Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002155.1 Hibiscus syriacus cultivar Beakdansim tig00004402_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: 180033
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:11812 original size:2 final size:2
Alignment explanation
Indices: 11805--11884 Score: 54
Period size: 2 Copynumber: 45.0 Consensus size: 2
11795 GAAAATATTT
*
11805 TA TA TA TA -A T- TA -A TA TA -A AA TA T- TA TA TA TA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
11840 TA -A TA TA AA AA TA TA -A AA TA T- 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
11879 TA TA TA
1 TA TA TA
11885 ATTAGAGATG
Statistics
Matches: 64, Mismatches: 4, Indels: 20
0.73 0.05 0.23
Matches are distributed among these distances:
1 10 0.16
2 54 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:11820 original size:9 final size:8
Alignment explanation
Indices: 11808--11886 Score: 54
Period size: 9 Copynumber: 9.2 Consensus size: 8
11798 AATATTTTAT
11808 ATATAATTA
1 ATATAA-TA
11817 ATATAA-A
1 ATATAATA
*
11824 ATATTATA
1 ATATAATA
11832 TATATAATTA
1 -ATATAA-TA
*
11842 ATATAAAA
1 ATATAATA
11850 ATATAA-A
1 ATATAATA
*
11857 ATATTATA
1 ATATAATA
11865 TATATATATA
1 -ATATA-ATA
11875 TATATATATA
1 -ATATA-ATA
11885 AT
1 AT
11887 TAGAGATGGC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
7 12 0.20
8 9 0.15
9 23 0.39
10 15 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATAATA
Found at i:11824 original size:25 final size:25
Alignment explanation
Indices: 11796--11888 Score: 106
Period size: 25 Copynumber: 3.8 Consensus size: 25
11786 CCCAAACCCG
*
11796 AAAATATTTTATATATAATTAATAT
1 AAAATATTATATATATAATTAATAT
11821 AAAATATTATATATATAATTAATAT
1 AAAATATTATATATATAATTAATAT
*
11846 AAAA-A-TATA-AAAT-ATT-ATAT
1 AAAATATTATATATATAATTAATAT
*
11866 ATATATATATATATATATAATTA
1 A-AAATAT-TATATATATAATTA
11889 GAGATGGCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
20 5 0.09
21 5 0.09
22 4 0.07
23 4 0.07
24 5 0.09
25 31 0.54
26 3 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAATATTATATATATAATTAATAT
Found at i:12599 original size:15 final size:15
Alignment explanation
Indices: 12576--12609 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12566 ATATTTGGCT
* *
12576 GGGCGGGCGGATGTG
1 GGGCAGGCGGATGCG
12591 GGGCAGGCGGATGCG
1 GGGCAGGCGGATGCG
12606 GGGC
1 GGGC
12610 GGATGCGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.18, G:0.65, T:0.09
Consensus pattern (15 bp):
GGGCAGGCGGATGCG
Found at i:12610 original size:11 final size:11
Alignment explanation
Indices: 12596--12620 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12586 ATGTGGGGCA
12596 GGCGGATGCGG
1 GGCGGATGCGG
12607 GGCGGATGCGG
1 GGCGGATGCGG
12618 GGC
1 GGC
12621 AGGTAATGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.20, G:0.64, T:0.08
Consensus pattern (11 bp):
GGCGGATGCGG
Found at i:21368 original size:2 final size:2
Alignment explanation
Indices: 21361--21388 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21351 CACTTGGAAA
21361 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
21389 TTTTCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:22811 original size:41 final size:41
Alignment explanation
Indices: 22749--22830 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
22739 TCTGATCGGA
* *
22749 CATAACTGCAGCGGAGAGGAGGCTATCCATGGTGCTCCAAT
1 CATAACTGCAGCAGAGAGGAGGCTAGCCATGGTGCTCCAAT
*
22790 CATAACTGCAGCAGAGCGGAGGCTAGCCATGGTGCTCCAAT
1 CATAACTGCAGCAGAGAGGAGGCTAGCCATGGTGCTCCAAT
22831 GGAGGACAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.27, C:0.26, G:0.29, T:0.18
Consensus pattern (41 bp):
CATAACTGCAGCAGAGAGGAGGCTAGCCATGGTGCTCCAAT
Found at i:24000 original size:15 final size:15
Alignment explanation
