Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002820.1 Hibiscus syriacus cultivar Beakdansim tig00005800_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: 76096
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:2947 original size:22 final size:23
Alignment explanation
Indices: 2913--2988 Score: 106
Period size: 22 Copynumber: 3.4 Consensus size: 23
2903 GTTGGTCTAT
2913 AAATATAAAGAAAAATGTAATAA
1 AAATATAAAGAAAAATGTAATAA
2936 AAATA-AAAGAAAAATGTAATAA
1 AAATATAAAGAAAAATGTAATAA
2958 ATAA-ATAAAG-AAAATGTAATAA
1 A-AATATAAAGAAAAATGTAATAA
2980 ATAA-ATAAA
1 A-AATATAAA
2989 CGTTGCTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
22 40 0.78
23 11 0.22
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (23 bp):
AAATATAAAGAAAAATGTAATAA
Found at i:5841 original size:21 final size:21
Alignment explanation
Indices: 5816--5860 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
5806 TGTTTTCATG
*
5816 TTTTAAA-AGCTTTAAAACCAT
1 TTTTAAATA-CTTTAAAAACAT
5837 TTTTAAATACTTTAAAAACAT
1 TTTTAAATACTTTAAAAACAT
5858 TTT
1 TTT
5861 AATCAACTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTTAAATACTTTAAAAACAT
Found at i:8208 original size:151 final size:149
Alignment explanation
Indices: 7920--8245 Score: 439
Period size: 151 Copynumber: 2.2 Consensus size: 149
7910 CCTGCGAAAG
*
7920 ATCACTTCAATTCAGTGATTTATCATACCATTGATGTTTTTAACTTATTTCCCTTTAATGAAAAC
1 ATCACTTCAATTCAGTGATATATCATACCATTGATGTTTTTAACTTATTTCCCTTTAATGAAAAC
* * *
7985 GTCATTTTCTCATAGACCATTTAGTACACAATTACAAAAACTTTTCAGTACACAATCACTTTATT
66 ATCATTTTCTCATAGACCATTTAGTACACAATGACAAAAACTTTTCAGTACACAATCACTTCATT
*
8050 TAGAAAC-TTTT-TAATGAT
131 TAAAAACTTTTTATAAT-AT
**
8068 ATCACTTCAATTCAGTGATATATCATACCATTGAATGATTTTT-TTTTACTTGTACCCTTTAATG
1 ATCACTTCAATTCAGTGATATATCATACCATTG-ATG-TTTTTAACTTA-TT-T-CCCTTTAATG
* *
8132 AAAACAT-ATTTTCTCATAGACCATTTTA-TACACAATGACAAAAACTTTT-AGTGCCCAATCAC
61 AAAACATCATTTTCTCATAGACCA-TTTAGTACACAATGACAAAAACTTTTCAGTACACAATCAC
8194 TTCATTTCAAAAACTTTTTAGTAATAT
125 TTCATTT-AAAAACTTTTTA-TAATAT
*
8221 ATCACTTCAGTTCAGTGATATATCA
1 ATCACTTCAATTCAGTGATATATCA
8246 GACAATAAAA
Statistics
Matches: 158, Mismatches: 10, Indels: 15
0.86 0.05 0.08
Matches are distributed among these distances:
148 32 0.20
149 6 0.04
150 24 0.15
151 42 0.27
152 24 0.15
153 26 0.16
154 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (149 bp):
ATCACTTCAATTCAGTGATATATCATACCATTGATGTTTTTAACTTATTTCCCTTTAATGAAAAC
ATCATTTTCTCATAGACCATTTAGTACACAATGACAAAAACTTTTCAGTACACAATCACTTCATT
TAAAAACTTTTTATAATAT
Found at i:10899 original size:13 final size:12
Alignment explanation
Indices: 10881--10933 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 12
10871 AGGATACATC
10881 GATGCATGGCAAG
1 GATGCATGGC-AG
*
10894 GATGCATCGCAG
1 GATGCATGGCAG
10906 GATGCAT--C--
1 GATGCATGGCAG
10914 GATGCATGGCAAG
1 GATGCATGGC-AG
10927 GATGCAT
1 GATGCAT
10934 CGATGCTAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
8 7 0.21
10 2 0.06
12 9 0.26
13 16 0.47
ACGTcount: A:0.28, C:0.19, G:0.34, T:0.19
Consensus pattern (12 bp):
GATGCATGGCAG
Found at i:10907 original size:33 final size:33
Alignment explanation
Indices: 10860--10935 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
10850 CTTGATGCAT
*
10860 GGATGCATCACAGGATACATCGATGCATGGCAA
1 GGATGCATCGCAGGATACATCGATGCATGGCAA
*
10893 GGATGCATCGCAGGATGCATCGATGCATGGCAA
1 GGATGCATCGCAGGATACATCGATGCATGGCAA
