Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006738.1 Hibiscus syriacus cultivar Beakdansim tig00016910_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: 41537
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2833 original size:20 final size:20
Alignment explanation
Indices: 2770--2824 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
2760 TTAAAATTCA
2770 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
2790 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGC
*
2810 GTTGTGAATTTGACT
1 GTTGCGAATTTGACT
2825 TCTGTGTTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGC
Found at i:2850 original size:40 final size:41
Alignment explanation
Indices: 2750--2856 Score: 118
Period size: 40 Copynumber: 2.7 Consensus size: 41
2740 AACTAAAACC
*
2750 TGTTGCGAATTTA-AAATTC-AGTTGCGAATTTGACTATCG
1 TGTTGCGAATTTACAAATTCGCGTTGCGAATTTGACTATCG
* * *
2789 CGTTGCGAATTTGAC-TA-TCGCGTTGTGAATTTGACT-TCTG
1 TGTTGCGAATTT-ACAAATTCGCGTTGCGAATTTGACTATC-G
2829 TGTTGCG-ATTTACAAATTCGCGTTGCGA
1 TGTTGCGAATTTACAAATTCGCGTTGCGA
2857 TTTACAGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
38 2 0.04
39 20 0.36
40 33 0.60
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (41 bp):
TGTTGCGAATTTACAAATTCGCGTTGCGAATTTGACTATCG
Found at i:2855 original size:20 final size:20
Alignment explanation
Indices: 2830--2917 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
2820 TGACTTCTGT
2830 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
* *
2850 GTTGCGATTTACAGATTTGC
1 GTTGCGATTTACAAATTCGC
* ** *
2870 GTTGTGAATTTGGAAAATCGC
1 GTTGCG-ATTTACAAATTCGC
** *
2891 AATGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
2911 GTTGCGA
1 GTTGCGA
2918 AATTGGAAAT
Statistics
Matches: 50, Mismatches: 17, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
20 38 0.76
21 12 0.24
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:2954 original size:20 final size:21
Alignment explanation
Indices: 2905--2958 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
2895 CGATTTACAT
2905 ATTCGCGTTGCGAAATTGGAA
1 ATTCGCGTTGCGAAATTGGAA
*
2926 ATT-GGGTTGCGAAATTGG-A
1 ATTCGCGTTGCGAAATTGGAA
*
2945 GTTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
2959 TTTGTTGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 23 0.79
21 3 0.10
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (21 bp):
ATTCGCGTTGCGAAATTGGAA
Found at i:3818 original size:41 final size:41
Alignment explanation
Indices: 3730--3810 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
3720 TACATATAAG
* * * * *
3730 TACTTTAGTGGTGTTTTTACACAAACACCACCACATAATCC
1 TACTTTAGTGGTGTTTCTAAACAAACACCACAAAAGAATCC
*
3771 TACTTTAGTGGTGTTTCTAAACAAACACCGCAAAAGAATC
1 TACTTTAGTGGTGTTTCTAAACAAACACCACAAAAGAATC
3811 GTTCTTTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (41 bp):
TACTTTAGTGGTGTTTCTAAACAAACACCACAAAAGAATCC
Found at i:9177 original size:19 final size:19
Alignment explanation
Indices: 9153--9191 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
9143 ATATTTATTA
9153 ATATTTCTAATAATATAAT
1 ATATTTCTAATAATATAAT
* *
9172 ATATTTTTAATATTATAAT
1 ATATTTCTAATAATATAAT
9191 A
1 A
9192 AAATAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTTCTAATAATATAAT
Found at i:9364 original size:22 final size:22
Alignment explanation
Indices: 9336--9415 Score: 62
Period size: 23 Copynumber: 3.6 Consensus size: 22
9326 TTTATATATT
9336 TAATATTAATATAATAATTTAA
1 TAATATTAATATAATAATTTAA
*
9358 TAATATTTTAATA-AAGATATTTAA
1 TAATA--TTAATATAATA-ATTTAA
9382 -AATATACTAAT-TAAT-ATTTAA
1 TAATAT--TAATATAATAATTTAA
*
9403 AAATA-TAATATAA
1 TAATATTAATATAA
9416 CACTATTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
