Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003314.1 Hibiscus syriacus cultivar Beakdansim tig00006976_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: 267825
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:190839 original size:26 final size:25
Alignment explanation
Indices: 190806--190865 Score: 56
Period size: 24 Copynumber: 2.5 Consensus size: 25
190796 GTATCAAATA
190806 ATTA-AATATTAATAATAAATCATT
1 ATTATAATATTAATAATAAATCATT
* *
190830 ATTAATAATA--ATTACTAAATCATT
1 ATT-ATAATATTAATAATAAATCATT
190854 ATTA-AATCATTA
1 ATTATAAT-ATTA
190866 TTATCATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
22 3 0.10
23 2 0.07
24 18 0.62
25 2 0.07
26 4 0.14
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATAATATTAATAATAAATCATT
Found at i:190873 original size:20 final size:23
Alignment explanation
Indices: 190851--190988 Score: 107
Period size: 23 Copynumber: 5.6 Consensus size: 23
190841 TTACTAAATC
*
190851 ATTATTAAATCATTATTATCATT
1 ATTATCAAATCATTATTATCATT
* *
190874 ATTATCAAATCATTATTATAATG
1 ATTATCAAATCATTATTATCATT
*
190897 ATTATTACTAAATCATTATTATAATGATT
1 ATTA-T-C-AAATCATTA-T-T-ATCATT
* *
190926 ATTATCAAATCATCAGTA-CATT
1 ATTATCAAATCATTATTATCATT
* *
190948 AAATATTTAAATCATTATTAAATCATT
1 -ATTA-TCAAATCATTATT--ATCATT
190975 ATTATCAAATCATT
1 ATTATCAAATCATT
190989 TCTAAATCAT
Statistics
Matches: 90, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
22 3 0.03
23 28 0.31
24 12 0.13
25 10 0.11
26 21 0.23
27 6 0.07
28 2 0.02
29 8 0.09
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTATCAAATCATTATTATCATT
Found at i:190900 original size:26 final size:26
Alignment explanation
Indices: 190851--190988 Score: 137
Period size: 26 Copynumber: 5.5 Consensus size: 26
190841 TTACTAAATC
*
190851 ATTATTAAATCATTA-T-T-ATCATT
1 ATTATCAAATCATTATTATAATCATT
*
190874 ATTATCAAATCATTATTATAATGATT
1 ATTATCAAATCATTATTATAATCATT
*
190900 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTATTATAATCATT
* * * * * *
190926 ATTATCAAATCATCAGTACATTAAAT
1 ATTATCAAATCATTATTATAATCATT
190952 ATT-T-AAATCATTATTA-AATCATT
1 ATTATCAAATCATTATTATAATCATT
190975 ATTATCAAATCATT
1 ATTATCAAATCATT
190989 TCTAAATCAT
Statistics
Matches: 95, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
23 21 0.22
24 12 0.13
25 11 0.12
26 50 0.53
27 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTATCAAATCATTATTATAATCATT
Found at i:190914 original size:49 final size:49
Alignment explanation
Indices: 190845--190988 Score: 157
Period size: 49 Copynumber: 2.9 Consensus size: 49
190835 TAATAATTAC
* *
190845 TAAATCATTATTAAATCATTATT-ATCATTATTATCAAATCATTATTATAA
1 TAAAT-ATTA-TAAATCATTATTAATCATTATTATCAAATCATTAGTACAA
* * * * *
190895 TGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATCAGTACAT
1 TAAATATTA-TAAATCATTA-T-TAATCATTATTATCAAATCATTAGTACAA
190947 TAAATATT-TAAATCATTATTAAATCATTATTATCAAATCATT
1 TAAATATTATAAATCATTATT-AATCATTATTATCAAATCATT
190989 TCTAAATCAT
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
48 1 0.01
49 34 0.44
50 14 0.18
51 1 0.01
52 28 0.36
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (49 bp):
TAAATATTATAAATCATTATTAATCATTATTATCAAATCATTAGTACAA
Found at i:191431 original size:14 final size:14
Alignment explanation
Indices: 191410--191480 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
191400 ATTAGTAATA
191410 ATTATTAAATCATT
1 ATTATTAAATCATT
* *
191424 AGTATTAAATAATT
1 ATTATTAAATCATT
* *
191438 ATTA-TAATTTCATG
1 ATTATTAA-ATCATT
*
191452 ATTACTAAATCATT
1 ATTATTAAATCATT
* *
191466 ACTATCAAATCATT
1 ATTATTAAATCATT
191480 A
1 A
191481 AATATTAATA
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
13 3 0.07
14 38 0.86
15 3 0.07
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:191534 original size:49 final size:49
Alignment explanation
Indices: 191427--191773 Score: 441
Period size: 49 Copynumber: 6.9 Consensus size: 49
191417 AATCATTAGT
* *
191427 ATTAAATAATT-ATTATAATTTCATGATTACTAAATCATTACTATCAAATC
1 ATTAAAT-ATTAATAATAATTTCATTATTACT-AATCATTACTATCAAATC
*
191477 ATTAAATATTAATAATAATTTCATTATTACTAATCGTTACTATCAAATC
1 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATC
*
191526 ATTAAATATTAATAATAATTTCTTTATTACTAATCATTACTATCAAATC
1 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATC
* *
191575 ATTAAATATTAATAATAATTTTC-TTATTACTAATCAATATTATCAAATC
1 ATTAAATATTAATAATAA-TTTCATTATTACTAATCATTACTATCAAATC
* * *
191624 ATTAAATATTAATAATAATTTCATTATTATTAATCATTACAAAAT-AATTAC
1 ATTAAATATTAATAATAATTTCATTATTACTAATCATTAC--TATCAAAT-C
*
191675 TATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATC
1 -ATTAAAT-ATT--A-A-TAA---TAATTTCATTATTACTAATCATTACTATCAAATC
191733 ATTAAATATTAATAATAATTTCATTATTA-TAATCATTACTA
1 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTA
191774 AATCAGTACT
Statistics
Matches: 264, Mismatches: 17, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
48 16 0.06
49 155 0.59
50 32 0.12
51 3 0.01
52 9 0.03
53 4 0.02
54 1 0.00
55 1 0.00
56 4 0.02
57 9 0.03
58 3 0.01
59 3 0.01
60 24 0.09
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.44
Consensus pattern (49 bp):
ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATC
Found at i:191575 original size:98 final size:99
Alignment explanation
Indices: 191427--191773 Score: 488
Period size: 98 Copynumber: 3.4 Consensus size: 99
