Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002978.1 Hibiscus syriacus cultivar Beakdansim tig00006157_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: 56596
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:11010 original size:60 final size:60
Alignment explanation
Indices: 10939--11068 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 60
10929 CGGTTAACTG
* *
10939 TCCCCAAACTATAACCCTCGTCT-TAAATT-GATCCTTAAACTTTTAAACATTCTAATTTCA
1 TCCCCAAACTATAACCCTC-TCTCTAAATTAG-TCCCTAAACATTTAAACATTCTAATTTCA
* * * * *
10999 TCCCCATACTATGACCCTCTTTCTAAATTAGTCCCTAAACATTTGAATATTCTAATTTCA
1 TCCCCAAACTATAACCCTCTCTCTAAATTAGTCCCTAAACATTTAAACATTCTAATTTCA
11059 TCCCCAAACT
1 TCCCCAAACT
11069 CATCCAAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.03
60 57 0.95
61 1 0.02
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (60 bp):
TCCCCAAACTATAACCCTCTCTCTAAATTAGTCCCTAAACATTTAAACATTCTAATTTCA
Found at i:11294 original size:60 final size:57
Alignment explanation
Indices: 11190--11378 Score: 164
Period size: 60 Copynumber: 3.2 Consensus size: 57
11180 TGTACGTATG
*
11190 GTTTGGGATGAAATTAGAATGTTCAAAAAGTTT-GTAACCAATTTAGAATAAGGGTCATA
1 GTTTGGGATGAAATTA-AATGTT-AAAAAGTTTAG-GACCAATTTAGAATAAGGGTCATA
* * ** *
11249 GTTTGGAGATGAAATTGAAATGTTAAAAAGTTTAAGGACCGATTTAGAATGATAGTCGTA
1 GTTTGG-GATGAAATT-AAATGTTAAAAAGTTT-AGGACCAATTTAGAATAAGGGTCATA
* * * * * *
11309 GTTTAGGGATGAAATCAAAATATTTAAAAGTTTAGGAATCAATTTAAAATAAGGGCCATA
1 GTTT-GGGATGAAAT-TAAATGTTAAAAAGTTTAGG-ACCAATTTAGAATAAGGGTCATA
*
11369 CTTTGAGGAT
1 GTTTG-GGAT
11379 ATGTCTAAAT
Statistics
Matches: 104, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
59 19 0.18
60 81 0.78
61 4 0.04
ACGTcount: A:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (57 bp):
GTTTGGGATGAAATTAAATGTTAAAAAGTTTAGGACCAATTTAGAATAAGGGTCATA
Found at i:11682 original size:2 final size:2
Alignment explanation
Indices: 11675--11699 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11665 AAATAAATAA
11675 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11700 ATTTTAAATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14991 original size:25 final size:25
Alignment explanation
Indices: 14957--15007 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
14947 ACTTCTGTAC
14957 TTATTTTTTGTTCCGTCTTAAGGAA
1 TTATTTTTTGTTCCGTCTTAAGGAA
14982 TTATTTTTTGTTCCGTCTTAAGGAA
1 TTATTTTTTGTTCCGTCTTAAGGAA
15007 T
1 T
15008 CTGAGGGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.53
Consensus pattern (25 bp):
TTATTTTTTGTTCCGTCTTAAGGAA
Found at i:15617 original size:20 final size:20
Alignment explanation
Indices: 15552--15801 Score: 229
Period size: 20 Copynumber: 12.5 Consensus size: 20
15542 CGATTTTCCA
* ** *
15552 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
15572 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
15592 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
15612 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
15632 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
15652 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
15672 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
15692 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
15712 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
15732 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
15752 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
15772 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
15792 AAATCACAAC
1 AAATCGCAAC
15802 ACTGAAATTT
Statistics
Matches: 195, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
20 194 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:16523 original size:24 final size:24
Alignment explanation
Indices: 16484--16530 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
16474 AAATTTGGTC
16484 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
16508 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
16531 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:16722 original size:12 final size:12
Alignment explanation
Indices: 16705--16729 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16695 ATATAATCCT
16705 GAAGAAGAAAAA
1 GAAGAAGAAAAA
16717 GAAGAAGAAAAA
1 GAAGAAGAAAAA
16729 G
1 G
16730 TCCCGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:19097 original size:19 final size:19
Alignment explanation
Indices: 19057--19173 Score: 181
Period size: 19 Copynumber: 6.4 Consensus size: 19
19047 GATTCTCTCG
19057 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
19077 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
19096 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
19110 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
19129 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
19148 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
19167 TTGCGAT
1 TTGCGAT
19174 AGTCAATTTT
Statistics
Matches: 90, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 6 0.07
16 7 0.08
17 7 0.08
19 55 0.61
20 15 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:19119 original size:33 final size:35
Alignment explanation
Indices: 19076--19173 Score: 146
Period size: 33 Copynumber: 2.8 Consensus size: 35
19066 TCATTTCCGC
19076 ATTGCGATTTTCATTTCGCATTGCGATTC-TCTCG
1 ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
*
19110 -TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCGCATTGCGA--TTCATCTCG
19146 CATTGCGATTTTCATTTCGCATTGCGAT
1 -ATTGCGATTTTCATTTCGCATTGCGAT
19174 AGTCAATTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
33 25 0.43
35 3 0.05
36 5 0.09
38 25 0.43
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (35 bp):
ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
Found at i:19151 original size:52 final size:53
Alignment explanation
Indices: 19038--19155 Score: 229
Period size: 53 Copynumber: 2.2 Consensus size: 53
19028 GAAATGAAAA
19038 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
19091 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
19143 TCGCATTGCGATT
1 TCGCATTGCGATT
19156 TTCATTTCGC
