Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 51 of 62
Found at i:11839686 original size:13 final size:12
Alignment explanation
Indices: 11839669--11839726 Score: 57
Period size: 13 Copynumber: 4.7 Consensus size: 12
11839659 CTCTTTTGAA
11839669 TTTCTTTTCTTT
1 TTTCTTTTCTTT
11839681 TCTTCTTTTCTGATT
1 T-TTCTTTTCT--TT
11839696 TTT-TTTTCTTT
1 TTTCTTTTCTTT
*
11839707 TTGTCTTTT-TCT
1 TT-TCTTTTCTTT
11839719 TTTCTTTT
1 TTTCTTTT
11839727 TGCACTCCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
11 10 0.25
12 6 0.15
13 19 0.47
14 2 0.05
15 3 0.08
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTCTTTTCTTT
Found at i:11839728 original size:19 final size:20
Alignment explanation
Indices: 11839673--11839728 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
11839663 TTTGAATTTC
11839673 TTTTCTTTTCTTCTTT-TCTGA
1 TTTTCTTTTCTT-TTTGTCT-A
*
11839694 TTTTTTTTTCTTTTTGTCT-
1 TTTTCTTTTCTTTTTGTCTA
11839713 TTTTCTTTTCTTTTTG
1 TTTTCTTTTCTTTTTG
11839729 CACTCCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 15 0.47
20 3 0.09
21 14 0.44
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTGTCTA
Found at i:11844931 original size:22 final size:22
Alignment explanation
Indices: 11844901--11844952 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
11844891 TTTGATACTT
*
11844901 GTGGTTCCTAGATTACTATCTA
1 GTGGGTCCTAGATTACTATCTA
11844923 GTGGGTCCTAGATTACTATCTA
1 GTGGGTCCTAGATTACTATCTA
11844945 GTGGGTCC
1 GTGGGTCC
11844953 ATGTCCTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (22 bp):
GTGGGTCCTAGATTACTATCTA
Found at i:11847170 original size:19 final size:20
Alignment explanation
Indices: 11847146--11847190 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
11847136 CAAGAGCATA
* *
11847146 TATTTTCA-TAAAAGTTATG
1 TATTTTCATTAAAAATAATG
11847165 TATTTTCATTAAAAATAATG
1 TATTTTCATTAAAAATAATG
11847185 TATTTT
1 TATTTT
11847191 GAAAGGGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (20 bp):
TATTTTCATTAAAAATAATG
Found at i:11848153 original size:16 final size:15
Alignment explanation
Indices: 11848129--11848164 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
11848119 GCTGCGGAAT
*
11848129 TGATGGTCTTGATGGA
1 TGATAGTCTTGAT-GA
11848145 TGATAGTCTTGATGA
1 TGATAGTCTTGATGA
11848160 TGATA
1 TGATA
11848165 TAAAGATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.39
Consensus pattern (15 bp):
TGATAGTCTTGATGA
Found at i:11850902 original size:22 final size:22
Alignment explanation
Indices: 11850877--11850919 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
11850867 TCACATATGT
11850877 ATTCATGTAGGCTGCCATGTGA
1 ATTCATGTAGGCTGCCATGTGA
11850899 ATTCATGTAGGCTGCCATGTG
1 ATTCATGTAGGCTGCCATGTG
11850920 CATCATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.33
Consensus pattern (22 bp):
ATTCATGTAGGCTGCCATGTGA
Found at i:11853881 original size:12 final size:13
Alignment explanation
Indices: 11853854--11853882 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
11853844 TTTCTTATCC
11853854 TTTCATTTCTTTA
1 TTTCATTTCTTTA
11853867 TTTCATTTC-TTA
1 TTTCATTTCTTTA
11853879 TTTC
1 TTTC
11853883 CAATATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:11857864 original size:16 final size:15
Alignment explanation
Indices: 11857834--11857876 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
11857824 CATCTCTATC
11857834 CATTTTATTTCTTAT
1 CATTTTATTTCTTAT
11857849 CATTTTATTTCTT-T
1 CATTTTATTTCTTAT
*
11857863 -ATTTCATTTCTTAT
1 CATTTTATTTCTTAT
11857877 TTCCAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 13 0.50
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (15 bp):
CATTTTATTTCTTAT
Found at i:11859613 original size:22 final size:22
Alignment explanation
Indices: 11859588--11859630 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
11859578 TCACATATGT
*
11859588 ATTCATGTATGCTGCCATGTGA
1 ATTCATGTAGGCTGCCATGTGA
11859610 ATTCATGTAGGCTGCCATGTG
1 ATTCATGTAGGCTGCCATGTG
11859631 CATCATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (22 bp):
ATTCATGTAGGCTGCCATGTGA
Found at i:11866517 original size:16 final size:15
Alignment explanation
Indices: 11866487--11866529 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
11866477 CATCTCTATC
11866487 CATTTTATTTCTTAT
1 CATTTTATTTCTTAT
11866502 CATTTTATTTCTT-T
1 CATTTTATTTCTTAT
*
11866516 -ATTTCATTTCTTAT
1 CATTTTATTTCTTAT
11866530 TTCCAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 13 0.50
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (15 bp):
CATTTTATTTCTTAT
Found at i:11868522 original size:16 final size:17
Alignment explanation
Indices: 11868481--11868522 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
11868471 AGTGCTTCAA
11868481 CTTCTTTCTTGTCTTTTT
1 CTTCTTT-TTGTCTTTTT
* *
11868499 TTTTTTTTTG-CTTTTT
1 CTTCTTTTTGTCTTTTT
11868515 CTTCTTTT
1 CTTCTTTT
11868523 GAGTGCTGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.79
Consensus pattern (17 bp):
CTTCTTTTTGTCTTTTT
Found at i:11874862 original size:28 final size:27
Alignment explanation
Indices: 11874809--11874871 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
11874799 TTTCTTTGCT
* *
11874809 TTTC-TTCTTTTGAGTGCTGGATTTTC
1 TTTCTTTCTTTTGAGTGCTGCAATTTC
*
11874835 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTCTTTCTTTT-GAGTGCTGCAATTTC
*
11874863 TTTTTTTCT
1 TTTCTTTCT
11874872 GATTTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.13
27 7 0.23
28 20 0.65
ACGTcount: A:0.08, C:0.16, G:0.14, T:0.62
Consensus pattern (27 bp):
TTTCTTTCTTTTGAGTGCTGCAATTTC
Found at i:11877319 original size:16 final size:16
Alignment explanation
Indices: 11877298--11877335 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
11877288 TGATTTAAAG
11877298 GAAATGATGAAGTATA
1 GAAATGATGAAGTATA
*
11877314 GAAATGATGAAGTATG
1 GAAATGATGAAGTATA
11877330 GAAATG
1 GAAATG
11877336 GAAGTAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (16 bp):
GAAATGATGAAGTATA
Found at i:11877341 original size:14 final size:15
Alignment explanation
Indices: 11877298--11877341 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
11877288 TGATTTAAAG
11877298 GAAATGATGAAGTATA
1 GAAATGA-GAAGTATA
*
11877314 GAAATGATGAAGTATG
1 GAAATGA-GAAGTATA
11877330 GAAATG-GAAGTA
1 GAAATGAGAAGTA
11877342 GAATGAATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 6 0.22
16 21 0.78
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.23
Consensus pattern (15 bp):
GAAATGAGAAGTATA
Found at i:11882797 original size:10 final size:10
Alignment explanation
Indices: 11882782--11882810 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
11882772 AATTTCATCC
11882782 ATTCATGCAT
1 ATTCATGCAT
11882792 ATTCATGCAT
1 ATTCATGCAT
11882802 ATTCATGCA
1 ATTCATGCA
11882811 AGAAGCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (10 bp):
ATTCATGCAT
Found at i:11883435 original size:17 final size:19
Alignment explanation
Indices: 11883403--11883447 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
11883393 AAGAGTAAGT
11883403 GAAAT-AATA-AAGAT-AA
1 GAAATGAATAGAAGATAAA
11883419 GAAATGAATAGAA-ATAAA
1 GAAATGAATAGAAGATAAA
11883437 GAAATG-ATAGA
1 GAAATGAATAGA
11883448 GATGGCTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 11 0.42
18 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (19 bp):
GAAATGAATAGAAGATAAA
Found at i:11887688 original size:6 final size:6
Alignment explanation
Indices: 11887677--11887730 Score: 58
Period size: 6 Copynumber: 8.8 Consensus size: 6
11887667 TCTTTTTGAA
*
11887677 TTTTTC TTTTTC TTTTTC -TTTTC TTTTCTTC TTTTTG TCTTTTC -TTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTT-TTC TTTTTC T-TTTTC TTTTTC
11887726 TTTTT
1 TTTTT
11887731 GCACTCCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
5 10 0.24
6 19 0.46
7 9 0.22
8 3 0.07
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:11887692 original size:5 final size:5
