Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 103 of 310
Found at i:32929954 original size:47 final size:47
Alignment explanation
Indices: 32929876--32930437 Score: 874
Period size: 47 Copynumber: 11.7 Consensus size: 47
32929866 CCCTTCGGGA
* * * * * *
32929876 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
32929923 CCTGTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32929970 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
32930017 CTTATCACATATATATACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930064 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930111 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930160 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930209 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930258 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930307 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
32930356 CTTGTCACATATATATACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
32930403 CTTATCACATATATGCA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
32930438 AGAATCCTAA
Statistics
Matches: 489, Mismatches: 23, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
46 1 0.00
47 246 0.50
49 242 0.49
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:32930144 original size:49 final size:49
Alignment explanation
Indices: 32929876--32930416 Score: 899
Period size: 49 Copynumber: 11.3 Consensus size: 49
32929866 CCCTTCGGGA
* * * * *
32929876 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
32929923 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32929970 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
32930017 CTTATCACATATATAT--ACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930064 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930111 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930160 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930209 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930258 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930307 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
32930356 CTTGTCACATATATAT--ACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
32930403 CTTATCACATATAT
1 CTTATCACATATAT
32930417 GCATGTTCAC
Statistics
Matches: 470, Mismatches: 16, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
45 6 0.01
46 1 0.00
47 207 0.44
49 256 0.54
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:32938806 original size:46 final size:45
Alignment explanation
Indices: 32938721--32938892 Score: 166
Period size: 46 Copynumber: 3.7 Consensus size: 45
32938711 ATCTCGTAGC
* * * * *
32938721 CGATACATGTCCCAGACATGTCATATACTGGCT-TACATCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCT-CATCT-GAGGT
* * * *
32938767 CAATGCATGTCCCAAACATGTCTTACACTAGCTCTCATCTAAATGT
1 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCT-GAGGT
* * * *
32938813 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCAT-CTGAGGT
32938861 CGATGCATGTCCCAGACATGTCTTACACTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC
32938893 ACACAATTAA
Statistics
Matches: 102, Mismatches: 20, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
46 49 0.48
47 28 0.27
48 24 0.24
49 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (45 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATCTGAGGT
Found at i:32938833 original size:47 final size:45
Alignment explanation
Indices: 32938769--32938892 Score: 162
Period size: 47 Copynumber: 2.7 Consensus size: 45
32938759 CTCGAGGCCA
*
32938769 ATGCATGTCCCAAACATGTCTTACACTAGCTCTCATCTAAATGT-T-G
1 ATGCATGTCCCAGACATGTCTTACACTAGCTCTCA--T-AATGTGTCG
*
32938815 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTCG
1 ATG-CATGTCCCAGACAT-GTCTTACACTAGCTCTCATAATGT-GTCG
32938863 ATGCATGTCCCAGACATGTCTTACACTAGC
1 ATGCATGTCCCAGACATGTCTTACACTAGC
32938893 ACACAATTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
45 5 0.07
46 16 0.23
47 28 0.40
48 21 0.30
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (45 bp):
ATGCATGTCCCAGACATGTCTTACACTAGCTCTCATAATGTGTCG
Found at i:32938849 original size:48 final size:47
Alignment explanation
Indices: 32938528--32938889 Score: 201
Period size: 48 Copynumber: 7.7 Consensus size: 47
32938518 GGTATAATGC
*
32938528 CGATGCCATGTCCCAGACATGGTCTTACATTGGCTCATCCATC-AAAGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC-T-CATCTAAAGT
* * * * * * *
32938576 CGATGCCATGTCCCGGACATAGTCTTCCACTGACTATCAGAATC-GAGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC---ATCTAAAGT
** * * * *
32938625 CGACACCATGTCCTAGACATGGTCTTATACTAGCTCTCA-CGTAACCGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATC-TAA-AGT
* * * * *
32938673 GCCTATGCCATGTCCCCGGCATGGTCTTACACTGGCATATC-TCGT--AGC
1 --CGATGCCATGTCCCAGACATGGTCTTACACTGGC-TCTCATC-TAAAGT
* * * * * *
32938721 CGAT-ACATGTCCCAGACAT-GTCATATACTGGCT-TACATCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATCT-AAAGT
* * *
32938767 CAATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTCATCTAAATGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTAAA-GT
* * ***
32938813 TGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-CTAAAGT
32938861 CGATG-CATGTCCCAGACAT-GTCTTACACT
1 CGATGCCATGTCCCAGACATGGTCTTACACT
32938890 AGCACACAAT
Statistics
Matches: 238, Mismatches: 55, Indels: 44
0.71 0.16 0.13
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 13 0.05
45 14 0.06
46 53 0.22
47 30 0.13
48 57 0.24
49 35 0.15
50 26 0.11
51 6 0.03
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCTAAAGT
Found at i:32940353 original size:23 final size:23
Alignment explanation
Indices: 32940327--32940381 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
32940317 TATCTTTGTC
32940327 TTTAAT-TTTAATTTAA-TCTTAAT
1 TTTAATATTT-ATTTAAGTC-TAAT
*
32940350 TTTAATATTTTTTTAAGTCTAAT
1 TTTAATATTTATTTAAGTCTAAT
32940373 TTTAATATT
1 TTTAATATT
32940382 ATTCATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 24 0.83
24 5 0.17
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTAATATTTATTTAAGTCTAAT
Found at i:32942358 original size:11 final size:11
Alignment explanation
Indices: 32942342--32942399 Score: 50
Period size: 10 Copynumber: 5.5 Consensus size: 11
32942332 GGGGAAATTA
32942342 TTTTTATTTAG
1 TTTTTATTTAG
*
32942353 TTTTTATTT-C
1 TTTTTATTTAG
**
32942363 TTTTTAGGT-G
1 TTTTTATTTAG
32942373 TTTTT-TTTAG
1 TTTTTATTTAG
*
32942383 TTTTTAGTTAG
1 TTTTTATTTAG
32942394 TATTTT
1 T-TTTT
32942400 GCTTTCGCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 1 0.03
10 18 0.49
11 14 0.38
12 4 0.11
ACGTcount: A:0.14, C:0.02, G:0.12, T:0.72
Consensus pattern (11 bp):
TTTTTATTTAG
Found at i:32943212 original size:14 final size:15
Alignment explanation
Indices: 32943193--32943248 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
32943183 AATCTTCAAT
32943193 GATATG-CAATCTTA
1 GATATGACAATCTTA
32943207 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
32943224 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
32943242 GATATGA
1 GATATGA
32943249 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:32943237 original size:35 final size:37
Alignment explanation
Indices: 32943191--32943269 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
32943181 ATAATCTTCA
32943191 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
32943227 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
32943263 A-GATATG
1 ATGATATG
32943270 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:32943269 original size:17 final size:19
Alignment explanation
Indices: 32943191--32943262 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
32943181 ATAATCTTCA
32943191 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32943210 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32943227 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32943245 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
32943263 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:32943288 original size:22 final size:22
Alignment explanation
Indices: 32943191--32943285 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 22
32943181 ATAATCTTCA
32943191 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32943210 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32943227 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32943245 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
32943267 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
32943286 GATTTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 15 0.22
22 8 0.12
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:32943576 original size:18 final size:17
Alignment explanation
Indices: 32943553--32943586 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
32943543 GTTTCCCTGT
*
32943553 TTTTTTTATATATTTTAA
1 TTTTTTAATA-ATTTTAA
32943571 TTTTTTAATAATTTTA
1 TTTTTTAATAATTTTA
