Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005351.1 Hibiscus syriacus cultivar Beakdansim tig00012148_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: 100932
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:432 original size:14 final size:15
Alignment explanation
Indices: 408--436 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
398 ACGAGGCTGG
408 AATTACAACAACAAC
1 AATTACAACAACAAC
423 AATT-CAACAACAAC
1 AATTACAACAACAAC
437 TATGAGAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:3800 original size:28 final size:29
Alignment explanation
Indices: 3763--3844 Score: 114
Period size: 29 Copynumber: 2.8 Consensus size: 29
3753 CAAACTAAAT
*
3763 TGATGTCATTACTTACATCA-TTAAGTAAA
1 TGATGTCATTGCTTACATCATTTAAGT-AA
*
3792 T-ATGTCATTGCTTACATTATTTAAGTAA
1 TGATGTCATTGCTTACATCATTTAAGTAA
3820 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
3845 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
28 19 0.40
29 23 0.49
30 5 0.11
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAAGTAA
Found at i:16217 original size:15 final size:16
Alignment explanation
Indices: 16180--16218 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
16170 CATAGCCTCC
*
16180 GAATCATTCATCATTT
1 GAATCATTCAGCATTT
*
16196 GAATCATTCAGCGTTT
1 GAATCATTCAGCATTT
16212 -AATCATT
1 GAATCATT
16219 ATGAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (16 bp):
GAATCATTCAGCATTT
Found at i:30789 original size:59 final size:59
Alignment explanation
Indices: 30670--30801 Score: 155
Period size: 59 Copynumber: 2.2 Consensus size: 59
30660 AATTTAAGGG
* * *
30670 TAAAAG-TACACAAATGATCACTGACTATAGGGTGTTGTTTAGTTAAGTCCCTCGATTAT
1 TAAAAGTTACA-AAATGATCACTGACTATAGGGCGTCGTTTAGTTAAGTCCCTCGACTAT
*
30729 TAAAAGTTACAAAATGATC-CTTCGACTATAGGGCGTCGCTTTA-TTGAGTCCC-CGACTAT
1 TAAAAGTTACAAAATGATCAC-T-GACTATAGGGCGTCG-TTTAGTTAAGTCCCTCGACTAT
*
30788 TAAAATTTACAAAA
1 TAAAAGTTACAAAA
30802 ATGGTCACCC
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
58 1 0.02
59 34 0.53
60 25 0.39
61 4 0.06
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (59 bp):
TAAAAGTTACAAAATGATCACTGACTATAGGGCGTCGTTTAGTTAAGTCCCTCGACTAT
Found at i:30803 original size:60 final size:60
Alignment explanation
Indices: 30670--30809 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 60
30660 AATTTAAGGG
* * * *
30670 TAAAAG-TACACAAATGATCACTGACTATAGGGTGTTGTTTAGTTAAGTCCCTCGATTAT
1 TAAAAGTTACAAAAATGATCACTGACTATAGGGCGTCGTTTAGTTAAGTCCCTCGACTAT
*
30729 TAAAAGTTAC-AAAATGATC-CTTCGACTATAGGGCGTCGCTTTA-TTGAGTCCC-CGACTAT
1 TAAAAGTTACAAAAATGATCAC-T-GACTATAGGGCGTCG-TTTAGTTAAGTCCCTCGACTAT
* *
30788 TAAAATTTACAAAAATGGTCAC
1 TAAAAGTTACAAAAATGATCAC
30810 CCGACTATTC
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
58 1 0.01
59 30 0.44
60 32 0.47
61 5 0.07
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (60 bp):
TAAAAGTTACAAAAATGATCACTGACTATAGGGCGTCGTTTAGTTAAGTCCCTCGACTAT
Found at i:31239 original size:2 final size:2
Alignment explanation
Indices: 31232--31292 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
31222 AGAATAGCTT
31232 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31274 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
31293 GGGCAAGATC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33127 original size:16 final size:16
Alignment explanation
Indices: 33102--33134 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
33092 TTTAGGGAAT
33102 ATAACCAATAAAATAA
1 ATAACCAATAAAATAA
*
33118 ATAACTAATAAAATAA
1 ATAACCAATAAAATAA
33134 A
1 A
33135 ATTCGGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (16 bp):
ATAACCAATAAAATAA
Found at i:35399 original size:31 final size:31
Alignment explanation
Indices: 35363--35421 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
35353 AACTTAAAAG
* *
35363 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
35394 AGTTTTACAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
35422 CTATGCAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:35475 original size:22 final size:22
Alignment explanation
Indices: 35447--35488 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
35437 AATAATTTTC
*
35447 TTAAAATAAATCAATCCATATT
1 TTAAAATAAATCAATACATATT
35469 TTAAAATAAATCAATACATA
1 TTAAAATAAATCAATACATA
35489 CTAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAAATAAATCAATACATATT
Found at i:35499 original size:22 final size:22
Alignment explanation
Indices: 35449--35501 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
35439 TAATTTTCTT
* * *
35449 AAAATAAATCAATCCATATTTT
1 AAAATAAATCAATACATATCTA
35471 AAAATAAATCAATACATA-CTA
1 AAAATAAATCAATACATATCTA
