Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000154.1 Hibiscus syriacus cultivar Beakdansim tig00000274_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: 49996
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2636 original size:20 final size:21
Alignment explanation
Indices: 2613--2692 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 21
2603 TTGGTGCAGA
*
2613 GGGAATCGATACCCCCATGAG
1 GGGAACCGATACCCCCATGAG
* * *
2634 GGAAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-ATG-AG
* *
2657 GGGAACCGATTCCCCCA-CAG
1 GGGAACCGATACCCCCATGAG
*
2677 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
2693 CTGGGGTTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 16 0.33
21 13 0.27
22 2 0.04
23 17 0.35
ACGTcount: A:0.26, C:0.34, G:0.25, T:0.15
Consensus pattern (21 bp):
GGGAACCGATACCCCCATGAG
Found at i:2698 original size:19 final size:20
Alignment explanation
Indices: 2655--2692 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2645 CCCCCTTTGA
*
2655 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
2675 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
2693 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:6481 original size:23 final size:23
Alignment explanation
Indices: 6446--6511 Score: 100
Period size: 22 Copynumber: 3.0 Consensus size: 23
6436 GGGGTATCAA
*
6446 TTCCCCTAC-AGGGGGGAATCGG
1 TTCCCCTTCAAGGGGGGAATCGG
6468 TTCCCCTTCAA-GGGGGAATCGG
1 TTCCCCTTCAAGGGGGGAATCGG
*
6490 TTCCCCTTCAAGGGGGGTATCG
1 TTCCCCTTCAAGGGGGGAATCG
6512 ATTCTCTCTG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
22 30 0.75
23 10 0.25
ACGTcount: A:0.17, C:0.27, G:0.33, T:0.23
Consensus pattern (23 bp):
TTCCCCTTCAAGGGGGGAATCGG
Found at i:10299 original size:22 final size:21
Alignment explanation
Indices: 10257--10296 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10247 GAGTTTGTTT
*
10257 TCATTTTTAAATTTTGAAACA
1 TCATTTTTAAATTTTAAAACA
*
10278 TCATTTTTATATTTTAAAA
1 TCATTTTTAAATTTTAAAA
10297 ACAATTTCTC
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:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTAAATTTTAAAACA
Found at i:17347 original size:54 final size:55
Alignment explanation
Indices: 17255--17370 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 55
17245 AATATAACAA
*
17255 AAATAAATAAATAAAAAATGAAGAAAATTTCAATTTT-AAAGGAA-ATAAATAAAT
1 AAATAAATAAATAAAAAATGAAGAAAATTTCAATTTTAAAAAGAAGATAAA-AAAT
*
17309 AAATAAAT-AATAAAAAGATTAA-AAAATGTT-AATTTTTAAAAAGAAGATAAAAAAT
1 AAATAAATAAATAAAAA-ATGAAGAAAAT-TTCAA-TTTTAAAAAGAAGATAAAAAAT
17364 AAATAAA
1 AAATAAA
17371 AGAAAGAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
53 15 0.27
54 18 0.33
55 17 0.31
56 5 0.09
ACGTcount: A:0.66, C:0.01, G:0.07, T:0.26
Consensus pattern (55 bp):
AAATAAATAAATAAAAAATGAAGAAAATTTCAATTTTAAAAAGAAGATAAAAAAT
Found at i:17405 original size:44 final size:45
Alignment explanation
Indices: 17301--17406 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 45
17291 TAAAGGAAAT
* *
17301 AAATAAATAAATAAATAATAAAAAGATTAAAAAATGTTAATTTTTAA
1 AAATAAGTAAA-AAATAATAAAAAGA-TAAAAAATGTAAATTTTTAA
* * *
17348 AAAGAAGATAAAAAATAA-ATAAAAGA-AAGAAATGTAAATTTTTTA
1 AAATAAG-TAAAAAATAATA-AAAAGATAAAAAATGTAAATTTTTAA
17393 AAATAAGTAAAAAA
1 AAATAAGTAAAAAA
17407 GCAGAATAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
44 7 0.14
45 22 0.43
46 1 0.02
47 17 0.33
48 4 0.08
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (45 bp):
AAATAAGTAAAAAATAATAAAAAGATAAAAAATGTAAATTTTTAA
Found at i:17425 original size:18 final size:17
Alignment explanation
Indices: 17402--17440 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
