Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007091.1 Hibiscus syriacus cultivar Beakdansim tig00018518_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: 54663
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:3542 original size:43 final size:43
Alignment explanation
Indices: 3456--3571 Score: 105
Period size: 43 Copynumber: 2.7 Consensus size: 43
3446 AAGGTAATTA
** *
3456 GCGGCGTTTGTATCCAAAAATTCCACTATAGATATAACATTTT
1 GCGGCGTTTGTATCCAAAAACGCCACTAAAGATATAACATTTT
* *
3499 GCGGCGTTTGTATCCAAACACGGCACTAAAGAGTCAT-AC-TTTT
1 GCGGCGTTTGTATCCAAAAACGCCACTAAAGA-T-ATAACATTTT
* * *
3542 GTGGTGTTT-T-TCCAACAAACGCCGCTAAAG
1 GCGGCGTTTGTATCCAA-AAACGCCACTAAAG
3572 GTTAGATATA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
41 5 0.08
42 12 0.20
43 38 0.63
44 3 0.05
45 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCACTAAAGATATAACATTTT
Found at i:3793 original size:41 final size:41
Alignment explanation
Indices: 3748--3856 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 41
3738 ATTTGTCAAG
*
3748 TAGTGGCATTT-TTTAGTAAACACCGCAATAGAGTTGGAATA
1 TAGTGGCATTTGTTTA-CAAACACCGCAATAGAGTTGGAATA
* * * *
3789 TAGTGGCGTTTGGTTTACAAACGCCGCAATAGAGTTGGCATG
1 TAGTGGCATTT-GTTTACAAACACCGCAATAGAGTTGGAATA
* * *
3831 TGGCGGCGTTTGGTTTACAAACACCG
1 TAGTGGCATTT-GTTTACAAACACCG
3857 TGAACTATTA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 10 0.17
42 44 0.76
43 4 0.07
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (41 bp):
TAGTGGCATTTGTTTACAAACACCGCAATAGAGTTGGAATA
Found at i:3820 original size:42 final size:42
Alignment explanation
Indices: 3765--3856 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
3755 ATTTTTTAGT
*
3765 AAACACCGCAATAGAGTTGGAATATAGTGGCGTTTGGTTTAC
1 AAACACCGCAATAGAGTTGGAATATAGCGGCGTTTGGTTTAC
* * * *
3807 AAACGCCGCAATAGAGTTGGCATGTGGCGGCGTTTGGTTTAC
1 AAACACCGCAATAGAGTTGGAATATAGCGGCGTTTGGTTTAC
3849 AAACACCG
1 AAACACCG
3857 TGAACTATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (42 bp):
AAACACCGCAATAGAGTTGGAATATAGCGGCGTTTGGTTTAC
Found at i:12111 original size:38 final size:38
Alignment explanation
Indices: 12059--12154 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
12049 CTCGTATAAA
* *
12059 TGTCCCGAATGACCTATCATCCCGAAGGATGCCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGCAATCTG
* * *
12097 TGTCCCGAAGGACCTGTCATCCTGAAGGATGTAATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGATGCAATCTG
*
12135 TGTCCCGTAGGACCTATCAT
1 TGTCCCGAAGGACCTATCAT
12155 ATGTCTTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (38 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGATGCAATCTG
Found at i:12359 original size:46 final size:46
Alignment explanation
Indices: 12306--12415 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
12296 TGTAACCATG
*
12306 TATTTCATATCATATCACATGTATCACGTATTACATATTCATATGT
1 TATTTCATATCATATCACATGTATCACGTATTACATATTCATATAT
*
12352 TATTTCATATCATATCACATGTATCACGTATTGCATATTCATATAT
1 TATTTCATATCATATCACATGTATCACGTATTACATATTCATATAT
12398 TATTTCATAT-AT-TCACAT
