Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014881.1 Kokia drynarioides strain JFW-HI SEQ_129924, 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: 216788
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 697 characters in sequence are not A, C, G, or T
Found at i:18637 original size:14 final size:14
Alignment explanation
Indices: 18618--18650 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
18608 TCAACTCACC
18618 TATATTAATT-TTTT
1 TATATT-ATTATTTT
18632 TATATTATTATTTT
1 TATATTATTATTTT
18646 TATAT
1 TATAT
18651 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATATTATTATTTT
Found at i:27850 original size:16 final size:15
Alignment explanation
Indices: 27829--27866 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 15
27819 AATAAATAAT
27829 TTAAAATTTATAAAAA
1 TTAAAATTT-TAAAAA
27845 TTAAAATTTTAAAAA
1 TTAAAATTTTAAAAA
27860 TATAAAA
1 T-TAAAA
27867 AAATTCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTAAAATTTTAAAAA
Found at i:28283 original size:18 final size:18
Alignment explanation
Indices: 28262--28296 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28252 AATACTTAAA
28262 TTTAGTAATTAAATTTAT
1 TTTAGTAATTAAATTTAT
*
28280 TTTAGTCATTAAATTTA
1 TTTAGTAATTAAATTTA
28297 AAATTACGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (18 bp):
TTTAGTAATTAAATTTAT
Found at i:30623 original size:25 final size:25
Alignment explanation
Indices: 30578--30630 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
30568 AATTGATATA
* *
30578 TTATATTTTTTAAATTCATTAAATT
1 TTATATTTCTTAAATTCATTAAAAT
*
30603 TTATATTTCTT-AATTATATTAAAAT
1 TTATATTTCTTAAATT-CATTAAAAT
30628 TTA
1 TTA
30631 ATGTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (25 bp):
TTATATTTCTTAAATTCATTAAAAT
Found at i:30745 original size:17 final size:16
Alignment explanation
Indices: 30709--30759 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
30699 ATTTAATAAT
*
30709 TTTTATAACTATTATATA
1 TTTTATAA-T-TTGTATA
30727 TTTTATGAATTTGTATA
1 TTTTAT-AATTTGTATA
*
30744 TTTTATATTTTGTATA
1 TTTTATAATTTGTATA
30760 AATTTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 9 0.30
17 12 0.40
18 7 0.23
19 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (16 bp):
TTTTATAATTTGTATA
Found at i:31797 original size:23 final size:23
Alignment explanation
Indices: 31771--31822 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
31761 AAAAACGTAC
31771 CACAAAGTAGAGAAAAAACATGT
1 CACAAAGTAGAGAAAAAACATGT
* * * *
31794 CACAAGGTAGAGGAAATACGTGT
1 CACAAAGTAGAGAAAAAACATGT
31817 CACAAA
1 CACAAA
31823 TATAAATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.15, G:0.21, T:0.13
Consensus pattern (23 bp):
CACAAAGTAGAGAAAAAACATGT
Found at i:33637 original size:7 final size:7
Alignment explanation
Indices: 33625--33654 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
33615 CAAGCTGTGA
33625 GAAGCTT
1 GAAGCTT
33632 GAAGCTT
1 GAAGCTT
33639 GAAGCTT
1 GAAGCTT
33646 GAAGCTT
1 GAAGCTT
33653 GA
1 GA
33655 CTCAAGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (7 bp):
GAAGCTT
Found at i:47755 original size:21 final size:21
Alignment explanation
Indices: 47685--47756 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
47675 CTCATAATCC
* *
47685 AAGGTTCAAGATCTAA-AGTCT
1 AAGGTTTAAGATTTAATA-TCT
*
47706 AGGGTTTAAGATTTAATATCT
1 AAGGTTTAAGATTTAATATCT
** *
47727 AAAATTTAAGATTTAATATTT
1 AAGGTTTAAGATTTAATATCT
*
47748 GAGGTTTAA
1 AAGGTTTAA
47757 AGTTCAGATT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (21 bp):
AAGGTTTAAGATTTAATATCT
Found at i:59203 original size:10 final size:9
Alignment explanation
Indices: 59179--59203 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
59169 TTTTTACTAA
59179 TTAAAAATT
1 TTAAAAATT
59188 TTAAAAATT
1 TTAAAAATT
59197 TTAAAAA
1 TTAAAAA
59204 CATAGATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TTAAAAATT
Found at i:65324 original size:23 final size:22
Alignment explanation
Indices: 65291--65333 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
65281 GGTGTGTATT
65291 TAAAAATAGTATGTAAAAAAAA
1 TAAAAATAGTATGTAAAAAAAA
*
65313 TAAAATATAGTATTTAAAAAA
1 TAAAA-ATAGTATGTAAAAAA
65334 TACATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (22 bp):
TAAAAATAGTATGTAAAAAAAA
Found at i:79827 original size:226 final size:226
Alignment explanation
Indices: 79433--79859 Score: 809
Period size: 226 Copynumber: 1.9 Consensus size: 226
79423 TAAGAAAGAT
*
79433 CCATAGGAATTTCAAATTCATCACTTATATAGGCATCCCACAAATCCATAAATTTCAAAAATAGT
1 CCATAGGAATTTCAAATTCATCACTTATATAGGCATCCCACAAATCAATAAATTTCAAAAATAGT
79498 CAAGGATGTTAAACTTACAAGTTTTTGTATCACACAACTTACACCATATTGAAATTCAAATCCAT
66 CAAGGATGTTAAACTTACAAGTTTTTGTATCACACAACTTACACCATATTGAAATTCAAATCCAT
*
79563 CTTCTGAAAATCAAATTCCTAAGTACAATCTAAGTGAACATTTCACAGCTATCAATTATTTTATG
131 CTTCTGAAAATCAAATTCCTAAGTACAACCTAAGTGAACATTTCACAGCTATCAATTATTTTATG
79628 CCTTCTATGTTATTGTATCACACAACTTACA
196 CCTTCTATGTTATTGTATCACACAACTTACA
79659 CCATAGGAATTTCAAATTCATCACTTATATAGGCATCCCACAAATCAATAAATTTCAAAAATAGT
1 CCATAGGAATTTCAAATTCATCACTTATATAGGCATCCCACAAATCAATAAATTTCAAAAATAGT
*
79724 CAAGGATGTTAAACTTATAAGTTTTTGTATCACACAACTTACACCATATTGAAATTCAAATCCAT
66 CAAGGATGTTAAACTTACAAGTTTTTGTATCACACAACTTACACCATATTGAAATTCAAATCCAT
* *
79789 CTTCTGAAACTCAAATTCCTAAGTACAACCTAAGTGAACATTTCACAGCTATCTATTATTTTATG
131 CTTCTGAAAATCAAATTCCTAAGTACAACCTAAGTGAACATTTCACAGCTATCAATTATTTTATG
79854 CCTTCT
196 CCTTCT
79860 TAGTTCATAT
Statistics
Matches: 196, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
226 196 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.33
Consensus pattern (226 bp):
CCATAGGAATTTCAAATTCATCACTTATATAGGCATCCCACAAATCAATAAATTTCAAAAATAGT
CAAGGATGTTAAACTTACAAGTTTTTGTATCACACAACTTACACCATATTGAAATTCAAATCCAT
CTTCTGAAAATCAAATTCCTAAGTACAACCTAAGTGAACATTTCACAGCTATCAATTATTTTATG
CCTTCTATGTTATTGTATCACACAACTTACA
Found at i:82773 original size:13 final size:12
Alignment explanation
Indices: 82757--82799 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
82747 TAGTTTTTTT
82757 TTTTTCAAATTTA
1 TTTTT-AAATTTA
*
82770 TTTTTATATTTTA
1 TTTTTA-AATTTA
82783 TTTTTAAA-TTA
1 TTTTTAAATTTA
82794 TTTTTA
1 TTTTTA
82800 CTAATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 9 0.33
12 2 0.07
13 16 0.59
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTTTAAATTTA
Found at i:82864 original size:16 final size:17
Alignment explanation
Indices: 82835--82867 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
82825 ATGATCAGAA
*
82835 TAAAAATAACTATAATT
1 TAAAAACAACTATAATT
82852 TAAAAACAA-TATAATT
1 TAAAAACAACTATAATT
82868 CAAAGGCCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAAACAACTATAATT
Found at i:83926 original size:9 final size:9
Alignment explanation
Indices: 83866--83926 Score: 50
Period size: 9 Copynumber: 6.2 Consensus size: 9
83856 TGACAAAAAT
83866 AACAACAAA
1 AACAACAAA
83875 AACAACAAGA
1 AACAACAA-A
83885 AATGCAACACCAA
1 AA--CAACA--AA
83898 AACAACAAA
1 AACAACAAA
** *
83907 AAGTACCAA
1 AACAACAAA
83916 AACAACAAA
1 AACAACAAA
83925 AA
1 AA
83927 ACAATAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
9 24 0.59
10 3 0.07
11 5 0.12
12 5 0.12
13 3 0.07
14 1 0.02
ACGTcount: A:0.69, C:0.23, G:0.05, T:0.03
