Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004478.1 Hibiscus syriacus cultivar Beakdansim tig00009871_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: 70678
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:14889 original size:2 final size:2
Alignment explanation
Indices: 14884--14910 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14874 ACACGCATAC
14884 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
14911 CCGACAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20104 original size:30 final size:31
Alignment explanation
Indices: 20063--20123 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
20053 ATGAGTGAAC
*
20063 ACATCAGTGATTAAAATGTAAT-AATCAATA
1 ACATAAGTGATTAAAATGTAATAAATCAATA
* *
20093 ACATAAGTGATTAAATTTTAATAAATCAATA
1 ACATAAGTGATTAAAATGTAATAAATCAATA
20124 GTGTAAGTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 19 0.70
31 8 0.30
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (31 bp):
ACATAAGTGATTAAAATGTAATAAATCAATA
Found at i:20895 original size:31 final size:31
Alignment explanation
Indices: 20857--20917 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
20847 TTATACGGCG
20857 TAGAATAGTCGTGCTCAACCCCAAATTGGCA
1 TAGAATAGTCGTGCTCAACCCCAAATTGGCA
* *
20888 TAGAATAGTCGTGCTCAACCTCGAATTGGC
1 TAGAATAGTCGTGCTCAACCCCAAATTGGC
20918 GAATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (31 bp):
TAGAATAGTCGTGCTCAACCCCAAATTGGCA
Found at i:22857 original size:60 final size:59
Alignment explanation
Indices: 22758--22884 Score: 245
Period size: 60 Copynumber: 2.1 Consensus size: 59
22748 TTTAAGCGAC
22758 TTACACAAATTTGGGATATTTTCACCAATTTCATTCTATGTAAATGTACAAAGGGTAAA
1 TTACACAAATTTGGGATATTTTCACCAATTTCATTCTATGTAAATGTACAAAGGGTAAA
22817 TTACACAAATTTGGGATATTTTTCACCAATTTCATTCTATGTAAATGTACAAAGGGTAAA
1 TTACACAAATTTGGGATA-TTTTCACCAATTTCATTCTATGTAAATGTACAAAGGGTAAA
22877 TTACACAA
1 TTACACAA
22885 TTAATCATTC
Statistics
Matches: 67, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
59 18 0.27
60 49 0.73
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (59 bp):
TTACACAAATTTGGGATATTTTCACCAATTTCATTCTATGTAAATGTACAAAGGGTAAA
Found at i:23670 original size:153 final size:153
Alignment explanation
Indices: 23392--23706 Score: 533
Period size: 153 Copynumber: 2.1 Consensus size: 153
23382 CCAAGCATTG
* * * * * * *
23392 AATTTGTGTACTAAAAAAATCAATATCGTGCTTGCATAATTTCTAATTGAAGTTGTTGTCCAAAA
1 AATTTGTGTACTAAAAAAACCAACACCGTGCTTACATAATTTCTAAATGAAATTATTGTCCAAAA
23457 CAGTATAGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGGGGGTCATAACTCCC
66 CAGTATAGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGGGGGTCATAACTCCC
23522 ACCTAAACCCAATTTCAATTAGA
131 ACCTAAACCCAATTTCAATTAGA
23545 AATTTGTGTACTAAAAAAACCAACACCGTGCTTACATAATTTCTAAATGAAATTATTGTCCAAAA
1 AATTTGTGTACTAAAAAAACCAACACCGTGCTTACATAATTTCTAAATGAAATTATTGTCCAAAA
*
23610 TAGT-TCAGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGGGGGTCATAACTCC
66 CAGTAT-AGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGGGGGTCATAACTCC
23674 CACCTAAACCCAATTTCAATTAGA
130 CACCTAAACCCAATTTCAATTAGA
23698 AATTATGTG
1 AATT-TGTG
23707 AACATTATGT
Statistics
Matches: 152, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
152 1 0.01
153 147 0.97
154 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (153 bp):
AATTTGTGTACTAAAAAAACCAACACCGTGCTTACATAATTTCTAAATGAAATTATTGTCCAAAA
CAGTATAGTTGCATTTAATTAATTTATTTTTATTATACCCTAAATTAGTGGGGGTCATAACTCCC
ACCTAAACCCAATTTCAATTAGA
Found at i:24658 original size:55 final size:56
Alignment explanation
Indices: 24578--24692 Score: 187
Period size: 55 Copynumber: 2.1 Consensus size: 56
24568 GATGAGCATT
* *
24578 ATTAATTTAATTTATAAAAAATTAAAATTCTAAAAGA-CTCAACGTATAATTATAA
1 ATTAATTTAATTTATAAAAAATTAAAATTCTAAAAAAGCCCAACGTATAATTATAA
* *
24633 ATTAATTTAATTTATAAAAATTTAAAATTTTAAAAAAGCCCAACGTATAATTATAA
1 ATTAATTTAATTTATAAAAAATTAAAATTCTAAAAAAGCCCAACGTATAATTATAA
24689 ATTA
1 ATTA
24693 GTATGATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
55 34 0.62
56 21 0.38
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.37
Consensus pattern (56 bp):
