Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006783.1 Hibiscus syriacus cultivar Beakdansim tig00017185_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: 55606
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Found at i:802 original size:15 final size:16
Alignment explanation
Indices: 781--826 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
771 AAAAAAAGCG
781 AAGATAATAAATAAAT
1 AAGATAATAAATAAAT
*
797 -AGATAATAAATTAAT
1 AAGATAATAAATAAAT
*
812 AAAATAATAAATAAA
1 AAGATAATAAATAAA
827 CAAACACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (16 bp):
AAGATAATAAATAAAT
Found at i:1070 original size:17 final size:18
Alignment explanation
Indices: 1034--1080 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
1024 CACCGAAATA
*
1034 GAAAAAGGGATACGAATT
1 GAAAAAAGGATACGAATT
*
1052 GAAAAAAGGATA-GATTT
1 GAAAAAAGGATACGAATT
1069 GAAAAAAGGATA
1 GAAAAAAGGATA
1081 AAGGTTTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.55, C:0.02, G:0.26, T:0.17
Consensus pattern (18 bp):
GAAAAAAGGATACGAATT
Found at i:1372 original size:33 final size:32
Alignment explanation
Indices: 1330--1412 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 32
1320 ATATAAAAAG
*
1330 AATAGAAATAAATATAAA-A-AAAGAAATAATAGT
1 AATATAAATAAATA-AAATATAAAGAAA-AATA-T
*
1363 AATATAAATAAATAAAATATTAAGAAAAATAT
1 AATATAAATAAATAAAATATAAAGAAAAATAT
1395 ACATATAAATAAATAAAA
1 A-ATATAAATAAATAAAA
1413 CAAATAGATG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
32 5 0.11
33 34 0.76
34 6 0.13
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (32 bp):
AATATAAATAAATAAAATATAAAGAAAAATAT
Found at i:3218 original size:102 final size:105
Alignment explanation
Indices: 2964--3635 Score: 834
Period size: 103 Copynumber: 6.6 Consensus size: 105
2954 CTGAAATTAG
* * *
2964 GAAATTGGGAAATTGTTCGTTGACAACCAGCCGTCCAC-T--T-GTG-AG-TGAACTTGTGTTGT
1 GAAATTAGGAAATTGTT-GTTGACAACCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGT
* * * *
3023 CTCGAGTGCACGATATCC-TC-CATCGTGGAGTTAAAATT-GCTC-
64 CTGGAGT-C-CAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCT
* * * *
3065 GAAACT--GAAATTGTTGTTGACAACCA-C-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTTT
1 GAAATTAGGAAATTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
3126 CG-GTCCAATATCCTTCGCTGTGAAGTTG-AATTGGCTCT
66 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
* * * *
3164 G-AATTGGGAAATTGTTTATTGACAACCAAC-GTCCCTTCGTCGTGAAGTTAAACTTGCG-TGTC
1 GAAATTAGGAAATTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
3226 TGGAGT-CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
65 TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
* * * *
3266 GACATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCT
1 GAAATTAGGAAATTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
3331 GGAGTCCAATATCC-TCGCTGTGAAGTTGAAATTGGCTCT
66 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
*
3370 GAAATT-GGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
1 GAAATTAGGAAATTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
3434 GGAGTCCAATAT-CTTCGCTGTGAAGTTGAAATTGGCTCT
