Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002379.1 Hibiscus syriacus cultivar Beakdansim tig00004863_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: 75272
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3817 original size:74 final size:76
Alignment explanation
Indices: 3647--3852 Score: 265
Period size: 75 Copynumber: 2.7 Consensus size: 76
3637 CCGTTGTACA
* * * * *
3647 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
** *
3711 CAAAACTGTTT
66 CAAAACCATTC
*
3722 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
*
3786 CCAAACCATTC
66 CAAAACCATTC
** *
3797 A-GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTATGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAA
3853 TTTTTGGCTT
Statistics
Matches: 115, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
74 21 0.18
75 64 0.56
76 30 0.26
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAA
CAAAACCATTC
Found at i:4911 original size:15 final size:16
Alignment explanation
Indices: 4891--4920 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4881 TTAAGATATT
4891 TTAAAA-AATTTTAAC
1 TTAAAATAATTTTAAC
4906 TTAAAATAATTTTAA
1 TTAAAATAATTTTAA
4921 GAAGAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAAAATAATTTTAAC
Found at i:6361 original size:3 final size:3
Alignment explanation
Indices: 6353--6377 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6343 TAAATGGGTG
6353 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
6378 CTTGGAGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:7229 original size:15 final size:16
Alignment explanation
Indices: 7203--7242 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7193 CTTTTGATAT
*
7203 AAAATCAAAATTAAAG
1 AAAATGAAAATTAAAG
*
7219 AAAA-GAAAATTAAAT
1 AAAATGAAAATTAAAG
7234 AAAATGAAA
1 AAAATGAAA
7243 TGAAATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.17
Consensus pattern (16 bp):
AAAATGAAAATTAAAG
Found at i:13512 original size:21 final size:21
Alignment explanation
Indices: 13444--13513 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
13434 CAATTCCCAT
*
13444 AATCGCGTTGCGATTATGA-AG
1 AATCGCATTGCGATTAT-ACAG
*
13465 AATCGCAATGCGA-TAGTACA-
1 AATCGCATTGCGATTA-TACAG
* *
13485 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCATTGCGATTATACAG
13507 AATCGCA
1 AATCGCA
13514 ACGCGAACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 5 0.13
21 31 0.79
22 3 0.08
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (21 bp):
AATCGCATTGCGATTATACAG
Found at i:13592 original size:20 final size:20
Alignment explanation
Indices: 13548--13796 Score: 238
Period size: 20 Copynumber: 12.4 Consensus size: 20
13538 GATTCTGACT
* * *
13548 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGAATACGT-AA
* * *
13569 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGAATACGTAA
13589 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGAATACGT-AA
* *
13610 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGAATACGTAA
*
13630 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGAATACGTAA
*
13650 ATCGCAACGCGTAT-CTGTAA
1 ATCGCAACGCGAATAC-GTAA
*
13670 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGAATACGTAA
* * * *
13690 ATCGCAATGTGTATCCGTAA
1 ATCGCAACGCGAATACGTAA
*
13710 ATCGCAA--CGATTACGTAA
1 ATCGCAACGCGAATACGTAA
* *
13728 ATCGCAATGCGATTACGTAA
1 ATCGCAACGCGAATACGTAA
*
13748 ATCGCAATGCGAATACGTAA
1 ATCGCAACGCGAATACGTAA
*
13768 ATCGCAATGCGAAT-CTGTAA
1 ATCGCAACGCGAATAC-GTAA
13788 ATCGCAACG
1 ATCGCAACG
13797 AGATTCTGAC
Statistics
Matches: 196, Mismatches: 24, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
18 14 0.07
19 2 0.01
20 146 0.74
