Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 53 of 276
Found at i:16522113 original size:12 final size:12
Alignment explanation
Indices: 16522089--16522126 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16522079 CGGCTCTACC
16522089 TTAT-TAATATTT
1 TTATATAAT-TTT
*
16522101 TTATATTATTTT
1 TTATATAATTTT
16522113 TTATATAATTTT
1 TTATATAATTTT
16522125 TT
1 TT
16522127 TTAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 20 0.87
13 3 0.13
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATATAATTTT
Found at i:16522376 original size:21 final size:22
Alignment explanation
Indices: 16522352--16522398 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
16522342 AAATGGTAAC
* *
16522352 AAAATAGTAA-AAAACAATAAG
1 AAAATAGTAACAAAAAAAAAAG
16522373 AAAATAGTAACAAAAAAAAAAG
1 AAAATAGTAACAAAAAAAAAAG
16522395 AAAA
1 AAAA
16522399 ACAATAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.77, C:0.04, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAATAGTAACAAAAAAAAAAG
Found at i:16529889 original size:5 final size:5
Alignment explanation
Indices: 16529881--16529908 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
16529871 CTTCATTTCA
16529881 TTTGC TTTGC TTTGC TTTGC TTTGC TTT
1 TTTGC TTTGC TTTGC TTTGC TTTGC TTT
16529909 CATCTCTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.18, T:0.64
Consensus pattern (5 bp):
TTTGC
Found at i:16532588 original size:111 final size:111
Alignment explanation
Indices: 16532449--16532670 Score: 435
Period size: 111 Copynumber: 2.0 Consensus size: 111
16532439 TTGTTTTCCA
*
16532449 TAGTATTTAATTGATCCTAATTTGGGTAGCACAGTAAGGATGATTTTGATTTTTGATGAATTATT
1 TAGTATTTAATTGATCCCAATTTGGGTAGCACAGTAAGGATGATTTTGATTTTTGATGAATTATT
16532514 GGCAACCTGAAGATGATGGATGAAAGAATTGCATGTTACCAATAGG
66 GGCAACCTGAAGATGATGGATGAAAGAATTGCATGTTACCAATAGG
16532560 TAGTATTTAATTGATCCCAATTTGGGTAGCACAGTAAGGATGATTTTGATTTTTGATGAATTATT
1 TAGTATTTAATTGATCCCAATTTGGGTAGCACAGTAAGGATGATTTTGATTTTTGATGAATTATT
16532625 GGCAACCTGAAGATGATGGATGAAAGAATTGCATGTTACCAATAGG
66 GGCAACCTGAAGATGATGGATGAAAGAATTGCATGTTACCAATAGG
16532671 CTGGCAGAGG
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.35
Consensus pattern (111 bp):
TAGTATTTAATTGATCCCAATTTGGGTAGCACAGTAAGGATGATTTTGATTTTTGATGAATTATT
GGCAACCTGAAGATGATGGATGAAAGAATTGCATGTTACCAATAGG
Found at i:16535513 original size:7 final size:7
Alignment explanation
Indices: 16535483--16535525 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
16535473 CTTTTAAAAA
16535483 AATATTT
1 AATATTT
16535490 ATATTATTT
1 A-A-TATTT
*
16535499 TA-ATTT
1 AATATTT
16535505 AATATTT
1 AATATTT
16535512 AATATTT
1 AATATTT
16535519 AATATTT
1 AATATTT
16535526 TTTTATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
6 5 0.16
7 19 0.61
8 2 0.06
9 5 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
AATATTT
Found at i:16543071 original size:31 final size:31
Alignment explanation
Indices: 16543036--16543101 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
16543026 CTTAACGTAC
*
16543036 TTTTGAATGATTATTCAATGTTAATTGTGAA
1 TTTTGAATGATTATTCAATGCTAATTGTGAA
* *
16543067 TTTTGGATGATTATTCGATGCTAATTGTGAA
1 TTTTGAATGATTATTCAATGCTAATTGTGAA
16543098 TTTT
1 TTTT
16543102 ATACTCCTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (31 bp):
TTTTGAATGATTATTCAATGCTAATTGTGAA
Found at i:16549990 original size:19 final size:20
Alignment explanation
Indices: 16549953--16549991 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
16549943 TTTTTGAATT
*
16549953 CATTTCATGCATCTGCATTG
1 CATTTCATGCATATGCATTG
16549973 CATTTCAT-CATATGCATTG
1 CATTTCATGCATATGCATTG
16549992 AATGTCACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (20 bp):
CATTTCATGCATATGCATTG
Found at i:16550288 original size:83 final size:83
Alignment explanation
Indices: 16550149--16550316 Score: 291
Period size: 83 Copynumber: 2.0 Consensus size: 83
16550139 AAGGAGATGC
* * * * *
16550149 AAGAATAGATGCAATCACAAATGCAAGAGCAATTGGCTAAGATCCAACAAGATATGAGGGATCAA
1 AAGAACAGATGCAAACACAAATGCAAGAGCAATTGGCTAAAATCCAACAAGATATGAGAGACCAA
16550214 ATGCTGGAATCACAAAGA
66 ATGCTGGAATCACAAAGA
16550232 AAGAACAGATGCAAACACAAATGCAAGAGCAATTGGCTAAAATCCAACAAGATATGAGAGACCAA
1 AAGAACAGATGCAAACACAAATGCAAGAGCAATTGGCTAAAATCCAACAAGATATGAGAGACCAA
16550297 ATGCTGGAATCACAAAGA
66 ATGCTGGAATCACAAAGA
16550315 AA
1 AA
16550317 CATGATGAAC
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (83 bp):
AAGAACAGATGCAAACACAAATGCAAGAGCAATTGGCTAAAATCCAACAAGATATGAGAGACCAA
ATGCTGGAATCACAAAGA
Found at i:16553041 original size:10 final size:10
Alignment explanation
Indices: 16553026--16553056 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
16553016 CATGAGAGAC
16553026 AACAAAAAAA
1 AACAAAAAAA
*
16553036 AACAAAACAA
1 AACAAAAAAA
16553046 AACAAAAAAA
1 AACAAAAAAA
16553056 A
1 A
16553057 GATTGTGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
AACAAAAAAA
Found at i:16553582 original size:19 final size:20
Alignment explanation
Indices: 16553558--16553608 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
16553548 AAAATTTTTC
16553558 CAAAAAAAGAAACAAAA-AA
1 CAAAAAAAGAAACAAAAGAA
*
16553577 CAAAAAAAGAAGAGAAAAGAA
1 CAAAAAAAGAA-ACAAAAGAA
16553598 -AAAAAAAGAAA
1 CAAAAAAAGAAA
16553609 ATGAGAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.41
20 15 0.52
21 2 0.07
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (20 bp):
CAAAAAAAGAAACAAAAGAA
Found at i:16553594 original size:10 final size:10
Alignment explanation
Indices: 16553559--16553609 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
16553549 AAATTTTTCC
16553559 AAAAAAAGAA
1 AAAAAAAGAA
* *
16553569 ACAAAAA-AC
1 AAAAAAAGAA
16553578 AAAAAAAGAA
1 AAAAAAAGAA
* *
16553588 GAGAAAAGAA
1 AAAAAAAGAA
16553598 AAAAAAAGAA
1 AAAAAAAGAA
16553608 AA
1 AA
16553610 TGAGAAGTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:16554007 original size:25 final size:25
Alignment explanation
Indices: 16553977--16554026 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
16553967 GATTAACTTA
16553977 TTCATTTTGAGTTAATTTCCTTATT
1 TTCATTTTGAGTTAATTTCCTTATT
16554002 TTCATTTTGAGTTAATTTCCTTATT
1 TTCATTTTGAGTTAATTTCCTTATT
16554027 ATTATATTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.08, T:0.60
Consensus pattern (25 bp):
TTCATTTTGAGTTAATTTCCTTATT
Found at i:16554531 original size:46 final size:46
Alignment explanation
Indices: 16554461--16554638 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
16554451 CTCAGATCAA
* * *
16554461 TGAAGAAGATACAAATCCTGTACCCCTGAGTTGCAGTGGGATGGAT
1 TGAAGAAAATACAAATCCTATACCCCTGAGTTGTAGTGGGATGGAT
*
16554507 TGAAGAAAATACAAATCCTATACCCCTGAGCTGTAGTGGGATGGAT
1 TGAAGAAAATACAAATCCTATACCCCTGAGTTGTAGTGGGATGGAT
*** *
16554553 TGAAGATGGTACAAATCCTATACCCCTGAGTTGTAGTAGGATGGAT
1 TGAAGAAAATACAAATCCTATACCCCTGAGTTGTAGTGGGATGGAT
* ** **
16554599 GGAAGAAACCACAAATTTTAT-CTCCCTGAAGTTGTAGTGG
1 TGAAGAAAATACAAATCCTATAC-CCCTG-AGTTGTAGTGG
16554639 AGCAAACCAG
Statistics
Matches: 113, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
45 1 0.01
46 102 0.90
47 10 0.09
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (46 bp):
TGAAGAAAATACAAATCCTATACCCCTGAGTTGTAGTGGGATGGAT
Found at i:16555105 original size:45 final size:45
Alignment explanation
Indices: 16555054--16555350 Score: 183
Period size: 45 Copynumber: 6.4 Consensus size: 45
16555044 TATCTCCCTA
* *
16555054 AAGTTGCAGCGGAACAGACTGAAGACAGCGAATCTTATTTCCTTG
1 AAGTTGCAGTGGAACAGATTGAAGACAGCGAATCTTATTTCCTTG
* * * * *
16555099 AAGTTGCAGTGGAGCAGATTGAAGCCA--TAAGTCTTATCT-CTCTA
1 AAGTTGCAGTGGAACAGATTGAAGACAGCGAA-TCTTATTTCCT-TG
* * *
16555143 AAGTTGCAGTGGAGCAGATTAAAGACAGCGAATCTTATTTCCCTG
1 AAGTTGCAGTGGAACAGATTGAAGACAGCGAATCTTATTTCCTTG
* * ** * *
16555188 AAGTTGCAGTTGAACAGATTAAAGCTACAAATTATGGCGAATCTTACCTCCCTA
1 AAGTTGCAGTGGAACAGATTGAAG--AC-----A--GCGAATCTTATTTCCTTG
* * * * *
16555242 AAGTTGTAGTGGAGCAGATTGAAGCCA-C-AAGTTTTATCTCCTTG
1 AAGTTGCAGTGGAACAGATTGAAGACAGCGAA-TCTTATTTCCTTG
* * * * * *
16555286 AAGTTAG-AGCGGAGCAGACTAAAGACAGCGAATCTTATTTCCCTA
1 AAGTT-GCAGTGGAACAGATTGAAGACAGCGAATCTTATTTCCTTG
*
16555331 AAGTTGTAGTGGAACAGATT
1 AAGTTGCAGTGGAACAGATT
16555351 AAAGCTAAAA
Statistics
Matches: 195, Mismatches: 38, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
43 6 0.03
44 65 0.33
45 79 0.41
46 5 0.03
47 3 0.02
52 2 0.01
54 35 0.18
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (45 bp):
AAGTTGCAGTGGAACAGATTGAAGACAGCGAATCTTATTTCCTTG
Found at i:16555144 original size:89 final size:88
Alignment explanation
Indices: 16554991--16555212 Score: 286
Period size: 89 Copynumber: 2.5 Consensus size: 88
16554981 AAGTCATCAT
*
16554991 AGCGAATCTTATCTTTCTGAAGTTGCAAG-GGAGCAGATTGAAGCCACTAGCCATATCTCCCTAA
1 AGCGAATCTTAT-TTCCTGAAGTTGC-AGTGGAGCAGATTGAAGCCACTAGCCATATCTCCCTAA
*
16555055 AGTTGCAGCGGAACAGACTGAAGAC
64 AGTTGCAGCGGAACAGACTAAAGAC
* * *
16555080 AGCGAATCTTATTTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCA-TAAGTCTTATCTCTCTAA
1 AGCGAATCTTATTTCC-TGAAGTTGCAGTGGAGCAGATTGAAGCCACT-AGCCATATCTCCCTAA
* * *
16555144 AGTTGCAGTGGAGCAGATTAAAGAC
64 AGTTGCAGCGGAACAGACTAAAGAC
* * *
16555169 AGCGAATCTTATTTCCCTGAAGTTGCAGTTGAACAGATTAAAGC
1 AGCGAATCTTATTT-CCTGAAGTTGCAGTGGAGCAGATTGAAGC
16555213 TACAAATTAT
Statistics
Matches: 118, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
88 6 0.05
89 110 0.93
90 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (88 bp):
AGCGAATCTTATTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCATATCTCCCTAAAG
TTGCAGCGGAACAGACTAAAGAC
Found at i:16555149 original size:44 final size:45
Alignment explanation
Indices: 16554997--16555451 Score: 176
Period size: 44 Copynumber: 9.8 Consensus size: 45
16554987 TCATAGCGAA
* *
16554997 TCTTATCTTTCTGAAGTTGCAAG-GGAGCAGATTGAAGCCACT-AG
1 TCTTATCTCTCTAAAGTTGC-AGTGGAGCAGATTGAAGCCACTAAG
* * * * * * * *
16555041 CCATATCTCCCTAAAGTTGCAGCGGAACAGACTGAAGACAGCGAA-
1 TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTGAAGCCA-CTAAG
* *
16555086 TCTTATTTC-CTTGAAGTTGCAGTGGAGCAGATTGAAGCCA-TAAG
1 TCTTATCTCTC-TAAAGTTGCAGTGGAGCAGATTGAAGCCACTAAG
* * *
16555130 TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGACAGCGAA-
1 TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTGAAGCCA-CTAAG
* * * * * * * *
16555175 TCTTATTTCCCTGAAGTTGCAGTTGAACAGATTAAAGCTACAAATTATGGCGAA
1 TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTGAAGC--C--ACTA-----AG
* * *
16555229 TCTTACCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCCAC-AAG
1 TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAAG
* * * * * * *
16555273 TTTTATCTC-CTTGAAGTTAG-AGCGGAGCAGACTAAAGACAGCGAA-
1 TCTTATCTCTC-TAAAGTT-GCAGTGGAGCAGATTGAAGCCA-CTAAG
* * * * * * * *
16555318 TCTTATTTCCCTAAAGTTGTAGTGGAACAGATTAAAGCTAAAAATTATGGTGAA
1 TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTGAAGC----CACTA-----AG
* * *
16555372 TCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGCCAC-CAG
1 TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAAG
* * * *
16555416 CCTTATCTCTCTGAAGTTACAGTGGAGCAGGTTGAA
1 TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTGAA
16555452 ATTACCAATT
Statistics
Matches: 305, Mismatches: 72, Indels: 68
0.69 0.16 0.15
Matches are distributed among these distances:
43 5 0.02
44 128 0.42
45 93 0.30
46 6 0.02
47 1 0.00
48 2 0.01
49 3 0.01
50 2 0.01
52 1 0.00
53 2 0.01
54 62 0.20
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (45 bp):
TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAAG
Found at i:16555346 original size:143 final size:143
Alignment explanation
Indices: 16555081--16555445 Score: 518
Period size: 143 Copynumber: 2.6 Consensus size: 143
16555071 ACTGAAGACA
* * * *
16555081 GCGAATCTTATTTCCTTGAAGTTGCAGTGGAGCAGATTGAAGCCATAAGTCTTATCTCTCTAAAG
1 GCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAGTCTTATCTCTCTGAAG
* * *
16555146 TT-GCAGTGGAGCAGATTAAAGACAGCGAATCTTATTTCCCTGAAGTTGCAGTTGAACAGATTAA
66 TTAG-AGTGGAGCAGACTAAAGACAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAA
*
16555210 AGCTACAAATTATG
130 AGCTAAAAATTATG
* * * *
16555224 GCGAATCTTACCTCCCTAAAGTTGTAGTGGAGCAGATTGAAGCCACAAGTTTTATCTC-CTTGAA
1 GCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAGTCTTATCTCTC-TGAA
* *
16555288 GTTAGAGCGGAGCAGACTAAAGACAGCGAATCTTATTTCCCTAAAGTTGTAGTGGAACAGATTAA
65 GTTAGAGTGGAGCAGACTAAAGACAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAA
16555353 AGCTAAAAATTATG
130 AGCTAAAAATTATG
* * * * *
16555367 GTGAATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCTCTGAAG
1 GCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAGTCTTATCTCTCTGAAG
*
16555432 TTACAGTGGAGCAG
66 TTAGAGTGGAGCAG
16555446 GTTGAAATTA
Statistics
Matches: 194, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
142 1 0.01
143 191 0.98
144 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (143 bp):
GCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAGTCTTATCTCTCTGAAG
TTAGAGTGGAGCAGACTAAAGACAGCGAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATTAAA
