Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009141.1 Hibiscus syriacus cultivar Beakdansim tig00112649_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: 919200
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:875018 original size:165 final size:165
Alignment explanation
Indices: 874757--875272 Score: 574
Period size: 165 Copynumber: 3.1 Consensus size: 165
874747 AGGCCTTTGG
* * * * * * * * ** *
874757 TTGGTAGATAACCCTTCTCGACTTAAGTTATATTGCAAAAGATGTACCCTCGAAGTTGAGTATAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGT-GCCTTGGAGCTGAGCGTAG
* *
874822 TCGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTATAACCTTGAGTTATGCTGTAAATGATGT
65 TCGAACTCAAAGGTCTTTTTGTGACAGATAACCCTTCTAACCTTGAGTTATGCTGTAAATGATGT
*
874887 GCCCTCAAAGCTGAGTGTAATCGAACTTGAGGGTCT
130 GCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTCT
* *
874923 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGTAAATGATGTGCCTTGGAGCTGAGCGTTGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
** * * * * * *
874988 CGAACTTTAAGGTCTTTTTTTGGA-AGATAACCCTTCTAGA-CTTAAGTTGTACTGCAGATGATG
66 CGAACTCAAAGGTCTTTTTGT-GACAGATAACCCTTCTA-ACCTTGAGTTATGCTGTAAATGATG
* * **
875051 TGCCCTCGAATCTGAGTGTAATTAAACTCGAGGGTCT
129 TGCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTCT
*
875088 TTGGCAGATAACTCTTCTCGACTTAAGCTATGA-TGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGCTAT-ACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
* * * * *
875152 TCGAACTCGAAGGT-TTTTTGTCACAGATAACCCTTCTAGCTTTGAGTTATGCTGTAAATGATAT
65 TCGAACTCAAAGGTCTTTTTGTGACAGATAACCCTTCTAACCTTGAGTTATGCTGTAAATGATGT
* * * * *
875216 G-CCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
130 GCCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTC-T
875252 TTGGTGACAGATAACCCTTCT
1 TT-G-G-CAGATAACCCTTCT
875273 AGCCTTGAGT
Statistics
Matches: 288, Mismatches: 53, Indels: 17
0.80 0.15 0.05
Matches are distributed among these distances:
163 25 0.09
164 41 0.14
165 164 0.57
166 45 0.16
167 13 0.05
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (165 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCAAAGGTCTTTTTGTGACAGATAACCCTTCTAACCTTGAGTTATGCTGTAAATGATGTG
CCCTCAAAGCTGAGTGTAATCGAACTCGAGGGTCT
Found at i:875112 original size:81 final size:81
Alignment explanation
Indices: 874675--875158 Score: 332
Period size: 85 Copynumber: 5.9 Consensus size: 81
874665 GTCTTTGGTA
* * * * * * * *
874675 GGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTG-AGCTGAGCGTAGTC
1 GGCAGATAACCCTTCTCGACTTAAGTTGTACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
** * *
874739 GAACTCAAAGGCCTTTGGTT
66 GAACT-TGAGG-GTCT--TT
* * * * * * *
874759 GGTAGATAACCCTTCTCGACTTAAGTTATATTGCAAAAGATGTACCCTCGAAGTTGAGTATAATC
1 GGCAGATAACCCTTCTCGACTTAAGTTGTACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
** *
874824 GAACTCAAAGGTCTTTT
66 GAACTTGAGGGTC-TTT
* * * * * * *
874841 GGTGACAGATAACCCTTAT-AACCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTGAGTGT
1 -G-G-CAGATAACCCTTCTCGA-CTTAAGTTGTACTGCAAATGATGTGCCCTCGAAGCTGAGTGT
874905 AATCGAACTTGAGGGTCTTT
62 AATCGAACTTGAGGGTCTTT
* * * * * * **
874925 GGCAGATAACCCTTCTCGACTTAAGCTATACTGTAAATGATGTG-CCTTGGAGCTGAGCGTTGTC
