Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 21
Found at i:4160713 original size:20 final size:20
Alignment explanation
Indices: 4160651--4160728 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
4160641 GCAAAGCGAA
*
4160651 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
4160671 TT-AGCTTTCGCATTACGATT
1 TTGA-CTTTCGCATTGCGATT
4160691 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
* * *
4160711 TTGAGTTTAGCGTTGCGA
1 TTGACTTTCGCATTGCGA
4160729 AAGTGTACCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:4160849 original size:13 final size:13
Alignment explanation
Indices: 4160831--4160870 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
4160821 TTATTTACAC
4160831 ATCAATTAAACAA
1 ATCAATTAAACAA
**
4160844 ATCAATTTTTACAA
1 ATCAA-TTAAACAA
4160858 ATCAATTAAACAA
1 ATCAATTAAACAA
4160871 GCAAAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
ATCAATTAAACAA
Found at i:4162296 original size:42 final size:42
Alignment explanation
Indices: 4162237--4162330 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
4162227 GTGAATCGGG
*
4162237 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAAGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAAGGGC
* ** * *
4162279 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAAGGGC
4162321 CTCTTGAACG
1 CTCTTGAACG
4162331 ATAGGAGAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 41 0.91
43 4 0.09
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAAGGGC
Found at i:4162303 original size:21 final size:20
Alignment explanation
Indices: 4162237--4162306 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
4162227 GTGAATCGGG
*
4162237 CTCTTGAATGGTGGGAGGGA
1 CTCTTGAACGGTGGGAGGGA
* * ** *
4162257 CCTCTTCAACGATGACAAGGGC
1 -CTCTTGAACGGTG-GGAGGGA
4162279 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGA-GGGA
4162300 CTCTTGA
1 CTCTTGA
4162307 GGGATGATAG
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 1 0.03
21 31 0.86
22 4 0.11
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGA
Found at i:4162356 original size:42 final size:42
Alignment explanation
Indices: 4162275--4162359 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
4162265 ACGATGACAA
* * * * *
4162275 GGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAG
1 GGGCCTCTTGAACGATAGGAGAGGACTCTTGAAGAATGATAG
* *
4162317 GGGCCTCTTGAACGATAGGAGAGGCCTCTTGAATAATGATAG
1 GGGCCTCTTGAACGATAGGAGAGGACTCTTGAAGAATGATAG
4162359 G
1 G
4162360 TGAGTCAGGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.22
Consensus pattern (42 bp):
GGGCCTCTTGAACGATAGGAGAGGACTCTTGAAGAATGATAG
Found at i:4162892 original size:20 final size:20
Alignment explanation
Indices: 4162869--4162913 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
4162859 ACTTAAAATT
4162869 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
**
4162889 GCAACGCGAATTTGACTATC
1 GCAACGCGAAAATGACTATC
4162909 GCAAC
1 GCAAC
4162914 AAGATAATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:4162942 original size:14 final size:14
Alignment explanation
Indices: 4162906--4162947 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
4162896 GAATTTGACT
* *
4162906 ATCGCAACAAGATA
1 ATCGCAACGAGAAA
4162920 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
*
4162934 ATCGCAACGTGAAA
1 ATCGCAACGAGAAA
4162948 CTAAATTCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:4162989 original size:14 final size:14
Alignment explanation
Indices: 4162970--4163002 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
4162960 TGCGATTTTC
4162970 ATTTTCACATTGCG
1 ATTTTCACATTGCG
*
4162984 ATTTTCACGTTGCG
1 ATTTTCACATTGCG
4162998 ATTTT
1 ATTTT
4163003 TATTTCGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (14 bp):
ATTTTCACATTGCG
Found at i:4163019 original size:33 final size:34
Alignment explanation
Indices: 4162957--4163032 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
4162947 ACTAAATTCG
*
4162957 CGTTGCGATTTTCATTTTCACATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCACATTGCGATTATCA
* * *
4162991 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCACATTGCGATTATCA
4163024 CGTTGCGAT
1 CGTTGCGAT
4163033 AGTCAAATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 25 0.66
34 13 0.34
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCACATTGCGATTATCA
Found at i:4163049 original size:20 final size:20
Alignment explanation
Indices: 4163024--4163092 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
4163014 GCGATTATCC
*
4163024 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
4163044 CGTTGCGATAGTC-ATTTCTG
1 CGTTGCGATAGTCAATTTC-G
* *
4163064 CGTTGCGATAGTTATTTTCG
1 CGTTGCGATAGTCAATTTCG
4163084 CGTTGCGAT
1 CGTTGCGAT
4163093 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.09
20 36 0.82
21 4 0.09
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:4165015 original size:20 final size:20
Alignment explanation
Indices: 4164976--4165045 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
4164966 CTTAAAATCA
* **
4164976 CAACACGAAAATGAAAATCG
1 CAACACGAAATTGACTATCG
4164996 CAACACGAAATTGACTATCG
1 CAACACGAAATTGACTATCG
**
4165016 CAATGCG-AATTCGACTATCG
1 CAACACGAAATT-GACTATCG
*
4165036 CAACGCGAAA
1 CAACACGAAA
4165046 CTAAAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 4 0.10
20 36 0.86
21 2 0.05
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (20 bp):
CAACACGAAATTGACTATCG
Found at i:4165452 original size:22 final size:22
Alignment explanation
Indices: 4165425--4165472 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
4165415 GGAGATAGAT
4165425 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGTCGGAGATGGGGAC
*
4165447 GGATTTCGTTGGAGATGGGGAC
1 GGATTTCGTCGGAGATGGGGAC
4165469 GGAT
1 GGAT
4165473 GTCGCCATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.19, C:0.10, G:0.46, T:0.25
Consensus pattern (22 bp):
GGATTTCGTCGGAGATGGGGAC
Found at i:4165689 original size:20 final size:20
Alignment explanation
Indices: 4165664--4165742 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
4165654 TCATAATCGC
4165664 TCAGAATCGCGTTGCGATAG
1 TCAGAATCGCGTTGCGATAG
*
4165684 TCAGAATCGCGTTGCGATTTTG
1 TCAGAATCGCGTTGCGA--TAG
** *
4165706 T-ATTATCACGTTGCGATAG
1 TCAGAATCGCGTTGCGATAG
*
4165725 TCAGAATCGCATTGCGAT
1 TCAGAATCGCGTTGCGAT
4165743 TTTCCAAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
19 3 0.06
20 29 0.62
21 12 0.26
22 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGATAG
Found at i:4165852 original size:19 final size:19
Alignment explanation
Indices: 4165828--4165864 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4165818 TGTGATACTG
* *
4165828 GAGATCGCGTTGTGATTTA
1 GAGATCGCATTGCGATTTA
4165847 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
4165865 TGTTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:4170851 original size:24 final size:24
Alignment explanation
Indices: 4170819--4170869 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
4170809 TTTGATTTGA
4170819 CATAAGCGAGTCCATCTCATCTTT
1 CATAAGCGAGTCCATCTCATCTTT
4170843 CATAAGCGAGTCCATCTCATCTTT
1 CATAAGCGAGTCCATCTCATCTTT
4170867 CAT
1 CAT
4170870 GAAAAACTCT
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:0.25, C:0.29, G:0.12, T:0.33
Consensus pattern (24 bp):
CATAAGCGAGTCCATCTCATCTTT
Found at i:4172569 original size:15 final size:15
Alignment explanation
Indices: 4172549--4172581 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4172539 TAAAATCTTT
*
4172549 TTTTCCCCTTCTTGA
1 TTTTCCCCTTCTGGA
4172564 TTTTCCCCTTCTGGA
1 TTTTCCCCTTCTGGA
4172579 TTT
1 TTT
4172582 CGATCTGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.30, G:0.09, T:0.55
Consensus pattern (15 bp):
TTTTCCCCTTCTGGA
Found at i:4186762 original size:36 final size:36
Alignment explanation
Indices: 4186722--4186799 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
4186712 TAAGCCATAA
4186722 AGCTTCTTTTGCAACTTCAACCGCTGCCATGTATTC
1 AGCTTCTTTTGCAACTTCAACCGCTGCCATGTATTC
* * * *
4186758 AGCTTCTTTTGTAGCTTCAGCCGCTGCTATGTATTC
1 AGCTTCTTTTGCAACTTCAACCGCTGCCATGTATTC
4186794 AGCTTC
1 AGCTTC
4186800 AGTTGTAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (36 bp):
AGCTTCTTTTGCAACTTCAACCGCTGCCATGTATTC
Found at i:4186806 original size:36 final size:36
Alignment explanation
Indices: 4186736--4186807 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
4186726 TCTTTTGCAA
**
4186736 CTTCAACCGCTGCCATGTATTCAGCTTCTTTTGTAG
1 CTTCAACCGCTGCCATGTATTCAGCTTCAGTTGTAG
* *
4186772 CTTCAGCCGCTGCTATGTATTCAGCTTCAGTTGTAG
1 CTTCAACCGCTGCCATGTATTCAGCTTCAGTTGTAG
4186808 ATAATGCCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (36 bp):
CTTCAACCGCTGCCATGTATTCAGCTTCAGTTGTAG
Found at i:4191821 original size:10 final size:10
Alignment explanation
Indices: 4191786--4191828 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
4191776 ATCATTTAAA
*
4191786 TTTAGGTTTG
1 TTTATGTTTG
* *
4191796 TTTATATTTA
1 TTTATGTTTG
4191806 TTTATGTTTG
1 TTTATGTTTG
*
4191816 TTTATGTTCG
1 TTTATGTTTG
4191826 TTT
1 TTT
4191829 GTACTAGGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.14, C:0.02, G:0.16, T:0.67
Consensus pattern (10 bp):
TTTATGTTTG
Found at i:4200295 original size:25 final size:25
Alignment explanation
Indices: 4200261--4200322 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
4200251 ATCACTAGTA
4200261 AAGACTAAGGTAGTGAAAGATAACC
1 AAGACTAAGGTAGTGAAAGATAACC
4200286 AAGACTAAGGTAGTGAAAGATAACC
1 AAGACTAAGGTAGTGAAAGATAACC
*
4200311 AAGGCTAAGGTA
1 AAGACTAAGGTA
4200323 ATAGTGACCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.47, C:0.11, G:0.26, T:0.16
Consensus pattern (25 bp):
AAGACTAAGGTAGTGAAAGATAACC
