Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006256.1 Hibiscus syriacus cultivar Beakdansim tig00014931_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: 57878
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3239 original size:22 final size:22
Alignment explanation
Indices: 3203--3247 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3193 TAAACCCCAA
3203 AAACTACCCCAAAACAC-AAAAG
1 AAACTACCCCAAAAC-CTAAAAG
* *
3225 AAACTACTCCTAAACCTAAAAG
1 AAACTACCCCAAAACCTAAAAG
3247 A
1 A
3248 GACACAAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.56, C:0.29, G:0.04, T:0.11
Consensus pattern (22 bp):
AAACTACCCCAAAACCTAAAAG
Found at i:4192 original size:135 final size:134
Alignment explanation
Indices: 3956--4310 Score: 446
Period size: 135 Copynumber: 2.6 Consensus size: 134
3946 TCAGAGTAGG
* *
3956 TTGAACCGAACTTGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCT-AAGAGAAAAAATATCT
1 TTGAATCGAACTTGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAA-AGAAAAGA-ATCT
* * *
4020 GCTCCACTACTCTTTGGGGGAGATCAAACTCGTAAAAAAC-TTCAATCCATTTCATTACTCTTCA
64 GCTCCACTACTCTTTAGGGGAGATCAAACTCG-AAAAAACTTTCAATCCACTTCACTACTCTTCA
4084 GGGAAGA
128 GGGAAGA
* * * * * *
4091 TTGAATCGAATTTGATTTTCTTTACTGATCTTCAAGAATACCAAATCTGAAAGAAGAAGAATCTA
1 TTGAATCGAACTTGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAAGAA-AAGAATCTG
* * ** * *
4156 CTCCACTACTTTTTAGGGGAGATCAGACTCGAAAAAACTTTTGATCCACTTCACTGCTCTTCATG
65 CTCCACTACTCTTTAGGGGAGATCAAACTCGAAAAAACTTTCAATCCACTTCACTACTCTTCAGG
4221 GAAGA
130 GAAGA
* *
4226 TTGAATCGAACTTGATTTGCTTCGA-TGCTCTTCAGGAAGACCAAATCTGAAAGAAAAAGAATAT
1 TTGAATCGAACTTGATTTGCTTC-ACTGCTCTTCAAGAAGACCAAATCTGAAAG-AAAAGAATCT
**
4290 GCTCTGCTACTCTTTAGGGGA
64 GCTCCACTACTCTTTAGGGGA
4311 AACCAAATCT
Statistics
Matches: 187, Mismatches: 28, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
134 7 0.04
135 172 0.92
136 8 0.04
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (134 bp):
TTGAATCGAACTTGATTTGCTTCACTGCTCTTCAAGAAGACCAAATCTGAAAGAAAAGAATCTGC
TCCACTACTCTTTAGGGGAGATCAAACTCGAAAAAACTTTCAATCCACTTCACTACTCTTCAGGG
AAGA
Found at i:5694 original size:21 final size:22
Alignment explanation
Indices: 5669--5720 Score: 81
Period size: 21 Copynumber: 2.5 Consensus size: 22
5659 TTTAACCCCC
*
5669 CTTTATTTTTTT-TTTCTTTTT
1 CTTTATTTTTTTCTTTATTTTT
5690 CTTTATTTTTTTCTTTATTTTT
1 CTTTATTTTTTTCTTTATTTTT
5712 CTTT-TTTTT
1 CTTTATTTTT
5721 CATATGCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 17 0.59
22 12 0.41
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.85
Consensus pattern (22 bp):
CTTTATTTTTTTCTTTATTTTT
Found at i:5700 original size:12 final size:12
Alignment explanation
Indices: 5669--5711 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
5659 TTTAACCCCC
5669 CTTTA-TTTTTT
1 CTTTATTTTTTT
*
5680 -TTT-TCTTTTT
1 CTTTATTTTTTT
5690 CTTTATTTTTTT
1 CTTTATTTTTTT
5702 CTTTATTTTT
