Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 144 of 235
Found at i:48302980 original size:19 final size:19
Alignment explanation
Indices: 48302956--48303068 Score: 154
Period size: 19 Copynumber: 5.8 Consensus size: 19
48302946 AATCATATAT
*
48302956 TCTAAGATTGCATATCATG
1 TCTAAGATTGCATATCATA
** *
48302975 TCTAAGATTATATATCATC
1 TCTAAGATTGCATATCATA
48302994 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
48303013 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
**
48303034 TCTTGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
48303053 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
48303069 CTCAAAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
19 65 0.79
21 17 0.21
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:48303043 original size:40 final size:40
Alignment explanation
Indices: 48302956--48303067 Score: 174
Period size: 40 Copynumber: 2.9 Consensus size: 40
48302946 AATCATATAT
* *
48302956 TCTAAGATTGCATATCATGTCTAAGATT--ATATATCATC
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
48302994 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
**
48303034 TCTTGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTGCATATCATATCTAAGATTGCATAT
48303068 CCTCAAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 27 0.40
40 41 0.60
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (40 bp):
TCTAAGATTGCATATCATATCTAAGATTGCATATATCATA
Found at i:48303212 original size:71 final size:71
Alignment explanation
Indices: 48303096--48303238 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
48303086 CATATGTGAG
48303096 TCCGGGCTAAAATTGGGTATTACACAAGTTTTAAAAAATAATTTGAAGAATATTTGCCAAATAAC
1 TCCGGGCTAAAATTGGGTATTACACAAGTTTTAAAAAATAATTTGAAGAATATTTGCCAAATAAC
48303161 CTGAAA
66 CTGAAA
48303167 TCCGGGCTAAAATTGGGTATTACACAAGTTTTAAAAAATAATTTGAAGAATATTTGCCAAATAAC
1 TCCGGGCTAAAATTGGGTATTACACAAGTTTTAAAAAATAATTTGAAGAATATTTGCCAAATAAC
48303232 CTGAAA
66 CTGAAA
48303238 T
1 T
48303239 ATTTTATACA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (71 bp):
TCCGGGCTAAAATTGGGTATTACACAAGTTTTAAAAAATAATTTGAAGAATATTTGCCAAATAAC
CTGAAA
Found at i:48310111 original size:20 final size:20
Alignment explanation
Indices: 48310086--48310134 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
48310076 TGAGTTATTT
48310086 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
48310106 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
48310126 AAG-AAGCAA
1 AAGTAAGCAA
48310135 AGACTATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:48319473 original size:37 final size:37
Alignment explanation
Indices: 48319412--48319557 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
48319402 TACGTATGAT
* *
48319412 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
48319447 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
48319484 CACTTATCACTTTGTTTCTTGATCAGATAAGTGCAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
48319521 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
48319558 TAAAGCTATC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 90 0.88
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:48319640 original size:52 final size:52
Alignment explanation
Indices: 48319564--48320557 Score: 1814
Period size: 52 Copynumber: 19.3 Consensus size: 52
48319554 TAGCTAAAGC
* *
48319564 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48319617 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48319669 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48319721 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48319773 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48319825 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48319877 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48319929 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48319981 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48320033 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48320085 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48320137 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48320189 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48320241 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48320293 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48320345 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48320397 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
48320443 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
48320489 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48320541 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
48320558 ATCAGAAGTA
Statistics
Matches: 924, Mismatches: 10, Indels: 14
0.97 0.01 0.01
Matches are distributed among these distances:
46 87 0.09
47 2 0.00
48 1 0.00
50 1 0.00
51 3 0.00
52 812 0.88
53 18 0.02
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:48320449 original size:38 final size:41
Alignment explanation
Indices: 48320361--48320496 Score: 152
Period size: 46 Copynumber: 3.1 Consensus size: 41
48320351 TTTTCACTTG
48320361 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTA
1 TCACTTGATCAGATAAGTATAGCCGAAG-----ACTTATCACTTTA
48320407 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTA
1 TCACTTGATCAGATAAGTATAGCCGAAG-----ACTTATCACTTTA
*
48320453 TCACTTGATCAGATAAGTATAGCCGAAG-C-TATTAC-TTA
1 TCACTTGATCAGATAAGTATAGCCGAAGACTTATCACTTTA
48320491 TCACTT
1 TCACTT
48320497 TCCACTTGTC
Statistics
Matches: 89, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
38 9 0.10
39 5 0.06
40 1 0.01
46 74 0.83
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.33
Consensus pattern (41 bp):
TCACTTGATCAGATAAGTATAGCCGAAGACTTATCACTTTA
Found at i:48323999 original size:21 final size:22
Alignment explanation
Indices: 48323952--48324008 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
48323942 TTGGGTAATT
48323952 TCAATCCCTCAATTTTCCACCA
1 TCAATCCCTCAATTTTCCACCA
*
48323974 CCAATCCCTCAATTTT-CACCA
1 TCAATCCCTCAATTTTCCACCA
*
48323995 TCAATCCATCAATT
1 TCAATCCCTCAATT
48324009 ATCATCTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.30, C:0.39, G:0.00, T:0.32
Consensus pattern (22 bp):
TCAATCCCTCAATTTTCCACCA
Found at i:48325884 original size:41 final size:41
Alignment explanation
Indices: 48325838--48325949 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
48325828 TTCAACTTCA
* * *
48325838 ATCTGCTCCACTGCCACTTTAGGGAGATGAGATTTGTTTTG
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTTTG
*
48325879 ATCTGCTCTACTGCAACTTTAGGGAGATAAGACTTGTTTTG
1 ATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTTTG
* * * * *
48325920 ATTTGTTCTACTGCAACTTCAGAGAGATAA
1 ATCTGCTCCACTGCAACTTTAGGGAGATAA
48325950 AACCTATGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (41 bp):
ATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTTTG
Found at i:48326055 original size:34 final size:34
Alignment explanation
Indices: 48326011--48326077 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
48326001 GATGTGCTAT
* * *
48326011 CTTCAGTCTACTCCACTGCAACTTCAGGGAGATA
1 CTTCAATCTACTCCACTGAAACTTCAAGGAGATA
*
48326045 CTTCAATCTACTCCGCTGAAACTTCAAGGAGAT
1 CTTCAATCTACTCCACTGAAACTTCAAGGAGAT
48326078 CTGCTGTGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (34 bp):
CTTCAATCTACTCCACTGAAACTTCAAGGAGATA
Found at i:48326264 original size:68 final size:68
Alignment explanation
Indices: 48326056--48326263 Score: 344
Period size: 68 Copynumber: 3.1 Consensus size: 68
48326046 TTCAATCTAC
48326056 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
48326121 AGA
66 AGA
* *
48326124 TCCGCTGAAACTTTAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTTAGGGAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
48326189 AGA
66 AGA
* * * * * *
48326192 TCCGTTGAAACTTCAAGAAAATCTGTTATGGCTTCAAGCCGCTCCAACGCCATTTCAGGGAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
48326257 AGA
66 AGA
48326260 TCCG
1 TCCG
48326264 TAATTCCCAG
Statistics
Matches: 130, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 130 1.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.24
Consensus pattern (68 bp):
TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
AGA
Found at i:48338573 original size:3 final size:3
Alignment explanation
Indices: 48338565--48338616 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
48338555 AATAATGTGG
* * *
48338565 TAA TAA TAA TAA TAA TAA TATA TACA TGAA TAA TAA CAG TAA CAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TA-A T-AA TAA TAA TAA TAA TAA TAA
48338613 TAA T
1 TAA T
48338617 GACACAACAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
3 32 0.80
4 7 0.17
5 1 0.03
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:48338825 original size:3 final size:3
Alignment explanation
Indices: 48338817--48338961 Score: 55
Period size: 3 Copynumber: 47.0 Consensus size: 3
48338807 TAGTCCTAAG
*
48338817 ATA ATA ATA ATA ATG ATA ATA ATA ATAA ATAA ATAA ATAA ATAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A AT-A AT-A ATA
** * * * *
48338864 ATA ACG ATA ATA CATT A-A ATT ATA ATA GTA A-A GTA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
48338908 GTG ATA ATC CTA AT- ATA TTA GACA ATA ATA GTA A-A ATA ATA AGCA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA
48338953 ATA ATA ATA
1 ATA ATA ATA
48338962 TATTAAATTA
Statistics
Matches: 104, Mismatches: 30, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
2 6 0.06
3 74 0.71
4 24 0.23
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:48338849 original size:4 final size:4
Alignment explanation
Indices: 48338840--48338864 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
48338830 TGATAATAAT
48338840 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
48338865 TAACGATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:48340077 original size:24 final size:25
Alignment explanation
Indices: 48340049--48340097 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
48340039 TGGGTTAGGA
*
48340049 TAGGTTGGGTTTTGGGC-TGTTGGG
1 TAGGTTGAGTTTTGGGCTTGTTGGG
*
48340073 TAGGTTTAGTTTTGGGCTTGTTGGG
1 TAGGTTGAGTTTTGGGCTTGTTGGG
48340098 GCCCGGGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.06, C:0.04, G:0.45, T:0.45
Consensus pattern (25 bp):
TAGGTTGAGTTTTGGGCTTGTTGGG
Found at i:48342437 original size:18 final size:17
Alignment explanation
Indices: 48342404--48342442 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
48342394 TTGTATAAAT
* *
48342404 TGTGAATTATTTTTGATA
1 TGTGAATTAATATTGA-A
48342422 TGTGAATTAATATTGAA
1 TGTGAATTAATATTGAA
48342439 TGTG
1 TGTG
48342443 GAAGGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TGTGAATTAATATTGAA
Found at i:48342537 original size:75 final size:75
Alignment explanation
Indices: 48342447--48342594 Score: 296
Period size: 75 Copynumber: 2.0 Consensus size: 75
48342437 AATGTGGAAG
48342447 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
1 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
48342512 GGTTGAACAT
66 GGTTGAACAT
48342522 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
1 GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
48342587 GGTTGAAC
66 GGTTGAAC
48342595 TTAGGAATAG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (75 bp):
GAAAGTTGTTCATGAATTATTCAAGTGATAAAGTGTTGAAAATAAAGTGTTAAGTGTAAATTCCC
GGTTGAACAT
Found at i:48342770 original size:23 final size:23
Alignment explanation
Indices: 48342743--48342840 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
48342733 AGTGTTATTG