10926 GGATGCATCG
1 GGATGCATCG
10936 ATGCTAGCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.29, C:0.21, G:0.32, T:0.18
Consensus pattern (33 bp):
GGATGCATCGCAGGATACATCGATGCATGGCAA
Found at i:10909 original size:12 final size:13
Alignment explanation
Indices: 10881--10914 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
10871 AGGATACATC
*
10881 GATGCATGGCAAG
1 GATGCATCGCAAG
10894 GATGCATCGC-AG
1 GATGCATCGCAAG
10906 GATGCATCG
1 GATGCATCG
10915 ATGCATGGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.26, C:0.21, G:0.35, T:0.18
Consensus pattern (13 bp):
GATGCATCGCAAG
Found at i:10930 original size:21 final size:21
Alignment explanation
Indices: 10894--10959 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
10884 GCATGGCAAG
*
10894 GATGCATCGC-AGGATGCATC
1 GATGCATAGCAAGGATGCATC
*
10914 GATGCATGGCAAGGATGCATC
1 GATGCATAGCAAGGATGCATC
10935 GATGC-TAGCAA-GATGCATC
1 GATGCATAGCAAGGATGCATC
10954 GATGCA
1 GATGCA
10960 CTAATTGCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.31
20 14 0.33
21 15 0.36
ACGTcount: A:0.29, C:0.21, G:0.30, T:0.20
Consensus pattern (21 bp):
GATGCATAGCAAGGATGCATC
Found at i:11034 original size:21 final size:21
Alignment explanation
Indices: 11010--11067 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
11000 GCATTGTGCA
*
11010 GATGCATGGATGCATTGCAGG
1 GATGCATGGATGCACTGCAGG
11031 GATGCATGGATGCACTGCAGG
1 GATGCATGGATGCACTGCAGG
11052 GATGCATGGATGCACT
1 GATGCATGGATGCACT
11068 TTGACACCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.22
Consensus pattern (21 bp):
GATGCATGGATGCACTGCAGG
Found at i:12996 original size:14 final size:15
Alignment explanation
Indices: 12977--13005 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12967 ATGCCTACCT
12977 CTTTCTT-ATCTTCC
1 CTTTCTTCATCTTCC
12991 CTTTCTTCATCTTCC
1 CTTTCTTCATCTTCC
13006 TTTACCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.07, C:0.38, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTTCTTCATCTTCC
Found at i:14433 original size:20 final size:20
Alignment explanation
Indices: 14408--14482 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
14398 TTGCAGCCTT
* *
14408 GATGCATGGATGCATCGCAG
1 GATGCATCGATGCATAGCAG
* *
14428 GATGCATCGATGCATGGAAAG
1 GATGCATCGATGCATAG-CAG
* *
14449 GATGCATCGATGCATATCAA
1 GATGCATCGATGCATAGCAG
14469 GATGCATCGATGCA
1 GATGCATCGATGCA
14483 CTAATTGCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 30 0.64
21 17 0.36
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (20 bp):
GATGCATCGATGCATAGCAG
Found at i:14560 original size:19 final size:20
Alignment explanation
Indices: 14502--14612 Score: 110
Period size: 19 Copynumber: 5.8 Consensus size: 20
14492 TTCGATGTTT
14502 GGATGCATGGATGCATTGCA
1 GGATGCATGGATGCATTGCA
* * *
14522 TGAT-CGAT-GAT-TAGTGCA
1 GGATGC-ATGGATGCATTGCA
14540 -GATGCATGGATGCATTGCA
1 GGATGCATGGATGCATTGCA
*
14559 -GATGCATGGATGCACTGCA
1 GGATGCATGGATGCATTGCA
14578 GGGATGCATGGATGCA-TGCA
1 -GGATGCATGGATGCATTGCA
14598 TGGAT-CATGGATGCA
1 -GGATGCATGGATGCA
14613 CTTTGACACC
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
17 5 0.06
18 9 0.12
19 37 0.47
20 13 0.17
21 14 0.18
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.25
Consensus pattern (20 bp):
GGATGCATGGATGCATTGCA
Found at i:14607 original size:40 final size:39
Alignment explanation
Indices: 14502--14614 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 39
