Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009221.1 Hibiscus syriacus cultivar Beakdansim tig00112812_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: 265395
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:193029 original size:4 final size:4
Alignment explanation
Indices: 192777--193023 Score: 485
Period size: 4 Copynumber: 61.8 Consensus size: 4
192767 TATAGTTTAT
192777 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
192825 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
192873 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
192921 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
192969 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
193017 ATAC ATA
1 ATAC ATA
193024 TATATAGAGA
Statistics
Matches: 241, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 241 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:193290 original size:17 final size:18
Alignment explanation
Indices: 193250--193292 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
193240 CCCCCAAAAT
193250 TTCTCAATTTCTCAGTAAA
1 TTCTCAATTTCTCA-TAAA
*
193269 TTCTCAATTTCTC-TATA
1 TTCTCAATTTCTCATAAA
193286 TTCTCAA
1 TTCTCAA
193293 AATTTCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.43
19 13 0.57
ACGTcount: A:0.28, C:0.23, G:0.02, T:0.47
Consensus pattern (18 bp):
TTCTCAATTTCTCATAAA
Found at i:193392 original size:2 final size:2
Alignment explanation
Indices: 193385--193586 Score: 85
Period size: 2 Copynumber: 104.0 Consensus size: 2
193375 ACTTTGAATA
193385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * * * * * *
193426 AA AT -T AT AG CT -T AT AA ACT AT AT ACT TT TT AT AGT TT AT AC
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT
* *
193467 AT AT AT AGT -T AT AT AT AT AGT -T CAT AT AA AC AT A- AT AT AT
1 AT AT AT A-T AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT
* *
193507 AT AT AT AT AT A- AT TT AT A- AT A- AT -T AT AT AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
*
193546 A- AT TT AT AT AT GA- ACT -T AT AT -T AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
193585 AT
1 AT
193587 TTTTTTAATT
Statistics
Matches: 152, Mismatches: 22, Indels: 52
0.67 0.10 0.23
Matches are distributed among these distances:
1 16 0.11
2 126 0.83
3 10 0.07
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:193532 original size:9 final size:11
Alignment explanation
Indices: 193501--193580 Score: 64
Period size: 11 Copynumber: 7.6 Consensus size: 11
193491 TATAAACATA
*
193501 ATATAT-ATAT
1 ATATATAATTT
193511 ATATATAATTT
1 ATATATAATTT
193522 ATA-ATAA--T
1 ATATATAATTT
*
193530 -TATATAGTTT
1 ATATATAATTT
193540 ATATATAATTT
1 ATATATAATTT
*
193551 ATATATGAACTT
1 ATATAT-AATTT
*
193563 ATAT-TATATAT
1 ATATATA-ATTT
193574 ATATATA
1 ATATATA
193581 TTATATTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
7 2 0.04
8 4 0.07
10 12 0.21
11 28 0.50
12 10 0.18
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (11 bp):
ATATATAATTT
Found at i:193549 original size:29 final size:27
Alignment explanation
Indices: 193498--193578 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 27
193488 TCATATAAAC
193498 ATAATATATATATATATATAATTTATA
1 ATAATATATATATATATATAATTTATA
*
193525 ATAATTATATAGTTTATATATAATTTATA
1 ATAA-TATATA-TATATATATAATTTATA
193554 TATGAACTTATATTATATATATATA
1 -AT-AA--TATA-TATATATATATA
193579 TATTATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
27 4 0.09
28 6 0.13
29 16 0.35
30 2 0.04
31 2 0.04
32 14 0.30
