Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011950.1 Kokia drynarioides strain JFW-HI SEQ_126948, 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: 522875
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:4888 original size:15 final size:15
Alignment explanation
Indices: 4870--4901 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4860 TAAAAAAATC
*
4870 ATAAAAATTAAAAAA
1 ATAAAAACTAAAAAA
4885 ATAAAAACTAAAAAA
1 ATAAAAACTAAAAAA
4900 AT
1 AT
4902 TAGGGTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAAAACTAAAAAA
Found at i:7102 original size:24 final size:24
Alignment explanation
Indices: 7075--7120 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
7065 AGAAATAATC
*
7075 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGATTATTTG
7099 TTTCAATTAAACTCTGATTATT
1 TTTCAATTAAACTCTGATTATT
7121 CTAGATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.13, G:0.07, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTGATTATTTG
Found at i:13268 original size:25 final size:24
Alignment explanation
Indices: 13214--13268 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
13204 TTGTCTGATT
*
13214 CTATGAAGTATATTGTGATGTATG
1 CTATGATGTATATTGTGATGTATG
*
13238 CT-TGATGTGTATTGATGAATGTATG
1 CTATGATGTATATTG-TG-ATGTATG
13263 -TATGAT
1 CTATGAT
13269 AACGCCTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.38
24 5 0.19
25 11 0.42
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.44
Consensus pattern (24 bp):
CTATGATGTATATTGTGATGTATG
Found at i:14107 original size:18 final size:19
Alignment explanation
Indices: 14072--14127 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
14062 AAAGATTAGT
14072 AAATATATATAAAGAATAA
1 AAATATATATAAAGAATAA
*
14091 AAATATA-AT-AAGTAATAT
1 AAATATATATAAAG-AATAA
* *
14109 ATATATATATATAGAATAA
1 AAATATATATAAAGAATAA
14128 TATGTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 3 0.10
18 12 0.40
19 13 0.43
20 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AAATATATATAAAGAATAA
Found at i:14127 original size:29 final size:29
Alignment explanation
Indices: 14095--14156 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
14085 GAATAAAAAT
* *
14095 ATAATAAGTA-ATATATATATATATATAGA
1 ATAATAAGTATATA-AAATATATATAAAGA
* *
14124 ATAATATGTATTTAAAATATATATAAAGA
1 ATAATAAGTATATAAAATATATATAAAGA
14153 ATAA
1 ATAA
14157 ACGAAATGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.93
30 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.37
Consensus pattern (29 bp):
ATAATAAGTATATAAAATATATATAAAGA
Found at i:14187 original size:31 final size:32
Alignment explanation
Indices: 14139--14220 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 32
14129 ATGTATTTAA
* *
14139 AATATATATAA-AG-AATAAACGAAATGCTG-
1 AATATATAAAATAGAAATAAACGAAATACTGT
* *
14168 AATATATAAAATAGAAATAAACTAAGTACTGT
1 AATATATAAAATAGAAATAAACGAAATACTGT
14200 AA-ATATAAAGAATAGAAATAA
1 AATATAT-AA-AATAGAAATAA
14221 TAGAATATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 10 0.23
30 2 0.05
31 17 0.39
32 4 0.09
33 11 0.25
ACGTcount: A:0.60, C:0.05, G:0.11, T:0.24
Consensus pattern (32 bp):
AATATATAAAATAGAAATAAACGAAATACTGT
Found at i:14357 original size:15 final size:15
Alignment explanation
Indices: 14337--14366 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14327 AATTTAAATA
14337 CAAGAAAATAAATTG
1 CAAGAAAATAAATTG
*
14352 CAAGAAAGTAAATTG
1 CAAGAAAATAAATTG
14367 GTAAACAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (15 bp):
CAAGAAAATAAATTG
Found at i:21047 original size:37 final size:37
Alignment explanation
Indices: 20979--21165 Score: 187
Period size: 37 Copynumber: 5.0 Consensus size: 37
20969 AGTTCTCTAA
* * * * * *
20979 TCACCGGCACAAAGGCTTGCTAGGTATATAGCCGGAGT
1 TCACCGACACAAA-GCCTGCTAGGCACATAGCCTGAAT
* * *
21017 TCACCGACACAAAGCTTGCTAGGCACATAGCCCGATT
1 TCACCGACACAAAGCCTGCTAGGCACATAGCCTGAAT
* *
21054 TCACC-AGCACAAAGCCTGCTAGGCACATAGCTTGAAA
1 TCACCGA-CACAAAGCCTGCTAGGCACATAGCCTGAAT
* * *
21091 TCATCAACACGAAGCCTGCTAGGCACATAGCCTGAAT
1 TCACCGACACAAAGCCTGCTAGGCACATAGCCTGAAT
* * * *
21128 ACACCGGCACGAAGCCTGCTAGGCACATAGCCCGAAT
1 TCACCGACACAAAGCCTGCTAGGCACATAGCCTGAAT
21165 T
1 T
21166 ATTTAAATGA
Statistics
Matches: 127, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
36 1 0.01
37 113 0.89
38 13 0.10
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (37 bp):
TCACCGACACAAAGCCTGCTAGGCACATAGCCTGAAT
Found at i:27755 original size:20 final size:20
Alignment explanation
Indices: 27730--27768 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27720 CCAATTCAAC
*
27730 AACAACATCCAGCA-CATATA
1 AACAAC-TCAAGCATCATATA
27750 AACAACTCAAGCATCATAT
1 AACAACTCAAGCATCATAT
27769 TAACTAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.28, G:0.05, T:0.18
Consensus pattern (20 bp):
AACAACTCAAGCATCATATA
Found at i:28136 original size:37 final size:36
Alignment explanation
Indices: 28071--28200 Score: 116
Period size: 37 Copynumber: 3.5 Consensus size: 36
28061 TGGCACAAAG
* * * * * *
28071 GCCTGCTAAGCATATAGCCCGAGTTCACCACCATGAA
1 GCCTGCTAGGCACATAGCCTGA-ATCACCAGCACGAA
* * *
28108 GCCTGCTAGGTACATAGCTTGAAATCACCGGCACGAA
1 GCCTGCTAGGCACATAGCCTG-AATCACCAGCACGAA
* * * *
28145 GCTTACTAGGCATATAGCCTGAATACACAAGCACGAA
1 GCCTGCTAGGCACATAGCCTGAAT-CACCAGCACGAA
28182 GCCTGCTAGGCACATAGCC
1 GCCTGCTAGGCACATAGCC
28201 CAAATTACTT
Statistics
Matches: 72, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
36 3 0.04
37 68 0.94
38 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (36 bp):
GCCTGCTAGGCACATAGCCTGAATCACCAGCACGAA
Found at i:30480 original size:18 final size:19
Alignment explanation
Indices: 30457--30521 Score: 100
Period size: 18 Copynumber: 3.6 Consensus size: 19
30447 TCTTATCCTC
30457 AAGCAAACAAAAG-AAGAA
1 AAGCAAACAAAAGCAAGAA
*
30475 AAGCAAA-TAAAGCAAGAA
1 AAGCAAACAAAAGCAAGAA
30493 AAGCAAAC-AAAGCAAGAA
1 AAGCAAACAAAAGCAAGAA
30511 AAGCAAACAAA
1 AAGCAAACAAA
30522 TGAGCTTGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
17 4 0.09
18 37 0.86
19 2 0.05
ACGTcount: A:0.69, C:0.14, G:0.15, T:0.02
Consensus pattern (19 bp):
AAGCAAACAAAAGCAAGAA
Found at i:30488 original size:9 final size:8
Alignment explanation
Indices: 30473--30517 Score: 54
Period size: 9 Copynumber: 5.1 Consensus size: 8
30463 ACAAAAGAAG
30473 AAAAGCAA
1 AAAAGCAA
30481 ATAAAGCAA
1 A-AAAGCAA
30490 GAAAAGCAA
1 -AAAAGCAA
30499 ACAAAGCAA
1 A-AAAGCAA
30508 GAAAAGCAA
1 -AAAAGCAA
30517 A
1 A
30518 CAAATGAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 3 0.09
9 28 0.85
10 2 0.06
ACGTcount: A:0.69, C:0.13, G:0.16, T:0.02
Consensus pattern (8 bp):
AAAAGCAA
Found at i:30922 original size:37 final size:37
Alignment explanation
Indices: 30872--30946 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
30862 TAAGCATAAA
30872 GGATTACAAGCACGAAAACAGTTTGGATCATTGTATT
1 GGATTACAAGCACGAAAACAGTTTGGATCATTGTATT
*
30909 GGATTACAAGCACGAAAATAGTTTGGATCATTGTATT
1 GGATTACAAGCACGAAAACAGTTTGGATCATTGTATT
30946 G
1 G
30947 TTCCCTATTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (37 bp):
GGATTACAAGCACGAAAACAGTTTGGATCATTGTATT
Found at i:37056 original size:23 final size:23
Alignment explanation
Indices: 37026--37072 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
37016 GGTTGTCAGA
37026 CATAGTGTTTGTTTCATGTTCTT
1 CATAGTGTTTGTTTCATGTTCTT
37049 CATAGTGTTTGTTTCATGTTCTT
1 CATAGTGTTTGTTTCATGTTCTT
37072 C
1 C
37073 CTTTCTCAAA
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:0.13, C:0.15, G:0.17, T:0.55
Consensus pattern (23 bp):
CATAGTGTTTGTTTCATGTTCTT
Found at i:47148 original size:19 final size:18
Alignment explanation
Indices: 47118--47153 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
47108 AACTAAATTT
47118 ACAAAAAGAAATGCAATG
1 ACAAAAAGAAATGCAATG
47136 ACAAAATAGAAATGCAAT
1 ACAAAA-AGAAATGCAAT
47154 AACAGTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.11, G:0.14, T:0.14
Consensus pattern (18 bp):
ACAAAAAGAAATGCAATG
Found at i:49462 original size:15 final size:15
Alignment explanation
Indices: 49433--49470 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
49423 CTTGCAAAGA
49433 AATTAAAA-CGAAAC
1 AATTAAAAGCGAAAC
*
49447 AATTAAAAGTGAAAC
1 AATTAAAAGCGAAAC
*
49462 AAATAAAAG
1 AATTAAAAG
49471 AAAATGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.66, C:0.08, G:0.11, T:0.16
Consensus pattern (15 bp):
AATTAAAAGCGAAAC
Found at i:65646 original size:2 final size:2
Alignment explanation
Indices: 65639--65665 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65629 ATAATAAGTA
65639 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 A
65666 AGTGCTAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:70155 original size:2 final size:2
Alignment explanation
Indices: 70148--70177 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
70138 AGAACACAAA
70148 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
