Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2308
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: 385994
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
File 2 of 3
Found at i:185357 original size:2 final size:2
Alignment explanation
Indices: 185350--185380 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
185340 AGTTTGTGTT
185350 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
185381 GATTATAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:185387 original size:14 final size:15
Alignment explanation
Indices: 185351--185392 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
185341 GTTTGTGTTT
*
185351 ATATATATATATATAT
1 ATATATATAT-TATAG
185367 ATATATATATTATAG
1 ATATATATATTATAG
*
185382 AT-TATAGATTA
1 ATATATATATTA
185393 ATGATGCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 8 0.33
15 6 0.25
16 10 0.42
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (15 bp):
ATATATATATTATAG
Found at i:186753 original size:28 final size:28
Alignment explanation
Indices: 186720--186775 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
186710 TGATTCAATT
*
186720 AGAATTTACGTGTGATGTGATGTTAGTC
1 AGAATTTACGTGTGAGGTGATGTTAGTC
186748 AGAATTTACGTGTGAGGTGATGTTAGTC
1 AGAATTTACGTGTGAGGTGATGTTAGTC
186776 CACTTAACGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.38
Consensus pattern (28 bp):
AGAATTTACGTGTGAGGTGATGTTAGTC
Found at i:187151 original size:69 final size:69
Alignment explanation
Indices: 187069--187208 Score: 237
Period size: 69 Copynumber: 2.0 Consensus size: 69
187059 ACGACAGTCT
*
187069 CAGATACATGTCTTCAAAGCTTGTG-GTTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAGCCTGTGTG-TTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
187133 GTTCC
65 GTTCC
* *
187138 CAGATATATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
187203 TTCC
66 TTCC
187207 CA
1 CA
187209 ACGTCTGTTG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 66 0.99
70 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (69 bp):
CAGATACATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
TTCC
Found at i:187340 original size:231 final size:231
Alignment explanation
Indices: 186934--187370 Score: 752
Period size: 231 Copynumber: 1.9 Consensus size: 231
186924 AGTGTGAAGT
* *
186934 TTGTAGAGATAGACAGCTGTAATAATTTGAAATGTCTGTTCCCAACTTCTGTTGCTAATAGCCTT
1 TTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTT
* * *
186999 GGGCATCTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGAC
66 GGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTCGGATTGGAAGAAATAATCCAAGCAACGAC
* * *
187064 AGTCTCAGATACATGTCTTCAAAGCTTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAAT
131 AGTCTCAGATACATGTCTTCAAAGCCTGTGGTCTGTAGAGATAGACAGCTGCAATAATTTGAAAT
187129 ATCTGTTCCCAGATATATGTCTTCAAAGCCTGTGTG
196 ATCTGTTCCCAGATATATGTCTTCAAAGCCTGTGTG
187165 TTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTT
1 TTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTT
187230 GGGAAACT-GAAAGGACTGAAGATAAAGAGCTGTTTCGGATTGGAAGAAATAATCCAAGCAACGA
66 GGGAAACTGGAAA-GACTGAAGATAAAGAGCTGTTTCGGATTGGAAGAAATAATCCAAGCAACGA
* *
187294 CAGTGTCAGATACATGTCTTCAAAGCCTG-GAGTCTGTAGTGATAGACAGCTGCAATAATTTGAA
130 CAGTCTCAGATACATGTCTTCAAAGCCTGTG-GTCTGTAGAGATAGACAGCTGCAATAATTTGAA
187358 ATATCTGTTCCCA
194 ATATCTGTTCCCA
187371 ACGTCTGTTG
Statistics
Matches: 194, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
230 5 0.03
231 189 0.97
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.29
Consensus pattern (231 bp):
TTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTT
GGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTCGGATTGGAAGAAATAATCCAAGCAACGAC
AGTCTCAGATACATGTCTTCAAAGCCTGTGGTCTGTAGAGATAGACAGCTGCAATAATTTGAAAT
ATCTGTTCCCAGATATATGTCTTCAAAGCCTGTGTG
Found at i:187412 original size:162 final size:162
Alignment explanation
Indices: 187138--187694 Score: 897
Period size: 162 Copynumber: 3.4 Consensus size: 162
187128 TATCTGTTCC
* * *
187138 CAGATATATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGTGAGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
* *
187203 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACT-GAAAGGACTGAAGATAAAGAGCTGTTTCG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAA-GACTGAAGATAAAGAGCTGTTTGG
*
187267 GATTGGAAGAAATAATCCAAGCAACGACAGTGT
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
* *
187300 CAGATACATGTCTTCAAAGCCTG-GAGTCTGTAGTGATAGACAGCTGCAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAGCCTGTGAGT-TGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
*
187364 GTTCCCAACGTCTGTTGCTAATAGTCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
65 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
*
187429 GATTGGAAGAAATAATCCAAGCAACGACCGTCT
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
* * * * *
187462 CCGATACATGTCTTCAAAGCCTG-AAGGATGTAGAGATAGACAACTGTAATAATTTGAAATCTCT
1 CAGATACATGTCTTCAAAGCCTGTGA-GTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
* *
187526 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGCTACTGAAAAGACTGAAGATAAAGAGCTGTTTGG
65 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
187591 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
187624 CAGATACATGTCTTCAAAGCCTGTG-GTTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAGCCTGTGAG-TTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
187688 GTTCCCA
65 GTTCCCA
187695 GATACATGTC
Statistics
Matches: 364, Mismatches: 26, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
161 4 0.01
162 355 0.98
163 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (162 bp):
CAGATACATGTCTTCAAAGCCTGTGAGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
TTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
ATTGGAAGAAATAATCCAAGCAACGACAGTCT
Found at i:187699 original size:393 final size:393
Alignment explanation
Indices: 187300--188087 Score: 1283
Period size: 393 Copynumber: 2.0 Consensus size: 393
187290 ACGACAGTGT
*
187300 CAGATACATGTCTTCAAAGCCTG-GAGTCTGTAGTGATAGACAGCTGCAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAGCCTGCGAGT-TGTAGAGATAGACAGCTGCAATAATTTGAAATATCT
* * *
187364 GTTCCCAACGTCTGTTGCTAATAGTCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
65 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTCG
* * *
187429 GATTGGAAGAAATAATCCAAGCAACGACCGTCTCCGATACATGTCTTCAAAGCCTGAAGGATGTA
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAAGGACGTA
* *
187494 GAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCT
195 GAGATAGACAACTGTAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCA
187559 ACTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCT
260 ACTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCT
* * * * *
187624 CAGATACATGTCTTCAAAGCCTG-TGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
325 CAGATACATATCTTCAAAGCCTGAAGG-ATGTACAGATAGACAACTGTAATAATTTGAAATATCT
187688 GTTCC
389 GTTCC
* * * *
187693 CAGATACATGTCTTCAAAGCCTGCGCGTTGTAGAGATAGAGAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGCGAGTTGTAGAGATAGACAGCTGCAATAATTTGAAATATCTG
*
187758 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAGGACTGAAGATAAAGAGCTGTTTCGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTCGG
* **
187823 ATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGGAGTCCGTAG
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAAGGACGTAG
* *
187888 TGATAGACAGCTGTAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAA
196 AGATAGACAACTGTAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAA
* * *
187953 CTGGAAAGATTGGAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCTC
261 CTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCTC
* *
188018 CGATACATATCTTCAAAGCCTGAAGGATGTACAGATAGACAACTGTAATAATTTGAAATCTCTGT
326 AGATACATATCTTCAAAGCCTGAAGGATGTACAGATAGACAACTGTAATAATTTGAAATATCTGT
188083 TCC
391 TCC
188086 CA
1 CA
188088 ACATCTGTTG
Statistics
Matches: 364, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
393 359 0.99
394 5 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (393 bp):
CAGATACATGTCTTCAAAGCCTGCGAGTTGTAGAGATAGACAGCTGCAATAATTTGAAATATCTG
TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTCGG
ATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAAGGACGTAG
AGATAGACAACTGTAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAA
CTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCTC
AGATACATATCTTCAAAGCCTGAAGGATGTACAGATAGACAACTGTAATAATTTGAAATATCTGT
TCC
Found at i:187705 original size:69 final size:69
Alignment explanation
Indices: 187624--187763 Score: 237
Period size: 69 Copynumber: 2.0 Consensus size: 69
187614 ACGACAGTCT
*
187624 CAGATACATGTCTTCAAAGCCTGTG-GTTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAGCCTGCGCG-TTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
187688 GTTCC
65 GTTCC
* *
187693 CAGATACATGTCTTCAAAGCCTGCGCGTTGTAGAGATAGAGAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGCGCGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
187758 TTCC
66 TTCC
187762 CA
1 CA
187764 ACGTCTGTTG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 66 0.99
70 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (69 bp):
CAGATACATGTCTTCAAAGCCTGCGCGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
TTCC
Found at i:187740 original size:555 final size:555
Alignment explanation
Indices: 186935--188804 Score: 3233
Period size: 555 Copynumber: 3.4 Consensus size: 555
186925 GTGTGAAGTT
* * *
186935 TGTAGAGATAGACAGCTGTAATAATTTGAAATGTCTGTTCCCAACTTCTGTTGCTAATAGCCTTG
1 TGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTG
*
187000 GGC-ATCTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGAC
66 GGCTA-CTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGAC
*
187064 AGTCTCAGATACATGTCTTCAAAGCTTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAAT
130 AGTCTCAGATACATGTCTTCAAAGCCTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAAT
*
187129 ATCTGTTCCCAGATATATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTG
195 ATCTGTTCCCAGATACATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTG
187194 AAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGAAAGGACTGAAGATAAAGAG
260 AAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGAAAGGACTGAAGATAAAGAG
*
187259 CTGTTTCGGATTGGAAGAAATAATCCAAGCAACGACAGTGTCAGATACATGTCTTCAAAGCCTGG
325 CTGTTTCGGATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGG
* *
187324 AGTCTGTAGTGATAGACAGCTGCAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGT
390 AGTCTGTAGTGATAGACAGCTGTAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGC
187389 CTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAAC
455 CTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAAC
*
187454 GACCGTCTCCGATACATGTCTTCAAAGCCTGAAGGA
520 GACAGTCTCCGATACATGTCTTCAAAGCCTGAAGGA
187490 TGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTG
1 TGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTG
187555 GGCTACTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACA
66 GGCTACTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACA
187620 GTCTCAGATACATGTCTTCAAAGCCTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATA
131 GTCTCAGATACATGTCTTCAAAGCCTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATA
* * *
187685 TCTGTTCCCAGATACATGTCTTCAAAGCCTGCGCGTTGTAGAGATAGAGAGCTGTAATAATTTGA
196 TCTGTTCCCAGATACATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTGA
*
187750 AATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAGGACTGAAGATAAAGAGC
261 AATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGAAAGGACTGAAGATAAAGAGC
187815 TGTTTCGGATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGGA
326 TGTTTCGGATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGGA
*
187880 GTCCGTAGTGATAGACAGCTGTAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGCC
391 GTCTGTAGTGATAGACAGCTGTAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGCC
* *
187945 TTGGGCAACTGGAAAGATTGGAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACG
456 TTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACG
*
188010 ACAGTCTCCGATACATATCTTCAAAGCCTGAAGGA
521 ACAGTCTCCGATACATGTCTTCAAAGCCTGAAGGA
* * *
188045 TGTACAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACATCTGTTGCTAGTAGCCTTG
1 TGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTG
*
188110 GGCTACTGAAAAGACTAAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACA
66 GGCTACTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACA
188175 GTCTCAGATACATGTCTTCAAAGCCTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATA
131 GTCTCAGATACATGTCTTCAAAGCCTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATA
* * * *
188240 TCTGTTCCCAGATACATGTCTTCAAAACCTATGTATTGTAGAGATAAACAGCTGTAATAATTTGA
196 TCTGTTCCCAGATACATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTGA
* * *
188305 AATCTCTGTTCTCAACATCTGTTGCTGATAGCCTTGGGAAACTGGAAA-GACTGAAGATAAAGAG
261 AATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACT-GAAAGGACTGAAGATAAAGAG
* *
188369 CTGTTTGGGATTGGAAGAAATAATCCAAGCAGCGACAGTCTCAGATACATGTCTTCAAAGCCTGA
325 CTGTTTCGGATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTG-
* * * *
188434 GGGT-TGTAGAGATAGACAGCTGTAATAATTTGAAATTTCTGTTCTCAACGTCTGTTGCTAATAG
389 GAGTCTGTAGTGATAGACAGCTGTAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAG
* *
188498 CCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAG
454 CCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAA
* * *
188563 CGACAGTCTCAGATACATGTCTTCAAAGCCTGAGGGT
519 CGACAGTCTCCGATACATGTCTTCAAAGCCTGAAGGA
* * * *
188600 TGTAGAGATAGACAGCTGTAATAATTTGAAATTTCTGTTCTCAACGTCTGTCGCTAATAGCCTTG
1 TGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTG
** * *
188665 GGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAGGAAATAATCCAAGCAACGACA
66 GGCTACTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACA
* * *
188730 GTCTCAGCTACATGTCTTCAAAGCCTATGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATC
131 GTCTCAGATACATGTCTTCAAAGCCTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATA
188795 TCTGTTCCCA
196 TCTGTTCCCA
188805 ACGTCTGTTG
Statistics
Matches: 1249, Mismatches: 63, Indels: 6
0.95 0.05 0.00
Matches are distributed among these distances:
555 1242 0.99
556 7 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (555 bp):
TGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTG
GGCTACTGAAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACA
GTCTCAGATACATGTCTTCAAAGCCTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATA
TCTGTTCCCAGATACATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTGA
AATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGAAAGGACTGAAGATAAAGAGC
TGTTTCGGATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGGA
GTCTGTAGTGATAGACAGCTGTAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGCC
TTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACG
ACAGTCTCCGATACATGTCTTCAAAGCCTGAAGGA
Found at i:187867 original size:231 final size:231
Alignment explanation
Indices: 187464--187925 Score: 784
Period size: 231 Copynumber: 2.0 Consensus size: 231
187454 GACCGTCTCC
187464 GATACATGTCTTCAAAGCCTGAAGGATGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGTT
1 GATACATGTCTTCAAAGCCTGAAGGATGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGTT
** *
187529 CCCAACGTCTGTTGCTAATAGCCTTGGGCTACTGAAAAGACTGAAGATAAAGAGCTGTTTGGGAT
66 CCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGAAAAGACTGAAGATAAAGAGCTGTTTCGGAT
**
187594 TGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGTG-GTTTGTAGA
131 TGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTG-GAGTCCGTAGA
187658 GATAGACAGCTGTAATAATTTGAAATATCTGTTCCCA
195 GATAGACAGCTGTAATAATTTGAAATATCTGTTCCCA
* * * *
187695 GATACATGTCTTCAAAGCCTG-CGCGTTGTAGAGATAGAGAGCTGTAATAATTTGAAATCTCTGT
1 GATACATGTCTTCAAAGCCTGAAG-GATGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGT
* *
187759 TCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAGGACTGAAGATAAAGAGCTGTTTCGGA
65 TCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGAAAAGACTGAAGATAAAGAGCTGTTTCGGA
*
187824 TTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGGAGTCCGTAGT
130 TTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGGAGTCCGTAGA
187889 GATAGACAGCTGTAATAATTTGAAATATCTGTTCCCA
195 GATAGACAGCTGTAATAATTTGAAATATCTGTTCCCA
187926 ACGTCTGTTG
Statistics
Matches: 217, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
230 2 0.01
231 215 0.99
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (231 bp):
GATACATGTCTTCAAAGCCTGAAGGATGTAGAGATAGACAACTGTAATAATTTGAAATCTCTGTT
CCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGAAAAGACTGAAGATAAAGAGCTGTTTCGGAT
TGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGGAGTCCGTAGAG
ATAGACAGCTGTAATAATTTGAAATATCTGTTCCCA
Found at i:187972 original size:162 final size:162
Alignment explanation
Indices: 187693--188249 Score: 859
Period size: 162 Copynumber: 3.4 Consensus size: 162
187683 TATCTGTTCC
* * *
187693 CAGATACATGTCTTCAAAGCCTGCGCGTTGTAGAGATAGAGAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGCGAGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
* * *
187758 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAGGACTGAAGATAAAGAGCTGTTTCGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
187823 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
* *
187855 CAGATACATGTCTTCAAAGCCTG-GAGTCCGTAGTGATAGACAGCTGTAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAGCCTGCGAGT-TGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
* *
187919 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGATTGGAGATAAAGAGCTGTTTGG
65 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
187984 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
* * * * * * *
188017 CCGATACATATCTTCAAAGCCTG-AAGGATGTACAGATAGACAACTGTAATAATTTGAAATCTCT
1 CAGATACATGTCTTCAAAGCCTGCGA-GTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
* * * * *
188081 GTTCCCAACATCTGTTGCTAGTAGCCTTGGGCTACTGAAAAGACTAAAGATAAAGAGCTGTTTGG
65 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
188146 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
*
188179 CAGATACATGTCTTCAAAGCCTGTG-GTTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAGCCTGCGAG-TTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
188243 GTTCCCA
65 GTTCCCA
188250 GATACATGTC
Statistics
Matches: 358, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
161 4 0.01
162 353 0.99
163 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (162 bp):
CAGATACATGTCTTCAAAGCCTGCGAGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
TTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
ATTGGAAGAAATAATCCAAGCAACGACAGTCT
Found at i:188254 original size:393 final size:393
Alignment explanation
Indices: 187855--188639 Score: 1259
Period size: 393 Copynumber: 2.0 Consensus size: 393
187845 ACGACAGTCT
* * *
187855 CAGATACATGTCTTCAAAGCCTGGA-GT-CCGTAGTGATAGACAGCTGTAATAATTTGAAATATC
1 CAGATACATGTCTTCAAAACCT--ATGTACCGTAGAGATAAACAGCTGTAATAATTTGAAATATC
* * * *
187918 TGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGATTGGAGATAAAGAGCTGTTTG
64 TGTTCCCAACATCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTG
*
187983 GGATTGGAAGAAATAATCCAAGCAACGACAGTCTCCGATACATATCTTCAAAGCCTGAAGGATGT
129 GGATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATATCTTCAAAGCCTGAAGGATGT
* *
188048 ACAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACATCTGTTGCTAGTAGCCTTGGGC
194 ACAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACATCTGTTGCTAATAGCCTTGGGA
*
188113 TACTGAAAAGACTAAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTC
259 AACTGAAAAGACTAAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTC
* *
188178 TCAGATACATGTCTTCAAAGCCTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
324 TCAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
188243 GTTCC
389 GTTCC
** *
188248 CAGATACATGTCTTCAAAACCTATGTATTGTAGAGATAAACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAACCTATGTACCGTAGAGATAAACAGCTGTAATAATTTGAAATATCTG
* *
188313 TTCTCAACATCTGTTGCTGATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
66 TTCCCAACATCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
* * * * *
188378 ATTGGAAGAAATAATCCAAGCAGCGACAGTCTCAGATACATGTCTTCAAAGCCTGAGGGTTGTAG
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATATCTTCAAAGCCTGAAGGATGTAC
* * * *
188443 AGATAGACAGCTGTAATAATTTGAAATTTCTGTTCTCAACGTCTGTTGCTAATAGCCTTGGGAAA
196 AGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACATCTGTTGCTAATAGCCTTGGGAAA
* * *
188508 CTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAGCGACAGTCTC
261 CTGAAAAGACTAAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCTC
*
188573 AGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATTTCTGT
326 AGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTGT
188638 TC
391 TC
188640 TCAACGTCTG
Statistics
Matches: 359, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
391 1 0.00
392 2 0.01
393 356 0.99
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (393 bp):
CAGATACATGTCTTCAAAACCTATGTACCGTAGAGATAAACAGCTGTAATAATTTGAAATATCTG
TTCCCAACATCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
ATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATATCTTCAAAGCCTGAAGGATGTAC
AGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACATCTGTTGCTAATAGCCTTGGGAAA
CTGAAAAGACTAAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCTC
AGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTGT
TCC
Found at i:188260 original size:69 final size:69
Alignment explanation
Indices: 188179--188315 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 69
188169 ACGACAGTCT
* * *
188179 CAGATACATGTCTTCAAAGCCTGTGGT-TTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAACCTAT-GTATTGTAGAGATAAACAGCTGTAATAATTTGAAATATCT
188243 GTTCC
65 GTTCC
*
188248 CAGATACATGTCTTCAAAACCTATGTATTGTAGAGATAAACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAACCTATGTATTGTAGAGATAAACAGCTGTAATAATTTGAAATATCTG
188313 TTC
66 TTC
188316 TCAACATCTG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 2 0.03
69 61 0.97
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (69 bp):
CAGATACATGTCTTCAAAACCTATGTATTGTAGAGATAAACAGCTGTAATAATTTGAAATATCTG
TTCC
Found at i:188422 original size:231 final size:231
