Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007609.1 Hibiscus syriacus cultivar Beakdansim tig00022473_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: 35736
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.24
Found at i:2315 original size:31 final size:30
Alignment explanation
Indices: 2254--2330 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
2244 GTGTGCGTGC
** * *
2254 GCCTCGTCACCATCGGTAATCCAAGGCGGT
1 GCCTCGTCACCATCGACAAACCAAGACGGT
*
2284 GGCCTCGTCACCATCGACAAACCCAGACGGT
1 -GCCTCGTCACCATCGACAAACCAAGACGGT
*
2315 GTCTCGGTCACCATCG
1 GCCTC-GTCACCATCG
2331 GCAACCCCGC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 4 0.10
31 35 0.90
ACGTcount: A:0.21, C:0.36, G:0.25, T:0.18
Consensus pattern (30 bp):
GCCTCGTCACCATCGACAAACCAAGACGGT
Found at i:2486 original size:164 final size:166
Alignment explanation
Indices: 2120--2681 Score: 903
Period size: 164 Copynumber: 3.4 Consensus size: 166
2110 ACGTGTGCGT
* *
2120 GCCTCGGTCACCATCGGCAAA--AACACGGGTG-CTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
2182 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
65 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
2247 TGCGTGCGCCTCGTCACCATCGGTAATCCAAGGCGGTG
130 TGCGTGAGCCTCGTCACCATCGGCAATCC-AGGCGGTG
*
2285 GCCTC-GTCACCATCGACAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCC-GCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
* *
2347 TGCGGGAGTGCCGCACAGTACCGAGC-TTTGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
*
2411 GCGTGAGCCTCGTCACCATCGGCAATCCTGGCGGTG
131 GCGTGAGCCTCGTCACCATCGGCAATCCAGGCGGTG
2447 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATC-GCAACCCCGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
* *
2511 TGCGGGAGTGCCGCACA-AACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG--CCCTTGT
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
2573 GCGTGAGCCTCGTCACCATCGGCAATCCCAGGCGGGTG
131 GCGTGAGCCTCGTCACCATCGGCAAT-CCAGGC-GGTG
*
2611 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTG
2676 GTGCGG
65 GTGCGG
2682 AGCCTCGGTC
Statistics
Matches: 371, Mismatches: 15, Indels: 21
0.91 0.04 0.05
Matches are distributed among these distances:
162 44 0.12
163 104 0.28
164 168 0.45
165 16 0.04
166 39 0.11
ACGTcount: A:0.17, C:0.35, G:0.31, T:0.17
Consensus pattern (166 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGG
TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGT
GCGTGAGCCTCGTCACCATCGGCAATCCAGGCGGTG
Found at i:2622 original size:33 final size:33
Alignment explanation
Indices: 2579--2762 Score: 178
Period size: 33 Copynumber: 5.5 Consensus size: 33
2569 TTGTGCGTGA
*
2579 GCCTC-GTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
2611 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * * *
2643 GTCTCGGTCACCATCGGTAACCCCGGGCCATTGGTGCGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C---GG-G-TG
**
2682 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
2716 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
2748 GTCTC-GTCACCATCG
1 GCCTCGGTCACCATCG
2763 CAACCCCGGC
Statistics
Matches: 125, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
31 10 0.08
32 31 0.25
33 54 0.43
34 1 0.01
35 1 0.01
36 4 0.03
37 1 0.01
39 1 0.01
40 22 0.18
ACGTcount: A:0.17, C:0.36, G:0.30, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
Found at i:2733 original size:105 final size:101
Alignment explanation
