Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006108.1 Hibiscus syriacus cultivar Beakdansim tig00014477_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: 98908
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3779 original size:34 final size:34
Alignment explanation
Indices: 3736--3805 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
3726 TCCCCTTAGC
3736 TGAGTTCTCGAACTGATAAACTCAAAAACAACAT
1 TGAGTTCTCGAACTGATAAACTCAAAAACAACAT
3770 TGAGTTCTCGAACTGATAAACTCAAAAACAACAT
1 TGAGTTCTCGAACTGATAAACTCAAAAACAACAT
3804 TG
1 TG
3806 TCAGATTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (34 bp):
TGAGTTCTCGAACTGATAAACTCAAAAACAACAT
Found at i:19204 original size:23 final size:23
Alignment explanation
Indices: 19172--19215 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19162 CGTAATAACA
19172 TAACAGGTTGCACCTATTTAAGG
1 TAACAGGTTGCACCTATTTAAGG
* * *
19195 TAACATGTTGCGCCTGTTTAA
1 TAACAGGTTGCACCTATTTAA
19216 AGGTGATGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (23 bp):
TAACAGGTTGCACCTATTTAAGG
Found at i:19734 original size:19 final size:18
Alignment explanation
Indices: 19698--19736 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
19688 TAAAATATAT
**
19698 TTGTAAAAATATTGATAC
1 TTGTAAAAATATCAATAC
19716 TTGTAGAAAATATCAATAC
1 TTGTA-AAAATATCAATAC
19735 TT
1 TT
19737 CGATTTCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (18 bp):
TTGTAAAAATATCAATAC
Found at i:21109 original size:18 final size:18
Alignment explanation
Indices: 21072--21118 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
21062 TGTGGAATTG
* *
21072 GATTCCAACT-CTTGACA
1 GATTCCAATTCCTTCACA
21089 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
21107 GATTCCAATTCC
1 GATTCCAATTCC
21119 CTCAGAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.32
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:21518 original size:100 final size:99
Alignment explanation
Indices: 21384--21786 Score: 419
Period size: 100 Copynumber: 4.0 Consensus size: 99
21374 AAATTCAAAT
* *
21384 GGTTAAGTTGTAAATATTTTACTGTTTAGATTATTATTATACCTTTAAACATATCAATAGCTAGT
1 GGTTAAGTTGTAAATATTTTACTGTTTACATTATTATTATACCTTTAAACA-ATCGATAGCTAGT
* **
21449 TCAACGTAATAGGTTGCGTCTATTTTATTTTAATT
65 TTAACGTAATAGGTTGCGTCTATTTTATTTTAACC
* * * *
21484 GGTTGAGTTGTAAATATTTTACTGTTTACATTATTATTATTATTATATCTTTAAACAAACCGGTA
1 GGTTAAGTTGTAAATATTTTACTGTTTAC------ATTATTATTATACCTTTAAAC-AATCGATA
* * **
21549 GCTAGTTTAATGTAATAGCTTGCACCTATTTTATTTTAACC
59 GCTAGTTTAACGTAATAGGTTGCGTCTATTTTATTTTAACC
* * * * * * * * *
21590 AGTTAATTTGTAATTATTTTAATGTTTACATTATTATTATGCCTTTAAGCAAACTGGTAGCTGGT
1 GGTTAAGTTGTAAATATTTTACTGTTTACATTATTATTATACCTTTAAACAATC-GATAGCTAGT
* * * *
21655 TTAACGTAATATGTTGCCTTTTTTTTATTTTAACC
65 TTAACGTAATAGGTTGCGTCTATTTTATTTTAACC
* * **
21690 GATTAAGTTCTAAATATTTTACCATTTACATTATTATTATACCTTTAAACAATCCGATAGCTAGT
1 GGTTAAGTTGTAAATATTTTACTGTTTACATTATTATTATACCTTTAAACAAT-CGATAGCTAGT
* **
21755 TTAACATAATAGGTTGCGAGTATTTTATTTTA
65 TTAACGTAATAGGTTGCGTCTATTTTATTTTA
21787 CCATTTACAT
Statistics
Matches: 245, Mismatches: 49, Indels: 18
0.79 0.16 0.06
Matches are distributed among these distances:
99 3 0.01
100 158 0.64
101 1 0.00
106 82 0.33
107 1 0.00
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (99 bp):
GGTTAAGTTGTAAATATTTTACTGTTTACATTATTATTATACCTTTAAACAATCGATAGCTAGTT
TAACGTAATAGGTTGCGTCTATTTTATTTTAACC
Found at i:21842 original size:82 final size:76
Alignment explanation
Indices: 21704--21941 Score: 270
Period size: 73 Copynumber: 3.1 Consensus size: 76
21694 AAGTTCTAAA
* *
21704 TATTTTACCATTTACATTATTATTATAC-CTTTAAACAATCCGATAGCTAGTTTAACATAATAGG
1 TATTTTACCATTTACATTATTATTATACTCTTTAAACAAACAG-TAGCTAGTTTAACATAATAGG
**
21768 TTGCGAGTATTT
65 TTGCGCCTATTT
*