Indices: 23980--24008 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23970 AAATATATTT
23980 TAAAATAATTTTAAG
1 TAAAATAATTTTAAG
23995 TAAAATAATTTTAA
1 TAAAATAATTTTAA
24009 AAGATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TAAAATAATTTTAAG
Found at i:24617 original size:18 final size:19
Alignment explanation
Indices: 24582--24618 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
24572 CACGGAATGT
24582 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
24602 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
24619 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:25133 original size:27 final size:30
Alignment explanation
Indices: 25074--25135 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
25064 TAAGATATAA
*
25074 TATTTATTATATCTTCTATATATAATAATT
1 TATTTATTATATCTTCTATATATAATAACT
* *
25104 TATTTATT-TATCTTTTATAT-TTAT-ACT
1 TATTTATTATATCTTCTATATATAATAACT
25131 TATTT
1 TATTT
25136 CTGCATACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 7 0.24
28 3 0.10
29 11 0.38
30 8 0.28
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (30 bp):
TATTTATTATATCTTCTATATATAATAACT
Found at i:28035 original size:14 final size:14
Alignment explanation
Indices: 28016--28045 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28006 GCTTCTCCTA
28016 TCTCTATTTTCTTT
1 TCTCTATTTTCTTT
*
28030 TCTCTATTTTTTTT
1 TCTCTATTTTCTTT
28044 TC
1 TC
28046 CTTTCGTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (14 bp):
TCTCTATTTTCTTT
Found at i:28578 original size:3 final size:3
Alignment explanation
Indices: 28572--28607 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
28562 AATTATTATT
* *
28572 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA GAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28608 ATAAATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:42716 original size:18 final size:18
Alignment explanation
Indices: 42693--42746 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
42683 AAATTATCTT
*
42693 TATTATATAATTTTATAA
1 TATTATATAATTTTAAAA
*
42711 TATTATA-AATTGTAAAA
1 TATTATATAATTTTAAAA
*
42728 TATTTATATATTTTTAAAA
1 TA-TTATATAATTTTAAAA
42747 AAAATTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 10 0.33
18 12 0.40
19 8 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TATTATATAATTTTAAAA
Found at i:54443 original size:27 final size:26
Alignment explanation
Indices: 54404--54456 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
54394 AATTGCTTAT
*
54404 TCAATACATGTGCATATGTCTTTAACA
1 TCAATACACGTGCATAT-TCTTTAACA
*
54431 TCAATACACGTGCATGTTCTTTAACA
1 TCAATACACGTGCATATTCTTTAACA
54457 GCAGTCTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (26 bp):
TCAATACACGTGCATATTCTTTAACA
Found at i:54625 original size:72 final size:71
Alignment explanation
Indices: 54509--54643 Score: 216
Period size: 72 Copynumber: 1.9 Consensus size: 71
54499 AAGATGAAAA
* *
54509 CTTGAATCGAAAGTGTGATGCCTCATTCCGTTCAACTTGAATCGAAAGTGTCGATGTTTCCTTCT
1 CTTGAATCGAAAGTGTAATGCCTCATTCCGTTCAACTTGAATCGAAAGTGTCGATGCTTCCTTCT
54574 ATTCGT
66 ATTCGT
* * *
54580 CTTGAATTGAAAGTGTCAATGCTTCATTCCGTTCGACTTGAATCGAAAGTGTCGATGCTTCCTT
1 CTTGAATCGAAAGTGT-AATGCCTCATTCCGTTCAACTTGAATCGAAAGTGTCGATGCTTCCTT
54644 ACGTTCTTCG
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
71 15 0.26
72 43 0.74
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (71 bp):
CTTGAATCGAAAGTGTAATGCCTCATTCCGTTCAACTTGAATCGAAAGTGTCGATGCTTCCTTCT
ATTCGT
Found at i:54649 original size:36 final size:36
Alignment explanation
Indices: 54508--54649 Score: 178
Period size: 36 Copynumber: 4.0 Consensus size: 36
54498 AAAGATGAAA
* *
54508 ACTTGAATCGAAAGTGT-GATGCCTCATTCCGTTCA
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
