Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007460.1 Kokia drynarioides strain JFW-HI SEQ_122081, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 612245
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 56 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:402005 original size:149 final size:149
Alignment explanation
Indices: 401662--402005 Score: 390
Period size: 149 Copynumber: 2.3 Consensus size: 149
401652 CAGTACCATG
* * * * *
401662 AAGATATGAAGGGAAAGG-TGAAGGCTGCAATGATGAATCCAGTACCTTAGAAGATGTGATAGGA
1 AAGATGTGATGGGAAAGGTTG-AGGCTGCAATGGTGAATCTAGTACCTTAAAAGATGTGATAGGA
* * * *
401726 AAGATTGATGCCGCAACGACGAATCTGATACCATGAAGATATGAAGGGAAATGTTGAGGCTGCAA
65 AAGATTGATGCCGCAACGACGAATCCGATACCATGAAGATATGAAGGGAAAGGTGGAGGCTACAA
* *
401791 CGGTGAACCCGATACCCTAA
130 CGGTAAACCCGAGACCCTAA
*** *
401811 AAGATGTGATGGGAAAGGTTGAGGCCATAATGGTGAACCTAGTACCTTAAAAGATGTGATAGG-A
1 AAGATGTGATGGGAAAGGTTGAGGCTGCAATGGTGAATCTAGTACCTTAAAAGATGTGATAGGAA
* ** * *
401875 AGAATT-TTGGTTGCAACGGCGAATCCGGTACCATGAAGATATGAAGGGAAAGGTGGAGGCTACA
66 AG-ATTGAT-GCCGCAACGACGAATCCGATACCATGAAGATATGAAGGGAAAGGTGGAGGCTACA
* * * *
401939 ACGGTAAACTCGGGACCTTAG
129 ACGGTAAACCCGAGACCCTAA
* *
401960 AAGATGTGATGGG-AAGGATTGAGGCTGCAATGGCGAATCTTGTACC
1 AAGATGTGATGGGAAAGG-TTGAGGCTGCAATGGTGAATCTAGTACC
402006 ATGGAAATAT
Statistics
Matches: 161, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
148 8 0.05
149 151 0.94
150 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.21
Consensus pattern (149 bp):
AAGATGTGATGGGAAAGGTTGAGGCTGCAATGGTGAATCTAGTACCTTAAAAGATGTGATAGGAA
AGATTGATGCCGCAACGACGAATCCGATACCATGAAGATATGAAGGGAAAGGTGGAGGCTACAAC
GGTAAACCCGAGACCCTAA
Found at i:402040 original size:99 final size:99
Alignment explanation
Indices: 401854--402040 Score: 232
Period size: 99 Copynumber: 1.9 Consensus size: 99
401844 TGAACCTAGT
** *
401854 ACCTTAAAAGATGTGATAGGAAGAATTTTGGTTGCAACGGCGAATCCGGTACCATGAAGATATGA
1 ACCTTAAAAGATGTGATAGGAAGAATTGAGGCTGCAACGGCGAATCCGGTACCATGAAGATATGA
* *
401919 AGGGAAAGGTGGAGGCTACAACGGTAAACTCGGG
66 AGGGAAAGGTGGAAGCCACAACGGTAAACTCGGG
* * * * **
401953 ACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGCAATGGCGAATCTTGTACCATGGAA-ATATG
1 ACCTTAAAAGATGTGATAGGAAGAATTGAGGCTGCAACGGCGAATCCGGTACCAT-GAAGATATG
* * *
402017 GAGGGAAAGGTTGAAGCCGCAACG
65 AAGGGAAAGGTGGAAGCCACAACG
402041 ATGAACTTTA
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
99 70 0.96
100 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (99 bp):
ACCTTAAAAGATGTGATAGGAAGAATTGAGGCTGCAACGGCGAATCCGGTACCATGAAGATATGA
AGGGAAAGGTGGAAGCCACAACGGTAAACTCGGG
Found at i:402056 original size:99 final size:99
Alignment explanation
Indices: 401853--402082 Score: 230
Period size: 99 Copynumber: 2.3 Consensus size: 99
401843 GTGAACCTAG
* * * ** *
401853 TACCTTAAAAGATGTGATAGGAAGAATTTTGGTTGCAACGGCGAATCCGGTACCATGAAGATATG
1 TACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGCAACGGCGAATCCGGTACCATGAAGATATG
* * * *
401918 AAGGGAAAGGTGGAGGCTACAACGGTAAACTCGG
66 AAGGGAAAGGTGGAAGCCACAACGATAAACTCGA
* * **
401952 GACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGCAATGGCGAATCTTGTACCATGGAA-ATAT
1 TACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGCAACGGCGAATCCGGTACCAT-GAAGATAT
* * * * **
402016 GGAGGGAAAGGTTGAAGCCGCAACGATGAACTTTA
65 GAAGGGAAAGGTGGAAGCCACAACGATAAACTCGA
* * *
402051 TACCTTAG-AGATATGAAGGGAAAGATTGAGGC
1 TACCTTAGAAGATGTGATGGGAAGGATTGAGGC
402083 CGTAATGATG
Statistics
Matches: 106, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
98 21 0.20
99 82 0.77
100 3 0.03
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.22
Consensus pattern (99 bp):
TACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGCAACGGCGAATCCGGTACCATGAAGATATG
AAGGGAAAGGTGGAAGCCACAACGATAAACTCGA
Found at i:402103 original size:49 final size:49
Alignment explanation
Indices: 401953--402103 Score: 133
Period size: 49 Copynumber: 3.1 Consensus size: 49
401943 TAAACTCGGG
* * * * ** *
401953 ACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGCAATGGCGAATCTTGT
1 ACCTTAG-AGATATGAAGGGAAAGATTGAGGCCGCAATGATGAATCTTAT
* * * * * * *
402003 ACCATGGAAATATGGAGGGAAAGGTTGAAGCCGCAACGATGAA-CTTTAT
1 ACCTTAGAGATATGAAGGGAAAGATTGAGGCCGCAATGATGAATC-TTAT
* *
402052 ACCTTAGAGATATGAAGGGAAAGATTGAGGCCGTAATGATGAATCTCAT
1 ACCTTAGAGATATGAAGGGAAAGATTGAGGCCGCAATGATGAATCTTAT
402101 ACC
1 ACC
402104 CTAAAGATGA
Statistics
Matches: 76, Mismatches: 23, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
48 1 0.01
49 69 0.91
50 6 0.08
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (49 bp):
ACCTTAGAGATATGAAGGGAAAGATTGAGGCCGCAATGATGAATCTTAT
Found at i:402376 original size:42 final size:42
Alignment explanation
Indices: 402329--402489 Score: 256
Period size: 42 Copynumber: 3.9 Consensus size: 42
402319 GAAGCTGTCT
402329 AATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCC
1 AATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCC
* * *
402371 AATCTCTTACCCCGATCATGGGGCATATTCAAG---TCATCC
1 AATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCC
*
402410 AATCTCTTACCCCGATCATGAGGTAGATTGAAGACATCATCC
1 AATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCC
*
402452 AATCTCTTACCCCGATCATGGGGTAGATTGAAGTCATC
1 AATCTCTTACCCCGATCATGGGGTAGATTGAAGACATC
402490 TAATCTTTTA
Statistics
Matches: 107, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
39 35 0.33
42 72 0.67
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (42 bp):
AATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCC
Found at i:402464 original size:81 final size:81
Alignment explanation
Indices: 402329--402502 Score: 294
Period size: 81 Copynumber: 2.1 Consensus size: 81
402319 GAAGCTGTCT
*
402329 AATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
1 AATCTCTTACCCCGATCATGAGGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
*
402394 CATATTCAAGTCATCC
66 CAGATTCAAGTCATCC
402410 AATCTCTTACCCCGATCATGAGGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
1 AATCTCTTACCCCGATCATGAGGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
* * *
402475 TAGATTGAAGTCATCT
66 CAGATTCAAGTCATCC
*
402491 AATCTTTTACCC
1 AATCTCTTACCC
402503 TTAAGTCAAG
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 87 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.29
Consensus pattern (81 bp):
AATCTCTTACCCCGATCATGAGGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
CAGATTCAAGTCATCC
Found at i:404401 original size:28 final size:29
Alignment explanation
Indices: 404369--404464 Score: 90
Period size: 28 Copynumber: 3.3 Consensus size: 29
404359 AAAAAATCAA
* *
404369 ATTTT-ACCCCCAAACTTTCTAAAATTTC
1 ATTTTAACCCTCAAACTTTCTAAAATTGC
* * *
404397 ATTTTGA-CCTTAGACTTT-TGAAAATTGC
1 ATTTTAACCCTCAAACTTTCT-AAAATTGC
*
404425 ATTTTAACCCTCGAACTTTCTAAAAATTGC
1 ATTTTAACCCTCAAACTTTCT-AAAATTGC
*
404455 AATTTAACCC
1 ATTTTAACCC
404465 CCTTTTTTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 1 0.02
28 26 0.48
29 9 0.17
30 18 0.33
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (29 bp):
ATTTTAACCCTCAAACTTTCTAAAATTGC
Found at i:404453 original size:30 final size:29
Alignment explanation
Indices: 404381--404464 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 29
404371 TTTACCCCCA
* * *
404381 AACTTTCTAAAATTTCATTTTGACCTTAG
1 AACTTTCTAAAATTGCATTTTAACCCTAG
*
404410 -ACTTT-TGAAAATTGCATTTTAACCCTCG
1 AACTTTCT-AAAATTGCATTTTAACCCTAG
*
404438 AACTTTCTAAAAATTGCAATTTAACCC
1 AACTTTCT-AAAATTGCATTTTAACCC
404465 CCTTTTTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
27 1 0.02
28 22 0.48
29 5 0.11
30 18 0.39
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.39
Consensus pattern (29 bp):
AACTTTCTAAAATTGCATTTTAACCCTAG
Found at i:404603 original size:18 final size:18
Alignment explanation
Indices: 404582--404625 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
404572 CTTTTAAAAT
404582 TTTTTATATAAAA-TTTCA
1 TTTTTAT-TAAAACTTTCA
* *
404600 TTTTGATTAAAACTTTCC
1 TTTTTATTAAAACTTTCA
404618 TTTTTATT
1 TTTTTATT
404626 TTGACTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTTATTAAAACTTTCA
Found at i:414940 original size:14 final size:16
Alignment explanation
Indices: 414921--414956 Score: 58
Period size: 14 Copynumber: 2.4 Consensus size: 16
414911 GAATAAAGTG
414921 TTTTTGAGAC-T-TAA
1 TTTTTGAGACTTGTAA
414935 TTTTTGAGACTTGTAA
1 TTTTTGAGACTTGTAA
414951 TTTTTG
1 TTTTTG
414957 GATTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.50
15 1 0.05
16 9 0.45
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (16 bp):
TTTTTGAGACTTGTAA
Found at i:418902 original size:24 final size:24
Alignment explanation
Indices: 418851--418925 Score: 91
Period size: 22 Copynumber: 3.2 Consensus size: 24
418841 TCTTTTAGTT
* * * * *
418851 AAACTCAGTTTATTTGGTTCAATT
1 AAACTCTGTTTATTTGTTTGAGTC
418875 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTGAGTC
418899 AAA--CTGTTTATTTGTTTGAGTC
1 AAACTCTGTTTATTTGTTTGAGTC
418921 AAACT
1 AAACT
418926 AATATTAGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
22 22 0.50
24 22 0.50
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.47
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTGAGTC
Found at i:418908 original size:22 final size:22
Alignment explanation
Indices: 418880--418925 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
418870 CAATTAAACT
418880 CTGTTTATTTGTTTGAGTCAAA
1 CTGTTTATTTGTTTGAGTCAAA
