Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007148.1 Hibiscus syriacus cultivar Beakdansim tig00018693_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: 69380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:327 original size:32 final size:33
Alignment explanation
Indices: 290--355 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
280 TGCGGTTGCA
290 AGAAAGTTGAAGC-AATTATTGTTTAATACAAG
1 AGAAAGTTGAAGCAAATTATTGTTTAATACAAG
322 AGAAAGTTGAAGCAAATTATTGTTTAATACAAG
1 AGAAAGTTGAAGCAAATTATTGTTTAATACAAG
355 A
1 A
356 TGAATGAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (33 bp):
AGAAAGTTGAAGCAAATTATTGTTTAATACAAG
Found at i:8924 original size:20 final size:20
Alignment explanation
Indices: 8888--8927 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
8878 AAAAAATTAC
*
8888 TTTAAAAATTATTATTTTTA
1 TTTAAAAATTATAATTTTTA
8908 TTTAAAACATTA-AATTTTTA
1 TTTAAAA-ATTATAATTTTTA
8928 ATATTTTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAAAAATTATAATTTTTA
Found at i:9742 original size:33 final size:35
Alignment explanation
Indices: 9667--9755 Score: 119
Period size: 33 Copynumber: 2.6 Consensus size: 35
9657 ATACATAATC
* * * *
9667 ATATAATATAGTTTTTAATATACTTTTGAAAACAT
1 ATATAATATGGTTTTGAAAACACTTTTGAAAACAT
*
9702 ATATAATATGGTTTTGAAAACATTTTTG-AAA-AT
1 ATATAATATGGTTTTGAAAACACTTTTGAAAACAT
9735 ATATAATATGGTTTTGAAAAC
1 ATATAATATGGTTTTGAAAAC
9756 GTATATAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
33 23 0.47
34 3 0.06
35 23 0.47
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (35 bp):
ATATAATATGGTTTTGAAAACACTTTTGAAAACAT
Found at i:9764 original size:23 final size:21
Alignment explanation
Indices: 9725--9780 Score: 85
Period size: 23 Copynumber: 2.6 Consensus size: 21
9715 TTGAAAACAT
9725 TTTTGAAAATATATAATATGG
1 TTTTGAAAATATATAATATGG
9746 TTTTGAAAACGTATATAATATGG
1 TTTTGAAAA--TATATAATATGG
*
9769 TTTTAAAAATAT
1 TTTTGAAAATAT
9781 TTTTGAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 12 0.38
23 20 0.62
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (21 bp):
TTTTGAAAATATATAATATGG
Found at i:9788 original size:35 final size:37
Alignment explanation
Indices: 9746--9817 Score: 114
Period size: 35 Copynumber: 2.0 Consensus size: 37
9736 TATAATATGG
9746 TTTTGAAAACGTAT-ATAATATGGTTTT-AAAA-ATAT
1 TTTTGAAAACGTATAAT-ATATGGTTTTGAAAACATAT
9781 TTTTGAAAACGTATAATATATGGTTTTGAAAACATAT
1 TTTTGAAAACGTATAATATATGGTTTTGAAAACATAT
9818 ATATGGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 24 0.71
36 6 0.18
37 4 0.12
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (37 bp):
TTTTGAAAACGTATAATATATGGTTTTGAAAACATAT
Found at i:9830 original size:21 final size:22
Alignment explanation
Indices: 9780--9836 Score: 82
Period size: 21 Copynumber: 2.6 Consensus size: 22
9770 TTTAAAAATA
9780 TTTTTGAAAACGTATAATATATGG
1 TTTTTGAAAAC--ATAATATATGG
9804 -TTTTGAAAACAT-ATATATGG
1 TTTTTGAAAACATAATATATGG
9824 TTTTTGAAAACAT
1 TTTTTGAAAACAT
9837 TTTTGAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.25
21 14 0.44
23 10 0.31
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.42
Consensus pattern (22 bp):
TTTTTGAAAACATAATATATGG
Found at i:9841 original size:12 final size:12
Alignment explanation
Indices: 9824--9848 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9814 ATATATATGG
9824 TTTTTGAAAACA
1 TTTTTGAAAACA
9836 TTTTTGAAAACA
1 TTTTTGAAAACA
9848 T
1 T
9849 ATAATATAGT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:9856 original size:56 final size:57
Alignment explanation
Indices: 9690--9856 Score: 243
Period size: 56 Copynumber: 2.9 Consensus size: 57
9680 TTTAATATAC
*
9690 TTTTGAAAACATATATAATATGGTTTTGAAAACATTTTTGAAAATATAT-A-ATATGG