32943587 GTATCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAATAATTTTAA
Found at i:32949270 original size:33 final size:34
Alignment explanation
Indices: 32949233--32949301 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
32949223 CATAAGAAAG
32949233 AGGCAGTAGA-AATGTAGCCCTAGAGGAAGGGAA
1 AGGCAGTAGAGAATGTAGCCCTAGAGGAAGGGAA
32949266 AGGCAGTAGAGAATGTAGCCCTAGAGGAAGGGAA
1 AGGCAGTAGAGAATGTAGCCCTAGAGGAAGGGAA
32949300 AG
1 AG
32949302 AGGTGAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 10 0.29
34 25 0.71
ACGTcount: A:0.39, C:0.12, G:0.38, T:0.12
Consensus pattern (34 bp):
AGGCAGTAGAGAATGTAGCCCTAGAGGAAGGGAA
Found at i:32951891 original size:44 final size:45
Alignment explanation
Indices: 32951698--32951965 Score: 260
Period size: 44 Copynumber: 6.0 Consensus size: 45
32951688 GATGTCATTA
* *
32951698 GGCATCTCTGTATTAGACGAGGAGCAGATCGAAGACATAGCAGATCT
1 GGCATCTCTGTATTAGACGGGGAGCAGATCGAAG--ATAGCAGATTT
* * * * * *
32951745 GACCT-TCATGTGTTTACATC--GAAGCAGATCCAAGAT-GACAGATTT
1 GGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCGAAGATAG-CAGATTT
* * *
32951790 GGCATCTCTGTATTAGACGGGGAGCAAATCGAAGTTAACAGATTT
1 GGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATTT
*
32951835 GGCATCTCTGTATTAGACGGGGAGCAGATTGAAGA-AGCAGATTT
1 GGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATTT
* * ***
32951879 GGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA-AAAA
1 GGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATTT
* * *
32951923 AGCGTCTCTGTATTAGACGGGGAGCAGATCAAAGATAGCAGAT
1 GGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGAT
32951966 ATCACCTTCC
Statistics
Matches: 181, Mismatches: 30, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
43 1 0.01
44 84 0.46
45 69 0.38
46 4 0.02
47 18 0.10
48 4 0.02
49 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.24
Consensus pattern (45 bp):
GGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATTT
Found at i:32951900 original size:89 final size:89
Alignment explanation
Indices: 32951767--32951965 Score: 267
Period size: 89 Copynumber: 2.2 Consensus size: 89
32951757 TTTACATCGA
* *
32951767 AGCAGATCCAAGAT-GACAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGTTAACAG
1 AGCAGATCAAAGATAG-CAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACA-
****
32951831 ATTTGGCATCTCTGTATTAGACGGGG
64 AAAAAGCATCTCTGTATTAGACGGGG
** * *
32951857 AGCAGATTGAAGA-AGCAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACAAA
1 AGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAAA
*
32951921 AAAGCGTCTCTGTATTAGACGGGG
66 AAAGCATCTCTGTATTAGACGGGG
32951945 AGCAGATCAAAGATAGCAGAT
1 AGCAGATCAAAGATAGCAGAT
32951966 ATCACCTTCC
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
88 32 0.34
89 51 0.54
90 12 0.13
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (89 bp):
AGCAGATCAAAGATAGCAGATTTGGCATCTCTGTATTAGACGGGGAGCAAATCGAAGATAACAAA
AAAGCATCTCTGTATTAGACGGGG
Found at i:32952333 original size:14 final size:15
Alignment explanation
Indices: 32952314--32952369 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
32952304 AATCTTCAAT
32952314 GATATG-CAATCTTA
1 GATATGACAATCTTA
32952328 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
32952345 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
32952363 GATATGA
1 GATATGA
32952370 TATGCAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:32952358 original size:35 final size:37
Alignment explanation
Indices: 32952312--32952390 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 37
32952302 ATAATCTTCA
32952312 ATGATATGCAATCTTAGATATGATA-CAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
32952348 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATA-GCAATCTTAGAT
32952384 A-GATATG
1 ATGATATG
32952391 ATTTTGTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 22 0.55
36 8 0.20
37 10 0.25
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATCTTAGAT
Found at i:32952390 original size:17 final size:19
Alignment explanation
Indices: 32952312--32952383 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
32952302 ATAATCTTCA
32952312 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32952331 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32952348 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32952366 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
32952384 AGATATGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
17 16 0.32
18 16 0.32
19 18 0.36
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:32952409 original size:22 final size:22
Alignment explanation
Indices: 32952312--32952406 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 22
32952302 ATAATCTTCA
32952312 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32952331 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32952348 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32952366 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
32952388 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
32952407 GATTTAATTT
Statistics
Matches: 67, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 15 0.22
22 8 0.12
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:32956412 original size:40 final size:40
Alignment explanation
Indices: 32956357--32956437 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
32956347 AGGAACTTCA
32956357 TGTAGTCTTTAGGAATTTTTCAGAGTAATTCTCGAAACAT
1 TGTAGTCTTTAGGAATTTTTCAGAGTAATTCTCGAAACAT
32956397 TGTAGTCTTTAGGAATTTTTCAGAGTAATTCTCGAAACAT
1 TGTAGTCTTTAGGAATTTTTCAGAGTAATTCTCGAAACAT
32956437 T
1 T
32956438 CTTGTTACTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (40 bp):
TGTAGTCTTTAGGAATTTTTCAGAGTAATTCTCGAAACAT
Found at i:32956881 original size:24 final size:24
Alignment explanation
Indices: 32956854--32956902 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
32956844 GCAGTAGAGA
32956854 ATGTAGCCCTAGAGGAAGGGAAAG
1 ATGTAGCCCTAGAGGAAGGGAAAG
*
32956878 ATGTAGCCCTGGAGGAAGGGAAAG
1 ATGTAGCCCTAGAGGAAGGGAAAG
32956902 A
1 A
32956903 GGTGAAAATT
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:0.37, C:0.12, G:0.39, T:0.12
Consensus pattern (24 bp):
ATGTAGCCCTAGAGGAAGGGAAAG
Found at i:32959963 original size:46 final size:46
Alignment explanation
Indices: 32959893--32960068 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 46
32959883 TGTTTGGGCA
*
32959893 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACG
* * *** * ** *
32959939 TCTGAACTCGTTGAGTTGAGTCCGAGTTTGAGAGATGTA-ACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAG-TTCACTTATGGATAC-AAACG
* * *
32959986 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACG
* *
32960032 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
32960069 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 21, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
46 73 0.69
47 33 0.31
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACG
Found at i:32960048 original size:93 final size:93
Alignment explanation
Indices: 32959889--32960059 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
32959879 AGGATGTTTG
*** *
32959889 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAATGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACACCCGAACTCGTTGAG
32959954 TTGAGTCCGAGTTTGAGAGATGTAACTA
66 TTGAGTCCGAGTTTGAGAGATGTAACTA
* * *
32959982 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACACCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACACCCGAACTCGTTGAG
32960047 TTGAGTCCGAGTT
66 TTGAGTCCGAGTT
32960060 CACTTATGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACACCCGAACTCGTTGAG
TTGAGTCCGAGTTTGAGAGATGTAACTA
Found at i:32964294 original size:78 final size:78
Alignment explanation
Indices: 32964192--32964486 Score: 412
Period size: 78 Copynumber: 3.8 Consensus size: 78
32964182 CGAGGAAACA
* * * * *
32964192 GATTTAGCATCTCCATATTCGACGGAGAGTAGATCGAAGACATAGCAGATCTGACATTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACATTCATTGAA
32964257 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * * * * *
32964270 GATTTGGCATCTCTGTATTAGACGGGAAGCAGATCGAAAACACAGTAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACATTCATTGAA
32964335 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * * * *
32964348 GATTTGGCATCTCTATATTAGACGGGGAACAGATCAAAGACATAACAGAT-TGGACCTGCATTGA
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-GACATTCATTGA
32964412 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
* *
32964426 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGTACATCTGACATTCAT
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACATTCAT
32964487 GTGTTTACAT
Statistics
Matches: 188, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
77 1 0.01
78 186 0.99
79 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.25
Consensus pattern (78 bp):
GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTGACATTCATTGAA
GCAGATCCAAGAT