66 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
* *
3473 GAAATTAGG-AA--GTTGTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
1 GAAATTAGGAAATTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
3535 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
66 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
*
3575 GAAATTAGGAAGTTGTTGTTGAC-ACCAGCGG----TTCGTCGTGAAGTTGAAC-TGCG-TGTCT
1 GAAATTAGGAAATTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
3633 GGA
66 GGA
3636 AATCGGAGTT
Statistics
Matches: 521, Mismatches: 24, Indels: 55
0.87 0.04 0.09
Matches are distributed among these distances:
95 1 0.00
96 5 0.01
97 5 0.01
98 41 0.08
99 20 0.04
100 30 0.06
101 123 0.24
102 89 0.17
103 141 0.27
104 49 0.09
105 17 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
GAAATTAGGAAATTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT
Found at i:3314 original size:103 final size:105
Alignment explanation
Indices: 3075--3635 Score: 840
Period size: 103 Copynumber: 5.5 Consensus size: 105
3065 GAAACTGAAA
* * * *
3075 TTGTTGTTGACAACCA-C-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTTTCG-GTCCAATAT
1 TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
3137 CCTTCGCTGTGAAGTTG-AATTGGCTCTG-AATTGGGAAA
66 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAG
* * *
3175 TTGTTTATTGACAACCAAC-GTCCCTTCGTCGTGAAGTTAAACTTGCG-TGTCTGGAGT-CAATA
1 TTG-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
3237 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGACATTGGGAAG
65 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAG
*
3278 TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGGAGTCCAATAT
1 TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
3343 CC-TCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGAAG
66 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAG
3381 TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
3446 -CTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAA-
66 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAG
* *
3484 --GTTGTTGACAACTAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAATAT
1 TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
3547 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAG
66 CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAG
3587 TTGTTGTTGAC-ACCAGCGG----TTCGTCGTGAAGTTGAAC-TGCG-TGTCTGGA
1 TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
3636 AATCGGAGTT
Statistics
Matches: 431, Mismatches: 16, Indels: 30
0.90 0.03 0.06
Matches are distributed among these distances:
98 8 0.02
99 3 0.01
100 21 0.05
101 101 0.23
102 91 0.21
103 139 0.32
104 51 0.12
105 17 0.04
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (105 bp):
TTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
CCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAG
Found at i:13809 original size:6 final size:6
Alignment explanation
Indices: 13798--13841 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
13788 GTAAACAGTT
*
13798 AAATAA AAATAA ATAATAA TAAA-AA CAATAA AAATAA AAATAA A
