Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007843.1 Hibiscus syriacus cultivar Beakdansim tig00110197_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: 60695
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1469 original size:175 final size:177
Alignment explanation
Indices: 1173--1535 Score: 642
Period size: 175 Copynumber: 2.1 Consensus size: 177
1163 ATTGGAAGAA
*
1173 GGTTAGTTGTGATAGTTTACTGAGTATCTTTATTGTTTGCTGACTTGTGATTAAACTTTGTTTAG
1 GGTT-GTTGTGATAGTTTACTGAGTATCTTTATTGTTTGCTGACTTGTGATTAAACTTTGGTTAG
1238 ATGGCACACGTTCTAGGTATGCTACTCTAATTTTCTATATATATATATAAAATT-AAAAATCTAC
65 ATGGCACACGTTCTAGGTATGCTACTCTAATTTTCTATATATATATATAAAATTAAAAAATCTAC
*
1302 -TTAATATAGTTTATTTTATGGTCATGTAGTTGTGATATCTGGCTTTT
130 TTTAATATAGTTTATTTTATGGTCATGTAGTTGGGATATCTGGCTTTT
*
1349 GGTTGTTGTGATAGTTTACTGAGTATCTTTATTGTTTGTTGACTTGTGATTAAACTTTGGTTAGA
1 GGTTGTTGTGATAGTTTACTGAGTATCTTTATTGTTTGCTGACTTGTGATTAAACTTTGGTTAGA
*
1414 TGGCACACGTTCTAGGTATTGCTACTCTAATTTT-TATATATATTTATAAAATTAAAAAATCTAC
66 TGGCACACGTTCTAGGTA-TGCTACTCTAATTTTCTATATATATATATAAAATTAAAAAATCTAC
*
1478 TTTAATATAGTTTCTTTTATGGTCATGTAGTTGGGATATCTGGCTTTT
130 TTTAATATAGTTTATTTTATGGTCATGTAGTTGGGATATCTGGCTTTT
1526 GGTTGTTGTG
1 GGTTGTTGTG
1536 GTTTTACCAT
Statistics
Matches: 179, Mismatches: 5, Indels: 5
0.95 0.03 0.03
Matches are distributed among these distances:
175 95 0.53
176 29 0.16
177 55 0.31
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.47
Consensus pattern (177 bp):
GGTTGTTGTGATAGTTTACTGAGTATCTTTATTGTTTGCTGACTTGTGATTAAACTTTGGTTAGA
TGGCACACGTTCTAGGTATGCTACTCTAATTTTCTATATATATATATAAAATTAAAAAATCTACT
TTAATATAGTTTATTTTATGGTCATGTAGTTGGGATATCTGGCTTTT
Found at i:15380 original size:54 final size:54
Alignment explanation
Indices: 15316--15492 Score: 191
Period size: 54 Copynumber: 3.3 Consensus size: 54
15306 AGCGCTCACA
* * *
15316 TAAGGCGTGGGCACGACTTTTTCATCCAGACCTAACGAAGAAGAAGTCTTCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCAGAACTAACGCAGAAGAAGTCTTCAGT
* * *
15370 TAAGGCGTGGGCACAACTTATCCAT-CATGAGA-T-ACTGCAGAAGAAGTCTCCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCA-GA-ACTAAC-GCAGAAGAAGTCTTCAGT
* * * *
15424 TAAGGCGTAGGCACGGCTTATTCATCCAAAACTACCGCAGAAGAA-TCCTTCAGT
1 TAAGGCGTGGGCACGACTTATTCATCCAGAACTAACGCAGAAGAAGT-CTTCAGT
*
15478 TAAGGCGTGAGCACG
1 TAAGGCGTGGGCACG
15493 CCATCTATTG
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
53 6 0.06
54 92 0.91
55 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (54 bp):
TAAGGCGTGGGCACGACTTATTCATCCAGAACTAACGCAGAAGAAGTCTTCAGT
Found at i:16487 original size:21 final size:20
Alignment explanation
Indices: 16461--16519 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
16451 AAAAGGCAAC
*
16461 CTTCTTCATTTTGTTCTTCTT
1 CTTCTTC-TTTTCTTCTTCTT
*
16482 CTTCTTCTCTTTCTTCTTTTT
1 CTTCTTCT-TTTCTTCTTCTT
16503 CTTCTTCTTTTTCTTCT
1 CTTCTTC-TTTTCTTCT
16520 GTTTTGGTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (20 bp):
CTTCTTCTTTTCTTCTTCTT
Found at i:16488 original size:9 final size:9
Alignment explanation
Indices: 16461--16519 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
16451 AAAAGGCAAC
16461 CTTCTTCATT
1 CTTCTTC-TT
*
16471 -TTGTTCTT
1 CTTCTTCTT
16479 CTTCTTCTT
1 CTTCTTCTT
16488 C-TCTTTCTT
1 CTTC-TTCTT
*
16497 CTTTTTCTT
1 CTTCTTCTT
*
16506 CTTCTTTTT
1 CTTCTTCTT
16515 CTTCT
1 CTTCT
16520 GTTTTGGTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
8 4 0.10
9 36 0.88
10 1 0.02
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (9 bp):
CTTCTTCTT
Found at i:16489 original size:12 final size:12
Alignment explanation
Indices: 16461--16519 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
16451 AAAAGGCAAC
16461 CTTCTTCATT-TT
1 CTTCTTC-TTCTT
*
16473 GTTCTTCTTCTT
1 CTTCTTCTTCTT
16485 CTTC-TCTTTCTT
1 CTTCTTC-TTCTT
*
16497 CTTTTTCTTCTT
1 CTTCTTCTTCTT
*
16509 CTTTTTCTTCT
1 CTTCTTCTTCT
