Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008193.1 Hibiscus syriacus cultivar Beakdansim tig00110812_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1025831
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 5
Found at i:366039 original size:28 final size:31
Alignment explanation
Indices: 366008--366070 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 31
365998 TTAAAAATTT
*
366008 TATTTTCATGTTTAT-T-ATTTAAAAA-AAA
1 TATTTTCATGTTTATATCAATTAAAAATAAA
*
366036 TATTTTCTTGTTTATATCAATTAAAAATAAA
1 TATTTTCATGTTTATATCAATTAAAAATAAA
366067 TATT
1 TATT
366071 AAAAATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 14 0.47
29 1 0.03
30 8 0.27
31 7 0.23
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (31 bp):
TATTTTCATGTTTATATCAATTAAAAATAAA
Found at i:371044 original size:2 final size:2
Alignment explanation
Indices: 371039--371066 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
371029 TTAAATTACA
371039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
371067 TAATAAGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:372770 original size:70 final size:71
Alignment explanation
Indices: 372656--372796 Score: 234
Period size: 70 Copynumber: 2.0 Consensus size: 71
372646 TTTTGGTCTT
*
372656 TTCCTTATCCAAGTCAAAGAAAGCAAGTAAATTAATTTCATAAGGCTCACATGA-TTATTATTCT
1 TTCCTTATCCAAGTCAAAGAAAGCAAATAAATTAATTTCATAAGG-TCACATGATTTA-TATTCT
372720 TGT-GTTA
64 TGTAGTTA
372727 TTCCTTATCCAAGTC-AAGAAAGCAAATAAATTAATTTCATAAGGTCACATGATTTATATTCTTG
1 TTCCTTATCCAAGTCAAAGAAAGCAAATAAATTAATTTCATAAGGTCACATGATTTATATTCTTG
372791 TAGTTA
66 TAGTTA
372797 ATTATTTCAC
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
69 17 0.25
70 35 0.52
71 15 0.22
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (71 bp):
TTCCTTATCCAAGTCAAAGAAAGCAAATAAATTAATTTCATAAGGTCACATGATTTATATTCTTG
TAGTTA
Found at i:377599 original size:58 final size:61
Alignment explanation
Indices: 377529--377644 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 61
377519 CCACTCAACT
377529 ATTTAAATGTATTC-A-TAAGTCACTAACCGTTAATATTTAATGG-AAAACTGATGTGTGC
1 ATTTAAATGTATTCAATTAAGTCACTAACCGTTAATATTTAATGGAAAAACTGATGTGTGC
377587 ATTTAAATGTATTCAATTAAGTCACTAACCGTTAATATTTAATGGAAAAACTGATGTG
1 ATTTAAATGTATTCAATTAAGTCACTAACCGTTAATATTTAATGGAAAAACTGATGTG
377645 CAGTTTGGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
58 14 0.25
59 1 0.02
60 28 0.51
61 12 0.22
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (61 bp):
ATTTAAATGTATTCAATTAAGTCACTAACCGTTAATATTTAATGGAAAAACTGATGTGTGC
Found at i:378844 original size:2 final size:2
Alignment explanation
Indices: 378837--378868 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
378827 ATAACACTAA
378837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
378869 TTAGAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:379059 original size:38 final size:39
Alignment explanation
Indices: 378987--379063 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
378977 TTATTAAAAT
378987 AATATTCAAAATATCAAAAAAAATTAATTATGATTCAAA
1 AATATTCAAAATATCAAAAAAAATTAATTATGATTCAAA
379026 AATATTCAAAATATCAAAAAAAATTAATT-TGATTCAAA
1 AATATTCAAAATATCAAAAAAAATTAATTATGATTCAAA
379064 TCATTTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 9 0.24
39 29 0.76
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (39 bp):
AATATTCAAAATATCAAAAAAAATTAATTATGATTCAAA
Found at i:386116 original size:18 final size:18
Alignment explanation
Indices: 386081--386131 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
386071 TCTTTATTCT
* *
386081 CTTTTTTTTACTTAAATTA
1 CTTTTATTTA-TTTAATTA
*
386100 CTTTTATTTATTTAATTG
1 CTTTTATTTATTTAATTA
386118 CTTTTA-TTATTTAA
1 CTTTTATTTATTTAA
386132 ATATATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 8 0.28
18 12 0.41
19 9 0.31
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (18 bp):
CTTTTATTTATTTAATTA
Found at i:386219 original size:626 final size:624
Alignment explanation
Indices: 385094--386327 Score: 2083
Period size: 626 Copynumber: 2.0 Consensus size: 624
385084 ACATGTGGGA
** *
385094 GGAAGATTCGGCTTATTGAAAACACATTCGACTTCCTGGGAACACACTTGATGAGATAGCTTCGC
1 GGAAGATTCGGCTTATTGAAAACACATTCGACTTCCTGGGAACACACTTGACAAGATAACTTCGC
* * * * *
385159 CAAGAGAGATTTTAGATCGGAATTGACGGTTATATAAGAAACAATCTGAGTCGGTCGCCACAAAT
66 CAAGAGAGATATGAGATCGGAATTGACGGTTATAGAAGAAACAATCCGAGTCGGACGCCACAAAT
* * *
385224 TTAAACGGTAATTGATCTACGACAATTGATGTTGTTAGAATCAATTTTCGAAGCCGGAATCAAAG
131 TTAAACGGTAAATGATCTACGAAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAG
*
385289 ATTGCCTTGGGTATTCGGTACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCTAC
196 ATTGCCTTGGGTATTCGGTACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCGAC
*
385354 GTGAATCCCGAAGGGAAAATCTAATTCGATGATCAAAGGGGAATTGAGTCAAAGCAAGGCTTGAG
261 GTGAATCCCGAAGGGAAAATCTAATTCGATGATCAAAGGGGAATTAAGTCAAAGCAAGGCTTGAG
* * *
385419 GTTACTTTTACCGTATTTATTCAGAATCTTTATTCTCTTATTTTTACTTAAATTGCTTTTATTTA
326 GCTACTTTTACCGTATTTATTCACAATCTTTATTCTCTTATTTTTACTTAAATTACTTTTATTTA
* *
385484 TTTAATCACTTTTATTATTTAAATATCTATTTACCAAACCCCCCCATTTACTATTTTTACGCCTC
391 TTTAATCACTTTTATTATTTAAATATATATTTACCAAACCCCCCCATTTACTATTTTCACGCCTC
385549 GAGTAAACCAATCAGACATAAATTAAGAATTTTCTAAGCCCTGTGGATTCGACCCTTACTTCTCT
456 GAGTAAACCAATCAGACATAAATTAAGAATTTTCTAAGCCCTGTGGATTCGACCCTTACTTCTCT
* * * *
385614 ATACTGCGAATTTCCTTATTTATTATCCGAGAATAAGAAATTTTATTTTGACATCGAAATGATAG
521 ATACTACGAATTTCCTTATTTATTATCCAAGAAGAAGAAATTTTATTTTGACATCGAAATGACAG
* *
385679 TTGTCAAATTGATGTCGTTGCCGGGGAGATAATCAAATT
586 TTGTCAAATTGACGCCGTTGCCGGGGAGATAATCAAATT
* *
385718 GGAAGATTTGGCTTATTGAAAACACATTCGACTTCCTGGGAACACACTTGGCAAGATAACTTCGC
1 GGAAGATTCGGCTTATTGAAAACACATTCGACTTCCTGGGAACACACTTGACAAGATAACTTCGC
* * *
385783 CAAGAGGGATATGAGATCGGAATTGACGGTTATAGAAGCAACAATCCGAGTCGGACGCCACGAAT
66 CAAGAGAGATATGAGATCGGAATTGACGGTTATAGAAGAAACAATCCGAGTCGGACGCCACAAAT
385848 TTAAACGGTAAATGATCTACGAAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAG
131 TTAAACGGTAAATGATCTACGAAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAG
385913 ATTGCCTTGGGTATTCGGTATACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCG
196 ATTGCCTTGGGTATTCGG--TACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCG
* * *
385978 ACGTGAATCCTGGAGGGAAAATCTAATTCGATGATCAAAGGGGAATTAAGTTAAAGCAAGGCTTG
259 ACGTGAATCCCGAAGGGAAAATCTAATTCGATGATCAAAGGGGAATTAAGTCAAAGCAAGGCTTG
*
386043 AGGCTACTTTTACCGTATTTATTCACAATCTTTATTCTCTTTTTTTTACTTAAATTACTTTTATT
324 AGGCTACTTTTACCGTATTTATTCACAATCTTTATTCTCTTATTTTTACTTAAATTACTTTTATT
** * *
386108 TATTTAATTGCTTTTATTATTTAAATATATATTTACCAAA-CTCCCCGTTTACTATTTTCACGCC
389 TATTTAATCACTTTTATTATTTAAATATATATTTACCAAACCCCCCCATTTACTATTTTCACGCC
*
386172 TGGAGTAAACCAATCAGACATAAATTAAGAATTTTCTAAGTCCCTGTGGATTCGACCCTTACTTC
454 TCGAGTAAACCAATCAGACATAAATTAAGAATTTTCTAAG-CCCTGTGGATTCGACCCTTACTTC
*
386237 TCTATACTACGAATTTCCTTATTTATTATCCAAGAAGAAGGAATTTTATTTTGACATCGAAATGA
518 TCTATACTACGAATTTCCTTATTTATTATCCAAGAAGAAGAAATTTTATTTTGACATCGAAATGA
386302 CAGTTGTCAAATTGACGCCGTTGCCG
583 CAGTTGTCAAATTGACGCCGTTGCCG
386328 AGACTTCGCC
Statistics
Matches: 568, Mismatches: 39, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
624 197 0.35
625 60 0.11
626 311 0.55
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (624 bp):
GGAAGATTCGGCTTATTGAAAACACATTCGACTTCCTGGGAACACACTTGACAAGATAACTTCGC
CAAGAGAGATATGAGATCGGAATTGACGGTTATAGAAGAAACAATCCGAGTCGGACGCCACAAAT
TTAAACGGTAAATGATCTACGAAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAG
ATTGCCTTGGGTATTCGGTACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCGAC
GTGAATCCCGAAGGGAAAATCTAATTCGATGATCAAAGGGGAATTAAGTCAAAGCAAGGCTTGAG
GCTACTTTTACCGTATTTATTCACAATCTTTATTCTCTTATTTTTACTTAAATTACTTTTATTTA
TTTAATCACTTTTATTATTTAAATATATATTTACCAAACCCCCCCATTTACTATTTTCACGCCTC
GAGTAAACCAATCAGACATAAATTAAGAATTTTCTAAGCCCTGTGGATTCGACCCTTACTTCTCT
ATACTACGAATTTCCTTATTTATTATCCAAGAAGAAGAAATTTTATTTTGACATCGAAATGACAG
TTGTCAAATTGACGCCGTTGCCGGGGAGATAATCAAATT
Found at i:388567 original size:17 final size:17
Alignment explanation
Indices: 388547--388581 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
388537 ATAAAAAAAA
388547 TCTAAAAAACTAAAATC
1 TCTAAAAAACTAAAATC
*
388564 TCTAAAAATCTAAAATC
1 TCTAAAAAACTAAAATC
388581 T
1 T
388582 GTTATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (17 bp):
TCTAAAAAACTAAAATC
Found at i:401140 original size:617 final size:613
Alignment explanation
Indices: 400179--401362 Score: 1973
Period size: 617 Copynumber: 1.9 Consensus size: 613
400169 TATTGAAAGC
* * *
400179 ACATTCGACTTCCTGGGAACACACTTGATGAGAAGCTTCGCCAAGAGGGATTTTAGATCGGAATT
1 ACATTCGACTTCCTGGGAACACACTTGAAGAGAAGCTTCGCCAAGAGGGATATGAGATCGGAATT
* * * *
400244 GACGGTTATATAAGAAACAATCTGAGTCGGTCGCCACAAATTTAAACGGTAATTGATCTACGACA
66 GACGGTTATAGAAGAAACAATCCGAGTCGGTCGCCACAAATTTAAACGGTAAATGATCTACGAAA
*
400309 ATTGATGTTGTTAGAATCAATTTTCGAAGCCGGAATCAAAGATTGCCTTGGGTATTCGGTACAAG
131 ATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAGATTGCCTTGGGTATTCGGTACAAG
*
400374 ATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCTACGTGAATCCCGAAGGGAAAATCTAA
196 ATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCGACGTGAATCCCGAAGGGAAAATCTAA
* * *
400439 TTCAATGATCAAAGGGGAATTGAGTCAAAGCAAGGCTTGAGGTTACTTTTACCGTATTTATTCAG
261 TTCAATGATCAAAGGGGAATTAAGTCAAAGCAAGGCTTGAGGCTACTTTTACCGTATTTATTCAC
*
400504 AATCTTTATTCTCTTA-TTTTACTTAAATTGCTTTTATTTATTTAATCACTTTTATTATTTAAAT
326 AATCTTTATTCTCTTATTTTTACTTAAATTACTTTTATTTATTTAATCACTTTTATTATTTAAAT
* *
400568 ATCTATTTACCAAACCCCCCATTTACTATTTTTACGCCTCGAGTAAACCAATCAGACATAAATTA
391 ATATATTTACCAAACCCCCCATTTACTATTTTCACGCCTCGAGTAAACCAATCA-ACATAAATTA
* *
400633 AGAATTTTCTAAG-CCCTGTGGATTCGACCCTTACTTCTCTATACTGCGAATTTCCTTATTTATT
455 AGAATTTTCTAAGTCCCTCTGGATTCGA-CCTTACTTCTCTATACTACGAATTTCCTTATTTATT
* *
400697 ATCCGAGAATAAGGAATTTTATTTTGACATCGAAA-GATAGTTGTCAAATTGATGTCGTTGCCGG
519 ATCC--GAAGAAGGAATTTTATTTTGACATCGAAATGACAGTTGTCAAATTGATGTCGTTGCCGG
400761 GGAGATAATCAAATTGGAAGATTCTTATTGAA
582 GGAGATAATCAAATTGGAAGATTCTTATTGAA
*
400793 ACATTCGACTTCCTGGGAACACACTTGGCAAGATAA-CTTCGCCAAGAGGGATATGAGATCGGAA
1 ACATTCGACTTCCTGGGAACACACTT-G-AAGAGAAGCTTCGCCAAGAGGGATATGAGATCGGAA
*
400857 TTGACGGTTATAGAA-ACAACAATCCGAGTCGGTCGCCACGAATTTAAACGGTAAATGATCTACG
64 TTGACGGTTATAGAAGA-AACAATCCGAGTCGGTCGCCACAAATTTAAACGGTAAATGATCTACG
400921 AAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAGATTGCCTTGGGTATTCGGTAT
128 AAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAGATTGCCTTGGGTATTCGG--T
* *
400986 ACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCGACGTGAATCCTGGAGGGAAAA
191 ACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCGACGTGAATCCCGAAGGGAAAA
* * *
401051 TCTAATTCGATGATCAAAGGGGAATTAAGTTAAAGCAAGGCTTGATGCTACTTTTACCGTATTTA
256 TCTAATTCAATGATCAAAGGGGAATTAAGTCAAAGCAAGGCTTGAGGCTACTTTTACCGTATTTA
**
401116 TTCACAATCTTTATTCTCTTATTTTTACTTAAATTACTTTTATTTATTTAATTGCTTTTATTATT
321 TTCACAATCTTTATTCTCTTATTTTTACTTAAATTACTTTTATTTATTTAATCACTTTTATTATT
* * *
401181 TAAATATATATTTACCAAACTCCCCGTTTACTATTTTCACGCCTGGAGTAAACCAATCAACATAA
386 TAAATATATATTTACCAAACCCCCCATTTACTATTTTCACGCCTCGAGTAAACCAATCAACATAA
401246 ATTAAGAATTTTCTAAGTCCCTCTGGATTCGACCTTACTTCTCTATACTACGAATTTCCTTATTT
451 ATTAAGAATTTTCTAAGTCCCTCTGGATTCGACCTTACTTCTCTATACTACGAATTTCCTTATTT
401311 ATTATCCGAAGAAGGAATTTTATTTTGACATCGAAATGACAGTTGTCAAATT
516 ATTATCCGAAGAAGGAATTTTATTTTGACATCGAAATGACAGTTGTCAAATT
401363 CGCCGTTGCC
Statistics
Matches: 531, Mismatches: 31, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
614 27 0.05
615 173 0.33
616 19 0.04
617 205 0.39
618 107 0.20
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (613 bp):
ACATTCGACTTCCTGGGAACACACTTGAAGAGAAGCTTCGCCAAGAGGGATATGAGATCGGAATT
GACGGTTATAGAAGAAACAATCCGAGTCGGTCGCCACAAATTTAAACGGTAAATGATCTACGAAA
ATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAGATTGCCTTGGGTATTCGGTACAAG
ATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCGACGTGAATCCCGAAGGGAAAATCTAA
TTCAATGATCAAAGGGGAATTAAGTCAAAGCAAGGCTTGAGGCTACTTTTACCGTATTTATTCAC
AATCTTTATTCTCTTATTTTTACTTAAATTACTTTTATTTATTTAATCACTTTTATTATTTAAAT
ATATATTTACCAAACCCCCCATTTACTATTTTCACGCCTCGAGTAAACCAATCAACATAAATTAA
GAATTTTCTAAGTCCCTCTGGATTCGACCTTACTTCTCTATACTACGAATTTCCTTATTTATTAT
CCGAAGAAGGAATTTTATTTTGACATCGAAATGACAGTTGTCAAATTGATGTCGTTGCCGGGGAG
ATAATCAAATTGGAAGATTCTTATTGAA
Found at i:401173 original size:18 final size:17
Alignment explanation
Indices: 401147--401183 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
401137 TTTTTACTTA
401147 AATTACTTTTATTTATTT
1 AATTACTTTTA-TTATTT
*
401165 AATTGCTTTTATTATTT
1 AATTACTTTTATTATTT
401182 AA
1 AA
401184 ATATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (17 bp):
AATTACTTTTATTATTT
Found at i:403592 original size:17 final size:17
Alignment explanation
Indices: 403572--403606 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
403562 ATAAAAAAAA
403572 TCTAAAAAACTAAAATC
1 TCTAAAAAACTAAAATC
*
403589 TCTAAAAATCTAAAATC
1 TCTAAAAAACTAAAATC
403606 T
1 T
403607 GTTATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (17 bp):
TCTAAAAAACTAAAATC
Found at i:408246 original size:215 final size:209
Alignment explanation
Indices: 407888--408311 Score: 760
Period size: 215 Copynumber: 2.0 Consensus size: 209
407878 ATTCGATTCT
*
407888 TGGGGTAACTAGTGTCTTGACTTGTTTTTTAAAATGTCTGGCCTTAGACTTAACGCCTAATGCGA
1 TGGGGTAACTAGTGTCTTGACTTGTTTTATAAAATGTCTGGCCTTAGACTTAACGCCTAATGCGA
407953 GTTATTACGGCTGGCATGAACTTTCCTACTCTTGAAAATCACTCTTCTCACTGGGTTTAAAATTG
66 GTTATTACGGCTGGCATGAACTTTCCTACTCTTGAAAATCACTCTTCTCACTGGGTTTAAAATTG
408018 GTTCTCTTCCTGTTAGGTATCTGGCATCCTTTAGTCACTAGAAAAGTCTCCCAAAAGGATTGTGT
131 GTTCTCTTCCTGTTAGGTATCTGGCATCCTTTAGTCACTAGAAAAGTCTCCCAAAAGGATTGTGT
408083 GGCCCTCATTGACA
196 GGCCCTCATTGACA
*
408097 TGGGGTAACTAGTGTTCTTGACTTGTTTTATAAAATGTCTGGCCTTATACTTAACGCCTCTAAAT
1 TGGGGTAACTAGTG-TCTTGACTTGTTTTATAAAATGTCTGGCCTTAGACTTAACG-C-CT-AAT
408162 GCGAGTTATTTACGGCT-GCATGAACTTTCCTACTCTTGAAAACATCACTCTTCTCACTGGGTTT
62 GCGAGTTA-TTACGGCTGGCATGAACTTTCCTACTCTTG-AAA-ATCACTCTTCTCACTGGGTTT
408226 AAAATTGGTTCTCTTCCTGTTAGGTATCTGGCATCCTTTAGTCACTAGAAAAGTCTCCCAAAAGG
124 AAAATTGGTTCTCTTCCTGTTAGGTATCTGGCATCCTTTAGTCACTAGAAAAGTCTCCCAAAAGG
408291 ATTGTGTGGCCCTCATTGACA
189 ATTGTGTGGCCCTCATTGACA
408312 ACATTAAGGC
Statistics
Matches: 206, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
209 14 0.07
210 39 0.19
211 1 0.00
212 2 0.01
213 32 0.16
214 11 0.05
215 107 0.52
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (209 bp):
TGGGGTAACTAGTGTCTTGACTTGTTTTATAAAATGTCTGGCCTTAGACTTAACGCCTAATGCGA
GTTATTACGGCTGGCATGAACTTTCCTACTCTTGAAAATCACTCTTCTCACTGGGTTTAAAATTG
GTTCTCTTCCTGTTAGGTATCTGGCATCCTTTAGTCACTAGAAAAGTCTCCCAAAAGGATTGTGT
GGCCCTCATTGACA
Found at i:414602 original size:3 final size:3
Alignment explanation
Indices: 414594--414621 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
414584 ACGGTTCTTA
414594 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
414622 GTTCTTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:416299 original size:18 final size:17
Alignment explanation
Indices: 416273--416309 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
416263 TTTTTACTTA
416273 AATTACTTTTATTTATTT
1 AATTACTTTTA-TTATTT
*
416291 AATTGCTTTTATTATTT
1 AATTACTTTTATTATTT
416308 AA
1 AA
416310 ATATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (17 bp):
AATTACTTTTATTATTT
Found at i:416461 original size:626 final size:624
Alignment explanation
Indices: 415272--416506 Score: 2012
Period size: 626 Copynumber: 2.0 Consensus size: 624
415262 ACATGTGGGA
* **
415272 GGAAGATTTGGCTTATTGAAAGCACATTCGACTTCCTGGGAACACACTTGATGAGAAAGCTTCGC
1 GGAAGATTCGGCTTATTGAAAGCACATTCGACTTCCTGGGAACACACTTGACAAGAAAGCTTCGC
* * * *
415337 CAAGAGGGATTTTAGATCGGAATTGACGGTTATATAAGAAACAATCTGAGTCGGTCGCCACAAAT
66 CAAGAGGGATATGAGATCGGAATTGACGGTTATAGAAGAAACAATCCGAGTCGGTCGCCACAAAT
* * *
415402 TTAAACGGTAATTGATCTACGACAATTGATGTTGTTAGAATCAATTTTCGAAGCCGGAATCAAAG
131 TTAAACGGTAAATGATCTACGAAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAG
*
415467 ATTGCCTTGGGTATTCGGTACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCTAC
196 ATTGCCTTGGGTATTCGGTACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCGAC
*
415532 GTGAATCCCGAAGGGAAAATCTAATTCAATGATCAAAGGGGAATTGAGTCAAAGCAAGGCTTGAG
261 GTGAATCCCGAAGGGAAAATCTAATTCAATGATCAAAGGGGAATTAAGTCAAAGCAAGGCTTGAG
* * * *
415597 GTTACTTTTATCGTATTTATTCAGAATCTTTATTCTCTTATTTTTTACTTAAATTGCTTTTATTT
326 GCTACTTTTACCGTATTTATTCACAATCTTTATTCTCTTATTTTTTACTTAAATTACTTTTATTT
*
415662 ATTTAATCACTTTTATTATTTAAATATCTATTTACCAAACCCCCCATTTACTACTTTTACGCCTC
391 ATTTAATCACTTTTATTATTTAAATATATATTTACCAAACCCCCCATTTACTACTTTTACGCCTC
* *
415727 GAGTAAACCAATCAGACATAAATTAAGAATTTTCTAAGCCCTGTGGATTCGACCCTTACTTCTCT
456 GAGTAAACCAATCAAACATAAATTAAGAATTTTCTAAGCCCTCTGGATTCGACCCTTACTTCTCT
* * * *
415792 ATACTGCGAATTTCCTTATTTATTATCCGAGAATAAGGAATTTTATTTTGACATCGAAACGATAG
521 ACACTACGAATTTCCTTATTTATTATCCGAGAAGAAGGAATTTTATTTTGACATCGAAACGACAG
* * *
415857 TTGTCAAATTGACGTCGTTGCCGGGGAGATAGTCAAATT
586 TTGTCAAATTAACGCCATTGCCGGGGAGATAGTCAAATT
*
415896 GGAAGATTCGGCTTATTGAAAGCACATTCGACTTCCTGGGAACACACTTGGCAAGATAA-CTTCG
1 GGAAGATTCGGCTTATTGAAAGCACATTCGACTTCCTGGGAACACACTTGACAAGA-AAGCTTCG
*
415960 CCAAGAGGGATATGAGATCGGAATTGACGGTTATAGAA-ACAACAATCCGAGTCGGTCGCCACGA
65 CCAAGAGGGATATGAGATCGGAATTGACGGTTATAGAAGA-AACAATCCGAGTCGGTCGCCACAA
*
416024 ATTTAAATGGTAAATGATCTACGAAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAA
129 ATTTAAACGGTAAATGATCTACGAAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAA
416089 AGATTGCCTTGGGTATTCGGTATACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAAC
194 AGATTGCCTTGGGTATTCGG--TACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAAC
* * * *
416154 CGACGTGAATCCTGGAGGGAAAATCTAATTCGATGATCAAAGGGGAATTAAGTTAAAGCAAGGCT
257 CGACGTGAATCCCGAAGGGAAAATCTAATTCAATGATCAAAGGGGAATTAAGTCAAAGCAAGGCT
*
416219 TGATGCTACTTTTACCGTATTTATTCACAATCTTTATTCTCTTA-TTTTTACTTAAATTACTTTT
322 TGAGGCTACTTTTACCGTATTTATTCACAATCTTTATTCTCTTATTTTTTACTTAAATTACTTTT
** * *
416283 ATTTATTTAATTGCTTTTATTATTTAAATATATATTTACCAAACTCCCCGTTTACTA-TTTTCAC
387 ATTTATTTAATCACTTTTATTATTTAAATATATATTTACCAAACCCCCCATTTACTACTTTT-AC
*
416347 GCCTGGAGTAAACCAATCAAACATAAATTAAGAATTTTCTAAGTCCCTCTGGATTCGA-CCTATA
451 GCCTCGAGTAAACCAATCAAACATAAATTAAGAATTTTCTAAG-CCCTCTGGATTCGACCCT-TA
416411 CTTCTCTACACTACGAATTTCCTTATTTATTATCCGAGAAGAAGGAATTTTATTTTGACATCGAA
514 CTTCTCTACACTACGAATTTCCTTATTTATTATCCGAGAAGAAGGAATTTTATTTTGACATCGAA
*
416476 ATGACAGTTGTCAAATTAACGCCATTGCCGG
579 ACGACAGTTGTCAAATTAACGCCATTGCCGG
416507 AGACTTCGCC
Statistics
Matches: 564, Mismatches: 40, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
623 1 0.00
624 199 0.35
625 119 0.21
626 245 0.43
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (624 bp):
GGAAGATTCGGCTTATTGAAAGCACATTCGACTTCCTGGGAACACACTTGACAAGAAAGCTTCGC
CAAGAGGGATATGAGATCGGAATTGACGGTTATAGAAGAAACAATCCGAGTCGGTCGCCACAAAT
TTAAACGGTAAATGATCTACGAAAATTGATGTTGTTAGAATCAATTTTCGAAGCCAGAATCAAAG
ATTGCCTTGGGTATTCGGTACAAGATAGAGTCACGGGGATTGCCCTTGTAGACAAAGTAACCGAC
GTGAATCCCGAAGGGAAAATCTAATTCAATGATCAAAGGGGAATTAAGTCAAAGCAAGGCTTGAG
GCTACTTTTACCGTATTTATTCACAATCTTTATTCTCTTATTTTTTACTTAAATTACTTTTATTT
ATTTAATCACTTTTATTATTTAAATATATATTTACCAAACCCCCCATTTACTACTTTTACGCCTC
GAGTAAACCAATCAAACATAAATTAAGAATTTTCTAAGCCCTCTGGATTCGACCCTTACTTCTCT
ACACTACGAATTTCCTTATTTATTATCCGAGAAGAAGGAATTTTATTTTGACATCGAAACGACAG
TTGTCAAATTAACGCCATTGCCGGGGAGATAGTCAAATT
Found at i:418733 original size:8 final size:8
Alignment explanation
Indices: 418722--418766 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
418712 AAAATTATAA
418722 AAAAATCT
1 AAAAATCT
*
418730 AAAAAACT
1 AAAAATCT
*
418738 AAAAAACT
1 AAAAATCT
*
418746 AAAATCTCT
1 AAAA-ATCT
418755 AAAAATCT
1 AAAAATCT
418763 AAAA
1 AAAA
418767 TCTCTTATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 26 0.81
9 6 0.19
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAAATCT
Found at i:418756 original size:17 final size:17
Alignment explanation
Indices: 418736--418771 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
418726 ATCTAAAAAA
418736 CTAAAAAACTAAAATCT
1 CTAAAAAACTAAAATCT
*
418753 CTAAAAATCTAAAATCT
1 CTAAAAAACTAAAATCT
418770 CT
1 CT
418772 TATTGCAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (17 bp):
CTAAAAAACTAAAATCT
Found at i:428637 original size:66 final size:66
Alignment explanation
Indices: 428531--428660 Score: 260
Period size: 66 Copynumber: 2.0 Consensus size: 66
428521 GGAGGCTGTC
428531 GCCTTCCCTAAAATATAAAATTATCATACATTTTAATTTTTTTCTGTTTATTTTTAATTGAAAAT
1 GCCTTCCCTAAAATATAAAATTATCATACATTTTAATTTTTTTCTGTTTATTTTTAATTGAAAAT
428596 A
66 A
428597 GCCTTCCCTAAAATATAAAATTATCATACATTTTAATTTTTTTCTGTTTATTTTTAATTGAAAA
1 GCCTTCCCTAAAATATAAAATTATCATACATTTTAATTTTTTTCTGTTTATTTTTAATTGAAAA
428661 CATATTTTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (66 bp):
GCCTTCCCTAAAATATAAAATTATCATACATTTTAATTTTTTTCTGTTTATTTTTAATTGAAAAT
A
Found at i:430320 original size:15 final size:15
Alignment explanation
Indices: 430283--430321 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
430273 AGTAGTTAGT
* *
430283 GGGCGGGCGGATGTG
1 GGGCGGGTGGATGCG
430298 GGGCGGGTGGATGCG
1 GGGCGGGTGGATGCG
*
430313 GGGTGGGTG
1 GGGCGGGTG
430322 CATACGAGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.10, G:0.69, T:0.15
Consensus pattern (15 bp):
GGGCGGGTGGATGCG
Found at i:431039 original size:12 final size:12
Alignment explanation
Indices: 431022--431059 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
431012 AAAAGAATTC
431022 TTTTGAATTGGT
1 TTTTGAATTGGT
*
431034 TTTTGAGTT-GT
1 TTTTGAATTGGT
431045 TTTTGAATTGTGT
1 TTTTGAATTG-GT
431058 TT
1 TT
431060 AACCTAGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 8 0.36
13 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.24, T:0.63
Consensus pattern (12 bp):
TTTTGAATTGGT
Found at i:431276 original size:21 final size:20
Alignment explanation
Indices: 431224--431267 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
431214 CAAAACAGAT
431224 TTTGA-AAAAATATTCTCTA
1 TTTGAGAAAAATATTCTCTA
431243 TTTGAGAAAAATA-TCTCATA
1 TTTGAGAAAAATATTCTC-TA
431263 TTTGA
1 TTTGA
431268 ATTAAAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTGAGAAAAATATTCTCTA
Found at i:441400 original size:128 final size:127
Alignment explanation
Indices: 441156--441405 Score: 333
Period size: 128 Copynumber: 2.0 Consensus size: 127
441146 ATAATAATAT
441156 TTATTTATTTATTTTAATATTAAGAAAGAGGTTGTCTTAAAATAACTAGATGTCATTTTCTGATA
1 TTATTTATTTATTTTAATATTAAGAAAGAGGTTGTCTTAAAATAACTAGATGTCATTTTCTGATA
* * *** *
441221 TTTTTAAATAAATAAATATCCTACTTTTATAAATTATATTTAATTTAATTTAATTTAAATTA
66 TTTTTAAATAAATAAATATACTACTTTTATAAACTATAAAAAATATAATTTAATTTAAATTA
* * * *
441283 TTATTTATTTATTTTTAATATTAAGAAAGGGGTTGTCTTAAAGTAACTAGATGTCCTTTTTTGAT
1 TTATTTATTTA-TTTTAATATTAAGAAAGAGGTTGTCTTAAAATAACTAGATGTCATTTTCTGAT
* * * *
441348 ATTTTTAAGTAAATAAATATATTA--TTTATAAAACTCTAAAAAATATATATTTACTTTA
65 ATTTTTAAATAAATAAATATACTACTTTTAT-AAACTATAAAAAATATA-ATTTAATTTA
441406 GTTTTATAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
126 5 0.05
127 22 0.21
128 79 0.75
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.48
Consensus pattern (127 bp):
TTATTTATTTATTTTAATATTAAGAAAGAGGTTGTCTTAAAATAACTAGATGTCATTTTCTGATA
TTTTTAAATAAATAAATATACTACTTTTATAAACTATAAAAAATATAATTTAATTTAAATTA
Found at i:448019 original size:110 final size:110
Alignment explanation
Indices: 447864--448067 Score: 309
Period size: 110 Copynumber: 1.9 Consensus size: 110
447854 GCATCCCAAT
*
447864 TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
* *
447929 CGACGAAGGGGCGGCTGATTGTCAACAAATAACTTTTCAATTTCA
