Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014240.1 Kokia drynarioides strain JFW-HI SEQ_129273, 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: 412615
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 62 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:367138 original size:48 final size:48
Alignment explanation
Indices: 367066--367352 Score: 285
Period size: 48 Copynumber: 6.0 Consensus size: 48
367056 CTTCAAACCA
*
367066 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAATAATGAAGCGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGGT
* *
367114 TATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGGT
* * * *
367162 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAATAGAGCT
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATG--A-AGCGGT
* * * * * * ** * * * * ***
367213 CAACATCCT--TGAAGTTATAGTGGAGTAAAGTGAAACT--TCAAACCCC
1 CATCTTCCTGATG-AGATACAGAGAAGTGGA-TCAAAATAATGAAGCGGT
*
367259 CATCTTCCTGATGAGATACAGAGAAGTGAATCAAAATAATGAAGCGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGGT
*
367307 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCG
1 CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCG
367353 AAACTCAATG
Statistics
Matches: 188, Mismatches: 42, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
46 14 0.07
47 13 0.07
48 132 0.70
49 3 0.02
50 12 0.06
51 14 0.07
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGGT
Found at i:367203 original size:316 final size:316
Alignment explanation
Indices: 366799--367474 Score: 917
Period size: 316 Copynumber: 2.1 Consensus size: 316
366789 CTTCAAACTC
* * * * ** * *
366799 CATCTTCCTG-ATAGATACAAAAAAATAGATTAAAAAAATGAAGCGATCATCTTCTTGATGAGAT
1 CATCTTCCTGAAGAGATACAAAGAAGTAAACCAAAATAATGAAGCGATCATCTTCCTGATGAGAT
* * *
366863 ACAGAGAAAGGGATCAAAACAATGAAGTAGAGCTCAACATCCTT-AAGATTACAGTAGAGTAGAG
66 ACAGAGAAAGGGACCAAAACAATGAAATAGAGCTCAACATCCTTGAAG-TTACAGTAGAGTAAAG
* * * *
366927 TGAAACTTCAAACCAACATCTTCTTGATGAGATATAGAAAAGTGGATCAAAACAATGTAGCGATC
130 TGAAACTTCAAACCAACATCTTCCTGATGAGATACAGAAAAGTGAATCAAAACAATGAAGCGATC
* *
366992 ATCTTCCTGATGAGATACAGAGAAGTGAACCAAAACAATGAAACGAAGCTCAATGTGAGCGAAAC
195 ATCTTCCTGATGAGATACAGAGAAGTGAACCAAAACAATGAAACGAAACTCAATGTGAACGAAAC
* ** *
367057 TTCAAACCACATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAATAATGAAGCGGT
260 TTCAAACCACATCTTCCTGATGAGATACAGAGAAATGAATCAAAACAATGAAGCGGT
* * * * ** * *
367114 TATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGGTCATCTTCCTGATGAGAT
1 CATCTTCCTGAAGAGATACAAAGAAGTAAACCAAAATAATGAAGCGATCATCTTCCTGATGAGAT
* *
367179 ACAGAG-AAGTGGACCAAAACAATGAAATAGAGCTCAACATCCTTGAAGTTATAGTGGAGTAAAG
66 ACAGAGAAAG-GGACCAAAACAATGAAATAGAGCTCAACATCCTTGAAGTTACAGTAGAGTAAAG
** * * *
367243 TGAAACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGAATCAAAATAATGAAGCGGTC
130 TGAAACTTCAAACCAACATCTTCCTGATGAGATACAGAAAAGTGAATCAAAACAATGAAGCGATC
* * * *
367308 ATCTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCGAAACTCAATGTGAATGAAAC
195 ATCTTCCTGATGAGATACAGAGAAGTGAACCAAAACAATGAAACGAAACTCAATGTGAACGAAAC
* *
367373 TTCAAACCCCATCTTCCTGATGAGATATAGAGAAATGAATCAAAACAATGAAGCGGT
260 TTCAAACCACATCTTCCTGATGAGATACAGAGAAATGAATCAAAACAATGAAGCGGT
* *
367430 CATCTTCCTGAAGAGATATAAATAAGTAAACCAAAATAATGAAGC
1 CATCTTCCTGAAGAGATACAAAGAAGTAAACCAAAATAATGAAGC
367475 AAAGCTCAAT
Statistics
Matches: 311, Mismatches: 47, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
315 11 0.04
316 297 0.95
317 3 0.01
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (316 bp):
CATCTTCCTGAAGAGATACAAAGAAGTAAACCAAAATAATGAAGCGATCATCTTCCTGATGAGAT
ACAGAGAAAGGGACCAAAACAATGAAATAGAGCTCAACATCCTTGAAGTTACAGTAGAGTAAAGT
GAAACTTCAAACCAACATCTTCCTGATGAGATACAGAAAAGTGAATCAAAACAATGAAGCGATCA
TCTTCCTGATGAGATACAGAGAAGTGAACCAAAACAATGAAACGAAACTCAATGTGAACGAAACT
TCAAACCACATCTTCCTGATGAGATACAGAGAAATGAATCAAAACAATGAAGCGGT
Found at i:367396 original size:268 final size:259
Alignment explanation
Indices: 367240--368331 Score: 1075
Period size: 268 Copynumber: 4.2 Consensus size: 259
367230 TAGTGGAGTA
* * * *
367240 AAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGAATCAAAATAATGAAGCG
1 AAGTGAAACTTCAAA-CCCCATCTTCCTGAAGAGATACAGAGAAATGGATCAAAACAATGAAGCG
* * *
367305 GTCATCTTCCTGATGAGATACAGAG-AAGTGGACCAAAATAATGAAGC-GA-AAC-T-C-AA-T-
65 ATCATCTTCTTGATGAGATACAGAGAAAG-GGATCAAAATAATGAAGCAGACAACATCCTAAGTA
* *
367362 GT-G-A-A-TGAAACTTCAAA-CCCCATCTTCCTGATGAGATATAGAGAAATGAATCAAAACAAT
129 GTGGTAGAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAAT
* * * * * *
367422 GAAGCGGTCATCTTCCTGAAGAGATATAAATAAGTAAACCAAAATAATG--AAGCA-AAGCTCAA