1 TATTTCATATCATATCACAT
12416 AGCTTATCTC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
44 6 0.10
45 2 0.03
46 54 0.87
ACGTcount: A:0.33, C:0.17, G:0.05, T:0.45
Consensus pattern (46 bp):
TATTTCATATCATATCACATGTATCACGTATTACATATTCATATAT
Found at i:19148 original size:46 final size:46
Alignment explanation
Indices: 19095--19195 Score: 166
Period size: 46 Copynumber: 2.2 Consensus size: 46
19085 GTAACCATGT
*
19095 ATTTCATATCATATCACATGTATCACGAATTACATATTCATATGCC
1 ATTTCATATCATATCACATGTATCACGAATTACATATTCATATACC
* * *
19141 ATTTCATATCATATCACATGTATCACGTATTGCATATTCATATATC
1 ATTTCATATCATATCACATGTATCACGAATTACATATTCATATACC
19187 ATTTCATAT
1 ATTTCATAT
19196 ATTTACATAG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 51 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.41
Consensus pattern (46 bp):
ATTTCATATCATATCACATGTATCACGAATTACATATTCATATACC
Found at i:22210 original size:22 final size:22
Alignment explanation
Indices: 22185--22265 Score: 126
Period size: 22 Copynumber: 3.7 Consensus size: 22
22175 GGGTATATTA
22185 GTCCTTCGGGACATATCCAGTG
1 GTCCTTCGGGACATATCCAGTG
*
22207 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACATATCCAGTG
* * *
22229 GTCCTTCAGGACGTATCTAGTG
1 GTCCTTCGGGACATATCCAGTG
22251 GTCCTTCGGGACATA
1 GTCCTTCGGGACATA
22266 GTGGTCATTC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.28
Consensus pattern (22 bp):
GTCCTTCGGGACATATCCAGTG
Found at i:22269 original size:18 final size:19
Alignment explanation
Indices: 22203--22282 Score: 81
Period size: 22 Copynumber: 3.9 Consensus size: 19
22193 GGACATATCC
22203 AGTGGTCCTTCGGGACGTAT
1 AGTGGTCCTTCGGGACG-AT
*
22223 CCAGTGGTCCTTCAGGACGTATCT
1 --AGTGGTCCTTCGGGACG-A--T
22247 AGTGGTCCTTCGGGAC-AT
1 AGTGGTCCTTCGGGACGAT
*
22265 AGTGGTCATTCGGGACGA
1 AGTGGTCCTTCGGGACGA
22283 ATACTGAACA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
18 16 0.31
19 1 0.02
20 1 0.02
22 33 0.63
24 1 0.02
ACGTcount: A:0.17, C:0.23, G:0.33, T:0.28
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACGAT
Found at i:23277 original size:18 final size:18
Alignment explanation
Indices: 23251--23293 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
23241 CAGGCAGGGA
*
23251 GAAGAGCGAACACCTCAG
1 GAAGTGCGAACACCTCAG
23269 GAAGTGCGAACACCTCAG
1 GAAGTGCGAACACCTCAG
23287 GAAGTGC
1 GAAGTGC
23294 CTGTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.30, T:0.09
Consensus pattern (18 bp):
GAAGTGCGAACACCTCAG
Found at i:25537 original size:66 final size:63
Alignment explanation
Indices: 25431--25593 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 63
25421 TTGTTGAAGG
* *
25431 TGCATCGATGCATAAGGAGTGCATCGATGCACTCATTTAAATTA-ATTGAACATCGAAT-GCCAT
1 TGCATCGATACATAAGGAGTGCATCGATGCAC-CATTTAAAATACA---AACATCGAATAG-CAT
25494 TTA
61 TTA
* * *
25497 TGCATCGATTCATAAGGAGTGCATCGATGCACCTTCTTAAAATACAAACATCGAATAGGATTTA
1 TGCATCGATACATAAGGAGTGCATCGATGCACCAT-TTAAAATACAAACATCGAATAGCATTTA
* *
25561 TGCACCGATACAT-GGGTAGTGCATCGATGCACC
1 TGCATCGATACATAAGG-AGTGCATCGATGCACC