1 GGCAGATAACCCTTCTCGACTTAAGTTGTACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
* *
874989 GAACTTTAAGGTCTTTTTTT
66 GAACTTGAGGGTC----TTT
* * * * *
875009 GGAAGATAACCCTTCTAGACTTAAGTTGTACTGCAGATGATGTGCCCTCGAATCTGAGTGTAATT
1 GGCAGATAACCCTTCTCGACTTAAGTTGTACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
* *
875074 AAACTCGAGGGTCTTT
66 GAACTTGAGGGTCTTT
* * * * *
875090 GGCAGATAACTCTTCTCGACTTAAGCTATG-A-TGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 GGCAGATAACCCTTCTCGACTTAAG-T-TGTACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
875152 TCGAACT
64 TCGAACT
875159 CGAAGGTTTT
Statistics
Matches: 313, Mismatches: 73, Indels: 32
0.75 0.17 0.08
Matches are distributed among these distances:
80 43 0.14
81 72 0.23
82 6 0.02
83 5 0.02
84 91 0.29
85 96 0.31
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (81 bp):
GGCAGATAACCCTTCTCGACTTAAGTTGTACTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATC
GAACTTGAGGGTCTTT
Found at i:875299 original size:84 final size:84
Alignment explanation
Indices: 874653--875297 Score: 544
Period size: 84 Copynumber: 7.8 Consensus size: 84
874643 CTGAATGAAA
* * * *
874653 TCGAACTCGAAGGTC-TTTGGTAGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCGAAGGTCTTTTGGT-GACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
*
874717 TGCCTTTGAGCTGAGCGTAG
65 TGCCTTAGAGCTGAGCGTAG
* * ** * ** *
874737 TCGAACTCAAAGG-CCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTATATTGCAAAAGATG
1 TCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * * ** *
874801 TACCCTCGAAGTTGAGTATAA
65 TGCCTTAG-AGCTGAGCGTAG
* * * *
874822 TCGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTATA-ACCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGA-CTTAAGTTATGCTGCAAATGATG
* * * *
874886 TGCCCTCAAAGCTGAGTGTAA
65 TG-CCTTAGAGCTGAGCGTAG
* * * * * *
874907 TCGAACTTGAGGGTC-TTT-G-G-CAGATAACCCTTCTCGACTTAAGCTATACTGTAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* *
874968 GCCTTGGAGCTGAGCGTTG
66 GCCTTAGAGCTGAGCGTAG
** ** * * *
874987 TCGAACTTTAAGGTCTTTTTTTGGA-AGATAACCCTTCTAGACTTAAGTTGTACTGCAGATGATG
1 TCGAACTCGAAGGTCTTTTGGT-GACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * * * *
875051 TGCCCTCGAATCTGAGTGTAA
65 TGCCTTAG-AGCTGAGCGTAG
** * * * * *
875072 TTAAACTCGAGGGTC-TTT-G-G-CAGATAACTCTTCTCGACTTAAGCTATGATGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
875133 GCCTTGGAGCTGAGCGTAG
66 GCCTTAGAGCTGAGCGTAG
* * * * *
875152 TCGAACTCGAAGGT-TTTTTGTCACAGATAACCCTTCTAG-CTTTGAGTTATGCTGTAAATGATA
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGAC-TTAAGTTATGCTGCAAATGATG
875215 TGCCTTAGAGCTGAGCGTAG
65 TGCCTTAGAGCTGAGCGTAG
* * *
875235 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT
1 TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT
875298 ATCTTTAAAA
Statistics
Matches: 449, Mismatches: 91, Indels: 42
0.77 0.16 0.07
Matches are distributed among these distances:
80 48 0.11
81 78 0.17
82 3 0.01
83 66 0.15
84 150 0.33
85 96 0.21
86 8 0.02
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
GCCTTAGAGCTGAGCGTAG
Found at i:879401 original size:9 final size:10
Alignment explanation
Indices: 879382--879411 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
