Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 61 of 190
Found at i:17587334 original size:28 final size:29
Alignment explanation
Indices: 17587292--17587359 Score: 111
Period size: 28 Copynumber: 2.3 Consensus size: 29
17587282 TACTGCATTG
17587292 CACTGTTACTATATTGGGCTAAGGCC-CA
1 CACTGTTACTATATTGGGCTAAGGCCACA
*
17587320 CACTGTTACTTTATTGGGCTAAGGCCTACA
1 CACTGTTACTATATTGGGCTAAGGCC-ACA
17587350 CACTGTTACT
1 CACTGTTACT
17587360 GTAATTGTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 25 0.68
30 12 0.32
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (29 bp):
CACTGTTACTATATTGGGCTAAGGCCACA
Found at i:17588633 original size:50 final size:50
Alignment explanation
Indices: 17588568--17588741 Score: 215
Period size: 50 Copynumber: 3.5 Consensus size: 50
17588558 AGAGGTTTCC
*
17588568 TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGGTGAGAGGTCCCA
1 TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGTCCCA
* * * * * *
17588618 TGTAAGACCATGTCTGGCATATGGCGTTGGCACCAAGTTGAGAGGTCCTC-
1 TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGTCC-CA
* * * **
17588668 CGTAGGACCATGTCTGGGACATGGCATGGGCACCGACATGAGAACATCCCA
1 TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAG-AGGTCCCA
17588719 TGTAAGACCATGTCTGGGACATG
1 TGTAAGACCATGTCTGGGACATG
17588742 ACTTTGGCAT
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
50 76 0.75
51 26 0.25
ACGTcount: A:0.25, C:0.23, G:0.32, T:0.21
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAGGTCCCA
Found at i:17590377 original size:31 final size:32
Alignment explanation
Indices: 17590341--17590415 Score: 118
Period size: 31 Copynumber: 2.4 Consensus size: 32
17590331 AGTTTTTCCT
17590341 TGAATATTTAAAACTGCTA-ATTAGGAGATGA
1 TGAATATTTAAAACTGCTAGATTAGGAGATGA
*
17590372 TGAATATTTTAAACTGCTAGATTAGGAGATGA
1 TGAATATTTAAAACTGCTAGATTAGGAGATGA
*
17590404 CGAAT-TTTAAAA
1 TGAATATTTAAAA
17590416 TAATTATCGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 24 0.60
32 16 0.40
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (32 bp):
TGAATATTTAAAACTGCTAGATTAGGAGATGA
Found at i:17602042 original size:17 final size:17
Alignment explanation
Indices: 17602012--17602051 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
17602002 ATTTTTCTTC
17602012 TTTATTGTTTCAATTTTA
1 TTTATTGTTTCAA-TTTA
17602030 TTTATTG-TTCAATTTA
1 TTTATTGTTTCAATTTA
17602046 TTTATT
1 TTTATT
17602052 TTAGTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTATTGTTTCAATTTA
Found at i:17602059 original size:9 final size:9
Alignment explanation
Indices: 17602042--17602076 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
17602032 TATTGTTCAA
17602042 TTTATTTAT
1 TTTATTTAT
*
17602051 TTTAGTTAT
1 TTTATTTAT
17602060 TTATATTTAT
1 TT-TATTTAT
17602070 TTTATTT
1 TTTATTT
17602077 GATCTAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:17611423 original size:29 final size:29
Alignment explanation
Indices: 17611369--17611483 Score: 131
Period size: 29 Copynumber: 3.9 Consensus size: 29
17611359 ATGACGTATC
* *
17611369 GACGAGCATCGATTAATGAAAAGGGATGGT
1 GACGACCATCGAAT-ATGAAAAGGGATGGT
*
17611399 GACGACCATCGAATATGAAAAGGGATTGT
1 GACGACCATCGAATATGAAAAGGGATGGT
** * * * *
17611428 TTCGATCATAGATTATGAAAAGGCATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
*
17611457 GATGACCATCGAATATGAAAAGGGATG
1 GACGACCATCGAATATGAAAAGGGATG
17611484 AACTGATAAG
Statistics
Matches: 68, Mismatches: 17, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
29 56 0.82
30 12 0.18
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (29 bp):
GACGACCATCGAATATGAAAAGGGATGGT
Found at i:17611932 original size:10 final size:10
Alignment explanation
Indices: 17611917--17611944 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
17611907 CAAGTTTATG
17611917 ATTGAAATAC
1 ATTGAAATAC
17611927 ATTGAAATAC
1 ATTGAAATAC
17611937 ATTGAAAT
1 ATTGAAAT
17611945 GGTAAGTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.32
Consensus pattern (10 bp):
ATTGAAATAC
Found at i:17615259 original size:11 final size:11
Alignment explanation
Indices: 17615243--17615273 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
17615233 ATATATACTA
17615243 AATAAAATAAT
1 AATAAAATAAT
*
17615254 AATAAAATGAT
1 AATAAAATAAT
17615265 AATAAAATA
1 AATAAAATA
17615274 TCATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:17617011 original size:29 final size:29
Alignment explanation
Indices: 17616976--17617194 Score: 246
Period size: 30 Copynumber: 7.4 Consensus size: 29
17616966 TCATCGATGA
17616976 ATGAAAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* *
17617005 ACGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAAT
* * *
17617034 ATGAAAAGGGAT-GGTAACGAC-ATCGAAAT
1 ATGAAAAGGGATAGCT-TCGGCTATCG-AAT
* *
17617063 ATGAAAAGGGATGGCTTCGGCTATCGATCT
1 ATGAAAAGGGATAGCTTCGGCTATCGA-AT
*
17617093 ATGAAAAAGGATAGCTTCGGCTATC-AATTT
1 ATGAAAAGGGATAGCTTCGGCTATCGAA--T
* *
17617123 ATGAAAACGGATAGCTTCGGTTATCGAACT
1 ATGAAAAGGGATAGCTTCGGCTATCGAA-T
* *
17617153 ATGAAAAGGGATAACTTCGGTTATCGAATT
1 ATGAAAAGGGATAGCTTCGGCTATCGAA-T
17617183 ATGAAAAGGGAT
1 ATGAAAAGGGAT
17617195 GTGTCAACCA
Statistics
Matches: 162, Mismatches: 20, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
28 6 0.04
29 60 0.37
30 94 0.58
31 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAAT
Found at i:17617140 original size:60 final size:60
Alignment explanation
Indices: 17616976--17617194 Score: 277
Period size: 60 Copynumber: 3.7 Consensus size: 60
17616966 TCATCGATGA
*
17616976 ATGAAAAGGGATAGCTTCGGCTATCGAA-TACGAAAAGGGATAGCTTCGGCTATCGAT-T
1 ATGAAAAGGGATAGCTTCGGCTATCGAATTATGAAAAGGGATAGCTTCGGCTATCGATCT
* * * * *
17617034 ATGAAAAGGGAT-GGTAACGAC-ATCGAAATATGAAAAGGGATGGCTTCGGCTATCGATCT
1 ATGAAAAGGGATAGCT-TCGGCTATCGAATTATGAAAAGGGATAGCTTCGGCTATCGATCT
* * * *
17617093 ATGAAAAAGGATAGCTTCGGCTATC-AATTTATGAAAACGGATAGCTTCGGTTATCGAACT
1 ATGAAAAGGGATAGCTTCGGCTATCGAA-TTATGAAAAGGGATAGCTTCGGCTATCGATCT
* *
17617153 ATGAAAAGGGATAACTTCGGTTATCGAATTATGAAAAGGGAT
1 ATGAAAAGGGATAGCTTCGGCTATCGAATTATGAAAAGGGAT
17617195 GTGTCAACCA
Statistics
Matches: 136, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
57 8 0.06
58 42 0.31
59 17 0.12
60 67 0.49
61 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (60 bp):
ATGAAAAGGGATAGCTTCGGCTATCGAATTATGAAAAGGGATAGCTTCGGCTATCGATCT
Found at i:17622713 original size:39 final size:39
Alignment explanation
Indices: 17622670--17622866 Score: 207
Period size: 39 Copynumber: 5.1 Consensus size: 39
17622660 TAAAATTGTG
* *
17622670 AATGTTATGTGATTATACGAGTATTGTAACATATGCTTA
1 AATGTTATGTGATTATACGAGTATTGTGATATATGCTTA
* * * * *
17622709 AATGTTATGCGATTATATGAATATTGTGTTATATGCTTG
1 AATGTTATGTGATTATACGAGTATTGTGATATATGCTTA
*
17622748 GATGTTATGTGATTATACGAGTATTGTGATATATGCTTA
1 AATGTTATGTGATTATACGAGTATTGTGATATATGCTTA
* * * * *
17622787 AATGTTAAGAGATTATATCTA-TATTGTGATATATACTTG
1 AATGTTATGTGATTATA-CGAGTATTGTGATATATGCTTA
* * * * * *
17622826 ATTGTTAGGTGATTATATGTGTAATATGATATATGCTTA
1 AATGTTATGTGATTATACGAGTATTGTGATATATGCTTA
17622865 AA
1 AA
17622867 AGTGAATATG
Statistics
Matches: 126, Mismatches: 30, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
39 124 0.98
40 2 0.02
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (39 bp):
AATGTTATGTGATTATACGAGTATTGTGATATATGCTTA
Found at i:17622801 original size:78 final size:77
Alignment explanation
Indices: 17622671--17622866 Score: 257
Period size: 78 Copynumber: 2.5 Consensus size: 77
17622661 AAAATTGTGA
* * * * *
17622671 ATGTTATGTGATTATACGAGTATTGTAACATATGCTTAAATGTTATGCGATTATATGAATATTGT
1 ATGTTATGTGATTATACGAGTATTGTGATATATGCTTAAATGTTAAGAGATTATATCAATATTGT
* *
17622736 GTTATATGCTTGG
66 GATATATACTT-G
*
17622749 ATGTTATGTGATTATACGAGTATTGTGATATATGCTTAAATGTTAAGAGATTATATCTATATTGT
1 ATGTTATGTGATTATACGAGTATTGTGATATATGCTTAAATGTTAAGAGATTATATCAATATTGT
17622814 GATATATACTTG
66 GATATATACTTG
* * * * *
17622826 ATTGTTAGGTGATTATATGTGTAATATGATATATGCTTAAA
1 A-TGTTATGTGATTATACGAGTATTGTGATATATGCTTAAA
17622867 AGTGAATATG
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
77 2 0.02
78 102 0.98
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (77 bp):
ATGTTATGTGATTATACGAGTATTGTGATATATGCTTAAATGTTAAGAGATTATATCAATATTGT
GATATATACTTG
Found at i:17623991 original size:18 final size:18
Alignment explanation
Indices: 17623962--17624005 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
17623952 GTGTGCACGC
17623962 TTATGTTCAAGACAAC-AT
1 TTATG-TCAAGACAACAAT
17623980 TTAGTGTCAAGACAACAAT
1 TTA-TGTCAAGACAACAAT
17623999 TTATGTC
1 TTATGTC
17624006 GTATGGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (18 bp):
TTATGTCAAGACAACAAT
Found at i:17634710 original size:55 final size:55
Alignment explanation
Indices: 17634577--17634689 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
17634567 GAATTAGAGG
* *
17634577 ATGATCAAAATATGGAATTAAATCTTTTTGAGTCTAGTTTCTCATAGAAGAAACT
1 ATGAACAAAATATGGAATTAAATCTTATTGAGTCTAGTTTCTCATAGAAGAAACT
* *
17634632 ATGAACAAAATATGGAACTAAATCTTATTGAGTCTAGTTTCTCATAGAGGAAACT
1 ATGAACAAAATATGGAATTAAATCTTATTGAGTCTAGTTTCTCATAGAAGAAACT
17634687 ATG
1 ATG
17634690 TAAGTAATGG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (55 bp):
ATGAACAAAATATGGAATTAAATCTTATTGAGTCTAGTTTCTCATAGAAGAAACT
Found at i:17639885 original size:17 final size:17
Alignment explanation
Indices: 17639842--17639891 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
17639832 CACATTTGGC
17639842 TCATTGAATGGAATA-A
1 TCATTGAATGGAATAGA
* *
17639858 -CGTGGGAATGGAATAGA
1 TCAT-TGAATGGAATAGA
17639875 TCATTGAATGGAATAGA
1 TCATTGAATGGAATAGA
17639892 AGGGTGATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 2 0.07
16 10 0.37
17 13 0.48
18 2 0.07
ACGTcount: A:0.40, C:0.06, G:0.28, T:0.26
Consensus pattern (17 bp):
TCATTGAATGGAATAGA
Found at i:17645839 original size:25 final size:25
Alignment explanation
Indices: 17645791--17645888 Score: 115
Period size: 25 Copynumber: 3.9 Consensus size: 25
17645781 ACAAGATGTG
* ** *
17645791 ATCGGTATGCTCACTTGAGTTGTAA
1 ATCGGTATGCTCTCAAGAGCTGTAA
* *
17645816 ATCAGTATGCTCTCACGAGCTGTAA
1 ATCGGTATGCTCTCAAGAGCTGTAA
* **
17645841 ATCGGTATGCTCACTTGAGCTGTAA
1 ATCGGTATGCTCTCAAGAGCTGTAA
17645866 ATCGGTATGCTCTCAAGAGCTGT
1 ATCGGTATGCTCTCAAGAGCTGT
17645889 GGGTCAAAAC
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (25 bp):
ATCGGTATGCTCTCAAGAGCTGTAA
Found at i:17645848 original size:50 final size:50