25594 CGTCAAGGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
63 2 0.02
64 42 0.49
65 3 0.03
66 38 0.44
67 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (63 bp):
TGCATCGATACATAAGGAGTGCATCGATGCACCATTTAAAATACAAACATCGAATAGCATTTA
Found at i:26218 original size:2 final size:2
Alignment explanation
Indices: 26211--26253 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
26201 CATGAGTTAG
26211 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
26253 A
1 A
26254 GGAATTTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26735 original size:22 final size:22
Alignment explanation
Indices: 26710--26765 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
26700 GGTATATTAA
26710 TCCTTCGGGACGTATCCAGTGG
1 TCCTTCGGGACGTATCCAGTGG
* *
26732 TCCTTCGAGACGTATCTAGTGG
1 TCCTTCGGGACGTATCCAGTGG
26754 TCCTTCGGGACG
1 TCCTTCGGGACG
26766 AATACTAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (22 bp):
TCCTTCGGGACGTATCCAGTGG
Found at i:29027 original size:21 final size:21
Alignment explanation
Indices: 28997--29087 Score: 110
Period size: 21 Copynumber: 4.3 Consensus size: 21
28987 AAGTAGGGAA
* *
28997 AGAAGTAGCGGCAACAAAGAG
1 AGAAGCAGCGGCAACACAGAG
* *
29018 AGAAGCAGCGGCAGCATAGAG
1 AGAAGCAGCGGCAACACAGAG
*
29039 AGAAGCAGCGACAACACAGAG
1 AGAAGCAGCGGCAACACAGAG
* * *
29060 AGAAGCTGTGGCAGCACAGAG
1 AGAAGCAGCGGCAACACAGAG
29081 AGAAGCA
1 AGAAGCA
29088 ACATATCAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.43, C:0.19, G:0.34, T:0.04
Consensus pattern (21 bp):
AGAAGCAGCGGCAACACAGAG
Found at i:29043 original size:42 final size:42
Alignment explanation
Indices: 28997--29087 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
28987 AAGTAGGGAA
* * *
28997 AGAAGTAGCGGCAACAAAGAGAGAAGCAGCGGCAGCATAGAG
1 AGAAGCAGCGACAACAAAGAGAGAAGCAGCGGCAGCACAGAG
* * *
29039 AGAAGCAGCGACAACACAGAGAGAAGCTGTGGCAGCACAGAG
1 AGAAGCAGCGACAACAAAGAGAGAAGCAGCGGCAGCACAGAG
29081 AGAAGCA
1 AGAAGCA
29088 ACATATCAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.43, C:0.19, G:0.34, T:0.04
Consensus pattern (42 bp):
AGAAGCAGCGACAACAAAGAGAGAAGCAGCGGCAGCACAGAG
Found at i:29607 original size:43 final size:43
Alignment explanation
Indices: 29501--29671 Score: 141
Period size: 43 Copynumber: 4.0 Consensus size: 43
29491 CATTTTTAGC
* * * * *
29501 AAAAATGCCGCAAAACATCAAAACCTACACTGCGACATTTATG-G
1 AAAAACGCCGCAAAACATCAACACCT--ACTGCGGCGTTTGTGAG
*
29545 GAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTGTGAG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTGTGAG
* * ** *
29588 AAAAACGCCGCTAAACATCATA-ACCTATTATGGCGTTTGTCTA-
1 AAAAACGCCGCAAAACATCA-ACACCTACTGCGGCGTTTGT-GAG
* * * * *
29631 AAAAACGCCGCTAAATATCAACATCTATTGTGGCGTTTGTG
1 AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTGTG
29672 TATATCAATA
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 13 0.12
43 69 0.64
44 25 0.23
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.23
Consensus pattern (43 bp):
AAAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTGTGAG
Found at i:30552 original size:23 final size:23
