Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007944.1 Hibiscus syriacus cultivar Beakdansim tig00110366_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: 85748
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:724 original size:19 final size:17
Alignment explanation
Indices: 697--741 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 17
687 AATTTCGTCC
*
697 TTATGTTATAATATATATA
1 TTATATTATAA-AT-TATA
716 TTATATTATAAATTATA
1 TTATATTATAAATTATA
733 TTATATTAT
1 TTATATTAT
742 TTACATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 13 0.52
18 2 0.08
19 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTATATTATAAATTATA
Found at i:2059 original size:15 final size:14
Alignment explanation
Indices: 2027--2085 Score: 59
Period size: 15 Copynumber: 4.1 Consensus size: 14
2017 TATTTTATTT
* *
2027 TTATTATATCTTTC
1 TTATTATATTTTTA
2041 TTATGTATATTTTTA
1 TTAT-TATATTTTTA
2056 TTA-TATATTTTTA
1 TTATTATATTTTTA
2069 CTTATTAT-TTTATTA
1 -TTATTATATTT-TTA
2084 TT
1 TT
2086 CAATATTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 10 0.26
14 12 0.31
15 17 0.44
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (14 bp):
TTATTATATTTTTA
Found at i:2073 original size:14 final size:13
Alignment explanation
Indices: 2022--2084 Score: 69
Period size: 13 Copynumber: 4.9 Consensus size: 13
2012 ATATATATTT
2022 TATTTTTATTATA
1 TATTTTTATTATA
* *
2035 TCTTTCTTA-TGTA
1 TATTT-TTATTATA
2048 TATTTTTATTATA
1 TATTTTTATTATA
2061 TATTTTTACTTAT-
1 TATTTTTA-TTATA
2074 TA-TTTTATTAT
1 TATTTTTATTAT
2085 TCAATATTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
11 4 0.09
12 8 0.19
13 24 0.56
14 7 0.16
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTTTTATTATA
Found at i:2077 original size:26 final size:27
Alignment explanation
Indices: 2021--2084 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
2011 TATATATATT
*
2021 TTATTTTTATTATATCTTTCTTATGTA
1 TTATTTTTATTATATATTTCTTATGTA
2048 -TATTTTTATTATATATTT-TTACT-TA
1 TTATTTTTATTATATATTTCTTA-TGTA
2073 TTA-TTTTATTAT
1 TTATTTTTATTAT
2085 TCAATATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 14 0.41
26 20 0.59
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.69
Consensus pattern (27 bp):
TTATTTTTATTATATATTTCTTATGTA
Found at i:13518 original size:105 final size:105
Alignment explanation
Indices: 13336--13892 Score: 1033
Period size: 105 Copynumber: 5.3 Consensus size: 105
13326 TTTTACCCAT
13336 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
13401 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
*
13441 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
13506 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
13546 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
13611 AAGGGACCGCTGGTTGTCAACAAACGTTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
13651 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
13716 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* *
13756 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
13821 AAGGGACCGCTGGTTGTCACCAAACATTTCTCCAACTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
*
13861 AGCCAATTTCAACTTCACAGCGAAGGATATTG
1 AGCCAATTTCAACTTCACAACGAAGGATATTG
13893 AAACTCAAGA
Statistics
Matches: 440, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 440 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
Found at i:14390 original size:22 final size:22
Alignment explanation
Indices: 14360--14407 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
14350 AATTTCGTCC
*
14360 TTATGTTATATAA-TATATATAT
1 TTATATTATA-AATTATATATAT
14382 TTATATTATAAATTATATATAT
1 TTATATTATAAATTATATATAT
14404 TTAT
1 TTAT
14408 TTACATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTATATTATAAATTATATATAT
Found at i:15714 original size:11 final size:11
Alignment explanation
Indices: 15671--15736 Score: 53
Period size: 11 Copynumber: 5.5 Consensus size: 11
15661 TACATATATA
*
15671 TATTTTATTTT
1 TATTATATTTT
15682 TATTATATCTTTCT
1 TATTATA--TTT-T
15696 TATGTATATTTT
1 TAT-TATATTTT
15708 TATTATATATTT
1 TATTATAT-TTT
*
15720 TACTTAT-TATT
1 TA-TTATATTTT
15731 TATTAT
1 TATTAT
15737 TCAATATTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 4 0.09
11 15 0.32
12 10 0.21
13 10 0.21
14 4 0.09
15 4 0.09
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (11 bp):
TATTATATTTT
Found at i:15718 original size:13 final size:13
Alignment explanation
Indices: 15676--15737 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
15666 ATATATATTT
15676 TATTTTTATTATA
1 TATTTTTATTATA
* *
15689 TCTTTCTTA-TGTA
1 TATTT-TTATTATA
15702 TATTTTTATTATA
1 TATTTTTATTATA
15715 TA-TTTTACTTAT-
1 TATTTTTA-TTATA
15727 TATTTATTATT
1 TATTT-TTATT
15738 CAATATTTGG
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
12 10 0.25
13 24 0.60
14 6 0.15
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTTTTATTATA
Found at i:15736 original size:26 final size:24
Alignment explanation
Indices: 15675--15754 Score: 65
Period size: 26 Copynumber: 3.2 Consensus size: 24
15665 TATATATATT
*
15675 TTATTTTTATTATAT-CTTTCTTA
1 TTATTTTTATTATATATTTTCTTA
15698 TGTATATTTTTATTATATATTTTACTTA
1 --T-TATTTTTATTATATATTTT-CTTA
**
15726 TTATTTATTATTCA-ATATTTGGTTA
1 TTATTT-TTATT-ATATATTTTCTTA
15751 TTAT
1 TTAT
15755 GTATATATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
25 13 0.28
26 26 0.55
27 4 0.09