879372 TTAGTGAGGT
*
879382 AAATCAAAAA
1 AAATAAAAAA
879392 AAATAAAAAA
1 AAATAAAAAA
879402 AAATAAAAAA
1 AAATAAAAAA
879412 TCCTACCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (10 bp):
AAATAAAAAA
Found at i:880501 original size:2 final size:2
Alignment explanation
Indices: 880496--880558 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
880486 AAAAAAGGTA
880496 AT 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 AT
880538 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
880559 GATAAATAGG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:881876 original size:13 final size:13
Alignment explanation
Indices: 881858--881882 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
881848 AAATGAAAAG
881858 AAATAATAATAAT
1 AAATAATAATAAT
881871 AAATAATAATAA
1 AAATAATAATAA
881883 CAATAATATA
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:882066 original size:41 final size:38
Alignment explanation
Indices: 882003--882158 Score: 125
Period size: 35 Copynumber: 4.2 Consensus size: 38
881993 ATAATATAAG
*
882003 TTTTCAAAATGTTTTTTAAAACTATATATTATATAAAT
1 TTTTCAAAATGTTTTTTAAAACTATACATTATATAAAT
882041 TTTTCAAAAATGGTTTTTTAAAAACTATACA-T-TAT--A-
1 TTTTC-AAAAT-GTTTTTT-AAAACTATACATTATATAAAT
* * *
882077 TTTTCAAAATG-ATTTCAAAACTATATATTATAT-AA-
1 TTTTCAAAATGTTTTTTAAAACTATACATTATATAAAT
* * * *
882112 CTTTCAAAATG--TTTTAAAACTTATATATTGTATATAAG
1 TTTTCAAAATGTTTTTTAAAAC-TATACATTATATA-AAT
882150 TTTTCAAAA
1 TTTTCAAAA
882159 ACATTTTTAA
Statistics
Matches: 100, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
32 10 0.10
33 4 0.04
34 12 0.12
35 27 0.27
36 5 0.05
37 3 0.03
38 13 0.13
39 8 0.08
40 8 0.08
41 10 0.10
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTTCAAAATGTTTTTTAAAACTATACATTATATAAAT
Found at i:882068 original size:110 final size:108
Alignment explanation
Indices: 881946--882193 Score: 274
Period size: 108 Copynumber: 2.3 Consensus size: 108
881936 CTTAAAAACG
* * *
881946 TTTTCAAAACTATATATTATATAGTTTTCAAAAATAATTTTAAAA-ATATA-ATATAAGTTTTCA
1 TTTTAAAAACTATATATTATATA-TTTTC-AAAATAATTTCAAAACATATATATATAA-CTTTCA
* **
882009 AAATGTTTTTTAAAAC-TATATATTATATA-AATTTTTCAAAAATGGTT
63 AAATG--TTTTAAAACTTATATATTATATATAAGTTTTCAAAAA-CATT
* *
882056 TTTTAAAAACTATACA-T-TATATTTTCAAAATGATTTCAAAACTATATATTATATAACTTTCAA
1 TTTTAAAAACTATATATTATATATTTTCAAAATAATTTCAAAAC-ATATA-TATATAACTTTCAA
*
882119 AATGTTTTAAAACTTATATATTGTATATAAGTTTTCAAAAACATT
64 AATGTTTTAAAACTTATATATTATATATAAGTTTTCAAAAACATT
*
882164 TTTAAAAAACTATATTATATATATATTTTC
1 TTTTAAAAACTATA-TAT-TATATATTTTC
882194 GGAAACCGTT
Statistics
Matches: 117, Mismatches: 11, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
106 13 0.11
107 14 0.12
108 36 0.31
109 24 0.21
110 20 0.17
111 1 0.01
112 9 0.08
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (108 bp):
TTTTAAAAACTATATATTATATATTTTCAAAATAATTTCAAAACATATATATATAACTTTCAAAA
TGTTTTAAAACTTATATATTATATATAAGTTTTCAAAAACATT
Found at i:882101 original size:73 final size:70
Alignment explanation
Indices: 881908--882111 Score: 213
Period size: 73 Copynumber: 2.9 Consensus size: 70
881898 TATAATATAA
** * * *
881908 AAAAAT-ATTTTTTAAACTATATATTATA-CTTAAAAACGTTTTCAAAACTATATATTATAT--A