Consensus pattern (9 bp):
AACAACAAA
Found at i:85723 original size:14 final size:13
Alignment explanation
Indices: 85700--85750 Score: 57
Period size: 14 Copynumber: 3.8 Consensus size: 13
85690 ATTCGTTAGC
*
85700 AATTATAAAATTAA
1 AATTA-AAAAATAA
85714 AATTAAAAAATATA
1 AATTAAAAAATA-A
* *
85728 ATTTAAATAATAA
1 AATTAAAAAATAA
85741 AATTAAAAAA
1 AATTAAAAAA
85751 ACTATATGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 15 0.48
14 16 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATTAAAAAATAA
Found at i:88295 original size:15 final size:15
Alignment explanation
Indices: 88271--88304 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
88261 TTACGTATCA
88271 TATTTTTGTA-TTTT
1 TATTTTTGTAGTTTT
88285 TATTGTTTGTAGTTTT
1 TATT-TTTGTAGTTTT
88301 TATT
1 TATT
88305 AATGACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 6 0.33
16 8 0.44
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.74
Consensus pattern (15 bp):
TATTTTTGTAGTTTT
Found at i:90710 original size:6 final size:6
Alignment explanation
Indices: 90699--90723 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
90689 ACACCTGTTT
90699 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
90724 ATATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:91931 original size:33 final size:33
Alignment explanation
Indices: 91871--91934 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
91861 TTTGTTGTAA
* * *
91871 TATTATTATTTTACTATCATATTACTATTTTAT
1 TATTATTATTTAAATATCATATAACTATTTTAT
* *
91904 TATTATTGTTTAAATATTATATAACTATTTT
1 TATTATTATTTAAATATCATATAACTATTTT
91935 TTTAGAGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (33 bp):
TATTATTATTTAAATATCATATAACTATTTTAT
Found at i:99444 original size:3 final size:3
Alignment explanation
Indices: 99436--99464 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
99426 GCTGTTGTAA
99436 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
99465 TAAGCAGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:108385 original size:31 final size:31
Alignment explanation
Indices: 108322--108404 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
108312 TTAGGTCCTA
* *
108322 AACTTGACAATTATTCTCACATTGAGATTTG
1 AACTTGACAATTATTCTCACATGGAGACTTG
* *
108353 AACTTGATAATTTTTCTCACATGG-GAGCTTG
1 AACTTGACAATTATTCTCACATGGAGA-CTTG
* *
108384 AATTTGGCAATTATTCTCACA
1 AACTTGACAATTATTCTCACA
108405 ATAAGACTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 2 0.05
31 41 0.95
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (31 bp):
AACTTGACAATTATTCTCACATGGAGACTTG
Found at i:112359 original size:16 final size:17
Alignment explanation
Indices: 112331--112366 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
112321 TTGATACATG
*
112331 CATATGAAATTTTTATA
1 CATATGAAATTTTGATA
112348 CATATG-AATTTTGATA
1 CATATGAAATTTTGATA
112364 CAT
1 CAT
112367 GCATATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (17 bp):
CATATGAAATTTTGATA
Found at i:112373 original size:20 final size:21
Alignment explanation
Indices: 112320--112380 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
112310 CAATGTGCAA
112320 TTTGATACATGCATATGAAAT
1 TTTGATACATGCATATGAAAT
*
112341 TTT--T--ATACATATG-AAT
1 TTTGATACATGCATATGAAAT
112357 TTTGATACATGCATATGAAAT
1 TTTGATACATGCATATGAAAT
112378 TTT
1 TTT
112381 TATTGCGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
16 6 0.18
17 8 0.24
18 1 0.03
19 1 0.03
20 8 0.24
21 9 0.27
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (21 bp):
TTTGATACATGCATATGAAAT
Found at i:112475 original size:29 final size:29
Alignment explanation
Indices: 112441--112511 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 29
112431 ATATTTAAAG
112441 AAATAAATACATTAATTTATTTATATAT-C
1 AAATAAATACATTAA-TTATTTATATATGC
112470 AAATAAAT--A-TAATTATTTATATATGC
1 AAATAAATACATTAATTATTTATATATGC
112496 AACATATAA-ACATTAA
1 AA-ATA-AATACATTAA
112512 ATGATTCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
25 12 0.33
26 6 0.17
27 4 0.11
28 2 0.06
29 9 0.25
30 3 0.08
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (29 bp):
AAATAAATACATTAATTATTTATATATGC
Found at i:120393 original size:40 final size:39
Alignment explanation
Indices: 120343--120441 Score: 153
Period size: 40 Copynumber: 2.5 Consensus size: 39
120333 TGGAACAAGT
120343 CTCTTCCAAAAGGTGTCCATCCAATATGAAAAGAGTTGTGA
1 CTCTT-CAAAAGGTGTCCATCCAATATGAAAAG-GTTGTGA
* *
120384 CTTTTCAAAAAGTGTCCATCCAATATGAAAAGGTTGTGA
1 CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGTTGTGA
*
120423 CTCTTCAAAAGATGTCCAT
1 CTCTTCAAAAGGTGTCCAT
120442 TGAGTGCATA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
39 23 0.43
40 26 0.49
41 4 0.08
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.29
Consensus pattern (39 bp):
CTCTTCAAAAGGTGTCCATCCAATATGAAAAGGTTGTGA
Found at i:125235 original size:24 final size:24
Alignment explanation
Indices: 125208--125350 Score: 214
Period size: 24 Copynumber: 6.0 Consensus size: 24
125198 TGGTACTCCA
* *
125208 CCATCATCTGGAGGTGGTAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
*
125232 CCATCATATGGAGGAGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
*
125256 CCATCTTATGGAGGTGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
* *
125280 CCATCTTATGGAGGTGGCAGTCCA
1 CCATCATATGGAGGTGGCAGTCCC
*
125304 CCATCTTATGGAGGTGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
*
125328 CCATCATACGGAGGTGGCAGTCC
1 CCATCATATGGAGGTGGCAGTCC
125351 ACCAACTACT
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 110 1.00
ACGTcount: A:0.20, C:0.29, G:0.29, T:0.22
Consensus pattern (24 bp):
CCATCATATGGAGGTGGCAGTCCC
Found at i:125279 original size:48 final size:48
Alignment explanation
Indices: 125204--125354 Score: 239
Period size: 48 Copynumber: 3.1 Consensus size: 48
125194 CGCATGGTAC
* * * *
125204 TCCACCATCATCTGGAGGTGGTAGTCCCCCATCATATGGAGGAGGCAG
1 TCCACCATCTTATGGAGGTGGCAGTCCCCCATCATATGGAGGTGGCAG
* *
125252 TCCCCCATCTTATGGAGGTGGCAGTCCCCCATCTTATGGAGGTGGCAG
1 TCCACCATCTTATGGAGGTGGCAGTCCCCCATCATATGGAGGTGGCAG
*
125300 TCCACCATCTTATGGAGGTGGCAGTCCCCCATCATACGGAGGTGGCAG
1 TCCACCATCTTATGGAGGTGGCAGTCCCCCATCATATGGAGGTGGCAG
125348 TCCACCA
1 TCCACCA
125355 ACTACTCCTA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 94 1.00
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.22
Consensus pattern (48 bp):
TCCACCATCTTATGGAGGTGGCAGTCCCCCATCATATGGAGGTGGCAG
Found at i:135796 original size:96 final size:96
Alignment explanation
Indices: 135623--135807 Score: 275
Period size: 96 Copynumber: 1.9 Consensus size: 96
135613 GAAAAGGATG
**
135623 TTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCAA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCAA
**
135688 AGATAAGGGAACATTGCCTCGATTAAGGGTA
66 AGATAAAAGAACATTGCCTCGATTAAGGGTA
* *
135719 TTCGATTATTTCTATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCA-AATCCC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAAT--C
*
135783 GAA-ATAAAAGAACATTGCCTCGATT
64 AAAGATAAAAGAACATTGCCTCGATT
135808 TTAAAGTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 3 0.04
96 74 0.93
97 3 0.04
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAGAATCAA
AGATAAAAGAACATTGCCTCGATTAAGGGTA