Alignment explanation
Indices: 17645791--17645888 Score: 169
Period size: 50 Copynumber: 2.0 Consensus size: 50
17645781 ACAAGATGTG
* *
17645791 ATCGGTATGCTCACTTGAGTTGTAAATCAGTATGCTCTCACGAGCTGTAA
1 ATCGGTATGCTCACTTGAGCTGTAAATCAGTATGCTCTCAAGAGCTGTAA
*
17645841 ATCGGTATGCTCACTTGAGCTGTAAATCGGTATGCTCTCAAGAGCTGT
1 ATCGGTATGCTCACTTGAGCTGTAAATCAGTATGCTCTCAAGAGCTGT
17645889 GGGTCAAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.32
Consensus pattern (50 bp):
ATCGGTATGCTCACTTGAGCTGTAAATCAGTATGCTCTCAAGAGCTGTAA
Found at i:17648720 original size:15 final size:15
Alignment explanation
Indices: 17648702--17648730 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17648692 CCAATCTATT
17648702 AATGAATTATTAAAA
1 AATGAATTATTAAAA
17648717 AATGAATTATTAAA
1 AATGAATTATTAAA
17648731 TATAACTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (15 bp):
AATGAATTATTAAAA
Found at i:17652559 original size:743 final size:743
Alignment explanation
Indices: 17651127--17652618 Score: 2396
Period size: 743 Copynumber: 2.0 Consensus size: 743
17651117 AACCAATCAA
* *
17651127 AATCATACATAATGTATCTTATACGAGCCCTCAAGGCCCTAAATATGCAATAGAAACAAGTCAGG
1 AATCATACATAATGTATCTTATACGAGCCCCCAAGGCCCTAAATATGCAATAGAAACAAGTCAAG
17651192 ATCAAATCAGAAACTCAGAGAATTTTTCAGAAAACATTGAAAATTTTCAACTGCAGGGGTCACAC
66 ATCAAATCAGAAACTCAGAGAATTTTTCAGAAAACATTGAAAATTTTCAACTGCAGGGGTCACAC
* * * * *
17651257 AGGCGTTTGACCAGGCCGTGTGGGCATTCAATGTAGGGACACAGAGCCGTGTCCCAGCCCGTGGC
131 AGACGTGTGACCAGGCCGTGTGGGCATTCAAAGCAGGGACACAGAGCCATGTCCCAGCCCGTGGC
* * *
17651322 TGTGCCCGTGTAACTCACTGACTTGGGTCACACGACCAAGCCACACACCCGTGTGCCAGGCTGTA
196 CGTGCCCGTGTAACTCACTAACTTGGCTCACACGACCAAGCCACACACCCGTGTGCCAGGCTGTA
* * *
17651387 TACCCTTCGAAGTAACCTCACACGCCCGTGTACCAGTCCATGTGCTAGGCTGTGTAACAGCCTGA
261 CACCCTTCGAAGTAACCTCACACGCCCGTGTACCAGGCCATGTGCTAGGCGGTGTAACAGCCTGA
* *
17651452 CTTGCAACCCTTTGAAAGCTACAGAGAACTCACGGTAGTGTCGCCTCGCCATGTGTCACACACGG
326 CTTGCAACCCATTGAAAGCTACAGAGAACTCACGGCAGTGTCGCCTCGCCATGTGTCACACACGG
* * *
17651517 TGAAGACACATGCTCGTGTCTCTGCCCGTGTGGGCGAAAATAGGCCATTTTACAAGCCATTTTTC
391 CGAAGACACACGCTCGTGTCTCTGCCCGTGTGGACGAAAATAGGCCATTTTACAAGCCATTTTTC
* *
17651582 TCACCCATCAAGGCATATACCTATAACCAAAAATGCACATATATATAAGTCATAACAAGGCATCC
456 TCACCCATCAAGGCATATAACTATAACCAAAAATGCACATATATATAAGCCATAACAAGGCATCC
*
17651647 AAATCAAGCATAAGCAAGTCCTATACATATGGTATAACATCATACAACCAATATGCCCTTAGGCA
521 AAATCAAGCATAAGAAAGTCCTATACATATGGTATAACATCATACAACCAATATGCCCTTAGGCA
* *
17651712 CCTCAAATAACAATATCTAAACATATCTAACCATGTATTCAATTTTACCAAATAATCAACTAACT
586 CCTCAAATAACAATATATAAACATATCTAACCATGTATTCAATTTGACCAAATAATCAACTAACT
* * *
17651777 TATATGCATATTTGCATCAATACATATCATGTAATTTACTTACCAAAATATATCAAATGGTAGTA
651 TATATGCATATTTGCATCAATACATATCATGTAATTTACTTACCAAAATATACCAAATGATACTA
*
17651842 ATCATACCATTCAACCACTAGTATCTAT
716 ATAATACCATTCAACCACTAGTATCTAT
*
17651870 AATCATACATAATGTCTCTTATACGAGCCCCCAAGGCCCTAAATATGCAATAGAAACAAGTCAAG
1 AATCATACATAATGTATCTTATACGAGCCCCCAAGGCCCTAAATATGCAATAGAAACAAGTCAAG
* *
17651935 ATCAAATCAGAAACTCAGAGAATTTTTCAGAAAGCATTGAAAATTTTCAACTGCAGGTGTCACAC
66 ATCAAATCAGAAACTCAGAGAATTTTTCAGAAAACATTGAAAATTTTCAACTGCAGGGGTCACAC
*
17652000 AGACGTGTGACCAGGCCGTGTGGGCATTCAAAGCAGGGACACA-ACGCCATGTCCCAGCCCGTGT
131 AGACGTGTGACCAGGCCGTGTGGGCATTCAAAGCAGGGACACAGA-GCCATGTCCCAGCCCGTGG
* * * *
17652064 CCGTGCCCGTGTAACTCACTAACTTGGCTCCCACGGCCAAGCCACACACCCGTGTGCTAGGCTTT
195 CCGTGCCCGTGTAACTCACTAACTTGGCTCACACGACCAAGCCACACACCCGTGTGCCAGGCTGT
* * * * *
17652129 GCACCCTTCGAAGTAACCTCACACGCCCTTGTACTAGGCCGTGTGCTAGGCGGTGTAACAGTCTG
260 ACACCCTTCGAAGTAACCTCACACGCCCGTGTACCAGGCCATGTGCTAGGCGGTGTAACAGCCTG
* * * * * * * * * *
17652194 ACTTGTAACCCATTGAAAGCTATAGGGGACTCAGGGCCGTGTCGCTTGGCCGTGTGTCATACACG
325 ACTTGCAACCCATTGAAAGCTACAGAGAACTCACGGCAGTGTCGCCTCGCCATGTGTCACACACG
* * *
17652259 GCCG-AGACACACG-TCTGTGTCTCTGCCTGTGTGGACGAAAATAGGTCATTTTACAAGTCATTT
390 G-CGAAGACACACGCTC-GTGTCTCTGCCCGTGTGGACGAAAATAGGCCATTTTACAAGCCATTT
*
17652322 TTCTCACCCATCAAGGCATATAACTATAACCAAAAATGCACATATATATAAGCCATAACAAGGCG
453 TTCTCACCCATCAAGGCATATAACTATAACCAAAAATGCACATATATATAAGCCATAACAAGGCA
* *
17652387 TCCAAATCAAGCATAAGAAAGTTCTATACATATGGTATAACATCATACAACCAATATTCCCTTAG
518 TCCAAATCAAGCATAAGAAAGTCCTATACATATGGTATAACATCATACAACCAATATGCCCTTAG
* *
17652452 GCACCTCAAATGACAATATATAAACATGTCTAACCATGTATTCAATTTGACCAAATAATCAACTA
583 GCACCTCAAATAACAATATATAAACATATCTAACCATGTATTCAATTTGACCAAATAATCAACTA
*
17652517 ACTTATATGCATATTTGCATCAATACATATCATGTCATTTACTTACCAAAATATACCAAATGATA
648 ACTTATATGCATATTTGCATCAATACATATCATGTAATTTACTTACCAAAATATACCAAATGATA
*
17652582 CTAATAATTCCATTCAACCACTAGTATCTAT
713 CTAATAATACCATTCAACCACTAGTATCTAT
17652613 AATCAT
1 AATCAT
17652619 TTAAGCCATT
Statistics
Matches: 686, Mismatches: 60, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
742 3 0.00
743 682 0.99
744 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (743 bp):
AATCATACATAATGTATCTTATACGAGCCCCCAAGGCCCTAAATATGCAATAGAAACAAGTCAAG
ATCAAATCAGAAACTCAGAGAATTTTTCAGAAAACATTGAAAATTTTCAACTGCAGGGGTCACAC
AGACGTGTGACCAGGCCGTGTGGGCATTCAAAGCAGGGACACAGAGCCATGTCCCAGCCCGTGGC
CGTGCCCGTGTAACTCACTAACTTGGCTCACACGACCAAGCCACACACCCGTGTGCCAGGCTGTA
CACCCTTCGAAGTAACCTCACACGCCCGTGTACCAGGCCATGTGCTAGGCGGTGTAACAGCCTGA
CTTGCAACCCATTGAAAGCTACAGAGAACTCACGGCAGTGTCGCCTCGCCATGTGTCACACACGG
CGAAGACACACGCTCGTGTCTCTGCCCGTGTGGACGAAAATAGGCCATTTTACAAGCCATTTTTC
TCACCCATCAAGGCATATAACTATAACCAAAAATGCACATATATATAAGCCATAACAAGGCATCC
AAATCAAGCATAAGAAAGTCCTATACATATGGTATAACATCATACAACCAATATGCCCTTAGGCA
CCTCAAATAACAATATATAAACATATCTAACCATGTATTCAATTTGACCAAATAATCAACTAACT
TATATGCATATTTGCATCAATACATATCATGTAATTTACTTACCAAAATATACCAAATGATACTA
ATAATACCATTCAACCACTAGTATCTAT
Found at i:17653438 original size:25 final size:24
Alignment explanation
Indices: 17653410--17653503 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 24
17653400 TCCTGTACAT
*
17653410 GTATGCTCGTACGAGCTGTGAATCG
1 GTATGCTC-TACGAGCTGTAAATCG
* *
17653435 GTATGCTC-ACTTGAGCTATAAATCA
1 GTATGCTCTAC--GAGCTGTAAATCG
*
17653460 GTATGCTCTCGCGAGCTGTAAATCG
1 GTATGCTCT-ACGAGCTGTAAATCG
*
17653485 GTATGCTCTCAAGAGCTGT
1 GTATGCTCT-ACGAGCTGT
17653504 GGGTCGAAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
23 2 0.04
25 54 0.95
27 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (24 bp):
GTATGCTCTACGAGCTGTAAATCG
Found at i:17655642 original size:21 final size:21
Alignment explanation
Indices: 17655618--17655685 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
17655608 GGACACGGTT
*
17655618 GTGTGTTCAAGGCATACGCCC
1 GTGTGTTCAAGGCACACGCCC
* * * *
17655639 GTGTG-GCTAAGGGACACGGCT
1 GTGTGTTC-AAGGCACACGCCC
*
17655660 GTGTGTTCAAGGTACACGCCC
1 GTGTGTTCAAGGCACACGCCC
17655681 GTGTG
1 GTGTG
17655686 GAAATCGATA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.24
Consensus pattern (21 bp):
GTGTGTTCAAGGCACACGCCC
Found at i:17655646 original size:42 final size:42
Alignment explanation
Indices: 17655599--17655686 Score: 149
Period size: 42 Copynumber: 2.1 Consensus size: 42
17655589 ACATGCCTGA
* *
17655599 GTGGCTAAGGGACACGGTTGTGTGTTCAAGGCATACGCCCGT
1 GTGGCTAAGGGACACGGCTGTGTGTTCAAGGCACACGCCCGT
*
17655641 GTGGCTAAGGGACACGGCTGTGTGTTCAAGGTACACGCCCGT
1 GTGGCTAAGGGACACGGCTGTGTGTTCAAGGCACACGCCCGT
17655683 GTGG
1 GTGG
17655687 AAATCGATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.18, C:0.22, G:0.38, T:0.23
Consensus pattern (42 bp):
GTGGCTAAGGGACACGGCTGTGTGTTCAAGGCACACGCCCGT
Found at i:17657514 original size:26 final size:27
Alignment explanation
Indices: 17657481--17657540 Score: 88
Period size: 26 Copynumber: 2.2 Consensus size: 27
17657471 ATACTATTAA
17657481 TTATTTGTAAAATTT-AT-TATCAAAAT
1 TTATTTGTAAAATTTAATATAT-AAAAT
17657507 TTATTTGTAAAATTTGAATATATAAAAT
1 TTATTTGTAAAATTT-AATATATAAAAT
17657535 TTATTT
1 TTATTT
17657541 TTTATATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
26 15 0.48
28 13 0.42
29 3 0.10
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (27 bp):
TTATTTGTAAAATTTAATATATAAAAT
Found at i:17657518 original size:13 final size:13
Alignment explanation
Indices: 17657481--17657540 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
17657471 ATACTATTAA
17657481 TTATTTGTAAAAT
1 TTATTTGTAAAAT
*
17657494 TTATTAT-CAAAAT
1 TTATT-TGTAAAAT
17657507 TTATTTGTAAAAT
1 TTATTTGTAAAAT
* *
17657520 TTGAATATATAAAAT
1 TT--ATTTGTAAAAT
17657535 TTATTT
1 TTATTT
17657541 TTTATATTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 1 0.03
13 25 0.66
14 1 0.03
15 11 0.29
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (13 bp):
TTATTTGTAAAAT
Found at i:17661498 original size:15 final size:15
Alignment explanation
Indices: 17661480--17661512 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17661470 CAAATGCTAT
17661480 AATAATAAATACAAC
1 AATAATAAATACAAC
*
17661495 AATAATAAATACATC
1 AATAATAAATACAAC
17661510 AAT
1 AAT
17661513 GGCATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:17661591 original size:17 final size:16
Alignment explanation
Indices: 17661561--17661603 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
17661551 CCATGACATG
17661561 CAAAATATTAAATGTAAA
1 CAAAATA-TAAATG-AAA
17661579 CAAAATATAAATGAAA
1 CAAAATATAAATGAAA
*
17661595 -AAAACATAA
1 CAAAATATAA
17661604 GTCAATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 3 0.12
17 6 0.25
18 7 0.29
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (16 bp):
CAAAATATAAATGAAA
Found at i:17661889 original size:19 final size:18
Alignment explanation
Indices: 17661860--17661901 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
17661850 ACATATATAG
17661860 ATTAT-AAAAATAATTAC
1 ATTATAAAAAATAATTAC
17661877 ATATATAAAAAATAATTAC
1 AT-TATAAAAAATAATTAC
17661896 ATTATA
1 ATTATA
17661902 TTTAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.09
18 7 0.30
19 14 0.61
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (18 bp):
ATTATAAAAAATAATTAC
Found at i:17661891 original size:25 final size:23
Alignment explanation
Indices: 17661822--17661891 Score: 59
Period size: 25 Copynumber: 2.9 Consensus size: 23
17661812 ACCTACATAT
* * *
17661822 ATATATATATATACAAGAATAAAT
1 ATATACATATATA-AAAAATAAAA
* **
17661846 ATATACATATATAGATTATAAAA
1 ATATACATATATAAAAAATAAAA
17661869 ATAATTACATATATAAAAAATAA
1 AT-A-TACATATATAAAAAATAA
17661892 TTACATTATA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 8 0.22
24 13 0.36
25 15 0.42
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (23 bp):