194 GAAGCAGTCATCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAG-AGAA-CTCAA
367484 TGT
257 TGT
* * * * * * * *
367487 GAGAGAAACTTCAAACTCCATCTTCTTGAAGAGTTATAGAGAAATGGATAAAAACAATGAAGCGG
1 AAGTGAAACTTCAAACCCCATCTTCCTGAAGAGATACAGAGAAATGGATCAAAACAATGAAGCGA
367552 TCATCTTCTTGATGAGATACAGAGAAAGGGATCAAAATAATGAAGCAGAGCTCAACATCCCTAAG
66 TCATCTTCTTGATGAGATACAGAGAAAGGGATCAAAATAATGAAGCAGA---CAACAT-CCTAA-
** * *
367617 GTTACAGTGGAGTAGAGTGAAACTTCAAACCCCCATCTTCCAAATGAAATATAGAGAAGTAGATC
126 G-T--AGT-G-GTAGAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGATC
* * *
367682 AAAACAATAAAGTAATCATCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGA-A
186 AAAACAATGAAGCAGTCATCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGAGA
*
367746 GCTCAATGT
251 ACTCAATGT
* * *
367755 AAGTGAAACTTCAAACCCCATCTTCCTGAAGAGTTATAGAGAAATGGATCAAAACAATGAAGTGA
1 AAGTGAAACTTCAAACCCCATCTTCCTGAAGAGATACAGAGAAATGGATCAAAACAATGAAGCGA
*
367820 TCATCTTCTTGATGAGATACAGAGAAAGGGATCAAAATAATGAAGCAAAACTCAACATCCCTAAG
66 TCATCTTCTTGATGAGATACAGAGAAAGGGATCAAAATAATGAAGC-AGA--CAACAT-CCTAA-
** *
367885 GTTACAGTGGAGTAGAGTGAAACTTCAAACCCCCATCTTCCAAATGAGATATAGAGAAGTAGATC
126 G-T--AGT-G-GTAGAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGATC
* * * *
367950 AAAACAATAAAGCAATCATCTTCCTGATGAGATATAAAGAAGTGGACCAAAACAATG--AAGAGA
186 AAAACAATGAAGCAGTCATCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGAGA
368013 AGCTCAATGT
251 A-CTCAATGT
* *
368023 AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGA-GGATCAAAACAACGAAGCG
1 AAGTGAAACTTCAAACCCCATCTTCCTGAAGAGATACAGAGAA-ATGGATCAAAACAATGAAGCG
* *
368087 ATCATCTTCTTGATGAGATACAGAG-AAGTGGATCAAAACAATGAAGC-GA-AGC-T-C--A--A
65 ATCATCTTCTTGATGAGATACAGAGAAAG-GGATCAAAATAATGAAGCAGACAACATCCTAAGTA
*** * * * *
368143 -T-GT-GAGTGAAACTTCAAA-TTTCATATTTCTGATGAGATACAGAGAAGTGGATCAAAATAAT
129 GTGGTAGAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAAT
* * * ** *
368204 GAAGCAGTCATCTTCTTTATGAGATACAGAGAAGTGAACCAAAACAATGAAGCG-GAGCTCAATA
194 GAAGCAGTCATCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGAGAACTCAAT-
*
368268 GG
258 GT
* * * ** * * *
368270 GAGTGAAACTTTAAACCCCATCTTCTTGTTGACATACAGAGAAGTGGATCAAAA-GATGAAGC
1 AAGTGAAACTTCAAACCCCATCTTCCTGAAGAGATACAGAGAAATGGATCAAAACAATGAAGC
368332 TATAACACCA
Statistics
Matches: 732, Mismatches: 79, Indels: 69
0.83 0.09 0.08
Matches are distributed among these distances:
246 168 0.23
247 83 0.11
248 3 0.00
251 4 0.01
252 2 0.00
254 1 0.00
255 2 0.00
258 2 0.00
260 1 0.00
261 2 0.00
262 1 0.00
263 2 0.00
264 1 0.00
265 1 0.00
266 6 0.01
267 16 0.02
268 429 0.59
269 5 0.01
270 3 0.00
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (259 bp):
AAGTGAAACTTCAAACCCCATCTTCCTGAAGAGATACAGAGAAATGGATCAAAACAATGAAGCGA
TCATCTTCTTGATGAGATACAGAGAAAGGGATCAAAATAATGAAGCAGACAACATCCTAAGTAGT
GGTAGAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGA
AGCAGTCATCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGAGAACTCAATGT
Found at i:367446 original size:123 final size:124
Alignment explanation
Indices: 367240--368331 Score: 874
Period size: 123 Copynumber: 8.5 Consensus size: 124
367230 TAGTGGAGTA
* * *
367240 AAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGAATCAAAATAATGAAGCG
1 AAGTGAAACTTCAAA-CCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCG
* *
367305 GTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCGAAACTCAATGTG
65 ATCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAACTCAATGTG
* * *
367365 AA-TGAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAATGAATCAAAACAATGAAGCGG
1 AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGA
* * * * ** *
367429 TCATCTTCCTGAAGAGATATAAATAAGTAAACCAAAATAATGAAGC-AAAGCTCAATGTG
66 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAA-CTCAATGTG
* * * * * * * *
367488 -AGAGAAACTTCAAACTCCATCTTCTTGAAGAGTTATAGAGAAATGGATAAAAACAATGAAGCGG
1 AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGA
* * *
367552 TCATCTTCTTGATGAGATACAGAGAAAG-GGATCAAAATAATGAAGCAGAGCTCAACATCCCTAA
66 TCATCTTCCTGATGAGATACAGAG-AAGTGGACCAAAACAATGAAGC-GA----AAC-T--C-AA
* *
367616 GGTT
121 TGTG
* ** ** * *
367620 ACAGTGGAGTAGAGTGAAACTTCAAACCCCCATCTTCCAAATGAAATATAGAGAAGTAGATCAAA
1 A-AGT-GA--A-ACT-TCA-----AA-CCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAA
* ** * * ** *
367685 ACAATAAAGTAATCATCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGAAGCTC
54 ACAATGAAGCGATCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAACTC
367750 AATGT-
119 AATGTG
* * * *
