Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006977.1 Hibiscus syriacus cultivar Beakdansim tig00017967_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: 53399
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:48 original size:2 final size:2
Alignment explanation
Indices: 35--165 Score: 111
Period size: 2 Copynumber: 68.5 Consensus size: 2
25 TAACTTAATA
* *
35 AT AT AA AT AT AT AT AA AT AT A- AT ACT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
*
76 AT AT AT AT A- AT AT AT AT AC A- AT AT AT A- AT AT AT AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
116 AT GT AT A- AT AC ACT AT AT AT -T AT AT A- AT AT A- 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
155 ACT AT A- AT AT A
1 A-T AT AT AT AT A
166 ACATAAACAG
Statistics
Matches: 106, Mismatches: 9, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
1 10 0.09
2 89 0.84
3 7 0.07
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:58 original size:21 final size:21
Alignment explanation
Indices: 32--166 Score: 102
Period size: 19 Copynumber: 6.4 Consensus size: 21
22 TAATAACTTA
32 ATAATATAAATATATATAAAT
1 ATAATATAAATATATATAAAT
*
53 ATAATACTATAATATATATATAT
1 ATAATA-TA-AATATATATAAAT
76 AT-ATATATAATATATATACAAT
1 ATAATATA-AATATATATA-AAT
* **
98 AT-ATAATATATATATACTATGT
1 ATAAT-ATAAATATATA-TAAAT
* * *
120 ATAATA-CACTATATAT-TAT
1 ATAATATAAATATATATAAAT
*
139 ATAATATAA-TATATAT-ACT
1 ATAATATAAATATATATAAAT
158 ATAATATAA
1 ATAATATAA
167 CATAAACAGG
Statistics
Matches: 95, Mismatches: 12, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
19 25 0.26
20 2 0.02
21 25 0.26
22 22 0.23
23 21 0.22
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (21 bp):
ATAATATAAATATATATAAAT
Found at i:6218 original size:29 final size:32
Alignment explanation
Indices: 6186--6251 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
6176 ATATTTTTAA
* *
6186 TATTTTTGA-TAAAAGTATT-ATA-TAAATAT
1 TATTTTTGATTAAAAATATTAATATTAAATAC
*
6215 TATTTTTTATTAAAAATATTAATATTAAATAC
1 TATTTTTGATTAAAAATATTAATATTAAATAC
6247 TATTT
1 TATTT
6252 AAAATATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 8 0.26
30 9 0.29
31 3 0.10
32 11 0.35
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (32 bp):
TATTTTTGATTAAAAATATTAATATTAAATAC
Found at i:6233 original size:19 final size:19
Alignment explanation
Indices: 6209--6275 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 19
6199 AGTATTATAT
6209 AAATATTATTTTTTATTAA
1 AAATATTATTTTTTATTAA
* *
6228 AAATATTAATATTAAATACTATTTA
1 AAATATT-AT-TT---T-TTATTAA
6253 AAATATTATTTTTTATTAA
1 AAATATTATTTTTTATTAA
6272 AAAT
1 AAAT
6276 TAAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
19 16 0.42
20 3 0.08
21 2 0.05
23 2 0.05
24 3 0.08
25 12 0.32
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATATTATTTTTTATTAA
Found at i:6303 original size:18 final size:18
Alignment explanation
Indices: 6275--6319 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
6265 TTATTAAAAA
*
6275 TTAAAAAAAAATTAACATT
1 TTAAATAAAAA-TAACATT
* *
6294 TTTAATAAAAATAATATT
1 TTAAATAAAAATAACATT
6312 TTAAATAA
1 TTAAATAA
6320 TACTTGATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATAAAAATAACATT
Found at i:10311 original size:210 final size:208
Alignment explanation
Indices: 9644--10443 Score: 1107
Period size: 210 Copynumber: 3.8 Consensus size: 208
9634 ATTTAAGAAT
*
9644 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A---A--AG
