Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004424.1 Hibiscus syriacus cultivar Beakdansim tig00009702_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: 76728
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2378 original size:12 final size:12
Alignment explanation
Indices: 2361--2386 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2351 TCGACATATG
2361 GGTACGGAAGTT
1 GGTACGGAAGTT
2373 GGTACGGAAGTT
1 GGTACGGAAGTT
2385 GG
1 GG
2387 GTTTGAGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.46, T:0.23
Consensus pattern (12 bp):
GGTACGGAAGTT
Found at i:7709 original size:7 final size:7
Alignment explanation
Indices: 7691--7737 Score: 67
Period size: 7 Copynumber: 6.6 Consensus size: 7
7681 TTATCGGAGG
7691 GAAACAAA
1 GAAA-AAA
*
7699 GAAACAA
1 GAAAAAA
7706 GAAAAAA
1 GAAAAAA
7713 GAAAAAA
1 GAAAAAA
7720 GAAAAAA
1 GAAAAAA
*
7727 GAAAAAG
1 GAAAAAA
7734 GAAA
1 GAAA
7738 GGCAAAATTG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
7 32 0.89
8 4 0.11
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:10348 original size:14 final size:14
Alignment explanation
Indices: 10325--10354 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10315 AATACCAATA
*
10325 TTAAATATAAAAAT
1 TTAAAAATAAAAAT
10339 TTAAAAATAAAAAT
1 TTAAAAATAAAAAT
10353 TT
1 TT
10355 TGATTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAAAATAAAAAT
Found at i:10907 original size:2 final size:2
Alignment explanation
Indices: 10900--10939 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
10890 TACCAAACGC
10900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10940 CCAAAAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13757 original size:2 final size:2
Alignment explanation
Indices: 13750--13786 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
13740 CTCGATGTGA
*
13750 AG AG AG AG AG AG AG AG CG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
13787 TTAATTCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:15166 original size:59 final size:60
Alignment explanation
Indices: 15054--15167 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 60
15044 AAACTAAGAC
* **
15054 TCATTCTAAATTAGTCCTCAAACTTTTAAGCATTTGAATTTCATCCACAAACTATGGCCT
1 TCATTCTAAATTAGTCCCCAAACTTTTAAGCATTCCAATTTCATCCACAAACTATGGCCT
* *
15114 TCATTCT-AATTGGTCCCCAAACTTTTTTAA-CATTCCAATTTCA-CCTCAAACTAT
1 TCATTCTAAATTAGTCCCCAAAC--TTTTAAGCATTCCAATTTCATCCACAAACTAT
15168 ACGTATATGC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 23 0.49
60 18 0.38
61 6 0.13
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (60 bp):
TCATTCTAAATTAGTCCCCAAACTTTTAAGCATTCCAATTTCATCCACAAACTATGGCCT
Found at i:15967 original size:3 final size:3
Alignment explanation
Indices: 15959--15986 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15949 CCTTTAATGA
15959 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
15987 ATACATCAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:16610 original size:16 final size:16
Alignment explanation
Indices: 16585--16615 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16575 AATAAATAGT
16585 AAATGGTAAAATAAAA
1 AAATGGTAAAATAAAA
*
16601 AAATGTTAAAATAAA
1 AAATGGTAAAATAAA
16616 TGAAAAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (16 bp):
AAATGGTAAAATAAAA
Found at i:16632 original size:19 final size:20
Alignment explanation
Indices: 16593--16630 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16583 GTAAATGGTA
16593 AAATAAAAAAATGTTAAAAT
1 AAATAAAAAAATGTTAAAAT
16613 AAATGAAAAAAA-GTTAAA
1 AAAT-AAAAAAATGTTAAA
16631 TACAACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (20 bp):
AAATAAAAAAATGTTAAAAT
Found at i:16742 original size:26 final size:26
Alignment explanation
Indices: 16713--16762 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
16703 CGAATAAACT
16713 AAAAAAAATGATAAAT-T-TTAAAAGAG
1 AAAAAAAA-GA-AAATATGTTAAAAGAG
16739 AAAAAAAAGAAAATATGTTAAAAG
1 AAAAAAAAGAAAATATGTTAAAAG
16763 GAAGAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.18
25 3 0.14
26 15 0.68
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (26 bp):
AAAAAAAAGAAAATATGTTAAAAGAG
Found at i:17082 original size:2 final size:2
Alignment explanation
Indices: 17077--17110 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17067 AAAAAACCAA
