Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_273 ID=scaffold_273-JGI_221_v2.0
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: 9773
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.25
Warning! 1013 characters in sequence are not A, C, G, or T
Found at i:5492 original size:42 final size:42
Alignment explanation
Indices: 5444--5548 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
5434 TCCGATTCAA
*
5444 AAAAAAAGGAAAATGAAAAGAGAGAAA-AAATTAAAATCAAAAT
1 AAAAAAA-GAAAA-GAAAAGAGAGAAATAAATCAAAATCAAAAT
* * *
5487 AAAAAAACAAAAAGAAAA-AGAGAAATCAATCAAAGTCAAAAT
1 AAAAAAA-GAAAAGAAAAGAGAGAAATAAATCAAAATCAAAAT
*
5529 AAAAATATGAAAAGAAAAGA
1 AAAAA-AAGAAAAGAAAAGA
5549 AAAGAAAAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
41 7 0.13
42 32 0.62
43 13 0.25
ACGTcount: A:0.72, C:0.05, G:0.12, T:0.10
Consensus pattern (42 bp):
AAAAAAAGAAAAGAAAAGAGAGAAATAAATCAAAATCAAAAT
Found at i:7333 original size:86 final size:86
Alignment explanation
Indices: 7188--8071 Score: 1149
Period size: 86 Copynumber: 10.2 Consensus size: 86
7178 GTGAAAATAA
*
7188 AAAACAAAGCCTTGCCTTCATTAGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
7253 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
*
7274 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAACTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
7339 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
* * *
7360 AAAACAAAGCCTTACCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTTCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
7425 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
7446 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
7511 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
* *
7532 AAAACAAAGCCTTGCCTTCATTGTTTGCAGTGGAGCTGGTTAAAGAAGCAGATTTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
7597 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
* * *
7618 AAAACAAAGCCTTGCCTTCATTAGTTACAGTGGAGGTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
7683 CGTTAACAGCGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
*
7704 AAAACAAAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
*
7769 CGTTAACAACGAAGCAGATCG
66 CGTTAACAGCGAAGCAGATCG
* * * **
7790 AAGACACAAA-CCTTGCCTCTC-TCGGTTG-TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCT
1 AA-A-ACAAAGCCTTGCCT-TCATTGGTTGCAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCT
** ** * *
7852 TTTTGTATTGACAGCGAAGCAGGTCG
61 TCCTGCGTTAACAGCGAAGCAGATCG
* * * **
7878 AAGACACAAA-CCTTGCCTCTC-TCGGTTG-TGATGGAGCTGGTTGAAGACAATAGATCTTGCCT
1 AA-A-ACAAAGCCTTGCCT-TCATTGGTTGCAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCT
* * *
7940 TCCTGCATTGACAGCGAAGCAGGTCG
61 TCCTGCGTTAACAGCGAAGCAGATCG
* * * * * **
7966 AAGACACAAA-TCTTGCCCCTC-TCGGTTG-TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCT
1 AA-A-ACAAAGCCTTG-CCTTCATTGGTTGCAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCT
* * * * *
8028 TTCTGCATTGATAGCGAAGCAGGTC-
61 TCCTGCGTTAACAGCGAAGCAGATCG
*
8053 AAAGACACAAACCTTGCCT
1 AAA-ACA-AAGCCTTGCCT
8072 CTGGTTGAAG
Statistics
Matches: 745, Mismatches: 45, Indels: 15
0.93 0.06 0.02
Matches are distributed among these distances:
86 502 0.67
87 36 0.05
88 205 0.28
89 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (86 bp):
AAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
CGTTAACAGCGAAGCAGATCG
Found at i:7474 original size:172 final size:172
Alignment explanation
Indices: 7188--8433 Score: 1200
Period size: 172 Copynumber: 7.3 Consensus size: 172
7178 GTGAAAATAA
* *
7188 AAAACAAAGCCTTGCCTTCATTAGTTGCAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
*
7253 CGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAACTGGTTAAA
66 CGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
