Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005343.1 Hibiscus syriacus cultivar Beakdansim tig00012103_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: 91994
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10021 original size:12 final size:12
Alignment explanation
Indices: 10004--10042 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 12
9994 AAGGTTGTGA
10004 TTTGGTATTCCC
1 TTTGGTATTCCC
10016 TTTGGTTGATTGCCC
1 TTTGG-T-ATT-CCC
10031 TTTGGTATTCCC
1 TTTGGTATTCCC
10043 ATTTAGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 8 0.33
13 4 0.17
14 4 0.17
15 8 0.33
ACGTcount: A:0.08, C:0.23, G:0.21, T:0.49
Consensus pattern (12 bp):
TTTGGTATTCCC
Found at i:12353 original size:2 final size:2
Alignment explanation
Indices: 12346--12396 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
12336 TTTTATGAAC
12346 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
12388 AT AT AT AT A
1 AT AT AT AT A
12397 GTTATAAGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24686 original size:64 final size:65
Alignment explanation
Indices: 24605--24736 Score: 239
Period size: 64 Copynumber: 2.0 Consensus size: 65
24595 GAAGCACCAA
* *
24605 CGAGCGGGAAAAGAAGAATCTGATTCTTTCGGCTGGTTGCATCTACGATGATTGGGATGTGAATC
1 CGAGCGGGAAAAAAAGAATCTGATTCTTTCGGCTGGTTGCATCTACGACGATTGGGATGTGAATC
24670 CGAGC-GGAAAAAAAGAATCTGATTCTTTCGGCTGGTTGCATCTACGACGATTGGGATGTGAATC
1 CGAGCGGGAAAAAAAGAATCTGATTCTTTCGGCTGGTTGCATCTACGACGATTGGGATGTGAATC
24734 CGA
1 CGA
24737 ACAGTGAATG
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 60 0.92
65 5 0.08
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (65 bp):
CGAGCGGGAAAAAAAGAATCTGATTCTTTCGGCTGGTTGCATCTACGACGATTGGGATGTGAATC
Found at i:25381 original size:23 final size:23
Alignment explanation
Indices: 25339--25382 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
25329 GTTATATCTA
*
25339 TATTTTATATTATATGTATTATT
1 TATTTTATATTATATATATTATT
* *
25362 TATTTTATTTTATTTATATTA
1 TATTTTATATTATATATATTA
25383 ATGTACTCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TATTTTATATTATATATATTATT
Found at i:26184 original size:15 final size:16
Alignment explanation
Indices: 26147--26184 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
26137 TGAACAACAT
26147 ATAAAATTGTATGTAA
1 ATAAAATTGTATGTAA
*
26163 TTAAAATTGTAT-TAA
1 ATAAAATTGTATGTAA
26178 ATAAAAT
1 ATAAAAT
26185 ATTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (16 bp):
ATAAAATTGTATGTAA
Found at i:26923 original size:16 final size:16
Alignment explanation
Indices: 26902--26936 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
26892 ATTTATTATT
26902 TATTATTTACGTTACA
1 TATTATTTACGTTACA
* *
26918 TATTATTTGCGTTATA
1 TATTATTTACGTTACA
26934 TAT
1 TAT
26937 AACTTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (16 bp):
TATTATTTACGTTACA
Found at i:27896 original size:23 final size:23
Alignment explanation
Indices: 27865--27909 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
27855 CTCAAACTAG
27865 ATTTATTTTATTAAATAGTTTAA
1 ATTTATTTTATTAAATAGTTTAA
*
27888 ATTTCTTTTATTAAATAGTTTA
1 ATTTATTTTATTAAATAGTTTA
27910 GAGTGGTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (23 bp):
ATTTATTTTATTAAATAGTTTAA
Found at i:30132 original size:40 final size:40
Alignment explanation
Indices: 30078--30167 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
30068 AAATAAACTG
* * * *
30078 AATAAA-ATAATAAATCAAAGTAAGATATAATAATACAAT
1 AATAAAGATGATAAATAAAAGCAAGATATAACAATACAAT
*
30117 AATAAAGATGATAAATAAAAGCAAGATATGACAATACAAT
1 AATAAAGATGATAAATAAAAGCAAGATATAACAATACAAT
30157 AATAAAGATGA
1 AATAAAGATGA
30168 ATATTTACCG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 6 0.13
40 39 0.87
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.22
Consensus pattern (40 bp):