17077 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
17111 CATTTTTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17756 original size:26 final size:26
Alignment explanation
Indices: 17727--17778 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17717 GTAGGATTAG
17727 ATAACTAAAAAAATTATCGATTCAAT
1 ATAACTAAAAAAATTATCGATTCAAT
17753 ATAACTAAAAAAATTATCGATTCAAT
1 ATAACTAAAAAAATTATCGATTCAAT
17779 GTGACATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.12, G:0.04, T:0.31
Consensus pattern (26 bp):
ATAACTAAAAAAATTATCGATTCAAT
Found at i:19580 original size:3 final size:3
Alignment explanation
Indices: 19574--19610 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
19564 TTTTTTTAAT
19574 TTA TTA TTA TTA TTA TTA TTGA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
19611 ATTTTGTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:19602 original size:22 final size:21
Alignment explanation
Indices: 19574--19622 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
19564 TTTTTTTAAT
19574 TTATTATTATTATT-ATTATTG
1 TTATTATTATTATTAATT-TTG
19595 ATTATTATTATTATTAATTTTG
1 -TTATTATTATTATTAATTTTG
19617 TTATTA
1 TTATTA
19623 CATATTTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.23
22 17 0.65
23 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (21 bp):
TTATTATTATTATTAATTTTG
Found at i:21042 original size:30 final size:29
Alignment explanation
Indices: 21008--21102 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
20998 CTATTTTTAT
21008 TATTTTAGTCCTGTAA-ATTCATGTTTATGC
1 TATTTTAGTCCTGTAACATTC-TGTTT-TGC
* * * *
21038 TATTTCAGTCCTTTAACTTTCTGTTTTGT
1 TATTTTAGTCCTGTAACATTCTGTTTTGC
** *
21067 TATTTTAG-CCATGTAAGTTTCTGTTTTATC
1 TATTTTAGTCC-TGTAACATTCTGTTTT-GC
21097 TATTTT
1 TATTTT
21103 GATCATTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.04
29 23 0.43
30 25 0.47
31 3 0.06
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.56
Consensus pattern (29 bp):
TATTTTAGTCCTGTAACATTCTGTTTTGC
Found at i:21116 original size:29 final size:28
Alignment explanation
Indices: 21002--21132 Score: 67
Period size: 29 Copynumber: 4.5 Consensus size: 28
20992 AAATGTCTAT
21002 TTTTATTATTTTAGTCC-TGTAAA-TTCATG
1 TTTTATTATTTTAG-CCAT-TAAATTTC-TG
* * *
21031 -TTTATGCTATTTCAGTCCTTTAACTTTCTG
1 TTTTAT--TATTTTAG-CCATTAAATTTCTG
* *
21061 TTTTGTTATTTTAGCCATGTAAGTTTCTG
1 TTTTATTATTTTAGCCAT-TAAATTTCTG
*
21090 TTTTATCTATTTT-GATCATTAAATTTCCT-
1 TTTTAT-TATTTTAG-CCATTAAATTT-CTG
21119 TATTTA-TATTTTAG
1 T-TTTATTATTTTAG
21133 TCCTATTATT
Statistics
Matches: 82, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
28 14 0.17
29 30 0.37
30 30 0.37
31 8 0.10
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTTATTATTTTAGCCATTAAATTTCTG
Found at i:27259 original size:36 final size:35
Alignment explanation
Indices: 27196--27303 Score: 117
Period size: 38 Copynumber: 2.9 Consensus size: 35
27186 ATCTTATTAA
* * * *
27196 AAAAACAAAGTGTCGTCTCACTAGAGACAGTTTTCTT
1 AAAAACAAA-TTTTGTCTCGCTTGAGACA-TTTTCTT
27233 AAAAACAAATTTTGTCTCGCTTGAGACAACTTTCTCTT
1 AAAAACAAATTTTGTCTCGCTTGAGAC-A-TTT-TCTT
* *
27271 TAAAACAAATTATGTCTCGCTTGAGACATTTTC
1 AAAAACAAATTTTGTCTCGCTTGAGACATTTTC
27304 CACCAATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
35 2 0.03
36 17 0.27
37 14 0.23
38 29 0.47
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.34
Consensus pattern (35 bp):
AAAAACAAATTTTGTCTCGCTTGAGACATTTTCTT
Found at i:27345 original size:21 final size:21
Alignment explanation
Indices: 27321--27379 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
27311 TTTGAGAATT
27321 TTAAAACAAATTTTGTCTCGC
1 TTAAAACAAATTTTGTCTCGC
*
27342 TTAAGAC-AA--TT-TCT--C
1 TTAAAACAAATTTTGTCTCGC
27357 TTAAAACAAATTTTGTCTCGC
1 TTAAAACAAATTTTGTCTCGC
27378 TT
1 TT
27380 GAGACATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
15 7 0.23
16 2 0.07
17 3 0.10
18 4 0.13
19 3 0.10
20 2 0.07
21 9 0.30
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (21 bp):
TTAAAACAAATTTTGTCTCGC
Found at i:27540 original size:104 final size:105
Alignment explanation
Indices: 27359--27555 Score: 263
Period size: 104 Copynumber: 1.9 Consensus size: 105
27349 AATTTCTCTT
* * * ** *
27359 AAAACAAATTTTGTCTCGCTTGAGACATTTTTCCTATAAGATACAAATTTTGAATTTGCTTCACA
1 AAAACAAATTTCGTCTCACTTGAGACATTTTCCCTATAAGATACAAATTTCAAAGTTGCTTCACA
*