ATATACATATATAAAAAATAAAA
Found at i:17662005 original size:21 final size:20
Alignment explanation
Indices: 17661976--17662028 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
17661966 CATAGATTTT
17661976 TAAAAAAAATAATTAAAT-A
1 TAAAAAAAATAATTAAATAA
* *
17661995 TGAAAATAAAAAAATTAATTAA
1 T-AAAA-AAAATAATTAAATAA
17662017 TAAAAAAAATAA
1 TAAAAAAAATAA
17662029 AAAAAACTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.04
20 10 0.36
21 15 0.54
22 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
TAAAAAAAATAATTAAATAA
Found at i:17662013 original size:25 final size:25
Alignment explanation
Indices: 17661976--17662040 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
17661966 CATAGATTTT
**
17661976 TAAAAAAAATAATTAA-ATATGAAAA
1 TAAAAAAAATAATTAATA-AAAAAAA
*
17662001 TAAAAAAATTAATTAATAAAAAAAA
1 TAAAAAAAATAATTAATAAAAAAAA
17662026 TAAAAAAAACTAATT
1 TAAAAAAAA-TAATT
17662041 TGAACTATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 28 0.82
26 6 0.18
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (25 bp):
TAAAAAAAATAATTAATAAAAAAAA
Found at i:17663085 original size:14 final size:14
Alignment explanation
Indices: 17663066--17663103 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
17663056 CATCAGTCCT
17663066 GGGCCTCTGTATTC
1 GGGCCTCTGTATTC
17663080 GGGCCTCTGTATTC
1 GGGCCTCTGTATTC
**
17663094 TTGCCTCTGT
1 GGGCCTCTGT
17663104 TTGTTTTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.05, C:0.29, G:0.26, T:0.39
Consensus pattern (14 bp):
GGGCCTCTGTATTC
Found at i:17663606 original size:44 final size:44
Alignment explanation
Indices: 17663426--17663874 Score: 137
Period size: 44 Copynumber: 10.2 Consensus size: 44
17663416 TATCTTAGAA
* *
17663426 AGATAATATTTGCCATCTTTAATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
17663470 AGATAAGATCTACAAT-TTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTT-AATCTGCTCCACTACTGCTTAGGG
** ** ** * * *
17663514 AGACCAGGCTTGGTGGCTTAAATCTGCTTCTCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTTAATCTGC-TC-CACTACTGCTTAGG-G
*
17663558 AGATAAGATTTGCCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
17663602 AGATAAGATCTACAAT-TTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCGTCTTT-AATCTGCTCCACTACTGCTTAGGG
* ** ** * * * *
17663646 AGACAAGGCTTGGTGGCTTAAATATGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* ** *
17663690 AGATAAGATTGGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * ** *
17663734 AGATAAGATCTACAATCTTCAACCTTCTCCGCTGTTGCTCAGGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** ** * * *
17663778 AGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCGTCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * *
17663822 AGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAAGG
1 AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
17663866 AGATAAGAT
1 AGATAAGAT
17663875 CTACAATTTT
Statistics
Matches: 271, Mismatches: 112, Indels: 44
0.63 0.26 0.10
Matches are distributed among these distances:
42 16 0.06
43 19 0.07
44 209 0.77
45 16 0.06
46 11 0.04
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTGCCGTCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:17663617 original size:132 final size:132
Alignment explanation
Indices: 17663380--17663981 Score: 1033
Period size: 132 Copynumber: 4.6 Consensus size: 132
17663370 GTAACTTCAA
* * *
17663380 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTAGAAAGATAATATTTGCCATCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
*
17663445 TAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTC
17663510 AG
131 AG
* *
17663512 GGAGACCAGGCTTGGTGGCTTAAATCTGCTTCTCACTATCTTGGAAAGATAAGATTTGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
17663577 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTC
17663642 AG
131 AG
* *
17663644 GGAGACAAGGCTTGGTGGCTTAAATATGCTTCCCACTATCTTGGAAAGATAAGATTGGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
* * * * *
17663709 CGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGTTGCTC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTC
17663774 AG
131 AG
* *
17663776 GGAGACAAGGCTTGGTGACTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGTCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
* *
17663841 TGATCTGCTCCACTACTGCTTAAGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGTTGCTC
66 TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTC
17663906 AG
131 AG
*
17663908 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTGGCCGTCTT
1 GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
*
17663973 CGATCTGCT
66 TGATCTGCT
17663982 TTACTGTTGG
Statistics
Matches: 442, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 442 1.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (132 bp):
GGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTT
TGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATTTTCAACCTACTCCGCTGCTGCTC
AG
Found at i:17675856 original size:15 final size:15
Alignment explanation
Indices: 17675838--17675870 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17675828 CAAATGCTAT
17675838 AATAATAAATACAAC
1 AATAATAAATACAAC
*
17675853 AATAATAAATACATC
1 AATAATAAATACAAC
17675868 AAT
1 AAT
17675871 GGCATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:17675964 original size:17 final size:17
Alignment explanation
Indices: 17675942--17675975 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17675932 TGCAAAATAT
* *
17675942 TAAATGTAAACAACATA
1 TAAATGAAAAAAACATA
17675959 TAAATGAAAAAAACATA
1 TAAATGAAAAAAACATA
17675976 AGTCAATAAA
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:0.65, C:0.09, G:0.06, T:0.21
Consensus pattern (17 bp):
TAAATGAAAAAAACATA
Found at i:17677459 original size:14 final size:14
Alignment explanation
Indices: 17677440--17677476 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17677430 ATCAGTCCTG
17677440 GGCCTCTGTATTCA
1 GGCCTCTGTATTCA
**
17677454 GGCCTCTGTATTTG
1 GGCCTCTGTATTCA
17677468 GGCCTCTGT
1 GGCCTCTGT
17677477 TTGTTTTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.27, G:0.27, T:0.38
Consensus pattern (14 bp):
GGCCTCTGTATTCA
Found at i:17679899 original size:131 final size:131
Alignment explanation
Indices: 17679662--17679902 Score: 342
Period size: 131 Copynumber: 1.8 Consensus size: 131
17679652 AACGATTTTC
* * * *
17679662 GATTTACTATCATGAACCATTTTCTCTAAGTTAGTTGATTTACTATCGGCACTCGAAATAGGTCG
1 GATTTACTATCATGAACAATGTTCTCTAAGTTAGTTGATTTACTATCGGCACTCCAAATAGCTCG
* *
17679727 CTTATTTAATATCACAACTAATATTATTAAGGCTCACTGATTTACAATTACAGCCTAAATTCATT
66 CTTATTTAAGATAACAACTAATATTATTAAGGCTCACTGATTTACAATTACAGCCTAAATTCATT
17679792 T
131 T
* *
17679793 GATTTACTATCATGAACAATGTTCTCTAAGTTAGTTGATTTACTAT-TGCTACTCCAAATAGCTT
1 GATTTACTATCATGAACAATGTTCTCTAAGTTAGTTGATTTACTATCGGC-ACTCCAAATAGCTC
* * * *
17679857 G-TTGATTTAAGATAATAGCTGATATTATTAAGGCTCATTGATTTAC
65 GCTT-ATTTAAGATAACAACTAATATTATTAAGGCTCACTGATTTAC
17679903 GATCACAACT
Statistics
Matches: 96, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
130 4 0.04
131 92 0.96
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (131 bp):
GATTTACTATCATGAACAATGTTCTCTAAGTTAGTTGATTTACTATCGGCACTCCAAATAGCTCG
CTTATTTAAGATAACAACTAATATTATTAAGGCTCACTGATTTACAATTACAGCCTAAATTCATT
T
Found at i:17692998 original size:18 final size:18
Alignment explanation
Indices: 17692951--17693001 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
17692941 AAATATTAAA
*
17692951 AAAAATATTTA-AAATTTT
1 AAAAAT-TTTATAAATTCT
* *
17692969 AAAAA-ATAATAAATTCT
1 AAAAATTTTATAAATTCT
17692986 AAAAATTTTATAAATT
1 AAAAATTTTATAAATT
17693002 TATGAAAGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 2 0.08
17 11 0.42
18 13 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTTTATAAATTCT
Found at i:17695645 original size:21 final size:22
Alignment explanation
Indices: 17695621--17695661 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17695611 GCTCTATACT
* *
17695621 TATAA-ACCATAACCGAATCTA
1 TATAATACCAAAACCAAATCTA
17695642 TATAATACCAAAACCAAATC
1 TATAATACCAAAACCAAATC
17695662 ATACCATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.22
Consensus pattern (22 bp):
TATAATACCAAAACCAAATCTA
Found at i:17697828 original size:31 final size:31
Alignment explanation
Indices: 17697735--17697830 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
17697725 GGCAAATTAC
*
17697735 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
17697766 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
17697798 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
17697829 AA
1 AA
17697831 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:17712796 original size:36 final size:36
Alignment explanation
Indices: 17712756--17712836 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
17712746 GAAGCCATTG
17712756 GTGTGTTTTGGATGGATTAGCTCTTATGAACATCTA
1 GTGTGTTTTGGATGGATTAGCTCTTATGAACATCTA
* * * * *
17712792 GTGTGCTTCGGATGGATTAGCTCTTATGAGCATTTG
1 GTGTGTTTTGGATGGATTAGCTCTTATGAACATCTA
17712828 GTGTGTTTT
1 GTGTGTTTT
17712837 AGTTAGAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.17, C:0.11, G:0.28, T:0.43
Consensus pattern (36 bp):
GTGTGTTTTGGATGGATTAGCTCTTATGAACATCTA
Found at i:17715553 original size:17 final size:18
Alignment explanation
Indices: 17715522--17715565 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
17715512 TCTAATGAAC
**
17715522 TACAAATAATTAATA-AA
1 TACAAATAAACAATACAA
17715539 TACAAATAAACAATACAA
1 TACAAATAAACAATACAA
*
17715557 TACACATAA
1 TACAAATAA
17715566 GAGCAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.64, C:0.14, G:0.00, T:0.23
Consensus pattern (18 bp):
TACAAATAAACAATACAA
Found at i:17716150 original size:16 final size:14
Alignment explanation
Indices: 17716129--17716168 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 14
17716119 AGGATAATTT
17716129 TAAAATAATTAATATA
1 TAAAATAATTAA-A-A
17716145 TAAAATAATTTAAAA
1 TAAAATAA-TTAAAA
17716160 TAAAATAAT
1 TAAAATAAT
17716169 ATACAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.04
15 9 0.39
16 9 0.39
17 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATAATTAAAA
Found at i:17716210 original size:26 final size:26
Alignment explanation
Indices: 17716128--17716215 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
17716118 TAGGATAATT
* * **
17716128 TTAAAATAATTAATATATAAA-ATAAT
