Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007940.1 Hibiscus syriacus cultivar Beakdansim tig00110356_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: 1348078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:362494 original size:74 final size:75
Alignment explanation
Indices: 362393--362569 Score: 205
Period size: 74 Copynumber: 2.4 Consensus size: 75
362383 AACTTTATAA
* * * *
362393 CATATGTATCGATATTTTAACTATCGATCATTTTCATCAACTTGTTCAATATCTAAAAGTATTG-
1 CATAAGTATCGATATTTTAAATTTCGATCATTTTCATCAACTTGTTCAATATCTAAAAGTATCGA
**
362457 ATCATCGTCG
66 ATCATCACCG
* * * * *
362467 CATAAGTATCGATATTTTAAATTTCGAT-ATTTTTATCAATTTTTTCAATTTTTAAAAGTATCGA
1 CATAAGTATCGATATTTTAAATTTCGATCATTTTCATCAACTTGTTCAATATCTAAAAGTATCGA
* *
362531 ATCTTTACCG
66 ATCATCACCG
* *
362541 CATAATTATTGATATTTTAAATTTCGATC
1 CATAAGTATCGATATTTTAAATTTCGATC
362570 TTATCTTTAA
Statistics
Matches: 86, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
73 29 0.34
74 57 0.66
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (75 bp):
CATAAGTATCGATATTTTAAATTTCGATCATTTTCATCAACTTGTTCAATATCTAAAAGTATCGA
ATCATCACCG
Found at i:362755 original size:79 final size:77
Alignment explanation
Indices: 362622--362845 Score: 227
Period size: 79 Copynumber: 2.9 Consensus size: 77
362612 TTGCGCGACG
* * * * * * *
362622 TATTTTATTAATAAAAAT-ATTAACATAACATATCACAACCTATTTCTTAGTGAACTATTATATT
1 TATTTTATTAA-AAAAATAATTAACATTACAGATCACAACATATTTCTTAATGAACCATAACATT
* *
362686 ATTGGGTGCAACC
65 ATTGGGCGCAAAC
* *
362699 TATTTTATTAAAAAAATAATATTACATTATAGATCACAACATACTTTCTTAATGAACCATAACAT
1 TATTTTATTAAAAAAATAAT-TAACATTACAGATCACAACATA-TTTCTTAATGAACCATAACAT
*
362764 TCTTGGGCGCAAAC
64 TATTGGGCGCAAAC
* * * * * * * *
362778 AATTTTATTAATAAAA-AATTAACATTACAGATCACAACCTGTTTCTTAGTGAATCATGACATTG
1 TATTTTATTAAAAAAATAATTAACATTACAGATCACAACATATTTCTTAATGAACCATAACATTA
362842 TTGG
66 TTGG
362846 ACACAACTGT
Statistics
Matches: 122, Mismatches: 22, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
76 29 0.24
77 31 0.25
78 20 0.16
79 42 0.34
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.37
Consensus pattern (77 bp):
TATTTTATTAAAAAAATAATTAACATTACAGATCACAACATATTTCTTAATGAACCATAACATTA
TTGGGCGCAAAC
Found at i:370914 original size:8 final size:8
Alignment explanation
Indices: 370901--370948 Score: 51
Period size: 8 Copynumber: 5.5 Consensus size: 8
370891 TCGTTCGTTT
370901 AAACGAAC
1 AAACGAAC
370909 AAACGAATGC
1 AAACGAA--C
*
370919 AAATGAAC
1 AAACGAAC
370927 AAACGAAC
1 AAACGAAC
370935 GTAAACGAAC
1 --AAACGAAC
370945 AAAC
1 AAAC
370949 ATAAAATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
8 19 0.56
10 15 0.44
ACGTcount: A:0.58, C:0.21, G:0.15, T:0.06
Consensus pattern (8 bp):
AAACGAAC
Found at i:370928 original size:18 final size:18
Alignment explanation
Indices: 370901--370948 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
370891 TCGTTCGTTT
*
370901 AAACGAACAAACGAATGC
1 AAACGAACAAACGAACGC
* *
370919 AAATGAACAAACGAACGT
1 AAACGAACAAACGAACGC
370937 AAACGAACAAAC
1 AAACGAACAAAC
370949 ATAAAATGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.58, C:0.21, G:0.15, T:0.06
Consensus pattern (18 bp):
AAACGAACAAACGAACGC
Found at i:371947 original size:2 final size:2
Alignment explanation
Indices: 371940--371964 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
371930 AGTAATAGTA
371940 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
371965 TAAGTGGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:381676 original size:25 final size:24
Alignment explanation
Indices: 381635--381689 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
381625 ATATAGTTAT
*
381635 TAAAAAAAAGAAGGAAAAATATGA
1 TAAAAAAAAGAAAGAAAAATATGA
*
381659 TAAAAGAAAATAAAGAAAAATAT-A
1 TAAAA-AAAAGAAAGAAAAATATGA
381683 -AAAAAAA
1 TAAAAAAA
381690 TCTACTGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 4 0.14
24 6 0.21
25 15 0.54
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (24 bp):
TAAAAAAAAGAAAGAAAAATATGA
Found at i:382834 original size:120 final size:120
Alignment explanation
Indices: 382642--382881 Score: 367
Period size: 120 Copynumber: 2.0 Consensus size: 120
382632 AAGTTGTACA
* * * *
382642 AATTATAATTACAAAAATATAAATTTAATTTTATAAATAACTACAAATTATTTTTACAATTATTC
1 AATTATAATTACAAAAAAATAAAATAAATTTAATAAATAACTACAAATTATTTTTACAATTATTC
382707 AAATATTCAATGATAGAATTACCAATAAAACAAATAACTAAAGTTAAAAAAATGT
66 AAATATTCAATGATAGAATTACCAATAAAACAAATAACTAAAGTTAAAAAAATGT
* *
382762 AATTATAATTACCAATAAAAATAAAATAAATTTAAT-TATAATTACAAATTATTTTTACAATTAT
1 AATTATAATTA-CAA-AAAAATAAAATAAATTTAATAAATAACTACAAATTATTTTTACAATTAT
* * *
382826 T-AAGTATTCAATGATAGAATTACCAATAAAATAAATAACTAAAGTTCAAAAAATGT
64 TCAAATATTCAATGATAGAATTACCAATAAAACAAATAACTAAAGTTAAAAAAATGT
382882 GTTATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
120 63 0.58
121 30 0.28
122 16 0.15
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (120 bp):
AATTATAATTACAAAAAAATAAAATAAATTTAATAAATAACTACAAATTATTTTTACAATTATTC
AAATATTCAATGATAGAATTACCAATAAAACAAATAACTAAAGTTAAAAAAATGT
Found at i:392427 original size:42 final size:41
Alignment explanation
Indices: 392368--392454 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 41
392358 CAACATCTTA
*
392368 ATTTTTAAAAAAATTGTTGA-ATGAATAATTATTTTCACATC
1 ATTTTTAAAAAAATTGTT-ATATGAATAATCATTTTCACATC
* *
392409 ATTTTTCAAAAAAATTGTTATATGAATAATCCTTTTCACGTC
1 ATTTTT-AAAAAAATTGTTATATGAATAATCATTTTCACATC
392451 ATTT
1 ATTT
392455 ATAGTATCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
41 7 0.17
42 34 0.83
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (41 bp):
ATTTTTAAAAAAATTGTTATATGAATAATCATTTTCACATC
Found at i:392625 original size:16 final size:15
Alignment explanation
Indices: 392578--392635 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
392568 CCATTTCACC
*
392578 TAAAATCATTTTAT-
1 TAAAATAATTTTATA
392592 TAAACA-AATTCTTATA
1 TAAA-ATAATT-TTATA
*
392608 -AATATAATTTTATA
1 TAAAATAATTTTATA
*
392622 TAAAATATTTTTAT
1 TAAAATAATTTTAT
392636 TTATCCACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
14 13 0.37
15 22 0.63
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATAATTTTATA
Found at i:394482 original size:165 final size:165
Alignment explanation
Indices: 394210--394540 Score: 662
Period size: 165 Copynumber: 2.0 Consensus size: 165
394200 ACGATGGGTG
394210 ACCATGAAGAGAGGGATATAGTGAAATCGACAATATATCTGAGGACTTGAGGGATTGTATTGATG
1 ACCATGAAGAGAGGGATATAGTGAAATCGACAATATATCTGAGGACTTGAGGGATTGTATTGATG
394275 ACAACCCTGGATGCAAAAACACCAAAAATTGCAACAAGAACAATGAAACAAAGGCTTTTGGGATT
66 ACAACCCTGGATGCAAAAACACCAAAAATTGCAACAAGAACAATGAAACAAAGGCTTTTGGGATT
394340 CATTGTGTTTTTAGTATATGTTATATACGGGATAA
131 CATTGTGTTTTTAGTATATGTTATATACGGGATAA
394375 ACCATGAAGAGAGGGATATAGTGAAATCGACAATATATCTGAGGACTTGAGGGATTGTATTGATG
1 ACCATGAAGAGAGGGATATAGTGAAATCGACAATATATCTGAGGACTTGAGGGATTGTATTGATG
394440 ACAACCCTGGATGCAAAAACACCAAAAATTGCAACAAGAACAATGAAACAAAGGCTTTTGGGATT
66 ACAACCCTGGATGCAAAAACACCAAAAATTGCAACAAGAACAATGAAACAAAGGCTTTTGGGATT
394505 CATTGTGTTTTTAGTATATGTTATATACGGGATAA
131 CATTGTGTTTTTAGTATATGTTATATACGGGATAA
394540 A
1 A
394541 TGGGACGTTT
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 166 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (165 bp):
ACCATGAAGAGAGGGATATAGTGAAATCGACAATATATCTGAGGACTTGAGGGATTGTATTGATG
ACAACCCTGGATGCAAAAACACCAAAAATTGCAACAAGAACAATGAAACAAAGGCTTTTGGGATT
CATTGTGTTTTTAGTATATGTTATATACGGGATAA
Found at i:395732 original size:21 final size:20
Alignment explanation
Indices: 395655--395740 Score: 59
Period size: 21 Copynumber: 4.3 Consensus size: 20
395645 AAAAATATAT
*
395655 ATTAAATTCAAATTTATCTA
1 ATTAAATTAAAATTTATCTA
* * *
395675 AATAAA--AAAATTAATTTA
1 ATTAAATTAAAATTTATCTA
* **
395693 ATTCAAATGAAAAAATATCTA
1 ATT-AAATTAAAATTTATCTA
*
395714 TATTAAATTCAAATTTATCTA
1 -ATTAAATTAAAATTTATCTA
*
395735 AATAAA
1 ATTAAA
395741 AAATAATTTA
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
18 11 0.23
19 3 0.06
20 10 0.21
21 21 0.44
22 3 0.06
ACGTcount: A:0.55, C:0.07, G:0.01, T:0.37
Consensus pattern (20 bp):
ATTAAATTAAAATTTATCTA
Found at i:395742 original size:58 final size:56
Alignment explanation
Indices: 395632--395754 Score: 194
Period size: 60 Copynumber: 2.1 Consensus size: 56
395622 ACACTCAAAT
*
395632 TTTAACTCAAATGAAAAATATATATTAAATTCAAATTTATCTAAATAAAAAAATTAA
1 TTTAATTCAAATGAAAAATATATATTAAATTCAAATTTATCTAAATAAAAAAA-TAA
395689 TTTAATTCAAATGAAAAAATATCTATATTAAATTCAAATTTATCTAAAT-AAAAAATAA
1 TTTAATTCAAATG-AAAAATA--TATATTAAATTCAAATTTATCTAAATAAAAAAATAA
395747 TTTAATTC
1 TTTAATTC
395755 GTTTTGACTA
Statistics
Matches: 62, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
57 12 0.19
58 18 0.29
59 6 0.10
60 26 0.42
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (56 bp):
TTTAATTCAAATGAAAAATATATATTAAATTCAAATTTATCTAAATAAAAAAATAA
Found at i:396592 original size:64 final size:64
Alignment explanation
Indices: 396491--396619 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
396481 ATCTTTCCAA
396491 GGCCAACGGCTGGACCACTTCGCCCCATTGTCCATGGCCAGACTTTGAAGTACAACATGAAGTT
1 GGCCAACGGCTGGACCACTTCGCCCCATTGTCCATGGCCAGACTTTGAAGTACAACATGAAGTT
396555 GGCCAACGGCTGGACCACTTCGCCCCATTGTCCATGGCCAGACTTTGAAGTACAACATGAAGTT
1 GGCCAACGGCTGGACCACTTCGCCCCATTGTCCATGGCCAGACTTTGAAGTACAACATGAAGTT
396619 G
1 G
396620 AGAGCTGGCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.25, C:0.29, G:0.24, T:0.22