7318 GAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
131 GAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
* *
7360 AAAACAAAGCCTTACCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTTCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
7425 CGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
66 CGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
7490 GAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
131 GAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
* * *
7532 AAAACAAAGCCTTGCCTTCATTGTTTGCAGTGGAGCTGGTTAAAGAAGCAGATTTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
* * *
7597 CGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTAGTTACAGTGGAGGTGGTTAAA
66 CGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
7662 GAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
131 GAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
7704 AAAACAAAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
1 AAAACAAAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
* * *
7769 CGTTAACAACGAAGCAGATCGAAGACACAAA-CCTTGCCTCTC-TCGGTTG-TGATGGAGCTGGT
66 CGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCT-TCATTGGTTGCAG-TGGAGCTGGT
* ** ** ** * *
7831 TGAAGACAAAAGATCTTGCCTTTTTGTATTGACAGCGAAGCAGGTCG
127 TAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
* * **
7878 AAGACACAAA-CCTTGCCTCTC-TCGGTTGT-GATGGAGCTGGTTGAAGACAATAGATCTTGCCT
1 AA-A-ACAAAGCCTTGCCT-TCATTGGTTGTAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCT
* * * * * * *
7940 TCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAA-TCTTGCCCCTC-TCGGTTG-TGATGGAG
61 TCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTG-CCTTCATTGGTTGCAG-TGGAG
* ** * * * * *
8002 CTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTGATAGCGAAGCAGGTC-
122 CTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
* * *
8053 AAAGACACAAACCTTGCC-TC--TGGTTG-A----A----G--ACA-AA--AGATCTTGCATTCC
1 AAA-ACA-AAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCC
* * * * * *
8101 TGCATTGACAGCGAAGCAGGTC-AAAGACATAAACCTTGCCTCTC-TCGGTTG-TGATGGAGCTG
64 TGCGTTAACAGCGAAGCAGATCGAAA-ACA-AAGCCTTGCCT-TCATTGGTTGCAG-TGGAGCTG
** * * * *
8163 GTTAAAGATAAAAGATCTTGCCTTCCTGCATTGACGGCGAAGCAGGTC-
125 GTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
* * * **
8211 AAAGACACAAACCTTGCCTCTC-TCGGTTGT-GATGGAGCTGGTTGAAGACAAAAGATCTTGCCT
1 AAA-ACA-AAGCCTTGCCT-TCATTGGTTGTAG-TGGAGCTGGTTAAAGA-AGCAGATCTTGCCT
** * * * * * *
8274 TCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAA-CCTTGCCTCCCTCGGTT--ATGATGGAT
61 TCCTGCGTTAACAGCGAAGCAGATCGAA-A-ACAAAGCCTTGCCTTCATTGGTTGCA-G-TGGAG
* * * * * *
8336 CTGGTTGAAGACAACAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGGTCG
122 CTGGTTAAAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
* * * * *
8388 AAGACGAA-CCTTACCTCTC-TCGGTTGTAGTGGAGCTGGCTAAAGAA
1 AAAACAAAGCCTTGCCT-TCATTGGTTGTAGTGGAGCTGGTTAAAGAA
8434 TTTCAGATCT
Statistics
Matches: 956, Mismatches: 76, Indels: 83
0.86 0.07 0.07
Matches are distributed among these distances:
156 4 0.00
157 6 0.01
158 120 0.13
160 3 0.00
161 6 0.01
162 1 0.00
164 1 0.00
166 1 0.00
168 1 0.00
170 1 0.00
172 417 0.44
173 34 0.04
174 81 0.08
175 39 0.04
176 229 0.24
177 8 0.01
178 4 0.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (172 bp):
AAAACAAAGCCTTGCCTTCATTGGTTGTAGTGGAGCTGGTTAAAGAAGCAGATCTTGCCTTCCTG
CGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTTCATTGGTTGCAGTGGAGCTGGTTAAA
GAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG
Found at i:7849 original size:44 final size:44
Alignment explanation
Indices: 7801--8027 Score: 191
Period size: 44 Copynumber: 5.2 Consensus size: 44
7791 AGACACAAAC
7801 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
