Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003134.1 Hibiscus syriacus cultivar Beakdansim tig00006573_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: 84300
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:8170 original size:22 final size:21
Alignment explanation
Indices: 8124--8184 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
8114 TTTTGGTACA
*
8124 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
8144 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
*
8165 GAAGGGAACCGATTTCCCCC
1 G-AGGGAACCGATTCCCCCC
8185 ACAAGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 16 0.46
ACGTcount: A:0.21, C:0.34, G:0.25, T:0.20
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:8204 original size:21 final size:21
Alignment explanation
Indices: 8166--8205 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
8156 TCCCCCTTTG
**
8166 AAGGGAACCGATTTCCCCCAC
1 AAGGGAACCGATACCCCCCAC
*
8187 AAGGGAATCGATACCCCCC
1 AAGGGAACCGATACCCCCC
8206 TGGGGTTCTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.38, G:0.20, T:0.12
Consensus pattern (21 bp):
AAGGGAACCGATACCCCCCAC
Found at i:12753 original size:49 final size:51
Alignment explanation
Indices: 12693--12800 Score: 123
Period size: 50 Copynumber: 2.1 Consensus size: 51
12683 ATTAAAAAAC
* * * *
12693 ACTATATATACTATCTTC-ATAACTTTATATTATTTTCAAGACTATATA-AT
1 ACTATTTATACTATCTTCAAAAACTATATA-TATTTTCAAAACTATATATAT
* *
12743 AC-ATTTATACTATTTTCAAAAAACTATATATATTTTGAAAACTATATATAT
1 ACTATTTATACTATCTTC-AAAAACTATATATATTTTCAAAACTATATATAT
12794 ACTATTT
1 ACTATTT
12801 TAAAAAGCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
49 13 0.27
50 18 0.38
51 13 0.27
52 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (51 bp):
ACTATTTATACTATCTTCAAAAACTATATATATTTTCAAAACTATATATAT
Found at i:12812 original size:20 final size:21
Alignment explanation
Indices: 12748--12813 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 21
12738 ATAATACATT
12748 TATACTATTTTCAAAAAACTA
1 TATACTATTTTCAAAAAACTA
*
12769 TATA-TATTTTGAAAACTATA-TA
1 TATACTATTTTCAAAA--A-ACTA
*
12791 TATACTATTTT-AAAAAGCTA
1 TATACTATTTTCAAAAAACTA
12811 TAT
1 TAT
12814 CTTATATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
20 16 0.42
21 4 0.11
22 11 0.29
23 7 0.18
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (21 bp):
TATACTATTTTCAAAAAACTA
Found at i:12821 original size:22 final size:22
Alignment explanation
Indices: 12767--12822 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
12757 TTCAAAAAAC
*
12767 TATATATATTTTGAAAACTATA
1 TATATATATTTTAAAAACTATA
12789 TATATACTATTTTAAAAAGCTATA
1 TATATA-TATTTTAAAAA-CTATA
*
12813 TCT-TATATTT
1 TATATATATTT
12823 ATGTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 11 0.37
23 12 0.40
24 7 0.23
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (22 bp):
TATATATATTTTAAAAACTATA
Found at i:12849 original size:17 final size:16
Alignment explanation
Indices: 12827--12892 Score: 57
Period size: 17 Copynumber: 4.2 Consensus size: 16
12817 ATATTTATGT
*
12827 TATTTTCAACAATTATA
1 TATTTTCAA-AACTATA
12844 TATTTTCAAAACTATA
1 TATTTTCAAAACTATA
* * *
12860 TA-TAT--ATATTATA
1 TATTTTCAAAACTATA
12873 TTATTTTCAAAACTATA
1 -TATTTTCAAAACTATA
12890 TAT
1 TAT
12893 ATTTTATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
13 6 0.16
14 2 0.05
15 4 0.11
16 11 0.29
17 15 0.39
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTTCAAAACTATA
