Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007225.1 Hibiscus syriacus cultivar Beakdansim tig00019119_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: 58962
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:766 original size:23 final size:24
Alignment explanation
Indices: 740--805 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
730 TTAAAATAAT
*
740 ATTAATTAAATTAAAATTT-TAAA
1 ATTAATTAAATTAAAATTTCCAAA
*
763 ATT-ATTGAAATAAAAAATTTCCCAAA
1 ATTAATT-AAAT-TAAAATTT-CCAAA
789 ATTATATTAAATTAAAA
1 ATTA-ATTAAATTAAAA
806 AAGTATTCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 3 0.09
23 7 0.21
24 7 0.21
26 10 0.29
27 4 0.12
28 3 0.09
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTAATTAAATTAAAATTTCCAAA
Found at i:12066 original size:7 final size:7
Alignment explanation
Indices: 12051--12110 Score: 111
Period size: 7 Copynumber: 8.6 Consensus size: 7
12041 ACTACCAGTC
*
12051 TTCTCAT
1 TTCTTAT
12058 TTCTTAT
1 TTCTTAT
12065 TTCTTAT
1 TTCTTAT
12072 TTCTTAT
1 TTCTTAT
12079 TTCTTAT
1 TTCTTAT
12086 TTCTTAT
1 TTCTTAT
12093 TTCTTAT
1 TTCTTAT
12100 TTCTTAT
1 TTCTTAT
12107 TTCT
1 TTCT
12111 GTTTGTACGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 52 1.00
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (7 bp):
TTCTTAT
Found at i:15276 original size:47 final size:47
Alignment explanation
Indices: 15181--15277 Score: 108
Period size: 48 Copynumber: 2.0 Consensus size: 47
15171 CAAACGTGAG
**
15181 AATAATAAATAAAACAAAAAAAAAGGAAAATAAAAAAACATGTAAAA
1 AATAATAAATAAAACAAAAAAAAAACAAAATAAAAAAACATGTAAAA
* * *
15228 AATAAT-AATAAAATAATAAAAATAAACAAAATGAATAAA-ATGTTAAAA
1 AATAATAAATAAAACAA-AAAAA-AAACAAAATAAAAAAACATG-TAAAA
15276 AA
1 AA
15278 CAAAGACACA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
46 9 0.21
47 14 0.33
48 19 0.45
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (47 bp):
AATAATAAATAAAACAAAAAAAAAACAAAATAAAAAAACATGTAAAA
Found at i:15442 original size:36 final size:35
Alignment explanation
Indices: 15387--15576 Score: 122
Period size: 37 Copynumber: 5.3 Consensus size: 35
15377 AGTATTTACT
* *
15387 AAAACAAA-TAAAAATAATAAATATATAATACTAAG
1 AAAATAAATTAAAAA-AATAAATATATAATATTAAG
*
15422 TAAAATAAATTAAAAAAATAAAGATATACATGATATTAAG
1 -AAAATAAATTAAAAAAAT-AA-ATAT--ATAATATTAAG
* *
15462 AAAA-AAA-TAAAAAAATAAAGTA-AAAATA-TAAT
1 AAAATAAATTAAAAAAATAAA-TATATAATATTAAG
* * * * *
15494 ATATATAAATAAATAAAAACAAAAATAGAATATTAAG
1 A-AAATAAATTAA-AAAAATAAATATATAATATTAAG
*
15531 AAAATATATATAAAAACATATAAA-ATATAATATTAAG
1 AAAATAAAT-TAAAAA-A-ATAAATATATAATATTAAG
*
15568 AAAAAAAAT
1 AAAATAAAT
15577 ATATACATAG
Statistics
Matches: 120, Mismatches: 19, Indels: 29
0.71 0.11 0.17
Matches are distributed among these distances:
32 4 0.03
33 6 0.05
34 3 0.03
35 4 0.03
36 36 0.30
37 43 0.36
38 11 0.09
39 4 0.03
40 9 0.08
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (35 bp):
AAAATAAATTAAAAAAATAAATATATAATATTAAG
Found at i:15508 original size:38 final size:37
Alignment explanation
Indices: 15424--15512 Score: 92
Period size: 38 Copynumber: 2.4 Consensus size: 37
15414 ATACTAAGTA
* *
15424 AAATAAATTAAAAAAATAAAGATATACATGATATTAAG
1 AAATAAA-TAAAAAAATAAAGATAAAAATGATATTAAG
* *
15462 AAAAAAATAAAAAAATAAAG-TAAAAAT-ATAATATATAT
1 AAATAAATAAAAAAATAAAGATAAAAATGAT-AT-TA-AG
15500 AAATAAATAAAAA
1 AAATAAATAAAAA
15513 CAAAAATAGA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
35 2 0.05
36 7 0.16
37 15 0.35
38 19 0.44
ACGTcount: A:0.71, C:0.01, G:0.04, T:0.24
Consensus pattern (37 bp):
AAATAAATAAAAAAATAAAGATAAAAATGATATTAAG
Found at i:17502 original size:106 final size:103
Alignment explanation
Indices: 17128--17640 Score: 376
Period size: 106 Copynumber: 5.0 Consensus size: 103
17118 TATTGTTCCA
* * *