* * **
54543 ACTTGAATCGAAAGTGTCGATGTTTCCTTCTATTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
* * *
54579 TCTTGAATTGAAAGTGTCAATGCTTCATTCCGTTCG
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
* *
54615 ACTTGAATCGAAAGTGTCGATGCTTCCTTACGTTC
1 ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTC
54650 TTCGTATTCA
Statistics
Matches: 88, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 17 0.19
36 71 0.81
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGTCGATGCTTCATTCCGTTCG
Found at i:57548 original size:2 final size:2
Alignment explanation
Indices: 57541--57584 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
57531 ATGAGATAGA
*
57541 AT AT AT AT AT AT AT AT AT AT AT GT 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
57583 AT
1 AT
57585 TCATGTTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76269 original size:19 final size:20
Alignment explanation
Indices: 76245--76283 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
76235 CAAGAACATT
76245 AGTGAAAATAGC-AATTCAA
1 AGTGAAAATAGCAAATTCAA
76264 AGTGAAAATAGCAAATTCAA
1 AGTGAAAATAGCAAATTCAA
76284 GTGGAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (20 bp):
AGTGAAAATAGCAAATTCAA
Found at i:79643 original size:13 final size:13
Alignment explanation
Indices: 79627--79651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79617 TAATATTTTG
79627 TTTTATTTTTTAT
1 TTTTATTTTTTAT
79640 TTTTATTTTTTA
1 TTTTATTTTTTA
79652 ATAAAAGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:80426 original size:27 final size:27
Alignment explanation
Indices: 80396--80481 Score: 97
Period size: 27 Copynumber: 3.2 Consensus size: 27
80386 TATAGATTAT
*
80396 TTTACAATGAATTAATGTAATATATAA
1 TTTACAATGAGTTAATGTAATATATAA
* * *
80423 TTTA-AATTAGTTTAT-TAATAAATTAGA
1 TTTACAATGAGTTAATGTAATATA-TA-A
80450 -TTACAATGAGTTAATGTAATATATAA
1 TTTACAATGAGTTAATGTAATATATAA
80476 TTTACA
1 TTTACA
80482 TTAATAATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
25 6 0.13
26 14 0.30
27 21 0.45
28 6 0.13
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (27 bp):
TTTACAATGAGTTAATGTAATATATAA
Found at i:82996 original size:7 final size:7
Alignment explanation
Indices: 82984--83017 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
82974 AACTTAAAAC
82984 CTTAAAT
1 CTTAAAT
82991 CTTAAAT
1 CTTAAAT
82998 CTTAAAT
1 CTTAAAT
* *
83005 CTTTAAC
1 CTTAAAT
83012 CTTAAA
1 CTTAAA
83018 GCAATAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (7 bp):
CTTAAAT
Found at i:83003 original size:14 final size:14
Alignment explanation
Indices: 82980--83017 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
82970 TATTAACTTA
82980 AAACCTTAAATCTT
1 AAACCTTAAATCTT
*
82994 AAATCTTAAATCTT
1 AAACCTTAAATCTT
*
83008 TAACCTTAAA
1 AAACCTTAAA
83018 GCAATAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (14 bp):
AAACCTTAAATCTT
Found at i:83258 original size:56 final size:56
Alignment explanation
Indices: 83116--83259 Score: 191
Period size: 56 Copynumber: 2.6 Consensus size: 56
83106 ATTTATTTTT
* * *
83116 TAGATATATTCGATTTC-AGGGCCCCTATTTGTATGCTTCTTAATGGCAACAACTGA
1 TAGATATACTCGATTTCGA-GGCCCCTATTTTTATACTTCTTAATGGCAACAACTGA
* * * * *
83172 TATATATACTCGATTTTGGGGTCTCTATTTTTATACTTCTTAATGGCAACAACTGA
1 TAGATATACTCGATTTCGAGGCCCCTATTTTTATACTTCTTAATGGCAACAACTGA
*
83228 TAGATATACTCGATTTCGAGACCCCTATTTTT
1 TAGATATACTCGATTTCGAGGCCCCTATTTTT
83260 TGAGGCCCTG
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (56 bp):
TAGATATACTCGATTTCGAGGCCCCTATTTTTATACTTCTTAATGGCAACAACTGA
Found at i:83994 original size:2 final size:2
Alignment explanation
Indices: 83987--84018 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
83977 AAGCTTCCTA
83987 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
