Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007968.1 Hibiscus syriacus cultivar Beakdansim tig00110403_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: 1361854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:303940 original size:22 final size:20
Alignment explanation
Indices: 303905--303952 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
303895 ATAATTATTT
303905 AAAAAAATTAAATAAAAATAC
1 AAAAAAATTAAATAAAAA-AC
*
303926 AAAAAACATTTAATAAAAAAC
1 AAAAAA-ATTAAATAAAAAAC
303947 TAAAAA
1 -AAAAA
303953 TATCCCCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAAAAATTAAATAAAAAAC
Found at i:304356 original size:20 final size:20
Alignment explanation
Indices: 304327--304382 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 20
304317 TAATTATTTT
*
304327 ATAATGATTTAATAAATATA
1 ATAATTATTTAATAAATATA
* * *
304347 ATAATTATTTTAT-AATCTC
1 ATAATTATTTAATAAATATA
*
304366 ATAAAT-TTTAATAAATA
1 ATAATTATTTAATAAATA
304383 AAAATATCCT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
18 5 0.18
19 12 0.43
20 11 0.39
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAATTATTTAATAAATATA
Found at i:315748 original size:15 final size:15
Alignment explanation
Indices: 315723--315763 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
315713 ATAATAAATA
315723 ATTAT-AAATATATT
1 ATTATAAAATATATT
315737 ATTATAAAATATATT
1 ATTATAAAATATATT
*
315752 ATTTTAAAATAT
1 ATTATAAAATAT
315764 TAATATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:315770 original size:28 final size:28
Alignment explanation
Indices: 315672--315771 Score: 96
Period size: 28 Copynumber: 3.6 Consensus size: 28
315662 ATTAAAAATA
* *
315672 TAAAA-ATTATTATATAATATATTGTTT
1 TAAAATATTAATATATAATATATTATTT
* * * *
315699 TAAGAAT-TTAAAATATAATAAATAATTA
1 TAA-AATATTAATATATAATATATTATTT
* *
315727 TAAATATATTATTATAAAATATATTATTT
1 TAAA-ATATTAATATATAATATATTATTT
315756 TAAAATATTAATATAT
1 TAAAATATTAATATAT
315772 TTAGGTCAGA
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
27 4 0.07
28 32 0.58
29 19 0.35
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TAAAATATTAATATATAATATATTATTT
Found at i:320118 original size:2 final size:2
Alignment explanation
Indices: 320113--320144 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
320103 ACACACACAC
320113 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
320145 GAAAGCTAAC
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:322189 original size:2 final size:2
Alignment explanation
Indices: 322182--322233 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
322172 CATCTTTGCT
322182 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
322224 TA TA TA TA TA
1 TA TA TA TA TA
322234 CACATTATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:329230 original size:109 final size:109
Alignment explanation
Indices: 328936--330006 Score: 1215
Period size: 109 Copynumber: 9.8 Consensus size: 109
328926 CTAGTTTCAA
* * ** * * * *
328936 GTGTACGAATTCTCAGCGCGATTATGTTAATCAATTACACACATTAGAGCGAATTTGTTTCTAAA
1 GTGTACGAATTCTCGGAGCGATCGTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCTAAA
* * * *
329001 GTAGTGGTTTTCACCACGACACAAATTT-AGTTTTTAAGTTTTGG
66 GCAGTGGTTTTCACCACGACAC-GATTTCAGTTGTTAAGTTTCGG
* * * ** * * *** *
329045 GTATATGCATTCT-AAAGCGATCGTGTTAAACGATTGA-ATACATTGGGATAAATTTGTGTCTAA
1 GTGTACGAATTCTCGGAGCGATCGTGTTAAGCGATT-ACACACATTGGGGCGAATTTGTTTCTAA
* * * * *
329108 AGTAGTGGTTTTCACCATGACATGGTTTCAGTTGTTAAGTTTTGG
65 AGCAGTGGTTTTCACCACGACACGATTTCAGTTGTTAAGTTTCGG
* * * * *
329153 GTGTACAAATTCTCAGAGTGACCGTGTTAAGCGATTACACATATTGGGGCGAATTTGTTTCTAAA
1 GTGTACGAATTCTCGGAGCGATCGTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCTAAA
*
329218 GCAGTAGTTTTCACCACGACACGATTTC-GATTGTTAAGTTTCGG
66 GCAGTGGTTTTCACCACGACACGATTTCAG-TTGTTAAGTTTCGG
* * *
329262 GTGTACGAATTCTCGGAGCGA-CGGTGTTAGGTGATTACACACATTGGGTCGAATTTGTTTCTAA
1 GTGTACGAATTCTCGGAGCGATC-GTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCTAA
* * **
329326 ATCAGTGGTTTTCACCATGACACGATTTTGGTTGTTAAGTTTCGG
65 AGCAGTGGTTTTCACCACGACACGATTTCAGTTGTTAAGTTTCGG
* * ** * *
329371 ATGTACGAATTCTCGAAATGA-CTGTGTTAAGCGATTACACACATTGGGGCTAATTTGTTTATAA
1 GTGTACGAATTCTCGGAGCGATC-GTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCT-A
* * * ** *
329435 AAGCAATGGTTTTCACCATGACACAATTTTGGTTGTCAAGTTTCGG
64 AAGCAGTGGTTTTCACCACGACACGATTTCAGTTGTTAAGTTTCGG
* * * * * *
329481 GTGTATGAATTCTCAGAGCGGTCGTGTTAAGCAATTACATACATTGGGGCAAATTTGTTTCTAAA
1 GTGTACGAATTCTCGGAGCGATCGTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCTAAA
* *
329546 GTAGTGGTTTTCACCA-GAACACGATTTCAGTTGTGAAGTTTCGG
66 GCAGTGGTTTTCACCACG-ACACGATTTCAGTTGTTAAGTTTCGG
* * *
329590 GTGTACGAATTCTCGAAGTGATCGTGTTAAGAGATTACACACATTGGGGCGAATTTGTTTCTAAA
1 GTGTACGAATTCTCGGAGCGATCGTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCTAAA
* * * *
329655 GCAATTGTTTTCACCACGACACGGTTTCAGTTGTTAAGTTTTGG
66 GCAGTGGTTTTCACCACGACACGATTTCAGTTGTTAAGTTTCGG
* * * * *
329699 GTGTATGAATTCTTGGAGCGATTGTGTTAAGTGATTACACACATTGGGGCGAATTTGTGTCTAAA
1 GTGTACGAATTCTCGGAGCGATCGTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCTAAA
* * *
329764 GCAATGGTTTTCACCACAACACGGTTTCAGTTGTTAAGTTTCGG
66 GCAGTGGTTTTCACCACGACACGATTTCAGTTGTTAAGTTTCGG
* * * * * *
329808 GTGTATGAATTCTTGGAGCGACCGTGTTAGGCGATTACACATATTGGGACGAATTTGTTTCTAAA
1 GTGTACGAATTCTCGGAGCGATCGTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCTAAA
* *
329873 GCAGTGGTTTTCACCACGACACGGTTTC-GATTGTTAAGTTTCGA
66 GCAGTGGTTTTCACCACGACACGATTTCAG-TTGTTAAGTTTCGG
* * * *
329917 GTGTACGAATTCTTGGAGCGATCGTGTTAAGCGACTACACACATTGCGGCG-ATTTGTTTATAAA
1 GTGTACGAATTCTCGGAGCGATCGTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCTAAA
329981 GCAGTGGTTTTCACCACGACACGATT
66 GCAGTGGTTTTCACCACGACACGATT
330007 ACGGCGAATT
Statistics
Matches: 823, Mismatches: 127, Indels: 25
0.84 0.13 0.03
Matches are distributed among these distances:
107 3 0.00
108 122 0.15
109 603 0.73
110 94 0.11
111 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.35
Consensus pattern (109 bp):
GTGTACGAATTCTCGGAGCGATCGTGTTAAGCGATTACACACATTGGGGCGAATTTGTTTCTAAA
GCAGTGGTTTTCACCACGACACGATTTCAGTTGTTAAGTTTCGG
Found at i:330029 original size:46 final size:44
Alignment explanation
Indices: 329955--330049 Score: 136
Period size: 46 Copynumber: 2.1 Consensus size: 44
329945 AAGCGACTAC
* *
329955 ACACATTGCGGCGATTTGTTTATAAAGCAGTGGTTTTCACCACG
1 ACACATTACGGCGATTTATTTATAAAGCAGTGGTTTTCACCACG
* *
329999 ACACGATTACGGCGAATTTATTTTTAAAGCAGTGGTTTTCATCACG
1 ACAC-ATTACGGCG-ATTTATTTATAAAGCAGTGGTTTTCACCACG
330045 ACACA
1 ACACA
330050 AATTTTTTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
44 4 0.09
45 9 0.20
46 32 0.71
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
ACACATTACGGCGATTTATTTATAAAGCAGTGGTTTTCACCACG
Found at i:330148 original size:154 final size:153
Alignment explanation
Indices: 329857--330157 Score: 383
Period size: 154 Copynumber: 2.0 Consensus size: 153
329847 CATATTGGGA
* ** **
329857 CGAATTTGTTTCTAAAGCAGTGGTTTTCACCACGACACGGTTTCGATTGTTAAGTTTCGAGTGTA
1 CGAATTTATTTCTAAAGCAGTGGTTTTCACCACGACACAATTTC-ATTGCCAAGTTTCGAGTGTA
* *
329922 CGAATTCTTGGAGCGATCGTGTTAAGCGACTACACACATTGCGGCGATTTGTTTATAAAGCAGTG
65 CGAATTCTCGGAGCGACCGTGTTAAGCGACTACACACATTGCGGCGATTTGTTTATAAAGCAGTG
*
329987 GTTTTCACCACGACACGATTACGG
130 ATTTTCACCACGACACGATTACGG
* * *
330011 CGAATTTATTTTTAAAGCAGTGGTTTTCATCACGACACAAATTT-TTTGCCAAGTTTC-AGGTGT
1 CGAATTTATTTCTAAAGCAGTGGTTTTCACCACGACAC-AATTTCATTGCCAAGTTTCGA-GTGT
* * * * *
330074 ATGAATTCTCGTAGCGACCGTGTTAAGCGATTACACACATTG-GGACGAATTTGTTTCTATAGCA
64 ACGAATTCTCGGAGCGACCGTGTTAAGCGACTACACACATTGCGG-CG-ATTTGTTTATAAAGCA
*
330138 TTGATTTTCACCACGACACG
127 GTGATTTTCACCACGACACG
330158 GTTTCGATTG
Statistics
Matches: 126, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
152 3 0.02
153 53 0.42
154 67 0.53
155 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (153 bp):
CGAATTTATTTCTAAAGCAGTGGTTTTCACCACGACACAATTTCATTGCCAAGTTTCGAGTGTAC
GAATTCTCGGAGCGACCGTGTTAAGCGACTACACACATTGCGGCGATTTGTTTATAAAGCAGTGA
TTTTCACCACGACACGATTACGG
Found at i:330950 original size:60 final size:60
Alignment explanation
Indices: 330880--331005 Score: 252
Period size: 60 Copynumber: 2.1 Consensus size: 60
330870 TAAAAATGAG
330880 ACCAACCCTAATTTAACTAAGCACAAGCAATTTACTTAATTTAGCTAACACTAATTTCAT
1 ACCAACCCTAATTTAACTAAGCACAAGCAATTTACTTAATTTAGCTAACACTAATTTCAT
330940 ACCAACCCTAATTTAACTAAGCACAAGCAATTTACTTAATTTAGCTAACACTAATTTCAT
1 ACCAACCCTAATTTAACTAAGCACAAGCAATTTACTTAATTTAGCTAACACTAATTTCAT
331000 ACCAAC
1 ACCAAC
331006 TTAAAGAAAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (60 bp):
ACCAACCCTAATTTAACTAAGCACAAGCAATTTACTTAATTTAGCTAACACTAATTTCAT
Found at i:330952 original size:32 final size:32
Alignment explanation
Indices: 330916--331005 Score: 82
Period size: 28 Copynumber: 2.9 Consensus size: 32
330906 GCAATTTACT
330916 TAATTTAGCTAACACTAATTTCATACCAACCC
1 TAATTTAGCTAACACTAATTTCATACCAACCC
* * *** *
330948 TAATTTAACTAAGCAC-AA--GCA-ATTTA-CT
1 TAATTTAGCTAA-CACTAATTTCATACCAACCC
330976 TAATTTAGCTAACACTAATTTCATACCAAC
1 TAATTTAGCTAACACTAATTTCATACCAAC
331006 TTAAAGAAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 12
0.64 0.17 0.19
Matches are distributed among these distances:
27 3 0.07
28 14 0.34
29 2 0.05
30 4 0.10
31 2 0.05
32 13 0.32
33 3 0.07
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.32
Consensus pattern (32 bp):
TAATTTAGCTAACACTAATTTCATACCAACCC
Found at i:330979 original size:28 final size:28
Alignment explanation
Indices: 330888--330987 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
