Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007904.1 Hibiscus syriacus cultivar Beakdansim tig00110295_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 354395
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1498 original size:28 final size:30
Alignment explanation
Indices: 1447--1521 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
1437 TAGCATATTT
1447 AAACTATTATATCATTCTAAATTAATCCAC
1 AAACTATTATATCATTCTAAATTAATCCAC
* * *
1477 -AACTATTATGT-ATTCTATATTAATCCTC
1 AAACTATTATATCATTCTAAATTAATCCAC
*
1505 AAACTATCATTATCATT
1 AAACTATTA-TATCATT
1522 ATTTTAATCC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
28 15 0.41
29 17 0.46
30 2 0.05
31 3 0.08
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (30 bp):
AAACTATTATATCATTCTAAATTAATCCAC
Found at i:3402 original size:18 final size:18
Alignment explanation
Indices: 3379--3422 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
3369 GGCAATTGGT
3379 CCAGCAGATACGGGTAGC
1 CCAGCAGATACGGGTAGC
3397 CCAGCAGATACGGGTAGC
1 CCAGCAGATACGGGTAGC
3415 CCAGCAGA
1 CCAGCAGA
3423 AGCCCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.32, T:0.09
Consensus pattern (18 bp):
CCAGCAGATACGGGTAGC
Found at i:7949 original size:18 final size:18
Alignment explanation
Indices: 7926--7969 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
7916 GGCAATTGGT
7926 CCAGCAGATACGGGTAGC
1 CCAGCAGATACGGGTAGC
7944 CCAGCAGATACGGGTAGC
1 CCAGCAGATACGGGTAGC
7962 CCAGCAGA
1 CCAGCAGA
7970 AGCCCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.32, T:0.09
Consensus pattern (18 bp):
CCAGCAGATACGGGTAGC
Found at i:14737 original size:13 final size:15
Alignment explanation
Indices: 14705--14738 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
14695 CATCTCGAAA
14705 AGAGTTAATACTTAT
1 AGAGTTAATACTTAT
14720 AGAGTTAATA-TT-T
1 AGAGTTAATACTTAT
14733 AGAGTT
1 AGAGTT
14739 GAATTCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 2 0.11
15 10 0.53
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (15 bp):
AGAGTTAATACTTAT
Found at i:18257 original size:2 final size:2
Alignment explanation
Indices: 18250--18284 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
18240 ACTAAGTTTC
18250 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18285 AAACAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22758 original size:74 final size:75
Alignment explanation
Indices: 22637--22778 Score: 214
Period size: 74 Copynumber: 1.9 Consensus size: 75
22627 AATGTCATAG
* * *
22637 CTTTGACATTTGTGTCAAGCTTTGCTTTATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGA-A
1 CTTTGACATTTGTATCAAGCTCTGCTATATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGACA
22701 AATTCTATAC
66 AATTCTATAC
* * * *
22711 CTTTGGCATTTGTATCAAGCTCTGGTATATTTCTTCTTGTCATGCAGAGACTTTGGTTTAAGACA
1 CTTTGACATTTGTATCAAGCTCTGCTATATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGACA
22776 AAT
66 AAT
22779 CTAAAGCTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
74 56 0.93
75 4 0.07
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (75 bp):
CTTTGACATTTGTATCAAGCTCTGCTATATTGCTTCTTGTCATGCAGAGACTCTGGTTTAAGACA
AATTCTATAC
Found at i:28112 original size:30 final size:31
Alignment explanation
Indices: 28045--28129 Score: 127
Period size: 33 Copynumber: 2.7 Consensus size: 31
28035 GAGTTAAATC
*
28045 AAATATAAATTTTAGAAATGTTTGTACCAAAAA
1 AAATGTAAATTTTAGAAATGTTTGTACC--AAA
28078 AAATGTAAATTTTAGAAATGTTTGTACC-AA
1 AAATGTAAATTTTAGAAATGTTTGTACCAAA
*
28108 AAATGAAAATTTTAGAAATGTT
1 AAATGTAAATTTTAGAAATGTT
28130 ATGGAATAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
30 23 0.46
33 27 0.54
ACGTcount: A:0.48, C:0.05, G:0.12, T:0.35
Consensus pattern (31 bp):
AAATGTAAATTTTAGAAATGTTTGTACCAAA
Found at i:32395 original size:18 final size:19
Alignment explanation
Indices: 32354--32396 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
32344 AAAATGTTCT
* *
32354 TAAATTTATATATTTTTTG
1 TAAATTTATATATTATTTA
32373 T-AATTTAT-TATTATTTA
1 TAAATTTATATATTATTTA
32390 TAAATTT
1 TAAATTT
32397 TAAACTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 12 0.57
19 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TAAATTTATATATTATTTA
Found at i:32653 original size:35 final size:36
Alignment explanation
Indices: 32596--32664 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
32586 ATACTATCAC
*
32596 CAATAATTCGTTTTTTTTATTAAACCAATAATTCAG
1 CAATAATTCGCTTTTTTTATTAAACCAATAATTCAG
32632 CAATAATTC-CTTTTTTTATTAAACCAATAATTC
1 CAATAATTCGCTTTTTTTATTAAACCAATAATTC
32665 GTTTTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 23 0.72
36 9 0.28
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (36 bp):
CAATAATTCGCTTTTTTTATTAAACCAATAATTCAG
Found at i:32664 original size:24 final size:24
Alignment explanation
Indices: 32632--32687 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
32622 AATAATTCAG
32632 CAATAATTCCTTTTTTTATTAAAC
1 CAATAATTCCTTTTTTTATTAAAC
*
32656 CAATAATTCGTTTTTTTATTAAAC
1 CAATAATTCCTTTTTTTATTAAAC
32680 CAATAATT
1 CAATAATT
32688 AGTTAGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (24 bp):
CAATAATTCCTTTTTTTATTAAAC
Found at i:32697 original size:24 final size:24
Alignment explanation
Indices: 32646--32697 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
32636 AATTCCTTTT
* **
32646 TTTATTAAACCAATAATTCGTTTT
1 TTTATTAAACCAATAATTAGTTAG
32670 TTTATTAAACCAATAATTAGTTAG
1 TTTATTAAACCAATAATTAGTTAG
32694 TTTA
1 TTTA
32698 ATAGAATGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (24 bp):
TTTATTAAACCAATAATTAGTTAG
Found at i:32965 original size:20 final size:21
Alignment explanation
Indices: 32930--32972 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
32920 AACTGAAATT
*
32930 TTTTAGATGATCGATCAGTTAA
1 TTTTAGAT-ATCGATCAATTAA
32952 TTTTAGAT-TCGATCAATTAA
1 TTTTAGATATCGATCAATTAA
32972 T
1 T
32973 GATTAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
22 8 0.40
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (21 bp):
TTTTAGATATCGATCAATTAA
Found at i:39893 original size:20 final size:21
Alignment explanation
Indices: 39868--39907 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39858 CCGAAAATGT
* *
39868 TAAAAA-ATTAATGTTTTAAG
1 TAAAAATAATAATATTTTAAG
39888 TAAAAATAATAATATTTTAA
1 TAAAAATAATAATATTTTAA
39908 ATACTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAG
Found at i:45974 original size:60 final size:60
Alignment explanation
Indices: 45846--45960 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
45836 ACCATATGTC
** * * *
45846 CCCAAACTATAACTCTCATTTTAAATAGGTCCTTAAACTTTTAAATATTCTAATTTAATT
1 CCCAAACTATGGCTTTCATTCTAAATAGGTCATTAAACTTTTAAATATTCTAATTTAATT
45906 CCCAAACTATGGCTTTCATTCTAAATTA-GTCATTAAACTTTTGAAA-ATTCTAATT
1 CCCAAACTATGGCTTTCATTCTAAA-TAGGTCATTAAACTTTT-AAATATTCTAATT
45961 ACATCCCTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 43 0.90
61 5 0.10
