Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000659.1 Kokia drynarioides strain JFW-HI SEQ_111641, 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: 82432
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5072 original size:14 final size:13
Alignment explanation
Indices: 5031--5080 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
5021 TAATAATTTT
5031 AAATATTTTTAAA
1 AAATATTTTTAAA
* *
5044 AAATACTTATAAAA
1 AAATA-TTTTTAAA
5058 AAATATTTTTCAAA
1 AAATATTTTT-AAA
5072 AAATTATTT
1 AAA-TATTT
5081 ATGTTTTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 8 0.27
14 17 0.57
15 5 0.17
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATATTTTTAAA
Found at i:6814 original size:20 final size:21
Alignment explanation
Indices: 6789--6830 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
6779 TAACATTATT
6789 AAAAAAACTAA-ATAAAACAA
1 AAAAAAACTAATATAAAACAA
* *
6809 AAAAAAATTAATTTAAAACAA
1 AAAAAAACTAATATAAAACAA
6830 A
1 A
6831 TAACTAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (21 bp):
AAAAAAACTAATATAAAACAA
Found at i:25655 original size:33 final size:33
Alignment explanation
Indices: 25600--25662 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
25590 TTTACTAGTA
* *
25600 TTATATATTATTATATTTAATTATTTAAATATT
1 TTATATATAATTATATTAAATTATTTAAATATT
*
25633 TTATGTATAATTATATTAAATTATTTAAAT
1 TTATATATAATTATATTAAATTATTTAAAT
25663 CTGATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
TTATATATAATTATATTAAATTATTTAAATATT
Found at i:25993 original size:21 final size:20
Alignment explanation
Indices: 25960--26002 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
25950 GTCTTAACGG
* *
25960 AACTACTGATGTGGCAAGTT
1 AACTACTAATGTGACAAGTT
*
25980 AACTAGCTAATGTGACCAGTT
1 AACTA-CTAATGTGACAAGTT
26001 AA
1 AA
26003 TTTGTCACGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (20 bp):
AACTACTAATGTGACAAGTT
Found at i:29234 original size:23 final size:23
Alignment explanation
Indices: 29189--29234 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
29179 TACGGTGTTG
* *
29189 TTAATATATCTTTGTATTAATTA
1 TTAATATATCCTTATATTAATTA
29212 TTAATATATCCTTAT-TTATATTA
1 TTAATATATCCTTATATTA-ATTA
29235 ATTATTGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.57
Consensus pattern (23 bp):
TTAATATATCCTTATATTAATTA
Found at i:30010 original size:18 final size:18
Alignment explanation
Indices: 29987--30024 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
29977 AAATATAGTT
29987 TTATTC-AGTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
30005 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
30023 TT
1 TT
30025 CAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:30765 original size:14 final size:14
Alignment explanation
Indices: 30742--30775 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30732 TGTCATTTTG
*
30742 TTATTATATTGTAA
1 TTATTTTATTGTAA
*
30756 TTATTTTATTGTTA
1 TTATTTTATTGTAA
30770 TTATTT
1 TTATTT
30776 GGATATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (14 bp):
