
1 TAATGATTTAGTAA
3755847 T
1 T
3755848 TATTATTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
11 9 0.20
12 10 0.23
13 7 0.16
14 18 0.41
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.44
Consensus pattern (14 bp):
TAATGATTTAGTAA
Found at i:3755880 original size:24 final size:25
Alignment explanation
Indices: 3755782--3755881 Score: 75
Period size: 26 Copynumber: 4.0 Consensus size: 25
3755772 GAATTGATAG
*
3755782 TAATGATTTAGTAA-TAATCATTATAA
1 TAATGATTCAGTAATTAAT-ATT-TAA
*
3755808 TAATGATT-TGATAA-TAATGATTTAA
1 TAATGATTCAG-TAATTAAT-ATTTAA
* *
3755833 TAATGATTTAGTAATTATTA-TTAA
1 TAATGATTCAGTAATTAATATTTAA
* *
3755857 TAGTGATTCA-TTATTAATATTTAA
1 TAATGATTCAGTAATTAATATTTAA
3755881 T
1 T
3755882 GATTTGATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
23 7 0.11
24 17 0.27
25 16 0.26
26 22 0.35
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (25 bp):
TAATGATTCAGTAATTAATATTTAA
Found at i:3755959 original size:11 final size:11
Alignment explanation
Indices: 3755793--3755941 Score: 61
Period size: 11 Copynumber: 12.4 Consensus size: 11
3755783 AATGATTTAG
*
3755793 TAATAATCATT
1 TAATAATGATT
3755804 ATAATAATGATTT
1 -TAATAATGA-TT
3755817 GATAATAATGATT
1 --TAATAATGATT
3755830 TAATAATGATT
1 TAATAATGATT
* *
3755841 TAGTAATTATTAT
1 TAATAATGA-T-T
*
3755854 TAATAGTGATT
1 TAATAATGATT
* * * *
3755865 CATTATTAATAT
1 TAATAATGAT-T
3755877 T--TAATGATT
1 TAATAATGATT
3755886 TGATATTAATGA-T
1 T-A-A-TAATGATT
3755899 TAAGTAATGATT
1 TAA-TAATGATT
3755911 AGTAATAATGAAATT
1 --TAATAATG--ATT
3755926 GTAATAATGATT
1 -TAATAATGATT
3755938 TAAT
1 TAAT
3755942 CATTAATAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 31
0.71 0.09 0.20
Matches are distributed among these distances:
9 2 0.02
10 5 0.05
11 36 0.33
12 16 0.15
13 18 0.17
14 28 0.26
15 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.11, T:0.45
Consensus pattern (11 bp):
TAATAATGATT
Found at i:3756251 original size:19 final size:22
Alignment explanation
Indices: 3756237--3756314 Score: 70
Period size: 24 Copynumber: 3.4 Consensus size: 22
3756227 TAATATTTAA
3756237 TAATGATTTTAATATTTGATAG
1 TAATGATTTTAATATTTGATAG
*
3756259 TAATGATTTACTAATGTTT-ACTAG
1 TAATGATTT--TAATATTTGA-TAG
* *
3756283 TAATGAAATTATAATA-ATGATAG
1 TAATG--ATTTTAATATTTGATAG
3756306 TAATGATTT
1 TAATGATTT
3756315 GATACGAATG
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
21 3 0.07
22 9 0.20
23 10 0.22
24 20 0.44
26 3 0.07
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.45
Consensus pattern (22 bp):
TAATGATTTTAATATTTGATAG
Found at i:3756305 original size:47 final size:49
Alignment explanation
Indices: 3756253--3756353 Score: 161
Period size: 50 Copynumber: 2.1 Consensus size: 49
3756243 TTTTAATATT
* *
3756253 TGATAGTAATGA-TT-TACTAATGTTTACTAGTAATGAAATTATAATAA
1 TGATAGTAATGATTTATACGAATGATTACTAGTAATGAAATTATAATAA
3756300 TGATAGTAATGATTTGATACGAATGATTACTAGTAATGAAATTATAATAA
1 TGATAGTAATGATTT-ATACGAATGATTACTAGTAATGAAATTATAATAA
3756350 TGAT
1 TGAT
3756354 TTGATACTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
47 12 0.24
48 2 0.04
50 35 0.71
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.39
Consensus pattern (49 bp):
TGATAGTAATGATTTATACGAATGATTACTAGTAATGAAATTATAATAA
Found at i:3756351 original size:27 final size:27
Alignment explanation
Indices: 3756270--3756354 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
3756260 AATGATTTAC
*
3756270 TAATGTTTACTAGTAATGAAATTATAA
1 TAATGATTACTAGTAATGAAATTATAA
* *
3756297 TAATG---A-TAGTAATG-ATTTGATAC
1 TAATGATTACTAGTAATGAAATT-ATAA
*
3756320 GAATGATTACTAGTAATGAAATTATAA
1 TAATGATTACTAGTAATGAAATTATAA
3756347 TAATGATT
1 TAATGATT
3756355 TGATACTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
22 3 0.07