Consensus pattern (64 bp):
GGCCAACGGCTGGACCACTTCGCCCCATTGTCCATGGCCAGACTTTGAAGTACAACATGAAGTT
Found at i:401845 original size:18 final size:18
Alignment explanation
Indices: 401808--401847 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
401798 TACCACCCAA
**
401808 CTCCGCCGCCCAAATGTC
1 CTCCGCCGCCCAAACATC
*
401826 CTCCGGCGCCCAAACATC
1 CTCCGCCGCCCAAACATC
401844 CTCC
1 CTCC
401848 CATTGTGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.53, G:0.15, T:0.15
Consensus pattern (18 bp):
CTCCGCCGCCCAAACATC
Found at i:401934 original size:72 final size:72
Alignment explanation
Indices: 401870--402117 Score: 399
Period size: 72 Copynumber: 3.4 Consensus size: 72
401860 TCCGTTTCAC
* * * * *
401870 CCTAAACCACCAAAACATCCACCGCACCCTCCC-AAACCACCGAAGCCTCCGGTGGTTAACCCTC
1 CCTAAACCACCTAAACATCCACCGCATCCTCCCGAAA-CGCCGAAGCCTCCGGTTGTTAACCCGC
*
401934 CATATCAT
65 CCTATCAT
401942 CCTAAACCACCTAAACATCCACCGCATCCTCCCGAAACGCCGAAGCCTCCGGTTGTTAACCCGCC
1 CCTAAACCACCTAAACATCCACCGCATCCTCCCGAAACGCCGAAGCCTCCGGTTGTTAACCCGCC
402007 CTATCAT
66 CTATCAT
*
402014 CCTAAACCGCCTAAACATCCACCGCATCCTCCCGAAACGCCGAAGCCTCCGGTTGTTAACCCGCC
1 CCTAAACCACCTAAACATCCACCGCATCCTCCCGAAACGCCGAAGCCTCCGGTTGTTAACCCGCC
402079 CTATCAT
66 CTATCAT
* *
402086 CCTAAACCGCCTAAGCATCCACCGCATCCTCC
1 CCTAAACCACCTAAACATCCACCGCATCCTCC
402118 TAAGCCTCCT
Statistics
Matches: 167, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
72 164 0.98
73 3 0.02
ACGTcount: A:0.27, C:0.44, G:0.12, T:0.17
Consensus pattern (72 bp):
CCTAAACCACCTAAACATCCACCGCATCCTCCCGAAACGCCGAAGCCTCCGGTTGTTAACCCGCC
CTATCAT
Found at i:402173 original size:33 final size:35
Alignment explanation
Indices: 402125--402201 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
402115 TCCTAAGCCT
* * *
402125 CCTGTCGTAAGGCCTCC-CC-ATGTACCCAAACCA
1 CCTGTTGTAAAGCCTCCACCTACGTACCCAAACCA
*
402158 CCTGTTGTAAAGCCTCCACCTTACGTACCCAAACCT
1 CCTGTTGTAAAGCCTCCACC-TACGTACCCAAACCA
*
402194 CCGGTTGT
1 CCTGTTGT
402202 TAAACCCCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 15 0.42
34 2 0.06
36 19 0.53
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.23
Consensus pattern (35 bp):
CCTGTTGTAAAGCCTCCACCTACGTACCCAAACCA
Found at i:404950 original size:21 final size:21
Alignment explanation
Indices: 404925--404965 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
404915 CCGTGAACAG
* *
404925 TGCTACAGTGCATCGATGCAT
1 TGCTACAGTACATAGATGCAT
*
404946 TGCTATAGTACATAGATGCA
1 TGCTACAGTACATAGATGCA
404966 CTAAAATTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (21 bp):
TGCTACAGTACATAGATGCAT
Found at i:405833 original size:32 final size:32
Alignment explanation
Indices: 405792--405867 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
405782 CATAGGCATA
*
405792 CTGTCCATATGTCTCAAAAGACAAAGGTAATT
1 CTGTCCATATGTCCCAAAAGACAAAGGTAATT
* *
405824 CTGTCCATATGTCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTCCCAAAAGACAAAGGTAATT
*
405856 ATGTCCATATGT
1 CTGTCCATATGT
405868 TCCGTAGAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (32 bp):
CTGTCCATATGTCCCAAAAGACAAAGGTAATT
Found at i:405880 original size:32 final size:32
Alignment explanation
Indices: 405762--405885 Score: 112
Period size: 32 Copynumber: 3.9 Consensus size: 32
405752 CTAGGTAAAC
* *
405762 TGTCCATATGTTCCTTAGAACATAGG-CA-TA
1 TGTCCATATGTTCCGTAGAACATAGGTAATTA
*** * *
405792 CTGTCCATATGTCTCAAAAG-ACAAAGGTAATTC
1 -TGTCCATATGT-TCCGTAGAACATAGGTAATTA
* *
405825 TGTCCATATGTCCCG-AAAGACATAGGTAATTA
1 TGTCCATATGTTCCGTAGA-ACATAGGTAATTA
405857 TGTCCATATGTTCCGTAGAACATAGGTAA
1 TGTCCATATGTTCCGTAGAACATAGGTAA
405886 ACCCTCGACT
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
30 1 0.01
31 18 0.25
32 51 0.70
33 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (32 bp):
TGTCCATATGTTCCGTAGAACATAGGTAATTA
Found at i:417600 original size:14 final size:14
Alignment explanation
Indices: 417581--417609 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
417571 TTTGAATGAA
417581 ATATTATCTTAATT
1 ATATTATCTTAATT
417595 ATATTATCTTAATT
1 ATATTATCTTAATT
417609 A
1 A
417610 AGTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTATCTTAATT
Found at i:421612 original size:2 final size:2
Alignment explanation
Indices: 421607--421636 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
421597 ACACACACGC
421607 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
421637 GAGAAGCAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:427423 original size:5 final size:5
Alignment explanation
Indices: 427413--427438 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
427403 AGATCGATAA
427413 TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC T
427439 CAGAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:433347 original size:23 final size:22
Alignment explanation
Indices: 433303--433348 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
433293 GATATTTTTC
*
433303 TAAAATTTATATTTATAGATAT
1 TAAAATTTATATATATAGATAT
433325 TAAAATTATATATAATATA-ATAT
1 TAAAATT-TATAT-ATATAGATAT
433348 T
1 T
433349 TTAATCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 10 0.48
24 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TAAAATTTATATATATAGATAT
Found at i:445689 original size:21 final size:20
Alignment explanation
Indices: 445664--445762 Score: 101
Period size: 21 Copynumber: 4.8 Consensus size: 20
445654 AATCAGTTTC
445664 GACTATCGCAATGCGAACTTG
1 GACTATCGCAATGCGAA-TTG
*
445685 GACTATCACAATGCGAATATG
1 GACTATCGCAATGCGAAT-TG
* * * *
445706 TA-AATCGCAATGCGATAGTC
1 GACTATCGCAATGCGA-ATTG
445726 GACTATCGCAATGCGAACTTG
1 GACTATCGCAATGCGAA-TTG
*
445747 GACTATCGCATTGCGA
1 GACTATCGCAATGCGA
445763 TTTACATATT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 15 0.24
21 48 0.76
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (20 bp):
GACTATCGCAATGCGAATTG
Found at i:445777 original size:20 final size:20
Alignment explanation
Indices: 445752--445807 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
445742 ACTTGGACTA
445752 TCGCATTGCGATTTACATA-T
1 TCGCATTGCGATTTACA-AGT
* *
445772 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGAT-TTACAAGT
445793 TCGCATTGCGATTTA
1 TCGCATTGCGATTTA
445808 TTTCAAATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAGT
Found at i:445839 original size:42 final size:40
Alignment explanation
Indices: 445751--445839 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 40
445741 AACTTGGACT
* *
445751 ATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1 ATCGCATTGCGATTTACAAATTCG-ATTGCGATAGTCCAAA
* *
445792 TTCGCATTGCGATTTATTTCAAATTCG-TTGTGATAGTCCAAA
1 ATCGCATTGCGATTTA---CAAATTCGATTGCGATAGTCCAAA
445834 ATCGCA
1 ATCGCA
445840 AGAATTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 15 0.38
42 18 0.45
44 7 0.17
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (40 bp):
ATCGCATTGCGATTTACAAATTCGATTGCGATAGTCCAAA
Found at i:446579 original size:42 final size:42
Alignment explanation
Indices: 446518--447031 Score: 875
Period size: 42 Copynumber: 12.2 Consensus size: 42
446508 GCGATTTTGA
* * *
446518 ACTATCACAACGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
446560 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
* * * *
446602 ACTATCGCAACAAATTTAGAATAAATCGCAACACGAACTTGG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
* *
446644 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
*
446686 ACTATCGCAACGAACTTGGAATAAATCGCAACACGAACTTGG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
* *
446728 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
446770 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
446812 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
* *
446854 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
* *
446896 ACTATCGCAACGAACTTGGAAAAAATTGCAACGCGAACTTGG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
*
446938 ACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
446980 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
1 ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
447022 ACTATCGCAA
1 ACTATCGCAA
447032 TGCGAATATG
Statistics
Matches: 443, Mismatches: 29, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 443 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (42 bp):
ACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGG
Found at i:449278 original size:15 final size:15
Alignment explanation
Indices: 449258--449328 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
449248 AATACATAAC
449258 ATAAATATAAAATT-T
1 ATAAAT-TAAAATTAT
*
449273 ATAAATTCAAATTAT
1 ATAAATTAAAATTAT
* *
449288 ATAATTTAAAAATATAA
1 ATAAATT-AAAAT-TAT
* *
449305 AAAAAGTAAAATTAT
1 ATAAATTAAAATTAT
449320 A-AAATTAAA
1 ATAAATTAAA
449329 GCTAAATTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
14 13 0.30
15 16 0.36
16 9 0.20
17 6 0.14
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (15 bp):
ATAAATTAAAATTAT
Found at i:451219 original size:23 final size:21
Alignment explanation
Indices: 451181--451223 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
451171 ATAATTATTT
451181 AAAAAATTAAATAAAAATATA
1 AAAAAATTAAATAAAAATATA
*
451202 AAAAATATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATA
451223 A
1 A
451224 TTTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATA
Found at i:467701 original size:7 final size:7