Found at i:32964654 original size:45 final size:45
Alignment explanation
Indices: 32964426--32964654 Score: 189
Period size: 45 Copynumber: 5.1 Consensus size: 45
32964416 GATCCAAGAT
* *
32964426 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGTA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAG--ATAGCA
* * * * * * * *
32964473 CATCTGACAT-TCATGTGTTTACATC--GAAACAGATCCAAGAT-GACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGGAGCAGATCGAAGATAG-CA
* * *
32964518 GATTTGGCATCTCTGTATTAGGCAGGGAGCAGATTGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCA
* * ** *
32964562 AATTTTGTGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCA
* *
32964607 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAATATAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCA
32964652 GAT
1 GAT
32964655 ATCATCTTCT
Statistics
Matches: 138, Mismatches: 35, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
43 1 0.01
44 39 0.28
45 69 0.50
46 4 0.03
47 20 0.14
48 4 0.03
49 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCA
Found at i:32965024 original size:19 final size:19
Alignment explanation
Indices: 32965000--32965073 Score: 141
Period size: 19 Copynumber: 3.9 Consensus size: 19
32964990 ATAATCTTCA
32965000 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32965019 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32965038 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
32965056 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
32965074 AGATATGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
18 18 0.33
19 36 0.67
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:32965047 original size:37 final size:38
Alignment explanation
Indices: 32965000--32965080 Score: 141
Period size: 37 Copynumber: 2.2 Consensus size: 38
32964990 ATAATCTTCA
32965000 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
32965038 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGA-
1 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
32965074 A-GATATG
1 ATGATATG
32965081 ATTTTGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
35 3 0.07
36 3 0.07
37 31 0.74
38 5 0.12
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (38 bp):
ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:32965099 original size:22 final size:22
Alignment explanation
Indices: 32965000--32965096 Score: 97
Period size: 19 Copynumber: 4.8 Consensus size: 22
32964990 ATAATCTTCA
32965000 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32965019 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32965038 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
32965056 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
32965078 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
32965097 GATTTAATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
18 18 0.25
19 33 0.46
22 8 0.11
23 12 0.17
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:32965759 original size:57 final size:57
Alignment explanation
Indices: 32965671--32965784 Score: 210
Period size: 57 Copynumber: 2.0 Consensus size: 57
32965661 TCACGAGATA
*
32965671 ATTTCAGTTACGAGAGTCTAAGAATATCGTGTCCTATCATGCTGGATGTGATGTTTG
1 ATTTCAGTTACGAGAGTCTAAGAATATCGTGTCCTATAATGCTGGATGTGATGTTTG
*
32965728 ATTTCAGTTACGAGAGTTTAAGAATATCGTGTCCTATAATGCTGGATGTGATGTTTG
1 ATTTCAGTTACGAGAGTCTAAGAATATCGTGTCCTATAATGCTGGATGTGATGTTTG
32965785 TATTCTTTCG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (57 bp):
ATTTCAGTTACGAGAGTCTAAGAATATCGTGTCCTATAATGCTGGATGTGATGTTTG
Found at i:32965954 original size:18 final size:18
Alignment explanation
Indices: 32965931--32965968 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
32965921 GTTGCGAGGG
32965931 TGCTAATCCTTCCTCGTA
1 TGCTAATCCTTCCTCGTA
32965949 TGCTAATCCTTCCTCGTA
1 TGCTAATCCTTCCTCGTA
32965967 TG
1 TG
32965969 TAACCGACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.32, G:0.13, T:0.39
Consensus pattern (18 bp):
TGCTAATCCTTCCTCGTA
Found at i:32969564 original size:46 final size:48
Alignment explanation
Indices: 32969492--32969594 Score: 147
Period size: 46 Copynumber: 2.2 Consensus size: 48
32969482 GATAGGACAG
* * * *
32969492 GACAGAAATGAGCCATGTAAGTCCATATCA-AT-TATATGGCTTTGGA
1 GACAGGAATGACCCATGTAAGCCCATATCATATATATATGGCATTGGA
*
32969538 GACAGGAATGACCCATGTAAGCCCATATTATATATATATGGCATTGGA
1 GACAGGAATGACCCATGTAAGCCCATATCATATATATATGGCATTGGA
32969586 GACAGGAAT
1 GACAGGAAT
32969595 AATTCATGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
46 26 0.52
47 2 0.04
48 22 0.44
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (48 bp):
GACAGGAATGACCCATGTAAGCCCATATCATATATATATGGCATTGGA
Found at i:32969603 original size:48 final size:46
Alignment explanation
Indices: 32969504--32969611 Score: 144
Period size: 48 Copynumber: 2.3 Consensus size: 46
32969494 CAGAAATGAG
* *
32969504 CCATGTAAGTCCATATCAATTATATGGCTTTGGAGACAGGAATGAC
1 CCATGTAAGTCCATATCAATTATATGGCATTGGAGACAGGAATAAC
* * *
32969550 CCATGTAAGCCCATATTATATATATATGGCATTGGAGACAGGAATAAT
1 CCATGTAAGTCCATATCA-AT-TATATGGCATTGGAGACAGGAATAAC
*
32969598 TCATGTAAGTCCAT
1 CCATGTAAGTCCAT
32969612 GTCGAAGACA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
46 16 0.30
47 2 0.04
48 35 0.66
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (46 bp):
CCATGTAAGTCCATATCAATTATATGGCATTGGAGACAGGAATAAC
Found at i:32972788 original size:62 final size:62
Alignment explanation
Indices: 32972717--32972841 Score: 225
Period size: 62 Copynumber: 2.0 Consensus size: 62
32972707 TGTAAGGACG
*
32972717 TTTTTGAAAAAAAGAAGAGGTTATTCTTTATTTT-AGTGCTGAATATGTTGGTTTTCAGCTCT
1 TTTTTGAAAAAAAGAAGAGGTCATTCTTTATTTTCA-TGCTGAATATGTTGGTTTTCAGCTCT
32972779 TTTTTGAAAAAAAGAAGAGGTCATTCTTTATTTTCATGCTGAATATGTTGGTTTTCAGCTCT
1 TTTTTGAAAAAAAGAAGAGGTCATTCTTTATTTTCATGCTGAATATGTTGGTTTTCAGCTCT
32972841 T
1 T
32972842 CTGCCTATGT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 60 0.98
63 1 0.02
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (62 bp):
TTTTTGAAAAAAAGAAGAGGTCATTCTTTATTTTCATGCTGAATATGTTGGTTTTCAGCTCT
Found at i:32973721 original size:67 final size:67
Alignment explanation
Indices: 32973613--32973749 Score: 247
Period size: 67 Copynumber: 2.0 Consensus size: 67
32973603 AAGAAACCCC
* *
32973613 ATTTTGATTTCTATATTCATGTAACAATGTTACATTCCCAATTGGGTTAATTCTGAAACCAAAAC
1 ATTTTGATTTCTATATTCATGTAACAATGCTACATTCCCAATTGGGTTAATTCTAAAACCAAAAC
32973678 CT
66 CT
*
32973680 ATTTTGATTTCTATATTCATGTAACAATGCTACATTTCCAATTGGGTTAATTCTAAAACCAAAAC
1 ATTTTGATTTCTATATTCATGTAACAATGCTACATTCCCAATTGGGTTAATTCTAAAACCAAAAC
32973745 CT
66 CT
32973747 ATT
1 ATT
32973750 AGAGGAGGGA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (67 bp):
ATTTTGATTTCTATATTCATGTAACAATGCTACATTCCCAATTGGGTTAATTCTAAAACCAAAAC
CT
Found at i:32985451 original size:3 final size:3
Alignment explanation
Indices: 32985443--32985470 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
32985433 CACTAATCTC
32985443 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
32985471 GTTACCTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32986142 original size:22 final size:22
Alignment explanation
Indices: 32986117--32986170 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
32986107 ATTTATTTTA
*
32986117 TAATATAATATTATGATATAAT
1 TAATATAATATTATAATATAAT
* *
32986139 TAATATAATAATATAATCTAAT
1 TAATATAATATTATAATATAAT
32986161 TAA-ATAATAT
1 TAATATAATAT
32986171 ATTTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAATATAATATTATAATATAAT
Found at i:32986166 original size:18 final size:17
Alignment explanation
Indices: 32986115--32986176 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
32986105 TGATTTATTT
* *
32986115 TATAATATAATATTATGA
1 TATAAT-TAATATAATAA
32986133 TATAATTAATATAATAA
1 TATAATTAATATAATAA
32986150 TATAATCTAAT-TAAATAA
1 TATAAT-TAATAT-AATAA
*
32986168 TATATTTAA
1 TATAATTAA
32986177 AAAAAATCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
17 19 0.49
18 20 0.51
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TATAATTAATATAATAA
Found at i:32987712 original size:24 final size:24
Alignment explanation
Indices: 32987684--32987738 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
32987674 CTATATAATG
* *
32987684 GGAAGTTCATAAGAGTCATAATCA
1 GGAAGCTCATAAGAGCCATAATCA
*
32987708 GGAAGCTCATAAGAGCCATAATTA
1 GGAAGCTCATAAGAGCCATAATCA
32987732 GGAAGCT
1 GGAAGCT
32987739 TATATATCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.22
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCA
Found at i:32989642 original size:24 final size:23
Alignment explanation
Indices: 32989615--32989668 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
32989605 ATTTCGATTG
* **
32989615 TTAATTTGTGTTATTTACTTTTAA
1 TTAATTTATGTTATTT-CGGTTAA
32989639 TTAATTTATGTTATTTCGGTTAA
1 TTAATTTATGTTATTTCGGTTAA
32989662 TTAATTT
1 TTAATTT
32989669 TTATTTGATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (23 bp):
TTAATTTATGTTATTTCGGTTAA
