Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001803.1 Hibiscus syriacus cultivar Beakdansim tig00003645_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: 54845
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:11803 original size:23 final size:23
Alignment explanation
Indices: 11763--11860 Score: 69
Period size: 22 Copynumber: 4.2 Consensus size: 23
11753 GAAAGAAAAG
11763 AAAAAATAATAAGTAAAATAAATATA
1 AAAAAAT-ATAAGTAAAA-AAA-ATA
*
11789 AAAAAATA-AAG-AAAAAGAATAA
1 AAAAAATATAAGTAAAAAAAAT-A
* * *
11811 AAAAATATATAAATAAAACAAGTA
1 AAAAA-ATATAAGTAAAAAAAATA
*
11835 AATAAA-ATAA-TAAAAAAAAGTA
1 AAAAAATATAAGTAAAAAAAA-TA
11857 AAAA
1 AAAA
11861 TATTATATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
21 9 0.16
22 17 0.29
23 8 0.14
24 10 0.17
25 7 0.12
26 7 0.12
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.17
Consensus pattern (23 bp):
AAAAAATATAAGTAAAAAAAATA
Found at i:11862 original size:37 final size:36
Alignment explanation
Indices: 11759--11862 Score: 102
Period size: 37 Copynumber: 2.8 Consensus size: 36
11749 TAAAGAAAGA
** *
11759 AAAGAAAAAATAATAAGTAAAATAAATATAAAAAAAT
1 AAAG-AAAAATAATAAAAAAAATAAAAATAAAAAAAT
* * *
11796 AAAGAAAAAGAATAAAAAAATATATAAATAAAACAAGT
1 AAAGAAAAATAATAAAAAAA-ATAAAAATAAAA-AAAT
*
11834 AAA-TAAAATAATAAAAAAAAGTAAAAATA
1 AAAGAAAAATAATAAAAAAAA-TAAAAATA
11863 TTATATATAT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
36 14 0.25
37 35 0.64
38 6 0.11
ACGTcount: A:0.76, C:0.01, G:0.06, T:0.17
Consensus pattern (36 bp):
AAAGAAAAATAATAAAAAAAATAAAAATAAAAAAAT
Found at i:12993 original size:39 final size:36
Alignment explanation
Indices: 12935--13029 Score: 129
Period size: 39 Copynumber: 2.6 Consensus size: 36
12925 AACTCGAGGG
*
12935 TTTG-GTGTTTCAAGAGAAACATTTTCAAAGGGTTTT
1 TTTGTGTGTTTCAAGAGAAACAATTTC-AAGGGTTTT
*
12971 TGTGTGTGTGTTTCAAGAGAAACAATTTCGAGGGTTTT
1 T-T-TGTGTGTTTCAAGAGAAACAATTTCAAGGGTTTT
*
13009 TTTTTGTGTTTCAAGAGAAAC
1 TTTGTGTGTTTCAAGAGAAAC
13030 TGTCTCAAGA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
36 19 0.36
37 2 0.04
38 11 0.21
39 21 0.40
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.41
Consensus pattern (36 bp):
TTTGTGTGTTTCAAGAGAAACAATTTCAAGGGTTTT
Found at i:13056 original size:36 final size:36
Alignment explanation
Indices: 13016--13131 Score: 146
Period size: 36 Copynumber: 3.2 Consensus size: 36
13006 TTTTTTTTGT
* * *
13016 GTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATTG
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
*
13052 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACATA
1 GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TTA
*
13089 G-TTCTAAAAGAAACTGTCTCAATG-GAGACAAAATTT
1 GTTTC-AAAAGAAACTGTCTCAA-GAGAGACAAAATTA
13125 GTTTCAA
1 GTTTCAA
13132 GGAAAATATA
Statistics
Matches: 70, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
36 38 0.54
37 31 0.44
38 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (36 bp):
GTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTA
Found at i:13237 original size:37 final size:37
Alignment explanation
Indices: 13146--13244 Score: 128
Period size: 36 Copynumber: 2.7 Consensus size: 37
13136 AATATATTCA
* **
13146 AAGATTTTATTTCAAGGGAAACTGTCTCAAGAAAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCAAAAGAAAGAC
* * *
13183 AA-AATTTGTTTCAAGGGAAATTGTCAAAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCAAAAGAAAGAC
*
13219 AAGATTTTGTTACAAGGGAAACTGTC
1 AAGATTTTGTTTCAAGGGAAACTGTC
13245 TCAAAACTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 30 0.58
37 22 0.42
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.27
Consensus pattern (37 bp):
AAGATTTTGTTTCAAGGGAAACTGTCAAAAGAAAGAC