* *
9709 AGATCAAATCGAAATAATTTTAAATTGTGAGGTTTAAATTAATACAAAAAAAGTACTAAATTATA
60 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-AAAAAAGTACTAAATTATA
*
9774 CCCATTTAAAAAGTTATGGGCCAATTTAAAAAATAGAATTAAGTAATAAGTATGGATCAATTTCA
124 CCCATTTAAAAAGTTAT-GGCCAATTTAAAAAATA-AA-TAAGTAATAAGTATGGGTCAATTTCA
* *
9839 TATGCAAATAAAAGTTGGAGGAC
186 GATGCAAATAAAATTTGGAGGAC
* * * *** **
9862 TAAATTGAACAAATATGAAATTACAAATAAAATTTTAAATA-A-CACAC-ATTGATGAGGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
* *
9924 AATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCTATTT
66 AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
* *
9989 AAAAAGTTATGGTCAATTT----AA-AAAT-AGTAATAAGTATGGGTCAATTTCAGATGAAAATA
131 AAAAAGTTATGGCCAATTTAAAAAATAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAAATA
10048 AAATTTGGAGGAC
196 AAATTTGGAGGAC
* *
10061 TAAATTGAATAAATATGAAATTAAAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
* * *
10126 AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAAGTATTAAATTATACCCATTT
66 AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
*
10191 AAAAAGTTATGAGCCAATTTAAAAATATAAATAAGTAATAAGTATGGGTCAATTTCAGGTGCAAA
131 AAAAAGTTATG-GCCAATTTAAAAA-ATAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAAA
10256 TAAAATTTGGAGGAC
194 TAAAATTTGGAGGAC
* * * *
10271 TAAATTGAAAAAATATGAAATTATAAATAAAAAATTAAATATATTAAACAACACAAAAGGGATAA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
* * *
10336 AATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATACTCATTT
66 AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
*
10401 AAAAAGTTATGGACCAA-TTAATAAATAGAAATAAGTAATAAGT
131 AAAAAGTTATGG-CCAATTTAA-AAA-ATAAATAAGTAATAAGT
10444 TGAGAAAAAA
Statistics
Matches: 525, Mismatches: 44, Indels: 34
0.87 0.07 0.06
Matches are distributed among these distances:
199 81 0.15
200 2 0.00
201 5 0.01
202 82 0.16
203 9 0.02
207 9 0.02
208 36 0.07
209 53 0.10
210 202 0.38
215 2 0.00
216 3 0.01
217 1 0.00
218 40 0.08
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (208 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACCCATTT
AAAAAGTTATGGCCAATTTAAAAAATAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAAATA
AAATTTGGAGGAC
Found at i:10493 original size:20 final size:20
Alignment explanation
Indices: 10468--10777 Score: 100
Period size: 20 Copynumber: 14.8 Consensus size: 20
10458 AAACAACTAA
10468 TATATA-TATATAATATAAAC
1 TATATAGTATAT-ATATAAAC
* *
10488 TATATAGTTTATATATAAAG
1 TATATAGTATATATATAAAC
* *
10508 TATATTTGTTATGTATATAAAC
1 TATA-TAG-TATATATATAAAC
** * *
10530 TGCATAGTTTATATATATA-
1 TATATAGTATATATATAAAC
*
10549 TATATTATGTATAAAGTATAAAC
1 TATA-TA-GTATATA-TATAAAC
*
10572 TATATATACCATGTATAGACTATAATAC
1 --TATAT---A-GTATATA-TATAA-AC
* *
10600 TATATAGTTTATATATGAAC
1 TATATAGTATATATATAAAC
* *
10620 TAT-T-GAACTATATAGAAAC
1 TATATAGTA-TATATATAAAC
* * *
10639 TACATAGTTTATATATAAAT
1 TATATAGTATATATATAAAC
*
10659 TATATATGAATTATATATAAAC
1 TATATA-GTA-TATATATAAAC
* * * * *
10681 TATACAATTTATATTTATA-
1 TATATAGTATATATATAAAC
10700 TAT-TATGTATA-ATTATAAA-
1 TATATA-GTATATA-TATAAAC
* *
10719 TA-ATA-TATATTGTATAAAT
1 TATATAGTATA-TATATAAAC
*
10738 TATATAGTTTATTAATATAAAC
1 TATATAGTATA-T-ATATAAAC
*
10760 TATATAGTTTTATATATA
1 TATATAG-TATATATATA
10778 TTATATGGTT
Statistics
Matches: 212, Mismatches: 50, Indels: 55
0.67 0.16 0.17
Matches are distributed among these distances:
17 4 0.02
18 9 0.04
19 30 0.14
