Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004865.1 Hibiscus syriacus cultivar Beakdansim tig00010971_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: 76869
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13477 original size:25 final size:25
Alignment explanation
Indices: 13439--13486 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
13429 CTCGCCTTAA
*
13439 AAAATCCTAAACCAGTTTAACCTAC
1 AAAATCCTAAACCACTTTAACCTAC
** *
13464 AAAATCCTTCACCACTTTCACCT
1 AAAATCCTAAACCACTTTAACCT
13487 TAACGAACCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.38, C:0.33, G:0.02, T:0.27
Consensus pattern (25 bp):
AAAATCCTAAACCACTTTAACCTAC
Found at i:13488 original size:51 final size:51
Alignment explanation
Indices: 13392--13513 Score: 120
Period size: 51 Copynumber: 2.4 Consensus size: 51
13382 TTGAACCTTG
* * * * * *
13392 TCCTAAATCACTTTAATCTACACAACCCTTGATCACTCTCGCCTTAAAAAA
1 TCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAAAAAA
* * * **
13443 TCCTAAACCAGTTTAACCTACAAAATCCTTCACCACTTTCACCTTAACGAA
1 TCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAAAAAA
*
13494 -CCATATACCACTTTAACCTA
1 TCC-TAAACCACTTTAACCTA
13514 AAATCACTCC
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
50 2 0.04
51 55 0.96
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.29
Consensus pattern (51 bp):
TCCTAAACCACTTTAACCTACAAAACCCTTCACCACTCTCACCTTAAAAAA
Found at i:14207 original size:21 final size:22
Alignment explanation
Indices: 14170--14219 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
14160 ATTAATCCTT
*
14170 AATGTTTTAATTTTTTTGTCAA
1 AATGATTTAATTTTTTTGTCAA
14192 AATGATTTAA-TTTTTTGTCAA
1 AATGATTTAATTTTTTTGTCAA
14213 AATGATT
1 AATGATT
14220 CTTGTTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (22 bp):
AATGATTTAATTTTTTTGTCAA
Found at i:15421 original size:14 final size:14
Alignment explanation
Indices: 15399--15441 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
15389 GAGTTTGGGC
*
15399 TGAATATAAACGAA
1 TGAACATAAACGAA
*
15413 TGAACATAAATGAA
1 TGAACATAAACGAA
* *
15427 TGAGCATAATCGAA
1 TGAACATAAACGAA
15441 T
1 T
15442 AAATTACCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.23
Consensus pattern (14 bp):
TGAACATAAACGAA
Found at i:16228 original size:17 final size:18
Alignment explanation
Indices: 16192--16229 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
16182 TAGATATTTA
*
16192 AAATAAAATCATAAATAT
1 AAATAAAATCATAAAAAT
*
16210 AAATTAAAT-ATAAAAAT
1 AAATAAAATCATAAAAAT
16227 AAA
1 AAA
16230 ATTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATAAAATCATAAAAAT
Found at i:16228 original size:23 final size:25
Alignment explanation
Indices: 16174--16229 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 25
16164 AAACCCACAT
16174 AATAAATATAGATATTTAAAATAAA
1 AATAAATATAGATATTTAAAATAAA
16199 ATCATAAATATA-A-A-TTAAATATAAA
1 A--ATAAATATAGATATTTAAA-ATAAA
16224 AATAAA
1 AATAAA
16230 ATTTAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
23 5 0.18
24 5 0.18
25 8 0.29
26 1 0.04
27 9 0.32
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (25 bp):
AATAAATATAGATATTTAAAATAAA
Found at i:16423 original size:18 final size:17
Alignment explanation
Indices: 16402--16451 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
16392 TTGAAGTGAT
*
16402 CAACTCAATAAAGATGAA
1 CAACTCAA-AAAGATAAA
16420 CAACTCAAAGAAGATAAA
1 CAACTCAAA-AAGATAAA
*
16438 TAACTCAACAAAGA
1 CAACTCAA-AAAGA