191417 AATCATTAGT
* *
191427 ATTAAATAATT-ATTATAATTTCATGATTACTAAATCATTACTATCAAATCATTAAATATTAATA
1 ATTAAAT-ATTAATAATAATTTCATTATTACTAAATCATTACTATCAAATCATTAAATATTAATA
*
191491 ATAATTTCATTATTACTAATCGTTACTATCAAATC
65 ATAATTTCATTATTACTAATCATTACTATCAAATC
*
191526 ATTAAATATTAATAATAATTTCTTTATTACT-AATCATTACTATCAAATCATTAAATATTAATAA
1 ATTAAATATTAATAATAATTTCATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAA
* *
191590 TAATTTTC-TTATTACTAATCAATATTATCAAATC
66 TAA-TTTCATTATTACTAATCATTACTATCAAATC
*
191624 ATTAAATATTAATAATAATTTCATTATTATTAATCATTACAAAATAATTACTATCAAATCATTAA
1 ATTAAATATTAATAATAATTTC---ATTATT-A-C--T---AAATCATTACTATCAAATCATTAA
191689 ATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATC
56 ATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATC
191733 ATTAAATATTAATAATAATTTCATTATTA-T-AATCATTACTA
1 ATTAAATATTAATAATAATTTCATTATTACTAAATCATTACTA
191774 AATCAGTACT
Statistics
Matches: 223, Mismatches: 11, Indels: 30
0.84 0.04 0.11
Matches are distributed among these distances:
97 10 0.04
98 84 0.38
99 28 0.13
101 6 0.03
102 1 0.00
103 1 0.00
105 2 0.01
106 6 0.03
108 4 0.02
109 81 0.36
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.44
Consensus pattern (99 bp):
ATTAAATATTAATAATAATTTCATTATTACTAAATCATTACTATCAAATCATTAAATATTAATAA
TAATTTCATTATTACTAATCATTACTATCAAATC
Found at i:191683 original size:109 final size:108
Alignment explanation
Indices: 191561--191801 Score: 412
Period size: 109 Copynumber: 2.2 Consensus size: 108
191551 ATTACTAATC
*
191561 ATTACTATCAAATCATTAAATATTAATAATAATTTTC-TTATTACTAATCAATATTATCAAATCA
1 ATTACTATCAAATCATTAAATATTAATAATAA-TTTCATTATTACTAATCAATACTATCAAATCA
191625 TTAAATATTAATAATAATTTCATTATTATTAATCATTACAAAATA
65 TTAAATATTAATAATAATTTCATTATTA-TAATCATTACAAAATA
*
191670 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCAT
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCAATACTATCAAATCAT
* *
191735 TAAATATTAATAATAATTTCATTATTATAATCATTACTAAATC
66 TAAATATTAATAATAATTTCATTATTATAATCATTACAAAATA
*
191778 AGTACTATCAAATCATTAAATATT
1 ATTACTATCAAATCATTAAATATT
191802 GGTTGACTCA
Statistics
Matches: 126, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
108 41 0.33
109 85 0.67
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (108 bp):
ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCAATACTATCAAATCAT
TAAATATTAATAATAATTTCATTATTATAATCATTACAAAATA
Found at i:191696 original size:25 final size:26
Alignment explanation
Indices: 191655--191745 Score: 61
Period size: 25 Copynumber: 3.7 Consensus size: 26
191645 CATTATTATT
*
191655 AATCATTACAA-AATAATTACTATCA
1 AATCATTATAATAATAATTACTATCA
*
191680 AATCATTA-AATATTAA-TA--AT-A
1 AATCATTATAATAATAATTACTATCA
* * *
191701 ATTTCATTATTACTAATCATTACTATCA
1 A-ATCATTA-TAATAATAATTACTATCA
*
191729 AATCATTA-AATATTAAT
1 AATCATTATAATAATAAT
191746 AATAATTTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
21 2 0.04
22 8 0.16
24 9 0.18
25 20 0.41
27 8 0.16
28 2 0.04
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (26 bp):
AATCATTATAATAATAATTACTATCA
Found at i:194962 original size:14 final size:14
Alignment explanation
Indices: 194945--194971 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
194935 TAATATACAC
194945 AACAACAAAAAATG
1 AACAACAAAAAATG
194959 AACAACAAAAAAT
1 AACAACAAAAAAT
194972 AATAAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
AACAACAAAAAATG
Found at i:195579 original size:15 final size:16
Alignment explanation
Indices: 195549--195583 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
195539 TGTCCCTTTA
*
195549 TTCTTCTTCTTTTCCT
1 TTCTTCTTCCTTTCCT
195565 TTCTT-TTCCTTTCCT
1 TTCTTCTTCCTTTCCT
195580 TTCT
1 TTCT
195584 CTCGCCAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTCTTCCTTTCCT
Found at i:197451 original size:14 final size:15
Alignment explanation
Indices: 197424--197481 Score: 54
Period size: 14 Copynumber: 4.2 Consensus size: 15
197414 TTTCTTCCTG
* *
197424 TTATTATTTATATTG
1 TTATTATATATATTA
197439 TTATT-TATATATTA
1 TTATTATATATATTA
*
197453 TTATTGTAT-TATTA
1 TTATTATATATATTA
197467 TTA-TA-A-ATATTA
1 TTATTATATATATTA
197479 TTA
1 TTA
197482 ATAAATACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.24
13 1 0.03
14 20 0.53
15 8 0.21
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTATTATATATATTA
Found at i:197476 original size:26 final size:26
Alignment explanation
Indices: 197424--197481 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
197414 TTTCTTCCTG
* *
197424 TTATTATTTATATTGTTATTTATATA
1 TTATTATTTATATTATTATTTAAATA
*
197450 TTATTA-TTGTATTATTATTATAAATA
1 TTATTATTTATATTATTATT-TAAATA
197476 TTATTA
1 TTATTA
197482 ATAAATACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (26 bp):
TTATTATTTATATTATTATTTAAATA
Found at i:198840 original size:2 final size:2
Alignment explanation
Indices: 198833--198866 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
198823 ACACATTAAG
198833 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
198867 GAAAATTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:199769 original size:7 final size:7
Alignment explanation
Indices: 199757--199790 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
199747 TTCAATTCAT
199757 TTTTTTA
1 TTTTTTA
199764 TTTTTTA
1 TTTTTTA
199771 TTTTTTA
1 TTTTTTA
