Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008345.1 Hibiscus syriacus cultivar Beakdansim tig00111073_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: 297766
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 1 of 2
Found at i:11181 original size:22 final size:22
Alignment explanation
Indices: 11153--11198 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
11143 CATTATGCCC
11153 ATAGTTAACACAACACAGAACA
1 ATAGTTAACACAACACAGAACA
11175 ATAGTTAACACAACACAGAACA
1 ATAGTTAACACAACACAGAACA
11197 AT
1 AT
11199 GCTTCTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.22, G:0.09, T:0.15
Consensus pattern (22 bp):
ATAGTTAACACAACACAGAACA
Found at i:17451 original size:21 final size:21
Alignment explanation
Indices: 17426--17465 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17416 GTATTTTTGG
*
17426 GTGTCAGTAACGGTATTGTAT
1 GTGTCAGTAACGATATTGTAT
*
17447 GTGTCAGTATCGATATTGT
1 GTGTCAGTAACGATATTGT
17466 TCTTATACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.10, G:0.28, T:0.40
Consensus pattern (21 bp):
GTGTCAGTAACGATATTGTAT
Found at i:25262 original size:14 final size:14
Alignment explanation
Indices: 25239--25278 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
25229 AAAAATATTT
*
25239 AAATTAAAATCTAAG
1 AAATT-AAATATAAG
25254 AAATTAAATATAAG
1 AAATTAAATATAAG
25268 AAATTAAATAT
1 AAATTAAATAT
25279 GCAGGGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (14 bp):
AAATTAAATATAAG
Found at i:26585 original size:20 final size:21
Alignment explanation
Indices: 26535--26585 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
26525 TTTGCATGTA
26535 AATAA-ATATTTAATAATAAT
1 AATAATATATTTAATAATAAT
* *
26555 AATATTTTATTT-ATAATAAT
1 AATAATATATTTAATAATAAT
26575 AATAATATATT
1 AATAATATATT
26586 GGTTGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAATATATTTAATAATAAT
Found at i:27278 original size:19 final size:19
Alignment explanation
Indices: 27254--27290 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27244 TTATTAAAAG
*
27254 TTATAAAATAATTTTTTAA
1 TTATAAAATAATGTTTTAA
*
27273 TTATAAGATAATGTTTTA
1 TTATAAAATAATGTTTTA
27291 TTAAGACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
TTATAAAATAATGTTTTAA
Found at i:28909 original size:16 final size:17
Alignment explanation
Indices: 28878--28911 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
28868 CGTTGATGTA
*
28878 TACATGAATAAAACTCT
1 TACATCAATAAAACTCT
28895 TACATCAAT-AAACTCT
1 TACATCAATAAAACTCT
28911 T
1 T
28912 GGCATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.21, G:0.03, T:0.32
Consensus pattern (17 bp):
TACATCAATAAAACTCT
Found at i:31683 original size:21 final size:22
Alignment explanation
Indices: 31659--31699 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
31649 TTAGGAATGT
* *
31659 TGGAGCAAAGTAG-GGAAAATA
1 TGGAGAAAAATAGAGGAAAATA
31680 TGGAGAAAAATAGAGGAAAA
1 TGGAGAAAAATAGAGGAAAA
31700 GAAGTAGAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.54, C:0.02, G:0.32, T:0.12
Consensus pattern (22 bp):
TGGAGAAAAATAGAGGAAAATA
Found at i:33973 original size:29 final size:29
Alignment explanation
Indices: 33931--33988 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
33921 CTTCCTTGAA
33931 CGAGAGGATCATTTTTGAATTGTTTTATG
1 CGAGAGGATCATTTTTGAATTGTTTTATG
33960 CGAGAGGATCATTTTTGAATTGTTTTATG
1 CGAGAGGATCATTTTTGAATTGTTTTATG
33989 TGACAACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (29 bp):
CGAGAGGATCATTTTTGAATTGTTTTATG
Found at i:35322 original size:29 final size:29
Alignment explanation
Indices: 35280--35337 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
35270 CTTCCTTGAA
35280 CGAGAGGATCATTTTTGAATTGTTTTATG
1 CGAGAGGATCATTTTTGAATTGTTTTATG
35309 CGAGAGGATCATTTTTGAATTGTTTTATG
1 CGAGAGGATCATTTTTGAATTGTTTTATG
35338 TGACAACAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (29 bp):
CGAGAGGATCATTTTTGAATTGTTTTATG
Found at i:38578 original size:21 final size:22
Alignment explanation
Indices: 38548--38588 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38538 TACTAATTGT
*
38548 TGGAGCAAAGTAG-GGAAAATA
1 TGGAGAAAAGTAGAGGAAAATA
38569 TGGAGAAAAGTAGAGGAAAA
1 TGGAGAAAAGTAGAGGAAAA
38589 CAAGAAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.51, C:0.02, G:0.34, T:0.12
Consensus pattern (22 bp):
TGGAGAAAAGTAGAGGAAAATA
Found at i:47637 original size:60 final size:60
Alignment explanation
Indices: 47524--47637 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
47514 CATACCCTCG
* * * *
47524 TTTTAAATTGGTCCCTAAAATTTTAATTATTTTAATTTCATCCTTAAATTATAATTATTA
1 TTTTAAATTAGTCCCTAAAATTTTAATCATTTTAATTTCATCCTCAAACTATAATTATTA
* *
47584 TTTTAAATTAGTCCTTAAAATTTTGAA-CATTTTAATTTCATTCTCAAACTATAA
1 TTTTAAATTAGTCCCTAAAATTTT-AATCATTTTAATTTCATCCTCAAACTATAA
47638 CCTTCATTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 45 0.96
61 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (60 bp):
TTTTAAATTAGTCCCTAAAATTTTAATCATTTTAATTTCATCCTCAAACTATAATTATTA
Found at i:47651 original size:60 final size:59
Alignment explanation
Indices: 47527--47696 Score: 157
Period size: 60 Copynumber: 2.8 Consensus size: 59
47517 ACCCTCGTTT
* * * * * *
47527 TAAATTGGTCCCTAAAATTTT-AATTATTTTAATTTCATCCTTAAATTATAATTATTATTT
1 TAAATTGGT-CCTAAAATTTTGAA-CATTTTAATTTCATCCTCAAACTATAACTATCATTC
* *
47587 TAAATTAGTCCTTAAAATTTTGAACATTTTAATTTCATTCTCAAACTATAACCT-TCATTC
1 TAAATTGGTCC-TAAAATTTTGAACATTTTAATTTCATCCTCAAACTATAA-CTATCATTC
* * * *
47647 TAAATTGGTCCCAAAACTTCTTGAACATTCTGATTTCATCC-CAAATTATA
1 TAAATTGGTCCTAAAA-TT-TTGAACATTTTAATTTCATCCTCAAACTATA
47697 CATATATATC
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
59 6 0.07
60 64 0.70
61 21 0.23
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (59 bp):
TAAATTGGTCCTAAAATTTTGAACATTTTAATTTCATCCTCAAACTATAACTATCATTC
Found at i:47731 original size:29 final size:29
Alignment explanation
Indices: 47686--47768 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
47676 CTGATTTCAT
*
47686 CCCAAATTATACATATATATCAGTCCCTG
1 CCCAAATTATACGTATATATCAGTCCCTG
*
47715 CCCAAATTATACGTATATATCAGTCCCTT
1 CCCAAATTATACGTATATATCAGTCCCTG
*
47744 CCCAAATTATACGTATATATTAGTC
1 CCCAAATTATACGTATATATCAGTC
47769 ACATCTCTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (29 bp):
CCCAAATTATACGTATATATCAGTCCCTG
Found at i:50772 original size:19 final size:19
Alignment explanation
Indices: 50711--50772 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
50701 TTAATATTAT
* *
50711 AATTTTATTATAATATTTA
1 AATTTAATTATAATTTTTA
* * *
50730 AA-TTAGTTTTAATTTTTTTC
1 AATTTAATTATAA--TTTTTA
50750 AATTTAATTATAATTTTTA
1 AATTTAATTATAATTTTTA
50769 AATT
1 AATT
50773 AGTTTACGAT
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 7 0.22
19 11 0.34
20 6 0.19
21 8 0.25
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
AATTTAATTATAATTTTTA
Found at i:51447 original size:2 final size:2
Alignment explanation
Indices: 51440--51487 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
51430 AAAAATTTAA
51440 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
51482 AT AT AT
1 AT AT AT
51488 GTGTTGGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52196 original size:8 final size:8
Alignment explanation
Indices: 52183--52235 Score: 88
Period size: 8 Copynumber: 6.6 Consensus size: 8
52173 GATTCGATTA
*
52183 ACGTATGT
1 ACGTAGGT
*
52191 ACGTATGT
1 ACGTAGGT
52199 ACGTAGGT
1 ACGTAGGT
52207 ACGTAGGT
1 ACGTAGGT
52215 ACGTAGGT
1 ACGTAGGT
52223 ACGTAGGT
1 ACGTAGGT
52231 ACGTA
1 ACGTA
52236 CATACGTACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.26, C:0.13, G:0.32, T:0.28
Consensus pattern (8 bp):
ACGTAGGT
Found at i:52241 original size:8 final size:8
Alignment explanation
Indices: 52230--52254 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
52220 GGTACGTAGG
52230 TACGTACA
1 TACGTACA
52238 TACGTACA
1 TACGTACA
52246 TACGTACA
1 TACGTACA
52254 T
1 T
