Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014971.1 Kokia drynarioides strain JFW-HI SEQ_130015, 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: 274434
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 270 characters in sequence are not A, C, G, or T
Found at i:13301 original size:190 final size:190
Alignment explanation
Indices: 12972--13354 Score: 669
Period size: 190 Copynumber: 2.0 Consensus size: 190
12962 CAACTTCCAA
* * *
12972 TGAGCGAACTTTAGGTAAGCTTCAGATCTGGGTTACTAAGTAGATATTCCAACTTTCTTTCTTAA
1 TGAGCGAACTTTAGGTAAGCTTCAGATCAGGGTTACTAAGCAGATATTCCAACCTTCTTTCTTAA
* *
13037 CAATCAGCCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGAATGGCAACAATCCCAGTGTGGA
66 CAATCAACCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGAATGGCAACAATCCCAGCGTGGA
*
13102 ATTTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAG
131 ATCTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAG
13162 TGAGCGAACTTTAGGTAAGCTTCAGAAT-AGGGTTACTAAGCAGATATTCCAACCTTCTTTCTTA
1 TGAGCGAACTTTAGGTAAGCTTCAG-ATCAGGGTTACTAAGCAGATATTCCAACCTTCTTTCTTA
* *
13226 ACAATCAACCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGGATGGCAACGATCCCAGCGTGG
65 ACAATCAACCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGAATGGCAACAATCCCAGCGTGG
*
13291 AATCTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTATAAG
130 AATCTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAG
13352 TGA
1 TGA
13355 TAGCAAGAAG
Statistics
Matches: 183, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
190 181 0.99
191 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (190 bp):
TGAGCGAACTTTAGGTAAGCTTCAGATCAGGGTTACTAAGCAGATATTCCAACCTTCTTTCTTAA
CAATCAACCAACAAATTACTTAAACCTGTTGCAGCCCTTTGGAATGGCAACAATCCCAGCGTGGA
ATCTGAACCCGAGGAAACATTGGCAGCTCTGAAAAGCAAAATGAAACCAAAATCTAAAAG
Found at i:14068 original size:12 final size:11
Alignment explanation
Indices: 14030--14070 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
14020 TTGAATTATA
14030 TTTTTAA-AAT
1 TTTTTAATAAT
14040 TTTTT-ATGAAT
1 TTTTTAAT-AAT
14051 TTTTTAATAAT
1 TTTTTAATAAT
14062 TTATTTAAT
1 TT-TTTAAT
14071 GATTAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.04
10 5 0.19
11 13 0.48
12 8 0.30
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:16256 original size:21 final size:20
Alignment explanation
Indices: 16202--16321 Score: 82
Period size: 21 Copynumber: 6.2 Consensus size: 20
16192 CCACGAACTA
16202 AAAAAATT-TAAAAAT-TGTT
1 AAAAAATTGTAAAAATAT-TT
16221 AAAAATCATTG-AAAAATATTT
1 AAAAA--ATTGTAAAAATATTT
16242 ATAAAAATTGTAAAAATATTT
1 A-AAAAATTGTAAAAATATTT
*
16263 --AAAATTAT-AAAA-ATTT
1 AAAAAATTGTAAAAATATTT
* *
16279 AAATAACTG-AAAAA-ATTT
1 AAAAAATTGTAAAAATATTT
16297 -AAAAA-TGTAAACAAATATTT
1 AAAAAATTGT-AA-AAATATTT
16317 AAAAA
1 AAAAA
16322 TAAAAAAATC
Statistics
Matches: 82, Mismatches: 5, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
16 6 0.07
17 8 0.10
18 21 0.26
19 8 0.10
20 8 0.10
21 26 0.32
22 5 0.06
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (20 bp):
AAAAAATTGTAAAAATATTT
Found at i:16312 original size:18 final size:18
Alignment explanation
Indices: 16232--16322 Score: 75
Period size: 18 Copynumber: 4.9 Consensus size: 18
16222 AAAATCATTG
16232 AAAAATATTTATAAAAATTGT
1 AAAAATA-TT-TAAAAA-TGT
16253 AAAAATATTT-AAAAT-T
1 AAAAATATTTAAAAATGT
16269 ATAAAA-ATTTAAATAACTG-
1 A-AAAATATTTAAA-AA-TGT
16288 AAAAA-ATTTAAAAATGT
1 AAAAATATTTAAAAATGT
16305 AAACAAATATTTAAAAAT
1 -AA-AAATATTTAAAAAT
16323 AAAAAAATCC
Statistics
Matches: 61, Mismatches: 0, Indels: 19
0.76 0.00 0.24
Matches are distributed among these distances:
16 8 0.13
17 9 0.15
18 19 0.31
19 6 0.10
20 12 0.20
21 7 0.11
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (18 bp):
AAAAATATTTAAAAATGT
Found at i:16320 original size:27 final size:27
Alignment explanation
Indices: 16240--16330 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
16230 TGAAAAATAT
16240 TTATAAAAATTGT-AAAAATATTTAAAA
1 TTATAAAAA-TGTAAAAAATATTTAAAA
* * *
16267 TTATAAAAATTTAAATAACTGA--AAAAA
1 TTATAAAAATGTAAA-AAAT-ATTTAAAA
16294 TT-TAAAAATGTAAACAAATATTTAAAA
1 TTATAAAAATGTAAA-AAATATTTAAAA
* *
16321 ATAAAAAAAT
1 TTATAAAAAT
16331 CCTAGATCCA
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
25 1 0.02
26 16 0.33
27 22 0.45
28 9 0.18
29 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (27 bp):
TTATAAAAATGTAAAAAATATTTAAAA
Found at i:16322 original size:10 final size:10
Alignment explanation
Indices: 16200--16323 Score: 68