21780 TATTTTACCATTTACATTATTATTATTACTAAACTTTTAAACAAACTAGTAGTTAGTTTAACATA
1 TATTTTACCATTTACATTATTATTA-TACT---C-TTTAAACAAAC-AGTAGCTAGTTTAACATA
*
21845 ATGGGTTGCGCCTATTT
60 ATAGGTTGCGCCTATTT
** * *
21862 TA--TT-CTGTTTACATTATTATTATA-TCTTTAAACAAACAAGTAGCTAGTTTAACGTAATATG
1 TATTTTACCATTTACATTATTATTATACTCTTTAAACAAAC-AGTAGCTAGTTTAACATAATAGG
*
21923 TTACGCCTATTT
65 TTGCGCCTATTT
21935 TATTTTA
1 TATTTTA
21942 ACCAGATAAG
Statistics
Matches: 138, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
73 43 0.31
74 1 0.01
75 2 0.01
76 25 0.18
77 4 0.03
78 2 0.01
79 16 0.12
80 2 0.01
81 1 0.01
82 41 0.30
83 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (76 bp):
TATTTTACCATTTACATTATTATTATACTCTTTAAACAAACAGTAGCTAGTTTAACATAATAGGT
TGCGCCTATTT
Found at i:21995 original size:100 final size:102
Alignment explanation
Indices: 21857--22041 Score: 293
Period size: 100 Copynumber: 1.8 Consensus size: 102
21847 GGGTTGCGCC
* *
21857 TATTTTATTCTGTTTACATTATTATTATATCTTTAAACAAACAAGTAGCTAGTTTAACGTAATAT
1 TATTTTATTCTGTTTACATTATTAGTATACCTTTAAACAAACAAGTAGCTAGTTTAACGTAATAT
21922 GTTACGCCTATTTTATTTTAACCAGATAAGTTGCCAA
66 GTTACGCCTATTTTATTTTAACCAGATAAGTTGCCAA
** *
21959 TATTTTA-TC-GTTTACATTATTAGTATACCTTTAAACAAACTGGTAGCTAGTTTAATGTAATAT
1 TATTTTATTCTGTTTACATTATTAGTATACCTTTAAACAAACAAGTAGCTAGTTTAACGTAATAT
**
22022 GTTGTGCCTATTTTATTTTA
66 GTTACGCCTATTTTATTTTA
22042 CCGTTTACAT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
100 67 0.88
101 2 0.03
102 7 0.09
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45
Consensus pattern (102 bp):
TATTTTATTCTGTTTACATTATTAGTATACCTTTAAACAAACAAGTAGCTAGTTTAACGTAATAT
GTTACGCCTATTTTATTTTAACCAGATAAGTTGCCAA
Found at i:22062 original size:76 final size:76
Alignment explanation
Indices: 21959--22117 Score: 221
Period size: 76 Copynumber: 2.1 Consensus size: 76
21949 AAGTTGCCAA
* * ** **
21959 TATTTTATCGTTTACATTATTAGTATACCTTTAAACAAA-CTGGTAGCTAGTTTAATGTAATATG
1 TATTTTACCGTTTACATTATTAGTATACCTTTAAACAAATC-GATAGCTAGTTTAACATAATAAA
**
22023 TTGTGCCTATTT
65 TTGCACCTATTT
*
22035 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAATCGATAGCTAGTTTAACATAATAAAT
1 TATTTTACCGTTTACATTATTAGTATACCTTTAAACAAATCGATAGCTAGTTTAACATAATAAAT
22100 TGCACCTATTT
66 TGCACCTATTT
22111 TATTTTA
1 TATTTTA
22118 ACTGATTAAG
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
76 72 0.99
77 1 0.01
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.45
Consensus pattern (76 bp):
TATTTTACCGTTTACATTATTAGTATACCTTTAAACAAATCGATAGCTAGTTTAACATAATAAAT
TGCACCTATTT
Found at i:22088 original size:176 final size:175
Alignment explanation
Indices: 21801--22216 Score: 524
Period size: 175 Copynumber: 2.4 Consensus size: 175
21791 TTACATTATT
* * * * * * *
21801 ATTATTACTAAACTTTTAAACAAACTAGTAGTTAGTTTAACATAATGGGTTGCGCCTATTTTA--
1 ATTATTAGTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAGGTTGCGCCTATTTTATT
* * * ** *
21864 TT-CTGTTTACATTATTATTATATCTTTAAACAAACAAGTAGCTAGTTTAACGTAATATGTTACG
66 TTACCGTTTACATTATTATTATACCTTTAAACAAACAAGTAGCTAGTTTAACATAATAAATTACA
*
21928 CCTATTTTATTTTAACCAGA-TAAGTTGCCAATATTTTAT-CGTTTAC
131 CCTATTTTATTTTAA-CAGATTAAGTTG-AAATATTTT-TCCGTTTAC
* * *
21974 ATTATTAGTATACCTTTAAACAAACTGGTAGCTAGTTTAATGTAATATGTTGTGCCTATTTTATT
1 ATTATTAGTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAGGTTGCGCCTATTTTATT
* *
22039 TTACCGTTTACATTATTATTATACCTTTAAACAAATCGA-TAGCTAGTTTAACATAATAAATTGC
66 TTACCGTTTACATTATTATTATACCTTTAAACAAA-CAAGTAGCTAGTTTAACATAATAAATTAC
*
22103 ACCTATTTTATTTTAACTGATTAAGTTGAAATATTTTTCCGTTTAC
130 ACCTATTTTATTTTAACAGATTAAGTTGAAATATTTTTCCGTTTAC
* *
22149 ATTATT-GTTATACCTTTAAACAAA-TCGGTAGCTAGTTTAACGAAATAGGTTGCGCCCATTTTA
1 ATTATTAG-TATACCTTTAAACAAACT-GGTAGCTAGTTTAACGTAATAGGTTGCGCCTATTTTA
22212 TTTTA
64 TTTTA
22217 ACTGGTTAAG
Statistics