23 15 0.33
24 1 0.02
26 1 0.02
27 23 0.50
28 3 0.07
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.39
Consensus pattern (27 bp):
TAATGATTACTAGTAATGAAATTATAA
Found at i:3758995 original size:21 final size:22
Alignment explanation
Indices: 3758971--3759014 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3758961 TTGTTTATGT
*
3758971 ATAATATAA-CTTAAACTAACA
1 ATAATATAACCCTAAACTAACA
3758992 ATAATATAACCCTAAACTAACA
1 ATAATATAACCCTAAACTAACA
3759014 A
1 A
3759015 ACTAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.57, C:0.18, G:0.00, T:0.25
Consensus pattern (22 bp):
ATAATATAACCCTAAACTAACA
Found at i:3759201 original size:26 final size:26
Alignment explanation
Indices: 3759161--3759218 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
3759151 CATGTTCTTT
*
3759161 CTTTC-TCGGTTGCAATCTCTTCTCA
1 CTTTCTTCGGTTGCAATATCTTCTCA
*
3759186 CTTTCTTCGGTTGCAATATCTTCTCC
1 CTTTCTTCGGTTGCAATATCTTCTCA
3759212 CTTTCTT
1 CTTTCTT
3759219 TCTTTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.10, C:0.31, G:0.10, T:0.48
Consensus pattern (26 bp):
CTTTCTTCGGTTGCAATATCTTCTCA
Found at i:3759647 original size:29 final size:29
Alignment explanation
Indices: 3759605--3759681 Score: 136
Period size: 29 Copynumber: 2.7 Consensus size: 29
3759595 TCACCTTCTT
*
3759605 GGAAGGCATGGCGACCTACAAGGTCGCCC
1 GGAAGGAATGGCGACCTACAAGGTCGCCC
*
3759634 GGAAGGAATGGCGACCTATAAGGTCGCCC
1 GGAAGGAATGGCGACCTACAAGGTCGCCC
3759663 GGAAGGAATGGCGACCTAC
1 GGAAGGAATGGCGACCTAC
3759682 GACCACACTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.27, C:0.26, G:0.35, T:0.12
Consensus pattern (29 bp):
GGAAGGAATGGCGACCTACAAGGTCGCCC
Found at i:3760720 original size:32 final size:32
Alignment explanation
Indices: 3760675--3760740 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
3760665 TATAAGATCA
*
3760675 AAGGGTTCTCATACATTGTACAGTAAAAACAC
1 AAGGGTTCCCATACATTGTACAGTAAAAACAC
*
3760707 AAGGGTTCCCATACATTGTCCAGTAAAAACAC
1 AAGGGTTCCCATACATTGTACAGTAAAAACAC
3760739 AA
1 AA
3760741 ACTTGTTGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.23
Consensus pattern (32 bp):
AAGGGTTCCCATACATTGTACAGTAAAAACAC
Found at i:3761393 original size:19 final size:21
Alignment explanation
Indices: 3761369--3761417 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
3761359 TACTATTGTC
*
3761369 ATAATTAT-TT-TTTAGAAAA
1 ATAATTATATTATTTAAAAAA
3761388 ATAATTAAATATTATTTAAAAAA
1 ATAATT--ATATTATTTAAAAAA
3761411 ATAATTA
1 ATAATTA
3761418 GTCTGTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 6 0.24
21 3 0.12
22 2 0.08
23 14 0.56
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAATTATATTATTTAAAAAA
Found at i:3761405 original size:23 final size:23
Alignment explanation
Indices: 3761374--3761417 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3761364 TTGTCATAAT
* *
3761374 TATTTTTTAGAAAAATAATTAAA
1 TATTATTTAAAAAAATAATTAAA
3761397 TATTATTTAAAAAAATAATTA
1 TATTATTTAAAAAAATAATTA
3761418 GTCTGTGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TATTATTTAAAAAAATAATTAAA
Found at i:3762198 original size:28 final size:28
Alignment explanation
Indices: 3762174--3762233 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
3762164 TAGAATAATT
3762174 TAAACAAATTAATAAAAATAAAATAAAA
1 TAAACAAATTAATAAAAATAAAATAAAA
*
3762202 TAAATAAATTAATAAATAA-ATAAAT-AAA
1 TAAACAAATTAATAAA-AATA-AAATAAAA
3762230 TAAA
1 TAAA
3762234 ATAAAGTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAACAAATTAATAAAAATAAAATAAAA
Found at i:3762207 original size:20 final size:20
Alignment explanation
Indices: 3762179--3762238 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
3762169 TAATTTAAAC
*
3762179 AAATTAATAAAAATAAAATA
1 AAATAAATAAAAATAAAATA
3762199 AAATAAATAAATTAAT-AAAT-