1 AAATAA AAATAA A-AATAA -AAATAA AAATAA AAATAA AAATAA A
13842 TGGCAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 2 0.06
6 23 0.70
7 7 0.21
8 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:13827 original size:15 final size:16
Alignment explanation
Indices: 13798--13842 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
13788 GTAAACAGTT
13798 AAATAAAAATAAATAA
1 AAATAAAAATAAATAA
* *
13814 TAATAAAAA-CAATAA
1 AAATAAAAATAAATAA
13829 AAATAAAAATAAAT
1 AAATAAAAATAAAT
13843 GGCAAGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (16 bp):
AAATAAAAATAAATAA
Found at i:13853 original size:31 final size:30
Alignment explanation
Indices: 13798--13858 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
13788 GTAAACAGTT
* *
13798 AAATAAAAATAAATAATAATAAAAACAATAA
1 AAATAAAAATAAATAACAAGAAAAA-AATAA
**
13829 AAATAAAAATAAATGGCAAGAAAAAAATAA
1 AAATAAAAATAAATAACAAGAAAAAAATAA
13859 GAGAAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (30 bp):
AAATAAAAATAAATAACAAGAAAAAAATAA
Found at i:14887 original size:16 final size:16
Alignment explanation
Indices: 14860--14899 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
14850 AAAAAAAGAG
14860 AAGATAAATAAATAAAT
1 AAGAT-AATAAATAAAT
*
14877 AAGATAATAAATTAAT
1 AAGATAATAAATAAAT
*
14893 AAAATAA
1 AAGATAA
14900 AAACAAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (16 bp):
AAGATAATAAATAAAT
Found at i:15173 original size:19 final size:19
Alignment explanation
Indices: 15118--15165 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
15108 CGAAAATAGG
*
15118 AAAAGGGATACAGATTTGA
1 AAAAAGGATACAGATTTGA
15137 AAAAAGGATACAGATTTGA
1 AAAAAGGATACAGATTTGA
15156 AAAAAGGATA
1 AAAAAGGATA
15166 AAGGTTTGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.54, C:0.04, G:0.23, T:0.19
Consensus pattern (19 bp):
AAAAAGGATACAGATTTGA
Found at i:15254 original size:16 final size:17
Alignment explanation
Indices: 15230--15265 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
15220 GTTAGGTTAT
15230 ATATATATATAAT-ATA
1 ATATATATATAATAATA
*
15246 ATATCTATATAATAATA
1 ATATATATATAATAATA
15263 ATA
1 ATA
15266 AGATATGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATATATAATAATA
Found at i:15451 original size:20 final size:20
Alignment explanation
Indices: 15417--15505 Score: 64
Period size: 20 Copynumber: 4.6 Consensus size: 20
15407 ATATTAACGT
* *
15417 ATATAAAGAATAGAAATAAA
1 ATATAAATAAAAGAAATAAA
*
15437 ATATAAATAAAAGAAA-ATA
1 ATATAAATAAAAGAAATAAA
*
15456 ATAGT-AATATAAATAAATAAA
1 ATA-TAAATA-AAAGAAATAAA
*
15477 ATAT---TAAAA-AAATATAC
1 ATATAAATAAAAGAAATA-AA
15494 ATATAAATAAAA
1 ATATAAATAAAA
15506 TAAAACAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
16 5 0.09
17 8 0.14
18 2 0.04
19 9 0.16
20 27 0.48
21 5 0.09
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (20 bp):
ATATAAATAAAAGAAATAAA
Found at i:15474 original size:16 final size:15
Alignment explanation
Indices: 15451--15508 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
15441 AAATAAAAGA
15451 AAAT-AATAGTAATAT
1 AAATAAATA-TAATAT
*
15466 AAATAAATAAAATATT
1 AAATAAATATAATA-T