AATAAAGATGATAAATAAAAGCAAGATATAACAATACAAT
Found at i:32668 original size:31 final size:31
Alignment explanation
Indices: 32626--32689 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
32616 AAGTGACTAC
*
32626 ATCTTAGTTAAATAAAAA-CGAAATTGACCAA
1 ATCTTAATTAAATAAAAATCGAAA-TGACCAA
*
32657 ATCTTAATTAAATAAAAATGGAAATGACCAA
1 ATCTTAATTAAATAAAAATCGAAATGACCAA
32688 AT
1 AT
32690 ATTATGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.87
32 4 0.13
ACGTcount: A:0.53, C:0.11, G:0.09, T:0.27
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAATCGAAATGACCAA
Found at i:35839 original size:45 final size:44
Alignment explanation
Indices: 35771--35873 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 44
35761 TGCACAGGAA
* * *
35771 GTGCATCGATGCACCTATTAAAATGGAAACATCGAATGCAATTG
1 GTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTG
* ** *
35815 GTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTGATTT
1 GTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTG
35860 GTGCATCGATGCAC
1 GTGCATCGATGCAC
35874 GGGTACTGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 14 0.27
45 37 0.73
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (44 bp):
GTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTG
Found at i:35926 original size:20 final size:20
Alignment explanation
Indices: 35861--35937 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
35851 AGGTGATTTG
* * *
35861 TGCATCGATGCACGGGT-AC
1 TGCATCGATGCACTGTTGAA
*
35880 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TG-T--TGAA
35904 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
35924 TGCATCGATGCACT
1 TGCATCGATGCACT
35938 TCAAGGGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 13 0.27
20 18 0.38
22 1 0.02
23 2 0.04
24 14 0.29
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (20 bp):
TGCATCGATGCACTGTTGAA
Found at i:36685 original size:2 final size:2
Alignment explanation
Indices: 36678--36722 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
36668 AGTATACGTG
*
36678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36720 AT A
1 AT A
36723 AGTTATTGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:37123 original size:30 final size:30
Alignment explanation
Indices: 37078--37180 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
37068 GGTTCTTCGG
* *
37078 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
37108 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
37138 GACCTCTGGATAGTTACCGAAGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
37168 GACCTCTGGATAG
1 GACCTCTGGATAG
37181 GTCCTTCGGG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:38880 original size:17 final size:17
Alignment explanation
Indices: 38844--38891 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
38834 GTTACAAAAT
*
38844 AATATAATATTATAACA
1 AATATAAAATTATAACA
* *
38861 AATATAAAATTTTAATA
1 AATATAAAATTATAACA
*
38878 AATTTAACAATTAT
1 AATATAA-AATTAT
38892 TTTATAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAAAATTATAACA
Found at i:38898 original size:31 final size:31
Alignment explanation
Indices: 38863--38947 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 31
38853 TTATAACAAA
38863 TATAA-AATTTTAAT-AAATTTAACAATTATTT
1 TATAATAA-TTTAATAAAATTTAA-AATTATTT
38894 TATAATAATTTAATAAAATTTAAAATTATTT
1 TATAATAATTTAATAAAATTTAAAATTATTT
* * **
38925 TAAAATTATTTGGTAAAATTTAA
1 TATAATAATTTAATAAAATTTAA
38948 TTACTATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 38 0.79
32 10 0.21
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (31 bp):
TATAATAATTTAATAAAATTTAAAATTATTT
Found at i:38911 original size:42 final size:41
Alignment explanation
Indices: 38864--38948 Score: 100
Period size: 42 Copynumber: 2.0 Consensus size: 41
38854 TATAACAAAT
* *
38864 ATAAAATTT-TAATAAATTTAACAATTATTTTATAATAATTTA