GCTAAAAATTATG
Found at i:16555531 original size:89 final size:87
Alignment explanation
Indices: 16555432--16555712 Score: 246
Period size: 89 Copynumber: 3.2 Consensus size: 87
16555422 CTCTCTGAAG
*
16555432 TTACAGTGGAGCAGGTTGAAATTACCAATTCTTACCTCCTTGAAGTTCTAGCGGAGTAGATCGAA
1 TTACAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTGAAGTTC-AGCGGAGTAGATCGAA
*
16555497 ACTACAAATCTATTCTTCCTTAAA
65 ACTACAAATCT-TTCTCCCTTAAA
* * * *** * ** **
16555521 TTACATTGGAGCAGATTTAAGCCA-CAATCCTTATCT-CTCTGAAGTTACAGTAGAGTAGGATAA
1 TTACAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCT-TGAAGTT-CAGCGGAGTA-GATCG
* *
16555584 AATAC-ACAAACCTTATC-CCCCTAAA
63 AA-ACTACAAATCTT-TCTCCCTTAAA
* ** *
16555609 GTTGCAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTCAAAGTTCCAGCGGAGTATATCGA
1 -TTACAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTGAAGTT-CAGCGGAGTAGATCGA
* *
16555674 AGCTACAAATCTCTTCTCCCTGAAA
64 AACTACAAATCT-TTCTCCCTTAAA
*
16555699 TTACATTGGAGCAG
1 TTACAGTGGAGCAG
16555713 ATCGAAGCCA
Statistics
Matches: 144, Mismatches: 37, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
87 2 0.01
88 32 0.22
89 75 0.52
90 33 0.23
91 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (87 bp):
TTACAGTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTTGAAGTTCAGCGGAGTAGATCGAAA
CTACAAATCTTTCTCCCTTAAA
Found at i:16555682 original size:178 final size:178
Alignment explanation
Indices: 16555373--16555805 Score: 607
Period size: 178 Copynumber: 2.4 Consensus size: 178
16555363 TATGGTGAAT
* ** ** * * *
16555373 CTTATCTCTCTGAAGTTGCAGTGGAGTA-GATTGAAGCCACCAGCCTTATCTCTCTGAAGTTACA
1 CTTATCTCTCTGAAGTTGCAGTAGAGTAGGATAAAATACACAAACCTTATCTCTCTGAAGTTGCA
** *
16555437 GTGGAGCAGGTTGAAATTACCAATTCTTACCTCCTTGAAGTTCTAGCGGAGTAGATCGAAACTAC
66 GTGGAGCAGGTTGAAATTACCAATTCTTACCTCCTCAAAGTTCCAGCGGAGTAGATCGAAACTAC
* * **
16555502 AAATCTATTCTTCCTTAAATTACATTGGAGCAGATTTAAGCCACAATC
131 AAATCTATTCTCCCTGAAATTACATTGGAGCAGATCGAAGCCACAATC
* * * *
16555550 CTTATCTCTCTGAAGTTACAGTAGAGTAGGATAAAATACACAAACCTTATCCCCCTAAAGTTGCA
1 CTTATCTCTCTGAAGTTGCAGTAGAGTAGGATAAAATACACAAACCTTATCTCTCTGAAGTTGCA
* * *
16555615 GTGGAGCAGGTTGAAATTACCAATTCTTATCTCCTCAAAGTTCCAGCGGAGTATATCGAAGCTAC
66 GTGGAGCAGGTTGAAATTACCAATTCTTACCTCCTCAAAGTTCCAGCGGAGTAGATCGAAACTAC
*
16555680 AAATCTCTTCTCCCTGAAATTACATTGGAGCAGATCGAAGCCACAATC
131 AAATCTATTCTCCCTGAAATTACATTGGAGCAGATCGAAGCCACAATC
* * * *
16555728 CTTATCTCTTTGAAGTTGCAGCAGAGAAGGATAAAAATATACAAACCTTATCTCTCTGAAGTTGC
1 CTTATCTCTCTGAAGTTGCAGTAGAGTAGGAT-AAAATACACAAACCTTATCTCTCTGAAGTTGC
16555793 AGTGGAGCAGGTT
65 AGTGGAGCAGGTT
16555806 AAAGATAGGG
Statistics
Matches: 223, Mismatches: 31, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
177 26 0.12
178 156 0.70
179 41 0.18
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (178 bp):
CTTATCTCTCTGAAGTTGCAGTAGAGTAGGATAAAATACACAAACCTTATCTCTCTGAAGTTGCA
GTGGAGCAGGTTGAAATTACCAATTCTTACCTCCTCAAAGTTCCAGCGGAGTAGATCGAAACTAC
AAATCTATTCTCCCTGAAATTACATTGGAGCAGATCGAAGCCACAATC
Found at i:16555799 original size:90 final size:89
Alignment explanation
Indices: 16555527--16555802 Score: 236
Period size: 90 Copynumber: 3.1 Consensus size: 89
16555517 TAAATTACAT
* * * *
16555527 TGGAGCAGATTTAAGCCACAATCCTTATCTCTCTGAAGTTACAGTAGAGTAGGAT-AAAATACAC
1 TGGAGCAGATTGAAGCCACAATCCTTATCTCTTTGAAGTTACAGCAGAG-AGGATAAAAATATAC
* *
16555591 AAACCTTATCCCCCTAAAGTTGCAG
65 AAACCTTATCTCCCTGAAGTTGCAG
* *** * * ** * * ** **
16555616 TGGAGCAGGTTGAAATTACCAATTCTTATCTCCTCAAAGTTCCAGC-G-GAGTATATCGAAGCTA
1 TGGAGCAGATTGAAGCCA-CAATCCTTATCTCTTTGAAGTTACAGCAGAGAGGATA-AAAATATA
* * * *
16555679 CAAATCTCT-TCTCCCTGAAATTACAT
64 CAAACCT-TATCTCCCTGAAGTTGCAG
* *
16555705 TGGAGCAGATCGAAGCCACAATCCTTATCTCTTTGAAGTTGCAGCAGAGAAGGATAAAAATATAC
1 TGGAGCAGATTGAAGCCACAATCCTTATCTCTTTGAAGTTACAGCAGAG-AGGATAAAAATATAC
*
16555770 AAACCTTATCTCTCTGAAGTTGCAG
65 AAACCTTATCTCCCTGAAGTTGCAG
16555795 TGGAGCAG
1 TGGAGCAG
16555803 GTTAAAGATA
Statistics
Matches: 135, Mismatches: 44, Indels: 15
0.70 0.23 0.08
Matches are distributed among these distances:
87 4 0.03
88 23 0.17
89 50 0.37
90 53 0.39
91 5 0.04
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (89 bp):
TGGAGCAGATTGAAGCCACAATCCTTATCTCTTTGAAGTTACAGCAGAGAGGATAAAAATATACA
AACCTTATCTCCCTGAAGTTGCAG
Found at i:16558849 original size:361 final size:360
Alignment explanation
Indices: 16558242--16558976 Score: 1326
Period size: 361 Copynumber: 2.0 Consensus size: 360
16558232 CATGAGATAT
* *
16558242 AATAGATTTTGTGAGATAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTTGAAAATCAT
1 AATA-ATTTAGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTTGAAAATCAT
16558307 AAAAAATTGGAGAAAAATAATTAGGGGCTTAAATTTATATTTTTAAAATACTTAATGAGTCTATT
65 AAAAAATTGGAGAAAAATAATTAGGGGCTTAAATTTATATTTTTAAAATACTTAATGAGTCTATT
*
16558372 TTCAATAGAAATAAACATGGAAATCATCCAAATTCTGTACGAAGAGATAATTAATTTTTAGTGAA
130 TTCAATAGAAATAAACATGGAAATCATCCAAATTCTGTACGAAGAGATAATTAATTTTTAGTAAA
*
16558437 GAAGGGTTGGAATTGTCAGACAGTAGAACAGGGGTGACATTAAAGAATAAACTGTACTTATTAGA
195 GAAGGGTCGGAATTGTCAGACAGTAGAACAGGGGTGACATTAAAGAATAAACTGTACTTATTAGA
*
16558502 TAAACCAAAAATTCTAAAAATTTTATGATAAGAGGAAATATGAATCTAGTTTCAGGGAAAATTAG
260 TAAACCAAAAATTCTAAAAATTTTATGATAAGAAGAAATATGAATCTAGTTTCAGGGAAAATTAG
16558567 CGGATCCTAATTTGGAGCTCTTTAGCTAAAGATAAA
325 CGGATCCTAATTTGGAGCTCTTTAGCTAAAGATAAA
16558603 AATAATTTAGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTTGAAAATCATA
1 AATAATTTAGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTTGAAAATCAT-
*
16558668 AAAAAATTGGAGAAAAATAATTAGGGGCTTAAATTTATATTTTTAAAATCCTTAATGAGTCTATT
65 AAAAAATTGGAGAAAAATAATTAGGGGCTTAAATTTATATTTTTAAAATACTTAATGAGTCTATT
* * * *
16558733 TTCAATAGAAATAAACATGGACATTATCCGAATTCTGTATGAAGAGATAATTAATTTTTAGTAAA
130 TTCAATAGAAATAAACATGGAAATCATCCAAATTCTGTACGAAGAGATAATTAATTTTTAGTAAA
*
16558798 GAAGGGTCGGAATTGTCAGACAGTAGAACAGGGGTGACTTTAAAGAATAAACTGTACTTATTAGA
195 GAAGGGTCGGAATTGTCAGACAGTAGAACAGGGGTGACATTAAAGAATAAACTGTACTTATTAGA
*
16558863 TAAACCAAAAATTCTAAAAATTTTATGATAAGAAGAAATATGAATCTGGTTTCAGGGAAAATTAG
260 TAAACCAAAAATTCTAAAAATTTTATGATAAGAAGAAATATGAATCTAGTTTCAGGGAAAATTAG
* *
16558928 TGGATCCTAATTTGGAGTTCTTTAGCTAAAGATAAA
325 CGGATCCTAATTTGGAGCTCTTTAGCTAAAGATAAA
16558964 AATAATTTAGTGA
1 AATAATTTAGTGA
16558977 CTATGGCATT
Statistics
Matches: 359, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
360 58 0.16
361 301 0.84
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (360 bp):
AATAATTTAGTGAGACAATGTCAGAATGATTTCGGGTTCCCCTGTTCTGACTTTTGAAAATCATA
AAAAATTGGAGAAAAATAATTAGGGGCTTAAATTTATATTTTTAAAATACTTAATGAGTCTATTT
TCAATAGAAATAAACATGGAAATCATCCAAATTCTGTACGAAGAGATAATTAATTTTTAGTAAAG
AAGGGTCGGAATTGTCAGACAGTAGAACAGGGGTGACATTAAAGAATAAACTGTACTTATTAGAT
AAACCAAAAATTCTAAAAATTTTATGATAAGAAGAAATATGAATCTAGTTTCAGGGAAAATTAGC
GGATCCTAATTTGGAGCTCTTTAGCTAAAGATAAA
Found at i:16559488 original size:51 final size:51
Alignment explanation
Indices: 16559412--16559576 Score: 303
Period size: 51 Copynumber: 3.2 Consensus size: 51
16559402 AGTGACAAGC
* * *
16559412 GACAAGCGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
16559463 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
16559514 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
1 GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
16559565 GACAAGTGATAA
1 GACAAGTGATAA
16559577 ATGTGATCAG
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 111 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (51 bp):
GACAAGTGATAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAGT
Found at i:16562140 original size:42 final size:42
Alignment explanation
Indices: 16562093--16562177 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
16562083 ATTTAATATG
*
16562093 TCGTAATTGTCCACTGAAAGTGAAAGGCTGTGAATTTCCTGC
1 TCGTAATTGTCCACTGAAAGTGAAAGGCTGTGAATTCCCTGC
16562135 TCGTAATTGTCCACTGAAAGTGAAAGGCTGTGAATTCCCTGC
1 TCGTAATTGTCCACTGAAAGTGAAAGGCTGTGAATTCCCTGC
16562177 T
1 T
16562178 GATTTAATGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (42 bp):
TCGTAATTGTCCACTGAAAGTGAAAGGCTGTGAATTCCCTGC
Found at i:16567126 original size:150 final size:150
Alignment explanation
Indices: 16566855--16567155 Score: 593
Period size: 150 Copynumber: 2.0 Consensus size: 150
16566845 TAATTTAGTG
*
16566855 ACTATGGCATTGATGGACAGCATTGGAATATACATAAGTAAATAATGAAATTATAGATAATATTA
1 ACTATGGCATTGATGGACAACATTGGAATATACATAAGTAAATAATGAAATTATAGATAATATTA
16566920 CTTATAAGCGGGTTGAAGATGAAGTCAATACTGATAAGTGAATGATTTTACAATGATAGATCGAG
66 CTTATAAGCGGGTTGAAGATGAAGTCAATACTGATAAGTGAATGATTTTACAATGATAGATCGAG
16566985 AACCTGATGTAAGTCGAGGA
131 AACCTGATGTAAGTCGAGGA
16567005 ACTATGGCATTGATGGACAACATTGGAATATACATAAGTAAATAATGAAATTATAGATAATATTA
1 ACTATGGCATTGATGGACAACATTGGAATATACATAAGTAAATAATGAAATTATAGATAATATTA
16567070 CTTATAAGCGGGTTGAAGATGAAGTCAATACTGATAAGTGAATGATTTTACAATGATAGATCGAG
66 CTTATAAGCGGGTTGAAGATGAAGTCAATACTGATAAGTGAATGATTTTACAATGATAGATCGAG
16567135 AACCTGATGTAAGTCGAGGA
131 AACCTGATGTAAGTCGAGGA
16567155 A
1 A
16567156 AAGAAAAAGT
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (150 bp):
ACTATGGCATTGATGGACAACATTGGAATATACATAAGTAAATAATGAAATTATAGATAATATTA
CTTATAAGCGGGTTGAAGATGAAGTCAATACTGATAAGTGAATGATTTTACAATGATAGATCGAG
AACCTGATGTAAGTCGAGGA
Found at i:16572832 original size:182 final size:182
Alignment explanation
Indices: 16572525--16572888 Score: 728
Period size: 182 Copynumber: 2.0 Consensus size: 182
16572515 TTTGGAAATT
16572525 CGAGAGATCGTGCCCTAACGTACTGGGTTTCGATTTTTCTCGTTTGGCCCAAATGACTGAATATC
1 CGAGAGATCGTGCCCTAACGTACTGGGTTTCGATTTTTCTCGTTTGGCCCAAATGACTGAATATC
16572590 TTTTTAAAATTAAAATACATGAGTTTTGAAAATCAAAAGACAAGCTTATTCTCGAGGGTTTAAAA
66 TTTTTAAAATTAAAATACATGAGTTTTGAAAATCAAAAGACAAGCTTATTCTCGAGGGTTTAAAA
16572655 TGTCGTGTCCTAACGTGATGGATATGACATTTTATTACTTTAAGACAAGAAA
131 TGTCGTGTCCTAACGTGATGGATATGACATTTTATTACTTTAAGACAAGAAA
16572707 CGAGAGATCGTGCCCTAACGTACTGGGTTTCGATTTTTCTCGTTTGGCCCAAATGACTGAATATC
1 CGAGAGATCGTGCCCTAACGTACTGGGTTTCGATTTTTCTCGTTTGGCCCAAATGACTGAATATC
16572772 TTTTTAAAATTAAAATACATGAGTTTTGAAAATCAAAAGACAAGCTTATTCTCGAGGGTTTAAAA
66 TTTTTAAAATTAAAATACATGAGTTTTGAAAATCAAAAGACAAGCTTATTCTCGAGGGTTTAAAA
16572837 TGTCGTGTCCTAACGTGATGGATATGACATTTTATTACTTTAAGACAAGAAA
131 TGTCGTGTCCTAACGTGATGGATATGACATTTTATTACTTTAAGACAAGAAA
16572889 GTCTTTAGCA
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 182 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (182 bp):
CGAGAGATCGTGCCCTAACGTACTGGGTTTCGATTTTTCTCGTTTGGCCCAAATGACTGAATATC
TTTTTAAAATTAAAATACATGAGTTTTGAAAATCAAAAGACAAGCTTATTCTCGAGGGTTTAAAA
TGTCGTGTCCTAACGTGATGGATATGACATTTTATTACTTTAAGACAAGAAA
Found at i:16574464 original size:26 final size:24
Alignment explanation
Indices: 16574434--16574483 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
16574424 TAAATAAAAA
*
16574434 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
16574460 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
16574484 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:16577280 original size:22 final size:24
Alignment explanation
Indices: 16577228--16577280 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 24
16577218 AAGTTAGGTA
* *
16577228 AAATAAAACTGCAATTTTTAATGC
1 AAATAAAGCTGCAATTTTTAATCC
*
16577252 AGA-AAAGCTGC-A-TTTTAATCC
1 AAATAAAGCTGCAATTTTTAATCC
16577273 AAATAAAG
1 AAATAAAG
16577281 ACAATGCCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 7 0.29
24 2 0.08
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.28
Consensus pattern (24 bp):
AAATAAAGCTGCAATTTTTAATCC
Found at i:16578525 original size:22 final size:24
Alignment explanation
Indices: 16578473--16578525 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 24
16578463 AAGTTAGGTA
* *
16578473 AAATAAAACTGCAATTTTTAATGC
1 AAATAAAGCTGCAATTTTTAATCC
*
16578497 AGA-AAAGCTGC-A-TTTTAATCC
1 AAATAAAGCTGCAATTTTTAATCC
16578518 AAATAAAG
1 AAATAAAG
16578526 ACAATGTCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
21 10 0.42
22 5 0.21
23 7 0.29
24 2 0.08
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.28
Consensus pattern (24 bp):
AAATAAAGCTGCAATTTTTAATCC
Found at i:16582225 original size:17 final size:17
Alignment explanation
Indices: 16582177--16582244 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
16582167 ATTTATAAAA
*
16582177 TAATTATTTATATTTCTAT
1 TAATTTTTTATA-TT-TAT
*
16582196 T-ATTATTTCATATTTAT
1 TAATT-TTTTATATTTAT
16582213 TAATTTTTTATATTT-T
1 TAATTTTTTATATTTAT
*
16582229 TGAATTTTTTTTATTT
1 T-AATTTTTTATATTT
16582245 TATCATGATG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
16 2 0.05
17 26 0.62
18 8 0.19
19 6 0.14
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (17 bp):
TAATTTTTTATATTTAT
Found at i:16583173 original size:14 final size:16
Alignment explanation
Indices: 16583149--16583182 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
16583139 TTATGAACTT
16583149 TTTTATATTTTTA-AA
1 TTTTATATTTTTATAA
16583164 TTTT-TATTTTTATAA
1 TTTTATATTTTTATAA
16583179 TTTT
1 TTTT
