Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold867
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1160077
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.29
Warning! 150854 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:319709 original size:32 final size:31
Alignment explanation
Indices: 319627--319709 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 31
319617 AATAACCATA
319627 CCGTCACGCTATCACAACTTTTATACCACAAG
1 CCGTCACGCTA-CACAACTTTTATACCACAAG
* * * *
319659 CTGTCACGCTAAACCAACTTTTA-CCCAACATG
1 CCGTCACGCTACA-CAACTTTTATACC-ACAAG
319691 CCGTCACGCTGACACAACT
1 CCGTCACGCT-ACACAACT
319710 CTGTCACAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
31 3 0.07
32 37 0.88
33 2 0.05
ACGTcount: A:0.30, C:0.36, G:0.11, T:0.23
Consensus pattern (31 bp):
CCGTCACGCTACACAACTTTTATACCACAAG
Found at i:319885 original size:21 final size:21
Alignment explanation
Indices: 319859--319900 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
319849 TATGCAACTA
* *
319859 TACACAATATGCAGTAACGCT
1 TACACAACACGCAGTAACGCT
319880 TACACAACACGCAGTAACGCT
1 TACACAACACGCAGTAACGCT
319901 AATACAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.29, G:0.14, T:0.19
Consensus pattern (21 bp):
TACACAACACGCAGTAACGCT
Found at i:319907 original size:21 final size:21
Alignment explanation
Indices: 319869--319908 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
319859 TACACAATAT
*
319869 GCAGTAACGCTTACACAACAC
1 GCAGTAACGCTAACACAACAC
*
319890 GCAGTAACGCTAATACAAC
1 GCAGTAACGCTAACACAAC
319909 TTTATACAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.30, G:0.15, T:0.15
Consensus pattern (21 bp):
GCAGTAACGCTAACACAACAC
Found at i:319943 original size:31 final size:31
Alignment explanation
Indices: 319879--319957 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
319869 GCAGTAACGC
* * *
319879 TTACACAACACGCAGTAACGCTAATACAACT
1 TTACACAACACACAGTAACCCTAACACAACT
* * *
319910 TTATACAACACACAGTGACCCTAACACAGCT
1 TTACACAACACACAGTAACCCTAACACAACT
319941 TTACACAACACACAGTA
1 TTACACAACACACAGTA
319958 CGCCATCGCG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.42, C:0.30, G:0.09, T:0.19
Consensus pattern (31 bp):
TTACACAACACACAGTAACCCTAACACAACT
Found at i:325485 original size:38 final size:38
Alignment explanation
Indices: 325466--326301 Score: 1057
Period size: 38 Copynumber: 22.2 Consensus size: 38
325456 TACAACTGGC
* *
325466 TGTTTGATTACAATCCACGACCCTTTACAACGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
325504 TGTTTGATTACAATTCACGACCCTTTA-TAACGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACT-ACGACAGAT
*
325542 TGTTTGATTACAATTCACGACCCTTTACAACGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* *
325580 TGTTTGATTACAATTCACGACCCTATACTATGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
325618 TG-TTGATTACAATTCACGACCCTTTACTACGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* *
325655 TG-TTGATTACAATTCACGACCCTATACTATGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
*
325692 TG-TTGATTACAATTCACGACCCTTTACAACGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* *
325729 TGTTTGATTACAATTCACGACCCTATACTATGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
*
325767 TG-TTGATTACAATTCACGACCCTTTACAACGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* *
325804 TGTTTGATTACAATTCACGACCCTATACTATGACAGAT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* * **
325842 TG-TTGATTACAATTCACGACCCTTTATTAAGACAGGC
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* * **
325879 GGTTTGATAACAATTCACGACCCTTTACTACGACAGGC
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
*
325917 TGTTTGATTACAATTCACGACCCTTTACTACGACAGGT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* *
325955 TG-TTGATTACAATTCACGACCCTATACTACGACAGGT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* *
325992 TGTTTGGTTACATTTCACGACCCTTTACTACGACA-AGT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGA-T
* * *
326030 TATTTGATTACATTTCACGACCCTTTGCTACGACAGGA-
1 TGTTTGATTACAATTCACGACCCTTTACTACGACA-GAT
* * ** * *
326068 TGTTTGATAAGAACGCACGATCCTTTACTACGACAGTT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* **
326106 TGTTTTATTACAATTCACGACCCTTTACTACGACAGGC
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* * * * *
326144 TGTTTGGTTAGAATTCACGACTCTTTACTGCGACAGGT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* * * * *
326182 TGTTTGGTTAGAATTCACGACCTTTTACCACGACAGGT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
* * *
326220 TGTTTGATTAGAA-TCTACGACCCTTTACTATGACAGGT
1 TGTTTGATTACAATTC-ACGACCCTTTACTACGACAGAT
* * *
326258 TGATTGATTAC-ACTCACGACCCCTTT-CTACGACAGGT
1 TGTTTGATTACAATTCACGA-CCCTTTACTACGACAGAT
326295 TGTTTGA
1 TGTTTGA
326302 GAAGTTCCCG
Statistics
Matches: 708, Mismatches: 77, Indels: 27
0.87 0.09 0.03
Matches are distributed among these distances:
37 229 0.32
38 478 0.68
40 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (38 bp):
TGTTTGATTACAATTCACGACCCTTTACTACGACAGAT
Found at i:325561 original size:76 final size:76
Alignment explanation
Indices: 325466--326301 Score: 1057
Period size: 75 Copynumber: 11.1 Consensus size: 76
325456 TACAACTGGC
* *
325466 TGTTTGATTACAATCCACGACCCTTTACAACGACAGATTGTTTGATTACAATTCACGACCCTTTA
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
325531 -TAACGACAGAT
66 CT-ACGACAGAT
* *
325542 TGTTTGATTACAATTCACGACCCTTTACAACGACAGATTGTTTGATTACAATTCACGACCCTATA
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
*
325607 CTATGACAGAT
66 CTACGACAGAT
*
325618 TG-TTGATTACAATTCACGACCCTTTACTACGACAGATTG-TTGATTACAATTCACGACCCTATA
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
*
325681 CTATGACAGAT
66 CTACGACAGAT
* *
325692 TG-TTGATTACAATTCACGACCCTTTACAACGACAGATTGTTTGATTACAATTCACGACCCTATA
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
*
325756 CTATGACAGAT
66 CTACGACAGAT
* *
325767 TG-TTGATTACAATTCACGACCCTTTACAACGACAGATTGTTTGATTACAATTCACGACCCTATA
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
*
325831 CTATGACAGAT
66 CTACGACAGAT
* * *** *
325842 TG-TTGATTACAATTCACGACCCTTTATTAAGACAGGCGGTTTGATAACAATTCACGACCCTTTA
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
**
325906 CTACGACAGGC
66 CTACGACAGAT
* *
325917 TGTTTGATTACAATTCACGACCCTTTACTACGACAGGTTG-TTGATTACAATTCACGACCCTATA
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
*
325981 CTACGACAGGT
66 CTACGACAGAT
* * * *
325992 TGTTTGGTTACATTTCACGACCCTTTACTACGACA-AGTTATTTGATTACATTTCACGACCCTTT
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGA-TTGTTTGATTACAATTCACGACCCTTT
*
326056 GCTACGACAGGA-
65 ACTACGACA-GAT
* * ** * * *
326068 TGTTTGATAAGAACGCACGATCCTTTACTACGACAGTTTGTTTTATTACAATTCACGACCCTTTA
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
**
326133 CTACGACAGGC
66 CTACGACAGAT
* * * * * * * *
326144 TGTTTGGTTAGAATTCACGACTCTTTACTGCGACAGGTTGTTTGGTTAGAATTCACGACCTTTTA
1 TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
* *
326209 CCACGACAGGT
66 CTACGACAGAT
* * * * *
326220 TGTTTGATTAGAA-TCTACGACCCTTTACTATGACAGGTTGATTGATTAC-ACTCACGACCCCTT
1 TGTTTGATTACAATTC-ACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGA-CCCTT
*
326283 T-CTACGACAGGT
64 TACTACGACAGAT
326295 TGTTTGA
1 TGTTTGA
326302 GAAGTTCCCG
Statistics
Matches: 682, Mismatches: 68, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
74 73 0.11
75 306 0.45
76 301 0.44
77 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (76 bp):
TGTTTGATTACAATTCACGACCCTTTACTACGACAGATTGTTTGATTACAATTCACGACCCTTTA
CTACGACAGAT
Found at i:327040 original size:78 final size:78
Alignment explanation
Indices: 326949--327095 Score: 181
Period size: 78 Copynumber: 1.9 Consensus size: 78
326939 ATTTTAACAA
* * * * *
326949 ATGTTTATTAATGAA-AAATGAAATCTAGTATTTTGACATATGTTTATTAAA-AAACACTGAATT
1 ATGTTTATAAATGAACAAA-GAAATATAGCATTTTGACATATGTTTA-TAAATAAACACAGAAAT
327012 CTAGCACTTTGGTGT
64 CTAGCACTTTGGTGT
* ***
327027 ATGTTTATAAATGAACACAGAAATATAGCATTTTGGTGTATGTTTATAAATAAACACAGAAATCT
1 ATGTTTATAAATGAACAAAGAAATATAGCATTTTGACATATGTTTATAAATAAACACAGAAATCT
327092 AGCA
66 AGCA
327096 TCTATACTAC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
77 4 0.07
78 52 0.90
79 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (78 bp):
ATGTTTATAAATGAACAAAGAAATATAGCATTTTGACATATGTTTATAAATAAACACAGAAATCT
AGCACTTTGGTGT
Found at i:327096 original size:39 final size:39
Alignment explanation
Indices: 326968--327096 Score: 161
Period size: 39 Copynumber: 3.3 Consensus size: 39
326958 AATGAAAAAT
* *** *
326968 GAAATCTAGTATTTTGACATATGTTTATTAAA-AAACACT
1 GAAATCTAGCATTTTGGTGTATGTTTA-TAAATAAACACA
* * *
327007 GAATTCTAGCACTTTGGTGTATGTTTATAAATGAACACA
1 GAAATCTAGCATTTTGGTGTATGTTTATAAATAAACACA
*
327046 GAAATATAGCATTTTGGTGTATGTTTATAAATAAACACA
1 GAAATCTAGCATTTTGGTGTATGTTTATAAATAAACACA
327085 GAAATCTAGCAT
1 GAAATCTAGCAT
327097 CTATACTACC
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
38 4 0.05
39 72 0.95
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.36
Consensus pattern (39 bp):
GAAATCTAGCATTTTGGTGTATGTTTATAAATAAACACA
Found at i:336833 original size:26 final size:26
Alignment explanation
Indices: 336797--336848 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
336787 AAAAGTGAGA
336797 CTGAGATCAAAAGTGAGCTCATCAAT
1 CTGAGATCAAAAGTGAGCTCATCAAT
336823 CTGAGATCAAAAGTGAGCTCATCAAT
1 CTGAGATCAAAAGTGAGCTCATCAAT
336849 ATTTGCTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (26 bp):
CTGAGATCAAAAGTGAGCTCATCAAT
Found at i:338848 original size:2 final size:2
Alignment explanation
Indices: 338841--338925 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
338831 TGTATTTAAC
338841 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
338883 AG AG AG GG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
338925 A
1 A
338926 TGTTCATTTG
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:341228 original size:2 final size:2
Alignment explanation
Indices: 341221--341261 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
341211 GTTGCATAAG
341221 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
341262 GAGATAAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:341963 original size:17 final size:17
Alignment explanation
Indices: 341949--341984 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
341939 CAAAAAACCC
341949 AACAACAGCAAAAACAA
1 AACAACAGCAAAAACAA
* *
341966 AACAACATCAAAAATAA
1 AACAACAGCAAAAACAA
341983 AA
1 AA
341985 ATGCCCAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.72, C:0.19, G:0.03, T:0.06
Consensus pattern (17 bp):
AACAACAGCAAAAACAA
Found at i:350403 original size:2 final size:2
Alignment explanation
Indices: 350396--350436 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
350386 TACTCATAGA
350396 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
350437 TGTAATTGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:351344 original size:2 final size:2
Alignment explanation
Indices: 351337--351394 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
351327 CATATAATAC
* *
351337 AG AG AG AG AG AG AG AA AC AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
351379 AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
351395 CGAGCATTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.52, C:0.02, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:361192 original size:46 final size:46