TTATTTTATTGTAA
Found at i:37012 original size:18 final size:18
Alignment explanation
Indices: 36954--37014 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
36944 TCGAAACAAT
36954 AAAAAACCAAAACAGT-A
1 AAAAAACCAAAACAGTAA
*
36971 AAAAAA-CACAA-A--AA
1 AAAAAACCAAAACAGTAA
* *
36985 CAACAACCAAAACAGTAA
1 AAAAAACCAAAACAGTAA
37003 AAAAAACCAAAA
1 AAAAAACCAAAA
37015 AAAAAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
14 5 0.15
15 5 0.15
16 5 0.15
17 6 0.18
18 12 0.36
ACGTcount: A:0.74, C:0.20, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAAAACCAAAACAGTAA
Found at i:37626 original size:17 final size:17
Alignment explanation
Indices: 37603--37639 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
37593 AATTATATAC
37603 TTTT-TTTT-ATTCTAA
1 TTTTATTTTAATTCTAA
*
37618 TTTTATTTTAATTTTAA
1 TTTTATTTTAATTCTAA
37635 TTTTA
1 TTTTA
37640 AATCCTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 4 0.21
17 11 0.58
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATTTTAATTCTAA
Found at i:40860 original size:69 final size:69
Alignment explanation
Indices: 40749--40886 Score: 276
Period size: 69 Copynumber: 2.0 Consensus size: 69
40739 CTGTTTCCTA
40749 AGCAGAAGGTCATAGGTTCGACCCCTATCTGGCGCGAAGATATTTTGTTTTTGAAATGTGTCGAC
1 AGCAGAAGGTCATAGGTTCGACCCCTATCTGGCGCGAAGATATTTTGTTTTTGAAATGTGTCGAC
40814 CCAT
66 CCAT
40818 AGCAGAAGGTCATAGGTTCGACCCCTATCTGGCGCGAAGATATTTTGTTTTTGAAATGTGTCGAC
1 AGCAGAAGGTCATAGGTTCGACCCCTATCTGGCGCGAAGATATTTTGTTTTTGAAATGTGTCGAC
40883 CCAT
66 CCAT
40887 TAAGCTCCAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (69 bp):
AGCAGAAGGTCATAGGTTCGACCCCTATCTGGCGCGAAGATATTTTGTTTTTGAAATGTGTCGAC
CCAT
Found at i:58459 original size:21 final size:20
Alignment explanation
Indices: 58435--58489 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
58425 TAGAAACTAG
*
58435 TATATTTAAATTTGTAATGAT-
1 TATATTTAAATTT-TAA-AATA
58456 TATATTTTAATATTTTAAAATA
1 TATA-TTTAA-ATTTTAAAATA
58478 TATATTTAAATT
1 TATATTTAAATT
58490 AAATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.10
21 11 0.37
22 12 0.40
23 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (20 bp):
TATATTTAAATTTTAAAATA
Found at i:58544 original size:12 final size:13
Alignment explanation
Indices: 58519--58543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58509 ATACGTAATT
58519 TTATTTTTTAAAA
1 TTATTTTTTAAAA
58532 TTATTTTTTAAA
1 TTATTTTTTAAA
58544 TAATATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTTTTAAAA
Found at i:58866 original size:15 final size:15
Alignment explanation
Indices: 58846--58892 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
58836 ATTTTTGGGC
58846 TATATTTTAATTATT
1 TATATTTTAATTATT
* * *
58861 TATATTTGAA-AAAT
1 TATATTTTAATTATT
*
58875 TATGTTTTAATTATT
1 TATATTTTAATTATT
58890 TAT
1 TAT
58893 TTTAACGTGT
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (15 bp):
TATATTTTAATTATT
Found at i:59597 original size:20 final size:20
Alignment explanation