28 4 0.09
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (24 bp):
TTATTTTTATTATATATTTTCTTA
Found at i:15847 original size:14 final size:14
Alignment explanation
Indices: 15828--15857 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
15818 CTTTTAATTT
*
15828 TTTTATATTCCTTA
1 TTTTATATTCATTA
15842 TTTTATATTCATTA
1 TTTTATATTCATTA
15856 TT
1 TT
15858 ATTTCCTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATATTCATTA
Found at i:18063 original size:223 final size:211
Alignment explanation
Indices: 17672--18101 Score: 630
Period size: 223 Copynumber: 2.0 Consensus size: 211
17662 GTAAATTATC
* * *
17672 TATCCTTTTTATAAAAGTGTCCATACTTTCACTGTGAAAATATATTTATTATTATCTTTAGTTAA
1 TATCATTTTTATAAAAGTGTCCATACTTTCACTGTGAAAACATATTTATTATTATATTTAGTTAA
**
17737 TATTGTTAAAAATCTAAATAATATTTTAATATCAAAACAATCAAATAATTTTTGTGTAAATGAAA
66 TATTGTTAAAAATCTAAATAATATTTTAATATCAAAACAATCAAATAAAATTTGTGTAAATGAAA
*
17802 TTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTAC
131 -TATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAACATAAATTAC
17867 ATAACTTTCAAAAAAGTA
195 ATAACTTT-AAAAAAGTA
*
17885 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATAC---TTTCACTG-TGAAAACATATTTATTATTATATTTAG
17950 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
62 TTAATATTGTT-AA---AAA-TCTAAATAATA-TTT-T--AATATCAAAACAATCAAATAAAATT
* *
18015 TGTGTAAAT-TAA-ATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATTGA
118 TGTGTAAATGAAATATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGA
18078 AACATAAATTACATAACTTTAAAA
183 AACATAAATTACATAACTTTAAAA
18102 GCAGTTTTAA
Statistics
Matches: 195, Mismatches: 9, Indels: 17
0.88 0.04 0.08
Matches are distributed among these distances:
213 25 0.13
216 8 0.04
217 35 0.18
218 2 0.01
221 3 0.02
222 15 0.08
223 72 0.37
224 1 0.01
225 2 0.01
226 32 0.16
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (211 bp):
TATCATTTTTATAAAAGTGTCCATACTTTCACTGTGAAAACATATTTATTATTATATTTAGTTAA
TATTGTTAAAAATCTAAATAATATTTTAATATCAAAACAATCAAATAAAATTTGTGTAAATGAAA
TATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGAAACATAAATTACA
TAACTTTAAAAAAGTA
Found at i:18189 original size:20 final size:19
Alignment explanation
Indices: 18166--18214 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
18156 CGATATACCA
18166 GGTAAAATTATGATAAAACC
1 GGTAAAATTATGAT-AAACC
*
18186 GGTAACAA-AATGATAAACC
1 GGTAA-AATTATGATAAACC
18205 GGTAAAATTA
1 GGTAAAATTA
18215 AAAGTGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 2 0.08
19 11 0.44
20 10 0.40
21 2 0.08
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.22
Consensus pattern (19 bp):
GGTAAAATTATGATAAACC
Found at i:18352 original size:20 final size:19
Alignment explanation
Indices: 18329--18375 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
18319 CGATATAACA
*
18329 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
18349 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
18369 GGTAAAA
1 GGTAAAA
18376 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:22542 original size:19 final size:19
Alignment explanation
Indices: 22479--22541 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
22469 AATGTCGAGT
*
22479 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
22498 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
22517 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
22536 T-ATTTT
1 TAATTTT
22542 TTTATGAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
18 5 0.12
19 38 0.88
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:23007 original size:199 final size:198
Alignment explanation
Indices: 22621--23638 Score: 1753
Period size: 199 Copynumber: 5.1 Consensus size: 198
22611 TTAAGGGTCA
* * *
22621 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTATTACAAGGTGCATCA
22686 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
22751 -ATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT-AATA
131 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
22813 ATG
196 ATG
** *
22816 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-ATTACAAGGTGCATC
*
22881 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
22946 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT-AA
129 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
23010 TAATG
194 TAATG
** *
23015 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-ATTACAAGGTGCATC
*
23080 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
23144 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
23209 TAATG
194 TAATG
* * * *
23214 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTTCCAGAATGAATTTTTACGAGGTGAAT
1 TGTCGACACTAATATAGTTTGTGTCGATA--TTTTTTTCCCAGAATGAATTATTACAAGGTGCAT
23279 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
64 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
23344 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
23409 TAATG
194 TAATG
*
23414 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATT-TTACAAGGTGAATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTATTACAAGGTGCATCA
23477 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
* *
23542 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATA
131 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
23607 ATG
196 ATG
*
23610 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
23639 CTAATTTAAA
Statistics