33 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (27 bp):
ATAATATATATATATATATAATTTATA
Found at i:201218 original size:13 final size:13
Alignment explanation
Indices: 201200--201235 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
201190 GACTTATTAA
*
201200 AAAATAAATCTGC
1 AAAATAAATATGC
*
201213 AAAATAGATATGC
1 AAAATAAATATGC
201226 AAAATAAATA
1 AAAATAAATA
201236 CTATAGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.22
Consensus pattern (13 bp):
AAAATAAATATGC
Found at i:203522 original size:13 final size:13
Alignment explanation
Indices: 203504--203528 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
203494 ATGACCAAAT
203504 AATTAAAAAATAA
1 AATTAAAAAATAA
203517 AATTAAAAAATA
1 AATTAAAAAATA
203529 TATAGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AATTAAAAAATAA
Found at i:204210 original size:14 final size:14
Alignment explanation
Indices: 204181--204223 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
204171 AAAAAAAGTG
*
204181 TATTAATT-ACATA
1 TATTAATTAAAATA
*
204194 TATTTATTAAAATA
1 TATTAATTAAAATA
204208 TATTAATTAAAATA
1 TATTAATTAAAATA
204222 TA
1 TA
204224 AACTATAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 7 0.27
14 19 0.73
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTAATTAAAATA
Found at i:204417 original size:16 final size:16
Alignment explanation
Indices: 204398--204433 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
204388 ACATGGCTCG
*
204398 AGACACACTCTGACTC
1 AGACACACTCAGACTC
204414 AGACACACTCAGACTC
1 AGACACACTCAGACTC
204430 AGAC
1 AGAC
204434 CTATACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (16 bp):
AGACACACTCAGACTC
Found at i:215608 original size:17 final size:18
Alignment explanation
Indices: 215581--215614 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
215571 AATTAAGAAA
*
215581 TAAGAATAAAAATAAAGT
1 TAAGAATAAAAAGAAAGT
215599 TAAG-ATAAAAAGAAAG
1 TAAGAATAAAAAGAAAG
215615 AATAATAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.18
Consensus pattern (18 bp):
TAAGAATAAAAAGAAAGT
Found at i:215653 original size:4 final size:4
Alignment explanation
Indices: 215644--215671 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
215634 ATTAAAAGAG
215644 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
215672 GAAGAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:215737 original size:45 final size:44
Alignment explanation
Indices: 215656--215819 Score: 181
Period size: 45 Copynumber: 3.7 Consensus size: 44
215646 ATAAATAAAT
* *
215656 AAATAAATAAATAAATGAAGAAAATGTTAAAATTTAAAAGAAATTTA
1 AAATAAAT-AA-AAATGAAGAAAATGTTAAATTTTAAAAGAAA-TAA
* *
215703 AAATAAATAAAAATGAAGAAAATATTAATTTTTAAAAGAAATAA
1 AAATAAATAAAAATGAAGAAAATGTTAAATTTTAAAAGAAATAA
* * *
215747 AAATAAAATAAAAAT-ATAAAGAAATGTTAAATATTATAAGAAATAA
1 AAAT-AAATAAAAATGA-AGA-AAATGTTAAATTTTAAAAGAAATAA
*
215793 AAAT-AA-AAAAATGAAGAAAGTGTTAAA
1 AAATAAATAAAAATGAAGAAAATGTTAAA
215820 GGATCAAATT
Statistics
Matches: 102, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
42 9 0.09
43 8 0.08
44 10 0.10
45 40 0.39
46 27 0.26
47 8 0.08
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (44 bp):
AAATAAATAAAAATGAAGAAAATGTTAAATTTTAAAAGAAATAA
Found at i:215801 original size:41 final size:40
Alignment explanation
Indices: 215743--215819 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 40
215733 TTTAAAAGAA
*
215743 ATAAAAATAAAATAAAAATATAAAGAAA-TGTTAAATATT
1 ATAAAAATAAAATAAAAAAATAAAGAAAGTGTTAAATATT
*
215782 ATAAGAAATAAAAATAAAAAAATGAAGAAAGTGTTAAA
