Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000449.1 Hibiscus syriacus cultivar Beakdansim tig00000824_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: 54144
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:13631 original size:13 final size:13
Alignment explanation
Indices: 13613--13637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13603 AATGAATTTT
13613 AAGATTTTCTAAA
1 AAGATTTTCTAAA
13626 AAGATTTTCTAA
1 AAGATTTTCTAA
13638 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:15185 original size:14 final size:14
Alignment explanation
Indices: 15168--15203 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
15158 AAAAGACAGA
*
15168 AAATTAAAGTAATG
1 AAATTAAAGGAATG
*
15182 AAATTAAAGGACTG
1 AAATTAAAGGAATG
15196 AAATTAAA
1 AAATTAAA
15204 CTAAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.14, T:0.25
Consensus pattern (14 bp):
AAATTAAAGGAATG
Found at i:15229 original size:21 final size:22
Alignment explanation
Indices: 15196--15236 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
15186 TAAAGGACTG
*
15196 AAATTAAACTAAATAAAAAGGC
1 AAATCAAACTAAATAAAAAGGC
*
15218 AAATCAAA-TAAATTAAAAG
1 AAATCAAACTAAATAAAAAG
15237 TAATTAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (22 bp):
AAATCAAACTAAATAAAAAGGC
Found at i:15499 original size:81 final size:83
Alignment explanation
Indices: 15368--15534 Score: 302
Period size: 81 Copynumber: 2.0 Consensus size: 83
15358 ATAAAGCTAG
15368 AAATTAAAGGATTAAAACATAATAAAATATATAAAAAAGTGAATAAATCACAAATAAAATAGTGA
1 AAATTAAAGGATTAAAACATAATAAAATATAT-AAAAAGTGAATAAATCACAAATAAAATAGTGA
15433 CTAAAACATAATAAATACA
65 CTAAAACATAATAAATACA
*
15452 AAATTAAAGGATT-AAACATAATAAAATATAT-AAAAGTGAATAAATCACAAATAAAATTGTGAC
1 AAATTAAAGGATTAAAACATAATAAAATATATAAAAAGTGAATAAATCACAAATAAAATAGTGAC
15515 TAAAACATAATAAATACA
66 TAAAACATAATAAATACA
15533 AA
1 AA
15535 TATCACAATA
Statistics
Matches: 82, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
81 51 0.62
83 18 0.22
84 13 0.16
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (83 bp):
AAATTAAAGGATTAAAACATAATAAAATATATAAAAAGTGAATAAATCACAAATAAAATAGTGAC
TAAAACATAATAAATACA
Found at i:16270 original size:23 final size:22
Alignment explanation
Indices: 16224--16271 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
16214 ATTTCAAAGA
* * *
16224 GAAAAAAATGAAAAATAAAGTT
1 GAAAAAAACGAAAAACAAAATT
16246 GAAAATAAACGAAAAACAAAATT
1 GAAAA-AAACGAAAAACAAAATT
16269 GAA
1 GAA
16272 TAGAACCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.15
Consensus pattern (22 bp):
GAAAAAAACGAAAAACAAAATT
Found at i:29044 original size:30 final size:29
Alignment explanation
Indices: 29010--29069 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
29000 TCAAACGCTT
29010 AATTCTA-ACAAACTAAAAATCCTAAATAAA
1 AATTCTATACAAACT-AAAATCCT-AATAAA
* *
29040 AATTCTATGCAAACTAAATTCCTAATAAA
1 AATTCTATACAAACTAAAATCCTAATAAA
29069 A
1 A
29070 TAATAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 7 0.26
30 14 0.52
31 6 0.22
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.27
Consensus pattern (29 bp):
AATTCTATACAAACTAAAATCCTAATAAA
Found at i:30096 original size:4 final size:4
Alignment explanation
Indices: 30087--30112 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
30077 GATAGGAGAA
30087 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
30113 GGATTCAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:31339 original size:3 final size:3
Alignment explanation
Indices: 31331--31356 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31321 GATAATGAGT
31331 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
31357 GGAGCTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:34193 original size:19 final size:19
Alignment explanation
Indices: 34169--34206 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
34159 TGAGTAAGTG
34169 AATTCAACTTCATGTAATC
1 AATTCAACTTCATGTAATC
34188 AATTCAACTTCATGTAATC
1 AATTCAACTTCATGTAATC
34207 GATGCAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (19 bp):
AATTCAACTTCATGTAATC
Found at i:41397 original size:8 final size:8
Alignment explanation
Indices: 41384--41423 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
41374 TCATTTTCAA
41384 AGAATTTG
1 AGAATTTG
41392 AGAATTT-
1 AGAATTTG
*
41399 AGAGTTTG
1 AGAATTTG
*
41407 GGAATTTG
1 AGAATTTG
41415 AGAATTTG
1 AGAATTTG
41423 A
1 A
41424 AAGATTGTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.38
Consensus pattern (8 bp):
AGAATTTG
Found at i:41724 original size:128 final size:128