418902 CTGTTTATTTGTTTGAGTCAAA
1 CTGTTTATTTGTTTGAGTCAAA
418924 CT
1 CT
418926 AATATTAGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (22 bp):
CTGTTTATTTGTTTGAGTCAAA
Found at i:423977 original size:65 final size:65
Alignment explanation
Indices: 423874--424005 Score: 237
Period size: 65 Copynumber: 2.0 Consensus size: 65
423864 ACTTCCAATA
*
423874 TGGTGGTGCATCTCTCTCTTTACCTGGAGCACAAATCACCTGCAATCATTAACCGAGGCTATTGG
1 TGGTGGTGCATCTCTCTCATTACCTGGAGCACAAATCACCTGCAATCATTAACCGAGGCTATTGG
* *
423939 TGGTGGTGCATCTCTCTCATTACCTGGAGCACAGATCACCTGCAATCATTATCCGAGGCTATTGG
1 TGGTGGTGCATCTCTCTCATTACCTGGAGCACAAATCACCTGCAATCATTAACCGAGGCTATTGG
424004 TG
1 TG
424006 ATCTAGGCAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.30
Consensus pattern (65 bp):
TGGTGGTGCATCTCTCTCATTACCTGGAGCACAAATCACCTGCAATCATTAACCGAGGCTATTGG
Found at i:430718 original size:81 final size:81
Alignment explanation
Indices: 430590--430754 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 81
430580 ATTTGATTGG
430590 AAAAAAATAAGAAAACTAAAATGGGAGGTAAAAGGCTGCTAAAAGATGAAAAAAGGGGTTTAAAT
1 AAAAAAATAAGAAAACTAAAATGGGAGGTAAAAGGCTGCTAAAAGATGAAAAAAGGGGTTTAAAT
430655 ACCCAATAAATTGGGT
66 ACCCAATAAATTGGGT
*
430671 AAAAAAGTAAGAAAACTAAAATGGGAGGTAAAAGGCTGCTAAAAGATGAAAAAAGGGGTTTAAAT
1 AAAAAAATAAGAAAACTAAAATGGGAGGTAAAAGGCTGCTAAAAGATGAAAAAAGGGGTTTAAAT
*
430736 ACCTAATAAATTGGGT
66 ACCCAATAAATTGGGT
430752 AAA
1 AAA
430755 TTTCACAAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.52, C:0.07, G:0.22, T:0.19
Consensus pattern (81 bp):
AAAAAAATAAGAAAACTAAAATGGGAGGTAAAAGGCTGCTAAAAGATGAAAAAAGGGGTTTAAAT
ACCCAATAAATTGGGT
Found at i:430898 original size:30 final size:29
Alignment explanation
Indices: 430858--430931 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
430848 AATTAAAGCT
*
430858 CAATTAAGTCCTTAAACTTCACTAAATATAC
1 CAATT-AGTCCTTAAACTTCACAAAAT-TAC
* * * *
430889 GAATTAGTCCATAAATTTCACAAAATTTC
1 CAATTAGTCCTTAAACTTCACAAAATTAC
430918 CAATTTAGTCCTTA
1 CAA-TTAGTCCTTA
430932 GTATAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 4 0.11
30 27 0.77
31 4 0.11
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.35
Consensus pattern (29 bp):
CAATTAGTCCTTAAACTTCACAAAATTAC
Found at i:432463 original size:27 final size:27
Alignment explanation
Indices: 432424--432600 Score: 221
Period size: 27 Copynumber: 6.5 Consensus size: 27
432414 TCATTTCAGC
*
432424 AATAACAGAATATCGCTCGTTCGAGCCA
1 AATAA-AGAATATCGCTCATTCGAGCCA
* *
432452 AATAAAGAATATCGCTTATTCGAACCA
1 AATAAAGAATATCGCTCATTCGAGCCA
** *
432479 AATACAA-AATGCCGCTCATTCGAGCGA
1 AATA-AAGAATATCGCTCATTCGAGCCA
* *
432506 GATAAAAAATATCGCTCATTCGAGCCA
1 AATAAAGAATATCGCTCATTCGAGCCA
* *
432533 AATACAGAATATCGCTCATTCGAACCA
1 AATAAAGAATATCGCTCATTCGAGCCA
*
432560 AATACAGAATATCGCTCATTCGAGCCA
1 AATAAAGAATATCGCTCATTCGAGCCA
*
432587 AATATAGAATATCG
1 AATAAAGAATATCG
432601 ATTATTGCTC
Statistics
Matches: 129, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.02
27 120 0.93
28 7 0.05
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (27 bp):
AATAAAGAATATCGCTCATTCGAGCCA
Found at i:432598 original size:81 final size:81
Alignment explanation
Indices: 432424--432600 Score: 255
Period size: 81 Copynumber: 2.2 Consensus size: 81
432414 TCATTTCAGC
* *
432424 AATAACAGAATATCGCTCGTTCGAGCCAAATAAAGAATATCGCTTATTCGAACCAAATACAAAAT
1 AATAA-AGAATATCGCTCATTCGAGCCAAATAAAGAATATCGCTCATTCGAACCAAATACAAAAT
* *
432489 GCCGCTCATTCGAGCGA
65 ACCGCTCATTCGAGCCA
* * * *
432506 GATAAAAAATATCGCTCATTCGAGCCAAATACAGAATATCGCTCATTCGAACCAAATACAGAATA
1 AATAAAGAATATCGCTCATTCGAGCCAAATAAAGAATATCGCTCATTCGAACCAAATACAAAATA
*
432571 TCGCTCATTCGAGCCA
66 CCGCTCATTCGAGCCA
*
432587 AATATAGAATATCG
1 AATAAAGAATATCG
432601 ATTATTGCTC
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
81 79 0.95
82 4 0.05
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (81 bp):
AATAAAGAATATCGCTCATTCGAGCCAAATAAAGAATATCGCTCATTCGAACCAAATACAAAATA
CCGCTCATTCGAGCCA
Found at i:440620 original size:27 final size:27
Alignment explanation
Indices: 440578--440635 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
440568 TGGTGTCCAT
440578 CATGTAAATCTCTGATTGTGATCGCAC
1 CATGTAAATCTCTGATTGTGATCGCAC
*
440605 CATGTAAATCTGTGATTGTGATCGCAC
1 CATGTAAATCTCTGATTGTGATCGCAC
440632 CATG
1 CATG
440636 ACGAAATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (27 bp):
CATGTAAATCTCTGATTGTGATCGCAC
Found at i:446634 original size:41 final size:41
Alignment explanation
Indices: 446589--446712 Score: 167
Period size: 41 Copynumber: 3.0 Consensus size: 41
446579 GTCAATGCTT
*
446589 GTTAGCTTAAACTGTTGCTGCACCTTCCAATGACAGTGATC
1 GTTAGCTTAAACTGTTGCTGCACCTTCCAGTGACAGTGATC
* * * * *
446630 GTTAGCTTAAACTGTCGCTGTACCTTTCAGTGATAGTGACC
1 GTTAGCTTAAACTGTTGCTGCACCTTCCAGTGACAGTGATC
* * *
446671 GTTAGCTTAAACTATTGCTGCACCTCCCAGTGACAATGATC
1 GTTAGCTTAAACTGTTGCTGCACCTTCCAGTGACAGTGATC
446712 G
1 G
446713 CAATAACACT
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (41 bp):
GTTAGCTTAAACTGTTGCTGCACCTTCCAGTGACAGTGATC
Found at i:449723 original size:10 final size:10
Alignment explanation
Indices: 449694--449729 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
449684 AATTTTAGAT
449694 AAATAAAGAA
1 AAATAAAGAA
*
449704 AAAT-ATGAA
1 AAATAAAGAA
449713 AAATAAAGAA
1 AAATAAAGAA
449723 AAATAAA
1 AAATAAA
449730 TAATGTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (10 bp):
AAATAAAGAA
Found at i:463794 original size:24 final size:24
Alignment explanation
Indices: 463767--463813 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
463757 ATTACAAAAA
463767 ATTTT-CTATTAATTT-TTGTCTTTT
1 ATTTTACT-TTAATTTGTT-TCTTTT
463791 ATTTTACTTTAATTTGTTTCTTT
1 ATTTTACTTTAATTTGTTTCTTT
463814 AGTTTTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.17, C:0.09, G:0.04, T:0.70
Consensus pattern (24 bp):
ATTTTACTTTAATTTGTTTCTTTT
Found at i:478373 original size:19 final size:18
Alignment explanation
Indices: 478351--478386 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
478341 CATGTCAGGA
478351 AAAAAATAATTATTTTTTT
1 AAAAAATAATT-TTTTTTT
*
478370 AAAATATAATTTTTTTT
1 AAAAAATAATTTTTTTT
478387 AAATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAAAATAATTTTTTTTT
Found at i:478375 original size:17 final size:17
Alignment explanation
Indices: 478353--478391 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
478343 TGTCAGGAAA
*
478353 AAAATAATTATTTTTTT
1 AAAATAATAATTTTTTT
478370 AAAAT-ATAATTTTTTT
1 AAAATAATAATTTTTTT
*
478386 TAAATA
1 AAAATA
478392 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAAATAATAATTTTTTT
Found at i:479266 original size:27 final size:23
Alignment explanation
Indices: 479213--479266 Score: 54
Period size: 26 Copynumber: 2.2 Consensus size: 23
479203 AATTTTATAT
* *
479213 TTAAAAAATATTTTTAAAATATT
1 TTAAAAAATATTTTTAAAAAATA
479236 TTAAAAAATTTATATTTTAAAAAATAA
1 TTAAAAAA--TAT-TTTTAAAAAAT-A
479263 TTAA
1 TTAA
479267 TTTTTTTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 8 0.32
25 3 0.12
26 10 0.40
27 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTAAAAAATATTTTTAAAAAATA
Found at i:479799 original size:8 final size:8
Alignment explanation
Indices: 479786--479816 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
479776 TATTATTAGC
479786 TTTTTTTA
1 TTTTTTTA
479794 -TTTTTTA
1 TTTTTTTA
479801 TTTTTTTA
1 TTTTTTTA
479809 TTTTTTTA
1 TTTTTTTA
479817 ATGTTTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:479806 original size:15 final size:15
Alignment explanation
Indices: 479786--479814 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
479776 TATTATTAGC
479786 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
479801 TTTTTTTATTTTTT
1 TTTTTTTATTTTTT
479815 TAATGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:486614 original size:27 final size:26
Alignment explanation
Indices: 486552--486615 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
486542 TTCTTTTGAA
486552 TTAATAAAA-TTCTCTGTGTTTTTCTT
1 TTAA-AAAATTTCTCTGTGTTTTTCTT
*
486578 TTAAAGAATTTCTCT-TGTATTTTCTT
1 TTAAAAAATTTCTCTGTGT-TTTTCTT
486604 TTAGAAAAATTT
1 TTA-AAAAATTT
486616 TAACAATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 6 0.18
26 20 0.61
27 7 0.21
ACGTcount: A:0.28, C:0.09, G:0.08, T:0.55
Consensus pattern (26 bp):
TTAAAAAATTTCTCTGTGTTTTTCTT
Found at i:488538 original size:35 final size:36
Alignment explanation
Indices: 488487--488566 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
488477 GTTGGGAAAG
**
488487 CTCTACGAAATAGCATCA-TGAAAATGGTCTACTGA
1 CTCTACGAAATAGCATCACAAAAAATGGTCTACTGA
* * *
488522 CTCTACGAAATGGCATCACAAAAAATGGTTTACTGT
1 CTCTACGAAATAGCATCACAAAAAATGGTCTACTGA
488558 CTCTACGAA
1 CTCTACGAA
488567 GCAACACCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
35 17 0.44
36 22 0.56
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.26
Consensus pattern (36 bp):
CTCTACGAAATAGCATCACAAAAAATGGTCTACTGA
Found at i:489754 original size:65 final size:65
Alignment explanation
Indices: 489674--489800 Score: 245
Period size: 65 Copynumber: 2.0 Consensus size: 65
489664 ATTATGGACT
*
489674 GATTATTTAATTAGTAGACGAAGTATAATATTATTTAATTACATAAACAATATAATGATTTTACC
1 GATTATTTAACTAGTAGACGAAGTATAATATTATTTAATTACATAAACAATATAATGATTTTACC
489739 GATTATTTAACTAGTAGACGAAGTATAATATTATTTAATTACATAAACAATATAATGATTTT
1 GATTATTTAACTAGTAGACGAAGTATAATATTATTTAATTACATAAACAATATAATGATTTT
489801 TCCTTTTAAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.40