16583183 GAATTATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTATATTTTTATAA
Found at i:16585649 original size:65 final size:65
Alignment explanation
Indices: 16585544--16585679 Score: 236
Period size: 65 Copynumber: 2.1 Consensus size: 65
16585534 TTGAACTTGG
**
16585544 TAGGAAATTGCGTAGTGTTGAAGAAGATGAGGATAAAGTCAGGGCGAGGAGTTTTCGGGGGAGGT
1 TAGGAAATTGAATAGTGTTGAAGAAGATGAGGATAAAGTCAGGGCGAGGAGTTTTCGGGGGAGGT
* *
16585609 TAGGAAATTGAATAGTGTTGAAGAATATGAGGATAGAGTCAGGGCGAGGAGTTTTCGGGGGAGGT
1 TAGGAAATTGAATAGTGTTGAAGAAGATGAGGATAAAGTCAGGGCGAGGAGTTTTCGGGGGAGGT
16585674 TAGGAA
1 TAGGAA
16585680 TTTGGCGATG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 67 1.00
ACGTcount: A:0.31, C:0.05, G:0.40, T:0.24
Consensus pattern (65 bp):
TAGGAAATTGAATAGTGTTGAAGAAGATGAGGATAAAGTCAGGGCGAGGAGTTTTCGGGGGAGGT
Found at i:16586439 original size:19 final size:19
Alignment explanation
Indices: 16586417--16586478 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
16586407 ATTAAAATAC
16586417 TTTTAAATAATATAAATTA
1 TTTTAAATAATATAAATTA
* ** *
16586436 TTTTAATTACGA-AAATAA
1 TTTTAAATAATATAAATTA
** *
16586454 CATTGAATAATATAAATTA
1 TTTTAAATAATATAAATTA
16586473 TTTTAA
1 TTTTAA
16586479 TTAAAAAAGA
Statistics
Matches: 28, Mismatches: 14, Indels: 2
0.64 0.32 0.05
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (19 bp):
TTTTAAATAATATAAATTA
Found at i:16588661 original size:18 final size:18
Alignment explanation
Indices: 16588605--16588663 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
16588595 ATCCTAAGGT
*
16588605 CATTTTCTTTCTCCTGGA
1 CATTTTCTTTCTCATGGA
** * *
16588623 CATTAGCATTCATGATGGA
1 CATTTTCTTTC-TCATGGA
*
16588642 CATTTTCTTTCTCTTGGA
1 CATTTTCTTTCTCATGGA
16588660 CATT
1 CATT
16588664 GTCTCTGGTA
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.46
Consensus pattern (18 bp):
CATTTTCTTTCTCATGGA
Found at i:16592665 original size:20 final size:20
Alignment explanation
Indices: 16592637--16592704 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
16592627 TTTTTCAAAG
*
16592637 AAATATTAAGAA-TATTATTT
1 AAATATTAA-AATTATTATTA
*
16592657 AAATTTTAAAATTATTATTA
1 AAATATTAAAATTATTATTA
*
16592677 AAATA--AAATTTTATTATTA
1 AAATATTAAA-ATTATTATTA
*
16592696 TAATATTAA
1 AAATATTAA
16592705 GTTTGATTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 19 0.49
21 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (20 bp):
AAATATTAAAATTATTATTA
Found at i:16594333 original size:34 final size:34
Alignment explanation
Indices: 16594266--16594333 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
16594256 TACTAATTAA
**
16594266 TTTTTAAAAATTAAAAAATCTTTTTAATTTTTAT
1 TTTTTAAAAATTAAAAAATCTAATTAATTTTTAT
*
16594300 TTTTTAAAATTTAAAAAAT-TAATTAATTATTTAT
1 TTTTTAAAAATTAAAAAATCTAATTAATT-TTTAT
16594334 ATGGTATCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 7 0.23
34 23 0.77
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (34 bp):
TTTTTAAAAATTAAAAAATCTAATTAATTTTTAT
Found at i:16595872 original size:7 final size:8
Alignment explanation
Indices: 16595854--16595879 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
16595844 TAATTATATT
16595854 AAAATTGA
1 AAAATTGA
16595862 AAAATTGA
1 AAAATTGA
16595870 AAAATTGA
1 AAAATTGA
16595878 AA
1 AA
16595880 CAAATTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (8 bp):
AAAATTGA
Found at i:16600622 original size:627 final size:627
Alignment explanation
Indices: 16599368--16600593 Score: 1864
Period size: 627 Copynumber: 2.0 Consensus size: 627
16599358 AACTAGTTTG
* * *
16599368 AGCATATGATATATAGTTGTGAAGGTCTCATGGAGTAGAGTATGAAGCCATAATTTTATGATTCA
1 AGCATATGATATACAGTTGTAAAGGTCTCATGGAGTAGAATATGAAGCCATAATTTTATGATTCA
* *
16599433 ACTCTCCACCTTTATCTATTGAGAATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCCAACAA
66 ACTCTCCACCTTTACCTATTGAGAATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCAAACAA
* * *
16599498 CGGGTATGTTCAAACCTTGTGGCTAGCAAGGATGTTTGCCAAGTAGGTGGATTGTTTCTAGAAGC
131 CGGCTATGTTCAAACCTTGTGGCTAGCAAAGATGTTTGCCAAGCAGGTGGATTGTTTCTAGAAGC
*
16599563 GGGTGGTTTAGGTGTTTCAAGAACACGTAATGCAGTCCAAGTCTCTTGCTAAGATAGAGGGTCAA
196 GGGTGGTTTAGGTGTTTCAAGAACACGTAATGCAGTCCAAGTCTCTTGCTAAGATAAAGGGTCAA
* * * * *
16599628 ACGGAGAGTAAGAATCTGGGAGAGATAGTCACCAAGGCATTCGAGTAGAGCAGAATGATTGGTCA
261 ACGGAGAGTAAAAATCTGGGAGAGACAGTCACCAAGACATTCGAGTAGAACAGAATAATTGGTCA
* * * ***
16599693 CGATTATTTCTTAGATGGCTTGTCACGCTAGCACGTGTCCACCTGTAGTGGAAGTATAATAATTT
326 CGATTATGTCTCAGATGCCTTGTCACGCTAGCACGTGTCCACCTGTAACAGAAGTATAATAATTT
* * * *
16599758 ACGGTTTATTTTTTGTCTAATTATCTAAACTTTTAATAAATACATATTGATAAAATCGAGTATTA
391 ACGATATATTTTTTGTCTAATTATCTAAACATTTAATAAATACATATTGATAAAATCAAGTATTA
* *
16599823 TTAATGCTATTGAATGGTTATTATTGCATAATTAAATAACTTGCATTACTTAAAATCTGATTGGT
456 TTAATGCTATTGAATGGTTATTATTGCAAAAGTAAATAACTTGCATTACTTAAAATCTGATTGGT
* * ** * * *
16599888 GTTGGATTTCGAGTTTAAGAATTTGATTCGTGTCTAAATTTAATTGATGTTTAATGTAATTATTT
521 GTTAGATTTCGAGTTTAAAAATTTGATTCGACTCTAAATTTAATTGATGGTTAATGTAATAAATT
16599953 TTTTGTTGGTAACTCTCTTGTCTATTTAACAATTCATATTTA
586 TTTTGTTGGTAACTCTCTTGTCTATTTAACAATTCATATTTA
* *
16599995 AGCATATGATATACCGTTGTAAAGGTCTCATGGAGTAGAATGTGAAGCCATAATTTTATGATTCA
1 AGCATATGATATACAGTTGTAAAGGTCTCATGGAGTAGAATATGAAGCCATAATTTTATGATTCA
16600060 ACTCTCCACCTTTACCTATTGAGAATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCAAACAA
66 ACTCTCCACCTTTACCTATTGAGAATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCAAACAA
* *
16600125 CGGCTATGTTGAAAGCTTGTGGCTAGCAAAGATGTTTGCCAAGCAGGTGGATTGTCTT-TAGAAG
131 CGGCTATGTTCAAACCTTGTGGCTAGCAAAGATGTTTGCCAAGCAGGTGGATTGT-TTCTAGAAG
* ** * * *
16600189 CGGGTGGTTTAGGTGTTTCAAGAAGACG-CGTGCAGTCTAAGTCTCTTGTTGAGATAAAGGGTCA
195 CGGGTGGTTTAGGTGTTTCAAGAACACGTAATGCAGTCCAAGTCTCTTGCTAAGATAAAGGGTCA
* * * * *
16600253 AACGGAGAGTAAAAATTTGGGAGAGGCAGTCACCACGACGTTCGAGTAGAACCGAATAATTGGTC
260 AACGGAGAGTAAAAATCTGGGAGAGACAGTCACCAAGACATTCGAGTAGAACAGAATAATTGGTC
* * *
16600318 ATGATTATGTCTCAGATTCCTTGTCACGCTGGCACGTGTCCACCTGTAACAGAAGTATAATAATT
325 ACGATTATGTCTCAGATGCCTTGTCACGCTAGCACGTGTCCACCTGTAACAGAAGTATAATAATT
* * * *
16600383 TACGATATATTTTTTTGTTTGATTATCTAACCATTTAATAAATACATATTGATCAAATCAAGTAT
390 TACGATATA-TTTTTTGTCTAATTATCTAAACATTTAATAAATACATATTGATAAAATCAAGTAT
* * **
16600448 TATTAATGCTATTTAATGGTTATTATTGTAAAAGTAAATAACTTGTGTTACTTAAAATCTGATTG
454 TATTAATGCTATTGAATGGTTATTATTGCAAAAGTAAATAACTTGCATTACTTAAAATCTGATTG
*
16600513 GTGTTAGATTGT-GGGTTTAAAAATTTGATTCGACTCTAAATTTAATTGATGGTTAATGTAATAA
519 GTGTTAGATT-TCGAGTTTAAAAATTTGATTCGACTCTAAATTTAATTGATGGTTAATGTAATAA
16600577 ATTTTTTGTTGGTAACT
583 ATTTTTTGTTGGTAACT
16600594 TTCATTTTTA
Statistics
Matches: 536, Mismatches: 60, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
626 148 0.28
627 385 0.72
628 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (627 bp):
AGCATATGATATACAGTTGTAAAGGTCTCATGGAGTAGAATATGAAGCCATAATTTTATGATTCA
ACTCTCCACCTTTACCTATTGAGAATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCAAACAA
CGGCTATGTTCAAACCTTGTGGCTAGCAAAGATGTTTGCCAAGCAGGTGGATTGTTTCTAGAAGC
GGGTGGTTTAGGTGTTTCAAGAACACGTAATGCAGTCCAAGTCTCTTGCTAAGATAAAGGGTCAA
ACGGAGAGTAAAAATCTGGGAGAGACAGTCACCAAGACATTCGAGTAGAACAGAATAATTGGTCA
CGATTATGTCTCAGATGCCTTGTCACGCTAGCACGTGTCCACCTGTAACAGAAGTATAATAATTT
ACGATATATTTTTTGTCTAATTATCTAAACATTTAATAAATACATATTGATAAAATCAAGTATTA
TTAATGCTATTGAATGGTTATTATTGCAAAAGTAAATAACTTGCATTACTTAAAATCTGATTGGT
GTTAGATTTCGAGTTTAAAAATTTGATTCGACTCTAAATTTAATTGATGGTTAATGTAATAAATT
TTTTGTTGGTAACTCTCTTGTCTATTTAACAATTCATATTTA
Found at i:16601873 original size:938 final size:920
Alignment explanation
Indices: 16600003--16605357 Score: 3933
Period size: 973 Copynumber: 5.6 Consensus size: 920
16599993 TAAGCATATG
* * * *
16600003 ATATACCGTTGTAAAGGTCTCATGGAGTAGAATGTGAAGCCATAATTTTATGATTCAACTCTCCA
1 ATATATCGTTGTAAAGGTCTCATGGAGTAGAATATGAAACCATAATTTTATGATTCAACTCTTCA
* *
16600068 CCTTTACCTATTG-AGAATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCAAACAACGGCTAT
66 CCTTTACCTATTGCA-AATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCCAACAACGGGTAT
* * * *
16600132 GTTGAAAGCTTGTGGCTAGCAAAGATGTTTGCCAAGCAGGTGGATTGTCTTTAGAAGCGGGTGGT
130 GTTCAAAGGTTGTGGCTAGCAAAGATGTTTACCAAGCAGGTGGATTGTCTCTAGAAGCGGGTGGT
** * * * *
16600197 TTAGGTGTTTCAAGAAGACGCGTGCAGTCTAAGTCTCTTGTTGAGATAAAGGGTCAAACGGAGAG
195 TTAGGTGTTTCAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGGGTCAAATGGAGAG
* * * * * *
16600262 TAAAAATTTGGGAGAGGCAGTCACCACGACGTTCGAGTAGAACCGAATAATTGGTCATGATTATG
260 TAAGAATTTGGGAGAGACAGTCACCAAGACGTTCGAGTAGAGCCGAATGATTGGTCATGATTATT
** * **
16600327 TCTCAGATTCCTTGTCACGCTGGCACGTGTCCACCTGTAA-CAGAAGTATAATAATTTACGATAT
325 TCTCAGATGGCTTGTCACGCTGGCACGTGTCCACCT-AAAGTGGAAGTATAATAATTTACGAT-T
* *
16600391 ATTTTTTTGTTTGATTATCTAACCATTTAATAAATACATATTGATCAAATCA-AGTATTATTAAT
388 ATTTTTTTGTCTGTTTATCTAACCATTTAATAAATACATATTGATCAAAT-AGAGTATTATTAAT
* * * *
16600455 GCTATTTAATGGTTATTATTGTAAAAGTAAATAACTTGTGTTACTTAAAATCTGATTGGTGTTAG
452 GCTATTTAATGGTTATTA-TGAAAAATTAAATAACTTGCGTTACTTAAAATCTGATTGGTGTTGG
* * * * * *
16600520 ATTGT-GGGTTTAAAAATTTGATTCGACTCTAAATTTAATTGATGGTTAATGTAATAAATTTTTT
516 ATT-TCGGTTTTAAGAATTTGATTCGAGTCTAAATTTAATTGATGTTTAATGTAATTAATTTGTT
* * * * * * *
16600584 GTTGGTAACTTTCATTTTTATTTCATGGTTTATATTTAATGCACAAATGATGCCTTTTTCTATCA
580 ATTGGTAGCTTTCATATTTATTTCACGGTTTATATTCAATGCACAAACGATGTCTTTTTCTATCA
* *
16600649 ACGAAACTATGAAAAAAATAAGAAGCCTATTTTTTCATGTTGGGCTCAAATATCCACCAATTTTG
645 ACAAAACTATGAAAAAAATAAGAAGCCTATTTTTTCATGTTGGGCTAAAATATCCACCAATTTTG
* *
16600714 GGCATGACCACATTCTAGACATTTTGCGTCGCTTCCTTGCACCCAAGGCAAGGAACCATACTTAG
710 GGCATGACCACATGCTAGACATTTTGCGTCGCTTACTTGCACCCAAGGCAAGGAACCATACTTAG
* **
16600779 TCATTCAGTCATCTTTCAAAAGGTTTTCATATATAAACACATCCCACACTTGGTATTTAACCAAT
775 TCATTCAATCATCTTTCAAAAGGTTCCCATATATAAACACATCCCACACTTGGTATTTAACCAAT
* * *
16600844 GTGGGATGTAAGCTTTTCTTTTCCTTAACAAATATTTTTAAGTAGCTTACATTGAGCATCAATTT
840 GTGGCATCTAAGCTTTTCTTTTCCTCAACAAATA--TTT-A-TA-C-T-CA-T-AG--------T
*
16600909 CTCATTCATCACTCAACCATTTTGAG-C-T-T-A-T-T
888 -TCATGCAT--CT-AA-CATTTTGAGTCATCTCATTAT
* *
16600941 ATATATCGTTGTAAAGGTCTCATGGAGTAGGATATGAAACCATAATTTTTTGATTCAACTCTTCA
1 ATATATCGTTGTAAAGGTCTCATGGAGTAGAATATGAAACCATAATTTTATGATTCAACTCTTCA
* *
16601006 CATTTACCTATTGCAAATATGCCTCAAAGCTCCCATAAAATGCAATTTTTCCAACAACGGGTATG
66 CCTTTACCTATTGCAAATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCCAACAACGGGTATG
* * *
16601071 TTCAAAGGTTGTGGCTAGCAAGGATGTTTACCAAGTAGGTGGATTGTCTCTAGAAGTGGGTGGTT
131 TTCAAAGGTTGTGGCTAGCAAAGATGTTTACCAAGCAGGTGGATTGTCTCTAGAAGCGGGTGGTT
** * * * *
16601136 TAGGCATTTCAGGAAGACGTATACAGTCCAACTCTCTTGCTGAGATAGAGGGTCAAATGGAGAGT
196 TAGGTGTTTCAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGGGTCAAATGGAGAGT
*
16601201 AAGAATTTGGGAGAGACAGTCACCAAGACGTTCGAGTAGAGCCGAATGATTGGTCACGATTATTT
261 AAGAATTTGGGAGAGACAGTCACCAAGACGTTCGAGTAGAGCCGAATGATTGGTCATGATTATTT
* * * *
16601266 CTCAGCTGGCTTGTCACGTTGGCACGTGTCCACCTAAAGTGGAAGTATAATATTTTACGGCTTAT
326 CTCAGATGGCTTGTCACGCTGGCACGTGTCCACCTAAAGTGGAAGTATAATAATTTAC-GATTAT
16601331 TTTTTTGTCTGTTTAT-TAACCATTTAATAAATACATATTGATCAAATAGAGTATTATTAATGCT
390 TTTTTTGTCTGTTTATCTAACCATTTAATAAATACATATTGATCAAATAGAGTATTATTAATGCT
*
16601395 ATTTAATGGTTATTATGGAAAAATTAAATAACTTGCGTTACTTAAAATCTGATTGATGTTGGATT
455 ATTTAATGGTTATTAT-GAAAAATTAAATAACTTGCGTTACTTAAAATCTGATTGGTGTTGGATT
*
16601460 TCAGTTTTAAGAATTTGATTCGAGTCTAAATTTAATTGATGTTTAATGTAATTAATTTGTTATTG
519 TCGGTTTTAAGAATTTGATTCGAGTCTAAATTTAATTGATGTTTAATGTAATTAATTTGTTATTG
* *
16601525 GTAGCTTTCATGTTTATTTCACGGTTTATATTCAATGCACAAACGATGTCTTTTTCTATCAGCAA
584 GTAGCTTTCATATTTATTTCACGGTTTATATTCAATGCACAAACGATGTCTTTTTCTATCAACAA
* * * *
16601590 AACTTTGAAAAAACATAATAAGCC-ACTTTTTTCGTGTTGGGCTAAAATATCTGCAGGCCGATTT
649 AACTATGAAAAAA-ATAAGAAGCCTA-TTTTTTCATGTTGGGCTAAAATATC--CA--CCAATTT
** * *
16601654 TGGGCAT-TTCACGTCGCTCATGTCATTTTGGTACGCCCCAACTCTGACAGGTATAAACTTGCAC
708 TGGGCATGACCACAT-GCT-A-GACATTTT-G--CG-------TC-G-C---T-T--ACTTGCA-
* **
16601718 CCTCTTGCGTGCGAGGCAAGGTTCCATACTTAGTCATTCAATCATCTTTCAAAAGGGTTCCCATA
751 ---C---C---CAAGGCAAGGAACCATACTTAGTCATTCAATCATCTTTCAAAA-GGTTCCCATA
*
16601783 TATAAACACATCTCACACTTGGGT-TTTAACCAATGTGGCATCTAAGCTTTTCTTTTCCTCAACA
806 TATAAACACATCCCACACTT-GGTATTTAACCAATGTGGCATCTAAGCTTTTCTTTTCCTCAACA
* * * * *
16601847 AATATTTCCAAGTAGCTTA-ATTTGA-GCATC--A-ATTTCTCATTCATCACTCAACCATTTTGA
870 AATATTT---A-TA-CTCATAGTTCATGCATCTAACATTT-TGAGTCAT--CT----CA--TT--
16601907 GCAT
919 --AT
*
16601911 ATGATATACCGTTGTAAAGGTCTCATGAAGTAGAATATGAAACCATAATTTTATGATTCAACTCT
1 AT-ATAT--CGTTGTAAAGGTCTCATGGAGTAGAATATGAAACCATAATTTTATGATTCAACTCT
* * **
16601976 TCACCTTTACCTATTGCGAATATGCCTCAAAGTTCCCATAAAATGTAATTTTTCCAACAACTAGT
63 TCACCTTTACCTATTGCAAATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCCAACAACGGGT
* * * * *
16602041 ATGTTCAAAGGTTGTGGCTAGCAATGATGTTTTCCAAGCAAGTGGATTGTCTCTAAAAGCGGATG
128 ATGTTCAAAGGTTGTGGCTAGCAAAGATGTTTACCAAGCAGGTGGATTGTCTCTAGAAGCGGGTG
16602106 GTTTAGGTGTTTCAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGGGTCAAATGGAG
193 GTTTAGGTGTTTCAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGGGTCAAATGGAG
* ** * * * * * * **
16602171 AGTAAGAATCTGATAAAGATAGTTACCAAGGCATTCAAGTAGAGCTTAATGATTGGTCATGATTA
258 AGTAAGAATTTGGGAGAGACAGTCACCAAGACGTTCGAGTAGAGCCGAATGATTGGTCATGATTA
* * * * *
16602236 TTTCTCAGATGGCTTGTCATGCTGACACGTGTCCACC-AGTAGTGGAAGTATAATAATTTATAGT
323 TTTCTCAGATGGCTTGTCACGCTGGCACGTGTCCACCTA-AAGTGGAAGTATAATAATTTA-CGA
* * * *
16602300 TTA-TTTTTTATCT-TATTATCTAATC-TTGTAATAAATATATATTGATCAAATCGAGTATTATT
386 TTATTTTTTTGTCTGT-TTATCTAACCATT-TAATAAATACATATTGATCAAATAGAGTATTATT
*
16602362 AATGCTATTTAATGGTTATTATGACAAAATTAAATAACTTGCATTACTTAAAATCTGATTGGTGT
449 AATGCTATTTAATGGTTATTATGA-AAAATTAAATAACTTGCGTTACTTAAAATCTGATTGGTGT
*
16602427 TGGATTTCGGTTTTAAGAATTTGATTCGAGTATAAATTTAATTGATGTTTAATGTAATTAATTTG
513 TGGATTTCGGTTTTAAGAATTTGATTCGAGTCTAAATTTAATTGATGTTTAATGTAATTAATTTG
* *
16602492 TTATTTGTAGCTTTCATATTTATTTCACGGTTCATATTCAATGCACAAACGATGTCTTTTTCTAT
578 TTATTGGTAGCTTTCATATTTATTTCACGGTTTATATTCAATGCACAAACGATGTCTTTTTCTAT
* * * *
16602557 C--C---AC---G-------T----CG-CTCA---TGTC--GTTCGGG-T---GT-GCC-CC-A-
643 CAACAAAACTATGAAAAAAATAAGAAGCCT-ATTTTTTCATGTT-GGGCTAAAATATCCACCAAT
* * * * * * **
16602589 -----GC-T--CCGACAGGTATAGAC--TTT-C-AC-CCT-CTTGCGCGCAAGGCAAGGTTCCAT
706 TTTGGGCATGACC-ACATG-CTAGACATTTTGCGTCGCTTACTTGCACCCAAGGCAAGGAACCAT
** *
16602640 ACAAAGTCATTCAATCATCTTTCAAAAGGGTTCCCATATATAAACACATCTCACACTTGGGT-TT
769 ACTTAGTCATTCAATCATCTTTCAAAA-GGTTCCCATATATAAACACATCCCACACTT-GGTATT
* * * * * *
16602704 TAACCGATGTGGGATCTAAGCTTTTCTTTTCCTCAACAAATATTTATAAGTAGCTTACTTTGA-G
832 TAACCAATGTGGCATCTAAGCTTTTCTTTTCCTCAACAAATATTTAT-ACT--CATA-GTTCATG
* *
16602768 CATC--A-ATTTCTCATTCATTACTCAACCATTTTGAGCAT
893 CATCTAACATTT-TGAGTCA-T-CT----CA--TT----AT
* *
16602806 ATGATATACCGTTGGAAAGGTCTCATGGAGAAGAATATGAAACCATAATTTTATGATTCAACTCT
1 AT-ATAT--CGTTGTAAAGGTCTCATGGAGTAGAATATGAAACCATAATTTTATGATTCAACTCT
* *
16602871 TCACCTTTACCTATTG-AGAATATGCCTCAAAGTTCCCATAAAATGTAATTTTTCCAACAACTGG
63 TCACCTTTACCTATTGCA-AATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCCAACAACGGG
* * * *
16602935 TATGTTCAAAGGTTGTGGCTAGCAAGGATGTTTGCCAAGCAAGTGGATTGTCTCTAGAAGCGGAT
127 TATGTTCAAAGGTTGTGGCTAGCAAAGATGTTTACCAAGCAGGTGGATTGTCTCTAGAAGCGGGT
* *
16603000 AGTTTAGGTGTTTCAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGAGTCAAATGGA
192 GGTTTAGGTGTTTCAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGGGTCAAATGGA
* * * * * *
16603065 GAGTAAGAATCTGAGAGAGACAATTACTAATG-CGTTCGAGTAGAGCTGAATGATTGGTCATGAT
257 GAGTAAGAATTTGGGAGAGACAGTCACCAA-GACGTTCGAGTAGAGCCGAATGATTGGTCATGAT
* * * *
16603129 TATATT-TCAGATGGCTTG-CACTCTGACACGTGTCCACCTATAGTGGAAGTATAATAATTTATA
321 TAT-TTCTCAGATGGCTTGTCACGCTGGCACGTGTCCACCTAAAGTGGAAGTATAATAATTTA-C
* * *
16603192 GTTTA-TTTTTTGTCT-TATTATCTAATC-TTGTAATAAATACATATTGATCAAATCGAGTATTA
384 GATTATTTTTTTGTCTGT-TTATCTAACCATT-TAATAAATACATATTGATCAAATAGAGTATTA
* * * * *
16603254 TTAATGTTATTCAATGGTTATTATTGCAGAATTAAATAACTTGCGTTACTTAAATTCTGATTGGT
447 TTAATGCTATTTAATGGTTATTA-TGAAAAATTAAATAACTTGCGTTACTTAAAATCTGATTGGT
** * * * *
16603319 GCAGGATTTTGGGTTTAAGAATTTGATTCAAGTCTAAATTTAATTGATGTTTAATGTAATTATTT
511 GTTGGATTTCGGTTTTAAGAATTTGATTCGAGTCTAAATTTAATTGATGTTTAATGTAATTA-AT
* * * *
16603384 TTTTTGTTGGTAGCTTTCATGTCTGTTTCACGATTCATATTCAATGCACATTACACGATTCATAT
575 TTGTTATT-G--G---T-A-G-C--TTT--C-A-T-AT-TT--AT-----TT-CACGGTTTATAT
* * * * *
16603449 TCAATGCACAAACGATGCCTTTTCCTATCAACAAAACTTTG--AAAATTAAGGAGCCTATTTTTT
615 TCAATGCACAAACGATGTCTTTTTCTATCAACAAAACTATGAAAAAAATAAGAAGCCTATTTTTT
* *
16603512 CGTGTTGGGCTAAAATATCCGCAGGCCAATTTTAGGAATTACCAGTTCAAACATTCCAAACATTT
680 CATGTTGGGCTAAAATAT-C-CA--CCAATTTT-GG--------G------CA-T---GAC----
* *
16603577 CACATCGCTA-ACGTGTGCTAGTGCGCCCCAAACCCCGACAGGTATGGACTTGCACCCATTTACG
718 CACAT-GCTAGACAT-T--T--TGCG---------TCG-C---T-T--ACTTGCACCCA---A-G
* *** * * *
16603641 CGCGAGGCAAGGTTCCATACTAATTCATTCAATTATCTTTCAAAAGGGTTCCCATATATAAACAC
757 -GCAAGG-AACCAT----ACTTAGTCATTCAATCATCTTTCAAAA-GGTTCCCATATATAAACAC
* **** * *** *
16603706 ATCTCAC-CCAAATATTT--CCAA----G----T-AGC-TTGC-TTTGAGCATC--A-A-TT-T-
815 ATCCCACACTTGGTATTTAACCAATGTGGCATCTAAGCTTTTCTTTTCCTCAACAAATATTTATA
* *
16603751 CTC---GTTCAT-TA-CTCAACCATTTTGAG-CA--T-A-T-G
880 CTCATAGTTCATGCATCT-AA-CATTTTGAGTCATCTCATTAT
* * * *
16603783 ATATACCGTTGTAAAGGACTCATGGAGTAGAATATGAAATCATAATTTTATGATTCAGCT-TTCC
1 ATATATCGTTGTAAAGGTCTCATGGAGTAGAATATGAAACCATAATTTTATGATTCAACTCTT-C
* * * *
16603847 ACCTTTACCTATTG-AGAATATGCCTCAAAGTTACCACACAATGTAATTTTTCCAACAACGGGTA
65 ACCTTTACCTATTGCA-AATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCCAACAACGGGTA
* * * * * * *
16603911 TGTTCAAAGCTTGTGGCTAGCAAGGATGTTTGCCAAGCAGGTGGATTATCTCTAGCATCGTGTGG
129 TGTTCAAAGGTTGTGGCTAGCAAAGATGTTTACCAAGCAGGTGGATTGTCTCTAGAAGCGGGTGG
* * **
16603976 TTTAGGTGTTTCAAGAAGATGCATGCAGTCCAAGTCTCTTGCTGAGATAGAGGGTCAAACAGAGA
194 TTTAGGTGTTTCAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGGGTCAAATGGAGA
* * * * *
16604041 GTAAGAATCTAGGAGAGACAGTCACCATTG-TGTTCGAGTAGAGCCGAATGATTGGTCACGATTA
259 GTAAGAATTTGGGAGAGACAGTCACCA-AGACGTTCGAGTAGAGCCGAATGATTGGTCATGATTA
* ** *
16604105 TTTCTCAGATGGCTTGTCATGCTGGCACGTGTCCACCTGTAGTGGAAGTATAATAATTTATGATT
323 TTTCTCAGATGGCTTGTCACGCTGGCACGTGTCCACCTAAAGTGGAAGTATAATAATTTACGA-T
* * * * * *
16604170 TATTTTTTTGTTTGATTATCTAACCTTTTAATATATACGTATTAATCAAATCA-AGTATTATTAA
387 TATTTTTTTGTCTGTTTATCTAACCATTTAATAAATACATATTGATCAAAT-AGAGTATTATTAA
* * *
16604234 TGCTATTTAATGGTTATTATTGCAAAAGTAAATAACTTGCGTTACTTAAAATCTGATTGGTGTTC
451 TGCTATTTAATGGTTATTA-TGAAAAATTAAATAACTTGCGTTACTTAAAATCTGATTGGTGTTG
* * * * *
16604299 GATTTCGGGTTTAAGAATTTGATTCGAGTCAAAATTTATTTGATGTTTAATGTAATCAATTTTTT
515 GATTTCGGTTTTAAGAATTTGATTCGAGTCTAAATTTAATTGATGTTTAATGTAATTAATTTGTT
** * ** * * * *
16604364 GCTAGTAATTTTCATGTTTATTTCACGGTTCATATTCAATGCACAAACGATGCCTGTTTCTATCA
580 ATTGGTAGCTTTCATATTTATTTCACGGTTTATATTCAATGCACAAACGATGTCTTTTTCTATCA
* * * * **
16604429 GCGAAACTTTGAAAAAAA-AAG-AGCCTATTTTTTCGTGTTGAGCGCCCATTTTGGGAAT-TACC
645 ACAAAACTATGAAAAAAATAAGAAGCCTATTTTTTCATGTTG-G-G--C----T-AAAATAT-CC
* * * * ***
16604491 AGTTCAAACATTCTGGACATTTATGATCGCTCACATTGTGCTGGTGCACTCCAACCCTGACAGGT
700 A---C-CA-ATTTTGGGC----ATGA---C-CACA---TGCT--AG-A---C-ATTTTG-C--GT
* * * ** * * *
16604556 ACAGACTTGCACCCCTTTGCGCACGAGGCAAGGTTCCATACTTATTCATTCAATTATCTTTTAAA
739 -C-G-CTT--A---C-TTGCACCCAAGGCAAGGAACCATACTTAGTCATTCAATCATCTTTCAAA
* * * *
16604621 AGGGTTCCCATATATAAACATATCTCACACTTGGTATTTAACCAATGTGGGATCTAAGGTTTT-T
795 A-GGTTCCCATATATAAACACATCCCACACTTGGTATTTAACCAATGTGGCATCTAAGCTTTTCT
* * * * * *
16604685 TTTCTTCAACAAATATTTCCAAGTAGCT--TACTTTAAGCATC--A-ATTTCTCATTCATCACTC
859 TTTCCTCAACAAATATTT---A-TA-CTCATAGTTCATGCATCTAACATTT-TGAGTCAT--CT-
16604745 AACCATTTTGAACAT
915 ---CA--TT----AT
* * * *
16604760 ATAATATACCATTGTAAAGGTCTCATGGAGTAGAATTTGAAACTATAATTTTATGATTCAACTCG
1 AT-ATAT--CGTTGTAAAGGTCTCATGGAGTAGAATATGAAACCATAATTTTATGATTCAACTCT
* * * * * *
16604825 CCACATTTACCTATTG-AGAATATGCCTCAAAGTTCTCATAAAGTGTAATTTTTCCAACAACGGT
63 TCACCTTTACCTATTGCA-AATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCCAACAACGGG
* * * ** * * *
16604889 TATGTTTAAAGCTTGTGGCTAGCAAAGATGTTTGCTGAGCAGGTGGAGTGTCTCTAAAAGCGGGA
127 TATGTTCAAAGGTTGTGGCTAGCAAAGATGTTTACCAAGCAGGTGGATTGTCTCTAGAAGCGGGT
* * * **
16604954 GGTTTAGGTGTTTCAAGAAGACGCATGTAGTCCAAGTCTCTTGCT-ATGATAGAGGGTCTAACAG
192 GGTTTAGGTGTTTCAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGA-GATAGAGGGTCAAATGG
* * * ** * * *
16605018 AGAGTAAGAATCTGAGAGAGACAGTTACCAAGGTGTTCGAGCAGAGCCAAAGGATTGGTCATGAT
256 AGAGTAAGAATTTGGGAGAGACAGTCACCAAGACGTTCGAGTAGAGCCGAATGATTGGTCATGAT
* * ** *
16605083 TATTTCTCAGATGGCTTGTCACGCTGACACGTGTCTACCTGTAGTGGAAGTATAATAATTTACGG
321 TATTTCTCAGATGGCTTGTCACGCTGGCACGTGTCCACCTAAAGTGGAAGTATAATAATTTACGA
* *
16605148 TT-TATTTTTTGTCT-TATTATCTAATC-TTGTAATAAATATATATTGATCAAATCA-AGTATTA
386 TTAT-TTTTTTGTCTGT-TTATCTAACCATT-TAATAAATACATATTGATCAAAT-AGAGTATTA
* * * * *
16605209 TTAATGTTATTCAATGGTTATTATTGCAGAATTAAATAACTTGCGTTATTTAAAATCTGATTGGT
447 TTAATGCTATTTAATGGTTATTA-TGAAAAATTAAATAACTTGCGTTACTTAAAATCTGATTGGT
** * * *
16605274 GTTGGATTTCGAATTTAAGAATTTGATTCGAGCCTAAATTTAATTGATGTTTGATGTAATTATTT
511 GTTGGATTTCGGTTTTAAGAATTTGATTCGAGTCTAAATTTAATTGATGTTTAATGTAATTAATT
* * *
16605339 TTTTGTGGGTAGCTTTCAT
576 TGTTATTGGTAGCTTTCAT
16605358 GTCTATTTAA
Statistics
Matches: 3653, Mismatches: 429, Indels: 629
0.78 0.09 0.13
Matches are distributed among these distances:
891 2 0.00
892 2 0.00
894 214 0.06
895 489 0.13
896 4 0.00
898 1 0.00
901 2 0.00
902 1 0.00
903 1 0.00
904 1 0.00
905 5 0.00
906 3 0.00
908 2 0.00
909 1 0.00
910 1 0.00
911 2 0.00
912 3 0.00
914 2 0.00
915 1 0.00
919 2 0.00
920 38 0.01
922 1 0.00
923 1 0.00
925 2 0.00
927 3 0.00
928 1 0.00
929 2 0.00
930 3 0.00
931 4 0.00
932 2 0.00
933 1 0.00
936 54 0.01
937 239 0.07
938 387 0.11
939 9 0.00
940 6 0.00
941 12 0.00
942 24 0.01
943 4 0.00
944 8 0.00
945 12 0.00
946 9 0.00
947 7 0.00
948 10 0.00
949 12 0.00
950 72 0.02
951 15 0.00
952 10 0.00
953 6 0.00
954 6 0.00
955 1 0.00
956 4 0.00
957 4 0.00
958 14 0.00
959 12 0.00
960 12 0.00
961 4 0.00
962 9 0.00
963 1 0.00
964 4 0.00
965 2 0.00
966 1 0.00
967 1 0.00
968 4 0.00
969 3 0.00
970 3 0.00
971 10 0.00
972 60 0.02
973 640 0.18
974 298 0.08
975 51 0.01
976 162 0.04
977 6 0.00
978 6 0.00
979 180 0.05
980 333 0.09
982 3 0.00
983 5 0.00
984 2 0.00
985 2 0.00
987 1 0.00
989 1 0.00
990 2 0.00
991 1 0.00
992 4 0.00
994 3 0.00
995 2 0.00
996 5 0.00
998 1 0.00
1000 2 0.00
1001 2 0.00
1002 2 0.00
1003 1 0.00
1005 6 0.00
1006 4 0.00
1007 3 0.00
1008 1 0.00
1009 8 0.00
1012 2 0.00
1013 1 0.00
1014 5 0.00
1015 1 0.00
1016 3 0.00
1017 1 0.00
1018 4 0.00
1019 51 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (920 bp):
ATATATCGTTGTAAAGGTCTCATGGAGTAGAATATGAAACCATAATTTTATGATTCAACTCTTCA
CCTTTACCTATTGCAAATATGCCTCAAAGTTCCCATAAAATGCAATTTTTCCAACAACGGGTATG
TTCAAAGGTTGTGGCTAGCAAAGATGTTTACCAAGCAGGTGGATTGTCTCTAGAAGCGGGTGGTT
TAGGTGTTTCAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGGGTCAAATGGAGAGT
AAGAATTTGGGAGAGACAGTCACCAAGACGTTCGAGTAGAGCCGAATGATTGGTCATGATTATTT
CTCAGATGGCTTGTCACGCTGGCACGTGTCCACCTAAAGTGGAAGTATAATAATTTACGATTATT
TTTTTGTCTGTTTATCTAACCATTTAATAAATACATATTGATCAAATAGAGTATTATTAATGCTA
TTTAATGGTTATTATGAAAAATTAAATAACTTGCGTTACTTAAAATCTGATTGGTGTTGGATTTC
GGTTTTAAGAATTTGATTCGAGTCTAAATTTAATTGATGTTTAATGTAATTAATTTGTTATTGGT
AGCTTTCATATTTATTTCACGGTTTATATTCAATGCACAAACGATGTCTTTTTCTATCAACAAAA
CTATGAAAAAAATAAGAAGCCTATTTTTTCATGTTGGGCTAAAATATCCACCAATTTTGGGCATG
ACCACATGCTAGACATTTTGCGTCGCTTACTTGCACCCAAGGCAAGGAACCATACTTAGTCATTC
AATCATCTTTCAAAAGGTTCCCATATATAAACACATCCCACACTTGGTATTTAACCAATGTGGCA
TCTAAGCTTTTCTTTTCCTCAACAAATATTTATACTCATAGTTCATGCATCTAACATTTTGAGTC
ATCTCATTAT
Found at i:16603399 original size:895 final size:895
Alignment explanation
Indices: 16601663--16603433 Score: 2933
Period size: 895 Copynumber: 2.0 Consensus size: 895
16601653 TTGGGCATTT
** * *
16601663 CACGTCGCTCATGTCATTTTGGTACGCCCCAACTCTGACAGGTATAAACTTGCACCCTCTTGCGT
1 CACGTCGCTCATGTCATTCGGGTACGCCCCAACTCCGACAGGTATAAACTTGCACCCTCTTGCGC
* **
16601728 GCGAGGCAAGGTTCCATACTTAGTCATTCAATCATCTTTCAAAAGGGTTCCCATATATAAACACA
66 GCAAGGCAAGGTTCCATACAAAGTCATTCAATCATCTTTCAAAAGGGTTCCCATATATAAACACA
*
16601793 TCTCACACTTGGGTTTTAACCAATGTGGCATCTAAGCTTTTCTTTTCCTCAACAAATATTTCCAA
131 TCTCACACTTGGGTTTTAACCAATGTGGCATCTAAGCTTTTCTTTTCCTCAACAAATATTTACAA
16601858 GTAGCTTAATTTGAGCATCAATTTCTCATTCATCACTCAACCATTTTGAGCATATGATATACCGT
196 GTAGCTTAATTTGAGCATCAATTTCTCATTCATCACTCAACCATTTTGAGCATATGATATACCGT
* *
16601923 TGTAAAGGTCTCATGAAGTAGAATATGAAACCATAATTTTATGATTCAACTCTTCACCTTTACCT
261 TGGAAAGGTCTCATGAAGAAGAATATGAAACCATAATTTTATGATTCAACTCTTCACCTTTACCT
*
16601988 ATTGCGAATATGCCTCAAAGTTCCCATAAAATGTAATTTTTCCAACAACTAGTATGTTCAAAGGT
326 ATTGAGAATATGCCTCAAAGTTCCCATAAAATGTAATTTTTCCAACAACTAGTATGTTCAAAGGT
* * *
16602053 TGTGGCTAGCAATGATGTTTTCCAAGCAAGTGGATTGTCTCTAAAAGCGGATGGTTTAGGTGTTT
391 TGTGGCTAGCAAGGATGTTTGCCAAGCAAGTGGATTGTCTCTAAAAGCGGATAGTTTAGGTGTTT
*
16602118 CAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGGGTCAAATGGAGAGTAAGAATCTG
456 CAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGAGTCAAATGGAGAGTAAGAATCTG
* * * *
16602183 ATAAAGATAGTTACCAAGGCATTCAAGTAGAGCTTAATGATTGGTCATGATTATTTCTCAGATGG
521 AGAAAGACAATTACCAAGGCATTCAAGTAGAGCTGAATGATTGGTCATGATTATTTCTCAGATGG
16602248 CTTGTCATGCTGACACGTGTCCACCAGTAGTGGAAGTATAATAATTTATAGTTTATTTTTTATCT
586 CTTGTCATGCTGACACGTGTCCACCAGTAGTGGAAGTATAATAATTTATAGTTTATTTTTTATCT
* *
16602313 TATTATCTAATCTTGTAATAAATATATATTGATCAAATCGAGTATTATTAATGCTATTTAATGGT
651 TATTATCTAATCTTGTAATAAATACATATTGATCAAATCGAGTATTATTAATGCTATTCAATGGT
** *
16602378 TATTATGACAAAATTAAATAACTTGCATTACTTAAAATCTGATTGGTGTTGGATTTCGGTTTTAA
716 TATTATGACAAAATTAAATAACTTGCATTACTTAAAATCTGATTGGTGCAGGATTTCGGGTTTAA
*
16602443 GAATTTGATTCGAGTATAAATTTAATTGATGTTTAATGTAATTAATTTGTTATTTGTAGCTTTCA
781 GAATTTGATTCAAGTATAAATTTAATTGATGTTTAATGTAATTAATTTGTTATTTGTAGCTTTCA