14492 TTCGATGTTT
* *
14502 GGATGCATGGATGCATTGCATGATCGAT-GAT-TAGTGCA
1 GGATGCATGGATGCATTGCATGATC-ATGGATGCACTGCA
14540 -GATGCATGGATGCATTGCA-GATGCATGGATGCACTGCA
1 GGATGCATGGATGCATTGCATGAT-CATGGATGCACTGCA
14578 GGGATGCATGGATGCA-TGCATGGATCATGGATGCACT
1 -GGATGCATGGATGCATTGCAT-GATCATGGATGCACT
14615 TTGACACCCT
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
36 5 0.08
37 23 0.35
38 5 0.08
39 4 0.06
40 26 0.39
41 3 0.05
ACGTcount: A:0.26, C:0.16, G:0.33, T:0.26
Consensus pattern (39 bp):
GGATGCATGGATGCATTGCATGATCATGGATGCACTGCA
Found at i:14753 original size:30 final size:30
Alignment explanation
Indices: 14696--14755 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
14686 AACTTTGAAT
14696 AAATTCAATTCAAATCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
*
14726 AAATTCAATTCAAGTCCAAAAACATTTTGC
1 AAATTCAATTCAAATCCAAAAACATTTTGC
14756 CTTAAATTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (30 bp):
AAATTCAATTCAAATCCAAAAACATTTTGC
Found at i:15118 original size:22 final size:22
Alignment explanation
Indices: 15087--15130 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
15077 AGTCGAGTGT
15087 TACATAGGTCATTCAGGACATA
1 TACATAGGTCATTCAGGACATA
* *
15109 TACATGGGTCCTTCAGGACATA
1 TACATAGGTCATTCAGGACATA
15131 CATGAGGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (22 bp):
TACATAGGTCATTCAGGACATA
Found at i:15148 original size:21 final size:20
Alignment explanation
Indices: 15087--15149 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 20
15077 AGTCGAGTGT
* *
15087 TACATAGGTCATTCAGGACATA
1 TACATGGGTCCTTCAGGAC--A
15109 TACATGGGTCCTTCAGGACA
1 TACATGGGTCCTTCAGGACA
* *
15129 TACATGAGGTCTTTCGGGACA
1 TACATG-GGTCCTTCAGGACA
15150 AATTTCACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 7 0.19
21 12 0.33
22 17 0.47
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (20 bp):
TACATGGGTCCTTCAGGACA
Found at i:20151 original size:17 final size:17
Alignment explanation
Indices: 20125--20157 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20115 TCATGCAATT
*
20125 CAAATTAGAATCATTTC
1 CAAATGAGAATCATTTC
20142 CAAATGAGAATCATTT
1 CAAATGAGAATCATTT
20158 TCATTCATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (17 bp):
CAAATGAGAATCATTTC
Found at i:29636 original size:14 final size:14
Alignment explanation
Indices: 29617--29646 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29607 TTTAGATTTT
*
29617 TTAAAATTACATTA
1 TTAAAAATACATTA
29631 TTAAAAATACATTA
1 TTAAAAATACATTA
29645 TT
1 TT
29647 GATAATTATA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:30778 original size:107 final size:105
Alignment explanation
Indices: 30638--30846 Score: 312
Period size: 107 Copynumber: 2.0 Consensus size: 105
30628 GTCAGGGTAA
* * *
30638 GAGGGGCGCTTGTTCAGGAACCATAAATTAAAAAAATTATTAATATAATATTTTCTCTTATTTTT
1 GAGGGGCGCTTATCCAGGAACCATAAATTAAAAAAATTATTAATATAATACTTTCTCTTATTTTT
30703 ATAATAAATTTTTAAAAAAA-ATTAAAATAAAATTATGGGGAG
66 ATAATAAA---TTAAAAAAACATTAAAATAAAATTATGGGGAG
* * *
30745 GAGGGGCGCTTATCCGGGAACCATAAATTAAAAATATTCTTAATATAATACTTTCTCTTATTTTT
1 GAGGGGCGCTTATCCAGGAACCATAAATTAAAAAAATTATTAATATAATACTTTCTCTTATTTTT
* *
30810 GTAATAAATTAAAAAAACTTTAAAATAAAATTATGGG
66 ATAATAAATTAAAAAAACATTAAAATAAAATTATGGG
30847 CCCATAAATT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
104 9 0.10
105 18 0.19
107 66 0.71
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (105 bp):