35492 AAATATAAAT
1 AAA-ATAAAT
35502 TAGTTTACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAATAAATCAATACATATCTA
Found at i:37037 original size:16 final size:16
Alignment explanation
Indices: 37018--37051 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
37008 AATAAATAAT
*
37018 ATATAAAAAATTTAAA
1 ATATAAAAAAATTAAA
37034 ATATAAAAAAATTAAA
1 ATATAAAAAAATTAAA
37050 AT
1 AT
37052 TTTTAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATATAAAAAAATTAAA
Found at i:37900 original size:26 final size:26
Alignment explanation
Indices: 37864--37917 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
37854 AGATAAGGTC
37864 CATGTCACCAAAATAAAGTCAACTTG
1 CATGTCACCAAAATAAAGTCAACTTG
37890 CATGTCACCAAAATAAAGTCAACTTG
1 CATGTCACCAAAATAAAGTCAACTTG
37916 CA
1 CA
37918 AAATAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.24, G:0.11, T:0.22
Consensus pattern (26 bp):
CATGTCACCAAAATAAAGTCAACTTG
Found at i:39187 original size:19 final size:19
Alignment explanation
Indices: 39143--39179 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39133 CGGTCAACGG
*
39143 TCGGCTCGGGTCGATCGGA
1 TCGGGTCGGGTCGATCGGA
39162 TCGGGTCGGGTCGATCGG
1 TCGGGTCGGGTCGATCGG
39180 GTTGGGTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.24, G:0.46, T:0.22
Consensus pattern (19 bp):
TCGGGTCGGGTCGATCGGA
Found at i:41659 original size:2 final size:2
Alignment explanation
Indices: 41654--41683 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41644 CACTAGTATC
41654 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41684 TCACTTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:42200 original size:26 final size:26
Alignment explanation
Indices: 42162--42221 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
42152 CATGTCTTAT
* *
42162 TTTTTACGTTAATATCGCATTAGTTA
1 TTTTTCCGATAATATCGCATTAGTTA
*
42188 TTTTTCCGATAATATCGCGTTAGTTA
1 TTTTTCCGATAATATCGCATTAGTTA
42214 TTTTTCCG
1 TTTTTCCG
42222 CTTATGAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.50
Consensus pattern (26 bp):
TTTTTCCGATAATATCGCATTAGTTA
Found at i:48836 original size:4 final size:4
Alignment explanation
Indices: 48800--48853 Score: 55
Period size: 4 Copynumber: 14.8 Consensus size: 4
48790 AAATAATTGT
* *
48800 AATA TATA AATT AAT- AAT- AAT- AAT- AAT- AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
48843 AATA AATA AAT
1 AATA AATA AAT
48854 GTTTTAAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
3 15 0.33
4 31 0.67
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
AATA
Found at i:48842 original size:24 final size:25
Alignment explanation
Indices: 48790--48843 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
48780 TCGGCCTACA
** *
48790 AAATAATTGTAATATATAAATTAAT
1 AAATAATAATAATATATAAATAAAT
48815 -AATAATAATAATA-ATAAATAAAT
1 AAATAATAATAATATATAAATAAAT
48838 AAATAA
1 AAATAA
48844 ATAAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATAATAATAATATATAAATAAAT
Found at i:48951 original size:2 final size:2
Alignment explanation
Indices: 48942--48994 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
48932 TTTTAAAAAC
*
48942 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
48983 TA TA TA TG TA TA
1 TA TA TA TA TA TA
48995 AAATAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:49481 original size:2 final size:2
Alignment explanation
Indices: 49474--49520 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
49464 AATTCTATGA
49474 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
49516 AT AT A
1 AT AT A
49521 ATGGCCAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56012 original size:2 final size:2
Alignment explanation
Indices: 56005--56036 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55995 TCCTCCGTAC
56005 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
56037 CCCAACGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61577 original size:4 final size:4
Alignment explanation
Indices: 61568--61600 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
61558 CAACATCTAC
*
61568 ACAT ACAT ACAT ACAT ACAT ATAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
61601 AGTTTATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:65068 original size:16 final size:16
Alignment explanation
Indices: 65049--65110 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
65039 GAAAGCAAGC
65049 CGAACCGAAATTAACT
1 CGAACCGAAATTAACT
* *
65065 CGAATCGAAATTAACC
1 CGAACCGAAATTAACT
* **
65081 CGAACTGAAAACAACT
1 CGAACCGAAATTAACT
*
65097 CGAACCAAAATTAA
1 CGAACCGAAATTAA
65111 TCTGAATCAA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.48, C:0.24, G:0.11, T:0.16
Consensus pattern (16 bp):