84019 GGGTTAATAC
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:95733 original size:16 final size:16
Alignment explanation
Indices: 95712--95742 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
95702 TATACATTTA
*
95712 TATATTTTGTTTTAAG
1 TATATTTTATTTTAAG
95728 TATATTTTATTTTAA
1 TATATTTTATTTTAA
95743 AAATTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TATATTTTATTTTAAG
Found at i:96364 original size:2 final size:2
Alignment explanation
Indices: 96310--96349 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
96300 ATTTTATCAA
96310 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
96350 CATTTCAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:115641 original size:3 final size:3
Alignment explanation
Indices: 115635--115723 Score: 171
Period size: 3 Copynumber: 30.0 Consensus size: 3
115625 TGAAACCATC
115635 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
115682 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
115724 GGTTTGTAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 83 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:118608 original size:63 final size:63
Alignment explanation
Indices: 118539--118658 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 63
118529 AAAAAACCTG
* * * *
118539 ACCCGAATATCAAAATTAAAAAAATCCGATCCGAACCCGAATTTTTTTTAAAAAAAACACACA
1 ACCCGAATATCAAAATTAAAAAAACCCGACCCGAAACCAAATTTTTTTTAAAAAAAACACACA
*
118602 ACCCGAATATCAAACTTAAAAAAACCCGACCCGAAACCAAATTTTTTTTAAAAAAAA
1 ACCCGAATATCAAAATTAAAAAAACCCGACCCGAAACCAAATTTTTTTTAAAAAAAA
118659 TTCAACCCGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.50, C:0.23, G:0.06, T:0.22
Consensus pattern (63 bp):
ACCCGAATATCAAAATTAAAAAAACCCGACCCGAAACCAAATTTTTTTTAAAAAAAACACACA
Found at i:118633 original size:28 final size:29
Alignment explanation
Indices: 118511--118636 Score: 80
Period size: 28 Copynumber: 4.2 Consensus size: 29
118501 CCCGACCCCA
* * *
118511 ACCCGTATATCACACTTAAAAAAAC-CTG
1 ACCCGAATATCAAACTTAAAAAAACACCG
*
118539 ACCCGAATATCAAAATTAAAAAAATCCGATCCG
1 ACCCGAATATCAAACTTAAAAAAA--C-A-CCG
**** *
118572 AACCCGAAT-T-TTTTTTAAAAAAAACACACA
1 -ACCCGAATATCAAACTT-AAAAAAACAC-CG
118602 ACCCGAATATCAAACTTAAAAAAAC-CCG
1 ACCCGAATATCAAACTTAAAAAAACACCG
118630 ACCCGAA
1 ACCCGAA
118637 ACCAAATTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 20
0.69 0.13 0.19
Matches are distributed among these distances:
28 29 0.39
29 10 0.14
30 12 0.16
31 3 0.04
32 2 0.03
33 10 0.14
34 8 0.11
ACGTcount: A:0.48, C:0.26, G:0.07, T:0.19
Consensus pattern (29 bp):
ACCCGAATATCAAACTTAAAAAAACACCG
Found at i:118656 original size:33 final size:31
Alignment explanation
Indices: 118619--118707 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
118609 TATCAAACTT
*
118619 AAAAAAACCCGACCCGAAACCAAATTTTTTTTA
1 AAAAAAATCCGACCCGAAACCAAA--TTTTTTA
* * ** *
118652 AAAAAAATTCAACCCGATCCCGAATTTTTTA
1 AAAAAAATCCGACCCGAAACCAAATTTTTTA
*
118683 AAAAAAATCCGACCTGAATACCAAA
1 AAAAAAATCCGACCCGAA-ACCAAA
118708 AAATTGATGA
Statistics
Matches: 43, Mismatches: 12, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
31 21 0.49
32 4 0.09
33 18 0.42
ACGTcount: A:0.47, C:0.24, G:0.07, T:0.22
Consensus pattern (31 bp):
AAAAAAATCCGACCCGAAACCAAATTTTTTA
Found at i:123229 original size:19 final size:19
Alignment explanation
Indices: 123205--123243 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
123195 CAATCCGTGG
*
123205 GAATACAATGGACTCTTAT
1 GAATACAATAGACTCTTAT
123224 GAATACAATAGACTCTTAT
1 GAATACAATAGACTCTTAT
123243 G
1 G
123244 CATGCAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (19 bp):
GAATACAATAGACTCTTAT
Found at i:127886 original size:39 final size:37
Alignment explanation
Indices: 127843--128111 Score: 157