Period size: 10 Copynumber: 12.8 Consensus size: 10
16190 GACCACGAAC
*
16200 TAAAAAAATT
1 TAAAAATATT
16210 TAAAAAT-TGT
1 TAAAAATAT-T
16220 TAAAAATCATT
1 TAAAAAT-ATT
*
16231 GAAAAATATT
1 TAAAAATATT
16241 TATAAAA-ATT
1 TA-AAAATATT
16251 GTAAAAATATT
1 -TAAAAATATT
*
16262 T-AAAAT-TA
1 TAAAAATATT
16270 T-AAAA-ATT
1 TAAAAATATT
* *
16278 TAAATA-ACT
1 TAAAAATATT
*
16287 GAAAAA-ATT
1 TAAAAATATT
*
16296 TAAAAAT-GT
1 TAAAAATATT
*
16305 AAACAAATATT
1 TAA-AAATATT
16316 TAAAAATA
1 TAAAAATA
16324 AAAAAATCCT
Statistics
Matches: 88, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
8 8 0.09
9 25 0.28
10 35 0.40
11 19 0.22
12 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (10 bp):
TAAAAATATT
Found at i:16330 original size:18 final size:19
Alignment explanation
Indices: 16253--16330 Score: 51
Period size: 18 Copynumber: 4.3 Consensus size: 19
16243 TAAAAATTGT
*
16253 AAAAATATTT-AAAA-TTA
1 AAAAATATTTAAAAACTAA
* *
16270 TAAAA-ATTTAAATAACT-G
1 AAAAATATTTAAA-AACTAA
*
16288 AAAAA-ATTTAAAAATGTAA
1 AAAAATATTTAAAAA-CTAA
*
16307 ACAAATATTTAAAAA-TAA
1 AAAAATATTTAAAAACTAA
16325 AAAAAT
1 AAAAAT
16331 CCTAGATCCA
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
16 4 0.08
17 8 0.17
18 22 0.46
19 5 0.10
20 9 0.19
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAATATTTAAAAACTAA
Found at i:19776 original size:23 final size:23
Alignment explanation
Indices: 19750--19897 Score: 190
Period size: 23 Copynumber: 6.3 Consensus size: 23
19740 ACACTAGCGC
19750 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
19773 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
19796 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
19821 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
19844 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
19867 ACTCTCTGTTTAGCATTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
19890 GCTCTCTG
1 GCTCTCTG
19898 TTGCCCAGCA
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
22 3 0.03
23 86 0.79
25 17 0.16
26 3 0.03
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.43
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:19818 original size:46 final size:44
Alignment explanation
Indices: 19750--19925 Score: 165
Period size: 48 Copynumber: 3.8 Consensus size: 44
19740 ACACTAGCGC
19750 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACT-TGTGTGCTCTCTGTTTAGCACGTCT-GT
* * *
19796 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTG--ATTAGCACT-TGTGTGCTCTCTGTTTAGCAC-GTCTGT
* * * *
19844 GCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCATTGTGTGT
1 GCTCTCTGATTAGCAC-TTGTGTGCTCTCTGTTTAGCA-CGTCTGT
*
19890 GCTCTCTG-TTGCCCAGCACTTATGTGCTCTCTGTTT
1 GCTCTCTGATT----AGCACTTGTGTGCTCTCTGTTT
19926 GTTCCGTCTA
Statistics
Matches: 110, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
45 2 0.02
46 46 0.42
47 1 0.01
48 55 0.50
49 6 0.05
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.43
Consensus pattern (44 bp):
GCTCTCTGATTAGCACTTGTGTGCTCTCTGTTTAGCACGTCTGT
Found at i:24066 original size:43 final size:43
Alignment explanation
Indices: 24001--24197 Score: 238
Period size: 43 Copynumber: 4.6 Consensus size: 43
23991 AAACATTTGA
*
24001 TGTATAAAAAGGAAGACTCATGTCTTGGGTTGAGCATGAGAATT
1 TGTAT-AAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATT
* *
24045 TGTATAAATGGAATACTCATGTCTCGGGTTGAGCATGAGAATT
1 TGTATAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATT
**
24088 TGTATAAAAGGAAGACTCATAACTCGGAG-TGAGCATGAGAATT
1 TGTATAAAAGGAAGACTCATGTCTCGG-GTTGAGCATGAGAATT
* * * * *
24131 TGCATAAATGGAAGACTCATGTATCGGGATGAGAATGAG-ATT
1 TGTATAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATT
* *
24173 ATG-ATTAAAGGAAGACTTATGTCTC
1 -TGTATAAAAGGAAGACTCATGTCTC
24198 TGGATAAGAA
Statistics
Matches: 133, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
42 22 0.17
43 105 0.79
44 6 0.05
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (43 bp):
TGTATAAAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATT
Found at i:24208 original size:42 final size:42
Alignment explanation
Indices: 24008--24240 Score: 141
Period size: 43 Copynumber: 5.5 Consensus size: 42
23998 TGATGTATAA
* * * * *
24008 AAAGGAAGACTCATGTCT-TGGGTTGAGCATGAGAATTTG-TAT
1 AAAGGAAGACTTATGTCTCT-GGATAAGAATGAGAATATGAT-T
* * * * * * * *
24050 AAATGGAATACTCATGTCTCGGGTTGAGCATGAGAATTTGTATA
1 AAA-GGAAGACTTATGTCTCTGGATAAGAATGAGAATATG-ATT
* ** * * *
24094 AAAGGAAGACTCATAACTC-GGAGTGAGCATGAGAATTTGCA-T
