Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007736.1 Hibiscus syriacus cultivar Beakdansim tig00109993_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70637
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:3292 original size:20 final size:22
Alignment explanation
Indices: 3247--3304 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
3237 ATGGGGTTAG
3247 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
3271 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
* *
3291 TGTATCGACGCACT
1 TGCATCGATGCACT
3305 TCAAATGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 2 0.06
24 13 0.41
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:4884 original size:23 final size:23
Alignment explanation
Indices: 4840--4884 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
4830 CATTTGATAT
*
4840 GGCACTTCAGTGCAATTCTACGC
1 GGCACTTCAGTGCAATTATACGC
** *
4863 GGCACTTTGGTGCATTTATACG
1 GGCACTTCAGTGCAATTATACG
4885 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCAGTGCAATTATACGC
Found at i:8277 original size:17 final size:17
Alignment explanation
Indices: 8255--8287 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
8245 TTGAAGCCAT
8255 GGGCGAAGAGAGTGTTA
1 GGGCGAAGAGAGTGTTA
8272 GGGCGAAGAGAGTGTT
1 GGGCGAAGAGAGTGTT
8288 GGAACGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.48, T:0.18
Consensus pattern (17 bp):
GGGCGAAGAGAGTGTTA
Found at i:8295 original size:17 final size:17
Alignment explanation
Indices: 8258--8296 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
8248 AAGCCATGGG
*
8258 CGAAGAGAGTGTTAGGG
1 CGAAGAGAGTGTTAGGA
8275 CGAAGAGAGTGTT-GGAA
1 CGAAGAGAGTGTTAGG-A
8292 CGAAG
1 CGAAG
8297 GAAAGTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.33, C:0.08, G:0.44, T:0.15
Consensus pattern (17 bp):
CGAAGAGAGTGTTAGGA
Found at i:9847 original size:21 final size:21
Alignment explanation
Indices: 9823--9864 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9813 GTGGGAGATT
*
9823 GTTGGAAGTCAAAATTGGGGG
1 GTTGGAAATCAAAATTGGGGG
9844 GTTGGAAATCAAAATTGGGGG
1 GTTGGAAATCAAAATTGGGGG
9865 CACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.40, T:0.24
Consensus pattern (21 bp):
GTTGGAAATCAAAATTGGGGG
Found at i:12323 original size:29 final size:32
Alignment explanation
Indices: 12290--12352 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
12280 GTGATTATTG
*
12290 TTATTG-TT-GTTTATGTTCGT-TTATTTCAT
1 TTATTGATTCGTTTATGTTCGTGTTAATTCAT
*
12319 TTATTGTATTCGTTTATGTTTGTGTTAATTCAT
1 TTATTG-ATTCGTTTATGTTCGTGTTAATTCAT
12352 T
1 T
12353 ATTTCGGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 6 0.21
31 2 0.07
32 11 0.39
33 9 0.32
ACGTcount: A:0.16, C:0.06, G:0.14, T:0.63
Consensus pattern (32 bp):
TTATTGATTCGTTTATGTTCGTGTTAATTCAT
Found at i:13840 original size:40 final size:37
Alignment explanation
Indices: 13755--13840 Score: 84
Period size: 39 Copynumber: 2.2 Consensus size: 37
13745 TTATTTTTTA
*
13755 TAACATTTTAGATTCAACTAAAAATGTTATAAAAAAG
1 TAACATTTTAGATTCAACTAAAAATATTATAAAAAAG
* * * *
13792 AAATATTTTCGATTGTCAAC-AGAAAATATTATGAAAAAGG
1 TAACATTTTAGA-T-TCAACTA-AAAATATTAT-AAAAAAG
13832 TAACATTTT
1 TAACATTTT
13841 TTATTGAACC
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
37 9 0.24
38 2 0.05
39 14 0.37
40 13 0.34
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (37 bp):
TAACATTTTAGATTCAACTAAAAATATTATAAAAAAG
