Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015351.1 Kokia drynarioides strain JFW-HI SEQ_130398, 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: 277395
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 214 characters in sequence are not A, C, G, or T
Found at i:4912 original size:22 final size:23
Alignment explanation
Indices: 4880--4923 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
4870 CTTGAAAATG
4880 GAAGAAAGGAAGAAAATGAAAGA
1 GAAGAAAGGAAGAAAATGAAAGA
*
4903 GAAG-AAGGAAGGAAATGAAAG
1 GAAGAAAGGAAGAAAATGAAAG
4924 GGGAGAAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (23 bp):
GAAGAAAGGAAGAAAATGAAAGA
Found at i:5074 original size:123 final size:122
Alignment explanation
Indices: 4930--5174 Score: 445
Period size: 123 Copynumber: 2.0 Consensus size: 122
4920 AAAGGGGAGA
*
4930 AGACAAATTTTGGAAGGAAAAAAAGAAGAAATTGGTGCCCGTGTCTAAGGCTAAAAAGGTAATTA
1 AGACAAATTTTGGAAGAAAAAAAAGAAGAAATTGGTGCCCGTGTCTAAGGCTAAAAAGGTAATTA
*
4995 AACTTTCTAAAAGCCCGTTTAGGCTGCTACTGGTGATATTTTTAACTTTTTTAATGGT
66 AACTTTCTAAAAGCCCGTTTAGGCTGCTACTGGTAATA-TTTTAACTTTTTTAATGGT
*
5053 AGACTAATTTTGGAAGAAAAAAAAGAAGAAATTGGTGCCCGTGTCTAAGGCTAAAAAGGTAATTA
1 AGACAAATTTTGGAAGAAAAAAAAGAAGAAATTGGTGCCCGTGTCTAAGGCTAAAAAGGTAATTA
*
5118 AACTTTCTAAAAGCCCGTTTGGGCTGCTACTGGTAATATTTTAACTTTTTTAATGGT
66 AACTTTCTAAAAGCCCGTTTAGGCTGCTACTGGTAATATTTTAACTTTTTTAATGGT
5175 TTAAGAAACC
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
122 19 0.16
123 99 0.84
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (122 bp):
AGACAAATTTTGGAAGAAAAAAAAGAAGAAATTGGTGCCCGTGTCTAAGGCTAAAAAGGTAATTA
AACTTTCTAAAAGCCCGTTTAGGCTGCTACTGGTAATATTTTAACTTTTTTAATGGT
Found at i:13072 original size:5 final size:5
Alignment explanation
Indices: 13062--13100 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
13052 GCCATACATT
* * *
13062 GGATG GGATG GGATG GGATA GGATA GGATA GGATA GGAT
1 GGATA GGATA GGATA GGATA GGATA GGATA GGATA GGAT
13101 GGGGGTTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.49, T:0.21
Consensus pattern (5 bp):
GGATA
Found at i:13085 original size:15 final size:15
Alignment explanation
Indices: 13062--13103 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
13052 GCCATACATT
* *
13062 GGATGGGATGGGATG
1 GGATAGGATGGGATA
*
13077 GGATAGGATAGGATA
1 GGATAGGATGGGATA
13092 GGATAGGATGGG
1 GGATAGGATGGG
13104 GGTTGTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.52, T:0.19
Consensus pattern (15 bp):
GGATAGGATGGGATA
Found at i:13747 original size:1 final size:1
Alignment explanation
Indices: 13702--13727 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
13692 TTAAATTTAG
13702 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
13728 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15498 original size:2 final size:2
Alignment explanation
Indices: 15491--15527 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
15481 GGTAAGGAAG
*
15491 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
15528 GAATTTACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20834 original size:71 final size:71
Alignment explanation
Indices: 20675--20820 Score: 229
Period size: 71 Copynumber: 2.1 Consensus size: 71
20665 GGTTCTACCA
* * *
20675 ATACAACCAAGACTTTTATCGATAGAACAAACTCCAGAGAGCAAAGAAATTGTGGCCTAGGACTT
1 ATACAACCAAGAGTTCTATCGATAAAACAAACTCCAGAGAGCAAAGAAATTGTGGCCTAGGACTT
20740 CTATCG
66 CTATCG
* * * *
20746 ATACAACCAAGAGTTCTATCGGTAAAACAAACTCCAGAGAGCAAAGAAGTTGTGGCTTGGGACTT
1 ATACAACCAAGAGTTCTATCGATAAAACAAACTCCAGAGAGCAAAGAAATTGTGGCCTAGGACTT
20811 CTATCG
66 CTATCG
20817 ATAC
1 ATAC
20821 TTGGAAGGCT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (71 bp):
ATACAACCAAGAGTTCTATCGATAAAACAAACTCCAGAGAGCAAAGAAATTGTGGCCTAGGACTT
CTATCG
Found at i:21673 original size:23 final size:23
Alignment explanation
Indices: 21630--21673 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
21620 TCACTTGGCA
*
21630 TTATTTTATAAAAAATGTACATT
1 TTATTTTATAAAAAATATACATT
* *
21653 TTATTTTATTAAATATATACA
1 TTATTTTATAAAAAATATACA
21674 AATTTTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
TTATTTTATAAAAAATATACATT
Found at i:21695 original size:25 final size:25
Alignment explanation
Indices: 21662--21719 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
21652 TTTATTTTAT
* *
21662 TAAATATATACAAATTTTAAAAATTA
1 TAAAAATATACAAA-TATAAAAATTA
* *
21688 -AAAAATATATATATATAAAAATTA
1 TAAAAATATACAAATATAAAAATTA
21712 TAAAAATA
1 TAAAAATA
21720 AATATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (25 bp):
TAAAAATATACAAATATAAAAATTA
Found at i:21724 original size:25 final size:24
Alignment explanation
Indices: 21679--21725 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
21669 ATACAAATTT
*
21679 TAAAAATTAAAAAATATATATATA
1 TAAAAATTAAAAAATAAATATATA
21703 TAAAAATTATAAAAATAAATATA
1 TAAAAATTA-AAAAATAAATATA
21726 AAATCTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (24 bp):
TAAAAATTAAAAAATAAATATATA
Found at i:21815 original size:15 final size:16
Alignment explanation
Indices: 21797--21833 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
21787 ACTCTAAAAT
*
21797 ATATATAATAATT-AA
1 ATATATAAAAATTCAA
21812 ATATATAAAAATTCAA
1 ATATATAAAAATTCAA
21828 A-ATATA
1 ATATATA
21834 CAATCTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATATAAAAATTCAA
Found at i:21830 original size:17 final size:18
Alignment explanation
Indices: 21791--21833 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
21781 TATAAAACTC
21791 TAAAATATATATAATAAT
1 TAAAATATATATAATAAT
21809 T-AAATATATA-AA-AAT
1 TAAAATATATATAATAAT
21824 TCAAAATATA
1 T-AAAATATA
21834 CAATCTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.17
16 2 0.09
17 16 0.70
18 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATATATAATAAT
Found at i:21851 original size:9 final size:9
Alignment explanation
Indices: 21791--21864 Score: 57
Period size: 9 Copynumber: 8.7 Consensus size: 9
21781 TATAAAACTC
21791 TAAAATATA
1 TAAAATATA
*
21800 TATAATA-A
1 TAAAATATA
*
21808 TTAAATATA
1 TAAAATATA
21817 TAAAA-AT-
1 TAAAATATA
*
21824 TCAAA-ATA
1 TAAAATATA
* *
21832 TACAATCTA
1 TAAAATATA
21841 TAAAATATA
1 TAAAATATA