*
15482 AAAAAAATATACATAT
1 AAATAAATATA-ATAT
15498 AAATAAA-ATAA
1 AAATAAATATAA
15509 AACAAATAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 1 0.03
15 11 0.31
16 21 0.58
17 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AAATAAATATAATAT
Found at i:18302 original size:3 final size:3
Alignment explanation
Indices: 18294--18325 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
18284 TTATGTGGGG
18294 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
18326 GTGTGTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:22149 original size:26 final size:26
Alignment explanation
Indices: 22129--22178 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
22119 TAAAATGTAA
22129 ATTAAAAATATATTTTAAAAAATAAT
1 ATTAAAAATATATTTTAAAAAATAAT
* * *
22155 ATTATATATATTTTTTAAAAAATA
1 ATTAAAAATATATTTTAAAAAATA
22179 TTTTCAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTAAAAATATATTTTAAAAAATAAT
Found at i:22173 original size:39 final size:39
Alignment explanation
Indices: 22130--22245 Score: 123
Period size: 38 Copynumber: 3.0 Consensus size: 39
22120 AAAATGTAAA
22130 TTAAAAATATATTTTAAAAAATA-ATATTATATATATTTT
1 TTAAAAATATATTTT-AAAAATAGATATTATATATATTTT
*
22169 TTAAAAA-ATATTTTCAAAATCAGATATTATATATA-TTT
1 TTAAAAATATATTTTAAAAAT-AGATATTATATATATTTT
* * * * *
22207 TCAAAAATAT-TTTTCTATATTATATATTATATATATTTT
1 TTAAAAATATATTTT-AAAAATAGATATTATATATATTTT
22246 CCAAAACGTT
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
37 5 0.08
38 34 0.52
39 27 0.41
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (39 bp):
TTAAAAATATATTTTAAAAATAGATATTATATATATTTT
Found at i:22271 original size:75 final size:73
Alignment explanation
Indices: 22133--22324 Score: 208
Period size: 75 Copynumber: 2.6 Consensus size: 73
22123 ATGTAAATTA
* * * **
22133 AAAATATATTTTAAAAAATA-ATATTATATATATTTTTTAAAAAATATTTTCAAAATCAGATATT
1 AAAATAT-TTTTCAAAACTATATATTATATATA--TTTT-CAAAACGTTTTCAAAATCAGATATT
22197 ATATATATTTTC
62 ATATATATTTTC
* * * *
22209 AAAAATATTTTTCTATATTATATATTATATATATTTTCCAAAACGTTTTCAAAA-CTGTATATTA
1 -AAAATATTTTTCAAAACTATATATTATATATATTTT-CAAAACGTTTTCAAAATCAG-ATATTA
22273 TATATATTTTC
63 TATATATTTTC
* *
22284 AAAATGTTTTTCAAAACTATATATTATATATGTTTTCAAAA
1 AAAATATTTTTCAAAACTATATATTATATATATTTTCAAAA
22325 TTATATATTA
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
73 5 0.05
74 33 0.33
75 34 0.34
76 8 0.08
77 19 0.19
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (73 bp):
AAAATATTTTTCAAAACTATATATTATATATATTTTCAAAACGTTTTCAAAATCAGATATTATAT
ATATTTTC
Found at i:22325 original size:37 final size:37
Alignment explanation
Indices: 22153--22325 Score: 188
Period size: 37 Copynumber: 4.6 Consensus size: 37
22143 TTAAAAAATA
* ** *
22153 ATATTATATATATTTTTTAAAAAATATTTTCAAAA-TCAG
1 ATATTATATATA-TTTTCAAAATGT-TTTTCAAAACT-AT
* * * *
22192 ATATTATATATATTTTCAAAAATATTTTTCTATATTAT
1 ATATTATATATATTTTC-AAAATGTTTTTCAAAACTAT
* *
22230 ATATTATATATATTTTCCAAAACG-TTTTCAAAACTGT
1 ATATTATATATATTTT-CAAAATGTTTTTCAAAACTAT
22267 ATATTATATATATTTTCAAAATGTTTTTCAAAACTAT
1 ATATTATATATATTTTCAAAATGTTTTTCAAAACTAT
*
22304 ATATTATATATGTTTTCAAAAT