1 CTTTATTTTT
5712 CTTTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 8 0.30
11 3 0.11
12 16 0.59
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (12 bp):
CTTTATTTTTTT
Found at i:5700 original size:18 final size:18
Alignment explanation
Indices: 5677--5719 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5667 CCCTTTATTT
5677 TTTTTTTCTTT-TTCTTTA
1 TTTTTTTCTTTATT-TTTA
*
5695 TTTTTTTCTTTATTTTTC
1 TTTTTTTCTTTATTTTTA
5713 TTTTTTT
1 TTTTTTT
5720 TCATATGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTTCTTTATTTTTA
Found at i:22472 original size:3 final size:3
Alignment explanation
Indices: 22464--22515 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
22454 GTGTAAGTTA
** * *
22464 AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
22509 AAT AAT A
1 AAT AAT A
22516 TATATAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:22976 original size:28 final size:29
Alignment explanation
Indices: 22935--23004 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 29
22925 AGGAGTTATG
* *
22935 GTTTCAAGAGAAACCA-AATTAAAGATTT
1 GTTTCAAGAAAAACCAGAATCAAAGATTT
* *
22963 GTTTCAA-AAAAAACAGACTCAAAGATTT
1 GTTTCAAGAAAAACCAGAATCAAAGATTT
22991 GTTTCAAGAAAAAC
1 GTTTCAAGAAAAAC
23005 AAGCTCAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 6 0.17
28 24 0.69
29 5 0.14
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (29 bp):
GTTTCAAGAAAAACCAGAATCAAAGATTT
Found at i:23025 original size:31 final size:28
Alignment explanation
Indices: 22955--23030 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 28
22945 AAACCAAATT
22955 AAAGATTTGTTTCAAAAAAAACAGACTC
1 AAAGATTTGTTTCAAAAAAAACAGACTC
*
22983 AAAGATTTGTTTCAAGAAAAACA-AGCTC
1 AAAGATTTGTTTCAAAAAAAACAGA-CTC
23011 AAAGATAATGTGTTTCAAAA
1 AAAGAT--T-TGTTTCAAAA
23031 GCAACTGTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 1 0.02
28 31 0.74
30 1 0.02
31 9 0.21
ACGTcount: A:0.49, C:0.12, G:0.13, T:0.26
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAAAAACAGACTC
Found at i:23762 original size:30 final size:30
Alignment explanation
Indices: 23696--23762 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
23686 ATTTGTTTTT
* * *
23696 AAAGAAATAAACTCAAAGATGATTTTGTTA
1 AAAGAAACAAACTCAAAGATGATTTTCTCA
** **
23726 GTAGAAACAAACTCAAAGATTTTTTTCTCA
1 AAAGAAACAAACTCAAAGATGATTTTCTCA
23756 AAAGAAA
1 AAAGAAA
23763 TTGTCTCAAG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.28
Consensus pattern (30 bp):
AAAGAAACAAACTCAAAGATGATTTTCTCA
Found at i:23836 original size:96 final size:91
Alignment explanation
Indices: 23621--23933 Score: 282
Period size: 96 Copynumber: 3.4 Consensus size: 91
23611 GTGAGACGAA
* * * * *
23621 TTTT-TTTCAAAGGAGACAATCTCAAAGGTTGGTTTTTCATTAGAAACTGTCTCAAGAGAGACAC
1 TTTTGTTTCAAAAGAAACAA-CTCAAAGATT-TTTTTTCA--AGAAATTGTCTCAAGAGAGACA-
*
23685 AA-TTTGTTTTTAAAGAAATAAACTCAAAGAT
61 AACTTTG-TTTCAAAGAAATAAACTCAAAGAT