Found at i:32995077 original size:3 final size:3
Alignment explanation
Indices: 32995069--32995102 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
32995059 TTATTTTTTC
*
32995069 CTT CTT CTT CTT CTT CTT CTT CTT CTT CGT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
32995103 CTCTCTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:33000194 original size:22 final size:22
Alignment explanation
Indices: 33000166--33000210 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
33000156 AGTCAATATC
33000166 GTTCCAGTATTATATTTTCAGT
1 GTTCCAGTATTATATTTTCAGT
33000188 GTTCCAGTATTATATTTTCAGT
1 GTTCCAGTATTATATTTTCAGT
33000210 G
1 G
33000211 CTACTGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (22 bp):
GTTCCAGTATTATATTTTCAGT
Found at i:33004773 original size:46 final size:45
Alignment explanation
Indices: 33004723--33004898 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
33004713 TGTTTGGGCA
33004723 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
33004769 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
33004816 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
33004862 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
33004899 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:33004878 original size:93 final size:93
Alignment explanation
Indices: 33004719--33004890 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
33004709 AGGATGTTTG
* *
33004719 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
33004784 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
33004812 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
33004877 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
33004891 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:33007875 original size:15 final size:15
Alignment explanation
Indices: 33007836--33007915 Score: 76
Period size: 15 Copynumber: 5.4 Consensus size: 15
33007826 GTATCTTGGG
*
33007836 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
33007851 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
33007866 TTTCTTTATT-TCGA
1 TTTCTTTATTCTGGA
*
33007880 GTTTCTCTA-TCTTGGA
1 -TTTCTTTATTC-TGGA
*
33007896 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
33007910 TTTCTT
1 TTTCTT
33007916 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
14 12 0.23
15 36 0.68
16 5 0.09
ACGTcount: A:0.11, C:0.17, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:33013249 original size:27 final size:27
Alignment explanation
Indices: 33013205--33013257 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
33013195 TAATAAATAT
* *
33013205 ATATTAATTTATCAATAAATTAATAAA
1 ATATTAATTCATCAATAAACTAATAAA
* *
33013232 ATATTCATTCATCGATAAACTAATAA
1 ATATTAATTCATCAATAAACTAATAA
33013258 CCTCGATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (27 bp):
ATATTAATTCATCAATAAACTAATAAA
Found at i:33020796 original size:5 final size:5
Alignment explanation
Indices: 33020786--33020826 Score: 64
Period size: 5 Copynumber: 8.0 Consensus size: 5
33020776 TAAGAGTCAT
*
33020786 TAAAA TAAAA TATAA TAAAA TATAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA
33020827 ACCAAAGGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:33023479 original size:20 final size:21
Alignment explanation
Indices: 33023445--33023485 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
33023435 ATAAAATATT
*
33023445 AAAAATAAATAAATATTTTTA
1 AAAAATAAATAAATAATTTTA
*
33023466 AAAAATACAT-AATAATTTTA
1 AAAAATAAATAAATAATTTTA
33023486 TAAGTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATAAATAAATAATTTTA
Found at i:33041901 original size:47 final size:47
Alignment explanation
Indices: 33041791--33041902 Score: 138
Period size: 47 Copynumber: 2.4 Consensus size: 47
33041781 TCCGAGATAA
* * *
33041791 ACACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGT
1 ACACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGT
* * *
33041838 ACACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-
1 ACACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGT
33041885 ACACATAGTG-TCTCATCG
1 ACACATAGTGCT-TCATCG
33041903 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (47 bp):
ACACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGT
Found at i:33042305 original size:21 final size:21
Alignment explanation
Indices: 33042267--33042352 Score: 118
Period size: 21 Copynumber: 4.1 Consensus size: 21
33042257 CCTGATCAGT
** *
33042267 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTA
* *
33042288 AAACTACACACGAGGTGCCTA
1 ATACGACACACGAGGTGCCTA
*
33042309 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTA
33042330 ATACGACACACGAGGTGCCTA
1 ATACGACACACGAGGTGCCTA
33042351 AT
1 AT
33042353 CGATAAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTA
Found at i:33042746 original size:15 final size:15
Alignment explanation
Indices: 33042721--33042778 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
33042711 TCATATATAT
33042721 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
33042737 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
33042752 AATAATTTCAATCAA
1 TATAAATTCAATCAA
33042767 TATAAATTCAAT
1 TATAAATTCAAT
33042779 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:33045531 original size:29 final size:30
Alignment explanation
Indices: 33045499--33045562 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
33045489 AAATTTTATG
**
33045499 TATAAAATTACACA-AAATCGTAGTTCATA
1 TATAAAATTACACATAAATCAAAGTTCATA
* *
33045528 TATACAATTATACATTAAATCAAAGTTCATA
1 TATAAAATTACACA-TAAATCAAAGTTCATA
33045559 TATA
1 TATA
33045563 GTTTTGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.48, C:0.12, G:0.05, T:0.34
Consensus pattern (30 bp):
TATAAAATTACACATAAATCAAAGTTCATA
Found at i:33045696 original size:30 final size:30
Alignment explanation
Indices: 33045639--33045696 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
33045629 TTTAAATAAT
* * *
33045639 ATAATTTATTTTTATAACTTTATAAAATGC
1 ATAAATTATTTTTATAACTTAAGAAAATGC
33045669 ATAAATTATTTTTATAA-TATAAGAAAAT
1 ATAAATTATTTTTATAACT-TAAGAAAAT
33045697 TTTTACCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (30 bp):
ATAAATTATTTTTATAACTTAAGAAAATGC
Found at i:33055704 original size:3 final size:3
Alignment explanation
Indices: 33055696--33055738 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
33055686 GGCAAAGTTC
33055696 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
33055739 TGATGATGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:33059524 original size:6 final size:6
Alignment explanation
Indices: 33059498--33059551 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
33059488 TAAGTATAAG
33059498 AAAAT- AAAAT- AAAAT- AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
33059543 AAAATA AAA
1 AAAATA AAA
33059552 GAAAACAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.31
6 33 0.69
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:33064174 original size:20 final size:19
Alignment explanation
Indices: 33064144--33064184 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
33064134 AGCTGAAAGA
33064144 AAGAAATAAAATAAAATAT
1 AAGAAATAAAATAAAATAT
33064163 AAGAAGATAAAATAAAATAT
1 AAGAA-ATAAAATAAAATAT
33064183 AA
1 AA
33064185 ACATGTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (19 bp):
AAGAAATAAAATAAAATAT
Found at i:33065591 original size:24 final size:26
Alignment explanation
Indices: 33065544--33065628 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 26
33065534 GTAACTGGAG
*
33065544 TAATAAT-ATATTGATAAAATGAATA
1 TAATAATAATAGTGATAAAATGAATA
33065569 -AA-AATAATAGTGATAATAA-GAATA
1 TAATAATAATAGTGATAA-AATGAATA
* *
33065593 TTAATAATAATAGTCATAAGGAT-AATA
1 -TAATAATAATAGTGATAA-AATGAATA
33065620 TAAATAATA
1 T-AATAATA
33065629 TTTAAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
23 3 0.06
24 16 0.33
25 2 0.04
26 3 0.06
27 25 0.51
ACGTcount: A:0.58, C:0.01, G:0.09, T:0.32
Consensus pattern (26 bp):
TAATAATAATAGTGATAAAATGAATA
Found at i:33065619 original size:27 final size:27
Alignment explanation
Indices: 33065566--33065628 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
33065556 GATAAAATGA
* *
33065566 ATAAA-AATAATAGTGATAATAAGAAT
1 ATAAATAATAATAGTCATAAGAAGAAT
* * *
33065592 ATTAATAATAATAGTCATAAGGATAAT
1 ATAAATAATAATAGTCATAAGAAGAAT
33065619 ATAAATAATA
1 ATAAATAATA
33065629 TTTAAAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.59, C:0.02, G:0.10, T:0.30
Consensus pattern (27 bp):
ATAAATAATAATAGTCATAAGAAGAAT
Found at i:33070206 original size:46 final size:46
Alignment explanation
Indices: 33070025--33070206 Score: 231
Period size: 46 Copynumber: 4.0 Consensus size: 46
33070015 TTTGACATGA
* * * * *
33070025 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
* ** * * *
33070071 TTCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
33070117 TGCCATGGTATCTTTCAACCATGGTCATACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