1 ATATTATATATATTTTCAAAAT
22326 TATATATTAT
Statistics
Matches: 116, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
36 6 0.05
37 58 0.50
38 32 0.28
39 20 0.17
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (37 bp):
ATATTATATATATTTTCAAAATGTTTTTCAAAACTAT
Found at i:22341 original size:27 final size:25
Alignment explanation
Indices: 22291--22339 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
22281 TTCAAAATGT
22291 TTTTCAAAACTATATATTATATATG
1 TTTTCAAAACTATATATTATATATG
*
22316 TTTTCAAAATTATATATTATATAT
1 TTTTCAAAACTATATATTATATAT
22340 ATTCAAAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (25 bp):
TTTTCAAAACTATATATTATATATG
Found at i:22344 original size:23 final size:24
Alignment explanation
Indices: 22293--22348 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
22283 CAAAATGTTT
*
22293 TTCAAAACTATATATTATATATGTT
1 TTCAAAACTATATATTATATA-GTA
*
22318 TTCAAAATTATATATTATATA-TA
1 TTCAAAACTATATATTATATAGTA
22341 TTCAAAAC
1 TTCAAAAC
22349 GTTTTCAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 8 0.29
25 20 0.71
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (24 bp):
TTCAAAACTATATATTATATAGTA
Found at i:31818 original size:37 final size:38
Alignment explanation
Indices: 31721--31920 Score: 279
Period size: 37 Copynumber: 5.4 Consensus size: 38
31711 AAAAATAATA
*
31721 ATATTATATATATTTTCAAAAAATG-TTTTCAAAACCAT
1 ATATTATATATATTTTC-AAAAATGTTTTTCAAAACTAT
* *
31759 ATATTATATATATTTTCAAAAATGTTTTTCTAAATTAT
1 ATATTATATATATTTTCAAAAATGTTTTTCAAAACTAT
*
31797 ATATTATATATTTTTTC-AAAATGTTTTTCAAAACTAT
1 ATATTATATATATTTTCAAAAATGTTTTTCAAAACTAT
* *
31834 ATATTATATATGTTTTCAAAAATG-TTTTCAAAATTAT
1 ATATTATATATATTTTCAAAAATGTTTTTCAAAACTAT
*
31871 ATATTATATATA--TTC-AAAACGTTTTT-AAAACTAT
1 ATATTATATATATTTTCAAAAATGTTTTTCAAAACTAT
31905 ATATTATATATATTTT
1 ATATTATATATATTTT
31921 ATGTATACTA
Statistics
Matches: 146, Mismatches: 11, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
34 24 0.16
35 7 0.05
36 2 0.01
37 64 0.44
38 49 0.34
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (38 bp):
ATATTATATATATTTTCAAAAATGTTTTTCAAAACTAT
Found at i:32978 original size:15 final size:15
Alignment explanation
Indices: 32958--32990 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
32948 CTTAAAAAAC
32958 CTTTTCATTTCATTT
1 CTTTTCATTTCATTT
32973 CTTTTCATTTCATTT
1 CTTTTCATTTCATTT
32988 CTT
1 CTT
32991 ACCTATTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTTCATTTCATTT
Found at i:33938 original size:19 final size:21
Alignment explanation
Indices: 33913--33969 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
33903 AAAACTATAC
* * *
33913 AATATATTATATTTTTAAAAT
1 AATATAATATGTTTTCAAAAT
33934 AATATAATATGTTTTCAAAAT
1 AATATAATATGTTTTCAAAAT
33955 -ATAATAATATGTTTT
1 AAT-ATAATATGTTTT
33970 TTTAAAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (21 bp):
AATATAATATGTTTTCAAAAT
Found at i:33942 original size:26 final size:28
Alignment explanation
Indices: 33882--33943 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 28
33872 TAATAAGCTA
33882 AATAT-ATATATATATATATTAAAAACT
