Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000801.1 Hibiscus syriacus cultivar Beakdansim tig00001556_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: 103805
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:729 original size:16 final size:16
Alignment explanation
Indices: 708--754 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
698 TATAAATTAA
708 ATTAATGGTGTTCATC
1 ATTAATGGTGTTCATC
724 ATTAATGGTGTTCATC
1 ATTAATGGTGTTCATC
740 ATTAATGGTGTTCAT
1 ATTAATGGTGTTCAT
755 TGCTTCGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (16 bp):
ATTAATGGTGTTCATC
Found at i:5391 original size:23 final size:23
Alignment explanation
Indices: 5365--5422 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
5355 TAAACTACCA
5365 AAAGGCAGAGAAAAACATGACAC
1 AAAGGCAGAGAAAAACATGACAC
* * * * *
5388 AAAGGTAGAGATAAACGTGTCAT
1 AAAGGCAGAGAAAAACATGACAC
*
5411 AAAGACAGAGAA
1 AAAGGCAGAGAA
5423 CATGTCACAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.53, C:0.12, G:0.24, T:0.10
Consensus pattern (23 bp):
AAAGGCAGAGAAAAACATGACAC
Found at i:8276 original size:2 final size:2
Alignment explanation
Indices: 8269--8299 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8259 TGGACATGGA
8269 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8300 AAGACAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9049 original size:38 final size:37
Alignment explanation
Indices: 8984--9105 Score: 208
Period size: 37 Copynumber: 3.3 Consensus size: 37
8974 TTATTTTGTC
8984 CGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGT
1 CGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGT
*
9021 CGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGT
1 CGGGTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGT
* *
9059 CGGGTCGAGTCGGGTTTTTTAAGTGTGATATTCAGGT
1 CGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGT
9096 CGGGTCGGGT
1 CGGGTCGGGT
9106 TTAGGGTGAA
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
37 44 0.56
38 35 0.44
ACGTcount: A:0.12, C:0.11, G:0.39, T:0.37
Consensus pattern (37 bp):
CGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGT
Found at i:9789 original size:2 final size:2
Alignment explanation
Indices: 9782--9815 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9772 CAATAAATAC
9782 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9816 GGAATACAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9884 original size:7 final size:7
Alignment explanation
Indices: 9872--9899 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
9862 AAATATGCCA
9872 CATTTCC
1 CATTTCC
9879 CATTTCC
1 CATTTCC
9886 CATTTCC
1 CATTTCC
9893 CATTTCC
1 CATTTCC
9900 ATGCATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
CATTTCC
Found at i:21713 original size:21 final size:21
Alignment explanation
Indices: 21681--21741 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
21671 AGTCACTCGT
*
21681 CAGAAATGATCGATCCCTT-A
1 CAGAAAGGATCGATCCCTTAA
* * * *
21701 GAGAAAAGGATCGGTACCTCAA
1 CAG-AAAGGATCGATCCCTTAA
21723 CAGAAAGGATCGATCCCTT
1 CAGAAAGGATCGATCCCTT
21742 CTCTGTTTTG
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.83
22 3 0.10
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.20
Consensus pattern (21 bp):
CAGAAAGGATCGATCCCTTAA
Found at i:21738 original size:42 final size:41
Alignment explanation
Indices: 21643--21741 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 41
21633 TCTGTCCAGT
* **
21643 AAAGGATCGATCCCTTAGAAAAATAATCAGTCACTCGTCAG
1 AAAGGATCGATCCCTTAGAAAAAGAATCAGTCACTCAACAG
* * *
21684 AAATGATCGATCCCTTAGAGAAAAGGATCGGT-ACCTCAACAG
1 AAAGGATCGATCCCTTAGA-AAAAGAATCAGTCA-CTCAACAG
21726 AAAGGATCGATCCCTT
1 AAAGGATCGATCCCTT
21742 CTCTGTTTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 19 0.39