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (60 bp):
CCCAAACTATGGCTTTCATTCTAAATAGGTCATTAAACTTTTAAATATTCTAATTTAATT
Found at i:49402 original size:21 final size:21
Alignment explanation
Indices: 49378--49421 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
49368 CCGTTGATGA
* *
49378 AACTAAAACTTTTAATTAAGC
1 AACTAAAACATGTAATTAAGC
*
49399 AACTAAAACATGTCATTAAGC
1 AACTAAAACATGTAATTAAGC
49420 AA
1 AA
49422 ATAGCAAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (21 bp):
AACTAAAACATGTAATTAAGC
Found at i:57429 original size:2 final size:2
Alignment explanation
Indices: 57422--57449 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
57412 TATTTTGTTA
57422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57450 TAGTGCTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61268 original size:18 final size:18
Alignment explanation
Indices: 61245--61317 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
61235 GTTCTTAAAG
61245 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
61263 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
* *
61282 CAGTGGTCTTTCGGGATAT
1 -AGTGGTCCTTCGGGACAT
61301 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
61318 AATATTCAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 29 0.64
19 4 0.09
20 12 0.27
ACGTcount: A:0.19, C:0.19, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:61296 original size:38 final size:38
Alignment explanation
Indices: 61245--61318 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
61235 GTTCTTAAAG
*
61245 AGTGGTCCTTCGGGACATAGTGGTTCTTCGGAACAATC
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATC
* * *
61283 AGTGGTCTTTCGGGATATAGTGGTCCTTCGGGACAA
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAA
61319 ATATTCAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.20, C:0.19, G:0.31, T:0.30
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCGGAACAATC
Found at i:67289 original size:18 final size:19
Alignment explanation
Indices: 67252--67289 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
67242 AAAAAAAATT
**
67252 AAAAAATAAAATATTCAAA
1 AAAAAATAAAATATAAAAA
67271 AAAAAAT-AAATATAAAAA
1 AAAAAATAAAATATAAAAA
67289 A
1 A
67290 TACCAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAAATAAAATATAAAAA
Found at i:67296 original size:26 final size:26
Alignment explanation
Indices: 67242--67298 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
67232 ACACTTTTAG
* *
67242 AAAAAAAATTAAAAAATAAAATATTC
1 AAAAAAAAATAAAAAATAAAATATCC
67268 AAAAAAAAATAAATATAA-AAAATA-CC
1 AAAAAAAAATAAA-A-AATAAAATATCC
67294 AAAAA
1 AAAAA
67299 TATATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 18 0.67
27 7 0.26
28 2 0.07
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (26 bp):
AAAAAAAAATAAAAAATAAAATATCC
Found at i:67297 original size:25 final size:27
Alignment explanation
Indices: 67242--67298 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 27
67232 ACACTTTTAG
* *
67242 AAAAAAAATTAAAAAATAAAATATTCA
1 AAAAAAAATTAAAAAATAAAAAATACA
* *
67269 AAAAAAAA-T-AAATATAAAAAATACC
1 AAAAAAAATTAAAAAATAAAAAATACA
67294 AAAAA
1 AAAAA
67299 TATATATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 17 0.65
26 1 0.04
27 8 0.31
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (27 bp):
AAAAAAAATTAAAAAATAAAAAATACA
Found at i:69575 original size:2 final size:2
Alignment explanation
Indices: 69570--69599 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
69560 CATTTTTAAA
69570 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69600 GCATTATACT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75386 original size:20 final size:20
Alignment explanation
Indices: 75338--75386 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
75328 TTTTTGCGCA
* *
75338 AAAGTTTTAAAACTTTCGGT
1 AAAGTTTCAAAACTTTCGAT
75358 AAGAGTTTCAAAACTTT-GAT
1 AA-AGTTTCAAAACTTTCGAT
75378 GAAAGTTTC
1 -AAAGTTTC
75387 CCTTGAGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (20 bp):
AAAGTTTCAAAACTTTCGAT
Found at i:88677 original size:18 final size:18
Alignment explanation
Indices: 88654--88693 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
88644 TGAGGAAGAT
*
88654 GATATAGAGAGTGAGAGA
1 GATATAGAGAGAGAGAGA
* *
88672 GATATATAGAGAGAGGGA
1 GATATAGAGAGAGAGAGA
88690 GATA
1 GATA
88694 CAAACAGAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.38, T:0.17
Consensus pattern (18 bp):
GATATAGAGAGAGAGAGA
Found at i:88691 original size:20 final size:21
Alignment explanation
Indices: 88650--88691 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
88640 GAGTTGAGGA
*
88650 AGATGATATAGAGAGTGAGAG
1 AGATGATATAGAGAGAGAGAG
*
88671 AGAT-ATATAGAGAGAGGGAG
1 AGATGATATAGAGAGAGAGAG
88691 A
1 A
88692 TACAAACAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.38, T:0.17
Consensus pattern (21 bp):
AGATGATATAGAGAGAGAGAG
Found at i:89041 original size:38 final size:38
Alignment explanation
Indices: 88990--89074 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 38
88980 ACTATAAGAT
* *
88990 ATTTATAT-ATTTTCTTTAAAAAAATT-AAATTCATAAA
1 ATTTATTTAATTTTCTTTAAAAAAATTGAAAAT-ATAAA
* *
89027 ATTTATTTAATTTTCTTTTACAAAATTGAAAATATAAA
1 ATTTATTTAATTTTCTTTAAAAAAATTGAAAATATAAA
*
89065 AATT-TTTAAT
1 ATTTATTTAAT
89075 GAAAGGGTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 13 0.32
38 24 0.59
39 4 0.10
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (38 bp):
ATTTATTTAATTTTCTTTAAAAAAATTGAAAATATAAA
Found at i:101676 original size:23 final size:23
Alignment explanation
Indices: 101650--101727 Score: 129
Period size: 23 Copynumber: 3.4 Consensus size: 23
101640 TATATCATCA
101650 ATTCAAACTCGATTTTGAATTCG
1 ATTCAAACTCGATTTTGAATTCG
*
101673 ATTCAAGCTCGATTTTGAATTCG
1 ATTCAAACTCGATTTTGAATTCG
* *
101696 ATTCAAACTCGATTTTGAGTTCA
1 ATTCAAACTCGATTTTGAATTCG
101719 ATTCAAACT
1 ATTCAAACT
101728 TAAGACTGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (23 bp):
ATTCAAACTCGATTTTGAATTCG
Found at i:103985 original size:11 final size:11
Alignment explanation
Indices: 103969--104031 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
103959 GTATTATAGA
103969 ATTTTTAATAT
1 ATTTTTAATAT
103980 ATTTTTAA-AT
1 ATTTTTAATAT
103990 -TTTTATAAT-T
1 ATTTT-TAATAT
*** *
104000 ATCAATAATGT
1 ATTTTTAATAT
*
104011 AGTTTTAATAT
1 ATTTTTAATAT
104022 ATTTTTAATA
1 ATTTTTAATA
104032 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 4 0.10
10 10 0.26
11 25 0.64
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:109290 original size:2 final size:2
Alignment explanation
Indices: 109283--109328 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
109273 TGGTTCACTA
109283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
109325 AT AT
1 AT AT
109329 GGGAAGACTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:110103 original size:15 final size:16
Alignment explanation