17392 AAAATAAGTA
17402 AAAAAGCAGAATAAAAAT
1 AAAAAGCAGAA-AAAAAT
*
17420 AAAAAGTAGAAAAAAAT
1 AAAAAGCAGAAAAAAAT
17437 AAAA
1 AAAA
17441 TAAGAAACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (17 bp):
AAAAAGCAGAAAAAAAT
Found at i:20084 original size:20 final size:20
Alignment explanation
Indices: 20061--20103 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
20051 AATCCACCAC
*
20061 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
20081 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
20101 ATG
1 ATG
20104 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:22737 original size:13 final size:13
Alignment explanation
Indices: 22721--22760 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
22711 AGGAAACTAG
22721 AAAGTGAAAGTAA
1 AAAGTGAAAGTAA
* *
22734 AAAGAGAAAGTGA
1 AAAGTGAAAGTAA
22747 AAAGTGAAAAGTAA
1 AAAGTG-AAAGTAA
22761 GTGGGGTAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (13 bp):
AAAGTGAAAGTAA
Found at i:30085 original size:20 final size:20
Alignment explanation
Indices: 30062--30104 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30052 AATCCACCAC
*
30062 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
30082 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
30102 ATG
1 ATG
30105 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:30554 original size:34 final size:34
Alignment explanation
Indices: 30515--30582 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
30505 TACATATTAC
30515 ATATATTCTAGAAAATGTTTTCAAAATCATATAT
1 ATATATTCTAGAAAATGTTTTCAAAATCATATAT
* * * *
30549 ATATATTTTCGAAAATGTTTTCTAAATTATATAT
1 ATATATTCTAGAAAATGTTTTCAAAATCATATAT
30583 TTTTTCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (34 bp):
ATATATTCTAGAAAATGTTTTCAAAATCATATAT
Found at i:30610 original size:40 final size:38
Alignment explanation
Indices: 30554--30630 Score: 111
Period size: 37 Copynumber: 2.0 Consensus size: 38
30544 TATATATATA
*
30554 TTTTCGAAAATGTTTTCTAAATTATATATTTTTTCAAAACG
1 TTTTCGAAAATGTTTTC-AAA-AATAT-TTTTTTCAAAACG
30595 TTTTC-AAAATGTTTTCAAAAATATTTTTTTCAAAAC
1 TTTTCGAAAATGTTTTCAAAAATATTTTTTTCAAAAC
30631 TATATATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
37 12 0.34
38 4 0.11
39 3 0.09
40 11 0.31
41 5 0.14
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.48
Consensus pattern (38 bp):
TTTTCGAAAATGTTTTCAAAAATATTTTTTTCAAAACG
Found at i:30616 original size:12 final size:11
Alignment explanation
Indices: 30584--30614 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
30574 ATTATATATT
*
30584 TTTTCAAAACG
1 TTTTCAAAATG
30595 TTTTCAAAATG
1 TTTTCAAAATG
30606 TTTTCAAAA
1 TTTTCAAAA
30615 ATATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (11 bp):
TTTTCAAAATG
Found at i:30671 original size:38 final size:38
Alignment explanation
Indices: 30603--30932 Score: 215
Period size: 36 Copynumber: 8.8 Consensus size: 38
30593 CGTTTTCAAA
* *
30603 ATGTTTTCAAAAATATTTTTTTCAAAACTATATATTATAT
1 ATGTTTTC-AAAA-ACTGTTTTCAAAACTATATATTATAT
30643 ATGTTTTCAAAAACTGTTTTCAAAACTATATA--ATAT
1 ATGTTTTCAAAAACTGTTTTCAAAACTATATATTATAT
* * * *
30679 ATATTTTCAAAAATTATTTTCAAAACTATATAATATAT
1 ATGTTTTCAAAAACTGTTTTCAAAACTATATATTATAT
* * *
30717 ATATTTTCAAAAATTGTTTTCAAAAC-A-AGA-TA-AT
1 ATGTTTTCAAAAACTGTTTTCAAAACTATATATTATAT
*
30751 ATGTTTTCAAAAA-TGTGATTTCAAAA-T-TATATAATAT
1 ATGTTTTCAAAAACTGT--TTTCAAAACTATATATTATAT
* * * *
30788 ATGTTTT-TAAATCGTATTTTCAAAAC--CATATTATAT
1 ATGTTTTCAAAAAC-TGTTTTCAAAACTATATATTATAT
* * * *
30824 ATATTTTCAAAATCTGATTTCTTTAAAA-AATATA-TATTAT
1 ATGTTTTCAAAAACTG--TT-TTCAAAACTATATATTA-TAT