20 59 0.28
21 29 0.14
22 51 0.24
23 5 0.02
24 1 0.00
25 4 0.02
26 5 0.02
27 13 0.06
28 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (20 bp):
TATATAGTATATATATAAAC
Found at i:10526 original size:42 final size:41
Alignment explanation
Indices: 10466--10577 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 41
10456 TAAAACAACT
*
10466 AATATA-TATATAT-AATATAAACTATATAGTTTATATATA
1 AATATATTATGTATAAATATAAACTATATAGTTTATATATA
** **
10505 AAGTATATT-TGTTATGTATATAAACTGCATAGTTTATATATA
1 AA-TATATTATG-TATAAATATAAACTATATAGTTTATATATA
*
10547 TATATATTATGTATAAAGTATAAACTATATA
1 AATATATTATGTATAAA-TATAAACTATATA
10578 TACCATGTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
39 2 0.03
40 5 0.09
41 14 0.24
42 37 0.64
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (41 bp):
AATATATTATGTATAAATATAAACTATATAGTTTATATATA
Found at i:10578 original size:27 final size:28
Alignment explanation
Indices: 10545--10605 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
10535 AGTTTATATA
** *
10545 TATATATATTATGTATAAAGTATAA-AC
1 TATATATACCATGTATAAACTATAATAC
*
10572 TATATATACCATGTATAGACTATAATAC
1 TATATATACCATGTATAAACTATAATAC
10600 TATATA
1 TATATA
10606 GTTTATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (28 bp):
TATATATACCATGTATAAACTATAATAC
Found at i:10661 original size:11 final size:11
Alignment explanation
Indices: 10647--10684 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
10637 ACTACATAGT
10647 TTATATATAAA
1 TTATATATAAA
*
10658 TTATATATGAA
1 TTATATATAAA
10669 TTATATATAAA
1 TTATATATAAA
*
10680 CTATA
1 TTATA
10685 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:10692 original size:42 final size:43
Alignment explanation
Indices: 10623--10721 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 43
10613 TATGAACTAT
* * * *
10623 TGAACTATATAGAAACTACATAGTTTATA-TATAAATTATATA
1 TGAATTATATATAAACTACACAATTTATATTATAAATTATATA
* * *
10665 TGAATTATATATAAACTATACAATTTATATTTATATATTATGTA
1 TGAATTATATATAAACTACACAATTTATA-TTATAAATTATATA
*
10709 T-AATTATAAATAA
1 TGAATTATATATAA
10722 TATATATTGT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 24 0.51
43 11 0.23
44 12 0.26
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (43 bp):
TGAATTATATATAAACTACACAATTTATATTATAAATTATATA
Found at i:10710 original size:17 final size:17
Alignment explanation
Indices: 10690--10743 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
10680 CTATACAATT
* *
10690 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
10707 TATAATTATAAATAATA
1 TATATTTATAAATTATA
10724 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
10742 TA
1 TA
10744 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 18 0.60
18 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:10859 original size:20 final size:20
Alignment explanation
Indices: 10834--10906 Score: 83
Period size: 20 Copynumber: 3.4 Consensus size: 20
10824 TATAAACTAC
10834 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
*
10854 ATACTATATTTTATACTAGTTAT
1 ATACTATAATTTATA-T--TTAT
*
10877 ATAAACTATAGTTTATATTTAT
1 AT--ACTATAATTTATATTTAT
10899 ATACTATA
1 ATACTATA
10907 TATATGAACT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
20 20 0.43
21 1 0.02
22 6 0.13
23 6 0.13
24 1 0.02
25 12 0.26
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.51
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:10870 original size:12 final size:13
Alignment explanation