48342743 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
48342766 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
48342789 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
48342811 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
48342834 ATCAGTG
1 ATCAGTG
48342841 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:48342809 original size:45 final size:45
Alignment explanation
Indices: 48342745--48342833 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
48342735 TGTTATTGAT
* *
48342745 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
48342790 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
48342834 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:48347994 original size:18 final size:17
Alignment explanation
Indices: 48347961--48347999 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
48347951 TTGTATAAAT
* *
48347961 TGTGAATTATTTTTGATA
1 TGTGAATTAATATTGA-A
48347979 TGTGAATTAATATTGAA
1 TGTGAATTAATATTGAA
48347996 TGTG
1 TGTG
48348000 GAAGGAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (17 bp):
TGTGAATTAATATTGAA
Found at i:48348252 original size:23 final size:23
Alignment explanation
Indices: 48348225--48348322 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
48348215 AGTGTTATTG
48348225 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
48348248 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
48348271 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
48348293 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
48348316 ATCAGTG
1 ATCAGTG
48348323 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:48348291 original size:45 final size:45
Alignment explanation
Indices: 48348227--48348315 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
48348217 TGTTATTGAT
* *
48348227 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
48348272 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
48348316 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:48350433 original size:55 final size:55
Alignment explanation
Indices: 48350367--48350481 Score: 221
Period size: 55 Copynumber: 2.1 Consensus size: 55
48350357 ATCAAGGCTG
*
48350367 AAGAATTGAGCAAAGAGAAAAGAAAGGTGGAAAGTGAAGCAAGAGATGAAAGAAA
1 AAGATTTGAGCAAAGAGAAAAGAAAGGTGGAAAGTGAAGCAAGAGATGAAAGAAA
48350422 AAGATTTGAGCAAAGAGAAAAGAAAGGTGGAAAGTGAAGCAAGAGATGAAAGAAA
1 AAGATTTGAGCAAAGAGAAAAGAAAGGTGGAAAGTGAAGCAAGAGATGAAAGAAA
48350477 AAGAT
1 AAGAT
48350482 CAAGGGGCAA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.56, C:0.03, G:0.30, T:0.10
Consensus pattern (55 bp):
AAGATTTGAGCAAAGAGAAAAGAAAGGTGGAAAGTGAAGCAAGAGATGAAAGAAA
Found at i:48353669 original size:8 final size:8
Alignment explanation
Indices: 48353656--48353684 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
48353646 CACTAGAGAC
48353656 CAGTGTTA
1 CAGTGTTA
48353664 CAGTGTTA
1 CAGTGTTA
48353672 CAGTGTTA
1 CAGTGTTA
48353680 CAGTG
1 CAGTG
48353685 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:48353798 original size:23 final size:23
Alignment explanation
Indices: 48353771--48353843 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
48353761 AGTGTTATTG
48353771 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
48353794 TTCAGTGGTAACTAT-GGCTACAT
1 ATCAGTGGTAGCT-TCGGCTACAT
48353817 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
48353840 ATCA
1 ATCA
48353844 ATGTGGCACT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 42 0.95
24 1 0.02
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:48360444 original size:19 final size:19
Alignment explanation
Indices: 48360401--48360446 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
48360391 TTTTTATTTT
*
48360401 TTATTTTTTTAATTTCATA
1 TTATTTTTTAAATTTCATA
*
48360420 TAATTTTTTAAATTTTC-TA
1 TTATTTTTTAAA-TTTCATA
48360439 TTATTTTT
1 TTATTTTT
48360447 GAATATCTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTTTTAAATTTCATA
Found at i:48360493 original size:18 final size:18
Alignment explanation
Indices: 48360472--48360559 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 18
48360462 TTTTTTTGTA
48360472 ATTTTATATTTTTTCCAT
1 ATTTTATATTTTTTCCAT
** *
48360490 ATTTTATAAGTTTTGCACT
1 ATTTTATATTTTTTCCA-T
*
48360509 -TTTCTATATTTTTAT-AAT
1 ATTT-TATATTTTT-TCCAT
*
48360527 ATTTT-TAATATTTTTCTAT
1 ATTTTAT-AT-TTTTTCCAT
48360546 ATTTTCATATTTTT
1 ATTTT-ATATTTTT
48360560 ACAAATTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
17 1 0.02
18 22 0.41
19 27 0.50
20 3 0.06
21 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.65
Consensus pattern (18 bp):
ATTTTATATTTTTTCCAT
Found at i:48360571 original size:39 final size:39
Alignment explanation
Indices: 48360508--48360600 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 39
48360498 AGTTTTGCAC
*
48360508 TTTTCTATATTTTTATAATATTTTTAATATTTTTCTAT-A
1 TTTTC-ATATTTTTAAAATATTTTTAATATTTTTCTATAA
* ** *
48360547 TTTTCATATTTTTACAAATTTTTTTTTTATTTTTCTTTAA
1 TTTTCATATTTTTA-AAATATTTTTAATATTTTTCTATAA
*
48360587 TTTATAATATTTTT
1 TTT-TCATATTTTT
48360601 TATAATTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 9 0.20
39 23 0.51
40 4 0.09
41 9 0.20
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (39 bp):
TTTTCATATTTTTAAAATATTTTTAATATTTTTCTATAA
Found at i:48360606 original size:19 final size:20
Alignment explanation
Indices: 48360574--48360611 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
48360564 ATTTTTTTTT
*
48360574 TATTTTTCTTTAATTTATAA
1 TATTTTTCTATAATTTATAA
48360594 TATTTTT-TATAATTTATA
1 TATTTTTCTATAATTTATA
48360612 TAAATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTTTCTATAATTTATAA
Found at i:48360686 original size:19 final size:17
Alignment explanation
Indices: 48360633--48360722 Score: 56
Period size: 19 Copynumber: 4.9 Consensus size: 17
48360623 TCATTTTAAT
*
48360633 TTTTATAATTCATTTTCACA
1 TTTTATAATT--TTTT-ATA
*
48360653 TTTTAT-ATATTTTATAA
1 TTTTATAATTTTTTAT-A
*
48360670 TTTTCATAATTTTTTATGG
1 TTTT-ATAATTTTTTAT-A
*
48360689 TTTTTTATATTTTTTATA
1 TTTTATA-ATTTTTTATA
*
48360707 TTTTTATGATTTTTTA
1 -TTTTATAATTTTTTA
48360723 ATTATTTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 12
0.73 0.12 0.16
Matches are distributed among these distances:
16 1 0.02
17 9 0.16
18 12 0.21
19 28 0.50
20 6 0.11
ACGTcount: A:0.26, C:0.04, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTATAATTTTTTATA
Found at i:48360692 original size:10 final size:9
Alignment explanation
Indices: 48360653--48360731 Score: 72
Period size: 9 Copynumber: 8.6 Consensus size: 9
48360643 CATTTTCACA
*
48360653 TTTTATATA
1 TTTTATATT
*
48360662 TTTTATAAT
1 TTTTATATT
*
48360671 TTTCATAATT
1 TTTTAT-ATT
*
48360681 TTTTATGGTT
1 TTTTAT-ATT
48360691 TTTTATATT
1 TTTTATATT
48360700 TTTTATA-T
1 TTTTATATT
48360708 TTTTATGATT
1 TTTTAT-ATT
48360718 TTTTA-ATT
1 TTTTATATT
48360726 ATTTTA
1 -TTTTA
48360732 AATATAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
8 10 0.17
9 27 0.47
10 21 0.36
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (9 bp):
TTTTATATT
Found at i:48360730 original size:27 final size:27
Alignment explanation
Indices: 48360653--48360731 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
48360643 CATTTTCACA
* * *
48360653 TTTTAT-ATATTTTATAATTTTCATAATT
1 TTTTATGATTTTTTATATTTTTTAT-A-T
*
48360681 TTTTATGGTTTTTTATATTTTTTATAT
1 TTTTATGATTTTTTATATTTTTTATAT
48360708 TTTTATGATTTTTTA-ATTATTTTA
1 TTTTATGATTTTTTATATT-TTTTA
48360732 AATATAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
26 3 0.07
27 20 0.45
28 7 0.16
29 14 0.32
ACGTcount: A:0.25, C:0.01, G:0.04, T:0.70
Consensus pattern (27 bp):
TTTTATGATTTTTTATATTTTTTATAT
Found at i:48362549 original size:32 final size:29
Alignment explanation
Indices: 48362513--48362577 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
48362503 TTAATAAATG
*
48362513 AATATACATAATTATTAAATATTAAATTAAAA
1 AATATAAAT-ATTATTAAA-A-TAAATTAAAA
* *
48362545 AATATAAATATTTTTAAAATAAATTTAAA
1 AATATAAATATTATTAAAATAAATTAAAA
48362574 AATA
1 AATA
48362578 ATATGAGTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 13 0.43
30 1 0.03
31 8 0.27
32 8 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AATATAAATATTATTAAAATAAATTAAAA
Found at i:48362581 original size:32 final size:34
Alignment explanation
Indices: 48362495--48362581 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 34
48362485 TTATTTATTT
* *
48362495 ATATAATTTTAATAAATGAATATACATAATTATTAA
1 ATATAAATTTAA-AAAT-AATATAAATAATTATTAA
*
48362531 ATATTAAA-TT-AAAA-AATATAAAT-ATTTTTAA
1 ATA-TAAATTTAAAAATAATATAAATAATTATTAA
48362562 A-ATAAATTTAAAAATAATAT
1 ATATAAATTTAAAAATAATAT
48362582 GAGTGGACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
29 4 0.09
30 3 0.07
31 12 0.27
32 13 0.30
34 3 0.07
35 1 0.02
36 5 0.11
37 3 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (34 bp):
ATATAAATTTAAAAATAATATAAATAATTATTAA
Found at i:48364022 original size:8 final size:8
Alignment explanation
Indices: 48364009--48364037 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
48363999 AATTTGGATA
48364009 TTATAATT
1 TTATAATT
48364017 TTATAATT
1 TTATAATT
48364025 TTATAATT
1 TTATAATT
48364033 TTATA
1 TTATA
48364038 TTCAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TTATAATT
Found at i:48381187 original size:20 final size:20
Alignment explanation
Indices: 48381125--48381188 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
48381115 TTTTAAACTT
*
48381125 TTTTAAAAATATAAATTTTGAA
1 TTTTAAAAA-AT-TATTTTGAA
* *
48381147 ATTTATATAAA-TATTTTGAA
1 TTTTA-AAAAATTATTTTGAA
48381167 TTTTAAAAAATTATTTTGAA
1 TTTTAAAAAATTATTTTGAA
48381187 TT
1 TT
48381189 ATTTTATTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.11
20 23 0.66
22 5 0.14
23 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTTAAAAAATTATTTTGAA
Found at i:48383015 original size:15 final size:15
Alignment explanation
Indices: 48382984--48383014 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
48382974 TAGAATAACC
48382984 TTCTTTTTTTTCTTT
1 TTCTTTTTTTTCTTT
48382999 TTCTTTTTTTT-TTT
1 TTCTTTTTTTTCTTT
48383013 TT
1 TT
48383015 TTTGTGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (15 bp):
TTCTTTTTTTTCTTT
Found at i:48383697 original size:12 final size:12
Alignment explanation
Indices: 48383679--48383710 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
48383669 ATTAAACCAA
48383679 AAAGGCTTGACC
1 AAAGGCTTGACC
*
48383691 CAAGGCTTGACC
1 AAAGGCTTGACC
48383703 AAAGGCTT
1 AAAGGCTT
48383711 CCCATATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (12 bp):
AAAGGCTTGACC
Found at i:48399724 original size:21 final size:20
Alignment explanation
Indices: 48399693--48399735 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
48399683 TTTATACTGA
48399693 AATTTTTTTA-TTCTATGATT
1 AATTTTTTTATTTCTAT-ATT
48399713 AATTTGTTTTATTTCTATATT
1 AATTT-TTTTATTTCTATATT
48399734 AA
1 AA
48399736 AGATGTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.63
Consensus pattern (20 bp):
AATTTTTTTATTTCTATATT
Found at i:48408728 original size:38 final size:38
Alignment explanation
Indices: 48408677--48409061 Score: 598
Period size: 38 Copynumber: 10.1 Consensus size: 38
48408667 ATATTCGATG
48408677 TATATCC-AGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGA-GTTAAATCCCGCAGGCTTCGTGCTGGTAA
*
48408715 TATATCCGAGTTAAATCCCGCAAGCTTCGTGCTGGTAA
1 TATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGTAA
48408753 TATATCC-AGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGA-GTTAAATCCCGCAGGCTTCGTGCTGGTAA
*
48408791 TATATCCGAGTTAAATCCCGCAAGCTTCGTGCTGGTAA
