Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004677.1 Hibiscus syriacus cultivar Beakdansim tig00010487_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: 55244
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5542 original size:24 final size:24
Alignment explanation
Indices: 5513--5559 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
5503 CCACCGCCAC
5513 CTCCTAGA-CTATTACCTCCTCCAT
1 CTCCTAGAGC-ATTACCTCCTCCAT
5537 CTCCTAGAGCATTACCTCCTCCA
1 CTCCTAGAGCATTACCTCCTCCA
5560 CCACCTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.21, C:0.43, G:0.06, T:0.30
Consensus pattern (24 bp):
CTCCTAGAGCATTACCTCCTCCAT
Found at i:11311 original size:27 final size:27
Alignment explanation
Indices: 11269--11332 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 27
11259 AGAACTGGAC
11269 TTAGATGACAAAAAGAATTTTGAGATTT
1 TTAG-TGACAAAAAGAATTTTGAGATTT
*
11297 TTAGTGACAATAAGAATTTTGAGATTT
1 TTAGTGACAAAAAGAATTTTGAGATTT
11324 TTAGTGACA
1 TTAGTGACA
11333 GTCAATCAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 31 0.89
28 4 0.11
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.38
Consensus pattern (27 bp):
TTAGTGACAAAAAGAATTTTGAGATTT
Found at i:12138 original size:30 final size:30
Alignment explanation
Indices: 12102--12171 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
12092 TGTTTTAGCT
*
12102 GGTCTCCTAGAAACAAGAGAAGCAGGAGCA
1 GGTCTCCCAGAAACAAGAGAAGCAGGAGCA
**
12132 GGTCTCCCAGAAACCGGAGAAGCAGGAGCA
1 GGTCTCCCAGAAACAAGAGAAGCAGGAGCA
12162 GGTCTCCCAG
1 GGTCTCCCAG
12172 TTTTCTGCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.33, C:0.26, G:0.31, T:0.10
Consensus pattern (30 bp):
GGTCTCCCAGAAACAAGAGAAGCAGGAGCA
Found at i:13038 original size:24 final size:24
Alignment explanation
Indices: 13011--13056 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
13001 AGTACCCCTT
13011 CCCTTAATTAAAATCCCTAACCTC
1 CCCTTAATTAAAATCCCTAACCTC
* *
13035 CCCTTAATTGAAATTCCTAACC
1 CCCTTAATTAAAATCCCTAACC
13057 CTATTTCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.30
Consensus pattern (24 bp):
CCCTTAATTAAAATCCCTAACCTC
Found at i:15795 original size:24 final size:24
Alignment explanation
Indices: 15768--15817 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
15758 TGGCAGTACC
15768 CCTCCCCTTAATTAAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
*
15792 CCTCCCCTTAATTGAAATCCCTAA
1 CCTCCCCTTAATTAAAATCCCTAA
15816 CC
1 CC
15818 CTATTTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.40, G:0.02, T:0.28
Consensus pattern (24 bp):
CCTCCCCTTAATTAAAATCCCTAA
Found at i:23261 original size:12 final size:12
Alignment explanation
Indices: 23246--23287 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
23236 AAAACACACA
23246 AAAAAAAGAAAG
1 AAAAAAAGAAAG
23258 AAAAAAA-ACAAG
1 AAAAAAAGA-AAG
*
23270 AAAAACAG-AAG
1 AAAAAAAGAAAG
23281 AAAAAAA
1 AAAAAAA
23288 ATAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:23273 original size:24 final size:24
Alignment explanation
Indices: 23219--23307 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 24
23209 ACACAGAGAG
23219 AAAAAGAAGAGATATAAAAAACACACAAA
1 AAAAAGAA-AGA-A-AAAAAACA-A-AAA
*
23248 AAAAAGAAAGAAAAAAAACAAGAA
1 AAAAAGAAAGAAAAAAAACAAAAA
* *
23272 AAACAG-AAGAAAAAAAATAAAAA
1 AAAAAGAAAGAAAAAAAACAAAAA
*
23295 AATAAAAAAAGAA
1 AA-AAAGAAAGAA
23308 TAAAGAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
23 17 0.33
24 9 0.17
25 6 0.12
26 8 0.15
27 1 0.02
