Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020960.1 Corchorus olitorius cultivar O-4 contig20993, 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: 56388
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:412 original size:119 final size:123
Alignment explanation
Indices: 126--441 Score: 353
Period size: 127 Copynumber: 2.6 Consensus size: 123
116 TAAAGTGCAT
*
126 TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACAGGGTTTTCCGACTTAAGGTTTTTAATGA
1 TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACTTAAGGTTTTTAATGA
* * * *
191 GGCAACAATAGCACATTTAGATGTAATTGTCCTGAAGACATTTACATGGACTTAAATTGCTC
66 GGCAAAAAGAGCACATGTAGA-GTAATTGTCCAGAAGACA--TACATGGACTTAAATTGC-C
* * **
253 TAGCACTC-TTTTCCCTTTTGTTCGGTTTTGTCCCACTGGGTTTTCCGACACAAGGTTTTTAATG
1 T-GCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACTTAAGGTTTTTAATG
* * *
317 AGGCAATAAAGAGCACATGTA-A-TATTTGTTCAGAAGACA-A-ATGGACTT-GATATG-C
65 AGGCAA-AAAGAGCACATGTAGAGTAATTGTCCAGAAGACATACATGGACTTAAAT-TGCC
* * *
372 TGCACTCTTTTTTCCTTATGA-CTGGTTTTGTCCCATTGGGTTTTCC-AGCTTAAGGTTTTTAAC
1 TGCACTCTTTTTCCCTTATGATC-GGTTTTGTCCCACTGGGTTTTCCGA-CTTAAGGTTTTTAAT
435 GAGGCAA
64 GAGGCAA
442 CCATAATACG
Statistics
Matches: 164, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
118 8 0.05
119 53 0.32
120 2 0.01
121 10 0.06
122 1 0.01
125 14 0.09
127 59 0.36
128 17 0.10
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (123 bp):
TGCACTCTTTTTCCCTTATGATCGGTTTTGTCCCACTGGGTTTTCCGACTTAAGGTTTTTAATGA
GGCAAAAAGAGCACATGTAGAGTAATTGTCCAGAAGACATACATGGACTTAAATTGCC
Found at i:1338 original size:54 final size:54
Alignment explanation
Indices: 1256--1365 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
1246 AAAGCATCGC
1256 AACAATATCATATACTAAGGAAGCTTCCTGCCAAAGAGAGTCTCTGCCTTTGTG
1 AACAATATCATATACTAAGGAAGCTTCCTGCCAAAGAGAGTCTCTGCCTTTGTG
1310 AACAATATCATATACTAAGGAAGCTTCCTGCCAAAGAGAGTCTCTGCCTTTGTG
1 AACAATATCATATACTAAGGAAGCTTCCTGCCAAAGAGAGTCTCTGCCTTTGTG
1364 AA
1 AA
1366 TTTCATCCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (54 bp):
AACAATATCATATACTAAGGAAGCTTCCTGCCAAAGAGAGTCTCTGCCTTTGTG
Found at i:3826 original size:15 final size:15
Alignment explanation
Indices: 3806--3883 Score: 88
Period size: 15 Copynumber: 5.2 Consensus size: 15
3796 AGTAAACACT
3806 TTCGGTGCCATCATC
1 TTCGGTGCCATCATC
*
3821 TTCGGTGCCATCGA-A
1 TTCGGTGCCATC-ATC
*
3836 TTGGGTGCCATCATC
1 TTCGGTGCCATCATC
*
3851 TTCGGTGCCGTCGAT-
1 TTCGGTGCCATC-ATC
*
3866 TTTGGTGCCATCATC
1 TTCGGTGCCATCATC
3881 TTC
1 TTC
3884 TTCCATGACA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.06
15 45 0.88
16 3 0.06
ACGTcount: A:0.13, C:0.28, G:0.24, T:0.35
Consensus pattern (15 bp):
TTCGGTGCCATCATC
Found at i:3845 original size:30 final size:30
Alignment explanation
Indices: 3809--3883 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
3799 AAACACTTTC
3809 GGTGCCATCATCTTCGGTGCCATCGAATTG
1 GGTGCCATCATCTTCGGTGCCATCGAATTG
* * *
3839 GGTGCCATCATCTTCGGTGCCGTCGATTTT
1 GGTGCCATCATCTTCGGTGCCATCGAATTG
3869 GGTGCCATCATCTTC
1 GGTGCCATCATCTTC
3884 TTCCATGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.13, C:0.28, G:0.25, T:0.33
Consensus pattern (30 bp):
GGTGCCATCATCTTCGGTGCCATCGAATTG
Found at i:5149 original size:18 final size:18
Alignment explanation
Indices: 5090--5177 Score: 104
Period size: 18 Copynumber: 4.9 Consensus size: 18
5080 AAGTGTGGCA
5090 ACTTGGTGCGGTGCGACC
1 ACTTGGTGCGGTGCGACC
* *
5108 ACTAGATGCGGTGCGACC
1 ACTTGGTGCGGTGCGACC
*
5126 ACTTGGTGTGGTGCGACC
1 ACTTGGTGCGGTGCGACC
* * * **
5144 ATTTGGTGTGGTGCAAAT
1 ACTTGGTGCGGTGCGACC
5162 ACTTGGTGCGGTGCGA
1 ACTTGGTGCGGTGCGA
5178 TTTGTTGTTG
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.16, C:0.20, G:0.38, T:0.26
Consensus pattern (18 bp):
ACTTGGTGCGGTGCGACC
Found at i:5816 original size:49 final size:47
Alignment explanation
Indices: 5711--5852 Score: 178
Period size: 49 Copynumber: 3.0 Consensus size: 47
5701 GAGCGTGCCA
* *
5711 ATCAATTTTGTCCAAAAATTGATAAAAAGTGCAATAAAAAGTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATAAAAAGTAAAAG
*
5758 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGTAAGTAAAAA-TAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAA-TAAAAAGTAAAAG
* * **
5807 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGCAGGAAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATAAAAAGTAAA
5853 GGATTGCTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
47 17 0.21
48 22 0.27
49 37 0.45
50 6 0.07
ACGTcount: A:0.52, C:0.06, G:0.15, T:0.27
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATAAAAAGTAAAAG
Found at i:12937 original size:22 final size:22
Alignment explanation
Indices: 12909--12951 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12899 AAAATCTAAT
