Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007923.1 Hibiscus syriacus cultivar Beakdansim tig00110328_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: 8415618
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 40 of 40
Found at i:8366300 original size:15 final size:15
Alignment explanation
Indices: 8366265--8366300 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
8366255 TATATTATTA
8366265 TTATTTATTTTTAAT
1 TTATTTATTTTTAAT
* *
8366280 TAATTTATTTTTCAT
1 TTATTTATTTTTAAT
8366295 TTATTT
1 TTATTT
8366301 TTGTGCAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTTATTTTTAAT
Found at i:8374839 original size:29 final size:30
Alignment explanation
Indices: 8374744--8374836 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
8374734 GTGGTCCTTA
8374744 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
8374774 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
8374804 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
8374833 TGGA
1 TGGA
8374837 TAGGTCCTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
29 18 0.30
30 42 0.70
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:8375562 original size:21 final size:21
Alignment explanation
Indices: 8375538--8375580 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
8375528 AAAGAAGATA
8375538 TTGTATAAT-CTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
8375559 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
8375580 T
1 T
8375581 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:8378976 original size:13 final size:13
Alignment explanation
Indices: 8378958--8379006 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
8378948 AGTAAAAGCA
8378958 ATTAAATACAAAC
1 ATTAAATACAAAC
8378971 ATTAAATACAAAC
1 ATTAAATACAAAC
* *
8378984 GTTACAATTCAAAC
1 ATTA-AATACAAAC
8378998 AATTAAATA
1 -ATTAAATA
8379007 ATAACAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 16 0.53
14 11 0.37
15 3 0.10
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (13 bp):
ATTAAATACAAAC
Found at i:8383742 original size:3 final size:3
Alignment explanation
Indices: 8383736--8383773 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
8383726 AAAAATGAAA
8383736 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
8383774 TATATATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:8383897 original size:34 final size:34
Alignment explanation
Indices: 8383859--8384056 Score: 139
Period size: 36 Copynumber: 5.5 Consensus size: 34
8383849 TATACGAATG
* *
8383859 TTTTCCAACATGTTTTCAAAAAAGATTATATAAA
1 TTTTCCAAAATGTTTTCAAAAAATATTATATAAA
*
8383893 TTTTCCCAAAATGTTTT-AAAAACTATATAATATAAA
1 TTTT-CCAAAATGTTTTCAAAAA--ATATTATATAAA
* * * * **
8383929 TGTTTTCAAAATGCTTTCAAAACTATAATATATATG
1 T-TTTCCAAAATGTTTTCAAAA-AATATTATATAAA
*
8383965 TTTTCAAAAATGTTTTCAAAAACTATATATATATATAA
1 TTTTCCAAAATGTTTTCAAAAA--ATAT-TATATA-AA
* *
8384003 GTTTTCC-AAATGATTTTAAAAATTATATATTATATATA
1 -TTTTCCAAAATG-TTTTCAAAA--A-ATATTATATAAA
*
8384041 TTTTCTAAAATGTTTT
1 TTTTCCAAAATGTTTT
8384057 TTAATACTAT
Statistics
Matches: 128, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
34 9 0.07
35 28 0.22
36 33 0.26
37 22 0.17
38 11 0.09
39 19 0.15
40 5 0.04
41 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.43
Consensus pattern (34 bp):
TTTTCCAAAATGTTTTCAAAAAATATTATATAAA
Found at i:8383939 original size:36 final size:36
Alignment explanation
Indices: 8383838--8384074 Score: 189
Period size: 38 Copynumber: 6.4 Consensus size: 36
8383828 TTTTTTTTTT
*
8383838 AAACTATATAATATACGAATGTTTTCCAACATGTTTTCAA
1 AAACTATATAATATA--AATGTTTT-CAAAATGTTTT-AA
* * *
8383878 AAA--AGATTATATAAAT-TTTCCCAAAATGTTTTAA
1 AAACTATATAATATAAATGTTT-TCAAAATGTTTTAA
* *
8383912 AAACTATATAATATAAATGTTTTCAAAATGCTTTCA
1 AAACTATATAATATAAATGTTTTCAAAATGTTTTAA
*
8383948 AAAC--TATAATATATATGTTTTCAAAAATGTTTTCAA
1 AAACTATATAATATAAATGTTTTC-AAAATGTTTT-AA
*
8383984 AAACTATATATATATATAA-GTTTTCCAAATGATTTTAA
1 AAACTATATA-ATATA-AATGTTTTCAAAATG-TTTTAA