Matches: 210, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
173 53 0.25
174 3 0.01
175 79 0.38
176 73 0.35
177 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (175 bp):
ATTATTAGTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAGGTTGCGCCTATTTTATT
TTACCGTTTACATTATTATTATACCTTTAAACAAACAAGTAGCTAGTTTAACATAATAAATTACA
CCTATTTTATTTTAACAGATTAAGTTGAAATATTTTTCCGTTTAC
Found at i:22210 original size:99 final size:99
Alignment explanation
Indices: 22035--22242 Score: 310
Period size: 99 Copynumber: 2.1 Consensus size: 99
22025 GTGCCTATTT
22035 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAATCGATAGCTAGTTTAACATAATAAAT
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAATCGATAGCTAGTTTAACATAATAAAT
*
22100 TGCACCTATTTTATTTTAACTGATTAAGTTGAAA
66 TGCACCCATTTTATTTTAACTGATTAAGTTGAAA
* * * **
22134 TATTTTTCCGTTTACATTATTGTTATACCTTTAAACAAATCGGTAGCTAGTTTAACGA-AATAGG
1 TATTTTACCGTTTACATTATTATTATACCTTTAAACAAATCGATAGCTAGTTTAAC-ATAATAAA
* *
22198 TTGCGCCCATTTTATTTTAACTGGTTAAGTTGAAA
65 TTGCACCCATTTTATTTTAACTGATTAAGTTGAAA
22233 TTATTATTAC
1 -TATT-TTAC
22243 ACTATCGATA
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
99 89 0.92
100 5 0.05
101 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (99 bp):
TATTTTACCGTTTACATTATTATTATACCTTTAAACAAATCGATAGCTAGTTTAACATAATAAAT
TGCACCCATTTTATTTTAACTGATTAAGTTGAAA
Found at i:26503 original size:70 final size:70
Alignment explanation
Indices: 26410--26619 Score: 214
Period size: 71 Copynumber: 3.0 Consensus size: 70
26400 AAAAAAAAGT
* *
26410 TTGATACTTTGCAATC-TACTCATTTCCTATGTTTTTTTAATTCGAAAGTATTGATATTTGTGGA
1 TTGATACTTTGCAACCTTA-TCATTTTCTATGTTTTTTTAATTCGAAAGTATTGATATTTGTGGA
26474 AAAATA
65 AAAATA
* * *
26480 TTGAAACTTTGCAACCTTATCATTTTCTATGTTTTTTTTAATTTGAAAGTATCGATATTAT-TGG
1 TTGATACTTTGCAACCTTATCATTTTCTATG-TTTTTTTAATTCGAAAGTATTGATATT-TGTGG
*
26544 AAAATTA
64 AAAAATA
* * *** * * * *
26551 TTTATACTTTGTAGGTTTCTCATTTTC-AT-TTTTTTAAATTCGAAAGTATCT-ATACTTGTGAA
1 TTGATACTTTGCAACCTTATCATTTTCTATGTTTTTTTAATTCGAAAGTAT-TGATATTTGTGGA
26613 AAAATA
65 AAAATA
26619 T
1 T
26620 CAATACTTAC
Statistics
Matches: 116, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
67 1 0.01
68 31 0.27
70 27 0.23
71 56 0.48
72 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.48
Consensus pattern (70 bp):
TTGATACTTTGCAACCTTATCATTTTCTATGTTTTTTTAATTCGAAAGTATTGATATTTGTGGAA
AAATA
Found at i:31693 original size:22 final size:20
Alignment explanation
Indices: 31662--31702 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
31652 ATGACTAAAT
*
31662 TTATTGAATTGAATTAAAATTA
1 TTATTAAATT-AA-TAAAATTA
31684 TTATTAAATTAATAAAATT
1 TTATTAAATTAATAAAATT
31703 TATAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TTATTAAATTAATAAAATTA
Found at i:32066 original size:20 final size:20
Alignment explanation
Indices: 32043--32094 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
32033 AACGCGATCC
32043 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
32063 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
32083 CCAAAATCGCAA
1 CCAGAATCGCAA
32095 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:32111 original size:21 final size:20
Alignment explanation
Indices: 32084--32182 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
32074 AATCAGTTTC
32084 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
32105 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
32126 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
32146 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
32167 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
32183 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:32211 original size:20 final size:20
Alignment explanation
Indices: 32149--32342 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