** * * * * *
7845 CTTGCCT-T-TTTGTAT-TGACAGCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCTCTCGGT-TGTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
*
7889 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAATAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
** * * * *
7933 CTTGCCT-TC-CTGCAT-TGACAGCGAAGCAGGTCGAAGACACAA-AT
1 CTTGCCTCTCTC-GGTTGTGA-TG-G-AGCTGGTTGAAGACAAAAGAT
*
7977 CTTGCCCCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
8021 CTTGCCT
1 CTTGCCT
8028 TTCTGCATTG
Statistics
Matches: 137, Mismatches: 30, Indels: 32
0.69 0.15 0.16
Matches are distributed among these distances:
42 10 0.07
43 37 0.27
44 43 0.31
45 37 0.27
46 10 0.07
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
Found at i:8069 original size:44 final size:44
Alignment explanation
Indices: 7755--8071 Score: 177
Period size: 44 Copynumber: 7.2 Consensus size: 44
7745 AAAGAAGCAG
* * * * * *
7755 ATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAGACACAA
1 ATCTTGCCTTTCTGCATTGATAGCGAAGCAGGTCGAAGACACAA
* * ** * * *
7799 ACCTTGCCTCTCTCGGTTGTGAT-G-G-AGCTGGTTGAAGACAAAA
1 ATCTTGCCTTTCT-GCAT-TGATAGCGAAGCAGGTCGAAGACACAA
* * *
7842 GATCTTGCCTTTTTGTATTGACAGCGAAGCAGGTCGAAGACACAA
1 -ATCTTGCCTTTCTGCATTGATAGCGAAGCAGGTCGAAGACACAA
* * ** * *
7887 ACCTTGCCTCTCTCGGTTGTGAT-G-G-AGCTGGTTGAAGACA-ATA
1 ATCTTGCCTTTCT-GCAT-TGATAGCGAAGCAGGTCGAAGACACA-A
* *
7930 GATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAA
1 -ATCTTGCCTTTCTGCATTGATAGCGAAGCAGGTCGAAGACACAA
** ** * * *
7975 ATCTTGCCCCTCTCGGTTGTGAT-G-G-AGCTGGTTGAAGACAAAA
1 ATCTTGCCTTTCT-GCAT-TGATAGCGAAGCAGGTCGAAGACACAA
*
8018 GATCTTGCCTTTCTGCATTGATAGCGAAGCAGGTCAAAGACACAA
1 -ATCTTGCCTTTCTGCATTGATAGCGAAGCAGGTCGAAGACACAA
*
8063 ACCTTGCCT
1 ATCTTGCCT
8072 CTGGTTGAAG
Statistics
Matches: 198, Mismatches: 55, Indels: 40
0.68 0.19 0.14
Matches are distributed among these distances:
42 11 0.06
43 52 0.26
44 75 0.38
45 51 0.26
46 9 0.05
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (44 bp):
ATCTTGCCTTTCTGCATTGATAGCGAAGCAGGTCGAAGACACAA
Found at i:8115 original size:70 final size:70
Alignment explanation
Indices: 8002--8143 Score: 248
Period size: 70 Copynumber: 2.0 Consensus size: 70
7992 TGTGATGGAG
* * *
8002 CTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTGATAGCGAAGCAGGTCAAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
8067 TGCCT
66 TGCCT
*
8072 CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACATAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
8137 TGCCT
66 TGCCT
8142 CT
1 CT
8144 CTCGGTTGTG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (70 bp):
CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
TGCCT
Found at i:8162 original size:334 final size:334
Alignment explanation
Indices: 7753--8392 Score: 1050
Period size: 334 Copynumber: 1.9 Consensus size: 334
7743 TTAAAGAAGC
* * *
7753 AGATCTTGCCTTCCTGCGTTAACAACGAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCATTCCTGCATTAACAACGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTTG
* ** * *
7818 TGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTTTGTATTGACAGCGAAGCAGGTCGAAGAC
66 TGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGAC
*
7883 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAATAGATCTTGCCTTCCTGCAT
131 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCAT
* *
7948 TGACAGCGAAGCAGGTCGAAGACACAAATCTTGCC-CCTCTCGGTTGTGATGGAGCTGGTTGAAG
196 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCC-CTCGGTTATGATGGAGCTGGTTGAAG
*
8012 ACAAAAGATCTTGCCTT-TCTGCATTGATAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCTGG
260 ACAAAAGATCTTGCCTTCT-TGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCTGG
8076 TTGAAGACAAA
324 TTGAAGACAAA
* * * *
8087 AGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACATAAACCTTGCCTCTCTCGGTTG