52255 GATATAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (8 bp):
TACGTACA
Found at i:52241 original size:16 final size:16
Alignment explanation
Indices: 52190--52254 Score: 67
Period size: 16 Copynumber: 4.1 Consensus size: 16
52180 TTAACGTATG
* **
52190 TACGTATGTACGTAGG
1 TACGTAGGTACGTACA
**
52206 TACGTAGGTACGTAGG
1 TACGTAGGTACGTACA
52222 TACGTAGGTACGTACA
1 TACGTAGGTACGTACA
**
52238 TACGTACATACGTACA
1 TACGTAGGTACGTACA
52254 T
1 T
52255 GATATAAGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (16 bp):
TACGTAGGTACGTACA
Found at i:52241 original size:24 final size:24
Alignment explanation
Indices: 52190--52243 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
52180 TTAACGTATG
* **
52190 TACGTATGTACGTAGGTACGTAGG
1 TACGTAGGTACGTAGGTACGTACA
52214 TACGTAGGTACGTAGGTACGTACA
1 TACGTAGGTACGTAGGTACGTACA
52238 TACGTA
1 TACGTA
52244 CATACGTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (24 bp):
TACGTAGGTACGTAGGTACGTACA
Found at i:52249 original size:24 final size:24
Alignment explanation
Indices: 52198--52251 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
52188 TGTACGTATG
** **
52198 TACGTAGGTACGTAGGTACGTAGG
1 TACGTAGGTACGTACATACGTACA
52222 TACGTAGGTACGTACATACGTACA
1 TACGTAGGTACGTACATACGTACA
52246 TACGTA
1 TACGTA
52252 CATGATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (24 bp):
TACGTAGGTACGTACATACGTACA
Found at i:54856 original size:2 final size:2
Alignment explanation
Indices: 54851--54875 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54841 ATATATATAT
54851 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
54876 TTGGATAGAG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55962 original size:28 final size:30
Alignment explanation
Indices: 55926--55982 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
55916 TCGCTCTCAT
55926 TAATCAAATTTGTTA-TTATAAAAAATATA
1 TAATCAAATTTGTTACTTATAAAAAATATA
*
55955 TAAT-AAATTTTTTACGTTATAAAAAATA
1 TAATCAAATTTGTTAC-TTATAAAAAATA
55983 GAATTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 4 0.16
30 12 0.48
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (30 bp):
TAATCAAATTTGTTACTTATAAAAAATATA
Found at i:60093 original size:32 final size:32
Alignment explanation
Indices: 60055--60132 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
60045 TCGGGGTCGT
*
60055 AGGGCCTACCTAAGAACAT-ATCTTAGGGCCGC
1 AGGGCCTACCTAAGAA-ATGATCTCAGGGCCGC
**
60087 AGGGCCTACCCGAG-AATGATCTCAGGGCCGC
1 AGGGCCTACCTAAGAAATGATCTCAGGGCCGC
*
60118 AGAGCCTACCTAAGA
1 AGGGCCTACCTAAGA
60133 GTCACATTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
30 2 0.05
31 24 0.63
32 12 0.32
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.15
Consensus pattern (32 bp):
AGGGCCTACCTAAGAAATGATCTCAGGGCCGC
Found at i:66522 original size:28 final size:28
Alignment explanation
Indices: 66482--66536 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
66472 CTCTATAAAC
66482 CATTCTTCAGGTATTTACTCAATTCGAT
1 CATTCTTCAGGTATTTACTCAATTCGAT
66510 CATTCTTCAGGTATTTACTCAATTCGA
1 CATTCTTCAGGTATTTACTCAATTCGA
66537 CAATTTCCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (28 bp):
CATTCTTCAGGTATTTACTCAATTCGAT
Found at i:71537 original size:23 final size:23
Alignment explanation
Indices: 71510--71583 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
71500 TTATATATGA
71510 ATATGTAATACGTGATACATGTG
1 ATATGTAATACGTGATACATGTG
* ** *
71533 ATATG--ATATGAAATGACATATG
1 ATATGTAATACGTGAT-ACATGTG
71555 AATATGTAATACGTGATACATGTG
1 -ATATGTAATACGTGATACATGTG
71579 ATATG
1 ATATG
71584 ATATGAAATA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
21 6 0.15
22 6 0.15
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (23 bp):
ATATGTAATACGTGATACATGTG
Found at i:71543 original size:46 final size:46
Alignment explanation
Indices: 71492--71596 Score: 185
Period size: 46 Copynumber: 2.3 Consensus size: 46
71482 CTATATGACT
* *
71492 ATATGAAATTATATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
71538 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
71584 ATATGAAAT-ACAT
1 ATATGAAATGACAT
71597 GGTTACACAT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 4 0.07
46 53 0.93
ACGTcount: A:0.43, C:0.06, G:0.17, T:0.34
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
Found at i:71796 original size:17 final size:17
Alignment explanation
Indices: 71774--71838 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
71764 ACAGATTACA
71774 TCCTTCGGGATGACAGG
1 TCCTTCGGGATGACAGG
*
71791 TCCTTCGGGA-CACAGATG
1 TCCTTCGGGATGACAG--G
*
71809 ACATCCTTCGGGATGATAGG
1 ---TCCTTCGGGATGACAGG
71829 TCCTTCGGGA
1 TCCTTCGGGA
71839 CATTTGTACG
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.10
17 20 0.51
18 1 0.03
20 1 0.03
21 10 0.26
22 3 0.08
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.25
Consensus pattern (17 bp):
TCCTTCGGGATGACAGG
Found at i:71801 original size:38 final size:38
Alignment explanation
Indices: 71745--71840 Score: 165
Period size: 38 Copynumber: 2.5 Consensus size: 38
71735 TATAAGACAT
* *
71745 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
71783 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
71821 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
71841 TTTGTACGAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:71817 original size:21 final size:21
Alignment explanation
Indices: 71753--71821 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
71743 ATATGATAGG
* *
71753 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
71774 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
71791 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
71812 TCCTTCGGGA
1 TCCTTCGGGA
71822 TGATAGGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
16 4 0.11
17 10 0.26
18 1 0.03
21 19 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:72031 original size:20 final size:21
Alignment explanation
Indices: 71995--72036 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
71985 TGACATGATT
*
71995 TATATATATGTCATATTGAAA
1 TATATACATGTCATATTGAAA
72016 TATATACATG-CATATTGAAA
1 TATATACATGTCATATTGAAA
72036 T
1 T
72037 GTTATGATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
TATATACATGTCATATTGAAA
Found at i:78432 original size:51 final size:51
Alignment explanation
Indices: 78372--78474 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
78362 CTATGTGACT
*
78372 ATATGAAATGATATATGAATATGCAATACGTGATACATGTGATATGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATGATATG
*
78423 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATGATATG
1 ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATGATATG
78474 A
1 A
78475 AATACATGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (51 bp):
ATATGAAATGACATATGAATATGCAATACGTGATACATGTGATATGATATG
Found at i:78686 original size:38 final size:38
Alignment explanation
Indices: 78643--78725 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
78633 ATAGGTCCTA
* *
78643 CGGGACACAGATTACATCCTTCGGGGTGACAGGTCATT
1 CGGGACACAGATGACATCCTTCGGGATGACAGGTCATT
*
78681 CGGGACACAGATGACATCCTTCGGGATGATAGGTCATT
1 CGGGACACAGATGACATCCTTCGGGATGACAGGTCATT
78719 CGGGACA
1 CGGGACA
78726 TTTGTACGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (38 bp):
CGGGACACAGATGACATCCTTCGGGATGACAGGTCATT
Found at i:78904 original size:21 final size:20
Alignment explanation
Indices: 78880--78922 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
78870 GACATGATTT
* *
78880 ATATATATATGTCATGTTGAA
1 ATATATACATG-CATATTGAA
78901 ATATATACATGCATATTGAA
1 ATATATACATGCATATTGAA
78921 AT
1 AT
78923 GTTATGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (20 bp):
ATATATACATGCATATTGAA
Found at i:81208 original size:16 final size:16
Alignment explanation
Indices: 81180--81216 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
81170 TGACGTGGCA
81180 GCGG-TGGAAGCAGAG
1 GCGGCTGGAAGCAGAG
*
81195 GCGGCTGGAGGCAGAG
1 GCGGCTGGAAGCAGAG