Found at i:4203465 original size:20 final size:20
Alignment explanation
Indices: 4203440--4203483 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
4203430 TAAGATGATG
*
4203440 ACACAAGATAAATTCTGGAA
1 ACACAAGATAAATTCTAGAA
4203460 ACACAAGATAAATTCTAGAA
1 ACACAAGATAAATTCTAGAA
4203480 ACAC
1 ACAC
4203484 CGAAAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.18
Consensus pattern (20 bp):
ACACAAGATAAATTCTAGAA
Found at i:4204723 original size:30 final size:32
Alignment explanation
Indices: 4204688--4204776 Score: 137
Period size: 32 Copynumber: 2.8 Consensus size: 32
4204678 GAAGGACCTA
* * *
4204688 TCCATATGTTCCGAAGAACATAGGTAA-C-TG
1 TCCATATGTCCCAAAGGACATAGGTAATCTTG
4204718 TCCATATGTCCCAAAGGACATAGGTAATCTTG
1 TCCATATGTCCCAAAGGACATAGGTAATCTTG
4204750 TCCATATGTCCCAAAGGACATAGGTAA
1 TCCATATGTCCCAAAGGACATAGGTAA
4204777 ACTACCCATA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
30 24 0.44
31 1 0.02
32 29 0.54
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (32 bp):
TCCATATGTCCCAAAGGACATAGGTAATCTTG
Found at i:4204757 original size:32 final size:30
Alignment explanation
Indices: 4204688--4204790 Score: 134
Period size: 32 Copynumber: 3.3 Consensus size: 30
4204678 GAAGGACCTA
* * *
4204688 TCCATATGTTCCGAAGAACATAGGTAACTG
1 TCCATATGTCCCAAAGGACATAGGTAACTG
4204718 TCCATATGTCCCAAAGGACATAGGTAATCTTG
1 TCCATATGTCCCAAAGGACATAGGTAA-C-TG
*
4204750 TCCATATGTCCCAAAGGACATAGGTAAACTA
1 TCCATATGTCCCAAAGGACATAGGT-AACTG
*
4204781 CCCATATGTC
1 TCCATATGTC
4204791 TCGTAAGATA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
30 24 0.37
31 11 0.17
32 28 0.43
33 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCAAAGGACATAGGTAACTG
Found at i:4206963 original size:21 final size:21
Alignment explanation
Indices: 4206937--4206983 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
4206927 TGATCAAGTT
4206937 GGTGATTCCTTACAGACCTAA
1 GGTGATTCCTTACAGACCTAA
4206958 GGTGATTCCTTACAGACCTAA
1 GGTGATTCCTTACAGACCTAA
*
4206979 TGTGA
1 GGTGA
4206984 CACCTTGGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (21 bp):
GGTGATTCCTTACAGACCTAA
Found at i:4206989 original size:21 final size:21
Alignment explanation
Indices: 4206944--4206989 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
4206934 GTTGGTGATT
**
4206944 CCTTACAGACCTAAGGTGATT
1 CCTTACAGACCTAAGGTGACA
*
4206965 CCTTACAGACCTAATGTGACA
1 CCTTACAGACCTAAGGTGACA
4206986 CCTT
1 CCTT
4206990 GGATCGGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (21 bp):
CCTTACAGACCTAAGGTGACA
Found at i:4217914 original size:22 final size:22
Alignment explanation
Indices: 4217889--4217933 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4217879 TATCTAAAAG
4217889 GTGATTTGAAGACGAGAAAATA
1 GTGATTTGAAGACGAGAAAATA
4217911 GTGATTTGAAGACGAGAAAATA
1 GTGATTTGAAGACGAGAAAATA
4217933 G
1 G
4217934 CAATATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.29, T:0.22
Consensus pattern (22 bp):
GTGATTTGAAGACGAGAAAATA
Found at i:4217942 original size:22 final size:22
Alignment explanation
Indices: 4217895--4217942 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
4217885 AAAGGTGATT
** *
4217895 TGAAGACGAGAAAATAGTGATT
1 TGAAGACGAGAAAATAGCAATA
4217917 TGAAGACGAGAAAATAGCAATA
1 TGAAGACGAGAAAATAGCAATA
4217939 TGAA
1 TGAA
4217943 ACTACTCGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.25, T:0.19
Consensus pattern (22 bp):
TGAAGACGAGAAAATAGCAATA
Found at i:4225870 original size:19 final size:19
Alignment explanation
Indices: 4225846--4225899 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
4225836 ATAAGACTCA
4225846 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
4225865 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
*
4225884 GTGCATCGGTGCACTA
1 GTGCATCGGTACACTA
4225900 ATTACATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.20, C:0.22, G:0.35, T:0.22
Consensus pattern (19 bp):
GTGCATCGGTACACTAGGG
Found at i:4225937 original size:46 final size:45
Alignment explanation
Indices: 4225884--4225981 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 45
4225874 TACACTAGGG
* * * *
4225884 GTGCATCGGTGCACTAATTACATTTGATGTTTCAA-ACAAGCCTAGA
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAATA-AAGCCT-GA
* *
4225930 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATAAATCCTGA
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAATAAAGCCTGA
4225975 GTGCATC
1 GTGCATC
4225982 TATGCATGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
45 9 0.20
46 35 0.78
47 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (45 bp):
GTGCATCGGTACACAAAATACATTCGATGTTTCAATAAAGCCTGA
Found at i:4228700 original size:23 final size:22
Alignment explanation
Indices: 4228666--4228744 Score: 97
Period size: 23 Copynumber: 3.6 Consensus size: 22
4228656 CACAGCAAAG
4228666 TGCATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
* * * *
4228689 TACATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
4228710 TGTATCGATGCACATTCAAGGA
1 TGCATCGATGCACATTCAAGGA
4228732 TGCATCGATGCAC
1 TGCATCGATGCAC
4228745 TGTCTAGTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
21 16 0.36
22 12 0.27
23 17 0.38
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:4228719 original size:44 final size:42
Alignment explanation
Indices: 4228664--4228763 Score: 130
Period size: 44 Copynumber: 2.3 Consensus size: 42
4228654 TGCACAGCAA
* *
4228664 AGTGCATCGATGCACATTCAAGGAATACATCGGTGCACCT-TCAT
1 AGTGTATCGATGCACATTCAAGG-ATACATCGATGCA-CTGTC-T
* *
4228708 GGTGTATCGATGCACATTCAAGGATGCATCGATGCACTGTCT
1 AGTGTATCGATGCACATTCAAGGATACATCGATGCACTGTCT
4228750 AGTGTATCGATGCA
1 AGTGTATCGATGCA
4228764 TTATGCACTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 16 0.32
43 13 0.26
44 21 0.42
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (42 bp):
AGTGTATCGATGCACATTCAAGGATACATCGATGCACTGTCT
Found at i:4228721 original size:21 final size:21
Alignment explanation
Indices: 4228692--4228763 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
4228682 CAAGGAATAC
*
4228692 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACCTTCATGGTGT
* * *
4228713 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACCTTCATGG-TGT
*
4228735 ATCGATGCA-CTGTC-TAGTGT
1 ATCGATGCACCT-TCATGGTGT
4228755 ATCGATGCA
1 ATCGATGCA
4228764 TTATGCACTA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 11 0.27
21 17 0.41
22 13 0.32
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (21 bp):
ATCGATGCACCTTCATGGTGT
Found at i:4234226 original size:64 final size:65
Alignment explanation
Indices: 4234094--4234249 Score: 217
Period size: 64 Copynumber: 2.4 Consensus size: 65
4234084 TACACTAGGG
* * * * *
4234094 GTGCATCGGTGCACTAATTACATTCGATGTTTTAAACAAGCCTGGAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAACAAGCATGGAGTGCATCGATGCATGGTCT
* * *
4234159 GTGCATCGGTACACAAAATGCATTCGATGTTTCAATA-AA-CATTGAGTGCATCGATGCATGGTG
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAA-ACAAGCATGGAGTGCATCGATGCATGGTC
4234222 T
65 T
4234223 GTGCATCGGTACACTAAATGCATTCGA
1 GTGCATCGGTACACTAAATGCATTCGA
4234250 AATGGGGTGT
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 48 0.59
65 32 0.40
66 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACTAAATGCATTCGATGTTTCAAACAAGCATGGAGTGCATCGATGCATGGTCT
Found at i:4236550 original size:13 final size:13
Alignment explanation
Indices: 4236536--4236581 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
4236526 GGCAGCTGAT
4236536 TTTAA-TAGTTGA
1 TTTAATTAGTTGA
**
4236548 TTTAATTAACTGA
1 TTTAATTAGTTGA
4236561 TTTAATTAGTTGA
1 TTTAATTAGTTGA
*
4236574 TTTGATTA
1 TTTAATTA
4236582 ATTGTTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 5 0.18
13 23 0.82
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (13 bp):
TTTAATTAGTTGA
Found at i:4236560 original size:26 final size:26
Alignment explanation
Indices: 4236531--4236582 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
4236521 TTATTGGCAG
4236531 CTGATTTTAA-TAGTTGATTTAATTAA
1 CTGA-TTTAATTAGTTGATTTAATTAA
*
4236557 CTGATTTAATTAGTTGATTTGATTAA
1 CTGATTTAATTAGTTGATTTAATTAA
4236583 TTGTTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (26 bp):
CTGATTTAATTAGTTGATTTAATTAA
Found at i:4238055 original size:58 final size:58
Alignment explanation
Indices: 4237967--4238078 Score: 147
Period size: 58 Copynumber: 1.9 Consensus size: 58
4237957 TTAATTCCAT
*
4237967 CCCTAAAATATGACTCCTATTCTAAATTAGTCACC-ATACTTTTAAACATTTCAAATTCA
1 CCCTAAAATATGACT-CTATTCTAAATTAGTC-CCAAAACTTTTAAACATTTCAAATTCA
* * *
4238026 CCCTCAAACTATGACT-TATTCTAAATTAGTCCCAAAACTTTTGAATATTTCAA
1 CCCT-AAAATATGACTCTATTCTAAATTAGTCCCAAAACTTTTAAACATTTCAA
4238079 TAATATCCCC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
57 2 0.04
58 31 0.66
59 4 0.09
60 10 0.21
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (58 bp):
CCCTAAAATATGACTCTATTCTAAATTAGTCCCAAAACTTTTAAACATTTCAAATTCA
Found at i:4241311 original size:21 final size:20
Alignment explanation
Indices: 4241260--4241311 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
4241250 CAGTAGAACA
*
4241260 CTACCTAAAATGTTATTTTT
1 CTACCTAAAATGTTATTTTG
**
4241280 CTACCGGAAATGTTAATTTTG
1 CTACCTAAAATGTT-ATTTTG
4241301 CTACCTAAAAT
1 CTACCTAAAAT
4241312 AAATATTTCC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (20 bp):
CTACCTAAAATGTTATTTTG
Found at i:4241390 original size:45 final size:45
Alignment explanation
Indices: 4241320--4241409 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
4241310 ATAAATATTT
*
4241320 CCGATATTAACATTTCAGTATAAAAAATAACATTTTA-AGTAACAC
1 CCGATATTAACATTTCAGTAGAAAAAATAACATTTTAGA-TAACAC
*
4241365 CCGATATTAATATTTC-GATAGAAAAAATAACATTTTAGATAACAC