1 AAAGGAAGACTTATGTCTCTGGA-TAAGAATGAGAATATG-ATT
* * * * *
24136 AAATGGAAGACTCATGTATCGGGATGAGAATGAGATTATGATT
1 AAA-GGAAGACTTATGTCTCTGGATAAGAATGAGAATATGATT
24179 AAAGGAAGACTTATGTCTCTGGATAAGAATGAGAATATGATT
1 AAAGGAAGACTTATGTCTCTGGATAAGAATGAGAATATGATT
* *
24221 TAAGGAAGACTTATGACTCT
1 AAAGGAAGACTTATGTCTCT
24241 ATAGAGCATA
Statistics
Matches: 161, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
42 61 0.38
43 93 0.58
44 6 0.04
45 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (42 bp):
AAAGGAAGACTTATGTCTCTGGATAAGAATGAGAATATGATT
Found at i:38327 original size:58 final size:58
Alignment explanation
Indices: 38237--38356 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
38227 GAAAAGAGTT
*
38237 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGAGTTTAAAAATATTTGGATTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGGATTTA
* * *
38295 GTTTATGAGTGTT-TTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTT-AAGAATAAAATTATATTTGAGTTTAAAAATATTTGGATTTA
38353 GTTT
1 GTTT
38357 GTTGATGGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
57 3 0.05
58 54 0.95
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGGATTTA
Found at i:40748 original size:191 final size:196
Alignment explanation
Indices: 40449--40830 Score: 506
Period size: 195 Copynumber: 2.0 Consensus size: 196
40439 TCGAGAAATG
* * * *
40449 AGAAAAGAAATATGGATTCTAAATGGATTATAGGCCCCACGATAGCTGAGATTTACGCATAAGTG
1 AGAAAAGAAATATGGATTCTAAATAGATTACAAGCCCCACGATAGCTGAGATCTACGCATAAGTG
* * *
40514 CATATTCTCGATAGCTCGTGTGAGCAGTATCGTTAGGGAACAG-T-TA-TACACACAGATACCGT
66 CATACTCTCGATAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATAGTACACACAGACACCGT
* * *
40576 ATCGATGGCTGAGGTACCGCATATGTTGCAAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACT
131 ACCGATGGCTGAGGTACCGCATACGTTGCAAGTCCTCGACAGCTCGTATGAGCAGCATCGTGACT
40641 C
196 C
* * * * * *
40642 AGAAAAGAAATATGGA-TCGTAAATAGATTACAAGCCCTACGATGGCTGTGA-CTATGCTTTA-T
1 AGAAAAGAAATATGGATTC-TAAATAGATTACAAGCCCCACGATAGCTGAGATCTACGCATAAGT
* * *
40704 GCATACTCTCGATAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTTATAGTACAGACAGGCACT
65 GCATACTCTCGATAGCTCGTGTGAGCAGCATCGTTAGGGAACAG-TTATAGTACACACAGACACC
* * *
40769 GTACCGATGGCTGGGGTACTGCATACGTTGCGAGTCCTCGACAGCTCGTATGAGCAGCATCG
129 GTACCGATGGCTGAGGTACCGCATACGTTGCAAGTCCTCGACAGCTCGTATGAGCAGCATCG
40831 AGTATTGGTA
Statistics
Matches: 162, Mismatches: 22, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
191 43 0.27
192 8 0.05
193 43 0.27
194 2 0.01
195 66 0.41
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (196 bp):
AGAAAAGAAATATGGATTCTAAATAGATTACAAGCCCCACGATAGCTGAGATCTACGCATAAGTG
CATACTCTCGATAGCTCGTGTGAGCAGCATCGTTAGGGAACAGTTATAGTACACACAGACACCGT
ACCGATGGCTGAGGTACCGCATACGTTGCAAGTCCTCGACAGCTCGTATGAGCAGCATCGTGACT
C
Found at i:41608 original size:21 final size:21
Alignment explanation
Indices: 41560--41611 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
41550 GGAGTTTTTA
41560 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATGACAT
* * *
41581 GTTTCGGTTGAAGTCAT-ACTT
1 GTATCGGTAGAAG-CATGACAT
41602 GTATCGGTAG
1 GTATCGGTAG
41612 TATTGTCTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACAT
Found at i:50839 original size:31 final size:31
Alignment explanation
Indices: 50780--50879 Score: 119
Period size: 31 Copynumber: 3.2 Consensus size: 31
50770 ACAATATTAA
* * *
50780 TCATTAAACTATATAGATAAGTTCTTATTTTGG
1 TCATTAAACTAT-TTGA-AAGTTTTTATTTAGG
* *
50813 TCATTGAACTATTTGAAAGTTTTTATTTAAG
1 TCATTAAACTATTTGAAAGTTTTTATTTAGG
*
50844 TCATTAAACTATTTAAAAGTTTTTATTTAGG
1 TCATTAAACTATTTGAAAGTTTTTATTTAGG
*
50875 CCATT
1 TCATT
50880 GGGATGTTAG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 44 0.76
32 3 0.05
33 11 0.19
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (31 bp):
TCATTAAACTATTTGAAAGTTTTTATTTAGG
Found at i:64065 original size:24 final size:25
Alignment explanation
Indices: 64038--64084 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
64028 TAATGTTCGT
64038 TTAACCGAATTAAC-AAAATTAAAA
1 TTAACCGAATTAACTAAAATTAAAA
**
64062 TTAATTGAATTAACTAAAATTAA
1 TTAACCGAATTAACTAAAATTAA
64085 CCGATTTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (25 bp):
TTAACCGAATTAACTAAAATTAAAA
Found at i:64385 original size:18 final size:18
Alignment explanation
Indices: 64362--64399 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
64352 AATAAGAATT
*
64362 TTATAA-TAACATTTATAA
1 TTATAATTAA-ATTAATAA
64380 TTATAATTAAATTAATAA
1 TTATAATTAAATTAATAA
64398 TT