Alignment explanation
Indices: 11887678--11887729 Score: 61
Period size: 5 Copynumber: 9.8 Consensus size: 5
11887668 CTTTTTGAAT
11887678 TTTTC TTTTTC TTTTTC TTTTC TTTTC TTCTT- TTTGTC TTTTC TTTTC
1 TTTTC -TTTTC -TTTTC TTTTC TTTTC TT-TTC TTT-TC TTTTC TTTTC
11887726 TTTT
1 TTTT
11887730 TGCACTCCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
4 1 0.02
5 26 0.60
6 16 0.37
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:11887719 original size:21 final size:22
Alignment explanation
Indices: 11887678--11887727 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
11887668 CTTTTTGAAT
* *
11887678 TTTTCTTTTTCTTTTTCTTTTC
1 TTTTCTTCTTCTTTGTCTTTTC
11887700 TTTTCTTCTT-TTTGTCTTTTC
1 TTTTCTTCTTCTTTGTCTTTTC
11887721 TTTTCTT
1 TTTTCTT
11887728 TTTGCACTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTCTTCTTCTTTGTCTTTTC
Found at i:11890639 original size:15 final size:14
Alignment explanation
Indices: 11890619--11890658 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
11890609 AAGAATAAAG
11890619 GAAATGATAAGAAAT
1 GAAATGA-AAGAAAT
11890634 GAAATGGAAAGAAAT
1 GAAAT-GAAAGAAAT
*
11890649 GATATGAAAG
1 GAAATGAAAG
11890659 TGGGCTGCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 16 0.70
16 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.17
Consensus pattern (14 bp):
GAAATGAAAGAAAT
Found at i:11894954 original size:27 final size:27
Alignment explanation
Indices: 11894924--11894980 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
11894914 ATCAGCAAAG
*
11894924 AAATTGAAGCACTCAAAAGGAAGAAGA
1 AAATTCAAGCACTCAAAAGGAAGAAGA
*
11894951 AAATTCAAGCACTCAAAATGAAGAAGA
1 AAATTCAAGCACTCAAAAGGAAGAAGA
11894978 AAA
1 AAA
11894981 AAAGAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.58, C:0.12, G:0.18, T:0.12
Consensus pattern (27 bp):
AAATTCAAGCACTCAAAAGGAAGAAGA
Found at i:11894990 original size:13 final size:13
Alignment explanation
Indices: 11894965--11895006 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
11894955 TCAAGCACTC
*
11894965 AAAATGAAG-AAG
1 AAAATAAAGAAAG
11894977 AAAA-AAAGAAAAG
1 AAAATAAAG-AAAG
11894990 AAAATAAAGAAAG
1 AAAATAAAGAAAG
11895003 AAAA
1 AAAA
11895007 GTTGATGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 3 0.12
12 4 0.15
13 15 0.58
14 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (13 bp):
AAAATAAAGAAAG
Found at i:11909850 original size:16 final size:16
Alignment explanation
Indices: 11909817--11909865 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
11909807 TAAGGTAATG
11909817 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
11909835 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
11909851 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
11909866 GATAATTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:11910084 original size:12 final size:12
Alignment explanation
Indices: 11910069--11910107 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
11910059 AGACTTTTTC
11910069 TTTTCTTTTTGT
1 TTTTCTTTTTGT
*
11910081 TTTTCTTCTTTCT
1 TTTTCTT-TTTGT
11910094 TTTCTCTTTTTGT
1 TTT-TCTTTTTGT
11910107 T
1 T
11910108 GCTTTTGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 12 0.52
14 4 0.17
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (12 bp):
TTTTCTTTTTGT
Found at i:11910092 original size:7 final size:6
Alignment explanation
Indices: 11910062--11910104 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
11910052 ATTTAGGAGA
*
11910062 CTTTTT C-TTTT CTTTTT GTTTTT CTTCTTT CTTTTCT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT-TTT CTTTT-T CTTTTT
11910105 GTTGCTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.16
6 15 0.47
7 12 0.38
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:11910355 original size:6 final size:6
Alignment explanation
Indices: 11910339--11910381 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
11910329 ATTTAGGAGA
*
11910339 CTTTTT C-TTTT CTTTTT GTTTTT CTTCTTT CTTTTT CTCTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTT-TTT CTTTTT CT-TTTT
11910382 TGTTGCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 5 0.16
6 17 0.53
7 10 0.31
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (6 bp):
CTTTTT
Found at i:11910361 original size:12 final size:12
Alignment explanation
Indices: 11910339--11910381 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
11910329 ATTTAGGAGA
11910339 CTTTTTC-TTTT
1 CTTTTTCTTTTT
*
11910350 CTTTTTGTTTTT
1 CTTTTTCTTTTT
11910362 CTTCTTTCTTTTT
1 CTT-TTTCTTTTT
11910375 CTCTTTT
1 CT-TTTT
11910382 TGTTGCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 6 0.22
12 7 0.26
13 13 0.48
14 1 0.04
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (12 bp):
CTTTTTCTTTTT
Found at i:11910491 original size:273 final size:268
Alignment explanation
Indices: 11909939--11910492 Score: 887
Period size: 273 Copynumber: 2.0 Consensus size: 268
11909929 TCCTTCTAGT
11909939 TTGTTGTTAGGCATATTATAATATGCTTCTCTTTTAGTCTACTTTGCAACTTTGTTCACTTTTTC
1 TTGTTGTTAGGCATATTATAATATGCTTCTCTTTTAGTCTACTTTGCAACTTTGTTCACTTTTTC
11910004 TTTTTCTTTGAATTTTCTTTTATTTACTTTCTTTTGCACTCCAATTTGATTTAGGAGACTTTTTC
66 TTTTTCTTTGAATTTTCTTTTATTTACTTTCTTTTGCACTCCAATTTGATTTAGGAGACTTTTTC
11910069 TTTTCTTTTTGTTTTTCTTCTTTCTTTTCTCTTTTTGTTGCTTTTGTTGCAGTACTTGATTGTCA
131 TTTTCTTTTTGTTTTTCTTCTTTCTTTTCTCTTTTTGTTGCTTTTGTTGCAGTACTTGATTGTCA
*
11910134 ATCCACCAAAGCTCTGATTACCGCTTGATGTAAGGCTAACCAGGCTTCTAAGAAACAACAAGGAT
196 ATCCACCAAAGCTCTGATTACCGCTTGATGTAAGGCTAACCAGGCTTCT----AACAACAAGGAG
* *** **
11910199 ACCTCCTTCTAGT
257 AACT-CTGAAACC
11910212 TTGTTGTTAGGCATATTATAATATGCTTCTCTTTTAGTCTACTTTGCAACTTTGTTCACTTTTTC
1 TTGTTGTTAGGCATATTATAATATGCTTCTCTTTTAGTCTACTTTGCAACTTTGTTCACTTTTTC
*
11910277 TTTTTCTTTGAATTTTCTTCTTTTATTTTCTTTCTTTTGCACTCCAAATTTGATTTAGGAGACTT
66 TTTTTCTTTGAA--TT-TTCTTTTATTTACTTTCTTTTGCACTCC-AATTTGATTTAGGAGACTT
11910342 TTTCTTTTCTTTTTGTTTTTCTTCTTTCTTTTTCTCTTTTTGTTGCTTTTGTTGCAGTACTTGAT
127 TTTCTTTTCTTTTTGTTTTTCTTCTTTC-TTTTCTCTTTTTGTTGCTTTTGTTGCAGTACTTGAT
* *
11910407 TGTCAATCCACCAAAGCTCTGATTACCGCTTGATGTAAGGCTAACCAGGCTTCT-TCAATAATGG
191 TGTCAATCCACCAAAGCTCTGATTACCGCTTGATGTAAGGCTAACCAGGCTTCTAACAACAA-GG
*
11910471 AGAAGT-TGGAAACC
255 AGAACTCT-GAAACC
11910485 TTGTTGTT
1 TTGTTGTT
11910493 TTCCGATCTA
Statistics
Matches: 263, Mismatches: 11, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
272 1 0.00
273 91 0.35
274 5 0.02
275 2 0.01
276 27 0.10
277 47 0.18
278 90 0.34
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.50
Consensus pattern (268 bp):
TTGTTGTTAGGCATATTATAATATGCTTCTCTTTTAGTCTACTTTGCAACTTTGTTCACTTTTTC
TTTTTCTTTGAATTTTCTTTTATTTACTTTCTTTTGCACTCCAATTTGATTTAGGAGACTTTTTC
TTTTCTTTTTGTTTTTCTTCTTTCTTTTCTCTTTTTGTTGCTTTTGTTGCAGTACTTGATTGTCA
ATCCACCAAAGCTCTGATTACCGCTTGATGTAAGGCTAACCAGGCTTCTAACAACAAGGAGAACT
CTGAAACC
Found at i:11911211 original size:18 final size:19
Alignment explanation
Indices: 11911165--11911214 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
11911155 GAAACCCCTT
*
11911165 TGAAAATACATGATTTTTGA
1 TGAAAATACATGA-TTTTAA
11911185 TGAAAATACATGA-TTTAA
1 TGAAAATACATGATTTTAA
*
11911203 TGAAGATACATG
1 TGAAAATACATG
11911215 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.54
20 13 0.46
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:11919410 original size:12 final size:12
Alignment explanation
Indices: 11919393--11919419 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
11919383 ACAACCCTAT
11919393 GCTTGCTAGCTA
1 GCTTGCTAGCTA
11919405 GCTTGCTAGCTA
1 GCTTGCTAGCTA
11919417 GCT
1 GCT
11919420 CCACACTCAA
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:0.15, C:0.26, G:0.26, T:0.33
Consensus pattern (12 bp):
GCTTGCTAGCTA
Found at i:11931130 original size:105 final size:105
Alignment explanation
Indices: 11930983--11931193 Score: 422
