Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1899
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: 50959
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:10147 original size:89 final size:87
Alignment explanation
Indices: 10018--10179 Score: 209
Period size: 89 Copynumber: 1.8 Consensus size: 87
10008 ATTCAACGGA
* * * *
10018 GAGCAGATCGAAGACATAGTAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATG
1 GAGCAGATCGAAGACATAGCAGATCTAACATTCAGATGTTTACAC-T-GAAGCAGATCCAAGATG
10083 ATTTGGCATCCTTGCATTTACAAG
64 ATTTGGCATCCTTGCATTTACAAG
* ** * *
10107 GAGCAGATCGAAGACATAGCAGATTTGGCATTCACG-TGTTTACGCTGAAGCAGATCTAAGATGA
1 GAGCAGATCGAAGACATAGCAGATCTAACATTCA-GATGTTTACACTGAAGCAGATCCAAGATGA
10171 TTTGGCATC
65 TTTGGCATC
10180 TCTGTACTGT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 25 0.40
88 1 0.02
89 36 0.57
90 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (87 bp):
GAGCAGATCGAAGACATAGCAGATCTAACATTCAGATGTTTACACTGAAGCAGATCCAAGATGAT
TTGGCATCCTTGCATTTACAAG
Found at i:10255 original size:220 final size:220
Alignment explanation
Indices: 9682--10271 Score: 948
Period size: 219 Copynumber: 2.7 Consensus size: 220
9672 CAGGCTAAAG
* * * **
9682 CATAGCAGATTTGACCTTCAGGTGTTTACGCTGAAGCGGATCCAAGATGATTTAACATCTCTGTA
1 CATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
* * *
9747 TTGTCAGAGAACAAATCGAAGAAAAAGATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAG
66 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCAACGGAGAGCAGATCGAAG
* **
9812 ACATAGCAGATCTAACCTTTGGATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
131 ACATAGTAGATCTAACCTTCAGATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
* *
9877 GCGTTGATAAGGAGCAGATCGAAGA
196 GCATTGACAAGGAGCAGATCGAAGA
* * *
9902 CATAGCAGATTTGACCTTCACATGTTTA-GCTGAAGCAGATCTAAGATGATTTGGTATCTCTATA
1 CATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
* *
9966 CTGTTAGAGAACAAATCGAAGAAATAGATTTGGCATATCCATATTCAACGGAGAGCAGATCGAAG
66 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCAACGGAGAGCAGATCGAAG
*
10031 ACATAGTAGATCTAACCTTCAGATGTTTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
131 ACATAGTAGATCTAACCTTCAGATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
*
10096 GCATTTACAAGGAGCAGATCGAAGA
196 GCATTGACAAGGAGCAGATCGAAGA
* *
10121 CATAGCAGATTTGGCATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
1 CATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
*
10186 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATTTTCAACGGAGAGCAGATCGAAG
66 CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCAACGGAGAGCAGATCGAAG
* *
10251 ACATAATAGATCTGACCTTCA
131 ACATAGTAGATCTAACCTTCA
10272 TTGAAGCAGA
Statistics
Matches: 339, Mismatches: 30, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
219 198 0.58
220 141 0.42
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (220 bp):
CATAGCAGATTTGACCTTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
CTGTCAGAGAACAAATCGAAGAAATAGATTTGGCATCTCCATATTCAACGGAGAGCAGATCGAAG
ACATAGTAGATCTAACCTTCAGATGTCTTCACATCGAAGTAGATCCAAGATGATTTGGCATCCTT
GCATTGACAAGGAGCAGATCGAAGA
Found at i:10322 original size:78 final size:78
Alignment explanation
Indices: 10233--10583 Score: 562
Period size: 78 Copynumber: 4.5 Consensus size: 78
10223 TCCATTTTCA
* *
10233 ACGGAGAGCAGATCGAAGACATAATAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
1 ACGGGGAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
10298 ATCTCTGTATTAG
66 ATCTCTGTATTAG
*
10311 ACGGGGAGCAGATCGAAGACACAACAGAT-TGGACCTTCATTGAAGCAGATCCAAGATGATTTGG
1 ACGGGGAGCAGATCGAAGACATAACAGATCT-GACCTTCATTGAAGCAGATCCAAGATGATTTGG
** *
10375 CATCTCCATATTCG
65 CATCTCTGTATTAG
* * *
10389 ACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTTATTGAAGCAGATCCAAGATGATTTGGC
1 ACGGGGAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
10454 ATCTCTGTATTAG
66 ATCTCTGTATTAG
* *
10467 ACGGGGAGCAGATCGAAGACACAACAGAT-TGGACCTTTATTGAAGCAGATCCAAGATGATTTGG
1 ACGGGGAGCAGATCGAAGACATAACAGATCT-GACCTTCATTGAAGCAGATCCAAGATGATTTGG
10531 CATCTCTGTATTAG
65 CATCTCTGTATTAG
*
10545 ACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCA
1 ACGGGGAGCAGATCGAAGACATAACAGATCTGACCTTCA
10584 CGTGTTTACG
Statistics
Matches: 250, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
77 2 0.01
78 246 0.98
79 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (78 bp):
ACGGGGAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
ATCTCTGTATTAG
Found at i:10423 original size:156 final size:156
Alignment explanation
Indices: 10212--10583 Score: 654
Period size: 156 Copynumber: 2.4 Consensus size: 156
10202 CGAAGAAATA
* * **
10212 GATTTGGCATCTCCATTTTCAACGGAGAGCAGATCGAAGACATAATAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
10277 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
66 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
10342 GACCTTCATTGAAGCAGATCCAAGAT
131 GACCTTCATTGAAGCAGATCCAAGAT
*
10368 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTTATTGAA
1 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
10433 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
66 GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
*
10498 GACCTTTATTGAAGCAGATCCAAGAT
131 GACCTTCATTGAAGCAGATCCAAGAT
** * *
10524 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCA
1 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCA
10584 CGTGTTTACG
Statistics
Matches: 205, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 205 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (156 bp):
GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTG
GACCTTCATTGAAGCAGATCCAAGAT
Found at i:10629 original size:443 final size:442
Alignment explanation
Indices: 10066--10930 Score: 1351
Period size: 443 Copynumber: 2.0 Consensus size: 442
10056 TTTTCACATC
* *
10066 GAAGTAGATCCAAGATGATTTGGCATCCTTGCATTTACAAGGAGCAGATCGAAGACATAGCAGAT
1 GAAGCAGATCCAAGATGATTTGGCATCCTTGCATTGACAAGGAGCAGATCGAAGACATAGCAGAT
* *
10131 TTGGCATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGA
66 CTGACATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGA
* * ** *
10196 ACAAATCGAAGAAATAGATTTGGCATCTCCATTTTCAACGGAGAGCAGATCGAAGACATAATAGA
131 ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCAACAAAGAGCAGATCGAAGACATAACAGA
* *
10261 TCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCG
196 TCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGGAAGCAGATCG
*
10326 AAGACACAACAGAT-TGGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCCATATTCGA
261 AAGACACAACAGATCT-GACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCCATATTAGA
* * * * * *
10390 C-GGAGAGCAGATCGAAGACATAGCAGATCT-GACCTTTATTGAAGCAGATCCAAGATGATTTGG
325 CAGG-GAGCAGATCAAAGACATAACACAT-TGGACCTTCATTGAAACAGATCCAAGATAATTTGG
10453 CATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTGGACCTTTATT
388 CATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTGGACCTTTATT
* **
10508 GAAGCAGATCCAAGATGATTTGGCAT-CTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAG
1 GAAGCAGATCCAAGATGATTTGGCATCCT-TGCATT-GACAAGGAGCAGATCGAAGACATAGCAG
* * * *
10572 ATCTGACCTTCACGTGTTTACGTTGAAGTAGATCTAAGATGATTTGGCATTTCTGTACTGTCAGA
64 ATCTGACATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGA
* *
10637 GAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCGACAAAGAGCAGATCGAAGACATAGCA
129 GAACAAATCGAAGAAACAGATTTGGCATCTCCATATTCAACAAAGAGCAGATCGAAGACATAACA
*
10702 GATCTGACCTTCATTGAAGCAGATCCAAGTTGATTTGGCATCTCTATATTAGACGGGAAGCAGAT
194 GATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGGAAGCAGAT
* * **
10767 TGAAGACACAACATATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAG
259 CGAAGACACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCCATATTAG
*
10832 ACAGGGAGTAGATCAAAGACATAACACATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGC
324 ACAGGGAGCAGATCAAAGACATAACACATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGC
*
10897 ATCTCTGTATTAGATGGGGAGCAGATCGAAGACA
389 ATCTCTGTATTAGACGGGGAGCAGATCGAAGACA
10931 TAGTAGATCT
Statistics
Matches: 384, Mismatches: 34, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
441 2 0.01
442 31 0.08
443 348 0.91
444 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (442 bp):