1 TTAAAATAAATAATATACAAAGA-ACC
17716154 TTAAAATAAAATAATATACAAAGAACC
1 TTAAAAT-AAATAATATACAAAGAACC
* * *
17716181 TTAACATAAATAATTTACAAAGCAA-G
1 TTAAAATAAATAATATACAAAG-AACC
17716207 TTAAAATAA
1 TTAAAATAA
17716216 TCATATAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
26 29 0.57
27 21 0.41
28 1 0.02
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.30
Consensus pattern (26 bp):
TTAAAATAAATAATATACAAAGAACC
Found at i:17716296 original size:16 final size:15
Alignment explanation
Indices: 17716249--17716296 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
17716239 TATATATAAG
17716249 AAAAATTTTAAAATA
1 AAAAATTTTAAAATA
*
17716264 AAACAA-ATTAAAGATA
1 AAA-AATTTTAAA-ATA
17716280 AATAAATTTTAAAATA
1 AA-AAATTTTAAAATA
17716296 A
1 A
17716297 CATATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 8 0.30
16 13 0.48
17 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAAATTTTAAAATA
Found at i:17717581 original size:20 final size:20
Alignment explanation
Indices: 17717556--17717595 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17717546 CTTTCTTGGA
*
17717556 CTTTTAATTTATTTTTATTT
1 CTTTTAATTTATTTGTATTT
*
17717576 CTTTTATTTTATTTGTATTT
1 CTTTTAATTTATTTGTATTT
17717596 GTTGAATTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (20 bp):
CTTTTAATTTATTTGTATTT
Found at i:17718030 original size:142 final size:142
Alignment explanation
Indices: 17717774--17718112 Score: 462
Period size: 142 Copynumber: 2.4 Consensus size: 142
17717764 CATCTTCAAA
* ** *
17717774 GGAATAAGATTCGCTATCTTCATTCTGCTCCACTGCAACTCCAGGGAGATAAGGCTAGTGGCTTC
1 GGAATAAGATTCGCTATCTTCACTCTGCTCCACTGCAACTTTAAGGAGATAAGGCTAGTGGCTTC
* *
17717839 GATCTGCTCCACTACAACTTCAGGAAGATAGGATCCGCCATAACTTGTAGCTTTAATCTGTTACA
66 AATCTGCTCCACTACAACTTCAGGAAGATAAGATCCGCCATAACTTGTAGCTTTAATCTGTTACA
* *
17717904 CTGTAACGTCAG
131 CTGCAACGCCAG
* * * * *
17717916 GGAATAAGATTTGTTATCTTCACTCTGCTCCGCTGCAACTTTAAGAAGATAAGGCTGGTGGCTTC
1 GGAATAAGATTCGCTATCTTCACTCTGCTCCACTGCAACTTTAAGGAGATAAGGCTAGTGGCTTC
* * * * *
17717981 AATCTGCTGCACTGCAACTTTAGGAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCA
66 AATCTGCTCCACTACAACTTCAGGAAGATAAGATCCGCCATAACTTGTAGCTTTAATCTGTTACA
17718046 CTGCAACGCCAG
131 CTGCAACGCCAG
* * ** *
17718058 GGAAATAAGATTCGCTGTCTTCAGTCCACTCCACTGTAACTTTAAGGAGATAAGG
1 GG-AATAAGATTCGCTATCTTCACTCTGCTCCACTGCAACTTTAAGGAGATAAGG
17718113 TTTGTGGCCT
Statistics
Matches: 169, Mismatches: 27, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
142 126 0.75
143 43 0.25
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (142 bp):
GGAATAAGATTCGCTATCTTCACTCTGCTCCACTGCAACTTTAAGGAGATAAGGCTAGTGGCTTC
AATCTGCTCCACTACAACTTCAGGAAGATAAGATCCGCCATAACTTGTAGCTTTAATCTGTTACA
CTGCAACGCCAG
Found at i:17718349 original size:41 final size:40
Alignment explanation
Indices: 17718274--17718352 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
17718264 CTTTAATTTG
* * *
17718274 TTCCACTACAACGCCGGGGAAAAAAATTCTCTGCCTTCTA
1 TTCCACTACAACGCCAGAGAAAAAAATTCGCTGCCTTCTA
* *
17718314 TTCCACTACAATGCCAAGAGAAAAAGATTCGCTGCCTTC
1 TTCCACTACAACGCC-AGAGAAAAAAATTCGCTGCCTTC
17718353 AGCTTTAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 14 0.42
41 19 0.58
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (40 bp):
TTCCACTACAACGCCAGAGAAAAAAATTCGCTGCCTTCTA
Found at i:17718390 original size:51 final size:51
Alignment explanation
Indices: 17718334--17718544 Score: 279
Period size: 51 Copynumber: 4.2 Consensus size: 51
17718324 ATGCCAAGAG
* *
17718334 AAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCTACTACAACGCCAGGGA
1 AAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAGGGA
* * *
17718385 AAAAAGATTTGCTGCCTTTAGCTTTAATC---T--ACTGCAACGCCAAGGAAA
1 AAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCC-AGG-GA
17718433 AAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAGGGA
1 AAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAGGGA
* * * *
17718484 AATAAGATTCACTGCCTTCAGCTTTAATCTATCCCACTGCAACGCCAGGGA
1 AAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAGGGA
*
17718535 AATAAGATTC
1 AAAAAGATTC
17718545 ACTATGCTAA
Statistics
Matches: 142, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 10 0.07
47 3 0.02
48 29 0.20
51 86 0.61
52 3 0.02
53 11 0.08
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (51 bp):
AAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAGGGA
Found at i:17718456 original size:48 final size:46
Alignment explanation
Indices: 17718131--17718544 Score: 250
Period size: 51 Copynumber: 8.6 Consensus size: 46
17718121 CTTCTGTTCC
* * *
17718131 ACTGCAACTCCAGGGAAAAAAGATTCTCTACCTTCAGCTTTAATCTGTT
1 ACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATC---T
* * * * ** *
17718180 CCTTTGTAACACCAGGGAAATAATTTTCGCTACCTTCAGCTTTAATCT
1 AC--TGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCT
* * * * *
17718228 ACTGCAGCGCTAGGG-AAAAAGATTTGTTGCCTTCAGCTTTAATTTGTTCC
1 ACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAA-----TCT
* * * * *
17718278 ACTACAACGCCGGGGAAAAAA-ATTCTCTGCCTT---C--TATTCC
1 ACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCT
* * *
17718318 ACTACAATGCCA-AGAGAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCT
1 ACTGCAACGCCAGGGA-AAAAAGATTCGCTGCCTTCAGCTTTAA-----TCT
* * *
17718369 ACTACAACGCCAGGGAAAAAAGATTTGCTGCCTTTAGCTTTAATCT
1 ACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCT
*
17718415 ACTGCAACGCCAAGGAAAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTT
1 ACTGCAACGCC-AGG-GAAAAAAGATTCGCTGCCTTCAGCTTTAATC---T
* *
17718466 CCACTGCAACGCCAGGGAAATAAGATTCACTGCCTTCAGCTTTAATCTAT
1 --ACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATC--T
*
17718516 CCCACTGCAACGCCAGGGAAATAAGATTC
1 ---ACTGCAACGCCAGGGAAAAAAGATTC
17718545 ACTATGCTAA
Statistics
Matches: 290, Mismatches: 46, Indels: 56
0.74 0.12 0.14
Matches are distributed among these distances:
39 2 0.01
40 18 0.06
41 11 0.04
44 1 0.00
45 23 0.08
46 24 0.08
47 4 0.01
48 30 0.10
49 1 0.00
50 23 0.08
51 137 0.47
52 5 0.02
53 11 0.04
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (46 bp):
ACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAATCT
Found at i:17718457 original size:99 final size:97
Alignment explanation
Indices: 17718131--17718514 Score: 383
Period size: 99 Copynumber: 4.0 Consensus size: 97
17718121 CTTCTGTTCC
* * * * ** ** *
17718131 ACTGCAACTCC-AGGGAAAAAAGATTCTCTACCTTCAGCTTTAATCTGTTCCTTTGTAACACCAG
1 ACTGCAACGCCAAGGAAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
* * *
17718195 GGAAATAATTTTCGCTACCTTCAGCTTTAATCT
66 GGAAAAAAATTT-GCTGCCTTCAGCTTTAATCT
* * * * * * *
17718228 ACTGCAGCG-CTAGG-GAAAAAGATTTGTTGCCTTCAGCTTTAATTTGTTCCACTACAACGCCGG
1 ACTGCAACGCCAAGGAAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
* *
17718291 GGAAAAAAATTCT-CTGCCTT---C--TATTCC
66 GGAAAAAAATT-TGCTGCCTTCAGCTTTAATCT
* * * *
17718318 ACTACAATGCCAA-GAGAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCTACTACAACGCCAG
1 ACTGCAACGCCAAGGAAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
*
17718382 GGAAAAAAGATTTGCTGCCTTTAGCTTTAATCT
66 GGAAAAAA-ATTTGCTGCCTTCAGCTTTAATCT
*
17718415 ACTGCAACGCCAAGGAAAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCA
1 ACTGCAACGCCAAGG-AAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCA
* **
17718480 GGGAAATAAGATTCACTGCCTTCAGCTTTAATCT
65 GGGAAA-AAAATTTGCTGCCTTCAGCTTTAATCT
17718514 A
1 A
17718515 TCCCACTGCA
Statistics
Matches: 234, Mismatches: 39, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
90 11 0.05
91 55 0.24
92 11 0.05
95 7 0.03
96 47 0.20
97 26 0.11
98 1 0.00
99 74 0.32
100 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (97 bp):
ACTGCAACGCCAAGGAAAAAAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
GGAAAAAAATTTGCTGCCTTCAGCTTTAATCT
Found at i:17718547 original size:51 final size:51
Alignment explanation
Indices: 17718310--17718544 Score: 275
Period size: 51 Copynumber: 4.7 Consensus size: 51
17718300 TTCTCTGCCT
* * *
17718310 TCTATTCCACTACAATGCCA-AGAGAAAAAGATTCGCTGCCTTCAGCTTTAA
1 TCTATTCCACTGCAACGCCAGGGA-AAAAAGATTCGCTGCCTTCAGCTTTAA
* * * * *
17718361 TCTGTTCTACTACAACGCCAGGGAAAAAAGATTTGCTGCCTTTAGCTTTAA
1 TCTATTCCACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAA
*
17718412 TC---T--ACTGCAACGCCAAGGAAAAAAAAGATTCGCTGCCTTCAGCTTTAA
1 TCTATTCCACTGCAACGCC-AGG-GAAAAAAGATTCGCTGCCTTCAGCTTTAA
* * *
17718460 TCTGTTCCACTGCAACGCCAGGGAAATAAGATTCACTGCCTTCAGCTTTAA
1 TCTATTCCACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAA
* *
17718511 TCTATCCCACTGCAACGCCAGGGAAATAAGATTC
1 TCTATTCCACTGCAACGCCAGGGAAAAAAGATTC
17718545 ACTATGCTAA
Statistics
Matches: 161, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
46 10 0.06
47 3 0.02
48 29 0.18
51 103 0.64
52 5 0.03
53 11 0.07
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (51 bp):
TCTATTCCACTGCAACGCCAGGGAAAAAAGATTCGCTGCCTTCAGCTTTAA
Found at i:17718714 original size:51 final size:51
Alignment explanation
Indices: 17718555--17718902 Score: 344
Period size: 51 Copynumber: 7.3 Consensus size: 51
17718545 ACTATGCTAA
* * *
17718555 GGAAATAAGATTTGCTGCCTTCAGCTTTAATCT-TTCCACTTCAATGCCAG
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
* * *
17718605 GGAAAAAAGATTCGCTACCTTCAGCTTTAATC---T--ACTGCAACGCCAG
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
* * *
17718651 GGAAATAAGATTCGCTACCTTCAGCTTTAATCTGTTCCACTGCAACGCCAA
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
* *
17718702 GGAAATAAGATTCACTG----C--C--T--TCTGTTCCACTACAATGCCAG
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
* * * * *
17718743 GGAAAAAAGATTTGTTGCCTTCAGCTTTAACCTGTTCCTCTACAACGCCAG
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
* * *
17718794 GGAAATAAGATTCGTTGGCTTCAGCTTTAATC---T--ACTACAACGCTAG
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
* *
17718840 GGAAA-AAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAATGCCAG
1 GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
*
17718890 GGAAAAAAGATTC
1 GGAAATAAGATTC
17718903 ACCATAATGA
Statistics
Matches: 247, Mismatches: 30, Indels: 41
0.78 0.09 0.13
Matches are distributed among these distances:
41 31 0.13
43 1 0.00
45 26 0.11
46 58 0.23
47 2 0.01
48 3 0.01
49 2 0.01
50 44 0.18
51 80 0.32
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (51 bp):
GGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTACAACGCCAG
Found at i:17718878 original size:188 final size:188