Indices: 110078--110117 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
110068 ATGTAGTGTG
*
110078 TTTATAAAATT-TTATT
1 TTTA-AAAATTATTAAT
110094 TTTAAAAATTATTAAT
1 TTTAAAAATTATTAAT
110110 TTTAAAAA
1 TTTAAAAA
110118 ATCCTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAAATTATTAAT
Found at i:110476 original size:16 final size:16
Alignment explanation
Indices: 110455--110494 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
110445 ATATGTGCCT
110455 TGATACATGTAACTAG
1 TGATACATGTAACTAG
*
110471 TGATACATGTCACTAG
1 TGATACATGTAACTAG
*
110487 TGACACAT
1 TGATACAT
110495 TTCATATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (16 bp):
TGATACATGTAACTAG
Found at i:111366 original size:21 final size:22
Alignment explanation
Indices: 111339--111388 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
111329 GACTTAACCT
111339 AATTTTTTTA-TA-TTTTATTA
1 AATTTTTTTAGTATTTTTATTA
* *
111359 AATATTTTTAGTATTTTTATTT
1 AATTTTTTTAGTATTTTTATTA
111381 AATTTTTT
1 AATTTTTT
111389 AAATAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.36
21 2 0.08
22 14 0.56
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
AATTTTTTTAGTATTTTTATTA
Found at i:112689 original size:23 final size:25
Alignment explanation
Indices: 112663--112712 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 25
112653 AATCCTAAAT
*
112663 TCTAATCCTAGCC-C-ACCTCTACC
1 TCTAATCCTAGCCACGACCACTACC
* *
112686 TCTATTTCTAGCCACGACCACTACC
1 TCTAATCCTAGCCACGACCACTACC
112711 TC
1 TC
112713 CGACTTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 11 0.50
24 1 0.05
25 10 0.45
ACGTcount: A:0.22, C:0.44, G:0.06, T:0.28
Consensus pattern (25 bp):
TCTAATCCTAGCCACGACCACTACC
Found at i:114077 original size:23 final size:23
Alignment explanation
Indices: 114051--114098 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
114041 ATATTAATAA
114051 ATTTAATTTAAATAAAAATATAT
1 ATTTAATTTAAATAAAAATATAT
* *
114074 ATTTAATTTAAATATATATATAT
1 ATTTAATTTAAATAAAAATATAT
114097 AT
1 AT
114099 ACCCGGCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATTTAAATAAAAATATAT
Found at i:114141 original size:12 final size:12
Alignment explanation
Indices: 114097--114161 Score: 69
Period size: 12 Copynumber: 5.5 Consensus size: 12
114087 ATATATATAT
*
114097 ATACCCGGCCCG
1 ATACCCGGCCCA
*
114109 ATTCCCGGCCCA
1 ATACCCGGCCCA
*
114121 ATA-CCGACCCA
1 ATACCCGGCCCA
* *
114132 ATACCCGACCTA
1 ATACCCGGCCCA
*
114144 ATACCCGGTCCA
1 ATACCCGGCCCA
114156 ATACCC
1 ATACCC
114162 ATTTAAATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
11 10 0.23
12 34 0.77
ACGTcount: A:0.26, C:0.46, G:0.14, T:0.14
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:114338 original size:11 final size:11
Alignment explanation
Indices: 114317--114352 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
114307 GGACGGGAGA
114317 CCAATACCCGGC
1 CCAA-ACCCGGC
114329 CCAAACCCGGC
1 CCAAACCCGGC
*
114340 CCGAACCCGGC
1 CCAAACCCGGC
114351 CC
1 CC
114353 GTTGCCATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.22, C:0.56, G:0.19, T:0.03
Consensus pattern (11 bp):
CCAAACCCGGC
Found at i:114353 original size:11 final size:11
Alignment explanation
Indices: 114322--114353 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
114312 GGAGACCAAT
*
114322 ACCCGGCCCAA
1 ACCCGGCCCGA
114333 ACCCGGCCCGA
1 ACCCGGCCCGA
114344 ACCCGGCCCG
1 ACCCGGCCCG
114354 TTGCCATCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.56, G:0.25, T:0.00
Consensus pattern (11 bp):
ACCCGGCCCGA
Found at i:120429 original size:22 final size:22
Alignment explanation
Indices: 120403--120446 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
120393 TATATATAGA
120403 AATGATGAAAGTAGTGCTCTAG
1 AATGATGAAAGTAGTGCTCTAG
120425 AATGATGAAAGTAGTGCTCTAG
1 AATGATGAAAGTAGTGCTCTAG
120447 TTTATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (22 bp):
AATGATGAAAGTAGTGCTCTAG
Found at i:124579 original size:60 final size:60
Alignment explanation
Indices: 124503--124641 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
124493 TAATATTTTA
* * ** * *
124503 TATAAATTTTACTAGTCGGGAGACTCAACAAAATAACACTCTATAGTCAAAGAACCATTT
1 TATAACTTTTAATAGTCGAAAGACTCAACAAAATAACACCCTATAATCAAAGAACCATTT
* * * * * *
124563 TGTAATTTTTAATAGTCGAAAGATTCAACAAAATAATACCCTATAATCAAAGGACTATTT
1 TATAACTTTTAATAGTCGAAAGACTCAACAAAATAACACCCTATAATCAAAGAACCATTT
*
124623 TATAACTTTTAATAATCGA
1 TATAACTTTTAATAGTCGA
124642 TTGACTATTT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.32
Consensus pattern (60 bp):
TATAACTTTTAATAGTCGAAAGACTCAACAAAATAACACCCTATAATCAAAGAACCATTT
Found at i:124637 original size:29 final size:29
Alignment explanation
Indices: 124605--124668 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
124595 ATAATACCCT
124605 ATAATCAAAGGACTATTTTATAACTTTTA
1 ATAATCAAAGGACTATTTTATAACTTTTA
* **
124634 ATAATCGATTGACTATTTTATAACTTTTA
1 ATAATCAAAGGACTATTTTATAACTTTTA
124663 ATAATC
1 ATAATC
124669 GATAAACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (29 bp):
ATAATCAAAGGACTATTTTATAACTTTTA
Found at i:124669 original size:29 final size:29
Alignment explanation
Indices: 124615--124671 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
124605 ATAATCAAAG
124615 GACTATTTTATAACTTTTAATAATCGATT
1 GACTATTTTATAACTTTTAATAATCGATT
124644 GACTATTTTATAACTTTTAATAATCGAT
1 GACTATTTTATAACTTTTAATAATCGAT
124672 AAACTTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (29 bp):
GACTATTTTATAACTTTTAATAATCGATT
Found at i:124792 original size:2 final size:2
Alignment explanation
Indices: 124785--124809 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
124775 TCTATTTATC
124785 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
124810 TTTACAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:125953 original size:60 final size:62
Alignment explanation
Indices: 125872--126008 Score: 147
Period size: 64 Copynumber: 2.2 Consensus size: 62
125862 AATAGGTAAA
* * *
125872 TTATACAAATGGTCCCTAACTATA-AGA-TA-TTGTTTTGTTGAGTTA-TCCGACTATTAAAAG
1 TTATA-AAATGATCCCTAACTATATAGAGTAGTTGCTTTGTTGAGTCACT-CGACTATTAAAAG
* * *
125932 TTATAAAATGATCTCTCAACTATATATATGTAGTTGCTTTGTTGAGTCACTTGACTATTAAAAG
1 TTATAAAATGATCCCT-AACTATATAGA-GTAGTTGCTTTGTTGAGTCACTCGACTATTAAAAG
*
125996 TTACAAAATGATC
1 TTATAAAATGATC
126009 ATCCGACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
59 9 0.14
60 12 0.19
61 2 0.03
63 2 0.03
64 38 0.59
65 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (62 bp):
TTATAAAATGATCCCTAACTATATAGAGTAGTTGCTTTGTTGAGTCACTCGACTATTAAAAG
Found at i:128578 original size:31 final size:28
Alignment explanation
Indices: 128501--128595 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 28
128491 ATAAGAGTAC
* * * *
128501 TTTATGTATTTATTTTAATCAAAAAGTAC
1 TTTAAGTATTTACTTTAA-CAAAAAATAT
* *
128530 TTTAGGTATTTAGTTTAACCAAAATAATAAT
1 TTTAAGTATTTACTTTAA-CAAAA-AAT-AT
128561 TTTAAGTATTTACTTTAACAAAAAATAT