66 CAACGAAGGGGCGGCTGACTGTCAACAAATAACTTTTCAATTTCA
* * * * **
447974 TTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTAGACTCAAGACAGTACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
* *
448039 CAACGAAGGGGCGGTTGGCTGTCAACAAA
66 CAACGAAGGGGCGGCTGACTGTCAACAAA
448068 CAATTTCCCA
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 83 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGGCTGACTGTCAACAAATAACTTTTCAATTTCA
Found at i:448083 original size:110 final size:110
Alignment explanation
Indices: 447864--448102 Score: 306
Period size: 110 Copynumber: 2.2 Consensus size: 110
447854 GCATCCCAAT
*
447864 TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
* * * *
447929 CGACGAAGGGGCGGCTGATTGTCAACAAATAACTTTTCAATTTCA
66 CAACGAAGGGGCGGCTGACTGTCAACAAACAACTTTCCAATTTCA
* * * * **
447974 TTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTAGACTCAAGACAGTACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
* * * *
448039 CAACGAAGGGGCGGTTGGCTGTCAACAAACAA-TTTCCCA-GT--
66 CAACGAAGGGGCGGCTGACTGTCAACAAACAACTTTCCAATTTCA
*
448080 TTCAGAACCAATTTCAACTTCAC
1 TTCAGAGCCAATTTCAACTTCAC
448103 GACGAAGGAT
Statistics
Matches: 111, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
106 20 0.18
108 1 0.01
109 5 0.05
110 85 0.77
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTAGACCCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGGCTGACTGTCAACAAACAACTTTCCAATTTCA
Found at i:448571 original size:63 final size:65
Alignment explanation
Indices: 448471--448645 Score: 246
Period size: 67 Copynumber: 2.7 Consensus size: 65
448461 AATTTACTCA
448471 AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTG-ACA-GTTTCCCTT
1 AAACAAA-TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAACAGGTTTCCCTT
448534 G
65 G
* * * * *
448535 AAACAAATTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACACCAATCTTTGAATAGGTTTCTCTT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAACAGGTTTCCCTT
448600 G
65 G
* *
448601 AAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACAAAA
1 AAAC-AAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
448646 AAAAACCTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
63 32 0.33
64 15 0.15
65 2 0.02
66 15 0.15
67 33 0.34
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAACAGGTTTCCCTTG
Found at i:448638 original size:67 final size:64
Alignment explanation
Indices: 448471--448645 Score: 244
Period size: 63 Copynumber: 2.7 Consensus size: 64
448461 AATTTACTCA
*
448471 AAACAAAGTTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGACAGTTTCCCTTG
1 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGACAGTTTCCCTTG
* * * * *
448535 AAAC-AAATTTTGTCTCTCTTAAGACAGTTTCCCTTGAAACACCAATCTTTGAATAGGTTTCTCT
1 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTG-ACA-GTTTCCCT
448599 TG
63 TG
* *
448601 AAACAAAATTTTGCCTCCCTTGAGACAGTTTCTCTTGAAACAAAA
1 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAA
448646 AAAAACCTTT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
63 34 0.35
64 12 0.12
65 2 0.02
66 15 0.16
67 33 0.34
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (64 bp):
AAACAAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGACAGTTTCCCTTG
Found at i:448829 original size:84 final size:84
Alignment explanation
Indices: 448681--448852 Score: 227
Period size: 84 Copynumber: 2.0 Consensus size: 84
448671 GAAACACCAA
* * * *
448681 ACCTTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAAG
1 ACCTTCAAGTTCGACTACACTCAGCTCCAAGACACATCATTTGCAACATAACTCAAGGCAAGAAG
* *
448746 GGCTATTTTCCAACCAAAG
66 GGCTATCTGCCAACCAAAG
* * * * * *
448765 ACCTTCAAGTTCGACTACGCTCAGCTCCGAGACACATCATTTGCAGCATAACTTAAGTCGAGAAG
1 ACCTTCAAGTTCGACTACACTCAGCTCCAAGACACATCATTTGCAACATAACTCAAGGCAAGAAG
*
448830 GGTTATCTGCCAACCAAAG
66 GGCTATCTGCCAACCAAAG
448849 ACCT
1 ACCT
448853 GACGAGTTCA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (84 bp):
ACCTTCAAGTTCGACTACACTCAGCTCCAAGACACATCATTTGCAACATAACTCAAGGCAAGAAG
GGCTATCTGCCAACCAAAG
Found at i:459776 original size:52 final size:53
Alignment explanation
Indices: 459693--459799 Score: 191
Period size: 52 Copynumber: 2.0 Consensus size: 53
459683 TCCCATCAGG
459693 TAAAGACTCGATTATTTTCCCCTACTGAACAAAAGTTAATT-TATGCATGAATC
1 TAAAGACTCGATTATTTTCCCCTACTGAACAAAAGTTAATTATATGCATG-ATC
459746 TAAAGACTCGATTA-TTTCCCCTACTGAACAAAAGTTAATTATATGCATGATC
1 TAAAGACTCGATTATTTTCCCCTACTGAACAAAAGTTAATTATATGCATGATC
459798 TA
1 TA
459800 TAAAATGTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 31 0.58
53 22 0.42
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (53 bp):
TAAAGACTCGATTATTTTCCCCTACTGAACAAAAGTTAATTATATGCATGATC
Found at i:465633 original size:30 final size:30
Alignment explanation
Indices: 465564--465633 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 30
465554 AAACTTAATA
*
465564 GACTAAAACAGTTAAAAAAGAAATTTAAAG
1 GACTAAAATAGTTAAAAAAGAAATTTAAAG
*
465594 GAC-ATAAATAG-TAAAAATTGAAATTT-AAG
1 GACTA-AAATAGTTAAAAA-AGAAATTTAAAG
465623 TGACTAAAATA
1 -GACTAAAATA
465634 AAATAATAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
29 10 0.29
30 23 0.68
31 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.24
Consensus pattern (30 bp):
GACTAAAATAGTTAAAAAAGAAATTTAAAG
Found at i:466379 original size:3 final size:3
Alignment explanation
Indices: 466371--466453 Score: 112
Period size: 3 Copynumber: 27.3 Consensus size: 3
466361 GTAGGTTTTA
* * *
466371 AAT AAT AAT AGT AAT AAT AAT AAT AGT AAT AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
466419 AAT AAT AAT AAT GAT AAT AAT AAT ATTT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A
466454 TTTTTTCGAT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
3 67 0.97
4 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:467013 original size:43 final size:43
Alignment explanation
Indices: 466952--467067 Score: 169
Period size: 43 Copynumber: 2.7 Consensus size: 43
466942 TGTTGATAGA
* * * *
466952 CACGATATCCTTCATCGTGAAGTTGAAATCATGGATGTGCGGG
1 CACGATATCCTCCGTCGTGGAGTTGAAATCATGGATCTGCGGG
*
466995 CACGATATCCTCCGTCGTGGAGTTGAAATCATGGATCTGTGGG
1 CACGATATCCTCCGTCGTGGAGTTGAAATCATGGATCTGCGGG
* *
467038 TACAATATCCTCCGTCGTGGAGTTGAAATC
1 CACGATATCCTCCGTCGTGGAGTTGAAATC
467068 GTGAATGGCC
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (43 bp):
CACGATATCCTCCGTCGTGGAGTTGAAATCATGGATCTGCGGG
Found at i:467249 original size:43 final size:43
Alignment explanation
Indices: 467183--467274 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
467173 TGTGAAGTTA
* * *
467183 AAATCGTGGTTGTGTGGGCACGATATCCTCTGTCGTGGAATTG
1 AAATCGTGGATATGTGGGCACGATATCCTCCGTCGTGGAATTG
* * *
467226 AAATCGTGGATATGTGGGTACGATGTCCTCCGTCGTGGAGTTG
1 AAATCGTGGATATGTGGGCACGATATCCTCCGTCGTGGAATTG
467269 AAATCG
1 AAATCG
467275 CAGATGGCCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.21, C:0.16, G:0.33, T:0.30
Consensus pattern (43 bp):
AAATCGTGGATATGTGGGCACGATATCCTCCGTCGTGGAATTG
Found at i:467527 original size:43 final size:43
Alignment explanation
Indices: 467479--467582 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
467469 TTTGTCGTGA
*
467479 AGTTGAAA-CTGTGGATGTGTGGGCACGATATCCTCTGCCGTAG
1 AGTTGAAATC-GTGGATGTGTGGGCACGATATCCTCCGCCGTAG
** * * *
467522 AGTTGAAATCGTGGATCCGTGGGTACGATATCCTCCGTCGTGG
1 AGTTGAAATCGTGGATGTGTGGGCACGATATCCTCCGCCGTAG
467565 AGTTGAAATCGTGGATGT
1 AGTTGAAATCGTGGATGT
467583 CCCTTTCGTC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 51 0.98
44 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (43 bp):
AGTTGAAATCGTGGATGTGTGGGCACGATATCCTCCGCCGTAG
Found at i:467871 original size:64 final size:64
Alignment explanation
Indices: 467784--467958 Score: 230
Period size: 61 Copynumber: 2.8 Consensus size: 64
467774 TTCTATCGTT
* *
467784 TTGAGTTCAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGTAAAATTGTTTG
1 TTGAGTACAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAAATTGTTTG
** * ** *
467848 TTGAGTACAATATCCTTCACTGTGAAGTTGAAATTGACTATG---AAAGTTGGAAAGTTGTTTG
1 TTGAGTACAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAAATTGTTTG
* *
467909 TTGAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGACTCTTAATGAAAA
1 TTGAGTACAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAAT-AAAA
467959 TAGGAAGCCC
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
61 52 0.56
64 38 0.41
65 3 0.03
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (64 bp):
TTGAGTACAATATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGGAAAATTGTTTG
Found at i:469500 original size:14 final size:14
Alignment explanation
Indices: 469481--469513 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
469471 ATTCTCATCC
469481 CTTTTTCTTTCTTT
1 CTTTTTCTTTCTTT
*
469495 CTTTTTGTTTCTTT
1 CTTTTTCTTTCTTT
469509 -TTTTT
1 CTTTTT
469514 ATTTATTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (14 bp):
CTTTTTCTTTCTTT
Found at i:470831 original size:65 final size:64
Alignment explanation
Indices: 470714--470914 Score: 187
Period size: 65 Copynumber: 3.1 Consensus size: 64
470704 TTTCAAAGTG
* * * *
470714 ATGCACCAATGCACTAATCCATGCATCGATGCAC-CATGG-AATAAATTG-AACATCGAATGCAT
1 ATGCATCAATGCAC-AAGCCATGCATCGATGCACTCA-GGCTAT-TA-TGAAACATCGAATGCAT
470776 TTC
62 TTC
* * * *
470779 ATGCATCAATGCACATA-CTATGCATCGATGTATTGAGGGCT-TTATGAAAACATCGAATGCATT
1 ATGCATCAATGCACA-AGCCATGCATCGATGCACTCA-GGCTATTATG-AAACATCGAATGCATT
*
470842 TG
63 TC
* * * *
470844 ATGCGTCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCACTTC
1 ATGCATCAATGCACAAGCCATGCATCGATGCACTCAGGCTATTATGAAACATCGAATGCATTTC
470908 ATGCATC
1 ATGCATC
470915 GCTGCACTCT
Statistics
Matches: 110, Mismatches: 19, Indels: 15
0.76 0.13 0.10
Matches are distributed among these distances:
63 2 0.02
64 42 0.38
65 66 0.60
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (64 bp):
ATGCATCAATGCACAAGCCATGCATCGATGCACTCAGGCTATTATGAAACATCGAATGCATTTC
Found at i:479452 original size:65 final size:64
Alignment explanation
Indices: 479383--479525 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 64
479373 GGAATAAATT
* *
479383 AAACATCGAATGCATTTCATGCATCGATGCACATA-CCATGCATCGAAGCTCTGACGGCT-TTAT
1 AAACATCGAATGCATTTCATGCATCGATGCACA-AGCCATGCATCGAAGCACTCA-GGCTATTAT
479446 G
64 G
* * * *
479447 AAAACATCAAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTG
1 -AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGAAGCACTCAGGCTATTATG
479512 AAACATCGAATGCA
1 AAACATCGAATGCA
479526 CTCTTAGTGC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 18 0.26
65 51 0.74
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (64 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGAAGCACTCAGGCTATTATG
Found at i:485437 original size:22 final size:22
Alignment explanation
Indices: 485409--485472 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
485399 TTTTGGTGCA
*
485409 GAGGGAATCGATTCCCCCCCTT
1 GAGGGAACCGATTCCCCCCCTT
* *
485431 GAGGGAACCGATT-CCTCCTTT
1 GAGGGAACCGATTCCCCCCCTT
485452 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
485473 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 7 0.20
22 13 0.37
23 11 0.31
24 4 0.11
ACGTcount: A:0.20, C:0.34, G:0.25, T:0.20
Consensus pattern (22 bp):
GAGGGAACCGATTCCCCCCCTT
Found at i:485480 original size:21 final size:21
Alignment explanation
Indices: 485454--485493 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
485444 CCTCCTTTGA
*
485454 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
485475 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
485494 TGGGTTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:488539 original size:46 final size:46
Alignment explanation
Indices: 488487--488632 Score: 131
Period size: 46 Copynumber: 3.2 Consensus size: 46
488477 TATTCATCTT
488487 TGAGGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTTG
1 TGAGGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTTG
** * *** * *
488533 TGAGGTTTCTTGTAAGTTTG--C-A-AATTGTGCTCATTGTATTCATCTT-
1 TGAGG-TTCTT-T-TCTTTGTTCTAGAATTGTGC-AAACATCTT-ACCTTG
488579 TGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTTG
1 TGAG-GTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTTG
488626 TGAGGTT
1 TGAGGTT
488633 TTCTTGTAAG
Statistics
Matches: 73, Mismatches: 16, Indels: 22
0.66 0.14 0.20
Matches are distributed among these distances:
44 4 0.05
45 9 0.12
46 27 0.37
47 20 0.27
48 9 0.12
49 4 0.05
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.47
Consensus pattern (46 bp):
TGAGGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTACCTTG
Found at i:488623 original size:93 final size:94
Alignment explanation
Indices: 488464--488652 Score: 355
Period size: 93 Copynumber: 2.0 Consensus size: 94
488454 AAGAACACTT
488464 TTGTGCTCAATTGTATTCATCTTTGAGGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTAC
1 TTGTGCTCAATTGTATTCATCTTTGAGGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTAC
488529 CTTGTGAGG-TTTCTTGTAAGTTTGCAAA
66 CTTGTGAGGTTTTCTTGTAAGTTTGCAAA
488557 TTGTGCTC-ATTGTATTCATCTTTGAGTGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTA
1 TTGTGCTCAATTGTATTCATCTTTGAG-GTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTA
488621 CCTTGTGAGGTTTTCTTGTAAGTTTGCAAA
65 CCTTGTGAGGTTTTCTTGTAAGTTTGCAAA
488651 TT
1 TT
488653 TGTAATCTTC
Statistics
Matches: 94, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
92 18 0.19
93 55 0.59
94 21 0.22
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.48
Consensus pattern (94 bp):
TTGTGCTCAATTGTATTCATCTTTGAGGTTCTTTTCTTTGTTCTAGAATTGTGCAAACATCTTAC
CTTGTGAGGTTTTCTTGTAAGTTTGCAAA
Found at i:491985 original size:30 final size:30
Alignment explanation
Indices: 491906--492001 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 30
491896 GTAAGATAAA
* *
491906 AAACTTAA-TAGACTAAAACAGTTAAAACAG
1 AAACTTAAGT-GACTAAAATAGTAAAAACAG
* *
491936 AAATTTAAAG-GAC-ATAAATAGTAAAAACTG
1 AAACTT-AAGTGACTA-AAATAGTAAAAACAG
491966 AAACTTAAGTGACTAAAATA--AAATAACAG
1 AAACTTAAGTGACTAAAATAGTAAA-AACAG
491995 AAA-TTAA
1 AAACTTAA
492002 AGTGTCAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
28 7 0.13
29 11 0.20
30 33 0.61
31 3 0.06
ACGTcount: A:0.58, C:0.09, G:0.10, T:0.22
Consensus pattern (30 bp):
AAACTTAAGTGACTAAAATAGTAAAAACAG
Found at i:492714 original size:3 final size:3
Alignment explanation
Indices: 492698--492764 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
492688 GTAGGTTTTA
* * *
492698 AAT AAT AA- AGT AAT AAT AAT AAT AAT AAT AGT AAT -AT AGT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
492743 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
492765 TTTTTTTCGA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.07
3 51 0.93
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:494581 original size:46 final size:46
Alignment explanation
Indices: 494531--494624 Score: 152
Period size: 46 Copynumber: 2.0 Consensus size: 46
494521 CATAATGTCG
494531 TTACAAAATTAACGACCGAGTGATAAAAAAAATTTAATGGCCAAAA
1 TTACAAAATTAACGACCGAGTGATAAAAAAAATTTAATGGCCAAAA
* * * *
494577 TTACAAAATTAACGATCGAGTTATAAAAAAAGTTTAATGGTCAAAA
1 TTACAAAATTAACGACCGAGTGATAAAAAAAATTTAATGGCCAAAA
494623 TT
1 TT
494625 CAGTGAGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.50, C:0.11, G:0.13, T:0.27
Consensus pattern (46 bp):
TTACAAAATTAACGACCGAGTGATAAAAAAAATTTAATGGCCAAAA
Found at i:504480 original size:11 final size:12
Alignment explanation
Indices: 504464--504492 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
504454 ATTTTATTTT
504464 AAAAAATTA-TA
1 AAAAAATTATTA
504475 AAAAAATTATTA
1 AAAAAATTATTA
504487 AAAAAA
1 AAAAAA
504493 ATTAAACTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAAAATTATTA
Found at i:504486 original size:14 final size:13
Alignment explanation
Indices: 504464--504496 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
504454 ATTTTATTTT
504464 AAAAAATTA-T-A
1 AAAAAATTATTAA
504475 AAAAAATTATTAA
1 AAAAAATTATTAA
504488 AAAAAATTA
1 AAAAAATTA
504497 AACTCCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 1 0.05
13 10 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAAATTATTAA
Found at i:505923 original size:31 final size:31
Alignment explanation
Indices: 505885--505946 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
505875 GAAAGAAAGA
505885 AAGAAATCATGTTGAGAAATTGGTGTACGAG
1 AAGAAATCATGTTGAGAAATTGGTGTACGAG
505916 AAGAAATCATGTTGAGAAATTGGTGTACGAG
1 AAGAAATCATGTTGAGAAATTGGTGTACGAG
505947 TCCTTTGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.29, T:0.26
Consensus pattern (31 bp):
AAGAAATCATGTTGAGAAATTGGTGTACGAG
Found at i:506676 original size:29 final size:29
Alignment explanation
Indices: 506627--506700 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
506617 ACGGAAAATA
*
506627 TAAAA-TTATAATAAAGGATAAA-ACTTTT
1 TAAAATTTATAATAAAGAATAAAGA-TTTT
506655 TAAAATTTACT-ATAAAGAATAAAGATTTT
1 TAAAATTTA-TAATAAAGAATAAAGATTTT
506684 TAAAATTTATAATAAAG
1 TAAAATTTATAATAAAG
506701 GACAATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
28 6 0.15
29 33 0.80
30 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAAATTTATAATAAAGAATAAAGATTTT
Found at i:506718 original size:27 final size:28
Alignment explanation
Indices: 506680--506733 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
506670 AGAATAAAGA
*
506680 TTTTTAAAATTTATAAT-AAAGGACAAT
1 TTTTTAAAATTTACAATAAAAGGACAAT
*
506707 TTTTTAGAATTTACAATAAAAGGACAA
1 TTTTTAAAATTTACAATAAAAGGACAA
506734 AACTTACAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (28 bp):
TTTTTAAAATTTACAATAAAAGGACAAT
Found at i:506729 original size:28 final size:27
Alignment explanation
Indices: 506651--506733 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 27
506641 AGGATAAAAC
* * * *
506651 TTTTTAAAATTTACTATAAAGAATAAAGA
1 TTTTTAAAATTTACAATAAAGGA-CAA-T
*
506680 TTTTTAAAATTTATAATAAAGGACAAT
1 TTTTTAAAATTTACAATAAAGGACAAT
*
506707 TTTTTAGAATTTACAATAAAAGGACAA
1 TTTTTAAAATTTACAAT-AAAGGACAA
506734 AACTTACAGG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
27 15 0.33
28 11 0.24
29 20 0.43
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.37
Consensus pattern (27 bp):
TTTTTAAAATTTACAATAAAGGACAAT
Found at i:510154 original size:2 final size:2
Alignment explanation
Indices: 510147--510203 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
510137 TTTCGTAAAT
510147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
510189 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
510204 GTAGATTGAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:510947 original size:16 final size:14
Alignment explanation
Indices: 510911--510939 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
510901 CTATCAATAT
510911 TCTTATAATTTATA
1 TCTTATAATTTATA
510925 TCTTATAA-TTATA
1 TCTTATAATTTATA
510938 TC
1 TC
510940 CTCTTATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTTATAATTTATA
Found at i:511293 original size:23 final size:23
Alignment explanation
Indices: 511275--511335 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
511265 CTCGTATAAA
511275 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
511298 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
511321 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
511336 TATAAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:512911 original size:21 final size:21
Alignment explanation
Indices: 512881--512921 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
512871 GTTCATTTAT
512881 TTGAAAGTGCATCGATACACA
1 TTGAAAGTGCATCGATACACA
*
512902 TTGAATGTGCATCGATACAC
1 TTGAAAGTGCATCGATACAC
512922 TTTGCCCAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (21 bp):
TTGAAAGTGCATCGATACACA
Found at i:518199 original size:30 final size:30
Alignment explanation
Indices: 518165--518227 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
518155 CAAATCTTTT
*
518165 ACTAATGTTATTATTTATTACAAAATGGTC
1 ACTAATGTTATCATTTATTACAAAATGGTC
* *
518195 ACTAATGTTATCGTTTGTTACAAAATGGTC
1 ACTAATGTTATCATTTATTACAAAATGGTC
518225 ACT
1 ACT
518228 CGACGTTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (30 bp):
ACTAATGTTATCATTTATTACAAAATGGTC
Found at i:519119 original size:3 final size:3
Alignment explanation
Indices: 519111--519137 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
519101 ATCAGCTGAT
519111 AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA
519138 GTCAAACGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:527039 original size:3 final size:3
Alignment explanation
Indices: 527031--527104 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
527021 TTTTTATCCA
* *
527031 TAT TAT TAT TAT TAA TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
527079 TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
527105 AATATATATT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:527049 original size:12 final size:12
Alignment explanation
Indices: 527034--527115 Score: 103
Period size: 12 Copynumber: 6.7 Consensus size: 12
527024 TTATCCATAT
527034 TATTATTATTAA
1 TATTATTATTAA
*
527046 TATTATTATTAC
1 TATTATTATTAA
*
527058 TATTATTATTAT
1 TATTATTATTAA
527070 TATTATTATT-A
1 TATTATTATTAA
*
527081 TCATTATTATTAT
1 T-ATTATTATTAA
527094 TATTATTATTAAA
1 TATTATTATT-AA
527107 TATATATTA
1 TAT-TATTA
527116 AACATATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
11 1 0.02
12 50 0.82
13 5 0.08
14 5 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:528498 original size:14 final size:14
Alignment explanation
Indices: 528479--528524 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
528469 AATTTAGTCA
528479 TTTATTTTATATGT
1 TTTATTTTATATGT
* *
528493 TTTATTTTATTTAT
1 TTTATTTTATATGT
528507 TTT-TTTTATATTGT
1 TTTATTTTATA-TGT
528521 TTTA
1 TTTA
528525 ATAGAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 6 0.23
14 20 0.77
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (14 bp):
TTTATTTTATATGT
Found at i:528576 original size:22 final size:21
Alignment explanation
Indices: 528537--528579 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
528527 AGAATTTTTC
**
528537 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
528558 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
528580 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:529238 original size:23 final size:23
Alignment explanation
Indices: 529212--529255 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
529202 AAATTAAAAA
529212 TTCAAAAATATTTAATTTTTTCT
1 TTCAAAAATATTTAATTTTTTCT
** *
529235 TTCAAATTTTTTTAATTTTTT
1 TTCAAAAATATTTAATTTTTT
529256 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (23 bp):
TTCAAAAATATTTAATTTTTTCT
Found at i:530953 original size:14 final size:14
Alignment explanation
Indices: 530915--530968 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
530905 ATTTTAAATA
*
530915 ATTTACATTTACA-
1 ATTTACATTTGCAT
530928 ATTTTACATTTGCAT
1 A-TTTACATTTGCAT
530943 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
530958 CTTTGCATTTG
1 ATTTACATTTG
530969 TATTGCACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 1 0.03
14 21 0.60
15 13 0.37
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:530957 original size:15 final size:15
Alignment explanation
Indices: 530930--530968 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
530920 CATTTACAAT
530930 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
530944 TTTACATTTGGCATC
1 TTTACATTTGGCATA
*
530959 TTTGCATTTG
1 TTTACATTTG
530969 TATTGCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:534247 original size:6 final size:6
Alignment explanation
Indices: 534231--534281 Score: 68
Period size: 6 Copynumber: 8.3 Consensus size: 6
534221 CTCATCCAAC
*
534231 AAAGAA AGAAGAA GAAGAA AAAGAA AAAGAA AAA-AA AAAGAA AAAGGAA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA-GAA
