Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005705.1 Kokia drynarioides strain JFW-HI SEQ_119919, 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: 44267
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:16136 original size:10 final size:10
Alignment explanation
Indices: 16121--16173 Score: 61
Period size: 10 Copynumber: 5.0 Consensus size: 10
16111 AAACAATCAC
16121 AAAAAGAAAG
1 AAAAAGAAAG
16131 AAAAAGAAAG
1 AAAAAGAAAG
*
16141 AAGAAGAAAG
1 AAAAAGAAAG
*
16151 AAGAAAAAAAG
1 AA-AAAGAAAG
16162 AATAAAAGAAAG
1 -A-AAAAGAAAG
16174 GAAATATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
10 21 0.58
11 6 0.17
12 8 0.22
13 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:21743 original size:18 final size:18
Alignment explanation
Indices: 21694--21749 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
21684 TGCAGTCTAC
*
21694 TGTGGCTGCATAC-GAGCA
1 TGTGACTGCAT-CTGAGCA
* *
21712 CGTGACTGTATCTGAGCA
1 TGTGACTGCATCTGAGCA
* *
21730 TGTGACTGCGTCTGATCA
1 TGTGACTGCATCTGAGCA
21748 TG
1 TG
21750 ATGTGTATGC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (18 bp):
TGTGACTGCATCTGAGCA
Found at i:35356 original size:44 final size:44
Alignment explanation
Indices: 35262--35493 Score: 333
Period size: 44 Copynumber: 5.2 Consensus size: 44
35252 GTTACATCAT
* * *
35262 CATCCAATCTTTTACCCTTAAGTCAAGAAGG-CAGATTGAAGAC
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGACAGATTGAAGAA
35305 CATCCAATCTTTTACCCCTAAGTCAAGAGGGACAGATTGAAGAA
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGACAGATTGAAGAA
* ** * *
35349 CATCCAATCTTTTACCCATAAGTCAAGAGGGGTAGACTGAAGAC
1 CATCCAATCTTTTACCCCTAAGTCAAGAGGGACAGATTGAAGAA
*
35393 CATCCAATCTTTTACCCCTAAGTCAAGAGGGGA-AGATTGAAGTCAT
1 CATCCAATCTTTTACCCCTAAGTCAAGA-GGGACAGATTGAAG--AA
35439 CATCCAATCTTTTACCCCCTAAGTCAAGAGGGACAGATTGAAGAA
1 CATCCAATCTTTTA-CCCCTAAGTCAAGAGGGACAGATTGAAGAA
35484 CATCCAATCT
1 CATCCAATCT
35494 AGGGACAGAT
Statistics
Matches: 170, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
43 29 0.17
44 85 0.50
45 14 0.08
46 19 0.11
47 23 0.14
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (44 bp):
CATCCAATCTTTTACCCCTAAGTCAAGAGGGACAGATTGAAGAA
Found at i:35505 original size:27 final size:27
Alignment explanation
Indices: 35467--35520 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
35457 CTAAGTCAAG
35467 AGGGACAGATTGAAGAACATCCAATCT
1 AGGGACAGATTGAAGAACATCCAATCT
35494 AGGGACAGATTGAAGAACATCCAATCT
1 AGGGACAGATTGAAGAACATCCAATCT
35521 TTTACCCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (27 bp):