* *
16602508 TATTTATTTCACGGTTCATATTCAATGCACAAACGATGTCTTTTTCTATC
846 TATCTATTTCACGATTCATATTCAATGCACAAACGATGTCTTTTTCTATC
* ** * * *
16602558 CACGTCGCTCATGTCGTTCGGGTGTGCCCCAGCTCCGACAGGTATAGACTTTCACCCTCTTGCGC
1 CACGTCGCTCATGTCATTCGGGTACGCCCCAACTCCGACAGGTATAAACTTGCACCCTCTTGCGC
16602623 GCAAGGCAAGGTTCCATACAAAGTCATTCAATCATCTTTCAAAAGGGTTCCCATATATAAACACA
66 GCAAGGCAAGGTTCCATACAAAGTCATTCAATCATCTTTCAAAAGGGTTCCCATATATAAACACA
* * *
16602688 TCTCACACTTGGGTTTTAACCGATGTGGGATCTAAGCTTTTCTTTTCCTCAACAAATATTTATAA
131 TCTCACACTTGGGTTTTAACCAATGTGGCATCTAAGCTTTTCTTTTCCTCAACAAATATTTACAA
* *
16602753 GTAGCTTACTTTGAGCATCAATTTCTCATTCATTACTCAACCATTTTGAGCATATGATATACCGT
196 GTAGCTTAATTTGAGCATCAATTTCTCATTCATCACTCAACCATTTTGAGCATATGATATACCGT
*
16602818 TGGAAAGGTCTCATGGAGAAGAATATGAAACCATAATTTTATGATTCAACTCTTCACCTTTACCT
261 TGGAAAGGTCTCATGAAGAAGAATATGAAACCATAATTTTATGATTCAACTCTTCACCTTTACCT
*
16602883 ATTGAGAATATGCCTCAAAGTTCCCATAAAATGTAATTTTTCCAACAACTGGTATGTTCAAAGGT
326 ATTGAGAATATGCCTCAAAGTTCCCATAAAATGTAATTTTTCCAACAACTAGTATGTTCAAAGGT
*
16602948 TGTGGCTAGCAAGGATGTTTGCCAAGCAAGTGGATTGTCTCTAGAAGCGGATAGTTTAGGTGTTT
391 TGTGGCTAGCAAGGATGTTTGCCAAGCAAGTGGATTGTCTCTAAAAGCGGATAGTTTAGGTGTTT
16603013 CAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGAGTCAAATGGAGAGTAAGAATCTG
456 CAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGAGTCAAATGGAGAGTAAGAATCTG
* * * * *
16603078 AGAGAGACAATTACTAATGCGTTCGAGTAGAGCTGAATGATTGGTCATGATTATATT-TCAGATG
521 AGAAAGACAATTACCAAGGCATTCAAGTAGAGCTGAATGATTGGTCATGATTAT-TTCTCAGATG
*
16603142 GCTTG-CACT-CTGACACGTGTCCACCTA-TAGTGGAAGTATAATAATTTATAGTTTATTTTTTG
585 GCTTGTCA-TGCTGACACGTGTCCACC-AGTAGTGGAAGTATAATAATTTATAGTTTATTTTTTA
*
16603204 TCTTATTATCTAATCTTGTAATAAATACATATTGATCAAATCGAGTATTATTAATGTTATTCAAT
648 TCTTATTATCTAATCTTGTAATAAATACATATTGATCAAATCGAGTATTATTAATGCTATTCAAT
* * * *
16603269 GGTTATTATTG-CAGAATTAAATAACTTGCGTTACTTAAATTCTGATTGGTGCAGGATTTTGGGT
713 GGTTATTA-TGACAAAATTAAATAACTTGCATTACTTAAAATCTGATTGGTGCAGGATTTCGGGT
* * *
16603333 TTAAGAATTTGATTCAAGTCTAAATTTAATTGATGTTTAATGTAATT-ATTTTTTTTGTTGGTAG
777 TTAAGAATTTGATTCAAGTATAAATTTAATTGATGTTTAATGTAATTAATTTGTTAT-TT-GTAG
* *
16603397 CTTTCATGTCTGTTTCACGATTCATATTCAATGCACA
840 CTTTCATATCTATTTCACGATTCATATTCAATGCACA
16603434 TTACACGATT
Statistics
Matches: 813, Mismatches: 57, Indels: 12
0.92 0.06 0.01
Matches are distributed among these distances:
893 7 0.01
894 215 0.26
895 589 0.72
896 2 0.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Consensus pattern (895 bp):
CACGTCGCTCATGTCATTCGGGTACGCCCCAACTCCGACAGGTATAAACTTGCACCCTCTTGCGC
GCAAGGCAAGGTTCCATACAAAGTCATTCAATCATCTTTCAAAAGGGTTCCCATATATAAACACA
TCTCACACTTGGGTTTTAACCAATGTGGCATCTAAGCTTTTCTTTTCCTCAACAAATATTTACAA
GTAGCTTAATTTGAGCATCAATTTCTCATTCATCACTCAACCATTTTGAGCATATGATATACCGT
TGGAAAGGTCTCATGAAGAAGAATATGAAACCATAATTTTATGATTCAACTCTTCACCTTTACCT
ATTGAGAATATGCCTCAAAGTTCCCATAAAATGTAATTTTTCCAACAACTAGTATGTTCAAAGGT
TGTGGCTAGCAAGGATGTTTGCCAAGCAAGTGGATTGTCTCTAAAAGCGGATAGTTTAGGTGTTT
CAAGAAGACGAATGCAGTCCAAGTCTCTTGCTGAGATAGAGAGTCAAATGGAGAGTAAGAATCTG
AGAAAGACAATTACCAAGGCATTCAAGTAGAGCTGAATGATTGGTCATGATTATTTCTCAGATGG
CTTGTCATGCTGACACGTGTCCACCAGTAGTGGAAGTATAATAATTTATAGTTTATTTTTTATCT
TATTATCTAATCTTGTAATAAATACATATTGATCAAATCGAGTATTATTAATGCTATTCAATGGT
TATTATGACAAAATTAAATAACTTGCATTACTTAAAATCTGATTGGTGCAGGATTTCGGGTTTAA
GAATTTGATTCAAGTATAAATTTAATTGATGTTTAATGTAATTAATTTGTTATTTGTAGCTTTCA
TATCTATTTCACGATTCATATTCAATGCACAAACGATGTCTTTTTCTATC
Found at i:16605938 original size:5 final size:5
Alignment explanation
Indices: 16605928--16605953 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16605918 AGTGAGAAAC
16605928 CTGCA CTGCA CTGCA CTGCA CTGCA C
1 CTGCA CTGCA CTGCA CTGCA CTGCA C
16605954 CCTTTTCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (5 bp):
CTGCA
Found at i:16608565 original size:29 final size:29
Alignment explanation
Indices: 16608523--16608581 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
16608513 GTCTCAAATG
16608523 TATGAAACAAGTAAAACCCTAATCCCATT
1 TATGAAACAAGTAAAACCCTAATCCCATT
16608552 TATGAAACAAGTAAAACCCTAATCCCATT
1 TATGAAACAAGTAAAACCCTAATCCCATT
16608581 T
1 T
16608582 CTTTCATCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (29 bp):
TATGAAACAAGTAAAACCCTAATCCCATT
Found at i:16609552 original size:30 final size:30
Alignment explanation
Indices: 16609525--16609582 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16609515 TTTATAAATT
* * *
16609525 TAAATTTAAATTTAAATATTTAAATAAAAA
1 TAAAATTAAATATAAACATTTAAATAAAAA
*
16609555 TAAAATTAGATATAAACATTTAAATAAA
1 TAAAATTAAATATAAACATTTAAATAAA
16609583 GAAAATTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (30 bp):
TAAAATTAAATATAAACATTTAAATAAAAA
Found at i:16609555 original size:20 final size:20
Alignment explanation
Indices: 16609513--16609555 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
16609503 CCATACTAGT
**
16609513 AATTTATAAATTTAAATTTA
1 AATTTATAAATTTAAATAAA
16609533 AATTTA-AATATTTAAATAAA
1 AATTTATAA-ATTTAAATAAA
16609553 AAT
1 AAT
16609556 AAAATTAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTATAAATTTAAATAAA
Found at i:16631947 original size:9 final size:10
Alignment explanation
Indices: 16631902--16631951 Score: 55
Period size: 11 Copynumber: 4.6 Consensus size: 10
16631892 ACATTAGTCT
16631902 TCTCACAATTC
1 TCTCA-AATTC
16631913 TCTCTAAATTC
1 TCTC-AAATTC
*
16631924 TCTCCACATTC
1 TCT-CAAATTC
16631935 TCTCAAATTTC
1 TCTCAAA-TTC
16631946 TCTCAA
1 TCTCAA
16631952 TTTTTGTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 3 0.09
11 29 0.85
12 2 0.06
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (10 bp):
TCTCAAATTC
Found at i:16631961 original size:21 final size:21
Alignment explanation
Indices: 16631937--16631983 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
16631927 CCACATTCTC
16631937 TCAAA-TTTCTCTCAATTTTTG
1 TCAAACTTTCT-TCAATTTTTG
*
16631958 TCAAAGCTTTCTTTAATTTTTG
1 TCAAA-CTTTCTTCAATTTTTG
16631980 -CAAA
1 TCAAA
16631984 AGAAAGCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.28, C:0.17, G:0.06, T:0.49
Consensus pattern (21 bp):
TCAAACTTTCTTCAATTTTTG
Found at i:16633104 original size:7 final size:7
Alignment explanation
Indices: 16633092--16633124 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
16633082 TAGTCGTTTC
16633092 GTATTTA
1 GTATTTA
16633099 GTATTTA
1 GTATTTA
16633106 GTATTTA
1 GTATTTA
*
16633113 TTATTTA
1 GTATTTA
16633120 GTATT
1 GTATT
16633125 ACCTATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (7 bp):
GTATTTA
Found at i:16633687 original size:30 final size:30
Alignment explanation
Indices: 16633621--16633688 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
16633611 GATGATGATG
* * *
16633621 CTGGCCCATCAGCGACGCCCACACAATCAC
1 CTGGCCCATCAACAACGCCCACACAACCAC
** * *
16633651 GGGGCCCATCAACAATGCCCACACAGCCAC
1 CTGGCCCATCAACAACGCCCACACAACCAC
16633681 CTGGCCCA
1 CTGGCCCA
16633689 ACACTTCAAC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.26, C:0.46, G:0.19, T:0.09
Consensus pattern (30 bp):
CTGGCCCATCAACAACGCCCACACAACCAC
Found at i:16634325 original size:128 final size:126
Alignment explanation
Indices: 16634191--16634557 Score: 491
Period size: 128 Copynumber: 2.9 Consensus size: 126
16634181 GTAGAAACGT
*
16634191 TTTTTATATAGTTTCATATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTTTT
1 TTTTTATATAGTTTCATATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGAACTTTACTTTT
*
16634256 TTTAATTTTATTAAAATAATTG-T-TTTTAAATTAGGCAATATTTTTTATTATTTTTATATTTAA
66 TTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATA-TTTTTATTA---TTATATTTAA
* *
16634319 TTTTTATATAGTTTCA-ATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGCACTTCACTTT
1 TTTTTATATAGTTTCATA-TAATAAAATAAAAGTTGTTTTTAATATTTTAATTGAACTTTACTTT
* * * *
16634383 TCTTAATTTTATTGAAATAAATGTTCTTTTAAATTAGTCAATA--TTT-TTATTATATTTAT
65 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTATTATTATATTTAA
* *
16634442 TTTTTATATAGTTATAAT-TAATAAAATAAAAGTTGTTTTTAAT-TTTTTATTGAACTTTACTTT
1 TTTTTATATAGTT-TCATATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGAACTTTACTTT
* *
16634505 TTTTAATTTTAATACAATAAATGTTCTTTTAAATTA-GCTAATAATTTTTATTA
65 TTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGC-AAT-ATTTTTATTA
16634558 AAATAAATGT
Statistics
Matches: 213, Mismatches: 16, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
121 1 0.00
122 52 0.24
123 48 0.23
124 2 0.01
125 3 0.01
126 6 0.03
127 4 0.02
128 80 0.38
129 1 0.00
130 16 0.08
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (126 bp):
TTTTTATATAGTTTCATATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGAACTTTACTTTT
TTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGGCAATATTTTTATTATTATATTTAA
Found at i:16637831 original size:125 final size:126
Alignment explanation
Indices: 16637608--16637916 Score: 435
Period size: 125 Copynumber: 2.5 Consensus size: 126
16637598 AGTCCAAGGC
* *
16637608 TTTTTTCAGATACGACTGTAGTAAAAGAGCGT-C-CATGTAGGAGCTTTTTTCTGTAATTTTGCT
1 TTTTTTCAGATACTACTGTAGTAAAAGAGCGTCCACATG-A-GAGCTTTTTTCCGTAATTTTGCT
*
16637671 GACAGTGCATCCTTCTTGAAACGTTTTTAACACTATTTGTTCAAAAACATCTTCTTAAAATTA
64 GACAGTGCATCCTTCTTGAAACGTTTTTAACACTATTTGTTCAAAAACATCTTCTCAAAATTA
* ** *
16637734 TTTTTTCAGATACTACTGTAGCAAAA-AAAGTCCACATGAGAGTTTTTTTCCGTAATTTTGCTGA
1 TTTTTTCAGATACTACTGTAGTAAAAGAGCGTCCACATGAGAGCTTTTTTCCGTAATTTTGCTGA
* * * * *
16637798 CTGTGCATCCTTCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATATCTTCTCAAAATTA
66 CAGTGCATCCTTCTTGAAACGTTTTTAACACTATTTGTTCAAAAACATCTTCTCAAAATTA
* * * *
16637859 TTTTTTCAGATACTACTATAGTAAAAGAGCGTCCACGTAAAAGCTTTTTTCCGTAATT
1 TTTTTTCAGATACTACTGTAGTAAAAGAGCGTCCACATGAGAGCTTTTTTCCGTAATT
16637917 AATAGTTAAT
Statistics
Matches: 160, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
125 105 0.66
126 51 0.32
127 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (126 bp):
TTTTTTCAGATACTACTGTAGTAAAAGAGCGTCCACATGAGAGCTTTTTTCCGTAATTTTGCTGA
CAGTGCATCCTTCTTGAAACGTTTTTAACACTATTTGTTCAAAAACATCTTCTCAAAATTA
Found at i:16638055 original size:24 final size:24
Alignment explanation
Indices: 16638027--16638076 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
16638017 TTTTCCCTTA
*
16638027 AAAAAT-ATTAAAACTCTAAATCCT
1 AAAAATCA-TAAAACACTAAATCCT
*
16638051 AAAAATCATAAACCACTAAATCCT
1 AAAAATCATAAAACACTAAATCCT
16638075 AA
1 AA
16638077 CTTTAAACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAAATCATAAAACACTAAATCCT
Found at i:16642888 original size:29 final size:29
Alignment explanation
Indices: 16642843--16642899 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
16642833 AGCCGTCTCA
16642843 TCAAATTTTGGTAGGCCCTCAGCTTCCAC
1 TCAAATTTTGGTAGGCCCTCAGCTTCCAC
*
16642872 TCAAATTTTGGTGGGCCCTCAGCTTCCA
1 TCAAATTTTGGTAGGCCCTCAGCTTCCA
16642900 TCATCTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (29 bp):
TCAAATTTTGGTAGGCCCTCAGCTTCCAC
Found at i:16647823 original size:21 final size:21
Alignment explanation
Indices: 16647797--16647837 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16647787 AGACGAGCAA
* *
16647797 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
16647818 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
16647838 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:16649776 original size:16 final size:16
Alignment explanation
Indices: 16649743--16649776 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16649733 GGAGATTGTT
* *
16649743 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
16649759 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
16649775 AA
1 AA
16649777 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:16654314 original size:14 final size:14
Alignment explanation
Indices: 16654295--16654322 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16654285 CTCCAAACGG
16654295 AAGGCTTATTCTAA
1 AAGGCTTATTCTAA
16654309 AAGGCTTATTCTAA
1 AAGGCTTATTCTAA
16654323 GGAAGCAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (14 bp):
AAGGCTTATTCTAA
Found at i:16657314 original size:28 final size:26
Alignment explanation
Indices: 16657269--16657334 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
16657259 TTATGATAAG
*
16657269 TAAAA-AACATAAAAATTTATTAAATAT
1 TAAAATAAAATAAAAATTT-TTAAA-AT
*
16657296 TAAAATAAAATAAATATTTTTAAAAT
1 TAAAATAAAATAAAAATTTTTAAAAT
*
16657322 AAAAATAATAATA
1 TAAAATAA-AATA
16657335 TCGGCAGACT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.26
27 14 0.41
28 11 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
TAAAATAAAATAAAAATTTTTAAAAT
Found at i:16657940 original size:10 final size:10
Alignment explanation
Indices: 16657925--16657955 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
16657915 TTTATATATC
16657925 ACAATAAATT
1 ACAATAAATT
16657935 ACAATAAATT
1 ACAATAAATT
16657945 ACAATAAATT
1 ACAATAAATT
16657955 A
1 A
16657956 TTTTATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (10 bp):
ACAATAAATT
Found at i:16664074 original size:34 final size:34
