Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002251.1 Hibiscus syriacus cultivar Beakdansim tig00004577_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: 85879
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2105 original size:39 final size:40
Alignment explanation
Indices: 2048--2128 Score: 155
Period size: 39 Copynumber: 2.0 Consensus size: 40
2038 TCACATTCTA
2048 CCTCATCCTGACACTCATTGATTTCTTCAAGACATATGGG
1 CCTCATCCTGACACTCATTGATTTCTTCAAGACATATGGG
2088 CCTCATCCT-ACACTCATTGATTTCTTCAAGACATATGGG
1 CCTCATCCTGACACTCATTGATTTCTTCAAGACATATGGG
2127 CC
1 CC
2129 GCTCCAAGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 32 0.78
40 9 0.22
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32
Consensus pattern (40 bp):
CCTCATCCTGACACTCATTGATTTCTTCAAGACATATGGG
Found at i:10562 original size:2 final size:2
Alignment explanation
Indices: 10555--10588 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10545 GCATTAGAGA
10555 AT AT AT AT A- 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 AT A
10589 ATGCACATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13880 original size:29 final size:30
Alignment explanation
Indices: 13820--13885 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
13810 CTGGCATAGG
* * *
13820 TTTT-TTTAGCCTATTAGGGTATTCGGTTT
1 TTTTATTTAGCCCATTAGGGTATCCGGATT
*
13849 TTTTATTTAGCCCATTAGGGTA-CCTGATT
1 TTTTATTTAGCCCATTAGGGTATCCGGATT
13878 TTTTATTT
1 TTTTATTT
13886 TGGAGAATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.55
Consensus pattern (30 bp):
TTTTATTTAGCCCATTAGGGTATCCGGATT
Found at i:17891 original size:19 final size:20
Alignment explanation
Indices: 17849--17897 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
17839 GAATTAAAAT
*
17849 ATATTTTTTAAATATAAGTG
1 ATATTTTTTAAATATAAGTA
17869 ATATTTTTTAAAT-TATA-TA
1 ATATTTTTTAAATATA-AGTA
17888 ATATTTTTTA
1 ATATTTTTTA
17898 TCATCATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
ATATTTTTTAAATATAAGTA
Found at i:17895 original size:20 final size:19
Alignment explanation
Indices: 17845--17897 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
17835 ATTGGAATTA
17845 AAATATATTTTTTAAATAT
1 AAATATATTTTTTAAATAT
*
17864 AAGTGATATTTTTTAAAT-T
1 AAAT-ATATTTTTTAAATAT
*
17883 ATATAATATTTTTTA
1 AAAT-ATATTTTTTA
17898 TCATCATCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
AAATATATTTTTTAAATAT
Found at i:26253 original size:20 final size:19
Alignment explanation
Indices: 26214--26265 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
26204 TTTATTTAAT
26214 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
26233 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
26253 ATTTATAAAATAA
1 A-TTAAAAAATAA
26266 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:26342 original size:120 final size:118
Alignment explanation
Indices: 26123--26359 Score: 264
Period size: 120 Copynumber: 2.0 Consensus size: 118
26113 GAAATATATT
* * * * * *
26123 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGT
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAGAACATCCAGGT
* *
26188 ACCTTAAGACAGCTCTTTTATTTAATATT-AAAAAATAAATAAATAATTAAAAC
66 ACCTTAAGACAGCCCTTTTATTCAATATTAAAAAAATAAATAAAT-ATTAAAAC
*
26241 AATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAAAAAATGAACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAAAAAA-GAACATCCA
* *** * * *
26306 GTTGTTTTAAGACTA-CCCTTTTCTTCGATA-TGAAAAAATAAATAAATATTAAAA
63 GGTACCTTAAGAC-AGCCCTTTTATTCAATATTAAAAAAATAAATAAATATTAAAA
26360 TATGATAAAA
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
118 10 0.10
119 6 0.06
120 41 0.41
121 41 0.41
122 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (118 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAGAACATCCAGGT
ACCTTAAGACAGCCCTTTTATTCAATATTAAAAAAATAAATAAATATTAAAAC
