Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002887.1 Hibiscus syriacus cultivar Beakdansim tig00005969_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: 88196
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:7759 original size:15 final size:13
Alignment explanation
Indices: 7731--7776 Score: 60
Period size: 14 Copynumber: 3.5 Consensus size: 13
7721 TTTTTGGCTC
7731 TTTTTTTG--TTT
1 TTTTTTTGCCTTT
7742 TTTTTTTGCCGTTT
1 TTTTTTTGCC-TTT
7756 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
7769 TTTGTTTT
1 TTT-TTTT
7777 TTTTTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.26
13 6 0.19
14 17 0.55
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:12708 original size:21 final size:22
Alignment explanation
Indices: 12682--12722 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12672 ATATGATGGA
*
12682 AAAATG-AAAAAGAAGAAAATG
1 AAAATGAAAAAAAAAGAAAATG
12703 AAAATGAAAAAAAAAGAAAA
1 AAAATGAAAAAAAAAGAAAA
12723 AAAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (22 bp):
AAAATGAAAAAAAAAGAAAATG
Found at i:12715 original size:15 final size:15
Alignment explanation
Indices: 12681--12715 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12671 AATATGATGG
12681 AAAAATGAAAAAGAA
1 AAAAATGAAAAAGAA
* *
12696 GAAAATGAAAATGAA
1 AAAAATGAAAAAGAA
12711 AAAAA
1 AAAAA
12716 AAGAAAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (15 bp):
AAAAATGAAAAAGAA
Found at i:13870 original size:43 final size:43
Alignment explanation
Indices: 13805--13996 Score: 128
Period size: 43 Copynumber: 4.4 Consensus size: 43
13795 TGATTAGATC
*
13805 TCCTCATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGACA
1 TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGACA
* * **
13848 TCCTCATCACGTAGGAACCGTGTTATCGCCCTTCCTAAAGATGGCCAGA-A
1 TCCTCATCACGTAGGAGCCGTG---TC-ACC--CCT--AGATAACCAGACA
* *
13898 CTCTTCATCACGTATGAGCCGTGTCATCCCC--G---ACCAGATC-
1 -TCCTCATCACGTAGGAGCCGTGTCA-CCCCTAGATAACCAGA-CA
* * * *
13938 TCCTCATCGCGTAGGAGCTGTGTCACCCCTAGATAACCAGCCG
1 TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGACA
*
13981 TCCTCATCGCGTAGGA
1 TCCTCATCACGTAGGA
13997 ACCGAGTTAT
Statistics
Matches: 116, Mismatches: 15, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
38 4 0.03
39 26 0.22
40 1 0.01
42 2 0.02
43 41 0.35
46 4 0.03
47 2 0.02
48 4 0.03
49 3 0.03
50 1 0.01
51 28 0.24
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (43 bp):
TCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGACA
Found at i:13961 original size:39 final size:38
Alignment explanation
Indices: 13892--13966 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
13882 CTAAAGATGG
* *
13892 CCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCGA
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCA-CCCCGA
* * *
13931 CCAGATCTCCTCATCGCGTAGGAGCTGTGTCACCCC
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCC
13967 TAGATAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 4 0.13
39 27 0.87
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.23
Consensus pattern (38 bp):
CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCGA
Found at i:14049 original size:134 final size:134
Alignment explanation
Indices: 13749--14105 Score: 549
Period size: 133 Copynumber: 2.7 Consensus size: 134
13739 ATTATCGCTA
**
13749 TAAA-ATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTGATTAGATCTCCTCATC
1 TAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCC-GACCAGATCTCCTCATC
* *
13813 ACGTAGGAG-TCGTGTCACCCCTAGATAACCAGACATCCTCATCACGTAGGAACCGTGTTATCGC
65 ACGTAGGAGCT-GTGTCACCCCTAGATAACCAGACATCCTCATCACGTAGGAACCGAGTTATCAC
13877 CCTTCC
129 CCTTCC
* *
13883 TAAAGATGGCC-AGAACTCTTCATCACGTATGAGCCGTGTCATCCCCGACCAGATCTCCTCATCG
1 TAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCGACCAGATCTCCTCATCA
* * *
13947 CGTAGGAGCTGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACCC
66 CGTAGGAGCTGTGTCACCCCTAGATAACCAGACATCCTCATCACGTAGGAACCGAGTTATCACCC
14012 TTCC
131 TTCC
*
14016 TAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACCAGATTTCCTCATC
1 TAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCC-CGACCAGATCTCCTCATC
* * *
14081 ACGTAGGAACCGTGTCACCCTTAGA
65 ACGTAGGAGCTGTGTCACCCCTAGA
14106 CGACCCGAAC
Statistics
Matches: 204, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
133 88 0.43
134 72 0.35
135 44 0.22
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (134 bp):
TAAAGATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCGACCAGATCTCCTCATCA
CGTAGGAGCTGTGTCACCCCTAGATAACCAGACATCCTCATCACGTAGGAACCGAGTTATCACCC
TTCC
Found at i:14139 original size:43 final size:40
Alignment explanation
Indices: 14028--14144 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 40
14018 AAGATGGCCA
14028 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
** * * * *
14068 AGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC-T---CGACC
* *
14111 CGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC
14145 CAACAACTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
39 3 0.05
40 25 0.43