16452 ATAACATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.58, C:0.18, G:0.10, T:0.14
Consensus pattern (17 bp):
CAACTCAAAAAGATAAA
Found at i:16957 original size:67 final size:67
Alignment explanation
Indices: 16878--17012 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
16868 AAATGACTTG
*
16878 CCAGTGTTAATATGTTAAATTATGTTAGGTAGATGTAAAAAGATTATGCTAAAAATTATTTAATG
1 CCAGTGTTAATATATTAAATTATGTTAGGTAGATGTAAAAAGATTATGCTAAAAATTATTTAATG
16943 AA
66 AA
*
16945 CCAGTGTTAATATATTAAATTATGTTAGGTAGATGTAAAAGGATTATGCTAAAAATTATTTAATG
1 CCAGTGTTAATATATTAAATTATGTTAGGTAGATGTAAAAAGATTATGCTAAAAATTATTTAATG
17010 AA
66 AA
17012 C
1 C
17013 AATTCTAGAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.37
Consensus pattern (67 bp):
CCAGTGTTAATATATTAAATTATGTTAGGTAGATGTAAAAAGATTATGCTAAAAATTATTTAATG
AA
Found at i:17194 original size:16 final size:16
Alignment explanation
Indices: 17173--17209 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
17163 ATGCACTTCA
17173 AATATTATACACACTC
1 AATATTATACACACTC
17189 AATATTATACACACTC
1 AATATTATACACACTC
*
17205 GATAT
1 AATAT
17210 CAAAAATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.22, G:0.03, T:0.32
Consensus pattern (16 bp):
AATATTATACACACTC
Found at i:18992 original size:31 final size:31
Alignment explanation
Indices: 18954--19073 Score: 138
Period size: 31 Copynumber: 3.9 Consensus size: 31
18944 GAGTCGAGGG
*
18954 TTTACCTATGTTCTTCAGGACATATGGACAA
1 TTTACCTATGTTCTTCAGGACATATGGACAT
18985 TTTACCTATG-TCTTTC-GAGACATATGGACAT
1 TTTACCTATGTTC-TTCAG-GACATATGGACAT
* *
19016 TTTACCTATGTTC-TAAGGAACATATGGATAT
1 TTTACCTATGTTCTTCAGG-ACATATGGACAT
* * *
19047 TTTACCTAGGTTCTTCGGGACCTATGG
1 TTTACCTATGTTCTTCAGGACATATGG
19074 TGTAACACCC
Statistics
Matches: 76, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
30 5 0.07
31 66 0.87
32 5 0.07
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (31 bp):
TTTACCTATGTTCTTCAGGACATATGGACAT
Found at i:19947 original size:149 final size:149
Alignment explanation
Indices: 19776--20077 Score: 541
Period size: 149 Copynumber: 2.0 Consensus size: 149
19766 AAGTGCAGCA
* *
19776 TAGATTTGCACCGTAGTTCCATATAACAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
* *
19841 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCACAGAATATATA
66 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
19906 TATATCCCGAAGGACCGCG
131 TATATCCCGAAGGACCGCG
*
19925 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
19990 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
* *
20055 TATGTCCCGAAGGACCGTG
131 TATATCCCGAAGGACCGCG
20074 TAGA
1 TAGA
20078 CCCTCGACTC
Statistics
Matches: 146, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 146 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTATTCCTTAAGAATCA
TATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATACA
TATATCCCGAAGGACCGCG
Found at i:20197 original size:14 final size:14
Alignment explanation
Indices: 20178--20205 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20168 AACTTGTAAT
20178 TCACGTATCACATA
1 TCACGTATCACATA
20192 TCACGTATCACATA
1 TCACGTATCACATA
20206 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:20629 original size:2 final size:2
Alignment explanation
Indices: 20624--20665 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
20614 TCTCTCAGAC
20624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20666 TCACATGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21634 original size:21 final size:21
Alignment explanation
