Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 30
Found at i:4037263 original size:14 final size:14
Alignment explanation
Indices: 4037237--4037266 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
4037227 TTCTTTTTGA
4037237 CTTTTCTTTTTTTT
1 CTTTTCTTTTTTTT
4037251 CTTTTCTTTTTTTT
1 CTTTTCTTTTTTTT
4037265 CT
1 CT
4037267 GAATGTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
CTTTTCTTTTTTTT
Found at i:4037291 original size:8 final size:8
Alignment explanation
Indices: 4037280--4037307 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4037270 TGTTTTCTTC
4037280 TTTTTTCT
1 TTTTTTCT
4037288 TTTTTTCT
1 TTTTTTCT
4037296 TTTTTTCT
1 TTTTTTCT
4037304 TTTT
1 TTTT
4037308 GTACTCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTCT
Found at i:4037298 original size:14 final size:13
Alignment explanation
Indices: 4037237--4037307 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 13
4037227 TTCTTTTTGA
4037237 CTTTTCTTTTTTTT
1 CTTTT-TTTTTTTT
4037251 CTTTTCTTTTTTTT
1 CTTTT-TTTTTTTT
** * *
4037265 CTGAATGTTTTCTT
1 CT-TTTTTTTTTTT
4037279 CTTTTTTCTTTTTTT
1 C-TTTTT-TTTTTTT
4037294 CTTTTTTTCTTTTT
1 CTTTTTTT-TTTTT
4037308 GTACTCCAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
13 2 0.04
14 34 0.76
15 9 0.20
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:4037634 original size:22 final size:21
Alignment explanation
Indices: 4037608--4037648 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4037598 GGCTGCGGAA
*
4037608 TTGATGATCTTGATGGATGATG
1 TTGATGATATTGAT-GATGATG
*
4037630 TTGATGGTATTGATGATGA
1 TTGATGATATTGATGATGA
4037649 AATGGAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.24, C:0.02, G:0.32, T:0.41
Consensus pattern (21 bp):
TTGATGATATTGATGATGATG
Found at i:4038923 original size:23 final size:23
Alignment explanation
Indices: 4038897--4038941 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4038887 TAACTATAGA
*
4038897 TATAATAT-ATATATGATAATAAT
1 TATAATATAACATATGA-AATAAT
*
4038920 TATATTATAACATATGAAATAA
1 TATAATATAACATATGAAATAA
4038942 GCATATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TATAATATAACATATGAAATAAT
Found at i:4040685 original size:21 final size:21
Alignment explanation
Indices: 4040648--4040698 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
4040638 CGCGAATATG
* *
4040648 TAAA-TCGCATTGTAATTTTT
1 TAAATTCGCATTGCAATTTTC
*
4040668 TAAATTCGCGTTGCAATTTTC
1 TAAATTCGCATTGCAATTTTC
*
4040689 CAAATTCGCA
1 TAAATTCGCA
4040699 ATACGAATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
TAAATTCGCATTGCAATTTTC
Found at i:4040719 original size:20 final size:20
Alignment explanation
Indices: 4040689--4040742 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4040679 TGCAATTTTC
*
4040689 CAAATTCGCAATACGAATATG
1 CAAA-TCGCAACACGAATATG
* * *
4040710 TAAATCGCAACGCGAATTTG
1 CAAATCGCAACACGAATATG
4040730 CAAATCGCAACAC
1 CAAATCGCAACAC
4040743 AAAAGTCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (20 bp):
CAAATCGCAACACGAATATG
Found at i:4040757 original size:20 final size:20
Alignment explanation
Indices: 4040714--4040901 Score: 184
Period size: 20 Copynumber: 9.4 Consensus size: 20
4040704 AATATGTAAA
**
4040714 TCGCAACGCGAATTTGCAAA-
1 TCGCAACGCGAAAGT-CAAAT
* *
4040734 TCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
* *
4040754 TCGCAACGCGATAGTTAAAT
1 TCGCAACGCGAAAGTCAAAT
* *
4040774 TCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
*
4040794 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
* * * *
4040814 TCACAACGCG-AATTTATAAA
1 TCGCAACGCGAAAGTCA-AAT
* *
4040834 TAGCAACAC-AGAAGTCAAAT
1 TCGCAACGCGA-AAGTCAAAT
*
4040854 TCGCAACGCGATAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
4040874 TCGCAACGCGAAAGTCAAAT
1 TCGCAACGCGAAAGTCAAAT
4040894 TCGCAACG
1 TCGCAACG
4040902 TGATCTCGAA
Statistics
Matches: 133, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
19 7 0.05
20 121 0.91
21 5 0.04
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAGTCAAAT
Found at i:4040779 original size:60 final size:58
Alignment explanation
Indices: 4040746--4040900 Score: 211
Period size: 60 Copynumber: 2.6 Consensus size: 58
4040736 GCAACACAAA
*
4040746 AGTCAAATTCGCAACGCGATAGTTAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGA-AGTTAAATTCGCAACAC-GAAGTCAAATTCGCAACGCGAT
* * * *
4040806 AGTCAAATTCACAACGCGAATTTATAAATAGCAACACAGAAGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAAGTTA-AATTCGCAACAC-GAAGTCAAATTCGCAACGCGAT
*
4040866 AGTCAAATTCGCAACGCGAAAGTCAAATTCGCAAC
1 AGTCAAATTCGCAACGCG-AAGTTAAATTCGCAAC
4040901 GTGATCTCGA
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 4 0.05
60 75 0.90
61 4 0.05
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.19
Consensus pattern (58 bp):
AGTCAAATTCGCAACGCGAAGTTAAATTCGCAACACGAAGTCAAATTCGCAACGCGAT
Found at i:4040901 original size:40 final size:40
Alignment explanation
Indices: 4040689--4040900 Score: 191
Period size: 40 Copynumber: 5.3 Consensus size: 40
4040679 TGCAATTTTC
* **
4040689 CAAATTCGCAATACGAATATGT-AAA-TCGCAACGCGAATTT
1 CAAATTCGCAACACGAA-A-GTCAAATTCGCAACGCGAAAGT
* *
4040729 GCAAA-TCGCAACACAAAAGTCAAATTCGCAACGCGATAGT
1 -CAAATTCGCAACACGAAAGTCAAATTCGCAACGCGAAAGT
* * *
4040769 TAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGT
1 CAAATTCGCAACACGAAAGTCAAATTCGCAACGCGAAAGT
* * * * * * *
4040809 CAAATTCACAACGCG-AATTTATAAATAGCAACAC-AGAAGT
1 CAAATTCGCAACACGAAAGTCA-AATTCGCAACGCGA-AAGT
* *
4040849 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACACGAAAGTCAAATTCGCAACGCGAAAGT
4040889 CAAATTCGCAAC
1 CAAATTCGCAAC
4040901 GTGATCTCGA
Statistics
Matches: 141, Mismatches: 23, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.01
39 12 0.09
40 119 0.84
41 8 0.06
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (40 bp):
CAAATTCGCAACACGAAAGTCAAATTCGCAACGCGAAAGT
Found at i:4040948 original size:80 final size:80
Alignment explanation
Indices: 4040770--4040981 Score: 196
Period size: 80 Copynumber: 2.6 Consensus size: 80
4040760 CGCGATAGTT
* * * * * * *
4040770 AAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCACAACGCGAATTTATAAAT
1 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATCTAGAAAT
*
4040835 AGCAACACAGAAGTC
66 AGCAACACAGAACTC
* * *
4040850 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGTG-ATCTCGAATT
1 AAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATCTAGAAAT
* *
4040914 CGTAACAC-GAACTCC
66 AGCAACACAGAACT-C
* * * * * * *
4040929 AATTTCTCAACGTGAATAGT-AAAATCGCAACGTGAATAGTAAAAATCGCAACG
1 AAATTCGCAACGCG-ATAGTCAAATTCGCAACGCGAA-AGTCAAATTCGCAACG
4040982 AATCTATATG
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
78 4 0.04
79 38 0.35
80 67 0.61
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (80 bp):
AAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGTCAAATTCGCAACGCGAATCTAGAAAT
AGCAACACAGAACTC
Found at i:4040961 original size:20 final size:21
Alignment explanation
Indices: 4040936--4040981 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
4040926 TCCAATTTCT
4040936 CAACGTGAATAGT-AAAATCG
1 CAACGTGAATAGTAAAAATCG
4040956 CAACGTGAATAGTAAAAATCG
1 CAACGTGAATAGTAAAAATCG
4040977 CAACG
1 CAACG
4040982 AATCTATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (21 bp):
CAACGTGAATAGTAAAAATCG
Found at i:4041359 original size:21 final size:21
Alignment explanation
Indices: 4041335--4041382 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
4041325 GCGATTTTGT
*
4041335 GATTTTCTA-AATTCGCGTTGC
1 GATTTT-TACAATTCACGTTGC
*
4041356 GATTTTTACTATTCACGTTGC
1 GATTTTTACAATTCACGTTGC
4041377 GATTTT
1 GATTTT
4041383 GGAAACTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.48
Consensus pattern (21 bp):
GATTTTTACAATTCACGTTGC
Found at i:4046282 original size:102 final size:102
Alignment explanation
Indices: 4046164--4046359 Score: 259
Period size: 102 Copynumber: 1.9 Consensus size: 102
4046154 GGTTAGATAA
** *
4046164 AATTTTGTTTTGAGTGAAACAATTTCAAAATTTGCA-TTTCAAGGGAAAACTGCCTCAAGCGATA
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTG-AGTTTCAAGGGAAAACTGCCTCAAGCGAGA
* * *
4046228 CGATATTTATTTTTAGGAAAAAAATCTCAAGTGAGATC
65 CGAAATTTATTTTTAAGAAAAAAATATCAAGTGAGATC
** * * * *
4046266 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGAGTTTTTAGGGGAAACTGTCTTAAGTGAGAC
1 AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGAGTTTCAAGGGAAAACTGCCTCAAGCGAGAC
*
4046331 GAAATTTGTTTTTAAGAAAAAAATATCAA
66 GAAATTTATTTTTAAGAAAAAAATATCAA
4046360 ATGTCTGTGT
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
101 1 0.01
102 79 0.99
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (102 bp):
AATTTTGTTTCAAGTGAAACAATTTCAAAATTTGAGTTTCAAGGGAAAACTGCCTCAAGCGAGAC
GAAATTTATTTTTAAGAAAAAAATATCAAGTGAGATC
Found at i:4046360 original size:66 final size:67
Alignment explanation
Indices: 4046252--4046484 Score: 246
Period size: 67 Copynumber: 3.5 Consensus size: 67
4046242 AGGAAAAAAA
* * ** * * *
4046252 TCTCAAGTGAGATC-AATTTTG-TTTCAAGTGAAACAATTTCAAAAT-TTGAGTTTTTAGGGGAA
1 TCTCAAGTGAGA-CGAAATTTGTTTTTAAGAAAAACAATATC-AAATGTTGAGTTCTTA-AGGAA
4046314 -ACTG
63 GACTG
* *
4046318 TCTTAAGTGAGACGAAATTTGTTTTTAAGAAAAA-AATATCAAATGTCTGTG-TCTTAAGGAAGA
1 TCTCAAGTGAGACGAAATTTGTTTTTAAGAAAAACAATATCAAATGT-TGAGTTCTTAAGGAAGA
4046381 CTG
65 CTG
* * *
4046384 TCTCAAGTGAGACGAAATTTGTTTTTAATAAAAACAATCTCAAATGTT-CGTATCTTAAGGAAGA
1 TCTCAAGTGAGACGAAATTTGTTTTTAAGAAAAACAATATCAAATGTTGAGT-TCTTAAGGAAGA
*
4046448 CTA
65 CTG
*
4046451 TCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAA
1 TCTCAAGTGAGACGAAATTTGTTTTTAAGAAAAA
4046485 TAATCTCATG
Statistics
Matches: 143, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
65 10 0.07
66 64 0.45
67 69 0.48
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (67 bp):
TCTCAAGTGAGACGAAATTTGTTTTTAAGAAAAACAATATCAAATGTTGAGTTCTTAAGGAAGAC
TG
Found at i:4046457 original size:67 final size:66
Alignment explanation
Indices: 4046322--4046492 Score: 263
Period size: 67 Copynumber: 2.6 Consensus size: 66
4046312 AAACTGTCTT
* * *
4046322 AAGTGAGACGAAATTTGTTTTTAAGAAAAAAATATCAAATGTCTGTGTCTTAAGGAAGACTGTCT
1 AAGTGAGACGAAATTTGTTTTTAAGAAAAAAATCTCAAATGTCTGTATCTTAAGGAAGACTATCT
4046387 C
66 C
*
4046388 AAGTGAGACGAAATTTGTTTTTAATAAAAACAATCTCAAATGT-TCGTATCTTAAGGAAGACTAT
1 AAGTGAGACGAAATTTGTTTTTAAGAAAAA-AATCTCAAATGTCT-GTATCTTAAGGAAGACTAT
4046452 CTC
64 CTC
*
4046455 AAGTGAGACAAAATTTGTTTTTAAGAAAAATAATCTCA
1 AAGTGAGACGAAATTTGTTTTTAAGAAAAA-AATCTCA
4046493 TGGTTTATGT
Statistics
Matches: 96, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
66 30 0.31
67 66 0.69
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (66 bp):
AAGTGAGACGAAATTTGTTTTTAAGAAAAAAATCTCAAATGTCTGTATCTTAAGGAAGACTATCT
C
Found at i:4048736 original size:25 final size:24