16520 GTTTTGGTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.10
12 35 0.85
13 2 0.05
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (12 bp):
CTTCTTCTTCTT
Found at i:18651 original size:35 final size:35
Alignment explanation
Indices: 18605--18678 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
18595 TTCTACAAAC
**
18605 TATATAATATATATTTCAAAAGTATTTTAAAATTA
1 TATATAATATATATTTCAAAAACATTTTAAAATTA
* * * *
18640 TATATTATATATATTTTAAAAACGTTTTCAAATTA
1 TATATAATATATATTTCAAAAACATTTTAAAATTA
18675 TATA
1 TATA
18679 GTTTTCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (35 bp):
TATATAATATATATTTCAAAAACATTTTAAAATTA
Found at i:18723 original size:66 final size:71
Alignment explanation
Indices: 18629--18793 Score: 181
Period size: 66 Copynumber: 2.5 Consensus size: 71
18619 TTCAAAAGTA
* * *
18629 TTTTAAAATTATATATTATATATATTTTAAAAACGTTTTC-AAA-T-T-ATATA-GTTTTCAAAA
1 TTTTTAAACTATATATTATATATATTTT-AAAACGATTTCAAAACTATAATATATGTTTTCAAAA
18689 TGTTT-T
65 TGTTTCT
* *
18695 TTTTTAAACTATATATTATA-AGTTTTTTAAAATGATTTCAAAACTATAATATATGTTTTCAAAA
1 TTTTTAAACTATATATTATATA-TATTTTAAAACGATTTCAAAACTATAATATATGTTTTCAAAA
18759 TGTTTCT
65 TGTTTCT
*
18766 TTTTTAAA--A-A-ATTATATTTATTTTAAAA
1 TTTTTAAACTATATATTATATATATTTTAAAA
18794 ATGTTTTTTA
Statistics
Matches: 84, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
65 10 0.12
66 26 0.31
67 16 0.19
68 2 0.02
69 6 0.07
70 15 0.18
71 9 0.11
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (71 bp):
TTTTTAAACTATATATTATATATATTTTAAAACGATTTCAAAACTATAATATATGTTTTCAAAAT
GTTTCT
Found at i:18854 original size:35 final size:36
Alignment explanation
Indices: 18778--18928 Score: 151
Period size: 36 Copynumber: 4.1 Consensus size: 36
18768 TTTAAAAAAT
* **
18778 TATATTTATTTTAAAAATGTTTTTTAAAACCGTATAA
1 TATATTTATTTTAAAAATG-TTTTAAAAACTATATAA
* * *
18815 TATATTT-TCTTAAAAACGTTTTAAAAACTATATAT
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
* *
18850 TATATTTATTTTCAAAGTGTTTTAAAAACTATATAA
1 TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
** * * *
18886 TATATAGATGTTTCAAATATGTTTTCAAAACTATATTA
1 TATATTTAT-TTT-AAAAATGTTTTAAAAACTATATAA
18924 TATAT
1 TATAT
18929 ATATGTATAT
Statistics
Matches: 93, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
35 20 0.22
36 39 0.42
37 10 0.11
38 24 0.26
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATTTATTTTAAAAATGTTTTAAAAACTATATAA
Found at i:19862 original size:105 final size:105
Alignment explanation
Indices: 19563--20429 Score: 1229
Period size: 105 Copynumber: 8.3 Consensus size: 105
19553 CATTGTTCCA
* * **
19563 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTG-TTGTTGACAA
* * * *
19627 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
19669 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
19729 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
19769 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGTTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
*
19834 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
19874 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTATTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
19934 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
19974 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAC
*
20038 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
20079 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
20144 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
20184 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAATTG-TTGTTGACAA
20249 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
20291 AGTCC-ATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTG-TTGTTGACAAC
* * * *
20355 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
20396 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
20430 CGCGGATGGC
Statistics
Matches: 695, Mismatches: 48, Indels: 33
0.90 0.06 0.04