Alignment explanation
Indices: 467689--467722 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
467679 GGGTAGGTTA
467689 GGCAATG
1 GGCAATG
467696 GGCAATG
1 GGCAATG
467703 GGCAATG
1 GGCAATG
467710 GGCAATG
1 GGCAATG
467717 GGCAAT
1 GGCAAT
467723 TGGGTTTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.41, T:0.15
Consensus pattern (7 bp):
GGCAATG
Found at i:471231 original size:30 final size:31
Alignment explanation
Indices: 471185--471247 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
471175 AAATATATTT
*
471185 TTTGTTTTCCTTAAAATTTTACGTATTTAAA
1 TTTGTTCTCCTTAAAATTTTACGTATTTAAA
*
471216 TTTGTTCTCC-TAAAATTTTATGTATTTAAA
1 TTTGTTCTCCTTAAAATTTTACGTATTTAAA
471246 TT
1 TT
471248 CGTCACTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 21 0.70
31 9 0.30
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.56
Consensus pattern (31 bp):
TTTGTTCTCCTTAAAATTTTACGTATTTAAA
Found at i:473716 original size:29 final size:29
Alignment explanation
Indices: 473683--473787 Score: 165
Period size: 29 Copynumber: 3.6 Consensus size: 29
473673 TCCCCAAGCA
* *
473683 TAGGTCGTCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
473712 TAGGTCGCCATGCACTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
* *
473741 TGGGTCGCCATGCACTCCTGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
*
473770 TGGGTCGCCATGCACTCC
1 TAGGTCGCCATGCACTCC
473788 CTCCTGCTCC
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 72 1.00
ACGTcount: A:0.11, C:0.35, G:0.30, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:473858 original size:14 final size:14
Alignment explanation
Indices: 473841--473874 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
473831 GCTCAGATAG
473841 CCTCGGTCGGATGC
1 CCTCGGTCGGATGC
*
473855 CCTCGGTCGGATGG
1 CCTCGGTCGGATGC
473869 CCTCGG
1 CCTCGG
473875 ATGCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.35, G:0.38, T:0.21
Consensus pattern (14 bp):
CCTCGGTCGGATGC
Found at i:483759 original size:2 final size:2
Alignment explanation
Indices: 483752--483779 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
483742 AATCCTGAGC
483752 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
483780 AAAGATAATA
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):
TA
Found at i:484191 original size:60 final size:60
Alignment explanation
Indices: 484063--484191 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 60
484053 TGAATGATAC
* * * * * *
484063 AAAGTTTAAGGACTAATTTAGAAAAAGGGTCATATTTTGGGGATGAAATTGGAATTTTCA
1 AAAGTTTAAAGACTAATTTAGAAAAAGAGTCATAGTTTAGGGATAAAATTAGAATTTTCA
* * * *
484123 AAATTTTAAAGACTAATTTA-AAATAATAGTTATAGTTTAGGGATAAAATTATAATATTT-A
1 AAAGTTTAAAGACTAATTTAGAAA-AAGAGTCATAGTTTAGGGATAAAATTAGAAT-TTTCA
484183 AAAGTTTAA
1 AAAGTTTAA
484192 GGATCAATAT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
59 3 0.05
60 50 0.89
61 3 0.05
ACGTcount: A:0.44, C:0.03, G:0.16, T:0.36
Consensus pattern (60 bp):
AAAGTTTAAAGACTAATTTAGAAAAAGAGTCATAGTTTAGGGATAAAATTAGAATTTTCA
Found at i:486768 original size:22 final size:22
Alignment explanation
Indices: 486743--486797 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
486733 AACTTTAAAT
*
486743 TATAAACCCTAAATCATAACCC
1 TATAAACCCTAAATCATAAACC
*
486765 TAT-AACCTTTAAATCATAAACC
1 TATAAACC-CTAAATCATAAACC
*
486787 T-CAAACCCTAA
1 TATAAACCCTAA
486798 CTTAGAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (22 bp):
TATAAACCCTAAATCATAAACC
Found at i:492573 original size:3 final size:3
Alignment explanation
Indices: 492565--492634 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
492555 AGTTTCTCTG
*
492565 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTC CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
492613 CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT C
492635 ACGGGTAAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:495473 original size:16 final size:17
Alignment explanation
Indices: 495454--495499 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
495444 CATATGCAGT
495454 TAAATATATA-TAAATA
1 TAAATATATATTAAATA
*
495470 TAAATATATATTAAATT
1 TAAATATATATTAAATA
*
495487 TAAA-ATCTATTAA
1 TAAATATATATTAA
495500 TGTCATAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATATATATTAAATA
Found at i:496600 original size:58 final size:58
Alignment explanation
Indices: 496476--496667 Score: 323
Period size: 59 Copynumber: 3.3 Consensus size: 58
496466 TAATCCAGGG
*
496476 ATCATTTCGTAACTTTCAATAGTTATGAGACAAAAAAAATAACATCCTATAGTCGAAGA
1 ATCATTTCGTAACTTTCAATAGTTATGAGAC-AAAAAAATAACACCCTATAGTCGAAGA
496535 ATCATTTCGTAACTTTCAATAGTTATGAGACAAAAAAATAACACCCTATAGTCGAAGA
1 ATCATTTCGTAACTTTCAATAGTTATGAGACAAAAAAATAACACCCTATAGTCGAAGA
* *
496593 ATTATTTCGTAACTTTCAATAGTTATGAGATCAAAAAAATAACACCCTATAATCGAAGA
1 ATCATTTCGTAACTTTCAATAGTTATGAGA-CAAAAAAATAACACCCTATAGTCGAAGA
496652 ATCATTT-GTAAACTTT
1 ATCATTTCGT-AACTTT
496668 ACCCTTTGAT
Statistics
Matches: 127, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
58 57 0.45
59 70 0.55
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.31
Consensus pattern (58 bp):
ATCATTTCGTAACTTTCAATAGTTATGAGACAAAAAAATAACACCCTATAGTCGAAGA
Found at i:498504 original size:21 final size:21
Alignment explanation
Indices: 498478--498530 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
498468 GTTTCCAGAT
*
498478 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
498499 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
498520 TCGCAATGCGA
1 TCGCAATGCGA
498531 TTTACATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:498565 original size:21 final size:21
Alignment explanation
Indices: 498539--498613 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
498529 GATTTACATA
498539 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
498560 TTCGCATTGCAATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
498581 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
498602 TTCGCGTTGCGA
1 TTCGCATTGCGA
498614 ATCTGAAAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:498773 original size:2 final size:2
Alignment explanation
Indices: 498766--498807 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
498756 CTCTTGTATT
498766 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
498808 AACGAGCCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:501689 original size:4 final size:4
Alignment explanation
Indices: 501680--501711 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
501670 CAATGCATGT
*
501680 ATAA ATAA ATAA ATAA ATAA ATAA ATAC ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
501712 TTGAAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Found at i:502548 original size:6 final size:6
Alignment explanation
Indices: 502531--502560 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
502521 TTTACATATA
*
502531 CCGGTG CGGGTG CCGGTG CCGGTG CCGGTG
1 CCGGTG CCGGTG CCGGTG CCGGTG CCGGTG
502561 TCGGACTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.30, G:0.53, T:0.17
Consensus pattern (6 bp):
CCGGTG
Found at i:516943 original size:15 final size:15
Alignment explanation
Indices: 516923--516954 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
516913 TGATGTATTT
516923 TCAAGAATGTCAAAA
1 TCAAGAATGTCAAAA
516938 TCAAGAATGTCAAAA
1 TCAAGAATGTCAAAA
516953 TC
1 TC
516955 CCAATGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (15 bp):
TCAAGAATGTCAAAA
Found at i:523853 original size:32 final size:28
Alignment explanation
Indices: 523817--523877 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 28
523807 AAATGAAGTT
*
523817 AAAATCAAAGACAGACACAAAAAACATAGATC
1 AAAAT-AAA-ACA-ACACAAAAAAAATA-ATC
*
523849 AAAATAAAACAACCCAAAAAAAATAATC
1 AAAATAAAACAACACAAAAAAAATAATC
523877 A
1 A
523878 TCCCCTGTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 4 0.15
29 12 0.44
30 3 0.11
31 3 0.11
32 5 0.19
ACGTcount: A:0.67, C:0.18, G:0.05, T:0.10
Consensus pattern (28 bp):
AAAATAAAACAACACAAAAAAAATAATC
Found at i:527806 original size:24 final size:24
Alignment explanation
Indices: 527774--527824 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
527764 TCGACATAAG
527774 GTGTAGGCAATGGCGGGAGTTTAT
1 GTGTAGGCAATGGCGGGAGTTTAT
*
527798 GTGTAGGCAATGGCTGGAGTTTAT
1 GTGTAGGCAATGGCGGGAGTTTAT
527822 GTG
1 GTG
527825 CAGCCAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.08, G:0.41, T:0.31
Consensus pattern (24 bp):
GTGTAGGCAATGGCGGGAGTTTAT
Found at i:528384 original size:21 final size:20
Alignment explanation
Indices: 528317--528455 Score: 73
Period size: 21 Copynumber: 6.8 Consensus size: 20
528307 AAATGACCAA
***
528317 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
528337 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
528357 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
528378 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
528399 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
528419 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* *
528440 GAAAATCACAACGCGA
1 CAAAATCGCAACGCGA
528456 ACACATAAAT
Statistics
Matches: 89, Mismatches: 25, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
19 1 0.01
20 41 0.46
21 47 0.53
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:528484 original size:20 final size:20
Alignment explanation
Indices: 528461--528615 Score: 204
Period size: 20 Copynumber: 7.7 Consensus size: 20