Alignment explanation
Indices: 361125--361451 Score: 460
Period size: 46 Copynumber: 7.1 Consensus size: 46
361115 CACGGTGTCT
*
361125 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTGACC
1 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACC
*
361171 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTGACC
1 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACC
* * *
361217 GTATGTAAACCCTCCCGTTCTGGCA-TGTTAAGGCTCGCCTGTAACC
1 GTATGTAAACCCTCCCATTATGACACT-TTAAGGCTCGCCTGTAACC
361263 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACC
1 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACC
*
361309 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTTGCCTGTAACC
1 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACC
* * * * * *
361355 GTATGTAAACCCTCCCATTCTGGCACGTTGAGGTTCGCCTGTAATC
1 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACC
* * * * * *
361401 GTATGTAAACCCTTCCATTCTGGCACATTGAGGCAT-GCCTGTAATC
1 GTATGTAAACCCTCCCATTATGACACTTTAAGGC-TCGCCTGTAACC
361447 GTATG
1 GTATG
361452 CATATCCTTT
Statistics
Matches: 260, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
45 1 0.00
46 257 0.99
47 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACC
Found at i:361376 original size:138 final size:138
Alignment explanation
Indices: 361125--361451 Score: 512
Period size: 138 Copynumber: 2.4 Consensus size: 138
361115 CACGGTGTCT
*
361125 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTGACCGTATGTAAACCCTCCCATT
1 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACCGTATGTAAACCCTCCCATT
* * *
361190 ATGACACTTTAAGGCTCGCCTGTGACCGTATGTAAACCCTCCCGTTCTGGCATGTTAAGGCTCGC
66 ATGACACTTTAAGGCTCGCCTGTAACCGTATGTAAACCCTCCCATTCTGGCACGTTAAGGCTCGC
361255 CTGTAACC
131 CTGTAACC
361263 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACCGTATGTAAACCCTCCCATT
1 GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACCGTATGTAAACCCTCCCATT
* * *
361328 ATGACACTTTAAGGCTTGCCTGTAACCGTATGTAAACCCTCCCATTCTGGCACGTTGAGGTTCGC
66 ATGACACTTTAAGGCTCGCCTGTAACCGTATGTAAACCCTCCCATTCTGGCACGTTAAGGCTCGC
*
361393 CTGTAATC
131 CTGTAACC
* * * * * *
361401 GTATGTAAACCCTTCCATTCTGGCACATTGAGGCAT-GCCTGTAATCGTATG
1 GTATGTAAACCCTCCCATTATGACACTTTAAGGC-TCGCCTGTAACCGTATG
361452 CATATCCTTT
Statistics
Matches: 174, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
138 173 0.99
139 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (138 bp):
GTATGTAAACCCTCCCATTATGACACTTTAAGGCTCGCCTGTAACCGTATGTAAACCCTCCCATT
ATGACACTTTAAGGCTCGCCTGTAACCGTATGTAAACCCTCCCATTCTGGCACGTTAAGGCTCGC
CTGTAACC
Found at i:361556 original size:2 final size:2
Alignment explanation
Indices: 361549--361598 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
361539 TGTAAACAAA
361549 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
361591 CT CT CT CT
1 CT CT CT CT
361599 GAGACATGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:367481 original size:2 final size:2
Alignment explanation
Indices: 367474--367558 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
367464 AATTAAGTAT
*
367474 GA GA GA GA GA GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
367516 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
367558 G
1 G
367559 TGTGTGTTAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.48, C:0.01, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:380750 original size:6 final size:6
Alignment explanation
Indices: 380739--380765 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
380729 CAAATAAAAC
380739 AAACAA AAACAA AAACAA AAACAA AAA
1 AAACAA AAACAA AAACAA AAACAA AAA
380766 ACCAACAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:383300 original size:15 final size:16
Alignment explanation
Indices: 383273--383302 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
383263 AAGTTTTCAA
383273 ATATAATCAATATTAT
1 ATATAATCAATATTAT
383289 ATATAA-CAATATTA
1 ATATAATCAATATTA
383303 GAAACGATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAATCAATATTAT
Found at i:386561 original size:15 final size:15
Alignment explanation
Indices: 386541--386596 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
386531 GCATAGTCTT
386541 CATTTGTTGTTTTTG
1 CATTTGTTGTTTTTG
* *
386556 CATTTGCTGATTTTG
1 CATTTGTTGTTTTTG
* **
386571 CATTTGTTGTTGTAA
1 CATTTGTTGTTTTTG
386586 CATTTGTTGTT
1 CATTTGTTGTT
386597 GCTGCTGCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.12, C:0.09, G:0.20, T:0.59
Consensus pattern (15 bp):
CATTTGTTGTTTTTG
Found at i:390045 original size:11 final size:11
Alignment explanation
Indices: 390029--390056 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
390019 AGAATTCAAA
390029 TATTACCCCAG
1 TATTACCCCAG
390040 TATTACCCCAG
1 TATTACCCCAG
390051 TATTAC
1 TATTAC
390057 GAAATAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.32
Consensus pattern (11 bp):
TATTACCCCAG
Found at i:395214 original size:17 final size:17
Alignment explanation
Indices: 395192--395228 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
395182 TCATCGAGGT
*
395192 AAATGCCAAAATCGGGA
1 AAATGCCAAAATAGGGA
*
395209 AAATGCCATAATAGGGA
1 AAATGCCAAAATAGGGA
395226 AAA
1 AAA
395229 AGGAAACGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.14, G:0.22, T:0.14
Consensus pattern (17 bp):
AAATGCCAAAATAGGGA
Found at i:397875 original size:21 final size:21
Alignment explanation
Indices: 397849--397891 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
397839 TTATGGGGAC
*
397849 AGCACCCAGCAAGTGAATTAG
1 AGCACCCAGAAAGTGAATTAG
397870 AGCACCCAGAAAGTGAATTAG
1 AGCACCCAGAAAGTGAATTAG
397891 A
1 A
397892 AAGTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (21 bp):
AGCACCCAGAAAGTGAATTAG
Found at i:397967 original size:21 final size:21
Alignment explanation
Indices: 397941--397983 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
397931 TTTTGGGGAT
397941 AGCACCCA-ACAAGTGAATTAG
1 AGCACCCAGA-AAGTGAATTAG
397962 AGCACCCAGAAAGTGAATTAG
1 AGCACCCAGAAAGTGAATTAG
397983 A
1 A
397984 AAGTATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (21 bp):
AGCACCCAGAAAGTGAATTAG
Found at i:397986 original size:92 final size:92
Alignment explanation
Indices: 397829--398013 Score: 334
Period size: 92 Copynumber: 2.0 Consensus size: 92
397819 TAGTACATTA
*
397829 TGGTTGTGAATTATGGGGACAGCACCCAGCAAGTGAATTAGAGCACCCAGAAAGTGAATTAGAAA
1 TGGTTGTGAATTATGGGGACAGCACCCAACAAGTGAATTAGAGCACCCAGAAAGTGAATTAGAAA
*
397894 GTATATATTTAAATTTTTGTAAGAAAT
66 GTATACATTTAAATTTTTGTAAGAAAT
* *
397921 TGGTTGTGAATTTTGGGGATAGCACCCAACAAGTGAATTAGAGCACCCAGAAAGTGAATTAGAAA
1 TGGTTGTGAATTATGGGGACAGCACCCAACAAGTGAATTAGAGCACCCAGAAAGTGAATTAGAAA
397986 GTATACATTTAAATTTTTGTAAGAAAT
66 GTATACATTTAAATTTTTGTAAGAAAT
398013 T
1 T
398014 ATTATGTGTT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 89 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (92 bp):
TGGTTGTGAATTATGGGGACAGCACCCAACAAGTGAATTAGAGCACCCAGAAAGTGAATTAGAAA
GTATACATTTAAATTTTTGTAAGAAAT
Found at i:403155 original size:20 final size:20
Alignment explanation
Indices: 403130--403170 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
403120 TAGTCGAATT
403130 ATATATCAAATATATGGTAC
1 ATATATCAAATATATGGTAC
403150 ATATATCAAATATATGGTAC
1 ATATATCAAATATATGGTAC
403170 A
1 A
403171 GCTACACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (20 bp):
ATATATCAAATATATGGTAC
Found at i:406466 original size:4 final size:4
Alignment explanation
Indices: 406459--406492 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
406449 ATTTATCGTT
406459 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA AT
406493 AATCGTTGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:407099 original size:89 final size:88
Alignment explanation
Indices: 406943--407120 Score: 295
Period size: 89 Copynumber: 2.0 Consensus size: 88
406933 CAATACTCTC
*
406943 CAAATAAACGTTATGCCCCAGTCACACATTCACGGATCAACTCCACGGTTCTACTACGGAATATT
1 CAAATAAACGTTATGCCCCAGTCACACATTCACAGATCAACTCCACGGTTCTACTACGGAATATT
407008 TTCCACGGTTGACACCGGAAAAT
66 TTCCACGGTTGACACCGGAAAAT
* * *
407031 CAAATAATCGTTAATGCCCCAGTCACACATTCACAGATCAACTCCTA-GGTTCTACTACGGATTT
1 CAAATAAACGTT-ATGCCCCAGTCACACATTCACAGATCAACTCC-ACGGTTCTACTACGGAATA
407095 TTTTCCACGGTTGACACCGGAAAAT
64 TTTTCCACGGTTGACACCGGAAAAT
407120 C
1 C
407121 TAATGATACG
Statistics
Matches: 84, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
88 11 0.13
89 72 0.86
90 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (88 bp):
CAAATAAACGTTATGCCCCAGTCACACATTCACAGATCAACTCCACGGTTCTACTACGGAATATT
TTCCACGGTTGACACCGGAAAAT
Found at i:420211 original size:2 final size:2
Alignment explanation
Indices: 420204--420297 Score: 179
Period size: 2 Copynumber: 47.0 Consensus size: 2
420194 CAATTTTGCC
*
420204 AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
420246 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
420288 AG AG AG AG AG
1 AG AG AG AG AG
420298 GGCAGGAGCG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 90 1.00
ACGTcount: A:0.50, C:0.00, G:0.49, T:0.01
Consensus pattern (2 bp):
AG
Found at i:421111 original size:11 final size:11
Alignment explanation
Indices: 421095--421120 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
421085 GGGTCAGTCT
421095 ATGTACAGGTG
1 ATGTACAGGTG
421106 ATGTACAGGTG
1 ATGTACAGGTG
421117 ATGT
1 ATGT
421121 TGGGCAGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.08, G:0.35, T:0.31
Consensus pattern (11 bp):
ATGTACAGGTG
Found at i:421924 original size:1 final size:1
Alignment explanation
Indices: 421918--421998 Score: 54
Period size: 1 Copynumber: 81.0 Consensus size: 1
421908 CATTTTGGCC
* * ** * *** * * *
421918 AAAAAAAAAAAAAAAAGAAGAAGCAAAAAACAAAAAAAAAAACCCAAAAAAAACAAACAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
421983 AAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAA
421999 CATATGTTCA
Statistics
Matches: 61, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:421983 original size:28 final size:27
Alignment explanation
Indices: 421917--422000 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 27
421907 CCATTTTGGC
* *
421917 CAAAAAAAAAAAAAAAAGAAGAAGCAAAAAA
1 CAAAAAAAAAAACAAAA-AA-AA--AACAAA
**
421948 CAAAAAAAAAAACCCAAAAAAAACAAA
1 CAAAAAAAAAAACAAAAAAAAAACAAA
421975 CAAACAAAAAAAACAAAAAAAAAACA
1 CAAA-AAAAAAAACAAAAAAAAAACA
422001 TATGTTCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 9 0.20
28 19 0.41
29 2 0.04
30 2 0.04
31 14 0.30
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (27 bp):
CAAAAAAAAAAACAAAAAAAAAACAAA
Found at i:425495 original size:22 final size:22
Alignment explanation
Indices: 425469--425510 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
425459 GCATCAGGGA
*
425469 AATGTTTCTTTGATCTCGCGGG
1 AATGTTTCTTTGAACTCGCGGG
425491 AATGTTTCTTTGAACTCGCG
1 AATGTTTCTTTGAACTCGCG
425511 CGGTGATTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (22 bp):
AATGTTTCTTTGAACTCGCGGG
Found at i:437351 original size:32 final size:32
Alignment explanation
Indices: 437305--437398 Score: 152
Period size: 32 Copynumber: 2.9 Consensus size: 32
437295 AATGACCGGG
* *
437305 GGTCATTTTTCTACGTAGAATAATGACCCCCC
1 GGTCATTATTCTACGTAGAAAAATGACCCCCC
* *
437337 GGTCATTATGCTACGCAGAAAAATGACCCCCC