17128 AGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTG---GA-AATTGTTTGTTGATAGTCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAATGAGAATTGTTTGTTGATAATCAG
* *
17189 CCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCG
66 CCGTCCCTTTACTGTGAAGTTGAGCTTGTGCTGTCTCG
* * * *
17227 AGTCTAATATCTTTCGTT-T---G---AAATTGACTCTGAATG-GAA-T-TTTGTTGACAATCAG
1 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAATGAGAATTGTTTGTTGATAATCAG
* * * * *
17282 CC-TCCCCTTATTCGTGAAGTTGAGCATGTGTTGTCTTG
66 CCGTCCCTTTACT-GTGAAGTTGAGCTTGTGCTGTCTCG
* * * * * * * * *
17320 GGTCCAATATCCTTCGCTGGGAAGTTGAAATTGGCCCTGAAATTGGGAAGTTATTTGTTGACAGT
1 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTG-AA-TGAGAA-TTGTTTGTTGATAAT
* * *
17385 CAGCCGCCCCTTTACTGTGAAGTTGAGCTTGTGCTATCTTG
63 CAGCCGTCCCTTTACTGTGAAGTTGAGCTTGTGCTGTCTCG
*
17426 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGGAATTGAGAAGTTGTTTGTTGATAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCT-GAA-TGAGAA-TTGTTTGTTGATAAT
* *** * **
17491 CAACCGTCCCTTCGTTGTGAAGTTGAACTTGTATTGTCTCG
63 CAGCCGTCCCTTTACTGTGAAGTTGAGCTTGTGCTGTCTCG
* * *** * * * * *
17532 AATTCAATATCCTTTACTGTGAAGTTGAAATTGGTTCTAAAACTGGGAAATTGTTTGTTGATAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCT-GAA-TGAG-AATTGTTTGTTGATAAT
* * *
17597 CAGCCGTCCC-TT-CGTGTTGAAGTTGAACTTGTGTTGTGTCG
63 CAGCCGTCCCTTTAC-TG-TGAAGTTGAGCTTGTGCTGTCTCG
17638 AGT
1 AGT
17641 GGCACGATAT
Statistics
Matches: 326, Mismatches: 65, Indels: 39
0.76 0.15 0.09
Matches are distributed among these distances:
92 17 0.05
93 51 0.16
94 1 0.00
95 4 0.01
97 1 0.00
98 1 0.00
99 14 0.04
100 10 0.03
101 2 0.01
102 2 0.01
103 3 0.01
105 4 0.01
106 206 0.63
107 10 0.03
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (103 bp):
AGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTGAATGAGAATTGTTTGTTGATAATCAG
CCGTCCCTTTACTGTGAAGTTGAGCTTGTGCTGTCTCG
Found at i:18429 original size:67 final size:65
Alignment explanation
Indices: 18313--18633 Score: 248
Period size: 65 Copynumber: 4.8 Consensus size: 65
18303 AAGATATCTG
* * * * * *
18313 TTGTTTCATGA-AAACGGTTTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAATAAATTTAAAGA-
18377 TT
64 TT
*
18379 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAGGGGAAATAAATTTAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAAATTTAAAGAT
18444 T
65 T
* * * * * ***
18445 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGAGAAACTGTCTTAAGAGAG
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA------TAA-ATTT
* *
18510 ACAAAACT
59 A-AAGATT
* * * * *** * * * * *
18518 TAGTTCCAAAAGAAATTGTCTCAAGGGAGACAAAATTTGTTTCAAATAAAACATATTCAAATAAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAAATTTAAAGATT
* * *
18583 TTATTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA
18634 CTGTCTCAAG
Statistics
Matches: 199, Mismatches: 46, Indels: 21
0.75 0.17 0.08
Matches are distributed among these distances:
65 89 0.45
66 6 0.03
67 35 0.18
68 20 0.10
71 3 0.02
72 2 0.01
73 44 0.22
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAAATTTAAAGATT
Found at i:18481 original size:65 final size:67
Alignment explanation
Indices: 18248--18495 Score: 218
Period size: 65 Copynumber: 3.7 Consensus size: 67
18238 TAGATGATGC
** * * * ** * *
18248 TTCAAGAGAAGTTGTCTCGAA-AGAGATATAATTCGTTTCAAGGGAAA-CGATCTCAAAGATATC
1 TTCAAGAGAAACTGTCTC-AAGAGAGACAAAATTTGTTTCAAGGGAAATAAAT-TTAAAGAT-TT
18311 TGTTGT
63 TG-TGT
* * * * * * *
18317 TTCATGA-AAACGGTTTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTG
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAATAAATTTAAAGATTTTG
18381 TGT
65 TGT
* *
18384 TTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAGGGGAAATAAATTTAAAGA-TTT-T
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAAATTTAAAGATTTTGT
18447 GT
66 GT