Indices: 21610--21651 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
21600 TGTTGTTCGT
* *
21610 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
21631 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
21652 ATGCCCAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.26, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:25198 original size:149 final size:149
Alignment explanation
Indices: 24948--25262 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
24938 TATAATTGCA
*
24948 CCGAAGTG-CCGCGTAGATTTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTA
*
25012 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATT
* *
25077 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
*
25097 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
25162 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATTC
*
25227 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
25246 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
25263 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATATTC
CAAAGAATATACATATATC
Found at i:25382 original size:14 final size:14
Alignment explanation
Indices: 25363--25390 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25353 AACTTGTAAT
25363 TCACGTATCACATA
1 TCACGTATCACATA
25377 TCACGTATCACATA
1 TCACGTATCACATA
25391 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:25814 original size:2 final size:2
Alignment explanation
Indices: 25809--25864 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
25799 TCTCTCAGAC
25809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25851 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
25865 TCACATGTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36866 original size:34 final size:34
Alignment explanation
Indices: 36823--36946 Score: 120
Period size: 34 Copynumber: 3.8 Consensus size: 34
36813 TTCGTCCTAC
36823 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
36857 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
36892 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
36921 TATGATTTAAACTCCT-AAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
36947 CCACAAGCAC
Statistics
Matches: 73, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
33 9 0.12
34 29 0.40
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:37251 original size:13 final size:15
Alignment explanation
Indices: 37233--37265 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
37223 ATATGGATAT
37233 TTATTCAT-TT-TTA
1 TTATTCATGTTATTA
37246 TTATTCATGTTATTA
1 TTATTCATGTTATTA
37261 TTATT
1 TTATT
37266 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 2 0.11
15 8 0.44
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (15 bp):
TTATTCATGTTATTA
Found at i:37347 original size:22 final size:22
Alignment explanation
Indices: 37309--37378 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
37299 ATTTTTTTAC
*
37309 TATATTT-TATTATTATTATATA
1 TATATTTCT-TTAATATTATATA
* *
37331 TATATTTCTTTAATATTTTATT
1 TATATTTCTTTAATATTATATA
**
37353 TATAAGTC--TAATATTACTATA
1 TATATTTCTTTAATATTA-TATA
37374 TATAT
1 TATAT
37379 ATATAATTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
20 7 0.18
21 7 0.18
22 23 0.61
23 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (22 bp):
TATATTTCTTTAATATTATATA
Found at i:48841 original size:105 final size:105
Alignment explanation
Indices: 48585--49031 Score: 452
Period size: 105 Copynumber: 4.3 Consensus size: 105