Found at i:136088 original size:58 final size:58
Alignment explanation
Indices: 136020--136466 Score: 383
Period size: 58 Copynumber: 7.6 Consensus size: 58
136010 ACTCGGGGGC
* * * * *
136020 AAAATGGTAATTTTGGGAAAATTCGAGGTTAAAAATGAAATTTTAGGCA-TTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCG-GGTCAAAAATGGAATTTTAGGAAGTTCGAGGGT
** *
136078 AAAATGGTAATTTTTGGAAAGAATCGGGATCAAAAAT-GAATTTTTTTTGAAGTT-TAGGGGT
1 AAAATGGTAATTTTTGGAAA-AATCGGG-TCAAAAATGGAA--TTTTAGGAAGTTCGA-GGGT
* * * * * *
136139 AAAATGGTAATTTTGGGAAGAATTGGGGTAAAAAATGGAAGTTTAGGAAGTT-TAGGGGT
1 AAAATGGTAATTTTTGGAA-AAATCGGGTCAAAAATGGAATTTTAGGAAGTTCGA-GGGT
* * * *
136198 AAAATGGTAATTTTTGGAGAAATAGGGTTAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCGGGTCAAAAATGGAATTTTAGGAAGTTCGAGGGT
** ** *
136256 AAAATGGTAATTTTTGGAAAAATCGGGTCCAAAAATGGAATTTTAATAAGTTTAAGGGAAA
1 AAAATGGTAATTTTTGGAAAAATCGGGT-CAAAAATGGAATTTTAGGAAGTTCGAGGG--T
* * * *
136317 AAAAT-GCAA-TTTTGGGAAAATCAAGGTCAAAAATGGAATTTT-GGAAAGTTCAAGGGT
1 AAAATGGTAATTTTTGGAAAAATC-GGGTCAAAAATGGAATTTTAGG-AAGTTCGAGGGT
* * * * *
136374 AAAAAT-GTAATTTTTGGAAAATTGGGGTTAAAAATGGAATTTTAGAAATTTCGAGGGT
1 -AAAATGGTAATTTTTGGAAAAATCGGGTCAAAAATGGAATTTTAGGAAGTTCGAGGGT
*
136432 AAAAAT-GTAA-TTTTGGAAAAATCGAGGACAAAAAT
1 -AAAATGGTAATTTTTGGAAAAATCG-GGTCAAAAAT
136467 ATAATTATAG
Statistics
Matches: 319, Mismatches: 52, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
57 12 0.04
58 133 0.42
59 116 0.36
60 20 0.06
61 37 0.12
62 1 0.00
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.31
Consensus pattern (58 bp):
AAAATGGTAATTTTTGGAAAAATCGGGTCAAAAATGGAATTTTAGGAAGTTCGAGGGT
Found at i:136089 original size:28 final size:30
Alignment explanation
Indices: 136020--136450 Score: 150
Period size: 29 Copynumber: 14.7 Consensus size: 30
136010 ACTCGGGGGC
* *
136020 AAAATGGTAATTTTGGGAAAATTCGAGGTTA
1 AAAATGGTAATTTTAGG-AAATTCGAGGGTA
* *
136051 AAAAT-GAAATTTTAGG-CATTCGAGGGT-
1 AAAATGGTAATTTTAGGAAATTCGAGGGTA
* * *
136078 AAAATGGTAATTTTTGGAAAGAATCG-GGATCA
1 AAAATGGTAATTTTAGG-AA-ATTCGAGGGT-A
** * *
136110 AAAAT-G-AATTTTTTTTGAAGTT-TAGGGGT-
1 AAAATGGTAA--TTTTAGGAAATTCGA-GGGTA
*
136139 AAAATGGTAATTTTGGGAAGAATT-G-GGGTAA
1 AAAATGGTAATTTTAGG-A-AATTCGAGGGT-A
* * *
136170 AAAATGG-AAGTTTAGGAAGTT-TAGGGGT-
1 AAAATGGTAATTTTAGGAAATTCGA-GGGTA
* *
136198 AAAATGGTAATTTTTGGAGAAAT--AGGGTTA
1 AAAATGGTAATTTTAGGA-AATTCGAGGG-TA
* *
136228 AAAATGG-AATTTTTGGAAGTTCGAGGGT-
1 AAAATGGTAATTTTAGGAAATTCGAGGGTA
* *
136256 AAAATGGTAATTTTTGGAAAAATC--GGGTCCA
1 AAAATGGTAATTTTAGG-AAATTCGAGGGT--A
** * ** *
136287 AAAATGG-AATTTTAATAAGTTTAAGGGAAA
1 AAAATGGTAATTTTAGGAAATTCGAGGG-TA
* * * *
136317 AAAAT-GCAATTTTGGGAAAATC-AAGGTCA
1 AAAATGGTAATTTTAGGAAATTCGAGGGT-A
*
136346 AAAATGG-AATTTT-GGAAAGTTCAAGGGTA
1 AAAATGGTAATTTTAGGAAA-TTCGAGGGTA
*
136375 AAAAT-GTAATTTTTGGAAAATT-G-GGGTTA
1 AAAATGGTAATTTTAGG-AAATTCGAGGG-TA
136404 AAAATGG-AATTTTA-GAAATTTCGAGGGTA
1 AAAATGGTAATTTTAGGAAA-TTCGAGGGTA
136433 AAAAT-GTAATTTT-GGAAA
1 AAAATGGTAATTTTAGGAAA
136451 AATCGAGGAC
Statistics
Matches: 304, Mismatches: 49, Indels: 96
0.68 0.11 0.21
Matches are distributed among these distances:
27 8 0.03
28 57 0.19
29 109 0.36
30 79 0.26
31 40 0.13
32 11 0.04
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.31
Consensus pattern (30 bp):
AAAATGGTAATTTTAGGAAATTCGAGGGTA
Found at i:136197 original size:30 final size:31
Alignment explanation
Indices: 136126--136201 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
136116 AATTTTTTTT
* *
136126 GAAGTTTAGGGGT--AAAATGGTAATTTTGG
1 GAAGTTTAGGGGTAAAAAATGGTAAGTTTAG
*
136155 GAAGAATT-GGGGTAAAAAATGG-AAGTTTAG
1 GAAG-TTTAGGGGTAAAAAATGGTAAGTTTAG
136185 GAAGTTTAGGGGTAAAA
1 GAAGTTTAGGGGTAAAA
136202 TGGTAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
29 11 0.28
30 21 0.54
31 7 0.18
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (31 bp):
GAAGTTTAGGGGTAAAAAATGGTAAGTTTAG
Found at i:137026 original size:3 final size:3
Alignment explanation
Indices: 137020--137096 Score: 55
Period size: 3 Copynumber: 25.0 Consensus size: 3
137010 ATTGTTAGGG
* * * *
137020 TTA TTA TTA CTA TTTA TTA TTA TTA TTA ATG TTA TTA TCA TTA TTTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * *
137067 TTA TTA ATA TTG TAA TTA ATA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
137097 ATGATACCTA
Statistics
Matches: 54, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
3 49 0.91
4 5 0.09
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:137056 original size:12 final size:12
Alignment explanation
Indices: 137037--137098 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
137027 TACTATTTAT
137037 TATTATTATTAA
1 TATTATTATTAA
* * *
137049 TGTTATTATCAT
1 TATTATTATTAA
137061 TATTTATTATTAA
1 TA-TTATTATTAA
* *
137074 TATTGTAATTAA
1 TATTATTATTAA
*
137086 TATTAATATTAA
1 TATTATTATTAA
137098 T
1 T
137099 GATACCTATT
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
12 28 0.74
13 10 0.26
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:137057 original size:31 final size:31
Alignment explanation
Indices: 137019--137077 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
137009 AATTGTTAGG
* *
137019 GTTATTATTACTATTTATTATTATTATTAAT
1 GTTATTATCACTATTTATTATTAATATTAAT
*
137050 GTTATTATCATTATTTATTATTAATATT
1 GTTATTATCACTATTTATTATTAATATT
137078 GTAATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (31 bp):
GTTATTATCACTATTTATTATTAATATTAAT
Found at i:137793 original size:17 final size:17
Alignment explanation
Indices: 137769--137886 Score: 157
Period size: 17 Copynumber: 6.8 Consensus size: 17
137759 GACTTCTATT
*
137769 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
*
137786 ATTTTAAATTTAAAAATA
1 AATTTAAATTT-AAAATA
* * *
137804 AATTTAAACTTGAATTA
1 AATTTAAATTTAAAATA
137821 AATTTAAATTTAAAATAA
1 AATTTAAATTTAAAAT-A
137839 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
137856 AATTT-AATCTTAAAATA
1 AATTTAAAT-TTAAAATA
137873 AATTTAAATTTAAA
1 AATTTAAATTTAAA
137887 GAAAAGTGGG
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
16 3 0.03
17 51 0.58
18 34 0.39
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:137809 original size:35 final size:34
Alignment explanation
Indices: 137769--137884 Score: 155
Period size: 35 Copynumber: 3.4 Consensus size: 34
137759 GACTTCTATT
*
137769 AATTTAAATTTAGAATAATTTTAAATTTAAAAATA
1 AATTTAAATTTAGAATAAATTTAAATTT-AAAATA
*
137804 AATTTAAACTT-GAATTAAATTTAAATTTAAAATAA
1 AATTTAAATTTAGAA-TAAATTTAAATTTAAAAT-A
*
137839 AATTTAAATTTAAAATAAATTT-AATCTTAAAATA
1 AATTTAAATTTAGAATAAATTTAAAT-TTAAAATA
137873 AATTTAAATTTA
1 AATTTAAATTTA
137885 AAGAAAAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
34 24 0.33
35 47 0.64
36 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (34 bp):
AATTTAAATTTAGAATAAATTTAAATTTAAAATA
Found at i:137830 original size:52 final size:52
Alignment explanation
Indices: 137769--137886 Score: 175
Period size: 52 Copynumber: 2.3 Consensus size: 52
137759 GACTTCTATT
* * * *
137769 AATTTAAATTTAGAAT-AATTTTAAATTTAAAAATAAATTTAAACTTGAATTA
1 AATTTAAATTTAAAATAAAATTTAAATTT-AAAATAAATTTAAACTTAAAATA
*
137821 AATTTAAATTTAAAATAAAATTTAAATTTAAAATAAATTTAATCTTAAAATA