Period size: 105 Copynumber: 2.0 Consensus size: 105
11930973 AGTTACATTG
11930983 CTCAAGGTAATGAATAAGTAATAAGTAACATTCTAATGTAACACATGATGCCATGGCTAATATAA
1 CTCAAGGTAATGAATAAGTAATAAGTAACATTCTAATGTAACACATGATGCCATGGCTAATATAA
11931048 TAATGCAATTTATATGATAACATAAATAAGGAATGTGTAA
66 TAATGCAATTTATATGATAACATAAATAAGGAATGTGTAA
11931088 CTCAAGGTAATGAATAAGTAATAAGTAACATTCTAATGTAACACATGATGCCATGGCTAATATAA
1 CTCAAGGTAATGAATAAGTAATAAGTAACATTCTAATGTAACACATGATGCCATGGCTAATATAA
11931153 TAATGCAATTTATATGATAACATAAATAAGGAATGTGTAA
66 TAATGCAATTTATATGATAACATAAATAAGGAATGTGTAA
11931193 C
1 C
11931194 ATATGCATGA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (105 bp):
CTCAAGGTAATGAATAAGTAATAAGTAACATTCTAATGTAACACATGATGCCATGGCTAATATAA
TAATGCAATTTATATGATAACATAAATAAGGAATGTGTAA
Found at i:11956745 original size:17 final size:17
Alignment explanation
Indices: 11956720--11956763 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
11956710 GCCATGGCTA
* *
11956720 ATATAATAATGAAATTT
1 ATATGATAACGAAATTT
11956737 ATATGATAACGAAATTT
1 ATATGATAACGAAATTT
11956754 ATATGATAAC
1 ATATGATAAC
11956764 ATATGTAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (17 bp):
ATATGATAACGAAATTT
Found at i:11969315 original size:66 final size:66
Alignment explanation
Indices: 11969238--11969372 Score: 252
Period size: 66 Copynumber: 2.0 Consensus size: 66
11969228 TTTGAAATTT
11969238 CTCTTCTTCACACACCTCTCGTATGCTCTCTTTGCATTCCAGTTCTTTTTGAATTCCACTCTCAC
1 CTCTTCTTCACACACCTCTCGTATGCTCTCTTTGCATTCCAGTTCTTTTTGAATTCCACTCTCAC
11969303 A
66 A
* *
11969304 CTCTTCTTCACACTCCTCTCGTATGCTCTCTTTTCATTCCAGTTCTTTTTGAATTCCACTCTCAC
1 CTCTTCTTCACACACCTCTCGTATGCTCTCTTTGCATTCCAGTTCTTTTTGAATTCCACTCTCAC
11969369 A
66 A
11969370 CTC
1 CTC
11969373 ATGTGTCTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.16, C:0.36, G:0.07, T:0.42
Consensus pattern (66 bp):
CTCTTCTTCACACACCTCTCGTATGCTCTCTTTGCATTCCAGTTCTTTTTGAATTCCACTCTCAC
A
Found at i:11974206 original size:19 final size:20
Alignment explanation
Indices: 11974182--11974233 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
11974172 CGGCCAAGAG
* *
11974182 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
11974201 CATGTATTTTCATCAAAAAAT
1 CATGTATTTTCAT-AAAAAAT
11974222 CATGTATTTTCA
1 CATGTATTTTCA
11974234 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
21 17 0.59
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:11974995 original size:18 final size:18
Alignment explanation
Indices: 11974942--11974987 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
11974932 TTGGAGTGCA
*
11974942 AAAAGAAGAGAAAAAAATCAG
1 AAAAGAAGA-AAAGAAA--AG
11974963 AAAAGAAGAAAAGAAAAG
1 AAAAGAAGAAAAGAAAAG
11974981 AAAAGAA
1 AAAAGAA
11974988 AAAGAGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 9 0.38
20 6 0.25
21 9 0.38
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAAAAGAAAAG
Found at i:11978362 original size:19 final size:20
Alignment explanation
Indices: 11978338--11978388 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
11978328 CGGCCAAGAG
* *
11978338 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
11978357 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
11978377 CATGTATTTTCA
1 CATGTATTTTCA
11978389 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:11982329 original size:66 final size:66
Alignment explanation
Indices: 11982252--11982386 Score: 261
Period size: 66 Copynumber: 2.0 Consensus size: 66
11982242 TTTAAAATTT
11982252 CTCTTCTTCACACACCTCTCGTATGCTCTCTTTGCATTCCAGTTCTTTTTGAATTCCACTCTCAC
1 CTCTTCTTCACACACCTCTCGTATGCTCTCTTTGCATTCCAGTTCTTTTTGAATTCCACTCTCAC
11982317 A
66 A
*
11982318 CTCTTCTTCACACTCCTCTCGTATGCTCTCTTTGCATTCCAGTTCTTTTTGAATTCCACTCTCAC
1 CTCTTCTTCACACACCTCTCGTATGCTCTCTTTGCATTCCAGTTCTTTTTGAATTCCACTCTCAC
11982383 A
66 A
11982384 CTC
1 CTC
11982387 ATGTGTCTTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.16, C:0.36, G:0.07, T:0.41
Consensus pattern (66 bp):
CTCTTCTTCACACACCTCTCGTATGCTCTCTTTGCATTCCAGTTCTTTTTGAATTCCACTCTCAC
A
Found at i:11992450 original size:22 final size:22
Alignment explanation
Indices: 11992410--11992451 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11992400 AAATATGTGG
*
11992410 TTCATAATAATATCTTCATACA
1 TTCATAATAATATCATCATACA
11992432 TTCATAAT-ATCATCATCATA
1 TTCATAATAAT-ATCATCATA
11992452 ACTATAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (22 bp):
TTCATAATAATATCATCATACA
Found at i:11993133 original size:23 final size:23
Alignment explanation
Indices: 11993088--11993133 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11993078 TTATACCTAT
*
11993088 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
11993111 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
11993134 TATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:11997736 original size:23 final size:23
Alignment explanation
Indices: 11997691--11997736 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11997681 TTATACCTAT
*
11997691 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
11997714 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
11997737 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:11999080 original size:20 final size:20
Alignment explanation
Indices: 11999052--11999095 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11999042 CAGCCATCTC
*
11999052 TTTCATTTATT-TCTATTTCA
1 TTTCATTTATTATATA-TTCA
*
11999072 TTTCCTTTATTATATATTCA
1 TTTCATTTATTATATATTCA
11999092 TTTC
1 TTTC
11999096 TTAAGACCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTTATTATATATTCA
Found at i:12004922 original size:17 final size:17
Alignment explanation
Indices: 12004887--12004922 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12004877 TTGCATTGGC
*
12004887 TATAGAAATGGTTAGGG
1 TATAGAAATGGATAGGG
*
12004904 TATAGAAATGGATATGG
1 TATAGAAATGGATAGGG
12004921 TA
1 TA
12004923 GGATAGAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (17 bp):
TATAGAAATGGATAGGG
Found at i:12005226 original size:19 final size:21
Alignment explanation
Indices: 12005183--12005227 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
12005173 ATGTAGGAGT
*
12005183 CTTTTTCTTTTCTTCTTTTTG
1 CTTTTTCTTATCTTCTTTTTG
12005204 -TTTTTCTTAT-TTC-TTTTG
1 CTTTTTCTTATCTTCTTTTTG
12005222 CTTTTT
1 CTTTTT
12005228 ATTGCAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.78
Consensus pattern (21 bp):
CTTTTTCTTATCTTCTTTTTG
Found at i:12007335 original size:25 final size:24
Alignment explanation
Indices: 12007307--12007358 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
12007297 TCAGGAAAAT
**
12007307 AAATTGAAGCACTGTAAAAGAAAGA
1 AAATTGAAGCACTCAAAAAG-AAGA
**
12007332 AAATTTCAGCACTCAAAAAGAAGA
1 AAATTGAAGCACTCAAAAAGAAGA
12007356 AAA
1 AAA
12007359 AAAGAAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (24 bp):
AAATTGAAGCACTCAAAAAGAAGA
Found at i:12007377 original size:14 final size:14
Alignment explanation
Indices: 12007348--12007383 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
12007338 CAGCACTCAA
12007348 AAAGAAGAAAAAAAG
1 AAAGAA-AAAAAAAG
*
12007363 AAAGAAAAGAAAAG
1 AAAGAAAAAAAAAG
12007377 AAAGAAA
1 AAAGAAA
12007384 GTTGAAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAG
Found at i:12008602 original size:24 final size:21
Alignment explanation
Indices: 12008568--12008610 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
12008558 TCCAAAAGAC
*
12008568 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
12008590 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
12008611 AGAATATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:12013956 original size:25 final size:25
Alignment explanation
Indices: 12013935--12013986 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
12013925 ATCAGAAAAT
*
12013935 AAATTGAAGCACTCCAAAAGAAAGA
1 AAATTGAAGCACTCAAAAAGAAAGA
