Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001755.1 Kokia drynarioides strain JFW-HI SEQ_113470, 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: 90449
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 150 characters in sequence are not A, C, G, or T
Found at i:190 original size:14 final size:14
Alignment explanation
Indices: 171--198 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
161 TACATTCAAA
171 CATAATCTATATGT
1 CATAATCTATATGT
185 CATAATCTATATGT
1 CATAATCTATATGT
199 TAAATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
CATAATCTATATGT
Found at i:6627 original size:5 final size:5
Alignment explanation
Indices: 6617--6643 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
6607 CTCAGTTCCC
6617 CAGGG CAGGG CAGGG CAGGG CAGGG CA
1 CAGGG CAGGG CAGGG CAGGG CAGGG CA
6644 TGTTTACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.56, T:0.00
Consensus pattern (5 bp):
CAGGG
Found at i:11177 original size:19 final size:19
Alignment explanation
Indices: 11155--11191 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
11145 ATCTAAATAG
11155 TTACAATAAAATTAAATTA
1 TTACAATAAAATTAAATTA
*
11174 TTACAATATAATTAAATT
1 TTACAATAAAATTAAATT
11192 GATAATTAAA
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:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TTACAATAAAATTAAATTA
Found at i:11204 original size:23 final size:22
Alignment explanation
Indices: 11173--11224 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
11163 AAATTAAATT
*
11173 ATTACAATATAATT-AAATTGATA
1 ATTAAAATAT-ATTCAAATT-ATA
*
11196 ATTAAAATATATTCAAATTTTA
1 ATTAAAATATATTCAAATTATA
11218 ATTAAAA
1 ATTAAAA
11225 AAAATCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
ATTAAAATATATTCAAATTATA
Found at i:18313 original size:15 final size:15
Alignment explanation
Indices: 18287--18332 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
18277 CAACTTGATC
18287 AATTTGAAAAATATAA
1 AATTT-AAAAATATAA
18303 AATTTAAAAATA-ACTA
1 AATTTAAAAATATA--A
18319 AATTT-AAAATATAA
1 AATTTAAAAATATAA
18333 GGATTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 2 0.07
15 13 0.48
16 12 0.44
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AATTTAAAAATATAA
Found at i:27013 original size:102 final size:103
Alignment explanation
Indices: 26861--27046 Score: 250
Period size: 102 Copynumber: 1.8 Consensus size: 103
26851 GTGTGTTAGA
* * * * *
26861 CTGAGTAACCGGGGTGGAATGCTTGGTTGTCATTTCATTTTGCGTTAAAAGGGCTAACACATTC-
1 CTGAGTAACCGGGATGGAATGCTTGGGTGTCATTTCATTTCGCGTCAAAAGGGCCAACACATTCT
26925 TAAA-AAAAAAAGAAAAAAATGATTACGAGCATGTTGGG
66 TAAAGAAAAAAA-AAAAAAATGATTACGAGCATGTTGGG
* * * * * *
26963 CTGAGTAATCGGGATGGAGTGCTTGGGTGTCATTTCGTTTCGCGTCAAAAGGTCCAATATATTCT
1 CTGAGTAACCGGGATGGAATGCTTGGGTGTCATTTCATTTCGCGTCAAAAGGGCCAACACATTCT
27028 TAAAGAAAAAAAAAAAAAA
66 TAAAGAAAAAAAAAAAAAA
27047 CCGACAAAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
102 53 0.75
103 11 0.15
104 7 0.10
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (103 bp):
CTGAGTAACCGGGATGGAATGCTTGGGTGTCATTTCATTTCGCGTCAAAAGGGCCAACACATTCT
TAAAGAAAAAAAAAAAAAATGATTACGAGCATGTTGGG
Found at i:27673 original size:11 final size:11
Alignment explanation