Found at i:17207 original size:22 final size:23
Alignment explanation
Indices: 17181--17227 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
17171 AACTAAGCAT
17181 AAACATCTTGAC-AAAAAAAGTA
1 AAACATCTTGACAAAAAAAAGTA
*
17203 AAACATTTTGACAAAAAAAAGTA
1 AAACATCTTGACAAAAAAAAGTA
17226 AA
1 AA
17228 CTTTACCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.19
Consensus pattern (23 bp):
AAACATCTTGACAAAAAAAAGTA
Found at i:17228 original size:22 final size:21
Alignment explanation
Indices: 17180--17228 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 21
17170 CAACTAAGCA
17180 TAAACATCTTGACAAAAAAAG
1 TAAACATCTTGACAAAAAAAG
*
17201 TAAAACATTTTGACAAAAAAAAG
1 T-AAACATCTTGAC-AAAAAAAG
17224 TAAAC
1 TAAAC
17229 TTTACCCAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.60
23 9 0.36
ACGTcount: A:0.59, C:0.12, G:0.08, T:0.20
Consensus pattern (21 bp):
TAAACATCTTGACAAAAAAAG
Found at i:22322 original size:33 final size:32
Alignment explanation
Indices: 22276--22408 Score: 152
Period size: 33 Copynumber: 4.2 Consensus size: 32
22266 TTTTCACCAT
*
22276 AAACCCGAACCGA-CTGAAATATCACACTTAAA
1 AAACCCGACCCGACCTG-AATATCACACTTAAA
22308 AAACCCCGACCCGACCTGAATATCACACTTAAA
1 AAA-CCCGACCCGACCTGAATATCACACTTAAA
*
22341 AAA-AC--CCCGA-CTCGAATATCACACTTAAA
1 AAACCCGACCCGACCT-GAATATCACACTTAAA
* *
22370 AAACCCGACCCGACCCGAAT-TCAAACTTAAAA
1 AAACCCGACCCGACCTGAATATCACACTT-AAA
22402 AAACCCG
1 AAACCCG
22409 TCCGACCCGA
Statistics
Matches: 88, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
28 2 0.02
29 24 0.27
30 1 0.01
31 8 0.09
32 22 0.25
33 28 0.32
34 3 0.03
ACGTcount: A:0.44, C:0.33, G:0.09, T:0.14
Consensus pattern (32 bp):
AAACCCGACCCGACCTGAATATCACACTTAAA
Found at i:22363 original size:62 final size:60
Alignment explanation
Indices: 22285--22407 Score: 194
Period size: 62 Copynumber: 2.0 Consensus size: 60
22275 TAAACCCGAA
* *
22285 CCGACTGAAATATCACACTTAAAAAACCCCGACCCGACCTGAATATCACACTTAAAAAAACC
1 CCGACTGAAATATCACACTTAAAAAA-CCCGACCCGACCCGAAT-TCAAACTTAAAAAAACC
22347 CCGACTCG-AATATCACACTTAAAAAACCCGACCCGACCCGAATTCAAACTTAAAAAAACC
1 CCGACT-GAAATATCACACTTAAAAAACCCGACCCGACCCGAATTCAAACTTAAAAAAACC
22407 C
1 C
22408 GTCCGACCCG
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
60 17 0.29
61 16 0.28
62 24 0.41
63 1 0.02
ACGTcount: A:0.43, C:0.33, G:0.08, T:0.15
Consensus pattern (60 bp):
CCGACTGAAATATCACACTTAAAAAACCCGACCCGACCCGAATTCAAACTTAAAAAAACC
Found at i:22401 original size:31 final size:31
Alignment explanation
Indices: 22293--22419 Score: 152
Period size: 29 Copynumber: 4.1 Consensus size: 31
22283 AACCGACTGA
*
22293 AATATCACACTTAAAAAACCCCGACCCGACCTG
1 AATATCACACTTAAAAAA-CCCG-CCCGACCCG
* *
22326 AATATCACACTTAAAAAA-AC-CCCGACTCG
1 AATATCACACTTAAAAAACCCGCCCGACCCG
22355 AATATCACACTTAAAAAACCCGACCCGACCCG
1 AATATCACACTTAAAAAACCCG-CCCGACCCG
* *
22387 AAT-TCAAACTTAAAAAAACCCGTCCGACCCG
1 AATATCACACTT-AAAAAACCCGCCCGACCCG
22418 AA
1 AA
22420 CCTGAAATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
29 25 0.30
30 1 0.01
31 18 0.22
32 21 0.25
33 18 0.22
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.15
Consensus pattern (31 bp):
AATATCACACTTAAAAAACCCGCCCGACCCG
Found at i:22435 original size:32 final size:32
Alignment explanation
Indices: 22365--22436 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
22355 AATATCACAC
*
22365 TTAAAAAACCCGACCCGACCCGAATTCAAACT
1 TTAAAAAACCCGACCCGACCCGAACTCAAACT
* * * *