33070163 TGCCGTGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
33070207 AGAGCACACT
Statistics
Matches: 118, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
45 4 0.03
46 114 0.97
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:33073525 original size:18 final size:18
Alignment explanation
Indices: 33073502--33073539 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
33073492 TAATTAGATA
33073502 ATTAGTTTTTGATAAAAC
1 ATTAGTTTTTGATAAAAC
33073520 ATTAGTTTTTGATAAAAC
1 ATTAGTTTTTGATAAAAC
33073538 AT
1 AT
33073540 ACTCTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (18 bp):
ATTAGTTTTTGATAAAAC
Found at i:33078037 original size:17 final size:18
Alignment explanation
Indices: 33078015--33078048 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33078005 TGCGATAACA
*
33078015 TTCTATT-TTCATATTCT
1 TTCTATTATTCAAATTCT
33078032 TTCTATTATTCAAATTC
1 TTCTATTATTCAAATTC
33078049 CAGCTAAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCTATTATTCAAATTCT
Found at i:33086705 original size:16 final size:16
Alignment explanation
Indices: 33086686--33086747 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
33086676 TAGTTAAGAT
33086686 TATTTACAAATTTTAA
1 TATTTACAAATTTTAA
*
33086702 TATTTTCAAATTCTTAA
1 TATTTACAAATT-TTAA
* *
33086719 TGCTTTACACACTTTTAA
1 T-ATTTACA-AATTTTAA
*
33086737 T-TTTAAAAATT
1 TATTTACAAATT
33086748 AGGTAGGATC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
15 3 0.08
16 16 0.43
17 5 0.14
18 10 0.27
19 3 0.08
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (16 bp):
TATTTACAAATTTTAA
Found at i:33094208 original size:24 final size:24
Alignment explanation
Indices: 33094181--33094228 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
33094171 GATTGTAAGG
33094181 GAGAAGTAGGTGTAACATTG-GGCT
1 GAGAAGTAGGTGTAAC-TTGTGGCT
* *
33094205 GAGAGGTTGGTGTAACTTGTGGCT
1 GAGAAGTAGGTGTAACTTGTGGCT
33094229 AAGATGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.23, C:0.08, G:0.40, T:0.29
Consensus pattern (24 bp):
GAGAAGTAGGTGTAACTTGTGGCT
Found at i:33108371 original size:39 final size:39
Alignment explanation
Indices: 33108304--33108443 Score: 208
Period size: 39 Copynumber: 3.6 Consensus size: 39
33108294 GCTCTGATGA
*
33108304 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* **
33108343 GCTTCAGTTAGCCTTCGAGCTTTTGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* *
33108382 GCTTCAGTTAGCCTTTGGGCTGCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
**
33108421 GCTTCAGTTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
33108444 AGATCACGAT
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.14, C:0.24, G:0.24, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:33118048 original size:17 final size:18
Alignment explanation
Indices: 33118017--33118050 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33118007 TATTCTTCAT
*
33118017 TTTAATTTTCGCAATTTA
1 TTTAATTTTCACAATTTA
33118035 TTTAA-TTTCACAATTT
1 TTTAATTTTCACAATTT
33118051 TTAATTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (18 bp):
TTTAATTTTCACAATTTA
Found at i:33121081 original size:4 final size:4
Alignment explanation
Indices: 33121058--33121153 Score: 53
Period size: 4 Copynumber: 23.8 Consensus size: 4
33121048 TATTTTTATT
*
33121058 TTTA TTT- TATTA TTTA -TTA TTTA -TTA TTTTA TTT- CTTA TTTA TTTA
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
*
33121104 TTCA -TTA CTTTA TTTTA TTTTA TTTTA TTTTA TTT- TTTA -TTA CTTTA
1 TTTA TTTA -TTTA -TTTA -TTTA -TTTA -TTTA TTTA TTTA TTTA -TTTA
33121151 TTT
1 TTT
33121154 TGTTTGAGTG
Statistics
Matches: 76, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
3 17 0.22
4 30 0.39
5 29 0.38
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:33121142 original size:27 final size:26
Alignment explanation
Indices: 33121035--33121144 Score: 96
Period size: 27 Copynumber: 3.9 Consensus size: 26
33121025 GCAACCCAAT
33121035 TTTTATTTTTCTTTA-TTTTTATTTTTA
1 TTTTATTTTT-TTTATTTTTTA-TTTTA
* *
33121062 TTTTATTATTTATTATTTATTATTTTA
1 TTTTATT-TTTTTTATTTTTTATTTTA
*
33121089 TTTCTTATTTATTTATTCATTACTTTATTTTA
1 -TT-TTATTT-TTT-TT-ATT-TTTTATTTTA
33121121 TTTTATTTTATTTTATTTTTTATT
1 TTTTATTTT-TTTTATTTTTTATT
33121145 ACTTTATTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
27 21 0.31
28 14 0.21
29 10 0.15
30 10 0.15
31 5 0.07
32 8 0.12
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTATTTTTTTTATTTTTTATTTTA
Found at i:33121150 original size:15 final size:15
Alignment explanation
Indices: 33121053--33121154 Score: 86
Period size: 15 Copynumber: 6.8 Consensus size: 15
33121043 TTCTTTATTT
*
33121053 TTATTTT-TATTTTA
1 TTATTTTATTTTTTA
*
33121067 TTA-TTTATTATTTA
1 TTATTTTATTTTTTA
*
33121081 TTATTTTATTTCTTA
1 TTATTTTATTTTTTA
**
33121096 TT-TATTTATTCATTA
1 TTAT-TTTATTTTTTA
33121111 CTTTATTTTATTTTATT-
1 --TTATTTTATTTT-TTA
33121128 TTATTTTATTTTTTA
1 TTATTTTATTTTTTA
*
33121143 TTACTTTATTTT
1 TTATTTTATTTT
33121155 GTTTGAGTGG
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
13 3 0.04
14 14 0.20
15 43 0.61
17 8 0.11
18 3 0.04
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (15 bp):
TTATTTTATTTTTTA
Found at i:33123915 original size:17 final size:18
Alignment explanation
Indices: 33123882--33123915 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33123872 TATTCTTCAT
*
33123882 TTTAATGTTCGCAATTTA
1 TTTAATGTTCACAATTTA
33123900 TTTAAT-TTCACAATTT
1 TTTAATGTTCACAATTT
33123916 TTAATTCAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTAATGTTCACAATTTA
Found at i:33124547 original size:59 final size:61
Alignment explanation
Indices: 33124477--33124677 Score: 171
Period size: 68 Copynumber: 3.2 Consensus size: 61
33124467 ATCACTTTAA
** * *
33124477 TATTAAATTAATCTAATATTCA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATATTCATTAAAAGATAAATATTAAATTAAATTTAATATTAAATCT
*
33124536 TATTAAATTAATAGAATATTTATTTAAAAGATAAATATTAAATTAAATTTAATATTAAGATAATC
1 TATTAAATTAATAGAATATTCA-TTAAAAGATAAATATTAAATTAAATTTAATATT---A-AAT-
33124601 ACTTT
60 -C--T
* * * *
33124606 AATATTGAATTAATAAAATACT-ATT--AAGATAAGTATTAAATTAAATTTAATATTAAAT-T
1 --TATTAAATTAATAGAATATTCATTAAAAGATAAATATTAAATTAAATTTAATATTAAATCT
*
33124665 TATTAAAATAATA
1 TATTAAATTAATA
33124678 TTATTTTTGG
Statistics
Matches: 118, Mismatches: 11, Indels: 28
0.75 0.07 0.18
Matches are distributed among these distances:
57 11 0.09
59 20 0.17
61 1 0.01
62 28 0.24
64 3 0.03
65 2 0.02
66 3 0.03
68 29 0.25
70 3 0.03
71 1 0.01
72 17 0.14
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (61 bp):
TATTAAATTAATAGAATATTCATTAAAAGATAAATATTAAATTAAATTTAATATTAAATCT
Found at i:33142724 original size:16 final size:16
Alignment explanation
Indices: 33142703--33142734 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33142693 TGTTGTTTTA
33142703 ATATAAATGAATCTAT
1 ATATAAATGAATCTAT
*
33142719 ATATAAATGTATCTAT
1 ATATAAATGAATCTAT
33142735 GTTGTGATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (16 bp):
ATATAAATGAATCTAT
Found at i:33148066 original size:16 final size:16
Alignment explanation
Indices: 33148042--33148072 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33148032 AGTAGAGTCA
*
33148042 CATCTATAATGTGTTG
1 CATCCATAATGTGTTG
33148058 CATCCATAATGTGTT
1 CATCCATAATGTGTT
33148073 TCATGTTTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (16 bp):
CATCCATAATGTGTTG
Found at i:33148939 original size:15 final size:15
Alignment explanation
Indices: 33148911--33148943 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
33148901 AGAAGTCAGG
33148911 ATTCTAAGTATTTTT
1 ATTCTAAGTATTTTT
33148926 ATTC-AAGTATTTTT
1 ATTCTAAGTATTTTT
33148940 ATTC
1 ATTC
33148944 GATTACTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (15 bp):
ATTCTAAGTATTTTT
Found at i:33149064 original size:18 final size:19
Alignment explanation
Indices: 33149027--33149064 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
33149017 TAAGTAGTTA
* *
33149027 TTGACATTGATTTTTTGTT
1 TTGACAATGATTTTTGGTT
33149046 TTGACAATG-TTTTTGGTT
1 TTGACAATGATTTTTGGTT
33149064 T
1 T
33149065 GGGAAAAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.16, C:0.05, G:0.18, T:0.61
Consensus pattern (19 bp):
TTGACAATGATTTTTGGTT
Found at i:33150152 original size:21 final size:21
Alignment explanation
Indices: 33150117--33150184 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
33150107 CTCAAACCCA
33150117 AGGTAT-AAGAACATAGGTATG
1 AGGTATCAA-AACATAGGTATG
* ** *
33150138 AGTTATCAAAACATAGACAAG
1 AGGTATCAAAACATAGGTATG
* *
33150159 AGGTATCAAAATATAGGTATA
1 AGGTATCAAAACATAGGTATG
33150180 AGGTA
1 AGGTA
33150185 CTAGAACATA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.24
Consensus pattern (21 bp):
AGGTATCAAAACATAGGTATG
Found at i:33151667 original size:6 final size:6
Alignment explanation
Indices: 33151656--33151685 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
33151646 ATATGACAAA