1 AATATAATATATATATATATTAAAAACT
* * *
33909 -ATACAATATAT-TATATTTTTAAAA-T
1 AATATAATATATATATATATTAAAAACT
33934 AATATAATAT
1 AATATAATAT
33944 GTTTTCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.03
26 22 0.76
27 6 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (28 bp):
AATATAATATATATATATATTAAAAACT
Found at i:34011 original size:22 final size:22
Alignment explanation
Indices: 33986--34241 Score: 171
Period size: 22 Copynumber: 11.2 Consensus size: 22
33976 ATCTCTGCTA
33986 TATATTTTCAAAAACTATATATT
1 TATATTTTCAAAAACTATATA-T
34009 ATATATTTTCAAAAACTATATAT
1 -TATATTTTCAAAAACTATATAT
** *
34032 TATATGTTTTTTAAAACTATATAA
1 TATA--TTTTCAAAAACTATATAT
* *
34056 TATGTTTTCAAAAACTATACCA-
1 TATATTTTCAAAAACTATA-TAT
* **
34078 TATGTCTTTTTAAAACTATACTA-
1 TATAT-TTTCAAAAACTATA-TAT
*
34101 TATATTTTCAAAAACTATACAT
1 TATATTTTCAAAAACTATATAT
** *
34123 TATATGTTTTTTAAAACTATATAA
1 TATA--TTTTCAAAAACTATATAT
* * * *
34147 CATGTTTTCAAAAAATATACCA-
1 TATATTTTCAAAAACTATA-TAT
*
34169 TATATTTTTAAAAACTATACT-T
1 TATATTTTCAAAAACTATA-TAT
34191 ATATATTTTCAAAAA-TCATATAT
1 -TATATTTTCAAAAACT-ATATAT
* * *
34214 TATTTTTTGAAAAAAATATATAT
1 TATATTTT-CAAAAACTATATAT
34237 TATAT
1 TATAT
34242 GATATAAAAA
Statistics
Matches: 185, Mismatches: 33, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
21 1 0.01
22 75 0.41
23 53 0.29
24 56 0.30
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (22 bp):
TATATTTTCAAAAACTATATAT
Found at i:34011 original size:24 final size:24
Alignment explanation
Indices: 33984--34241 Score: 202
Period size: 24 Copynumber: 11.2 Consensus size: 24
33974 AAATCTCTGC
33984 TATATATTTTCAAAAACTATATAT
1 TATATATTTTCAAAAACTATATAT
34008 TATATATTTTCAAAAACTATATAT
1 TATATATTTTCAAAAACTATATAT
* **
34032 TATATGTTTTTTAAAACTATATA-
1 TATATATTTTCAAAAACTATATAT
* *
34055 -ATATGTTTTCAAAAACTATACCA-
1 TATATATTTTCAAAAACTATA-TAT
* * * *
34078 TATGTCTTTT-TAAAAC--TATAC
1 TATATATTTTCAAAAACTATATAT
*
34099 TATATATTTTCAAAAACTATACAT
1 TATATATTTTCAAAAACTATATAT
* **
34123 TATATGTTTTTTAAAACTATATA-
1 TATATATTTTCAAAAACTATATAT
* * *
34146 -ACATGTTTTCAAAAA--ATATAC
1 TATATATTTTCAAAAACTATATAT
* * *
34167 CATATATTTTTAAAAACTATA-CT
1 TATATATTTTCAAAAACTATATAT
34190 TATATATTTTCAAAAA-TCATATAT
1 TATATATTTTCAAAAACT-ATATAT
* *
34214 TAT-T-TTTTGAAAAAAATATATAT
1 TATATATTTT-CAAAAACTATATAT
34237 TATAT
1 TATAT
34242 GATATAAAAA
Statistics
Matches: 188, Mismatches: 31, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
20 6 0.03
21 10 0.05
22 52 0.28
23 38 0.20
24 82 0.44
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.45
Consensus pattern (24 bp):
TATATATTTTCAAAAACTATATAT
Found at i:34055 original size:115 final size:115
Alignment explanation
Indices: 33884--34146 Score: 329
Period size: 115 Copynumber: 2.3 Consensus size: 115
33874 ATAAGCTAAA
* *
33884 TATATATATATATATATTAAAAACTATACAATATATTATATTTTTAAAATAATATAATATGTTTT
1 TATATAT-TATATATTTTAAAAACTATATAATATATTATATTTTTAAAATAATATAATATGTTTT
* * *
33949 CAAAATA-TAATA-ATATGTTTTTTTAAAATCTCTGCTATATATTTTCAAAAAC
65 CAAAA-ACT-ATACATATGTCTTTTTAAAA-CTATACTATATATTTTCAAAAAC
* *