GAGGGGCGCTTATCCAGGAACCATAAATTAAAAAAATTATTAATATAATACTTTCTCTTATTTTT
ATAATAAATTAAAAAAACATTAAAATAAAATTATGGGGAG
Found at i:37382 original size:258 final size:253
Alignment explanation
Indices: 36955--37507 Score: 771
Period size: 258 Copynumber: 2.2 Consensus size: 253
36945 ATAAAGTTTC
*
36955 ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAT
1 ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAA
*
37020 ATATAGAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTG
66 ATATAGAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTT-
* * *
37085 GGTTGGGTCGGGTATTTTTCACCCTAAACTCGAACCCGACCCGAATATTACACTT-AAAAA-AA-
130 -GTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTTAAAAAACAAC
* * *
37147 CCGACCCGACCAAAATAAAGTTTCAC-CGACCCGACTCGAATATATGAATTAGAAATCCGACTCG
194 CCGACCCAACCAAAATAAAGTTTCACTCGACCCGACCCGAATATATAAATTAGAAA--C--C-CG
* *
37211 ACCCGACCCAAAATAATAAAAAATATATTTTTATTCAATAAAAACAGTGACTTAATTGGAAAAAA
1 ACCCGACCCGAAATAATAAAAAA-ATATTTTTATTCAATAAAAACAATGACTTAATTGG-AAAAA
* *
37276 AAATTTATG-TAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA-TAT
64 AAATATA-GAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTAT
* *
37339 TT-TCGGGTC-GTTATTTTTCACCCTAAACCCGAACTCGACCCGACCTGAATATCACACTTAAAA
128 TTGTCGGGTCGGGTATTTTTCACCCTAAACCCG-A----ACCCGACCCGAATATCACACTTAAAA
37402 AACCAACCCGACCCAACCAAAATAAAGTTTCACTCGACCCGACCCGAATATATAAATTAGAAACC
188 AA-CAACCCGACCCAACCAAAATAAAGTTTCACTCGACCCGACCCGAATATATAAATTAGAAACC
37467 CG
252 CG
*
37469 ACCTGACCCGAAATAATAAAAAAATATTTTTATTCAATA
1 ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
37508 TATGAATAAG
Statistics
Matches: 268, Mismatches: 16, Indels: 25
0.87 0.05 0.08
Matches are distributed among these distances:
253 20 0.07
254 7 0.03
256 22 0.08
257 54 0.20
258 103 0.38
259 7 0.03
261 3 0.01
262 25 0.09
263 27 0.10
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (253 bp):
ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTGGAAAAAAA
ATATAGAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTATTTG
TCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTTAAAAAACAACCC
GACCCAACCAAAATAAAGTTTCACTCGACCCGACCCGAATATATAAATTAGAAACCCG
Found at i:39277 original size:96 final size:96
Alignment explanation
Indices: 39113--39304 Score: 375
Period size: 96 Copynumber: 2.0 Consensus size: 96
39103 AGCATAACTA
39113 CCGTTGAATTATGATCCGTATTGTATTCTCACACTTGTGTTTGGGTAAAAAGGCAGTATATAGGA
1 CCGTTGAATTATGATCCGTATTGTATTCTCACACTTGTGTTTGGGTAAAAAGGCAGTATATAGGA
39178 TAAACTACAGCACAAGTCACTCTATTATTAG
66 TAAACTACAGCACAAGTCACTCTATTATTAG
39209 CCGTTGAATTATGATCCGTATTGTATTCTCACACTTGTGTTTGGGTAAAAAGGCAGTATATAGGA
1 CCGTTGAATTATGATCCGTATTGTATTCTCACACTTGTGTTTGGGTAAAAAGGCAGTATATAGGA
*
39274 TAAATTACAGCACAAGTCACTCTATTATTAG
66 TAAACTACAGCACAAGTCACTCTATTATTAG
39305 TCGTAAGTCT
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (96 bp):
CCGTTGAATTATGATCCGTATTGTATTCTCACACTTGTGTTTGGGTAAAAAGGCAGTATATAGGA
TAAACTACAGCACAAGTCACTCTATTATTAG
Found at i:43436 original size:32 final size:32
Alignment explanation
Indices: 43400--43576 Score: 185
Period size: 32 Copynumber: 5.5 Consensus size: 32
43390 TAGTTTCAAC
* *
43400 ATTGCATTCAGATAATGCATATCAGAGTTAGT
1 ATTGCATTCAGATAATGCATAACAGAGTCAGT
* * *
43432 ATTGCATTTAGATAATGCACAACAGAGTTAGT
1 ATTGCATTCAGATAATGCATAACAGAGTCAGT
* * * *
43464 ATTGCATTCAGATAATGCACAGA-AAAATCAAT
1 ATTGCATTCAGATAATGCATA-ACAGAGTCAGT
