Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003791.1 Hibiscus syriacus cultivar Beakdansim tig00008114_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: 75070
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:146 original size:18 final size:18
Alignment explanation
Indices: 119--266 Score: 197
Period size: 18 Copynumber: 7.9 Consensus size: 18
109 TTCTTAAGGC
* *
119 GTGGTTCTTCAGGATATA
1 GTGGTCCTTCAGGACATA
137 GTGGTCCTTCAGGACAAATCA
1 GTGGTCCTTCAGGAC--AT-A
*
158 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCAGGACATA
176 GTGGTCCTTCAGGACAAATCA
1 GTGGTCCTTCAGGAC--AT-A
*
197 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCAGGACATA
215 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCAGGACATA
233 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCAGGACATA
*
251 GTGGTCCTTTAGGACA
1 GTGGTCCTTCAGGACA
267 AATATACAGT
Statistics
Matches: 117, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
18 79 0.68
19 4 0.03
20 4 0.03
21 30 0.26
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.28
Consensus pattern (18 bp):
GTGGTCCTTCAGGACATA
Found at i:177 original size:39 final size:39
Alignment explanation
Indices: 119--269 Score: 236
Period size: 39 Copynumber: 3.9 Consensus size: 39
109 TTCTTAAGGC
* *
119 GTGGTTCTTCAGGATATAGTGGTCCTTCAGGACAAATCA
1 GTGGTCCTTCAGGACATAGTGGTCCTTCAGGACAAATCA
*
158 GTGGTCCTTCGGGACATAGTGGTCCTTCAGGACAAATCA
1 GTGGTCCTTCAGGACATAGTGGTCCTTCAGGACAAATCA
*
197 GTGGTCCTTCGGGACATAGTGGTCCTTCAGGAC--AT-A
1 GTGGTCCTTCAGGACATAGTGGTCCTTCAGGACAAATCA
*
233 GTGGTCCTTCAGGACATAGTGGTCCTTTAGGACAAAT
1 GTGGTCCTTCAGGACATAGTGGTCCTTCAGGACAAAT
270 ATACAGTGCC
Statistics
Matches: 105, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
36 32 0.30
37 2 0.02
38 2 0.02
39 69 0.66
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (39 bp):
GTGGTCCTTCAGGACATAGTGGTCCTTCAGGACAAATCA
Found at i:189 original size:57 final size:56
Alignment explanation
Indices: 119--270 Score: 200
Period size: 57 Copynumber: 2.7 Consensus size: 56
109 TTCTTAAGGC
* * *
119 GTGGTTCTTCAGGATATAGTGGTCCTTCAGGACAAATCAGTGGTCCTTCGGGACATA
1 GTGGTCCTTCAGGAAATAGTGGTCCTTCAGGACAAAT-AGTGGTCCTTCAGGACATA
*
176 GTGGTCCTTCAGGACAAATCAGTGGTCCTTCGGGAC--ATAGTGGTCCTTCAGGACATA
1 GTGGTCCTTCAGG--AAAT-AGTGGTCCTTCAGGACAAATAGTGGTCCTTCAGGACATA
* *
233 GTGGTCCTTCAGGACATAGTGGTCCTTTAGGACAAATA
1 GTGGTCCTTCAGGAAATAGTGGTCCTTCAGGACAAATA
271 TACAGTGCCC
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
54 14 0.17
55 3 0.04
56 3 0.04
57 43 0.52
58 2 0.02
59 3 0.04
60 15 0.18
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (56 bp):
GTGGTCCTTCAGGAAATAGTGGTCCTTCAGGACAAATAGTGGTCCTTCAGGACATA
Found at i:5163 original size:18 final size:18
Alignment explanation
Indices: 5130--5220 Score: 110
Period size: 18 Copynumber: 4.9 Consensus size: 18
5120 TTCTTAAGGT
*
5130 GTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
* *
5148 GCGGTACTTCGGGACAAATCA
1 GTGGTCCTTCGGGAC--AT-A
*
5169 GTGGTCCTTCGGGATATA
1 GTGGTCCTTCGGGACATA
*
5187 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCGGGACATA
5205 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
5221 AATATACAGT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
18 44 0.72
19 2 0.03
20 2 0.03
21 13 0.21
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:5173 original size:39 final size:36
Alignment explanation
Indices: 5130--5220 Score: 110
Period size: 39 Copynumber: 2.4 Consensus size: 36
5120 TTCTTAAGGT
* *
5130 GTGGTCCTTTGGGACATAGCGGTACTTCGGGACAAATCA