48575 AACATCCACG
* * * *
48585 ATTTCAACTCCACGATGGAGGATATCGTGCCACTCAAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACGACGGAGGATAT--TG-GACCCAAGACAACACAAGTTCAACTTCACAACGAA
* * * * **
48650 GGGACGACTGGTTGTCAACGAACAACTTTCCAATTTCAAAGCTG
63 GGGACGGCTGGTTGTCAACAAACAA-TTTCCAGTTTCAGAGCCA
* * * *
48694 ATTT----TCCACGACGGAGGATATCATGCTACCTATGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACGACGGAGGATAT--TG-GACCCAAGACAACACAAGTTCAACTTCACAACGAA
* *
48755 GGGACGGTTGGTTGTCAAC-AACAATTTCCCAGTTTCAGGGCCA
63 GGGACGGCTGGTTGTCAACAAACAATTT-CCAGTTTCAGAGCCA
* * *
48798 ATTTCAACTTCAC-AGCGGAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGG
1 ATTTCAACTTCACGA-CGGAGGATATTGGACCCAAGACAACACAAGTTCAACTTCACAACGAAGG
* **
48862 GGCGGCTGACTGTCAACAAACAATTT-C-G-----GAGCCA
65 GACGGCTGGTTGTCAACAAACAATTTCCAGTTTCAGAGCCA
* * * * *
48896 ATCTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACGACGGAGGATATTGGACCCAAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
48961 ACGGCTGGTTGTCAACAAACAATTTTCCGGTTCCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAA-TTTCCAGTTTCAGAGCCA
49002 ATTTCAACTTCACGACGGAGGATATTGGAC
1 ATTTCAACTTCACGACGGAGGATATTGGAC
49032 TTGGAACAAT
Statistics
Matches: 284, Mismatches: 38, Indels: 35
0.80 0.11 0.10
Matches are distributed among these distances:
98 80 0.28
99 4 0.01
100 1 0.00
101 1 0.00
103 4 0.01
104 20 0.07
105 112 0.39
106 43 0.15
107 1 0.00
108 14 0.05
109 4 0.01
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (105 bp):
ATTTCAACTTCACGACGGAGGATATTGGACCCAAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAAACAATTTCCAGTTTCAGAGCCA
Found at i:48933 original size:98 final size:98
Alignment explanation
Indices: 48727--48985 Score: 295
Period size: 98 Copynumber: 2.6 Consensus size: 98
48717 TGCTACCTAT
* * **
48727 GACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAAC-AACAATTTCCCAGTTTC
1 GACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTT--C-G----
* * * *
48791 AGGGCCAATTTCAACTTCACAGCGGAGGATATTGGACCCAA
59 -GAGCCAATCTCAACTTCACAACGAAGGATATTGGACCCAA
* * *
48832 GACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCGGAGCCAA
1 GACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTCGGAGCCAA
* *
48897 TCTCAACTTCACAACGAAGGATATTGGACTCGA
66 TCTCAACTTCACAACGAAGGATATTGGACCCAA
* **
48930 GACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT
1 GACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTT
48986 TCCGGTTCCA
Statistics
Matches: 134, Mismatches: 19, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
98 84 0.63
103 1 0.01
104 1 0.01
105 40 0.30
106 8 0.06
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (98 bp):
GACAACACAAGCTCAACTTCACAACGAAGGGACGGCTGACTGTCAACAAACAATTTCGGAGCCAA
TCTCAACTTCACAACGAAGGATATTGGACCCAA
Found at i:49624 original size:34 final size:34
Alignment explanation
Indices: 49581--49705 Score: 129
Period size: 34 Copynumber: 3.8 Consensus size: 34
49571 TTCGTCCTAC
49581 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* *
49615 TAGGATTCAAACTCCTAAAGATATGATAGAATTTT
1 TAGGATTCAAACTCCTAAAAATAGGATAGAA-TTT
49650 GCTAGGATTC--A-----AAAAATAGGATAGAATTT
1 --TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
* * *
49679 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
49706 CCACAAGCAC
Statistics
Matches: 74, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.08
29 4 0.05
30 13 0.18
34 39 0.53
35 4 0.05
37 8 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.31