81211 GCGGCT
1 GCGGCT
81217 AGGGATTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.19, C:0.19, G:0.54, T:0.08
Consensus pattern (16 bp):
GCGGCTGGAAGCAGAG
Found at i:81335 original size:9 final size:10
Alignment explanation
Indices: 81302--81340 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
81292 TGGGCTTGTA
81302 ATTTAATATT
1 ATTTAATATT
81312 ATTTATATATGT
1 ATTTA-ATAT-T
81324 ATTTAATA-T
1 ATTTAATATT
81333 ATTTAATA
1 ATTTAATA
81341 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:81344 original size:3 final size:3
Alignment explanation
Indices: 81336--81392 Score: 87
Period size: 3 Copynumber: 19.0 Consensus size: 3
81326 TTAATATATT
* * *
81336 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TTA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
81384 TAA TAA TAA
1 TAA TAA TAA
81393 ATTAATATGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:82498 original size:113 final size:112
Alignment explanation
Indices: 81717--82491 Score: 1302
Period size: 113 Copynumber: 6.9 Consensus size: 112
81707 ATAGAATTAT
* * * * *
81717 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
81782 ATTATGAACTTCTCTGGAAAAGATAATCCATCA-ATTGAT-GAATTCA
66 ATTATGAACTTCTCTGGAAAAGATAATCCATCAGA-TGATGGATTTGA
* *
81828 GGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
81893 CATTATGAACTTCTCTGGAAAAGATAATCCATCAGATGATGGATTTGA
65 CATTATGAACTTCTCTGGAAAAGATAATCCATCAGATGATGGATTTGA
81941 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
82006 ATTATGAACTTTTTCTGGAAAAGATAATCCATCAGATGATGGATTTGA
66 ATTATGAAC-TTCTCTGGAAAAGATAATCCATCAGATGATGGATTTGA
82054 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
82119 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
66 ATTATGAAC-TTCTCTGGAAAAGATAATCCATCAGATGATGGATTTGA
*
82167 GCAAAAAGGTTGAACAAATTCTTCTCATTAAGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* *
82232 CATTATGAACTTCTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
65 CATTATGAACTTCTCTGGAAAAGATAATCCATCAGATGATGGATTTGA
82280 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
82345 ATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
66 ATTATGAAC-TTCTCTGGAAAAGATAATCCATCAGATGATGGATTTGA
82393 GCAAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
82458 CATTATGAACTTCTCTGGAAAAGATAATCCATCA
65 CATTATGAACTTCTCTGGAAAAGATAATCCATCA
82492 ATTGATGAAT
Statistics
Matches: 638, Mismatches: 19, Indels: 11
0.96 0.03 0.02
Matches are distributed among these distances:
112 240 0.38
113 255 0.40
114 143 0.22
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTCTCTGGAAAAGATAATCCATCAGATGATGGATTTGA
Found at i:84288 original size:16 final size:16
Alignment explanation
Indices: 84269--84305 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
84259 AATTTTCAAA
84269 AAATAAATTGAATCTT-
1 AAATAAATTGAA-CTTG
84285 AAATAAATTGAACTTG
1 AAATAAATTGAACTTG
84301 AAATA
1 AAATA
84306 GATAGAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.32
Consensus pattern (16 bp):
AAATAAATTGAACTTG
Found at i:84630 original size:1 final size:1
Alignment explanation
Indices: 84624--84678 Score: 65
Period size: 1 Copynumber: 55.0 Consensus size: 1
84614 CCTTGACCCC
* * * * *
84624 TTTTTTTTTTTCTCTTTTTTTTTCTTTTTTTTTCTTTTTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
84679 CTTCAAGCAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (1 bp):
T
Found at i:84651 original size:22 final size:21
Alignment explanation
Indices: 84626--84681 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
84616 TTGACCCCTT
84626 TTTTTTTTTCTCTTTTTTTTTC
1 TTTTTTTTTCT-TTTTTTTTTC
*
84648 TTTTTTTTTCTTTTTTTTTTT
1 TTTTTTTTTCTTTTTTTTTTC
84669 TTTCTTTTTTCTT
1 TTT-TTTTTTCTT
84682 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (21 bp):
TTTTTTTTTCTTTTTTTTTTC
Found at i:84678 original size:10 final size:10
Alignment explanation
Indices: 84627--84676 Score: 75
Period size: 10 Copynumber: 4.9 Consensus size: 10
84617 TGACCCCTTT
84627 TTTTTTTTCTC
1 TTTTTTTT-TC
84638 TTTTTTTTTC
1 TTTTTTTTTC
84648 TTTTTTTTTC
1 TTTTTTTTTC
84658 TTTTTTTTT-
1 TTTTTTTTTC
84667 TTTTTCTTTT
1 TTTTT-TTTT
84677 TTCTTCAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
9 5 0.13
10 25 0.66
11 8 0.21
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:95353 original size:15 final size:15
Alignment explanation
Indices: 95329--95378 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
95319 AATAAAACAT
*
95329 ATAAATATTATGAAA
1 ATAAAAATTATGAAA
* *
95344 ATAATAATTA--AAT
1 ATAAAAATTATGAAA
*
95357 ATAAAAATTTTGAAA
1 ATAAAAATTATGAAA
95372 ATAAAAA
1 ATAAAAA
95379 ATTAAAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 10 0.37
15 17 0.63
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (15 bp):
ATAAAAATTATGAAA
Found at i:95358 original size:28 final size:29
Alignment explanation
Indices: 95285--95399 Score: 98
Period size: 28 Copynumber: 4.1 Consensus size: 29
95275 TTTGACAAAA
* *
95285 AAAATAAATAATGAAATA-AAATACT-TG
1 AAAATAAATAATTAAATATAAATATTATG
*
95312 CAAATAAAATAA--AACATATAAATATTATG
1 AAAAT-AAATAATTAA-ATATAAATATTATG
* *
95341 AAAAT-AATAATTAAATATAAAAATTTTG
1 AAAATAAATAATTAAATATAAATATTATG
* *
95369 AAAATAAAAAATTAAAAATTAAATA-TATG
1 AAAATAAATAATTAAATA-TAAATATTATG
95398 AA
1 AA
95400 TTTTTAATTA
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
26 2 0.03
27 12 0.17
28 29 0.41
29 23 0.32
30 5 0.07
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (29 bp):
AAAATAAATAATTAAATATAAATATTATG
Found at i:97273 original size:16 final size:16
Alignment explanation
Indices: 97245--97281 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
97235 TGACGTGGCA
97245 GCGG-TGGAAGCAGAG
1 GCGGCTGGAAGCAGAG
*
97260 GCGGCTGGAGGCAGAG
1 GCGGCTGGAAGCAGAG
97276 GCGGCT
1 GCGGCT
97282 AGGGATTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.19, C:0.19, G:0.54, T:0.08
Consensus pattern (16 bp):
GCGGCTGGAAGCAGAG
Found at i:97400 original size:9 final size:10
Alignment explanation
Indices: 97367--97405 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
97357 TGGGCTTGTA
97367 ATTTAATATT
1 ATTTAATATT
97377 ATTTATATATGT
1 ATTTA-ATAT-T
97389 ATTTAATA-T
1 ATTTAATATT
97398 ATTTAATA
1 ATTTAATA
97406 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:97409 original size:3 final size:3
Alignment explanation
Indices: 97401--97495 Score: 174
Period size: 3 Copynumber: 32.0 Consensus size: 3
97391 TTAATATATT
97401 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
97449 TAA TAA TAA T-A TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
97496 ATTAATATGG
Statistics
Matches: 89, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 87 0.98
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:100939 original size:2 final size:2
Alignment explanation
Indices: 100932--100967 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
100922 GATCTTAACT
100932 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
100968 GGGTTAATAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:101767 original size:2 final size:2
Alignment explanation
Indices: 101762--101787 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
101752 ACACACACAC
101762 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
101788 CTATTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:109673 original size:39 final size:39
Alignment explanation
Indices: 109619--109956 Score: 523
Period size: 39 Copynumber: 8.7 Consensus size: 39
109609 TTTAAAGAAT
* * * * *
109619 ATTTTATCTCACTTGAGATGGTTTCTCTCGAAATATAAT
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAAG
*
109658 ATTTTATCTTGCTTGAGATAGTTTCCCTCGAAATAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAAG
* *
109697 ATTTTATCTCCCTTGAGATAGTTTCCCTCGAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAAG
* *
109736 ATTTTATCTCGCTTGAGATAGTTTCCCTCAAAATAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAAG
* * * *