Indices: 27654--27686 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
27644 TTAGGATATT
27654 ATTTATATTTA
1 ATTTATATTTA
*
27665 ATTTGTATTTA
1 ATTTATATTTA
27676 ATTTATATTTA
1 ATTTATATTTA
27687 TCATTTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:28058 original size:109 final size:110
Alignment explanation
Indices: 27922--28130 Score: 375
Period size: 109 Copynumber: 1.9 Consensus size: 110
27912 CTGTACAATA
*
27922 ATTATATTGTGTTTTTTCCCAAAAACATGAGTAACTGAAAACCCTTTTAGCCGAAGGTTATCAAA
1 ATTATATTGTGTTTTTTCCCAAAAACATGAGCAACTGAAAACCCTTTTAGCCGAAGGTTATCAAA
27987 TATTCCTTCAAGGTTCATGAGGCTTAGAACTCACATATATTTTTT
66 TATTCCTTCAAGGTTCATGAGGCTTAGAACTCACATATATTTTTT
* * *
28032 ATTATCTTGTG-TTTTTCCCAAAAACATGAGCAACTGAAAATCCTTTTAGTCGAAGGTTATCAAA
1 ATTATATTGTGTTTTTTCCCAAAAACATGAGCAACTGAAAACCCTTTTAGCCGAAGGTTATCAAA
28096 TATTCCTTCAAGGTTCATGAGGCTTAGAACTCACA
66 TATTCCTTCAAGGTTCATGAGGCTTAGAACTCACA
28131 CTTAATTCCT
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
109 85 0.89
110 10 0.11
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (110 bp):
ATTATATTGTGTTTTTTCCCAAAAACATGAGCAACTGAAAACCCTTTTAGCCGAAGGTTATCAAA
TATTCCTTCAAGGTTCATGAGGCTTAGAACTCACATATATTTTTT
Found at i:31220 original size:16 final size:17
Alignment explanation
Indices: 31184--31220 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
31174 ATTAGCACCC
31184 AAAATAATTCGAACTTG
1 AAAATAATTCGAACTTG
*
31201 -AAATGATTCGAAC-TG
1 AAAATAATTCGAACTTG
31216 AAAAT
1 AAAAT
31221 TGATAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (17 bp):
AAAATAATTCGAACTTG
Found at i:37322 original size:20 final size:20
Alignment explanation
Indices: 37277--37323 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
37267 GCCATAAAAA
*
37277 AATTAATTTAAATTTAATAG
1 AATTATTTTAAATTTAATAG
* *
37297 ATTTATTTTTAATTTCAA-AG
1 AATTATTTTAAATTT-AATAG
37317 AATTATT
1 AATTATT
37324 CGAATTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (20 bp):
AATTATTTTAAATTTAATAG
Found at i:51511 original size:13 final size:13
Alignment explanation
Indices: 51493--51523 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
51483 TCGTATCAAA
*
51493 TTTTTTATATTAT
1 TTTTTTATATAAT
51506 TTTTTTATATAAT
1 TTTTTTATATAAT
51519 TTTTT
1 TTTTT
51524 AAAAATCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTATATAAT
Found at i:53133 original size:32 final size:32
Alignment explanation
Indices: 53088--53169 Score: 137
Period size: 32 Copynumber: 2.6 Consensus size: 32
53078 CAAAAAAAAA
*
53088 ATGTTTATGTTTATGTTTGTATTTAATTAATT
1 ATGTTTATATTTATGTTTGTATTTAATTAATT
* *
53120 ATGTTTACATTTATTTTTGTATTTAATTAATT
1 ATGTTTATATTTATGTTTGTATTTAATTAATT
53152 ATGTTTATATTTATGTTT
1 ATGTTTATATTTATGTTT
53170 ATGTTTGGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.26, C:0.01, G:0.10, T:0.63
Consensus pattern (32 bp):
ATGTTTATATTTATGTTTGTATTTAATTAATT
Found at i:53162 original size:20 final size:20
Alignment explanation
Indices: 53098--53164 Score: 60
Period size: 20 Copynumber: 3.8 Consensus size: 20
53088 ATGTTTATGT
*
53098 TTATGTTTGTATTTAATTAA
1 TTATGTTTATATTTAATTAA
*
53118 TTATGTTTACATTT-ATT--
1 TTATGTTTATATTTAATTAA
53135 TT-TG----TATTTAATTAA
1 TTATGTTTATATTTAATTAA
53150 TTATGTTTATATTTA
1 TTATGTTTATATTTA