22397 TAAAAAAACCCG-TCCGACCCGAACCTGAAATT
1 TTAAAAAACCCGACCCGACCCGAA-CTCAAACT
22429 TTAAAAAA
1 TTAAAAAA
22437 AAAATCCGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.44, C:0.29, G:0.10, T:0.17
Consensus pattern (32 bp):
TTAAAAAACCCGACCCGACCCGAACTCAAACT
Found at i:22904 original size:16 final size:16
Alignment explanation
Indices: 22883--22923 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
22873 AATCAAACTT
22883 AAAATAATTACAAAAG
1 AAAATAATTACAAAAG
22899 AAAATAATTACAAAAG
1 AAAATAATTACAAAAG
22915 AAAATAATT
1 AAAATAATT
22924 CGGATTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (16 bp):
AAAATAATTACAAAAG
Found at i:49701 original size:21 final size:21
Alignment explanation
Indices: 49663--49704 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
49653 GTTAGTCTGT
49663 TAGCATATTTTGCTAGTTTAA
1 TAGCATATTTTGCTAGTTTAA
49684 TAGCATATTTTGCTAGTTTAA
1 TAGCATATTTTGCTAGTTTAA
49705 CATACTAGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.48
Consensus pattern (21 bp):
TAGCATATTTTGCTAGTTTAA
Found at i:54915 original size:2 final size:2
Alignment explanation
Indices: 54908--54935 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54898 AAAGTGAACC
54908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54936 GAATATGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55268 original size:31 final size:30
Alignment explanation
Indices: 55230--55445 Score: 155
Period size: 31 Copynumber: 6.9 Consensus size: 30
55220 GTCAAGGAAT
55230 TACCTATGTCTTTCGGGACATATGGACAATA
1 TACCTATGT-TTTCGGGACATATGGACAATA
*
55261 TACCTATGTTTTACGGAACATATGGAC-ATAA
1 TACCTATGTTTT-CGGGACATATGGACAAT-A
*
55292 TTACCTATGTCTTTCGGGACATATGGACAGTA
1 -TACCTATGT-TTTCGGGACATATGGACAATA
* * * * *
55324 TACCTATGTTCTACGGAATATATAGACAAAA
1 TACCTATGTT-TTCGGGACATATGGACAATA
* * * * *
55355 TTAGCTATGTCTTTTGAGACTTATGGACAGTA
1 -TACCTATGT-TTTCGGGACATATGGACAATA
* ** * * *
55387 TACATATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTT-TTCGGGACATATGGACAATA
* *
55418 TACCTAGGTTCTTCGGGACTTATGGACA
1 TACCTATGTT-TTCGGGACATATGGACA
55446 GTTGCCGAGG
Statistics
Matches: 143, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
30 7 0.05
31 89 0.62
32 42 0.29
33 5 0.03
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (30 bp):
TACCTATGTTTTCGGGACATATGGACAATA
Found at i:55305 original size:63 final size:63
Alignment explanation
Indices: 55227--55447 Score: 286
Period size: 63 Copynumber: 3.5 Consensus size: 63
55217 AGAGTCAAGG
* *
55227 AATTACCTATGTCTTTCGGGACATATGGACAATATACCTATGTTTTACGGAACATATGGACAT
1 AATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACAT
* * *
55290 AATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAATATATAGACAA
1 AATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACAT
* * * * * *
55353 AATTAGCTATGTCTTTTGAGACTTATGGACAGTATACATATGTTCTAAGGAACATATGGACAGT
1 AATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACA-T
* *
55417 --TTACCTAGGT-TCTTCGGGACTTATGGACAGT
1 AATTACCTATGTCT-TTCGGGACATATGGACAGT
55448 TGCCGAGGTT
Statistics
Matches: 138, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
61 1 0.01
62 25 0.18
63 112 0.81
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (63 bp):
AATTACCTATGTCTTTCGGGACATATGGACAGTATACCTATGTTCTACGGAACATATGGACAT
Found at i:56197 original size:12 final size:12
Alignment explanation
Indices: 56178--56220 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