109775 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACACAAC
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAAG
*
109814 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAAAAG
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAAG
*
109853 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAAG
*
109892 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAGAAG
1 ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAAG
109931 ATTTTATCTCGCTTGAGATAGTTTCC
1 ATTTTATCTCGCTTGAGATAGTTTCC
109957 ATTGAAACAA
Statistics
Matches: 276, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 276 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (39 bp):
ATTTTATCTCGCTTGAGATAGTTTCCCTCGAAATAAAAG
Found at i:109998 original size:36 final size:35
Alignment explanation
Indices: 109944--110039 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 35
109934 TTATCTCGCT
* *
109944 TGAGATAGTTTCCATTGAAACAAGTTTTGTCTTTCC
1 TGAGACAGTTTCC-TTGAAACAAGTTTTGTCTCTCC
* * *
109980 TGTGACAGTTTCTCTTGAAACAAATTTTGTCTCTCT
1 TGAGACAGTTTC-CTTGAAACAAGTTTTGTCTCTCC
110016 TGAGACAGTTTCCCTTGAAACAAG
1 TGAGACAGTTT-CCTTGAAACAAG
110040 AAATGTATCT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
36 49 0.96
37 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (35 bp):
TGAGACAGTTTCCTTGAAACAAGTTTTGTCTCTCC
Found at i:110095 original size:74 final size:76
Alignment explanation
Indices: 109987--110134 Score: 192
Period size: 74 Copynumber: 2.0 Consensus size: 76
109977 TCCTGTGACA
* * **
109987 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGAC-AGTTTCCCTTGAAACAAGAAA-TGTATCT
1 GTTTCTCTTAAAACAAATTTCGTCTCGATTGAGACAAGTTTCCCTTGAAACAAGAAATTGTATCT
*
110050 CACTTGAGATG
66 CACTCGAGATG
* * * * *
110061 GTTTTTCTTAAAACCAATTTCGTCTCGATTGAGACAATTTTCTCTTGAAACAAGAAATTTTATCT
1 GTTTCTCTTAAAACAAATTTCGTCTCGATTGAGACAAGTTTCCCTTGAAACAAGAAATTGTATCT
110126 CACTCGAGA
66 CACTCGAGA
110135 GAGATTATCT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
74 29 0.47
75 19 0.31
76 14 0.23
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (76 bp):
GTTTCTCTTAAAACAAATTTCGTCTCGATTGAGACAAGTTTCCCTTGAAACAAGAAATTGTATCT
CACTCGAGATG
Found at i:110156 original size:75 final size:73
Alignment explanation
Indices: 109992--110156 Score: 172
Period size: 75 Copynumber: 2.2 Consensus size: 73
109982 TGACAGTTTC
* * ** *
109992 TCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGAAATGTATCTCACTTGA
1 TCTTAAAAC-AATTTCGTCTCGATTGAGACAGTTTCCCTTGAAACAAGAAATGTATCTCACTCGA
* *
110057 GATGGTTTT
65 GATGGATTA
* * *
110066 TCTTAAAACCAATTTCGTCTCGATTGAGACAATTTTCTCTTGAAACAAGAAATTTTATCTCACTC
1 TCTTAAAA-CAATTTCGTCTCGATTGAGAC-AGTTTCCCTTGAAACAAGAAA-TGTATCTCACTC
110131 GAGA-GAGATTA
63 GAGATG-GATTA
110142 TCTT-AAACATATTTC
1 TCTTAAAACA-ATTTC
110157 TTATTCATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
74 26 0.34
75 29 0.38
76 21 0.28
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (73 bp):
TCTTAAAACAATTTCGTCTCGATTGAGACAGTTTCCCTTGAAACAAGAAATGTATCTCACTCGAG
ATGGATTA
Found at i:113606 original size:25 final size:25
Alignment explanation
Indices: 113578--113627 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
113568 CATTATTTTC
*
113578 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
113603 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
113628 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:114039 original size:18 final size:18
Alignment explanation
Indices: 114016--114051 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
114006 AAGTTGGTTG
114016 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
*
114034 TGATTGCGATTTTGATTT
1 TGATTGAGATTTTGATTT
114052 CCTTTTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:116132 original size:5 final size:6
Alignment explanation
Indices: 116116--116140 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
116106 TCTTCGGGGA
116116 CTTTTT CTTTTT CTTTTT CTTTTT C
1 CTTTTT CTTTTT CTTTTT CTTTTT C
116141 AGGGTTATAT
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:117146 original size:14 final size:15
Alignment explanation
Indices: 117110--117147 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
117100 AAATCATTGG
117110 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
117125 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
117140 AAAAATTA
1 AAAAATTA
117148 GAGATGGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:119278 original size:5 final size:5
Alignment explanation
Indices: 119268--119294 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
119258 GAGAGGAAGA
119268 GATAG GATAG GATAG GATAG GATAG GA
1 GATAG GATAG GATAG GATAG GATAG GA
119295 ACTGTTGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (5 bp):
GATAG
Found at i:125054 original size:37 final size:37
Alignment explanation
Indices: 124974--125057 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 37
124964 TGAAATCGGG
* * * * *
124974 GCAATTACAATTTAGAAAATTGATACAGGGAGCAGAA
1 GCAATTGCAATTCAGAAAATTGATAAAGGAAACAGAA
*
125011 GCAATTGCAATTCAGAAAATTGATAAAGGAAACATAA
1 GCAATTGCAATTCAGAAAATTGATAAAGGAAACAGAA
*
125048 GTAATTGCAA
1 GCAATTGCAA
125058 AGAAGATTAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.23
Consensus pattern (37 bp):
GCAATTGCAATTCAGAAAATTGATAAAGGAAACAGAA
Found at i:125516 original size:16 final size:16
Alignment explanation
Indices: 125495--125532 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
125485 CACATTTGTA
125495 GAAATAAAAAGCAGAG
1 GAAATAAAAAGCAGAG
125511 GAAAT--AAAGCAGAG
1 GAAATAAAAAGCAGAG
*
125525 GATATAAA
1 GAAATAAA
125533 GGAAAATCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
14 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.05, G:0.24, T:0.11
Consensus pattern (16 bp):
GAAATAAAAAGCAGAG
Found at i:125521 original size:14 final size:14
Alignment explanation
Indices: 125502--125533 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
125492 GTAGAAATAA
125502 AAAGCAGAGGAAAT
1 AAAGCAGAGGAAAT
*
125516 AAAGCAGAGGATAT
1 AAAGCAGAGGAAAT
125530 AAAG
1 AAAG
125534 GAAAATCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.06, G:0.28, T:0.09
Consensus pattern (14 bp):
AAAGCAGAGGAAAT
Found at i:129302 original size:21 final size:22
Alignment explanation
Indices: 129220--129303 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 22
129210 CAGAACCCCA
*
129220 GGGGGGTATCGATTCCC-C-TGT
1 GGGGGGAATCGATTCCCTCAT-T
* *
129241 GGGGGGAATCGGTTCCCCTTCA-A
1 GGGGGGAATCGATT-CCC-TCATT
* *
129264 AGGGGGAATCGGTTCCCTCATT
1 GGGGGGAATCGATTCCCTCATT
129286 GGGGGG-ATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
129304 TGCACCAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
21 26 0.51
22 11 0.22
23 13 0.25
24 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGGGGAATCGATTCCCTCATT
Found at i:137682 original size:20 final size:20
Alignment explanation
Indices: 137657--137750 Score: 70
Period size: 20 Copynumber: 4.6 Consensus size: 20
137647 ATATTTAATT
137657 TTTTATAATAATTAACTTAA
1 TTTTATAATAATTAACTTAA
*
137677 TTTTATAATAATTTATGCATAATAA
1 TTTTATAATAA-TTA-AC-T--TAA
* * *
137702 TTTGTGT-AT-A-T-ATTTGA
1 TTT-TATAATAATTAACTTAA
137719 TTTTATAATAATTAACTTAA
1 TTTTATAATAATTAACTTAA
137739 TTTTATAATAAT
1 TTTTATAATAAT
137751 GTATTCAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 20
0.67 0.10 0.24
Matches are distributed among these distances:
16 2 0.04
17 7 0.12
18 1 0.02
19 2 0.04
20 27 0.48
21 3 0.05
22 2 0.04
23 1 0.02
24 1 0.02
25 8 0.14
26 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTATAATAATTAACTTAA
Found at i:137741 original size:62 final size:63
Alignment explanation
Indices: 137642--137765 Score: 196
Period size: 62 Copynumber: 2.0 Consensus size: 63
137632 TTTCTATGTA
* *
137642 TGTATATATTTAATTTTTTATAATAATTAACTTAATTTTATAATAATTTATGCATAATAATTTG
1 TGTATATATTTAA-TTTTTATAATAATTAACTTAATTTTATAATAATGTATGCAAAATAATTTG
* *