Consensus pattern (34 bp):
TAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:50084 original size:15 final size:15
Alignment explanation
Indices: 50062--50100 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
50052 ATTATATGGA
*
50062 TATT-TTATTCATTT
1 TATTATTATTCATGT
*
50076 TTTTATTATTCATGT
1 TATTATTATTCATGT
50091 TATTATTATT
1 TATTATTATT
50101 ATATGTATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (15 bp):
TATTATTATTCATGT
Found at i:61106 original size:42 final size:41
Alignment explanation
Indices: 61047--61145 Score: 126
Period size: 42 Copynumber: 2.4 Consensus size: 41
61037 GGTAAGTCCT
* *
61047 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCG
1 TCGGGCCATCAGTAAGTCTTTCGAACAAGATGA-TAAATCCG
* * * *
61089 TCGGGTCATCTGTAAGTCTTTCGAACAAGATGATAAGTCCT
1 TCGGGCCATCAGTAAGTCTTTCGAACAAGATGATAAATCCG
*
61130 TCGGGCCATCCGTAAG
1 TCGGGCCATCAGTAAG
61146 ACATTTGGGT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 20 0.41
42 29 0.59
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.28
Consensus pattern (41 bp):
TCGGGCCATCAGTAAGTCTTTCGAACAAGATGATAAATCCG
Found at i:61382 original size:257 final size:250
Alignment explanation
Indices: 60921--61544 Score: 919
Period size: 257 Copynumber: 2.5 Consensus size: 250
60911 AGTTGTTTCA
* *
60921 AAAATGAGAAAGCGATTTATAAAGTTTCTCCTTTAATATTTTCTGAAAAATGAAATTTTTGAAAA
1 AAAATGAGAAAGCGATTTCTAAAGTTTCTCATTTAATATTTTCT-AAAAATGAAATTTTTGAAAA
* * *
60986 GTAAGAAAGCGATTTCCAAAGTTTCTTACCCAGTAAACTATTTCCTAAATTGGTAAGTCCTTCGG
65 GTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGA
*
61051 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCGTCGGGTCATCTGTAAGTCTTTCGAACA
130 GCCATCACTAAGTCTTTCGAGCATGATGATTAAATCCGTCGGGTCATCTGTAAGTCTTTCGAACA
* * *
61116 AGATGATAAGTCCTTCGGGCCATCCGTAAGACATTTGGGTAGGATGTTTTCACATG
195 AGATGATAAGTCATTCGGGCCATCCGTAAGACATTCGAGTAGGATGTTTTCACATG
*
61172 AATTTTAAAAGTGAGAAAGCGATTTCTAAAGTTTCTCATTTAATATTTTCTTAAAATGAAATTTT
1 ------AAAA-TGAGAAAGCGATTTCTAAAGTTTCTCATTTAATATTTTCTAAAAATGAAATTTT
* * * * *
61237 TGAAAAGTAAAAAAGTGATTACCAAAGTTTCTTACCCAATAAATTATTTCCGAAATTGGTAAGTC
59 TGAAAAGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTC
* *
61302 CTTCGAGCCATCACTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTGTAAGTCTTT
124 CTTCGAGCCATCACTAAGTCTTTCGAGCATGATGATTAAATCCGTCGGGTCATCTGTAAGTCTTT
* * *
61367 CGAGCAAGATGATAAGTCATTTGGGCCATCCGTAAGACCTTCGAGTAGGATGTTTTCACATG
189 CGAACAAGATGATAAGTCATTCGGGCCATCCGTAAGACATTCGAGTAGGATGTTTTCACATG
* * * *
61429 AAAATGAGAAAACGATTTTTCCAAAGTTTCTCATTTAATGTTTTCAAAAAATGAAA-TTTTGAAA
1 AAAATGAGAAAGCGA--TTTCTAAAGTTTCTCATTTAATATTTTCTAAAAATGAAATTTTTGAAA
*
61493 AGTAAGAAAGCGATTACCAAA-TTTCTTACCCAGTAAACAATTTCCAAAATTG
64 AGTAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTG
61545 ATCTAACAAC
Statistics
Matches: 334, Mismatches: 30, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
250 37 0.11
251 31 0.09
252 35 0.10
257 193 0.58
258 38 0.11
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (250 bp):
AAAATGAGAAAGCGATTTCTAAAGTTTCTCATTTAATATTTTCTAAAAATGAAATTTTTGAAAAG
TAAGAAAGCGATTACCAAAGTTTCTTACCCAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGAG
CCATCACTAAGTCTTTCGAGCATGATGATTAAATCCGTCGGGTCATCTGTAAGTCTTTCGAACAA
GATGATAAGTCATTCGGGCCATCCGTAAGACATTCGAGTAGGATGTTTTCACATG
Found at i:61402 original size:41 final size:42
Alignment explanation
Indices: 61308--61411 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 42
61298 AGTCCTTCGA