43 27 0.47
44 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
Found at i:14316 original size:3 final size:3
Alignment explanation
Indices: 14301--14353 Score: 61
Period size: 3 Copynumber: 17.0 Consensus size: 3
14291 CTATTTTAAT
* * *
14301 TTA TTA CTA TTA TTA TTT TTAA TAA TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA
14348 TTA TTA
1 TTA TTA
14354 ATACAAATGG
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
3 38 0.90
4 4 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:14322 original size:23 final size:25
Alignment explanation
Indices: 14294--14353 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
14284 GTCTTTTCTA
14294 TTTTAAT-TTATTA-CTATTATTAT
1 TTTTAATATTATTATCTATTATTAT
*
14317 TTTTAATAATTATTATTTATTATTAT
1 TTTTAAT-ATTATTATCTATTATTAT
* *
14343 TATTATTATTA
1 TTTTAATATTA
14354 ATACAAATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 7 0.23
25 10 0.32
26 14 0.45
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTAATATTATTATCTATTATTAT
Found at i:19863 original size:18 final size:18
Alignment explanation
Indices: 19840--19875 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19830 AGGGATTTAC
*
19840 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCAGGACAT
19858 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
19876 TTCATATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:19886 original size:23 final size:23
Alignment explanation
Indices: 19855--19930 Score: 98
Period size: 23 Copynumber: 3.2 Consensus size: 23
19845 TCCTTCGGGA
19855 CATAGTGGTCCTTCAGGACATTT
1 CATAGTGGTCCTTCAGGACATTT
* * *
19878 CATATTGGTCCTTCGGGATATTT
1 CATAGTGGTCCTTCAGGACATTT
*
19901 CATAGTGGTCCTTCAAGACAAATTT
1 CATAGTGGTCCTTCAGGAC--ATTT
19926 CATAG
1 CATAG
19931 CCCCTAGTGG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 35 0.80
25 9 0.20
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (23 bp):
CATAGTGGTCCTTCAGGACATTT
Found at i:36633 original size:34 final size:32
Alignment explanation
Indices: 36563--36633 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 32
36553 AAATATCAAA
* *
36563 AATAGAAATTTAAATGACTAAAATAAAATAAC
1 AATATAAACTTAAATGACTAAAATAAAATAAC
*
36595 ---ATAAACTTAAGTGACTAAAATAAAATAAC
1 AATATAAACTTAAATGACTAAAATAAAATAAC
36624 AGAATATAAA
1 --AATATAAA
36634 GTGACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
29 26 0.84
34 5 0.16
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (32 bp):
AATATAAACTTAAATGACTAAAATAAAATAAC
Found at i:36635 original size:29 final size:29
Alignment explanation
Indices: 36573--36653 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
36563 AATAGAAATT
*
36573 TAAA-TGACTAAAATAAAATAACATAAAC
1 TAAAGTGACTAAAATAAAATAACAGAAAC
*
36601 TTAAGTGACTAAAATAAAATAACAGAATA-
1 TAAAGTGACTAAAATAAAATAACAGAA-AC
*
36630 TAAAGTGACAAAAATCAGAAATAA
1 TAAAGTGACTAAAAT-A-AAATAA
36654 ACAAAATAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 3 0.07
29 34 0.76
30 2 0.04
31 6 0.13
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.21
Consensus pattern (29 bp):
TAAAGTGACTAAAATAAAATAACAGAAAC
Found at i:38521 original size:85 final size:85
Alignment explanation
Indices: 38399--39148 Score: 820
Period size: 85 Copynumber: 8.9 Consensus size: 85
38389 ATGTGTCATC
* * ** * * ** * *
38399 GAGCAGAATGAAATCGAACTCGACAACT-TTTATTGACAGATCACTTTTCTCGACTTAAGCTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
38463 TTGTAAATTTGACT-TGCCCTTT
65 CTGTAAATTTGA-TATG-CCTTT
* *
38485 -AGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAAATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
38549 TGT-AATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * * *
38568 GACCTGAATGTTATCGAACTCAAAAGGTCTTTGTTGATAGATAACCCTTCTCGCCGTGAGTTATG
1 GAGCTGAATGTAATCGAACTC-GAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
38633 CTGTAAATTTGATACGTCC-TT
65 CTGTAAATTTGATATG-CCTTT
* * ** * *
38654 GAGCTGAATGTAATCGAACTCGAAGGACTTTGCTGGTAGATAGCCCTTCTCGCCTTGAGCTATAC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
38719 TGTAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * *** * *
38739 GAGCTGAATCTAATTGAACAAAAAATGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAAC-TCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
38804 CTGTAAATTTTATATG-TTCTT
65 CTGTAAATTTGATATGCCT-TT
* * *
38825 GAGCTCAATGTAATCGAACTCGAAGGTCTTTGCTAACAGATAACCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
38890 TGTAAATTTGATATGTCTTT
66 TGTAAATTTGATATGCCTTT
* * * * * **
38910 GAGCTAAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAACCTTTATCGCCTTGAGTTATTA
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
38975 TGT-AA----ATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* *
38990 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* * **
39055 CTATAAATTTGATGTATCTTT
65 CTGTAAATTTGATATGCCTTT
*** * * * *
39076 GAGCTGAATGTAATCGAACTCGAAGGTCACGGTTGACAGATAACCATTTTCGCCTTGAGTTATGA
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
39141 TGTAAATT
66 TGTAAATT
39149 GGTAATCGAA
Statistics
Matches: 559, Mismatches: 89, Indels: 33