33151656 AATTAT AATTAT AATTAT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AATTAT AATTAT
33151686 TAGTTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTAT
Found at i:33157445 original size:26 final size:26
Alignment explanation
Indices: 33157414--33157521 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
33157404 TGAAATTCCC
*
33157414 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
33157440 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
33157466 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
33157492 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
33157518 ATCA
1 ATCA
33157522 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:33159801 original size:18 final size:18
Alignment explanation
Indices: 33159736--33159850 Score: 97
Period size: 18 Copynumber: 6.3 Consensus size: 18
33159726 AGCAATTAAT
*
33159736 CAATCAGTAATATTCATTAA
1 CAATCAGT--TATTCAGTAA
* *
33159756 CAATCAGTCAATCAG-AA
1 CAATCAGTTATTCAGTAA
* *
33159773 CAATTATTTATTCAGTAA
1 CAATCAGTTATTCAGTAA
* *
33159791 CAGTCAGTTATTCGGTAA
1 CAATCAGTTATTCAGTAA
* *
33159809 CAATCAATTATTCAATAA
1 CAATCAGTTATTCAGTAA
* * *
33159827 TAATCAGTTTTTCAGTAT
1 CAATCAGTTATTCAGTAA
33159845 CAATCA
1 CAATCA
33159851 ATTGATCGGT
Statistics
Matches: 73, Mismatches: 21, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
17 13 0.18
18 52 0.71
20 8 0.11
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.35
Consensus pattern (18 bp):
CAATCAGTTATTCAGTAA
Found at i:33159820 original size:36 final size:36
Alignment explanation
Indices: 33159746--33159853 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
33159736 CAATCAGTAA
* * * * *
33159746 TATTCATTAACAATCAGTCAATCAG-AACAATTATT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* * *
33159781 TATTCAGTAACAGTCAGTTATTCGGTAACAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* * *
33159817 TATTCAATAATAATCAGTTTTTCAGTATCAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
33159853 T
1 T
33159854 GATCGGTTAT
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
35 20 0.34
36 39 0.66
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (36 bp):
TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
Found at i:33160118 original size:59 final size:58
Alignment explanation
Indices: 33160043--33160179 Score: 164
Period size: 53 Copynumber: 2.4 Consensus size: 58
33160033 CCGAAGCCAG
33160043 AACAGTAACAGTAACAGTAGCAGTACGGTACACAGAGTACCTCATCA-GAACAAATCTGG-
1 AACAGTAACAGTAACAGTA-CAGTACGGTACACAGAGTACCTCAT-AGGAACAAATC-GGA
33160102 AAC-G----A-TAACAGTAACAGTACGGTACACAGAGTACCTCATAGGAACAAATCGGA
1 AACAGTAACAGTAACAGT-ACAGTACGGTACACAGAGTACCTCATAGGAACAAATCGGA
*
33160155 AACAGTAACAGTAACGGTAACAGTA
1 AACAGTAACAGTAACAGT-ACAGTA
33160180 ACAATATCCG
Statistics
Matches: 68, Mismatches: 1, Indels: 18
0.78 0.01 0.21
Matches are distributed among these distances:
52 3 0.04
53 44 0.65
54 3 0.04
58 2 0.03
59 16 0.24
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.16
Consensus pattern (58 bp):
AACAGTAACAGTAACAGTACAGTACGGTACACAGAGTACCTCATAGGAACAAATCGGA
Found at i:33160120 original size:53 final size:53
Alignment explanation
Indices: 33160049--33160169 Score: 185
Period size: 53 Copynumber: 2.3 Consensus size: 53
33160039 CCAGAACAGT
*
33160049 AACAGTAACAGTAGCAGTACGGTACACAGAGTACCTCATCA-GAACAAATCTGG-
1 AACAGTAACAGTAACAGTACGGTACACAGAGTACCTCAT-AGGAACAAATC-GGA
33160102 AAC-GATAACAGTAACAGTACGGTACACAGAGTACCTCATAGGAACAAATCGGA
1 AACAG-TAACAGTAACAGTACGGTACACAGAGTACCTCATAGGAACAAATCGGA
33160155 AACAGTAACAGTAAC
1 AACAGTAACAGTAAC
33160170 GGTAACAGTA
Statistics
Matches: 63, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
52 4 0.06
53 58 0.92
54 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATAGGAACAAATCGGA
Found at i:33160388 original size:16 final size:16
Alignment explanation
Indices: 33160341--33160392 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
33160331 AATAGGGTAT
*
33160341 TTAATTCACTTTTCAA
1 TTAATTCAATTTTCAA
33160357 TT--TTCAATTTTCAA
1 TTAATTCAATTTTCAA
33160371 TTAATTCATATTTT-AA
1 TTAATTCA-ATTTTCAA
33160387 TTAATT
1 TTAATT
33160393 AACTATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 13 0.41
16 14 0.44
17 5 0.16
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATTCAATTTTCAA
Found at i:33161181 original size:24 final size:22
Alignment explanation
Indices: 33161153--33161199 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
33161143 TGTATTACAA
33161153 ATGTATGTACATTGTTTATCACAC
1 ATGTAT-TACATT-TTTATCACAC
**
33161177 ATGTATTTTATTTTTATCACAC
1 ATGTATTACATTTTTATCACAC
33161199 A
1 A
33161200 CTTGGCACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 11 0.52
23 4 0.19
24 6 0.29
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.47
Consensus pattern (22 bp):
ATGTATTACATTTTTATCACAC
Found at i:33161658 original size:14 final size:14
Alignment explanation
Indices: 33161639--33161669 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
33161629 AATTTTTTCT
33161639 ATTATAATATATGA
1 ATTATAATATATGA
33161653 ATTATAATATATGA
1 ATTATAATATATGA
33161667 ATT
1 ATT
33161670 GACAAGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (14 bp):
ATTATAATATATGA
Found at i:33164730 original size:13 final size:13
Alignment explanation
Indices: 33164714--33164738 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33164704 AAACCTTAAG
33164714 AAAAAAACAAAAA
1 AAAAAAACAAAAA
33164727 AAAAAAACAAAA
1 AAAAAAACAAAA
33164739 GCACAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:33166027 original size:22 final size:22
Alignment explanation
Indices: 33165977--33166027 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
33165967 ATATGACGCA
*
33165977 ATTTAA-AAATTTTATTGGTGT
1 ATTTAATAAATTTTATTGGTGG
* *
33165998 ATTAAATAATTTTTCATT-GTGG
1 ATTTAATAAATTTT-ATTGGTGG
33166020 ATTTAATA
1 ATTTAATA
33166028 CCTATACTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 5 0.21
22 16 0.67
23 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (22 bp):
ATTTAATAAATTTTATTGGTGG
Found at i:33179292 original size:15 final size:16
Alignment explanation
Indices: 33179266--33179295 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
33179256 TTGTGAGTGT
33179266 TTTTTATATTTATTTG
1 TTTTTATATTTATTTG
33179282 TTTTTAT-TTTATTT
1 TTTTTATATTTATTT
33179296 TTTATAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTTATATTTATTTG
Found at i:33179923 original size:21 final size:21
Alignment explanation
Indices: 33179899--33179951 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
33179889 GTGTCCCCTC
* *
33179899 CACACGGGCGTATGTGGCCTT
1 CACACGGGCATATATGGCCTT
*
33179920 CACACGAGCATATATGGCCTT
1 CACACGGGCATATATGGCCTT
*
33179941 CACATGGGCAT
1 CACACGGGCAT
33179952 GTAAACCCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (21 bp):
CACACGGGCATATATGGCCTT
Found at i:33180649 original size:21 final size:20
Alignment explanation
Indices: 33180616--33180654 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
33180606 AATATACGTT
33180616 TGTTTGTCAGAACATTTTGTC
1 TGTTTGTCAGAAC-TTTTGTC
**
33180637 TGTTTGTGTGAACTTTTG
1 TGTTTGTCAGAACTTTTG
33180655 GTTATTGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.15, C:0.10, G:0.23, T:0.51
Consensus pattern (20 bp):
TGTTTGTCAGAACTTTTGTC
Found at i:33181192 original size:12 final size:12
Alignment explanation
Indices: 33181159--33181197 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
33181149 ATGTTGGTTA
*
33181159 ATATTAAATTAT
1 ATATTATATTAT
33181171 ATTAATTATATTAT
1 A-T-ATTATATTAT
33181185 ATATTATATTAT
1 ATATTATATTAT
33181197 A
1 A
33181198 ATGAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.50
13 2 0.08
14 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATATTATATTAT
Found at i:33181474 original size:9 final size:9
Alignment explanation
Indices: 33181439--33181472 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
33181429 AATAGATATC
33181439 TATTATAAT
1 TATTATAAT
33181448 TATTATAAT
1 TATTATAAT
*
33181457 GTATTATTAT
1 -TATTATAAT
33181467 TATTAT
1 TATTAT
33181473 TAACTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (9 bp):
TATTATAAT
Found at i:33186205 original size:21 final size:21
Alignment explanation
Indices: 33186179--33186224 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
33186169 CTGCTTACAT
33186179 GGGCGTGTGTGCCCTCCACAC
1 GGGCGTGTGTGCCCTCCACAC
* * *
33186200 GGGCGTGTGTGGCCTTCACAT
1 GGGCGTGTGTGCCCTCCACAC
33186221 GGGC
1 GGGC
33186225 ATGTAGACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.30, G:0.39, T:0.22
Consensus pattern (21 bp):
GGGCGTGTGTGCCCTCCACAC
Found at i:33186639 original size:21 final size:20
Alignment explanation
Indices: 33186606--33186644 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
33186596 AATATATGTT
33186606 TGTTTGTCAGAACATTTTGTC
1 TGTTTGTCAGAAC-TTTTGTC
33186627 TGTTTGT-ATGAACTTTTG
1 TGTTTGTCA-GAACTTTTG