27424 TGAAACAAAATTAATCTCACTTGAGATTGTTCTTTATTTC
66 TGAAACAAAATTAATATCACTTGAGATTGTTCTTTATTTC
* * *
27464 AAAACAAATTTCGTCTCACTTGAGACATTTTCCC--TCAGAATACAAATTTCAAAGTTGTTTTAC
1 AAAACAAATTTCGTCTCACTTGAGACATTTTCCCTATAAG-ATACAAATTTCAAAGTTGCTTCAC
* *
27527 TTGAAACAAAATTAATATCATTTGAGATT
65 ATGAAACAAAATTAATATCACTTGAGATT
27556 TTCAAAATCG
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
103 3 0.04
104 45 0.57
105 31 0.39
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (105 bp):
AAAACAAATTTCGTCTCACTTGAGACATTTTCCCTATAAGATACAAATTTCAAAGTTGCTTCACA
TGAAACAAAATTAATATCACTTGAGATTGTTCTTTATTTC
Found at i:27842 original size:90 final size:92
Alignment explanation
Indices: 27733--27910 Score: 252
Period size: 92 Copynumber: 2.0 Consensus size: 92
27723 TTTTGAATAT
* * * * * * *
27733 AAAAATTTTTGAGTTGTTTCTTGTGAGA-AAAAAAT-TTTGAGTCTATGTCTTTTGAAACAAAGT
1 AAAAATCTTTGAGTAGTTTCTTGTGAAACAAAAAATCTTTGAATATATGTCTTTGGAAACAAAAT
27796 TTTGTCTCTCTTGAGACAATTTCGTGA
66 TTTGTCTCTCTTGAGACAATTTCGTGA
* * *
27823 AAAAATCTTTGAGTAGTTTCTTTTGAAACAAAAAATCTTTGAATATGTTTCTTTGGAAACAAAAT
1 AAAAATCTTTGAGTAGTTTCTTGTGAAACAAAAAATCTTTGAATATATGTCTTTGGAAACAAAAT
27888 TTTGTCTCTCTTGAGACAATTTC
66 TTTGTCTCTCTTGAGACAATTTC
27911 TTTTGAGAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
90 24 0.32
91 7 0.09
92 45 0.59
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (92 bp):
AAAAATCTTTGAGTAGTTTCTTGTGAAACAAAAAATCTTTGAATATATGTCTTTGGAAACAAAAT
TTTGTCTCTCTTGAGACAATTTCGTGA
Found at i:27858 original size:30 final size:31
Alignment explanation
Indices: 27822--27886 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
27812 CAATTTCGTG
* *
27822 AAAAAATCTTTGAGTA-GTTTCTTTTGAAAC
1 AAAAAATCTTTGAATATGTTTCTTTGGAAAC
27852 AAAAAATCTTTGAATATGTTTCTTTGGAAAC
1 AAAAAATCTTTGAATATGTTTCTTTGGAAAC
27883 AAAA
1 AAAA
27887 TTTTGTCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (31 bp):
AAAAAATCTTTGAATATGTTTCTTTGGAAAC
Found at i:27873 original size:121 final size:123
Alignment explanation
Indices: 27671--27891 Score: 301
Period size: 120 Copynumber: 1.8 Consensus size: 123
27661 TTAAAACGAT
** * *
27671 TTTTGTCTCTCTTGAGACGGTTTCTCTTGAAACAAATCTTTGAGTATGTTCCTTTTGAATATAAA
1 TTTTGTCTCTCTTGAGACGAATTCTCGTGAAACAAATCTTTGAGTATGTTCCTTTTGAATAAAAA
* *
27736 AATTTTTGAGTTGTTTCTTGTGAGAAA-AAAATTTTGAGTCTATGTCTTTTGAAACAAAG
66 AATCTTTGAATTGTTTCTT-TG-GAAACAAAATTTTGAGTCTATGTCTTTTGAAACAAAG
*
27795 TTTTGTCTCTCTTGAGAC-AATT-TCGTGAAA-AAATCTTTGAGTA-GTTTCTTTTGAA-ACAAA
1 TTTTGTCTCTCTTGAGACGAATTCTCGTGAAACAAATCTTTGAGTATGTTCCTTTTGAATA-AAA
27855 AAATCTTTGAATATGTTTCTTTGGAAACAAAATTTTG
65 AAATCTTTGAAT-TGTTTCTTTGGAAACAAAATTTTG
27892 TCTCTCTTGA
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
119 5 0.06
120 34 0.39
121 21 0.24
122 7 0.08
123 2 0.02
124 18 0.21
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (123 bp):
TTTTGTCTCTCTTGAGACGAATTCTCGTGAAACAAATCTTTGAGTATGTTCCTTTTGAATAAAAA
AATCTTTGAATTGTTTCTTTGGAAACAAAATTTTGAGTCTATGTCTTTTGAAACAAAG
Found at i:28168 original size:119 final size:118
Alignment explanation
Indices: 27953--28169 Score: 287
Period size: 120 Copynumber: 1.8 Consensus size: 118
27943 CTAACAAAAT
*
27953 CATCTTTGAGTTTATTTCTTTAAAAACAAATTGTGTCTCTCTTGAGACAGTTTCTAATGAAAAAC
1 CATCTTTGAGTCTATTTCTTTAAAAACAAATTGTGTCTCTCTTGAGACAGTTTCTAATGAAAAA-
28018 CAACCTTTGAGATTGTTTCCTTTGAAAAAAATTCGTCTCACTTAAGACGTAATC
65 CAACCTTTGAGATTGTTTCCTTTGAAAAAAATTCGTCTCACTTAAGACGTAATC
* ** * ** *
28072 CATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCTTTTGAGAAA
1 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATTGTGTCTCTCTTGAGACAGTTTCTAATGAAAAA
*
28137 -AATCTTTGAG-TCTGTTT-CTTTGGAAACAAAATT
65 CAACCTTTGAGAT-TGTTTCCTTT-GAAA-AAAATT
28170 TACCATCTTT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
117 5 0.06
118 18 0.21
119 29 0.34
120 33 0.39
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.40
Consensus pattern (118 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAATTGTGTCTCTCTTGAGACAGTTTCTAATGAAAAAC
AACCTTTGAGATTGTTTCCTTTGAAAAAAATTCGTCTCACTTAAGACGTAATC
Found at i:28189 original size:36 final size:35
Alignment explanation
Indices: 28138--28229 Score: 96
Period size: 36 Copynumber: 2.6 Consensus size: 35
28128 TTTGAGAAAA
* ** *
28138 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTACC
1 ATCTTTGAGTTTGTTTCTTTGGAAACAAAA-CAAAC
*