534280 AA
1 AA
534282 TCGAATAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
5 5 0.12
6 25 0.62
7 10 0.25
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:535274 original size:16 final size:17
Alignment explanation
Indices: 535240--535280 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
535230 AAAAAAAAGT
535240 AAAAAAAA-AACAAACA
1 AAAAAAAAGAACAAACA
*
535256 AAAAAAAAGAATAAA-A
1 AAAAAAAAGAACAAACA
*
535272 AAAAGAAAG
1 AAAAAAAAG
535281 TGATGGATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.85, C:0.05, G:0.07, T:0.02
Consensus pattern (17 bp):
AAAAAAAAGAACAAACA
Found at i:536587 original size:83 final size:83
Alignment explanation
Indices: 536448--536703 Score: 458
Period size: 83 Copynumber: 3.1 Consensus size: 83
536438 CTGAAAGAGA
* *
536448 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTGGACAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
536513 ATTTAGAAGATGAATCTG
66 ATTTAGAAGATGAATCTG
536531 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
*
536596 ATTTAGAAGATGAATGTG
66 ATTTAGAAGATGAATCTG
* *
536614 CTCATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTATACAGAACCAATCATTGA
1 CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
*
536679 ATTTAGAAGATGAATTTG
66 ATTTAGAAGATGAATCTG
536697 CTCATAG
1 CTCATAG
536704 GAGAAATAAG
Statistics
Matches: 167, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 167 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (83 bp):
CTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGA
ATTTAGAAGATGAATCTG
Found at i:538923 original size:40 final size:40
Alignment explanation
Indices: 538868--538946 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
538858 TGAGCAGAGT
538868 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
* *
538908 CCACAGAAAAGGATGAATGTGTTGTCAAGTGTTTTACAT
1 CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACAT
538947 ATAAGCTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (40 bp):
CCACAGAAAAGGATGAATGCGTTGTCAAATGTTTTACATC
Found at i:539328 original size:33 final size:33
Alignment explanation
Indices: 539286--539353 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
539276 GAACAGACTT
539286 TACTCTCCTAATTAATCCCCGCTGAGTCAGGCA
1 TACTCTCCTAATTAATCCCCGCTGAGTCAGGCA
539319 TACTCTCCTAATTAATCCCCGCTGAGTCAGGCA
1 TACTCTCCTAATTAATCCCCGCTGAGTCAGGCA
539352 TA
1 TA
539354 TCTACATCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (33 bp):
TACTCTCCTAATTAATCCCCGCTGAGTCAGGCA
Found at i:539400 original size:22 final size:22
Alignment explanation
Indices: 539369--539423 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
539359 ATCTACACTC
**
539369 TTCAAAGATGGTAGATTC-CTTT
1 TTCAAAGATGACAGATTCTC-TT
*
539391 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
539413 TTCAAAGATGA
1 TTCAAAGATGA
539424 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 27 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:540011 original size:112 final size:113
Alignment explanation
Indices: 539860--540268 Score: 653
Period size: 112 Copynumber: 3.6 Consensus size: 113
539850 TTCCAGGTCG
*
539860 AGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
*
539925 AACCTTTTGCTCAAATCCATCATTTGATGGATTAACATTTCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATTAACATTTCCAGAGAA
* *
539973 AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* *
540037 AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATTAACATTTCCAGAGAA
* *
540085 AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* * *
540149 AACCTTTTGC-CTGAATTCATCACTTGATGGATTAACTTTTCCAGAGAA
66 AACCTTTTGCTC-AAATCCATCACTTGATGGATTAACATTTCCAGAGAA
* * **
540197 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
540262 AACCTTT
66 AACCTTT
540269 GTTTGATGCT
Statistics
Matches: 281, Mismatches: 13, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
111 1 0.00
112 215 0.77
113 65 0.23
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATTAACATTTCCAGAGAA
Found at i:540539 original size:113 final size:113
Alignment explanation
Indices: 540377--540925 Score: 803
Period size: 113 Copynumber: 4.8 Consensus size: 113
540367 TCCTTCAAAT
* * *
540377 ATCAGTATTTCCAGAAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCA
1 ATCAGCATTGCCAG-AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
** * *
540442 TAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCACTTGATGG
65 TAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCCATCATTTGATGG
* * *
540491 ATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCAT
1 ATCAGCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
540556 AATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGG
66 AATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCCATCATTTGATGG
* * * *
540604 ATCAGCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAGCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
540669 AATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGG
66 AATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCCATCATTTGATGG
* * *
540717 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAGCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
540782 AATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGG
66 AATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCCATCATTTGATGG
* * *
540830 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAGT
1 ATCAGCATTGCCAGAGAAG-GTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGT
* * *
540894 TCATAATAAGAAGAACTTGTTCAACTTTTTGC
62 TCATAATGAGAAGAATTTGTTCAACCTTTTGC
540926 ATAATTCTAT
Statistics
Matches: 402, Mismatches: 29, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
112 2 0.00
113 337 0.84
114 10 0.02
115 1 0.00
116 52 0.13
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
ATCAGCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAATTTGTTCAACCTTTTGCCTGAATCCATCATTTGATGG
Found at i:541250 original size:3 final size:3
Alignment explanation
Indices: 541242--541318 Score: 127
Period size: 3 Copynumber: 25.7 Consensus size: 3
541232 TTTTTATCCA
* *
541242 TAT TAT TAT TAT TAA TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
541290 TAT TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
541319 AATATATATT
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:541260 original size:12 final size:12
Alignment explanation
Indices: 541245--541329 Score: 98
Period size: 12 Copynumber: 6.7 Consensus size: 12
541235 TTATCCATAT
541245 TATTATTATTAA
1 TATTATTATTAA
*
541257 TATTATTATTAC
1 TATTATTATTAA
*
541269 TATTATTATTAT
1 TATTATTATTAA
541281 TATTATTATTATTA
1 TATTATTATTA--A
*
541295 TCATTATTATTAT
1 T-ATTATTATTAA
541308 TATTATTATTAAA
1 TATTATTATT-AA
541321 TATATATTA
1 TAT-TATTA
541330 AACATATATA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
12 42 0.67
13 5 0.08
14 6 0.10
15 10 0.16
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:542711 original size:14 final size:14
Alignment explanation
Indices: 542692--542738 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
542682 AATTTAGTCA
542692 TTTATTTTATATGT
1 TTTATTTTATATGT
* *
542706 TTTATTTTATTTTAT
1 TTTATTTTA-TATGT
542721 TTTA-TTTATATTGT
1 TTTATTTTATA-TGT
542735 TTTA
1 TTTA
542739 ATAGAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 19 0.70
15 7 0.26
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (14 bp):
TTTATTTTATATGT
Found at i:542790 original size:22 final size:21
Alignment explanation
Indices: 542751--542793 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
542741 AGAAATTTTC
**
542751 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
542772 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
542794 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:544247 original size:226 final size:225
Alignment explanation
Indices: 543834--544271 Score: 747
Period size: 227 Copynumber: 1.9 Consensus size: 225
543824 TTATCTATCC
* *
543834 TTTTATAAAAGTGTCCTACTTATTCACTGTGAAAATATATTTATTATTATCTTTAGTTAATATTG
1 TTTTATAAAAGTGTCCTACTTATTCACTGTGAAAACATATTTATTATTATATTTAGTTAATATTG
**
543899 TTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAA
66 TTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGTAAA
543964 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
131 TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
544029 ATTACATAACTTTCAAAAAAGTATATATCAT
196 ATTACATAACTTT-AAAAAAGTATATATCAT
*
544060 TTTTAT-AAAGTGTCCATACTTATTTCACTGTTGAAAACATA-TTATTATTATATTTGGTTAATA
1 TTTTATAAAAGTGTCC-TACTTA-TTCACTG-TGAAAACATATTTATTATTATATTTAGTTAATA
*
544123 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGT
63 TTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGT
* *
544188 AAAT-TAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATTGAAACA
128 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACA
544252 TAAATTACATAACTTTAAAA
193 TAAATTACATAACTTTAAAA
544272 GCAGTTTTAA
Statistics
Matches: 201, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
225 13 0.06
226 86 0.43
227 93 0.46
228 9 0.04
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (225 bp):
TTTTATAAAAGTGTCCTACTTATTCACTGTGAAAACATATTTATTATTATATTTAGTTAATATTG
TTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTTTGTGTAAA
TGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAA
ATTACATAACTTTAAAAAAGTATATATCAT
Found at i:544358 original size:19 final size:18
Alignment explanation
Indices: 544336--544379 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
544326 CGATATACCA
*
544336 GGTAAAATATGATAAAACC
1 GGTAAAAAATGATAAAA-C
544355 GGTAACAAAATGATAAAAC
1 GGTAA-AAAATGATAAAAC
544374 GGTAAA
1 GGTAAA
544380 TTTAAAAGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 11 0.48
20 11 0.48
ACGTcount: A:0.55, C:0.09, G:0.18, T:0.18
Consensus pattern (18 bp):
GGTAAAAAATGATAAAAC
Found at i:546773 original size:21 final size:22
Alignment explanation
Indices: 546744--546784 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
546734 TGCAAAGACA
546744 ATCAGAGTCGAAGAGAAACTTG
1 ATCAGAGTCGAAGAGAAACTTG
*
546766 ATCA-AGTCGTAGAGAAACT
1 ATCAGAGTCGAAGAGAAACT
546785 CGAGGCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (22 bp):
ATCAGAGTCGAAGAGAAACTTG
Found at i:546875 original size:31 final size:32
Alignment explanation
Indices: 546822--546884 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
546812 AAATAGATGG
*
546822 AGTGGTGAAAGAAGTAGAGGTG-TGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
***
546853 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
546885 TATTAAGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.44, T:0.24
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:548695 original size:17 final size:19
Alignment explanation
Indices: 548649--548688 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
548639 AATGTCGAGT
548649 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
548668 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
548687 TA
1 TA
548689 TTTGTATGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:549293 original size:201 final size:198
Alignment explanation
Indices: 548812--550553 Score: 2920
Period size: 201 Copynumber: 8.9 Consensus size: 198
548802 ACAATAGGCC
* * * *
548812 AACAGGGTGCACCCAT-AAGTGTCGATCCATATAAAAAAAGTGTCAATCCCAAAA-CATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
548875 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
548939 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCG--ATTTTTTTCCAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
549002 GGAA
195 GGAA
549006 AAC-AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGAT-CCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
549069 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTTTTATGA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG---TTTTATGA
549134 GAGAATATGTCTAAATAAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
128 GAGAATATGTCTAAAT-AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
**
549199 AATTAAA
192 AATGGAA
549206 AACAAGGTGCACCCAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
549270 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGATACAATTATACCGGTTTTATAAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
549335 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTTTCCAGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA----TTTTTTTCCAGAATG
**
549400 AATTAAA
192 AATGGAA
*
549407 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
549472 CC-AAAGTATAATGTAATA-GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
549535 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCAGAATGAAT
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
549599 GG-A
195 GGAA
549602 AAC-AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
549666 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT--GAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
549728 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
*
549793 AAA
196 GAA
*
549796 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG--AA
*
549861 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
549926 AGGATATGTCTAAATAATGTGTCGAC-CTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
549990 TGGAA
194 TGGAA
*
549995 AACAGGGTGCACCCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATC--AC
1 AACAAGGTGCACCC-ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAC
550057 CCAAAAGTATAATGTAATATGT-A-TTTTCAATCTAA-CGGTACAA-T-TACC-GTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
550116 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAA
550181 TGGAA
194 TGGAA
*
550186 AACAAGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATAATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
550250 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
550315 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
550380 GGAA
195 GGAA
*
550384 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTGGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
550449 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGATACAATTATACC-G-TTTAT--GAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
550510 AATATGTCTAAA-AATGTGTCGACACTAATATAGTTTG-GTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
550554 CTAATTTAAA
Statistics
Matches: 1476, Mismatches: 33, Indels: 79
0.93 0.02 0.05
Matches are distributed among these distances:
189 56 0.04
190 57 0.04
191 26 0.02
192 80 0.05
193 129 0.09
194 178 0.12
195 106 0.07
196 18 0.01
197 69 0.05
198 204 0.14
199 179 0.12
200 102 0.07
201 208 0.14
202 60 0.04
203 4 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:549858 original size:389 final size:392
Alignment explanation
Indices: 548812--550553 Score: 2904
Period size: 389 Copynumber: 4.4 Consensus size: 392
548802 ACAATAGGCC
* * *
548812 AACAGGGTGCACCCAT-AAGTGTCGATCCATATAAAAAAAGTGTCAATCCCAAAA-CATCGAAAA
1 AACA-GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
548875 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGAGAG
64 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGAGA-
548940 GATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCG--ATTTTTTTCCAGAATGAATG
128 -ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
*
549003 GAAAAC-AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGAT-CCAAAATCATCGA
192 AAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
*
549066 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTTTTA
257 AACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG---TTTTA
549131 TGAGAGAATATGTCTAAATAAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGA
319 TGAGAGAATATGTCTAAAT-AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGA
**
549196 ATGAATTAAA
383 ATGAATGGAA
549206 AACAAGGTGCACCCAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AAC-AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
549270 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGATACAATTATACCGGTTTTATAAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTAT--GAG
549335 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTTTCCAGAATG
127 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA----TTTTTTTCCAGAATG
*
549400 AATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
188 AATGAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCA
549465 TCGAAAACC-AAAGTATAATGTAATA-GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
253 TCG-AAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
*
549528 TATGAGAGGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCAG
317 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAG
549592 AATGAATGG-A
382 AATGAATGGAA
549602 AACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
1 AACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
549667 -AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAAT
66 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTATGAGAAT
*
549731 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAA
130 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGAAA
*
549796 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAATCATCGAAAA
195 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG--AA
549861 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
258 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
549926 AGGATATGTCTAAATAATGTGTCGAC-CTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
323 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
549990 TGGAA
388 TGGAA
549995 AACAGGGTGCACCCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATC--AC
1 AACA-GGTGCACCC-ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAC
550057 CCAAAAGTATAATGTAATATGT-A-TTTTCAATCTAA-CGGTACAA-T-TACCGTTTTATGAGAG
64 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTAT--GAG
550117 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
127 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
* *
550182 GGAAAACAAGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATAATCG
191 GAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
550246 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
256 AAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
550311 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAAT
321 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAAT
550376 GAATGGAA
385 GAATGGAA
*
550384 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTGGATCCCAAAATCATCGAACC
1 AAC-AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
550449 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGATACAATTATACCG-TTTATGAGAAT
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGAGAAT
550513 ATGTCTAAA-AATGTGTCGACACTAATATAGTTTG-GTCGATA
130 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
550554 CTAATTTAAA
Statistics
Matches: 1291, Mismatches: 20, Indels: 77
0.93 0.01 0.06
Matches are distributed among these distances:
387 98 0.08
388 53 0.04
389 236 0.18
390 39 0.03
391 80 0.06
392 120 0.09
393 100 0.08
394 144 0.11
395 151 0.12
396 58 0.04
397 22 0.02
398 33 0.03
399 23 0.02
401 23 0.02
402 79 0.06
403 28 0.02
404 4 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (392 bp):
AACAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGAGAATA
TGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGAAAA
ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAACC
AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGG
AA
Found at i:549922 original size:198 final size:196
Alignment explanation
Indices: 548812--550553 Score: 2858
Period size: 198 Copynumber: 8.9 Consensus size: 196
548802 ACAATAGGCC
* * * *
548812 AACAGGGTGCACCCAT-AAGTGTCGATCCATATAAAAAAAGTGTCAATCCCAAAA-CATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
548875 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACC-GTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
548939 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCG--ATTTTTTTCCAGAATGAAT
130 --ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
549002 GGAA
193 GGAA
549006 AAC-AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGAT-CCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
549069 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTTTTATGA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGG---TTTTAT--
549134 GAGAATATGTCTAAATAAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
126 GAGAATATGTCTAAAT-AATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
**
549199 AATTAAA
190 AATGGAA
549206 AACAAGGTGCACCCAT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
549270 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGATACAATTATACCGGTTTTATAAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT--GAG
549335 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTTTTCCAGAATG
129 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA----TTTTTTTCCAGAATG
**
549400 AATTAAA
190 AATGGAA
*
549407 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
549472 CC-AAAGTATAATGTAATA-GTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
549535 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTCCAGAATGAAT
130 --ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAAT
549599 GG-A
193 GGAA
549602 AAC-AGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
549666 C-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAA
**
549730 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAA
131 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGA
549795 A
196 A
*
549796 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTATCGATCCCAAAATCATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG--AA
*
549861 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
549926 AGGATATGTCTAAATAATGTGTCGAC-CTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
129 A--ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
549990 TGGAA
192 TGGAA
*
549995 AACAGGGTGCACCCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATC--AC
1 AACAAGGTGCACCC-ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAAC
550057 CCAAAAGTATAATGTAATATGT-A-TTTTCAATCTAA-CGGTACAA-T-TACC-GTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT--GA
550116 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
128 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAA
550181 TGGAA
192 TGGAA
*
550186 AACAAGGTGCA-CCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATAATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
550250 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT--GAG
550315 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
129 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
550380 GGAA
193 GGAA
*
550384 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTGGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
550449 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGATACAATTATACC-G-TTTATGAGAA
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAA
550512 TATGTCTAAA-AATGTGTCGACACTAATATAGTTTG-GTCGATA
131 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
550554 CTAATTTAAA
Statistics
Matches: 1476, Mismatches: 27, Indels: 91
0.93 0.02 0.06
Matches are distributed among these distances:
189 51 0.03
190 57 0.04
191 30 0.02
192 77 0.05
193 129 0.09
194 182 0.12
195 106 0.07
196 18 0.01
197 64 0.04
198 208 0.14
199 187 0.13
200 99 0.07
201 204 0.14
202 60 0.04
203 4 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (196 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAA
TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGA
A
Found at i:550242 original size:21 final size:21
Alignment explanation