1 GGTCATTATTCTACGTAGAAAAATGACCCCCC
437369 GGTCATTATTCTACGTAGAAAAATGACCCC
1 GGTCATTATTCTACGTAGAAAAATGACCCC
437399 TTTGCCTGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (32 bp):
GGTCATTATTCTACGTAGAAAAATGACCCCCC
Found at i:437808 original size:29 final size:28
Alignment explanation
Indices: 437755--437809 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
437745 GACCTAAGTT
*
437755 GCAAAGGCGATAATGCGAAGGCGAAGGA
1 GCAAAGGCGATAATGCGAAGACGAAGGA
*
437783 GCAAAGTGCGA-AGATGCGACGACGAAG
1 GCAAAG-GCGATA-ATGCGAAGACGAAG
437810 CGCGAAGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.38, C:0.16, G:0.38, T:0.07
Consensus pattern (28 bp):
GCAAAGGCGATAATGCGAAGACGAAGGA
Found at i:438399 original size:16 final size:16
Alignment explanation
Indices: 438380--438414 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
438370 TCACCGAGAC
438380 GAGGCATCACCTTTAT
1 GAGGCATCACCTTTAT
438396 GAGGCATCACCTTTAT
1 GAGGCATCACCTTTAT
438412 GAG
1 GAG
438415 ACCACCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (16 bp):
GAGGCATCACCTTTAT
Found at i:438422 original size:14 final size:16
Alignment explanation
Indices: 438380--438425 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
438370 TCACCGAGAC
*
438380 GAGGCATCACCTTTAT
1 GAGGCACCACCTTTAT
*
438396 GAGGCATCACCTTTAT
1 GAGGCACCACCTTTAT
438412 GA-G-ACCACCTTTAT
1 GAGGCACCACCTTTAT
438426 CATATTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
16 18 0.62
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (16 bp):
GAGGCACCACCTTTAT
Found at i:440279 original size:177 final size:175
Alignment explanation
Indices: 439965--440483 Score: 641
Period size: 177 Copynumber: 2.9 Consensus size: 175
439955 CAAGAATCAT
* * *
439965 AAACCTATGGCTCTGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACTA-TATCA
1 AAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACCATTATCC
* * * ***
440029 ATGCAAGGTTGGTGAAGTTAGGACCAGTAATAACTAAGATATTGTCATCAGAGGGCACCTGTTTC
66 ATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAGATATT-TCATTAGAGGGCACCTGCAAC
** *
440094 AAAAACTTTAACCAGCTCTTAAAATCTTAACCTCCTCAGGCATCCG
130 AAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCAGGCATCCG
* * * *
440140 AAACCTGTGGCTCAGATTCAGCATTTAAGCCTGTCAGGTGCATCACTATAATAAGACGCATTATC
1 AAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGAC-CATTATC
* **
440205 CATACAAGTTTAATGAAGTTAGGACCAGTAGTAACTAAGATATTATCATTAGAGGGCACCTGCAA
65 CATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAGATATT-TCATTAGAGGGCACCTGCAA
* * **
440270 CAGAAACTTTAACCAGCTCCAAAAACCTTTACCTCCTCCTGCATCCG
129 CAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCAGGCATCCG
* * * * * *
440317 AAACCTATAGTTCAGATTCAGCACTCAAGCCTGTCTGGTGTATCAGTATCATAAGACACATCATC
1 AAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGAC-CATTATC
* * *
440382 CATGCAAGTTTGGTGAAG-TACGGACCAGCAGTAACTTAGATATTGCTATTTA-A-GGCACCTGC
65 CATGCAAGTTTGGTGAAGTTA-GGACCAGTAGTAACTAAGATATTTC-A-TTAGAGGGCACCTGC
* *
440444 AACAAAAACTTTAAACTGCTCCAAAAACCTTAACCTCCTC
127 AACAAAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTC
440484 CAGCATCTGA
Statistics
Matches: 294, Mismatches: 45, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
175 52 0.18
176 49 0.17
177 190 0.65
178 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (175 bp):
AAACCTATGGCTCAGATTCAGCATTCAAGCCTGTCAGGTGCATCAGTATCATAAGACCATTATCC
ATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACTAAGATATTTCATTAGAGGGCACCTGCAACA
AAAACTTTAACCAGCTCCAAAAACCTTAACCTCCTCAGGCATCCG
Found at i:440484 original size:19 final size:19
Alignment explanation
Indices: 440446--440485 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
440436 GCACCTGCAA
* *
440446 CAAAAACTTTAAACTGCTC
1 CAAAAACCTTAAACTCCTC
*
440465 CAAAAACCTTAACCTCCTC
1 CAAAAACCTTAAACTCCTC
440484 CA
1 CA
440486 GCATCTGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.40, C:0.35, G:0.03, T:0.23
Consensus pattern (19 bp):
CAAAAACCTTAAACTCCTC
Found at i:445257 original size:185 final size:179
Alignment explanation
Indices: 444642--445256 Score: 868
Period size: 177 Copynumber: 3.4 Consensus size: 179
444632 ACGTTAATAA
* *
444642 TAGCTGACGACATAAAGAGAGATATCTGAATAATTGTGTCGTAATATTATGTGGATGACTTGAAG
1 TAGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGAAG
* *
444707 GAAAT-TTGAT-AC-TAGCAAGACTGGCATATATCTTCAATATATATATATACAGTTGCTTGAGA
66 G-AATGTTGATAACATAGCAAGACTGGCATATATCTTCAAT-T-TATATATACAGCTACTTGAGA
444769 TATATTGACAAAACCGCCTAAACATAAAGATATTTGTAACAAAATGCACTAG
128 TATATTGACAAAACCGCCTAAACATAAAGATATTTGTAACAAAATGCACTAG
* *
444821 TAGCTGACTACATAAAGAGAGAT-T-TGAGTAATAGTGTTGTAATATTATGTGGATGACTTGAAG
1 TAGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGAAG
* * * * * * *
444884 AAATATTGGTAA-A-AGCATGTCTGGCATATATCTTCAATTTAAATATACAGCTACTTGAGGTAT
66 GAATGTTGATAACATAGCAAGACTGGCATATATCTTCAATTTATATATACAGCTACTTGAGATAT
* *
444947 ATTAACAAAACCGCCTAAACATAAAGATATTTGTAACAAAATGTACTAG
131 ATTGACAAAACCGCCTAAACATAAAGATATTTGTAACAAAATGCACTAG
**
444996 TAGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGAGATGACA
1 TAGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGA-A
* *
445061 -GAATGTTGATATCAACATTAGCAAGACTGGCATATATCCTCAATTTATATGTACAGCTACTTGA
65 GGAATGTTG--AT-AACA-TAGCAAGACTGGCATATATCTTCAATTTATATATACAGCTACTTGA
* *
445125 GATATATTGACAAAACCGCCAAAAAATATAAAGATATTTGTAACAAAATGCACTAG
126 GATATATTGACAAAACCGCC--TAAACATAAAGATATTTGTAACAAAATGCACTAG
* * *
445181 TAGCTGACTACATAAATAGAGATATCTGAGTAATTGTGTCGTAATATGATGTGGATGACCTGAAG
1 TAGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGAAG
445246 GAATGTTGATA
66 GAATGTTGATA
445257 TTAACAACCC
Statistics
Matches: 386, Mismatches: 35, Indels: 27
0.86 0.08 0.06
Matches are distributed among these distances:
175 90 0.23
176 5 0.01
177 102 0.26
178 3 0.01
179 23 0.06
180 2 0.01
181 1 0.00
182 1 0.00
183 60 0.16
184 1 0.00
185 98 0.25
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (179 bp):
TAGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATTATGTGGATGACTTGAAG
GAATGTTGATAACATAGCAAGACTGGCATATATCTTCAATTTATATATACAGCTACTTGAGATAT
ATTGACAAAACCGCCTAAACATAAAGATATTTGTAACAAAATGCACTAG
Found at i:448858 original size:180 final size:179
Alignment explanation
Indices: 448556--448914 Score: 700
Period size: 180 Copynumber: 2.0 Consensus size: 179
448546 CACATTCTGT
448556 CATGGTAACAGATTTACACTTCCATTTACAATACATCCAATGATTTTTACAATAAGTGAACAAGG
1 CATGGTAACAGATTTACACTTCCATTTACAATACATCCAATGATTTTTACAATAAGTGAACAAGG
448621 AGGACCGATTTGCACTCAAATTTATGGATAAAATGGGATTTTTGTGTGTGATGGAAACAAACTAT
66 AGGACCGATTTGCACTCAAATTTATGGATAAAATGGGATTTTTGTGTGTGATGGAAACAAACTAT
448686 ATGGTCATTCTGCAAAGGGGAATCCGTGTGTCGCTGTTGCTAATGCGAA
131 ATGGTCATTCTGCAAAGGGGAATCCGTGTGTCGCTGTTGCTAATGCGAA
*
448735 NCATGGTAACAGATTTACACTTCCATTTACAATACATCCAATGATTTTTACAATATGTGAACAAG
1 -CATGGTAACAGATTTACACTTCCATTTACAATACATCCAATGATTTTTACAATAAGTGAACAAG
448800 GAGGACCGATTTGCACTCAAATTTATGGATAAAATGGGATTTTTGTGTGTGATGGAAACAAACTA
65 GAGGACCGATTTGCACTCAAATTTATGGATAAAATGGGATTTTTGTGTGTGATGGAAACAAACTA
448865 TATGGTCATTCTGCAAAGGGGAATCCGTGTGTCGCTGTTGCTAATGCGAA
130 TATGGTCATTCTGCAAAGGGGAATCCGTGTGTCGCTGTTGCTAATGCGAA
448915 AAATTCATTT
Statistics
Matches: 178, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 178 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (179 bp):
CATGGTAACAGATTTACACTTCCATTTACAATACATCCAATGATTTTTACAATAAGTGAACAAGG
AGGACCGATTTGCACTCAAATTTATGGATAAAATGGGATTTTTGTGTGTGATGGAAACAAACTAT
ATGGTCATTCTGCAAAGGGGAATCCGTGTGTCGCTGTTGCTAATGCGAA
Found at i:454498 original size:145 final size:146
Alignment explanation
Indices: 454164--454725 Score: 749
Period size: 145 Copynumber: 3.9 Consensus size: 146
454154 TTTTAAACAA
* * * * * *
454164 TGACCTTGAACTTCCTCAATTGACCTTGGGTCCAGGTCATGACACACCCTCAGGTTATAAGCAAT
1 TGACCTTGACCTTCCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * * * * *
454229 C-TTGATGTGAATTATGAACTTCCAAGGTTTCTCCATAAGATAGATATTGACCGGACACGAATTT
66 CTTTG-TGTGAAGTAAGAACTTCCAATGTTTCTCCTTAAGAAAGATATGGACCGGACACGAATTT
454293 TGCACTTTTTCTGCCAG
130 TGCACTTTTTCTGCCAG
* * * * *
454310 TGACCTTGACCTTGCTCAAATTACCTT-GGTCAAGGTCATGACACACCCTTTGGTCATAAGGAAT
1 TGACCTTGACCTTCCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * * * *
454374 CTTTGTGTGAAGCAAGAACTTCCAATGTTTTTTCTTTA-AAGGATATGGACCGGACACGAATTTT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCTTAAGAAAGATATGGACCGGACACGAATTTT
454438 GCACTTTTTCTGCCAG
131 GCACTTTTTCTGCCAG
* ** *
454454 TGTCCTTGACCTTCCCCAAATGACCTTGGGTCAAGGTCATGACACTTCCTTAGGTCATAAACAAT
1 TGACCTTGACCTTCCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * *
454519 CTTTGTGTGAAGTAAAAAC-TCAAAATATTTCTCCTTAAGAAAGATATGGACCGGACACGAATTT
66 CTTTGTGTGAAGTAAGAACTTC-CAATGTTTCTCCTTAAGAAAGATATGGACCGGACACGAATTT
454583 TGCACTTTTTCTGCCAG
130 TGCACTTTTTCTGCCAG
* * * *
454600 TGAACTTGACC-TGCCCAAATGACCTTGGGTTAAGGTCAAGACACACCCTT-GGTCATAAGCAAT
1 TGACCTTGACCTTCCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* *
454663 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCATAAGAAAAATATGGACCGGACACGAATT
66 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCTTAAGAAAGATATGGACCGGACACGAATT
454726 GAACAGACGG
Statistics
Matches: 361, Mismatches: 50, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
144 131 0.36
145 154 0.43
146 76 0.21
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (146 bp):
TGACCTTGACCTTCCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
CTTTGTGTGAAGTAAGAACTTCCAATGTTTCTCCTTAAGAAAGATATGGACCGGACACGAATTTT
GCACTTTTTCTGCCAG
Found at i:455375 original size:18 final size:18
Alignment explanation
Indices: 455354--455388 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
455344 GAAAACGGAG
455354 CAAAAAACAAACACAAAA
1 CAAAAAACAAACACAAAA
**
455372 CAAAACCCAAACACAAA
1 CAAAAAACAAACACAAA
455389 CCATTTGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (18 bp):
CAAAAAACAAACACAAAA
Found at i:456137 original size:8 final size:8
Alignment explanation
Indices: 456095--456139 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
456085 ATCACATTTT
456095 GTCTGT-C
1 GTCTGTCC
*
456102 GTCTGTCT
1 GTCTGTCC
*
456110 GTCAGTCC
1 GTCTGTCC
*
456118 GTCCGTCC
1 GTCTGTCC
456126 GTCTGTCC
1 GTCTGTCC
456134 GTCTGT
1 GTCTGT
456140 AAACTTTTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.02, C:0.33, G:0.27, T:0.38
Consensus pattern (8 bp):
GTCTGTCC
Found at i:456332 original size:1 final size:1
Alignment explanation
Indices: 456288--456312 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
456278 TCAAAACTGT
456288 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
456313 GGGGGGGCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:471324 original size:80 final size:79
Alignment explanation
Indices: 471186--471351 Score: 296
Period size: 80 Copynumber: 2.1 Consensus size: 79
471176 GCACTGTAAA
*
471186 ATTTTATGTAATGGTGAAATTTGTAAATATTAAGTCTTTAACTCATGATTTACTAATATCATATT
1 ATTTTATGTAATGGTGAAATTTGTAAATATTAAGTCTTTAACTCATGATTTACTAATATCAAATT
*
471251 GGGGCTTTGACATG
66 AGGGCTTTGACATG
*
471265 ATTTTCATGTAATGGTGAAATTTGTAAATATTCAGTCTTTAACTCATGATTTACTAATATCAAAT
1 ATTTT-ATGTAATGGTGAAATTTGTAAATATTAAGTCTTTAACTCATGATTTACTAATATCAAAT
471330 TAGGGCTTTGACATG
65 TAGGGCTTTGACATG
471345 ATTTTAT
1 ATTTTAT
471352 TTTCTTCAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