33186645 GTTATTGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.18, C:0.10, G:0.21, T:0.51
Consensus pattern (20 bp):
TGTTTGTCAGAACTTTTGTC
Found at i:33187454 original size:22 final size:22
Alignment explanation
Indices: 33187426--33187468 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
33187416 AATAGTACCA
*
33187426 CATGCCCGTGTGGTTGATGTGG
1 CATGCCCGTGTGGCTGATGTGG
33187448 CATGCCCGTGTGGCTGATGTG
1 CATGCCCGTGTGGCTGATGTG
33187469 ACACGCCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.40, T:0.30
Consensus pattern (22 bp):
CATGCCCGTGTGGCTGATGTGG
Found at i:33187476 original size:22 final size:22
Alignment explanation
Indices: 33187429--33187476 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
33187419 AGTACCACAT
* * *
33187429 GCCCGTGTGGTTGATGTGGCAT
1 GCCCGTGTGGCTGATGTGACAC
33187451 GCCCGTGTGGCTGATGTGACAC
1 GCCCGTGTGGCTGATGTGACAC
33187473 GCCC
1 GCCC
33187477 ATGTCATCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.10, C:0.27, G:0.38, T:0.25
Consensus pattern (22 bp):
GCCCGTGTGGCTGATGTGACAC
Found at i:33190035 original size:30 final size:30
Alignment explanation
Indices: 33190001--33190060 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
33189991 TGAAATCACG
*
33190001 ATATGCTAGTATCGTAACCGGTTCTTCTTC
1 ATATGCCAGTATCGTAACCGGTTCTTCTTC
*
33190031 ATATGCCAGTATCTTAACCGGTTCTTCTTC
1 ATATGCCAGTATCGTAACCGGTTCTTCTTC
33190061 TGTAATTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (30 bp):
ATATGCCAGTATCGTAACCGGTTCTTCTTC
Found at i:33194383 original size:39 final size:40
Alignment explanation
Indices: 33194338--33194469 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
33194328 GCTCCTCGTT
* * *
33194338 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
33194378 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
33194417 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
33194457 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
33194470 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 34 0.43
40 46 0.57
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:33194531 original size:41 final size:41
Alignment explanation
Indices: 33194454--33194531 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
33194444 TTAGTATCTC
* * *
33194454 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
33194495 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
33194532 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:33202309 original size:40 final size:40
Alignment explanation
Indices: 33202211--33202473 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
33202201 TCCTCGTTCA
* * * ** *
33202211 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
33202250 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
33202290 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
33202330 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
33202370 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
33202410 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
33202450 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
33202474 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:33212338 original size:46 final size:48
Alignment explanation
Indices: 33212288--33212423 Score: 172
Period size: 48 Copynumber: 2.9 Consensus size: 48
33212278 TGCTACTGTA
* * *
33212288 TAAGACTATATCTGGGATATGGCATC-A-ATGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGATATGGCATCAATATGAGATATGTGATCCGTG
* *
33212334 TAAGACCATAGCTGGGCTATGGCATCAATATGTGATATGTGATCCGTG
1 TAAGACCATAGCTGGGATATGGCATCAATATGAGATATGTGATCCGTG
33212382 TAAGACCATAGCT-GGACTATGGCATCGATATATGA-ATATGTG
1 TAAGACCATAGCTGGGA-TATGGCATC-A-ATATGAGATATGTG
33212424 TAAGACAATA
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
46 23 0.29
47 3 0.04
48 39 0.50
49 8 0.10
50 5 0.06
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (48 bp):
TAAGACCATAGCTGGGATATGGCATCAATATGAGATATGTGATCCGTG
Found at i:33212385 original size:48 final size:47
Alignment explanation
Indices: 33212168--33212407 Score: 189
Period size: 46 Copynumber: 5.0 Consensus size: 47
33212158 CCATGGCAAC
*
33212168 ATGTGATATGTGATTTCCATATAAGACCATAGCTGGGCTATGGCATCGGAGAG
1 ATGTGATATGTGA--TCCGTATAAGACCATAGCTGGGCTATGGCATC----AG
* * * * * *
33212221 ATGTAATTATGTGCTTCCGTATAAGACCATATCTAGGATATGACATC-G
1 ATGTGA-TATGTG-ATCCGTATAAGACCATAGCTGGGCTATGGCATCAG
* * * * * * *
33212269 GTGT-ATATATGCTACTGTATAAGACTATATCTGGGATATGGCATCA-
1 ATGTGATATGTGAT-CCGTATAAGACCATAGCTGGGCTATGGCATCAG
* * * *
33212315 ATGAGATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATCAAT
1 ATGTGATATGTGATCCGTATAAGACCATAGCTGGGCTATGGCATC-AG
* *
33212363 ATGTGATATGTGATCCGTGTAAGACCATAGCTGGACTATGGCATC
1 ATGTGATATGTGATCCGTATAAGACCATAGCTGGGCTATGGCATC
33212408 GATATATGAA
Statistics
Matches: 153, Mismatches: 27, Indels: 19
0.77 0.14 0.10
Matches are distributed among these distances:
45 1 0.01
46 59 0.39
47 9 0.06
48 46 0.30
53 32 0.21
54 6 0.04
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (47 bp):
ATGTGATATGTGATCCGTATAAGACCATAGCTGGGCTATGGCATCAG
Found at i:33212425 original size:42 final size:43
Alignment explanation
Indices: 33212379--33212493 Score: 144
Period size: 42 Copynumber: 2.7 Consensus size: 43
33212369 TATGTGATCC
* *
33212379 GTGTAAGACCATAGCTGGACTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGTTGGACTATGGCATCGATTATATGAAGAT
* ** * *
33212421 GTGTAAGACAATAGTTGGGGTTTGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGTTGGACTATGGCATCGATTATATGAAGAT
*
33212463 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGTTGGACTATGGCATCGA
33212494 GAAAATGAAG
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.02
42 57 0.97
43 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATAGTTGGACTATGGCATCGATTATATGAAGAT
Found at i:33217029 original size:22 final size:22
Alignment explanation
Indices: 33217001--33217056 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
33216991 GAATAGTACC
*
33217001 ACACGCCCGTGTGATTGATGTG
1 ACACGCCCGTGTGACTGATGTG
*
33217023 ACACGCCCGTGTGGCTGATGTG
1 ACACGCCCGTGTGACTGATGTG
*
33217045 ACACGCCTGTGT
1 ACACGCCCGTGT
33217057 TATCAACCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.16, C:0.27, G:0.32, T:0.25
Consensus pattern (22 bp):
ACACGCCCGTGTGACTGATGTG
Found at i:33218962 original size:49 final size:49
Alignment explanation
Indices: 33218904--33219008 Score: 192
Period size: 49 Copynumber: 2.1 Consensus size: 49
33218894 TTTTTCTTTC
*
33218904 TTTCTTTCCCTGCTATTCGTGCCTTTCTTTCTCTTTTTCTTTATGTTTTA
1 TTTC-TTCCCTACTATTCGTGCCTTTCTTTCTCTTTTTCTTTATGTTTTA
33218954 TTTCTTCCCTACTATTCGTGCCTTTCTTTCTCTTTTTCTTTATGTTTTA
1 TTTCTTCCCTACTATTCGTGCCTTTCTTTCTCTTTTTCTTTATGTTTTA
33219003 TTTCTT
1 TTTCTT
33219009 TTATTTTCTT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
49 50 0.93
50 4 0.07
ACGTcount: A:0.07, C:0.24, G:0.07, T:0.63
Consensus pattern (49 bp):
TTTCTTCCCTACTATTCGTGCCTTTCTTTCTCTTTTTCTTTATGTTTTA
Found at i:33222477 original size:45 final size:46
Alignment explanation
Indices: 33222412--33222502 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 46
33222402 GCAATTAGAC
*
33222412 CCAAAATTTATTATGGCTGGATGGCAACGG-ATGAAATCAGCAGGA
1 CCAAAATTTATTATGACTGGATGGCAACGGCATGAAATCAGCAGGA
*
33222457 CCAAAATTTATTATGACTGGATGGCAAGGGCATGAAATCAGCAGGA
1 CCAAAATTTATTATGACTGGATGGCAACGGCATGAAATCAGCAGGA
33222503 AAATTGATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 28 0.65
46 15 0.35
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.22
Consensus pattern (46 bp):
CCAAAATTTATTATGACTGGATGGCAACGGCATGAAATCAGCAGGA
Found at i:33224628 original size:44 final size:44
Alignment explanation
Indices: 33224565--33224651 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
33224555 ATATTAGGTA
33224565 AGTATAATTCTTGTAACATGACCTTACTAAGCACGAAGTGCTTC
1 AGTATAATTCTTGTAACATGACCTTACTAAGCACGAAGTGCTTC
* *
33224609 AGTATAATTCTTGTTACATGAGCTTACTAAGCACGAAGTGCTT
1 AGTATAATTCTTGTAACATGACCTTACTAAGCACGAAGTGCTT
33224652 ACCCCGTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (44 bp):
AGTATAATTCTTGTAACATGACCTTACTAAGCACGAAGTGCTTC
Found at i:33234203 original size:15 final size:15
Alignment explanation
Indices: 33234183--33234214 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33234173 TTTAATTAAG
*
33234183 AAATTAATTTAAATA
1 AAATTAATTAAAATA
33234198 AAATTAATTAAAATA
1 AAATTAATTAAAATA
33234213 AA
1 AA
33234215 TAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTAATTAAAATA
Found at i:33238779 original size:32 final size:32
Alignment explanation
Indices: 33238738--33238798 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
33238728 ATTGCAATTT
*
33238738 TGCATTCTTCTCATATTACGCCAACATTGTCG
1 TGCATTCTTCTCATATTACACCAACATTGTCG
33238770 TGCATTCTTCTCATATTACACCAACATTG
1 TGCATTCTTCTCATATTACACCAACATTG
33238799 CCGCACCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (32 bp):
TGCATTCTTCTCATATTACACCAACATTGTCG
Found at i:33241314 original size:3 final size:3