1 TTTAAGTATTTACTTTAACAAAAAATAT
128589 TTTAAGT
1 TTTAAGT
128596 GATTGAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.16
29 24 0.42
30 7 0.12
31 17 0.30
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.45
Consensus pattern (28 bp):
TTTAAGTATTTACTTTAACAAAAAATAT
Found at i:144031 original size:3 final size:3
Alignment explanation
Indices: 144023--144101 Score: 56
Period size: 3 Copynumber: 26.0 Consensus size: 3
144013 AATGATATCA
* * * *
144023 ATT ATT ATT AATT CTTT ATA ATT ATT -TT ACT -TT ATT -TG ATT ATAT
1 ATT ATT ATT -ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
144068 AAT ATT TATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
144102 TTCGATTAGT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
2 4 0.07
3 45 0.76
4 10 0.17
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:147986 original size:53 final size:53
Alignment explanation
Indices: 147886--148198 Score: 414
Period size: 53 Copynumber: 5.9 Consensus size: 53
147876 TCTTCAAATG
* * * ****
147886 ACGGGTCCGCTCCCTCTTG-TTCCGGGATTAAGGAACTCGAACAATCTTCTAAAA
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCCT
* * * *
147940 ATGGGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * *
147993 ACGGGTTCGCTCCCTCTTGCTTCAGGGGGTAGAACTCGAATAATCTTCTACC-
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * *
148045 AGCGGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCAAACAATCTTCTGTCT
1 A-CGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* *
148099 ACGGGTTTGCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
148152 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTT
1 ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTT
148199 ATGGTTTGAT
Statistics
Matches: 228, Mismatches: 28, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
52 1 0.00
53 201 0.88
54 18 0.08
55 8 0.04
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
Found at i:159400 original size:30 final size:31
Alignment explanation
Indices: 159366--159423 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
159356 ATAATATTAA
* *
159366 TTTGACTC-TAAACTTTAGATGAAATATCAT
1 TTTGACCCTTAAACTTTAGATAAAATATCAT
*
159396 TTTGACCCTTAAATTTTAGATAAAATAT
1 TTTGACCCTTAAACTTTAGATAAAATAT
159424 TAAGTTAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (31 bp):
TTTGACCCTTAAACTTTAGATAAAATATCAT
Found at i:161546 original size:23 final size:23
Alignment explanation
Indices: 161516--161563 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
161506 ATTAAGGGTA
161516 TACTACACCTTTAGTATCCCAAT
1 TACTACACCTTTAGTATCCCAAT
161539 TACTACACCTTTAGTATCCCAAT
1 TACTACACCTTTAGTATCCCAAT
161562 TA
1 TA
161564 TCATTGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.35
Consensus pattern (23 bp):
TACTACACCTTTAGTATCCCAAT
Found at i:168314 original size:31 final size:31
Alignment explanation
Indices: 168276--168381 Score: 212
Period size: 31 Copynumber: 3.4 Consensus size: 31
168266 CATCTATCCT
168276 ATGTATGCATGCAACCATCAATCACATTGAC
1 ATGTATGCATGCAACCATCAATCACATTGAC
168307 ATGTATGCATGCAACCATCAATCACATTGAC
1 ATGTATGCATGCAACCATCAATCACATTGAC
168338 ATGTATGCATGCAACCATCAATCACATTGAC
1 ATGTATGCATGCAACCATCAATCACATTGAC
168369 ATGTATGCATGCA
1 ATGTATGCATGCA
168382 TAAATCCATA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (31 bp):
ATGTATGCATGCAACCATCAATCACATTGAC
Found at i:173854 original size:193 final size:193
Alignment explanation
Indices: 173652--174007 Score: 694
Period size: 193 Copynumber: 1.8 Consensus size: 193
173642 ATATAATCCC
173652 ATATATATATATATATATCATATTGCTTCTTCAAAGATTGAAGGATCATCTTGCTTAAAATACTT
1 ATATATATATATATATATCATATTGCTTCTTCAAAGATTGAAGGATCATCTTGCTTAAAATACTT
173717 CGTAAACACTCTACTGCCAAAAACCTTTGTTTCCTTGTTTCTTCTAATCTTTTACATTGATTACT
66 CGTAAACACTCTACTGCCAAAAACCTTTGTTTCCTTGTTTCTTCTAATCTTTTACATTGATTACT
173782 GTCACTATACTATCATTGTTATAATAGTTGCATTGATCCTTCAATCTTTGAAGAAGCAATATG
131 GTCACTATACTATCATTGTTATAATAGTTGCATTGATCCTTCAATCTTTGAAGAAGCAATATG
173845 ATATATATATATATATATCATATTGCTTCTTCAAAGATTGAAGGATCATCTTGCTTAAAATACTT
1 ATATATATATATATATATCATATTGCTTCTTCAAAGATTGAAGGATCATCTTGCTTAAAATACTT
173910 CGTAAACACTCTACTGCCAAAAACCTTTGTTTCCTTGTTTCTTCTAATCTTTTACATTGATTACT
66 CGTAAACACTCTACTGCCAAAAACCTTTGTTTCCTTGTTTCTTCTAATCTTTTACATTGATTACT
* *
173975 GTCATTATACTATCATTGTTATAATATTTGCAT
131 GTCACTATACTATCATTGTTATAATAGTTGCAT
174008 ATGGTTCTCT
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 161 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (193 bp):
ATATATATATATATATATCATATTGCTTCTTCAAAGATTGAAGGATCATCTTGCTTAAAATACTT
CGTAAACACTCTACTGCCAAAAACCTTTGTTTCCTTGTTTCTTCTAATCTTTTACATTGATTACT
GTCACTATACTATCATTGTTATAATAGTTGCATTGATCCTTCAATCTTTGAAGAAGCAATATG
Found at i:187223 original size:2 final size:2
Alignment explanation
Indices: 187212--187241 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
187202 AATGAATTTT
187212 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
187242 TTCTTCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:196197 original size:20 final size:19
Alignment explanation
Indices: 196172--196211 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
196162 TCCTATTCCC
*
196172 TGGTAATCTTTTATTCTCGT
1 TGGTAATCTTATATTC-CGT
196192 TGGTAATCTTATATTCCGT
1 TGGTAATCTTATATTCCGT
196211 T
1 T
196212 AACCAAACGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (19 bp):
TGGTAATCTTATATTCCGT
Found at i:196600 original size:2 final size:2
Alignment explanation
Indices: 196589--196619 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
196579 TAGGGATAAT
196589 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
196620 AGTTAAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:201390 original size:5 final size:6
Alignment explanation
Indices: 201375--201399 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
201365 TTATTGATTG
201375 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
201400 AAATAGCCTA
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:206430 original size:30 final size:31
Alignment explanation
Indices: 206395--206722 Score: 291
Period size: 30 Copynumber: 10.9 Consensus size: 31
206385 GTGGTTGTTA
* * *
206395 TGAAAGT-GGTGGTGTAGAAGTGGATAATGC
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* * *
206425 TGAAAGT-GGTGGTGTAGAAATGGATATTGC
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* *
206455 TGAAA-TGGGTAGTGTAGAAAGGGACAATGT
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* *
206485 TGAAA-TGGGTAGTGTTGAAAGGGACAATGC
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* *
206515 TGAAA-TGGGTAGTGTTGAAAGGGACAATGC
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* * * *
206545 TGAAAGT-GGTGGTGTAGAAATAGATAGTGC
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* * * *
206575 TGAAAGT-GCTGGTGTAGAAATTGATAATGC
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* * *
206605 T-AAAATGGGTAGTGTAAAAATAGACAATGC