Alignment explanation
Indices: 16664009--16664078 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 34
16663999 AAGTCGTCCC
* **
16664009 AACAATGTCAACTCTAGAATTGGTCTTTACCTTT
1 AACAATGTCAACTCTAGAATTCGTCCCTACCTTT
* * *
16664043 AACAATGTTAACTCTGGGATTCGTCCCTACCTTT
1 AACAATGTCAACTCTAGAATTCGTCCCTACCTTT
16664077 AA
1 AA
16664079 AATTTTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (34 bp):
AACAATGTCAACTCTAGAATTCGTCCCTACCTTT
Found at i:16666184 original size:21 final size:23
Alignment explanation
Indices: 16666148--16666190 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
16666138 TTAACCTATA
*
16666148 GATTAACCGTAATTAA-TCGGTC
1 GATTAACAGTAATTAATTCGGTC
16666170 GATTAACAG-AATTAATTCGGT
1 GATTAACAGTAATTAATTCGGT
16666191 TGGGGGTCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (23 bp):
GATTAACAGTAATTAATTCGGTC
Found at i:16686056 original size:32 final size:32
Alignment explanation
Indices: 16686020--16686082 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
16686010 AGTGGTACAG
16686020 AGTACAAGACATGAACCATCGGATGACAGAAT
1 AGTACAAGACATGAACCATCGGATGACAGAAT
16686052 AGTACAAGACATGAACCATCGGATGACAGAA
1 AGTACAAGACATGAACCATCGGATGACAGAA
16686083 GAGAGGGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.14
Consensus pattern (32 bp):
AGTACAAGACATGAACCATCGGATGACAGAAT
Found at i:16687603 original size:18 final size:18
Alignment explanation
Indices: 16687569--16687603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16687559 TTATAATTCC
* *
16687569 AAAAATTATATATTTTTA
1 AAAAATTATAAAATTTTA
16687587 AAAAATTATAAAATTTT
1 AAAAATTATAAAATTTT
16687604 CTTTTAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAAATTATAAAATTTTA
Found at i:16688134 original size:21 final size:23
Alignment explanation
Indices: 16688109--16688153 Score: 60
Period size: 21 Copynumber: 2.0 Consensus size: 23
16688099 CTTGTGTTAT
16688109 AAATTATAATA-AT-AA-AAATAA
1 AAATTA-AATACATCAATAAATAA
16688130 AAATTAAATACATCAATAAATAA
1 AAATTAAATACATCAATAAATAA
16688153 A
1 A
16688154 TACTTGTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.19
21 8 0.38
22 2 0.10
23 7 0.33
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATTAAATACATCAATAAATAA
Found at i:16688249 original size:44 final size:44
Alignment explanation
Indices: 16688186--16688277 Score: 157
Period size: 44 Copynumber: 2.1 Consensus size: 44
16688176 TTAAAACCTT
* *
16688186 CACAAGCTATGTATTAAATGAAACACTTAATATTATATGCGGCA
1 CACAAGCCATGTATTAAATGAAACACCTAATATTATATGCGGCA
*
16688230 CACAAGCCATGTATTAAATGAAACACCTAATATTCTATGCGGCA
1 CACAAGCCATGTATTAAATGAAACACCTAATATTATATGCGGCA
16688274 CACA
1 CACA
16688278 TTTGTATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (44 bp):
CACAAGCCATGTATTAAATGAAACACCTAATATTATATGCGGCA
Found at i:16694474 original size:46 final size:47
Alignment explanation
Indices: 16694236--16694637 Score: 232
Period size: 46 Copynumber: 8.5 Consensus size: 47
16694226 ATTGAGTACT
* * *
16694236 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-TTTTGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGT-AGAGCC
* * * * *
16694282 AGTGTAAGACCATGTCTGAGACATGGCATCGGCATTGAGACG-AGTGCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTAGAGCC
* * * * * *
16694330 TGTGTAAGACATGTCTGGGACATGTATCGACCAC-A-TTTTGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGT-AGAGCC
* * ** ** * * *
16694376 AATGTAAGACCATGTCTGAGACATTGCATCGGTATTAAGACG-AGTGCT
1 AGTGTAAGA-CATGTCTGGGACA-TGCATCGGCCTCGAGATGTAGAGCC
* *
16694424 AGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
* * * *
16694470 AGTGTAAGACATGTTTGGGACATGTATTGG-CTACGAGATGT---GTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGATGTAGAGCC
* * * * * *
16694514 AATGTAAGATATTGTCTGGGACATGGCATCGGCATAGATATGCTAGAGCT
1 AGTGTAAGACA-TGTCTGGGACAT-GCATCGGCCTCGAGATG-TAGAGCC
* * * * *
16694564 TGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGATATGCTAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATG-TAGAGCC
*
16694614 TGTGTAAGACCATGTCTGGGACAT
1 AGTGTAAGA-CATGTCTGGGACAT
16694638 TAAATCGACA
Statistics
Matches: 277, Mismatches: 59, Indels: 36
0.74 0.16 0.10
Matches are distributed among these distances:
44 11 0.04
45 14 0.05
46 87 0.31
47 53 0.19
48 39 0.14
49 2 0.01
50 70 0.25
51 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (47 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATGTAGAGCC
Found at i:16694479 original size:94 final size:94
Alignment explanation
Indices: 16694229--16694455 Score: 366
Period size: 94 Copynumber: 2.4 Consensus size: 94
16694219 ATGAGCTATT
*
16694229 GAGTACTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTTTGAGAGCCAGTGTAAGACCA
1 GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTTTGAGAGCCAGTGTAAGACCA
*
16694294 TGTCTGAGACATGGCATCGGCATTGAGAC
66 TGTCTGAGACATGGCATCGGCATTAAGAC
* * *
16694323 GAGTGCCT-GTGTAAGACATGTCTGGGACATGTATCGACCACATTTTGAGAGCCAATGTAAGACC
1 GAGTG-CTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTTTGAGAGCCAGTGTAAGACC
* *
16694387 ATGTCTGAGACATTGCATCGGTATTAAGAC
65 ATGTCTGAGACATGGCATCGGCATTAAGAC
*
16694417 GAGTGCTAGTGTAAGACATGTCTGGGACATGCATTGGCC
1 GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCC
16694456 TCGAGACGTA
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
93 2 0.02
94 117 0.97
95 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (94 bp):
GAGTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTTTGAGAGCCAGTGTAAGACCA
TGTCTGAGACATGGCATCGGCATTAAGAC
Found at i:16694580 original size:50 final size:50
Alignment explanation
Indices: 16694526--16694637 Score: 224
Period size: 50 Copynumber: 2.2 Consensus size: 50
16694516 TGTAAGATAT
16694526 TGTCTGGGACATGGCATCGGCATAGATATGCTAGAGCTTGTGTAAGACCA
1 TGTCTGGGACATGGCATCGGCATAGATATGCTAGAGCTTGTGTAAGACCA
16694576 TGTCTGGGACATGGCATCGGCATAGATATGCTAGAGCTTGTGTAAGACCA
1 TGTCTGGGACATGGCATCGGCATAGATATGCTAGAGCTTGTGTAAGACCA
16694626 TGTCTGGGACAT
1 TGTCTGGGACAT
16694638 TAAATCGACA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (50 bp):
TGTCTGGGACATGGCATCGGCATAGATATGCTAGAGCTTGTGTAAGACCA
Found at i:16696165 original size:19 final size:20
Alignment explanation
Indices: 16696141--16696180 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
16696131 CCCTGTTTAG
16696141 TGAAAAATTTTCT-AAGTTT
1 TGAAAAATTTTCTAAAGTTT
16696160 TGAAAAATTTTCTAAAGTTT
1 TGAAAAATTTTCTAAAGTTT
16696180 T
1 T
16696181 CGGTTTAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (20 bp):
TGAAAAATTTTCTAAAGTTT
Found at i:16698453 original size:41 final size:41
Alignment explanation
Indices: 16698375--16698459 Score: 98
Period size: 41 Copynumber: 2.1 Consensus size: 41
16698365 TTACTTGATA
** * *
16698375 CAATACACCAGCACAAAGCCTACTAGGCTCAAGGCCTAATT
1 CAATACACCAGCACAAAGCCTACTAGGAACAAAGCCTAAAT
* * * *
16698416 CAATACACCGGCTCAAAGCCTGCTGGGAACAAAGCCTAAAT
1 CAATACACCAGCACAAAGCCTACTAGGAACAAAGCCTAAAT
16698457 CAA
1 CAA
16698460 CACATTGGCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.38, C:0.31, G:0.16, T:0.15
Consensus pattern (41 bp):
CAATACACCAGCACAAAGCCTACTAGGAACAAAGCCTAAAT
Found at i:16704063 original size:17 final size:18
Alignment explanation
Indices: 16704026--16704063 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
16704016 TGTAGGAATG
16704026 TTTTTATCTCAAAAGTGA
1 TTTTTATCTCAAAAGTGA
16704044 TTTTTATC-CTAAAAGT-A
1 TTTTTATCTC-AAAAGTGA
16704061 TTT
1 TTT
16704064 CTTAGAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (18 bp):
TTTTTATCTCAAAAGTGA
Found at i:16708053 original size:7 final size:7
Alignment explanation
Indices: 16708032--16708065 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
16708022 TAAAAGAACT
16708032 AAAAGAAG
1 AAAA-AAG
*
16708040 AATAAAG
1 AAAAAAG
16708047 AAAAAAG
1 AAAAAAG
16708054 AAAAAAG
1 AAAAAAG
16708061 AAAAA
1 AAAAA
16708066 CAAGCAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 21 0.88
8 3 0.12
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:16713759 original size:5 final size:5
Alignment explanation
Indices: 16713749--16713804 Score: 51
Period size: 5 Copynumber: 11.0 Consensus size: 5
16713739 AATGTAAAGT
* * * *
16713749 TTTAA TTTAA TTAAA TTTAA TTT-T TTATAA TTAAA TTTAT TTTAA TTTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TT-TAA TTTAA TTTAA TTTAA -TTTAA
16713800 TTTAA
1 TTTAA
16713805 ATGTTTCACA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
4 2 0.05
5 31 0.77
6 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:16716355 original size:22 final size:22
Alignment explanation
Indices: 16716309--16716355 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
16716299 TATTAGATAT
**
16716309 TAAATAGATATTTATTATTTTA
1 TAAATAGATATTTATTATTAAA
16716331 TAAA-AGATATTTATTAATTAAA
1 TAAATAGATATTTATT-ATTAAA
16716353 TAA
1 TAA
16716356 TTATATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATAGATATTTATTATTAAA
Found at i:16718486 original size:23 final size:24
Alignment explanation
Indices: 16718441--16718491 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
16718431 CCGAAATACA
* *
16718441 GCTCTTCGTGAGCTTCCCCATAG-
1 GCTCTTCGTGAGCCTCCCAATAGT
* *
16718464 GCTCTTTGTGAGCCTCTCAATAGT
1 GCTCTTCGTGAGCCTCCCAATAGT
16718488 GCTC
1 GCTC
16718492 GCTTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.14, C:0.31, G:0.22, T:0.33
Consensus pattern (24 bp):
GCTCTTCGTGAGCCTCCCAATAGT
Found at i:16718979 original size:46 final size:46
Alignment explanation
Indices: 16718927--16719055 Score: 188
Period size: 46 Copynumber: 2.8 Consensus size: 46
16718917 GCTCTCTGAA
*
16718927 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGAAACTTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGAAACATGAT
* *
16718973 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGAAACATGAT
* * *
16719019 A-GAAAACGAGTAAGACCATAGTTGAAAGATACTATGG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACTATGG
16719056 CATCATGTCG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
45 1 0.01
46 74 0.99
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGAAACATGAT
Found at i:16719442 original size:20 final size:20
Alignment explanation
Indices: 16719417--16719487 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 20
16719407 TAAGAGAATA
16719417 ATATATTTTGTGACATGTAC
1 ATATATTTTGTGACATGTAC
* *
16719437 ATATATAATTATCTTTGATATGTTA-
1 --ATAT-ATT-T-TGTGACATG-TAC
*
16719462 ATATGTTTTGTGACATGTAC
1 ATATATTTTGTGACATGTAC
16719482 ATATAT
1 ATATAT
16719488 AATTATCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
19 2 0.05
20 12 0.32
21 1 0.03
22 6 0.16
23 7 0.18
24 1 0.03
25 7 0.18
26 2 0.05
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (20 bp):
ATATATTTTGTGACATGTAC
Found at i:16719465 original size:25 final size:25
Alignment explanation
Indices: 16719437--16719509 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
16719427 TGACATGTAC
16719437 ATATATAATTATCTTTGATATGTT-
1 ATATATAATTATCTTTGATATGTTA
* * *
16719461 A-ATAT-GTT-T-TGTGACATG-TA
1 ATATATAATTATCTTTGATATGTTA
16719481 CATATATAATTATCTTTGATATGTTA
1 -ATATATAATTATCTTTGATATGTTA
16719507 ATA
1 ATA
16719510 CAAGAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 13
0.65 0.11 0.24
Matches are distributed among these distances:
19 1 0.03
20 7 0.19
21 2 0.06
22 6 0.17
23 6 0.17
24 2 0.06
25 10 0.28
26 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.49
Consensus pattern (25 bp):
ATATATAATTATCTTTGATATGTTA
Found at i:16719479 original size:45 final size:45
Alignment explanation
Indices: 16719415--16719509 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
16719405 AGTAAGAGAA
16719415 TAATATATTTTGTGACATGTACATATATAATTATCTTTGATATGT
1 TAATATATTTTGTGACATGTACATATATAATTATCTTTGATATGT
*
16719460 TAATATGTTTTGTGACATGTACATATATAATTATCTTTGATATGT
1 TAATATATTTTGTGACATGTACATATATAATTATCTTTGATATGT
16719505 TAATA
1 TAATA
16719510 CAAGAAAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (45 bp):
TAATATATTTTGTGACATGTACATATATAATTATCTTTGATATGT
Found at i:16726320 original size:42 final size:42
Alignment explanation
Indices: 16726216--16726372 Score: 115
Period size: 43 Copynumber: 3.7 Consensus size: 42
16726206 TGTGTTATCG
* * * *
16726216 TGTAAGACCATGTCTAGGACGTTGGCATC-AACTTATGATTTACG
1 TGTAAGACCCTGTCTGGGACGTTGGCATCGTAC-T-TGATTT-CA
* * *
16726260 TGTAAGAACAC-GTTTGGGACGTTGGTATCGTACTTGATTTCA
1 TGTAAG-ACCCTGTCTGGGACGTTGGCATCGTACTTGATTTCA
* * *
16726302 TGTAAGACCCTGTCTGGGATAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCCTGTCTGGGA-CGTTGGCATCG-TACTTGATTTCA
* *
16726345 TGTAAGACCAC-ATCTGGGATGTTGGCAT
1 TGTAAGACC-CTGTCTGGGACGTTGGCAT
16726373 TGTATGAGCT
Statistics
Matches: 91, Mismatches: 15, Indels: 15
0.75 0.12 0.12
Matches are distributed among these distances:
41 3 0.03
42 22 0.24
43 39 0.43
44 23 0.25
45 4 0.04
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (42 bp):
TGTAAGACCCTGTCTGGGACGTTGGCATCGTACTTGATTTCA
Found at i:16735878 original size:16 final size:17
Alignment explanation
Indices: 16735852--16735885 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