*
12909 TCAACCTTTGGAGAGGTCGAAC
1 TCAACCTTCGGAGAGGTCGAAC
*
12931 TCAACCTTCGTAGAGGTCGAA
1 TCAACCTTCGGAGAGGTCGAA
12952 ACAACAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (22 bp):
TCAACCTTCGGAGAGGTCGAAC
Found at i:16685 original size:24 final size:25
Alignment explanation
Indices: 16635--16685 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
16625 ATTGGAGTAT
* *
16635 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTATA
* *
16660 TTATTT-TCTTGTTTATTTATTATA
1 TTATTTATCTTGTTGATTAATTATA
16684 TT
1 TT
16686 GTTCACATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.20, C:0.06, G:0.06, T:0.69
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTATA
Found at i:18518 original size:26 final size:27
Alignment explanation
Indices: 18484--18544 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
18474 CACTTTTAGT
*
18484 TTAGGTTAGCTAATTCATATTTAGGC-
1 TTAGATTAGCTAATTCATATTTAGGCA
*
18510 TTAGATTAGCTAATTCATCTTTAGGCA
1 TTAGATTAGCTAATTCATATTTAGGCA
18537 TCTAGATT
1 T-TAGATT
18545 GCATTTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 24 0.77
27 1 0.03
28 6 0.19
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (27 bp):
TTAGATTAGCTAATTCATATTTAGGCA
Found at i:21301 original size:35 final size:35
Alignment explanation
Indices: 21218--22010 Score: 691
Period size: 35 Copynumber: 21.8 Consensus size: 35
21208 CAAATTGGTC
*
21218 AAAGACTTAATTCAGGGTAATTAAGTAAATAACAGT
1 AAAGACTTAATTCAGGGTAATTAAGTAAA-ATCAGT
* *
21254 CAAAGACTTAATTTAGGGTAATTAAGTAAAATCGGT
1 -AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
* *
21290 AAAGACTTAATTCAGGGTAATTAAGTGAAATCAGC
1 AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
*
21325 AAAGACTTAATTCAGGGTAATTAAGTAATATCAGT
1 AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
* * *
21360 CAAGTATTTAATTTAGGGTAATTAAGTAAAATCAGT
1 AAAG-ACTTAATTCAGGGTAATTAAGTAAAATCAGT
* * * **
21396 ACAGACTTAATTCAGGGTATTTAAGTGAAATCAAC
1 AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
*
21431 AAAGACTTAATTCAGGTTAATTAAGTAAAATCAGT
1 AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
* *
21466 CAAATACTTAATTCAGGGTAATTAAGTCAAATCAGT
1 -AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
* * * *
21502 AAATACTTAATTCAGGGTAATTAAGTGAAATTAGA
1 AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
*
21537 AAAGACTTAATCCAGGGTAATTAAGTAAAATCAGT
1 AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
*
21572 CAAAGACTTAATTCAGGGTAATTAAGTAAACAACAGT
1 -AAAGACTTAATTCAGGGTAATTAAGTAAA-ATCAGT
* * *
21609 CAAAGACTTAATTTAGGGTAATTAAGTAAAATCGGC
1 -AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
* *
21645 AAAGACTTAATTCATGGTAATTAAGTGAAAAAT-AAT
1 AAAGACTTAATTCAGGGTAATTAAGT--AAAATCAGT
* ** * * ** * * *
21681 TAAGTAAAATCAGTCAAAGATTTAATCTAGGGT-AATTAAGT
1 AAAG--ACTTAATTC--AG-GGTAAT-TA-AGTAAAATCAGT
* *
21722 AAACAACAGTCAAAGACTTGATTCAGGGTAATTATGT-AAATCAGT
1 -----------AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
*
21767 CAAAGACTTAATTCAGAGTAATTAAGTAAAATCAGT
1 -AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
21803 CAAAGACTTAATTCAGGGTAATTAAGTAAAAGT-AGT
1 -AAAGACTTAATTCAGGGTAATTAAGTAAAA-TCAGT
*
21839 CAAAGACTTAATTCAGGGTAATTAAGT-AAACCAGT
1 -AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
* * * * *
21874 CAAGGACTTAATTCAGAGTAAATAAGTAAAGTCAAT
1 -AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
* * * * *
21910 CAAGGAACTTAATTCTGGGTAATTAAGTAGAGTCAAT
1 -AAAG-ACTTAATTCAGGGTAATTAAGTAAAATCAGT
* * * *
21947 -AAGTAACTTAATTC-TGGTAATTAAGTAGAGTCAAT
1 AAAG--ACTTAATTCAGGGTAATTAAGTAAAATCAGT
*
21982 AAAGAACTTAATTCAAGGTAATTAAGTAA
1 AAAG-ACTTAATTCAGGGTAATTAAGTAA
22011 GACATTAAAT
Statistics
Matches: 633, Mismatches: 90, Indels: 67
0.80 0.11 0.08
Matches are distributed among these distances:
35 292 0.46
36 203 0.32
37 95 0.15
38 5 0.01
40 4 0.01
41 6 0.01
42 2 0.00
43 2 0.00
45 8 0.01
46 2 0.00
47 4 0.01
48 2 0.00
50 5 0.01
52 3 0.00
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (35 bp):
AAAGACTTAATTCAGGGTAATTAAGTAAAATCAGT
Found at i:21402 original size:71 final size:70
Alignment explanation
Indices: 21219--22010 Score: 613
Period size: 71 Copynumber: 10.9 Consensus size: 70
21209 AAATTGGTCA
* *
21219 AAGACTTAATTCAGGGTAATTAAGTAAATAACAGTCAAAGACTTAATTTAGGGTAATTAAGTAAA
1 AAGACTTAATTCAGGGTAATTAAGTAAA-ATCAGTCAAAGACTTAATTCAGGGTAATTAAGT-AA
* *
21284 ATCGGTA
64 ATCAGTC
*
21291 AAGACTTAATTCAGGGTAATTAAGTGAAATCAG-CAAAGACTTAATTCAGGGTAATTAAGTAATA
1 AAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAA-A
21355 TCAGTC
65 TCAGTC
* * * *
21361 AAGTATTTAATTTAGGGTAATTAAGTAAAATCAGT-ACAGACTTAATTCAGGGTATTTAAGTGAA
1 AAG-ACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGT-AA
*