367755 AAGTGAAACTTCAAACCCCATCTTCCTGAAGAGTTATAGAGAAATGGATCAAAACAATGAAGTGA
1 AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGA
* * * *
367820 TCATCTTCTTGATGAGATACAGAGAAAG-GGATCAAAATAATGAAGCAAAACTCAACATCCCTAA
66 TCATCTTCCTGATGAGATACAGAG-AAGTGGACCAAAACAATGAAGCGAAACTC-A-A----T--
*
367884 GGTT
122 -GTG
* ** ** *
367888 ACAGTGGAGTAGAGTGAAACTTCAAACCCCCATCTTCCAAATGAGATATAGAGAAGTAGATCAAA
1 A-AGT-GA--A-ACT-TCA-----AA-CCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAA
* * * * * *
367953 ACAATAAAGCAATCATCTTCCTGATGAGATATAAAGAAGTGGACCAAAACAATGAAGAGAAGCTC
54 ACAATGAAGCGATCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAACTC
368018 AATGT-
119 AATGTG
* * *
368023 AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGAGGATCAAAACAACGAAGCGA
1 AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGA
* * *
368088 TCATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCGAAGCTCAATGTG
66 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAACTCAATGTG
*** * * * *
368147 -AGTGAAACTTCAAATTTCATATTTCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGC-A
1 AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGA
* * * * *
368210 GTCATCTTCTTTATGAGATACAGAGAAGTGAACCAAAACAATGAAGCGGAGCTCAATAG-G
66 -TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAACTCAAT-GTG
* * * * * * *
368270 GAGTGAAACTTTAAACCCCATCTTCTTGTTGACATACAGAGAAGTGGATCAAAA-GATGAAGC
1 AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGC
368332 TATAACACCA
Statistics
Matches: 780, Mismatches: 132, Indels: 112
0.76 0.13 0.11
Matches are distributed among these distances:
122 5 0.01
123 475 0.61
124 68 0.09
125 4 0.01
128 1 0.00
129 6 0.01
130 4 0.01
131 3 0.00
132 6 0.01
133 5 0.01
134 11 0.01
135 6 0.01
136 6 0.01
137 3 0.00
138 4 0.01
139 4 0.01
140 2 0.00
143 1 0.00
144 13 0.02
145 153 0.20
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (124 bp):
AAGTGAAACTTCAAACCCCATCTTCCTGATGAGATATAGAGAAGTGGATCAAAACAATGAAGCGA
TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAAACTCAATGTG
Found at i:367465 original size:48 final size:48
Alignment explanation
Indices: 367382--367474 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
367372 CTTCAAACCC
* * * *
367382 CATCTTCCTGATGAGATATAGAGAAATGAATCAAAACAATGAAGCGGT
1 CATCTTCCTGAAGAGATATAAAGAAATAAACCAAAACAATGAAGCGGT
* * *
367430 CATCTTCCTGAAGAGATATAAATAAGTAAACCAAAATAATGAAGC
1 CATCTTCCTGAAGAGATATAAAGAAATAAACCAAAACAATGAAGC
367475 AAAGCTCAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (48 bp):
CATCTTCCTGAAGAGATATAAAGAAATAAACCAAAACAATGAAGCGGT
Found at i:367576 original size:48 final size:48
Alignment explanation
Indices: 367505--367597 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
367495 CTTCAAACTC
* * *
367505 CATCTTCTTGAAGAGTTATAGAGAAATGGATAAAAACAATGAAGCGGT
1 CATCTTCTTGAAGAGATACAGAGAAAGGGATAAAAACAATGAAGCGGT
* * *
367553 CATCTTCTTGATGAGATACAGAGAAAGGGATCAAAATAATGAAGC
1 CATCTTCTTGAAGAGATACAGAGAAAGGGATAAAAACAATGAAGC
367598 AGAGCTCAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.24
Consensus pattern (48 bp):
CATCTTCTTGAAGAGATACAGAGAAAGGGATAAAAACAATGAAGCGGT
Found at i:367712 original size:391 final size:391
Alignment explanation
Indices: 367115--367838 Score: 1060
Period size: 391 Copynumber: 1.9 Consensus size: 391
367105 TGAAGCGGTT
* * * *
367115 ATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCGGTCATCTTCCTGATGAGATA
1 ATCTTCTTGAAGAGATACAGAGAAATGGATAAAAACAATGAAGCGGTCATCTTCCTGATGAGATA
* * *
367180 CAGAGAAGTGGACCAAAACAATGAAATAGAGCTCAACATCCTTGAAGTTATAGTGGAGTAAAGTG
66 CAGAGAAGTGGACCAAAACAATGAAACAGAGCTCAACATCCCTGAAGTTACAGTGGAGTAAAGTG
** * * * **
367245 AAACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGAATCAAAATAATGAAGCGGTCAT
131 AAACTTCAAACCCCCATCTTCCAAATGAAATACAGAGAAGTGAATCAAAACAATAAAGCAATCAT
* * * **
367310 CTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCGAAACTCAATGTGAA-TGAAACT
196 CTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGAAACTCAATGT-AAGTGAAACT
* *
367374 TCAAACCCCATCTTCCTGATGAGATATAGAGAAATGAATCAAAACAATGAAGCGGTCATCTTCCT
260 TCAAACCCCATCTTCCTGAAGAGATATAGAGAAATGAATCAAAACAATGAAGCGATCATCTTCCT
367439 GAAGAGATATAAATAAGTAAACCAAAATAATGAAGCAAAGCTCAATGTGAGAGAAACTTCAAACT
325 GAAGAGATATAAATAAGTAAACCAAAATAATGAAGCAAAGCTCAATGTGAGAGAAACTTCAAACT
367504 CC
390 CC
* * *
367506 ATCTTCTTGAAGAGTTATAGAGAAATGGATAAAAACAATGAAGCGGTCATCTTCTTGATGAGATA
1 ATCTTCTTGAAGAGATACAGAGAAATGGATAAAAACAATGAAGCGGTCATCTTCCTGATGAGATA
* * * *
367571 CAGAGAAAG-GGATCAAAATAATGAAGCAGAGCTCAACATCCCT-AAGGTTACAGTGGAGTAGAG
66 CAGAG-AAGTGGACCAAAACAATGAAACAGAGCTCAACATCCCTGAA-GTTACAGTGGAGTAAAG