330878 AGACCAACCC
330888 TAATTTAACTAAGCACAAGCAATTTACT
1 TAATTTAACTAAGCACAAGCAATTTACT
* * *** *
330916 TAATTTAGCTAA-CACTAATTTCATACCAACCC
1 TAATTTAACTAAGCAC-AA--GCA-ATTTA-CT
330948 TAATTTAACTAAGCACAAGCAATTTACT
1 TAATTTAACTAAGCACAAGCAATTTACT
*
330976 TAATTTAGCTAA
1 TAATTTAACTAA
330988 CACTAATTTC
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
27 3 0.06
28 25 0.47
29 2 0.04
30 4 0.08
31 2 0.04
32 14 0.26
33 3 0.06
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (28 bp):
TAATTTAACTAAGCACAAGCAATTTACT
Found at i:333958 original size:2 final size:2
Alignment explanation
Indices: 333951--333989 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
333941 TCTTTTACTT
333951 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
333990 CCCTCTCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:335163 original size:6 final size:6
Alignment explanation
Indices: 335152--335183 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
335142 CTTAATACCG
*
335152 CCCGTC CCCGTC CCCGTC CCCGTC CCCCTC CC
1 CCCGTC CCCGTC CCCGTC CCCGTC CCCGTC CC
335184 TCCCTCCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.72, G:0.12, T:0.16
Consensus pattern (6 bp):
CCCGTC
Found at i:335186 original size:4 final size:4
Alignment explanation
Indices: 335177--335225 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
335167 GTCCCCGTCC
* *
335177 CCCT CCCT CCCT CCCT TCCT CCCT CCCT CCCT -CCT CCCT CCAT CCCT
1 CCCT CCCT CCCT CCCT CCCT CCCT CCCT CCCT CCCT CCCT CCCT CCCT
335224 CC
1 CC
335226 TATAAGTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 3 0.08
4 37 0.93
ACGTcount: A:0.02, C:0.71, G:0.00, T:0.27
Consensus pattern (4 bp):
CCCT
Found at i:335375 original size:26 final size:26
Alignment explanation
Indices: 335344--335393 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
335334 CTAGAATTTT
335344 TTTATTATATT-ATAATTATTTAATAG
1 TTTATTATATTAAT-ATTATTTAATAG
*
335370 TTTATTATTTTAATATTATTTAAT
1 TTTATTATATTAATATTATTTAAT
335394 TTACTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTATTATATTAATATTATTTAATAG
Found at i:337565 original size:18 final size:20
Alignment explanation
Indices: 337523--337569 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
337513 ATTTTTAAAG
* *
337523 TTGGTTGTTTCTTGAATTTT
1 TTGGTTGGTTCTTGAATTCT
337543 TTGGTTGGTT-TTGAA-TCT
1 TTGGTTGGTTCTTGAATTCT
337561 TTGGTTGGT
1 TTGGTTGGT
337570 ATAGAAGCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.44
19 5 0.20
20 9 0.36
ACGTcount: A:0.09, C:0.04, G:0.28, T:0.60
Consensus pattern (20 bp):
TTGGTTGGTTCTTGAATTCT
Found at i:338508 original size:15 final size:15
Alignment explanation
Indices: 338484--338570 Score: 93
Period size: 15 Copynumber: 5.7 Consensus size: 15
338474 TTATTAGTAT
*
338484 GTGAATATGTTCTAC
1 GTGAAAATGTTCTAC
* *
338499 GTGAAAATGTTTTAT
1 GTGAAAATGTTCTAC
*
338514 GTGAATATGTTCTAC
1 GTGAAAATGTTCTAC
* *
338529 GTGAAAATGTTTTAT
1 GTGAAAATGTTCTAC
*
338544 GTGAAAATGTTATAC
1 GTGAAAATGTTCTAC
338559 TGTGAATAATGT
1 -GTGAA-AATGT
338571 AATATGAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
15 49 0.83
16 5 0.08
17 5 0.08
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (15 bp):
GTGAAAATGTTCTAC
Found at i:338515 original size:30 final size:30
Alignment explanation
Indices: 338481--338570 Score: 144
Period size: 30 Copynumber: 2.9 Consensus size: 30
338471 ATTTTATTAG
338481 TATGTGAATATGTTCTACGTGAAAATGTTT
1 TATGTGAATATGTTCTACGTGAAAATGTTT
338511 TATGTGAATATGTTCTACGTGAAAATGTTT
1 TATGTGAATATGTTCTACGTGAAAATGTTT
* *
338541 TATGTGAAAATGTTATACTGTGAATAATGT
1 TATGTGAATATGTTCTAC-GTGAA-AATGT
338571 AATATGAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
30 46 0.82
31 5 0.09
32 5 0.09
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (30 bp):
TATGTGAATATGTTCTACGTGAAAATGTTT
Found at i:338700 original size:23 final size:23
Alignment explanation
Indices: 338674--338739 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
338664 CCTTCAGAAT
338674 AATTCTACGTGGTCATTCGGGAC
1 AATTCTACGTGGTCATTCGGGAC
* *
338697 AATTCTACGCT-GTCCTTCAGGAC
1 AATTCTACG-TGGTCATTCGGGAC
* *
338720 AAATCTATGTGG-CACTTCGG
1 AATTCTACGTGGTCA-TTCGG
338740 TGCATATTCT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
22 2 0.06
23 31 0.91
24 1 0.03
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (23 bp):
AATTCTACGTGGTCATTCGGGAC
Found at i:342013 original size:15 final size:15
Alignment explanation
Indices: 341989--342019 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
341979 TTCAGTGATC
*
341989 ACTTGTAATCTTTCA
1 ACTTGCAATCTTTCA
342004 ACTTGCAATCTTTCA
1 ACTTGCAATCTTTCA
342019 A
1 A
342020 AAACATGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (15 bp):
ACTTGCAATCTTTCA
Found at i:349157 original size:3 final size:3
Alignment explanation
Indices: 349151--349203 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
349141 TCTATTTTTT
*
349151 TTA TTA TTA TTA TTA -TA TTA TTA TT- TATA TTA CTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA
349195 TTA TTA TTA
1 TTA TTA TTA
349204 AATAAATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
2 5 0.11
3 35 0.80
4 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:349218 original size:38 final size:36
Alignment explanation
Indices: 349152--349225 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 36
349142 CTATTTTTTT
* * * *
349152 TATTATTATTATTATATTATTATTTATATTACTATATA
1 TATTATTATTATTAAATAAATATATATA-TA-TATATA
349190 TATTATTATTATTAAATAAATATATATATATATATA
1 TATTATTATTATTAAATAAATATATATATATATATA
349226 CAAGCCTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 6 0.19
37 2 0.06
38 24 0.75
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (36 bp):
TATTATTATTATTAAATAAATATATATATATATATA
Found at i:350470 original size:21 final size:20
Alignment explanation
Indices: 350444--350489 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
350434 CATTATTATT
*
350444 TATTATTTGT-TATTAATTTTA
1 TATTATTT-TATATT-ATTTCA
350465 TATTATTTTATATTATTTCA
1 TATTATTTTATATTATTTCA
350485 TATTA
1 TATTA
350490 GTCACATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTATTTTATATTATTTCA
Found at i:350487 original size:10 final size:10
Alignment explanation
Indices: 350424--350489 Score: 64
Period size: 10 Copynumber: 6.3 Consensus size: 10
350414 GCTTTTTAAT
350424 TTATTTTAATCA
1 TTATTTT-AT-A
350436 TTATTATT-TA
1 TTATT-TTATA
350446 TTATTTGT-TA
1 TTATTT-TATA
350456 TTAATTTTATA
1 TT-ATTTTATA
350467 TTATTTTATA
1 TTATTTTATA
*
350477 TTATTTCATA
1 TTATTTTATA
350487 TTA
1 TTA
350490 GTCACATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
9 1 0.02
10 32 0.65
11 9 0.18
12 5 0.10
13 2 0.04
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (10 bp):
TTATTTTATA
Found at i:350489 original size:31 final size:33
Alignment explanation
Indices: 350426--350489 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 33
350416 TTTTTAATTT
**
350426 ATTTTAATCATTATTATTTATTATTTGTTATTA
1 ATTTTAATCATTATTATTTATTATTTCATATTA
350459 ATTTT-AT-ATTATT-TTATATTATTTCATATTA
1 ATTTTAATCATTATTATT-TATTATTTCATATTA
350490 GTCACATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.07
31 19 0.68
32 2 0.07
33 5 0.18
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (33 bp):
ATTTTAATCATTATTATTTATTATTTCATATTA
Found at i:350756 original size:11 final size:10
Alignment explanation
Indices: 350711--350757 Score: 58
Period size: 10 Copynumber: 4.5 Consensus size: 10
350701 TGTCTTAAAT
*
350711 TATTATTTTG
1 TATTATTTTA
*
350721 TATAATTTTA
1 TATTATTTTA
350731 TATTATTTTA
1 TATTATTTTA
350741 TTATTATTTTCA
1 -TATTATTTT-A
350753 TATTA
1 TATTA
350758 GTCACATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 17 0.53
11 14 0.44
12 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (10 bp):
TATTATTTTA
Found at i:351073 original size:115 final size:116
Alignment explanation
Indices: 350943--351151 Score: 285
Period size: 115 Copynumber: 1.8 Consensus size: 116
350933 TAATATTTAA
** * * * * * *
350943 TTATTTATTTATTAATATTGAAGGAAAGGGTTGTCTTAAAGCAACTAGAAATCCTTTTCTAATAT
1 TTATTTATTTATTAATATCAAAAGAAAGAGCTATCTTAAAACAACTAGAAACCCTTTTCTAATAT
*
351008 TTTTAAATAAATAAATATCTTAT-TATATTAAAATAATTTATTATTATTAT
66 TTCTAAATAAATAAATATCTTATATATATTAAAATAATTTATTATTATTAT
* * * *
351058 TTATTTATTTTTTAATATCAAAAGAAAGAGCTATCTTAAAACACCTAGAAGCCCTTTTCTGATAT
1 TTATTTATTTATTAATATCAAAAGAAAGAGCTATCTTAAAACAACTAGAAACCCTTTTCTAATAT
*
351123 TTCTAAATAAATAAATATGTTATATATAT
66 TTCTAAATAAATAAATATCTTATATATAT
351152 ATATATATAT
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
115 74 0.94
116 5 0.06
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.44
Consensus pattern (116 bp):
TTATTTATTTATTAATATCAAAAGAAAGAGCTATCTTAAAACAACTAGAAACCCTTTTCTAATAT
TTCTAAATAAATAAATATCTTATATATATTAAAATAATTTATTATTATTAT
Found at i:351136 original size:271 final size:268
Alignment explanation
Indices: 350484--351140 Score: 721
Period size: 270 Copynumber: 2.5 Consensus size: 268
350474 ATATTATTTC
* *
350484 ATATTAGTCACATAATTAT--ATATTTTTAAATAATAATCTTTATTTATTTTCAATATCAAAGAA
1 ATATTAGT-ACATAATTATAAATATATTTAAATAATAATATTTATTTATTTTCAATATCAAAGAA
* * * * * *
350547 AAGGGCAGTCTTAATACAATTAGATGTCCTATTCTGGTATTTTAAA-ATATTAAATATTATAAAA
65 AAGAGCAGTCTTAAAACAACTAGAAGCCCTATTCTGATATTTTAAATA-ATTAAATATTATAAAA
*
350611 ATTATAATTTAGTTTATTTAAATTATTTTTAGGAAAAATTATTACATATTTTATATTTATTTATT
129 ATTATAATTTAGTTTATTTAAATTATTTTTAGGAAAAATTATTACATATTTTATATTTAATTATT
** * * * *
350676 TATTTATTAATATTGAAGGAAAGGGTGTCTTAAATTATTATTTTGTATAATTTTATATTATTTTA