**
23716 GATTTTG-TT-AGTAGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGAC
1 --TTTTGTTTCAAAAGAAAC-AACTCAAAGATTTTTTT-TC--AAGAAATTGTCTCAAGAGAGAC
* *
23779 AAACTTTTGTTTCCAAAGAAACATACTCAAAGAT
60 AAAC-TTTGTTT-CAAAGAAATAAACTCAAAGAT
* *
23813 TTTTGTTTCAAAAGAAACTACTCAAAGA--TTTTTTCACGAAATTGTCTCAAGAGAGACAAAACT
1 TTTTGTTTCAAAAGAAACAACTCAAAGATTTTTTTTCAAGAAATTGTCTCAAGAGAGAC-AAACT
* *
23876 TTGTTTCAAAGACATAGACTCAAA-AT
65 TTGTTTCAAAGAAATAAACTCAAAGAT
* * *
23902 TTTT-TCTCACAAGAAACAACTCAAAAATTTTT
1 TTTTGTTTCAAAAGAAACAACTCAAAGATTTTT
23934 GTATTCAAAA
Statistics
Matches: 182, Mismatches: 21, Indels: 33
0.77 0.09 0.14
Matches are distributed among these distances:
88 19 0.10
89 6 0.03
90 18 0.10
91 28 0.15
92 4 0.02
93 2 0.01
94 5 0.03
95 11 0.06
96 51 0.28
97 37 0.20
98 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (91 bp):
TTTTGTTTCAAAAGAAACAACTCAAAGATTTTTTTTCAAGAAATTGTCTCAAGAGAGACAAACTT
TGTTTCAAAGAAATAAACTCAAAGAT
Found at i:23846 original size:30 final size:30
Alignment explanation
Indices: 23783--23845 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
23773 AGAGACAAAC
*
23783 TTTTGTTTCCAAAGAAACATACTCAAAGAT
1 TTTTGTTTCAAAAGAAACATACTCAAAGAT
23813 TTTTGTTTCAAAAGAAAC-TACTCAAAGAT
1 TTTTGTTTCAAAAGAAACATACTCAAAGAT
23842 TTTT
1 TTTT
23846 TCACGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACATACTCAAAGAT
Found at i:23923 original size:27 final size:29
Alignment explanation
Indices: 23893--23965 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
23883 AAAGACATAG
*
23893 ACTCAAAATTTTTT-CTCACAAGAAACA-
1 ACTCAAAATTTTTTACTCAAAAGAAACAT
* *
23920 ACTCAAAAATTTTTGTATTCAAAAGGAACAT
1 ACTC-AAAATTTTT-TACTCAAAAGAAACAT
23951 ACTCAAAGATTTTTT
1 ACTCAAA-ATTTTTT
23966 TACGAAATTG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 4 0.11
28 9 0.24
29 1 0.03
30 14 0.37
31 10 0.26
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.34
Consensus pattern (29 bp):
ACTCAAAATTTTTTACTCAAAAGAAACAT
Found at i:24027 original size:26 final size:25
Alignment explanation
Indices: 23988--24094 Score: 70
Period size: 28 Copynumber: 3.8 Consensus size: 25
23978 TCAAGAGAGA
* *
23988 CAAAACTTTGTTTCAAAAGACATAGACT
1 CAAAA-TTT-TTTCAAAAGAAACA-ACT
*
24016 CAAAATTTTTTCACAAGAAACAACT
1 CAAAATTTTTTCAAAAGAAACAACT
*
24041 CAAAAATTTTTATATTCAAAAGGAACATACT
1 C-AAAA--TTT-T-TTCAAAAGAAACA-ACT
*
24072 CAAAGATTTGTTTCAAGAGAAAC
1 CAAA-ATTT-TTTCAAAAGAAAC
24095 CGTCTCAAGA
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
25 4 0.06
26 15 0.23
27 3 0.05
28 18 0.28
29 5 0.08
30 14 0.22
31 5 0.08
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (25 bp):
CAAAATTTTTTCAAAAGAAACAACT
Found at i:24061 original size:118 final size:119
Alignment explanation
Indices: 23794--24113 Score: 495
Period size: 118 Copynumber: 2.7 Consensus size: 119
23784 TTTGTTTCCA
* * *
23794 AAGAAACATACTCAAAGATTTTTGT-TTCAAAAGAAAC-TACTCAAAGATTTTTTCACGAAATTG