* *
367634 TGAAACTTCAAACCCCCATCTTCCAAATGAAATATAGAGAAGT-AGATCAAAACAATAAAGTAAT
129 TGAAACTTCAAACCCCCATCTTCCAAATGAAATACAGAGAAGTGA-ATCAAAACAATAAAGCAAT
*
367698 CATCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGAAGCTCAATGTAAGTGAAA
193 CATCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGAAACTCAATGTAAGTGAAA
* * *
367763 CTTCAAACCCCATCTTCCTGAAGAGTTATAGAGAAATGGATCAAAACAATGAAGTGATCATCTTC
258 CTTCAAACCCCATCTTCCTGAAGAGATATAGAGAAATGAATCAAAACAATGAAGCGATCATCTTC
* *
367828 TTGATGAGATA
323 CTGAAGAGATA
367839 CAGAGAAAGG
Statistics
Matches: 293, Mismatches: 36, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
390 5 0.02
391 285 0.97
392 3 0.01
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (391 bp):
ATCTTCTTGAAGAGATACAGAGAAATGGATAAAAACAATGAAGCGGTCATCTTCCTGATGAGATA
CAGAGAAGTGGACCAAAACAATGAAACAGAGCTCAACATCCCTGAAGTTACAGTGGAGTAAAGTG
AAACTTCAAACCCCCATCTTCCAAATGAAATACAGAGAAGTGAATCAAAACAATAAAGCAATCAT
CTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATGAAAAGAAACTCAATGTAAGTGAAACTT
CAAACCCCATCTTCCTGAAGAGATATAGAGAAATGAATCAAAACAATGAAGCGATCATCTTCCTG
AAGAGATATAAATAAGTAAACCAAAATAATGAAGCAAAGCTCAATGTGAGAGAAACTTCAAACTC
C
Found at i:367846 original size:48 final size:48
Alignment explanation
Indices: 367773--367864 Score: 130
Period size: 48 Copynumber: 1.9 Consensus size: 48
367763 CTTCAAACCC
* * *
367773 CATCTTCCTGAAGAGTTATAGAGAAATGGATCAAAACAATGAAGTGAT
1 CATCTTCCTGAAGAGATACAGAGAAAGGGATCAAAACAATGAAGTGAT
* * *
367821 CATCTTCTTGATGAGATACAGAGAAAGGGATCAAAATAATGAAG
1 CATCTTCCTGAAGAGATACAGAGAAAGGGATCAAAACAATGAAG
367865 CAAAACTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (48 bp):
CATCTTCCTGAAGAGATACAGAGAAAGGGATCAAAACAATGAAGTGAT
Found at i:368095 original size:48 final size:48
Alignment explanation
Indices: 368041--368135 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
368031 CTTCAAACCC
368041 CATCTTCCTGATGAGATACAGAGAAGAGGATCAAAACAACGAAGCGAT
1 CATCTTCCTGATGAGATACAGAGAAGAGGATCAAAACAACGAAGCGAT
* * *
368089 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCGA
1 CATCTTCCTGATGAGATACAGAGAAGAGGATCAAAACAACGAAGCGA
368136 AGCTCAATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAGAGAAGAGGATCAAAACAACGAAGCGAT
Found at i:370019 original size:29 final size:29
Alignment explanation
Indices: 369951--370023 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
369941 TGAAGCCCCT
369951 TTTTATTTTTGACCCTAAACTTTCAAAAA
1 TTTTATTTTTGACCCTAAACTTTCAAAAA
* ** * *
369980 ATTTAAATTTGGCCCTCAAAC-TTCCAAAA
1 TTTTATTTTTGACCCT-AAACTTTCAAAAA
370009 TTTTATTTTTGACCC
1 TTTTATTTTTGACCC
370024 CGTTTTTCCC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (29 bp):
TTTTATTTTTGACCCTAAACTTTCAAAAA
Found at i:373089 original size:10 final size:10
Alignment explanation
Indices: 373074--373110 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
373064 AATATAAATA
373074 TTTTTTCTTT
1 TTTTTTCTTT
373084 TTTTTTCTTT
1 TTTTTTCTTT
373094 TTTTATTCTTT
1 TTTT-TTCTTT
373105 TTTTTT
1 TTTTTT
373111 TATAAATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:373095 original size:11 final size:11
Alignment explanation
Indices: 373074--373111 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
373064 AATATAAATA
373074 TTTTTTC-TTT
1 TTTTTTCTTTT
373084 TTTTTTCTTTT
1 TTTTTTCTTTT
*
373095 TTTATTCTTTT
1 TTTTTTCTTTT
373106 TTTTTT
1 TTTTTT
373112 ATAAATGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.03, C:0.08, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:394329 original size:20 final size:20
Alignment explanation
Indices: 394294--394331 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
394284 AAGTGGTGAA
394294 GAAGAGAAATGCAAGAAAAT
1 GAAGAGAAATGCAAGAAAAT
394314 GAAGAAGAAATG-AAGAAA
1 GAAG-AGAAATGCAAGAAA
394332 TTCTTGACAA
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:0.63, C:0.03, G:0.26, T:0.08
Consensus pattern (20 bp):
GAAGAGAAATGCAAGAAAAT
Found at i:396182 original size:30 final size:29
Alignment explanation
Indices: 396146--396248 Score: 100
Period size: 29 Copynumber: 3.5 Consensus size: 29
396136 AAAAACGTAA
***
396146 TTTTTGAGAAATTCGAGGTTAAAATCGGGT
1 TTTTTGA-AAATTCGAGGTTAAAATCGAAC
*
396176 TTTTTGAAAATTTG-GAGTTAAAATCGAAC
1 TTTTTGAAAATTCGAG-GTTAAAATCGAAC
* * *
396205 TTTTGGAAAATTCGAGGTCAAAATCAAAC
1 TTTTTGAAAATTCGAGGTTAAAATCGAAC
*
396234 TTTTGGAAAAGTTCG
1 TTTTTGAAAA-TTCG
396249 GGGGCAAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
28 1 0.02
29 49 0.79
30 12 0.19
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (29 bp):
TTTTTGAAAATTCGAGGTTAAAATCGAAC