70178 TTTTGAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:70311 original size:23 final size:23
Alignment explanation
Indices: 70285--70361 Score: 93
Period size: 23 Copynumber: 3.2 Consensus size: 23
70275 TCAACGGTAC
70285 AGATTAAAGTACATCAATGGTTA
1 AGATTAAAGTACATCAATGGTTA
* *
70308 AGATTGAAAAGTTAAATCAACGG-TA
1 AGATT--AAAG-TACATCAATGGTTA
70333 CAGATTAAAGTACATCAATGGTTA
1 -AGATTAAAGTACATCAATGGTTA
70357 AGATT
1 AGATT
70362 GTCTATCTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
23 19 0.42
24 6 0.13
25 6 0.13
26 14 0.31
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (23 bp):
AGATTAAAGTACATCAATGGTTA
Found at i:70327 original size:26 final size:24
Alignment explanation
Indices: 70272--70362 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 24
70262 AGCCTCCCCA
*
70272 AAATCAACGG-TACAGATT-AAAGT
1 AAATCAATGGTTA-AGATTGAAAGT
*
70295 ACATCAATGGTTAAGATTGAAAAGTT
1 AAATCAATGGTTAAGATTG-AAAG-T
*
70321 AAATCAACGG-TACAGATT-AAAGT
1 AAATCAATGGTTA-AGATTGAAAGT
*
70344 ACATCAATGGTTAAGATTG
1 AAATCAATGGTTAAGATTG
70363 TCTATCTTGA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
23 27 0.49
24 8 0.15
25 6 0.11
26 14 0.25
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (24 bp):
AAATCAATGGTTAAGATTGAAAGT
Found at i:75843 original size:18 final size:17
Alignment explanation
Indices: 75822--75858 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
75812 AAATAATATA
75822 TTTTGAATTTTTTCTTTT
1 TTTTGAA-TTTTTCTTTT
*
75840 TTTTGTATTTTTCTTTT
1 TTTTGAATTTTTCTTTT
75857 TT
1 TT
75859 CTGCACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTTGAATTTTTCTTTT
Found at i:75868 original size:17 final size:17
Alignment explanation
Indices: 75831--75877 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
75821 ATTTTGAATT
* * *
75831 TTTTCTTTTTTTTGTAT
1 TTTTCTTTTTTCTGCAC
75848 TTTTCTTTTTTCTGCAC
1 TTTTCTTTTTTCTGCAC
75865 TTTT-TTTATTTCT
1 TTTTCTTT-TTTCT
75878 TTTTTTCTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 3 0.12
17 23 0.88
ACGTcount: A:0.06, C:0.13, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTCTTTTTTCTGCAC
Found at i:75868 original size:18 final size:17
Alignment explanation
Indices: 75830--75869 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
75820 TATTTTGAAT
* *
75830 TTTTTCTTTTTTTTGTA
1 TTTTTCTTTTTTCTGCA
75847 TTTTTCTTTTTTCTGCA
1 TTTTTCTTTTTTCTGCA
75864 CTTTTT
1 -TTTTT
75870 TTATTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTTTCTGCA
Found at i:87700 original size:77 final size:77
Alignment explanation
Indices: 87610--87763 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
87600 TTTTAAAAAG
* * *
87610 ATGATAATCGTTTTATATTTTATTAAATAATTTATTTAGATCTAAGATATTAATAATATACTTAA
1 ATGATAATAGTTTTATATTTTATTAAATAATTTATTTAGATATAAGATATTAATAATATAATTAA
87675 AATACTATTGTT
66 AATACTATTGTT
87687 ATGATAATAGTTTTATATTTTATTAAATAATTTATTTAGATATAAGATATTAATAATATAATTAA
1 ATGATAATAGTTTTATATTTTATTAAATAATTTATTTAGATATAAGATATTAATAATATAATTAA
87752 AATACTATTGTT
66 AATACTATTGTT
87764 CTCTAAGGGT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (77 bp):
ATGATAATAGTTTTATATTTTATTAAATAATTTATTTAGATATAAGATATTAATAATATAATTAA
AATACTATTGTT
Found at i:87751 original size:39 final size:39
Alignment explanation
Indices: 87631--87752 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 39
87621 TTTATATTTT
*
87631 ATTAAATAATTTATTTAGATCTAAGATATTAATAATATA
1 ATTAAATAATTTATTTAGATATAAGATATTAATAATATA
* * * * * *
87670 CTTAAAATACTATT-GTTATGATA-ATAG-T-TTTAT-ATTTT
1 ATT-AAATAAT-TTATTTA-GATATA-AGATATTAATAATATA
87708 ATTAAATAATTTATTTAGATATAAGATATTAATAATATA
1 ATTAAATAATTTATTTAGATATAAGATATTAATAATATA
87747 ATTAAA
1 ATTAAA
87753 ATACTATTGT
Statistics
Matches: 61, Mismatches: 13, Indels: 18
0.66 0.14 0.20
Matches are distributed among these distances:
36 8 0.13
37 11 0.18
38 9 0.15
39 15 0.25
40 11 0.18
41 7 0.11
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (39 bp):
ATTAAATAATTTATTTAGATATAAGATATTAATAATATA
Found at i:89442 original size:4 final size:4
Alignment explanation
Indices: 89433--89460 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
89423 GGATCCCTCA
89433 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
89461 CATGCATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:89465 original size:4 final size:4
Alignment explanation
Indices: 89458--89484 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
89448 GTATGTATGT
89458 ATGC ATGC ATGC ATGC ATGC ATGC ATG
1 ATGC ATGC ATGC ATGC ATGC ATGC ATG
89485 TCTAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (4 bp):
ATGC
Found at i:94732 original size:2 final size:2
Alignment explanation
Indices: 94725--94759 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
94715 CTGCAATAAT
94725 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
94760 TAGAGAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:95667 original size:31 final size:31
Alignment explanation
Indices: 95629--95695 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
95619 AATATAGTGA
**
95629 TTAATTTGATTTACTTAATAATAAGACTATT
1 TTAATTTGATCCACTTAATAATAAGACTATT
95660 TTAATTTGATCCACTTAATAATAAGACTATT
1 TTAATTTGATCCACTTAATAATAAGACTATT
95691 TTAAT
1 TTAAT
95696 CTAGTCCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (31 bp):
TTAATTTGATCCACTTAATAATAAGACTATT
Found at i:112339 original size:15 final size:16
Alignment explanation
Indices: 112305--112355 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
112295 TATTGAGGAT
112305 GAAGAAAAAGAAAGAA
1 GAAGAAAAAGAAAGAA
*
112321 -AAGAATAAGAAA-AA
1 GAAGAAAAAGAAAGAA
* *
112335 GAAG-AGAAGGAAGAA
1 GAAGAAAAAGAAAGAA
112350 GAAGAA
1 GAAGAA
112356 GATGTTGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 8 0.28
15 20 0.69
16 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (16 bp):
GAAGAAAAAGAAAGAA
Found at i:112351 original size:21 final size:21
Alignment explanation
Indices: 112300--112357 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
112290 ATGGGTATTG
*
112300 AGGATGAAGAAAAAGAAAGAA
1 AGGAAGAAGAAAAAGAAAGAA
* *
112321 AAGAATAAGAAAAAG-AAGAGA
1 AGGAAGAAGAAAAAGAAAGA-A
*
112342 AGGAAGAAGAAGAAGA
1 AGGAAGAAGAAAAAGA
112358 TGTTGTCTCG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.03
Consensus pattern (21 bp):
AGGAAGAAGAAAAAGAAAGAA
Found at i:115056 original size:15 final size:15
Alignment explanation
Indices: 115024--115055 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
115014 GAATTAACTC
115024 TTTGAATTGTGTAGT
1 TTTGAATTGTGTAGT
115039 TTTGAATTGTGTA-T
1 TTTGAATTGTGTAGT
115053 TTT
1 TTT
115056 TTAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (15 bp):
TTTGAATTGTGTAGT
Found at i:118595 original size:17 final size:16
Alignment explanation
Indices: 118573--118614 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
118563 TATAAATTCA
*
118573 ATTTTTTTTATTGTATT
1 ATTTTTATTATT-TATT
118590 ATTTTTATTATTTATT
1 ATTTTTATTATTTATT
118606 -TTCTTTATT
1 ATT-TTTATT
118615 TAATTTCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 2 0.09
16 10 0.43
17 11 0.48
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (16 bp):
ATTTTTATTATTTATT
Found at i:128326 original size:21 final size:22
Alignment explanation
Indices: 128285--128327 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
128275 CTTTTCAAGA
*
128285 ATACTTTTGATTTGCCGATTGG
1 ATACTTTAGATTTGCCGATTGG
128307 ATACTTTAG-TTTGGCC-ATTGG
1 ATACTTTAGATTT-GCCGATTGG
128328 TTTGGGGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.19, C:0.14, G:0.23, T:0.44
Consensus pattern (22 bp):
ATACTTTAGATTTGCCGATTGG
Found at i:138292 original size:26 final size:26
Alignment explanation
Indices: 138255--138354 Score: 103
Period size: 26 Copynumber: 3.8 Consensus size: 26
138245 TTGAATTCTG
138255 GCTCGATAAGAGTGTTATTCTGTCTAA
1 GCTCG-TAAGAGTGTTATTCTGTCTAA
*
138282 GCTCGTAAGAGTGTTATT-TGTTTAA
1 GCTCGTAAGAGTGTTATTCTGTCTAA
* * ** * *
138307 GCTAGTATGAGCATTATTTTGTCTGA
1 GCTCGTAAGAGTGTTATTCTGTCTAA
* *
138333 GCTTGTAAGAGTGATATTCTGT
1 GCTCGTAAGAGTGTTATTCTGT
138355 TCGGGCTTGT
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
25 20 0.34
26 34 0.58
27 5 0.08
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (26 bp):
GCTCGTAAGAGTGTTATTCTGTCTAA
Found at i:149720 original size:18 final size:18
Alignment explanation
Indices: 149697--149758 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
149687 CAACAAGTTG
*
149697 AAGAAGAAGAAGACCCTA
1 AAGAAGAAGAAGATCCTA
149715 AAGAAGAAGAAGGGGATCCTA
1 AAGAAGAAGAA---GATCCTA
*
149736 AGGAAGAAGAAGATCCTA
1 AAGAAGAAGAAGATCCTA
149754 AAGAA
1 AAGAA
149759 AATCCCGTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 22 0.58
21 16 0.42
ACGTcount: A:0.53, C:0.11, G:0.27, T:0.08
Consensus pattern (18 bp):
AAGAAGAAGAAGATCCTA
Found at i:149722 original size:21 final size:21
Alignment explanation
Indices: 149696--149748 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
149686 ACAACAAGTT