Found at i:13399 original size:36 final size:37
Alignment explanation
Indices: 13323--13399 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
13313 TGTTTGAAGA
* * * ** *
13323 GAAACTATCTCGAGGGAGACAAAACTTTGTTTCAAGG
1 GAAACTATCTCAAGAGAGACAAAAATTAATTTCAAAG
13360 GAAACTATCTCAAGAGAGA-AAAAATTAATTTCAAAG
1 GAAACTATCTCAAGAGAGACAAAAATTAATTTCAAAG
13396 GAAA
1 GAAA
13400 TGTTTTCAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 17 0.50
37 17 0.50
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.22
Consensus pattern (37 bp):
GAAACTATCTCAAGAGAGACAAAAATTAATTTCAAAG
Found at i:13414 original size:102 final size:101
Alignment explanation
Indices: 13290--13633 Score: 429
Period size: 102 Copynumber: 3.3 Consensus size: 101
13280 TTTGTGTTTT
* ** * *
13290 AAGGGAAACGTTTTCAGGGTTTATGTTTGAAGAGAAACTATCTCGAGGGAGACAAAACTTTGTTT
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-TTTGTTT
* *
13355 CAAGGGAAACTATCTCAAGAGAGAAAAAATTAATTTC
65 CAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTC
*
13392 AAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTT
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAA-TTTGTTT
* * *
13457 CAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTC
65 CAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTC
* * * *
13494 AAGGGAAATG-TTTCAATGTTTACGTTTCAAGGGAGACAAAATTTCGTTTCAAGGAAGACAAAAT
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAA--GAG--AAACTATC---TCAAGGGAGACAAAAT
* * *
13558 TTCGTTTCAAGGGAAACTATCTTAATCGAGATAAAATTCATTTC
59 TT-GTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTC
13602 AAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 AAGGGAAATGTTTTCAATGTTTATGTTTCAAG
13634 GGAGACCAAA
Statistics
Matches: 210, Mismatches: 23, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
101 19 0.09
102 99 0.47
103 3 0.01
105 6 0.03
107 4 0.02
108 60 0.29
109 19 0.09
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
AAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTGTTTC
AAGGGAAACTATCTCAAGCGAGATAAAATTAATTTC
Found at i:13466 original size:37 final size:36
Alignment explanation
Indices: 13415--13501 Score: 111
Period size: 37 Copynumber: 2.4 Consensus size: 36
13405 TCAATGTTTA
* * * *
13415 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAA-TT
*
13452 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAATT
*
13488 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
13502 TGTTTCAATG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 15 0.34
37 29 0.66
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAATT
Found at i:13544 original size:22 final size:22
Alignment explanation
Indices: 13516--13571 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
13506 TCAATGTTTA
13516 CGTTTCAAGGGAGACAAAATTT
1 CGTTTCAAGGGAGACAAAATTT
*
13538 CGTTTCAAGGAAGACAAAATTT
1 CGTTTCAAGGGAGACAAAATTT
13560 CGTTTCAAGGGA
1 CGTTTCAAGGGA
13572 AACTATCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (22 bp):
CGTTTCAAGGGAGACAAAATTT
Found at i:13570 original size:108 final size:108
Alignment explanation
Indices: 13339--13656 Score: 418
Period size: 108 Copynumber: 3.0 Consensus size: 108
13329 ATCTCGAGGG
* * *
13339 AGACAAAACTTTGTTTCAAGGGAAACTATCTCAAGAGAGAAAAAATTAATTTCAAAGGAAATGTT
1 AGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTCAAGGGAAATGTT
* * *
13404 TTCAATGTTTATGTTTCAA--GAG--AAACTATC---TCAAGGG
65 TTCAATGTTTATGTTTCAAGGGAGACAAAATTTCGTTTCAAGGA
* * *
13441 AGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGGAAATG-T
1 AGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTCAAGGGAAATGTT
*
13505 TTCAATGTTTACGTTTCAAGGGAGACAAAATTTCGTTTCAAGGA