Alignment explanation
Indices: 188019--188477 Score: 742
Period size: 231 Copynumber: 2.0 Consensus size: 231
188009 GACAGTCTCC
* *
188019 GATACATATCTTCAAAGCCTGAAGGATGTACAGATAGACAACTGTAATAATTTGAAATCTCTGTT
1 GATACATATCTTCAAAACCTGAAGGATGTACAGATAAACAACTGTAATAATTTGAAATCTCTGTT
**
188084 CCCAACATCTGTTGCTAGTAGCCTTGGGCTACTGAAAAGACTAAAGATAAAGAGCTGTTTGGGAT
66 CCCAACATCTGTTGCTAGTAGCCTTGGGAAACTGAAAAGACTAAAGATAAAGAGCTGTTTGGGAT
* *
188149 TGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGTGGTTTGTAGAG
131 TGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAG
188214 ATAGACAGCTGTAATAATTTGAAATATCTGTTCCCA
196 ATAGACAGCTGTAATAATTTGAAATATCTGTTCCCA
* * * * *
188250 GATACATGTCTTCAAAACCT-ATGTATTGTAGAGATAAACAGCTGTAATAATTTGAAATCTCTGT
1 GATACATATCTTCAAAACCTGAAGGA-TGTACAGATAAACAACTGTAATAATTTGAAATCTCTGT
* * *
188314 TCTCAACATCTGTTGCT-GATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
65 TCCCAACATCTGTTGCTAG-TAGCCTTGGGAAACTGAAAAGACTAAAGATAAAGAGCTGTTTGGG
*
188378 ATTGGAAGAAATAATCCAAGCAGCGACAGTCTCAGATACATGTCTTCAAAGCCTGAGGGTTGTAG
129 ATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAGGGTTGTAG
*
188443 AGATAGACAGCTGTAATAATTTGAAATTTCTGTTC
194 AGATAGACAGCTGTAATAATTTGAAATATCTGTTC
188478 TCAACGTCTG
Statistics
Matches: 210, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
230 4 0.02
231 206 0.98
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (231 bp):
GATACATATCTTCAAAACCTGAAGGATGTACAGATAAACAACTGTAATAATTTGAAATCTCTGTT
CCCAACATCTGTTGCTAGTAGCCTTGGGAAACTGAAAAGACTAAAGATAAAGAGCTGTTTGGGAT
TGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAG
ATAGACAGCTGTAATAATTTGAAATATCTGTTCCCA
Found at i:188515 original size:162 final size:162
Alignment explanation
Indices: 188248--190225 Score: 3280
Period size: 162 Copynumber: 12.2 Consensus size: 162
188238 TATCTGTTCC
* ** *
188248 CAGATACATGTCTTCAAAACCT-ATGTATTGTAGAGATAAACAGCTGTAATAATTTGAAATCTCT
1 CAGATACATGTCTTCAAAGCCTGA-GGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCT
* * *
188312 GTTCTCAACATCTGTTGCTGATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
65 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
*
188377 GATTGGAAGAAATAATCCAAGCAGCGACAGTCT
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
*
188410 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATTTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
*
188475 TTCTCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
*
188540 ATTGGAAGAAATAATCCAAGCAGCGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
*
188572 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATTTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* *
188637 TTCTCAACGTCTGTCGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
*
188702 ATTGGAGGAAATAATCCAAGCAACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
* *
188734 CAGCTACATGTCTTCAAAGCCT-ATGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCT
1 CAGATACATGTCTTCAAAGCCTGA-GGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCT
*
188798 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGGAGATAAAGAGCTGTTTGG
65 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
188863 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
* *
188896 CAGATACATGTCTTCAAAGCCTGAAGGTTGTAGAGAGAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* * * *
188961 TTCTCAACGTCTGTTGCTGATAGCCTTGGGAAACTGAAAAGACTGAAGATAAAGAGCTGTTTCGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
*
189026 ATTGGAAGAAATAATCCAAGGAACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
* *
189058 CAGATACATGTCTTCAAAGCCTGAAGGTTGTAGAGATAGATAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* *
189123 TTCCCAACGTCTGTTGCTGATAGCCTTGGGAAACTGAAAAGACTGAAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
* *
189188 ATTGGAAGAAATAATTCAAGGAACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
*
189220 CAGATACATGTCTTCAAAGCCTGAAGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* * *
189285 TTCCCAACGTCTATTGTTGATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
*
189350 ATTGGAGGAAATAATCCAAGCAACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
* * *
189382 CAGATACATGTCTTCAAAGTCTGTGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* *
189447 TTCCCAACGTCTGTTGTTGATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
*
189512 ATTGAAAGAAATAATCCAAGCAACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
*
189544 CCGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* ** *
189609 TTCCCAATGTCTGTTGCTAATAGCCTTGGGAAACTAAAAAGACCGAAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
* *
189674 ATTGGAGGAAATAATCCAAGCAATGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
* *
189706 CAGATACATGTCTTCAAAGCCTGAAGGTTGTAAAGATAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
*
189771 TTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
189836 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
* * * **
189868 CAAATACATGTCTTCAAAGCCTAAAGGTTGTAGAGATAGACAGCTGTGTTAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* * *
189933 TTCCCAACGTCGGTTGCTAATAGCCTTGGGAAACTGAAAAGACTGGAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
189998 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
*
190030 CAGATACATGTCTTCAAAGCCTGAAGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* * * * *
190095 TTCCCAACGTCTGTTGCTAATAGCCTTCGGCAATTGGAAAGACTGGAGATAAAGAGCTGTTTTGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
* *
190160 ATTGGAAGAAATAATCAAAGCGACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
190192 C-GAATACATGTCTTCAAAGCCTG-GAGGTTGTAGA
1 CAG-ATACATGTCTTCAAAGCCTGAG-GGTTGTAGA
190226 TATAAGTTTG
Statistics
Matches: 1720, Mismatches: 91, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
161 2 0.00
162 1716 1.00
163 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (162 bp):
CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
ATTGGAAGAAATAATCCAAGCAACGACAGTCT
Found at i:188521 original size:717 final size:707
Alignment explanation
Indices: 187138--189117 Score: 2435
Period size: 717 Copynumber: 2.8 Consensus size: 707
187128 TATCTGTTCC
* * * *
187138 CAGATATATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGAGAGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
*
187203 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACT-GAAAGGACTGAAGATAAAGAGCTGTTTCG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAA-GACTGAAGATAAAGAGCTGTTTGG
* * **
187267 GATTGGAAGAAATAATCCAAGCAACGACAGTGTCAGATACATGTCTTCAAAGCCTGGAGTCTGTA
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAAGGATGTA
* * * *
187332 GTGATAGACAGCTGCAATAATTTGAAATATCTGTTCCCAACGTCTGTTGCTAATAGTCTTGGGCA
195 GAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCA
*
187397 ACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACCGTCT
260 ACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCT
* * *
187462 CCGATACATGTCTTCAAAGCCTGAAGGATGTAGAGATAGACAACTGTAATAATTTGAAATCTCTG
325 CAGATACATGTCTTCAAAGCCTGAAGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* * * *
187527 TTCCCAACGTCTGTTGCTAATAGCCTTGGGCTACTGAAAAGACTGAAGATAAAGAGCTGTTTGGG
390 TTCCCAAC-TCTGTTGCTAATAACCTT-GGCTACTG---AGAC-GAAGATAAACAGCTGTAT-GA
* **
187592 ATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGTGGTTTGTAG
448 ATTGGAAGAAATAATCC-AGCAACGACAGTCTCAGATA-ATGCCTTCAAA-CCTGTGGACTGTAG
* * * * *
187657 AGATAGACAGCTGTAATAATTTGAAATATCTGTTCCCAGATACATGTCTTCAAAGCCTGCGCGTT
510 AGATAAACAGCTGTAATAATTAGAAATATCCGGTCCCAGATACATGTCTTCAAAGCCTGAGCGTT
*
187722 GTAGAGATAGAGAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGG
575 GTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGG
*
187787 GAAACTGGAAGGACTGAAGATAAAGAGCTGTTTCGGATTGGAAGAAATAATCCAAGCAACGACAG
640 GAAACTGGAAAGACTGAAGATAAAGAGCTGTTTCGGATTGGAAGAAATAATCCAAGCAACGACAG
187852 TCT
705 TCT
* *
187855 CAGATACATGTCTTCAAAGCCTG-GAGTCCGTAGTGATAGACAGCTGTAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAGCCTGAGAGT-TGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
* * *
187919 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAAGATTGGAGATAAAGAGCTGTTTGG
65 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGG
* *
187984 GATTGGAAGAAATAATCCAAGCAACGACAGTCTCCGATACATATCTTCAAAGCCTGAAGGATGTA
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAAGGATGTA
* * * * *
188049 CAGATAGACAACTGTAATAATTTGAAATCTCTGTTCCCAACATCTGTTGCTAGTAGCCTTGGGCT
195 GAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCA
* *
188114 ACTGAAAAGACTAAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCT
260 ACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCT
* *
188179 CAGATACATGTCTTCAAAGCCTG-TGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
325 CAGATACATGTCTTCAAAGCCTGAAGG-TTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCT
* * *
188243 GTTCCCAGA-TACATGTCTTC-AA-AACCTAT-G-TATTG-TA-G-AGATAAACAGCTGTAAT-A
389 GTTCCCA-ACT-C-TGT-TGCTAATAACCT-TGGCTACTGAGACGAAGATAAACAGCTGT-ATGA
* ** ** * * * * *
188299 ATTTGAA-ATCTCTGTTC-TCAAC-ATCTGT-TGCTGAT-A-GCCTTGGGAAA-CTG-GAAAGAC
448 ATTGGAAGAAAT-AATCCAGCAACGA-CAGTCT-CAGATAATGCCTT--CAAACCTGTG---GAC
* * * *
188356 TG-A-AGATAAAGAGCTGT-TTGGGATTGGAAGAAATAATCCAAGCAGCGACAGTCTCAGATACA
505 TGTAGAGATAAACAGCTGTAAT--AATT---AGAAAT-AT-----C--CG---GTCCCAGATACA
* * *
188418 TGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATTTCTGTTCTCAAC
554 TGTCTTCAAAGCCTGAGCGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAAC
*
188483 GTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAG
619 GTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTCGGATTGGAAG
*
188548 AAATAATCCAAGCAGCGACAGTCT
684 AAATAATCCAAGCAACGACAGTCT
* *
188572 CAGATACATGTCTTCAAAGCCTGAGGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATTTCTG
1 CAGATACATGTCTTCAAAGCCTGAGAGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
* *
188637 TTCTCAACGTCTGTCGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
* * * *
188702 ATTGGAGGAAATAATCCAAGCAACGACAGTCTCAGCTACATGTCTTCAAAGCCT-ATGGTTTGTA
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAAGG-ATGTA
*
188766 GAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGAA
195 GAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCA
*
188831 ACTGGAAAGACTGGAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCT
260 ACTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCT
*
188896 CAGATACATGTCTTCAAAGCCTGAAGGTTGTAGAGAGAGACAGCTGTAATAATTTGAAATCTCTG
325 CAGATACATGTCTTCAAAGCCTGAAGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
* * * ** * * *
188961 TTCTCAACGTCTGTTGCTGATAGCCTTGGGAAACTGAAAAGACTGAAGATAAAGAGCTGTTTCGG
390 TTCCCAAC-TCTGTTGCTAATAACCTT-GGCTACTG---AGAC-GAAGATAAACAGCTGTAT-GA
* * * *
189026 ATTGGAAGAAATAATCCAAGGAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAAGG-TTGTA
448 ATTGGAAGAAATAATCC-AGCAACGACAGTCTCAGATA-ATGCCTTCAAA-CCTG-TGGACTGTA
* * *
189090 GAGATAGATAGCTGTAATAATTTGAAAT
509 GAGATAAACAGCTGTAATAATTAGAAAT
189118 CTCTGTTCCC
Statistics
Matches: 1073, Mismatches: 123, Indels: 123
0.81 0.09 0.09
Matches are distributed among these distances:
701 2 0.00
702 19 0.02
703 5 0.00
704 8 0.01
705 11 0.01
706 7 0.01
707 10 0.01
708 13 0.01
709 2 0.00
711 1 0.00
712 1 0.00