* * * * *
8384022 AAATTATATATTATATATATTTTCTAAAATGTTTTTTA
1 AAACTATATAATATAAATGTTTTC-AAAATG-TTTTAA
* *
8384060 ATACTATATATTATA
1 AAACTATATAATATA
8384075 TTTTAAAAAC
Statistics
Matches: 161, Mismatches: 23, Indels: 28
0.76 0.11 0.13
Matches are distributed among these distances:
34 22 0.14
35 22 0.14
36 35 0.22
37 12 0.07
38 51 0.32
39 15 0.09
40 4 0.02
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (36 bp):
AAACTATATAATATAAATGTTTTCAAAATGTTTTAA
Found at i:8383979 original size:12 final size:12
Alignment explanation
Indices: 8383962--8383986 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8383952 TATAATATAT
8383962 ATGTTTTCAAAA
1 ATGTTTTCAAAA
8383974 ATGTTTTCAAAA
1 ATGTTTTCAAAA
8383986 A
1 A
8383987 CTATATATAT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:8384972 original size:84 final size:83
Alignment explanation
Indices: 8384775--8385686 Score: 1066
Period size: 84 Copynumber: 10.9 Consensus size: 83
8384765 GGGGTCTTTG
* * * *
8384775 GCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGC
1 GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* *
8384840 ACTCGAAGGTC-TTTGAT
66 ACTCAAAGGTCTTTTGTT
* * * * *
8384857 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCGTT-GAGCTGAGCGTAGTC
1 G-CAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTC
*
8384921 AAACTCAAAGGTCTTTTGTT
64 GAACTCAAAGGTCTTTTGTT
* * * * * * * * * *
8384941 AACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATC
1 -GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTC
* *
8385006 GAACTTAAGGGTC-TTTG--
64 GAACTCAAAGGTCTTTTGTT
* *
8385023 GCAGATAACCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
8385088 ACTCAAAGGTCTTTGGTT
66 ACTCAAAGGTCTTTTGTT
* * * * * * * * *
8385106 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
* * *
8385171 AACTTAAGGGTCTTTAGTT
65 AACTCAAAGGTCTTTTGTT
* * *
8385190 GGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTC
1 -GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTC
* *
8385255 GAACTCGAGGGTC-TTTG--
64 GAACTCAAAGGTCTTTTGTT
* * * *
8385272 GCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
1 GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
8385337 ACTCAAAGGTCTTTGGTT
66 ACTCAAAGGTCTTTTGTT
* * * * * * * * *
8385355 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCG
1 GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
* * *
8385420 AACTTAAGGGTCTTTAGTT
65 AACTCAAAGGTCTTTTGTT
*
8385439 GGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
1 -GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
8385504 AACTCAAAGGTCTTTTGTT
65 AACTCAAAGGTCTTTTGTT
8385523 AGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
1 -GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG
8385588 AACTCAAAGGTCTTTTGTT
65 AACTCAAAGGTCTTTTGTT
** *
8385607 AGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTCAAAGCTGAACGTAGTC
1 -GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTC
*
8385672 GAACTCGAAGGTCTT
64 GAACTCAAAGGTCTT
8385687 GGTGGACAGA
Statistics
Matches: 709, Mismatches: 103, Indels: 33
0.84 0.12 0.04
Matches are distributed among these distances:
80 53 0.07
81 83 0.12
82 1 0.00
83 131 0.18
84 293 0.41
85 148 0.21
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (83 bp):
GCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
ACTCAAAGGTCTTTTGTT
Found at i:8385309 original size:249 final size:248
Alignment explanation
Indices: 8384742--8385652 Score: 1338
Period size: 249 Copynumber: 3.6 Consensus size: 248
8384732 ATATGACCTC
* * * * * *
8384742 GAAGTTGAGTGTAATCGAACCCAGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTG
1 GAAGCTGAGCGTAGTCGAACTCAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTG
* * * * *
8384807 CAAATGATGTGCCTTAGAGCTGAGCGTAGTCGCACTCGAAGGTCTTTGATGACAGATAACCCTTC
66 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTTC
* * * * * *
8384872 TAGCCTTGAGTTATGCTGTAAATGATATGCCGTTG-AGCTGAGCGTAGTCAAACTCAAAGGTCTT