Consensus pattern (65 bp):
GATTATTTAACTAGTAGACGAAGTATAATATTATTTAATTACATAAACAATATAATGATTTTACC
Found at i:498553 original size:5 final size:5
Alignment explanation
Indices: 498543--498631 Score: 54
Period size: 5 Copynumber: 17.8 Consensus size: 5
498533 TCAAAACGTG
* * * * * * *
498543 TCATA TCATA TTATA ACATA ACGA-A TCTTA TCATA TGATA ACAAA TCATA
1 TCATA TCATA TCATA TCATA TC-ATA TCATA TCATA TCATA TCATA TCATA
* * * * *
498593 TTATA TCATA ACATA TCATA TTATA TCGTA ACATA TCAT
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCAT
498632 GTCCTACCCC
Statistics
Matches: 60, Mismatches: 22, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
5 59 0.98
6 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.03, T:0.37
Consensus pattern (5 bp):
TCATA
Found at i:498589 original size:20 final size:20
Alignment explanation
Indices: 498547--498631 Score: 80
Period size: 20 Copynumber: 4.2 Consensus size: 20
498537 AACGTGTCAT
* * *
498547 ATCATATTATAACATAACGA
1 ATCATATCATATCATAACAA
* *
498567 ATCTTATCATATGATAACAA
1 ATCATATCATATCATAACAA
* *
498587 ATCATATTATATCATAACAT
1 ATCATATCATATCATAACAA
* * *
498607 ATCATATTATATCGTAACAT
1 ATCATATCATATCATAACAA
498627 ATCAT
1 ATCAT
498632 GTCCTACCCC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (20 bp):
ATCATATCATATCATAACAA
Found at i:498625 original size:40 final size:40
Alignment explanation
Indices: 498547--498631 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
498537 AACGTGTCAT
*
498547 ATCATATTATAACATAACGAATCTTATCATATGATAACAA
1 ATCATATTATAACATAACGAATCATATCATATGATAACAA
* * *
498587 ATCATATTATATCATAAC-ATATCATATTATATCG-TAACAT
1 ATCATATTATAACATAACGA-ATCATATCATAT-GATAACAA
498627 ATCAT
1 ATCAT
498632 GTCCTACCCC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
39 1 0.03
40 37 0.95
41 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (40 bp):
ATCATATTATAACATAACGAATCATATCATATGATAACAA
Found at i:501291 original size:2 final size:2
Alignment explanation
Indices: 501284--501315 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
501274 TTACCAGACG
501284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
501316 CTTCTTTCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:502102 original size:24 final size:24
Alignment explanation
Indices: 502065--502128 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
502055 GGCAACACAG
* *
502065 AATATGCCATAAAGGCATTTACAA
1 AATATGCCACAAAGGAATTTACAA
*
502089 AATATACCACAAAGGAATTTACAA
1 AATATGCCACAAAGGAATTTACAA
*
502113 AATATGCCACATAGGA
1 AATATGCCACAAAGGA
502129 TAAACAGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.22
Consensus pattern (24 bp):
AATATGCCACAAAGGAATTTACAA
Found at i:502144 original size:23 final size:23
Alignment explanation
Indices: 502113--502277 Score: 109
Period size: 23 Copynumber: 7.1 Consensus size: 23
502103 GAATTTACAA
* *
502113 AATATGCCACATAGGATAAACAG
1 AATACGCCACATAGGCTAAACAG
*
502136 AATACGCCACATAGG-TGAAACAA
1 AATACGCCACATAGGCT-AAACAG
* *
502159 AATACGTCACATAGCCTAAACA-
1 AATACGCCACATAGGCTAAACAG
* * * * *
502181 AAGCACGCCACACAAGCCAAACTG
1 AA-TACGCCACATAGGCTAAACAG
* * *
502205 AATACGCCACATAGGTTAAGCAT
1 AATACGCCACATAGGCTAAACAG
* * * *
502228 AATACGCCACAAAAGCTAAAAAA
1 AATACGCCACATAGGCTAAACAG
* * *
502251 AAGTATGCCACAAAGGCCAAACAG
1 AA-TACGCCACATAGGCTAAACAG
502275 AAT
1 AAT
502278 GCAGCACAAA
Statistics
Matches: 107, Mismatches: 30, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
22 3 0.03
23 83 0.78
24 21 0.20
ACGTcount: A:0.47, C:0.24, G:0.15, T:0.13
Consensus pattern (23 bp):
AATACGCCACATAGGCTAAACAG
Found at i:506996 original size:7 final size:7
Alignment explanation
Indices: 506986--507011 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
506976 GAAAAGAATG
506986 GAGAAGA
1 GAGAAGA
506993 GAGAAGA
1 GAGAAGA
507000 GAGAAGA
1 GAGAAGA
507007 GAGAA
1 GAGAA
507012 TTTTCATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
GAGAAGA
Found at i:507918 original size:21 final size:19
Alignment explanation
Indices: 507868--507939 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
507858 AATGTTTTAT
* *
507868 AAATTTATATTTTTTAAAA
1 AAATTTAAACTTTTTAAAA
507887 AAATTTAAACTTTTTAAAA
1 AAATTTAAACTTTTTAAAA
*
507906 ATAATTTTTAACTTTTTAAAA
1 A-AA-TTTAAACTTTTTAAAA
507927 GAAA-TTAAACTTT
1 -AAATTTAAACTTT
507940 AAAATAATGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 26 0.57
20 2 0.04
21 17 0.37
22 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (19 bp):
AAATTTAAACTTTTTAAAA
Found at i:516260 original size:28 final size:25
Alignment explanation
Indices: 516209--516289 Score: 74
Period size: 27 Copynumber: 3.1 Consensus size: 25
516199 AATATACTAG
* **
516209 AAAAT-AAAATAAAAATAAGCATAA
1 AAAATAAAAAGAAAAATAAAAATAA
516233 AAAGATAAATAAGCAAAAATAAAAATAA
1 AAA-ATAAA-AAG-AAAAATAAAAATAA
*
516261 ATAATAAAAAGAAATAATATAAAATAA
1 AAAATAAAAAGAAA-AATA-AAAATAA
516288 AA
1 AA
516290 GATGTAACGA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 3 0.07
25 5 0.11
26 9 0.20
27 15 0.33
28 14 0.30
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.17
Consensus pattern (25 bp):
AAAATAAAAAGAAAAATAAAAATAA
Found at i:516268 original size:13 final size:13
Alignment explanation
Indices: 516250--516288 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
516240 AATAAGCAAA
516250 AATAAAAATAAAT
1 AATAAAAATAAAT
*
516263 AATAAAAAGAAAT
1 AATAAAAATAAAT
516276 AATATAAAATAAA
1 AATA-AAAATAAA
516289 AGATGTAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (13 bp):
AATAAAAATAAAT
Found at i:516270 original size:20 final size:19
Alignment explanation
Indices: 516247--516289 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
516237 ATAAATAAGC
* *
516247 AAAAATAAAAATAAATAAT
1 AAAAAGAAAAATAAAAAAT
*
516266 AAAAAGAAATAATATAAAAT
1 AAAAAGAAA-AATAAAAAAT
516286 AAAA
1 AAAA
516290 GATGTAACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (19 bp):
AAAAAGAAAAATAAAAAAT
Found at i:516285 original size:33 final size:34
Alignment explanation
Indices: 516212--516289 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 34
516202 ATACTAGAAA
* *
516212 ATAAAATAAAAATAAGCATAAAAAGATAAATAAGC
1 ATAAAATAAAAATAA-CATAAAAAAAGAAATAAGC
*
516247 A-AAAATAAAAATAA-ATAATAAAAAGAAATAA-T
1 ATAAAATAAAAATAACATAA-AAAAAGAAATAAGC
516279 ATAAAATAAAA
1 ATAAAATAAAA
516290 GATGTAACGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 5 0.13
33 19 0.50
34 13 0.34
35 1 0.03
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (34 bp):
ATAAAATAAAAATAACATAAAAAAAGAAATAAGC
Found at i:517288 original size:160 final size:161
Alignment explanation
Indices: 517019--517318 Score: 394
Period size: 160 Copynumber: 1.9 Consensus size: 161
517009 TTTGATGAAT
** *
517019 ATATGTTGTCAGTTTAATTGACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCTAGACACTAGG
1 ATATGTTGTCAGTTTAACCGACTAGAGCTGGGCTCACAATTGCGATTTATCCGCTAGACACTAGG
* *
517084 TGCCAAGATTTGACAAATATTTGTCGGTTTAATCGACTAGAGCTGGGCTTACATTTGTGGTTTAT
66 TGCCAAGATTTGACAAATATTTGTCGGTTTAACCGACTAGAGCTGGGCTTACATTTGCGGTTTAT
517149 CTGCTAAGCACAGGGTGCTAAATTTTGATGG
131 CTGCTAAGCACAGGGTGCTAAATTTTGATGG
* * *
517180 ATAT-TTGTCAGTTTAACCGACTAGAGTTGGGCTCACATTTGCGATTTATCTGCTA-AGCA-TAG
1 ATATGTTGTCAGTTTAACCGACTAGAGCTGGGCTCACAATTGCGATTTATCCGCTAGA-CACTA-
* * * * * * *
517242 GGTG-CTAGAATTTTA-AGGATATTTTTTGGTTTTACCGACTAGAGCTGGTCTTACATTTGCGGT
64 GGTGCCAAG-ATTTGACA-AATATTTGTCGGTTTAACCGACTAGAGCTGGGCTTACATTTGCGGT
517305 TTATCTGCTAAGCA
127 TTATCTGCTAAGCA
517319 TTGGGTGTTA
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
159 7 0.06
160 109 0.91
161 4 0.03
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (161 bp):
ATATGTTGTCAGTTTAACCGACTAGAGCTGGGCTCACAATTGCGATTTATCCGCTAGACACTAGG
TGCCAAGATTTGACAAATATTTGTCGGTTTAACCGACTAGAGCTGGGCTTACATTTGCGGTTTAT
CTGCTAAGCACAGGGTGCTAAATTTTGATGG
Found at i:517319 original size:80 final size:80
Alignment explanation
Indices: 517038--517367 Score: 330
Period size: 80 Copynumber: 4.1 Consensus size: 80
517028 CAGTTTAATT
* * * * *
517038 GACTAGAGCTGGGCTCACAATTGCGGTTTATCCGCT-AGACACTA-GGTGCCA-AGATTTGACA-
1 GACTAGAGCTGGGCTTACATTTGCGGTTTATCTGCTAAG-CA-TAGGGTGCTAGA-ATTTTA-AG
* * *
517099 AATATTTGTCGGTTTAATC
62 GATATTTGTTGGTTTAACC
* * *
517118 GACTAGAGCTGGGCTTACATTTGTGGTTTATCTGCTAAGCACAGGGTGCTA-AATTTTGATGGAT
1 GACTAGAGCTGGGCTTACATTTGCGGTTTATCTGCTAAGCATAGGGTGCTAGAATTTT-AAGGAT
**
517182 ATTTGTCAGTTTAACC
65 ATTTGTTGGTTTAACC
* * *
517198 GACTAGAGTTGGGCTCACATTTGCGATTTATCTGCTAAGCATAGGGTGCTAGAATTTTAAGGATA
1 GACTAGAGCTGGGCTTACATTTGCGGTTTATCTGCTAAGCATAGGGTGCTAGAATTTTAAGGATA
* *
517263 TTTTTTGGTTTTACC
66 TTTGTTGGTTTAACC
* * * * * * *
517278 GACTAGAGCTGGTCTTACATTTGCGGTTTATCTGCTAAGCATTGGGTGTTAGGATTTGACGAATA
1 GACTAGAGCTGGGCTTACATTTGCGGTTTATCTGCTAAGCATAGGGTGCTAGAATTTTAAGGATA
517343 TTTGTTGG-TTAATCC
66 TTTGTTGGTTTAA-CC
*
517358 AACTAGAGCT
1 GACTAGAGCT
517368 CACTTTCGCA
Statistics
Matches: 210, Mismatches: 34, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
79 8 0.04
80 194 0.92
81 8 0.04
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (80 bp):
GACTAGAGCTGGGCTTACATTTGCGGTTTATCTGCTAAGCATAGGGTGCTAGAATTTTAAGGATA
TTTGTTGGTTTAACC
Found at i:518369 original size:18 final size:17
Alignment explanation
Indices: 518334--518378 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
518324 TTGAAGGATT
518334 AAATTGAAAACAAAATAA
1 AAATT-AAAACAAAATAA
*
518352 AAATTAAAGCAAACATAA
1 AAATTAAAACAAA-ATAA