194 TATTTATTAATATTGAAGGAAAGGGTGTCTTAAAGCA-TATCTAGAATAATTTTATAATATTTTA
* * ** **
350741 TTATTATTTTC
258 TAAATAAATAA
* * *
350752 ATATTAGTCACATAATTATATATATTTTTAAATAATAATCTTTATTTATTTTCAATATCAAAGAA
1 ATATTAGT-ACATAATTATAAATATATTTAAATAATAATATTTATTTATTTTCAATATCAAAGAA
* * * * * *
350817 AAGGGCAGTCTTAATACAATTAGATGTCCTATTCTGGTATTTTAAATAATTAAATATTATAAAAA
65 AAGAGCAGTCTTAAAACAACTAGAAGCCCTATTCTGATATTTTAAATAATTAAATATTATAAAAA
350882 TTATAATTTAGTTTTATTTAAATTATTTTTAGGAAAAATTATTACATATTTTAATATTTAATTAT
130 TTATAATTTAG-TTTATTTAAATTATTTTTAGGAAAAATTATTACATATTTT-ATATTTAATTAT
** *
350947 TTATTTATTAATATTGAAGGAAAGGGTTGTCTTAAAGCA-A-CTAGAAATCCTTTTCTAATATTT
193 TTATTTATTAATATTGAAGGAAAGGG-TGTCTTAAAGCATATCTAG-AATAATTTTATAATATTT
351010 T-TAAATAAATAA
256 TATAAATAAATAA
* * * * *
351022 ATATCT--TA-TTATATTA-AAATA-ATTT-ATTATTATTATTTATTTATTTTTTAATATCAAA-
1 ATAT-TAGTACATA-ATTATAAATATATTTAAATAATAATATTTATTTA-TTTTCAATATCAAAG
* * *
351080 AGAAAGAGCTA-TCTTAAAACACCTAGAAGCCCTTTTCTGATATTTCTAAATAAATAAATAT
63 A-AAAGAGC-AGTCTTAAAACAACTAGAAGCCCTATTCTGATATTT-TAAATAATTAAATAT
351141 GTTATATATA
Statistics
Matches: 343, Mismatches: 33, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
265 15 0.04
266 49 0.14
267 21 0.06
268 24 0.07
269 1 0.00
270 129 0.38
271 57 0.17
272 37 0.11
273 10 0.03
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (268 bp):
ATATTAGTACATAATTATAAATATATTTAAATAATAATATTTATTTATTTTCAATATCAAAGAAA
AGAGCAGTCTTAAAACAACTAGAAGCCCTATTCTGATATTTTAAATAATTAAATATTATAAAAAT
TATAATTTAGTTTATTTAAATTATTTTTAGGAAAAATTATTACATATTTTATATTTAATTATTTA
TTTATTAATATTGAAGGAAAGGGTGTCTTAAAGCATATCTAGAATAATTTTATAATATTTTATAA
ATAAATAA
Found at i:352319 original size:80 final size:80
Alignment explanation
Indices: 352186--352346 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
352176 TGGGGGCAAA
352186 TATTTTAATGGAGCAATCATCTTCATTAGCAGACATTTGCTTGCCATAGATGATAATGGACTGAA
1 TATTTTAATGGAGCAATCATCTTCATTAGCAGACATTTGCTTGCCATAGATGATAATGGACTGAA
352251 CATATACTCTTATTT
66 CATATACTCTTATTT
352266 TATTTTAATGGAGCAATCATCTTCATTAGCAGACATTTGCTTGCCATAGATGATAATGGACTGAA
1 TATTTTAATGGAGCAATCATCTTCATTAGCAGACATTTGCTTGCCATAGATGATAATGGACTGAA
352331 CATATACTCTTATTT
66 CATATACTCTTATTT
352346 T
1 T
352347 TATACTATTT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (80 bp):
TATTTTAATGGAGCAATCATCTTCATTAGCAGACATTTGCTTGCCATAGATGATAATGGACTGAA
CATATACTCTTATTT
Found at i:360389 original size:10 final size:10
Alignment explanation
Indices: 360376--360410 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
360366 TAAAAACATT
360376 TAAAATATAA
1 TAAAATATAA
*
360386 T-AAATAAAA
1 TAAAATATAA
360395 TAAAATATAA
1 TAAAATATAA
360405 TAAAAT
1 TAAAAT
360411 TCAATTACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAAATATAA
Found at i:367910 original size:21 final size:21
Alignment explanation
Indices: 367884--367924 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
367874 GGAAGCCATT
*
367884 GATGAAAGATTTAAACTTTGG
1 GATGAAAGATTGAAACTTTGG
*
367905 GATGAAAGATTGGAACTTTG
1 GATGAAAGATTGAAACTTTG
367925 AGAAGATGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.32
Consensus pattern (21 bp):
GATGAAAGATTGAAACTTTGG
Found at i:376020 original size:33 final size:33
Alignment explanation
Indices: 375981--376053 Score: 80
Period size: 33 Copynumber: 2.2 Consensus size: 33
375971 ATACCAAAAC
375981 TTATAATTAGGTA-C-TTAACATGTAATTTACCCT
1 TTATAATTAGGTAGCATT--CATGTAATTTACCCT
**
376014 TTATAA-TATTTATGCATTCATGTAATTTACCCT
1 TTATAATTAGGTA-GCATTCATGTAATTTACCCT
376047 TTATAAT
1 TTATAAT
376054 ATTTATCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
32 4 0.12
33 27 0.79
34 1 0.03
35 2 0.06
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.47
Consensus pattern (33 bp):
TTATAATTAGGTAGCATTCATGTAATTTACCCT
Found at i:376904 original size:21 final size:21
Alignment explanation
Indices: 376878--377019 Score: 148
Period size: 21 Copynumber: 6.8 Consensus size: 21
376868 TTTCCAAATC
*
376878 CGTTGCGATAGTCCAAGTTTG
1 CGTTGCGATAGTCCAAGTTCG
* *
376899 CGTTGCGATTTATTCCAAATTCG
1 CGTTGCGA--TAGTCCAAGTTCG
376922 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
* *
376941 CGTTGCGATAGTCGAACTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
376962 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
376983 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
377004 CGTTGTGATAGTCCAA
1 CGTTGCGATAGTCCAA
377020 AATCGCAACG
Statistics
Matches: 100, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
19 26 0.26
21 48 0.48
23 26 0.26
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:376945 original size:42 final size:40
Alignment explanation
Indices: 376870--377019 Score: 169
Period size: 42 Copynumber: 3.6 Consensus size: 40
376860 AATGCGATTT
*
376870 TCCAAA-TC-CGTTGCGATAGTCCAAGTTTGCGTTGCGATTTAT
1 TCCAAATTCGCGTTGCGATAGTCCAAG-TT-CGTTGCGA--TAG
376912 TCCAAATTCGCGTTGCGATAGTCCAAGTTCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAGTCCAAGTTCGTTGCGATAG
* * * *
376952 TCGAACTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
1 TCCAAATTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAG
* *
376994 TCCAAGTTCGCGTTGTGATAGTCCAA
1 TCCAAATTCGCGTTGCGATAGTCCAA
377020 AATCGCAACG
Statistics
Matches: 95, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
40 25 0.26
42 49 0.52
43 4 0.04
44 17 0.18
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (40 bp):
TCCAAATTCGCGTTGCGATAGTCCAAGTTCGTTGCGATAG
Found at i:376965 original size:63 final size:61
Alignment explanation
Indices: 376878--377019 Score: 212
Period size: 63 Copynumber: 2.3 Consensus size: 61
376868 TTTCCAAATC
* *
376878 CGTTGCGATAGTCCAAGTTTGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTT
1 CGTTGCGATAGTCCAACTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATAGTCCAAGTT
*
376941 CGTTGCGATAGTCGAACTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
1 CGTTGCGATAGTCCAACTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
*
377002 CGCGTTGTGATAGTCCAA
1 --CGTTGCGATAGTCCAA
377020 AATCGCAACG
Statistics
Matches: 72, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
61 19 0.26
63 53 0.74
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (61 bp):
CGTTGCGATAGTCCAACTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
Found at i:377949 original size:42 final size:42
Alignment explanation
Indices: 377890--378089 Score: 255
Period size: 42 Copynumber: 4.7 Consensus size: 42
377880 TGCGATTTTG
*
377890 GACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTC
*
377932 GACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTC
* * *
377974 GACTATCACAACGAATTTGGAATCGACTATCGCAACG--AACTTG
1 GACTATCGCAACGAATTTGGAAT--A-AATCGCAACGCAAACTTC
* * *
378017 GACTATCGCAACGCGAATTTGGAATAAATCTCAACGCGAACTTG
1 GACTATCGCAA--CGAATTTGGAATAAATCGCAACGCAAACTTC
378061 GACTATCGCAACGAATTTGG-A-AAATCGCA
1 GACTATCGCAACGAATTTGGAATAAATCGCA
378090 TTGCGATAGT
Statistics
Matches: 143, Mismatches: 8, Indels: 16
0.86 0.05 0.10
Matches are distributed among these distances:
40 7 0.05
41 1 0.01
42 80 0.56
43 16 0.11
44 18 0.13
45 21 0.15
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTC
Found at i:378000 original size:24 final size:24
Alignment explanation
Indices: 377972--378018 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
377962 AACGCAAACT
*
377972 TCGACTATCACAACGAATTTGGAA
1 TCGACTATCACAACGAACTTGGAA
*
377996 TCGACTATCGCAACGAACTTGGA
1 TCGACTATCACAACGAACTTGGA
378019 CTATCGCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (24 bp):
TCGACTATCACAACGAACTTGGAA
Found at i:378046 original size:87 final size:83
Alignment explanation
Indices: 377890--378089 Score: 253
Period size: 87 Copynumber: 2.4 Consensus size: 83
377880 TGCGATTTTG
*
377890 GACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAACGAACTTGGAAT
1 GACTATCGCAACGAATTTGGAATAAATCGCAACG-AAACTTCGACTATCGCAACGAACTTGGAAT
377955 AAATCGCAACGCAAACTTC
65 AAATCGCAACGCAAACTTC
* * * *
377974 GACTATCACAACGAATTTGGAATCGACTATCGCAACG-AACTTGGACTATCGCAACGCGAATTTG
1 GACTATCGCAACGAATTTGGAAT--A-AATCGCAACGAAACTTCGACTATCGCAA--CGAACTTG
* * *
378038 GAATAAATCTCAACGCGAACTTG
61 GAATAAATCGCAACGCAAACTTC
378061 GACTATCGCAACGAATTTGG-A-AAATCGCA
1 GACTATCGCAACGAATTTGGAATAAATCGCA
378090 TTGCGATAGT
Statistics
Matches: 101, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
82 6 0.06
83 1 0.01
84 21 0.21
85 16 0.16
86 2 0.02
87 55 0.54
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (83 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGAAACTTCGACTATCGCAACGAACTTGGAATA
AATCGCAACGCAAACTTC
Found at i:378087 original size:19 final size:20
Alignment explanation
Indices: 377894--378089 Score: 69
Period size: 21 Copynumber: 9.3 Consensus size: 20
377884 ATTTTGGACT
377894 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAACCGAACTTGG-A-AA
* * **
377915 ATCGCAACGCAAACTTCGACT
1 ATCGCAAC-CGAACTTGGAAA
377936 ATCGCAA-CGAACTTGGAATAA
1 ATCGCAACCGAACTTGG-A-AA
* * **
377957 ATCGCAACGCAAACTTCGACT
1 ATCGCAAC-CGAACTTGGAAA
* *
377978 ATCACAA-CGAATTTGGAATCGA
1 ATCGCAACCGAACTTGGAA---A
**
378000 CTATCGCAA-CGAACTTGGACT
1 --ATCGCAACCGAACTTGGAAA
*
378021 ATCGCAACGCGAATTTGGAATAA
1 ATCGCAAC-CGAACTTGG-A-AA
* **
378044 ATCTCAACGCGAACTTGGACT
1 ATCGCAAC-CGAACTTGGAAA
*
378065 ATCGCAA-CGAATTTGGAAA
1 ATCGCAACCGAACTTGGAAA
378084 ATCGCA
1 ATCGCA
378090 TTGCGATAGT
Statistics
Matches: 127, Mismatches: 33, Indels: 32
0.66 0.17 0.17
Matches are distributed among these distances:
19 36 0.28
20 1 0.01
21 41 0.32
22 4 0.03
23 30 0.24
24 15 0.12
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACCGAACTTGGAAA
Found at i:380606 original size:20 final size:20
Alignment explanation
Indices: 380581--380636 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
380571 ATTATCATTA
380581 AAAAATTTCAACTTGTTTCT
1 AAAAATTTCAACTTGTTTCT
*
380601 AAAAATTTGC-TCATTGTTTCT
1 AAAAATTT-CAAC-TTGTTTCT
380622 AAAAATTTCAACTTG
1 AAAAATTTCAACTTG
380637 GTTGTTCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (20 bp):
AAAAATTTCAACTTGTTTCT
Found at i:383786 original size:2 final size:2
Alignment explanation
Indices: 383779--383803 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
383769 AGTTAGTATC
383779 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
383804 GAGTGATTTT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:385703 original size:10 final size:10
Alignment explanation
Indices: 385688--385712 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
385678 AAGTGGAAAC
385688 TATAAGCCTA
1 TATAAGCCTA
385698 TATAAGCCTA
1 TATAAGCCTA
385708 TATAA
1 TATAA
385713 AACATGTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (10 bp):
TATAAGCCTA
Found at i:388471 original size:17 final size:18
Alignment explanation
Indices: 388434--388472 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
388424 ATATTATGTA
388434 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
388452 TTTACTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
388469 TTTA
1 TTTA
388473 GTAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:390287 original size:18 final size:18
Alignment explanation
Indices: 390261--390295 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
390251 CAGCAACTAC
*
390261 CGCAACCATTTATGATGT
1 CGCAACCATATATGATGT
*
390279 CGCATCCATATATGATG
1 CGCAACCATATATGATG
390296 CCGTCATCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (18 bp):
CGCAACCATATATGATGT
Found at i:392485 original size:17 final size:19
Alignment explanation
Indices: 392463--392497 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
392453 CCCCGGGAAA
392463 TTTAAAA-AAAA-ACTTTG
1 TTTAAAACAAAATACTTTG
392480 TTTAAAACAAAATACTTT
1 TTTAAAACAAAATACTTT
392498 AATTTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTAAAACAAAATACTTTG
Found at i:393068 original size:15 final size:15
Alignment explanation
Indices: 393048--393082 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
393038 CCGTAGGACC
*
393048 ACTACGTCCCGAAGT
1 ACTACGTCCCGAAGG
393063 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
393078 ACTAC
1 ACTAC
393083 AATACCCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:411643 original size:22 final size:23
Alignment explanation
Indices: 411618--411663 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
411608 ATATCAATTT
411618 ATATGAGAAAAAT-TAATAT-AAA
1 ATATGA-AAAAATATAATATGAAA
*
411640 ATATTAAAAAATATAATATGAAA
1 ATATGAAAAAATATAATATGAAA
411663 A
1 A
411664 CCTTTTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (23 bp):
ATATGAAAAAATATAATATGAAA
Found at i:417657 original size:33 final size:33
Alignment explanation
Indices: 417615--417716 Score: 150
Period size: 33 Copynumber: 3.1 Consensus size: 33
417605 GTGGTGACAT
** *
417615 CGACAATGACAACAGTAGCGGCAATAACGATGG
1 CGACAATGACAACAGTAGCATCAACAACGATGG
* *
417648 CGACAATGACAATAGTATCATCAACAACGATGG
1 CGACAATGACAACAGTAGCATCAACAACGATGG
*
417681 CGACAATGGCAACAGTAGCATCAACAACGATGG
1 CGACAATGACAACAGTAGCATCAACAACGATGG
417714 CGA
1 CGA
417717 TGGTAGTAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.14
Consensus pattern (33 bp):
CGACAATGACAACAGTAGCATCAACAACGATGG
Found at i:417733 original size:39 final size:38
Alignment explanation
Indices: 417690--417788 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 38
417680 GCGACAATGG
* *
417690 CAACAGTAGCATCAACAACGATGGCGATGGTAGTAACAA
1 CAACAGTAGCA-CAACAACGATGGCGATGGCAATAACAA
* * *
417729 CAACAATAGCGACAATAACGATGGCGATGGCAATAACAT
1 CAACAGTAGC-ACAACAACGATGGCGATGGCAATAACAA
* *
417768 CTACTGTAGCAGCAACAACGA
1 CAACAGTAGCA-CAACAACGA
417789 CGACAATGGC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
38 1 0.02
39 47 0.96
40 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.21, T:0.15
Consensus pattern (38 bp):
CAACAGTAGCACAACAACGATGGCGATGGCAATAACAA
Found at i:424658 original size:2 final size:2
Alignment explanation
Indices: 424651--424676 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
424641 TCGAACAAAC
424651 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
424677 CCATGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:427200 original size:33 final size:33
Alignment explanation
Indices: 427158--427224 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
427148 GGTCAGGCTC
427158 CGACCCCATCCCATCCCTAATTGTTGATATTAA
1 CGACCCCATCCCATCCCTAATTGTTGATATTAA
*
427191 CGACCCCATCCCATCCCTAATTGTTGATGTTAA
1 CGACCCCATCCCATCCCTAATTGTTGATATTAA
427224 C
1 C
427225 AATGTGTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.34, G:0.10, T:0.30
Consensus pattern (33 bp):
CGACCCCATCCCATCCCTAATTGTTGATATTAA
Found at i:429152 original size:24 final size:24
Alignment explanation
Indices: 429125--429173 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
429115 CTGCTTTTCT
429125 TTTAAAGTCTCGAGCTTCAATTCC
1 TTTAAAGTCTCGAGCTTCAATTCC
429149 TTTAAAGTCTCGAGCTTCAATTCC
1 TTTAAAGTCTCGAGCTTCAATTCC
429173 T
1 T
429174 CAGACTCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (24 bp):
TTTAAAGTCTCGAGCTTCAATTCC
Found at i:429737 original size:3 final size:3
Alignment explanation
Indices: 429724--429804 Score: 67
Period size: 3 Copynumber: 27.0 Consensus size: 3
429714 ATCAAATAGT
* * **
429724 AGA AGGA AGA AGA AGA AGA AGA AGA AGA AGA A-A CA-A ATA ATA CTA
1 AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA -AGA AGA AGA AGA
* * *
429769 AGT AGA AGT AGA AGA AGA AGA AGA AGA AAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
429805 GAACATTTTC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
2 2 0.03
3 61 0.92
4 3 0.05
ACGTcount: A:0.64, C:0.02, G:0.27, T:0.06
Consensus pattern (3 bp):
AGA
Found at i:433041 original size:15 final size:15
Alignment explanation
Indices: 433017--433046 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
433007 ATGAGTTTAA
*
433017 TTAGGTATATGAAAG
1 TTAGGAATATGAAAG
433032 TTAGGAATATGAAAG
1 TTAGGAATATGAAAG
433047 GGGTTGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (15 bp):
TTAGGAATATGAAAG
Found at i:433252 original size:64 final size:63
Alignment explanation
Indices: 433184--433404 Score: 220
Period size: 64 Copynumber: 3.5 Consensus size: 63
433174 TTGAAGGTGT
* * * *
433184 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAAACTAA-ATACATCGAATGCAATTTGTG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CTATT-AA-TAAGAAACATCGAATGCAATTAGTG
433247 C
63 C
433248 ATCGATGCATCA-GTAGTGCATCGATGCATCCTATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCTATTAATAA-GAAACATCGAATGCAATTAGTGC
* * * * * *
433312 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTTA-TG
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCTATTAATAAGA-AACATCGAATGCA-ATTAGTG
433375 C
63 C
*
433376 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
433405 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 14, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
62 3 0.02
63 5 0.04
64 121 0.90
65 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (63 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCTATTAATAAGAAACATCGAATGCAATTAGTGC
Found at i:433759 original size:18 final size:18
Alignment explanation
Indices: 433724--433759 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
433714 AAATTGGGTA
* *
433724 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
433742 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
433760 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:438446 original size:64 final size:63
Alignment explanation
Indices: 438378--438507 Score: 165
Period size: 64 Copynumber: 2.0 Consensus size: 63
438368 TTGAAGGTGT
** * * *
438378 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAAACTAA-ATACATCGAATGCAATTTGTG
1 ATCGATGCATCAGTAGTGCATCGATGCATC-CTATT-AA-TAAGAAACATCGAATGCAATTAGTG
438441 C
63 C
438442 ATCGATGCATCAGTAGTGCATCGATGCATCCTATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATCAGTAGTGCATCGATGCATCCTATTAATAA-GAAACATCGAATGCAATTAGTGC
438506 AT
1 AT
438508 TAGTGCACAA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
62 3 0.05
63 2 0.03
64 52 0.90
65 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Consensus pattern (63 bp):
ATCGATGCATCAGTAGTGCATCGATGCATCCTATTAATAAGAAACATCGAATGCAATTAGTGC
Found at i:442624 original size:14 final size:14
Alignment explanation
Indices: 442605--442660 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
442595 CGTTCATGAA
442605 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
442619 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
442632 --TT-GTTTATGTT
1 CGTTCGATTATGTT
442643 CGTTCGATTATGTT
1 CGTTCGATTATGTT
442657 CGTT
1 CGTT
442661 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:442639 original size:24 final size:24
Alignment explanation
Indices: 442612--442681 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
442602 GAACGTTCGA
*
442612 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
442636 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
442660 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
442682 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:443420 original size:10 final size:10
Alignment explanation