53165 TGTTTATGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 16
0.65 0.05 0.29
Matches are distributed among these distances:
12 4 0.11
13 3 0.08
15 2 0.06
16 4 0.11
17 2 0.06
19 3 0.08
20 18 0.50
ACGTcount: A:0.28, C:0.01, G:0.07, T:0.63
Consensus pattern (20 bp):
TTATGTTTATATTTAATTAA
Found at i:53519 original size:26 final size:26
Alignment explanation
Indices: 53512--53583 Score: 117
Period size: 26 Copynumber: 2.8 Consensus size: 26
53502 AATTAAATAC
* *
53512 AAATATAAACATAAACATAATTAATT
1 AAATACAAATATAAACATAATTAATT
*
53538 AAATACAAACATAAACATAATTAATT
1 AAATACAAATATAAACATAATTAATT
53564 AAATACAAATATAAACATAA
1 AAATACAAATATAAACATAA
53584 ACATTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (26 bp):
AAATACAAATATAAACATAATTAATT
Found at i:53525 original size:32 final size:32
Alignment explanation
Indices: 53484--53587 Score: 148
Period size: 32 Copynumber: 3.4 Consensus size: 32
53474 AAACATAATA
* *
53484 ATAAGCATAAATATAATTAATTAAATACAAAT
1 ATAAACATAAACATAATTAATTAAATACAAAT
53516 ATAAACATAAACATAATTAATTAAATAC----
1 ATAAACATAAACATAATTAATTAAATACAAAT
53544 --AAACATAAACATAATTAATTAAATACAAAT
1 ATAAACATAAACATAATTAATTAAATACAAAT
53574 ATAAACATAAACAT
1 ATAAACATAAACAT
53588 TTTTTTTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
26 26 0.41
32 38 0.59
ACGTcount: A:0.62, C:0.10, G:0.01, T:0.28
Consensus pattern (32 bp):
ATAAACATAAACATAATTAATTAAATACAAAT
Found at i:54280 original size:2 final size:2
Alignment explanation
Indices: 54273--54313 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
54263 ATGTTCATAG
54273 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
54314 TTGCCAAAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:56846 original size:21 final size:21
Alignment explanation
Indices: 56798--56849 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
56788 GGAGTTTTTA
* *
56798 GTATCGATAGAAGAGTCACTT
1 GTATCGGTAGAACAGTCACTT
*
56819 GTATCGGTAGAACTGTCACTT
1 GTATCGGTAGAACAGTCACTT
56840 GTATCGGTAG
1 GTATCGGTAG
56850 GAGTTTGCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAACAGTCACTT
Found at i:61093 original size:18 final size:17
Alignment explanation
Indices: 61062--61124 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 17
61052 GGTAGTCAAT
61062 TTATTAGAAT-GATAATCC
1 TTATTA-AATAGAT-ATCC
*
61080 TTATTAAATAGATATTC
1 TTATTAAATAGATATCC
* * *
61097 TGATTAAAAATATTATCC
1 TTATTAAATAGA-TATCC
61115 TTATTAAATA
1 TTATTAAATA
61125 TATGTTTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
17 15 0.42
18 21 0.58
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (17 bp):
TTATTAAATAGATATCC
Found at i:61127 original size:18 final size:18
Alignment explanation
Indices: 61076--61127 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
61066 TAGAATGATA
*
61076 ATCCTTATTAAATAGA-T
1 ATCCTTATTAAATATATT
* * *
61093 ATTCTGATTAAAAATATT
1 ATCCTTATTAAATATATT
61111 ATCCTTATTAAATATAT
1 ATCCTTATTAAATATAT
61128 GTTTTTTTCT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (18 bp):
ATCCTTATTAAATATATT
Found at i:61198 original size:18 final size:17
Alignment explanation
Indices: 61175--61209 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
61165 CATTACGTAG
61175 CTGTATACCACACTTTTT
1 CTGTATACCACA-TTTTT
*