Found at i:12859 original size:47 final size:49
Alignment explanation
Indices: 12789--12898 Score: 138
Period size: 48 Copynumber: 2.3 Consensus size: 49
12779 GAAAACTATA
* *
12789 TATATACTATTTTAAAAAGCTATATCT-TATATTTATGTTATTTTCAACAA-
1 TATATA-TATTTTAAAAAGCTATATATATATA-TTATATTATTTTCAA-AAC
*
12839 T-TATATATTTTCAAAA-CTATATATATATATTATATTATTTTCAAAAC
1 TATATATATTTTAAAAAGCTATATATATATATTATATTATTTTCAAAAC
12886 TATATATATTTTA
1 TATATATATTTTA
12899 TTTATGACTC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
46 2 0.04
47 22 0.42
48 24 0.45
49 4 0.08
50 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (49 bp):
TATATATATTTTAAAAAGCTATATATATATATTATATTATTTTCAAAAC
Found at i:12880 original size:30 final size:29
Alignment explanation
Indices: 12838--12894 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 29
12828 ATTTTCAACA
12838 ATTATATATTTTCAAAACTATATATATAT
1 ATTATATATTTTCAAAACTATATATATAT
12867 ATTATATTATTTTCAAAACTATATATAT
1 ATTATA-TATTTTCAAAACTATATATAT
12895 TTTATTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTATATATTTTCAAAACTATATATATAT
Found at i:12892 original size:26 final size:27
Alignment explanation
Indices: 12838--12900 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 27
12828 ATTTTCAACA
12838 ATTATA-TATTTTCAAAACTATATATATAT
1 ATTATATTATTTTCAAAAC---ATATATAT
12867 ATTATATTATTTTCAAAAC-TATATAT
1 ATTATATTATTTTCAAAACATATATAT
*
12893 ATTTTATT
1 ATTATATT
12901 TATGACTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 14 0.44
29 6 0.19
30 12 0.38
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTATATTATTTTCAAAACATATATAT
Found at i:13271 original size:24 final size:26
Alignment explanation
Indices: 13243--13296 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
13233 ATTTAAAAGA
*
13243 TTTAATGATTTACA-AAT-TTTATT-T
1 TTTAATAATTTA-ATAATATTTATTAT
13267 TTTAATAATTTAATAATATTTATTAT
1 TTTAATAATTTAATAATATTTATTAT
13293 TTTA
1 TTTA
13297 TAACTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 1 0.04
24 14 0.54
25 6 0.23
26 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (26 bp):
TTTAATAATTTAATAATATTTATTAT
Found at i:13354 original size:10 final size:9
Alignment explanation
Indices: 13340--13394 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
13330 ATAGTGCTTT
13340 TATTTTTAA
1 TATTTTTAA
13349 TTATTTTTAA
1 -TATTTTTAA
13359 TATTTATT-A
1 TATTT-TTAA
*
13368 T-TTTTGAA
1 TATTTTTAA
13376 TA-TTTTAA
1 TATTTTTAA
*
13384 TATTTTAAA
1 TATTTTTAA
13393 TA
1 TA
13395 ATTTCATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
7 1 0.03
8 12 0.32
9 14 0.37
10 11 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
TATTTTTAA
Found at i:13364 original size:17 final size:18
Alignment explanation
Indices: 13343--13394 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
13333 GTGCTTTTAT
13343 TTTTAATTATTTTTAATA
1 TTTTAATTATTTTTAATA
13361 -TTT-ATTATTTTTGAATA
1 TTTTAATTATTTTT-AATA
*
13378 TTTTAA-TATTTTAAATA
1 TTTTAATTATTTTTAATA
13395 ATTTCATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.30
17 11 0.37
18 9 0.30
19 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTAATTATTTTTAATA
Found at i:13390 original size:26 final size:26
Alignment explanation
Indices: 13339--13388 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
13329 AATAGTGCTT
13339 TTATTTTTAATTATTTTTAATATTTA
1 TTATTTTTAATTATTTTTAATATTTA
13365 TTATTTTTGAA-TA-TTTTAATATTT
1 TTATTTTT-AATTATTTTTAATATTT