Indices: 443405--443479 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
443395 GGGTCTCCAA
443405 CGTTTATGTT
1 CGTTTATGTT
443415 CGTTTATGTT
1 CGTTTATGTT
443425 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
443436 ATGTTCGTGTT
1 -CGTTTATGTT
443447 CGTTTATGTT
1 CGTTTATGTT
443457 CG----TGTT
1 CGTTTATGTT
443463 CGTTTATGTT
1 CGTTTATGTT
443473 CGTTTAT
1 CGTTTAT
443480 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:443436 original size:16 final size:16
Alignment explanation
Indices: 443411--443475 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
443401 CCAACGTTTA
443411 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
443427 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
443443 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
443459 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
443475 T
1 T
443476 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:443566 original size:16 final size:16
Alignment explanation
Indices: 443545--443577 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
443535 AAAAAAATTT
443545 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
443561 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
443577 T
1 T
443578 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:456938 original size:20 final size:20
Alignment explanation
Indices: 456913--456973 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
456903 ACATTCCCTC
456913 TCTTTGAGACCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
*
456933 TCTTTGAGACCTTAAAACAT
1 TCTTTGAGACCTTGAAACAT
* *
456953 TCTTTGTGGCCTTGAAACAT
1 TCTTTGAGACCTTGAAACAT
456973 T
1 T
456974 GCATTTATCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (20 bp):
TCTTTGAGACCTTGAAACAT
Found at i:457605 original size:14 final size:14
Alignment explanation
Indices: 457586--457625 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
457576 CAAAGAAAAT
457586 CAAAGAGAAAGAAA
1 CAAAGAGAAAGAAA
457600 CAAAGAG-AA-AAA
1 CAAAGAGAAAGAAA
457612 C-AAGCAGAAAGAAA
1 CAAAG-AGAAAGAAA
457626 AAGAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 3 0.13
12 6 0.26
13 4 0.17
14 10 0.43
ACGTcount: A:0.70, C:0.10, G:0.20, T:0.00
Consensus pattern (14 bp):
CAAAGAGAAAGAAA
Found at i:458884 original size:4 final size:4
Alignment explanation
Indices: 458851--458877 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
458841 ATACATCAAC
458851 ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA
458878 CATACATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (4 bp):
ACAT
Found at i:459440 original size:105 final size:105
Alignment explanation
Indices: 459238--459579 Score: 469
Period size: 105 Copynumber: 3.3 Consensus size: 105
459228 GCAGTTTCTT
* * * * *
459238 TTGAAATAAAATTAATCTCAATTGAGATTGCTGTTTCTTTCAAAAAAAAAATTT-GTCTCGTTTG
1 TTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTCTTTC--AAAACAAATTTCGTCTCGCTTG
459302 AGATATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCAC
64 AGATATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCAC
*
459344 TTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTCTTTCAAAACAAATTTCGTCTCGCCTGAG
1 TTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTCTTTCAAAACAAATTTCGTCTCGCTTGAG
459409 ATATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCAC
66 ATATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCAC
*
459449 TTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTATTTCAAAACAAATTTCGTCTCGCTTGAG
1 TTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTCTTTCAAAACAAATTTCGTCTCGCTTGAG
* * * ** * *
459514 ACATTTTCCCTCAT-A-ATACAAATTTCAAAGTTGATAT-AC
66 ATATTTTTCCT-TTGAGATACAAATTTTGAATTTGCT-TCAC
*
459553 TTGAAAAAAAATTAATC-CTACTTGAGA
1 TTGAAACAAAATTAATCTC-ACTTGAGA
459580 ATTTTAAAGT
Statistics
Matches: 216, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
103 1 0.00
104 52 0.24
105 124 0.57
106 39 0.18
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (105 bp):
TTGAAACAAAATTAATCTCACTTGAGATTGTTGTTTCTTTCAAAACAAATTTCGTCTCGCTTGAG
ATATTTTTCCTTTGAGATACAAATTTTGAATTTGCTTCAC
Found at i:459791 original size:28 final size:27
Alignment explanation
Indices: 459755--459842 Score: 108
Period size: 26 Copynumber: 3.2 Consensus size: 27
459745 GACAATTTCG
459755 TGAAAAAAATATTTGAGTCTGTTCCTTT
1 TGAAAAAAATATTTGAGTCTGTT-CTTT
* *
459783 TGAATAAAAATCTTTGTGT-TGTT-TTT
1 TGAA-AAAAATATTTGAGTCTGTTCTTT
459809 TGAAAAAAAATATTTGAGTCTGTTTCTTT
1 TG-AAAAAAATATTTGAGTCTG-TTCTTT
459838 TGAAA
1 TGAAA
459843 CAAAGTTTTG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
26 17 0.33
27 4 0.08
28 13 0.25
29 17 0.33
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (27 bp):
TGAAAAAAATATTTGAGTCTGTTCTTT
Found at i:459817 original size:26 final size:28
Alignment explanation
Indices: 459757--459842 Score: 113
Period size: 29 Copynumber: 3.1 Consensus size: 28
459747 CAATTTCGTG
459757 AAAAAAATATTTGAGTCTGTTCCTTTTGA
1 AAAAAAATATTTGAGTCTGTT-CTTTTGA
* * *
459786 ATAAAAATCTTTGTGT-TGTT-TTTTGA
1 AAAAAAATATTTGAGTCTGTTCTTTTGA
459812 AAAAAAATATTTGAGTCTGTTTCTTTTGA
1 AAAAAAATATTTGAGTCTG-TTCTTTTGA
459841 AA
1 AA
459843 CAAAGTTTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
26 19 0.40
27 2 0.04
28 6 0.12
29 21 0.44
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (28 bp):
AAAAAAATATTTGAGTCTGTTCTTTTGA
Found at i:459911 original size:62 final size:62
Alignment explanation
Indices: 459813--460224 Score: 249
Period size: 62 Copynumber: 6.5 Consensus size: 62
459803 GTTTTTTGAA
* *
459813 AAAAAATATTTGAGTCTGTTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGGA-AATTTCGTG
1 AAAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGA-GACAATTTCGTG
* * * * * * **
459875 CAAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTTTATTAAGATAATTTTGAAA
1 AAAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCG-TG
* * * *
459938 AAAAAATCTTTGAGTTTATTTCTTTGGAAACACAGTTTTGTCTCTCTTGAGACAATTTCTTTTG
1 AAAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTC--GTG
* * ** *** *
460002 AGAAAAATCTTTGAGTCTGTTTC-TTTGAAAACAAA-ATTTAACGTCT-TTGAGATTGTTTCCCT
1 A-AAAAATCTTTGAGTCTATTTCTTTTG-AAACAAAGTTTTGTC-TCTCTTGAGACAATTT--CG
460064 TG
61 TG
* * * **
460066 AAACAAAACCCATCTTTGAGTCTTTTTCTCTTGAAACAAAAGTCTTTGAGTCGTTTCTTTTGA-A
1 --A-AAAA---ATCTTTGAGTCTATTTCTTTTGAAAC-AAAGT-TTT--GTC-TCTCTTGAGACA
460130 A---C---
55 ATTTCGTG
* * * *
460132 -AAAAATCTTTAAGTTTGTTTCTTTTAAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG
1 AAAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG
* *
460193 -AAATATCTTTGAGT-TGTTTCTTTTGAAACAAA
1 AAAAAATCTTTGAGTCTATTTCTTTTGAAACAAA
460225 TATTTGAGTC
Statistics
Matches: 269, Mismatches: 53, Indels: 58
0.71 0.14 0.15
Matches are distributed among these distances:
54 7 0.03
55 5 0.02
57 3 0.01
58 6 0.02
59 21 0.08
60 17 0.06
61 14 0.05
62 54 0.20
63 50 0.19
64 20 0.07
65 28 0.10
66 6 0.02
69 21 0.08
70 6 0.02
72 3 0.01
74 4 0.01
75 4 0.01
ACGTcount: A:0.30, C:0.13, G:0.14, T:0.42
Consensus pattern (62 bp):
AAAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG
Found at i:460114 original size:30 final size:30
Alignment explanation
Indices: 460063--460164 Score: 109
Period size: 30 Copynumber: 3.3 Consensus size: 30
460053 ATTGTTTCCC
*
460063 TTGAAACAAAACCCATCTTTGAGTCTTTTTCTC
1 TTGAAACAAAA---ATCTTTGAGTCTTTTTCTT
* *
460096 TTGAAACAAAAGTCTTTGAGTC-GTTTCTT
1 TTGAAACAAAAATCTTTGAGTCTTTTTCTT
*
460125 TTGAAACAAAAATCTTTAAGT-TTGTTTCTT
1 TTGAAACAAAAATCTTTGAGTCTT-TTTCTT
*
460155 TTAAAACAAA
1 TTGAAACAAA
460165 GTTTTGTCTC
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
29 24 0.40
30 25 0.42
33 11 0.18
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (30 bp):
TTGAAACAAAAATCTTTGAGTCTTTTTCTT
Found at i:460129 original size:29 final size:29
Alignment explanation
Indices: 460004--460164 Score: 108
Period size: 30 Copynumber: 5.1 Consensus size: 29
459994 TTCTTTTGAG
460004 AAAAATCTTTGAGTCTGTTTC-TTTGAAAAC
1 AAAAATCTTTGAGTC-GTTTCTTTTG-AAAC
* **
460034 AAAATTTAACGTCTTTGAGATTGTTTCCCTTGAAAC
1 -AAA---AA--TCTTTGAG-TCGTTTCTTTTGAAAC
* *
460070 AAAACCCATCTTTGAGTCTTTTTCTCTTGAAAC
1 AAAA---ATCTTTGAGTC-GTTTCTTTTGAAAC
*
460103 AAAAGTCTTTGAGTCGTTTCTTTTGAAAC
1 AAAAATCTTTGAGTCGTTTCTTTTGAAAC
* * *
460132 AAAAATCTTTAAGTTTGTTTCTTTTAAAAC
1 AAAAATCTTTGAG-TCGTTTCTTTTGAAAC
460162 AAA
1 AAA
460165 GTTTTGTCTC
Statistics
Matches: 106, Mismatches: 12, Indels: 25
0.74 0.08 0.17
Matches are distributed among these distances:
29 23 0.22
30 27 0.25
31 3 0.03
32 2 0.02
33 24 0.23
34 2 0.02
35 4 0.04
36 17 0.16
37 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (29 bp):
AAAAATCTTTGAGTCGTTTCTTTTGAAAC
Found at i:460232 original size:27 final size:26
Alignment explanation
Indices: 460200--460268 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 26
460190 GTGAAATATC
460200 TTTGAGTTGTTTCTTTTGAAACAAATA
1 TTTGAGTTGTTTCTTTTGAAA-AAATA
* *
460227 TTTGAGTCTGTTTATTTTGAAAAAATC
1 TTTGAGT-TGTTTCTTTTGAAAAAATA
460254 TTTGAGTTTGTTTCT
1 TTTGAG-TTGTTTCT
460269 ACTAACAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (26 bp):
TTTGAGTTGTTTCTTTTGAAAAAATA
Found at i:460700 original size:28 final size:29
Alignment explanation
Indices: 460668--460746 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 29
460658 GAAACACGTC
*
460668 ATCTTTGAGTCTGTTT-TTCTTT-AAACAA
1 ATCTTTGAGTCTGTTTCTT-TTTAAAAAAA
*
460696 ATCTTTGAGTTTGTTTCTTTTTAAAAAAAAA
1 ATCTTTGAGTCTGTTTCTTTTT--AAAAAAA
460727 ATCTTTGAGTCTGTTTCTTT
1 ATCTTTGAGTCTGTTTCTTT
460747 GGTAACAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