1 TATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* *
48408829 TATATCCGGGTTAAATCCCGCAAGCTTCGTGCTGGTAA
1 TATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGTAA
48408867 TATATCC-AGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGA-GTTAAATCCCGCAGGCTTCGTGCTGGTAA
*
48408905 TATATCCGAGTTAAATCCCGCAAGCTTCGTGCTGGTAA
1 TATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGTAA
48408943 TATATCC-AGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGA-GTTAAATCCCGCAGGCTTCGTGCTGGTAA
* * *
48408981 TATACCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGTAA
* * * *
48409019 TATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTAT
1 TATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGTAA
48409057 TATAT
1 TATAT
48409062 TCGGGCCTTT
Statistics
Matches: 326, Mismatches: 14, Indels: 14
0.92 0.04 0.04
Matches are distributed among these distances:
37 2 0.01
38 321 0.98
39 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (38 bp):
TATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGTAA
Found at i:48421195 original size:13 final size:13
Alignment explanation
Indices: 48421177--48421201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48421167 TTCTCTATTT
48421177 TCACACGGCCGTA
1 TCACACGGCCGTA
48421190 TCACACGGCCGT
1 TCACACGGCCGT
48421202 GTTGCCCCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (13 bp):
TCACACGGCCGTA
Found at i:48423775 original size:12 final size:12
Alignment explanation
Indices: 48423758--48423782 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48423748 TTGAATTGTG
48423758 TTAGGTTTTAGT
1 TTAGGTTTTAGT
48423770 TTAGGTTTTAGT
1 TTAGGTTTTAGT
48423782 T
1 T
48423783 CAAAATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (12 bp):
TTAGGTTTTAGT
Found at i:48427441 original size:14 final size:14
Alignment explanation
Indices: 48427422--48427450 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
48427412 AGATGAGATT
48427422 GTGTATAGACTACC
1 GTGTATAGACTACC
48427436 GTGTATAGACTACC
1 GTGTATAGACTACC
48427450 G
1 G
48427451 ACAGCTCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (14 bp):
GTGTATAGACTACC
Found at i:48430890 original size:110 final size:110
Alignment explanation
Indices: 48430692--48430908 Score: 398
Period size: 110 Copynumber: 2.0 Consensus size: 110
48430682 GAAAATGAAT
* * *
48430692 CATAGTTATGAAATAAATAACTTTTTTGAAAAGATTTCTCATGAAAACCCTAAAAAGGACCATTT
1 CATAGTTATGAAATAAACAACTTTTGTGAAAAGATTTATCATGAAAACCCTAAAAAGGACCATTT
*
48430757 TGCATAAGTTGTAAAATAGGTGATAAAGATGTGAAATATTGAAAC
66 TGCATAAGTTGTAAAATAAGTGATAAAGATGTGAAATATTGAAAC
48430802 CATAGTTATGAAATAAACAACTTTTGTGAAAAGATTTATCATGAAAACCCTAAAAAGGACCATTT
1 CATAGTTATGAAATAAACAACTTTTGTGAAAAGATTTATCATGAAAACCCTAAAAAGGACCATTT
48430867 TGCATAAGTTGTAAAATAAGTGATAAAGATGTGAAATATTGA
66 TGCATAAGTTGTAAAATAAGTGATAAAGATGTGAAATATTGA
48430909 GAATTTTGGA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 103 1.00
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (110 bp):
CATAGTTATGAAATAAACAACTTTTGTGAAAAGATTTATCATGAAAACCCTAAAAAGGACCATTT
TGCATAAGTTGTAAAATAAGTGATAAAGATGTGAAATATTGAAAC
Found at i:48431418 original size:47 final size:47
Alignment explanation
Indices: 48431352--48431528 Score: 159
Period size: 47 Copynumber: 3.7 Consensus size: 47
48431342 TTTATGTGCT
*
48431352 AGTGTAAGA-CATGTTTGGGACATG-CATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGACATCGG-CACATTATGAGAGCC
* * *
48431398 AGTGTAAGACCATGTCTGGGACATGACATTGGCACGGA-TACGGGAAAGCC
1 AGTGTAAGACCATGTCTGGGACATGACATCGGCAC--ATTA--TGAGAGCC
* *
48431448 AGTGTAAGACCATGTTTGGGACATGATATC-G-AC-TTGATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGACATCGGCACATT-AT-GA-GAGCC
* * *
48431495 AGTGTAAGACCGTGTCTGGGACATGGCATTGGCA
1 AGTGTAAGACCATGTCTGGGACATGACATCGGCA
48431529 TTATACCCAA
Statistics
Matches: 105, Mismatches: 14, Indels: 21
0.75 0.10 0.15
Matches are distributed among these distances:
46 12 0.11
47 47 0.45
48 10 0.10
49 3 0.03
50 33 0.31
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGACATCGGCACATTATGAGAGCC
Found at i:48431457 original size:50 final size:49
Alignment explanation
Indices: 48431394--48431528 Score: 152
Period size: 50 Copynumber: 2.8 Consensus size: 49
48431384 ACATTATGAG
48431394 AGCCAGTGTAAGACCATGTCTGGGACATGACATTGGCAC-GGATACGGGA-A
1 AGCCAGTGTAAGACCATGTCTGGGACATGACATTGGCACTGGAT---GGATA
* * * * *
48431444 AGCCAGTGTAAGACCATGTTTGGGACATGATA-TCG-ACTTGATGGATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGACATTGGCACTGGATGGATA
* *
48431491 AGCCAGTGTAAGACCGTGTCTGGGACATGGCATTGGCA
1 AGCCAGTGTAAGACCATGTCTGGGACATGACATTGGCA
48431529 TTATACCCAA
Statistics
Matches: 71, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
46 3 0.04
47 28 0.39
48 4 0.06
49 6 0.08
50 30 0.42
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (49 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGACATTGGCACTGGATGGATA
Found at i:48431494 original size:97 final size:95
Alignment explanation
Indices: 48431352--48431528 Score: 252
Period size: 97 Copynumber: 1.8 Consensus size: 95
48431342 TTTATGTGCT
48431352 AGTGTAAGACATGTTTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTTTGGGACATGCATCGG-CACATTATGAGAGCCAGTGTAAGACCATGTCTGG
48431417 GACATGACATTGGCACGGATACGGGAAAGCC
65 GACATGACATTGGCACGGATACGGGAAAGCC
* *
48431448 AGTGTAAGACCATGTTTGGGACATGATATC-G-AC-TTGATGGATGAGCCAGTGTAAGACCGTGT
1 AGTGTAAGA-CATGTTTGGGACATG-CATCGGCACATT-AT-GA-GAGCCAGTGTAAGACCATGT
*
48431510 CTGGGACATGGCATTGGCA
61 CTGGGACATGACATTGGCA
48431529 TTATACCCAA
Statistics
Matches: 73, Mismatches: 3, Indels: 9
0.86 0.04 0.11
Matches are distributed among these distances:
94 2 0.03
95 4 0.05
96 11 0.15
97 53 0.73
98 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (95 bp):
AGTGTAAGACATGTTTGGGACATGCATCGGCACATTATGAGAGCCAGTGTAAGACCATGTCTGGG
ACATGACATTGGCACGGATACGGGAAAGCC
Found at i:48433249 original size:27 final size:26
Alignment explanation
Indices: 48433201--48433281 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 26
48433191 GCAAGGCTGC
* * * *
48433201 CAGATATTGCGACGGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
48433228 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
48433254 CAGATATATGTGGCAGAGCCACTAGAA
1 CAGATAT-TGTGGCAGAGCCACCAGAA
48433281 C
1 C
48433282 GCTTCCTCCA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 8 0.17
27 40 0.83
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:48434697 original size:15 final size:15
Alignment explanation
Indices: 48434677--48434707 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
48434667 GATAGAAGCA
48434677 AACTACCATGAACTT
1 AACTACCATGAACTT
48434692 AACTACCATGAACTT
1 AACTACCATGAACTT
48434707 A
1 A
48434708 CCTTCAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (15 bp):
AACTACCATGAACTT
Found at i:48434921 original size:26 final size:26
Alignment explanation
Indices: 48434891--48434998 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
48434881 TGAAATTCCC
48434891 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
48434917 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
48434943 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
48434969 ACCATGGAACATTAACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
48434995 ATCA
1 ATCA
48434999 ATTTGTATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.37, C:0.28, G:0.06, T:0.29
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:48437286 original size:25 final size:26
Alignment explanation
Indices: 48437253--48437306 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
48437243 AGACTAGGAG
*
48437253 TTCATTTTTTAAGTTTAAATAAACTT
1 TTCATTTTTTAAGTTGAAATAAACTT
48437279 TTCATTTTTTAAGTTGAAATAAACTT
1 TTCATTTTTTAAGTTGAAATAAACTT
48437305 TT
1 TT
48437307 ACAATTCAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.54
Consensus pattern (26 bp):
TTCATTTTTTAAGTTGAAATAAACTT
Found at i:48442551 original size:23 final size:23
Alignment explanation
Indices: 48442506--48443194 Score: 439
Period size: 23 Copynumber: 30.2 Consensus size: 23
48442496 ACATAAATTA
*
48442506 AATTT-CAGCAAC-TAAACAATTC
1 AATTTGCAGC-ACTTAAACACTTC
* *
48442528 AATTTGCAGTACTTAAAAACTTC
1 AATTTGCAGCACTTAAACACTTC
* * *
48442551 AATTTACAACACTTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
48442574 AATTAGCAGCACTTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
48442597 AATTTGCAGCACTTTAACAATTC
1 AATTTGCAGCACTTAAACACTTC
* * *
48442620 AATTTACAACATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
*
48442643 AATTTGCAGCACTTTAACA-TCTC
1 AATTTGCAGCACTTAAACACT-TC
** * * * * *
48442666 AATTAACAACATTTATACTCCTC
1 AATTTGCAGCACTTAAACACTTC
* *
48442689 AA-TTACAGC-GTTAAA-ACATCTC
1 AATTTGCAGCACTTAAACAC-T-TC
*
48442711 AATTTCCAGCAAC-TAAACACTTC
1 AATTTGCAGC-ACTTAAACACTTC
*
48442734 AATTTGCAGTACTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* * *
48442757 AATTTAC-GACATTTGAACACTTC
1 AATTTGCAG-CACTTAAACACTTC
* * *
48442780 AATTTACAACA-TTCAAACACTTA
1 AATTTGCAGCACTT-AAACACTTC
*
48442803 AATTTGCAGCACTTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
48442826 AATTTACAGCATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
**
48442849 AATTTGCAGCACTTTTACA-TCTC
1 AATTTGCAGCACTTAAACACT-TC
** * * * *
48442872 AATTAACAACATTTATACACCTC
1 AATTTGCAGCACTTAAACACTTC
** *
48442895 AA-TCACAGCGA-TAAAACA-TCTC
1 AATTTGCAGC-ACTTAAACACT-TC
*
48442917 AATTTCCAGCAAC-T--ACACTTC
1 AATTTGCAGC-ACTTAAACACTTC
* *
48442938 AATTTGTAGTACTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* * *
48442961 AATTTACAACATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* * *
48442984 AATTTACAGTATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
*
48443007 AATTTGCAGCACTTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
48443030 AATTTGCAACACTTTAACACTTC
1 AATTTGCAGCACTTAAACACTTC
* *
48443053 AATTTACAGCATTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
*
48443076 AATTTGCAGCACTTTAACA-TCTC
1 AATTTGCAGCACTTAAACACT-TC
** * * * * *
48443099 AATTAACAACATTTATACTCCTC
1 AATTTGCAGCACTTAAACACTTC
**
48443122 AATTAT--AG-TGTTAAA-ACATCTC
1 AATT-TGCAGCACTTAAACAC-T-TC
* * *
48443144 AATTTCCAGCAATTATACACTTC
1 AATTTGCAGCACTTAAACACTTC
*
48443167 AATTTGCAGTACTTAAACACTTC
1 AATTTGCAGCACTTAAACACTTC
48443190 AATTT
1 AATTT
48443195 ACTTCAATTT
Statistics
Matches: 516, Mismatches: 117, Indels: 67
0.74 0.17 0.10
Matches are distributed among these distances:
20 4 0.01
21 22 0.04
22 46 0.09
23 428 0.83
24 12 0.02
25 4 0.01
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.34
Consensus pattern (23 bp):
AATTTGCAGCACTTAAACACTTC
Found at i:48442596 original size:46 final size:45
Alignment explanation
Indices: 48442546--48443705 Score: 603
Period size: 46 Copynumber: 25.2 Consensus size: 45
48442536 GTACTTAAAA
*
48442546 ACTTCAATTTACAACACTTTAACACTTCAATTAGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAACACTTCAATTA-CAGCACTTTAAC
* * *
48442592 ACTTCAATTTGCAGCACTTTAACAATTCAATTTACAACA-TTTAAAC
1 ACTTCAATTTACAGCACTTTAACACTTCAA-TTACAGCACTTT-AAC
* *
48442638 ACTTCAATTTGCAGCACTTTAACA-TCTCAATTAACAACA-TTTATAC
1 ACTTCAATTTACAGCACTTTAACACT-TCAATT-ACAGCACTTTA-AC
* * * * * *
48442684 TCCTCAA-TTACAG--CGTTAAAACATCTCAATTTCCAGCAAC-TAAAC
1 ACTTCAATTTACAGCACTTTAACAC-T-TCAA-TTACAGC-ACTTTAAC
* * *
48442729 ACTTCAATTTGCAGTACTTAAACACTTCAATTTAC-G-ACATTTGAAC
1 ACTTCAATTTACAGCACTTTAACACTTCAA-TTACAGCAC-TTT-AAC
* * * *
48442775 ACTTCAATTTACAACA-TTCAAACACTTAAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTT-TAACACTTCAA-TTACAGCACTTTAAC
* *
48442821 ACTTCAATTTACAGCA-TTTAAACACTTCAATTTGCAGCACTTTTAC