1 CCGATATTAACATTTCAG-TAGAAAAAATAACATTTTAGATAACAC
4241410 TTTACCGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 1 0.02
45 39 0.95
46 1 0.02
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (45 bp):
CCGATATTAACATTTCAGTAGAAAAAATAACATTTTAGATAACAC
Found at i:4241635 original size:2 final size:2
Alignment explanation
Indices: 4241630--4241655 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4241620 ACACATTATT
4241630 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
4241656 CACCAGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4246528 original size:61 final size:61
Alignment explanation
Indices: 4246427--4246723 Score: 287
Period size: 61 Copynumber: 4.9 Consensus size: 61
4246417 AATAATTAAC
* * * * *
4246427 TAAGGACGTAATTG-AAG-AAGTTAAATTTA-TAGACTCAATTATTAATTAATTTAACTAAT
1 TAAGGACCTAATTGCAAGCAA-CTAAACTTATTAGGCTCAATTATTAATTAATTTAACTAAA
* * * *
4246486 TAAGGACCCAGTTGCAAGCAACTAAACTTATTAGGTTCAATTATTAAATAATTTAACTAAA
1 TAAGGACCTAATTGCAAGCAACTAAACTTATTAGGCTCAATTATTAATTAATTTAACTAAA
* * * * * * *
4246547 TAAAGACCTAGTTGCAAGTAGCTAATCTTATGAGGCTCAATTATTAATTAATTTAACTAAT
1 TAAGGACCTAATTGCAAGCAACTAAACTTATTAGGCTCAATTATTAATTAATTTAACTAAA
* * * * * * * * *
4246608 TGAGTACCTAACTGCAAGCATCCAAACTTGTTAAGTTCAATTATTAGTTAATTTAACTAAA
1 TAAGGACCTAATTGCAAGCAACTAAACTTATTAGGCTCAATTATTAATTAATTTAACTAAA
*
4246669 TAAGGACCTAATTGCAA-AAAGCTAAACTTATTAGGCTCATATGTAATTAATTAAT
1 TAAGGACCTAATTGCAAGCAA-CTAAACTTATTAGGCTCA-AT-T-ATTAATTAAT
4246724 GTTGAGAAGA
Statistics
Matches: 188, Mismatches: 43, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
59 11 0.06
60 11 0.06
61 154 0.82
62 2 0.01
63 1 0.01
64 9 0.05
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (61 bp):
TAAGGACCTAATTGCAAGCAACTAAACTTATTAGGCTCAATTATTAATTAATTTAACTAAA
Found at i:4246627 original size:122 final size:122
Alignment explanation
Indices: 4246435--4246723 Score: 348
Period size: 122 Copynumber: 2.4 Consensus size: 122
4246425 ACTAAGGACG
* * * * **
4246435 TAATTG-AAGAAGTTAAATTTAT-AGACTCAATTATTAATTAATTTAACTAATTAAGGACCCAGT
1 TAATTGCAAAAAGCTAAACTTATGAGGCTCAATTATTAATTAATTTAACTAATTAAGGACCCAAC
* *
4246498 TGCAAGCAACTAAACTTATTAGGTTCAATTATTAAATAATTTAACTAAATAAAGACC
66 TGCAAGCAACCAAACTTATTAAGTTCAATTATTAAATAATTTAACTAAATAAAGACC
* ** * * * *
4246555 TAGTTGCAAGTAGCTAATCTTATGAGGCTCAATTATTAATTAATTTAACTAATTGAGTACCTAAC
1 TAATTGCAAAAAGCTAAACTTATGAGGCTCAATTATTAATTAATTTAACTAATTAAGGACCCAAC
* * ** *
4246620 TGCAAGCATCCAAACTTGTTAAGTTCAATTATTAGTTAATTTAACTAAATAAGGACC
66 TGCAAGCAACCAAACTTATTAAGTTCAATTATTAAATAATTTAACTAAATAAAGACC
*
4246677 TAATTGCAAAAAGCTAAACTTATTAGGCTCATATGTAATTAATTAAT
1 TAATTGCAAAAAGCTAAACTTATGAGGCTCA-AT-T-ATTAATTAAT
4246724 GTTGAGAAGA
Statistics
Matches: 141, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
120 5 0.04
121 12 0.09
122 111 0.79
123 2 0.01
124 1 0.01
125 10 0.07
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (122 bp):
TAATTGCAAAAAGCTAAACTTATGAGGCTCAATTATTAATTAATTTAACTAATTAAGGACCCAAC
TGCAAGCAACCAAACTTATTAAGTTCAATTATTAAATAATTTAACTAAATAAAGACC
Found at i:4247427 original size:45 final size:45
Alignment explanation
Indices: 4247377--4247470 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
4247367 ATACCAATAT
*
4247377 TACCTTTAACAGTAGTACCAATACTCCAAATAATAGTATCGATAC
1 TACCTTTAACAGTAGTACCAATACTCCAAATAATAATATCGATAC
* * * *
4247422 TACCTTTAACAGTAGTATCAATACTCCGAATGATAATATTGATAC
1 TACCTTTAACAGTAGTACCAATACTCCAAATAATAATATCGATAC
4247467 TACC
1 TACC
4247471 CTTGTTTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (45 bp):
TACCTTTAACAGTAGTACCAATACTCCAAATAATAATATCGATAC
Found at i:4247437 original size:24 final size:24
Alignment explanation
Indices: 4247371--4247446 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
4247361 ATTTCAATAC
* *
4247371 CAATATTACCTTTAACAGTAGTAC
1 CAATACTACCTTTAACAGTAGTAT
* * *
4247395 CAATACT-CC--AAATAATAGTAT
1 CAATACTACCTTTAACAGTAGTAT
*
4247416 CGATACTACCTTTAACAGTAGTAT
1 CAATACTACCTTTAACAGTAGTAT
4247440 CAATACT
1 CAATACT
4247447 CCGAATGATA
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
21 14 0.36
22 2 0.05
23 2 0.05
24 21 0.54
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (24 bp):
CAATACTACCTTTAACAGTAGTAT
Found at i:4249055 original size:131 final size:131
Alignment explanation
Indices: 4248896--4249253 Score: 581
Period size: 131 Copynumber: 2.7 Consensus size: 131
4248886 TCAATATTGA
* * *
4248896 AAATAGTAATATCTTTTCATTTCGATTGGAGTAATAAATGACTACTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
* * *
4248961 TTATTCTTGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAATCAATATTCAATTTTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCAAATCAATATTCAATTCTAAGAC
4249026 G
131 G
* *
4249027 AAATAGTGATATCTCTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGCTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
* *
4249092 TTATTCTCGATTGGAAATAATTAGATATTATTGTTTTCTCTCAAATCAATATTGAATTCTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCAAATCAATATTCAATTCTAAGAC
4249157 G
131 G
* * * * *
4249158 AAATAGTGATATCTCTTCATTTTGATTGGAGTGATAAATTAATGTTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
4249223 TTATTCTCGATTGGAAATAATTAGATATTAT
66 TTATTCTCGATTGGAAATAATTAGATATTAT
4249254 CATTTTCTTT
Statistics
Matches: 210, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
131 210 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (131 bp):
AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCAAATCAATATTCAATTCTAAGAC
G
Found at i:4251245 original size:6 final size:6
Alignment explanation
Indices: 4251234--4251272 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
4251224 ATTAACACCT
* *
4251234 TTTGCA TTTGCA TTTTGCA TCTGCA TTTGAA TTTGCA TT
1 TTTGCA TTTGCA -TTTGCA TTTGCA TTTGCA TTTGCA TT
4251273 GTATTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.51
Consensus pattern (6 bp):
TTTGCA
Found at i:4251251 original size:13 final size:13
Alignment explanation
Indices: 4251233--4251272 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
4251223 AATTAACACC
4251233 TTTTGCATTTGCA
1 TTTTGCATTTGCA
*
4251246 TTTTGCATCTGCA
1 TTTTGCATTTGCA
*
4251259 -TTTGAATTTGCA
1 TTTTGCATTTGCA
4251271 TT
1 TT
4251273 GTATTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (13 bp):
TTTTGCATTTGCA
Found at i:4255428 original size:41 final size:40
Alignment explanation
Indices: 4255333--4255431 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 40
4255323 TTTCCAAAAT
* * * *
4255333 TAATAAGCCCTTCGAGCATCAGTAAGTCTTTTGAGCATGA
1 TAATAAGTCCTTCGAGCATCAGTAAGCCTTTCGAGCAAGA
* *
4255373 TAATTAAATTCTTCGAGTCATCTA-TAAGCCTTTCGAGCAAGA
1 TAA-TAAGTCCTTCGAG-CATC-AGTAAGCCTTTCGAGCAAGA
*
4255415 TGATAAGTCCTTCGAGC
1 TAATAAGTCCTTCGAGC
4255432 CATCCCTAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
40 4 0.09
41 21 0.45
42 21 0.45
43 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.31
Consensus pattern (40 bp):
TAATAAGTCCTTCGAGCATCAGTAAGCCTTTCGAGCAAGA
Found at i:4255674 original size:192 final size:197
Alignment explanation
Indices: 4255349--4255699 Score: 552
Period size: 192 Copynumber: 1.8 Consensus size: 197
4255339 GCCCTTCGAG
* *
4255349 CATCAGTAAGTCTTTTGAGCATGATAATTAAATTCTTCGAGTCATCTATAAGCCTTTCGAGCAAG
1 CATCAGTAAGTCTTTTAAGCATGATAATTAAATCCTTCGAGTCATCTATAAGCCTTTCGAGCAAG
* * * *
4255414 ATGATAAGTCCTTCGAGCCATCCCTAAGACCTTCAGGCATGATGTTTTCATATGTTTTTCGAAAA
66 ATGATAAGTCCTTCGAGCCATCCATAAGACCTTCAGGCAGGATGTTTTCACATGTTTTTCAAAAA
4255479 GTAAGAAAATGATTTCCAAAGTTTCTTACCAAGTAAACTATTTCCAAGATTGGTAAGTCCTTCAG
131 GTAAGAAAATGATTTCCAAAGTTTCTTACCAAGTAAACTATTTCCAAGATTGGTAAGTCCTTCAG
4255544 GC
196 GC
* *
4255546 CATCAGTAAGTC-TTTAAGCATGATGATTAAATCCTTC-AGGTCATCTATAAG-CTTTC-CG-AA
1 CATCAGTAAGTCTTTTAAGCATGATAATTAAATCCTTCGA-GTCATCTATAAGCCTTTCGAGCAA
* **
4255606 GATGATAAGTCCTTC-AGGCATCCATAAGACCTTTGGGCAGGATGTTTTCACATGTTTTTCAAAA
65 GATGATAAGTCCTTCGAGCCATCCATAAGACCTTCAGGCAGGATGTTTTCACATGTTTTTCAAAA
4255670 AGTAAGAAAATGATTTCCAAAGTTTCTTAC
130 AGTAAGAAAATGATTTCCAAAGTTTCTTAC
4255700 TAGTAAGTCC
Statistics
Matches: 142, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
192 72 0.51
193 17 0.12
194 1 0.01
195 6 0.04
196 34 0.24
197 12 0.08
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (197 bp):
CATCAGTAAGTCTTTTAAGCATGATAATTAAATCCTTCGAGTCATCTATAAGCCTTTCGAGCAAG
ATGATAAGTCCTTCGAGCCATCCATAAGACCTTCAGGCAGGATGTTTTCACATGTTTTTCAAAAA
GTAAGAAAATGATTTCCAAAGTTTCTTACCAAGTAAACTATTTCCAAGATTGGTAAGTCCTTCAG
GC
Found at i:4256326 original size:132 final size:132
Alignment explanation
Indices: 4256098--4256575 Score: 588
Period size: 132 Copynumber: 3.6 Consensus size: 132
4256088 AATCGAACTT
* * *
4256098 GATTCAATATTCCCTAG-AGAACAGTTGAATGAATCAATGTCTCTAGATCTAATTTTCCCTGAAG
1 GATTCAATCTTCCC-AGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTAATTTTCCCTGAAG
* * * * * *
4256162 AAGCAACCGAATATAT-CCCTCTTTCCATATTTGATCTTACCTGAGTAGCAGTGGAACAAGTCTA
65 AAGCAACGGAACAGATCCCCTCTTTCTAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCT-
4256226 CCTC
129 CCTC
*
4256230 GATTCAATCTTCCCAGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTGA-TTTCCCTGAAGA
1 GATTCAATCTTCCCAGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTAATTTTCCCTGAAGA
* *
4256294 AGCAGCGGAACAGATCCCCCCTTTCTAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTCC
66 AGCAACGGAACAGATCCCCTCTTTCTAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTCC
4256359 TC
131 TC
* ** * * * * *
4256361 GATTCAATTTTCCTTGAAGAACATTGGAATAAATCAATGTCTCTAGATATGATTTTCCCTGAAGA
1 GATTCAATCTTCCCAGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTAATTTTCCCTGAAGA
* * * * *
4256426 AGCAATGGAATAGATCCCCTCTTTCTAGATTTGATCTTCCCTGAGTAGTAATAGAACAAGTCTGC