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* * *
206635 TGAAA-TGGGTAGTGTTGAAAAGGACAATGT
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* * *
206665 TGAAAGT-GTTGGTGTAGAAATGGATAATGC
1 TGAAAGTGGGTAGTGTAGAAATGGACAATGC
* * *
206695 TGAAA-TGGGTAATGTTGAAAGGGACAAT
1 TGAAAGTGGGTAGTGTAGAAATGGACAAT
206723 AAGAAAGACA
Statistics
Matches: 251, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
29 6 0.02
30 240 0.96
31 5 0.02
ACGTcount: A:0.35, C:0.05, G:0.34, T:0.26
Consensus pattern (31 bp):
TGAAAGTGGGTAGTGTAGAAATGGACAATGC
Found at i:206474 original size:15 final size:15
Alignment explanation
Indices: 206436--206534 Score: 76
Period size: 15 Copynumber: 6.6 Consensus size: 15
206426 GAAAGTGGTG
* *
206436 GTGTAGAAATGGATA
1 GTGTTGAAATGGGTA
* *
206451 TTGCTGAAATGGGTA
1 GTGTTGAAATGGGTA
* *
206466 GTGTAGAAA-GGGACA
1 GTGTTGAAATGGG-TA
*
206481 ATGTTGAAATGGGTA
1 GTGTTGAAATGGGTA
*
206496 GTGTTGAAA-GGGACA
1 GTGTTGAAATGGG-TA
* *
206511 ATGCTGAAATGGGTA
1 GTGTTGAAATGGGTA
206526 GTGTTGAAA
1 GTGTTGAAA
206535 GGGACAATGC
Statistics
Matches: 62, Mismatches: 18, Indels: 8
0.70 0.20 0.09
Matches are distributed among these distances:
14 6 0.10
15 50 0.81
16 6 0.10
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.26
Consensus pattern (15 bp):
GTGTTGAAATGGGTA
Found at i:206489 original size:60 final size:60
Alignment explanation
Indices: 206406--206722 Score: 336
Period size: 60 Copynumber: 5.3 Consensus size: 60
206396 GAAAGTGGTG
* *
206406 GTGTAG-AAGTGGATAATGCTGAAAGTGGTGGTGTAGAAATGGATATTGCTGAAATGGGTA
1 GTGTAGAAAG-GGACAATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAATGGGTA
* * * * *
206466 GTGTAGAAAGGGACAATGTTGAAA-TGGGTAGTGTTGAAAGGGACAATGCTGAAATGGGTA
1 GTGTAGAAAGGGACAATGCTGAAAGT-GGTGGTGTAGAAATGGATAATGCTGAAATGGGTA
* * * * *
206526 GTGTTGAAAGGGACAATGCTGAAAGTGGTGGTGTAGAAATAGATAGTGCTGAAA-GTGCTG
1 GTGTAGAAAGGGACAATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAATG-GGTA
** * * * * * *
206586 GTGTAGAAATTGATAATGCT-AAAATGGGTAGTGTAAAAATAGACAATGCTGAAATGGGTA
1 GTGTAGAAAGGGACAATGCTGAAAGT-GGTGGTGTAGAAATGGATAATGCTGAAATGGGTA
* * * *
206646 GTGTTGAAAAGGACAATGTTGAAAGTGTTGGTGTAGAAATGGATAATGCTGAAATGGGTA
1 GTGTAGAAAGGGACAATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAATGGGTA
* *
206706 ATGTTGAAAGGGACAAT
1 GTGTAGAAAGGGACAAT
206723 AAGAAAGACA
Statistics
Matches: 209, Mismatches: 41, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
59 6 0.03
60 194 0.93
61 9 0.04
ACGTcount: A:0.35, C:0.05, G:0.34, T:0.26
Consensus pattern (60 bp):
GTGTAGAAAGGGACAATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAATGGGTA
Found at i:206548 original size:15 final size:15
Alignment explanation
Indices: 206471--206550 Score: 74
Period size: 15 Copynumber: 5.3 Consensus size: 15
206461 GGGTAGTGTA
206471 GAAAGGGACAATGTT
1 GAAAGGGACAATGTT
* *
206486 GAAATGGG-TAGTGTT
1 GAAA-GGGACAATGTT
*
206501 GAAAGGGACAATGCT
1 GAAAGGGACAATGTT
* *
206516 GAAATGGG-TAGTGTT
1 GAAA-GGGACAATGTT
*
206531 GAAAGGGACAATGCT
1 GAAAGGGACAATGTT
206546 GAAAG
1 GAAAG
206551 TGGTGGTGTA
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 6 0.12
15 38 0.76
16 6 0.12
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (15 bp):
GAAAGGGACAATGTT
Found at i:206590 original size:120 final size:120
Alignment explanation
Indices: 206420--206722 Score: 410
Period size: 120 Copynumber: 2.5 Consensus size: 120
206410 AGAAGTGGAT
* * *
206420 AATGCTGAAAGTGGTGGTGTAGAAATGGATATTGCTGAAATGGGTAGTGTAGAAAGGGACAATGT
1 AATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAATGGCTAGTGTAGAAAGGGACAATGC
* ** * *
206485 TGAAATGGGTAGTGTTGAAAGGGACAATGCTGAAATGGGTAGTGTTGAAAGGGAC
66 TAAAATGGGTAGTGTAAAAAGAGACAATGCTGAAATGGGTAGTGTTGAAAAGGAC
* * * ** *
206540 AATGCTGAAAGTGGTGGTGTAGAAATAGATAGTGCTGAAA-GTGCTGGTGTAGAAATTGATAATG
1 AATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAATG-GCTAGTGTAGAAAGGGACAATG
*
206604 CTAAAATGGGTAGTGTAAAAATAGACAATGCTGAAATGGGTAGTGTTGAAAAGGAC
65 CTAAAATGGGTAGTGTAAAAAGAGACAATGCTGAAATGGGTAGTGTTGAAAAGGAC
* * * * *
206660 AATGTTGAAAGTGTTGGTGTAGAAATGGATAATGCTGAAATGGGTAATGTTGAAAGGGACAAT
1 AATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAATGGCTAGTGTAGAAAGGGACAAT
206723 AAGAAAGACA
Statistics
Matches: 156, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
119 1 0.01
120 154 0.99
121 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.33, T:0.26
Consensus pattern (120 bp):
AATGCTGAAAGTGGTGGTGTAGAAATGGATAATGCTGAAATGGCTAGTGTAGAAAGGGACAATGC
TAAAATGGGTAGTGTAAAAAGAGACAATGCTGAAATGGGTAGTGTTGAAAAGGAC
Found at i:206653 original size:15 final size:15
Alignment explanation
Indices: 206630--206714 Score: 55
Period size: 15 Copynumber: 5.7 Consensus size: 15
206620 AAAAATAGAC
* *
206630 AATGCTGAAATGGGT
1 AATGTTGAAATGGAT
* * *
206645 AGTGTTGAAAAGGAC
1 AATGTTGAAATGGAT
*
206660 AATGTTGAAA-GTGTT
1 AATGTTGAAATG-GAT
** *
206675 GGTGTAGAAATGGAT
1 AATGTTGAAATGGAT
* *
206690 AATGCTGAAATGGGT
1 AATGTTGAAATGGAT
206705 AATGTTGAAA
1 AATGTTGAAA
206715 GGGACAATAA
Statistics
Matches: 50, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
14 1 0.02
15 48 0.96
16 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.32, T:0.28
Consensus pattern (15 bp):
AATGTTGAAATGGAT
Found at i:209810 original size:22 final size:21
Alignment explanation
Indices: 209778--209818 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
209768 CTTGCAGTTC
209778 AATGCAAAATGAAGAAAAATTA
1 AATGCAAAATGAA-AAAAATTA
* *
209800 AATGCACAATGCAAAAAAT
1 AATGCAAAATGAAAAAAAT
209819 CAAAGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.17
Consensus pattern (21 bp):
AATGCAAAATGAAAAAAATTA
Found at i:217185 original size:36 final size:35
Alignment explanation
Indices: 217138--217214 Score: 118
Period size: 36 Copynumber: 2.2 Consensus size: 35
217128 AAAACAGTCC
* *
217138 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAAT-AAT
*
217174 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
217209 TCAATT
1 TCAATT
217215 AAATTCAACT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
35 9 0.24
36 29 0.76
ACGTcount: A:0.40, C:0.23, G:0.01, T:0.35
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:217771 original size:130 final size:130
Alignment explanation
Indices: 217612--217858 Score: 404
Period size: 130 Copynumber: 1.9 Consensus size: 130
217602 TATTTATATA
* * **
217612 ATCAATTTGGTCCTAAATTAAGTAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
217677 TTAGCACATGATCATGACACGTGTCATTTGTGACACATGTCACCACCTAATTGTTTATATATGTT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTGTTTATATATGTT
217742 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
217807 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATT
217859 AGAAGAAAAT
Statistics
Matches: 107, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTGTTTATATATGTT
Found at i:217890 original size:130 final size:129