1 ACTTCAATTTACAGCACTTT-AACACTTCAA-TTACAGCACTTTAAC
* * * * **
48442867 A-TCTCAATTAACAACA-TTTATACACCTCAATCACAGCGA-TAAAAC
1 ACT-TCAATTTACAGCACTTTA-ACACTTCAATTACAGC-ACTTTAAC
* ** * *
48442912 A-TCTCAATTTCCAGCAAC--T-ACACTTCAATTTGTAGTACTTAAAC
1 ACT-TCAATTTACAGC-ACTTTAACACTTCAA-TTACAGCACTTTAAC
* *
48442956 ACTTCAATTTACAACA-TTTAAACACTTCAATTTACAGTA-TTTAAAC
1 ACTTCAATTTACAGCACTTT-AACACTTCAA-TTACAGCACTTT-AAC
* * *
48443002 ACTTCAATTTGCAGCACTTTAACACTTCAATTTGCAACACTTTAAC
1 ACTTCAATTTACAGCACTTTAACACTTCAA-TTACAGCACTTTAAC
*
48443048 ACTTCAATTTACAGCA-TTTAAACACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCACTTT-AACACTTCAA-TTACAGCACTTTAAC
* * * * * *
48443094 A-TCTCAATTAACAACA-TTTATACTCCTCAATTATAG---TGTTAAA
1 ACT-TCAATTTACAGCACTTTA-ACACTTCAATTACAGCACT-TTAAC
* * * * *
48443137 ACATCTCAATTTCCAGCA-ATTATACACTTCAATTTGCAGTACTTAAAC
1 AC-T-TCAATTTACAGCACTTTA-ACACTTCAA-TTACAGCACTTTAAC
* * **
48443185 ACTTCAATTTACTTCAATTTACAACATTCAAACACTTCAATTTGTAGCACTTTAAC
1 ACTTCAATTTA---C-A---GC-AC-TT-TAACACTTCAA-TTACAGCACTTTAAC
* **
48443241 ACTTCAATTTGCAGCACTTTAACACTTCAATTTGTAGCACTTTAAC
1 ACTTCAATTTACAGCACTTTAACACTTCAA-TTACAGCACTTTAAC
* * * * **
48443287 A-TCTCAATTAACAACA-TTTATACCCCTCAATTACAGCGA-TCAAAC
1 ACT-TCAATTTACAGCACTTTA-ACACTTCAATTACAGC-ACTTTAAC
* * * * * * *
48443332 A-TCTCAATTTCCATCAAC-TAAATACTTCAATTTGCAGTACTTAAAC
1 ACT-TCAATTTACAGC-ACTTTAACACTTCAA-TTACAGCACTTTAAC
*
48443378 ACTTCAATTTACAACA-TTTAAACACTTCAATTTACAGCA-TTTAAAC
1 ACTTCAATTTACAGCACTTT-AACACTTCAA-TTACAGCACTTT-AAC
* *
48443424 ACTTCAATTTGCAGCACTTTAACA-TCTCAATTAACAACA-TTTATAC
1 ACTTCAATTTACAGCACTTTAACACT-TCAATT-ACAGCACTTTA-AC
* ** *
48443470 ACCTCAA-TTACAGCGA-TAAAACA-TCTCAATTTACAACA-TTTAAGC
1 ACTTCAATTTACAGC-ACTTTAACACT-TCAA-TTACAGCACTTTAA-C
*
48443515 ACTTCAATTTACAGCA-TTTAAACACTTCAATTTACAACA-TTTAAC
1 ACTTCAATTTACAGCACTTT-AACACTTCAA-TTACAGCACTTTAAC
*
48443560 ACTTCAATTTGCAGCACTTTAACACTTCAATTTACAGCAC-TTAAC
1 ACTTCAATTTACAGCACTTTAACACTTCAA-TTACAGCACTTTAAC
*
48443605 ACTTCAATTTGCAGCACTTTAACACTTCAATTTACAGCA-TTTAAAC
1 ACTTCAATTTACAGCACTTTAACACTTCAA-TTACAGCACTTT-AAC
* * *
48443651 ACTTCAATTTGCTGCACTTTAACA-TCTCAATTAACAACA-TTTATAC
1 ACTTCAATTTACAGCACTTTAACACT-TCAATT-ACAGCACTTTA-AC
*
48443697 ACCTCAATT
1 ACTTCAATT
48443706 AACATCTCAG
Statistics
Matches: 904, Mismatches: 126, Indels: 168
0.75 0.11 0.14
Matches are distributed among these distances:
42 1 0.00
43 23 0.03
44 21 0.02
45 251 0.28
46 529 0.59
47 22 0.02
48 15 0.02
49 3 0.00
50 1 0.00
52 1 0.00
53 2 0.00
54 1 0.00
56 33 0.04
57 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (45 bp):
ACTTCAATTTACAGCACTTTAACACTTCAATTACAGCACTTTAAC
Found at i:48442598 original size:69 final size:67
Alignment explanation
Indices: 48442520--48443660 Score: 707
Period size: 69 Copynumber: 16.5 Consensus size: 67
48442510 TCAGCAACTA
* * *
48442520 AACAATTCAATTTGCAGTACTTAAAAACTTCAATTTACAACACTTTAACACTTCAATTAGCAGCA
1 AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACA-TTTAACACTTCAATTA-CAGCA
48442585 CTTT
64 CTTT
* * *
48442589 AACACTTCAATTTGCAGCACTTTAACAATTCAATTTACAACATTTAAACACTTCAATTTGCAGCA
1 AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTT-AACACTTCAA-TTACAGCA
48442654 CTTT
64 CTTT
** * * * * * * * * *
48442658 AACA-TCTCAATTAACAACATTTATACTCCTCAA-TTACAGC-GTTAAAACATCTCAATTTCCAG
1 AACACT-TCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAACAC-T-TCAA-TTACAG
*
48442720 CAAC-TA
62 C-ACTTT
* * *
48442726 AACACTTCAATTTGCAGTACTTAAACACTTCAATTTACGACATTTGAACACTTCAATTTACAACA
1 AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTT-AACACTTCAA-TTACAGCA
*
48442791 -TTCA
64 CTT-T
* * * *
48442795 AACACTTAAATTTGCAGCACTTTAACACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCA
1 AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTT-AACACTTCAA-TTACAGCA
48442860 CTTT
64 CTTT
* ** * * * * * * ** *
48442864 TACA-TCTCAATTAACAACATTTATACACCTCAA-TCACAGCGATAAAACA-TCTCAATTTCCAG
1 AACACT-TCAATTTGCAGCACTTAAACACTTCAATTTACAAC-ATTTAACACT-TCAA-TTACAG
48442926 CAAC--T
62 C-ACTTT
* * *
48442931 -ACACTTCAATTTGTAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTACAGTA
1 AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTT-AACACTTCAA-TTACAGCA
48442995 -TTT
64 CTTT
* *
48442998 AAACACTTCAATTTGCAGCACTTTAACACTTCAATTTGCAACACTTTAACACTTCAATTTACAGC
1 -AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACA-TTTAACACTTCAA-TTACAGC
48443063 A-TTT
63 ACTTT
* * * * *
48443067 AAACACTTCAATTTGCAGCACTTTAACA-TCTCAATTAACAACATTTATACTCCTCAATTATAG-
1 -AACACTTCAATTTGCAGCACTTAAACACT-TCAATTTACAACATTTA-ACACTTCAATTACAGC
48443130 --TGTT
63 ACT-TT
* * * * * *
48443134 AAAACATCTCAATTTCCAGCAATTATACACTTCAATTTGCAGTAC-TTAAACACTTCAATTTACT
1 AACAC-T-TCAATTTGCAGCACTTAAACACTTCAATTTACA--ACATTTAACACTTCAA-TTA--
* *
48443198 TCAATTTACAACATTCA
59 -C-A---GC-AC-TT-T
* * * * **
48443215 AACACTTCAATTTGTAGCACTTTAACACTTCAATTTGCAGCACTTTAACACTTCAATTTGTAGCA
1 AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACA-TTTAACACTTCAA-TTACAGCA
48443280 CTTT
64 CTTT
** * * * * * * ** * *
48443284 AACA-TCTCAATTAACAACATTTATACCCCTCAA-TTACAGCGATCAAACA-TCTCAATTTCCAT
1 AACACT-TCAATTTGCAGCACTTAAACACTTCAATTTACAAC-ATTTAACACT-TCAA-TTACAG
*
48443346 CAAC-TA
62 C-ACTTT
* *
48443352 AATACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTACAGCA
1 AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTT-AACACTTCAA-TTACAGCA
48443417 -TTT
64 CTTT
* * *
48443420 AAACACTTCAATTTGCAGCACTTTAACA-TCTCAATTAACAACATTTATACACCTCAATTACAGC
1 -AACACTTCAATTTGCAGCACTTAAACACT-TCAATTTACAACATTTA-ACACTTCAATTACAGC
**
48443484 GA-TAA
63 -ACTTT
* * * * * *
48443489 AACA-TCTCAATTTACAACATTTAAGCACTTCAATTTACAGCATTTAAACACTTCAATTTACAAC
1 AACACT-TCAATTTGCAGCACTTAAACACTTCAATTTACAACATTT-AACACTTCAA-TTACAGC
48443553 A-TTT
63 ACTTT
* * * *
48443557 AACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAGCACTTAACACTTCAATTTGCAGCAC
1 AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAACACTTCAA-TTACAGCAC
48443622 TTT
65 TTT
* *
48443625 AACACTTCAATTTACAGCATTTAAACACTTCAATTT
1 AACACTTCAATTTGCAGCACTTAAACACTTCAATTT
48443661 GCTGCACTTT
Statistics
Matches: 838, Mismatches: 165, Indels: 139
0.73 0.14 0.12
Matches are distributed among these distances:
66 34 0.04
67 48 0.06
68 286 0.34
69 395 0.47
70 15 0.02
71 6 0.01
72 1 0.00
73 1 0.00
75 1 0.00
77 1 0.00
79 43 0.05
80 2 0.00
81 5 0.01
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (67 bp):
AACACTTCAATTTGCAGCACTTAAACACTTCAATTTACAACATTTAACACTTCAATTACAGCACT
TT
Found at i:48443282 original size:193 final size:183
Alignment explanation
Indices: 48442974--48443648 Score: 685
Period size: 193 Copynumber: 3.7 Consensus size: 183
48442964 TTACAACATT
* * * * *
48442974 TAAACACTTCAATTTACAGTATTTAAACACTTCAATTTGCAGCACTT-TAACACTTCAATTTGCA
1 TAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACA-TTCAAACACTTCAATTTGCA
* *
48443038 ACACTTTAACACTTCAATTTACAGCA-TTTAAACACTTCAATTTGCAGCACTTTAACATCTCAAT
65 GCACTTTAACACTTCAATTTGCAGCACTTT-AACACTTCAATTTGCAGCACTTTAACATCTCAAT
* * * * *
48443102 TAACAACATTTATACTCCTCAATTATAGTGTTAAAACATCTCAATTTCCAGCAAT
129 TAACAACATTTATACCCCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAAC
*
48443157 TATACACTTCAATTTGCAGTACTTAAACACTTCAATTTACTTCAATTTACAACATTCAAACACTT
1 TAAACACTTCAATTTGCAGTACTT-AA-A---C-----ACTTCAATTTACAACATTCAAACACTT
* *
48443222 CAATTTGTAGCACTTTAACACTTCAATTTGCAGCACTTTAACACTTCAATTTGTAGCACTTTAAC
56 CAATTTGCAGCACTTTAACACTTCAATTTGCAGCACTTTAACACTTCAATTTGCAGCACTTTAAC
* *
48443287 ATCTCAATTAACAACATTTATACCCCTCAATTACAGCGATCAAACATCTCAATTTCCATCAAC
121 ATCTCAATTAACAACATTTATACCCCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAAC
* * *
48443350 TAAATACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTACAG
1 TAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTCAAACACTTCAATTTGCAG
** * *
48443415 CA-TTTAAACACTTCAATTTGCAGCACTTTAACA-TCTCAATTAACAACA-TTTATACACCTCAA
66 CACTTT-AACACTTCAATTTGCAGCACTTTAACACT-TCAATTTGCAGCACTTTA-ACATCTCAA
* * * ** * * * * **
48443477 TT-ACAGCGA-TAAAACATCTCAATTTACAAC-ATTTAAGCA-CTTCAATTTACAGCATT
128 TTAACAAC-ATTTATACCCCTCAA-TTACAGCGA-TAAAACATC-TCAATTTCCAGCAAC
* * * * * *
48443533 TAAACACTTCAATTTACA--ACATTTAACACTTCAATTTGCAGCACTT-TAACACTTCAATTTAC
1 TAAACACTTCAATTTGCAGTAC-TTAAACACTTCAATTTACAACA-TTCAAACACTTCAATTTGC
*
48443595 AGCAC-TTAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAGCA-TTTAA
64 AGCACTTTAACACTTCAATTTGCAGCACTTTAACACTTCAATTTGCAGCACTTTAA
48443649 ACACTTCAAT
Statistics
Matches: 422, Mismatches: 47, Indels: 49
0.81 0.09 0.09
Matches are distributed among these distances:
180 1 0.00
181 44 0.10
182 64 0.15
183 144 0.34
184 2 0.00
185 1 0.00
188 2 0.00
191 1 0.00
192 4 0.01
193 156 0.37
194 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (183 bp):
TAAACACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTCAAACACTTCAATTTGCAG
CACTTTAACACTTCAATTTGCAGCACTTTAACACTTCAATTTGCAGCACTTTAACATCTCAATTA
ACAACATTTATACCCCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAAC
Found at i:48443458 original size:160 final size:159
Alignment explanation
Indices: 48443195--48443613 Score: 603
Period size: 160 Copynumber: 2.6 Consensus size: 159
48443185 ACTTCAATTT
* ** *
48443195 ACTTCAATTTACAACA-TTCAAACACTTCAATTTGTAGCACTTTAACACTTCAATTTGCAGCACT
1 ACTTCAATTTACAGCACTT-AAACACTTCAATTTACAACA-TTTAACACTTCAATTTGCAGCACT
* *
48443259 TTAACACTTCAATTTGTAGCACTTTAACATCTCAATTAACAACATTTATACCCCTCAATTACAGC
64 TTAACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGC
* * * *
48443324 GATCAAACATCTCAATTTCCATCAACTAAAT
129 GATAAAACATCTCAATTTACAACAACTAAAC
* * *
48443355 ACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACATTTAAACACTTCAATTTACAGCA-TT
1 ACTTCAATTTACAGCACTTAAACACTTCAATTTACAACATTT-AACACTTCAATTTGCAGCACTT
48443419 TAAACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGC
65 T-AACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGC
** *
48443484 GATAAAACATCTCAATTTACAACATTTAAGC
129 GATAAAACATCTCAATTTACAACAACTAAAC
*
48443515 ACTTCAATTTACAGCATTTAAACACTTCAATTTACAACATTTAACACTTCAATTTGCAGCACTTT
1 ACTTCAATTTACAGCACTTAAACACTTCAATTTACAACATTTAACACTTCAATTTGCAGCACTTT
*
48443580 AACACTTCAATTTACAGCAC-TTAACA-CTTCAATT
66 AACACTTCAATTTGCAGCACTTTAACATC-TCAATT
48443614 TGCAGCACTT
Statistics
Matches: 233, Mismatches: 21, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
157 1 0.00
158 12 0.05
159 43 0.18
160 175 0.75
161 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.33
Consensus pattern (159 bp):
ACTTCAATTTACAGCACTTAAACACTTCAATTTACAACATTTAACACTTCAATTTGCAGCACTTT
AACACTTCAATTTGCAGCACTTTAACATCTCAATTAACAACATTTATACACCTCAATTACAGCGA
TAAAACATCTCAATTTACAACAACTAAAC
Found at i:48443522 original size:68 final size:69
Alignment explanation
Indices: 48443195--48443660 Score: 397
Period size: 68 Copynumber: 6.8 Consensus size: 69
48443185 ACTTCAATTT
* ** * *
48443195 ACTTCAATTTACAACA-TTCAAACACTTCAATTTGTAGCACTTTAACACTTCAATTTGCAGCACT
1 ACTTCAATTTACAGCACTT-AAACACTTCAATTTACAGCACTTTAACACTTCAATTTACAACA-T
48443259 TT-AAC
64 TTAAAC
** * * * * * *
48443264 ACTTCAATTTGTAGCACTTTAACA-TCTCAATTAACAACA-TTTATACCCCTCAA-TTACAGCGA
1 ACTTCAATTTACAGCACTTAAACACT-TCAATTTACAGCACTTTA-ACACTTCAATTTACAAC-A
*
48443326 -TCAAAC
63 TTTAAAC
* * * * * *
48443332 A-TCTCAATTTCCATCAAC-TAAATACTTCAATTTGCAGTACTTAAACACTTCAATTTACAACAT
1 ACT-TCAATTTACAGC-ACTTAAACACTTCAATTTACAGCACTTTAACACTTCAATTTACAACAT
48443395 TTAAAC
64 TTAAAC
* * *
48443401 ACTTCAATTTACAGCATTTAAACACTTCAATTTGCAGCACTTTAACA-TCTCAATTAACAACATT
1 ACTTCAATTTACAGCACTTAAACACTTCAATTTACAGCACTTTAACACT-TCAATTTACAACATT
*