1 GTGGTCCTTCGGGACATAGCGGTACTTCAGGAC--AT-A
* * *
5169 GTGGTCCTTCGGGATATAGTGGTCCTTCAGGACATA
1 GTGGTCCTTCGGGACATAGCGGTACTTCAGGACATA
5205 GTGGTCCTTCGGGACA
1 GTGGTCCTTCGGGACA
5221 AATATACAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 16 0.35
37 2 0.04
39 28 0.61
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.27
Consensus pattern (36 bp):
GTGGTCCTTCGGGACATAGCGGTACTTCAGGACATA
Found at i:10088 original size:2 final size:2
Alignment explanation
Indices: 10081--10145 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
10071 ATGTAAGATA
10081 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
10123 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
10146 AAGTATTATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12594 original size:15 final size:15
Alignment explanation
Indices: 12574--12610 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
12564 ATGGACCCTT
12574 CATGCGCGATTAATC
1 CATGCGCGATTAATC
12589 CATGCGCGATTAATC
1 CATGCGCGATTAATC
12604 CATGCGC
1 CATGCGC
12611 TAAGCGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (15 bp):
CATGCGCGATTAATC
Found at i:21149 original size:19 final size:19
Alignment explanation
Indices: 21125--21233 Score: 92
Period size: 19 Copynumber: 5.4 Consensus size: 19
21115 ACTTATTTTA
21125 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
21144 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
21166 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* * *
21188 ATTTTAACTATCACAACAC
1 TTTTTCACTATCGCAACAC
* * *
21207 ATTTTAACTATCACAACAC
1 TTTTTCACTATCGCAACAC
21226 ATTTTTCA
1 -TTTTTCA
21234 AAATCGCGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
19 43 0.57
20 5 0.07
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:21283 original size:21 final size:21
Alignment explanation
Indices: 21235--21295 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
21225 CATTTTTCAA
*
21235 AATCGCGTTGCGAATCT-TAC
1 AATCGCGTTGCGAATCTGGAC
*
21255 AATCGCGTTGCGAATCTGGAT
1 AATCGCGTTGCGAATCTGGAC
* *
21276 ATTCGCGTTGCGAATTTGGA
1 AATCGCGTTGCGAATCTGGA
21296 AACTGAGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (21 bp):
AATCGCGTTGCGAATCTGGAC
Found at i:23967 original size:26 final size:26
Alignment explanation
Indices: 23921--23986 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
23911 GAAGGGGTGG
* *
23921 ACTTATAAAA-CTTAAATAATGGAGA
1 ACTTATAAAATTTTAAATAATGCAGA
23946 ACTTATAAAATTTTAAATAATGCAGA
1 ACTTATAAAATTTTAAATAATGCAGA
23972 ACTTATAAAATTTTA
1 ACTTATAAAATTTTA
23987 CTGGAAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 10 0.26
26 28 0.74
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (26 bp):
ACTTATAAAATTTTAAATAATGCAGA
Found at i:31187 original size:22 final size:22
Alignment explanation
Indices: 31161--31264 Score: 138
Period size: 22 Copynumber: 4.7 Consensus size: 22
31151 TTGGTGCAGA
*
31161 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
31183 GGGAACCGATACCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAG
* *
31205 GGGAACCAATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-TTGAAG
* *
31228 GGGAACCGATTCCCCC-TGTAG
1 GGGAACCGATACCCCCTTGAAG
*
31249 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
31265 AGGAGGTTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.24
22 35 0.47
23 21 0.28
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (22 bp):
GGGAACCGATACCCCCTTGAAG
Found at i:36983 original size:13 final size:13
Alignment explanation