28 18 0.41
29 2 0.05
31 24 0.55
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (29 bp):
ATCTTTGAGTCTGTTTCTTTTTAAAAAAA
Found at i:460806 original size:63 final size:63
Alignment explanation
Indices: 460723--460883 Score: 223
Period size: 63 Copynumber: 2.5 Consensus size: 63
460713 TTTTTAAAAA
* * * *
460723 AAAAATCTTTGAGTCTGTTTCTTTGGTAACAAAATTTTGTCTCTTTTGAGACAGTTTCTTTTG
1 AAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTG
460786 AAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAG
1 AAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTT--G
* * *
460851 AAAATCATCTTTAAGTCTGTTTCTTTCGAAACA
1 AAAA--ATCTTTGAGTATGTTTCTTTGGAAACA
460884 TCATCTTTGA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
63 58 0.67
65 5 0.06
67 24 0.28
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (63 bp):
AAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTG
Found at i:460886 original size:29 final size:30
Alignment explanation
Indices: 460840--460903 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
460830 CTTGAGACAA
* *
460840 TTTCTTTTGAGAAAATCATCTTTAAGTCTG
1 TTTCTTTCGAGAAAATCATCTTTAAGTCGG
* *
460870 TTTCTTTCGA-AACATCATCTTTGAGTCGG
1 TTTCTTTCGAGAAAATCATCTTTAAGTCGG
460899 TTTCT
1 TTTCT
460904 CTTGGAACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.22, C:0.17, G:0.14, T:0.47
Consensus pattern (30 bp):
TTTCTTTCGAGAAAATCATCTTTAAGTCGG
Found at i:461160 original size:134 final size:134
Alignment explanation
Indices: 460920--461269 Score: 452
Period size: 134 Copynumber: 2.6 Consensus size: 134
460910 ACCATTATCT
* * * *
460920 CTAAAGATGGCTAGAACTCTTCATCACGTATGAGCCGTACCATCCCCTGACCAGATCTCCTCATA
1 CTAAAGATGGCCAAAACTCTTCATCGCGTATGAGCCGTACCATCCCCTGACCAGATCTCCTCATC
** *
460985 ACGTAGGAGCAGCGTCAACTTTAGATAACCAGTCGTCCTCATCACGTAGGAACCGAGTTATCACC
66 ACGTAGGAGCAGCGTCAACCGTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACC
**
461050 TTTC
131 ACTC
*
461054 CTAAAGATGGCCAAAACTCTTCATCGCGTATGAGTCGTACCATCCCCTGACCAGATCTCCTCATC
1 CTAAAGATGGCCAAAACTCTTCATCGCGTATGAGCCGTACCATCCCCTGACCAGATCTCCTCATC
** *
461119 ACGTAGGAGCAGCGTCAACCGTAGATAACCAGCCGTCCTCATCGTGTAGGAACTGAGTTATCACC
66 ACGTAGGAGCAGCGTCAACCGTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACC
461184 ACTC
131 ACTC
* * * * * * * * * *
461188 CTAAATATGACC-AACCGTCCTCATCGCGTAGGAACCTTATCATCCCCCGACCATATCTCCTCAT
1 CTAAAGATGGCCAAAAC-TCTTCATCGCGTATGAGCCGTACCATCCCCTGACCAGATCTCCTCAT
*
461252 CAAGTAGGAGTCA-CGTCA
65 CACGTAGGAG-CAGCGTCA
461270 CCTTTAGACG
Statistics
Matches: 189, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
133 3 0.02
134 184 0.97
135 2 0.01
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.23
Consensus pattern (134 bp):
CTAAAGATGGCCAAAACTCTTCATCGCGTATGAGCCGTACCATCCCCTGACCAGATCTCCTCATC
ACGTAGGAGCAGCGTCAACCGTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACC
ACTC
Found at i:464589 original size:2 final size:2
Alignment explanation
Indices: 464582--464606 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
464572 GTATGCTTTC
464582 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
464607 GTTGAGTGTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:467318 original size:3 final size:3
Alignment explanation
Indices: 467310--467339 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
467300 AACTAATGGA
467310 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
467340 GGTGGGTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:474355 original size:37 final size:37
Alignment explanation
Indices: 474305--474378 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
474295 GACCCCACAC
*
474305 GAGGTACTTCTTAGAGGAAAAGGGTTATGTTCTGGAT
1 GAGGTACTTCTTAGAGGAAAAGGGTTATGCTCTGGAT
*
474342 GAGGTACTTCTTAGAGGAGAAGGGTTATGCTCTGGAT
1 GAGGTACTTCTTAGAGGAAAAGGGTTATGCTCTGGAT
474379 TCGTACTCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.31
Consensus pattern (37 bp):
GAGGTACTTCTTAGAGGAAAAGGGTTATGCTCTGGAT
Found at i:480770 original size:12 final size:12
Alignment explanation
Indices: 480753--480788 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
480743 AGTTAATGCC
480753 TGATGTGGCAGT
1 TGATGTGGCAGT
*
480765 TGATGTGGC-GA
1 TGATGTGGCAGT
480776 TGATGTGGCAGT
1 TGATGTGGCAGT
480788 T
1 T
480789 AACGTGGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.17, C:0.08, G:0.42, T:0.33
Consensus pattern (12 bp):
TGATGTGGCAGT
Found at i:480779 original size:23 final size:23
Alignment explanation
Indices: 480753--480806 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
480743 AGTTAATGCC
* *
480753 TGATGTGGCAGTTGATGTGGCGA
1 TGATGTGGCAGTTAACGTGGCGA
*
480776 TGATGTGGCAGTTAACGTGGTGA
1 TGATGTGGCAGTTAACGTGGCGA
*
480799 TGAAGTGG
1 TGATGTGG
480807 TAGCTGACGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.07, G:0.43, T:0.30
Consensus pattern (23 bp):
TGATGTGGCAGTTAACGTGGCGA
Found at i:480781 original size:11 final size:12
Alignment explanation
Indices: 480753--480786 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
480743 AGTTAATGCC
*
480753 TGATGTGGCAGT
1 TGATGTGGCAGA
480765 TGATGTGGC-GA
1 TGATGTGGCAGA
480776 TGATGTGGCAG
1 TGATGTGGCAG
480787 TTAACGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.18, C:0.09, G:0.44, T:0.29
Consensus pattern (12 bp):
TGATGTGGCAGA
Found at i:480859 original size:23 final size:23
Alignment explanation
Indices: 480833--480888 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
480823 CAATTAACAT
480833 CTTCTAGAAGGCCCAATCATCAA
1 CTTCTAGAAGGCCCAATCATCAA
*
480856 CTTCTAGAAGGTCCAATCATCAA
1 CTTCTAGAAGGCCCAATCATCAA
480879 CTTCTAGAAG
1 CTTCTAGAAG
480889 ATTCAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (23 bp):
CTTCTAGAAGGCCCAATCATCAA
Found at i:480895 original size:23 final size:23
Alignment explanation
Indices: 480833--480897 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
480823 CAATTAACAT
**
480833 CTTCTAGAAGGCCCAATCATCAA
1 CTTCTAGAAGATCCAATCATCAA
*
480856 CTTCTAGAAGGTCCAATCATCAA
1 CTTCTAGAAGATCCAATCATCAA
*
480879 CTTCTAGAAGATTCAATCA
1 CTTCTAGAAGATCCAATCA
480898 ACAGTGGCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (23 bp):
CTTCTAGAAGATCCAATCATCAA
Found at i:487321 original size:34 final size:34
Alignment explanation
Indices: 487260--487326 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 34
487250 TTCTTGAGAG
487260 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTTATC-AGAGAGAAGTTGTTA
487294 TTGTTTTCTCCTTGTTATATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-TATCAGAGAGAAGTTGT
487327 AATTCCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 20 0.67
35 6 0.20
36 4 0.13
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTTATCAGAGAGAAGTTGTTA
Found at i:508333 original size:25 final size:25
Alignment explanation
Indices: 508305--508387 Score: 64
Period size: 25 Copynumber: 3.2 Consensus size: 25
508295 TTATATTAAG
508305 AAATGCCAAGCCAAACATTATTTGT
1 AAATGCCAAGCCAAACATTATTTGT
**
508330 AAATTG--AATATCAAACATCTTATATTAAG-
1 AAA-TGCCAA-GCCAAACA--TTAT-TT--GT
508359 AAATGCCAAGCCAAACATTATTTGT
1 AAATGCCAAGCCAAACATTATTTGT
508384 AAAT
1 AAAT
508388 TGCGTTACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 20
0.65 0.06 0.29
Matches are distributed among these distances:
24 3 0.07
25 13 0.30
26 4 0.09
27 8 0.18
28 4 0.09
29 9 0.20
30 3 0.07
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.30
Consensus pattern (25 bp):
AAATGCCAAGCCAAACATTATTTGT
Found at i:508364 original size:54 final size:54
Alignment explanation
Indices: 508282--508389 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
508272 CACCAAACTC
508282 AATATAAAACATCTTATATTAAGAAATGCCAAGCCAAACATTATTTGTAAATTG
1 AATATAAAACATCTTATATTAAGAAATGCCAAGCCAAACATTATTTGTAAATTG
*
508336 AATATCAAACATCTTATATTAAGAAATGCCAAGCCAAACATTATTTGTAAATTG
1 AATATAAAACATCTTATATTAAGAAATGCCAAGCCAAACATTATTTGTAAATTG
508390 CGTTACAACT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.31
Consensus pattern (54 bp):
AATATAAAACATCTTATATTAAGAAATGCCAAGCCAAACATTATTTGTAAATTG
Found at i:508373 original size:29 final size:29
Alignment explanation
Indices: 508288--508376 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
508278 ACTCAATATA
508288 AAACATCTTATATTAAGAAATGCCAAGCC
1 AAACATCTTATATTAAGAAATGCCAAGCC
**
508317 AAACA--TTAT-TT--GTAAATTG--AATATC
1 AAACATCTTATATTAAG-AAA-TGCCAA-GCC
508342 AAACATCTTATATTAAGAAATGCCAAGCC
1 AAACATCTTATATTAAGAAATGCCAAGCC
508371 AAACAT
1 AAACAT
508377 TATTTGTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 20
0.66 0.06 0.29
Matches are distributed among these distances:
24 3 0.07
25 9 0.20
26 4 0.09
27 8 0.17
28 4 0.09
29 15 0.33
30 3 0.07
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (29 bp):
AAACATCTTATATTAAGAAATGCCAAGCC
Found at i:509728 original size:8 final size:8
Alignment explanation
Indices: 509717--509743 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
509707 CCATTGTAGT
509717 TTGATTGG
1 TTGATTGG
509725 TTGATTGG
1 TTGATTGG
509733 TTGATTGG
1 TTGATTGG
509741 TTG
1 TTG
509744 TAGCAACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.37, T:0.52
Consensus pattern (8 bp):
TTGATTGG
Found at i:514384 original size:29 final size:29
Alignment explanation
Indices: 514339--514395 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
514329 CTAGATTAAT
*
514339 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGATTACATCAATTTAGTA
514368 TTGATGTCATTGATTACATCAATTTAGT
1 TTGATGTCATTGATTACATCAATTTAGT
514396 TATGTGAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (29 bp):
TTGATGTCATTGATTACATCAATTTAGTA
