Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 120 of 193
Found at i:38044071 original size:58 final size:58
Alignment explanation
Indices: 38044009--38044167 Score: 134
Period size: 58 Copynumber: 2.8 Consensus size: 58
38043999 TCGGGGTCAG
* * *
38044009 AAATGGAATTTTTAGACA-TCGGGGGTAAAATGATAATTTTT-GAAAAGTTCGAGGTTAA
1 AAATGGAAATTTTAGA-AGTCGAGGGTAAAATGATAATTTTTGGAAAA-TTCAAGGTTAA
* * * *
38044067 AAAT-GAAATTTTGGAAGTTTGATGGTAAAATGATAATTTTTGGAGAATTCAAGGTTAA
1 AAATGGAAATTTTAGAAG-TCGAGGGTAAAATGATAATTTTTGGAAAATTCAAGGTTAA
* * *
38044125 AAAT-G-ATTTTTGAAAATTCGA-GGTAAAAAT-ATAATTTTTGGAA
1 AAATGGAAATTTT-AGAAGTCGAGGGT-AAAATGATAATTTTTGGAA
38044168 GTTTAGGGGC
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
56 16 0.19
57 22 0.27
58 41 0.49
59 4 0.05
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.35
Consensus pattern (58 bp):
AAATGGAAATTTTAGAAGTCGAGGGTAAAATGATAATTTTTGGAAAATTCAAGGTTAA
Found at i:38044160 original size:56 final size:59
Alignment explanation
Indices: 38044032--38044167 Score: 174
Period size: 58 Copynumber: 2.4 Consensus size: 59
38044022 AGACATCGGG
* * * *
38044032 GGTAAAATGATAATTTTT-GAAAAGTTCGAGGTTAAAAATGAAATTTTGGAAGTTTGAT
1 GGTAAAATGATAATTTTTGGAAAAGTTCAAGGTTAAAAATGAAATTTTGAAAATTCGAT
* *
38044090 GGTAAAATGATAATTTTTGGAGAA-TTCAAGGTTAAAAATG-ATTTTTGAAAATTCGA-
1 GGTAAAATGATAATTTTTGGAAAAGTTCAAGGTTAAAAATGAAATTTTGAAAATTCGAT
38044146 GGTAAAAAT-ATAATTTTTGGAA
1 GGT-AAAATGATAATTTTTGGAA
38044168 GTTTAGGGGC
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
56 15 0.22
57 17 0.25
58 33 0.48
59 4 0.06
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (59 bp):
GGTAAAATGATAATTTTTGGAAAAGTTCAAGGTTAAAAATGAAATTTTGAAAATTCGAT
Found at i:38044189 original size:85 final size:85
Alignment explanation
Indices: 38044043--38044251 Score: 214
Period size: 85 Copynumber: 2.4 Consensus size: 85
38044033 GTAAAATGAT
* * * *
38044043 AATTTTTGAAAAGTTCGAGGTTAAAAATGA-AA-TTTTGGAAGTTTGATGGTAAAATGATAATTT
1 AATTTTTGAAAA-TTCGAGG-TAAAAAT-ATAATTTTTGGAAGTTTGAGGGAAAAAAGATAATTG
38044106 TTG-GAGAATTCAAGGTTAAAAATG
63 TTGTGA-AATTCAAGG-TAAAAATG
38044130 -ATTTTTGAAAATTCGAGGTAAAAATATAATTTTTGGAAGTTT-AGGGGCAAAAAAG-TAATTGT
1 AATTTTTGAAAATTCGAGGTAAAAATATAATTTTTGGAAGTTTGA-GGG-AAAAAAGATAATTGT
* * *
38044192 TGTGAAGTTTAAGGTCAAAATG
64 TGTGAAATTCAAGGTAAAAATG
* *
38044214 TAATTTTTGAAAGTTCGAAGGTCAAAATATAATTTTTG
1 -AATTTTTGAAAATTCG-AGGTAAAAATATAATTTTTG
38044252 AACAATTCAG
Statistics
Matches: 105, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
83 1 0.01
84 17 0.16
85 36 0.34
86 32 0.30
87 19 0.18
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.36
Consensus pattern (85 bp):
AATTTTTGAAAATTCGAGGTAAAAATATAATTTTTGGAAGTTTGAGGGAAAAAAGATAATTGTTG
TGAAATTCAAGGTAAAAATG
Found at i:38044247 original size:58 final size:56
Alignment explanation
Indices: 38044032--38044253 Score: 165
Period size: 58 Copynumber: 3.9 Consensus size: 56
38044022 AGACATCGGG
* *
38044032 GGTAAAATGATAATTTTTGAAAAGTTCG-AGGTTAAAAATGAAATTTTG-GAAGTTTGAT
1 GGTAAAATGATAATTTTTG-AAAGTTCGAAGGTCAAAAAT--AATTTTGTGAAGTTT-AA
* * * **
38044090 GGTAAAATGATAATTTTTGGAGAA-TTC-AAGGTTAAAAATGATTTT-TGAAAATTCGA
1 GGTAAAATGATAATTTTT-GA-AAGTTCGAAGGTCAAAAATAATTTTGTG-AAGTTTAA
* * * *
38044146 GGTAAAAAT-ATAATTTTTGGAAGTT-TAGGGGCAAAAAAGTAATTGTTGTGAAGTTTAA
1 GGT-AAAATGATAATTTTTGAAAGTTCGAAGGTC-AAAAA-TAATT-TTGTGAAGTTTAA
38044204 GGTCAAAATG-TAATTTTTGAAAGTTCGAAGGTCAAAATATAATTTT-TGAA
1 GGT-AAAATGATAATTTTTGAAAGTTCGAAGGTCAAAA-ATAATTTTGTGAA
38044254 CAATTCAGAG
Statistics
Matches: 131, Mismatches: 18, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
54 2 0.02
55 6 0.05
56 27 0.21
57 15 0.11
58 71 0.54
59 10 0.08
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (56 bp):
GGTAAAATGATAATTTTTGAAAGTTCGAAGGTCAAAAATAATTTTGTGAAGTTTAA
Found at i:38044252 original size:29 final size:29
Alignment explanation
Indices: 38044035--38044253 Score: 143
Period size: 29 Copynumber: 7.6 Consensus size: 29
38044025 CATCGGGGGT
*
38044035 AAAATGATAATTTTTGAAAAGTTCG-AGGTT
1 AAAAT-ATAATTTTTG-AAAGTTCGAAGGTC
* * * *
38044065 AAAA-ATGAAATTTTGGAAGTTTGATGGT-
1 AAAATAT-AATTTTTGAAAGTTCGAAGGTC
*
38044093 AAAATGATAATTTTTGGAGAA-TTC-AAGGTT
1 AAAAT-ATAATTTTT-GA-AAGTTCGAAGGTC
* * *
38044123 AAAA-ATGATTTTTGAAAATTCG-AGGTA
1 AAAATATAATTTTTGAAAGTTCGAAGGTC
* * * *
38044150 AAAATATAATTTTTGGAAGTT-TAGGGGC
1 AAAATATAATTTTTGAAAGTTCGAAGGTC
* *
38044178 AAAAAAGTAATTGTTGTG-AAGTT-TAAGGTC
1 AAAATA-TAATT-TT-TGAAAGTTCGAAGGTC
*
38044208 AAAATGTAATTTTTGAAAGTTCGAAGGTC
1 AAAATATAATTTTTGAAAGTTCGAAGGTC
38044237 AAAATATAATTTTTGAA
1 AAAATATAATTTTTGAA
38044254 CAATTCAGAG
Statistics
Matches: 149, Mismatches: 24, Indels: 33
0.72 0.12 0.16
Matches are distributed among these distances:
26 2 0.01
27 15 0.10
28 47 0.32
29 52 0.35
30 29 0.19
31 4 0.03
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.36
Consensus pattern (29 bp):
AAAATATAATTTTTGAAAGTTCGAAGGTC
Found at i:38049517 original size:10 final size:10
Alignment explanation
Indices: 38049502--38049535 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
38049492 GGGAGAAACA
*
38049502 AAAAAAAATG
1 AAAAAAAAGG
38049512 AAAAAAAAGG
1 AAAAAAAAGG
38049522 AAAAAAAAGG
1 AAAAAAAAGG
38049532 AAAA
1 AAAA
38049536 GTTCAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:38055851 original size:31 final size:29
Alignment explanation
Indices: 38055812--38055876 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 29
38055802 TTCTAAATTT
* *
38055812 AAATTTATTTGAAAAATGAGATATATTAAA
1 AAATTTATTAGAAAAATG-CATATATTAAA
* *
38055842 ACAATTTATTAGAGAAATGCATTTATTAAA
1 A-AATTTATTAGAAAAATGCATATATTAAA
38055872 AAATT
1 AAATT
38055877 AAAATACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 4 0.13
30 11 0.37
31 15 0.50
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (29 bp):
AAATTTATTAGAAAAATGCATATATTAAA
Found at i:38073466 original size:2 final size:2
Alignment explanation
Indices: 38073461--38073489 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38073451 AGAAAAAATA
38073461 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
38073490 ATGATATTTT
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:38073898 original size:17 final size:19
Alignment explanation
Indices: 38073857--38073898 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
38073847 CGAAAAATTC
38073857 AAAAAATATAAAAATTATT
1 AAAAAATATAAAAATTATT
*
38073876 CAAAAAT-T-AAAATTATT
1 AAAAAATATAAAAATTATT
38073893 AAAAAA
1 AAAAAA
38073899 AGCATAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 14 0.67
18 1 0.05
19 6 0.29
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATATAAAAATTATT
Found at i:38080174 original size:40 final size:40
Alignment explanation
Indices: 38080110--38080186 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
38080100 ACTAATATTA
* *
38080110 TTAATTTGTGATGATGTGAAAATGACAATCGATCACACTG
1 TTAATTTGTGATGATATGAAAATGACAACCGATCACACTG
*
38080150 TTAATTTGTGATGATATGATAATGACAACCGATCACA
1 TTAATTTGTGATGATATGAAAATGACAACCGATCACA
38080187 TATTGACACG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.32
Consensus pattern (40 bp):
TTAATTTGTGATGATATGAAAATGACAACCGATCACACTG
Found at i:38080421 original size:23 final size:22
Alignment explanation
Indices: 38080369--38080423 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
38080359 TATATATATA
*
38080369 TATATATATATTAATTTTGGAT
1 TATATATATATTAATTTTGAAT
* *
38080391 TTTTTATAGTATT-ATTTTGAAAT
1 TATATATA-TATTAATTTTG-AAT
38080414 TATATATATA
1 TATATATATA
38080424 AATATAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (22 bp):
TATATATATATTAATTTTGAAT
Found at i:38080452 original size:15 final size:16
Alignment explanation
Indices: 38080432--38080465 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38080422 TAAATATAAA
*
38080432 AAATTAA-AAATATAC
1 AAATTAATAAAAATAC
38080447 AAATTAATAAAAATAC
1 AAATTAATAAAAATAC
38080463 AAA
1 AAA
38080466 ACATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTAATAAAAATAC
Found at i:38080629 original size:8 final size:7
Alignment explanation
Indices: 38080628--38080678 Score: 59
Period size: 8 Copynumber: 6.9 Consensus size: 7
38080618 TAATATTATA
38080628 ATAAATAT
1 ATAAAT-T
38080636 ATAAATT
1 ATAAATT
38080643 ATAAATAT
1 ATAAAT-T
38080651 ATAAATT
1 ATAAATT
38080658 ATAAATAT
1 ATAAAT-T
38080666 ATACAATT
1 ATA-AATT
38080674 A-AAAT
1 ATAAAT
38080679 GTATTAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 3 0.08
7 15 0.38
8 19 0.47
9 3 0.08
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (7 bp):
ATAAATT
Found at i:38080665 original size:13 final size:15
Alignment explanation
Indices: 38080628--38080678 Score: 86
Period size: 15 Copynumber: 3.4 Consensus size: 15
38080618 TAATATTATA
38080628 ATAAATATATAAATT
1 ATAAATATATAAATT
38080643 ATAAATATATAAATT
1 ATAAATATATAAATT
38080658 ATAAATATATACAATT
1 ATAAATATATA-AATT
38080674 A-AAAT
1 ATAAAT
38080679 GTATTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 30 0.86
16 5 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAAATATATAAATT
Found at i:38081885 original size:11 final size:11
Alignment explanation
Indices: 38081852--38081885 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
38081842 TTTTAAAAAT
38081852 TAAATAATAAA
1 TAAATAATAAA
* *
38081863 CAAGTAATAAA
1 TAAATAATAAA
38081874 TAAATAATAAA
1 TAAATAATAAA
38081885 T
1 T
38081886 TGTTTTAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:38090473 original size:15 final size:15
Alignment explanation
Indices: 38090453--38090483 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38090443 TAAATTACAA
38090453 AGAGAGAATTAAACT
1 AGAGAGAATTAAACT
38090468 AGAGAGAATTAAACT
1 AGAGAGAATTAAACT
38090483 A
1 A
38090484 AGGAAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.19, T:0.19
Consensus pattern (15 bp):
AGAGAGAATTAAACT
Found at i:38094357 original size:52 final size:52
Alignment explanation
Indices: 38094241--38094481 Score: 306
Period size: 52 Copynumber: 4.6 Consensus size: 52
38094231 GTAAATGCAA
* * *
38094241 AAGGTCCGATGACTTTGTGTCATCGTGAGTTATATGAATCTTTTACGAATT-T
1 AAGGTCCGATGACTATGTGTCATCGTGAG-TATATGAATCCTTTACGGATTAT
** * * *
38094293 CTGGGTCCGATGATTATGAGTCATCATGAGTATATGAATCCTTTACGGATTAT
1 -AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
38094346 AAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAC
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
38094398 GAGGTTCGATGACTATGTGTCATCATGAGTATATGAAT-CTTTGACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTT-ACGGATTAT
*
38094450 GAGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
38094482 TAAATGAAAA
Statistics
Matches: 162, Mismatches: 24, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
51 3 0.02
52 135 0.83
53 24 0.15
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:38094422 original size:104 final size:104
Alignment explanation
Indices: 38094241--38094481 Score: 369
Period size: 104 Copynumber: 2.3 Consensus size: 104
38094231 GTAAATGCAA
* *
38094241 AAGGTCCGATGACTTTGTGTCATCGTGAGTTATATGAATCTTTTACGAATTTCTGGGTCCGATGA
1 AAGGTCCGATGACTATGTGTCATCGTGAG-TATATGAATCTTTTACGAATTACTGGGTCCGATGA
*
38094306 TTATGAGTCATCATGAGTATATGAATCCTTT-ACGGATTAT
65 CTATGAGTCATCATGAGTATATGAAT-CTTTGACGGATTAT
* * *
38094346 AAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTAC-GAGGTTCGATGA
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGAATTACTG-GGTCCGATGA
*
38094410 CTATGTGTCATCATGAGTATATGAATCTTTGACGGATTAT
65 CTATGAGTCATCATGAGTATATGAATCTTTGACGGATTAT
*
38094450 GAGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
38094482 TAAATGAAAA
Statistics
Matches: 125, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