149696 GAAGAAGAAGAAGACCCTAAA
1 GAAGAAGAAGAAGACCCTAAA
** * *
149717 GAAGAAGAAGGGGATCCTAAG
1 GAAGAAGAAGAAGACCCTAAA
149738 GAAGAAGAAGA
1 GAAGAAGAAGA
149749 TCCTAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.53, C:0.09, G:0.32, T:0.06
Consensus pattern (21 bp):
GAAGAAGAAGAAGACCCTAAA
Found at i:155981 original size:21 final size:20
Alignment explanation
Indices: 155941--155983 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
155931 TTCTCTTCAT
155941 TCTTCTCATCTTCTTCCTTC
1 TCTTCTCATCTTCTTCCTTC
*
155961 TCTTCCTCATTTTCCTT-CTTC
1 TCTT-CTCATCTT-CTTCCTTC
155982 TC
1 TC
155984 CTCAAGGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 13 0.65
22 3 0.15
ACGTcount: A:0.05, C:0.40, G:0.00, T:0.56
Consensus pattern (20 bp):
TCTTCTCATCTTCTTCCTTC
Found at i:155985 original size:18 final size:19
Alignment explanation
Indices: 155934--155987 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
155924 ATGTTCCTTC
* *
155934 TCTTCATTCTTCTCATC-T
1 TCTTCCTTCTTCTCCTCAT
155952 TCTTCCTTC-TCTTCCTCAT
1 TCTTCCTTCTTC-TCCTCAT
155971 T-TTCCTTCTTCTCCTCA
1 TCTTCCTTCTTCTCCTCA
155988 AGGTCCTCCT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 2 0.06
18 25 0.81
19 4 0.13
ACGTcount: A:0.07, C:0.39, G:0.00, T:0.54
Consensus pattern (19 bp):
TCTTCCTTCTTCTCCTCAT
Found at i:163592 original size:39 final size:39
Alignment explanation
Indices: 163547--163627 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
163537 TCATGATGAC
163547 ACTAAGTCATCGAACCCTTAATTCATCATGGATTCATTT
1 ACTAAGTCATCGAACCCTTAATTCATCATGGATTCATTT
163586 ACTAAGTCATCGAACCCTTAATTCATCATGGATTCATTT
1 ACTAAGTCATCGAACCCTTAATTCATCATGGATTCATTT
163625 ACT
1 ACT
163628 CATGATAACA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (39 bp):
ACTAAGTCATCGAACCCTTAATTCATCATGGATTCATTT
Found at i:163630 original size:19 final size:19
Alignment explanation
Indices: 163569--163630 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
163559 AACCCTTAAT
163569 TCATCATGGATTCATTTAC
1 TCATCATGGATTCATTTAC
* * ** * * *
163588 TAAGTCATCGAACCCTTAAT
1 TCA-TCATGGATTCATTTAC
163608 TCATCATGGATTCATTTAC
1 TCATCATGGATTCATTTAC
163627 TCAT
1 TCAT
163631 GATAACACTT
Statistics
Matches: 28, Mismatches: 14, Indels: 2
0.64 0.32 0.05
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (19 bp):
TCATCATGGATTCATTTAC
Found at i:169957 original size:21 final size:22
Alignment explanation
Indices: 169903--169960 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
169893 AAATAGTGCA
*
169903 AATTTCTACC-AGTACATGTACT
1 AATTTCTACCGA-TACAAGTACT
*
169925 AATTT-TATCGATACAAGTA-T
1 AATTTCTACCGATACAAGTACT
169945 AATTTCTACCGATACA
1 AATTTCTACCGATACA
169961 TGTCATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 6 0.19
21 19 0.61
22 6 0.19
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (22 bp):
AATTTCTACCGATACAAGTACT
Found at i:170812 original size:51 final size:51
Alignment explanation
Indices: 170679--170816 Score: 240
Period size: 51 Copynumber: 2.7 Consensus size: 51
170669 CTGTATAGGA
* **
170679 ATTCATTTACCCATGATGACACTTAGTCATCAAACCTTTAATCCGTAAAGG
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
*
170730 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAATG
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
170781 ATTCATTTACTCATGATGACACTTAGTCATCGGACC
1 ATTCATTTACTCATGATGACACTTAGTCATCGGACC
170817 CCTTTCGTTT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 83 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (51 bp):
ATTCATTTACTCATGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
Found at i:181124 original size:12 final size:12
Alignment explanation
Indices: 181107--181131 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
181097 TGTTATGATG
181107 ATGAATGCTATT
1 ATGAATGCTATT
181119 ATGAATGCTATT
1 ATGAATGCTATT
181131 A
1 A
181132 ATTCTTTAAT
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:182712 original size:45 final size:45
Alignment explanation
Indices: 182662--182751 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
182652 TCGTGAGATG
182662 TTTAAATTATGATTCAATTGAGTCCTTGATAAATTTTAGAATGCT
1 TTTAAATTATGATTCAATTGAGTCCTTGATAAATTTTAGAATGCT
182707 TTTAAATTATGATTCAATTGAGTCCTTGATAAATTTTAGAATGCT
1 TTTAAATTATGATTCAATTGAGTCCTTGATAAATTTTAGAATGCT
182752 GTAGATATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (45 bp):
TTTAAATTATGATTCAATTGAGTCCTTGATAAATTTTAGAATGCT
Found at i:203574 original size:51 final size:51
Alignment explanation
Indices: 203472--203795 Score: 443
Period size: 51 Copynumber: 6.3 Consensus size: 51
203462 CAATGACGTA
** * * *
203472 TAGTCATCGGATCCCTTGTTCCGTATAGGAATTCATATACTCACAATGACACT
1 TAGTCATCGGA-CCCTTAATCCGTAAAGG-ATTCATTTACTCACGATGACACT
* * * * *
203525 GAGTCATCGGACCCTTAATTCATCATGGATTCATTTACTCACGATGACACT
1 TAGTCATCGGACCCTTAATCCGTAAAGGATTCATTTACTCACGATGACACT
*
203576 TAGTCATCGGA-CCTGTAATCCGTAAAGGATTCATTTACTCACGACGACACT
1 TAGTCATCGGACCCT-TAATCCGTAAAGGATTCATTTACTCACGATGACACT
* * * *
203627 TAGTCATCGAACCTTTAATCCGTAAAGGATTCATTTACTCATGATGACTCT
1 TAGTCATCGGACCCTTAATCCGTAAAGGATTCATTTACTCACGATGACACT
* * *
203678 TAGTCATTGGACCTTTAATCCGTAAAGGATTCATTTACTCATGATGACACT
1 TAGTCATCGGACCCTTAATCCGTAAAGGATTCATTTACTCACGATGACACT
*
203729 TAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACT
1 TAGTCATCGGACCCTTAATCCGTAAAGGATTCATTTACTCACGATGACACT
203780 TAGTCATCGGACCCTT
1 TAGTCATCGGACCCTT
203796 TCGTTTATAG
Statistics
Matches: 242, Mismatches: 27, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
50 3 0.01
51 217 0.90
52 12 0.05
53 10 0.04
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
TAGTCATCGGACCCTTAATCCGTAAAGGATTCATTTACTCACGATGACACT
Found at i:204607 original size:2 final size:2
Alignment explanation
Indices: 204602--204626 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
204592 TTCTTTTAAT
204602 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
204627 TAATGACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:206009 original size:26 final size:26
Alignment explanation
Indices: 205947--206016 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 26
205937 GAATTCTAGC
*
205947 TCGATAAGAGCGTATTCTGTTTGAGCT
1 TCGA-AAGAGCGTATTCTATTTGAGCT
*
205974 T-GTATA-AGCGTTATTCTATTTGAG-T
1 TCG-AAAGAGCG-TATTCTATTTGAGCT
205999 TCGAAAGAGCGATATTCT
1 TCGAAAGAGCG-TATTCT
206017 GTCTAGGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
25 8 0.23
26 25 0.71
27 2 0.06
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (26 bp):
TCGAAAGAGCGTATTCTATTTGAGCT
Found at i:206056 original size:26 final size:26
Alignment explanation
Indices: 206015--206100 Score: 73
Period size: 26 Copynumber: 3.3 Consensus size: 26
206005 GAGCGATATT
* *
206015 CTGTCTAGGCACATAATAGTTAAACC
1 CTGTCTAGGCACATAAGAGCTAAACC
** *
206041 CTGTCTAGGCTTATAAGAGCTAAACT
1 CTGTCTAGGCACATAAGAGCTAAACC
* * * * **
206067 CTGTTTGGGCTCGTAAGAGCTAAATT
1 CTGTCTAGGCACATAAGAGCTAAACC
206093 CTGTCTAG
1 CTGTCTAG
206101 CCTCGTATGA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (26 bp):
CTGTCTAGGCACATAAGAGCTAAACC
Found at i:206105 original size:26 final size:26
Alignment explanation
Indices: 206035--206107 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 26
206025 ACATAATAGT
* * **
206035 TAAACCCTGTCTAGGCTTATAAGAGC
1 TAAACTCTGTCTAGCCTCGTAAGAGC
* * *
206061 TAAACTCTGTTTGGGCTCGTAAGAGC
1 TAAACTCTGTCTAGCCTCGTAAGAGC
*
206087 TAAATTCTGTCTAGCCTCGTA
1 TAAACTCTGTCTAGCCTCGTA
206108 TGATTTAAAT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (26 bp):
TAAACTCTGTCTAGCCTCGTAAGAGC
Found at i:210994 original size:27 final size:27
Alignment explanation
Indices: 210964--211022 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
210954 TGTGCTTTGT
*
210964 ATAGAATGTAGCTCATT-TGAGCCCAAA
1 ATAGAATGTAGCTC-TTACGAGCCCAAA
* * *
210991 ATAGAGTTTAGCTCTTACGAGCCCAGA
1 ATAGAATGTAGCTCTTACGAGCCCAAA
211018 ATAGA
1 ATAGA
211023 GATTTGATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
ATAGAATGTAGCTCTTACGAGCCCAAA
Found at i:217037 original size:7 final size:7
Alignment explanation
Indices: 216980--217044 Score: 75
Period size: 6 Copynumber: 9.4 Consensus size: 7
216970 GGAGGCATAA
216980 TTTTA-T
1 TTTTATT
216986 TTTTA-T
1 TTTTATT
216992 TTTTA-T
1 TTTTATT
216998 TTTTA-T
1 TTTTATT
217004 TTTTATCT
1 TTTTAT-T
217012 TTTTATT
1 TTTTATT
217019 TTTTATCT
1 TTTTAT-T
217027 TTTTATT
1 TTTTATT
217034 TTTTAATT
1 TTTT-ATT
217042 TTT
1 TTT
217045 GGGTTTTTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
6 23 0.42
7 12 0.22
8 20 0.36
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTATT
Found at i:217044 original size:15 final size:14
Alignment explanation
Indices: 216985--217036 Score: 81
Period size: 15 Copynumber: 3.8 Consensus size: 14
216975 CATAATTTTA
216985 TTTTTATTTTTA--
1 TTTTTATTTTTATC
216997 TTTTTATTTTTATC
1 TTTTTATTTTTATC
217011 TTTTTATTTTTTATC
1 TTTTTA-TTTTTATC
217026 TTTTTATTTTT
1 TTTTTATTTTT