56168 GTAATTTTTC
56178 ACTGTTCATGGT
1 ACTGTTCATGGT
*
56190 ATTGTTCATGGT
1 ACTGTTCATGGT
56202 ACTGTTCAT--T
1 ACTGTTCATGGT
56212 ACTGTTCAT
1 ACTGTTCAT
56221 ATGATATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 10 0.34
12 19 0.66
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.47
Consensus pattern (12 bp):
ACTGTTCATGGT
Found at i:56257 original size:19 final size:20
Alignment explanation
Indices: 56210--56261 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
56200 GTACTGTTCA
56210 TTACTGTTCATATGATATTG
1 TTACTGTTCATATGATATTG
56230 TTCACTGTTCATATCG-TATT-
1 TT-ACTGTTCATAT-GATATTG
56250 TTACTGTTCATA
1 TTACTGTTCATA
56262 AAACATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.33
20 4 0.13
21 15 0.50
22 1 0.03
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.50
Consensus pattern (20 bp):
TTACTGTTCATATGATATTG
Found at i:60732 original size:13 final size:14
Alignment explanation
Indices: 60714--60747 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
60704 GCAAAATAAA
60714 ATTTAAATA-TAGG
1 ATTTAAATACTAGG
60727 ATTTAAATACTAGG
1 ATTTAAATACTAGG
60741 ACTTTAA
1 A-TTTAA
60748 CTTCCTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.47
14 5 0.26
15 5 0.26
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (14 bp):
ATTTAAATACTAGG
Found at i:62861 original size:30 final size:30
Alignment explanation
Indices: 62827--62888 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
62817 GTGGCAGATC
* *
62827 CACGTAGACTAAATGCTGACGTGGTATGTA
1 CACGTAGACTAAATACTGACGTGGAATGTA
*
62857 CACGTAGACTAAATACTGATGTGGAATGTA
1 CACGTAGACTAAATACTGACGTGGAATGTA
62887 CA
1 CA
62889 TGTTTACTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (30 bp):
CACGTAGACTAAATACTGACGTGGAATGTA
Found at i:63268 original size:17 final size:18
Alignment explanation
Indices: 63243--63280 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
63233 TTAAATTCAT
*
63243 ATTTAAAATTT-TAATTA
1 ATTTAAAATTTATAACTA
*
63260 ATTTTAAATTTATAACTA
1 ATTTAAAATTTATAACTA
63278 ATT
1 ATT
63281 AATATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAAATTTATAACTA
Found at i:63364 original size:17 final size:16
Alignment explanation
Indices: 63316--63411 Score: 62
Period size: 17 Copynumber: 6.2 Consensus size: 16
63306 TTTTATTCAA
*
63316 AATTTATAA-CTAATT
1 AATTTATAATATAATT
* *
63331 AATATA-AATTTAA--
1 AATTTATAATATAATT
63344 AATTTATAACTATAATT
1 AATTTATAA-TATAATT
*
63361 AATTAATAATACTAATT
1 AATTTATAATA-TAATT
* *
63378 AATAT-TAATTTAA--
1 AATTTATAATATAATT
63391 AATTTATAATTATAATT
1 AATTTATAA-TATAATT
63408 AATT
1 AATT
63412 AATATACTAA
Statistics
Matches: 61, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
13 9 0.15
14 7 0.11
15 19 0.31
16 6 0.10
17 20 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AATTTATAATATAATT
Found at i:63392 original size:47 final size:46
Alignment explanation
Indices: 63316--63422 Score: 171
Period size: 47 Copynumber: 2.3 Consensus size: 46
63306 TTTTATTCAA
*
63316 AATTTATA-ACTAATTAATATAAATTTAAAATTTATAACTATAATT
1 AATTAATATACTAATTAATATAAATTTAAAATTTATAACTATAATT
* *
63361 AATTAATAATACTAATTAATATTAATTTAAAATTTATAATTATAATT
1 AATTAAT-ATACTAATTAATATAAATTTAAAATTTATAACTATAATT
63408 AATTAATATACTAAT
1 AATTAATATACTAAT
63423 ACTATAATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
45 6 0.11
46 9 0.16
47 42 0.74
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (46 bp):