103 5 0.04
104 93 0.74
105 27 0.22
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (104 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTTACGAATTACTGGGTCCGATGAC
TATGAGTCATCATGAGTATATGAATCTTTGACGGATTAT
Found at i:38108374 original size:11 final size:11
Alignment explanation
Indices: 38108358--38108383 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38108348 TAGTCTAGAG
38108358 TAACATTGAAT
1 TAACATTGAAT
38108369 TAACATTGAAT
1 TAACATTGAAT
38108380 TAAC
1 TAAC
38108384 GGCATGTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (11 bp):
TAACATTGAAT
Found at i:38111444 original size:8 final size:9
Alignment explanation
Indices: 38111419--38111457 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
38111409 AGCCCTTTTC
*
38111419 AAATTTTAA
1 AAATTATAA
38111428 AAATTATTAAA
1 AAATTA-T-AA
38111439 AAATTATAA
1 AAATTATAA
38111448 AAATTATAA
1 AAATTATAA
38111457 A
1 A
38111458 CAAAATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 17 0.63
10 2 0.07
11 8 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
AAATTATAA
Found at i:38111448 original size:20 final size:21
Alignment explanation
Indices: 38111419--38111469 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
38111409 AGCCCTTTTC
* *
38111419 AAATTTTAAAAATTATTAA-A
1 AAATTATAAAAATTATAAACA
38111439 AAATTATAAAAATTATAAACA
1 AAATTATAAAAATTATAAACA
38111460 AAATTTATAA
1 AAA-TTATAA
38111470 GAAAAAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 17 0.63
21 4 0.15
22 6 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATTATAAAAATTATAAACA
Found at i:38113258 original size:42 final size:41
Alignment explanation
Indices: 38113211--38113345 Score: 173
Period size: 42 Copynumber: 3.2 Consensus size: 41
38113201 TCAGTTTAGA
*
38113211 CGATGATGCACTTATGTGTCAATATATTTGCTTTGATTTATC
1 CGATGATGCACTTATGTGTCAATATA-TTGCTTTGGTTTATC
* *
38113253 CGATGATGCACTTATGTGCTAAAT-TAATTGCTTTGGTATATC
1 CGATGATGCACTTATGTG-TCAATAT-ATTGCTTTGGTTTATC
* * *
38113295 TGATGATGCACTTATGTGCCAACATGATTGCTTTGGTTTATC
1 CGATGATGCACTTATGTGTCAATAT-ATTGCTTTGGTTTATC
38113337 CGATGATGC
1 CGATGATGC
38113346 GTTATGCGTG
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
41 2 0.03
42 73 0.91
43 5 0.06
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.41
Consensus pattern (41 bp):
CGATGATGCACTTATGTGTCAATATATTGCTTTGGTTTATC
Found at i:38113433 original size:47 final size:47
Alignment explanation
Indices: 38113360--38113454 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 47
38113350 TGCGTGTCAG
* *
38113360 TATAATTGCTTCGATTCGTTCCATGATGCACCT-CGTGTGCTAGTATA
1 TATAATTGCTTCGATTCGTCCCATGATGCA-CTACGTATGCTAGTATA
*
38113407 TATAATTGCTTCGACTT-G-CCCGATGATGCACTATGTATGCTAGTATA
1 TATAATTGCTTCGA-TTCGTCCC-ATGATGCACTACGTATGCTAGTATA
38113454 T
1 T
38113455 TTCCTTTGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
46 4 0.10
47 36 0.86
48 2 0.05
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (47 bp):
TATAATTGCTTCGATTCGTCCCATGATGCACTACGTATGCTAGTATA
Found at i:38121520 original size:6 final size:6
Alignment explanation
Indices: 38121509--38121558 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
38121499 TTTAATTCTA
38121509 TCACCC TCACCC TCACCC TCACCC TCACCC TCACCC TCACCC TCACCC
1 TCACCC TCACCC TCACCC TCACCC TCACCC TCACCC TCACCC TCACCC
38121557 TC
1 TC
38121559 CTCCCCCAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.16, C:0.66, G:0.00, T:0.18
Consensus pattern (6 bp):
TCACCC
Found at i:38125861 original size:12 final size:12
Alignment explanation
Indices: 38125844--38125873 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
38125834 ATATACTTAT
38125844 TTATAAAAAAAA
1 TTATAAAAAAAA
38125856 TTATAAAAAAAA
1 TTATAAAAAAAA
38125868 -TATAAA
1 TTATAAA
38125874 CACAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
TTATAAAAAAAA
Found at i:38130943 original size:5 final size:6
Alignment explanation
Indices: 38130933--38131050 Score: 58
Period size: 6 Copynumber: 20.5 Consensus size: 6
38130923 AATAGTATTT
*
38130933 TATTAA T-TTAA TATTAAA GTGATT-A TCTTAA TATTAA -ATTAA -ATTTAA
1 TATTAA TATTAA TATT-AA -T-ATTAA TATTAA TATTAA TATTAA TA-TTAA
* * * * * *
38130981 TGTTTA TCTTACA TATAAA TATT-T TATTAA T-TTAA TAAT-A T-TTAA
1 TATTAA TATTA-A TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
38131026 TATTAA T-TTAA TA-TAA TATTAA TAT
1 TATTAA TATTAA TATTAA TATTAA TAT
38131051 AAGAAAAAGA
Statistics
Matches: 85, Mismatches: 13, Indels: 28
0.67 0.10 0.22
Matches are distributed among these distances:
4 1 0.01
5 36 0.42
6 37 0.44
7 7 0.08
8 1 0.01
9 3 0.04
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (6 bp):
TATTAA
Found at i:38131025 original size:10 final size:11
Alignment explanation
Indices: 38131008--38131049 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
38130998 AATATTTTAT
38131008 TAATTTAATAA
1 TAATTTAATAA
*
38131019 T-ATTTAATAT
1 TAATTTAATAA
38131029 TAATTTAAT-A
1 TAATTTAATAA
38131039 TAATATTAATA
1 TAAT-TTAATA
38131050 TAAGAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTTAATAA
Found at i:38131031 original size:21 final size:19
Alignment explanation
Indices: 38130998--38131038 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
38130988 CTTACATATA
38130998 AATATTTTATTAATTTAAT
1 AATATTTTATTAATTTAAT
38131017 AATATTTAATATTAATTTAAT
1 AATATTT--TATTAATTTAAT
38131038 A
1 A
38131039 TAATATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTTTATTAATTTAAT
Found at i:38131036 original size:11 final size:11
Alignment explanation
Indices: 38131005--38131050 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
38130995 ATAAATATTT
38131005 TATTAATTTAA
1 TATTAATTTAA
*
38131016 TAAT-ATTTAA
1 TATTAATTTAA
38131026 TATTAATTTAA
1 TATTAATTTAA
38131037 TA-TAATATTAA
1 TATTAAT-TTAA
38131048 TAT
1 TAT
38131051 AAGAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 13 0.43
11 17 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATTAATTTAA
Found at i:38139143 original size:6 final size:6
Alignment explanation
Indices: 38139132--38139167 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
38139122 TCTACCTCTT
38139132 TGAGCG TGAGCG TGAGCG TGAGCG TGAGCG TGAGCG
1 TGAGCG TGAGCG TGAGCG TGAGCG TGAGCG TGAGCG
38139168 AGAAGGAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.17
Consensus pattern (6 bp):
TGAGCG
Found at i:38140843 original size:17 final size:17
Alignment explanation
Indices: 38140818--38140851 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38140808 TGTTTATCAA
38140818 TAAAATAAATATTAAAT
1 TAAAATAAATATTAAAT
*
38140835 TAAATTAAATATTAAAT
1 TAAAATAAATATTAAAT
38140852 CCTATTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAATAAATATTAAAT
Found at i:38140942 original size:96 final size:97
Alignment explanation
Indices: 38140816--38141265 Score: 530
Period size: 94 Copynumber: 4.6 Consensus size: 97
38140806 CATGTTTATC
* * * * *
38140816 AATAAAATAAATATTAAATTAAATTAAATATTAAATCCTATTAAAATAATACAATATTTATTTAC
1 AATAAGATAAATATTAAATTTAATTTAATATTAAATCTTATTAAAATAATACAATATTTATCTAC
38140881 AATA-TAACTATTTCAAAAATAATATTATTTT
66 AATATTAACTATTTCAAAAATAATATTATTTT
* *
38140912 AATAAGATAAATATTAAATTTAATTTAATATTAAA---TATTAAAATAATACAACATTTATCTAT
1 AATAAGATAAATATTAAATTTAATTTAATATTAAATCTTATTAAAATAATACAATATTTATCTAC
38140974 AATATTAACTATTTCAAAAATAATATTATTTT
66 AATATTAACTATTTCAAAAATAATATTATTTT
* * *
38141006 AATAAGATAAACATTAAATTTAATTTAATATTAAATCTTATT-AAATAATATAATATTTATCTAT
1 AATAAGATAAATATTAAATTTAATTTAATATTAAATCTTATTAAAATAATACAATATTTATCTAC
* * *
38141070 AAAATAAACATTAATTAAATTAAAGTTAGATTAATATAATATTTT
66 AATATTAAC--T-ATT---TCAAA---A-A-TAATAT--TATTTT
*
38141115 AATAAGATAAATATTAAACTTAA-TTAATATTAAATCTTATTAAAATAATACAATATTTATCTAC
1 AATAAGATAAATATTAAATTTAATTTAATATTAAATCTTATTAAAATAATACAATATTTATCTAC
38141179 AATATTAACTATTTC-AAAATAATATTATTTT
66 AATATTAACTATTTCAAAAATAATATTATTTT
* * *
38141210 AAT---A-AAAT-TTAATTTTAAATTTAATATTAAATATT-TTAAAATAATATAATATTTAT
1 AATAAGATAAATATTAAATTT-AATTTAATATTAAATCTTATTAAAATAATACAATATTTAT
38141266 AAACATTAAA
Statistics
Matches: 311, Mismatches: 23, Indels: 45
0.82 0.06 0.12
Matches are distributed among these distances:
90 6 0.02
91 26 0.08
92 15 0.05
93 28 0.09
94 61 0.20
95 9 0.03
96 59 0.19
97 10 0.03
98 2 0.01
99 4 0.01
102 6 0.02
103 1 0.00
105 1 0.00
106 4 0.01
107 7 0.02
108 18 0.06
109 54 0.17
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (97 bp):
AATAAGATAAATATTAAATTTAATTTAATATTAAATCTTATTAAAATAATACAATATTTATCTAC
AATATTAACTATTTCAAAAATAATATTATTTT
Found at i:38140951 original size:44 final size:44
Alignment explanation
Indices: 38140901--38141047 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 44
38140891 TTTCAAAAAT
38140901 AATATTATTTTAATAAGATAAATATTAAATTTAATTTAATATTA
1 AATATTATTTTAATAAGATAAATATTAAATTTAATTTAATATTA
*** * ** * *
38140945 AATATTAAAATAATACA-ACATTTATCTATAATATTAACTATTTCAAAAAT-
1 AATATTATTTTAATA-AGATAAATAT-TA-AAT-TT-A--ATTT-AATATTA
*
38140995 AATATTATTTTAATAAGATAAACATTAAATTTAATTTAATATTA
1 AATATTATTTTAATAAGATAAATATTAAATTTAATTTAATATTA
*
38141039 AATCTTATT
1 AATATTATT
38141048 AAATAATATA
Statistics
Matches: 75, Mismatches: 18, Indels: 20
0.66 0.16 0.18
Matches are distributed among these distances:
43 4 0.05
44 29 0.39
45 3 0.04
46 4 0.05
47 4 0.05
48 4 0.05
49 3 0.04
50 20 0.27
51 4 0.05
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (44 bp):
AATATTATTTTAATAAGATAAATATTAAATTTAATTTAATATTA
Found at i:38141143 original size:16 final size:16
Alignment explanation
Indices: 38141124--38141157 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
38141114 TAATAAGATA
38141124 AATATTAAA-CTTAATT
1 AATATTAAATCTT-ATT
38141140 AATATTAAATCTTATT
1 AATATTAAATCTTATT
38141156 AA
1 AA
38141158 AATAATACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATTAAATCTTATT
Found at i:38141240 original size:108 final size:108
Alignment explanation
Indices: 38141000--38141200 Score: 289
Period size: 109 Copynumber: 1.9 Consensus size: 108
38140990 AAAATAATAT
* * *
38141000 TATTTTAATAAGATAAACATTAAATTTAATTTAATATTAAATCTTATTAAATAATATAATATTTA
1 TATTTTAATAAGATAAATATTAAACTTAATTTAATATTAAATCTTATTAAATAATACAATATTTA
* * *
38141065 TCTATAAAATAAACATTAATTAAATTAAAGTTAGATTAATATAA
66 TCTACAAAATAAACATT-ATCAAAATAAAGTTAGATTAATATAA
38141109 TATTTTAATAAGATAAATATTAAACTTAA-TTAATATTAAATCTTATTAAAATAATACAATATTT
1 TATTTTAATAAGATAAATATTAAACTTAATTTAATATTAAATCTTATT-AAATAATACAATATTT
* *
38141173 ATCTACAATATTAACTATT-TCAAAATAA
65 ATCTACAAAATAAAC-ATTATCAAAATAA
38141201 TATTATTTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
108 25 0.30
109 54 0.66
110 3 0.04
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (108 bp):
TATTTTAATAAGATAAATATTAAACTTAATTTAATATTAAATCTTATTAAATAATACAATATTTA
TCTACAAAATAAACATTATCAAAATAAAGTTAGATTAATATAA
Found at i:38141245 original size:53 final size:54
Alignment explanation
Indices: 38141179--38141292 Score: 144
Period size: 53 Copynumber: 2.1 Consensus size: 54
38141169 ATTTATCTAC
* * * *
38141179 AATATTAACTATTTCAAAATAATATTAT-TTTAATAAA-ATTTAATT-TTAAATTT
1 AATATTAAATATTTCAAAATAATATAATATTT-ATAAACATTAAATTATTAAA-AT
*
38141232 AATATTAAATATTTTAAAATAATATAATATTTATAAACATTAAATTATTAAAAT
1 AATATTAAATATTTCAAAATAATATAATATTTATAAACATTAAATTATTAAAAT
38141286 AATATTA
1 AATATTA
38141293 TTTTTGAAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
53 30 0.57
54 18 0.34
55 5 0.09
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (54 bp):
AATATTAAATATTTCAAAATAATATAATATTTATAAACATTAAATTATTAAAAT
Found at i:38141309 original size:87 final size:89
Alignment explanation
Indices: 38141138--38141309 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 89
38141128 TTAAACTTAA
* *