1 TT
64400 TTTAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATAATTAAATTAATAA
Found at i:78501 original size:21 final size:21
Alignment explanation
Indices: 78472--78512 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
78462 TCTCCTTGGA
* *
78472 TTTTTTTAACTATTTTATTTG
1 TTTTATTAAATATTTTATTTG
*
78493 TTTTATTAAATTTTTTATTT
1 TTTTATTAAATATTTTATTT
78513 TTAATAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTATTAAATATTTTATTTG
Found at i:90373 original size:19 final size:18
Alignment explanation
Indices: 90351--90403 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
90341 TAAAAATATC
90351 ATTATAATATAATTTCAA
1 ATTATAATATAATTTCAA
* * **
90369 TATTAAAATACTTATTTTTA
1 -ATTATAATA-TAATTTCAA
90389 ATTATAATATAATTT
1 ATTATAATATAATTT
90404 TTATTAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 5 0.19
19 16 0.59
20 6 0.22
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTATAATATAATTTCAA
Found at i:92426 original size:29 final size:29
Alignment explanation
Indices: 92394--92456 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
92384 AATATGTCTT
92394 TTTTTATTATTTAG-AATTTAATTTTTATA
1 TTTTTATT-TTTAGAAATTTAATTTTTATA
* * *
92423 TTTTTGTTTTTAGAAATTTAGTTTTTTTA
1 TTTTTATTTTTAGAAATTTAATTTTTATA
92452 TTTTT
1 TTTTT
92457 TAGATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 25 0.83
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (29 bp):
TTTTTATTTTTAGAAATTTAATTTTTATA
Found at i:93389 original size:29 final size:30
Alignment explanation
Indices: 93356--93423 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
93346 GAAAAAACCA
** * *
93356 AGAATCTCGGGAT-AAGTTTTTGAAACCCG
1 AGAATCTCAAGATAAAGTTTCTAAAACCCG
* *
93385 AGAATCCCAAGATAAAGTTTCTAAAACCTG
1 AGAATCTCAAGATAAAGTTTCTAAAACCCG
93415 AGAATCTCA
1 AGAATCTCA
93424 GGAAAAAATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (30 bp):
AGAATCTCAAGATAAAGTTTCTAAAACCCG
Found at i:93748 original size:3 final size:3
Alignment explanation
Indices: 93740--93774 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
93730 TAATGAGTAC
93740 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
93775 GTATGTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:118963 original size:2 final size:2
Alignment explanation
Indices: 118956--118997 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
118946 TTCAATTGTT
118956 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
118998 ATCGAATCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:119877 original size:19 final size:17
Alignment explanation
Indices: 119823--119884 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
119813 TTTTTTTTTG
119823 TTTTAAATATTATTAATATA
1 TTTTAAAT-TTA--AATATA
119843 TTTTAAATTTAAATATA
1 TTTTAAATTTAAATATA
* * *
119860 TTTTTAAGTTATATATA
1 TTTTAAATTTAAATATA
119877 TTTTAAAT
1 TTTTAAAT
119885 ATTATTTCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
17 26 0.70
19 3 0.08
20 8 0.22
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATATA
Found at i:123689 original size:17 final size:16
Alignment explanation
Indices: 123643--123718 Score: 62
Period size: 17 Copynumber: 4.2 Consensus size: 16
123633 AAAATTCATG
123643 AAAATATACAATCTAGAAA
1 AAAATATA-AAT-TA-AAA
123662 ACAACATATAAATTATAAA
1 A-AA-ATATAAATTA-AAA
123681 AAAATATAAATTACAAA
1 AAAATATAAATTA-AAA
* *
123698 AATAAGATAAATGAAAA
1 AA-AATATAAATTAAAA
123715 AAAA
1 AAAA
123719 GAGTTGAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
16 2 0.04
17 20 0.40
18 11 0.22
19 7 0.14
20 5 0.10
21 5 0.10
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.21
Consensus pattern (16 bp):
AAAATATAAATTAAAA
Found at i:123782 original size:17 final size:17
Alignment explanation
Indices: 123755--123807 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
123745 AAAATGTAAA
123755 AAAAACTTATAAAAATTT
1 AAAAA-TTATAAAAATTT
*
123773 -AAAATATATAATAATTT
1 AAAAAT-TATAAAAATTT
123790 AAAAATTATTAAAAATTT
1 AAAAATTA-TAAAAATTT
123808 GTGAAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
16 1 0.03
17 16 0.53
18 13 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAAATTATAAAAATTT
Found at i:123852 original size:20 final size:21
Alignment explanation
Indices: 123827--123870 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
123817 ATTAATTTTT
123827 AAAAAAATTAAAAATTGT-AA
1 AAAAAAATTAAAAATTGTGAA
* *
123847 AAAAAAATTAGAATTTGTGAA
1 AAAAAAATTAAAAATTGTGAA
123868 AAA
1 AAA
123871 TATAAGAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (21 bp):