**
12013960 AAATTTCAGCACTCAAAAAG-AAGA
1 AAATTGAAGCACTCAAAAAGAAAGA
12013984 AAA
1 AAA
12013987 AAACAAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.58, C:0.15, G:0.13, T:0.13
Consensus pattern (25 bp):
AAATTGAAGCACTCAAAAAGAAAGA
Found at i:12020393 original size:90 final size:89
Alignment explanation
Indices: 12020236--12020399 Score: 301
Period size: 90 Copynumber: 1.8 Consensus size: 89
12020226 CCTAACACAC
12020236 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
12020301 TTTAATTAAATGAAATTTAATAAT
66 TTTAATTAAATGAAATTTAATAAT
**
12020325 CCTTTTATATTCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
12020390 ATTTAATTAA
65 ATTTAATTAA
12020400 TTAAAATTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 33 0.46
90 39 0.54
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAAATGAAATTTAATAAT
Found at i:12022659 original size:21 final size:21
Alignment explanation
Indices: 12022633--12022681 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
12022623 GTAATGGAAG
12022633 GATGATGATATAGGCATTAAT
1 GATGATGATATAGGCATTAAT
12022654 GATGATGATATAGGCATTAAT
1 GATGATGATATAGGCATTAAT
*
12022675 GGTGATG
1 GATGATG
12022682 GAGGATGGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (21 bp):
GATGATGATATAGGCATTAAT
Found at i:12025906 original size:45 final size:45
Alignment explanation
Indices: 12025823--12025912 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
12025813 AAGACACGTT
** **
12025823 CTTTGAATGAAAAATGGTGTCCTTTTGCTGTTTGATGGACATTTC
1 CTTTGAATGAAAAATGGTGTCCTTTTGCTACTCAATGGACATTTC
* * * *
12025868 CTTTGAATGAAAAATTGTTTCCTTTTGTTACTCAATGGATATTTC
1 CTTTGAATGAAAAATGGTGTCCTTTTGCTACTCAATGGACATTTC
12025913 TTTTAGATTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.44
Consensus pattern (45 bp):
CTTTGAATGAAAAATGGTGTCCTTTTGCTACTCAATGGACATTTC
Found at i:12032958 original size:15 final size:12
Alignment explanation
Indices: 12032928--12032953 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12032918 ACAAATTGAA
12032928 GAAGAAAGTTTG
1 GAAGAAAGTTTG
12032940 GAAGAAAGTTTG
1 GAAGAAAGTTTG
12032952 GA
1 GA
12032954 TGAAGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (12 bp):
GAAGAAAGTTTG
Found at i:12042314 original size:12 final size:13
Alignment explanation
Indices: 12042287--12042317 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
12042277 ATTCTTATCC
12042287 TTTCATTTCTTTA
1 TTTCATTTCTTTA
12042300 TTTCATTTC-TTA
1 TTTCATTTCTTTA
12042312 TTTCAT
1 TTTCAT
12042318 ATATATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:12049279 original size:12 final size:12
Alignment explanation
Indices: 12049262--12049295 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
12049252 GTGCTTCAAC
12049262 TTTCTTTCTTTG
1 TTTCTTTCTTTG
12049274 TTTCTTTCTTTG
1 TTTCTTTCTTTG
12049286 TTTC-TTCTTT
1 TTTCTTTCTTT
12049296 TTAATGCTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.27
12 16 0.73
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (12 bp):
TTTCTTTCTTTG
Found at i:12049312 original size:23 final size:24
Alignment explanation
Indices: 12049286--12049338 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
12049276 TCTTTCTTTG
*
12049286 TTTCTTCTTTT-TAATGCTTGAAT
1 TTTCTTCTTTTGGAATGCTTGAAT
* *
12049309 TTTCTTCTTTTGGAGTGCTTGACT
1 TTTCTTCTTTTGGAATGCTTGAAT
12049333 TTTCTT
1 TTTCTT
12049339 TACTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.60
Consensus pattern (24 bp):
TTTCTTCTTTTGGAATGCTTGAAT
Found at i:12051682 original size:13 final size:11
Alignment explanation
Indices: 12051662--12051795 Score: 103
Period size: 13 Copynumber: 11.3 Consensus size: 11
12051652 AATATAGGCG
12051662 TGATATGGTGA
1 TGATATGGTGA
12051673 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
12051686 TGATATAGGCG-
1 TGATAT-GGTGA
12051697 TGATAATGGTGA
1 TGAT-ATGGTGA
12051709 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
12051722 TGATATAGG-GG
1 TGATAT-GGTGA
12051733 TGATATGGTGA
1 TGATATGGTGA
12051744 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
12051757 TGATATAGGCG-
1 TGATAT-GGTGA
12051768 TGATAATGGTGA
1 TGAT-ATGGTGA
12051780 TGGACTATGGTGA
1 T-GA-TATGGTGA
12051793 TGA
1 TGA
12051796 ACAGATTGTA
Statistics
Matches: 101, Mismatches: 6, Indels: 31
0.73 0.04 0.22
Matches are distributed among these distances:
10 2 0.02
11 35 0.35
12 22 0.22
13 40 0.40
14 2 0.02
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:12051692 original size:35 final size:36
Alignment explanation
Indices: 12051645--12051795 Score: 252
Period size: 36 Copynumber: 4.2 Consensus size: 36
12051635 ATTTATAAGT
*
12051645 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
12051680 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
12051716 TGGTGATGATATAGGGGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
12051751 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
12051787 TGGTGATGA
1 TGGTGATGA
12051796 ACAGATTGTA
Statistics
Matches: 108, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
35 53 0.49
36 55 0.51
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:12051728 original size:71 final size:71
Alignment explanation
Indices: 12051645--12051795 Score: 284
Period size: 71 Copynumber: 2.1 Consensus size: 71
12051635 ATTTATAAGT
*
12051645 TGGTGATAATATAGGCGTGATATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGAT
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGAT
12051710 GGACTA
66 GGACTA
*
12051716 TGGTGATGATATAGGGGTGATATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGAT
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGAT
12051781 GGACTA
66 GGACTA
12051787 TGGTGATGA
1 TGGTGATGA
12051796 ACAGATTGTA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.28, C:0.03, G:0.37, T:0.31
Consensus pattern (71 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGAT
GGACTA
Found at i:12054386 original size:24 final size:25
Alignment explanation
Indices: 12054353--12054402 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
12054343 ATCAGCAAAG
*
12054353 AAATTGAAGCACTC-AAAAGAAGAA
1 AAATTCAAGCACTCAAAAAGAAGAA
12054377 AAATTCAAGCACTCAAAAAGAAGAA
1 AAATTCAAGCACTCAAAAAGAAGAA
12054402 A
1 A
12054403 GAAAAGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (25 bp):
AAATTCAAGCACTCAAAAAGAAGAA
Found at i:12060443 original size:21 final size:20
Alignment explanation
Indices: 12060401--12060445 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
12060391 TGTTTGAATA
*
12060401 ATATGAGCTATGAATGATTG
1 ATATGAGCTATCAATGATTG
12060421 ATATGAGCTAATCATAT-ATTG
1 ATATGAGCT-ATCA-ATGATTG
12060442 ATAT
1 ATAT
12060446 AGCATATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 11 0.50
22 2 0.09
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (20 bp):
ATATGAGCTATCAATGATTG
Found at i:12069625 original size:45 final size:45
Alignment explanation
Indices: 12069556--12069859 Score: 495
Period size: 45 Copynumber: 6.8 Consensus size: 45
12069546 TATAAAATTT
* *
12069556 CTTATCATTTA-TCCTATAAGCTCGTAAGCTTATTGTACCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
12069601 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
12069646 CTTACCATTTACTCCTTAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
12069691 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTATACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
12069736 CTTACCATTTACTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
12069781 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTCACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
** *
12069826 CTTGTCA-TTATTCCATAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
12069860 GCATGCTTAC
Statistics
Matches: 244, Mismatches: 14, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
44 26 0.11
45 215 0.88
46 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:12070022 original size:40 final size:40