528451 CGCGAACACA
*
528461 TAAATCGCAACTCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
528481 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGCGTATCCG
**
528501 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
528521 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
528541 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* * *
528561 TAAATCGCAACG-ATAATACA
1 TAAATCGCAACGCGT-ATCCG
528581 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACGCGTATCCG
528602 TAAATCGCAACGCG
1 TAAATCGCAACGCG
528616 ATATTTAAAG
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 98 0.85
21 15 0.13
22 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:528486 original size:40 final size:39
Alignment explanation
Indices: 528422--528616 Score: 183
Period size: 40 Copynumber: 4.9 Consensus size: 39
528412 CGATTTTCCA
* ** * *
528422 AAATCGCAACGCGAATATGAAAATCACAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CAT
* * * *
528462 AAATCGCAACTCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
** * * *
528502 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCAT
* ** *
528542 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT
528582 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
528617 TATTTAAAGC
Statistics
Matches: 126, Mismatches: 26, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 92 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.19
Consensus pattern (39 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACCAT
Found at i:528506 original size:60 final size:60
Alignment explanation
Indices: 528422--528615 Score: 228
Period size: 60 Copynumber: 3.2 Consensus size: 60
528412 CGATTTTCCA
* ** * * *
528422 AAATCGCAACGCGAATATGAAAATCACAACGCGAACACATAAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACTCGTATCCGT
* * ***
528482 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAA-TGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACT-CGTATCCGT
* ** *
528542 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACTCGTATCCGT
528603 AAATCGCAACGCG
1 AAATCGCAACGCG
528616 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
59 1 0.01
60 79 0.72
61 30 0.27
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACTCGTATCCGT
Found at i:529038 original size:33 final size:33
Alignment explanation
Indices: 528999--529069 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
528989 TTCACTTAGA
*
528999 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
529032 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
529065 TTTCA
1 TTTCA
529070 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:529205 original size:41 final size:41
Alignment explanation
Indices: 529147--529224 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
529137 TTGCAGAAGA
*
529147 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
529188 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
529225 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:529221 original size:21 final size:21
Alignment explanation
Indices: 529148--529223 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
529138 TGCAGAAGAG
*
529148 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
529169 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
529189 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
529210 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
529224 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:529227 original size:14 final size:14
Alignment explanation
Indices: 529208--529263 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
529198 GAGAAATGAA
529208 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
529222 AATCGCAACGCGATATG
1 AATCGCAA--CGAGA-G
529239 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
529254 AATCGCAACG
1 AATCGCAACG
529264 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 18 0.50
15 1 0.03
16 8 0.22
17 1 0.03
18 8 0.22
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:529315 original size:14 final size:14
Alignment explanation
Indices: 529296--529385 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
529286 TTTCATTTCG
529296 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
529310 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
529329 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
529343 CGTTGCGATTGTCATTTCA
1 CGTTGCGA-T-TC---TCT
529362 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
529376 CGTTGCGATT
1 CGTTGCGATT
529386 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:529327 original size:33 final size:33
Alignment explanation
Indices: 529280--529393 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
529270 CAAAATCGCA
529280 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
529312 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
529345 TTGCGATTGTCATTTCACGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
529378 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
529394 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 6 0.08
33 72 0.92
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:529334 original size:19 final size:18
Alignment explanation
Indices: 529275--529371 Score: 84
Period size: 19 Copynumber: 5.7 Consensus size: 18
529265 GAAACCAAAA
*
529275 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
529293 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
529307 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
529326 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
529340 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATT-TCATT
*
529359 TCACGTTGCGATT
1 TCGCGTTGCGATT
529372 CTCTCGTTGC
Statistics
Matches: 64, Mismatches: 5, Indels: 19
0.73 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 1 0.02
16 5 0.08
17 6 0.09
18 10 0.16
19 22 0.34
ACGTcount: A:0.11, C:0.24, G:0.22, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:531262 original size:92 final size:93
Alignment explanation
Indices: 531072--531715 Score: 1186
Period size: 92 Copynumber: 7.1 Consensus size: 93
531062 TAGATTGCTT
* *
531072 AGTAAATTT-ATC-GTTTCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
531135 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
531163 AGT-AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
531226 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
531254 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
531319 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
531347 AGT-AATTTGTTCGGTTGCTGCC-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
531410 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
531437 AGTAAATTTGTTCGG-TGCTGCC-ATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
531500 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
531528 AGTAAATTTG-TCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
531592 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
531620 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG-GTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
531684 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
531711 AGTAA
1 AGTAA
531716 TGCATCCATT
Statistics
Matches: 542, Mismatches: 2, Indels: 18
0.96 0.00 0.03
Matches are distributed among these distances:
90 87 0.16
91 145 0.27
92 245 0.45
93 65 0.12
ACGTcount: A:0.21, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:531787 original size:20 final size:19
Alignment explanation
Indices: 531762--531888 Score: 91
Period size: 18 Copynumber: 7.3 Consensus size: 19
531752 TAGTTTACTT
*
531762 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
531782 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
531800 TCGCAACGCGAAA-TAAAAA
1 TCGCAACGCGAAACT-AAAA
*
531819 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACTAAAA
*
531833 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
*
531851 TCGCAA--CG--AC-AAGA
1 TCGCAACGCGAAACTAAAA
*
531865 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
531884 TCGCA
1 TCGCA
531889 TTGCGATTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 25
0.72 0.08 0.21
Matches are distributed among these distances:
14 19 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 28 0.33
19 17 0.20
20 13 0.15
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:531802 original size:18 final size:18
Alignment explanation
Indices: 531779--531888 Score: 96
Period size: 18 Copynumber: 6.4 Consensus size: 18
531769 ACGAAACTTA
531779 AAATCGCAACGCGAAACC
1 AAATCGCAACGCGAAACC
**
531797 AAATCGCAACGCGAAATAA
1 AAATCGCAACGCGAAA-CC
531816 AAATCGCAA--CG--A-C
1 AAATCGCAACGCGAAACC
531829 AGAATCGCAACGCGAAACC
1 A-AATCGCAACGCGAAACC
531848 AAATCGCAA--CG--A-C
1 AAATCGCAACGCGAAACC
531861 AAGATCGCAACGCGAAACC
1 AA-ATCGCAACGCGAAACC
531880 AAAATCGCA
1 -AAATCGCA
531889 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 27
0.71 0.03 0.26
Matches are distributed among these distances:
13 4 0.05
14 16 0.21
15 1 0.01
16 6 0.08
17 2 0.03
18 26 0.35
19 18 0.24
20 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.07
Consensus pattern (18 bp):
AAATCGCAACGCGAAACC
Found at i:531857 original size:32 final size:31
Alignment explanation
Indices: 531796--531888 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 31
531786 AACGCGAAAC