1 TTTTGAAAAC-TATATAATATGGTTTTGAAAACATTTTTGAAAACATATAATATATGG
* * *
9746 TTTTGAAAACGTATATAATATGGTTTTAAAAATATTTTTGAAAACGTATAATATATGG
1 TTTTGAAAAC-TATATAATATGGTTTTGAAAACATTTTTGAAAACATATAATATATGG
9804 TTTTGAAAAC-ATAT-ATATGGTTTTTGAAAACATTTTTGAAAACATATAATATA
1 TTTTGAAAACTATATAATATGG-TTTTGAAAACATTTTTGAAAACATATAATATA
9857 GTTAAAAAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
55 6 0.06
56 77 0.77
57 1 0.01
58 16 0.16
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (57 bp):
TTTTGAAAACTATATAATATGGTTTTGAAAACATTTTTGAAAACATATAATATATGG
Found at i:9867 original size:33 final size:34
Alignment explanation
Indices: 9804--9895 Score: 89
Period size: 33 Copynumber: 2.7 Consensus size: 34
9794 TAATATATGG
* ***
9804 TTTTGAAAACATAT-ATATGGTTTTTGAAAAC-AT
1 TTTTGAAAACATATAATATAG-TTAAAAAAACGAT
*
9837 TTTTGAAAACATATAATATAGTTAAAAAAACGGT
1 TTTTGAAAACATATAATATAGTTAAAAAAACGAT
*
9871 TTTTAAAAACGTATATAATATAGTT
1 TTTTGAAAAC--ATATAATATAGTT
9896 TTGAATATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
33 21 0.43
34 15 0.31
36 13 0.27
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (34 bp):
TTTTGAAAACATATAATATAGTTAAAAAAACGAT
Found at i:9912 original size:112 final size:112
Alignment explanation
Indices: 9690--9925 Score: 255
Period size: 112 Copynumber: 2.1 Consensus size: 112
9680 TTTAATATAC
* * ***
9690 TTTTGAAAACATATATAATATGGTTTTGAAAACATTTTTGAAAATATATAATATGGTTTTGAAAA
1 TTTTGAAAACA-ATATAATATGGTTTTGAAAACATTTTTGAAAACATATAATATAGTTAAAAAAA
* ** * *
9755 CGTATATAATATGGTTTTAAAAATATTTTTGAAAACGTATAATATATGG
65 CGTATATAAAAACGTTATAAAAATAGTTTTGAAAAC-TATAATATATGG
9804 TTTTGAAAAC-ATAT-ATATGGTTTTTGAAAACATTTTTGAAAACATATAATATAGTTAAAAAAA
1 TTTTGAAAACAATATAATATGG-TTTTGAAAACATTTTTGAAAACATATAATATAGTTAAAAAAA
* * * *
9867 CGGTTTTTAAAAACG-TATATAATATAGTTTTGAATA-TATATATATATGG
65 C-GTATATAAAAACGTTATA-AAAATAGTTTTGAAAACTATA-ATATATGG
*
9916 TTTTTAAAAC
1 TTTTGAAAAC
9926 GATTTTTGAA
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
111 10 0.10
112 62 0.60
113 21 0.20
114 10 0.10
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (112 bp):
TTTTGAAAACAATATAATATGGTTTTGAAAACATTTTTGAAAACATATAATATAGTTAAAAAAAC
GTATATAAAAACGTTATAAAAATAGTTTTGAAAACTATAATATATGG
Found at i:10007 original size:3 final size:3
Alignment explanation
Indices: 9999--10049 Score: 77
Period size: 3 Copynumber: 16.7 Consensus size: 3
9989 TATATAGTTT
9999 TTA TTA TTA TTA -TA TTA TTA TTTA TATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA T-TA TTA TTA TTA TTA TTA TTA
10045 TTA TT
1 TTA TT
10050 TATTTGTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.04
3 37 0.82
4 6 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:10018 original size:14 final size:14
Alignment explanation
Indices: 9999--10049 Score: 77
Period size: 14 Copynumber: 3.6 Consensus size: 14
9989 TATATAGTTT
9999 TTATTATTATTATA
1 TTATTATTATTATA
10013 TTATTATT-TATATA
1 TTATTATTAT-TATA
10027 TTATTATTATTATTA
1 TTATTATTATTA-TA
10042 TTATTATT
1 TTATTATT
10050 TATTTGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.03
14 22 0.65
15 11 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:10053 original size:25 final size:25
Alignment explanation
Indices: 9998--10053 Score: 87
Period size: 25 Copynumber: 2.2 Consensus size: 25
9988 ATATATAGTT
9998 TTTATTATTATTATATTATTATTTA
1 TTTATTATTATTATATTATTATTTA
*
10023 TATATTATTATTATTATTATTA-TTA
1 TTTATTATTATTA-TATTATTATTTA
10048 TTTATT
1 TTTATT
10054 TGTTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 20 0.71
26 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTATTATTATTATATTATTATTTA
Found at i:19053 original size:45 final size:45
Alignment explanation