34001 TATATATTATATATTTTCAAAAACTATATATTATA-TGT-TTTTTAAAACT-ATATAATATGTTT
1 TATATATTATATATTTT-AAAAACTATATAATATATTATATTTTTAAAA-TAATATAATATGTTT
34063 TCAAAAACTATACCATATGTCTTTTTAAAACTATACTATATATTTTCAAAAAC
64 TCAAAAACTATA-CATATGTCTTTTTAAAACTATACTATATATTTTCAAAAAC
* * *
34116 TATACATTATATGTTTTTTAAAACTATATAA
1 TATATATTATAT-ATTTTAAAAACTATATAA
34147 CATGTTTTCA
Statistics
Matches: 129, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
114 4 0.03
115 72 0.56
116 31 0.24
117 22 0.17
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (115 bp):
TATATATTATATATTTTAAAAACTATATAATATATTATATTTTTAAAATAATATAATATGTTTTC
AAAAACTATACATATGTCTTTTTAAAACTATACTATATATTTTCAAAAAC
Found at i:34064 original size:46 final size:46
Alignment explanation
Indices: 33996--34216 Score: 247
Period size: 45 Copynumber: 4.8 Consensus size: 46
33986 TATATTTTCA
33996 AAAACTATATATTATATATTTTCAAAAACTATATATTATATGTTTTTT
1 AAAACTATATA--ATATATTTTCAAAAACTATATATTATATGTTTTTT
* **
34044 AAAACTATATAATATGTTTTCAAAAAC--TATACCATATGTCTTTTT
1 AAAACTATATAATATATTTTCAAAAACTATATATTATATGT-TTTTT
*
34089 AAAACTATACT-ATATATTTTCAAAAACTATACATTATATGTTTTTT
1 AAAACTATA-TAATATATTTTCAAAAACTATATATTATATGTTTTTT
* * ** * *
34135 AAAACTATATAACATGTTTTCAAAAA--ATATACCATATATTTTTA
1 AAAACTATATAATATATTTTCAAAAACTATATATTATATGTTTTTT
*
34179 AAAACTATACTTATATATTTTCAAAAA-TCATATATTAT
1 AAAACTATA-TAATATATTTTCAAAAACT-ATATATTAT
34217 TTTTTGAAAA
Statistics
Matches: 146, Mismatches: 19, Indels: 17
0.80 0.10 0.09
Matches are distributed among these distances:
44 32 0.22
45 44 0.30
46 43 0.29
47 16 0.11
48 11 0.08
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (46 bp):
AAAACTATATAATATATTTTCAAAAACTATATATTATATGTTTTTT
Found at i:34252 original size:91 final size:91
Alignment explanation
Indices: 33985--34216 Score: 360
Period size: 91 Copynumber: 2.5 Consensus size: 91
33975 AATCTCTGCT
* *
33985 ATATATTTTCAAAAACTATATATTATATATTTTCAAAAACTATATATTATATGTTTTTTAAAACT
1 ATATATTTTTAAAAACTATA-CTTATATATTTTCAAAAACTATATATTATATGTTTTTTAAAACT
*
34050 ATATAATATGTTTTCAAAAACTATACC
65 ATATAATATGTTTTCAAAAAATATACC
* * *
34077 ATATGTCTTTTTAAAACTATAC-TATATATTTTCAAAAACTATACATTATATGTTTTTTAAAACT
1 ATATAT-TTTTAAAAACTATACTTATATATTTTCAAAAACTATATATTATATGTTTTTTAAAACT
*
34141 ATATAACATGTTTTCAAAAAATATACC
65 ATATAATATGTTTTCAAAAAATATACC
34168 ATATATTTTTAAAAACTATACTTATATATTTTCAAAAA-TCATATATTAT
1 ATATATTTTTAAAAACTATACTTATATATTTTCAAAAACT-ATATATTAT
34217 TTTTTGAAAA
Statistics
Matches: 127, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
90 15 0.12
91 95 0.75
92 5 0.04
93 12 0.09
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (91 bp):
ATATATTTTTAAAAACTATACTTATATATTTTCAAAAACTATATATTATATGTTTTTTAAAACTA
TATAATATGTTTTCAAAAAATATACC
Found at i:36368 original size:19 final size:16
Alignment explanation
Indices: 36322--36377 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 16
36312 TATCATATTC
36322 TCATGTAATCACATAGA
1 TCATGTAA-CACATAGA
*
36339 TCATTTAACACATAGTA
1 TCATGTAACACATAG-A
*
36356 TGACATGTAACACATAGC
1 T--CATGTAACACATAGA
36374 TCAT
1 TCAT
36378 ACATAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 10 0.30