32139 CGATTTTCCA
* ** *
32149 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
32169 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
32189 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32209 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
32229 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
32249 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
32269 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
32289 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
32309 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
32330 AAATCGCAACGCG
1 AAATCGCAACGCG
32343 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:32233 original size:60 final size:60
Alignment explanation
Indices: 32149--32342 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
32139 CGATTTTCCA
* ** * *
32149 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
32209 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
32269 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
32330 AAATCGCAACGCG
1 AAATCGCAACGCG
32343 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:32763 original size:33 final size:33
Alignment explanation
Indices: 32724--32794 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
32714 TTCACTTAGA
*
32724 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
32757 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
32790 TTTCA
1 TTTCA
32795 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:32934 original size:14 final size:14
Alignment explanation
Indices: 32915--32969 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
32905 AGAATGACTG
32915 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
32929 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
32948 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
32962 TCGCAACG
1 TCGCAACG
32970 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:32952 original size:33 final size:33
Alignment explanation
Indices: 32915--32985 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
32905 AGAATGACTG
**
32915 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
32948 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
32981 TCGCA
1 TCGCA
32986 TTGCGTAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:33144 original size:12 final size:12
Alignment explanation
Indices: 33127--33151 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
33117 TCTTCGGGGA
33127 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33139 CTTTTTCTTCTT
1 CTTTTTCTTCTT
33151 C
1 C
33152 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:33360 original size:24 final size:24
Alignment explanation
Indices: 33326--33372 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
33316 CTGAAACATC
33326 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
33350 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
33373 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:34074 original size:20 final size:20
Alignment explanation
Indices: 34046--34414 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
34036 AAATTTCAGT
* * * *
34046 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
34066 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
34086 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
34106 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
34126 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
34146 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
34166 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
34186 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
34206 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
34226 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