Period size: 37 Copynumber: 7.4 Consensus size: 37
127833 ATATTATATG
*
127843 ATATATAATATAT-GTTTTTTTCGAAAACATTTTAAAAAT
1 ATATATAATATATAG--TCTTT-GAAAACATTTTAAAAAT
*
127882 ATATATAATATATAGTCTTTGAAAACATTTTGAAAAT
1 ATATATAATATATAGTCTTTGAAAACATTTTAAAAAT
* * * * * * * *
127919 GTATAT-ATATATA-TATAT--ATATA-TATATATAT
1 ATATATAATATATAGTCTTTGAAAACATTTTAAAAAT
* * * * * * *
127951 ATATAT-ATATATA-TATAT-ATATATATATTGAAAAC
1 ATATATAATATATAGTCTTTGA-AAACATTTTAAAAAT
**
127986 ATATATAATATATAGT-TTTGAAAACATTTTTGGAAAT
1 ATATATAATATATAGTCTTTGAAAACA-TTTTAAAAAT
* *
128023 TTATATGATATATAGT-TTTGAAAACATTTTGAAAACAT
1 ATATATAATATATAGTCTTTGAAAACATTTT-AAAA-AT
* * * *
128061 TTATAT-ATATATAGTTTTTAAAAATATTTTAAAAAT
1 ATATATAATATATAGTCTTTGAAAACATTTTAAAAAT
128097 ATATATATATATATA
1 ATATATA-ATATATA
128112 TATATATATA
Statistics
Matches: 186, Mismatches: 31, Indels: 27
0.76 0.13 0.11
Matches are distributed among these distances:
32 22 0.12
33 3 0.02
34 5 0.03
35 12 0.06
36 30 0.16
37 69 0.37
38 31 0.17
39 13 0.07
40 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATAATATATAGTCTTTGAAAACATTTTAAAAAT
Found at i:127998 original size:2 final size:2
Alignment explanation
Indices: 127920--127978 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
127910 TTTGAAAATG
127920 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
127962 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
127979 TGAAAACATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:128006 original size:25 final size:25
Alignment explanation
Indices: 127935--128012 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
127925 ATATATATAT
* *
127935 ATATATATATATATATATAT-ATATAT
1 ATATATATATATATATAT-TGA-AAAC
127961 ATATATATATATATATATTGAAAAC
1 ATATATATATATATATATTGAAAAC
*
127986 ATATATA-ATATATAGTTTTGAAAAC
1 ATATATATATATATA-TATTGAAAAC
128011 AT
1 AT
128013 TTTTGGAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
24 7 0.15
25 21 0.45
26 19 0.40
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (25 bp):
ATATATATATATATATATTGAAAAC
Found at i:128054 original size:11 final size:11
Alignment explanation
Indices: 128038--128062 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
128028 TGATATATAG
128038 TTTTGAAAACA
1 TTTTGAAAACA
128049 TTTTGAAAACA
1 TTTTGAAAACA
128060 TTT
1 TTT
128063 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:128090 original size:38 final size:38
Alignment explanation
Indices: 127949--128111 Score: 149
Period size: 38 Copynumber: 4.4 Consensus size: 38
127939 ATATATATAT
* * * * *
127949 ATATATATATATATA-TATATATATATATATTGAAAAC
1 ATATATATATATATAGTTTTTAAAAATATTTTGAAAAC
* *
127986 ATATATA-ATATATAGTTTTGAAAACAT-TTTTG-GAA-
1 ATATATATATATATAGTTTTTAAAA-ATATTTTGAAAAC
* * *
128021 ATTTATATGATATATAG-TTTTGAAAACATTTTGAAAAC
1 ATATATAT-ATATATAGTTTTTAAAAATATTTTGAAAAC
* * *
128059 ATTTATATATATATAGTTTTTAAAAATATTTTAAAAAT
1 ATATATATATATATAGTTTTTAAAAATATTTTGAAAAC
128097 ATATATATATATATA
1 ATATATATATATATA
128112 TATATATATA
Statistics
Matches: 101, Mismatches: 17, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
35 7 0.07
36 20 0.20
37 33 0.33
38 41 0.41
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (38 bp):
ATATATATATATATAGTTTTTAAAAATATTTTGAAAAC
Found at i:128102 original size:2 final size:2
Alignment explanation
Indices: 128095--128130 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
128085 TATTTTAAAA
128095 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
128131 TATTATTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:128128 original size:3 final size:3
Alignment explanation
Indices: 128120--128190 Score: 74
Period size: 3 Copynumber: 23.3 Consensus size: 3
128110 TATATATATA
* *
128120 TAT TAT TA- TAT TAT TAT TATT TAT TAT TAT CATT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT
*
128166 AAT TAT T-T TATT TAT TAT TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT T
128191 TCTTATTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 4 0.07
3 45 0.79
4 8 0.14
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:128146 original size:13 final size:13
Alignment explanation
Indices: 128120--128197 Score: 97
Period size: 13 Copynumber: 6.1 Consensus size: 13
128110 TATATATATA
128120 TATTATTATATTAT
1 TATTATT-TATTAT
128134 TATTATTTATTAT
1 TATTATTTATTAT
*
128147 TATCATTTATTAT
1 TATTATTTATTAT
* *
128160 TATT-GTAATTAT
1 TATTATTTATTAT
128172 T-TTATTTATTAT
1 TATTATTTATTAT
*
128184 TATTATTTCTTAT
1 TATTATTTATTAT
128197 T
1 T
128198 TAATTATTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
11 2 0.04
12 14 0.25
13 32 0.58
14 7 0.13
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:128177 original size:37 final size:37
Alignment explanation
Indices: 128120--128197 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
128110 TATATATATA
128120 TATTATTATATTATTATTATTTATTATTATCATTTAT
1 TATTATTATATTATTATTATTTATTATTATCATTTAT
* * *
128157 TATTATTGTAATTATT-TTATTTATTATTATTATTTCT
1 TATTATTAT-ATTATTATTATTTATTATTATCATTTAT
128194 TATT
1 TATT
128198 TAATTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 31 0.84
38 6 0.16
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (37 bp):
TATTATTATATTATTATTATTTATTATTATCATTTAT
Found at i:132774 original size:20 final size:20
Alignment explanation
Indices: 132718--132777 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
132708 AGTTTGGGGT
* *
132718 TTTTTTTTTATAAATAAAATA
1 TTTTTTATTATTAA-AAAATA
*
132739 TTTTTTAAGTTTTTAAAAAATA
1 TTTTTT-A-TTATTAAAAAATA
132761 TTTTTTATTATTAAAAA
1 TTTTTTATTATTAAAAA
132778 TTAAAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 9 0.27
21 7 0.21
22 12 0.36
23 5 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTTTATTATTAAAAAATA
Found at i:133952 original size:21 final size:21
Alignment explanation
Indices: 133911--133952 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
133901 AAGTTTCGTT
*
133911 AATAAATAAATGAATAGTACA
1 AATAAATAAATGAATAATACA
*
133932 AATAATTAAAT-AATTAATACA
1 AATAAATAAATGAA-TAATACA
133953 TCAAAGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (21 bp):
AATAAATAAATGAATAATACA
Found at i:139900 original size:25 final size:25
Alignment explanation
Indices: 139871--139924 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
139861 AAAATATGTT
139871 TTCGTC-TCCTTTAAAATTTTATAAG
1 TTCGTCTTCC-TTAAAATTTTATAAG
* *
139896 TTCGTCTTTCCTTCAAATTTTATTAG
1 TTCGTC-TTCCTTAAAATTTTATAAG
139922 TTC
1 TTC
139925 ACTTCCGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 16 0.64
27 3 0.12
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (25 bp):
TTCGTCTTCCTTAAAATTTTATAAG
Found at i:146121 original size:17 final size:17
Alignment explanation
Indices: 146098--146141 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
146088 TATAAAATTT
146098 ATAAAAATAAAAATAAAA
1 ATAAAAAT-AAAATAAAA
* **
146116 ATAAAAATAAATTATTA
1 ATAAAAATAAAATAAAA
146133 ATAAAAATA
1 ATAAAAATA
146142 TTATAGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAAAATAAAATAAAA
Found at i:146141 original size:6 final size:6
Alignment explanation
Indices: 146098--146126 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
146088 TATAAAATTT
146098 ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
146127 TTATTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:158362 original size:19 final size:19
Alignment explanation
Indices: 158340--158387 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
158330 TTATTTTGAT
158340 TATTATAATTTTAA-CTAAA
1 TATT-TAATTTTAATCTAAA
*