714 1 0.00
715 6 0.01
716 16 0.01
717 873 0.81
718 18 0.02
719 5 0.00
723 1 0.00
725 2 0.00
726 13 0.01
727 8 0.01
728 7 0.01
729 10 0.01
730 7 0.01
731 6 0.01
732 19 0.02
733 1 0.00
734 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (707 bp):
CAGATACATGTCTTCAAAGCCTGAGAGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
TTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAAGACTGAAGATAAAGAGCTGTTTGGG
ATTGGAAGAAATAATCCAAGCAACGACAGTCTCAGATACATGTCTTCAAAGCCTGAAGGATGTAG
AGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAA
CTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGACAGTCTC
AGATACATGTCTTCAAAGCCTGAAGGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGT
TCCCAACTCTGTTGCTAATAACCTTGGCTACTGAGACGAAGATAAACAGCTGTATGAATTGGAAG
AAATAATCCAGCAACGACAGTCTCAGATAATGCCTTCAAACCTGTGGACTGTAGAGATAAACAGC
TGTAATAATTAGAAATATCCGGTCCCAGATACATGTCTTCAAAGCCTGAGCGTTGTAGAGATAGA
CAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTTGGGAAACTGGAAA
GACTGAAGATAAAGAGCTGTTTCGGATTGGAAGAAATAATCCAAGCAACGACAGTCT
Found at i:194255 original size:30 final size:31
Alignment explanation
Indices: 194221--194289 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 31
194211 TTATTGTCCT
194221 AAAATATTAAATATTTACTCT-GATTGAT-AA
1 AAAATATTAAATATTTA-TCTGGATTGATCAA
* *
194251 AAAATATTGAATATTTATTTGGATTGATCAA
1 AAAATATTAAATATTTATCTGGATTGATCAA
194282 ATAAATAT
1 A-AAATAT
194290 CTTAAGATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 2 0.06
30 23 0.68
31 3 0.09
32 6 0.18
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (31 bp):
AAAATATTAAATATTTATCTGGATTGATCAA
Found at i:196371 original size:2 final size:2
Alignment explanation
Indices: 196364--196396 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
196354 AGTTCGTGTT
196364 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
196397 GATTAATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:197126 original size:5 final size:5
Alignment explanation
Indices: 197118--197147 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
197108 TCTTTATTTA
197118 TTATT TTATT TTATT TTATT TTATT ATTAT
1 TTATT TTATT TTATT TTATT TTATT -TTAT
197148 CTTCTGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:201785 original size:14 final size:14
Alignment explanation
Indices: 201754--201791 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
201744 ATTTGAATTT
201754 AAAATT-ATATAAA
1 AAAATTAATATAAA
*
201767 AAAATTAATATATA
1 AAAATTAATATAAA
*
201781 TAAATTAATAT
1 AAAATTAATAT
201792 TACTCAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATTAATATAAA
Found at i:202317 original size:23 final size:23
Alignment explanation
Indices: 202285--202360 Score: 73
Period size: 23 Copynumber: 3.1 Consensus size: 23
202275 TTAAATTTAA
*
202285 TAATTTAAATATAATATAAATAT
1 TAATTAAAATATAATATAAATAT
202308 TAATTAAAATATAA-ATAAAATAT
1 TAATTAAAATATAATAT-AAATAT
* *
202331 TTATATATAAATATATGTATAAATTAT
1 TAAT-TA-AAATATA-ATATAAA-TAT
202358 TAA
1 TAA
202361 AATATTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
22 2 0.05
23 22 0.51
24 2 0.05
25 7 0.16
26 3 0.07
27 7 0.16
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
TAATTAAAATATAATATAAATAT
Found at i:202764 original size:19 final size:19
Alignment explanation
Indices: 202740--202777 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
202730 TTGAATAGAT
202740 TTTAAATATAATATTTTTA
1 TTTAAATATAATATTTTTA
* *
202759 TTTAAATTTAATTTTTTTA
1 TTTAAATATAATATTTTTA
202778 AATATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTAAATATAATATTTTTA
Found at i:202777 original size:15 final size:16
Alignment explanation
Indices: 202740--202786 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
202730 TTGAATAGAT
202740 TTTAAATATAATATTTTTA
1 TTTAAATAT-A-A-TTTTA
*
202759 TTTAAATTTAATTTT-
1 TTTAAATATAATTTTA
202774 TTTAAATATAATT
1 TTTAAATATAATT
202787 AAAATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 12 0.46
16 4 0.15
17 1 0.04
18 1 0.04
19 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAAATATAATTTTA
Found at i:204959 original size:21 final size:21
Alignment explanation
Indices: 204934--204981 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
204924 ATATTTTTGA
204934 ATGAAATG-ATGCATTGATTGG
1 ATGAAA-GAATGCATTGATTGG
**
204955 ATGAAAGAATGCATTTTTTGG
1 ATGAAAGAATGCATTGATTGG
204976 ATGAAA
1 ATGAAA
204982 AATACAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (21 bp):
ATGAAAGAATGCATTGATTGG
Found at i:204991 original size:21 final size:21
Alignment explanation
Indices: 204951--204993 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
204941 GATGCATTGA
*
204951 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATACATTTT
*
204972 TTGGATGAAA-AATACAATTT
1 TTGGATGAAAGAATACATTTT
204992 TT
1 TT
204994 AATAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.40
Consensus pattern (21 bp):
TTGGATGAAAGAATACATTTT
Found at i:208433 original size:25 final size:25
Alignment explanation
Indices: 208386--208436 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
208376 ATTAAAAATG
* *
208386 ATTATATAAATATAACATAAATAAA
1 ATTATATAAACATAAAATAAATAAA
208411 ATTATATAAAACATAAAATAATATAA
1 ATTATAT-AAACATAAAATAA-ATAA
208437 TACTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 11 0.50
27 4 0.18
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
ATTATATAAACATAAAATAAATAAA
Found at i:208662 original size:16 final size:16
Alignment explanation
Indices: 208621--208670 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
208611 TCATTCAAAT
208621 TTTAAAA-AATTT-AA
1 TTTAAAATAATTTAAA
* *
208635 TTGTGAATTAATTTAAA
1 TT-TAAAATAATTTAAA
208652 TTTAAAATAATTTAAA
1 TTTAAAATAATTTAAA
208668 TTT
1 TTT
208671 GAACAACTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 3 0.10
16 20 0.69
17 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (16 bp):
TTTAAAATAATTTAAA
Found at i:208848 original size:2 final size:2
Alignment explanation
Indices: 208841--208873 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
208831 GAACACAATT
208841 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
208874 TTATGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:209944 original size:23 final size:22
Alignment explanation
Indices: 209913--209958 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
209903 TGAGCTAATC
*
209913 TAATTAAATTATTATTATTTAAA
1 TAATAAAATTATTA-TATTTAAA
*
209936 TAATAAAATTTTTATATTTAAA
1 TAATAAAATTATTATATTTAAA
209958 T
1 T
209959 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATAAAATTATTATATTTAAA
Found at i:219581 original size:63 final size:63
Alignment explanation
Indices: 219503--219629 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
219493 AAGAAGGTAG
219503 TCAGCATGTAAAGAGATTTTGTGACTCGGATTATTCTGATGATTTAGACAAGCATCGATCAAC
1 TCAGCATGTAAAGAGATTTTGTGACTCGGATTATTCTGATGATTTAGACAAGCATCGATCAAC
219566 TCAGCATGTAAAGAGATTTTGTGACTCGGATTATTCTGATGATTTAGACAAGCATCGATCAAC
1 TCAGCATGTAAAGAGATTTTGTGACTCGGATTATTCTGATGATTTAGACAAGCATCGATCAAC
219629 T
1 T
219630 ACTGGTGGAG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.32
Consensus pattern (63 bp):
TCAGCATGTAAAGAGATTTTGTGACTCGGATTATTCTGATGATTTAGACAAGCATCGATCAAC
Found at i:223798 original size:14 final size:14
Alignment explanation
Indices: 223775--223813 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
223765 TCAAATAACT
223775 AAAAGAAAAAAAATA
1 AAAAG-AAAAAAATA
*
223790 AAAAGAAAAACATA
1 AAAAGAAAAAAATA
*
223804 AAAATAAAAA
1 AAAAGAAAAA
223814 TCATGCCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.85, C:0.03, G:0.05, T:0.08
Consensus pattern (14 bp):
AAAAGAAAAAAATA
Found at i:224235 original size:29 final size:28
Alignment explanation
Indices: 224203--224261 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
224193 ATAATTTTTT
224203 TTTTAAAATGAAAAAATTA-TCCTTAAAAA
1 TTTTAAAATG-AAAAA-TAGTCCTTAAAAA
**
224232 TTTTAGGATGAAAAATAGTCCTTAAAAA
1 TTTTAAAATGAAAAATAGTCCTTAAAAA
224260 TT
1 TT
224262 ATCGTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 2 0.07
28 17 0.63
29 8 0.30
ACGTcount: A:0.49, C:0.07, G:0.08, T:0.36
Consensus pattern (28 bp):
TTTTAAAATGAAAAATAGTCCTTAAAAA
Found at i:226749 original size:27 final size:28
Alignment explanation
Indices: 226710--226765 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
226700 TCAATAATTT
226710 TTTTAAAAGAAAAAATA-TCCTTAAAAA
1 TTTTAAAAGAAAAAATAGTCCTTAAAAA
* * *
226737 TTTTAAGATAAAAAATAGTCTTTAAAAA
1 TTTTAAAAGAAAAAATAGTCCTTAAAAA
226765 T
1 T
226766 CATCTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (28 bp):
TTTTAAAAGAAAAAATAGTCCTTAAAAA
Found at i:228625 original size:15 final size:15
Alignment explanation
Indices: 228605--228633 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
228595 TTGTTTCTCT
228605 TTTTCTTTATATTAG
1 TTTTCTTTATATTAG
228620 TTTTCTTTATATTA
1 TTTTCTTTATATTA
228634 ATGGTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTCTTTATATTAG
Found at i:228915 original size:20 final size:19
Alignment explanation
Indices: 228890--228963 Score: 74
Period size: 20 Copynumber: 4.3 Consensus size: 19
228880 TTAAATTTAA
228890 TAATAAAAATATATAAATAT
1 TAATAAAAATAT-TAAATAT
228910 TAATAAAAAT-TT--A-A-
1 TAATAAAAATATTAAATAT
228924 TAAT-AAAATATTAAATAT
1 TAATAAAAATATTAAATAT
*
228942 TAATATAAATA-TAAA-AT
1 TAATAAAAATATTAAATAT
228959 TAATA
1 TAATA
228964 TTTTAATATA
Statistics
Matches: 47, Mismatches: 1, Indels: 15
0.75 0.02 0.24
Matches are distributed among these distances:
13 5 0.11
14 6 0.13
15 1 0.02
16 2 0.04
17 8 0.17
18 9 0.19
19 6 0.13
20 10 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATAAAAATATTAAATAT
Found at i:228937 original size:14 final size:13
Alignment explanation
Indices: 228897--228958 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
228887 TAATAATAAA
228897 AATATATAAATATT
1 AATATA-AAATATT
228911 AATA-AAAAT-TT
1 AATATAAAATATT
228922 AATAATAAAATATT
1 AAT-ATAAAATATT
* *
228936 AA-ATATTAATATA
1 AATATA-AAATATT
228949 AATATAAAAT
1 AATATAAAAT
228959 TAATATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
11 5 0.12
12 8 0.20
13 16 0.40
14 11 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAAAATATT
Found at i:228944 original size:32 final size:34
Alignment explanation
Indices: 228882--228951 Score: 117
Period size: 32 Copynumber: 2.1 Consensus size: 34
228872 ATTTTAATTT
228882 AAATTTAATAATAAAAATATATAAATATTAATAA
1 AAATTTAATAATAAAAATATATAAATATTAATAA
*
228916 AAATTTAATAAT-AAAATAT-TAAATATTAATAT
1 AAATTTAATAATAAAAATATATAAATATTAATAA
228948 AAAT
1 AAAT
228952 ATAAAATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 16 0.46
33 7 0.20
34 12 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (34 bp):
AAATTTAATAATAAAAATATATAAATATTAATAA
Found at i:230836 original size:28 final size:28
Alignment explanation
Indices: 230796--230851 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
230786 CAATTTTTAC
230796 AAACCACCATATTTGACAAATACAAAGG
1 AAACCACCATATTTGACAAATACAAAGG
230824 AAACCACCATATTTGACAAATACAAAGG
1 AAACCACCATATTTGACAAATACAAAGG
230852 GTGGCATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.21, G:0.11, T:0.18
Consensus pattern (28 bp):
AAACCACCATATTTGACAAATACAAAGG