28174 ATCTTTGAGTTTGTTTCCCTT-GAAACAAAACAAAC
1 ATCTTTGAGTTTGTTT-CTTTGGAAACAAAACAAAC
* *
28209 ATCTTTGAGATTGCTTCTTTG
1 ATCTTTGAGTTTGTTTCTTTG
28230 AAATGATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
34 3 0.07
35 16 0.35
36 24 0.52
37 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.41
Consensus pattern (35 bp):
ATCTTTGAGTTTGTTTCTTTGGAAACAAAACAAAC
Found at i:28436 original size:28 final size:28
Alignment explanation
Indices: 28405--28469 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
28395 AAAACATATC
28405 ATCTTTGAGTTTGTTTT-TCTTGAAACAA
1 ATCTTTGAGTTT-TTTTCTCTTGAAACAA
* *
28433 ATCTTTGGGTTTTTTTCTTTTGAAACAA
1 ATCTTTGAGTTTTTTTCTCTTGAAACAA
28461 ATCTTTGAG
1 ATCTTTGAG
28470 CCGGTTTCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.23, C:0.11, G:0.15, T:0.51
Consensus pattern (28 bp):
ATCTTTGAGTTTTTTTCTCTTGAAACAA
Found at i:28689 original size:40 final size:40
Alignment explanation
Indices: 28645--28876 Score: 177
Period size: 41 Copynumber: 5.5 Consensus size: 40
28635 CCTGTCGTCC
*
28645 TCATCACGTAGGAACCGTGTCATCACCTGACCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATCACCTGACCAGAACTCT
28685 TCATCACGTAGGAGCCGTGTCA--ACCTGATAACCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATCACCTG---ACCAGAACTCT
*
28726 TCATCACGTAGGAGTCGTGTCA--ACCTGATAACCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATCACCTG---ACCAGAACTCT
** *
28767 TCATCACGTATTAGCCGTGTTATCACCTTACTAAAGATGACCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATCA-C---C------TGACCAGAACTCT
* * ** *
28817 TCATCACGTATGAGCAGTGTCATC-CCTCGACCAGATTTCC
1 TCATCACGTAGGAGCCGTGTCATCACCT-GACCAGAACTCT
*
28857 TCATCACGTAGGAACCGTGT
1 TCATCACGTAGGAGCCGTGT
28877 AACCCTTAGA
Statistics
Matches: 161, Mismatches: 15, Indels: 32
0.77 0.07 0.15
Matches are distributed among these distances:
38 5 0.03
39 1 0.01
40 47 0.29
41 69 0.43
43 1 0.01
44 1 0.01
45 1 0.01
47 1 0.01
48 1 0.01
50 32 0.20
53 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (40 bp):
TCATCACGTAGGAGCCGTGTCATCACCTGACCAGAACTCT
Found at i:28731 original size:41 final size:41
Alignment explanation
Indices: 28645--28786 Score: 209
Period size: 41 Copynumber: 3.5 Consensus size: 41
28635 CCTGTCGTCC
*
28645 TCATCACGTAGGAACCGTGTCATCACCTG---ACCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCA--ACCTGATAACCAGAACTCT
28685 TCATCACGTAGGAGCCGTGTCAACCTGATAACCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCAACCTGATAACCAGAACTCT
*
28726 TCATCACGTAGGAGTCGTGTCAACCTGATAACCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCAACCTGATAACCAGAACTCT
**
28767 TCATCACGTATTAGCCGTGT
1 TCATCACGTAGGAGCCGTGT
28787 TATCACCTTA
Statistics
Matches: 94, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
38 5 0.05
40 21 0.22
41 68 0.72
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (41 bp):
TCATCACGTAGGAGCCGTGTCAACCTGATAACCAGAACTCT
Found at i:29088 original size:3 final size:3
Alignment explanation
Indices: 29082--29122 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
29072 TTTTTTTAAT
29082 TTA TTA TTA TTA TTA TTA TTGA TTGA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TT-A TTA TTA TTA TTA TTA
29123 ATTTTGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 30 0.81
4 7 0.19
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:30634 original size:29 final size:28
Alignment explanation
Indices: 30520--30650 Score: 74
Period size: 29 Copynumber: 4.5 Consensus size: 28
30510 AAATGTCTAT
*
30520 TTTTATTATTTTAGTCCAGTAAA-TTCATG
1 TTTTATTATTTTAG-CCATTAAATTTC-TG
* * *
30549 -TTTATGCTATTTCAGTCCTTTAACTTTCTG
1 TTTTAT--TATTTTAG-CCATTAAATTTCTG
* *
30579 TTTTGTTATTTTAGCCATGTAAGTTTCTG
1 TTTTATTATTTTAGCCAT-TAAATTTCTG
*
30608 TTTTATCTATTTT-GATCATTAAATTTCCT-
1 TTTTAT-TATTTTAG-CCATTAAATTT-CTG
30637 TATTTA-TATTTTAG
1 T-TTTATTATTTTAG
30651 TCCTATTATT
Statistics
Matches: 81, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
28 14 0.17
29 30 0.37
30 30 0.37
31 7 0.09
ACGTcount: A:0.22, C:0.12, G:0.10, T:0.56
Consensus pattern (28 bp):
TTTTATTATTTTAGCCATTAAATTTCTG
Found at i:35837 original size:21 final size:21
Alignment explanation
Indices: 35811--35971 Score: 213
Period size: 21 Copynumber: 7.7 Consensus size: 21
35801 GTTTCCAGAT
*
35811 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
35832 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
