Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002316.1 Hibiscus syriacus cultivar Beakdansim tig00004717_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 75263
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:1515 original size:78 final size:78
Alignment explanation
Indices: 1406--1549 Score: 243
Period size: 78 Copynumber: 1.8 Consensus size: 78
1396 GAATTTCAAG
* * * *
1406 AGAGTTTTACTCTAACTAAAACTCTTTTAATATCTAAATTTAAATGGATAATGATATCTTTTAAA
1 AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAA
1471 TAAATTAAACCTA
66 TAAATTAAACCTA
*
1484 AGAGTTTTACTCAAACCAAAACTCTTTTAATATTTAAATTTAAATAGATAATAATATCTTTTAAA
1 AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAA
1549 T
66 T
1550 TTAAATATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 61 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (78 bp):
AGAGTTTTACTCAAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAA
TAAATTAAACCTA
Found at i:3365 original size:21 final size:21
Alignment explanation
Indices: 3339--3394 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
3329 ACAGTGATAT
*
3339 AGTGTATCGATGCATTGCTAC
1 AGTGTACCGATGCATTGCTAC
3360 AGTGTACCGATGCATTGCTAC
1 AGTGTACCGATGCATTGCTAC
3381 AGTGTACCGATGCA
1 AGTGTACCGATGCA
3395 CAAAAACATC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (21 bp):
AGTGTACCGATGCATTGCTAC
Found at i:3441 original size:21 final size:21
Alignment explanation
Indices: 3416--3480 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
3406 AATATAAATT
* *
3416 GTGTATCGATGCACTGCTACA
1 GTGTACCGATGCACTTCTACA
3437 GTGTACCGATGCACTTCTACA
1 GTGTACCGATGCACTTCTACA
3458 GTGTACCGATGCACTTCTACA
1 GTGTACCGATGCACTTCTACA
3479 GT
1 GT
3481 AACTTCAGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (21 bp):
GTGTACCGATGCACTTCTACA
Found at i:11256 original size:82 final size:83
Alignment explanation
Indices: 11095--11259 Score: 314
Period size: 82 Copynumber: 2.0 Consensus size: 83
11085 TTTTTTCAAA
*
11095 GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGATTTTAGGTTTAAATAACCTATCTTCA
1 GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGATATTAGGTTTAAATAACCTATCTTCA
11160 CTTAGTGCTTAAAATAAT
66 CTTAGTGCTTAAAATAAT
11178 GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGA-ATTAGGTTTAAATAACCTATCTTCA
1 GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGATATTAGGTTTAAATAACCTATCTTCA
11242 CTTAGTGCTTAAAATAAT
66 CTTAGTGCTTAAAATAAT
11260 TTAGCACTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
82 42 0.52
83 39 0.48
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (83 bp):
GCCTTTAGACAAGGAAAGATTTTGGACACTTAGGAGAGATATTAGGTTTAAATAACCTATCTTCA
CTTAGTGCTTAAAATAAT
Found at i:11529 original size:21 final size:21
Alignment explanation
Indices: 11505--11585 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
11495 TTGGTGCAGA
*
11505 GGGAATCGATACCCCCTGAAG
1 GGGAACCGATACCCCCTGAAG
*
11526 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC--TGAAG
* * *
11549 GGGAACCAATTCCCCCTGTAG
1 GGGAACCGATACCCCCTGAAG
* *
11570 GAGAATCGATACCCCC
1 GGGAACCGATACCCCC
11586 CTGGGGTTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
21 30 0.60
23 20 0.40
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCCCTGAAG
Found at i:11551 original size:23 final size:22
Alignment explanation
Indices: 11505--11565 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
11495 TTGGTGCAGA
* *
11505 GGGAATCGATACCCCC-TGAAG
1 GGGAACCGATTCCCCCTTGAAG
11526 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
*
11549 GGGAACCAATTCCCCCT
1 GGGAACCGATTCCCCCT
11566 GTAGGAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.40
22 1 0.03
23 20 0.57
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:16965 original size:57 final size:57
Alignment explanation
Indices: 16824--17087 Score: 177
Period size: 57 Copynumber: 4.5 Consensus size: 57
16814 CGAGACTTTC
** * *
16824 AAGAAATAAATTCAACAATTTA-TTTCTTTTTACAAGAA-AGAATCATACTTGATTTTC
1 AAGAAATAAATTCAACAATTTATTTTC-TTTTACAA-AATAGAATCATACAAGATTCTA
* ** *
16881 AAGAGATAAATTCAATGATTTAATTTCTTTTACAAAATAGAATCATACAAGATTCT-