1 ATAA-AAAT-AAAATAAAAAAATAAAGAAAGTGTTAAA
215820 GGATCAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 4 0.12
40 4 0.12
41 18 0.55
42 7 0.21
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.23
Consensus pattern (40 bp):
ATAAAAATAAAATAAAAAAATAAAGAAAGTGTTAAATATT
Found at i:216927 original size:17 final size:17
Alignment explanation
Indices: 216905--217022 Score: 96
Period size: 17 Copynumber: 7.4 Consensus size: 17
216895 AAATAATATA
216905 ATAAATAAATATATAAT
1 ATAAATAAATATATAAT
216922 ATAAAT-AATA-ATAAT
1 ATAAATAAATATATAAT
216937 ATATAATAAATATA-AAT
1 ATA-AATAAATATATAAT
* *
216954 ATATATAAATACA-AAT
1 ATAAATAAATATATAAT
216970 A-ATAATAAATA-AT-AT
1 ATA-AATAAATATATAAT
216985 -T-AATATAATATATAAT
1 ATAAATA-AATATATAAT
*
217001 AT-AATATAGTATATAAT
1 ATAAATA-AATATATAAT
217018 A-AAAT
1 ATAAAT
217023 CTATATAATA
Statistics
Matches: 86, Mismatches: 4, Indels: 22
0.77 0.04 0.20
Matches are distributed among these distances:
13 4 0.05
14 4 0.05
15 14 0.16
16 28 0.33
17 35 0.41
18 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.36
Consensus pattern (17 bp):
ATAAATAAATATATAAT
Found at i:217013 original size:10 final size:10
Alignment explanation
Indices: 216897--217038 Score: 82
Period size: 10 Copynumber: 13.7 Consensus size: 10
216887 AAAATAAAAA
216897 ATAATATAAT
1 ATAATATAAT
*
216907 A-AATAAATAT
1 ATAATATA-AT
216917 ATAATATAA-
1 ATAATATAAT
216926 ATAATAATAAT
1 ATAAT-ATAAT
216937 AT-ATAATAAAT
1 ATAAT-AT-AAT
216948 ATAA-ATATAT
1 ATAATATA-AT
*
216958 ATAA-ATACAA
1 ATAATATA-AT
216968 ATAATAATAA-
1 ATAAT-ATAAT
216978 ATAATATTAAT
1 ATAATA-TAAT
216989 ATAATATATAAT
1 AT-A-ATATAAT
217001 ATAATATAGTAT
1 ATAATATA--AT
*
217013 ATAATAAAAT
1 ATAATATAAT
*
217023 CT-ATATAAT
1 ATAATATAAT
*
217032 ATTATAT
1 ATAATAT
217039 TTTCAAAAAT
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
9 19 0.18
10 50 0.46
11 16 0.15
12 20 0.19
13 3 0.03
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (10 bp):
ATAATATAAT
Found at i:217017 original size:42 final size:39
Alignment explanation
Indices: 216896--217020 Score: 141
Period size: 37 Copynumber: 3.2 Consensus size: 39
216886 AAAAATAAAA
216896 AATAATATAATAAATA-AATATATAATATAAATAATA-AT
1 AATAA-ATAATAAATATAATATATAATATAAATAATATAT
* *
216934 AATATATAATAAATATAA-ATAT-ATATAAATACAAATAAT
1 AATAAATAATAAATATAATATATAATATAAATA-ATAT-AT
*
216973 AATAAATAATATTAATATAATATATAATATAATATAGTATAT
1 AATAAATAATA--AATATAATATATAATATAA-ATAATATAT
217015 AATAAA
1 AATAAA
217021 ATCTATATAA
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
36 9 0.12
37 16 0.22
38 6 0.08
39 12 0.16
41 7 0.10
42 12 0.16
43 8 0.11
44 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (39 bp):
AATAAATAATAAATATAATATATAATATAAATAATATAT
Found at i:217733 original size:15 final size:15
Alignment explanation
Indices: 217713--217769 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
217703 AACCGGGTAT
217713 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
217728 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
*
217745 CGGATACCCGATTAC
1 CGGGTACCCGATTAC
217760 CGGGTACCCG
1 CGGGTACCCG
217770 TAACATCCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.23, C:0.35, G:0.26, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:217758 original size:32 final size:32
Alignment explanation
Indices: 217717--217779 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
217707 GGGTATCGGG
217717 TACCCGATTACCGGGTACCCGCAAAATCCGGA
1 TACCCGATTACCGGGTACCCGCAAAATCCGGA
* *
217749 TACCCGATTACCGGGTACCCGTAACATCCGG