GAAGCAGATCCAAGATGATTTGGCATCCTTGCATTGACAAGGAGCAGATCGAAGACATAGCAGAT
CTGACATTCACGTGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTACTGTCAGAGA
ACAAATCGAAGAAACAGATTTGGCATCTCCATATTCAACAAAGAGCAGATCGAAGACATAACAGA
TCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGGAAGCAGATCG
AAGACACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCCATATTAGAC
AGGGAGCAGATCAAAGACATAACACATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCAT
CTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTGGACCTTTATT
Found at i:10717 original size:365 final size:368
Alignment explanation
Indices: 10290--11065 Score: 1085
Period size: 365 Copynumber: 2.1 Consensus size: 368
10280 GATCCAAGAT
** ***
10290 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAACAGATTGGACCTTCATTGAA
1 GATTTGGCATCTCCATATTAGACAAAGAGCAGATCGAAGACACAACAGATTGGACCTTCATTGAA
* * *
10355 GCAGATCCAAGATGATTTGGCATCTCCATATTCGAC-GGAGAGCAGATCGAAGACATAGCAGATC
66 GCAGATCCAAGATGATTTGGCATCTCCATATTAGACGGGA-AGCAGATCGAAGACACAACAGATC
* * *
10419 TGACCTTTATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAA
130 TGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAA
* * * *
10484 GACACAACAGATTGGACCTTTATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGG
195 GACACAACACATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGACGG
* * * * *
10549 GGAGCAGATCGAAGACATAGCAGATCTGACCTTCACGTGTTTACGTTGAAGTAGATCTAAGAT-G
260 GGAGCAGATCGAAGACATAGCAGATCTGACCTTCACATGTTTACATCGAAGCAGATCCAAGATAG
* *
10613 ATTTGGCATTTCTGTACT-GTCAGAGAACAAATCGAAGA-AACA
325 ATTTGGCATCTCTGTACTAGACAGAGAACAAATCGAAGATAACA
* * *
10655 GATTTGGCATCTCCATATTCGACAAAGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGA
1 GATTTGGCATCTCCATATTAGACAAAGAGCAGATCGAAGACACAACAGAT-TGGACCTTCATTGA
* * * *
10719 AGCAGATCCAAGTTGATTTGGCATCTCTATATTAGACGGGAAGCAGATTGAAGACACAACATATC
65 AGCAGATCCAAGATGATTTGGCATCTCCATATTAGACGGGAAGCAGATCGAAGACACAACAGATC
*
10784 TGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGGGAGTAGATCAAA
130 TGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAA
* *
10849 GACATAACACATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGATGG
195 GACACAACACATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGACGG
* *
10914 GGAGCAGATCGAAGACATAGTAGATCTGACCTTCATATGTTTACATCGAAGCAGATCCAAGATGA
260 GGAGCAGATCGAAGACATAGCAGATCTGACCTTCACATGTTTACATCGAAGCAGATCCAAGAT--
* * * *
10979 CAGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGGAGATAACA
323 -AGATTTGGCATCTCTGTACTAGACAGAGAACAAATCGAAGATAACA
** * * *
11026 GATTTGGCATCTCTGTATTAGACGAGGAGCAGATTGAAGA
1 GATTTGGCATCTCCATATTAGACAAAGAGCAGATCGAAGA
11066 AGAAGATTTG
Statistics
Matches: 359, Mismatches: 44, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
365 284 0.79
366 4 0.01
369 17 0.05
370 16 0.04
371 38 0.11
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (368 bp):
GATTTGGCATCTCCATATTAGACAAAGAGCAGATCGAAGACACAACAGATTGGACCTTCATTGAA
GCAGATCCAAGATGATTTGGCATCTCCATATTAGACGGGAAGCAGATCGAAGACACAACAGATCT
GACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAAG
ACACAACACATTGGACCTTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGG
GAGCAGATCGAAGACATAGCAGATCTGACCTTCACATGTTTACATCGAAGCAGATCCAAGATAGA
TTTGGCATCTCTGTACTAGACAGAGAACAAATCGAAGATAACA
Found at i:10785 original size:78 final size:78
Alignment explanation
Indices: 10655--10949 Score: 362
Period size: 78 Copynumber: 3.8 Consensus size: 78
10645 CGAAGAAACA
* * ** *
10655 GATTTGGCATCTCCATATTCGAC-AAAGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGA
1 GATTTGGCATCTCTATATTAGACGGGA-AGCAGATCGAAGACATAACAGATCTGACCTTCATTGA
*
10719 AGCAGATCCAAGTT
65 AGCAGATCCAAGAT
* * *
10733 GATTTGGCATCTCTATATTAGACGGGAAGCAGATTGAAGACACAACATATCTGACCTTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGGAAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAA
10798 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * * *
10811 GATTTGGCATCTCTGTATTAGACAGGG-AGTAGATCAAAGACATAACACAT-TGGACCTTCATTG
1 GATTTGGCATCTCTATATTAGAC-GGGAAGCAGATCGAAGACATAACAGATCT-GACCTTCATTG
*
10874 AAACAGATCCAAGAT
64 AAGCAGATCCAAGAT
* * * * **