Indices: 2571--2785 Score: 367
Period size: 105 Copynumber: 2.1 Consensus size: 101
2561 TCAGGCCCTT
2571 GTGCGTGAGCCTCGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
1 GTGCG-GAGCCTCGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
*
2636 GACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
65 GACGGGTGTCTC-GTCACCATC-GCAACCCC-GGCCATTG
*
2676 GTGCGGAGCCTCGGTCACCATCGGCAGTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
1 GTGCGGAGCCTC-GTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCA
2741 GACGGGTGTCTCGTCACCATCGCAACCCCGGCCATTG
65 GACGGGTGTCTCGTCACCATCGCAACCCCGGCCATTG
2778 GTGCGGAG
1 GTGCGGAG
2786 TGCCGCACAG
Statistics
Matches: 107, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
102 16 0.15
103 7 0.07
104 16 0.15
105 68 0.64
ACGTcount: A:0.17, C:0.35, G:0.32, T:0.16
Consensus pattern (101 bp):
GTGCGGAGCCTCGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAG
ACGGGTGTCTCGTCACCATCGCAACCCCGGCCATTG
Found at i:3164 original size:11 final size:11
Alignment explanation
Indices: 3148--3179 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3138 TTCCCGTGGT
3148 GCTCCGGCGAC
1 GCTCCGGCGAC
*
3159 GCTCCGGCGAT
1 GCTCCGGCGAC
3170 GCTCCGGCGA
1 GCTCCGGCGA
3180 GACATTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.38, T:0.12
Consensus pattern (11 bp):
GCTCCGGCGAC
Found at i:11134 original size:31 final size:31
Alignment explanation
Indices: 11090--11170 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
11080 GTGTGCGTGC
* * *
11090 GCCTCGGTCACCATCGTAATCCAAGGCGGGT
1 GCCTCGGTCACCATCGCAAACCAAGACGGGT
*
11121 GGCCTC-GTCACCATCGCAAACCCAGACGGGT
1 -GCCTCGGTCACCATCGCAAACCAAGACGGGT
*
11152 GTCTCGGTCACCATCGCAA
1 GCCTCGGTCACCATCGCAA
11171 CCCCGGCCAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.09
31 34 0.79
32 5 0.12
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.17
Consensus pattern (31 bp):
GCCTCGGTCACCATCGCAAACCAAGACGGGT
Found at i:11244 original size:164 final size:167
Alignment explanation
Indices: 10957--11520 Score: 879
Period size: 163 Copynumber: 3.4 Consensus size: 167
10947 ACGTGTGCGT
**
10957 GCCTCGGTCACCATCGGCAAAAACAGACGGTGTCTC-GTCACCATCGGCAACCCCGGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
*
11021 TGC-GGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACCATCAGCCCCCGTGTG
66 TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGCCCCCGTGTG
* *
11085 CGTGCGCCTCGGTCACCATC-GTAATCCAAGGCGGGTG
131 CGTGAGCCTCGGTCACCATCGGCAATCC-AGGCGGGTG
11122 GCCTC-GTCACCATC-GCAAACCCAGACGGGTGTCTCGGTCACCATC-GCAACCCC-GGCCATT-
1 GCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
11182 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
65 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCA-GCCCCCGTG
*
11247 TGCGTGAGCCTC-GTCACCATCGGCAATCCTGGCGGGTG
129 TGCGTGAGCCTCGGTCACCATCGGCAATCCAGGCGGGTG
11285 GCCTC-GTCACCATCGGCAAACCCA-ACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGAC-GGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
11348 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGC-GGAGTCTCGGTCACCATCAG-CCCCTTGT
65 GTGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGCCCCCGTGT
11411 GCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
130 GCGTGAGCCTCGGTCACCATCGGCAAT-CCAGGCGGGTG
*
11450 GCCTCGGTCACCATCGGCAAACCCAGACGG-GTCTCGGTCACCATC-GTAACCCCGGGCCATTGG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
11513 TGCGGGAG
66 TGCGGGAG
11521 CCTCGGTCAC
