Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006342.1 Hibiscus syriacus cultivar Beakdansim tig00015159_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: 72222
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:719 original size:15 final size:15
Alignment explanation
Indices: 699--735 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
689 ATGTCACATT
699 CAGAGCCAATTCATA
1 CAGAGCCAATTCATA
714 CAGAGCCAATTCATA
1 CAGAGCCAATTCATA
729 CAGAGCC
1 CAGAGCC
736 TTTGAATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.30, G:0.16, T:0.16
Consensus pattern (15 bp):
CAGAGCCAATTCATA
Found at i:2280 original size:3 final size:3
Alignment explanation
Indices: 2274--2418 Score: 206
Period size: 3 Copynumber: 49.0 Consensus size: 3
2264 TTTATCCATT
* * *
2274 TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2322 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA -TA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* *
2370 TTA TCA TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TCA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2416 TTA
1 TTA
2419 AATATATTAA
Statistics
Matches: 126, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
2 6 0.05
3 118 0.94
4 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:15180 original size:6 final size:6
Alignment explanation
Indices: 15163--15240 Score: 67
Period size: 6 Copynumber: 13.2 Consensus size: 6
15153 ATTATGCTTG
* *
15163 AAGAAA AA-AAA AAGAAA AA-AGAA AAGAAA AA-TAA GAGAAA AA-AAA
1 AAGAAA AAGAAA AAGAAA AAGA-AA AAGAAA AAGAAA AAGAAA AAGAAA
15208 AAGGAAAA GAAGAAA AAGAAA AAGAAA AA-AAA A
1 AA-G-AAA -AAGAAA AAGAAA AAGAAA AAGAAA A
15241 GGGGTCAAGG
Statistics
Matches: 60, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
5 18 0.30
6 32 0.53
7 4 0.07
8 4 0.07
9 2 0.03
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.01
Consensus pattern (6 bp):
AAGAAA
Found at i:15203 original size:28 final size:28
Alignment explanation
Indices: 15162--15237 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 28
15152 TATTATGCTT
15162 GAAGAAAAA-AAAAAGAAAAAA-GAAAA
1 GAAGAAAAAGAAAAAGAAAAAAGGAAAA
15188 GAA-AAATAAGAGAAAA-AAAAAAGGAAAA
1 GAAGAAA-AAGA-AAAAGAAAAAAGGAAAA
15216 GAAGAAAAAGAAAAAGAAAAAA
1 GAAGAAAAAGAAAAAGAAAAAA
15238 AAAGGGGTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
25 3 0.07
26 5 0.11
27 11 0.25
28 22 0.50
29 3 0.07
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (28 bp):
GAAGAAAAAGAAAAAGAAAAAAGGAAAA
Found at i:15234 original size:32 final size:33
Alignment explanation
Indices: 15163--15240 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 33
15153 ATTATGCTTG
15163 AAGAAAAAAAAAAGAAAAAAGAAAAGAAAAATA
1 AAGAAAAAAAAAAGAAAAAAGAAAAGAAAAATA
*
15196 AGAGAAAAAAAAAAGGAAAAGAAGAAAAAGAAAAAGA
1 A-AGAAAAAAAAAA-GAAAA-AAG-AAAAGAAAAATA
15233 AA-AAAAAA
1 AAGAAAAAA
15241 GGGGTCAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
33 1 0.03
34 12 0.30
35 11 0.28
36 4 0.10
37 12 0.30
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.01
Consensus pattern (33 bp):
AAGAAAAAAAAAAGAAAAAAGAAAAGAAAAATA
Found at i:15237 original size:22 final size:20
Alignment explanation
Indices: 15168--15239 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 20
15158 GCTTGAAGAA
15168 AAAAAAAAGAAAAAAGAAAAG
1 AAAAAAAAGAAAAAA-AAAAG
15189 AAAAATAAGAGAAAAAAAAAAG
1 AAAAA-AA-AGAAAAAAAAAAG
* *
15211 GAAAAGAAGAAAAAGAAAAAG
1 AAAAAAAAGAAAAA-AAAAAG
15232 AAAAAAAA
1 AAAAAAAA
15240 AGGGGTCAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
20 7 0.16
21 18 0.41
22 11 0.25
23 8 0.18
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.01
Consensus pattern (20 bp):
AAAAAAAAGAAAAAAAAAAG
Found at i:15238 original size:34 final size:34
Alignment explanation
Indices: 15167--15240 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 34
15157 TGCTTGAAGA
15167 AAAAAAAAAGAAAAAAGAAAAGAAAAATAAGAGAA
1 AAAAAAAAAGAAAAAAGAAAAGAAAAATAAGA-AA
* *
15202 AAAAAAAAGGAAAAGAAGAAAA-AGAAA-AAGAAA
1 AAAAAAAAAGAAAA-AAGAAAAGAAAAATAAGAAA