Indices: 59564--59611 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
59554 TTTTTTCTTG
*
59564 AAAAAAATTTAAATTTAAGT
1 AAAAAAATTAAAATTTAAGT
*
59584 AAAAATATTAAAATTTAAG-
1 AAAAAAATTAAAATTTAAGT
59603 AAGAAAAAT
1 AA-AAAAAT
59612 CTAATTTACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (20 bp):
AAAAAAATTAAAATTTAAGT
Found at i:60368 original size:15 final size:15
Alignment explanation
Indices: 60348--60396 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
60338 TATTTTTGGG
60348 TTATATTTTAATTAT
1 TTATATTTTAATTAT
* ** *
60363 TTATATTTGAAAAAA
1 TTATATTTTAATTAT
*
60378 TTATGTTTTAATTAT
1 TTATATTTTAATTAT
60393 TTAT
1 TTAT
60397 TTTAACGTGT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (15 bp):
TTATATTTTAATTAT
Found at i:73931 original size:49 final size:49
Alignment explanation
Indices: 73851--74367 Score: 350
Period size: 49 Copynumber: 10.6 Consensus size: 49
73841 CCAGTACTAC
* *
73851 GAAGACATG-AGGGAAA-AGTTTAAGTCACAACGGTGAACCGTGTACCTCA
1 GAAGACATGAAGGGAAAGA-TTTAAGTCGCAACGGCGAACC-TGTACCTCA
* * *
73900 GAAG-CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACA
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAA-CCTGTACCTCA
* * * * * * *
73949 -ACGAAATCAAGGGAACGGTTTAAGTCGCAATGGCGAACCTAGTACCTTA
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCT-GTACCTCA
* * * * *
73998 GAAGACATTAAGGGAAAGATCTAAG-CTGCAACAGCGGATCCTGTACCAC-
1 GAAGACATGAAGGGAAAGATTTAAGTC-GCAACGGC-GAACCTGTACCTCA
* * * ** * * *
74047 GAAGGCA-CAAGGGAAAGGTTTAAGTTACAATGGAGAACCTAGTACCTAA
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCT-GTACCTCA
* * * * *
74096 G-AGACATGAAGGGGAAGATCTAAGCCGCAACGGCAGATCCTGTACCAC-
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGC-GAACCTGTACCTCA
* * * * *
74144 GAAGACAT-AAGGGAAAGGTTTAAGTCGTAATGGCGAACCTAGAACCTAA
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCT-GTACCTCA
* * *
74193 G-AGACATGAAGGG-AAGATCTAAG-CTGCAATGGCGAATCCTGTACCAC-
1 GAAGACATGAAGGGAAAGATTTAAGTC-GCAACGGCGAA-CCTGTACCTCA
* * * *
74240 GAAAACA-CAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGTACCTCA
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCT-GTACCTCA
* * * *
74289 G-AGACATGAAGGGAAAGATCTAAGTCGCAACGGCGGATCTAGTACCGC-
1 GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCT-GTACCTCA
* *
74337 GAAGACA-CAAGGGGAAAGGTTTAAGTCGCAA
1 GAAGACATGAA-GGGAAAGATTTAAGTCGCAA
74368 TGGAAAACAT
Statistics
Matches: 358, Mismatches: 83, Indels: 54
0.72 0.17 0.11
Matches are distributed among these distances:
47 20 0.06
48 124 0.35
49 172 0.48
50 37 0.10
51 5 0.01
ACGTcount: A:0.37, C:0.20, G:0.27, T:0.16
Consensus pattern (49 bp):
GAAGACATGAAGGGAAAGATTTAAGTCGCAACGGCGAACCTGTACCTCA
Found at i:74144 original size:97 final size:97
Alignment explanation
Indices: 73806--74370 Score: 699
Period size: 97 Copynumber: 5.8 Consensus size: 97
73796 GCACCATGAA
* * * * * ** *
73806 ACATGAAGGGAAAGATCTAAGCTGTAACAGCGGATCCAGTACTACGAAGACATGAGGGAAAAGTT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCTGTACCACGAAGACACAAGGGAAAGGTT