19 4 0.08
20 3 0.06
21 7 0.15
22 9 0.19
23 13 0.27
24 12 0.25
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
TAATATTAATATAATAATTTAA
Found at i:9369 original size:19 final size:19
Alignment explanation
Indices: 9307--9371 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
9297 TATTATTAAA
*
9307 TTTAATAA-TGAAT-ATATT
1 TTTAATAATTTAATAATA-T
* * *
9325 TTTTATATATTTAATATTAA
1 TTTAATA-ATTTAATAATAT
*
9345 TATAATAATTTAATAATAT
1 TTTAATAATTTAATAATAT
9364 TTTAATAA
1 TTTAATAA
9372 AGATATTTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
18 6 0.17
19 18 0.51
20 9 0.26
21 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATAATTTAATAATAT
Found at i:9746 original size:14 final size:14
Alignment explanation
Indices: 9713--9753 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
9703 AAATGTAATT
*
9713 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
9727 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
* *
9741 CTTTTTCCAGAAA
1 CATTTTCCGGAAA
9754 TGTAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:9805 original size:14 final size:14
Alignment explanation
Indices: 9764--9815 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
9754 TGTAATTTAT
*
9764 TTTCTAGAATTCAA
1 TTTCCAGAATTCAA
* *
9778 ATTCCAGTAATTCAT
1 TTTCCAG-AATTCAA
9793 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
*
9807 TTTCAAGAA
1 TTTCCAGAA
9816 AACCAATTAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (14 bp):
TTTCCAGAATTCAA
Found at i:9809 original size:15 final size:15
Alignment explanation
Indices: 9762--9809 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
9752 AATGTAATTT
*
9762 ATTTTCTAGAATTCA
1 ATTTTCCAGAATTCA
*
9777 A-ATTCCAGTAATTC-
1 ATTTTCCAG-AATTCA
9791 ATTTTCCAGAATTCA
1 ATTTTCCAGAATTCA
9806 ATTT
1 ATTT
9810 CAAGAAAACC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTTTCCAGAATTCA
Found at i:10106 original size:22 final size:22
Alignment explanation
Indices: 10078--10121 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
10068 ACTATACGGT
* *
10078 ATGAACAGTACCGTGAACAGTA
1 ATGAACAATACCATGAACAGTA
*
10100 ATGAACAATATCATGAACAGTA
1 ATGAACAATACCATGAACAGTA
10122 CCGAATGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.20
Consensus pattern (22 bp):
ATGAACAATACCATGAACAGTA
Found at i:11063 original size:24 final size:24
Alignment explanation
Indices: 11019--11065 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
11009 CTCGTATAAA
*
11019 TTGCATCGAAGTGCCATGTAGAAT
1 TTGCATCGAAGTGCCACGTAGAAT
*
11043 TTGCATCGAAGTGCCGCGTAGAA
1 TTGCATCGAAGTGCCACGTAGAA
11066 ATGCACCGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (24 bp):
TTGCATCGAAGTGCCACGTAGAAT
Found at i:11222 original size:23 final size:23
Alignment explanation
Indices: 11194--11237 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11184 AATACATACA
11194 TGTCCCAAAGGACCACGTAGAAT
1 TGTCCCAAAGGACCACGTAGAAT
* *
11217 TGTCCCGAAGGACCGCGTAGA
1 TGTCCCAAAGGACCACGTAGA
11238 CCCTCTACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
TGTCCCAAAGGACCACGTAGAAT
Found at i:12892 original size:30 final size:30
Alignment explanation
Indices: 12858--12925 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
12848 CAACCATTTA
*
12858 CAACTTTTCCAAAAATTA-TGAATTGGTCCC
1 CAACTTTTCCAAAAATTACAGAA-TGGTCCC
12888 CAACTTTT-CAAAAATTACAGAATGGTCCC
1 CAACTTTTCCAAAAATTACAGAATGGTCCC
*
12917 CAAATTTTC
1 CAACTTTTC
12926 TAAAGCTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (30 bp):
CAACTTTTCCAAAAATTACAGAATGGTCCC
Found at i:13735 original size:29 final size:30
Alignment explanation