* * * *
30864 ATGTTTTCAATAACCGTTTTCTAAAAACTATATGTTATAC
1 ATGTTTTCAAAAACTGTTTTC--AAAACTATATATTATAT
* * *
30904 GT-TTTTCGAAAA-TATTTTCAAAAACTATA
1 ATGTTTTCAAAAACTGTTTTC-AAAACTATA
30933 CTATATTATT
Statistics
Matches: 235, Mismatches: 33, Indels: 47
0.75 0.10 0.15
Matches are distributed among these distances:
33 3 0.01
34 14 0.06
35 12 0.05
36 62 0.26
37 27 0.11
38 58 0.25
39 24 0.10
40 33 0.14
41 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (38 bp):
ATGTTTTCAAAAACTGTTTTCAAAACTATATATTATAT
Found at i:30680 original size:36 final size:36
Alignment explanation
Indices: 30603--30932 Score: 229
Period size: 38 Copynumber: 8.8 Consensus size: 36
30593 CGTTTTCAAA
* *
30603 ATGTTTTCAAAAATATTTTTTTCAAAACTATATATTATAT
1 ATGTTTTC-AAAA-ACTGTTTTCAAAACTATATA--ATAT
30643 ATGTTTTCAAAAACTGTTTTCAAAACTATATAATAT
1 ATGTTTTCAAAAACTGTTTTCAAAACTATATAATAT
* * *
30679 ATATTTTCAAAAATTATTTTCAAAACTATATAATATAT
1 ATGTTTTCAAAAACTGTTTTCAAAACTATAT-A-ATAT
* * * *
30717 ATATTTTCAAAAATTGTTTTCAAAACAAGAT-A-AT
1 ATGTTTTCAAAAACTGTTTTCAAAACTATATAATAT
*
30751 ATGTTTTCAAAAA-TGTGATTTCAAAATTATATAATAT
1 ATGTTTTCAAAAACTGT--TTTCAAAACTATATAATAT
* * * * *
30788 ATGTTTT-TAAATCGTATTTTCAAAACCATATTATAT
1 ATGTTTTCAAAAAC-TGTTTTCAAAACTATATAATAT
* * * * *
30824 ATATTTTCAAAATCTGATTTCTTTAAAAAATATATATTAT
1 ATGTTTTCAAAAACTG---T-TTTCAAAACTATATAATAT
* * **
30864 ATGTTTTCAATAACCGTTTTCTAAAAACTATATGTTAT
1 ATGTTTTCAAAAACTGTTTTC--AAAACTATATAATAT
* * *
30902 ACGTTTTTCGAAAA-TATTTTCAAAAACTATA
1 ATG-TTTTCAAAAACTGTTTTC-AAAACTATA
30933 CTATATTATT
Statistics
Matches: 236, Mismatches: 38, Indels: 35
0.76 0.12 0.11
Matches are distributed among these distances:
33 3 0.01
34 14 0.06
35 12 0.05
36 62 0.26
37 26 0.11
38 72 0.31
39 13 0.06
40 34 0.14
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (36 bp):
ATGTTTTCAAAAACTGTTTTCAAAACTATATAATAT
Found at i:30784 original size:109 final size:106
Alignment explanation
Indices: 30641--30835 Score: 284
Period size: 109 Copynumber: 1.8 Consensus size: 106
30631 TATATATTAT
* *
30641 ATATGTTTTCAAAAACTGTTTTCAAAACTATATAATATATATTTTCAAAAATTATTTTCAAAACT
1 ATATGTTTTCAAAAACTGTTTTCAAAACTATATAATATATATTTTCAAAAAGTATTTTCAAAACC
30706 ATATAATATATATATTTTCAAAAATTGTTTTCAAAACAAGATA
66 ATAT--TATATATATTTTCAAAAATTGTTTTCAAAACAAGATA
* * * **
30749 ATATGTTTTCAAAAA-TGTGATTTCAAAATTATATAATATATGTTTTTAAATCGTATTTTCAAAA
1 ATATGTTTTCAAAAACTGT--TTTCAAAACTATATAATATATATTTTCAAAAAGTATTTTCAAAA
30813 CCATATTATATATATTTTCAAAA
64 CCATATTATATATATTTTCAAAA
30836 TCTGATTTCT
Statistics
Matches: 78, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
107 20 0.26
108 15 0.19
109 43 0.55
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.43
Consensus pattern (106 bp):
ATATGTTTTCAAAAACTGTTTTCAAAACTATATAATATATATTTTCAAAAAGTATTTTCAAAACC
ATATTATATATATTTTCAAAAATTGTTTTCAAAACAAGATA
Found at i:31190 original size:3 final size:3
Alignment explanation
Indices: 31182--31221 Score: 53
Period size: 3 Copynumber: 12.3 Consensus size: 3
31172 TTCGATTACA
31182 AAT AAT AAT AAT AAT AATT AATT AAT AAT AAT AATT AAT A
1 AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AA-T AAT A
31222 TTATTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 25 0.71
4 10 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:31209 original size:17 final size:17
Alignment explanation
Indices: 31187--31220 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31177 TTACAAATAA
31187 TAATAATAATAATTAAT
1 TAATAATAATAATTAAT
31204 TAATAATAATAATTAAT
1 TAATAATAATAATTAAT
31221 ATTATTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATAATAATTAAT
Found at i:31226 original size:3 final size:3
Alignment explanation
Indices: 31215--31260 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
31205 AATAATAATA
* *
31215 ATT AAT ATT ATT ATT ATT ATT ATT AATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
31261 GTAAACAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:31241 original size:25 final size:25
Alignment explanation
Indices: 31213--31260 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
31203 TTAATAATAA
31213 TAATTAATATTATTATTATTATTAT
1 TAATTAATATTATTATTATTATTAT
* *
31238 TAATTATTATTGTTATTATTATT
1 TAATTAATATTATTATTATTATT
31261 GTAAACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TAATTAATATTATTATTATTATTAT
Found at i:31243 original size:19 final size:19
Alignment explanation
Indices: 31221--31258 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31211 AATAATTAAT
31221 ATTATTATTATTATTATTA
1 ATTATTATTATTATTATTA
*
31240 ATTATTATTGTTATTATTA
1 ATTATTATTATTATTATTA
31259 TTGTAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:32968 original size:18 final size:18
Alignment explanation
Indices: 32938--32985 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
32928 ATAACAATTA
*
32938 TTTTTGTATTTAC-TTAT
1 TTTTTATATTTACTTTAT
32955 TTTTTATATGTTACTTTAT
1 TTTTTATAT-TTACTTTAT
*
32974 TTTTTTTATTTA
1 TTTTTATATTTA
32986 TATTTTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 8 0.30
18 7 0.26
19 12 0.44
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTTATATTTACTTTAT
Found at i:45039 original size:31 final size:31
Alignment explanation
Indices: 44964--45056 Score: 141
Period size: 32 Copynumber: 3.0 Consensus size: 31
44954 CAAAGAACAT
44964 AACTGTCCATATGTCCCGAAGGACATAGGTA
1 AACTGTCCATATGTCCCGAAGGACATAGGTA
*
44995 ATCCTGTCCATATGTCCCGAAGGACATAGGTA
1 A-ACTGTCCATATGTCCCGAAGGACATAGGTA
* * *
45027 AACTATCCATATGTCTCGAAAGACATAGGT
1 AACTGTCCATATGTCCCGAAGGACATAGGT
45057 GACCCTCGAC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 26 0.46
32 30 0.54
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGGACATAGGTA
Found at i:47820 original size:28 final size:28
Alignment explanation
Indices: 47788--47873 Score: 145
Period size: 28 Copynumber: 3.1 Consensus size: 28
47778 TTTTAAGACA
47788 AGAAGTTCATAATGAGAAGAACTTGTTC
1 AGAAGTTCATAATGAGAAGAACTTGTTC
47816 AGAAGTTCATAATGAGAAGAACTTGTTC
1 AGAAGTTCATAATGAGAAGAACTTGTTC
* * *
47844 AGAAGTTCATAATGAAAAGCACGTGTTC
1 AGAAGTTCATAATGAGAAGAACTTGTTC
47872 AG
1 AG
47874 CCTTTGCTGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.27
Consensus pattern (28 bp):
AGAAGTTCATAATGAGAAGAACTTGTTC
Found at i:48216 original size:3 final size:3
Alignment explanation
Indices: 48208--48274 Score: 68
Period size: 3 Copynumber: 22.7 Consensus size: 3
48198 TTGATTATAA
* *
48208 ATT ATT ATT ATT ATT ATT ATTT ATT AAT -TT AAT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT A-TT ATT ATT
*
48254 ATT AAT A-T ATT ATT ATT -TT AT
1 ATT ATT ATT ATT ATT ATT ATT AT
48275 AAACAAATAT
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
2 5 0.09
3 43 0.80
4 6 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:48243 original size:24 final size:24
Alignment explanation
Indices: 48216--48274 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
48206 AAATTATTAT
*
48216 TATTATTATTATTTATTAATTTAA
1 TATTATTATTATTTATTAATATAA
*
48240 TATTATTTATTA-TTATTAATATAT
1 TATTA-TTATTATTTATTAATATAA
48264 TATTATT-TTAT
1 TATTATTATTAT
48275 AAACAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 3 0.10
23 2 0.06
24 20 0.65
25 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTATTATTATTTATTAATATAA
Done.