217037 TAATTTTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.32
14 11 0.30
15 14 0.38
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTATTTTTATC
Found at i:225343 original size:20 final size:20
Alignment explanation
Indices: 225318--225363 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
225308 AGAGCCGATA
*
225318 TTAAACCAAATGGGAACATC
1 TTAAACCAAATGGAAACATC
*
225338 TTAAACGAAATGGAAACATC
1 TTAAACCAAATGGAAACATC
225358 TTAAAC
1 TTAAAC
225364 AAAAAGTAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (20 bp):
TTAAACCAAATGGAAACATC
Found at i:232509 original size:2 final size:2
Alignment explanation
Indices: 232492--232526 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
232482 AAATTAAAAA
* *
232492 AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
232527 CATGATTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:234836 original size:14 final size:14
Alignment explanation
Indices: 234819--234847 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
234809 AGTAGGGTCG
234819 ATTCCACAGGGACT
1 ATTCCACAGGGACT
234833 ATTCCACAGGGACT
1 ATTCCACAGGGACT
234847 A
1 A
234848 GTTGCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.21
Consensus pattern (14 bp):
ATTCCACAGGGACT
Found at i:236502 original size:18 final size:19
Alignment explanation
Indices: 236479--236524 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
236469 ACCCAACATG
236479 TATATTTTTCTCTTTTTT-
1 TATATTTTTCTCTTTTTTA
*
236497 TATATTTTTTTCTTTTTTA
1 TATATTTTTCTCTTTTTTA
236516 TATATTTTT
1 TATATTTTT
236525 TGAGACATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (19 bp):
TATATTTTTCTCTTTTTTA
Found at i:236513 original size:19 final size:18
Alignment explanation
Indices: 236479--236525 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
236469 ACCCAACATG
* *
236479 TATATTTTTCTCTTTTTT
1 TATATTTTTTTCTTTTTA
236497 TATATTTTTTTCTTTTTTA
1 TATATTTTTTTC-TTTTTA
236516 TATATTTTTT
1 TATATTTTTT
236526 GAGACATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (18 bp):
TATATTTTTTTCTTTTTA
Found at i:239544 original size:17 final size:18
Alignment explanation
Indices: 239507--239576 Score: 69
Period size: 17 Copynumber: 4.1 Consensus size: 18
239497 ATAAGAATGG
*
239507 AAATGCAACT-ACAA-TGC
1 AAATGCAACTGACAAGT-A
*
239524 AAATG-AACTAACAAGTA
1 AAATGCAACTGACAAGTA
*
239541 AAATGCAAC-GACAACTA
1 AAATGCAACTGACAAGTA
239558 AAATGCAA-TGACAAGTA
1 AAATGCAACTGACAAGTA
239575 AA
1 AA
239577 TAAGATGCAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.09
17 37 0.82
18 4 0.09
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.16
Consensus pattern (18 bp):
AAATGCAACTGACAAGTA
Found at i:239562 original size:34 final size:34
Alignment explanation
Indices: 239507--239576 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
239497 ATAAGAATGG
* *
239507 AAATGCAACTACAATGCAAATG-AACTAACAAGTA
1 AAATGCAACGACAATGAAAATGCAA-TAACAAGTA
*
239541 AAATGCAACGACAACT-AAAATGCAATGACAAGTA
1 AAATGCAACGACAA-TGAAAATGCAATAACAAGTA
239575 AA
1 AA
239577 TAAGATGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 28 0.90
35 3 0.10
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.16
Consensus pattern (34 bp):
AAATGCAACGACAATGAAAATGCAATAACAAGTA
Found at i:240022 original size:15 final size:16
Alignment explanation
Indices: 239969--240023 Score: 69
Period size: 15 Copynumber: 3.5 Consensus size: 16
239959 CGGGGTAACA
239969 TCTTCTTCCTCTTTGT
1 TCTTCTTCCTCTTTGT
239985 T-TTCTTCCTCTTTGGT
1 TCTTCTTCCTCTTT-GT
* *
240001 CCTTCTTCTTCTTT-T
1 TCTTCTTCCTCTTTGT
240016 TCTTCTTC
1 TCTTCTTC
240024 ATTCACCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 20 0.59
16 3 0.09
17 11 0.32
ACGTcount: A:0.00, C:0.31, G:0.05, T:0.64
Consensus pattern (16 bp):
TCTTCTTCCTCTTTGT
Found at i:250593 original size:27 final size:27
Alignment explanation
Indices: 250562--250615 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
250552 ATTTTGCTAT
250562 TGACAAATTCAACTAAAAATATCTTTG
1 TGACAAATTCAACTAAAAATATCTTTG
250589 TGACAAATTCAACTAAAAATATCTTTG
1 TGACAAATTCAACTAAAAATATCTTTG
250616 CACGTAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (27 bp):
TGACAAATTCAACTAAAAATATCTTTG
Found at i:251551 original size:80 final size:80
Alignment explanation
Indices: 251416--251577 Score: 191
Period size: 80 Copynumber: 2.0 Consensus size: 80
251406 TCTACTTATA
* * * * * * **
251416 AATAGGGGTTTACGTAGTGGAGAGTTTTAGGATGAGTTTGGATAAATGATGTGTTTATTTATGAT
1 AATAGGGGTTGAAGCAGTGGAGAGTTTTAGGATGAGTTTAGATAAATGATATGTTTATCTACAAT
*
251481 TAGTATAAAAATAAT
66 TAATATAAAAATAAT
* **
251496 AATAGGGGTTGAAGCAGTGGAGAGTTTTAGGGT-AGATTTAGATGGATGATATGTTTATCTACAA
1 AATAGGGGTTGAAGCAGTGGAGAGTTTTAGGATGAG-TTTAGATAAATGATATGTTTATCTACAA
*
251560 TTAATGTAAAAATAAT
65 TTAATATAAAAATAAT
251576 AA
1 AA
251578 GAATCCCCTT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
79 2 0.03
80 66 0.97
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (80 bp):
AATAGGGGTTGAAGCAGTGGAGAGTTTTAGGATGAGTTTAGATAAATGATATGTTTATCTACAAT
TAATATAAAAATAAT
Found at i:252268 original size:27 final size:29
Alignment explanation
Indices: 252219--252281 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
252209 AAGTTGAAAA
* *
252219 AAAAAAATTTAATATCTTAAAAA-TTGGT
1 AAAAAAATTTAATACCTTAAAAAGTTGAT
*
252247 AAAAAAATTTAA-ACCTTTAAAAGTTGAT
1 AAAAAAATTTAATACCTTAAAAAGTTGAT
252275 AAAAAAA
1 AAAAAAA
252282 ATTTTGAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAAAATTTAATACCTTAAAAAGTTGAT
Found at i:252297 original size:30 final size:28
Alignment explanation
Indices: 252205--252301 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 28
252195 TTTAGATTCA
* *
252205 TTAAAAGTTGAAAAAAAAAAATTTAATATC
1 TTAAAAGTTG-ATAAAAAAAATTTAA-CTC
* *
252235 TTAAAAATTGGT-AAAAAAATTTAAAC-C
1 TTAAAAGTTGATAAAAAAAATTT-AACTC
252262 TTTAAAAGTTGATAAAAAAAATTTTGAACTC
1 -TTAAAAGTTGATAAAAAAAA-TTT-AACTC
252293 TTAAAAGTT
1 TTAAAAGTT
252302 AAAATTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
27 1 0.02
28 20 0.36
29 9 0.16
30 24 0.44
31 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (28 bp):
TTAAAAGTTGATAAAAAAAATTTAACTC
Found at i:252753 original size:6 final size:6
Alignment explanation
Indices: 252742--252775 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
252732 AATTTCCAAG
252742 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
252776 ATCTTCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:258995 original size:29 final size:30
Alignment explanation
Indices: 258957--259018 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
258947 AAGAAAAAAG
258957 TTTAAATATTT-AAAT-AAAGTTTTGATTTT
1 TTTAAATATTTCAAATAAAAG-TTTGATTTT
*
258986 TTTAACTATTTCGAAATAAAAGTTTGATTTT
1 TTTAAATATTTC-AAATAAAAGTTTGATTTT
259017 TT
1 TT
259019 AAGTAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 10 0.34
31 15 0.52
32 4 0.14
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTAAATATTTCAAATAAAAGTTTGATTTT
Found at i:259084 original size:149 final size:146
Alignment explanation
Indices: 258844--259272 Score: 553
Period size: 148 Copynumber: 2.9 Consensus size: 146
258834 GTTTTATATA
* * * *
258844 ATTTCGAAATAAAATTTTTGATTTTTAAGAAAAATAGTGATTTTCTTTTAAAAAGAGAAAGTTTA
1 ATTTCGAAATAAAA-ATTTGATTTTTAAGTAAAATAGTGATTTTC-ATTAAAAAAAGAAAGTTTA
* * *
258909 GATTTT-TAAATAAAAATATGTTTTTTTTATTTATTTTAAAGAAAAAAGTTTAAATATTTAAAT-
64 GATTTTAAAAATAAAAATATG-TTTTTTTAGTCATTTTAAAGAAAAAA-TTTAAA-ATTTAAATC
258972 AAAGTTTTGATTTTTTTAACT
126 AAAGTTTTGATTTTTTTAACT
* *
258993 ATTTCGAAATAAAAGTTTGATTTTTTAAGTAAAATAGTGATTTTCATTAAAAAAAATAAAGTTTA
1 ATTTCGAAATAAAAATTTGA-TTTTTAAGTAAAATAGTGATTTTCATT-AAAAAAAGAAAGTTTA
* *
259058 GATTTGTAAAAATAAAAATATG--TTTTTAGGCATTTTAAAAGAAAAAATTTAAAATTTTAATCA
64 GATTT-TAAAAATAAAAATATGTTTTTTTAGTCATTTT-AAAGAAAAAATTTAAAATTTAAATCA
259121 AAGTTTTGATTTTTTTAACT
127 AAGTTTTGATTTTTTTAACT
* *
259141 ATTTCGAAATAAAAATTTAGATTTTTAAATAAAATAGTGATTTTCATTAAAAAAAGAAAGTTCAG
1 ATTTCGAAATAAAAATTT-GATTTTTAAGTAAAATAGTGATTTTCATTAAAAAAAGAAAGTTTAG
*
259206 ATTTTTTAAAAAATAAAAATATGATTTTTTTAGTGATTTTAAAG-AAAAATTTAAAAATTTTAAA
65 A--TTTT-AAAAATAAAAATATG-TTTTTTTAGTCATTTTAAAGAAAAAATTT-AAAA-TTTAAA
259270 TCA
124 TCA
259273 TTGAGCTCTC
Statistics
Matches: 248, Mismatches: 17, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
147 23 0.09
148 89 0.36
149 86 0.35
150 9 0.04
151 21 0.08
152 20 0.08
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (146 bp):
ATTTCGAAATAAAAATTTGATTTTTAAGTAAAATAGTGATTTTCATTAAAAAAAGAAAGTTTAGA
TTTTAAAAATAAAAATATGTTTTTTTAGTCATTTTAAAGAAAAAATTTAAAATTTAAATCAAAGT
TTTGATTTTTTTAACT
Found at i:274372 original size:15 final size:16
Alignment explanation
Indices: 274343--274372 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
274333 AACAACACGA
274343 TGAAAAGTGAAATAAC
1 TGAAAAGTGAAATAAC
274359 TGAAAAGT-AAATAA
1 TGAAAAGTGAAATAA
274373 AAAATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (16 bp):
TGAAAAGTGAAATAAC