Found at i:396234 original size:29 final size:30
Alignment explanation
Indices: 396195--396258 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
396185 ATTTGGAGTT
* *
396195 AAAATCGAACTTTTGGAAAA-TTCGAGGTC
1 AAAATCAAACTTTTGGAAAAGTTCGAGGGC
*
396224 AAAATCAAACTTTTGGAAAAGTTCGGGGGC
1 AAAATCAAACTTTTGGAAAAGTTCGAGGGC
396254 AAAAT
1 AAAAT
396259 GTGATTTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (30 bp):
AAAATCAAACTTTTGGAAAAGTTCGAGGGC
Found at i:396266 original size:29 final size:29
Alignment explanation
Indices: 396205--396357 Score: 127
Period size: 30 Copynumber: 5.3 Consensus size: 29
396195 AAAATCGAAC
* * ** *
396205 TTTTGGAAAATTCGAGGTCAAAATCAAAC
1 TTTTGGAAAATTCGGGGGCAAAATGTAAT
*
396234 TTTTGGAAAAGTTCGGGGGCAAAATGTGAT
1 TTTTGGAAAA-TTCGGGGGCAAAATGTAAT
* * *
396264 TTTT-GAAAGTTCGAGGG--AAATAATAAT
1 TTTTGGAAAATTCGGGGGCAAAAT-GTAAT
*
396291 TTTTGGAAGATTCGGGGGCAAAAATGTAAT
1 TTTTGGAAAATTCGGGGGC-AAAATGTAAT
* *
396321 TTTT-GAAATATTCGTGGCCAAAATGT-AT
1 TTTTGGAAA-ATTCGGGGGCAAAATGTAAT
396349 TTTTGGAAA
1 TTTTGGAAA
396358 TTTTTAAGGG
Statistics
Matches: 99, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
26 4 0.04
27 7 0.07
28 23 0.23
29 28 0.28
30 33 0.33
31 4 0.04
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (29 bp):
TTTTGGAAAATTCGGGGGCAAAATGTAAT
Found at i:396358 original size:29 final size:31
Alignment explanation
Indices: 396234--396358 Score: 101
Period size: 29 Copynumber: 4.3 Consensus size: 31
396224 AAAATCAAAC
*
396234 TTTTGGAAA-AGTTCGGGGGC-AAAATGTGAT
1 TTTTGGAAATA-TTCGGGGGCAAAAATGTAAT
* *
396264 TTTT-GAAA-GTTCGAGGG-AAATAA--TAAT
1 TTTTGGAAATATTCGGGGGCAAA-AATGTAAT
*
396291 TTTTGG-AAGATTCGGGGGCAAAAATGTAAT
1 TTTTGGAAATATTCGGGGGCAAAAATGTAAT
* *
396321 TTTT-GAAATATTC-GTGGCCAAAATGT-AT
1 TTTTGGAAATATTCGGGGGCAAAAATGTAAT
396349 TTTTGGAAAT
1 TTTTGGAAAT
396359 TTTTAAGGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
27 9 0.12
28 25 0.32
29 26 0.33
30 18 0.23
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (31 bp):
TTTTGGAAATATTCGGGGGCAAAAATGTAAT
Found at i:396397 original size:29 final size:30
Alignment explanation
Indices: 396360--396448 Score: 121
Period size: 29 Copynumber: 3.1 Consensus size: 30
396350 TTTGGAAATT
396360 TTTAAGGGTTAAAATATAATTTTAGAAAAG
1 TTTAAGGGTTAAAATATAATTTTAGAAAAG
* *
396390 TTT-AGGGTCAAAATGTAATTTT-GAAAAG
1 TTTAAGGGTTAAAATATAATTTTAGAAAAG
* *
396418 TTTAAGGG-TCAAATAAAATTTTAGAAAAG
1 TTTAAGGGTTAAAATATAATTTTAGAAAAG
396447 TT
1 TT
396449 GTCAAAATGC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
28 19 0.37
29 29 0.57
30 3 0.06
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (30 bp):
TTTAAGGGTTAAAATATAATTTTAGAAAAG
Found at i:396504 original size:30 final size:29
Alignment explanation
Indices: 396339--396505 Score: 107
Period size: 30 Copynumber: 5.8 Consensus size: 29
396329 TATTCGTGGC
* **
396339 CAAAATGTATTTTTGGAAATTTTTAAGGGT
1 CAAAATATATTTTT-GAAAAGTTTAAGGGT
* *
396369 TAAAATATAATTTTAGAAAAGTTT-AGGGT
1 CAAAATAT-ATTTTTGAAAAGTTTAAGGGT
* *
396398 CAAAATGTAATTTTGAAAAGTTTAAGGGT
1 CAAAATATATTTTTGAAAAGTTTAAGGGT
* *
396427 C-AAATAAAATTTTAGAAAAG-TT----GT
1 CAAAAT-ATATTTTTGAAAAGTTTAAGGGT
* **
396451 CAAAATGCA-ATTTTGGAGGAGTTTAAGGGT
1 CAAAAT--ATATTTTTGAAAAGTTTAAGGGT
*
396481 CAAAATATGATTTTTGGAAAGTTTA
1 CAAAATAT-ATTTTTGAAAAGTTTA
396506 GGGACCTACT
Statistics
Matches: 104, Mismatches: 21, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
24 3 0.03
25 13 0.12
26 3 0.03
28 20 0.19
29 27 0.26
30 33 0.32
31 5 0.05
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.37
Consensus pattern (29 bp):
CAAAATATATTTTTGAAAAGTTTAAGGGT
Found at i:398530 original size:78 final size:78
Alignment explanation
Indices: 398409--398663 Score: 276
Period size: 78 Copynumber: 3.3 Consensus size: 78
398399 TTGGTAAGAT
* * * * * * * * * *
398409 ATTGGATGGTTGCAATCTGCCCCTGTCGCGGGGGAAGAGATTGGCTGACGATGATCTGCCCCATG
1 ATTGGATGGCTGCAATCTGCCTCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAG
*
398474 ATCGGGGTAAAAG
66 CTCGGGGTAAAAG
* * * * **
398487 ATTGAATGGTTGCAATCTGCCTTAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTACCTTAAG
1 ATTGGATGGCTGCAATCTGCCTCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAG
*
398552 CTCAGGGTAAAAG
66 CTCGGGGTAAAAG
* * * * *
398565 ATCGGATGGCTGCAATCTGCCTCAGGCTCAGGGTAAGAGATTAGTTGATGGTGACCTGCCCCAGG
1 ATTGGATGGCTGCAATCTGCCTCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAG
*
398630 CTCGGGGTAAGAG
66 CTCGGGGTAAAAG
**
398643 ATTGGATGGCTATAATCTGCC
1 ATTGGATGGCTGCAATCTGCC
398664 CTAAGCTCGA
Statistics