1 ATAAAATTTAAAATAAATTTAA-AATTATTTGATAA-AATTTA
* * *
38906 ATAAAATTTAAAATTATTTTAAAATTATTTGGTAAAATTTA
1 ATAAAATTTAAAATAAATTTAAAATTATTTGATAAAATTTA
38947 AT
1 AT
38949 TACTATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 8 0.22
42 20 0.54
43 9 0.24
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (41 bp):
ATAAAATTTAAAATAAATTTAAAATTATTTGATAAAATTTA
Found at i:39072 original size:20 final size:21
Alignment explanation
Indices: 39013--39081 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 21
39003 ATAATTAAAA
39013 TAAT-TATTTAAAT-ATGA-TT
1 TAATATATTTAAATGAT-ATTT
*
39032 TAATA-ATTAAAATGATATTT
1 TAATATATTTAAATGATATTT
*
39052 TAGTATATTTAAATGAT-TTT
1 TAATATATTTAAATGATATTT
39072 TAATATATTT
1 TAATATATTT
39082 TTATCCAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 12 0.29
20 20 0.48
21 10 0.24
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
TAATATATTTAAATGATATTT
Found at i:46675 original size:33 final size:33
Alignment explanation
Indices: 46633--46700 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
46623 GTTAACATAC
* *
46633 TTCTTAGTATGTGAATGAATATGAAGGGAGTTT
1 TTCTTAGTATGTGAACGAATACGAAGGGAGTTT
46666 TTCTTAGTATGTGAACGAATACGAAGGGAGTTT
1 TTCTTAGTATGTGAACGAATACGAAGGGAGTTT
46699 TT
1 TT
46701 AATGAGACCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.38
Consensus pattern (33 bp):
TTCTTAGTATGTGAACGAATACGAAGGGAGTTT
Found at i:47404 original size:2 final size:2
Alignment explanation
Indices: 47397--47421 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47387 TGTCATTTCC
47397 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
47422 TGATAGGATG
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:53429 original size:33 final size:33
Alignment explanation
Indices: 53392--53486 Score: 91
Period size: 33 Copynumber: 2.9 Consensus size: 33
53382 TTGTTCCGGA
* *
53392 CAAGTAGCAGGGATGATGCCCCCACATGCAGCC
1 CAAGTAGCAGCGATGATGCCCCCACAAGCAGCC
* * * * *
53425 CAAGTAGTAGCAATGATGCCCCTATAAGCAGGC
1 CAAGTAGCAGCGATGATGCCCCCACAAGCAGCC
* * * *
53458 CTAGTAGCAGTGATGATGCCTCCATAAGC
1 CAAGTAGCAGCGATGATGCCCCCACAAGC
53487 TGGTTAAATA
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.18
Consensus pattern (33 bp):
CAAGTAGCAGCGATGATGCCCCCACAAGCAGCC
Found at i:55704 original size:60 final size:60
Alignment explanation
Indices: 55625--55790 Score: 158
Period size: 60 Copynumber: 2.8 Consensus size: 60
55615 ATTCTCATTT
* * ** * * * *
55625 TAAATTAGTCTTTAAACTTTTAAATGTTTCAATTTCGTCTCTAAACTATGA-CTATAATTC
1 TAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCCAAACCATGACCT-TAATTC
* * *
55685 TAAATTAGTCCTCAAACTTTTGAACATTTCAATTTCATCCCCAAACCATTACCTTCATTC
1 TAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCCAAACCATGACCTTAATTC
* * *
55745 TAAATTGGTCCCCAAACTTTTTTAACA-TTCTAATTTCAT-CCCAAAC
1 TAAATTAGTCCTCAAAC-TTTTAAACATTTC-AATTTCATCCCCAAAC
55791 TATACGATAT
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
60 71 0.80
61 18 0.20
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.40
Consensus pattern (60 bp):
TAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCCCCAAACCATGACCTTAATTC
Found at i:58756 original size:16 final size:16
Alignment explanation
Indices: 58735--58765 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
58725 TTGTACCTGC
58735 AAGTATTGACATAAAA
1 AAGTATTGACATAAAA
58751 AAGTATTGACATAAA
1 AAGTATTGACATAAA
58766 TGTTCCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (16 bp):
AAGTATTGACATAAAA
Found at i:68710 original size:19 final size:19
Alignment explanation
Indices: 68686--68722 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
68676 ATGACCAACA
*
68686 AAATCGCAATGTGATCTCT
1 AAATCGCAACGTGATCTCT
68705 AAATCGCAACGTGATCTC
1 AAATCGCAACGTGATCTC
68723 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (19 bp):