Found at i:286238 original size:21 final size:21
Alignment explanation
Indices: 286192--286257 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
286182 GTGCAGGCTC
* *
286192 CTACCAATACAAGTGATAGTT
1 CTACCGATACAAGTGATACTT
*
286213 TTACCGATACAAGTGACT-CTT
1 CTACCGATACAAGTGA-TACTT
**
286234 CTACCGATACAAGTCTTACTT
1 CTACCGATACAAGTGATACTT
286255 CTA
1 CTA
286258 TCAATACCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (21 bp):
CTACCGATACAAGTGATACTT
Found at i:286557 original size:20 final size:20
Alignment explanation
Indices: 286521--286558 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
286511 CAACATGAGA
*
286521 TACATAGACTCTTAAGTCAT
1 TACATAGACTCTCAAGTCAT
286541 TACATAGCACT-TCAAGTC
1 TACATAG-ACTCTCAAGTC
286559 TATATTCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (20 bp):
TACATAGACTCTCAAGTCAT
Found at i:302601 original size:41 final size:41
Alignment explanation
Indices: 302512--302662 Score: 167
Period size: 41 Copynumber: 3.7 Consensus size: 41
302502 CGAATCACTT
** * **
302512 GATTATATTAAAGGAAGACTCATGACTCAAAACAAGCATGA
1 GATTATATTAAAGGAAGACTCATGACTTGAGATGAGCATGA
* * * * *
302553 GATTATATTAAAGGAGGACTCATGTCTTGGGGTGAGCACGA
1 GATTATATTAAAGGAAGACTCATGACTTGAGATGAGCATGA
* *
302594 GAATATATTAAAGGAAGACTCGTGACTTGAGATGAGCATGA
1 GATTATATTAAAGGAAGACTCATGACTTGAGATGAGCATGA
* *
302635 CATTATATTTAAAGGAAGACTTATGACT
1 GATTATA-TTAAAGGAAGACTCATGACT
302663 CGGTAAAGCA
Statistics
Matches: 88, Mismatches: 21, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
41 70 0.80
42 18 0.20
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.26
Consensus pattern (41 bp):
GATTATATTAAAGGAAGACTCATGACTTGAGATGAGCATGA
Found at i:305895 original size:30 final size:30
Alignment explanation
Indices: 305807--305897 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
305797 GAGTGTTTGG
* ** * *
305807 AGCTCTAGTGTTCGCGACATGAGTGCTCAC
1 AGCTCTAGTGTTCGCAACACCAATGCTCGC
**
305837 AGCTCTAGTGTTTACAACACCAATGCTCGC
1 AGCTCTAGTGTTCGCAACACCAATGCTCGC
305867 AGCTCTAGTGTTCGCAACACCAATGCTCGC
1 AGCTCTAGTGTTCGCAACACCAATGCTCGC
305897 A
1 A
305898 TCTTCTAAGT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.25
Consensus pattern (30 bp):
AGCTCTAGTGTTCGCAACACCAATGCTCGC
Found at i:310301 original size:36 final size:36
Alignment explanation
Indices: 310231--310302 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
310221 TTGTTTAAAT
*
310231 AAAAAAAAACAACAAAACAAAAAAAGAGAGAGAGAG
1 AAAAAAAAACAACAAAACAAAAAAAGAGAAAGAGAG
* *
310267 AAAAAAAGAACAA-AAAAGAAGAAAAA-ATAAAGAGAG
1 AAAAAAA-AACAACAAAACAA-AAAAAGAGAAAGAGAG
310303 TAAGAGAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
36 21 0.68
37 10 0.32
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.01
Consensus pattern (36 bp):
AAAAAAAAACAACAAAACAAAAAAAGAGAAAGAGAG
Found at i:310792 original size:42 final size:42
Alignment explanation
Indices: 310703--310798 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
310693 GCACTCATTG
* * *
310703 CATTTAGAGGCCTAGGTGTGGAGGTCCATTTACTTTTCATCG
1 CATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTCATCC
*
310745 TATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTCATCC
1 CATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTCATCC
*
310787 CATTTAGTGGCC
1 CATTTAGAGGCC
310799 CAAGTACCCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (42 bp):
CATTTAGAGGCCAAGGTGTGGAGGCCCATTTACTTTTCATCC
Found at i:310872 original size:42 final size:42
Alignment explanation
Indices: 310825--311205 Score: 453
Period size: 42 Copynumber: 9.1 Consensus size: 42
310815 TTTCATTACA
* * * *
310825 GTGGAGGTCCATTTATTTTTCATTACATTTAAAGGCCTAAGT
1 GTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGT
** *
310867 GTGGAGACCCATTTACTTTTCATCT-CATTTAGAGGCCCAGGT
1 GTGGAGGTCCATTTACTTTTCAT-TGCATTTAGAGGCCTAGGT
*
310909 GTGGAGGTCCATTTATTTTTCATTGCATTTAGAGGCCTAGGT
1 GTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGT
* * * * *
310951 GTGGAGATCCATTTATTTTTCATTGCATTTTGAGGCCCAAGT
1 GTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGT
* * * **
310993 GTGGAGGCCCATTTACTTTTCATCGCATTTAGAGGCCCAAAT
1 GTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGT
* *
311035 GTGGAGGTCCATTTAC-TTTCAATCGTATTTAGAGGCCTAGGT
1 GTGGAGGTCCATTTACTTTTC-ATTGCATTTAGAGGCCTAGGT
* * *
311077 GTGGAGGTCCATTTACTTTTCATCGCATTTAAAAG-CTCAGGT
1 GTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCT-AGGT
* * *
311119 GTTGAGGTCCATTTAATTTTCATTGCATTTAGAGGTCTAGGT
1 GTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGT
* * *
311161 GTGGAGGTCCATTTACTTTTCGTTGCATTTAGAGTCCTAAGT
1 GTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGT
311203 GTG
1 GTG
311206 ATGTCTATTT
Statistics
Matches: 294, Mismatches: 39, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
41 7 0.02
42 280 0.95
43 7 0.02
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (42 bp):
GTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCTAGGT
Found at i:311564 original size:3 final size:3
Alignment explanation
Indices: 311556--311603 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
311546 AAGAGCCCAA
* * * * *
311556 ATT ATT ATT ATC ATT ATT ACT ACT AGT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
311604 TAGGGTTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:312204 original size:147 final size:145
Alignment explanation
Indices: 312023--312305 Score: 394
Period size: 147 Copynumber: 1.9 Consensus size: 145
312013 AAATTTTGAA
* * * * *
312023 TTTTTTAAATAATTTCGGAAGAAAAGTTTCGATTTTTAAGTAAAATAGTGATTTTCTTTAAAAAA
1 TTTTTTAAATAATTTCGAAAGAAAAGTTTAGATTTTTAAATAAAATAGTAATTTTCATTAAAAAA
312088 GAGAAAGTTTAGA-CTTTTAAAAATAAAAATATGATTTTTAGTCATTTTAAA-AGAAAA-TTTAA
66 -AGAAAGTTTAGATCTTTTAAAAA-AAAAA-AT--TTTTTAGTCATTTTAAATA-AAAAGTTTAA
312150 ATTTTTAAACAATTTTTTTAT
125 ATTTTTAAACAATTTTTTTAT
* *
312171 TTTTTTAACT-ATTTCGAAATAAAAGTTTAGATTTTTAAATAAAATAGTAATTTTCATTAAAAAA
1 TTTTTTAAATAATTTCGAAAGAAAAGTTTAGATTTTTAAATAAAATAGTAATTTTCATTAAAAAA
* * *
312235 AGAAAGTTTAGATTTTTTAAAAAAATAAATTTTTTAGTGATTTTAAATAAAAAGTTTAAATTTTT
66 AGAAAGTTTAGATCTTTTAAAAAAAAAAATTTTTTAGTCATTTTAAATAAAAAGTTTAAATTTTT
312300 AAACAA
131 AAACAA
312306 AGTTTTGATT
Statistics
Matches: 122, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
143 20 0.16
144 18 0.15
145 2 0.02
146 16 0.13
147 57 0.47
148 9 0.07
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (145 bp):
TTTTTTAAATAATTTCGAAAGAAAAGTTTAGATTTTTAAATAAAATAGTAATTTTCATTAAAAAA
AGAAAGTTTAGATCTTTTAAAAAAAAAAATTTTTTAGTCATTTTAAATAAAAAGTTTAAATTTTT
AAACAATTTTTTTAT
Found at i:318491 original size:26 final size:26
Alignment explanation
Indices: 318457--318539 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
318447 AACCCGGAAT
*
318457 AGAGATTAGCTCTTACGAGCCCAAAC
1 AGAGTTTAGCTCTTACGAGCCCAAAC
*
318483 AGAGTTTAGCT-TATACGAGACCAAAC
1 AGAGTTTAGCTCT-TACGAGCCCAAAC
* * **
318509 AAAGTTTAGCTCATACGAGCCCGGAC
1 AGAGTTTAGCTCTTACGAGCCCAAAC
318535 AGAGT
1 AGAGT
318540 ATTTCTCCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
25 1 0.02
26 46 0.98
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (26 bp):
AGAGTTTAGCTCTTACGAGCCCAAAC
Found at i:318583 original size:27 final size:27
Alignment explanation
Indices: 318553--318642 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
318543 TCTCCAAGAT
* *
318553 AGAATCAGAATAACGCTCTTTTGAGTC
1 AGAATCAGAATAACGCTCTTTCGAGCC
* * *
318580 AGAATCAAAATGACGTTCTTTCGAGCC
1 AGAATCAGAATAACGCTCTTTCGAGCC
* * *
318607 AGAATCAGAATAACACTCTTACGAGCT
1 AGAATCAGAATAACGCTCTTTCGAGCC
*
318634 AGAACCAGA
1 AGAATCAGA
318643 TTACTCCTCA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (27 bp):
AGAATCAGAATAACGCTCTTTCGAGCC
Found at i:320284 original size:14 final size:15
Alignment explanation
Indices: 320265--320298 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
320255 ACTAACTTTT
320265 AATTCAATAATT-AA
1 AATTCAATAATTCAA
*
320279 AATTCATTAATTCAA
1 AATTCAATAATTCAA
320294 AATTC
1 AATTC
320299 CATATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTCAATAATTCAA
Found at i:322544 original size:28 final size:28
Alignment explanation
Indices: 322517--322647 Score: 122
Period size: 28 Copynumber: 4.7 Consensus size: 28
322507 CGATACTCTA
322517 ATTT-TAGCTTGGGTAGAGTTTTGATCT
1 ATTTATAGCTTGGGTAGAGTTTTGATCT
* * * * * *
322544 ATTTACAGCTCGAGTAAAGCTTTGATTT
1 ATTTATAGCTTGGGTAGAGTTTTGATCT
* *
322572 GTTTACAGCTTGGGTAGAGTTTTGAT-T
1 ATTTATAGCTTGGGTAGAGTTTTGATCT
** *
322599 CATTTATAGCTCAGGTAGAGATTTGATCT
1 -ATTTATAGCTTGGGTAGAGTTTTGATCT
* *
322628 ATTTATGGCTTGAGTAGAGT
1 ATTTATAGCTTGGGTAGAGT
322648 GATATACTGT
Statistics
Matches: 80, Mismatches: 21, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
27 5 0.06
28 74 0.93
29 1 0.01
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (28 bp):
ATTTATAGCTTGGGTAGAGTTTTGATCT
Found at i:322639 original size:56 final size:56
Alignment explanation
Indices: 322522--322647 Score: 148