Alignment explanation
Indices: 33241306--33241368 Score: 92
Period size: 3 Copynumber: 21.3 Consensus size: 3
33241296 AGTAGATTTA
* * *
33241306 ATT ATT ATT ATT ATT ATT AGT ATA ACT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
33241353 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
33241369 AAATGAAGCC
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:33245734 original size:44 final size:44
Alignment explanation
Indices: 33245685--33245776 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
33245675 TGTTCAGGGA
*
33245685 TACTTCGACCTTGAGTCGATAAGGCAC-TATAAGTGTCGTACTGT
1 TACTTCGACCTTAAGTCGATAAGGCACAT-TAAGTGTCGTACTGT
* * **
33245729 TACTTCGACTTTAAGTCGATGAGGCACATTGTGTGTCGTACTGT
1 TACTTCGACCTTAAGTCGATAAGGCACATTAAGTGTCGTACTGT
33245773 TACT
1 TACT
33245777 GTTACTTCGA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (44 bp):
TACTTCGACCTTAAGTCGATAAGGCACATTAAGTGTCGTACTGT
Found at i:33245824 original size:47 final size:49
Alignment explanation
Indices: 33245723--33245831 Score: 134
Period size: 47 Copynumber: 2.2 Consensus size: 49
33245713 ATAAGTGTCG
* * *
33245723 TACTGTTACTTCGACTTTAAGTCGATGAGGCACATTGTGTGTCGTACTGT
1 TACTGTTACTTCGACTTTAAGTCGATAAGGCACA-TGAGTATCGTACTGT
*
33245773 TACTGTTACTTCGA-TTTAA-TCCGATAAGGTAC-TGAGTATCGTACTGT
1 TACTGTTACTTCGACTTTAAGT-CGATAAGGCACATGAGTATCGTACTGT
33245820 TACTGTTTACTT
1 TACTG-TTACTT
33245832 TGGCAAAGCC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
47 18 0.34
48 7 0.13
49 14 0.26
50 14 0.26
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.40
Consensus pattern (49 bp):
TACTGTTACTTCGACTTTAAGTCGATAAGGCACATGAGTATCGTACTGT
Found at i:33248276 original size:25 final size:25
Alignment explanation
Indices: 33248248--33248328 Score: 110
Period size: 25 Copynumber: 3.2 Consensus size: 25
33248238 CAGCTTGTAT
33248248 GAGCTTACCGATT-TGCAGCTCGTGA
1 GAGCTTACCGATTCT-CAGCTCGTGA
*
33248273 GAGCTTACCGATTCTCAGCTCGTAA
1 GAGCTTACCGATTCTCAGCTCGTGA
* * *
33248298 AAGCTTATCGATTCTCAGCTCGTGT
1 GAGCTTACCGATTCTCAGCTCGTGA
33248323 GAGCTT
1 GAGCTT
33248329 TGACAATTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
25 48 0.98
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (25 bp):
GAGCTTACCGATTCTCAGCTCGTGA
Found at i:33248508 original size:13 final size:13
Alignment explanation
Indices: 33248490--33248515 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33248480 CATGAGAGTA
33248490 CTTTTAGGAAACC
1 CTTTTAGGAAACC
33248503 CTTTTAGGAAACC
1 CTTTTAGGAAACC
33248516 TTATCAAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
CTTTTAGGAAACC
Found at i:33249095 original size:40 final size:38
Alignment explanation
Indices: 33249003--33249099 Score: 115
Period size: 40 Copynumber: 2.5 Consensus size: 38
33248993 ACCATCTCCG
* *
33249003 TCCAACCCAACACACCATGTGGGGATAAAATCGACCCA
1 TCCAACCCTACACACCATATGGGGATAAAATCGACCCA
* * *
33249041 -CCAATCTCTGCACACCGTATATGGGGATATAATCGACCCA
1 TCCAA-CCCTACACACC--ATATGGGGATAAAATCGACCCA
33249081 TCCAACCCTACACACCATA
1 TCCAACCCTACACACCATA
33249100 AAGTACCGCA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
37 4 0.08
38 11 0.23
40 29 0.60
41 4 0.08
ACGTcount: A:0.34, C:0.35, G:0.13, T:0.18
Consensus pattern (38 bp):
TCCAACCCTACACACCATATGGGGATAAAATCGACCCA
Found at i:33251117 original size:13 final size:13
Alignment explanation
Indices: 33251099--33251129 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
33251089 CTGAGTCATC
*
33251099 ATTTTACGTCTCG
1 ATTTTACGTATCG
33251112 ATTTTACGTATCG
1 ATTTTACGTATCG
33251125 ATTTT
1 ATTTT
33251130 GGCAGAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (13 bp):
ATTTTACGTATCG
Found at i:33255784 original size:13 final size:13
Alignment explanation
Indices: 33255766--33255790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
33255756 TCACATGATA
33255766 TTTTAGGAAACCC
1 TTTTAGGAAACCC
33255779 TTTTAGGAAACC
1 TTTTAGGAAACC
33255791 TTATCAAGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTTTAGGAAACCC
Found at i:33258527 original size:29 final size:30
Alignment explanation
Indices: 33258482--33258542 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 30
33258472 TCTTGTTTGT
*
33258482 ACCCAATTTCTTTAATAATTTC-TTTTCTA
1 ACCCAATTTCTTCAATAATTTCTTTTTCTA
33258511 ACCCAATTTCTTCAATAATTTCTTTTTCTA
1 ACCCAATTTCTTCAATAATTTCTTTTTCTA
33258541 AC
1 AC
33258543 TAACCACTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (30 bp):
ACCCAATTTCTTCAATAATTTCTTTTTCTA
Found at i:33262909 original size:459 final size:458
Alignment explanation
Indices: 33262040--33262961 Score: 1551
Period size: 459 Copynumber: 2.0 Consensus size: 458
33262030 TCCAGTGTGC
*
33262040 GCAAATGTTGATTTTTTTTAACAACCAGGGATTGTCGCAAAGAGGCATTATAATTACCTCGGGAG
1 GCAAATGTTGATTTTTTTTAACAACCAGGGATTGTCGCAAAGAGGCATTATAATTACCCCGGGAG
* *
33262105 GAAAGAAGACACAATCCAGCAAGTGGCGTGGTGGTAAGGTACGGGTGGTGTAGTTGAAGGGTACG
66 GAAAGAAGACACAATCCAGCAAGTAGCGTGGTGGTAAGGTACGGGTGGTATAGTTGAAGGGTACG
* * * * *
33262170 GGTTTGAGTTTGGTAACTAGCGATGTTTTTGTTTTATTTTTAAATGAACCGGGACTGCAGTAGAT
131 GGTTCGAGTCTAGTAACTAGCAATGTTTTTGTTTTATTTTTAAATGAACCAGGACTGCAGTAGAT
*
33262235 AAGTCTTAAAATTAATTGTGAGTAGATTATATCATGAGAGGAGCTTCAGTGCAGTGGCAAGTAGC
196 AAGTCTTAAAATTAATTGTGAGTAGATTATATCATGAGAGGAGCTTCAGTGCAGTGGCAAGCAGC
* * * *
33262300 GTATGTGGGTGCCTGGAGGTCTCGGTTTCGAGCTGCTGTACACGCACTGGGCGACCAATTTTGCT
261 ATATGTGGCTGCCTGGAGGTCTCAGTTTCGAGCTGCTGTACACGCAATGGGCGACCAATTTTGCT
* *
33262365 GCTCACGTGGAGTAGAGTTAGAGTTTGACCGAAACTCTCCTAGCAGTGGCTTAAGTCAGTCAAGT
326 GCTCACGTGGAGGAGAGTTAGAGTTTGACCGAAACTCTCCTAGCAGTGGCTTAAGTCAGTCAAGC
33262430 GGTGGACTGCTGCTGATGGTGCAAGGAATTTGGATGGGATTTAAATTGGTGGTGGCTGAAATTTA
391 GGTGGACTGCTGCTGATGGTGCAAGGAATTTGGATGGGATTTAAATTGGTGGTGGCTGAAATTTA
33262495 GGA
456 GGA
*
33262498 GCAAATGTTGATTTTTTTTTAACAACCAGGGATTGTCG-AAAGGAGGCCTTATAATTACCCCGGG
1 GCAAATGTTGA-TTTTTTTTAACAACCAGGGATTGTCGCAAA-GAGGCATTATAATTACCCCGGG
* * *
33262562 AGGAAAGAAGACACAATCGAGCAAGTAGCGTGGTGGTAAGGTACGGGTGGTATAGTTGGAGTGTA
64 AGGAAAGAAGACACAATCCAGCAAGTAGCGTGGTGGTAAGGTACGGGTGGTATAGTTGAAGGGTA
*
33262627 -GAGGTTCGAGTCTAGTAAGTAGCAATGTTTTTGTTTTATTTTTAAATGAACCAGGACTGCAGTA
129 CG-GGTTCGAGTCTAGTAACTAGCAATGTTTTTGTTTTATTTTTAAATGAACCAGGACTGCAGTA
* *
33262691 GATAAGTCTTAAAATTAATTGTGAGTAGATTATGTCATGAGAGGAGCTTCAGTGCAGTGGTAAGC
193 GATAAGTCTTAAAATTAATTGTGAGTAGATTATATCATGAGAGGAGCTTCAGTGCAGTGGCAAGC
* * *
33262756 AGCATATGTGGCTGTCTGGAGGTCTCAGTTTCGAGCTGCTGTACGCGCAATGGGCGACTAATTTT
258 AGCATATGTGGCTGCCTGGAGGTCTCAGTTTCGAGCTGCTGTACACGCAATGGGCGACCAATTTT
* * *
33262821 GCTGCTCACGTGGGGGAGAGTTAGAGTTTGACCGAAACTCTCCTAGCAGTGGCTTGAGTCGGTCA
323 GCTGCTCACGTGGAGGAGAGTTAGAGTTTGACCGAAACTCTCCTAGCAGTGGCTTAAGTCAGTCA
33262886 AGCGGTGGACTGCTGCTGATGGTGCAAGGAATTTGGATGGGATTTAAATTGGTGGTGGCTGAAAT
388 AGCGGTGGACTGCTGCTGATGGTGCAAGGAATTTGGATGGGATTTAAATTGGTGGTGGCTGAAAT
33262951 TTAGGA
453 TTAGGA
33262957 GCAAA
1 GCAAA
33262962 ACATGGAATT
Statistics
Matches: 433, Mismatches: 28, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
458 15 0.03
459 418 0.97
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (458 bp):
GCAAATGTTGATTTTTTTTAACAACCAGGGATTGTCGCAAAGAGGCATTATAATTACCCCGGGAG
GAAAGAAGACACAATCCAGCAAGTAGCGTGGTGGTAAGGTACGGGTGGTATAGTTGAAGGGTACG
GGTTCGAGTCTAGTAACTAGCAATGTTTTTGTTTTATTTTTAAATGAACCAGGACTGCAGTAGAT
AAGTCTTAAAATTAATTGTGAGTAGATTATATCATGAGAGGAGCTTCAGTGCAGTGGCAAGCAGC
ATATGTGGCTGCCTGGAGGTCTCAGTTTCGAGCTGCTGTACACGCAATGGGCGACCAATTTTGCT
GCTCACGTGGAGGAGAGTTAGAGTTTGACCGAAACTCTCCTAGCAGTGGCTTAAGTCAGTCAAGC
GGTGGACTGCTGCTGATGGTGCAAGGAATTTGGATGGGATTTAAATTGGTGGTGGCTGAAATTTA
GGA
Found at i:33263048 original size:14 final size:14
Alignment explanation
Indices: 33263029--33263055 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33263019 GCAAATAAGT
33263029 GCCGTTTATTTTTG
1 GCCGTTTATTTTTG
33263043 GCCGTTTATTTTT
1 GCCGTTTATTTTT
33263056 CATTTTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.19, T:0.59
Consensus pattern (14 bp):
GCCGTTTATTTTTG
Found at i:33266070 original size:27 final size:27
Alignment explanation
Indices: 33266026--33266099 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
33266016 TATAGAAATG
* * *
33266026 CCCTCGACTTGTAAAATTACCAAAGTA
1 CCCTCGATTTATAGAATTACCAAAGTA
*****
33266053 CCCTCGATTTATAGAATTACTGTTTTA
1 CCCTCGATTTATAGAATTACCAAAGTA
*
33266080 CCCTTGATTTATAGAATTAC
1 CCCTCGATTTATAGAATTAC
33266100 TGTTTTACCC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCAAAGTA
Found at i:33266100 original size:27 final size:27
Alignment explanation
Indices: 33266051--33266135 Score: 125
Period size: 27 Copynumber: 3.1 Consensus size: 27
33266041 ATTACCAAAG
33266051 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
*
33266078 TACCCTTGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTGTTT
* * **
33266105 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTATAGAATTACTGTTT
33266132 TACC
1 TACC
33266136 TTCAATTGTG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACTGTTT
Done.