13389 TAAATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.48
26 10 0.43
27 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTATTTTTAATTATTTTTAATATTTA
Found at i:14972 original size:3 final size:3
Alignment explanation
Indices: 14964--15013 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
14954 AAAAAGAGAA
14964 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
15012 AA
1 AA
15014 ACAATCGCTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19221 original size:5 final size:5
Alignment explanation
Indices: 19211--19240 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
19201 CGTTATTTTA
*
19211 AAATT AAATT AATTT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT AAATT
19241 TTTCTCGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AAATT
Found at i:26976 original size:2 final size:2
Alignment explanation
Indices: 26969--27004 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
26959 ATTAGCTTTA
26969 AT 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 AT
27005 TCTACTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35218 original size:16 final size:16
Alignment explanation
Indices: 35201--35231 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35191 TTGTTTATAT
35201 TTTAAAT-TTAAATAA
1 TTTAAATATTAAATAA
35216 TTTAAATATTAAATAA
1 TTTAAATATTAAATAA
35232 GTCATCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAATATTAAATAA
Found at i:35746 original size:2 final size:2
Alignment explanation
Indices: 35741--35770 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35731 ACACACAAAA
35741 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
35771 TCATTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37099 original size:22 final size:22
Alignment explanation
Indices: 37071--37131 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
37061 AGCGTTCTTC
*
37071 TTAAAATTATTATATATATTTT
1 TTAAAATTATTATATATACTTT
*
37093 TTAAAATTACTT-T-TAAACTTT
1 TTAAAATTA-TTATATATACTTT
37114 TTAAAATT-TTATAATATA
1 TTAAAATTATTAT-ATATA
37132 AAATTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 14 0.44
22 13 0.41
23 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAAATTATTATATATACTTT
Found at i:37406 original size:46 final size:42
Alignment explanation
Indices: 37353--37456 Score: 111
Period size: 46 Copynumber: 2.4 Consensus size: 42
37343 GTTAATTACA
*
37353 AATATATTTGTATTTTAAAT-TGTTTTCAATTTTTTTCATTGAACAT
1 AATATATTTGTATTTTAAATCT-TTTT-AA--TTCTTCATT-AACAT
** *
37399 AATATATTAATATTTTAAATCTTTTTAATTCTTCATTAACTT
1 AATATATTTGTATTTTAAATCTTTTTAATTCTTCATTAACAT
*
37441 AATATATTTGTTTTTT
1 AATATATTTGTATTTT
37457 TTTCACTCAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
42 17 0.34
43 8 0.16
45 2 0.04
46 22 0.44
47 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.58
Consensus pattern (42 bp):
AATATATTTGTATTTTAAATCTTTTTAATTCTTCATTAACAT
Found at i:41200 original size:12 final size:12
Alignment explanation
Indices: 41183--41225 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
41173 AAACGTATTT
41183 ATGAACAGTACC
1 ATGAACAGTACC
41195 ATGAACAGTA--
1 ATGAACAGTACC
*
41205 ATGAACAGTGCC
1 ATGAACAGTACC
*
41217 ATAAACAGT
1 ATGAACAGT
41226 GCTACAGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:41211 original size:22 final size:22
Alignment explanation
Indices: 41183--41225 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
41173 AAACGTATTT
*
41183 ATGAACAGTACCATGAACAGTA
1 ATGAACAGTACCATAAACAGTA