Indices: 10845--10894 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
10835 TACTATAATT
10845 TATATTTATATAC
1 TATATTTATATAC
10858 TATATTT-TATAC
1 TATATTTATATAC
* *
10870 TAGT-TATATAAAC
1 TA-TATTTATATAC
10883 TATAGTTTATAT
1 TATA-TTTATAT
10895 TTATATACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
12 10 0.34
13 14 0.48
14 5 0.17
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (13 bp):
TATATTTATATAC
Found at i:10904 original size:33 final size:32
Alignment explanation
Indices: 10858--10945 Score: 108
Period size: 33 Copynumber: 2.8 Consensus size: 32
10848 ATTTATATAC
10858 TATATTTTATACTAGT-TATATAAACTATAGTT
1 TATATTTTATACTA-TATATATAAACTATAGTT
*
10890 TATATTTATATACTATATATATGAACTATAGTT
1 TATATTT-TATACTATATATATAAACTATAGTT
* * *
10923 TACATATGA-ACTATATATATAAA
1 TATATTTTATACTATATATATAAA
10946 TATGTATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
31 13 0.27
32 9 0.18
33 27 0.55
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (32 bp):
TATATTTTATACTATATATATAAACTATAGTT
Found at i:10989 original size:18 final size:18
Alignment explanation
Indices: 10968--11136 Score: 90
Period size: 18 Copynumber: 9.4 Consensus size: 18
10958 AAGGTTGATA
10968 TTTATATATGAACTATAG
1 TTTATATATGAACTATAG
* *
10986 TTTACATATAAACTATATAG
1 TTTATATATGAAC--TATAG
*
11006 TTTATATACT-AACTATAC
1 TTTATATA-TGAACTATAG
* *
11024 TTTACATATAAACTATAG
1 TTTATATATGAACTATAG
11042 TTAATATTTACATATGAACTATAG
1 TT--TA--T--ATATGAACTATAG
*
11066 TTTACATATGAACTATA-
1 TTTATATATGAACTATAG
11083 --TATATA--AACTATATAG
1 TTTATATATGAAC--TATAG
* *
11099 TTTACATATGACCTATA-
1 TTTATATATGAACTATAG
11116 --TATATAT--ACTATAG
1 TTTATATATGAACTATAG
11130 TTTATAT
1 TTTATAT
11137 TCATATACTA
Statistics
Matches: 117, Mismatches: 14, Indels: 42
0.68 0.08 0.24
Matches are distributed among these distances:
13 8 0.07
15 15 0.13
16 5 0.04
17 1 0.01
18 52 0.44
20 19 0.16
21 1 0.01
22 2 0.02
24 14 0.12
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (18 bp):
TTTATATATGAACTATAG
Found at i:11010 original size:38 final size:39
Alignment explanation
Indices: 10965--11087 Score: 160
Period size: 38 Copynumber: 3.1 Consensus size: 39
10955 ACTAAGGTTG
10965 ATATTTATATATGAACTATAGTTTACATATAAACTATAT
1 ATATTTATATATGAACTATAGTTTACATATAAACTATAT
* *
11004 A-GTTTATATACT-AACTATACTTTACATATAAACTATAGTT
1 ATATTTATATA-TGAACTATAGTTTACATATAAACTATA--T
* *
11044 AATATTTACATATGAACTATAGTTTACATATGAACTATAT
1 -ATATTTATATATGAACTATAGTTTACATATAAACTATAT
11084 ATAT
1 ATAT
11088 AAACTATATA
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
38 32 0.44
39 6 0.08
40 2 0.03
41 2 0.03
42 30 0.42
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (39 bp):
ATATTTATATATGAACTATAGTTTACATATAAACTATAT
Found at i:11093 original size:31 final size:31
Alignment explanation
Indices: 11053--11133 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 31
11043 TAATATTTAC
*
11053 ATATGAACTATAGTTTACATATGAACTATAT
1 ATATAAACTATAGTTTACATATGAACTATAT
*
11084 ATATAAACTATATAGTTTACATATGACCTATAT
1 ATATAAAC--TATAGTTTACATATGAACTATAT
*
11117 ATATATACTATAGTTTA
1 ATATAAACTATAGTTTA
11134 TATTCATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
31 16 0.36
33 29 0.64
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATATAAACTATAGTTTACATATGAACTATAT
Found at i:11100 original size:33 final size:33
Alignment explanation
Indices: 11061--11128 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