* *
21850 TAAACTCTA
1 TAAAATATA
21859 TAAAAT
1 TAAAAT
21865 TATTAAAAAT
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
7 6 0.12
8 11 0.22
9 32 0.65
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAATATA
Found at i:22479 original size:20 final size:21
Alignment explanation
Indices: 22430--22479 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
22420 ATAACATGAC
* *
22430 TAAAATTAAAAATCAGTTATA
1 TAAAATTTAAAAGCAGTTATA
* *
22451 TATAATTTAAAAGCATTTA-A
1 TAAAATTTAAAAGCAGTTATA
22471 TAAAATTTA
1 TAAAATTTA
22480 TATAGAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAAATTTAAAAGCAGTTATA
Found at i:24126 original size:226 final size:225
Alignment explanation
Indices: 23709--24309 Score: 669
Period size: 226 Copynumber: 2.6 Consensus size: 225
23699 ATATCGACGA
* * * *
23709 TATAGGATGTATTTTAAAACGGTTAAAATATGTTATAGATCCTTATAATTGTTGTAAATTTAAAA
1 TATA-GATGTATTTTAAAAAGGTTAAAATATGTCATAGATCC-TAT-ATTTTTGTAAAATTAAAA
* * * *
23774 TTTAG-TCTTTATACTTTTATTTTTATTAATTTAATCCTTTTACTTTTTAGAATTTCAAGTCTAA
63 TTTAGTTC-TTATACTTTTATTTCTA-AAATTTAATTCTTTTACTTTTCAGAATTTCAAGTCTAA
* * * *
23838 TTGTTAACACTATTAGTGTCAGTATAGGAGTATCTATAATGACAGATTCATTTGTTCGTC-A-A-
126 TTGTTAACACTATTAGTGTCAGTATAAGAGTATCTATAATGACAAATTAATTTATTCGTCAATAG
*
23900 TA-TATATA-CCGATGATATGATTAGGGTCGTTCG
191 TATTATATAGCCGATGATATGATTAGGGTCGTCCG
* * *
23933 TATAGTATGTATTCTAAAAAGGTTAAAAATATGTCATAAATACCTATACTTTTTGTAAAATTGAA
1 TATAG-ATGTATTTTAAAAAGGTT-AAAATATGTCATAGAT-CCTATA-TTTTTGTAAAATTAAA
* *
23998 ATTTAGTTCTTATACTTTTACTTTCTAGAAATCTAATTCTTTTACTTTTCAGAATTTCAAGTCCA
62 ATTTAGTTCTTATACTTTTA-TTTCTA-AAATTTAATTCTTTTACTTTTCAGAATTTCAAGTCTA
* *
24063 ATTGTTAACACCATTAGTGTC-GATATAAGAGTATTTATAATGACAAATTAATTTATTCGTCAAT
125 ATTGTTAACACTATTAGTGTCAG-TATAAGAGTATCTATAATGACAAATTAATTTATTCGTC-A-
* *
24127 ATAGGTATTATATATGCCGATGATATTATTAGTGTCGTCCG
187 ATA-GTATTATATA-GCCGATGATATGATTAGGGTCGTCCG
* * * * *
24168 TATAAGATGTATTTTAAAAAGATTAAAATATGTCATAGATCTCTATTTTTTTATAAATTTAAATT
1 TAT-AGATGTATTTTAAAAAGGTTAAAATATGTCATAGATC-CTATATTTTTGTAAAATTAAAAT
* * * * * * *
24233 TTAGTCCCTATACTTTTATTTCTAATAATTTAA-TCCTTTCCTTCTCAGAATTTCTAGACTAATT
64 TTAGTTCTTATACTTTTATTTCTAA-AATTTAATTCTTTTACTTTTCAGAATTTCAAGTCTAATT
24297 GTTAACACTATTA
128 GTTAACACTATTA
24310 AAATTATTTT
Statistics
Matches: 317, Mismatches: 41, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
223 1 0.00
224 21 0.07
225 48 0.15
226 94 0.30
229 1 0.00
230 1 0.00
231 38 0.12
232 14 0.04
233 37 0.12
234 19 0.06
235 41 0.13
236 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (225 bp):
TATAGATGTATTTTAAAAAGGTTAAAATATGTCATAGATCCTATATTTTTGTAAAATTAAAATTT
AGTTCTTATACTTTTATTTCTAAAATTTAATTCTTTTACTTTTCAGAATTTCAAGTCTAATTGTT
AACACTATTAGTGTCAGTATAAGAGTATCTATAATGACAAATTAATTTATTCGTCAATAGTATTA
TATAGCCGATGATATGATTAGGGTCGTCCG
Found at i:28389 original size:44 final size:44
Alignment explanation
Indices: 28341--28428 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
28331 AATGGATTTA
*
28341 ATTGTCAAGTTGAAAGATCAAATTAAAGAATAAAATATAAATAT
1 ATTGTCAAGCTGAAAGATCAAATTAAAGAATAAAATATAAATAT
28385 ATTGTCAAGCTGAAAGATCAAATTAAAGAATAAAATATAAATAT
1 ATTGTCAAGCTGAAAGATCAAATTAAAGAATAAAATATAAATAT
28429 CAAAGTGGAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (44 bp):
ATTGTCAAGCTGAAAGATCAAATTAAAGAATAAAATATAAATAT
Found at i:30248 original size:10 final size:10
Alignment explanation
Indices: 30233--30262 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
30223 TTTAATTATA
30233 AAAATAAATT
1 AAAATAAATT
30243 AAAAT-AATT
1 AAAATAAATT
30252 AAAATAAATT
1 AAAATAAATT
30262 A
1 A
30263 TATTATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAATAAATT
Found at i:43339 original size:10 final size:10
Alignment explanation
Indices: 43324--43355 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
43314 GACTCGAGTT
*
43324 CGGCCCGGCC
1 CGGCCCGACC
43334 CGGCCCGACC
1 CGGCCCGACC
43344 CGGCCCGACC
1 CGGCCCGACC
43354 CG
1 CG
43356 ACCTGAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.06, C:0.59, G:0.34, T:0.00
Consensus pattern (10 bp):
CGGCCCGACC
Found at i:43347 original size:15 final size:15
Alignment explanation
Indices: 43327--43358 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43317 TCGAGTTCGG
*
43327 CCCGGCCCGGCCCGA
1 CCCGGCCCGACCCGA
43342 CCCGGCCCGACCCGA
1 CCCGGCCCGACCCGA
43357 CC
1 CC
43359 TGAATTCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.62, G:0.28, T:0.00
Consensus pattern (15 bp):
CCCGGCCCGACCCGA
Found at i:44103 original size:24 final size:24
Alignment explanation
Indices: 44072--44117 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
44062 AAACTTTTTT
44072 ACTTTTTCCCAAAAACTTTTACTC
1 ACTTTTTCCCAAAAACTTTTACTC
*
44096 ACTTTTTCCCCAAAACTTTTAC
1 ACTTTTTCCCAAAAACTTTTAC
44118 CCCTTCCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.41
Consensus pattern (24 bp):
ACTTTTTCCCAAAAACTTTTACTC
Found at i:44267 original size:5 final size:5
Alignment explanation
Indices: 44257--44281 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44247 AAAACTATTA
44257 CTCCC CTCCC CTCCC CTCCC CTCCC
1 CTCCC CTCCC CTCCC CTCCC CTCCC
44282 ACCTCCCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (5 bp):
CTCCC
Found at i:44579 original size:19 final size:19
Alignment explanation
Indices: 44555--44601 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
44545 ATATTTATAT
*
44555 TATTGAATTTTTTTAATAA
1 TATTGAATTTTTATAATAA
* *
44574 TATTGAATATTTATATTAA
1 TATTGAATTTTTATAATAA
*
44593 AATTGAATT
1 TATTGAATT
44602 ATTAATGATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TATTGAATTTTTATAATAA
Found at i:44592 original size:22 final size:21
Alignment explanation
Indices: 44540--44592 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 21
44530 AAATTCACAG
* *
44540 TTTTAATATTTATATTATTGAA
1 TTTT-ATATTAATAATATTGAA
44562 TTTT-T-TTAATAATATTGAA
1 TTTTATATTAATAATATTGAA
44581 TATTTATATTAA
1 T-TTTATATTAA
44593 AATTGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 13 0.50
20 4 0.15
21 1 0.04
22 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (21 bp):
TTTTATATTAATAATATTGAA
Found at i:45302 original size:22 final size:23