137706 TGTATATATTTGA-TTTTATAATAATTAACTTAATTTTATAATAATGTATTCAAAATAATT
1 TGTATATATTTAATTTTTATAATAATTAACTTAATTTTATAATAATGTATGCAAAATAATT
137766 AACTTTATTT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
62 44 0.79
64 12 0.21
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (63 bp):
TGTATATATTTAATTTTTATAATAATTAACTTAATTTTATAATAATGTATGCAAAATAATTTG
Found at i:137886 original size:35 final size:37
Alignment explanation
Indices: 137821--137889 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 37
137811 TTTTAAGTCA
137821 AATTTATGTTTTATAACTAATAATTATTAAATCTTCG
1 AATTTATGTTTTATAACTAATAATTATTAAATCTTCG
* *
137858 AATTTATGTTTT-TTA-TTATAATTATTAAATCT
1 AATTTATGTTTTATAACTAATAATTATTAAATCT
137890 ATTTATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 16 0.53
36 2 0.07
37 12 0.40
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (37 bp):
AATTTATGTTTTATAACTAATAATTATTAAATCTTCG
Found at i:138135 original size:147 final size:145
Alignment explanation
Indices: 137940--138219 Score: 429
Period size: 147 Copynumber: 1.9 Consensus size: 145
137930 ATGAGGATTT
* * * * *
137940 TATTGTTATTGTTATTTATAAGTCTTCGAATTTAATCAATTTGTTAAGGTAAACAAA-TTATAAC
1 TATTGTTATTGTTATTTATAAATATTCAAATTTAATCAATCTGGTAAGGTAAA-AAATTTATAAC
**
138004 TAATAATTATTAAATATTCGAATTTAAGTTAAGGTAAAAATTTTCAAAAAACAATATATTTACTC
65 TAATAATTATTAAATATTCGAATTTAAGTTAAGGTAAAAAAATTC-AAAAA-AA-ATATTTACTC
138069 ATGTTTATGATTGTTATTA
127 ATGTTTATGATTGTTATTA
138088 TATT-TTATTGTTATTTATAAATATTCAAATTTAATCAATCTGGTAAGGTAAAAAATTTATAACT
1 TATTGTTATTGTTATTTATAAATATTCAAATTTAATCAATCTGGTAAGGTAAAAAATTTATAACT
* *
138152 GATAATTATTAAATCTTCGAATTTAAGTTAAGGTAAAAAAATTCAAAAAAAATATTTACTCATGT
66 AATAATTATTAAATATTCGAATTTAAGTTAAGGTAAAAAAATTCAAAAAAAATATTTACTCATGT
138217 TTA
131 TTA
138220 CAAAATAAAA
Statistics
Matches: 122, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
144 17 0.14
145 2 0.02
146 8 0.07
147 91 0.75
148 4 0.03
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (145 bp):
TATTGTTATTGTTATTTATAAATATTCAAATTTAATCAATCTGGTAAGGTAAAAAATTTATAACT
AATAATTATTAAATATTCGAATTTAAGTTAAGGTAAAAAAATTCAAAAAAAATATTTACTCATGT
TTATGATTGTTATTA
Found at i:139228 original size:18 final size:19
Alignment explanation
Indices: 139205--139250 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
139195 TACGTAAAAT
139205 TATAAATAAAGAAATAAA-
1 TATAAATAAAGAAATAAAG
**
139223 TATAAATAACTAAATAAAG
1 TATAAATAAAGAAATAAAG
139242 T-TAAATAAA
1 TATAAATAAA
139251 TTAATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (19 bp):
TATAAATAAAGAAATAAAG
Found at i:140720 original size:20 final size:20
Alignment explanation
Indices: 140682--140741 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
140672 TGAATCGAGA
*
140682 TTCTCTTCT-TCTTCTTTCT
1 TTCTCTTTTCTCTTCTTTCT
*
140701 TTCTCTTTTCTCTTCATTCT
1 TTCTCTTTTCTCTTCTTTCT
* *
140721 TCCTCATTTCTCTTCTTTCT
1 TTCTCTTTTCTCTTCTTTCT
140741 T
1 T
140742 CTCCTATGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 8 0.23
20 27 0.77
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (20 bp):
TTCTCTTTTCTCTTCTTTCT
Found at i:140730 original size:27 final size:27
Alignment explanation
Indices: 140682--140743 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
140672 TGAATCGAGA
*
140682 TTCTCTTCTTCTTCTTTCTTTCTCTT-
1 TTCTCTTCTTCTTCTCTCTTTCTCTTC
140708 TTCTCTTCATTCTTC-CTCATTTCTCTTC
1 TTCTCTTC-TTCTTCTCTC-TTTCTCTTC
140736 TT-TCTTCT
1 TTCTCTTCT
140744 CCTATGCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 11 0.34
27 19 0.59
28 2 0.06
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (27 bp):
TTCTCTTCTTCTTCTCTCTTTCTCTTC
Found at i:142576 original size:24 final size:25
Alignment explanation
Indices: 142521--142578 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
142511 CATGGGTTTA
142521 ATATAT-TTTTAAAAAAGCTATAAT
1 ATATATATTTTAAAAAAGCTATAAT
* *
142545 ATAAATATTTTCAAAAA-CTATATATT
1 ATATATATTTTAAAAAAGCTATA-A-T
142571 ATATATAT
1 ATATATAT
142579 GTTTTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 10 0.36
25 10 0.36
26 8 0.29
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (25 bp):
ATATATATTTTAAAAAAGCTATAAT
Found at i:146833 original size:27 final size:27
Alignment explanation
Indices: 146794--146845 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
146784 TTGTACTTGT
* * *
146794 TACGGGACGATAATGGTAAATATAATA
1 TACGAGACAATAACGGTAAATATAATA
146821 TACGAGACAATAACGGTAAATATAA
1 TACGAGACAATAACGGTAAATATAA
146846 GTGTATAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.23
Consensus pattern (27 bp):
TACGAGACAATAACGGTAAATATAATA
Found at i:150122 original size:15 final size:15
Alignment explanation
Indices: 150102--150139 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
150092 TCCTCGAAAT
*
150102 GCAAGATTATGTTTA
1 GCAAGATAATGTTTA
150117 GCAAGATAATGTTTA
1 GCAAGATAATGTTTA
150132 GCAAGATA
1 GCAAGATA
150140 TTTCACAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (15 bp):
GCAAGATAATGTTTA
Found at i:152418 original size:33 final size:33
Alignment explanation
Indices: 152375--152439 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
152365 GCCTCTACCA
* *
152375 ACCTTGCACCATTCCATGTTTTCTTCTTCCACT
1 ACCTTCCACCATTCCATGTTTCCTTCTTCCACT
*
152408 ACCTTCCACCATTCTATGTTTCCTTCTTCCAC
1 ACCTTCCACCATTCCATGTTTCCTTCTTCCAC
152440 CCACAACAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.15, C:0.38, G:0.05, T:0.42
Consensus pattern (33 bp):
ACCTTCCACCATTCCATGTTTCCTTCTTCCACT
Found at i:153233 original size:17 final size:17
Alignment explanation
Indices: 153211--153244 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
153201 AGTTTTATTT
153211 TTTAGATGTAAT-TTTAA
1 TTTAGAT-TAATATTTAA
153228 TTTAGATTAATATTTAA
1 TTTAGATTAATATTTAA
153245 ATCAAGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (17 bp):
TTTAGATTAATATTTAA
Found at i:161437 original size:23 final size:21
Alignment explanation
Indices: 161404--161532 Score: 77
Period size: 21 Copynumber: 6.0 Consensus size: 21
161394 TCTATACACT
*
161404 ATGAAGCTGCATCGATGCATCC
1 ATGAAGATGCATCGATGCAT-C
* * *
161426 TTTGAATG-TGCATCAATACATC
1 -ATGAA-GATGCATCGATGCATC
* *
161448 ATGAAGATGCACCGATACATC
1 ATGAAGATGCATCGATGCATC
*
161469 ATGAAGATGCACCGATGCACTCC
1 ATGAAGATGCATCGATGCA-T-C
*
161492 TTGAATG-TGCATCGATGCACTC
1 ATGAA-GATGCATCGATGCA-TC
**
161514 -TG-CCATGCATCGATGCATC
1 ATGAAGATGCATCGATGCATC
161533 CGTTGGGTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.02
20 13 0.15
21 36 0.40
22 3 0.03
23 33 0.37
24 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (21 bp):
ATGAAGATGCATCGATGCATC
Found at i:161458 original size:21 final size:21
Alignment explanation
Indices: 161434--161481 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
161424 CCTTTGAATG
*
161434 TGCATCAATACATCATGAAGA
1 TGCACCAATACATCATGAAGA
*
161455 TGCACCGATACATCATGAAGA
1 TGCACCAATACATCATGAAGA
161476 TGCACC
1 TGCACC
161482 GATGCACTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (21 bp):
TGCACCAATACATCATGAAGA
Found at i:161482 original size:21 final size:21
Alignment explanation
Indices: 161441--161484 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
161431 ATGTGCATCA
161441 ATACATCATGAAGATGCACCG
1 ATACATCATGAAGATGCACCG
161462 ATACATCATGAAGATGCACCG
1 ATACATCATGAAGATGCACCG
161483 AT
1 AT
161485 GCACTCCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (21 bp):
ATACATCATGAAGATGCACCG
Found at i:165381 original size:29 final size:28
Alignment explanation
Indices: 165327--165381 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
165317 CACTCCCATT
* * *
165327 TTTGCATCTTTGTATTTGTATGTACATC
1 TTTGCATCTTTGCATTAGTATATACATC
165355 TTTGCATCTTTTGCATTAGTATATACA
1 TTTGCATC-TTTGCATTAGTATATACA
165382 CATTGTGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.51
Consensus pattern (28 bp):
TTTGCATCTTTGCATTAGTATATACATC
Found at i:167489 original size:16 final size:17
Alignment explanation