Period size: 56 Copynumber: 2.2 Consensus size: 56
322512 CTCTAATTTT
* * *
322522 AGCTTGGGTAGAGTTTTGATCTATTTACAGCTCGAGTAAAGCTTTGATTTGTTTAC
1 AGCTTGGGTAGAGTTTTGATCTATTTACAGCTCGAGTAAAGATTTGATCTATTTAC
* * *
322578 AGCTTGGGTAGAGTTTTGAT-TCATTTATAGCTC-AGGTAGAGATTTGATCTATTTAT
1 AGCTTGGGTAGAGTTTTGATCT-ATTTACAGCTCGA-GTAAAGATTTGATCTATTTAC
* *
322634 GGCTTGAGTAGAGT
1 AGCTTGGGTAGAGT
322648 GATATACTGT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
55 2 0.03
56 58 0.97
ACGTcount: A:0.24, C:0.10, G:0.25, T:0.40
Consensus pattern (56 bp):
AGCTTGGGTAGAGTTTTGATCTATTTACAGCTCGAGTAAAGATTTGATCTATTTAC
Found at i:322685 original size:28 final size:28
Alignment explanation
Indices: 322605--322715 Score: 75
Period size: 28 Copynumber: 4.0 Consensus size: 28
322595 GATTCATTTA
* * * *
322605 TAGCTCAGGTAGAGATTTGATCTATTTA
1 TAGCTCAAGTAGAGAGTTGATCTGTTTC
* ** * *
322633 TGGCTTGAGTAGAGTGAT-ATACTGTTTC
1 TAGCTCAAGTAGAGAGTTGAT-CTGTTTC
322661 TAGCTCAAGTAGAGAGTTGATCTGTTTC
1 TAGCTCAAGTAGAGAGTTGATCTGTTTC
* *
322689 T-G-TCTAGAGTAGAGCGTTAATCTGTTT
1 TAGCTC-A-AGTAGAGAGTTGATCTGTTT
322716 TCGGCTCGGA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
26 2 0.03
27 4 0.06
28 55 0.87
29 2 0.03
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (28 bp):
TAGCTCAAGTAGAGAGTTGATCTGTTTC
Found at i:327456 original size:165 final size:165
Alignment explanation
Indices: 327184--327515 Score: 601
Period size: 165 Copynumber: 2.0 Consensus size: 165
327174 AAGGTATATG
327184 AGTTTCTCGAGGTAAACACCGATAAAGATATGGAAAGATGGTGGTACAAATTTTGAGAAAGAGAT
1 AGTTTCTCGAGGTAAACACCGATAAAGATATGGAAAGATGGTGGTACAAATTTTGAGAAAGAGAT
*
327249 AAACGCTAGAGAATAGCTTGGCACGATGGCTACTGGATGAACAACGATAAAATAGACCAGTCACA
66 AAACGCTAGAGAATAGCTTGGCACAATGGCTACTGGATGAACAACGATAAAATAGACCAGTCACA
*
327314 ATGAACCCTCACTATGAACGTCACAGCAATGTGCA
131 ATGAACCCGCACTATGAACGTCACAGCAATGTGCA
327349 AGTTTCTCGAGGTAAACACCGATAAAGATATGGAAAGATGGTGGTACAAATTTTGAGAAAGAGAT
1 AGTTTCTCGAGGTAAACACCGATAAAGATATGGAAAGATGGTGGTACAAATTTTGAGAAAGAGAT
* * *
327414 AAACGCTAGAGAATATCTTGGCACAATGGCTGCTGGATGAACAATGATAAAATAGACCAGTCACA
66 AAACGCTAGAGAATAGCTTGGCACAATGGCTACTGGATGAACAACGATAAAATAGACCAGTCACA
* *
327479 GTGCACCCGCACTATGAACGTCACAGCAATGTGCA
131 ATGAACCCGCACTATGAACGTCACAGCAATGTGCA
327514 AG
1 AG
327516 CGTACATTGT
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 160 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (165 bp):
AGTTTCTCGAGGTAAACACCGATAAAGATATGGAAAGATGGTGGTACAAATTTTGAGAAAGAGAT
AAACGCTAGAGAATAGCTTGGCACAATGGCTACTGGATGAACAACGATAAAATAGACCAGTCACA
ATGAACCCGCACTATGAACGTCACAGCAATGTGCA
Found at i:327688 original size:16 final size:16
Alignment explanation
Indices: 327667--327697 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
327657 ATAATGTGAA
327667 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
327683 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
327698 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:328551 original size:26 final size:26
Alignment explanation
Indices: 328498--328551 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
328488 ATTTTTGGCG
*
328498 CAATTCTGGACACGTTCATGCAGTGA
1 CAATTCTGGACACGTTCATGCAGCGA
* *
328524 CAATTCTGGACATGTTCATGTAGCGA
1 CAATTCTGGACACGTTCATGCAGCGA
328550 CA
1 CA
328552 TTCCTAGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (26 bp):
CAATTCTGGACACGTTCATGCAGCGA
Found at i:331832 original size:16 final size:16
Alignment explanation
Indices: 331811--331841 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
331801 ATAACGTGAA
331811 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
331827 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
331842 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:332673 original size:26 final size:26
Alignment explanation
Indices: 332643--332694 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
332633 TCTGGGTGCG
332643 ATTCTAGACACGTTCATGCAGCGACA
1 ATTCTAGACACGTTCATGCAGCGACA
* * *
332669 ATTCTGGACATGTTCATGCAGTGACA
1 ATTCTAGACACGTTCATGCAGCGACA
332695 TTCCTCGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (26 bp):
ATTCTAGACACGTTCATGCAGCGACA
Found at i:332847 original size:37 final size:37
Alignment explanation
Indices: 332797--332880 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
332787 GAAATATTCC
* * * *
332797 TGCAGTGATAGTTTTGGGTGCAATCTGGAAGTGCTCA
1 TGCAGCGACAGTTTTGGGCGCAATCTAGAAGTGCTCA
*
332834 TGCGGCGACAGTTTTGGGCGCAATCTAGAAGTGCTCA
1 TGCAGCGACAGTTTTGGGCGCAATCTAGAAGTGCTCA
332871 TGCAGCGACA
1 TGCAGCGACA
332881 TTAGTAGTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
TGCAGCGACAGTTTTGGGCGCAATCTAGAAGTGCTCA
Found at i:347314 original size:19 final size:19
Alignment explanation
Indices: 347257--347314 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
347247 AGATTGTGAT
* *
347257 TTAATTATGTCATGCATTA
1 TTAAATATGACATGCATTA
*
347276 TT-AATCT-ACAT-C-TT-
1 TTAAATATGACATGCATTA
347290 TTAAATATGACATGCATTA
1 TTAAATATGACATGCATTA
347309 TTAAAT
1 TTAAAT
347315 GATCTGCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 2 0.07
15 6 0.20
16 5 0.17
17 4 0.13
18 5 0.17
19 8 0.27
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (19 bp):
TTAAATATGACATGCATTA
Found at i:347437 original size:50 final size:50
Alignment explanation
Indices: 347370--347513 Score: 157
Period size: 50 Copynumber: 2.8 Consensus size: 50
347360 ACTCTCATAA
* *
347370 TTAGTTAAGTTTGCATCATAAATAATGACATGCATTAAGTAACTTACATG
1 TTAGTTAAATTTGCATCATAAATAATGACATGCATTAAGTAACTCACATG
* ** * *
347420 TTAGTTAAATATGCATCATAAATCCT-ATCATGCATTATGTAACTCCCATG
1 TTAGTTAAATTTGCATCATAAATAATGA-CATGCATTAAGTAACTCACATG
* *
347470 TTAGTTAAAGTTTGCATCATTAAATCAA-GTCATGCATTTAGTAA
1 TTAGTTAAA-TTTGCATCA-TAAAT-AATGACATGCATTAAGTAA
347514 TCCATTATTT
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 50 0.66
51 8 0.11
52 17 0.22
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (50 bp):
TTAGTTAAATTTGCATCATAAATAATGACATGCATTAAGTAACTCACATG
Found at i:348769 original size:29 final size:32
Alignment explanation
Indices: 348718--348776 Score: 88
Period size: 29 Copynumber: 1.9 Consensus size: 32
348708 TTTTGAAAAA
348718 AAAGAAAAATATTGAAATATTGAAAAAAAATC
1 AAAGAAAAATATTGAAATATTGAAAAAAAATC
*
348750 AAAG-AAAAT-TTGAAGT-TTGAAAAAAAA
1 AAAGAAAAATATTGAAATATTGAAAAAAAA
348777 GAAGAGAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 6 0.23
31 5 0.19
32 4 0.15
ACGTcount: A:0.64, C:0.02, G:0.12, T:0.22
Consensus pattern (32 bp):
AAAGAAAAATATTGAAATATTGAAAAAAAATC
Found at i:348784 original size:29 final size:27
Alignment explanation
Indices: 348709--348809 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 27
348699 TTTTTCGTGT
*
348709 TTTGAAAAAAAAGAAA-AATATTGAAA
1 TTTGAAAAAAAAGAAAGAAAATTGAAA
* *
348735 TATTGAAAAAAAATCAAAGAAAATTTGAAG
1 T-TTGAAAAAAAA-GAAAGAAAA-TTGAAA
*
348765 TTTGAAAAAAAAG-AAGAGAAATTCAAA
1 TTTGAAAAAAAAGAAAGA-AAATTGAAA
*
348792 -TT--AAAAAAAGAAAAAAAA
1 TTTGAAAAAAAAGAAAGAAAA
348810 AGAATCGAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
24 11 0.18
25 3 0.05
26 3 0.05
27 19 0.31
28 6 0.10
29 14 0.23
30 6 0.10
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (27 bp):
TTTGAAAAAAAAGAAAGAAAATTGAAA
Found at i:349780 original size:20 final size:20
Alignment explanation
Indices: 349735--349782 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
349725 AGAGATATTG
349735 AAAAA-AAAAAGATAATGAA
1 AAAAAGAAAAAGATAATGAA
*
349754 AGGAAAGAAAAAGA-AATTGAA
1 A-AAAAGAAAAAGATAA-TGAA
349775 AAAAAGAA
1 AAAAAGAA
349783 TGAGAGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 11 0.46
21 12 0.50
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (20 bp):
AAAAAGAAAAAGATAATGAA
Found at i:364455 original size:21 final size:20
Alignment explanation
Indices: 364431--364481 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
364421 GTGATGTAGC
364431 TGCATTTGATTCTGGTGTGAA
1 TGCATTTGATT-TGGTGTGAA
* * *
364452 TGCATTTGGCTTTGTTGTGGA
1 TGCATTT-GATTTGGTGTGAA
364473 TGCATTTGA
1 TGCATTTGA
364482 GTGTGCTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 21 0.84
22 3 0.12
ACGTcount: A:0.16, C:0.10, G:0.29, T:0.45
Consensus pattern (20 bp):
TGCATTTGATTTGGTGTGAA
Found at i:365584 original size:25 final size:25
Alignment explanation
Indices: 365530--365578 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
365520 TTCCATAAAT
*
365530 GCTCCTCTTGTGTCGCACTTAGGAC
1 GCTCCTCTTGTGTCGCACTTAGAAC
365555 GCTCCTCTTGTGTCGCACTTAGAA
1 GCTCCTCTTGTGTCGCACTTAGAA
365579 TCCTCCGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.33
Consensus pattern (25 bp):
GCTCCTCTTGTGTCGCACTTAGAAC
Found at i:379488 original size:21 final size:21
Alignment explanation
Indices: 379472--379510 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
379462 ACTTTTTCTT
379472 TTATTT-GTTTT-AGTTTTAC
1 TTATTTCGTTTTAAGTTTTAC
379491 TTATTTCGTTTTAAGTTTTA
1 TTATTTCGTTTTAAGTTTTA