Alignment explanation
Indices: 4048706--4048787 Score: 78
Period size: 25 Copynumber: 3.3 Consensus size: 24
4048696 CTCATATCAG
4048706 TTTTCTCTTTTCT-TTTTCTTCTTT
1 TTTTCT-TTTTCTATTTTCTTCTTT
*
4048730 TCTTTCTTTTTCTCTATTTTTTTC-TT
1 T-TTTC-TTTT-TCTATTTTCTTCTTT
* *
4048756 TTTTCTTTTTCTCTCATTCTTCTTT
1 TTTTCTTTTTCTAT-TTTCTTCTTT
4048781 TTTTCTT
1 TTTTCTT
4048788 CAGGTGTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
23 4 0.08
24 10 0.21
25 20 0.42
26 7 0.15
27 7 0.15
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (24 bp):
TTTTCTTTTTCTATTTTCTTCTTT
Found at i:4048737 original size:18 final size:17
Alignment explanation
Indices: 4048713--4048787 Score: 82
Period size: 17 Copynumber: 4.4 Consensus size: 17
4048703 CAGTTTTCTC
4048713 TTTTCTTTTTCTTCTTT
1 TTTTCTTTTTCTTCTTT
*
4048730 TCTTTCTTTTTCTCTATTT
1 T-TTTCTTTTTCT-TCTTT
4048749 TTTTC-TTTT-TTCTTT
1 TTTTCTTTTTCTTCTTT
* **
4048764 TTCTCTCATTCTTCTTT
1 TTTTCTTTTTCTTCTTT
4048781 TTTTCTT
1 TTTTCTT
4048788 CAGGTGTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
15 8 0.17
16 3 0.06
17 16 0.34
18 15 0.32
19 5 0.11
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCTTTTTCTTCTTT
Found at i:4048741 original size:31 final size:29
Alignment explanation
Indices: 4048706--4048787 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 29
4048696 CTCATATCAG
4048706 TTTTCTCTTTTCTTTTTCTTCTTTTCTTTCT
1 TTTTCTCTTTTCTTTTTCTTCTTTTC-TT-T
*
4048737 TTTTCTCTATT-TTTTTCTT-TTTTCTTT
1 TTTTCTCTTTTCTTTTTCTTCTTTTCTTT
*
4048764 TTCTCTCATTCTTCTTTTT-TTCTT
1 TTTTCTC-TT-TTCTTTTTCTTCTT
4048788 CAGGTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
27 7 0.16
28 3 0.07
29 9 0.20
30 15 0.34
31 10 0.23
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTCTCTTTTCTTTTTCTTCTTTTCTTT
Found at i:4048760 original size:29 final size:31
Alignment explanation
Indices: 4048706--4048763 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4048696 CTCATATCAG
*
4048706 TTTTCTCTTTTCTTTTTCTTCTTTTCTTTCT
1 TTTTCTCTATTCTTTTTCTTCTTTTCTTTCT
4048737 TTTTCTCTATT-TTTTTCTT-TTTTCTTT
1 TTTTCTCTATTCTTTTTCTTCTTTTCTTT
4048764 TTCTCTCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.31
30 8 0.31
31 10 0.38
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (31 bp):
TTTTCTCTATTCTTTTTCTTCTTTTCTTTCT
Found at i:4056952 original size:31 final size:30
Alignment explanation
Indices: 4056917--4056990 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 30
4056907 TCCAGTTAAA
4056917 ATTAACCACTAACCACTAACTTTGCTAATTT
1 ATTAACCACTAACCACTAACTTTGCTAA-TT
* *
4056948 ATTAACCATTAATCACTAACTTTGCTAATT
1 ATTAACCACTAACCACTAACTTTGCTAATT
*
4056978 ATTAACCTCTAAC
1 ATTAACCACTAAC
4056991 TGCTAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
30 12 0.32
31 26 0.68
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
ATTAACCACTAACCACTAACTTTGCTAATT
Found at i:4056981 original size:23 final size:21
Alignment explanation
Indices: 4056955--4056998 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
4056945 TTTATTAACC
*
4056955 ATTAATCACTAACTTTGCTAATT
1 ATTAACCACTAAC--TGCTAATT
*
4056978 ATTAACCTCTAACTGCTAATT
1 ATTAACCACTAACTGCTAATT
4056999 TTTATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (21 bp):
ATTAACCACTAACTGCTAATT
Found at i:4057343 original size:19 final size:17
Alignment explanation
Indices: 4057319--4057357 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4057309 TTCATTTGTA
4057319 TTTGTTAATTGCTTTTAAT
1 TTTGTTAATT--TTTTAAT
*
4057338 TTTGTTCATTTTTTAAT
1 TTTGTTAATTTTTTAAT
4057355 TTT
1 TTT
4057358 CTTCAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
19 9 0.47
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (17 bp):
TTTGTTAATTTTTTAAT
Found at i:4057832 original size:11 final size:11
Alignment explanation
Indices: 4057818--4057875 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 11
4057808 ATATATTATA
4057818 ATTTTGAAAAT
1 ATTTTGAAAAT
4057829 ATTTTGAAAAT
1 ATTTTGAAAAT
* *
4057840 ATATATGATATAT
1 AT-TTTGA-AAAT
*
4057853 AGTTTTTAAAAT
1 A-TTTTGAAAAT
4057865 ATTTTTGAAAA
1 A-TTTTGAAAA
4057876 CATATATATT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 13 0.35
12 16 0.43
13 7 0.19
14 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.47
Consensus pattern (11 bp):
ATTTTGAAAAT
Found at i:4057881 original size:37 final size:36
Alignment explanation
Indices: 4057804--4058192 Score: 240
Period size: 37 Copynumber: 10.2 Consensus size: 36
4057794 ATATATGTAT
* * * *
4057804 ATATATATATTATAATTTTGAAAATA-TTTTGAAAAT
1 ATATATATA-TATAGTTTTTAAAACATTTTTGAAAAC
*
4057840 ATATATGATATATAGTTTTTAAAATATTTTTGAAAAC
1 ATATAT-ATATATAGTTTTTAAAACATTTTTGAAAAC
* * *
4057877 ATATATAT-TATAGAGTTTT-AAACA-TTTTGAATAT
1 ATATATATATATAG-TTTTTAAAACATTTTTGAAAAC
*
4057911 ATATATAATATATAG-TTTTAAAACA-TTTTGAAAAA
1 ATATAT-ATATATAGTTTTTAAAACATTTTTGAAAAC
* *
4057946 ATTTATATATTATATAGTTTTTAAAACGTTTTTGAAAAT
1 A--TATATA-TATATAGTTTTTAAAACATTTTTGAAAAC
* * *
4057985 AAATATAATATATAGTTTTTAAAACGTTTTTGAATATAT
1 ATATAT-ATATATAGTTTTTAAAACATTTTTGAA-A-AC
* *
4058024 ATATATATATATA-TATATATATAATATAGTTTTT-AAAAC
1 ATATATATATATAGT-T-T-T-TAAAACA-TTTTTGAAAAC
*
4058063 ATTTTGAAAATATATAATATATAGTTTTTAAAAGCATTTTTTAAAAC
1 ---------ATATAT-ATATATAGTTTTTAAAA-CATTTTTGAAAAC
* *
4058110 ATATATATATTATATAGTTTTTAAAAAAACCTTTTGAAAAGC
1 --ATATATA-TATATAGTTTTT-AAAACA-TTTTTGAAAA-C
*
4058152 ATATA-ATATATAGTTTTAAAAACATTTTTGAAAAC
1 ATATATATATATAGTTTTTAAAACATTTTTGAAAAC
4058187 -TATATA
1 ATATATA
4058193 ATTTTGAAAA
Statistics
Matches: 290, Mismatches: 26, Indels: 75
0.74 0.07 0.19
Matches are distributed among these distances:
34 22 0.08
35 27 0.09
36 41 0.14
37 66 0.23
38 30 0.10
39 21 0.07
40 27 0.09
41 18 0.06
42 6 0.02
46 9 0.03
47 7 0.02
48 7 0.02
49 8 0.03
50 1 0.00
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATATATATATAGTTTTTAAAACATTTTTGAAAAC
Found at i:4057881 original size:71 final size:72
Alignment explanation
Indices: 4057806--4058185 Score: 281
Period size: 71 Copynumber: 5.0 Consensus size: 72
4057796 ATATGTATAT
* *
4057806 ATATATATTATA-A-TTTTGAAAATATTTTGAAAATATATATGATATATAGTTTTTAAAATATTT
1 ATATATATTATAGAGTTTT-AAAATATTTTGAAAATATATATAATATATAGTTTTTAAAACATTT
*
4057869 TTGAAAAC
65 TTGAAAAA
* *
4057877 ATATATATTATAGAGTTTT-AAACATTTTGAATATATATATAATATATAG-TTTTAAAACA-TTT
1 ATATATATTATAGAGTTTTAAAATATTTTGAAAATATATATAATATATAGTTTTTAAAACATTTT
4057939 TGAAAAA
66 TGAAAAA
* *
4057946 ATTTATATATTATATAGTTTTTAAAACGT-TTTTGAAAATAAATATAATATATAGTTTTTAAAAC
1 A--TATATATTATAGAG-TTTTAAAA--TATTTTGAAAATATATATAATATATAGTTTTTAAAAC
*
4058010 GTTTTTGAATATATA
61 ATTTTTGAA-A-A-A
* * * *
4058025 TATATATATATATATA-TATATAATATAGTTTTTAAAACATTTTGAAAATATATAATATATAGTT
1 -ATATATAT-TATAGAGT-TTTAAAATA--TTTTGAAA-A---T----ATATATAATATATAGTT
*
4058089 TTTAAAAGCATTTTTTAAAACA
53 TTTAAAA-CATTTTTGAAAA-A
* * ** *
4058111 TATATATATTATATAGTTTTTAAAAAAACCTTTTGAAAA-GCATATAATATATAGTTTTAAAAAC
1 -ATATATATTATAGAG-TTTT-AAAATA--TTTTGAAAATATATATAATATATAGTTTTTAAAAC
4058175 ATTTTTGAAAA
61 ATTTTTGAAAA
4058186 CTATATAATT
Statistics
Matches: 251, Mismatches: 27, Indels: 56
0.75 0.08 0.17
Matches are distributed among these distances:
69 10 0.04
70 9 0.04
71 52 0.21
72 5 0.02
73 7 0.03
74 23 0.09
75 9 0.04
76 8 0.03
77 13 0.05
78 34 0.14
79 14 0.06
80 2 0.01
83 1 0.00
85 6 0.02
86 14 0.06
87 36 0.14
88 8 0.03
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (72 bp):
ATATATATTATAGAGTTTTAAAATATTTTGAAAATATATATAATATATAGTTTTTAAAACATTTT
TGAAAAA
Found at i:4058025 original size:2 final size:2
Alignment explanation
Indices: 4058018--4058051 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4058008 ACGTTTTTGA
4058018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4058052 GTTTTTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4058054 original size:53 final size:49
Alignment explanation
Indices: 4057987--4058085 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 49
4057977 TTGAAAATAA
* *
4057987 ATATAATATATAGTTTTTAAAACGTTTTTGAATATATATATATATATATAT
1 ATATAATATATAGTTTTTAAAAC-ATTTTGAAAATATATA-ATATATATAT
4058038 ATATATATAATATAGTTTTTAAAACATTTTGAAAATATATAATATATA
1 ATATA-AT-ATATAGTTTTTAAAACATTTTGAAAATATATAATATATA
4058086 GTTTTTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
51 12 0.27
52 16 0.36
53 16 0.36
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (49 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAATATATAATATATATAT
Found at i:4058058 original size:90 final size:87
Alignment explanation
Indices: 4057949--4058125 Score: 257
Period size: 87 Copynumber: 2.0 Consensus size: 87
4057939 TGAAAAAATT
* * *
4057949 TATATATTATATAGTTTTTAAAACGTTTTTGAAAATAAATATAATATATAGTTTTTAAAA-CGTT
1 TATATATAATATAGTTTTTAAAAC-ATTTTGAAAAT--ATATAATATATAGTTTTTAAAAGCATT
* *
4058013 TTTGAATATATATATATATATATATA
63 TTTGAAAACATATATATAT-TATATA
4058039 TATATATAATATAGTTTTTAAAACATTTTGAAAATATATAATATATAGTTTTTAAAAGCATTTTT
1 TATATATAATATAGTTTTTAAAACATTTTGAAAATATATAATATATAGTTTTTAAAAGCATTTTT
*
4058104 TAAAACATATATATATTATATA
66 GAAAACATATATATATTATATA
4058126 GTTTTTAAAA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
87 28 0.35
88 19 0.24
89 10 0.12
90 23 0.29
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (87 bp):
TATATATAATATAGTTTTTAAAACATTTTGAAAATATATAATATATAGTTTTTAAAAGCATTTTT
GAAAACATATATATATTATATA
Found at i:4058124 original size:127 final size:123
Alignment explanation
Indices: 4057907--4058135 Score: 327
Period size: 127 Copynumber: 1.8 Consensus size: 123
4057897 AACATTTTGA
*
4057907 ATATATATATAATATATAGTTTTAAAACATTTTGAAAAAATTTATATATTATATAGTTTTTAAAA
1 ATATATATATAATATATAGTTTTAAAACATTTTG-AAAAA-TTATATAATATATAGTTTTTAAAA
*
4057972 CGTTTTTGAAAATAAATATAATATATAGTTTTTAAAACGTTTTTGAATATATATATATAT
64 CGTTTTTAAAAATAAATATAATATATAGTTTTTAAAACGTTTTTGAATATATATATATAT
4058032 ATATATATATATATAATATAGTTTTTAAAACATTTTG-AAAA-TATATAATATATAGTTTTTAAA
1 ATATATATATA-AT-ATATAG-TTTTAAAACATTTTGAAAAATTATATAATATATAGTTTTTAAA
* * *
4058095 AGCATTTTTTAAAACATATATATATTATATAGTTTTTAAAA
63 A-C-GTTTTTAAAA-ATAAATATAATATATAGTTTTTAAAA
4058136 AAACCTTTTG
Statistics
Matches: 93, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
124 22 0.24
125 12 0.13
126 14 0.15
127 30 0.32
128 15 0.16
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (123 bp):
ATATATATATAATATATAGTTTTAAAACATTTTGAAAAATTATATAATATATAGTTTTTAAAACG
TTTTTAAAAATAAATATAATATATAGTTTTTAAAACGTTTTTGAATATATATATATAT
Found at i:4058156 original size:40 final size:39
Alignment explanation
Indices: 4058038--4058192 Score: 129
Period size: 40 Copynumber: 4.2 Consensus size: 39
4058028 ATATATATAT
*
4058038 ATATATATAATATAGTTTTT---AAAACATTTTG-AAA-
1 ATATATATTATATAGTTTTTAAAAAAACATTTTGAAAAC
* * *
4058072 ATATATAATATATAGTTTTT--AAAAGCATTTTTTAAAAC