15235 AAAAAA
1 AAAAAA
15241 GGGGTCAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
33 8 0.22
34 4 0.11
35 17 0.47
36 7 0.19
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (34 bp):
AAAAAAAAAGAAAAAAGAAAAGAAAAATAAGAAA
Found at i:16474 original size:52 final size:52
Alignment explanation
Indices: 16396--16712 Score: 557
Period size: 52 Copynumber: 6.1 Consensus size: 52
16386 AATATGCTCA
16396 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
16448 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
*
16500 AACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
* *
16552 AACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
*
16604 AACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
*
16656 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCT-AGTCTGATTGGACAGAATCA-
1 AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA-TCTGGTTGGACAGAA-CAT
16708 AGCAT
1 AGCAT
16713 TGAATTTAGA
Statistics
Matches: 258, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
51 1 0.00
52 255 0.99
53 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.36
Consensus pattern (52 bp):
AGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACAT
Found at i:16793 original size:83 final size:83
Alignment explanation
Indices: 16654--16858 Score: 349
Period size: 83 Copynumber: 2.5 Consensus size: 83
16644 TGGACAGAAC
*
16654 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT-AGTCTGATTGGACAGAATCAAGCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGA-TCTAATTGGACAGAATCAAGCATTGAAT
16718 TTAGAAGATAAATTTGCCA
65 TTAGAAGATAAATTTGCCA
16737 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTGGACAGAATCAAGCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTGGACAGAATCAAGCATTGAATT
* *
16802 TGGAAGATGAATTTGCCA
66 TAGAAGATAAATTTGCCA
* *
16820 ATAGCATCTTCTGGAAGCGTTCTTTGAGTTATTTGATCT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
16859 GAAGAAGTGC
Statistics
Matches: 116, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
83 115 0.99
84 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAATTGGACAGAATCAAGCATTGAATT
TAGAAGATAAATTTGCCA
Found at i:17607 original size:113 final size:113
Alignment explanation
Indices: 17409--18074 Score: 1010
Period size: 113 Copynumber: 5.8 Consensus size: 113
17399 TAGCAAAGAT
* *
17409 TTGAATCCGTCATTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
17474 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
17522 TTGAATCCGTCATTTGATGGATTAACTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
17587 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
17635 TTGAATCCGTCATTTGATGGATTAACTTTTCCAGAGAAGAGTTCATAATGAGAAGAACTCGTCAT
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAA--C-TCAT
* * *
17700 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGT
62 CTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
17752 TTAAATTCATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
1 TTGAATCCATCATTTGATGGATCA-ACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
17817 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
17866 TTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
17931 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
17979 TTAAATCCATCATTTGGTGGATCAACATTGCTAG-GTAAAGTTCATAATGAGAAGAACTCATCTG
1 TTGAATCCATCATTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
18043 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAA
65 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAA
18075 CTCATCAAGA
Statistics
Matches: 515, Mismatches: 32, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
112 1 0.00
113 321 0.62
114 90 0.17
115 1 0.00
116 1 0.00
117 88 0.17
118 13 0.03
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (113 bp):
TTGAATCCATCATTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:18331 original size:3 final size:3
Alignment explanation
Indices: 18325--18473 Score: 219
Period size: 3 Copynumber: 50.0 Consensus size: 3
18315 TTTATCCATT
* * *