Matches: 145, Mismatches: 32, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
78 145 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (78 bp):
ATTGGATGGCTGCAATCTGCCTCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAG
CTCGGGGTAAAAG
Found at i:398663 original size:39 final size:39
Alignment explanation
Indices: 398401--398878 Score: 179
Period size: 39 Copynumber: 12.3 Consensus size: 39
398391 TTTTTTTTTT
* * ** * *
398401 GGTAAGATATTGGATGGTTGCAATCTGCCCC-TGTCGCGG
1 GGTAAGAGATTGGATGGCTATAATCTGCCCCAAG-CTCGG
* * * * * * *
398440 GGGAAGAGATTGGCTGACGATGATCTGCCCCATGATCGG
1 GGTAAGAGATTGGATGGCTATAATCTGCCCCAAGCTCGG
* * * ** ** * *
398479 GGTAAAAGATTGAATGGTTGCAATCTGCCTTAGGCTCAG
1 GGTAAGAGATTGGATGGCTATAATCTGCCCCAAGCTCGG
* * * * * ** *
398518 GGTAAGAGATTGGCT-GATGGTGATCTACCTTAAGCTCAG
1 GGTAAGAGATTGGATGGCT-ATAATCTGCCCCAAGCTCGG
* * ** * * *
398557 GGTAAAAGATCGGATGGCTGCAATCTGCCTCAGGCTCAG
1 GGTAAGAGATTGGATGGCTATAATCTGCCCCAAGCTCGG
* * *
398596 GGTAAGAGATTAGTTGATGG---TGACCTGCCCCAGGCTCGG
1 GGTAAGAGATT-G--GATGGCTATAATCTGCCCCAAGCTCGG
* *
398635 GGTAAGAGATTGGATGGCTATAATCTGCCCTAAGCTCGA
1 GGTAAGAGATTGGATGGCTATAATCTGCCCCAAGCTCGG
* * * * *
398674 GCTAAAATATCGGATGGTTATAATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGATGGCTATAATCTGCCCCAAGCTCGG
* *
398713 GGTAAGAGATTGACTGATGG-TGAT--T-TGCCCTAAGCTCGA
1 GGTAAGAGATTG---GATGGCT-ATAATCTGCCCCAAGCTCGG
* *** * *
398752 GGTAAAAGATCATATGGCTACAATCTGCCTCAAGCTCGG
1 GGTAAGAGATTGGATGGCTATAATCTGCCCCAAGCTCGG
* * **
398791 GGTAAGAGATTGGTTTATGG---TGATCTACCTTAAGCTCGG
1 GGTAAGAGATTGG---ATGGCTATAATCTGCCCCAAGCTCGG
* * * * *
398830 GGTAAAAGATCGGATGGCTGTGATCTGCCCTAAGCTCGG
1 GGTAAGAGATTGGATGGCTATAATCTGCCCCAAGCTCGG
*
398869 GGTAAAAGAT
1 GGTAAGAGAT
398879 CGAATTACTG
Statistics
Matches: 328, Mismatches: 88, Indels: 46
0.71 0.19 0.10
Matches are distributed among these distances:
36 14 0.04
37 1 0.00
38 4 0.01
39 286 0.87
40 6 0.02
41 1 0.00
42 16 0.05
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (39 bp):
GGTAAGAGATTGGATGGCTATAATCTGCCCCAAGCTCGG
Found at i:398669 original size:117 final size:115
Alignment explanation
Indices: 398548--398800 Score: 265
Period size: 117 Copynumber: 2.2 Consensus size: 115
398538 TGATCTACCT
* * * *
398548 TAAGCTCAGGGTAAAAGATCGGATGGCTGCAATCTGCCTCAGGCTCAGGGTAAGAGATT-AGTTG
1 TAAGCTC-GGGTAAAAGATCGGATGGCTACAATCTGCCCCAAGCTCAGGGTAAGAGATTGA-CTG
* * * ** *
398612 ATGGTGACCTGCCCCAGGCTCGGGGTAAGAGATTGGATGGCTATAATCTGCCC
64 ATGGTGACCTGCCCCAAGCTCGAGGTAAAAGATCAGATGGCTACAATCTG-CC
* * * * *
398665 TAAGCTCGAGCTAAAATATCGGATGGTTATAATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGA
1 TAAGCTCG-GGTAAAAGATCGGATGGCTACAATCTGCCCCAAGCTCAGGGTAAGAGATTGACTGA
** * *
398730 TGGTGATTTGCCCTAAGCTCGAGGTAAAAGATCATATGGCTACAATCTGCC
65 TGGTGACCTGCCCCAAGCTCGAGGTAAAAGATCAGATGGCTACAATCTGCC
*
398781 TCAAGCTCGGGGTAAGAGAT
1 T-AAGCTC-GGGTAAAAGAT
398801 TGGTTTATGG
Statistics
Matches: 110, Mismatches: 22, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
116 4 0.04
117 104 0.95
118 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (115 bp):
TAAGCTCGGGTAAAAGATCGGATGGCTACAATCTGCCCCAAGCTCAGGGTAAGAGATTGACTGAT
GGTGACCTGCCCCAAGCTCGAGGTAAAAGATCAGATGGCTACAATCTGCC
Found at i:398702 original size:78 final size:75
Alignment explanation
Indices: 398620--398878 Score: 250
Period size: 78 Copynumber: 3.3 Consensus size: 75
398610 TGATGGTGAC
* *
398620 CTGCCCCAGGCTCGGGGTAAGAGATTGGATGGCT-ATAATCTGCCCTAAGCTCGAGCTAAAATAT
1 CTGCCCCAAGCTCGGGGTAAGAGATTGGATGG-TGAT--T-TGCCCTAAGCTCGAGCTAAAAGAT
* * *
398684 CGGATGGTTATAAT
62 CAGATGGCTACAAT
*
398698 CTGCCCCAAGCTCGGGGTAAGAGATTGACTGATGGTGATTTGCCCTAAGCTCGAGGTAAAAGATC
1 CTGCCCCAAGCTCGGGGTAAGAGATTG---GATGGTGATTTGCCCTAAGCTCGAGCTAAAAGATC
*
398763 ATATGGCTACAAT
63 AGATGGCTACAAT
* * * * * *
398776 CTGCCTCAAGCTCGGGGTAAGAGATTGGTTTATGGTGATCTACCTTAAGCTCGGGGTAAAAGATC
1 CTGCCCCAAGCTCGGGGTAAGAGATTGG---ATGGTGATTTGCCCTAAGCTCGAGCTAAAAGATC
* ***
398841 GGATGGCTGTGAT
63 AGATGGCTACAAT
* *
398854 CTGCCCTAAGCTCGGGGTAAAAGAT
1 CTGCCCCAAGCTCGGGGTAAGAGAT
398879 CGAATTACTG
Statistics
Matches: 154, Mismatches: 20, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
75 1 0.01
78 144 0.94
79 1 0.01
80 1 0.01
81 7 0.05
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (75 bp):
CTGCCCCAAGCTCGGGGTAAGAGATTGGATGGTGATTTGCCCTAAGCTCGAGCTAAAAGATCAGA
TGGCTACAAT
Found at i:398879 original size:39 final size:39
Alignment explanation
Indices: 398460--398898 Score: 217
Period size: 39 Copynumber: 11.3 Consensus size: 39
398450 TGGCTGACGA
* * * * * *
398460 TGATCTGCCCCATGATCGGGGTAAAAGATTGAATGGTTG