1 ATATATATTATATAGTTTTTAAAAAAACA-TTTTGAAAAC
*
4058110 ATATATATATTATATAGTTTTTAAAAAAACCTTTTGAAAAGC
1 --ATATATATTATATAGTTTTTAAAAAAACATTTTGAAAA-C
4058152 ATATA-A-TATATAG-TTTT--AAAAACATTTTTGAAAAC
1 ATATATATTATATAGTTTTTAAAAAAACA-TTTTGAAAAC
4058187 -TATATA
1 ATATATA
4058193 ATTTTGAAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
34 22 0.22
35 13 0.13
36 13 0.13
37 7 0.07
38 7 0.07
39 1 0.01
40 24 0.24
41 8 0.08
42 6 0.06
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (39 bp):
ATATATATTATATAGTTTTTAAAAAAACATTTTGAAAAC
Found at i:4058158 original size:78 final size:73
Alignment explanation
Indices: 4058036--4058192 Score: 217
Period size: 77 Copynumber: 2.1 Consensus size: 73
4058026 ATATATATAT
* *
4058036 ATATATATATAATATAGTTTTTAAAACATTTTGAAAATATATAATATATAGTTTTTAAAAGCATT
1 ATATATATATAATATAGTTTTTAAAACATTTTGAAAACATATAATATATAG-TTTTAAAAACATT
*
4058101 TTTTAAAAC
65 TTTGAAAAC
* *
4058110 ATATATATATTATATAGTTTTTAAAAAAACCTTTTGAAAAGCATATAATATATAGTTTTAAAAAC
1 ATATATATATAATATAGTTTTT---AAAACATTTTGAAAA-CATATAATATATAGTTTTAAAAAC
4058175 ATTTTTGAAAAC
62 ATTTTTGAAAAC
4058187 -TATATA
1 ATATATA
4058193 ATTTTGAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
74 21 0.28
76 6 0.08
77 34 0.46
78 13 0.18
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (73 bp):
ATATATATATAATATAGTTTTTAAAACATTTTGAAAACATATAATATATAGTTTTAAAAACATTT
TTGAAAAC
Found at i:4058173 original size:36 final size:36
Alignment explanation
Indices: 4058037--4058194 Score: 169
Period size: 36 Copynumber: 4.2 Consensus size: 36
4058027 TATATATATA
*
4058037 TATATATATAATATAGTTTTTAAAACA-TTTTGAAAA-
1 TATATA-AT-ATATAGTTTTAAAAACATTTTTGAAAAC
* *
4058073 TATATAATATATAGTTTTTAAAAGCATTTTTTAAAAC
1 TATATAATATATAG-TTTTAAAAACATTTTTGAAAAC
* *
4058110 ATATATATATTATATAGTTTTTAAAAAAACCTTTTGAAAAGC
1 -TATATA-A-TATATAG-TTTTAAAAACA-TTTTTGAAAA-C
4058152 -ATATAATATATAGTTTTAAAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTAAAAACATTTTTGAAAAC
4058187 TATATAAT
1 TATATAAT
4058195 TTTGAAAACA
Statistics
Matches: 104, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
34 6 0.06
35 12 0.12
36 30 0.29
37 10 0.10
38 13 0.12
39 2 0.02
40 22 0.21
41 8 0.08
42 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (36 bp):
TATATAATATATAGTTTTAAAAACATTTTTGAAAAC
Found at i:4058209 original size:77 final size:77
Alignment explanation
Indices: 4058058--4058213 Score: 192
Period size: 77 Copynumber: 2.0 Consensus size: 77
4058048 TATAGTTTTT
* * *
4058058 AAAACATTTTGAAAATATATAATATATAGTTTTTAAAAGCATTTTTTAAAACATATATATATTAT
1 AAAACATTTTGAAAACATATAATATATAGTTTTTAAAAACATTTTTGAAAACATATATATATTAT
* **
4058123 ATAGTTTTTAAA
66 AAACATTTTAAA
* *
4058135 AAAACCTTTTGAAAAGCATATAATATATAG-TTTTAAAAACATTTTTGAAAAC-TATATA-ATTT
1 AAAACATTTTGAAAA-CATATAATATATAGTTTTTAAAAACATTTTTGAAAACATATATATATTA
4058197 TGAAAACATTTTAAA
65 T--AAACATTTTAAA
4058212 AA
1 AA
4058214 TATTTATATA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
75 4 0.06
76 6 0.09
77 45 0.66
78 13 0.19
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (77 bp):
AAAACATTTTGAAAACATATAATATATAGTTTTTAAAAACATTTTTGAAAACATATATATATTAT
AAACATTTTAAA
Found at i:4058234 original size:27 final size:25
Alignment explanation
Indices: 4058204--4058253 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
4058194 TTTTGAAAAC
4058204 ATTTTAAAAATATTTATATAATATATA
1 ATTTT-AAAATATTTATA-AATATATA
*
4058231 ATTTTAAAATATTTTTAAATATA
1 ATTTTAAAATATTTATAAATATA
4058254 GATTTTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 11 0.50
27 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTTAAAATATTTATAAATATATA
Found at i:4058323 original size:13 final size:13
Alignment explanation
Indices: 4058307--4058339 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4058297 TTATTGACCT
*
4058307 TTATTATTATTTA
1 TTATTATTACTTA
4058320 TTATTATTACTTA
1 TTATTATTACTTA
4058333 TT-TTATT
1 TTATTATT
4058340 TTCATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTATTACTTA
Found at i:4058349 original size:23 final size:25
Alignment explanation
Indices: 4058280--4058351 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 25
4058270 TATTTTTTAG
*
4058280 TTTATTTTTATTTTAATTTATTGACC
1 TTTA-TTTTATTTTATTTTATTGACC
4058306 TTTATTATTA-TTTATTATTATT-A-C
1 TTTATT-TTATTTTATT-TTATTGACC
4058330 -TTATTTTATTTTCATTTTATTG
1 TTTATTTTATTTT-ATTTTATTG
4058352 CAGGGTCCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
22 3 0.08
23 13 0.32
24 4 0.10
25 8 0.20
26 12 0.30
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (25 bp):
TTTATTTTATTTTATTTTATTGACC
Found at i:4059399 original size:14 final size:14
Alignment explanation
Indices: 4059375--4059431 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
4059365 TGTATATACC
4059375 TTTATTTTATTTTCG
1 TTTA-TTTATTTTCG
*
4059390 TTTATTTATTTTTTTCT
1 TTTATTTA---TTTTCG
4059407 TTTATTTATTTAT-G
1 TTTATTTATTT-TCG
4059421 TTTATTTATTT
1 TTTATTTATTT
4059432 CTTTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
14 18 0.50
15 5 0.14
17 13 0.36
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.77
Consensus pattern (14 bp):
TTTATTTATTTTCG
Found at i:4059411 original size:27 final size:27
Alignment explanation
Indices: 4059379--4059456 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 27
4059369 TATACCTTTA
*
4059379 TTTTATTT-TCGTTTATTTATTTTTTTC
1 TTTTATTTATC-TTTATTTATTTATTTC
*
4059406 TTTTATTTAT-TTATGTTTATTTATTTC
1 TTTTATTTATCTT-TATTTATTTATTTC
4059433 TTTT-TTTATCTTTATTTTATTTAT
1 TTTTATTTATCTTTA-TTTATTTAT
4059457 CGAATTTTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
26 8 0.18
27 35 0.80
28 1 0.02
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (27 bp):
TTTTATTTATCTTTATTTATTTATTTC
Found at i:4059415 original size:31 final size:30
Alignment explanation
Indices: 4059375--4059456 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 30
4059365 TGTATATACC
4059375 TTTATTTTATTTTCGTTTATTTATTT-TTTTCT
1 TTTA-TTTATTTT-GTTTATTTATTTCTTTT-T
4059407 TTTATTTATTTATGTTTATTTATTTCTTTTT
1 TTTATTTATTT-TGTTTATTTATTTCTTTTT
* *
4059438 TTATCTTTATTTTATTTAT
1 TT-TATTTATTTTGTTTAT
4059457 CGAATTTTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 28 0.62
32 17 0.38
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (30 bp):
TTTATTTATTTTGTTTATTTATTTCTTTTT
Found at i:4063793 original size:95 final size:96
Alignment explanation
Indices: 4063621--4063820 Score: 240
Period size: 95 Copynumber: 2.1 Consensus size: 96
4063611 ATATTATAAT
* * ** *
4063621 ATTATATATATACAATAAAGCTCGAGTTGTCCCTCTAAAGCAACTGGTTAAGTGCCCCGACTTTA
1 ATTATATATATACAATAAAACTCGAGTTATCCCTCTAAAGCAACTGGTTAAACGCCCCGACTCTA
*
4063686 TGGATAAGATTCAGCTAGCCTAATAAAGGTG
66 TGGATAAGATTCAGCTAACCTAATAAAGGTG
* * * * * *
4063717 ATTATA-ATATACAATAAAACTTGAGTTATCCCTGTAGAGCAATTTGTTAAACGCCCCGGCTCTA
1 ATTATATATATACAATAAAACTCGAGTTATCCCTCTAAAGCAACTGGTTAAACGCCCCGACTCTA
* * *
4063781 TTGATAATATTCAGCTAACCTGATAAAGGTG
66 TGGATAAGATTCAGCTAACCTAATAAAGGTG
* *
4063812 TTTACATAT
1 ATTATATAT
4063821 TGAGCTGTCC
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
95 78 0.91
96 8 0.09
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (96 bp):
ATTATATATATACAATAAAACTCGAGTTATCCCTCTAAAGCAACTGGTTAAACGCCCCGACTCTA
TGGATAAGATTCAGCTAACCTAATAAAGGTG
Found at i:4065123 original size:84 final size:82
Alignment explanation
Indices: 4064989--4065430 Score: 431
Period size: 80 Copynumber: 5.5 Consensus size: 82
4064979 ACTCACGGCT
* * *
4064989 AGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTTGACTACGCTTAGCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGCC-ACAAAAGACCTTCGAGTTTGACTACACTCAGCTC-AAGGCACATCATT
*
4065054 TGCAGAATAACTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * * *
4065073 AGATGGGCTATCTGCCATCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCA-CAAAAGACCTTCGAGTTTGACTACACTCAGCT-CAAGGCACATCATT
*
4065138 TACAGCATAACTTAAGTCG
64 TGCAGCATAACTTAAGTCG
* * **
4065157 AGAAGGGTTATCTTCCAC-AAAGACCTTCGAGTTCGACTATGCTCAGC-CAAGGCACATCATTTG
1 AGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTTGACTACACTCAGCTCAAGGCACATCATTTG
* *
4065220 CAGGATAGCTTAAGTCG
66 CAGCATAACTTAAGTCG
* * * * * *
4065237 AGAAGGGATATCTG-C-C-AAAGACCCTCGAGTTTGATTACACTAAGCTTTGAGGGCACATCATT
1 AGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTTGACTACACTCAGC--TCAAGGCACATCATT
* * * * *
4065299 TACAGTATAACTCAAGGCT
64 TGCAGCATAACTTAAGTCG
* * * *
4065318 AGAAAGGTTA--T-AC-CAAAAGACCTTCGAGTTTGACTACACTCAGCTCCA-G--TATCATTTG
1 AGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTTGACTACACTCAGCTCAAGGCACATCATTTG
*
4065376 CAGCATAACTTAAGTCT
66 CAGCATAACTTAAGTCG
* * *
4065393 AAAAGGGTTATCTGCCAACCAAAGACCTTCGATTTTGA
1 AGAAGGGTTATCTGCC-ACAAAAGACCTTCGAGTTTGA
4065431 AAAGACCTTC
Statistics
Matches: 294, Mismatches: 52, Indels: 28
0.79 0.14 0.07
Matches are distributed among these distances:
75 29 0.10
77 2 0.01
78 26 0.09
79 4 0.01
80 85 0.29
81 33 0.11
82 27 0.09
83 2 0.01
84 85 0.29
85 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (82 bp):
AGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTTGACTACACTCAGCTCAAGGCACATCATTTG
CAGCATAACTTAAGTCG
Found at i:4065430 original size:80 final size:81
Alignment explanation
Indices: 4064989--4065430 Score: 393
Period size: 84 Copynumber: 5.5 Consensus size: 81
4064979 ACTCACGGCT
** * *
4064989 AGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTTGACTACGCTTAGCTCAAAGGCACATCATT
1 AGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTTGACTACACTCAGCTC-AAGG-ACATCATT
*
4065054 TGCAGAATAACTTAAGTCG
63 TGCAGCATAACTTAAGTCG
* * * * *
4065073 AGATGGGCTATCTGCCATCAAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCA-CCAAAGACCTTCGAGTTTGACTACACTCAGCT-CAAGG-ACATCATT
*
4065138 TACAGCATAACTTAAGTCG
63 TGCAGCATAACTTAAGTCG
* * **
4065157 AGAAGGGTTATCTTCCA-CAAAGACCTTCGAGTTCGACTATGCTCAGC-CAAGGCACATCATTTG
1 AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTTGACTACACTCAGCTCAAGG-ACATCATTTG
* *
4065220 CAGGATAGCTTAAGTCG
65 CAGCATAACTTAAGTCG
* * * * * *
4065237 AGAAGGGATATCTG---CCAAAGACCCTCGAGTTTGATTACACTAAGCTTTGAGGGCACATCATT
1 AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTTGACTACACTCAGC--TCAAGG-ACATCATT
* * * * *
4065299 TACAGTATAACTCAAGGCT
63 TGCAGCATAACTTAAGTCG
* * * *
4065318 AGAAAGGTTA--TACCA--AAAGACCTTCGAGTTTGACTACACTCAGCTCCA-G-TATCATTTGC
1 AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTTGACTACACTCAGCTCAAGGACATCATTTGC
*
4065377 AGCATAACTTAAGTCT
66 AGCATAACTTAAGTCG
* *
4065393 AAAAGGGTTATCTGCCAACCAAAGACCTTCGATTTTGA
1 AGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTTGA
4065431 AAAGACCTTC
Statistics
Matches: 291, Mismatches: 53, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
75 29 0.10
77 4 0.01
78 26 0.09