Statistics
Matches: 372, Mismatches: 14, Indels: 27
0.90 0.03 0.07
Matches are distributed among these distances:
162 4 0.01
163 134 0.36
164 109 0.29
165 69 0.19
166 54 0.15
167 2 0.01
ACGTcount: A:0.17, C:0.35, G:0.31, T:0.17
Consensus pattern (167 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGG
TGCGGGAGTGCCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGCCCCCGTGTG
CGTGAGCCTCGGTCACCATCGGCAATCCAGGCGGGTG
Found at i:11292 original size:31 final size:30
Alignment explanation
Indices: 11254--11334 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
11244 GTGTGCGTGA
* ***
11254 GCCTCGTCACCATCGGCAATCCTGGCGGGT
1 GCCTCGTCACCATCGGCAAACCCAACGGGT
11284 GGCCTCGTCACCATCGGCAAACCCAACGGGT
1 -GCCTCGTCACCATCGGCAAACCCAACGGGT
*
11315 GTCTCGGTCACCATCGGCAA
1 GCCTC-GTCACCATCGGCAA
11335 CCCCGGGCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 4 0.09
31 40 0.91
ACGTcount: A:0.19, C:0.37, G:0.27, T:0.17
Consensus pattern (30 bp):
GCCTCGTCACCATCGGCAAACCCAACGGGT
Found at i:11459 original size:33 final size:33
Alignment explanation
Indices: 11417--11597 Score: 144
Period size: 33 Copynumber: 5.5 Consensus size: 33
11407 TTGTGCGTGA
*
11417 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
11450 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * *
11482 --CTCGGTCACCATC-GTAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
**
11519 AGCCTCGGTCACCATC-GC-GTCCCAGGCGGGTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
11551 GCCTCGGTCACCATCGGCAAACCCAGAC-GGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
11582 GTCTCGGTCACCATCG
1 GCCTCGGTCACCATCG
11598 CAACCCCGGC
Statistics
Matches: 119, Mismatches: 16, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
29 7 0.06
30 14 0.12
31 30 0.25
32 7 0.06
33 37 0.31
34 2 0.02
35 1 0.01
36 1 0.01
38 1 0.01
39 5 0.04
40 14 0.12
ACGTcount: A:0.17, C:0.37, G:0.30, T:0.16
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
Found at i:11561 original size:101 final size:103
Alignment explanation
Indices: 11409--11618 Score: 363
Period size: 101 Copynumber: 2.1 Consensus size: 103
11399 TCAGCCCCTT
*
11409 GTGCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
*
11474 AGACGG-GTCTCGGTCACCATCGTAACCCCGGGCCATTG
66 AGACGGTGTCTCGGTCACCATCGCAACCCC-GGCCATTG
*
11512 GTGCGGGAGCCTCGGTCACCATC-GC-GTCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
1 GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
11575 AGACGGTGTCTCGGTCACCATCGCAACCCCGGCCATTG
66 AGACGGTGTCTCGGTCACCATCGCAACCCCGGCCATTG
11613 GTGCGG
1 GTGCGG
11619 AGTGCCGCAC
Statistics
Matches: 103, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
101 57 0.55
102 24 0.23
103 22 0.21
ACGTcount: A:0.16, C:0.36, G:0.31, T:0.16
Consensus pattern (103 bp):
GTGCGGGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCC
AGACGGTGTCTCGGTCACCATCGCAACCCCGGCCATTG
Found at i:19602 original size:33 final size:32
Alignment explanation
Indices: 19563--19649 Score: 102
Period size: 33 Copynumber: 2.7 Consensus size: 32
19553 CCGTGTGCGT
* *
19563 GTGCCTCGGTCACCATCGGTAATCCAAGGCGG
1 GTGCCTCGGTCACCATCGGTAAACCAAGACGG
* ** *
19595 GTGGCCTCGATCACCATCGACAAACCCAGACGG
1 GT-GCCTCGGTCACCATCGGTAAACCAAGACGG
*
19628 GTGTCTCGGTCACCATCGGTAA
1 GTGCCTCGGTCACCATCGGTAA
19650 CCCCGGCCAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
32 18 0.41
33 26 0.59
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.18