Alignment explanation
Indices: 217626--217890 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
217616 ATTTGGTCCT
* * ** *
217626 AAATTAAGTAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
217691 TGACACGTGTCATTTGTGACACATGTCACCACCTAATTGTTTATATATGTTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTGAGAAAATAAGTTATCAAAGAAGT-CA
217756 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *
217821 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT-G-AGAAAA-TAAGTTATCAAAGAAGT
217885 -A
128 CA
217886 AAATT
1 AAATT
217891 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 98 0.88
131 1 0.01
132 7 0.06
133 6 0.05
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTGAGAAAATAAGTTATCAAAGAAGTCA
Found at i:218219 original size:28 final size:27
Alignment explanation
Indices: 218188--218250 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
218178 AGTTGATACA
*
218188 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
218216 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
218244 ATATTTT
1 ATATTTT
218251 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:218351 original size:16 final size:17
Alignment explanation
Indices: 218330--218361 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
218320 ATTTCTTATT
218330 AAAATAAAAT-ATTCAA
1 AAAATAAAATGATTCAA
218346 AAAATAAAATGATTCA
1 AAAATAAAATGATTCA
218362 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.66, C:0.06, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAATAAAATGATTCAA
Found at i:228663 original size:16 final size:16
Alignment explanation
Indices: 228642--228675 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
228632 TTTCGTTGCC
228642 ATTGCTTCGTTTACGG
1 ATTGCTTCGTTTACGG
228658 ATTGCTTCGTTTACGG
1 ATTGCTTCGTTTACGG
228674 AT
1 AT
228676 AGCTCTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.44
Consensus pattern (16 bp):
ATTGCTTCGTTTACGG
Found at i:231364 original size:4 final size:4
Alignment explanation
Indices: 231355--231384 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
231345 TCTTATTTTG
231355 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
231385 CTCATTTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:237972 original size:16 final size:16
Alignment explanation
Indices: 237951--238043 Score: 50
Period size: 16 Copynumber: 5.7 Consensus size: 16
237941 TCTTTACTTT
237951 ATTAAATTTTATATTA
1 ATTAAATTTTATATTA
*
237967 ATTAAATATTATAGTT-
1 ATTAAATTTTATA-TTA
*
237983 -TTAAATTTATTATATCA
1 ATTAAA-TT-TTATATTA
* *
238000 AATAAATATTAT-TTA
1 ATTAAATTTTATATTA
*
238015 TATATAATTTTTA-ATTA
1 -AT-TAAATTTTATATTA
*
238032 ATATAATTTTTA
1 AT-TAAATTTTA
238044 AATATATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 16
0.71 0.11 0.19
Matches are distributed among these distances:
15 7 0.12
16 31 0.52
17 18 0.30
18 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (16 bp):
ATTAAATTTTATATTA
Found at i:238418 original size:2 final size:2
Alignment explanation
Indices: 238411--238446 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
238401 GCATGCTCCA
238411 TC TC TC 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 TC TC TC
238447 ATTAACATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:244005 original size:13 final size:13
Alignment explanation
Indices: 243987--244011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
243977 TTAAATTGAG
243987 TTATTTAAATTTT
1 TTATTTAAATTTT
244000 TTATTTAAATTT
1 TTATTTAAATTT
244012 AATTATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTAAATTTT
Found at i:244032 original size:27 final size:26
Alignment explanation
Indices: 243917--244032 Score: 58
Period size: 27 Copynumber: 4.4 Consensus size: 26
243907 AGAGTCTTGC
**
243917 TTTATAATTTAAATTCT-ATTTAAACT
1 TTTATAATTTAAATT-TAATTTAAAAA
* * *
243943 TTTGTAAAGTTAAATATAATTTATAAAA
1 TTTAT-AATTTAAATTTAATTTA-AAAA
* * * **
243971 -TT-TAAGTTAAATTGAGTTATTTAAA
1 TTTATAATTTAAATTTAATT-TAAAAA
* *
243996 TTTTTTATTTAAATTTAATTATAAAAA
1 TTTATAATTTAAATTTAATT-TAAAAA
244023 TTTATAATTT
1 TTTATAATTT
244033 TTTAATGTTA
Statistics
Matches: 66, Mismatches: 18, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
25 15 0.23
26 9 0.14
27 40 0.61
28 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (26 bp):
TTTATAATTTAAATTTAATTTAAAAA
Found at i:258875 original size:173 final size:173
Alignment explanation
Indices: 258582--259104 Score: 931
Period size: 173 Copynumber: 3.0 Consensus size: 173
258572 TAATTTAGTT
**
258582 TTACAGTCCCATTGTTGACTTTCCCATAGTTGCGGTCTACTAAGAATCGATGATAAATAAAGGGA
1 TTACAGTCCCATTGTTGACTTTCCCATAGTTGCGGTAGACTAAGAATCGATGATAAATAAAGGGA
* *
258647 TGGAGTAAGATTAGCGGTTCCAGACCCAATAACTTTGGCTTTTGACCCA-TTGGCTAAAGTTACA
66 TGGAGTAAGATTAGCGGTTCCAGACCCAATAACTTTTGCTGTTGA-CCATTTGGCTAAAGTTACA
*
258711 GGCTGATAGACTTATGGTGATGAAAATCAGAAAGTAAACTGGGA
130 GGGTGATAGACTTATGGTGATGAAAATCAGAAAGTAAACTGGGA
*
258755 TTACAGTCCCATTGTTGACTTTCCCATAGTTGCGGTAGACTAAGAATCGATGATAAATAAAGAGA
1 TTACAGTCCCATTGTTGACTTTCCCATAGTTGCGGTAGACTAAGAATCGATGATAAATAAAGGGA
* *
258820 TGGAGTAAGATTAGCGGTTCCAGACCCAATAACTTTTTCTGTTGACCATTTGGCTAAAGTTTCAG
66 TGGAGTAAGATTAGCGGTTCCAGACCCAATAACTTTTGCTGTTGACCATTTGGCTAAAGTTACAG
258885 GGTGATAGACTTATGGTGATGAAAATCAGAAAGTAAACTGGGA
131 GGTGATAGACTTATGGTGATGAAAATCAGAAAGTAAACTGGGA
* *
258928 TTACAGTCCCATTGTTGACTTTCCCATAGTTGCGGCAGACTAAGAATCGATGATAAATAAAGGGG
1 TTACAGTCCCATTGTTGACTTTCCCATAGTTGCGGTAGACTAAGAATCGATGATAAATAAAGGGA
258993 TGGAGTAAGATTAGCGGTTCCAGACCCAATAACTTTTGCTGTTGACCATTTGGCTAAAGTTACAG
66 TGGAGTAAGATTAGCGGTTCCAGACCCAATAACTTTTGCTGTTGACCATTTGGCTAAAGTTACAG
*
259058 GGTGATAGACATATGGTGATGAAAATCAGAAAGTAAACTGGGA
131 GGTGATAGACTTATGGTGATGAAAATCAGAAAGTAAACTGGGA
259101 TTAC
1 TTAC
259105 CTGTCATATG
Statistics
Matches: 335, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
172 3 0.01
173 332 0.99
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (173 bp):
TTACAGTCCCATTGTTGACTTTCCCATAGTTGCGGTAGACTAAGAATCGATGATAAATAAAGGGA
TGGAGTAAGATTAGCGGTTCCAGACCCAATAACTTTTGCTGTTGACCATTTGGCTAAAGTTACAG
GGTGATAGACTTATGGTGATGAAAATCAGAAAGTAAACTGGGA
Found at i:270090 original size:17 final size:18
Alignment explanation
Indices: 270068--270116 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
270058 TTTTAAAAAG
270068 AATTTATTTTAATTGA-T
1 AATTTATTTTAATTGATT
**
270085 AATTTATTTTTTTTGATT
1 AATTTATTTTAATTGATT
270103 AATTTAATTTTAAT
1 AATTT-ATTTTAAT
270117 AAAAAAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 14 0.54
18 6 0.23
19 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (18 bp):
AATTTATTTTAATTGATT
Found at i:276180 original size:12 final size:12
Alignment explanation
Indices: 276150--276198 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
276140 ACATACTAAA
276150 AAATATATTTAT
1 AAATATATTTAT
** *
276162 ATTTATATTTCT
1 AAATATATTTAT
* *
276174 AAATATATTAAA
1 AAATATATTTAT
276186 AAATATATTTAT