Found at i:235441 original size:28 final size:28
Alignment explanation
Indices: 235401--235456 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
235391 CAATTTTTAC
235401 AAACCACCATATTTGACAAATACAAAGG
1 AAACCACCATATTTGACAAATACAAAGG
*
235429 AAACCACTATATTTGACAAATACAAAGG
1 AAACCACCATATTTGACAAATACAAAGG
235457 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.50, C:0.20, G:0.11, T:0.20
Consensus pattern (28 bp):
AAACCACCATATTTGACAAATACAAAGG
Found at i:236593 original size:19 final size:21
Alignment explanation
Indices: 236545--236596 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
236535 ATATTTAAAT
*
236545 TATTAAATT-TAAAATTTATA
1 TATTTAATTATAAAATTTATA
236565 TATTT-A-TATAAAATTTA-A
1 TATTTAATTATAAAATTTATA
236583 -ATTTAATTATAAAA
1 TATTTAATTATAAAA
236597 AAAAATGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 4 0.14
18 3 0.11
19 17 0.61
20 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATTTAATTATAAAATTTATA
Found at i:237169 original size:18 final size:17
Alignment explanation
Indices: 237139--237210 Score: 67
Period size: 18 Copynumber: 4.2 Consensus size: 17
237129 ATTTATAATA
*
237139 TAATAT-TATATATTAAT
1 TAATATATA-ATATAAAT
*
237156 TAATTATATGATATAAAT
1 TAA-TATATAATATAAAT
*
237174 TACATATATAATATAAAA
1 TA-ATATATAATATAAAT
*
237192 TAATATATTATAT-AAT
1 TAATATATAATATAAAT
237208 TAA
1 TAA
237211 AAAATAAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
16 5 0.11
17 13 0.28
18 26 0.57
19 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (17 bp):
TAATATATAATATAAAT
Found at i:237871 original size:21 final size:20
Alignment explanation
Indices: 237841--237882 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
237831 AATAATAAAA
237841 ATATTTTCAT-ATTAATATTT
1 ATATTTTCATAATTAA-ATTT
237861 ATATATTTCATAATTAAATTT
1 ATAT-TTTCATAATTAAATTT
237882 A
1 A
237883 ACCAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTTCATAATTAAATTT
Found at i:240818 original size:21 final size:21
Alignment explanation
Indices: 240793--240837 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
240783 ATTAAAATAT
*
240793 TATTTTAT-ATTAATATTTATA
1 TATTTTATAATTAA-ATTTAAA
240814 TATTTTATAATTAAATTTAAA
1 TATTTTATAATTAAATTTAAA
240835 TAT
1 TAT
240838 AAATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTTATAATTAAATTTAAA
Found at i:241567 original size:16 final size:16
Alignment explanation
Indices: 241532--241585 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
241522 TTATTTATAT
241532 TTTAATTGAATAAA-AAA
1 TTTAATT-AA-AAATAAA
241549 TTTAATTAAAAATAAA
1 TTTAATTAAAAATAAA
*
241565 TTTAAATTCAAAAT-AA
1 TTT-AATTAAAAATAAA
241581 TTTAA
1 TTTAA
241586 ATTTGAACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 5 0.15
16 13 0.38
17 16 0.47
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
TTTAATTAAAAATAAA
Found at i:241586 original size:16 final size:16
Alignment explanation
Indices: 241543--241588 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
241533 TTAATTGAAT
241543 AAAA-AATTT-AATTA
1 AAAATAATTTAAATTA
*
241557 AAAATAAATTTAAATTC
1 AAAAT-AATTTAAATTA
241574 AAAATAATTTAAATT
1 AAAATAATTTAAATT
241589 TGAACAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 4 0.14
16 15 0.54
17 9 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATAATTTAAATTA
Found at i:242146 original size:47 final size:47
Alignment explanation
Indices: 242090--242186 Score: 176
Period size: 47 Copynumber: 2.1 Consensus size: 47
242080 AAAGAGTGAG
242090 AGGAATTTCAAATTTGAATGTAAAAGAATTTAGGAAAAAAAAAACTA
1 AGGAATTTCAAATTTGAATGTAAAAGAATTTAGGAAAAAAAAAACTA
* *
242137 AGGAATTTCAAATTTGAATGTAAAAGAATTTAGGGAAAAAAAGACTA
1 AGGAATTTCAAATTTGAATGTAAAAGAATTTAGGAAAAAAAAAACTA
242184 AGG
1 AGG
242187 TTAAAATGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (47 bp):
AGGAATTTCAAATTTGAATGTAAAAGAATTTAGGAAAAAAAAAACTA
Found at i:242873 original size:20 final size:21
Alignment explanation
Indices: 242854--242891 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
242844 ATAATCTAAT
242854 TAAA-TTAT-TATTTAAATAA
1 TAAAGTTATATATTTAAATAA
*
242873 TAAAGTTTTATATTTAAAT
1 TAAAGTTATATATTTAAAT
242892 TTTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 3 0.19
21 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (21 bp):
TAAAGTTATATATTTAAATAA
Found at i:245105 original size:4 final size:4
Alignment explanation
Indices: 245096--245129 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
245086 TTTGATTTTC
245096 TTAT TTAT TTA- TTATT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TT
245130 CATCCTCACC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
4 22 0.79
5 3 0.11
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:245117 original size:16 final size:17
Alignment explanation
Indices: 245096--245129 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
245086 TTTGATTTTC
245096 TTATTTATTTA-TTATT
1 TTATTTATTTATTTATT
245112 TTATTTATTTATTTATT
1 TTATTTATTTATTTATT
245129 T
1 T
245130 CATCCTCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTATTTATTTATT
Found at i:246369 original size:17 final size:19
Alignment explanation
Indices: 246330--246368 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
246320 ATTTAAGGTA
*
246330 ATTTTTTTTTTCTTCTTTAT
1 ATTTTTATTTTCTTC-TTAT
246350 ATTTTTATTTTCTTCTTAT
1 ATTTTTATTTTCTTCTTAT
246369 TCATTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTTTATTTTCTTCTTAT
Found at i:250097 original size:2 final size:2
Alignment explanation
Indices: 250090--250125 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
250080 GTATTAAGTG
*
250090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
250126 ATACTTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:253259 original size:2 final size:2
Alignment explanation
Indices: 253252--253280 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
253242 TGATGATAAA
253252 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
253281 ATTTGACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:255549 original size:19 final size:18
Alignment explanation
Indices: 255527--255579 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
255517 ATATTTTTAT
255527 TTAAATTACATATTTAAAA
1 TTAAATTACA-ATTTAAAA
*
255546 TTAAATATA-AATTTTAAA
1 TTAAAT-TACAATTTAAAA
* *
255564 TTAATTTACAAATTAA
1 TTAAATTACAATTTAA
255580 TTATTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 2 0.07
18 17 0.61
19 7 0.25
20 2 0.07
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATTACAATTTAAAA
Found at i:255573 original size:37 final size:37
Alignment explanation
Indices: 255503--255573 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
255493 TATTTTTTAA
* * * * *
255503 TTAAAATTTATTATATATTTTTATTTAAATTACATAT
1 TTAAAATTAAATATAAATTTTAAATTAAATTACATAT
*
255540 TTAAAATTAAATATAAATTTTAAATTAATTTACA
1 TTAAAATTAAATATAAATTTTAAATTAAATTACA
255574 AATTAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 28 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (37 bp):
TTAAAATTAAATATAAATTTTAAATTAAATTACATAT
Found at i:255649 original size:43 final size:48
Alignment explanation
Indices: 255581--255720 Score: 123
Period size: 43 Copynumber: 2.9 Consensus size: 48
255571 ACAAATTAAT
*
255581 TATTTT-AAATATATTATTTAAAAATAAAAATAATTAATAAAATAAATT-
1 TATTTTAAAATA-AATATTT-AAAATAAAAATAATTAATAAAATAAATTA
** * *
255629 TATTTTAAAAT-AA-A-TT-AAATATGAAT-ATTAAATCAATTAAATTAA
1 TATTTTAAAATAAATATTTAAAATAAAAATAATT-AATAAAATAAATT-A
*
255674 TTTTTTAAAATAAATTATTTAAAATAAAAATTAATTAATAAAATAAA
1 TATTTTAAAATAAA-TATTTAAAATAAAAA-TAATTAATAAAATAAA
255721 ATTTTAAGAA
Statistics
Matches: 71, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
42 3 0.04
43 19 0.27
45 12 0.17
46 3 0.04
47 1 0.01
48 7 0.10
49 6 0.08
50 7 0.10
51 10 0.14
52 3 0.04
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (48 bp):
TATTTTAAAATAAATATTTAAAATAAAAATAATTAATAAAATAAATTA
Found at i:255684 original size:14 final size:14
Alignment explanation
Indices: 255667--255701 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
255657 TAAATCAATT
* *
255667 AAATTAATTTTTTA
1 AAATAAATTATTTA
255681 AAATAAATTATTTA
1 AAATAAATTATTTA
255695 AAATAAA
1 AAATAAA
255702 AATTAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:255691 original size:94 final size:96
Alignment explanation
Indices: 255543--255720 Score: 265
Period size: 94 Copynumber: 1.9 Consensus size: 96
255533 TACATATTTA
* * *
255543 AAATTAAATATAAATTTTAAATTAATTTACAAATTAATTATTTTAAATATATTATTTAAAAATAA
1 AAATTAAATATAAATATTAAATCAATTTA-AAATTAATTATTTTAAATAAATTATTT-AAAATAA
255608 AAA-TAATTAATAAAATAAATTTATTTTAAAAT
64 AAATTAATTAATAAAATAAATTTATTTTAAAAT
*
255640 AAATTAAATATGAATATTAAATCAA-TT-AAATTAATT-TTTTAAAATAAATTATTTAAAATAAA
1 AAATTAAATATAAATATTAAATCAATTTAAAATTAATTATTTT-AAATAAATTATTTAAAATAAA
255702 AATTAATTAATAAAATAAA
65 AATTAATTAATAAAATAAA
255721 ATTTTAAGAA
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
93 14 0.19
94 37 0.49
96 2 0.03
97 22 0.29
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (96 bp):
AAATTAAATATAAATATTAAATCAATTTAAAATTAATTATTTTAAATAAATTATTTAAAATAAAA
ATTAATTAATAAAATAAATTTATTTTAAAAT
Found at i:255709 original size:20 final size:19
Alignment explanation
Indices: 255680--255721 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
255670 TTAATTTTTT
*
255680 AAAATAAATTATTTAAAATA
1 AAAATAAATTA-ATAAAATA
*
255700 AAAATTAATTAATAAAATA
1 AAAATAAATTAATAAAATA
255719 AAA
1 AAA
255722 TTTTAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATAAATTAATAAAATA
Found at i:256168 original size:19 final size:19
Alignment explanation
Indices: 256127--256169 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
256117 GATAAATGTA
* * * *
256127 AAATGTTAATATATAATTT
1 AAATATTAATAAATAAGTG
256146 AAATATTAATAAATAAGTG
1 AAATATTAATAAATAAGTG
256165 AAATA
1 AAATA
256170 AAAATATAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (19 bp):
AAATATTAATAAATAAGTG
Found at i:257904 original size:27 final size:28
Alignment explanation
Indices: 257852--257913 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
257842 TACTTAATAC
257852 TATAAA-ATTAAATATATTTTTATTAAA
1 TATAAATATTAAATATATTTTTATTAAA
*
257879 TATAAATATTAAA-AT-TTTATTTTTAAA
1 TATAAATATTAAATATATTT-TTATTAAA
*
257906 TTTAAATA
1 TATAAATA
257914 ATATAAGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 3 0.10
27 22 0.71
28 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
TATAAATATTAAATATATTTTTATTAAA
Found at i:258466 original size:24 final size:24
Alignment explanation
Indices: 258434--258484 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
258424 TTAAAAATTT
* *
258434 ATAATATTATTATATTAAT-TAAA
1 ATAATATTAATACATTAATATAAA
*
258457 ATAATAATTAATCCATTAATATAAA
1 ATAAT-ATTAATACATTAATATAAA
258482 ATA
1 ATA
258485 TTGAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 5 0.22
24 11 0.48
25 7 0.30
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAATATTAATACATTAATATAAA
Found at i:258553 original size:24 final size:23
Alignment explanation
Indices: 258522--258567 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
258512 AATAAATAAA
* *
258522 ATAAAAATATAATTTTTTTTAAT
1 ATAAAAATATAAATTTATTTAAT
258545 ATAATAAATATAAATTTATTTAA
1 ATAA-AAATATAAATTTATTTAA