1 AAGAAACA-ACTCAAAAATTTTTGTATTCAAAAGGAACATACTCAAAGATTTTTTAACGAAATTG
23857 TCTCAAGAGAGACAAAACTTTGTTTCAAAGACATAGACTCAAAATTTTTTCTCAC
65 TCTCAAGAGAGACAAAACTTTGTTTCAAAGACATAGACTCAAAATTTTTTCTCAC
*
23912 AAGAAACAACTCAAAAATTTTTGTATTCAAAAGGAACATACTCAAAGATTTTTTTACGAAATTGT
1 AAGAAACAACTCAAAAATTTTTGTATTCAAAAGGAACATACTCAAAGATTTTTTAACGAAATTGT
23977 CTCAAGAGAGACAAAACTTTGTTTCAAAAGACATAGACTCAAAA-TTTTT-TCAC
66 CTCAAGAGAGACAAAACTTTGTTTC-AAAGACATAGACTCAAAATTTTTTCTCAC
* * *
24030 AAGAAACAACTCAAAAATTTTTATATTCAAAAGGAACATACTCAAAGATTTGTTTCAAGAGAAAC
1 AAGAAACAACTCAAAAATTTTTGTATTCAAAAGGAACATACTCAAAGATTT-TTT-AA-CGAAAT
*
24095 CGTCTCAAGAGAGACAAAA
63 TGTCTCAAGAGAGACAAAA
24114 ATCGTTTTAA
Statistics
Matches: 188, Mismatches: 8, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
117 15 0.08
118 73 0.39
119 59 0.31
120 19 0.10
121 22 0.12
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.29
Consensus pattern (119 bp):
AAGAAACAACTCAAAAATTTTTGTATTCAAAAGGAACATACTCAAAGATTTTTTAACGAAATTGT
CTCAAGAGAGACAAAACTTTGTTTCAAAGACATAGACTCAAAATTTTTTCTCAC
Found at i:24409 original size:21 final size:21
Alignment explanation
Indices: 24348--24409 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
24338 GGTGGAAAAA
*
24348 TGTCTCAAGCGAGACATAATT
1 TGTCTCAAGCGAGACAAAATT
* * * *
24369 TGTTTTAA---AGA-GAAAGT
1 TGTCTCAAGCGAGACAAAATT
24386 TGTCTCAAGCGAGACAAAATT
1 TGTCTCAAGCGAGACAAAATT
24407 TGT
1 TGT
24410 TTTTAAGAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 8
0.62 0.20 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (21 bp):
TGTCTCAAGCGAGACAAAATT
Found at i:24426 original size:36 final size:36
Alignment explanation
Indices: 24342--24450 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 36
24332 AAAATTGGTG
* *
24342 GAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
*
24378 GAGAAAGTTGTCTCAAGCGAGACAAAATTTGTTTTTAA
1 GA-AAA-ATGTCTCAAGCGAGACAAAATTTGTTTTTAA
* * * * *
24416 GAAAACTGTCTCTAGTGAGACGACACTTTGTTTTT
1 GAAAAATGTCTCAAGCGAGAC-AAAATTTGTTTTT
24451 TTTTTTTTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
36 15 0.24
37 17 0.27
38 30 0.48
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
Found at i:31824 original size:3 final size:3
Alignment explanation
Indices: 31816--31867 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
31806 GTGTAAGTTA
** * *
31816 AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAC GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
31861 AAT AAT A
1 AAT AAT A
31868 TATATAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:32374 original size:13 final size:13
Alignment explanation
Indices: 32340--32374 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
32330 AATTGGAGGA
*
32340 GAAGAAGAAAGTT
1 GAAGAAGAGAGTT
32353 GAAGAAGAGAGTT
1 GAAGAAGAGAGTT
32366 GAAGAAGAG
1 GAAGAAGAG
32375 TTTGAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.37, T:0.11