Matches are distributed among these distances:
100 171 0.25
101 7 0.01
102 8 0.01
103 5 0.01
104 8 0.01
105 335 0.48
106 84 0.12
107 56 0.08
109 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:19916 original size:205 final size:207
Alignment explanation
Indices: 19563--20429 Score: 1242
Period size: 205 Copynumber: 4.1 Consensus size: 207
19553 CATTGTTCCA
* * * **
19563 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
* * ** *
19628 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
** *
19693 TTGAAATTGAATCTGAA-TGAAATTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
131 TTGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
19757 TGCGTTGTCTGG
196 TGCGTTGTCTGG
* * ** * *
19769 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGTTCTGGGATTGGGAAGTTG-TTGTTGACAAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
*
19833 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
* *
19898 TTGAAATTGGCTCTGAA-TGAAATTTTATTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
131 TTGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
19962 TGCGTTGTCTGG
196 TGCGTTGTCTGG
*
19974 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTG-TTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTGTTGACAA
*
20037 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
*
20102 GTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 GTTGAAATTGGCTCTGA-ATT--GAAATT-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
20167 GAACTTGCGTTGTCTGG
191 GAACTTGCGTTGTCTGG
* *
20184 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAATTGTTTGTTGACAA
* *
20249 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC-ATATCCTTCATTGTGAA
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* *
20313 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
130 GTTGAAATTGGCTCTG-AATTGA-AA--T-TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
20378 TGAACTTGTGTTGTCTCG
190 TGAACTTGCGTTGTCTGG
* * *
20396 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
20430 CGCGGATGGC
Statistics
Matches: 602, Mismatches: 42, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
204 4 0.01
205 276 0.46
206 46 0.08
207 1 0.00
209 7 0.01
210 93 0.15
211 40 0.07
212 110 0.18
213 4 0.01
215 21 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (207 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
TTGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGG
Found at i:20125 original size:310 final size:311
Alignment explanation
Indices: 19563--20429 Score: 1300
Period size: 310 Copynumber: 2.8 Consensus size: 311
19553 CATTGTTCCA
* * *
19563 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAA-C-TGAAATTGTTTATTGACAA
* * * *
19627 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
62 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
19692 GTTGAAATTGAATCTGAA-TGAAA-TT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
127 GTTGAAATTGGCTCTGAATTGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
* * *
19754 ACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGTTCTGGGATTGGGAAG
192 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAG
19819 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
257 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
19874 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-T-TTTATTGACAAGCAG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTATTGACAACCAG
19936 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
20001 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGA-ATT-GAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
20066 TTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
194 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
* *
20131 GTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
259 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