79 1 0.00
80 84 0.29
81 33 0.11
82 27 0.09
83 1 0.00
84 85 0.29
85 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (81 bp):
AGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTTGACTACACTCAGCTCAAGGACATCATTTGC
AGCATAACTTAAGTCG
Found at i:4065436 original size:18 final size:18
Alignment explanation
Indices: 4065413--4065448 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4065403 TCTGCCAACC
*
4065413 AAAGACCTTCGATTTTGA
1 AAAGACCTTCGAGTTTGA
4065431 AAAGACCTTCGAGTTTGA
1 AAAGACCTTCGAGTTTGA
4065449 CTACACTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (18 bp):
AAAGACCTTCGAGTTTGA
Found at i:4065504 original size:101 final size:98
Alignment explanation
Indices: 4065332--4065531 Score: 373
Period size: 101 Copynumber: 2.0 Consensus size: 98
4065322 AGGTTATACC
4065332 AAAAGACCTTCGAGTTTGACTACACTCAGCTCCAGTATCATTTGCAGCATAACTTAAGTCTAAAA
1 AAAAGACCTTCGAGTTTGACTACACTCAGCTCCAGTATCATTTGCAGCATAACTTAAGTCTAAAA
4065397 GGGTTATCTGCCAACCAAAGACCTTCGATTTTG
66 GGGTTATCTGCCAACCAAAGACCTTCGATTTTG
4065430 AAAAGACCTTCGAGTTTGACTACACTCAGCTCCAAGCATATCATTTGCAGCATAACTTAAGTCTA
1 AAAAGACCTTCGAGTTTGACTACACTCAGCTCC-AG--TATCATTTGCAGCATAACTTAAGTCTA
4065495 AAAGGGTTATCTGCCAACCAAAGACCTTCGATTTTG
63 AAAGGGTTATCTGCCAACCAAAGACCTTCGATTTTG
4065531 A
1 A
4065532 CTACGCTCAG
Statistics
Matches: 99, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
98 33 0.33
99 2 0.02
101 64 0.65
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (98 bp):
AAAAGACCTTCGAGTTTGACTACACTCAGCTCCAGTATCATTTGCAGCATAACTTAAGTCTAAAA
GGGTTATCTGCCAACCAAAGACCTTCGATTTTG
Found at i:4065948 original size:84 final size:84
Alignment explanation
Indices: 4065431--4065945 Score: 549
Period size: 84 Copynumber: 6.2 Consensus size: 84
4065421 TCGATTTTGA
* * *
4065431 AAAGACCTTCGAGTTTGACTACACTCAGCTCCAA-GCATATCATTTGCAGCATAACTTAAGTCTA
1 AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
*
4065495 AAAGGGTTATCTGCCAACC
66 GAAGGGTTATCTGCCAACC
* * * * *
4065514 AAAGACCTTCGATTTTGACTACGCTCAGCTCAAAGGCACATCATTTGCAACATAGCTTGAGTCGA
1 AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
**
4065579 GAAGGGTTATCT----TTC
66 GAAGGGTTATCTGCCAACC
* * * * * * * * * *
4065594 AAAGACCCTT-GAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAACATAACTCAAGGC
1 AAAGA-CCTTCGAGTTTGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
4065658 TAGAAGGGTTATCTGTC-ACC
64 GAGAAGGGTTATCTGCCAACC
* ** *
4065678 AAAAGACCTTCGAGTTTGACTATGCTCAGCTCCAAATCACATCATTTGCAGAATAACTTAAGTCG
1 -AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * *
4065743 AGAAGGGCTATCTGCCATCA
65 AGAAGGGTTATCTGCCAACC
* *
4065763 AAAGACCTTCGATTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGA
1 AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
* **
4065828 GAAGGGTTATCTGACAATT
66 GAAGGGTTATCTGCCAACC
* * * * * *
4065847 AAAGATCTTTGAGTTCGACTACGTTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
* **
4065912 GAAAGACTATCTGCCAACC
66 GAAGGGTTATCTGCCAACC
*
4065931 GAAGACCTTCGAGTT
1 AAAGACCTTCGAGTT
4065946 CGATTACACT
Statistics
Matches: 350, Mismatches: 73, Indels: 17
0.80 0.17 0.04
Matches are distributed among these distances:
80 20 0.06
81 44 0.13
83 31 0.09
84 235 0.67
85 20 0.06
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.27
Consensus pattern (84 bp):
AAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
GAAGGGTTATCTGCCAACC
Found at i:4066029 original size:168 final size:162
Alignment explanation
Indices: 4065530--4066032 Score: 412
Period size: 168 Copynumber: 3.0 Consensus size: 162
4065520 CTTCGATTTT
* * * **
4065530 GACTACGCTCAGC-TCAAAGGCACATCATTTGCAACATAGCTTGAGTCGAGAAGGGTTATCTTTC
1 GACTACGCTCAGCTTC-AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
**
4065594 -A-AAGACCCTT-GAGTTCGATTACACTCAACTTC-GAGGGCACATCATTTACAACATAACTCAA
65 AACAAGA-CCTTCGAGTTCGATTACACTCAAC-TCAGAGGAAACA--ATTTACAA-ATAACTCAA
* ** * *
4065655 GGCTAGAAGGGTTATCTGTCACCAAAA-GACCTTCGAGTTT
125 GGCAAGAAGGGTTATCTGTCAATAAAATTA--TT-GAGTTC
* * ** * *
4065695 GACTATGCTCAGCTCCAAATCACATCATTTGCAGAATAACTTAAGTCGAGAAGGGCTATCTGCCA
1 GACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
* * * * * * * * * *
4065760 TCAAAAGACCTTCGATTTTGACTACGCTCAGCTCCA-AGGCATATC-ATTTGCAGCATAACTTAA
66 --ACAAGACCTTCGAGTTCGATTACACTCAACT-CAGAGG-A-AACAATTTACA-AATAACTCAA
* * *
4065823 GTCGAGAAGGGTTATCTGACAATTAAAGATCT-TTGAGTTC
125 GGCAAGAAGGGTTATCTGTCAA-TAAA-AT-TATTGAGTTC
* * *
4065863 GACTACGTTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAAGACTATCTGCCA
1 GACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
*
4065928 ACCGAAGACCTTCGAGTTCGATTACACTCAACTCAGAGGAAAACCAAATTTACATAATAGCTCAA
66 A-C-AAGACCTTCGAGTTCGATTACACTCAACTCAGAGG-AAA-C-AATTTACA-AATAACTCAA
4065993 GGCAAGAAGGGTTATCTGTCAATAAAATTATTGAGTTC
125 GGCAAGAAGGGTTATCTGTCAATAAAATTATTGAGTTC
4066031 GA
1 GA
4066033 TTCCATTCAG
Statistics
Matches: 262, Mismatches: 54, Indels: 41
0.73 0.15 0.11
Matches are distributed among these distances:
165 51 0.19
166 2 0.01
167 4 0.02
168 140 0.53
169 31 0.12
170 33 0.13
171 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (162 bp):
GACTACGCTCAGCTTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA
ACAAGACCTTCGAGTTCGATTACACTCAACTCAGAGGAAACAATTTACAAATAACTCAAGGCAAG
AAGGGTTATCTGTCAATAAAATTATTGAGTTC
Found at i:4066716 original size:38 final size:38
Alignment explanation
Indices: 4066596--4066984 Score: 433
Period size: 38 Copynumber: 10.2 Consensus size: 38
4066586 TATAATATAT
* * * *
4066596 ATATGTATATATTATAAAATTTTAAAAACATTTTGAAA
1 ATATATATATATTATATAGTTTTTAAAACATTTTGAAA
*
4066634 ATATATAT-GA-TATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATATATTATATAGTTTTTAAAACA-TTTTGAAA
4066671 ACT-TATATATATTATATAGTTTTTAAAACATTTTGAAA
1 A-TATATATATATTATATAGTTTTTAAAACATTTTGAAA
* *
4066709 ATATATATATAATATAGAGTTTTTAAAACATTTTGAAA
1 ATATATATATATTATATAGTTTTTAAAACATTTTGAAA
* * *
4066747 ACATTTATATATTATATAGTTTTTAAAACGTTTTTGAAA
1 ATATATATATATTATATAGTTTTTAAAAC-ATTTTGAAA
*
4066786 ATA-A-ATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATATATTATATAGTTTTTAAAACA-TTTTGAAA
*
4066823 ATATATATATATTATATAGTTTATAAAACATTTTG-AA
1 ATATATATATATTATATAGTTTTTAAAACATTTTGAAA
4066860 A-ATATATA-A-TATATAGTTTTTAAAAGCATTTTGTAAAA
1 ATATATATATATTATATAGTTTTTAAAA-CATTTTG--AAA
*
4066898 CATATATATATATTATATAGTTTTTAAAAAAAATCTTTTGAAA
1 -ATATATATATATTATATAGTTTTT--AAAACA--TTTTGAAA
* *
4066941 A-ACATATA-A-TATATAGTTTTAAAAACATTTGTGAAA
1 ATATATATATATTATATAGTTTTTAAAACATTT-TGAAA
4066977 ACTATATA
1 A-TATATA
4066985 ATTTTGAAAA
Statistics
Matches: 302, Mismatches: 25, Indels: 48
0.81 0.07 0.13
Matches are distributed among these distances:
34 15 0.05
35 11 0.04
36 28 0.09
37 57 0.19
38 88 0.29
39 62 0.21
40 8 0.03
41 7 0.02
42 13 0.04
43 4 0.01
44 4 0.01
45 5 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (38 bp):
ATATATATATATTATATAGTTTTTAAAACATTTTGAAA
Found at i:4066865 original size:152 final size:152
Alignment explanation
Indices: 4066596--4066984 Score: 540
Period size: 152 Copynumber: 2.5 Consensus size: 152
4066586 TATAATATAT
* * * * * * *
4066596 ATATGTATATATTATAAAATTTTAAAAACATTTTGAAAATATATATGATATATAGTTTTTAAAAC
1 ATATATATATATTATATAGTTTTTAAAACTTTTTGAAAATAAATATAATATATAGTTTTTAAAAC
*
4066661 ATTTTTGAAAACT-TATATATATTATATAGTTTTTAAAACATTTTGAAAATATATATATAATATA
66 ATTTTTGAAAACTATATATATATTATATAGTTTATAAAACATTTTGAAAATATATA-AT-ATAT-
4066725 GAGTTTTTAAAA-CATTTTG-AAAAC
128 -AGTTTTTAAAAGCATTTTGTAAAAC
4066749 AT-T-TATATATTATATAGTTTTTAAAACGTTTTTGAAAATAAATATAATATATAGTTTTTAAAA
1 ATATATATATATTATATAGTTTTTAAAAC-TTTTTGAAAATAAATATAATATATAGTTTTTAAAA
4066812 CATTTTTGAAAA-TATATATATATTATATAGTTTATAAAACATTTTGAAAATATATAATATATAG
65 CATTTTTGAAAACTATATATATATTATATAGTTTATAAAACATTTTGAAAATATATAATATATAG
4066876 TTTTTAAAAGCATTTTGTAAAAC
130 TTTTTAAAAGCATTTTGTAAAAC
* * *
4066899 ATATATATATATTATATAGTTTTTAAAAAAAATCTTTTGAAAA-ACATATAATATATAGTTTTAA
1 ATATATATATATTATATAGTTTTT---AAAACT-TTTTGAAAATAAATATAATATATAGTTTTTA
*
4066963 AAACATTTGTGAAAACTATATA
62 AAACATTTTTGAAAACTATATA
4066985 ATTTTGAAAA
Statistics
Matches: 214, Mismatches: 11, Indels: 20
0.87 0.04 0.08
Matches are distributed among these distances:
148 11 0.05
149 7 0.03
150 11 0.05
151 25 0.12
152 105 0.49
153 2 0.01
154 34 0.16
155 19 0.09
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (152 bp):
ATATATATATATTATATAGTTTTTAAAACTTTTTGAAAATAAATATAATATATAGTTTTTAAAAC
ATTTTTGAAAACTATATATATATTATATAGTTTATAAAACATTTTGAAAATATATAATATATAGT
TTTTAAAAGCATTTTGTAAAAC
Found at i:4066994 original size:29 final size:30
Alignment explanation
Indices: 4066948--4067018 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
4066938 AAAAACATAT
* *
4066948 AATATATAGTTTTAAAAACATTTGT-GAAA
1 AATATATAATTTTAAAAACATTTGTAAAAA
* * *
4066977 ACTATATAATTTTGAAAACATTTTTAAAAA
1 AATATATAATTTTAAAAACATTTGTAAAAA
4067007 AATATATAATTT
1 AATATATAATTT
4067019 ATAATTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (30 bp):
AATATATAATTTTAAAAACATTTGTAAAAA
Found at i:4067047 original size:34 final size:36
Alignment explanation
Indices: 4066979--4067061 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 36
4066969 TTGTGAAAAC
4066979 TATATAATTTTGAAAACATTTTTAAAAAAATATATAAT
1 TATATAATTTTGAAAACATTTTT-AAAAAATATAT-AT
*
4067017 T-TATAATTTT-AAAATATTTTT-AAAAATATATAT
1 TATATAATTTTGAAAACATTTTTAAAAAATATATAT
4067050 TATATAGATTTT
1 TATATA-ATTTT
4067062 TGGAAAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
33 3 0.07
34 14 0.33
35 5 0.12
36 10 0.24
37 9 0.21
38 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (36 bp):
TATATAATTTTGAAAACATTTTTAAAAAATATATAT
Found at i:4067094 original size:22 final size:22
Alignment explanation
Indices: 4067069--4067110 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4067059 TTTTGGAAAA
*
4067069 TATTATTT-TTTTAGTTTATTTT
1 TATT-TTTATTTTAATTTATTTT
4067091 TATTTTTATTTTAATTTATT
1 TATTTTTATTTTAATTTATT
4067111 GACATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (22 bp):
TATTTTTATTTTAATTTATTTT
Found at i:4068242 original size:5 final size:5
Alignment explanation
Indices: 4068232--4068315 Score: 50
Period size: 5 Copynumber: 16.6 Consensus size: 5
4068222 TGTATATACC
** * *
4068232 TTTAT TTTAT TTTCG TTTA- TTTAT TTATTT TTTCT TTTA- TTTA- TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT TTTAT TTTAT TTTAT TTTAT
*
4068280 GTTTA- TTTAT TTCATAT TTTGT CTTTAT TTTAT TTT
1 -TTTAT TTTAT TT--TAT TTTAT -TTTAT TTTAT TTT
4068316 CTTTATCGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
4 16 0.25
5 30 0.48
6 12 0.19
7 5 0.08
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.75
Consensus pattern (5 bp):
TTTAT
Found at i:4068270 original size:20 final size:20
Alignment explanation