42 30 0.61
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
AAAGGATCGATCCCTTAGAAAAAGAATCAGTCACTCAACAG
Found at i:27232 original size:37 final size:37
Alignment explanation
Indices: 27177--27275 Score: 90
Period size: 41 Copynumber: 2.6 Consensus size: 37
27167 GATCGACCCC
* * * *
27177 TTTTCGAAATGATCGATCTTTCGGGATTAACGATCCA
1 TTTTCAAAAGGATCGATCTCTCGGGAGTAACGATCCA
* * *
27214 TTTTCAAAAGGATTGATCTCTCGGGAGTAATGATCAATCCC
1 TTTTCAAAAGGATCGATCTCTCGGGAGT-A--A-CGATCCA
*
27255 TTTTCAAAAGGATCAATCTCT
1 TTTTCAAAAGGATCGATCTCT
27276 TGGAGAAAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
37 23 0.47
38 1 0.02
40 1 0.02
41 24 0.49
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (37 bp):
TTTTCAAAAGGATCGATCTCTCGGGAGTAACGATCCA
Found at i:27287 original size:41 final size:41
Alignment explanation
Indices: 27209--27294 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
27199 GGGATTAACG
** *
27209 ATCCATTTTCAAAAGGATTGATCTCTCGGGAGTAATGATCA
1 ATCCATTTTCAAAAGGATCAATCTCTCGGGAGAAATGATCA
* * *
27250 ATCCCTTTTCAAAAGGATCAATCTCT-TGGAGAAAATGATCG
1 ATCCATTTTCAAAAGGATCAATCTCTCGGGAG-AAATGATCA
27291 ATCC
1 ATCC
27295 TCGACAGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (41 bp):
ATCCATTTTCAAAAGGATCAATCTCTCGGGAGAAATGATCA
Found at i:30756 original size:18 final size:18
Alignment explanation
Indices: 30733--30780 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
30723 TCAAGGTGTA
30733 ACATTTCTTCTCATGAAG
1 ACATTTCTTCTCATGAAG
30751 ACATTTCTTCTCATGAAG
1 ACATTTCTTCTCATGAAG
30769 ACATTT-TTCTCA
1 ACATTTCTTCTCA
30781 ATTTTTCGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 6 0.20
18 24 0.80
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (18 bp):
ACATTTCTTCTCATGAAG
Found at i:31176 original size:16 final size:15
Alignment explanation
Indices: 31155--31184 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
31145 AAATCGATCC
31155 AAAAAATTGATAACCA
1 AAAAAATTGA-AACCA
31171 AAAAAATTGAAACC
1 AAAAAATTGAAACC
31185 GAGTGTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.63, C:0.13, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAAAATTGAAACCA
Found at i:39932 original size:91 final size:91
Alignment explanation
Indices: 39771--39952 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
39761 ACCAGTTTCG
*
39771 CAACACAGTTTTCAAATTCGCAACGCGATTCTCCAAAATCGCAACGCGAATTTCGTTTTCGCAAC
1 CAACACAGTTTTCAAATTCGCAACGCGATTCTCCAAAATCGCAACACGAATTTCGTTTTCGCAAC
*
39836 GCTAATTACCGA-TATAAGTAAACACA
66 ACTAATTACC-ATTATAAGTAAACACA
* * *
39862 CAACTCAGTTTTCAAATTCGTAACGCGATTCTCCAAAATCGCAACACGAATTTCGTTTTCGTAAC
1 CAACACAGTTTTCAAATTCGCAACGCGATTCTCCAAAATCGCAACACGAATTTCGTTTTCGCAAC
*
39927 ACTAATTACCATTATAGGTAAACACA
66 ACTAATTACCATTATAAGTAAACACA
39953 ACTATTCGCA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
90 1 0.01
91 83 0.99
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (91 bp):
CAACACAGTTTTCAAATTCGCAACGCGATTCTCCAAAATCGCAACACGAATTTCGTTTTCGCAAC
ACTAATTACCATTATAAGTAAACACA
Found at i:40159 original size:21 final size:20
Alignment explanation
Indices: 40130--40179 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
40120 CGAAATTCGT
* * *
40130 GTTGCGAATTTAAAGAATTGC
1 GTTGTGAATTTAAA-AACTGA
*
40151 GTTGTGAATTTGAAAACTGA
1 GTTGTGAATTTAAAAACTGA
40171 GTTGTGAAT
1 GTTGTGAAT
40180 AGTTGTGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGTGAATTTAAAAACTGA
Found at i:40260 original size:113 final size:113
Alignment explanation
Indices: 40110--40340 Score: 363
Period size: 113 Copynumber: 2.0 Consensus size: 113
40100 AGTAATTAGC
* * **
40110 GTTGCGAAAACGAAATTCGTGTTGCGAATTTAAAGAATTGCGTTGTGAATTTGAAAACTGAGTTG
1 GTTGCGAAAACGAAATTCGCGTTGCGAATTTAAAGAATCGCGTTACGAATTTGAAAACTGAGTTG