0.82 0.13 0.05
Matches are distributed among these distances:
80 36 0.06
81 33 0.06
82 2 0.00
83 6 0.01
84 33 0.06
85 314 0.56
86 133 0.24
87 2 0.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTTT
Found at i:38808 original size:171 final size:169
Alignment explanation
Indices: 38431--39148 Score: 845
Period size: 171 Copynumber: 4.2 Consensus size: 169
38421 ACAACTTTTA
* ** * * * * * *
38431 TTGACAGATCACTTTTCTCGACTTAAGCTATGTTGTAAATTTGACTTGCCCTTTAGCTGAATGTA
1 TTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGA-TTGTCCTTGAGCTGAATGTA
* * *
38496 ATCGAACTCGAAGGTCTTTGTTGACAAATAGCCCTTCTCGCCTTGAGCTATGCTGT-AATTTGAT
65 ATCGAACTCGAAGGTCTTTGCTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGAT
* *
38560 ATGCCTTTGACCTGAATGTTATCGAACTCAAAAGGTCTTTG
130 ATGCCTTTGAGCTGAATGTAATCGAACT-AAAAGGTCTTTG
* * * *
38601 TTGATAGATAACCCTTCTCGCCGTGAGTTATGCTGTAAATTTGATACGTCCTTGAGCTGAATGTA
1 TTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGAT-TGTCCTTGAGCTGAATGTA
* ** * *
38666 ATCGAACTCGAAGGACTTTGCTGGTAGATAGCCCTTCTCGCCTTGAGCTATACTGTAAATTTGAT
65 ATCGAACTCGAAGGTCTTTGCTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGAT
* * * *
38731 ATGCCTTTGAGCTGAATCTAATTGAACAAAAAATGTCTTTG
130 ATGCCTTTGAGCTGAATGTAATCGAAC-TAAAAGGTCTTTG
* * * *
38772 TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTTATATGTTCTTGAGCTCAATGTA
1 TTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGAT-TGTCCTTGAGCTGAATGTA
*
38837 ATCGAACTCGAAGGTCTTTGCTAACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGAT
65 ATCGAACTCGAAGGTCTTTGCTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGAT
* * * **
38902 ATGTCTTTGAGCTAAATATAATCGAACTCGAAGGTCTTTG
130 ATGCCTTTGAGCTGAATGTAATCGAACTAAAAGGTCTTTG
* * * *
38942 TTGACAGATAACCTTTATCGCCTTGAGTTATTATGTAAA--T-A-TG-CCTTTGAGCTGAGTGTA
1 TTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGATTGTCC-TTGAGCTGAATGTA
* * *
39002 ATCGAACTCGAAGGTCTTGTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTGA
65 ATCGAACTCGAAGGTCTT-TGCTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* ** ** ***
39067 TGTATCTTTGAGCTGAATGTAATCGAACTCGAAGGTCACGG
129 TATGCCTTTGAGCTGAATGTAATCGAACTAAAAGGTCTTTG
* *
39108 TTGACAGATAACCATTTTCGCCTTGAGTTATGATGTAAATT
1 TTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAAATT
39149 GGTAATCGAA
Statistics
Matches: 476, Mismatches: 65, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
164 1 0.00
165 32 0.07
166 112 0.24
167 1 0.00
168 1 0.00
169 1 0.00
170 145 0.30
171 183 0.38
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (169 bp):
TTGACAGATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGATTGTCCTTGAGCTGAATGTAA
TCGAACTCGAAGGTCTTTGCTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATA
TGCCTTTGAGCTGAATGTAATCGAACTAAAAGGTCTTTG
Found at i:38868 original size:256 final size:255
Alignment explanation
Indices: 38399--40058 Score: 1589
Period size: 256 Copynumber: 6.6 Consensus size: 255
38389 ATGTGTCATC
* * ** * * ** * * *
38399 GAGCAGAATGAAATCGAACTCGACAACT-TTTATTGACAGATCACTTTTCTCGACTTAAGCTATG
1 GAGCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATA
* * * ** *
38463 TTGTAAATTTGACT-TGCCCTTT-AGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAAATA
65 CTATAAATTTGA-TATG-CCTTTGAGCTGAATGTAATCGAACTCAAAGGTCACTGTTGACAGATA
* * * * *
38526 GCCCTTCTCGCCTTGAGCTATGCTGT-AATTTGATATG-CCTTTGACCTGAATGTTATCGAACTC
128 ACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTTCTTTGAGCTGAATGTAATCGAACTC
* * * *
38589 AAAAGGTCTTTGTTGATAGATAACCCTTCTCGCCGTGAGTTATGCTGTAAATTTGATACGTCC-T
193 -GAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTT-ATA-GTCCTT
38653 T
255 T
* * ** *
38654 GAGCTGAATGTAATCGAACTCGAAGGACTTTGCTGGTAGATAGCCCTTCTCGCCTTGAGCTATAC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATAC
* * * ** * **
38719 TGTAAATTTGATATGCCTTTGAGCTGAATCTAATTGAACAAAAAATGTCTTTGTTGACAGATAAC
66 TATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAAC-TCAAAGGTCACTGTTGACAGATAAC
* *
38784 CCTTCTCGCCTTGAGTTATGCTGTAAATTTTATATGTTC-TTGAGCTCAATGTAATCGAACTCGA
130 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTTCTTTGAGCTGAATGTAATCGAACTCGA
* *
38848 AGGTCTTTGCTAACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGT-CTTT
195 AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTT-ATA-GTCCTTT
* * * *
38910 GAGCTAAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAACCTTTATCGCCTTGAG-T-TA-
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATAC
** * * **
38972 T-T--ATGTAAATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGACAGATAA
66 TATAAAT-TTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGGTC-ACTGTTGACAGATAA
*
39034 CCCTTCTCGCCTTGAGTTATGCTATAAATTTG--ATGTATCTTTGAGCTGAATGTAATCGAACTC
129 CCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGT-TCTTTGAGCTGAATGTAATCGAACTC
*** * * * *
39097 GAAGGTCACGGTTGACAGATAACCATTTTCGCCTTGAGTTATGATGT--A---A-A------T
193 GAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTATAGTCCTTT
* * * *
39148 ----TG---GTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTATCGTCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATA
* * * * *
39206 TTGTAAATTTGATGTGCCTTTGAGCTGAATGTAATTGAACTCAAAGGTCACGGTTGACAGATAAC
65 CTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGGTCACTGTTGACAGATAAC
* * ** *
39271 CCTTCTCTCCTTGAGTTATGCTGTAAATTGGATAT-ACCTTTGAGCTAAATGTAATCGAACTCGA
130 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTTCTTTGAGCTGAATGTAATCGAACTCGA
* * *
39335 AGGTCTTGGTTGACGGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA--TAT-G-CCTTT
195 AGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTATAGTCCTTT
* * * * *
39392 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGAGAGATAGCCCTTCTCACCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTT-TGTTGACAGATAACCCTTCTCGCCTTGAGCTATA
* * * * *
39457 CTATAAATTTGATGTGTCTTTGAGCTAAATGTAATCGAACTCGAAGGTCACGGTTGACAGATAAC
65 CTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGGTCACTGTTGACAGATAAC
* * * * *
39522 CCTTCTTGCCTTGAGTTATGCTGTAAATTAGATATG--CATTTTAGTTGAATGTAATTGAACTCG
130 CCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTTC-TTTGAGCTGAATGTAATCGAACTCG
* *
39585 AAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCCATGCTGTAAATTTA-ATGTGCCTTT
194 AAGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTATA-GT-CCTTT
* * * *** * * *
39649 GAGCTAAATGTAATCAAACCCGAAGGTCACAGTTGATAGATAACCCTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATAC
* * * *
39714 TATAAATTGGATATGCCTTTGAGCTAAATGTAATCGAATTCAAAGGTCACAGTTGACAGATAACC
66 TATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGGTCACTGTTGACAGATAACC
* * * *
39779 CTTCTTGCCTTGAGTTATGCTGTAAATTAGATATG--CATTTGAGTTGAATGTAATTGAACTCGA
131 CTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTTC-TTTGAGCTGAATGTAATCGAACTCGA
* * * *
39842 AGGTCTTTTGTTGACATATAGCCCTTCTCACCTTGAGCTATGCTTTAAATTTGAT-GTGCCTTT
195 AGGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTT-ATAGT-CCTTT
* * * * *
39905 GAGCTGAATGTAATCAAACCCGAAGGTCATAGTTGACAGATAACCCTTCTCGCCTTGAGTTA-AG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATA-
* * * * *
39969 CTATAAATTGGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGGT-ATTTTGTTGAAAGATA
65 CTATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGGTCA--CTGTTGACAGATA
* * * *
40033 GCTCTTCTCTCCTTGAGCTATGCTGT
128 ACCCTTCTCGCCTTGAGTTATGCTGT
40059 CATAATTCTC
Statistics
Matches: 1196, Mismatches: 158, Indels: 100
0.82 0.11 0.07
Matches are distributed among these distances:
231 18 0.02
232 28 0.02
233 1 0.00
234 2 0.00
235 1 0.00
236 107 0.09
237 35 0.03
238 6 0.01
239 1 0.00
244 2 0.00
245 1 0.00
248 2 0.00
249 5 0.00
250 12 0.01
251 296 0.25
252 39 0.03
253 1 0.00
254 11 0.01
255 79 0.07
256 457 0.38
257 91 0.08
258 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (255 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATAC
TATAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCAAAGGTCACTGTTGACAGATAACC
CTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGTTCTTTGAGCTGAATGTAATCGAACTCGAA
GGTCTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTATAGTCCTTT
Found at i:39200 original size:66 final size:65
Alignment explanation
Indices: 39085--39214 Score: 170
Period size: 66 Copynumber: 2.0 Consensus size: 65
39075 TGAGCTGAAT
* *
39085 GTAATCGAACTCGAAGGTCACGGTTGACAGATAACCATTTTCGCCTTGAGTTATGATGTAAATTG
1 GTAATCGAACTCGAAGGTCACGGTTGACAGATAACCATTATCGCCTTGAGCTATGATGTAAATTG
*** * * * *
39150 GTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTATCGTCTTGAGCTATGTTGTAAATT
1 GTAATCGAACTCGAAGGTC-ACGGTTGACAGATAACCATTATCGCCTTGAGCTATGATGTAAATT
39215 TGATGTGCCT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
65 19 0.35
66 36 0.65
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (65 bp):
GTAATCGAACTCGAAGGTCACGGTTGACAGATAACCATTATCGCCTTGAGCTATGATGTAAATTG
Found at i:39283 original size:151 final size:151
Alignment explanation
Indices: 38999--39301 Score: 471
Period size: 151 Copynumber: 2.0 Consensus size: 151
38989 TGAGCTGAGT
* *
38999 GTAATCGAACTCGAAGGTCTTGTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATT
1 GTAATCGAACTCGAAGGTCTTGTGTTGACAGATAACCCTTATCGCCTTGAGCTATGCTATAAATT
* * *
39064 TGATGTATCTTTGAGCTGAATGTAATCGAACTCGAAGGTCACGGTTGACAGATAACCATTTTCGC
66 TGATGTACCTTTGAGCTGAATGTAATCGAACTCAAAGGTCACGGTTGACAGATAACCATTCTCGC
39129 CTTGAGTTATGATGTAAATTG
131 CTTGAGTTATGATGTAAATTG
* * * * *
39150 GTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTATCGTCTTGAGCTATGTTGTAAATT
1 GTAATCGAACTCGAAGGTCTTGTGTTGACAGATAACCCTTATCGCCTTGAGCTATGCTATAAATT
* * * *
39215 TGATGTGCCTTTGAGCTGAATGTAATTGAACTCAAAGGTCACGGTTGACAGATAACCCTTCTCTC
66 TGATGTACCTTTGAGCTGAATGTAATCGAACTCAAAGGTCACGGTTGACAGATAACCATTCTCGC
*
39280 CTTGAGTTATGCTGTAAATTG
131 CTTGAGTTATGATGTAAATTG
39301 G
1 G
39302 ATATACCTTT
Statistics
Matches: 137, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
151 137 1.00
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (151 bp):
GTAATCGAACTCGAAGGTCTTGTGTTGACAGATAACCCTTATCGCCTTGAGCTATGCTATAAATT
TGATGTACCTTTGAGCTGAATGTAATCGAACTCAAAGGTCACGGTTGACAGATAACCATTCTCGC
CTTGAGTTATGATGTAAATTG