66 AGCAACGGAACAGATCCCCTCTTTCTAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCT-C
4256491 CTC
130 CTC
* * * * *
4256494 GATTTAATCTT-CCTGAAGAACAGTGGAATGAATCAATGTTTCTCA-ATCTAATCTACCCTGAAG
1 GATTCAATCTTCCCAGAAGAACAGTGGAATGAATCAATGTCTC-CAGATCTAATTTTCCCTGAAG
* **
4256557 AAACAGTGGAACAGATCCC
65 AAGCAACGGAACAGATCCC
4256576 TTATCAGATT
Statistics
Matches: 301, Mismatches: 40, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
131 74 0.25
132 213 0.71
133 14 0.05
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (132 bp):
GATTCAATCTTCCCAGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTAATTTTCCCTGAAGA
AGCAACGGAACAGATCCCCTCTTTCTAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTCC
TC
Found at i:4256570 original size:264 final size:263
Alignment explanation
Indices: 4256098--4256575 Score: 685
Period size: 263 Copynumber: 1.8 Consensus size: 263
4256088 AATCGAACTT
* *
4256098 GATTCAATATTCCCTAGAGAACAGTTGAATGAATCAATGTCTCTAGATCTAATTTTCCCTGAAGA
1 GATTCAATATTCCCTAGAGAACAGTTGAATAAATCAATGTCTCTAGATATAATTTTCCCTGAAGA
* * * *
4256163 AGCAACCGAATATATCCCTCTTTCCATATTTGATCTTACCTGAGTAGCAGTGGAACAAGTCTACC
66 AGCAACCGAATAGATCCCTCTTTCCAGATTTGATCTTACCTGAGTAGCAATAGAACAAGTCTACC
* *
4256228 TCGATTCAATCTTCCCAGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTGATTTCCCTGAAG
131 TCGATTCAATCTTCCCAGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTAATTACCCTGAAG
*
4256293 AAGCAGCGGAACAGATCCCCCCTTTCTAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTC
196 AAACAGCGGAACAGATCCCCCCTTTCTAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTC
4256358 CTC
261 CTC
* * *
4256361 GATTCAAT-TTTCCTTGAAGAACA-TTGGAATAAATCAATGTCTCTAGATATGATTTTCCCTGAA
1 GATTCAATATTCCCTAG-AGAACAGTT-GAATAAATCAATGTCTCTAGATATAATTTTCCCTGAA
** * * *
4256424 GAAGCAATGGAATAGATCCCCTCTTTCTAGATTTGATCTTCCCTGAGTAGTAATAGAACAAGTCT
64 GAAGCAACCGAATAGAT-CCCTCTTTCCAGATTTGATCTTACCTGAGTAGCAATAGAACAAGTCT
* * * *
4256489 GCCTCGATTTAATCTT-CCTGAAGAACAGTGGAATGAATCAATGTTTCTCA-ATCTAATCTACCC
128 ACCTCGATTCAATCTTCCCAGAAGAACAGTGGAATGAATCAATGTCTC-CAGATCTAAT-TACCC
*
4256552 TGAAGAAACAGTGGAACAGATCCC
191 TGAAGAAACAGCGGAACAGATCCC
4256576 TTATCAGATT
Statistics
Matches: 188, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
262 8 0.04
263 97 0.52
264 83 0.44
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (263 bp):
GATTCAATATTCCCTAGAGAACAGTTGAATAAATCAATGTCTCTAGATATAATTTTCCCTGAAGA
AGCAACCGAATAGATCCCTCTTTCCAGATTTGATCTTACCTGAGTAGCAATAGAACAAGTCTACC
TCGATTCAATCTTCCCAGAAGAACAGTGGAATGAATCAATGTCTCCAGATCTAATTACCCTGAAG
AAACAGCGGAACAGATCCCCCCTTTCTAGATTTGATCTTCCCTGAGTAGCAGTGGAACAAGTCTC
CTC
Found at i:4258167 original size:2 final size:2
Alignment explanation
Indices: 4258160--4258218 Score: 56
Period size: 2 Copynumber: 32.0 Consensus size: 2
4258150 GCAATTTACA
* *
4258160 AT AT AT AT AT AT AT AT AT AT AT GT A- AT A- AG AT AT -T A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
4258198 TT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
4258219 TATTATTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
1 5 0.11
2 42 0.89
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4258968 original size:130 final size:131
Alignment explanation
Indices: 4258734--4259098 Score: 536
Period size: 130 Copynumber: 2.8 Consensus size: 131
4258724 TCAATATTGA
* * *
4258734 AAATAGTAATATCTTTTCATTTCAGTTGGAGTAATAAATGAATGCTTTAAGGTATGAGAGGTCAT
1 AAATAGTGATATCTATTCATTTCAATTGGAGTAATAAATGAATGCTTTAAGGTATGAGAGGTCAT
* * * * * * *
4258799 TTATTCTCAATTGCAAATAATTAGTTATTATGGTTTTCTCTTGAATCAATATTGAATTTTAAGAT
66 TTATTCTCGATTGAAAATAATTAGATATTATCGTTTTCTCTTAAATCAATATTGAATTCTAAGAC
4258864 G
131 G
* * *
4258865 AAATAGTGATATATCTTCATTTCAATTGGAGTAATAAATGACTG-TTTAAGGTATGAGAGGTCAT
1 AAATAGTGATATCTATTCATTTCAATTGGAGTAATAAATGAATGCTTTAAGGTATGAGAGGTCAT
4258929 TTATTCTCGATT-AGAAATAATTAGATATTATCGTTTTCTCTTAAATCAATATTGAATTCTAAGA
66 TTATTCTCGATTGA-AAATAATTAGATATTATCGTTTTCTCTTAAATCAATATTGAATTCTAAGA
4258993 CG
130 CG
* * * * * *
4258995 AAATAGTGATATCTATTCATTTCGATCGGAGTGATAAATGATTGTTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTATTCATTTCAATTGGAGTAATAAATGAATGCTTTAAGGTATGAGAGGTCAT
4259060 TTATTCTCGATTGAAAATAATTAGATATTATCGTTTTCT
66 TTATTCTCGATTGAAAATAATTAGATATTATCGTTTTCT
4259099 TTATTAAAAT
Statistics
Matches: 212, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
130 116 0.55
131 95 0.45
132 1 0.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (131 bp):
AAATAGTGATATCTATTCATTTCAATTGGAGTAATAAATGAATGCTTTAAGGTATGAGAGGTCAT
TTATTCTCGATTGAAAATAATTAGATATTATCGTTTTCTCTTAAATCAATATTGAATTCTAAGAC
G
Found at i:4262605 original size:15 final size:15
Alignment explanation
Indices: 4262585--4262626 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
4262575 TCATAAAATG
4262585 GAATTTAATATTTTA
1 GAATTTAATATTTTA
4262600 GAATTTAATATTTTA
1 GAATTTAATATTTTA
4262615 GAATTTAATATT
1 GAATTTAATATT
4262627 GTAGGCCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (15 bp):
GAATTTAATATTTTA
Found at i:4263125 original size:56 final size:56
Alignment explanation
Indices: 4263039--4263149 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 56
4263029 ACATAAAACT
4263039 ACAAAGATGGAGGAAAACAAGAGAGGTTAAGGCCTAGAATCCCACCCAGCTCTACC
1 ACAAAGATGGAGGAAAACAAGAGAGGTTAAGGCCTAGAATCCCACCCAGCTCTACC
*
4263095 ACAAAGATGGAGGAAAACAAGAGAGGTTAAGGCCTAGAATCCCACCCTGCTCTAC
1 ACAAAGATGGAGGAAAACAAGAGAGGTTAAGGCCTAGAATCCCACCCAGCTCTAC
4263150 TTAGTTATTG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.14
Consensus pattern (56 bp):
ACAAAGATGGAGGAAAACAAGAGAGGTTAAGGCCTAGAATCCCACCCAGCTCTACC
Found at i:4264690 original size:15 final size:15
Alignment explanation
Indices: 4264670--4264701 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4264660 TGGCAGATCG
*
4264670 AAATCAAGAAGGGGA
1 AAATCAAGAACGGGA
4264685 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
4264700 AA
1 AA
4264702 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.28, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:4270458 original size:196 final size:198
Alignment explanation
Indices: 4270124--4270517 Score: 774
Period size: 196 Copynumber: 2.0 Consensus size: 198
4270114 TGAATCAAAT
4270124 TAAGTGTGAATTCAACAAGAGAGTAAGTGAATCTGACGTTGTTTAAAAGCATCGTTTGAAGTCTA
1 TAAGTGTGAATTCAACAAGAGAGTAAGTGAATCTGACGTTGTTTAAAAGCATCGTTTGAAGTCTA
4270189 AGGTATCTGACTATCACACGACCAGACATAACATACGCTGTGGAATTAGTAAGCAGATTCATGGA
66 AGGTATCTGACTATCACACGACCAGACATAACATACGCTGTGGAATTAGTAAGCAGATTCATGGA
4270254 GCATCCGAAA-TAGATCATTGGATTGCAACAAAAAGAATCAT-AGATATGTCAAAGGTACAACAG
131 GCATCCGAAACTAGATCATTGGATTGCAACAAAAAGAATCATCAGATATGTCAAAGGTACAACAG
4270317 GTC
196 GTC
4270320 TAAGTGTGAATTCAACAAGAGAGTAAGTGAATCTGACGTTGTTTAAAAGCATCGTTTGAAGTCTA
1 TAAGTGTGAATTCAACAAGAGAGTAAGTGAATCTGACGTTGTTTAAAAGCATCGTTTGAAGTCTA
4270385 AGGTATCTGACTATCACACGACCAGACATAACATACGCTGTGGAATTAGTAAGCAGATTCATGGA
66 AGGTATCTGACTATCACACGACCAGACATAACATACGCTGTGGAATTAGTAAGCAGATTCATGGA
4270450 GCATCCGAAACTAGATCATTGGATTGCAACAAAAAGAATCATCAGATATGTCAAAGGTACAACAG
131 GCATCCGAAACTAGATCATTGGATTGCAACAAAAAGAATCATCAGATATGTCAAAGGTACAACAG
4270515 GTC
196 GTC
4270518 ATGATTTGTT
Statistics
Matches: 196, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
196 140 0.71
197 31 0.16
198 25 0.13
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (198 bp):
TAAGTGTGAATTCAACAAGAGAGTAAGTGAATCTGACGTTGTTTAAAAGCATCGTTTGAAGTCTA
AGGTATCTGACTATCACACGACCAGACATAACATACGCTGTGGAATTAGTAAGCAGATTCATGGA
GCATCCGAAACTAGATCATTGGATTGCAACAAAAAGAATCATCAGATATGTCAAAGGTACAACAG
GTC
Found at i:4274480 original size:8 final size:8
Alignment explanation
Indices: 4274467--4274491 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4274457 ATTCTAAGTT
4274467 TTTTTTTC
1 TTTTTTTC
4274475 TTTTTTTC
1 TTTTTTTC
4274483 TTTTTTTC
1 TTTTTTTC
4274491 T
1 T
4274492 GGATACTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTC
Found at i:4275208 original size:2 final size:2
Alignment explanation
Indices: 4275201--4275227 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4275191 TGAAATGATG
4275201 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
4275228 ATGAAATAAA
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:4275402 original size:19 final size:18
Alignment explanation
Indices: 4275370--4275419 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
4275360 TATATATCGT
4275370 AAATAAAA-AAAGAATAAA
1 AAATAAAATAAAGAAT-AA
*
4275388 AAATAAAATAAAGAATTA
1 AAATAAAATAAAGAATAA
4275406 AAATAAATATAAAG
1 AAATAAA-ATAAAG
4275420 GCAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (18 bp):
AAATAAAATAAAGAATAA
Found at i:4275407 original size:13 final size:12
Alignment explanation
Indices: 4275370--4275412 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 12
4275360 TATATATCGT
4275370 AAATAAAAAA-A
1 AAATAAAAAATA
*
4275381 GAATAAAAAATA
1 AAATAAAAAATA
*
4275393 AAATAAAGAATTA
1 AAATAAA-AAATA
4275406 AAATAAA
1 AAATAAA
4275413 TATAAAGGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 9 0.33
12 7 0.26
13 11 0.41
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (12 bp):
AAATAAAAAATA
Found at i:4277515 original size:42 final size:41
Alignment explanation
Indices: 4277425--4277516 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 41
4277415 CGTGAAGTTG
*
4277425 AATCGTGGA-TATGGGCACAATATCCTCCTCGTAGAGTTAA
1 AATCGTGGATTATGGGCACAATATCCTCCTCGTAGAGATAA
* * * * *
4277465 AATTGTGGATTTATGGGTACGATATCCTCCATCGT-GGGATGA
1 AATCGTGGA-TTATGGGCACAATATCCTCC-TCGTAGAGATAA
4277507 AATCGTGGAT
1 AATCGTGGAT
4277517 GGCTCATTCG
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
40 8 0.19
41 1 0.02
42 29 0.69
43 4 0.10
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (41 bp):