11051 ACATATGAAC
11061 TATAGTTTACATATGAACTATATATATAAACTA
1 TATAGTTTACATATGAACTATATATATAAACTA
* *
11094 TATAGTTTACATATGACCTATATATATATACTA
1 TATAGTTTACATATGAACTATATATATAAACTA
11127 TA
1 TA
11129 GTTTATATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (33 bp):
TATAGTTTACATATGAACTATATATATAAACTA
Found at i:11135 original size:20 final size:20
Alignment explanation
Indices: 11112--11174 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
11102 ACATATGACC
11112 TATATATATATACTATAGT-T
1 TATATATATATACTATA-TAT
11132 TATAT-TCATATACTATATAT
1 TATATAT-ATATACTATATAT
*
11152 TATATATATAAACTATATAT
1 TATATATATATACTATATAT
11172 TAT
1 TAT
11175 GTAATATAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 2 0.05
20 36 0.92
21 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (20 bp):
TATATATATATACTATATAT
Found at i:11169 original size:33 final size:35
Alignment explanation
Indices: 11079--11169 Score: 80
Period size: 33 Copynumber: 2.5 Consensus size: 35
11069 ACATATGAAC
11079 TATATATATAAACTATATAGTTTACATATGACCTATATA
1 TATATATATAAAC--TATA--TTACATATGACCTATATA
***
11118 TATATACTATAGTTTATATT-CATAT-A-CTATATA
1 TATATA-TATAAACTATATTACATATGACCTATATA
11151 TTATATATATAAACTATAT
1 -TATATATATAAACTATAT
11170 ATTATGTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
33 16 0.36
34 7 0.16
35 5 0.11
36 2 0.05
38 4 0.09
39 6 0.14
40 4 0.09
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (35 bp):
TATATATATAAACTATATTACATATGACCTATATA
Found at i:11282 original size:33 final size:33
Alignment explanation
Indices: 11244--11397 Score: 161
Period size: 33 Copynumber: 4.5 Consensus size: 33
11234 CCCTAAACCC
*
11244 TAAACTATACATTATATAGTTTATTAGTATATA
1 TAAACTATACATTATATAGTTCATTAGTATATA
* *
11277 TAAACTATATAACA-TATATAGAAT-ATATGGTATATA
1 TAAAC--TAT-ACATTATATAG-TTCAT-TAGTATATA
11313 TAAACTA-ACATTATATATAGTTCATTAGTATATA
1 TAAACTATACA-T-TATATAGTTCATTAGTATATA
*
11347 TAAACTATATATTATATAGTTCATTAGTATATA
1 TAAACTATACATTATATAGTTCATTAGTATATA
* * *
11380 TAACCTATATAGTATATA
1 TAAACTATACATTATATA
11398 TAAACTATAT
Statistics
Matches: 104, Mismatches: 7, Indels: 20
0.79 0.05 0.15
Matches are distributed among these distances:
32 3 0.03
33 42 0.40
34 19 0.18
35 23 0.22
36 17 0.16
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (33 bp):
TAAACTATACATTATATAGTTCATTAGTATATA
Found at i:11295 original size:18 final size:18
Alignment explanation
Indices: 11272--11319 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
11262 GTTTATTAGT
11272 ATATATAAACTATATAAC
1 ATATATAAACTATATAAC
***
11290 ATATATAGAA-TATATGGT
1 ATATATA-AACTATATAAC
11308 ATATATAAACTA
1 ATATATAAACTA
11320 ACATTATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 2 0.08
18 21 0.84
19 2 0.08
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (18 bp):
ATATATAAACTATATAAC
Found at i:11344 original size:17 final size:17
Alignment explanation
Indices: 11324--11381 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
11314 AAACTAACAT
11324 TATATATAGTTCATTAG
1 TATATATAGTTCATTAG
**
11341 TATATATA-AAC-TATA-
1 TATATATAGTTCAT-TAG
11356 TATTATATAGTTCATTAG
1 TA-TATATAGTTCATTAG
11374 TATATATA
1 TATATATA
11382 ACCTATATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (17 bp):
TATATATAGTTCATTAG
Found at i:11551 original size:60 final size:60
Alignment explanation
Indices: 11484--11598 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
11474 AACAAATTTT