Found at i:39296 original size:85 final size:85
Alignment explanation
Indices: 39150--40058 Score: 963
Period size: 85 Copynumber: 10.7 Consensus size: 85
39140 ATGTAAATTG
* * * * * *
39150 GTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTATCGT-CTTGAGCTATGTTGTAAAT
1 GTAATCGAACTCGAAGGTC-ATGGTTGACAGATAACCCTTCTC-TCCTTGAGTTATGCTGTAAAT
*
39214 TTGATGTGCCTTTGAGCTGAAT
64 TTGATATGCCTTTGAGCTGAAT
* * * *
39236 GTAATTGAACTCAAAGGTCACGGTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATTG
1 GTAATCGAACTCGAAGGTCATGGTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATTT
* *
39301 GATATACCTTTGAGCTAAAT
66 GATATGCCTTTGAGCTGAAT
* * *
39321 GTAATCGAACTCGAAGGTCTTGGTTGACGGATAACCCTTCTCGCCTTGAGTTATGCTGT-AA---
1 GTAATCGAACTCGAAGGTCATGGTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATTT
*
39382 -ATATGCCTTTGAGCTGAGT
66 GATATGCCTTTGAGCTGAAT
* * * * * *
39401 GTAATCGAACTCGAAGGTCTTGTGTTGAGAGATAGCCCTTCTCACCTTGAGCTATGCTATAAATT
1 GTAATCGAACTCGAAGGTCATG-GTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATT
* * *
39466 TGATGTGTCTTTGAGCTAAAT
65 TGATATGCCTTTGAGCTGAAT
*
39487 GTAATCGAACTCGAAGGTCACGGTTGACAGATAACCCTTCT-TGCCTTGAGTTATGCTGTAAATT
1 GTAATCGAACTCGAAGGTCATGGTTGACAGATAACCCTTCTCT-CCTTGAGTTATGCTGTAAATT
* * * *
39551 AGATATGCATTTTAGTTGAAT
65 TGATATGCCTTTGAGCTGAAT
* * * * * **
39572 GTAATTGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCCATGCTGTAAATT
1 GTAATCGAACTCGAAGGTC-ATGGTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATT
* * *
39637 TAATGTGCCTTTGAGCTAAAT
65 TGATATGCCTTTGAGCTGAAT
* * ** * * * *
39658 GTAATCAAACCCGAAGGTCACAGTTGATAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTG
1 GTAATCGAACTCGAAGGTCATGGTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATTT
*
39723 GATATGCCTTTGAGCTAAAT
66 GATATGCCTTTGAGCTGAAT
* * **
39743 GTAATCGAATTCAAAGGTCACAGTTGACAGATAACCCTTCT-TGCCTTGAGTTATGCTGTAAATT
1 GTAATCGAACTCGAAGGTCATGGTTGACAGATAACCCTTCTCT-CCTTGAGTTATGCTGTAAATT
* * *
39807 AGATATGCATTTGAGTTGAAT
65 TGATATGCCTTTGAGCTGAAT
* * * * * * * *
39828 GTAATTGAACTCGAAGGTCTTTTGTTGACATATAGCCCTTCTCACCTTGAGCTATGCTTTAAATT
1 GTAATCGAACTCGAAGGTC-ATGGTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATT
*
39893 TGATGTGCCTTTGAGCTGAAT
65 TGATATGCCTTTGAGCTGAAT
* * * * * * *
39914 GTAATCAAACCCGAAGGTCATAGTTGACAGATAACCCTTCTCGCCTTGAGTTAAGCTATAAATTG
1 GTAATCGAACTCGAAGGTCATGGTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATTT
39979 GATATGCCTTTGAGCTGAAT
66 GATATGCCTTTGAGCTGAAT
* * * * * *
39999 GTAATCAAACTCGAAGGT-ATTTTGTTGAAAGATAGCTCTTCTCTCCTTGAGCTATGCTGT
1 GTAATCGAACTCGAAGGTCA--TGGTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGT
40059 CATAATTCTC
Statistics
Matches: 685, Mismatches: 123, Indels: 30
0.82 0.15 0.04
Matches are distributed among these distances:
80 38 0.06
81 31 0.05
82 2 0.00
84 4 0.01
85 391 0.57
86 219 0.32
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (85 bp):
GTAATCGAACTCGAAGGTCATGGTTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATTT
GATATGCCTTTGAGCTGAAT
Found at i:39512 original size:402 final size:411
Alignment explanation
Indices: 38431--39966 Score: 1664
Period size: 402 Copynumber: 3.7 Consensus size: 411
38421 ACAACTTTTA
* ** * * * * * *
38431 TTGACAGATCACTTTTCTCGACTTAAGCTATGTTGTAAATTTGACT-TGCCCTTT-AGCTGAATG
1 TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGA-TATG-CCTTTGAGCTAAATG
* * * *
38494 TAATCGAACTCGAAGGTCTTTGTTGACAAATAGCCCTTCTCGCCTTGAGCTATGCTGTAATTTGA
64 TAATCGAACTCGAAGGTCTTAGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAA----A
* * * * * * *
38559 TATGCCTTTGACCTGAATGTTATCGAACTCAAAAGGTCTT-TGTTGATAGATAACCCTTCTCGCC
125 TATGCCTTTGAGCTGAGTGTAATCGAACTC-GAAGGTCTTGTGTTGACAGATAGCCCTTCTCACC
* * * ** * * *** *
38623 GTGAGTTATGCTGTAAATTTGATACGTCCTTGAGCTGAATGTAATCGAACTCGAAGGACTTTGCT
189 TTGAGCTATGCTATAAATTTGATGTGTCTTTGAGCTGAATGTAATCGAACTCGAAGGTCACGGTT
** * * * * * *
38688 GGTAGATAGCCCTTCTCGCCTTGAGCTATACTGTAAATTTGATATGCCTTTGAGCTGAATCTAAT
254 GACAGATAACCCTTTTCGCCTTGAG-T-TACTG--AATTAGATA---C-AT-AGTTG-A-GTAAT
* *** * *
38753 TGAACAAAAAATGTC-TTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTTAT
308 CGAAC-TCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAA-TTTA-
* * ***
38817 ATGT-TC-TTGAGCTCAATGTAATCGAACTCGAAGGTCTTTG
370 ATGTGCCTTTGAGCTAAATGTAATCGAACTCGAAGGTCACAG
* * * * * *
38857 CTAACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGTCTTTGAGCTAAATATA
1 TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAATGTA
* * * **
38922 ATCGAACTCGAAGGTCTTTGTTGACAGATAACCTTTATCGCCTTGAGTTATTATGTAAATATGCC
66 ATCGAACTCGAAGGTCTTAGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATATGCC
* * *
38987 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGACAGATAACCCTTCTCGCCTTGAGTT
131 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGACAGATAGCCCTTCTCACCTTGAGCT
*
39052 ATGCTATAAATTTGATGTATCTTTGAGCTGAATGTAATCGAACTCGAAGGTCACGGTTGACAGAT
196 ATGCTATAAATTTGATGTGTCTTTGAGCTGAATGTAATCGAACTCGAAGGTCACGGTTGACAGAT
*
39117 AACCATTTTCGCCTTGAGTTA-TG-A-T-G-TA-A-A-TTG-GTAATCGAACTCGAAGGTCTTTT