48443465 TATAC
65 TAAAC
* * * *
48443470 ACCTCAA-TTACAGCGA-TAAAACA-TCTCAATTTACAACA-TTTAAGCACTTCAATTTACAGCA
1 ACTTCAATTTACAGC-ACTTAAACACT-TCAATTTACAGCACTTTAA-CACTTCAATTTACAACA
48443531 TTTAAAC
63 TTTAAAC
* * * * *
48443538 ACTTCAATTTACAACA-TTTAACACTTCAATTTGCAGCACTTTAACACTTCAATTTACAGCACTT
1 ACTTCAATTTACAGCACTTAAACACTTCAATTTACAGCACTTTAACACTTCAATTTACAACATTT
48443602 -AAC
66 AAAC
* *
48443605 ACTTCAATTTGCAGCACTTTAACACTTCAATTTACAGCA-TTTAAACACTTCAATTT
1 ACTTCAATTTACAGCACTTAAACACTTCAATTTACAGCACTTT-AACACTTCAATTT
48443661 GCTGCACTTT
Statistics
Matches: 323, Mismatches: 51, Indels: 47
0.77 0.12 0.11
Matches are distributed among these distances:
67 28 0.09
68 166 0.51
69 126 0.39
70 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (69 bp):
ACTTCAATTTACAGCACTTAAACACTTCAATTTACAGCACTTTAACACTTCAATTTACAACATTT
AAAC
Found at i:48443709 original size:23 final size:22
Alignment explanation
Indices: 48443195--48443705 Score: 406
Period size: 23 Copynumber: 22.4 Consensus size: 22
48443185 ACTTCAATTT
* *
48443195 ACTTCAATTTACAACATTCAAAC
1 ACTTCAATTTACAGCATT-TAAC
**
48443218 ACTTCAATTTGTAGCACTTTAAC
1 ACTTCAATTTACAGCA-TTTAAC
*
48443241 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCA-TTTAAC
**
48443264 ACTTCAATTTGTAGCACTTTAAC
1 ACTTCAATTTACAGCA-TTTAAC
* *
48443287 A-TCTCAATTAACAACATTTATAC
1 ACT-TCAATTTACAGCATTTA-AC
* * **
48443310 CCCTCAA-TTACAGCGATCAAAC
1 ACTTCAATTTACAGC-ATTTAAC
* * * * *
48443332 A-TCTCAATTTCCATCAACTAAAT
1 ACT-TCAATTTACAGC-ATTTAAC
* * *
48443355 ACTTCAATTTGCAGTACTTAAAC
1 ACTTCAATTTACAGCA-TTTAAC
*
48443378 ACTTCAATTTACAACATTTAAAC
1 ACTTCAATTTACAGCATTT-AAC
48443401 ACTTCAATTTACAGCATTTAAAC
1 ACTTCAATTTACAGCATTT-AAC
*
48443424 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCA-TTTAAC
* *
48443447 A-TCTCAATTAACAACATTTATAC
1 ACT-TCAATTTACAGCATTTA-AC
* **
48443470 ACCTCAA-TTACAGCGATAAAAC
1 ACTTCAATTTACAGC-ATTTAAC
*
48443492 A-TCTCAATTTACAACATTTAAGC
1 ACT-TCAATTTACAGCATTTAA-C
48443515 ACTTCAATTTACAGCATTTAAAC
1 ACTTCAATTTACAGCATTT-AAC
*
48443538 ACTTCAATTTACAACATTTAAC
1 ACTTCAATTTACAGCATTTAAC
*
48443560 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCA-TTTAAC
*
48443583 ACTTCAATTTACAGCACTTAAC
1 ACTTCAATTTACAGCATTTAAC
*
48443605 ACTTCAATTTGCAGCACTTTAAC
1 ACTTCAATTTACAGCA-TTTAAC
48443628 ACTTCAATTTACAGCATTTAAAC
1 ACTTCAATTTACAGCATTT-AAC
* *
48443651 ACTTCAATTTGCTGCACTTTAAC
1 ACTTCAATTTACAGCA-TTTAAC
* *
48443674 A-TCTCAATTAACAACATTTATAC
1 ACT-TCAATTTACAGCATTTA-AC
*
48443697 ACCTCAATT
1 ACTTCAATT
48443706 AACATCTCAG
Statistics
Matches: 398, Mismatches: 63, Indels: 54
0.77 0.12 0.10
Matches are distributed among these distances:
22 85 0.21
23 301 0.76
24 12 0.03
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (22 bp):
ACTTCAATTTACAGCATTTAAC
Found at i:48447979 original size:41 final size:41
Alignment explanation
Indices: 48447911--48448029 Score: 121
Period size: 41 Copynumber: 2.9 Consensus size: 41
48447901 GGTAAATAAT
* * ** * *
48447911 GGCGTTTTCAACAAAAACGAAATTATAGCTCAATTTTTTAC
1 GGCGTTTTTACCAAAAACGCTACTATAGCTTAATTTTTTAC
* * **
48447952 GGTGTTTTTATCAAAAACGCTACTATAGCTTAATTTTTTGT
1 GGCGTTTTTACCAAAAACGCTACTATAGCTTAATTTTTTAC
* * *
48447993 GGCGTTTTTCCCAAAAACGTTACTATTGCTTAATTTT
1 GGCGTTTTTACCAAAAACGCTACTATAGCTTAATTTT
48448030 ATTTTTTTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (41 bp):
GGCGTTTTTACCAAAAACGCTACTATAGCTTAATTTTTTAC
Found at i:48448180 original size:7 final size:7
Alignment explanation
Indices: 48448164--48448224 Score: 77
Period size: 7 Copynumber: 8.4 Consensus size: 7
48448154 ATATTAAATA
48448164 TTTAAGTT
1 TTTAA-TT
48448172 TTTAATT
1 TTTAATT
48448179 TTTAATT
1 TTTAATT
48448186 TTTAATT
1 TTTAATT
*
48448193 TTTAAAT
1 TTTAATT
*
48448200 TTTAAAT
1 TTTAATT
*
48448207 TTTAAAT
1 TTTAATT
48448214 TTTACATT
1 TTTA-ATT
48448222 TTT
1 TTT
48448225 TTGAAGATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
7 40 0.80
8 10 0.20
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (7 bp):
TTTAATT
Found at i:48448196 original size:21 final size:21
Alignment explanation
Indices: 48448157--48448224 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
48448147 GACTAAAATA
48448157 TTAAATATTTAAGTTTTTAATTT
1 TTAAAT-TTTAA-TTTTTAATTT
* *
48448180 TTAATTTTTAATTTTTAAATT
1 TTAAATTTTAATTTTTAATTT
*
48448201 TTAAATTTTAAATTTTACATTT
1 TTAAATTTTAATTTTTA-ATTT
48448223 TT
1 TT
48448225 TTGAAGATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 24 0.62
22 10 0.26
23 5 0.13
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (21 bp):
TTAAATTTTAATTTTTAATTT
Found at i:48448243 original size:9 final size:8
Alignment explanation
Indices: 48448157--48448250 Score: 74
Period size: 7 Copynumber: 11.9 Consensus size: 8
48448147 GACTAAAATA
*
48448157 TTAAATAT
1 TTAAATTT
*
48448165 TTAAGTTT
1 TTAAATTT
48448173 TT-AATTT
1 TTAAATTT
48448180 TT-AATTT
1 TTAAATTT
48448187 TT-AATTT
1 TTAAATTT
48448194 TTAAA-TT
1 TTAAATTT
48448201 TTAAA-TT
1 TTAAATTT
48448208 TTAAA-TT
1 TTAAATTT
*
48448215 TTACATTTTT
1 TTA-A-ATTT
48448225 TTGAAGATTT
1 TT-AA-ATTT
48448235 TTATAATTT
1 TTA-AATTT
48448244 TTAAATT
1 TTAAATT
48448251 ATCATATAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
7 39 0.53
8 15 0.20
9 8 0.11
10 11 0.15
11 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (8 bp):
TTAAATTT
Found at i:48449110 original size:21 final size:21
Alignment explanation
Indices: 48449069--48449110 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48449059 AACAATAAAT
* *
48449069 CATAAACCCCAAACTCTAAAC
1 CATAAACCCCAAAATCAAAAC
*
48449090 CATAAACCCTAAAATCAAAAC
1 CATAAACCCCAAAATCAAAAC
48449111 TCTAATAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.14
Consensus pattern (21 bp):
CATAAACCCCAAAATCAAAAC
Found at i:48449187 original size:36 final size:37
Alignment explanation
Indices: 48449126--48449215 Score: 96
Period size: 36 Copynumber: 2.5 Consensus size: 37
48449116 TAACAAAATA
* *
48449126 ATAAACATTATATCATAAACCCTAAAACCTC-AAACC
1 ATAAACATTAAATCATAAACCCTAAAACCCCTAAACC
* ** *
48449162 ATAAACATTAAATCTTAAATTCTAAACCCCCTAAACC
1 ATAAACATTAAATCATAAACCCTAAAACCCCTAAACC
48449199 ATAAATCA-TAAA-CATAA
1 ATAAA-CATTAAATCATAA
48449216 TCTCTAAACC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
36 29 0.64
37 14 0.31
38 2 0.04
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (37 bp):
ATAAACATTAAATCATAAACCCTAAAACCCCTAAACC
Found at i:48449308 original size:15 final size:15
Alignment explanation
Indices: 48449281--48449318 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
48449271 TACTCTTAAA
48449281 CCATAAA-CCATAAT
1 CCATAAACCCATAAT
*
48449295 CCCTAAACCCATAAT
1 CCATAAACCCATAAT
48449310 CCATAAACC
1 CCATAAACC
48449319 TTAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (15 bp):
CCATAAACCCATAAT
Found at i:48449323 original size:22 final size:21
Alignment explanation
Indices: 48449275--48449323 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
48449265 AACCCCTACT
*
48449275 CTTAAACCATAAACCATAATC
1 CTTAAACCATAAACCATAAAC
* *
48449296 CCTAAACCCATAATCCATAAAC
1 CTTAAA-CCATAAACCATAAAC
48449318 CTTAAA
1 CTTAAA
48449324 ATATTTAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (21 bp):
CTTAAACCATAAACCATAAAC
Found at i:48463725 original size:39 final size:40
Alignment explanation
Indices: 48463680--48463864 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
48463670 GCTCCTCGTT
* * *
48463680 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
48463720 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
48463759 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
48463799 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
48463840 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
48463865 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:48463780 original size:40 final size:39
Alignment explanation
Indices: 48463647--48463864 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
48463637 AAATCACGTA
* * **
48463647 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
48463686 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
48463725 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
48463765 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
48463805 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
48463845 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
48463865 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:48471642 original size:40 final size:40
Alignment explanation
Indices: 48471544--48471846 Score: 380
Period size: 40 Copynumber: 7.6 Consensus size: 40
48471534 TCCTCGTTCA
* * * ** *
48471544 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
48471583 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
48471623 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
48471663 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
48471703 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
48471743 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
48471783 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
48471823 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
48471847 CAGCATTCAA
Statistics
Matches: 239, Mismatches: 20, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 194 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:48495362 original size:12 final size:12
Alignment explanation
Indices: 48495345--48495369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48495335 TATCTCCAAA
48495345 ATGAAAATGGAG
1 ATGAAAATGGAG
48495357 ATGAAAATGGAG
1 ATGAAAATGGAG
48495369 A
1 A
48495370 AATGGAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (12 bp):
ATGAAAATGGAG
Found at i:48495383 original size:63 final size:62
Alignment explanation
Indices: 48495296--48495416 Score: 181
Period size: 63 Copynumber: 1.9 Consensus size: 62
48495286 ATAGAAATGG
* *
48495296 TGAAAATGGAAAATGGGGATATTTGGAAATGATTATGGTTATCTCCAAAATGAAAATGGAGA
1 TGAAAATGGAAAATGGAGATATTTGGAAATGAATATGGTTATCTCCAAAATGAAAATGGAGA
* *
48495358 TGAAAATGGAGAAATGGAG-TCATTTGGAAATGAATGTGGTTTTCTCCAAAATGAAAATG
1 TGAAAATGGA-AAATGGAGAT-ATTTGGAAATGAATATGGTTATCTCCAAAATGAAAATG
48495417 ACCTGAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
62 11 0.21
63 42 0.79
ACGTcount: A:0.40, C:0.06, G:0.26, T:0.28
Consensus pattern (62 bp):
TGAAAATGGAAAATGGAGATATTTGGAAATGAATATGGTTATCTCCAAAATGAAAATGGAGA
Found at i:48500714 original size:22 final size:24
Alignment explanation
Indices: 48500642--48500751 Score: 97
Period size: 23 Copynumber: 4.8 Consensus size: 24
48500632 GATATATATT
*
48500642 AGCTCGTA-AGAGCTTACTGTTTTT
1 AGCTCGTATAGAGCTTACTG-TTTC
* * *
48500666 AGCTCAT-TGGAGCTTACCGTTTC
1 AGCTCGTATAGAGCTTACTGTTTC
48500689 AGCTCGTAT-GAGCTTACTG-TTC
1 AGCTCGTATAGAGCTTACTGTTTC
**
48500711 AGCTCG-ATAGAGCTTACCATTTC
1 AGCTCGTATAGAGCTTACTGTTTC
* *
48500734 AGGTC-AATAGAGCTTACT
1 AGCTCGTATAGAGCTTACT
48500752 CTCCATCAGC
Statistics
Matches: 71, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
21 2 0.03
22 17 0.24
23 36 0.51
24 16 0.23
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (24 bp):
AGCTCGTATAGAGCTTACTGTTTC
Found at i:48500734 original size:45 final size:46
Alignment explanation
Indices: 48500642--48500735 Score: 120
Period size: 45 Copynumber: 2.0 Consensus size: 46
48500632 GATATATATT
* * *
48500642 AGCTCGTAAGAGCTTACTGTTTTTAGCTCATTGGAGCTTACCGTTTC
1 AGCTCGTAAGAGCTTACTG-TTTCAGCTCATTAGAGCTTACCATTTC
*
48500689 AGCTCGTATGAGCTTACTG-TTCAGCTCGA-TAGAGCTTACCATTTC
1 AGCTCGTAAGAGCTTACTGTTTCAGCTC-ATTAGAGCTTACCATTTC
48500734 AG
1 AG