18325 TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
18373 TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
18421 TTA TTA TCA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TCA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18468 TTA TTA
1 TTA TTA
18474 AATATATTAA
Statistics
Matches: 129, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
2 2 0.02
3 127 0.98
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:18980 original size:15 final size:16
Alignment explanation
Indices: 18960--18989 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18950 ACAGAACCGA
18960 AGAGAA-AAAAAAAAC
1 AGAGAAGAAAAAAAAC
18975 AGAGAAGAAAAAAAA
1 AGAGAAGAAAAAAAA
18990 AACAACAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAGAAGAAAAAAAAC
Found at i:18987 original size:20 final size:21
Alignment explanation
Indices: 18958--18996 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18948 AAACAGAACC
*
18958 GAAGAGAAAAAAAA-AACAGA
1 GAAGAAAAAAAAAACAACAGA
18978 GAAGAAAAAAAAAACAACA
1 GAAGAAAAAAAAAACAACA
18997 AACTATACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (21 bp):
GAAGAAAAAAAAAACAACAGA
Found at i:21283 original size:38 final size:38
Alignment explanation
Indices: 21232--21307 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
21222 CACATATTAG
21232 ATCATCCAATGGCATGATCATGGGGATTGGTAGAAAGT
1 ATCATCCAATGGCATGATCATGGGGATTGGTAGAAAGT
21270 ATCATCCAATGGCATGATCATGGGGATTGGTAGAAAGT
1 ATCATCCAATGGCATGATCATGGGGATTGGTAGAAAGT
21308 CTAAGGGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (38 bp):
ATCATCCAATGGCATGATCATGGGGATTGGTAGAAAGT
Found at i:21852 original size:15 final size:16
Alignment explanation
Indices: 21832--21867 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
21822 TTTGTTTGAT
21832 TAAAAAT-AAAGAAAG
1 TAAAAATAAAAGAAAG
21847 TAAAAATAAAAGAAAG
1 TAAAAATAAAAGAAAG
21863 TAAAA
1 TAAAA
21868 TTGAATTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (16 bp):
TAAAAATAAAAGAAAG
Found at i:24156 original size:30 final size:31
Alignment explanation
Indices: 24116--24180 Score: 98
Period size: 30 Copynumber: 2.1 Consensus size: 31
24106 CTTTATTGCA
*
24116 CAAATTAACCCTTCAAA-TTGAC-ATTTTTAT
1 CAAATCAACCCTT-AAACTTGACAATTTTTAT
24146 CAAATCAACCCTTAAACTTGACAATTTTTAT
1 CAAATCAACCCTTAAACTTGACAATTTTTAT
24177 CAAA
1 CAAA
24181 CTTTAACGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 3 0.09
30 17 0.53
31 12 0.38
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (31 bp):
CAAATCAACCCTTAAACTTGACAATTTTTAT
Found at i:26758 original size:49 final size:49
Alignment explanation
Indices: 26701--26796 Score: 147
Period size: 49 Copynumber: 2.0 Consensus size: 49
26691 GACACTTGTA
*
26701 GAGGGGTTGCTTGGGATACCCCGGGCACCATGGAGGTCCACCCCTGGAT
1 GAGGGGTTGCTCGGGATACCCCGGGCACCATGGAGGTCCACCCCTGGAT
* * * *
26750 GAGGGGTTGCTCGGGATATCCCGGGCTCTATGGAGGTCCGCCCCTGG
1 GAGGGGTTGCTCGGGATACCCCGGGCACCATGGAGGTCCACCCCTGG
26797 TATAAATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.14, C:0.28, G:0.39, T:0.20
Consensus pattern (49 bp):
GAGGGGTTGCTCGGGATACCCCGGGCACCATGGAGGTCCACCCCTGGAT
Found at i:28879 original size:20 final size:20
Alignment explanation
Indices: 28854--28898 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
28844 ATGCTAGATA
28854 AATTTAATGGTCAGACTTTG
1 AATTTAATGGTCAGACTTTG
28874 AATTTAATGGTCAGACTTTG
1 AATTTAATGGTCAGACTTTG
28894 AATTT
1 AATTT
28899 TGTTAAGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (20 bp):
AATTTAATGGTCAGACTTTG
Found at i:36395 original size:3 final size:3
Alignment explanation
Indices: 36387--36430 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
36377 GTAATATTTG
* * *
36387 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAG TAG TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
36431 ATATAATTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:36881 original size:42 final size:43
Alignment explanation
Indices: 36816--36896 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 43