21425 ATCA-AC
64 ATCAGTC
* *
21431 AAAGACTTAATTCAGGTTAATTAAGTAAAATCAGTCAAATACTTAATTCAGGGTAATTAAGTCAA
1 -AAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGT-AA
*
21496 ATCAGTA
64 ATCAGTC
* * * * *
21503 AATACTTAATTCAGGGTAATTAAGTGAAATTAG-AAAAGACTTAATCCAGGGTAATTAAGTAAAA
1 AAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGT-AAA
21567 TCAGTC
65 TCAGTC
* *
21573 AAAGACTTAATTCAGGGTAATTAAGTAAACAACAGTCAAAGACTTAATTTAGGGTAATTAAGTAA
1 -AAGACTTAATTCAGGGTAATTAAGTAAA-ATCAGTCAAAGACTTAATTCAGGGTAATTAAGT-A
*
21638 AATC-GGC
63 AATCAGTC
* * * ** * * **
21645 AAAGACTTAATTCATGGTAATTAAGTGAAAAAT-AAT-TAAGTAAAATCAGTCAAAGATTTAATC
1 -AAGACTTAATTCAGGGTAATTAAGT--AAAATCAGTCAAAG--ACTTAATTC--AG-GGTAAT-
* * *
21708 TAGGGTAATTAAGT-
57 TA-AGTAAATCAGTC
* * ** * * *
21722 AA-AC-AACAGTCAAAGACTTGATTCAGGGTAATTATGTAAATCAGTCAAAGACTTAATTCAGAG
1 AAGACTTA-ATTC--AG-GGTAATT-A----AG-TA---AAATCAGTCAAAGACTTAATTCAGGG
21785 TAATTAAGTAAAATCAGTC
53 TAATTAAGT-AAATCAGTC
21804 AAAGACTTAATTCAGGGTAATTAAGTAAAAGT-AGTCAAAGACTTAATTCAGGGTAATTAAGTAA
1 -AAGACTTAATTCAGGGTAATTAAGTAAAA-TCAGTCAAAGACTTAATTCAGGGTAATTAAGTAA
*
21868 ACCAGTC
64 ATCAGTC
* * * * * *
21875 AAGGACTTAATTCAGAGTAAATAAGTAAAGTCAATCAAGGAACTTAATTCTGGGTAATTAAGTAG
1 AA-GACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAG-ACTTAATTCAGGGTAATTAAGTA-
* *
21940 AGTCAAT-
63 AATCAGTC
* * * * *
21947 AAGTAACTTAATTC-TGGTAATTAAGTAGAGTCAAT-AAAGAACTTAATTCAAGGTAATTAAGTA
1 AAG--ACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAG-ACTTAATTCAGGGTAATTAAGTA
22010 A
63 A
22011 GACATTAAAT
Statistics
Matches: 579, Mismatches: 94, Indels: 96
0.75 0.12 0.12
Matches are distributed among these distances:
69 2 0.00
70 99 0.17
71 213 0.37
72 134 0.23
73 49 0.08
74 4 0.01
75 9 0.02
76 7 0.01
77 6 0.01
78 7 0.01
79 1 0.00
80 3 0.01
81 12 0.02
82 7 0.01
83 5 0.01
84 6 0.01
85 10 0.02
86 2 0.00
87 3 0.01
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (70 bp):
AAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAT
CAGTC
Found at i:21403 original size:106 final size:104
Alignment explanation
Indices: 21217--22010 Score: 734
Period size: 106 Copynumber: 7.3 Consensus size: 104
21207 ACAAATTGGT
*
21217 CAAAGACTTAATTCAGGGTAATTAAGTAAATAACAGTCAAAGACTTAATTTAGGGTAATTAAGTA
1 CAAAGACTTAATTCAGGGTAATTAAGTAAA-ATCAGTC-AAGACTTAATTTAGGGTAATTAAGTA
*
21282 AAATCGGTAAAGACTTAATTCAGGGTAATTAAGTGAAATCAG
64 AAATCAGTAAAGACTTAATTCAGGGTAATTAAGT-AAATCAG
* *
21324 CAAAGACTTAATTCAGGGTAATTAAGTAATATCAGTCAAGTATTTAATTTAGGGTAATTAAGTAA
1 CAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAG-ACTTAATTTAGGGTAATTAAGTAA
* * *
21389 AATCAGTACAGACTTAATTCAGGGTATTTAAGTGAAATCAA
65 AATCAGTAAAGACTTAATTCAGGGTAATTAAGT-AAATCAG
* * * *
21430 CAAAGACTTAATTCAGGTTAATTAAGTAAAATCAGTCAAATACTTAATTCAGGGTAATTAAGTCA
1 CAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTC-AAGACTTAATTTAGGGTAATTAAGTAA
* *
21495 AATCAGTAAATACTTAATTCAGGGTAATTAAGTGAAATTAG
65 AATCAGTAAAGACTTAATTCAGGGTAATTAAGT-AAATCAG
* * *
21536 AAAAGACTTAATCCAGGGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAA
1 CAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTC-AAGACTTAATTTAGGGTAATTAAGTAA
* * *
21601 ACAACAGTCAAAGACTTAATTTAGGGTAATTAAGTAAAATCGG
65 A-ATCAGT-AAAGACTTAATTCAGGGTAATTAAGT-AAATCAG
* * * * * * ** **
21644 CAAAGACTTAATTCATGGTAATTAAGTGAAAAAT-AATTAAGTAAAATCAGTCAAAGATTTAATC
1 CAAAGACTTAATTCAGGGTAATTAAGT--AAAATCAGTCAAG---ACTTAAT-TTAG-GGTAAT-
* * * *
21708 TAGGGTAATTAAGTAAACAACAGTCAAAGACTTGATTCAGGGTAATTATGTAAATCAG
58 TA-AGTAA--AA-T--C----AGT-AAAGACTTAATTCAGGGTAATTAAGTAAATCAG
* *
21766 TCAAAGACTTAATTCAGAGTAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTA
1 -CAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTC-AAGACTTAATTTAGGGTAATTAAGTA
*
21831 AAAGT-AGTCAAAGACTTAATTCAGGGTAATTAAGTAAACCAG
64 AAA-TCAGT-AAAGACTTAATTCAGGGTAATTAAGTAAATCAG
* * * * *
21873 TCAAGGACTTAATTCAGAGTAAATAAGTAAAGTCAATCAAGGAACTTAATTCT-GGGTAATTAAG
1 -CAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAA-G-ACTTAATT-TAGGGTAATTAAG
* * * * * *
21937 TAGAGTCAAT-AAGTAACTTAATTC-TGGTAATTAAGTAGAGTCAA
62 TAAAATCAGTAAAG--ACTTAATTCAGGGTAATTAAGTA-AATCAG
* *
21981 TAAAGAACTTAATTCAAGGTAATTAAGTAA
1 CAAAG-ACTTAATTCAGGGTAATTAAGTAA
22011 GACATTAAAT
Statistics
Matches: 574, Mismatches: 80, Indels: 65
0.80 0.11 0.09
Matches are distributed among these distances:
105 3 0.01
106 224 0.39
107 121 0.21
108 113 0.20
109 2 0.00
110 5 0.01
111 4 0.01
112 2 0.00
113 4 0.01
114 6 0.01
115 4 0.01
116 5 0.01
117 3 0.01
118 4 0.01
119 2 0.00
120 4 0.01
121 5 0.01
122 8 0.01
123 55 0.10
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (104 bp):
CAAAGACTTAATTCAGGGTAATTAAGTAAAATCAGTCAAGACTTAATTTAGGGTAATTAAGTAAA