Alignment explanation
Indices: 41496--42760 Score: 2293
Period size: 128 Copynumber: 9.9 Consensus size: 128
41486 ATCGGAGTAT
*
41496 TATTCACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
* *
41561 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAATACCTATTATTTTAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
41624 TATTCACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
41689 TTGCCCTATTATGTCACTCATGTCCCTCGGAGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
41752 TATTCACATGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
41817 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
41880 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
41945 TTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
42007 TATTCACATGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
42072 TTGCCATATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
42134 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
42199 TTGCCCTATTATGTCACTTATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
42262 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTTCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
42327 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
* *
42390 TATTCATATGAAGGCGTGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
42455 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
42518 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCATCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
* * *
42583 TTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAATACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * ** *
42646 -AGGGGACATGAAGGCGCGTTCCTGGGGGCGCGCCTTCCATTATTTTATCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
42710 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
42761 AATCAGGTAA
Statistics
Matches: 1102, Mismatches: 33, Indels: 4
0.97 0.03 0.00
Matches are distributed among these distances:
127 250 0.23
128 852 0.77
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:43205 original size:33 final size:33
Alignment explanation
Indices: 43162--43257 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
43152 ATTTAATGTT
*
43162 AATTTCGAATACTATAATTTATATTTTAAATTTA
1 AATTT-GAATAATATAATTTATATTTTAAATTTA
* * *
43196 AATTTGAATAATATTATTTTTATTTT-ATTTTA
1 AATTTGAATAATATAATTTATATTTTAAATTTA
*
43228 AATTTTGAATAATATAATTTGTATTTTAAA
1 AA-TTTGAATAATATAATTTATATTTTAAA
43258 AACATTTATC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 7 0.13
33 40 0.75
34 6 0.11
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (33 bp):
AATTTGAATAATATAATTTATATTTTAAATTTA
Found at i:43808 original size:21 final size:20
Alignment explanation
Indices: 43784--43849 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 20
43774 TAAAACCCTA
*
43784 CGGGCTAGGCATGTAACCTGG
1 CGGGCTAGGAATGTAACCT-G
*
43805 CGGGCTTGGAATGTAACCCTG
1 CGGGCTAGGAATGTAA-CCTG
*
43826 CGGGCTCGGAATGTAACCCTG
1 CGGGCTAGGAATGTAA-CCTG
43847 CGG
1 CGG
43850 AGATGGCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 38 0.93
22 3 0.07
ACGTcount: A:0.18, C:0.26, G:0.36, T:0.20
Consensus pattern (20 bp):
CGGGCTAGGAATGTAACCTG
Found at i:43879 original size:21 final size:21
Alignment explanation
Indices: 43853--43900 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
43843 CCTGCGGAGA
*
43853 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
43874 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
43895 GGGCAT
1 TGGCAT
43901 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:45661 original size:17 final size:19
Alignment explanation
Indices: 45639--45677 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
45629 TATATAATAT
45639 TATTTA-ATAAA-ATATAA
1 TATTTACATAAATATATAA
45656 TATTTACATAAATATATAA
1 TATTTACATAAATATATAA
45675 TAT
1 TAT
45678 AAAAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 5 0.25
19 9 0.45
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
TATTTACATAAATATATAA
Found at i:45717 original size:32 final size:33
Alignment explanation
Indices: 45647--45717 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
45637 ATTATTTAAT
*
45647 AAAAT-ATAATATTTACATAAATATATAATATA
1 AAAATAATAATATTTACATAAATATATAACATA
45679 AAAATAATAACTATTTA-A-AAA-ATACTAACATA
1 AAAATAATAA-TATTTACATAAATATA-TAACATA
45711 AAAATAA
1 AAAATAA
45718 ATTTCTTACC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
31 3 0.09
32 21 0.60
33 5 0.14
34 6 0.17
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (33 bp):
AAAATAATAATATTTACATAAATATATAACATA