Found at i:26378 original size:120 final size:119
Alignment explanation
Indices: 26134--26359 Score: 267
Period size: 121 Copynumber: 1.9 Consensus size: 119
26124 ATTTATATAT
* * * * *
26134 ATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTACCTTAAGACA
1 ATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAGAACATCCAGGTACCTTAAGACA
* * * *
26199 GCTCTTTTATTTAATATTAAAAAATAAATAAATAATTAAAACAATTAATATATA
66 GCCCTTTTATTCAATATGAAAAAATAAATAAATAATTAAAACAATTAATAAATA
* * ***
26253 ATTTATAAAATAAGATATTTATTTATTTAAAAATATCAAAAAATGAACATCCAGTTGTTTTAAGA
1 ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAAAAAA-GAACATCCAGGTACCTTAAGA
* *
26318 CTA-CCCTTTTCTTCGATATGAAAAAATAAATAAAT-ATTAAAA
64 C-AGCCCTTTTATTCAATATGAAAAAATAAATAAATAATTAAAA
26360 TATGATAAAA
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
119 6 0.07
120 40 0.45
121 42 0.47
122 1 0.01
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.37
Consensus pattern (119 bp):
ATTTATAAATAAAATATTTATTTATTTAAAAATATCAAAAAAGAACATCCAGGTACCTTAAGACA
GCCCTTTTATTCAATATGAAAAAATAAATAAATAATTAAAACAATTAATAAATA
Found at i:26453 original size:22 final size:23
Alignment explanation
Indices: 26428--26491 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
26418 TTATATGACT
*
26428 ATATAATAAA-AATAATATTTAA
1 ATATAATAAACAATAATATTAAA
*
26450 ATAT-ATAAACAAGTAAAATTAAA
1 ATATAATAAACAA-TAATATTAAA
*
26473 ACATAAATAAACAATAATA
1 ATAT-AATAAACAATAATA
26492 AAAATACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.15
22 6 0.18
23 11 0.32
24 4 0.12
25 8 0.24
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (23 bp):
ATATAATAAACAATAATATTAAA
Found at i:27873 original size:2 final size:2
Alignment explanation
Indices: 27868--27892 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27858 TTTTTATTAT
27868 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
27893 TTAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28443 original size:113 final size:113
Alignment explanation
Indices: 28160--28941 Score: 1026
Period size: 113 Copynumber: 7.0 Consensus size: 113
28150 TAGAGTCATT
* * * * *
28160 CAAAAGGTTGAATAAGCTCTTCTCATTATGAA---CTTCTT-CTTCTTCAGACGAATTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
**** * * * *
28221 TTATGAACTTTCTCTGGAAAAGCTGATTCATC-AAGTGATGGATTT-AG
66 TTATGAACTCGAACTGGAAATGTTGATCCATCGAA-TGATGAATTTAAG
* * * *
28268 CAAAAGGTTGAACAAATTATTCTCATTATGAA-TT-TTCTT-CTTTTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
* * * * *
28330 TTATTATGAACTCTATCTGGCAATGTTGATCCATCAAATGATGAATTTAAG
63 TCATTATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAG
28381 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
28446 TTATGAACTCGAACTGGTAATGCTGATCCATTGAATCATGAATTCAAG
66 TTATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAG
** *
28494 CAAAAAGTTGAGTAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
28559 TTATGAACTCGAACTGGTAATGCTGATCCATTGAATCATGAATTCAAG
66 TTATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAG
* **
28607 CAAAAGGTTGAGTAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* *
28672 TTATGAACTCGAACTGGAAATGTTGATCCACCGAATGATGGATTTAAG
66 TTATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAG
*
28720 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTT-TTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
28784 TTATGAACTCGAACTGGAAATGTCGATCCACCGAATGATGGATTTAAG
66 TTATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAG
*
28832 CAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
28897 TTATGAACTCGAACTGGAAATGTCGATCCACCGACTGATGAATTT
66 TTATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTT
28942 TAATCTTTGC
Statistics
Matches: 614, Mismatches: 49, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
108 28 0.05
109 14 0.02