79 7 0.08
80 76 0.92
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (79 bp):
ATTTTATGTAATGGTGAAATTTGTAAATATTAAGTCTTTAACTCATGATTTACTAATATCAAATT
AGGGCTTTGACATG
Found at i:478734 original size:146 final size:146
Alignment explanation
Indices: 478470--479262 Score: 994
Period size: 146 Copynumber: 5.4 Consensus size: 146
478460 CCCAATTCCA
* *
478470 TCCGGTCCATATCTTTCTTATGGAGAAACATTGTAAGTTCTTACTTCACACAAAGATTGCTTATG
1 TCCGGTCCATATCTTTCTTATGGAGAGACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATG
*
478535 ACCTAATGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAA
66 ACCTAAGGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAA
*
478600 AAATACAAAATTCGTG
131 AAGTACAAAATTCGTG
** * *
478616 TCCGGTCCATATCTTTCCAATGGAGAGTCATTGGAAGTTCTTACTTCACACAAAGAGTGCTTATG
1 TCCGGTCCATATCTTTCTTATGGAGAGACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATG
* ** * * *
478681 ACCGACTGGTGTGTCATGACCTTGATTC-AAGGTTATTTGGGCAAGATCAAGGTCACTGGCAGAA
66 ACCTAAGGGTGTGTCATGACCTTGA-CCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAA
* *
478745 AAAATACAAAAAATCGTG
130 AAAGTAC-AAAATTCGTG
* ** * *
478763 TCTGGTCCATATCTTTCTTATGGAGAGTTATTGGAAGTTCTTACTTCAAACAAAGGTTGCTTATG
1 TCCGGTCCATATCTTTCTTATGGAGAGACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATG
** * *
478828 ACCTAAGAATGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTAGCAGAAA
66 ACCTAAGGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAA
* *
478893 AAGTGCAAAATTTGTG
131 AAGTACAAAATTCGTG
* *
478909 TCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTAATTCACACAAAGATTGCTTATG
1 TCCGGTCCATATCTTTCTTATGGAGAGACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATG
* * *** *
478974 ACCTAAGGGTGTGTCATGACC-TAATCAAAGGTCATTTGGGCAAGGTCAAGGTTGTTGG-GGAAA
66 ACCTAAGGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAA
* * * *
479037 ATGGTGCAACATTTGTG
131 A-AGTACAAAATTCGTG
* * *
479054 TCCGGT-TATTATCTTTCTTATGGAGA-AGCATT-GAATGTTCTAACTTCACACAAATATTGCTT
1 TCCGGTCCA-TATCTTTCTTATGGAGAGA-CATTGGAA-GTTCTTACTTCACACAAAGATTGCTT
* *
479116 ATGACCAAAGGGTGTGTCATGACCTTGACCTAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAG
63 ATGACCTAAGGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAG
479181 AAAAAGTGA-AAAATTCGTG
128 AAAAAGT-ACAAAATTCGTG
* * * *
479200 TCCGGT-CATTATCTTTCTTATGGATA-AGCATT-GAATGTTCGTACTTCCCACAAATATTGCTT
1 TCCGGTCCA-TATCTTTCTTATGGAGAGA-CATTGGAA-GTTCTTACTTCACACAAAGATTGCTT
479262 A
63 A
479263 CATTTGTATG
Statistics
Matches: 565, Mismatches: 72, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
144 10 0.02
145 116 0.21
146 308 0.55
147 131 0.23
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (146 bp):
TCCGGTCCATATCTTTCTTATGGAGAGACATTGGAAGTTCTTACTTCACACAAAGATTGCTTATG
ACCTAAGGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAA
AAGTACAAAATTCGTG
Found at i:479187 original size:291 final size:292
Alignment explanation
Indices: 478470--479262 Score: 1035
Period size: 293 Copynumber: 2.7 Consensus size: 292
478460 CCCAATTCCA
*
478470 TCCGGTCCATATCTTTCTTATGGAGAAACATTGTAAGTTCTTACTTCACACAAAGATTGCTTATG
1 TCCGGTCCATATCTTTCTTATGGAGAAGCATTG-AAGTTCTTACTTCACACAAAGATTGCTTATG
*
478535 ACCTAATGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAA
65 ACCTAAGGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAA
* * ** **
478600 AAATACAAAATTCGTGTCCGGTCCATATCTTTCCAATGGAGAGTCATTGGAAGTTCTTACTTCAC
130 AAGTGCAAAATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCAC
* ** * *
478665 ACAAAGAGTGCTTATGACCGACTGGTGTGTCATGACCTTGATTCAAGGTTATTTGGGCAAGATCA
195 ACAAAGATTGCTTATGACCGAAGGGTGTGTCATGACCTTGAATCAAGGTCATTTGGGCAAGATCA
478730 AGGTCACTGGCAGAAAAAATACAAAAAATCGTG
260 AGGTCACTGGCAGAAAAAATACAAAAAATCGTG
* * * *
478763 TCTGGTCCATATCTTTCTTATGGAG-AGTTATTGGAAGTTCTTACTTCAAACAAAGGTTGCTTAT
1 TCCGGTCCATATCTTTCTTATGGAGAAG-CATT-GAAGTTCTTACTTCACACAAAGATTGCTTAT
** * *
478827 GACCTAAGAATGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTAGCAGAA
64 GACCTAAGGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAA
* *
478892 AAAGTGCAAAATTTGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTAATTCA
129 AAAGTGCAAAATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCA
* *
478957 CACAAAGATTGCTTATGACCTAAGGGTGTGTCATGACC-T-AATCAAAGGTCATTTGGGCAAGGT
194 CACAAAGATTGCTTATGACCGAAGGGTGTGTCATGACCTTGAATC-AAGGTCATTTGGGCAAGAT
*** * ** * * * *
479020 CAAGGTTGTTGG-GGAAAATGGTGC-AACATTTGTG
258 CAAGGTCACTGGCAGAAAA-AATACAAAAAATCGTG
* * *
479054 TCCGGT-TATTATCTTTCTTATGGAGAAGCATTGAATGTTCTAACTTCACACAAATATTGCTTAT
1 TCCGGTCCA-TATCTTTCTTATGGAGAAGCATTGAA-GTTCTTACTTCACACAAAGATTGCTTAT
* *
479118 GACCAAAGGGTGTGTCATGACCTTGACCTAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAA
64 GACCTAAGGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAA
* * * *
479183 AAAGTGAAAAATTCGTGTCCGGT-CATTATCTTTCTTATGGATAAGCATT-GAATGTTCGTACTT
129 AAAGTGCAAAATTCGTGTCCGGTCCA-TATCTTTCTTATGGAGAAACATTGGAA-GTTCTTACTT
* *
479246 CCCACAAATATTGCTTA
192 CACACAAAGATTGCTTA
479263 CATTTGTATG
Statistics
Matches: 436, Mismatches: 55, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
290 9 0.02
291 188 0.43
292 32 0.07
293 206 0.47
294 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.31
Consensus pattern (292 bp):
TCCGGTCCATATCTTTCTTATGGAGAAGCATTGAAGTTCTTACTTCACACAAAGATTGCTTATGA
CCTAAGGGTGTGTCATGACCTTGACCAAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAAA
AGTGCAAAATTCGTGTCCGGTCCATATCTTTCTTATGGAGAAACATTGGAAGTTCTTACTTCACA
CAAAGATTGCTTATGACCGAAGGGTGTGTCATGACCTTGAATCAAGGTCATTTGGGCAAGATCAA
GGTCACTGGCAGAAAAAATACAAAAAATCGTG
Found at i:484273 original size:37 final size:36
Alignment explanation
Indices: 484223--484322 Score: 139
Period size: 37 Copynumber: 2.7 Consensus size: 36
484213 AAAGATAGGT
*
484223 AAAGTTAGCTACTAGTAACTGGCTACGAGAAGTAAGA-
1 AAAGTTAGCTACTAGTAACTGGCTACGAG-A-TAAAAC
*
484260 AAAGTTAGCTACTAGTAACTGGCTAAGAGATAAAATC
1 AAAGTTAGCTACTAGTAACTGGCTACGAGATAAAA-C
*
484297 AAAGTTGGCTACTAGTAACTGGCTAC
1 AAAGTTAGCTACTAGTAACTGGCTAC
484323 TAGTAACTGG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 4 0.07
36 1 0.02
37 52 0.91
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (36 bp):
AAAGTTAGCTACTAGTAACTGGCTACGAGATAAAAC
Found at i:484321 original size:14 final size:14
Alignment explanation
Indices: 484302--484334 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
484292 AAATCAAAGT
484302 TGGCTACTAGTAAC
1 TGGCTACTAGTAAC
484316 TGGCTACTAGTAAC
1 TGGCTACTAGTAAC
484330 TGGCT
1 TGGCT
484335 TCGAGAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (14 bp):
TGGCTACTAGTAAC
Found at i:485580 original size:175 final size:177
Alignment explanation
Indices: 485030--485764 Score: 980
Period size: 175 Copynumber: 4.2 Consensus size: 177
485020 TAATAATAGA
*
485030 ATGTGGATGACTTGAAGGAATGTTGATATTAGCAAGACTGGCATATATCTTCAATTTATATATAC
1 ATGTGGATGACTTGAAGGAATGTTGATATTAGCAACACTGGCATATATCTTCAATTTATATATAC
* * * * *
485095 AGCTACTCGAGATATATTGACAAAACCA-CCAAAAAATAAAGACATTTGTAACAAAATACACTAG
66 AGCTACTTGAGATATATTGACAAAACCAGCC-ACAAATAAAGATATATGTAACAAAATGCACTAG
* *
485159 TAGCTGACTACATAAAAAGAGATATCTGAGTAATTGTGTCGTAATAAT
130 TAGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATT
*** *
485207 ATGTGGATGACTTGAAGGAATGTTGATATTAGCATGTCTGGCATATATCTTCAATATATATTTAT
1 ATGTGGATGACTTGAAGGAATGTTGATATTAGCAACACTGGCATATATCTTCAAT-T-TATATAT
* * * * *
485272 ACAGGTACTGTGAGATATATTGTCAAAATC-GCCA-AATATAAAGATATTTGTAACAAAATGTAC
64 ACAGCTACT-TGAGATATATTGACAAAACCAGCCACAA-ATAAAGATATATGTAACAAAATGCAC
* *
485335 TAGCAGCTGACTACATAAA-A-AG--A---GAGTAATTGTGTCGTAACATT
127 TAGTAGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATT
* * * * * * *
485379 ATGTTGATGACTTGAAGGATTGTTGATATTAGCAACATTAGCATATATCTTCAATTTCTTTGTAC
1 ATGTGGATGACTTGAAGGAATGTTGATATTAGCAACACTGGCATATATCTTCAATTTATATATAC
*
485444 AGCTACTTGAGATATATTGACAAAA-CAGCCACAAA-AAAGATATATGTAACAAAATGCATTAGT
66 AGCTACTTGAGATATATTGACAAAACCAGCCACAAATAAAGATATATGTAACAAAATGCACTAGT
485507 AGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAAT-TAT
131 AGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATAT-T
*
485554 ATGTGGATGACTTGAAGGAATGTTGATATTAGCAAGACTGGCATATATCTTCAATTTATATATAC
1 ATGTGGATGACTTGAAGGAATGTTGATATTAGCAACACTGGCATATATCTTCAATTTATATATAC
*
485619 AGCTACTTGAAATATATTGACAAAA-CAGCCACAAA-AAAGATATATGTAACAAAATGCACTAGT
66 AGCTACTTGAGATATATTGACAAAACCAGCCACAAATAAAGATATATGTAACAAAATGCACTAGT
* *
485682 AGCTGACTACATAAAGAAAAATATCTGAGTAATTGTGTCGTAATATT
131 AGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATT
* * * *
485729 ATGTAGATGACCTGATA-TAATGTTGATATTATCAAC
1 ATGTGGATGACTTGA-AGGAATGTTGATATTAGCAAC
485765 CCTTGAAGAT
Statistics
Matches: 495, Mismatches: 46, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
168 40 0.08
169 23 0.05
170 17 0.03
171 1 0.00
172 68 0.14
174 1 0.00
175 209 0.42
176 2 0.00
177 55 0.11
178 4 0.01
179 56 0.11
180 19 0.04
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (177 bp):
ATGTGGATGACTTGAAGGAATGTTGATATTAGCAACACTGGCATATATCTTCAATTTATATATAC
AGCTACTTGAGATATATTGACAAAACCAGCCACAAATAAAGATATATGTAACAAAATGCACTAGT
AGCTGACTACATAAAGAGAGATATCTGAGTAATTGTGTCGTAATATT
Found at i:486093 original size:42 final size:42
Alignment explanation
Indices: 486039--486147 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 42
486029 CAAAACCTTC
* *
486039 CGAAACGAAACGAAACCTAT-CGAAACGAAGCGAAATAAAAAT
1 CGAAACGAAACGAAACCTATCCAAAACGAAACGAAA-AAAAAT
* **
486081 CGAAACGAAACGAAACCT-TCCAAAATGAAACGAAACCAAAT
1 CGAAACGAAACGAAACCTATCCAAAACGAAACGAAAAAAAAT
*
486122 CGAAACAAAACGAAACCTA-CCAAAAC
1 CGAAACGAAACGAAACCTATCCAAAAC
486148 AATATTAACA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
41 28 0.48
42 30 0.52
ACGTcount: A:0.55, C:0.24, G:0.13, T:0.08
Consensus pattern (42 bp):
CGAAACGAAACGAAACCTATCCAAAACGAAACGAAAAAAAAT
Found at i:486112 original size:62 final size:63
Alignment explanation
Indices: 486019--486136 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 63
486009 CGAAATCTGC
* * * *
486019 CGAAACGAAACAAAACCTTCCGAAACGAAACGAAACC-TATCGAAACGAAGCGAAATAAAAAT
1 CGAAACGAAACAAAACCTTCCAAAACGAAACGAAACCAAATCGAAACAAAACGAAATAAAAAT
* *
486081 CGAAACGAAACGAAACCTTCCAAAATGAAACGAAACCAAATCGAAACAAAACGAAA
1 CGAAACGAAACAAAACCTTCCAAAACGAAACGAAACCAAATCGAAACAAAACGAAA
486137 CCTACCAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 34 0.69
63 15 0.31
ACGTcount: A:0.55, C:0.23, G:0.14, T:0.08
Consensus pattern (63 bp):
CGAAACGAAACAAAACCTTCCAAAACGAAACGAAACCAAATCGAAACAAAACGAAATAAAAAT
Found at i:486149 original size:20 final size:20
Alignment explanation
Indices: 485980--486147 Score: 138
Period size: 20 Copynumber: 8.2 Consensus size: 20
485970 GAAACGAAAT
*
485980 GAAACGAAACGAAATCTACC
1 GAAACGAAACGAAACCTACC
* * *
486000 GAAACAAAACGAAATCTGCC
1 GAAACGAAACGAAACCTACC
* *
486020 GAAACGAAACAAAACCTTCC
1 GAAACGAAACGAAACCTACC
*
486040 GAAACGAAACGAAACCTATC
1 GAAACGAAACGAAACCTACC
* *** *
486060 GAAACGAAGCGAAATAAAAATC
1 GAAACGAAACG-AA-ACCTACC
*
486082 GAAACGAAACGAAACCTTCC
1 GAAACGAAACGAAACCTACC
* * * *
486102 AAAATGAAACGAAACCAAATC
1 GAAACGAAACGAAACC-TACC
*
486123 GAAACAAAACGAAACCTACC
1 GAAACGAAACGAAACCTACC
*
486143 AAAAC
1 GAAAC
486148 AATATTAACA
Statistics
Matches: 115, Mismatches: 30, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