* * * *
18449 TTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGAGAAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
18496 CTGTCTTAAG
Statistics
Matches: 146, Mismatches: 29, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
65 44 0.30
66 3 0.02
67 36 0.25
68 35 0.24
69 26 0.18
70 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (67 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATAAATTTAAAGATTTTGT
GT
Found at i:18496 original size:36 final size:36
Alignment explanation
Indices: 18448--18771 Score: 216
Period size: 36 Copynumber: 9.3 Consensus size: 36
18438 AAAGATTTTG
*
18448 TTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
* * *
18484 TTTCAAGAGAAACTGTCTTAAGAGAGACAAAACTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
* ** * * *
18520 GTTCCAAAAGAAATTGTCTCAAGGGAGACAAAATTTG
1 -TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
*** * *
18557 TTTCAAATAAAACATAT-TC-----A-A-ATAATTTA
1 TTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATTTA
* *
18586 TTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
* *
18622 TTTCAAGGGAAACTGTCTCAAGAGAGACGAAGTTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
* *
18658 TTTCAAGGGAAA-TGTTTTC-A-A-TG------TTTA
1 TTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTTA
* * *
18685 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCG
1 --TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT-A
* * **
18724 TTTCAAGGAAAACTATCTCAAGAGAGACAAAATTCG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
18760 TTTCAAGGGAAA
1 TTTCAAGGGAAA
18772 TGTTTTCAAT
Statistics
Matches: 223, Mismatches: 41, Indels: 48
0.71 0.13 0.15
Matches are distributed among these distances:
27 4 0.02
28 2 0.01
29 32 0.14
30 4 0.02
31 1 0.00
32 1 0.00
33 1 0.00
34 2 0.01
35 4 0.02
36 108 0.48
37 61 0.27
38 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:18538 original size:37 final size:36
Alignment explanation
Indices: 18456--18552 Score: 122
Period size: 37 Copynumber: 2.7 Consensus size: 36
18446 TGTTTCAAGG
* * * *
18456 GAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAA
*
18492 GAAACTGTCTTAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAA
* *
18529 GAAATTGTCTCAAGGGAGACAAAA
1 GAAACTGTCTCAAGAGAGACAAAA
18553 TTTGTTTCAA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 25 0.48
37 27 0.52
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAA
Found at i:18549 original size:138 final size:138
Alignment explanation
Indices: 18390--18649 Score: 376
Period size: 138 Copynumber: 1.9 Consensus size: 138
18380 GTGTTTCAAG
** * * * * *
18390 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAGGGGAAATAAATTTAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTATTTCAAG
* *
18455 GGAAACTGTCTCAAGAGAGACGAAATTTATTTCAAGAGAAACTGTCTTAAGAGAGACAAAACTTA
66 GGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
18520 GTTCCAAA
131 GTTCCAAA
* * * *
18528 AGAAATTGTCTCAAGGGAGACAAAATTTGTTTCAAATAAAACATATTCAAATAATTTATTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTATTTCAAG
* * *
18593 GGAAACTGTCTCAAGTGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
66 GGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGAC
18650 GAAGTTTATT
Statistics
Matches: 106, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 106 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAAGAATTTATTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:18602 original size:102 final size:101
Alignment explanation
Indices: 18478--18818 Score: 278
Period size: 102 Copynumber: 3.4 Consensus size: 101
18468 AGAGAGACGA
* *
18478 AATTTATTTCAAGAGAAACTGTCTTAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAG
1 AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAAGAAACTGTCTCAAG
* *
18543 GGAGACAAAATTTGTTTCAAATAAAACATATTCAAAT
65 AGAGACAAAATTTATTTCAAATAAAACATATTCAAAT
* * * * **
18580 AATTTATTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGA
1 AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGA
* * *** ** *
18645 GAGACGAAGTTTATTTCAAGGGAAATGTTTTC-AAT
66 GAGACAAAATTTATTTCAAATAAAACATATTCAAAT
* * * * * *
18680 -GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCGTTTC-AAGGAAAACTATCTC
1 AATTTA--TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAAG-AAACTGTCTC
** *** ** *
18743 AAGAGAGACAAAATTCGTTTCAAGGGAAATGTTTTC-AAT
62 AAGAGAGACAAAATTTATTTCAAATAAAACATATTCAAAT
* *
18782 -GTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAA
1 AATTTA--TTTCAAGAGAAACTGTCTCAAGAGAGACAA
18819 TATTTTGTTT
Statistics
Matches: 207, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
99 4 0.02
100 3 0.01
101 77 0.37
102 123 0.59
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (101 bp):
AATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGA
GAGACAAAATTTATTTCAAATAAAACATATTCAAAT
Found at i:18693 original size:203 final size:203
Alignment explanation
Indices: 18484--18852 Score: 483
Period size: 203 Copynumber: 1.8 Consensus size: 203
18474 ACGAAATTTA
* * * *
18484 TTTCAAGAGAAACTGTCTTAAGAGAGACAAAACTTAGTTCCAAA-AGAAATTGTCTCAAGGGAGA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAGA-AAACTATCTCAAGAGAGA
* * * *
18548 CAAAATTTGTTTCAAATAAAACATATTCAAATAATTTA-TTTCAAGGGAAACTGTCTCAAGTGAG
65 CAAAATTCGTTTCAAAGAAAACATATTC-AAT-ATTTAGTTTCAAGAGAAACTGTCTCAAGGGAG
*
18612 ACAA-AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAGTTTATTTCAAGGGAAATGTTTT
128 ACAATAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAGTTTATTTCAAGGGAAATGTTTT
18676 CAATGTTTATG
193 CAATGTTTATG
* * * * *
18687 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCGTTTCAAGGAAAACTATCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAGAAAACTATCTCAAGAGAGAC
* * ** * *
18752 AAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
66 AAAATTCGTTTCAAAGAAAACATATTCAATATTTA-GTTTCAAGAGAAACTGTCTCAAGGGAGAC
* *
18817 AATATTTTGTTTCAAGGGAAACTATCTCAAGCGAGA
130 AATAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
18853 TAAAATCTTC
Statistics
Matches: 140, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
201 4 0.03
202 3 0.02
203 102 0.73
204 31 0.22
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (203 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAGAAAACTATCTCAAGAGAGAC
AAAATTCGTTTCAAAGAAAACATATTCAATATTTAGTTTCAAGAGAAACTGTCTCAAGGGAGACA
ATAATTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAGTTTATTTCAAGGGAAATGTTTTCAA
TGTTTATG
Found at i:18737 original size:37 final size:37
Alignment explanation
Indices: 18686--18771 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
18676 CAATGTTTAT
* *
18686 GTTTCAA-GAGAAACTGTCTCAAGGGAGACAAAATTTC
1 GTTTCAAGGAGAAACTATCTCAAGAGAGACAAAA-TTC
18723 GTTTCAAGGA-AAACTATCTCAAGAGAGACAAAATTC
1 GTTTCAAGGAGAAACTATCTCAAGAGAGACAAAATTC
18759 GTTTCAAGG-GAAA
1 GTTTCAAGGAGAAA
18772 TGTTTTCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
36 15 0.33
37 28 0.62
38 2 0.04
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (37 bp):
GTTTCAAGGAGAAACTATCTCAAGAGAGACAAAATTC
Found at i:18829 original size:102 final size:101
Alignment explanation
Indices: 18586--18858 Score: 420
Period size: 102 Copynumber: 2.7 Consensus size: 101
18576 AAATAATTTA
* * * * *
18586 TTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACG
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
* *
18651 AAGTTTATTTCAAGGGAAATGTTTTCAATGTTTATG
66 AAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
* *
18687 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTCGTTTCAAGGAAAACTATCTCAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGGGAGAC-AAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