38141138 TTAATATTAAATCTTATTAAAATAATACAATATTTATCTACAATATTAACTATTTCAAAATAATA
1 TTAATATTAAATATTATTAAAATAATACAATATTTA-CTACAACATTAAC-ATTTCAAAATAATA
*
38141203 TTATTTTAATAAAATTTAATTTTAAAT
64 TTATTTT-ATAAAAATTAATTTTAAAT
* *
38141230 TTAATATTAAATATT-TTAAAATAATATAATATTTA-TA-AACATTAA-ATTATTAAAATAATAT
1 TTAATATTAAATATTATTAAAATAATACAATATTTACTACAACATTAACATT-TCAAAATAATAT
38141291 TATTTT-TGAAATAATTAAT
65 TATTTTAT-AAA-AATTAAT
38141310 ATGAAATCAA
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
85 1 0.01
86 6 0.08
87 23 0.32
88 7 0.10
89 2 0.03
91 19 0.26
92 14 0.19
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (89 bp):
TTAATATTAAATATTATTAAAATAATACAATATTTACTACAACATTAACATTTCAAAATAATATT
ATTTTATAAAAATTAATTTTAAAT
Found at i:38147899 original size:30 final size:30
Alignment explanation
Indices: 38147864--38147987 Score: 130
Period size: 30 Copynumber: 4.2 Consensus size: 30
38147854 GATCAAAACG
*
38147864 TAATTTTGGGAAGTTTCGGGGTCAAAAATA
1 TAATTTTGGGAAGTTTCAGGGTCAAAAATA
* * * *
38147894 TAATTTTCGGAAG-TTCTAGTGT-AGAAATG
1 TAATTTTGGGAAGTTTC-AGGGTCAAAAATA
*
38147923 TAATTTTGGGAAGTTTTAGGGTCAAAAATA
1 TAATTTTGGGAAGTTTCAGGGTCAAAAATA
*
38147953 TAATTTTTGGAAGTTTC-GGGATC-AAAATA
1 TAATTTTGGGAAGTTTCAGGG-TCAAAAATA
*
38147982 CAATTT
1 TAATTT
38147988 CTGAACAGTT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
29 38 0.49
30 39 0.51
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (30 bp):
TAATTTTGGGAAGTTTCAGGGTCAAAAATA
Found at i:38149165 original size:21 final size:21
Alignment explanation
Indices: 38149112--38149190 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
38149102 TCGTGTATTT
* *
38149112 TATTATTAATA-A-TTAATAA
1 TATTATTAAAACATTTATTAA
38149131 TATTATTATAAAACATTTATTAA
1 TATTA-T-TAAAACATTTATTAA
* * *
38149154 TATTATTAAAACGTTTGTTAT
1 TATTATTAAAACATTTATTAA
*
38149175 TATTATCAAAAC-TTTA
1 TATTATTAAAACATTTA
38149191 ATGTTGCTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.10
20 4 0.08
21 27 0.55
22 2 0.04
23 11 0.22
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (21 bp):
TATTATTAAAACATTTATTAA
Found at i:38149962 original size:17 final size:16
Alignment explanation
Indices: 38149942--38150003 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
38149932 AAATCATTTT
38149942 AATTCAAAATAAATTCA
1 AATTCAAAATAAATT-A
* *
38149959 AATTTAACATAAATTTA
1 AATTCAAAATAAA-TTA
*
38149976 AATTTAAAATAAATTA
1 AATTCAAAATAAATTA
38149992 AGATTTCAAAAT
1 A-A-TTCAAAAT
38150004 TAAAAGTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
16 4 0.11
17 25 0.66
18 9 0.24
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (16 bp):
AATTCAAAATAAATTA
Found at i:38150837 original size:201 final size:199
Alignment explanation
Indices: 38150340--38150974 Score: 844
Period size: 206 Copynumber: 3.2 Consensus size: 199
38150330 ATTTGGCCTT
* * * * * *
38150340 CTTCTCAGTGTCTCATCAGGAAGATAACCGCATCACTTGCTTCAATTCACTTCTCTGTGTCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCTCTG-ATCTCCT
* * * * *
38150405 CAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCTTCAGGAAGCTAACCATTTTATTGCTCCAA
65 CAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
*
38150470 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATTGAGCTTGGGTTT
130 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA-TGAGC----G-TT
* * *
38150535 GATTTGTTC-TT
189 GAGTTG-GCATA
* *
38150546 CTTCTCAGTGTCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCTCTGGATATCCT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCTCT-GATCTCCT
* *
38150611 CAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTACTTCGA
65 CAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * *
38150676 CCTGCTTCTCAGTATCTTATCAAGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTCGAGTT
130 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT-GAGCGTTGAGTT
38150741 GGCATA
194 GGCATA
* * *
38150747 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTTGTTTCAATTCGCTTCTCTAGATCTCCT
1 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCTCT-GATCTCCT
* *
38150812 CAGGAAGATGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACC-GTTTATTGCTTCGA
65 CAGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * * * * *
38150876 CCTGCTTCTCTGTGTCTCATCAGGAAGCT-GGGTTCGAAGGTTTGCTCGCATGAACTTTGAGTTG
130 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATGAGCGTTGAGTTG
38150940 GCATA
195 GCATA
*
38150945 CTTCTCTGTATCTCATCAGGAAGATGACCG
1 CTTCTCAGTATCTCATCAGGAAGATGACCG
38150975 TCTCAATGTT
Statistics
Matches: 387, Mismatches: 39, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
198 45 0.12
199 20 0.05
200 38 0.10
201 114 0.29
202 1 0.00
205 1 0.00
206 167 0.43
207 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (199 bp):
CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCTCTGATCTCCTC
AGGAAGACGAATTTGGTCCGCTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGAC
CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATGAGCGTTGAGTTGG
CATA
Found at i:38151494 original size:49 final size:49
Alignment explanation
Indices: 38151254--38151525 Score: 142
Period size: 49 Copynumber: 5.5 Consensus size: 49
38151244 ACTAGATTTG
* * * * * *
38151254 CCGTTGCGGCTTAAATTTTTCCCGTCATATCTTCATGGTACT-AGATTTA
1 CCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCGTGGTACTGA-ATTCA
** * * * *
38151303 CCGTTATGGCTTAAATCTTTCCCTTATTGTCTTCTGAGGTAC--AAGGTCTG
1 CCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTC-GTGGTACTGAA-TTC-A
* * * * * *
38151353 CCGTTGCGACTTAGACCTTTCCCTT-TTGTATCTT-GTGGTACTGGATCCG
1 CCGTTGCGGCTTAAATCTTTCCCTTCTTG--TCTTCGTGGTACTGAATTCA
* * * * * ** *
38151402 CCGTTGCAGTCTTAGATCTTTCCATCCATGTCTTTATGATACTGAATTCA
1 CCGTTGC-GGCTTAAATCTTTCCCTTCTTGTCTTCGTGGTACTGAATTCA
* * *
38151452 CCGTTGCGGCTTAAATCTTTCTCTTCTTGTCTTCGTGGTACTGGA-TCTG
1 CCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCGTGGTACTGAATTC-A
* *
38151501 CCGTTGTGGTCTTAGATCTTTCCCT
1 CCGTTGCGG-CTTAAATCTTTCCCT
38151526 GTCAAACCTG
Statistics
Matches: 166, Mismatches: 45, Indels: 23
0.71 0.19 0.10
Matches are distributed among these distances:
48 3 0.02
49 86 0.52
50 70 0.42
51 7 0.04
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (49 bp):
CCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCGTGGTACTGAATTCA
Found at i:38152466 original size:105 final size:99
Alignment explanation
Indices: 38152304--38152512 Score: 222
Period size: 105 Copynumber: 2.1 Consensus size: 99
38152294 CATGATCGCA
** **
38152304 AGGTGAATGAATTTCATGGAGGCAAAGCTCACAAAAGGTTTAAAAATGACATGTATTGGTCAAAA
1 AGGTGAATGAATTTCATGGAGGCAAAGCTCACAAAAAATTTAAAAATGACACATATTGGTCAAAA
* * *
38152369 GTTGCAAAACCTAAGGTGAACAAAGAA-TGAGGTT
66 GATGCAAAACATAAAGTGAACAAAGAATTG-GGTT
* * *
38152403 AGGTGAATGAATTTTATTGGAGGCAAAGCTCACATGAATGAAATATTAAAAGTGACCCATATTGG
1 AGGTGAATGAATTTCA-TGGAGGCAAAGCTCACA--AA--AAAT-TTAAAAATGACACATATTGG
* * * *
38152468 TTAAAGGATGCCAAACATAAAGTGAGCAAAGAATTGGGTT
60 TCAAAAGATGCAAAACATAAAGTGAACAAAGAATTGGGTT
38152508 AGGTG
1 AGGTG
38152513 CCCCATATAT
Statistics
Matches: 89, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
99 15 0.17
100 17 0.19
102 2 0.02
104 2 0.02
105 51 0.57
106 2 0.02
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (99 bp):
AGGTGAATGAATTTCATGGAGGCAAAGCTCACAAAAAATTTAAAAATGACACATATTGGTCAAAA
GATGCAAAACATAAAGTGAACAAAGAATTGGGTT
Found at i:38152790 original size:13 final size:11
Alignment explanation
Indices: 38152766--38152835 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 11
38152756 TCGACCTCTC
38152766 CTTTTCTTTTTCT
1 CTTTT-TTTTT-T
*
38152779 CTCTTTTTTTT
1 CTTTTTTTTTT
38152790 CTTTTTTTTTT
1 CTTTTTTTTTT
* *
38152801 -TTTGCTTTCTT
1 CTTT-TTTTTTT
38152812 CTTCTTCTTTTTT
1 CTT-TT-TTTTTT
38152825 CTTTTCTTTTT
1 CTTTT-TTTTT
38152836 ATTCATTGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
10 3 0.06
11 16 0.34
12 15 0.32
13 13 0.28
ACGTcount: A:0.00, C:0.19, G:0.01, T:0.80
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:38152811 original size:28 final size:27
Alignment explanation
Indices: 38152767--38152829 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
38152757 CGACCTCTCC
* * *
38152767 TTTTCTTTTTCTCTCTTTTTTTTCTTT
1 TTTTTTTTTTCTCTCTTCTTCTTCTTT
*
38152794 TTTTTTTTTTGCTTTCTTCTTCTTCTTT
1 TTTTTTTTTT-CTCTCTTCTTCTTCTTT
*
38152822 TTTCTTTT
1 TTTTTTTT
38152830 CTTTTTATTC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (27 bp):
TTTTTTTTTTCTCTCTTCTTCTTCTTT
Found at i:38155594 original size:117 final size:117
Alignment explanation
Indices: 38155388--38155621 Score: 459
Period size: 117 Copynumber: 2.0 Consensus size: 117
38155378 ACAATACTAA
38155388 GTGAGAGTCCAGGACCGATGCCTATTCCTTTTAACATCAAGTAAGTCAAAATATTCTTGATTAGA
1 GTGAGAGTCCAGGACCGATGCCTATTCCTTTTAACATCAAGTAAGTCAAAATATTCTTGATTAGA
*
38155453 CATCTGCCTTGTTTGGTCTTCCATATTTCATTGAACTCTAGCTTTTATGTAC
66 CATCTGCCTTGTTTGGTCTTCCATATTTCATTCAACTCTAGCTTTTATGTAC
38155505 GTGAGAGTCCAGGACCGATGCCTATTCCTTTTAACATCAAGTAAGTCAAAATATTCTTGATTAGA
1 GTGAGAGTCCAGGACCGATGCCTATTCCTTTTAACATCAAGTAAGTCAAAATATTCTTGATTAGA
38155570 CATCTGCCTTGTTTGGTCTTCCATATTTCATTCAACTCTAGCTTTTATGTAC
66 CATCTGCCTTGTTTGGTCTTCCATATTTCATTCAACTCTAGCTTTTATGTAC
38155622 TTGGGTGCAA
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
117 116 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.38
Consensus pattern (117 bp):
GTGAGAGTCCAGGACCGATGCCTATTCCTTTTAACATCAAGTAAGTCAAAATATTCTTGATTAGA
CATCTGCCTTGTTTGGTCTTCCATATTTCATTCAACTCTAGCTTTTATGTAC
Found at i:38160056 original size:29 final size:29
Alignment explanation
Indices: 38160024--38160089 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
38160014 GACATCCGGG
38160024 GGTTAAAACGTAATTTTGAGAAGTTTCAA
1 GGTTAAAACGTAATTTTGAGAAGTTTCAA
* *
38160053 GGTTAAAATGTAATTTTGGGAAGTTTCAA
1 GGTTAAAACGTAATTTTGAGAAGTTTCAA
*
38160082 GGTAAAAA
1 GGTTAAAA
38160090 ATATAATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (29 bp):
GGTTAAAACGTAATTTTGAGAAGTTTCAA
Found at i:38160097 original size:30 final size:30
Alignment explanation
Indices: 38160034--38160186 Score: 100
Period size: 29 Copynumber: 5.2 Consensus size: 30
38160024 GGTTAAAACG
* * *
38160034 TAATTTTGAGAAGTTTCAAGGT-TAAAATG
1 TAATTTTGGGAAGTTTCAAGGTAAAAAATA
38160063 TAATTTTGGGAAGTTTCAAGGTAAAAAATA
1 TAATTTTGGGAAGTTTCAAGGTAAAAAATA
*** * * ** *
38160093 TAATTTTCAAAAGTTT--TGGGATTGAAATG
1 TAATTTTGGGAAGTTTCAAGGTA-AAAAATA
* *
38160122 TAATTTTGGGAAGGTTT-AGGGTCAAAAATA
1 TAATTTTGGGAA-GTTTCAAGGTAAAAAATA
* * **
38160152 TAATTTTCGAAAGTTTCAA-GTTCAAAATA
1 TAATTTTGGGAAGTTTCAAGGTAAAAAATA
38160181 TAATTT
1 TAATTT
38160187 CTGAACAGTT
Statistics
Matches: 94, Mismatches: 25, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
28 3 0.03
29 52 0.55
30 37 0.39
31 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.38
Consensus pattern (30 bp):
TAATTTTGGGAAGTTTCAAGGTAAAAAATA
Found at i:38160107 original size:59 final size:59
Alignment explanation
Indices: 38160034--38160186 Score: 177
Period size: 59 Copynumber: 2.6 Consensus size: 59
38160024 GGTTAAAACG
* *
38160034 TAATTTTGAGAAGTTTCAAGGTTAAAATGTAATTTTGGGAA-GTTTCAAGGTAAAAAATA
1 TAATTTTCAAAAGTTTCAAGGTTAAAATGTAATTTTGGGAAGGTTT-AAGGTAAAAAATA
** * * *
38160093 TAATTTTCAAAAGTTT-TGGGATTGAAATGTAATTTTGGGAAGGTTTAGGGTCAAAAATA
1 TAATTTTCAAAAGTTTCAAGG-TTAAAATGTAATTTTGGGAAGGTTTAAGGTAAAAAATA
* *
38160152 TAATTTTCGAAAGTTTCAA-GTTCAAAATATAATTT
1 TAATTTTCAAAAGTTTCAAGGTT-AAAATGTAATTT
38160187 CTGAACAGTT
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
58 4 0.05
59 70 0.90
60 4 0.05
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.38
Consensus pattern (59 bp):
TAATTTTCAAAAGTTTCAAGGTTAAAATGTAATTTTGGGAAGGTTTAAGGTAAAAAATA
Found at i:38161194 original size:21 final size:21