1 AAGAAATAAATTCAACAATTTATTTTCTTTTACAAAATAGAATCATACAAGATTCTA
* * * * *
16937 ATGAATATAAATTTAACAATTTATTTTCTTCTACAAGAT-GAATTCGAT-CAAGATT-TCC
1 AAGAA-ATAAATTCAACAATTTATTTTCTTTTACAAAATAGAA-TC-ATACAAGATTCT-A
** * *
16995 AAGAAAATAAATTTC-ACGTTTTATTTCCTTTT-CAAAGTTAGAATCA-ACGCAAGATTCTA
1 AAG-AAATAAA-TTCAACAATTTATTTTCTTTTACAAA-ATAGAATCATA--CAAGATTCTA
*
17054 AGGTGAAATAAATTCAACAATTTATTTCTCTTTT
1 A--AGAAATAAATTCAACAATTTATTT-TCTTTT
17088 TCCAATGCTA
Statistics
Matches: 161, Mismatches: 27, Indels: 34
0.73 0.12 0.15
Matches are distributed among these distances:
56 9 0.06
57 82 0.51
58 29 0.18
59 18 0.11
60 17 0.11
61 6 0.04
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (57 bp):
AAGAAATAAATTCAACAATTTATTTTCTTTTACAAAATAGAATCATACAAGATTCTA
Found at i:18703 original size:82 final size:83
Alignment explanation
Indices: 18540--18782 Score: 393
Period size: 82 Copynumber: 2.9 Consensus size: 83
18530 TTCGAGAAAG
* *
18540 TTTTGCTCCAACTAAAACTCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTA
1 TTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTA
18605 AAATATTAAATC-TGAGAA
66 AAATATTAAA-CATGAGAA
18623 TTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAA-AAATAATAATATCTTTTAAATTTA
1 TTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTA
*
18687 AAATAATAAACATGAGAA
66 AAATATTAAACATGAGAA
* * *
18705 TTTTACTCAAACCAAAACTCTTTTAATAACTAAATTTAAACATATAATAATATCTTTTTAAATTT
1 TTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAAATAATAATATC-TTTTAAATTT
18770 -AAATATTAAACAT
65 AAAATATTAAACAT
18783 ATATTTCCTC
Statistics
Matches: 150, Mismatches: 7, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
81 1 0.01
82 77 0.51
83 62 0.41
84 10 0.07
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (83 bp):
TTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAACAAATAATAATATCTTTTAAATTTA
AAATATTAAACATGAGAA
Found at i:21585 original size:2 final size:2
Alignment explanation
Indices: 21578--21608 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
21568 AAATAAAAAT
*
21578 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21609 TAAAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25983 original size:29 final size:29
Alignment explanation
Indices: 25948--26029 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
25938 AAACTAAATT
25948 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTACTTACATCATTTAATTAAA
* *
25977 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTACTTACATCATTTAATTAAA
*
26006 GATGTCATTTCTTACATCAATTTA
1 GATGTCATTACTTACATC-ATTTA
26030 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.44
Consensus pattern (29 bp):
GATGTCATTACTTACATCATTTAATTAAA
Found at i:26447 original size:18 final size:20
Alignment explanation
Indices: 26424--26461 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
26414 AAATCGAGTT
26424 GAGTCA-CCGAGTT-GAGCC
1 GAGTCAGCCGAGTTGGAGCC
26442 GAGTCAGCCGAGTTGGAGCC
1 GAGTCAGCCGAGTTGGAGCC
26462 CTTGACCGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 7 0.39
20 5 0.28
ACGTcount: A:0.21, C:0.26, G:0.37, T:0.16
Consensus pattern (20 bp):
GAGTCAGCCGAGTTGGAGCC
Found at i:30748 original size:29 final size:29
Alignment explanation
Indices: 30713--30794 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
30703 AAACTAAATT
*
30713 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
30742 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
30771 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
30795 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:33577 original size:21 final size:21
Alignment explanation
Indices: 33551--33619 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
33541 CGAACCCTGC
33551 AGCTGTGTTCAAACAACATAT
1 AGCTGTGTTCAAACAACATAT
* * *
33572 AGCTGT-TT--ACCATTCATTT
1 AGCTGTGTTCAAACA-ACATAT
33591 GAAGCTGTGTTCAAACAACATAT
1 --AGCTGTGTTCAAACAACATAT
33614 AGCTGT
1 AGCTGT
33620 TTACCATTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 3 0.08
19 4 0.11
20 2 0.06
21 18 0.50
22 2 0.06
23 4 0.11
24 3 0.08
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (21 bp):
AGCTGTGTTCAAACAACATAT