34246 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
34266 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
34286 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
34306 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
34326 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
34346 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
34366 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
34386 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
34406 GTTGCGATT
1 GTTGCGATT
34415 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:47632 original size:60 final size:60
Alignment explanation
Indices: 47516--47632 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
47506 CCTTTGACAC
* * * * *
47516 GATGCCTTCAAGTTCCAATGGGAGGCATTCAACTGCAAGGTTCTTCAACCTCAATGTAGA
1 GATGCCTTCAAGTTCCAAAGGGAGACATTCAACTACAAGCTTCTTCAACCTAAATGTAGA
* * * *
47576 GATGCCTTCAAGTT-CAAAGGGAAGACATTCAACTACCAGCTTGTTCTACTTAAATGT
1 GATGCCTTCAAGTTCCAAAGGG-AGACATTCAACTACAAGCTTCTTCAACCTAAATGT
47633 CGATATCGTG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 6 0.13
60 41 0.87
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (60 bp):
GATGCCTTCAAGTTCCAAAGGGAGACATTCAACTACAAGCTTCTTCAACCTAAATGTAGA
Found at i:51525 original size:13 final size:14
Alignment explanation
Indices: 51511--51558 Score: 53
Period size: 13 Copynumber: 3.3 Consensus size: 14
51501 ATAACAATAA
51511 AAAATAGTATAAAAAT
1 AAAATAGTAT--AAAT
51527 AAAATAGTAT-AAT
1 AAAATAGTATAAAT
*
51540 ATAATAGTAATAAAT
1 AAAATAGT-ATAAAT
51555 AAAA
1 AAAA
51559 ACCAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 10 0.36
14 2 0.07
15 6 0.21
16 10 0.36
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (14 bp):
AAAATAGTATAAAT
Found at i:51545 original size:18 final size:17
Alignment explanation
Indices: 51506--51545 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
51496 TAATAATAAC
51506 AATAA-AAAATAGTATA
1 AATAATAAAATAGTATA
51522 AA-AATAAAATAGTATA
1 AATAATAAAATAGTATA
51538 ATATAATA
1 A-ATAATA
51546 GTAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.10
16 14 0.67
17 1 0.05
18 4 0.19
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
AATAATAAAATAGTATA
Found at i:51597 original size:12 final size:11
Alignment explanation
Indices: 51563--51600 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
51553 ATAAAAACCA
51563 AAAATAAA-AT
1 AAAATAAATAT
51573 AAAATAAATAT
1 AAAATAAATAT
*
51584 AAAGATATATAT
1 AAA-ATAAATAT
51596 AAAAT
1 AAAAT
51601 GATAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 8 0.32
11 7 0.28
12 10 0.40
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AAAATAAATAT
Found at i:51610 original size:19 final size:17
Alignment explanation
Indices: 51566--51612 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 17
51556 AAAACCAAAA
51566 ATAAAATA-AAATAAAT
1 ATAAAATATAAATAAAT
*
51582 ATAAAGATATATATAAAAT
1 ATAAA-ATATAAAT-AAAT
51601 GATAAAATATAA
1 -ATAAAATATAA
51613 TACTTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 5 0.20
17 3 0.12
18 3 0.12
19 9 0.36
20 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (17 bp):
ATAAAATATAAATAAAT
Found at i:51638 original size:17 final size:17
Alignment explanation
Indices: 51618--51656 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
51608 TATAATACTT
51618 AAATAAAAAGAA-TAACC
1 AAATAAAAAGAATTAA-C
*
51635 AAATAAAAATAATTAAC
1 AAATAAAAAGAATTAAC
51652 AAATA
1 AAATA
51657 TACATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.72, C:0.08, G:0.03, T:0.18
Consensus pattern (17 bp):
AAATAAAAAGAATTAAC
Found at i:54039 original size:65 final size:64
Alignment explanation
Indices: 53918--54109 Score: 178
Period size: 65 Copynumber: 3.0 Consensus size: 64
53908 CGATGTATCA
* ** ** *