*
41205 ATGAACAGTGCCATAAACAGT
1 ATGAACAGTACCATAAACAGT
41226 GCTACAGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (22 bp):
ATGAACAGTACCATAAACAGTA
Found at i:42147 original size:30 final size:30
Alignment explanation
Indices: 42106--42174 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
42096 TCACATAGTG
*
42106 TATCTCATAGACATATTATTTT-CATAC-TTT
1 TATCACATAGACATA--ATTTTCCATACATTT
42136 TATCACATAGACATAATTTTCCATACATTT
1 TATCACATAGACATAATTTTCCATACATTT
42166 T-TCACATAG
1 TATCACATAG
42175 CTCATATAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 5 0.14
29 13 0.36
30 18 0.50
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.43
Consensus pattern (30 bp):
TATCACATAGACATAATTTTCCATACATTT
Found at i:43781 original size:21 final size:20
Alignment explanation
Indices: 43726--43787 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
43716 TTTTACCCTA
*
43726 ATTCATCTAGTATCGACACT
1 ATTCATCTAGTATCGATACT
* * *
43746 GTTCATCCCAATATCGATACT
1 ATTCAT-CTAGTATCGATACT
43767 ATTCATCATAGTATCGATACT
1 ATTCATC-TAGTATCGATACT
43788 CAAACCCTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 6 0.18
21 27 0.82
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (20 bp):
ATTCATCTAGTATCGATACT
Found at i:54133 original size:159 final size:156
Alignment explanation
Indices: 53933--54345 Score: 537
Period size: 159 Copynumber: 2.6 Consensus size: 156
53923 GTAAAAAGTA
* * * * *
53933 AGAATTGAAATTACATAAGTATTCTATTG-TAGTATATGAGCATGTGGTTCAAATTTGGTAAAAG
1 AGAATTAAAAGTACATATGTATTCTA-CGATAGTTTATGAGCATGTGGTTCAAATTTGGTAAAAG
* * *
53997 AAAAACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAAATATGAAAGATTAAGGGACAAAATT
65 AAGAACTTAAAATAAAGGATGAATTGAAGAAATAAAGAAAATATGAAAAATTAA-GGACAAAATT
54062 GAAAAATAAAAAAATTGTTA-CCAAAAAG
129 GAAAAATAAAAAAATTGTTATCC-AAAAG
54090 AGAAATTAAAAAGTACATATGTATTCTACGAT-GATTTATGAGCATGTGGTTCAAATTTGGTAAA
1 AG-AATT-AAAAGTACATATGTATTCTACGATAG-TTTATGAGCATGTGGTTCAAATTTGGTAAA
* * * * *
54154 AGACGGACTTAAAATAAATGATAAATTGAAGAAATAAAGAAAATATGAAAAATTAAGGACTAAAT
63 AGAAGAACTTAAAATAAAGGATGAATTGAAGAAATAAAGAAAATATGAAAAATTAAGGACAAAAT
* *
54219 TGAAAAATAAAAAATTTGTTATTCAAAAG
128 TGAAAAATAAAAAAATTGTTATCCAAAAG
* * * * *
54248 AGGATTTAATGTACATATGTATTCTACGATAGTTTATGAGGATGTGGTTCAAATTTAGTAAAA-A
1 AGAATTAAAAGTACATATGTATTCTACGATAGTTTATGAGCATGTGGTTCAAATTTGGTAAAAGA
* *
54312 ATGAACTTAAAATAAAGGAGGAATTGAAGGAATA
66 A-GAACTTAAAATAAAGGATGAATTGAAGAAATA
54346 TTGAAATTAT
Statistics
Matches: 223, Mismatches: 26, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
155 1 0.00
156 78 0.35
157 6 0.03
158 41 0.18
159 97 0.43
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.28
Consensus pattern (156 bp):
AGAATTAAAAGTACATATGTATTCTACGATAGTTTATGAGCATGTGGTTCAAATTTGGTAAAAGA
AGAACTTAAAATAAAGGATGAATTGAAGAAATAAAGAAAATATGAAAAATTAAGGACAAAATTGA
AAAATAAAAAAATTGTTATCCAAAAG
Found at i:54190 original size:20 final size:18
Alignment explanation
Indices: 54164--54229 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 18
54154 AGACGGACTT
54164 AAAATAAATGATAAATTGA
1 AAAATAAA-GATAAATTGA
54183 AGAAATAAAGA-AAATATGA
1 A-AAATAAAGATAAAT-TGA
*
54202 AAAATTAAGGACTAAATTGA
1 AAAA-TAAAGA-TAAATTGA
54222 AAAATAAA
1 AAAATAAA
54230 AAATTTGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
18 7 0.17
19 15 0.38
20 14 0.35
21 4 0.10
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.21
Consensus pattern (18 bp):
AAAATAAAGATAAATTGA