ATTAATTTAATTTATAAAAAATTAAAATTCTAAAAAAGCCCAACGTATAATTATAA
Found at i:24889 original size:23 final size:24
Alignment explanation
Indices: 24859--24917 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
24849 ATTTCAAATG
24859 TAGTTTTTTTAAA-TATATAATATA
1 TAGTTTTTTTAAACT-TATAATATA
**
24883 TA-TTTTTGAAAACTTATAATATA
1 TAGTTTTTTTAAACTTATAATATA
24906 TAGTTTTTTTAA
1 TAGTTTTTTTAA
24918 TATTTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (24 bp):
TAGTTTTTTTAAACTTATAATATA
Found at i:24957 original size:37 final size:36
Alignment explanation
Indices: 24882--25091 Score: 217
Period size: 38 Copynumber: 5.7 Consensus size: 36
24872 TATATAATAT
* **
24882 ATATTTTTGAAAACTTATAATATATAGTTTTT-TTA
1 ATATTTTTGAAAACGTATAATATATAGTTTTTAAAA
*
24917 ATATTTTTGAAAATGTATAATATATAGCTTTTTAAAA
1 ATATTTTTGAAAACGTATAATATATAG-TTTTTAAAA
* * **
24954 ATATTTTTAAAAACATATAATATATAGTTTTTTTTTTAA
1 ATATTTTTGAAAACGTATAATATATAG---TTTTTAAAA
*
24993 ATATTTTTG-AAACGTATAATATATGGTTTTCTAAAAA
1 ATATTTTTGAAAACGTATAATATATAGTTTT-T-AAAA
*
25030 ATATTTTTGAAAACGTATAATATATATATTTTTAAAA
1 ATATTTTTGAAAACGTATAATATATA-GTTTTTAAAA
* * *
25067 ACGATTTTTGAAAACATGTAATATA
1 A-TATTTTTGAAAACGTATAATATA
25092 ATATTATATA
Statistics
Matches: 146, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
35 29 0.20
36 6 0.04
37 41 0.28
38 51 0.35
39 19 0.13
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (36 bp):
ATATTTTTGAAAACGTATAATATATAGTTTTTAAAA
Found at i:25823 original size:20 final size:19
Alignment explanation
Indices: 25800--25851 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
25790 TGCGATTTAA
25800 AAAATCGCAACGTAAAAAAG
1 AAAATCGCAACGT-AAAAAG
*
25820 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAAC-GTAAAAAG
25840 AAAATCGCAACG
1 AAAATCGCAACG
25852 CGAGCTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.54, C:0.19, G:0.17, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGTAAAAAG
Found at i:25911 original size:20 final size:20
Alignment explanation
Indices: 25886--26239 Score: 573
Period size: 20 Copynumber: 17.4 Consensus size: 20
25876 TTTAGAAGAA
25886 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
25906 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
25926 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
25946 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
25966 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
*
25986 AATCGCAATGCGATTTAGAAGAG
1 AATCGCAATGCGA-TT-G-ATAG
26009 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
26029 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
26049 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
26069 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
26089 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
26109 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
*
26129 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAG
* *
26149 AATCGCAATGCGATTAAGAG
1 AATCGCAATGCGATTGATAG
* * *
26169 ATTCGCAACGCGAGTTAGAAGAG
1 AATCGCAATGCGA-TT-G-ATAG
*
26192 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAG
*
26212 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAG
26232 AATCGCAA
1 AATCGCAA
26240 CGTTGAAAAT
Statistics
Matches: 316, Mismatches: 12, Indels: 12
0.93 0.04 0.04
Matches are distributed among these distances:
20 275 0.87
21 5 0.02
22 5 0.02
23 31 0.10
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:26013 original size:123 final size:123
Alignment explanation
Indices: 25865--26239 Score: 603
Period size: 123 Copynumber: 3.0 Consensus size: 123
25855 GCTTCCAAGT
* *
25865 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
1 TCGCAATGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
25930 GCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAA
66 GCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAA
25988 TCGCAATGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
1 TCGCAATGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
26053 GCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAA
66 GCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAA
* * * * *
26111 TCGCAATGCGA-TT-G-ATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTAAGAGATTC
1 TCGCAATGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
* * * *
26173 GCAACGCGAGTTAGAAGAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTTATAGAA
66 GCAATGCGA-TT-G-ATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAA
26234 TCGCAA
1 TCGCAA
26240 CGTTGAAAAT
Statistics
Matches: 238, Mismatches: 11, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
120 51 0.21
121 3 0.01
122 3 0.01
123 181 0.76
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (123 bp):
TCGCAATGCGATTTAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATC
GCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAA
Found at i:26063 original size:163 final size:163
Alignment explanation
Indices: 25886--26239 Score: 606
Period size: 163 Copynumber: 2.2 Consensus size: 163
25876 TTTAGAAGAA
25886 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCG
25951 CAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTTAGAAGAGAATCGCA
66 CAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGA-TT--AAGAGAATCGCA
* *
26016 ATGCGA-TT-G-ATAGAATCGCAATGCGATTGATAG
128 ACGCGAGTTAGAAGAGAATCGCAATGCGATTGATAG
26049 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCG
1 AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCG
* *
26114 CAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTAAGAGATTCGCAACG
66 CAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTAAGAGAATCGCAACG
*
26179 CGAGTTAGAAGAGAATCGCAATGCGATTTATAG
131 CGAGTTAGAAGAGAATCGCAATGCGATTGATAG
*
26212 AATCGCAATGCGATTTATAGAATCGCAA
1 AATCGCAATGCGATTGATAGAATCGCAA
26240 CGTTGAAAAT
Statistics
Matches: 182, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
160 16 0.09
161 2 0.01
162 3 0.02
163 161 0.88
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (163 bp):
AATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCG
CAATGCGATTGATAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTAAGAGAATCGCAACG
CGAGTTAGAAGAGAATCGCAATGCGATTGATAG
Found at i:26369 original size:5 final size:5
Alignment explanation
Indices: 26353--26386 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
26343 CGTATTACCA
26353 CGACC ACGACC CGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC CGACC CGACC CGACC CGACC CGA
26387 GACGAGACGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.24, C:0.56, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:27090 original size:6 final size:6
Alignment explanation
Indices: 27074--27105 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
27064 TCTCGTCTCG
27074 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
27106 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:27216 original size:20 final size:20
Alignment explanation
Indices: 27193--27470 Score: 193
Period size: 20 Copynumber: 13.6 Consensus size: 20
27183 TTCTTTTTAA
27193 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
27213 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
27233 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
27253 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
27276 CGTTGCGAATCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
27296 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
27316 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
27336 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
27359 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
27380 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
27398 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
27420 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
27440 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
27459 CGTTGCGATTTT
1 CGTTGCGATTTT
27471 ATTGGTCATT
Statistics
Matches: 207, Mismatches: 40, Indels: 23
0.77 0.15 0.09
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 140 0.68
21 15 0.07
22 5 0.02
23 28 0.14
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:27276 original size:63 final size:62
Alignment explanation