1 AAATAAATAAA--AATAAAATA
3762219 AAATAAAT--AAATAAAATA
1 AAATAAATAAAAATAAAATA
3762237 AA
1 AA
3762239 GTTAGTGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 3 0.09
17 4 0.11
18 3 0.09
20 18 0.51
21 4 0.11
22 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAAATAAAAATAAAATA
Found at i:3762208 original size:4 final size:4
Alignment explanation
Indices: 3762189--3762238 Score: 64
Period size: 4 Copynumber: 11.8 Consensus size: 4
3762179 AAATTAATAA
*
3762189 AAAT AAAAT AAAAT AAAT AAAT TAAT AAAT AAAT AAAT AAAT AAAAT AAA
1 AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAA
3762239 GTTAGTGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
4 29 0.69
5 13 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3763702 original size:139 final size:138
Alignment explanation
Indices: 3763447--3763956 Score: 653
Period size: 139 Copynumber: 3.7 Consensus size: 138
3763437 TCAATTTGGA
* * * ** *
3763447 GATAATTTGGTGACAACATGGTTCCTACGTGATGAGGAAATCTGATTGTTTGAGGATGACATTGT
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTGCATGAGGATGACATTGC
* * * ** *
3763512 TCTTATGCGTTGAGGAGATCTAGTCGGTGGACGACATTGTTATTACGTGATGAGGACACATAGCT
66 TCCTATGCGTTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACTC-TAGCT
3763577 GTCTTTAGG
130 GTCTTTAGG
* * * * **
3763586 GATACTTTGGAGACAACACAGTTTCTACGTGATGAGGAAGTCTGATTGCCTGAGGATGATGTTGC
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTGCATGAGGATGACATTGC
* *
3763651 TCCTACGAGTTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACGTCTAGCT
66 TCCTATGCGTTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGAC-TCTAGCT
3763716 GTCTTTAGG
130 GTCTTTAGG
* * * *
3763725 GATAATTTGTAGACAAGACGGTTCCTACGTGATGAGGAAGTCTGATTACATGAGGATGACACTGC
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTGCATGAGGATGACATTGC
* *
3763790 TCCTATGCGTTGAGGAGATCTGGTCAGTGGATGACATTGTTCCTACGTGATGAGGATGTCTAGCT
66 TCCTATGCGTTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGA-CTCTAGCT
3763855 GTCTTTAGG
130 GTCTTTAGG
* * * * * * *
3763864 GATAATTTGGAGACAAAACGGTTCCTACGTGATGAGGAAGTATGGTTATC-TAAAGATGACACTG
1 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATT-GCATGAGGATGACATTG
* * *
3763928 CTCCTACGCGTTGATGTGATCTGGTCGGT
65 CTCCTATGCGTTGAGGAGATCTGGTCGGT
3763957 TGCCAATGAT
Statistics
Matches: 324, Mismatches: 44, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
139 322 0.99
140 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.29, T:0.31
Consensus pattern (138 bp):
GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTGCATGAGGATGACATTGC
TCCTATGCGTTGAGGAGATCTGGTCGGTGGATGACATTGTTCCTACGTGATGAGGACTCTAGCTG
TCTTTAGG
Found at i:3763844 original size:40 final size:43
Alignment explanation
Indices: 3763745--3763850 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 43
3763735 AGACAAGACG
*
3763745 GTTCCTACGTGATGAGGAAGTCTGATTACATGAGGATGACACT
1 GTTCCTACGTGATGAGGAAGTCTGAGTACATGAGGATGACACT
* * * * * *
3763788 GCTCCTATGCGTTGAGG-AGATCTG-GT-CA-GTGGATGACATT
1 GTTCCTACGTGATGAGGAAG-TCTGAGTACATGAGGATGACACT
*
3763828 GTTCCTACGTGATGAGGATGTCT
1 GTTCCTACGTGATGAGGAAGTCT
3763851 AGCTGTCTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
40 26 0.53
41 3 0.06
42 3 0.06
43 17 0.35
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
GTTCCTACGTGATGAGGAAGTCTGAGTACATGAGGATGACACT
Found at i:3764291 original size:30 final size:30
Alignment explanation
Indices: 3764255--3764359 Score: 77
Period size: 30 Copynumber: 3.3 Consensus size: 30
3764245 CTTTGTTGCG
3764255 AGAGAAACAATATCAAAGGTTTATGTTTCA
1 AGAGAAACAATATCAAAGGTTTATGTTTCA
** * * *
3764285 AGAGAAACTGTCTCAAGCGAGATAAAACTT-TGTTTCG
1 AGAGAAACAATATCAA---AGGT-----TTATGTTTCA
*
3764322 AGAGGAACAATATCAAAGGTTTATGTTTCA
1 AGAGAAACAATATCAAAGGTTTATGTTTCA