Found at i:46791 original size:21 final size:21
Alignment explanation
Indices: 46749--46797 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
46739 TTATCAAAAA
*
46749 TATTATTATTTTTATCAGTTT
1 TATTATTATTTTTATCAATTT
*
46770 TATTATT-TTTTCTATTAATTT
1 TATTATTATTTT-TATCAATTT
*
46791 TGTTATT
1 TATTATT
46798 GTTAGACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.69
Consensus pattern (21 bp):
TATTATTATTTTTATCAATTT
Found at i:46881 original size:12 final size:12
Alignment explanation
Indices: 46860--46885 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
46850 ATATTTTAAG
46860 TAATTTTTTTAT
1 TAATTTTTTTAT
46872 TAATTTTTTTAT
1 TAATTTTTTTAT
46884 TA
1 TA
46886 TTTAAATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TAATTTTTTTAT
Found at i:48327 original size:21 final size:22
Alignment explanation
Indices: 48301--48344 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
48291 GATTACAAAT
*
48301 AGGGTATCGATA-CCATGCTAC
1 AGGGTACCGATAGCCATGCTAC
*
48322 AGGGTACCGATAGCCCTGCTAC
1 AGGGTACCGATAGCCATGCTAC
48344 A
1 A
48345 ATACTGCTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
AGGGTACCGATAGCCATGCTAC
Found at i:48353 original size:11 final size:11
Alignment explanation
Indices: 48337--48366 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
48327 ACCGATAGCC
48337 CTGCTACAATA
1 CTGCTACAATA
48348 CTGCTACAATA
1 CTGCTACAATA
*
48359 TTGCTACA
1 CTGCTACA
48367 GTATTTCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (11 bp):
CTGCTACAATA
Found at i:48371 original size:11 final size:11
Alignment explanation
Indices: 48338--48371 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
48328 CCGATAGCCC
*
48338 TGCTACAATAC
1 TGCTACAATAT
48349 TGCTACAATAT
1 TGCTACAATAT
*
48360 TGCTACAGTAT
1 TGCTACAATAT
48371 T
1 T
48372 TCCATAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (11 bp):
TGCTACAATAT
Found at i:48900 original size:24 final size:24
Alignment explanation
Indices: 48873--48947 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
48863 ATCTCGTATA
48873 AATTTACACCGAAGTACCACGTAG
1 AATTTACACCGAAGTACCACGTAG
* * *
48897 AATTTGTC-CCGAAGGACCGCGTAG
1 AATTT-ACACCGAAGTACCACGTAG
* * *
48921 AA-ATGCACCGAAGTGCCACGTAG
1 AATTTACACCGAAGTACCACGTAG
48944 AATT
1 AATT
48948 GCACCGTAGT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
22 1 0.03
23 16 0.41
24 21 0.54
25 1 0.03
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (24 bp):
AATTTACACCGAAGTACCACGTAG
Found at i:48942 original size:23 final size:23
Alignment explanation
Indices: 48879--48961 Score: 89
Period size: 23 Copynumber: 3.6 Consensus size: 23
48869 TATAAATTTA
*
48879 CACCGAAGTACCACGTAGAATTTG
1 CACCGAAGTGCCACGTAGAA-TTG
* *
48903 TC-CCGAAG-GACCGCGTAGAAATG
1 -CACCGAAGTG-CCACGTAGAATTG
48926 CACCGAAGTGCCACGTAGAATTG
1 CACCGAAGTGCCACGTAGAATTG
*
48949 CACCGTAGTGCCA
1 CACCGAAGTGCCA
48962 TATAATATGT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
22 1 0.02
23 31 0.63
24 16 0.33
25 1 0.02
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTG
Found at i:49244 original size:30 final size:31
Alignment explanation
Indices: 49185--49245 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
49175 TCACAATTCA
* * *
49185 CATATCTTTATCACATAGACATATCATTTTC
1 CATACCTTTATCACATACACATATAATTTTC
*
49216 CATACCTTTATCATA-ACACATATAATTTTC
1 CATACCTTTATCACATACACATATAATTTTC
49246 ATGCATATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (31 bp):
CATACCTTTATCACATACACATATAATTTTC
Found at i:49595 original size:20 final size:21
Alignment explanation
Indices: 49556--49597 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
49546 CTTCAACTTT
49556 TCCTTAGGGGTATCGATACCC
1 TCCTTAGGGGTATCGATACCC
49577 TCCTTA-GGGTATC-AGTACCC
1 TCCTTAGGGGTATCGA-TACCC
49597 T
1 T
49598 TATACATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.05
20 13 0.65
21 6 0.30
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (21 bp):
TCCTTAGGGGTATCGATACCC
Found at i:53951 original size:23 final size:23
Alignment explanation
Indices: 53920--54001 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
53910 CATATAAATT
*
53920 TGCACCGAAGTGCCACGTAGAATT
1 TGCACCGAAGTGCCACGTAGAA-A
* *
53944 TTC-CCGAAG-GACCGCGTAGAAA
1 TGCACCGAAGTG-CCACGTAGAAA
* *
53966 TGCACCGAAGTTCCACGTAG-AT
1 TGCACCGAAGTGCCACGTAGAAA
*
53988 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
54002 CTATAATATG
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
22 16 0.35
23 28 0.61
24 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAA
Done.