258568 CGTGATTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAAAATATAAATTTATTTAAT
Found at i:258876 original size:22 final size:22
Alignment explanation
Indices: 258834--258877 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
258824 TTATTAAAAT
* *
258834 TTTATTTTTATATTACTATTTA
1 TTTATATTTATATTACAATTTA
258856 TTTATATTTATAATTA-AATTTA
1 TTTATATTTAT-ATTACAATTTA
258878 AATAAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTATATTTATATTACAATTTA
Found at i:261709 original size:24 final size:24
Alignment explanation
Indices: 261682--261734 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
261672 GTTTTTGTAT
* *
261682 TATTTATTTTTAA-TTTTTAATTAA
1 TATTTACTTTTAAGTTTTTAA-AAA
*
261706 TATTTCCTTTTAAGTTTTTAAAAA
1 TATTTACTTTTAAGTTTTTAAAAA
261730 TATTT
1 TATTT
261735 GCCTTTTATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (24 bp):
TATTTACTTTTAAGTTTTTAAAAA
Found at i:261723 original size:25 final size:24
Alignment explanation
Indices: 261689--261742 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 24
261679 TATTATTTAT
*
261689 TTTTAATTTTTAATTAATATTT-CC
1 TTTTAATTTTTAA-AAATATTTGCC
261713 TTTTAAGTTTTTAAAAATATTTGCC
1 TTTTAA-TTTTTAAAAATATTTGCC
261738 TTTTA
1 TTTTA
261743 TCTCAATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (24 bp):
TTTTAATTTTTAAAAATATTTGCC
Found at i:261972 original size:15 final size:14
Alignment explanation
Indices: 261928--261976 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
261918 AATTGATAGG
261928 AATAATTTTTTTAA
1 AATAATTTTTTTAA
** *
261942 AA-AAAATTTTAAA
1 AATAATTTTTTTAA
261955 AATATATTTTTTTAA
1 AATA-ATTTTTTTAA
261970 AATAATT
1 AATAATT
261977 ATTGATAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 10 0.37
14 6 0.22
15 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATAATTTTTTTAA
Found at i:269740 original size:12 final size:12
Alignment explanation
Indices: 269723--269748 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
269713 TTCTTCAAAT
269723 CAAATTTTATAG
1 CAAATTTTATAG
269735 CAAATTTTATAG
1 CAAATTTTATAG
269747 CA
1 CA
269749 TAATCAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (12 bp):
CAAATTTTATAG
Found at i:272344 original size:530 final size:530
Alignment explanation
Indices: 271343--272401 Score: 2091
Period size: 530 Copynumber: 2.0 Consensus size: 530
271333 TATGAATATC
271343 TCTAATATGTTTTTATTACATACGAATAAATTTAAGTTGGTCATTGAGTGACTAATAGGTATCAT
1 TCTAATATGTTTTTATTACATACGAATAAATTTAAGTTGGTCATTGAGTGACTAATAGGTATCAT
271408 TATAAAATTTTTAAGAATTGAGGATGATCAATAATTATTTTTTAAAAGAAAAAAATTGTTTTTAA
66 TATAAAATTTTTAAGAATTGAGGATGATCAATAATTATTTTTTAAAAGAAAAAAATTGTTTTTAA
271473 AAGTTTTAGAATGAAAAGTAATGCCTAAAAATTATCTTTTAGAACTGTGTTTCTGACTAAAATGT
131 AAGTTTTAGAATGAAAAGTAATGCCTAAAAATTATCTTTTAGAACTGTGTTTCTGACTAAAATGT
271538 TTTGAGGACGATATTATCTATAATACTGTTAAACTGGGGATAACATTTGCTCTCAACAACACCTA
196 TTTGAGGACGATATTATCTATAATACTGTTAAACTGGGGATAACATTTGCTCTCAACAACACCTA
271603 AGTTCAAGATAAAAGATATTTTTCTTAATCTGTCTATTTTTTGACCCTAAAGATCTCTTATTTTG
261 AGTTCAAGATAAAAGATATTTTTCTTAATCTGTCTATTTTTTGACCCTAAAGATCTCTTATTTTG
271668 TAATGTATCACTTAAAATTAAACTTTTATTTAATCACTAATCTCGAAAAAGAATTAATACTCAAA
326 TAATGTATCACTTAAAATTAAACTTTTATTTAATCACTAATCTCGAAAAAGAATTAATACTCAAA
271733 CTCATTATATTATAACATAACATCCTCAAAGTGTTTATATGAGTTGAATTTGATTGATTGTTAAG
391 CTCATTATATTATAACATAACATCCTCAAAGTGTTTATATGAGTTGAATTTGATTGATTGTTAAG
*
271798 AAAAATTGTTACAGTTAGTAACATATTCATTAGATCCTATTTTATCTTCCTAGCATGAAATGTGG
456 AAAAATTGTTACAGTTAGTAACATATTCATCAGATCCTATTTTATCTTCCTAGCATGAAATGTGG
271863 ATTGCCTCTT
521 ATTGCCTCTT
271873 TCTAATATGTTTTTATTACATACGAATAAATTTAAGTTGGTCATTGAGTGACTAATAGGTATCAT
1 TCTAATATGTTTTTATTACATACGAATAAATTTAAGTTGGTCATTGAGTGACTAATAGGTATCAT
271938 TATAAAATTTTTAAGAATTGAGGATGATCAATAATTATTTTTTAAAAGAAAAAAATTGTTTTTAA
66 TATAAAATTTTTAAGAATTGAGGATGATCAATAATTATTTTTTAAAAGAAAAAAATTGTTTTTAA
272003 AAGTTTTAGAATGAAAAGTAATGCCTAAAAATTATCTTTTAGAACTGTGTTTCTGACTAAAATGT
131 AAGTTTTAGAATGAAAAGTAATGCCTAAAAATTATCTTTTAGAACTGTGTTTCTGACTAAAATGT
*
272068 TTTGAGGACGATATTGTCTATAATACTGTTAAACTGGGGATAACATTTGCTCTCAACAACACCTA
196 TTTGAGGACGATATTATCTATAATACTGTTAAACTGGGGATAACATTTGCTCTCAACAACACCTA
272133 AGTTCAAGATAAAAGATATTTTTCTTAATCTGTCTATTTTTTGACCCTAAAGATCTCTTATTTTG
261 AGTTCAAGATAAAAGATATTTTTCTTAATCTGTCTATTTTTTGACCCTAAAGATCTCTTATTTTG
*
272198 TAATGTATCACTTAAAATTAAACTTTTATTTAATCACTAATCTCGAAAAAGAATTAATACTCATA
326 TAATGTATCACTTAAAATTAAACTTTTATTTAATCACTAATCTCGAAAAAGAATTAATACTCAAA
272263 CTCATTATATTATAACATAACATCCTCAAAGTGTTTATATGAGTTGAATTTGATTGATTGTTAAG
391 CTCATTATATTATAACATAACATCCTCAAAGTGTTTATATGAGTTGAATTTGATTGATTGTTAAG
272328 AAAAATTGTTACAGTTAGTAACATATTCATCAGATCCTATTTTATCTTCCTAGCATGAAATGTGG
456 AAAAATTGTTACAGTTAGTAACATATTCATCAGATCCTATTTTATCTTCCTAGCATGAAATGTGG
272393 ATTGCCTCT
521 ATTGCCTCT
272402 CATCTTTTTG
Statistics
Matches: 526, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
530 526 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (530 bp):
TCTAATATGTTTTTATTACATACGAATAAATTTAAGTTGGTCATTGAGTGACTAATAGGTATCAT
TATAAAATTTTTAAGAATTGAGGATGATCAATAATTATTTTTTAAAAGAAAAAAATTGTTTTTAA
AAGTTTTAGAATGAAAAGTAATGCCTAAAAATTATCTTTTAGAACTGTGTTTCTGACTAAAATGT
TTTGAGGACGATATTATCTATAATACTGTTAAACTGGGGATAACATTTGCTCTCAACAACACCTA
AGTTCAAGATAAAAGATATTTTTCTTAATCTGTCTATTTTTTGACCCTAAAGATCTCTTATTTTG
TAATGTATCACTTAAAATTAAACTTTTATTTAATCACTAATCTCGAAAAAGAATTAATACTCAAA
CTCATTATATTATAACATAACATCCTCAAAGTGTTTATATGAGTTGAATTTGATTGATTGTTAAG
AAAAATTGTTACAGTTAGTAACATATTCATCAGATCCTATTTTATCTTCCTAGCATGAAATGTGG
ATTGCCTCTT
Found at i:275450 original size:28 final size:28
Alignment explanation
Indices: 275417--275472 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
275407 TGATTCAATT
275417 AGAATTTACGTGTGATGTGATGTTAGTC
1 AGAATTTACGTGTGATGTGATGTTAGTC
275445 AGAATTTACGTGTGATGTGATGTTAGTC
1 AGAATTTACGTGTGATGTGATGTTAGTC
275473 CACTTAACGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.29, T:0.39
Consensus pattern (28 bp):
AGAATTTACGTGTGATGTGATGTTAGTC
Found at i:275848 original size:69 final size:69
Alignment explanation
Indices: 275766--275905 Score: 228
Period size: 69 Copynumber: 2.0 Consensus size: 69
275756 ACGACAGTCT
*
275766 CAGATACATGTCTTCAAAGCTTGCGGT-TTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
1 CAGATACATGTCTTCAAAGCCTG-GGTGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
275830 GTTCC
65 GTTCC
* * *
275835 CAGATATATGTCTTCAAAGCCTGTGTGTTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTG
1 CAGATACATGTCTTCAAAGCCTGGGTGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
275900 TTCC
66 TTCC
275904 CA
1 CA
275906 ACGTCTGTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
68 2 0.03
69 64 0.97
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (69 bp):
CAGATACATGTCTTCAAAGCCTGGGTGTTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
TTCC
Found at i:276034 original size:231 final size:231
Alignment explanation
Indices: 275631--276067 Score: 786
Period size: 231 Copynumber: 1.9 Consensus size: 231
275621 AGTGTGAAGT
* *
275631 TTGTAGAGATAGACAGCTGTAATAATTTGAAATGTCTGTTCCCAACTTCTGTTGCTAATAGCCTT
1 TTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTT
275696 GGGCATCTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGAC
66 GGGCATCTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGAC
* *
275761 AGTCTCAGATACATGTCTTCAAAGCTTGCGGTTTGTAGAGATAGACAGCTGTAATAATTTGAAAT
131 AGTCTCAGATACATGTCTTCAAAGATTGCGGTCTGTAGAGATAGACAGCTGTAATAATTTGAAAT
275826 ATCTGTTCCCAGATATATGTCTTCAAAGCCTGTGTG
196 ATCTGTTCCCAGATATATGTCTTCAAAGCCTGTGTG
275862 TTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTT
1 TTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTT
*
275927 GGGCAAT-TGGAAATACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGA
66 GGGC-ATCTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGA
* **
275991 CAGTCTCTGATACATGTCTTCAAAGATTGTTGTCTGTAGAGATAGACAGCTGTAATAATTTGAAA
130 CAGTCTCAGATACATGTCTTCAAAGATTGCGGTCTGTAGAGATAGACAGCTGTAATAATTTGAAA
276056 TATCTGTTCCCA
195 TATCTGTTCCCA
276068 ACGTCTGTTG
Statistics
Matches: 197, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
231 195 0.99
232 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (231 bp):
TTGTAGAGATAGACAGCTGTAATAATTTGAAATCTCTGTTCCCAACGTCTGTTGCTAATAGCCTT
GGGCATCTGGAAAGACTGAAGATAAAGAGCTGTTTGGGATTGGAAGAAATAATCCAAGCAACGAC
AGTCTCAGATACATGTCTTCAAAGATTGCGGTCTGTAGAGATAGACAGCTGTAATAATTTGAAAT
ATCTGTTCCCAGATATATGTCTTCAAAGCCTGTGTG
Found at i:276114 original size:162 final size:162
Alignment explanation
Indices: 275835--276312 Score: 807
Period size: 162 Copynumber: 3.0 Consensus size: 162
275825 TATCTGTTCC
* ** *
275835 CAGATATATGTCTTCAAAGCCTGTGTGT-TGTAGAGATAGACAGCTGTAATAATTTGAAATCTCT
1 CAGATACATGTCTTCAAAGATTGT-TGTCTGTAGAGATAGACAGCTGTAATAATTTGAAATATCT
* * *
275899 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAATTGGAAATACTGAAGATAAAGAGCTGTTTGG
65 GTTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAACACTGGAGATAAAGAGCTGTTTGG
275964 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
130 GATTGGAAGAAATAATCCAAGCAACGACAGTCT
*
275997 CTGATACATGTCTTCAAAGATTGTTGTCTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
1 CAGATACATGTCTTCAAAGATTGTTGTCTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
* * *
276062 TTCCCAACGTCTGTTGCTAATAGCCTTGGGCGACTGGGAAGACTGGAGATAAAGAGCTGTTTGGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAACACTGGAGATAAAGAGCTGTTTGGG
276127 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
131 ATTGGAAGAAATAATCCAAGCAACGACAGTCT
*
276159 CAGATACATGTCTTCAAAGATTGTGGTCTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
1 CAGATACATGTCTTCAAAGATTGTTGTCTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
276224 TTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAACACT-GACGATAAAGAGCTGTTTGG
66 TTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAACACTGGA-GATAAAGAGCTGTTTGG
*
276288 GATTGGAAGTAATAATCCAAGCAAC
130 GATTGGAAGAAATAATCCAAGCAAC
276313 AGAAGTGCCC
Statistics
Matches: 298, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
161 5 0.02
162 293 0.98
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (162 bp):
CAGATACATGTCTTCAAAGATTGTTGTCTGTAGAGATAGACAGCTGTAATAATTTGAAATATCTG
TTCCCAACGTCTGTTGCTAATAGCCTTGGGCAACTGGAAACACTGGAGATAAAGAGCTGTTTGGG
ATTGGAAGAAATAATCCAAGCAACGACAGTCT
Found at i:281523 original size:202 final size:201
Alignment explanation
Indices: 281177--281552 Score: 619
Period size: 202 Copynumber: 1.9 Consensus size: 201
281167 AAGAAATAAA
* * *
281177 GAGAAGTTGAGATTTGAATCTTAAACCTTAATATGAGAGATGAAAATTAAAATCAAACTTGAAAG
1 GAGAAGTTGAGATTTCAATCTTAAACCTTAATATGAGAGATAAAAAATAAAATCAAACTTGAAAG
* * *
281242 TTAGGGTGCTGGGTTCAAAATTAAATGTGCTACTATTAGTACTTGAAGCTGCTTCAAGTTGTCCA
66 TCAGGATGCTGGGTTCAAAATTAAATGTGCTACTATTAGTACTTGAAGCTGCTTCAACTTGTCCA
*
281307 TTGATAGAATGAATGGGTGGGTATTTGCTGTGAATAAAGGGACCTAGAGCATTGTCTAGAGAGAA
131 TTGATAGAATGAATGGGTGGGTATCTGCTGTGAATAAA-GGACCTAGAGCATTGTCTAGAGAGAA
281372 GGGATAT
195 GGGATAT
* *
281379 GAGAAGTTGAGATTTCAATTTTAAACCTTAATATGAGAGATAAAAAATAAAATCAAATTTGAAAG
1 GAGAAGTTGAGATTTCAATCTTAAACCTTAATATGAGAGATAAAAAATAAAATCAAACTTGAAAG
*
281444 TCAGGATGCTGGGTTCAAAATTAAATGTGCTACTATT-GTTACTTGTAGCTGCTTCAACTTGTCC