Consensus pattern (13 bp):
GAAGAAGAGAGTT
Found at i:42733 original size:21 final size:21
Alignment explanation
Indices: 42678--42726 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
42668 AAGGATATGG
42678 AAGACAAAGTCAAGATTAATC
1 AAGACAAAGTCAAGATTAATC
42699 AAGACAAAGTCAAGATTAATC
1 AAGACAAAGTCAAGATTAATC
42720 AAGACAA
1 AAGACAA
42727 TCTCAAGGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.16
Consensus pattern (21 bp):
AAGACAAAGTCAAGATTAATC
Found at i:44004 original size:38 final size:38
Alignment explanation
Indices: 43941--44032 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
43931 CTTTCCAAAA
* * * * *
43941 AAAGTCAACTTTTGGCCAAAATCAACGCTGGTCAATGTC
1 AAAGTCAA-ATTTGGTCAAAATCAACACTAGTCAATATC
* *
43980 AAAGTCAAATTTGGTCAAAGTCAACACTAGTTAATATC
1 AAAGTCAAATTTGGTCAAAATCAACACTAGTCAATATC
44018 AAAGTCAAATTTGGT
1 AAAGTCAAATTTGGT
44033 AGTCAACAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 38 0.83
39 8 0.17
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.28
Consensus pattern (38 bp):
AAAGTCAAATTTGGTCAAAATCAACACTAGTCAATATC
Found at i:44055 original size:32 final size:36
Alignment explanation
Indices: 43974--44056 Score: 102
Period size: 38 Copynumber: 2.4 Consensus size: 36
43964 AACGCTGGTC
43974 AATGTCAAAGTCAAATTTGGTCAAAGTCAACACTAGTT
1 AATGTCAAAGTCAAATTTGGT--AAGTCAACACTAGTT
*
44012 AATATCAAAGTCAAATTTGGT-AGTC-A-AC-AGTT
1 AATGTCAAAGTCAAATTTGGTAAGTCAACACTAGTT
*
44044 CATGTCAAAGTCA
1 AATGTCAAAGTCA
44057 TTGGTTCGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 15 0.36
33 2 0.05
34 1 0.02
35 4 0.10
38 20 0.48
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (36 bp):
AATGTCAAAGTCAAATTTGGTAAGTCAACACTAGTT
Found at i:44114 original size:20 final size:20
Alignment explanation
Indices: 44089--44171 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
44079 TTTGGATTGG
44089 TTCAAGTTGACTCAGACTGA
1 TTCAAGTTGACTCAGACTGA
*
44109 TTCAAGTTGACTC-GATTCGA
1 TTCAAGTTGACTCAGACT-GA
* * *
44129 TAT-GAGTTGACTCAGTCTGG
1 T-TCAAGTTGACTCAGACTGA
* *
44149 TTCAAGTTGACACAGACCGA
1 TTCAAGTTGACTCAGACTGA
44169 TTC
1 TTC
44172 TAGAAGGTTT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.08
20 42 0.86
21 3 0.06
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (20 bp):
TTCAAGTTGACTCAGACTGA
Found at i:49619 original size:748 final size:749
Alignment explanation
Indices: 47920--50165 Score: 4403
Period size: 748 Copynumber: 3.0 Consensus size: 749
47910 ATGAAATTTA
47920 TAATTTATCTCATTTGATAAGGTATGGAAATACGTCGATTGGGTAAAATTATGAAATTACCCTTA
1 TAATTTATCTCATTTGATAAGGTATGGAAATACGTCGATTGGGTAAAATTATGAAATTACCCTTA
*
47985 TATTGGAAAATGACAAGAATTGTCCCTGGAAATTGGTTAATAACTCTGAAAAGACATATTGATTC
66 TATTGGAAAATGACAAGAATTGTCCCTGGAAATTGGTTAATAACTCTGAAAAGACATATTGATCC
48050 AATATAATTACAAATGTGCATAAGAAATGATAGTTTTGCTTAAAAAATTTGGATAACTGGTTTTT
131 AATATAATTACAAATGTGCATAAGAAATGATAGTTTTGCTTAAAAAATTTGGATAACTGGTTTTT