65 TTCAATGTTTATGTTTCAAGGGAGACAAAATTTCGTTTCAAGGA
* * *
13549 AGACAAAATTTCGTTTCAAGGGAAACTATCTTAATCGAGATAAAATTCATTTCAAGGGAAATGTT
1 AGACAAAATTT-GTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTCAAGGGAAATGTT
* *
13614 TTCAATGTTTATGTTTCAAGGGAGACCAAATTTTGTTTCAAGG
65 TTCAATGTTTATGTTTCAAGGGAGACAAAATTTCGTTTCAAGG
13657 GAAACTATCT
Statistics
Matches: 188, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
101 19 0.10
102 56 0.30
103 3 0.02
105 6 0.03
107 3 0.02
108 60 0.32
109 41 0.22
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (108 bp):
AGACAAAATTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATTAATTTCAAGGGAAATGTTT
TCAATGTTTATGTTTCAAGGGAGACAAAATTTCGTTTCAAGGA
Found at i:13685 original size:87 final size:87
Alignment explanation
Indices: 13539--13720 Score: 319
Period size: 87 Copynumber: 2.1 Consensus size: 87
13529 ACAAAATTTC
*
13539 GTTTCAAGGAAGACAAAATTTCGTTTCAAGGGAAACTATCTTAATCGAGATAAAATTCATTTCAA
1 GTTTCAAGGAAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAA
13604 GGGAAATGTTTTCAATGTTTAT
66 GGGAAATGTTTTCAATGTTTAT
* * *
13626 GTTTCAAGGGAGACCAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAA
1 GTTTCAAGGAAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAA
*
13691 GGGAAATGTTTTTAATGTTTAT
66 GGGAAATGTTTTCAATGTTTAT
13713 GTTTCAAG
1 GTTTCAAG
13721 AGAAACTGTC
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 90 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (87 bp):
GTTTCAAGGAAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAA
GGGAAATGTTTTCAATGTTTAT
Found at i:14058 original size:93 final size:93
Alignment explanation
Indices: 13943--14128 Score: 309
Period size: 93 Copynumber: 2.0 Consensus size: 93
13933 GTATTGTTCT
13943 GAGTCCAATATCATTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCATTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
** * *
14008 CCAGTCGTCCCTTCGTTGTGAAGTTGAA
66 CCAACCATCCCTTCATTGTGAAGTTGAA
* *
14036 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCATTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
*
14101 CCAACCATCCCTTCATTGTGGAGTTGAA
66 CCAACCATCCCTTCATTGTGAAGTTGAA
14129 CTCGTGTTGT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 86 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (93 bp):
GAGTCCAATATCATTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
CCAACCATCCCTTCATTGTGAAGTTGAA
Found at i:14750 original size:32 final size:32
Alignment explanation
Indices: 14714--14790 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
14704 ATTCCCAAAG
* *
14714 ATGCCCCAATATTCAATATTGAATCTCAAAA-A
1 ATGCCCCAACATTCAATATTAAATCT-AAAATA
** *
14746 ATGCCCCAACATTTGATGTTAAATCTAAAATA
1 ATGCCCCAACATTCAATATTAAATCTAAAATA
14778 ATGCCCCAACATT
1 ATGCCCCAACATT
14791 TGATGTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 4 0.10
32 35 0.90
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (32 bp):
ATGCCCCAACATTCAATATTAAATCTAAAATA
Found at i:14791 original size:32 final size:32
Alignment explanation
Indices: 14735--14802 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
14725 TTCAATATTG
14735 AATCTCAAAAAATGCCCCAACATTTGATGTTA
1 AATCTCAAAAAATGCCCCAACATTTGATGTTA
*
14767 AATCT-AAAATAATGCCCCAACATTTGATGTTG
1 AATCTCAAAA-AATGCCCCAACATTTGATGTTA
14799 AATC
1 AATC
14803 CTCACAAGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 4 0.12
32 30 0.88
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (32 bp):
AATCTCAAAAAATGCCCCAACATTTGATGTTA
Found at i:15295 original size:65 final size:64
Alignment explanation
Indices: 15215--15363 Score: 196
Period size: 65 Copynumber: 2.3 Consensus size: 64
15205 GGGTGGATCG
* * *
15215 ATGCATAAAAAGCATTCGATGTTT-CA-AACAAGCCTGGAGTGCATCGATGCATGGTCTGTGCAT