20 83 0.72
21 18 0.16
22 14 0.12
ACGTcount: A:0.54, C:0.24, G:0.13, T:0.09
Consensus pattern (20 bp):
GAAACGAAACGAAACCTACC
Found at i:494225 original size:3 final size:3
Alignment explanation
Indices: 494219--494247 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
494209 TGTTAATGTA
494219 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
494248 AGAATACTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:495108 original size:443 final size:442
Alignment explanation
Indices: 494282--495166 Score: 1761
Period size: 443 Copynumber: 2.0 Consensus size: 442
494272 AGAGCAATGC
494282 GACTGAAAAACATTGACTGCCATCATAACTTGCTATTGAGGTGTTATATAGTGCATTTTCCCCCT
1 GACTGAAAAACATTGACTGCCATCATAACTTGCTATTGAGGTGTTATATAGTGCATTTTCCCCCT
494347 AGCCATCTTTCCCCCGGAAAAATGGCTATATAGCAGTTTTCCCCACGGAAAAATGGCTATATAGT
66 AGCCATCTTTCCCCCGGAAAAATGGCTATATAGCAGTTTTCCCCACGGAAAAATGGCTATATAGT
494412 GGGCTTTCCCCCTTTTTATAGCCAGATTACCCCCACGGAAAACCTCATATATAGTGGATTTTCCC
131 GGGCTTTCCCCCTTTTTATAGCCAGATTACCCCCACGGAAAACCTCATATATAGTGGATTTTCCC
494477 CCATTTTTACTTTCCGGCCATGTTTATTGCGGACCATTCGTGACAATAATTTGCAATAATTGATA
196 CCATTTTTACTTTCCGGCCATGTTTATTGCGGACCATTCGTGACAATAATTTGCAATAATTGATA
494542 TGATATTAATTTCTCACAAAAAAGGATAATTATGGCATTTATTAATACATAGAATAAAATACATG
261 TGATATTAATTTCTCACAAAAAAGGATAATTATGGCATTTATTAATACATAGAATAAAATACATG
494607 GTTTTTCAACCCCAAATATGAACTAAGGCATGCGCCTTCATAACATTCATGTGTCATCATCGTTT
326 GTTTTTCAACCCCAAATATGAACTAAGGCATGCGCCTTCATAACATTCATGTGTCATCATCGTTT
494672 ATTTCACCTGTTCTCACACCTTTTTGGAACGCCTTTTACACGGATTTCGGAA
391 ATTTCACCTGTTCTCACACCTTTTTGGAACGCCTTTTACACGGATTTCGGAA
494724 NGACTGAAAAACATTGACTGCCATCATAACTTGCTATTGAGGTGTTATATAGTGCATTTTCCCCC
1 -GACTGAAAAACATTGACTGCCATCATAACTTGCTATTGAGGTGTTATATAGTGCATTTTCCCCC
494789 TAGCCATCTTTCCCCCGGAAAAATGGCTATATAGCAGTTTTCCCCACGGAAAAATGGCTATATAG
65 TAGCCATCTTTCCCCCGGAAAAATGGCTATATAGCAGTTTTCCCCACGGAAAAATGGCTATATAG
494854 TGGGCTTTCCCCCTTTTTATAGCCAGATTACCCCCACGGAAAACCTCATATATAGTGGATTTTCC
130 TGGGCTTTCCCCCTTTTTATAGCCAGATTACCCCCACGGAAAACCTCATATATAGTGGATTTTCC
494919 CCCATTTTTACTTTCCGGCCATGTTTATTGCGGACCATTCGTGACAATAATTTGCAATAATTGAT
195 CCCATTTTTACTTTCCGGCCATGTTTATTGCGGACCATTCGTGACAATAATTTGCAATAATTGAT
494984 ATGATATTAATTTCTCACAAAAAAGGATAATTATGGCATTTATTAATACATAGAATAAAATACAT
260 ATGATATTAATTTCTCACAAAAAAGGATAATTATGGCATTTATTAATACATAGAATAAAATACAT
495049 GGTTTTTCAACCCCAAATATGAACTAAGGCATGCGCCTTCATAACATTCATGTGTCATCATCGTT
325 GGTTTTTCAACCCCAAATATGAACTAAGGCATGCGCCTTCATAACATTCATGTGTCATCATCGTT
495114 TATTTCACCTGTTCTCACACCTTTTTGGAACGCCTTTTACACGGATTTCGGAA
390 TATTTCACCTGTTCTCACACCTTTTTGGAACGCCTTTTACACGGATTTCGGAA
495167 TACCTCGAAT
Statistics
Matches: 442, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
443 442 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (442 bp):
GACTGAAAAACATTGACTGCCATCATAACTTGCTATTGAGGTGTTATATAGTGCATTTTCCCCCT
AGCCATCTTTCCCCCGGAAAAATGGCTATATAGCAGTTTTCCCCACGGAAAAATGGCTATATAGT
GGGCTTTCCCCCTTTTTATAGCCAGATTACCCCCACGGAAAACCTCATATATAGTGGATTTTCCC
CCATTTTTACTTTCCGGCCATGTTTATTGCGGACCATTCGTGACAATAATTTGCAATAATTGATA
TGATATTAATTTCTCACAAAAAAGGATAATTATGGCATTTATTAATACATAGAATAAAATACATG
GTTTTTCAACCCCAAATATGAACTAAGGCATGCGCCTTCATAACATTCATGTGTCATCATCGTTT
ATTTCACCTGTTCTCACACCTTTTTGGAACGCCTTTTACACGGATTTCGGAA
Found at i:500640 original size:12 final size:11
Alignment explanation
Indices: 500611--500639 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
500601 AATCCAGGTT
500611 GTTTTTTGTGG
1 GTTTTTTGTGG
500622 GTTTTTTGTGG
1 GTTTTTTGTGG
500633 GTTTTTT
1 GTTTTTT
500640 TTTTATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (11 bp):
GTTTTTTGTGG
Found at i:500761 original size:24 final size:24
Alignment explanation
Indices: 500731--500779 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
500721 TGTGGAATCA
500731 TTTTTGTTTGTTGGGGTCAATGTT
1 TTTTTGTTTGTTGGGGTCAATGTT
*
500755 TTTTTGTTTGTTGGGTTCAATGTT
1 TTTTTGTTTGTTGGGGTCAATGTT
500779 T
1 T
500780 GTGGTTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.04, G:0.27, T:0.61
Consensus pattern (24 bp):
TTTTTGTTTGTTGGGGTCAATGTT
Found at i:501364 original size:4 final size:4
Alignment explanation
Indices: 501355--501408 Score: 90
Period size: 4 Copynumber: 13.5 Consensus size: 4
501345 TTTGTCCGTC
* *
501355 GTCT GTCT GTCC GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCC
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
501403 GTCT GT
1 GTCT GT
501409 AAACTTTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.00, C:0.28, G:0.26, T:0.46
Consensus pattern (4 bp):
GTCT
Found at i:511601 original size:26 final size:26
Alignment explanation
Indices: 511572--511622 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
511562 TTTGTTTACA
**
511572 CGATGATGATGATGTTGATCAGATGT
1 CGATGATGATGAAATTGATCAGATGT
511598 CGATGATGATGAAATTGATCAGATG
1 CGATGATGATGAAATTGATCAGATG
511623 ACAACAGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.31
Consensus pattern (26 bp):
CGATGATGATGAAATTGATCAGATGT
Found at i:511649 original size:35 final size:35
Alignment explanation
Indices: 511599--511703 Score: 131
Period size: 35 Copynumber: 3.0 Consensus size: 35
511589 ATCAGATGTC
*
511599 GATGATGATGAAATTGATCAGATGACAACAG-TGAT
1 GATGATGATGTAATTGATCAGATGACAA-AGATGAT
* * *
511634 GATGATGATCTAATTGATCAGATGTCAATGATGAT
1 GATGATGATGTAATTGATCAGATGACAAAGATGAT
* * *
511669 GATGATGATGTAATTGATAAGATGTCAATGATGAT
1 GATGATGATGTAATTGATCAGATGACAAAGATGAT
511704 AATAAAATTG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 1 0.02
35 62 0.98
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (35 bp):
GATGATGATGTAATTGATCAGATGACAAAGATGAT
Found at i:513642 original size:4 final size:4
Alignment explanation
Indices: 513627--513672 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
513617 ATCACCCGTT
*
513627 GTCC GT-C GTCC GTCC GTCC GTCC GTCC GTCC GTCT GTCC GTCC GTC
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTC
513673 TGTAAACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 36 0.92
ACGTcount: A:0.00, C:0.46, G:0.26, T:0.28
Consensus pattern (4 bp):
GTCC
Found at i:513673 original size:12 final size:12
Alignment explanation
Indices: 513622--513675 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
513612 TTCTGATCAC
513622 CCGT-TGTCCGT
1 CCGTCTGTCCGT
*
513633 -CGTCCGTCCGT
1 CCGTCTGTCCGT
*
513644 CCGTCCGTCCGT
1 CCGTCTGTCCGT
513656 CCGTCTGTCCGT
1 CCGTCTGTCCGT
513668 CCGTCTGT
1 CCGTCTGT
513676 AAACTTTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
10 3 0.08
11 6 0.15
12 30 0.77
ACGTcount: A:0.00, C:0.43, G:0.26, T:0.31
Consensus pattern (12 bp):
CCGTCTGTCCGT
Found at i:514894 original size:16 final size:17
Alignment explanation
Indices: 514875--514908 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
514865 CGTCACAATA
514875 TACT-GGCGAGAAATGG
1 TACTCGGCGAGAAATGG
514891 TACTCGGCGAGAAATGG
1 TACTCGGCGAGAAATGG
514908 T
1 T
514909 CGCACTCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.21
Consensus pattern (17 bp):
TACTCGGCGAGAAATGG
Found at i:520575 original size:2 final size:2
Alignment explanation
Indices: 520568--520619 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
520558 CCCCCTACCC
520568 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
520610 AG AG AG AG AG
1 AG AG AG AG AG
520620 CCCGGTACCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:524470 original size:14 final size:14
Alignment explanation
Indices: 524451--524480 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
524441 ACACTAACGC
524451 TTACATTGATACCA
1 TTACATTGATACCA
524465 TTACATTGATACCA
1 TTACATTGATACCA
524479 TT
1 TT
524481 GATACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (14 bp):
TTACATTGATACCA
Found at i:527474 original size:2 final size:2
Alignment explanation
Indices: 527467--527528 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
527457 ACTCTTTACC
527467 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
527509 CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
527529 GTGTATTTTC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:539067 original size:2 final size:2
Alignment explanation
Indices: 539060--539129 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
539050 TAAGACCGAT
*
539060 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
539102 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
539130 NNNNNNNNNN
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:542330 original size:5 final size:5
Alignment explanation
Indices: 542308--542343 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
542298 CCCCCCCCAC
542308 AAAC- AAAC- AAAC- AAACA AAACA AAACA AAACA AAAC
1 AAACA AAACA AAACA AAACA AAACA AAACA AAACA AAAC
542344 GATAGTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.39
5 19 0.61
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (5 bp):
AAACA
Found at i:560089 original size:18 final size:18
Alignment explanation
Indices: 560066--560101 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
560056 ATCACTTCGC
560066 AACCACTATTGAAATAAA
1 AACCACTATTGAAATAAA
560084 AACCACTATTGAAATAAA
1 AACCACTATTGAAATAAA
560102 TTAGTTCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.22
Consensus pattern (18 bp):
AACCACTATTGAAATAAA
Found at i:560131 original size:85 final size:84
Alignment explanation
Indices: 560021--560185 Score: 226
Period size: 85 Copynumber: 2.0 Consensus size: 84
560011 GTGTATGTGT
* *
560021 TTCAATAGTGGTTGGGAATGCATTTCAT-TAGAAAAATCACTTCGCAACCACTATTGAAATAAAA
1 TTCAATACTGGTTGGGAATGCATTTCATCT-GAAAAATCACTTCACAACCACTATTGAAAT-AAA
560085 ACCACTA-TTGAAATAAATTAG
64 ACCACTACTT-AAATAAATTAG
* * * * *
560106 TTCAATACTGGTTGGGAATGTATTTCATCTGAAGAATCACTTTACAACCAGTATTGAAATACAAC
1 TTCAATACTGGTTGGGAATGCATTTCATCTGAAAAATCACTTCACAACCACTATTGAAATAAAAC
560171 CACTACTTAAATAAA
66 CACTACTTAAATAAA
560186 ATATTTAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
84 16 0.23
85 54 0.76
86 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (84 bp):
TTCAATACTGGTTGGGAATGCATTTCATCTGAAAAATCACTTCACAACCACTATTGAAATAAAAC
CACTACTTAAATAAATTAG
Found at i:560672 original size:53 final size:53
Alignment explanation
Indices: 560482--560673 Score: 201
Period size: 53 Copynumber: 3.6 Consensus size: 53
560472 TTATAAATAT
* * * * * *
560482 CACTATT-AATATAAATTATTTCAATAGGGGTTGGGGGTTA-C-TTCACTACGAC
1 CACTATTGAA-ATAAATTATTTCAATAGTGGTT-GAGGATACCATTCATTCCAAC
* * * * *
560534 CACTATTGAAATATATTATTTCAATAGTGGTTAAGGATGCGATTCATTTCAAC
1 CACTATTGAAATAAATTATTTCAATAGTGGTTGAGGATACCATTCATTCCAAC
* * * *
560587 CACTATTGAAATAATTTATTTCAATAGTGGTTGGGGATACCTTTTATTCCAAC
1 CACTATTGAAATAAATTATTTCAATAGTGGTTGAGGATACCATTCATTCCAAC
*
560640 CACTATTGAAATAAAGTATTTCAATAGTGGTTGA
1 CACTATTGAAATAAATTATTTCAATAGTGGTTGA
560674 TGATGCATTT
Statistics
Matches: 115, Mismatches: 22, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
51 3 0.03
52 27 0.23
53 85 0.74
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (53 bp):
CACTATTGAAATAAATTATTTCAATAGTGGTTGAGGATACCATTCATTCCAAC
Found at i:561086 original size:53 final size:53
Alignment explanation
Indices: 560901--561084 Score: 255
Period size: 53 Copynumber: 3.5 Consensus size: 53
560891 ATAACATCCT
* * *
560901 ACCACTATTAAAATATTTTATTTCAATAATGGTTGTAAT-AAACCGCAT-CCTTA
1 ACCACTATTGAAATAATTTATTTCAATAGTGGTTGTAATGAAA-CGCATACC-TA