AGGGACAGATTGAAGAACATCCAATCT
Found at i:35548 original size:71 final size:72
Alignment explanation
Indices: 35422--35564 Score: 202
Period size: 71 Copynumber: 2.0 Consensus size: 72
35412 AAGTCAAGAG
*
35422 GGGAAGATTGAAGTCATCATCCAATCTTTTACCCCCTAAGTCAAGAGGGACAGATTGAAGAACAT
1 GGGAAGATTGAAG-CAACATCCAATCTTTTACCCCCTAAGTCAAGAGGGACAGATTGAAGAACAT
35487 CCAATCTA
65 CCAATCTA
* * *
35495 GGGACAGATTGAAG-AACATCCAATCTTTTA-CCCGTAAGTTAAGA-GGAGCAGATTGAAGACCA
1 GGGA-AGATTGAAGCAACATCCAATCTTTTACCCCCTAAGTCAAGAGGGA-CAGATTGAAGAACA
35557 TCCAATCT
64 TCCAATCT
35565 TTTAACCCTA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
70 3 0.05
71 33 0.52
72 15 0.23
73 4 0.06
74 9 0.14
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (72 bp):
GGGAAGATTGAAGCAACATCCAATCTTTTACCCCCTAAGTCAAGAGGGACAGATTGAAGAACATC
CAATCTA
Found at i:35685 original size:46 final size:44
Alignment explanation
Indices: 35494--36020 Score: 359
Period size: 38 Copynumber: 12.8 Consensus size: 44
35484 CATCCAATCT
* * * * *
35494 AGGGACAGATTGAAGAACATCCAATCTTTTACCCGTAAGTTAAG
1 AGGGGCAGATTGAAGACCATCCAATCTTTTACCCCTAAATCAAG
* * *
35538 AGGAGCAGATTGAAGACCATCCAATCTTTTAACCCTAAGTCAAG
1 AGGGGCAGATTGAAGACCATCCAATCTTTTACCCCTAAATCAAG
* *
35582 AGGAGCAGATTGAAGACCATCAAATCTTTTACCCCT-AATCAAG
1 AGGGGCAGATTGAAGACCATCCAATCTTTTACCCCTAAATCAAG
* *
35625 AGGGGTAGATTGAAGCCACCATCCAATCTTTTACCCTTAAATCAAG
1 AGGGGCAGATTGAAG--ACCATCCAATCTTTTACCCCTAAATCAAG
* * *
35671 AGGGGCAGACTGAAGTCACAATCCAATCTTTTACCCCT-AATCAAA
1 AGGGGCAGATTGAAG--ACCATCCAATCTTTTACCCCTAAATCAAG
* * *
35716 AGGGGCAGATTGAA-ACCATCGTCTAATCTCTTACCCC--GATC-AT
1 AGGGGCAGATTGAAGACCATC--C-AATCTTTTACCCCTAAATCAAG
*
35759 A-GGGTAGATTGAAG--CATCCAATCTTTTA-CCCT-AATC-AG
1 AGGGGCAGATTGAAGACCATCCAATCTTTTACCCCTAAATCAAG
* *
35797 A-GGGCAGATTGAAGACACA-CCAATCTCTTACCCC--GATC-A-
1 AGGGGCAGATTGAAGAC-CATCCAATCTTTTACCCCTAAATCAAG
* * *
35836 TGGGGCAGATTGAAG--CATCCAATCTTTTA-CCCT-AGT-TAG
1 AGGGGCAGATTGAAGACCATCCAATCTTTTACCCCTAAATCAAG
* * * *
35875 A-GGGCAGATTAAAGA-CA-CTAATCTCTTACCCCGT---TCATG
1 AGGGGCAGATTGAAGACCATCCAATCTTTTACCCC-TAAATCAAG
*
35914 A--GGTAGATTGAAG--CATCCAATCTTTTA-CCCT-AATC-AG
1 AGGGGCAGATTGAAGACCATCCAATCTTTTACCCCTAAATCAAG
* * *
35951 A-GAGCAAATTGAAGACACA-CCAATCTCTTACCCC--AATC-A-
1 AGGGGCAGATTGAAGAC-CATCCAATCTTTTACCCCTAAATCAAG
*
35990 TGGGGCAGATTGAAG--CATCCAATCTTTTACC
1 AGGGGCAGATTGAAGACCATCCAATCTTTTACC
36021 TTAGTTAGAG
Statistics
Matches: 398, Mismatches: 54, Indels: 68
0.77 0.10 0.13
Matches are distributed among these distances:
36 1 0.00