Indices: 18996--19237 Score: 367
Period size: 45 Copynumber: 5.4 Consensus size: 45
18986 TATTTATTAT
* *
18996 TTTCATTCATGGCATCCTTTCATGCCTGTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
19041 TTTTATTTATGGCATCCTTTTATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
19086 TTTTATTTATGGCATCCTTTCATGCCTTTAATACACTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
19131 TTTCATTTATGGTATCCTTTCATACCTTTAATGCACCGTTATACA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
19176 TTTCATTTATGTCATCCTTTCATGCCTTTAATGTACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
19221 TTTCATTTATGTGCATC
1 TTTCATTTATG-GCATC
19238 AAAAATTTAT
Statistics
Matches: 177, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
45 173 0.98
46 4 0.02
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:25112 original size:45 final size:45
Alignment explanation
Indices: 25061--25296 Score: 346
Period size: 45 Copynumber: 5.2 Consensus size: 45
25051 TATTCATTAT
*
25061 TTTCATTTATGGCATCCTTTCATGCCTGTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
25106 TTTCATTTATAGCATTCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* **
25151 TTTCATTTACGGCATCCTTTCATGCCTTTAATGCATTGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* ** *
25196 TTTCATTTATGTCATTTTTTCATGCCTTTAAAGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * * *
25241 TTTTATTTATGGCATCCTTTCATGCCTTCAATACACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
25286 TTTCATTTATG
1 TTTCATTTATG
25297 TACATCGAAA
Statistics
Matches: 167, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 167 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:29438 original size:21 final size:21
Alignment explanation
Indices: 29412--29451 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29402 CAGAACCCCA
*
29412 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
29433 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
29452 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:41755 original size:14 final size:15
Alignment explanation
Indices: 41737--41777 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
41727 CATATTAAAT
41737 AATAAATATAATT-A
1 AATAAATATAATTAA
* *
41751 TATAACTATAATTAA
1 AATAAATATAATTAA
41766 AATAAATA-AATT
1 AATAAATATAATT
41778 TGAGGCTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAAATATAATTAA
Found at i:42087 original size:16 final size:16
Alignment explanation
Indices: 42063--42093 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42053 TTCTAAATTT
*
42063 TTTTTGAGTTCAAGTC
1 TTTTCGAGTTCAAGTC
42079 TTTTCGAGTTCAAGT
1 TTTTCGAGTTCAAGT
42094 TTCAATATTA
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:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTCGAGTTCAAGTC
Found at i:44003 original size:36 final size:36
Alignment explanation
Indices: 43932--44004 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
43922 GTTGGAAAAT
* *
43932 ATTTATATATTTTCTTTAAAAATTTAAAGTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
43968 ATTTATATAATTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTGAAAATCATAAA
44004 A
1 A
44005 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:44448 original size:9 final size:9
Alignment explanation
Indices: 44434--44475 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
44424 TTATTAACTA
44434 ATTAAAAAT
1 ATTAAAAAT
**
44443 ATTAAATTT
1 ATTAAAAAT
44452 AATTAAAAAT
1 -ATTAAAAAT
44462 ATTAAAAA-
1 ATTAAAAAT
44470 ATTAAA
1 ATTAAA
44476 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
8 6 0.21
9 15 0.54
10 7 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:44786 original size:29 final size:31
Alignment explanation