3764352 AGAGAAAC
1 AGAGAAAC
3764360 TGTCTCAAGC
Statistics
Matches: 54, Mismatches: 12, Indels: 18
0.64 0.14 0.21
Matches are distributed among these distances:
29 2 0.04
30 26 0.48
33 3 0.06
34 3 0.06
37 18 0.33
38 2 0.04
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (30 bp):
AGAGAAACAATATCAAAGGTTTATGTTTCA
Found at i:3764302 original size:67 final size:67
Alignment explanation
Indices: 3764102--3764394 Score: 403
Period size: 67 Copynumber: 4.4 Consensus size: 67
3764092 TATCTTAGGT
* * * * ** *
3764102 GAGATAAAATTTTGTTTCGAGTGAAAC-ATTTCAAA-ATTTGCGTTTCAAGGGAAAACTGTCTCA
1 GAGATAAAACTTTGTTTCGAGAGAAACAATATCAAAGGTTTATGTTTCAAGAG-AAACTGTCTCA
*
3764165 AGT
65 AGC
* * * *
3764168 GAGATGAAACTTTGTTTCAAGAGAAACAATTCTCAATGGTTTATGTTTCAAGAGAAACTGTCTCA
1 GAGATAAAACTTTGTTTCGAGAGAAACAA-TATCAAAGGTTTATGTTTCAAGAGAAACTGTCTCA
3764233 AGC
65 AGC
*
3764236 GAGATAAAACTTTGTTGCGAGAGAAACAATATCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAA
1 GAGATAAAACTTTGTTTCGAGAGAAACAATATCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAA
3764301 GC
66 GC
*
3764303 GAGATAAAACTTTGTTTCGAGAGGAACAATATCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAA
1 GAGATAAAACTTTGTTTCGAGAGAAACAATATCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAA
3764368 GC
66 GC
* *
3764370 AAGATAAAA-TTTGTTTCAAGAGAAA
1 GAGATAAAACTTTGTTTCGAGAGAAA
3764395 TTGTCTCTAG
Statistics
Matches: 203, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
66 37 0.18
67 110 0.54
68 44 0.22
69 12 0.06
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (67 bp):
GAGATAAAACTTTGTTTCGAGAGAAACAATATCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAA
GC
Found at i:3764392 original size:36 final size:36
Alignment explanation
Indices: 3764211--3764421 Score: 117
Period size: 36 Copynumber: 6.1 Consensus size: 36
3764201 CAATGGTTTA
*
3764211 TGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGCAAGATAAAA-TT
* * ** * *
3764248 TGTTGCGAGAGAAACAATATC-A--AAGGT----TT
1 TGTTTCAAGAGAAACTGTCTCAAGCAAGATAAAATT
*
3764277 ATGTTTCAAGAGAAACTGTCTCAAGCGAGATAAAACTT
1 -TGTTTCAAGAGAAACTGTCTCAAGCAAGATAAAA-TT
* * ** * *
3764315 TGTTTCGAGAGGAACAATATC-A--AAGGT----TT
1 TGTTTCAAGAGAAACTGTCTCAAGCAAGATAAAATT
3764344 ATGTTTCAAGAGAAACTGTCTCAAGCAAGATAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGCAAGATAAAATT
* * * * *
3764381 TGTTTCAAGAGAAATTGTCTCTAGCGATACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGCAAGATAAAATT
3764417 TGTTT
1 TGTTT
3764422 TTAGTTAAAA
Statistics
Matches: 125, Mismatches: 32, Indels: 35
0.65 0.17 0.18
Matches are distributed among these distances:
29 4 0.03
30 32 0.26
31 2 0.02
33 7 0.06
34 6 0.05
36 38 0.30
37 34 0.27
38 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGCAAGATAAAATT
Found at i:3764638 original size:66 final size:66
Alignment explanation
Indices: 3764519--3764766 Score: 216
Period size: 67 Copynumber: 3.7 Consensus size: 66
3764509 TTTATTTTGA
* * * * * *
3764519 GAAAACAATCTCAATTGAGA-TAAATTT-TGTTTCAAGTAAAACAATTTCAAAATTTGTATTTC-
1 GAAAACTATCTCAAGTGAGACGAAATTTGT-TTTCAAGAAAAACAATCTC-AAATTT-TATGTCT
*
3764581 TAGG
63 TAAG
* *
3764585 GAAAACTATCTCAAGTGAGACGAAATTTGTTTTCAAGAAAAATAATCTCAAATTTTCGTGTCTTA
1 GAAAACTATCTCAAGTGAGACGAAATTTGTTTTCAAGAAAAACAATCTCAAATTTT-ATGTCTTA
3764650 AG
65 AG
* * * * * * * * * *
3764652 GAAGATTGTATCAAGTTAGACGACATTTGTTTTTAAGGAAAACAATCTCAAGTGTTCATGTCTTA
1 GAAAACTATCTCAAGTGAGACGAAATTTGTTTTCAAGAAAAACAATCTCAAAT-TTTATGTCTTA
3764717 AG
65 AG
* * * *
3764719 GAAGACTGTCTCAAGTGAGACAAAATTTGTTTT-GAGAAAAACAATCTC
1 GAAAACTATCTCAAGTGAGACGAAATTTGTTTTCAAGAAAAACAATCTC
3764767 TAGTAAGATA
Statistics
Matches: 149, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
65 1 0.01
66 40 0.27
67 105 0.70