16735842 CAACTTGTGA
16735852 AAAATAAAATAAAAAAT
1 AAAATAAAATAAAAAAT
16735869 AAAA-AAAATAAAAAAT
1 AAAATAAAATAAAAAAT
16735885 A
1 A
16735886 CACAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAATAAAATAAAAAAT
Found at i:16736742 original size:43 final size:42
Alignment explanation
Indices: 16736684--16736896 Score: 268
Period size: 43 Copynumber: 5.0 Consensus size: 42
16736674 ATATCATACA
* * *
16736684 ATGCCAATGTTCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCACTGTCCCAGACG-GGTCTTACACGTAATCACATATCG
* *
16736727 ATGCCACTGTCCCAGAAAGGGTCTTATACGTAATCACATATCG
1 ATGCCACTGTCCCAG-ACGGGTCTTACACGTAATCACATATCG
16736770 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCACATATCG
1 ATGCCACTGTCCCAGAC-GGGTCTTACACGTAATCACATATCG
* *
16736813 ATGCCAAC-GTCCCAGACGCAGTCTTACACGTAATCACATTTCG
1 ATGCC-ACTGTCCCAGACG-GGTCTTACACGTAATCACATATCG
* *
16736856 ATGCCAAC-GTCCCGGACGTGGTCTTACATGTAATCACATAT
1 ATGCC-ACTGTCCCAGACG-GGTCTTACACGTAATCACATAT
16736897 ACATCCATGT
Statistics
Matches: 152, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
42 2 0.01
43 146 0.96
44 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACGGGTCTTACACGTAATCACATATCG
Found at i:16740786 original size:40 final size:40
Alignment explanation
Indices: 16740726--16740803 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
16740716 GGTACTTTAT
* * *
16740726 GGTGTGTAGGGTTGGATGAGTCGATTATATCCCCATATAC
1 GGTGTGCAGGGATGGATGAGTCAATTATATCCCCATATAC
* * *
16740766 GGTGTGCAGGGATGGGTGAGTTAATTTTATCCCCATAT
1 GGTGTGCAGGGATGGATGAGTCAATTATATCCCCATAT
16740804 GGTGTGTTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (40 bp):
GGTGTGCAGGGATGGATGAGTCAATTATATCCCCATATAC
Found at i:16762317 original size:43 final size:43
Alignment explanation
Indices: 16762262--16762506 Score: 320
Period size: 43 Copynumber: 5.7 Consensus size: 43
16762252 TGCCAACATT
*
16762262 CCAGAC-GTGGTCTTACATGTAATCACATATCGATGCCACTGTC
1 CCAGACAG-GGTCTTACACGTAATCACATATCGATGCCACTGTC
* *
16762305 CTAGACAGGGTCTTACACGTAATCACATATCGATGCCATTGTC
1 CCAGACAGGGTCTTACACGTAATCACATATCGATGCCACTGTC
* * * *
16762348 CCAGTCAAGGTCTTACACGTAATCACATATTGATGCCAATGTC
1 CCAGACAGGGTCTTACACGTAATCACATATCGATGCCACTGTC
*
16762391 CCAGACATGGTCTTACACGTAATCACATATCGATGCCAAC-GTC
1 CCAGACAGGGTCTTACACGTAATCACATATCGATGCC-ACTGTC
* *
16762434 CCAGAC-GTAGTCTTACACGTAATCACATATCGATGCCAAC-ATC
1 CCAGACAG-GGTCTTACACGTAATCACATATCGATGCC-ACTGTC
16762477 CCAGAC-GTGGTCTTACACGTAATCACATAT
1 CCAGACAG-GGTCTTACACGTAATCACATAT
16762507 ACATCTATGT
Statistics
Matches: 183, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
43 181 0.99
44 2 0.01
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (43 bp):
CCAGACAGGGTCTTACACGTAATCACATATCGATGCCACTGTC
Found at i:16762489 original size:129 final size:129
Alignment explanation
Indices: 16762262--16762506 Score: 368
Period size: 129 Copynumber: 1.9 Consensus size: 129
16762252 TGCCAACATT
* * * *
16762262 CCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTGTCCTAGACAGGGTCTTACACGTAA
1 CCAGACATGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGACAGAGTCTTACACGTAA
*** *
16762327 TCACATATCGATGCCATTGTCCCAGTCAAGGTCTTACACGTAATCACATATTGATGCCAATGTC
66 TCACATATCGATGCCAACATCCCAGACAAGGTCTTACACGTAATCACATATTGATGCCAATGTC
16762391 CCAGACATGGTCTTACACGTAATCACATATCGATGCCAAC-GTCCCAGAC-GTAGTCTTACACGT
1 CCAGACATGGTCTTACACGTAATCACATATCGATGCC-ACTGTCCCAGACAG-AGTCTTACACGT
**
16762454 AATCACATATCGATGCCAACATCCCAGACGTGGTCTTACACGTAATCACATAT
64 AATCACATATCGATGCCAACATCCCAGACAAGGTCTTACACGTAATCACATAT
16762507 ACATCTATGT
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
128 1 0.01
129 101 0.97
130 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (129 bp):
CCAGACATGGTCTTACACGTAATCACATATCGATGCCACTGTCCCAGACAGAGTCTTACACGTAA
TCACATATCGATGCCAACATCCCAGACAAGGTCTTACACGTAATCACATATTGATGCCAATGTC
Found at i:16764917 original size:43 final size:43
Alignment explanation
Indices: 16764869--16764961 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
16764859 ATTCTAGAAA
16764869 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
* *
16764912 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
16764955 TATTTTC
1 TATTTTC
16764962 CCAATTAGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (43 bp):
TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
Found at i:16769590 original size:19 final size:19
Alignment explanation
Indices: 16769544--16769591 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
16769534 ATATATATTT
16769544 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
16769562 TAAATCTTATTT-GGATAGA
1 TAAATTTTATTTAGG-TAGA
*
16769581 TAAGTTTTATT
1 TAAATTTTATT
16769592 CATATTCTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:16769653 original size:43 final size:43
Alignment explanation
Indices: 16769605--16769697 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 43
16769595 ATTCTAGAAA
16769605 TATTTT-TATTTTATCTTTTAGTAGTTTACTAAAATAAGGGAAC
1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAAAATAAGGGAAC
* * *
16769648 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAAAATAAGGGAAC
*
16769691 AATTTTC
1 TATTTTC
16769698 CCAATTAGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 44 0.98
44 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (43 bp):
TATTTTCTTTTTATCTTTTAGTAGTTTACTAAAATAAGGGAAC
Found at i:16771155 original size:13 final size:13
Alignment explanation
Indices: 16771137--16771172 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
16771127 TATATTATAA
16771137 TAAAAATCTTAAC
1 TAAAAATCTTAAC
16771150 TAAAAATCTTAAC
1 TAAAAATCTTAAC
16771163 TAAAAATCTT
1 TAAAAATCTT
16771173 TGATATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAAATCTTAAC
Found at i:16777029 original size:12 final size:13
Alignment explanation
Indices: 16777012--16777044 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
16777002 AAACAACATG
16777012 ATATATTTTTTT-
1 ATATATTTTTTTC
16777024 ATATATATTTTTTC
1 ATATAT-TTTTTTC
16777038 ATATATT
1 ATATATT
16777045 AATAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 7 0.37
14 6 0.32
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
ATATATTTTTTTC
Found at i:16777031 original size:14 final size:14
Alignment explanation
Indices: 16777012--16777043 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16777002 AAACAACATG
*
16777012 ATATATTTTTTTAT
1 ATATATTTTTTCAT
16777026 ATATATTTTTTCAT
1 ATATATTTTTTCAT
16777040 ATAT
1 ATAT
16777044 TAATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATATTTTTTCAT
Found at i:16779559 original size:23 final size:23
Alignment explanation
Indices: 16779533--16779610 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 23
16779523 TAATTGATTA
16779533 TTTAAATAAAAAATTATTAAAAT
1 TTTAAATAAAAAATTATTAAAAT
*
16779556 TTTAAA-AATATAATT-TATAAAA-
1 TTTAAATAA-AAAATTAT-TAAAAT
16779578 TTT--ATAAAAGAATTATTAGAAAT
1 TTTAAATAAAA-AATTATTA-AAAT
16779601 TTATAAATAA
1 TT-TAAATAA
16779611 TTATAAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 17
0.69 0.03 0.27
Matches are distributed among these distances:
20 2 0.05
21 8 0.19
22 10 0.23
23 18 0.42
24 1 0.02
26 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTAAATAAAAAATTATTAAAAT
Found at i:16779609 original size:44 final size:40
Alignment explanation
Indices: 16779538--16779638 Score: 114
Period size: 41 Copynumber: 2.4 Consensus size: 40
16779528 GATTATTTAA
16779538 ATAAAAAATTATTAAAATTTTAAAAATATAATTTATAAAATTT
1 ATAAAAAATTATTAAAATTTT-AAAA-ATAA-TTATAAAATTT
*
16779581 ATAAAAGAATTATTAGAAA-TTTATAAATAATTATAAAATTT
1 ATAAAA-AATTATTA-AAATTTTAAAAATAATTATAAAATTT
* * *
16779622 ATTAAAAACTATAAAAA
1 ATAAAAAATTATTAAAA
16779639 ATATAGAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
39 3 0.06
40 6 0.12
41 16 0.31
42 4 0.08
43 9 0.17
44 11 0.21
45 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (40 bp):
ATAAAAAATTATTAAAATTTTAAAAATAATTATAAAATTT
Found at i:16779623 original size:41 final size:43
Alignment explanation
Indices: 16779538--16779656 Score: 121
Period size: 50 Copynumber: 2.6 Consensus size: 43
16779528 GATTATTTAA
16779538 ATAAAAAATTATTAAAATTTTAAAAATATAATTTATAAAATTT
1 ATAAAAAATTATTAAAATTTTAAAAATATAATTTATAAAATTT
**
16779581 ATAAAAGAATTATTAGAAATTTATAAATAATTATAAAATTTATTAAAAACT
1 ATAAAA-AATTATTA-AAATTT-TAAA-AA-TAT--AATTTA-TAAAATTT
**
16779632 ATAAAAAATATAGAAAAATTTTAAA
1 ATAAAAAAT-TATTAAAATTTTAAA
16779657 TGTTATATGT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
43 6 0.10
44 8 0.13
45 6 0.10
46 4 0.06
47 2 0.03
48 3 0.05
49 4 0.06
50 15 0.24
51 15 0.24
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.37
Consensus pattern (43 bp):
ATAAAAAATTATTAAAATTTTAAAAATATAATTTATAAAATTT
Found at i:16779627 original size:10 final size:9
Alignment explanation
Indices: 16779567--16779628 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 9
16779557 TTAAAAATAT
16779567 AATTTATAA
1 AATTTATAA
16779576 AATTTATAAA
1 AATTTAT-AA
*
16779586 AGAATTATTAGA
1 A-ATTTA-TA-A
16779598 AATTTATAA
1 AATTTATAA
*
16779607 ATAATTATAA
1 A-ATTTATAA
16779617 AATTTATTAA
1 AATTTA-TAA
16779627 AA
1 AA
16779629 ACTATAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
9 13 0.30
10 18 0.42
11 9 0.21
12 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (9 bp):
AATTTATAA
Found at i:16783950 original size:100 final size:100
Alignment explanation
Indices: 16783825--16784024 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
16783815 GTTGACACCG
*
16783825 TTGCTCATCGTTTCTATAGTGATTGATGCCATACAAGGCGTATTATCAGGTTTGGATTATGTTCG
1 TTGCTCATCGTTCCTATAGTGATTGATGCCATACAAGGCGTATTATCAGGTTTGGATTATGTTCG
16783890 ACAATTCATATTTACATTTTGAAATGATCGATTCT
66 ACAATTCATATTTACATTTTGAAATGATCGATTCT
*
16783925 TTGCTCATTGTTCCTATAGTGATTGATGCCATACAAGGCGTATTATCAGGTTTGGATTATGTTCG
1 TTGCTCATCGTTCCTATAGTGATTGATGCCATACAAGGCGTATTATCAGGTTTGGATTATGTTCG
16783990 ACAATTCATATTTACATTTTGAAATGATCGATTCT
66 ACAATTCATATTTACATTTTGAAATGATCGATTCT
16784025 AACTTAAAAC
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (100 bp):
TTGCTCATCGTTCCTATAGTGATTGATGCCATACAAGGCGTATTATCAGGTTTGGATTATGTTCG
ACAATTCATATTTACATTTTGAAATGATCGATTCT
Found at i:16785415 original size:7 final size:7
Alignment explanation
Indices: 16785403--16785427 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16785393 GTTTTGAGGA
16785403 TCAGGGT
1 TCAGGGT
16785410 TCAGGGT
1 TCAGGGT
16785417 TCAGGGT
1 TCAGGGT
16785424 TCAG
1 TCAG
16785428 AGTAAGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.40, T:0.28
Consensus pattern (7 bp):
TCAGGGT
Found at i:16785968 original size:19 final size:19
Alignment explanation
Indices: 16785945--16786016 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 19
16785935 AAAAATTAAA
16785945 AAAAATTCAAAAATATTTT
1 AAAAATTCAAAAATATTTT
*
16785964 CAAAAAGTTTAAATAAT-TTTT
1 -AAAAA-TTCAAA-AATATTTT
16785985 -AAAATTC-AAAATATTTAT
1 AAAAATTCAAAAATATTT-T
16786003 AAAAAATT-AAAAAT
1 -AAAAATTCAAAAAT
16786017 TTATGTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
16 3 0.07
17 5 0.12
18 3 0.07
19 4 0.09
20 16 0.37
21 9 0.21
22 3 0.07
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (19 bp):
AAAAATTCAAAAATATTTT
Found at i:16791628 original size:23 final size:23
Alignment explanation
Indices: 16791598--16791718 Score: 127
Period size: 23 Copynumber: 5.3 Consensus size: 23
16791588 ATATATGCTA
*
16791598 ATACTGTTATCAAACTGATTTTG
1 ATACTGTTACCAAACTGATTTTG
*
16791621 ATACTGTTACCAAA-TTATTTTTG
1 ATACTGTTACCAAACTGA-TTTTG
* ***
16791644 ATATTGTTACTGTACTGATTTTG
1 ATACTGTTACCAAACTGATTTTG
*
16791667 ATACTGTTACCAAACTAATTTTG
1 ATACTGTTACCAAACTGATTTTG
* * * *
16791690 TTATTGTTACCGAACTGATTTTC
1 ATACTGTTACCAAACTGATTTTG
16791713 ATACTG
1 ATACTG
16791719 AAATGCATAA
Statistics
Matches: 77, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
22 2 0.03
23 73 0.95
24 2 0.03
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.45
Consensus pattern (23 bp):
ATACTGTTACCAAACTGATTTTG
Found at i:16791669 original size:46 final size:46
Alignment explanation
Indices: 16791610--16791718 Score: 164
Period size: 46 Copynumber: 2.4 Consensus size: 46
16791600 ACTGTTATCA
* * *
16791610 AACTGATTTTGATACTGTTACCAAATTATTTTTGATATTGTTACTG
1 AACTGATTTTGATACTGTTACCAAACTAATTTTGATATTGTTACCG
* *
16791656 TACTGATTTTGATACTGTTACCAAACTAATTTTGTTATTGTTACCG
1 AACTGATTTTGATACTGTTACCAAACTAATTTTGATATTGTTACCG
*
16791702 AACTGATTTTCATACTG
1 AACTGATTTTGATACTG
16791719 AAATGCATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 56 1.00
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.46
Consensus pattern (46 bp):
AACTGATTTTGATACTGTTACCAAACTAATTTTGATATTGTTACCG
Found at i:16796160 original size:20 final size:18
Alignment explanation
Indices: 16796124--16796164 Score: 64
Period size: 20 Copynumber: 2.2 Consensus size: 18
16796114 AAACCTTCAA
16796124 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
16796142 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