** * *
11484 AAATATGAAGTTTAAATTAATAAATTGTAACATTAAATTTAGATTAAATTAAAAAAAATG
1 AAATATGAAACTTAAATTAATAAATTATAACATTAAATTTAGACTAAATTAAAAAAAATG
* * *
11544 AAATATGAAACTTAAATTAATATATTATATCATTAAATTTGGACTAAATTAAAAA
1 AAATATGAAACTTAAATTAATAAATTATAACATTAAATTTAGACTAAATTAAAAA
11599 TTAAGAGACA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (60 bp):
AAATATGAAACTTAAATTAATAAATTATAACATTAAATTTAGACTAAATTAAAAAAAATG
Found at i:14050 original size:20 final size:20
Alignment explanation
Indices: 14025--14066 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
14015 TTCTGATCTA
*
14025 ACCTTCGATAAGGAGAATTG
1 ACCTTCGATAAGGAGAACTG
*
14045 ACCTTCGGTAAGGAGAACTG
1 ACCTTCGATAAGGAGAACTG
14065 AC
1 AC
14067 ATGTCTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (20 bp):
ACCTTCGATAAGGAGAACTG
Found at i:16770 original size:18 final size:16
Alignment explanation
Indices: 16747--16781 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
16737 ATCAAATTTA
16747 TAATATACAAATTATAAT
1 TAATATA-AAATTA-AAT
16765 TAATATAAAATTAAAT
1 TAATATAAAATTAAAT
16781 T
1 T
16782 TTAAAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 6 0.35
18 7 0.41
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATAAAATTAAAT
Found at i:16814 original size:17 final size:17
Alignment explanation
Indices: 16792--16878 Score: 67
Period size: 17 Copynumber: 5.3 Consensus size: 17
16782 TTAAAAAGTA
*
16792 ATCATATTAATTTAATT
1 ATCATAATAATTTAATT
16809 ATCATAATAA--T--TT
1 ATCATAATAATTTAATT
* **
16822 ATGATAA-AATTTCAAAA
1 ATCATAATAATTT-AATT
* *
16839 AGTAATATTAATTTAATT
1 A-TCATAATAATTTAATT
16857 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
16874 ATCAT
1 ATCAT
16879 TAGTTTATTA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
12 2 0.04
13 8 0.15
14 1 0.02
15 1 0.02
17 29 0.55
18 7 0.13
19 5 0.09
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:17016 original size:16 final size:16
Alignment explanation
Indices: 16995--17029 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16985 TCAATTACAA
*
16995 GTCAGGTTCATAACAG
1 GTCAGGTTCAAAACAG
*
17011 GTCAGGTTGAAAACAG
1 GTCAGGTTCAAAACAG
17027 GTC
1 GTC
17030 GGGTAATACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (16 bp):
GTCAGGTTCAAAACAG
Found at i:24281 original size:3 final size:3
Alignment explanation
Indices: 24273--24299 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
24263 TCTAAAGTTA
24273 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
24300 TTTCTTAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:33912 original size:28 final size:28
Alignment explanation
Indices: 33872--33929 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
33862 AAACGTTTGA
33872 TATAATTACACATCCAGTCATTGATACT
1 TATAATTACACATCCAGTCATTGATACT
33900 TATAATTACACATCCAGTCATTGATACT
1 TATAATTACACATCCAGTCATTGATACT
33928 TA
1 TA
33930 CATATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (28 bp):
TATAATTACACATCCAGTCATTGATACT
Found at i:34623 original size:18 final size:18
Alignment explanation
Indices: 34594--34641 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
34584 TTCCATATAT
*
34594 TTAAATTTAAATTTACATA
1 TTAAA-TTAAATTCACATA
*
34613 TTAAATTAAATTCACATC
1 TTAAATTAAATTCACATA
34631 TTAACATTAAA
1 TTAA-ATTAAA
34642 AAAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATTAAATTCACATA
Found at i:34709 original size:60 final size:60
Alignment explanation
Indices: 34631--34801 Score: 197