Found at i:523585 original size:40 final size:39
Alignment explanation
Indices: 523517--523599 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 39
523507 TTTTAAGGAT
* *
523517 CCAAAGATGAAATTCTCATGTACACAAGTTGGCCACCTA
1 CCAAAGATGAAATTCCCATGTACACAAGTTGGCCACCAA
* **
523556 CCAAAGATGAATTTTCCCATGTGTACAAGTTGGCCACCAA
1 CCAAAGATGAA-ATTCCCATGTACACAAGTTGGCCACCAA
523596 CCAA
1 CCAA
523600 CTTGTCAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
39 11 0.29
40 27 0.71
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.23
Consensus pattern (39 bp):
CCAAAGATGAAATTCCCATGTACACAAGTTGGCCACCAA
Found at i:528312 original size:39 final size:40
Alignment explanation
Indices: 528269--528352 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
528259 TATTTTAAGG
* *
528269 ACCAAAGATGAA-ACTCTCATGTGTCCAAGTTGGCCACCT
1 ACCAAAGATGAATACTCTCATGTGTACAAGTTGGCCACCA
** *
528308 ACCAAAGATGAATTTTCTCATGTGTACAAGTTGGTCACCA
1 ACCAAAGATGAATACTCTCATGTGTACAAGTTGGCCACCA
528348 ACCAA
1 ACCAA
528353 CTTGTCAACT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 12 0.31
40 27 0.69
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (40 bp):
ACCAAAGATGAATACTCTCATGTGTACAAGTTGGCCACCA
Found at i:528382 original size:17 final size:17
Alignment explanation
Indices: 528349--528382 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
528339 TGGTCACCAA
* *
528349 CCAACTTGTCAACTTTG
1 CCAACTTGCCAAATTTG
528366 CCAACTTGCCAAATTTG
1 CCAACTTGCCAAATTTG
528383 ACAATTTGCA
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:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (17 bp):
CCAACTTGCCAAATTTG
Found at i:535918 original size:15 final size:14
Alignment explanation
Indices: 535891--535931 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
535881 CTCTCAAGAC
535891 TATCTATTATTTTT
1 TATCTATTATTTTT
535905 TATCTATCTATTTTT
1 TATCTAT-TATTTTT
*
535920 TCTCTAGTTATT
1 TATCTA-TTATT
535932 CATTAGAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 16 0.67
16 1 0.04
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (14 bp):
TATCTATTATTTTT
Found at i:537758 original size:24 final size:24
Alignment explanation
Indices: 537731--537786 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
537721 GAACGAAGAG
* *
537731 GTCTACGAATTGGAGAACGGCTTC
1 GTCTACGAATCGGAGAACGGCTAC
*
537755 GTCTACGAATCGGAGAAGGGCTAC
1 GTCTACGAATCGGAGAACGGCTAC
537779 GTCTACGA
1 GTCTACGA
537787 TTGATGGGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.21
Consensus pattern (24 bp):
GTCTACGAATCGGAGAACGGCTAC
Found at i:545055 original size:12 final size:12
Alignment explanation
Indices: 545038--545063 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
545028 TCACTTAATC
545038 CAAAATACACCA
1 CAAAATACACCA
545050 CAAAATACACCA
1 CAAAATACACCA
545062 CA
1 CA
545064 CTGGATGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.35, G:0.00, T:0.08
Consensus pattern (12 bp):
CAAAATACACCA
Found at i:546351 original size:13 final size:13
Alignment explanation
Indices: 546307--546352 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
546297 TTCATTCTCA
546307 TTTCTCTTCTTTT
1 TTTCTCTTCTTTT
* *
546320 ATTTCCTCTTCTCTA
1 -TTT-CTCTTCTTTT
546335 TTTCTCTTCTTTT
1 TTTCTCTTCTTTT
546348 TTTCT
1 TTTCT
546353 TCCCTCTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 13 0.48
14 6 0.22
15 8 0.30
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTCTCTTCTTTT
Found at i:546360 original size:28 final size:27
Alignment explanation
Indices: 546302--546360 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
546292 TGTGTTTCAT
*
546302 TCTCATTTCTCTTCTTTTATTTCCTCT
1 TCTCATTTCTCTTCTTTTATTTCCTCC
*
546329 TCTCTATTTCTCTTCTTTT-TTTCTTCCC
1 TCTC-ATTTCTCTTCTTTTATTTCCT-CC
546357 TCTC
1 TCTC
546361 CAAGTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (27 bp):
TCTCATTTCTCTTCTTTTATTTCCTCC
Found at i:547380 original size:48 final size:49
Alignment explanation
Indices: 547324--547419 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 49
547314 AATTCAAAAG
* *
547324 TAAACCCTAAAATGCTTAAATAACCAAATCTTTAC-AAATTTATGAATA
1 TAAACCCTAAAATGCTTAAACAACCAAATCTTTACAAAATCTATGAATA
547372 TAAACCCTAAAATGCTTAAACAACCAAATCTTTACAAAATCTATGAAT
1 TAAACCCTAAAATGCTTAAACAACCAAATCTTTACAAAATCTATGAAT
547420 TGATGAAAGC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 34 0.76
49 11 0.24
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.29
Consensus pattern (49 bp):
TAAACCCTAAAATGCTTAAACAACCAAATCTTTACAAAATCTATGAATA
Found at i:547710 original size:21 final size:19
Alignment explanation
Indices: 547685--547723 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
547675 GGAAGAAGAA
547685 GAAGAAAATGGAAAATGAGAG
1 GAAGAAAAT-G-AAATGAGAG
547706 GAAGAAAATGAAATGAGA
1 GAAGAAAATGAAATGAGA
547724 TAATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.10
Consensus pattern (19 bp):
GAAGAAAATGAAATGAGAG
Found at i:549460 original size:60 final size:60
Alignment explanation
Indices: 549396--549535 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 60
549386 TTCAAATATC
** * * **
549396 TCAATTTCATCATTAAACTATGA-GTATCATTTTAAATTAATCCTTAAAC-TTTTGAACACT
1 TCAATTTCATCACCAAACTATGACCT-TAATTTTAAATTAATCCCCAAACTTTTTGAACA-T
* *
549456 TCAATTTCATCCCCAAACTATGACCTTAATTTTAAATTGATCCCCAAACTTTTTGAACAT
1 TCAATTTCATCACCAAACTATGACCTTAATTTTAAATTAATCCCCAAACTTTTTGAACAT
549516 TCTAATTTCATC-CC-AACTAT
1 TC-AATTTCATCACCAAACTAT
549536 ATATATATTA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
59 6 0.09
60 44 0.64
61 19 0.28
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.39
Consensus pattern (60 bp):
TCAATTTCATCACCAAACTATGACCTTAATTTTAAATTAATCCCCAAACTTTTTGAACAT
Found at i:550168 original size:3 final size:3
Alignment explanation
Indices: 550162--550186 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
550152 AAAAAAAAAA
550162 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
550187 GAATTAGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:550605 original size:31 final size:31
Alignment explanation
Indices: 550561--550624 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
550551 TAGTCGTTAG
*
550561 AAATTCTAGGATCATATTATATCATATCCCA
1 AAATTCTAGGATCAGATTATATCATATCCCA
550592 AAATTCT-GAGATCAGATTATATCATATCCCA
1 AAATTCTAG-GATCAGATTATATCATATCCCA
550623 AA
1 AA
550625 TTAACATCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.33
Consensus pattern (31 bp):
AAATTCTAGGATCAGATTATATCATATCCCA
Found at i:553465 original size:23 final size:23
Alignment explanation
Indices: 553416--553473 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
553406 ATAACTCTAA
*
553416 TTTTATGACACATTTTCATTTGT
1 TTTTATGACACATTTTCATTTGC
*
553439 TTTTATGACATATTTTCATCTT-C
1 TTTTATGACACATTTTCAT-TTGC
*
553462 TTTTATAACACA
1 TTTTATGACACA
553474 CATGCTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (23 bp):
TTTTATGACACATTTTCATTTGC
Found at i:561398 original size:14 final size:14
Alignment explanation
Indices: 561369--561414 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
561359 CGTTCGTGAA
561369 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
561385 CGTTCATTTATGTT
1 CGTTCATTTATGTT
*
561399 CATTCATTTATGTT
1 CGTTCATTTATGTT
561413 CG
1 CG
561415 AACAGAGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 20 0.71
15 3 0.11
16 5 0.18
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.52
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:561695 original size:10 final size:10
Alignment explanation
Indices: 561677--561757 Score: 62
Period size: 10 Copynumber: 8.1 Consensus size: 10
561667 GTATTTGTAT
*
561677 TGTTTGTTTA
1 TGTTCGTTTA
561687 TGTTCGTTTA
1 TGTTCGTTTA
561697 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
561710 TGTTCATTTA
1 TGTTCGTTTA
561720 T-TAT-G-TT-
1 TGT-TCGTTTA
* *
561727 CGTTCGTTTG
1 TGTTCGTTTA
561737 TGTTCGTTTA
1 TGTTCGTTTA
561747 TGTTCGTTTA
1 TGTTCGTTTA
561757 T
1 T
561758 CATTTAAATG
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
7 1 0.02
8 4 0.07
9 3 0.05
10 39 0.68
13 10 0.18
ACGTcount: A:0.10, C:0.09, G:0.20, T:0.62
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:561698 original size:27 final size:26
Alignment explanation
Indices: 561668--561747 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 26
561658 TTGTTTTTTG
*
561668 TATTTGTATTGTTTGTTTATGTTCGTT
1 TATTTGT-TTGTTCGTTTATGTTCGTT
*
561695 TA-TTG--TGTTCGTTTATGTTCATT
1 TATTTGTTTGTTCGTTTATGTTCGTT
* *
561718 TATTATGTTCGTTCGTTTGTGTTCGTT
1 TATT-TGTTTGTTCGTTTATGTTCGTT
561745 TAT
1 TAT
561748 GTTCGTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 18 0.41
24 1 0.02
25 2 0.05
26 3 0.07
27 20 0.45
ACGTcount: A:0.11, C:0.07, G:0.19, T:0.62
Consensus pattern (26 bp):
TATTTGTTTGTTCGTTTATGTTCGTT
Found at i:561705 original size:13 final size:13
Alignment explanation
Indices: 561687--561747 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
561677 TGTTTGTTTA
561687 TGTTCGTTTATTG
1 TGTTCGTTTATTG
561700 TGTTCGTTTA---
1 TGTTCGTTTATTG
* *
561710 TGTTCATTTATTA
1 TGTTCGTTTATTG
561723 TGTTCGTTCGT-TTG
1 TGTTCGTT--TATTG
561737 TGTTCGTTTAT
1 TGTTCGTTTAT
561748 GTTCGTTTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
10 9 0.23
12 1 0.03
13 18 0.46
14 10 0.26
15 1 0.03
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.61
Consensus pattern (13 bp):
TGTTCGTTTATTG
Found at i:561708 original size:23 final size:23
Alignment explanation
Indices: 561674--561730 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
561664 TTTGTATTTG
*
561674 TATTGT-TT-GTTTATGTTCGTT
1 TATTGTGTTCGTTTATGTTCATT