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 31 0.48
53 34 0.52
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:19288 original size:19 final size:19
Alignment explanation
Indices: 19232--19347 Score: 108
Period size: 19 Copynumber: 6.6 Consensus size: 19
19222 CCATTACATT
*
19232 TCGCGATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
19252 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
19266 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
19285 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
19304 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
19318 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
19337 TCGCATTGCGA
1 TCGCAATGCGA
19348 TTCTCCCATT
Statistics
Matches: 79, Mismatches: 7, Indels: 21
0.74 0.07 0.20
Matches are distributed among these distances:
14 20 0.25
15 2 0.03
16 4 0.05
17 3 0.04
18 3 0.04
19 42 0.53
20 5 0.06
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:19316 original size:52 final size:52
Alignment explanation
Indices: 19232--19347 Score: 196
Period size: 52 Copynumber: 2.2 Consensus size: 52
19222 CCATTACATT
*
19232 TCGCGATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
19285 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
19337 TCGCATTGCGA
1 TCGCAATGCGA
19348 TTCTCCCATT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 52 0.87
53 8 0.13
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:19396 original size:19 final size:19
Alignment explanation
Indices: 19354--19453 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
19344 GCGATTCTCC
19354 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
19374 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
19393 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
19409 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
19426 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
19445 CATTGCGAT
1 CATTGCGAT
19454 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:19450 original size:52 final size:53
Alignment explanation
Indices: 19337--19453 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
19327 GAAATTAAAA
19337 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
19390 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
19442 TCGCATTGCGAT
1 TCGCATTGCGAT
19454 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:19578 original size:14 final size:14
Alignment explanation
Indices: 19559--19595 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19549 CATCAATTAC
19559 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
19573 ACAAATCATCTTTT
1 ACAAATCAACTTTT
19587 ACAAATCAA
1 ACAAATCAA
19596 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:21593 original size:14 final size:14
Alignment explanation
Indices: 21574--21630 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
21564 GCGAAATGAA
*
21574 AATCGCAACGACAG
1 AATCGCAACGAAAG
21588 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
21605 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
21621 AATCGCAACG
1 AATCGCAACG
21631 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:21601 original size:33 final size:33
Alignment explanation
Indices: 21555--21643 Score: 160
Period size: 33 Copynumber: 2.7 Consensus size: 33
21545 GCGAAACCAA
*
21555 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
21588 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
21621 AATCGCAACGCGAAATGAAAATC
1 AATCGCAACGCGAAATGAAAATC
21644 ACAATGCGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:21652 original size:19 final size:19
Alignment explanation
Indices: 21518--21643 Score: 119
Period size: 19 Copynumber: 7.1 Consensus size: 19
21508 TAGTTTACTT
* *
21518 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
21538 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
21557 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
21576 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
21590 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
21609 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
21623 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
21642 TC
1 TC
21644 ACAATGCGAT
Statistics
Matches: 89, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
14 16 0.18
16 11 0.12
17 11 0.12
19 39 0.44
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:21670 original size:19 final size:19
Alignment explanation
Indices: 21648--21776 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
21638 AAAATCACAA
21648 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
21667 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
21681 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
21700 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
21714 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
21733 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
21752 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
21772 TGCGA
1 TGCGA
21777 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:21690 original size:33 final size:33
Alignment explanation
Indices: 21648--21739 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
21638 AAAATCACAA
21648 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
21681 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
21714 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
21740 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:22092 original size:93 final size:93
Alignment explanation
Indices: 21820--22199 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
21810 TTGAATGGAT
21820 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
21885 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
21913 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
21977 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
22005 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
22070 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
22098 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
22163 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