* * *
560954 ACCACTATTGAAATAAATTAATTCAATAGTGGTTGTAATGAAATGCATACCTA
1 ACCACTATTGAAATAATTTATTTCAATAGTGGTTGTAATGAAACGCATACCTA
* * *
561007 GCCACTATTGAAATAATTTATTTCATTAGTGGTTATAATGAAACGCATACCTA
1 ACCACTATTGAAATAATTTATTTCAATAGTGGTTGTAATGAAACGCATACCTA
561060 ACCACTATTGAAATAATTTATTTCA
1 ACCACTATTGAAATAATTTATTTCA
561085 TTCAATATTG
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
53 111 0.96
54 5 0.04
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (53 bp):
ACCACTATTGAAATAATTTATTTCAATAGTGGTTGTAATGAAACGCATACCTA
Found at i:561578 original size:67 final size:66
Alignment explanation
Indices: 561435--561583 Score: 235
Period size: 67 Copynumber: 2.2 Consensus size: 66
561425 ATAGTGGTTG
* *
561435 TATTTCAATAGTGTTTGCAAAGTGATTTCTCTAATGAATACGTCCCCAACCACTATTGAAATAAT
1 TATTTCAATAGTGGTTGCAAAGTGATTTCTCTAATGAATACATCCCCAACCACTATTGAAATAAT
561500 T
66 T
* * * *
561501 TATTTCAATAGTGGTTGCAAGGTGATTTTTCTAATGAAATACATTCCGAACCACTATTGAAATAA
1 TATTTCAATAGTGGTTGCAAAGTGATTTCTCTAATG-AATACATCCCCAACCACTATTGAAATAA
561566 TT
65 TT
561568 TATTTCAATAGTGGTT
1 TATTTCAATAGTGGTT
561584 TTATTTCAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
66 33 0.43
67 43 0.57
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (66 bp):
TATTTCAATAGTGGTTGCAAAGTGATTTCTCTAATGAATACATCCCCAACCACTATTGAAATAAT
T
Found at i:561588 original size:17 final size:17
Alignment explanation
Indices: 561566--561600 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
561556 ATTGAAATAA
561566 TTTATTTCAATAGTGGT
1 TTTATTTCAATAGTGGT
561583 TTTATTTCAATAGTGGT
1 TTTATTTCAATAGTGGT
561600 T
1 T
561601 GCAACAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.17, T:0.54
Consensus pattern (17 bp):
TTTATTTCAATAGTGGT
Found at i:567004 original size:96 final size:94
Alignment explanation
Indices: 566972--568751 Score: 1435
Period size: 96 Copynumber: 18.6 Consensus size: 94
566962 ATCACCCCCG
*
566972 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCAAAATGTCCATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
** * *
567037 ACAGGCAGCTGTAAGTGGTGTCCACTTCCCA
66 ACAGGCTTCTGTAAGTGGTGTTC-C-TACCA
* * *
567068 TCATTTAGGTTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACAACATTTAAATGTCCATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
* *
567133 ACAGGCTTCTGTAAGTGGTGTCCTCTTACTA
66 ACAGGCTTCTGTAAGTGGTGT--TCCTACCA
* *
567164 TCATTTAGATTGACTTCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGGCCATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
567229 ACAGGCTTCTGTAAGTGGTGTTCTCTTACCA
66 ACAGGCTTCTGTAAGTGGTGTTC-C-TACCA
567260 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
** * *
567325 ACAGGCAGCTGTAAGTGGTGTCCACTTCCCA
66 ACAGGCTTCTGTAAGTGGTGTTC-C-TACCA
* * *
567356 TCATTTAGGTTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACAACATTTAAATGTCCATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
* *
567421 ACAGGCTTCTGTAAGTGGTGTCCTCTTACTA
66 ACAGGCTTCTGTAAGTGGTGT--TCCTACCA
* *
567452 TCATTTAGATTGACTTCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGGCCATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
567517 ACAGGCTTCTGTAAGTGGTGTTCTCTTACCA
66 ACAGGCTTCTGTAAGTGGTGTTC-C-TACCA
567548 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
*
567613 ACAGGCTTCTGTAAGTGGTGTTCTGTCACCA
66 ACAGGCTTCTGTAAGTGGTGTTC-CT-ACCA
* **
567644 TCATTGAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTATT
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
* * *
567709 ACAGGCTGCTGTAAGTGGTGTATTTGCT-CCG
66 ACAGGCTTCTGTAAGTGGTG---TTCCTACCA
567740 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
* *
567805 ACAGGCTTCTGTAAGTGGTGTCCTCTTACTA
66 ACAGGCTTCTGTAAGTGGTGT--TCCTACCA
567836 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCA--AAT
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAA-
** * * *
567899 GAACAGGCCACTGTAAGTGGTGTATCATCCCCG
65 G-ACAGGCTTCTGTAAGTGGTGT-TCCT-ACCA
* * ** ** * * ** ** * * * *
567932 TAAATTCTATTGACATCAGCGCTT-GTTCCAATCAATTTCTCTACTATTTGCGAATTAT-CGTTG
1 TCATTTAGATTGACATCAGCTTTTCCTT-CAATCAGTTTCTGAACTACAT-CTAAATGTCCATT-
* * * * * ** *
567995 TA-ACATGCTGCTATTAGTGGTGTTAATATTCCG
63 AAGACAGGCTTCTGTAAGTGGTGTTCCTA--CCA
* * * *** * * * * * * * *
568028 TTATCTAGGTTGACATCAGCGCCTGCTTCAATTAATTTCTGAGCTATC-GCTAAATATCCATCAT
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTA-CATCTAAATGTCCATTAA
* * * * ** *
568092 TACTAGCCGATAT-TAA-TGGTGTTTGATTTCCGA
65 GAC-AGGC-TTCTGTAAGTGGTG-TT-CCTACC-A
* * *** ** * * *
568125 -C-TTTAAAATTAACATCAGCGCCTGATTCGATCAGTTTTTGAGCTACATCTAAATGTCCA-TAA
1 TCATTT-AGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAA
* * * * *
568187 CAACATGCTGCTGTTAGTGGTGTATATGCT-CC-
65 -GACAGGCTTCTGTAAGTGGTG--T-TCCTACCA
* * *** * *
568219 TCATTAACATTGACATCAGCGCCTGCTCCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
* * * ** * *
568284 ACAGGCTGCTATTAGTGGTGTATATTTTCCG
66 ACAGGCTTCTGTAAGTGGTGT-T-CCTACCA
* *** * * * * *
568315 TCATTTAGTTTGACATCAGCGCCTGCTTCAATTAATTTCTGAACTACATCCAAATGTCC-TCTCT
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCAT-T-A
* * * * * *
568379 TG-CATGCTGCTGTAAGTGGTGTGTCATCCCGG
64 AGACAGGCTTCTGTAAGTGGTGT-TCCTACC-A
* * * ***** * * ** ** * *
568411 TAAATTT-CATAGACATCAGCGCCAGCTCCAATCAATTTCTCTACTATTTGTGAATGTCCATTAT
1 T-CATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTA-
* * * * * * *
568475 A-ACATGCTGCTATTAGAGGTGTAT-ATAATCCG
64 AGACAGGCTTCTGTAAGTGGTGT-TCCT-A-CCA
* * * * * *
568507 TCATCTAGGTTGACATTAGCTTTTCCTTCTATCAGTTTCTGAACTACATCCAAATGTCTATTAAG
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
* * *
568572 ACAGGCTGCTGTAAGTGGTGTATATGCT-CCG
66 ACAGGCTTCTGTAAGTGGTG--T-TCCTACCA
*
568603 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTTTGAACTACATCTAAATGTCCATTATA
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTA-A
* * *
568668 -ACAGGCTGCTGTAAGTGGTGTATTAGCT-CCG
65 GACAGGCTTCTGTAAGTGGTG--TT-CCTACCA
568699 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAA
1 TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAA
568752 NNNNNNNNNN
Statistics
Matches: 1394, Mismatches: 227, Indels: 126
0.80 0.13 0.07
Matches are distributed among these distances:
93 4 0.00
94 8 0.01
95 105 0.08
96 1239 0.89
97 24 0.02
98 10 0.01
99 4 0.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (94 bp):
TCATTTAGATTGACATCAGCTTTTCCTTCAATCAGTTTCTGAACTACATCTAAATGTCCATTAAG
ACAGGCTTCTGTAAGTGGTGTTCCTACCA
Found at i:585032 original size:2 final size:2
Alignment explanation
Indices: 585025--585073 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
585015 NNNNNNNNNN
585025 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
585067 AG AG AG A
1 AG AG AG A
585074 TTTCACCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:585473 original size:21 final size:21
Alignment explanation
Indices: 585413--585488 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
585403 ACTTAAAGGG
*
585413 AACTTAAAGATGGTTTAAAGAC
1 AACTTAAAGAT-GCTTAAAGAC
* *
585435 AACTTAAAGGA-GCGTAAATAC
1 AACTTAAA-GATGCTTAAAGAC
* **
585456 CACTTAAAGATGCTTAAAGGT
1 AACTTAAAGATGCTTAAAGAC
*
585477 AGCTTAAAGATG
1 AACTTAAAGATG
585489 GCTGAAAGGT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
20 2 0.05
21 30 0.71
22 8 0.19
23 2 0.05
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
AACTTAAAGATGCTTAAAGAC
Found at i:585504 original size:22 final size:21
Alignment explanation
Indices: 585458--585508 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
585448 GTAAATACCA
*
585458 CTTAAAGATGCTTAAAGGTAG
1 CTTAAAGATGCTGAAAGGTAG
**
585479 CTTAAAGATGGCTGAAAGGTTT
1 CTTAAAGAT-GCTGAAAGGTAG
585501 CTTAAAGA
1 CTTAAAGA
585509 AGTTTGGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
CTTAAAGATGCTGAAAGGTAG
Found at i:585593 original size:11 final size:11
Alignment explanation
Indices: 585577--585617 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
585567 GATTGTATAT
585577 CCTTTAAGCCA
1 CCTTTAAGCCA
* *
585588 CCTTTACGCTA
1 CCTTTAAGCCA
585599 CCTTTAAGCCA
1 CCTTTAAGCCA
585610 CCTTTAAG
1 CCTTTAAG
585618 GACTTGCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.24, C:0.34, G:0.10, T:0.32
Consensus pattern (11 bp):
CCTTTAAGCCA
Found at i:588800 original size:20 final size:20
Alignment explanation
Indices: 588744--588800 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 20
588734 TTTTACAATA
* * *
588744 TAACATATGATATTATATTG
1 TAACATATTATATAATAGTG
** * *
588764 TATTATATTAAACAATAGTG
1 TAACATATTATATAATAGTG
588784 TAACATATTATATAATA
1 TAACATATTATATAATA
588801 CTTTATTATA
Statistics
Matches: 26, Mismatches: 11, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
TAACATATTATATAATAGTG
Found at i:589984 original size:176 final size:174
Alignment explanation
Indices: 589590--590236 Score: 652
Period size: 177 Copynumber: 3.7 Consensus size: 174
589580 CATGTTCCAA
* * * * * * * * * * *
589590 AAAACTTAACCTTATCCAGCATCCAAAACCTATAACTAAAATTCAGAATTCTACCCTGTTTGGGG
1 AAAACTTCACC-TCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTATGGTG
* ** * ** * * * * ** *
589655 CATCAGTACCATTCGACGCACCAACCATATAAGATTGGTGAAGTTAGAACAAGTAATAGTGAAGA
65 CATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTA-ACAAAA
* * * * * **
589720 TATCATCATCAGACGTCAACTGTTTCAAAAAC-TTTAACCAGCTTTTT
129 TATAATCATCAGA-GGCACCTG-CTCAAAAACGTTTAACCAGCTCTAG
* * * * * * * *
589767 AAACCTTAACTTCATCAAGCATCCCAAACCTTTGGCTCAGATTCAGCATTCAAGCATGTATGGTG
1 AAAACTTCACCTC-TCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTATGGTG
* * * * *
589832 CATCAGTTTCATAAGACGCACCATCCGTGCAAGTTTGATGAAGTTAGGACTAGTAGTAACTAAGA
65 CATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAAC-AAAA
* * * *
589897 TTTAAT-ATCAGGGGGCACCTGCTCCAAAACTTTTAACCAGCTCTAG
129 TATAATCATCA-GAGGCACCTGCTCAAAAACGTTTAACCAGCTCTAG
* * *
589943 AAAACTTCACCTCCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCATGCCTGTCTGGAG
1 AAAACTTCACCT-CTCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTATGGTG
**
590008 CATCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTTAATACCAGTAGTAACAA
65 ---CATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACAA
590073 AATATAATCATCAGAGGCACCTGCTCAAAAACGTTTAACCAGCTCTAG
127 AATATAATCATCAGAGGCACCTGCTCAAAAACGTTTAACCAGCTCTAG
* * *
590121 AAAACTTCACCTCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCAATCAGGCCTCTA-GGTGC
1 AAAACTTCACCTCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTATGGTGC
* *
590185 ATCAGTATCATAAGATGCACCATCCATGCAAGTTTGGTGAAGTTAGAACCAG
66 ATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTTAGGACCAG
590237 CAGTTACTGA
Statistics
Matches: 390, Mismatches: 71, Indels: 22
0.81 0.15 0.05
Matches are distributed among these distances:
173 50 0.13
175 7 0.02
176 78 0.20
177 145 0.37
178 52 0.13
179 58 0.15
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (174 bp):
AAAACTTCACCTCTCCAGCATCCGAAACCTATAGCTCAGATTCAGCATTCAAGCCTGTATGGTGC
ATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGTTAGGACCAGTAGTAACAAAATA
TAATCATCAGAGGCACCTGCTCAAAAACGTTTAACCAGCTCTAG
Found at i:590223 original size:173 final size:173
Alignment explanation
Indices: 589744--590229 Score: 609
Period size: 176 Copynumber: 2.8 Consensus size: 173
589734 GTCAACTGTT
* ** * * * * * * *
589744 TCAAAAACTTTAACCAGCTTTTTAAACCTTAACTTCATCAAGCATCCCAAACCTTTGGCTCAGAT