Indices: 13703--13774 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 30
13693 AAAAATTACC
*
13703 ATTTGGTCCCTAAACTTTCC-AAATTTTAT-
1 ATTTGGTCCCTAAAC-TTCCAAAATCTTATA
* *
13732 ATTTAGTCACC-AAGCTTCCAAAATCTTATA
1 ATTTGGTC-CCTAAACTTCCAAAATCTTATA
*
13762 ATTTGGTCACTAA
1 ATTTGGTCCCTAA
13775 CTAAATCCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.12
29 19 0.56
30 11 0.32
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (30 bp):
ATTTGGTCCCTAAACTTCCAAAATCTTATA
Found at i:14028 original size:2 final size:2
Alignment explanation
Indices: 14021--14150 Score: 71
Period size: 2 Copynumber: 73.5 Consensus size: 2
14011 CCGCCCCGAT
* *
14021 TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA TA T- TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
14060 T- TA CT- TA TA TA TA TA -A TA T- TT TA TA TA T- TT TA TA T- TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
14097 -A T- TA TA TA TA TA TA TA -A TA T- TT TA TA TA TC T- TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14133 TA -A T- TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA T
14151 TTTATATTTT
Statistics
Matches: 103, Mismatches: 6, Indels: 38
0.70 0.04 0.26
Matches are distributed among these distances:
1 18 0.17
2 84 0.82
3 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:14070 original size:34 final size:34
Alignment explanation
Indices: 14031--14181 Score: 232
Period size: 34 Copynumber: 4.3 Consensus size: 34
14021 TATATATATA
*
14031 TATATATATAATATTTTATATATTTTATATTACT
1 TATATATATAATATTTTATATATTTTATATTAAT
14065 TATATATATAATATTTTATATATTTTATATTAATTAT
1 TATATATATAATATTTTATATATTTTATATT-A--AT
*
14102 ATATATATATAATATTTTATATATCTTATATTAAT
1 -TATATATATAATATTTTATATATTTTATATTAAT
14137 TATATATATAATATTTTATAT-TTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
14170 TATATAATATAA
1 TATAT-ATATAA
14182 ATCCTAAACC
Statistics
Matches: 109, Mismatches: 3, Indels: 10
0.89 0.02 0.08
Matches are distributed among these distances:
33 16 0.15
34 58 0.53
35 3 0.03
37 2 0.02
38 30 0.28
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:14114 original size:72 final size:71
Alignment explanation
Indices: 14027--14180 Score: 274
Period size: 72 Copynumber: 2.2 Consensus size: 71
14017 CGATTATATA
* *
14027 TATATATATATATAATATTTTATATATTTTATATTACTTATATATATAATATTTTATATATTTTA
1 TATATATATATATAATATTTTATATATCTTATATTAATTATATATATAATATTTTATAT-TTTTA
14092 TATTAAT
65 TATTAAT
14099 TATATATATATATAATATTTTATATATCTTATATTAATTATATATATAATATTTTATATTTTTAT
1 TATATATATATATAATATTTTATATATCTTATATTAATTATATATATAATATTTTATATTTTTAT
14164 ATTAAT
66 ATTAAT
14170 TATATA-ATATA
1 TATATATATATA
14181 AATCCTAAAC
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
70 5 0.06
71 18 0.22
72 57 0.71
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (71 bp):
TATATATATATATAATATTTTATATATCTTATATTAATTATATATATAATATTTTATATTTTTAT
ATTAAT
Found at i:15258 original size:18 final size:18
Alignment explanation
Indices: 15220--15264 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
15210 TCAGTACATA
*
15220 AATTATATTATATAATTT
1 AATTATATTATATAATAT
*
15238 AATTATATTATATAGTAT
1 AATTATATTATATAATAT
*
15256 AATTTTATT
1 AATTATATT
15265 TACATTTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
AATTATATTATATAATAT
Found at i:23202 original size:14 final size:14
Alignment explanation
Indices: 23183--23212 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23173 TTCGTGAACA
*
23183 TTCGGTTATGTTCG
1 TTCGGTTATATTCG
23197 TTCGGTTATATTCG
1 TTCGGTTATATTCG
23211 TT
1 TT
23213 TATGTTCATT
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:0.10, C:0.13, G:0.23, T:0.53
Consensus pattern (14 bp):
TTCGGTTATATTCG