Alignment explanation
Indices: 30521--30570 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
30511 TTTGATTTTT
*
30521 AAAACTATTACCAAGAAATATTG
1 AAAAATATTACCAAGAAATATTG
** *
30544 AAAAATATTACTTAGATATATTG
1 AAAAATATTACCAAGAAATATTG
30567 AAAA
1 AAAA
30571 TATCAAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (23 bp):
AAAAATATTACCAAGAAATATTG
Found at i:31438 original size:20 final size:20
Alignment explanation
Indices: 31426--31477 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
31416 TCCATACTCT
*
31426 TCCATAAGGTTCCACACTAC
1 TCCATAAGGTTCCAAACTAC
*
31446 TCTATAAGGTTCCAAACTAC
1 TCCATAAGGTTCCAAACTAC
*
31466 TCCAAAAGGTTC
1 TCCATAAGGTTC
31478 AACGCATCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.27
Consensus pattern (20 bp):
TCCATAAGGTTCCAAACTAC
Found at i:35787 original size:7 final size:7
Alignment explanation
Indices: 35775--35964 Score: 380
Period size: 7 Copynumber: 27.1 Consensus size: 7
35765 TAATTTAAGT
35775 GGTTTAG
1 GGTTTAG
35782 GGTTTAG
1 GGTTTAG
35789 GGTTTAG
1 GGTTTAG
35796 GGTTTAG
1 GGTTTAG
35803 GGTTTAG
1 GGTTTAG
35810 GGTTTAG
1 GGTTTAG
35817 GGTTTAG
1 GGTTTAG
35824 GGTTTAG
1 GGTTTAG
35831 GGTTTAG
1 GGTTTAG
35838 GGTTTAG
1 GGTTTAG
35845 GGTTTAG
1 GGTTTAG
35852 GGTTTAG
1 GGTTTAG
35859 GGTTTAG
1 GGTTTAG
35866 GGTTTAG
1 GGTTTAG
35873 GGTTTAG
1 GGTTTAG
35880 GGTTTAG
1 GGTTTAG
35887 GGTTTAG
1 GGTTTAG
35894 GGTTTAG
1 GGTTTAG
35901 GGTTTAG
1 GGTTTAG
35908 GGTTTAG
1 GGTTTAG
35915 GGTTTAG
1 GGTTTAG
35922 GGTTTAG
1 GGTTTAG
35929 GGTTTAG
1 GGTTTAG
35936 GGTTTAG
1 GGTTTAG
35943 GGTTTAG
1 GGTTTAG
35950 GGTTTAG
1 GGTTTAG
35957 GGTTTAG
1 GGTTTAG
35964 G
1 G
35965 CACCTCCACA
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 183 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:36093 original size:10 final size:10
Alignment explanation
Indices: 36054--36094 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
36044 AAAACTCTAC
*
36054 ACTCTTCCAC
1 ACTCTTCCAT
36064 ACTCTTCCAT
1 ACTCTTCCAT
*
36074 ATTCTTCCAT
1 ACTCTTCCAT
36084 ACTCTTCCAT
1 ACTCTTCCAT
36094 A
1 A
36095 AGGTTCCACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.22, C:0.39, G:0.00, T:0.39
Consensus pattern (10 bp):
ACTCTTCCAT
Found at i:36102 original size:40 final size:40
Alignment explanation
Indices: 36058--36145 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
36048 CTCTACACTC
** *
36058 TTCCACACT-CTTCCATATTCTTCCATACT-CTTCCATAAGG
1 TTCCACACTAC-TCCATAAGCTTCCACACTAC-TCCATAAGG
* *
36098 TTCCACACTACTCTATAAGGTTCCACACTACTCCATAAGG
1 TTCCACACTACTCCATAAGCTTCCACACTACTCCATAAGG
36138 TTCCACAC
1 TTCCACAC
36146 ATCTCCAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
40 39 0.95
41 2 0.05
ACGTcount: A:0.26, C:0.35, G:0.07, T:0.32
Consensus pattern (40 bp):
TTCCACACTACTCCATAAGCTTCCACACTACTCCATAAGG
Found at i:36152 original size:20 final size:20
Alignment explanation
Indices: 36089--36145 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
36079 TCCATACTCT
36089 TCCATAAGGTTCCACACTAC
1 TCCATAAGGTTCCACACTAC