1 TCAAAAACTTTAACCAGCTCTAGAAAACTTCACCTC-TCCAGCATCCGAAACCTATAGCTCAGAT
* * * * *
589809 TCAGCATTCAAGCATGTATGGTGCATCAGTTTCATAAGACGCACCATCCGTGCAAGTTTGATGAA
65 TCAGCATTCAAGCCTCTA-GGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAA
* * * * *
589874 GTTAGGACTAGTAGTAACTAAGATTTAATATCAGGGGGCACCTGC
129 GTTAAGACCAGTAGTAACTAAAATATAATATCAGGAGGCACCTGC
*
589919 TCCAAAACTTTTAACCAGCTCTAGAAAACTTCACCTCCTCCAGCATCCGAAACCTATAGCTCAGA
1 TCAAAAAC-TTTAACCAGCTCTAGAAAACTTCACCT-CTCCAGCATCCGAAACCTATAGCTCAGA
* *
589984 TTCAGCATTCATGCCTGTCT-GGAGCATCATCAGTATCATAAGACGCACCATCCATGCAAGTTTG
64 TTCAGCATTCAAGCC--TCTAGGTG---CATCAGTATCATAAGACGCACCATCCATGCAAGTTTG
*
590048 GTGAAGTTAATACCAGTAGTAAC-AAAATATAATCATCA-GAGGCACCTGC
124 GTGAAGTTAAGACCAGTAGTAACTAAAATATAAT-ATCAGGAGGCACCTGC
590097 TCAAAAACGTTTAACCAGCTCTAGAAAACTTCACCTCTCCAGCATCCGAAACCTATAGCTCAGAT
1 TCAAAAAC-TTTAACCAGCTCTAGAAAACTTCACCTCTCCAGCATCCGAAACCTATAGCTCAGAT
* * *
590162 TCAGCAATCAGGCCTCTAGGTGCATCAGTATCATAAGATGCACCATCCATGCAAGTTTGGTGAAG
65 TCAGCATTCAAGCCTCTAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAG
590227 TTA
130 TTA
590230 GAACCAGCAG
Statistics
Matches: 272, Mismatches: 30, Indels: 20
0.84 0.09 0.06
Matches are distributed among these distances:
173 45 0.17
175 10 0.04
176 63 0.23
177 42 0.15
178 54 0.20
179 58 0.21
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (173 bp):
TCAAAAACTTTAACCAGCTCTAGAAAACTTCACCTCTCCAGCATCCGAAACCTATAGCTCAGATT
CAGCATTCAAGCCTCTAGGTGCATCAGTATCATAAGACGCACCATCCATGCAAGTTTGGTGAAGT
TAAGACCAGTAGTAACTAAAATATAATATCAGGAGGCACCTGC
Found at i:591947 original size:7 final size:7
Alignment explanation
Indices: 591932--591998 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
591922 TTTAGATATT
591932 GAATCTC
1 GAATCTC
*
591939 GAATTTC
1 GAATCTC
*
591946 GAATCTT
1 GAATCTC
591953 GAATCTC
1 GAATCTC
* *
591960 GTATTTC
1 GAATCTC
591967 GAATCTC
1 GAATCTC
* * *
591974 GTATTTT
1 GAATCTC
591981 GAATCTC
1 GAATCTC
591988 GAATCTC
1 GAATCTC
591995 GAAT
1 GAAT
591999 GATCCTTCTC
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (7 bp):
GAATCTC
Found at i:596548 original size:24 final size:24
Alignment explanation
Indices: 596513--596575 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
596503 AATAAATCGC
*
596513 GGAAAAGAGGGAATTTCAAGTGTT
1 GGAAAAGGGGGAATTTCAAGTGTT
*
596537 GGAAAAGGGGGAAATTCAAGTGTT
1 GGAAAAGGGGGAATTTCAAGTGTT
*
596561 -AAAAAGGGGGGAATT
1 GGAAAA-GGGGGAATT
596576 GAAGTAATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 4 0.12
24 30 0.88
ACGTcount: A:0.40, C:0.03, G:0.37, T:0.21
Consensus pattern (24 bp):
GGAAAAGGGGGAATTTCAAGTGTT
Found at i:602214 original size:5 final size:5
Alignment explanation
Indices: 602204--602241 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
602194 ATCGAGTTTG
602204 TTGTT TTGTT TTGTT TTGTTT TTGTTT TTGTT TT-TT TT
1 TTGTT TTGTT TTGTT TTG-TT TTG-TT TTGTT TTGTT TT
602242 TTTGGGGGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.12
5 17 0.53
6 11 0.34
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
TTGTT
Found at i:602219 original size:10 final size:10
Alignment explanation
Indices: 602204--602241 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
602194 ATCGAGTTTG
602204 TTGTTTTGTT
1 TTGTTTTGTT
602214 TTGTTTTGTTT
1 TTGTTTTG-TT
602225 TTGTTTTTGTT
1 TTG-TTTTGTT
602236 TT-TTTT
1 TTGTTTT
602242 TTTGGGGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.15
10 8 0.31
11 9 0.35
12 5 0.19
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (10 bp):
TTGTTTTGTT
Found at i:602228 original size:6 final size:6
Alignment explanation
Indices: 602207--602245 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
602197 GAGTTTGTTG
*
602207 TTTTG- TTTTG- TTTTGT TTTTGT TTTTGT TTTTTT TTTTG
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTTG
602246 GGGGGGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:602228 original size:16 final size:16
Alignment explanation
Indices: 602207--602242 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
602197 GAGTTTGTTG
602207 TTTTG-TTTTGTTTTGT
1 TTTTGTTTTTGTTTT-T
602223 TTTTGTTTTTGTTTTT
1 TTTTGTTTTTGTTTTT
602239 TTTT
1 TTTT
602243 TTGGGGGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (16 bp):
TTTTGTTTTTGTTTTT
Found at i:610531 original size:3 final size:3
Alignment explanation
Indices: 610523--610553 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
610513 TATTTCTTAC
*
610523 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
610554 TATATCTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:622421 original size:172 final size:172
Alignment explanation
Indices: 622018--622646 Score: 985
Period size: 172 Copynumber: 3.6 Consensus size: 172
622008 GTATCGAGTC
* * ** * * *
622018 TATCGACCAAGGCTGATTTAGGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAA-AT
1 TATCGACTAATGCTGATTTTCGAACTTGACCAAGGTAATAGTAGTATAAACATTTGGTATAACTT
* * * *
622082 TAATGAAAATCCTTCAAAATTTGTAGGCATAAAAGCGCTTACAAGGTAAATTTTTGGATACATGT
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGAT--A---
*
622147 AATACAGATTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAA-
126 AA-ACGGATTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
622194 TATCGACTAATGCTGATTTTCGAACTTGACCAAGGTAATAGTAGTATAAACATTTGGTATAACTT
1 TATCGACTAATGCTGATTTTCGAACTTGACCAAGGTAATAGTAGTATAAACATTTGGTATAACTT
*
622259 TAATGAAAATCTGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
* *
622324 GAGTCATTATTGTTGTCAAAGTCCCATAACGCCAACAAAAAG
131 GATTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
* *
622366 TATCGACTAATGATGATTTTCGAACTTGACCAAGGTAATAGTAGTATAAACATTTGGTATAAATT
1 TATCGACTAATGCTGATTTTCGAACTTGACCAAGGTAATAGTAGTATAAACATTTGGTATAACTT
* *
622431 TAATGAAAATCCGTCAAAAATTGAAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
*
622496 GATTCATTATTGTGGTCAAAGTCCAATAACGCCAACAAAAAG
131 GATTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
*
622538 TATCGACTAATGCTGATTTTCGAACTTGACCAAGGTAATAGTGGTATAAACATTTGGTAT-ACAT
1 TATCGACTAATGCTGATTTTCGAACTTGACCAAGGTAATAGTAGTATAAACATTTGGTATAAC-T
622602 TTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
65 TTAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
622647 AAAAGTGTGC
Statistics
Matches: 422, Mismatches: 28, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
171 42 0.10
172 268 0.64
175 1 0.00
176 56 0.13
177 55 0.13
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (172 bp):
TATCGACTAATGCTGATTTTCGAACTTGACCAAGGTAATAGTAGTATAAACATTTGGTATAACTT
TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
GATTCATTATTGTGGTCAAAGTCCCATAACGCCAACAAAAAG
Found at i:623393 original size:31 final size:32
Alignment explanation
Indices: 623350--623409 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 32
623340 ATAAAAAAAA
*
623350 TACTGTCGTCCCCTGT-CACCCCCTGTGTTTT
1 TACTGTCATCCCCTGTACACCCCCTGTGTTTT
*
623381 TACTGTCATCCCCTGTACATCCCCTGTGT
1 TACTGTCATCCCCTGTACACCCCCTGTGT
623410 GCCACTGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 15 0.58
32 11 0.42
ACGTcount: A:0.10, C:0.38, G:0.15, T:0.37
Consensus pattern (32 bp):
TACTGTCATCCCCTGTACACCCCCTGTGTTTT
Found at i:623417 original size:31 final size:31
Alignment explanation
Indices: 623351--623417 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
623341 TAAAAAAAAT
* ***
623351 ACTGTCGTCCCCTGTCACCCCCTGTGTTTTT
1 ACTGTCATCCCCTGTCACCCCCTGTGTTGCC
*
623382 ACTGTCATCCCCTGTACATCCCCTGTG-TGCC
1 ACTGTCATCCCCTGT-CACCCCCTGTGTTGCC
623413 ACTGT
1 ACTGT
623418 ACAGAGCCCC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.10, C:0.39, G:0.16, T:0.34
Consensus pattern (31 bp):
ACTGTCATCCCCTGTCACCCCCTGTGTTGCC
Found at i:623471 original size:42 final size:43
Alignment explanation
Indices: 623391--623472 Score: 103
Period size: 42 Copynumber: 1.9 Consensus size: 43
623381 TACTGTCATC
* * * *
623391 CCCTGTACATCCCCTGTGTGCCACTGTACAGAGCCCCTGTATA
1 CCCTGTACATCCCCTGAGCGCCACTGTACACAGACCCTGTATA
* *
623434 CCCTGT-CATCCCCTGAGCGCCCCTGTACACATACCCTGT
1 CCCTGTACATCCCCTGAGCGCCACTGTACACAGACCCTGT
623473 GTGTCACTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 27 0.82
43 6 0.18
ACGTcount: A:0.17, C:0.41, G:0.17, T:0.24
Consensus pattern (43 bp):
CCCTGTACATCCCCTGAGCGCCACTGTACACAGACCCTGTATA
Found at i:623532 original size:20 final size:20
Alignment explanation
Indices: 623479--623561 Score: 78
Period size: 20 Copynumber: 4.0 Consensus size: 20
623469 CTGTGTGTCA
* *
623479 CTGTAGGCCCCTGTCACCCC
1 CTGTAAGCCCCTGTCATCCC
*
623499 CTGTACGCCCCTGTCATCCC
1 CTGTAAGCCCCTGTCATCCC
*
623519 CTGTAAGCCACTGT-ATACCC
1 CTGTAAGCCCCTGTCAT-CCC
* *
623539 CTGTGCATGCCCCTGACATCCC
1 CTGT--AAGCCCCTGTCATCCC
623561 C
1 C
623562 ATCGGTCTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.04
20 37 0.71
22 11 0.21
23 2 0.04
ACGTcount: A:0.14, C:0.46, G:0.17, T:0.23
Consensus pattern (20 bp):
CTGTAAGCCCCTGTCATCCC
Found at i:631809 original size:3 final size:3
Alignment explanation
Indices: 631786--631833 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
631776 CTGAAAAACA
* * *
631786 AAT AA- AAT AA- AAT ATT AAT AAT AAA AAT AAT AAT AAT AAT AAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
631832 AA
1 AA
631834 ATAAATAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:632836 original size:135 final size:131
Alignment explanation
Indices: 632582--632841 Score: 315
Period size: 135 Copynumber: 2.0 Consensus size: 131
632572 GATTGAAGTA
* * * * * *
632582 TATCGAATCAATATTAAAATTATTATTTTTGTTGGAATTATTTTTGCTTCATGTATTTAACCACT
1 TATCGAATCAATATCAAAATAATCATTTTTGTCGGAAATATTTGTGCTTCATGTATTTAACCACT
* * * * *
632647 GATTTGAAAAACCAGAAAGTTACCCGCAATATTTACTTAAGCGGTGACAGCATAAGAACTTATAA
66 AATCTGAAAAACCAGAAAGTGACCCGCAATATATACTAAAGCGGTGACAGCATAAGAACTTATAA
632712 T
131 T
* * *
632713 TATCGAATCAATATCAGAATAATCATTTTTGTCGGAAATGTTTGTGCTTCATGTATTTAGCTTAG
1 TATCGAATCAATATCAAAATAATCATTTTTGTCGGAAATATTTGTGCTTCATGTATTTA----AC
* * *
632778 TACTAATCTGAAAAATCAGAAAGTGACCCGCAATATATACTAAAGCGGTGA-TGTCATAAGAACT
62 CACTAATCTGAAAAACCAGAAAGTGACCCGCAATATATACTAAAGCGGTGACAG-CATAAGAACT
632842 ACTGTCAAAG
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
131 51 0.48
134 1 0.01
135 55 0.51
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (131 bp):
TATCGAATCAATATCAAAATAATCATTTTTGTCGGAAATATTTGTGCTTCATGTATTTAACCACT
AATCTGAAAAACCAGAAAGTGACCCGCAATATATACTAAAGCGGTGACAGCATAAGAACTTATAA
T
Found at i:633739 original size:40 final size:40
Alignment explanation
Indices: 633549--633723 Score: 251
Period size: 40 Copynumber: 4.4 Consensus size: 40
633539 TATAGCTGAT
* * * *
633549 ACAAACCATGCCTTAAAAGTAGGGCGGATCTCATGATTTA
1 ACAAATCATTCCTTAAAATTAGGGCGGATCTTATGATTTA
* *
633589 ACAAATCATTCCTTAAAACTAGGGCAGATCTTATGATTTA
1 ACAAATCATTCCTTAAAATTAGGGCGGATCTTATGATTTA
*
633629 GCAAATCATTCCTTAAAATTAGGGCGGATCTTATGATTTA
1 ACAAATCATTCCTTAAAATTAGGGCGGATCTTATGATTTA
* * *
633669 GCAAGTCATTCCTTAAAATAAGGGCGGATCTTATGATTTA
1 ACAAATCATTCCTTAAAATTAGGGCGGATCTTATGATTTA
*
633709 ACAAATCATGCCTTA
1 ACAAATCATTCCTTA
633724 TATTCTAGAT
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 122 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (40 bp):
ACAAATCATTCCTTAAAATTAGGGCGGATCTTATGATTTA
Found at i:634515 original size:14 final size:15
Alignment explanation