561695 TATTGTGTTCGTTTATGTTCATT
1 TATTGTGTTCGTTTATGTTCATT
*
561718 TATTATGTTCGTT
1 TATTGTGTTCGTT
561731 CGTTTGTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 6 0.19
22 2 0.06
23 24 0.75
ACGTcount: A:0.12, C:0.07, G:0.18, T:0.63
Consensus pattern (23 bp):
TATTGTGTTCGTTTATGTTCATT
Found at i:561744 original size:37 final size:36
Alignment explanation
Indices: 561684--561757 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 36
561674 TATTGTTTGT
561684 TTATGTTCGTTTATTGTGTTCGTTTATGTTCATTTA
1 TTATGTTCGTTTATTGTGTTCGTTTATGTTCATTTA
*
561720 TTATGTTCGTTCGT-TTGTGTTCGTTTATGTTCGTTTA
1 TTATGTTCGTT--TATTGTGTTCGTTTATGTTCATTTA
561757 T
1 T
561758 CATTTAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
36 11 0.31
37 23 0.66
38 1 0.03
ACGTcount: A:0.11, C:0.09, G:0.19, T:0.61
Consensus pattern (36 bp):
TTATGTTCGTTTATTGTGTTCGTTTATGTTCATTTA
Found at i:564323 original size:21 final size:21
Alignment explanation
Indices: 564299--564339 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
564289 TTTTCGTCGT
*
564299 TGACAGTTTATTTTATTGACA
1 TGACAGTTTATTTTACTGACA
564320 TGACAGTTTATTTTACTGAC
1 TGACAGTTTATTTTACTGAC
564340 GTAATAATCT
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:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (21 bp):
TGACAGTTTATTTTACTGACA
Found at i:575936 original size:180 final size:180
Alignment explanation
Indices: 575635--575998 Score: 712
Period size: 180 Copynumber: 2.0 Consensus size: 180
575625 TATAAATATT
575635 GTTATATTACCCCTCTGTCTATTGTTTTTTTAATTAAATTCTTATTTATATTAGGTTGGATTAAC
1 GTTATATTACCCCTCTGTCTATTGTTTTTTTAATTAAATTCTTATTTATATTAGGTTGGATTAAC
575700 TCGAATCTAATTTATATTTTAAAAATTCAAGTCGGATTAGATTCGGATGAAATGTATATATTTTT
66 TCGAATCTAATTTATATTTTAAAAATTCAAGTCGGATTAGATTCGGATGAAATGTATATATTTTT
575765 TGAATTGGATCAAGTAAATGATATATAA-TTTCAGATCAAATCAAGTTGG
131 TGAATTGGATCAAGTAAATGATATATAATTTTCAGATCAAATCAAGTTGG
575814 GTTATATTACCCCTCTGTCTATTGTTTTTTTAATTAAATTCTTATTTTATATTAGGTTGGATTAA
1 GTTATATTACCCCTCTGTCTATTGTTTTTTTAATTAAATTCTTA-TTTATATTAGGTTGGATTAA
575879 CTCGAATCTAATTTATATTTTAAAAATTCAAGTCGGATTAGATTCGGATGAAATGTATATATTTT
65 CTCGAATCTAATTTATATTTTAAAAATTCAAGTCGGATTAGATTCGGATGAAATGTATATATTTT
575944 TTGAATTGGATCAAGTAAATGATATATAATTTTCAGATCAAATCAAGTTGG
130 TTGAATTGGATCAAGTAAATGATATATAATTTTCAGATCAAATCAAGTTGG
575995 GTTA
1 GTTA
575999 ATAATATATT
Statistics
Matches: 183, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
179 44 0.24
180 114 0.62
181 25 0.14
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (180 bp):
GTTATATTACCCCTCTGTCTATTGTTTTTTTAATTAAATTCTTATTTATATTAGGTTGGATTAAC
TCGAATCTAATTTATATTTTAAAAATTCAAGTCGGATTAGATTCGGATGAAATGTATATATTTTT
TGAATTGGATCAAGTAAATGATATATAATTTTCAGATCAAATCAAGTTGG
Found at i:579639 original size:40 final size:40
Alignment explanation
Indices: 579561--579858 Score: 191
Period size: 40 Copynumber: 7.3 Consensus size: 40
579551 CTTAAACTAT
** * *
579561 TAAAGG-AAAAAGTTTGATTAAAAAATTATGGACTTCAATTA
1 TAAAGGTAAAAAGTGAGA-TAAAAAATTA-GGGCCTCAATTA
*
579602 T-AAGGTAAAAAGTGAGATAAAAAATTAGGTGCCTCAATTT
1 TAAAGGTAAAAAGTGAGATAAAAAATTAGG-GCCTCAATTA
* * *
579642 TAAAGGTAAAAAGTGAGACAGAAAAAATTAGGGAACTAAATTA
1 TAAAGGTAAAAAGTGAG--ATAAAAAATTAGGG-CCTCAATTA
* *
579685 T-AA-G-AAAAA-TGGGATTGAAAAAATTAGAGACCTCAATTA
1 TAAAGGTAAAAAGTGAGA-T-AAAAAATTAG-GGCCTCAATTA
* * * **
579724 TAAACGTAAAAAATGAGATTAAAAATTAGGGGTTCAATTA
1 TAAAGGTAAAAAGTGAGATAAAAAATTAGGGCCTCAATTA
*
579764 TAAAGGTAGAAAGTGAGATTGAAAAAATTAGGAG-CTCAA-T-
1 TAAAGGTAAAAAGTGAGA-T-AAAAAATTAGG-GCCTCAATTA
** * * * *
579804 TAAAGGTTTAAAGTGTGATTGAAAAACTTAGAGTCATCAATTA
1 TAAAGGTAAAAAGTGAGA-T-AAAAAATTAG-GGCCTCAATTA
*
579847 TAAATGTAAAAA
1 TAAAGGTAAAAA
579859 AATGAGATTG
Statistics
Matches: 204, Mismatches: 33, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
37 1 0.00
39 23 0.11
40 80 0.39
41 43 0.21
42 24 0.12
43 33 0.16
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (40 bp):
TAAAGGTAAAAAGTGAGATAAAAAATTAGGGCCTCAATTA
Found at i:579667 original size:82 final size:82
Alignment explanation
Indices: 579580--579805 Score: 225
Period size: 82 Copynumber: 2.8 Consensus size: 82
579570 AAGTTTGATT
*
579580 AAAAAATTATGGACTTCAATTATAAGGTAAAAAGTGAGA-T-AAAAAATTAGGTGCCTCAATTTT
1 AAAAAATTA-GGACTTCAATTATAAGGTAAAAAGTGAGATTGAAAAAATTAGG-GCCTCAATTAT
* *
579643 AAAGGTAAAAAGTGAGACAG
64 AAACGTAAAAAATGAGA-AG
* * *
579663 AAAAAATTAGGGAAC-TAAATTATAA-G-AAAAA-TGGGATTGAAAAAATTAGAGACCTCAATTA
1 AAAAAATTA-GG-ACTTCAATTATAAGGTAAAAAGTGAGATTGAAAAAATTAG-GGCCTCAATTA
*
579724 TAAACGTAAAAAATGAG-AT
63 TAAACGTAAAAAATGAGAAG
* ** *
579743 TAAAAATTAGGGGTTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGGAG-CTCAATTA
1 AAAAAATTAGGACTTCAATTAT-AAGGTAAAAAGTGAGATTGAAAAAATTAGG-GCCTCAATTA
579806 AAGGTTTAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 21
0.77 0.10 0.14
Matches are distributed among these distances:
79 9 0.08
80 15 0.13
81 7 0.06
82 47 0.40
83 38 0.32
84 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (82 bp):
AAAAAATTAGGACTTCAATTATAAGGTAAAAAGTGAGATTGAAAAAATTAGGGCCTCAATTATAA
ACGTAAAAAATGAGAAG
Found at i:579761 original size:122 final size:123
Alignment explanation
Indices: 579559--579867 Score: 326
Period size: 122 Copynumber: 2.5 Consensus size: 123
579549 GGCTTAAACT
** * * *
579559 ATTAAAGG-AAAAAGTTTGATT-AAAAAATTATG-GACTTCAATTAT-AAGGTAAAAAGTGAGAT
1 ATTAAAGGTAAAAA-TGGGATTGAAAAAATTA-GAGACATCAATTATAAACGTAAAAAATGAGAT
* *
579620 AAAAAATTAGGTGCCTCAATTTTAAAGGTAAAAAGTGAGACAGAAAAAATTAGGGAACTAA
64 TAAAAATTAGGTGCCTCAATTATAAAGGTAAAAAGTGAGACAGAAAAAATTA-GGAACTAA
*
579681 ATTATAA-G-AAAAATGGGATTGAAAAAATTAGAGACCTCAATTATAAACGTAAAAAATGAGATT
1 ATTA-AAGGTAAAAATGGGATTGAAAAAATTAGAGACATCAATTATAAACGTAAAAAATGAGATT
** * ** * *
579744 AAAAATTAGG-GGTTCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGGAGCTCA
65 AAAAATTAGGTGCCTCAATTATAAAGGTAAAAAGTGAGACAGAAAAAATTAGGAACTAA
* * * * * *
579802 ATTAAAGGTTTAAAGTGTGATTGAAAAACTTAGAGTCATCAATTATAAATGTAAAAAAATGAGAT
1 ATTAAAGG-TAAAAATGGGATTGAAAAAATTAGAGACATCAATTATAAACGT-AAAAAATGAGAT
579867 T
64 T
579868 GATAAAAATT
Statistics
Matches: 158, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
120 2 0.01
121 17 0.11
122 64 0.41
123 62 0.39
124 13 0.08
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.27
Consensus pattern (123 bp):
ATTAAAGGTAAAAATGGGATTGAAAAAATTAGAGACATCAATTATAAACGTAAAAAATGAGATTA
AAAATTAGGTGCCTCAATTATAAAGGTAAAAAGTGAGACAGAAAAAATTAGGAACTAA
Found at i:579845 original size:123 final size:123
Alignment explanation
Indices: 579576--579867 Score: 326
Period size: 123 Copynumber: 2.4 Consensus size: 123
579566 GAAAAAGTTT
* * * *
579576 GATT-AAAAAATTATG-GACTTCAATTAT-AAGGTAAAAAGTGAGATAAAAAATTAGGTGCCTCA
1 GATTGAAAAAATTA-GAGACATCAATTATAAACGTAAAAAATGAGATTAAAAATTAGGTGCCTCA
*
579638 ATTTTAAAGGTAAAAAGTGAGACAGAAAAAATTAGGGAACTAAATTATAAGAAAAATGG
65 ATTATAAAGGTAAAAAGTGAGACAGAAAAAATTAGGGAACTAAATTATAAGAAAAATGG
* **
579697 GATTGAAAAAATTAGAGACCTCAATTATAAACGTAAAAAATGAGATTAAAAATTAGG-GGTTCAA
1 GATTGAAAAAATTAGAGACATCAATTATAAACGTAAAAAATGAGATTAAAAATTAGGTGCCTCAA
* ** * * * * *
579761 TTATAAAGGTAGAAAGTGAGATTGAAAAAATTA-GGAGCTCAATTA-AAGGTTTAAAGTGT
66 TTATAAAGGTAAAAAGTGAGACAGAAAAAATTAGGGAACTAAATTATAA-G--AAAAATGG
* * *
579820 GATTGAAAAACTTAGAGTCATCAATTATAAATGTAAAAAAATGAGATT
1 GATTGAAAAAATTAGAGACATCAATTATAAACGT-AAAAAATGAGATT
579868 GATAAAAATT
Statistics
Matches: 145, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
120 2 0.01
121 16 0.11
122 54 0.37
123 60 0.41
124 13 0.09
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (123 bp):
GATTGAAAAAATTAGAGACATCAATTATAAACGTAAAAAATGAGATTAAAAATTAGGTGCCTCAA
TTATAAAGGTAAAAAGTGAGACAGAAAAAATTAGGGAACTAAATTATAAGAAAAATGG
Found at i:580115 original size:19 final size:19
Alignment explanation
Indices: 580091--580127 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
580081 ATGACCAACA
*
580091 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
580110 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
580128 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:580176 original size:20 final size:20
Alignment explanation
Indices: 580153--580340 Score: 123
Period size: 20 Copynumber: 9.2 Consensus size: 20
580143 GTTTCCAGAT
*
580153 TCGCAACGCGATTTTGACCA
1 TCGCAACGCGATTTTGACTA
* *
580173 TCGCAATGCGATTTTCGA-AA
1 TCGCAACGCGATTTT-GACTA
***
580193 TCCGCGTTGCGATTTTAGA-TAA
1 T-CGCAACGCGATTTT-GACT-A
* **
580215 TCGCAATGCGATAAT-ACGTGA
1 TCGCAACGCGATTTTGAC-T-A
*
580236 TCGTAACGCGATTTTGACTA
1 TCGCAACGCGATTTTGACTA
*
580256 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGACTA
* **
580276 TCGCAACGTGATAAT-ACGTGA
1 TCGCAACGCGATTTTGAC-T-A
*
580297 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGACTA
* *
580317 TCGCAACGAGATTCTGACTA
1 TCGCAACGCGATTTTGACTA
580337 TCGC
1 TCGC
580341 GTTGCGATAT
Statistics
Matches: 135, Mismatches: 24, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
19 3 0.02
20 72 0.53
21 54 0.40
22 6 0.04
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTTTGACTA
Found at i:580224 original size:21 final size:19
Alignment explanation
Indices: 580153--580226 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 19
580143 GTTTCCAGAT
* *
580153 TCGCAACGCGATTTTGACCA
1 TCGCAATGCGATTTTGA-AA
580173 TCGCAATGCGATTTTCGAAA
1 TCGCAATGCGATTTT-GAAA
**
580193 TCCGCGTTGCGATTTTAGATAA
1 T-CGCAATGCGATTTT-GA-AA
580215 TCGCAATGCGAT
1 TCGCAATGCGAT
580227 AATACGTGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 16 0.36
21 25 0.57
22 3 0.07
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (19 bp):
TCGCAATGCGATTTTGAAA
Done.