10889 AATTTGGCATCTCTGTATTAGATGGGGAGCAGATCGAAGACATAGTAGATCTGACCTTCAT
1 GATTTGGCATCTCTATATTAGACGGGAAGCAGATCGAAGACATAACAGATCTGACCTTCAT
10950 ATGTTTACAT
Statistics
Matches: 189, Mismatches: 23, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
77 4 0.02
78 180 0.95
79 5 0.03
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (78 bp):
GATTTGGCATCTCTATATTAGACGGGAAGCAGATCGAAGACATAACAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:11042 original size:45 final size:45
Alignment explanation
Indices: 10963--11156 Score: 248
Period size: 45 Copynumber: 4.3 Consensus size: 45
10953 TTTACATCGA
* * *
10963 AGCAGATCCAAGATGACAGATTTGGCATCTCTGTATTAGACAGGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* * *
11008 AGCAAATCGGAGATAACAGATTTGGCATCTCTGTATTAGACGAGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
* * * *
11053 AGCAGATTGAAGA-AGA-AGATTTGACGTCTCTGTATTATACGGGG
1 AGCAGATCGAAGATA-ACAGATTTGGCATCTCTGTATTAGACGGGG
**
11097 AGCAGATCGAAGATAACAGATTTGGTGTCTCTGTATTAGACGGGG
1 AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
*
11142 AGCAGATCAAAGATA
1 AGCAGATCGAAGATA
11157 GCATATATCG
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
44 38 0.30
45 90 0.70
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (45 bp):
AGCAGATCGAAGATAACAGATTTGGCATCTCTGTATTAGACGGGG
Found at i:11131 original size:89 final size:89
Alignment explanation
Indices: 10980--11148 Score: 257
Period size: 89 Copynumber: 1.9 Consensus size: 89
10970 CCAAGATGAC
* *
10980 AGATTTGGCATCTCTGTATTAGACAGGGAGCAAATCGGAGATAACAGATTTGGCATCTCTGTATT
1 AGATTTGACATCTCTGTATTAGACAGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATT
11045 AGACGAGGAGCAGATTGAAGAAGA
66 AGACGAGGAGCAGATTGAAGAAGA
* * * * **
11069 AGATTTGACGTCTCTGTATTATACGGGGAGCAGATCGAAGATAACAGATTTGGTGTCTCTGTATT
1 AGATTTGACATCTCTGTATTAGACAGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATT
*
11134 AGACGGGGAGCAGAT
66 AGACGAGGAGCAGAT
11149 CAAAGATAGC
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 71 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (89 bp):
AGATTTGACATCTCTGTATTAGACAGGGAGCAAATCGAAGATAACAGATTTGGCATCTCTGTATT
AGACGAGGAGCAGATTGAAGAAGA
Found at i:11381 original size:21 final size:20
Alignment explanation
Indices: 11355--11393 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
11345 CGAACCCAGA
*
11355 AATAAATCCAAAAAGAAAAAT
1 AATAAACCCAAAAA-AAAAAT
11376 AATAAACCCAAAAAAAAA
1 AATAAACCCAAAAAAAAA
11394 CGAAGTCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.74, C:0.13, G:0.03, T:0.10
Consensus pattern (20 bp):
AATAAACCCAAAAAAAAAAT
Found at i:11544 original size:36 final size:35
Alignment explanation
Indices: 11504--11581 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 35
11494 ATGGAAATAT
11504 AATCTTCA-ATGATATGCAATCTTAGATATGATATGA
1 AATCTTCATATGATA--CAATCTTAGATATGATATGA
* *
11540 AATCTTTGATATGATACAATCTTAGATATGATATGC
1 AATC-TTCATATGATACAATCTTAGATATGATATGA
11576 AATCTT
1 AATCTT
11582 AGAAGATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
35 2 0.05
36 27 0.71
37 3 0.08
38 6 0.16
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (35 bp):
AATCTTCATATGATACAATCTTAGATATGATATGA
Found at i:11574 original size:22 final size:20
Alignment explanation
Indices: 11511--11593 Score: 62
Period size: 19 Copynumber: 4.5 Consensus size: 20
11501 TATAATCTTC
11511 AATGATATG--CAATCTTAG
1 AATGATATGATCAATCTTAG
11529 ATATGATATGA--AATCTT--
1 A-ATGATATGATCAATCTTAG
11546 --TGATATGATACAATCTTAG
1 AATGATATGAT-CAATCTTAG
11565 ATATGATATG--CAATCTTAG
1 A-ATGATATGATCAATCTTAG
11584 AA-GATATGAT
1 AATGATATGAT
11594 TTTGTAATCT
Statistics
Matches: 53, Mismatches: 0, Indels: 23
0.70 0.00 0.30
Matches are distributed among these distances:
14 8 0.15
17 12 0.23
18 2 0.04
19 24 0.45
22 7 0.13
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (20 bp):
AATGATATGATCAATCTTAG
Found at i:11591 original size:17 final size:19
Alignment explanation
Indices: 11512--11584 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
11502 ATAATCTTCA
11512 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
* *
11531 ATGATATGAAATCTTTGAT