Indices: 634488--634517 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
634478 TTATCTTTTA
634488 AGTAACTCTTTTATT
1 AGTAACTCTTTTATT
634503 AGTAACT-TTTTATT
1 AGTAACTCTTTTATT
634517 A
1 A
634518 AACGACCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (15 bp):
AGTAACTCTTTTATT
Found at i:645218 original size:20 final size:20
Alignment explanation
Indices: 645141--645316 Score: 176
Period size: 21 Copynumber: 8.7 Consensus size: 20
645131 CAAATTTCTT
* *
645141 ATTCGTCCGAACAAATTGCTT
1 ATTCGTCCGAACAAATCG-TA
*
645162 ATTCGTCCGAACAAATAGCTA
1 ATTCGTCCGAACAAATCG-TA
* * *
645183 ATCCGTCAGAATAAATCGTA
1 ATTCGTCCGAACAAATCGTA
*
645203 ATTTGTCCGAACAAATCGTA
1 ATTCGTCCGAACAAATCGTA
* *
645223 ATTCGTTCGAACAAATAAC-TT
1 ATTCGTCCGAACAAAT--CGTA
* * *
645244 ATTTGTCCGAATAAAACGCTA
1 ATTCGTCCGAACAAATCG-TA
*
645265 ATTCGTCCAAACAAATCGTA
1 ATTCGTCCGAACAAATCGTA
645285 ATTCGT-CGAACAAATCGTA
1 ATTCGTCCGAACAAATCGTA
645304 ATTCGTCCGAACA
1 ATTCGTCCGAACA
645317 CAAAAGTTAT
Statistics
Matches: 127, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
19 19 0.15
20 46 0.36
21 61 0.48
22 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (20 bp):
ATTCGTCCGAACAAATCGTA
Found at i:645352 original size:81 final size:82
Alignment explanation
Indices: 645141--645381 Score: 251
Period size: 82 Copynumber: 3.0 Consensus size: 82
645131 CAAATTTCTT
** * * *
645141 ATTCGTCCGAACAAATTGCTTATTCGTCCGAACAAATA-GCTAATCCGT-CAGAATAAATCGTAA
1 ATTCGTCCGAACAAATAACTTATTTGTCCGAACAAA-ACGCTAATTCGTCCA-AACAAATCGTAA
*
645204 TTTGTCCGAACAAATCGTA
64 TTCGTCCGAACAAATCGTA
* *
645223 ATTCGTTCGAACAAATAACTTATTTGTCCGAATAAAACGCTAATTCGTCCAAACAAATCGTAATT
1 ATTCGTCCGAACAAATAACTTATTTGTCCGAACAAAACGCTAATTCGTCCAAACAAATCGTAATT
645288 CGT-CGAACAAATCGTA
66 CGTCCGAACAAATCGTA
* * * * * * * *
645304 ATTCGTCCGAACACAA-AAGTTATTTTTGCGAACAATTA-GCTTCA-TCGTCCCAACAAACCCTA
1 ATTCGTCCGAACA-AATAACTTATTTGTCCGAACAA-AACGC-TAATTCGTCCAAACAAATCGTA
645366 ATTCGTCCGAACAAAT
63 ATTCGTCCGAACAAAT
645382 AACATTTTTT
Statistics
Matches: 135, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
81 64 0.47
82 69 0.51
83 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (82 bp):
ATTCGTCCGAACAAATAACTTATTTGTCCGAACAAAACGCTAATTCGTCCAAACAAATCGTAATT
CGTCCGAACAAATCGTA
Found at i:646875 original size:13 final size:12
Alignment explanation
Indices: 646857--646902 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
646847 AGGCATTTTG
646857 CAAAAAAAAAGAA
1 CAAAAAAAAA-AA
*
646870 CAAAAACAAAAA
1 CAAAAAAAAAAA
*
646882 CAAAAAAAGCAAA
1 CAAAAAAA-AAAA
646895 CAAAAAAA
1 CAAAAAAA
646903 TTACAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 9 0.31
13 20 0.69
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAA
Found at i:648262 original size:2 final size:2
Alignment explanation
Indices: 648255--648308 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
648245 GAACCAAATT
648255 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
648297 GA GA GA GA GA GA
1 GA GA GA GA GA GA
648309 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:652074 original size:18 final size:18
Alignment explanation
Indices: 652051--652086 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
652041 CCGTTTGTGT
*
652051 TTTACTAAAGATTTCTTC
1 TTTACTAAACATTTCTTC
652069 TTTACTAAACATTTCTTC
1 TTTACTAAACATTTCTTC
652087 AAAGCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.19, G:0.03, T:0.50
Consensus pattern (18 bp):
TTTACTAAACATTTCTTC
Found at i:654780 original size:2 final size:2
Alignment explanation
Indices: 654773--654798 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
654763 TTCTGGAGTA
654773 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
654799 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:663124 original size:15 final size:17
Alignment explanation
Indices: 663104--663142 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
663094 CACTCGATAG
663104 CTCGAA-CT-TTGATCT
1 CTCGAAGCTCTTGATCT
*
663119 CTCGAAGGTCTTGATCT
1 CTCGAAGCTCTTGATCT
663136 CTCGAAG
1 CTCGAAG
663143 TGAACTCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.29
16 1 0.05
17 14 0.67
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (17 bp):
CTCGAAGCTCTTGATCT
Found at i:668970 original size:2 final size:2
Alignment explanation
Indices: 668963--668999 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
668953 NNNNNNNNNN
668963 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
669000 AATATAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:669194 original size:2 final size:2
Alignment explanation
Indices: 669189--669228 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
669179 TCTCTCGCGT
* * *
669189 TC TC TC TC TC TG TT TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
669229 ATGATTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.42, G:0.03, T:0.55
Consensus pattern (2 bp):
TC
Found at i:669196 original size:12 final size:12
Alignment explanation
Indices: 669179--669222 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
669169 AACCTCTCTT
*
669179 TCTCTCGCGTTC
1 TCTCTCTCGTTC
669191 TCTCTCTCTGTT-
1 TCTCTCTC-GTTC
*
669203 TCTCTCTCTTTC
1 TCTCTCTCGTTC
669215 TCTCTCTC
1 TCTCTCTC
669223 TCTCTCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 2 0.07
12 23 0.82
13 3 0.11
ACGTcount: A:0.00, C:0.41, G:0.07, T:0.52
Consensus pattern (12 bp):
TCTCTCTCGTTC
Found at i:669204 original size:24 final size:24
Alignment explanation
Indices: 669172--669225 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
669162 TCAATGCAAC
669172 CTCTCTTTCTCTCGCGTTCTCTCT
1 CTCTCTTTCTCTCGCGTTCTCTCT
* * *
669196 CTCTGTTTCTCTCTCTTTCTCTCT
1 CTCTCTTTCTCTCGCGTTCTCTCT
669220 CTCTCT
1 CTCTCT
669226 CTCATGATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.00, C:0.41, G:0.06, T:0.54
Consensus pattern (24 bp):
CTCTCTTTCTCTCGCGTTCTCTCT
Found at i:669206 original size:10 final size:10
Alignment explanation
Indices: 669172--669228 Score: 60
Period size: 10 Copynumber: 5.3 Consensus size: 10
669162 TCAATGCAAC
669172 CTCTCTTTCT
1 CTCTCTTTCT
*
669182 CTCGCGTTCTCT
1 CTCTC-TT-TCT
669194 CTCTCTGTTTCT
1 CTCTC--TTTCT
669206 CTCTCTTTCT
1 CTCTCTTTCT
*
669216 CTCTCTCTCT
1 CTCTCTTTCT
669226 CTC
1 CTC
669229 ATGATTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
10 21 0.51
11 2 0.05
12 15 0.37
13 3 0.07
ACGTcount: A:0.00, C:0.42, G:0.05, T:0.53
Consensus pattern (10 bp):
CTCTCTTTCT
Found at i:669915 original size:35 final size:35
Alignment explanation
Indices: 669869--669938 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
669859 TTGAACTTCA
669869 AAGGACTACATGCCCTGAGGGCTTTCACACCTATC
1 AAGGACTACATGCCCTGAGGGCTTTCACACCTATC
669904 AAGGACTACATGCCCTGAGGGCTTTCACACCTATC
1 AAGGACTACATGCCCTGAGGGCTTTCACACCTATC
669939 GAAAATAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (35 bp):
AAGGACTACATGCCCTGAGGGCTTTCACACCTATC
Found at i:670506 original size:61 final size:61
Alignment explanation
Indices: 670184--670503 Score: 496
Period size: 61 Copynumber: 5.2 Consensus size: 61
670174 CAAAAGCCGA
* * * * * *
670184 ACAGGGGATGACAGGAGCATACATAGGGAAGTACATTGCCTTACAGGGGATGAGAGGGGCGT
1 ACAGGGG-TGACAGGAGCATACATAAGGATGTACAGTGGCTTACAGGGGATGACAGAGGCGT
670246 ACAGGGGTGACAGGAGCATACATAAGGATGTACAGTGGCTTACAGGGGATGACAGAGGCGT
1 ACAGGGGTGACAGGAGCATACATAAGGATGTACAGTGGCTTACAGGGGATGACAGAGGCGT
* * *
670307 ACAGGGGGGACAGGAGCATACATATGGATGTATAGTGGCTTACAGGGGATGACAGAGGCGT
1 ACAGGGGTGACAGGAGCATACATAAGGATGTACAGTGGCTTACAGGGGATGACAGAGGCGT
* * *
670368 ACAGGGGTGACAGGGGCATACATATGGATGTACAGTGGCTTACAGGGGATGACAGAGGTGT
1 ACAGGGGTGACAGGAGCATACATAAGGATGTACAGTGGCTTACAGGGGATGACAGAGGCGT
* * *
670429 ACAGGGGTGACAGGGGCATACATAAGAATTTACAGTGGCTTACAGGGGATGACAGAGGCGT
1 ACAGGGGTGACAGGAGCATACATAAGGATGTACAGTGGCTTACAGGGGATGACAGAGGCGT
670490 ACAGGGGTGACAGG
1 ACAGGGGTGACAGG
670504 GGCTTCCAGT
Statistics
Matches: 241, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
61 234 0.97
62 7 0.03
ACGTcount: A:0.30, C:0.14, G:0.39, T:0.17
Consensus pattern (61 bp):
ACAGGGGTGACAGGAGCATACATAAGGATGTACAGTGGCTTACAGGGGATGACAGAGGCGT
Found at i:685711 original size:18 final size:18
Alignment explanation
Indices: 685684--685725 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
685674 AAGGACAGTC
685684 AATATAGATAGCTA-ATAT
1 AATATAGATAG-TACATAT
*
685702 AATATTGATAGTATCATAT
1 AATATAGATAGTA-CATAT
685721 AATAT
1 AATAT
685726 CAAATTGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 10 0.48
19 9 0.43
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (18 bp):
AATATAGATAGTACATAT
Found at i:694591 original size:2 final size:2
Alignment explanation
Indices: 694584--694630 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
694574 TGACTTGCAC
694584 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
694626 AG AG A
1 AG AG A
694631 TATGAATCTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:697536 original size:15 final size:15
Alignment explanation
Indices: 697516--697545 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
697506 CCCCCCCCCC
697516 AAAAAAAAAAAAATT
1 AAAAAAAAAAAAATT
*
697531 AAAAAAAAAAGAATT
1 AAAAAAAAAAAAATT
697546 TTATTTTGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAAAAAAAAAAATT
Found at i:702662 original size:24 final size:25
Alignment explanation
Indices: 702616--702665 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
702606 TAGCGACCAA
702616 TTTTTATAGGAAAGATTTCAAAAAC
1 TTTTTATAGGAAAGATTTCAAAAAC
*
702641 TTTTTATAGGAAAGATTTAAAAAAC
1 TTTTTATAGGAAAGATTTCAAAAAC
702666 AATTCAAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (25 bp):
TTTTTATAGGAAAGATTTCAAAAAC
Found at i:706870 original size:150 final size:151
Alignment explanation
Indices: 706598--706871 Score: 480
Period size: 150 Copynumber: 1.8 Consensus size: 151
706588 GACCTAGCTA
* *
706598 TATCCACCTTATAGCTTGGTGTGATTTCGAGAAACTTCAAACTCACTGGACCTTGAAAATCGGAG
1 TATCCACCTTATAGCTTGGTGTGATTTCGAGAAACTTCAAACTCACTGGACCATGAAAATCGGAA
*
706663 ACCTAGCTATATCCTGCTTGATGTGATTTTAGCACCTCACCAGTCCAGGGCAAAGTTACCTCCGA
66 ACCTAGCTATATCCTGCTTAATGTGATTTTAGCACCTCACCAGTCCAGGGCAAAGTTACCTCCGA
706728 GTCCCCTTGAGGTACTAAAAG
131 GTCCCCTTGAGGTACTAAAAG
* *
706749 TATCCACCTTATAGCTTGGTGTGATTTCGGGAAACTT-ATAACTCACTGGACCATG-AAATCTGA
1 TATCCACCTTATAGCTTGGTGTGATTTCGAGAAACTTCA-AACTCACTGGACCATGAAAATCGGA
706812 AACCTAGCTATATCCTGCTTAATGTGATTTTAGCACCTCACCAGTCCAGGGCAAAGTTAC
65 AACCTAGCTATATCCTGCTTAATGTGATTTTAGCACCTCACCAGTCCAGGGCAAAGTTAC
706872 TTCCCCTGAG
Statistics
Matches: 117, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
150 66 0.56
151 51 0.44
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (151 bp):
TATCCACCTTATAGCTTGGTGTGATTTCGAGAAACTTCAAACTCACTGGACCATGAAAATCGGAA
ACCTAGCTATATCCTGCTTAATGTGATTTTAGCACCTCACCAGTCCAGGGCAAAGTTACCTCCGA
GTCCCCTTGAGGTACTAAAAG
Found at i:715073 original size:16 final size:16
Alignment explanation
Indices: 715052--715099 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
715042 CCCGAATGCT
715052 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
715068 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
715084 GGAGAAAACGTACCCA
1 GGAGAAAACGTACCCA
715100 ATTTCTAGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.44, C:0.25, G:0.25, T:0.06
Consensus pattern (16 bp):
GGAGAAAACGTACCCA
Done.