66 TCAGGATGCTGGGTTCAAAATTAAATGTGCTACTATTAG-TACTTGAAGCTGCTTCAACTTGTCC
* *
281508 ATTGATAGAATGAATGGGTGGGTATCTGTTGTGAATAGAGGACCT
130 ATTGATAGAATGAATGGGTGGGTATCTGCTGTGAATAAAGGACCT
281553 GGAGAGAGAA
Statistics
Matches: 161, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
201 7 0.04
202 154 0.96
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (201 bp):
GAGAAGTTGAGATTTCAATCTTAAACCTTAATATGAGAGATAAAAAATAAAATCAAACTTGAAAG
TCAGGATGCTGGGTTCAAAATTAAATGTGCTACTATTAGTACTTGAAGCTGCTTCAACTTGTCCA
TTGATAGAATGAATGGGTGGGTATCTGCTGTGAATAAAGGACCTAGAGCATTGTCTAGAGAGAAG
GGATAT
Found at i:282802 original size:2 final size:2
Alignment explanation
Indices: 282795--282826 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
282785 ACCAGCTTCC
*
282795 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
282827 GGTAAGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:283484 original size:15 final size:14
Alignment explanation
Indices: 283465--283501 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
283455 GAAAGATAGG
283465 AGAAAAAAAGAAAA
1 AGAAAAAAAGAAAA
*
283479 AGGAAAGAAAGAAAA
1 A-GAAAAAAAGAAAA
283494 AGAAAAAA
1 AGAAAAAA
283502 TATATGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAAAAGAAAA
Found at i:283487 original size:19 final size:18
Alignment explanation
Indices: 283447--283500 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
283437 AATAGAGCTA
283447 AAAAAAAAGAAAGATAGGAG
1 AAAAAAAAGAAA-A-AGGAG
283467 -AAAAAAAGAAAAAGGAAAG
1 AAAAAAAAGAAAAAGG--AG
283486 AAAGAAAAAGAAAAA
1 AAA-AAAAAGAAAAA
283501 ATATATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.10
18 1 0.03
19 13 0.43
20 2 0.07
21 11 0.37
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (18 bp):
AAAAAAAAGAAAAAGGAG
Found at i:290533 original size:16 final size:16
Alignment explanation
Indices: 290500--290533 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
290490 AATATAACAT
*
290500 AAATAAAATTATTAAA
1 AAATAAAATAATTAAA
290516 AAATAAAATAATATAAA
1 AAATAAAATAAT-TAAA
290533 A
1 A
290534 TATTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAAAATAATTAAA
Found at i:291479 original size:23 final size:23
Alignment explanation
Indices: 291452--291499 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
291442 AATTTTTGAG
291452 TTAATATT-AAATATTAACCCACC
1 TTAATATTCAAATATTAA-CCACC
* *
291475 TTAATTTTCAAATTTTAACCACC
1 TTAATATTCAAATATTAACCACC
291498 TT
1 TT
291500 GAGTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.42
Consensus pattern (23 bp):
TTAATATTCAAATATTAACCACC
Found at i:291645 original size:26 final size:26
Alignment explanation
Indices: 291599--291650 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
291589 TAATTTAAAT
* *
291599 ATTACACTAGGAATACTTCAAAAAAA
1 ATTACACTAGGAAAACATCAAAAAAA
* *
291625 ATTACACTAGGAAAAGATCAATAAAA
1 ATTACACTAGGAAAACATCAAAAAAA
291651 TGAATGAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (26 bp):
ATTACACTAGGAAAACATCAAAAAAA
Found at i:292072 original size:19 final size:19
Alignment explanation
Indices: 292028--292075 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
292018 TAATAAAAAA
*
292028 TATTTTATA-TTTAAAATT
1 TATTTTAAATTTTAAAATT
*
292046 TATTTTTAAATTTTTAAATT
1 TA-TTTTAAATTTTAAAATT
292066 TATTTTAAAT
1 TATTTTAAAT
292076 AATAATATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 10 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTAAATTTTAAAATT
Found at i:292614 original size:2 final size:2
Alignment explanation
Indices: 292607--292652 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
292597 AATTATCATT
* * * *
292607 TA TA TA TA CA TA GA CA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
292649 TA TA
1 TA TA
292653 CGTATTGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:294411 original size:24 final size:24
Alignment explanation
Indices: 294374--294423 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
294364 TATAAGTGCA
* *
294374 TTTTTTTCTGATAAAGTGAGTAGT
1 TTTTTTTCTAATAAAGTGAATAGT
*
294398 TTTTTTTTTAATAAAGTGAATAGT
1 TTTTTTTCTAATAAAGTGAATAGT
294422 TT
1 TT
294424 CTTTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.16, T:0.54
Consensus pattern (24 bp):
TTTTTTTCTAATAAAGTGAATAGT
Found at i:294434 original size:24 final size:24
Alignment explanation
Indices: 294384--294436 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
294374 TTTTTTTCTG
* * ***
294384 ATAAAGTGAGTAGTTTTTTTTTTA
1 ATAAAGTGAATAGTTTCTTTAAAA
294408 ATAAAGTGAATAGTTTCTTTAAAA
1 ATAAAGTGAATAGTTTCTTTAAAA
294432 ATAAA
1 ATAAA
294437 TAGGTTTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.43
Consensus pattern (24 bp):
ATAAAGTGAATAGTTTCTTTAAAA
Found at i:295300 original size:22 final size:24
Alignment explanation
Indices: 295248--295314 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 24
295238 AAAATATTTT
* *
295248 AATTTCATATTAAATGATATTTTTAT
1 AATTTCATATTTAA--ATATTTTTAA
*
295274 TATTT-AT-TTTAAATATTTTTAA
1 AATTTCATATTTAAATATTTTTAA
*
295296 AATTTCATATTTATATATT
1 AATTTCATATTTAAATATT
295315 AATAAGGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
22 13 0.38
23 2 0.06
24 13 0.38
25 2 0.06
26 4 0.12
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (24 bp):
AATTTCATATTTAAATATTTTTAA
Found at i:299162 original size:149 final size:149
Alignment explanation
Indices: 298872--299178 Score: 460
Period size: 149 Copynumber: 2.1 Consensus size: 149
298862 TTTGACATAG
*
298872 TTTTAGTTAAAAAGTACATTTATTTATGAACAAAATATTAAATAAGTAAATAAATTATTTTTACG
1 TTTTAGTTAAAAAGTACATTTATTTACGAACAAAATATTAAATAAGTAAATAAATTA-TTTTACG
* *
298937 ATTAAATAATAATTTAATAATTTAAATCATAAAATTAAAAAATTAAAGTTTTTATAATTTAAAAA
65 ATTAAATAATAATTTAACAATTTAAATCATAAAATTAAAAAATTAAAGCTTTTATAATTTAAAAA
* *
299002 TTGACTTTTAAATAAAATAA
130 CTAACTTTTAAATAAAATAA
* *
299022 TTTTAGTTAAAAAGTACATTTCA-TTACGGATAAAATATTAAATAAGTAAATAAATTA-TTTACG
1 TTTTAGTTAAAAAGTACATTT-ATTTACGAACAAAATATTAAATAAGTAAATAAATTATTTTACG
* * *
299085 GTTAAAATAATAATTTAACAATTTAAATTATAAAGTTAAAAAAATTAAA-CTTTTATAATTTAAA
65 ATT-AAATAATAATTTAACAATTTAAATCATAAAATT-AAAAAATTAAAGCTTTTATAATTTAAA
299149 AACTAACTTTTAAATAAAATAA
128 AACTAACTTTTAAATAAAATAA
299171 TTTT-GTTA
1 TTTTAGTTA
299179 TTCTCGTATC
Statistics
Matches: 144, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
148 12 0.08
149 68 0.47
150 63 0.44
151 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.40
Consensus pattern (149 bp):
TTTTAGTTAAAAAGTACATTTATTTACGAACAAAATATTAAATAAGTAAATAAATTATTTTACGA
TTAAATAATAATTTAACAATTTAAATCATAAAATTAAAAAATTAAAGCTTTTATAATTTAAAAAC
TAACTTTTAAATAAAATAA
Found at i:301560 original size:17 final size:18
Alignment explanation
Indices: 301527--301560 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
301517 AATATAATTT
*
301527 TTTAAATACATAATAAAA
1 TTTAAATACAAAATAAAA
301545 TTTAAATA-AAAATAAA
1 TTTAAATACAAAATAAA
301561 TATATTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
TTTAAATACAAAATAAAA
Found at i:304481 original size:13 final size:13
Alignment explanation
Indices: 304463--304489 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
304453 GTCCCTTTTA
304463 ATTGTACAGTTAT
1 ATTGTACAGTTAT
304476 ATTGTACAGTTAT
1 ATTGTACAGTTAT
304489 A
1 A
304490 CTATAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
ATTGTACAGTTAT
Found at i:306082 original size:39 final size:40
Alignment explanation
Indices: 306024--306111 Score: 115
Period size: 39 Copynumber: 2.2 Consensus size: 40
306014 GAACATTTAA
* *
306024 TATTAAATGAAATAAATATAATAAAAATAATATGAATAAAT
1 TATTAAAT-ACATAAATATAATAAAAATAATATAAATAAAT
* * *
306065 TA-TAAATACATAAATATATTAAAATTTATATAAATAAAT
1 TATTAAATACATAAATATAATAAAAATAATATAAATAAAT
306104 TATTAAAT
1 TATTAAAT
306112 TATTAAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 29 0.71
40 10 0.24
41 2 0.05
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.36
Consensus pattern (40 bp):
TATTAAATACATAAATATAATAAAAATAATATAAATAAAT
Found at i:306087 original size:24 final size:23
Alignment explanation
Indices: 306060--306119 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
306050 ATAATATGAA
*
306060 TAAATTATAAATACATAAATATAT
1 TAAATTATAAATAAATAAAT-TAT
*
306084 TAAAATT-TATATAAATAAATTAT
1 T-AAATTATAAATAAATAAATTAT
306107 TAAATTATTAAAT
1 TAAATTA-TAAAT
306120 TTTATATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 5 0.17
23 4 0.13
24 16 0.53
25 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAAATTATAAATAAATAAATTAT
Found at i:311006 original size:2 final size:2
Alignment explanation
Indices: 310999--311029 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
310989 ACCTAATGGG
310999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
311030 TAATATTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:312991 original size:118 final size:115
Alignment explanation
Indices: 312865--313101 Score: 296
Period size: 117 Copynumber: 2.0 Consensus size: 115
312855 TATTATATTT
* * * * ** *
312865 TTAGTAATTTAATCATTTAAATTATATTAAAAAGAATTAAAATGAAATT-CAAAACTAATTAATG
1 TTAGTAATTTAACCATTTAAACTACATTAAAAAG--TTAAAATGAAATTAAAAAAC-AACAAATA
* * *
312929 AAATTATTATATTCTATTAAATTTAATAAATAAGACTGAAATAAAATTAATATA
63 AAATTAATATATTATATTAAATTTAATAAATAAGAATGAAAT-AAATTAATATA
312983 TTAGTAATTTAACCATTTAAACTACATTAAAAAGTTAAAATGAAATTAAAAAAACAACAAATAAA
1 TTAGTAATTTAACCATTTAAACTACATTAAAAAGTTAAAATGAAATT-AAAAAACAACAAATAAA
* * * *
313048 ATTAATATATTATGTTAAATTTAATGATTAAGAATGAGATAAATTAATATA
65 ATTAATATATTATATTAAATTTAATAAATAAGAATGAAATAAATTAATATA
313099 TTA
1 TTA
313102 TATTAAACAT
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
116 27 0.26
117 40 0.39
118 36 0.35
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (115 bp):
TTAGTAATTTAACCATTTAAACTACATTAAAAAGTTAAAATGAAATTAAAAAACAACAAATAAAA
TTAATATATTATATTAAATTTAATAAATAAGAATGAAATAAATTAATATA
Found at i:313280 original size:21 final size:22
Alignment explanation
Indices: 313243--313283 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
313233 AAAGTCTATT
313243 AAAAAGAATTAACATGAAATTC
1 AAAAAGAATTAACATGAAATTC
313265 AAAAAGCAA-TAA-ATGAAAT
1 AAAAAG-AATTAACATGAAAT
313284 AAAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 9 0.50
23 2 0.11
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (22 bp):
AAAAAGAATTAACATGAAATTC
Found at i:313536 original size:2 final size:2
Alignment explanation
Indices: 313529--313559 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
313519 AATTGTATTT
313529 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
313560 GATAAGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:314665 original size:11 final size:11
Alignment explanation
Indices: 314649--314677 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
314639 GTTAGTAAAT
314649 TTATTATTATA
1 TTATTATTATA
314660 TTATTATTATA
1 TTATTATTATA
314671 TTATTAT
1 TTATTAT
314678 ATTATCTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTATTATA
Found at i:315054 original size:16 final size:17
Alignment explanation
Indices: 315002--315052 Score: 79
Period size: 16 Copynumber: 3.1 Consensus size: 17
314992 TTTTAATAAT
315002 AAATAAATA-TTAAATA
1 AAATAAATATTTAAATA
315018 AAATAAATATTT-AATA
1 AAATAAATATTTAAATA
*
315034 AAATATATATTTAAATA
1 AAATAAATATTTAAATA
315051 AA
1 AA
315053 TAATATGATC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