Indices: 4068232--4068279 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
4068222 TGTATATACC
4068232 TTTATTT-TATTTTCGTTTA
1 TTTATTTATATTTTCGTTTA
* *
4068251 TTTATTTATTTTTTCTTTTA
1 TTTATTTATATTTTCGTTTA
4068271 TTTATTTAT
1 TTTATTTAT
4068280 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 7 0.27
20 19 0.73
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTATTTATATTTTCGTTTA
Found at i:4068320 original size:14 final size:14
Alignment explanation
Indices: 4068231--4068321 Score: 57
Period size: 14 Copynumber: 6.4 Consensus size: 14
4068221 GTGTATATAC
4068231 CTTTATTTTATTTT
1 CTTTATTTTATTTT
4068245 CGTTTA-TTTA-TTT
1 C-TTTATTTTATTTT
* *
4068258 -ATT-TTTTCTTTT
1 CTTTATTTTATTTT
*
4068270 ATTTA-TTTATGTTT
1 CTTTATTTTAT-TTT
*
4068284 ATTTATTTCATATTTTGT
1 CTTTATTT--TA-TTT-T
4068302 CTTTATTTTATTTT
1 CTTTATTTTATTTT
4068316 CTTTAT
1 CTTTAT
4068322 CGAATTTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
11 5 0.08
12 3 0.05
13 9 0.15
14 20 0.33
15 9 0.15
16 2 0.03
17 4 0.07
18 9 0.15
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (14 bp):
CTTTATTTTATTTT
Found at i:4070973 original size:2 final size:2
Alignment explanation
Indices: 4070966--4071001 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4070956 ATTGAAAATA
4070966 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4071002 ATAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4071008 original size:6 final size:6
Alignment explanation
Indices: 4070962--4071026 Score: 60
Period size: 6 Copynumber: 9.8 Consensus size: 6
4070952 AATTATTGAA
4070962 AATAAT ATATATAT ATATATAT ATATATAT ATATAAT -ATAAT AATAAT
1 AATAAT A-ATA-AT A-ATA-AT A-ATA-AT A-ATAAT AATAAT AATAAT
4071010 AATAAT AATAAT AATAA
1 AATAAT AATAAT AATAA
4071027 GATATGATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.09
6 23 0.41
7 5 0.09
8 23 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (6 bp):
AATAAT
Found at i:4071022 original size:18 final size:19
Alignment explanation
Indices: 4070962--4071031 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 19
4070952 AATTATTGAA
4070962 AATAATATATATATATATATAT
1 AATAATATATA-ATA-ATA-AT
4070984 ATATATATATATAAT-ATAAT
1 A-ATA-ATATATAATAATAAT
4071004 AATAATA-ATAATAATAAT
1 AATAATATATAATAATAAT
*
4071022 AATAAGATAT
1 AATAATATAT
4071032 GATATATTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
17 5 0.12
18 14 0.33
19 5 0.12
20 3 0.07
21 3 0.07
22 1 0.02
23 5 0.12
24 7 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (19 bp):
AATAATATATAATAATAAT
Found at i:4080406 original size:32 final size:32
Alignment explanation
Indices: 4080361--4080444 Score: 114
Period size: 32 Copynumber: 2.6 Consensus size: 32
4080351 GTAACTATTG
4080361 TGCATTATCTGAATACGACACTGACACTACGA
1 TGCATTATCTGAATACGACACTGACACTACGA
* * * * *
4080393 TGCATTATTTGAATGCGACATTGACATTACTA
1 TGCATTATCTGAATACGACACTGACACTACGA
*
4080425 TGCATTATCTGAACACGACA
1 TGCATTATCTGAATACGACA
4080445 GACATCTAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (32 bp):
TGCATTATCTGAATACGACACTGACACTACGA
Found at i:4082664 original size:6 final size:6
Alignment explanation
Indices: 4082653--4082678 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4082643 TCAAGAAGAT
4082653 GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GA
4082679 GCTTGGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GATGAA
Found at i:4088901 original size:19 final size:19
Alignment explanation
Indices: 4088855--4088901 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
4088845 CCCCTACTAG
4088855 GAGTATCGATACTCTTGCCCT
1 GAGTATCGATACTCTTG--CT
4088876 G-GTATCGATACTCTATG-T
1 GAGTATCGATACTCT-TGCT
4088894 GAGTATCG
1 GAGTATCG
4088902 GTACCGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.08
19 6 0.25
20 13 0.54
21 3 0.12
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (19 bp):
GAGTATCGATACTCTTGCT
Found at i:4090750 original size:12 final size:12
Alignment explanation
Indices: 4090733--4090775 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
4090723 TATTGGATAA
*
4090733 TATTGATAATAG
1 TATTGATAATGG
***
4090745 TATTGATGCGGG
1 TATTGATAATGG
4090757 TATTGATAATGG
1 TATTGATAATGG
4090769 TATTGAT
1 TATTGAT
4090776 GCTGATATCA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (12 bp):
TATTGATAATGG
Found at i:4090762 original size:24 final size:23
Alignment explanation
Indices: 4090733--4090806 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 23
4090723 TATTGGATAA
4090733 TATTGATAATAGTATTGATGCGGG
1 TATTGATAAT-GTATTGATGCGGG
* *
4090757 TATTGATAATGGTATTGATGCTGA
1 TATTGATAAT-GTATTGATGCGGG
** *
4090781 TATCAATACTGTATTGATGCGGG
1 TATTGATAATGTATTGATGCGGG
4090804 TAT
1 TAT
4090807 CGACACCAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 14 0.33
24 28 0.67
ACGTcount: A:0.28, C:0.07, G:0.26, T:0.39
Consensus pattern (23 bp):
TATTGATAATGTATTGATGCGGG
Found at i:4091433 original size:29 final size:29
Alignment explanation
Indices: 4091391--4091460 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
4091381 CTTGGAGAAG
*
4091391 AAGGAGGAGAAGGAAATGTGAAAGGATGA
1 AAGGAGGAGAAGGAAATATGAAAGGATGA
*
4091420 AAGGAGGAGAAGGAAATATGAAAGGATTA
1 AAGGAGGAGAAGGAAATATGAAAGGATGA
* *
4091449 AATGAAGAGAAG
1 AAGGAGGAGAAG
4091461 AAGATGAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.37, T:0.11
Consensus pattern (29 bp):
AAGGAGGAGAAGGAAATATGAAAGGATGA
Found at i:4092120 original size:40 final size:39
Alignment explanation
Indices: 4092016--4092124 Score: 141
Period size: 39 Copynumber: 2.8 Consensus size: 39
4092006 TTTTGAATGT
*
4092016 GATACTAAAATAAAATAAAAACTAAAGTTTTTAACGGTA
1 GATACTAAAATAAAATAAAAACTAAAGCTTTTAACGGTA
* * * *
4092055 GGTACTAAAATGAAACAAAAGCTAAAGCTTTTAACGACG-A
1 GATACTAAAATAAAATAAAAACTAAAGCTTTTAACG--GTA
4092095 GATACTAAAATAAAATAAAAACTAAA-CTTT
1 GATACTAAAATAAAATAAAAACTAAAGCTTT
4092125 AGGTATGATT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
39 35 0.59
40 23 0.39
41 1 0.02
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.25
Consensus pattern (39 bp):
GATACTAAAATAAAATAAAAACTAAAGCTTTTAACGGTA
Found at i:4092167 original size:21 final size:21
Alignment explanation
Indices: 4092143--4092187 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4092133 TTTTTTTTAA
* *
4092143 AAAATTAAAAATTTAGGTACT
1 AAAACTAAAAACTTAGGTACT
* *
4092164 AAAACTAATAGCTTAGGTACT
1 AAAACTAAAAACTTAGGTACT
4092185 AAA
1 AAA
4092188 TGTATAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (21 bp):
AAAACTAAAAACTTAGGTACT
Found at i:4092334 original size:7 final size:7
Alignment explanation
Indices: 4092322--4092346 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4092312 AATAAATTAT
4092322 TTATATA
1 TTATATA
4092329 TTATATA
1 TTATATA
4092336 TTATATA
1 TTATATA
4092343 TTAT
1 TTAT
4092347 CAATACTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTATATA
Found at i:4093192 original size:30 final size:28
Alignment explanation
Indices: 4093156--4093227 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
4093146 TAGTTAGTGT
*
4093156 AAATAATTAACACTATTAACTAATCTATTA
1 AAATAATTAACAC-A-TAACTAATATATTA
*
4093186 AAATAA-TAATACATAACTAATATATTA
1 AAATAATTAACACATAACTAATATATTA
*
4093213 AAATAA-TAATACATA
1 AAATAATTAACACATA
4093228 CTTTTTTCTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 28 0.70
28 1 0.03
29 5 0.12
30 6 0.15
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (28 bp):
AAATAATTAACACATAACTAATATATTA
Found at i:4093242 original size:27 final size:27
Alignment explanation
Indices: 4093172--4093227 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
4093162 TTAACACTAT
*
4093172 TAACTAATCTATTAAAATAATAATACA
1 TAACTAATATATTAAAATAATAATACA
4093199 TAACTAATATATTAAAATAATAATACA
1 TAACTAATATATTAAAATAATAATACA
4093226 TA
1 TA
4093228 CTTTTTTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (27 bp):
TAACTAATATATTAAAATAATAATACA
Found at i:4093266 original size:3 final size:3
Alignment explanation
Indices: 4093258--4093290 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
4093248 CTTCCCATAT
*
4093258 TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4093291 ATCATCTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:4106475 original size:20 final size:20
Alignment explanation
Indices: 4106450--4106501 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
4106440 ATACTCGTAG
4106450 GAGTATCGATACCAATGGGT
1 GAGTATCGATACCAATGGGT
4106470 GAGTATCGATACCAATGGGT
1 GAGTATCGATACCAATGGGT
*
4106490 GAGTATCAATAC
1 GAGTATCGATAC
4106502 TCTCCATCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (20 bp):
GAGTATCGATACCAATGGGT
Found at i:4109674 original size:24 final size:24
Alignment explanation
Indices: 4109647--4109711 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
4109637 CGTTCGATAA
*
4109647 TATGTTCATTCATTTATGTTCATT
1 TATGTTCATTAATTTATGTTCATT
* * *
4109671 TATGTTCATTTACTTT-GGTTCGTT
1 TATGTTCA-TTAATTTATGTTCATT
4109695 TATGTTCATTAATTTAT
1 TATGTTCATTAATTTAT
4109712 ATTTAGCGCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
23 6 0.18
24 22 0.67
25 5 0.15
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (24 bp):
TATGTTCATTAATTTATGTTCATT
Found at i:4109701 original size:10 final size:10
Alignment explanation
Indices: 4109655--4109682 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
4109645 AATATGTTCA
4109655 TTCATTTATG
1 TTCATTTATG
4109665 TTCATTTATG
1 TTCATTTATG
4109675 TTCATTTA
1 TTCATTTA
4109683 CTTTGGTTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.07, T:0.61
Consensus pattern (10 bp):
TTCATTTATG
Found at i:4109981 original size:23 final size:23
Alignment explanation
Indices: 4109918--4109989 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
4109908 TTTTTTTTCA
* * *
4109918 TTTATTATGTTTGTTTACGTTCA
1 TTTATTGTGTTTGTTTACATTCG
**
4109941 TTCGT-TTGTGTTCATTTACATTCG
1 TT--TATTGTGTTTGTTTACATTCG
4109965 TTTATTGTGTTTGTTTACATTCG
1 TTTATTGTGTTTGTTTACATTCG
4109988 TT
1 TT
4109990 CGTTAATGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
22 1 0.03
23 21 0.54
24 16 0.41
25 1 0.03
ACGTcount: A:0.14, C:0.11, G:0.15, T:0.60
Consensus pattern (23 bp):
TTTATTGTGTTTGTTTACATTCG
Found at i:4111275 original size:34 final size:34
Alignment explanation
Indices: 4111237--4111355 Score: 150
Period size: 34 Copynumber: 3.4 Consensus size: 34
4111227 AAAATGACTG
*
4111237 AAGTGATATAAAATGTTTCAAGAGAAAATATCTC
1 AAGTGAGATAAAATGTTTCAAGAGAAAATATCTC
*
4111271 AAGTGAGATAAAAATTTGTTTCAAGGGAAAATATCTC
1 AAGTGAGAT-AAAA--TGTTTCAAGAGAAAATATCTC
* * *
4111308 GAGTGAGA-ATAAATTTTTCAAGAGAAAATATCTA
1 AAGTGAGATA-AAATGTTTCAAGAGAAAATATCTC
4111342 AAGTGAGATAAAAT
1 AAGTGAGATAAAAT
4111356 TTATTTCAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
34 37 0.51
35 6 0.08
36 3 0.04
37 27 0.37