Matches: 796, Mismatches: 19, Indels: 15
0.96 0.02 0.02
Matches are distributed among these distances:
195 47 0.06
196 206 0.26
197 56 0.07
198 92 0.12
199 238 0.30
200 138 0.17
201 19 0.02
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTATTACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:25110 original size:18 final size:18
Alignment explanation
Indices: 25087--25148 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
25077 AATCGTCGCA
* * *
25087 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
25105 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
25123 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
25141 GAAGATGA
1 GAAGATGA
25149 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:25111 original size:6 final size:6
Alignment explanation
Indices: 25087--25148 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
25077 AATCGTCGCA
* * * * * *
25087 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
25135 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
25149 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:25122 original size:3 final size:3
Alignment explanation
Indices: 25102--25152 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
25092 TGAAGCTGAC
* * * *
25102 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
25150 GAT
1 GAT
25153 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:25149 original size:12 final size:12
Alignment explanation
Indices: 25090--25152 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
25080 CGTCGCAGAA
* *
25090 GATGAAGCTGAC
1 GATGAAGATGAT
*
25102 GATGAAGATGAC
1 GATGAAGATGAT
*
25114 GATGATGATGAT
1 GATGAAGATGAT
*
25126 GATGACGATGAT
1 GATGAAGATGAT
25138 GATGAAGATGAT
1 GATGAAGATGAT
25150 GAT
1 GAT
25153 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:27098 original size:184 final size:184
Alignment explanation
Indices: 26515--27183 Score: 1272
Period size: 184 Copynumber: 3.7 Consensus size: 184
26505 CTTTCAACAT
**
26515 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
26580 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
26645 AATGTGTCGATACGATTT-AAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
26698 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
26762 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
26826 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
26880 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
26945 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
27010 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
27064 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
27129 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
27184 CCATTTAAAA
Statistics
Matches: 478, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
181 19 0.04
182 161 0.34
183 124 0.26
184 174 0.36
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:29761 original size:23 final size:23
Alignment explanation
Indices: 29730--29792 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
29720 ATAGGTAAAC
*
29730 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
29753 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
29776 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
29793 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:29800 original size:23 final size:23
Alignment explanation
Indices: 29730--29802 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
29720 ATAGGTAAAC
* * **
29730 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
29753 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
29776 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
29799 ATAT
1 ATAT
29803 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:30190 original size:23 final size:23
Alignment explanation
Indices: 30159--30221 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
30149 ATAGGTAAAC
*
30159 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
30182 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
30205 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
30222 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:30229 original size:23 final size:23
Alignment explanation
Indices: 30159--30231 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
30149 ATAGGTAAAC
* * **
30159 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
30182 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
30205 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
30228 ATAT
1 ATAT
30232 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:30620 original size:23 final size:23
Alignment explanation
Indices: 30589--30651 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
30579 ATAGGTAAAC
*
30589 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
30612 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
30635 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
30652 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:30659 original size:23 final size:23
Alignment explanation
Indices: 30589--30661 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
30579 ATAGGTAAAC
* * **
30589 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
30612 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
30635 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
30658 ATAT
1 ATAT