199778 --TTTTA
1 TTTTTTA
199783 TTTTTTA
1 TTTTTTA
199790 T
1 T
199791 ATCCTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.20
7 20 0.80
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:199781 original size:12 final size:12
Alignment explanation
Indices: 199766--199790 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
199756 TTTTTTTATT
199766 TTTTATTTTTTA
1 TTTTATTTTTTA
199778 TTTTATTTTTTA
1 TTTTATTTTTTA
199790 T
1 T
199791 ATCCTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:200835 original size:22 final size:21
Alignment explanation
Indices: 200810--200879 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
200800 GCATATATGC
*
200810 ATTTGCATTTTATTTGTGTTAT
1 ATTTGCATTTTATTTGTATT-T
200832 ATTTGCATTATTATATT-TATTT
1 ATTTGCATT-TTAT-TTGTATTT
* * *
200854 ATTTAGCATTTTTTTTGCATTC
1 ATTT-GCATTTTATTTGTATTT
200876 ATTT
1 ATTT
200880 TCAAAACTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 2 0.05
22 24 0.60
23 12 0.30
24 2 0.05
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (21 bp):
ATTTGCATTTTATTTGTATTT
Found at i:209053 original size:137 final size:136
Alignment explanation
Indices: 208794--209444 Score: 907
Period size: 137 Copynumber: 4.8 Consensus size: 136
208784 TTGATATTTG
* * * *
208794 AGCAACATCATCCCTAGATAACTAGATGTCCTCATCAC----GAACCGTGTTATCTCAAATATCT
1 AGCAGCATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
*
208855 TTAAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATTAGAACTCCTCATC
66 TTAAAGATGG-CAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATC
208920 ACGAAGA
130 ACGAAGA
* *
208927 AACAGCATCATCATTAGATAACCAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
1 AGCAGCATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
* * ** * *
208992 TTAAAGATGGTCAAACGTCCTTATCACGAAGGAACAATGTCATCCATTGATCAAAATTCCTCATC
66 TTAAAGATGG-CAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATC
209057 ACGAAGA
130 ACGAAGA
*
209064 AGCATCATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
1 AGCAGCATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
* *
209129 TTAAAGATGGCCAGACGTCCTCATCATGAAGGAATAATGTCATCCACCGATCAGAACTCCTCATC
66 TTAAAGATGG-CAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATC
209194 ACGAAGA
130 ACGAAGA
* * *
209201 AGTATCATCATCCTTAGATAACCAGATATCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
1 AGCAGCATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
* ** *
209266 TTAAAGATGGCTAGACGTCCTCATCACAAAGGAACAATGTCATCCATTG-TCAGAATTCCTCATC
66 TTAAAGATGGC-AGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATC
** *
209330 ATAAAGG
130 ACGAAGA
* * * *** *
209337 AGCAGCATCATCCTTAGATAGCCAGATGTCCTTATCACGAATGAACCAAGTTATCTGAAATATCT
1 AGCAGCATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
* *
209402 TTAAAGATGGCTAAACGTCCTCATCACGGAGGAACAATGTCAT
66 TTAAAGATGGC-AGACGTCCTCATCACGAAGGAACAATGTCAT
209445 ACACTAGTTT
Statistics
Matches: 464, Mismatches: 49, Indels: 7
0.89 0.09 0.01
Matches are distributed among these distances:
133 33 0.07
136 114 0.25
137 317 0.68
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.26
Consensus pattern (136 bp):
AGCAGCATCATCCTTAGATAACCAGATGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCT
TTAAAGATGGCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCA
CGAAGA
Found at i:209758 original size:17 final size:18
Alignment explanation
Indices: 209718--209760 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
209708 AACCCGAGTC
*
209718 AGGCCCAAATAACCCAGC
1 AGGCCCAAATAACCCAGA
*
209736 AGGCCCAAATAACTC-GA
1 AGGCCCAAATAACCCAGA
209753 AGGCCCAA
1 AGGCCCAA
209761 CAAGACCAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.35, G:0.19, T:0.07
Consensus pattern (18 bp):
AGGCCCAAATAACCCAGA
Found at i:211239 original size:30 final size:30
Alignment explanation
Indices: 211205--211277 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
211195 CCCGAAGGAC
211205 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
211235 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
211265 CTGTCCATAGGTC
1 CTATCCAGAGGTC
211278 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:211373 original size:63 final size:61
Alignment explanation
Indices: 211260--211388 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
211250 AAAGATCCTC
* *
211260 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
211321 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
211384 GGTAA
1 GGTAA
211389 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:211383 original size:32 final size:31
Alignment explanation
Indices: 211263--211390 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
211253 GATCCTCGGT
* * * *
211263 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
211294 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
211325 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
211357 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
211388 AAC
1 AAC
211391 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:212598 original size:21 final size:21
Alignment explanation
Indices: 212574--212618 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
212564 TGTTGTTCGT
* *
212574 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
212595 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