21 34 0.17
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAATACGTAA
Found at i:13663 original size:40 final size:40
Alignment explanation
Indices: 13548--13799 Score: 339
Period size: 40 Copynumber: 6.3 Consensus size: 40
13538 GATTCTGACT
* *
13548 ATCGCAACGAGTATCCGTAAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
* *
13589 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
* *
13630 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
*
13670 ATCGCAACGAGAATACGTAAATCGCAATGTGTATCCGTAA
1 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
* *
13710 ATCGCAAC--GATTACGTAAATCGCAATGCG-ATTACGTAA
1 ATCGCAACGAGAATACGTAAATCGCAATGCGTA-TCCGTAA
* * * *
13748 ATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
13788 ATCGCAACGAGA
1 ATCGCAACGAGA
13800 TTCTGACTAT
Statistics
Matches: 189, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
37 1 0.01
38 32 0.17
40 101 0.53
41 55 0.29
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
Found at i:13767 original size:118 final size:120
Alignment explanation
Indices: 13507--13799 Score: 380
Period size: 118 Copynumber: 2.4 Consensus size: 120
13497 GATTTTCCAG
* ** * * *
13507 AATCGCAACGCGAACATATAAATCGCAACGCGATTCTG-ACTATCGCAACGAGTATCCGTAAAAT
1 AATCGCAACGCGAATACGTAAATCGCAACGCGA-TCTGTA-AATCGCAACGAGAATACGTAAAAT
*
13571 CGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
64 CGCAATGCGTATCCGTAAATCGCAACGA-AATACGTAAAATCGCAACGCGTATACGTA
*
13629 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT-AAATC
1 AATCGCAACGCGAATACGTAAATCGCAACGCG-ATCTGTAAATCGCAACGAGAATACGTAAAATC
* * *
13693 GCAATGTGTATCCGTAAATCGCAACG-ATTACGT-AAATCGCAATGCG-ATTACGTA
65 GCAATGCGTATCCGTAAATCGCAACGAAATACGTAAAATCGCAACGCGTA-TACGTA
* *
13747 AATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAAATCGCAACGAGA
1 AATCGCAACGCGAATACGTAAATCGCAACGCG-ATCTGTAAATCGCAACGAGA
13800 TTCTGACTAT
Statistics
Matches: 153, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
117 1 0.01
118 66 0.43
119 6 0.04
121 30 0.20
122 48 0.31
123 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (120 bp):
AATCGCAACGCGAATACGTAAATCGCAACGCGATCTGTAAATCGCAACGAGAATACGTAAAATCG
CAATGCGTATCCGTAAATCGCAACGAAATACGTAAAATCGCAACGCGTATACGTA
Found at i:13804 original size:20 final size:19
Alignment explanation
Indices: 13525--13802 Score: 161
Period size: 20 Copynumber: 13.9 Consensus size: 19
13515 CGCGAACATA
*
13525 TAAATCGCAACGCGATTC-
1 TAAATCGCAACGAGATTCG
* *
13543 TGACTATCGCAACGAGTATCCG
1 T-A-AATCGCAACGAG-ATTCG
* * *
13565 TAAAATCGCAATGCGTATCCG
1 T-AAATCGCAACGAG-ATTCG
* *
13586 TAAATCGCAACGACAATACG
1 TAAATCGCAACGA-GATTCG
* *
13606 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGAG-ATTCG
*
13627 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGAG-ATTCG
*
13647 TAAATCGCAACGCG-TATCTG
1 TAAATCGCAACGAGAT-TC-G
*
13667 TAAATCGCAACGAGAATACG
1 TAAATCGCAACGAG-ATTCG
* * *
13687 TAAATCGCAATGTGTATCCG
1 TAAATCGCAACGAG-ATTCG
13707 TAAATCGCAAC--GATTACG
1 TAAATCGCAACGAGATT-CG
* *
13725 TAAATCGCAATGCGATTACG
1 TAAATCGCAACGAGATT-CG
*
13745 TAAATCGCAATGCGA-ATACG
1 TAAATCGCAA--CGAGATTCG
* * *
13765 TAAATCGCAATGCGAATCTG
1 TAAATCGCAACGAGATTC-G
13785 TAAATCGCAACGAGATTC
1 TAAATCGCAACGAGATTC
13803 TGACTATCGC
Statistics
Matches: 204, Mismatches: 38, Indels: 34
0.74 0.14 0.12
Matches are distributed among these distances:
17 2 0.01
18 16 0.08
19 4 0.02
20 140 0.69
21 38 0.19
22 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (19 bp):
TAAATCGCAACGAGATTCG
Found at i:14468 original size:33 final size:32
Alignment explanation
Indices: 14426--14509 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 32