30662 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:30762 original size:430 final size:430
Alignment explanation
Indices: 29632--30928 Score: 2541
Period size: 429 Copynumber: 3.0 Consensus size: 430
29622 AATTCGCAGT
*
29632 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAATGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
29697 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
66 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
29762 AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATA
131 AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATA
29827 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
196 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
29892 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
261 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
29957 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATC-AATAATTTTTTGTGCAA
326 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
30021 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
30061 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGATCCTTTTTTATA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCC-TTTTTATA
30125 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
65 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
30190 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
130 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
30255 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
195 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
30320 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
260 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
30385 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
325 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCA
30450 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
390 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
30491 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
30556 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
66 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
30621 AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATA
131 AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATA
30686 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
196 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
30751 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGG--TATA-TATTA
261 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
30813 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
326 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
30878 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
30918 ACACTGTTAAA
1 ACACTGTTAAA
30929 GTATCGATCC
Statistics
Matches: 864, Mismatches: 1, Indels: 8
0.99 0.00 0.01
Matches are distributed among these distances:
427 121 0.14
428 19 0.02
429 355 0.41
430 353 0.41
431 16 0.02
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (430 bp):
ACACTGTTAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATAA
AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
AATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTATA
AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
TTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:40808 original size:30 final size:31
Alignment explanation
Indices: 40751--40810 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
40741 TATAAAGATT
*
40751 GGTGACTAGAATATAAAAGGGATAATAATTC
1 GGTGACTAGAATATAAAAGAGATAATAATTC
* *
40782 GGTGACTATAATATAAAA-ATATAATAATT
1 GGTGACTAGAATATAAAAGAGATAATAATT
40811 TGATGACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.30
Consensus pattern (31 bp):
GGTGACTAGAATATAAAAGAGATAATAATTC
Found at i:83614 original size:31 final size:31
Alignment explanation
Indices: 83556--83615 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
83546 TGCCAAAGCT
*
83556 TAATATAAATTTAGATGAATTTGATTTGAAA
1 TAATATAAATTTAGATGAATTTAATTTGAAA
* ** *
83587 TAATATTAATTTATTTGATTTTAATTTGA
1 TAATATAAATTTAGATGAATTTAATTTGA
83616 CAAAGTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (31 bp):
TAATATAAATTTAGATGAATTTAATTTGAAA
Found at i:83630 original size:2 final size:2
Alignment explanation
Indices: 83623--83666 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
83613 TGACAAAGTT
83623 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
83665 TA
1 TA
83667 ATTTTTGTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83970 original size:25 final size:27
Alignment explanation
Indices: 83923--83990 Score: 106
Period size: 26 Copynumber: 2.6 Consensus size: 27
83913 CCCGCCCCGA
83923 TTATA-TATATATAATATTTTATA-TTT
1 TTATATTATATAT-ATATTTTATATTTT
83949 TTA-ATTATATATATATTTTATATTTT
1 TTATATTATATATATATTTTATATTTT
83975 TTATATTATATATATA
1 TTATATTATATATATA
83991 ATATTTTCGG
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
25 11 0.28
26 16 0.41
27 12 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTATATTATATATATATTTTATATTTT
Found at i:83979 original size:18 final size:16
Alignment explanation
Indices: 83934--83981 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
83924 TATATATATA
*
83934 TAATATTTTATATTTT
1 TAATTTTTTATATTTT
* *
83950 TAATTATATATATATTT
1 TAATTTTTTATAT-TTT
83967 TATATTTTTTATATT
1 TA-ATTTTTTATATT
83982 ATATATATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATTTTTTATATTTT
Done.