Alignment explanation
Indices: 17718555--17718904 Score: 540
Period size: 188 Copynumber: 1.9 Consensus size: 188
17718545 ACTATGCTAA
* * * *
17718555 GGAAATAAGATTTGCTGCCTTCAGCTTTAATCTTTCCACTTCAATGCCAGGGAAAAAAGATTCGC
1 GGAAAAAAGATTTGCTGCCTTCAGCTTTAACCTTTCCACTACAACGCCAGGGAAAAAAGATTCGC
*
17718620 TACCTTCAGCTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGCTACCTTCAGCTTTAATCTG
66 TACCTTCAGCTTTAATCTACTACAACGCCAGGGAAATAAGATTCGCTACCTTCAGCTTTAATCTG
*
17718685 TTCCACTGCAACGCCAAGGAAATAAGATTCACTGCCTTCTGTTCCACTACAATGCCAG
131 TTCCACTGCAACGCCAAGGAAAAAAGATTCACTGCCTTCTGTTCCACTACAATGCCAG
* * *
17718743 GGAAAAAAGATTTGTTGCCTTCAGCTTTAACCTGTTCCTCTACAACGCCAGGGAAATAAGATTCG
1 GGAAAAAAGATTTGCTGCCTTCAGCTTTAACCT-TTCCACTACAACGCCAGGGAAAAAAGATTCG
* ** * *
17718808 TTGGCTTCAGCTTTAATCTACTACAACGCTAGGGAAA-AAGATTCGCTGCCTTCAGCTTTAATCT
65 CTACCTTCAGCTTTAATCTACTACAACGCCAGGGAAATAAGATTCGCTACCTTCAGCTTTAATCT
* *
17718872 GTTCCACTGCAATGCCAGGGAAAAAAGATTCAC
130 GTTCCACTGCAACGCCAAGGAAAAAAGATTCAC
17718905 CATAATGACT
Statistics
Matches: 145, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
188 86 0.59
189 59 0.41
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.28
Consensus pattern (188 bp):
GGAAAAAAGATTTGCTGCCTTCAGCTTTAACCTTTCCACTACAACGCCAGGGAAAAAAGATTCGC
TACCTTCAGCTTTAATCTACTACAACGCCAGGGAAATAAGATTCGCTACCTTCAGCTTTAATCTG
TTCCACTGCAACGCCAAGGAAAAAAGATTCACTGCCTTCTGTTCCACTACAATGCCAG
Found at i:17720645 original size:22 final size:23
Alignment explanation
Indices: 17720613--17720666 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
17720603 CCTGGTAGAG
*
17720613 GTTTTTGTTATTTGTT-CTTTTT
1 GTTTTTTTTATTTGTTACTTTTT
* *
17720635 GTTTTTTTTATTTTTTATTTTTT
1 GTTTTTTTTATTTGTTACTTTTT
*
17720658 ATTTTTTTT
1 GTTTTTTTT
17720667 CCTCTACTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.83
Consensus pattern (23 bp):
GTTTTTTTTATTTGTTACTTTTT
Found at i:17720662 original size:7 final size:7
Alignment explanation
Indices: 17720615--17720664 Score: 55
Period size: 7 Copynumber: 6.9 Consensus size: 7
17720605 TGGTAGAGGT
17720615 TTTTGTTA
1 TTTT-TTA
* *
17720623 TTTGTTC
1 TTTTTTA
*
17720630 TTTTTGTT
1 TTTTT-TA
17720638 TTTTTTA
1 TTTTTTA
17720645 TTTTTTA
1 TTTTTTA
17720652 TTTTTTA
1 TTTTTTA
17720659 TTTTTT
1 TTTTTT
17720665 TTCCTCTACT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
7 27 0.75
8 9 0.25
ACGTcount: A:0.08, C:0.02, G:0.06, T:0.84
Consensus pattern (7 bp):
TTTTTTA
Found at i:17725736 original size:17 final size:18
Alignment explanation
Indices: 17725705--17725749 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
17725695 TCTAATGAAC
**
17725705 TACAAATAATTAATA-AA
1 TACAAATAAGCAATACAA
17725722 TACAAATAAGCAATACAA
1 TACAAATAAGCAATACAA
*
17725740 TACATATAAG
1 TACAAATAAG
17725750 AGTAATAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.60, C:0.11, G:0.04, T:0.24
Consensus pattern (18 bp):
TACAAATAAGCAATACAA
Found at i:17726316 original size:26 final size:26
Alignment explanation
Indices: 17726278--17726331 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
17726268 ATTTAAACTA
*
17726278 AAATAATACACAAAGCAACTTAACAT
1 AAATAATACACAAAGCAACTTAAAAT
** *
17726304 AAATAATTTACAAAGCAAGTTAAAAT
1 AAATAATACACAAAGCAACTTAAAAT
17726330 AA
1 AA
17726332 TCATATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.59, C:0.13, G:0.06, T:0.22
Consensus pattern (26 bp):
AAATAATACACAAAGCAACTTAAAAT
Found at i:17726383 original size:17 final size:17
Alignment explanation
Indices: 17726358--17726410 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
17726348 TGTAATATAT
*
17726358 ATAAGAAAAATTTTAAA
1 ATAAAAAAAATTTTAAA
17726375 ATAAAAAAAA--TTAAA
1 ATAAAAAAAATTTTAAA
*
17726390 GAT-AAACAAATTTTAAA
1 -ATAAAAAAAATTTTAAA
17726407 ATAA
1 ATAA
17726411 CATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 11 0.37
16 4 0.13
17 15 0.50
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (17 bp):
ATAAAAAAAATTTTAAA
Found at i:17726410 original size:16 final size:15
Alignment explanation
Indices: 17726363--17726410 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
17726353 TATATATAAG
17726363 AAAAATTTTAAAATA
1 AAAAATTTTAAAATA
**
17726378 AAAAAAATTAAAGATA
1 AAAAATTTTAAA-ATA
17726394 AACAAATTTTAAAATA
1 AA-AAATTTTAAAATA
17726410 A
1 A
17726411 CATATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 10 0.37
16 9 0.33
17 8 0.30
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAAATTTTAAAATA
Found at i:17728333 original size:27 final size:27
Alignment explanation
Indices: 17728303--17728355 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
17728293 GACAGTTCTG
17728303 ACCTCTCTTCACTAAAAATTAATTATA
1 ACCTCTCTTCACTAAAAATTAATTATA
17728330 ACCTCTCTTCACTAAAAATTAATTAT
1 ACCTCTCTTCACTAAAAATTAATTAT
17728356 CTCATTGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.38
Consensus pattern (27 bp):
ACCTCTCTTCACTAAAAATTAATTATA
Found at i:17728819 original size:23 final size:22
Alignment explanation
Indices: 17728776--17728819 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
17728766 TTCTAAGCCG
17728776 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
17728799 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
17728820 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:17728979 original size:51 final size:50
Alignment explanation
Indices: 17728917--17729104 Score: 243
Period size: 51 Copynumber: 3.7 Consensus size: 50
17728907 TTCGGTTCAT
* *
17728917 ATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACAC
1 ATAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATCCGGTACAC
* * * * *
17728968 ATAGTACCCTGCACATAGTACTACACACGTGATCGAAACTATCCGGTACGC
1 ATAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATCCGGTACAC
* *
17729019 ATAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCGGTACAC
1 ATAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TCCGGTACAC
* *
17729069 GTAGTAGCCTGCACATAGTATTACACACGTGACCAT
1 ATAGTAGCCTGCACATAGTACTACACACGTGACCAT
17729105 CACTTTCACT
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.02
50 41 0.35
51 72 0.62
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (50 bp):
ATAGTAGCCTGCACATAGTACTACACACGTGACCATACCATCCGGTACAC
Found at i:17729100 original size:101 final size:101
Alignment explanation
Indices: 17728917--17729100 Score: 298
Period size: 101 Copynumber: 1.8 Consensus size: 101
17728907 TTCGGTTCAT
17728917 ATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACATAGTACCCTGCAC
1 ATAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGATACACATAGTACCCTGCAC
17728982 ATAGTACTACACACGTGATCGAAACTATCCGGTACGC
65 ATAGTACTACACACGTGATCGAAACTATCCGGTACGC
* * * *
17729019 ATAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCGGTACACGTAGTAGCCTGCAC
1 ATAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCGATACACATAGTACCCTGCAC
*
17729083 ATAGTATTACACACGTGA
65 ATAGTACTACACACGTGA
17729101 CCATCACTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 38 0.50
102 34 0.45
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
ATAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCGATACACATAGTACCCTGCACA
TAGTACTACACACGTGATCGAAACTATCCGGTACGC
Found at i:17729124 original size:101 final size:101
Alignment explanation
Indices: 17728909--17729100 Score: 278
Period size: 102 Copynumber: 1.9 Consensus size: 101
17728899 CAATGATGTT
*
17728909 CGGTTCATATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACATAGTA
1 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGATACACATAGTA
*
17728974 CCCTGCACATAGTACTACACACGTGATCGAAACTATC
65 CCCTGCACATAGTACTACACACGTGATCCAAACTATC
* * * * *
17729011 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGTGACC-TATCATTCCGGTACACGTAGTA
1 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCGATACACATAGTA
* *
17729075 GCCTGCACATAGTATTACACACGTGA
65 CCCTGCACATAGTACTACACACGTGA
17729101 CCATCACTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 4 0.05
101 38 0.47
102 39 0.48
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (101 bp):
CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATACCATCCGATACACATAGTAC
CCTGCACATAGTACTACACACGTGATCCAAACTATC
Found at i:17730673 original size:17 final size:18
Alignment explanation
Indices: 17730641--17730676 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
17730631 ATTACAAAAA
17730641 TTATTTATTTTATATTTT
1 TTATTTATTTTATATTTT
*
17730659 TTATTT-TTTTCTATTTT
1 TTATTTATTTTATATTTT
17730676 T
1 T
17730677 CTGTTATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (18 bp):
TTATTTATTTTATATTTT
Found at i:17730976 original size:20 final size:20
Alignment explanation
Indices: 17730951--17730990 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17730941 CTTTATTGAA
*
17730951 CTTTTAATTTATTTTTATTT
1 CTTTTAATTTATTTGTATTT
*
17730971 CTTTTATTTTATTTGTATTT
1 CTTTTAATTTATTTGTATTT
17730991 GTTGAATTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.75
Consensus pattern (20 bp):
CTTTTAATTTATTTGTATTT
Found at i:17737132 original size:9 final size:9
Alignment explanation
Indices: 17737108--17737171 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
17737098 GAACAAGAGC
*
17737108 TTGAGAAAA
1 TTGAGAGAA
17737117 TTGAGAGAA
1 TTGAGAGAA
* *
17737126 TTTAGAGAG
1 TTGAGAGAA
* *
17737135 TTAAGAGAG
1 TTGAGAGAA
*
17737144 TTGAGAAAA
1 TTGAGAGAA
* *
17737153 TAGAGAGAT
1 TTGAGAGAA
17737162 TTGAGAGAA
1 TTGAGAGAA
17737171 T
1 T
17737172 AGGATGTGAG
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.25
Consensus pattern (9 bp):
TTGAGAGAA
Found at i:17740060 original size:45 final size:45
Alignment explanation
Indices: 17739892--17740134 Score: 200
Period size: 45 Copynumber: 5.4 Consensus size: 45
17739882 CTACAGGTAC
* * * ** * * * *
17739892 AGGAAAGAAGAAGTTTCCATGAAGCCGGAAACAGGCTATGGATAC
1 AGGAAACAAGAAGTTTCCTTGATGCTAGCAACAGGATATAGATAT
* * ** * * * * *
17739937 AGGAAACAAGAAGTCTCCATGGA-GCCGGAAACATGCTATGGATAC
1 AGGAAACAAGAAGTTTCC-TTGATGCTAGCAACAGGATATAGATAT
* * * * **
17739982 AGGAATCAAGGAGTTTCCTTGGTGCCATAAACAGGATATAGATAT
1 AGGAAACAAGAAGTTTCCTTGATGCTAGCAACAGGATATAGATAT
*
17740027 AGGAAACAAGAAGTTTCGTTGATGCTAGCAACAGGATATAGATAT
1 AGGAAACAAGAAGTTTCCTTGATGCTAGCAACAGGATATAGATAT
* * * *
17740072 AGGAAATAAGAAGTTTCCTTGATGCTAGCAACAGGATATGGACAG
1 AGGAAACAAGAAGTTTCCTTGATGCTAGCAACAGGATATAGATAT
*
17740117 AGGAAACAAGATGTTTCC
1 AGGAAACAAGAAGTTTCC
17740135 CTAATGCAGG
Statistics