AAAAAAATTAAAAATTGTGAA
Found at i:124417 original size:21 final size:21
Alignment explanation
Indices: 124391--124435 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
124381 ATTTTGTAAA
*
124391 TTGGATTTCTAATCTTTATAT
1 TTGGATTTCTAAACTTTATAT
124412 TTGGATTTCTAAACTTTATAT
1 TTGGATTTCTAAACTTTATAT
124433 TTG
1 TTG
124436 AATTATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.09, G:0.11, T:0.56
Consensus pattern (21 bp):
TTGGATTTCTAAACTTTATAT
Found at i:128050 original size:21 final size:21
Alignment explanation
Indices: 128021--128064 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
128011 TATTTTATAA
128021 TATTAATTAATAA-AATATTAT
1 TATTAATT-ATAACAATATTAT
* *
128042 TATTTATTATAACACTATTAT
1 TATTAATTATAACAATATTAT
128063 TA
1 TA
128065 ATGAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTAATTATAACAATATTAT
Found at i:130910 original size:156 final size:156
Alignment explanation
Indices: 130626--130938 Score: 581
Period size: 156 Copynumber: 2.0 Consensus size: 156
130616 ATAAAGCTGC
*
130626 TTTTCTCGTAATTTCTGCAACATAATTCTTAAATGTTGATCATGCTCTTCCTTAGTCTTTGAATA
1 TTTTCTCGTAATTTCTGCAACATAATTCTTAAATGTTGATCATGCTCTTCCTCAGTCTTTGAATA
130691 AATTAAACTATCATCAATAAACACCACTACAAACTAATCTAAAAATGGCTAAAAATACGATTTAT
66 AATTAAACTATCATCAATAAACACCACTACAAACTAATCTAAAAATGGCTAAAAATACGATTTAT
*
130756 GAGATCCATAAATACTACAAGAGCAT
131 AAGATCCATAAATACTACAAGAGCAT
130782 TTTTCTCGTAATTTCTGCAACATAATTCTTAAATGTTGATCATGCTCTTCCTCAGTCTTTGAATA
1 TTTTCTCGTAATTTCTGCAACATAATTCTTAAATGTTGATCATGCTCTTCCTCAGTCTTTGAATA
* *
130847 AATTAAACTATCATCAATAAACACCACTACAAACTGATCTAAAAATGGCTGAAAATACGATTTAT
66 AATTAAACTATCATCAATAAACACCACTACAAACTAATCTAAAAATGGCTAAAAATACGATTTAT
*
130912 AAGATCCATAAATACTACAGGAGCAT
131 AAGATCCATAAATACTACAAGAGCAT
130938 T
1 T
130939 ACTCAACCCA
Statistics
Matches: 152, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 152 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (156 bp):
TTTTCTCGTAATTTCTGCAACATAATTCTTAAATGTTGATCATGCTCTTCCTCAGTCTTTGAATA
AATTAAACTATCATCAATAAACACCACTACAAACTAATCTAAAAATGGCTAAAAATACGATTTAT
AAGATCCATAAATACTACAAGAGCAT
Found at i:156281 original size:31 final size:30
Alignment explanation
Indices: 156194--156281 Score: 72
Period size: 31 Copynumber: 2.8 Consensus size: 30
156184 ATTTATTTAA
*
156194 ATGTGTATAATTAAATCAAAATT-AAAGTTTT
1 ATGTGTATAATT-AATC-AAATTAAAAGTTTC
* * * *
156225 ATGTATACATTTGAACCATAA-TAAAAGTTTC
1 ATGTGTATAATT-AATCA-AATTAAAAGTTTC
156256 ATGTGTATAATTACATCAAATTAAAA
1 ATGTGTATAATTA-ATCAAATTAAAA
156282 TTTATATATC
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
30 5 0.12
31 38 0.88
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (30 bp):
ATGTGTATAATTAATCAAATTAAAAGTTTC
Found at i:157343 original size:17 final size:17
Alignment explanation
Indices: 157321--157394 Score: 53
Period size: 17 Copynumber: 4.2 Consensus size: 17
157311 ATTTTTAAAA
157321 AATATTTTTATTATTTT
1 AATATTTTTATTATTTT
* *
157338 AATA-TTTAATAATTTT
1 AATATTTTTATTATTTT
*
157354 ATATATTTTTTATT-TATTG
1 A-ATA-TTTTTATTAT-TTT
*
157373 AAAATTTTTATATAGTTTT
1 AATATTTTTAT-TA-TTTT
157392 AAT
1 AAT
157395 GTTTATTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
16 11 0.26
17 14 0.33
18 4 0.10
19 12 0.29
20 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
AATATTTTTATTATTTT
Found at i:157360 original size:28 final size:26
Alignment explanation
Indices: 157319--157399 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 26
157309 TTATTTTTAA
157319 AAAATATTTT-TATTATTTTAATATTT
1 AAAAT-TTTTATATTATTTTAATATTT
* *
157345 AATAATTTTATATATT-TTTTATTTATTG
1 AA-AATTTT-TATATTATTTTA-ATATTT
*
157373 AAAATTTTTATA-TAGTTTTAATGTTT
1 AAAATTTTTATATTA-TTTTAATATTT
157399 A
1 A
157400 TTTTAGATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
25 1 0.02
26 13 0.30
27 20 0.45
28 10 0.23
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (26 bp):
AAAATTTTTATATTATTTTAATATTT
Found at i:159659 original size:31 final size:31
Alignment explanation
Indices: 159617--159687 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
159607 TTAACGCATA
* * *
159617 GGTGACTAAAATGAAAACGCCCTAAAAGTTG
1 GGTGACCAAAATAAAAACGCCCTAAAAATTG
*
159648 GGTGACCAAAATAAAAACGTCCTAAAAATTG
1 GGTGACCAAAATAAAAACGCCCTAAAAATTG
*
159679 AGTGACCAA
1 GGTGACCAA
159688 CTAAGTAGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (31 bp):
GGTGACCAAAATAAAAACGCCCTAAAAATTG
Found at i:164784 original size:18 final size:19
Alignment explanation