AAATCGCAACGTGATCTCT
Found at i:68828 original size:21 final size:21
Alignment explanation
Indices: 68804--68879 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
68794 TGAATATGTA
68804 AATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
* **
68825 AATCGTAACGCGATTCTGAC-T
1 AATCGCAACGCGATAAT-ACAT
68846 -ATCGCAACGCGATAATACAT
1 AATCGCAACGCGATAATACAT
*
68866 AAGCGCAACGCGAT
1 AATCGCAACGCGAT
68880 TCTAACTATC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
19 2 0.04
20 14 0.31
21 27 0.60
22 2 0.04
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (21 bp):
AATCGCAACGCGATAATACAT
Found at i:68854 original size:20 final size:20
Alignment explanation
Indices: 68826--68936 Score: 125
Period size: 20 Copynumber: 5.5 Consensus size: 20
68816 ATAATACATA
*
68826 ATCGTAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
68846 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* *
68866 AAGCGCAACGCGATTCTAACT
1 -ATCGCAACGCGATTCTGACT
68887 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
68907 GTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
68927 GTCGTAACGC
1 ATCGCAACGC
68937 TGAATTTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 60 0.77
21 14 0.18
22 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:68862 original size:41 final size:41
Alignment explanation
Indices: 68805--68899 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
68795 GAATATGTAA
* * *
68805 ATCGCAACGCGATAATACATAATCGTAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAAGCGCAACGCGATTCTAACT
68846 ATCGCAACGCGATAATACATAAGCGCAACGCGATTCTAACT
1 ATCGCAACGCGATAATACATAAGCGCAACGCGATTCTAACT
68887 ATCGCAACGCGAT
1 ATCGCAACGCGAT
68900 TCTGACTGTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGATAATACATAAGCGCAACGCGATTCTAACT
Found at i:69788 original size:24 final size:24
Alignment explanation
Indices: 69756--69809 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
69746 GTATTCGAAA
69756 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
69780 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
69804 TTTGAT
1 TTTGAT
69810 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:70028 original size:14 final size:14
Alignment explanation
Indices: 69999--70035 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
69989 AGAAAAAGAA
69999 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
70014 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
70028 GAAGAAAA
1 GAAGAAAA
70036 TACCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:72080 original size:12 final size:12
Alignment explanation
Indices: 72065--72095 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
72055 CAAGAAAAAG
72065 GCAATCAAAATC
1 GCAATCAAAATC
72077 GCAATCAAAATC
1 GCAATCAAAATC
72089 GCAATCA
1 GCAATCA
72096 CAACCGGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:72405 original size:140 final size:140
Alignment explanation
Indices: 72153--72435 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
72143 GCAAACGTTG
*
72153 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTATGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
72218 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
72283 CGAATTTGAC
131 CGAATTTGAC
*
72293 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAAGTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
72358 TTGAACATTGCTATGATATGTTTAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAATG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
72423 TGAATTTGAC
131 CGAATTTGAC
72433 TAT
1 TAT
72436 CGCAACTCAA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.45
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:72473 original size:20 final size:20
Alignment explanation
Indices: 72448--72570 Score: 134