Found at i:23229 original size:24 final size:24
Alignment explanation
Indices: 23182--23229 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
23172 GTTCGTGAAC
* *
23182 ATTCGGTTATGTTCGTTCGGTTAT
1 ATTCGGTTATGTTCATTCAGTTAT
* *
23206 ATTCGTTTATGTTCATTCATTTAT
1 ATTCGGTTATGTTCATTCAGTTAT
23230 GTTTAACCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (24 bp):
ATTCGGTTATGTTCATTCAGTTAT
Found at i:24264 original size:10 final size:10
Alignment explanation
Indices: 24249--24323 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
24239 GGGTCTCTAA
24249 CGTTTATGTT
1 CGTTTATGTT
24259 CGTTTATGTT
1 CGTTTATGTT
24269 C----ATGTT
1 CGTTTATGTT
*
24275 CATTTATGTT
1 CGTTTATGTT
24285 CGTGTT-TGTTT
1 CGT-TTATG-TT
* **
24296 ATGTTCGTGTT
1 -CGTTTATGTT
24307 CGTTTATGTT
1 CGTTTATGTT
24317 CGTTTAT
1 CGTTTAT
24324 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:24287 original size:26 final size:26
Alignment explanation
Indices: 24251--24301 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
24241 GTCTCTAACG
24251 TTTATGTTCGT-TTATGTTCATGTTCA
1 TTTATGTTCGTGTT-TGTTCATGTTCA
*
24277 TTTATGTTCGTGTTTGTTTATGTTC
1 TTTATGTTCGTGTTTGTTCATGTTC
24302 GTGTTCGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.91
27 2 0.09
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (26 bp):
TTTATGTTCGTGTTTGTTCATGTTCA
Found at i:24318 original size:16 final size:16
Alignment explanation
Indices: 24255--24319 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
24245 CTAACGTTTA
*
24255 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGTTCG
*
24271 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
24287 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24303 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24319 T
1 T
24320 TTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:24409 original size:16 final size:16
Alignment explanation
Indices: 24388--24420 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
24378 AAAAAAAAAT
24388 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24404 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
24420 T
1 T
24421 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:25623 original size:22 final size:23
Alignment explanation
Indices: 25598--25642 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
25588 TAATTGTTAA
25598 ATTTATTAAGT-TAAATTATATT
1 ATTTATTAAGTATAAATTATATT
* *
25620 ATTTATTATGTATAAATTTTATT
1 ATTTATTAAGTATAAATTATATT
25643 TAGTTTCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (23 bp):
ATTTATTAAGTATAAATTATATT
Found at i:31124 original size:31 final size:31
Alignment explanation
Indices: 31088--31146 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
31078 AACTTAAAAG
*
31088 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
31119 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
31147 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:31195 original size:22 final size:22
Alignment explanation
Indices: 31170--31290 Score: 172
Period size: 22 Copynumber: 5.5 Consensus size: 22
31160 ATAATAAATT
31170 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
31192 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
31214 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
* *
31236 TTTTAAAATGAATCAATCCTTA
1 TTTTAAAATAAATCAATCCATA
**
31258 GATTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
31280 TTTTAAAATAA
1 TTTTAAAATAA
31291 CATGCAGATC
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
21 3 0.04
22 78 0.92
23 4 0.05
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.38
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Done.