* * *
40175 TGAATAGTTGTGTTTACCTATATTGGTAATTAGCGTTGCGAAATTCGA
66 TGAATAGTTGTGTTGACCTATATCGGTAATTAGCATTGCGAAATTCGA
* **
40223 GTTGCGAAAACGAAATTCGCGTTGCGATTTTGGAGAATCGCGTTACGAATTTGAAAACTGAGTTG
1 GTTGCGAAAACGAAATTCGCGTTGCGAATTTAAAGAATCGCGTTACGAATTTGAAAACTGAGTTG
*
40288 TGAATAGTTGTGTTGACCTATATCGGTAATTAGCATTGCGAAATTCGT
66 TGAATAGTTGTGTTGACCTATATCGGTAATTAGCATTGCGAAATTCGA
40336 GTTGC
1 GTTGC
40341 AATTTTGGAG
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
113 107 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.34
Consensus pattern (113 bp):
GTTGCGAAAACGAAATTCGCGTTGCGAATTTAAAGAATCGCGTTACGAATTTGAAAACTGAGTTG
TGAATAGTTGTGTTGACCTATATCGGTAATTAGCATTGCGAAATTCGA
Found at i:44052 original size:3 final size:3
Alignment explanation
Indices: 44026--44087 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
44016 CACGGGAAAA
* *
44026 AAT AA- AAT AA- AAT AAGT GAT AAT AAT AAT AAT AAAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT AAT
44071 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
44088 ATATAAAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.08
3 42 0.82
4 5 0.10
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:44148 original size:14 final size:14
Alignment explanation
Indices: 44129--44171 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
44119 ACTGTTTCTT
44129 TTAAAAAATATATA
1 TTAAAAAATATATA
* * *
44143 TTAAAAAAAACATT
1 TTAAAAAATATATA
44157 TTAAAAAACTATATA
1 TTAAAAAA-TATATA
44172 ATTTTCAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 19 0.86
15 3 0.14
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
TTAAAAAATATATA
Found at i:44303 original size:39 final size:36
Alignment explanation
Indices: 44207--44428 Score: 175
Period size: 37 Copynumber: 6.0 Consensus size: 36
44197 CCATATAATT
* * * *
44207 TTTTAAAAATGTTTTAAAAATTACATATTATATATG
1 TTTTCAAAATGTTTTAAAAACTATATATTATATATA
* *
44243 CTTTCAAAATGTTTTTCAAAAAATTATATATTATATATTAA
1 TTTTCAAAATG-TTTT--AAAAACTATATATTATATA-T-A
* * *
44284 TTTTCAAAACGTTTTAAAAACTATATAATATATAAATG
1 TTTTCAAAATGTTTTAAAAACTATAT-AT-TATATATA
* * *
44322 TTTTTAAAATG-TTT--ATA-TATATATTATATACA
1 TTTTCAAAATGTTTTAAAAACTATATATTATATATA
*
44354 TTTTCAAAATGTTTTCAAAGACTATATATTATATATA
1 TTTTCAAAATGTTTT-AAAAACTATATATTATATATA
*
44391 TTTTTAAAATGTTTTCGAAAAAAAC-ATATATTATATAT
1 TTTTCAAAATGTTTT----AAAAACTATATATTATATAT
44429 CATATAATAT
Statistics
Matches: 150, Mismatches: 21, Indels: 27
0.76 0.11 0.14
Matches are distributed among these distances:
32 15 0.10
33 5 0.03
34 5 0.03
35 2 0.01
36 11 0.07
37 35 0.23
38 19 0.13
39 34 0.23
40 15 0.10
41 9 0.06
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTTCAAAATGTTTTAAAAACTATATATTATATATA
Found at i:44357 original size:70 final size:70
Alignment explanation
Indices: 44267--44404 Score: 190
Period size: 69 Copynumber: 2.0 Consensus size: 70
44257 TTCAAAAAAT
*
44267 TATATATTATATATTAATTTTCAAAACGTTTT-AAAAACTATATAATATATAAATGTTTTTAAAA
1 TATATATTATATA-TAATTTTCAAAACGTTTTCAAAAACTATAT-AT-TATAAATATTTTTAAAA
44331 TGTTTATA
63 TGTTTATA
* * * *
44339 TATATATTATATA-CATTTTCAAAATGTTTTCAAAGACTATATATTATATATATTTTTAAAATGT
1 TATATATTATATATAATTTTCAAAACGTTTTCAAAAACTATATATTATAAATATTTTTAAAATGT
44403 TT
66 TT
44405 TCGAAAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
69 20 0.33
70 17 0.28
71 10 0.17
72 13 0.22
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (70 bp):
TATATATTATATATAATTTTCAAAACGTTTTCAAAAACTATATATTATAAATATTTTTAAAATGT
TTATA
Found at i:45278 original size:84 final size:81
Alignment explanation
Indices: 45138--45896 Score: 765
Period size: 84 Copynumber: 9.2 Consensus size: 81
45128 TTGAATATAA
* * * * *
45138 TCGAACTCGAGGGTCTTTAG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