Consensus pattern (32 bp):
GTGCCTCGGTCACCATCGGTAAACCAAGACGG
Found at i:19715 original size:169 final size:170
Alignment explanation
Indices: 19428--20009 Score: 961
Period size: 169 Copynumber: 3.4 Consensus size: 170
19418 ACGTGTGCGT
** *
19428 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
19493 GTGCGGGAGTACCGCATAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
19558 TGCGTGTGCCTCGGTCACCATCGGTAATCCAAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
* * *
19598 GCCTCGATCACCATCGACAAACCCAGACGGGTGTCTCGGTCACCATCGGTAACCCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
19662 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
**
19727 TGCGTGAGCCTCGGTCACCATCGGCAATCCTGGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
19767 GCCTCGGTCACCATCGGTAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
19832 GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCCCTTG
66 GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* *
19896 TACGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
*
19936 GCCTCGGTCACCATCGGTAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
20001 GTGCGGGAG
66 GTGCGGGAG
20010 CCTCGGTCAC
Statistics
Matches: 386, Mismatches: 25, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
169 273 0.71
170 113 0.29
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.18
Consensus pattern (170 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TGCGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTG
Found at i:19810 original size:32 final size:33
Alignment explanation
Indices: 19734--19818 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
19724 GTGTGCGTGA
* ** *
19734 GCCTCGGTCACCATCGGCAATCCTGGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
19767 GCCTCGGTCACCATCGGTAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
19799 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
19819 CCCCGGGCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 18 0.40
33 27 0.60
ACGTcount: A:0.18, C:0.34, G:0.31, T:0.18
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
Found at i:19945 original size:33 final size:33
Alignment explanation
Indices: 19903--20125 Score: 177
Period size: 32 Copynumber: 6.6 Consensus size: 33
19893 TTGTACGTGA
*
19903 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* *
19936 GCCTCGGTCACCATCGGTAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
* * * *
19968 GTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCCAGG-C----G-G-GTG
** * *
20008 AGCCTCGGTCACCATCAGGC---CCCTTGTGCGTG
1 -GCCTCGGTCACCATC-GGCAAACCCAGGCGGGTG
** *
20040 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGTTG
1 -GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
20074 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
*
20106 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
20126 CCCCGGGCCA
Statistics
Matches: 152, Mismatches: 25, Indels: 27
0.75 0.12 0.13
Matches are distributed among these distances:
31 3 0.02
32 59 0.39
33 58 0.38
34 8 0.05
37 1 0.01
38 1 0.01
39 5 0.03
41 14 0.09
42 3 0.02
ACGTcount: A:0.17, C:0.36, G:0.30, T:0.17
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGGCGGGTG
Found at i:19977 original size:65 final size:64
Alignment explanation
Indices: 19905--20125 Score: 212
Period size: 65 Copynumber: 3.3 Consensus size: 64
19895 GTACGTGAGC
19905 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGTAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGG-AAACCCAGACGGGTGT