261 AACCCTTTTCGCCTTGAGTTACTGAATTAGATACATAGTTGAGTAATCGAACTCGAAGGTCTTTT
* * * * * *
39173 GTTGACATATAACCCTTATCGTCTTGAGCTATGTTGTAAATTTGATGTGCCTTTGAGCTGAATGT
326 GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTAATGTGCCTTTGAGCTAAATGT
* * *
39238 AATTGAACTCAAAGGTCACGG
391 AATCGAACTCGAAGGTCACAG
* *
39259 TTGACAGATAACCCTTCTCTCCTTGAGTTATGCTGTAAATTGGATATACCTTTGAGCTAAATGTA
1 TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAATGTA
* *
39324 ATCGAACTCGAAGGTCTTGGTTGACGGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATATGCC
66 ATCGAACTCGAAGGTCTTAGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATATGCC
*
39389 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGAGAGATAGCCCTTCTCACCTTGAGCT
131 TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGACAGATAGCCCTTCTCACCTTGAGCT
*
39454 ATGCTATAAATTTGATGTGTCTTTGAGCTAAATGTAATCGAACTCGAAGGTCACGGTTGACAGAT
196 ATGCTATAAATTTGATGTGTCTTTGAGCTGAATGTAATCGAACTCGAAGGTCACGGTTGACAGAT
*
39519 AACCCTTCTT-GCCTTGAGTTATGCTGTAAATTAGATATGCATTTTAGTTGAATGTAATTGAACT
261 AACCCTT-TTCGCCTTGAGTTA--CTG--AATTAGATA--CA---TAGTTG-A-GTAATCGAACT
* *
39583 CGAAGGTCTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCCATGCTGTAAATTTAATGTGCCTT
314 CGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTAATGTGCCTT
* *
39648 TGAGCTAAATGTAATCAAACCCGAAGGTCACAG
379 TGAGCTAAATGTAATCGAACTCGAAGGTCACAG
* *
39681 TTGATAGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTGGATATGCCTTTGAGCTAAATGTA
1 TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAATGTA
* * ** *
39746 ATCGAATTCAAAGGTCACAGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAATTAGAT
66 ATCGAACTCGAAGGTCTTAGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT--A--A-AT
* * * * * *
39811 ATGCATTTGAGTTGAATGTAATTGAACTCGAAGGTCTTTTGTTGACATATAGCCCTTCTCACCTT
126 ATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGACAGATAGCCCTTCTCACCTT
* * * * **
39876 GAGCTATGCTTTAAATTTGATGTGCCTTTGAGCTGAATGTAATCAAACCCGAAGGTCATAGTTGA
191 GAGCTATGCTATAAATTTGATGTGTCTTTGAGCTGAATGTAATCGAACTCGAAGGTCACGGTTGA
*
39941 CAGATAACCCTTCTCGCCTTGAGTTA
256 CAGATAACCCTTTTCGCCTTGAGTTA
39967 AGCTATAAAT
Statistics
Matches: 956, Mismatches: 121, Indels: 65
0.84 0.11 0.06
Matches are distributed among these distances:
400 4 0.00
401 9 0.01
402 331 0.35
403 2 0.00
405 4 0.00
406 1 0.00
408 1 0.00
409 1 0.00
410 1 0.00
411 2 0.00
413 2 0.00
414 2 0.00
415 1 0.00
416 1 0.00
418 1 0.00
419 5 0.01
420 2 0.00
421 9 0.01
422 330 0.35
424 1 0.00
425 5 0.01
426 100 0.10
427 141 0.15
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.35
Consensus pattern (411 bp):
TTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAATGTA
ATCGAACTCGAAGGTCTTAGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATATGCC
TTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGACAGATAGCCCTTCTCACCTTGAGCT
ATGCTATAAATTTGATGTGTCTTTGAGCTGAATGTAATCGAACTCGAAGGTCACGGTTGACAGAT
AACCCTTTTCGCCTTGAGTTACTGAATTAGATACATAGTTGAGTAATCGAACTCGAAGGTCTTTT
GTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTAATGTGCCTTTGAGCTAAATGT
AATCGAACTCGAAGGTCACAG
Found at i:40024 original size:171 final size:171
Alignment explanation
Indices: 39150--40058 Score: 1010
Period size: 171 Copynumber: 5.4 Consensus size: 171
39140 ATGTAAATTG
* * * * *
39150 GTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTATCGTCTTGAGCTATGTTGTAAATT
1 GTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATT
* * * ** *
39215 TGATGTGCCTTTGAGCTGAATGTAATTGAACTCAAAGGTCACGGTTGACAGATAACCCTTCTCTC
66 TGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCATAGTTGACAGATAACCCTTCTCGC
*
39280 CTTGAGTTATGCTGTAAATTGGATATACCTTTGAGCTAAAT
131 CTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAAT
* * * *
39321 GTAATCGAACTCGAAGGT-CTTGGTTGACGGATAACCCTTCTCGCCTTGAGTTATGCTGT-AA--
1 GTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATT
* * * * * *
39382 --ATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGTGTTGAGAGATAGCCCTTCTCA
66 TGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCAT-AGTTGACAGATAACCCTTCTCG
* * * * *
39445 CCTTGAGCTATGCTATAAATTTGATGTGTCTTTGAGCTAAAT
130 CCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAAT
** * *
39487 GTAATCGAACTCGAAGGTCA--CGGTTGACAGATAACCCTTCTTGCCTTGAGTTATGCTGTAAAT
1 GTAATCGAACTCGAAGGT-ATTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAAT
* * * * * * * *
39550 TAGATATGCATTTTAGTTGAATGTAATTGAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTC
65 TTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTC-ATAGTTGACAGATAACCCTTCTC
** ** *
39615 GCCTTGAGCCATGCTGTAAATTTAATGTGCCTTTGAGCTAAAT
129 GCCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAAT
* * ** * * *
39658 GTAATCAAACCCGAAGGTCA--CAGTTGATAGATAACCCTTCTCGCCTTGAGTTATGCTATAAAT
1 GTAATCGAACTCGAAGGT-ATTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAAT
* * * * * *
39721 TGGATATGCCTTTGAGCTAAATGTAATCGAATTCAAAGGTCACAGTTGACAGATAACCCTTCTTG
65 TTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCATAGTTGACAGATAACCCTTCTCG
* * * *
39786 CCTTGAGTTATGCTGTAAATTAGATATGCATTTGAGTTGAAT