68 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (66 bp):
GAAAACTATCTCAAGTGAGACGAAATTTGTTTTCAAGAAAAACAATCTCAAATTTTATGTCTTAA
G
Found at i:3764666 original size:67 final size:66
Alignment explanation
Indices: 3764595--3764766 Score: 227
Period size: 67 Copynumber: 2.6 Consensus size: 66
3764585 GAAAACTATC
* * * *
3764595 TCAAGTGAGACGAAATTTGTTTTCAAGAAAAATAATCTCAAATTTTCGTGTCTTAAGGAAGATTG
1 TCAAGTGAGACGAAATTTGTTTT-AAGAAAAACAATCTCAAATGTTCATGTCTTAAGGAAGACTG
3764660 TA
65 TA
* * * *
3764662 TCAAGTTAGACGACATTTGTTTTTAAGGAAAACAATCTCAAGTGTTCATGTCTTAAGGAAGACTG
1 TCAAGTGAGACGAAATTTG-TTTTAAGAAAAACAATCTCAAATGTTCATGTCTTAAGGAAGACTG
*
3764727 TC
65 TA
* *
3764729 TCAAGTGAGACAAAATTTGTTTTGAGAAAAACAATCTC
1 TCAAGTGAGACGAAATTTGTTTTAAGAAAAACAATCTC
3764767 TAGTAAGATA
Statistics
Matches: 90, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
66 17 0.19
67 69 0.77
68 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.33
Consensus pattern (66 bp):
TCAAGTGAGACGAAATTTGTTTTAAGAAAAACAATCTCAAATGTTCATGTCTTAAGGAAGACTGT
A
Found at i:3764938 original size:35 final size:37
Alignment explanation
Indices: 3764878--3764965 Score: 117
Period size: 35 Copynumber: 2.4 Consensus size: 37
3764868 CAAATGTTCA
* *
3764878 TGTTTCAAGAGAAAATTATCTCAAGTGAGAC-AAATTT
1 TGTTTCAAGAG-AAACTGTCTCAAGTGAGACAAAATTT
*
3764915 T-TTTTAAGAGAAACTGTCTCAAGTGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTT
*
3764951 TGTTTCGAGAGAAAC
1 TGTTTCAAGAGAAAC
3764966 AATCTTAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 17 0.39
36 15 0.34
37 12 0.27
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAATTT
Found at i:3767896 original size:17 final size:17
Alignment explanation
Indices: 3767856--3767900 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3767846 CTTCTTTTTC
*
3767856 TTTCTTT-CT-TTTCTT
1 TTTCTTTGCTCTTTATT
3767871 TTCTCTTTGCTCTTTATT
1 TT-TCTTTGCTCTTTATT
3767889 TTTCTTTGCTCT
1 TTTCTTTGCTCT
3767901 CTTTTTCCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 5 0.19
17 12 0.46
18 7 0.27
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTCTTTGCTCTTTATT
Found at i:3767902 original size:19 final size:19
Alignment explanation
Indices: 3767850--3767904 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
3767840 ACTTGTCTTC
* *
3767850 TTTTTCTTT-CTTTCTTTTC
1 TTTTTCTTTGCTCTC-TTTA
3767869 TTTTCTCTTTG--CTCTTTA
1 TTTT-TCTTTGCTCTCTTTA
3767887 TTTTTCTTTGCTCTCTTT
1 TTTTTCTTTGCTCTCTTT
3767905 TTCCCCTTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 6 0.20
18 7 0.23
19 12 0.40
20 5 0.17
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTTCTTTGCTCTCTTTA
Found at i:3773354 original size:133 final size:133
Alignment explanation
Indices: 3773104--3773588 Score: 569
Period size: 133 Copynumber: 3.6 Consensus size: 133
3773094 GGAATATGAT
* * * * * * ** * ** *
3773104 GAGGGATCTGTTCTGCTTCTTCTCGAGGAAAAATCAGATCTAGGGTTGTTGAATCATTATACTAT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAAT-AAATTTAGGGACGTTGATTCATTCCACTGT
* * * * *
3773169 CACTCAAGGAAGATTGAATCGAGGTAGACTTGTTCCACTATTACTTAGGAAATATCAAATATTGA
65 CACTCAAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCACGAAATATCAAATCTTGA
3773234 AAGA
130 AAGA
* ** * *
3773238 GAGGGATCTGTTTTGCTTTTTCTTGAGGGAAAATAAGATTTAGGGACGTTGATTCATTCTACTGT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATAA-ATTTAGGGACGTTGATTCATTCCACTGT
* * * *
3773303 CAC-CAAGGAAGATTGAATAGAGGCAGACTTGTTCCACTGTTACTCATGAAATATCAGATCCTGA
65 CACTCAAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCACGAAATATCAAATCTTGA
*
3773367 AATA
130 AAGA
* *
3773371 GAGGGATATGTTCCACTTCTTCTTGAGGGAAAATCAAATAT-GGGACGTTGATTCATTCCACTGT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAAT-AAATTTAGGGACGTTGATTCATTCCACTGT