28 3 0.06
29 8 0.15
ACGTcount: A:0.80, C:0.06, G:0.10, T:0.04
Consensus pattern (24 bp):
AAAAAGAAAGAAAAAAAACAAAAA
Found at i:23293 original size:20 final size:20
Alignment explanation
Indices: 23256--23304 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
23246 AAAAAAAGAA
23256 AGAAAAAAAACAAGAAAAAC
1 AGAAAAAAAACAAGAAAAAC
* *
23276 AGAAGAAAAAA-AATAAAAAA
1 AGAA-AAAAAACAAGAAAAAC
*
23296 ATAAAAAAA
1 AGAAAAAAA
23305 GAATAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 14 0.56
21 6 0.24
ACGTcount: A:0.84, C:0.04, G:0.08, T:0.04
Consensus pattern (20 bp):
AGAAAAAAAACAAGAAAAAC
Found at i:25069 original size:4 final size:4
Alignment explanation
Indices: 25060--25848 Score: 1442
Period size: 4 Copynumber: 198.2 Consensus size: 4
25050 TAAGTGCATT
25060 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25108 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25156 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25204 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25250 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25298 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25346 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25394 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25442 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
25490 CATA CATA CATA CATA CATA CATA CATA CAAA CGTA CGTA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
25538 CATA CATA CATA CGTA CATA TATA CGTA TATA CATA CATA CATA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
25586 CATA CGTA CATA CATA CATA CGTA CATA CATA CGTA CATA CGTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25634 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25682 CATA CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25728 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25776 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
25824 CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA C
25849 TTCTTACAGA
Statistics
Matches: 759, Mismatches: 22, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
2 4 0.01
4 755 0.99
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:26082 original size:54 final size:54
Alignment explanation
Indices: 26016--26321 Score: 270
Period size: 54 Copynumber: 5.7 Consensus size: 54
26006 GCTAATGAGT
* ** * *
26016 TTTTAAATAAACTAATTCTAATTTTCAGAAGTTTCTTGACGATTTTTAAATGAG
1 TTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGACGATTTTTAAATGAA
* * * * *
26070 TTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAAAGAA
1 TTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGACGATTTTTAAATGAA
* * * * * *
26124 CTTTCAAAGAAATTAAGCTTAATTTTTAGGGGTTTCTTGAC-ATTTTCAAATGAA
1 -TTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGACGATTTTTAAATGAA
* * * *
26178 TTTGAAAGAAGCTAAGCTTGATTTTCAGGAGTTTCTT----ATTGTTTCAAATGAA
1 TTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGACGATT-TTT-AAATGAA
* * *
26230 TTTTAAAGAAA-TCAAGCCTAACTTTT-AGGGGTTTCTTGATG-TTTTCAAATGAA
1 TTTTAAAGAAACT-AAGCCTAA-TTTTCAGGAGTTTCTTGACGATTTTTAAATGAA
* *
26283 TATTTAAAGAAACTAAGCCTAATTTTTAGG-GGTTCTTGA
1 T-TTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGA
26322 TGATAACTGT
Statistics
Matches: 209, Mismatches: 31, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
50 3 0.01
51 3 0.01
52 32 0.15
53 55 0.26
54 82 0.39
55 34 0.16
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.41