1 AATTTAAATTTAAAATAAAATTTAAATTTAAAATAAATTTAAACTTAAAATA
137873 AATTTAAATTTAAA
1 AATTTAAATTTAAA
137887 GAAAAGTGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 49 0.82
53 11 0.18
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (52 bp):
AATTTAAATTTAAAATAAAATTTAAATTTAAAATAAATTTAAACTTAAAATA
Found at i:138665 original size:49 final size:47
Alignment explanation
Indices: 138547--138881 Score: 170
Period size: 49 Copynumber: 6.8 Consensus size: 47
138537 AGGTTTCTAG
* * * *
138547 GGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTGCCT-TCGT
1 GGTAC-AGGTTCGCCATTGCG-CTTAAACCTTTCCCTTCATGTCTCT-GA
* * ** * * *
138596 GGTACTGGATTTGCTGTTGCAGCTTAGATCTTTCCCTTCATGTCTCCGA
1 GGTACAGG-TTCGCCATTGC-GCTTAAACCTTTCCCTTCATGTCTCTGA
* * * ** * * *
138645 GGTACAAGGTTCGCCATTGCAACCTAAACCCTTCCCTTTGTGCCTTTGC
1 GGTAC-AGGTTCGCCATTGC-GCTTAAACCTTTCCCTTCATGTCTCTGA
* * * * * * *
138694 GGTACTGGATCCACCGTTGCGGCTTAGATCTTTCCCTTCATGTCTGTGA
1 GGTACAGG-TTCGCCATTGC-GCTTAAACCTTTCCCTTCATGTCTCTGA
* *
138743 GGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTT-GTGTCTTCATTGC
1 GGTAC-AGGTTCGCCATTGCG-CTTAAACCTTTCCCTTCATGTC-TC--TGA
* * * * * * *
138794 GGTACTGGATCCGCCGTTGTGGCTTAGATCTTTCCCTTCATGTCTTCTAA
1 GGTACAGG-TTCGCCATTG-CGCTTAAACCTTTCCCTTCATGTC-TCTGA
138844 GGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTT
1 GGTAC-AGGTTCGCCATTGCG-CTTAAACCTTTCCCTT
138882 GCGTCTTTGT
Statistics
Matches: 206, Mismatches: 65, Indels: 29
0.69 0.22 0.10
Matches are distributed among these distances:
48 9 0.04
49 123 0.60
50 35 0.17
51 31 0.15
52 8 0.04
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.36
Consensus pattern (47 bp):
GGTACAGGTTCGCCATTGCGCTTAAACCTTTCCCTTCATGTCTCTGA
Found at i:138698 original size:98 final size:97
Alignment explanation
Indices: 138547--138929 Score: 496
Period size: 98 Copynumber: 3.9 Consensus size: 97
138537 AGGTTTCTAG
* * * ** *
138547 GGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTGCCTTCGTGGTACTGGATTTGCTG
1 GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTT-GTGCCTTTGCGGTACTGGATCCGCCG
* *
138612 TTGCAGCTTAGATCTTTCCCTTCATGTCTCCGA
65 TTGCGGCTTAGATCTTTCCCTTCATGTCTCTGA
* * * *
138645 GGTACAAGGTTCGCCATTGCAACCTAAACCCTTCCCTTTGTGCCTTTGCGGTACTGGATCCACCG
1 GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCC-TTGTGCCTTTGCGGTACTGGATCCGCCG
*
138710 TTGCGGCTTAGATCTTTCCCTTCATGTCTGTGA
65 TTGCGGCTTAGATCTTTCCCTTCATGTCTCTGA
* *
138743 GGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCATTGCGGTACTGGATCCGC
1 GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTG-C--CTTTGCGGTACTGGATCCGC
* *
138808 CGTTGTGGCTTAGATCTTTCCCTTCATGTCTTCTAA
63 CGTTGCGGCTTAGATCTTTCCCTTCATGTC-TCTGA
* * * * *
138844 GGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTGCGTCTTTGTGGTACTGGATCTGCCGT
1 GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGCCTTTGCGGTACTGGATCCGCCGT
* *
138909 TGTGGCTTAGATATTTCCCTT
66 TGCGGCTTAGATCTTTCCCTT
138930 TTGTATCTTT
Statistics
Matches: 252, Mismatches: 28, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
97 5 0.02
98 155 0.62
99 2 0.01
100 47 0.19
101 43 0.17
ACGTcount: A:0.15, C:0.27, G:0.22, T:0.36
Consensus pattern (97 bp):
GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTGTGCCTTTGCGGTACTGGATCCGCCGT
TGCGGCTTAGATCTTTCCCTTCATGTCTCTGA
Found at i:138835 original size:198 final size:196
Alignment explanation
Indices: 138547--138929 Score: 518
Period size: 198 Copynumber: 1.9 Consensus size: 196
138537 AGGTTTCTAG
* * ** *
138547 GGTACAAGGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTGCCTTCGTGGTACTGGATTTGCTG
1 GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTGCCTTCGCGGTACTGGATCCGCCG
*
138612 TTGCAGCTTAGATCTTTCCCTTCATGTC-TCCGAGGTACAAGGTTCGCCATTGCAACCTAAACCC
66 TTGCAGCTTAGATCTTTCCCTTCATGTCTTCCAAGGTACAAGGTTCGCCATTGCAACCTAAACCC
* *
138676 TTCCCTTTGTGCCTTTGCGGTACTGGATCCACCGTTGCGGCTTAGATCTTTCCCTTCATGTCTGT
131 TTCCC-TTGCGCCTTTGCGGTACTGGATCCACCGTTGCGGCTTAGATATTTCCCTTCATGTCTGT
138741 GA
195 GA
* *
138743 GGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTT-GTGTCTTCATTGCGGTACTGGATCCG
1 GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTGCCTTC---GCGGTACTGGATCCG
** * * * *
138807 CCGTTGTGGCTTAGATCTTTCCCTTCATGTCTTCTAAGGTACTAGGTTCGCCATTGCGACTTAAA
63 CCGTTGCAGCTTAGATCTTTCCCTTCATGTCTTCCAAGGTACAAGGTTCGCCATTGCAACCTAAA
* * * ** *
138872 CCTTTCCCTTGCGTCTTTGTGGTACTGGATCTGCCGTTGTGGCTTAGATATTTCCCTT
128 CCCTTCCCTTGCGCCTTTGCGGTACTGGATCCACCGTTGCGGCTTAGATATTTCCCTT
138930 TTGTATCTTT
Statistics
Matches: 161, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
195 7 0.04
196 36 0.22
198 83 0.52
199 35 0.22
ACGTcount: A:0.15, C:0.27, G:0.22, T:0.36
Consensus pattern (196 bp):
GGTACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCGTGCCTTCGCGGTACTGGATCCGCCG
TTGCAGCTTAGATCTTTCCCTTCATGTCTTCCAAGGTACAAGGTTCGCCATTGCAACCTAAACCC
TTCCCTTGCGCCTTTGCGGTACTGGATCCACCGTTGCGGCTTAGATATTTCCCTTCATGTCTGTG
A
Found at i:138950 original size:50 final size:50
Alignment explanation
Indices: 138688--138979 Score: 186
Period size: 50 Copynumber: 5.9 Consensus size: 50
138678 CCCTTTGTGC
* * * *
138688 CTTTGCGGTACTGGATCCACCGTTGCGGCTTAGATCTTTCCCTTCATG--T
1 CTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATATTTCCCTT-TTGTAT
* * * * * * ** * *
138737 CTGTGAGGTACTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTT
1 CTTTGTGGTACT-GGATCCGCCGTTGCGGCTTAGATATTTCCCTTTTGT-AT
* * * * *
138788 CATTGCGGTACTGGATCCGCCGTTGTGGCTTAGATCTTTCCCTTCATG--T
1 CTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATATTTCCCTT-TTGTAT
** * * * * ** **
138837 CTTCTAAGGTACTAGG-TTCGCCATTGCGACTTAAACCTTTCCC--TTGCGT
1 CTT-TGTGGTACT-GGATCCGCCGTTGCGGCTTAGATATTTCCCTTTTGTAT
* *
138886 CTTTGTGGTACTGGATCTGCCGTTGTGGCTTAGATATTTCCCTTTTGTAT
1 CTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATATTTCCCTTTTGTAT
*
138936 CTTTGTGGTTCTGGATCCGCCGTTGCGGCTTAGATATTTCCCTT
1 CTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATATTTCCCTT
138980 CATGTTTCAT
Statistics
Matches: 186, Mismatches: 44, Indels: 25
0.73 0.17 0.10
Matches are distributed among these distances:
47 4 0.02
48 28 0.15
49 40 0.22
50 77 0.41
51 35 0.19
52 2 0.01
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.39
Consensus pattern (50 bp):
CTTTGTGGTACTGGATCCGCCGTTGCGGCTTAGATATTTCCCTTTTGTAT
Found at i:142319 original size:22 final size:24
Alignment explanation
Indices: 142280--142339 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
142270 AAACGGAACA
* *
142280 AACAGAGAGTACCGAAGTACT-G-
1 AACAGAGAGCACAGAAGTACTGGT
* *
142302 AACAGAGAGCACATAAGTGCTGGGT
1 AACAGAGAGCACAGAAGTACT-GGT
142327 AACAGAGAGCACA
1 AACAGAGAGCACA
142340 CAAAGTGCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 17 0.55
24 1 0.03
25 13 0.42
ACGTcount: A:0.42, C:0.18, G:0.28, T:0.12
Consensus pattern (24 bp):
AACAGAGAGCACAGAAGTACTGGT
Found at i:142379 original size:23 final size:23
Alignment explanation
Indices: 142349--142416 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
142339 ACAAAGTGCT
*
142349 GAGCACACGAAATGCTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
142372 GAGCACACGAAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
*
142395 GAGCACACGCAGTGCTAATCAG