36806 AAGGACTTAT
* *
36816 CATCTTGCTCGAAAGACTGACAGATGACCCGAA-GATTTTAAG
1 CATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTTAAG
36858 CATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTT
1 CATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTT
36897 ACAAATTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 31 0.86
43 5 0.14
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (43 bp):
CATCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTTAAG
Found at i:36922 original size:249 final size:249
Alignment explanation
Indices: 36482--36990 Score: 831
Period size: 249 Copynumber: 2.0 Consensus size: 249
36472 AGTTGCCCTT
* *
36482 CTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATATGTGAACATCCTACCCAAAGGCTTTA
1 CTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATATATGAACATCATACCCAAAGGCTTTA
* * *
36547 CGGATGCCCTAAGGACTTATCATATTGCTCGAAAGACTGACAGATGACCTGAAGGTTTTATGCAT
66 CGGATGCCCTAAGGACTTATCATATTGCTCGAAAGACTGACAGATGACCCGAAGATTTTAAGCAT
* * *
36612 CATGCTCGAAAGACTAATAGATGACCTGAAGGATTTACAAATTTGTGGGAAATATTTTACTGAGT
131 CATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACAAATTTGTGGGAAATACTTTACTGAGT
* * *
36677 AATAAACTTCTTACTTTTCAAAAATTTGATTTTCT-AGAACATTAAATGAGAAA
196 AAGAAACTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAA
*
36730 CTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATATATGAACATTATACCCAAAGGCTTTA
1 CTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATATATGAACATCATACCCAAAGGCTTTA
* *
36795 CGGATGGCTCTAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGACCCGAAGATTTTAAGCA
66 CGGAT-GCCCTAAGGACTTATCATATTGCTCGAAAGACTGACAGATGACCCGAAGATTTTAAGCA
*
36860 TCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACAAATTTGTGGGAAATACTTTACTGGG
130 TCATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACAAATTTGTGGGAAATACTTTACTGAG
* * *
36925 TAAGAAGCTTCTTACTTTTCAAGAATTTCATTTTCTAAAAAAGATTAAATGAGAAA
195 TAAGAAACTTCTTACTTTTCAAAAATTTCATTTTCT-AAAAACATTAAATGAGAAA
36981 CTTTGAAAAT
1 CTTTGAAAAT
36991 TATTTTATCA
Statistics
Matches: 240, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
248 67 0.28
249 147 0.61
251 26 0.11
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (249 bp):
CTTTGAAAATCGCTATCTCATTTTCATGCGAAAATCATATATGAACATCATACCCAAAGGCTTTA
CGGATGCCCTAAGGACTTATCATATTGCTCGAAAGACTGACAGATGACCCGAAGATTTTAAGCAT
CATGCTCGAAAGACTAACAGATGACCCGAAGGATTTACAAATTTGTGGGAAATACTTTACTGAGT
AAGAAACTTCTTACTTTTCAAAAATTTCATTTTCTAAAAACATTAAATGAGAAA
Found at i:39933 original size:9 final size:9
Alignment explanation
Indices: 39902--39961 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
39892 ATTCAATTTC
39902 TTTTCCTTTT
1 TTTTCC-TTT
*
39912 TTTGTCATCTT
1 TTT-TCCT-TT
39923 TTTTCCTTT
1 TTTTCCTTT
39932 TTTTCCTTT
1 TTTTCCTTT
39941 TTCTT--TTT
1 TT-TTCCTTT
*
39949 TTTTTCTTT
1 TTTTCCTTT
39958 TTTT
1 TTTT
39962 AATGATAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
7 2 0.05
8 5 0.12
9 20 0.47
10 9 0.21
11 7 0.16
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (9 bp):
TTTTCCTTT
Found at i:39947 original size:21 final size:22
Alignment explanation
Indices: 39898--39947 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
39888 CTTGATTCAA
*
39898 TTTCTTTTCCTTTTTTTGTCAT
1 TTTCTTTTCCTTTTTTTGCCAT
* *
39920 CTT-TTTTCCTTTTTTT-CCTT
1 TTTCTTTTCCTTTTTTTGCCAT
39940 TTTCTTTT
1 TTTCTTTT
39948 TTTTTTCTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.17
21 17 0.74
22 2 0.09
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTCTTTTCCTTTTTTTGCCAT
Found at i:42451 original size:20 final size:20
Alignment explanation
Indices: 42412--42461 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
42402 TACAAACGTA
*
42412 AAAATGCAAAGATGCAAATG
1 AAAATGCAAAGATACAAATG
* **
42432 CAAATGCAAAGATATGAATG
1 AAAATGCAAAGATACAAATG
42452 AAAATGCAAA
1 AAAATGCAAA
42462 AACGTAGAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATGCAAAGATACAAATG
Found at i:46481 original size:3 final size:3
Alignment explanation