1 ATGCATAAAATGCATTCAATGTTTCCATAA-AAGCCT-GAGTGCATCGATGCATGG-CAGTGCAT
15278 CA
63 CA
** *
15280 ATGCATAAAATGCATTCAATGTTTCCATAAAATTCTGAGTGCATCGATGCATGGCAGTGCATCG
1 ATGCATAAAATGCATTCAATGTTTCCATAAAAGCCTGAGTGCATCGATGCATGGCAGTGCATCA
15344 ATGCATAAAATGCA-TCAATG
1 ATGCATAAAATGCATTCAATG
15364 AGTGCATCGG
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
63 6 0.08
64 22 0.29
65 40 0.53
66 6 0.08
67 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (64 bp):
ATGCATAAAATGCATTCAATGTTTCCATAAAAGCCTGAGTGCATCGATGCATGGCAGTGCATCA
Found at i:15984 original size:27 final size:27
Alignment explanation
Indices: 15945--16001 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
15935 CTAAATGATG
* *
15945 CAAAAATCTAATAAACCAA-TATAAGTT
1 CAAAAACCAAATAAA-CAATTATAAGTT
* *
15972 CAAAAACCAAATATATAATTATAAGTT
1 CAAAAACCAAATAAACAATTATAAGTT
15999 CAA
1 CAA
16002 GCATTCAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (27 bp):
CAAAAACCAAATAAACAATTATAAGTT
Found at i:18014 original size:23 final size:23
Alignment explanation
Indices: 17984--18062 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
17974 TGCACTGCTA
17984 AGTGCATCGATGCACATTCAAGG
1 AGTGCATCGATGCACATTCAAGG
* * *
18007 AGTGCATCGGTGCACCTTC-ATG
1 AGTGCATCGATGCACATTCAAGG
*
18029 -GTGTATCGATGCACATTCACAGG
1 AGTGCATCGATGCACATTCA-AGG
18052 A-TGCATCGATG
1 AGTGCATCGATG
18063 TACTGGATAG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 28 0.62
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (23 bp):
AGTGCATCGATGCACATTCAAGG
Found at i:23347 original size:65 final size:64
Alignment explanation
Indices: 23277--23452 Score: 212
Period size: 65 Copynumber: 2.7 Consensus size: 64
23267 TGGAACACTT
* * * *
23277 AGTGCATCGGTGCACTACAGGTGGATCGATGCATAAAATGCATTCGATGTTT-CA-AACAAGTCT
1 AGTGCATCGATGCA-TGCAAGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAA-AAGTCT
23340 GG
64 -G
*** * *
23342 AGTGCATCGATGCATGGTTTGTGCATCGATGCATAAAATGCATTTGATGTTTCCATAAAATTCTG
1 AGTGCATCGATGCAT-GCAAGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGTCTG
*
23407 AGTGCATCGATGCATGGAAGTGCATCGATGCATAAAATGCATTCGA
1 AGTGCATCGATGCATGCAAGTGCATCGATGCATAAAATGCATTCGA
23453 AATGGGGTGT
Statistics
Matches: 96, Mismatches: 12, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
64 28 0.29
65 59 0.61
66 7 0.07
67 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATGCAAGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAAGTCTG
Found at i:23452 original size:18 final size:18
Alignment explanation
Indices: 23409--23448 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
23399 AAATTCTGAG
* *
23409 TGCATCGATGCATGGAAG
1 TGCATCGATGCATGAAAA
23427 TGCATCGATGCAT-AAAA
1 TGCATCGATGCATGAAAA
23444 TGCAT
1 TGCAT
23449 TCGAAATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (18 bp):
TGCATCGATGCATGAAAA
Found at i:29646 original size:19 final size:19
Alignment explanation
Indices: 29624--29662 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
29614 TAAAAGGGAA
29624 AATAGTA-AAAATAATAAAT
1 AATAGTAGAAAATAA-AAAT
29643 AATAGTAGTAAAATAAAAAT
1 AATAGTAG-AAAATAAAAAT
29663 GGGTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (19 bp):
AATAGTAGAAAATAAAAAT
Found at i:29725 original size:17 final size:18
Alignment explanation
Indices: 29685--29726 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
29675 GTTGTTTTTA
29685 AAATAAAAGATAAGAATG
1 AAATAAAAGATAAGAATG
* *
29703 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATG
29720 AAATAAA
1 AAATAAA
29727 TAATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (18 bp):
AAATAAAAGATAAGAATG
Found at i:29729 original size:12 final size:13
Alignment explanation