1 AAAAATAATTTTAAAAACTATA-ATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAAA
881969 GTTTTC
65 GTTTTC
*
881975 AAAAATAATTTTAAAAA-TATAA-TATAAGTTTTCAAAATGTTTTTTAAAACTATATATTATATA
1 AAAAATAATTTTAAAAACTATAATTAT-A-TTTTCAAAATG-TTTTCAAAACTATATATTATATA
*
882038 AATTTTTC
63 AAGTTTTC
** *
882046 AAAAATGGTTTTTTAAAAACTATACATTATATTTTCAAAATGATTTCAAAACTATATATTATATA
1 AAAAAT--AATTTTAAAAACTATA-ATTATATTTTCAAAATGTTTTCAAAACTATATATTATATA
882111 A
63 A
882112 CTTTCAAAAT
Statistics
Matches: 114, Mismatches: 11, Indels: 18
0.80 0.08 0.13
Matches are distributed among these distances:
65 3 0.03
66 2 0.02
67 10 0.09
68 15 0.13
69 21 0.18
71 12 0.11
73 31 0.27
74 15 0.13
75 2 0.02
76 3 0.03
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (70 bp):
AAAAATAATTTTAAAAACTATAATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAAAG
TTTTC
Found at i:882148 original size:37 final size:36
Alignment explanation
Indices: 881947--882158 Score: 140
Period size: 32 Copynumber: 5.9 Consensus size: 36
881937 TTAAAAACGT
* *
881947 TTTCAAAACTATATATTATAT-AGTTTTCAAAAATAA
1 TTTCAAAACTATATATTATATAAGCTTTC-AAAATGA
* * *
881983 TTTTAAAA--ATATA--ATATAAGTTTTCAAAATGTT
1 TTTCAAAACTATATATTATATAAGCTTTCAAAATG-A
* ** *
882016 TTTTAAAACTATATATTATATAAATTTTTCAAAAATGGTTT
1 TTTCAAAACTATATATTATAT-AAGCTTTC-AAAAT-G--A
* *
882057 TTTAAAAACTATACATTATAT----TTTCAAAATGA
1 TTTCAAAACTATATATTATATAAGCTTTCAAAATGA
882089 TTTCAAAACTATATATTATATAA-CTTTCAAAATG-
1 TTTCAAAACTATATATTATATAAGCTTTCAAAATGA
* *
882123 TTTTAAAACTTATATATTGTATATAAGTTTTCAAAA
1 TTTCAAAAC-TATATA-T-TATATAAGCTTTCAAAA
882159 ACATTTTTAA
Statistics
Matches: 148, Mismatches: 11, Indels: 32
0.77 0.06 0.17
Matches are distributed among these distances:
32 28 0.19
33 15 0.10
34 14 0.09
35 26 0.18
36 12 0.08
37 11 0.07
38 15 0.10
39 5 0.03
40 1 0.01
41 21 0.14
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTCAAAACTATATATTATATAAGCTTTCAAAATGA
Found at i:882154 original size:73 final size:76
Alignment explanation
Indices: 881947--882158 Score: 197
Period size: 73 Copynumber: 2.9 Consensus size: 76
881937 TTAAAAACGT
* **
881947 TTTCAAAACTATATATTATAT-AGT-TTTCAAAAAT-AATTTTAAAAA-TAT--A-ATATAAGTT
1 TTTCAAAACTATATATTATATAAATCTTTCAAAAATGGTTTTTAAAAACTATACATATATAAGTT
*
882005 TTCAAAATGTT
66 TTCAAAATGTA
* *
882016 TTTTAAAACTATATATTATATAAATTTTTCAAAAATGGTTTTTTAAAAACTATACAT-TAT-A-T
1 TTTCAAAACTATATATTATATAAATCTTTCAAAAATGG-TTTTTAAAAACTATACATATATAAGT
882078 TTTCAAAATG-A
65 TTTCAAAATGTA
*
882089 TTTCAAAACTATATATTATAT-AA-CTTTC-AAAAT-G-TTTT-AAAACTTATATATTGTATATA
1 TTTCAAAACTATATATTATATAAATCTTTCAAAAATGGTTTTTAAAAAC-TATACA---TATATA
882148 AGTTTTCAAAA
62 AGTTTTCAAAA
882159 ACATTTTTAA
Statistics
Matches: 120, Mismatches: 8, Indels: 26
0.78 0.05 0.17
Matches are distributed among these distances:
66 5 0.04
67 9 0.08
69 21 0.17
70 8 0.07
71 17 0.14
72 3 0.03
73 38 0.32
74 14 0.12
75 1 0.01
76 4 0.03
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (76 bp):
TTTCAAAACTATATATTATATAAATCTTTCAAAAATGGTTTTTAAAAACTATACATATATAAGTT
TTCAAAATGTA
Found at i:882185 original size:39 final size:37
Alignment explanation
Indices: 881951--882260 Score: 134
Period size: 41 Copynumber: 8.4 Consensus size: 37
881941 AAACGTTTTC