212616 TTG
1 TTG
212619 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:215829 original size:30 final size:30
Alignment explanation
Indices: 215757--215816 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
215747 CCCGAAGGAC
215757 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
215787 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
215817 TTGTCCATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:215920 original size:32 final size:32
Alignment explanation
Indices: 215818--215941 Score: 96
Period size: 31 Copynumber: 3.9 Consensus size: 32
215808 CCTCGGTAAT
* * *
215818 TGTCCATAGGTCCCG-AAGAACCTAGGT-AAAC
1 TGTCCATATGTCTCGTAA-AACATAGGTAAAAC
* * * *
215849 TGTCTATATGT-TCCTTAGAACATAGGT-ATAC
1 TGTCCATATGTCT-CGTAAAACATAGGTAAAAC
215880 TGTCCATATGTCTCG-AAAGACATAGGTAAAAC
1 TGTCCATATGTCTCGTAAA-ACATAGGTAAAAC
* * *
215912 TGTTCATATGTTTCGTATAACATAGGTAAA
1 TGTCCATATGTCTCGTAAAACATAGGTAAA
215942 CCCTCGACTC
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
30 2 0.03
31 40 0.55
32 29 0.40
33 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (32 bp):
TGTCCATATGTCTCGTAAAACATAGGTAAAAC
Found at i:215934 original size:63 final size:62
Alignment explanation
Indices: 215818--215939 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 62
215808 CCTCGGTAAT
* *
215818 TGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCTATATGTTCCTTAGAACATAGGTATAC
1 TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCTATATGTTCCGTAGAACATAGGTATAC
* * * *
215880 TGTCCATATGTCTCGAA-AGACATAGGTAAAACTGT-TCATATGTTTCGTATAACATAGGTA
1 TGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCT-ATATGTTCCGTAGAACATAGGTA
215940 AACCCTCGAC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
61 1 0.02
62 23 0.45
63 27 0.53
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (62 bp):
TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCTATATGTTCCGTAGAACATAGGTATAC
Found at i:217151 original size:21 final size:21
Alignment explanation
Indices: 217127--217171 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
217117 TGTTGTTCGT
* *
217127 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
217148 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
217169 TTG
1 TTG
217172 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:218422 original size:2 final size:2
Alignment explanation
Indices: 218415--218452 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
218405 ACATATTAAG
218415 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
218453 GAAAAATTGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:219539 original size:133 final size:135
Alignment explanation
Indices: 219342--219586 Score: 433
Period size: 134 Copynumber: 1.8 Consensus size: 135
219332 ATGATTATAA
*
219342 AAATAAATATATAATAATAATTTTTAATTTTGACATTATTTTATGTAGTAATTTTTCATCTTTTC
1 AAATAAATATATAATAATAATTTTTAATATTGACATTATTTTATGTAGTAATTTTTCATCTTTTC
* *
219407 AATTT-TTTTTATTTTTCCAAGCAAAACTTAAAGAGATGGAAACTAGCACAAAAATGAGAGAGAT
66 AATTTCTTTTTATTTTTCCAAGAAAAACTTAAAGAGATGAAAACTAGCACAAAAATGAGAGAGAT
219471 GGGGG
131 GGGGG
219476 AAATAAATATATAATAATAATTTTTAATAATT-ACA-TATTTTATGTAGTAATTTTTCATCTTTT
1 AAATAAATATATAATAATAATTTTTAAT-ATTGACATTATTTTATGTAGTAATTTTTCATCTTTT
219539 CAATTTCTTTTTATTTTTCCAAGAAAAACTTAAAGAGATGAAAACTAG
65 CAATTTCTTTTTATTTTTCCAAGAAAAACTTAAAGAGATGAAAACTAG
219587 GGCTGGCAAT
Statistics
Matches: 106, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
133 34 0.32
134 70 0.66
135 2 0.02
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (135 bp):
AAATAAATATATAATAATAATTTTTAATATTGACATTATTTTATGTAGTAATTTTTCATCTTTTC
AATTTCTTTTTATTTTTCCAAGAAAAACTTAAAGAGATGAAAACTAGCACAAAAATGAGAGAGAT
GGGGG
Found at i:221284 original size:2 final size:2
Alignment explanation
Indices: 221239--221268 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
221229 ACCTGCCATG
221239 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
221269 GGATGGATAG
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:221290 original size:20 final size:22
Alignment explanation
Indices: 221257--221296 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
221247 ATATATATAT
221257 ATATATATATATGGATGGATAG
1 ATATATATATATGGATGGATAG
*
221279 ATATAT-TA-ATGGGTGGAT
1 ATATATATATATGGATGGAT
221297 GGATGTTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (22 bp):
ATATATATATATGGATGGATAG
Found at i:224129 original size:24 final size:26
Alignment explanation
Indices: 224074--224129 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
224064 TTTTCGATGT
* *
224074 TCTGTTTTGTCGTTGGTTGTTTGCTC
1 TCTGTTTTGGCGTTGGTTCTTTGCTC
*
224100 TCTGTTTTGGC-TTTGTTCTTT-CTC
1 TCTGTTTTGGCGTTGGTTCTTTGCTC
224124 TCTGTT
1 TCTGTT
224130 GGTTGTTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 9 0.33
25 8 0.30
26 10 0.37
ACGTcount: A:0.00, C:0.18, G:0.21, T:0.61
Consensus pattern (26 bp):
TCTGTTTTGGCGTTGGTTCTTTGCTC
Found at i:224585 original size:3 final size:3
Alignment explanation
Indices: 224577--224615 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
224567 ATTTTTTATT
* *
224577 TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
224616 ACAAAATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:224914 original size:45 final size:45
Alignment explanation