35853 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
35874 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
35895 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
35915 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
35936 TCGCAATCCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
35957 TCGCAATGCGAACTT
1 TCGCAATGCGAACTT
35972 GCGAACTTGG
Statistics
Matches: 126, Mismatches: 8, Indels: 12
0.86 0.05 0.08
Matches are distributed among these distances:
20 17 0.13
21 109 0.87
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:35997 original size:21 final size:20
Alignment explanation
Indices: 35971--36076 Score: 87
Period size: 21 Copynumber: 5.3 Consensus size: 20
35961 AATGCGAACT
*
35971 TGCGAACTTGGACTATCGCAA
1 TGCGAA-TTCGACTATCGCAA
*
35992 TGCGAATAT-GTA-AATCGCAA
1 TGCGAAT-TCG-ACTATCGCAA
*
36012 TGCGATAGTCGACTATCGCAA
1 TGCGA-ATTCGACTATCGCAA
36033 TGCGAACTTCGACTATCGCAA
1 TGCGAA-TTCGACTATCGCAA
* *
36054 T--G-AGTCGACTATTGCAA
1 TGCGAATTCGACTATCGCAA
36071 TGCGAA
1 TGCGAA
36077 CTTGCGAACT
Statistics
Matches: 70, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
17 13 0.19
18 1 0.01
19 2 0.03
20 18 0.26
21 36 0.51
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (20 bp):
TGCGAATTCGACTATCGCAA
Found at i:36039 original size:91 final size:91
Alignment explanation
Indices: 35880--36055 Score: 343
Period size: 91 Copynumber: 1.9 Consensus size: 91
35870 ACTATCGCAA
35880 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATCC
1 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATCC
35945 GAACTTCGACTATCGCAATGCGAACT
66 GAACTTCGACTATCGCAATGCGAACT
*
35971 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGC
1 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATCC
36036 GAACTTCGACTATCGCAATG
66 GAACTTCGACTATCGCAATG
36056 AGTCGACTAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (91 bp):
TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATCC
GAACTTCGACTATCGCAATGCGAACT
Found at i:36063 original size:17 final size:18
Alignment explanation
Indices: 36018--36072 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
36008 GCAATGCGAT
36018 AGTCGACTATCGCAATGCGA
1 AGTCGACTATCGCAAT--GA
*
36038 ACTTCGACTATCGCAATG-
1 A-GTCGACTATCGCAATGA
*
36056 AGTCGACTATTGCAATG
1 AGTCGACTATCGCAATG
36073 CGAACTTGCG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 14 0.45
18 1 0.03
19 1 0.03
20 1 0.03
21 14 0.45
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (18 bp):
AGTCGACTATCGCAATGA
Found at i:36109 original size:108 final size:110
Alignment explanation
Indices: 35859--36132 Score: 373
Period size: 108 Copynumber: 2.5 Consensus size: 110
35849 ACTATCGCAA
* *
35859 TGCGAACTTGGACTATCGCAATGCGAACT-TGGACTATCGCAATGCGAATA-T-GTAAATCGCAA
1 TGCGAACTTGGACTATCGCAATGCGAA-TATGTA-AATCGCAATGCG-ATAGTCG-AAATCGCAA
*
35921 TGCGATAGTCGACTATCGCAATCCGAACTTCGACTATCGCAATGCGAACT
62 TGCGATAGTCGACTATCGCAAT-CGAACGTCGACTATCGCAATGCGAACT
*
35971 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCAATGC
1 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGA-AATCGCAATGC
* *
36036 GA-ACTTCGACTATCGCAAT-G-A-GTCGACTATTGCAATGCGAACT
65 GATA-GTCGACTATCGCAATCGAACGTCGACTATCGCAATGCGAACT
*
36079 TGCGAACTTTGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAA
1 TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAA
36133 TGCGAATATG
Statistics
Matches: 149, Mismatches: 8, Indels: 15
0.87 0.05 0.09
Matches are distributed among these distances:
108 72 0.48
109 1 0.01
110 4 0.03
111 15 0.10
112 57 0.38
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (110 bp):
TGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAATCGCAATGCG
ATAGTCGACTATCGCAATCGAACGTCGACTATCGCAATGCGAACT
Found at i:36140 original size:33 final size:33
Alignment explanation
Indices: 36098--36161 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
36088 TGACTATCGC
36098 AATGCGAATATGTAAATCGCAATGCGATAGTCG
1 AATGCGAATATGTAAATCGCAATGCGATAGTCG
36131 AATGCGAATATGTAAATCGCAATGCGATAGT
1 AATGCGAATATGTAAATCGCAATGCGATAGT
36162 GAACTATCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.25
Consensus pattern (33 bp):
AATGCGAATATGTAAATCGCAATGCGATAGTCG
Found at i:36172 original size:21 final size:22
Alignment explanation
Indices: 36146--36332 Score: 98