Found at i:57032 original size:27 final size:27
Alignment explanation
Indices: 56999--57058 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
56989 AATATTACTT
* *
56999 TAAAAAAGAAAAATAAAGTTTGATTAAC
1 TAAAAAA-ATAAATAAAGTTTCATTAAC
** *
57027 TAAAAAAATAAATGGATTTTCATTAAC
1 TAAAAAAATAAATAAAGTTTCATTAAC
57054 TAAAA
1 TAAAA
57059 CAATTACAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.28
Consensus pattern (27 bp):
TAAAAAAATAAATAAAGTTTCATTAAC
Found at i:59815 original size:21 final size:21
Alignment explanation
Indices: 59791--59832 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
59781 TGTATTTTTT
59791 TTAGAAAAAATGATCGATCCC
1 TTAGAAAAAATGATCGATCCC
* *
59812 TTAGGAGAAATGATCGATCCC
1 TTAGAAAAAATGATCGATCCC
59833 AAAGTTTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
TTAGAAAAAATGATCGATCCC
Found at i:66615 original size:2 final size:2
Alignment explanation
Indices: 66608--66637 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
66598 CGGTTTGTGA
66608 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
66638 GTATTCTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69461 original size:27 final size:27
Alignment explanation
Indices: 69420--69474 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
69410 ACATGCTCTA
*
69420 ATAGCATCGAAACTGTATAACGTCCAC
1 ATAGCATCGAAACTGTACAACGTCCAC
** *
69447 ATAGCATCGTCACTGTACGACGTCCAC
1 ATAGCATCGAAACTGTACAACGTCCAC
69474 A
1 A
69475 CGAACTACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (27 bp):
ATAGCATCGAAACTGTACAACGTCCAC
Found at i:70126 original size:26 final size:26
Alignment explanation
Indices: 70082--70131 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
70072 TTTATCGTCA
70082 AAAAATTACAATAACATAAACTAAACC
1 AAAAATTACAATAACATAAA-TAAACC
**
70109 AAAAATTA-AATATTATAAATAAA
1 AAAAATTACAATAACATAAATAAA
70132 TAAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 9 0.43
27 8 0.38
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (26 bp):
AAAAATTACAATAACATAAATAAACC
Found at i:70142 original size:14 final size:15
Alignment explanation
Indices: 70120--70149 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
70110 AAAATTAAAT
70120 ATTATAAATAAATAA
1 ATTATAAATAAATAA
70135 ATTA-AAATAAATAA
1 ATTATAAATAAATAA
70149 A
1 A
70150 CATGGATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTATAAATAAATAA
Found at i:70635 original size:18 final size:17
Alignment explanation
Indices: 70611--70680 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 17
70601 AAGTTCAAAA
70611 TAAATAAATAAATTATT
1 TAAATAAATAAATTATT
70628 TGAAATAAATTAAAAATTATT
1 T-AAATAAA-T--AAATTATT
* *
70649 CAAAATAAATAAATAATT
1 -TAAATAAATAAATTATT
*
70667 TAGAGTAAATAAAT
1 TA-AATAAATAAAT
70681 AAATAAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
17 2 0.05
18 24 0.56
19 1 0.02
20 1 0.02
21 15 0.35
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (17 bp):
TAAATAAATAAATTATT
Found at i:70636 original size:22 final size:22
Alignment explanation
Indices: 70589--70687 Score: 101
Period size: 22 Copynumber: 4.5 Consensus size: 22
70579 ATATCACTTC
*
70589 AAATAAATAAATAAGTTCAAAAT
1 AAATAAATAAATTA-TTCAAAAT
**
70612 AAATAAATAAATTATTTGAAAT
1 AAATAAATAAATTATTCAAAAT
*
70634 AAATTAA-AAATTATTCAAAAT
1 AAATAAATAAATTATTCAAAAT
* ****
70655 AAATAAATAATTTAGAGTAAAT
1 AAATAAATAAATTATTCAAAAT
70677 AAATAAATAAA
1 AAATAAATAAA
70688 AATCACCTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
21 18 0.29