*
45202 TTGGAGCTGAGCGGAG
66 TTGGAGCTGAGCGTAG
* * * *
45218 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
45283 GCCGTT-GAGCTGAGCGTAG
63 GCC-TTGGAGCTGAGCGTAG
* * * * ** *
45302 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTATTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTTG--GTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
45367 GCCTTGGAGCTGGGCGTAG
63 GCCTTGGAGCTGAGCGTAG
* *
45386 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTCCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGG-T--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * * *
45451 GCCCTCGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
* * ** * * *
45471 ACGAACTTGGGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
45535 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * *
45551 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * * *
45616 GCCCTCGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
** * * * *
45636 TCGAACTCGGGGGTCTTTGG-CAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
45700 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * * * * * *
45716 TCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATG
1 TCGAACTCGAAGGTCTTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* * *
45781 CCCTTGAAGCTGAGTGTAA
64 -CCTTGGAGCTGAGCGTAG
* * * * *
45800 TCGAACT-TAAGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGC
1 TCGAACTCGAA-GGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
*
45863 CTTGGAGCTGAGCGTAT
65 CTTGGAGCTGAGCGTAG
45880 TCGAACTCGAAGGTCTT
1 TCGAACTCGAAGGTCTT
45897 GGTGGTAGGT
Statistics
Matches: 551, Mismatches: 105, Indels: 46
0.78 0.15 0.07
Matches are distributed among these distances:
80 97 0.18
81 119 0.22
83 41 0.07
84 235 0.43
85 58 0.11
86 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.30
Consensus pattern (81 bp):
TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAG
Found at i:45319 original size:164 final size:165
Alignment explanation
Indices: 45075--45896 Score: 1103
Period size: 165 Copynumber: 5.0 Consensus size: 165
45065 AATTTTATTG
* * * * * * * * *
45075 ACAGATAACCCTTCTTGCCTTGAGCTATTCTGTAAGCTTGATTTG-CCTCTAAGTTGAATATAAT
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATGTGCCCTCGAAGCTGAGTGTAAT
*
45139 CGAACTCGAGGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
64 CGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
*
45204 GGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTC
129 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* * * * *
45241 ACAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATGATGTGCCGTTG-AGCTGAGCGTAGTCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
* * * * * * * ** *
45305 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTATTGCAAATGATATGCC
66 AACTCGAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
* *
45370 TTGGAGCTGGGCGTAGTCGAACTCGAAGGTC-TTTGGTTG
127 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TC
* * * * * * *
45409 GCAGATAACCCTCCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAAACG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
* *
45474 AACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
45539 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
45574 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
* * *
45639 AACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
* * *
45704 AGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTA
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* * *
45738 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
** *
45803 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
*
45868 AGCTGAGCGTATTCGAACTCGAAGGTCTT
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