1 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
** * * * * * * *
398499 CAATCTGCCTTAGGCTCAGGGTAAGAGATTGGCT-GATGG
1 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCT-G
* * *
398538 TGATCTACCTTAAGCTCAGGGTAAAAGATCGGATGGCTG
1 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
** * * * ** * *
398577 CAATCTG-CCTCAGGCTCAGGGTAAGAGATTAG-TTGATGG
1 TGATCTGCCCT-AAGCTCGGGGTAAAAGATCGGATGGCT-G
* * * * * *
398616 TGACCTGCCCCAGGCTCGGGGTAAGAGATTGGATGGCTA
1 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
* * * * * *
398655 TAATCTGCCCTAAGCTCGAGCTAAAATATCGGATGGTTA
1 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
* * * * *
398694 TAATCTGCCCCAAGCTCGGGGTAAGAGAT-TGACT-GATGG
1 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGA-TGGCT-G
* * ** *
398733 TGATTTGCCCTAAGCTCGAGGTAAAAGATCATATGGCTA
1 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
** * * ***
398772 CAATCTG-CCTCAAGCTCGGGGTAAGAGATTGG-TTTATGG
1 TGATCTGCCCT-AAGCTCGGGGTAAAAGATCGGATGGCT-G
* *
398811 TGATCTACCTTAAGCTCGGGGTAAAAGATCGGATGGCTG
1 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
* **
398850 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGAATTACTG
1 TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
398889 TGATCTGCCC
1 TGATCTGCCC
398899 CATGATCAAG
Statistics
Matches: 295, Mismatches: 91, Indels: 28
0.71 0.22 0.07
Matches are distributed among these distances:
38 16 0.05
39 265 0.90
40 14 0.05
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (39 bp):
TGATCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGCTG
Found at i:398892 original size:78 final size:78
Alignment explanation
Indices: 398657--398921 Score: 264
Period size: 78 Copynumber: 3.4 Consensus size: 78
398647 GATGGCTATA
* * * * *
398657 ATCTGCCCTAAGCTCGAGCTAAAATATCGGATGGTTATAATCTGCCCCAAGCTCGGGGTAAGAGA
1 ATCTACCCTAAGCTCGAGGTAAAAGATCGGATGGCTATAATCTGCCCTAAGCTCGGGGTAAGAGA
* *
398722 TTGACTGATGGTG
66 TTGAATTATGGTG
* * ** *
398735 ATTTGCCCTAAGCTCGAGGTAAAAGATCATATGGCTACAATCTG-CCTCAAGCTCGGGGTAAGAG
1 ATCTACCCTAAGCTCGAGGTAAAAGATCGGATGGCTATAATCTGCCCT-AAGCTCGGGGTAAGAG
**
398799 ATTGGTTTATGGTG
65 ATTGAATTATGGTG
* * * * *
398813 ATCTACCTTAAGCTCGGGGTAAAAGATCGGATGGCTGTGATCTGCCCTAAGCTCGGGGTAAAAGA
1 ATCTACCCTAAGCTCGAGGTAAAAGATCGGATGGCTATAATCTGCCCTAAGCTCGGGGTAAGAGA
*
398878 TCGAATTACT-GTG
66 TTGAATTA-TGGTG
* * * * * *
398891 ATCTGCCCCATGATCAAGGTAAGAGATCGGA
1 ATCTACCCTAAGCTCGAGGTAAAAGATCGGA
398922 ATCTTCAATC
Statistics
Matches: 152, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
77 2 0.01
78 146 0.96
79 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (78 bp):
ATCTACCCTAAGCTCGAGGTAAAAGATCGGATGGCTATAATCTGCCCTAAGCTCGGGGTAAGAGA
TTGAATTATGGTG
Found at i:398912 original size:39 final size:39
Alignment explanation
Indices: 398830--398919 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
398820 TTAAGCTCGG
* * * * **
398830 GGTAAAAGATCGGATGGCTGTGATCTGCCCTAAGCTCGG
1 GGTAAAAGATCGAATGACTGTGATCTGCCCCAAGATCAA
* *
398869 GGTAAAAGATCGAATTACTGTGATCTGCCCCATGATCAA
1 GGTAAAAGATCGAATGACTGTGATCTGCCCCAAGATCAA
*
398908 GGTAAGAGATCG
1 GGTAAAAGATCG
398920 GAATCTTCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (39 bp):
GGTAAAAGATCGAATGACTGTGATCTGCCCCAAGATCAA
Found at i:400310 original size:22 final size:21
Alignment explanation
Indices: 400284--400340 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
400274 TCACCTCGAC
400284 CTCTTATTTTTCTT-TTTTTCTT
1 CTCTT-TTTTT-TTCTTTTTCTT
400306 CTCTTTTCTTTTTCTTTTTCTT
1 CTCTTTT-TTTTTCTTTTTCTT
*
400328 TTCTTCTTTTTTT
1 CTCTT-TTTTTTT
400341 AATTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 4 0.13
22 25 0.81
23 2 0.06
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (21 bp):
CTCTTTTTTTTTCTTTTTCTT
Found at i:400314 original size:7 final size:6
Alignment explanation
Indices: 400290--400329 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
400280 CGACCTCTTA
*
400290 TTTTTC TTTTT- TTCTTC TCTTTTC TTTTTC TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTT
400330 CTTCTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.13
6 21 0.70
7 5 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:400315 original size:27 final size:25
Alignment explanation
Indices: 400285--400354 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 25
400275 CACCTCGACC
400285 TCTTATTTTTCTTTTTTTCTTCTCTTT
1 TCTTATTTTT-TTTTTTTCTTCT-TTT
400312 TCTT-TTTCTTTTTCTTTTCTTCTTTT
1 TCTTATTT-TTTTT-TTTTCTTCTTTT
400338 T-TTAATTTTTTTTTTTT
1 TCTT-ATTTTTTTTTTTT
400355 GAAATTTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