Matches: 166, Mismatches: 30, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
44 2 0.01
45 162 0.98
46 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (45 bp):
AGGAAACAAGAAGTTTCCTTGATGCTAGCAACAGGATATAGATAT
Found at i:17743642 original size:20 final size:20
Alignment explanation
Indices: 17743600--17743643 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
17743590 TAAGATATCA
* *
17743600 ATTTTAAAATTTTTATAAAT
1 ATTTGAAAATTTTGATAAAT
17743620 ATTTGAAAATTTTGA-AAATT
1 ATTTGAAAATTTTGATAAA-T
17743640 ATTT
1 ATTT
17743644 TGATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (20 bp):
ATTTGAAAATTTTGATAAAT
Found at i:17745483 original size:24 final size:23
Alignment explanation
Indices: 17745456--17745538 Score: 77
Period size: 24 Copynumber: 3.7 Consensus size: 23
17745446 TGTTATAAAG
17745456 AGATGAAAGGTGAAGAGTTAAGGA
1 AGATGAAAGGTGAA-AGTTAAGGA
*
17745480 AGATGAAA---GATAG--AAGGTA
1 AGATGAAAGGTGAAAGTTAAGG-A
*
17745499 AGATGAAAGGTGGAATGTTAAGGA
1 AGATGAAAGGT-GAAAGTTAAGGA
*
17745523 AAATGAAAGGTGAAAG
1 AGATGAAAGGTGAAAG
17745539 GTTGAACATC
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
18 4 0.09
19 9 0.19
20 2 0.04
21 2 0.04
23 7 0.15
24 19 0.40
25 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.17
Consensus pattern (23 bp):
AGATGAAAGGTGAAAGTTAAGGA
Found at i:17746889 original size:4 final size:4
Alignment explanation
Indices: 17746876--17746909 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
17746866 TAATGAAGAC
*
17746876 AAAT -AAT AAAT AAAT AAAT AAGT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
17746910 CATAAAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:17747028 original size:12 final size:12
Alignment explanation
Indices: 17747002--17747035 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
17746992 AAGATACATA
17747002 AATAAATAGTAAT
1 AATAAATA-TAAT
17747015 AATAAATATAAT
1 AATAAATATAAT
17747027 AATAAATAT
1 AATAAATAT
17747036 GGTAAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AATAAATATAAT
Found at i:17757662 original size:25 final size:25
Alignment explanation
Indices: 17757549--17757664 Score: 119
Period size: 25 Copynumber: 4.6 Consensus size: 25
17757539 ATACATGTAT
* * *
17757549 GCTCATACGAGCTATGAATTGGTAT
1 GCTCATACGAGCTGTGAATCGGTAA
17757574 GCTC-TCACGAGCTGTGAATCGGTAA
1 GCTCAT-ACGAGCTGTGAATCGGTAA
* * * *
17757599 GCTTATACGAACTGGGAATCGATAA
1 GCTCATACGAGCTGTGAATCGGTAA
* *
17757624 GCTC-TCACGAGCTGTAAATCAGTAA
1 GCTCAT-ACGAGCTGTGAATCGGTAA
17757649 GCTCATACGAGCTGTG
1 GCTCATACGAGCTGTG
17757665 GTGTGTCCGT
Statistics
Matches: 73, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
24 2 0.03
25 69 0.95
26 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (25 bp):
GCTCATACGAGCTGTGAATCGGTAA
Found at i:17761369 original size:60 final size:60
Alignment explanation
Indices: 17761276--17761408 Score: 248
Period size: 60 Copynumber: 2.2 Consensus size: 60
17761266 ATACACACCG
17761276 AAAATATTACAAGGTTAGTGAGTTCACATATGCAAAACATATAATAACTTTATCATGTCA
1 AAAATATTACAAGGTTAGTGAGTTCACATATGCAAAACATATAATAACTTTATCATGTCA
*
17761336 AAAATCTTACAAGGTTAGTGAGTTCACATATGCAAAACATATAATAACTTTATCATGTCA
1 AAAATATTACAAGGTTAGTGAGTTCACATATGCAAAACATATAATAACTTTATCATGTCA
*
17761396 AAAATATTGCAAG
1 AAAATATTACAAG
17761409 TAAACACAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.31
Consensus pattern (60 bp):
AAAATATTACAAGGTTAGTGAGTTCACATATGCAAAACATATAATAACTTTATCATGTCA
Found at i:17761546 original size:40 final size:40
Alignment explanation
Indices: 17761491--17761568 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
17761481 ATCAAATGTT
*
17761491 CCATTTCATATATCTATTTTCATATAACTGATTCATATTA
1 CCATTCCATATATCTATTTTCATATAACTGATTCATATTA
*
17761531 CCATTCCATATATCTATTTTTATATAACTGATTCATAT
1 CCATTCCATATATCTATTTTCATATAACTGATTCATAT
17761569 AAACACTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (40 bp):
CCATTCCATATATCTATTTTCATATAACTGATTCATATTA
Found at i:17761581 original size:40 final size:39
Alignment explanation
Indices: 17761495--17761582 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 39
17761485 AATGTTCCAT
* *
17761495 TTCATATATCTATTTTCATATAACTGATTCATATTACCA
1 TTCATATATCTATTTTCATATAACTGATTCATATAAACA
*
17761534 TTCCATATATCTATTTTTATATAACTGATTCATATAAACA
1 TT-CATATATCTATTTTCATATAACTGATTCATATAAACA
17761574 CTTCATATA
1 -TTCATATA
17761583 ACCATTTCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 2 0.05
40 40 0.91
41 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.45
Consensus pattern (39 bp):
TTCATATATCTATTTTCATATAACTGATTCATATAAACA
Found at i:17765687 original size:8 final size:8
Alignment explanation
Indices: 17765676--17765702 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
17765666 AAAAATTTTG
17765676 AAATAATA
1 AAATAATA
17765684 AAATAATA
1 AAATAATA
17765692 AAATAATA
1 AAATAATA
17765700 AAA
1 AAA
17765703 GCTGATAAAA
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATAATA
Found at i:17772490 original size:2 final size:2
Alignment explanation
Indices: 17772485--17772519 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17772475 TTTAATTGTA
17772485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17772520 AATTTCTACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17773154 original size:20 final size:20
Alignment explanation
Indices: 17773129--17773218 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 20
17773119 ACTTACAAGA
17773129 TGTATGGATAGAAGTGAACT
1 TGTATGGATAGAAGTGAACT
* * * *
17773149 TGTATGGGTAGAAATGGATT
1 TGTATGGATAGAAGTGAACT
* * * * *
17773169 TGTATAGATAAAACTTAACA
1 TGTATGGATAGAAGTGAACT
* *
17773189 TGTATGGATAGAAGTGGAGT
1 TGTATGGATAGAAGTGAACT
*
17773209 TGTATTGATA
1 TGTATGGATA
17773219 CATTGCACAT
Statistics
Matches: 50, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (20 bp):
TGTATGGATAGAAGTGAACT
Found at i:17774629 original size:72 final size:72
Alignment explanation
Indices: 17774530--17774676 Score: 197
Period size: 72 Copynumber: 2.0 Consensus size: 72
17774520 TTAAAATTAA
* * *
17774530 TTTTTAATAAAAATAGTAAAAAAAAGTGAGCTATGGGAGTATTCTCTAGTCAATTTAAGATTAAA
1 TTTTTAATAAAAATAG-AAAAAAAAGTGAACTATGAGAGTATTCTCTAGTCAATAT-AGATTAAA
17774595 ATTAACTTT
64 ATTAACTTT
** * * *
17774604 TTTTTAATAAAAATAG-CGAAGAAGTGAACTATGAGAGTGTTCTCTAGTCAATATGGATTAAAAT
1 TTTTTAATAAAAATAGAAAAAAAAGTGAACTATGAGAGTATTCTCTAGTCAATATAGATTAAAAT
17774668 TAACTTT
66 TAACTTT
17774675 TT
1 TT
17774677 AATGGAAACG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
71 18 0.28
72 31 0.48
74 16 0.25
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (72 bp):
TTTTTAATAAAAATAGAAAAAAAAGTGAACTATGAGAGTATTCTCTAGTCAATATAGATTAAAAT
TAACTTT
Found at i:17776262 original size:26 final size:26
Alignment explanation
Indices: 17776220--17776295 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
17776210 TTCTTTCCAT
* *
17776220 AGAT-CGCTACAATGGCTTCCATTTC
1 AGATACGCCACAAAGGCTTCCATTTC
* *
17776245 AGTTACGCCACTAAGGCTTCCATTTC
1 AGATACGCCACAAAGGCTTCCATTTC
*
17776271 AGATACGCCACAAAGGCTTCTATTT
1 AGATACGCCACAAAGGCTTCCATTT
17776296 TCTGACGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 3 0.07
26 40 0.93
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (26 bp):
AGATACGCCACAAAGGCTTCCATTTC
Found at i:17802609 original size:28 final size:28
Alignment explanation
Indices: 17802572--17802669 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 28
17802562 ACAAAGTGCA
*
17802572 AATAACGATAAGCACCGAAGTGCAAAAT
1 AATAACGATAAGCACAGAAGTGCAAAAT
* * *
17802600 AATAATGATAAGCACAAAAGTGCAAATTTT
1 AATAACGATAAGCACAGAAGTGCAAA--AT
* * * **
17802630 TACAACGATAAGCACTGAAGTGCGTAAT
1 AATAACGATAAGCACAGAAGTGCAAAAT
*
17802658 AAT-ATGATAAGC
1 AATAACGATAAGC
17802670 GCACTAATTT
Statistics
Matches: 53, Mismatches: 15, Indels: 5
0.73 0.21 0.07
Matches are distributed among these distances:
27 8 0.15
28 25 0.47
30 20 0.38
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.21
Consensus pattern (28 bp):
AATAACGATAAGCACAGAAGTGCAAAAT
Found at i:17804660 original size:23 final size:23
Alignment explanation
Indices: 17804625--17804669 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17804615 TGGAGTATAA
* *
17804625 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
17804648 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
17804670 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:17804714 original size:2 final size:2
Alignment explanation
Indices: 17804709--17804747 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17804699 AAGGTATATA
17804709 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
17804748 ACTTAAGATT
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:17805105 original size:2 final size:2
Alignment explanation
Indices: 17805098--17805124 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17805088 TGTATTAAGT
17805098 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 T
17805125 GTCGGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17805459 original size:42 final size:42
Alignment explanation
Indices: 17805400--17805601 Score: 252
Period size: 42 Copynumber: 4.9 Consensus size: 42
17805390 NNNNNNNNNN
17805400 TCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATT
1 TCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATT
* *
17805442 TCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAACAATA
1 TCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATT
*
17805484 TCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA-CATT
1 TCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATT
* * * *
17805525 TCAGACTATATGTCTAGCAGGC-TAAGTGCCGGTGTACTGAA--
1 TCAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTGAAAT-AATT
* * *
17805566 TCAGGCTTTAAGTCTAGCAGGC-TAAGTGCCAGTGAA
1 TCAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTGAA
17805602 TCTGTTTAAA
Statistics
Matches: 143, Mismatches: 14, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
40 3 0.02
41 62 0.43
42 77 0.54
43 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (42 bp):
TCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATT
Found at i:17809050 original size:11 final size:11
Alignment explanation
Indices: 17809027--17809067 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
17809017 TCGAATCTGC
17809027 CTATTATTTTTG
1 CTATTA-TTTTG
17809039 CTATTATTTTG
1 CTATTATTTTG
* *
17809050 CTGTCATTTTG
1 CTATTATTTTG
17809061 CTATTAT