* *
61308 GCCATCAC-TAAGTCTTTCGAGCATGATGATTAAATCCTTTGG
1 GCCATC-CGTAAGTCTTTCGAGCAAGATGATTAAATCATTTGG
* * *
61350 GTCATCTGTAAGTCTTTCGAGCAAGATGA-TAAGTCATTTGG
1 GCCATCCGTAAGTCTTTCGAGCAAGATGATTAAATCATTTGG
* *
61391 GCCATCCGTAAGACCTTCGAG
1 GCCATCCGTAAGTCTTTCGAG
61412 TAGGATGTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 27 0.52
42 25 0.48
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
GCCATCCGTAAGTCTTTCGAGCAAGATGATTAAATCATTTGG
Found at i:61686 original size:79 final size:81
Alignment explanation
Indices: 61537--61695 Score: 187
Period size: 79 Copynumber: 2.0 Consensus size: 81
61527 AAACAATTTC
* * ** *
61537 CAAAATTGATCTAACAACCTGAAAAAAGAGGAATAGATCAAGTCTGATCTCTCCTAAAGAAGAAT
1 CAAAATTGATCTAACAACCCGAAAAAAGAGGAATAGATCAAGCCCAATCTCCCCTAAAGAAGAAT
61602 AGAGCA-ACATGTCTA
66 AGAGCAGACATGTCTA
* * * * * *
61617 CAAAATTGATCTGACTACCCG-AAAAAGAGGAATATATCATGCCCAATCTCCCCTAAAGAATAGT
1 CAAAATTGATCTAACAACCCGAAAAAAGAGGAATAGATCAAGCCCAATCTCCCCTAAAGAAGAAT
* *
61681 GGAGCAGACCTGTCT
66 AGAGCAGACATGTCT
61696 TCCTTCAGAC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 40 0.62
80 25 0.38
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (81 bp):
CAAAATTGATCTAACAACCCGAAAAAAGAGGAATAGATCAAGCCCAATCTCCCCTAAAGAAGAAT
AGAGCAGACATGTCTA
Found at i:61918 original size:3 final size:3
Alignment explanation
Indices: 61908--61964 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
61898 AATAATAATA
61908 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
61955 ATT ATT ATT A
1 ATT ATT ATT A
61965 CATTTTTATA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:67072 original size:19 final size:19
Alignment explanation
Indices: 67040--67098 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
67030 AATAAAAAAT
67040 TAATAAATAA-TATATAATA
1 TAATAAA-AACTATATAATA
67059 TAATAAAAACTATATTAA-A
1 TAATAAAAACTATA-TAATA
**
67078 TTTTCAAAAACTATATAATA
1 TAAT-AAAAACTATATAATA
67098 T
1 T
67099 GTTTTCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 2 0.06
19 17 0.50
20 15 0.44
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATAAAAACTATATAATA
Found at i:67120 original size:17 final size:17
Alignment explanation
Indices: 67063--67131 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 17
67053 ATAATATAAT
67063 AAAAACTATATTAAATTTTC
1 AAAAACTATA-T--ATTTTC
67083 AAAAACTATATAATATGTTTTC
1 AAAAAC--TAT-ATA--TTTTC
*
67105 AAAAATTATATATTTTC
1 AAAAACTATATATTTTC
67122 AAAAACTATA
1 AAAAACTATA
67132 CTATATATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
17 14 0.33
19 3 0.07
20 10 0.24
22 14 0.33
23 1 0.02
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.39
Consensus pattern (17 bp):
AAAAACTATATATTTTC
Found at i:67156 original size:15 final size:15
Alignment explanation
Indices: 67136--67165 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
67126 ACTATACTAT
67136 ATATGTTTTCAAAAA
1 ATATGTTTTCAAAAA
67151 ATATGTTTTCAAAAA
1 ATATGTTTTCAAAAA
67166 CTATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (15 bp):
ATATGTTTTCAAAAA
Found at i:67193 original size:23 final size:24
Alignment explanation
Indices: 67151--67195 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
67141 TTTTCAAAAA
67151 ATATGTTTTCAAAAACTATATTAT
1 ATATGTTTTCAAAAACTATATTAT
67175 ATATGTTTTCAAAAA-TATATT
1 ATATGTTTTCAAAAACTATATT
67196 TTCAAAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (24 bp):
ATATGTTTTCAAAAACTATATTAT
Found at i:67198 original size:38 final size:39