61193 CTGTATACGACATTTTT
1 CTGTATACCACATTTTT
61210 ATCCAACTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.46
Consensus pattern (17 bp):
CTGTATACCACATTTTT
Found at i:69862 original size:91 final size:85
Alignment explanation
Indices: 69738--69947 Score: 210
Period size: 91 Copynumber: 2.4 Consensus size: 85
69728 CCTTACTTTC
* * * * *
69738 TTTTTGCACTCAATTAGATA-TTTAAACTGTCAAAATGCATAAAAAA-GACCCTCAAAATTTTTT
1 TTTTTTCACTCAATTGGGTACTTT-AACTGTCAAAAAGCATAAAAAATG-CCCTC-AAA--CTTT
* *
69801 AAAA-AAAGCAATTAAGCCCCTGCTTTTT
61 AAAAGAAAACAATTAAGCCCCTG----AT
* *
69829 TTTTTTCACTCAATTGGGTACTTTAACTTTCAAAAAGCATAAAAAATGCCTTCAAACTTTAAAAG
1 TTTTTTCACTCAATTGGGTACTTTAACTGTCAAAAAGCATAAAAAATGCCCTCAAACTTTAAAAG
*
69894 AAAATAATTAAGCCCCTGAT
66 AAAACAATTAAGCCCCTGAT
* *
69914 TTTTTTCACTCAATTGAGTACTTGAACTGTCAAA
1 TTTTTTCACTCAATTGGGTACTTTAACTGTCAAA
69948 TGTATCAAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
85 32 0.31
88 7 0.07
89 16 0.16
90 3 0.03
91 41 0.40
92 4 0.04
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.35
Consensus pattern (85 bp):
TTTTTTCACTCAATTGGGTACTTTAACTGTCAAAAAGCATAAAAAATGCCCTCAAACTTTAAAAG
AAAACAATTAAGCCCCTGAT
Found at i:70154 original size:12 final size:12
Alignment explanation
Indices: 70137--70161 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
70127 AATTTTTTAT
70137 AAAAATTATAAA
1 AAAAATTATAAA
70149 AAAAATTATAAA
1 AAAAATTATAAA
70161 A
1 A
70162 TGCATAAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:71293 original size:11 final size:11
Alignment explanation
Indices: 71253--71299 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
71243 TTCTTTATTC
71253 ATTA-AAAAAA
1 ATTATAAAAAA
*
71263 ATTATAATAAA
1 ATTATAAAAAA
71274 ATTATTAAAAAA
1 ATTA-TAAAAAA
*
71286 ATTGTAAAACAA
1 ATTATAAAA-AA
71298 AT
1 AT
71300 CAATATATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 4 0.13
11 14 0.45
12 13 0.42
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
ATTATAAAAAA
Found at i:71772 original size:19 final size:19
Alignment explanation
Indices: 71732--71774 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
71722 TCATCCTTCA
*
71732 AAATTGTTTAAAATTTTGG
1 AAATTGTTTAAAACTTTGG
*
71751 AAATTGTTTTGAAACTTT-G
1 AAATTG-TTTAAAACTTTGG
71770 AAATT
1 AAATT
71775 AAAGTAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (19 bp):
AAATTGTTTAAAACTTTGG
Found at i:73018 original size:31 final size:31
Alignment explanation
Indices: 72958--73018 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
72948 TCCTGAAAAT
* ***
72958 AAAAATATGAAAATTTAAATTTAAATTTACG
1 AAAAATATAAAAATTTAAAAAGAAATTTACG
*
72989 AAAAATATAAAAATTTAAAAAGAATTTTAC
1 AAAAATATAAAAATTTAAAAAGAAATTTAC
73019 CCATACCTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (31 bp):
AAAAATATAAAAATTTAAAAAGAAATTTACG
Found at i:80212 original size:34 final size:33
Alignment explanation
Indices: 80152--80233 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
80142 TTTTTGGTCC
80152 AATTTGGTACTCAAACTTGACATTTTTTTTTCT
1 AATTTGGTACTCAAACTTGACATTTTTTTTTCT
*
80185 AATTTGGTAC-CTAAACTTGACA-CTTTTTTT-T
1 AATTTGGTACTC-AAACTTGACATTTTTTTTTCT
* *
80216 AAGTTGGTACTTAAACTT
1 AATTTGGTACTCAAACTT
80234 TTTGGGGTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