*
18752 AAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTATG
65 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
* *
18789 TTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAACTATCTCAAGCGAGAT
1 TTTCAAGAGAAACTGTCTCAAGGGAGACAA-ATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
18854 AAAAT
65 AAAAT
18859 CTTCTTTTTA
Statistics
Matches: 156, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
101 28 0.18
102 128 0.82
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (101 bp):
TTTCAAGAGAAACTGTCTCAAGGGAGACAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACA
AAATTCATTTCAAGGGAAATGTTTTCAATGTTTATG
Found at i:18838 original size:37 final size:38
Alignment explanation
Indices: 18778--18852 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
18768 GAAATGTTTT
* * *
18778 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
*
18816 CAATATTT-TGTTTCAAGGGAAACTATCTCAAGCGAGA
1 CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
18853 TAAAATCTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (38 bp):
CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
Found at i:21663 original size:7 final size:7
Alignment explanation
Indices: 21651--21679 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
21641 TGAAATGTAG
21651 ATGCAAA
1 ATGCAAA
21658 ATGCAAA
1 ATGCAAA
21665 ATGCAAA
1 ATGCAAA
21672 ATGCAAA
1 ATGCAAA
21679 A
1 A
21680 ATGTATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (7 bp):
ATGCAAA
Found at i:23210 original size:18 final size:18
Alignment explanation
Indices: 23187--23255 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
23177 TAATAAATAA
23187 AACAAAAAAATGAAAAAT
1 AACAAAAAAATGAAAAAT
* *
23205 AACAAAACACATAAAAAAT
1 AACAAAA-AAATGAAAAAT
* *
23224 AATAATAAAAT-AATAAA-
1 AACAAAAAAATGAA-AAAT
*
23241 AATAAACAAAATGAA
1 AACAAA-AAAATGAA
23256 TAAAATGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 7 0.17
18 18 0.44
19 16 0.39
ACGTcount: A:0.75, C:0.07, G:0.03, T:0.14
Consensus pattern (18 bp):
AACAAAAAAATGAAAAAT
Found at i:23224 original size:39 final size:40
Alignment explanation
Indices: 23176--23251 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
23166 AAACGTAAGA
*
23176 ATAATAAATAA-AACAAAAAAATGAAAAAT-AACAAAACAC
1 ATAAAAAATAATAACAAAAAAAT-AAAAATAAACAAAACAC
* *
23215 ATAAAAAATAATAATAAAATAATAAAAATAAACAAAA
1 ATAAAAAATAATAACAAAAAAATAAAAATAAACAAAA
23252 TGAATAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 16 0.50
40 16 0.50
ACGTcount: A:0.76, C:0.07, G:0.01, T:0.16
Consensus pattern (40 bp):
ATAAAAAATAATAACAAAAAAATAAAAATAAACAAAACAC
Found at i:23233 original size:11 final size:10
Alignment explanation
Indices: 23175--23260 Score: 54
Period size: 10 Copynumber: 8.7 Consensus size: 10
23165 CAAACGTAAG
*
23175 AATAATAAAT
1 AATAAAAAAT
*
23185 AA-AACAAAAA
1 AATAA-AAAAT
*
23195 AATGAAAAAT
1 AATAAAAAAT
* *
23205 AACAAAACA-
1 AATAAAAAAT
*
23214 CATAAAAAAT
1 AATAAAAAAT
23224 AATAATAAAAT
1 AATAA-AAAAT
23235 AAT-AAAAAT
1 AATAAAAAAT
*
23244 AA-ACAAAAT
1 AATAAAAAAT
23253 GAATAAAA
1 -AATAAAA
23261 TGTTAAAAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 13
0.68 0.16 0.16
Matches are distributed among these distances:
9 20 0.36
10 24 0.43
11 12 0.21
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (10 bp):
AATAAAAAAT
Found at i:23260 original size:40 final size:38
Alignment explanation
Indices: 23172--23260 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 38
23162 GTGCAAACGT
*
23172 AAGAATAATAAATAAAACAAAAAAATGAAAAATAACAA
1 AAGAATAAAAAATAAAACAAAAAAATGAAAAATAACAA
* * *
23210 AACACATAAAAAATAATAATAAAATAAT-AAAAATAAACAA
1 AAGA-ATAAAAAATAA-AACAAAAAAATGAAAAAT-AACAA
23250 AATGAATAAAA
1 AA-GAATAAAA