Indices: 550201--550242 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
550191 GGTGCACCAT
*
550201 AAAGTGTCGATCCATATATAA
1 AAAGTGTCGATCCATAAATAA
550222 AAAGTGTCGATCCCA-AAATAA
1 AAAGTGTCGAT-CCATAAATAA
550243 TCGAACCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (21 bp):
AAAGTGTCGATCCATAAATAA
Found at i:552004 original size:18 final size:18
Alignment explanation
Indices: 551983--552050 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
551973 AGCGGTCGCA
551983 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
552001 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
552022 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
552043 GAAGATGA
1 GAAGATGA
552051 TGAGATGATG
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:552007 original size:6 final size:6
Alignment explanation
Indices: 551983--552077 Score: 64
Period size: 6 Copynumber: 15.3 Consensus size: 6
551973 AGCGGTCGCA
* * * * * *
551983 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * *
552031 GAAGCT GGCGAT GAAGAT GATGAGAT GATGAT GATGAT GAAAGAT GA
1 GAAGAT GAAGAT GAAGAT GA--AGAT GAAGAT GAAGAT G-AAGAT GA
552078 TCCAAACAGT
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
6 59 0.84
7 5 0.07
8 6 0.09
ACGTcount: A:0.38, C:0.06, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:552018 original size:3 final size:3
Alignment explanation
Indices: 551998--552070 Score: 67
Period size: 3 Copynumber: 24.7 Consensus size: 3
551988 TGAAGCTGAC
* * * * * ** *
551998 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
552046 GAT GAT GA- GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
552071 AAGATGATCC
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (3 bp):
GAT
Found at i:553840 original size:183 final size:183
Alignment explanation
Indices: 553525--553864 Score: 547
Period size: 183 Copynumber: 1.9 Consensus size: 183
553515 CTTTCAACAT
* *
553525 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
*
553590 GGTCTACAACCTATATCGACACTTTTTAATAGTGTGTCGGTACTTTATGTACAATTGGAAGAAAA
66 GGTCTACAACCTATATCGACACTTTATAATAGTGTGTCGGTACTTTATGTACAATTGGAAGAAAA
*
553655 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGCAACCCATA
131 ATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTACACATCGCAACCCATA
** * * *
553708 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
* * * *
553773 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTAC-TTATGTCCCCATTGGAATAAA
66 GGTCTACAACCTATATCGACACTTTATAATAGTGTGTCGGTACTTTATGT-ACAATTGGAAGAAA
553837 AATGTGTCGATACCATTTAAAAAAGTGT
130 AATGTGTCGATACCATTTAAAAAAGTGT
553865 TAGTTTGTTA
Statistics
Matches: 143, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 6 0.04
183 137 0.96
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (183 bp):
ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTCTTATGAGCGAATA
GGTCTACAACCTATATCGACACTTTATAATAGTGTGTCGGTACTTTATGTACAATTGGAAGAAAA
ATGTGTCGATACCATTTAAAAAAGTGTCGACATTTTACACATCGCAACCCATA
Found at i:556329 original size:23 final size:23
Alignment explanation
Indices: 556298--556361 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
556288 ATAGGTAAAC
*
556298 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
556321 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
556344 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
556362 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:556368 original size:23 final size:23
Alignment explanation
Indices: 556298--556370 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
556288 ATAGGTAAAC
* **
556298 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
556321 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
556344 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
556367 ATAT
1 ATAT
556371 TGTAAAGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:556557 original size:29 final size:30
Alignment explanation
Indices: 556514--556579 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
556504 GTTACGGTAT
* *
556514 ATATTATTATTAAAT-TAAAA-ATTCTAAATA
1 ATATT-TTATAAAATATAAAACAATC-AAATA
556544 ATATTTTATAAAATATAAAACAATCAAATA
1 ATATTTTATAAAATATAAAACAATCAAATA
556574 AT-TTTT
1 ATATTTT
556580 CTGCAAATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 12 0.38
30 17 0.53
31 3 0.09
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (30 bp):
ATATTTTATAAAATATAAAACAATCAAATA
Found at i:556754 original size:22 final size:23
Alignment explanation
Indices: 556721--556781 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 23
556711 ATAGGTAAAC
*
556721 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
**
556744 ATAT-ATGTAATAGGT--CGTTT
1 ATATAATGTAATAGGTAGCCCTT
556764 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
556782 TGGTTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 7 0.21
21 11 0.33
22 11 0.33
23 4 0.12
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:556789 original size:21 final size:20
Alignment explanation
Indices: 556726--556782 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 20
556716 TAAACATATG
*
556726 ATGTAATAGGTAGCCCTTATA
1 ATGTAATAGGTAG-TCTTATA
* *
556747 TATGTAATAGGTCGTTTATATA
1 -ATGTAATAGGTAGTCT-TATA
556769 ATGTAATAGGTAGT
1 ATGTAATAGGTAGT
556783 GGTTATATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (20 bp):
ATGTAATAGGTAGTCTTATA
Found at i:556794 original size:21 final size:20
Alignment explanation
Indices: 556721--556795 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 20
556711 ATAGGTAAAC
*
556721 ATATGATGTAATAGGTAGCCCTT
1 ATAT-ATGTAATAGGTAG--TTT
*
556744 ATATATGTAATAGGTCGTTT
1 ATATATGTAATAGGTAGTTT
556764 ATATAATGTAATAGGTAGTGGTT
1 ATAT-ATGTAATAGGTAGT--TT
556787 ATAT-TGTAA
1 ATATATGTAA
556796 AGTTTCTATC
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.13
21 18 0.39
22 12 0.26
23 10 0.22
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.40
Consensus pattern (20 bp):
ATATATGTAATAGGTAGTTT
Found at i:557195 original size:22 final size:23
Alignment explanation
Indices: 557146--557208 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
557136 ATAGGTAAAC
*
557146 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
**
557169 ATATAATGTAATAGGTA-CGTTT
1 ATATAATGTAATAGGTAGCCCTT
557191 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
557209 TGGTTATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.37
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:557221 original size:21 final size:20
Alignment explanation
Indices: 557170--557222 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
557160 GTAGCCCTTA
*
557170 TATAATGTAATAGGTACGTT
1 TATATTGTAATAGGTACGTT
557190 TATATAATGTAATAGGTA-GTGGT
1 TATAT--TGTAATAGGTACGT--T
557213 TATATTGTAA
1 TATATTGTAA
557223 AGTTTCTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 7 0.25
22 11 0.39
23 6 0.21
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.42
Consensus pattern (20 bp):
TATATTGTAATAGGTACGTT
Found at i:557552 original size:22 final size:22
Alignment explanation
Indices: 557507--557552 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
557497 ATTACATAAG
*
557507 TTTTAAAAAAAGTATCGATCCT
1 TTTTAAAAAAAGTATCGAACCT
*
557529 TTTTATAAAAAGTAT-GAACACT
1 TTTTAAAAAAAGTATCGAAC-CT
557551 TT
1 TT
557553 CAATATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTTAAAAAAAGTATCGAACCT
Found at i:557568 original size:424 final size:428
Alignment explanation
Indices: 556200--558720 Score: 4469
Period size: 425 Copynumber: 5.9 Consensus size: 428
556190 AATTCGCAGT
*
556200 ACACTGTTAAAAAATTTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAA
556265 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
66 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
*
556330 AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTTTCTATCCTTTTTATA
131 AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATA
*
556395 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAATATTA-ATTTTGAGTGAGTTTTA
196 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGATTATATTTTGAGTGAGTTTTA
556459 AGATATTAATTTAGT-ATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTA
261 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGT-TATATTATTA
556523 TTAAATTAAAAATTCTAAATAATATTTTATAAAATAT-AAAACAATCAAATAATTTTTCTGCAAA
325 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTCTGCAAA
556587 TGAAATTATTAAATCAATATTGTAGGTGG-AAACATGAA
390 TGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
556625 ACACTGTT--AAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAA
556688 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATAT-ATGT
66 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
*
556752 AATAGG--TCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTTTCTATCCTTTTTATA
131 AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATA
* *
556815 AAAGTGTCCATACTTTTTTTACTGTGGAAAACATTAATTTAATATTA-ATTTTTGAGTGAGTTTT
196 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGATTATA-TTTTGAGTGAGTTTT
556879 AAGATATTAA-TTAGTAA-TATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
260 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGT-TATATTATT
556942 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTCTGCAA
324 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTCTGCAA
557007 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
389 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
557047 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGATCCTTTTTATA
557112 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
65 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
*
557177 TAATAGGTA-CGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTTTCTATCCTTTTTAT
130 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
*
557241 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAATATTA-ATTTTGAGTGAGTTTT
195 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGATTATATTTTGAGTGAGTTTT
557305 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGG-TATA-TATTA
260 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTTATATTATTA
557367 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTCTGCAA
325 TTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAA-TTTTTCTGCAA
557432 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
389 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
557472 ACACTGTT-AAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGATCCTTTTTATA
*
557536 AAAAGTATGAACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
65 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
557601 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTG-AAAGTGTCTATCCTTTTTAT
130 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
* *
557665 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
195 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGATTATATTTTGAGTGAGTTTT
557730 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTTATATATTAT
260 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGG-T-TATATTAT
557795 TATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTCTGC
323 TATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAA-TTTTTCTGC
557860 AAATGAAATTA-TAAATCAATATTGTAGGTGGAAAACATGAA
387 AAATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
557901 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCC-TTTTAT-
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTT-AAAAAAGTATCGATCCTTTTTATA
* *
557964 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATAATATAATA-GTAGCCCTTATATAATG
65 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
* *
558028 AAATAGATATCG-TTATATAATGTAATAGGTAGTGGTTAT-TTGTAAAGTGTCTATCCTTTTTAT
130 TAATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTAT
* * *
558091 -AAAGTGTCCATACTTTTTTCAATGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