ATCAGTAAAGACTTAATTCAGGGTAATTAAGTAAATCAG
Found at i:21724 original size:36 final size:36
Alignment explanation
Indices: 21677--22010 Score: 360
Period size: 36 Copynumber: 9.3 Consensus size: 36
21667 AAGTGAAAAA
*
21677 TAATTAAGTAAAATCAGTCAAAGATTTAA-TCTAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTC-AGGG
* *
21713 TAATTAAGTAAACAACAGTCAAAGACTTGATTCAGGG
1 TAATTAAGTAAA-ATCAGTCAAAGACTTAATTCAGGG
* *
21750 TAATTATGT-AAATCAGTCAAAGACTTAATTCAGAG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
21785 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
21821 TAATTAAGTAAAAGT-AGTCAAAGACTTAATTCAGGG
1 TAATTAAGTAAAA-TCAGTCAAAGACTTAATTCAGGG
* * *
21857 TAATTAAGT-AAACCAGTCAAGGACTTAATTCAGAG
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
* * * * *
21892 TAAATAAGTAAAGTCAATCAAGGAACTTAATTCTGGG
1 TAATTAAGTAAAATCAGTCAAAG-ACTTAATTCAGGG
* * * *
21929 TAATTAAGTAGAGTCAAT--AAGTAACTTAATTC-TGG
1 TAATTAAGTAAAATCAGTCAAAG--ACTTAATTCAGGG
* * * *
21964 TAATTAAGTAGAGTCAAT-AAAGAACTTAATTCAAGG
1 TAATTAAGTAAAATCAGTCAAAG-ACTTAATTCAGGG
22000 TAATTAAGTAA
1 TAATTAAGTAA
22011 GACATTAAAT
Statistics
Matches: 264, Mismatches: 24, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
35 91 0.34
36 117 0.44
37 54 0.20
38 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (36 bp):
TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGG
Found at i:21773 original size:123 final size:122
Alignment explanation
Indices: 21554--21797 Score: 386
Period size: 123 Copynumber: 2.0 Consensus size: 122
21544 TAATCCAGGG
21554 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAACAACAGTCAAAGACTTA
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAACAACAGTCAAAGACTTA
*
21619 ATTTAGGGTAATTAAGTAAAATCGGCAAAGACTTAATTCATG-GTAATTAAGTGAAAAA
66 ATTCAGGGTAATTAAGTAAAATCGGCAAAGACTTAATTCA-GAGTAATTAAGT-AAAAA
*
21677 TAATTAAGTAAAATCAGTCAAAGATTTAA-TCTAGGGTAATTAAGTAAACAACAGTCAAAGACTT
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTC-AGGGTAATTAAGTAAACAACAGTCAAAGACTT
* * *
21741 GATTCAGGGTAATTATGT-AAATCAGTCAAAGACTTAATTCAGAGTAATTAAGTAAAA
65 AATTCAGGGTAATTAAGTAAAATC-GGCAAAGACTTAATTCAGAGTAATTAAGTAAAA
21798 TCAGTCAAAG
Statistics
Matches: 113, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
122 12 0.11
123 101 0.89
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (122 bp):
TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAACAACAGTCAAAGACTTA
ATTCAGGGTAATTAAGTAAAATCGGCAAAGACTTAATTCAGAGTAATTAAGTAAAAA
Found at i:21884 original size:107 final size:108
Alignment explanation
Indices: 21677--21938 Score: 384
Period size: 107 Copynumber: 2.4 Consensus size: 108
21667 AAGTGAAAAA
*
21677 TAATTAAGTAAAATCAGTCAAAGATTTAA-TCTAGGGTAATTAAGTAAACAACAGTCAAAGACTT
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTC-AGGGTAATTAAGTAAACAACAGTCAAAGACTT
* * *
21741 GATTCAGGGTAATTATGTAAATCAGTCAAAGACTTAATTCAGAG
65 AATTCAGGGTAATTAAGTAAACCAGTCAAAGACTTAATTCAGAG
**
21785 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAA-AGTAGTCAAAGACTTA
1 TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAACAACAGTCAAAGACTTA
*
21849 ATTCAGGGTAATTAAGTAAACCAGTCAAGGACTTAATTCAGAG
66 ATTCAGGGTAATTAAGTAAACCAGTCAAAGACTTAATTCAGAG
* * * * *
21892 TAAATAAGTAAAGTCAATCAAGGAACTTAATTCTGGGTAATTAAGTA
1 TAATTAAGTAAAATCAGTCAAAG-ACTTAATTCAGGGTAATTAAGTA
21939 GAGTCAATAA
Statistics
Matches: 140, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
107 72 0.51
108 66 0.47
109 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (108 bp):
TAATTAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAACAACAGTCAAAGACTTA
ATTCAGGGTAATTAAGTAAACCAGTCAAAGACTTAATTCAGAG
Found at i:21966 original size:107 final size:105
Alignment explanation
Indices: 21681--21973 Score: 333
Period size: 107 Copynumber: 2.7 Consensus size: 105
21671 GAAAAATAAT
* * ** *
21681 TAAGTAAAATCAGTCAAAGATTTAA-TCTAGGGTAATTAAGTAAACAACAGTCAAAGACTTGATT
1 TAAGTAAAATCAATCAAAGACTTAATTC-AGGGTAATTAAGT--A-AGTAGTCAAAGACTTAATT
* * *
21745 CAGGGTAATTATGTAAATCAGTCAAAGACTTAATTCAGAGTAAT
62 CAGGGTAATTAAGTAAACCAGTCAAAGACTTAATTCAGAGTAAA
*
21789 TAAGTAAAATCAGTCAAAGACTTAATTCAGGGTAATTAAGTAAAAGTAGTCAAAGACTTAATTCA
1 TAAGTAAAATCAATCAAAGACTTAATTCAGGGTAATTAAGT--AAGTAGTCAAAGACTTAATTCA
*
21854 GGGTAATTAAGTAAACCAGTCAAGGACTTAATTCAGAGTAAA
64 GGGTAATTAAGTAAACCAGTCAAAGACTTAATTCAGAGTAAA
* * *
21896 TAAGTAAAGTCAATCAAGGAACTTAATTCTGGGTAATTAAGT-AG-AGTCAATAAGTAACTTAAT
1 TAAGTAAAATCAATCAAAG-ACTTAATTCAGGGTAATTAAGTAAGTAGTC-A-AAG--ACTTAAT
*
21959 TC-TGGTAATTAAGTA
61 TCAGGGTAATTAAGTA
21974 GAGTCAATAA
Statistics
Matches: 166, Mismatches: 13, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
104 4 0.02
105 3 0.02
106 3 0.02
107 84 0.51
108 70 0.42
109 2 0.01
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.29