Period size: 20 Copynumber: 6.5 Consensus size: 20
72438 CAACTCAAAA
*
72448 ATCGCAACGCAAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
72468 ATCGCAACACGAATATGACT
1 ATCGCAACGCGAATTTGACT
*
72488 ATCGCAACGC-AA----A-A
1 ATCGCAACGCGAATTTGACT
72502 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* *
72522 ATCGCAACGTGAATTTGATT
1 ATCGCAACGCGAATTTGACT
72542 ATCGCAACAG-GAATTTGACT
1 ATCGCAAC-GCGAATTTGACT
72562 ATCGCAACG
1 ATCGCAACG
72571 AGAAAAACGC
Statistics
Matches: 87, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.11
15 3 0.03
19 4 0.05
20 69 0.79
21 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:72488 original size:54 final size:54
Alignment explanation
Indices: 72406--72549 Score: 216
Period size: 54 Copynumber: 2.7 Consensus size: 54
72396 TTACACATTC
* * *
72406 ATTTGAATATCGCAATGTGAATTTGACTATCGCAACTCAAAAATCGCAACGCAA
1 ATTTGACTATCGCAACGTGAATTTGACTATCGCAACGCAAAAATCGCAACGCAA
** * *
72460 ATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCGA
1 ATTTGACTATCGCAACGTGAATTTGACTATCGCAACGCAAAAATCGCAACGCAA
*
72514 ATTTGACTATCGCAACGTGAATTTGATTATCGCAAC
1 ATTTGACTATCGCAACGTGAATTTGACTATCGCAAC
72550 AGGAATTTGA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (54 bp):
ATTTGACTATCGCAACGTGAATTTGACTATCGCAACGCAAAAATCGCAACGCAA
Found at i:72492 original size:40 final size:39
Alignment explanation
Indices: 72448--72570 Score: 148
Period size: 40 Copynumber: 3.2 Consensus size: 39
72438 CAACTCAAAA
*
72448 ATCGCAACGCAAATTTGACTATCGCAACACGAATATGACT
1 ATCGCAACGCAAATTTGA-TATCGCAACACGAATTTGACT
*
72488 ATCGCAACGCAAA----A-ATCGCAACGCGAATTTGACT
1 ATCGCAACGCAAATTTGATATCGCAACACGAATTTGACT
** *
72522 ATCGCAACGTGAATTTGATTATCGCAACAGGAATTTGACT
1 ATCGCAACGCAAATTTGA-TATCGCAACACGAATTTGACT
72562 ATCGCAACG
1 ATCGCAACG
72571 AGAAAAACGC
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
34 29 0.41
36 1 0.01
38 1 0.01
40 40 0.56
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (39 bp):
ATCGCAACGCAAATTTGATATCGCAACACGAATTTGACT
Found at i:72610 original size:74 final size:74
Alignment explanation
Indices: 72448--72619 Score: 206
Period size: 74 Copynumber: 2.3 Consensus size: 74
72438 CAACTCAAAA
* * *
72448 ATCGCAACGCAAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAAACGCAAAGCG
*
72513 AATTTGACT
66 AATTAGACT
* * * *
72522 ATCGCAACGTGAATTTGATTATCGCAACAGGAATTTGACTATCGCAACG-AGAAAAACGCAAAGC
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCA-AAAAACGCAAAGC
72586 -ATATTAGACT
65 GA-ATTAGACT
* * *
72596 ATCGTAATGCGAA-TTGACTTTCGC
1 ATCGCAACGCGAATTTGACTATCGC
72620 GTTGCGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
73 11 0.13
74 72 0.87
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAAAACGCAAAGCG
AATTAGACT
Found at i:72657 original size:40 final size:40
Alignment explanation
Indices: 72609--72705 Score: 158
Period size: 40 Copynumber: 2.4 Consensus size: 40
72599 GTAATGCGAA
*
72609 TTGACTTTCGCGTTGCGATTTTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATTTTGACTTTCGCATTGCGATT
*
72649 TTGACTTTCGCATTGCGATTTTGACTTTCGCATTGCGATT
1 TTGACTTTCGCGTTGCGATTTTGACTTTCGCATTGCGATT
* *
72689 TTGAGTTTAGCGTTGCG
1 TTGACTTTCGCGTTGCG
72706 GAAGTGTATC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (40 bp):
TTGACTTTCGCGTTGCGATTTTGACTTTCGCATTGCGATT
Found at i:72705 original size:20 final size:20
Alignment explanation
Indices: 72609--72692 Score: 150
Period size: 20 Copynumber: 4.2 Consensus size: 20
72599 GTAATGCGAA
*
72609 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCGATT
*
72629 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
72649 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
72669 TTGACTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCGATT
72689 TTGA
1 TTGA
72693 GTTTAGCGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGACTTTCGCATTGCGATT
Found at i:72822 original size:36 final size:36
Alignment explanation
Indices: 72781--72889 Score: 119
Period size: 36 Copynumber: 3.3 Consensus size: 36
72771 TTACATTTCA
72781 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
* * *
72817 ATCAA-T---TAA--ACAAAT--CAACT-TTTACAA
1 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
*
72844 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
72880 ATCAATTAAA
1 ATCAATTAAA
72890 CAAATCAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
27 11 0.19
28 4 0.07
30 6 0.11
31 2 0.04
32 3 0.05
33 6 0.11
35 4 0.07
36 21 0.37
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.28
Consensus pattern (36 bp):
ATCAATTAAATAAGCACAAATAAGAATTATTTACAC
Found at i:72842 original size:27 final size:27
Alignment explanation
Indices: 72810--72919 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
72800 ATAAGAATTA
*
72810 TTTACACATCAATTAAACAAATCAACT
1 TTTACAAATCAATTAAACAAATCAACT
* *
72837 TTTACAAATCAATTAAACAAGCACAAATAAGAATT
1 TTTACAAATCAATT----AA--ACAAAT--CAACT
*
72872 ATTTACACATCAATTAAACAAATCAACT
1 -TTTACAAATCAATTAAACAAATCAACT
*
72900 TTTACAAAACAATTAAACAA
1 TTTACAAATCAATTAAACAA
72920 GCAAAAAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
27 31 0.47
28 3 0.05
30 6 0.09
31 2 0.03
32 2 0.03
33 6 0.09
35 3 0.05
36 13 0.20
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.27
Consensus pattern (27 bp):
TTTACAAATCAATTAAACAAATCAACT
Found at i:72866 original size:63 final size:63
Alignment explanation
Indices: 72758--72922 Score: 276
Period size: 63 Copynumber: 2.6 Consensus size: 63
72748 GATTGAAATC
*
72758 AACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAAT
1 AACAAATCAACTTTTACA----AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAAT
72823 TA
62 TA
72825 AACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
*
72888 AACAAATCAACTTTTACAAAACAATTAAACAAGCA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCA
72923 AAAAATGCTA
Statistics
Matches: 96, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
63 78 0.81
67 18 0.19
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.27
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATTA
Found at i:74356 original size:42 final size:42
Alignment explanation
Indices: 74297--74390 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 42
74287 ATGAATCGGG
**
74297 CTCTTGAATAGTGGGA-GGGACCTCTTCAACG-ATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTT-AACGAATGACAGGGGC
* * *
74339 CTCTTGAACGGTGGGAGGGGACTCTTGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTAACGAATGACAGGGGC
74381 CTCTTGAACG
1 CTCTTGAACG
74391 ATGACAGGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
41 2 0.04
42 39 0.87
43 4 0.09
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTAACGAATGACAGGGGC
Found at i:74357 original size:21 final size:21
Alignment explanation
Indices: 74297--74366 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
74287 ATGAATCGGG
** *
74297 CTCTTGAATAGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
74318 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
74339 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
74360 CTCTTGA
1 CTCTTGA
74367 GGAATGATAG
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:74394 original size:21 final size:21
Alignment explanation
Indices: 74312--74398 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
74302 GAATAGTGGG
* *
74312 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* **
74333 AGGGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* * *
74354 AGGGGACTCTTG-AGGAATGAT
1 AGGGGCCTCTTGAACG-ATGAC
74375 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
74396 AGG
1 AGG
74399 TGAGTCGGGC
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 47 0.92