*
518370 AAAATAAAA
1 AAATTAAAA
518379 AAATGAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.73, C:0.07, G:0.04, T:0.16
Consensus pattern (17 bp):
AAATTAAAACAAAATAA
Found at i:518569 original size:15 final size:14
Alignment explanation
Indices: 518542--518568 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
518532 AAAATGAATT
518542 AAAATTAAAAAAAC
1 AAAATTAAAAAAAC
518556 AAAATTAAAAAAA
1 AAAATTAAAAAAA
518569 ATACGGAAGG
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:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATTAAAAAAAC
Found at i:519550 original size:24 final size:24
Alignment explanation
Indices: 519512--519562 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
519502 TGGGTACGTG
* *
519512 TATTTAAGTTAGTTGGGCTTTTGGT
1 TATTTAAGGTAGTTGGG-TTTGGGT
519537 TATTT-AGGTAGTTGGGTTTGGGT
1 TATTTAAGGTAGTTGGGTTTGGGT
519560 TAT
1 TAT
519563 GTAAATGGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.16, C:0.02, G:0.31, T:0.51
Consensus pattern (24 bp):
TATTTAAGGTAGTTGGGTTTGGGT
Found at i:520202 original size:101 final size:101
Alignment explanation
Indices: 520076--520476 Score: 459
Period size: 101 Copynumber: 4.0 Consensus size: 101
520066 GGATTTGACG
* *
520076 TTGTAACTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAATATTTGC-TTCTGTAGCTTTAAT
1 TTGTAACTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAATATTTGCTTTC-GTAGCTTCAAT
* *
520140 TTGACCCACTGCAACTTCAAGGATATAAGATTTGGTT
65 TCGATCCACTGCAACTTCAAGGATATAAGATTTGGTT
* * *
520177 TTGTAGCTTCATCCTGCTCTACTGCAACTTCAAAGAGATAAGA-ATTTGCTTTCGTAGCTTCAAT
1 TTGTAACTTCATCTTGCTCTACTGCAACTTCAGAGAGATAA-ATATTTGCTTTCGTAGCTTCAAT
* * * * *
520241 AT-GATCCACTACAACTTCATGGATATAGGATTTGATG
65 -TCGATCCACTGCAACTTCAAGGATATAAGATTTGGTT
* * ** * * * * * * *
520278 TTGTAGCTTTATCTTGCTCTTTTGTAACTTAAGGGAGATAAATATTTGTTTTTGTAGTTTCAATC
1 TTGTAACTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAATATTTGCTTTCGTAGCTTCAATT
* * * *
520343 CGATCCACTGTAACTTTAGGGGTATAAGATTTGGTT
66 CGATCCACTGCAACTTCAAGGATATAAGATTTGGTT
* * *
520379 TTGTAACTTCATCTTGCTCTATTGCAACTTCAGAGAGATAAAGATTTGCTTTCATAGCTTCAATT
1 TTGTAACTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAATATTTGCTTTCGTAGCTTCAATT
*
520444 CGATCCACTGCAACTTC-AGGTATATAGGATTTG
66 CGATCCACTGCAACTTCAAGG-ATATAAGATTTG
520477 ATGTTGTCCC
Statistics
Matches: 246, Mismatches: 48, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
100 3 0.01
101 238 0.97
102 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (101 bp):
TTGTAACTTCATCTTGCTCTACTGCAACTTCAGAGAGATAAATATTTGCTTTCGTAGCTTCAATT
CGATCCACTGCAACTTCAAGGATATAAGATTTGGTT
Found at i:520318 original size:202 final size:201
Alignment explanation
Indices: 520043--520483 Score: 568
Period size: 202 Copynumber: 2.2 Consensus size: 201
520033 AGTTTTAATC
* * *
520043 CGATCCACTATAACTTCAGG--GTAGGATTTGACGTTGTAACTTCATCTTGCTCCACTGCAACTT
1 CGATCCACTACAACTTCAGGATATAGGATTTGATGTTGTAACTTCATCTTGCTCCACTGCAACTT
* **
520106 CAGAGAGATAAATATTTGCTTCTGTAGCTTT-AATTTGACCCACTGCAACTTCAAGGATATAAGA
66 AAGAGAGATAAATATTTGCTTCTGTAG-TTTCAATCCGACCCACTGCAACTTCAAGGATATAAGA
* *
520170 TTTGGTTTTGTAGCTTCATCCTGCTCTACTGCAACTTCAAAGAGAT-AAGAATTTGCTTTCGTAG
130 TTTGGTTTTGTAACTTCATCCTGCTCTACTGCAACTTCAAAGAGATAAAG-ATTTGCTTTCATAG
520234 CTTCAATAT
194 CTTCAAT-T
* * *** *
520243 -GATCCACTACAACTTCATGGATATAGGATTTGATGTTGTAGCTTTATCTTGCTCTTTTGTAACT
1 CGATCCACTACAACTTCA-GGATATAGGATTTGATGTTGTAACTTCATCTTGCTCCACTGCAACT
* * * * * * * *
520307 TAAGGGAGATAAATATTTGTTTTTGTAGTTTCAATCCGATCCACTGTAACTTTAGGGGTATAAGA
65 TAAGAGAGATAAATATTTGCTTCTGTAGTTTCAATCCGACCCACTGCAACTTCAAGGATATAAGA
* * *
520372 TTTGGTTTTGTAACTTCATCTTGCTCTATTGCAACTTCAGAGAGATAAAGATTTGCTTTCATAGC
130 TTTGGTTTTGTAACTTCATCCTGCTCTACTGCAACTTCAAAGAGATAAAGATTTGCTTTCATAGC
520437 TTCAATT
195 TTCAATT
*
520444 CGATCCACTGCAACTTCAGGTATATAGGATTTGATGTTGT
1 CGATCCACTACAACTTCAGG-ATATAGGATTTGATGTTGT
520484 CCCTCACGTC
Statistics
Matches: 208, Mismatches: 26, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
199 16 0.08
200 2 0.01
201 6 0.03
202 181 0.87
203 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (201 bp):
CGATCCACTACAACTTCAGGATATAGGATTTGATGTTGTAACTTCATCTTGCTCCACTGCAACTT
AAGAGAGATAAATATTTGCTTCTGTAGTTTCAATCCGACCCACTGCAACTTCAAGGATATAAGAT
TTGGTTTTGTAACTTCATCCTGCTCTACTGCAACTTCAAAGAGATAAAGATTTGCTTTCATAGCT
TCAATT
Found at i:520425 original size:51 final size:51
Alignment explanation
Indices: 520076--520462 Score: 258
Period size: 51 Copynumber: 7.6 Consensus size: 51
520066 GGATTTGACG
* *
520076 TTGTAACTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAATATTTGCTT
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAAGATTTGCTT
* * *
520127 CTGTAGCTTTAAT-TTGAC-CCACTGCAACTTCA-AG-GATATAAGATTTGGTT
1 TTGTAGC-TTCATCTTG-CTCCACTGCAACTTCAGAGAGATA-AAGATTTGCTT
* * *
520177 TTGTAGCTTCATCCTGCTCTACTGCAACTTCAAAGAGAT-AAGAATTTGCTT
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAAG-ATTTGCTT
* * * * * * * *
520228 TCGTAGCTTCAAT-ATGATCCACTACAACTTCA-TG-GATATAGGATTTGATG
1 TTGTAGCTTC-ATCTTGCTCCACTGCAACTTCAGAGAGATA-AAGATTTGCTT
* *** * * * * *
520278 TTGTAGCTTTATCTTGCTCTTTTGTAACTTAAGGGAGATAAATATTTGTTT
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAAGATTTGCTT
* * * * * * *
520329 TTGTAGTTTCAATC-CGATCCACTGTAACTTTAG-G-GGTATAAGATTTGGTT
1 TTGTAGCTTC-ATCTTGCTCCACTGCAACTTCAGAGAGATA-AAGATTTGCTT
* * *
520379 TTGTAACTTCATCTTGCTCTATTGCAACTTCAGAGAGATAAAGATTTGCTT
1 TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAAGATTTGCTT
** * *
520430 TCATAGCTTCAAT-TCGATCCACTGCAACTTCAG
1 TTGTAGCTTC-ATCTTGCTCCACTGCAACTTCAG
520463 GTATATAGGA
Statistics
Matches: 254, Mismatches: 62, Indels: 40
0.71 0.17 0.11
Matches are distributed among these distances:
49 20 0.08
50 92 0.36
51 120 0.47
52 22 0.09
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (51 bp):
TTGTAGCTTCATCTTGCTCCACTGCAACTTCAGAGAGATAAAGATTTGCTT
Found at i:521324 original size:20 final size:20
Alignment explanation
Indices: 521302--521339 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
521292 GATCTCTCCT
*
521302 TTTTCTTTT-TTCTTTTTTA
1 TTTTATTTTCTTCTTTTTTA
521321 TTTTATTTTCTTCTTTTTT
1 TTTTATTTTCTTCTTTTTT
521340 TAAAAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (20 bp):
TTTTATTTTCTTCTTTTTTA
Found at i:521331 original size:17 final size:16
Alignment explanation
Indices: 521300--521341 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
521290 TCGATCTCTC
521300 CTTTTTCTT-TTTTCTT
1 CTTTTT-TTATTTTCTT
*
521316 TTTTATTTTATTTTCTT
1 CTTT-TTTTATTTTCTT
521333 CTTTTTTTA
1 CTTTTTTTA
521342 AAAAACTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (16 bp):
CTTTTTTTATTTTCTT
Found at i:529117 original size:19 final size:19
Alignment explanation
Indices: 529086--529231 Score: 125
Period size: 19 Copynumber: 7.7 Consensus size: 19
529076 AAAACGAAAT
*
529086 TGGCTCGTGAGAGCGATAC
1 TGGCTCGTAAGAGCGATAC
* *
529105 TGACTCGTAAGAGAGATAC
1 TGGCTCGTAAGAGCGATAC
* * *
529124 TGGCTCATAAGAGTGATAT
1 TGGCTCGTAAGAGCGATAC
* *
529143 TGGCTCGTGAGAGCAATAC
1 TGGCTCGTAAGAGCGATAC
*
529162 TGGATCGT-AGA-CTGATAC
1 TGGCTCGTAAGAGC-GATAC
* *
529180 TGGCTCGTAAGAGCAATAT
1 TGGCTCGTAAGAGCGATAC
* * * * *
529199 TGGCTCATAGGAGTGTTAT
1 TGGCTCGTAAGAGCGATAC
529218 TGGCTCGTAAGAGC
1 TGGCTCGTAAGAGC
529232 AATTTAATGA
Statistics
Matches: 99, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
17 1 0.01
18 14 0.14
19 83 0.84
20 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.26
Consensus pattern (19 bp):
TGGCTCGTAAGAGCGATAC
Found at i:529128 original size:38 final size:37
Alignment explanation
Indices: 529086--529234 Score: 140
Period size: 38 Copynumber: 3.9 Consensus size: 37
529076 AAAACGAAAT
*
529086 TGGCTCGTGAGAGCGATACTGACTCGTAAGAG-AGATAC
1 TGGCTCGT-AGAGCGATACTGGCTCGTAAGAGCA-ATAC
* * * *
529124 TGGCTCATAAGAGTGATATTGGCTCGTGAGAGCAATAC
1 TGGCTCGT-AGAGCGATACTGGCTCGTAAGAGCAATAC
* *
529162 TGGATCGTAGA-CTGATACTGGCTCGTAAGAGCAATAT
1 TGGCTCGTAGAGC-GATACTGGCTCGTAAGAGCAATAC
* * * *
529199 TGGCTCATAGGAGTGTTATTGGCTCGTAAGAGCAAT
1 TGGCTCGTA-GAGCGATACTGGCTCGTAAGAGCAAT
529235 TTAATGACTA
Statistics
Matches: 90, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
37 31 0.34
38 58 0.64
39 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (37 bp):
TGGCTCGTAGAGCGATACTGGCTCGTAAGAGCAATAC
Found at i:529204 original size:56 final size:57
Alignment explanation
Indices: 529084--529204 Score: 165
Period size: 56 Copynumber: 2.1 Consensus size: 57
529074 TAAAAACGAA
* * **
529084 ATTGGCTCGTGAGAGCGATACTGACTCGTAAGAGAGATACTGGCTCATAAGAGTGAT
1 ATTGGCTCGTGAGAGCAATACTGACTCGTAAGACAGATACTGGCTCATAAGAGCAAT
* *
529141 ATTGGCTCGTGAGAGCAATACTGGA-TCGT-AGACTGATACTGGCTCGTAAGAGCAAT
1 ATTGGCTCGTGAGAGCAATACT-GACTCGTAAGACAGATACTGGCTCATAAGAGCAAT
529197 ATTGGCTC
1 ATTGGCTC
529205 ATAGGAGTGT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 30 0.53
57 25 0.44
58 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (57 bp):
ATTGGCTCGTGAGAGCAATACTGACTCGTAAGACAGATACTGGCTCATAAGAGCAAT
Found at i:530520 original size:98 final size:97
Alignment explanation
Indices: 530347--530539 Score: 260
Period size: 98 Copynumber: 2.0 Consensus size: 97
530337 ATCTTGAAAA
* * * * *
530347 AGGGTATTAGATTATCCCGGTTTGAAGAAAAGTCGCGCCTAGAAAGTTAAGGCATAAATTTTCAA
1 AGGGTATTAGATTATCCCGATTTGAAAAAAAATCGCACCTAGAAAGTTAAGGCACAAATTTTCAA
*
530412 AACCCGAAATAAAAGAATATTACCTCGATTTG
66 AACCCAAAATAAAAGAATATTACCTCGATTTG
* * * * *