17 9 0.27
18 1 0.03
19 13 0.39
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (16 bp):
TCATGTAACACATAGA
Found at i:36710 original size:22 final size:20
Alignment explanation
Indices: 36679--36731 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
36669 ACCCAAGGTA
* *
36679 CAGTACCGATACTTCTTACTT
1 CAGTATCGATACTT-ATACTT
*
36700 ATAGTATCGATA-TTATACTT
1 -CAGTATCGATACTTATACTT
36720 CAGTATCGATAC
1 CAGTATCGATAC
36732 CTATTCTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 10 0.38
20 5 0.19
21 2 0.08
22 9 0.35
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (20 bp):
CAGTATCGATACTTATACTT
Found at i:41920 original size:16 final size:16
Alignment explanation
Indices: 41899--41934 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
41889 ATGAGGTGTC
41899 ACATTTACTTTTCAAA
1 ACATTTACTTTTCAAA
*
41915 ACATTTACTTTTTAAA
1 ACATTTACTTTTCAAA
41931 ACAT
1 ACAT
41935 AGTTGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (16 bp):
ACATTTACTTTTCAAA
Found at i:42575 original size:23 final size:23
Alignment explanation
Indices: 42549--42623 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
42539 GAAGTGCCAT
42549 ATAGAAATGTCCCGAAGGACTAC
1 ATAGAAATGTCCCGAAGGACTAC
* * *
42572 ATAGTATTATCCCGAAGGA-TCAC
1 ATAGAAATGTCCCGAAGGACT-AC
* * *
42595 GTAGAAATGTCCTGAAGGACCAC
1 ATAGAAATGTCCCGAAGGACTAC
*
42618 GTAGAA
1 ATAGAA
42624 TTATCCTGAA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
22 1 0.02
23 40 0.98
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (23 bp):
ATAGAAATGTCCCGAAGGACTAC
Found at i:42600 original size:46 final size:46
Alignment explanation
Indices: 42550--42646 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
42540 AAGTGCCATA
* *
42550 TAGAAATGTCCCGAAGGACTACATAGTATTATCCCGAAGGATCACG
1 TAGAAATGTCCCGAAGGACCACATAGAATTATCCCGAAGGATCACG
* * * *
42596 TAGAAATGTCCTGAAGGACCACGTAGAATTATCCTGAAGGATCGCG
1 TAGAAATGTCCCGAAGGACCACATAGAATTATCCCGAAGGATCACG
42642 TAGAA
1 TAGAA
42647 CCCTCGACTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.22
Consensus pattern (46 bp):
TAGAAATGTCCCGAAGGACCACATAGAATTATCCCGAAGGATCACG
Found at i:42630 original size:23 final size:23
Alignment explanation
Indices: 42562--42646 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
42552 GAAATGTCCC
* * * *
42562 GAAGGACTACATAGTATTATCCC
1 GAAGGACCACGTAGAATTATCCT
* * *
42585 GAAGGATCACGTAGAAATGTCCT
1 GAAGGACCACGTAGAATTATCCT
42608 GAAGGACCACGTAGAATTATCCT
1 GAAGGACCACGTAGAATTATCCT
* *
42631 GAAGGATCGCGTAGAA
1 GAAGGACCACGTAGAA
42647 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (23 bp):
GAAGGACCACGTAGAATTATCCT
Found at i:51348 original size:23 final size:23
Alignment explanation
Indices: 51298--51364 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
51288 TACAGAGGCA
**
51298 TGTGCTTTTGCAGCAGACAAAACT
1 TGTGCTTTTGCAGCAGA-TGAACT
*
51322 TGTGCTTTTGCAGTAGATGAACT
1 TGTGCTTTTGCAGCAGATGAACT
* * *
51345 TGTGATTTTACAGGAGATGA
1 TGTGCTTTTGCAGCAGATGA
51365 GTTCCTTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.34
Consensus pattern (23 bp):
TGTGCTTTTGCAGCAGATGAACT
Done.