1 GAGCACACGAAGTGCTAATCAG
142417 TAGGCGCACA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.38, C:0.24, G:0.25, T:0.13
Consensus pattern (23 bp):
GAGCACACGAAGTGCTAATCAGA
Found at i:142438 original size:46 final size:47
Alignment explanation
Indices: 142349--142448 Score: 109
Period size: 46 Copynumber: 2.2 Consensus size: 47
142339 ACAAAGTGCT
* *
142349 GAGCACACGAAATGCTAATCAGAGAGCACACGAAGTGCTAATCAG-A
1 GAGCACACGAAATGCTAATCAGAGAGCACACGAAGCGCAAATCAGTA
* * *
142395 GAGCACACGCAGTGCTAATCAGTAG-GCGCAC-ATAGCGCAAATCAGTA
1 GAGCACACGAAATGCTAATCAG-AGAGCACACGA-AGCGCAAATCAGTA
142442 G-GCACAC
1 GAGCACAC
142449 AAGGTGTGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
45 1 0.02
46 41 0.89
47 4 0.09
ACGTcount: A:0.37, C:0.25, G:0.25, T:0.13
Consensus pattern (47 bp):
GAGCACACGAAATGCTAATCAGAGAGCACACGAAGCGCAAATCAGTA
Found at i:142463 original size:23 final size:23
Alignment explanation
Indices: 142437--142534 Score: 114
Period size: 23 Copynumber: 4.3 Consensus size: 23
142427 TAGCGCAAAT
*
142437 CAGTAGGCACAC-AAGGTGTGAAA
1 CAGTAAGCACACGAA-GTGTGAAA
*
142460 CAGTAAGCAAACGAAGTGTGAAA
1 CAGTAAGCACACGAAGTGTGAAA
* *
142483 CAGTAAGCACACGAAGAGCGAAA
1 CAGTAAGCACACGAAGTGTGAAA
142506 CAGTAAGCACAC--AGTGCTG-AA
1 CAGTAAGCACACGAAGTG-TGAAA
142527 CAGTAAGC
1 CAGTAAGC
142535 GCGCTAGCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
21 13 0.20
22 1 0.02
23 50 0.76
24 2 0.03
ACGTcount: A:0.43, C:0.19, G:0.27, T:0.11
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGTGAAA
Found at i:142635 original size:24 final size:26
Alignment explanation
Indices: 142597--142644 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
142587 TCTACATGGG
142597 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
142623 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
142645 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:152717 original size:3 final size:3
Alignment explanation
Indices: 152709--152785 Score: 55
Period size: 3 Copynumber: 25.0 Consensus size: 3
152699 AATGTTAGGG
* * * *
152709 TTA TTA TTA CTA TTAA TTA TTA TTA TTA ATG TTA TTA TCA TTA TTTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * *
152756 TTA TTA ATA TTG TAA TTA ATA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
152786 GTGATACCTA
Statistics
Matches: 54, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:152743 original size:28 final size:27
Alignment explanation
Indices: 152712--152785 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
152702 GTTAGGGTTA
*
152712 TTATTACTATTAATTATTATTATTAATG
1 TTATTA-TATTAATTATTATTAATAATG
* *
152740 TTATTATCATTATTTATTATTAATATTG
1 TTATTAT-ATTAATTATTATTAATAATG
*
152768 TAATTAATATTAA-TATTA
1 TTATT-ATATTAATTATTA
152786 GTGATACCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 6 0.15
28 31 0.79
29 2 0.05
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (27 bp):
TTATTATATTAATTATTATTAATAATG
Found at i:152743 original size:31 final size:31
Alignment explanation
Indices: 152708--152766 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
152698 TAATGTTAGG
* *
152708 GTTATTATTACTATTAATTATTATTATTAAT
1 GTTATTATCACTATTAATTATTAATATTAAT
* *
152739 GTTATTATCATTATTTATTATTAATATT
1 GTTATTATCACTATTAATTATTAATATT
152767 GTAATTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
GTTATTATCACTATTAATTATTAATATTAAT
Found at i:153502 original size:18 final size:18
Alignment explanation
Indices: 153462--153510 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
153452 GACTTCTATT
*
153462 AATTTAAATTT-AGAATA
1 AATTTAAATTTAAAAATA
*
153479 AGTTTAAATTTAAAAATA
1 AATTTAAATTTAAAAATA
153497 AATTTAAATTTAAA
1 AATTTAAATTTAAA
153511 GAAAAGTGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (18 bp):
AATTTAAATTTAAAAATA
Found at i:154608 original size:6 final size:6
Alignment explanation
Indices: 154597--154621 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
154587 CTTGCACAAT
154597 ATTTTA ATTTTA ATTTTA ATTTTA A
1 ATTTTA ATTTTA ATTTTA ATTTTA A
154622 ATCCGTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTTA
Found at i:155888 original size:18 final size:19
Alignment explanation
Indices: 155865--155900 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
155855 ATTTTGTTGT
155865 TAAATTTTAT-TATTAAAA
1 TAAATTTTATATATTAAAA
*
155883 TAAATTTTTTATATTAAA
1 TAAATTTTATATATTAAA
155901 TAATTTACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATTTTATATATTAAAA
Found at i:159658 original size:6 final size:6
Alignment explanation
Indices: 159647--159713 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
159637 CAAATGTATT
** **
159647 TTTAAA TTTAAA TTTATCT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
159695 TTT-AA TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
159714 GATTTAAAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 7 0.15
6 37 0.77
7 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:159687 original size:17 final size:17
Alignment explanation
Indices: 159646--159718 Score: 92
Period size: 17 Copynumber: 4.2 Consensus size: 17
159636 TCAAATGTAT
159646 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
*
159663 TCTTTTAAATTTAAATTTG
1 --TTTTAAATTTAAATTTA
159682 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
* * *
159699 ATTAAAATTTAAATTGA
1 TTTTAAATTTAAATTTA
159716 TTT
1 TTT
159719 AAAACTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
17 32 0.67
19 16 0.33
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:159720 original size:17 final size:17
Alignment explanation
Indices: 159650--159727 Score: 68
Period size: 17 Copynumber: 4.5 Consensus size: 17
159640 ATGTATTTTT
* *
159650 AAATTTAAATTTATCTTTT
1 AAATTTAAATTGA--TTTA
*
159669 AAATTTAAATTTG-TTTT
1 AAATTTAAA-TTGATTTA
* *
159686 AAATTTAAATTTAATTA
1 AAATTTAAATTGATTTA
159703 AAATTTAAATTGATTTA
1 AAATTTAAATTGATTTA
*
159720 AAACTTAA
1 AAATTTAA
159728 TTAAATTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 2 0.04
17 37 0.74
19 9 0.18
20 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
AAATTTAAATTGATTTA
Found at i:159736 original size:16 final size:17
Alignment explanation
Indices: 159690--159738 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
159680 TGTTTTAAAT
* *
159690 TTAAATTTAATTAAAAT
1 TTAAATTAAATTAAAAC
* *
159707 TTAAATTGATTTAAAAC
1 TTAAATTAAATTAAAAC
159724 TT-AATTAAATTAAAA
1 TTAAATTAAATTAAAA
159739 GTCCAAAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAATTAAATTAAAAC
Found at i:160488 original size:16 final size:16
Alignment explanation
Indices: 160469--160500 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
160459 ACATTAATAA
160469 TAATGATAATATTAAT
1 TAATGATAATATTAAT
*
160485 TAATGTTAATATTAAT
1 TAATGATAATATTAAT
160501 AATAAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TAATGATAATATTAAT
Found at i:161543 original size:29 final size:29
Alignment explanation
Indices: 161488--161872 Score: 318
Period size: 29 Copynumber: 13.5 Consensus size: 29
161478 GGAGGTCCCT
* *
161488 AAACTCCCAAAAATTCCATGTTT-ACCCCC
1 AAACTTCCAAAAATTCCATTTTTGA-CCCC
*
161517 GAACTTCC-AAAATTCCATTTTTGA---C
1 AAACTTCCAAAAATTCCATTTTTGACCCC
** *
161542 ---C--CCAAAAATTCCATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