1 TACCCGATTACCGGGTACCCGCAAAATCCGG
217780 GTCGGGACAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.35, G:0.22, T:0.17
Consensus pattern (32 bp):
TACCCGATTACCGGGTACCCGCAAAATCCGGA
Found at i:217781 original size:17 final size:16
Alignment explanation
Indices: 217713--217781 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 16
217703 AACCGGGTAT
**
217713 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
217728 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
* **
217745 CGGATACCCGATTA-C
1 CGGGTACCCGAAAATC
*
217760 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
217777 CGGGT
1 CGGGT
217782 CGGGACACGG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:217839 original size:15 final size:16
Alignment explanation
Indices: 217807--217861 Score: 76
Period size: 15 Copynumber: 3.4 Consensus size: 16
217797 GAAATCGTCG
*
217807 ACCCGGAAGTTCCGGGT
1 ACCCGGAA-ATCCGGGT
217824 ACCCGGAAAT-CGGGT
1 ACCCGGAAATCCGGGT
*
217839 ACCCGAAAATCCGGGT
1 ACCCGGAAATCCGGGT
217855 ACCCGGA
1 ACCCGGA
217862 TTTGCACACC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
15 14 0.41
16 12 0.35
17 8 0.24
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.13
Consensus pattern (16 bp):
ACCCGGAAATCCGGGT
Found at i:229953 original size:20 final size:20
Alignment explanation
Indices: 229928--229975 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
229918 ACAGGCTAAC
229928 TGGGAAACTACCAGCTTCAA
1 TGGGAAACTACCAGCTTCAA
229948 TGGGAAACTACCAGCTTCAA
1 TGGGAAACTACCAGCTTCAA
229968 TGGGAAAC
1 TGGGAAAC
229976 CTTGTCACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (20 bp):
TGGGAAACTACCAGCTTCAA
Found at i:232138 original size:18 final size:16
Alignment explanation
Indices: 232117--232179 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 16
232107 CCCCTCCATT
232117 TCCTCCACCACCTCCGCC
1 TCCTCC-CCACCTCC-CC
*
232135 TCCTCCCC-CTTCCCC
1 TCCTCCCCACCTCCCC
*
232150 TCCTCCGCCACCCTCACC
1 TCCTCC-CCA-CCTCCCC
232168 TCCTCCTCCACC
1 TCCTCC-CCACC
232180 ATTCCCGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.21
16 6 0.16
17 4 0.11
18 20 0.53
ACGTcount: A:0.08, C:0.68, G:0.03, T:0.21
Consensus pattern (16 bp):
TCCTCCCCACCTCCCC
Found at i:232154 original size:33 final size:33
Alignment explanation
Indices: 232091--232173 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 33
232081 GCCCCCACCG
**
232091 CCACCGCCACCTCCTCCCCCTCCATTTCCTCCA
1 CCACCGCCACCTCCTCCCCCTCCACCTCCTCCA
* * *
232124 CCACCTCCGCCTCCTCCCCCTTCC-CCTCCTCCG
1 CCACCGCCACCTCCTCCCCC-TCCACCTCCTCCA
232157 CCACC-CTCACCTCCTCC
1 CCACCGC-CACCTCCTCC
232174 TCCACCATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
32 1 0.02
33 38 0.90
34 3 0.07
ACGTcount: A:0.08, C:0.67, G:0.04, T:0.20
Consensus pattern (33 bp):
CCACCGCCACCTCCTCCCCCTCCACCTCCTCCA
Found at i:233762 original size:28 final size:28
Alignment explanation
Indices: 233714--233777 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
233704 TTTATTATGT
* *
233714 TAAAAATTTATTTAATCTTAAAATAA-AAC
1 TAAAAA-TTATTAAATATTAAAA-AATAAC
*
233743 TAAAAATTATTAAATATTAAAAAATGAC
1 TAAAAATTATTAAATATTAAAAAATAAC
233771 TAAAAAT
1 TAAAAAT
233778 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 23 0.74
29 6 0.19
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (28 bp):
TAAAAATTATTAAATATTAAAAAATAAC
Found at i:233810 original size:18 final size:16
Alignment explanation
Indices: 233785--233827 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
233775 AATAAAATAA
233785 AATTATAAATATATATG
1 AATTATAAATAT-TATG