Alignment explanation
Indices: 12069964--12070045 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
12069954 ACCGTAGTGC
* *
12069964 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
12070004 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
12070044 TA
1 TA
12070046 TAAACCTACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCATGCCCACCATATACACCGAAGTGTAT
Found at i:12075172 original size:67 final size:67
Alignment explanation
Indices: 12075059--12075324 Score: 408
Period size: 67 Copynumber: 4.0 Consensus size: 67
12075049 TAAAAGATTA
* * * *
12075059 TTGATGCCTAACTGTGCATTGAC-GAAAATGTGACAATTGTGTCAGTTAGATGAAAGGCTAAGTG
1 TTGAGGCCTAACTGTGCATTGACAG-AAAGGTGTCAATTGTGCCAGTTAGATGAAAGGCTAAGTG
12075123 CCT
65 CCT
* * *
12075126 TTGAGGCCTAACTGTGCATTAACAGAAAGGTGTCAATTATTCCAGTTAGATGAAAGGCTAAGTGC
1 TTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTGTGCCAGTTAGATGAAAGGCTAAGTGC
12075191 CT
66 CT
* *
12075193 TTGAGGCCTAACTGTGCATTGACGGAAAGGTGTCAATTGTGCTAGTTAGATGAAAGGCTAAGTGC
1 TTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTGTGCCAGTTAGATGAAAGGCTAAGTGC
12075258 CT
66 CT
* * *
12075260 TTGAGGCCTAACTGTGTATTGATAGAAATGTGTCAATTGTGCCAGTTAGATGAAAGGCTAAGTGC
1 TTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTGTGCCAGTTAGATGAAAGGCTAAGTGC
12075325 TTGATGTGAT
Statistics
Matches: 181, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
67 180 0.99
68 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (67 bp):
TTGAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTGTGCCAGTTAGATGAAAGGCTAAGTGC
CT
Found at i:12076734 original size:22 final size:22
Alignment explanation
Indices: 12076707--12076750 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
12076697 TTCCATTCTA
12076707 CATCAACACCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
*
12076729 CATCAACGCCATCAACATCTTC
1 CATCAACACCATCAACATCTTC
12076751 ATAATTCCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.41, G:0.02, T:0.23
Consensus pattern (22 bp):
CATCAACACCATCAACATCTTC
Found at i:12076845 original size:23 final size:23
Alignment explanation
Indices: 12076799--12076845 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
12076789 ATTACTTATC
* *
12076799 TTATTTATCTATTTCTTATTCTA
1 TTATTAATCTATTTCTTATCCTA
12076822 TTATTAATCATATTTCTT-TCCTA
1 TTATTAATC-TATTTCTTATCCTA
12076845 T
1 T
12076846 CTTTGTTGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTAATCTATTTCTTATCCTA
Found at i:12082206 original size:21 final size:23
Alignment explanation
Indices: 12082180--12082231 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
12082170 AGTTCTCATT
12082180 GTATCGATACCCTC-TACATA-G
1 GTATCGATACCCTCATACATAGG
* *
12082201 GTATCGAT-GCCTCATCCATAGG
1 GTATCGATACCCTCATACATAGG
12082223 GTATCGATA
1 GTATCGATA
12082232 TTGTTCGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 13 0.50
22 9 0.35
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (23 bp):
GTATCGATACCCTCATACATAGG
Found at i:12083319 original size:164 final size:164
Alignment explanation
Indices: 12083132--12083459 Score: 620
Period size: 164 Copynumber: 2.0 Consensus size: 164
12083122 GAGGTGCTGA
12083132 CCTATCTTGCTCCTCTAAGCTTCTCTTCTCGCTTTCTGAAACCTACGTGTGAAACACTCACACGC
1 CCTATCTTGCTCCTCTAAGCTTCTCTTCTCGCTTTCTGAAACCTACGTGTGAAACACTCACACGC
**
12083197 TAAGTCAATGACTTAGTTAGGCATAATAAAATTACTATACCACATCATAACTAATTCCTACTATA
66 TAAGTCAATGACTTAGTTAGGCATAATAAAATTACTATAAAACATCATAACTAATTCCTACTATA
12083262 CATACTTCATGTAATCATACACTATAAAATGCAT
131 CATACTTCATGTAATCATACACTATAAAATGCAT
12083296 CCTATCTTGCTCCTCTAAGCTTCTCTTCTCGCTTTCTGAAACCTACGTGTGAAACACTCACACGC
1 CCTATCTTGCTCCTCTAAGCTTCTCTTCTCGCTTTCTGAAACCTACGTGTGAAACACTCACACGC
* *
12083361 TAAGTCAATGACTTAGTTAGGCATAATAAACTTACTATAAAACATCATAACTAATTCCTATTATA
66 TAAGTCAATGACTTAGTTAGGCATAATAAAATTACTATAAAACATCATAACTAATTCCTACTATA
12083426 CATACTTCATGTAATCATACACTATAAAATGCAT
131 CATACTTCATGTAATCATACACTATAAAATGCAT
12083460 TATGCATCAA
Statistics
Matches: 160, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 160 1.00
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (164 bp):
CCTATCTTGCTCCTCTAAGCTTCTCTTCTCGCTTTCTGAAACCTACGTGTGAAACACTCACACGC
TAAGTCAATGACTTAGTTAGGCATAATAAAATTACTATAAAACATCATAACTAATTCCTACTATA
CATACTTCATGTAATCATACACTATAAAATGCAT
Found at i:12088909 original size:28 final size:29
Alignment explanation
Indices: 12088872--12088928 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
12088862 GAGTTGTTTG
12088872 TGTCTCCC-AAATGCTCCACCAAGCTGTT
1 TGTCTCCCAAAATGCTCCACCAAGCTGTT
*
12088900 TGTCTTCCAAAAATGCTCCACCAAGCTGT
1 TGTC-TCCCAAAATGCTCCACCAAGCTGT
12088929 ATATGTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 4 0.15
29 3 0.12
30 19 0.73
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (29 bp):
TGTCTCCCAAAATGCTCCACCAAGCTGTT
Found at i:12092894 original size:21 final size:21
Alignment explanation
Indices: 12092854--12092894 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12092844 AATGCATGCT
*
12092854 TATGATAAAATAAAATATATA
1 TATGATAAAATAAAAGATATA
* *
12092875 TATGATATAATATAAGATAT
1 TATGATAAAATAAAAGATAT
12092895 GATAAAGAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (21 bp):
TATGATAAAATAAAAGATATA
Found at i:12094169 original size:90 final size:89
Alignment explanation
Indices: 12094055--12094229 Score: 269
Period size: 90 Copynumber: 2.0 Consensus size: 89
12094045 TCTCGAATAT
* * * *
12094055 TTAATTTCAATTAATTAAATATAGATTTAATTAATTCAAAATAATAAAATCCCTGATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTCAAAATAATAAAAACCCTAATATGACTAG
12094120 GGTAACTTGGATATAAAAGGATTA
66 GGTAACTTGGATATAAAAGGATTA
** *
12094144 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTCAAAATAATAAAAACCCTAATATGACTA
*
12094209 GGGTAACTTGGCTATAAAAGG
65 GGGTAACTTGGATATAAAAGG
12094230 GTGTGTTAGG
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
89 7 0.09
90 70 0.91
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTCAAAATAATAAAAACCCTAATATGACTAG
GGTAACTTGGATATAAAAGGATTA
Found at i:12097604 original size:23 final size:24
Alignment explanation
Indices: 12097576--12097629 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
12097566 AAAATCAGCA
12097576 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
12097599 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
12097623 AAGAAAA
1 AAGAAAA
12097630 GAAAGAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:12102345 original size:16 final size:16
Alignment explanation
Indices: 12102324--12102362 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
12102314 ATCTATTCTT
*
12102324 AGCACTTTGGGAGAAA
1 AGCACTTTAGGAGAAA
*
12102340 AGCACTTTAGGAGAAG
1 AGCACTTTAGGAGAAA
12102356 AGCACTT
1 AGCACTT
12102363 ATACGCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.28, T:0.21
Consensus pattern (16 bp):
AGCACTTTAGGAGAAA
Found at i:12109759 original size:21 final size:22
Alignment explanation
Indices: 12109732--12109780 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
12109722 GTGCTACAAC
* *
12109732 AAAAAAAGCAACAAAAA-AGAAG
1 AAAAAAA-AAACAAAAAGAAAAG
12109754 AAAAAAAAAACAAAAAGAAAAG
1 AAAAAAAAAACAAAAAGAAAAG
12109776 AAAAA
1 AAAAA
12109781 GACTCCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAACAAAAAGAAAAG
Found at i:12109774 original size:11 final size:10
Alignment explanation
Indices: 12109732--12109782 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
12109722 GTGCTACAAC
12109732 AAAAAAAGCAA
1 AAAAAAAG-AA
*
12109743 CAAAAAAGAA
1 AAAAAAAGAA
12109753 GAAAAAAA-AA
1 -AAAAAAAGAA
*
12109763 ACAAAAAGAA
1 AAAAAAAGAA
12109773 AAGAAAAAGA
1 AA-AAAAAGA
12109783 CTCCTACAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 6 0.18
10 7 0.21
11 20 0.61
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:12111979 original size:22 final size:22