Indices: 36967--36997 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
36957 TAGAAAATAT
36967 TTTTCTATTTTTG
1 TTTTCTATTTTTG
*
36980 TTTTCTGTTTTTG
1 TTTTCTATTTTTG
36993 TTTTC
1 TTTTC
36998 AGAAAATAGT
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:0.03, C:0.10, G:0.10, T:0.77
Consensus pattern (13 bp):
TTTTCTATTTTTG
Found at i:38115 original size:27 final size:27
Alignment explanation
Indices: 38074--38126 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
38064 GGATTGAAGA
38074 TCCACAAGCGAAGTGAGTTTAAGGCAT
1 TCCACAAGCGAAGTGAGTTTAAGGCAT
*
38101 TCCACAAGCGGAGTGAGTTTAAGGCA
1 TCCACAAGCGAAGTGAGTTTAAGGCA
38127 CAATCGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.21
Consensus pattern (27 bp):
TCCACAAGCGAAGTGAGTTTAAGGCAT
Found at i:38128 original size:22 final size:23
Alignment explanation
Indices: 38075--38134 Score: 59
Period size: 27 Copynumber: 2.5 Consensus size: 23
38065 GATTGAAGAT
38075 CCACAAGCGAAGTGAGTTTAAGG
1 CCACAAGCGAAGTGAGTTTAAGG
*
38098 CATTCCACAAGCGGAGTGAGTTTAAGG
1 ----CCACAAGCGAAGTGAGTTTAAGG
*
38125 -CACAATCGAA
1 CCACAAGCGAA
38135 TCCTTTGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 8 0.27
27 22 0.73
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (23 bp):
CCACAAGCGAAGTGAGTTTAAGG
Found at i:43584 original size:2 final size:2
Alignment explanation
Indices: 43577--43665 Score: 101
Period size: 2 Copynumber: 44.5 Consensus size: 2
43567 TTATATGCAC
*
43577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT TT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* ** *
43619 AT AC CC AT AA AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43661 AT AT A
1 AT AT A
43666 CATGACTACA
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.03
2 71 0.95
3 2 0.03
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:44138 original size:54 final size:54
Alignment explanation
Indices: 44073--44254 Score: 192
Period size: 54 Copynumber: 3.4 Consensus size: 54
44063 GTCCTTCAGA
* * ** * *
44073 GAGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGTTCCCTCTTTATCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
* * *
44127 GAGTGTGGAACTCGAACGTC-T-TT-AAACGGGTTCACTCCCTCTTTCT-TCAGG
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGG
* * * *
44178 GAGAATAGAACTCGAATATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTCTAGG
1 GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
*
44232 GAGTATGAAACTCGAACAATCTT
1 GAGTATGGAACTCGAAC-ATCTT
44255 AAACAATCGT
Statistics
Matches: 102, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
50 1 0.01
51 36 0.35
52 3 0.03
53 3 0.03
54 53 0.52
55 6 0.06
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (54 bp):
GAGTATGGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGG
Found at i:44257 original size:105 final size:105
Alignment explanation
Indices: 44066--44258 Score: 262
Period size: 105 Copynumber: 1.8 Consensus size: 105
44056 TTCCCCAGTC
* ** *
44066 CTTCAGAGAGTATAGAACTCAAACATCTTCTTCTTACGGGTTCGTTCCCTCTTTATCTAGGGAGT
1 CTTCAGAGAGAATAGAACTCAAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTATCTAGGGAGT
* * *
44131 GTGGAACTCGAACGTCTTTAAACGGGTTCACTCCCTCTTT
66 ATGAAACTCGAACATCTTTAAACGGGTTCACTCCCTCTTT
* * * * *
44171 CTTCAGGGAGAATAGAACTCGAATATCTTCTTCAAACGGGTTTGCTCCCTCTTTCTCTAGGGAGT
1 CTTCAGAGAGAATAGAACTCAAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTATCTAGGGAGT
44236 ATGAAACTCGAACAATC-TTAAAC
66 ATGAAACTCGAAC-ATCTTTAAAC
44259 AATCGTGTCT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