530444 AGGGTATTCGATTATCCTGATTTGAAAAAAAAATTGCACCTAGTAAGTTAAGGCACGAATTTTCA
1 AGGGTATTAGATTATCCCGATTTG-AAAAAAAATCGCACCTAGAAAGTTAAGGCACAAATTTTCA
* *
530509 AAACCCAAAATAAATGAATATTGCCTCGATT
65 AAACCCAAAATAAAAGAATATTACCTCGATT
530540 AAATATTTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
97 21 0.26
98 61 0.74
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (97 bp):
AGGGTATTAGATTATCCCGATTTGAAAAAAAATCGCACCTAGAAAGTTAAGGCACAAATTTTCAA
AACCCAAAATAAAAGAATATTACCTCGATTTG
Found at i:530944 original size:57 final size:56
Alignment explanation
Indices: 530811--530952 Score: 153
Period size: 57 Copynumber: 2.5 Consensus size: 56
530801 TGAAGTTTTT
* * * * *
530811 GAGAGTTTGGGGTTAAAACATA-ATTTTAGAAAGTTTTAGGGGTAAAAATGTCATTTTGG
1 GAGAGTTCGGGG-TAAAATATATTTTTTAG-AAG--TTAGGGGCAAAAATGTAATTTTGG
* *
530870 GAGAGTTCGGGGTAAAATTTGATTTTTTAGAAGTTAGGGGCAAAAATGTAATTTTTG
1 GAGAGTTCGGGGTAAAATAT-ATTTTTTAGAAGTTAGGGGCAAAAATGTAATTTTGG
530927 GA-AGTTCGGGGTAAAAATATATTTTT
1 GAGAGTTCGGGGT-AAAATATATTTTT
530953 GGAAAAGTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
56 16 0.22
57 29 0.40
58 6 0.08
59 15 0.21
60 6 0.08
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.37
Consensus pattern (56 bp):
GAGAGTTCGGGGTAAAATATATTTTTTAGAAGTTAGGGGCAAAAATGTAATTTTGG
Found at i:530961 original size:57 final size:58
Alignment explanation
Indices: 530796--530984 Score: 167
Period size: 58 Copynumber: 3.3 Consensus size: 58
530786 AAAAGGGGTA
* * * * *
530796 AAAAATG-AAGTTTTT-GAGAGTTTGGGGTTAAAACATAATTTTAG-AAAGTTTTAGGGGT
1 AAAAATGTAA-TTTTTGGAGAGTTCGGGG-TAAAATATGATTTTTGAAAAG-TTTAGGGGC
* * * * *
530854 AAAAATGTCATTTTGGGAGAGTTCGGGGTAAAATTTGATTTTTTAGAAG-TTAGGGGC
1 AAAAATGTAATTTTTGGAGAGTTCGGGGTAAAATATGATTTTTGAAAAGTTTAGGGGC
*
530911 AAAAATGTAATTTTTGGA-AGTTCGGGGTAAAAATAT-ATTTTTGGAAAAGTTTGGGGGTC
1 AAAAATGTAATTTTTGGAGAGTTCGGGGT-AAAATATGATTTTT-GAAAAGTTTAGGGG-C
*
530970 -AAAATGTGATTTTTG
1 AAAAATGTAATTTTTG
530985 AAAAGTTTAA
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
56 16 0.15
57 33 0.31
58 42 0.39
59 16 0.15
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (58 bp):
AAAAATGTAATTTTTGGAGAGTTCGGGGTAAAATATGATTTTTGAAAAGTTTAGGGGC
Found at i:530974 original size:30 final size:30
Alignment explanation
Indices: 530790--530992 Score: 95
Period size: 28 Copynumber: 7.0 Consensus size: 30
530780 GAAAAAAAAA
*
530790 GGGGTAAAAA-ATGAAGTTTTTG-AGAGTTTG
1 GGGGTAAAAATATG-A-TTTTTGAAAAGTTTG
* * *
530820 GGGTTAAAACATA--ATTTTAG-AAAGTTTTA
1 GGGGTAAAA-ATATGATTTTTGAAAAG-TTTG
* * * * * *
530849 GGGGTAAAAATGTCATTTTGGGAGAG-TTC
1 GGGGTAAAAATATGATTTTTGAAAAGTTTG
* * * *
530878 GGGGT-AAAATTTGATTTTTTAGAAG-TTA
1 GGGGTAAAAATATGATTTTTGAAAAGTTTG
* * * * *
530906 GGGGCAAAAATGTAATTTTTG-GAAG-TTC
1 GGGGTAAAAATATGATTTTTGAAAAGTTTG
530934 GGGGTAAAAATAT-ATTTTTGGAAAAGTTTG
1 GGGGTAAAAATATGATTTTT-GAAAAGTTTG
* *
530964 GGGGTCAAAATGTGATTTTTGAAAAGTTT
1 GGGGTAAAAATATGATTTTTGAAAAGTTT
530993 AAGGACCTTT
Statistics
Matches: 134, Mismatches: 28, Indels: 22
0.73 0.15 0.12
Matches are distributed among these distances:
27 6 0.04
28 47 0.35
29 34 0.25
30 36 0.27
31 10 0.07
32 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (30 bp):
GGGGTAAAAATATGATTTTTGAAAAGTTTG
Found at i:532628 original size:17 final size:17
Alignment explanation
Indices: 532606--532682 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
532596 GGACATTATT
*
532606 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
* *
532623 ATTTTAATTTTAAAAATA
1 AATTTAAATTT-AAAATA
*
532641 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
**
532658 AATTTAACCTTAAAATA
1 AATTTAAATTTAAAATA
532675 AATTTAAA
1 AATTTAAA
532683 AAGAATGGGT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
17 38 0.75
18 13 0.25
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:532647 original size:35 final size:34
Alignment explanation
Indices: 532606--532682 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 34
532596 GGACATTATT
* * * **
532606 AATTTAAATTTAGAATAATTTTAATTTTAAAAATA
1 AATTTAAACTTAAAATAAATTTAACCTT-AAAATA
532641 AATTTAAACTTAAAATAAATTTAACCTTAAAATA
1 AATTTAAACTTAAAATAAATTTAACCTTAAAATA
532675 AATTTAAA
1 AATTTAAA
532683 AAGAATGGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 14 0.38
35 23 0.62
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (34 bp):
AATTTAAACTTAAAATAAATTTAACCTTAAAATA
Found at i:533169 original size:39 final size:38
Alignment explanation
Indices: 533046--533644 Score: 324
Period size: 39 Copynumber: 15.4 Consensus size: 38
533036 TGGCCCATGA
* *
533046 TCGGGGTAAGAGATTGACTGATGATGATCTACCCAAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCC-AGGC
* * * ** ** * *
533085 TCAGGGTAAAAGATCGAATGACT-ACAATCTACCCCAAGC
1 TCGGGGTAAGAGATTGGCTGA-TGATGATCT-GCCCAGGC
* * *
533124 TTGGGGTAAGAGTTTTGCTGATGATGATCTGCCTCAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCC-CAGGC
* * * ** * *
533163 TCGGGGTAAGAGATCGGATAGCT-ACAATATGTCCCAGGT
1 TCGGGGTAAGAGATTGGCT-GATGATGATCTG-CCCAGGC
* *
533202 TCGAGGTAAGAGATTGGCTGAT-AGTGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGCTGATGA-TGATCTG-CCCAGGC
** * ** *
533241 TCGGGGTAAGAGATTGAATGGCT-ACAATCTACCCTAGGC
1 TCGGGGTAAGAGATTGGCT-GATGATGATCTGCCC-AGGC
* ** * *
533280 TCGGGGTAAGAGATCGAATGACT-ATAATTTGACCCAGGC
1 TCGGGGTAAGAGATTGGCTGA-TGATGATCTG-CCCAGGC
*
533319 TCGGGGTAAGAGATTGGCTGATGATGATCTGTCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTG-CCCAGGC
* * * * *
533358 TCGAGGTAAGAGATCGGAT-A-GCTGCAATCTGTCCCAGAC
1 TCGGGGTAAGAGATTGGCTGATGATG--ATCTG-CCCAGGC
* * * * *
533397 TCGGGGTAAGAAATTAGCTGATGGTGATTTGCCTTAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCC-CAGGC
* *
533436 TCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCTAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTGCCC-AGGC
* * ** * *
533475 TCGGGGTAAAAGATCGAATG--GCTGCAATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGCTGATGATG--ATCTG-CCCAGGC
** * *
533514 TCAAGGTAATAGATTGGCTGATGGTGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTG-CCCAGGC
* *
533553 TCGGGGTAAGAGATCAAATGGCT-A-GA--ATTTACCTCAGGC
1 TCGGGGTAAGAGAT----TGGCTGATGATGATCTGCC-CAGGC
533592 TCGGGGTAAGAGATTGGCTGATGATGATCTGTCCCAGGC
1 TCGGGGTAAGAGATTGGCTGATGATGATCTG-CCCAGGC
533631 TCGGGGTAAGAGAT
1 TCGGGGTAAGAGAT
533645 CGGATGGCTG
Statistics
Matches: 426, Mismatches: 101, Indels: 66
0.72 0.17 0.11
Matches are distributed among these distances:
35 5 0.01
36 1 0.00
37 8 0.02
38 16 0.04
39 363 0.85
40 20 0.05
41 7 0.02
42 1 0.00
43 5 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (38 bp):
TCGGGGTAAGAGATTGGCTGATGATGATCTGCCCAGGC
Found at i:533386 original size:117 final size:116
Alignment explanation
Indices: 533150--533515 Score: 375
Period size: 117 Copynumber: 3.1 Consensus size: 116
533140 GCTGATGATG
* * * * *
533150 ATCTG-CCTCAGGCTCGGGGTAAGAGATCGGAT-AGCTACAATATGTCCCAGGTTCGAGGTAAGA
1 ATCTGACC-CAGGCTCGGGGTAAGAGATCGAATGA-CTATAATTTG-CCCAGGCTCGGGGTAAGA
* * * *
533213 GATTGGCTGAT-AGTGATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCTACA
63 GATTGGCTGATGA-TGATCTGCCCTAGGCTCGGGGTAAGAGATCGAATGGCTGCA
533267 ATCT-ACCCTAGGCTCGGGGTAAGAGATCGAATGACTATAATTTGACCCAGGCTCGGGGTAAGAG
1 ATCTGACCC-AGGCTCGGGGTAAGAGATCGAATGACTATAATTTG-CCCAGGCTCGGGGTAAGAG
* * * *
533331 ATTGGCTGATGATGATCTGTCCTAGGCTCGAGGTAAGAGATCGGATAGCTGCA
64 ATTGGCTGATGATGATCTGCCCTAGGCTCGGGGTAAGAGATCGAATGGCTGCA
* * * * * * * *
533384 ATCTGTCCCAGACTCGGGGTAAGAAAT-TAGCTGA-TGGTGATTTGCCTTAGGCTCGGGGTAAGA
1 ATCTGACCCAGGCTCGGGGTAAGAGATCGA-ATGACT-ATAATTTGCC-CAGGCTCGGGGTAAGA
* * *
533447 GATTGGCTGATGGTGATTTGCCCTAGGCTCGGGGTAAAAGATCGAATGGCTGCA
63 GATTGGCTGATGATGATCTGCCCTAGGCTCGGGGTAAGAGATCGAATGGCTGCA
* *
533501 ATCTGCCCCAAGCTC
1 ATCTGACCCAGGCTC
533516 AAGGTAATAG
Statistics
Matches: 209, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
116 5 0.02
117 199 0.95
118 5 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (116 bp):
ATCTGACCCAGGCTCGGGGTAAGAGATCGAATGACTATAATTTGCCCAGGCTCGGGGTAAGAGAT
TGGCTGATGATGATCTGCCCTAGGCTCGGGGTAAGAGATCGAATGGCTGCA
Found at i:533522 original size:117 final size:116
Alignment explanation
Indices: 533195--533566 Score: 408
Period size: 117 Copynumber: 3.2 Consensus size: 116
533185 TACAATATGT
* * * * * *
533195 CCCAGGTTCGAGGTAAGAGATTGGCTGATAGTGATCTGCCCCAAGCTCGGGGTAAGAGATTGAAT
1 CCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGAAT
* * * * * * * *
533260 GGCTACAATCTACCCTAGGCTCGGGGTAAGAGA-TCGAATGACT-ATAATTTG
66 GGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTAG-CTGA-TGGTGATTTG
* * * *
533311 ACCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGTCCTAGGCTCGAGGTAAGAGATCGGA
1 -CCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGAA
* * *
533376 TAGCTGCAATCTGTCCC-AGACTCGGGGTAAGAAATTAGCTGATGGTGATTTG
65 TGGCTGCAATCTGCCCCAAG-CTCGGGGTAAGAGATTAGCTGATGGTGATTTG
* * *
533428 CCTTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCTAGGCTCGGGGTAAAAGATCGAA
1 CC-CAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGAA
** * * *
533493 TGGCTGCAATCTGCCCCAAGCTCAAGGTAATAGATTGGCTGATGGTGATCTG
65 TGGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTAGCTGATGGTGATTTG
533545 CCCCAGGCTCGGGGTAAGAGAT
1 -CCCAGGCTCGGGGTAAGAGAT
533567 CAAATGGCTA
Statistics
Matches: 212, Mismatches: 37, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
116 4 0.02
117 202 0.95
118 6 0.03
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (116 bp):
CCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAGAGATCGAAT
GGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTAGCTGATGGTGATTTG
Found at i:533666 original size:39 final size:38
Alignment explanation
Indices: 533150--533721 Score: 264
Period size: 39 Copynumber: 14.7 Consensus size: 38
533140 GCTGATGATG
* *
533150 ATCTG-CCTCAGGCTCGGGGTAAGAGATCGGATAGCTACA
1 ATCTGTCC-CAGGCTCGGGGTAAGAGATCGGATGGCT-GA
* * * * *
533189 ATATGTCCCAGGTTCGAGGTAAGAGATTGGCTGATAG-TG-
1 ATCTGTCCCAGGCTCGGGGTAAGAGA-T--CGGATGGCTGA
* * * * *
533228 ATCTGCCCCAAGCTCGGGGTAAGAGATTGAATGGCTACA
1 ATCTGTCCCAGGCTCGGGGTAAGAGATCGGATGGCT-GA
* * * *
533267 ATCT-ACCCTAGGCTCGGGGTAAGAGATCGAATGACTATA
1 ATCTGTCCC-AGGCTCGGGGTAAGAGATCGGATGGCT-GA
* * * * *
533306 ATTTGACCCAGGCTCGGGGTAAGAGATTGGCT-GATGA
1 ATCTGTCCCAGGCTCGGGGTAAGAGATCGGATGGCTGA
* * *
533343 TGATCTGTCCTAGGCTCGAGGTAAGAGATCGGATAGCTGCA
1 --ATCTGTCCCAGGCTCGGGGTAAGAGATCGGATGGCTG-A
* * *
533384 ATCTGTCCCAGACTCGGGGTAAGAAATTAGCTGATGG-TG-
1 ATCTGTCCCAGGCTCGGGGTAAGAGA-T--CGGATGGCTGA
* * *
533423 ATTTG-CCTTAGGCTCGGGGTAAGAGATTGGCTGATGG-TG-
1 ATCTGTCC-CAGGCTCGGGGTAAGAGA-T--CGGATGGCTGA
* * *
533462 ATTTG-CCCTAGGCTCGGGGTAAAAGATCGAATGGCTGCA
1 ATCTGTCCC-AGGCTCGGGGTAAGAGATCGGATGGCTG-A
* * ** * *
533501 ATCTGCCCCAAGCTCAAGGTAATAGATTGGCTGATGG-TG-
1 ATCTGTCCCAGGCTCGGGGTAAGAGA-T--CGGATGGCTGA
* **
533540 ATCTGCCCCAGGCTCGGGGTAAGAGATCAAATGGCTAGA
1 ATCTGTCCCAGGCTCGGGGTAAGAGATCGGATGGCT-GA
* * *
533579 AT-T-TACCTCAGGCTCGGGGTAAGAGATTGGCT-GATGA
1 ATCTGT-CC-CAGGCTCGGGGTAAGAGATCGGATGGCTGA
533616 TGATCTGTCCCAGGCTCGGGGTAAGAGATCGGATGGCTGCA
1 --ATCTGTCCCAGGCTCGGGGTAAGAGATCGGATGGCTG-A
* * * * *
533657 ATTTATCCCAAGCTCGGGGTAAGAGAT-TGACTGG-TTA
1 ATCTGTCCCAGGCTCGGGGTAAGAGATCGGA-TGGCTGA
* *
533694 ATCT-TCCCCAAGCTCGGGGTAAAAGATC
1 ATCTGT-CCCAGGCTCGGGGTAAGAGATC
533722 AAATCTTTAA
Statistics
Matches: 416, Mismatches: 78, Indels: 79
0.73 0.14 0.14
Matches are distributed among these distances:
36 14 0.03
37 31 0.07
38 18 0.04
39 308 0.74
40 21 0.05
41 8 0.02
42 16 0.04
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.24
Consensus pattern (38 bp):
ATCTGTCCCAGGCTCGGGGTAAGAGATCGGATGGCTGA
Found at i:533682 original size:78 final size:77
Alignment explanation
Indices: 533028--533685 Score: 482
Period size: 78 Copynumber: 8.4 Consensus size: 77
533018 CTTCGAATTA
** * * * * *
533028 CTGCAATCTGGCCCATGATCGGGGTAAGAGATTGACTGATGATGATCTACCCAAGGCTCAGGGTA
1 CTGCAATCTATCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCC-AGGCTCGGGGTA
* *
533093 AAAGATCGAATGA
65 AGAGATCGAATGG
* * * * * *
533106 CTACAATCTACCCCAAGCTTGGGGTAAGAGTTTTGCTGATGATGATCTGCCTCAGGCTCGGGGTA
1 CTGCAATCTATCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCC-CAGGCTCGGGGTA
* *
533171 AGAGATCGGATAG
65 AGAGATCGAATGG
* * * * * *
533184 CTACAATATGTCCCAGGTTCGAGGTAAGAGATTGGCTGAT-AGTGATCTGCCCCAAGCTCGGGGT
1 CTGCAATCTATCCCAGGCTCGGGGTAAGAGATTGGCTGATGA-TGATCTG-CCCAGGCTCGGGGT
*
533248 AAGAGATTGAATGG
64 AAGAGATCGAATGG
* * ** * *
533262 CTACAATCTA-CCCTAGGCTCGGGGTAAGAGATCGAATGACT-ATAATTTGACCCAGGCTCGGGG
1 CTGCAATCTATCCC-AGGCTCGGGGTAAGAGATTGGCTGA-TGATGATCTG-CCCAGGCTCGGGG
* **
533325 TAAGAGATTGGCT-G
63 TAAGAGATCGAATGG
* * * * * * * *
533339 ATG-ATGATCTGTCCTAGGCTCGAGGTAAGAGATCGGAT-A-GCTGCAATCTGTCCCAGACTCGG
1 CTGCA--ATCTATCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG--ATCTG-CCCAGGCTCGG
*
533401 GGTAAGAAATTAGCTG-ATGG
61 GGTAAGAGA-T--C-GAATGG
* * *
533421 -TG--AT-T-TGCCTTAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCTAGGCTCGGGG
1 CTGCAATCTAT-CC-CAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCC-AGGCTCGGGG
*
533481 TAAAAGATCGAATGG
63 TAAGAGATCGAATGG
** * ** * *
533496 CTGCAATCTGCCCCAAGCTCAAGGTAATAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTA
1 CTGCAATCTATCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTG-CCCAGGCTCGGGGTA
*
533561 AGAGATCAAATGG
65 AGAGATCGAATGG
*
533574 CTAG-AATTTA-CCTCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGTCCCAGGCTCGGGG
1 CT-GCAATCTATCC-CAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTG-CCCAGGCTCGGGG
*
533637 TAAGAGATCGGATGG
63 TAAGAGATCGAATGG
* *
533652 CTGCAATTTATCCCAAGCTCGGGGTAAGAGATTG
1 CTGCAATCTATCCCAGGCTCGGGGTAAGAGATTG
533686 ACTGGTTAAT
Statistics
Matches: 465, Mismatches: 83, Indels: 64
0.76 0.14 0.10
Matches are distributed among these distances:
74 1 0.00
75 5 0.01
76 5 0.01
77 17 0.04
78 411 0.88
79 18 0.04
80 3 0.01
81 3 0.01
82 2 0.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (77 bp):
CTGCAATCTATCCCAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCAGGCTCGGGGTAA
GAGATCGAATGG
Found at i:533732 original size:37 final size:37
Alignment explanation
Indices: 533663--533734 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
533653 TGCAATTTAT
* ** * *
533663 CCCAAGCTCGGGGTAAGAGATTGACTGGTTAATCTTC
1 CCCAAGCTCGGGGTAAAAGATCAAATCGTTAATCTTC
*
533700 CCCAAGCTCGGGGTAAAAGATCAAATCTTTAATCT
1 CCCAAGCTCGGGGTAAAAGATCAAATCGTTAATCT
533735 GCCCTTCTTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (37 bp):
CCCAAGCTCGGGGTAAAAGATCAAATCGTTAATCTTC
Found at i:545619 original size:59 final size:60
Alignment explanation
Indices: 545542--545802 Score: 196
Period size: 58 Copynumber: 4.5 Consensus size: 60
545532 AATAGGGTCG
* * * * * *
545542 AAAATG-AAGTTTCGGAGAGTTTAAGGTTAAAATATAATTTT-GAAAAGTTTTAGGGGTA
1 AAAATGTAATTTTGGGAAAGTTTAGGGTAAAAATGTAATTTTAGAAAAGTTTTAGGGGTA
* * * * * * *
545600 AAAATGTCATTTTGGGAGAGTTTGGGGTAAAAATGTGATTTTTGAGAAG-TTCA-GGGTA
1 AAAATGTAATTTTGGGAAAGTTTAGGGTAAAAATGTAATTTTAGAAAAGTTTTAGGGGTA
** * * *
545658 AAAATGTAATTTT-TCAAAGTTCGAGGGTAAAAATGTAATTTTGGAAAA-TTTTAGGGGTT
1 AAAATGTAATTTTGGGAAAGTT-TAGGGTAAAAATGTAATTTTAGAAAAGTTTTAGGGGTA
** * * * * *
545717 AAAATAAAATTTTAGGAAAATTTTAGGGTTAAAATGTAATTTTAGAAAAG-TTTA-AGGTT
1 AAAATGTAATTTT-GGGAAAGTTTAGGGTAAAAATGTAATTTTAGAAAAGTTTTAGGGGTA
* * *
545776 AATATGTGATTTTTGGAAAGTTTAGGG
1 AAAATGTAATTTTGGGAAAGTTTAGGG
545803 ACCTTTTGGG
Statistics
Matches: 158, Mismatches: 37, Indels: 16
0.75 0.18 0.08
Matches are distributed among these distances:
57 5 0.03
58 58 0.37
59 58 0.37
60 32 0.20
61 5 0.03
ACGTcount: A:0.38, C:0.02, G:0.24, T:0.36
Consensus pattern (60 bp):
AAAATGTAATTTTGGGAAAGTTTAGGGTAAAAATGTAATTTTAGAAAAGTTTTAGGGGTA
Found at i:545735 original size:31 final size:30
Alignment explanation
Indices: 545694--545777 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
545684 GTAAAAATGT
545694 AATTTT-GGAAAATTTTAGGGGTTAAAATAA
1 AATTTTAGGAAAATTTTA-GGGTTAAAATAA
**
545724 AATTTTAGGAAAATTTTAGGGTTAAAATGT
1 AATTTTAGGAAAATTTTAGGGTTAAAATAA
* *
545754 AATTTTA-GAAAAGTTTAAGGTTAA
1 AATTTTAGGAAAATTTTAGGGTTAA
545778 TATGTGATTT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 15 0.31
30 23 0.47
31 11 0.22
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (30 bp):
AATTTTAGGAAAATTTTAGGGTTAAAATAA
Found at i:545775 original size:29 final size:28
Alignment explanation
Indices: 545559--545802 Score: 173
Period size: 29 Copynumber: 8.3 Consensus size: 28
545549 AGTTTCGGAG
* * *
545559 AGTTTAAGGTTAAAATATAATTTTGAAA
1 AGTTTAGGGTAAAAATGTAATTTTGAAA
* * *
545587 AGTTTTAGGGGTAAAAATGTCATTTTGGGAG
1 AG-TTTA-GGGTAAAAATGTAATTTT-GAAA
* * *
545618 AGTTTGGGGTAAAAATGTGATTTTTGAGA
1 AGTTTAGGGTAAAAATGT-AATTTTGAAA
* **
545647 AGTTCAGGGTAAAAATGTAATTTTTCAA
1 AGTTTAGGGTAAAAATGTAATTTTGAAA
*
545675 AGTTCGAGGGTAAAAATGTAATTTTGGAAA
1 AGTT-TAGGGTAAAAATGTAATTTT-GAAA
* * **
545705 ATTTTAGGGGTTAAAATAAAATTTTAGGAAA
1 AGTTTA-GGGTAAAAATGTAATTTT--GAAA
* *
545736 ATTTTAGGGTTAAAATGTAATTTTAGAAA
1 AGTTTAGGGTAAAAATGTAATTTT-GAAA
* * * * *
545765 AGTTTAAGGTTAATATGTGATTTTTGGAA
1 AGTTTAGGGTAAAAATGT-AATTTTGAAA
545794 AGTTTAGGG
1 AGTTTAGGG
545803 ACCTTTTGGG
Statistics
Matches: 172, Mismatches: 35, Indels: 17
0.77 0.16 0.08
Matches are distributed among these distances:
28 12 0.07
29 83 0.48
30 62 0.36
31 15 0.09
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (28 bp):
AGTTTAGGGTAAAAATGTAATTTTGAAA
Found at i:547336 original size:6 final size:6
Alignment explanation
Indices: 547325--547453 Score: 76
Period size: 6 Copynumber: 22.3 Consensus size: 6
547315 GGACATTATT
* ** *
547325 AATTTA AATTT- -ATTATA ATTTTA AATTTA AAAATA AATTTA AACTTA
1 AATTTA AATTTA AATT-TA AATTTA AATTTA AATTTA AATTTA AATTTA
* * *
547372 AA-TTA AATTTA AATTTTTA AA--CA AATTTA AACTTA AA-ATA AATTTA
1 AATTTA AATTTA AA--TTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* ** *
547418 AATTTA AA-ATA AATTTA ACGTTA AA-ATA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
547454 AAGAATGGTT
Statistics
Matches: 93, Mismatches: 19, Indels: 22
0.69 0.14 0.16
Matches are distributed among these distances:
4 6 0.06
5 18 0.19
6 61 0.66
7 2 0.02
8 6 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:547366 original size:35 final size:33
Alignment explanation
Indices: 547325--547435 Score: 107
Period size: 35 Copynumber: 3.2 Consensus size: 33
547315 GGACATTATT
547325 AATTTAAATTTATTATAATTTTAAATTTAAAAATA
1 AATTTAAATTTATTATAA-TTTAAATTT-AAAATA
* * *
547360 AATTTAAACTTAAATTA-AATTTAAATTTTTAAACA
1 AATTTAAA-TT-TATTATAATTTAAA-TTTAAAATA
* **
547395 AATTTAAACTTAAAATAAATTTAAATTTAAAATA
1 AATTTAAATTTATTAT-AATTTAAATTTAAAATA
547429 AATTTAA
1 AATTTAA
547436 CGTTAAAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
33 2 0.03
34 15 0.24
35 34 0.55
36 7 0.11
37 4 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (33 bp):
AATTTAAATTTATTATAATTTAAATTTAAAATA