Alignment explanation
Indices: 38161136--38161218 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
38161126 ACCTTTCATG
*
38161136 TATT-TTATTATTAATA-ATT
1 TATTATTATTATTAAAACATT
38161155 AATATTATTATTA-TAAAACATT
1 --TATTATTATTATTAAAACATT
* *
38161177 TATTAATATTATTAAAACGTT
1 TATTATTATTATTAAAACATT
* *
38161198 TGTTATTATTATCAAAACATT
1 TATTATTATTATTAAAACATT
38161219 AATGCTGCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.19
21 33 0.63
22 9 0.17
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTATTATTATTAAAACATT
Found at i:38161260 original size:11 final size:11
Alignment explanation
Indices: 38161244--38161269 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
38161234 AATTAAATTC
38161244 ATATATATAAT
1 ATATATATAAT
38161255 ATATATATAAT
1 ATATATATAAT
38161266 ATAT
1 ATAT
38161270 TTATTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATATATATAAT
Found at i:38162985 original size:50 final size:50
Alignment explanation
Indices: 38162678--38162995 Score: 194
Period size: 50 Copynumber: 6.5 Consensus size: 50
38162668 CCTTAACCTT
* * * * *
38162678 TCCCTTCATATCTTC-ATGGTGCAGGGTTCGCCATTGCGGCCTCAA-TCC
1 TCCCTTCATATCTTCTAAGGTACTGGGTTCGCCGTTGCGGCCTCAACTTC
* * * ** *
38162726 TTCCCATCATATCTTCTAAGGTA-TCGGGTTCACCATTATGGCCTCAAC-CC
1 -TCCCTTCATATCTTCTAAGGTACT-GGGTTCGCCGTTGCGGCCTCAACTTC
* * *
38162776 TTCCTATCATATCTTCTGAGGTACTGGGTTCGCCGTTGCGGCTTCAACCTT-
1 TCCCT-TCATATCTTCTAAGGTACTGGGTTCGCCGTTGCGGCCTCAA-CTTC
* * * * *
38162827 TCCCTTCAAATC-TCTAGGGTACTAGATTCACCGTTGCGGCCTCAATCTTC
1 TCCCTTCATATCTTCTAAGGTACTGGGTTCGCCGTTGCGGCCTCAA-CTTC
* * * * * * *
38162877 -CCCATCA-A-CTT-TCATGGTACCGGATTTGTCGTTGCGGCCTCAGGCTT-
1 TCCCTTCATATCTTCT-AAGGTACTGGGTTCGCCGTTGCGGCCTCA-ACTTC
* * * *
38162924 T-CCTATTATATCTTCTAAGGTACTGGGTTTGCCGTTGTGGCTTCAACTTC
1 TCCCT-TCATATCTTCTAAGGTACTGGGTTCGCCGTTGCGGCCTCAACTTC
*
38162974 TCCCTTCATATCTT-TATGGTAC
1 TCCCTTCATATCTTCTAAGGTAC
38162996 CGAATTCTCC
Statistics
Matches: 207, Mismatches: 44, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
47 4 0.02
48 30 0.14
49 64 0.31
50 99 0.48
51 10 0.05
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (50 bp):
TCCCTTCATATCTTCTAAGGTACTGGGTTCGCCGTTGCGGCCTCAACTTC
Found at i:38163414 original size:345 final size:345
Alignment explanation
Indices: 38162764--38163446 Score: 943
Period size: 345 Copynumber: 2.0 Consensus size: 345
38162754 TTCACCATTA
* * * *
38162764 TGGCCTCAACCCTTCCTATCATATCTTCTGAGGTACTGGGTTCGCCGTTGCGGCTTCAACCTTTC
1 TGGCCTCAACCCTTCCCATCATATCTTCTAAGGTACTGGGTTCGCCATTGCAGCTTCAACCTTTC
* * *
38162829 CCTTCAAATCTCTAGGGTACTAGATTCACCGTTGCGGCCTCAATCTTCCCCATCAACTTTCATGG
66 CCTCCAAATCTCTAGGGTACTAGAGTCACCATTGCGGCCTCAATCTTCCCCATCAACTTTCATGG
* * * * * * **
38162894 TACCGGATTTGTCGTTGCGGCCTCAGGCTTTCCTATTATATCTTCTAAGGTACTGGGTTTGCCGT
131 TACCGAATTTATCGTTACGGCCTCAAGCCTTCCCATTATATCTTCTAAGGTACTGGGTTCCCCGT
* * * * * * *
38162959 TGTGGCTTCAACTTCTCCCTTCATATCTTTATGGTACCGAATTCTCCGTTGTGGCCTAAATCCTT
196 TGTGACTTCAACCTCCCCCTTCATATCTTCATGGTACCGAATTCGCCATTGCGGCCTAAATCCTT
* ** ** *
38163024 CCCATAACATCTTCTGAGGTATCGGGTTCGTTATTACGACCTCAACCTTTCCCTCTATATCTTCG
261 CCAATAACATCTTCTGAGGTATCGGGTTCGCCACCACGACCTCAACCTTTCCCTCCATATCTTCG
*
38163089 TGGTACCATATTCATCGTTC
326 TGGTACCAGATTCATCGTTC
* * *
38163109 TGGCTTCAACCCTTCCCATCATATGTTCTAAGGTATTGGGTTCGCCATTGCAGCTTCAACCTTTC
1 TGGCCTCAACCCTTCCCATCATATCTTCTAAGGTACTGGGTTCGCCATTGCAGCTTCAACCTTTC
** *
38163174 CCTCCAAATCTCTAGGGTACTAGAGTCGTCATTGCGGCCTTAATCTTCCCCATCAACTTTCATGG
66 CCTCCAAATCTCTAGGGTACTAGAGTCACCATTGCGGCCTCAATCTTCCCCATCAACTTTCATGG
* * *
38163239 TACCGAATTTATCGTTACGGCCTCAATCCTTCCCATTATATCTTTTAAGGTATTGGGTTCCCCGT
131 TACCGAATTTATCGTTACGGCCTCAAGCCTTCCCATTATATCTTCTAAGGTACTGGGTTCCCCGT
* * * *
38163304 TGTGACTTCAACCTCCCCCTTCATATCTTCATGGTATCGGATTCGCCATTGCGTCCTCAATCCTT
196 TGTGACTTCAACCTCCCCCTTCATATCTTCATGGTACCGAATTCGCCATTGCGGCCTAAATCCTT
* * * * *
38163369 CCAATCACATCTTTTGAGGTATCGGGTTCGCCACCGCGGCCTCAACCTTTCCCTCCATATCTTTG
261 CCAATAACATCTTCTGAGGTATCGGGTTCGCCACCACGACCTCAACCTTTCCCTCCATATCTTCG
38163434 TGGTACCAGATTC
326 TGGTACCAGATTC
38163447 GCTGTTGTAA
Statistics
Matches: 291, Mismatches: 47, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
345 291 1.00
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (345 bp):
TGGCCTCAACCCTTCCCATCATATCTTCTAAGGTACTGGGTTCGCCATTGCAGCTTCAACCTTTC
CCTCCAAATCTCTAGGGTACTAGAGTCACCATTGCGGCCTCAATCTTCCCCATCAACTTTCATGG
TACCGAATTTATCGTTACGGCCTCAAGCCTTCCCATTATATCTTCTAAGGTACTGGGTTCCCCGT
TGTGACTTCAACCTCCCCCTTCATATCTTCATGGTACCGAATTCGCCATTGCGGCCTAAATCCTT
CCAATAACATCTTCTGAGGTATCGGGTTCGCCACCACGACCTCAACCTTTCCCTCCATATCTTCG
TGGTACCAGATTCATCGTTC
Found at i:38166908 original size:52 final size:52
Alignment explanation
Indices: 38166836--38167183 Score: 525
Period size: 52 Copynumber: 6.7 Consensus size: 52
38166826 AATGAAAAAG
** *
38166836 GGTCCGATAACTATGTGTCATCGTGAGTATTTGAATCCTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * *
38166888 GGTTCGATGGCTATGTGTCATCATGAGTATATGAACCCTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * *
38166940 GGTCCGATGGCTATGTGTCATCATGAGTATATGAACCCTTTACGAATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * *
38166992 GGTCCGATAGCTATGTGTCATTGTGAGTATATGAATCTTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
38167044 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
38167096 GGTTCGATGGCTATGTGTCATCGTGAGTATATGAATCTTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * * *
38167148 GGTCCGGTTGCAATGTGTCATTGTGAGTATATGAAT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAAT
38167184 GAAATGAAAT
Statistics
Matches: 270, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 270 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (52 bp):
GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:38171927 original size:52 final size:52
Alignment explanation
Indices: 38171839--38171978 Score: 217
Period size: 52 Copynumber: 2.7 Consensus size: 52
38171829 AATGAAAAAG
* * *
38171839 GGTCTGATGACTATGTGTCATAGTGAGTATATGAATCCTTTACGGATTATAA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAA
* * *
38171891 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACTGATTGTGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAA
*
38171943 GGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAAT
38171979 GAAATGAAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.36
Consensus pattern (52 bp):
GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAA
Found at i:38187861 original size:7 final size:7
Alignment explanation
Indices: 38187851--38187920 Score: 50
Period size: 7 Copynumber: 11.0 Consensus size: 7
38187841 ATTAAATTAA
38187851 ATTAAAT
1 ATTAAAT
38187858 ATTAAAT
1 ATTAAAT
38187865 ATTAAATT
1 ATTAAA-T
*
38187873 AATATAAT
1 ATTA-AAT
38187881 ATT---T
1 ATTAAAT
38187885 ATTAAA-
1 ATTAAAT
38187891 A-TAAAT
1 ATTAAAT
38187897 ATT-AA-
1 ATTAAAT
38187902 ATTAAAT
1 ATTAAAT
38187909 -TT-AAT
1 ATTAAAT
38187914 ATTAAAT
1 ATTAAAT
38187921 CCTATTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 22
0.68 0.03 0.30
Matches are distributed among these distances:
4 4 0.08
5 10 0.20
6 10 0.20
7 17 0.34
8 7 0.14
9 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATTAAAT
Found at i:38187894 original size:56 final size:57
Alignment explanation
Indices: 38187831--38187945 Score: 169
Period size: 56 Copynumber: 2.0 Consensus size: 57
38187821 TGTTTATCAA
* *
38187831 TAAAATAAACATTAAATTAAATTAAATATTAAA-TATTAAATTAATATAATATTTAT
1 TAAAATAAACATTAAATTAAATTAAATATTAAACTATTAAAATAATACAATATTTAT
* *
38187887 TAAAATAAATATTAAATTAAATTTAATATTAAATCCTATTAAAATAATACAATATTTAT
1 TAAAATAAACATTAAATTAAATTAAATATTAAA--CTATTAAAATAATACAATATTTAT
38187946 CTACAATATT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 31 0.60
59 21 0.40
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (57 bp):
TAAAATAAACATTAAATTAAATTAAATATTAAACTATTAAAATAATACAATATTTAT
Found at i:38188010 original size:97 final size:96
Alignment explanation
Indices: 38187889--38188137 Score: 382
Period size: 97 Copynumber: 2.6 Consensus size: 96
38187879 ATATTTATTA
* *
38187889 AAATAAATATTAAATTAAATTTAATATTAAATCCTATTAAAATAATACAATATTTATCTACAATA
1 AAATAAATATTAAATTTAATTTAATATTAAATCATATTAAAATAATACAATATTTATCTACAATA
*
38187954 TTAATTATTTCAAAAATAATATTATTTTAAT
66 TTAACTATTTCAAAAATAATATTATTTTAAT
*
38187985 AAGATAAATATTAAATTTAATTTAATATTAAATCTTATTAAAATAATACAATATTTATCTACAAT
1 AA-ATAAATATTAAATTTAATTTAATATTAAATCATATTAAAATAATACAATATTTATCTACAAT
38188050 ATTAACTATTTCAAAAATAATATTATTTTAAT
65 ATTAACTATTTCAAAAATAATATTATTTTAAT
* * *
38188082 --A-AAAT-TTAATTTTAAATTTAATATTAAAT-ATTTTTAAATAATACAATATTTATCTA
1 AAATAAATATTAAATTT-AATTTAATATTAAATCATATTAAAATAATACAATATTTATCTA
38188138 TAGGATAAAC
Statistics
Matches: 144, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
92 31 0.22
93 19 0.13
94 1 0.01
96 2 0.01
97 91 0.63
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (96 bp):
AAATAAATATTAAATTTAATTTAATATTAAATCATATTAAAATAATACAATATTTATCTACAATA
TTAACTATTTCAAAAATAATATTATTTTAAT
Found at i:38188178 original size:93 final size:92
Alignment explanation
Indices: 38187876--38188180 Score: 285
Period size: 97 Copynumber: 3.2 Consensus size: 92
38187866 TTAAATTAAT
* * * **
38187876 ATAATATT-TATTAAAATAAATATTAAATTAAATTTAATATTAAATCCTATTAAAATAATACAAT
1 ATAATATTAAATTAATA-AAATATTAAATTTAATTTAATATTAAATATTATTAAAATAATACAAT
* * *
38187940 ATTTATCTACAATATTAATTATTTCAAAA
65 ATTTATCTACAAGATAAACTATTT-AAAA
** *
38187969 ATAATATTATTTTAATAAGATAAATATTAAATTTAATTTAATATTAAATCTTATTAAAATAATAC
1 ATAATATTAAATTAAT---A-AAATATTAAATTTAATTTAATATTAAATATTATTAAAATAATAC
* *
38188034 AATATTTATCTACAATATTAACTATTTCAAAA
62 AATATTTATCTACAAGATAAACTATTT-AAAA
** * *
38188066 ATAATATTATTTTAATAAAAT-TTAATTTTAAATTTAATATTAAATATT-TTTAAATAATACAAT
1 ATAATATTAAATTAATAAAATATTAAATTT-AATTTAATATTAAATATTATTAAAATAATACAAT
* * *
38188129 ATTTATCTATAGGATAAACATTAATTT-AAT
65 ATTTATCTACAAGATAAAC--T-ATTTAAAA
* *
38188159 GTAATATTAAATTATTAAAATA
1 ATAATATTAAATTAATAAAATA
38188181 ATATTATTTT
Statistics
Matches: 186, Mismatches: 17, Indels: 17
0.85 0.08 0.08
Matches are distributed among these distances:
92 36 0.19
93 48 0.26
94 7 0.04
95 4 0.02
97 91 0.49
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (92 bp):
ATAATATTAAATTAATAAAATATTAAATTTAATTTAATATTAAATATTATTAAAATAATACAATA
TTTATCTACAAGATAAACTATTTAAAA
Found at i:38197203 original size:26 final size:27
Alignment explanation
Indices: 38197174--38197232 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
38197164 AATATTAAAT
*
38197174 TATTTATATAA-TTGTATTATATATTA
1 TATTTATAAAATTTGTATTATATATTA
* * *
38197200 TATTTTTAAAATTTGTATTTTCTATTA
1 TATTTATAAAATTTGTATTATATATTA
*
38197227 TTTTTA
1 TATTTA
38197233 ATGTTGTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (27 bp):
TATTTATAAAATTTGTATTATATATTA
Found at i:38199250 original size:62 final size:62
Alignment explanation
Indices: 38199173--38199293 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 62
38199163 ATCACTCCAG
*
38199173 ATATGTCGCGCTTGAGTTGTAACAAAGCCAATTGTCAATTGTTATGTTGATGAAACTTGTCT
1 ATATGTCGCGCTTGAGTTGTAACAAAACCAATTGTCAATTGTTATGTTGATGAAACTTGTCT
* *
38199235 ATATGTCGTGCTTGAGTTGTAACAAAACCAATTGTCAATTGTTATGTTGATGGAACTTG
1 ATATGTCGCGCTTGAGTTGTAACAAAACCAATTGTCAATTGTTATGTTGATGAAACTTG
38199294 CCTTTCACCA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.37
Consensus pattern (62 bp):
ATATGTCGCGCTTGAGTTGTAACAAAACCAATTGTCAATTGTTATGTTGATGAAACTTGTCT
Found at i:38204079 original size:42 final size:42
Alignment explanation
Indices: 38203950--38204164 Score: 159
Period size: 42 Copynumber: 5.0 Consensus size: 42
38203940 TCAACAGGAA
* * * *