**
531796 CAAATCGCAACGCGAAATAAAAATCGCAACGA
1 CAAATCGCAACGCGAAA-CCAAATCGCAACGA
531828 CAGAATCGCAACGCGAAACCAAATCGCAACGA
1 CA-AATCGCAACGCGAAACCAAATCGCAACGA
531860 CAAGATCGCAACGCGAAACCAAAATCGCA
1 CAA-ATCGCAACGCGAAACC-AAATCGCA
531889 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 32 0.57
33 23 0.41
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.08
Consensus pattern (31 bp):
CAAATCGCAACGCGAAACCAAATCGCAACGA
Found at i:531886 original size:51 final size:51
Alignment explanation
Indices: 531762--531888 Score: 127
Period size: 51 Copynumber: 2.5 Consensus size: 51
531752 TAGTTTACTT
* **
531762 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
*** *
531813 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAATCGCAACG-CGAA-A
531865 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
531889 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
50 3 0.05
51 46 0.78
52 7 0.12
53 3 0.05
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (51 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAATCGCAACGCGAAA
Found at i:531906 original size:19 final size:19
Alignment explanation
Indices: 531884--532002 Score: 114
Period size: 19 Copynumber: 6.8 Consensus size: 19
531874 GAAACCAAAA
*
531884 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
531903 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
531919 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
531936 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
531952 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
531969 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
531988 TCGCGTTTCGATTTT
1 TCGCGTTGCGATTTT
532003 AAGTTTTCGT
Statistics
Matches: 82, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
14 15 0.18
16 11 0.13
17 11 0.13
19 45 0.55
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.48
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:531925 original size:14 final size:14
Alignment explanation
Indices: 531906--531962 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
531896 TTTCATTTCG
531906 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
531920 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
531937 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
531953 CGTTGCGATT
1 CGTTGCGATT
531963 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:531931 original size:33 final size:33
Alignment explanation
Indices: 531889--531981 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
531879 CAAAATCGCA
*
531889 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
531922 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
531955 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
531982 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:533692 original size:13 final size:14
Alignment explanation
Indices: 533667--533701 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
533657 ATTGTTTAAT
533667 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
533681 TGATTTGT-AAAGT
1 TGATTTGTAAAAGA
533694 TGATTTGT
1 TGATTTGT
533702 GTAATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:533822 original size:19 final size:19
Alignment explanation
Indices: 533806--533850 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
533796 CAAAATGACT
533806 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
533825 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
533844 ATCGCAA
1 ATCGCAA
533851 CGAGAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:533912 original size:33 final size:33
Alignment explanation
Indices: 533875--534026 Score: 143
Period size: 33 Copynumber: 4.5 Consensus size: 33
533865 TGCGTTTATA
*
533875 ATTTCGCATTGCGATTCCCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
533908 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * *
533948 -TTT-GCGATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGC-A-TTGCGATTCTCTCGTTGCGATTTTC
533979 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
534012 -TTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
534027 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 9, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
31 5 0.05
32 23 0.24
33 38 0.39
35 5 0.05
36 3 0.03
37 2 0.02
38 10 0.10
39 6 0.06
40 5 0.05
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:533921 original size:19 final size:19
Alignment explanation
Indices: 533897--534091 Score: 217
Period size: 19 Copynumber: 11.1 Consensus size: 19
533887 GATTCCCTCG
533897 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
533916 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
533935 TTGCGA--TTC---TCTCT
1 TTGCGATTTTCATTTCGCA
533949 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
533968 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
533987 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
534001 TTGCGATTTTC-TTTCGCA
1 TTGCGATTTTCATTTCGCA
534019 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
534038 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
534052 TTGTGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
534070 TTGCGATTTTTCATTTCGCA
1 TTGCGA-TTTTCATTTCGCA
534090 TT
1 TT
534092 CTCTCGTTGC
Statistics
Matches: 150, Mismatches: 10, Indels: 31
0.79 0.05 0.16
Matches are distributed among these distances:
14 20 0.13
15 3 0.02
16 22 0.15
17 9 0.06
18 16 0.11
19 66 0.44
20 14 0.09
ACGTcount: A:0.13, C:0.22, G:0.16, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:534037 original size:51 final size:52
Alignment explanation
Indices: 533875--534130 Score: 411
Period size: 52 Copynumber: 5.0 Consensus size: 52
533865 TGCGTTTATA
*
533875 ATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
533927 ATTTCGCATTGCGATTCTCTCTTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
533979 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC-TTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
534030 ATTTCGCATTGCGATTCTCTCGTTGTGA-TTTCATTTCGCATTGCGATTTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA-TTTTC
534082 ATTT--C---GC-ATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
534129 AT
1 AT
534131 GTTGGGATTC
Statistics
Matches: 195, Mismatches: 5, Indels: 13
0.92 0.02 0.06
Matches are distributed among these distances:
46 14 0.07
47 17 0.09
48 10 0.05
50 5 0.03
51 58 0.30
52 91 0.47
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:534065 original size:32 final size:33
Alignment explanation
Indices: 533916--534077 Score: 161
Period size: 33 Copynumber: 4.8 Consensus size: 33
533906 TCATTTCGCA
*
533916 TTGCGATTTTCATTTCGCATTGCGATTCTCTCT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
533949 TTGCGATTTTCATTTCGCATTGCGATT-T-TCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
* * * * *
533980 TTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCTTTCG
1 TTGCG-ATTTTC-ATT-TCGCATTGCGA--TTCTCTCG
534017 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
534052 TTGTGA-TTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
534078 TTTCATTTCG
Statistics
Matches: 107, Mismatches: 12, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
31 9 0.08
32 25 0.23
33 41 0.38
35 9 0.08
36 1 0.01
37 11 0.10
38 4 0.04
39 7 0.07
ACGTcount: A:0.13, C:0.22, G:0.17, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:535847 original size:12 final size:12
Alignment explanation
Indices: 535830--535854 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
535820 TCTTCGGGGA
535830 CTTTTTCTTCTT
1 CTTTTTCTTCTT
535842 CTTTTTCTTCTT
1 CTTTTTCTTCTT
535854 C
1 C
535855 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:536932 original size:20 final size:20
Alignment explanation
Indices: 536723--536931 Score: 210
Period size: 20 Copynumber: 10.6 Consensus size: 20
536713 TTTAGATTCT
*
536723 CGTTGCGATTTACGGATTA-T
1 CGTTGCGATTTACGGA-TACG
* * *
536743 CGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGATACG
* *
536763 CGTTGCGATTTACGTATTA-T
1 CGTTGCGATTTACGGA-TACG
536783 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
536803 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
* **
536823 CATTGCGATTTACCCATACG
1 CGTTGCGATTTACGGATACG
*
536843 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
536863 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* * *
536883 AGTTGCGATTTA-TG-TTCG
1 CGTTGCGATTTACGGATACG
* ** *
536901 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
536921 CGTTGCGATTT
1 CGTTGCGATTT
536932 TGGAAAATCG
Statistics
Matches: 160, Mismatches: 24, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
18 13 0.08
19 4 0.03
20 142 0.89
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:536948 original size:21 final size:21
Alignment explanation
Indices: 536918--537000 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
536908 ATTTTCATAT
*
536918 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
536939 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
536960 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
536981 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
537001 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:536991 original size:42 final size:43
Alignment explanation
Indices: 536898--536996 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
536888 CGATTTATGT
* *
536898 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