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.29
Consensus pattern (34 bp):
AAGTGAGATAAAATGTTTCAAGAGAAAATATCTC
Found at i:4111301 original size:37 final size:37
Alignment explanation
Indices: 4111250--4111370 Score: 160
Period size: 34 Copynumber: 3.4 Consensus size: 37
4111240 TGATATAAAA
4111250 TGTTTCAAGAGAAAATATCTCAAGTGAGATAAAAATT
1 TGTTTCAAGAGAAAATATCTCAAGTGAGATAAAAATT
* * *
4111287 TGTTTCAAGGGAAAATATCTCGAGTGAGA-ATAAA-T
1 TGTTTCAAGAGAAAATATCTCAAGTGAGATAAAAATT
*
4111322 T-TTTCAAGAGAAAATATCTAAAGTGAGAT-AAAATT
1 TGTTTCAAGAGAAAATATCTCAAGTGAGATAAAAATT
* *
4111357 TATTTCAAAAGAAA
1 TGTTTCAAGAGAAA
4111371 TTGTCTTGAG
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
34 27 0.37
35 4 0.05
36 15 0.21
37 27 0.37
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGAGAAAATATCTCAAGTGAGATAAAAATT
Found at i:4111356 original size:34 final size:34
Alignment explanation
Indices: 4111237--4111431 Score: 160
Period size: 36 Copynumber: 5.5 Consensus size: 34
4111227 AAAATGACTG
* *
4111237 AAGTGATATAAAATGTTTCAAGAGAAAATATCTC
1 AAGTGAGATAAAATTTTTCAAGAGAAAATATCTC
*
4111271 AAGTGAGATAAAAATTTGTTTCAAGGGAAAATATCTC
1 AAGTGAGAT-AAAA-TT-TTTCAAGAGAAAATATCTC
* *
4111308 GAGTGAGA-ATAAATTTTTCAAGAGAAAATATCTA
1 AAGTGAGATA-AAATTTTTCAAGAGAAAATATCTC
* * * *
4111342 AAGTGAGATAAAATTTATTTCAAAAGAAATTGTCTT
1 AAGTGAGATAAAA-TT-TTTCAAGAGAAAATATCTC
* * * *
4111378 GAGTGAAATGAAACTTGTTTTAAG-GAAAACTATCTC
1 AAGTGAGAT-AAAATT-TTTCAAGAGAAAA-TATCTC
* *
4111414 AAATGATATAAAATTTTT
1 AAGTGAGATAAAATTTTT
4111432 GTTTTGAGAG
Statistics
Matches: 128, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
34 38 0.30
35 19 0.15
36 43 0.34
37 28 0.22
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (34 bp):
AAGTGAGATAAAATTTTTCAAGAGAAAATATCTC
Found at i:4111406 original size:71 final size:71
Alignment explanation
Indices: 4111244--4111429 Score: 209
Period size: 71 Copynumber: 2.6 Consensus size: 71
4111234 CTGAAGTGAT
* * * **
4111244 ATAAAATGTTTCAAGAGAAAATATCTCAAGTGAGATAAAAATTTGTTTCAAGGGAAAATATCTCG
1 ATAAATTGTTTCAAGAGAAAATATCTAAAGTGAGAT-AAAATTTATTTCAAAAGAAAATATCTCG
4111309 AGTGAGA
65 AGTGAGA
* * *
4111316 ATAAATT-TTTCAAGAGAAAATATCTAAAGTGAGATAAAATTTATTTCAAAAGAAATTGTCTTGA
1 ATAAATTGTTTCAAGAGAAAATATCTAAAGTGAGATAAAATTTATTTCAAAAGAAAATATCTCGA
4111380 GTGA-A
66 GTGAGA
* *
4111385 ATGAAACTTGTTTTAAG-GAAAACTATCTCAAA-TGATATAAAATTT
1 AT-AAA-TTGTTTCAAGAGAAAA-TATCT-AAAGTGAGATAAAATTT
4111430 TTGTTTTGAG
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
69 3 0.03
70 30 0.30
71 34 0.34
72 29 0.29
73 3 0.03
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (71 bp):
ATAAATTGTTTCAAGAGAAAATATCTAAAGTGAGATAAAATTTATTTCAAAAGAAAATATCTCGA
GTGAGA
Found at i:4125301 original size:29 final size:29
Alignment explanation
Indices: 4125250--4125425 Score: 161
Period size: 29 Copynumber: 6.3 Consensus size: 29
4125240 TTTACACATT
* * *
4125250 TATCACCCTTTTTAAAAACAATTACAAAAA
1 TATCACCC-TTTTCAAAATAATTACGAAAA
*
4125280 TATCACCCTTTTCAAAATAATTACTAAAA
1 TATCACCCTTTTCAAAATAATTACGAAAA
* ** *
4125309 TATCA--TTTTTTTAAAT--TTACGAAAT
1 TATCACCCTTTTCAAAATAATTACGAAAA
*
4125334 TATCA--CTTTTTAAAA-AATTACGAAAA
1 TATCACCCTTTTCAAAATAATTACGAAAA
* *
4125360 TAGCACCATTTTCAAAATAATTATC-AAAA
1 TATCACCCTTTTCAAAATAATTA-CGAAAA
* *
4125389 TATCACCATTTTCAAAATAATTACTAAAA
1 TATCACCCTTTTCAAAATAATTACGAAAA
4125418 TATCACCC
1 TATCACCC
4125426 AGTCAACGGG
Statistics
Matches: 123, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
25 20 0.16
26 12 0.10
27 8 0.07
28 9 0.07
29 65 0.53
30 9 0.07
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (29 bp):
TATCACCCTTTTCAAAATAATTACGAAAA
Found at i:4126800 original size:14 final size:14
Alignment explanation
Indices: 4126781--4126809 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4126771 GGTGGTAGTG
4126781 TGATAACAAATGGA
1 TGATAACAAATGGA
4126795 TGATAACAAATGGA
1 TGATAACAAATGGA
4126809 T
1 T
4126810 ATGTCGTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.24
Consensus pattern (14 bp):
TGATAACAAATGGA
Found at i:4126939 original size:18 final size:18
Alignment explanation
Indices: 4126916--4126950 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4126906 ATCGGCCAAG
4126916 AAGGCAAAATAAAATGTC
1 AAGGCAAAATAAAATGTC
4126934 AAGGCAAAATAAAATGT
1 AAGGCAAAATAAAATGT
4126951 AAACAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (18 bp):
AAGGCAAAATAAAATGTC
Found at i:4127943 original size:2 final size:2
Alignment explanation
Indices: 4127936--4127999 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
4127926 AGCCAATTGA
4127936 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4127978 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
4128000 CTTAAGCTGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4130171 original size:23 final size:23
Alignment explanation
Indices: 4130094--4130177 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
4130084 ATAACCTCCA
* * *
4130094 GGGGGTATCGATTCCCCTAC-AG
1 GGGGGAATCGGTTCCCCTTCAAG
* *
4130116 GGGGGAATCAGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAG
*
4130139 GGGGGAATCGGTTTCCCTTCAAG
1 GGGGGAATCGGTTCCCCTTCAAG
* *
4130162 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
4130178 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
22 16 0.32
23 34 0.68
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.24
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAG
Found at i:4146294 original size:29 final size:29
Alignment explanation
Indices: 4146262--4146435 Score: 146
Period size: 29 Copynumber: 6.1 Consensus size: 29
4146252 CACATCTATT
* *
4146262 ACCCTTTTTAAAA-AATTTACAAAAATATC
1 ACCCTTTTCAAAATAA-TTACGAAAATATC
*
4146291 ACCCTTTTCAAAATAATTACTAAAATATC
1 ACCCTTTTCAAAATAATTACGAAAATATC
*** * * *
4146320 ATTTTTTTTTAAAA-ATTTACGAAATTATC
1 A-CCCTTTTCAAAATAATTACGAAAATATC
* *
4146349 A--CTTTT-AAAA-AATTATGAAAATAGC
1 ACCCTTTTCAAAATAATTACGAAAATATC
*
4146374 ACCATTTTCAAAATAATTATC-AAAATATC
1 ACCCTTTTCAAAATAATTA-CGAAAATATC
* *
4146403 ACCATTTTCAAAATAATTACTAAAATATC
1 ACCCTTTTCAAAATAATTACGAAAATATC
4146432 ACCC
1 ACCC
4146436 GGTCAACGGT
Statistics
Matches: 119, Mismatches: 18, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
25 16 0.13
26 4 0.03
27 4 0.03
28 5 0.04
29 80 0.67
30 10 0.08
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.36
Consensus pattern (29 bp):
ACCCTTTTCAAAATAATTACGAAAATATC
Found at i:4146432 original size:83 final size:84
Alignment explanation
Indices: 4146267--4146433 Score: 196
Period size: 83 Copynumber: 2.0 Consensus size: 84
4146257 CTATTACCCT
* * *** *
4146267 TTTTAAAAAATTTACAAAAATATCACCCTTTTCAAAATAATTACTAAAATATCATTTTTTTTTAA
1 TTTTAAAAAATTTACAAAAATAGCACCATTTTCAAAATAATTACTAAAATATCATCCATTTTCAA
* *
4146332 AAATTTACGAAATTATCAC
66 AAAATTACGAAAATATCAC
**
4146351 TTTTAAAAAA-TTATGAAAATAGCACCATTTTCAAAATAATTA-TCAAAATATCA-CCATTTTCA
1 TTTTAAAAAATTTACAAAAATAGCACCATTTTCAAAATAATTACT-AAAATATCATCCATTTTCA
*
4146413 AAATAATTACTAAAATATCAC
65 AAA-AATTACGAAAATATCAC
4146434 CCGGTCAACG
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
82 9 0.13
83 51 0.73
84 10 0.14
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (84 bp):
TTTTAAAAAATTTACAAAAATAGCACCATTTTCAAAATAATTACTAAAATATCATCCATTTTCAA
AAAATTACGAAAATATCAC
Found at i:4147323 original size:2 final size:2
Alignment explanation
Indices: 4147316--4147344 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4147306 TCAAAATTAA
4147316 AT 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 AT A
4147345 ATAAATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4153333 original size:21 final size:21
Alignment explanation
Indices: 4153309--4153366 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
4153299 TATGTAAACC
*
4153309 TTTGGAACATATATATGGTTA
1 TTTGGAACATATATATGGTCA
* * * *
4153330 TTTGGGACACATATTTGGTCC
1 TTTGGAACATATATATGGTCA
* *
4153351 TTTGAAATATATATAT
1 TTTGGAACATATATAT
4153367 ATATGTGGTC
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (21 bp):
TTTGGAACATATATATGGTCA
Found at i:4153424 original size:21 final size:21
Alignment explanation
Indices: 4153365--4153417 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
4153355 AAATATATAT
*
4153365 ATATATGTGGTCCTTCGGTAC
1 ATATATGTGGTCCTTCGGGAC
*
4153386 ATCTATGTGGTCCTTCGGGAC
1 ATATATGTGGTCCTTCGGGAC
4153407 ATATATGTGGT
1 ATATATGTGGT
4153418 TTTTCGGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (21 bp):
ATATATGTGGTCCTTCGGGAC
Found at i:4159386 original size:14 final size:14
Alignment explanation
Indices: 4159367--4159399 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
4159357 CAAGATTTAG
4159367 GATGAAATATTGAA
1 GATGAAATATTGAA
4159381 GATGAAATATTGAA
1 GATGAAATATTGAA
4159395 GATGA
1 GATGA
4159400 GTTATATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.27
Consensus pattern (14 bp):
GATGAAATATTGAA
Found at i:4159441 original size:19 final size:19
Alignment explanation
Indices: 4159417--4159464 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
4159407 GAATATATGA
4159417 TAGGTTAAGTAAGTTGAGT
1 TAGGTTAAGTAAGTTGAGT
4159436 TAGGTTAAGTAAGTTGAGT
1 TAGGTTAAGTAAGTTGAGT
*
4159455 TAAGTTAAGT
1 TAGGTTAAGT
4159465 TTAGTAGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.29, T:0.38
Consensus pattern (19 bp):
TAGGTTAAGTAAGTTGAGT
Found at i:4159455 original size:5 final size:5
Alignment explanation
Indices: 4159420--4159465 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
4159410 TATATGATAG
* * *
4159420 GTTAA G-TAA GTTGA GTTAG GTTAA G-TAA GTTGA GTTAA GTTAA GTT
1 GTTAA GTTAA GTTAA GTTAA GTTAA GTTAA GTTAA GTTAA GTTAA GTT
4159466 TAGTAGTATG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 8 0.24
5 25 0.76
ACGTcount: A:0.33, C:0.00, G:0.28, T:0.39
Consensus pattern (5 bp):
GTTAA
Found at i:4160491 original size:21 final size:21
Alignment explanation
Indices: 4160467--4160526 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
4160457 CATTTTGAAT
*
4160467 ACATATTTTGTCCTTTGGGAC
1 ACATATTTAGTCCTTTGGGAC
* *
4160488 ACATATTTGGTCATTTGGGAC
1 ACATATTTAGTCCTTTGGGAC
4160509 ACATATTTAGTCCTTTGG
1 ACATATTTAGTCCTTTGG
4160527 AATATATATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.42
Consensus pattern (21 bp):
ACATATTTAGTCCTTTGGGAC
Found at i:4160535 original size:21 final size:21
Alignment explanation
Indices: 4160456--4160535 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
4160446 ATATATATAA
* *
4160456 TCATTTTGAATACATATTTTG
1 TCATTTGGAATACATATTTAG
* * * *
4160477 TCCTTTGGGACACATATTTGG
1 TCATTTGGAATACATATTTAG
* *
4160498 TCATTTGGGACACATATTTAG
1 TCATTTGGAATACATATTTAG
* *
4160519 TCCTTTGGAATATATAT
1 TCATTTGGAATACATAT
4160536 ATGTGATCCT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (21 bp):