130 CCTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAAT
* * * * * *
39828 GTAATTGAACTCGAAGGTCTTTTGTTGACATATAGCCCTTCTCACCTTGAGCTATGCTTTAAATT
1 GTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATT
* * *
39893 TGATGTGCCTTTGAGCTGAATGTAATCAAACCCGAAGGTCATAGTTGACAGATAACCCTTCTCGC
66 TGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCATAGTTGACAGATAACCCTTCTCGC
* * *
39958 CTTGAGTTAAGCTATAAATTGGATATGCCTTTGAGCTGAAT
131 CTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAAT
* * * * *
39999 GTAATCAAACTCGAAGGTATTTTGTTGAAAGATAGCTCTTCTCTCCTTGAGCTATGCTGT
1 GTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGT
40059 CATAATTCTC
Statistics
Matches: 628, Mismatches: 99, Indels: 22
0.84 0.13 0.03
Matches are distributed among these distances:
165 34 0.05
166 108 0.17
167 2 0.00
169 2 0.00
170 101 0.16
171 379 0.60
172 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (171 bp):
GTAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATT
TGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCATAGTTGACAGATAACCCTTCTCGC
CTTGAGTTATGCTGTAAATTGGATATGCCTTTGAGCTAAAT
Found at i:41385 original size:95 final size:95
Alignment explanation
Indices: 41188--41442 Score: 334
Period size: 95 Copynumber: 2.7 Consensus size: 95
41178 GGCTAGCTGG
* * *
41188 ATCCATAAAGCCGGGGTGTTTAACCAATTGA-TCTAGAGGGACAACTTAATATCATTGTATAG-A
1 ATCCATAAAGCCGGGGTGTTTAACCAATT-ACTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTA
41251 TATTATAATCACCTTTATCAGGCTAGCTAAATATT
61 TATTATAATCACCTTTATCAGGCTAGCTAAATATT
* * *
41286 ATCCATAAAGCCGGGGCGTTTAACCAATTACTCTAGAGGAAAAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGTGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* *
41351 TAATCACCTTTATCAGGCTAGCTTAATCTT
66 TAATCACCTTTATCAGGCTAGCTAAATATT
* * * * *
41381 ATCCATAAAGTCGGGGTGTTTAACAAATTGCTCTAGAGGGACAGCTCAAGCTTTATTATATA
1 ATCCATAAAGCCGGGGTGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATA
41443 GATATAATAT
Statistics
Matches: 139, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
94 4 0.03
95 90 0.65
96 2 0.01
97 3 0.02
98 40 0.29
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGTGTTTAACCAATTACTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTAAATATT
Found at i:44393 original size:29 final size:29
Alignment explanation
Indices: 44359--44420 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
44349 AAATATCAAA
44359 AACAGAAATTTAAATGACTAAAATAAAAT
1 AACAGAAATTTAAATGACTAAAATAAAAT
*
44388 AACAGAAATTTAAGTGACTAAAATAAAAT
1 AACAGAAATTTAAATGACTAAAATAAAAT
44417 AACA
1 AACA
44421 TAATATAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.23
Consensus pattern (29 bp):
AACAGAAATTTAAATGACTAAAATAAAAT
Found at i:44431 original size:29 final size:29
Alignment explanation
Indices: 44359--44442 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
44349 AAATATCAAA
44359 AACAGAAATTTAAA-TGACTAAAATAAAAT
1 AACAGAAA-TTAAAGTGACTAAAATAAAAT
*
44388 AACAGAAATTTAAGTGACTAAAATAAAAT
1 AACAGAAATTAAAGTGACTAAAATAAAAT
* * *
44417 AACA-TAATATAAAGTGCCCAAAATAA
1 AACAGAAAT-TAAAGTGACTAAAATAA
44443 GAAATAAACA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 7 0.15
29 41 0.85
ACGTcount: A:0.60, C:0.10, G:0.08, T:0.23
Consensus pattern (29 bp):
AACAGAAATTAAAGTGACTAAAATAAAAT
Found at i:51888 original size:150 final size:151
Alignment explanation
Indices: 51719--52020 Score: 597
Period size: 150 Copynumber: 2.0 Consensus size: 151
51709 CTTTTTATAT
51719 TATCATGTTCTTCTTATCTTTAATACATATACACATCATATAATATCACATCACCAAACAAACAT
1 TATCATGTTCTTCTTATCTTTAATACATATACACATCATATAATATCACATCACCAAACAAACAT
51784 GTAACATCACATAGAAATTTCGCATATTATATTTTTAATGGCCCATGTACACATATGA-AACTAT
66 GTAACATCACATAGAAATTTCGCATATTATATTTTTAATGGCCCATGTACACATATGAGAACTAT
51848 AGATATGTGAGTTTATAGAGG
131 AGATATGTGAGTTTATAGAGG
51869 TATCATGTTCTTCTTATCTTTAATACATATACACATCATATAATATCACATCACCAAACAAACAT
1 TATCATGTTCTTCTTATCTTTAATACATATACACATCATATAATATCACATCACCAAACAAACAT
51934 GTAACATCACATAGAAATTTCGCATATTATATTTTTAATGGCCCATGTACACATATGAGAACTAT
66 GTAACATCACATAGAAATTTCGCATATTATATTTTTAATGGCCCATGTACACATATGAGAACTAT
51999 AGATATGTGAGTTTATAGAGG
131 AGATATGTGAGTTTATAGAGG
52020 T
1 T
52021 TGTGCACTAA
Statistics
Matches: 151, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
150 123 0.81
151 28 0.19
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (151 bp):
TATCATGTTCTTCTTATCTTTAATACATATACACATCATATAATATCACATCACCAAACAAACAT
GTAACATCACATAGAAATTTCGCATATTATATTTTTAATGGCCCATGTACACATATGAGAACTAT
AGATATGTGAGTTTATAGAGG
Found at i:52081 original size:23 final size:24
Alignment explanation
Indices: 52046--52116 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 24
52036 TCACCACAGC
* *
52046 TCGTATAAATGCACCGGAGTGCCA
1 TCGTAGAAATGCACCGAAGTGCCA
52070 T-GTA-AAATTGCACCGAAGTGCC-
1 TCGTAGAAA-TGCACCGAAGTGCCA
*
52092 TCGTAGAAATGCACCGTAGTGCCA
1 TCGTAGAAATGCACCGAAGTGCCA
52116 T
1 T
52117 ATAAGATGTC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
22 4 0.10
23 32 0.78
24 5 0.12
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.23