1 CTATTAT
17809068 ATTATTACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 19 0.76
12 6 0.24
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.61
Consensus pattern (11 bp):
CTATTATTTTG
Found at i:17810098 original size:12 final size:12
Alignment explanation
Indices: 17810081--17810142 Score: 65
Period size: 12 Copynumber: 5.1 Consensus size: 12
17810071 TTTCCATCTA
*
17810081 TCTTCTTTATTT
1 TCTTATTTATTT
*
17810093 TCTTCTTTATTAT
1 TCTTATTTATT-T
17810106 TC-TATTTATTT
1 TCTTATTTATTT
17810117 ATCTTATTTATTT
1 -TCTTATTTATTT
17810130 AT-TTATTTATTT
1 -TCTTATTTATTT
17810142 T
1 T
17810143 GTTTGACTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
11 2 0.04
12 30 0.65
13 14 0.30
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTTATTTATTT
Found at i:17810117 original size:4 final size:4
Alignment explanation
Indices: 17810098--17810141 Score: 63
Period size: 4 Copynumber: 10.8 Consensus size: 4
17810088 TATTTTCTTC
17810098 TTTA -TTA TTCTA TTTA TTTA TCTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TT-TA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTT
17810142 TGTTTGACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.08
4 26 0.70
5 8 0.22
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:17810127 original size:25 final size:24
Alignment explanation
Indices: 17810086--17810142 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
17810076 ATCTATCTTC
*
17810086 TTTATTTTCTTCTTTA-TTATTCTA
1 TTTATTTTCTTATTTATTTATT-TA
17810110 TTTATTTATCTTATTTATTTATTTA
1 TTTATTT-TCTTATTTATTTATTTA
17810135 TTTATTTT
1 TTTATTTT
17810143 GTTTGACTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 8 0.27
25 17 0.57
26 5 0.17
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (24 bp):
TTTATTTTCTTATTTATTTATTTA
Found at i:17811474 original size:20 final size:20
Alignment explanation
Indices: 17811449--17811495 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 20
17811439 TATTTTCTTC
17811449 TTTATTATTCTAATCT-TTTA
1 TTTATTATTCTAAT-TATTTA
17811469 TTTATTATTCTAATTATTTA
1 TTTATTATTCTAATTATTTA
17811489 TCTTATT
1 T-TTATT
17811496 TATTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.76
21 5 0.20
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTATTATTCTAATTATTTA
Found at i:17837179 original size:2 final size:2
Alignment explanation
Indices: 17837166--17837196 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
17837156 GAAAATATGG
*
17837166 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17837197 AACAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:17837575 original size:3 final size:3
Alignment explanation
Indices: 17837569--17837625 Score: 96
Period size: 3 Copynumber: 19.0 Consensus size: 3
17837559 TAGTTATTAG
**
17837569 TAA TAA TAA TGT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17837617 TAA TAA TAA
1 TAA TAA TAA
17837626 ATGATAATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17839707 original size:44 final size:44
Alignment explanation
Indices: 17839635--17839890 Score: 159
Period size: 44 Copynumber: 5.8 Consensus size: 44
17839625 ATCTGATGTG
* * * *
17839635 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTAT-TTTA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGA--CTATTATCTTCA
* * * *
17839679 ATCTGCTCCACTGTAATTTCAGGGAGATAGGATTACTATCTTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGACTATTATCTTCA
* * **
17839723 ATCTGCTCCGCTGTAATCTT-AGAGAGATAAGACCTGAATT-TCTTTG
1 ATCTGCTCCACTGTAA-CTTCAGGGAGATAAGA-CT--ATTATCTTCA
* * * *
17839769 GTCTACTCCACTGTAACCTCAGGGAGATAAGACT-TGTATATTCA
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGACTAT-TATCTTCA
* * * * * *
17839813 ACCTGCCCCACTGTAACTTCAGGGAGATAAG-GT-TTGTGGCTCCG
1 ATCTGCTCCACTGTAACTTCAGGGAGATAAGACTATTAT--CTTCA
*
17839857 ATCTGCTCCTCTGTAA-TCTCAGGGAGATAAGACT
1 ATCTGCTCCACTGTAACT-TCAGGGAGATAAGACT
17839891 TGATGCGATC
Statistics
Matches: 161, Mismatches: 38, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
42 4 0.02
43 7 0.04
44 112 0.70
45 8 0.05
46 28 0.17
47 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGTAACTTCAGGGAGATAAGACTATTATCTTCA
Found at i:17839722 original size:98 final size:98
Alignment explanation
Indices: 17839537--17839727 Score: 269
Period size: 98 Copynumber: 1.9 Consensus size: 98
17839527 AGTGTCCTCA
* *
17839537 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTAAATTTTAATCCGCTCCACTGTAACTTCA
1 ATCTACTCCACTGTAATCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTGTAACTTCA
*
17839602 GGGAGATAGGATTATCGGCTTCAATCTGATGTG
66 GGGAGATAGGATTATCAGCTTCAATCTGATGTG
* ** * *
17839635 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATTTC
1 ATCTACTCCACTGTAATC-TCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTGTAACTTC
*
17839699 AGGGAGATAGGATTA-CTATCTTCAATCTG
65 AGGGAGATAGGATTATC-AGCTTCAATCTG
17839728 CTCCGCTGTA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
97 2 0.02
98 80 0.98
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (98 bp):
ATCTACTCCACTGTAATCTCAGAGAGATAAGATCCTAAATTTTAATCCGCTCCACTGTAACTTCA
GGGAGATAGGATTATCAGCTTCAATCTGATGTG
Found at i:17839861 original size:134 final size:133
Alignment explanation
Indices: 17839636--17839889 Score: 314
Period size: 134 Copynumber: 1.9 Consensus size: 133
17839626 TCTGATGTGA
* * * * * *
17839636 TCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATTTCAG
1 TCTACTCCACTGTAACCTCAGAGAGATAAGA-CCTTTATTTCAACCTGCCCCACTGTAACTTCAG
* * *
17839701 GGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAATCTTAGAGAGATAAGACCTGAATTTCT
65 GGAGATAGGATTACTAGCTCCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGACCTGAATTTCT
17839766 TTGG
130 TTGG
*
17839770 TCTACTCCACTGTAACCTCAGGGAGATAAGA-CTTGTATATTCAACCTGCCCCACTGTAACTTCA
1 TCTACTCCACTGTAACCTCAGAGAGATAAGACCTT-TAT-TTCAACCTGCCCCACTGTAACTTCA
** * * * *
17839834 GGGAGATAAGG-TTTGTGGCTCCGATCTGCTCCTCTGTAATCTCAGGGAGATAAGAC
64 GGGAGAT-AGGATTACTAGCTCCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGAC
17839890 TTGATGCGAT
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
132 3 0.03
133 3 0.03
134 92 0.91
135 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (133 bp):
TCTACTCCACTGTAACCTCAGAGAGATAAGACCTTTATTTCAACCTGCCCCACTGTAACTTCAGG
GAGATAGGATTACTAGCTCCAATCTGCTCCGCTGTAATCTCAGAGAGATAAGACCTGAATTTCTT
TGG
Found at i:17852048 original size:2 final size:2
Alignment explanation
Indices: 17852041--17852067 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17852031 GAAAATATGG
17852041 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17852068 AACAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17852448 original size:3 final size:3
Alignment explanation
Indices: 17852442--17852495 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
17852432 TAGTTATTAG
**
17852442 TAA TAA TAA TGT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17852490 TAA TAA
1 TAA TAA
17852496 ATGATAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17863835 original size:41 final size:41
Alignment explanation
Indices: 17863790--17864014 Score: 242
Period size: 41 Copynumber: 5.5 Consensus size: 41
17863780 AGTCCAAAAA
*
17863790 GCTTCGTGCCGATGTATACTCA-CAGGCTTTGTGCCTAGCAG
1 GCTTCGTGCCGATGTATA-TTATCAGGCTTTGTGCCTAGCAG
* *
17863831 GCTTCGTGCCGGTGTATATTATCAGGTTTTGTGCCTAGCAG
1 GCTTCGTGCCGATGTATATTATCAGGCTTTGTGCCTAGCAG
* * *
17863872 GCTTCGTGCC-AGTGTATATTATCAGCCTTTGTGCCTCGCAA
1 GCTTCGTGCCGA-TGTATATTATCAGGCTTTGTGCCTAGCAG
* * *
17863913 GCTTCGTGCTGGTGTAGATTATCAGGCTTTGTGCCTAGCAG
1 GCTTCGTGCCGATGTATATTATCAGGCTTTGTGCCTAGCAG
* * * * * * * *
17863954 GCTTTGAGTCGGTGTATATTATTAGGCATTGAGTCTAGCAG
1 GCTTCGTGCCGATGTATATTATCAGGCTTTGTGCCTAGCAG
*
17863995 GCTTTGTGCC-A-GTATATTAT
1 GCTTCGTGCCGATGTATATTAT
17864015 ATTAGGTAAC
Statistics
Matches: 155, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
39 9 0.06
40 2 0.01
41 144 0.93
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.35
Consensus pattern (41 bp):
GCTTCGTGCCGATGTATATTATCAGGCTTTGTGCCTAGCAG
Found at i:17868018 original size:6 final size:6
Alignment explanation
Indices: 17868007--17868043 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
17867997 TCTAACCTGA
*
17868007 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAGAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
17868044 TGGACGAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:17869648 original size:95 final size:95
Alignment explanation
Indices: 17869453--17869660 Score: 238
Period size: 95 Copynumber: 2.2 Consensus size: 95
17869443 TATTTTATCA
* * * * *
17869453 AATTATATATTTTATTTAAAATGTATTGGCCCTTTTGATGTGAAGTGGGATGACAACTCAAGCAC
1 AATT-TAT-TTTTATTTAAAATGTATTAGCCCTTTTGACGCGAAGTGGAATGACAACCCAAGCAC
* * * * * *
17869518 CCCACCCCGATTACTTAGCCCGACACGCTCTT
64 CCCACCACGATTACTCAACCCAACACACTCCT
*
17869550 AATTT-TTTTTGTTTAAGAATGTATTAGCCCTTTTGACGCGAAGTGGAATGACAACCCAAGCACC
1 AATTTATTTTTATTTAA-AATGTATTAGCCCTTTTGACGCGAAGTGGAATGACAACCCAAGCACC
* * *
17869614 TCACCATGGTTACTCAACCCAACACACTCCT
65 CCACCACGATTACTCAACCCAACACACTCCT
17869645 AATTTATTTTTTATTT
1 AATTTA-TTTTTATTT
17869661 CCATAATTTC
Statistics
Matches: 92, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
94 9 0.10
95 70 0.76
96 1 0.01
97 12 0.13
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (95 bp):
AATTTATTTTTATTTAAAATGTATTAGCCCTTTTGACGCGAAGTGGAATGACAACCCAAGCACCC
CACCACGATTACTCAACCCAACACACTCCT
Found at i:17871523 original size:42 final size:42
Alignment explanation
Indices: 17871477--17871567 Score: 182
Period size: 42 Copynumber: 2.2 Consensus size: 42
17871467 CTTGTGATTT
17871477 TATTTTCTCAATTGACGTGGTCAACTCTTTTATAGATTCATC
1 TATTTTCTCAATTGACGTGGTCAACTCTTTTATAGATTCATC
17871519 TATTTTCTCAATTGACGTGGTCAACTCTTTTATAGATTCATC
1 TATTTTCTCAATTGACGTGGTCAACTCTTTTATAGATTCATC
17871561 TATTTTC
1 TATTTTC
17871568 GTTTGAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.23, C:0.19, G:0.11, T:0.47
Consensus pattern (42 bp):
TATTTTCTCAATTGACGTGGTCAACTCTTTTATAGATTCATC
Found at i:17873839 original size:24 final size:22
Alignment explanation
Indices: 17873800--17874115 Score: 114
Period size: 24 Copynumber: 13.8 Consensus size: 22
17873790 GCATATACAT
17873800 ACCAAATTTAACAGCACTTTTAC
1 ACCAAATTTAACAGCA-TTTTAC
* *
17873823 ACCAAAATTTAATAGCATATATAC
1 ACC-AAATTTAACAGCAT-TTTAC
* * * * *
17873847 AGCAAA--TAGGCAGCATATAAT
1 ACCAAATTTA-ACAGCATTTTAC
17873868 ACCAAATTTAACAGCACTTTTAC