45897 GGTGGTAGGT
Statistics
Matches: 571, Mismatches: 76, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
164 179 0.31
165 220 0.39
166 37 0.06
167 6 0.01
168 109 0.19
169 20 0.04
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (165 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
AACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
Found at i:47320 original size:59 final size:59
Alignment explanation
Indices: 47228--47345 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
47218 ATAACCAATT
47228 GCCTTAGCGGAATAGCTCAGTTTTTACGGATTTAATTTCTTAAGATTGTTAAGAAGAAC
1 GCCTTAGCGGAATAGCTCAGTTTTTACGGATTTAATTTCTTAAGATTGTTAAGAAGAAC
47287 GCCTTAGCGGAATAGCTCAGTTTTTACGGATTTAATTTCTTAAGATTGTTAAGAAGAAC
1 GCCTTAGCGGAATAGCTCAGTTTTTACGGATTTAATTTCTTAAGATTGTTAAGAAGAAC
47346 CTGTTATAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (59 bp):
GCCTTAGCGGAATAGCTCAGTTTTTACGGATTTAATTTCTTAAGATTGTTAAGAAGAAC
Found at i:49365 original size:19 final size:19
Alignment explanation
Indices: 49341--49386 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
49331 AGTTAATGTG
49341 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
49360 AATGCAAAGAAAATAACGA
1 AATGCAAAGAAAATAACAA
49379 AATGCAAA
1 AATGCAAA
49387 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:52526 original size:3 final size:3
Alignment explanation
Indices: 52499--52561 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
52489 CACGGGAAAA
* * *
52499 AAT AA- AAT AAA AAT AAGT GAT AAT AAT AAT AAT AAAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT -AAT AAT AAT AAT
52545 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
52562 ATATAAAAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 44 0.86
4 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:52530 original size:22 final size:21
Alignment explanation
Indices: 52499--52559 Score: 88
Period size: 22 Copynumber: 2.9 Consensus size: 21
52489 CACGGGAAAA
52499 AATAA-AATAAAAATAAGTGAT
1 AATAATAATAAAAATAA-TGAT
52520 AATAATAATAATAAATAATGAT
1 AATAATAATAA-AAATAATGAT
*
52542 AATAATAATAATAATAAT
1 AATAATAATAAAAATAAT
52560 AAATATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 11 0.30
22 20 0.54
23 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AATAATAATAAAAATAATGAT
Found at i:52830 original size:70 final size:71
Alignment explanation
Indices: 52740--52878 Score: 192
Period size: 70 Copynumber: 2.0 Consensus size: 71
52730 TTCAAAAAAT
*
52740 TATATATTATATATTAATTTTCAAAACGTTTT-AAAAACTATATAATATATAAATGTTTTTAAAA
1 TATATATTATATA-TAATTTTCAAAACGTTTTCAAAAACTATATAATATATAAAT-ATTTTAAAA
52804 TGTTTATA
64 TGTTTATA
* * * * *
52812 TATATATTATATA-CATTTTCAAAATGTTTTCAAAGACTATATATTATATATATATTTTAAAATG
1 TATATATTATATATAATTTTCAAAACGTTTTCAAAAACTATATAATATATAAATATTTTAAAATG
52876 TTT
66 TTT
52879 TCGAAAAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
70 28 0.47
71 19 0.32
72 13 0.22
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.48
Consensus pattern (71 bp):
TATATATTATATATAATTTTCAAAACGTTTTCAAAAACTATATAATATATAAATATTTTAAAATG
TTTATA
Found at i:52900 original size:38 final size:37
Alignment explanation
Indices: 52680--52902 Score: 174
Period size: 38 Copynumber: 6.0 Consensus size: 37
52670 CCATATAATT
* * * *
52680 TTTTTAAAATGTTTT-AAAAATTACATATTATATATG
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATA
* *
52716 CTTTCAAAATGTTTTTCAAAAAATTATATATTATATATTAA
1 TTTTCAAAATG-TTTTC-AAAAACTATATATTATATA-T-A
* * *
52757 TTTTCAAAACGTTTT-AAAAACTATATAATATATAAATG
1 TTTTCAAAATGTTTTCAAAAACTATAT-AT-TATATATA
* * *
52795 TTTTTAAAATG-TTT---ATA-TATATATTATATACA
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATA
*
52827 TTTTCAAAATGTTTTCAAAGACTATATATTATATATA