Consensus pattern (105 bp):
TAAGTAAAATCAATCAAAGACTTAATTCAGGGTAATTAAGTAAGTAGTCAAAGACTTAATTCAGG
GTAATTAAGTAAACCAGTCAAAGACTTAATTCAGAGTAAA
Found at i:24075 original size:6 final size:6
Alignment explanation
Indices: 24064--24113 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
24054 TTGACAGCGC
* *
24064 AACAAA AAC-AA AACGAA AAC-AA AACAAA AACAAA AACAGAA AACGAA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACA-AA AACAAA
24111 AAC
1 AAC
24114 GATGTCAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
5 10 0.25
6 25 0.62
7 5 0.12
ACGTcount: A:0.76, C:0.18, G:0.06, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:24084 original size:11 final size:12
Alignment explanation
Indices: 24064--24113 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
24054 TTGACAGCGC
24064 AACAAAAAC-AA
1 AACAAAAACGAA
*
24075 AACGAAAAC-AA
1 AACAAAAACGAA
*
24086 AACAAAAACAAA
1 AACAAAAACGAA
24098 AACAGAAAACGAA
1 AACA-AAAACGAA
24111 AAC
1 AAC
24114 GATGTCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
11 18 0.53
12 6 0.18
13 10 0.29
ACGTcount: A:0.76, C:0.18, G:0.06, T:0.00
Consensus pattern (12 bp):
AACAAAAACGAA
Found at i:24084 original size:17 final size:18
Alignment explanation
Indices: 24064--24115 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
24054 TTGACAGCGC
24064 AACAAAAAC-AAAACGAA
1 AACAAAAACAAAAACGAA
*
24081 AAC-AAAACAAAAACAAA
1 AACAAAAACAAAAACGAA
*
24098 AACAGAAAACGAAAACGA
1 AACA-AAAACAAAAACGA
24116 TGTCAAACGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 5 0.17
17 13 0.45
19 11 0.38
ACGTcount: A:0.75, C:0.17, G:0.08, T:0.00
Consensus pattern (18 bp):
AACAAAAACAAAAACGAA
Found at i:25131 original size:109 final size:109
Alignment explanation
Indices: 25003--25216 Score: 401
Period size: 109 Copynumber: 2.0 Consensus size: 109
24993 TATATATATT
*
25003 ATTATTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAAA
1 ATTATTAATTATGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAAA
25068 ATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATG
66 ATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATG
*
25112 ATTATTAATTATGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAAA
1 ATTATTAATTATGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAAA
*
25177 GTGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
66 ATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACC
25217 AAAATGACTA
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 102 1.00
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.29
Consensus pattern (109 bp):
ATTATTAATTATGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAAA
ATGCAATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATG
Found at i:31033 original size:78 final size:78
Alignment explanation
Indices: 30950--31117 Score: 239
Period size: 78 Copynumber: 2.2 Consensus size: 78
30940 GTTTTTTAAT
** * *
30950 TAAAATAGTAAAATGGTAAAATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATAAAATAAATATAAAGATATTAGATTTAATTAAATAAAAATAAA
* *
31015 GTTTTTAGTTGAG
66 GTTTTTAATTGAA
* * *
31028 TAAAATAGTAAAATGGTAAGATAAAATAAATATAAAGATATTAGATTTAATTAAATTAAATTAAA
1 TAAAATAGTAAAATGGTAAAATAAAATAAATATAAAGATATTAGATTTAATTAAATAAAAATAAA
31093 GTTTTTAATTGAA
66 GTTTTTAATTGAA
*
31106 AAAAATA-TAAAA
1 TAAAATAGTAAAA
31118 GTTTAAACAA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
77 5 0.06
78 75 0.94
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATAAAATAAATATAAAGATATTAGATTTAATTAAATAAAAATAAA
GTTTTTAATTGAA
Found at i:32914 original size:23 final size:24
Alignment explanation
Indices: 32885--32930 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
32875 GATCCTCTTG
32885 TATTATATAT-TTGTAATACCCGT
1 TATTATATATATTGTAATACCCGT
32908 TATTATATATAATTGTAATACCC
1 TATTATATAT-ATTGTAATACCC
32931 ATTACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.46
Consensus pattern (24 bp):
TATTATATATATTGTAATACCCGT
Found at i:36510 original size:22 final size:22
Alignment explanation
Indices: 36467--36511 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
36457 AATATTCATA
*
36467 TAAAATATGATAATCTTCCTAT
1 TAAAATATGATAATCTACCTAT
*
36489 TAAATTATGATAAT-TACACTAT
1 TAAAATATGATAATCTAC-CTAT
36511 T
1 T
36512 TTTGATGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (22 bp):
TAAAATATGATAATCTACCTAT
Found at i:36610 original size:22 final size:22
Alignment explanation
Indices: 36584--36647 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
36574 GAATTTCGAG
* *
36584 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
36606 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
* * *
36628 AACCTCCCTAAGAAATTTTG
1 AACCTTCTTATGAAATTTTG