112 154 0.25
113 401 0.65
114 2 0.00
115 5 0.01
116 10 0.02
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCGAACTGGAAATGTTGATCCATCGAATGATGAATTTAAG
Found at i:29828 original size:114 final size:114
Alignment explanation
Indices: 29628--29840 Score: 327
Period size: 114 Copynumber: 1.9 Consensus size: 114
29618 GATCATGCAG
* * * * ** *
29628 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACTGAACCAGATCAGATGACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
29693 ACATTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
*
29742 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
29807 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATT
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATT
29841 AATGTGGTAC
Statistics
Matches: 88, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 88 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:31040 original size:19 final size:17
Alignment explanation
Indices: 31016--31064 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
31006 AAAATAAAAG
31016 AATAAATTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
31035 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
31051 AATAAATTGAATTT
1 AATAAATTGAATTT
31065 AAAGAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 3 0.11
19 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:31444 original size:10 final size:10
Alignment explanation
Indices: 31429--31458 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
31419 TTTTTCTTCT
31429 TTTCTTTTTC
1 TTTCTTTTTC
31439 TTTCTTTTTC
1 TTTCTTTTTC
31449 TTTCTTTTTC
1 TTTCTTTTTC
31459 CCTTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:31455 original size:34 final size:32
Alignment explanation
Indices: 31417--31492 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 32
31407 CTTGATCCCC
* * *
31417 TCTTTTTCTTCTTTTCTTTTTCTTTCTTTTTCTT
1 TCTTTTTCTTATTTT-TTTTCCTTT-TTGTTCTT
31451 TCTTTTTCCCTTATTTTTTTTCCTTTTTGTTCTT
1 TCTTTTT--CTTATTTTTTTTCCTTTTTGTTCTT
*
31485 TTTTTTTC
1 TCTTTTTC
31493 AAGCATAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
32 1 0.03
34 20 0.56
35 8 0.22
36 7 0.19
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.78
Consensus pattern (32 bp):
TCTTTTTCTTATTTTTTTTCCTTTTTGTTCTT
Found at i:38827 original size:15 final size:15
Alignment explanation
Indices: 38804--38835 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38794 TGAAATGAAT
38804 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
38819 AATGCATGTATGCAA
1 AATGAATGTATGCAA
38834 AA
1 AA
38836 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:42116 original size:13 final size:15
Alignment explanation
Indices: 42098--42134 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
42088 CTGACAGAAA
42098 AAATAAAATA-ATG-
1 AAATAAAATACATGT
*
42111 AAATAAAATACTTGT
1 AAATAAAATACATGT
42126 AAATAAAAT
1 AAATAAAAT
42135 GAAATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.48
14 2 0.10
15 9 0.43
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (15 bp):
AAATAAAATACATGT
Found at i:42801 original size:20 final size:19
Alignment explanation
Indices: 42762--42813 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
42752 TTTCTTTAAT
42762 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
42781 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
42801 ATTTATAAAATAA
1 A-TTAAAAAATAA
42814 GTTATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:42820 original size:120 final size:118
Alignment explanation
Indices: 42671--42907 Score: 296
Period size: 121 Copynumber: 2.0 Consensus size: 118
42661 GAAATATATT
* * * * *
42671 AATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAA-GGACTTCTAGG
1 AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGAACATCCAGG
* * *