Alignment explanation
Indices: 45277--45319 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
45267 GTTTTTAATG
45277 TTTATTTATTTTATTA-TTTAGT
1 TTTATTTATTTTATTAGTTTAGT
* *
45299 TTTATTTTTTTTGTTAGTTTA
1 TTTATTTATTTTATTAGTTTA
45320 ATACTCGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (23 bp):
TTTATTTATTTTATTAGTTTAGT
Found at i:46436 original size:6 final size:6
Alignment explanation
Indices: 46425--46452 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
46415 CTCAAACGCA
46425 TGTGGG TGTGGG TGTGGG TGTGGG TGTG
1 TGTGGG TGTGGG TGTGGG TGTGGG TGTG
46453 TACAAATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (6 bp):
TGTGGG
Found at i:49579 original size:28 final size:29
Alignment explanation
Indices: 49539--49594 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
49529 GATTAGTCAT
*
49539 TTTTTAGAGGGATCGAAATTAA-ATTTTAA
1 TTTTTAGAAGGAT-GAAATTAAGATTTTAA
*
49568 TTTTTA-AAGGATTAAATTAAGATTTTA
1 TTTTTAGAAGGATGAAATTAAGATTTTA
49595 TCATTTTAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.29
28 11 0.46
29 6 0.25
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (29 bp):
TTTTTAGAAGGATGAAATTAAGATTTTAA
Found at i:49601 original size:29 final size:27
Alignment explanation
Indices: 49554--49622 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 27
49544 AGAGGGATCG
49554 AAATTAAATTTTAATTTTTAAAG-GATT
1 AAATTAAATTTTAATTTTT-AAGTGATT
49581 AAATTAAGATTTT-ATCATTTTAAGTGATT
1 AAATTAA-ATTTTAAT--TTTTAAGTGATT
49610 AAAATATAAATTT
1 -AAAT-TAAATTT
49623 ACTTTTACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
27 9 0.25
28 8 0.22
29 8 0.22
30 8 0.22
31 3 0.08
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (27 bp):
AAATTAAATTTTAATTTTTAAGTGATT
Found at i:60626 original size:33 final size:34
Alignment explanation
Indices: 60584--60666 Score: 123
Period size: 33 Copynumber: 2.4 Consensus size: 34
60574 AAAGTTCAAG
*
60584 TAAATAATATTTGGGTAAGGTAAAAGATAAAAAAT
1 TAAA-AATATTTGGGTAAGATAAAAGATAAAAAAT
* *
60619 T-AAAATATTTTGATAAGATAAAAGATAAAAAAT
1 TAAAAATATTTGGGTAAGATAAAAGATAAAAAAT
60652 TAAAAATATTTGGGT
1 TAAAAATATTTGGGT
60667 TTAGTTTACG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 28 0.67
34 13 0.31
35 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (34 bp):
TAAAAATATTTGGGTAAGATAAAAGATAAAAAAT
Found at i:62820 original size:26 final size:26
Alignment explanation
Indices: 62750--62820 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
62740 TACTTTTATG
62750 TTATTTAAAATTTTAGTTTGTACTAAA
1 TTATTTAAAATTTTA-TTTGTACTAAA
** * *
62777 TTCA-AAAAAAATTAATTTGTACTAAA
1 TT-ATTTAAAATTTTATTTGTACTAAA
62803 TTATTTAAAATTTTATTT
1 TTATTTAAAATTTTATTT
62821 CTAAAATTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
25 1 0.03
26 23 0.68
27 9 0.26
28 1 0.03
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (26 bp):
TTATTTAAAATTTTATTTGTACTAAA
Found at i:70540 original size:53 final size:53
Alignment explanation
Indices: 70477--70582 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
70467 CTTGAATTCT
*
70477 GGGTTTCTGTCAGATTTGGCATTACTGTATATGTGATTTGTCCTTAGGGTCCA
1 GGGTTTCTGTCAGATTTGGCATTACCGTATATGTGATTTGTCCTTAGGGTCCA
70530 GGGTTTCTGTCAGATTTGGCATTACCGTATATGTGATTTGTCCTTAGGGTCCA
1 GGGTTTCTGTCAGATTTGGCATTACCGTATATGTGATTTGTCCTTAGGGTCCA
70583 ATGTTCTAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.17, C:0.16, G:0.26, T:0.41
Consensus pattern (53 bp):
GGGTTTCTGTCAGATTTGGCATTACCGTATATGTGATTTGTCCTTAGGGTCCA
Found at i:73249 original size:2 final size:2
Alignment explanation
Indices: 73242--73271 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
73232 TCTTCCTCAA
73242 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
73272 CTTTTTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:73834 original size:29 final size:30
Alignment explanation
Indices: 73787--73845 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
73777 GAATTAGATC
* * *
73787 AAATCAAAATTTCTTGTATAAAATTACACA
1 AAATCAAAAGTTCATGTATAAAATAACACA
*
73817 AAATC-AAAGTTCATGTATATAATAACACA
1 AAATCAAAAGTTCATGTATAAAATAACACA
73846 TTAAACCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 20 0.80
30 5 0.20
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAAGTTCATGTATAAAATAACACA
Found at i:81819 original size:23 final size:23
Alignment explanation
Indices: 81792--81837 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
81782 AAGTAAGAAA
81792 TAAAGAAAACATTTATATCAAAT
1 TAAAGAAAACATTTATATCAAAT
* *
81815 TAAAGATAACATTTATATTAAAT
1 TAAAGAAAACATTTATATCAAAT
81838 GTTTACTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (23 bp):
TAAAGAAAACATTTATATCAAAT
Found at i:86367 original size:47 final size:48
Alignment explanation
Indices: 86275--86368 Score: 113
Period size: 47 Copynumber: 2.0 Consensus size: 48
86265 TGAAGCATGA
* ** *
86275 GAATTTTAGGTTTTAAATTTTAGTTTTTTTTTTATGTAAATTATGTGT
1 GAATTTTAGCTTTTAAATTTTAGTTTTGATTTAATGTAAATTATGTGT
86323 GAATTTTA-CTTTTAAATTTTA-TTTTGATTTAAT-TATAATATATGTG
1 GAATTTTAGCTTTTAAATTTTAGTTTTGATTTAATGTA-AAT-TATGTG
86369 ATTATAATGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
45 2 0.05
46 12 0.30
47 18 0.45
48 8 0.20
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.59
Consensus pattern (48 bp):
GAATTTTAGCTTTTAAATTTTAGTTTTGATTTAATGTAAATTATGTGT
Found at i:86527 original size:28 final size:29
Alignment explanation
Indices: 86487--86542 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
86477 GGATTTTATC
* *
86487 AATTTAGTCCCTT-TATTATTAAATAAATT
1 AATTTAATCCCTTGTACTATTAAA-AAATT
86516 AATTTAAT-CCTTGTACTATTAAAAAAT
1 AATTTAATCCCTTGTACTATTAAAAAAT
86543 CAAACAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (29 bp):
AATTTAATCCCTTGTACTATTAAAAAATT
Found at i:87476 original size:12 final size:12
Alignment explanation
Indices: 87447--87486 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
87437 CGGTTTGATT
87447 AAAT-AATTTAA
1 AAATAAATTTAA
87458 AATATAAATTTAA
1 AA-ATAAATTTAA
87471 AAATAAA-TTAA
1 AAATAAATTTAA
87482 AAATA
1 AAATA
87487 GAGAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.41
12 7 0.26
13 9 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATAAATTTAA
Found at i:101591 original size:3 final size:3
Alignment explanation
Indices: 101583--101607 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
101573 GAAGATGCAA
101583 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
101608 TCTAAAGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:102636 original size:24 final size:24
Alignment explanation
Indices: 102609--102657 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
102599 ATCATTCTTC
*
102609 TCCAATTAATAAATAAGGAAAATG
1 TCCAATTAACAAATAAGGAAAATG
102633 TCCAATTAACAAATAAGGAAAATG
1 TCCAATTAACAAATAAGGAAAATG
102657 T
1 T
102658 ATTCTTCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
TCCAATTAACAAATAAGGAAAATG
Found at i:104251 original size:90 final size:91
Alignment explanation
Indices: 104142--104323 Score: 348
Period size: 90 Copynumber: 2.0 Consensus size: 91
104132 TCAAATTTTC
104142 TTATGTTTTTCTTTTAATTCTTTTATTCAACATAAGAGTTTTATTAAATTATTTATTAATTATGT
1 TTATGTTTTTCTTTTAATTCTTTTATTCAACATAAGAGTTTTATTAAATTATTTATTAATTATGT
104207 TGTTTTCTC-AAACATCATGATGACT
66 TGTTTTCTCAAAACATCATGATGACT
*
104232 TTATGTTTTTCTTTTAATTCTTTTATTTAACATAAGAGTTTTATTAAATTATTTATTAATTATGT
1 TTATGTTTTTCTTTTAATTCTTTTATTCAACATAAGAGTTTTATTAAATTATTTATTAATTATGT
104297 TGTTTTCTCAAAACATCATGATGACT
66 TGTTTTCTCAAAACATCATGATGACT
104323 T
1 T
104324 CTTCAATAAA
Statistics
Matches: 90, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
90 73 0.81
91 17 0.19
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (91 bp):
TTATGTTTTTCTTTTAATTCTTTTATTCAACATAAGAGTTTTATTAAATTATTTATTAATTATGT
TGTTTTCTCAAAACATCATGATGACT
Found at i:105269 original size:31 final size:30
Alignment explanation
Indices: 105208--105270 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
105198 TAAACTTTAA
* * *
105208 AATTCAAAAAATGCAAAATTAAAATGAATT
1 AATTCAAAAAATGAAAAACTAAAATAAATT
* *
105238 AATTCAAAAAATATAAAAACTAAATTAAATT
1 AATTCAAAAAAT-GAAAAACTAAAATAAATT
105269 AA
1 AA
105271 ATTAAAATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.27
Consensus pattern (30 bp):
AATTCAAAAAATGAAAAACTAAAATAAATT
Found at i:108576 original size:19 final size:19
Alignment explanation
Indices: 108552--108588 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
108542 TTAATTAAAA
108552 ATAAAATA-ATATTTATTAT
1 ATAAAATACATA-TTATTAT
108571 ATAAAATACATATTATTA
1 ATAAAATACATATTATTA
108589 ACAATACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
ATAAAATACATATTATTAT
Found at i:108783 original size:30 final size:29
Alignment explanation
Indices: 108715--108784 Score: 70
Period size: 30 Copynumber: 2.3 Consensus size: 29
108705 AATTTTATAT
**
108715 AATTATATATTAATTAATTGAAATGTTTA
1 AATTATATATTAATTAATTGAAACATTTA
* *
108744 AATAAATATATTAA-TAATGTGTCAACATTTA
1 AAT-TATATATTAATTAAT-TG-AAACATTTA
108775 AATTATATAT
1 AATTATATAT
108785 AAAATTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
29 7 0.21
30 17 0.52
31 9 0.27
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (29 bp):
AATTATATATTAATTAATTGAAACATTTA
Found at i:132603 original size:12 final size:12
Alignment explanation
Indices: 132586--132612 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
132576 ATTATACTAC
132586 TCTCCTTCTTCT
1 TCTCCTTCTTCT
132598 TCTCCTTCTTCT
1 TCTCCTTCTTCT
132610 TCT
1 TCT
132613 TCTCCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTCCTTCTTCT
Found at i:132625 original size:15 final size:15
Alignment explanation
Indices: 132590--132619 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
132580 TACTACTCTC
132590 CTTCTTCTTCTCCTT
1 CTTCTTCTTCTCCTT
132605 CTTCTTCTTCTCCTT
1 CTTCTTCTTCTCCTT
132620 TCTCTTGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
CTTCTTCTTCTCCTT
Found at i:141197 original size:15 final size:17
Alignment explanation
Indices: 141177--141214 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
141167 AATCCTTTAA
141177 AAATTATAAAAAT-AT-
1 AAATTATAAAAATGATG
*
141192 AAATTATTAAAATGATG
1 AAATTATAAAAATGATG
141209 AAATTA
1 AAATTA
141215 CATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AAATTATAAAAATGATG
Found at i:150173 original size:30 final size:29
Alignment explanation
Indices: 150104--150177 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 29
150094 ATATAATCTA
* *
150104 ATTAAATTTTTAAATAATTAATATTAATT
1 ATTAAAATATTAAATAATTAATATTAATT
*
150133 ACTTAGAAATATTAAA-AATTAATATTTCATAT
1 A-TTA-AAATATTAAATAATTAATA-TTAAT-T
150165 ATTAAAATATTAA
1 ATTAAAATATTAA
150178 CAAAAAGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 1 0.03
30 20 0.53
31 15 0.39
32 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (29 bp):
ATTAAAATATTAAATAATTAATATTAATT
Found at i:153209 original size:77 final size:78
Alignment explanation
Indices: 153082--153236 Score: 294
Period size: 77 Copynumber: 2.0 Consensus size: 78
153072 TGGAGGAAAG
153082 ATTTGGGGGTATGTTTTGAGAATGTGAAAAGCCAAGGGAAGGTGAAGTGAAGATGTCAGAAAGGG
1 ATTTGGGGGTATGTTTTGAGAATGTGAAAAGCCAAGGGAAGGTGAAGTGAAGATGTCAGAAAGGG
153147 G-TTTATTTTTAT
66 GTTTTATTTTTAT
*
153159 ATTTGGGGGTATGTTTTGAGAATGTGAAAAGCTAAGGGAAGGTGAAGTGAAGATGTCAGAAAGGG
1 ATTTGGGGGTATGTTTTGAGAATGTGAAAAGCCAAGGGAAGGTGAAGTGAAGATGTCAGAAAGGG
153224 GTTTTATTTTTAT
66 GTTTTATTTTTAT
153237 TTTATTTTTT
Statistics
Matches: 76, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
77 65 0.86
78 11 0.14
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.32
Consensus pattern (78 bp):
ATTTGGGGGTATGTTTTGAGAATGTGAAAAGCCAAGGGAAGGTGAAGTGAAGATGTCAGAAAGGG
GTTTTATTTTTAT
Found at i:160921 original size:22 final size:21
Alignment explanation
Indices: 160830--160922 Score: 78
Period size: 22 Copynumber: 4.2 Consensus size: 21
160820 TTTAATATTT
*
160830 ATATTAAAATAATATTAAATGA
1 ATATTAAAATAA-ATTAAATAA
* * *
160852 TTATATAAAAAAAATTCAATAA
1 ATAT-TAAAATAAATTAAATAA
** * *
160874 ATAAAAAATATAAATTTATTAA
1 ATATTAAA-ATAAATTAAATAA
160896 ATATTAAAATAAATTAAATTAA
1 ATATTAAAATAAATTAAA-TAA
160918 ATATT
1 ATATT
160923 TTTAAAAATT
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
21 11 0.20
22 36 0.67
23 7 0.13
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (21 bp):
ATATTAAAATAAATTAAATAA
Found at i:161444 original size:3 final size:3