AATCGTGGATTATGGGCACAATATCCTCCTCGTAGAGATAA
Found at i:4278444 original size:5 final size:5
Alignment explanation
Indices: 4278422--4278458 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
4278412 AACCATCTTA
*
4278422 TTTTCC TTTTC TTCTC TTTTC TTTTC TTTTC TTTTC T
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
4278459 ATTTTTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:4279635 original size:21 final size:23
Alignment explanation
Indices: 4279584--4279636 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 23
4279574 TCTGTCATGT
4279584 ACTTCTTCCAGTATCATTTTTTG
1 ACTTCTTCCAGTATCATTTTTTG
4279607 TACTTCTTCCAGTATCA-TTTTTG
1 -ACTTCTTCCAGTATCATTTTTTG
4279630 -CTTCTTC
1 ACTTCTTC
4279637 TGCATCGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.24
23 6 0.21
24 16 0.55
ACGTcount: A:0.15, C:0.25, G:0.08, T:0.53
Consensus pattern (23 bp):
ACTTCTTCCAGTATCATTTTTTG
Found at i:4279637 original size:24 final size:24
Alignment explanation
Indices: 4279581--4279628 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4279571 TACTCTGTCA
4279581 TGTACTTCTTCCAGTATCATTTTT
1 TGTACTTCTTCCAGTATCATTTTT
4279605 TGTACTTCTTCCAGTATCATTTTT
1 TGTACTTCTTCCAGTATCATTTTT
4279629 GCTTCTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.08, T:0.54
Consensus pattern (24 bp):
TGTACTTCTTCCAGTATCATTTTT
Found at i:4284452 original size:22 final size:22
Alignment explanation
Indices: 4284418--4284459 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4284408 AACGTTGTGT
*
4284418 GTATTATCGGAAACTCTCGTGC
1 GTATTATCAGAAACTCTCGTGC
*
4284440 GTATTGTCAGAAACTCTCGT
1 GTATTATCAGAAACTCTCGT
4284460 TGTACTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
GTATTATCAGAAACTCTCGTGC
Found at i:4287856 original size:32 final size:35
Alignment explanation
Indices: 4287781--4287850 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 35
4287771 ATATATATAT
*
4287781 ATAAATGAAATAAATAAAATACAATAAAGGAAAGGAA
1 ATAAA-GAAACAAATAAAATACAATAAAGGAAAGG-A
*
4287818 TATAAAGAAACAAATAAAATA-AATAAAGTAAAG
1 -ATAAAGAAACAAATAAAATACAATAAAGGAAAG
4287851 ATAAAGGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
36 11 0.37
37 14 0.47
38 5 0.17
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (35 bp):
ATAAAGAAACAAATAAAATACAATAAAGGAAAGGA
Found at i:4289848 original size:3 final size:3
Alignment explanation
Indices: 4289840--4289875 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
4289830 TATTAACAGC
4289840 AAG AAG AAG AAG AAG AAG AA- AATG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG
4289876 GGTTAACTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:4289914 original size:36 final size:36
Alignment explanation
Indices: 4289874--4289971 Score: 133
Period size: 36 Copynumber: 2.7 Consensus size: 36
4289864 AAGAAGAAGA
* *
4289874 AGGGTTAACTTCTACGTTAGCAAAAAATATTAGTAG
1 AGGGTTAACTTCCACGTCAGCAAAAAATATTAGTAG
* *
4289910 AGGGTTAACTTCCACGTCATCAAAAAATATTAGTGG
1 AGGGTTAACTTCCACGTCAGCAAAAAATATTAGTAG
* * *
4289946 AGGGTTAACTGCCACATCAACAAAAA
1 AGGGTTAACTTCCACGTCAGCAAAAA
4289972 CTAACGGAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (36 bp):
AGGGTTAACTTCCACGTCAGCAAAAAATATTAGTAG
Found at i:4292913 original size:33 final size:33
Alignment explanation
Indices: 4292861--4292923 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
4292851 ATTTAAAATT
* *
4292861 TATATTAAATTATTCTAAAA-AGTTTATTTATAA
1 TATATGAAAATATTCTAAAATA-TTTATTTATAA
*
4292894 TATATGAAAATATTTTAAAATATTTATTTA
1 TATATGAAAATATTCTAAAATATTTATTTA
4292924 CTTTTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 25 0.96
34 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (33 bp):
TATATGAAAATATTCTAAAATATTTATTTATAA
Found at i:4292932 original size:21 final size:20
Alignment explanation
Indices: 4292906--4292953 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
4292896 TATGAAAATA
4292906 TTTTAAAAT-ATTTATTTACTT
1 TTTTAAAATCA-TTATTTA-TT
4292927 TTTT-AAATCATTATTTATT
1 TTTTAAAATCATTATTTATT
4292946 TATTTAAA
1 T-TTTAAA
4292954 TAATATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
19 3 0.12
20 14 0.58
21 7 0.29
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAAAATCATTATTTATT
Found at i:4292954 original size:20 final size:20
Alignment explanation
Indices: 4292917--4292954 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4292907 TTTAAAATAT
4292917 TTATTTACTTTTTTAAATCA
1 TTATTTACTTTTTTAAATCA
4292937 TTATTTA-TTTATTTAAAT
1 TTATTTACTTT-TTTAAAT
4292955 AATATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTTACTTTTTTAAATCA
Found at i:4293129 original size:15 final size:16
Alignment explanation
Indices: 4293109--4293141 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4293099 AATTAATTGA
4293109 ATTTAA-AAAATAAAT
1 ATTTAACAAAATAAAT
*
4293124 ATTTAACAATATAAAT
1 ATTTAACAAAATAAAT
4293140 AT
1 AT
4293142 AGCTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTAACAAAATAAAT
Found at i:4293257 original size:24 final size:24
Alignment explanation
Indices: 4293212--4293257 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
4293202 TATTTCTAAA
* *
4293212 TAAAGTGAAAATTAACTTTTAATT
1 TAAAATGAAAATTAACTATTAATT
* *
4293236 TAAAATGATAATTAAGTATTAA
1 TAAAATGAAAATTAACTATTAA
4293258 ATTCAATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (24 bp):
TAAAATGAAAATTAACTATTAATT
Found at i:4299707 original size:15 final size:15
Alignment explanation
Indices: 4299687--4299728 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
4299677 GTACATTGAA
4299687 ATTAGACATCATTTC
1 ATTAGACATCATTTC
*
4299702 ATTAGACTTCATTTC
1 ATTAGACATCATTTC
*
4299717 ATTAGAGATCAT
1 ATTAGACATCAT
4299729 GTCACTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (15 bp):
ATTAGACATCATTTC
Found at i:4300645 original size:19 final size:20
Alignment explanation
Indices: 4300623--4300665 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
4300613 TCGAAATAAT
*
4300623 TTTTTTTTTTAAAT-TGTTG
1 TTTTTTATTTAAATATGTTG
*
4300642 TTTTTTATTTAATTATGTTG
1 TTTTTTATTTAAATATGTTG
4300662 TTTT
1 TTTT
4300666 CATGAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.16, C:0.00, G:0.09, T:0.74
Consensus pattern (20 bp):
TTTTTTATTTAAATATGTTG
Found at i:4304260 original size:12 final size:12
Alignment explanation
Indices: 4304243--4304269 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4304233 GATTTTCTCA
4304243 TCGCCACCGCCG
1 TCGCCACCGCCG
4304255 TCGCCACCGCCG
1 TCGCCACCGCCG
4304267 TCG
1 TCG
4304270 ATTTTATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.56, G:0.26, T:0.11
Consensus pattern (12 bp):
TCGCCACCGCCG
Found at i:4305229 original size:21 final size:22
Alignment explanation
Indices: 4305177--4305230 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
4305167 CCTATAATGC
*
4305177 ATGG-CCAATTCGAAAATTTAA
1 ATGGACCAATTTGAAAATTTAA
4305198 ATGGA-CAATTTG-AAATATTAA
1 ATGGACCAATTTGAAAAT-TTAA
4305219 AT-GACCAATTTG
1 ATGGACCAATTTG
4305231 GGAAATCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (22 bp):
ATGGACCAATTTGAAAATTTAA
Found at i:4309672 original size:18 final size:18
Alignment explanation
Indices: 4309649--4309690 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
4309639 GAGGGTCTAC
4309649 GTGGTCCTTCGGGACAAA
1 GTGGTCCTTCGGGACAAA
* *
4309667 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGACAAA
4309685 GTGGTC
1 GTGGTC
4309691 TACGAGACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.19, G:0.36, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACAAA
Found at i:4309869 original size:7 final size:7
Alignment explanation
Indices: 4309857--4309883 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4309847 GTGAAATGGT
4309857 ATATGTG
1 ATATGTG
4309864 ATATGTG
1 ATATGTG
4309871 ATATGTG
1 ATATGTG
4309878 ATATGT
1 ATATGT
4309884 ATTAGTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (7 bp):
ATATGTG
Found at i:4315586 original size:3 final size:3
Alignment explanation
Indices: 4315569--4315658 Score: 96
Period size: 3 Copynumber: 30.0 Consensus size: 3
4315559 TTTCATCCAT
*
4315569 TTA TTT TTA -TA TTA TTA TTA TTA -TA TTTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA
* * *
4315614 ATA -TA TTA TTA TTA TTA TATA TTA TTA TTA ATA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
4315659 AATAAATAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
2 6 0.08
3 60 0.81
4 8 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:4318993 original size:36 final size:36
Alignment explanation
Indices: 4318946--4319015 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
4318936 TGAGCTATGC
** *
4318946 ACACAAAGATCCTGTTATATTGATACCAAAAGTATT
1 ACACAAAGATCCTGCCAGATTGATACCAAAAGTATT
*
4318982 ACACAAAGATCCTGCCAGGTTGATACCAAAAGTA
1 ACACAAAGATCCTGCCAGATTGATACCAAAAGTA
4319016 GTCTACGGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (36 bp):
ACACAAAGATCCTGCCAGATTGATACCAAAAGTATT
Found at i:4319488 original size:19 final size:20
Alignment explanation
Indices: 4319464--4319510 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
4319454 AGAAAATGGG
4319464 AAAGTTTTCCCCTATATGT-
1 AAAGTTTTCCCCTATATGTA
4319483 AAAGTTTTCCCCTATATGTA
1 AAAGTTTTCCCCTATATGTA
4319503 AAAGTTTT
1 AAAGTTTT
4319511 GTTTGATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (20 bp):
AAAGTTTTCCCCTATATGTA
Found at i:4319606 original size:13 final size:13
Alignment explanation
Indices: 4319588--4319621 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
4319578 TTTTCATACA
4319588 TGCATTTGCATTT
1 TGCATTTGCATTT
*
4319601 TGCATTTTCATTT
1 TGCATTTGCATTT
4319614 TGCATTTG
1 TGCATTTG
4319622 TTGTTTGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (13 bp):