42735 TACCTTAAGACAGCTCTTTTCTTTAATATTAAAAAATAAATAAATAATTAAAAC
66 TACCTTAAGACAGCCCTTTTCTTCAATATGAAAAAATAAATAAAT-ATTAAAAC
**
42789 AATTAATATATAATTTATAAAATAAGTTATTTATTTATTTAAAAATATCAGAAAATGAACATCCA
1 AATTAATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGAACATCCA
* *** * *
42854 GTTGTTTTAAGACTGCCCTTTTCTTCGATATGAAAAAATAAATAAATATTAAAA
64 GGTACCTTAAGACAGCCCTTTTCTTCAATATGAAAAAATAAATAAATATTAAAA
42908 TATGATAAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
118 10 0.10
119 6 0.06
120 40 0.40
121 44 0.44
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.38
Consensus pattern (118 bp):
AATTAATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGAACATCCAGG
TACCTTAAGACAGCCCTTTTCTTCAATATGAAAAAATAAATAAATATTAAAAC
Found at i:42995 original size:22 final size:23
Alignment explanation
Indices: 42970--43033 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
42960 TTATATGACT
*
42970 ATATAATAAA-AATAATATTTAA
1 ATATAATAAACAATAATATTAAA
*
42992 ATAT-ATAAACAAGTAAAATTAAA
1 ATATAATAAACAA-TAATATTAAA
*
43015 ACATAAATAAACAATAATA
1 ATAT-AATAAACAATAATA
43034 AAAATACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 5 0.15
22 6 0.18
23 11 0.32
24 4 0.12
25 8 0.24
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (23 bp):
ATATAATAAACAATAATATTAAA
Found at i:44427 original size:2 final size:2
Alignment explanation
Indices: 44420--44468 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
44410 TTATTATTAT
*
44420 TA TA TA TA TA TA TA TA TA TT TA -A TA -A TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44459 TA TA TA TA TA
1 TA TA TA TA TA
44469 ATAATAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:44448 original size:3 final size:3
Alignment explanation
Indices: 44440--44493 Score: 65
Period size: 3 Copynumber: 17.0 Consensus size: 3
44430 TATATATATT
44440 TAA TAA TAA T-A TATA TATA TATA TATA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TA-A TA-A TA-A TAA TAA TAA TAA TAA TAA TAA
44488 TAA TAA
1 TAA TAA
44494 ATAAAAATGG
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 32 0.65
4 15 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:44453 original size:21 final size:21
Alignment explanation
Indices: 44427--44492 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
44417 TATTATATAT
44427 ATATATATATATTTAATAATA
1 ATATATATATATTTAATAATA
44448 ATATATATATATATATATATAATA
1 ATATATATATAT-T-TA-ATAATA
*
44472 ATA-ATA-ATA-ATAATAATA
1 ATATATATATATTTAATAATA
44490 ATA
1 ATA
44493 AATAAAAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 9 0.22
19 2 0.05
21 12 0.29
22 4 0.10
23 5 0.12
24 9 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATATATATATTTAATAATA
Found at i:44459 original size:27 final size:27
Alignment explanation
Indices: 44421--44477 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
44411 TATTATTATT
*
44421 ATATATATATATATATATTTAATAATA
1 ATATATATATATATATATATAATAATA
44448 ATATATATATATATATATATAATAATA
1 ATATATATATATATATATATAATAATA
44475 ATA
1 ATA
44478 ATAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATATATATATATATATATAATAATA
Found at i:44462 original size:33 final size:33
Alignment explanation
Indices: 44420--44483 Score: 105
Period size: 31 Copynumber: 2.0 Consensus size: 33
44410 TTATTATTAT
*
44420 TATATATATATATATAT-AT-TTAATAATAATA
1 TATATATATATATATATAATAATAATAATAATA
44451 TATATATATATATATATAATAATAATAATAATA
1 TATATATATATATATATAATAATAATAATAATA
44484 ATAATAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 17 0.57
32 2 0.07
33 11 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
TATATATATATATATATAATAATAATAATAATA
Found at i:45023 original size:16 final size:17
Alignment explanation
Indices: 44997--45028 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
44987 GCTCCGATTT
44997 TTTTAATTAATTATATA
1 TTTTAATTAATTATATA