* * * *
73871 TAAGTCACAACGGTGAACCGT-GTACCTCAGA-
66 TAAGTCGCAATGGCGAACC-TAGTACCTAAGAG
* * * * *
73902 AGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AACGAAATCAAGGGAACG
1 A-CATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCTGTACCACGAA-GACA-CAAGGGAAAG
*
73966 GTTTAAGTCGCAATGGCGAACCTAGTACCTTAGAAG
63 GTTTAAGTCGCAATGGCGAACCTAGTACCTAAG-AG
* * * *
74002 ACATTAAGGGAAAGATCTAAGCTGCAACAGCGGATCCTGTACCACGAAGGCACAAGGGAAAGGTT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCTGTACCACGAAGACACAAGGGAAAGGTT
** *
74067 TAAGTTACAATGGAGAACCTAGTACCTAAGAG
66 TAAGTCGCAATGGCGAACCTAGTACCTAAGAG
* * *
74099 ACATGAAGGGGAAGATCTAAGCCGCAACGGCAGATCCTGTACCACGAAGACATAAGGGAAAGGTT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCTGTACCACGAAGACACAAGGGAAAGGTT
* *
74164 TAAGTCGTAATGGCGAACCTAGAACCTAAGAG
66 TAAGTCGCAATGGCGAACCTAGTACCTAAGAG
* * * *
74196 ACATGAAGGG-AAGATCTAAGCTGCAATGGCGAATCCTGTACCACGAAAACACAAGGGAAAGGTT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCTGTACCACGAAGACACAAGGGAAAGGTT
*
74260 TAAGTCGCAATGGCGAACCTAGTACCTCAGAG
66 TAAGTCGCAATGGCGAACCTAGTACCTAAGAG
* *
74292 ACATGAAGGGAAAGATCTAAGTCGCAACGGCGGAT-CTAGTACCGCGAAGACACAAGGGGAAAGG
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCT-GTACCACGAAGACACAA-GGGAAAGG
74356 TTTAAGTCGCAATGG
64 TTTAAGTCGCAATGG
74371 AAAACATTAT
Statistics
Matches: 404, Mismatches: 55, Indels: 18
0.85 0.12 0.04
Matches are distributed among these distances:
96 92 0.23
97 174 0.43
98 94 0.23
99 41 0.10
100 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.16
Consensus pattern (97 bp):
ACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCTGTACCACGAAGACACAAGGGAAAGGTT
TAAGTCGCAATGGCGAACCTAGTACCTAAGAG
Found at i:74258 original size:193 final size:194
Alignment explanation
Indices: 73806--74370 Score: 746
Period size: 196 Copynumber: 2.9 Consensus size: 194
73796 GCACCATGAA
* * * ** *
73806 ACATGAAGGGAAAGATCTAAGCTGTAACAGCGGATCCAGTACTACGAAGACATGAGGGAAAAGTT
1 ACATGAAGGGAAAGATCTAAGCTGCAACAGCGGATCCTGTACCACGAAGACACAAGGGAAAGGTT
* * *
73871 TAAGTCACAACGGTGAACCGT-GTACCTCAGA-AGCATGAAGGGAAAGATTTAAGCCGCAACGGC
66 TAAGTCACAATGGAGAACC-TAGTACCTCAGAGA-CATGAAGGGAAAGATCTAAGCCGCAACGGC
* * * * *
73934 GAATCCAGTACCAC-AACGAAATCAAGGGAACGGTTTAAGTCGCAATGGCGAACCTAGTACCTTA
129 G-ATCCTGTACCACGAA-GACAT-AAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGAACCTAA
73998 GAAG
191 GAAG
* *
74002 ACATTAAGGGAAAGATCTAAGCTGCAACAGCGGATCCTGTACCACGAAGGCACAAGGGAAAGGTT
1 ACATGAAGGGAAAGATCTAAGCTGCAACAGCGGATCCTGTACCACGAAGACACAAGGGAAAGGTT
* * *
74067 TAAGTTACAATGGAGAACCTAGTACCTAAGAGACATGAAGGGGAAGATCTAAGCCGCAACGGCAG
66 TAAGTCACAATGGAGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGCCGCAACGGC-G
*
74132 ATCCTGTACCACGAAGACATAAGGGAAAGGTTTAAGTCGTAATGGCGAACCTAGAACCTAAG-AG
130 ATCCTGTACCACGAAGACATAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGAACCTAAGAAG
** * *
74196 ACATGAAGGG-AAGATCTAAGCTGCAATGGCGAATCCTGTACCACGAAAACACAAGGGAAAGGTT
1 ACATGAAGGGAAAGATCTAAGCTGCAACAGCGGATCCTGTACCACGAAGACACAAGGGAAAGGTT