16 24 0.75
17 8 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATAAATATTTAAATA
Found at i:316543 original size:20 final size:20
Alignment explanation
Indices: 316505--316543 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
316495 ATTTAAACTA
* **
316505 TAATTAAAAATTTTCATTAT
1 TAATTAAAAAATTAAATTAT
316525 TAATTAAAAAATTAAATTA
1 TAATTAAAAAATTAAATTA
316544 AGTTTTCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATTAAAAAATTAAATTAT
Found at i:317110 original size:25 final size:26
Alignment explanation
Indices: 317082--317136 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 26
317072 AATATGACAG
*
317082 TAAAATATAAA-TCATTTAATTT-AT
1 TAAAATATAAATTCATTCAATTTAAT
* * *
317106 TTAAATTTAAATTTATTCAATTTAAT
1 TAAAATATAAATTCATTCAATTTAAT
317132 TAAAA
1 TAAAA
317137 AATTAATAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 9 0.38
25 9 0.38
26 6 0.25
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TAAAATATAAATTCATTCAATTTAAT
Found at i:317154 original size:14 final size:15
Alignment explanation
Indices: 317135--317168 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
317125 ATTTAATTAA
*
317135 AAAATTAA-TAGTTT
1 AAAATTAATTAATTT
317149 AAAATTAATTAATTT
1 AAAATTAATTAATTT
317164 AAAAT
1 AAAAT
317169 ATTTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAATTAATTAATTT
Found at i:317185 original size:23 final size:25
Alignment explanation
Indices: 317129--317188 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 25
317119 TATTCAATTT
317129 AATTAAAAAA-TT--AATAGTTTAA
1 AATTAAAAAATTTAAAATAGTTTAA
**
317151 AATTAATTAATTTAAAATA-TTTAA
1 AATTAAAAAATTTAAAATAGTTTAA
317175 AA-TAAAAAATTTAA
1 AATTAAAAAATTTAA
317189 CTTGAAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 8 0.26
23 12 0.39
24 7 0.23
25 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AATTAAAAAATTTAAAATAGTTTAA
Found at i:317843 original size:13 final size:13
Alignment explanation
Indices: 317813--317866 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
317803 ACTTATATTT
*
317813 AAATAAACA-TAA
1 AAATAAATATTAA
317825 AAATAAATATTAA
1 AAATAAATATTAA
*
317838 ATATAAATATTTAAA
1 AAATAAATA-TT-AA
317853 AAATAAA-ATTAA
1 AAATAAATATTAA
317865 AA
1 AA
317867 TAACATCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
12 12 0.33
13 13 0.36
14 3 0.08
15 8 0.22
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAAATATTAA
Found at i:317866 original size:11 final size:12
Alignment explanation
Indices: 317807--317869 Score: 56
Period size: 12 Copynumber: 5.0 Consensus size: 12
317797 TTTTATACTT
*
317807 ATATTTAAATAA
1 ATATTAAAATAA
* *
317819 ACATAAAAATAA
1 ATATTAAAATAA
317831 ATATTAAATATAA
1 ATATTAAA-ATAA
317844 ATATTTAAAAAATAA
1 ATA-TT--AAAATAA
317859 A-ATTAAAATAA
1 ATATTAAAATAA
317870 CATCATTTGA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 7 0.17
12 15 0.36
13 9 0.21
14 3 0.07
15 5 0.12
16 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATTAAAATAA
Found at i:319802 original size:2 final size:2
Alignment explanation
Indices: 319797--319835 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
319787 AAAAAAAAAA
319797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
319836 GACTTGTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:319906 original size:2 final size:2
Alignment explanation
Indices: 319899--319927 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
319889 TTGAAGCTTG
319899 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
319928 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:319958 original size:2 final size:2
Alignment explanation
Indices: 319948--319986 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
319938 TATAAATATA
* * *
319948 TG TG CG TG TG TG TG TG TG TG TG TG GG TG TG GG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
319987 AGATGTCGAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.03, G:0.54, T:0.44
Consensus pattern (2 bp):
TG
Found at i:320429 original size:23 final size:22
Alignment explanation
Indices: 320386--320428 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
320376 TTATATAAAT
*
320386 TTTTAAAAAGATTGATCTTTTC
1 TTTTAAAAAAATTGATCTTTTC
*
320408 TTTTAAAAAAATTGATATTTT
1 TTTTAAAAAAATTGATCTTTT
320429 TTAAGAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTTAAAAAAATTGATCTTTTC
Found at i:327264 original size:22 final size:20
Alignment explanation
Indices: 327214--327266 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
327204 AATAAAAAAA
*
327214 ATATTATAAATTTTTAAATTT
1 ATATT-TAAATTTTTAAATTC
*
327235 AAACTTTAAATTTATTAAATATC
1 ATA-TTTAAATTT-TTAAAT-TC
327258 ATATTTAAA
1 ATATTTAAA
327267 AGTAATTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 9 0.35
22 14 0.54
23 3 0.12
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTTAAATTTTTAAATTC
Found at i:327917 original size:20 final size:21
Alignment explanation
Indices: 327894--327943 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
327884 TTAATTTTGT
327894 TTGAATTATTTTTTATTT-AA
1 TTGAATTATTTTTTATTTAAA
*
327914 TTGAAATATTTTTTATTTAAA
1 TTGAATTATTTTTTATTTAAA
*
327935 TTTAATTAT
1 TTGAATTAT
327944 AAATAGTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTGAATTATTTTTTATTTAAA
Found at i:328110 original size:15 final size:16
Alignment explanation
Indices: 328080--328112 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
328070 ATGTAGCTTC
*
328080 ATAAAACTTTTTAAAA
1 ATAAAACTTTTAAAAA
328096 ATAAAA-TTTTAAAAA
1 ATAAAACTTTTAAAAA
328111 AT
1 AT
328113 GATTGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAAACTTTTAAAAA
Found at i:328162 original size:21 final size:22
Alignment explanation
Indices: 328118--328168 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
328108 AAAATGATTG
* *
328118 TTAAAAATAATTTTTTATTTTT
1 TTAAAAATAATTTATTATTATT
*
328140 TTATAAATAA-TTATTATTATT
1 TTAAAAATAATTTATTATTATT
328161 TTAAAAAT
1 TTAAAAAT
328169 TTTTAAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAAAAATAATTTATTATTATT
Found at i:328415 original size:11 final size:11
Alignment explanation
Indices: 328375--328424 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
328365 TTTTAATAAA
328375 TTTATA-TATT
1 TTTATATTATT
328385 TTTATATTA-T
1 TTTATATTATT
*
328395 ATTATAATTATT
1 TTTAT-ATTATT
*
328407 TTTATATTATA
1 TTTATATTATT
328418 TTTATAT
1 TTTATAT
328425 AGAATAATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 11 0.32
11 18 0.53
12 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTTATATTATT
Found at i:331006 original size:23 final size:21
Alignment explanation
Indices: 330980--331036 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 21
330970 AATTTAAAAT
330980 TTTAAATAATAAAAAATTATTAA
1 TTTAAA-AATAAAAAA-TATTAA
*
331003 TTTATAAAATATATAAATATTAA
1 TTTA-AAAATA-AAAAATATTAA
*
331026 TATAAAAATAA
1 TTTAAAAATAA
331037 TTTTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 1 0.03
22 6 0.20
23 17 0.57
24 6 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTAAAAATAAAAAATATTAA
Found at i:332916 original size:20 final size:21
Alignment explanation
Indices: 332891--332942 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 21
332881 AATGATGACT
332891 TTTAAAAATAATTTTTCAT-C
1 TTTAAAAATAATTTTTCATAC
* *
332911 TTT-AAAAT-ATTTTTTATAT
1 TTTAAAAATAATTTTTCATAC
332930 TTTAAAAATAATT
1 TTTAAAAATAATT
332943 ATTAATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 8 0.30
21 3 0.11
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAAAAATAATTTTTCATAC
Found at i:332950 original size:19 final size:19
Alignment explanation
Indices: 332890--332951 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
332880 AAATGATGAC
*
332890 TTTTAAAAATAATTTTTCA
1 TTTTAAAAATAATTTTTAA
*
332909 TCTTT-AAAATATTTTTTATA
1 T-TTTAAAAATAATTTTTA-A
*
332929 TTTTAAAAATAATTATTAA
1 TTTTAAAAATAATTTTTAA
332948 TTTT
1 TTTT
332952 TTTTAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 20 0.56
20 16 0.44
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATAATTTTTAA
Found at i:332952 original size:20 final size:20
Alignment explanation
Indices: 332890--332952 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
332880 AAATGATGAC
*
332890 TTTTAAAAATAATTTTTCAT
1 TTTTAAAAATAATTTTTAAT
* *
332910 CTTT-AAAAT-ATTTTTTAT
1 TTTTAAAAATAATTTTTAAT
*
332928 ATTTTAAAAATAATTATTAAT
1 -TTTTAAAAATAATTTTTAAT
332949 TTTT
1 TTTT
332953 TTTAAATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 8 0.23
19 8 0.23
20 12 0.34
21 7 0.20
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTAAAAATAATTTTTAAT
Found at i:334333 original size:13 final size:13
Alignment explanation
Indices: 334317--334341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
334307 TTTTATTTAA
334317 AATATTTATATTT
1 AATATTTATATTT
334330 AATATTTATATT
1 AATATTTATATT
334342 CGATATATTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:335691 original size:2 final size:2
Alignment explanation
Indices: 335684--335721 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
335674 TAAACGACGC
*
335684 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
335722 AAATTAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:336363 original size:44 final size:44
Alignment explanation
Indices: 336263--336356 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
336253 AATAAATTTG
* *
336263 TGTTCAACATTTGTACCCAAATCTAAATAACATAAATATTAATAT
1 TGTT-AACATTTATGCCCAAATCTAAATAACATAAATATTAATAT
* *
336308 TGTTAACATTTATGCCCAAATCTAAGA-AACATAGATGTTAATAT
1 TGTTAACATTTATGCCCAAATCTAA-ATAACATAAATATTAATAT
336352 TGTTA
1 TGTTA
336357 CTATTTAACA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 39 0.89
45 5 0.11
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (44 bp):
TGTTAACATTTATGCCCAAATCTAAATAACATAAATATTAATAT
Found at i:339170 original size:27 final size:26
Alignment explanation
Indices: 339137--339188 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
339127 TATATTTTTT
*
339137 ATAATTAAATATTTTTACATTAAATAA
1 ATAATTAAATAATTTTA-ATTAAATAA
*
339164 ATAATTAAATAATTTTAATTTAATA
1 ATAATTAAATAATTTTAATTAAATA
339189 TATACAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
ATAATTAAATAATTTTAATTAAATAA
Found at i:340843 original size:6 final size:6
Alignment explanation
Indices: 340829--340899 Score: 88
Period size: 6 Copynumber: 11.8 Consensus size: 6
340819 TCAAGGAAAA
* * * *
340829 CTCCTG CTCCGG CTCCAG CTCCAG CTCCAG CTCCAG CTCCCG CTCCCG
1 CTCCAG CTCCAG CTCCAG CTCCAG CTCCAG CTCCAG CTCCAG CTCCAG
* *
340877 CTCCGG CTCCAG CTTCAG CTCCA
1 CTCCAG CTCCAG CTCCAG CTCCA
340900 TTTCAAGCTC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.10, C:0.52, G:0.18, T:0.20
Consensus pattern (6 bp):
CTCCAG
Found at i:344309 original size:21 final size:21
Alignment explanation
Indices: 344284--344335 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
344274 ATAAATTATT
344284 TATATATTATATAA-TATAAA
1 TATATATTATATAATTATAAA
*
344304 TGATATATTATATAATTTTAAA
1 T-ATATATTATATAATTATAAA
344326 T-TATATTATA
1 TATATATTATA
344336 AAACATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 10 0.34
21 13 0.45
22 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TATATATTATATAATTATAAA
Done.