38203950 GATGGCTTCAATCTGCCCCTCTTGACTAAGGGTAAAAGATTGGA-
1 GATGTCTTCAATCTG--CCTCATGA-TTAGGGTAAGAGATTGGAT
* *
38203994 -AT-TCTTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGGAT
1 GATGTCTTCAATCTG--CCTCATGA-TTA-GGGTAAGAGATTGGAT
* *
38204038 AAGGTCTTCAATCTGCCTCATGATTAGGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCTCATGATTAGGGTAAGAGATTGGAT
* * * ** *
38204080 GATGTTTTCAATTTGCCCCATGATCGGGGTAAGAGATTAGAT
1 GATGTCTTCAATCTGCCTCATGATTAGGGTAAGAGATTGGAT
* * * * *
38204122 GATTTTTTTAATCTACC-CTATGATTGGGGTAAGAGATTGGAT
1 GATGTCTTCAATCTGCCTC-ATGATTAGGGTAAGAGATTGGAT
38204164 G
1 G
38204165 GTGACGTAAC
Statistics
Matches: 146, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 106 0.73
43 20 0.14
44 7 0.05
45 1 0.01
46 11 0.08
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (42 bp):
GATGTCTTCAATCTGCCTCATGATTAGGGTAAGAGATTGGAT
Found at i:38204791 original size:98 final size:98
Alignment explanation
Indices: 38204495--38205032 Score: 661
Period size: 98 Copynumber: 5.4 Consensus size: 98
38204485 CCTTTTATGT
* * * ** *
38204495 TTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCATTCCCTTTAAATCTTCGTGGTACTAGAT
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGAT
* *
38204560 TCGCCGTTATGGCTTAAATCTTTCCCATCAT-A
66 TCGCCGTTATGGCTTAAATCTTTCCCTTCATGC
* * ** * **
38204592 TCCTTGTGGTACTGAA--TTTACCGTTGCGGCTTAAGTCTTTCCCTTCATATCATATCTTCGTGG
1 TTC-TGAGGTAC--AAGGTTCGCCGTTGCGACTTAAACCTTTCCC-TC----CATATCTTCGTGG
*
38204655 TACTAGATTCGCCGTTGCT-GCTTAAATCTTTCCCTTCATGC
58 TACTAGATTCGCCGTT-ATGGCTTAAATCTTTCCCTTCATGC
*
38204696 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGAT
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGAT
*
38204761 TCGCCGTTATGACTTAAATCTTTCCCTTCATGC
66 TCGCCGTTATGGCTTAAATCTTTCCCTTCATGC
* * *
38204794 TTCTGAGGTACAAGGTTCGCTGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTAGAT
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGAT
* ** *
38204859 TCACCGTTGCGGCTTAAATCTTTCCCTTCACGC
66 TCGCCGTTATGGCTTAAATCTTTCCCTTCATGC
* * *
38204892 TTCTGAGGTACAAGGTTCGCTGTTGTGACTTAAACCTTTCCCTCCATATCTTTGTGGTACTAGAT
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGAT
* * * *
38204957 ACACCGTTACGGCTTCAATCTTTCCCTTCATGC
66 TCGCCGTTATGGCTTAAATCTTTCCCTTCATGC
**
38204990 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATTTTTCCCT
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT
38205033 TCATGTTGCG
Statistics
Matches: 381, Mismatches: 47, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
97 3 0.01
98 293 0.77
99 1 0.00
100 2 0.01
101 2 0.01
102 2 0.01
103 75 0.20
104 3 0.01
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (98 bp):
TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGAT
TCGCCGTTATGGCTTAAATCTTTCCCTTCATGC
Found at i:38205034 original size:49 final size:49
Alignment explanation
Indices: 38204495--38205037 Score: 397
Period size: 49 Copynumber: 11.0 Consensus size: 49
38204485 CCTTTTATGT
* * * * *
38204495 TTCTAAGGTACAAGGTTCGTCGTTGCGACTTAAACCATTCCCTTTAAAT-C
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCC-TT-CATGC
* * * ** * * *
38204545 TTC-GTGGTACTAGATTCGCCGTTATGGCTTAAATCTTTCCCATCAT-A
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATGC
* * ** * * *
38204592 TCCTTGTGGTACTGAA--TTTACCGTTGCGGCTTAAGTCTTTCCCTTCATATC
1 TTC-TGAGGTAC--AAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCAT-GC
* * *
38204643 ATATCTTCGTGGTACTAGATTCGCCGTTGCTG-CTTAAATCTTTCCCTTCATGC
1 -T-TC-T-GAGGTACAAGGTTCGCCGTTGC-GACTTAAATCTTTCCCTTCATGC
* * *
38204696 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATC
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCAT-GC
* * **
38204746 TTC-GTGGTAC-TGGATTCGCCGTTATGACTTAAATCTTTCCCTTCATGC
1 TTCTGAGGTACAAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGC
* *
38204794 TTCTGAGGTACAAGGTTCGCTGTTGCGACTTAAACCTTTCCCTTCAAAT-C
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTC--ATGC
* * * * * *
38204844 TTC-GTGGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCACGC
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATGC
* * * * *
38204892 TTCTGAGGTACAAGGTTCGCTGTTGTGACTTAAACCTTTCCCTCCATATC
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCAT-GC
* * * * * * * *
38204942 TT-TGTGGTACTAGATACACCGTTACGGCTTCAATCTTTCCCTTCATGC
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATGC
*
38204990 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATTTTTCCCTTCATG
1 TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATG
38205038 TTGCGACTTA
Statistics
Matches: 382, Mismatches: 88, Indels: 47
0.74 0.17 0.09
Matches are distributed among these distances:
47 5 0.01
48 15 0.04
49 298 0.78
50 17 0.04
51 5 0.01
52 3 0.01
53 4 0.01
54 34 0.09
55 1 0.00
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (49 bp):
TTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTCATGC
Found at i:38205047 original size:26 final size:26
Alignment explanation
Indices: 38205011--38205061 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
38205001 AAGGTTCGCC
**
38205011 GTTGCGACTTAAATTTTTCCCTTCAT
1 GTTGCGACTTAAACCTTTCCCTTCAT
38205037 GTTGCGACTTAAACCTTTCCCTTCA
1 GTTGCGACTTAAACCTTTCCCTTCA
38205062 AATCTTCGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (26 bp):
GTTGCGACTTAAACCTTTCCCTTCAT
Found at i:38205137 original size:124 final size:124
Alignment explanation
Indices: 38204912--38205147 Score: 366
Period size: 124 Copynumber: 1.9 Consensus size: 124
38204902 CAAGGTTCGC
* * * *
38204912 TGTTGTGACTTAAACCTTTCCCTCCATATCTTTGTGGTACTAGATACACCGTTACGGCTTCAATC
1 TGTTGCGACTTAAACCTTTCCCTCCAAATCTTCGTGGTACTAGATACACCGTTACGACTTCAATC
*
38204977 TTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAATTTTTCCCTTCA
66 TTTCCCTTCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAATTTTTCCCTTCA
* * **
38205036 TGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTAGATTCGTCGTTACGACTT-ATAT
1 TGTTGCGACTTAAACCTTTCCCTCCAAATCTTCGTGGTACTAGATACACCGTTACGACTTCA-AT
*
38205100 CTTTCCCTTCATGCTTCTGAGGTACAAGTTTCACCGTTGCGACTTAAA
65 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAA
38205148 CCTTTCCTCC
Statistics
Matches: 101, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
123 1 0.01
124 100 0.99
ACGTcount: A:0.20, C:0.26, G:0.16, T:0.38
Consensus pattern (124 bp):
TGTTGCGACTTAAACCTTTCCCTCCAAATCTTCGTGGTACTAGATACACCGTTACGACTTCAATC
TTTCCCTTCATGCTTCTGAGGTACAAGGTTCACCGTTGCGACTTAAATTTTTCCCTTCA
Found at i:38205143 original size:49 final size:48
Alignment explanation
Indices: 38205037--38205154 Score: 130
Period size: 49 Copynumber: 2.4 Consensus size: 48
38205027 TTCCCTTCAT
* * **
38205037 GTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTAGATTCGTC
1 GTTGCGACTTAAACCTTTCCCTTC-AATCTTCGAGGTACAAGATTCACC
* * * *
38205086 GTTACGACTTATATCTTTCCCTTC-ATGCTTCTGAGGTACAAGTTTCACC
1 GTTGCGACTTAAACCTTTCCCTTCAAT-CTTC-GAGGTACAAGATTCACC
38205135 GTTGCGACTTAAACCTTTCC
1 GTTGCGACTTAAACCTTTCC
38205155 TCCATATCCT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
47 2 0.04
48 4 0.07
49 50 0.89
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.37
Consensus pattern (48 bp):
GTTGCGACTTAAACCTTTCCCTTCAATCTTCGAGGTACAAGATTCACC
Found at i:38206091 original size:10 final size:10
Alignment explanation
Indices: 38206076--38206108 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
38206066 CTCCTTTTTA
38206076 TTTTTTCTTT
1 TTTTTTCTTT
38206086 TTTTTTCTTT
1 TTTTTTCTTT
38206096 ATTTTTTCTTT
1 -TTTTTTCTTT
38206107 TT
1 TT
38206109 GGGTAAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:38206100 original size:11 final size:11
Alignment explanation
Indices: 38206072--38206106 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
38206062 AACTCTCCTT
38206072 TTTATTTTTTC
1 TTTATTTTTTC
38206083 TTT-TTTTTTC
1 TTTATTTTTTC
38206093 TTTATTTTTTC
1 TTTATTTTTTC
38206104 TTT
1 TTT
38206107 TTGGGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTATTTTTTC
Found at i:38207005 original size:51 final size:52
Alignment explanation
Indices: 38206928--38207034 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 52
38206918 CATATATAGA
* * ** * *
38206928 TTTTTCAAGATGCCCTTTGCGGGTTTTCATC-TTGA-CTTTCTTTTTCTTTTT
1 TTTTTAAAGATGCCCTTTACAAGTTTTCATCTTTGACCTTT-TCTTTCCTTTT
38206979 TTTTTAAAGATGCCCTTTACAAGTTTTCATCTTTGACCTTTTCTTTCCTTTT
1 TTTTTAAAGATGCCCTTTACAAGTTTTCATCTTTGACCTTTTCTTTCCTTTT
38207031 TTTT
1 TTTT
38207035 CTTTTTTTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 27 0.56
52 17 0.35
53 4 0.08
ACGTcount: A:0.13, C:0.20, G:0.10, T:0.57
Consensus pattern (52 bp):
TTTTTAAAGATGCCCTTTACAAGTTTTCATCTTTGACCTTTTCTTTCCTTTT
Found at i:38213521 original size:11 final size:11
Alignment explanation
Indices: 38213455--38213526 Score: 54
Period size: 11 Copynumber: 6.5 Consensus size: 11
38213445 AGAAAAAAAA
*
38213455 ATTATTTTCTT
1 ATTATTTTGTT
* * *
38213466 GTTATTTTCTC
1 ATTATTTTGTT
*
38213477 GTTATTTTGTT
1 ATTATTTTGTT
* * *
38213488 GTCATTTTATT
1 ATTATTTTGTT
*
38213499 ATTATGTTGTT
1 ATTATTTTGTT
*
38213510 ACTATTTTGTT
1 ATTATTTTGTT
38213521 ATTATT
1 ATTATT
38213527 GTTTGAATAT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 48 1.00
ACGTcount: A:0.17, C:0.07, G:0.10, T:0.67
Consensus pattern (11 bp):
ATTATTTTGTT
Found at i:38216949 original size:20 final size:21
Alignment explanation
Indices: 38216921--38216959 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38216911 TTACAAAAAT
38216921 CTTAAATTTTGGG-GGACCTA
1 CTTAAATTTTGGGAGGACCTA
*
38216941 CTTATATTTTGGGAGGACC
1 CTTAAATTTTGGGAGGACC
38216960 ATAGTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (21 bp):
CTTAAATTTTGGGAGGACCTA
Found at i:38221010 original size:21 final size:21
Alignment explanation
Indices: 38220981--38221020 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38220971 TCCACCAATC
38220981 GGGTACACCG-CTGTCCGAACT
1 GGGTACACCGAC-GTCCGAACT
*
38221002 GGGTGCACCGACGTCCGAA
1 GGGTACACCGACGTCCGAA
38221021 TGCCTTACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.20, C:0.33, G:0.33, T:0.15
Consensus pattern (21 bp):
GGGTACACCGACGTCCGAACT
Found at i:38221787 original size:30 final size:31
Alignment explanation
Indices: 38221753--38221817 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
38221743 CTTGAATCAG
*
38221753 TTGTTTTCAAT-TTGT-T-ACTATTTATTGTTA
1 TTGTTTTAAATATTGTATAACTA-TTATT-TTA
38221783 TTG-TTTAAATATTGTATAACTATTATTTTA
1 TTGTTTTAAATATTGTATAACTATTATTTTA
38221813 TTGTT
1 TTGTT
38221818 AATTTTGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
29 6 0.20
30 13 0.43
31 7 0.23
32 4 0.13
ACGTcount: A:0.25, C:0.05, G:0.09, T:0.62
Consensus pattern (31 bp):
TTGTTTTAAATATTGTATAACTATTATTTTA
Found at i:38233835 original size:20 final size:22
Alignment explanation
Indices: 38233801--38233841 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
38233791 CAGTAAATGA
38233801 TTTTAAATTATTAAAATTATTT
1 TTTTAAATTATTAAAATTATTT
38233823 TTTTAAA-TA-TAAAATTATT
1 TTTTAAATTATTAAAATTATT
38233842 AAATAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTAAATTATTAAAATTATTT
Found at i:38234962 original size:28 final size:30
Alignment explanation
Indices: 38234932--38235002 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 30
38234922 ATTAAAATTA
38234932 TTTAATAATTTTAT-TATTT-AAAAAATAAT
1 TTTAATAATTTTATAT-TTTAAAAAAATAAT
38234961 TTTAA-AATTTTATATTTTAAAAAAATAAT
1 TTTAATAATTTTATATTTTAAAAAAATAAT
*
38234990 TTTAATTATTTTA
1 TTTAATAATTTTA
38235003 AAATCATTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
28 11 0.29
29 21 0.55
30 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTAATAATTTTATATTTTAAAAAAATAAT
Found at i:38234993 original size:14 final size:14
Alignment explanation