22 31 0.50
23 13 0.21
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AAATAAATAAATTATTCAAAAT
Found at i:70646 original size:21 final size:21
Alignment explanation
Indices: 70604--70666 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
70594 AATAAATAAG
*
70604 TTCAAAATAAATAAATAAATTA
1 TTCAAAATAAATTAA-AAATTA
**
70626 TTTGAAATAAATTAAAAATTA
1 TTCAAAATAAATTAAAAATTA
70647 TTCAAAATAAA-TAAATAATT
1 TTCAAAATAAATTAAA-AATT
70667 TAGAGTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 4 0.11
21 19 0.54
22 12 0.34
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (21 bp):
TTCAAAATAAATTAAAAATTA
Found at i:75812 original size:132 final size:135
Alignment explanation
Indices: 75505--75832 Score: 373
Period size: 132 Copynumber: 2.4 Consensus size: 135
75495 TACATCAATA
* * *
75505 TTTAATTTAGTCCTCACCTTTGCTTGAGGTTCTAAATTAATTATTCT-ATTCAATAAATTGTTAA
1 TTTAATTTAGTCCTCGCCTTTGCTAGAGGTTCCAAATTAATTATT-TGATTCAATAAATTGTTAA
*
75569 AAACCGTTAGGTTTTAATATTACAACCTACATTTTAGGTTTAACTTCACCTCAGTCTCTCAATTT
65 AAACCGTTAGGTTTTAATATTACAACC-AC--TTTAAGTTTAACTTCACCTCAGTCTCTCAATTT
* *
75634 AGGTGGATT
127 AGGAGAATT
* *
75643 TTTAATTTAGTCGTCGACTTTGCTAGAGGTTCCAAATTAATTATTTGATTCAATAAATTGTT-AA
1 TTTAATTTAGTCCTCGCCTTTGCTAGAGGTTCCAAATTAATTATTTGATTCAATAAATTGTTAAA
** * * *
75707 AATTGATTAGGTTTTAATATTATC-A-C-C-TTAAGTTTAATTTCACCTTAGTC-CATTAATTTA
66 AACCG-TTAGGTTTTAATATTA-CAACCACTTTAAGTTTAACTTCACCTCAGTCTC-TCAATTTA
75767 GGAGAATT
128 GGAGAATT
* * * * * *
75775 TTTAATTTGGTCCTTGCCTTTGCTCGAGATTCCAAATTAATTATTCGATTCAACAAAT
1 TTTAATTTAGTCCTCGCCTTTGCTAGAGGTTCCAAATTAATTATTTGATTCAATAAAT
75833 GGCTAGGTTT
Statistics
Matches: 165, Mismatches: 21, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
131 1 0.01
132 83 0.50
135 1 0.01
137 7 0.04
138 72 0.44
139 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (135 bp):
TTTAATTTAGTCCTCGCCTTTGCTAGAGGTTCCAAATTAATTATTTGATTCAATAAATTGTTAAA
AACCGTTAGGTTTTAATATTACAACCACTTTAAGTTTAACTTCACCTCAGTCTCTCAATTTAGGA
GAATT
Found at i:77270 original size:27 final size:27
Alignment explanation
Indices: 77195--77261 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
77185 TTTTTTTTTG
* *
77195 CCCATTAGGCCATGCGAAAAATGTTAG
1 CCCATTAGGTCATGCGAAAAATGTTAA
77222 CCCATTAGGTCATGCGAAAAATGTTAA
1 CCCATTAGGTCATGCGAAAAATGTTAA
77249 CCCATTAGGTCAT
1 CCCATTAGGTCAT
77262 ATCTAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (27 bp):
CCCATTAGGTCATGCGAAAAATGTTAA
Found at i:79025 original size:44 final size:44
Alignment explanation
Indices: 78973--79062 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 44
78963 ATATATATAT
78973 ATACAGACGACACTAAAAACACGTGTCACCAAAATATAACAGAG
1 ATACAGACGACACTAAAAACACGTGTCACCAAAATATAACAGAG
* * *
79017 ATACAGACGATAGTAAAAACACGTGTCACTAAAATATAACAGAG
1 ATACAGACGACACTAAAAACACGTGTCACCAAAATATAACAGAG
79061 AT
1 AT
79063 GGGCGAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.17
Consensus pattern (44 bp):
ATACAGACGACACTAAAAACACGTGTCACCAAAATATAACAGAG
Found at i:80966 original size:32 final size:32
Alignment explanation
Indices: 80930--81002 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
80920 ATAAGAGATG
80930 AAATTTAAGCATGTTTCAGTTTTATTTACAAT
1 AAATTTAAGCATGTTTCAGTTTTATTTACAAT
80962 AAATTTAAGCATGTTTCAGTTTTATTTACAAT
1 AAATTTAAGCATGTTTCAGTTTTATTTACAAT
80994 AAATTTAAG
1 AAATTTAAG
81003 GATTACGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (32 bp):
AAATTTAAGCATGTTTCAGTTTTATTTACAAT
Done.