* * *
74260 TAAGTCGCAATGGCGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGTCGCAACGGCGG
66 TAAGTCACAATGGAGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGCCGCAACGGC-G
* *
74325 AT-CTAGTACCGCGAAGACACAAGGGGAAAGGTTTAAGTCGCAATGG
130 ATCCT-GTACCACGAAGACATAA-GGGAAAGGTTTAAGTCGCAATGG
74371 AAAACATTAT
Statistics
Matches: 327, Mismatches: 36, Indels: 14
0.87 0.10 0.04
Matches are distributed among these distances:
192 2 0.01
193 124 0.38
194 33 0.10
195 39 0.12
196 125 0.38
197 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.16
Consensus pattern (194 bp):
ACATGAAGGGAAAGATCTAAGCTGCAACAGCGGATCCTGTACCACGAAGACACAAGGGAAAGGTT
TAAGTCACAATGGAGAACCTAGTACCTCAGAGACATGAAGGGAAAGATCTAAGCCGCAACGGCGA
TCCTGTACCACGAAGACATAAGGGAAAGGTTTAAGTCGCAATGGCGAACCTAGAACCTAAGAAG
Found at i:74849 original size:17 final size:17
Alignment explanation
Indices: 74829--74896 Score: 82
Period size: 17 Copynumber: 3.9 Consensus size: 17
74819 CTAACTCATT
74829 TTAAATTTATTTTAAGA
1 TTAAATTTATTTTAAGA
* *
74846 TTAAATTTATTCTAAAA
1 TTAAATTTATTTTAAGA
* *
74863 TTTAAATTTAATTTAAGT
1 -TTAAATTTATTTTAAGA
74881 TTAAATTTATATTTAA
1 TTAAATTTAT-TTTAA
74897 ATTTAAAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
17 24 0.57
18 18 0.43
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTAAATTTATTTTAAGA
Found at i:74868 original size:35 final size:35
Alignment explanation
Indices: 74828--74903 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
74818 CCTAACTCAT
*
74828 TTTAAATTTATTTTAAGATTAAATTTAT-TCTAAAA
1 TTTAAATTTAATTTAAGATTAAATTTATAT-TAAAA
* *
74863 TTTAAATTTAATTTAAGTTTAAATTTATATTTAAA
1 TTTAAATTTAATTTAAGATTAAATTTATATTAAAA
74898 TTTAAA
1 TTTAAA
74904 ACTATTATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 36 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTAAATTTAATTTAAGATTAAATTTATATTAAAA
Found at i:74871 original size:6 final size:6
Alignment explanation
Indices: 74860--74903 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
74850 ATTTATTCTA
* *
74860 AAATTT AAATTT -AATTT AAGTTT AAATTT ATATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAA
74904 ACTATTATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:75624 original size:3 final size:3
Alignment explanation
Indices: 75616--75742 Score: 78
Period size: 3 Copynumber: 42.0 Consensus size: 3
75606 ATAACTTTAT
* * * * *
75616 TAA TAA TAA TAT TAA TAA TAAA TAA TAT TAG TAT TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
75662 CAA TAA TAA TAAA TAA TAT TAG TAT TAA TAT TAA TAA CAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
75708 TAA -ATA TGA CAT TAA TAA TAT TAA TAA TAA -AA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
75743 AAGGAAATTT
Statistics
Matches: 93, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
2 3 0.03
3 84 0.90
4 6 0.06
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:75669 original size:37 final size:37
Alignment explanation
Indices: 75619--75713 Score: 172