48115 AACCCCAAAAGGGTTTGTATAAGATGCTAGAAGTATGTTAAGAGAATCATTTCAAGATCAGAGAA
196 AACCCCAAAAGGGTTTGTATAAGATGCTAGAAGTATGTTAAGAGAATCATTTCAAGATCAGAGAA
48180 TGTTCAAGAAAGAAATTAATCATAGGATCTCTAAATTATATTATTTTTGTTAAGAGTTAATACCG
261 TGTTCAAGAAAGAAATTAATCATAGGATCTCTAAATTATATTATTTTTGTTAAGAGTTAATACCG
48245 AAATTATCTGGTTAAGAAATTACGAAAATGCCCTTGAGAGGTAAAATAGTCCGAGTTGACCCTGA
326 AAATTATCTGGTTAAGAAATTACGAAAATGCCCTTGAGAGGTAAAATAGTCCGAGTTGACCCTGA
48310 ATGAG-AAGTACTTTGAGGATTCATACTTAACTTGATTAAGTACGGATTTAATTGTTAAGATCCT
391 ATGAGAAAGTACTTTGAGGATTCATACTTAACTTGATTAAGTACGGATTTAATTGTTAAGATCCT
48374 GACTTTGTGTAGAAAAATTCATGATATTCCGTTTGTAAAATCTGAGAAGGCACTTGACCCAAAAA
456 GACTTTGTGTAGAAAAATTCATGATATTCCGTTTGTAAAATCTGAGAAGGCACTTGACCCAAAAA
48439 TATCCGAGTTATGAGTAAATACTTGAATAACAATTTATCAGGAGAATTCTTTTGTCAGAATTGTT
521 TATCCGAGTTATGAGTAAATACTTGAATAACAATTTATCAGGAGAATTCTTTTGTCAGAATTGTT
48504 CGAATGGACTGAAATAAATGATAAGTTTGAAGTTAATAATAAGATTGGACGGAAAGAAATGATTG
586 CGAATGGACTGAAATAAATGATAAGTTTGAAGTTAATAATAAGATTGGACGGAAAGAAATGATTG
48569 AAGTACACTGGATCTGTAAAATGACCAGAATACCCATGTAATGGAAATGACCCAAGAATATCACC
651 AAGTACACTGGATCTGTAAAATGACCAGAATACCCATGTAATGGAAATGACCCAAGAATATCACC
48634 AAGCTTAGGAATGATGGGATATCCTCGAGCTCTG
716 AAGCTTAGGAATGATGGGATATCCTCGAGCTCTG
48668 T-ATTTATCTCATTTGATAAGGTATGGAAATACGTCGATTGGGTAAAATTATGAAATTACCCTTA
1 TAATTTATCTCATTTGATAAGGTATGGAAATACGTCGATTGGGTAAAATTATGAAATTACCCTTA
*
48732 TATTGGAAAATGACAAGAATTGTCCCTGGAAATTGATTAATAACTCTGAAAAGACATATTGATCC
66 TATTGGAAAATGACAAGAATTGTCCCTGGAAATTGGTTAATAACTCTGAAAAGACATATTGATCC
48797 AATATAATTACAAATGTGCATAAGAAATGATAGTTTTGCTTAAAAAATTTGGATAACTGGTTTTT
131 AATATAATTACAAATGTGCATAAGAAATGATAGTTTTGCTTAAAAAATTTGGATAACTGGTTTTT
48862 AACCCCAAAAGGGTTTGTATAAGATGCTAGAAGTATGTTAAGAGAATCATTTCAAGATCAGAGAA
196 AACCCCAAAAGGGTTTGTATAAGATGCTAGAAGTATGTTAAGAGAATCATTTCAAGATCAGAGAA
48927 TGTTCAAGAAAGAAATTAATCATAGGATCTCTAAATTATATTATTTTTGTTAAGAGTTAATACCG
261 TGTTCAAGAAAGAAATTAATCATAGGATCTCTAAATTATATTATTTTTGTTAAGAGTTAATACCG
48992 AAATTATCTGGTTAAGAAATTACGAAAATGCCCTTGAGAGGTAAAATAGTCCGAGTTGACCCTGA
326 AAATTATCTGGTTAAGAAATTACGAAAATGCCCTTGAGAGGTAAAATAGTCCGAGTTGACCCTGA
49057 ATGAGAAAGTACTTTGAGGATTCATACTTAACTTGATTAAGTACGGATTTAATTGTTAAGATCCT
391 ATGAGAAAGTACTTTGAGGATTCATACTTAACTTGATTAAGTACGGATTTAATTGTTAAGATCCT
*
49122 GACTTTGTGTAGAAAAATTCATGATATTCCGTTTGTAAAATCTGAGAAGACACTTGACCCAAAAA
456 GACTTTGTGTAGAAAAATTCATGATATTCCGTTTGTAAAATCTGAGAAGGCACTTGACCCAAAAA
49187 TATCCGAGTTATGAGTAAATACTTGAATAACAATTTATCAGGAGAATTCTTTTGTCAGAATTGTT
521 TATCCGAGTTATGAGTAAATACTTGAATAACAATTTATCAGGAGAATTCTTTTGTCAGAATTGTT
49252 CGAATGGACTGAAATAAATGATAAGTTTGAAGTTAATAATAAGATTGGACGGAAAGAAATGATTG
586 CGAATGGACTGAAATAAATGATAAGTTTGAAGTTAATAATAAGATTGGACGGAAAGAAATGATTG
*
49317 AAGTACACTGGATCTGTAAAATGATCAGAATACCCATGTAATGGAAATGACCCAAGAATATCACC
651 AAGTACACTGGATCTGTAAAATGACCAGAATACCCATGTAATGGAAATGACCCAAGAATATCACC