Indices: 167445--167482 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
167435 ATGTATAAGT
167445 TTATATGC--TATGTGA
1 TTATATGCAATATGTGA
167460 TTATATGCAATATGTGA
1 TTATATGCAATATGTGA
167477 -TATATG
1 TTATATG
167483 TTATATGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 6 0.29
17 7 0.33
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (17 bp):
TTATATGCAATATGTGA
Found at i:168700 original size:20 final size:21
Alignment explanation
Indices: 168675--168716 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
168665 TTTGAAAGTA
*
168675 CTGTAGCAG-GGTATCGGTAC
1 CTGTAGCAGAGGTATCGATAC
168695 CTGTAGCAGAGGTATCGATAC
1 CTGTAGCAGAGGTATCGATAC
168716 C
1 C
168717 CCTGAAGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (21 bp):
CTGTAGCAGAGGTATCGATAC
Found at i:170404 original size:36 final size:35
Alignment explanation
Indices: 170351--170488 Score: 107
Period size: 36 Copynumber: 3.7 Consensus size: 35
170341 TAATACAGAG
*
170351 GATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 GATTTGTCTCACTTGAGATTGTTTTTCTTAAAACA
**
170386 GACTTTGTCTCACTTGAGACAGTTTTTACTCAAAATAAAA-A
1 GA-TTTGTCTCACTTGAGATTGTTTTT-CT-----TAAAACA
* * ** *
170427 GATTTATTTCACTCAAGATTATTTTTCTTAAAACAA
1 GATTTGTCTCACTTGAGATTGTTTTTCTTAAAAC-A
* *
170463 GATTTGTCTCGCTTGAGATGGTTTTT
1 GATTTGTCTCACTTGAGATTGTTTTT
170489 ACTCAAAAGA
Statistics
Matches: 77, Mismatches: 17, Indels: 17
0.69 0.15 0.15
Matches are distributed among these distances:
34 5 0.06
35 2 0.03
36 41 0.53
37 2 0.03
39 2 0.03
40 17 0.22
41 3 0.04
42 5 0.06
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (35 bp):
GATTTGTCTCACTTGAGATTGTTTTTCTTAAAACA
Found at i:170452 original size:76 final size:75
Alignment explanation
Indices: 170351--170528 Score: 232
Period size: 76 Copynumber: 2.3 Consensus size: 75
170341 TAATACAGAG
* **
170351 GATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AGACTTTGTCTCACTTGAGACAGTTTTTAC
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGACAGTTTTTAC
170415 TCAAAATAAAAA
65 TCAAAA-AAAAA
* * **
170427 GATTTATTTCACTCAAGATTATTTTTCTTAAAACAAGATTTGTCTCGCTTGAGATGGTTTTTACT
1 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAGTTTTTACT
* *
170492 CAAAAGAAGA
66 CAAAAAAAAA
*
170502 CATTTCATTTCACTCAAGATTGTTTTT
1 GATTT-ATTTCACTCAAGATTGTTTTT
170529 AAAAAGATTT
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
75 7 0.08
76 79 0.89
77 3 0.03
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (75 bp):
GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAGTTTTTACT
CAAAAAAAAA
Found at i:170584 original size:39 final size:39
Alignment explanation
Indices: 170530--171084 Score: 903
Period size: 39 Copynumber: 14.2 Consensus size: 39
170520 ATTGTTTTTA
*
170530 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCTAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * *
170569 AAAAGATTTTGTCTCGCTTAAGATAGTTTTCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
170608 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
170647 ATAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
170686 ATAAGATTTTATCTCGCTTGAGATAGTTTACCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
170725 AGAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
170764 AAAAGATTTTATCTCACTTGAGATAGTTTCCCTCAAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
170803 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
170842 AAAATATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
170881 ATAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
*
170920 AAAAGATTTTATCTCGCTTGAGATAATTTCCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* *
170959 AGAAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
170998 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
* * * **
171037 AGAAGATTTTATCTCACTTAAGATAGTTTCGATCGAAAC
1 AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
171076 AAAAGATTT
1 AAAAGATTT
171085 AAAGAAACTA
Statistics
Matches: 478, Mismatches: 38, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 478 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (39 bp):
AAAAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAAC
Found at i:170653 original size:22 final size:22
Alignment explanation
Indices: 170628--170692 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
170618 ATCTCGCTTG
170628 AGATAGTTTCCCTCGAAACATA
1 AGATAGTTTCCCTCGAAACATA
** * *
170650 AGAT--TTTGTCTCG---CTTG
1 AGATAGTTTCCCTCGAAACATA
170667 AGATAGTTTCCCTCGAAACATA
1 AGATAGTTTCCCTCGAAACATA
170689 AGAT
1 AGAT
170693 TTTATCTCGC
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 6 0.20
19 7 0.23
20 7 0.23
22 10 0.33
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (22 bp):
AGATAGTTTCCCTCGAAACATA
Found at i:171747 original size:34 final size:34
Alignment explanation
Indices: 171701--171803 Score: 102
Period size: 34 Copynumber: 3.1 Consensus size: 34
171691 TACCACTACA
*
171701 ATGCCTCCACCAAGCTCCCACCATCCCATGTTTC
1 ATGCCTCCACCAACCTCCCACCATCCCATGTTTC
* * *
171735 ATGCCTCTACCAACCTTCCACCATTCCATGTTTCC
1 ATGCCTCCACCAACCTCCCACCATCCCATGTTT-C
* * * * *
171770 TTG-TTCCA-CTACCTTCCACCATTCCATGTTTC
1 ATGCCTCCACCAACCTCCCACCATCCCATGTTTC
171802 AT
1 AT
171804 TCTTCCCCCA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
32 2 0.03
33 22 0.37
34 32 0.54
35 3 0.05
ACGTcount: A:0.19, C:0.42, G:0.07, T:0.32
Consensus pattern (34 bp):
ATGCCTCCACCAACCTCCCACCATCCCATGTTTC
Found at i:172531 original size:21 final size:21
Alignment explanation
Indices: 172476--172541 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
172466 ACTTATTTTA
*
172476 TTTTTATTTGTTA--TTTATG
1 TTTTTATTTGTTATTTTTATT
* **
172495 TTGTT-TTTACTATTTTTATT
1 TTTTTATTTGTTATTTTTATT
*
172515 TTTTTATTTGTTATTTTAATT
1 TTTTTATTTGTTATTTTTATT
*
172536 ATTTTA
1 TTTTTA
172542 ATTAAGTTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
18 5 0.14
19 4 0.11
20 9 0.26
21 17 0.49
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (21 bp):
TTTTTATTTGTTATTTTTATT
Found at i:176598 original size:20 final size:21
Alignment explanation
Indices: 176573--176665 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
176563 TTTTCCCAAT
*
176573 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
176593 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
176614 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
176634 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
176655 TCGCAATGCGA
1 TCGCAATGCGA
176666 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:176618 original size:41 final size:41
Alignment explanation
Indices: 176573--176665 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
176563 TTTTCCCAAT
176573 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
176614 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
176655 TCGCAATGCGA
1 TCGCAATGCGA
176666 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:176678 original size:41 final size:41
Alignment explanation
Indices: 176592--176726 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
176582 GAATAAGTAA
* *
176592 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
176633 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
176674 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
176715 TTCGCAACGCGA
1 ATCGCAACGCGA
176727 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:176679 original size:20 final size:20
Alignment explanation
Indices: 176654--176748 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
176644 AATTGGGAAA
*
176654 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
176674 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
176695 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
176715 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
176735 TTCGCAACGCGATA
1 ATCGCAACGCGATA
176749 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:176963 original size:22 final size:22