37 17 0.04
38 101 0.25
39 8 0.02
40 54 0.14
41 14 0.04
42 16 0.04
43 21 0.05
44 76 0.19
45 50 0.13
46 40 0.10
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (44 bp):
AGGGGCAGATTGAAGACCATCCAATCTTTTACCCCTAAATCAAG
Found at i:35697 original size:206 final size:206
Alignment explanation
Indices: 35293--35699 Score: 606
Period size: 206 Copynumber: 2.0 Consensus size: 206
35283 GTCAAGAAGG
*
35293 CAGATTGAAGACCATCCAATCTTTTACCCCTAAGTCAAGAGGGACAGATTGAAGAACATCCAATC
1 CAGATTGAAGAACATCCAATCTTTTACCCCTAAGTCAAGAGGGACAGATTGAAGAACATCCAATC
* * *
35358 TTTTACCCATAAGTCAAGAGGGGTAGACTGAAGACCATCCAATCTTTTACCCCTAAGTCAAGAGG
66 TTTTACCCATAAGTCAAGAGGAGCAGACTGAAGACCATCAAATCTTTTACCCCTAAGTCAAGAGG
* * * *
35423 GGAAGATTGAAGTCATCATCCAATCTTTTACCCCCTAAGTCAAGAGGGACAGATTGAAGAACATC
131 GGAAGATTGAAGCCACCATCCAATCTTTTACCCCCTAAATCAAGAGGGACAGACTGAAGAACATC
35488 CAATCTAGGGA
196 CAATCTAGGGA
* * *
35499 CAGATTGAAGAACATCCAATCTTTTACCCGTAAGTTAAGA-GGAGCAGATTGAAGACCATCCAAT
1 CAGATTGAAGAACATCCAATCTTTTACCCCTAAGTCAAGAGGGA-CAGATTGAAGAACATCCAAT
*
35563 CTTTTAACCC-TAAGTCAAGAGGAGCAGATTGAAGACCATCAAATCTTTTACCCCTAA-TCAAGA
65 CTTTT-ACCCATAAGTCAAGAGGAGCAGACTGAAGACCATCAAATCTTTTACCCCTAAGTCAAGA
* * * *
35626 GGGGTAGATTGAAGCCACCATCCAATCTTTTA-CCCTTAAATCAAGAGGGGCAGACTGAAGTCAC
129 GGGGAAGATTGAAGCCACCATCCAATCTTTTACCCCCTAAATCAAGAGGGACAGACTGAAG-AAC
35690 AATCCAATCT
193 -ATCCAATCT
35700 TTTACCCCTA
Statistics
Matches: 181, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
204 24 0.13
205 40 0.22
206 113 0.62
207 4 0.02
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (206 bp):
CAGATTGAAGAACATCCAATCTTTTACCCCTAAGTCAAGAGGGACAGATTGAAGAACATCCAATC
TTTTACCCATAAGTCAAGAGGAGCAGACTGAAGACCATCAAATCTTTTACCCCTAAGTCAAGAGG
GGAAGATTGAAGCCACCATCCAATCTTTTACCCCCTAAATCAAGAGGGACAGACTGAAGAACATC
CAATCTAGGGA
Found at i:35710 original size:250 final size:248
Alignment explanation
Indices: 35262--35729 Score: 728
Period size: 250 Copynumber: 1.9 Consensus size: 248
35252 GTTACATCAT
* *
35262 CATCCAATCTTTTACCCTTAAGTCAAGAAGGCAGATTGAAGACCATCCAATCTTTTACCCCTAAG
1 CATCCAATCTTTTACCCGTAAGTCAAGAAGGCAGATTGAAGACCATCCAATCTTTTAACCCTAAG
*
35327 TCAAGAGGGACAGATTGAAGAACATCCAATCTTTTACCCATAAGTCAAGAGGGGTAGACTGAAGA
66 TCAAGAGGGACAGATTGAAGAACATCAAATCTTTTACCCATAAGTCAAGAGGGGTAGACTGAAGA
* *
35392 CCATCCAATCTTTTACCCCTAAGTCAAGAGGGGAAGATTGAAGTCATCATCCAATCTTTTACCCC
131 CCATCCAATCTTTTACCCCTAAATCAAGAGGGGAAGACTGAAGTCATCATCCAATCTTTTACCCC
*
35457 CTAAGTCAAGAGGGACAGATTGAAGAACATCCAATCTAGGGACAGATTGAAGAA
196 CTAA-TCAAAAGGGACAGATTGAAGAACATCCAATCTAGGGACAGATTGAAGAA