Indices: 27195--27366 Score: 199
Period size: 63 Copynumber: 2.8 Consensus size: 62
27185 CTTTTTAACG
* * *
27195 TTGCGA-T-TTTCTAAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTTTCTAAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCA
* * * *
27255 TTGCGATTCTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATAAATCGCA
1 TTGCGATTCT-TTCTAAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCA
* *
27318 TTGCGATTCTATC--AATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGATTCTTTCTAAATCGCGTTGCGA--TT-TTCTAAATCGCGTTGCGA
27367 ACTTGGAAGC
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
60 18 0.19
61 1 0.01
62 4 0.04
63 70 0.75
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (62 bp):
TTGCGATTCTTTCTAAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCA
Found at i:27337 original size:83 final size:83
Alignment explanation
Indices: 27193--27367 Score: 260
Period size: 83 Copynumber: 2.1 Consensus size: 83
27183 TTCTTTTTAA
* * * * * * * *
27193 CGTTGCGATTTTCTAAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAGTCGCATTG
1 CGTTGCGAATCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
27258 CGATTCTCTTCTAAATCG
66 CGATTCTCTTCTAAATCG
*
27276 CGTTGCGAATCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
1 CGTTGCGAATCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
*
27341 CGATTTTCTTCTAAATCG
66 CGATTCTCTTCTAAATCG
27359 CGTTGCGAA
1 CGTTGCGAA
27368 CTTGGAAGCT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (83 bp):
CGTTGCGAATCTCTAAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTG
CGATTCTCTTCTAAATCG
Found at i:27460 original size:19 final size:20
Alignment explanation
Indices: 27420--27470 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
27410 TTCTTTTTAA
*
27420 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
27440 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
27459 CGTTGCGATTTT
1 CGTTGCGATTTT
27471 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:27801 original size:15 final size:15
Alignment explanation
Indices: 27777--27810 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
27767 CCGTAGGACC
27777 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
27792 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
27807 ACTA
1 ACTA
27811 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:30666 original size:173 final size:173
Alignment explanation
Indices: 30377--30723 Score: 694
Period size: 173 Copynumber: 2.0 Consensus size: 173
30367 CCATTTAGGA
30377 ATTGAAATTGGTTGTAACAATCCTGACAGAACCTGATGCTCAGCTTTGACTTGTTGACAAGTCAA
1 ATTGAAATTGGTTGTAACAATCCTGACAGAACCTGATGCTCAGCTTTGACTTGTTGACAAGTCAA
30442 ACACTTTGATACAAATTTCGTAATGTCTTTCTTCATTCCCGGCCACCAATATCGACTCTTGAGAT
66 ACACTTTGATACAAATTTCGTAATGTCTTTCTTCATTCCCGGCCACCAATATCGACTCTTGAGAT
30507 CCATATATATTTTGTTCCCTCCCGGATGTATTGTCAATGGACT
131 CCATATATATTTTGTTCCCTCCCGGATGTATTGTCAATGGACT
30550 ATTGAAATTGGTTGTAACAATCCTGACAGAACCTGATGCTCAGCTTTGACTTGTTGACAAGTCAA
1 ATTGAAATTGGTTGTAACAATCCTGACAGAACCTGATGCTCAGCTTTGACTTGTTGACAAGTCAA
30615 ACACTTTGATACAAATTTCGTAATGTCTTTCTTCATTCCCGGCCACCAATATCGACTCTTGAGAT
66 ACACTTTGATACAAATTTCGTAATGTCTTTCTTCATTCCCGGCCACCAATATCGACTCTTGAGAT
30680 CCATATATATTTTGTTCCCTCCCGGATGTATTGTCAATGGACT
131 CCATATATATTTTGTTCCCTCCCGGATGTATTGTCAATGGACT
30723 A
1 A
30724 CAATGTGCTT
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 174 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (173 bp):
ATTGAAATTGGTTGTAACAATCCTGACAGAACCTGATGCTCAGCTTTGACTTGTTGACAAGTCAA
ACACTTTGATACAAATTTCGTAATGTCTTTCTTCATTCCCGGCCACCAATATCGACTCTTGAGAT
CCATATATATTTTGTTCCCTCCCGGATGTATTGTCAATGGACT
Found at i:34724 original size:15 final size:15
Alignment explanation
Indices: 34700--34733 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
34690 GTATCGTACC
34700 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
34715 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
34730 ACTA
1 ACTA
34734 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:35328 original size:64 final size:64
Alignment explanation
Indices: 35259--35415 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