36648 AAGACCTCAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 33 0.92
23 3 0.08
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:36654 original size:22 final size:22
Alignment explanation
Indices: 36617--36918 Score: 96
Period size: 22 Copynumber: 13.6 Consensus size: 22
36607 ACCTTCTTAT
*
36617 GAAATTTTGTTAACCTCCCTAA
1 GAAATTTTGATAACCTCCCTAA
* *
36639 GAAATTTTGA-AGACCTCACTAT
1 GAAATTTTGATA-ACCTCCCTAA
*
36661 GAAATTTTGATAACTTCCC-AA
1 GAAATTTTGATAACCTCCCTAA
* * *
36682 TGAAATTTTGATAACCAACACTAT
1 -GAAATTTTGATAACC-TCCCTAA
* * * *
36706 GAGATGTTGATAACCTCCATAT
1 GAAATTTTGATAACCTCCCTAA
* * * ** *
36728 GATATATTGATAACCACGTTAT
1 GAAATTTTGATAACCTCCCTAA
* * * * * *
36750 GAAAATTTAAAAAACTCCATAT
1 GAAATTTTGATAACCTCCCTAA
* * * **
36772 G-AATTGTT-AGTAATCACACTCT
1 GAAATT-TTGA-TAACCTCCCTAA
* * * *
36794 GAAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCTCCCTAA
* *
36816 GAAATTGTGATAACCTCGCTATA
1 GAAATTTTGATAACCTCCCTA-A
* *
36839 -AAATTTTGAAAAACCTTCCTATA
1 GAAATTTTG-ATAACCTCCCTA-A
*
36862 -AAATCTTGATAAACCTCCCTATA
1 GAAATTTTGAT-AACCTCCCTA-A
* * *
36885 -AAACTTTGATAACCTCCTTAT
1 GAAATTTTGATAACCTCCCTAA
*
36906 GAAATCTTGATAA
1 GAAATTTTGATAA
36919 GTACAAATTT
Statistics
Matches: 212, Mismatches: 55, Indels: 26
0.72 0.19 0.09
Matches are distributed among these distances:
21 6 0.03
22 147 0.69
23 58 0.27
24 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (22 bp):
GAAATTTTGATAACCTCCCTAA
Found at i:36662 original size:44 final size:45
Alignment explanation
Indices: 36614--36918 Score: 146
Period size: 44 Copynumber: 6.8 Consensus size: 45
36604 TTAACCTTCT
* *
36614 TATGAAATTTTGTTAACCTCCCTAA-GAAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATAACCTCCC-AATGAAATTTTGATA-ACCAACAC
*
36658 TATGAAATTTTGATAACTTCCCAATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
* * * * **
36703 TATGAGATGTTGATAACCT-CCATATGATATATTGATAACC-ACGT
1 TATGAAATTTTGATAACCTCCCA-ATGAAATTTTGATAACCAACAC
* * * * *
36747 TATGAAAATTTAAAAAACT-CCATATG-AATTGTT-AGTAATC-ACAC
1 TATGAAATTTTGATAACCTCCCA-ATGAAATT-TTGA-TAACCAACAC
* * * * * * * *
36791 TCTGAAATTTTGATAATCACACTATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
* * * * * * * *
36835 TATAAAATTTTGAAAAACCTTCCTATAAAATCTTGATAAACC-TCCC
1 TATGAAATTTTG-ATAACCTCCCAATGAAATTTTGAT-AACCAACAC
* * ** *
36881 TATAAAACTTTGATAACCTCCTTATGAAATCTTGATAA
1 TATGAAATTTTGATAACCTCCCAATGAAATTTTGATAA
36919 GTACAAATTT
Statistics
Matches: 201, Mismatches: 49, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
43 5 0.02
44 101 0.50
45 77 0.38
46 18 0.09
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (45 bp):
TATGAAATTTTGATAACCTCCCAATGAAATTTTGATAACCAACAC
Found at i:36860 original size:23 final size:23
Alignment explanation
Indices: 36827--36915 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 23
36817 AAATTGTGAT
*
36827 AACCTCGCTATAAAATTTTGAAA
1 AACCTCCCTATAAAATTTTGAAA
* * *
36850 AACCTTCCTATAAAATCTTGATA
1 AACCTCCCTATAAAATTTTGAAA
* *
36873 AACCTCCCTATAAAACTTTG-AT
1 AACCTCCCTATAAAATTTTGAAA
* * *
36895 AACCTCCTTATGAAATCTTGA
1 AACCTCCCTATAAAATTTTGA
36916 TAAGTACAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 16 0.31
23 36 0.69
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.33
Consensus pattern (23 bp):
AACCTCCCTATAAAATTTTGAAA
Found at i:37031 original size:22 final size:22
Alignment explanation
Indices: 37006--37085 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
36996 ATCTACATAC
37006 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCCTCT
* ***
37028 TATGAAATTTTGAAAACTAAAC-
1 TATGAAATTTTGATAAC-CCTCT
*
37050 TATGAAATTTTGATAA-CCTTT
1 TATGAAATTTTGATAACCCTCT
37071 ATATGAAATTTTGAT
1 -TATGAAATTTTGAT
37086 TACTCCATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 45 0.98
23 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCCTCT
Found at i:37032 original size:44 final size:42
Alignment explanation
Indices: 36984--37085 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 42
36974 TTAATCTCCG
36984 TATGAAATTTTGATCTACATACTATGAAATTTTGATAACCCTCT-
1 TATGAAATTTTGATCTA-A-ACTATGAAATTTTGATAA-CCTCTA
* *
37028 TATGAAATTTTGAAAACTAAACTATGAAATTTTGATAACCTTTA
1 TATGAAATTTTG--ATCTAAACTATGAAATTTTGATAACCTCTA
37072 TATGAAATTTTGAT
1 TATGAAATTTTGAT
37086 TACTCCATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
42 1 0.02
43 4 0.08
44 42 0.81
45 1 0.02
46 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (42 bp):
TATGAAATTTTGATCTAAACTATGAAATTTTGATAACCTCTA
Found at i:37216 original size:22 final size:21
Alignment explanation
Indices: 37193--37399 Score: 98
Period size: 22 Copynumber: 9.5 Consensus size: 21
37183 TCACATTTTG
37193 AAAATTTGATAACCTCTTTAT
1 AAAATTTGATAACCTCTTTAT
* * *
37214 GAAATTTTGATAACATCTCTAT