TCATTTGGAATACATATTTAG
Found at i:4160585 original size:21 final size:21
Alignment explanation
Indices: 4160559--4160605 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
4160549 GGAGTAGTAA
*
4160559 TTCGGGACATCTATGTGGTCC
1 TTCGGGACATATATGTGGTCC
4160580 TTCGGGACATATATGTGGTCC
1 TTCGGGACATATATGTGGTCC
4160601 TTCGG
1 TTCGG
4160606 AACAAATTCT
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:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (21 bp):
TTCGGGACATATATGTGGTCC
Found at i:4161991 original size:60 final size:60
Alignment explanation
Indices: 4161913--4162176 Score: 225
Period size: 60 Copynumber: 4.4 Consensus size: 60
4161903 AGCAATTAAT
* * *
4161913 ACATATTTACACCGGTGTAAATATGTACATCTCTC-AATATCTTGGTACCTAAAAATAAAC
1 ACATACTTACA-CTGTGTAAATATGTACACCTCTCAAATATCTTGGTACCTAAAAATAAAC
* * *
4161973 ACATACTTACATCTGTGTAAGTATGCATACCTCTC-AATA---TGGTACCTAAAAATAAAC
1 ACATACTTACA-CTGTGTAAATATGTACACCTCTCAAATATCTTGGTACCTAAAAATAAAC
* * * * *
4162030 ACATACTTACACATGTGTAAATGTGTACACCTGTCAAAAATCTTGGTACCAAAAAATAAGC
1 ACATACTTACAC-TGTGTAAATATGTACACCTCTCAAATATCTTGGTACCTAAAAATAAAC
* * * * * * * **
4162091 GCATATTTACACTAGTATAAGTATGTATATCTC-CTAATATCTTAATACCTAAAAATAAAC
1 ACATACTTACACT-GTGTAAATATGTACACCTCTCAAATATCTTGGTACCTAAAAATAAAC
* * * *
4162151 GCATAATTATATTAGTGTAAATATGT
1 ACATACTTACACT-GTGTAAATATGT
4162177 TTCTGTATTT
Statistics
Matches: 164, Mismatches: 34, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
56 1 0.01
57 46 0.28
58 3 0.02
60 75 0.46
61 39 0.24
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (60 bp):
ACATACTTACACTGTGTAAATATGTACACCTCTCAAATATCTTGGTACCTAAAAATAAAC
Found at i:4169606 original size:10 final size:9
Alignment explanation
Indices: 4169554--4169618 Score: 57
Period size: 8 Copynumber: 7.6 Consensus size: 9
4169544 GACTATATAT
4169554 AATAATAAA
1 AATAATAAA
4169563 AATAAT-AA
1 AATAATAAA
4169571 AAT-ATAAA
1 AATAATAAA
* *
4169579 CA-AGTAAA
1 AATAATAAA
* *
4169587 ATTAA-AAC
1 AATAATAAA
4169595 AATAATAAA
1 AATAATAAA
4169604 CAATAATAAA
1 -AATAATAAA
4169614 AATAA
1 AATAA
4169619 AATTAGAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
7 2 0.05
8 18 0.42
9 14 0.33
10 9 0.21
ACGTcount: A:0.72, C:0.05, G:0.02, T:0.22
Consensus pattern (9 bp):
AATAATAAA
Found at i:4171095 original size:3 final size:3
Alignment explanation
Indices: 4171087--4171130 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
4171077 TTGTAATATT
*
4171087 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TGA TAAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
4171131 AAACAAACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4171099 original size:16 final size:15
Alignment explanation
Indices: 4171080--4171130 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
4171070 TTATAATTTG
4171080 TAATATTTAATAATAA
1 TAATA-TTAATAATAA
*
4171096 TAATAAATAATAATAA
1 TAAT-ATTAATAATAA
*
4171112 TAATGATAAATAATAA
1 TAAT-ATTAATAATAA
4171128 TAA
1 TAA
4171131 AAACAAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 29 0.97
17 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
TAATATTAATAATAA
Found at i:4171111 original size:19 final size:19
Alignment explanation
Indices: 4171087--4171130 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
4171077 TTGTAATATT
4171087 TAATAATAATAATAAATAA
1 TAATAATAATAATAAATAA
*
4171106 TAATAATAATGATAAATAA
1 TAATAATAATAATAAATAA
4171125 TAATAA
1 TAATAA
4171131 AAACAAACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
TAATAATAATAATAAATAA
Found at i:4171835 original size:151 final size:151
Alignment explanation
Indices: 4171261--4172721 Score: 2513
Period size: 151 Copynumber: 9.7 Consensus size: 151
4171251 GAAATGTTGA
* * *
4171261 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGG-CTTGAAAACATCAAAAAGCTCCCGA
* * * *
4171326 AAGCTTTTTGGAAACATCATGCACTGTAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
65 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
* *
4171391 AAAGCTTCCAAAGGCTTTTTTGG
130 AAAGCTCCCGAAGGC-TTTTTGG
4171414 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAA
*
4171479 GGCTTTTTGGAAACATTATGCACTGCAGGACTTACAGATGACCCTAAGGC-TTGAAAACATCAAA
66 GGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAA
4171543 AAGCTCCCGAAGGCTTTTTGG
131 AAGCTCCCGAAGGCTTTTTGG
4171564 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAA
4171629 GGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAA
66 GGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAA
4171694 AAGCTCCCGAAGGCTTTTTGG
131 AAGCTCCCGAAGGCTTTTTGG
* *
4171715 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGA
* *
4171780 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATTAA
65 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
4171844 AAAGCTCCCGAAGGCTTTTTGG
130 AAAGCTCCCGAAGGCTTTTTGG
* *
4171866 AAACATCATGCACTGCATGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCTCTC
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTC-C-C
4171930 GAAGGCTTTTT-GAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC
63 GAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC
* *
4171994 AAAAA-CTACCGAATGCTTTTTGG
128 AAAAAGCTCCCGAAGGCTTTTTGG
* *
4172017 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTG-AAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGA
4172080 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
65 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
*
4172145 AAAACTCCCGAAGGCTTTTTGG
130 AAAGCTCCCGAAGGCTTTTTGG
4172167 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAA
*
4172232 GGCTTTTTGGAAACAACATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAA
66 GGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAA
4172297 AAGCTCCCGAAGGCTTTTTGG
131 AAGCTCCCGAAGGCTTTTTGG
* * *
4172318 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAAGCTTGAAAACATCAAAAAGCTCCCGAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAA
* * * *
4172383 GGCTTTTTGGAAATATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAA
66 GGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAA
4172448 AAGCTCCCGAAGGCTTTTTGG
131 AAGCTCCCGAAGGCTTTTTGG
*
4172469 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGA
4172534 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
65 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
4172599 AAAGCTCCCGAAGGCTTTTTGG
130 AAAGCTCCCGAAGGCTTTTTGG
* *
4172621 AAACATCATGCACTGCAGGACTTACAGATGACTCGAAGGCTTGAAAACATCAAAAAGCTCCCAAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAA
4172686 GGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
66 GGCTTTTTGGAAACATCATGCACTGCAGGACTTACA
4172722 AATGTAGGAA
Statistics
Matches: 1250, Mismatches: 48, Indels: 22
0.95 0.04 0.02
Matches are distributed among these distances:
148 12 0.01
149 62 0.05
150 204 0.16
151 620 0.50
152 315 0.25
153 37 0.03
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (151 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAA
GGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAA
AAGCTCCCGAAGGCTTTTTGG
Found at i:4172751 original size:75 final size:76
Alignment explanation
Indices: 4171261--4172721 Score: 2505
Period size: 76 Copynumber: 19.3 Consensus size: 76
4171251 GAAATGTTGA
* * * *
4171261 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4171326 AAGCTTTTTGG
66 AGGCTTTTTGG
* * * * *
4171337 AAACATCATGCACTGTAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4171402 AGGCTTTTTTGG
66 AGGC-TTTTTGG
*
4171414 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4171478 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4171489 AAACATTATGCACTGCAGGACTTACAGATGACCCTAAGGC-TTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4171553 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4171564 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4171628 AGGCTTTTTGG
66 AGGCTTTTTGG
4171639 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4171704 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4171715 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4171780 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
4171791 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATTAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4171855 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4171866 AAACATCATGCACTGCATGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAGCTCTCTC
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC-C-C
4171930 GAAGGCTTTTT-G
64 GAAGGCTTTTTGG
*
4171942 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAA-CTACCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
4172006 ATGCTTTTTGG
66 AGGCTTTTTGG
*
4172017 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTG-AAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4172080 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4172091 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4172156 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4172167 AAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4172231 AGGCTTTTTGG
66 AGGCTTTTTGG
*
4172242 AAACAACATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4172307 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
4172318 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAAGC-TTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4172382 AGGCTTTTTGG
66 AGGCTTTTTGG
* * * *
4172393 AAATATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4172458 AGGCTTTTTGG
66 AGGCTTTTTGG
4172469 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4172534 AGGCTTTTTGG
66 AGGCTTTTTGG
4172545 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4172610 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
4172621 AAACATCATGCACTGCAGGACTTACAGATGACTCGAAGGC-TTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
4172685 AGGCTTTTTGG
66 AGGCTTTTTGG
4172696 AAACATCATGCACTGCAGGACTTACA
1 AAACATCATGCACTGCAGGACTTACA
4172722 AATGTAGGAA
Statistics
Matches: 1326, Mismatches: 47, Indels: 25
0.95 0.03 0.02
Matches are distributed among these distances:
73 4 0.00
74 77 0.06
75 528 0.40
76 656 0.49
77 61 0.05
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:4173431 original size:22 final size:22
Alignment explanation
Indices: 4173403--4173457 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
4173393 CATAAAGCTT
*
4173403 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
4173425 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
4173447 TCATCTTTGAA
1 TCATCTTTGAA
4173458 GAGTGTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:4173920 original size:65 final size:63
Alignment explanation
Indices: 4173818--4173946 Score: 240