AATTAATATACTAATTAATATAAATTTAAAATTTATAACTATAATT
Found at i:63441 original size:47 final size:47
Alignment explanation
Indices: 63324--63552 Score: 163
Period size: 47 Copynumber: 4.9 Consensus size: 47
63314 AAAATTTATA
* * *
63324 ACTAATTAATATAAATTTAAAATTTATAACTATAATTAATTAATAAT
1 ACTAATTAATATTAATATAAAATTTATAATTATAATTAATTAATAAT
*
63371 ACTAATTAATATTAATTTAAAATTTATAATTATAATTAATTAAT-AT
1 ACTAATTAATATTAATATAAAATTTATAATTATAATTAATTAATAAT
* * *
63417 ACTAA-TACTATAATTAATAT-AAATTTAAAATTA-ATATTAATTATTTATT
1 ACTAATTA--AT-ATTAATATAAAATTTATAATTATA-ATTAATTA-ATAAT
* * * * * *
63466 ATTAATTAAT-TATAGT-TTAAATTTAAAATTA-ATATTAATTAGTATT
1 ACTAATTAATAT-TAATATAAAATTTATAATTATA-ATTAATTAATAAT
* * *
63512 ATTAATTAATA-T-ATTTATAAATTTAAAATTA-ATATTAATTA
1 ACTAATTAATATTAATATA-AAATTTATAATTATA-ATTAATTA
63553 GTATTATTAA
Statistics
Matches: 159, Mismatches: 11, Indels: 25
0.82 0.06 0.13
Matches are distributed among these distances:
44 1 0.01
45 4 0.03
46 47 0.30
47 90 0.57
48 10 0.06
49 5 0.03
50 2 0.01
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (47 bp):
ACTAATTAATATTAATATAAAATTTATAATTATAATTAATTAATAAT
Found at i:63505 original size:17 final size:17
Alignment explanation
Indices: 63374--63458 Score: 68
Period size: 17 Copynumber: 4.8 Consensus size: 17
63364 TAATAATACT
63374 AATTAATATTAATTTAA
1 AATTAATATTAATTTAA
63391 AATT--TA-TAATTATAA
1 AATTAATATTAATT-TAA
* *
63406 TTAATTAATATACTAATACTAT
1 --AATTAATAT--TAAT-TTAA
*
63428 AATTAATATAAATTTAA
1 AATTAATATTAATTTAA
63445 AATTAATATTAATT
1 AATTAATATTAATT
63459 ATTTATTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
14 5 0.09
15 5 0.09
17 23 0.43
18 3 0.06
19 2 0.04
20 9 0.17
22 6 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAATATTAATTTAA
Found at i:63518 original size:23 final size:22
Alignment explanation
Indices: 63445--63563 Score: 75
Period size: 23 Copynumber: 5.1 Consensus size: 22
63435 ATAAATTTAA
63445 AATTAATATTAATTATTTATTATT
1 AATTAATATTAATTA--TATTATT
* * *
63469 AATTAAT-TATAGTTTAAATT-TAA
1 AATTAATAT-TA-ATTATATTAT-T
63492 AATTAATATTAATTAGTATTATT
1 AATTAATATTAATTA-TATTATT
* *
63515 AATTAATA-TATTTATAAATT-TAA
1 AATTAATATTAATTAT--ATTAT-T
63538 AATTAATATTAATTAGTATTATT
1 AATTAATATTAATTA-TATTATT
63561 AAT
1 AAT
63564 GAATTATAGT
Statistics
Matches: 73, Mismatches: 10, Indels: 25
0.68 0.09 0.23
Matches are distributed among these distances:
21 1 0.01
22 10 0.14
23 41 0.56
24 17 0.23
25 4 0.05
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
AATTAATATTAATTATATTATT
Found at i:63584 original size:22 final size:22
Alignment explanation
Indices: 63570--63662 Score: 82
Period size: 22 Copynumber: 4.1 Consensus size: 22
63560 TAATGAATTA
63570 TAGTTATAAATTTAAAATTAAT
1 TAGTTATAAATTTAAAATTAAT
*
63592 TAGTTATAAATTTTGAATAAAATAA-
1 TAGTTATAAA-TTT--A-AAATTAAT
* * * *
63617 CAATGAATAAATTT-ATATTAAT
1 TAGT-TATAAATTTAAAATTAAT
63639 TAGTTATAAATTTAAAATTAAT
1 TAGTTATAAATTTAAAATTAAT
63661 TA
1 TA
63663 AAGTTTTAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
21 13 0.24
22 21 0.39
23 3 0.06
25 6 0.11
26 11 0.20
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (22 bp):
TAGTTATAAATTTAAAATTAAT
Found at i:64072 original size:30 final size:30
Alignment explanation
Indices: 64022--64086 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
64012 GTGGCAGCAC
* * *
64022 ACGTATACATGTCACTTCAACATTTAGTCT
1 ACGTGTACATGCCACGTCAACATTTAGTCT