Alignment explanation
Indices: 161438--161505 Score: 63
Period size: 3 Copynumber: 23.0 Consensus size: 3
161428 TATGTTATAG
* *
161438 TAT TAT TA- TAT TAT TAT TGCAG TAT T-T AAT T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT T--AT TAT TAT TAT TAT TAT TAT TAT TAT
161482 TAT TAT TAT TAT TA- TAT TAAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT
161506 GGAATATATT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
2 7 0.13
3 42 0.78
4 3 0.06
5 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:161466 original size:53 final size:51
Alignment explanation
Indices: 161406--161505 Score: 132
Period size: 53 Copynumber: 1.9 Consensus size: 51
161396 ATCTTGTGGT
* *
161406 GTATTTAA-TTTATTTTTTATTATATGTTATAGTATTATTATATT-ATTATTGCA
1 GTATTTAATTTTA-TTATTATTAT-TATTAT--TATTATTATATTAATTATTGCA
161459 GTATTTAATTTTATTATTATTATTATTATTATTATTATATTAATTAT
1 GTATTTAATTTTATTATTATTATTATTATTATTATTATATTAATTAT
161506 GGAATATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
50 12 0.28
51 5 0.12
52 5 0.12
53 17 0.40
54 4 0.09
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (51 bp):
GTATTTAATTTTATTATTATTATTATTATTATTATTATATTAATTATTGCA
Found at i:162728 original size:40 final size:39
Alignment explanation
Indices: 162671--162765 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 39
162661 GATGGATATA
* *
162671 AAAACTAAACCCTAAAAATC-CGAAAACAAAGAA-CTCTC
1 AAAACTAAACACTAAAAAACTCGAAAACAAAGAATC-CTC
162709 AAAACATAAACACTAAAAAACTCGAAAACAAAGAATCCTC
1 AAAAC-TAAACACTAAAAAACTCGAAAACAAAGAATCCTC
162749 AAAACGTAAACACTAAA
1 AAAAC-TAAACACTAAA
162766 TTCTCCAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
38 5 0.10
39 13 0.25
40 32 0.63
41 1 0.02
ACGTcount: A:0.59, C:0.23, G:0.05, T:0.13
Consensus pattern (39 bp):
AAAACTAAACACTAAAAAACTCGAAAACAAAGAATCCTC
Found at i:167319 original size:202 final size:203
Alignment explanation
Indices: 166962--167367 Score: 787
Period size: 202 Copynumber: 2.0 Consensus size: 203
166952 ATCCATAAGT
166962 TCAAATATTGTTTATTGTCTTGTGTATCATGTTCTTTAGGTAGGGATTATTGTTTGTGTTGTGTT
1 TCAAATATTGTTTATTGTCTTGTGTATCATGTTCTTTAGGTAGGGATTATTGTTTGTGTTGTGTT
167027 TTCTCTTTATACTGCATCTCGTTTGTATGGGTAACAATGCATTTTTTAGGTCTCTAATTTGACAA
66 TTCTCTTTATACTGCATCTCGTTTGTATGGGTAACAATGCATTTTTTAGGTCTCTAATTTGACAA
167092 AAAAATTGCCTGCTATATATTTAGTAGACAGTGAACGAAGCGTTTGACTGTGATTGAAATTTTGG
131 AAAAATTGCCTGCTATATATTTAGTAGACAGTGAACGAAGCGTTTGACTGTGATTGAAATTTTGG
167157 GCTGCATC
196 GCTGCATC
*
167165 TCAAATATTG-TTATTGTCTTGTGTTTCATGTTCTTTAGGTAGGGATTATTGTTTGTGTTGTGTT
1 TCAAATATTGTTTATTGTCTTGTGTATCATGTTCTTTAGGTAGGGATTATTGTTTGTGTTGTGTT
167229 TTCTCTTTATACTGCATCTCGTTTGTATGGGTAACAATGCATTTTTTAGGTCTCTAATTTGACAA
66 TTCTCTTTATACTGCATCTCGTTTGTATGGGTAACAATGCATTTTTTAGGTCTCTAATTTGACAA
*
167294 AAAAGTTGCCTGCTATATATTTAGTAGACAGTGAACGAAGCGTTTGACTGTGATTGAAATTTTGG
131 AAAAATTGCCTGCTATATATTTAGTAGACAGTGAACGAAGCGTTTGACTGTGATTGAAATTTTGG
167359 GCTGCATC
196 GCTGCATC
167367 T
1 T
167368 ATTATGAGAT
Statistics
Matches: 201, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
202 191 0.95
203 10 0.05
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (203 bp):
TCAAATATTGTTTATTGTCTTGTGTATCATGTTCTTTAGGTAGGGATTATTGTTTGTGTTGTGTT
TTCTCTTTATACTGCATCTCGTTTGTATGGGTAACAATGCATTTTTTAGGTCTCTAATTTGACAA
AAAAATTGCCTGCTATATATTTAGTAGACAGTGAACGAAGCGTTTGACTGTGATTGAAATTTTGG
GCTGCATC
Found at i:168680 original size:21 final size:20
Alignment explanation
Indices: 168628--168680 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
168618 AGCTATAAAG
168628 AAATTATAAAAAAAAATACTA
1 AAATTATAAAAAAAAATAC-A
*
168649 AAATTACAAAAAAAAATTA-A
1 AAATTATAAAAAAAAA-TACA
168669 AAATTGATAAAA
1 AAATT-ATAAAA
168681 GTTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 6 0.21
21 20 0.71
22 2 0.07
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.23
Consensus pattern (20 bp):
AAATTATAAAAAAAAATACA
Found at i:169960 original size:22 final size:22
Alignment explanation
Indices: 169936--169976 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
169926 TAAAACTATT
169936 TTTTATTTAGAT-TAATTAGAG
1 TTTTATTTAGATGTAATTAGAG
*
169957 TTTTATTTGGATGTAATTAG
1 TTTTATTTAGATGTAATTAG
169977 TTAGTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (22 bp):
TTTTATTTAGATGTAATTAGAG
Found at i:170414 original size:35 final size:35
Alignment explanation
Indices: 170364--170433 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
170354 GCAGGGAAAA
*
170364 CAAATATCTTCTTCTCTAAGGGAGTGGAGGACTTT
1 CAAATATCTTATTCTCTAAGGGAGTGGAGGACTTT
170399 CAAATATCTTATTCTCTAAGGGAGTGGAGGACTTT
1 CAAATATCTTATTCTCTAAGGGAGTGGAGGACTTT
170434 ATTGCTGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (35 bp):
CAAATATCTTATTCTCTAAGGGAGTGGAGGACTTT
Found at i:182407 original size:25 final size:25
Alignment explanation
Indices: 182347--182410 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
182337 ACCAAAGTAC
*
182347 TAACAGAAAGCACATAAGTGTTGAG
1 TAACAGAGAGCACATAAGTGTTGAG
182372 TAACAGAGAGCACATAAGTGTTGAG
1 TAACAGAGAGCACATAAGTGTTGAG
*
182397 TAACAGTGAGCACA
1 TAACAGAGAGCACA
182411 CACAGTGCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (25 bp):
TAACAGAGAGCACATAAGTGTTGAG
Found at i:182426 original size:48 final size:46
Alignment explanation
Indices: 182373--182526 Score: 168
Period size: 48 Copynumber: 3.2 Consensus size: 46
182363 AGTGTTGAGT
* * *
182373 AACAGAGAGCACATAAGTGTTGAGTAACAGTGAGCACACACAGTGCTA
1 AACAGAGAGCACAAAAGTGCT-A-TAACAGAGAGCACACACAGTGCTA
*
182421 AACAGAGAGCACACAAAGTGCTA-ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACA-AAAGTGCTATAACAGAGAGCACACACAGTGCT-A
* *
182468 TAACAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACA-TGCTA
1 -AACAGAGAGCACA-AAAGTGCT-ATAACAGAGAGCAC-ACACAGTGCTA
182517 AACAGAGAGC
1 AACAGAGAGC
182527 GCGCTAGTGT
Statistics
Matches: 93, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
46 20 0.22
47 1 0.01
48 45 0.48
49 8 0.09
50 15 0.16
51 4 0.04
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (46 bp):
AACAGAGAGCACAAAAGTGCTATAACAGAGAGCACACACAGTGCTA
Found at i:182430 original size:23 final size:23
Alignment explanation
Indices: 182398--182526 Score: 170