53918 ATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATTTATTTCA-AGCATCGATGCA
1 ATCCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATTTGATA-CATCGATGCA
*
53980 -T
63 CC
*
53981 ATACCATGCATCGATGCACTCAGGGT-TTTATGAAAACATCGAATGCATTTGATACATCGATGCA
1 AT-CCATGCATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCATTTGATACATCGATGCA
54045 CC
63 CC
* * * * *
54047 ATCCATGCATCGATGCACTTAGGCTATTTTGAAATATCGAATGCATTTTATGCATCGGTGCAC
1 ATCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTGATACATCGATGCAC
54110 TCTTAGTGCA
Statistics
Matches: 108, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
63 5 0.05
64 46 0.43
65 50 0.46
66 6 0.06
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (64 bp):
ATCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTGATACATCGATGCACC
Found at i:59896 original size:25 final size:25
Alignment explanation
Indices: 59862--59920 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
59852 TTTGGGGGAG
59862 TTTATGTTCTTTGGTGAAAATTAAC
1 TTTATGTTCTTTGGTGAAAATTAAC
59887 TTTATGTTCTTTGGTGAAAATTAAC
1 TTTATGTTCTTTGGTGAAAATTAAC
59912 TTTATGTTC
1 TTTATGTTC
59921 AAATGTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.51
Consensus pattern (25 bp):
TTTATGTTCTTTGGTGAAAATTAAC
Found at i:60142 original size:23 final size:23
Alignment explanation
Indices: 60073--60148 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
60063 ACACTTAACA
60073 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACTCCTTGAAT
* * *
60095 GTGCATCGAT--ACACCATGAAA
1 GTGCATCGATGCACTCCTTGAAT
*
60116 GTGCACCGATGCACTCCTTGAAT
1 GTGCATCGATGCACTCCTTGAAT
60139 GTGCATCGAT
1 GTGCATCGAT
60149 ACACAAGGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.35
22 10 0.23
23 17 0.40
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACTCCTTGAAT
Found at i:60142 original size:44 final size:43
Alignment explanation
Indices: 60054--60152 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 43
60044 TTGTGTTTAA
* *
60054 TGCATCGATACA-CTTAACAGTGCATCGATGCATCCTTGAATG
1 TGCATCGATACACCTGAACAGTGCACCGATGCATCCTTGAATG
60096 TGCATCGATACACCATGAA-AGTGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACC-TGAACAGTGCACCGATGCA-TCCTTGAATG
60140 TGCATCGATACAC
1 TGCATCGATACAC
60153 AAGGACATGC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
42 12 0.23
43 14 0.27
44 26 0.50
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (43 bp):
TGCATCGATACACCTGAACAGTGCACCGATGCATCCTTGAATG
Found at i:60170 original size:43 final size:43
Alignment explanation
Indices: 60072--60172 Score: 141
Period size: 44 Copynumber: 2.3 Consensus size: 43
60062 TACACTTAAC
* *
60072 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGAA
1 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGAA
* *
60115 AGTGCACCGATGCACTCCTTGAATGTGCATCGATACACAAGGAC
1 AGTGCATCGATGCA-TCCTTGAATGTGCATCGATACACAAGGAA
*
60159 A-TGCATTGATGCAT
1 AGTGCATCGATGCAT
60173 TCGTCGGGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.02
43 23 0.45
44 27 0.53
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (43 bp):
AGTGCATCGATGCATCCTTGAATGTGCATCGATACACAAGGAA
Found at i:62443 original size:16 final size:17
Alignment explanation
Indices: 62417--62449 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
62407 TGATTTAACA
62417 AAAAGGGGGAGAAGTGT
1 AAAAGGGGGAGAAGTGT
62434 AAAA-GGGGAGAAGTGT
1 AAAAGGGGGAGAAGTGT
62450 TAGAGTAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.12
Consensus pattern (17 bp):
AAAAGGGGGAGAAGTGT
Found at i:62966 original size:45 final size:46
Alignment explanation
Indices: 62871--62978 Score: 175
Period size: 45 Copynumber: 2.4 Consensus size: 46
62861 TGCACATACC
*
62871 ATGCATCGATGCACTCAGGGTTTTATGAAAACATCGAATGCATTTG
1 ATGCATCGATGCACTCAGGCTTTTATGAAAACATCGAATGCATTTG