Indices: 224848--225331 Score: 887
Period size: 45 Copynumber: 10.7 Consensus size: 45
224838 TCAAAAAGTT
*
224848 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGG--TTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
* *
224895 CCCGAATGTTTTGAAAACATCAAGCACTGAAGGGCTTATAGATGA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
*
224940 CCCGAAGGTTTTGAAAACATCAAGCACTAAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
224985 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
225030 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
*
225075 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATTA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
*
225120 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
225165 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
*
225210 CTCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
225255 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
225300 CCCGAAGGTTTTGAAAACATCAAGCACTGAAG
1 CCCGAAGGTTTTGAAAACATCAAGCACTGAAG
225332 ATGTGGGAAA
Statistics
Matches: 424, Mismatches: 13, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
45 417 0.98
47 7 0.02
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGA
Found at i:226059 original size:26 final size:22
Alignment explanation
Indices: 226000--226076 Score: 93
Period size: 22 Copynumber: 3.5 Consensus size: 22
225990 AATAAAGCTT
*
226000 TCATCTTTGAA-AATAGAATCTA
1 TCATCTTTGAAGAA-AGAGTCTA
* * * *
226022 TCATCTTTAAAGAGATAGGCTA
1 TCATCTTTGAAGAAAGAGTCTA
226044 TCATCTTTGAAGAAAGAGTCTA
1 TCATCTTTGAAGAAAGAGTCTA
226066 TCATCTTTGAA
1 TCATCTTTGAA
226077 AAGTGTAGAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAAAGAGTCTA
Found at i:230621 original size:11 final size:10
Alignment explanation
Indices: 230605--230668 Score: 69
Period size: 11 Copynumber: 6.2 Consensus size: 10
230595 TTAATTTTCC
230605 TTCTTTTGTTT
1 TTCTTTT-TTT
230616 TTC--TTTTT
1 TTCTTTTTTT
230624 TTCTTTTTTT
1 TTCTTTTTTT
230634 TTCTTTTTTTT
1 TTC-TTTTTTT
*
230645 TTGTTTTCTTT
1 TTCTTTT-TTT
230656 TTCTTTTTCTT
1 TTCTTTTT-TT
230667 TT
1 TT
230669 TTCCTTCTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
8 6 0.13
9 2 0.04
10 13 0.28
11 25 0.54
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:230623 original size:1 final size:1
Alignment explanation
Indices: 230608--230670 Score: 54
Period size: 1 Copynumber: 63.0 Consensus size: 1
230598 ATTTTCCTTC
* * * * * * * *
230608 TTTTGTTTTTCTTTTTTTCTTTTTTTTTCTTTTTTTTTTGTTTTCTTTTTCTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
230671 CCTTCTTCTT
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (1 bp):
T
Found at i:230633 original size:22 final size:21
Alignment explanation
Indices: 230599--230670 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
230589 CTTGATTTAA
* *
230599 TTTTCCTTCTTTTGTTTTTCTT
1 TTTTTCTT-TTTTTTTTTTCTT
*
230621 TTTTTCTTTTTTTTTCTTTTTT
1 TTTTTCTTTTTTTTT-TTTCTT
*
230643 TTTTGTTTTCTTTTTCTTTTTCTT
1 TTTT-TCTT-TTTTT-TTTTTCTT
230667 TTTT
1 TTTT
230671 CCTTCTTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
21 6 0.15
22 16 0.39
23 3 0.07
24 14 0.34
25 2 0.05
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (21 bp):
TTTTTCTTTTTTTTTTTTCTT
Found at i:230634 original size:12 final size:12
Alignment explanation
Indices: 230614--230670 Score: 69
Period size: 13 Copynumber: 4.5 Consensus size: 12
230604 CTTCTTTTGT
230614 TTTTCTTTTTTTC
1 TTTT-TTTTTTTC
*
230627 TTTTTTTTTCTTT
1 TTTTTTTTT-TTC
230640 TTTTTTTGTTTTC
1 TTTTTTT-TTTTC
*
230653 TTTTTCTTTTTC
1 TTTTTTTTTTTC
230665 TTTTTT
1 TTTTTT
230671 CCTTCTTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
12 15 0.39
13 21 0.55
14 2 0.05
ACGTcount: A:0.00, C:0.11, G:0.02, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTTTC
Found at i:230676 original size:11 final size:11
Alignment explanation
Indices: 230599--230685 Score: 70
Period size: 12 Copynumber: 7.7 Consensus size: 11
230589 CTTGATTTAA
*
230599 TTTTCCTTCTT
1 TTTTCTTTCTT
230610 TTGTT-TTTCTTT
1 TT-TTCTTTC-TT
230622 TTTTCTTT-TT
1 TTTTCTTTCTT
*
230632 TTTTCTTTTTT
1 TTTTCTTTCTT
*
230643 TTTTGTTTTCTT
1 TTTT-CTTTCTT
*
230655 TTTCTTTTTCTT
1 TTT-TCTTTCTT
*
230667 TTTTCCTTCTT
1 TTTTCTTTCTT
*
230678 CTTTCTTT
1 TTTTCTTT
230686 GTTGGATGAG
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
10 10 0.16
11 25 0.40
12 27 0.43
13 1 0.02
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:230684 original size:7 final size:6
Alignment explanation
Indices: 230608--230669 Score: 67
Period size: 6 Copynumber: 10.7 Consensus size: 6
230598 ATTTTCCTTC
* * *
230608 TTTTGT TTTTCT TTTT-T TCTTTTT TTTTCT TTTT-T TTTT-G TTTTCT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTTCT TTTTCT TTTTCT
230654 TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTT
230670 TCCTTCTTCT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
5 11 0.22
6 36 0.73
7 2 0.04
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (6 bp):
TTTTCT
Found at i:235616 original size:20 final size:18
Alignment explanation
Indices: 235599--235659 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
235589 AATTAATACC
235599 TGAATAAAATAAAAAATA
1 TGAATAAAATAAAAAATA
* *
235617 TTAATAAAATAATATAAAAA
1 TGAATAAAATAA-A-AAATA
*
235637 T-AATAAGTAATAAAAAATT
1 TGAATAA--AATAAAAAATA