48500736 GTCAATAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 23 0.55
46 1 0.02
47 18 0.43
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (46 bp):
AGCTCGTAAGAGCTTACTGTTTCAGCTCATTAGAGCTTACCATTTC
Found at i:48504091 original size:33 final size:33
Alignment explanation
Indices: 48504054--48504125 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
48504044 ATACAAAAAG
48504054 GTTATTTGCCATCTAGTATTTATGGGTTCTTAT
1 GTTATTTGCCATCTAGTATTTATGGGTTCTTAT
48504087 GTTATTTGCCATCTAGTATTTATGGGTTCTTAT
1 GTTATTTGCCATCTAGTATTTATGGGTTCTTAT
48504120 GTTATT
1 GTTATT
48504126 GTAGCACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (33 bp):
GTTATTTGCCATCTAGTATTTATGGGTTCTTAT
Found at i:48522521 original size:54 final size:55
Alignment explanation
Indices: 48522420--48522557 Score: 170
Period size: 54 Copynumber: 2.5 Consensus size: 55
48522410 CAAGCCCTAT
** *
48522420 GCCCGTGTTAATTTAACAGGTTCGACCACAGGTGTTCCACACAGGCGTGTCGAAC
1 GCCCGTGTTGTTTTAACAGGTTCGACCACAGGTCTTCCACACAGGCGTGTCGAAC
* * * * *
48522475 GCCTGTGTTGTTTTAACAGGTTC-ACCACTGTTCTTCCACACGGGCGTGTCGCAC
1 GCCCGTGTTGTTTTAACAGGTTCGACCACAGGTCTTCCACACAGGCGTGTCGAAC
** *
48522529 GCCCGTGTTGTTTTGGCAGGCTCGACCAC
1 GCCCGTGTTGTTTTAACAGGTTCGACCAC
48522558 GGCCATATCG
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
54 45 0.64
55 25 0.36
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.28
Consensus pattern (55 bp):
GCCCGTGTTGTTTTAACAGGTTCGACCACAGGTCTTCCACACAGGCGTGTCGAAC
Found at i:48527095 original size:23 final size:23
Alignment explanation
Indices: 48527067--48527141 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
48527057 CAACTCATTG
48527067 GAGCTTACCGTTTCAGCTCG-TA
1 GAGCTTACCGTTTCAGCTCGATA
* * *
48527089 TGTGCTTACTG-TTCATCTCGATA
1 -GAGCTTACCGTTTCAGCTCGATA
* *
48527112 GAGCTTACCGTTTTAGCTCTATA
1 GAGCTTACCGTTTCAGCTCGATA
*
48527135 AAGCTTA
1 GAGCTTA
48527142 TTGTCCATCA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
22 16 0.39
23 25 0.61
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (23 bp):
GAGCTTACCGTTTCAGCTCGATA
Found at i:48531667 original size:30 final size:31
Alignment explanation
Indices: 48531631--48531706 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
48531621 TAATAATTAT
*
48531631 AAATTATAAATTTACTAATAATTTAGT-AAA
1 AAATTATAAATTTACTAATAATTCAGTGAAA
* * * *
48531661 AAATTATAAAGTTATTAATAATTCATTGAAT
1 AAATTATAAATTTACTAATAATTCAGTGAAA
*
48531692 AAATTGTAAATTTAC
1 AAATTATAAATTTAC
48531707 CCTTTTCCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
30 23 0.62
31 14 0.38
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTATAAATTTACTAATAATTCAGTGAAA
Found at i:48532824 original size:17 final size:17
Alignment explanation
Indices: 48532802--48532910 Score: 65
Period size: 17 Copynumber: 6.4 Consensus size: 17
48532792 CAAACATCTG
*
48532802 TTCATATAAAATAACAA
1 TTCATACAAAATAACAA
* *
48532819 TTCATACCAAATGACAA
1 TTCATACAAAATAACAA
* * * *
48532836 CTCATGCAAAATAATAG
1 TTCATACAAAATAACAA
** ** *
48532853 TTCATATGAAATATTAG
1 TTCATACAAAATAACAA
** *
48532870 TTCATACTGAATAATAA
1 TTCATACAAAATAACAA
* *
48532887 TTCATACAAAATAATAG
1 TTCATACAAAATAACAA
48532904 TTCATAC
1 TTCATAC
48532911 TCCATCATAA
Statistics
Matches: 70, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 70 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (17 bp):
TTCATACAAAATAACAA
Found at i:48532859 original size:51 final size:51
Alignment explanation
Indices: 48532801--48532909 Score: 128
Period size: 51 Copynumber: 2.1 Consensus size: 51
48532791 TCAAACATCT
* *
48532801 GTTCATATAAAATAACAATTCATACCAAATGACAACTCATGCAAAATAATA
1 GTTCATATAAAATAACAATTCATACCAAATAACAACTCATACAAAATAATA
* ** * ** * *
48532852 GTTCATATGAAATATTAGTTCATACTGAATAATAATTCATACAAAATAATA
1 GTTCATATAAAATAACAATTCATACCAAATAACAACTCATACAAAATAATA
48532903 GTTCATA
1 GTTCATA
48532910 CTCCATCATA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (51 bp):
GTTCATATAAAATAACAATTCATACCAAATAACAACTCATACAAAATAATA
Found at i:48532883 original size:34 final size:34
Alignment explanation
Indices: 48532845--48532911 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
48532835 ACTCATGCAA
* ** *
48532845 AATAATAGTTCATATGAAATATTAGTTCATACTG
1 AATAATAATTCATACAAAATAATAGTTCATACTG
48532879 AATAATAATTCATACAAAATAATAGTTCATACT
1 AATAATAATTCATACAAAATAATAGTTCATACT
48532912 CCATCATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.46, C:0.10, G:0.07, T:0.36
Consensus pattern (34 bp):
AATAATAATTCATACAAAATAATAGTTCATACTG
Found at i:48532926 original size:34 final size:34
Alignment explanation
Indices: 48532861--48532926 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
48532851 AGTTCATATG
* * *
48532861 AAATATTAGTTCATACTGAATAATAATTCATACA
1 AAATAATAGTTCATACTCAATAATAACTCATACA
* *
48532895 AAATAATAGTTCATACTCCATCATAACTCATA
1 AAATAATAGTTCATACTCAATAATAACTCATA
48532927 TATTTCAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (34 bp):
AAATAATAGTTCATACTCAATAATAACTCATACA
Found at i:48543088 original size:40 final size:40
Alignment explanation
Indices: 48543005--48543347 Score: 467
Period size: 40 Copynumber: 8.6 Consensus size: 40
48542995 TTGAATGCTG
* * * * * *
48543005 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
48543045 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
48543085 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
48543125 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
48543165 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
48543205 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
48543245 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
48543285 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
48543324 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
48543348 TGAACGAGGA
Statistics
Matches: 281, Mismatches: 19, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.12
40 238 0.85
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:48548621 original size:56 final size:56
Alignment explanation
Indices: 48548535--48548760 Score: 452
Period size: 56 Copynumber: 4.0 Consensus size: 56
48548525 TGGTATCAGA
48548535 GCTATGGTTTAGTCGGTTCTAGGACTACCATAGCGCGTATGAGTCTAGCTATACAT
1 GCTATGGTTTAGTCGGTTCTAGGACTACCATAGCGCGTATGAGTCTAGCTATACAT
48548591 GCTATGGTTTAGTCGGTTCTAGGACTACCATAGCGCGTATGAGTCTAGCTATACAT
1 GCTATGGTTTAGTCGGTTCTAGGACTACCATAGCGCGTATGAGTCTAGCTATACAT
48548647 GCTATGGTTTAGTCGGTTCTAGGACTACCATAGCGCGTATGAGTCTAGCTATACAT
1 GCTATGGTTTAGTCGGTTCTAGGACTACCATAGCGCGTATGAGTCTAGCTATACAT
48548703 GCTATGGTTTAGTCGGTTCTAGGACTACCATAGCGCGTATGAGTCTAGCTATACAT
1 GCTATGGTTTAGTCGGTTCTAGGACTACCATAGCGCGTATGAGTCTAGCTATACAT
48548759 GC
1 GC
48548761 CTTAATGTTA
Statistics
Matches: 170, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 170 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (56 bp):
GCTATGGTTTAGTCGGTTCTAGGACTACCATAGCGCGTATGAGTCTAGCTATACAT
Found at i:48555011 original size:28 final size:28
Alignment explanation
Indices: 48554966--48555117 Score: 247
Period size: 27 Copynumber: 5.5 Consensus size: 28
48554956 TAAATTGTGC
48554966 AGCACTAAGTGTG-GAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48554993 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
48555021 AGCACTAAGTGTGCGAG-TTGACTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
48555048 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
* *
48555076 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGACTATGT
*
48555103 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
48555118 GACTTAATAT
Statistics
Matches: 120, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
27 63 0.52
28 57 0.47
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:48555031 original size:55 final size:55
Alignment explanation
Indices: 48554966--48555117 Score: 252
Period size: 55 Copynumber: 2.8 Consensus size: 55
48554956 TAAATTGTGC
48554966 AGCACTAAGTGTG-GAGTTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
48555021 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
48555076 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
48555118 GACTTAATAT
Statistics
Matches: 92, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
55 89 0.97
56 3 0.03
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.32
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:48574792 original size:22 final size:22
Alignment explanation
Indices: 48574764--48574808 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
48574754 AATAAGCAAG
48574764 TTGTTAATGTTATTGTTGTTTA
1 TTGTTAATGTTATTGTTGTTTA
48574786 TTGTTAATGTTATTGTTGTTTA
1 TTGTTAATGTTATTGTTGTTTA
48574808 T
1 T
48574809 GGCTAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (22 bp):
TTGTTAATGTTATTGTTGTTTA
Found at i:48574798 original size:12 final size:12
Alignment explanation
Indices: 48574764--48574802 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
48574754 AATAAGCAAG
48574764 TTGTTAATGTTA
1 TTGTTAATGTTA
*
48574776 TTGTT-GT-TTA
1 TTGTTAATGTTA
48574786 TTGTTAATGTTA
1 TTGTTAATGTTA
48574798 TTGTT
1 TTGTT
48574803 GTTTATGGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 8 0.35
11 2 0.09
12 13 0.57
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (12 bp):
TTGTTAATGTTA
Found at i:48575216 original size:43 final size:42
Alignment explanation
Indices: 48575151--48575260 Score: 148
Period size: 43 Copynumber: 2.6 Consensus size: 42
48575141 GGAATTAAGA
* *
48575151 AATCCGAGCTTGTTGAGCGGTCCGAGTTCGTGATATGTATGAG
1 AATCCGAGCTTGTTGAGTGGTCCGAGTTCGTGATATATATG-G
* * *
48575194 AATCCGAACTTGTTGAGTGGTCCAAGTTCGTGATATATGTGG
1 AATCCGAGCTTGTTGAGTGGTCCGAGTTCGTGATATATATGG
* *
48575236 CATCCGAGCTTGCTGAGTGGTCCGA
1 AATCCGAGCTTGTTGAGTGGTCCGA
48575261 ATTCATTATG
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
42 22 0.38
43 36 0.62
ACGTcount: A:0.21, C:0.18, G:0.31, T:0.30
Consensus pattern (42 bp):
AATCCGAGCTTGTTGAGTGGTCCGAGTTCGTGATATATATGG
Found at i:48578964 original size:22 final size:23
Alignment explanation
Indices: 48578921--48578966 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
48578911 TTTTAGGTCT
*
48578921 TTAGGAATTTATTTCTTTCATAA
1 TTAGGAATTTATTTCTTGCATAA
48578944 TTAGG-ATTTAATTTC-TGCATAA
1 TTAGGAATTT-ATTTCTTGCATAA
48578966 T
1 T
48578967 AAAACATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (23 bp):
TTAGGAATTTATTTCTTGCATAA
Found at i:48582510 original size:101 final size:102
Alignment explanation
Indices: 48582359--48582597 Score: 268
Period size: 101 Copynumber: 2.4 Consensus size: 102
48582349 AGACAAGGTT
* * * * * * * *
48582359 TTACTCGCACA-CATATATCCG-AATAACATTTCGATTCCAATGTATAAAACGTGGACTTACTTG
1 TTACTCACACATCACATATCAGAAATCACATATCGATGCCAACGTATAAAACGTGGACTTACTCG
* * * * *
48582422 TACATATATATCGAAATCACATATCGATGCCATGGTC
66 CACACATATATAGAAATCACACATCAATGCCATGGTC
* * *
48582459 TTACTCACATATCACATATCA-AAATCACATATCGATGCCAACGTATTAAACGTGGTCTTACTCG
1 TTACTCACACATCACATATCAGAAATCACATATCGATGCCAACGTATAAAACGTGGACTTACTCG
* *
48582523 CGCACATATATAGGAATCACACATCAATGCCATGGTC
66 CACACATATATAGAAATCACACATCAATGCCATGGTC
* * *
48582560 TTACTCGCACATCACATATCAGAATTCACATGTCGATG
1 TTACTCACACATCACATATCAGAAATCACATATCGATG
48582598 TCTCATATAC
Statistics
Matches: 114, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
100 9 0.08
101 91 0.80
102 14 0.12
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (102 bp):
TTACTCACACATCACATATCAGAAATCACATATCGATGCCAACGTATAAAACGTGGACTTACTCG
CACACATATATAGAAATCACACATCAATGCCATGGTC
Found at i:48584526 original size:7 final size:7
Alignment explanation