Alignment explanation
Indices: 176936--176979 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
176926 CACTCTCTCA
176936 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
176958 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
176980 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:177252 original size:20 final size:20
Alignment explanation
Indices: 177223--177266 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
177213 GCGATTTTAG
177223 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
177243 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
177263 TTTC
1 TTTC
177267 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:178574 original size:18 final size:18
Alignment explanation
Indices: 178553--178597 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
178543 TCCACTTCGG
*
178553 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
178571 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
178589 GAGCCATCA
1 GAGCCATCA
178598 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:179113 original size:20 final size:19
Alignment explanation
Indices: 179090--179199 Score: 72
Period size: 19 Copynumber: 6.1 Consensus size: 19
179080 TGCAACACGA
179090 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGC-G
* *
179110 AAATGGCTATCGCAATGCG
1 AAATGACTATCGCAACGCG
**
179129 AAATGAAAATCGCAA--CG
1 AAATGACTATCGCAACGCG
*
179146 ACAA--A--ATCGCAATGCG
1 A-AATGACTATCGCAACGCG
*
179162 AAATGA-AATCGCAACGCG
1 AAATGACTATCGCAACGCG
** *
179180 AAATGAAAATCGCAATGCG
1 AAATGACTATCGCAACGCG
179199 A
1 A
179200 TTTGTGTTTC
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.09
15 2 0.03
16 4 0.05
17 4 0.05
18 18 0.24
19 25 0.33
20 16 0.21
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (19 bp):
AAATGACTATCGCAACGCG
Found at i:179133 original size:19 final size:20
Alignment explanation
Indices: 179090--179145 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
179080 TGCAACACGA
179090 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
179110 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
179129 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
179146 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:179191 original size:19 final size:19
Alignment explanation
Indices: 179118--179199 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
179108 GGAAATGGCT
179118 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
179137 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
179151 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
179169 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
179188 ATCGCAATGCGA
1 ATCGCAATGCGA
179200 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 18 0.34
19 20 0.38
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:179289 original size:20 final size:19
Alignment explanation
Indices: 179255--179309 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
179245 TTGTGATTTT
*
179255 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
179274 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
179294 CATTTCGCGTAGCGAT
1 CATTTCGCGTTGCGAT
179310 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:179308 original size:19 final size:19
Alignment explanation
Indices: 179206--179309 Score: 78
Period size: 19 Copynumber: 5.7 Consensus size: 19
179196 GCGATTTGTG
*
179206 TTTCGCGTTGCGAT-TTCA
1 TTTCGCGTTGCGATAGTCA
179224 TTTCGCGTTGCG--A-T--
1 TTTCGCGTTGCGATAGTCA
* **
179238 TTT-GTCGTTGTGATTTTCA
1 TTTCG-CGTTGCGATAGTCA
* *
179257 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATAGTCA
179276 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATAGTCA
*
179296 TTTCGCGTAGCGAT
1 TTTCGCGTTGCGAT
179310 TTTAAGTTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
13 1 0.01
14 9 0.13
16 1 0.01
17 1 0.01
18 12 0.18
19 25 0.37
20 18 0.27
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.41
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:181196 original size:14 final size:14
Alignment explanation
Indices: 181177--181212 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
181167 ATTGTTTAAT
181177 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
181191 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
181205 TGATTTGT
1 TGATTTGT
181213 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:181335 original size:20 final size:20
Alignment explanation
Indices: 181298--181335 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
181288 GCAAAACAGA
*
181298 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
181318 CTATCGCAACGAGGAAAT
1 CTATCGCAACGAGAAAAT
181336 CGCAATGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:181356 original size:19 final size:19
Alignment explanation
Indices: 181332--181397 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
181322 CGCAACGAGG
181332 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
181351 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCGAAATGA
181370 AAATCGCAA--C--AA-GA
1 AAATCGCAATGCGAAATGA
181384 AAATCGCAATGCGA
1 AAATCGCAATGCGA
181398 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.26
15 2 0.05
16 1 0.02
17 1 0.02
19 28 0.65
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AAATCGCAATGCGAAATGA
Found at i:181446 original size:20 final size:20
Alignment explanation
Indices: 181423--181493 Score: 142
Period size: 20 Copynumber: 3.5 Consensus size: 20
181413 GCGATTTCCT
181423 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
181443 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
181463 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
181483 CGTTGCGATAG
1 CGTTGCGATAG
181494 TCAAATGAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:181449 original size:34 final size:34
Alignment explanation
Indices: 181404--181491 Score: 95
Period size: 40 Copynumber: 2.4 Consensus size: 34
181394 GCGATTTTCA
* *
181404 TTTCGCATTGCGATTTCCTCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTCCGCGTTGCGATAGCCAT
*
181438 TTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGC----G--ATTTCCGCGTTGCGATAGCCAT
181478 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
181492 AGTCAAATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
34 12 0.27
36 1 0.02
38 1 0.02
40 31 0.69
ACGTcount: A:0.14, C:0.25, G:0.24, T:0.38
Consensus pattern (34 bp):
TTTCGCGTTGCGATTTCCGCGTTGCGATAGCCAT
Found at i:182607 original size:24 final size:24
Alignment explanation
Indices: 182580--182633 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
182570 GTATTCAAAA
* *
182580 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
182604 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
182628 TTTGAT
1 TTTGAT
182634 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:185149 original size:19 final size:19
Alignment explanation
Indices: 185127--185191 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
185117 GGAAATTACT
185127 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
185146 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
185160 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
185179 ATCGCAACGCGAA
1 ATCGCAATGCGAA
185192 TTTAATTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:185150 original size:39 final size:36
Alignment explanation
Indices: 185107--185189 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 36
185097 CTTAATGTCC
*
185107 ATCGCAACGCGGAAATTACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAA-GA--ATCGCAATGCGAAATGAAA
*
185146 ATCGCAA--C-GAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
185179 ATCGCAACGCG
1 ATCGCAACGCG
185190 AATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
33 26 0.67
35 2 0.05
36 3 0.08
37 1 0.03
39 7 0.18
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (36 bp):
ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