* * *
881951 AAAACTATATATTATATAGTTTTCAAAAATAATTTT-A
1 AAAACTATATA-TATATAATTTTCAAAAACATTTTTAA
* ** *
881988 AAAA-TATA-ATATA-AGTTTTC-AAAATGTTTTT-T
1 AAAACTATATATATATAATTTTCAAAAACATTTTTAA
** *
882020 AAAACTATATATTATATAAATTTTTCAAAAATGGTTTTTTA
1 AAAACTATATA-TATAT-AA-TTTTCAAAAA-CATTTTTAA
* ** *
882061 AAAACTATACAT-TAT-ATTTTCAAAATGA--TTT-C
1 AAAACTATATATATATAATTTTCAAAAACATTTTTAA
*
882093 AAAACTATATATTATATAACTTTC--AAA-ATGTTTT--
1 AAAACTATATA-TATATAATTTTCAAAAACAT-TTTTAA
882127 AAAACTTATATATTGTATATAAGTTTTCAAAAACATTTTTAA
1 AAAAC-TATATA---TATATAA-TTTTCAAAAACATTTTTAA
* * * **
882169 AAAACTATATTATATATATATTTTCGGAAACCGTTTTTTTG
1 AAAACTATA-TATATATA-ATTTTC-AAAAAC-ATTTTTAA
*
882210 AAAACTATATAT-TATATTTTTCAAAAAACA-TTTTAA
1 AAAACTATATATATATAATTTTC-AAAAACATTTTTAA
*
882246 AAAAATATACTATAT
1 AAAACTATA-TATAT
882261 TACTATATAT
Statistics
Matches: 215, Mismatches: 28, Indels: 59
0.71 0.09 0.20
Matches are distributed among these distances:
32 24 0.11
33 17 0.08
34 13 0.06
35 20 0.09
36 25 0.12
37 16 0.07
38 19 0.09
39 22 0.10
40 22 0.10
41 30 0.14
42 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAACTATATATATATAATTTTCAAAAACATTTTTAA
Found at i:882928 original size:28 final size:29
Alignment explanation
Indices: 882881--882939 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
882871 TAGAATAATA
**
882881 ACTATTTTTATATATTTTTTAATACTTTT
1 ACTATTTTTATATAGATTTTAATACTTTT
882910 ACTA-TTTTATATAGATTTTAATACTTTT
1 ACTATTTTTATATAGATTTTAATACTTTT
882938 AC
1 AC
882940 CGTGTATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (29 bp):
ACTATTTTTATATAGATTTTAATACTTTT
Found at i:886894 original size:3 final size:3
Alignment explanation
Indices: 886886--886914 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
886876 AGTGAGGCAA
886886 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
886915 CAAGGAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:887165 original size:23 final size:23
Alignment explanation
Indices: 887135--887204 Score: 106
Period size: 23 Copynumber: 3.0 Consensus size: 23
887125 CTTGTATAAA
887135 TGCACAGAAGTGCCACGTAGAAT
1 TGCACAGAAGTGCCACGTAGAAT
887158 TGCACAGAAGTGCCACGTAGAAT
1 TGCACAGAAGTGCCACGTAGAAT
* *
887181 TGCATC-GAAGTACCGCGTAGAAT
1 TGCA-CAGAAGTGCCACGTAGAAT
887204 T
1 T
887205 ACACCGTAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACAGAAGTGCCACGTAGAAT
Found at i:890874 original size:17 final size:17
Alignment explanation
Indices: 890852--890884 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
890842 AGAACTTTGA
890852 AAAATATGTAAACAAAT
1 AAAATATGTAAACAAAT
890869 AAAATATGTAAACAAA
1 AAAATATGTAAACAAA
890885 ATGAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAATATGTAAACAAAT
Found at i:890886 original size:18 final size:18
Alignment explanation
Indices: 890852--890891 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 18
890842 AGAACTTTGA
890852 AAAATATGTAAACAAAT-
1 AAAATATGTAAACAAATG
890869 AAAATATGTAAACAAAATG
1 AAAATATGTAAAC-AAATG
890888 AAAA
1 AAAA
890892 ATATTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.62
18 4 0.19
19 4 0.19
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (18 bp):
AAAATATGTAAACAAATG
Found at i:893801 original size:32 final size:31