22 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.20
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:74914 original size:19 final size:20
Alignment explanation
Indices: 74872--74914 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
74862 AATAGTTTTT
*
74872 GAAACTTAAAACCGCAACAT
1 GAAACTTAAAACCGCAACAC
* *
74892 GAAACTT-AAATCGCAACGC
1 GAAACTTAAAACCGCAACAC
74911 GAAA
1 GAAA
74915 ATGACTATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAACCGCAACAC
Found at i:74926 original size:20 final size:20
Alignment explanation
Indices: 74901--74969 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
74891 TGAAACTTAA
74901 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
74921 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
74941 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
74961 ATCGCAACG
1 ATCGCAACG
74970 GGATAATCGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:74998 original size:19 final size:20
Alignment explanation
Indices: 74974--75012 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
74964 GCAACGGGAT
*
74974 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACTAAA
74993 AATCGCAACGCGAAACTAAA
1 AATCGCAACGCGAAACTAAA
75013 TTCGCGTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.51, C:0.21, G:0.15, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAAACTAAA
Found at i:75042 original size:20 final size:20
Alignment explanation
Indices: 75013--75050 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
75003 CGAAACTAAA
*
75013 TTCGCGTTGCGATATTCATT
1 TTCGCATTGCGATATTCATT
*
75033 TTCGCATTGCGATTTTCA
1 TTCGCATTGCGATATTCA
75051 CGTTGTGATT
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:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (20 bp):
TTCGCATTGCGATATTCATT
Found at i:77088 original size:19 final size:20
Alignment explanation
Indices: 77052--77123 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
77042 GAAACTTAAA
77052 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
77072 ATCGCAACGCG-AAATGAAA
1 ATCGCAACACGAAAATGACT
*
77091 ATCTCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
*
77111 ATCGCAACGCGAA
1 ATCGCAACACGAA
77124 TATCGCAACG
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 15 0.36
20 27 0.64
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.14
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:77103 original size:39 final size:39
Alignment explanation
Indices: 77049--77123 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
77039 TCTGAAACTT
77049 AAAATCGCAACACGAAAATGACTATCGCAACGCGAAATG
1 AAAATCGCAACACGAAAATGACTATCGCAACGCGAAATG
*
77088 AAAATCTCAACACGAAAATGACTATCGCAACGCGAA
1 AAAATCGCAACACGAAAATGACTATCGCAACGCGAA
77124 TATCGCAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.13
Consensus pattern (39 bp):
AAAATCGCAACACGAAAATGACTATCGCAACGCGAAATG
Found at i:77129 original size:14 final size:14
Alignment explanation
Indices: 77110--77138 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
77100 CGAAAATGAC
77110 TATCGCAACGCGAA
1 TATCGCAACGCGAA
77124 TATCGCAACGCGAA
1 TATCGCAACGCGAA
77138 T
1 T
77139 TAAACTATCG
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:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (14 bp):
TATCGCAACGCGAA
Found at i:77533 original size:22 final size:22
Alignment explanation
Indices: 77508--77561 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
77498 GAGATAGACG
*
77508 GATTTCGCCGGAGTTGGGGACA
1 GATTTCGCCGGAGATGGGGACA
* *
77530 GATTTCGTCGGAGATGGGGACG
1 GATTTCGCCGGAGATGGGGACA
*
77552 GATGTCGCCG
1 GATTTCGCCG
77562 TAGAGAGTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.43, T:0.22
Consensus pattern (22 bp):
GATTTCGCCGGAGATGGGGACA
Found at i:77723 original size:21 final size:21
Alignment explanation
Indices: 77698--77854 Score: 191