Period size: 23 Copynumber: 5.4 Consensus size: 23
182388 AGTGTTGAGT
*
182398 AACAGTGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
182421 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
182444 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
182468 TAACAGAGAGCACACACAGTGCTAA
1 -AACAGAGAGCACACACAGTGCT-A
*
182493 TAACAGAGAGCACGAGACA-TGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
182517 AACAGAGAGC
1 AACAGAGAGC
182527 GCGCTAGTGT
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
23 51 0.53
24 2 0.02
25 40 0.41
26 4 0.04
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:182452 original size:25 final size:25
Alignment explanation
Indices: 182372--182526 Score: 182
Period size: 25 Copynumber: 6.4 Consensus size: 25
182362 AAGTGTTGAG
* * *
182372 TAACAGAGAGCACATA-AGTGTTGAG
1 TAACAGAGAGCACACACAGTGCT-AA
*
182397 TAACAGTGAGCACACACAGTGCT-A
1 TAACAGAGAGCACACACAGTGCTAA
*
182421 -AACAGAGAGCACACAAAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
182445 T--CAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
182468 TAACAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
*
182493 TAACAGAGAGCACGAGACA-TGCT-A
1 TAACAGAGAGCAC-ACACAGTGCTAA
182517 -AACAGAGAGC
1 TAACAGAGAGC
182527 GCGCTAGTGT
Statistics
Matches: 116, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
23 52 0.45
24 2 0.02
25 53 0.46
26 9 0.08
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (25 bp):
TAACAGAGAGCACACACAGTGCTAA
Found at i:185954 original size:15 final size:15
Alignment explanation
Indices: 185934--185964 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
185924 TAATAAAAAT
185934 AAAGTCTGAATAATA
1 AAAGTCTGAATAATA
185949 AAAGTCTGAATAATA
1 AAAGTCTGAATAATA
185964 A
1 A
185965 TTATGTTAAA
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:0.13, T:0.26
Consensus pattern (15 bp):
AAAGTCTGAATAATA
Found at i:187291 original size:26 final size:26
Alignment explanation
Indices: 187250--187300 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
187240 CAAATATCAA
* *
187250 TTTCGTATATTTATTTCATATAAACC
1 TTTCGTATAATAATTTCATATAAACC
* *
187276 TTTCGTATAATAATTTTATCTAAAC
1 TTTCGTATAATAATTTCATATAAAC
187301 ATTACATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (26 bp):
TTTCGTATAATAATTTCATATAAACC
Found at i:187929 original size:30 final size:30
Alignment explanation
Indices: 187895--187953 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
187885 AGTGTCTTTC
187895 AACTATGGTCTTAATCATTAACTCCAAGCA
1 AACTATGGTCTTAATCATTAACTCCAAGCA
*
187925 AACTATGGTCTTTATCATTAACTCCAAGC
1 AACTATGGTCTTAATCATTAACTCCAAGC
187954 CAATAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (30 bp):
AACTATGGTCTTAATCATTAACTCCAAGCA
Found at i:189385 original size:16 final size:16
Alignment explanation
Indices: 189364--189395 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
189354 TATTTGACTC
189364 GTAAATATTAAATAAT
1 GTAAATATTAAATAAT
189380 GTAAATATTAAATAAT
1 GTAAATATTAAATAAT
189396 AATATTTACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (16 bp):
GTAAATATTAAATAAT
Found at i:192345 original size:91 final size:91
Alignment explanation
Indices: 192190--192373 Score: 368
Period size: 91 Copynumber: 2.0 Consensus size: 91
192180 GGCCAAAAAA
192190 TTGAAAGAATAGGGGAAAGAAGATGATCTATCCATAGCATTCACAATGTTTAACTGAAATGCGAA
1 TTGAAAGAATAGGGGAAAGAAGATGATCTATCCATAGCATTCACAATGTTTAACTGAAATGCGAA
192255 AAATACGAACAGTGTGTGCAAATAAC
66 AAATACGAACAGTGTGTGCAAATAAC
192281 TTGAAAGAATAGGGGAAAGAAGATGATCTATCCATAGCATTCACAATGTTTAACTGAAATGCGAA
1 TTGAAAGAATAGGGGAAAGAAGATGATCTATCCATAGCATTCACAATGTTTAACTGAAATGCGAA
192346 AAATACGAACAGTGTGTGCAAATAAC
66 AAATACGAACAGTGTGTGCAAATAAC
192372 TT
1 TT
192374 AATCAAGTAA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (91 bp):
TTGAAAGAATAGGGGAAAGAAGATGATCTATCCATAGCATTCACAATGTTTAACTGAAATGCGAA
AAATACGAACAGTGTGTGCAAATAAC
Found at i:194813 original size:15 final size:14
Alignment explanation
Indices: 194788--194822 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
194778 TGTTTCACTG
*
194788 AAAATGGTTTTTGA
1 AAAATGATTTTTGA
194802 AAAATGATTTTTGA
1 AAAATGATTTTTGA
194816 AAAATGA
1 AAAATGA
194823 CTTACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (14 bp):
AAAATGATTTTTGA
Found at i:195324 original size:17 final size:17
Alignment explanation
Indices: 195283--195324 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
195273 TTATATTATA
*
195283 AAATATTT-ATTTTAAT
1 AAATATTTAATTGTAAT
* *
195299 ATATTTTTAATTGTAAT
1 AAATATTTAATTGTAAT
195316 AAATATTTA
1 AAATATTTA
195325 TTATTAAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AAATATTTAATTGTAAT
Found at i:196828 original size:23 final size:24
Alignment explanation
Indices: 196783--196841 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
196773 GATCCCTATA
196783 TTTTTTTCATTTTAAGCAATTTAAC
1 TTTTTTTC-TTTTAAGCAATTTAAC
* *
196808 TTTTTTTCTTTTAATC-TTTTAAC
1 TTTTTTTCTTTTAAGCAATTTAAC
196831 TTTTTTTCTTT
1 TTTTTTTCTTT
196842 ATTTTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 17 0.53
24 7 0.22
25 8 0.25
ACGTcount: A:0.19, C:0.12, G:0.02, T:0.68
Consensus pattern (24 bp):
TTTTTTTCTTTTAAGCAATTTAAC
Found at i:206606 original size:29 final size:29
Alignment explanation
Indices: 206564--206622 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
206554 AATTTTTTTA
*
206564 GAGGATACAAAGGTGTTAGTTGTCTTGTT
1 GAGGATACAAAGGTATTAGTTGTCTTGTT
206593 GAGGATACAAAGGTATTAGTTGTCTTGTT
1 GAGGATACAAAGGTATTAGTTGTCTTGTT
206622 G
1 G
206623 TGATCATGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.31, T:0.37
Consensus pattern (29 bp):
GAGGATACAAAGGTATTAGTTGTCTTGTT
Found at i:214650 original size:24 final size:24
Alignment explanation
Indices: 214623--214667 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
214613 TACTTTAATT
*
214623 TTTTTGAA-TTTTATGAATTTTTA
1 TTTTTGAATTTTTATAAATTTTTA
214646 TTTTTGAATTTTTATAAATTTT
1 TTTTTGAATTTTTATAAATTTT
214668 AAATTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (24 bp):
TTTTTGAATTTTTATAAATTTTTA
Found at i:214655 original size:14 final size:15
Alignment explanation
Indices: 214630--214660 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