35249 TAATGAAGGT
*
35259 ATGCATCGATGCACTACTTGTGCATCTG-TGCA-TAAAAT-GCATTCGATG-TTTTATTATTAAT
1 ATGCATCGATGCACTACTTGTGCATC-GATGCACT--AATCGCATTCGATGTTTTTATT-TTAAA
*
35320 GGA
62 AGA
* * *
35323 ATGCATTGATGCA-TGCCTTATGCATCGATGCACTAATCGCATTCGATGTTTTTATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAATCGCATTCGATGTTTTTATTTTAAAAGA
* *
35387 GTGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
35416 ACACCTTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
63 5 0.06
64 63 0.82
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAATCGCATTCGATGTTTTTATTTTAAAAGA
Found at i:37388 original size:18 final size:18
Alignment explanation
Indices: 37365--37439 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
37355 AGGGATATAC
37365 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
37383 AGTGGTCATTTGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
* *
37403 ACAATGGTCTTTCGGGACAT
1 --AGTGGTCCTTCGGGACAT
*
37423 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
37440 AATATTCAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 28 0.62
20 4 0.09
22 13 0.29
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:37417 original size:40 final size:40
Alignment explanation
Indices: 37359--37439 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
37349 TAGTCGAGGG
*
37359 ATATACAGTGGTCCTTCGGGACATAGTGGTCATTTGGGAC
1 ATATACAATGGTCCTTCGGGACATAGTGGTCATTTGGGAC
* *
37399 ATATACAATGGTCTTTCGGGACATAGTGGTCCTTTGGGAC
1 ATATACAATGGTCCTTCGGGACATAGTGGTCATTTGGGAC
37439 A
1 A
37440 AATATTCAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (40 bp):
ATATACAATGGTCCTTCGGGACATAGTGGTCATTTGGGAC
Found at i:37901 original size:11 final size:11
Alignment explanation
Indices: 37882--37916 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
37872 GTAAATGTAT
*
37882 AGTATTGTAGC
1 AGTACTGTAGC
*
37893 AGTACTGTAGT
1 AGTACTGTAGC
37904 AGTACTGTAGC
1 AGTACTGTAGC
37915 AG
1 AG
37917 GGGAATCGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (11 bp):
AGTACTGTAGC
Found at i:39773 original size:2 final size:2
Alignment explanation
Indices: 39766--39790 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39756 CAACTTGTTA
39766 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39791 ATAAGGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39993 original size:14 final size:14
Alignment explanation
Indices: 39970--40000 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39960 AACACACCCT
*
39970 TAAATTCTAAACTC
1 TAAATCCTAAACTC
39984 TAAATCCTAAACTC
1 TAAATCCTAAACTC
39998 TAA
1 TAA
40001 CCCTTAGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATCCTAAACTC
Found at i:40466 original size:21 final size:21
Alignment explanation
Indices: 40440--40482 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40430 AAAATGAATT
** *
40440 ACTGGAATTTGAATTATTGGA
1 ACTGGAAAATGAATTACTGGA
40461 ACTGGAAAATGAATTACTGGA
1 ACTGGAAAATGAATTACTGGA
40482 A
1 A
40483 TTTGAATTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (21 bp):
ACTGGAAAATGAATTACTGGA
Found at i:40502 original size:14 final size:15
Alignment explanation
Indices: 40461--40506 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
40451 AATTATTGGA
40461 ACTGGAAAATGAATT
1 ACTGGAAAATGAATT
**
40476 ACTGGAATTTGAATT
1 ACTGGAAAATGAATT
40491 -CTGGAAAATGAATT
1 ACTGGAAAATGAATT
40505 AC
1 AC
40507 ATTTCTGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:40900 original size:23 final size:23
Alignment explanation
Indices: 40851--40913 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
40841 GTGTTATATT
* **
40851 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
40874 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
40897 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
40914 AAATAATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:40937 original size:24 final size:24
Alignment explanation
Indices: 40910--40968 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
40900 TTATTTAAAT
40910 ATATAAATAATTTATT-CATTATTA
1 ATATAAA-AATTTATTACATTATTA
*