14416 CAACGAGTGA
* *
14426 CGTTACGATTTCATTTTCGCATTGTGATTCACT
1 CGTTGCGATTTCA-TTTCGCATTGCGATTCACT
*
14459 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGA-TTTCATTTCGCATTGCGATTCACT
*
14492 CGTTGCGATAGTCATTTC
1 CGTTGCGAT-TTCATTTC
14510 CGCGTTGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 39 0.87
34 5 0.11
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTCATTTCGCATTGCGATTCACT
Found at i:16108 original size:42 final size:42
Alignment explanation
Indices: 16029--16119 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
16019 CCTCTTCAAC
* * *
16029 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
16071 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
16113 GATGACA
1 GATGACA
16120 AGTGAGTCGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:16624 original size:20 final size:20
Alignment explanation
Indices: 16601--16648 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
16591 GAAACTTAAA
16601 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
16621 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
16641 ATCGCAAC
1 ATCGCAAC
16649 AAGAGAATCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:16704 original size:19 final size:19
Alignment explanation
Indices: 16682--16725 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
16672 AAATCGCAAC
*
16682 GCGATTAT-AGTTTCGCGTT
1 GCGATTATCA-TTTCACGTT
*
16701 GCGATTTTCATTTCACGTT
1 GCGATTATCATTTCACGTT
16720 GCGATT
1 GCGATT
16726 TTGTCGTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.16, C:0.18, G:0.23, T:0.43
Consensus pattern (19 bp):
GCGATTATCATTTCACGTT
Found at i:16740 original size:33 final size:33
Alignment explanation
Indices: 16697--16788 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
16687 TATAGTTTCG
* * *
16697 CGTTGCGATTTTCATTTCACGTTGCGATTTTGT
1 CGTTGTGATTTTCATTTCACGTTGCGATTCTCT
* *
16730 CGTTGTGATTTTCATTTCTCGTTACGATTCTCT
1 CGTTGTGATTTTCATTTCACGTTGCGATTCTCT
16763 CGTTGTGA--TTCATTTCGA-GTTGCGAT
1 CGTTGTGATTTTCATTTC-ACGTTGCGAT
16789 AGTCATTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
31 15 0.29
33 36 0.71
ACGTcount: A:0.13, C:0.18, G:0.21, T:0.48
Consensus pattern (33 bp):
CGTTGTGATTTTCATTTCACGTTGCGATTCTCT
Found at i:16990 original size:94 final size:93
Alignment explanation
Indices: 16876--17243 Score: 524
Period size: 94 Copynumber: 4.1 Consensus size: 93
16866 ATGGATTGCA
* * *
16876 TTACTTCAGCCAAAAGACAAAACAAAGACAAATACTAACTTCAAAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
16941 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
16969 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
17034 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
17063 TTAATTTCAACCAAAAGACAAAACAAAGACAAATATTACCTTCACAGTGTTAAAGAATACACAGT
1 TT-ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
17128 TTAGCAGAATTGGCAGCAATCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
17157 TTACTTCAA-C------C---A-AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
* * *
17211 TAGCAGTATTGGCAGCAACTGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
17239 TTACT
1 TTACT
17244 AAGCAATCTA
Statistics
Matches: 257, Mismatches: 16, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
82 68 0.26
83 1 0.00
86 1 0.00
92 1 0.00
93 10 0.04
94 175 0.68
95 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:17224 original size:82 final size:82
Alignment explanation
Indices: 17087--17243 Score: 253
Period size: 82 Copynumber: 1.9 Consensus size: 82
17077 AAGACAAAAC
* * *
17087 AAAGACAAATATTACCTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAA-TCGA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACT-GA