214620 ATTTTTTTGA
214630 ATTTTATGAATTTTT
1 ATTTTATGAATTTTT
214645 ATTTT-TGAATTTTT
1 ATTTTATGAATTTTT
214659 AT
1 AT
214661 AAATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
ATTTTATGAATTTTT
Found at i:214668 original size:23 final size:23
Alignment explanation
Indices: 214623--214668 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
214613 TACTTTAATT
*
214623 TTTTTGAATTTTATGAATTTTTA
1 TTTTTGAATTTTATGAAATTTTA
214646 TTTTTGAATTTTTAT-AAATTTTA
1 TTTTTGAA-TTTTATGAAATTTTA
214669 AATTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (23 bp):
TTTTTGAATTTTATGAAATTTTA
Found at i:220062 original size:19 final size:19
Alignment explanation
Indices: 220025--220064 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
220015 ACCTTGACAA
* *
220025 TTGACTTTGATCGTTGACT
1 TTGACTTTAATCGTAGACT
*
220044 TTGACTTTAATTGTAGACT
1 TTGACTTTAATCGTAGACT
220063 TT
1 TT
220065 TTGACTAACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.50
Consensus pattern (19 bp):
TTGACTTTAATCGTAGACT
Found at i:221992 original size:28 final size:27
Alignment explanation
Indices: 221961--222115 Score: 107
Period size: 28 Copynumber: 5.6 Consensus size: 27
221951 TGAAATGTTA
221961 GAAAATGAATGCCTTTATGGTAATCTAT
1 GAAAATGAA-GCCTTTATGGTAATCTAT
* *
221989 GAAAATGAAAGCCTTTATAGCAATCTAT
1 GAAAATG-AAGCCTTTATGGTAATCTAT
*
222017 G-AAATGGAAGCCCTGT-TGGTAATCTAT
1 GAAAAT-GAAG-CCTTTATGGTAATCTAT
* * * * *
222044 GAAAATATAAGTCTTTGTGGCAATCTGT
1 GAAAAT-GAAGCCTTTATGGTAATCTAT
* * ** *
222072 GATAAAGGAAGCCTTTGTGACAATATAT
1 GA-AAATGAAGCCTTTATGGTAATCTAT
*
222100 GATAAAGGAAGCCTTT
1 GA-AAATGAAGCCTTT
222116 GTGGCGATTT
Statistics
Matches: 104, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
27 20 0.19
28 79 0.76
29 5 0.05
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (27 bp):
GAAAATGAAGCCTTTATGGTAATCTAT
Found at i:222039 original size:55 final size:56
Alignment explanation
Indices: 221978--222084 Score: 146
Period size: 55 Copynumber: 1.9 Consensus size: 56
221968 AATGCCTTTA
*
221978 TGGTAATCTATGAAAATGA-AAGCCTTTATAGCAATCTATGA-AATGGAAGCCCTGT
1 TGGTAATCTATGAAAAT-ATAAGCCTTTATAGCAATCTATGATAAAGGAAGCCCTGT
* * * *
222033 TGGTAATCTATGAAAATATAAGTCTTTGTGGCAATCTGTGATAAAGGAAGCC
1 TGGTAATCTATGAAAATATAAGCCTTTATAGCAATCTATGATAAAGGAAGCC
222085 TTTGTGACAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 1 0.02
55 35 0.78
56 9 0.20
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (56 bp):
TGGTAATCTATGAAAATATAAGCCTTTATAGCAATCTATGATAAAGGAAGCCCTGT
Found at i:222316 original size:27 final size:27
Alignment explanation
Indices: 222262--222323 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
222252 TATTCTTGGT
* * * *
222262 AAACTCTAAAGGAATAGTATGTATGGA
1 AAACTCTGAAGAAATAGTATGGAAGGA
*
222289 AAACTCTGAAGAAATGGTATGGAAGGA
1 AAACTCTGAAGAAATAGTATGGAAGGA
*
222316 AATCTCTG
1 AAACTCTG
222324 GAATTAAGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (27 bp):
AAACTCTGAAGAAATAGTATGGAAGGA
Found at i:228133 original size:148 final size:148
Alignment explanation
Indices: 227897--228176 Score: 316
Period size: 148 Copynumber: 1.9 Consensus size: 148
227887 GTGTTTTTGG
** ** * **
227897 ATTCAATCATGGCAGAACAGTATTCACCTTGACATCTTTCCCTTAATCCGTAATGTAAGATATAA
1 ATTCAATCATGGCAGAACAGTATTCACCTTGACATCTACCCCCCAAACCGTAACATAAGATATAA
* * ** * *
227962 ACATAAATGTGAATGAAACATAGAATATTAAATCAATGGTGAAAA-ACATTTGCATTGTTCACTA
66 ACATAAATGTGAAGGAAACATAGAAAAAAAAATCAATAG-CAAAAGACATTTGCATTGTTCACTA
228026 GATAAACAAAGGTATTATA
130 GATAAACAAAGGTATTATA
* *
228045 ATTCAATCATGGCAGAGCAGTATTCA-TTTCGACATCTACCCCCCAAACCGTAACATAAGATATA
1 ATTCAATCATGGCAGAACAGTATTCACCTT-GACATCTACCCCCCAAACCGTAACATAAGATATA
** * * *
228109 AATGCA-AGTTG-GAAGGAAATATAGAAAAAAAAATCAATAGCAAAAGGCATTTGCATTGTTCAT
65 AA--CATAAATGTGAAGGAAACATAGAAAAAAAAATCAATAGCAAAAGACATTTGCATTGTTCAC
228172 TAGAT
128 TAGAT
228177 TGCATTAGTG
Statistics
Matches: 108, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
147 6 0.06
148 97 0.90
149 3 0.03
150 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (148 bp):
ATTCAATCATGGCAGAACAGTATTCACCTTGACATCTACCCCCCAAACCGTAACATAAGATATAA
ACATAAATGTGAAGGAAACATAGAAAAAAAAATCAATAGCAAAAGACATTTGCATTGTTCACTAG
ATAAACAAAGGTATTATA
Found at i:232799 original size:31 final size:31
Alignment explanation
Indices: 232762--232822 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
232752 GGTTCACTTT
* *
232762 GTTTGATTTGGGTTTTAGGGTTATTGGGTTG
1 GTTTGATTTAGGTTTTAGGGTTAATGGGTTG
*
232793 GTTTGATTTAGGTTTTAGGTTTAATGGGTT
1 GTTTGATTTAGGTTTTAGGGTTAATGGGTT
232823 AAGAGAGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.13, C:0.00, G:0.34, T:0.52
Consensus pattern (31 bp):
GTTTGATTTAGGTTTTAGGGTTAATGGGTTG
Found at i:238516 original size:31 final size:32
Alignment explanation
Indices: 238449--238516 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 32
238439 GCTCGGTCCG
**
238449 AAGGCCCGCCCGAAAAATGGGCGGGTTTGGGTAAA
1 AAGGCCCGCCCGAAAAAT--G-GGGTTTGGACAAA
238484 AAGGCCCGCCCGAAAAAT-GGGTTTGGACAAA
1 AAGGCCCGCCCGAAAAATGGGGTTTGGACAAA
238515 AA
1 AA
238517 AACGAGGCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 13 0.42
35 18 0.58
ACGTcount: A:0.34, C:0.21, G:0.32, T:0.13
Consensus pattern (32 bp):
AAGGCCCGCCCGAAAAATGGGGTTTGGACAAA
Found at i:239357 original size:41 final size:40
Alignment explanation
Indices: 239285--239368 Score: 114
Period size: 41 Copynumber: 2.1 Consensus size: 40
239275 GTTTATTGTA
* *
239285 TTTTCAATTTGTTTGTTGTTTTACGAATTGTTTTAGTATCT
1 TTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAATAT-T
* * *
239326 TTTTTAATTTGTTTGTTGTTTTAATATTTGTTTTAATATT
1 TTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAATATT
239366 TTT
1 TTT
239369 AAGTGTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.18, C:0.04, G:0.12, T:0.67
Consensus pattern (40 bp):
TTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAATATT
Found at i:239358 original size:12 final size:12
Alignment explanation
Indices: 239341--239366 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
239331 AATTTGTTTG
239341 TTGTTTTAATAT
1 TTGTTTTAATAT
239353 TTGTTTTAATAT
1 TTGTTTTAATAT
239365 TT