64052 ACGTGTACATGCCACGTCAACATTTAGTCT
1 ACGTGTACATGCCACGTCAACATTTAGTCT
64082 ACGTG
1 ACGTG
64087 GATCTGACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (30 bp):
ACGTGTACATGCCACGTCAACATTTAGTCT
Found at i:64098 original size:30 final size:30
Alignment explanation
Indices: 64028--64100 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
64018 GCACACGTAT
* * *
64028 ACATGTCACTTCAACATTTAGTCTACGTGT
1 ACATGACACGTCAACATTTAGTCTACGTGG
*
64058 ACATGCCACGTCAACATTTAGTCTACGTGG
1 ACATGACACGTCAACATTTAGTCTACGTGG
64088 ATC-TGACACGTCA
1 A-CATGACACGTCA
64101 TCCTTTACTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 37 0.97
31 1 0.03
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.30
Consensus pattern (30 bp):
ACATGACACGTCAACATTTAGTCTACGTGG
Found at i:66683 original size:14 final size:14
Alignment explanation
Indices: 66664--66716 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
66654 CAACTACAAT
66664 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
66678 AATAAATCAATTCATATT
1 AATAAAT-TATT--TA-A
66696 AATAAATTATTTAA
1 AATAAATTATTTAA
66710 AATAAAT
1 AATAAAT
66717 CAATACATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:66704 original size:32 final size:32
Alignment explanation
Indices: 66663--66990 Score: 163
Period size: 32 Copynumber: 11.0 Consensus size: 32
66653 ACAACTACAA
*
66663 TAATAAATTATTTAAAATAAATCAATTCATAT
1 TAATAAATTATTTAAAATAAATCAATACATAT
66695 TAATAAATTATTTAAAATAAATCAATACATA-
1 TAATAAATTATTTAAAATAAATCAATACATAT
* * *
66726 CAACTACA--A--T---A-AAATCAATCCATAT
1 TAA-TAAATTATTTAAAATAAATCAATACATAT
* * ** * * *
66751 T-TTAAAATAAAT-CAATCAATCCATAC--A-
1 TAATAAATTATTTAAAATAAATCAATACATAT
* *
66778 -AATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATACATAT
*
66809 TAATAAATTATTTAAAATAAATCAATCCATAT
1 TAATAAATTATTTAAAATAAATCAATACATAT
* * *
66841 T-TTAAA--A--T-AAATCAATCTATACTA-AT
1 TAATAAATTATTTAAAATAAATCAATAC-ATAT
* * * ** * * *
66867 AAATTATTTAAAAT-AAATCAATCCATACAA--
1 TAATAAATT-ATTTAAAATAAATCAATACATAT
* *
66897 --ATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATACATAT
* *
66927 TAAT-AATTATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATACATAT
*
66958 TAATAAATTATTTAAAATAAATCAATCCATAT
1 TAATAAATTATTTAAAATAAATCAATACATAT
66990 T
1 T
66991 TTAAAATAAA
Statistics
Matches: 228, Mismatches: 39, Indels: 58
0.70 0.12 0.18
Matches are distributed among these distances:
23 3 0.01
24 12 0.05
25 2 0.01
26 13 0.06
27 14 0.06
28 29 0.13
29 2 0.01
30 10 0.04
31 37 0.16
32 106 0.46
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TAATAAATTATTTAAAATAAATCAATACATAT
Found at i:66814 original size:54 final size:57
Alignment explanation
Indices: 66737--67032 Score: 209
Period size: 63 Copynumber: 5.1 Consensus size: 57
66727 AACTACAATA
** *
66737 AAATCAATCCATATTTTAAA-ATAAATCAATCAATCCATACAAATAAATTATTTAAAAT
1 AAATCAATCCATA-CATAAATA-AAATAAATCAATCCATACAAATAAATTATTTAAAAT
* ** * * *
66795 AAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-CAT--A-T-TTTAAAAT
1 AAATCAATCCATAC--ATAAATAAAAT-AAATCAATCCATACAAATAAATTATTTAAAAT
*
66849 AAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTATTTAAAAT
1 AAATCAATCCATAC--AT-AA--A--TAAAATAAATCAATCCATACAAATAAATTATTTAAAAT
* *
66913 AAATCAATCCATACTAATAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAAT
1 AAATCAATCCATAC--ATAA--A--TAAAATAAATCAATCCATACAAATAAATTATTTAAAAT