22191 AAATTTACT
1 AAATTTACT
22200 AAGCAATCTA
Statistics
Matches: 283, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 91 0.32
93 192 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:23979 original size:14 final size:14
Alignment explanation
Indices: 23960--24016 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
23950 TTTGGTTTCG
23960 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
23974 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
23993 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
24007 CGTTGCGATT
1 CGTTGCGATT
24017 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:23992 original size:33 final size:33
Alignment explanation
Indices: 23944--24024 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
23934 AAAATCGCAA
**
23944 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
23977 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
24010 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
24025 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:24047 original size:20 final size:20
Alignment explanation
Indices: 24000--24056 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
23990 TCGCGTTGCG
***
24000 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
24020 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGACAGTC
24041 ATTCTCTCGTTGCGAC
1 ATTCTCTCGTTGCGAC
24057 TCTTCTGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.12, C:0.28, G:0.18, T:0.42
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:24182 original size:33 final size:33
Alignment explanation
Indices: 24135--24205 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
24125 AATACTAACT
* *
24135 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
24168 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
24201 TGAAA
1 TGAAA
24206 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:24612 original size:20 final size:20
Alignment explanation
Indices: 24587--24740 Score: 211
Period size: 20 Copynumber: 7.7 Consensus size: 20
24577 CTTTAAATAT
24587 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
24607 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
24629 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
24648 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
24668 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
24688 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
24708 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
24728 CGCGTTGCGATTT
1 CGCGTTGCGATTT
24741 TCATATTTGC
Statistics
Matches: 115, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
19 2 0.02
20 97 0.84
21 14 0.12
22 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:24724 original size:60 final size:60
Alignment explanation
Indices: 24589--24760 Score: 220
Period size: 60 Copynumber: 2.9 Consensus size: 60
24579 TTAAATATCG
*** * *
24589 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACCCATTAGCGTTGCGATTTACGGATACA
* *
24650 CGTTGCGATATACGGATACGCATTGCGATTTACCCA-TACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACCCATTA-GCGTTGCGATTTACGGATACA
* ** *
24710 CGTTGCGATTTACGGATACGCGTTGCGATTTTCATATTTGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACCCATTAGCGTTGCGATTT
24761 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
59 2 0.02
60 67 0.70
61 27 0.28
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACCCATTAGCGTTGCGATTTACGGATACA
Found at i:24754 original size:40 final size:40
Alignment explanation
Indices: 24587--24760 Score: 190
Period size: 40 Copynumber: 4.3 Consensus size: 40
24577 CTTTAAATAT
*
24587 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTA-TGTATTA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTACAG-A-TA
* * *
24629 -TCGTTGCGATTTACGGATACGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATA
* ** *
24668 CGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATA
* * * *
24708 CACGTTGCGATTTACGGATACGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATA
*
24748 TGCGTTGCGATTT
1 CGCGTTGCGATTT
24761 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
39 2 0.02
40 81 0.72
41 29 0.26
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (40 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTACAGATA
Found at i:32168 original size:20 final size:20
Alignment explanation
Indices: 32143--32192 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
32133 ACCTTCACTC
32143 ATTTGATTTAATAATTAAAG
1 ATTTGATTTAATAATTAAAG
* *
32163 ATTTGATGTAATAGTTAAAG
1 ATTTGATTTAATAATTAAAG
*
32183 -TTTAATTTAA
1 ATTTGATTTAA
32193 ATTTTCTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTTGATTTAATAATTAAAG
Found at i:32670 original size:2 final size:2
Alignment explanation
Indices: 32663--32688 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32653 TAACACATGC
32663 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
32689 GATCAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53784 original size:117 final size:114
Alignment explanation
Indices: 53620--53874 Score: 307
Period size: 117 Copynumber: 2.2 Consensus size: 114
53610 CAAAAATATA
* * * * ** * * *
53620 GACGATAACATAGTCGGTTAATTATTAAAAATTTATTAATTACAATAATATATTATGTAGCGTTT
1 GACGATAACATAATCAGTTAATTACTAAAAATTTATCAAGCACAATAACATATTAGGTAGCGCTT
* *
53685 ATATAACGTAATAGGTAGCGCCTTGTTAAAACTGATGGAGCTTTAGAAATCC
66 ATATAACGTAATAGGTA--GCATTGTTAAAACTGATGG-GCTTTAAAAATCC
*
53737 GACGATAACATAATCAGTTAATTACTAGAAAA-TTATCAAGCATAATAACATATTAGGTAGCGCT
1 GACGATAACATAATCAGTTAATTACTA-AAAATTTATCAAGCACAATAACATATTAGGTAGCGCT
* * *
53801 TATATAACGTAATAGGTAGCATTTTTTAAACTGATGGGCTTTAAAAATTC
65 TATATAACGTAATAGGTAGCATTGTTAAAACTGATGGGCTTTAAAAATCC
*
53851 GACGATAACAAAAT-AGGTTAATTA
1 GACGATAACATAATCA-GTTAATTA
53875 TTGGATTTGT
Statistics
Matches: 120, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
113 1 0.01
114 32 0.27
115 16 0.13
117 67 0.56
118 4 0.03
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (114 bp):
GACGATAACATAATCAGTTAATTACTAAAAATTTATCAAGCACAATAACATATTAGGTAGCGCTT
ATATAACGTAATAGGTAGCATTGTTAAAACTGATGGGCTTTAAAAATCC
Done.