CGAACCGAAATTAACT
Found at i:65084 original size:32 final size:32
Alignment explanation
Indices: 65048--65110 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
65038 TGAAAGCAAG
** * *
65048 CCGAACCGAAATTAACTCGAATCGAAATTAAC
1 CCGAACCGAAAACAACTCGAACCAAAATTAAC
*
65080 CCGAACTGAAAACAACTCGAACCAAAATTAA
1 CCGAACCGAAAACAACTCGAACCAAAATTAA
65111 TCTGAATCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.25, G:0.11, T:0.16
Consensus pattern (32 bp):
CCGAACCGAAAACAACTCGAACCAAAATTAAC
Found at i:65130 original size:48 final size:47
Alignment explanation
Indices: 65019--65139 Score: 129
Period size: 48 Copynumber: 2.5 Consensus size: 47
65009 ATTTGACCCC
* * * *
65019 AATCGAAAATAACCCAAAATGAAAGCAAGCCGAACCGAAATTAACTCG
1 AATC-AAAATAACCCGAACTGAAAACAAGCCGAACCAAAATTAACTCG
*
65067 AATCGAAATTAACCCGAACTGAAAACAA-CTCGAACCAAAATTAA-TCTG
1 AATC-AAAATAACCCGAACTGAAAACAAGC-CGAACCAAAATTAACTC-G
*
65115 AATCAAAAGTAACCCGAACTAAAAA
1 AATCAAAA-TAACCCGAACTGAAAA
65140 ATAGCCCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
47 6 0.10
48 57 0.90
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.15
Consensus pattern (47 bp):
AATCAAAATAACCCGAACTGAAAACAAGCCGAACCAAAATTAACTCG
Found at i:72752 original size:17 final size:17
Alignment explanation
Indices: 72730--72762 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
72720 ACACATAATT
*
72730 ATAAATTAGTTAAAATG
1 ATAAATTAATTAAAATG
72747 ATAAATTAATTAAAAT
1 ATAAATTAATTAAAAT
72763 AAAATATTAT
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:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAAATTAATTAAAATG
Found at i:73267 original size:2 final size:2
Alignment explanation
Indices: 73260--73284 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
73250 ATAAAGAAAT
73260 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
73285 CAATTATGTT
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:82770 original size:15 final size:15
Alignment explanation
Indices: 82747--82783 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
82737 GTTCACTCGT
*
82747 CATTTCTATTTAAGC
1 CATTCCTATTTAAGC
82762 CATTCCTATTTAAGC
1 CATTCCTATTTAAGC
82777 CATTCCT
1 CATTCCT
82784 GAACTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.43
Consensus pattern (15 bp):
CATTCCTATTTAAGC
Found at i:87807 original size:26 final size:26
Alignment explanation
Indices: 87771--87830 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
87761 TCTTGCTCCA
*
87771 AAATTTTGCAATTCGGTATAATGGGC
1 AAATTTAGCAATTCGGTATAATGGGC
* *
87797 AAATTTAGCAATTGGGTATGATGGGC
1 AAATTTAGCAATTCGGTATAATGGGC
87823 AGAATTTA
1 A-AATTTA
87831 TATTCGGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 24 0.80
27 6 0.20
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (26 bp):
AAATTTAGCAATTCGGTATAATGGGC
Found at i:92556 original size:21 final size:21
Alignment explanation
Indices: 92529--92585 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
92519 ACGGTCGTGA
* * *
92529 ATTTTTTAATAA-AAGATTTG
1 ATTTTTTTATAACAAAATCTG
92549 ATTTTTTTATAACAAAATCTG
1 ATTTTTTTATAACAAAATCTG
*
92570 ATTTTTTT-TAAAAAAA
1 ATTTTTTTATAACAAAA
92586 AAATAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (21 bp):
ATTTTTTTATAACAAAATCTG
Found at i:92585 original size:20 final size:20
Alignment explanation
Indices: 92530--92585 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 20
92520 CGGTCGTGAA
*
92530 TTTTTTAATAAAAGATTTGATT
1 TTTTTTAA-AAAA-ATCTGATT
*
92552 TTTTTATAACAAAATCTGATT
1 TTTTT-TAAAAAAATCTGATT
92573 TTTTTTAAAAAAA
1 TTTTTTAAAAAAA
92586 AAATAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
22 8 0.27
23 3 0.10
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTTTAAAAAAATCTGATT
Found at i:93637 original size:19 final size:19
Alignment explanation
Indices: 93584--93637 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
93574 TCGTTAGAAA
93584 AAATAAATATATCAATAAAAT
1 AAATAAAT-TAT-AATAAAAT
* *
93605 ATAAT-TATTTTAATAAAAT
1 A-AATAAATTATAATAAAAT
93624 AAATAAATTATAAT
1 AAATAAATTATAAT
93638 CCTGAAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 3 0.11
19 16 0.59
20 2 0.07
21 3 0.11
22 3 0.11
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATAAATTATAATAAAAT
Found at i:98322 original size:22 final size:21
Alignment explanation
Indices: 98294--98339 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
98284 CCGGAAATAT
* * *
98294 TAAAAAACATTAATGTTTTAGG
1 TAAAAAA-AATAAAGTTTTAAG
98316 TAAAAAAAATAAAGTTTTAAG
1 TAAAAAAAATAAAGTTTTAAG
98337 TAA
1 TAA
98340 TTTTTTACCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.33
Consensus pattern (21 bp):
TAAAAAAAATAAAGTTTTAAG
Done.