1 TTTTCAAAATGTTTTCAAAAACTATATATTATATATA
*
52864 TATTTTAAAATGTTTTCGAAAAAAAC-ATATATTATATAT
1 T-TTTCAAAATGTTTTC---AAAAACTATATATTATATAT
52903 CATATAATAT
Statistics
Matches: 151, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
32 15 0.10
33 5 0.03
34 5 0.03
35 2 0.01
36 11 0.07
37 22 0.15
38 33 0.22
39 21 0.14
40 23 0.15
41 14 0.09
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTTCAAAATGTTTTCAAAAACTATATATTATATATA
Found at i:54678 original size:31 final size:29
Alignment explanation
Indices: 54643--54709 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 29
54633 TTAAAGGTCC
54643 AAAATAGAAAAAAATATAAACTTAAGAGACT
1 AAAATAGAAAAAAA-A-AAACTTAAGAGACT
*
54674 AAAATAG---AAAAAAAACTTAAGGGACT
1 AAAATAGAAAAAAAAAAACTTAAGAGACT
54700 AAAATAGAAA
1 AAAATAGAAA
54710 TTACAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
26 20 0.62
27 1 0.03
28 4 0.12
31 7 0.22
ACGTcount: A:0.66, C:0.06, G:0.12, T:0.16
Consensus pattern (29 bp):
AAAATAGAAAAAAAAAAACTTAAGAGACT
Found at i:54690 original size:26 final size:26
Alignment explanation
Indices: 54660--54709 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
54650 AAAAAAATAT
54660 AAACTTAAGAGACTAAAATAGAAAAA
1 AAACTTAAGAGACTAAAATAGAAAAA
*
54686 AAACTTAAGGGACTAAAATAGAAA
1 AAACTTAAGAGACTAAAATAGAAA
54710 TTACAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.62, C:0.08, G:0.14, T:0.16
Consensus pattern (26 bp):
AAACTTAAGAGACTAAAATAGAAAAA
Found at i:55245 original size:2 final size:2
Alignment explanation
Indices: 55238--55270 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55228 TTTGCATTTA
55238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55271 ATCTAAGGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56276 original size:3 final size:3
Alignment explanation
Indices: 56263--56331 Score: 63
Period size: 3 Copynumber: 23.7 Consensus size: 3
56253 TGTGAATTGT
* * *
56263 TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAT TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
56310 -ATA TAT TTA TAA TAA T-A TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA TA
56332 TTTTTGTAGA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
2 5 0.10
3 46 0.88
4 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:60411 original size:25 final size:23
Alignment explanation
Indices: 60375--60458 Score: 64
Period size: 25 Copynumber: 3.5 Consensus size: 23
60365 TCAAACAATT
60375 AAATAATAAAAAATATTAAGAAACA
1 AAATAAT-AAAAA-ATTAAGAAACA
** * **
60400 AAATAA-ATAAAAATCCA-TAATT
1 AAATAATA-AAAAATTAAGAAACA
60422 AAATAATAAAAACATTAAGAAACA
1 AAATAATAAAAA-ATTAAGAAACA
60446 AAATAAATAAAAA
1 AAAT-AATAAAAA
60459 GTCCATAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 10
0.69 0.16 0.16
Matches are distributed among these distances:
22 12 0.27
23 8 0.18
24 10 0.23
25 14 0.32
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.20
Consensus pattern (23 bp):
AAATAATAAAAAATTAAGAAACA
Found at i:60496 original size:43 final size:43
Alignment explanation
Indices: 60383--60545 Score: 238
Period size: 43 Copynumber: 3.7 Consensus size: 43
60373 TTAAATAATA
*
60383 AAAAATATTAAGAAACAAAATAAATAAAAATCCATAATTAAATAAT
1 AAAAACATTAAGAAACAAAATAAATAAAAATCCATAATT--A-AAT
60429 AAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAAT
1 AAAAACATTAAGAAACAAAATAAATAAAAA-TCCATAATTAAAT
* * *
60473 -AAAATATTAAGAAACAAAATAAATAAAATTTTCATAATTAAAT
1 AAAAACATTAAGAAACAAAATAAATAAAA-ATCCATAATTAAAT
60516 AAAAACATTAAGAAACAAAATAAATAAAAA
1 AAAAACATTAAGAAACAAAATAAATAAAAA
60546 CATTAAGAAA
Statistics
Matches: 108, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
43 39 0.36
44 30 0.28
45 1 0.01
46 29 0.27
47 9 0.08
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (43 bp):
AAAAACATTAAGAAACAAAATAAATAAAAATCCATAATTAAAT