23261 TGTTAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
38 3 0.07
39 16 0.38
40 22 0.52
41 1 0.02
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.16
Consensus pattern (38 bp):
AAGAATAAAAAATAAAACAAAAAAATGAAAAATAACAA
Found at i:23323 original size:17 final size:17
Alignment explanation
Indices: 23303--23350 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
23293 AAATTAATGG
23303 AGTAAAAAAATAAAAAA
1 AGTAAAAAAATAAAAAA
* *
23320 AGTAAAAGAAATTAAAAC
1 AGTAAAA-AAATAAAAAA
23338 AG-AATAAAAATAA
1 AGTAA-AAAAATAA
23351 TGTGTACATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (17 bp):
AGTAAAAAAATAAAAAA
Found at i:23486 original size:2 final size:2
Alignment explanation
Indices: 23474--23505 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
23464 TAAAGTAAAA
23474 AT AT A- 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 AT AT AT A
23506 AAAACAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23573 original size:36 final size:35
Alignment explanation
Indices: 23497--23575 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 35
23487 ATATATATAT
23497 ATATATATAAAAACAAAAATAGAATATTTAGAAAA
1 ATATATATAAAAACAAAAATAGAATATTTAGAAAA
*
23532 A-ATATATAAAAACGTATAAAATATAATA-TTA-AAAA
1 ATATATATAAAAAC--A-AAAATAGAATATTTAGAAAA
23567 ATATATATA
1 ATATATATA
23576 CATAGTAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
34 12 0.31
35 6 0.15
36 11 0.28
37 10 0.26
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.29
Consensus pattern (35 bp):
ATATATATAAAAACAAAAATAGAATATTTAGAAAA
Found at i:23652 original size:20 final size:22
Alignment explanation
Indices: 23617--23656 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
23607 ATATATATAT
23617 ATATATATATATAATAAAAATA
1 ATATATATATATAATAAAAATA
23639 ATATA-ATATA-AATAAAAA
1 ATATATATATATAATAAAAA
23657 AAAGAGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATATATATATATAATAAAAATA
Found at i:29144 original size:26 final size:27
Alignment explanation
Indices: 29108--29162 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
29098 TACTTGGTCA
*
29108 TTTAGAGTTCAA-TGTATTTTAGTCCT
1 TTTAGAGTTCAAGAGTATTTTAGTCCT
* *
29134 TTTAGGGTTCAAGAGTATTTTGGTCCT
1 TTTAGAGTTCAAGAGTATTTTAGTCCT
29161 TT
1 TT
29163 GAATATTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.49
Consensus pattern (27 bp):
TTTAGAGTTCAAGAGTATTTTAGTCCT
Found at i:37165 original size:65 final size:64
Alignment explanation
Indices: 37028--37187 Score: 234
Period size: 65 Copynumber: 2.5 Consensus size: 64
37018 TGCACTAAGA
*
37028 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTACATCGATGCATGGATT
** * *
37092 GTGCATCGATGCATTTAATGCATTTGATGTTTTCATAAA-ATCCTGAGTACATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AAATAGCCTGAGTACATCGATGCATGGAT
37155 AT
64 -T
37157 GTGCATCGATGCATAAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
37188 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 31 0.36
65 51 0.60
66 3 0.04
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTACATCGATGCATGGATT
Found at i:37226 original size:65 final size:64
Alignment explanation
Indices: 37028--37229 Score: 232
Period size: 65 Copynumber: 3.1 Consensus size: 64
37018 TGCACTAAGA
* * *
37028 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTGCATCGATGCATGGATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATATATCCTGAGTGCATCGATGCATGGATT
** * * *
37092 GTGCATCGATGCATTTAATGCATTTGATGTTTTC-ATAAAATCCTGAGTACATCGATGCATGG-T
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAT-ATATCCTGAGTGCATCGATGCATGGAT
37155 AT
64 -T
* *
37157 GTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCAATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATATA-TC-CTGAGTGCATCGATGCATGGAT
37220 T
64 T
37221 GGTGCATCG
1 -GTGCATCG