1 -AAAATTTGATAACCTCTTTAT
* * * *
37236 AAAATTTTGTTGACCCCTCTAT
1 AAAA-TTTGATAACCTCTTTAT
* * *
37258 AAAATTTTGATAATCACATTAT
1 AAAA-TTTGATAACCTCTTTAT
*
37280 ATAATTATGATAACCTTGCTTT-T
1 AAAATT-TGATAACC-T-CTTTAT
* *
37303 AAATTTTGATAA-TTC-TTAT
1 AAAATTTGATAACCTCTTTAT
* *
37322 AAATTTTGATAATCCGATCTCTAT
1 AAAATTTGATAA-CC--TCTTTAT
* *
37346 AAAATTTCGATAATCACTTTAT
1 AAAATTT-GATAACCTCTTTAT
* * *
37368 GAGATTTGATAACCT-TCTAT
1 AAAATTTGATAACCTCTTTAT
*
37388 CAAATTTTGATA
1 -AAAATTTGATA
37400 CTCCTTATGA
Statistics
Matches: 138, Mismatches: 35, Indels: 25
0.70 0.18 0.13
Matches are distributed among these distances:
18 2 0.01
19 14 0.10
20 5 0.04
21 19 0.14
22 73 0.53
23 7 0.05
24 13 0.09
25 5 0.04
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.43
Consensus pattern (21 bp):
AAAATTTGATAACCTCTTTAT
Found at i:37344 original size:88 final size:83
Alignment explanation
Indices: 37166--37413 Score: 232
Period size: 88 Copynumber: 2.9 Consensus size: 83
37156 AGAAATACCA
* * * *
37166 CTATGAAATTTTGGTAATCACATTTTGAAAATTTGATAACC-TCTTTATGAAATTTTGATAACAT
1 CTATAAAATTTTGATAATCACA-TTT-ATAATTTGATAACCTTCTTT-T-AAATTTTGATAA-TT
* *
37230 CTCTATAAAATTTTGTTGACCCCT
61 CT-TATAAAATTTTGATAACCCCT
37254 CTATAAAATTTTGATAATCACATTATATAATTATGATAACCTTGCTTTTAAATTTTGATAATTCT
1 CTATAAAATTTTGATAATCACATT-TATAATT-TGATAACCTT-CTTTTAAATTTTGATAATTCT
*
37319 TAT-AAATTTTGATAATCCGATCT
63 TATAAAATTTTGATAA-CC--CCT
* * * * *
37342 CTATAAAATTTCGATAATCAC-TTTATGAGATTTGATAACCTTCTATCAAATTTTGATACTCCTT
1 CTATAAAATTTTGATAATCACATTTAT-A-ATTTGATAACCTTCTTTTAAATTTTGATAATTCTT
*
37406 ATGAAATT
64 ATAAAATT
37414 GAGACTTTTA
Statistics
Matches: 138, Mismatches: 12, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
85 10 0.07
86 28 0.20
87 28 0.20
88 66 0.48
89 2 0.01
90 4 0.03
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (83 bp):
CTATAAAATTTTGATAATCACATTTATAATTTGATAACCTTCTTTTAAATTTTGATAATTCTTAT
AAAATTTTGATAACCCCT
Found at i:37351 original size:44 final size:44
Alignment explanation
Indices: 37166--37399 Score: 157
Period size: 44 Copynumber: 5.4 Consensus size: 44
37156 AGAAATACCA
* * * *
37166 CTATGAAATTTTGGTAATCACATTTTGAAAATT-TGATAACCTCT
1 CTATAAAATTTTGATAATCACATTAT-ATAATTATGATAACCTCT
* * * * * * *
37210 TTATGAAATTTTGATAA-CATC-TCTATAAAATTTTGTTGACCCCT
1 CTATAAAATTTTGATAATCA-CAT-TATATAATTATGATAACCTCT
37254 CTATAAAATTTTGATAATCACATTATATAATTATGATAACCT-T
1 CTATAAAATTTTGATAATCACATTATATAATTATGATAACCTCT
* * * *
37297 GCTTTTAAATTTTGATAAT-TC-TTATA-AATTTTGATAATCCGATCT
1 -CTATAAAATTTTGATAATCACATTATATAATTATGATAA-CC--TCT
*
37342 CTATAAAATTTCGATAATCAC-TT-TATGAGATT-TGATAACCT-T
1 CTATAAAATTTTGATAATCACATTATAT-A-ATTATGATAACCTCT
*
37384 CTATCAAATTTTGATA
1 CTATAAAATTTTGATA
37400 CTCCTTATGA
Statistics
Matches: 153, Mismatches: 23, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
41 10 0.07
42 22 0.14
43 12 0.08
44 90 0.59
45 9 0.06
46 7 0.05
47 3 0.02
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (44 bp):
CTATAAAATTTTGATAATCACATTATATAATTATGATAACCTCT
Found at i:37448 original size:22 final size:21
Alignment explanation
Indices: 37341--37558 Score: 70
Period size: 22 Copynumber: 9.9 Consensus size: 21
37331 TAATCCGATC
* *
37341 TCTATAAAATTTCGATAATCACT
1 TCTATGAAATTTTGATAA-C-CT
*
37364 T-TATGAGA-TTTGATAACCT
1 TCTATGAAATTTTGATAACCT
* *
37383 TCTATCAAATTTTGATACTCCT
1 TCTATGAAATTTTGATA-ACCT
* *
37405 TATGAAATTGAGACTTTT-ATAACCT
1 TCT---A-TGA-AATTTTGATAACCT
*
37430 TCATATGAAATTTTGATAACCAC
1 TC-TATGAAATTTTGATAACC-T
* *
37453 ACTATGAAATTTTGATAACAT
1 TCTATGAAATTTTGATAACCT
* * **
37474 CCCCATGAAATAGT-AGTAATCTCT
1 -TCTATGAAATTTTGA-TAA-C-CT
* *
37498 T-TATGAAATTTTGTTAACCAC
1 TCTATGAAATTTTGATAACC-T
*
37519 ACTATGAAATTCTT-ATAACCT
1 TCTATGAAATT-TTGATAACCT
* *
37540 CGCTATGACATTTTGATAA
1 -TCTATGAAATTTTGATAA
37559 TCTCTTTGAA
Statistics
Matches: 142, Mismatches: 32, Indels: 43
0.65 0.15 0.20
Matches are distributed among these distances:
19 3 0.02
20 7 0.05
21 23 0.16
22 86 0.61
23 6 0.04
24 1 0.01
25 5 0.04
26 6 0.04
27 5 0.04
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.39
Consensus pattern (21 bp):
TCTATGAAATTTTGATAACCT
Found at i:37750 original size:22 final size:22
Alignment explanation
Indices: 37587--37798 Score: 80
Period size: 22 Copynumber: 9.5 Consensus size: 22
37577 TATAAAATAG
37587 TGATAACCACACTATGAAATTT
1 TGATAACCACACTATGAAATTT
** ** *
37609 CAATAACGTTC-CTAAGAAATTT
1 TGATAAC-CACACTATGAAATTT
* * *
37631 TAATAACCTGATTA-TATGGAATTT
1 TGATAACC--A-CACTATGAAATTT
* * * *
37655 TGGTAATCACACTGTGCAATTT
1 TGATAACCACACTATGAAATTT
** *
37677 TGATAATCTTC-CCATGAAATTT
1 TGATAA-CCACACTATGAAATTT
37699 TGATAACTTC-CA-TATTG-AATTT
1 TGATAAC--CACACTA-TGAAATTT
* *
37721 TGGTAACCACACTATGGAATTT