17151 ATAAATTTACTTCAACCA
65 ATAAATTTACTTCAACCA
* *
17169 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATAGTTTAGCAGTATTGGCAGCAACTGAA
1 AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACTGAA
17234 TAAATTTACT
66 TAAATTTACT
17244 AAGCAATCTA
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
82 68 0.99
83 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (82 bp):
AAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGCAGAATTGGCAGCAACTGAA
TAAATTTACTTCAACCA
Found at i:18960 original size:20 final size:20
Alignment explanation
Indices: 18937--18992 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
18927 TGAAATGAAA
18937 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
18957 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
18977 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
18993 CGTAACGCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:19102 original size:40 final size:40
Alignment explanation
Indices: 19044--19135 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
19034 GTTGCGATTA
* **
19044 TCTCGTTGAGATTTTCA-TTTCGCGTTGCGATTTTCATTT
1 TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTT
*
19083 CTCTCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTT
1 -TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTT
19124 TCAT-GTTGCGAT
1 TC-TCGTTGCGAT
19136 TTTAAGTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 24 0.52
41 22 0.48
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (40 bp):
TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTT
Found at i:19113 original size:20 final size:20
Alignment explanation
Indices: 19048--19138 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
19038 CGATTATCTC
* *
19048 GTTGAGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
19067 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
**
19087 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
*
19108 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
19128 GTTGCGATTTT
1 GTTGCGATTTT
19139 AAGTTTAGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
19 12 0.20
20 32 0.52
21 17 0.28
ACGTcount: A:0.13, C:0.16, G:0.20, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:19721 original size:20 final size:20
Alignment explanation
Indices: 19696--19868 Score: 177
Period size: 20 Copynumber: 8.6 Consensus size: 20
19686 CTTTAAAAAT
*
19696 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
* *
19716 CGCGTTACGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
19736 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
19757 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
19777 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
19797 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
19817 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
19837 CGCGTTGGGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
* *
19858 CTCGTTACGAT
1 CGCGTTGCGAT
19869 AGTCAGAATC
Statistics
Matches: 122, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
20 90 0.74
21 32 0.26
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:19782 original size:40 final size:41
Alignment explanation
Indices: 19698--19868 Score: 247
Period size: 40 Copynumber: 4.2 Consensus size: 41
19688 TTAAAAATCG
* * *
19698 CGTTGCGATTTATGGATACGCGTTACGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
19739 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
19779 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
19819 CGTTGCGATTTACGGATACGCGTTGGGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
19860 CGTTACGAT
1 CGTTGCGAT
19869 AGTCAGAATC