TGCATTTGCATTT
Found at i:4319634 original size:6 final size:7
Alignment explanation
Indices: 4319588--4319620 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
4319578 TTTTCATACA
4319588 TGCA-TT
1 TGCATTT
4319594 TGCATTT
1 TGCATTT
4319601 TGCATTT
1 TGCATTT
4319608 T-CATTT
1 TGCATTT
4319614 TGCATTT
1 TGCATTT
4319621 GTTGTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 10 0.40
7 15 0.60
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.58
Consensus pattern (7 bp):
TGCATTT
Found at i:4319710 original size:26 final size:27
Alignment explanation
Indices: 4319674--4319726 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
4319664 CACATCTTTG
* *
4319674 TATTTGCATTTGCA-TCTTTGCATTTT
1 TATTTACATTTACATTCTTTGCATTTT
*
4319700 TATTTACATTTACATTTTTTGCATTTT
1 TATTTACATTTACATTCTTTGCATTTT
4319727 CGTATTTGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.19, C:0.13, G:0.08, T:0.60
Consensus pattern (27 bp):
TATTTACATTTACATTCTTTGCATTTT
Found at i:4325064 original size:709 final size:710
Alignment explanation
Indices: 4323706--4325125 Score: 2680
Period size: 709 Copynumber: 2.0 Consensus size: 710
4323696 AAATTCTTTC
4323706 ATTCTTCGATAAAGAAAGGAGGAAAAACATTTTCAAACAGGATAGTCTCAGATGAGGAAGGTCCT
1 ATTCTTCGATAAAGAAAGGAGGAAAAACATTTTCAAACAGGATAGTCTCAGATGAGGAAGGTCCT
4323771 TGAATCAAGTTATTGTCTATTATACCTCTATTGAAGAAAAAGAATGAATGAGGTCAGAATAATGA
66 TGAATCAAGTTATTGTCTATTATACCTCTATTGAAGAAAAAGAATGAATGAGGTCAGAATAATGA
4323836 AGCATTTCACTTCCTTGAAAGCAAGGGGTCAAAGAAGGCAGAAAGTCTGGAGAATTGAACTTGTA
131 AGCATTTCACTTCCTTGAAAGCAAGGGGTCAAAGAAGGCAGAAAGTCTGGAGAATTGAACTTGTA
*
4323901 ACGATCTCCTGTGACATCATTAGCAATTCATCAAGAAAGATTATCCTATTTAAAAAAAGACACTT
196 ACGATCTCCTGTGACATCATTAGCAATTCATCAAGAAAGATTATCATATTTAAAAAAAGACACTT
*
4323966 ATCTCATGCGGAAGGCGATAAGCATCACCTGACAAATTATTCTCCCTAACCATCAATCCATGTTC
261 ATCTCATGCGGAAGGCGATAAGCATCACCTGACAAATTATTCTCCCCAACCATCAATCCATGTTC
4324031 TCTAGAAGATTACATCACAGAGCCATAAGTCTCATAAGAATGGGATATGTAGGTGTGTATCTTAA
326 TCTAGAAGATTACATCACAGAGCCATAAGTCTCATAAGAATGGGATATGTAGGTGTGTATCTTAA
4324096 AGCAACAAAAGAGACAGTCACTGTAGCAGTCATTGCAAGAAAATGCACTAACAAAGATCTTCTAG
391 AGCAACAAAAGAGACAGTCACTGTAGCAGTCATTGCAAGAAAATGCACTAACAAAGATCTTCTAG
* *
4324161 TACATCTCGATGATGTTTATTTCTTCCGGTAAGGTTGTTACACTAGATTCCACTGACAACAAGAT
456 TACATCTCGATGATGTTTATTTCTTCCGGTAAGGTTGTTACACTAGATGCCACTAACAACAAGAT
*
4324226 CAAATTCATCAAATCTACTCATCAATTTCTCCAACTGATCATCATTCAGTTCTTTCACATATGCT
521 CAAATTCATCAAATCTACTCATCAATTTCTCCAACTGATCATCATTCAGTTCTTGCACATATGCT
*
4324291 TTCAAAAGTATGCTGAGATAGTAGAAGGCAACCTCTACATCACTGATCCTAGAGAAAAGAGACAT
586 TTCAAAAGTATGCTGAGATAGTAGAAGGCAACCTCTACATCACTGATCCCAGAGAAAAGAGACAT
4324356 AACATTGATACCACCGGGGAACATGTCTCTAGCAGATCCTTCTCCTCGTGTATGGTTTTT
651 AACATTGATACCACCGGGGAACATGTCTCTAGCAGATCCTTCTCCTCGTGTATGGTTTTT
*
4324416 ATTCTTCGATAAAGAAAGGAGGAAAAACATTTTCAAATAGGATAGTCTCAGATGAGGAAGGTCCT
1 ATTCTTCGATAAAGAAAGGAGGAAAAACATTTTCAAACAGGATAGTCTCAGATGAGGAAGGTCCT
4324481 TGAATCAAGTTATTGTCTATTATACCTCTATTGAAGAAAAAGAATGAATGAGGTCAGAATAATGA
66 TGAATCAAGTTATTGTCTATTATACCTCTATTGAAGAAAAAGAATGAATGAGGTCAGAATAATGA
* *
4324546 AGCATTTCACTTTCTTGAAAGCAAGGGGTCCAAGAAGGCAGAAAGTCTGGAGAATTGAACTTGTA
131 AGCATTTCACTTCCTTGAAAGCAAGGGGTCAAAGAAGGCAGAAAGTCTGGAGAATTGAACTTGTA
4324611 ACGATCTCCTGTGACATCATTAGCAATTCATCAAGAAAGATTATCATATTT-AAAAAAGACACTT
196 ACGATCTCCTGTGACATCATTAGCAATTCATCAAGAAAGATTATCATATTTAAAAAAAGACACTT
4324675 ATCTCATGCGGAAGGCGATAAGCATCACCTGACAAATTATTCTCCCCAACCATCAATCCATGTTC
261 ATCTCATGCGGAAGGCGATAAGCATCACCTGACAAATTATTCTCCCCAACCATCAATCCATGTTC
4324740 TCTAGAAGATTACATCACAGAGCCATAAGTCTCATAAGAATGGGATATGTAGGTGTGTATCTTAA
326 TCTAGAAGATTACATCACAGAGCCATAAGTCTCATAAGAATGGGATATGTAGGTGTGTATCTTAA
* * *
4324805 ATCAGCAAAAGAGACAGTCACTGTAGTAGTCATTGCAAGAAAATGCACTAACAAAGATCTTCTAG
391 AGCAACAAAAGAGACAGTCACTGTAGCAGTCATTGCAAGAAAATGCACTAACAAAGATCTTCTAG
* *
4324870 TACATCTCGATGATGTTTATTTCTTTCGGTAAGGTTGTTACACTAGATGCCACTAACAACAATAT
456 TACATCTCGATGATGTTTATTTCTTCCGGTAAGGTTGTTACACTAGATGCCACTAACAACAAGAT
*
4324935 CAAATTCATCAAATCTACTCATCAATTTCTCCAACTGATCATCATTCAGTTCTTGCACATCTGCT
521 CAAATTCATCAAATCTACTCATCAATTTCTCCAACTGATCATCATTCAGTTCTTGCACATATGCT
4325000 TTCAAAAGTATGCTGAGATAGTAGAAGGCAACCTCTACATCACTGATCCCAGAGAAAAGAGACAT
586 TTCAAAAGTATGCTGAGATAGTAGAAGGCAACCTCTACATCACTGATCCCAGAGAAAAGAGACAT
* *
4325065 AACATTGATACCACCGGGGAATATGTCTCTAGCAGATCTTTCTCCTCGTGTATGGTTTTT
651 AACATTGATACCACCGGGGAACATGTCTCTAGCAGATCCTTCTCCTCGTGTATGGTTTTT
4325125 A
1 A
4325126 GGGAAACCTA
Statistics
Matches: 693, Mismatches: 17, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
709 451 0.65
710 242 0.35
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (710 bp):
ATTCTTCGATAAAGAAAGGAGGAAAAACATTTTCAAACAGGATAGTCTCAGATGAGGAAGGTCCT
TGAATCAAGTTATTGTCTATTATACCTCTATTGAAGAAAAAGAATGAATGAGGTCAGAATAATGA
AGCATTTCACTTCCTTGAAAGCAAGGGGTCAAAGAAGGCAGAAAGTCTGGAGAATTGAACTTGTA
ACGATCTCCTGTGACATCATTAGCAATTCATCAAGAAAGATTATCATATTTAAAAAAAGACACTT
ATCTCATGCGGAAGGCGATAAGCATCACCTGACAAATTATTCTCCCCAACCATCAATCCATGTTC
TCTAGAAGATTACATCACAGAGCCATAAGTCTCATAAGAATGGGATATGTAGGTGTGTATCTTAA
AGCAACAAAAGAGACAGTCACTGTAGCAGTCATTGCAAGAAAATGCACTAACAAAGATCTTCTAG
TACATCTCGATGATGTTTATTTCTTCCGGTAAGGTTGTTACACTAGATGCCACTAACAACAAGAT
CAAATTCATCAAATCTACTCATCAATTTCTCCAACTGATCATCATTCAGTTCTTGCACATATGCT
TTCAAAAGTATGCTGAGATAGTAGAAGGCAACCTCTACATCACTGATCCCAGAGAAAAGAGACAT
AACATTGATACCACCGGGGAACATGTCTCTAGCAGATCCTTCTCCTCGTGTATGGTTTTT
Found at i:4328227 original size:22 final size:22
Alignment explanation
Indices: 4328202--4328273 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
4328192 CATTCTCCAT
*
4328202 AGATGATAAATTCTCTCTTCAA
1 AGATGATAGATTCTCTCTTCAA
* *
4328224 AGATAATAGA-TCTTCTCTTTAA
1 AGATGATAGATTC-TCTCTTCAA
* *
4328246 CGATGATAGATTCTCTTTTCAA
1 AGATGATAGATTCTCTCTTCAA
4328268 AGATGA
1 AGATGA
4328274 ACGCTTTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 2 0.05
22 36 0.90
23 2 0.05
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (22 bp):
AGATGATAGATTCTCTCTTCAA
Found at i:4329050 original size:37 final size:36
Alignment explanation
Indices: 4328943--4329069 Score: 114
Period size: 36 Copynumber: 3.5 Consensus size: 36
4328933 TTCAAATAGT
4328943 AATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-A
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* ** ** **
4328978 AA-TTACGTCTTACTTGAGACAGTTTCACTCGAAACAA
1 AATTTA--TCTCACTTGAGATTGTTTTTCTTAAAACAA
4329015 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* ** *
4329052 GATTCGTCTCGCTTGAGA
1 AATTTATCTCACTTGAGA
4329070 CAATTTTACT
Statistics
Matches: 69, Mismatches: 18, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
34 3 0.04
35 2 0.03
36 35 0.51
37 24 0.35
38 2 0.03
39 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.39
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:4329093 original size:73 final size:73
Alignment explanation
Indices: 4328943--4329086 Score: 227
Period size: 73 Copynumber: 2.0 Consensus size: 73
4328933 TTCAAATAGT
* * *
4328943 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTACGTCTTACTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTACGTCTCACTTGAGACAATTTCACTA
4329008 GAAACAAC
66 GAAACAAC
* *
4329016 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATT-CGTCTCGCTTGAGACAATTTTACT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-ATTACGTCTCACTTGAGACAATTTCACT
4329080 AGAAACA
65 AGAAACA
4329087 GAAATTTCCA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 62 0.95
74 3 0.05
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.38
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTACGTCTCACTTGAGACAATTTCACTA
GAAACAAC
Found at i:4329325 original size:113 final size:112
Alignment explanation
Indices: 4329095--4329767 Score: 791
Period size: 113 Copynumber: 5.9 Consensus size: 112
4329085 CAGAAATTTC
* *
4329095 CATCACTCGATGGATCAACATTTCCAG-AGGAAGTTCATAATAAGAAGAACTCATCTGAAG-AGG
1 CATCACTCGATGGATCAACATTGCCAGTA-G-AGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
4329158 AATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTTCTTGAATT
64 AATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATT
**
4329207 CATCACTCGATGGATCAGTATTGCCATGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCA-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
4329272 ATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTTAATT
65 ATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATT
* * *
4329320 TATCACTCAATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCA-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
4329385 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTTAATT
65 ATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATT
* * * * *
4329433 CATTACTTGATGGATTAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
1 CATCACTCGATGGATCAACATTGCCA-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
4329498 ATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCGAATT
65 ATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATT
* * * * * * *
4329546 CATTACTCGATGCATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGA
1 CATCACTCGATGGATCAACATTGCCAG-TAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * *
4329610 AGAAGAAGTTCATAATGAGAAGAATTTGCTTAACC-TTTGCATG-ACT
65 ATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATT
* * * * * *
4329656 CTATCACAGAAAGAGATAGATCAGCATCAAAATTTCCAGAAGTGTTCATAATGAGAAGAACTCAT
1 C-ATCAC---------TCGAT--GGATCAACATTGCCAGTAGAGTTCATAATGAGAAGAACTCAT
* * * *
4329721 CTGAAGAAGG-AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT
54 CTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTT
4329768 ACCTTAATTC
Statistics