1 ATGATATGCAATCTTAGAT
11550 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
11567 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
11585 AGATATGATT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.31
19 33 0.69
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:13692 original size:118 final size:118
Alignment explanation
Indices: 13536--13773 Score: 467
Period size: 118 Copynumber: 2.0 Consensus size: 118
13526 TTTGGGCTAG
*
13536 TGTAAACATGGTGGCTTTTGTGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
1 TGTAAACATGGTGGCTTTTATGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
13601 GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
66 GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
13654 TGTAAACATGGTGGCTTTTATGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
1 TGTAAACATGGTGGCTTTTATGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
13719 GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
66 GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
13772 TG
1 TG
13774 CAAAGGATTT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 119 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (118 bp):
TGTAAACATGGTGGCTTTTATGACTTGAAAACTAAAAAATGTAGTTGTTTACCGGTGTTAGAGCA
GCTACCATCTAACATTGCAACAAAGGTGGATGCTATGCAGCGATGACGGAAAC
Found at i:14680 original size:20 final size:20
Alignment explanation
Indices: 14655--14700 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
14645 ATTTGCTTAT
14655 TATTTAAGTAAATATTAATG
1 TATTTAAGTAAATATTAATG
14675 TATTTAAGTAAATATTAATG
1 TATTTAAGTAAATATTAATG
14695 TATTTA
1 TATTTA
14701 TTATTATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (20 bp):
TATTTAAGTAAATATTAATG
Found at i:14858 original size:15 final size:16
Alignment explanation
Indices: 14817--14851 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
14807 GTATATTTAC
*
14817 TTATTATATAAGTATA
1 TTATTAAATAAGTATA
14833 TTATTAAATAA-TATA
1 TTATTAAATAAGTATA
14848 TTAT
1 TTAT
14852 ATAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTATTAAATAAGTATA
Found at i:16402 original size:18 final size:19
Alignment explanation
Indices: 16360--16427 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 19
16350 AAAGATCGAC
16360 TGTTACTGAATAATTTAAT
1 TGTTACTGAATAATTTAAT
* *
16379 TGTTACTGTAT-ATTTGAT
1 TGTTACTGAATAATTTAAT
* *
16397 TTTTACTGAATAA-TTAAC
1 TGTTACTGAATAATTTAAT
16415 TGTTACTGAATAA
1 TGTTACTGAATAA
16428 CCGATCAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 30 0.73
19 11 0.27
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (19 bp):
TGTTACTGAATAATTTAAT
Found at i:21250 original size:458 final size:458
Alignment explanation
Indices: 20460--21305 Score: 1264
Period size: 458 Copynumber: 1.8 Consensus size: 458
20450 TGCTAAAATG
** * * * * *
20460 TTACCATTCTGACCTATTTCATATTGTGCCCATTAAAGCAGTCGAGGTAAGACTTGATTTGTCCT
1 TTACCATTCTGACCTATCGCATATTGTGCCCATCAAAGAAATCGAGGTAAGACCTAATTTGTCCT
* * * *
20525 TTGAAGAAGAACACATTAGAATTATTTAAAAAGATGTGAAAGTTTTTATAAGGAAACAAATTCCA
66 TCGAAGAAGAACACATTAGAATTATTTAAAAAAATGTGAAAGTTCTGATAAGGAAACAAATTCCA
* * * * *
20590 TTAGTAAAAGTGTTGTGGCAAAACCATGGTGTTGAGGACGTTACAAGGGAAATGGAAGATTCACT
131 TTAGTAAAAGTGTTATGGCAAAACCATGGTGTTGAGGAAGCTACAAGGGAAATAGAAGATCCACT
** * * * *
20655 CCGTCAACAATATCCCCACTTATTCGAAATAGGTAAAATTTCGAGGATAAAATTTCTTTAAGAAG
196 CCACCAAAAATATCCCCACTTATTCGAAAAAGGTAAAATTTCGAGGAAAAAAATTCTTTAAGAAG
* **
20720 GGGAGAATTGTAACATCCCAAACAATAGGAGGTTAGATTCTTCGAAATTATCATGAATTGAATCC
261 GGGAGAATTCTAACATCCCAAACAATAGGAGGTTAGATTCTTAAAAATTATCATGAATTGAATCC
* *
20785 TAGTCTAGTGGTTAAGAGCCTGGTAGAAAGTATAGAGAACCAAAGTTCAAGCCTCTTAAATTGAA
326 TAGTCTAGTGGTTAAGAGCCTGGTAGAAAGTATAGAGAACCAAAGTTCAAGACTCCTAAATTGAA
20850 TTCAACTCTCCCCAATTCAACTAAAATTCTCATTTGTTATTTTAGCAAATAAAAACCATACTAAG
391 TTCAACTCTCCCCAATTCAACTAAAATTCTCATTTGTTATTTTAGCAAATAAAAACCATACTAAG
20915 ACA
456 ACA
* *
20918 TTACCGTTCTGACCTATCGCATATTGTGCCCATCAAAGAAATTGAGGTAAGACCTAATTTGTCCT
1 TTACCATTCTGACCTATCGCATATTGTGCCCATCAAAGAAATCGAGGTAAGACCTAATTTGTCCT
* * *
20983 TCGAAGAAGAACCCATTAGAATTCTTTAAAAAAATGTGAAAGTTCTGATAAGGAAACAAATTCTA