Found at i:60540 original size:87 final size:88
Alignment explanation
Indices: 60384--60545 Score: 274
Period size: 87 Copynumber: 1.8 Consensus size: 88
60374 TAAATAATAA
60384 AAAATATTAAGAAACAAAATAAATAAAAATCCATAATTAAATAATAAAAACATTAAGAAACAAAA
1 AAAATATTAAGAAACAAAATAAATAAAAATCCATAATT-AATAATAAAAACATTAAGAAACAAAA
60449 TAAATAAAAAGTCCATAATTAAAT
65 TAAATAAAAAGTCCATAATTAAAT
* *
60473 AAAATATTAAGAAACAAAATAAATAAAATTTTCATAATT-A-AATAAAAACATTAAGAAACAAAA
1 AAAATATTAAGAAACAAAATAAATAAAA-ATCCATAATTAATAATAAAAACATTAAGAAACAAAA
60536 TAAATAAAAA
65 TAAATAAAAA
60546 CATTAAGAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
87 33 0.47
88 1 0.01
89 28 0.40
90 8 0.11
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (88 bp):
AAAATATTAAGAAACAAAATAAATAAAAATCCATAATTAATAATAAAAACATTAAGAAACAAAAT
AAATAAAAAGTCCATAATTAAAT
Found at i:60541 original size:25 final size:25
Alignment explanation
Indices: 60511--60572 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
60501 TTTTCATAAT
60511 TAAATAAAAACATTAAGAAACAAAA
1 TAAATAAAAACATTAAGAAACAAAA
60536 TAAATAAAAACATTAAGAAACAAAA
1 TAAATAAAAACATTAAGAAACAAAA
60561 TAAATAAAAACA
1 TAAATAAAAACA
60573 AGTTTATCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.73, C:0.08, G:0.03, T:0.16
Consensus pattern (25 bp):
TAAATAAAAACATTAAGAAACAAAA
Found at i:61002 original size:21 final size:22
Alignment explanation
Indices: 60978--61018 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
60968 CATTTGAAAT
*
60978 GGTTGTCGTGGCATC-GAAAAC
1 GGTTGTCGTGCCATCTGAAAAC
*
60999 GGTTGTGGTGCCATCTGAAA
1 GGTTGTCGTGCCATCTGAAA
61019 TGGCTACGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.27
Consensus pattern (22 bp):
GGTTGTCGTGCCATCTGAAAAC
Found at i:68196 original size:18 final size:17
Alignment explanation
Indices: 68152--68197 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
68142 ATTTAGAATT
68152 AATGTAAAATAAATAAA
1 AATGTAAAATAAATAAA
*
68169 AGAAGTAAAATAAATAATA
1 A-ATGTAAAATAAATAA-A
*
68188 AATGAAAAAT
1 AATGTAAAAT
68198 CATGAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.88
19 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.22
Consensus pattern (17 bp):
AATGTAAAATAAATAAA
Found at i:68920 original size:23 final size:22
Alignment explanation
Indices: 68866--68920 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
68856 CTATTCATGC
68866 TAAAAAAATCCTAAAAGATAAAA
1 TAAAAAAAT-CTAAAAGATAAAA
**
68889 TAACTAAAT-TATAAAGATAAATA
1 TAAAAAAATCTA-AAAGATAAA-A
68912 TAAAAAAAT
1 TAAAAAAAT
68921 ATTTAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 9 0.35
23 15 0.58
ACGTcount: A:0.67, C:0.05, G:0.04, T:0.24
Consensus pattern (22 bp):
TAAAAAAATCTAAAAGATAAAA
Found at i:69752 original size:2 final size:2
Alignment explanation
Indices: 69741--69769 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
69731 TAGGTAAGGG
69741 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
69770 AATGTTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:85578 original size:22 final size:22
Alignment explanation
Indices: 85553--85595 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
85543 ATAAGTAAAG
85553 AAGAAAAAGAAGCAG-CAGACAC
1 AAGAAAAAGAAG-AGACAGACAC
*
85575 AAGAAGAAGAAGAGACAGACA
1 AAGAAAAAGAAGAGACAGACA
85596 ATAGATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.60, C:0.14, G:0.26, T:0.00
Consensus pattern (22 bp):
AAGAAAAAGAAGAGACAGACAC
Found at i:89158 original size:15 final size:15
Alignment explanation
Indices: 89138--89175 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
89128 ATTTTCCCCT
*
89138 TTATTCTTATATTTC
1 TTATTCTTATATCTC
89153 TTATTCTTATATCTC
1 TTATTCTTATATCTC
89168 TTATTCTT
1 TTATTCTT
89176 CTTGTTCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTCTTATATCTC
Found at i:92518 original size:21 final size:21
Alignment explanation
Indices: 92494--92537 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
92484 CCGGTGCCGG
*
92494 AGGAGGAGCACAAGAAGAGCT
1 AGGAGCAGCACAAGAAGAGCT
* **
92515 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACAAGAAGAGCT
92536 AG
1 AG
92538 CTCCCGGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACAAGAAGAGCT
Found at i:93560 original size:19 final size:18
Alignment explanation
Indices: 93536--93590 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
93526 GGAAAGGTTT
*
93536 TGAAAAATCATAATGTATA
1 TGAAAAATCATAAT-TAAA
*
93555 TGAAAACAACATAATTAAA
1 TGAAAA-ATCATAATTAAA
*
93574 TCAAAAATCA-AATTAAA
1 TGAAAAATCATAATTAAA
93591 AAAATTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 7 0.23
18 3 0.10
19 14 0.45
20 7 0.23
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.25
Consensus pattern (18 bp):
TGAAAAATCATAATTAAA
Found at i:99930 original size:56 final size:57
Alignment explanation
Indices: 99861--99979 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 57
99851 AGTGCAACGA
* * *
99861 TGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCAGAGTGCATCGATGCATGGT-TGG
1 TGCATCAAATGCATTCGATGTTTTCATAAA-AACCACAGTGCATCGATGCATGGTAT-G
*
99917 TGCATCAAATGCATTCGATGTTTTCATAAAAACCTCAGTGCATCGATGCATGGTATG
1 TGCATCAAATGCATTCGATGTTTTCATAAAAACCACAGTGCATCGATGCATGGTATG
99974 TGCATC
1 TGCATC
99980 GATGCATGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
56 19 0.34
57 33 0.59
58 4 0.07
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (57 bp):
TGCATCAAATGCATTCGATGTTTTCATAAAAACCACAGTGCATCGATGCATGGTATG
Found at i:101851 original size:23 final size:25
Alignment explanation
Indices: 101815--101860 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
101805 TAATTATATA
101815 TATATATTGAAATT-TTAAGTTAAAT
1 TATATATTGAAATTATT-AGTTAAAT
101840 TATAT-TTG-AATTATTAGTTAA
1 TATATATTGAAATTATTAGTTAA
101861 TTGTTACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.50
24 5 0.25
25 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (25 bp):
TATATATTGAAATTATTAGTTAAAT
Found at i:102202 original size:16 final size:16
Alignment explanation
Indices: 102181--102215 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
102171 TGAGTCAATT
102181 ACATGCCAGGTTCATA
1 ACATGCCAGGTTCATA
* *
102197 ACATGCCCGGTTGATA
1 ACATGCCAGGTTCATA
102213 ACA
1 ACA
102216 GGTCGGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (16 bp):
ACATGCCAGGTTCATA
Found at i:103066 original size:10 final size:10
Alignment explanation
Indices: 103051--103125 Score: 57
Period size: 10 Copynumber: 8.7 Consensus size: 10
103041 CATTTAATAA
103051 ATAAACGAAC
1 ATAAACGAAC
103061 ATAAACGAAC
1 ATAAACGAAC
103071 ----ACGAAC
1 ATAAACGAAC
103077 ATAAACG---
1 ATAAACGAAC
103084 A-AAACGAAC
1 ATAAACGAAC
*
103093 ATAAATGAAC
1 ATAAACGAAC
103103 ----ACGAAC
1 ATAAACGAAC
103109 ATAAACGAAC
1 ATAAACGAAC
103119 ATAAACG
1 ATAAACG
103126 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 2, Indels: 24
0.66 0.03 0.31
Matches are distributed among these distances:
6 16 0.31
7 1 0.02
9 1 0.02
10 33 0.65
ACGTcount: A:0.59, C:0.20, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:103076 original size:16 final size:16
Alignment explanation
Indices: 103055--103119 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
103045 TAATAAATAA
103055 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
103071 ACGAACATAAACGAAA
1 ACGAACATAAACGAAC
*
103087 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
103103 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
103119 A
1 A
103120 TAAACGTTGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Done.