37230 GTACACTCTT
Statistics
Matches: 115, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
63 4 0.03
64 48 0.42
65 63 0.55
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAATATATCCTGAGTGCATCGATGCATGGATT
Found at i:38339 original size:21 final size:21
Alignment explanation
Indices: 38305--38348 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
38295 CCGGAGGAGG
* *
38305 AGGAGGAGCACGTGAAGAGCT
1 AGGAGCAGCACGTGAAGAACT
*
38326 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGTGAAGAACT
38347 AG
1 AG
38349 CTCCCAGAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.16, G:0.39, T:0.11
Consensus pattern (21 bp):
AGGAGCAGCACGTGAAGAACT
Found at i:51228 original size:23 final size:22
Alignment explanation
Indices: 51197--51281 Score: 84
Period size: 23 Copynumber: 3.8 Consensus size: 22
51187 ATTTTTGTGC
*
51197 ATAGAGTATCGATACCGCCTTTGA
1 ATAG-GTATCAATACC-CCTTTGA
*
51221 ATAGGTATTAATA-CCC-TTGCA
1 ATAGGTATCAATACCCCTTTG-A
*
51242 ATAGGTATCAATACCATCTTTGA
1 ATAGGTATCAATACC-CCTTTGA
*
51265 ATAGGTATCGATACCCC
1 ATAGGTATCAATACCCC
51282 CTGATGGTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 3 0.06
21 15 0.29
22 3 0.06
23 23 0.45
24 7 0.14
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (22 bp):
ATAGGTATCAATACCCCTTTGA
Found at i:53384 original size:19 final size:19
Alignment explanation
Indices: 53360--53411 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
53350 AATAGTCTGA
53360 GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGGATT
53379 GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGGATT
53398 GTGCATCGATGCAT
1 GTGCATCGATGCAT
53412 TAAATGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGATT
Found at i:53448 original size:65 final size:64
Alignment explanation
Indices: 53379--53535 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 64
53369 TGCATGGATT
* * *
53379 GTGCATCGATGCATGGATTGTGCATCGATGCATTAAATGTATTCGATGTTTTC-ATAAAATC-CT
1 GTGCATCGATGCATGGATTGTGCATCGATGCATAAAATGCATTCGATG--TTCAATAAAATCAAT
53442 G
64 G
* ** *
53443 AGTGCATCGATGCATGG-TATGTGCATCGATGCATAAAATGCATTTGATGTTCAATTTATTCAAT
1 -GTGCATCGATGCATGGAT-TGTGCATCGATGCATAAAATGCATTCGATGTTCAATAAAATCAAT
53507 G
64 G
53508 GTGCATCGATGCATGGATTGGTGCATCG
1 GTGCATCGATGCATGGATT-GTGCATCG
53536 GTACACTCTT
Statistics
Matches: 80, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
63 3 0.04
64 23 0.29
65 54 0.68
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCATGGATTGTGCATCGATGCATAAAATGCATTCGATGTTCAATAAAATCAATG
Found at i:53470 original size:84 final size:83
Alignment explanation
Indices: 53315--53476 Score: 240
Period size: 84 Copynumber: 1.9 Consensus size: 83
53305 TGGACCCTTA
*
53315 GTGCATCGATGCGTAAAATGCATTCGATGTTTTAAAATAGTCTGAGTGCATCGATGCATGGATTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGTCTGAGTGCATCGATGCATGGATTG
53380 TGCATCGATGCATGGATT
66 TGCATCGATGCATGGATT
* *
53398 GTGCATCGATGCATTAAATGTATTCGATGTTTTCATAAA-A-TCCTGAGTGCATCGATGCATGG-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AAATAGT-CTGAGTGCATCGATGCATGGA
53460 TATGTGCATCGATGCAT
63 T-TGTGCATCGATGCAT
53477 AAAATGCATT
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
83 32 0.44
84 37 0.51
85 3 0.04
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (83 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGTCTGAGTGCATCGATGCATGGATTG
TGCATCGATGCATGGATT
Found at i:54890 original size:29 final size:29
Alignment explanation
Indices: 54840--54895 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
54830 CAAAGTATAT
54840 AACTTTTAAAAATCACACTTTAGTCACCA
1 AACTTTTAAAAATCACACTTTAGTCACCA
* * *
54869 AACTTTTAAAATTTACATTTTAGTCAC
1 AACTTTTAAAAATCACACTTTAGTCAC
54896 TAGTCAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (29 bp):
AACTTTTAAAAATCACACTTTAGTCACCA
Done.