* *
161566 AAACTTCCAAAAATT-CAATTTTGACCCTG
1 AAACTTCCAAAAATTCCATTTTTGACCC-C
* * *
161595 ATACTTCCAAAAATTTCA-TTTTGACCCTG
1 AAACTTCCAAAAATTCCATTTTTGACCC-C
* *
161624 ATACTTCCAAAAATTTCA-TTTTGACCCCC
1 AAACTTCCAAAAATTCCATTTTTGA-CCCC
161653 AAACTTCCAAAAATTCCA-TTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
*
161681 AAACTTCCAAAAATTCCATTTTT-ACCCT
1 AAACTTCCAAAAATTCCATTTTTGACCCC
* * *
161709 GAACTTCCAAAAATTCCATTTTTTACCCT
1 AAACTTCCAAAAATTCCATTTTTGACCCC
161738 AACACTTCCAAAAAATTCCATTTTT-ACCCTC
1 AA-ACTTCC-AAAAATTCCATTTTTGACCC-C
* *
161769 AAACTTCCAAAAATCCCATCTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
* * *
161798 AAAACTTCAAAAAATTACATTTTT-ATCCTC
1 -AAACTTCCAAAAATTCCATTTTTGA-CCCC
* * * *
161828 GAGCCTCCAAAATTTCCATTTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
*
161857 GAAACTTTCAAAAATT
1 -AAACTTCCAAAAATT
161873 AACATTTTGT
Statistics
Matches: 296, Mismatches: 37, Indels: 45
0.78 0.10 0.12
Matches are distributed among these distances:
20 2 0.01
21 14 0.05
22 1 0.00
24 1 0.00
25 1 0.00
27 1 0.00
28 69 0.23
29 132 0.45
30 58 0.20
31 17 0.06
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTGACCCC
Found at i:161548 original size:20 final size:19
Alignment explanation
Indices: 161523--161574 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
161513 CCCCGAACTT
161523 CCAAAATTCCATTTTTGACC
1 CCAAAATTCCATTTTT-ACC
161543 CCAAAAATTCCATTTTTACC
1 CC-AAAATTCCATTTTTACC
*
161563 CTCAAACTTCCA
1 C-CAAAATTCCA
161575 AAAATTCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.33, C:0.33, G:0.02, T:0.33
Consensus pattern (19 bp):
CCAAAATTCCATTTTTACC
Found at i:161551 original size:21 final size:21
Alignment explanation
Indices: 161525--161568 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
161515 CCGAACTTCC
161525 AAAATTCCATTTTTGACCC-CA
1 AAAATTCCATTTTT-ACCCTCA
161546 AAAATTCCATTTTTACCCTCA
1 AAAATTCCATTTTTACCCTCA
161567 AA
1 AA
161569 CTTCCAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (21 bp):
AAAATTCCATTTTTACCCTCA
Found at i:161603 original size:49 final size:49
Alignment explanation
Indices: 161493--161592 Score: 148
Period size: 49 Copynumber: 2.0 Consensus size: 49
161483 TCCCTAAACT
* *
161493 CCCAAAAATTCCATGTTTACCCCCGAACTTCCAAAATTCCATTTTTGAC
1 CCCAAAAATTCCATGTTTACCCCCAAACTTCCAAAATTCCAATTTTGAC
* *
161542 CCCAAAAATTCCATTTTTACCCTCAAACTTCCAAAAATT-CAATTTTGAC
1 CCCAAAAATTCCATGTTTACCCCCAAACTTCC-AAAATTCCAATTTTGAC
161591 CC
1 CC
161593 TGATACTTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 40 0.87
50 6 0.13
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (49 bp):
CCCAAAAATTCCATGTTTACCCCCAAACTTCCAAAATTCCAATTTTGAC
Found at i:161881 original size:30 final size:29
Alignment explanation
Indices: 161543--162029 Score: 340
Period size: 29 Copynumber: 16.8 Consensus size: 29
161533 ATTTTTGACC
*
161543 CCAAAAATTCCATTTTTACCCTC-AAACTT
1 CCAAAAATTCCATTTTGACCC-CGAAACTT
* * *
161572 CCAAAAATTCAATTTTGACCCTGATACTT
1 CCAAAAATTCCATTTTGACCCCGAAACTT
* * *
161601 CCAAAAATTTCATTTTGACCCTGATACTT
1 CCAAAAATTCCATTTTGACCCCGAAACTT
* *
161630 CCAAAAATTTCATTTTGACCCCCAAACTT
1 CCAAAAATTCCATTTTGACCCCGAAACTT
161659 CCAAAAATTCCATTTTGACCCC-AAACTT
1 CCAAAAATTCCATTTTGACCCCGAAACTT
* *
161687 CCAAAAATTCCATTTTTACCCTG-AACTT
1 CCAAAAATTCCATTTTGACCCCGAAACTT
* *
161715 CCAAAAATTCCATTTTTTA-CCCTAACACTT
1 CCAAAAATTCCA-TTTTGACCCCGAA-ACTT
*
161745 CCAAAAAATTCCATTTTTACCCTC-AAACTT
1 CC-AAAAATTCCATTTTGACCC-CGAAACTT
* *
161775 CCAAAAATCCCATCTTTGACCCCAAAACTT
1 CCAAAAATTCCAT-TTTGACCCCGAAACTT
* * * * * *
161805 CAAAAAATTACATTTTTATCCTCG-AGCCT
1 CCAAAAATTCCATTTTGA-CCCCGAAACTT
*
161834 CCAAAATTTCCATTTTTGACCCCGAAACTT
1 CCAAAAATTCCA-TTTTGACCCCGAAACTT
* * *
161864 TCAAAAATTAACATTTTGTCCCCG-AA-TGT
1 CCAAAAATT-CCATTTTGACCCCGAAACT-T
* * * **
161893 CCAAAAACTCTATTTTCAACCTTGAAAC-T
1 CCAAAAATTCCATTTT-GACCCCGAAACTT
*
161922 CTC-AAAATTACCCTTTT-ACCCCCG-AA-TGT
1 C-CAAAAATT-CCATTTTGA-CCCCGAAACT-T
* * * * **
161951 CTAAAAATTCCATTTTTAACTCTTAACTT
1 CCAAAAATTCCATTTTGACCCCGAAACTT
* * *
161980 CCCAAAATTACCATTTTGCCCCCGAAA-AT
1 CCAAAAATT-CCATTTTGACCCCGAAACTT
162009 CC-AAAATTACCATTTTG-CCCC
1 CCAAAAATT-CCATTTTGACCCC
162030 TCGGGTATCC
Statistics
Matches: 368, Mismatches: 62, Indels: 58
0.75 0.13 0.12
Matches are distributed among these distances:
27 4 0.01
28 77 0.21
29 181 0.49
30 89 0.24
31 16 0.04
32 1 0.00
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
CCAAAAATTCCATTTTGACCCCGAAACTT
Found at i:164738 original size:20 final size:20
Alignment explanation
Indices: 164713--164755 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
164703 CAAAGGGAAC
164713 TGCGCTAACCCCATTTTCCA
1 TGCGCTAACCCCATTTTCCA
164733 TGCGCTAACCCCATTTTCCA
1 TGCGCTAACCCCATTTTCCA
164753 TGC
1 TGC
164756 TCATATCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.40, G:0.12, T:0.30
Consensus pattern (20 bp):
TGCGCTAACCCCATTTTCCA
Found at i:174438 original size:17 final size:17
Alignment explanation
Indices: 174416--174454 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
174406 AGGTGGAGAA
* * *
174416 CTTGTTCGTTGAGAGTT
1 CTTGTTAGTAGAGAATT
174433 CTTGTTAGTAGAGAATT
1 CTTGTTAGTAGAGAATT
174450 CTTGT
1 CTTGT
174455 CAAGGTGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTAGTAGAGAATT
Found at i:175105 original size:17 final size:17
Alignment explanation
Indices: 175086--175162 Score: 111
Period size: 17 Copynumber: 4.5 Consensus size: 17
175076 CTATTGGAAA
175086 TTAAATTTATTTTTAAA-
1 TTAAATTTA-TTTTAAAT
*
175103 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAT
*
175120 TTAAATTTATTTGAAAT
1 TTAAATTTATTTTAAAT
*
175137 TTAAATTTATTATAAAT
1 TTAAATTTATTTTAAAT
175154 TTAAATTTA
1 TTAAATTTA
175163 AAATGTCCAA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
16 7 0.13
17 47 0.87
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:175138 original size:7 final size:6
Alignment explanation
Indices: 175086--175164 Score: 62
Period size: 6 Copynumber: 13.8 Consensus size: 6
175076 CTATTGGAAA
** * *
175086 TTAAAT TTATTT TTAAA- TTAAGT TT-ATT TTAAAT TTAAAT TT--AT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
175130 TTGAAAT TTAAAT TT--AT TATAAAT TTAAAT TTAAA
1 TT-AAAT TTAAAT TTAAAT T-TAAAT TTAAAT TTAAA
175165 ATGTCCAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
4 7 0.12
5 9 0.16
6 35 0.60
7 7 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:175240 original size:15 final size:15
Alignment explanation
Indices: 175198--175241 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
175188 AGGTACAGAT
175198 CAAATTGGCCCAATTA
1 CAAA-TGGCCCAATTA
*
175214 CAAAACGGCCCAATTA
1 C-AAATGGCCCAATTA
175230 CAAATGGCCCAA
1 CAAATGGCCCAA
175242 ATAGGCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 12 0.48
17 3 0.12
ACGTcount: A:0.41, C:0.30, G:0.14, T:0.16
Consensus pattern (15 bp):
CAAATGGCCCAATTA
Found at i:177054 original size:29 final size:30
Alignment explanation
Indices: 177032--177214 Score: 191
Period size: 29 Copynumber: 6.1 Consensus size: 30
177022 AAAAATTTTG
*
177032 TTTTT-ACCCTCGAACTTCCAAAAATCCCA
1 TTTTTGACCCTCGAACTTCCAAAAATTCCA
*
177061 TTTTTGACCC-CAAAAACTTCCAAAAA-TCCTA
1 TTTTTGACCCTC--GAACTTCCAAAAATTCC-A