131 TAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTT
* ** * * * * *
8384936 TTGTTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTT
196 TAGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTT
* * * *
8384990 GAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATTCTG
1 GAAGCTGAGCGTAGTCGAACTCAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTG
8385055 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTTC
66 CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTTC
8385120 TAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTT
131 TAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTT
* *
8385185 TAGTTGGCAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTT
196 TAGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
* * * * *
8385238 CGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCT
1 -GAAGCTGAGCGTAGTCGAACTCAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCT
8385303 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTT
65 GCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTT
8385368 CTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCT
130 CTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCT
*
8385433 TTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT
195 TTAGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
* * *
8385487 GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTAT
1 GAAGCTGAGCGTAGTCGAACTCAAGGGTC-TTTG---GCAGATAACCCTTCTTGACTTAAGCTAT
*
8385552 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAAC
62 GCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTA-CAGATAAC
* * * * *
8385617 CCTTCTTGACTTAAGTTATGCTGCAAATGATGTGCC
126 CCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCC
8385653 TTCAAAGCTG
Statistics
Matches: 606, Mismatches: 50, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
248 182 0.30
249 306 0.50
252 79 0.13
253 39 0.06
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (248 bp):
GAAGCTGAGCGTAGTCGAACTCAAGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTG
CAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTACAGATAACCCTTC
TAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTT
TAGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT
Found at i:8389081 original size:18 final size:19
Alignment explanation
Indices: 8389040--8389084 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
8389030 AGTTAATGTG
8389040 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
8389059 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
8389077 AATGCAAA
1 AATGCAAA
8389085 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:8391974 original size:3 final size:3
Alignment explanation
Indices: 8391968--8392005 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
8391958 AAAAATGAAA
8391968 AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A
8392006 TATATATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:8392140 original size:35 final size:35
Alignment explanation
Indices: 8392075--8392288 Score: 136
Period size: 38 Copynumber: 5.8 Consensus size: 35
8392065 TTTTTAAACT
*
8392075 ATATAATATACGAATGTTTTCCAACATGTTTTCAAAAA
1 ATATAATATA--AATG-TTTCCAAAATGTTTTCAAAAA
* *
8392113 AGATTATATAAAT-TTTCCCAAAATGTTTT-AAAAA
1 ATATAATATAAATGTTT-CCAAAATGTTTTCAAAAA
* *
8392147 CTATATAATATAAATGTTTTCAAAATGCTTTC-AAAA
1 --ATATAATATAAATGTTTCCAAAATGTTTTCAAAAA
* * *
8392183 CTATAATATATATGTTTTCAAAAATGTTTTCAAAAA
1 ATATAATATAAATG-TTTCCAAAATGTTTTCAAAAA
8392219 CTATATATATATATAA-GTTTTCC-AAATGATTTT-AAAAA
1 --ATATA-ATATA-AATG-TTTCCAAAATG-TTTTCAAAAA
* *
8392257 TTATATATTATATATAT-TTTCTAAAATGTTTT
1 --ATATA--ATATAAATGTTTCCAAAATGTTTT
8392289 TTTAATACTA
Statistics
Matches: 143, Mismatches: 18, Indels: 31
0.74 0.09 0.16
Matches are distributed among these distances:
34 20 0.14
35 24 0.17
36 32 0.22
37 11 0.08
38 34 0.24
39 21 0.15
40 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.43
Consensus pattern (35 bp):