Alignment explanation
Indices: 893760--893823 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
893750 ATAATTATTG
893760 AATAACTACACGCAACAATGACTGTGAAGAAA
1 AATAACTACACGCAACAATGACTGTGAA-AAA
* *
893792 AATAACTACACGCAACAATTATTGTGAAAAA
1 AATAACTACACGCAACAATGACTGTGAAAAA
893823 A
1 A
893824 TAGAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 4 0.13
32 26 0.87
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (31 bp):
AATAACTACACGCAACAATGACTGTGAAAAA
Found at i:896866 original size:55 final size:55
Alignment explanation
Indices: 896806--896918 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
896796 TACTATACTT
* * *
896806 AGTTCATTTTAGTCATACTATTAAAAATAATATTTTAGTCCATGAACATTTGAAA
1 AGTTCATTTTAGTCATACTATTAAAAAGAACATTTTAGTCCATGAACATTTAAAA
*
896861 AGTTCATTTTAGTCATACTATTAAAAGGAACATTTTAGTCCATGAACATTTAAAA
1 AGTTCATTTTAGTCATACTATTAAAAAGAACATTTTAGTCCATGAACATTTAAAA
896916 AGT
1 AGT
896919 GAATCTTTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (55 bp):
AGTTCATTTTAGTCATACTATTAAAAAGAACATTTTAGTCCATGAACATTTAAAA
Found at i:896870 original size:29 final size:28
Alignment explanation
Indices: 896837--896915 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
896827 TAAAAATAAT
*
896837 ATTTTAGTCCATGAACATTTGAAAAGTTC
1 ATTTTAGTCCATGAACATTT-AAAAGTAC
*
896866 ATTTTAGT-CAT--AC-TATTAAAAGGAAC
1 ATTTTAGTCCATGAACAT-TTAAAA-GTAC
896892 ATTTTAGTCCATGAACATTTAAAA
1 ATTTTAGTCCATGAACATTTAAAA
896916 AGTGAATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
25 5 0.12
26 14 0.33
27 3 0.07
28 3 0.07
29 16 0.38
30 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (28 bp):
ATTTTAGTCCATGAACATTTAAAAGTAC
Found at i:896899 original size:26 final size:25
Alignment explanation
Indices: 896810--896900 Score: 76
Period size: 26 Copynumber: 3.4 Consensus size: 25
896800 ATACTTAGTT
*
896810 CATTTTAGTCATACTATTAAAAATAA
1 CATTTTAGTCATACTATT-AAAAGAA
* **
896836 TATTTTAGTCCATGAAC-ATTTGAAAAGTT
1 CATTTTAGT-CAT--ACTA-TT-AAAAGAA
896865 CATTTTAGTCATACTATTAAAAGGAA
1 CATTTTAGTCATACTATTAAAA-GAA
896891 CATTTTAGTC
1 CATTTTAGTC
896901 CATGAACATT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
25 4 0.08
26 23 0.45
27 4 0.08
28 4 0.08
29 16 0.31
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (25 bp):
CATTTTAGTCATACTATTAAAAGAA
Found at i:903214 original size:26 final size:26
Alignment explanation
Indices: 903176--903239 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
903166 TGTCCCTCAG
* * *
903176 ATTCGTTCCATGCATGTAAATCAATC
1 ATTCCTTCAATGCATGCAAATCAATC
*
903202 ATTCCTTCAATGCGTGCAAATCAATC
1 ATTCCTTCAATGCATGCAAATCAATC
903228 ATTCCTTCAATG
1 ATTCCTTCAATG
903240 AAGATTTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (26 bp):
ATTCCTTCAATGCATGCAAATCAATC
Found at i:917972 original size:20 final size:19
Alignment explanation
Indices: 917933--917996 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
917923 GCATTGAATG
*
917933 TTCACACAGTACGATACTA
1 TTCATACAGTACGATACTA
*
917952 TTCATACAGTATCGGTACTA
1 TTCATACAGTA-CGATACTA
* *
917972 TTTATACAGTGC-ATTACTA
1 TTCATACAGTACGA-TACTA
917991 TTCATA
1 TTCATA
917997 AAAAAATTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (19 bp):
TTCATACAGTACGATACTA
Done.