235656 TGAA
1 TGAA
235660 AGAAAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 11 0.32
19 10 0.29
20 8 0.24
21 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
TGAATAAAATAAAAAATA
Found at i:241351 original size:29 final size:29
Alignment explanation
Indices: 241309--241397 Score: 169
Period size: 29 Copynumber: 3.1 Consensus size: 29
241299 ATACAGTGGT
241309 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
241338 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
*
241367 CTTGAAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
241396 CT
1 CT
241398 GTGTGTATTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.15, C:0.31, G:0.36, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:241483 original size:15 final size:15
Alignment explanation
Indices: 241443--241621 Score: 144
Period size: 15 Copynumber: 11.1 Consensus size: 15
241433 AACATGGGAC
241443 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
241459 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
241474 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
241489 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
241506 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* *
241524 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
241539 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
241556 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* * *
241571 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
241591 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
241606 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
241621 G
1 G
241622 GAGGGGATGG
Statistics
Matches: 131, Mismatches: 18, Indels: 29
0.74 0.10 0.16
Matches are distributed among these distances:
14 1 0.01
15 56 0.43
16 27 0.21
17 26 0.20
18 7 0.05
19 12 0.09
20 2 0.02
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:241516 original size:65 final size:66
Alignment explanation
Indices: 241430--241556 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
241420 TCGCCATGCA
241430 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG-GTGGGAATGCATGGGGGAGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
241494 G
66 G
*
241495 ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGA-GTGGGAATGCATGGGG
241557 TGGGAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.24, C:0.09, G:0.50, T:0.17
Consensus pattern (66 bp):
ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
G
Found at i:241554 original size:50 final size:48
Alignment explanation
Indices: 241435--241648 Score: 220
Period size: 50 Copynumber: 4.3 Consensus size: 48
241425 ATGCAATCAA
* * * *
241435 CATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGG-TGGGAATG
1 CATGGGACGTGGGAATGCAT-GGGGTGGGAATGCATGGGGAGGGGAGTG
* * *
241483 CATGGG-GGAGGG-ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGA-TG
1 CATGGGACGTGGGAAT--GCATGGG--GTGGGAATGCAT-GGGGAGGGGAGTG
241533 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGATGGTG
1 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGA--GTG
*
241583 CATTGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTG
1 CATGGGACGTGGGAATGCATGGGGTGGGAATGCAT-GGGGAGGGGA--GTG
*
241634 CATTGGACGTGGGAA
1 CATGGGACGTGGGAA
241649 CTGTGCATGG
Statistics
Matches: 144, Mismatches: 10, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
46 2 0.01
47 17 0.12
48 21 0.15
49 10 0.07
50 54 0.38
51 38 0.26
52 2 0.01
ACGTcount: A:0.21, C:0.08, G:0.52, T:0.18
Consensus pattern (48 bp):
CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGAGTG
Found at i:241569 original size:65 final size:64
Alignment explanation
Indices: 241433--241625 Score: 214
Period size: 65 Copynumber: 3.0 Consensus size: 64
241423 CCATGCAATC
*
241433 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGGAT
1 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
*
241497 CAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGGTG-GG
1 -AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG--GTGGGAATGCATGGGG-GAGG
241561 AAT
62 AAT
* * ** * *
241564 -GCATGGGGA-G-GGGATGGTGCATTGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGG
1 AACAT-GGGACGTGGGA--ATGCA-TGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGG
241626 GGATGGTGCA
Statistics
Matches: 112, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
64 5 0.04
65 62 0.55
66 8 0.07
67 36 0.32
68 1 0.01
ACGTcount: A:0.22, C:0.08, G:0.52, T:0.17
Consensus pattern (64 bp):
AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
Found at i:241578 original size:82 final size:82
Alignment explanation
Indices: 241445--241620 Score: 223
Period size: 82 Copynumber: 2.2 Consensus size: 82
241435 CATGGGACGT
* * * *
241445 GGGAATGCATGGG-GGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGGAT-CAACATGGGAT
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGATGCAACATGGGAC
241508 GTGGGAATGCATGGGGGA
66 GTGGGAATGCAT-GGGGA
* *** *
241526 GGGGATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCAT-GGGGAGGGGATGGTGCATTGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGA-GGGATGCAACATGGGA
*
241590 CGTGGGAATGCATGGGGT
65 CGTGGGAATGCATGGGGA
241608 GGGAATGCATGGG
1 GGGAATGCATGGG
241621 GGAGGGGATG
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
81 17 0.21
82 46 0.57
83 18 0.22