20184 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AACT--G-AAATTGTTTATTGACAA
*
20249 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC-ATATCCTTCATTGTGAA
62 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
20313 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
127 GTTGAAATTGGCTCTG-AATTGA-AAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
* * * * *
20378 TGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
189 TGAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
20430 CGCGGATGGC
Statistics
Matches: 510, Mismatches: 27, Indels: 29
0.90 0.05 0.05
Matches are distributed among these distances:
305 85 0.17
306 2 0.00
307 5 0.01
308 4 0.01
309 2 0.00
310 193 0.38
311 37 0.07
312 2 0.00
314 1 0.00
315 5 0.01
316 42 0.08
317 107 0.21
318 3 0.01
320 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (311 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTATTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAATTGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
TGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:21169 original size:67 final size:66
Alignment explanation
Indices: 21034--21191 Score: 176
Period size: 68 Copynumber: 2.4 Consensus size: 66
21024 AAGATATCTG
* * **
21034 TTGTTTCATGAGAAA-TGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGA
1 TTGTTTCAAGAGAAACT-ATCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
21098 TTT
65 -TT
* ** * *
21101 TGTGTTTCAAGAGTAACTATCTCAAGGGCGACAAAATT-TGTTTTAGGGGAAATAAATTCAAAGG
1 T-TGTTTCAAGAGAAACTATCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGA
21165 TT
65 TT
* *
21167 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTATCTCAAG
21192 ATAGACGAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
65 21 0.27
66 3 0.04
67 23 0.30
68 29 0.38
69 1 0.01
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTATCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:21208 original size:65 final size:67
Alignment explanation
Indices: 21035--21500 Score: 170
Period size: 73 Copynumber: 6.7 Consensus size: 67
21025 AGATATCTGT
* * * * ** *
21035 TGTTTCATGAGAAA-TGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TGTTTCAAGAGAAACT-ATCTCAAGAGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAG
21099 TTTG
64 TTTG
* * * *
21103 TGTTTCAAGAGTAACTATCTCAAGGGCGACAAAATTTGTTTTAGGGGAAATAAATTCAAAG-GTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
21167 T-
66 TG
* * * * * *
21168 TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT--GTCTCAAGAG
1 TGTTTCAAGAGAAACTATCTCAAGAGAGAC-AAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-AG
*
21230 AGACAAAACTT-
62 AG------TTTG
* * * * * ** * * * * * *
21241 AGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAATTTGTTTCAAAGAAAACATATTCAAATA-TT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
21305 T-
66 TG
* * * * *
21306 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACT--GTCTCAAGATA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-A
**
21369 GACGAAAAT-
61 GA-G--TTTG
* * *
21378 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACT--GTCTCAAGAGA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA-TAAAT-TCAA-AGA
*
21441 GAAAAAAATT-
63 G------TTTG
* *
21451 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAA
21501 CTGTCTCAAG
Statistics
Matches: 316, Mismatches: 54, Indels: 51
0.75 0.13 0.12
Matches are distributed among these distances:
64 2 0.01
65 84 0.27
66 11 0.03
67 24 0.08
68 31 0.10
69 2 0.01
70 4 0.01
71 1 0.00
72 60 0.19
73 96 0.30
74 1 0.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAGTT
TG
Found at i:21218 original size:36 final size:36
Alignment explanation
Indices: 21166--21520 Score: 408
Period size: 36 Copynumber: 10.0 Consensus size: 36
21156 ATTCAAAGGT
* *
21166 TTTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
21203 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * **
21238 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
21275 TTTGTTTCAA-AGAAAACATAT-TC-----A-A-ATAT
1 TTTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
21304 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * *
21340 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
21377 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
21412 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAG-ACAAAA
21449 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
21485 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
21521 CTCTTCTAGT
Statistics
Matches: 273, Mismatches: 29, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
28 2 0.01
29 17 0.06
30 2 0.01
31 1 0.00
34 1 0.00
35 11 0.04
36 170 0.62
37 69 0.25
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:21486 original size:73 final size:73
Alignment explanation
Indices: 21304--21520 Score: 382
Period size: 73 Copynumber: 3.0 Consensus size: 73
21294 ATTCAAATAT
* * *
21304 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
**
21369 GACGAAAA
66 GAAAAAAA
21377 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
21441 GAAAAAAA
66 GAAAAAAA
21449 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
21514 GAAAAAA
66 GAAAAAA
21521 CTCTTCTAGT
Statistics
Matches: 138, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
72 67 0.49
73 71 0.51
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (73 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
GAAAAAAA
Found at i:22546 original size:22 final size:22
Alignment explanation
Indices: 22447--22539 Score: 159
Period size: 22 Copynumber: 4.2 Consensus size: 22
22437 TTGTGTTTGG
* *
22447 TCAAAGGTTTGGCATTTGATAC
1 TCAAAGGTTTGACATTTGATGC
22469 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
22491 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
22513 TCAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
22535 TCAAA
1 TCAAA
22540 AGATTGATGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 68 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:23047 original size:11 final size:12
Alignment explanation
Indices: 23029--23057 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
23019 TGCTCATATG
23029 TGTTTCTCTGGA
1 TGTTTCTCTGGA
23041 T-TTTCTCTGGA
1 TGTTTCTCTGGA
23052 TGTTTC
1 TGTTTC
23058 ATGATCTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.07, C:0.17, G:0.21, T:0.55
Consensus pattern (12 bp):
TGTTTCTCTGGA
Found at i:23209 original size:16 final size:16
Alignment explanation
Indices: 23190--23275 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 16
23180 TCTTTTTGAT
23190 TTTTGCTCTTTTTTTC
1 TTTTGCTCTTTTTTTC
* *
23206 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTT-TTTTTC
* * *
23223 TTTTTCTTTGTTTTTTTT
1 TTTTGC--TCTTTTTTTC
23241 TTTTGCT-TTTTTGCTTC
1 TTTTGCTCTTTTT--TTC
*
23258 TTTT-CTTTTTTTGTTC
1 TTTTGCTCTTTTT-TTC
23274 TT
1 TT
23276 GATTGGATCT
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
15 5 0.09
16 17 0.31
17 20 0.37
18 9 0.17
19 3 0.06
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTGCTCTTTTTTTC
Found at i:23251 original size:25 final size:25
Alignment explanation
Indices: 23178--23270 Score: 75
Period size: 25 Copynumber: 3.7 Consensus size: 25
23168 TTTGTCCCTT
** *
23178 TTTCTTTTTGATTTTTGCTCTTTT-
1 TTTCTTTTTTTTTTTTGCTTTTTTC
*
23202 TTTCTTTTGTTCTTGTTT-CTCTTTTTC
1 TTTCTTTT-TT-TTTTTTGCT-TTTTTC
*
23229 TTTGTTTTTTTTTTTTGCTTTTTTGC
1 TTTCTTTTTTTTTTTTGCTTTTTT-C
*
23255 -TTCTTTTCTTTTTTTG
1 TTTCTTTTTTTTTTTTG
23271 TTCTTGATTG
Statistics
Matches: 55, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
24 8 0.15
25 27 0.49
26 13 0.24
27 7 0.13
ACGTcount: A:0.01, C:0.13, G:0.09, T:0.77
Consensus pattern (25 bp):
TTTCTTTTTTTTTTTTGCTTTTTTC
Found at i:23269 original size:8 final size:8
Alignment explanation
Indices: 23196--23269 Score: 69