* * * * *
19970 CTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGGAGCCTCGGTCACCATCAGG--CCCCTT
1 CTCGGTCACCATCGGCAATCCCAGG-C----G-G-GTG-GCCTCGGTCACCATC-GGAAACCC-A
* * * *
20033 GTGCGTGAGC
56 G-ACGGGTGT
* *
20043 CTCGGTCACCATCGGCAGTCCCAGGCGGTTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGT
1 CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGG-AAACCCAGACGGGTGT
20108 CTCGGTCACCATCGGCAA
1 CTCGGTCACCATCGGCAA
20126 CCCCGGGCCA
Statistics
Matches: 121, Mismatches: 21, Indels: 28
0.71 0.12 0.16
Matches are distributed among these distances:
64 2 0.02
65 59 0.49
66 3 0.02
67 4 0.03
68 1 0.01
70 1 0.01
71 4 0.03
72 4 0.03
73 41 0.34
74 2 0.02
ACGTcount: A:0.17, C:0.36, G:0.30, T:0.17
Consensus pattern (64 bp):
CTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGAAACCCAGACGGGTGT
Found at i:19979 original size:32 final size:33
Alignment explanation
Indices: 19903--20125 Score: 161
Period size: 33 Copynumber: 6.6 Consensus size: 33
19893 TTGTACGTGA
* *
19903 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
19936 GCCTCGGTCACCATCGGTAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
* * * * *
19968 GTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGG
1 GCCTCGGTCACCATCGGCAAACCC-AG--A--CG-G-GTG
* * *
20008 AGCCTCGGTCACCATCAGGC---CCCTTG-TGCGTG
1 -GCCTCGGTCACCATC-GGCAAACCC-AGACGGGTG
** * *
20040 AGCCTCGGTCACCATCGGCAGTCCCAGGCGGTTG
1 -GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
20074 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
20106 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
20126 CCCCGGGCCA
Statistics
Matches: 152, Mismatches: 24, Indels: 29
0.74 0.12 0.14
Matches are distributed among these distances:
31 3 0.02
32 58 0.38
33 59 0.39
34 7 0.05
35 1 0.01
37 1 0.01
38 1 0.01
39 5 0.03
41 14 0.09
42 3 0.02
ACGTcount: A:0.17, C:0.36, G:0.30, T:0.17
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
Found at i:20021 original size:138 final size:138
Alignment explanation
Indices: 19860--20147 Score: 531
Period size: 138 Copynumber: 2.1 Consensus size: 138
19850 GAACCGAGCG
*
19860 TTGGTGCGGGAGTCTCGGTCACCATCAGGCCCCTTGTACGTGAGCCTCGGTCACCATCGGCAATC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTACGTGAGCCTCGGTCACCATCGGCAATC
*
19925 CCAGGCGGGTGGCCTCGGTCACCATCGGTAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
66 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
19990 CCGGGCCA
131 CCGGGCCA
* *
19998 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTGCGTGAGCCTCGGTCACCATCGGCAGTC
1 TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTACGTGAGCCTCGGTCACCATCGGCAATC
*
20063 CCAGGCGGTTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
66 CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
20128 CCGGGCCA
131 CCGGGCCA
20136 TTGGTGCGGGAG
1 TTGGTGCGGGAG
20148 TGCCGCACAG
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
138 145 1.00
ACGTcount: A:0.16, C:0.34, G:0.32, T:0.18
Consensus pattern (138 bp):
TTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCTTGTACGTGAGCCTCGGTCACCATCGGCAATC
CCAGGCGGGTGGCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACC
CCGGGCCA
Found at i:20114 original size:339 final size:339
Alignment explanation
Indices: 19428--20125 Score: 977
Period size: 339 Copynumber: 2.1 Consensus size: 339
19418 ACGTGTGCGT
*