ACGTcount: A:0.22, C:0.08, G:0.53, T:0.18
Consensus pattern (82 bp):
GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGATGCAACATGGGAC
GTGGGAATGCATGGGGA
Found at i:241644 original size:51 final size:51
Alignment explanation
Indices: 241508--241648 Score: 245
Period size: 50 Copynumber: 2.8 Consensus size: 51
241498 AACATGGGAT
*
241508 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
241556 GTGGGAATGCAT-GGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
241606 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
241649 CTGTGCATGG
Statistics
Matches: 88, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
47 10 0.11
48 12 0.14
50 36 0.41
51 30 0.34
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
Found at i:242101 original size:21 final size:21
Alignment explanation
Indices: 242076--242119 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
242066 AATCTAGTTA
242076 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
242097 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
242118 AT
1 AT
242120 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:242129 original size:28 final size:30
Alignment explanation
Indices: 242096--242158 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
242086 TAGTATAAAT
*
242096 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
242124 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
242154 TATTA
1 TATTA
242159 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:242706 original size:20 final size:21
Alignment explanation
Indices: 242662--242706 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
242652 AAATATTGTG
**
242662 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
242683 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
242703 TTTA
1 TTTA
242707 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:242991 original size:26 final size:25
Alignment explanation
Indices: 242962--243020 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
242952 AAATCATATT
*
242962 ATTATTAAATTATTAAATATCAAATC
1 ATTATTAAA-TAGTAAATATCAAATC
*
242988 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
243014 ATTATTA
1 ATTATTA
243021 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 20 0.71
27 2 0.07
28 3 0.11
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:245175 original size:26 final size:25
Alignment explanation
Indices: 245140--245296 Score: 139
Period size: 26 Copynumber: 6.3 Consensus size: 25
245130 CAAACCTTGT
*
245140 TAATAATCATTATAGTAATGATTTGA
1 TAATAATCATTATAATAATGATTT-A
245166 TAATAATCATTATAATAATGATTTA
1 TAATAATCATTATAATAATGATTTA
*
245191 GTAATAATCATTATAAAAATGA-TT-
1 -TAATAATCATTATAATAATGATTTA
*
245215 TAATAATGATT-T-A-AAT-ATTTAA
1 TAATAATCATTATAATAATGATTT-A
* * * *
245237 TGATTTGATGATT-TAGTAATGATTTGA
1 T-A-ATAATCATTATAATAATGATTT-A
245264 TAATAATCATTATAATAATGATTTTA
1 TAATAATCATTATAATAATGA-TTTA
245290 TAATAAT
1 TAATAAT
245297 TATTTAGTTA
Statistics
Matches: 109, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.01
20 5 0.05
21 1 0.01
22 2 0.02
23 11 0.10
24 8 0.07
25 9 0.08
26 63 0.58
27 9 0.08
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (25 bp):
TAATAATCATTATAATAATGATTTA
Found at i:245529 original size:17 final size:17
Alignment explanation
Indices: 245504--245536 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
245494 ACTAAATATT
*
245504 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
245521 TAATGATTTGATACTA
1 TAATGATTTGATACTA
245537 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:245529 original size:25 final size:23
Alignment explanation
Indices: 245450--245529 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
245440 GATTTATTGT
245450 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
245471 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
245498 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
245520 GTAATGATTT
1 -TAAT-ATTT
245530 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:248001 original size:47 final size:47
Alignment explanation
Indices: 247898--247988 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
247888 CAACAAACAA
247898 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
* *
247946 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
247989 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 10 0.24
45 13 0.32
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
Found at i:248221 original size:4 final size:4
Alignment explanation
Indices: 248185--248250 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
248175 CCTTATCTCC
* **
248185 CTTT C-TT C-TT CTTA CTTT CCTTT CTCC CTTT CTTT CTTT CTTT CCTTT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT -CTTT
**
248233 CTCC CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CT
248251 CGGCTGCAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
3 6 0.12
4 35 0.71
5 8 0.16
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:248227 original size:25 final size:25
Alignment explanation
Indices: 248175--248250 Score: 116
Period size: 25 Copynumber: 2.9 Consensus size: 25
248165 AAAAAATTTA
*
248175 CCTTATCTCCCTTTCTTCTTCTTACTTT
1 CCTT-TCTCCCTTTC-T-TTCTTTCTTT
248203 CCTTTCTCCCTTTCTTTCTTTCTTT
1 CCTTTCTCCCTTTCTTTCTTTCTTT
248228 CCTTTCTCCCTTTCTTTCTTTCT