105 73 0.97
106 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (105 bp):
CTTCAGAGAGAATAGAACTCAAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTATCTAGGGAGT
ATGAAACTCGAACATCTTTAAACGGGTTCACTCCCTCTTT
Found at i:44281 original size:55 final size:55
Alignment explanation
Indices: 44161--44429 Score: 346
Period size: 55 Copynumber: 4.9 Consensus size: 55
44151 AACGGGTTCA
* * * * ** * * *
44161 CTCCCTCTTTCTTCAGGGAGAAT-AGAACTCGAA-TATCTTCTTCAAACGGGTTTG
1 CTCCCTATTTCTTCAGAGAGTATGAG-ACTCGAACAATCTTCAACAATCGTGTCTG
* * * *
44215 CTCCCTCTTTC-TCTAGGGAGTATGAAACTCGAACAATCTTAAACAATCGTGTCTG
1 CTCCCTATTTCTTC-AGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
*
44270 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTATG
1 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
* *
44325 GTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
*
44380 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAATAATCGT
1 CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGT
44430 TGGGAAATCT
Statistics
Matches: 193, Mismatches: 18, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
53 2 0.01
54 26 0.13
55 163 0.84
56 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (55 bp):
CTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTG
Found at i:45461 original size:20 final size:20
Alignment explanation
Indices: 45425--45492 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
45415 TCTTGAACCC
45425 TCATTTTTTCA-TTTTTTCAT
1 TCATTTTTT-ATTTTTTTCAT
45445 TCATTTTTTATTTTTTT-AT
1 TCATTTTTTATTTTTTTCAT
*
45464 T--TTTTATTATATATTTTTCAC
1 TCATTTT-TTAT-T-TTTTTCAT
45485 TCATTTTT
1 TCATTTTT
45493 CTTCTTCTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
17 4 0.10
18 4 0.10
19 5 0.12
20 20 0.50
21 2 0.05
22 1 0.03
23 4 0.10
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (20 bp):
TCATTTTTTATTTTTTTCAT
Found at i:49001 original size:8 final size:8
Alignment explanation
Indices: 48988--49015 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
48978 GAAAAAGAAG
48988 ATATATAC
1 ATATATAC
48996 ATATATAC
1 ATATATAC
49004 ATATATAC
1 ATATATAC
49012 ATAT
1 ATAT
49016 GGGAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:56311 original size:15 final size:15
Alignment explanation
Indices: 56288--56338 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
56278 AACCGCGTCA
*
56288 TTTTTAATTATTATC
1 TTTTCAATTATTATC
**
56303 TTTTCAATT-GGAT-
1 TTTTCAATTATTATC
56316 TTTT-AATTATTATC
1 TTTTCAATTATTATC
56330 TTTTCAATT
1 TTTTCAATT
56339 GGATTTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 6 0.21
15 12 0.43
ACGTcount: A:0.25, C:0.08, G:0.04, T:0.63
Consensus pattern (15 bp):
TTTTCAATTATTATC
Found at i:56325 original size:27 final size:27
Alignment explanation
Indices: 56287--56351 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
56277 AAACCGCGTC
56287 ATTTTTAATTATTATCTTTTCAATTGG
1 ATTTTTAATTATTATCTTTTCAATTGG
56314 ATTTTTAATTATTATCTTTTCAATTGG
1 ATTTTTAATTATTATCTTTTCAATTGG
56341 ATTTTTAATTA
1 ATTTTTAATTA
56352 AAAACAGTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (27 bp):
ATTTTTAATTATTATCTTTTCAATTGG
Found at i:62936 original size:21 final size:20
Alignment explanation
Indices: 62903--62941 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
62893 ATGAGAAAAC
62903 AAAAAGAGGGAAAAGTGTTTG
1 AAAAAGAGGGAAAA-TGTTTG
* *
62924 AAAAGGAGTGAAAATGTT
1 AAAAAGAGGGAAAATGTT
62942 AAATTAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.21
Consensus pattern (20 bp):
AAAAAGAGGGAAAATGTTTG