Period size: 21 Copynumber: 8.6 Consensus size: 22
36136 GAATATGTAA
36146 ATCGCAATGCGATAGT-GAACT
1 ATCGCAATGCGATAGTCGAACT
*
36167 ATCGCAATGCGA-ACTTCG-ACT
1 ATCGCAATGCGATA-GTCGAACT
*
36188 ATCGCAATGCGA-ACTTGCGAACTTGGACT
1 ATCGCAATGCGATA-GT-CG-A-----ACT
36217 ATCGCAATGCGAATA-T-GTAA--
1 ATCGCAATGCG-ATAGTCG-AACT
36237 ATCGCAATGCGATAGTCG-ACT
1 ATCGCAATGCGATAGTCGAACT
36258 ATCGCAATGCGAATA-T-GTAA--
1 ATCGCAATGCG-ATAGTCG-AACT
*
36278 ATCGCAATGCGATAGTCGAAAT
1 ATCGCAATGCGATAGTCGAACT
**
36300 -TCGCGTTGCGATAGTCG-ACT
1 ATCGCAATGCGATAGTCGAACT
*
36320 ATCGCATTGCGAT
1 ATCGCAATGCGAT
36333 TTACATATTC
Statistics
Matches: 136, Mismatches: 6, Indels: 48
0.72 0.03 0.25
Matches are distributed among these distances:
19 7 0.05
20 30 0.22
21 72 0.53
22 8 0.06
27 2 0.01
29 15 0.11
30 1 0.01
31 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (22 bp):
ATCGCAATGCGATAGTCGAACT
Found at i:36206 original size:124 final size:127
Alignment explanation
Indices: 36058--36293 Score: 388
Period size: 124 Copynumber: 1.8 Consensus size: 127
36048 TCGCAATGAG
* *
36058 TCGACTATTGCAATGCGAACTTGCGAACTTTGACTATCGCAATGCGAATATGTAAATCGCAATGC
1 TCGACTATCGCAATGCGAACTTGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGC
36123 GATA-G-TCG-AATGCGAATATGTAAATCGCAATGCGATAGTGAACTATCGCAATGCGAACT
66 GATACGATCGCAATGCGAATATGTAAATCGCAATGCGATAGTGAACTATCGCAATGCGAACT
36182 TCGACTATCGCAATGCGAACTTGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGC
1 TCGACTATCGCAATGCGAACTTGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGC
36247 GATAGTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGT
66 GATA--CG---ATCGCAATGCGAATATGTAAATCGCAATGCGATAGT
36294 CGAAATTCGC
Statistics
Matches: 102, Mismatches: 2, Indels: 8
0.91 0.02 0.07
Matches are distributed among these distances:
124 67 0.66
127 1 0.01
131 3 0.03
132 31 0.30
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (127 bp):
TCGACTATCGCAATGCGAACTTGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGC
GATACGATCGCAATGCGAATATGTAAATCGCAATGCGATAGTGAACTATCGCAATGCGAACT
Found at i:36216 original size:29 final size:29
Alignment explanation
Indices: 36174--36229 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
36164 ACTATCGCAA
36174 TGCGAACTTCGACTATCGCAATGCGAACT
1 TGCGAACTTCGACTATCGCAATGCGAACT
*
36203 TGCGAACTTGGACTATCGCAATGCGAA
1 TGCGAACTTCGACTATCGCAATGCGAA
36230 TATGTAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (29 bp):
TGCGAACTTCGACTATCGCAATGCGAACT
Found at i:36248 original size:41 final size:41
Alignment explanation
Indices: 36213--36296 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
36203 TGCGAACTTG
36213 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
36254 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
1 GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
36295 GA
1 GA
36297 AATTCGCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (41 bp):
GACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTC
Found at i:36331 original size:62 final size:62
Alignment explanation
Indices: 36244--36373 Score: 185
Period size: 62 Copynumber: 2.1 Consensus size: 62
36234 TAAATCGCAA
36244 TGCGATAGTCGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCGAAATTCGCGT
1 TGCGATAGTCGACTATCGCAATGCG-AT-T-TACATATTCGCAATGCGATAGTCGAAATTCGCGT
* * *
36306 TGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCACTGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCAATGCGATAGTCGAAATTCGCGT
36368 TGCGAT
1 TGCGAT
36374 TTATTCCAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
59 2 0.03
60 2 0.03
61 3 0.05
62 55 0.89
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (62 bp):
TGCGATAGTCGACTATCGCAATGCGATTTACATATTCGCAATGCGATAGTCGAAATTCGCGT
Found at i:36371 original size:21 final size:20
Alignment explanation
Indices: 36238--36373 Score: 82
Period size: 21 Copynumber: 6.6 Consensus size: 20
36228 AATATGTAAA
* *
36238 TCGCAATGCGATAGTCGACT
1 TCGCATTGCGATAGTCGAAT
* *
36258 ATCGCAATGCGAATA-T-GTAAA
1 -TCGCATTGCG-ATAGTCG-AAT
*
36279 TCGCAATGCGATAGTCGAAAT
1 TCGCATTGCGATAGTCG-AAT
* *
36300 TCGCGTTGCGATAGTCGACT
1 TCGCATTGCGATAGTCGAAT
*
36320 ATCGCATTGCGAT-TTAC-ATAT
1 -TCGCATTGCGATAGT-CGA-AT
*
36341 TCGCACTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAA-T
*
36362 TCGCGTTGCGAT
1 TCGCATTGCGAT
36374 TTATTCCAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