Period size: 37 Copynumber: 2.6 Consensus size: 37
75609 ACTTTATTAA
* *
75619 TAATAATATTAATAATAAATAATATTAGTATTAATAT
1 TAATAACAATAATAATAAATAATATTAGTATTAATAT
75656 TAATAACAATAATAATAAATAATATTAGTATTAATAT
1 TAATAACAATAATAATAAATAATATTAGTATTAATAT
75693 TAATAACAATAATAATAAATA
1 TAATAACAATAATAATAAATA
75714 TGACATTAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (37 bp):
TAATAACAATAATAATAAATAATATTAGTATTAATAT
Found at i:76875 original size:30 final size:29
Alignment explanation
Indices: 76841--77034 Score: 139
Period size: 30 Copynumber: 6.7 Consensus size: 29
76831 AAACTATCTA
*
76841 AAAATCATATTTTGACCACCAAACTTTTCT
1 AAAATTATATTTTGACC-CCAAACTTTTCT
* * *
76871 AAAATTACATTTT-A-ACCAAACTTTTCC
1 AAAATTATATTTTGACCCCAAACTTTTCT
* * * **
76898 AAAAATACATTTTAACCGTTAAA-TTTTCT
1 AAAATTATATTTTGACC-CCAAACTTTTCT
* *
76927 AAAATTATATTTTGACCCCTACACTTCTCT
1 AAAATTATATTTTGACCCC-AAACTTTTCT
*
76957 AAAATTATATTTTGACCCTCAAAC-TTTCAA
1 AAAATTATATTTTGACCC-CAAACTTTTC-T
* * * *
76987 AAAAATACATTTTTACCCCAAAC-TTTCC
1 AAAATTATATTTTGACCCCAAACTTTTCT
77015 AAAATTCCAT-TTTTGACCCC
1 AAAATT--ATATTTTGACCCC
77035 GATATTATCA
Statistics
Matches: 129, Mismatches: 26, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
27 23 0.18
28 6 0.05
29 43 0.33
30 56 0.43
31 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTATATTTTGACCCCAAACTTTTCT
Found at i:76895 original size:27 final size:27
Alignment explanation
Indices: 76858--76939 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
76848 TATTTTGACC
76858 ACCAAACTTTTCTAAAATTACATTTTA
1 ACCAAACTTTTCTAAAATTACATTTTA
* *
76885 ACCAAACTTTTCCAAAAATACATTTTA
1 ACCAAACTTTTCTAAAATTACATTTTA
*
76912 ACCGTTAAA-TTTTCTAAAATTATATTTT
1 ACC---AAACTTTTCTAAAATTACATTTT
76940 GACCCCTACA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
27 28 0.60
29 16 0.34
30 3 0.06
ACGTcount: A:0.40, C:0.17, G:0.01, T:0.41
Consensus pattern (27 bp):
ACCAAACTTTTCTAAAATTACATTTTA
Found at i:77008 original size:29 final size:30
Alignment explanation
Indices: 76957--77087 Score: 96
Period size: 29 Copynumber: 4.5 Consensus size: 30
76947 ACACTTCTCT
* *
76957 AAAATTATATTTTGACCCTC-AAACTTTCAA
1 AAAATTACATTTTTACCC-CGAAACTTTCAA
* *
76987 AAAAATACATTTTTACCCC-AAACTTTC-C
1 AAAATTACATTTTTACCCCGAAACTTTCAA
* *
77015 AAAATTCCATTTTTGACCCCGATA-TTATCAA
1 AAAATTACATTTTT-ACCCCGAAACTT-TCAA
* *
77046 AAAATTACA--ATTACCCCTAAACTTT-AA
1 AAAATTACATTTTTACCCCGAAACTTTCAA
* *
77073 AAAATTCCCTTTTTA
1 AAAATTACATTTTTA
77088 ACCATGATTT
Statistics
Matches: 79, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
27 9 0.11
28 20 0.25
29 23 0.29
30 19 0.24
31 8 0.10
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTTACCCCGAAACTTTCAA
Found at i:77048 original size:58 final size:57
Alignment explanation
Indices: 76981--77351 Score: 272
Period size: 58 Copynumber: 6.4 Consensus size: 57
76971 ACCCTCAAAC
* * * *
76981 TTTCAAAAAAATACATTTTTACCCCAAACTTTCCAAAATTCCATTTTTGACCCCGATAT
1 TTTCCAAAAATTACA-TTTTACCCCAAACTTTCAAAAATTCCATTTTTGACCTCGAT-T
* * * * * *