49382 AAGCTTAGGAATGATGGGATATCCTCGAGCTCTG
716 AAGCTTAGGAATGATGGGATATCCTCGAGCTCTG
49416 TAATTTATCTCATTTGATAAGGTATGGAAATACGTCGATTGGGTAAAATTATGAAATTACCCTTA
1 TAATTTATCTCATTTGATAAGGTATGGAAATACGTCGATTGGGTAAAATTATGAAATTACCCTTA
49481 TATTGGAAAATGACAAGAATTGTCCCTGGAAATTGGTTAATAACTCTGAAAAGACATATTGATCC
66 TATTGGAAAATGACAAGAATTGTCCCTGGAAATTGGTTAATAACTCTGAAAAGACATATTGATCC
49546 AATATAATTACAAATGTGCATAAGAAATGATAGTTTTGCTTAAAAAATTTGGATAACTGGTTTTT
131 AATATAATTACAAATGTGCATAAGAAATGATAGTTTTGCTTAAAAAATTTGGATAACTGGTTTTT
49611 AA-CCCAAAAGGGTTTGTATAAGATGCTAGAAGTATGTTAAGAGAATCATTTCAAGATCAGAGAA
196 AACCCCAAAAGGGTTTGTATAAGATGCTAGAAGTATGTTAAGAGAATCATTTCAAGATCAGAGAA
49675 TGTTCAAGAAAGAAATTAATCATAGGATCTCTAAATTATATTATTTTTGTTAAGAGTTAATACCG
261 TGTTCAAGAAAGAAATTAATCATAGGATCTCTAAATTATATTATTTTTGTTAAGAGTTAATACCG
*
49740 AAATTATCTGGTTAAGAAATTACGAAAATGCCATTGAGAGGTAAAATAGTCCGAGTTGACCCTGA
326 AAATTATCTGGTTAAGAAATTACGAAAATGCCCTTGAGAGGTAAAATAGTCCGAGTTGACCCTGA
49805 ATGAGAAAGTACTTTGAGGATTCATACTTAACTTGATTAAGTACGGATTTAATTGTTAAGATCCT
391 ATGAGAAAGTACTTTGAGGATTCATACTTAACTTGATTAAGTACGGATTTAATTGTTAAGATCCT
49870 GACTTTGTGTAGAAAAATTCATGATATTCCGTTTGTAAAATCTGAGAAGGCACTTGACCCAAAAA
456 GACTTTGTGTAGAAAAATTCATGATATTCCGTTTGTAAAATCTGAGAAGGCACTTGACCCAAAAA
*
49935 TATCCGAGTTATGAGTAAATACTTGAATAACAATTTATCGGGAGAATTCTTTTGTCAGAATTGTT
521 TATCCGAGTTATGAGTAAATACTTGAATAACAATTTATCAGGAGAATTCTTTTGTCAGAATTGTT
50000 CGAATGGACTGAAATAAATGATAAGTTTGAAGTTAATAATAAGATTGGACGGAAAGAAATGATTG
586 CGAATGGACTGAAATAAATGATAAGTTTGAAGTTAATAATAAGATTGGACGGAAAGAAATGATTG
50065 AAGTACA-TGGATCTGT-AAATGACCAGAATACCCATGTAATGGAAATGACCCAAGAATATCACC
651 AAGTACACTGGATCTGTAAAATGACCAGAATACCCATGTAATGGAAATGACCCAAGAATATCACC
50128 AAGCTTAGGAATGATGGGATATCCTCGAGCTCTG
716 AAGCTTAGGAATGATGGGATATCCTCGAGCTCTG
50162 TAAT
1 TAAT
50166 GATTAGAACA
Statistics
Matches: 1487, Mismatches: 9, Indels: 6
0.99 0.01 0.00
Matches are distributed among these distances:
746 84 0.06
747 400 0.27
748 809 0.54
749 194 0.13
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (749 bp):
TAATTTATCTCATTTGATAAGGTATGGAAATACGTCGATTGGGTAAAATTATGAAATTACCCTTA
TATTGGAAAATGACAAGAATTGTCCCTGGAAATTGGTTAATAACTCTGAAAAGACATATTGATCC
AATATAATTACAAATGTGCATAAGAAATGATAGTTTTGCTTAAAAAATTTGGATAACTGGTTTTT
AACCCCAAAAGGGTTTGTATAAGATGCTAGAAGTATGTTAAGAGAATCATTTCAAGATCAGAGAA
TGTTCAAGAAAGAAATTAATCATAGGATCTCTAAATTATATTATTTTTGTTAAGAGTTAATACCG
AAATTATCTGGTTAAGAAATTACGAAAATGCCCTTGAGAGGTAAAATAGTCCGAGTTGACCCTGA
ATGAGAAAGTACTTTGAGGATTCATACTTAACTTGATTAAGTACGGATTTAATTGTTAAGATCCT
GACTTTGTGTAGAAAAATTCATGATATTCCGTTTGTAAAATCTGAGAAGGCACTTGACCCAAAAA
TATCCGAGTTATGAGTAAATACTTGAATAACAATTTATCAGGAGAATTCTTTTGTCAGAATTGTT
CGAATGGACTGAAATAAATGATAAGTTTGAAGTTAATAATAAGATTGGACGGAAAGAAATGATTG
AAGTACACTGGATCTGTAAAATGACCAGAATACCCATGTAATGGAAATGACCCAAGAATATCACC
AAGCTTAGGAATGATGGGATATCCTCGAGCTCTG
Found at i:51171 original size:24 final size:24
Alignment explanation