45014 TTTT-ATTAATTATAT
1 TTTTAATTAATTATAT
45029 TCATCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAATTAATTATATA
Found at i:45431 original size:2 final size:2
Alignment explanation
Indices: 45424--45462 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
45414 CTAGAAGAAA
45424 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
45463 ATTCAACCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55474 original size:6 final size:6
Alignment explanation
Indices: 55463--55491 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
55453 TTATTGGTGC
55463 TGCCAG TGCCAG TGCCAG TGCCAG TGCCA
1 TGCCAG TGCCAG TGCCAG TGCCAG TGCCA
55492 CCGGTTATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.34, G:0.31, T:0.17
Consensus pattern (6 bp):
TGCCAG
Found at i:59329 original size:30 final size:30
Alignment explanation
Indices: 59298--59378 Score: 146
Period size: 30 Copynumber: 2.7 Consensus size: 30
59288 ACTAGTAAAT
*
59298 TTTTAGTTTT-TATCAATTATAACATTGAA
1 TTTTAATTTTATATCAATTATAACATTGAA
59327 TTTTAATTTTATATCAATTATAACATTGAA
1 TTTTAATTTTATATCAATTATAACATTGAA
59357 TTTTAATTTTATATCAATTATA
1 TTTTAATTTTATATCAATTATA
59379 TACTATATCG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 9 0.18
30 41 0.82
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (30 bp):
TTTTAATTTTATATCAATTATAACATTGAA
Found at i:60209 original size:16 final size:16
Alignment explanation
Indices: 60188--60218 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
60178 TTACACGACA
60188 TGTTATCAACTTGACC
1 TGTTATCAACTTGACC
*
60204 TGTTATGAACTTGAC
1 TGTTATCAACTTGAC
60219 TTGTAATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (16 bp):
TGTTATCAACTTGACC
Found at i:60476 original size:14 final size:14
Alignment explanation
Indices: 60435--60478 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
60425 TCTATATTAT
*
60435 TTATAATCATTATA
1 TTATAATCATTAAA
* *
60449 TTACAAT-TTTAAA
1 TTATAATCATTAAA
60462 TTATAATCATTAAA
1 TTATAATCATTAAA
60476 TTA
1 TTA
60479 ATTTTATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (14 bp):
TTATAATCATTAAA
Found at i:64373 original size:181 final size:181
Alignment explanation
Indices: 64069--64425 Score: 696
Period size: 181 Copynumber: 2.0 Consensus size: 181
64059 CCTGCAAAAC
*
64069 AACAATCATAACCCATCAAGCAAAAAAAAAAACTAATTTTTCATGAAACAAAGAAGAAAAACAAC
1 AACAATCATAACCCATCAAGCAAAAAAAAAAACAAATTTTTCATGAAACAAAGAAGAAAAACAAC
*
64134 GAAAAAAAACCATTCAATCTCAAACAAGGAAATTCGAAGATTAAAAAGGGAACAGAAGAGGAATC
66 GAAAAAAAACCATTCAATCTCAAACAAGGAAATTCGAAGATTAAAAAGGGAACAGAAGAAGAATC
64199 CTATGGAAGTGAGTGTTGGGGAAATCAATGGAGAGATGAGAAAAGAAGAAA
131 CTATGGAAGTGAGTGTTGGGGAAATCAATGGAGAGATGAGAAAAGAAGAAA
64250 AACAATCATAACCCATCAAGCAAAAAAAAAAACAAATTTTTCATGAAACAAAGAAGAAAAACAAC
1 AACAATCATAACCCATCAAGCAAAAAAAAAAACAAATTTTTCATGAAACAAAGAAGAAAAACAAC
64315 GAAAAAAAACCATTCAATCTCAAACAAGGAAATTCGAAGATTAAAAAGGGAACAGAAGAAGAATC
66 GAAAAAAAACCATTCAATCTCAAACAAGGAAATTCGAAGATTAAAAAGGGAACAGAAGAAGAATC
64380 CTATGGAAGTGAGTGTTGGGGAAATCAATGGAGAGATGAGAAAAGA
131 CTATGGAAGTGAGTGTTGGGGAAATCAATGGAGAGATGAGAAAAGA
64426 CTTTGTCCAT
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 174 1.00
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.15
Consensus pattern (181 bp):
AACAATCATAACCCATCAAGCAAAAAAAAAAACAAATTTTTCATGAAACAAAGAAGAAAAACAAC
GAAAAAAAACCATTCAATCTCAAACAAGGAAATTCGAAGATTAAAAAGGGAACAGAAGAAGAATC
CTATGGAAGTGAGTGTTGGGGAAATCAATGGAGAGATGAGAAAAGAAGAAA
Found at i:85692 original size:18 final size:19
Alignment explanation
Indices: 85649--85684 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
85639 TTAAACGACT
85649 ATTTTATATTTTTATATAA
1 ATTTTATATTTTTATATAA
*
85668 AATTTATA-TTTTATATA
1 ATTTTATATTTTTATATA
85685 GCTTTTATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATTTTTATATAA
Done.