*
177092 TTTTTGACCCT-AAACTTCCAAAAATTCCA
1 TTTTTGACCCTCGAACTTCCAAAAATTCCA
* * *
177121 TTTTT-TCCCCCGAACTTCCAAAAATCCCA
1 TTTTTGACCCTCGAACTTCCAAAAATTCCA
*
177150 TTTTTGACTCT-GAAACTTCCAAAAATTCCA
1 TTTTTGACCCTCG-AACTTCCAAAAATTCCA
*
177180 TTTTT-ACCCCCCGAACTTCCAAAAATTACCA
1 TTTTTGA-CCCTCGAACTTCCAAAAATT-CCA
177211 TTTT
1 TTTT
177215 ACCCCCGGAT
Statistics
Matches: 130, Mismatches: 12, Indels: 22
0.79 0.07 0.13
Matches are distributed among these distances:
28 3 0.02
29 48 0.37
30 48 0.37
31 31 0.24
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (30 bp):
TTTTTGACCCTCGAACTTCCAAAAATTCCA
Found at i:177115 original size:60 final size:59
Alignment explanation
Indices: 177032--177214 Score: 237
Period size: 60 Copynumber: 3.1 Consensus size: 59
177022 AAAAATTTTG
* ** *
177032 TTTTT-ACCCTCG-AACTTCCAAAAATCCCATTTTTGACCCCAAAAACTTCCAAAAATCCTA
1 TTTTTGACCCT-GAAACTTCCAAAAATTCCATTTTT-ACCCC-CGAACTTCCAAAAATCCCA
*
177092 TTTTTGACCCT-AAACTTCCAAAAATTCCATTTTTTCCCCCGAACTTCCAAAAATCCCA
1 TTTTTGACCCTGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCA
* *
177150 TTTTTGACTCTGAAACTTCCAAAAATTCCATTTTTACCCCCCGAACTTCCAAAAATTACCA
1 TTTTTGACCCTGAAACTTCCAAAAATTCCATTTTTA-CCCCCGAACTTCCAAAAA-TCCCA
177211 TTTT
1 TTTT
177215 ACCCCCGGAT
Statistics
Matches: 110, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
58 26 0.24
59 27 0.25
60 44 0.40
61 13 0.12
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (59 bp):
TTTTTGACCCTGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCA
Found at i:177197 original size:89 final size:90
Alignment explanation
Indices: 177032--177221 Score: 255
Period size: 89 Copynumber: 2.1 Consensus size: 90
177022 AAAAATTTTG
*
177032 TTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCAAAAACTTCCAAAAATCCTATTTTT
1 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAAACTTCCAAAAATCCTATTTTT
*
177097 GACCCTAAACTTCCAAAAATT-CCA
66 GACCCCAAACTTCCAAAAATTACCA
* * **
177121 TTTTTTCCCCCGAACTTCCAAAAATCCCATTTTTGA-CTCTGAAACTTCCAAAAATTCC-ATTTT
1 TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAAACTTCCAAAAA-TCCTATTTT
*
177184 T-ACCCCCCGAACTTCCAAAAATTACCA
65 TGA--CCCCAAACTTCCAAAAATTACCA
177211 -TTTTACCCCCG
1 TTTTTACCCCCG
177222 GATGTTCGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
87 1 0.01
88 21 0.24
89 64 0.72
90 3 0.03
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.32
Consensus pattern (90 bp):
TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAAACTTCCAAAAATCCTATTTTT
GACCCCAAACTTCCAAAAATTACCA
Found at i:188161 original size:29 final size:29
Alignment explanation
Indices: 188129--188185 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
188119 TTTTCAACTA
* *
188129 ATGATTGTTTCCTTTGATCCTTTTTTTTT
1 ATGATCGTTTCCTTTGATCCTCTTTTTTT
188158 ATGATCGTTTCCTTTGATCCTCTTTTTT
1 ATGATCGTTTCCTTTGATCCTCTTTTTT
188186 GGAATACGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.61
Consensus pattern (29 bp):
ATGATCGTTTCCTTTGATCCTCTTTTTTT
Found at i:189001 original size:208 final size:207
Alignment explanation
Indices: 188644--189045 Score: 723
Period size: 208 Copynumber: 1.9 Consensus size: 207
188634 TGTGATACCC
* * *
188644 ACAAATGACGCGGTTAGCTTCCTGATGAGATACTGAGAAGAAGATCAAATCAAACCCACGCTCAA
1 ACAAATGACGCGGTCAGCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCAA
188709 AGCAAGCAAAATCTTCGAACCCCAACTTCATGATGAGATACTGAGAAGCAGGTCGAAGTAATAAA
66 AGCAAGCAAAATCTTCGAACCCCAACTTCATGATGAGATACTGAGAAGCAGGTCGAAGTAATAAA
188774 ACGGATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
131 ACGGATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
188839 AAGCGGATTGAA
196 AAGCGGATTGAA
* *
188851 ACAAATGACGCGGTCAGCTTCCTGATGAGATACTAAGAAGAATACCAAAATCAAACCCACGTTCA
1 ACAAATGACGCGGTCAGCTTCCTGATGAGATACTAAGAAGAAGACC-AAATCAAACCCACGCTCA
* * *
188916 AAGCGAGCAAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAA
65 AAGCAAGCAAAATCTTCGAACCCCAACTTCATGATGAGATACTGAGAAGCAGGTCGAAGTAATAA
188981 AACGGATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGA
130 AACGGATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGA
189046 NNNNNNNNNN
Statistics
Matches: 186, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
207 42 0.23
208 144 0.77
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (207 bp):
ACAAATGACGCGGTCAGCTTCCTGATGAGATACTAAGAAGAAGACCAAATCAAACCCACGCTCAA
AGCAAGCAAAATCTTCGAACCCCAACTTCATGATGAGATACTGAGAAGCAGGTCGAAGTAATAAA
ACGGATAGCTTCCTGATGAGATACTGAGGAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAG
AAGCGGATTGAA
Found at i:189737 original size:17 final size:16
Alignment explanation
Indices: 189715--189776 Score: 79
Period size: 17 Copynumber: 3.8 Consensus size: 16
189705 GGCCTATTGG
189715 AAATTAAATTTATTTTT
1 AAATTAAATTTA-TTTT
* *
189732 AAATTAAGTTTATTTG
1 AAATTAAATTTATTTT
*
189748 AAATTTAAATTTATTAT
1 AAA-TTAAATTTATTTT
189765 AAATTAAATTTA
1 AAATTAAATTTA
189777 AAATGTCCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
16 15 0.38
17 24 0.62
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
AAATTAAATTTATTTT
Found at i:189768 original size:33 final size:33
Alignment explanation
Indices: 189709--189776 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
189699 TGTCTGGGCC
* *
189709 TATTGGAAATTAAATTTATTTTTAAATTAAGTT
1 TATTGGAAATTAAATTTATTTATAAATTAAATT
*
189742 TATTTGAAATTTAAATTTA-TTATAAATTAAATT
1 TATTGGAAA-TTAAATTTATTTATAAATTAAATT
189775 TA
1 TA
189777 AAATGTCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 22 0.71
34 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (33 bp):
TATTGGAAATTAAATTTATTTATAAATTAAATT
Found at i:191693 original size:30 final size:29
Alignment explanation
Indices: 191647--191787 Score: 149
Period size: 30 Copynumber: 4.8 Consensus size: 29
191637 AAAAATTCTG
**
191647 TTTACCCCCGAACTTCCAAAAATCCCATT
1 TTTACCCCAAAACTTCCAAAAATCCCATT
* *
191676 TTTGACCCTAAAACTTCCAAAAATTCCATT
1 TTT-ACCCCAAAACTTCCAAAAATCCCATT
***
191706 TTTACCCCCGTACTTCCAAAAATCCCATT
1 TTTACCCCAAAACTTCCAAAAATCCCATT
* *
191735 TTTGACCCCAAAACTTCCCAAAATTTCC-TT
1 TTT-ACCCCAAAACTT-CCAAAAATCCCATT
**
191765 TTTACCCCTGAACTTCCAAAAAT
1 TTTACCCCAAAACTTCCAAAAAT
191788 TATCATTTTA
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
28 7 0.08
29 37 0.40
30 39 0.42
31 9 0.10
ACGTcount: A:0.32, C:0.33, G:0.04, T:0.31
Consensus pattern (29 bp):
TTTACCCCAAAACTTCCAAAAATCCCATT
Found at i:191724 original size:59 final size:58
Alignment explanation
Indices: 191624--191787 Score: 242
Period size: 59 Copynumber: 2.8 Consensus size: 58
191614 ACCCGGAGGT
*
191624 CCCT-AAACTGTCCAAAAATT-CTGTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAACT-TCCAAAAATTCCTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
*
191681 CCCTAAAACTTCCAAAAATTCCATTTTTACCCCCGTACTTCCAAAAATCCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTCC-TTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * *
191740 CCCCAAAACTTCCCAAAATTTCCTTTTTACCCCTGAACTTCCAAAAAT
1 CCCTAAAACTT-CCAAAAATTCCTTTTTACCCCCGAACTTCCAAAAAT
191788 TATCATTTTA
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
57 14 0.14
58 6 0.06
59 67 0.69
60 10 0.10
ACGTcount: A:0.32, C:0.33, G:0.04, T:0.30
Consensus pattern (58 bp):