Indices: 29712--29740 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29702 GAAATAAAAG
29712 AAATAA-TTAAAT
1 AAATAATTTAAAT
29724 AAATAATTTAAAT
1 AAATAATTTAAAT
29737 AAAT
1 AAAT
29741 TGAGATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATAATTTAAAT
Found at i:32506 original size:14 final size:13
Alignment explanation
Indices: 32479--32511 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
32469 ATCTGCTAAA
32479 AAAT-AATAAATC
1 AAATAAATAAATC
32491 AAATAAATAGAATC
1 AAATAAATA-AATC
32505 AAATAAA
1 AAATAAA
32512 GTTTGCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 4 0.21
14 11 0.58
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (13 bp):
AAATAAATAAATC
Found at i:46830 original size:20 final size:21
Alignment explanation
Indices: 46784--46836 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 21
46774 GGCTATAATG
*
46784 AATAAA-GATAATAAATGGATT
1 AATAAATGATAAAAAATGGA-T
46805 ATATAAATGATAAAAAATGGA-
1 A-ATAAATGATAAAAAATGGAT
46826 AATAAAT-ATAA
1 AATAAATGATAA
46837 TGAAATGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 6 0.21
21 2 0.07
22 5 0.17
23 12 0.41
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.26
Consensus pattern (21 bp):
AATAAATGATAAAAAATGGAT
Found at i:46842 original size:20 final size:20
Alignment explanation
Indices: 46784--46843 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
46774 GGCTATAATG
*
46784 AATAAAGATAATAAATGGATT
1 AATAAATATAATAAATGGA-T
*
46805 ATATAAATGATAAAAAATGGA-
1 A-ATAAAT-ATAATAAATGGAT
46826 AATAAATATAATGAAATG
1 AATAAATATAAT-AAATG
46844 AATTAAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 4 0.12
20 11 0.33
21 2 0.06
22 5 0.15
23 11 0.33
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (20 bp):
AATAAATATAATAAATGGAT
Found at i:48108 original size:17 final size:18
Alignment explanation
Indices: 48071--48109 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
48061 GGTTTAAAAT
48071 TAAAAGATAAGAATCAAA
1 TAAAAGATAAGAATCAAA
* *
48089 TAAAAGA-AATAATTAAA
1 TAAAAGATAAGAATCAAA
48106 TAAA
1 TAAA
48110 TAATTTAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
TAAAAGATAAGAATCAAA
Found at i:50881 original size:5 final size:5
Alignment explanation
Indices: 50873--50921 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
50863 AAAAGTAAAT
* * *
50873 AAAAC AAAAC AAAAC AAAAT AAAAC AAAAAC AAAAC GAAA- TAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC -AAAAC AAAAC AAAAC AAAAC AAAA
50922 ATAAATGGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
4 3 0.08
5 29 0.78
6 5 0.14
ACGTcount: A:0.80, C:0.14, G:0.02, T:0.04
Consensus pattern (5 bp):
AAAAC
Found at i:50886 original size:20 final size:19
Alignment explanation
Indices: 50858--50921 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
50848 AAGTTTGCTA
*
50858 AAAATAAAAGTAAATAAAAC
1 AAAACAAAAG-AAATAAAAC
*
50878 AAAACAAAACAAAATAAAAC
1 AAAACAAAA-GAAATAAAAC
50898 AAAAACAAAACGAAAT-AAAC
1 -AAAACAAAA-GAAATAAAAC
50918 AAAA
1 AAAA
50922 ATAAATGGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.10
20 21 0.54
21 14 0.36
ACGTcount: A:0.78, C:0.11, G:0.03, T:0.08
Consensus pattern (19 bp):
AAAACAAAAGAAATAAAAC
Found at i:50922 original size:20 final size:20
Alignment explanation
Indices: 50869--50922 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
50859 AAATAAAAGT
50869 AAATAAA-ACAAAACAAAACA
1 AAATAAACA-AAAACAAAACA
*
50889 AAATAAAACAAAAACAAAACG
1 AAAT-AAACAAAAACAAAACA
50910 AAATAAACAAAAA
1 AAATAAACAAAAA
50923 TAAATGGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 13 0.42
21 17 0.55
22 1 0.03
ACGTcount: A:0.80, C:0.13, G:0.02, T:0.06
Consensus pattern (20 bp):
AAATAAACAAAAACAAAACA
Done.