77040 TATCAAAAAATTACA-ATTACCCCTAAACTTTAAAAAATTCCCTTTTTAACCAT-GATT
1 TTTCCAAAAATTACATTTTACCCC-AAACTTTCAAAAATTCCATTTTTGACC-TCGATT
* *
77097 TTTCCAAAAATTACCATTTTACCCCCAAA-TTTCGAAAAACTCTATTTTT-ACCTCGATT
1 TTTCCAAAAATTA-CATTTTA-CCCCAAACTTTC-AAAAATTCCATTTTTGACCTCGATT
* * ** *
77155 TTTCTAAAAATTACAATTTTCACCCTAAACTTTTTAAAATTCCA-TTTTGACCTTGATT
1 TTTCCAAAAATTAC-ATTTT-ACCCCAAACTTTCAAAAATTCCATTTTTGACCTCGATT
* * * *
77213 CTTCCCAAAATTACCATTTTACCCCAAACTTCCAAAAATTTCATTTTTGATCCT-GATT
1 TTTCCAAAAATTA-CATTTTACCCCAAACTTTCAAAAATTCCATTTTTGA-CCTCGATT
* * ** * * * * *
77271 TCTTCTAAAAATCACCATTTTACCCCCGGAC-GTCTAAAATTCCATTTTTCACCCCGAACT
1 T-TTCCAAAAATTA-CATTTTA-CCCCAAACTTTCAAAAATTCCATTTTTGACCTCG-ATT
77331 TTTCC-AAAATTACCATTTTAC
1 TTTCCAAAAATTA-CATTTTAC
77352 ACTTAGGTAC
Statistics
Matches: 249, Mismatches: 45, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
57 44 0.18
58 117 0.47
59 75 0.30
60 13 0.05
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (57 bp):
TTTCCAAAAATTACATTTTACCCCAAACTTTCAAAAATTCCATTTTTGACCTCGATT
Found at i:77174 original size:29 final size:29
Alignment explanation
Indices: 77093--77179 Score: 68
Period size: 29 Copynumber: 3.0 Consensus size: 29
77083 TTTTAACCAT
*
77093 GATTTTTCCAAAAATTACCATTTTACCCC
1 GATTTTTCCAAAAATTACAATTTTACCCC
* ** * * * *
77122 CAAATTTCGAAAAACT-CTATTTTTACCTC
1 GATTTTTCCAAAAATTAC-AATTTTACCCC
*
77151 GATTTTTCTAAAAATTACAATTTTCACCC
1 GATTTTTCCAAAAATTACAATTTT-ACCC
77180 TAAACTTTTT
Statistics
Matches: 40, Mismatches: 15, Indels: 5
0.67 0.25 0.08
Matches are distributed among these distances:
28 1 0.03
29 35 0.88
30 4 0.10
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.39
Consensus pattern (29 bp):
GATTTTTCCAAAAATTACAATTTTACCCC
Found at i:77271 original size:116 final size:116
Alignment explanation
Indices: 76997--77295 Score: 324
Period size: 116 Copynumber: 2.6 Consensus size: 116
76987 AAAAATACAT
* * * * *
76997 TTTTACCCCAAACTTTCC-AAAATTCCATTTTTGACCCCGATATTATCAAAAAATTACAA-TTAC
1 TTTTACCCCAAAC-TTCCAAAAATTTCATTTTTGA-CCTGAT-TTTTCTAAAAATTACAATTTTC
* *
77060 -CCCTAAACTTTAAAAAATTCCCTTTTTAACCATGATTTTTCCAAAAATTACCA
63 ACCCTAAACTTTAAAAAATTCCCATTTTAACCATGATTCTTCCAAAAATTACCA
* * *
77113 TTTTACCCCCAAATTTCGAAAAA-CTCTATTTTT-ACCTCGATTTTTCTAAAAATTACAATTTTC
1 TTTTA-CCCCAAACTTCCAAAAATTTC-ATTTTTGACCT-GATTTTTCTAAAAATTACAATTTTC
** * * *
77176 ACCCTAAACTTTTTAAAATT-CCATTTTGACCTTGATTCTTCCCAAAATTACCA
63 ACCCTAAACTTTAAAAAATTCCCATTTTAACCATGATTCTTCCAAAAATTACCA
* *
77229 TTTTACCCCAAACTTCCAAAAATTTCATTTTTGATCCTGATTTCTTCTAAAAATCACCATTTT-A
1 TTTTACCCCAAACTTCCAAAAATTTCATTTTTGA-CCTGATTT-TTCTAAAAATTACAATTTTCA
77293 CCC
64 CCC
77296 CCGGACGTCT
Statistics
Matches: 153, Mismatches: 20, Indels: 20
0.79 0.10 0.10
Matches are distributed among these distances:
115 38 0.25
116 61 0.40
117 54 0.35
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.38
Consensus pattern (116 bp):
TTTTACCCCAAACTTCCAAAAATTTCATTTTTGACCTGATTTTTCTAAAAATTACAATTTTCACC
CTAAACTTTAAAAAATTCCCATTTTAACCATGATTCTTCCAAAAATTACCA
Done.