* *
35511 CATCCAATCTTTTACCCGTAAGTTAAGAGGAGCAGATTGAAGACCATCCAATCTTTTAACCCTAA
1 CATCCAATCTTTTACCCGTAAGTCAAGAAG-GCAGATTGAAGACCATCCAATCTTTTAACCCTAA
* * *
35576 GTCAAGA-GGAGCAGATTGAAGACCATCAAATCTTTTACCCCTAA-TCAAGAGGGGTAGATTGAA
65 GTCAAGAGGGA-CAGATTGAAGAACATCAAATCTTTTACCCATAAGTCAAGAGGGGTAGACTGAA
* *
35639 GCCACCATCCAATCTTTTACCCTTAAATCAAGAGGGGCAGACTGAAGTCA-CAATCCAATCTTTT
129 G--ACCATCCAATCTTTTACCCCTAAATCAAGAGGGGAAGACTGAAGTCATC-ATCCAATCTTTT
*
35703 A-CCCCTAATCAAAAGGGGCAGATTGAA
191 ACCCCCTAATCAAAAGGGACAGATTGAA
35730 ACCATCGTCT
Statistics
Matches: 200, Mismatches: 14, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
249 66 0.33
250 78 0.39
251 56 0.28
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (248 bp):
CATCCAATCTTTTACCCGTAAGTCAAGAAGGCAGATTGAAGACCATCCAATCTTTTAACCCTAAG
TCAAGAGGGACAGATTGAAGAACATCAAATCTTTTACCCATAAGTCAAGAGGGGTAGACTGAAGA
CCATCCAATCTTTTACCCCTAAATCAAGAGGGGAAGACTGAAGTCATCATCCAATCTTTTACCCC
CTAATCAAAAGGGACAGATTGAAGAACATCCAATCTAGGGACAGATTGAAGAA
Found at i:35744 original size:91 final size:86
Alignment explanation
Indices: 35499--35867 Score: 288
Period size: 91 Copynumber: 4.3 Consensus size: 86
35489 AATCTAGGGA
* * * *
35499 CAGATTGAAGA-ACATCCAATCTTTTACCCGTAAGTTAAGAGGAGCAGATTGAAGACCATC-CAA
1 CAGACTGAAGACA-ATCCAATCTTTTACCCCTAA-TCAAGAGGGGCAGATTGAA-ACCATCTCAA
*
35562 TCTTTTAACCCTAAGTCAAGAGGAG
63 TCTTTT-ACCCTAAATCAAGAGGAG
* * * *
35587 CAGATTGAAGACCATCAAATCTTTTACCCCTAATCAAGAGGGGTAGATTGAAGCCACCATC-CAA
1 CAGACTGAAGACAATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAA---ACCATCTCAA
*
35651 TCTTTTACCCTTAAATCAAGAGGGG
63 TCTTTTACCC-TAAATCAAGAGGAG
*
35676 CAGACTGAAGTCACAATCCAATCTTTTACCCCTAATCAAAAGGGGCAGATTGAAACCATCGTCTA
1 CAGACTGAAG--ACAATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAACCATC-TC-A
* ** *
35741 ATCTCTTACCC-CGATC-ATAGG-G
62 ATCTTTTACCCTAAATCAAGAGGAG
* *
35763 TAGATTGAAG-C-ATCCAATCTTTTA-CCCTAATC-AGA-GGGCAGATTGAAGACACA-C-CAAT
1 CAGACTGAAGACAATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAA-AC-CATCTCAAT
* ** *
35821 CTCTTACCC-CGATCATG-GG-G
64 CTTTTACCCTAAATCAAGAGGAG
*
35841 CAGATTGAAG-C-ATCCAATCTTTTACCC
1 CAGACTGAAGACAATCCAATCTTTTACCC
35868 TAGTTAGAGG
Statistics
Matches: 244, Mismatches: 24, Indels: 35
0.81 0.08 0.12
Matches are distributed among these distances:
78 43 0.18
79 3 0.01
80 12 0.05
81 5 0.02
82 10 0.04
83 13 0.05
84 1 0.00
87 25 0.10
88 43 0.18
89 39 0.16
90 1 0.00
91 49 0.20
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (86 bp):
CAGACTGAAGACAATCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGAAACCATCTCAATCT
TTTACCCTAAATCAAGAGGAG
Found at i:35764 original size:133 final size:128
Alignment explanation
Indices: 35500--36020 Score: 361
Period size: 116 Copynumber: 4.2 Consensus size: 128
35490 ATCTAGGGAC
* * *
35500 AGATTGAAGAACATCCAATCTTTTACCCGTAAGTTAAGAGGAGCAGATTGAAG-ACCATCCAATC
1 AGATTGAAG--CATCCAATCTTTTACCC-TAAATCAAGAGGGGCAGATTGAAGCA-CATCCAATC
* * *
35564 TTTTAACCCTAAGTCAAGAGGAGCAGATTGAAGACCATCAAATCTTTTACCCCTAATCAAGAGGG
62 TTTTACCCCTAAGTCAAAAGGAGCAGATTGAAGACCATCAAATCTCTTACCCCTAATCAAGAGGG
35629 GT
127 GT
*
35631 AGATTGAAGCCACCATCCAATCTTTTACCCTTAAATCAAGAGGGGCAGACTGAAGTCACAATCCA
1 AGATTGAAG----CATCCAATCTTTTACCC-TAAATCAAGAGGGGCAGATTGAAG-CAC-ATCCA
* * *
35696 ATCTTTTACCCCTAA-TCAAAAGGGGCAGATTGAA-ACCATCGTCTAATCTCTTACCCC-GATC-
59 ATCTTTTACCCCTAAGTCAAAAGGAGCAGATTGAAGACCA---TCAAATCTCTTACCCCTAATCA
*
35757 ATA-GGGT
121 AGAGGGGT
*
35764 AGATTGAAGCATCCAATCTTTTACCCT-AATC-AGA-GGGCAGATTGAAGACACA-CCAATCTCT
1 AGATTGAAGCATCCAATCTTTTACCCTAAATCAAGAGGGGCAGATTGAAG-CACATCCAATCTTT
* * * * * * * *
35825 TACCCC-GA-TC--ATGGGGCAGATTGAAG--CATCCAATCTTTTA-CCCTAGT-TAGA-GGGC
65 TACCCCTAAGTCAAAAGGAGCAGATTGAAGACCATCAAATCTCTTACCCCTAATCAAGAGGGGT
* * * *** * *
35880 AGATTAAAGACA-CTAATCTCTTACCC-CGTTCATGA--GGTAGATTGAAG--CATCCAATCTTT
1 AGATTGAAG-CATCCAATCTTTTACCCTAAATCAAGAGGGGCAGATTGAAGCACATCCAATCTTT
* * * * *
35939 TA-CCCTAA-TC-AGA-GAGCAAATTGAAGACACA-CCAATCTCTTACCCC-AATC-A-TGGGGC
65 TACCCCTAAGTCAAAAGGAGCAGATTGAAGAC-CATCAAATCTCTTACCCCTAATCAAGAGGGGT
35996 AGATTGAAGCATCCAATCTTTTACC
1 AGATTGAAGCATCCAATCTTTTACC
36021 TTAGTTAGAG
Statistics
Matches: 323, Mismatches: 43, Indels: 63
0.75 0.10 0.15
Matches are distributed among these distances:
113 5 0.02
114 24 0.07
115 5 0.02
116 85 0.26
117 9 0.03
119 2 0.01
120 14 0.04
122 3 0.01
123 14 0.04
124 1 0.00
125 15 0.05
126 3 0.01
127 4 0.01
128 1 0.00
129 17 0.05
131 9 0.03
133 55 0.17
134 20 0.06
135 23 0.07
136 14 0.04
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (128 bp):
AGATTGAAGCATCCAATCTTTTACCCTAAATCAAGAGGGGCAGATTGAAGCACATCCAATCTTTT
ACCCCTAAGTCAAAAGGAGCAGATTGAAGACCATCAAATCTCTTACCCCTAATCAAGAGGGGT
Found at i:35788 original size:38 final size:38
Alignment explanation
Indices: 35691--36235 Score: 317
Period size: 38 Copynumber: 13.9 Consensus size: 38
35681 TGAAGTCACA
* * *
35691 ATCCAATCTTTTACCCCTAATCAAAAGGGGCAGATTGAAACC
1 ATCCAATCTCTTACCCC-AATC-ATA-GGGCAGATTG-AAGC
* *
35733 ATCGTCTAATCTCTTACCCCGATCATAGGGTAGATTGAAGC
1 ATC--C-AATCTCTTACCCCAATCATAGGGCAGATTGAAGC
* * *