Period size: 65 Copynumber: 2.0 Consensus size: 63
4173808 AGAATAGCAG
4173818 GTTCGTAAATATTTGCAGTGCATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTT
1 GTTCGTAAATATTTGCAGTGCATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTT
4173881 GTTCGTAAAATATTTGACAGTGCATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTT
1 GTTCGT-AAATATTTG-CAGTGCATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTT
4173946 G
1 G
4173947 ACAACACATT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 6 0.09
64 9 0.14
65 49 0.77
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (63 bp):
GTTCGTAAATATTTGCAGTGCATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTT
Found at i:4174010 original size:54 final size:52
Alignment explanation
Indices: 4173885--4174035 Score: 173
Period size: 54 Copynumber: 2.9 Consensus size: 52
4173875 ACACTTGTTC
* * * *
4173885 GTAAAATATTTGACAGTGCATTCATC-TTTTCCTGTGGTTTCTG-TC-GAGAT
1 GTAAAACATTTGACAATACATTCATCATTTT-CTGTGGCTTCTGCTCAGAGAT
* * *
4173935 GTAAAACACTTGACAACACATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTT
1 GTAAAACATTTGACAATACATTCATCATTTTCTGTGGCTTCTGCTCAGA-G-AT
* *
4173989 GTAAAGCATTTGACAATACATTCATCATTTTTTGTGGCTTCTGCTCA
1 GTAAAACATTTGACAATACATTCATCATTTTCTGTGGCTTCTGCTCA
4174036 AATTTCTCAA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
50 32 0.38
51 6 0.07
52 2 0.02
53 1 0.01
54 44 0.52
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (52 bp):
GTAAAACATTTGACAATACATTCATCATTTTCTGTGGCTTCTGCTCAGAGAT
Found at i:4176310 original size:114 final size:114
Alignment explanation
Indices: 4176110--4176333 Score: 385
Period size: 114 Copynumber: 2.0 Consensus size: 114
4176100 GATCATGCAG
* * *
4176110 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
4176175 ACATTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
4176224 TTCATCTTTCAAATCTAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
4176289 ACACTTCCAAAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
66 ACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
4176334 AACGTAGCAC
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAAAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:4178321 original size:22 final size:22
Alignment explanation
Indices: 4178293--4178351 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 22
4178283 ATTCTATTTC
4178293 TTTTTTTTTCTTTTCCTCCTTTT
1 TTTTTTTTTCTTTT-CTCCTTTT
*
4178316 TTTTTTTTTCTTTT-TTCTTTT
1 TTTTTTTTTCTTTTCTCCTTTT
4178337 TTTTTTCTTTCTTTT
1 TTTTTT-TTTCTTTT
4178352 TTCTTTGCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 12 0.35
22 8 0.24
23 14 0.41
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTTTTTTTCTTTTCTCCTTTT
Found at i:4178329 original size:11 final size:11
Alignment explanation
Indices: 4178289--4178383 Score: 88
Period size: 11 Copynumber: 8.6 Consensus size: 11
4178279 CTTGATTCTA
4178289 TTTCTTTTTT-
1 TTTCTTTTTTC
*
4178299 TTTCTTTTCCTCC
1 TTTCTTTT--TTC
*
4178312 TTT-TTTTTTT
1 TTTCTTTTTTC
4178322 TTTCTTTTTTC
1 TTTCTTTTTTC
*
4178333 TTTTTTTTTTC
1 TTTCTTTTTTC
4178344 TTTCTTTTTTC
1 TTTCTTTTTTC
***
4178355 TTTGCTAGATT-
1 TTT-CTTTTTTC
4178366 TTTCTTTTTTC
1 TTTCTTTTTTC
4178377 TTTCTTT
1 TTTCTTT
4178384 GTTGGATGGG
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
10 16 0.24
11 39 0.58
12 9 0.13
13 3 0.04
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:4178337 original size:15 final size:15
Alignment explanation
Indices: 4178295--4178357 Score: 69
Period size: 14 Copynumber: 4.2 Consensus size: 15
4178285 TCTATTTCTT
*
4178295 TTTTTTTCTTTTCCTCC
1 TTTTTTTCTTTT--TTC
4178312 TTTTTTT-TTTTTTC
1 TTTTTTTCTTTTTTC
4178326 -TTTTTTCTTTTTT-
1 TTTTTTTCTTTTTTC
4178339 TTTTCTTTCTTTTTTC
1 TTTT-TTTCTTTTTTC
4178355 TTT
1 TTT
4178358 GCTAGATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
13 6 0.15
14 11 0.27
15 10 0.24
16 7 0.17
17 7 0.17
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:4181196 original size:14 final size:14
Alignment explanation
Indices: 4181179--4181217 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
4181169 TAAAAGTATG
4181179 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
4181193 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
4181208 AATG-AAAATG
1 AATGCAAAATG
4181218 CATATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:4183305 original size:15 final size:16
Alignment explanation
Indices: 4183285--4183319 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
4183275 ATAAATAAAT
4183285 AAAATAAAAAGT-ATA
1 AAAATAAAAAGTAATA
*
4183300 AAAATAACAAGTAATA
1 AAAATAAAAAGTAATA
4183316 AAAA
1 AAAA
4183320 ATTTGAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAGTAATA
Found at i:4184082 original size:18 final size:17
Alignment explanation
Indices: 4184054--4184087 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4184044 TCAAATTAAG
4184054 ATTTAATATAAATTATT
1 ATTTAATATAAATTATT
*
4184071 ATTTATATATAATTTAT
1 ATTTA-ATATAAATTAT
4184088 ATGACTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTAATATAAATTATT
Found at i:4184607 original size:221 final size:218
Alignment explanation
Indices: 4184346--4184785 Score: 812
Period size: 221 Copynumber: 2.0 Consensus size: 218
4184336 ATTAATAAGT
4184346 GATTAAAATTATAATTATTAAATTAAAGACTCTAACTCGAATAATAAAAAGATCTAAGTGCTAAT
1 GATTAAAATTATAATTATTAAATTAAAGACTCTAACTCGAATAATAAAAAGATCTAAGTGCTAAT
4184411 AATGTAA-TATCC-TATTTAATTAATTCGGGTTAAAATGATAATTACTAAACTATAAGGGACTAA
66 AATGTAATTATCCTTATTTAATTAATTCGGGTTAAAATGATAATTACTAAACTATAAGGGACTAA
4184474 ATTAGGCATTTATCCTAAAGATATATTATATTATGTAAAGGACTAAAATAAAATGAAATAAAATT
131 ATTAGGCATTTATCCT-AA-ATATA-TATATTATGTAAAGGACTAAAATAAAATGAAATAAAATT
4184539 ACTAGATCGAATATATAATATATAAAA
193 ACTAGATCGAAT-TATAATATATAAAA
4184566 GATTAAAATTATAATTATTAAAATTAAAGACTCTAACTCGAATAATAAAAAGATCTAAGTGCTAA
1 GATTAAAATTATAATTATT-AAATTAAAGACTCTAACTCGAATAATAAAAAGATCTAAGTGCTAA
4184631 TAATGTAATTTATCCTTATTTAATTAATTCGGGTTAAAATGATAATTACTAAACTATAAGGGACT
65 TAATGTAA-TTATCCTTATTTAATTAATTCGGGTTAAAATGATAATTACTAAACTATAAGGGACT
4184696 AAATTAGGCATTTATCCTAAATATATATATTATGTAAAGGACTAAAATAAAATGAAATAAAATTA
129 AAATTAGGCATTTATCCTAAATATATATATTATGTAAAGGACTAAAATAAAATGAAATAAAATTA
4184761 CTAGATCGAATTATAATATATAAAA
194 CTAGATCGAATTATAATATATAAAA
4184786 ACATGCGATA
Statistics
Matches: 216, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
220 33 0.15
221 104 0.48
222 5 0.02
223 7 0.03
224 67 0.31
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (218 bp):
GATTAAAATTATAATTATTAAATTAAAGACTCTAACTCGAATAATAAAAAGATCTAAGTGCTAAT
AATGTAATTATCCTTATTTAATTAATTCGGGTTAAAATGATAATTACTAAACTATAAGGGACTAA
ATTAGGCATTTATCCTAAATATATATATTATGTAAAGGACTAAAATAAAATGAAATAAAATTACT
AGATCGAATTATAATATATAAAA
Found at i:4185733 original size:3 final size:3
Alignment explanation
Indices: 4185725--4185783 Score: 91
Period size: 3 Copynumber: 19.0 Consensus size: 3
4185715 TTGTAATATT
*
4185725 TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4185771 TAAA TAA TAA TAA
1 T-AA TAA TAA TAA
4185784 AAACAAACTG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
3 47 0.90
4 5 0.10
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4185765 original size:28 final size:28
Alignment explanation
Indices: 4185725--4185783 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
4185715 TTGTAATATT
4185725 TAATAATAATAATAAATAATAATAATAA
1 TAATAATAATAATAAATAATAATAATAA
*
4185753 TAATAATAATAAT-AATGATAAATAATAA
1 TAATAATAATAATAAATAAT-AATAATAA
4185781 TAA
1 TAA
4185784 AAACAAACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
TAATAATAATAATAAATAATAATAATAA
Found at i:4187325 original size:64 final size:63
Alignment explanation
Indices: 4187240--4187400 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
4187230 TTGTTTAAGG
* * * *
4187240 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
4187304 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
4187368 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
4187401 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:4187752 original size:18 final size:18
Alignment explanation
Indices: 4187717--4187752 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4187707 AAAATGGGTA
* *
4187717 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
4187735 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
4187753 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:4189065 original size:149 final size:149
Alignment explanation
Indices: 4188751--4189066 Score: 571
Period size: 149 Copynumber: 2.1 Consensus size: 149
4188741 GAGTCGAGGG
*
4188751 TTCTACGTGGTCCTTCGAGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TTCTACGTGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
* *
4188816 TACTTGATCCCTAGTATATGTGTATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATTATT
4188881 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
* *
4188900 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACATA
1 TTCTACGTGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
4188965 TACTTGATCCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATTATT
4189030 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
4189049 TTCTACGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
4189067 TGCAATTATA
Statistics
Matches: 160, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TTCTACGTGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
TACTTGATCCCTAGTATATGTATATGATTATTAAGGAATAATATGTGGTCCTTATGGACATTATT
ATATGGCACTACGGTGCAA
Found at i:4189067 original size:23 final size:23
Alignment explanation
Indices: 4189033--4189078 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
4189023 CATTATTATA
*
4189033 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
4189056 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
4189079 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:4192323 original size:64 final size:63
Alignment explanation
Indices: 4192238--4192398 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
4192228 TTGTTTAAGG
* * * *
4192238 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * *
4192302 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
*
4192366 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
4192399 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.73
65 21 0.25
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:4192750 original size:18 final size:18
Alignment explanation
Indices: 4192715--4192750 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4192705 AAAATGGGTA
* *
4192715 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
4192733 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
4192751 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Done.