*
43496 ATTGCATTCAAATAATGCATAACAGAGTCAGT
1 ATTGCATTCAGATAATGCATAACAGAGTCAGT
* ** *
43528 ATTGCATTCAAATAATGTGTAGCAGAGTCAGT
1 ATTGCATTCAGATAATGCATAACAGAGTCAGT
** *
43560 ATCACATTCTGATAATG
1 ATTGCATTCAGATAATG
43577 AGCGTCATAT
Statistics
Matches: 123, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
31 1 0.01
32 121 0.98
33 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (32 bp):
ATTGCATTCAGATAATGCATAACAGAGTCAGT
Found at i:43568 original size:96 final size:96
Alignment explanation
Indices: 43395--43576 Score: 238
Period size: 96 Copynumber: 1.9 Consensus size: 96
43385 CATAGTAGTT
* * * * *
43395 TCAACATTGCATTCAGATAATGCATATCAGAGTTAGTATTGCATTTAGATAATGCACAACAGAGT
1 TCAACATTGCATTCAAATAATGCATAACAGAGTCAGTATTGCATTCAAATAATGCACAACAGAGT
* **
43460 TAGTATTGCATTCAGATAATGCACAGAAAAA
66 CAGTATCACATTCAGATAATGCACAGAAAAA
* *** *
43491 TCAATATTGCATTCAAATAATGCATAACAGAGTCAGTATTGCATTCAAATAATGTGTAGCAGAGT
1 TCAACATTGCATTCAAATAATGCATAACAGAGTCAGTATTGCATTCAAATAATGCACAACAGAGT
*
43556 CAGTATCACATTCTGATAATG
66 CAGTATCACATTCAGATAATG
43577 AGCGTCATAT
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 72 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (96 bp):
TCAACATTGCATTCAAATAATGCATAACAGAGTCAGTATTGCATTCAAATAATGCACAACAGAGT
CAGTATCACATTCAGATAATGCACAGAAAAA
Found at i:45821 original size:6 final size:7
Alignment explanation
Indices: 45808--45832 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
45798 TTAAATCTTT
45808 AATAAAA
1 AATAAAA
45815 AATAAAA
1 AATAAAA
45822 AATAAAA
1 AATAAAA
45829 AATA
1 AATA
45833 CATATATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAA
Found at i:55835 original size:23 final size:23
Alignment explanation
Indices: 55805--55859 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
55795 TAGGAATAAG
*
55805 TCTGTCTTTGTGATCCGTTTATC
1 TCTGTCTTTGTGACCCGTTTATC
55828 TCTGTCTTTGTGACCCGTTTATC
1 TCTGTCTTTGTGACCCGTTTATC
*
55851 TATGTCTTT
1 TCTGTCTTT
55860 CGGTAGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.09, C:0.22, G:0.16, T:0.53
Consensus pattern (23 bp):
TCTGTCTTTGTGACCCGTTTATC
Found at i:56803 original size:2 final size:2
Alignment explanation
Indices: 56796--56824 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
56786 AAGAATAAGA
56796 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56825 GACAGGGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62038 original size:30 final size:29
Alignment explanation
Indices: 61987--62044 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
61977 GAACCAGTAA
*
61987 CTAAAATATAACTTTTGAAAGTTTAGGGG
1 CTAAAATATAACTTTTGAAAGTGTAGGGG
*
62016 CTAAAGTATAAAC-TTTGAAAAGTGTAGGG
1 CTAAAATAT-AACTTTTG-AAAGTGTAGGG
62045 ATTGAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (29 bp):
CTAAAATATAACTTTTGAAAGTGTAGGGG
Found at i:64274 original size:20 final size:20
Alignment explanation
Indices: 64249--64298 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
64239 GACCAACAAA
64249 TTCGCAACGCAAACTCCAAT
1 TTCGCAACGCAAACTCCAAT
* **
64269 TTCGCAACCCAATTTCCAAT
1 TTCGCAACGCAAACTCCAAT
64289 TTCGCAACGC
1 TTCGCAACGC
64299 GAATCTGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.36, G:0.10, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCAAACTCCAAT
Found at i:64313 original size:20 final size:20
Alignment explanation
Indices: 64290--64336 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