19428 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGTAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
19493 GTGCGGGAGTACCGCATAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACCATCAGGCCCCCGTG
66 GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* * *
19558 TGCGTGTGCCTCGGTCACCATCGGTAATCCAAGGCGGGTGGCCTCGATCACCATCGACAAACCCA
131 TACGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTGGCCTCGATCACCATCGACAAACCCA
* *
19623 GACGGGTGTCTCGGTCACCATCGGTAACCCCGGCCATTGGTGCGGGAGTGCCGCACAGTACCGAG
196 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGTGCGGGAGTGCCGCACAGTACAGAG
* * *
19688 CTTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTGTGCGTGAGCCTCGGTCACCATCGGCA
261 CCTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCAGTGCGCGTGAGCCTCGGTCACCATCGGCA
* ** *
19753 ATCCTGGGCGGGTG
326 AACCCAGACGGGTG
* **
19767 GCCTCGGTCACCATCGGTAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
19832 GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCCCTTG
66 GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
* * **
19896 TACGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTGGCCTCGGTCACCATCGGTAAACCCA
131 TACGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTGGCCTCGATCACCATCGACAAACCCA
*
19961 GACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTGGTGCGGGAGCCT-CGGTCACCA-T-
196 GACGGGTGTCTCGGTCACCATCGGCAACCCC-GGCCATTGGTGCGGGAG--TGCCG-CA-CAGTA
*
20023 CAG-GCCCCTT-GTGCGTGAGCCTCGGTCACCATC-GGCAGTCCCAG-GCG-GTTG-GCCTCGGT
256 CAGAG--CCTTGGTGCGGGAGCCTCGGTCACCATCAGGC---CCCAGTGCGCG-TGAGCCTCGGT
20082 CACCATCGGCAAACCCAGACGGGT-
315 CACCATCGGCAAACCCAGACGGGTG
*
20106 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
20126 CCCCGGGCCA
Statistics
Matches: 320, Mismatches: 28, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
338 94 0.29
339 154 0.48
340 55 0.17
341 11 0.03
342 6 0.02
ACGTcount: A:0.17, C:0.34, G:0.32, T:0.18
Consensus pattern (339 bp):
GCCTCGGTCACCATCGGCAAAAACAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCCGTG
TACGTGAGCCTCGGTCACCATCGGCAATCCAAGGCGGGTGGCCTCGATCACCATCGACAAACCCA
GACGGGTGTCTCGGTCACCATCGGCAACCCCGGCCATTGGTGCGGGAGTGCCGCACAGTACAGAG
CCTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCAGTGCGCGTGAGCCTCGGTCACCATCGGCA
AACCCAGACGGGTG
Found at i:20529 original size:11 final size:11
Alignment explanation
Indices: 20515--20546 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
20505 TCCCGGTGGT
20515 GCTCCGGCGAC
1 GCTCCGGCGAC
20526 GCTCCGGCGAC
1 GCTCCGGCGAC
20537 GCTCCGGCGA
1 GCTCCGGCGA
20547 GACAATATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.44, G:0.38, T:0.09
Consensus pattern (11 bp):
GCTCCGGCGAC
Found at i:20983 original size:48 final size:48
Alignment explanation
Indices: 20912--21006 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
20902 CAAGAAGGGC
20912 GATGGAGAAAGTGTCCTCGTTTCAGACATTTCAATGTCTACTGGTAGT
1 GATGGAGAAAGTGTCCTCGTTTCAGACATTTCAATGTCTACTGGTAGT
20960 GATGGAGAAAGTGTCCTCGTTTCAGACATTTCAATGTCTACTGGTAG
1 GATGGAGAAAGTGTCCTCGTTTCAGACATTTCAATGTCTACTGGTAG
21007 CGTTTCAGAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (48 bp):
GATGGAGAAAGTGTCCTCGTTTCAGACATTTCAATGTCTACTGGTAGT
Found at i:21013 original size:30 final size:30
Alignment explanation
Indices: 20977--21035 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
20967 AAAGTGTCCT
20977 CGTTTCAGACATTTCAATGTCTACTGGTAG
1 CGTTTCAGACATTTCAATGTCTACTGGTAG
21007 CGTTTCAGACATTTCAATGTCTACTGGTA