Indices: 38234951--38234994 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
38234941 TTTATTATTT
38234951 AAAAAATAATTTTA
1 AAAAAATAATTTTA
***
38234965 AAATTTTATATTTTA
1 AAAAAATA-ATTTTA
38234980 AAAAAATAATTTTA
1 AAAAAATAATTTTA
38234994 A
1 A
38234995 TTATTTTAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAAATAATTTTA
Found at i:38243864 original size:13 final size:13
Alignment explanation
Indices: 38243842--38243876 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
38243832 ACCCATATTA
*
38243842 ATTTTTTTAGATT
1 ATTTTATTAGATT
38243855 ATTTTATTAGATT
1 ATTTTATTAGATT
38243868 ATTTTATTA
1 ATTTTATTA
38243877 TATACAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (13 bp):
ATTTTATTAGATT
Found at i:38246199 original size:45 final size:44
Alignment explanation
Indices: 38246134--38246226 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 44
38246124 TTAAAGCTTG
*
38246134 AAAATTTTTACTAGTTTGGTACAAAATTGCAGGTTCGTCTCCAA
1 AAAATTTTTACTAGTCTGGTACAAAATTGCAGGTTCGTCTCCAA
38246178 AAAATTTTTTACTAGTCTGGTACAAAATTGCAGGTTCGTCTCCAA
1 AAAA-TTTTTACTAGTCTGGTACAAAATTGCAGGTTCGTCTCCAA
38246223 AAAA
1 AAAA
38246227 AATTACAGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (44 bp):
AAAATTTTTACTAGTCTGGTACAAAATTGCAGGTTCGTCTCCAA
Found at i:38247121 original size:48 final size:48
Alignment explanation
Indices: 38247050--38247172 Score: 167
Period size: 48 Copynumber: 2.6 Consensus size: 48
38247040 GATTTGGTCT
* *
38247050 ACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTG-TTTTAATCC
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGCTTTT-ACCC
* * * *
38247098 ACTTCTCTGTATATCATCAGGAAGGTGACCGCTTTATTGCTTTTACCC
1 ACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGCTTTTACCC
*
38247146 ACTTCTCTGTATCTCATCAAGAAGATG
1 ACTTCTCTGTATCTCATCAGGAAGATG
38247173 GGGGTTTGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
48 61 0.94
49 4 0.06
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.35
Consensus pattern (48 bp):
ACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGCTTTTACCC
Found at i:38247181 original size:172 final size:172
Alignment explanation
Indices: 38246983--38247293 Score: 498
Period size: 172 Copynumber: 1.8 Consensus size: 172
38246973 TTCTCTCCGT
* *
38246983 TATCTCATCAAAAAGATGGAGGTTTGAAGTTCCGCTCATATTGAG-TTTCGCTTCATCGATTTGG
1 TATCTCATCAAAAAGATGGAGGTTTGAAGTTCCACTCATATTGAGCTTT-GCTTCATCAATTTGG
* *
38247047 TCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTGTATAT
65 TCTACTTCTCAGTATATCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTATATAT
38247112 CATCAGGAAGGTGACCGCTTTATTGCTTTTACCCACTTCTCTG
130 CATCAGGAAGGTGACCGCTTTATTGCTTTTACCCACTTCTCTG
* * * *
38247155 TATCTCATCAAGAAGATGGGGGTTTGAAGTTTCACTCATATTGAGCTTTGTTTCATCAATTTGGT
1 TATCTCATCAAAAAGATGGAGGTTTGAAGTTCCACTCATATTGAGCTTTGCTTCATCAATTTGGT
* * * *
38247220 TTACTTCTTAGTATATCATCAGGAAGATGACTGCCTCATTGTTTTAATCCACTTCTCTATATCTC
66 CTACTTCTCAGTATATCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTATATATC
38247285 ATCAGGAAG
131 ATCAGGAAG
38247294 ACAGATTTGG
Statistics
Matches: 126, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
172 123 0.98
173 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (172 bp):
TATCTCATCAAAAAGATGGAGGTTTGAAGTTCCACTCATATTGAGCTTTGCTTCATCAATTTGGT
CTACTTCTCAGTATATCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTCTATATATC
ATCAGGAAGGTGACCGCTTTATTGCTTTTACCCACTTCTCTG
Found at i:38247357 original size:85 final size:85
Alignment explanation
Indices: 38247213--38247379 Score: 228
Period size: 85 Copynumber: 2.0 Consensus size: 85
38247203 TGTTTCATCA
* * *
38247213 ATTTGGTTTACTTCTTAGTATATCATCAGGAAGATGACTGCCTCATTGTTTTAATCCACTTCTCT
1 ATTTGGTTCACTTCTTAGTATATCATCAGGAAGATGACTGCCTCATTGCTTTAACCCACTTCTCT
38247278 ATATCTCATCAGGAAGACAG
66 ATATCTCATCAGGAAGACAG
* * * * *
38247298 ATTTGGTTCACTTCTTTGTATCTCATCAGGAAGGTGA-TCGCTTCATTGCTTTGACCCACTTCTC
1 ATTTGGTTCACTTCTTAGTATATCATCAGGAAGATGACT-GCCTCATTGCTTTAACCCACTTCTC
* *
38247362 TGTATCTCATTAGGAAGA
65 TATATCTCATCAGGAAGA
38247380 TGGGGGTTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
84 1 0.01
85 70 0.99
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (85 bp):
ATTTGGTTCACTTCTTAGTATATCATCAGGAAGATGACTGCCTCATTGCTTTAACCCACTTCTCT
ATATCTCATCAGGAAGACAG
Found at i:38247467 original size:209 final size:209
Alignment explanation
Indices: 38247097--38248016 Score: 1179
Period size: 209 Copynumber: 4.4 Consensus size: 209
38247087 TGTTTTAATC
* *
38247097 CACTTCTCTGTATATCATCAGGAAGGTGACCGCTTTATTGCTTTTACCCACTTCTCTGTATCTCA
1 CACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCA
* * * * * * *
38247162 TCAAGAAGATGGGGGTTTGAAGTTTCACTCATATTGAGCTTTGTTTCATCAATTTGGTTTACTTC
66 TCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTT
* * *
38247227 TTAGTATATCATCAGGAAGATGACTGCCTCATTGTTTTAATCCACTTCTCTATATCTCATCAGGA
131 TTAGTATCTCATCAGGAAGATGACCGCCTCATTATTTTAATCCACTTCTCTATATCTCATCAGGA
38247292 AGACAGATTTGGTT
196 AGACAGATTTGGTT
* * *
38247306 CACTTCTTTGTATCTCATCAGGAAGGTGATCGCTTCATTGCTTTGACCCACTTCTCTGTATCTCA
1 CACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCA
* *
38247371 TTAGGAAGATGGGGGTTTAAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTT
66 TCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTT
* * * * *
38247436 TTAGTATCTCATCAAGAAAATAACCGCCTCATTATTTTAATCCACTTCTTTGTATCTCATCAGGA
131 TTAGTATCTCATCAGGAAGATGACCGCCTCATTATTTTAATCCACTTCTCTATATCTCATCAGGA
38247501 AGACAGATTTGGTT
196 AGACAGATTTGGTT
* * *
38247515 TACTTCTCTGTATCTTATCAGGAAGGTGACCGTTTTATTGCTTTGACCCACTTCTCTGTATCTCA
1 CACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCA
* *
38247580 TCAGGAAGATGGGGGTTTGAAGTTTTACTCACATTAAGCTTCGCTTCATCGATTTGGTCTA-TTT
66 TCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTT
* * * *
38247644 CTCAGTATCTCATCAGGAAGATGACCGTCTAATTATTTTAATCTACTTCTCTATATCTCATCAGG
131 -TTAGTATCTCATCAGGAAGATGACCGCCTCATTATTTTAATCCACTTCTCTATATCTCATCAGG
*
38247709 AAGACGGATTTGGTT
195 AAGACAGATTTGGTT
** * * * * * * * *
38247724 CACTTCTCTACATCTCGTCAGGAAGATTACCACTTTATTGCTTCGACCCATTTTTTTGTATCTCA
1 CACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCA
* * ** * *
38247789 TCAAGAAGAT-GGGGTTTTAAGTTTCACTCGTATTGAGCTTTGCTTCATTGATTTGGTCTACTTC
66 TCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTT-
* * * * * * *
38247853 TCT-GTATCTCATTAGGAAGATGATCGTCTCATTGA-TTTAATCCACTTTTCTGTATCTCACCAG
130 TTTAGTATCTCATCAGGAAGATGACCGCCTCATT-ATTTTAATCCACTTCTCTATATCTCATCAG
38247916 GAAGAC-GAATTTGG-T
194 GAAGACAG-ATTTGGTT
* * * * * * *
38247931 CTACTTCTCTGTATCTCATAAGGAAGATGACCGTTTTATTGTTTTGACCCCATTTTTTTGTATCT
1 C-ACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTTGA-CCCACTTCTCTGTATCT
38247996 CATCAGGAAGAT-GGGGTTTGA
64 CATCAGGAAGATGGGGGTTTGA
38248017 TCTACCCCTC
Statistics
Matches: 621, Mismatches: 83, Indels: 14
0.86 0.12 0.02
Matches are distributed among these distances:
207 3 0.00
208 145 0.23
209 472 0.76
210 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (209 bp):
CACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTTGACCCACTTCTCTGTATCTCA
TCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCATCGATTTGGTCTACTTT
TTAGTATCTCATCAGGAAGATGACCGCCTCATTATTTTAATCCACTTCTCTATATCTCATCAGGA
AGACAGATTTGGTT
Found at i:38248088 original size:46 final size:45
Alignment explanation
Indices: 38248022--38248111 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 45
38248012 TTTGATCTAC
* * * *
38248022 CCCTCTTGACTAGGGGTAAAATATCATAATACGGCTTCAATCTGG
1 CCCTCTTAACTAGGGATAAAAGATCAGAATACGGCTTCAATCTGG
* *
38248067 CCCTCTTAACTTAGGGATAAAAGATTAGAATGCGGCTTCAATCTG
1 CCCTCTTAAC-TAGGGATAAAAGATCAGAATACGGCTTCAATCTG
38248112 CCTTTCTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
45 9 0.24
46 29 0.76
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (45 bp):
CCCTCTTAACTAGGGATAAAAGATCAGAATACGGCTTCAATCTGG
Found at i:38248170 original size:45 final size:45
Alignment explanation
Indices: 38248016--38248268 Score: 201
Period size: 45 Copynumber: 5.6 Consensus size: 45
38248006 ATGGGGTTTG
* *
38248016 ATCTACCCCTCTTGACTAGGGGTAAAAT-ATCATA-AT-ACGGCTTCA
1 ATCTACCCCTCTTGACTTGGGGT-AAATGA-C-TAGATGATGGCTTCA
** * * * * *
38248061 ATCTGGCCCTCTTAACTTAGGGATAAAAGATTAGAATG-CGGCTTCA
1 ATCTACCCCTCTTGACTT-GGGGTAAATGACTAG-ATGATGGCTTCA
* ** *
38248107 ATCTGCCTTTCTTGACTTGAGGTAAATGACTAGATGATGGCTGT-A
1 ATCTACCCCTCTTGACTTGGGGTAAATGACTAGATGATGGCT-TCA
38248152 ATCTACCCCTCTTGACTTGGGGTAAATGACTAGATGATGGCTTCA
1 ATCTACCCCTCTTGACTTGGGGTAAATGACTAGATGATGGCTTCA
* * * * * *
38248197 ATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGACTACA
1 ATCTACCCCTCTTGACTT-GGGGTAAATGACTAGATGATGGCTTCA
** * *
38248243 ATCGGCCCCTCTTGAATAGGGGTAAA
1 ATCTACCCCTCTTGACTTGGGGTAAA
38248269 AGTTTGGAAT
Statistics
Matches: 170, Mismatches: 29, Indels: 18
0.78 0.13 0.08
Matches are distributed among these distances:
44 6 0.04
45 97 0.57
46 67 0.39
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (45 bp):
ATCTACCCCTCTTGACTTGGGGTAAATGACTAGATGATGGCTTCA
Found at i:38248222 original size:91 final size:90
Alignment explanation
Indices: 38248100--38248268 Score: 212
Period size: 91 Copynumber: 1.9 Consensus size: 90
38248090 ATTAGAATGC
** * * ** *
38248100 GGCTTCAATCTGCCTTTCTTGACTTGAGGTAAATGACTAGATGATGGCTGTAATCTACCCCTCTT
1 GGCTTCAATCTGCCCCTCTTGACTTGAGGTAAAAGACTAGATGATGACTACAATCGACCCCTCTT
* *
38248165 GACTTGGGGTAAATGACTAGATGAT
66 GAATAGGGGTAAATGACTAGATGAT
* * * *
38248190 GGCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGGATGATGACTACAATCGGCCCCTCT
1 GGCTTCAATCTGCCCCTCTTGACTT-GAGGTAAAAGACTAGATGATGACTACAATCGACCCCTCT
38248255 TGAATAGGGGTAAA
65 TGAATAGGGGTAAA
38248269 AGTTTGGAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
90 23 0.35
91 42 0.65
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (90 bp):
GGCTTCAATCTGCCCCTCTTGACTTGAGGTAAAAGACTAGATGATGACTACAATCGACCCCTCTT
GAATAGGGGTAAATGACTAGATGAT
Found at i:38248267 original size:136 final size:136
Alignment explanation
Indices: 38248016--38248268 Score: 307
Period size: 136 Copynumber: 1.9 Consensus size: 136
38248006 ATGGGGTTTG
*
38248016 ATCTACCCCTCTTGACTAGGGGTAAAATATCATAATACGGCTTCAATCTGGCCCTCTTAACTTAG
1 ATCTACCCCTCTTGACTAGGGGTAAAATATCATAATACGGCTTCAATCTGCCCCTCTTAACTTAG
* * * ** * *
38248081 GGATAAAAGATTAGAATGCGGCTTCAATCTGCCTTTCTTGACTTGAGGTAAATGACTAGATGATG
66 GGATAAAAGATTAGAATGCGACTACAATCGGCCCCTCTTGAATAGAGGTAAATGACTAGATGATG
38248146 GCTGTA
131 GCTGTA
* * *
38248152 ATCTACCCCTCTTGACTTGGGGT-AAATGA-C-TAGATGATGGCTTCAATCTGCCCCTCTTGACT
1 ATCTACCCCTCTTGACTAGGGGTAAAAT-ATCATA-AT-ACGGCTTCAATCTGCCCCTCTTAACT
* * * *
38248214 TAGGGGTAAAAGATT-GGATGATGACTACAATCGGCCCCTCTTGAATAGGGGTAAA
63 TAGGGATAAAAGATTAGAATG-CGACTACAATCGGCCCCTCTTGAATAGAGGTAAA
38248269 AGTTTGGAAT
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
134 2 0.02
135 11 0.11
136 85 0.87
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (136 bp):
ATCTACCCCTCTTGACTAGGGGTAAAATATCATAATACGGCTTCAATCTGCCCCTCTTAACTTAG
GGATAAAAGATTAGAATGCGACTACAATCGGCCCCTCTTGAATAGAGGTAAATGACTAGATGATG
GCTGTA
Found at i:38254907 original size:16 final size:17
Alignment explanation
Indices: 38254886--38254917 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38254876 ACGAACAAGT
38254886 TTCGAAA-CTTTTTATA
1 TTCGAAATCTTTTTATA
38254902 TTCGAAATCTTTTTAT
1 TTCGAAATCTTTTTAT
38254918 TTTGTTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.28, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
TTCGAAATCTTTTTATA
Found at i:38256570 original size:15 final size:15
Alignment explanation
Indices: 38256538--38256577 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
38256528 TATAATTAAC
38256538 CACATA-ATATTTCA
1 CACATATATATTTCA
* *
38256552 CACATATATTTTTCT