1 TGATAACCACACTATGAAATTT
* *
37743 TGATAACCTC-CTCATGAAATTA
1 TGATAACCACACT-ATGAAATTT
* *
37765 TAATAACCATC-TTATGAAATTT
1 TGATAACCA-CACTATGAAATTT
*
37787 TAATAACCACAC
1 TGATAACCACAC
37799 AGAGACAAGA
Statistics
Matches: 137, Mismatches: 36, Indels: 34
0.66 0.17 0.16
Matches are distributed among these distances:
20 1 0.01
21 9 0.07
22 108 0.79
23 6 0.04
24 13 0.09
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
TGATAACCACACTATGAAATTT
Found at i:37786 original size:66 final size:65
Alignment explanation
Indices: 37590--37798 Score: 183
Period size: 66 Copynumber: 3.1 Consensus size: 65
37580 AAAATAGTGA
** *
37590 TAACCACACTATGAAATTTCAATAACGTTCCT-AAGAAATTTTAATAACCTGAT-TATATGGAAT
1 TAACCACACTATGAAATTTTGATAAC-TTCCTCATGAAATTTTAATAACC--ATCT-TAT-GAAT
37653 TTTGG
61 TTTGG
* * * * * *
37658 TAATCACACTGTGCAATTTTGATAATCTTCC-CATGAAATTTTGATAA-CTTCCATATTGAATTT
1 TAACCACACTATGAAATTTTGATAA-CTTCCTCATGAAATTTTAATAACCAT-CTTA-TGAATTT
37721 TGG
63 TGG
* * * *
37724 TAACCACACTATGGAATTTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAATTTTA
1 TAACCACACTATGAAATTTTGATAACTTCCTCATGAAATTTTAATAACCATCTTATG-AATTTTG
*
37789 A
65 G
37790 TAACCACAC
1 TAACCACAC
37799 AGAGACAAGA
Statistics
Matches: 114, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
65 7 0.06
66 65 0.57
67 4 0.04
68 37 0.32
69 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (65 bp):
TAACCACACTATGAAATTTTGATAACTTCCTCATGAAATTTTAATAACCATCTTATGAATTTTGG
Found at i:41263 original size:16 final size:15
Alignment explanation
Indices: 41242--41295 Score: 69
Period size: 16 Copynumber: 3.7 Consensus size: 15
41232 AAAATGTGTT
41242 AATATTATAAAAAAAC
1 AATATTAT-AAAAAAC
41258 AATATTATAAAAAAC
1 AATATTATAAAAAAC
41273 ---ATTATAAAAAAC
1 AATATTATAAAAAAC
41285 AATAATTATAA
1 AAT-ATTATAA
41296 GAAGTGAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 12 0.35
15 7 0.21
16 15 0.44
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (15 bp):
AATATTATAAAAAAC
Found at i:41278 original size:12 final size:12
Alignment explanation
Indices: 41261--41285 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41251 AAAAAACAAT
41261 ATTATAAAAAAC
1 ATTATAAAAAAC
41273 ATTATAAAAAAC
1 ATTATAAAAAAC
41285 A
1 A
41286 ATAATTATAA
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
ATTATAAAAAAC
Found at i:44594 original size:21 final size:21
Alignment explanation
Indices: 44556--44595 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
44546 GGCGCCCACA
* *
44556 TGGTTTGTCTGAAGACCCATG
1 TGGTTTGCCTGAACACCCATG
*
44577 TGGTTTGCCTGATCACCCA
1 TGGTTTGCCTGAACACCCA
44596 GGTAGGCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (21 bp):
TGGTTTGCCTGAACACCCATG
Found at i:47069 original size:10 final size:10
Alignment explanation
Indices: 47050--47078 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
47040 TATCAGTCCA
47050 TGCA-TCATC
1 TGCATTCATC
47059 TGCATTCATC
1 TGCATTCATC
47069 TGCATTCATC
1 TGCATTCATC
47079 AGTCCATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.21, C:0.31, G:0.10, T:0.38
Consensus pattern (10 bp):
TGCATTCATC
Found at i:47469 original size:31 final size:31
Alignment explanation
Indices: 47374--47472 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 31
47364 CGTTTCACGA
*
47374 AGGGACTAAATTGATCGTTTCTT-AATAGTAT
1 AGGGACTAAATTGATC-TTTTTTCAATAGTAT
* *** * **
47405 AGGGATTAAATTGA-CAGATTTC-ATAATGG
1 AGGGACTAAATTGATCTTTTTTCAATAGTAT
*
47434 AGGGACTAAAATGATCTTTTTTCAATAGTAT
1 AGGGACTAAATTGATCTTTTTTCAATAGTAT
47465 AGGGACTA
1 AGGGACTA
47473 TTTAGGTACT
Statistics
Matches: 49, Mismatches: 16, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
29 18 0.37
30 6 0.12
31 25 0.51
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.34
Consensus pattern (31 bp):
AGGGACTAAATTGATCTTTTTTCAATAGTAT
Found at i:48609 original size:25 final size:24
Alignment explanation
Indices: 48561--48608 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
48551 TATTACAATA
48561 CCCAAAAATATCCCTTACATTTTT
1 CCCAAAAATATCCCTTACATTTTT
48585 CCCAAAAATATCCCTTACATTTTT
1 CCCAAAAATATCCCTTACATTTTT
48609 TTTAGGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.00, T:0.38
Consensus pattern (24 bp):
CCCAAAAATATCCCTTACATTTTT
Found at i:49020 original size:16 final size:16
Alignment explanation
Indices: 48997--49046 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 16
48987 ACATAAAGTA
48997 AATT-AAATAGAAAGC
1 AATTAAAATAGAAAGC
49012 AATTAAAATAAGAAAAGC
1 AATTAAAAT-AG-AAAGC
*
49030 AATAAATAATA-AAAGC
1 AATTAA-AATAGAAAGC
49046 A
1 A
49047 CCATCCCATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 2 0.07
18 11 0.37
19 3 0.10
ACGTcount: A:0.66, C:0.06, G:0.10, T:0.18
Consensus pattern (16 bp):
AATTAAAATAGAAAGC
Done.