1 AGATCTTGCATTCCTGCATTAACAACGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTTG
* *
8152 TGATGGAGCTGGTTAAAGATAAAAGATCTTGCCTTCCTGCATTGACGGCGAAGCAGGTCAAAGAC
66 TGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGAC
*
8217 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTAT
131 ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCAT
*
8282 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTATGATGGATCTGGTTGAAGA
196 TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTATGATGGAGCTGGTTGAAGA
* *
8347 CAACAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGGTCGAAGAC
261 CAAAAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGGTCAAAGAC
8393 GAACCTTACC
Statistics
Matches: 282, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
334 279 0.99
335 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (334 bp):
AGATCTTGCATTCCTGCATTAACAACGAAGCAGATCAAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGAC
ACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCAT
TGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCCCTCGGTTATGATGGAGCTGGTTGAAGA
CAAAAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCTCTGGTT
GAAGACAAA
Found at i:8185 original size:44 final size:44
Alignment explanation
Indices: 8135--8361 Score: 137
Period size: 44 Copynumber: 5.2 Consensus size: 44
8125 AGACATAAAC
*
8135 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGATAAAAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGACAAAAGAT
** * * * * *
8179 CTTGCCT-TC-CTGCAT-TGACGGCGAAGCAGGTCAAAGACACAA-AC
1 CTTGCCTCTCTC-GGTTGTGA-TG-G-AGCTGGTTAAAGACAAAAGAT
*
8223 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGACAAAAGAT
* * * ** * *
8267 CTTGCCT-TC-CTGTAT-TGACAGCGAAGCAGGTCGAAGACACAA-AC
1 CTTGCCTCTCTCGGT-TGTGA-TG-G-AGCTGGTTAAAGACAAAAGAT
* * * * *
8311 CTTGCCTCCCTCGGTTATGATGGATCTGGTTGAAGACAACAGAT
1 CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGACAAAAGAT
8355 CTTGCCT
1 CTTGCCT
8362 TCTTGCATTG
Statistics
Matches: 136, Mismatches: 31, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
42 10 0.07
43 36 0.26
44 43 0.32
45 37 0.27
46 10 0.07
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.26
Consensus pattern (44 bp):
CTTGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGACAAAAGAT
Found at i:8203 original size:158 final size:162
Alignment explanation
Indices: 7913--8392 Score: 644
Period size: 158 Copynumber: 2.9 Consensus size: 162
7903 TTGTGATGGA
* *
7913 GCTGGTTGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAATC
1 GCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACC
* * *
7978 TTGCCCCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTTCTGCATTGATAGC
66 TTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC
8043 GAAGCAGGTCAAAGACACAAACCTTG-C-C-T
131 GAAGCAGGTCAAAGACACAAACCTTGCCTCGT
* * *
8072 -CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACATAAACC
1 GCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACC
* * *
8136 TTGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGATAAAAGATCTTGCCTTCCTGCATTGACGGC
66 TTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC
8201 GAAGCAGGTCAAAGACACAAACCTTGCCTCTCTCGGTTGTGAT
131 GAAGCAGGTCAAAGACACAAACCTTG---C-CTC------G-T
*
8244 GGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAA
1 ---GCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAA
* * * * *
8309 ACCTTGCCTCCCTCGGTTATGATGGATCTGGTTGAAGACAACAGATCTTGCCTTCTTGCATTGAC
63 ACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGAC
*
8374 AGCGAAGCAGGTCGAAGAC
128 AGCGAAGCAGGTCAAAGAC
8393 GAACCTTACC
Statistics
Matches: 279, Mismatches: 24, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
158 144 0.52
163 1 0.00
164 1 0.00
172 1 0.00
176 132 0.47
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (162 bp):
GCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACC
TTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC
GAAGCAGGTCAAAGACACAAACCTTGCCTCGT
Found at i:8223 original size:88 final size:88
Alignment explanation
Indices: 8072--8425 Score: 543
Period size: 88 Copynumber: 4.0 Consensus size: 88
8062 AACCTTGCCT
* *
8072 CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACATAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
8137 TGCCTCTCTCGGTTGTGATGGAG
66 TGCCTCTCTCGGTTGTGATGGAG
* * *
8160 CTGGTTAAAGATAAAAGATCTTGCCTTCCTGCATTGACGGCGAAGCAGGTCAAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
8225 TGCCTCTCTCGGTTGTGATGGAG
66 TGCCTCTCTCGGTTGTGATGGAG
* *
8248 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
* * *
8313 TGCCTCCCTCGGTTATGATGGAT
66 TGCCTCTCTCGGTTGTGATGGAG
* * * *
8336 CTGGTTGAAGACAACAGATCTTGCCTTCTTGCATTGACAGCGAAGCAGGTCGAAG--ACGAACCT
1 CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
*
8399 TACCTCTCTCGGTTGT-AGTGGAG
66 TGCCTCTCTCGGTTGTGA-TGGAG
8422 CTGG
1 CTGG
8426 CTAAAGAATT
Statistics
Matches: 244, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
85 1 0.00
86 28 0.11
88 215 0.88
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (88 bp):
CTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
TGCCTCTCTCGGTTGTGATGGAG
Found at i:8260 original size:246 final size:246
Alignment explanation
Indices: 7826--8318 Score: 833
Period size: 246 Copynumber: 2.0 Consensus size: 246
7816 TGTGATGGAG
* ** * *
7826 CTGGTTGAAGACAAAAGATCTTGCCTTTTTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
* *
7891 TGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAATAGATCTTGCCTTCCTGCATTGACAGCG
66 TGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCG
* *
7956 AAGCAGGTCGAAGACACAAATCTTGCCCCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
131 AAGCAGGTCAAAGACACAAACCTTGCCCCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
* *
8021 CTTGCCTTTCTGCATTGATAGCGAAGCAGGTCAAAGACACAAACCTTGCCT
196 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCT
*
8072 CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACATAAACCT
1 CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
* *
8137 TGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGATAAAAGATCTTGCCTTCCTGCATTGACGGCG
66 TGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCG
*
8202 AAGCAGGTCAAAGACACAAACCTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
131 AAGCAGGTCAAAGACACAAACCTTGCCCCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
* *
8267 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
196 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCT
8318 C
1 C
8319 CCTCGGTTAT
Statistics
Matches: 230, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
246 230 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (246 bp):
CTGGTTGAAGACAAAAGATCTTGCATTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCT
TGCCTCTCTCGGTTGTGATGGAGCTGGTTAAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCG
AAGCAGGTCAAAGACACAAACCTTGCCCCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGAT
CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCAAAGACACAAACCTTGCCT
Found at i:8536 original size:44 final size:44
Alignment explanation
Indices: 8439--8551 Score: 104
Period size: 44 Copynumber: 2.6 Consensus size: 44
8429 AAGAATTTCA
* * *
8439 GATCTTATCTCCCTGAGATTACAGCGGAGCAAATTGAAGTTAGT
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAAATTAAAATAAGT
* * * ***
8483 AATCCTATCTCCCTGAGATTACAGTGGAGTGGATTAAAATGAAG-
1 GATCTTATCTCCCTGAGATTACAGCGGAGCAAATTAAAAT-AAGT
*
8527 GATCTTATCTCTCTGA-AGTTACAGC
1 GATCTTATCTCCCTGAGA-TTACAGC
8552 AGAGTAGATC
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
43 1 0.02
44 51 0.94
45 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
GATCTTATCTCCCTGAGATTACAGCGGAGCAAATTAAAATAAGT
Done.