31 16 0.36
32 8 0.18
33 20 0.45
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.48
Consensus pattern (33 bp):
AATTTGGTACTCAAACTTGACATTTTTTTTTCT
Found at i:80223 original size:31 final size:33
Alignment explanation
Indices: 80155--80233 Score: 101
Period size: 31 Copynumber: 2.5 Consensus size: 33
80145 TTGGTCCAAT
* *
80155 TTGGTA-CTCAAACTTGACATTTTTTTTTCTAAT
1 TTGGTACCT-AAACTTGACATCTTTTTTTCTAAG
80188 TTGGTACCTAAACTTGACA-CTTTTTTT-TAAG
1 TTGGTACCTAAACTTGACATCTTTTTTTCTAAG
*
80219 TTGGTACTTAAACTT
1 TTGGTACCTAAACTT
80234 TTTGGGGTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
31 17 0.40
32 7 0.17
33 16 0.38
34 2 0.05
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (33 bp):
TTGGTACCTAAACTTGACATCTTTTTTTCTAAG
Found at i:80502 original size:31 final size:30
Alignment explanation
Indices: 80467--80613 Score: 92
Period size: 31 Copynumber: 4.9 Consensus size: 30
80457 AAAAAGATTG
80467 GGTACCAAATTAGGAAAACATGTCAAGTTTA
1 GGTACCAAATTAGGAAAA-ATGTCAAGTTTA
* * *
80498 GGTACCCAATTGGGTAAAAA---AAAGTTTA
1 GGTACCAAATTAGG-AAAAATGTCAAGTTTA
* *
80526 GGTACCAAATTAAGAAAAAGTGTCAAGTTCA
1 GGTACCAAATTAGGAAAAA-TGTCAAGTTTA
* * *
80557 AGTATCAAATTGAGTCAAAAA----AAGTTTTA
1 GGTACCAAATT-AG-GAAAAATGTCAAG-TTTA
* * *
80586 AGTACCAAATTACGAAAAGTGTCAAGTT
1 GGTACCAAATTAGGAAAAATGTCAAGTT
80614 CAAATACCAA
Statistics
Matches: 87, Mismatches: 17, Indels: 25
0.67 0.13 0.19
Matches are distributed among these distances:
27 9 0.10
28 22 0.25
29 13 0.15
30 2 0.02
31 31 0.36
32 5 0.06
33 5 0.06
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (30 bp):
GGTACCAAATTAGGAAAAATGTCAAGTTTA
Found at i:80530 original size:59 final size:58
Alignment explanation
Indices: 80455--80625 Score: 198
Period size: 59 Copynumber: 2.9 Consensus size: 58
80445 AATGAATATT
* * * * * * *
80455 AAAAAAAGATTGGGTACCAAATTAGGAAAACATGTCAAGTTTAGGTACCCAATTGGGTA
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAA-ATGTCAAGTTCAAGTACCAAATTGAGTA
* *
80514 AAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAAGTATCAAATTGAGTC
1 AAAAAAAGTTTAGGTACCAAATTAAGAAAAA-TGTCAAGTTCAAGTACCAAATTGAGTA
* * * *
80573 AAAAAAAGTTTTAAGTACCAAATTACGAAAAGTGTCAAGTTCAAATACCAAAT
1 AAAAAAAG-TTTAGGTACCAAATTAAGAAAAATGTCAAGTTCAAGTACCAAAT
80626 ATTATATTAA
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
58 1 0.01
59 75 0.78
60 20 0.21
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.25
Consensus pattern (58 bp):
AAAAAAAGTTTAGGTACCAAATTAAGAAAAATGTCAAGTTCAAGTACCAAATTGAGTA
Found at i:80544 original size:28 final size:28
Alignment explanation
Indices: 80455--80544 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
80445 AATGAATATT
* *
80455 AAAAAAAGATTGGGTACCAAATTAGGAA
1 AAAAAAAGTTTAGGTACCAAATTAGGAA
** * * *
80483 AACATGTCAAGTTTAGGTACCCAATTGGGTA
1 AA-A--AAAAGTTTAGGTACCAAATTAGGAA
*
80514 AAAAAAAGTTTAGGTACCAAATTAAGAA
1 AAAAAAAGTTTAGGTACCAAATTAGGAA
80542 AAA
1 AAA
80545 GTGTCAAGTT
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
28 24 0.52
29 1 0.02
30 1 0.02
31 20 0.43
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (28 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAA
Found at i:80796 original size:19 final size:20
Alignment explanation