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 75 0.64
41 43 0.36
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:19904 original size:81 final size:80
Alignment explanation
Indices: 19712--19910 Score: 195
Period size: 81 Copynumber: 2.5 Consensus size: 80
19702 GCGATTTATG
* * * ** * *
19712 GATACGCGTTACGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATTGCGATTTACGTATT
1 GATACACGTTGCGA-TTTACATATTCACGTTGCGATTTACGGATACGCATTGCGATTTACGGATA
* *
19777 CTCGTTGCGATTTACA
65 CTCGTTACGATGTACA
* * * * *
19793 GATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGGGATTTTACGGATA
1 GATACACGTTGCGATTTACATATTCACGTTGCGATTTACGGATACGCATTGCGA-TTTACGGATA
19858 CTCGTTACGATAGT-CA
65 CTCGTTACGAT-GTACA
* * *
19874 GA-ATCACGTTGTGATTTATATGTTCACGTTGCGATTT
1 GATA-CACGTTGCGATTTACATATTCACGTTGCGATTT
19911 TTATATTCGC
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
80 38 0.38
81 62 0.61
82 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (80 bp):
GATACACGTTGCGATTTACATATTCACGTTGCGATTTACGGATACGCATTGCGATTTACGGATAC
TCGTTACGATGTACA
Found at i:19916 original size:22 final size:20
Alignment explanation
Indices: 19877--19929 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
19867 ATAGTCAGAA
* * *
19877 TCACGTTGTGATTTATATGT
1 TCACGTTGCGATTTTTATAT
19897 TCACGTTGCGATTTTTATAT
1 TCACGTTGCGATTTTTATAT
*
19917 TCGCGTTGCGATT
1 TCACGTTGCGATT
19930 CTGGAAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (20 bp):
TCACGTTGCGATTTTTATAT
Found at i:22791 original size:90 final size:90
Alignment explanation
Indices: 22638--22817 Score: 315
Period size: 90 Copynumber: 2.0 Consensus size: 90
22628 GATTCGTATT
*
22638 GCTGCAGATCCAGAAGGTATTGCAAATGCACAGAAATCACTAGGGTTGGGACAGGAAGAAAAGGC
1 GCTGCAGATCCAGAAGGTATTGCAAATGCACAGAAATCACTAGGGTTGGAACAGGAAGAAAAGGC
*
22703 TTGTCGTGTACGCTAACTAGATGAA
66 TCGTCGTGTACGCTAACTAGATGAA
* *
22728 GCTGCAGGTCCAGAAGGTATTGCAAATGCACGGAAATCACTAGGGTTGGAACAGGAAGAAAAGGC
1 GCTGCAGATCCAGAAGGTATTGCAAATGCACAGAAATCACTAGGGTTGGAACAGGAAGAAAAGGC
*
22793 TCGTTGTGTACGCTAACTAGATGAA
66 TCGTCGTGTACGCTAACTAGATGAA
22818 ACCGACTTTT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 85 1.00
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (90 bp):
GCTGCAGATCCAGAAGGTATTGCAAATGCACAGAAATCACTAGGGTTGGAACAGGAAGAAAAGGC
TCGTCGTGTACGCTAACTAGATGAA
Found at i:28350 original size:28 final size:29
Alignment explanation
Indices: 28309--28363 Score: 87
Period size: 27 Copynumber: 1.9 Consensus size: 29
28299 AATGTTCAAA
28309 ATTTTATTTTAAAAAAAAT-TAAAATTAT
1 ATTTTATTTTAAAAAAAATCTAAAATTAT
28337 ATTTT-TTTTAAAAACAAATCTAAAATT
1 ATTTTATTTTAAAAA-AAATCTAAAATT
28364 TTCAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 9 0.36
28 9 0.36
29 7 0.28
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (29 bp):
ATTTTATTTTAAAAAAAATCTAAAATTAT
Found at i:32585 original size:18 final size:18
Alignment explanation
Indices: 32562--32603 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
32552 TAAACGTATT
32562 AGATTCCTGGAAAGAATC
1 AGATTCCTGGAAAGAATC
32580 AGATTCCTGGAAAGAATC
1 AGATTCCTGGAAAGAATC
32598 AGATTC
1 AGATTC
32604 TCCATGCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (18 bp):
AGATTCCTGGAAAGAATC
Found at i:36883 original size:25 final size:25
Alignment explanation
Indices: 36855--36909 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
36845 AATTCCATTT
36855 TAAATAGAACGGCCTAAA-TCAAATA
1 TAAATAGAACGGCC-AAATTCAAATA
*
36880 TAAATAGAATGGCCAAATTCAAATA
1 TAAATAGAACGGCCAAATTCAAATA
36905 TAAAT
1 TAAAT
36910 TCATAGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 3 0.11
25 25 0.89
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.24