Consensus pattern (54 bp):
TTTTAAAGAAACTAAGCCTAATTTTCAGGAGTTTCTTGACGATTTTTAAATGAA
Found at i:26264 original size:52 final size:53
Alignment explanation
Indices: 26063--26323 Score: 241
Period size: 53 Copynumber: 4.9 Consensus size: 53
26053 GACGATTTTT
* * * * ** *
26063 AAATGAGTTTTAAAGAAA-CTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTT
1 AAATGAATTTTAAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTGATG--TTTC
* * *
26117 AAAAGAACTTTCAAAGAAAT-TAAGCTTAATTTTTAGGGGTTTCTTGACAT-TTTC
1 AAATGAA-TTTTAAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTG--ATGTTTC
* * * * * *
26171 AAATGAATTTGAAAG-AAGCTAAGCTTGATTTTCAGGAGTTTCTT-ATTGTTTC
1 AAATGAATTTTAAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTGA-TGTTTC
*
26223 AAATGAATTTTAAAGAAATC-AAGCCTAACTTTTAGGGGTTTCTTGATGTTTTC
1 AAATGAATTTTAAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTC
26276 AAATGAATATTTAAAGAAA-CTAAGCCTAATTTTTAGGGG-TTCTTGATG
1 AAATGAAT-TTTAAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTGATG
26324 ATAACTGTAA
Statistics
Matches: 171, Mismatches: 24, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 41 0.24
53 55 0.32
54 41 0.24
55 30 0.18
57 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (53 bp):
AAATGAATTTTAAAGAAATCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTC
Found at i:26280 original size:105 final size:108
Alignment explanation
Indices: 26046--26325 Score: 322
Period size: 105 Copynumber: 2.6 Consensus size: 108
26036 ATTTTCAGAA
* *
26046 GTTTCTTGACGATTTTTAAATGAGTTTTAAAGAAACTAAG-TCTGATTTTCAGAAGTTTCTTGAT
1 GTTTCTTGACG-TTTTCAAATGAATTTTAAAGAAACTAAGCTCTGATTTTCAGAAGTTTCTTGAT
* * * *
26110 GATTTTTAAAAGAACTTTCAAAGAAATTAAGCTTAATTTTTAGGG
65 GA-TTTCAAAAGAACTTTCAAAGAAATCAAGCCTAACTTTTAGGG
* * * *
26155 GTTTCTTGACATTTTCAAATGAATTTGAAAGAAGCTAAGCT-TGATTTTCAGGAGTTTCTT-ATT
1 GTTTCTTGACGTTTTCAAATGAATTTTAAAGAAACTAAGCTCTGATTTTCAGAAGTTTCTTGA-T
* *
26218 G-TTTCAAATGAA-TTTTAAAGAAATCAAGCCTAACTTTTAGGG
65 GATTTCAAAAGAACTTTCAAAGAAATCAAGCCTAACTTTTAGGG
* * * * *
26260 GTTTCTTGATGTTTTCAAATGAATATTTAAAGAAACTAAGC-CTAATTTTTAG-GGGTTCTTGAT
1 GTTTCTTGACGTTTTCAAATGAAT-TTTAAAGAAACTAAGCTCTGATTTTCAGAAGTTTCTTGAT
26323 GAT
65 GAT
26326 AACTGTAAAC
Statistics
Matches: 145, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
105 56 0.39
106 33 0.23
107 1 0.01
108 44 0.30
109 11 0.08
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.41
Consensus pattern (108 bp):
GTTTCTTGACGTTTTCAAATGAATTTTAAAGAAACTAAGCTCTGATTTTCAGAAGTTTCTTGATG
ATTTCAAAAGAACTTTCAAAGAAATCAAGCCTAACTTTTAGGG
Found at i:26490 original size:41 final size:41
Alignment explanation
Indices: 26378--26490 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 41
26368 AGCGTTTCTT
* *
26378 GATGAGTAAGTCCTTTGGGCCAT-CACTAAGTCTTTCGAGCAT
1 GATGA-TAAGTCCTTCGGGCCATCCA-TAAGTCTTTCGAGCAA
* * * *
26420 GATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAA
1 GATG-ATAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAA
26462 GATGATAAGTCCTTCGGGCCATCCATAAG
1 GATGATAAGTCCTTCGGGCCATCCATAAG
26491 ACCTTCAGGC
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
41 21 0.36
42 37 0.63
43 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (41 bp):
GATGATAAGTCCTTCGGGCCATCCATAAGTCTTTCGAGCAA
Found at i:27807 original size:139 final size:139
Alignment explanation
Indices: 27553--27922 Score: 668
Period size: 139 Copynumber: 2.7 Consensus size: 139
27543 GGTAAATTAG
* *