Found at i:185209 original size:19 final size:20
Alignment explanation
Indices: 185187--185229 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
185177 AAATCGCAAC
185187 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
185206 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
185226 GCGA
1 GCGA
185230 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:185388 original size:14 final size:14
Alignment explanation
Indices: 185369--185405 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
185359 CATCAATTAA
185369 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
185383 ACAAATCACCTTTT
1 ACAAATCAACTTTT
185397 ACAAATCAA
1 ACAAATCAA
185406 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:186829 original size:21 final size:21
Alignment explanation
Indices: 186763--186829 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
186753 GTGAATCGGG
*
186763 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
186783 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
186805 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
186826 CTCT
1 CTCT
186830 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:186848 original size:42 final size:41
Alignment explanation
Indices: 186763--186885 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
186753 GTGAATCGGG
* * * * *
186763 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
186805 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
186847 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
186886 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:188968 original size:33 final size:33
Alignment explanation
Indices: 188910--188997 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
188900 ACGAGATAAT
*
188910 GAGAATCGCAACGCGAAAATGACTATCGCAACGA
1 GAGAATCGCAACGCG-AAATGACTATCGCAACCA
*
188944 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
188977 GACAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
188998 AAATTGCAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:189006 original size:19 final size:19
Alignment explanation
Indices: 188885--189069 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
188875 TCTTTTGGTT
*
188885 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
188904 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
188924 GAAAATGACTATCGCAA--C
1 G-AAATGAAAATCGCAACGC
*
188942 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
188958 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
188976 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
188991 GAAATGAAAATTGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
189011 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
189030 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
189049 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
189068 GA
1 GA
189070 TTTTGGTTTC
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
18 5 0.04
19 61 0.45
20 45 0.33
21 1 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:189023 original size:39 final size:38
Alignment explanation
Indices: 188980--189069 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
188970 GCGACCAGAC
*
188980 AATCGCAACGCGAAATGAAAATTGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
189019 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
189057 AATCGCAATGCGA
1 AATCGCAACGCGA
189070 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 22 0.46
39 26 0.54
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:189098 original size:19 final size:19
Alignment explanation
Indices: 189065--189131 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
189055 AAAATCGCAA
**
189065 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
189084 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
189103 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
189123 TGCGATTTT
1 TGCGATTTT
189132 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:189673 original size:20 final size:20
Alignment explanation
Indices: 189648--189700 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
189638 GCGCTATGTA
189648 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
189668 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
189688 TATCTCGTTGCGA
1 AATCGCGTTGCGA
189701 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:189734 original size:20 final size:20
Alignment explanation
Indices: 189709--189762 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
189699 GATTTTGTAT
189709 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
189729 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
189749 TATCGCATTGCGAT
1 TATCGCATTGCGAT
189763 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:189747 original size:61 final size:61
Alignment explanation
Indices: 189649--189765 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
189639 CGCTATGTAA
* * * * *
189649 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
189710 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
189766 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:189781 original size:61 final size:61
Alignment explanation
Indices: 189649--189783 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
189639 CGCTATGTAA
* * * * * ** *
189649 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
189710 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
189772 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
189784 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:192621 original size:24 final size:24
Alignment explanation
Indices: 192594--192644 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
192584 TTTAGAGGTT
*
192594 GTGACTGCTGCTTTTTAATCACAC
1 GTGACTGCTGATTTTTAATCACAC
192618 GTGACTGCTGATTTTTAATCACAC
1 GTGACTGCTGATTTTTAATCACAC
192642 GTG
1 GTG
192645 GCTGAACTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (24 bp):
GTGACTGCTGATTTTTAATCACAC
Found at i:193176 original size:58 final size:58
Alignment explanation
Indices: 193082--193402 Score: 340
Period size: 58 Copynumber: 5.5 Consensus size: 58
193072 ATGGCACTTT
* * * *
193082 GTGTGCTAAAATGATAGGGAAACCATACTGAGTGTATAGATTTTCGTATGGAGCACTGA
1 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
*
193141 GTGTGCTAAATGATAAGGAAATCATATTGAGTGTATAGATTTCCATATGGAGCACTGA
1 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
*
193199 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGTACTGA
1 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
* * * *** * * * *
193257 GCGTGCTAAATGACAAGGAAATCATATTGAAAATATGGATTTCCAGATAGG-GCATTTTA
1 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATAT-GGAGCA-CTGA
* * * * * ** * *
193316 -TGTGCTAAAAAGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAACACTAA
1 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
* *
193374 GGGTGCTACAAAGATAAGGAAATCATACT
1 GTGTGCTA-AATGATAAGGAAATCATACT
193403 AATGGTATGG
Statistics
Matches: 221, Mismatches: 35, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
58 152 0.69
59 69 0.31
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (58 bp):
GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
Found at i:193230 original size:30 final size:30
Alignment explanation
Indices: 193136--193232 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 30
193126 CGTATGGAGC
193136 ACTGAGTGTGCTAAATGATAAGGAAATCAT
1 ACTGAGTGTGCTAAATGATAAGGAAATCAT
* * * * * *
193166 ATTGAGTGT-ATAGATTTCCATATGG--AGC--
1 ACTGAGTGTGCTA-A-AT-GATAAGGAAATCAT
193194 ACTGAGTGTGCTAAATGATAAGGAAATCAT
1 ACTGAGTGTGCTAAATGATAAGGAAATCAT
193224 ACTGAGTGT
1 ACTGAGTGT
193233 ATAGATTTCC
Statistics
Matches: 47, Mismatches: 12, Indels: 16
0.63 0.16 0.21
Matches are distributed among these distances:
26 5 0.11
27 1 0.02
28 11 0.23
29 4 0.09
30 20 0.43
31 1 0.02
32 5 0.11
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (30 bp):
ACTGAGTGTGCTAAATGATAAGGAAATCAT
Done.