Found at i:33610 original size:42 final size:42
Alignment explanation
Indices: 33551--33658 Score: 180
Period size: 42 Copynumber: 2.6 Consensus size: 42
33541 CGAACCCTGC
33551 AGCTGTGTTCAAACAACATATAGCTGTTTACCATTCATTTGA
1 AGCTGTGTTCAAACAACATATAGCTGTTTACCATTCATTTGA
*
33593 AGCTGTGTTCAAACAACATATAGCTGTTTACCATTCATTTGC
1 AGCTGTGTTCAAACAACATATAGCTGTTTACCATTCATTTGA
* * *
33635 AGCTGTCTTCAAACCACATGTAGC
1 AGCTGTGTTCAAACAACATATAGC
33659 CGATACACTC
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (42 bp):
AGCTGTGTTCAAACAACATATAGCTGTTTACCATTCATTTGA
Found at i:33638 original size:21 final size:20
Alignment explanation
Indices: 33572--33640 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 20
33562 AACAACATAT
33572 AGCTGTTTACCATTCATTTG
1 AGCTGTTTACCATTCATTTG
* * *
33592 AAGCTGTGTTCAAACA-ACATAT-
1 -AGCTGT-TT--ACCATTCATTTG
33614 AGCTGTTTACCATTCATTTG
1 AGCTGTTTACCATTCATTTG
33634 CAGCTGT
1 -AGCTGT
33641 CTTCAAACCA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 3 0.08
19 4 0.11
20 2 0.06
21 18 0.50
22 2 0.06
23 4 0.11
24 3 0.08
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (20 bp):
AGCTGTTTACCATTCATTTG
Found at i:36313 original size:41 final size:41
Alignment explanation
Indices: 36247--36343 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
36237 CGATCTCTAA
* * **
36247 TTCGCATTGCGAT-CTTGAAAATCGCGTTACGATTTTGTAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCAT
*
36287 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCAT
* *
36328 TTCGTGTCGCGATAGT
1 TTCGCGTTGCGATAGT
36344 CTACAGTTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 12 0.24
41 37 0.76
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCAT
Found at i:36314 original size:21 final size:20
Alignment explanation
Indices: 36248--36320 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
36238 GATCTCTAAT
*
36248 TCGCATTGCGATCTTGAAAA
1 TCGCGTTGCGATCTTGAAAA
* * * **
36268 TCGCGTTACGATTTTGTATT
1 TCGCGTTGCGATCTTGAAAA
*
36288 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-CTTGAAAA
36309 TCGCGTTGCGAT
1 TCGCGTTGCGAT
36321 TTTCCATTTC
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 25 0.61
21 16 0.39
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATCTTGAAAA
Found at i:36465 original size:6 final size:6
Alignment explanation
Indices: 36454--36521 Score: 136
Period size: 6 Copynumber: 11.3 Consensus size: 6
36444 GTCGACAAAT
36454 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
36502 GACCAC GACCAC GACCAC GA
1 GACCAC GACCAC GACCAC GA
36522 GACGAGACGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.34, C:0.49, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:37207 original size:22 final size:24
Alignment explanation
Indices: 37182--37238 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
37172 AATTTAGAAA
*
37182 ATCGCAACGAC-C-ACTGTAGACT
1 ATCGCAACGACACTACGGTAGACT
*
37204 ATCGCAACAACAACTACGGTAGACT
1 ATCGCAACGAC-ACTACGGTAGACT
37229 ATCGCAACGA
1 ATCGCAACGA
37239 ATTTGGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.34
24 1 0.03
25 18 0.62
ACGTcount: A:0.37, C:0.30, G:0.18, T:0.16
Consensus pattern (24 bp):
ATCGCAACGACACTACGGTAGACT
Found at i:44171 original size:15 final size:14
Alignment explanation
Indices: 44151--44182 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
44141 AAGTAGTATC
44151 GTACTGATTCAATCA
1 GTACTGATTCAAT-A
44166 GTACTGATTCAATA
1 GTACTGATTCAATA
44180 GTA
1 GTA
44183 TCGATACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (14 bp):
GTACTGATTCAATA
Found at i:44206 original size:18 final size:20
Alignment explanation
Indices: 44180--44229 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
44170 TGATTCAATA
44180 GTATCGATACCAT-G-AA-G
1 GTATCGATACCATGGTAAGG
44197 GTAGTCGATACCATGGTAAGG
1 GTA-TCGATACCATGGTAAGG
44218 GTATCGATACCA
1 GTATCGATACCA
44230 AACATCATCG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.10
18 10 0.34
19 1 0.03
20 11 0.38
21 4 0.14
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (20 bp):
GTATCGATACCATGGTAAGG
Found at i:44689 original size:59 final size:59
Alignment explanation