Indices: 48584514--48584546 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
48584504 ACATTTCTAT
48584514 TCATCCC
1 TCATCCC
48584521 TCATCCC
1 TCATCCC
*
48584528 TCATCAC
1 TCATCCC
48584535 TCATCCC
1 TCATCCC
48584542 TCATC
1 TCATC
48584547 ATTCATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.18, C:0.52, G:0.00, T:0.30
Consensus pattern (7 bp):
TCATCCC
Found at i:48584531 original size:14 final size:14
Alignment explanation
Indices: 48584514--48584553 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
48584504 ACATTTCTAT
*
48584514 TCATCCCTCATCCC
1 TCATCACTCATCCC
48584528 TCATCACTCATCCC
1 TCATCACTCATCCC
*
48584542 TCATCATTCATC
1 TCATCACTCATC
48584554 ATTCTCTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.20, C:0.47, G:0.00, T:0.33
Consensus pattern (14 bp):
TCATCACTCATCCC
Found at i:48584552 original size:21 final size:21
Alignment explanation
Indices: 48584514--48584554 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48584504 ACATTTCTAT
*
48584514 TCATCCCTCATCCCTCATCAC
1 TCATCCCTCATCACTCATCAC
*
48584535 TCATCCCTCATCATTCATCA
1 TCATCCCTCATCACTCATCA
48584555 TTCTCTCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.46, G:0.00, T:0.32
Consensus pattern (21 bp):
TCATCCCTCATCACTCATCAC
Found at i:48586208 original size:48 final size:48
Alignment explanation
Indices: 48586149--48586288 Score: 174
Period size: 48 Copynumber: 2.9 Consensus size: 48
48586139 GGGTTATGTG
* * * * ** *
48586149 TGATCCTATGTAAGACCATGTCTGTGACAAGGCATTGACATCGTTATGA
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGACA-CA
*
48586198 -GATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCGACACA
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGACACA
* *
48586245 TGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCGA
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGA
48586289 TGTGAGACAT
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
47 1 0.01
48 78 0.99
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (48 bp):
TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGACACA
Found at i:48586305 original size:48 final size:45
Alignment explanation
Indices: 48586147--48586377 Score: 153
Period size: 48 Copynumber: 5.0 Consensus size: 45
48586137 TAGGGTTATG
* * * * * * *
48586147 TGTGATCCTATGTAAGACCATGTCTGTGACAAGGCATTGACATCGTTA
1 TGTGAACCCATGTAAGACCATATCTGGGATATGGCATTGGCATC---A
* * * * *
48586195 TGAGATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCGACA
1 TGTGAACCCATGTAAGACCATATCTGGGATATGGCATTGGCAT---CA
** *
48586243 CATGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCGA
1 TGTGAACCCATGTAAGACCATATCTGGGATATGGCATTGGCATC-A
* * * * * * *
48586289 TGTGAGACATCGTGTAAGACCATAGCTGGGCTATTAGC-TTTG-AT-T
1 TGTGA-AC-CCATGTAAGACCATATCTGGGATA-TGGCATTGGCATCA
48586334 TGTGAACCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 TGTGAACCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
48586378 TTACTATGTT
Statistics
Matches: 145, Mismatches: 28, Indels: 23
0.74 0.14 0.12
Matches are distributed among these distances:
42 3 0.02
43 23 0.16
44 4 0.03
45 6 0.04
46 4 0.03
47 3 0.02
48 98 0.68
49 3 0.02
51 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (45 bp):
TGTGAACCCATGTAAGACCATATCTGGGATATGGCATTGGCATCA
Found at i:48586318 original size:96 final size:91
Alignment explanation
Indices: 48586149--48586377 Score: 219
Period size: 96 Copynumber: 2.5 Consensus size: 91
48586139 GGGTTATGTG
* * * * * * *
48586149 TGATCCTATGTAAGACCATGTCTGTGACAAGGCATTGACATCGTTATGAGATCCCATGTAAGACC
1 TGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCGATATGAGATCCCATGTAAGACC
*
48586214 ATGTCTGGGACATGGAATTGGCATCGACACA
66 ATGTCTGGG-C-T---ATTAGCATCGACACA
* * *
48586245 TGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCGATGTGAGA-CATCGTGTAAGAC
1 TGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCGATATGAGATC-CCATGTAAGAC
* * ****
48586309 CATAG-CTGGGCTATTAGCTTTGATTTG
65 CAT-GTCTGGGCTATTAGCATCGACACA
*
48586336 TGAACCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
1 TGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATC
48586378 TTACTATGTT
Statistics
Matches: 113, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
91 49 0.43
94 1 0.01
95 2 0.02
96 60 0.53
97 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (91 bp):
TGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCGATATGAGATCCCATGTAAGACC
ATGTCTGGGCTATTAGCATCGACACA
Found at i:48588227 original size:40 final size:40
Alignment explanation
Indices: 48588181--48588405 Score: 263
Period size: 40 Copynumber: 5.6 Consensus size: 40
48588171 CTTGCACAAG
* * *
48588181 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * * *
48588221 GCCTTCGGGACTTAGCCCGAATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * * *
48588261 GCCTTCGAGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
48588301 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
48588341 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
48588382 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
48588406 CATTCGAATA
Statistics
Matches: 155, Mismatches: 27, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.01
40 125 0.81
41 29 0.19
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:48588277 original size:80 final size:79
Alignment explanation
Indices: 48588145--48588405 Score: 267
Period size: 80 Copynumber: 3.3 Consensus size: 79
48588135 CTCAAGTAAT
* * * * * * * *
48588145 CTTCGGGATTTAG-CTGGATATAACTACTTGCAC-AAGGCCTTCGGGTCTTAGCCCGGATGTGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTC-GGTCTTAGCCCGGATATAGT
*
48588208 CACTAGCATAAATGC
65 CACTAGCACAAATGC
* * * * *
48588223 CTTCGGGACTTAGCCCGAATATAATC-GCTAGCACAAATGCCTTCGAGTTTTAGCCCGGATATAA
1 CTTCGGGACTTAGCCCGGATAT-AGCAACTAGCACAAATGCCTTCG-GTCTTAGCCCGGATATAG
*
48588287 TCGCTAGCACAAATGC
64 TCACTAGCACAAATGC
* * * * *
48588303 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATCTTAGTCCGGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGG-TCTTAGCCCGGATATAGT
*
48588368 CACCTAGCACAAAAGC
65 CA-CTAGCACAAATGC
48588384 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
48588406 CATTCGAATA
Statistics
Matches: 150, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
78 12 0.08
79 16 0.11
80 89 0.59
81 33 0.22
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGTCTTAGCCCGGATATAGTC
ACTAGCACAAATGC
Found at i:48591805 original size:44 final size:42
Alignment explanation
Indices: 48591737--48591849 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 42
48591727 TTCCGATATG
** * * *
48591737 TGATTTCGTGTAAGACCACATCTGGGACGTTGGCATTG-ATT
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
*
48591778 TGAGATTTACGTGTAAGACAATGTCTGGGACATTGGCATCGTATA
1 T--GATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
*
48591823 TGATTTCGTGTAAGACCCTGTCTGGGA
1 TGATTTCGTGTAAGACCATGTCTGGGA
48591850 TAGTGACATC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 19 0.32
43 10 0.17
44 27 0.45
45 3 0.05
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
Found at i:48591845 original size:42 final size:41
Alignment explanation
Indices: 48591737--48591864 Score: 123
Period size: 42 Copynumber: 3.0 Consensus size: 41
48591727 TTCCGATATG
* * * *
48591737 TGATTTCGTGTAAGACCAC-ATCTGGGACGTTGGCATTGATT
1 TGATTTCGTGTAAGACC-CTGTCTGGGACATTGGCATCGATA
**
48591778 TGAGATTTACGTGTAAGACAATGTCTGGGACATTGGCATCGTATA
1 T--GATTT-CGTGTAAGACCCTGTCTGGGACATTGGCATCG-ATA
* * *
48591823 TGATTTCGTGTAAGACCCTGTCTGGGATAGTGACATCGATA
1 TGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCGATA
48591864 T
1 T
48591865 TTGATAACAT
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
41 5 0.07
42 27 0.38
43 10 0.14
44 26 0.37
45 3 0.04
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATCGATA
Found at i:48599377 original size:43 final size:43
Alignment explanation
Indices: 48599225--48599378 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 43
48599215 GATTTTGTGG
*
48599225 AAGACCACGTCTGGGACGTTGGCATCGAT-TTGAGATTTAAGTGT
1 AAGACCACGTCTGGGACGTTGGCATCGATATT-TGA-TTAAGTGT
* * * **
48599269 AAGACCATGTCTGGGACATTGGCATCG-TATATGATTTCGTGT
1 AAGACCACGTCTGGGACGTTGGCATCGATATTTGATTAAGTGT
*
48599311 ATGACC-C-TGCTTGGGACAG-TGGCATCGATATTTGA-TAAGATGT
1 AAGACCACGT-C-TGGGAC-GTTGGCATCGATATTTGATTAAG-TGT
*
48599354 AAGACCACATCTGGGACGTTGGCAT
1 AAGACCACGTCTGGGACGTTGGCAT
48599379 TGTACGAGTT
Statistics
Matches: 88, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 28 0.32
43 29 0.33
44 28 0.32
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
AAGACCACGTCTGGGACGTTGGCATCGATATTTGATTAAGTGT
Found at i:48605095 original size:49 final size:49
Alignment explanation
Indices: 48604930--48605112 Score: 165
Period size: 49 Copynumber: 3.7 Consensus size: 49
48604920 CTGGTACGCA
* *
48604930 TAGTAGCCT-ATACTTAGTACTACACACGTGACC--TAACCATCTGATACATG
1 TAGTAGCCTGA-ACTTAGTACTACACACGTGACCAATAACC--C-GGTACACG
* * * * * * * *
48604980 TAGTAACCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGAACTTAGTACTACACACGTGA-CCAA-TAACCCGGTACACG
* * *
48605031 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATAACCCGGTACACG
1 TAGTAGCCTGAACTTAGTACTACACACGTGACCAATAACCCGGTACACG
*
48605080 TAGTAGCCTGAACTTAGTACTACACATGTGACC
1 TAGTAGCCTGAACTTAGTACTACACACGTGACC
48605113 TCACAATAGA
Statistics
Matches: 107, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
49 40 0.37
50 31 0.29
51 33 0.31
54 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGAACTTAGTACTACACACGTGACCAATAACCCGGTACACG
Found at i:48616108 original size:47 final size:47
Alignment explanation
Indices: 48616047--48616176 Score: 181
Period size: 47 Copynumber: 2.8 Consensus size: 47
48616037 GTACGAATAA
* * *
48616047 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTCA-GAGAGGAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACT-ATGAGAGAAGT
* * *
48616094 TACCTTGATTTGGCTATGGGCCATGGTATAAGTACTATGGGATAAGT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTATGAGAGAAGT
*
48616141 TACCTTGATTTAGCTATGGGCCATGGTATAGGTACT
1 TACCTTGATTTGGCTATGGGCCATGGTATAGGTACT
48616177 TATCAATTGA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 1 0.01
47 73 0.99
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (47 bp):
TACCTTGATTTGGCTATGGGCCATGGTATAGGTACTATGAGAGAAGT
Found at i:48623177 original size:29 final size:29
Alignment explanation
Indices: 48623135--48623224 Score: 162
Period size: 29 Copynumber: 3.1 Consensus size: 29
48623125 GTGAAGAAGT
*
48623135 TAGCTTCGGTGAATTGATCTATTCAGAGA
1 TAGCTTCGGTGAATCGATCTATTCAGAGA
48623164 TAGCTTCGGTGAATCGATCTATTCAGAGA
1 TAGCTTCGGTGAATCGATCTATTCAGAGA
*
48623193 TAGCTTCAGTGAATCGATCTATTCAGAGA
1 TAGCTTCGGTGAATCGATCTATTCAGAGA
48623222 TAG
1 TAG
48623225 TTAAAGGAAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (29 bp):
TAGCTTCGGTGAATCGATCTATTCAGAGA
Found at i:48630196 original size:41 final size:42
Alignment explanation
Indices: 48630105--48630216 Score: 111
Period size: 44 Copynumber: 2.7 Consensus size: 42
48630095 TATTCAGCCA
**
48630105 AAGCTATATCGATATCGCACACTTAGTGCTATCACATTGAACCG
1 AAGCTATATCGATATCGCACACTTAGTGC--TCACATAAAACCG
* * *
48630149 AAGCTATCTCGGTATCGCACACTTAGTGC-CACATAAAATCG
1 AAGCTATATCGATATCGCACACTTAGTGCTCACATAAAACCG
* * * *
48630190 ACGCTATTTCAAT-TCGCACACTAAGTG
1 AAGCTATATCGATATCGCACACTTAGTG
48630217 TTGTATATAG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
40 13 0.22
41 18 0.31
44 27 0.47
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (42 bp):
AAGCTATATCGATATCGCACACTTAGTGCTCACATAAAACCG
Found at i:48631027 original size:15 final size:15