** * *
66976 AAATCAATCCAT--AT-TTTAAAATAAATCAA-CTATACTAATAAATTATTTAAAAT
1 AAATCAATCCATACATAAATAAAATAAATCAATCCATACAAATAAATTATTTAAAAT
67029 AAAT
1 AAAT
67033 TATTTTAAAA
Statistics
Matches: 200, Mismatches: 23, Indels: 35
0.78 0.09 0.14
Matches are distributed among these distances:
53 26 0.13
54 38 0.19
55 3 0.01
56 1 0.00
57 1 0.00
58 25 0.12
59 13 0.06
60 11 0.05
62 1 0.00
63 56 0.28
64 25 0.12
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (57 bp):
AAATCAATCCATACATAAATAAAATAAATCAATCCATACAAATAAATTATTTAAAAT
Found at i:66870 original size:22 final size:22
Alignment explanation
Indices: 66821--66869 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
66811 ATAAATTATT
**
66821 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
66843 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
66866 TAAA
1 TAAA
66870 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:66880 original size:86 final size:87
Alignment explanation
Indices: 66737--66988 Score: 364
Period size: 86 Copynumber: 2.8 Consensus size: 87
66727 AACTACAATA
*
66737 AAATCAATCCATATTTTAAAATAAATCAATCAATCCATACAAATAAATTATTTAAAATAAATCAA
1 AAATCAATCCATATTTTAAAATAAATCAATC--T-CATACTAATAAATTATTTAAAATAAATCAA
*
66802 TCCATACTAATAAATTATTTAAAAT
63 TCCATACAAATAAATTATTTAAAAT
66827 AAATCAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTATTTAAAATAAATCAATCC
1 AAATCAATCCATATTTTAAAATAAATCAATCTCATACTAATAAATTATTTAAAATAAATCAATCC
66891 ATACAAATAAATTATTTAAAAT
66 ATACAAATAAATTATTTAAAAT
66913 AAATCAATCCATACTAATAATTATTTAAAATAAATCAAT-TCATACTAATAAATTATTTAAAATA
1 AAATCAAT-C---C--AT-A-T-TTTAAAATAAATCAATCTCATACTAATAAATTATTTAAAATA
66977 AATCAATCCATA
57 AATCAATCCATA
66989 TTTTAAAATA
Statistics
Matches: 150, Mismatches: 2, Indels: 15
0.90 0.01 0.09
Matches are distributed among these distances:
86 60 0.40
87 1 0.01
88 1 0.01
90 32 0.21
92 2 0.01
93 1 0.01
94 2 0.01
95 51 0.34
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (87 bp):
AAATCAATCCATATTTTAAAATAAATCAATCTCATACTAATAAATTATTTAAAATAAATCAATCC
ATACAAATAAATTATTTAAAAT
Found at i:66959 original size:149 final size:149
Alignment explanation
Indices: 66759--67032 Score: 505
Period size: 149 Copynumber: 1.8 Consensus size: 149
66749 ATTTTAAAAT
*
66759 AAATCAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
66824 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
66 AATAAATCAATCCATATTTTAAAATAAATCAA-CTATACTAATAAATTATTTAAAATAAATCAAT
66889 CCATACAAATAAATTATTTA
130 CCATACAAATAAATTATTTA
* *
66909 AAATAAATCAATCCATACTAAT-AATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
66973 AATAAATCAATCCATATTTTAAAATAAATCAACTATACTAATAAATTATTTAAAATAAAT
66 AATAAATCAATCCATATTTTAAAATAAATCAACTATACTAATAAATTATTTAAAATAAAT
67033 TATTTTAAAA
Statistics
Matches: 121, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
148 28 0.23
149 73 0.60
150 20 0.17
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (149 bp):
AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
AATAAATCAATCCATATTTTAAAATAAATCAACTATACTAATAAATTATTTAAAATAAATCAATC
CATACAAATAAATTATTTA
Found at i:66963 original size:63 final size:63
Alignment explanation
Indices: 66841--67032 Score: 269
Period size: 63 Copynumber: 3.2 Consensus size: 63
66831 CAATCCATAT
* * *
66841 TTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAAT-AATTATTTAAAATAAATCAATTCATACTAATAAATTA
66905 TTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATCAATTCATACTAATAAATTA
*