Alignment explanation
Indices: 12111953--12111994 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12111943 TATCATAACA
12111953 TTTGCATTCATTCATT-ATATGG
1 TTTGCA-TCATTCATTGATATGG
*
12111975 TTTGCATCATTGATTGATAT
1 TTTGCATCATTCATTGATAT
12111995 TAAAGCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.50
Consensus pattern (22 bp):
TTTGCATCATTCATTGATATGG
Found at i:12115348 original size:23 final size:25
Alignment explanation
Indices: 12115309--12115362 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
12115299 TTCTTTTATT
12115309 TTTCTTCCTTTTTGAGTGCTTTAAA
1 TTTCTTCCTTTTTGAGTGCTTTAAA
* * *
12115334 TTTCTT-C-TTTTGAGTTCTTTGAC
1 TTTCTTCCTTTTTGAGTGCTTTAAA
12115357 TTTCTT
1 TTTCTT
12115363 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 19 0.73
24 1 0.04
25 6 0.23
ACGTcount: A:0.11, C:0.17, G:0.11, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTAAA
Found at i:12117489 original size:8 final size:9
Alignment explanation
Indices: 12117472--12117499 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12117462 GTGCCTTAAC
12117472 TTTTCTTTT
1 TTTTCTTTT
12117481 TTTTCTTTT
1 TTTTCTTTT
12117490 TTTTCTTTT
1 TTTTCTTTT
12117499 T
1 T
12117500 GAGTGCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:12119585 original size:11 final size:11
Alignment explanation
Indices: 12119569--12119596 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12119559 GATCAGCCCC
12119569 CATGTGCCTTG
1 CATGTGCCTTG
12119580 CATGTGCCTTG
1 CATGTGCCTTG
12119591 CATGTG
1 CATGTG
12119597 GTTCATTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.11, C:0.25, G:0.29, T:0.36
Consensus pattern (11 bp):
CATGTGCCTTG
Found at i:12122007 original size:21 final size:21
Alignment explanation
Indices: 12121968--12122007 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12121958 AAGGAAGATT
*
12121968 AATGAAATTATAAAGATAAGG
1 AATGAAATTATAAAAATAAGG
12121989 AATGAAATTA-AATAAATAA
1 AATGAAATTATAA-AAATAA
12122008 AGGATAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (21 bp):
AATGAAATTATAAAAATAAGG
Found at i:12125781 original size:19 final size:21
Alignment explanation
Indices: 12125757--12125807 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12125747 GGCCAAGAGC
*
12125757 ATGTATCTTCA-TTAAAA-TA
1 ATGTATTTTCATTTAAAAGTA
*
12125776 ATGTATTTTCATTTAAAAGTC
1 ATGTATTTTCATTTAAAAGTA
12125797 ATGTATTTTCA
1 ATGTATTTTCA
12125808 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (21 bp):
ATGTATTTTCATTTAAAAGTA
Found at i:12128057 original size:90 final size:91
Alignment explanation
Indices: 12127934--12128106 Score: 249
Period size: 90 Copynumber: 1.9 Consensus size: 91
12127924 CCCATGTGCC
* * *
12127934 TTGCATATGACCAGACCCCATATTCCTTGCATGTGGATCATTTAGGCACCAAGATGAAGAGTTCT
1 TTGCATATGAACAGACCCCATATGCCTTGCATGTGGATCATTTAGGCACCAAGATGAAGAGCTCT
*
12127999 CTCCCTATTCGGCCAAGCCATGTATT
66 CTCCATATTCGGCCAAGCCATGTATT
* * * * * *
12128025 TTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATGAAGTGCTCT
1 TTGCATATGAACAGACCCCATATGCCTTGCATGTGGATCATTTAGGCACCAAGATGAAGAGCTCT
12128089 CTCCATATTCGGCCAAGC
66 CTCCATATTCGGCCAAGC
12128107 ATCATTTCCC
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 60 0.83
91 12 0.17
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (91 bp):
TTGCATATGAACAGACCCCATATGCCTTGCATGTGGATCATTTAGGCACCAAGATGAAGAGCTCT
CTCCATATTCGGCCAAGCCATGTATT
Found at i:12134911 original size:24 final size:25
Alignment explanation
Indices: 12134865--12134919 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
12134855 ACAGTTATGC
*
12134865 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
12134889 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
12134914 CA-TTGA
1 CACTTGA
12134920 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:12147729 original size:71 final size:71
Alignment explanation
Indices: 12147597--12147744 Score: 201
Period size: 71 Copynumber: 2.1 Consensus size: 71
12147587 ATAAGATACT
* *
12147597 ACCTA-AACATCATCATCTTCCATCACCATTTTCACGCCTATAACATCACCATCTTCCATCACCA
1 ACCTATAACATCACCATCTTCCATCACCATTTGCACGCCTATAACATCACCATCTTCCATCACCA
12147661 TTTTCAC
66 -TTTCAC
* * * * * *
12147668 GCCTATAACATCACCATCTTCTATTACCA-TTGCACGCCTATATCATTACCATCTTCTATCACCA
1 ACCTATAACATCACCATCTTCCATCACCATTTGCACGCCTATAACATCACCATCTTCCATCACCA
12147732 TTTCAC
66 TTTCAC
12147738 ACCTATA
1 ACCTATA
12147745 TAACCACCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
70 12 0.18
71 35 0.52
72 20 0.30
ACGTcount: A:0.29, C:0.36, G:0.03, T:0.32
Consensus pattern (71 bp):
ACCTATAACATCACCATCTTCCATCACCATTTGCACGCCTATAACATCACCATCTTCCATCACCA
TTTCAC
Found at i:12147745 original size:35 final size:36
Alignment explanation
Indices: 12147598--12147744 Score: 201
Period size: 36 Copynumber: 4.2 Consensus size: 36
12147588 TAAGATACTA
*
12147598 CCTA-AACATCATCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
12147633 CCTATAACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
* * *
12147669 CCTATAACATCACCATCTTCTATTACCA-TTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
* * * *
12147704 CCTATATCATTACCATCTTCTATCACCA-TTTCACA
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
12147739 CCTATA
1 CCTATA
12147745 TAACCACCAA
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 46 0.45
36 56 0.55
ACGTcount: A:0.29, C:0.36, G:0.03, T:0.33
Consensus pattern (36 bp):
CCTATAACATCACCATCTTCCATCACCATTTTCACG
Found at i:12147916 original size:15 final size:15
Alignment explanation
Indices: 12147891--12147940 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
12147881 CTTTGATAAC
12147891 ATTTCTTTCCATTTCA
1 ATTT-TTTCCATTTCA
12147907 ATTTTTTCCATTTCA
1 ATTTTTTCCATTTCA
* *
12147922 ATTCTTTCCATTTCT
1 ATTTTTTCCATTTCA
12147937 ATTT
1 ATTT
12147941 CATTTCTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
15 27 0.87
16 4 0.13
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTTTCCATTTCA
Found at i:12149707 original size:11 final size:10
Alignment explanation
Indices: 12149691--12149724 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
12149681 AATTTCTGAA
12149691 TTTTTTTCTT
1 TTTTTTTCTT
12149701 CTTTTTTTCTT
1 -TTTTTTTCTT
12149712 TTCTTTTTCTT
1 TT-TTTTTCTT
12149723 TT
1 TT
12149725 GCACTCCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 2 0.09
11 20 0.91
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:12149917 original size:22 final size:23
Alignment explanation
Indices: 12149891--12149949 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 23
12149881 GGAAAATGAT
12149891 TAATAAAGGAAGATT-AATGAAA
1 TAATAAAGGAAGATTAAATGAAA
*
12149913 TAATAAAGATAAAGATTGAAATGAAA
1 TAATAAAG--GAAGATT-AAATGAAA
12149939 TAAATAAAGGA
1 T-AATAAAGGA
12149950 TAGAGATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
22 8 0.27
24 6 0.20
25 1 0.03
26 8 0.27
27 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (23 bp):
TAATAAAGGAAGATTAAATGAAA
Found at i:12152113 original size:69 final size:69
Alignment explanation
Indices: 12152002--12152136 Score: 270
Period size: 69 Copynumber: 2.0 Consensus size: 69
12151992 GAATAGAAAT
12152002 ATCAAACCAGGATGGATGTTTAATGGGAGTTGGTTGTTGAATTCTTTTCTGGATTGGCAATGCAC
1 ATCAAACCAGGATGGATGTTTAATGGGAGTTGGTTGTTGAATTCTTTTCTGGATTGGCAATGCAC
12152067 TGGA
66 TGGA
12152071 ATCAAACCAGGATGGATGTTTAATGGGAGTTGGTTGTTGAATTCTTTTCTGGATTGGCAATGCAC
1 ATCAAACCAGGATGGATGTTTAATGGGAGTTGGTTGTTGAATTCTTTTCTGGATTGGCAATGCAC
12152136 T
66 T
12152137 TGGATTGTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (69 bp):
ATCAAACCAGGATGGATGTTTAATGGGAGTTGGTTGTTGAATTCTTTTCTGGATTGGCAATGCAC
TGGA
Found at i:12155696 original size:23 final size:25
Alignment explanation
Indices: 12155670--12155724 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
12155660 AAATCCAGCA
12155670 AAGAAAATCAAAGCACTC-AAAA-G
1 AAGAAAATCAAAGCACTCAAAAAGG
* *
12155693 AAGAAATTGAAAGCACTCAAAAAGG