Period size: 8 Copynumber: 9.1 Consensus size: 8
23186 TGATTTTTGC
23196 TCTTTTTT
1 TCTTTTTT
*
23204 TCTTTTGT
1 TCTTTTTT
*
23212 TC-TTGTT
1 TCTTTTTT
*
23219 TCTCTTTT
1 TCTTTTTT
23227 TCTTTGTTT
1 TCTTT-TTT
*
23236 TTTTTTTT
1 TCTTTTTT
23244 TGCTTTTTT
1 T-CTTTTTT
* *
23253 GCTTCTTT
1 TCTTTTTT
23261 TCTTTTTT
1 TCTTTTTT
23269 T
1 T
23270 GTTCTTGATT
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
7 5 0.10
8 33 0.65
9 13 0.25
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (8 bp):
TCTTTTTT
Found at i:27521 original size:14 final size:14
Alignment explanation
Indices: 27493--27534 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
27483 TGGACAATTA
*
27493 AAATGAAAATAAAAT
1 AAATAAAAAT-AAAT
*
27508 TAATAAAAATAAAT
1 AAATAAAAATAAAT
27522 AAATAAAAATAAA
1 AAATAAAAATAAA
27535 CAACAACGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:27624 original size:36 final size:36
Alignment explanation
Indices: 27577--27652 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
27567 TTCTACAAAC
* *
27577 TATATAATATATATTTTCAAAA-GTATTTTAAAATTA
1 TATATAATATATATTTTAAAAACGT-TTTCAAAATTA
*
27613 TATATTATATATATTTTAAAAACGTTTTCAAAATTA
1 TATATAATATATATTTTAAAAACGTTTTCAAAATTA
27649 TATA
1 TATA
27653 GTTTTCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (36 bp):
TATATAATATATATTTTAAAAACGTTTTCAAAATTA
Found at i:27689 original size:68 final size:72
Alignment explanation
Indices: 27573--27750 Score: 178
Period size: 73 Copynumber: 2.6 Consensus size: 72
27563 TATTTTCTAC
* * * *
27573 AAACTATATAATATATATTTTCAAAA-G--T-ATTTTAAAATTATATATTATATA-TATTTTAAA
1 AAAC-ATATAATATATGTTTTCAAAATGTTTCTTTTTTAAACTATATATTATA-AGT-TTTTAAA
*
27633 AACGTTTTC-
63 AACGATTTCA
* * *
27642 AAA-AT-T-ATATA-GTTTTCAAAATGTTTTTTTTTTAAACTATATATTATAAGTTTTTTAAAAT
1 AAACATATAATATATGTTTTCAAAATGTTTCTTTTTTAAACTATATATTATAAGTTTTTAAAAAC
27703 GATTTCA
66 GATTTCA
27710 AAACTATATAATATATGTTTTCAAAATGTTTCTTTTTTAAA
1 AAAC-ATATAATATATGTTTTCAAAATGTTTCTTTTTTAAA
27751 AAATTATTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 18
0.78 0.07 0.16
Matches are distributed among these distances:
64 9 0.10
65 6 0.07
66 1 0.01
67 17 0.19
68 22 0.24
69 3 0.03
70 2 0.02
71 1 0.01
72 5 0.06
73 24 0.27
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (72 bp):
AAACATATAATATATGTTTTCAAAATGTTTCTTTTTTAAACTATATATTATAAGTTTTTAAAAAC
GATTTCA
Found at i:27846 original size:31 final size:33
Alignment explanation
Indices: 27808--27899 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 33
27798 TCTTAAAAAC
*
27808 GTTTTAAAAACTATATATATAT-TTTCAAA-GT
1 GTTTTAAAAACTATATATATATGTTTCAAATAT
27839 GTTTTAAAAACTATAAAATATATAGATGTTTCAAATAT
1 GTTTTAAAAACTAT---ATATAT--ATGTTTCAAATAT
*
27877 GTTTTCAAAACTATATTATATAT
1 GTTTTAAAAACTATA-TATATAT
27900 ATGTATATAC
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
31 14 0.27
34 8 0.16
35 1 0.02
36 7 0.14
37 7 0.14
38 14 0.27
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (33 bp):
GTTTTAAAAACTATATATATATGTTTCAAATAT
Found at i:27880 original size:38 final size:36
Alignment explanation
Indices: 27820--27900 Score: 99
Period size: 38 Copynumber: 2.2 Consensus size: 36
27810 TTTAAAAACT
* *
27820 ATATATATATTTTCAAAGTGTTTTAAAAACTATAAA
1 ATATATAGATTTTCAAAATGTTTTAAAAACTATAAA
* **
27856 ATATATAGATGTTTCAAATATGTTTTCAAAACTATATT
1 ATATATAGAT-TTTCAAA-ATGTTTTAAAAACTATAAA
27894 ATATATA
1 ATATATA
27901 TGTATATACA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
36 9 0.24
37 7 0.18
38 22 0.58
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.43
Consensus pattern (36 bp):
ATATATAGATTTTCAAAATGTTTTAAAAACTATAAA
Found at i:29153 original size:6 final size:6
Alignment explanation
Indices: 29118--29151 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
29108 AAGTTAAAAA
* *
29118 AACCCA AACCCT AACCCT AACCCT AACCTT AACC
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACC
29152 TTGACCTGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:31448 original size:55 final size:55
Alignment explanation
Indices: 31336--31465 Score: 154
Period size: 55 Copynumber: 2.4 Consensus size: 55
31326 AGGGAACTCA
* ** *
31336 AACTC-GGGTGGTGTCGGACACACGTATCAAACTCGATTAACAAAGCATTTCACG
1 AACTCGGGGTGGTGTCGGACACACGTATCAAACACGAGAAACAAAGCATTCCACG
* * **
31390 AACTCGGGGTGGTGTCGGACACACGTGTCAAACACGAGAAACAATGCATTCCTTG
1 AACTCGGGGTGGTGTCGGACACACGTATCAAACACGAGAAACAAAGCATTCCACG
***
31445 AACTCGATTTGGTGTCGGACA
1 AACTCGGGGTGGTGTCGGACA
31466 TACGAGTAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
54 5 0.08
55 59 0.92
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.22
Consensus pattern (55 bp):
AACTCGGGGTGGTGTCGGACACACGTATCAAACACGAGAAACAAAGCATTCCACG
Found at i:33351 original size:20 final size:20
Alignment explanation
Indices: 33326--33366 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
33316 TTCGTCTGTT
*
33326 GCCCGCTGGCCGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
* *
33346 GCCCGCCGTCTGCTGCCGCC
1 GCCCGCCGGCCGCTGCCGCC
33366 G
1 G
33367 TCAGCCGTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.54, G:0.34, T:0.12
Consensus pattern (20 bp):
GCCCGCCGGCCGCTGCCGCC
Found at i:33373 original size:20 final size:20
Alignment explanation
Indices: 33337--33375 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33327 CCCGCTGGCC
*
33337 GCTGCCGCCGCCCGCCGTCT
1 GCTGCCGCCGCCAGCCGTCT
*
33357 GCTGCCGCCGTCAGCCGTC
1 GCTGCCGCCGCCAGCCGTC
33376 CGCCGCCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.51, G:0.31, T:0.15
Consensus pattern (20 bp):
GCTGCCGCCGCCAGCCGTCT
Found at i:38932 original size:20 final size:20
Alignment explanation
Indices: 38895--38934 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
38885 ATGGAATCTG
*
38895 CTTTTCTTAATAAAAATAAT
1 CTTTTATTAATAAAAATAAT
* *
38915 CTTTTATTATTAATAATAAT
1 CTTTTATTAATAAAAATAAT
38935 AATAATTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (20 bp):
CTTTTATTAATAAAAATAAT
Found at i:40194 original size:12 final size:12
Alignment explanation
Indices: 40181--40223 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
40171 GTAATGAATT
*
40181 ATTAATTTAATT
1 ATTAATTTAATA
*
40193 ATTAATTTACTA
1 ATTAATTTAATA
40205 ATT-A-TTAATA
1 ATTAATTTAATA
40215 ATTAATTTA
1 ATTAATTTA
40224 CTATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 16 0.62
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTAATTTAATA
Found at i:40213 original size:22 final size:22
Alignment explanation
Indices: 40186--40243 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 22
40176 GAATTATTAA
40186 TTTAATTATTAATTTACTA-AT
1 TTTAATTATTAATTTACTATAT
*
40207 TATTAATAATTAATTTACTATAT
1 T-TTAATTATTAATTTACTATAT
40230 TTTATATCTATTAA
1 TTTA-AT-TATTAA
40244 AAGACAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 1 0.03
22 20 0.65
23 5 0.16
24 5 0.16
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAATTATTAATTTACTATAT
Found at i:54542 original size:21 final size:20
Alignment explanation
Indices: 54502--54543 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
54492 TAAAAATATT
*
54502 AAAAAATAATATTTTAAATA
1 AAAAAATAATATTATAAATA
*
54522 AAAATAATAATATTATCAATA
1 AAAA-AATAATATTATAAATA
54543 A
1 A
54544 TTTTTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATAATATTATAAATA
Found at i:55200 original size:33 final size:33
Alignment explanation
Indices: 55153--55226 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
55143 ATTTTAGTGA
*
55153 ATAACAGTTAATTCAAAAAGGTAATTTATAGCT
1 ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
*
55186 GTAATAGTTAATTCAAAAAGGTAATTTATAGCT
1 ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
55219 ATAATAGT
1 ATAATAGT
55227 GTTCGATAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.35
Consensus pattern (33 bp):
ATAATAGTTAATTCAAAAAGGTAATTTATAGCT
Done.