1 TT
239367 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:239723 original size:2 final size:2
Alignment explanation
Indices: 239716--239751 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
239706 CACAATTAAT
*
239716 CA CA CA CA CA CA CA CA CA CA CA TA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
239752 TATATAGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.47, G:0.00, T:0.03
Consensus pattern (2 bp):
CA
Found at i:239893 original size:18 final size:18
Alignment explanation
Indices: 239872--239906 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
239862 TAAATACCCG
239872 AAAATAAAATAATAAGTT
1 AAAATAAAATAATAAGTT
239890 AAAATAAAATAATAAGT
1 AAAATAAAATAATAAGT
239907 CTATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAATAAAATAATAAGTT
Found at i:240937 original size:20 final size:20
Alignment explanation
Indices: 240912--240949 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
240902 GGTTTCTCAT
*
240912 AAAAAGTCAATGGTCAACCC
1 AAAAAGTCAACGGTCAACCC
240932 AAAAAGTCAACGGTCAAC
1 AAAAAGTCAACGGTCAAC
240950 GGTTAACAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.13
Consensus pattern (20 bp):
AAAAAGTCAACGGTCAACCC
Found at i:248616 original size:18 final size:18
Alignment explanation
Indices: 248590--248665 Score: 98
Period size: 18 Copynumber: 4.2 Consensus size: 18
248580 AAAACAAACT
* *
248590 AGTATGCTCAAAAGAAAC
1 AGTATGCTCAAATGAACC
* *
248608 AGAATGCTCAAATGAGCC
1 AGTATGCTCAAATGAACC
248626 AGTATGCTCAAATGAACC
1 AGTATGCTCAAATGAACC
* *
248644 AGTATGCTCAAACGAGCC
1 AGTATGCTCAAATGAACC
248662 AGTA
1 AGTA
248666 CGCTATTCCT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (18 bp):
AGTATGCTCAAATGAACC
Found at i:248630 original size:36 final size:36
Alignment explanation
Indices: 248590--248665 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
248580 AAAACAAACT
*
248590 AGTATGCTCAAAAGAAACAGAATGCTCAAATGAGCC
1 AGTATGCTCAAAAGAAACAGAATGCTCAAACGAGCC
* * *
248626 AGTATGCTCAAATGAACCAGTATGCTCAAACGAGCC
1 AGTATGCTCAAAAGAAACAGAATGCTCAAACGAGCC
248662 AGTA
1 AGTA
248666 CGCTATTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (36 bp):
AGTATGCTCAAAAGAAACAGAATGCTCAAACGAGCC
Found at i:250498 original size:20 final size:21
Alignment explanation
Indices: 250460--250499 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
250450 TTAACCGAGC
*
250460 ATCACTGAGTTAGAAAATGCA
1 ATCACTAAGTTAGAAAATGCA
250481 ATCACTAAGTTA-AAAATGC
1 ATCACTAAGTTAGAAAATGC
250500 TAACAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (21 bp):
ATCACTAAGTTAGAAAATGCA
Found at i:250880 original size:18 final size:18
Alignment explanation
Indices: 250857--250931 Score: 73
Period size: 18 Copynumber: 4.3 Consensus size: 18
250847 CACATATAAA
250857 TTTTTTCTTCTTTTCCTT
1 TTTTTTCTTCTTTTCCTT
* * * **
250875 TTTTTTC-ACATAT-AAT
1 TTTTTTCTTCTTTTCCTT
250891 TTTTTTCTTCTTTTCCTT
1 TTTTTTCTTCTTTTCCTT
* *
250909 TTTTTTCTTTTTTTTCTT
1 TTTTTTCTTCTTTTCCTT
250927 TTTTT
1 TTTTT
250932 CTATGTGGCT
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
16 8 0.19
17 6 0.14
18 29 0.67
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTCTTCTTTTCCTT
Found at i:250913 original size:9 final size:9
Alignment explanation
Indices: 250890--250932 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
250880 TCACATATAA
250890 TTTTTTT-C
1 TTTTTTTCC
*
250898 TTCTTTTCC
1 TTTTTTTCC
*
250907 TTTTTTTTC
1 TTTTTTTCC
*
250916 TTTTTTTTC
1 TTTTTTTCC
250925 TTTTTTTC
1 TTTTTTTC
250933 TATGTGGCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
8 6 0.20
9 24 0.80
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCC
Found at i:250930 original size:34 final size:34
Alignment explanation
Indices: 250847--250915 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
250837 TAATAATATA
*
250847 CACATATAAATTTTTTCTTCTTTTCCTTTTTTTT
1 CACATATAATTTTTTTCTTCTTTTCCTTTTTTTT
250881 CACATATAATTTTTTTCTTCTTTTCCTTTTTTTT
1 CACATATAATTTTTTTCTTCTTTTCCTTTTTTTT
250915 C
1 C
250916 TTTTTTTTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (34 bp):
CACATATAATTTTTTTCTTCTTTTCCTTTTTTTT
Found at i:252562 original size:17 final size:17
Alignment explanation
Indices: 252526--252558 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
252516 GCGACATGAG
*
252526 TTTGCTTTTCCTCTTTC
1 TTTGCTTTTCCTCTTCC
252543 TTTGCTTTTCCT-TTCC
1 TTTGCTTTTCCTCTTCC
252559 CTTTTTTGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.00, C:0.30, G:0.06, T:0.64
Consensus pattern (17 bp):
TTTGCTTTTCCTCTTCC
Found at i:261894 original size:18 final size:16
Alignment explanation
Indices: 261865--261906 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
261855 AAAAAGTGAG
261865 AAAAAG-AAAGAAAAGA
1 AAAAAGAAAAG-AAAGA
*
261881 AAAAGAGAAAAGAATGA
1 AAAA-AGAAAAGAAAGA
261898 AAAAAGAAA
1 AAAAAGAAA
261907 TAATTTGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 10 0.43
18 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAAGAAAGA
Found at i:261902 original size:11 final size:11
Alignment explanation
Indices: 261865--261906 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
261855 AAAAAGTGAG
261865 AAAAAGAAAGA
1 AAAAAGAAAGA
261876 AAAGAA-AAAGA
1 AAA-AAGAAAGA
* *
261887 GAAAAGAATGA
1 AAAAAGAAAGA
261898 AAAAAGAAA
1 AAAAAGAAA
261907 TAATTTGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.08
11 21 0.84
12 2 0.08
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:271023 original size:20 final size:21
Alignment explanation
Indices: 270986--271024 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
270976 AAACCGAGCA
*
270986 TCACTGAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
271007 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
271025 TAACAATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:274788 original size:19 final size:19
Alignment explanation
Indices: 274752--274790 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
274742 TCAACTTCAA
* * *
274752 ATAATTTTTATAATTTTTT
1 ATAATTTTCAAAAGTTTTT
274771 ATAATTTTCAAAAGTTTTT
1 ATAATTTTCAAAAGTTTTT
274790 A
1 A
274791 AAAGTTCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
ATAATTTTCAAAAGTTTTT
Done.