*
36109 TCTATAAGGTTCCACACTAC
1 TCCATAAGGTTCCACACTAC
36129 TCCATAAGGTTCCACAC
1 TCCATAAGGTTCCACAC
36146 ATCTCCAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.33, G:0.11, T:0.26
Consensus pattern (20 bp):
TCCATAAGGTTCCACACTAC
Found at i:38140 original size:119 final size:119
Alignment explanation
Indices: 37928--38167 Score: 426
Period size: 119 Copynumber: 2.0 Consensus size: 119
37918 ATGGTAAAAT
* *
37928 AATCCAAATCAGATGCATGTTAAATCTGTAGGGTTACCACTAATAAGGGTTGTTTCAAGTGGTAA
1 AATCCAAATCAGATGCATGTTAAATCTGAAGGGTTACCACTAACAAGGGTTGTTTCAAGTGGTAA
* *
37993 ACAGTTTGCTATCATTTAAACAAGGTCTCAAGTTGGAGTCTTTGTGTATGCAGA
66 ACAGATTGCTATCATTTAAACAAGGTCTCAAGTTGGAGTATTTGTGTATGCAGA
*
38047 AATCCAAATCAGATGGATGTTAAATCTGAAGGGTTACCACTAACAAGGGTTGTTTCAAGTGGTAA
1 AATCCAAATCAGATGCATGTTAAATCTGAAGGGTTACCACTAACAAGGGTTGTTTCAAGTGGTAA
*
38112 ACAGATTGCTATCATTTAAACAATGTCTCAAGTTGGAGTATTTGTGTATGCAGA
66 ACAGATTGCTATCATTTAAACAAGGTCTCAAGTTGGAGTATTTGTGTATGCAGA
38166 AA
1 AA
38168 ATGCCTGTTG
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
119 115 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.32
Consensus pattern (119 bp):
AATCCAAATCAGATGCATGTTAAATCTGAAGGGTTACCACTAACAAGGGTTGTTTCAAGTGGTAA
ACAGATTGCTATCATTTAAACAAGGTCTCAAGTTGGAGTATTTGTGTATGCAGA
Found at i:40513 original size:29 final size:29
Alignment explanation
Indices: 40470--40557 Score: 104
Period size: 37 Copynumber: 2.8 Consensus size: 29
40460 TCTATTTGTT
40470 TCACTGAAAACATTTTTCGGAAAATGAAA
1 TCACTGAAAACATTTTTCGGAAAATGAAA
40499 TCACTGAAAATATTTTCGAATTTTTCGGAAAATGAAA
1 TCACTG-AAA-A----C--ATTTTTCGGAAAATGAAA
40536 TCACTGAAAACATTTTTCGGAA
1 TCACTGAAAACATTTTTCGGAA
40558 GAAAACATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
29 17 0.33
30 3 0.06
31 2 0.04
35 2 0.04
36 3 0.06
37 24 0.47
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (29 bp):
TCACTGAAAACATTTTTCGGAAAATGAAA
Found at i:40531 original size:37 final size:37
Alignment explanation
Indices: 40481--40551 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
40471 CACTGAAAAC
*
40481 ATTTTTCGGAAAATGAAATCACTGAAAATATTTTCGA
1 ATTTTTCGGAAAATGAAATCACTGAAAACATTTTCGA
40518 ATTTTTCGGAAAATGAAATCACTGAAAACATTTT
1 ATTTTTCGGAAAATGAAATCACTGAAAACATTTT
40552 TCGGAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (37 bp):
ATTTTTCGGAAAATGAAATCACTGAAAACATTTTCGA
Found at i:40563 original size:17 final size:17
Alignment explanation
Indices: 40541--40574 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40531 TGAAATCACT
40541 GAAAACATTTTTCGGAA
1 GAAAACATTTTTCGGAA
40558 GAAAACATTTTTCGGAA
1 GAAAACATTTTTCGGAA
40575 AATGAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (17 bp):
GAAAACATTTTTCGGAA
Found at i:43679 original size:21 final size:21
Alignment explanation
Indices: 43626--43683 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
43616 AACTAACCCA
*
43626 ATATAATTTTTTATAT-AATT
1 ATATAATTTTTTATTTAAATT
43646 -TATACATATTTTTATTTAAATT
1 ATATA-AT-TTTTTATTTAAATT
*
43668 ATATTATTTTTTATTT
1 ATATAATTTTTTATTT