Consensus pattern (24 bp):
TCGTAGAAATGCACCGAAGTGCCA
Found at i:52535 original size:2 final size:2
Alignment explanation
Indices: 52528--52590 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
52518 ATGACTTCTC
52528 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
52570 AT AT AT AT AT A- AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
52591 AACTTGCATT
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52647 original size:19 final size:21
Alignment explanation
Indices: 52623--52661 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52613 AATCTACTCA
52623 TAATAA-A-ATATATCATATT
1 TAATAATATATATATCATATT
52642 TAATAATATATATATCATAT
1 TAATAATATATATATCATAT
52662 AGGTATATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAATATATATATCATATT
Found at i:57085 original size:23 final size:23
Alignment explanation
Indices: 57059--57142 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
57049 CTCGTATAAA
57059 TGCACC-AGAGTGCCACGTAGAAT
1 TGCACCGA-AGTGCCACGTAGAAT
*
57082 TGCACCGGAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
57105 TGCACCGAAGTGCCGCGTAGAAA
1 TGCACCGAAGTGCCACGTAGAAT
*
57128 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
57143 TATAAGATGT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:61511 original size:31 final size:31
Alignment explanation
Indices: 61397--61517 Score: 133
Period size: 32 Copynumber: 4.0 Consensus size: 31
61387 CCCGAAGGAC
* *
61397 CTATCCATGT-TCC-GAAGAACATAGGT-AA
1 CTATCCATATGTCCTGAAGGACATAGGTAAA
* *
61425 CTGTCCATATGTCCTGAAGGACATAGGTAATC
1 CTATCCATATGTCCTGAAGGACATAGGTAA-A
* *
61457 CTTTCTATATGTCCTGAAGGACATAGGTAAA
1 CTATCCATATGTCCTGAAGGACATAGGTAAA
*
61488 CTATCCATATGT-CTCGAAAGACATAGGTAA
1 CTATCCATATGTCCT-GAAGGACATAGGTAA
61518 CCCTCGACTC
Statistics
Matches: 78, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.10
29 3 0.04
30 14 0.18
31 25 0.32
32 28 0.36
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (31 bp):
CTATCCATATGTCCTGAAGGACATAGGTAAA
Found at i:61773 original size:2 final size:2
Alignment explanation
Indices: 61755--61810 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
61745 TCACATTGTC
* *
61755 AT AT TT AT AT TT 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
61797 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
61811 CTCTTATGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:66234 original size:32 final size:30
Alignment explanation
Indices: 66153--66276 Score: 149
Period size: 30 Copynumber: 4.0 Consensus size: 30
66143 CCCGAAGGAC
* *
66153 CTATCCATATGTTCCGAAGAACATAGGTAA
1 CTATCCATATGTCCCGAAGGACATAGGTAA
* *
66183 CTGTCCATATGTCCTGAAGGACATAGGTAA
1 CTATCCATATGTCCCGAAGGACATAGGTAA
* *
66213 TCCTTTCTATATGTCCCGAAGGACATAGGTAAA
1 --CTATCCATATGTCCCGAAGGACATAGGT-AA
* *
66246 CTATCCATATGTCTCGAAAGACATAGGTAA
1 CTATCCATATGTCCCGAAGGACATAGGTAA
66276 C
1 C
66277 CCTCGACTCT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
30 29 0.36
31 24 0.30
32 25 0.31
33 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (30 bp):
CTATCCATATGTCCCGAAGGACATAGGTAA
Found at i:71052 original size:32 final size:30
Alignment explanation
Indices: 70974--71062 Score: 106
Period size: 32 Copynumber: 2.9 Consensus size: 30
70964 GAAAGACCTA
* *
70974 TCCATATGTTCTGAAGAACATAGGTAATTG
1 TCCATATGTCCTGAAGGACATAGGTAATTG
* *
71004 TTCATATATCCTGAAGGACATAGGTAATCATG
1 TCCATATGTCCTGAAGGACATAGGTAAT--TG
* *
71036 TCCATATGTCCCGAAGGACATAAGTAA
1 TCCATATGTCCTGAAGGACATAGGTAA
71063 ACCATCTATA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 24 0.49
32 25 0.51
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (30 bp):
TCCATATGTCCTGAAGGACATAGGTAATTG
Found at i:71386 original size:2 final size:2
Alignment explanation
Indices: 71379--71403 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
71369 TTCTTATTCT
71379 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
71404 TCTCATATAC
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:72821 original size:20 final size:20
Alignment explanation
Indices: 72796--72847 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
72786 CGTTACATAG
72796 TGCATCGATACATTCAGGGA
1 TGCATCGATACATTCAGGGA
*
72816 TGCATCGATACATTCAGGGG
1 TGCATCGATACATTCAGGGA
*
72836 TGTATCGATACA
1 TGCATCGATACA
72848 CATGCATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (20 bp):
TGCATCGATACATTCAGGGA
Found at i:73877 original size:2 final size:2
Alignment explanation
Indices: 73870--73901 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
73860 AGGTAAAATG
73870 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
73902 GTCTATGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74448 original size:23 final size:23
Alignment explanation
Indices: 74405--74463 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
74395 ATTTTATATG
* **
74405 GCACTACGGTGCAATTTTACGCA
1 GCACTTCGGTGCAATCCTACGCA
**
74428 GCACTTCGGTGCAATCCTACGTG
1 GCACTTCGGTGCAATCCTACGCA
*
74451 GTACTTCGGTGCA
1 GCACTTCGGTGCA
74464 TTTATACGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GCACTTCGGTGCAATCCTACGCA
Done.