Alignment explanation
Indices: 48631007--48631037 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
48630997 GCCATTAAGA
48631007 TGAATGAATCAAATT
1 TGAATGAATCAAATT
48631022 TGAATGAATCAAATT
1 TGAATGAATCAAATT
48631037 T
1 T
48631038 TGTCTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.35
Consensus pattern (15 bp):
TGAATGAATCAAATT
Found at i:48640020 original size:22 final size:23
Alignment explanation
Indices: 48639973--48640024 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
48639963 TTTAATTGAT
* * *
48639973 TAAAATATTAAAATATATTATAA
1 TAAAATAATAAAATAGATAATAA
48639996 TAAAATAATAAAA-AGATAATAA
1 TAAAATAATAAAATAGATAATAA
48640018 TAAAATA
1 TAAAATA
48640025 TTTCACCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
TAAAATAATAAAATAGATAATAA
Found at i:48642182 original size:40 final size:40
Alignment explanation
Indices: 48642137--48642298 Score: 256
Period size: 40 Copynumber: 4.1 Consensus size: 40
48642127 CTAAGATCCA
*
48642137 AAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCG
* *
48642177 AAGGCATTTGTGCGAGTTACTATATCCAGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCG
*
48642217 AAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCCG
1 AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCG
*
48642257 AAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCCCG
1 AAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTCCCG
48642296 AAG
1 AAG
48642299 ATACTTGGGT
Statistics
Matches: 115, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 14 0.12
40 100 0.87
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
AAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCG
Found at i:48644500 original size:15 final size:15
Alignment explanation
Indices: 48644480--48644509 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
48644470 CACCTTGAGT
48644480 ACATTTCATCATATA
1 ACATTTCATCATATA
48644495 ACATTTCATCATATA
1 ACATTTCATCATATA
48644510 CATATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
ACATTTCATCATATA
Found at i:48645998 original size:7 final size:7
Alignment explanation
Indices: 48645986--48646018 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
48645976 TATACGTGCG
48645986 TAATTAA
1 TAATTAA
48645993 TAATTAA
1 TAATTAA
48646000 TAATTAA
1 TAATTAA
*
48646007 TAA-AAA
1 TAATTAA
48646013 TAATTA
1 TAATTA
48646019 TGTTATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAATTAA
Found at i:48647255 original size:55 final size:53
Alignment explanation
Indices: 48647176--48647377 Score: 185
Period size: 55 Copynumber: 3.7 Consensus size: 53
48647166 TTAAGGATAC
* * * *
48647176 CATGTAAGACCATGCCAAGGCATGGAAACTGATAAGGTTTCTAAGGCAAGAAAAT
1 CATGTAAGACCATGTCAAGACATGG-CATTGATAA-GTTTCTAAGGCAAGAAAAT
* **
48647231 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC-A-AAGGT
1 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTT--TCTAAGGCAAGAAAAT
* * * * * *
48647284 CCCATGTAAGACCATGTCAAGGCATGGCATTGGTGAG-TTCATAAGGCAAGGATAC
1 --CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTTC-TAAGGCAAGAAAAT
* *
48647339 CATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTTC
1 CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTTC
48647378 AAAAGGATAC
Statistics
Matches: 121, Mismatches: 18, Indels: 17
0.78 0.12 0.11
Matches are distributed among these distances:
52 1 0.01
53 44 0.36
54 13 0.11
55 63 0.52
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (53 bp):
CATGTAAGACCATGTCAAGACATGGCATTGATAAGTTTCTAAGGCAAGAAAAT
Found at i:48647374 original size:108 final size:110
Alignment explanation
Indices: 48647175--48647375 Score: 282
Period size: 108 Copynumber: 1.8 Consensus size: 110
48647165 TTTAAGGATA
*
48647175 CCATGTAAGACCATGCCAAGGCATGGAAACTGATAAGGTTTCTAAGGCAAGAAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAACTGATAAGGTTTCTAAGGCAAGAAAACCATGTAAGA
*
48647240 CCATGTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
* * * * * * *
48647285 CCATGTAAGACCATGTCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAACTGATAAGGTTTC-TAAGGCAAGAAAACCATGTAAG
*
48647347 ACCATGTCAAGACATGGCAATGGTAAGTT
65 ACCATGTCAAGACATGGCAATGATAAGTT
48647376 TCAAAAGGAT
Statistics
Matches: 80, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.04
108 47 0.59
109 5 0.06
110 25 0.31
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAACTGATAAGGTTTCTAAGGCAAGAAAACCATGTAAGA
CCATGTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:48647640 original size:16 final size:16
Alignment explanation
Indices: 48647619--48647649 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48647609 ATAAATTTGA
48647619 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
48647635 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
48647650 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:48652764 original size:19 final size:19
Alignment explanation
Indices: 48652728--48652769 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
48652718 GGTAAATTGC
48652728 TAAATTGTAAAATGAGTTG
1 TAAATTGTAAAATGAGTTG
48652747 TAAATGTGTAAAAT-AGTTG
1 TAAAT-TGTAAAATGAGTTG
48652766 -AAAT
1 TAAAT
48652770 AATGAGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.18
19 10 0.45
20 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (19 bp):
TAAATTGTAAAATGAGTTG
Found at i:48652802 original size:86 final size:86
Alignment explanation
Indices: 48652696--48652867 Score: 308
Period size: 86 Copynumber: 2.0 Consensus size: 86
48652686 GAAAGAAATT
* *
48652696 GCATGAAAATACCTTAAAAAGGGGTAAATTGCTAAATTGTAAAATGAGTTGTAAATGTGTAAAAT
1 GCATGAAAACACCTTAAAAAGGGGTAAATTGCTAAATTGTAAAATGAGTTGTAAATGGGTAAAAT
48652761 AGTTGAAATAATGAGTTGCTA
66 AGTTGAAATAATGAGTTGCTA
*
48652782 GCATGAAAACACCTTAAAAAGGGGTAAATTGCTAAGTTGTAAAATGAGTTGTAAATGGGTAAAAT
1 GCATGAAAACACCTTAAAAAGGGGTAAATTGCTAAATTGTAAAATGAGTTGTAAATGGGTAAAAT
*
48652847 AGTTGAAATTATGAGTTGCTA
66 AGTTGAAATAATGAGTTGCTA
48652868 TAGTTATGAA
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (86 bp):
GCATGAAAACACCTTAAAAAGGGGTAAATTGCTAAATTGTAAAATGAGTTGTAAATGGGTAAAAT
AGTTGAAATAATGAGTTGCTA
Found at i:48653464 original size:46 final size:46
Alignment explanation
Indices: 48653413--48653771 Score: 564
Period size: 46 Copynumber: 7.8 Consensus size: 46
48653403 GGTTGAGCAT
* * *
48653413 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * * * *
48653459 TCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
48653504 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48653552 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48653598 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48653644 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48653690 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48653736 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
48653772 GCGGGTTACA
Statistics
Matches: 291, Mismatches: 13, Indels: 18
0.90 0.04 0.06
Matches are distributed among these distances:
42 2 0.01
43 4 0.01
45 3 0.01
46 246 0.85
47 25 0.09
48 4 0.01
50 4 0.01
51 3 0.01
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:48656406 original size:46 final size:45
Alignment explanation
Indices: 48656302--48656519 Score: 181
Period size: 46 Copynumber: 4.8 Consensus size: 45
48656292 AGATTTGTGT
* * * * *
48656302 GCCAGTGTAAGACCATGTATGGGACATGGCATC-GGCATTGAGACGAGG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCA--CAGATGAGA
*
48656350 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACAG-ATGAGA
* * **
48656396 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTTA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCAC-AGATGAGA
* * * * ** *
48656442 GCCAATGTCAGACATGTCTGGGACATGCGTCGGTTAC-GA-GATGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGA-GA
* *
48656486 GCTAGTGTAAGACATGTCTGGGACATGCGTCAGC
1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGC
48656520 ACGGTTACAT
Statistics
Matches: 141, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
43 1 0.01
44 31 0.22
45 2 0.01
46 78 0.55
47 18 0.13
48 11 0.08
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (45 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCACAGATGAGA
Found at i:48656456 original size:92 final size:90
Alignment explanation
Indices: 48656302--48656513 Score: 228
Period size: 92 Copynumber: 2.3 Consensus size: 90
48656292 AGATTTGTGT
* * * * *
48656302 GCCAGTGTAAGACCATGTATGGGACATGGCATCGGCATTGAGACGAGGGCTAGTGTAAGACATGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAGAGCCAATGTAAGACATGT
48656367 CTGGGACATGCATCAGCCAC-AGTATGAGA
64 CTGGGACATGCATCAGCCACGAG-AT--GA
* * ** *
48656396 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTTAGCCAATGTCAGACATGTCT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAATGTAAGACATGTCT
* * ** *
48656461 GGGACATGCGTCGGTTACGAGATGT
66 GGGACATGCATCAGCCACGAGATGA
*
48656486 GCTAGTGTAAGACATGTCTGGGACATGC
1 GCCAGTGTAAGACATGTCTGGGACATGC
48656514 GTCAGCACGG
Statistics
Matches: 101, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
90 28 0.28
92 46 0.46
93 15 0.15
94 12 0.12
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.23
Consensus pattern (90 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCCAATGTAAGACATGTCT
GGGACATGCATCAGCCACGAGATGA
Found at i:48659369 original size:19 final size:19
Alignment explanation
Indices: 48659333--48659374 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
48659323 GGTAAATTGC
48659333 TAAATTGTAAAATGAGTTG
1 TAAATTGTAAAATGAGTTG
48659352 TAAATGTGTAAAAT-AGTTG
1 TAAAT-TGTAAAATGAGTTG
48659371 -AAAT
1 TAAAT
48659375 AATGAGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.18
19 10 0.45
20 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (19 bp):
TAAATTGTAAAATGAGTTG
Found at i:48659983 original size:46 final size:46
Alignment explanation
Indices: 48659932--48660888 Score: 1742
Period size: 46 Copynumber: 20.8 Consensus size: 46
48659922 GGTTGAGCAT
* * * *
48659932 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGTTGCGAATGT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * * * * *
48659978 TCGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
*
48660023 ATTCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660071 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660117 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660163 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660209 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660255 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660301 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660347 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660393 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660439 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660485 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660531 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660577 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660623 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660669 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660715 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660761 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660807 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
48660853 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
48660889 GCGGGTTACA
Statistics
Matches: 888, Mismatches: 14, Indels: 18
0.97 0.02 0.02
Matches are distributed among these distances:
42 2 0.00
43 3 0.00
45 3 0.00
46 843 0.95
47 26 0.03
48 4 0.00
50 4 0.00
51 3 0.00
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Done.