19 3 0.03
20 29 0.32
21 56 0.62
22 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (20 bp):
TCGCATTGCGATAGTCGAAT
Found at i:36508 original size:5 final size:5
Alignment explanation
Indices: 36495--36527 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
36485 CGTATTACCA
*
36495 CGACC CGACA CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGACC CGA
36528 GACGAGACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.24, C:0.55, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:37254 original size:21 final size:20
Alignment explanation
Indices: 37228--37341 Score: 97
Period size: 21 Copynumber: 5.5 Consensus size: 20
37218 TTCGCAAGTA
37228 CGCATTGCGATAGTCGACTAT
1 CGCATTGCGATAGTCGACT-T
* *
37249 CGCATTGCGAT-TTAC-ATATT
1 CGCATTGCGATAGT-CGA-CTT
* *
37269 CGCATTGCGATAGTCCAAGTT
1 CGCATTGCGATAGT-CGACTT
*
37290 CGCATTGCGATAGTCGAAGTT
1 CGCATTGCGATAGTCG-ACTT
*
37311 CGCATTGCGATAGTCGAAGTT
1 CGCATTGCGATAGTCG-ACTT
*
37332 CGCGTTGCGA
1 CGCATTGCGA
37342 ATCTGGAAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
20 15 0.19
21 65 0.80
22 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (20 bp):
CGCATTGCGATAGTCGACTT
Found at i:42509 original size:21 final size:21
Alignment explanation
Indices: 42485--42545 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
42475 AACTTTGAAA
42485 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
* *
42506 AAAT--ATTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
42520 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
42541 AAATG
1 AAATG
42546 TTTCTTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 14
0.62 0.09 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.14
19 4 0.14
20 3 0.10
21 10 0.34
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:42584 original size:37 final size:36
Alignment explanation
Indices: 42477--42585 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
42467 TGGCAACCAA
*
42477 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
42514 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
42549 CTTTGAAAAATGATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATG-GTTTTCAAAGTTTGGTAAATGTTT
42586 GTTGAAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 34 0.51
36 6 0.09
37 27 0.40
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:43812 original size:15 final size:15
Alignment explanation
Indices: 43788--43819 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43778 TGGCAGATCC
*
43788 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
43803 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
43818 AA
1 AA
43820 GAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:47131 original size:21 final size:21
Alignment explanation
Indices: 47107--47167 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
47097 AACTTTGAAA
47107 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
47128 AAAT-G-TTTC----TTT-GT
1 AAATGGTTTTCAAAGTTTGGT
47142 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
47163 AAATG
1 AAATG
47168 TTTCTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
14 6 0.18
15 4 0.12
16 4 0.12
19 4 0.12
20 4 0.12
21 11 0.33
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:47198 original size:37 final size:36
Alignment explanation
Indices: 47099--47207 Score: 175
Period size: 35 Copynumber: 3.0 Consensus size: 36
47089 TGGCAACCAA
47099 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
47136 CTTTG-TAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
47171 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
47208 GTTGAAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 34 0.51
36 6 0.09
37 27 0.40
ACGTcount: A:0.28, C:0.06, G:0.20, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:64092 original size:2 final size:2
Alignment explanation
Indices: 64085--64123 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
64075 TTTGTGTTTT
64085 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64124 GAATAACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65933 original size:25 final size:25
Alignment explanation
Indices: 65901--65957 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
65891 GCATAGCATG
*
65901 ACTAAAAAAATTCTAAATAAAAACT
1 ACTAAAAAAATTCTAAACAAAAACT
*