158359 TATTTAAGTCTTAATCTAAA
1 TATTTAA-TTTTAATCTAAA
158379 TATTTAATT
1 TATTTAATT
158388 AACACAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.12
19 10 0.40
20 12 0.48
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (19 bp):
TATTTAATTTTAATCTAAA
Found at i:162769 original size:10 final size:10
Alignment explanation
Indices: 162754--162790 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
162744 TTTTTATATG
162754 ATAATTTTAT
1 ATAATTTTAT
*
162764 ATAATTTAAT
1 ATAATTTTAT
*
162774 AAAATTTTAT
1 ATAATTTTAT
162784 ATAATTT
1 ATAATTT
162791 CTTTATAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATAATTTTAT
Found at i:164136 original size:6 final size:6
Alignment explanation
Indices: 164125--164174 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
164115 TTTTTGTATG
* *
164125 ATATAA ATATAA ATA-AA ATTTAA ATATAA ATATAA TTAATAA A-ATAA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA AT-ATAA ATATAA
164172 ATA
1 ATA
164175 ATTATTCGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 9 0.24
6 24 0.65
7 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:164148 original size:17 final size:18
Alignment explanation
Indices: 164126--164175 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
164116 TTTTGTATGA
164126 TATAAATATAAATAAAAT
1 TATAAATATAAATAAAAT
*
164144 T-TAAATATAAATATAAT
1 TATAAATATAAATAAAAT
164161 TAATAAA-ATAAATAA
1 T-ATAAATATAAATAA
164176 TTATTCGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 8 0.29
19 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
TATAAATATAAATAAAAT
Found at i:170135 original size:18 final size:19
Alignment explanation
Indices: 170098--170154 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
170088 CATTTTGAAC
*
170098 CATTCTTCTTTTTCCATAAA
1 CATT-TTCTTCTTCCATAAA
170118 CATTTTCTTCTT-CATAAA
1 CATTTTCTTCTTCCATAAA
* *
170136 TA-CTTCTTCTTCCATAAA
1 CATTTTCTTCTTCCATAAA
170154 C
1 C
170155 CTATTTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.25
18 13 0.41
19 7 0.22
20 4 0.12
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.47
Consensus pattern (19 bp):
CATTTTCTTCTTCCATAAA
Found at i:170267 original size:20 final size:22
Alignment explanation
Indices: 170242--170290 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
170232 TACCCATTTT
170242 TTCTTCCACAAA-CATGT-TTC
1 TTCTTCCACAAACCATGTGTTC
*
170262 TTCTTCCATAAACTCATGTGTTC
1 TTCTTCCACAAAC-CATGTGTTC
170285 TTCTTC
1 TTCTTC
170291 TATAAACTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 11 0.44
22 5 0.20
23 9 0.36
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.45
Consensus pattern (22 bp):
TTCTTCCACAAACCATGTGTTC
Found at i:170289 original size:23 final size:22
Alignment explanation
Indices: 170242--170312 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 22
170232 TACCCATTTT
*
170242 TTCTTCCACAAA--CATGTTTC
1 TTCTTCCATAAACTCATGTTTC
170262 TTCTTCCATAAACTCATGTGTTC
1 TTCTTCCATAAACTCATGT-TTC
* *
170285 TTCTTCTATAAACTCATTTCTTC
1 TTCTTCCATAAACTCATGT-TTC
170308 TTCTT
1 TTCTT
170313 TCATTAGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 11 0.25
22 5 0.11
23 28 0.64
ACGTcount: A:0.21, C:0.27, G:0.04, T:0.48
Consensus pattern (22 bp):
TTCTTCCATAAACTCATGTTTC
Found at i:170972 original size:30 final size:30
Alignment explanation
Indices: 170927--170990 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
170917 GTATATTAAA
*
170927 TATTATAAAATTTTTTAAATAAAAA-TAAT
1 TATTAAAAAATTTTTTAAATAAAAACTAAT
**
170956 TATTAAAAATATTTTTTTCATAAAAACTAAT
1 TATTAAAAA-ATTTTTTAAATAAAAACTAAT
170987 TATT
1 TATT
170991 TTTTCATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 8 0.27
30 14 0.47
31 8 0.27
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (30 bp):
TATTAAAAAATTTTTTAAATAAAAACTAAT
Done.