Indices: 164740--164786 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
164730 ATTTAATTTG
164740 ATTTTTGTAAAAAAATTAAA
1 ATTTTT-TAAAAAAATTAAA
* * *
164760 ATATTTTAAAATAA-TATA
1 ATTTTTTAAAAAAATTAAA
164778 ATTTTTTAA
1 ATTTTTTAA
164787 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 11 0.48
19 7 0.30
20 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTTTTTAAAAAAATTAAA
Found at i:168365 original size:27 final size:26
Alignment explanation
Indices: 168321--168378 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
168311 TCTCATCCCT
168321 ATTTTACCCCTAACAAAAAATTTGACA
1 ATTTTACCCCTAAC-AAAAATTTGACA
** * *
168348 ATTTTACCCCTATTAAAATTTTGACG
1 ATTTTACCCCTAACAAAAATTTGACA
168374 ATTTT
1 ATTTT
168379 TCCCTTGGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.40
Consensus pattern (26 bp):
ATTTTACCCCTAACAAAAATTTGACA
Found at i:168555 original size:12 final size:12
Alignment explanation
Indices: 168535--168571 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
168525 AGGATTGCAA
168535 ATTTCCATTTTT
1 ATTTCCATTTTT
* *
168547 ATTTTCATTTTA
1 ATTTCCATTTTT
168559 ATTTCCATTTTT
1 ATTTCCATTTTT
168571 A
1 A
168572 AAAACCTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTCCATTTTT
Found at i:176943 original size:2 final size:2
Alignment explanation
Indices: 176936--176963 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
176926 ATACATTCAT
176936 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
176964 GGATACCTCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:183186 original size:2 final size:2
Alignment explanation
Indices: 183181--183209 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
183171 ATATTATATA
183181 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
183210 ATGTATGTAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:186081 original size:19 final size:20
Alignment explanation
Indices: 186044--186083 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
186034 CTGATTTAAT
186044 TGTAAAAGAAATTTAAAAAA
1 TGTAAAAGAAATTTAAAAAA
* *
186064 TGTAAAA-AGATTTTAAAAA
1 TGTAAAAGAAATTTAAAAAA
186083 T
1 T
186084 AACAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (20 bp):
TGTAAAAGAAATTTAAAAAA
Found at i:195868 original size:30 final size:28
Alignment explanation
Indices: 195814--195870 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
195804 AAGTGATTAA
*
195814 GTACCAAATTAAAAAATGTCAAATTTAT
1 GTACCAAATTAAAAAATATCAAATTTAT
195842 GTACCAAATTAAAAAATATATCAAATTTA
1 GTACCAAATT-AAAAA-ATATCAAATTTA
195871 AATATGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 10 0.38
29 5 0.19
30 11 0.42
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (28 bp):
GTACCAAATTAAAAAATATCAAATTTAT
Found at i:196358 original size:14 final size:15
Alignment explanation
Indices: 196336--196388 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
196326 ATTTTGATTT
*
196336 TATATAATTTT-ATA
1 TATAAAATTTTCATA
* *
196350 TATAAAATTTTGATT
1 TATAAAATTTTCATA
*
196365 TGATTAAATTTTCATA
1 T-ATAAAATTTTCATA
196381 TATAAAAT
1 TATAAAAT
196389 AATGGTTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 10 0.32
15 9 0.29
16 12 0.39
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
TATAAAATTTTCATA
Found at i:196360 original size:30 final size:31
Alignment explanation
Indices: 196324--196388 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
196314 TGTCGTACAT
*
196324 AAATTTTGATTTTA-TATAATTTT-ATATATA
1 AAATTTTGATTTGATTA-AATTTTCATATATA
196354 AAATTTTGATTTGATTAAATTTTCATATATA
1 AAATTTTGATTTGATTAAATTTTCATATATA
196385 AAAT
1 AAAT
196389 AATGGTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (31 bp):
AAATTTTGATTTGATTAAATTTTCATATATA
Found at i:202555 original size:9 final size:10
Alignment explanation
Indices: 202513--202575 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
202503 AATATTGTAA
202513 TTTTATATAT
1 TTTTATATAT
202523 TTTTA-ATA-
1 TTTTATATAT
* *
202531 ATTTACATACT
1 TTTTATATA-T
202542 TTTTATA-AT
1 TTTTATATAT
*
202551 TTTTAAATAT
1 TTTTATATAT
*
202561 TTTTTTATAT
1 TTTTATATAT
202571 TTTTA
1 TTTTA
202576 ATAAGTATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
8 4 0.10
9 13 0.31
10 20 0.48
11 5 0.12
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTATATAT
Found at i:202593 original size:21 final size:20
Alignment explanation
Indices: 202541--202593 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
202531 ATTTACATAC
*
202541 TTTTTATAATTTTTAAATATT
1 TTTTTA-AATTTTTAAATATA
*
202562 TTTTTATATTTTT-AATAAGTA