ATATAATATAAATGTTTCCAAAATGTTTTCAAAAA
Found at i:8392166 original size:72 final size:72
Alignment explanation
Indices: 8392070--8392288 Score: 237
Period size: 72 Copynumber: 3.0 Consensus size: 72
8392060 TTTTTTTTTT
* * *
8392070 AAACTATATAATATACGAATGTTTTCCAACATGTTTTCAAAAAAGATTATATAAATTTTCCCAAA
1 AAACTATATAATATAC-AATGTTTTCCAA-ATGTTTTCAAAAAATATTATATATATTTT-CAAAA
8392135 ATGTTTT-AA
63 ATGTTTTCAA
* * * * *
8392144 AAACTATATAATATA-AATGTTTTCAAAATGCTTTCAAAACTATAATATATATGTTTTCAAAAAT
1 AAACTATATAATATACAATGTTTTCCAAATGTTTTCAAAA-AATATTATATATATTTTCAAAAAT
8392208 GTTTTCAA
65 GTTTTCAA
* * *
8392216 AAACTATATATATATATAA-GTTTTCCAAATGATTTTAAAAATTATATATTATATATATTTTCTA
1 AAACTATATA-ATATACAATGTTTTCCAAATG-TTTTCAAAA--A-ATATTATATATATTTTCAA
8392280 AAATGTTTT
61 AAATGTTTT
8392289 TTTAATACTA
Statistics
Matches: 122, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
71 22 0.18
72 35 0.29
73 16 0.13
74 24 0.20
76 25 0.20
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (72 bp):
AAACTATATAATATACAATGTTTTCCAAATGTTTTCAAAAAATATTATATATATTTTCAAAAATG
TTTTCAA
Found at i:8392171 original size:36 final size:36
Alignment explanation
Indices: 8392070--8392288 Score: 189
Period size: 36 Copynumber: 5.9 Consensus size: 36
8392060 TTTTTTTTTT
*
8392070 AAACTATATAATATACGAATGTTTTCCAACATGTTTTCAA
1 AAACTATATAATATA--AATGTTTT-CAAAATGTTTT-AA
* * *
8392110 AAA--AGATTATATAAAT-TTTCCCAAAATGTTTTAA
1 AAACTATATAATATAAATGTTT-TCAAAATGTTTTAA
* *
8392144 AAACTATATAATATAAATGTTTTCAAAATGCTTTCA
1 AAACTATATAATATAAATGTTTTCAAAATGTTTTAA
*
8392180 AAAC--TATAATATATATGTTTTCAAAAATGTTTTCAA
1 AAACTATATAATATAAATGTTTTC-AAAATGTTTT-AA
*
8392216 AAACTATATATATATATAA-GTTTTCCAAATGATTTTAA
1 AAACTATATA-ATATA-AATGTTTTCAAAATG-TTTTAA
* * * *
8392254 AAATTATATATTATATATATTTTCTAAAATGTTTT
1 AAACTATATAATATAAATGTTTTC-AAAATGTTTT
8392289 TTTAATACTA
Statistics
Matches: 147, Mismatches: 19, Indels: 29
0.75 0.10 0.15
Matches are distributed among these distances:
34 22 0.15
35 22 0.15
36 35 0.24
37 16 0.11
38 33 0.22
39 15 0.10
40 4 0.03
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (36 bp):
AAACTATATAATATAAATGTTTTCAAAATGTTTTAA
Found at i:8392211 original size:12 final size:12
Alignment explanation
Indices: 8392194--8392218 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8392184 TATAATATAT
8392194 ATGTTTTCAAAA
1 ATGTTTTCAAAA
8392206 ATGTTTTCAAAA
1 ATGTTTTCAAAA
8392218 A
1 A
8392219 CTATATATAT
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:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:8392301 original size:37 final size:37
Alignment explanation
Indices: 8392115--8392318 Score: 122
Period size: 36 Copynumber: 5.5 Consensus size: 37
8392105 TTCAAAAAAG
* *
8392115 ATTATATAAATTTTCCCAAAATG-TTTTAAAA-ACTAT
1 ATTATATATATTTT-CTAAAATGTTTTTAAAATACTAT
* * * *
8392151 ATAATATAAATGTTT-TCAAAATG-CTTTCAAA-ACTAT
1 ATTATATATAT-TTTCT-AAAATGTTTTTAAAATACTAT
* * * *
8392187 AATATATATGTTTTCAAAAATGTTTTCAAAA-ACTAT
1 ATTATATATATTTTCTAAAATGTTTTTAAAATACTAT
* *
8392223 ATATATATATAAGTTTTC-CAAATGATTTTAAAAATTA-TAT
1 AT-TATATAT-A-TTTTCTAAAATG-TTTTTAAAA-TACTAT
**
8392263 ATTATATATATTTTCTAAAATGTTTTTTTAATACTAT
1 ATTATATATATTTTCTAAAATGTTTTTAAAATACTAT
*
8392300 A-TATTATATAATTT-TAAAA
1 ATTA-TATATATTTTCTAAAA
8392319 ACTATTAAAA
Statistics
Matches: 134, Mismatches: 21, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
35 9 0.07
36 54 0.40
37 34 0.25
38 11 0.08
39 20 0.15
40 5 0.04
41 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
ATTATATATATTTTCTAAAATGTTTTTAAAATACTAT
Found at i:8392301 original size:39 final size:37
Alignment explanation
Indices: 8392115--8392357 Score: 196
Period size: 38 Copynumber: 6.5 Consensus size: 37
8392105 TTCAAAAAAG
*
8392115 ATTATATAAATTTTCCCAAAATG-TTTTAAAAACTATAT
1 ATTATATATATTTT--CAAAATGTTTTTAAAAACTATAT
* * * * *
8392153 AATATAAATGTTTTCAAAATG-CTTTCAAAACTATA-
1 ATTATATATATTTTCAAAATGTTTTTAAAAACTATAT
* *
8392188 A-TATATATGTTTTCAAAAATGTTTTCAAAAACTATAT
1 ATTATATATATTTTC-AAAATGTTTTTAAAAACTATAT