Alignment explanation
Indices: 67077--67216 Score: 223
Period size: 39 Copynumber: 3.6 Consensus size: 39
67067 ACTATATTAA
67077 ATTTTCAAAAACTATA-TA-ATATGTTTTCAAAAATTATAT
1 ATTTTCAAAAACTATACTATATATGTTTTCAAAAA--ATAT
67116 ATTTTCAAAAACTATACTATATATGTTTTCAAAAAATAT
1 ATTTTCAAAAACTATACTATATATGTTTTCAAAAAATAT
* *
67155 GTTTTCAAAAACTATATTATATATGTTTTC-AAAAATAT
1 ATTTTCAAAAACTATACTATATATGTTTTCAAAAAATAT
67193 ATTTTCAAAAACTATACTATATAT
1 ATTTTCAAAAACTATACTATATAT
67217 TAAAAACTTT
Statistics
Matches: 95, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
38 30 0.32
39 48 0.51
40 2 0.02
41 15 0.16
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (39 bp):
ATTTTCAAAAACTATACTATATATGTTTTCAAAAAATAT
Found at i:67208 original size:15 final size:14
Alignment explanation
Indices: 67175--67208 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
67165 ACTATATTAT
*
67175 ATATGTTTTCAAAA
1 ATATATTTTCAAAA
67189 ATATATTTTCAAAA
1 ATATATTTTCAAAA
67203 ACTATA
1 A-TATA
67209 CTATATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (14 bp):
ATATATTTTCAAAA
Found at i:67231 original size:18 final size:19
Alignment explanation
Indices: 67050--67232 Score: 68
Period size: 20 Copynumber: 9.5 Consensus size: 19
67040 TAATAAATAA
*
67050 TATATAATATAAT-AAAAAC
1 TATAT-ATATATTCAAAAAC
* *
67069 TATATTAAATTTTCAAAAAC
1 TATA-TATATATTCAAAAAC
*
67089 TATATAATATGTTTTCAAAAA-
1 TATAT-ATA--TATTCAAAAAC
*
67110 T-TATATATTTTCAAAAAC
1 TATATATATATTCAAAAAC
67128 TATACTATATATGTTTTCAAAAA-
1 TATA-TATATA----TTCAAAAAC
*
67151 -ATATGT-T-TTCAAAAAC
1 TATATATATATTCAAAAAC
67167 TATATTATATATGTTTTC-AAAA-
1 TATA-TATATA----TTCAAAAAC
67189 -ATATAT-T-TTCAAAAAC
1 TATATATATATTCAAAAAC
67205 TATACTATATATT-AAAAAC
1 TATA-TATATATTCAAAAAC
*
67224 TTTATATAT
1 TATATATAT
67233 TATATATTTT
Statistics
Matches: 129, Mismatches: 8, Indels: 55
0.67 0.04 0.29
Matches are distributed among these distances:
14 3 0.02
15 12 0.09
17 16 0.12
18 11 0.09
19 26 0.20
20 27 0.21
21 6 0.05
22 13 0.10
23 4 0.03
24 11 0.09
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (19 bp):
TATATATATATTCAAAAAC
Found at i:72363 original size:24 final size:24
Alignment explanation
Indices: 72331--72403 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
72321 TTAGTTACAA
*
72331 AAGCTTGTGCTTTTGTAGCCGATG
1 AAGCTTGTGCTTTTGTAGCAGATG
* * * *
72355 AAGCTTGTGCTTTTGCAACATATA
1 AAGCTTGTGCTTTTGTAGCAGATG
*
72379 AAACTTGTGCTTTTGTAGCAGATG
1 AAGCTTGTGCTTTTGTAGCAGATG
72403 A
1 A
72404 GTCTCCTTGA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (24 bp):
AAGCTTGTGCTTTTGTAGCAGATG
Found at i:76136 original size:14 final size:13
Alignment explanation
Indices: 76088--76136 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
76078 TAAACAAAAC
76088 AAAA-TTAAATTA
1 AAAATTTAAATTA
* *
76100 AGAAATATAAAATA
1 A-AAATTTAAATTA
76114 AAAATTTAAATTA
1 AAAATTTAAATTA
76127 AAAGATTTAA
1 AAA-ATTTAA
76137 TGCAACAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 1 0.03
13 16 0.53
14 13 0.43
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (13 bp):
AAAATTTAAATTA
Found at i:76692 original size:13 final size:14
Alignment explanation
Indices: 76671--76699 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
76661 TTGTTTTTTT
76671 ATGCTTATTTTGTG
1 ATGCTTATTTTGTG
76685 ATGC-TATTTTGTG
1 ATGCTTATTTTGTG
76698 AT
1 AT
76700 ACTTGGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.17, C:0.07, G:0.21, T:0.55
Consensus pattern (14 bp):
ATGCTTATTTTGTG
Done.