536939 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
536981 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
536997 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:537236 original size:23 final size:23
Alignment explanation
Indices: 537210--537262 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
537200 TATTTTTTTT
*
537210 TTAATTTTATCTGT-TTTTTATAA
1 TTAATTATAT-TGTATTTTTATAA
* *
537233 TTAATTATATTTTATTTTTATGA
1 TTAATTATATTGTATTTTTATAA
537256 TTAATTA
1 TTAATTA
537263 CAATTTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
TTAATTATATTGTATTTTTATAA
Found at i:537269 original size:23 final size:23
Alignment explanation
Indices: 537224--537270 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
537214 TTTTATCTGT
* *
537224 TTTTTATAATTAATTATATTTTA
1 TTTTTATAATTAATTACAATTTA
*
537247 TTTTTATGATTAATTACAATTTA
1 TTTTTATAATTAATTACAATTTA
537270 T
1 T
537271 CCCTTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTTATAATTAATTACAATTTA
Found at i:549723 original size:214 final size:209
Alignment explanation
Indices: 549309--549731 Score: 801
Period size: 214 Copynumber: 2.0 Consensus size: 209
549299 CGTGTTCCTT
549309 TCTCCTCTCTCTTTTCTCTATCCTTGTGCAGCTGTCTAAACCTTTCCTGCAAAAGAGCAATTGAG
1 TCTCCTCTCTCTTTTCTCTATCCTTGTGCAGCTGTCTAAACCTTTCCTGCAAAAGAGCAATTGAG
549374 GAACTAACAATAGGAGAATGAGATGATCATAGTAATGAGGGTAGGTCAAATGGTTTCAGGTGATG
66 GAACTAACAATAGGAGAATGAGATGATCATAGTAATGAGGGTAGGTCAAATGGTTTCAGGTGATG
549439 TAAGAGAATGGGGGTGTTGTACAACTAAATCCAAGAAGATGAGGTGATGAGGAGGGTACATGTAT
131 TAAGAGAATGGGGGTGTTGTACAACTAAATCCAAGAAGATGAGGTGATGAGGAGGGTACATGTAT
549504 GGAATGATTTTCAG
196 GGAATGATTTTCAG
549518 TCTCCTCTCTCTTTTCTCTATCCTTGTGCAGCTGTCTAAACCTTTCCTGCAAAAGAGCAATTGAG
1 TCTCCTCTCTCTTTTCTCTATCCTTGTGCAGCTGTCTAAACCTTTCCTGCAAAAGAGCAATTGAG
549583 GAACTAACAATAGGAGAATGAGATGATCATATAGTTAATGAGGGTGTAGGTCAAATGGTTTCAGG
66 GAACTAACAATAGGAGAATGAGATGATC--ATAG-TAATGA-GG-GTAGGTCAAATGGTTTCAGG
549648 TGATGTAAGAGAATGGGGGTGTTGTACAACTAAATCCAAGAAGATGAGGTGATGAGGAGGGTACA
126 TGATGTAAGAGAATGGGGGTGTTGTACAACTAAATCCAAGAAGATGAGGTGATGAGGAGGGTACA
549713 TGTATGGAATGATTTTCAG
191 TGTATGGAATGATTTTCAG
549732 AGTTATGATG
Statistics
Matches: 209, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
209 93 0.44
211 4 0.02
212 6 0.03
213 2 0.01
214 104 0.50
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (209 bp):
TCTCCTCTCTCTTTTCTCTATCCTTGTGCAGCTGTCTAAACCTTTCCTGCAAAAGAGCAATTGAG
GAACTAACAATAGGAGAATGAGATGATCATAGTAATGAGGGTAGGTCAAATGGTTTCAGGTGATG
TAAGAGAATGGGGGTGTTGTACAACTAAATCCAAGAAGATGAGGTGATGAGGAGGGTACATGTAT
GGAATGATTTTCAG
Found at i:556859 original size:29 final size:30
Alignment explanation
Indices: 556817--556873 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
556807 ATCCACTATT
556817 ATCGGTTTGGGAAA-CGACTCCTGGCCCCA
1 ATCGGTTTGGGAAACCGACTCCTGGCCCCA
556846 ATCGGTTTGGGAAACCGACTCCTGGCCC
1 ATCGGTTTGGGAAACCGACTCCTGGCCC
556874 AAGGAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.19, C:0.32, G:0.28, T:0.21
Consensus pattern (30 bp):
ATCGGTTTGGGAAACCGACTCCTGGCCCCA
Found at i:573216 original size:16 final size:18
Alignment explanation
Indices: 573195--573238 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
573185 AACATTCTCA
573195 GTAATCTT-ATT-CACTG
1 GTAATCTTAATTCCACTG
573211 GTAATCTTACATTCCCACTG
1 GTAATCTTA-ATT-CCACTG
573231 GTAATCTT
1 GTAATCTT
573239 CCATTCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.33
18 3 0.12
20 13 0.54
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (18 bp):
GTAATCTTAATTCCACTG
Found at i:573231 original size:20 final size:20
Alignment explanation
Indices: 573206--573245 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
573196 TAATCTTATT
573206 CACTGGTAATCTTACATTCC
1 CACTGGTAATCTTACATTCC
*
573226 CACTGGTAATCTTCCATTCC
1 CACTGGTAATCTTACATTCC
573246 ATGAACCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.33, G:0.10, T:0.35
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCC
Found at i:575125 original size:11 final size:12
Alignment explanation
Indices: 575092--575125 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
575082 AAGTTTGTTT
575092 TTTAATATATAA
1 TTTAATATATAA
575104 TTTATATATATAA
1 TTTA-ATATATAA
575117 TTTAA-ATAT
1 TTTAATATAT
575126 TTATGGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 5 0.24
13 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTAATATATAA
Found at i:575836 original size:2 final size:2
Alignment explanation
Indices: 575829--575873 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
575819 AAAATAATTT
575829 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
575871 TA T
1 TA T
575874 GACAATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:576404 original size:31 final size:31
Alignment explanation
Indices: 576366--576425 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
576356 GTAGACTCAA
* *
576366 TTTATCATTTCCGCCTCTATCGTATTATCAC
1 TTTATCATTTCCGCCCCTATCATATTATCAC
* *
576397 TTTATCATTTTCTCCCCTATCATATTATC
1 TTTATCATTTCCGCCCCTATCATATTATC
576426 GCATCAATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.20, C:0.28, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTATCATTTCCGCCCCTATCATATTATCAC
Found at i:581962 original size:21 final size:21
Alignment explanation
Indices: 581936--581988 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
581926 GGACCTATAA
* *
581936 TCCCGAGGGATGTCATATGTG
1 TCCCGAAGGATGTAATATGTG
*
581957 TCCCGAAGGATGTAATCTGTG
1 TCCCGAAGGATGTAATATGTG
*
581978 TCCCGTAGGAT
1 TCCCGAAGGAT
581989 CTATCATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (21 bp):
TCCCGAAGGATGTAATATGTG
Found at i:582201 original size:46 final size:46
Alignment explanation
Indices: 582144--582248 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
582134 ATGTGTAACC
582144 ATGT-ATTTCATATCATATCACATGTATCACGTATTACACATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACACATTCAT
* *
582189 ATGTCATTTCATATCATATCACATGTATCACGTATTGCATATTCAT
1 ATGTCATTTCATATCATATCACATGTATCACGTATTACACATTCAT
*
582235 ATATCATTTCATAT
1 ATGTCATTTCATAT
582249 ACTCACATAG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.07
46 52 0.93
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (46 bp):
ATGTCATTTCATATCATATCACATGTATCACGTATTACACATTCAT
Found at i:587396 original size:12 final size:12
Alignment explanation
Indices: 587371--587411 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
587361 AAACTTTTTA
*
587371 AGATAGACAGAC
1 AGATAGATAGAC
*
587383 AGACAGATAGAC
1 AGATAGATAGAC
*
587395 AGATAGATAGAT
1 AGATAGATAGAC
587407 AGATA
1 AGATA
587412 TTGCTCCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.24, T:0.15
Consensus pattern (12 bp):
AGATAGATAGAC
Found at i:587411 original size:8 final size:8
Alignment explanation
Indices: 587371--587409 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
587361 AAACTTTTTA
587371 AGATAGAC
1 AGATAGAC
*
587379 AGACAGAC
1 AGATAGAC
587387 AGATAGAC
1 AGATAGAC
*
587395 AGATAGAT
1 AGATAGAC
587403 AGATAGA
1 AGATAGA
587410 TATTGCTCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.51, C:0.10, G:0.26, T:0.13
Consensus pattern (8 bp):
AGATAGAC
Found at i:592320 original size:56 final size:56
Alignment explanation
Indices: 592248--592354 Score: 135
Period size: 56 Copynumber: 1.9 Consensus size: 56
592238 ATATATATTG
592248 ATAGTTTGGAATGAAATTAAAATATTCAAAAGTTTG-GGATCAATTTAAAAGGGTC
1 ATAGTTTGGAATGAAATTAAAATATTCAAAAGTTTGAGGATCAATTTAAAAGGGTC
* ** * * * *
592303 ATAGTTTAGGGATGAAATTGGATTGTTTAAAAGTTTGAGGATTAATTTAAAA
1 ATAGTTT-GGAATGAAATTAAAATATTCAAAAGTTTGAGGATCAATTTAAAA
592355 TGAAAATCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 7 0.16
56 23 0.53
57 13 0.30
ACGTcount: A:0.40, C:0.03, G:0.21, T:0.36
Consensus pattern (56 bp):
ATAGTTTGGAATGAAATTAAAATATTCAAAAGTTTGAGGATCAATTTAAAAGGGTC
Found at i:600777 original size:35 final size:36
Alignment explanation
Indices: 600707--600777 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
600697 ACTATAATTT
* *
600707 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
600743 ATTTATATATTTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATATATTTTCTTTA-AAAATTAAAAATCATAAA
600778 TATGTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 9 0.28
36 23 0.72
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
Found at i:602888 original size:39 final size:39
Alignment explanation
Indices: 602845--602950 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
602835 TTTAAAAAGT
* *
602845 AATTTAGAATGTTAATGTGAAATAATTTAATAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAAAAAATAAG
* *
602884 AATTTAGAATGTT-ATGGTGGTAA-AATTTAAAAAAATAGG
1 AATTTAGAATGTTAAT-GT-GAAATAATTTAAAAAAATAAG
* ***
602923 AATTTTGAATGTTAGCATGAAATAATTT
1 AATTTAGAATGTTAATGTGAAATAATTT
602951 GAGAATTATA
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
38 5 0.09
39 46 0.85
40 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.16, T:0.38
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAAAAAATAAG
Found at i:603575 original size:22 final size:22
Alignment explanation
Indices: 603547--603666 Score: 156
Period size: 22 Copynumber: 5.5 Consensus size: 22
603537 ATAATAATTT
603547 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
* *
603569 TTTTAAAATAAATCAATCCATC
1 TTTTAAAATAAATCAATTCATA
*
603591 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