64280 ATTTCCAATT
64290 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
64310 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
64330 TCGCAAC
1 TCGCAAC
64337 ACAAAAGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:64353 original size:20 final size:20
Alignment explanation
Indices: 64330--64516 Score: 114
Period size: 20 Copynumber: 9.3 Consensus size: 20
64320 AATTTGTAAA
64330 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
64350 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
64370 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
64390 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
** *** *
64410 TTACAACGTGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* **
64430 TCGCAACGCGAACCTGT-AAA-
1 TCGCAACAC-AA-AAGTCAAAT
* *
64450 TCTCAACGA-AAATTTGT-AAA-
1 TCGCAAC-ACAAA--AGTCAAAT
*
64470 TCGCAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
64490 TCTCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
*
64510 TTGCAAC
1 TCGCAAC
64517 GTGGAATTTC
Statistics
Matches: 131, Mismatches: 28, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.02
19 6 0.05
20 117 0.89
21 4 0.03
22 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.21
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:64354 original size:40 final size:41
Alignment explanation
Indices: 64310--64537 Score: 167
Period size: 40 Copynumber: 5.7 Consensus size: 41
64300 AATCTGTAAA
*
64310 TCGCAACGCGAATTTGT-AAA-TCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAA-TAGTCAAATTCGCAACACAAAAGTCAAAT
64350 TCGCAACGCG-ATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATAGTCAAATTCGCAACACAAAAGTCAAAT
** *** *
64390 TCGCAACGCG-ATAGTCAAATTTACAACGTGATAGTCAAAT
1 TCGCAACGCGAATAGTCAAATTCGCAACACAAAAGTCAAAT
* *
64430 TCGCAACGCGAACCT-GT-AAA-TCTCAACGA-AAATTTGT-AAA-
1 TCGCAACGCGAA--TAGTCAAATTCGCAAC-ACAAA--AGTCAAAT
* *
64470 TCGCAACAC--ATAAGTCAAATTCTCAACACAAAAGTCAAAT
1 TCGCAACGCGAAT-AGTCAAATTCGCAACACAAAAGTCAAAT
* * *
64510 TTGCAACGTGGAAT-TTCAAATTCGCAAC
1 TCGCAACG-CGAATAGTCAAATTCGCAAC
64538 TGAATTTCAA
Statistics
Matches: 150, Mismatches: 20, Indels: 35
0.73 0.10 0.17
Matches are distributed among these distances:
36 1 0.01
38 8 0.05
39 11 0.07
40 104 0.69
41 19 0.13
42 4 0.03
43 3 0.02
ACGTcount: A:0.41, C:0.23, G:0.14, T:0.22
Consensus pattern (41 bp):
TCGCAACGCGAATAGTCAAATTCGCAACACAAAAGTCAAAT
Found at i:64374 original size:60 final size:59
Alignment explanation
Indices: 64289--64456 Score: 153
Period size: 60 Copynumber: 2.8 Consensus size: 59
64279 AATTTCCAAT
* *
64289 TTCGCAACGCGAATCTGT-AAA-TCGCAACGCGAATTTGTAAATCGCAACACAAAAGTCAAA
1 TTCGCAACGCG-AT-AGTCAAATTCGCAACGCGAA-ATGTAAATCGCAACACAAAAGTCAAA
* * * * *
64349 TTCGCAACGCGATAGTCAAATTCGCAACAC-AAAAGTCAAATTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACGCGAAATGT-AAA-TCGCAACACAAAAGTCAAA
** * * *
64409 TTTACAACGTGATAGTCAAATTCGCAACGCGAACCTGTAAATCTCAAC
1 TTCGCAACGCGATAGTCAAATTCGCAACGCGAA-ATGTAAATCGCAAC
64457 GAAAATTTGT
Statistics
Matches: 88, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
58 4 0.05
59 10 0.11
60 67 0.76
61 5 0.06
62 2 0.02
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (59 bp):
TTCGCAACGCGATAGTCAAATTCGCAACGCGAAATGTAAATCGCAACACAAAAGTCAAA
Found at i:64457 original size:60 final size:59
Alignment explanation
Indices: 64310--64461 Score: 155
Period size: 60 Copynumber: 2.5 Consensus size: 59