Matches: 495, Mismatches: 48, Indels: 26
0.87 0.08 0.05
Matches are distributed among these distances:
110 3 0.01
111 10 0.02
112 88 0.18
113 310 0.63
114 1 0.00
120 4 0.01
121 61 0.12
122 18 0.04
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
CATCACTCGATGGATCAACATTGCCAGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
TAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATT
Found at i:4330143 original size:3 final size:3
Alignment explanation
Indices: 4330126--4330202 Score: 88
Period size: 3 Copynumber: 26.0 Consensus size: 3
4330116 TTTCATCCAT
* *
4330126 TTA TTT TTA -TA TTA TTA TTA TTA -TA TTTA CATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA TTA TTA
*
4330171 -TA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4330203 AATAAATAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
2 6 0.10
3 53 0.84
4 4 0.06
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:4331708 original size:3 final size:3
Alignment explanation
Indices: 4331700--4331726 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4331690 TTAAATACAT
4331700 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
4331727 AATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4333445 original size:14 final size:15
Alignment explanation
Indices: 4333421--4333451 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4333411 TTAGTTAAAA
4333421 ATTTAATAATAAATT
1 ATTTAATAATAAATT
4333436 ATTTAA-AATAAATT
1 ATTTAATAATAAATT
4333450 AT
1 AT
4333452 AAATATATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTAATAATAAATT
Found at i:4339271 original size:35 final size:35
Alignment explanation
Indices: 4339204--4339274 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
4339194 CAATTTTACC
* ** *
4339204 ATAAAGAATTATCAGTTCGATCGGTCTGAACCTAT
1 ATAAAGAATTATCAGTTCAATCGAACTAAACCTAT
* *
4339239 ATAAGGAATTATCAGTTTAATCGAACTAAACCTAT
1 ATAAAGAATTATCAGTTCAATCGAACTAAACCTAT
4339274 A
1 A
4339275 GAGACTTCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (35 bp):
ATAAAGAATTATCAGTTCAATCGAACTAAACCTAT
Found at i:4340948 original size:17 final size:17
Alignment explanation
Indices: 4340922--4340955 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4340912 CGAAAAACAT
4340922 AAAATATGACTTTTTGG
1 AAAATATGACTTTTTGG
*
4340939 AAAATTTGACTTTTTGG
1 AAAATATGACTTTTTGG
4340956 GTCAAAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (17 bp):
AAAATATGACTTTTTGG
Found at i:4340983 original size:22 final size:22
Alignment explanation
Indices: 4340955--4341014 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
4340945 TGACTTTTTG
4340955 GGTCAAAGTCAACGGTTAGACC
1 GGTCAAAGTCAACGGTTAGACC
* *
4340977 GGTCAAAGTTAACGGTTAGGCC
1 GGTCAAAGTCAACGGTTAGACC
* *
4340999 AGTCAACGATCAACGG
1 GGTCAAAG-TCAACGG
4341015 GTCAGGTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.32, C:0.22, G:0.28, T:0.18
Consensus pattern (22 bp):
GGTCAAAGTCAACGGTTAGACC
Found at i:4343292 original size:569 final size:569
Alignment explanation
Indices: 4342214--4343353 Score: 2280
Period size: 569 Copynumber: 2.0 Consensus size: 569
4342204 GGCCAAGCCT
4342214 ATACAAATCTATAAATAGGCTTTGGCATTTATTTGTAAAACTCAACCCTTTGATAAATGAAAACT
1 ATACAAATCTATAAATAGGCTTTGGCATTTATTTGTAAAACTCAACCCTTTGATAAATGAAAACT
4342279 CTTGTGAGATTATTCTCTCTTCAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAA
66 CTTGTGAGATTATTCTCTCTTCAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAA
4342344 GTTTATGTCATCAATCTCTTCCTTGATACTTCTGGTTTCTAGTTCATATAACTAGTGGGTCAAAG
131 GTTTATGTCATCAATCTCTTCCTTGATACTTCTGGTTTCTAGTTCATATAACTAGTGGGTCAAAG
4342409 TCCTTCCTAACATCCCTTATAAAACTTATAGGAAATGGGTCTTTGTTCTTTATAACATTGGTTCC
196 TCCTTCCTAACATCCCTTATAAAACTTATAGGAAATGGGTCTTTGTTCTTTATAACATTGGTTCC
4342474 CTCTTAGTTTTATAAGATACTATTTCCTTCACCATTATCCATCACTTTCACGCCAACTCTATCAC
261 CTCTTAGTTTTATAAGATACTATTTCCTTCACCATTATCCATCACTTTCACGCCAACTCTATCAC
4342539 CATCCCATTACCATATTCATCACCATTCCTTAACCATTGAATTATTCATCAACATTCATCAATAA
326 CATCCCATTACCATATTCATCACCATTCCTTAACCATTGAATTATTCATCAACATTCATCAATAA
4342604 TCATGTGCATCATCACCAATGGTGGTCGAATTCATCAACATTTGAAGGACAATTCAACAACACTT
391 TCATGTGCATCATCACCAATGGTGGTCGAATTCATCAACATTTGAAGGACAATTCAACAACACTT
4342669 CCGCAGCCCATCTTTGATAACATTTCTATCCATTTCAATTCTTATCATTTCCTTTATTCTTCCGT
456 CCGCAGCCCATCTTTGATAACATTTCTATCCATTTCAATTCTTATCATTTCCTTTATTCTTCCGT
4342734 TTCTTATTTATATTTCTATATTAATCATTTCTTTCTTTAATTTTTGCTG
521 TTCTTATTTATATTTCTATATTAATCATTTCTTTCTTTAATTTTTGCTG
4342783 ATACAAATCTATAAATAGGCTTTGGCATTTATTTGTAAAACTCAACCCTTTGATAAATGAAAACT
1 ATACAAATCTATAAATAGGCTTTGGCATTTATTTGTAAAACTCAACCCTTTGATAAATGAAAACT
4342848 CTTGTGAGATTATTCTCTCTTCAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAA
66 CTTGTGAGATTATTCTCTCTTCAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAA
4342913 GTTTATGTCATCAATCTCTTCCTTGATACTTCTGGTTTCTAGTTCATATAACTAGTGGGTCAAAG
131 GTTTATGTCATCAATCTCTTCCTTGATACTTCTGGTTTCTAGTTCATATAACTAGTGGGTCAAAG
4342978 TCCTTCCTAACATCCCTTATAAAACTTATAGGAAATGGGTCTTTGTTCTTTATAACATTGGTTCC
196 TCCTTCCTAACATCCCTTATAAAACTTATAGGAAATGGGTCTTTGTTCTTTATAACATTGGTTCC
4343043 CTCTTAGTTTTATAAGATACTATTTCCTTCACCATTATCCATCACTTTCACGCCAACTCTATCAC
261 CTCTTAGTTTTATAAGATACTATTTCCTTCACCATTATCCATCACTTTCACGCCAACTCTATCAC
4343108 CATCCCATTACCATATTCATCACCATTCCTTAACCATTGAATTATTCATCAACATTCATCAATAA
326 CATCCCATTACCATATTCATCACCATTCCTTAACCATTGAATTATTCATCAACATTCATCAATAA
4343173 TCATGTGCATCATCACCAATGGTGGTCGAATTCATCAACATTTGAAGGACAATTCAACAACACTT
391 TCATGTGCATCATCACCAATGGTGGTCGAATTCATCAACATTTGAAGGACAATTCAACAACACTT
4343238 CCGCAGCCCATCTTTGATAACATTTCTATCCATTTCAATTCTTATCATTTCCTTTATTCTTCCGT
456 CCGCAGCCCATCTTTGATAACATTTCTATCCATTTCAATTCTTATCATTTCCTTTATTCTTCCGT
4343303 TTCTTATTTATATTTCTATATTAATCATTTCTTTCTTTAATTTTTGCTG
521 TTCTTATTTATATTTCTATATTAATCATTTCTTTCTTTAATTTTTGCTG
4343352 AT
1 AT
4343354 TACTTATTAA
Statistics
Matches: 571, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
569 571 1.00
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.40
Consensus pattern (569 bp):
ATACAAATCTATAAATAGGCTTTGGCATTTATTTGTAAAACTCAACCCTTTGATAAATGAAAACT
CTTGTGAGATTATTCTCTCTTCAAGTTCTTTTTAGAACTATATCGATTAAGCAAGCTTTTCTAAA
GTTTATGTCATCAATCTCTTCCTTGATACTTCTGGTTTCTAGTTCATATAACTAGTGGGTCAAAG
TCCTTCCTAACATCCCTTATAAAACTTATAGGAAATGGGTCTTTGTTCTTTATAACATTGGTTCC
CTCTTAGTTTTATAAGATACTATTTCCTTCACCATTATCCATCACTTTCACGCCAACTCTATCAC
CATCCCATTACCATATTCATCACCATTCCTTAACCATTGAATTATTCATCAACATTCATCAATAA
TCATGTGCATCATCACCAATGGTGGTCGAATTCATCAACATTTGAAGGACAATTCAACAACACTT
CCGCAGCCCATCTTTGATAACATTTCTATCCATTTCAATTCTTATCATTTCCTTTATTCTTCCGT
TTCTTATTTATATTTCTATATTAATCATTTCTTTCTTTAATTTTTGCTG
Found at i:4344393 original size:13 final size:13
Alignment explanation
Indices: 4344375--4344406 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
4344365 AATAATGTTT
4344375 GTCATATTTAATA
1 GTCATATTTAATA
4344388 GTCATATTTAATA
1 GTCATATTTAATA
4344401 GTCATA
1 GTCATA
4344407 ATCCATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (13 bp):
GTCATATTTAATA
Found at i:4348135 original size:2 final size:2
Alignment explanation
Indices: 4348128--4348172 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
4348118 TCAATTTACA
*
4348128 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4348170 AT A
1 AT A
4348173 ATTTACGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4348381 original size:26 final size:26
Alignment explanation
Indices: 4348331--4348393 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
4348321 TGACGTTAAT
4348331 TGTGCGTCATAAATTAGCATTATAAA
1 TGTGCGTCATAAATTAGCATTATAAA
*
4348357 TGTGTGTCATAAA-T-GCATGTCATAAA
1 TGTGCGTCATAAATTAGCAT-T-ATAAA
*
4348383 GGTGCGTCATA
1 TGTGCGTCATA
4348394 GATTTATGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 4 0.12
25 2 0.06
26 26 0.81
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (26 bp):
TGTGCGTCATAAATTAGCATTATAAA
Found at i:4349035 original size:12 final size:12
Alignment explanation
Indices: 4349018--4349048 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
4349008 AAATTGATGG
4349018 AGCATTCTGCAT
1 AGCATTCTGCAT
4349030 AGCATTCTGCAT
1 AGCATTCTGCAT
4349042 AGCATTC
1 AGCATTC
4349049 CTAGGCATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (12 bp):
AGCATTCTGCAT
Found at i:4350014 original size:22 final size:22
Alignment explanation
Indices: 4349989--4350057 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
4349979 GCTCAACTCA
4349989 ATTTTGCCACAACATTCTTTAC
1 ATTTTGCCACAACATTCTTTAC
* *
4350011 ATTTTGCCATAGCATTCTTTAC
1 ATTTTGCCACAACATTCTTTAC
* *
4350033 -TATTTGTCACAACATTTCATTAC
1 AT-TTTGCCACAACA-TTCTTTAC
4350056 AT
1 AT
4350058 ACTTTAATAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
21 1 0.03
22 29 0.76
23 7 0.18
24 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (22 bp):
ATTTTGCCACAACATTCTTTAC
Found at i:4352210 original size:56 final size:55
Alignment explanation
Indices: 4352120--4352285 Score: 210
Period size: 56 Copynumber: 3.0 Consensus size: 55
4352110 TTAAATCCCA
*
4352120 TAAACCTTTGAAACACTTTCCTTTACTTCA-AAAAATTATTAAACCCTCTAACATTC
1 TAAA-CTTTGAAACACTTTCCTTTACTT-ATAAAAATTATTAAACCCTTTAACATTC
*
4352176 TAAACGTTTGAAACACTTTCCTTTACTTATAAAAATTATTAAACTCTTTAACATTC
1 TAAAC-TTTGAAACACTTTCCTTTACTTATAAAAATTATTAAACCCTTTAACATTC
* **** * *
4352232 CAAA-AACAAAAAACTTTCCTTTCCTTATAAAAATTATTAAACCCTTTAACATTC
1 TAAACTTTGAAACACTTTCCTTTACTTATAAAAATTATTAAACCCTTTAACATTC
4352286 CAAAAACATA
Statistics
Matches: 98, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
54 43 0.44
55 2 0.02
56 53 0.54
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.37
Consensus pattern (55 bp):
TAAACTTTGAAACACTTTCCTTTACTTATAAAAATTATTAAACCCTTTAACATTC
Found at i:4352266 original size:54 final size:54