* * * *
3773435 CACTCAAGGTAGATTGAATCGAGGCATACTTATTCCACTGTTACTCACGGAATATCAAATCTTGA
65 CACTCAAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCACGAAATATCAAATCTTGA
3773500 AAGA
130 AAGA
* * * * *
3773504 GATGGATATGTTTCGCTTCTTCTTGAGGGAAAATTAAATTTGGGGATGTTGATTCATTCCACTTT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAA-TAAATTTAGGGACGTTGATTCATTCCACTGT
*
3773569 CACCCAAGGAAGATTGAATC
65 CACTCAAGGAAGATTGAATC
3773589 AAGTTCAATT
Statistics
Matches: 302, Mismatches: 44, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
132 25 0.08
133 180 0.60
134 97 0.32
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (133 bp):
GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATAAATTTAGGGACGTTGATTCATTCCACTGTC
ACTCAAGGAAGATTGAATCGAGGCAGACTTGTTCCACTGTTACTCACGAAATATCAAATCTTGAA
AGA
Found at i:3781276 original size:131 final size:131
Alignment explanation
Indices: 3781031--3781369 Score: 337
Period size: 131 Copynumber: 2.6 Consensus size: 131
3781021 ATACTTTTAA
* * * * * *
3781031 GAGTGAAAACAATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACA
1 GAGTGAAAACGATAATATCTAATTATTTCCAGTCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *** * *
3781096 -TTCATTTATTACCCCAATTGAAATAAAGAAATATTACTATTTTGCCTT-AAAATTCAATATCGA
66 GTT-ATTTATTACCCCAATCGAAATAAAGAAATATCAATATTCCACCTTAAAAACT-AATATCAA
3781159 -TT
129 TTT
* *
3781161 GAAGTGAAAACGATAATATCTAATGATTTCCAGTCGAGAATAAATGACCTCTCATACCTTAAAGC
1 G-AGTGAAAACGATAATATCTAATTATTTCCAGTCGAGAATAAATGACCTCTCATGCCTTAAAGC
* * * * * ** *
3781226 AGTTATTTATTGCTCCAATCGAAATGAAGAGATATCAATATTCCATCTTAAAAACTGGTATTAAT
65 AGTTATTTATTACCCCAATCGAAATAAAGAAATATCAATATTCCACCTTAAAAACTAATATCAAT
3781291 TT
130 TT
* * *
3781293 GAGAGAAAACG-TCAATATCAAATTATTTCCAAGT-GAGAATAAATGACCTCTCATGCCTTCAAG
1 GAGTGAAAACGAT-AATATCTAATTATTTCC-AGTCGAGAATAAATGACCTCTCATGCCTTAAAG
* *
3781356 AAGTCATTTATTAC
64 CAGTTATTTATTAC
3781370 TCTGACCAAA
Statistics
Matches: 171, Mismatches: 32, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
130 2 0.01
131 156 0.91
132 13 0.08
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (131 bp):
GAGTGAAAACGATAATATCTAATTATTTCCAGTCGAGAATAAATGACCTCTCATGCCTTAAAGCA
GTTATTTATTACCCCAATCGAAATAAAGAAATATCAATATTCCACCTTAAAAACTAATATCAATT
T
Found at i:3783366 original size:3 final size:3
Alignment explanation
Indices: 3783358--3783402 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
3783348 AAGAAAAAAG
* *
3783358 TAA TAA TAA TAA TAA TAA TAG TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3783403 ATAAATAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3783407 original size:4 final size:4
Alignment explanation
Indices: 3783398--3783426 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3783388 TAATAATAAT
3783398 AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA A
3783427 TCGGACGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:3789969 original size:19 final size:19
Alignment explanation
Indices: 3789945--3789991 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
3789935 GAAAGTTGAG
3789945 TACAAGATTCATCGACCCA
1 TACAAGATTCATCGACCCA
* *
3789964 TACAAGATTCATCGACTCG
1 TACAAGATTCATCGACCCA
3789983 TACAAGATT
1 TACAAGATT
3789992 ATTAAGAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (19 bp):
TACAAGATTCATCGACCCA
Found at i:3800649 original size:55 final size:53
Alignment explanation
Indices: 3800516--3800847 Score: 276
Period size: 55 Copynumber: 6.2 Consensus size: 53
3800506 GATTCACACG
* * * *
3800516 TAGTGCCTATACGG-TAGTTCATCAACTTATGATGAATTTCGTAGG-TTGC--ACA
1 TAGTGCATGTACGGTTA-TTCATCAACTCATGATGAATTT-GT-GGATTTCATACA
* * *
3800568 TAGTGTGCCTGTACGGTTATTTATCAACTCAAGATGAATTCTGTGGAATTTCATACA
1 TA--GTGCATGTACGGTTATTCATCAACTCATGATGAATT-TGTGG-ATTTCATACA