16796162 TTT
1 TTT
16796165 CNNNNNNNNN
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 6 0.29
20 10 0.48
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:16798153 original size:20 final size:18
Alignment explanation
Indices: 16798117--16798161 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
16798107 AAACCTTCAA
16798117 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
16798135 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
16798155 -TTTCCCT
1 TTTTCCCT
16798162 GCTTTTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:16798395 original size:20 final size:20
Alignment explanation
Indices: 16798372--16798411 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16798362 TATAATTATT
16798372 TAATTAATAAATATCTTTTA
1 TAATTAATAAATATCTTTTA
16798392 TAATTAATAAATATCTTTTA
1 TAATTAATAAATATCTTTTA
16798412 ATACTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTAATAAATATCTTTTA
Found at i:16800326 original size:21 final size:21
Alignment explanation
Indices: 16800287--16800341 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
16800277 TATTAATTCA
*
16800287 TATTTTAAT-AATTATTATAT
1 TATTTTATTAAATTATTATAT
*
16800307 TAATTTTTTTAAATTA-TATAT
1 T-ATTTTATTAAATTATTATAT
16800328 TATTTTATTAAATT
1 TATTTTATTAAATT
16800342 GTATTTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.43
21 12 0.40
22 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTTTATTAAATTATTATAT
Found at i:16800358 original size:29 final size:28
Alignment explanation
Indices: 16800292--16800359 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
16800282 ATTCATATTT
*
16800292 TAATAATTATTATATTAATTTTTTTAAA
1 TAATAATTATTATATTAATTTATTTAAA
* * *
16800320 TTATATATTATTTTATTAAATTGTATTT-CA
1 TAATA-ATTATTATATT-AATT-TATTTAAA
16800350 TAATAATTAT
1 TAATAATTAT
16800360 GTTAAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 4 0.12
29 15 0.47
30 9 0.28
31 4 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (28 bp):
TAATAATTATTATATTAATTTATTTAAA
Found at i:16800562 original size:39 final size:40
Alignment explanation
Indices: 16800507--16800608 Score: 100
Period size: 44 Copynumber: 2.4 Consensus size: 40
16800497 TTTCTTATGT
*
16800507 TATTACATCATCTATTCTATTCAACCAAAC-ACAAGAA-TAC
1 TATTACAGC-TCTATTCTATTCAACCAAACAAC-AGAATTAC
*
16800547 TATTACAGCTCTATTCCATTCTATTCAACCAAACAACTGAATTAC
1 TATTACAGCTC---T--ATTCTATTCAACCAAACAACAGAATTAC
16800592 TGATTACAGCTCTATTC
1 T-ATTACAGCTCTATTC
16800609 CATTACAGTC
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
39 2 0.04
40 8 0.15
41 4 0.08
42 1 0.02
43 1 0.02
44 20 0.38
45 6 0.12
46 10 0.19
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (40 bp):
TATTACAGCTCTATTCTATTCAACCAAACAACAGAATTAC
Found at i:16800570 original size:44 final size:46
Alignment explanation
Indices: 16800520--16800612 Score: 147
Period size: 44 Copynumber: 2.1 Consensus size: 46
16800510 TACATCATCT
16800520 ATTCTATTCAACCAAAC-ACAAGAA-TACT-ATTACAGCTCTATTCC
1 ATTCTATTCAACCAAACAAC-AGAATTACTGATTACAGCTCTATTCC
*
16800564 ATTCTATTCAACCAAACAACTGAATTACTGATTACAGCTCTATTCC
1 ATTCTATTCAACCAAACAACAGAATTACTGATTACAGCTCTATTCC
16800610 ATT
1 ATT
16800613 ACAGTCTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
44 20 0.44
45 6 0.13
46 19 0.42
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (46 bp):
ATTCTATTCAACCAAACAACAGAATTACTGATTACAGCTCTATTCC
Found at i:16800615 original size:16 final size:16
Alignment explanation
Indices: 16800594--16800628 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
16800584 TGAATTACTG
16800594 ATTACAG-CTCTATTCC
1 ATTACAGTCT-TATTCC
16800610 ATTACAGTCTTATTCC
1 ATTACAGTCTTATTCC
16800626 ATT
1 ATT
16800629 CCCCCCAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTACAGTCTTATTCC
Found at i:16801444 original size:47 final size:49
Alignment explanation
Indices: 16801391--16801485 Score: 122
Period size: 49 Copynumber: 2.0 Consensus size: 49
16801381 ATGATTTATG
* * * *
16801391 GGTTACAAGATAATGAATTT-A-GGGGTTATGGACATTCATTTTTTAAA
1 GGTTACAAGAGAATAAATTTGAGGGGGTTATGGACATCCATTTATTAAA
* *
16801438 GGTTACAATAGCATAAATTTGAGGGGGTTATGGACATCCATTTATTAA
1 GGTTACAAGAGAATAAATTTGAGGGGGTTATGGACATCCATTTATTAA
16801486 TGAGTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
47 16 0.40
48 1 0.03
49 23 0.57
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (49 bp):
GGTTACAAGAGAATAAATTTGAGGGGGTTATGGACATCCATTTATTAAA
Found at i:16804627 original size:12 final size:12
Alignment explanation
Indices: 16804610--16804634 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16804600 AATGGGTGCC
16804610 CAATTGAATTCT
1 CAATTGAATTCT
16804622 CAATTGAATTCT
1 CAATTGAATTCT
16804634 C
1 C
16804635 GATTATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (12 bp):
CAATTGAATTCT
Found at i:16807212 original size:22 final size:22
Alignment explanation
Indices: 16807170--16807213 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16807160 ATAAATTATA
* **
16807170 AATATATTTATAAATTTAAATT
1 AATATATTTAAAAATGAAAATT
16807192 AATATATTTAAAAATGAAAATT
1 AATATATTTAAAAATGAAAATT
16807214 TGAAGAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATATTTAAAAATGAAAATT
Found at i:16808260 original size:89 final size:87
Alignment explanation
Indices: 16808158--16808318 Score: 207
Period size: 87 Copynumber: 1.8 Consensus size: 87
16808148 AAATTTTTTC
* * * ** *
16808158 AAAACAAATAATTAAGCCCCTATTTTTTTTGTTGCACTCACTTCG-GTACTTAAACTTTCAAAAT
1 AAAAAAAACAATTAAGCCCCTA-CTTTTTT-TAACACTCAATT-GAGTACTTAAACTTTCAAAAT
16808222 GTATAAAAAAAGTCTTCAAACTTTA
63 GTATAAAAAAAGTCTTCAAACTTTA
* * *
16808247 AAAAAAAACAATTAAGCCCTTACTTTTTTTAACATTCAATTGAGTACTTAAACTTTCAAAATTTA
1 AAAAAAAACAATTAAGCCCCTACTTTTTTTAACACTCAATTGAGTACTTAAACTTTCAAAATGTA
16808312 TAAAAAA
66 TAAAAAA
16808319 TACCCCAAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
86 1 0.02
87 36 0.58
88 6 0.10
89 19 0.31
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.35
Consensus pattern (87 bp):
AAAAAAAACAATTAAGCCCCTACTTTTTTTAACACTCAATTGAGTACTTAAACTTTCAAAATGTA
TAAAAAAAGTCTTCAAACTTTA
Found at i:16808609 original size:3 final size:3
Alignment explanation
Indices: 16808597--16808632 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
16808587 CTCCCTAAAT
16808597 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16808633 ATTATAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:16808863 original size:28 final size:29
Alignment explanation
Indices: 16808814--16808869 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
16808804 AAATTTAACA
*
16808814 ATTCAAAATCAAATTAAGTAAA-AATAAT
1 ATTCAAAATCAAATTAAATAAATAATAAT
*
16808842 ATTCAAAAT-TAATTAAAATAAATAATAA
1 ATTCAAAATCAAATT-AAATAAATAATAA
16808870 AGGTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.17
28 15 0.62
29 5 0.21
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.30
Consensus pattern (29 bp):
ATTCAAAATCAAATTAAATAAATAATAAT
Found at i:16809562 original size:18 final size:18
Alignment explanation
Indices: 16809547--16809600 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
16809537 TATAAAATCA
16809547 AATAATTATTTCAAATAT
1 AATAATTATTTCAAATAT
* *
16809565 CATTATTATTTCAAATATGT
1 AATAATTATTTCAAATA--T
16809585 AA-AA-TATTTCAAATAT
1 AATAATTATTTCAAATAT
16809601 CATTGTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 1 0.03
18 26 0.87
19 1 0.03
20 2 0.07
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (18 bp):
AATAATTATTTCAAATAT
Found at i:16812477 original size:18 final size:18
Alignment explanation
Indices: 16812450--16812542 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
16812440 TACGACCGTT
*
16812450 TACGGTACTATTCACGTA
1 TACGGCACTATTCACGTA
16812468 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
16812486 TACAGTACTATTCACGTA
1 TACGGCACTATTCACGTA
16812504 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
16812522 TACGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
16812540 TAC
1 TAC
16812543 NNNNNNNNNN
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 70 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:16815373 original size:16 final size:16
Alignment explanation
Indices: 16815352--16815382 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16815342 TAGTATTATT
*
16815352 CTTTAAAATATTTTAC
1 CTTTAAAAAATTTTAC
16815368 CTTTAAAAAATTTTA
1 CTTTAAAAAATTTTA
16815383 AAGATTTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (16 bp):
CTTTAAAAAATTTTAC
Found at i:16815891 original size:11 final size:11
Alignment explanation
Indices: 16815875--16815905 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
16815865 ATACCCATAC
16815875 CCCATACCTTG
1 CCCATACCTTG
*
16815886 CCCATACCTTT
1 CCCATACCTTG
16815897 CCCATACCT
1 CCCATACCT
16815906 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:16819585 original size:24 final size:24
Alignment explanation
Indices: 16819488--16819647 Score: 139
Period size: 24 Copynumber: 6.6 Consensus size: 24
16819478 AAGGAAATTT
* * * *
16819488 GCACCCATAGTGCCATGTTAACCC
1 GCACACATAGTGCCATATAAATCC
*
16819512 GCACACATAGTGCCTTA-ATAATCC
1 GCACACATAGTGCCATATA-AATCC
** *
16819536 ATACACATA-TCGACGAT-TCAAATCC
1 GCACACATAGT-G-CCATAT-AAATCC
*
16819561 GCACACATAGTGCCGTATAAATCC
1 GCACACATAGTGCCATATAAATCC
* * *
16819585 GCACACATAGTGCTATACAAATCT
1 GCACACATAGTGCCATATAAATCC
16819609 GCACACATAGTGCCAT-TCAAATCC
1 GCACACATAGTGCCATAT-AAATCC
16819633 GCACACATAGTGCCA
1 GCACACATAGTGCCA
16819648 AGGTCATTTC
Statistics
Matches: 108, Mismatches: 20, Indels: 16
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.01
24 89 0.82
25 16 0.15
26 2 0.02
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.22
Consensus pattern (24 bp):
GCACACATAGTGCCATATAAATCC
Found at i:16822150 original size:9 final size:9
Alignment explanation
Indices: 16822131--16822310 Score: 57
Period size: 9 Copynumber: 18.9 Consensus size: 9
16822121 TGTTATTATT
16822131 TATTAAAAAA
1 TATT-AAAAA
16822141 TATTAAAAA
1 TATTAAAAA
* *
16822150 TATGAAAAT
1 TATTAAAAA
**
16822159 TGATATAAACT
1 T-AT-TAAAAA
16822170 TA-TAAAAA
1 TATTAAAAA
16822178 TAATT-AAAA
1 T-ATTAAAAA
16822187 TATTATAATAA
1 TATTA-AA-AA
*
16822198 T-TATAATAA
1 TAT-TAAAAA
16822207 T-TCTAATAAA
1 TAT-TAA-AAA
*
16822217 T-TATAAAAT
1 TAT-TAAAAA
*
16822226 TAATAAAACA
1 TATTAAAA-A
*
16822236 TATTTAAAA
1 TATTAAAAA
*
16822245 TAATTAAAAT
1 T-ATTAAAAA
*
16822255 TGTATAAAAA
1 TAT-TAAAAA
*
16822265 TATTTAAAA
1 TATTAAAAA
16822274 TCA-TAAAAA
1 T-ATTAAAAA
*
16822283 TTATAAAAAA
1 -TATTAAAAA
*
16822293 TATAAAAAA
1 TATTAAAAA
16822302 GTATTAAAA
1 -TATTAAAA
16822311 TTGATATCAA
Statistics
Matches: 129, Mismatches: 24, Indels: 34
0.69 0.13 0.18
Matches are distributed among these distances:
8 8 0.06
9 58 0.45
10 53 0.41
11 10 0.08
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (9 bp):
TATTAAAAA
Found at i:16822192 original size:20 final size:20
Alignment explanation
Indices: 16822169--16822274 Score: 58
Period size: 20 Copynumber: 5.0 Consensus size: 20
16822159 TGATATAAAC
16822169 TTATAAAAATAATTAAAATA
1 TTATAAAAATAATTAAAATA
16822189 TTATAATAATTATAA-TAATTCTAATAAA
1 TTATAA-AA--ATAATTAA----AAT--A
* *
16822217 TTATAAAATTAATAAAACATA
1 TTATAAAAATAATTAAA-ATA
16822238 TT-T-AAAATAATTAAAAT-
1 TTATAAAAATAATTAAAATA
*
16822255 TGTATAAAAATATTTAAAAT
1 T-TATAAAAATAATTAAAAT
16822275 CATAAAAATT
Statistics
Matches: 67, Mismatches: 5, Indels: 28
0.67 0.05 0.28
Matches are distributed among these distances:
17 1 0.01
18 3 0.04
19 11 0.16
20 20 0.30
21 5 0.07
22 4 0.06
23 6 0.09
25 3 0.04
26 5 0.07
27 2 0.03
28 7 0.10
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (20 bp):
TTATAAAAATAATTAAAATA
Found at i:16822201 original size:29 final size:28
Alignment explanation
Indices: 16822169--16822299 Score: 110
Period size: 29 Copynumber: 4.6 Consensus size: 28
16822159 TGATATAAAC
*
16822169 TTATAAAAATAATTAAAAT-ATTATAATAA
1 TTATAAAAATATTTAAAATAATTA-AA-AA
* * *
16822198 TTATAATAAT-TCTAATA-AATTATAAAA
1 TTATAAAAATATTTAAAATAATTA-AAAA
*
16822225 TTAATAAAACATATTTAAAATAATTAAAAT
1 TT-ATAAAA-ATATTTAAAATAATTAAAAA
*
16822255 TGTATAAAAATATTTAAAATCA-TAAAAA
1 T-TATAAAAATATTTAAAATAATTAAAAA
*
16822283 TTATAAAAA-ATATAAAA
1 TTATAAAAATATTTAAAA
16822300 AAGTATTAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 15
0.77 0.10 0.14
Matches are distributed among these distances:
26 7 0.08
27 12 0.14
28 22 0.26
29 23 0.27
30 15 0.18
31 6 0.07
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (28 bp):
TTATAAAAATATTTAAAATAATTAAAAA
Found at i:16822214 original size:26 final size:26
Alignment explanation
Indices: 16822176--16822227 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
16822166 AACTTATAAA
16822176 AATAATTAAAAT-ATTATAATAATTAT
1 AATAATTAAAATAATTATAA-AATTAT
**
16822202 AATAATTCTAATAAATTATAAAATTA
1 AATAATTAAAAT-AATTATAAAATTA
16822228 ATAAAACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 10 0.45
27 5 0.23
28 7 0.32
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AATAATTAAAATAATTATAAAATTAT
Done.