66 TCGAAGAAGAACACATTAGAATTATTTAAAAAAATGTGAAAGTTCTGATAAGGAAACAAATTCCA
* ** *
21048 TTAGT-AAAGTGTTATGGCGAAACCATGGTGTTGAGGAAGCTACGTGGGAAATAGAAGATCCATT
131 TTAGTAAAAGTGTTATGGCAAAACCATGGTGTTGAGGAAGCTACAAGGGAAATAGAAGATCCACT
*
21112 CCACCAAAAATATCCCCACTTATTCGAAAAAGGTAAAATTTCGA-GAAAAAGAATTCTTTAAGGA
196 CCACCAAAAATATCCCCACTTATTCGAAAAAGGTAAAATTTCGAGGAAAAA-AATTCTTTAAGAA
* * * * *
21176 GGGGGGAGTTCTAACATCCTACACAATAGGAGGTTAGATTCTTAAAAAATTATCATGAATTTAAT
260 GGGGAGAATTCTAACATCCCAAACAATAGGAGGTTAGATTCTT-AAAAATTATCATGAATTGAAT
* *
21241 CCTAGTCTAGTGGTTAAGAGCTTGGTAGAAAGTATAGTGAACCAAAGTTCAAGACTCCTAAATTG
324 CCTAGTCTAGTGGTTAAGAGCCTGGTAGAAAGTATAGAGAACCAAAGTTCAAGACTCCTAAATTG
21306 CACTTTTTCT
Statistics
Matches: 342, Mismatches: 44, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
456 5 0.01
457 139 0.41
458 198 0.58
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (458 bp):
TTACCATTCTGACCTATCGCATATTGTGCCCATCAAAGAAATCGAGGTAAGACCTAATTTGTCCT
TCGAAGAAGAACACATTAGAATTATTTAAAAAAATGTGAAAGTTCTGATAAGGAAACAAATTCCA
TTAGTAAAAGTGTTATGGCAAAACCATGGTGTTGAGGAAGCTACAAGGGAAATAGAAGATCCACT
CCACCAAAAATATCCCCACTTATTCGAAAAAGGTAAAATTTCGAGGAAAAAAATTCTTTAAGAAG
GGGAGAATTCTAACATCCCAAACAATAGGAGGTTAGATTCTTAAAAATTATCATGAATTGAATCC
TAGTCTAGTGGTTAAGAGCCTGGTAGAAAGTATAGAGAACCAAAGTTCAAGACTCCTAAATTGAA
TTCAACTCTCCCCAATTCAACTAAAATTCTCATTTGTTATTTTAGCAAATAAAAACCATACTAAG
ACA
Found at i:25658 original size:16 final size:17
Alignment explanation
Indices: 25627--25659 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
25617 TTCATAAGTA
25627 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
25644 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
25660 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:26003 original size:46 final size:45
Alignment explanation
Indices: 25938--26397 Score: 497
Period size: 46 Copynumber: 9.9 Consensus size: 45
25928 TTATCTTTGA
* * * * * *
25938 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTAT
* *** *
25984 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TAT
* ** * ** * **
26030 TACATAGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTAT
* *
26075 CATGTTGCCATGGTATCTTTCAATCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTAT
* *
26121 CCTGTTTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TAT
* *
26167 CATGTTGCCATGGTATCTTTCAACCATAGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTAT
26213 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TAT
* *
26259 CATGTTGCCATGGTGTCTTTCAACCATTGTCTTATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAA-C-----C--ATGGTCTTACACA-TTTCTAT
* *
26313 CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TAT
*
26359 CATGTTGCCATGGTATTTTTCAACCATGGTCTTACACAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
26398 ATCATTTCAG
Statistics
Matches: 357, Mismatches: 42, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
45 46 0.13
46 263 0.74
47 4 0.01
48 1 0.00
52 1 0.00
53 1 0.00
54 38 0.11
55 3 0.01
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (45 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTAT
Found at i:26202 original size:92 final size:92
Alignment explanation
Indices: 25938--26397 Score: 564
Period size: 92 Copynumber: 4.9 Consensus size: 92
25928 TTATCTTTGA
* * * * * * *
25938 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGGTATCT
*** * *
26002 TTCAACCATGGTCTTGTTCATTTCATGT
65 TTCAACCATGGTCTTACACATTTTATAT
* ** * ** ***
26030 TACATAGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCCCGTCATGTTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
*
26094 TCAATCATGGTCTTACACATTTTATAT
66 TCAACCATGGTCTTACACATTTTATAT
* *
26121 CCTGTTTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
*
26186 TCAACCATAGTCTTACACATTTTATAT
66 TCAACCATGGTCTTACACATTTTATAT
*
26213 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
26278 TCAACCATTGTCTTATGGTCTTACACATTTTATAT
66 TCAA-C-----C--ATGGTCTTACACATTTTATAT
* * *
26313 CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATTTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
26378 TCAACCATGGTCTTACACAT
66 TCAACCATGGTCTTACACAT