*
233802 AACTTATAAA-ATTATT
1 AA-TTATAAATATTATG
233818 AATTATAAAT
1 AATTATAAAT
233828 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 4 0.17
18 7 0.30
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
AATTATAAATATTATG
Found at i:235252 original size:41 final size:41
Alignment explanation
Indices: 235195--235305 Score: 186
Period size: 41 Copynumber: 2.7 Consensus size: 41
235185 AAATGTTGAC
* **
235195 ATCATATAACATCAATATATACTGTTTCTAGCAGTGCTAAG
1 ATCATATACCATCAATATATACTGTTTCTAGCAACGCTAAG
235236 ATCATATACCATCAATATATACTGTTTCTAGCAACGCTAAG
1 ATCATATACCATCAATATATACTGTTTCTAGCAACGCTAAG
*
235277 ATCATATACCATCAATGTATACTGTTTCT
1 ATCATATACCATCAATATATACTGTTTCT
235306 CCCATTCAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (41 bp):
ATCATATACCATCAATATATACTGTTTCTAGCAACGCTAAG
Found at i:238037 original size:17 final size:17
Alignment explanation
Indices: 238006--238051 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
237996 AAAAATATAT
*
238006 AATTT-TATTTTTTTTA
1 AATTTATATATTTTTTA
238022 AATTTATATATTTTTTA
1 AATTTATATATTTTTTA
*
238039 AAATTATCATATT
1 AATTTAT-ATATT
238052 GTGACATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 5 0.19
17 16 0.62
18 5 0.19
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTTATATATTTTTTA
Found at i:241046 original size:2 final size:2
Alignment explanation
Indices: 241039--241068 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
241029 GAATGAATTC
241039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
241069 TGAGTAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:246940 original size:20 final size:20
Alignment explanation
Indices: 246905--246945 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
246895 AAATTTTGGC
*
246905 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTCTTTTTTTGT
246925 TTTTTTGCCT-TTTTTTT-T
1 TTTTTTGCCTCTTTTTTTGT
246943 TTT
1 TTT
246946 GCCTTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
20 9 0.45
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (20 bp):
TTTTTTGCCTCTTTTTTTGT
Found at i:246942 original size:15 final size:15
Alignment explanation
Indices: 246918--246961 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 15
246908 TTTGGCTCTT
246918 TTTTTGTTTTTTTGCC
1 TTTTT-TTTTTTTGCC
246934 TTTTTTTTTTTTGCC
1 TTTTTTTTTTTTGCC
246949 TTTTTTGTTTTTT
1 TTTTTT-TTTTTT
246962 TGAAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTGCC
Found at i:251979 original size:2 final size:2
Alignment explanation
Indices: 251966--252005 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
251956 TAAGTGATAA
*
251966 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
252006 GAACACAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:253279 original size:16 final size:16
Alignment explanation
Indices: 253231--253279 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
253221 TAATTTTAGC
*
253231 TTAAGTTATTTTTGAT
1 TTAAATTATTTTTGAT
* *
253247 ATAAATCA-TTTTGAT
1 TTAAATTATTTTTGAT
*
253262 TTAAATTATTTTTTAT
1 TTAAATTATTTTTGAT
253278 TT
1 TT
253280 TGAATTAACT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (16 bp):
TTAAATTATTTTTGAT
Found at i:258816 original size:17 final size:18
Alignment explanation
Indices: 258787--258822 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
258777 AGTGGATTTA
258787 AATATTATAAATTCAAAT
1 AATATTATAAATTCAAAT
*
258805 AATATT-TAAATTTAAAT
1 AATATTATAAATTCAAAT
258822 A
1 A
258823 CGAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATTATAAATTCAAAT
Done.