1 CACATATATATTTCA
38256567 CACATATATAT
1 CACATATATAT
38256578 CATTATATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (15 bp):
CACATATATATTTCA
Found at i:38259801 original size:12 final size:12
Alignment explanation
Indices: 38259784--38259881 Score: 71
Period size: 12 Copynumber: 8.6 Consensus size: 12
38259774 ATAACATCCA
*
38259784 AACAACCAAAAT
1 AACAACAAAAAT
* *
38259796 AACAACCAAAAC
1 AACAACAAAAAT
** *
38259808 AGTAGCAAAAAT
1 AACAACAAAAAT
*
38259820 AACAGC-AAAAT
1 AACAACAAAAAT
*
38259831 AA-TA--AAAAT
1 AACAACAAAAAT
*
38259840 AGCAACAAAAAT
1 AACAACAAAAAT
*
38259852 AAC-ATAAAAAT
1 AACAACAAAAAT
38259863 AACAACAAAAAT
1 AACAACAAAAAT
38259875 AACAACA
1 AACAACA
38259882 TCAAAACAGG
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
9 6 0.09
10 1 0.01
11 17 0.25
12 43 0.64
ACGTcount: A:0.68, C:0.17, G:0.04, T:0.10
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:38259846 original size:23 final size:21
Alignment explanation
Indices: 38259791--38259876 Score: 84
Period size: 23 Copynumber: 3.9 Consensus size: 21
38259781 CCAAACAACC
**
38259791 AAAATAACAACCAAAACAGTAGCA
1 AAAATAACAA-CAAAA-A-TAATA
*
38259815 AAAATAACAGC-AAAATAATA
1 AAAATAACAACAAAAATAATA
*
38259835 AAAATAGCAACAAAAATAACATA
1 AAAATAACAACAAAAAT-A-ATA
38259858 AAAATAACAACAAAAATAA
1 AAAATAACAACAAAAATAA
38259877 CAACATCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
20 12 0.23
21 7 0.13
22 5 0.09
23 20 0.38
24 9 0.17
ACGTcount: A:0.70, C:0.14, G:0.05, T:0.12
Consensus pattern (21 bp):
AAAATAACAACAAAAATAATA
Found at i:38259879 original size:32 final size:32
Alignment explanation
Indices: 38259791--38259879 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 32
38259781 CCAAACAACC
* *
38259791 AAAATAACAACCAAAACAGTAGCAAAAATAACAGC
1 AAAATAACAA-CAAAA-A-TAACAAAAATAACAGA
* ** *
38259826 AAAATAATAA-AAATAGCAACAAAAATAACATA
1 AAAATAACAACAAA-AATAACAAAAATAACAGA
38259858 AAAATAACAACAAAAATAACAA
1 AAAATAACAACAAAAATAACAA
38259880 CATCAAAACA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
32 27 0.63
33 6 0.14
34 1 0.02
35 9 0.21
ACGTcount: A:0.70, C:0.15, G:0.04, T:0.11
Consensus pattern (32 bp):
AAAATAACAACAAAAATAACAAAAATAACAGA
Found at i:38259889 original size:23 final size:23
Alignment explanation
Indices: 38259814--38259878 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
38259804 AAACAGTAGC
*
38259814 AAAAATAACAGC-AAAAT-A-AT
1 AAAAATAACAACAAAAATAACAT
*
38259834 AAAAATAGCAACAAAAATAACAT
1 AAAAATAACAACAAAAATAACAT
38259857 AAAAATAACAACAAAAATAACA
1 AAAAATAACAACAAAAATAACA
38259879 ACATCAAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
20 10 0.26
21 5 0.13
22 1 0.03
23 23 0.59
ACGTcount: A:0.72, C:0.12, G:0.03, T:0.12
Consensus pattern (23 bp):
AAAAATAACAACAAAAATAACAT
Found at i:38274151 original size:43 final size:43
Alignment explanation
Indices: 38274014--38274151 Score: 179
Period size: 43 Copynumber: 3.2 Consensus size: 43
38274004 TTTGTTAATG
* *
38274014 TTAGTGGCGTTTGTGGGAAAAGCGCCGTTAAAGACCATGTT-T
1 TTAGCGGCGTTTGTGGGATAAGCGCCGTTAAAGACCATGTTCT
* * **
38274056 TTAGCGGCGTTTGCGGGATAAGCGTCGTTAAAGATTATGTTCT
1 TTAGCGGCGTTTGTGGGATAAGCGCCGTTAAAGACCATGTTCT
** * *
38274099 TTAATGGCGTTTGTGAGATAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGATAAGCGCCGTTAAAGACCATGTTCT
38274142 TTAGCGGCGT
1 TTAGCGGCGT
38274152 ATGGTTTTTA
Statistics
Matches: 79, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 35 0.44
43 44 0.56
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGATAAGCGCCGTTAAAGACCATGTTCT
Found at i:38275344 original size:25 final size:25
Alignment explanation
Indices: 38275316--38275367 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
38275306 AGAAATAATC
* *
38275316 TTTCAGTTAAACTTTGTTTATTTGT
1 TTTCAATTAAACTCTGTTTATTTGT
38275341 TTTCAATTAAACTCTGTTTATTTGT
1 TTTCAATTAAACTCTGTTTATTTGT
38275366 TT
1 TT
38275368 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.60
Consensus pattern (25 bp):
TTTCAATTAAACTCTGTTTATTTGT
Found at i:38277338 original size:25 final size:25
Alignment explanation
Indices: 38277309--38277360 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
38277299 AGAAATAATC
* *
38277309 TTTCAGTTAAACTTTGTTTATTTGT
1 TTTCAATTAAACTCTGTTTATTTGT
38277334 TTTCAATTAAACTCTGTTTATTTGT
1 TTTCAATTAAACTCTGTTTATTTGT
38277359 TT
1 TT
38277361 GAGTCAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.21, C:0.10, G:0.10, T:0.60
Consensus pattern (25 bp):
TTTCAATTAAACTCTGTTTATTTGT
Found at i:38279404 original size:28 final size:28
Alignment explanation
Indices: 38279227--38279523 Score: 127
Period size: 29 Copynumber: 10.3 Consensus size: 28
38279217 TTGGATATCG
*
38279227 GGGGTAAAATGGTAATTTT-G-G-ACTT
1 GGGGTAAAATGGTAATTTTGGTGAAATT
* * *
38279252 ACGGGGCAAAATGGTAATTTTCGATGAAATC
1 --GGGGTAAAATGGTAATTTT-GGTGAAATT
* * * * *
38279283 GGGGACAAAAAGGGAATCTTGG-AAAATTT
1 GGGG-TAAAATGGTAATTTTGGTGAAA-TT
* * *
38279312 AAGGGTAAAATAGTAATTTTTGGTGAAATC
1 -GGGGTAAAATGGTAA-TTTTGGTGAAATT
*
38279342 GAGGTCAAAAATGG-AATTTT-G-GAAAGTT
1 GGGGT--AAAATGGTAATTTTGGTGAAA-TT
*
38279370 CGAGGGT-AAATGGTAATTTTTGGCGAAATT
1 -G-GGGTAAAATGGTAA-TTTTGGTGAAATT
*
38279400 GGGGTTAAAATGG-AATTTT--AGAAAGTT
1 GGGG-TAAAATGGTAATTTTGGTGAAA-TT
** *
38279427 CAAGGTAAAATGGTAATTTTTGGTGAAATC
1 -GGGGTAAAATGGTAA-TTTTGGTGAAATT
38279457 GGGGTTAAAAATGG-AATTTT-G-GAAAGTT
1 GGGG-T-AAAATGGTAATTTTGGTGAAA-TT
*
38279485 CGGGGTAAAATGGTAATTTTGGTGAAATC
1 -GGGGTAAAATGGTAATTTTGGTGAAATT
38279514 GGGGTTAAAA
1 GGGG-TAAAA
38279524 ATATGATTAC
Statistics
Matches: 204, Mismatches: 32, Indels: 66
0.68 0.11 0.22
Matches are distributed among these distances:
26 4 0.02
27 49 0.24
28 31 0.15
29 50 0.25
30 44 0.22
31 26 0.13
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGTGAAATT
Found at i:38279496 original size:58 final size:58
Alignment explanation
Indices: 38279223--38279562 Score: 361
Period size: 57 Copynumber: 5.9 Consensus size: 58
38279213 ACTTTTGGAT
* * * * *
38279223 ATCGGGGGT-AAAATGGTAATTTTGG--ACTTACGGGGCAAAATGGTAATTTTCGATGAA
1 ATCGGGGTTAAAAATGG-AATTTTGGAAAGTT-CGGGGTAAAATGGTAATTTTTGGTGAA
** * * * ** *
38279280 ATCGGGGACAAAAAGGGAATCTTGGAAAATTTAAGGGTAAAATAGTAATTTTTGGTGAA
1 ATCGGGGTTAAAAATGGAATTTTGG-AAAGTTCGGGGTAAAATGGTAATTTTTGGTGAA
* * *
38279339 ATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT-AAATGGTAATTTTTGGCGAA
1 ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCG-GGGTAAAATGGTAATTTTTGGTGAA
* * **
38279397 ATTGGGGTT-AAAATGGAATTTTAGAAAGTTCAAGGTAAAATGGTAATTTTTGGTGAA
1 ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTTGGTGAA
38279454 ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATGGTAA-TTTTGGTGAA
1 ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTTGGTGAA
* ** *
38279511 ATCGGGGTTAAAAATATG-ATTACGGAAAGTTCGGGGGTAAAATAGTAATTTT
1 ATCGGGGTTAAAAAT-GGAATTTTGGAAAGTTC-GGGGTAAAATGGTAATTTT
38279563 GGACAGTCCA
Statistics
Matches: 238, Mismatches: 35, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
56 3 0.01
57 99 0.42
58 84 0.35
59 49 0.21
60 3 0.01
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.31
Consensus pattern (58 bp):
ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTTGGTGAA
Found at i:38279525 original size:115 final size:116
Alignment explanation
Indices: 38279223--38279525 Score: 375
Period size: 115 Copynumber: 2.6 Consensus size: 116
38279213 ACTTTTGGAT
* * * *
38279223 ATCGGGGGT-AAAATGGTAATTTTGG--ACTTACGGGGCAAAATGGTAATTTTCGATGAAATCGG
1 ATCGGGGTTAAAAATGG-AATTTTGGAAAGTT-CGGGGTAAAATGGTAATTTT-GGTGAAATCGG
** * * *
38279285 GGACAAAAAGGGAATCTTGGAAAATTTAAGGGTAAAATAGTAATTTTTGGTGAA
63 GGTTAAAAATGGAATCTTAGAAAATTCAAGGGTAAAATAGTAATTTTTGGTGAA
* * * *
38279339 ATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT-AAATGGTAATTTTTGGCGAAATTGGG
1 ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCG-GGGTAAAATGGTAA-TTTTGGTGAAATCGGG
* * *
38279403 GTT-AAAATGGAATTTTAGAAAGTTCAA-GGTAAAATGGTAATTTTTGGTGAA
64 GTTAAAAATGGAATCTTAGAAAATTCAAGGGTAAAATAGTAATTTTTGGTGAA
38279454 ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTGGTGAAATCGGGGT
1 ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTGGTGAAATCGGGGT
38279519 TAAAAAT
66 TAAAAAT
38279526 ATGATTACGG
Statistics
Matches: 160, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
114 21 0.13
115 68 0.43
116 33 0.21
117 28 0.17
118 10 0.06
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.30
Consensus pattern (116 bp):
ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGTAAAATGGTAATTTTGGTGAAATCGGGGT
TAAAAATGGAATCTTAGAAAATTCAAGGGTAAAATAGTAATTTTTGGTGAA
Found at i:38279564 original size:115 final size:115
Alignment explanation
Indices: 38279313--38279562 Score: 344
Period size: 115 Copynumber: 2.2 Consensus size: 115
38279303 GGAAAATTTA
38279313 AGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTA
1 AGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTA
* **
38279378 AATGGTAATTTTTGGCGAAATTGGGGTTAAAATGGAATTTTAGAAAGTTC
66 AATGGTAATTTTTGGCGAAATCGGGGTTAAAATGGAATTACAGAAAGTTC
* * * *
38279428 AAGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCG-GGGTA
1 AGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGT-
* * *
38279492 AAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATATG-ATTACGGAAAGTTC
65 AAATGGTAATTTTTGGCGAAATCGGGGTT-AAAAT-GGAATTACAGAAAGTTC
*
38279543 GGGGGTAAAATAGTAATTTT
1 -AGGGTAAAATAGTAATTTT
38279563 GGACAGTCCA
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
114 21 0.18
115 80 0.68
116 17 0.14
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (115 bp):
AGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTCGAGGGTA
AATGGTAATTTTTGGCGAAATCGGGGTTAAAATGGAATTACAGAAAGTTC
Found at i:38280429 original size:6 final size:6
Alignment explanation
Indices: 38280420--38280519 Score: 77
Period size: 6 Copynumber: 17.0 Consensus size: 6
38280410 TTAATATTAT
* *
38280420 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TAAGTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T--TTAAA
** *
38280467 TTTAAA TTTAAGA --TAAA TTTAAA AATAAA TTTAAA ATTAAA -TTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
38280513 CTTTAAA
1 -TTTAAA
38280520 AAATCAAAAG
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
4 3 0.04
5 16 0.21
6 45 0.60
7 6 0.08
8 5 0.07
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (6 bp):
TTTAAA
Found at i:38280429 original size:17 final size:16
Alignment explanation
Indices: 38280420--38280519 Score: 86
Period size: 17 Copynumber: 6.4 Consensus size: 16
38280410 TTAATATTAT
38280420 TTTAAATTTAATTAAA
1 TTTAAATTTAATTAAA
*
38280436 TTTAAATTTAAAATAAA
1 TTTAAATTT-AATTAAA
*
38280453 TTTAAA--TAAGTAAA
1 TTTAAATTTAATTAAA
*
38280467 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-TTAAA
38280484 TTTAAA---AA-TAAA
1 TTTAAATTTAATTAAA
*
38280496 TTTAAAATTAAATTAAA
1 TTT-AAATTTAATTAAA
38280513 CTTTAAA
1 -TTTAAA
38280520 AAATCAAAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 19
0.76 0.03 0.20
Matches are distributed among these distances:
12 7 0.10
13 3 0.04
14 14 0.20
15 1 0.01
16 14 0.20
17 29 0.41
18 3 0.04
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:38280512 original size:11 final size:12
Alignment explanation
Indices: 38280418--38280509 Score: 72
Period size: 11 Copynumber: 8.2 Consensus size: 12
38280408 GTTTAATATT
* *
38280418 ATTTTAAATTTA
1 ATTTAAAATTAA
*
38280430 A-TTAAATTTAA
1 ATTTAAAATTAA
38280441 ATTTAAAA-TAA
1 ATTTAAAATTAA
38280452 ATTT-AAA-T-A
1 ATTTAAAATTAA
* *
38280461 A-GTAAATTTAA
1 ATTTAAAATTAA
*
38280472 ATTTAAGA-TAA
1 ATTTAAAATTAA
*
38280483 ATTTAAAAATAA
1 ATTTAAAATTAA
38280495 ATTTAAAATTAA
1 ATTTAAAATTAA
38280507 ATT
1 ATT