1 CCTTTCTCCCTTTCTTTCTTTCT
248251 CGGCTGCAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
25 32 0.68
26 1 0.02
27 10 0.21
28 4 0.09
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.61
Consensus pattern (25 bp):
CCTTTCTCCCTTTCTTTCTTTCTTT
Found at i:248340 original size:25 final size:25
Alignment explanation
Indices: 248312--248363 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
248302 TTTCTTTTAT
*
248312 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
248337 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
248362 AA
1 AA
248364 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:248511 original size:23 final size:23
Alignment explanation
Indices: 248484--248530 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
248474 GAATCTATAT
248484 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
248507 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
248530 G
1 G
248531 AATGGACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.09, G:0.45, T:0.26
Consensus pattern (23 bp):
GGCTGCATGTGAATGGATGATGG
Found at i:248535 original size:13 final size:13
Alignment explanation
Indices: 248517--248548 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
248507 GGCTGCATGT
*
248517 GAATGGATGATGG
1 GAATGGACGATGG
248530 GAATGGACGATGG
1 GAATGGACGATGG
248543 GAATGG
1 GAATGG
248549 CGCCGGGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.47, T:0.19
Consensus pattern (13 bp):
GAATGGACGATGG
Found at i:248582 original size:29 final size:29
Alignment explanation
Indices: 248549--248657 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
248539 ATGGGAATGG
248549 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
*
248578 CGCCGGGAGTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
248607 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTACAAGGT
* *
248636 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
248658 CTCTATTCCA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 73 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.31, G:0.32, T:0.15
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTACAAGGT
Found at i:248713 original size:43 final size:43
Alignment explanation
Indices: 248652--248739 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
248642 GGCTGCATGG
248652 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
248695 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
248738 CG
1 CG
248740 CTCGTATGGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.20
Consensus pattern (43 bp):
CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
Found at i:248862 original size:35 final size:35
Alignment explanation
Indices: 248739--248861 Score: 219
Period size: 35 Copynumber: 3.5 Consensus size: 35
248729 TGGGGAGAAC
248739 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
*
248774 GCTCGTATGTCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
* *
248809 GCTCGTATGGCTCGTATGTATGGGGAGACCCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
248844 GCTCGTATGGCTCGTATG
1 GCTCGTATGGCTCGTATG
248862 TCACACCGTT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 84 1.00
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.28
Consensus pattern (35 bp):
GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
Found at i:248941 original size:35 final size:35
Alignment explanation
Indices: 248895--248973 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
248885 TGGGGAGAAC
248895 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
248930 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
248965 GCTCGTATG
1 GCTCGTATG
248974 TTCCCGTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (35 bp):
GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
Found at i:249411 original size:2 final size:2
Alignment explanation
Indices: 249404--249434 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
249394 ATAATTTTAA
249404 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 A
249435 ATTCGTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:263173 original size:28 final size:28
Alignment explanation
Indices: 263141--263196 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
263131 AACAAATGGC
*
263141 TCCTGGACTCCAAACCAATAGCACACAA
1 TCCTGGACTCCAAACCAATAACACACAA
263169 TCCTGGACTCCAAACCAATAACACACAA
1 TCCTGGACTCCAAACCAATAACACACAA
263197 AACACAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.36, G:0.09, T:0.14
Consensus pattern (28 bp):
TCCTGGACTCCAAACCAATAACACACAA
Found at i:264220 original size:16 final size:17
Alignment explanation
Indices: 264199--264231 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
264189 CAAACTAAAA
264199 CCTTTGAG-AGGACATT
1 CCTTTGAGCAGGACATT
264215 CCTTTGAGCAGGACATT
1 CCTTTGAGCAGGACATT
264232 GGCAAGCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
CCTTTGAGCAGGACATT
Found at i:267710 original size:18 final size:18
Alignment explanation
Indices: 267689--267741 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
267679 ATAAATTAAA
*
267689 CAATTAAAATTAAAGAAT
1 CAATTAAAATTAAAGAAG
* *
267707 CAA-TAAGATTTCAAGAAG
1 CAATTAA-AATTAAAGAAG
*
267725 GAATTAAAATTAAAGAA
1 CAATTAAAATTAAAGAA
267742 ACAAAATTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (18 bp):
CAATTAAAATTAAAGAAG
Done.