1 AAGAAAATCAAAGCACTCAAAAAGG
12155718 AAGAAAA
1 AAGAAAA
12155725 AAGAAATGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 16 0.59
24 4 0.15
25 7 0.26
ACGTcount: A:0.62, C:0.13, G:0.16, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAAAGG
Found at i:12158075 original size:19 final size:19
Alignment explanation
Indices: 12158051--12158088 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
12158041 CCAAAAGGGA
12158051 TCCCTAGATAAAGATCATT
1 TCCCTAGATAAAGATCATT
12158070 TCCCTAGATAAAGATCATT
1 TCCCTAGATAAAGATCATT
12158089 CCAAAGGGTA
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:0.21, G:0.11, T:0.32
Consensus pattern (19 bp):
TCCCTAGATAAAGATCATT
Found at i:12161589 original size:35 final size:37
Alignment explanation
Indices: 12161543--12161622 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
12161533 TTTGAGAATT
*
12161543 TGGTGATGATATAGGCGTGAT-ATGG-TGATAGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATAGACTA
* *
12161578 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATAGACTA
12161615 TGGTGATG
1 TGGTGATG
12161623 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATAGACTA
Found at i:12164986 original size:15 final size:15
Alignment explanation
Indices: 12164946--12164990 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
12164936 CTTGCTTCAC
12164946 TTTTCCTTTGCTTTTGA
1 TTTT-CTTT-CTTTTGA
*
12164963 TTTTC-TTCTTTTTA
1 TTTTCTTTCTTTTGA
12164977 TTTTCTTTCTTTTG
1 TTTTCTTTCTTTTG
12164991 CACTCCAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 11 0.44
15 9 0.36
16 1 0.04
17 4 0.16
ACGTcount: A:0.04, C:0.16, G:0.07, T:0.73
Consensus pattern (15 bp):
TTTTCTTTCTTTTGA
Found at i:12165516 original size:37 final size:35
Alignment explanation
Indices: 12165437--12165516 Score: 115
Period size: 35 Copynumber: 2.2 Consensus size: 35
12165427 TTTGAGAATT
*
12165437 TGGTGATGATATAGGCGTGATATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATATGGAGATGGACTA
* *
12165472 TGATGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGAT-ATGG-AGATGGACTA
12165509 TGGTGATG
1 TGGTGATG
12165517 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGAGATGGACTA
Found at i:12166759 original size:42 final size:46
Alignment explanation
Indices: 12166713--12166803 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 46
12166703 TATTATTACA
12166713 ACTATAGA-T-TAT-ATG-ATATCAATCAATGATGCAAACCATAGG
1 ACTATAGATTATATCATGAATATCAATCAATGATGCAAACCATAGG
12166755 ACTATAGATTATATGCATGAATATCAATCAATGATGCAAACCATAGG
1 ACTATAGATTATAT-CATGAATATCAATCAATGATGCAAACCATAGG
12166802 AC
1 AC
12166804 ATAATGAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
42 8 0.18
43 1 0.02
44 3 0.07
46 3 0.07
47 29 0.66
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (46 bp):
ACTATAGATTATATCATGAATATCAATCAATGATGCAAACCATAGG
Found at i:12167500 original size:19 final size:20
Alignment explanation
Indices: 12167443--12167492 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
12167433 ATAATGGGTT
*
12167443 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
12167462 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
12167482 TAAG-AATGAAA
1 TAAGTAATGAAA
12167493 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:12173010 original size:19 final size:20
Alignment explanation
Indices: 12172953--12173002 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
12172943 ATAATGGGTT
*
12172953 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
12172972 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
12172992 TAAG-AATGAAA
1 TAAGTAATGAAA
12173003 TGAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:12176243 original size:16 final size:16
Alignment explanation
Indices: 12176222--12176254 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12176212 TAGTTAGCTC
12176222 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
12176238 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
12176254 A
1 A
12176255 GGTGGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:12179547 original size:15 final size:16
Alignment explanation
Indices: 12179520--12179551 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12179510 TAGTTAGCTC
12179520 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
12179536 ATTTGC-TTCTAACAT
1 ATTTGCATTCTAACAT
12179551 A
1 A
12179552 GGTGGCAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:12181902 original size:21 final size:21
Alignment explanation
Indices: 12181863--12181902 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12181853 AAGGAAGATT
*
12181863 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
12181884 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
12181903 AGGATAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:12181951 original size:22 final size:21
Alignment explanation
Indices: 12181925--12181965 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12181915 GTTGCAGAAT
12181925 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
12181947 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
12181966 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:12186126 original size:24 final size:24
Alignment explanation
Indices: 12186099--12186150 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
12186089 TCTTGGCACT
* * *
12186099 TCAAGTGGCACATCTTTTTGAACA
1 TCAAGTGGCACAGCTGTTGGAACA
*
12186123 TCAAGTGGCATAGCTGTTGGAACA
1 TCAAGTGGCACAGCTGTTGGAACA
12186147 TCAA
1 TCAA
12186151 AGGACATGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
TCAAGTGGCACAGCTGTTGGAACA
Found at i:12187442 original size:24 final size:24
Alignment explanation
Indices: 12187415--12187469 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
12187405 CCAACTTTTC
12187415 TTTCTTTTTTCTTC-TTTTGAGTG
1 TTTCTTTTTTCTTCTTTTTGAGTG
**
12187438 TTT-TCAATTTCTTCTTTTTGAGTG
1 TTTCT-TTTTTCTTCTTTTTGAGTG
*
12187462 CTTCTTTT
1 TTTCTTTT
12187470 CTGATTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 5
0.71 0.15 0.15
Matches are distributed among these distances:
22 1 0.04
23 10 0.42
24 12 0.50
25 1 0.04
ACGTcount: A:0.07, C:0.15, G:0.11, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTTCTTCTTTTTGAGTG
Found at i:12194912 original size:19 final size:19
Alignment explanation
Indices: 12194890--12194940 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
12194880 CTTTTTGAAT
12194890 TTTTTTCTTTTTTTTCTTA
1 TTTTTTCTTTTTTTTCTTA
* ** *
12194909 TTTTCTGATTTTTTTCTTC
1 TTTTTTCTTTTTTTTCTTA
12194928 TTTTTGTCTTTTT
1 TTTTT-TCTTTTT
12194941 CTTTTCTTTT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (19 bp):
TTTTTTCTTTTTTTTCTTA
Found at i:12195716 original size:19 final size:20
Alignment explanation
Indices: 12195669--12195719 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
12195659 GAAACCCCTT
**
12195669 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
12195689 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
12195708 TGAAGATACATG
1 TGAAAATACATG
12195720 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:12199530 original size:19 final size:20
Alignment explanation
Indices: 12199506--12199555 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
12199496 GGCCAAGAGC
* *
12199506 ATGTATCTTCAT-TAAAATA
1 ATGTATTTTCATCAAAAATA
*
12199525 ATGTATTTTCATCAAAAATC
1 ATGTATTTTCATCAAAAATA
12199545 ATGTATTTTCA
1 ATGTATTTTCA
12199556 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (20 bp):
ATGTATTTTCATCAAAAATA
Found at i:12200335 original size:18 final size:18
Alignment explanation
Indices: 12200282--12200327 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
12200272 TTGGAGTGCA
*
12200282 AAAAGAAGAGAAAAAAATCAG
1 AAAAGAAGA-AAAGAAA--AG
12200303 AAAAGAAGAAAAGAAAAG
1 AAAAGAAGAAAAGAAAAG
12200321 AAAAGAA
1 AAAAGAA
12200328 AAAGAGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 9 0.38