43684 TTTTGAGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 17 0.53
22 6 0.19
23 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
ATATAATTTTTTATTTAAATT
Found at i:44597 original size:20 final size:20
Alignment explanation
Indices: 44572--44612 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
44562 TAGTTTTAAA
*
44572 TATAATTTTAAAAATAAATT
1 TATAATTTCAAAAATAAATT
44592 TATAATTTCAAAAATAAATT
1 TATAATTTCAAAAATAAATT
44612 T
1 T
44613 TGAAAATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAATTTCAAAAATAAATT
Found at i:46746 original size:18 final size:18
Alignment explanation
Indices: 46723--46762 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
46713 ATCCTCATCC
*
46723 TATCATT-ATCATTTTTAT
1 TATCATTCAT-ATTTCTAT
46741 TATCATTCATATTTCTAT
1 TATCATTCATATTTCTAT
46759 TATC
1 TATC
46763 TTGTTCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.28, C:0.15, G:0.00, T:0.57
Consensus pattern (18 bp):
TATCATTCATATTTCTAT
Found at i:53148 original size:2 final size:2
Alignment explanation
Indices: 53141--53165 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53131 ATTATTTAAC
53141 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
53166 TTTATTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53413 original size:23 final size:22
Alignment explanation
Indices: 53387--53464 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 22
53377 TTTGTACTCT
53387 TATTTATTTATTTAGTATGTATA
1 TATTTATTTATTTA-TATGTATA
*
53410 TA-TTATTTTATTATTTTAT-TATA
1 TATTTA-TTTA-T-TTATATGTATA
* *
53433 TATCTA-GTATTTATATGTATA
1 TATTTATTTATTTATATGTATA
*
53454 TATAT-TTTATT
1 TATTTATTTATT
53465 GTTTTACTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
20 5 0.12
21 13 0.30
22 5 0.12
23 12 0.28
24 6 0.14
25 2 0.05
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (22 bp):
TATTTATTTATTTATATGTATA
Found at i:53490 original size:40 final size:44
Alignment explanation
Indices: 53396--53494 Score: 109
Period size: 43 Copynumber: 2.3 Consensus size: 44
53386 TTATTTATTT
* *
53396 ATTTAGTATGTATATATTATTTTATTATTTTATTATATATCTAGT
1 ATTT-GTATGTATATATTATTTTATTATTTTACTATATATCTAGC
* *
53441 ATTTATATGTATATA-TATTTTATTGTTTTACT-T-TAT-T-GC
1 ATTTGTATGTATATATTATTTTATTATTTTACTATATATCTAGC
53480 ATGTTGTATGTATAT
1 AT-TTGTATGTATAT
53495 TCTACACACA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
39 3 0.06
40 12 0.25
41 3 0.06
42 1 0.02
43 15 0.31
44 10 0.21
45 4 0.08
ACGTcount: A:0.28, C:0.03, G:0.09, T:0.60
Consensus pattern (44 bp):
ATTTGTATGTATATATTATTTTATTATTTTACTATATATCTAGC
Found at i:54498 original size:27 final size:25
Alignment explanation
Indices: 54450--54505 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 25
54440 TGTCCCTATG
* * *
54450 TTTTTTCCTTTTTTTTTTTTTCTTC
1 TTTTTTCATTTTTTTTTATTTCTAC
54475 TTTTTTCATTTATTTATTTATTTCTAC
1 TTTTTTCATTT-TTT-TTTATTTCTAC
54502 TTTT
1 TTTT
54506 ACTAACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 10 0.38
26 3 0.12
27 13 0.50
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTTCATTTTTTTTTATTTCTAC
Done.