603613 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
603635 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
603657 TTTTAAAATA
1 TTTTAAAATA
603667 GATTTAAATA
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 80 0.94
23 1 0.01
24 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:603613 original size:44 final size:44
Alignment explanation
Indices: 603547--603666 Score: 179
Period size: 44 Copynumber: 2.7 Consensus size: 44
603537 ATAATAATTT
* *
603547 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATC
1 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
** *
603591 TTTTAAAATAAAAT-TTTCCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAAT-AAATCAATCCATATTTTAAAATAAATCAATCCATA
603635 TTTTAAAATAAATCAATCCATATTTTAAAATA
1 TTTTAAAATAAATCAATCCATATTTTAAAATA
603667 GATTTAAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 4 0.06
44 59 0.88
45 4 0.06
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (44 bp):
TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
Found at i:605952 original size:19 final size:18
Alignment explanation
Indices: 605919--605959 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
605909 GATATGTTTG
*
605919 TAAATTTTATTTAAATTT
1 TAAATTTTATTTAAATGT
*
605937 TAAATTATTTTTTAAATGT
1 TAAATT-TTATTTAAATGT
605956 TAAA
1 TAAA
605960 GCTTAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TAAATTTTATTTAAATGT
Found at i:606560 original size:15 final size:13
Alignment explanation
Indices: 606534--606587 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 13
606524 AATTTTTATT
606534 TTAAAATAAAATA
1 TTAAAATAAAATA
606547 TTAAGAATATAAATA
1 TTAA-AATA-AAATA
*
606562 TTTAAA-AAAA-A
1 TTAAAATAAAATA
606573 TTAAAA-AATAATA
1 TTAAAATAA-AATA
606586 TT
1 TT
606588 TAATCAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
11 8 0.23
12 5 0.14
13 8 0.23
14 6 0.17
15 8 0.23
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
TTAAAATAAAATA
Found at i:606566 original size:16 final size:14
Alignment explanation
Indices: 606533--606573 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
606523 GAATTTTTAT
606533 TTTAAAATAAAATA
1 TTTAAAATAAAATA
606547 -TTAAGAATATAAATA
1 TTTAA-AATA-AAATA
606562 TTTAAAA-AAAAT
1 TTTAAAATAAAAT
606574 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 7 0.29
16 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (14 bp):
TTTAAAATAAAATA
Found at i:608861 original size:17 final size:17
Alignment explanation
Indices: 608839--608874 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
608829 TATTTTATAT
608839 ATTATT-TTTTTAATTAA
1 ATTATTATTTTT-ATTAA
608856 ATTATTATTTTTATTAA
1 ATTATTATTTTTATTAA
608873 AT
1 AT
608875 AAAAATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATTATTTTTATTAA
Found at i:608863 original size:20 final size:21
Alignment explanation
Indices: 608838--608877 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
608828 ATATTTTATA
*
608838 TATTATTTTT-TTAATTAAAT
1 TATTATTTTTATTAAATAAAT
608858 TATTATTTTTATTAAATAAA
1 TATTATTTTTATTAAATAAA
608878 AATAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATTTTTATTAAATAAAT
Found at i:609020 original size:6 final size:6
Alignment explanation
Indices: 609009--609046 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
608999 CGCATGCCCC
609009 CTGCTA CTGCTA CTGCTA CTGCTA CTGCTA CTGCTA CT
1 CTGCTA CTGCTA CTGCTA CTGCTA CTGCTA CTGCTA CT
609047 AAAGTCTTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.34, G:0.16, T:0.34
Consensus pattern (6 bp):
CTGCTA
Found at i:610700 original size:9 final size:9
Alignment explanation
Indices: 610682--610715 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
610672 GTTGTCTCCA
*
610682 CCGCCGCCG
1 CCGCCACCG
610691 CCGCCACCG
1 CCGCCACCG
610700 CCGCCACCG
1 CCGCCACCG
610709 CCGCCAC
1 CCGCCAC
610716 TTCCATCGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.09, C:0.68, G:0.24, T:0.00
Consensus pattern (9 bp):
CCGCCACCG
Found at i:612351 original size:36 final size:36
Alignment explanation
Indices: 612311--612387 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
612301 GGCGCATAAA
612311 TTCCCAGTTCCAGTGAACCCAATGATGCAACAATCT
1 TTCCCAGTTCCAGTGAACCCAATGATGCAACAATCT
* * * **
612347 TTCCCAGTTCCGGTGAATCCGATGATGCCGCAATCT
1 TTCCCAGTTCCAGTGAACCCAATGATGCAACAATCT
612383 TTCCC
1 TTCCC
612388 CGGATTTCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.27
Consensus pattern (36 bp):
TTCCCAGTTCCAGTGAACCCAATGATGCAACAATCT
Found at i:620092 original size:2 final size:2
Alignment explanation
Indices: 620085--620118 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
620075 AAAACATCGA
620085 AT 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 AT
620119 CATCGATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:620201 original size:22 final size:21
Alignment explanation
Indices: 620152--620201 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
620142 GCACTAGTAT
*
620152 TAAAGTACCTCAACACTGATA
1 TAAAGTACATCAACACTGATA
* *
620173 TAGAAGTACATTAACATTGATA
1 TA-AAGTACATCAACACTGATA
620195 CTAAAGT
1 -TAAAGT
620202 GTCTTAGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 20 0.83
23 2 0.08
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (21 bp):
TAAAGTACATCAACACTGATA
Found at i:626053 original size:2 final size:2
Alignment explanation
Indices: 626046--626076 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
626036 ATAGAAATGG
626046 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
626077 GCTACATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:626545 original size:21 final size:21
Alignment explanation
Indices: 626516--626572 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
626506 GGGTTTCATA
*
626516 GGTCTTTCGGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
626537 GGTCCTTCGGGACAATACAGT
1 GGTCCTTCGGGACAATACAGT
626558 GGTCCTTCGGGACAA
1 GGTCCTTCGGGACAA
626573 ATTTCATATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.30, T:0.25
Consensus pattern (21 bp):
GGTCCTTCGGGACAATACAGT
Found at i:628340 original size:15 final size:14
Alignment explanation
Indices: 628313--628341 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
628303 AGCAACTCAC
628313 TCTTTTATTTTTTT
1 TCTTTTATTTTTTT
628327 TCTTTTATTTTTTT
1 TCTTTTATTTTTTT
628341 T
1 T
628342 GGGAATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (14 bp):
TCTTTTATTTTTTT
Found at i:635533 original size:165 final size:165
Alignment explanation
Indices: 635261--635592 Score: 655
Period size: 165 Copynumber: 2.0 Consensus size: 165
635251 AACTTTTACA
635261 ATGTACCTATTTCAATGGTATAACACAGTTCTTACACAATGTGGAATGATAACAAGTTCACTAGA
1 ATGTACCTATTTCAATGGTATAACACAGTTCTTACACAATGTGGAATGATAACAAGTTCACTAGA
635326 AATGATACAAGGTTTTCCAGGAAACAATGCCATATGCTGCTCCTGATCATAATTTTCTCTCCAAC
66 AATGATACAAGGTTTTCCAGGAAACAATGCCATATGCTGCTCCTGATCATAATTTTCTCTCCAAC
635391 CAAGCAAAGGCCATCTGATTGATCTCTGATCTACT
131 CAAGCAAAGGCCATCTGATTGATCTCTGATCTACT
635426 ATGTACCTATTTCAATGGTATAACACAGTTCTTACACAATGTGGAATGATAACAAGTTCACTAGA
1 ATGTACCTATTTCAATGGTATAACACAGTTCTTACACAATGTGGAATGATAACAAGTTCACTAGA
635491 AATGATACAAGGTTTTCCAGGAAACAATGCCATATGCTGCTCCTGATCATAATTTTCTCTCCAAC
66 AATGATACAAGGTTTTCCAGGAAACAATGCCATATGCTGCTCCTGATCATAATTTTCTCTCCAAC
*
635556 CAAGGAAAGGCCATCTGATTGATCTCTGATCTACT
131 CAAGCAAAGGCCATCTGATTGATCTCTGATCTACT
635591 AT
1 AT
635593 TTGCCAGTGA
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 166 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (165 bp):
ATGTACCTATTTCAATGGTATAACACAGTTCTTACACAATGTGGAATGATAACAAGTTCACTAGA
AATGATACAAGGTTTTCCAGGAAACAATGCCATATGCTGCTCCTGATCATAATTTTCTCTCCAAC
CAAGCAAAGGCCATCTGATTGATCTCTGATCTACT
Found at i:639159 original size:17 final size:17
Alignment explanation
Indices: 639134--639167 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
639124 ACTCGAAAAA
* *
639134 TTAATTTTTTTTTAATT
1 TTAAGTTTTTTTGAATT
639151 TTAAGTTTTTTTGAATT
1 TTAAGTTTTTTTGAATT
639168 GAGTCTAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTAAGTTTTTTTGAATT
Found at i:639420 original size:20 final size:18
Alignment explanation
Indices: 639395--639437 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
639385 TTTTTATAAT
*
639395 TTTTTTATTTCTTTAATTCA
1 TTTTTTA-TT-TTAAATTCA
639415 TTTTTTATTTTAAATTCA
1 TTTTTTATTTTAAATTCA
639433 TTTTT
1 TTTTT
639438 ATTAAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTATTTTAAATTCA
Found at i:639646 original size:157 final size:156
Alignment explanation
Indices: 639313--639650 Score: 342
Period size: 157 Copynumber: 2.2 Consensus size: 156
639303 CTAAACTATC
* * * *** *
639313 ATAGAATACATATGTATTGTCAA-CTCTTCTTTTTGATAATTTTTTTTCTATTGTCCAATTTAGC
1 ATAGAATACATATATACT-TCAATTTC-TCTTTTTGATAACAATTTTTCTATTGTCCAATTTAAC
* * * * ** * **
639377 CTCTCAATTTTTTATAATTTTTTTATTTCTTTAATTCATTTTTTATTTTAAATTCATTTTTATTA
64 CCCTCAATTTTTCATAATTTTCTTATTTCTTCAATTCATTCCTTACTTTAAATTCATTTTTACCA
* * * **
639442 AATTTGAACCACGTGCTCTTCAATCATT
129 AATTTGAACCACCTGCTCATCAACCACA
* * *
639470 GTAGAATACATATATACTTCCAATTTCTCTTTTTGATAACAATTTTTCTATTTTTCAATTTAACC
1 ATAGAATACATATATACTT-CAATTTCTCTTTTTGATAACAATTTTTCTATTGTCCAATTTAACC
* *
639535 CCTCAATTTTTCATAATTTTCTTATTTCTTCAATTCA-TCCTTACTTTAAGTAT-GTTTTTACCA
65 CCTCAATTTTTCATAATTTTCTTATTTCTTCAATTCATTCCTTACTTTAAAT-TCATTTTTACCA
639598 AATTTGAACCACCTGCTCAT-ATACCACA
129 AATTTGAACCACCTGCTCATCA-ACCACA