35774 ATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGAC
1 ATCCAATCTCTTACCCCAATCATAGGGCAGATTGAAG-C
* * *
35813 ACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGC
1 A-TCCAATCTCTTACCCCAATCATAGGGCAGATTGAAGC
* * * * * *
35852 ATCCAATCTTTTACCCTAGTTAGAGGGCAGATTAAAGAC
1 ATCCAATCTCTTACCCCAATCATAGGGCAGATTGAAG-C
* ** *
35891 A-CTAATCTCTTACCCCGTTCAT-GAGGTAGATTGAAGC
1 ATCCAATCTCTTACCCCAATCATAG-GGCAGATTGAAGC
* * * * *
35928 ATCCAATCTTTTACCCTAATCAGAGAGCAAATTGAAGAC
1 ATCCAATCTCTTACCCCAATCATAGGGCAGATTGAAG-C
* *
35967 ACACCAATCTCTTACCCCAATCATGGGGCAGATTGAAGC
1 A-TCCAATCTCTTACCCCAATCATAGGGCAGATTGAAGC
* ** * * * ** *
36006 ATCCAATCTTTTACCTTAGTTAGAGGATAGATTTAAGAC
1 ATCCAATCTCTTACCCCAATCATAGGGCAGATTGAAG-C
* * * *
36045 ACACCAATCTCTTACGCAAATCATGGGGCAGATTGAAGC
1 A-TCCAATCTCTTACCCCAATCATAGGGCAGATTGAAGC
* * * * *
36084 ATCCAATCT-TTAACCCTAGTTAGAGGGCAAATTGAAG-
1 ATCCAATCTCTT-ACCCCAATCATAGGGCAGATTGAAGC
* * * *
36121 ATACACCAATCTCTTACTCCAATCGT-GGAGCAGATTAAAAC
1 AT---CCAATCTCTTACCCCAATCATAGG-GCAGATTGAAGC
* * * * *
36162 ATCCAATCTGTTACCCTAATCAAATGACAGATTGAAGAC
1 ATCCAATCTCTTACCCCAATCATAGGGCAGATTGAAG-C
* *** *
36201 ACACCAATCTCTTACATTAATCAGAGGGCAGATTG
1 A-TCCAATCTCTTACCCCAATCATAGGGCAGATTG
36236 GAACATCTAA
Statistics
Matches: 374, Mismatches: 106, Indels: 48
0.71 0.20 0.09
Matches are distributed among these distances:
37 7 0.02
38 177 0.47
39 21 0.06
40 129 0.34
41 10 0.03
42 12 0.03
43 2 0.01
44 4 0.01
45 12 0.03
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (38 bp):
ATCCAATCTCTTACCCCAATCATAGGGCAGATTGAAGC
Found at i:35833 original size:78 final size:78
Alignment explanation
Indices: 35487--36235 Score: 650
Period size: 78 Copynumber: 9.2 Consensus size: 78
35477 TGAAGAACAT
*
35487 CCAATC-TAGGGACAGATTGAAGAACATCCAATCTTTTACCCGTAAGTTAAGAGGAGCAGATTGA
1 CCAATCATAGGG-CAGATTGAAG--CATCCAATCTTTTACCC-TAA--TCAGAGG-GCAGATTGA
*
35551 AGAC-CATCCAATCTTTTAACC
59 AGACACA-CCAATCTCTT-ACC
* * * *
35572 CTAAGTCAAGAGGAGCAGATTGAAGACCATCAAATCTTTTACCCCTAATCAAGAGGGGTAGATTG
1 CCAA-TC-ATAGG-GCAGATTGAAG--CATCCAATCTTTTA-CCCTAATC-AGA-GGGCAGATTG
* *
35637 AAGCCACCATCCAATCTTTTACC
58 AAGACA-CA-CCAATCTCTTACC
* * * *
35660 CTTAAATCAAGAGGGGCAGACTGAAGTCACAATCCAATCTTTTACCCCTAATCAAAAGGGGCAGA
1 C--CAATC-ATA-GGGCAGATTGAAG---C-ATCCAATCTTTTA-CCCTAATC-AGA-GGGCAGA
35725 TTGAA-AC-CATCGTCTAATCTCTTACC
55 TTGAAGACACA-C--C-AATCTCTTACC
* *
35751 CCGATCATAGGGTAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACA
1 CCAATCATAGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACA
35816 CCAATCTCTTACC