Period size: 61 Copynumber: 2.9 Consensus size: 60
34621 AATTCACATC
* * * * *
34631 TTAACATTAAAAAA-ATATTTTATTTTTATCTTAACTTATTAAATATATTTTATTTTTAT-
1 TTAACTTTAAAAAATATATTTTATTCTTATATTAACTTA-AAAATATATTTTATTCTTATA
* * *
34690 TTTA-TTTAAAAAAATATATTTTACTCTTATTTTAACTTAAAAA-ATATGTCTTATTCTTATA
1 TTAACTTT-AAAAAATATATTTTATTCTTATATTAACTTAAAAATATAT-T-TTATTCTTATA
*
34751 TTAACTTTAAAAAATATATCTTATTCTTATATTAACTTAAAAATATATTTT
1 TTAACTTTAAAAAATATATTTTATTCTTATATTAACTTAAAAATATATTTT
34802 TATATTGACT
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
58 6 0.06
59 13 0.14
60 32 0.34
61 36 0.38
62 7 0.07
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (60 bp):
TTAACTTTAAAAAATATATTTTATTCTTATATTAACTTAAAAATATATTTTATTCTTATA
Found at i:34733 original size:31 final size:30
Alignment explanation
Indices: 34631--34801 Score: 186
Period size: 30 Copynumber: 5.7 Consensus size: 30
34621 AATTCACATC
* *
34631 TTAACATTAAAAAA-ATATTTTATTTTTATC
1 TTAAC-TTAAAAAATATATTTTATTCTTATA
** *
34661 TTAACTTATTAAATATATTTTATTTTTAT-
1 TTAACTTAAAAAATATATTTTATTCTTATA
* * * *
34690 TTTATTTAAAAAAATATATTTTACTCTTATT
1 TTAACTT-AAAAAATATATTTTATTCTTATA
* *
34721 TTAACTTAAAAAATATGTCTTATTCTTATA
1 TTAACTTAAAAAATATATTTTATTCTTATA
*
34751 TTAACTTTAAAAAATATATCTTATTCTTATA
1 TTAAC-TTAAAAAATATATTTTATTCTTATA
34782 TTAACTT-AAAAATATATTTT
1 TTAACTTAAAAAATATATTTT
34802 TATATTGACT
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
29 23 0.19
30 64 0.53
31 34 0.28
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (30 bp):
TTAACTTAAAAAATATATTTTATTCTTATA
Found at i:34799 original size:24 final size:25
Alignment explanation
Indices: 34741--34834 Score: 84
Period size: 31 Copynumber: 3.6 Consensus size: 25
34731 AAATATGTCT
34741 TATTCTTATATTAACTTTAAAAAATATA
1 TATTCTTATATTAACTTT--AAAA-ATA
34769 TCTTATTCTTATATTAAC-TTAAAAATA
1 ---TATTCTTATATTAACTTTAAAAATA
* *
34796 TATTTTTATATTGACTTTTAAAAATA
1 TATTCTTATATTAAC-TTTAAAAATA
*
34822 TA-TCTTAAATTAA
1 TATTCTTATATTAA
34835 AATAAAAGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
24 13 0.23
25 8 0.14
26 11 0.20
27 3 0.05
28 4 0.07
30 2 0.04
31 15 0.27
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (25 bp):
TATTCTTATATTAACTTTAAAAATA
Found at i:34806 original size:55 final size:56
Alignment explanation
Indices: 34631--34828 Score: 170
Period size: 60 Copynumber: 3.4 Consensus size: 56
34621 AATTCACATC
* * * *
34631 TTAACATTAAAAAA-ATATTTTATTTTTATCTTAACTTATTAAATATATTTTATTTTTAT-
1 TTAACTTTAAAAAATATATCTTATTCTTATATTAACTTA--AAA-ATA--TTATTTTTATA
* * * * *
34690 TTTA-TTTAAAAAAATATATTTTACTCTTATTTTAACTTAAAAAATATGTCTTATTCTTATA
1 TTAACTTT-AAAAAATATATCTTATTCTTATATTAACTT-AAAAATA----TTATTTTTATA
34751 TTAACTTTAAAAAATATATCTTATTCTTATATTAACTTAAAAATA-TATTTTTATA
1 TTAACTTTAAAAAATATATCTTATTCTTATATTAACTTAAAAATATTATTTTTATA
* *
34806 TTGACTTTTAAAAATATATCTTA
1 TTAACTTTAAAAAATATATCTTA
34829 AATTAAAATA
Statistics
Matches: 118, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
55 30 0.25
58 5 0.04
59 12 0.10
60 37 0.31
61 31 0.26
62 3 0.03
ACGTcount: A:0.40, C:0.07, G:0.01, T:0.52
Consensus pattern (56 bp):
TTAACTTTAAAAAATATATCTTATTCTTATATTAACTTAAAAATATTATTTTTATA
Found at i:34923 original size:30 final size:29
Alignment explanation
Indices: 34832--34998 Score: 133
Period size: 29 Copynumber: 5.8 Consensus size: 29
34822 TATCTTAAAT
* * * * *
34832 TAAAATAAAAGTAAAATATATTTCATAAGT
1 TAAAATAAGATTAAAAAATATTT-TTAAGC