1 TTTTTAAATTTTTAAAT-A-TA
202583 TTTTTAAATTT
1 TTTTTAAATTT
202594 AACAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.11
20 7 0.26
21 17 0.63
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTTAAATTTTTAAATATA
Found at i:204043 original size:12 final size:12
Alignment explanation
Indices: 204026--204084 Score: 73
Period size: 12 Copynumber: 4.9 Consensus size: 12
204016 AACAGCAAAA
204026 CAACAAAAATAG
1 CAACAAAAATAG
*
204038 CAACAAAAATAA
1 CAACAAAAATAG
*
204050 CAGCAAAAATAG
1 CAACAAAAATAG
* *
204062 CAACAAAAACAT
1 CAACAAAAATAG
*
204074 CAATAAAAATA
1 CAACAAAAATA
204085 ACAGCACCAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.68, C:0.17, G:0.05, T:0.10
Consensus pattern (12 bp):
CAACAAAAATAG
Found at i:204051 original size:24 final size:24
Alignment explanation
Indices: 204024--204084 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
204014 AAAACAGCAA
*
204024 AACAACAAAAATAGCAACAAAAAT
1 AACAACAAAAATAGCAACAAAAAC
*
204048 AACAGCAAAAATAGCAACAAAAAC
1 AACAACAAAAATAGCAACAAAAAC
* *
204072 ATCAATAAAAATA
1 AACAACAAAAATA
204085 ACAGCACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.10
Consensus pattern (24 bp):
AACAACAAAAATAGCAACAAAAAC
Found at i:204082 original size:36 final size:37
Alignment explanation
Indices: 204026--204107 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 37
204016 AACAGCAAAA
*
204026 CAACAAAAATAGCAACAAAAATAACAGCA-AAAATAG
1 CAACAAAAACAGCAACAAAAATAACAGCACAAAATAG
* *
204062 CAACAAAAACATCAATAAAAATAACAGCACCAAAATAG
1 CAACAAAAACAGCAACAAAAATAACAGCA-CAAAATAG
*
204100 TAA-AAAAA
1 CAACAAAAA
204108 GCACCAAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 26 0.65
37 5 0.12
38 9 0.22
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.10
Consensus pattern (37 bp):
CAACAAAAACAGCAACAAAAATAACAGCACAAAATAG
Found at i:204127 original size:21 final size:20
Alignment explanation
Indices: 204087--204177 Score: 107
Period size: 21 Copynumber: 4.6 Consensus size: 20
204077 TAAAAATAAC
*
204087 AGCACCAAAATAGTAAAAAA
1 AGCACCAAAACAGTAAAAAA
204107 AGCACCAAAACAGT-AAAAA
1 AGCACCAAAACAGTAAAAAA
*
204126 A--ACCAAAACAATAAAAAA
1 AGCACCAAAACAGTAAAAAA
*
204144 AGCAACAAAAACAGTAAAAAA
1 AGC-ACCAAAACAGTAAAAAA
*
204165 TAGCATCAAAACA
1 -AGCACCAAAACA
204178 ACAATATAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.17
18 6 0.10
19 6 0.10
20 13 0.22
21 22 0.37
22 3 0.05
ACGTcount: A:0.67, C:0.18, G:0.08, T:0.08
Consensus pattern (20 bp):
AGCACCAAAACAGTAAAAAA
Found at i:204131 original size:37 final size:38
Alignment explanation
Indices: 204090--204164 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 38
204080 AAATAACAGC
* * *
204090 ACCAAAATAGTAAAAAAAGC-ACCAAAACAGTAAAAAA
1 ACCAAAACAATAAAAAAAGCAACAAAAACAGTAAAAAA
204127 ACCAAAACAATAAAAAAAGCAACAAAAACAGTAAAAAA
1 ACCAAAACAATAAAAAAAGCAACAAAAACAGTAAAAAA
204165 TAGCATCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 18 0.53
38 16 0.47
ACGTcount: A:0.71, C:0.16, G:0.07, T:0.07
Consensus pattern (38 bp):
ACCAAAACAATAAAAAAAGCAACAAAAACAGTAAAAAA
Found at i:216012 original size:19 final size:19
Alignment explanation
Indices: 215988--216024 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
215978 AAATTGTAAA
215988 AAATGTCACATTACAAAAG
1 AAATGTCACATTACAAAAG
*
216007 AAATGTCACATTTCAAAA
1 AAATGTCACATTACAAAA
216025 TCTTAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.24
Consensus pattern (19 bp):
AAATGTCACATTACAAAAG
Found at i:219517 original size:3 final size:3
Alignment explanation
Indices: 219509--219540 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
219499 GTTCATCCTT
219509 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
219541 TTGTGCGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:220496 original size:42 final size:44
Alignment explanation
Indices: 220429--220513 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 44
220419 CTTCCTACGA
*
220429 AAACGCCGCAAAAGAACATGGTCTTTAACGGCGCTTT-TCACAC
1 AAACGCCGCAAAAGAACATGGTCTTTAACGGCACTTTCTCACAC
* * * *
220472 AAACGGCGCTAAAG-ACATGTTCTTTAGCGGCACTTTCTCACA
1 AAACGCCGCAAAAGAACATGGTCTTTAACGGCACTTTCTCACA
220514 AATGTCACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 19 0.53
43 17 0.47
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (44 bp):
AAACGCCGCAAAAGAACATGGTCTTTAACGGCACTTTCTCACAC
Found at i:230753 original size:29 final size:29
Alignment explanation
Indices: 230720--230787 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
230710 TAAATATTGT