*
62917 ATGCATCGATGCACTCAGGCTATTT-TG-AAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGCT-TTTATGAAAACATCGAATGCATTTG
62962 ATGCATCGATGCACTCA
1 ATGCATCGATGCACTCA
62979 AATGATTTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
45 34 0.58
46 22 0.37
47 3 0.05
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGGCTTTTATGAAAACATCGAATGCATTTG
Found at i:65765 original size:13 final size:13
Alignment explanation
Indices: 65749--65782 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
65739 AATAAAAAAT
65749 AAATAAATATTAA
1 AAATAAATATTAA
*
65762 AAAT-TATATTAA
1 AAATAAATATTAA
65774 AAATAAATA
1 AAATAAATA
65783 AAATAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAAATATTAA
Found at i:65802 original size:29 final size:29
Alignment explanation
Indices: 65734--65802 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
65724 TTTTTCAGAT
* *
65734 ATAATAATAAAAAATAAATAAATATTAAAA
1 ATAAT-ATTAAAAATAAATAAATATAAAAA
*
65764 ATTATATTAAAAATAAATAAA-ATAAACAA
1 ATAATATTAAAAATAAATAAATATAAA-AA
*
65793 ATAATTTTAA
1 ATAATATTAA
65803 TTGTCTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 4 0.12
29 25 0.76
30 4 0.12
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (29 bp):
ATAATATTAAAAATAAATAAATATAAAAA
Found at i:65876 original size:12 final size:12
Alignment explanation
Indices: 65859--65900 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
65849 AATAAATGAA
65859 TTATAAACAAAT
1 TTATAAACAAAT
* *
65871 TTATAAA-GAAC
1 TTATAAACAAAT
*
65882 TAATAAACAAAT
1 TTATAAACAAAT
65894 TTATAAA
1 TTATAAA
65901 GAACTAATAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (12 bp):
TTATAAACAAAT
Found at i:65876 original size:23 final size:23
Alignment explanation
Indices: 65861--65915 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
65851 TAAATGAATT
65861 ATAAACAAATTTATAAAGAACTA
1 ATAAACAAATTTATAAAGAACTA
65884 ATAAACAAATTTATAAAGAACTA
1 ATAAACAAATTTATAAAGAACTA
65907 ATAAACAAA
1 ATAAACAAA
65916 CTTGTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.64, C:0.09, G:0.04, T:0.24
Consensus pattern (23 bp):
ATAAACAAATTTATAAAGAACTA
Found at i:75730 original size:34 final size:34
Alignment explanation
Indices: 75645--75732 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 34
75635 AAAACTTTAA
75645 ATATATATTTAAAAATTATAAAAAAAATAAAAATAG
1 ATATATATTTAAAAA-TAT-AAAAAAATAAAAATAG
* * * * *
75681 ATAAATATTTTAAAATAT-AAAAGATACATAATAT
1 ATATATATTTAAAAATATAAAAAAATA-AAAATAG
75715 ATATATATTTAAAAATAT
1 ATATATATTTAAAAATAT
75733 CACCCCAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
33 7 0.16
34 21 0.48
35 3 0.07
36 13 0.30
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.35
Consensus pattern (34 bp):
ATATATATTTAAAAATATAAAAAAATAAAAATAG
Found at i:80504 original size:10 final size:11
Alignment explanation
Indices: 80479--80503 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
80469 AAGATCCCAC
80479 AAAATCTAAAA
1 AAAATCTAAAA
80490 AAAATCTAAAA
1 AAAATCTAAAA
80501 AAA
1 AAA
80504 TGTAGACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATCTAAAA
Found at i:88426 original size:18 final size:18
Alignment explanation
Indices: 88388--88423 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
88378 AATTAACATT
88388 ATAATGGAGATAAAAACA
1 ATAATGGAGATAAAAACA
*
88406 ATAA-GGAGATTAAAACA
1 ATAATGGAGATAAAAACA
88423 A
1 A
88424 ATATTGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.06, G:0.17, T:0.17
Consensus pattern (18 bp):
ATAATGGAGATAAAAACA
Found at i:89070 original size:2 final size:2
Alignment explanation
Indices: 89063--89090 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
89053 AACATACACA
89063 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
89091 GCAATCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.