1 AAATATATTTAT
276198 A
1 A
276199 TTTTTAAACC
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATATATTTAT
Found at i:276186 original size:36 final size:36
Alignment explanation
Indices: 276130--276201 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
276120 AGGGCCACAA
276130 ATATTTCTAAACATACTAAAAAATATATTTATATTT
1 ATATTTCTAAACATACTAAAAAATATATTTATATTT
* *
276166 ATATTTCTAAATATATTAAAAAATATATTTATATTT
1 ATATTTCTAAACATACTAAAAAATATATTTATATTT
276202 TTAAACCTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (36 bp):
ATATTTCTAAACATACTAAAAAATATATTTATATTT
Found at i:276595 original size:14 final size:14
Alignment explanation
Indices: 276578--276608 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
276568 GTTAGATAAG
*
276578 TGAAAATAGACTAT
1 TGAAAATAGACGAT
276592 TGAAAATAGACGAT
1 TGAAAATAGACGAT
276606 TGA
1 TGA
276609 GATTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (14 bp):
TGAAAATAGACGAT
Found at i:279657 original size:22 final size:22
Alignment explanation
Indices: 279629--279673 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
279619 TCACAACCAA
279629 ACTTCGAGTTCCAACCTCCCTC
1 ACTTCGAGTTCCAACCTCCCTC
279651 ACTTCGAGTTCCAACCTCCCTC
1 ACTTCGAGTTCCAACCTCCCTC
279673 A
1 A
279674 ACTCTAAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.44, G:0.09, T:0.27
Consensus pattern (22 bp):
ACTTCGAGTTCCAACCTCCCTC
Found at i:281747 original size:24 final size:23
Alignment explanation
Indices: 281720--281768 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
281710 TAGGCATCAA
*
281720 ACTAGAAC-GAAATAAACGTTAGAC
1 ACTA-AACTGAAA-AAACATTAGAC
*
281744 ACTAAACTGAAAAAACATTGGAC
1 ACTAAACTGAAAAAACATTAGAC
281767 AC
1 AC
281769 CTTTTGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.16
Consensus pattern (23 bp):
ACTAAACTGAAAAAACATTAGAC
Found at i:281857 original size:28 final size:28
Alignment explanation
Indices: 281811--281865 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
281801 CTTTATTTAC
* * *
281811 ATTATGTCGTCGAGCTAGTGCATGAAAT
1 ATTATGTCATCAAGATAGTGCATGAAAT
*
281839 ATTATGTCATCAAGATAGTGCTTGAAA
1 ATTATGTCATCAAGATAGTGCATGAAA
281866 GTAAAAACAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (28 bp):
ATTATGTCATCAAGATAGTGCATGAAAT
Found at i:289589 original size:14 final size:15
Alignment explanation
Indices: 289570--289598 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
289560 GTATTTTTTA
289570 ATTTAAT-TATTGAT
1 ATTTAATCTATTGAT
289584 ATTTAATCTATTGAT
1 ATTTAATCTATTGAT
289599 CGATTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
ATTTAATCTATTGAT
Found at i:290125 original size:41 final size:41
Alignment explanation
Indices: 290074--290173 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 41
290064 GGTACAATAT
* * *
290074 TTTACGGTTGTAATTTATAGGACACTATGCAATAAATATTA
1 TTTAGGGTTGTAATTTATACGACACTATGCAATAAATATAA
* * * *
290115 TTTAGGGTTGTTATTTTATACGATATTATGCAATAATTATAA
1 TTTAGGGTTG-TAATTTATACGACACTATGCAATAAATATAA
*
290157 TTTAGGATTGTAATTTA
1 TTTAGGGTTGTAATTTA
290174 GGGTACAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 15 0.31
42 34 0.69
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (41 bp):
TTTAGGGTTGTAATTTATACGACACTATGCAATAAATATAA
Found at i:291047 original size:38 final size:39
Alignment explanation
Indices: 291004--291081 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
290994 CTTTCTATTG
* * *
291004 TTATAATTGAGGTCTTTAATTTTT-TATTTTTATTTTTT
1 TTATAATTGAAGCCCTTAATTTTTGTATTTTTATTTTTT
*
291042 TTATAATTGAAGCCCTTAGTTTTTGTATTTTTATTTTTT
1 TTATAATTGAAGCCCTTAATTTTTGTATTTTTATTTTTT
291081 T
1 T
291082 CCTTTATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 20 0.57
39 15 0.43
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.65
Consensus pattern (39 bp):
TTATAATTGAAGCCCTTAATTTTTGTATTTTTATTTTTT
Found at i:291108 original size:43 final size:38
Alignment explanation
Indices: 291004--291114 Score: 107
Period size: 43 Copynumber: 2.8 Consensus size: 38
290994 CTTTCTATTG
* **
291004 TTATAATTGAGGTCTTTAATTTTTTATTTTTATTTTTT
1 TTATAATTGAGATCCCTAATTTTTTATTTTTATTTTTT
* *
291042 TTATAATTGA-AGCCCTTAGTTTTTGTATTTTTATTTTTTTCCT
1 TTATAATTGAGATCCC-TAATTTTT-TATTTTTA--TTTTT--T
*
291085 TTATAATTGAGATCCCTAATTTTTAATTTT
1 TTATAATTGAGATCCCTAATTTTTTATTTT
291115 CACTTTCTAC
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
37 1 0.02
38 17 0.29
39 8 0.14
41 5 0.09
42 5 0.09
43 18 0.31
44 4 0.07
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.61
Consensus pattern (38 bp):
TTATAATTGAGATCCCTAATTTTTTATTTTTATTTTTT
Found at i:291300 original size:43 final size:43
Alignment explanation
Indices: 291150--291309 Score: 173
Period size: 44 Copynumber: 3.7 Consensus size: 43
291140 TCAATGCCCT
* ** * * *
291150 ATTTTTT-AATCTCATTTTTTAATTTTATAGTTGAGGCC-CTG
1 ATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCTCTA
* * * *
291191 ATTTTTTCATTCTCACTTTCTATCTTTATAATTGA-AGCTCCTA
1 ATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCT-CTA
291234 ATTTATTTCAATCTCACTTTTTACCTTTATAATTGAGACCTCTA
1 ATTT-TTTCAATCTCACTTTTTACCTTTATAATTGAGACCTCTA
* *
291278 ATTTTTTCAATTTCACTTTTTACTTTTATAAT
1 ATTTTTTCAATCTCACTTTTTACCTTTATAAT
291310 ATAGATCCCT
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
41 8 0.08
42 21 0.21
43 32 0.32
44 35 0.35
45 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.06, T:0.53
Consensus pattern (43 bp):
ATTTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCTCTA
Found at i:291309 original size:87 final size:84
Alignment explanation
Indices: 291150--291309 Score: 198
Period size: 86 Copynumber: 1.9 Consensus size: 84
291140 TCAATGCCCT
* * * * *
291150 ATTTTTTAATCTCATTTTTTAATTTTATAGTTGAGGCCCTGATTTTTTCATTCTCACTTTCTATC
1 ATTTTTTAATCTCACTTTTTAACTTTATAATTGAGACCCTAATTTTTTCATTCTCACTTTCTATC
291215 TTTATAATTGAAGCTCCTA
66 TTTATAATTGAAGCTCCTA
* *
291234 ATTTATTTCAATCTCACTTTTTACCTTTATAATTGAGACCTCTAATTTTTTCAATT-TCACTTTT
1 ATTT-TTT-AATCTCACTTTTTAACTTTATAATTGAGACC-CTAATTTTTTC-ATTCTCACTTTC
291298 TA-CTTTTATAAT
62 TATC-TTTATAAT
291310 ATAGATCCCT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
84 4 0.06
85 3 0.05
86 27 0.42
87 27 0.42
88 3 0.05
ACGTcount: A:0.24, C:0.17, G:0.06, T:0.53
Consensus pattern (84 bp):
ATTTTTTAATCTCACTTTTTAACTTTATAATTGAGACCCTAATTTTTTCATTCTCACTTTCTATC
TTTATAATTGAAGCTCCTA
Found at i:291322 original size:43 final size:43
Alignment explanation
Indices: 291146--291325 Score: 167
Period size: 43 Copynumber: 4.2 Consensus size: 43
291136 AGATTCAATG
* ** * *
291146 CCCT-ATTT-TTT-AATCTCATTTTTTAATTTTATAGTTGAGG
1 CCCTAATTTATTTCAATCTCACTTTTTACCTTTATAATTGAGA
* * * *
291186 CCCTGATTT-TTTCATTCTCACTTTCTATCTTTATAATTGA-A
1 CCCTAATTTATTTCAATCTCACTTTTTACCTTTATAATTGAGA
291227 GCTCCTAATTTATTTCAATCTCACTTTTTACCTTTATAATTGAGA
1 -C-CCTAATTTATTTCAATCTCACTTTTTACCTTTATAATTGAGA
* *
291272 CCTCTAATTT-TTTCAATTTCACTTTTTACTTTTATAATAT-AGA