* *
3800625 TAGTGCATGTACGGTTATTCATCAACTCATGATAAATTTCTTGG-----AT--A
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTT-GTGGATTTCATACA
* * *
3800672 TAGTGCATGTATGATTATTCATCAATTCATGATGAATTTCGTGGATTT-ACTCACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTT-GTGGATTTCA-T-ACA
* * *
3800727 TAGTGCATGTATGGTTATTCATCAACGT-ATGATGAATTTTGTGGTTTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAAC-TCATGATGAA-TTTGTGGATTT-CATACA
* *
3800782 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
1 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTT-GTGGATTT-CATACA
3800837 TAGTGCATGTA
1 TAGTGCATGTA
3800848 GTAGACTTAG
Statistics
Matches: 234, Mismatches: 23, Indels: 43
0.78 0.08 0.14
Matches are distributed among these distances:
47 40 0.17
49 2 0.01
51 1 0.00
52 3 0.01
53 2 0.01
54 36 0.15
55 140 0.60
56 4 0.02
57 6 0.03
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (53 bp):
TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTGTGGATTTCATACA
Found at i:3800681 original size:47 final size:47
Alignment explanation
Indices: 3800624--3800717 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
3800614 AATTTCATAC
* *
3800624 ATAGTGCATGTACGGTTATTCATCAACTCATGATAAATTTCTTGGAT
1 ATAGTGCATGTACGATTATTCATCAACTCATGATAAATTTCGTGGAT
* * *
3800671 ATAGTGCATGTATGATTATTCATCAATTCATGATGAATTTCGTGGAT
1 ATAGTGCATGTACGATTATTCATCAACTCATGATAAATTTCGTGGAT
3800718 TTACTCACAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (47 bp):
ATAGTGCATGTACGATTATTCATCAACTCATGATAAATTTCGTGGAT
Found at i:3800733 original size:102 final size:104
Alignment explanation
Indices: 3800516--3800847 Score: 302
Period size: 102 Copynumber: 3.1 Consensus size: 104
3800506 GATTCACACG
* * * * * *
3800516 TAGTGCCTATACGG-TAGTTCATCAACTTATGATGAATTTCGTAGGTTGCACATAGTGTGCCTGT
1 TAGTGCATGTACGGTTA-TTCATCAACGTATGATAAATTTTGT-GG-TGCACATA--GTGCATGT
* * *
3800580 ACGGTTATTTATCAACTCAAGATGAA-TTCTGTGGAATTTCAT-ACA
61 ACGATTATTCATCAACTCATGATGAATTTC-GTGG-ATTTC-TCACA
* *
3800625 TAGTGCATGTACGGTTATTCATCAAC-TCATGATAAATTTCT-T-G-G-ATATAGTGCATGTATG
1 TAGTGCATGTACGGTTATTCATCAACGT-ATGATAAATTT-TGTGGTGCACATAGTGCATGTACG
*
3800685 ATTATTCATCAATTCATGATGAATTTCGTGGATTTACTCACA
64 ATTATTCATCAACTCATGATGAATTTCGTGGATTT-CTCACA
* * *
3800727 TAGTGCATGTATGGTTATTCATCAACGTATGATGAATTTTGTGGTTTTGCACACATAGTGCCTGT
1 TAGTGCATGTACGGTTATTCATCAACGTATGATAAATTTTGTGG---TG--CACATAGTGCATGT
* *
3800792 ACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
61 ACGATTATTCATCAACTCATGATGAATTTCGTGGATTT-CTCACA
3800837 TAGTGCATGTA
1 TAGTGCATGTA
3800848 GTAGACTTAG
Statistics
Matches: 187, Mismatches: 20, Indels: 31
0.79 0.08 0.13
Matches are distributed among these distances:
101 6 0.03
102 72 0.39
103 5 0.03
104 4 0.02
105 1 0.01
107 2 0.01
108 1 0.01
109 32 0.17
110 64 0.34
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (104 bp):
TAGTGCATGTACGGTTATTCATCAACGTATGATAAATTTTGTGGTGCACATAGTGCATGTACGAT
TATTCATCAACTCATGATGAATTTCGTGGATTTCTCACA
Found at i:3807602 original size:27 final size:27
Alignment explanation
Indices: 3807565--3807618 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3807555 GAACAAGTTC
3807565 CCCTCATCACCTTGGAATTCGAAGGAT
1 CCCTCATCACCTTGGAATTCGAAGGAT
3807592 CCCTCATCACCTTGGAATTCGAAGGAT
1 CCCTCATCACCTTGGAATTCGAAGGAT
3807619 ATGCTCACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (27 bp):
CCCTCATCACCTTGGAATTCGAAGGAT
Found at i:3819498 original size:17 final size:17
Alignment explanation
Indices: 3819478--3819512 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3819468 ACTACTTCCC
3819478 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
3819495 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
3819512 T
1 T