1 CGTTTCAGACATTTCAATGTCTACTGGTA
21036 ACTGGTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (30 bp):
CGTTTCAGACATTTCAATGTCTACTGGTAG
Found at i:35296 original size:33 final size:31
Alignment explanation
Indices: 35215--35346 Score: 122
Period size: 33 Copynumber: 4.1 Consensus size: 31
35205 GAGCTTTGGT
* *
35215 GCGGGAGCCTCGGTCACCATCAGGC-TCCCGTG
1 GCGGGTGCCTCGGTCACCATC-GGCAACCCG-G
* *
35247 TGCGTGAGCCTCGGTCACCATCGGCAACCCTGG
1 -GCGGGTGCCTCGGTCACCATCGGCAACCC-GG
* *
35280 GCGGGTGGCCTTGGTCACCATCGGCAAACCCAG
1 GCGGGT-GCCTCGGTCACCATCGGC-AACCCGG
* *
35313 ACGGGTGTCTCGGTCACCATCGGCAACCCCGG
1 GCGGGTGCCTCGGTCACCATCGGCAA-CCCGG
35345 GC
1 GC
35347 CATTGGGCGG
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
31 2 0.02
32 28 0.34
33 47 0.57
34 6 0.07
ACGTcount: A:0.15, C:0.36, G:0.33, T:0.16
Consensus pattern (31 bp):
GCGGGTGCCTCGGTCACCATCGGCAACCCGG
Found at i:35482 original size:166 final size:168
Alignment explanation
Indices: 34953--35526 Score: 885
Period size: 166 Copynumber: 3.4 Consensus size: 168
34943 ACGTGTGCGT
** * *
34953 GCCTCGGTCACCATCGGCAAAAACAGACGGATGTCTCGGTCACCATCGACAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* * *
35018 GTGCGGGAGTACCGCACAGAACCGAGCGTTGGTGCGGGAGCCTCGTTCACC-TCAGGCCCCGTAT
66 GTGCGGGAGTGCCGCACAGAA-CGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGT
* * **
35082 GC-TGCGCCTCGGTCACCATC-GTAATCTAAGGCGGGTG
130 GCGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
* *
35119 GCCTCGGTCACCATCGACAAACCCAGACTGGTGTCTCGGTCACCATCGGCAA-CCC-GGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
35182 GTGCGGGAGTGCCGCACAGTACCGAGCTTTGGTGCGGGAGCCTCGGTCACCATCAGGCTCCCGTG
66 GTGCGGGAGTGCCGCACAG-AACGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGC-CCCGTG
*
35247 TGCGTGAGCCTCGGTCACCATCGGCAA-CCCTGGGCGGGTG
129 TGCGTGAGCCTCGGTCACCATCGGCAATCCC-AGGCGGGTG
*
35287 GCCTTGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
* *
35352 G-GCGGGAGTGCCGCACAGAACGAGCGTTGGTGCGGGAGTCTCGGTCACCATCAGG-CCCTTGTG
66 GTGCGGGAGTGCCGCACAGAACGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGTG
35415 CGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
131 CGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
35453 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
35518 GTGCGGGAG
66 GTGCGGGAG
35527 ACCCCCAAAA
Statistics
Matches: 373, Mismatches: 25, Indels: 19
0.89 0.06 0.05
Matches are distributed among these distances:
164 53 0.14
165 10 0.03
166 159 0.43
167 28 0.08
168 94 0.25
169 20 0.05
170 9 0.02
ACGTcount: A:0.18, C:0.33, G:0.32, T:0.17
Consensus pattern (168 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTGTCTCGGTCACCATCGGCAACCCCGGGCCATTG
GTGCGGGAGTGCCGCACAGAACGAGCGTTGGTGCGGGAGCCTCGGTCACCATCAGGCCCCGTGTG
CGTGAGCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
Found at i:35496 original size:32 final size:33
Alignment explanation
Indices: 35420--35504 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
35410 TTGTGCGTGA
* *
35420 GCCTCGGTCACCATCGGCAATCCCAGGCGGGTG
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
35453 GCCTCGGTCACCATCGGCAAACCCAGACGGGT-
1 GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
*
35485 GTCTCGGTCACCATCGGCAA
1 GCCTCGGTCACCATCGGCAA
35505 CCCCGGGCCA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
32 19 0.39
33 30 0.61
ACGTcount: A:0.19, C:0.36, G:0.29, T:0.15
Consensus pattern (33 bp):
GCCTCGGTCACCATCGGCAAACCCAGACGGGTG
Done.