38280510 AAACTTTAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
8 1 0.02
9 4 0.06
10 5 0.08
11 27 0.43
12 26 0.41
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (12 bp):
ATTTAAAATTAA
Found at i:38282259 original size:23 final size:24
Alignment explanation
Indices: 38282227--38282277 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
38282217 ACAAAGAACT
*
38282227 TAAAATTTTAAATT-TAAAAAATA
1 TAAAAATTTAAATTCTAAAAAATA
*
38282250 TAAAAATTTAAATTCTTAAAAATA
1 TAAAAATTTAAATTCTAAAAAATA
38282274 -AAAA
1 TAAAA
38282278 TAAAATGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
TAAAAATTTAAATTCTAAAAAATA
Found at i:38283012 original size:23 final size:23
Alignment explanation
Indices: 38282964--38283012 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
38282954 TTAGTTCTTT
*
38282964 ATATATATATATATAATTTTATA
1 ATATATATATATATAATTTTAAA
* *
38282987 ATATAT-TTTATATACTTTTCAAA
1 ATATATATATATATAATTTT-AAA
38283010 ATA
1 ATA
38283013 ATAATCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATATATATATATAATTTTAAA
Found at i:38286735 original size:30 final size:32
Alignment explanation
Indices: 38286665--38286740 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 32
38286655 ATAAAAGAAA
38286665 TTTAATTAAAAA-TTTCACAAATTTTAGAGAG
1 TTTAATTAAAAATTTTCACAAATTTTAGAGAG
* *
38286696 CTTAA-TAAAAATTTTCA-AATATTTT-GA-TG
1 TTTAATTAAAAATTTTCACAA-ATTTTAGAGAG
*
38286725 TTTAATTAAAATTTTT
1 TTTAATTAAAAATTTT
38286741 AAAAGCTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 5 0.13
30 19 0.50
31 14 0.37
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (32 bp):
TTTAATTAAAAATTTTCACAAATTTTAGAGAG
Found at i:38287964 original size:18 final size:18
Alignment explanation
Indices: 38287929--38287965 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38287919 TGAGTTTTCG
*
38287929 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCGAAT
*
38287947 AATTCGAATAAATTGAAT
1 AATTCGAATAAATCGAAT
38287965 A
1 A
38287966 TTAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.30
Consensus pattern (18 bp):
AATTCGAATAAATCGAAT
Found at i:38297171 original size:368 final size:367
Alignment explanation
Indices: 38296317--38297424 Score: 2121
Period size: 368 Copynumber: 3.0 Consensus size: 367
38296307 CTTTTTAAAC
*
38296317 AATCTTATCCCCTACCGAGTCATAAGTCTTACTTTTTAAAACATATTCTCACGCTCATTACGAGT
1 AATCTTATCCCCTACCGAGTCATAAGTCTTCCTTTTTAAAACATATTCTCACGCTCATTACGAGT
38296382 CATGAGTCTTTCTTTATCACATTCTCATTCTCATCCCAAGACATGAGTCTTCCATTTATACACCA
66 CATGAGTCTTTCTTTATCACATTCTCATTCTCATCCCAAGACATGAGTCTTCCATTTATACACCA
38296447 AGATTCTCAAGTACTTCCTCAATAGATAACGATTAGCAGTTCATATGTAAAATTTAACAAAACAA
131 AGATTCTCAAGTACTTCCTCAATAGATAACGATTAGCAGTTCATATGTAAAATTTAACAAAACAA
38296512 ACTTACCGGACGAAAATGCAGTTCGGGTGGAACTTCAGGGACTATTCTACGATTTTTCCCTTCTC
196 ACTTACCGGACGAAAATGCAGTTCGGGTGGAACTTCAGGGACTATTCTACGA-TTTTCCCTTCTC
*
38296577 ACGATTTGTGACTCGATCTTGATCTAATCACAACAATAAATCAAATCTCCTGTTAAATCATATAA
260 ACGATCTGTGACTCGATCTTGATCTAATCACAACAATAAATCAAATCTCCTGTTAAATCATATAA
38296642 TTT-ATCAATTTACAAATATAAGTCTTTTTCAAAAAATTACGG
325 TTTAATCAATTTACAAATATAAGTCTTTTTCAAAAAATTACGG
38296684 AATCTTATCCCCTACCGAGTCATAAGTC-TCCTTTTTAAAACATATTCTCACGCTCATTACGAGT
1 AATCTTATCCCCTACCGAGTCATAAGTCTTCCTTTTTAAAACATATTCTCACGCTCATTACGAGT
*
38296748 CATGAGTCTTTCTTTATCACATTCTCATTCTCATCCCAAGAAATGAGTATCTTCCATTTATACAC
66 CATGAGTCTTTCTTTATCACATTCTCATTCTCATCCCAAGACATGAG--TCTTCCATTTATACAC
38296813 CAAGATTCTCAAGTACTTCCTCAATAGATAACGATTAGCAGTTCATATGTAAAATTTAACAAAAC
129 CAAGATTCTCAAGTACTTCCTCAATAGATAACGATTAGCAGTTCATATGTAAAATTTAACAAAAC
38296878 AAACTTACCGGACGAAAATGCAGTTCGGGTGGAACTTCAGGGACTATTCTACGATTTTCCCTTTC
194 AAACTTACCGGACGAAAATGCAGTTCGGGTGGAACTTCAGGGACTATTCTACGATTTTCCC-TTC
38296943 TCACGATCTGTGACTCGATCTTGATCTAATCACAACAATAAATCAAATCTCCTGTTAAATCATAT
258 TCACGATCTGTGACTCGATCTTGATCTAATCACAACAATAAATCAAATCTCCTGTTAAATCATAT
38297008 AATTTAATCAATTTACAAATATAAGTCTTTTTCAAAAAATTACGG
323 AATTTAATCAATTTACAAATATAAGTCTTTTTCAAAAAATTACGG
38297053 AATCTTATCCCCTACCGAGTCATAAGTCTTCCTTTTTAAAACATATTCTCACGCTCATTACGAGT
1 AATCTTATCCCCTACCGAGTCATAAGTCTTCCTTTTTAAAACATATTCTCACGCTCATTACGAGT
38297118 CATGAGTCTTTCTTTATCACATTCTCATTCTCATCCCAAGACATGAGTCTTCCATTTATACACCA
66 CATGAGTCTTTCTTTATCACATTCTCATTCTCATCCCAAGACATGAGTCTTCCATTTATACACCA
38297183 AGATTCTCAAGTACTTCCTCAATAGATAACGATTAGCAGTTCATATGTAAAATTTAACAAAACAA
131 AGATTCTCAAGTACTTCCTCAATAGATAACGATTAGCAGTTCATATGTAAAATTTAACAAAACAA
38297248 ACTTACCGGACGAAAATGCAGTTCGGGTGGAACTTCAGGGACTATTCTACGATTTTCCCCTTCTC
196 ACTTACCGGACGAAAATGCAGTTCGGGTGGAACTTCAGGGACTATTCTACGATTTT-CCCTTCTC
38297313 ACGATCTGTGACTCGATCTTGATCTAATCACAACAATAAATCAAATCTCCTGTTAAATCATATAA
260 ACGATCTGTGACTCGATCTTGATCTAATCACAACAATAAATCAAATCTCCTGTTAAATCATATAA
*
38297378 TTTAATCAATTTACAAATATAAGACTTTTTCAAAAAATTACGG
325 TTTAATCAATTTACAAATATAAGTCTTTTTCAAAAAATTACGG
38297421 AATC
1 AATC
38297425 ACTCCTAAAC
Statistics
Matches: 730, Mismatches: 5, Indels: 11
0.98 0.01 0.01
Matches are distributed among these distances:
366 81 0.11
367 35 0.05
368 462 0.63
369 70 0.10
370 82 0.11
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (367 bp):
AATCTTATCCCCTACCGAGTCATAAGTCTTCCTTTTTAAAACATATTCTCACGCTCATTACGAGT
CATGAGTCTTTCTTTATCACATTCTCATTCTCATCCCAAGACATGAGTCTTCCATTTATACACCA
AGATTCTCAAGTACTTCCTCAATAGATAACGATTAGCAGTTCATATGTAAAATTTAACAAAACAA
ACTTACCGGACGAAAATGCAGTTCGGGTGGAACTTCAGGGACTATTCTACGATTTTCCCTTCTCA
CGATCTGTGACTCGATCTTGATCTAATCACAACAATAAATCAAATCTCCTGTTAAATCATATAAT
TTAATCAATTTACAAATATAAGTCTTTTTCAAAAAATTACGG
Found at i:38298418 original size:18 final size:18
Alignment explanation
Indices: 38298395--38298429 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38298385 AGAAATAGTT
*
38298395 GCAAAATAATACATAAAA
1 GCAAAACAATACATAAAA
38298413 GCAAAACAATACATAAA
1 GCAAAACAATACATAAA
38298430 TGCTCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.06, T:0.14
Consensus pattern (18 bp):
GCAAAACAATACATAAAA
Found at i:38306554 original size:81 final size:81
Alignment explanation
Indices: 38306419--38306581 Score: 247
Period size: 81 Copynumber: 2.0 Consensus size: 81
38306409 ATGAAAATGA
* * * *
38306419 GCCATTACAGGTATATTGCAATAGTCATTTCTTTTTCCACATGCAAATAGTGATTCATCATTCAT
1 GCCATTACAGGCATATTGCAACAGTAATTTCCTTTTCCACATGCAAATAGTGATTCATCATTCAT
38306484 ATATTTACTTGTGTAT
66 ATATTTACTTGTGTAT
* *
38306500 GCCATTACAGGCATGTTGCAACAGTAATTTCCTTTTCCACACT-TAAATAGTGATTCATCATTCA
1 GCCATTACAGGCATATTGCAACAGTAATTTCCTTTTCCACA-TGCAAATAGTGATTCATCATTCA
*
38306564 TATATTTACTTTTGTAT
65 TATATTTACTTGTGTAT
38306581 G
1 G
38306582 TTTTATCTTC
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
81 73 0.99
82 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (81 bp):
GCCATTACAGGCATATTGCAACAGTAATTTCCTTTTCCACATGCAAATAGTGATTCATCATTCAT
ATATTTACTTGTGTAT
Found at i:38309106 original size:22 final size:21
Alignment explanation
Indices: 38309075--38309145 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
38309065 TTTGTTAATG
38309075 TTTTGTTGTCATTTCATTATTA
1 TTTTGTTGTCATTT-ATTATTA
* *
38309097 TTTTGCTGTCATTTTACTATTA
1 TTTTGTTGTCA-TTTATTATTA
* * *
38309119 TATTGTTATTATTATATTATTA
1 TTTTGTTGTCATT-TATTATTA
38309141 TTTTG
1 TTTTG
38309146 ATATTACATA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
21 2 0.05
22 34 0.87
23 3 0.08
ACGTcount: A:0.21, C:0.07, G:0.08, T:0.63
Consensus pattern (21 bp):
TTTTGTTGTCATTTATTATTA
Found at i:38309133 original size:14 final size:14
Alignment explanation
Indices: 38309114--38309151 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
38309104 GTCATTTTAC
*
38309114 TATTATATTGTTAT
1 TATTATATTATTAT
38309128 TATTATATTATTAT
1 TATTATATTATTAT
38309142 T-TTGATATTA
1 TATT-ATATTA
38309152 CATAACTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:38315125 original size:61 final size:61
Alignment explanation
Indices: 38315030--38315152 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
38315020 ATGATCTGAT
38315030 ATCACTTCATCAACCGATGGTATATCTCCATTAATTTTAGGTACATGCTACACAATCACAA
1 ATCACTTCATCAACCGATGGTATATCTCCATTAATTTTAGGTACATGCTACACAATCACAA
*
38315091 ATCACTTCATCAATCGATGGTATATCTCCATTAATTTTAGGTACATGCTACACAATCACAA
1 ATCACTTCATCAACCGATGGTATATCTCCATTAATTTTAGGTACATGCTACACAATCACAA
38315152 A
1 A
38315153 ATTAGCAACG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.35, C:0.24, G:0.10, T:0.32
Consensus pattern (61 bp):
ATCACTTCATCAACCGATGGTATATCTCCATTAATTTTAGGTACATGCTACACAATCACAA
Found at i:38324770 original size:26 final size:26
Alignment explanation
Indices: 38324715--38324771 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
38324705 TAAATTATAT
* *
38324715 TTTTTAAAATATGTAATTATCACAAA
1 TTTTTAAAATATATAATTACCACAAA
38324741 TTTTT-AAATATATAATTACCACAAA
1 TTTTTAAAATATATAATTACCACAAA
*
38324766 CTTTTA
1 TTTTTA
38324772 TTTTATGTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTTTAAAATATATAATTACCACAAA
Found at i:38327769 original size:22 final size:22
Alignment explanation
Indices: 38327744--38327787 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
38327734 ATAATATAAT
*
38327744 AGTGAAATAGTAGCAAAACAAC
1 AGTGAAATAGAAGCAAAACAAC
*
38327766 AGTGAAATGGAAGCAAAACAAC
1 AGTGAAATAGAAGCAAAACAAC
38327788 TAATTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.14, G:0.20, T:0.11
Consensus pattern (22 bp):
AGTGAAATAGAAGCAAAACAAC
Found at i:38346446 original size:24 final size:24
Alignment explanation
Indices: 38346393--38346442 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
38346383 TTAGTTAAAT
*
38346393 TCTATTTATTTGTTTCAATTAAAC
1 TCTATTTATTTGTTTCAATCAAAC
* *
38346417 TCTATTTA-TTGTTTGAGTCAAAC
1 TCTATTTATTTGTTTCAATCAAAC
38346440 TCT
1 TCT
38346443 TATTAATCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.52
Consensus pattern (24 bp):
TCTATTTATTTGTTTCAATCAAAC
Found at i:38353376 original size:36 final size:36
Alignment explanation
Indices: 38353319--38353390 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
38353309 CTAGATTCAA
38353319 GATGTTCTTTCAACATATGTCCCAACAGAGAATGGT
1 GATGTTCTTTCAACATATGTCCCAACAGAGAATGGT
* * *
38353355 GATGTTCTTTCCACATGTGTCCCATCAGAGAATGGT
1 GATGTTCTTTCAACATATGTCCCAACAGAGAATGGT
38353391 TCTCCACATA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (36 bp):
GATGTTCTTTCAACATATGTCCCAACAGAGAATGGT
Found at i:38354570 original size:17 final size:17
Alignment explanation
Indices: 38354548--38354583 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
38354538 TCCCTTGACT
*
38354548 TTTAACCTTCCATATTC
1 TTTAACATTCCATATTC
*
38354565 TTTAACATTTCATATTC
1 TTTAACATTCCATATTC
38354582 TT
1 TT
38354584 GTTGTAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAACATTCCATATTC
Found at i:38360167 original size:24 final size:24
Alignment explanation
Indices: 38360122--38360169 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
38360112 ATGGATGTTC
* *
38360122 AACCTTTTATCTCTCTTGACCTTT
1 AACCTTTCATCTCTCTTAACCTTT
* *
38360146 AACCTTTCATCTTTTTTAACCTTT
1 AACCTTTCATCTCTCTTAACCTTT
38360170 CATATTCTTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.27, G:0.02, T:0.52
Consensus pattern (24 bp):
AACCTTTCATCTCTCTTAACCTTT
Found at i:38366516 original size:31 final size:32
Alignment explanation
Indices: 38366481--38366554 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 32
38366471 TAACCCAAAT
*
38366481 TTATTTTATTTTTAAT-TTT-TTAATATTTATA
1 TTATTTTATTTTTAATATTTGATAAT-TTTATA
*
38366512 TTATTTTA-ATTTAATATTTGATAATTTTATA
1 TTATTTTATTTTTAATATTTGATAATTTTATA
*
38366543 TAATTTTTATTT
1 TTA-TTTTATTT
38366555 ATTGAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 6 0.17
31 19 0.54
32 9 0.26
33 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (32 bp):
TTATTTTATTTTTAATATTTGATAATTTTATA
Done.