Found at i:547380 original size:17 final size:17
Alignment explanation
Indices: 547325--547453 Score: 134
Period size: 17 Copynumber: 7.5 Consensus size: 17
547315 GGACATTATT
* **
547325 AATTTAAATTTATTATA
1 AATTTAAACTTAAAATA
* *
547342 ATTTTAAATTTAAAAATA
1 AATTTAAACTT-AAAATA
*
547360 AATTTAAACTTAAATTA
1 AATTTAAACTTAAAATA
* * *
547377 AATTTAAATTTTTAAACA
1 AATTTAAA-CTTAAAATA
547395 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
*
547412 AATTTAAATTTAAAATA
1 AATTTAAACTTAAAATA
547429 AATTT-AACGTTAAAATA
1 AATTTAAAC-TTAAAATA
547446 AATTTAAA
1 AATTTAAA
547454 AAGAATGGTT
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
16 2 0.02
17 63 0.68
18 28 0.30
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:550583 original size:21 final size:21
Alignment explanation
Indices: 550552--550602 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
550542 TATAACATAC
*
550552 AATATAATAATAACA-AAAATA
1 AATAAAATAATAACACAAAA-A
* *
550573 AATTAAATAATCACACAAAAA
1 AATAAAATAATAACACAAAAA
550594 AATAAAATA
1 AATAAAATA
550603 CATTATAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AATAAAATAATAACACAAAAA
Found at i:550667 original size:15 final size:15
Alignment explanation
Indices: 550647--550678 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
550637 GATAGTAAAA
550647 AATGATAATAATGAC
1 AATGATAATAATGAC
*
550662 AATGATACTAATGAC
1 AATGATAATAATGAC
550677 AA
1 AA
550679 AAAATACGAT
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:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (15 bp):
AATGATAATAATGAC
Found at i:550852 original size:14 final size:12
Alignment explanation
Indices: 550807--550877 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 12
550797 AATATACTAG
*
550807 AAAATAAA-ATA
1 AAAATAAATACA
550818 AAAATAAGCATA-A
1 AAAATAA--ATACA
550831 AAAGATAAATAAGCA
1 AAA-ATAAAT-A-CA
550846 AAAATAAATACA
1 AAAATAAATACA
550858 AAAAT-AATACA
1 AAAATAAATACA
550869 AAAA-AAATA
1 AAAATAAATA
550878 ATACAAAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 16
0.76 0.00 0.24
Matches are distributed among these distances:
11 21 0.40
12 9 0.17
13 7 0.13
14 11 0.21
15 4 0.08
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAATAAATACA
Found at i:550890 original size:15 final size:14
Alignment explanation
Indices: 550857--550902 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
550847 AAATAAATAC
550857 AAAAATAATACAAA
1 AAAAATAATACAAA
550871 AAAAATAATACAAA
1 AAAAATAATACAAA
550885 ATAAAATATATA-AAA
1 A-AAAATA-ATACAAA
550900 AAA
1 AAA
550903 CGAGGGACTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 17 0.57
15 10 0.33
16 3 0.10
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAATAATACAAA
Found at i:550892 original size:26 final size:27
Alignment explanation
Indices: 550845--550902 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
550835 ATAAATAAGC
*
550845 AAAAATAAATACAAAAATAATACA-AA
1 AAAAATAAATACAAAAAAAATACATAA
*
550871 AAAAAT-AATACAAAATAAAATATATAA
1 AAAAATAAATACAAAA-AAAATACATAA
550898 AAAAA
1 AAAAA
550903 CGAGGGACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.32
26 12 0.43
27 7 0.25
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (27 bp):
AAAAATAAATACAAAAAAAATACATAA
Found at i:551206 original size:19 final size:17
Alignment explanation
Indices: 551172--551210 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
551162 CAAAAGGTAG
*
551172 AAATTAAAAATGAATTA
1 AAATTAAAAAAGAATTA
551189 AAATTAAAAAAAGAAATTA
1 AAATT-AAAAAAG-AATTA
551208 AAA
1 AAA
551211 AAATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 6 0.32
19 8 0.42
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (17 bp):
AAATTAAAAAAGAATTA
Found at i:551212 original size:12 final size:13
Alignment explanation
Indices: 551189--551213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
551179 AAATGAATTA
551189 AAATTAAAAAAAG
1 AAATTAAAAAAAG
551202 AAATTAAAAAAA
1 AAATTAAAAAAA
551214 TAAAAATGTG
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAATTAAAAAAAG
Found at i:552187 original size:24 final size:22
Alignment explanation
Indices: 552152--552210 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 22
552142 GGGCTTATAA
* *
552152 TTGGGTATGGGTATTTAACTTAG
1 TTGGGTTTGGGTATTTAA-GTAG
552175 TTGGGCTTTGGGTTATTTAAGTAG
1 TTGGG-TTTGGG-TATTTAAGTAG
552199 TTGGGTTTGGGT
1 TTGGGTTTGGGT
552211 TATGTAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 1 0.03
23 11 0.34
24 13 0.41
25 7 0.22
ACGTcount: A:0.15, C:0.03, G:0.36, T:0.46
Consensus pattern (22 bp):
TTGGGTTTGGGTATTTAAGTAG
Found at i:552211 original size:23 final size:24
Alignment explanation
Indices: 552152--552213 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
552142 GGGCTTATAA
* *
552152 TTGGGTATGGG-TATTTAACTTAG
1 TTGGGTTTGGGTTATTTAACGTAG
552175 TTGGGCTTTGGGTTATTTAA-GTAG
1 TTGGG-TTTGGGTTATTTAACGTAG
552199 TTGGGTTTGGGTTAT
1 TTGGGTTTGGGTTAT
552214 GTAAATGGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 15 0.43
24 13 0.37
25 7 0.20
ACGTcount: A:0.16, C:0.03, G:0.34, T:0.47
Consensus pattern (24 bp):
TTGGGTTTGGGTTATTTAACGTAG
Found at i:554879 original size:20 final size:20
Alignment explanation
Indices: 554854--554901 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
554844 GGAAAGTGAT
554854 ATTCTTTTGGAAAGAATATA
1 ATTCTTTTGGAAAGAATATA
554874 ATTCTTTTGGAAAGAATATA
1 ATTCTTTTGGAAAGAATATA
554894 ATTCTTTT
1 ATTCTTTT
554902 TCATTACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.46
Consensus pattern (20 bp):
ATTCTTTTGGAAAGAATATA
Found at i:560220 original size:24 final size:24
Alignment explanation
Indices: 560152--560220 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
560142 CCAAAATTTT
* * *
560152 GCTCATACAAGCCCAGACAAAATTA
1 GCTCTTACGAGCCCAGA-AAGATTA
* * *
560177 GCTCTTATGAGCCTAAAAAGATTA
1 GCTCTTACGAGCCCAGAAAGATTA
560201 GCTCTTACGAGCCCAGAAAG
1 GCTCTTACGAGCCCAGAAAG
560221 GTTAACCAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 23 0.66
25 12 0.34
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (24 bp):
GCTCTTACGAGCCCAGAAAGATTA
Found at i:565951 original size:24 final size:23
Alignment explanation
Indices: 565907--565951 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
565897 CTTATTCATT
*
565907 CAATTCATTTTTATTTAAACACG
1 CAATTCATTTTGATTTAAACACG
*
565930 CAATTCATTTATGATTTCAACA
1 CAATTCATTT-TGATTTAAACA
565952 AGCTAGCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (23 bp):
CAATTCATTTTGATTTAAACACG
Found at i:567819 original size:20 final size:19
Alignment explanation
Indices: 567794--567831 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
567784 TAACCCAATG
*
567794 TATAATTATGATACTATAAT
1 TATAATAATGATAC-ATAAT
567814 TATAATAATGATACATAA
1 TATAATAATGATACATAA
567832 CCTTAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
TATAATAATGATACATAAT
Found at i:569621 original size:27 final size:23
Alignment explanation
Indices: 569582--569645 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
569572 TCCCTCTTAT
* *
569582 ATTTTATTAATTTATTTTGCATT
1 ATTTTATTTATTTATTTTGCATG
569605 ATTTTATTTATTTATTTTGCATG
1 ATTTTATTTATTTATTTTGCATG
*
569628 ATTTTAATTATTTATTTT
1 ATTTTATTTATTTATTTT
569646 ATTTATTATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (23 bp):
ATTTTATTTATTTATTTTGCATG
Found at i:569878 original size:14 final size:14
Alignment explanation
Indices: 569857--569898 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
569847 TAATTAATTG
569857 TATTTATTTA-TTT
1 TATTTATTTATTTT
*
569870 TATTTTATTCATTTT
1 TA-TTTATTTATTTT
569885 TATTTATTTATTTT
1 TATTTATTTATTTT
569899 GTCATTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 18 0.72
15 5 0.20
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTATTTATTTT
Found at i:576445 original size:52 final size:52
Alignment explanation
Indices: 576367--576589 Score: 277
Period size: 52 Copynumber: 4.3 Consensus size: 52
576357 AATGATTTTA
* * * *
576367 TGTCATCGTGAGTATATGAACCCTTTACGAATTATAAGGTCTGATGGCTCTG
1 TGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCTGATGACTATG
* * * *
576419 TGTCATCATGAGCATATGAATCCTTTACGGATTATGAGGTCTGATGACTAAG
1 TGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCTGATGACTATG
* * *
576471 TGTCATCGTGAGTATATAAATCCTTTACGGATTATAAGTTCCGATGACTATG
1 TGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCTGATGACTATG
* * * * **
576523 TGTCATCGTGAGTGTATGATTCCTTTAAGTAACA-AGAGGTCTGATGACTATG
1 TGTCATCGTGAGTATATGAATCCTTTACGGATTATA-AGGTCTGATGACTATG
576575 TGTCATCGTGAGTAT
1 TGTCATCGTGAGTAT
576590 TAAAGGAAAA
Statistics
Matches: 145, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
51 1 0.01
52 144 0.99
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (52 bp):
TGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCTGATGACTATG
Found at i:584914 original size:52 final size:52
Alignment explanation
Indices: 584828--585025 Score: 211
Period size: 52 Copynumber: 3.8 Consensus size: 52
584818 ATGAAAAAGG
*
584828 TTCGATGACTCTGTGTTATCGTGAGTATATGAATCCTTTATAG-ATTATAAAGT
1 TTCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTA-AGAATTAT-AAGT
* * *
584881 TT-GATGGCTCTGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGT
1 TTCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTAAGAATTATAAGT
** * * * * *
584932 TTCGATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGG
1 TTCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTAAGAATTATAAGT
* * * * * *
584984 TCCAATGACTATGTGTCATTGTGAGTGTATGATTCCTTTAAG
1 TTCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTAAG
585026 GAACAAGAGG
Statistics
Matches: 125, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
51 6 0.05
52 117 0.94
53 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (52 bp):
TTCGATGACTCTGTGTCATCGTGAGTATATGAATCCTTTAAGAATTATAAGT
Found at i:585008 original size:104 final size:104
Alignment explanation
Indices: 584825--585063 Score: 264
Period size: 104 Copynumber: 2.3 Consensus size: 104
584815 TAAATGAAAA
* * * * *** *
584825 AGGTTCGATGACTCTGTGTTATCGTGAGTATATGAATCCTTTATAGATTATAAAGTTTGATGGCT
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATAAATCCTTTACAGATTATAAAGTCCAATGACT
* * *
584890 CTGTGTCATCGTGAGTATATGAATCCTTT-ACGAATTATG
66 ATGTGTCATCGTGAGTATATGAATCCTTTAACGAA-CAAG
* * * * *
584929 AGTTTCGATGACTAAGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCAATGACT
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATAAATCCTTTACAGATTATAAAGTCCAATGACT
* * * *
584994 ATGTGTCATTGTGAGTGTATGATTCCTTTAAGGAACAAG
66 ATGTGTCATCGTGAGTATATGAATCCTTTAACGAACAAG
* *
585033 AGGTCCGGTGACTATGTGTCATCGTGAGTAT
1 AGGTTCGATGACTATGTGTCATCGTGAGTAT
585064 TACAGGAAAA
Statistics
Matches: 110, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
104 106 0.96
105 4 0.04
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (104 bp):
AGGTTCGATGACTATGTGTCATCGTGAGTATATAAATCCTTTACAGATTATAAAGTCCAATGACT
ATGTGTCATCGTGAGTATATGAATCCTTTAACGAACAAG
Found at i:585036 original size:52 final size:52
Alignment explanation
Indices: 584891--585063 Score: 168
Period size: 52 Copynumber: 3.3 Consensus size: 52
584881 TTGATGGCTC
* * * * * * *
584891 TGTGTCATCGTGAGTATATGAATCCTTT-ACGAATTATGAGTTTCGATGACTA
1 TGTGTCATCGTGAGTATATAAATCCTTTAAGGAA-CAAGAGGTCCAATGACTA
* * ** *
584943 AGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCCAATGACTA
1 TGTGTCATCGTGAGTATATAAATCCTTTAAGGAACAAGAGGTCCAATGACTA
* * * * **
584995 TGTGTCATTGTGAGTGTATGATTCCTTTAAGGAACAAGAGGTCCGGTGACTA
1 TGTGTCATCGTGAGTATATAAATCCTTTAAGGAACAAGAGGTCCAATGACTA
585047 TGTGTCATCGTGAGTAT
1 TGTGTCATCGTGAGTAT
585064 TACAGGAAAA
Statistics
Matches: 99, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
52 97 0.98
53 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (52 bp):
TGTGTCATCGTGAGTATATAAATCCTTTAAGGAACAAGAGGTCCAATGACTA
Found at i:585688 original size:21 final size:21
Alignment explanation
Indices: 585650--585689 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
585640 GACTTTGGTT
*
585650 GTATCGGTAGTTGAATACTAA
1 GTATCGGTAGTTCAATACTAA
*
585671 GTATCGGTAGTTCTATACT
1 GTATCGGTAGTTCAATACT
585690 TGAAAGTATT
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:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (21 bp):
GTATCGGTAGTTCAATACTAA
Found at i:590874 original size:101 final size:104
Alignment explanation
Indices: 590618--590899 Score: 297
Period size: 106 Copynumber: 2.7 Consensus size: 104
590608 TAGCATACCT
* ** * * *
590618 TTATCTCCCTGAAGTTACAATGGAGCAAGATGAAGCTACAACATTAAATCTTATATCCCTGAAGT
1 TTATCTCTCTGAAGTTGTAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGT
* * * *
590683 TGCAGTGGATCGGATTGAAGCTACGAAAGTGAATTCTTATC
66 TGTAGTGGATCGGATTAAAGCTACGAAAGTCAAATC-T-TC
* * * *
590724 TTATCTCTCTGAAGTTGTAGTAGAGTAGGATGAAGCTACAA-AACTAAATCCTATA-CTCCTGAA
1 TTATCTCTCTGAAGTTGTAGTGGAGCAAGATGAAGCTACAACATC-AAATCCTATATC-CCTGAA
* * *
590787 GTTGTAGTGGGTCGGTTTAAAG-TCATGAAAG-CAAATC-T-
64 GTTGTAGTGGATCGGATTAAAGCT-ACGAAAGTCAAATCTTC
* * *
590825 TTATCTCTTTGAAGTTGTAGTGGAGCAAGATGAAGTTACAACATCAAATCCTATATCCCTAAAGT
1 TTATCTCTCTGAAGTTGTAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGT
590890 TGTAGTGGAT
66 TGTAGTGGAT
590900 TAGATTGAGG
Statistics
Matches: 146, Mismatches: 25, Indels: 15
0.78 0.13 0.08
Matches are distributed among these distances:
101 62 0.42
102 4 0.03
105 7 0.05
106 73 0.50
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (104 bp):
TTATCTCTCTGAAGTTGTAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCCTGAAGT
TGTAGTGGATCGGATTAAAGCTACGAAAGTCAAATCTTC
Found at i:590921 original size:101 final size:100
Alignment explanation
Indices: 590638--590978 Score: 287
Period size: 101 Copynumber: 3.3 Consensus size: 100
590628 GAAGTTACAA
* * *
590638 TGGAGCAAGATGAAGCTACAACATTAAATCTTATATCCCTGAAGTTGCAGTGGATCGGATTGAAG
1 TGGAGCAAGATGAAGCTACAA-ATCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTGAAG
* * *
590703 CTACGA-AAGTGAATTCTTATCTTATCTCTCTGAAGTTGTAG
65 CTAC-ATAAG-CAAATC---T-TTATCTCTTTGAAGTTGTAG
* * * * * * *
590744 TAGAGTAGGATGAAGCTACAAAACTAAATCCTATA-CTCCTGAAGTTGTAGTGGGTCGGTTTAAA
1 TGGAGCAAGATGAAGCTACAAATC-AAATCCTATATC-CCTGAAGTTGTAGTGGATCGGATTGAA
590808 G-T-CATGAAAGCAAATCTTTATCTCTTTGAAGTTGTAG
64 GCTACAT--AAGCAAATCTTTATCTCTTTGAAGTTGTAG
* * ** *
590845 TGGAGCAAGATGAAGTTACAACATCAAATCCTATATCCCTAAAGTTGTAGTGGATTAGATTGAGG
1 TGGAGCAAGATGAAGCTACAA-ATCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTGAAG
* * * * * * *
590910 CTACATTAGCAAGTC-CTATCTCCTTAAAGATATAG
65 CTACATAAGCAAATCTTTATCTCTTTGAAGTTGTAG
* *
590945 TGGAGCAAGATAAAGCTACAAAGTCGAATCCTAT
1 TGGAGCAAGATGAAGCTACAAA-TCAAATCCTAT
590979 CTTTCTGAGA
Statistics
Matches: 190, Mismatches: 35, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
99 1 0.01
100 44 0.23
101 74 0.39
102 5 0.03
103 4 0.02
104 1 0.01
105 7 0.04
106 54 0.28
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (100 bp):
TGGAGCAAGATGAAGCTACAAATCAAATCCTATATCCCTGAAGTTGTAGTGGATCGGATTGAAGC
TACATAAGCAAATCTTTATCTCTTTGAAGTTGTAG
Found at i:591401 original size:50 final size:52
Alignment explanation
Indices: 591326--591445 Score: 181
Period size: 50 Copynumber: 2.3 Consensus size: 52
591316 GGCCTTTACA
* *
591326 AAAACCCAAATTTTATTTATTATTTATTTATAAAT-GA-AAATTAATAAAAT
1 AAAACCCAAATTTTATTTATTATTTATTTATAAATAAAGAAATGAATAAAAT
* *
591376 AAAACCCAATTTTTATTTGTTATTTATTTATAAATAAAAGAAATGAATAAAAT
1 AAAACCCAAATTTTATTTATTATTTATTTATAAAT-AAAGAAATGAATAAAAT
591429 AAAACCCAAATTTTATT
1 AAAACCCAAATTTTATT
591446 AAACCAAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
50 33 0.53
52 1 0.02
53 28 0.45
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (52 bp):
AAAACCCAAATTTTATTTATTATTTATTTATAAATAAAGAAATGAATAAAAT
Found at i:592875 original size:24 final size:23
Alignment explanation
Indices: 592833--592895 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 23
592823 TCCCTCTTAT
*
592833 ATTTTAATTATTTATTTTGCATG
1 ATTTTAATTATTTAATTTGCATG
*
592856 ATTTTAATTTGTTTAATTTGCATG
1 ATTTTAA-TTATTTAATTTGCATG
592880 ATTTTTTAATTATTTA
1 A--TTTTAATTATTTA
592896 TTTTATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.21
24 15 0.44
25 6 0.18
26 6 0.18
ACGTcount: A:0.27, C:0.03, G:0.08, T:0.62
Consensus pattern (23 bp):
ATTTTAATTATTTAATTTGCATG
Found at i:593654 original size:22 final size:23
Alignment explanation
Indices: 593606--593654 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
593596 AAATTTATTG
* *
593606 ATTTATTTTTCATTATTTCGTGG
1 ATTTATTTTTAATTATTTCGTGA
593629 ATTTATTTTTGAATT-TTT-GTGA
1 ATTTATTTTT-AATTATTTCGTGA
593651 ATTT
1 ATTT
593655 GAATATGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 7 0.30
23 13 0.57
24 3 0.13
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.63
Consensus pattern (23 bp):
ATTTATTTTTAATTATTTCGTGA
Found at i:611023 original size:17 final size:17
Alignment explanation
Indices: 610995--611038 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
610985 CTTTTTTTTG
*
610995 AATTTGAATTTAAA-TT
1 AATTTAAATTTAAATTT
611011 AATCTTAAATTTAAATTT
1 AAT-TTAAATTTAAATTT
611029 AATTTAAATT
1 AATTTAAATT
611039 CAAAGTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 3 0.12
17 17 0.68
18 5 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AATTTAAATTTAAATTT
Found at i:611024 original size:6 final size:6
Alignment explanation
Indices: 610995--611048 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
610985 CTTTTTTTTG
* *
610995 AATTTG AATTTA AA-TT- AATCTTA AATTTA AATTT- AATTTA AATTCA
1 AATTTA AATTTA AATTTA AAT-TTA AATTTA AATTTA AATTTA AATTTA
*
611041 AAGTTA AA
1 AATTTA AA
611049 AAGTCCAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 2 0.05
5 7 0.17
6 28 0.70
7 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:611107 original size:15 final size:16
Alignment explanation
Indices: 611073--611109 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
611063 AATTACATAA
611073 CCCAAATTACAAATGG
1 CCCAAATTACAAATGG
611089 CCCAAATT-CGAAA-GG
1 CCCAAATTAC-AAATGG
611104 CCCAAA
1 CCCAAA
611110 CTTTACACTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.43, C:0.30, G:0.14, T:0.14
Consensus pattern (16 bp):
CCCAAATTACAAATGG
Found at i:611735 original size:3 final size:3
Alignment explanation
Indices: 611727--611756 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
611717 AATATTTTCT
611727 TAA TAA TAA TAA TAA TAA TAA TTAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TA
611757 TGATTAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:611762 original size:12 final size:13
Alignment explanation
Indices: 611727--611766 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
611717 AATATTTTCT
611727 TAATAATAA-TAA
1 TAATAATAATTAA
611739 TAATAATAATTAA
1 TAATAATAATTAA
*
611752 TAAT-ATGATTAA
1 TAATAATAATTAA
611764 TAA
1 TAA
611767 AAGAAAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
TAATAATAATTAA
Done.