1 ACCAAATTTAACAGCA-TTTTAC
* *
17873891 ACCAAAATTTAATAGCATATATAC
1 ACC-AAATTTAACAGCAT-TTTAC
* * *
17873915 AGCAAA--TAGGCAGCA-TATAC
1 ACCAAATTTA-ACAGCATTTTAC
*
17873935 ATACCAAATTTAATAGCACTTTTAC
1 --ACCAAATTTAACAGCA-TTTTAC
*
17873960 ACCAAAATTTAACAGCATATATAC
1 ACC-AAATTTAACAGCAT-TTTAC
* * *
17873984 AACAAA--TAGGCAGCA-TATAC
1 ACCAAATTTA-ACAGCATTTTAC
* *
17874004 ATACCAAATTGAGCAGCATTTTTAC
1 --ACCAAATTTAACAGCA-TTTTAC
*
17874029 ACCAAAATTTAACAGCATATATAC
1 ACC-AAATTTAACAGCAT-TTTAC
* * *
17874053 AACAAA--TAGGCAGCA-TATAC
1 ACCAAATTTA-ACAGCATTTTAC
* *
17874073 ATACCAAATTGAGCAGCATTTTTAC
1 --ACCAAATTTAACAGCA-TTTTAC
17874098 ACCAAAATTTAACAGCAT
1 ACC-AAATTTAACAGCAT
17874116 ATATACAACA
Statistics
Matches: 219, Mismatches: 40, Indels: 68
0.67 0.12 0.21
Matches are distributed among these distances:
20 15 0.07
21 14 0.06
22 39 0.18
23 53 0.24
24 86 0.39
25 12 0.05
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.26
Consensus pattern (22 bp):
ACCAAATTTAACAGCATTTTAC
Found at i:17873865 original size:69 final size:69
Alignment explanation
Indices: 17873718--17874144 Score: 651
Period size: 69 Copynumber: 6.2 Consensus size: 69
17873708 TCAATGTGGA
* * * * * ** *
17873718 CAGCATTTATATACCAAATTAAACAGCA-TTTATACAACAAAATTTGGACAGGTTATATACATCA
1 CAGCATATACATACCAAATTTAACAGCACTTT-TACACCAAAATTT-AACAGCATATATACAACA
17873782 AATAGG
64 AATAGG
* *
17873788 CAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAATAGCATATATACAGCAAA
1 CAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAA
17873853 TAGG
66 TAGG
* *
17873857 CAGCATATA-ATACCAAATTTAACAGCACTTTTACACCAAAATTTAATAGCATATATACAGCAAA
1 CAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAA
17873921 TAGG
66 TAGG
*
17873925 CAGCATATACATACCAAATTTAATAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAA
17873990 TAGG
66 TAGG
* * *
17873994 CAGCATATACATACCAAATTGAGCAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAA
17874059 TAGG
66 TAGG
* * *
17874063 CAGCATATACATACCAAATTGAGCAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAA
1 CAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAA
17874128 TAGG
66 TAGG
17874132 CAGCATATACATA
1 CAGCATATACATA
17874145 ATACATCATA
Statistics
Matches: 339, Mismatches: 16, Indels: 5
0.94 0.04 0.01
Matches are distributed among these distances:
68 68 0.20
69 231 0.68
70 37 0.11
71 3 0.01
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.26
Consensus pattern (69 bp):
CAGCATATACATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCATATATACAACAAA
TAGG
Found at i:17874157 original size:18 final size:17
Alignment explanation
Indices: 17874136--17874172 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
17874126 AATAGGCAGC
17874136 ATATACATAATACATCAT
1 ATATACATAATACA-CAT
*
17874154 ATATATATAATACACAT
1 ATATACATAATACACAT
17874171 AT
1 AT
17874173 TACTTTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (17 bp):
ATATACATAATACACAT
Found at i:17875034 original size:41 final size:41
Alignment explanation
Indices: 17874950--17875105 Score: 179
Period size: 41 Copynumber: 3.8 Consensus size: 41
17874940 TTGTATAAAA
* ** * *
17874950 CACCGGCATAAAGCCTGCTACG-CACAAAGCCCAATACATTT
1 CACCGGCATAAAGCCTGCTA-GACATAAAGCCTGATATAATT
* * * *
17874991 CACCGGAACAAAGCCTACTAGACATAAAGTCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCTGATATAATT
*
17875032 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCTGATATAATT
* * *
17875073 CACTGGCATAAAGCCTGCTAGGCACAAAGCCTG
1 CACCGGCATAAAGCCTGCTAGACATAAAGCCTG
17875106 CTAGGCACAA
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.01
41 97 0.99
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGCCTGATATAATT
Found at i:17875101 original size:16 final size:16
Alignment explanation
Indices: 17875077--17875121 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
17875067 ATAATTCACT
*
17875077 GGCATAAAGCCTGCTA
1 GGCACAAAGCCTGCTA
17875093 GGCACAAAGCCTGCTA
1 GGCACAAAGCCTGCTA
17875109 GGCACAAAGCCTG
1 GGCACAAAGCCTG
17875122 AACTTACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.27, T:0.13
Consensus pattern (16 bp):
GGCACAAAGCCTGCTA
Found at i:17878855 original size:16 final size:16
Alignment explanation
Indices: 17878834--17878872 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
17878824 TGTATATTAC
17878834 CAGGCTTTGTACCTAG
1 CAGGCTTTGTACCTAG
*
17878850 CAGGCTTTGTGCCTAG
1 CAGGCTTTGTACCTAG
*
17878866 CAAGCTT
1 CAGGCTT
17878873 CATGCCAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (16 bp):
CAGGCTTTGTACCTAG
Found at i:17878954 original size:41 final size:41
Alignment explanation
Indices: 17878850--17878954 Score: 129
Period size: 41 Copynumber: 2.6 Consensus size: 41
17878840 TTGTACCTAG
*
17878850 CAGGCTTTGTGCCTAGCAAGCTTCATGCCAGTGTAGATTAT
1 CAGGCTTTGTGCCTAGCAGGCTTCATGCCAGTGTAGATTAT
* * * * * *
17878891 CAGGCGTTGTGCCTAGCGGGCTTCGTGTCGGTGTATATTAT
1 CAGGCTTTGTGCCTAGCAGGCTTCATGCCAGTGTAGATTAT
* *
17878932 CAGGCTTTATGCCTAGTAGGCTT
1 CAGGCTTTGTGCCTAGCAGGCTT
17878955 TATCAAGCTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (41 bp):
CAGGCTTTGTGCCTAGCAGGCTTCATGCCAGTGTAGATTAT
Found at i:17880269 original size:28 final size:28
Alignment explanation
Indices: 17880229--17880286 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
17880219 ATCAAAACAT
17880229 AACTTACAATTTCAATTTGCATAATTTA
1 AACTTACAATTTCAATTTGCATAATTTA
17880257 AACTTACAATTTCAATTTGCATAATTTA
1 AACTTACAATTTCAATTTGCATAATTTA
17880285 AA
1 AA
17880287 GCATAAGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.41
Consensus pattern (28 bp):
AACTTACAATTTCAATTTGCATAATTTA
Found at i:17884292 original size:46 final size:46
Alignment explanation
Indices: 17884220--17884401 Score: 337
Period size: 46 Copynumber: 4.0 Consensus size: 46
17884210 ACATTGCTAT
* *
17884220 AACTCAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTTGC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCGC
17884266 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCGC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCGC
*
17884312 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCGC
17884358 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTC
17884402 ACATTTTGCC
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 133 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCGC
Found at i:17887407 original size:24 final size:24
Alignment explanation
Indices: 17887380--17887428 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
17887370 ATATATTTTT
*
17887380 AGTATGGATCATGTATATTATATA
1 AGTATGAATCATGTATATTATATA
*
17887404 AGTATGAATTATGTATATTATATA
1 AGTATGAATCATGTATATTATATA
17887428 A
1 A
17887429 AATAAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.43
Consensus pattern (24 bp):
AGTATGAATCATGTATATTATATA
Found at i:17887437 original size:24 final size:24
Alignment explanation
Indices: 17887390--17887434 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
17887380 AGTATGGATC
* *
17887390 ATGTATATTATATAAGTATGAATT
1 ATGTATATTATATAAATATAAATT
17887414 ATGTATATTATATAAA-ATAAA
1 ATGTATATTATATAAATATAAA
17887435 ATTGCTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (24 bp):
ATGTATATTATATAAATATAAATT
Found at i:17893690 original size:23 final size:23
Alignment explanation
Indices: 17893664--17893711 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
17893654 CAAAAACATG
17893664 AACTCATTCTTCCATAATTTTTT
1 AACTCATTCTTCCATAATTTTTT
17893687 AACTCATTCTTCCATAATTTTTT
1 AACTCATTCTTCCATAATTTTTT
17893710 AA
1 AA
17893712 GTCCTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (23 bp):
AACTCATTCTTCCATAATTTTTT
Found at i:17908129 original size:19 final size:20
Alignment explanation
Indices: 17908097--17908152 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 20
17908087 AAATTTAATT
*
17908097 TTTTTATAATTTTTTATG-A
1 TTTTTATAAGTTTTTATGAA
* *
17908116 TTTTTATAGGTTTTTAAGAA
1 TTTTTATAAGTTTTTATGAA
* *
17908136 TTTTAATACGTTTTTAT
1 TTTTTATAAGTTTTTAT
17908153 AAAATTCTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTTTATAAGTTTTTATGAA
Found at i:17908150 original size:21 final size:21
Alignment explanation
Indices: 17908126--17908176 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
17908116 TTTTTATAGG
*
17908126 TTTTTAAGAATT-TTAATACGT
1 TTTTTAA-AATTCTAAATACGT
*
17908147 TTTTATAAAATTCTAAATATGT
1 TTTT-TAAAATTCTAAATACGT
17908169 TTTATTAA
1 TTT-TTAA
17908177 TTTTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 8 0.32
22 16 0.64
23 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.53
Consensus pattern (21 bp):
TTTTTAAAATTCTAAATACGT
Found at i:17908282 original size:14 final size:15
Alignment explanation
Indices: 17908265--17908294 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
17908255 AATTTCAATA
17908265 TATTTTTAATA-TTT
1 TATTTTTAATACTTT
17908279 TATTTTTAATACTTT
1 TATTTTTAATACTTT
17908294 T
1 T
17908295 TATAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTTAATACTTT
Found at i:17908343 original size:20 final size:20
Alignment explanation
Indices: 17908294--17908331 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17908284 TTAATACTTT
17908294 TTATAA-TTTTTCTGATTTG
1 TTATAATTTTTTCTGATTTG
*
17908313 TTATAATTTTTTCTTATTT
1 TTATAATTTTTTCTGATTT
17908332 TTAATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TTATAATTTTTTCTGATTTG
Found at i:17912850 original size:50 final size:50
Alignment explanation
Indices: 17912782--17912985 Score: 189
Period size: 50 Copynumber: 4.1 Consensus size: 50
17912772 AAAGTGAAAG
* *
17912782 TGATAG-TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAA
1 TGATAGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA
* * * * * *
17912831 TGAAAGGTCTCATGTGTAGTACTATGTACAGGCTACTATGCGTACCGG-A
1 TGATAGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA
* * * * * *
17912880 TAGCTTCGATCACGTGTCTAGTACTATGTGCAGGCTACTACGTGAACTGGAA
1 T-G-ATAGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA
* * * * * *
17912932 AGTTTGATCACATGTATAGTACTATGTGAAGGCTACTACGTGTATC-GAA
1 TGATAGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA
17912981 TGATA
1 TGATA
17912986 ATAGTTAAAT
Statistics
Matches: 121, Mismatches: 30, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
49 12 0.10
50 73 0.60
51 35 0.29
52 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (50 bp):
TGATAGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAA
Done.