Period size: 21 Copynumber: 7.6 Consensus size: 21
77688 GCGCTTTGAA
* *
77698 AATCGCATTGCGATTTTGTAT
1 AATCGCGTTGCGATTATGTAT
* *
77719 TATCGCGTTGCGA-TA-GTCAG
1 AATCGCGTTGCGATTATGT-AT
77739 AATCGCGTTGCGATTATGTAT
1 AATCGCGTTGCGATTATGTAT
77760 AATCGCGTTGCGATTATGTAT
1 AATCGCGTTGCGATTATGTAT
*
77781 AATCGCGTTGCGA-TA-GTCAG
1 AATCGCGTTGCGATTATGT-AT
77801 AATCGCGTTGCGATTATGTAT
1 AATCGCGTTGCGATTATGTAT
*
77822 AATCGCGTTGCGA-TA-GTCAA
1 AATCGCGTTGCGATTATGT-AT
77842 AATCGCGTTGCGA
1 AATCGCGTTGCGA
77855 ATCTGGAAAT
Statistics
Matches: 120, Mismatches: 9, Indels: 15
0.83 0.06 0.10
Matches are distributed among these distances:
19 6 0.05
20 46 0.38
21 64 0.53
22 4 0.03
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (21 bp):
AATCGCGTTGCGATTATGTAT
Found at i:77759 original size:41 final size:42
Alignment explanation
Indices: 77698--77854 Score: 191
Period size: 41 Copynumber: 3.8 Consensus size: 42
77688 GCGCTTTGAA
* * * *
77698 AATCGCATTGCGATTTTGTATTATCGCGTTGCGA-TA-GTCAG
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATTATGT-AT
77739 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATTATGTAT
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATTATGTAT
*
77781 AATCGCGTTGCGA-TA-GTCAGAATCGCGTTGCGATTATGTAT
1 AATCGCGTTGCGATTATGT-ATAATCGCGTTGCGATTATGTAT
*
77822 AATCGCGTTGCGA-TA-GTCAAAATCGCGTTGCGA
1 AATCGCGTTGCGATTATGT-ATAATCGCGTTGCGA
77855 ATCTGGAAAT
Statistics
Matches: 107, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
40 2 0.02
41 87 0.81
42 16 0.15
43 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
AATCGCGTTGCGATTATGTATAATCGCGTTGCGATTATGTAT
Found at i:77795 original size:62 final size:62
Alignment explanation
Indices: 77698--77854 Score: 255
Period size: 62 Copynumber: 2.5 Consensus size: 62
77688 GCGCTTTGAA
* * *
77698 AATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTAT
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTAT
77760 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTAT
1 AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTAT
*
77822 AATCGCGTTGCGA-TA-GTCAAAATCGCGTTGCGA
1 AATCGCGTTGCGATTATGT-ATAATCGCGTTGCGA
77855 ATCTGGAAAT
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
60 2 0.02
61 16 0.18
62 72 0.80
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (62 bp):
AATCGCGTTGCGATTATGTATAATCGCGTTGCGATAGTCAGAATCGCGTTGCGATTATGTAT
Found at i:77895 original size:20 final size:20
Alignment explanation
Indices: 77697--77895 Score: 104
Period size: 20 Copynumber: 9.8 Consensus size: 20
77687 GGCGCTTTGA
* * *
77697 AAATCGCATTGCGATTTTGT
1 AAATCGCGTTGCGATATTGG
* * *
77717 ATTATCGCGTTGCGATAGT-C
1 A-AATCGCGTTGCGATATTGG
*
77737 AGAATCGCGTTGCGAT-TATGT
1 A-AATCGCGTTGCGATAT-TGG
*
77758 ATAATCGCGTTGCGAT-TATGT
1 A-AATCGCGTTGCGATAT-TGG
* *
77779 ATAATCGCGTTGCGATAGT-C
1 A-AATCGCGTTGCGATATTGG
*
77799 AGAATCGCGTTGCGAT-TATGT
1 A-AATCGCGTTGCGATAT-TGG
* **
77820 ATAATCGCGTTGCGATAGTCA
1 A-AATCGCGTTGCGATATTGG
77841 AAATCGCGTTGCGA-ATCTGG
1 AAATCGCGTTGCGATAT-TGG
* **
77861 AAATTGATTTGCGATATTGG
1 AAATCGCGTTGCGATATTGG
*
77881 AGATCGCGTTGCGAT
1 AAATCGCGTTGCGAT
77896 TTAGAGATCG
Statistics
Matches: 141, Mismatches: 29, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
19 1 0.01
20 71 0.50
21 69 0.49
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (20 bp):
AAATCGCGTTGCGATATTGG
Found at i:77904 original size:19 final size:19
Alignment explanation
Indices: 77869--77916 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
77859 GGAAATTGAT
* *
77869 TTGCGATATTGGAGATCGCG
1 TTGCGAT-TTAGAGATCGCA
77889 TTGCGATTTAGAGATCGCA
1 TTGCGATTTAGAGATCGCA
*
77908 TTGTGATTT
1 TTGCGATTT
77917 TATTGGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.21, C:0.12, G:0.29, T:0.38
Consensus pattern (19 bp):
TTGCGATTTAGAGATCGCA
Done.