3819513 TAATAAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:3821193 original size:19 final size:20
Alignment explanation
Indices: 3821163--3821200 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
3821153 CAAAGTTTCA
3821163 TTTTGTTTTTCAAAATCAAC
1 TTTTGTTTTTCAAAATCAAC
3821183 TTTTG-TTTTCAAAATCAA
1 TTTTGTTTTTCAAAATCAA
3821201 ATCATTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTGTTTTTCAAAATCAAC
Found at i:3824540 original size:19 final size:19
Alignment explanation
Indices: 3824516--3824553 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3824506 CTTACAAAGC
3824516 CCAGCAGTATAATCGCTAA
1 CCAGCAGTATAATCGCTAA
3824535 CCAGCAGTATAATCGCTAA
1 CCAGCAGTATAATCGCTAA
3824554 TCTAGAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (19 bp):
CCAGCAGTATAATCGCTAA
Found at i:3825811 original size:3 final size:3
Alignment explanation
Indices: 3825803--3825855 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
3825793 CCCTCTAATC
3825803 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3825851 TTA TT
1 TTA TT
3825856 TATTTTGAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3826504 original size:3 final size:3
Alignment explanation
Indices: 3826496--3826539 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
3826486 CCTCTCAACA
3826496 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3826540 CCATTTAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3827546 original size:15 final size:15
Alignment explanation
Indices: 3827528--3827582 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
3827518 TTTATTGAGT
3827528 TTATTAATCTTATAA
1 TTATTAATCTTATAA
3827543 TTATATTAA--TTATTAA
1 -T-TATTAATCTTA-TAA
*
3827559 ATATTAATCTTATAA
1 TTATTAATCTTATAA
*
3827574 TTATAAATC
1 TTATTAATC
3827583 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 6 0.19
15 13 0.41
16 7 0.22
17 6 0.19
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATTAATCTTATAA
Found at i:3827551 original size:17 final size:17
Alignment explanation
Indices: 3827529--3827578 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
3827519 TTATTGAGTT
3827529 TATTAATCTTATAATTA
1 TATTAATCTTATAATTA
3827546 TATTAA--TTATTAA--A
1 TATTAATCTTA-TAATTA
3827560 TATTAATCTTATAATTA
1 TATTAATCTTATAATTA
3827577 TA
1 TA
3827579 AATCATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
14 7 0.25
15 6 0.21
16 6 0.21
17 9 0.32
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAATCTTATAATTA
Found at i:3830173 original size:61 final size:61
Alignment explanation
Indices: 3830078--3830199 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
3830068 ATTAAGAAGC
3830078 CGTTTAATACGAAAAACCCACTTACATCCAACAAGGTTCTGCAGAGAATTAGATGGAACAA
1 CGTTTAATACGAAAAACCCACTTACATCCAACAAGGTTCTGCAGAGAATTAGATGGAACAA
3830139 CGTTTAATACGAAAAACCCACTTACATCCAACAAGGTTCTGCAGAGAATTAGATGGAACAA
1 CGTTTAATACGAAAAACCCACTTACATCCAACAAGGTTCTGCAGAGAATTAGATGGAACAA
3830200 GCTCCCAAGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (61 bp):
CGTTTAATACGAAAAACCCACTTACATCCAACAAGGTTCTGCAGAGAATTAGATGGAACAA
Found at i:3833235 original size:52 final size:53
Alignment explanation
Indices: 3833169--3833277 Score: 184
Period size: 52 Copynumber: 2.1 Consensus size: 53
3833159 ACACAAGATG
*
3833169 AGGCACATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACA
1 AGGCACATA-AAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACA
*
3833223 AGGCACAT-AAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATCACA
1 AGGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACA
3833275 AGG
1 AGG
3833278 ATATTATAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 45 0.85
54 8 0.15
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (53 bp):
AGGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACA
Done.