27553 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGTTGAGAGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
* *
27618 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAATACCTTA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
*
27683 CTTGAGGGA
131 CTCGAGGGA
*
27692 TCACCATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
27757 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
27822 CTCGAGGGA
131 CTCGAGGGA
* *
27831 TCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAAAAGAAGTTCATA
1 TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
27896 ATGAGAAGAACTTGTTCAACCTTAGCT
66 ATGAGAAGAACTTGTTCAACCTTAGCT
27923 TGTTTTCCAT
Statistics
Matches: 222, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
139 222 1.00
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (139 bp):
TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCA
CTCGAGGGA
Found at i:28722 original size:21 final size:21
Alignment explanation
Indices: 28697--28747 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
28687 GGAGAAAAAA
28697 AGGAGAAAGAATGAGGTTAGG
1 AGGAGAAAGAATGAGGTTAGG
28718 AGGAGAAAGAATGAGGTTAGG
1 AGGAGAAAGAATGAGGTTAGG
28739 AGGAGAAAG
1 AGGAGAAAG
28748 GGGTCCGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.43, T:0.12
Consensus pattern (21 bp):
AGGAGAAAGAATGAGGTTAGG
Found at i:35032 original size:192 final size:193
Alignment explanation
Indices: 34623--35046 Score: 514
Period size: 192 Copynumber: 2.2 Consensus size: 193
34613 AACTTGATTG
* * *
34623 TTGCAAAAGATGATGTTGCACTAACAGCTAAGGTTTCGGAGGTAGCACTAGGCAACAGAACAGGC
1 TTGCAAAAGACGATGTTACACTAACAGCTAAGGTTTCAGAGGTAGCACTAGGCAACAGAACAGGC
* ** *
34688 ACTGAATCTGATCTCAAAGGAAGTAAAAGAAAGAAACAAAAGGGGTCTTTGTGCAAGGATGAATA
66 ACTGAATCTGATCTCAAAGGAAGAAAAAGAAAGAAACAAAAGAAG--TTTGTGCAAGGATGAAGA
* * * *
34753 CCAAAAGGATGTTGAGATAGAAACCAAGATGGAAGAAGTTATTCCTTCTCCATTGGACTTGGCTG
129 CCAAAAGGATGTCGAGATAGAAACCAAGATGGAAGAAGTTATCCCTTCTCCATTGAACTTGGCTC
** * * * * * *
34818 TCACAACAGACGATGTTACACTAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAGAGCACAGGC
1 TTGCAAAAGACGATGTTACACTAACAGCTAAGGTTTCAGAGGTAGCACTAGGCAACAGAACAGGC
* * *
34883 ACTGAATCTGATC-CGAAAGGAAGAAAAAGAAAGAAGTC-GAAGAAG-TTGTGCAAGGATGGAGA
66 ACTGAATCTGATCTC-AAAGGAAGAAAAAGAAAGAA-ACAAAAGAAGTTTGTGCAAGGATGAAGA
* * *
34945 CCAAACA-GATGTCGAGATAGGAACTAAGATGGAAGAAGTTATCCCTTCTCCCTTGAACTTGGCT
129 CCAAA-AGGATGTCGAGATAGAAACCAAGATGGAAGAAGTTATCCCTTCTCCATTGAACTTGGCT
35009 C
193 C
* * * *
35010 TTGCAAAAGACCATGATACACTAACAGCCAATGTTTC
1 TTGCAAAAGACGATGTTACACTAACAGCTAAGGTTTC
35047 TCCTTCGATC
Statistics
Matches: 193, Mismatches: 33, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
192 100 0.52
193 1 0.01
194 1 0.01
195 90 0.47
196 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (193 bp):
TTGCAAAAGACGATGTTACACTAACAGCTAAGGTTTCAGAGGTAGCACTAGGCAACAGAACAGGC
ACTGAATCTGATCTCAAAGGAAGAAAAAGAAAGAAACAAAAGAAGTTTGTGCAAGGATGAAGACC
AAAAGGATGTCGAGATAGAAACCAAGATGGAAGAAGTTATCCCTTCTCCATTGAACTTGGCTC
Found at i:35244 original size:246 final size:246
Alignment explanation
Indices: 34809--35340 Score: 902
Period size: 246 Copynumber: 2.2 Consensus size: 246
34799 TCTCCATTGG
*
34809 ACTTGGCTGTCACAACAGACGATGTTACACTAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAG
1 ACTTGGCTGTCACAACAGACGATGTTACACTAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAC
* *
34874 AGCACAGGCACTGAATCTGATCCGAAAGGAAGAAAAAGAAAGAAGTCGAAGAAGTTGTGCAAGGA