195 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGATTATATTTTGAGTGAGTTTT
558155 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTA-TTTTTACGTTACGGTATATATTATT
260 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGT-TATATTATT
*
558219 ATT-AATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTGTGCAA
324 ATTAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTCTGCAA
558283 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
389 ATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
*
558323 ACAATGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCC-TTTTATAA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAA
558387 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATAT-ATGT
66 AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
558451 AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATA
131 AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATA
* *
558516 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTA
196 AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGATTATATTTTGAGTGAGTTTTA
* *
558581 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTGC-GATATA-TATTAT
261 AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTTATATTATTAT
* * *
558644 TAAATTAAAAATTCTAAATATTA-TTTATAAAATATCAAAACAATCAAATAATTTTTGTGCAAAT
326 TAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTCTGCAAAT
558708 GAAATTATTAAAT
391 GAAATTATTAAAT
558721 TAAATAATTC
Statistics
Matches: 2041, Mismatches: 25, Indels: 62
0.96 0.01 0.03
Matches are distributed among these distances:
420 193 0.09
421 123 0.06
422 204 0.10
423 228 0.11
424 344 0.17
425 452 0.22
426 107 0.05
427 151 0.07
428 64 0.03
429 48 0.02
430 127 0.06
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (428 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAGTATCGATCCTTTTTATAA
AAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATGT
AATAGGTATCGTTTATATAATGTAATAGGTAGTGGTTATATTGTAAAGTGTCTATCCTTTTTATA
AAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGATTATATTTTGAGTGAGTTTTA
AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTTATATTATTAT
TAAATTAAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTCTGCAAAT
GAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:557601 original size:23 final size:23
Alignment explanation
Indices: 557570--557633 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
557560 ATAGGTAAAC
*
557570 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
557593 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
557616 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
557634 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:557640 original size:23 final size:23
Alignment explanation
Indices: 557570--557642 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
557560 ATAGGTAAAC
* **
557570 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
557593 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
557616 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
557639 ATAT
1 ATAT
557643 TGAAAGTGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:558032 original size:22 final size:22
Alignment explanation
Indices: 557998--558055 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
557988 ATAGGTAAAC
557998 ATATAAT-ATAATAG-TAGCCCTT
1 ATATAATGA-AATAGATA-CCCTT
* *
558020 ATATAATGAAATAGATATCGTT
1 ATATAATGAAATAGATACCCTT
*
558042 ATATAATGTAATAG
1 ATATAATGAAATAG
558056 GTAGTGGTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (22 bp):
ATATAATGAAATAGATACCCTT
Found at i:558095 original size:20 final size:20
Alignment explanation
Indices: 558070--558108 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
558060 TGGTTATTTG
* *
558070 TAAAGTGTCTATCCTTTTTA
1 TAAAGTGTCCATACTTTTTA
558090 TAAAGTGTCCATACTTTTT
1 TAAAGTGTCCATACTTTTT
558109 TCAATGTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.10, T:0.49
Consensus pattern (20 bp):
TAAAGTGTCCATACTTTTTA
Found at i:558453 original size:22 final size:23
Alignment explanation
Indices: 558420--558482 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
558410 ATAGGTAAAC
*
558420 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
558443 ATAT-ATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
558465 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
558483 TGGTTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.54
23 16 0.46
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:558489 original size:23 final size:22
Alignment explanation
Indices: 558420--558496 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
558410 ATAGGTAAAC
**
558420 ATATGATGTAATAGGTAGCCCTT
1 ATAT-ATGTAATAGGTAGTGCTT
*
558443 ATATATGTAATAGGTA-TCGTTT
1 ATATATGTAATAGGTAGT-GCTT
*
558465 ATATAATGTAATAGGTAGTGGTT
1 ATAT-ATGTAATAGGTAGTGCTT
558488 ATAT-TGTAA
1 ATATATGTAA
558497 AGTGTCTATC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
21 5 0.11
22 18 0.38
23 23 0.49
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (22 bp):
ATATATGTAATAGGTAGTGCTT
Found at i:558789 original size:25 final size:25
Alignment explanation
Indices: 558755--558805 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
558745 ACAACAAATC
*
558755 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
558780 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
558805 A
1 A
558806 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:559026 original size:11 final size:11
Alignment explanation
Indices: 559010--559038 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
559000 TTTCATGTTG
559010 CATTTCAAATT
1 CATTTCAAATT
559021 CATTTCAAATT
1 CATTTCAAATT
559032 CATTTCA
1 CATTTCA
559039 TATGTAATTG
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:0.21, G:0.00, T:0.45
Consensus pattern (11 bp):
CATTTCAAATT
Found at i:559060 original size:24 final size:25
Alignment explanation
Indices: 559033--559087 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
559023 TTTCAAATTC
*
559033 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
559057 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
559081 ATTTCAA
1 ATTTCAA
559088 TATATATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:559073 original size:18 final size:18
Alignment explanation
Indices: 559052--559088 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
559042 GTAATTGGAG
559052 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
559070 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
559088 T
1 T
559089 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:559390 original size:39 final size:39
Alignment explanation
Indices: 559347--559433 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
559337 TCCGATGCTC
* *
559347 ATCAAAATCCAAAGCTCATATGGTGTCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
559386 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
559425 ATCAAAATC
1 ATCAAAATC
559434 TACAACTTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:559786 original size:23 final size:23
Alignment explanation
Indices: 559755--559818 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
559745 ATAGGTAAAC
*
559755 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
559778 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
559801 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
559819 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:559825 original size:23 final size:23
Alignment explanation
Indices: 559755--559827 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
559745 ATAGGTAAAC
* **
559755 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
559778 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
559801 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
559824 ATAT
1 ATAT
559828 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:560539 original size:2 final size:2
Alignment explanation
Indices: 560534--560561 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
560524 GTGTGTGTGT
560534 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
560562 TCGATTTGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:560723 original size:5 final size:5
Alignment explanation
Indices: 560710--560739 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
560700 CTTTTTTTAT
560710 TTTTCC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTT-C TTTTC TTTTC TTTTC TTTTC TTTT
560740 GCTGATTTTG
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:585227 original size:29 final size:29
Alignment explanation
Indices: 585173--585228 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
585163 GATTCATTTG
* *
585173 ATAAATATTAAAAAATTATAATTAATATT
1 ATAAATATTAAAAAAATATAAATAATATT
585202 ATAAATA-TAAAAAAATATAACATAATA
1 ATAAATATTAAAAAAATATAA-ATAATA
585229 ATATTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (29 bp):
ATAAATATTAAAAAAATATAAATAATATT
Found at i:585236 original size:16 final size:15
Alignment explanation
Indices: 585190--585250 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
585180 TTAAAAAATT
585190 ATAATTAATATTATAA
1 ATAA-TAATATTATAA
* * *
585206 ATATAAAAAAATATAA
1 ATA-ATAATATTATAA
585222 CATAATAATATTATAA
1 -ATAATAATATTATAA
*
585238 ACAA-AATATTATA
1 ATAATAATATTATA
585251 GTAGTAAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
14 9 0.25
15 3 0.08
16 20 0.56
17 4 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAATAATATTATAA
Found at i:586646 original size:29 final size:29
Alignment explanation
Indices: 586613--586668 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
586603 TCCCAACACA
*
586613 TAGGTCTCCATGC-CTTCCGGGCGACCTTG
1 TAGGTCGCCATGCAC-TCCGGGCGACCTTG
586642 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
586669 ATCCTCGCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.12, C:0.36, G:0.29, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:586713 original size:33 final size:33
Alignment explanation
Indices: 586672--586746 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
586662 GCGACCTATC
586672 CTCGCTCGGCTT-CCCTCGGAT-TCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGT-CCTCGCATAG
586705 CTCGCTCGGTTGCCCTCGGATGTCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGTCCTCGCATAG
*
586738 CTCGTTCGG
1 CTCGCTCGG
586747 ATGGCCTTGG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
32 2 0.05
33 36 0.92
34 1 0.03
ACGTcount: A:0.08, C:0.39, G:0.25, T:0.28
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGTCCTCGCATAG
Found at i:586772 original size:10 final size:10
Alignment explanation
Indices: 586757--586809 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
586747 ATGGCCTTGG
586757 TCGGATGGCC
1 TCGGATGGCC
586767 TCGGAT-G-C
1 TCGGATGGCC
586775 TCGGATGGCCC
1 TCGGATGG-CC
586786 TCGGAT-GCTC
1 TCGGATGGC-C
586796 TCGGATGGCC
1 TCGGATGGCC
586806 TCGG
1 TCGG
586810 TCGGATGGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
8 7 0.18
9 3 0.08
10 19 0.50
11 9 0.24
ACGTcount: A:0.09, C:0.30, G:0.38, T:0.23
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:586815 original size:14 final size:14
Alignment explanation
Indices: 586738--586821 Score: 65
Period size: 14 Copynumber: 6.2 Consensus size: 14
586728 CCTCGCATAG
*
586738 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
*
586752 CTTGGTCGGATGGC
1 CTCGGTCGGATGGC
586766 CTCGGATGCTCGGATGGC
1 CTC-G--G-TCGGATGGC
586784 C-C--TCGGAT-G-
1 CTCGGTCGGATGGC
586793 CTC--TCGGATGGC
1 CTCGGTCGGATGGC
586805 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
586819 CTC
1 CTC
586822 AGATACCCAG
Statistics
Matches: 58, Mismatches: 3, Indels: 18
0.73 0.04 0.23
Matches are distributed among these distances:
9 1 0.02
10 8 0.14
11 7 0.12
12 3 0.05
14 26 0.45
15 1 0.02
17 2 0.03
18 10 0.17
ACGTcount: A:0.08, C:0.30, G:0.37, T:0.25
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Done.