40934 ATATATAAAATTTATTATATTATTA
1 ATATA-AAAATTTATTACATTATTA
*
40959 AAATAAAAAT
1 ATATAAAAAT
40969 AATATCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 18 0.58
25 13 0.42
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATAAAAATTTATTACATTATTA
Found at i:41018 original size:28 final size:27
Alignment explanation
Indices: 40987--41057 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 27
40977 ATATTATTAT
* *
40987 AATATAATTGATTATTTTATATATTAA-A
1 AATATAA-T-ATTATATTATAAATTAATA
41015 AATATAATATTATATTATAAATTAATA
1 AATATAATATTATATTATAAATTAATA
*
41042 AATA-AATA-AATATTAT
1 AATATAATATTATATTAT
41058 TTTGATGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.18
26 19 0.49
27 6 0.15
28 7 0.18
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (27 bp):
AATATAATATTATATTATAAATTAATA
Found at i:41028 original size:19 final size:18
Alignment explanation
Indices: 41006--41041 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
40996 GATTATTTTA
41006 TATATTAAAAATATAATAT
1 TATATTAAAAAT-TAATAT
*
41025 TATATTATAAATTAATA
1 TATATTAAAAATTAATA
41042 AATAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATTAAAAATTAATAT
Found at i:41284 original size:42 final size:42
Alignment explanation
Indices: 41232--41359 Score: 229
Period size: 42 Copynumber: 3.0 Consensus size: 42
41222 ATGAATTACA
*
41232 TTCCGGAAAACAAATTACGTAAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAATATT
* *
41274 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAATATT
41316 TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAATATT
41358 TT
1 TT
41360 AAAAGTAAAA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.48, C:0.16, G:0.16, T:0.20
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTAAAACAAACACGGGAAAATATT
Found at i:53089 original size:23 final size:23
Alignment explanation
Indices: 53046--53089 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
53036 CGTGGAAAAA
* *
53046 ATAATTTTTTCATTTTTTGAATT
1 ATAATTTTTTCATTGTATGAATT
53069 ATAATTTTTT-ATTAGTATGAA
1 ATAATTTTTTCATT-GTATGAA
53090 GACATTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (23 bp):
ATAATTTTTTCATTGTATGAATT
Found at i:53403 original size:11 final size:11
Alignment explanation
Indices: 53387--53411 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
53377 AATTATTTTT
53387 TTAAAAAATTA
1 TTAAAAAATTA
53398 TTAAAAAATTA
1 TTAAAAAATTA
53409 TTA
1 TTA
53412 TATTTTAGTT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAAAAATTA
Found at i:53962 original size:29 final size:29
Alignment explanation
Indices: 53920--54001 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
53910 CTACTAAATT
53920 GATGTAATTGCTTACATCATTTAAGTAAA
1 GATGTAATTGCTTACATCATTTAAGTAAA
* *
53949 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTAATTGCTTACATCATTTAAGTAAA
*
53978 GATGTTATTGCTTACATCAATTTA
1 GATGTAATTGCTTACATC-ATTTA
54002 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (29 bp):
GATGTAATTGCTTACATCATTTAAGTAAA
Found at i:55267 original size:15 final size:15
Alignment explanation
Indices: 55247--55276 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
55237 TCGAGGCTGG
55247 AATTACAACAACAAC
1 AATTACAACAACAAC
55262 AATTACAACAACAAC
1 AATTACAACAACAAC
55277 TATGAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:58683 original size:29 final size:29
Alignment explanation
Indices: 58641--58722 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
58631 AAACTAAATT
*
58641 GATGTCATTGCTTAAATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
58670 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
58699 GATGTTATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
58723 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:64962 original size:14 final size:14
Alignment explanation
Indices: 64943--64973 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
64933 ATTGATAGAT
64943 AATGACAATAACTA
1 AATGACAATAACTA
*
64957 AATGACAATGACTA
1 AATGACAATAACTA
64971 AAT
1 AAT
64974 TTATATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.10, T:0.23
Consensus pattern (14 bp):
AATGACAATAACTA
Done.