* * *
8392225 A-TATATATAAGTTTTCCAAATGATTTTAAAAATTATAT
1 ATTATATAT-A-TTTTCAAAATGTTTTTAAAAACTATAT
* *
8392263 ATTATATATATTTTCTAAAATGTTTTTTTAATACTATAT
1 ATTATATATATTTTC-AAAATG-TTTTTAAAAACTATAT
** *
8392302 ATTATATA-ATTTT-AAAA-ACTATTAAAAACTATAT
1 ATTATATATATTTTCAAAATGTTTTTAAAAACTATAT
*
8392336 ATTATATACGTAGTTTCAAAAT
1 ATTATATA--TATTTTCAAAAT
8392358 ATGTATATAT
Statistics
Matches: 166, Mismatches: 26, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
34 32 0.19
35 7 0.04
36 34 0.20
37 17 0.10
38 44 0.27
39 32 0.19
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
ATTATATATATTTTCAAAATGTTTTTAAAAACTATAT
Found at i:8393193 original size:12 final size:12
Alignment explanation
Indices: 8393176--8393222 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
8393166 ATTTAACATT
8393176 TGGTACTGTTCA
1 TGGTACTGTTCA
8393188 TGGTACTGTTCA
1 TGGTACTGTTCA
*
8393200 T--TATTGTTCA
1 TGGTACTGTTCA
* *
8393210 TAGTATTGTTCA
1 TGGTACTGTTCA
8393222 T
1 T
8393223 ACGGTATAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 9 0.28
12 23 0.72
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (12 bp):
TGGTACTGTTCA
Found at i:8393249 original size:19 final size:19
Alignment explanation
Indices: 8393209--8393249 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
8393199 ATTATTGTTC
**
8393209 ATAGTATTGTTCATACGGT
1 ATAGTATTGTTCATACCCT
8393228 ATAGTATTGTTCATACCCT
1 ATAGTATTGTTCATACCCT
8393247 ATA
1 ATA
8393250 TTACTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (19 bp):
ATAGTATTGTTCATACCCT
Found at i:8394431 original size:76 final size:77
Alignment explanation
Indices: 8394303--8394510 Score: 282
Period size: 76 Copynumber: 2.8 Consensus size: 77
8394293 CCGTTGTACA
* * *
8394303 AGGGGGGAATCGGTACC-CCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
**
8394366 -CAAAACTGTTT
66 CCAAAACCATTT
*
8394377 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGG-ATATCTCGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAT-TCTCGGA
8394441 GCCAAAACCATTT
65 GCCAAAACCATTT
* * * *
8394454 A-GGGGGAATCAGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
8394511 TTTGGCTTTG
Statistics
Matches: 119, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
74 16 0.13
75 5 0.04
76 86 0.72
77 12 0.10
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
CCAAAACCATTT
Found at i:8397129 original size:21 final size:21
Alignment explanation
Indices: 8397075--8397137 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
8397065 TTCCCCTGTG
8397075 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTT-CCC-TCAA
*
8397098 AGGGGGAATCGGTTCCCTC-A
1 GGGGGGAATCGGTTCCCTCAA
*
8397118 GGGGGGAGATCGATTCCCTC
1 GGGGGGA-ATCGGTTCCCTC
8397138 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 7 0.19
21 13 0.36
22 3 0.08
23 13 0.36
ACGTcount: A:0.17, C:0.25, G:0.37, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTCAA
Found at i:8400973 original size:22 final size:21
Alignment explanation
Indices: 8400931--8400970 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8400921 GAGTTTGTTT
*
8400931 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
8400952 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
8400971 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:8403080 original size:77 final size:77
Alignment explanation
Indices: 8402889--8403088 Score: 282
Period size: 76 Copynumber: 2.6 Consensus size: 77
8402879 CCGTTGTACA
* * *
8402889 AGGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
**
8402952 GCAAAACTGTTT
66 GCAAAACCATTT
* *
8402964 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
8403028 GCCAAAACCATTT
66 G-CAAAACCATTT
* *
8403041 A-GGGGGAATCTGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCA
8403089 ATATGTAATT
Statistics
Matches: 112, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
75 25 0.22
76 53 0.47
77 34 0.30
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGA
GCAAAACCATTT
Done.