Indices: 44749--44811 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
44739 TAAAAAGTAA
* *
44749 AATTAATAATTAAATACAT-GTT-AATAATT
1 AATTAATAATTAAACACATAGTTAAATAACT
*
44778 AATTCATAATTAAACACATAGTTAAATAACT
1 AATTAATAATTAAACACATAGTTAAATAACT
44809 AAT
1 AAT
44812 GTAGTGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.59
30 3 0.10
31 9 0.31
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.37
Consensus pattern (31 bp):
AATTAATAATTAAACACATAGTTAAATAACT
Found at i:44790 original size:18 final size:19
Alignment explanation
Indices: 44749--44790 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
44739 TAAAAAGTAA
44749 AATTAATAATTAAATACAT
1 AATTAATAATTAAATACAT
* *
44768 -GTTAATAATT-AATTCAT
1 AATTAATAATTAAATACAT
44785 AATTAA
1 AATTAA
44791 ACACATAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTAATAATTAAATACAT
Found at i:46302 original size:15 final size:15
Alignment explanation
Indices: 46282--46311 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
46272 AATGCTGAAG
*
46282 GACAAGCATATAAAT
1 GACAAGCATAAAAAT
46297 GACAAGCATAAAAAT
1 GACAAGCATAAAAAT
46312 TTCTTGATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.13, T:0.17
Consensus pattern (15 bp):
GACAAGCATAAAAAT
Found at i:46652 original size:32 final size:32
Alignment explanation
Indices: 46616--46683 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
46606 GAACCAACCT
*
46616 AAGGGAGTACCTTGGGGCCTTAGAGCCTACCC
1 AAGGGAGTACCTTGGGGCCTAAGAGCCTACCC
46648 AAGGGAGTACCTTGGGGCCTAAGAGCCTACCC
1 AAGGGAGTACCTTGGGGCCTAAGAGCCTACCC
46680 AAGG
1 AAGG
46684 TGTAATACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.32, T:0.16
Consensus pattern (32 bp):
AAGGGAGTACCTTGGGGCCTAAGAGCCTACCC
Found at i:48214 original size:13 final size:13
Alignment explanation
Indices: 48196--48222 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48186 AAAAGAATTC
48196 ATAAAAGGTAGTT
1 ATAAAAGGTAGTT
48209 ATAAAAGGTAGTT
1 ATAAAAGGTAGTT
48222 A
1 A
48223 AATGGAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (13 bp):
ATAAAAGGTAGTT
Found at i:48865 original size:17 final size:17
Alignment explanation
Indices: 48843--48890 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
48833 TTTTGAGCTC
48843 GATTCAAGCTCGAACTA
1 GATTCAAGCTCGAACTA
48860 GATTCAAGCTCGAACTA
1 GATTCAAGCTCGAACTA
48877 GATTCAAGCTCGAA
1 GATTCAAGCTCGAA
48891 ATCAAACTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (17 bp):
GATTCAAGCTCGAACTA
Found at i:59454 original size:20 final size:20
Alignment explanation
Indices: 59425--59467 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
59415 ATTTCACCAC
*
59425 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
59445 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
59465 ATG
1 ATG
59468 GGCTCTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:62112 original size:23 final size:22
Alignment explanation
Indices: 62086--62130 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
62076 CTGAGTGGCA
62086 TATGAAATTTATCCCGAAGGACC
1 TATG-AATTTATCCCGAAGGACC
* *
62109 TATGTATTTGTCCCGAAGGACC
1 TATGAATTTATCCCGAAGGACC
62131 GCGTAGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (22 bp):
TATGAATTTATCCCGAAGGACC
Found at i:64461 original size:14 final size:14
Alignment explanation
Indices: 64437--64480 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
64427 TATCACATAA
64437 TTAGA-TTTAGGGT
1 TTAGAGTTTAGGGT
*
64450 TTATAGTTTAGGGT
1 TTAGAGTTTAGGGT
*
64464 TTAGGGTTTAGGGT
1 TTAGAGTTTAGGGT
64478 TTA
1 TTA
64481 AGGTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (14 bp):
TTAGAGTTTAGGGT
Found at i:64465 original size:7 final size:7
Alignment explanation
Indices: 64442--64487 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