65926 ACTAAAAAAATTCTAAACAGAAACT
1 ACTAAAAAAATTCTAAACAAAAACT
*
65951 ATTAAAA
1 ACTAAAA
65958 GATCATACTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.63, C:0.12, G:0.02, T:0.23
Consensus pattern (25 bp):
ACTAAAAAAATTCTAAACAAAAACT
Found at i:71144 original size:14 final size:14
Alignment explanation
Indices: 71110--71152 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
71100 TCGAAATACA
71110 GAAATCAGATATTAG
1 GAAATCA-ATATTAG
71125 GAAATCAATATTCAG
1 GAAATCAATATT-AG
71140 G-AATCAAGTATTA
1 GAAATCAA-TATTA
71153 TGTATTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (14 bp):
GAAATCAATATTAG
Found at i:71934 original size:29 final size:28
Alignment explanation
Indices: 71902--72032 Score: 105
Period size: 29 Copynumber: 4.8 Consensus size: 28
71892 TTTTTTTCAA
*
71902 AATTACAAAAATAGCATCATTTTAAAATT
1 AATTACAAAAATAGCACCATTTTAAAA-T
* *
71931 AATTACCAATATAGCACCATTTTCAAAAT
1 AATTACAAAAATAGCACCATTTT-AAAAT
* * *** *
71960 ATTTACTAAAAT-GTCATTTTTTTCAAA-
1 AATTACAAAAATAG-CACCATTTTAAAAT
71987 AATTAC-AAAATAG---CATTTTAAAA-
1 AATTACAAAAATAGCACCATTTTAAAAT
72010 AATTACAAAAATAGCACCATTTT
1 AATTACAAAAATAGCACCATTTT
72033 CGAATTAATT
Statistics
Matches: 81, Mismatches: 14, Indels: 16
0.73 0.13 0.14
Matches are distributed among these distances:
23 13 0.16
24 7 0.09
26 5 0.06
27 12 0.15
28 4 0.05
29 36 0.44
30 4 0.05
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (28 bp):
AATTACAAAAATAGCACCATTTTAAAAT
Found at i:71992 original size:27 final size:28
Alignment explanation
Indices: 71950--72005 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 28
71940 TATAGCACCA
71950 TTTTCAAAATATTTACTAAAAT-GTCATTT
1 TTTTCAAAATATTTAC-AAAATAG-CATTT
71979 TTTTCAAAA-A-TTACAAAATAGCATTT
1 TTTTCAAAATATTTACAAAATAGCATTT
72005 T
1 T
72006 AAAAAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 11 0.42
27 5 0.19
28 1 0.04
29 9 0.35
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.45
Consensus pattern (28 bp):
TTTTCAAAATATTTACAAAATAGCATTT
Found at i:72010 original size:23 final size:24
Alignment explanation
Indices: 71979--72025 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
71969 AATGTCATTT
*
71979 TTTTCAAAAATTAC-AAAATAGCA
1 TTTTAAAAAATTACAAAAATAGCA
72002 TTTTAAAAAATTACAAAAATAGCA
1 TTTTAAAAAATTACAAAAATAGCA
72026 CCATTTTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (24 bp):
TTTTAAAAAATTACAAAAATAGCA
Found at i:72053 original size:79 final size:81
Alignment explanation
Indices: 71892--72054 Score: 197
Period size: 79 Copynumber: 2.0 Consensus size: 81
71882 ATTAATATTT
* *
71892 TTTTTTTCAAAATTACAAAAATAGCATCATTTTAAAATTAATTACCAATATAGCACCATTTTCAA
1 TTTTTTTCAAAATTACAAAAATAG-A-CATTTTAAAA-TAATTACAAAAATAGCACCATTTTCAA
* *
71957 AATATTTACTAAAATGTCA
63 AATAATTACCAAAATGTCA
* *
71976 TTTTTTTCAAAAATTAC-AAAATAG-CATTTTAAAA-AATTACAAAAATAGCACCATTTTCGAAT
1 TTTTTTTC-AAAATTACAAAAATAGACATTTTAAAATAATTACAAAAATAGCACCATTTTCAAAA
* *
72038 TAATTCCCAATATGTCA
65 TAATTACCAAAATGTCA
72055 CCAATTTCAA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
79 37 0.53
81 10 0.14
84 15 0.21
85 8 0.11
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.37
Consensus pattern (81 bp):
TTTTTTTCAAAATTACAAAAATAGACATTTTAAAATAATTACAAAAATAGCACCATTTTCAAAAT
AATTACCAAAATGTCA
Found at i:72057 original size:29 final size:29
Alignment explanation
Indices: 72001--72085 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 29
71991 ACAAAATAGC
* *
72001 ATTTTAAAA-AATTACAAAAATAG-CACCA
1 ATTTCAAAATAATTACCAAAAT-GTCACCA
* * * * *
72029 TTTTCGAATTAATTCCCAATATGTCACCA
1 ATTTCAAAATAATTACCAAAATGTCACCA
*
72058 ATTTCAAAATAATTACTAAAATGTCACC
1 ATTTCAAAATAATTACCAAAATGTCACC
72086 GGTCAATAGT
Statistics
Matches: 42, Mismatches: 13, Indels: 3
0.72 0.22 0.05
Matches are distributed among these distances:
28 6 0.14
29 36 0.86
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.32
Consensus pattern (29 bp):
ATTTCAAAATAATTACCAAAATGTCACCA
Found at i:72117 original size:18 final size:18
Alignment explanation
Indices: 72094--72134 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
72084 CCGGTCAATA
**
72094 GTCAACGGGTCGGGTCGG
1 GTCAACGGGTCAAGTCGG
72112 GTCAACGGGTCAAGTCGG
1 GTCAACGGGTCAAGTCGG
72130 GTCAA
1 GTCAA
72135 AACTGGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.17
Consensus pattern (18 bp):
GTCAACGGGTCAAGTCGG
Done.