379511 TGCAGGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 5 0.28
21 7 0.39
ACGTcount: A:0.18, C:0.05, G:0.10, T:0.67
Consensus pattern (21 bp):
TTATTTCGTTTTAAGTTTTAC
Found at i:382320 original size:18 final size:18
Alignment explanation
Indices: 382292--382334 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
382282 TTTCAATCAC
*
382292 ATAAAAAGGAAAATG-AG
1 ATAAAAAGGAAAAAGAAG
382309 ATAAAGAAGGAAAAAGAAG
1 ATAAA-AAGGAAAAAGAAG
382328 ATAAAAA
1 ATAAAAA
382335 TTATGTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 5 0.22
18 11 0.48
19 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (18 bp):
ATAAAAAGGAAAAAGAAG
Found at i:397220 original size:22 final size:22
Alignment explanation
Indices: 397203--397251 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
397193 TGTTTTCTTC
397203 TTATTTTGCTACAATTTTATTA
1 TTATTTTGCTACAATTTTATTA
* * * *
397225 TTATGTTGCTACTATTTTGTTG
1 TTATTTTGCTACAATTTTATTA
397247 TTATT
1 TTATT
397252 GTTTGAATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.08, G:0.10, T:0.61
Consensus pattern (22 bp):
TTATTTTGCTACAATTTTATTA
Found at i:400022 original size:31 final size:29
Alignment explanation
Indices: 399984--400064 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 29
399974 TATATCAAAA
* *
399984 TTATACATTAATTATGGTTTAATATGTAA-T
1 TTATACATGAATTATGATTT--TATGTAACT
*
400014 TATATACATGAATTTTGATTTTATGTAACT
1 T-TATACATGAATTATGATTTTATGTAACT
*
400044 TTATACATGAAATTTTGATTT
1 TTATACATG-AATTATGATTT
400065 GATCCAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 15 0.33
30 14 0.31
31 16 0.36
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.51
Consensus pattern (29 bp):
TTATACATGAATTATGATTTTATGTAACT
Found at i:400038 original size:29 final size:30
Alignment explanation
Indices: 400006--400064 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
399996 TATGGTTTAA
400006 TATGTAA-TTATATACATG-AATTTTGATTT
1 TATGTAACTT-TATACATGAAATTTTGATTT
400035 TATGTAACTTTATACATGAAATTTTGATTT
1 TATGTAACTTTATACATGAAATTTTGATTT
400065 GATCCAATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 15 0.54
30 13 0.46
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (30 bp):
TATGTAACTTTATACATGAAATTTTGATTT
Found at i:400234 original size:31 final size:31
Alignment explanation
Indices: 400198--400291 Score: 84
Period size: 31 Copynumber: 3.1 Consensus size: 31
400188 AATATGTATT
400198 ATTGAATCAAAATAAAAATTTCAAGTATATA
1 ATTGAATCAAAATAAAAATTTCAAGTATATA
* * * * * *
400229 TTTGAACCACAATTAAAATTTCACGTTTATA
1 ATTGAATCAAAATAAAAATTTCAAGTATATA
* * * *
400260 ATTGTATC-AAAT-TAAAGTTCATGTATATA
1 ATTGAATCAAAATAAAAATTTCAAGTATATA
400289 ATT
1 ATT
400292 TCAAGTATAC
Statistics
Matches: 49, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 16 0.33
30 3 0.06
31 30 0.61
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (31 bp):
ATTGAATCAAAATAAAAATTTCAAGTATATA
Found at i:402962 original size:19 final size:19
Alignment explanation
Indices: 402929--402973 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
402919 ACTTTTATAT
*
402929 AATAAGATGTTTAAAAATTA
1 AATAA-ATGTCTAAAAATTA
*
402949 AATAAATGTCTAAACATTA
1 AATAAATGTCTAAAAATTA
*
402968 ACTAAA
1 AATAAA
402974 AATAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (19 bp):
AATAAATGTCTAAAAATTA
Found at i:403720 original size:140 final size:140
Alignment explanation
Indices: 403481--403793 Score: 572
Period size: 140 Copynumber: 2.2 Consensus size: 140
403471 TTTACATTTT
*
403481 AGTCACTCAACTTTGAAAATGTGACAAAACAGTTCTTTTTCACGTTTTTCGTCACAAACATCAAA
1 AGTCACTCAACTTTGAAAATGTGACAAAACAGTTCTTTTTCACGTTTTTCATCACAAACATCAAA
403546 GAACAGTGACATGGCAGTTGACGATGTCGGTGGAGTGTGGAAAACATCTAGCTGATCGGTTACAT
66 GAACAGTGACATGGCAGTTGACGATGTCGGTGGAGTGTGGAAAACATCTAGCTGATCGGTTACAT
403611 TTAACACAAC
131 TTAACACAAC
*
403621 AGTCACTCAACTTTGAAAATGTGACAAAACAGTTCTTTTTCACGTTTTTCATCACAGACATCAAA
1 AGTCACTCAACTTTGAAAATGTGACAAAACAGTTCTTTTTCACGTTTTTCATCACAAACATCAAA
**
403686 GAACAGTGACATGGCAGTTGACGATGTCGGTGGAGTGTGGAAAATGTCTAGCTGATCGGTTACAT
66 GAACAGTGACATGGCAGTTGACGATGTCGGTGGAGTGTGGAAAACATCTAGCTGATCGGTTACAT
403751 TTAACACAAC
131 TTAACACAAC
* *
403761 AGTCACTCAACTTTGAAAAAGTGACAGAACAGT
1 AGTCACTCAACTTTGAAAATGTGACAAAACAGT
403794 CACTGTTTAA
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 167 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (140 bp):
AGTCACTCAACTTTGAAAATGTGACAAAACAGTTCTTTTTCACGTTTTTCATCACAAACATCAAA
GAACAGTGACATGGCAGTTGACGATGTCGGTGGAGTGTGGAAAACATCTAGCTGATCGGTTACAT
TTAACACAAC
Found at i:404914 original size:41 final size:41
Alignment explanation
Indices: 404863--405103 Score: 275
Period size: 41 Copynumber: 5.8 Consensus size: 41
404853 TTAACCATAT
*
404863 TCTCATTCTCATCTCGAGACATGAGTCTTTCTTAATCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
* * * *
404904 TCTCATTCTCATTTCGAGACATGAGTCTTCCTTATTCATAG
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
*
404945 TCTCATTCTCATCTTGAGACATGAGTCTTCCTTAATCAAAA
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
* * * * *
404986 TCTCATTCTCATTTTGAGACATGAGTCTTCCTTATTCATAG
1 TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
* * * ***
405027 TCTCATTCTCATCTCTAGACATGGGTCTTCCATTTATACAGTT
1 TCTCATTCTCATCTCGAGACATGAGTCTTCC-TTAAT-CAAAA
* * *
405070 TCTCATGCTCAAACTCAAGACATGAGTCTTCCTT
1 TCTCATTCTC-ATCTCGAGACATGAGTCTTCCTT
405104 TTTATACACC
Statistics
Matches: 170, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
41 136 0.80
42 3 0.02
43 13 0.08
44 18 0.11
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.39
Consensus pattern (41 bp):
TCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAA
Found at i:404964 original size:82 final size:82
Alignment explanation
Indices: 404858--405057 Score: 339
Period size: 82 Copynumber: 2.4 Consensus size: 82
404848 TTCTTTTAAC
* * *
404858 CATATTCTCATTCTCATCTCGAGACATGAGTCTTTCTTAATCAAAATCTCATTCTCATTTCGAGA
1 CATAGTCTCATTCTCATCTTGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGA
404923 CATGAGTCTTCCTTATT
66 CATGAGTCTTCCTTATT
*
404940 CATAGTCTCATTCTCATCTTGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATTTTGAGA
1 CATAGTCTCATTCTCATCTTGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGA
405005 CATGAGTCTTCCTTATT
66 CATGAGTCTTCCTTATT
*
405022 CATAGTCTCATTCTCATCTCT-AGACATGGGTCTTCC
1 CATAGTCTCATTCTCATCT-TGAGACATGAGTCTTCC
405058 ATTTATACAG
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
82 111 0.99
83 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (82 bp):
CATAGTCTCATTCTCATCTTGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCATTTCGAGA
CATGAGTCTTCCTTATT
Found at i:405928 original size:22 final size:21
Alignment explanation
Indices: 405881--405928 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
405871 GACTTTCATA
* *
405881 ATTAACTTAATTAATCTTCTT
1 ATTAACTTAATTAATCCTATT
* *
405902 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCCTATT
405924 ATTAA
1 ATTAA
405929 TCTATATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTAACTTAATTAATCCTATT
Found at i:412095 original size:41 final size:41
Alignment explanation
Indices: 412027--412285 Score: 259
Period size: 41 Copynumber: 6.2 Consensus size: 41
412017 TCCAATCATA
* * * *
412027 AGTCTTCCTTTAACCATATTCTCATTCTCATCTCGAGATATG
1 AGTCTTCC-TTAATCAAAATCTCATTCTCATCTCGAGACATG
* * *
412069 AGTCTTTCTTAATCAAAATCCCATTCTCAT-TCGAGATATG
1 AGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATG
* * * *
412109 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCAAGACATG
1 AGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATG
* *
412150 AGTCTTCCTTAATCAAAATCTCATTATCATTTCGAGACATG
1 AGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATG
* * * * *
412191 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCGAAACACG
1 AGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATG
* ** * * *
412232 AGTCTTCCATTTATACAATTTCTCATGCTCAAACCCGAGACATG
1 AGTCTTCC-TTAAT-CAAAATCTCATTCTC-ATCTCGAGACATG
412276 AGTCTTCCTT
1 AGTCTTCCTT
412286 TTTATACACC
Statistics
Matches: 178, Mismatches: 35, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
40 35 0.20
41 103 0.58
42 10 0.06
43 13 0.07
44 17 0.10
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (41 bp):
AGTCTTCCTTAATCAAAATCTCATTCTCATCTCGAGACATG
Found at i:412137 original size:81 final size:82
Alignment explanation
Indices: 412027--412239 Score: 311
Period size: 82 Copynumber: 2.6 Consensus size: 82
412017 TCCAATCATA
** * * *
412027 AGTCTTCCTTTAACCATATTCTCATTCTCATCTCGAGATATGAGTCTTTCTTAATCAAAATCCCA
1 AGTCTTCC-TTATTCATAGTCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCCCA
* *
412092 TTCTCA-TTCGAGATATG
65 TTATCATTTCGAGACATG
* *
412109 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCAAGACATGAGTCTTCCTTAATCAAAATCTCAT
1 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCCCAT
412174 TATCATTTCGAGACATG
66 TATCATTTCGAGACATG
* *
412191 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCGAAACACGAGTCTTCC
1 AGTCTTCCTTATTCATAGTCTCATTCTCATCTCGAGACATGAGTCTTCC
412240 ATTTATACAA
Statistics
Matches: 118, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
81 54 0.46
82 64 0.54
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (82 bp):
AGTCTTCCTTATTCATAGTCTCATTCTCATCTCGAGACATGAGTCTTCCTTAATCAAAATCCCAT
TATCATTTCGAGACATG
Found at i:413130 original size:22 final size:21
Alignment explanation
Indices: 413083--413130 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
413073 GACTTTCATA
*
413083 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
413104 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
413126 ATTAA
1 ATTAA
413131 TCAATATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:413530 original size:12 final size:12
Alignment explanation
Indices: 413513--413543 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
413503 TGATAACAAC
413513 TGGGGCTGCAAA
1 TGGGGCTGCAAA
413525 TGGGGCTGCAAA
1 TGGGGCTGCAAA
*
413537 TGTGGCT
1 TGGGGCT
413544 AGTCCCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.42, T:0.23
Consensus pattern (12 bp):
TGGGGCTGCAAA
Found at i:414461 original size:30 final size:31
Alignment explanation
Indices: 414394--414464 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 31
414384 TTAGAATAAC
414394 AGTGACTGTTTTGTCACTTTTCGATAACGTT
1 AGTGACTGTTTTGTCACTTTTCGATAACGTT
414425 AGTGACTGTTTTGTCACATTTTC-A-AA-GTT
1 AGTGACTGTTTTGTCAC-TTTTCGATAACGTT
414454 GAGTGACTGTT
1 -AGTGACTGTT
414465 GTGTTAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.32
31 18 0.47
32 5 0.13
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTCGATAACGTT
Found at i:414969 original size:6 final size:6
Alignment explanation
Indices: 414958--414992 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
414948 ACACCTCTCT
414958 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
414993 TTCCCTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTTCA
Found at i:415685 original size:39 final size:39
Alignment explanation
Indices: 415640--415719 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
415630 CGACAGGACT
*
415640 CTCAATAACTTTTGACTTTGTTCATTGAAAAGGGTGTTG
1 CTCAATAACTTTTGACTTCGTTCATTGAAAAGGGTGTTG
415679 CTCAATAACTTTTGACTTCGTTCATTGAAAAGGGTGTTG
1 CTCAATAACTTTTGACTTCGTTCATTGAAAAGGGTGTTG
415718 CT
1 CT
415720 TTCCGGTGGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (39 bp):
CTCAATAACTTTTGACTTCGTTCATTGAAAAGGGTGTTG
Found at i:421925 original size:53 final size:53
Alignment explanation
Indices: 421868--421976 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
421858 ACGAGGTGAG
421868 CATTAACTTATAATCAAAATTATATGATGCCACAATTACTTAACATGCCAATT
1 CATTAACTTATAATCAAAATTATATGATGCCACAATTACTTAACATGCCAATT
421921 CATTAACTTATAATCAAAATTATATGATGCCACAATTACTTAACATGCCAATT
1 CATTAACTTATAATCAAAATTATATGATGCCACAATTACTTAACATGCCAATT
421974 CAT
1 CAT
421977 GTCATTTTAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (53 bp):
CATTAACTTATAATCAAAATTATATGATGCCACAATTACTTAACATGCCAATT
Found at i:422814 original size:94 final size:94
Alignment explanation
Indices: 422698--422887 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
422688 TTATGAGTAT
422698 GTTTCTTGGATTATTATGTAATAGTCTCAATATTACTCATAGTGATAACTATGTATATGATTTTC
1 GTTTCTTGGATTATTATGTAATAGTCTCAATATTACTCATAGTGATAACTATGTATATGATTTTC
422763 AGACTTGAGATCATCATTGTCCCAATATC
66 AGACTTGAGATCATCATTGTCCCAATATC
422792 GTTTCTTGGATTATTATGTAATAGTCTCAATATTACTCATAGTGATAACTATGTATATGATTTTC
1 GTTTCTTGGATTATTATGTAATAGTCTCAATATTACTCATAGTGATAACTATGTATATGATTTTC
422857 AGACTTGAGATCATCATTGTCCCAATATC
66 AGACTTGAGATCATCATTGTCCCAATATC
422886 GT
1 GT
422888 GAGTCATATA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (94 bp):
GTTTCTTGGATTATTATGTAATAGTCTCAATATTACTCATAGTGATAACTATGTATATGATTTTC
AGACTTGAGATCATCATTGTCCCAATATC
Found at i:423977 original size:138 final size:138
Alignment explanation
Indices: 423515--424071 Score: 840
Period size: 138 Copynumber: 4.1 Consensus size: 138
423505 GAGAACATAG
* *
423515 ATATAATTAATATATGAATTTGATTCATACCAAATATTAATTATATATATTTTA-CAGAA--T-T
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCA-AATTTAT
* *
423576 T-ATATAAACAATTATATTAATTAATTTC-GATCAAAATATAAAATATATGAAAATTAATATTCT
65 TAATATAAACAATTATATTAATTAATTTCAG-TCAAAATATAAAAAACATGAAAATTAATATTCT
423639 TTTGGAAAGA
129 TTTGGAAAGA
* *
423649 ATATAATTAGTATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAACAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
* **
423714 AATATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAACACATGAAAATTGCTATTCTT
66 AATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAA-ACATGAAAATTAATATTCTT
*
423779 TTGGAAATA
130 TTGGAAAGA
* *
423788 ATATAATTAACATATGAATTTGATTCATACAAAATATTAATTGTATGTATTTTACCGAAA-TTAT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACC-AAATTTAT
* *
423852 TAATATAAACAATTATATTAATTAATTTCAGTCAAAATCTAAAAGACATGAAAATTAATATTCTT
65 TAATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAAACATGAAAATTAATATTCTT
423917 TTGGAAAGA
130 TTGGAAAGA
*
423926 ATATAATTAATATATGAATTTGATTCATACAAAATGTTAATTGTATATATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
* * * * * *
423991 AATATAAATAGTTGTATTTATTAATTTCAGTCAAAATATAAAAAATATGAAAATTAATATTCTTC
66 AATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAAACATGAAAATTAATATTCTTT
424056 TGGAAAGA
131 TGGAAAGA
424064 ATATAATT
1 ATATAATT
424072 GTAAAAGAAT
Statistics
Matches: 384, Mismatches: 30, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
134 53 0.14
135 2 0.01
136 1 0.00
137 5 0.01
138 196 0.51
139 124 0.32
140 3 0.01
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
AATATAAACAATTATATTAATTAATTTCAGTCAAAATATAAAAAACATGAAAATTAATATTCTTT
TGGAAAGA
Found at i:424016 original size:277 final size:272
Alignment explanation
Indices: 423515--424071 Score: 882
Period size: 277 Copynumber: 2.0 Consensus size: 272
423505 GAGAACATAG
* *
423515 ATATAATTAATATATGAATTTGATTCATACCAAATATTAATTATATATATTTTACAGAATTTATA
1 ATATAATTAACATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACAGAATTTATA
* *
423580 TAAACAATTATATTAATTAATTTCGATCAAAATATAAAATATATGAAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
*
423645 AAGAATATAATTAGTATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAACAAATT
131 AAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAACAAATT
**
423710 TATTAATATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAACACATGAAAATTGCTAT
196 TATTAATATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAA-ACATGAAAATTAATAT
* *
423775 TCTTTTGGAAATA
260 TCTTCTGGAAAGA
* * *
423788 ATATAATTAACATATGAATTTGATTCATACAAAATATTAATTGTATGTATTTTACCGAAATTATT
1 ATATAATTAACATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACAG-AA-T-TT
*
423853 AATATAAACAATTATATTAATTAATTTC-AGTCAAAATCTAAAAGACATGAAAATTAATATTCTT
63 -ATATAAACAATTATATTAATTAATTTCGA-TCAAAATATAAAAGACATGAAAATTAATATTCTT
* *
423917 TTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATGTTAATTGTATATATTTTACC
126 TTGGAAAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAAC
* * * *
423982 AAATTTATTAATATAAATAGTTGTATTTATTAATTTCAGTCAAAATATAAAAAATATGAAAATTA
191 AAATTTATTAATATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAAACATGAAAATTA
424047 ATATTCTTCTGGAAAGA
256 ATATTCTTCTGGAAAGA
424064 ATATAATT
1 ATATAATT
424072 GTAAAAGAAT
Statistics
Matches: 260, Mismatches: 19, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
273 52 0.20
274 2 0.01
275 1 0.00
276 35 0.13
277 170 0.65
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (272 bp):
ATATAATTAACATATGAATTTGATTCATACAAAATATTAATTATATATATTTTACAGAATTTATA
TAAACAATTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
AAGAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTAACAAATT
TATTAATATAAACAGTTATATTAATTAATTTCAGTCAAAATATAAAAAACATGAAAATTAATATT
CTTCTGGAAAGA
Found at i:424793 original size:36 final size:36
Alignment explanation
Indices: 424710--424949 Score: 205
Period size: 36 Copynumber: 6.7 Consensus size: 36
424700 TCAGTGGAAA
** * * *
424710 GCTTACGTCTCGGTTAGAGCATAATGCTTTGTGACT
1 GCTTACGTCTCAATTAGAGCATAATGCTATGTAATT
* * * *
424746 GCATACATCTCAATTAGAGCGTATTGCTATGTAATT
1 GCTTACGTCTCAATTAGAGCATAATGCTATGTAATT
* * * *
424782 GCTTACGTCTCAGTTAGAGCGTAATGCTATATGATT
1 GCTTACGTCTCAATTAGAGCATAATGCTATGTAATT
* * * * *
424818 GCATATGTCTTAATTAGAGCGTATTGCTAAT-TAATT
1 GCTTACGTCTCAATTAGAGCATAATGCT-ATGTAATT
* *
424854 GCTTACGTCTCGATTAGAGCATAATGCTAAG-AGATT
1 GCTTACGTCTCAATTAGAGCATAATGCTATGTA-ATT
* * *
424890 GCATACGTCTCAATTAGAGCATAATGCTAAGTGATT
1 GCTTACGTCTCAATTAGAGCATAATGCTATGTAATT
* * **
424926 GCTTATGTATCGGTTAGAGCATAA
1 GCTTACGTCTCAATTAGAGCATAA
424950 GGCCATTTCA
Statistics
Matches: 164, Mismatches: 36, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
35 2 0.01
36 160 0.98
37 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (36 bp):
GCTTACGTCTCAATTAGAGCATAATGCTATGTAATT
Done.