64300 AATCTGTAAA
* * *
64310 TCGCAACGCGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACGCGAA-ATGTAAATCGCAACGCAAAAGTCAAATTCACAACGCGATAGTCAAAT
* * * * * *
64370 TCGCAACAC-AAAAGTCAAATTCGCAACGCGATAGTCAAATTTACAACGTGATAGTCAAAT
1 TCGCAACGCGAAATGT-AAA-TCGCAACGCAAAAGTCAAATTCACAACGCGATAGTCAAAT
* *
64430 TCGCAACGCGAACCTGTAAATCTCAACG-AAAA
1 TCGCAACGCGAA-ATGTAAATCGCAACGCAAAA
64462 TTTGTAAATC
Statistics
Matches: 73, Mismatches: 15, Indels: 9
0.75 0.15 0.09
Matches are distributed among these distances:
58 2 0.03
59 7 0.10
60 57 0.78
61 5 0.07
62 2 0.03
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (59 bp):
TCGCAACGCGAAATGTAAATCGCAACGCAAAAGTCAAATTCACAACGCGATAGTCAAAT
Found at i:64570 original size:20 final size:19
Alignment explanation
Indices: 64504--64595 Score: 87
Period size: 19 Copynumber: 4.7 Consensus size: 19
64494 AACACAAAAG
*
64504 TCAAATTTGCAACGTGGAATT
1 TCAAATTCGCAAC-T-GAATT
64525 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
64544 TCAAATTCACAACTAGATTT
1 TCAAATTCGCAACT-GAATT
* *
64564 TCGAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
64584 T-AATTTCGCAAC
1 TCAAATTCGCAAC
64596 AGGTTTTAGT
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
19 27 0.45
20 21 0.35
21 12 0.20
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:64787 original size:16 final size:15
Alignment explanation
Indices: 64752--64790 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
64742 TCCCCATCTC
*
64752 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
64767 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
64783 TAATTTTT
1 TAATTTTT
64791 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:65407 original size:12 final size:12
Alignment explanation
Indices: 65386--65419 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
65376 ACCACATTTC
*
65386 CAATACCAAACA
1 CAATATCAAACA
65398 CAATATCAAACA
1 CAATATCAAACA
*
65410 CAATCTCAAA
1 CAATATCAAA
65420 ACCCACAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:65572 original size:24 final size:24
Alignment explanation
Indices: 65545--65598 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
65535 GTATTCAAAA
*
65545 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
65569 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
65593 TTTGAT
1 TTTGAT
65599 GATGTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:67875 original size:18 final size:18
Alignment explanation
Indices: 67852--67887 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
67842 AAGCAAAAGG
*
67852 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
67870 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
67888 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:68411 original size:66 final size:64
Alignment explanation
Indices: 68340--68514 Score: 244
Period size: 66 Copynumber: 2.6 Consensus size: 64
68330 AATTTAAAAC
68340 AACAAATCAACTTTTACAAATCAATTAAACAAGAACAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAA-AAAAATAATTCTTATTTACACATC-AATT
68405 A
64 A
* * *
68406 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTA
68470 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGAAAAAAA
68515 AGTGTACCCC
Statistics
Matches: 99, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
64 16 0.16
65 24 0.24
66 34 0.34
68 4 0.04
69 21 0.21
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.28