CCCTAAAACTTCCAAAAATTCCTTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:191796 original size:29 final size:29
Alignment explanation
Indices: 191629--191805 Score: 164
Period size: 29 Copynumber: 6.1 Consensus size: 29
191619 GAGGTCCCTA
*
191629 AACTGTCCAAAAATT-C-TGTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTTACCCCCG
* ***
191657 AACTTCCAAAAATCCCATTTTTGACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
191687 AACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* * **
191716 TACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
* *
191746 AACTTCCCAAAATTTCC-TTTTTACCCCTG
1 AACTT-CCAAAAATTCCATTTTTACCCCCG
* *
191775 AACTTCCAAAAATTATCA-TTTTATCCCCG
1 AACTTCCAAAAATT-CCATTTTTACCCCCG
191804 AA
1 AA
191806 TGTCCGAAGA
Statistics
Matches: 120, Mismatches: 22, Indels: 13
0.77 0.14 0.08
Matches are distributed among these distances:
27 9 0.08
28 13 0.11
29 50 0.42
30 39 0.32
31 9 0.08
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.32
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCCG
Found at i:194546 original size:21 final size:20
Alignment explanation
Indices: 194496--194547 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
194486 AAATTTAAAG
194496 AATATATAAAAATAAAAAAT
1 AATATATAAAAATAAAAAAT
* * *
194516 GATTTTTAAAAA-AGAAATAAT
1 AATATATAAAAATA-AAA-AAT
194537 AATATATAAAA
1 AATATATAAAA
194548 TTTTAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 1 0.04
20 12 0.50
21 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
AATATATAAAAATAAAAAAT
Found at i:195646 original size:25 final size:25
Alignment explanation
Indices: 195600--195647 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
195590 TTTATGGGAT
* * *
195600 TTATTTTGAATGGGAAATTGTATTC
1 TTATTATGAATGGAAAAGTGTATTC
*
195625 TTATTATGAATTGAAAAGTGTAT
1 TTATTATGAATGGAAAAGTGTAT
195648 GTGTATGTGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (25 bp):
TTATTATGAATGGAAAAGTGTATTC
Found at i:197439 original size:26 final size:26
Alignment explanation
Indices: 197389--197439 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
197379 AAAATTCTCT
*
197389 TTGAGTTTTCTTTTTAAAAATTTTTC
1 TTGAGTTTTCTTTTTAAAAAGTTTTC
*
197415 TTGAGTTTT-TTTTTAGAAGAGTTTT
1 TTGAGTTTTCTTTTTA-AAAAGTTTT
197440 ATCAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.22, C:0.04, G:0.14, T:0.61
Consensus pattern (26 bp):
TTGAGTTTTCTTTTTAAAAAGTTTTC
Found at i:198361 original size:3 final size:3
Alignment explanation
Indices: 198353--198377 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
198343 CCCCACCCCT
198353 CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG C
198378 AGTAGAAAAC
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:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:201189 original size:19 final size:19
Alignment explanation
Indices: 201167--201221 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
201157 AAATAATGAG
*
201167 AAAACAATAAAAAAACAGC
1 AAAACAATAAAAAAACAGA
*
201186 AAAACAGTAAAAAAA-AGA
1 AAAACAATAAAAAAACAGA
201204 AAATAGCAA-AAAAAAACA
1 AAA-A-CAATAAAAAAACA
201222 ATATTTCCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.17
19 22 0.73
20 3 0.10
ACGTcount: A:0.76, C:0.11, G:0.07, T:0.05
Consensus pattern (19 bp):
AAAACAATAAAAAAACAGA
Found at i:214071 original size:11 final size:12
Alignment explanation
Indices: 214030--214070 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
214020 ATAAATAGAA
214030 TGTTCGATGAAC
1 TGTTCGATGAAC
214042 TGTTCGATGAAC
1 TGTTCGATGAAC
214054 TGTTCG-TGAAC
1 TGTTCGATGAAC
*
214065 CGTTCG
1 TGTTCG
214071 TATTGTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (12 bp):
TGTTCGATGAAC
Found at i:214150 original size:18 final size:18
Alignment explanation
Indices: 214110--214186 Score: 68
Period size: 18 Copynumber: 4.3 Consensus size: 18
214100 CCAAACTCCC
* *
214110 TTTAAGTTTATTT-TAAA
1 TTTAAATTTATTTAAAAA
*
214127 TATTAAATTTGTTTAAAAA
1 T-TTAAATTTATTTAAAAA
**
214146 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTAAAAA
* *
214164 TTTAAAATTA-TTATAAA
1 TTTAAATTTATTTAAAAA
214181 TTTAAA
1 TTTAAA
214187 ATAAGTAAAG
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
17 12 0.24
18 33 0.67
19 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (18 bp):
TTTAAATTTATTTAAAAA
Found at i:214973 original size:9 final size:9
Alignment explanation
Indices: 214959--215012 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
214949 TGCTGATAGC
*
214959 ATTAATGAT
1 ATTAATAAT
214968 ATTAATAAT
1 ATTAATAAT
*
214977 AATAATAAT
1 ATTAATAAT
*
214986 AATAATAAT
1 ATTAATAAT
214995 ATT--TAAT
1 ATTAATAAT
215002 AATTAATAAT
1 -ATTAATAAT
215012 A
1 A
215013 AAAAAGGGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
7 4 0.10
8 3 0.08
9 28 0.72
10 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (9 bp):
ATTAATAAT
Found at i:214978 original size:3 final size:3
Alignment explanation
Indices: 214970--215013 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
214960 TTAATGATAT
*
214970 TAA TAA TAA TAA TAA TAA TAA TAA TATT TAA TAA TTAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA -TAA TAA TAA
215014 AAAAGGGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:216124 original size:30 final size:30
Alignment explanation
Indices: 216037--216292 Score: 168
Period size: 31 Copynumber: 8.7 Consensus size: 30
216027 TTAAATTGTT
* * *
216037 CAAAAATTCCA-TTTTTACCCTCGAACTTC
1 CAAAAATCCCATTTTTTACCCCCAAACTTC
* *
216066 CAAAAATCCCATTTTTTGATCCCAAAACTTC
1 CAAAAATCCCATTTTTT-ACCCCCAAACTTC
216097 CAAAAATCCCATTTTTTACCCCCAAACTTC
1 CAAAAATCCCATTTTTTACCCCCAAACTTC
* ** * **
216127 TAAAAAATTACATTTTTAACCCAAAAACTTC
1 -CAAAAATCCCATTTTTTACCCCCAAACTTC
* *
216158 CAAAAATCCCA-TTTTT-CCCCCGAACTTT
1 CAAAAATCCCATTTTTTACCCCCAAACTTC
* * * * **
216186 AAAAAATCCCATTTTTGACCTCAAAACCAC
1 CAAAAATCCCATTTTTTACCCCCAAACTTC
* * * * *
216216 TAATAATCCCA-TTTTAAACCTCAAA-TT-
1 CAAAAATCCCATTTTTTACCCCCAAACTTC
* *
216243 CAAAAGGT-CCA-TTTTTACCCCCGAACTTC
1 CAAAA-ATCCCATTTTTTACCCCCAAACTTC
* * *
216272 TAAAAATCTCATTTTTAACCC
1 CAAAAATCCCATTTTTTACCC
216293 TAAATTTTCC
Statistics
Matches: 168, Mismatches: 49, Indels: 19
0.71 0.21 0.08
Matches are distributed among these distances:
27 16 0.10
28 22 0.13
29 33 0.20
30 47 0.28
31 50 0.30
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (30 bp):
CAAAAATCCCATTTTTTACCCCCAAACTTC
Found at i:216126 original size:61 final size:60
Alignment explanation
Indices: 216037--216201 Score: 210
Period size: 61 Copynumber: 2.8 Consensus size: 60
216027 TTAAATTGTT
* * * *
216037 CAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTTGATCCC-AAAACTTC
1 CAAAAATCCCATTTTTACCCCCGAACTTCAAAAAATCCCATTTTTT-AACCCAAAAACTTC
* **
216097 CAAAAATCCCATTTTTTACCCCCAAACTTCTAAAAAATTACA-TTTTTAACCCAAAAACTTC
1 CAAAAATCCCA-TTTTTACCCCCGAACTTC-AAAAAATCCCATTTTTTAACCCAAAAACTTC
*
216158 CAAAAATCCCATTTTT-CCCCCGAACTTTAAAAAATCCCATTTTT
1 CAAAAATCCCATTTTTACCCCCGAACTTCAAAAAATCCCATTTTT
216202 GACCTCAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
58 9 0.10
59 14 0.16
60 19 0.21
61 40 0.44
62 8 0.09
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (60 bp):
CAAAAATCCCATTTTTACCCCCGAACTTCAAAAAATCCCATTTTTTAACCCAAAAACTTC
Done.