Indices: 46473--46516 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
46463 GTAATATTTG
* *
46473 TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAG TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46517 ATATAATTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:46523 original size:9 final size:8
Alignment explanation
Indices: 46473--46523 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 8
46463 GTAATATTTG
46473 TAATAATAA
1 TAAT-ATAA
46482 TAATATAA
1 TAATATAA
46490 TAATAATAA
1 TAAT-ATAA
46499 TAATAGTAA
1 TAATA-TAA
46508 T-AT-TAA
1 TAATATAA
46514 TAAATATAA
1 T-AATATAA
46523 T
1 T
46524 TAGTATCGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 4 0.11
8 13 0.35
9 20 0.54
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (8 bp):
TAATATAA
Found at i:51336 original size:2 final size:2
Alignment explanation
Indices: 51331--51359 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
51321 ATTAAAAAAA
51331 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 A
51360 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51848 original size:17 final size:17
Alignment explanation
Indices: 51826--51863 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
51816 TTACCGTAAA
51826 TATGTTCATTTAACGTT
1 TATGTTCATTTAACGTT
*
51843 TATGTTTATTTAACGTT
1 TATGTTCATTTAACGTT
51860 TATG
1 TATG
51864 GAAATTTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.55
Consensus pattern (17 bp):
TATGTTCATTTAACGTT
Found at i:57722 original size:14 final size:15
Alignment explanation
Indices: 57691--57725 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
57681 GAGGCGACAT
*
57691 AAAATCCAACCCTAA
1 AAAATCCAACCATAA
*
57706 AAAATCCAACGATAA
1 AAAATCCAACCATAA
57721 AAAAT
1 AAAAT
57726 ATGCCATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.60, C:0.23, G:0.03, T:0.14
Consensus pattern (15 bp):
AAAATCCAACCATAA
Found at i:59506 original size:114 final size:114
Alignment explanation
Indices: 59302--59514 Score: 320
Period size: 114 Copynumber: 1.9 Consensus size: 114
59292 TAATAGCGAG
* * *
59302 TATCGAATTAAAACATAAACTAAATGTTAGGTATAATTTAAGAAAAATTTAAATAACAAAATAGA
1 TATCGAATTAAAACATAAACTAAATATTAGATATAATTTAAGAAAAAATTAAATAACAAAATAGA
* *
59367 ACAAAAGTAGTAGTTTAAGTATTAAACATCATTACTGAAGGAGATGTGA
66 AAAAAAGTAATAGTTTAAGTATTAAACATCATTACTGAAGGAGATGTGA
* *
59416 TATCGAATTAAAACATAAACTAAATATTATATATAATTTAA-AAAAAATTAGATAACAAAATAGA
1 TATCGAATTAAAACATAAACTAAATATTAGATATAATTTAAGAAAAAATTAAATAACAAAATAG-
* * *
59480 AAAAAAATTAATAGTTTAGGTGTTAAACATCATTA
65 AAAAAAAGTAATAGTTTAAGTATTAAACATCATTA
59515 TTCACGGTAA
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
113 20 0.23
114 68 0.77
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.30
Consensus pattern (114 bp):
TATCGAATTAAAACATAAACTAAATATTAGATATAATTTAAGAAAAAATTAAATAACAAAATAGA
AAAAAAGTAATAGTTTAAGTATTAAACATCATTACTGAAGGAGATGTGA
Found at i:63157 original size:22 final size:22
Alignment explanation
Indices: 63115--63157 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
63105 AGTTATTTAA
*
63115 TTTTATTATTTTATGTTTTATG
1 TTTTATTATTTTATGTATTATG
63137 TTTTATTATTATTAT-TATTAT
1 TTTTATTATT-TTATGTATTAT
63158 TATATTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (22 bp):
TTTTATTATTTTATGTATTATG
Found at i:63160 original size:25 final size:25
Alignment explanation
Indices: 63117--63166 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
63107 TTATTTAATT
* *
63117 TTATTATTTTATGTTTTATGTTTTA
1 TTATTATTTTATGTATTATATTTTA
63142 TTATTATTATTAT-TATTATATTTTA
1 TTATTATT-TTATGTATTATATTTTA
63167 GGATTAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (25 bp):
TTATTATTTTATGTATTATATTTTA
Found at i:67044 original size:24 final size:24
Alignment explanation
Indices: 67017--67066 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
67007 TGGTGGTTGA
*
67017 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
67041 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
67065 TT
1 TT
67067 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Done.