1 CC-CTAATTTATTTCAATCTCACTTTTTACCTTTATAAT-TGAGA
291315 TCCCTAATTTA
1 -CCCTAATTTA
291326 ATCATTTTTC
Statistics
Matches: 117, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
40 4 0.03
41 7 0.06
42 22 0.19
43 44 0.38
44 39 0.33
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.51
Consensus pattern (43 bp):
CCCTAATTTATTTCAATCTCACTTTTTACCTTTATAATTGAGA
Found at i:293055 original size:3 final size:3
Alignment explanation
Indices: 293047--293097 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
293037 TGTCCCAACC
293047 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
293095 AAG
1 AAG
293098 TTTGATTCTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:296366 original size:50 final size:51
Alignment explanation
Indices: 296286--296385 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 51
296276 CTCTTCCTTG
* *
296286 TTCCTTTTGCCACTTAATTTGTTTGTTGTGCACGTTTCTTTTATTACATAA
1 TTCCTTTTGCCACTTAATATGTTTGTTGTGCACGTTTCTTGTATTACATAA
* *
296337 TTCCTTTTGCTACTTGATAT-TTTGTTGTGCACGTTTCTTGTATTACATA
1 TTCCTTTTGCCACTTAATATGTTTGTTGTGCACGTTTCTTGTATTACATA
296386 CATTTGATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 28 0.62
51 17 0.38
ACGTcount: A:0.17, C:0.17, G:0.13, T:0.53
Consensus pattern (51 bp):
TTCCTTTTGCCACTTAATATGTTTGTTGTGCACGTTTCTTGTATTACATAA
Found at i:298235 original size:55 final size:54
Alignment explanation
Indices: 298151--298260 Score: 157
Period size: 55 Copynumber: 2.0 Consensus size: 54
298141 GAAATGTTTG
* *
298151 AAAGTTTTAATATTATTGTAGAAGCATTTTAATCCAAAATAATAGGAATTCTTC
1 AAAGTTTTAATATTATTGTAAAAGCATTTTAATCCAAAATAATAAGAATTCTTC
* * * *
298205 AAAGTTTTAGATATTATTGTAAAAGTATTTTAGTTCAAAATAATAAGAATTGTTC
1 AAAGTTTTA-ATATTATTGTAAAAGCATTTTAATCCAAAATAATAAGAATTCTTC
298260 A
1 A
298261 TTGTCTAAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
54 9 0.18
55 40 0.82
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (54 bp):
AAAGTTTTAATATTATTGTAAAAGCATTTTAATCCAAAATAATAAGAATTCTTC
Found at i:305996 original size:12 final size:13
Alignment explanation
Indices: 305981--306033 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 13
305971 TAAAGAAGCA
305981 GCTGCAGCT-CAG
1 GCTGCAGCTGCAG
*
305993 GCTGCGGCTGCA-
1 GCTGCAGCTGCAG
306005 GCT-CAGGCTGC-G
1 GCTGCA-GCTGCAG
306017 GCTGCAGCT-CAG
1 GCTGCAGCTGCAG
306029 GCTGC
1 GCTGC
306034 TTCTTCTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
11 2 0.06
12 28 0.82
13 4 0.12
ACGTcount: A:0.11, C:0.34, G:0.38, T:0.17
Consensus pattern (13 bp):
GCTGCAGCTGCAG
Found at i:306002 original size:18 final size:18
Alignment explanation
Indices: 305981--306033 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
305971 TAAAGAAGCA
305981 GCTGCAGCTCAGGCTGCG
1 GCTGCAGCTCAGGCTGCG
305999 GCTGCAGCTCAGGCTGCG
1 GCTGCAGCTCAGGCTGCG
306017 GCTGCAGCTCAGGCTGC
1 GCTGCAGCTCAGGCTGC
306034 TTCTTCTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.11, C:0.34, G:0.38, T:0.17
Consensus pattern (18 bp):
GCTGCAGCTCAGGCTGCG
Found at i:312431 original size:22 final size:22
Alignment explanation
Indices: 312406--312448 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
312396 TAGTATGGGG
312406 ATCTTTGGCATATTTAAACATC
1 ATCTTTGGCATATTTAAACATC
312428 ATCTTTGGCATATTTAAACAT
1 ATCTTTGGCATATTTAAACAT
312449 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (22 bp):
ATCTTTGGCATATTTAAACATC
Found at i:316077 original size:23 final size:23
Alignment explanation
Indices: 316047--316128 Score: 130
Period size: 23 Copynumber: 3.6 Consensus size: 23
316037 TTTGTATAAA
316047 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
316070 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
316093 TGCACCGTAA-TGCCGCGTAGAAT
1 TGCACCG-AAGTGCCACGTAGAAT
*
316116 TGCATCGAAGTGC
1 TGCACCGAAGTGC
316129 TATATAAGGT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.04
23 51 0.93
24 2 0.04
ACGTcount: A:0.28, C:0.26, G:0.27, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:317182 original size:2 final size:2
Alignment explanation
Indices: 317177--317212 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
317167 ACACACACAC
*
317177 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
317213 CAATATAATC
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:324479 original size:19 final size:19
Alignment explanation
Indices: 324455--324507 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
324445 TCTTAAGGGG
324455 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
324474 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
324493 ATGCATCGATGCACT
1 ATGCATCGATGCACT
324508 AATTGCATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.23, C:0.30, G:0.17, T:0.30
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:332359 original size:18 final size:18
Alignment explanation
Indices: 332336--332382 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
332326 CCAAATTGTC
*
332336 ATTATATATTTGTATAAT
1 ATTATATATTTGTAAAAT
*
332354 ATTATA-AATTGTAAAAT
1 ATTATATATTTGTAAAAT
332371 ATTTATATATTT
1 A-TTATATATTT
332383 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.42
18 11 0.46
19 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
ATTATATATTTGTAAAAT
Found at i:336582 original size:7 final size:7
Alignment explanation
Indices: 336572--336605 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
336562 AATATAAAGA
336572 TTAAATT
1 TTAAATT
336579 TTAAATT
1 TTAAATT
336586 TTAAATT
1 TTAAATT
336593 TTAAATT
1 TTAAATT
336600 TTAAAT
1 TTAAAT
336606 AGTATAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:336582 original size:21 final size:21
Alignment explanation
Indices: 336558--336604 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
336548 TGTCATAAGA
336558 TTAAAATATAAAGATTAAATT
1 TTAAAATATAAAGATTAAATT
* * **
336579 TTAAATTTTAAATTTTAAATT
1 TTAAAATATAAAGATTAAATT
336600 TTAAA
1 TTAAA
336605 TAGTATAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAAAATATAAAGATTAAATT
Found at i:336583 original size:14 final size:14
Alignment explanation
Indices: 336554--336597 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
336544 TTAATGTCAT
* *
336554 AAGATTAAAATATA
1 AAGATTAAATTTTA
336568 AAGATTAAATTTTA
1 AAGATTAAATTTTA
**
336582 AATTTTAAATTTTA
1 AAGATTAAATTTTA
336596 AA
1 AA
336598 TTTTAAATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (14 bp):
AAGATTAAATTTTA
Found at i:350275 original size:21 final size:21
Alignment explanation
Indices: 350245--350302 Score: 98
Period size: 21 Copynumber: 2.7 Consensus size: 21
350235 AATACCAAGT
350245 CAAGTGTATCGATACCCCTATA
1 CAAG-GTATCGATACCCCTATA
350267 CAAGGTATCGATACCCCTATA
1 CAAGGTATCGATACCCCTATA
*
350288 CAAGGTATTGATACC
1 CAAGGTATCGATACC
350303 TTAGGCCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 31 0.89
22 4 0.11
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.26
Consensus pattern (21 bp):
CAAGGTATCGATACCCCTATA
Done.