Indices: 80769--80807 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
80759 TATATATTTG
80769 ATATAAAATA-CGAAATTGA
1 ATATAAAATATCGAAATTGA
* *
80788 ATATCAAATATTGAAATTGA
1 ATATAAAATATCGAAATTGA
80808 GTCCAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (20 bp):
ATATAAAATATCGAAATTGA
Found at i:83580 original size:28 final size:28
Alignment explanation
Indices: 83550--83604 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
83540 TAAATGTTTT
* *
83550 TTTTTTAAAATTATTTTTT-GTTTTCAA
1 TTTTCTAAAATTATTTTTTAATTTTCAA
*
83577 TTTTCTAAAATTGTTTTTTAATTTTCAA
1 TTTTCTAAAATTATTTTTTAATTTTCAA
83605 GAAAACCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (28 bp):
TTTTCTAAAATTATTTTTTAATTTTCAA
Found at i:89693 original size:30 final size:29
Alignment explanation
Indices: 89583--89870 Score: 257
Period size: 30 Copynumber: 9.8 Consensus size: 29
89573 CTTTTAGACA
* *
89583 TTCGGGATAAAAAGGGTAA-TTTTGGGAGT
1 TTCGGGATAAAAATGG-AATTTTTGGAAGT
* * *
89612 TTTGAGGTTGAAAATGG-ATATTTTGGAAG-
1 TTCG-GGATAAAAATGGAAT-TTTTGGAAGT
*
89641 TTCGAGGACAAAAATGGAATTTTTGGAAGT
1 TTCG-GGATAAAAATGGAATTTTTGGAAGT
* * *
89671 TTCGGGATAAAAAACGGGATTTTTTGAAGT
1 TTCGGGAT-AAAAATGGAATTTTTGGAAGT
* *
89701 TTTGGAGGTAAAAATGGAATTTTTGGAAGT
1 TTCGG-GATAAAAATGGAATTTTTGGAAGT
*
89731 TTCGAGGGTAAAAATGGAATTTTTGGAAGT
1 TTCG-GGATAAAAATGGAATTTTTGGAAGT
* * *
89761 TTCGGGGTCAAAATGGAATTTTTGAAAG-
1 TTCGGGATAAAAATGGAATTTTTGGAAGT
89789 TTCAAGGG-TAAAAATGGAATTTTTGGAAGTT
1 TTC--GGGATAAAAATGGAATTTTTGGAAG-T
* * *
89820 TTAGGG-TCAAAATGGAATTTTTAGAAGT
1 TTCGGGATAAAAATGGAATTTTTGGAAGT
* *
89848 TTAGGGGT-AAAATGGAATTTTTG
1 TTCGGGATAAAAATGGAATTTTTG
89871 ATAGTTTTAG
Statistics
Matches: 219, Mismatches: 27, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
28 25 0.11
29 92 0.42
30 97 0.44
31 5 0.02
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
TTCGGGATAAAAATGGAATTTTTGGAAGT
Found at i:89898 original size:30 final size:29
Alignment explanation
Indices: 89602--89942 Score: 282
Period size: 29 Copynumber: 11.6 Consensus size: 29
89592 AAAAGGGTAA
* * *
89602 TTTTGGGAGTTTTGAGGTTGAAAATGG-AT
1 TTTTGGAAGTTTT-AGGGTAAAAATGGAAT
** **
89631 ATTTTGGAAGTTCGAGGACAAAAATGGAAT
1 -TTTTGGAAGTTTTAGGGTAAAAATGGAAT
* * *
89661 TTTTGGAAG-TTTCGGGATAAAAAACGGGAT
1 TTTTGGAAGTTTTAGGG-T-AAAAATGGAAT
* *
89691 TTTTTGAAGTTTTGGAGGTAAAAATGGAAT
1 TTTTGGAAGTTTTAG-GGTAAAAATGGAAT
*
89721 TTTTGGAAGTTTCGAGGGTAAAAATGGAAT
1 TTTTGGAAGTTT-TAGGGTAAAAATGGAAT
** *
89751 TTTTGGAAGTTTCGGGGTCAAAATGGAAT
1 TTTTGGAAGTTTTAGGGTAAAAATGGAAT
* **
89780 TTTTGAAAGTTCAAGGGTAAAAATGGAAT
1 TTTTGGAAGTTTTAGGGTAAAAATGGAAT
*
89809 TTTTGGAAGTTTTAGGGTCAAAATGGAAT
1 TTTTGGAAGTTTTAGGGTAAAAATGGAAT
*
89838 TTTTAGAAG-TTTAGGGGT-AAAATGGAAT
1 TTTTGGAAGTTTTA-GGGTAAAAATGGAAT
89866 TTTT-GATAGTTTTAGGGTTAAAAAT-GAGAT
1 TTTTGGA-AGTTTTAGGG-TAAAAATGGA-AT
** ** **
89896 TTTTAAAAGTTCGAGGGTAAAAATAAAAT
1 TTTTGGAAGTTTTAGGGTAAAAATGGAAT
89925 TTTTCGGACAG-TTTAGGG
1 TTTT-GGA-AGTTTTAGGG
89943 ACCTCCTAGG
Statistics
Matches: 254, Mismatches: 41, Indels: 32
0.78 0.13 0.10
Matches are distributed among these distances:
27 2 0.01
28 26 0.10
29 114 0.45
30 101 0.40
31 9 0.04
32 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
TTTTGGAAGTTTTAGGGTAAAAATGGAAT
Done.