25 6 0.15
26 15 0.38
27 18 0.46
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.81
Consensus pattern (25 bp):
TCTTATTTTTTTTTTTTCTTCTTTT
Found at i:400321 original size:24 final size:25
Alignment explanation
Indices: 400290--400337 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
400280 CGACCTCTTA
400290 TTTTTCTTTTT-TTCTTC-TCTTTTC
1 TTTTTCTTTTTCTT-TTCTTCTTTTC
400314 TTTTTCTTTTTCTTTTCTTCTTTT
1 TTTTTCTTTTTCTTTTCTTCTTTT
400338 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (25 bp):
TTTTTCTTTTTCTTTTCTTCTTTTC
Found at i:400340 original size:11 final size:10
Alignment explanation
Indices: 400290--400351 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 10
400280 CGACCTCTTA
400290 TTTTTCTTTTT
1 TTTTTC-TTTT
400301 TTCTTCTCTTTT
1 TT-TT-TCTTTT
400313 CTTTTTCTTTT
1 -TTTTTCTTTT
400324 TCTTTTCTTCTT
1 T-TTTTCTT-TT
*
400336 TTTTTAATTTT
1 TTTTT-CTTTT
400347 TTTTT
1 TTTTT
400352 TTTGAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
10 1 0.02
11 26 0.59
12 13 0.30
13 4 0.09
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:400340 original size:17 final size:17
Alignment explanation
Indices: 400291--400340 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 17
400281 GACCTCTTAT
400291 TTTTCTTTTTTTCTTCTC
1 TTTTCTTTTTTT-TTCTC
400309 TTTTCTTTTTCTTTT-TC
1 TTTTCTTTTT-TTTTCTC
400326 TTTTCTTCTTTTTTT
1 TTTTCTT-TTTTTTT
400341 AATTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 13 0.43
18 15 0.50
19 2 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTTTTTTCTC
Found at i:401275 original size:18 final size:18
Alignment explanation
Indices: 401252--401286 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
401242 CATCTTGACT
401252 TTCTTTTT-TCTTCTTTTC
1 TTCTTTTTCTCTT-TTTTC
401270 TTCTTTTTCTCTTTTTT
1 TTCTTTTTCTCTTTTTT
401287 ATCTCTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTCTTTTTCTCTTTTTTC
Found at i:406024 original size:29 final size:29
Alignment explanation
Indices: 405991--406064 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 29
405981 ATTGGGTTTC
* *
405991 TTGGAAAATTTGGAGTTAGAATCGAACTT
1 TTGGAAAATTTGGAGTTAAAATCAAACTT
*
406020 TTGG-AAA-TTCGAGGTTAAAATCAAACTT
1 TTGGAAAATTTGGA-GTTAAAATCAAACTT
406048 TTGGAAAAGTTCTGGAG
1 TTGGAAAA-TT-TGGAG
406065 CAAAATGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
27 4 0.11
28 20 0.56
29 7 0.19
31 2 0.06
32 3 0.08
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.32
Consensus pattern (29 bp):
TTGGAAAATTTGGAGTTAAAATCAAACTT
Found at i:406171 original size:30 final size:30
Alignment explanation
Indices: 406082--406247 Score: 160
Period size: 29 Copynumber: 5.6 Consensus size: 30
406072 TGATTTTTGG
**
406082 AAGTTTAAGGGCAAAAATGTAATTTTTAG--
1 AAGTTTAAGGGTTAAAATGTAA-TTTTAGAA
* *
406111 AAGTTTAAGGGTCAAAATGTAATTTTTGGAA
1 AAGTTTAAGGGTTAAAATGTAA-TTTTAGAA
* * *
406142 AATTTTAAGGGTTAAAATGTAAGTTTGGAA
1 AAGTTTAAGGGTTAAAATGTAATTTTAGAA
* **
406172 AAGTTT-GGGGTTAAAATACAATTTTAGAA
1 AAGTTTAAGGGTTAAAATGTAATTTTAGAA
* *
406201 AAGTTTAAGGG-TCAAATGAAATTTTAGAA
1 AAGTTTAAGGGTTAAAATGTAATTTTAGAA
* *
406230 AAGTTTAAGTGTCAAAAT
1 AAGTTTAAGGGTTAAAAT
406248 ATTATTTCTA
Statistics
Matches: 114, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
29 75 0.66
30 19 0.17
31 20 0.18
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (30 bp):
AAGTTTAAGGGTTAAAATGTAATTTTAGAA
Found at i:408589 original size:23 final size:24
Alignment explanation
Indices: 408553--408603 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
408543 GAGGATGAGA
408553 ATGAGAATAGAAATAAAATTGA-T
1 ATGAGAATAGAAATAAAATTGATT
* *
408576 ATGAGAA-AGAAAATGAGATTGATT
1 ATGAGAATAG-AAATAAAATTGATT
408600 ATGA
1 ATGA
408604 AAATTTGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 17 0.71
24 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (24 bp):
ATGAGAATAGAAATAAAATTGATT
Found at i:410874 original size:3 final size:3
Alignment explanation
Indices: 410866--410892 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
410856 GGAGTGTAAA
410866 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
410893 TAAGAAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:412468 original size:22 final size:22
Alignment explanation
Indices: 412427--412469 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
412417 ACATCTGTTT
*
412427 ACATAACACTTGAAATTATATG
1 ACATAACACATGAAATTATATG
412449 ACATAACACAT-AAATATATAT
1 ACATAACACATGAAAT-TATAT
412470 TTAATGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (22 bp):
ACATAACACATGAAATTATATG
Done.