* * * * *
34862 TAAGATAA-AATAAAATATTTTTTTGAGC
1 TAAAATAAGATTAAAAAATATTTTTAAGC
34890 TAAAATAAGATTAAAAAATATTTTTAAGAC
1 TAAAATAAGATTAAAAAATATTTTTAAG-C
* *
34920 TAAAATAATATTAAAAAATATTTTTAAGT
1 TAAAATAAGATTAAAAAATATTTTTAAGC
* * * *
34949 TAGAATAAGACTAAAATAT-TTTTTAAGT
1 TAAAATAAGATTAAAAAATATTTTTAAGC
* *
34977 TAAAATAA-AATAAAATATATTT
1 TAAAATAAGATTAAAAAATATTT
34999 AATAATTAAA
Statistics
Matches: 115, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
27 9 0.08
28 29 0.25
29 42 0.37
30 35 0.30
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (29 bp):
TAAAATAAGATTAAAAAATATTTTTAAGC
Found at i:35035 original size:87 final size:85
Alignment explanation
Indices: 34815--35068 Score: 246
Period size: 87 Copynumber: 2.9 Consensus size: 85
34805 ATTGACTTTT
*
34815 AAAAATATATCTT-AAATTAAAATAAAAGTAAAATATATTTCATAAGTTAAGATAAAATAAAATA
1 AAAAATATAT-TTAAAATTAAAATAAAAATAAAATATA-TTCATAAGTTAAGATAAAATAAAATA
* *
34879 TTTTTTTGAGCTAAAATAAGATTA
64 -TTTTTTAAGTTAAAATAAGA-TA
* * * * * * ** *
34903 AAAAATATTTTTAAGACTAAAATAATATTAAAAAATATTTTTAAGTT-AGAATAAGACTAAAATA
1 AAAAATATATTTAAAATTAAAATAAAAATAAAATATATTCATAAGTTAAG-ATAA-AATAAAATA
34967 TTTTTTAAGTTAAAATAA-A-A
64 TTTTTTAAGTTAAAATAAGATA
* *
34987 TAAAATATATTTAATAATTAAAGATAAAAATAAAATATATTCAATAAGTTAATATAAAAATAAAA
1 AAAAATATATTTAA-AATTAAA-ATAAAAATAAAATATATTC-ATAAGTTAAGAT-AAAATAAAA
35052 TATATTTTTAATGTTAA
62 TAT-TTTTTAA-GTTAA
35069 TATGTGAATT
Statistics
Matches: 134, Mismatches: 22, Indels: 19
0.77 0.13 0.11
Matches are distributed among these distances:
84 13 0.10
85 5 0.04
86 18 0.13
87 47 0.35
88 46 0.34
89 5 0.04
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (85 bp):
AAAAATATATTTAAAATTAAAATAAAAATAAAATATATTCATAAGTTAAGATAAAATAAAATATT
TTTTAAGTTAAAATAAGATA
Found at i:35071 original size:30 final size:29
Alignment explanation
Indices: 34816--35068 Score: 219
Period size: 30 Copynumber: 8.7 Consensus size: 29
34806 TTGACTTTTA
* * *
34816 AAAATATA-TCTTAAATTAAAATAAAAGT
1 AAAATATATTTTTAAGTTAAAATAAAAAT
* *
34844 AAAATATATTTCATAAGTTAAGAT-AAAAT
1 AAAATATATTT-TTAAGTTAAAATAAAAAT
* * * * *
34873 AAAATATTTTTTTGAGCTAAAATAAGATT
1 AAAATATATTTTTAAGTTAAAATAAAAAT
* * * *
34902 AAAAAATATTTTTAAGACTAAAATAATATT
1 AAAATATATTTTTAAG-TTAAAATAAAAAT
* * * *
34932 AAAAAATATTTTTAAGTTAGAATAAGACT
1 AAAATATATTTTTAAGTTAAAATAAAAAT
34961 AAAATAT-TTTTTAAGTTAAAAT-AAAAT
1 AAAATATATTTTTAAGTTAAAATAAAAAT
*
34988 AAAATATATTTAATAA-TTAAAGATAAAAAT
1 AAAATATATTT-TTAAGTTAAA-ATAAAAAT
** *
35018 AAAATATATTCAATAAGTTAATATAAAAAT
1 AAAATATATT-TTTAAGTTAAAATAAAAAT
35048 AAAATATATTTTTAATGTTAA
1 AAAATATATTTTTAA-GTTAA
35069 TATGTGAATT
Statistics
Matches: 185, Mismatches: 29, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
27 10 0.05
28 38 0.21
29 54 0.29
30 79 0.43
31 4 0.02
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (29 bp):
AAAATATATTTTTAAGTTAAAATAAAAAT
Found at i:36719 original size:39 final size:36
Alignment explanation
Indices: 36657--36732 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 36
36647 CACAATATAT
*
36657 AAAATTTAGTTTTTATTTCATTTTAGTACACAATCGTTA
1 AAAACTTAGTTTTTATTTCATTTTAG--CAC-ATCGTTA
* *
36696 AAAACTTAGTTTTTGTTTTATTTTAGCACATCGTTA
1 AAAACTTAGTTTTTATTTCATTTTAGCACATCGTTA
36732 A
1 A
36733 CGTTAAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 3 0.09
39 23 0.68
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (36 bp):
AAAACTTAGTTTTTATTTCATTTTAGCACATCGTTA
Done.