64432 CATAATTAGA
64442 TTTAGGG
1 TTTAGGG
**
64449 TTTATAG
1 TTTAGGG
64456 TTTAGGG
1 TTTAGGG
64463 TTTAGGG
1 TTTAGGG
64470 TTTAGGG
1 TTTAGGG
*
64477 TTTAAGG
1 TTTAGGG
64484 TTTA
1 TTTA
64488 TTACAATGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:64555 original size:7 final size:7
Alignment explanation
Indices: 64540--64616 Score: 86
Period size: 7 Copynumber: 11.3 Consensus size: 7
64530 ATAAGTATAA
64540 TTTAGGG
1 TTTAGGG
*
64547 TTTATGG
1 TTTAGGG
*
64554 TTTAAGG
1 TTTAGGG
64561 TTTAGGG
1 TTTAGGG
**
64568 TTTA-TA
1 TTTAGGG
64574 TTTAGGG
1 TTTAGGG
* *
64581 CTTA-AG
1 TTTAGGG
64587 TTTAGGG
1 TTTAGGG
64594 TTTAGGG
1 TTTAGGG
64601 TTTAGGG
1 TTTAGGG
64608 TTTAGGG
1 TTTAGGG
64615 TT
1 TT
64617 CATTATAAAG
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
6 8 0.14
7 49 0.86
ACGTcount: A:0.18, C:0.01, G:0.34, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:65995 original size:19 final size:19
Alignment explanation
Indices: 65971--66065 Score: 109
Period size: 19 Copynumber: 5.0 Consensus size: 19
65961 ATATGCATTG
*
65971 GCTATGAATTTGAAAATAA
1 GCTATGAATCTGAAAATAA
*
65990 GCTATGAATCTGACAATAA
1 GCTATGAATCTGAAAATAA
*
66009 GCTATGAGTCTGAAAATAA
1 GCTATGAATCTGAAAATAA
* * *
66028 GTTATGAGTCTGGAAATAA
1 GCTATGAATCTGAAAATAA
* * *
66047 GTTATGAGTCAGAAAATAA
1 GCTATGAATCTGAAAATAA
66066 ATTATGAAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 68 1.00
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.28
Consensus pattern (19 bp):
GCTATGAATCTGAAAATAA
Found at i:66023 original size:38 final size:38
Alignment explanation
Indices: 65971--66065 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 38
65961 ATATGCATTG
* *
65971 GCTATGAATTTGAAAATAAGCTATGAATCT-GACAATAA
1 GCTATGAGTCTGAAAATAAGCTATGAATCTGGA-AATAA
* *
66009 GCTATGAGTCTGAAAATAAGTTATGAGTCTGGAAATAA
1 GCTATGAGTCTGAAAATAAGCTATGAATCTGGAAATAA
* *
66047 GTTATGAGTCAGAAAATAA
1 GCTATGAGTCTGAAAATAA
66066 ATTATGAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
38 48 0.96
39 2 0.04
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.28
Consensus pattern (38 bp):
GCTATGAGTCTGAAAATAAGCTATGAATCTGGAAATAA
Found at i:66070 original size:19 final size:19
Alignment explanation
Indices: 65981--66072 Score: 121
Period size: 19 Copynumber: 4.8 Consensus size: 19
65971 GCTATGAATT
* *
65981 TGAAAATAAGCTATGAATC
1 TGAAAATAAGTTATGAGTC
* *
66000 TGACAATAAGCTATGAGTC
1 TGAAAATAAGTTATGAGTC
66019 TGAAAATAAGTTATGAGTC
1 TGAAAATAAGTTATGAGTC
*
66038 TGGAAATAAGTTATGAGTC
1 TGAAAATAAGTTATGAGTC
* *
66057 AGAAAATAAATTATGA
1 TGAAAATAAGTTATGA
66073 AATGTGAAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.28
Consensus pattern (19 bp):
TGAAAATAAGTTATGAGTC
Found at i:66117 original size:12 final size:12
Alignment explanation
Indices: 66090--66133 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
66080 AAGTACTTAT
*
66090 TATGAACATGGAA
1 TATGAAAAT-GAA
66103 TATGAAAATGAA
1 TATGAAAATGAA
**
66115 TATGTGAATGAA
1 TATGAAAATGAA
66127 TATGAAA
1 TATGAAA
66134 GTGGAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 18 0.69
13 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.20, T:0.27
Consensus pattern (12 bp):
TATGAAAATGAA
Found at i:69118 original size:22 final size:25
Alignment explanation
Indices: 69079--69124 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 25
69069 TTAGAGAATT
*
69079 GGTTATTTTAAAATAAAATAAATAG
1 GGTTATTTTAAAATAAAAGAAATAG
69104 GGTT-TTTT-AAA-AAAAGAAATA
1 GGTTATTTTAAAATAAAAGAAATA
69125 AGAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 4 0.20
25 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (25 bp):
GGTTATTTTAAAATAAAAGAAATAG
Done.