26398 ATCATTTCAG
Statistics
Matches: 320, Mismatches: 38, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
90 3 0.01
91 71 0.22
92 157 0.49
93 1 0.00
94 1 0.00
98 1 0.00
99 1 0.00
100 85 0.27
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (92 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTTATAT
Found at i:26320 original size:54 final size:53
Alignment explanation
Indices: 26238--26392 Score: 207
Period size: 54 Copynumber: 3.0 Consensus size: 53
26228 TCTTTCAACC
26238 ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATTGTCTT
1 ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCA-TGTCTT
* *
26292 ATGGTCTTACACATTTTATATCATGTTGCCATGATGTCTTTCAA-C----C--
1 ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGTCTT
* *
26338 ATGGTCTTACACATTTCATATCATGTTGCCATGGTATTTTTCAACCATGGTCTT
1 ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCAT-GTCTT
26392 A
1 A
26393 CACATATCAT
Statistics
Matches: 87, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
46 40 0.46
47 1 0.01
48 1 0.01
52 1 0.01
53 1 0.01
54 43 0.49
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (53 bp):
ATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTTTCAACCATGTCTT
Found at i:26357 original size:192 final size:183
Alignment explanation
Indices: 25938--26402 Score: 574
Period size: 183 Copynumber: 2.5 Consensus size: 183
25928 TTATCTTTGA
* * * * *
25938 CATGATGCCAT-AGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATC
1 CATGTTGCCATGA-TGTCTTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGGTATC
*** * * **
26001 TTTCAACCATGGTCTTGTTCATTTCATGTTACATAGCCATGGTATCTTTCAACCATGGTCTTATT
64 TTTCAACCATGGTCTTACACATTTCATATCACATAGCCATGGTATCTTTCAACCATGGTCTTACA
* *
26066 CATTCCCGTCATGTTGCCATGGTATCTTTCAATCATGGTCTTACACATTTTATAT
129 CATTCACATCATGTTGCCATGGTATCTTTCAATCATGGTCTTACACATTTTATAT
* * * *
26121 CCTGTTTCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
1 CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
* * ** *
26186 TCAACCATAGTCTTACACATTTTATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
66 TCAACCATGGTCTTACACATTTCATATCACATAGCCATGGTATCTTTCAACCATGGTCTTACACA
* *
26251 TTTCATATCATGTTGCCATGGTGTCTTTCAACCATTGTCTTATGGTCTTACACATTTTATAT
131 -TTCACATCATGTTGCCATGGTATCTTTC-A--A---TC--ATGGTCTTACACATTTTATAT
*
26313 CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATTTT
1 CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
*
26378 TCAACCATGGTCTTACACATATCAT
66 TCAACCATGGTCTTACACATTTCAT
26403 TTCAGAAAGC
Statistics
Matches: 238, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
182 4 0.02
183 103 0.43
184 24 0.10
185 1 0.00
187 1 0.00
190 2 0.01
192 103 0.43
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (183 bp):
CATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTCATATCACATAGCCATGGTATCTTTCAACCATGGTCTTACACA
TTCACATCATGTTGCCATGGTATCTTTCAATCATGGTCTTACACATTTTATAT
Found at i:26368 original size:100 final size:100
Alignment explanation
Indices: 26195--26392 Score: 351
Period size: 100 Copynumber: 2.0 Consensus size: 100
26185 TTCAACCATA
*
26195 GTCTTACACATTTTATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATC
1 GTCTTACACATTTTATATCATGTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATC
* *
26260 ATGTTGCCATGGTGTCTTTCAACCATTGTCTTATG
66 ATGTTGCCATGGTATCTTTCAACCATGGTCTTATG
*
26295 GTCTTACACATTTTATATCATGTTGCCATGATGTCTTTCAACCATGGTCTTACACATTTCATATC
1 GTCTTACACATTTTATATCATGTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATC
*
26360 ATGTTGCCATGGTATTTTTCAACCATGGTCTTA
66 ATGTTGCCATGGTATCTTTCAACCATGGTCTTA
26393 CACATATCAT
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.42
Consensus pattern (100 bp):
GTCTTACACATTTTATATCATGTTGCCATGATATCTTTCAACCATGGTCTTACACATTTCATATC
ATGTTGCCATGGTATCTTTCAACCATGGTCTTATG
Found at i:26368 original size:146 final size:138
Alignment explanation
Indices: 25938--26402 Score: 547
Period size: 137 Copynumber: 3.3 Consensus size: 138
25928 TTATCTTTGA
* * * * * * *
25938 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCAGGTTGCCATGGTATCT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCATGTTGCCATGGTATCT
*** * * ** * **
26002 TTCAACCATGGTCTTGTTCATTTCATGTTACATAGCCATGGTATCTTTCAACCATGGTCTTATTC
65 TTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
***
26067 A-TTCCCGT
130 ATTTCATAT
* * * *
26075 CATGTTGCCATGGTATCTTTCAATCATGGTCTTACACATTTTATATCCTGTTTCCATGGTATCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
*
26140 TCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATAGTCTTACACA
66 TCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
*
26205 TTTTATAT
131 TTTCATAT
*
26213 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTGTCTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
* * *
26278 TCAACCATTGTCTTATGGTCTTACACATTTTATATCATGTTGCCATGATGTCTTTCAACCATGGT
66 TCAA-C-----C--ATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGT
26343 CTTACACATTTCATAT
123 CTTACACATTTCATAT
* *
26359 CATGTTGCCATGGTATTTTTCAACCATGGTCTTACACATATCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
26403 TTCAGAAAGC
Statistics
Matches: 280, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
136 3 0.01
137 104 0.37
138 67 0.24
139 1 0.00
144 1 0.00
146 104 0.37
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (138 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTT
TCAACCATGGTCTTACACATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
TTTCATAT
Found at i:29177 original size:39 final size:39
Alignment explanation
Indices: 29114--29229 Score: 135
Period size: 39 Copynumber: 3.0 Consensus size: 39
29104 TGGGGTTTCA
* * * *
29114 GTTTAGCTCTGATGAGCTTCAGTTAACCTTCGGGCTTCC
1 GTTTAGCACTTATGTGCTTAAGTTAACCTTCGGGCTTCC
* * *
29153 GTTTAGCACTTGTGTGCTTTAGTTAGCCTTCGGGCTTCC
1 GTTTAGCACTTATGTGCTTAAGTTAACCTTCGGGCTTCC
* *
29192 GTTTAGTACTTATGTGCTTAAGCTAGA-CTTCGGGCTTC
1 GTTTAGCACTTATGTGCTTAAGTTA-ACCTTCGGGCTTC
29230 AAATCATGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (39 bp):
GTTTAGCACTTATGTGCTTAAGTTAACCTTCGGGCTTCC
Found at i:29935 original size:13 final size:13
Alignment explanation
Indices: 29912--29945 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
29902 GTTTTTTTTT
*
29912 AAATAATAATAATA
1 AAATAA-AATAAAA
29926 AAATAAAATAAAA
1 AAATAAAATAAAA
29939 AAATAAA
1 AAATAAA
29946 TTCTAGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:30412 original size:45 final size:45
Alignment explanation
Indices: 30361--30449 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
30351 GACAAGTAGT
30361 GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACATA
1 GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACATA
30406 GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACAT
1 GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACAT
30450 GATTATTGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (45 bp):
GATGTTCCAATTTCCTTGATACGAGAACAAGAACTTAGAAACATA
Found at i:37176 original size:40 final size:39
Alignment explanation
Indices: 37092--37275 Score: 212
Period size: 40 Copynumber: 4.6 Consensus size: 39
37082 TTGAATGATG
* * * *
37092 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
37132 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
37172 TCCGGGCTAAG-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
37210 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
37251 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
37276 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
38 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:37227 original size:78 final size:80
Alignment explanation
Indices: 37092--37275 Score: 216
Period size: 78 Copynumber: 2.3 Consensus size: 80
37082 TTGAATGATG
*
37092 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
37156 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
37171 TTCCGGGCTAAG-CCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
*
37233 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
37250 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAG-CCCGAAGGCATTTG
37276 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
77 1 0.01
78 57 0.63
79 8 0.09
80 24 0.27
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Done.