66968 TTTAAAATAAATCAAT-C---C--AT-A-T-TTTAAAATAAATCAACT-ATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATCAATTCATACTAATAAATTA
67021 TTTAAAATAAAT
1 TTTAAAATAAAT
67033 TATTTTAAAA
Statistics
Matches: 124, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
53 26 0.21
54 16 0.13
55 1 0.01
56 1 0.01
57 2 0.02
59 1 0.01
62 1 0.01
63 51 0.41
64 25 0.20
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (63 bp):
TTTAAAATAAATCAATCCATACTAATAATTATTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:66994 original size:22 final size:22
Alignment explanation
Indices: 66968--67067 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
66958 TAATAAATTA
66968 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
66990 TTTAAAATAAATCAA-CTATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
67012 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
67036 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
67058 TTTATAATAA
1 TTTAAAATAA
67068 TTTATTTTAA
Statistics
Matches: 56, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
21 4 0.07
22 35 0.62
23 6 0.11
24 9 0.16
25 2 0.04
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:67041 original size:15 final size:15
Alignment explanation
Indices: 67012--67164 Score: 123
Period size: 15 Copynumber: 9.5 Consensus size: 15
67002 CAACTATACT
67012 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
67026 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
67041 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
67063 AATAATTTATTTTAAA
1 AATAAATTATTTT-AA
*
67079 GTAATAAATAAATTATTTTAT
1 --AAT----AAATTATTTTAA
67100 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
67115 AATAAATTATTTTAT
1 AATAAATTATTTTAA
67130 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
67144 AAT-AATTATTTTAA
1 AATAAATTATTTTAA
67158 AATAAAT
1 AATAAAT
67165 AACCTTATTA
Statistics
Matches: 114, Mismatches: 8, Indels: 33
0.74 0.05 0.21
Matches are distributed among these distances:
13 5 0.04
14 24 0.21
15 51 0.45
16 1 0.01
17 1 0.01
18 5 0.04
19 6 0.05
20 1 0.01
21 1 0.01
22 19 0.17
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:67073 original size:37 final size:38
Alignment explanation
Indices: 67012--67121 Score: 145
Period size: 37 Copynumber: 3.0 Consensus size: 38
67002 CAACTATACT
* *
67012 AATAAATTA-TTTAAAATAAATTATTTTAAAATAAATC
1 AATAAATTATTTTATAATAAATTATTTTAAAATAAATA
** * *
67049 AATCCA-TATTTTATAATAATTTATTTTAAAGT-AATA
1 AATAAATTATTTTATAATAAATTATTTTAAAATAAATA
67085 AATAAATTATTTTATAATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTATAATAAATTATTTTAAAATAAAT
67122 TATTTTATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
36 9 0.15
37 48 0.80
38 3 0.05
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.45
Consensus pattern (38 bp):
AATAAATTATTTTATAATAAATTATTTTAAAATAAATA
Found at i:67120 original size:30 final size:29
Alignment explanation
Indices: 67084--67164 Score: 137
Period size: 30 Copynumber: 2.8 Consensus size: 29
67074 TTAAAGTAAT
67084 AAATAAATTATTTTATAATAAATTATTTTA
1 AAATAAATTATTTTATAATAAATTA-TTTA
67114 AAATAAATTATTTTATAATAAATTATTTA
1 AAATAAATTATTTTATAATAAATTATTTA
*
67143 AAAT-AATTATTTTAAAATAAAT
1 AAATAAATTATTTTATAATAAAT
67165 AACCTTATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 17 0.34
29 8 0.16
30 25 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (29 bp):
AAATAAATTATTTTATAATAAATTATTTA
Done.