Indices: 51144--51245 Score: 71
Period size: 24 Copynumber: 4.2 Consensus size: 24
51134 ATATTTTATC
* *
51144 TGATTTATGACTTGATTTCTGTTA
1 TGATTTATGACTTGAATTATGTTA
** * * *
51168 TGATACATTACCTGAATTATGTTC
1 TGATTTATGACTTGAATTATGTTA
* *
51192 TGATTTCTGATCTAG-ATTATGTTA
1 TGATTTATGA-CTTGAATTATGTTA
* * * *
51216 TGATATATGATTTGAATTCTGTTT
1 TGATTTATGACTTGAATTATGTTA
51240 TGATTT
1 TGATTT
51246 CTGATGTCTC
Statistics
Matches: 55, Mismatches: 21, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.51
Consensus pattern (24 bp):
TGATTTATGACTTGAATTATGTTA
Found at i:51250 original size:24 final size:24
Alignment explanation
Indices: 51179--51250 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
51169 GATACATTAC
*
51179 CTGAATTATGTTCTGATTTCTGAT
1 CTGAATTATGTTATGATTTCTGAT
* *
51203 CT-AGATTATGTTATGATATATGAT
1 CTGA-ATTATGTTATGATTTCTGAT
* * *
51227 TTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTATGTTATGATTTCTGAT
51251 GTCTCCATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
23 1 0.03
24 36 0.95
25 1 0.03
ACGTcount: A:0.24, C:0.08, G:0.17, T:0.51
Consensus pattern (24 bp):
CTGAATTATGTTATGATTTCTGAT
Found at i:52059 original size:18 final size:17
Alignment explanation
Indices: 52036--52071 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
52026 ATTTTTTAAA
52036 TTTATATTTAATATTTAG
1 TTTATATTTAA-ATTTAG
*
52054 TTTATATTTCAATTTAG
1 TTTATATTTAAATTTAG
52071 T
1 T
52072 ACTTTGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTATATTTAAATTTAG
Found at i:52568 original size:21 final size:21
Alignment explanation
Indices: 52542--52581 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
52532 TTATACCATC
52542 GAACATATATACTTAAATTTT
1 GAACATATATACTTAAATTTT
52563 GAACATATATACTTAAATT
1 GAACATATATACTTAAATT
52582 GTTAAATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (21 bp):
GAACATATATACTTAAATTTT
Found at i:54120 original size:54 final size:54
Alignment explanation
Indices: 54004--54228 Score: 301
Period size: 54 Copynumber: 4.2 Consensus size: 54
53994 TGTATTTACT
54004 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCA-AATGAGTTTATGAATTTCC
1 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCC
**
54057 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTTT
1 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCC
* * * *
54111 GTATTGGCACTATATGTGCAATTTAAGAAATTAATAATGAGTTTATGAATTTCC
1 GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCC
* * ** * * *
54165 ATATTGGCACTGTGTTTGCAATCCCACGTAATTCATAATGAGTTT-TGAATTACC
1 GTATTGGCACTGTGTGTGCAA-CTTAAGAAATTCATAATGAGTTTATGAATTTCC
*
54219 GTATTAGCAC
1 GTATTGGCAC
54229 ACGTGTGCAA
Statistics
Matches: 149, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
53 34 0.23
54 98 0.66
55 17 0.11
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.38
Consensus pattern (54 bp):
GTATTGGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCC
Done.