Consensus pattern (25 bp):
TAAATAGAACGGCCAAATTCAAATA
Found at i:37850 original size:20 final size:20
Alignment explanation
Indices: 37827--37870 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
37817 TAGTATCGAA
37827 ACTAGTACAAAGGTATCAAT
1 ACTAGTACAAAGGTATCAAT
* *
37847 ACTAGTACAAGGGTATCGAT
1 ACTAGTACAAAGGTATCAAT
37867 ACTA
1 ACTA
37871 CTATAGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (20 bp):
ACTAGTACAAAGGTATCAAT
Found at i:38611 original size:25 final size:25
Alignment explanation
Indices: 38560--38611 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
38550 AATATATGTA
* **
38560 AAATTATAAAGTTTAATATAACCAT
1 AAATTATAAAGTTTAACATAAAAAT
38585 AAATTATTAAA-TTTAACATAAAAAT
1 AAATTA-TAAAGTTTAACATAAAAAT
38610 AA
1 AA
38612 TTTAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATTATAAAGTTTAACATAAAAAT
Found at i:40217 original size:44 final size:45
Alignment explanation
Indices: 40135--40239 Score: 203
Period size: 44 Copynumber: 2.4 Consensus size: 45
40125 GTCACCTGCC
40135 AAGACATCACTCGGAAACTTTTTTTATTTATTATTATTTTGGAGT
1 AAGACATCACTCGGAAACTTTTTTTATTTATTATTATTTTGGAGT
40180 AAGACATCACTCGGAAACTTTTTTTA-TTATTATTATTTTGGAGT
1 AAGACATCACTCGGAAACTTTTTTTATTTATTATTATTTTGGAGT
40224 AAGACATCACTCGGAA
1 AAGACATCACTCGGAA
40240 CTAAAACACC
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 34 0.57
45 26 0.43
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (45 bp):
AAGACATCACTCGGAAACTTTTTTTATTTATTATTATTTTGGAGT
Found at i:44012 original size:3 final size:3
Alignment explanation
Indices: 43975--44002 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43965 TATTTAAATT
43975 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
44003 TTTTAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:45208 original size:2 final size:2
Alignment explanation
Indices: 45201--45237 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
45191 TGAGCAGGTC
45201 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
45238 GTTTTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:58302 original size:2 final size:2
Alignment explanation
Indices: 58295--58349 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
58285 TATTCTAATT
58295 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
58337 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
58350 TAATCTTGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64195 original size:110 final size:111
Alignment explanation
Indices: 64052--64315 Score: 406
Period size: 111 Copynumber: 2.4 Consensus size: 111
64042 AAATCGGTTA
** * *
64052 AAATAAATTTCAGTTCGATTAATCGAACCGAATTAACCAAATTTTTGCTTCGATTAATTCACTTA
1 AAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCGAATTTTTGCTTCGATTAATTCACTTA
*
64117 ATAA-TTTAAAAAAAATCGGTTAACTT-GTTTCGGTTAATAATTTTC
66 ATAATTTTAAAAAAAATCGGTTAA-TTCGGTTCGGTTAATAATTTTC
* * * * *
64162 AAATATATTTTGGTTTGATTAACCAAACCGAATTAACCGATTTTTTGCTTCGATTAATTTACTTA
1 AAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCGAATTTTTGCTTCGATTAATTCACTTA
*
64227 ATAATTTTAAAAAAAATCGGTTAATTCGGTTCGGTTAATCATTTTC
66 ATAATTTTAAAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTC
64273 AAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCGAATT
1 AAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCGAATT
64316 GTTTCTTTAA
Statistics
Matches: 137, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
110 62 0.45
111 75 0.55
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (111 bp):
AAATAAATTTTGGTTCGATTAACCGAACCGAATTAACCGAATTTTTGCTTCGATTAATTCACTTA
ATAATTTTAAAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTC
Done.