230720 TGAGTGTTCTCAGAGGGAAGATTTGGAAG
1 TGAGTGTTCTCAGAGGGAAGATTTGGAAG
230749 TGAGTGTTCTCAGAGGGAAGATTTGGAAG
1 TGAGTGTTCTCAGAGGGAAGATTTGGAAG
230778 TGAGTGTTCT
1 TGAGTGTTCT
230788 AGTCTTTAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.25, C:0.07, G:0.37, T:0.31
Consensus pattern (29 bp):
TGAGTGTTCTCAGAGGGAAGATTTGGAAG
Found at i:235574 original size:26 final size:26
Alignment explanation
Indices: 235545--235628 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
235535 TAAGAATCAA
235545 AATTAAATATTATATTTAACTTAATT
1 AATTAAATATTATATTTAACTTAATT
* * * * *
235571 AATT-AATCTTTGTTTTTAA--GAATCAA
1 AATTAAAT-ATTATATTTAACTTAAT--T
235597 AATTAAATATTATATTTAACTTAATT
1 AATTAAATATTATATTTAACTTAATT
235623 AATTAA
1 AATTAA
235629 TCTACACATC
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
24 3 0.07
25 3 0.07
26 30 0.71
27 3 0.07
28 3 0.07
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (26 bp):
AATTAAATATTATATTTAACTTAATT
Found at i:235605 original size:52 final size:52
Alignment explanation
Indices: 235527--235631 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
235517 TCTTCTAGTT
235527 TTTGTTTTTAAGAATCAAAATTAAATATTATATTTAACTTAATTAATTAATC
1 TTTGTTTTTAAGAATCAAAATTAAATATTATATTTAACTTAATTAATTAATC
235579 TTTGTTTTTAAGAATCAAAATTAAATATTATATTTAACTTAATTAATTAATC
1 TTTGTTTTTAAGAATCAAAATTAAATATTATATTTAACTTAATTAATTAATC
235631 T
1 T
235632 ACACATCCAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (52 bp):
TTTGTTTTTAAGAATCAAAATTAAATATTATATTTAACTTAATTAATTAATC
Found at i:240938 original size:31 final size:31
Alignment explanation
Indices: 240898--240993 Score: 83
Period size: 30 Copynumber: 3.1 Consensus size: 31
240888 ATAATAACAC
*
240898 ATTTAATTTTTAATATTTATATATTCTATCA
1 ATTTAATTTTTAATATTTATATATTCTATAA
* *
240929 ATTTGA-TTTTAAT-TTTAAATAATT-TAATAA
1 ATTTAATTTTTAATATTTATAT-ATTCT-ATAA
* * *
240959 ATTTAATCTTTT-ATATTTATAAAATCTATGA
1 ATTTAAT-TTTTAATATTTATATATTCTATAA
240990 ATTT
1 ATTT
240994 GATTCTCAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
29 7 0.14
30 18 0.35
31 16 0.31
32 10 0.20
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTTAATTTTTAATATTTATATATTCTATAA
Found at i:250763 original size:29 final size:29
Alignment explanation
Indices: 250719--250776 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
250709 TTTTCAGTCG
* * *
250719 TTCAATTATCAGAAGTTATAAAATAATCA
1 TTCAATTATAAAAAGTTACAAAATAATCA
250748 TTCAATTATAAAAAGTTACAAAATAATCA
1 TTCAATTATAAAAAGTTACAAAATAATCA
250777 CCCCAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.52, C:0.10, G:0.05, T:0.33
Consensus pattern (29 bp):
TTCAATTATAAAAAGTTACAAAATAATCA
Found at i:251325 original size:16 final size:16
Alignment explanation
Indices: 251300--251353 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
251290 ATAAATTATG
*
251300 TTTTCCATCCTTTTAA
1 TTTTCTATCCTTTTAA
* *
251316 TTTTCTATCCCTTCAA
1 TTTTCTATCCTTTTAA
*
251332 CTTTTC-ATCATTTTAA
1 -TTTTCTATCCTTTTAA
251348 TTTTCT
1 TTTTCT
251354 TTTTACTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 5 0.17
16 20 0.67
17 5 0.17
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTCTATCCTTTTAA
Found at i:252828 original size:11 final size:11
Alignment explanation
Indices: 252812--252837 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
252802 AATATTTTAC
252812 AATAAATTAAA
1 AATAAATTAAA
252823 AATAAATTAAA
1 AATAAATTAAA
252834 AATA
1 AATA
252838 TTTATACTTA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAAATTAAA
Found at i:260209 original size:13 final size:13
Alignment explanation
Indices: 260179--260208 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
260169 TCATTTCGAG
260179 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
260192 TTTTTCTTTTT-T
1 TTTTTCTTTTTCT
260204 TTTTT
1 TTTTT
260209 TATTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:261848 original size:14 final size:14
Alignment explanation
Indices: 261829--261860 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
261819 GAGAATAAAG
261829 ATTTAATTAAATAA
1 ATTTAATTAAATAA
*
261843 ATTTAATTAATTAA
1 ATTTAATTAAATAA
261857 ATTT
1 ATTT
261861 TTTAAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTAATTAAATAA
Found at i:270454 original size:6 final size:6
Alignment explanation
Indices: 270443--270473 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
270433 TGAAAAATGC
270443 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
270474 TCATCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Done.