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGAAAAAAATAATTCTTATTTACACATCAATTA
Found at i:69887 original size:21 final size:21
Alignment explanation
Indices: 69863--69961 Score: 80
Period size: 21 Copynumber: 4.7 Consensus size: 21
69853 GCGGGCGGGA
* *
69863 CCTCTTGAACGATGACATGGG
1 CCTCTTGAACGATGAAAGGGG
*
69884 CCTCTTGAACGGTGAAAGGGG
1 CCTCTTGAACGATGAAAGGGG
69905 CCTCTTCGATA--AT-AAGAGGGG
1 CCTCTT-GA-ACGATGAA-AGGGG
* *
69926 CCTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-AAGGGG
*
69947 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
69962 TAGGTGCATC
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
19 1 0.02
20 4 0.06
21 55 0.86
22 3 0.05
23 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGAAAGGGG
Found at i:72696 original size:20 final size:20
Alignment explanation
Indices: 72673--72799 Score: 209
Period size: 20 Copynumber: 6.3 Consensus size: 20
72663 TGTGTTTCGC
* *
72673 GTTGCAAATTTGACTTTTGC
1 GTTGCGAATTTGACTTTTGT
*
72693 GTTGCGAATTTGACTTTTAT
1 GTTGCGAATTTGACTTTTGT
72713 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
72733 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
72753 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
* *
72773 GTTGCGAATTTAACTTTTCT
1 GTTGCGAATTTGACTTTTGT
72793 GTTGCGA
1 GTTGCGA
72800 TTTACAAATT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.48
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:72816 original size:20 final size:20
Alignment explanation
Indices: 72793--72860 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
72783 TAACTTTTCT
72793 GTTGCGATTTACAAATTCGA
1 GTTGCGATTTACAAATTCGA
** *
72813 GTTGCGAATTTGGAAAATCGCA
1 GTTGCG-ATTTACAAATTCG-A
* * *
72835 -ATGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGA
72854 GTTGCGA
1 GTTGCGA
72861 AATTGGAAAC
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
20 20 0.57
21 14 0.40
22 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGA
Found at i:72817 original size:60 final size:60
Alignment explanation
Indices: 72673--72824 Score: 182
Period size: 60 Copynumber: 2.5 Consensus size: 60
72663 TGTGTTTCGC
* * * * * *
72673 GTTGCAAATTTGACTTTTGCGTTGCGAATTTGACTTTTATGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACATTCGAGTTGCGAATTTGACTTTTATGTTGCGAATTTAACTTTTCT
* * * *
72733 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTGTTGCGAATTTAACTTTTCT
1 GTTGCGAATTTGACATTCGAGTTGCGAATTTGACTTTTATGTTGCGAATTTAACTTTTCT
72793 GTTGCG-ATTT-ACAAATTCGAGTTGCGAATTTG
1 GTTGCGAATTTGAC--ATTCGAGTTGCGAATTTG
72825 GAAAATCGCA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.02
59 4 0.05
60 76 0.93
ACGTcount: A:0.19, C:0.12, G:0.22, T:0.47
Consensus pattern (60 bp):
GTTGCGAATTTGACATTCGAGTTGCGAATTTGACTTTTATGTTGCGAATTTAACTTTTCT
Found at i:73076 original size:36 final size:36
Alignment explanation
Indices: 73035--73133 Score: 180
Period size: 36 Copynumber: 2.8 Consensus size: 36
73025 GAGTATTATT
*
73035 AGCTTTGGTACATTTGTGTATCAATGTTATCATATC
1 AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
73071 AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
1 AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
*
73107 AGCTATGGTACATTCGTGTATCAATGT
1 AGCTTTGGTACATTCGTGTATCAATGT
73134 CCAGCACCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.41
Consensus pattern (36 bp):
AGCTTTGGTACATTCGTGTATCAATGTTATCATATC
Done.