66 AGCACAGGCACTGAATCTGACCCGAAAGGAAGAAAAAGAAAGAAGTCAAAGAAGTTGTGCAAGGA
*
34939 TGGAGACCAAACAGATGTCGAGATAGGAACTAAGATGGAAGAAGTTATCCCTTCTCCCTTGAACT
131 TGGAGACCAAACAGATGTCGAGATAGGAACTAAGATGGAAGAAGTAATCCCTTCTCCCTTGAACT
*
35004 TGGCTCTTGCAAAAGACCATGATACACTAACAGCCAATGTTTCTCCTTCGA
196 TGGCTCTTGCAAAAGACCATGATACACTAACAGCCAATGTTTCTCATTCGA
*
35055 TCTTGGCTGTCACAACAGACGATGTTACACTAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAC
1 ACTTGGCTGTCACAACAGACGATGTTACACTAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAC
* *
35120 AGCACAGGCACTGAATCTGACCCGAAAGGAAGAAAAAGAAAGAATTCAAAGAAGTTGTGGAAGGA
66 AGCACAGGCACTGAATCTGACCCGAAAGGAAGAAAAAGAAAGAAGTCAAAGAAGTTGTGCAAGGA
*
35185 TGGAGACCAAACAGATGTTGAGATAGGAACTAAGATGGAAGAAGTAATCCCTTCTCCCTTGAACT
131 TGGAGACCAAACAGATGTCGAGATAGGAACTAAGATGGAAGAAGTAATCCCTTCTCCCTTGAACT
* * *
35250 TGGCTGTTGCAAAATACCATGATACACTAACAGCTAATGTTTCTCATTCGA
196 TGGCTCTTGCAAAAGACCATGATACACTAACAGCCAATGTTTCTCATTCGA
* * * ** *
35301 ACTTGGCTGTCGCAAAAGATGATGCCACACTAACAGCTAA
1 ACTTGGCTGTCACAACAGACGATGTTACACTAATAGCTAA
35341 AGCTAGAGAG
Statistics
Matches: 267, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
246 267 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.22
Consensus pattern (246 bp):
ACTTGGCTGTCACAACAGACGATGTTACACTAATAGCTAAGGTTTCAGAGGTAGCATTGGGCAAC
AGCACAGGCACTGAATCTGACCCGAAAGGAAGAAAAAGAAAGAAGTCAAAGAAGTTGTGCAAGGA
TGGAGACCAAACAGATGTCGAGATAGGAACTAAGATGGAAGAAGTAATCCCTTCTCCCTTGAACT
TGGCTCTTGCAAAAGACCATGATACACTAACAGCCAATGTTTCTCATTCGA
Found at i:39032 original size:18 final size:18
Alignment explanation
Indices: 39009--39044 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
38999 ATGAAGTTCA
39009 AATAAAAAAATTATATAT
1 AATAAAAAAATTATATAT
*
39027 AATAAAATAATTATATAT
1 AATAAAAAAATTATATAT
39045 TTTTAGTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATAAAAAAATTATATAT
Found at i:40797 original size:3 final size:3
Alignment explanation
Indices: 40789--40816 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40779 GTTAATTCCC
40789 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
40817 ATGCGTGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:42352 original size:22 final size:23
Alignment explanation
Indices: 42319--42385 Score: 95
Period size: 22 Copynumber: 3.0 Consensus size: 23
42309 TCCAAACCGA
*
42319 TTTGATCG-GTCAGACCGTTGAC
1 TTTGACCGAGTCAGACCGTTGAC
42341 TTTGACC-AGTCAGACCGTTGAC
1 TTTGACCGAGTCAGACCGTTGAC
42363 TTTGACCGAGTCA-ACCCGTTGAC
1 TTTGACCGAGTCAGA-CCGTTGAC
42386 CGTTGACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
22 28 0.68
23 13 0.32
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (23 bp):
TTTGACCGAGTCAGACCGTTGAC
Found at i:44924 original size:54 final size:54
Alignment explanation
Indices: 44535--44925 Score: 518
Period size: 54 Copynumber: 7.2 Consensus size: 54
44525 TACCAAATAG
** * * * *
44535 GCACTAAACGTGCATTTCACGGAATTCATCCTTTGTGGAGGAAAAACTATTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCA
**
44588 GACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTCA
1 G-CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCA
* *
44643 GCACTAAGTGTACATTTCACGGAATTCATCATATGTGGATGAATAA-TCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACT-GTTTCA
* * * *
44697 ACACTAAGTGTGCATTTCACAGAATTCATCTTATGTGGATGAATAACCGTTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCA
* * *
44750 GACACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAATTGTTTCG
1 G-CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCA
* * * *
44805 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGGGGATGAATAACCGTTTCT
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCA
*
44859 GTACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCA
* *
44913 GCCCTATGTGTGC
1 GCACTAAGTGTGC
44926 GAAACACAAA
Statistics
Matches: 299, Mismatches: 33, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.00
54 296 0.99
55 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCA
Found at i:44972 original size:162 final size:162
Alignment explanation
Indices: 44544--44972 Score: 466
Period size: 162 Copynumber: 2.6 Consensus size: 162
44534 GGCACTAAAC
* * * * ** **
44544 GTGCATTTCACGGAATTCATCCTTTGTGGAGGAAAAACTATTTCGACACTAAGTGTGCATTTCAC
1 GTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATAACAC
** ** * * * * *
44609 GGAATTCATCCTATGTGGATGAATAACCATTTCAGCACTAAGTGTACATTTCACGGAATTCATCA
66 AAAATTCATAATATGTGGATGAATAATCGTATCGGCACTAAGTGTACATTTCACGAAATTCATCA
* *
44674 TATGTGGATGAATAATCGTTTCAACACTAAGT
131 TATGGGGATGAATAACCGTTTCAACACTAAGT
* **
44706 GTGCATTTCACAGAATTCATCTTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCAC
1 GTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATAACAC
* ** * * * *
44771 GAAATTCATCCTATGTGGATGAATAATTGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCC
66 AAAATTCATAATATGTGGATGAATAATCGTATCGGCACTAAGTGTACATTTCACGAAATTCATCA
***
44836 TATGGGGATGAATAACCGTTTCTGTACTAAGT
131 TATGGGGATGAATAACCGTTTCAACACTAAGT
* * * *
44868 GTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC-AGCCCTATGTGTGCGA-AAC
1 GTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGA-CACTAAGTGTGC-ATAAC
** * *
44931 ACAAAATTCATAATATGTTTATGAATGATCGTATGGGCACTA
64 ACAAAATTCATAATATGTGGATGAATAATCGTATCGGCACTA
44973 CGGGTGTATT
Statistics
Matches: 229, Mismatches: 36, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
161 1 0.00
162 227 0.99
163 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (162 bp):
GTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATAACAC
AAAATTCATAATATGTGGATGAATAATCGTATCGGCACTAAGTGTACATTTCACGAAATTCATCA
TATGGGGATGAATAACCGTTTCAACACTAAGT
Found at i:45049 original size:2 final size:2
Alignment explanation
Indices: 45042--45075 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
45032 AAGAATAATG
45042 AT 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
45076 TGATTTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49834 original size:30 final size:30
Alignment explanation
Indices: 49798--49866 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
49788 GTGACCCTTG
*
49798 GGTAGGCTCTGCAACCTCAAGATCTTCTTA
1 GGTAGGCTCTGCAACCCCAAGATCTTCTTA
* * * * *
49828 GGTAGGCCCTGCAGCCCCAATATTTTCTTG
1 GGTAGGCTCTGCAACCCCAAGATCTTCTTA
49858 GGTAGGCTC
1 GGTAGGCTC
49867 ACAGGCCCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.29
Consensus pattern (30 bp):
GGTAGGCTCTGCAACCCCAAGATCTTCTTA
Found at i:52130 original size:24 final size:25
Alignment explanation
Indices: 52095--52157 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 25
52085 ATATTTTTAA
*
52095 TAAT-TATCTTTTGTAAATAAAATT
1 TAATATATATTTTGTAAATAAAATT
52119 TAATATATTTTTATTTTGTAAATAAAATT
1 TAATATA----TATTTTGTAAATAAAATT
52148 TAATATATAT
1 TAATATATAT
52158 ATATCCAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
24 4 0.12
25 5 0.15
29 24 0.73
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (25 bp):
TAATATATATTTTGTAAATAAAATT
Done.