Alignment explanation
Indices: 4352134--4352298 Score: 206
Period size: 54 Copynumber: 3.0 Consensus size: 54
4352124 CCTTTGAAAC
* * **** *
4352134 ACTTTCCTTTACTTCA-AAAAATTATTAAACCCTCTAACATTCTAAACGTTTGAAAC
1 ACTTTCCTTTACTT-ATAAAAATTATTAAACCCTTTAACATTCCAAA--AACAAAAA
*
4352190 ACTTTCCTTTACTTATAAAAATTATTAAACTCTTTAACATTCCAAAAACAAAAA
1 ACTTTCCTTTACTTATAAAAATTATTAAACCCTTTAACATTCCAAAAACAAAAA
* *
4352244 ACTTTCCTTTCCTTATAAAAATTATTAAACCCTTTAACATTCCAAAAACATAAA
1 ACTTTCCTTTACTTATAAAAATTATTAAACCCTTTAACATTCCAAAAACAAAAA
4352298 A
1 A
4352299 TCATAGAATA
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
54 55 0.57
55 1 0.01
56 41 0.42
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.35
Consensus pattern (54 bp):
ACTTTCCTTTACTTATAAAAATTATTAAACCCTTTAACATTCCAAAAACAAAAA
Found at i:4358980 original size:10 final size:10
Alignment explanation
Indices: 4358965--4358994 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
4358955 ATTTAGAAGG
4358965 TAATATATTA
1 TAATATATTA
4358975 TAATATATTA
1 TAATATATTA
*
4358985 TAATAAATTA
1 TAATATATTA
4358995 ATATTTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TAATATATTA
Found at i:4359178 original size:27 final size:27
Alignment explanation
Indices: 4359148--4359199 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
4359138 TTGGTAATAA
* * *
4359148 TTTATTTATTTATTGTTTTATTATTAG
1 TTTATATATTAATTGTTTTAATATTAG
*
4359175 TTTATATATTAATTTTTTTAATATT
1 TTTATATATTAATTGTTTTAATATT
4359200 TATTAAATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTATATATTAATTGTTTTAATATTAG
Found at i:4367991 original size:20 final size:18
Alignment explanation
Indices: 4367947--4367998 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
4367937 TGTTTTTCTT
4367947 TAAAATT-TAAATTTTAA
1 TAAAATTATAAATTTTAA
4367964 TATTAAATTATAAATATTTGAA
1 TA--AAATTATAAAT-TTT-AA
4367986 TAAAATTCATAAA
1 TAAAATT-ATAAA
4367999 ATTATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 2 0.07
19 5 0.17
20 10 0.34
21 8 0.28
22 4 0.14
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TAAAATTATAAATTTTAA
Found at i:4368589 original size:60 final size:58
Alignment explanation
Indices: 4368483--4368595 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 58
4368473 GTTATTATTG
* *
4368483 ATAATAATCTTTTCCGTGAACCAAAGGTAATGATACAATTATGAAAAAATTATTTCTTTT
1 ATAATAATATTTTCCGTGAACCAAAAGTAA-GATACAATTATG-AAAAATTATTTCTTTT
* * *
4368543 ATAATAATATTTTTCGTGAATCAAAAGT-AGAATGCAATTATAGAAAAATTATT
1 ATAATAATATTTTCCGTGAACCAAAAGTAAG-ATACAATTAT-GAAAAATTATT
4368596 CCCCTTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 1 0.02
59 20 0.43
60 25 0.54
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (58 bp):
ATAATAATATTTTCCGTGAACCAAAAGTAAGATACAATTATGAAAAATTATTTCTTTT
Found at i:4374549 original size:33 final size:34
Alignment explanation
Indices: 4374507--4374577 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 34
4374497 AAAAAATTCA
4374507 AACCTTGGTCACTTAAGAAACT-AACATGTATCC
1 AACCTTGGTCACTTAAGAAACTAAACATGTATCC
*
4374540 AACCTTGGTCACTTAAGAAACTAAACTTGTATCC
1 AACCTTGGTCACTTAAGAAACTAAACATGTATCC
4374574 AACC
1 AACC
4374578 ATTAAAAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 22 0.61
34 14 0.39
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (34 bp):
AACCTTGGTCACTTAAGAAACTAAACATGTATCC
Found at i:4374697 original size:21 final size:24
Alignment explanation
Indices: 4374672--4374724 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 24
4374662 TATATATATA
4374672 TATTAACTTA-AAAATA-TTTT-T
1 TATTAACTTATAAAATATTTTTAT
*
4374693 TATTAACTTATTAAATATTTTTAT
1 TATTAACTTATAAAATATTTTTAT
4374717 TATTAACT
1 TATTAACT
4374725 AATTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 10 0.36
22 5 0.18
23 4 0.14
24 9 0.32
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTAACTTATAAAATATTTTTAT
Found at i:4374706 original size:24 final size:24
Alignment explanation
Indices: 4374679--4374724 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
4374669 ATATATTAAC
4374679 TTAAAAATATTTT-TTATTAACTTA
1 TTAAAAAT-TTTTATTATTAACTTA
*
4374703 TTAAATATTTTTATTATTAACT
1 TTAAAAATTTTTATTATTAACT
4374725 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAAAAATTTTTATTATTAACTTA
Found at i:4375417 original size:51 final size:51
Alignment explanation
Indices: 4375274--4375517 Score: 305
Period size: 50 Copynumber: 4.8 Consensus size: 51
4375264 AGATGTACAT
* *
4375274 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACATTTATTTTATTTTATTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTT-TTTTATTTTATTC
* * *
4375326 A-TGTATACCGTTGTAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
1 ACT-TACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTC
* *
4375377 ACTTACACCGGTGT-AGTATGTGTTAAGTGTTATATTTTTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTC
** * * *
4375427 ACTTACACCAATGTTAGTATGTGTTAAGTGCTACACTTGTTTATTTTATTC
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTC
* * * *
4375478 AC-TACATCGGTGTAAATATGTTTTAAGTGCTATATTTTTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTT
4375518 GTAGTATAAA
Statistics
Matches: 164, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
50 74 0.45
51 57 0.35
52 33 0.20
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (51 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTGCTACATTTTTTTATTTTATTC
Found at i:4375446 original size:101 final size:102
Alignment explanation
Indices: 4375274--4375517 Score: 350
Period size: 101 Copynumber: 2.4 Consensus size: 102
4375264 AGATGTACAT
* * * **
4375274 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTACATTTATTTTATTTTATTTATGTATACCGTTG
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTATATTT-TTTTATTTTATTCATGTACACCAATG
*
4375339 TAAGTATGTGTTAAGTGCTACACTTTTTTATTTTATTC
65 TAAGTATGTGTTAAGTGCTACACTTGTTTATTTTATTC
* *
4375377 ACTTACACCGGTGT-AGTATGTGTTAAGTGTTATATTTTTTTATTTTATTCACT-TACACCAATG
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTATATTTTTTTATTTTATTCA-TGTACACCAATG
*
4375440 TTAGTATGTGTTAAGTGCTACACTTGTTTATTTTATTC
65 TAAGTATGTGTTAAGTGCTACACTTGTTTATTTTATTC
* *
4375478 AC-TACATCGGTGTAAATATGTTTTAAGTGCTATATTTTTT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTGCTATATTTTTT
4375518 GTAGTATAAA
Statistics
Matches: 126, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
100 10 0.08
101 81 0.64
102 22 0.17
103 13 0.10
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (102 bp):
ACTTACATCGGTGTAAGTATGTGTTAAGTGCTATATTTTTTTATTTTATTCATGTACACCAATGT
AAGTATGTGTTAAGTGCTACACTTGTTTATTTTATTC
Found at i:4375796 original size:31 final size:31
Alignment explanation
Indices: 4375758--4375828 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
4375748 TAACTCGTGA
4375758 TGACCATATCCTAATTAAATAAAAATGAAAG
1 TGACCATATCCTAATTAAATAAAAATGAAAG
*
4375789 TGACCATATCTTAATTAAATAAAAATGAAAG
1 TGACCATATCCTAATTAAATAAAAATGAAAG
*
4375820 TGATCATAT
1 TGACCATAT
4375829 ATTGTGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (31 bp):
TGACCATATCCTAATTAAATAAAAATGAAAG
Found at i:4378061 original size:16 final size:17
Alignment explanation
Indices: 4378036--4378071 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
4378026 GATTTGAGAA
4378036 AAATTCAATTTAAATTT
1 AAATTCAATTTAAATTT
*
4378053 AAATT-AATTTAATTTT
1 AAATTCAATTTAAATTT
4378069 AAA
1 AAA
4378072 ATAACGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTAAATTT
Found at i:4385410 original size:17 final size:18
Alignment explanation
Indices: 4385384--4385417 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4385374 TGTGCTTCAA
4385384 TGATTAATGATC-CAATG
1 TGATTAATGATCTCAATG
*
4385401 TGATTGATGATCTCAAT
1 TGATTAATGATCTCAAT
4385418 TAAGCAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (18 bp):
TGATTAATGATCTCAATG
Found at i:4388285 original size:15 final size:15
Alignment explanation
Indices: 4388265--4388311 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
4388255 TACTATGAGT
*
4388265 ATATGTTATAGGTGA
1 ATATGTTATACGTGA
4388280 ATATGTTATACGTGAA
1 ATATGTTATACGTG-A
*
4388296 AAATGTTATACGTGA
1 ATATGTTATACGTGA
4388311 A
1 A
4388312 AAATGTTCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 15 0.52
16 14 0.48
ACGTcount: A:0.38, C:0.04, G:0.21, T:0.36
Consensus pattern (15 bp):
ATATGTTATACGTGA
Found at i:4388332 original size:15 final size:16
Alignment explanation
Indices: 4388267--4388329 Score: 83
Period size: 16 Copynumber: 4.0 Consensus size: 16
4388257 CTATGAGTAT
* *
4388267 ATGTTATAGGTG-AAT
1 ATGTTATACGTGAAAA
4388282 ATGTTATACGTGAAAA
1 ATGTTATACGTGAAAA
4388298 ATGTTATACGTGAAAA
1 ATGTTATACGTGAAAA
* *
4388314 ATGTTCTATGTGAAAA
1 ATGTTATACGTGAAAA
4388330 TGTGCTAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
15 11 0.26
16 32 0.74
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTTATACGTGAAAA
Found at i:4392479 original size:15 final size:15
Alignment explanation
Indices: 4392449--4392495 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
4392439 TACTATGAGT
4392449 ATATGTTATA-GCTGA
1 ATATGTTATACG-TGA
4392464 ATATGTTATACGTGAA
1 ATATGTTATACGTG-A
* *
4392480 AAATGTTATACTTGA
1 ATATGTTATACGTGA
4392495 A
1 A
4392496 AAATGTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (15 bp):
ATATGTTATACGTGA
Found at i:4392487 original size:16 final size:16
Alignment explanation
Indices: 4392466--4392513 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
4392456 ATAGCTGAAT
4392466 ATGTTATACGTGAAAA
1 ATGTTATACGTGAAAA
*
4392482 ATGTTATACTTGAAAA
1 ATGTTATACGTGAAAA
* *
4392498 ATGTTCTATGTGAAAA
1 ATGTTATACGTGAAAA
4392514 TGTGCTAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (16 bp):
ATGTTATACGTGAAAA
Done.