20 6 0.25
21 9 0.38
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAAAAGAAAAG
Found at i:12203703 original size:19 final size:20
Alignment explanation
Indices: 12203679--12203729 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
12203669 CGGCCAAGAG
* *
12203679 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
12203698 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
12203718 CATGTATTTTCA
1 CATGTATTTTCA
12203730 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:12205450 original size:11 final size:11
Alignment explanation
Indices: 12205434--12205501 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 11
12205424 ATTTTTTTTT
12205434 CAAAAAAAAAA
1 CAAAAAAAAAA
12205445 CAAAAAAAAAA
1 CAAAAAAAAAA
12205456 CAAAAAAGGCAAAA
1 CAAAAAA---AAAA
*
12205470 AAAAACAAAAAA
1 CAAAA-AAAAAA
12205482 GGC-AAAAAAAAA
1 --CAAAAAAAAAA
12205494 CAAAAAAA
1 CAAAAAAA
12205502 GAGCCAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
10 1 0.02
11 24 0.50
12 10 0.21
13 3 0.06
14 8 0.17
15 2 0.04
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:12205451 original size:10 final size:10
Alignment explanation
Indices: 12205436--12205501 Score: 73
Period size: 10 Copynumber: 6.7 Consensus size: 10
12205426 TTTTTTTTCA
12205436 AAAAAAAAAC
1 AAAAAAAAAC
12205446 AAAAAAAAA-
1 AAAAAAAAAC
**
12205455 ACAAAAAAGGC
1 A-AAAAAAAAC
12205466 AAAAAAAAAC
1 AAAAAAAAAC
**
12205476 -AAAAAAGGC
1 AAAAAAAAAC
12205485 AAAAAAAAAC
1 AAAAAAAAAC
12205495 AAAAAAA
1 AAAAAAA
12205502 GAGCCAAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 8 0.18
10 36 0.80
11 1 0.02
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:12205462 original size:20 final size:19
Alignment explanation
Indices: 12205437--12205502 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
12205427 TTTTTTTCAA
*
12205437 AAAAAAAACAAAAAAAAAAC
1 AAAAAAAGC-AAAAAAAAAC
*
12205457 AAAAAAGGCAAAAAAAAAC
1 AAAAAAAGCAAAAAAAAAC
*
12205476 AAAAAAGGCAAAAAAAAAC
1 AAAAAAAGCAAAAAAAAAC
12205495 AAAAAAAG
1 AAAAAAAG
12205503 AGCCAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
19 36 0.84
20 7 0.16
ACGTcount: A:0.83, C:0.09, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAAGCAAAAAAAAAC
Found at i:12205519 original size:20 final size:19
Alignment explanation
Indices: 12205447--12205519 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
12205437 AAAAAAAACA
*
12205447 AAAAAAAAACAAAAAAGGC
1 AAAAAAAACCAAAAAAGGC
*
12205466 AAAAAAAAACAAAAAAGGC
1 AAAAAAAACCAAAAAAGGC
*
12205485 AAAAAAAAACAAAAAAAGAGC
1 -AAAAAAAACCAAAAAAG-GC
* *
12205506 CAAAAAAGCCAAAA
1 AAAAAAAACCAAAA
12205520 TTTCAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
19 19 0.40
20 26 0.55
21 2 0.04
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAAAAAACCAAAAAAGGC
Found at i:12205519 original size:21 final size:20
Alignment explanation
Indices: 12205447--12205512 Score: 100
Period size: 19 Copynumber: 3.3 Consensus size: 20
12205437 AAAAAAAACA
12205447 AAAAAAAAAC-AAAAAAGGC
1 AAAAAAAAACAAAAAAAGGC
12205466 AAAAAAAAAC-AAAAAAGGC
1 AAAAAAAAACAAAAAAAGGC
12205485 AAAAAAAAACAAAAAAAGAGCC
1 AAAAAAAAACAAAAAAAG-G-C
12205507 AAAAAA
1 AAAAAA
12205513 GCCAAAATTT
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 29 0.66
20 7 0.16
21 1 0.02
22 7 0.16
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (20 bp):
AAAAAAAAACAAAAAAAGGC
Found at i:12216342 original size:24 final size:25
Alignment explanation
Indices: 12216315--12216366 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
12216305 AAGAAAAATC
* *
12216315 AGAAAAG-AAAGTGAAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
12216339 AG-AAAGAAAAATCAAGCACTCAAA
1 AGAAAAGAAAAATCAAGCACTCAAA
12216363 AGAA
1 AGAA
12216367 GAAAAAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 19 0.79
25 1 0.04
ACGTcount: A:0.62, C:0.13, G:0.17, T:0.08
Consensus pattern (25 bp):
AGAAAAGAAAAATCAAGCACTCAAA
Found at i:12216373 original size:24 final size:24
Alignment explanation
Indices: 12216328--12216372 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
12216318 AAAGAAAGTG
12216328 AAGCACTCAAAAGAAAGAAAAATC
1 AAGCACTCAAAAGAAAGAAAAATC
12216352 AAGCACTCAAAAG-AAGAAAAA
1 AAGCACTCAAAAGAAAGAAAAA
12216373 AGCAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.64, C:0.16, G:0.13, T:0.07
Consensus pattern (24 bp):
AAGCACTCAAAAGAAAGAAAAATC
Found at i:12223738 original size:11 final size:11
Alignment explanation
Indices: 12223717--12223784 Score: 104
Period size: 11 Copynumber: 6.2 Consensus size: 11
12223707 TTTTTTTTCG
12223717 AAAAAAC-AAA
1 AAAAAACAAAA
12223727 AAAAAACAAAA
1 AAAAAACAAAA
12223738 AAAAAACAAAA
1 AAAAAACAAAA
12223749 AAAAAACAAAA
1 AAAAAACAAAA
12223760 AAAACAA-AAAA
1 AAAA-AACAAAA
12223771 AAAAAGACAAAA
1 AAAAA-ACAAAA
12223783 AA
1 AA
12223785 GCCAAAATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
10 8 0.15
11 38 0.70
12 8 0.15
ACGTcount: A:0.90, C:0.09, G:0.01, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:12223754 original size:32 final size:34
Alignment explanation
Indices: 12223717--12223784 Score: 113
Period size: 32 Copynumber: 2.1 Consensus size: 34
12223707 TTTTTTTTCG
*
12223717 AAAAAACAAAAAAAA-ACAAAAAAAAA-ACAAAA
1 AAAAAACAAAAAAAACAAAAAAAAAAAGACAAAA
12223749 AAAAAACAAAAAAAACAAAAAAAAAAAGACAAAA
1 AAAAAACAAAAAAAACAAAAAAAAAAAGACAAAA
12223783 AA
1 AA
12223785 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 15 0.45
33 10 0.30
34 8 0.24
ACGTcount: A:0.90, C:0.09, G:0.01, T:0.00
Consensus pattern (34 bp):
AAAAAACAAAAAAAACAAAAAAAAAAAGACAAAA
Found at i:12223784 original size:1 final size:1
Alignment explanation
Indices: 12223717--12223775 Score: 73
Period size: 1 Copynumber: 59.0 Consensus size: 1
12223707 TTTTTTTTCG
* * * * *
12223717 AAAAAACAAAAAAAAACAAAAAAAAAACAAAAAAAAAACAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12223776 GACAAAAAAG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12223784 original size:10 final size:10
Alignment explanation
Indices: 12223717--12223773 Score: 89
Period size: 10 Copynumber: 5.6 Consensus size: 10
12223707 TTTTTTTTCG
12223717 AAAAAACAAA
1 AAAAAACAAA
12223727 AAAAAACAAAA
1 AAAAAAC-AAA
12223738 AAAAAACAAA
1 AAAAAACAAA
12223748 AAAAAA-ACAA
1 AAAAAACA-AA
12223758 AAAAAACAAA
1 AAAAAACAAA
12223768 AAAAAA
1 AAAAAA
12223774 AAGACAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
9 1 0.02
10 32 0.73
11 11 0.25
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:12223791 original size:32 final size:30
Alignment explanation
Indices: 12223717--12223791 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
12223707 TTTTTTTTCG
*
12223717 AAAAAACAAAAAAAAACAAAAAAAAAACAAA
1 AAAAAACCAAAAAAAACAAAAAAAAAAC-AA
*
12223748 AAAAAAACAAAAAAAACAAAAAAAAAA-AGA
1 AAAAAACCAAAAAAAACAAAAAAAAAACA-A
12223778 CAAAAAAGCCAAAA
1 -AAAAAA-CCAAAA
12223792 TTTCAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 1 0.03
30 1 0.03
31 31 0.82
32 5 0.13
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (30 bp):
AAAAAACCAAAAAAAACAAAAAAAAAACAA
Found at i:12233582 original size:2 final size:2
Alignment explanation
Indices: 12233571--12233602 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12233561 TAACTATAGT
12233571 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12233603 GAAAATAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12241431 original size:21 final size:20
Alignment explanation
Indices: 12241407--12241468 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
12241397 TCTTTTTGAA
12241407 CTTCTCTTTTTCTTTTCTTTT
1 CTTCT-TTTTTCTTTTCTTTT
** *
12241428 CTTCTTTTCTGATTTTTTTTT
1 CTTCTTTT-TTCTTTTCTTTT
12241449 CTTCTTTTTGTCTTTTCTTT
1 CTTCTTTTT-TCTTTTCTTT
12241469 CTTTTTGCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (20 bp):
CTTCTTTTTTCTTTTCTTTT
Done.