* *
639626 ATAGATTACATATGTAACTTCAATT
1 ATAGAATACATATAT-ACTTCAATT
639651 CTTATTTTTT
Statistics
Matches: 147, Mismatches: 29, Indels: 11
0.79 0.16 0.06
Matches are distributed among these distances:
155 1 0.01
156 56 0.38
157 88 0.60
158 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.05, T:0.49
Consensus pattern (156 bp):
ATAGAATACATATATACTTCAATTTCTCTTTTTGATAACAATTTTTCTATTGTCCAATTTAACCC
CTCAATTTTTCATAATTTTCTTATTTCTTCAATTCATTCCTTACTTTAAATTCATTTTTACCAAA
TTTGAACCACCTGCTCATCAACCACA
Found at i:639660 original size:157 final size:157
Alignment explanation
Indices: 639340--639638 Score: 343
Period size: 157 Copynumber: 1.9 Consensus size: 157
639330 TGTCAACTCT
*** * * * *
639340 TCTTTTTGATAATTTTTTTTCTATTGTCCAATTTAGCCTCTCAATTTTTTATAATTTTTTTATTT
1 TCTTTTTGATAACAATTTTTCTATTGTCCAATTTAACCCCTCAATTTTTCATAATTTTCTTATTT
* ** * ** * * * **
639405 CTTTAATTCATTTTTTATTTTAAATTCATTTTTATTAAATTTGAACCACGTGCTCTTCAATCATT
66 CTTCAATTCATTCCTTACTTTAAATTCATTTTTACCAAATTTGAACCACCTGCTCATCAACCACA
*
639470 GTAGAATACATATATACTTCCAATTTC
131 ATAGAATACATATATACTTCCAATTTC
* *
639497 TCTTTTTGATAACAATTTTTCTATTTTTCAATTTAACCCCTCAATTTTTCATAATTTTCTTATTT
1 TCTTTTTGATAACAATTTTTCTATTGTCCAATTTAACCCCTCAATTTTTCATAATTTTCTTATTT
* *
639562 CTTCAATTCA-TCCTTACTTTAAGTAT-GTTTTTACCAAATTTGAACCACCTGCTCAT-ATACCA
66 CTTCAATTCATTCCTTACTTTAAAT-TCATTTTTACCAAATTTGAACCACCTGCTCATCA-ACCA
*
639624 CAATAGATTACATAT
129 CAATAGAATACATAT
639639 GTAACTTCAA
Statistics
Matches: 116, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
155 1 0.01
156 49 0.42
157 66 0.57
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (157 bp):
TCTTTTTGATAACAATTTTTCTATTGTCCAATTTAACCCCTCAATTTTTCATAATTTTCTTATTT
CTTCAATTCATTCCTTACTTTAAATTCATTTTTACCAAATTTGAACCACCTGCTCATCAACCACA
ATAGAATACATATATACTTCCAATTTC
Found at i:645257 original size:20 final size:20
Alignment explanation
Indices: 645232--645269 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
645222 ATCCTATTCT
645232 CTGATAATCTTACATTCCCA
1 CTGATAATCTTACATTCCCA
*
645252 CTGATAATCTTTCATTCC
1 CTGATAATCTTACATTCC
645270 ATGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.05, T:0.39
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:646577 original size:20 final size:20
Alignment explanation
Indices: 646552--646671 Score: 87
Period size: 20 Copynumber: 5.6 Consensus size: 20
646542 AACACAAATG
* *
646552 AACGAACGTAAAGGAACACA
1 AACGAATGTAAAAGAACACA
** *
646572 AACGAATGTAAATTAACATA
1 AACGAATGTAAAAGAACACA
646592 AACGAATGAATGTAAAAGAACACA
1 AAC----GAATGTAAAAGAACACA
** *
646616 AACGAATGTAAATTAACATA
1 AACGAATGTAAAAGAACACA
646636 AACGAATGAATGTAAAAGAACACA
1 AAC----GAATGTAAAAGAACACA
*
646660 AACGAACGTAAA
1 AACGAATGTAAA
646672 TTAATTAGAT
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
20 44 0.56
24 34 0.44
ACGTcount: A:0.57, C:0.13, G:0.15, T:0.15
Consensus pattern (20 bp):
AACGAATGTAAAAGAACACA
Found at i:646607 original size:24 final size:24
Alignment explanation
Indices: 646542--646665 Score: 102
Period size: 24 Copynumber: 5.5 Consensus size: 24
646532 ATGATAAACA
* * * *
646542 AACACAAATGAACGAACGTAAAGG
1 AACACAAACGAATGAATGTAAAAG
**
646566 AACACAAAC----GAATGTAAATT
1 AACACAAACGAATGAATGTAAAAG
*
646586 AACATAAACGAATGAATGTAAAAG
1 AACACAAACGAATGAATGTAAAAG
**
646610 AACACAAAC----GAATGTAAATT
1 AACACAAACGAATGAATGTAAAAG
*
646630 AACATAAACGAATGAATGTAAAAG
1 AACACAAACGAATGAATGTAAAAG
646654 AACACAAACGAA
1 AACACAAACGAA
646666 CGTAAATTAA
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
20 33 0.42
24 45 0.58
ACGTcount: A:0.57, C:0.14, G:0.15, T:0.15
Consensus pattern (24 bp):
AACACAAACGAATGAATGTAAAAG
Found at i:646613 original size:44 final size:44
Alignment explanation
Indices: 646559--646675 Score: 216
Period size: 44 Copynumber: 2.7 Consensus size: 44
646549 ATGAACGAAC
*
646559 GTAAAGGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
1 GTAAAAGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
646603 GTAAAAGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
1 GTAAAAGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
*
646647 GTAAAAGAACACAAACGAACGTAAATTAA
1 GTAAAAGAACACAAACGAATGTAAATTAA
646676 TTAGATTTAT
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (44 bp):
GTAAAAGAACACAAACGAATGTAAATTAACATAAACGAATGAAT
Found at i:648449 original size:149 final size:151
Alignment explanation
Indices: 648134--648733 Score: 1147
Period size: 149 Copynumber: 4.0 Consensus size: 151
648124 CCTAAGAAGA
* *
648134 GTTATAGTGCATTCCTCCATAAAAGTTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
648199 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAAC-AACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
648263 ATAAAAAGGTAGGAATCTAAC
131 ATAAAAAGGTAGGAATCTAAC
648284 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAA-TT-TA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
648347 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
648412 ATAAAAAGGTAGGAATCTAAC
131 ATAAAAAGGTAGGAATCTAAC
648433 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
648498 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
648563 ATAAAAAGGTAGGAATCTAAC
131 ATAAAAAGGTAGGAATCTAAC
648584 G-T-TAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
648647 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
648712 ATAAAAAGGTAGGAATCTAAC
131 ATAAAAAGGTAGGAATCTAAC
648733 G
1 G
648734 ATGGAACTTG
Statistics
Matches: 445, Mismatches: 2, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
148 50 0.11
149 246 0.55
150 60 0.13
151 89 0.20
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.25
Consensus pattern (151 bp):
GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
ATAAAAAGGTAGGAATCTAAC
Found at i:648710 original size:300 final size:299
Alignment explanation
Indices: 648134--648733 Score: 1141
Period size: 300 Copynumber: 2.0 Consensus size: 299
648124 CCTAAGAAGA
* *
648134 GTTATAGTGCATTCCTCCATAAAAGTTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
648199 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAACGCATTTAATAATAA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAACGCATTTAATAATAA
648264 TAAAAAGGTAGGAATCTAACGTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAA
131 TAAAAAGGTAGGAATCTAACGTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAA
648329 ACAGGGTACCAAAATTTAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAA
196 ACAGGGTACCAAAATTTAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAA
648394 CAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
261 CAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
648433 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
1 GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
648498 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAAACGCATTTAATAATA
66 AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAAC-AACGCATTTAATAATA
648563 ATAAAAAGGTAGGAATCTAACG-T-TAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAA
130 ATAAAAAGGTAGGAATCTAACGTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAA
648626 AACAGGGTACCAAAATTTGTAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAA
195 AACAGGGTACCAAAA-TT-TAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAA
648691 GAACAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
258 GAACAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
648733 G
1 G
648734 ATGGAACTTG
Statistics
Matches: 296, Mismatches: 2, Indels: 5
0.98 0.01 0.02
Matches are distributed among these distances:
298 55 0.19
299 114 0.39
300 127 0.43
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.25
Consensus pattern (299 bp):
GTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAAACAGGGTACCAAAATTTGTA
AATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAACAACGCATTTAATAATAA
TAAAAAGGTAGGAATCTAACGTTATAATGCATTCCTCCATAAAAATTCATCAAAACGACACAAAA
ACAGGGTACCAAAATTTAAATGTATCTGCAGAATATCAAAATTATACCATGACATAATCTAAGAA
CAAACGCATTTAATAATAATAAAAAGGTAGGAATCTAAC
Found at i:664443 original size:108 final size:109
Alignment explanation
Indices: 664253--664470 Score: 429
Period size: 108 Copynumber: 2.0 Consensus size: 109
664243 ACACATATAA
664253 TATACGATTTTAATTAATTTTTTTCGGATTTGTCAAAATGACCAACAAAATCGCAATGCGATCGC
1 TATACGATTTTAATTAATTTTTTTCGGATTTGTCAAAATGACCAACAAAATCGCAATGCGATCGC
664318 TAATTCGCAACACGATCTCCATTATCGCAAATCAGTTTCCAGAT
66 TAATTCGCAACACGATCTCCATTATCGCAAATCAGTTTCCAGAT
664362 TATACGATTTTAATTAA-TTTTTTCGGATTTGTCAAAATGACCAACAAAATCGCAATGCGATCGC
1 TATACGATTTTAATTAATTTTTTTCGGATTTGTCAAAATGACCAACAAAATCGCAATGCGATCGC
664426 TAATTCGCAACACGATCTCCATTATCGCAAATCAGTTTCCAGAT
66 TAATTCGCAACACGATCTCCATTATCGCAAATCAGTTTCCAGAT
664470 T
1 T
664471 CGCAACGCGA
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 92 0.84
109 17 0.16
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (109 bp):
TATACGATTTTAATTAATTTTTTTCGGATTTGTCAAAATGACCAACAAAATCGCAATGCGATCGC
TAATTCGCAACACGATCTCCATTATCGCAAATCAGTTTCCAGAT
Found at i:664541 original size:21 final size:21
Alignment explanation
Indices: 664490--664542 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
664480 ATTATTACTA
664490 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
664511 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
664532 TCGCAATGCGA
1 TCGCAATGCGA
664543 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Done.