66 CCAATCTCTTACC
* * * * *
35829 CCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAGTTAGAGGGCAGATT-AA-AGACA
1 CCAATCATAGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACA
*
35892 CTAATCTCTTACC
66 CCAATCTCTTACC
** * * *
35905 CCGTTCAT-GAGGTAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGAGCAAATTGAAGACAC
1 CCAATCATAG-GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAC
35969 ACCAATCTCTTACC
65 ACCAATCTCTTACC
* * * * ** *
35983 CCAATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAGTTAGAGGATAGATTTAAGACACA
1 CCAATCATAGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACA
*
36048 CCAATCTCTTACG
66 CCAATCTCTTACC
* * * * * * *
36061 CAAATCATGGGGCAGATTGAAGCATCCAATCTTTAACCCTAGTTAGAGGGCAAATTGAAGATACA
1 CCAATCATAGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACA
*
36126 CCAATCTCTTACT
66 CCAATCTCTTACC
* * * * * * *
36139 CCAATCGT-GGAGCAGATTAAAACATCCAATCTGTTACCCTAATCAAATGACAGATTGAAGACAC
1 CCAATCATAGG-GCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAC
*
36203 ACCAATCTCTTACA
65 ACCAATCTCTTACC
** *
36217 TTAATCAGAGGGCAGATTG
1 CCAATCATAGGGCAGATTG
36236 GAACATCTAA
Statistics
Matches: 563, Mismatches: 76, Indels: 57
0.81 0.11 0.08
Matches are distributed among these distances:
75 1 0.00
76 64 0.11
77 6 0.01
78 284 0.50
79 4 0.01
80 12 0.02
81 5 0.01
82 10 0.02
83 13 0.02
84 1 0.00
85 3 0.01
86 3 0.01
87 25 0.04
88 42 0.07
89 36 0.06
90 7 0.01
91 47 0.08
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (78 bp):
CCAATCATAGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACA
CCAATCTCTTACC
Found at i:36320 original size:36 final size:35
Alignment explanation
Indices: 36273--36353 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 35
36263 TCGGAGTAAG
* * * *
36273 AGATTGGAGACACTATTTGATCTTTTATCAGAGGTC
1 AGATTGAAGACACCATTCGATCTTTT-TCAGAGGGC
36309 AGATTGAAGACACCATTCGATCTTTTTCAGAGGGC
1 AGATTGAAGACACCATTCGATCTTTTTCAGAGGGC
*
36344 AAATTGAAGA
1 AGATTGAAGA
36354 TATGTTACGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 17 0.43
36 23 0.57
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (35 bp):
AGATTGAAGACACCATTCGATCTTTTTCAGAGGGC
Found at i:36524 original size:21 final size:21
Alignment explanation
Indices: 36485--36524 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
36475 CACTCGGCCC
* * *
36485 AATAAAATGAAGCCCAATAGA
1 AATAAAATAAAACCAAATAGA
36506 AATAAAATAAAACCAAATA
1 AATAAAATAAAACCAAATA
36525 AAAAAATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (21 bp):
AATAAAATAAAACCAAATAGA
Done.