Found at i:63395 original size:20 final size:21
Alignment explanation
Indices: 63370--63416 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
63360 ACATATGGTA
* *
63370 AAATAAAATT-AAATTAAATT
1 AAATAAAATTAAAATGAAATG
63390 AAAT-AAATTAAAATGAAATG
1 AAATAAAATTAAAATGAAATG
63410 AAATAAA
1 AAATAAA
63417 GTATGCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 16 0.70
21 2 0.09
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
AAATAAAATTAAAATGAAATG
Found at i:67296 original size:17 final size:14
Alignment explanation
Indices: 67263--67307 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
67253 TAAACTATTT
67263 AAAATAAAATAATA
1 AAAATAAAATAATA
67277 AAAATAAAGATAAGATA
1 AAAATAAA-AT-A-ATA
*
67294 AAAATAATATAATA
1 AAAATAAAATAATA
67308 TTTAAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 3 0.11
17 10 0.37
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAAATAAAATAATA
Found at i:68471 original size:15 final size:15
Alignment explanation
Indices: 68447--68481 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
68437 GATAATCAAA
*
68447 ACTTTTTAAAAATTG
1 ACTTTGTAAAAATTG
68462 ACTTTGTAAAAATTG
1 ACTTTGTAAAAATTG
68477 ACTTT
1 ACTTT
68482 CGATGCTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (15 bp):
ACTTTGTAAAAATTG
Found at i:68909 original size:46 final size:44
Alignment explanation
Indices: 68836--68925 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 44
68826 AAGTGACGTC
68836 GTGACTATGCTGCCTTTAATAAACCTTTGTCAAATTGGACTCCA
1 GTGACTATGCTGCCTTTAATAAACCTTTGTCAAATTGGACTCCA
68880 GTGACTATGCTGCCCTTTTAATAAACCTTTGTCAAATTGGACTCCA
1 GTGACTATGCTG-CC-TTTAATAAACCTTTGTCAAATTGGACTCCA
68926 TTTATCAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
44 12 0.27
45 2 0.05
46 30 0.68
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (44 bp):
GTGACTATGCTGCCTTTAATAAACCTTTGTCAAATTGGACTCCA
Found at i:71711 original size:9 final size:9
Alignment explanation
Indices: 71681--71714 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
71671 ATTAACTTGG
71681 TTTTAAATT
1 TTTTAAATT
*
71690 TTTAAAATAT
1 TTTTAAAT-T
71700 TTTTAAATT
1 TTTTAAATT
71709 TTTTAA
1 TTTTAA
71715 TGAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTAAATT
Found at i:72062 original size:16 final size:16
Alignment explanation
Indices: 72028--72140 Score: 190
Period size: 16 Copynumber: 6.9 Consensus size: 16
72018 TTTGTATTTT
* *
72028 TTAATCGAATCAATGGA
1 TTAA-CGAATTAATAGA
72045 TTAACGAATTAATAGA
1 TTAACGAATTAATAGA
72061 TTAACGAATTAATAGA
1 TTAACGAATTAATAGA
72077 TTAACGAATTAATAGA
1 TTAACGAATTAATAGA
72093 TTAACGAATTAATAGA
1 TTAACGAATTAATAGA
72109 TTAACGAATTAATAGA
1 TTAACGAATTAATAGA
72125 TTAACGAATTGAATAG
1 TTAACGAATT-AATAG
72141 TTCTGATAAG
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
16 84 0.90
17 9 0.10
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (16 bp):
TTAACGAATTAATAGA
Found at i:72063 original size:8 final size:8
Alignment explanation
Indices: 72052--72128 Score: 54
Period size: 8 Copynumber: 9.6 Consensus size: 8
72042 GGATTAACGA
72052 ATTAATAG
1 ATTAATAG
*
72060 ATTAA-CG
1 ATTAATAG
72067 AATTAATAG
1 -ATTAATAG
*
72076 ATTAA-CG
1 ATTAATAG
72083 AATTAATAG
1 -ATTAATAG
*
72092 ATTAA-CG
1 ATTAATAG
72099 AATTAATAG
1 -ATTAATAG
*
72108 ATTAA-CG
1 ATTAATAG
72115 AATTAATAG
1 -ATTAATAG
72124 ATTAA
1 ATTAA
72129 CGAATTGAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
7 4 0.08
8 45 0.85
9 4 0.08
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (8 bp):
ATTAATAG
Done.