Indices: 44616--44816 Score: 321
Period size: 59 Copynumber: 3.4 Consensus size: 59
44606 ATTACCAAAT
* * * * *
44616 GGCACTACGTGTGCTAAAATGATAAGAAATTCATATTAAGTGTATGAATTTCTATATAT
1 GGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
* * * *
44675 GGCACTTTGTGTGCTAAAACGTTAAAAAATTCATACTAAGTCTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
44734 GGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
1 GGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
44793 GGCACTTCGTGTGCTAAAATGTTA
1 GGCACTTCGTGTGCTAAAATGTTA
44817 TAAAAATCAT
Statistics
Matches: 129, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 129 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (59 bp):
GGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
Found at i:44753 original size:49 final size:51
Alignment explanation
Indices: 44699--45471 Score: 247
Period size: 59 Copynumber: 13.8 Consensus size: 51
44689 TAAAACGTTA
44699 AAAAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATGTT
1 AAAAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC----A---T
*
44757 AAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC-T
1 AA-AAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGCAT
* * * * *
44808 -AAAATGTTATA-AAAATC-AT--A----C--ACAGGGTACTTCGTGTGCTAAAATGTT
1 AAAAAT-TCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC----A---T
* *
44856 AAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTGTGCTAAAATGTT
1 AA-AAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC----A---T
* * * **
44915 AATAAATTCATACTAAGTGTATAAAGTTCCATATTA----AAAT-G-GT--A-
1 AA-AAATTCATACTAAGTCTATGAATTTCCATA-TAGGGCACTTCGTGTGCAT
* * * *
44959 AGAAATTCATACTAAGTGTATGAATTTCCATATAAGGCACTTCATGTGCTAAAATGCT
1 AAAAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC----A---T
* * *
45017 AAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGAACTTCGTTTGCTAAAATGTT
1 AA-AAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC----A---T
* **
45076 AAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTTTTAAAATGTT
1 AA-AAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTG---T-GCA---T
* *
45135 AAAAAAATCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATGGT
1 -AAAAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC----A---T
*
45194 AAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATGAT
1 AA-AAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC-------AT
* * * *
45253 AAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTTGTGTGCTAAAATGAT
1 AA-AAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC-------AT
* *
45312 AAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTAAAATGAT
1 AA-AAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC-------AT
* * *
45371 AAGAAAGTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGCTAAAAGGAT
1 AA-AAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGC-------AT
* * *
45430 AAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACT
1 AA-AAATTCATACTAAGTCTATGAATTTCCATATAGGGCACT
45472 ATGCGTGCTA
Statistics
Matches: 610, Mismatches: 52, Indels: 105
0.80 0.07 0.14
Matches are distributed among these distances:
40 16 0.03
42 3 0.00
43 28 0.05
44 1 0.00
46 3 0.00
48 6 0.01
49 12 0.02
50 12 0.02
51 3 0.00
53 1 0.00
54 3 0.00
55 1 0.00
56 3 0.00
57 1 0.00
58 5 0.01
59 505 0.83
60 4 0.01
62 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (51 bp):
AAAAATTCATACTAAGTCTATGAATTTCCATATAGGGCACTTCGTGTGCAT
Found at i:44827 original size:118 final size:118
Alignment explanation
Indices: 44616--45639 Score: 951
Period size: 118 Copynumber: 8.5 Consensus size: 118
44606 ATTACCAAAT
* * * *
44616 GGCACTACGTGTGCTAAAATGATAAGAAATTCATATTAAGTGTATGAATTTCTATATATGGCACT
1 GGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT
* * *
44681 TTGTGTGCTAAAACGTTAAAAAATTCATACTAAGTCTATGAATTTCCATATAG
66 TCGTGTGCTAAAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCATATAG
*
44734 GGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT
1 GGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT
* *** * * *
44799 TCGTGTGCTAAAATGTTATAAAAA-TCATAC-ACAGGGTACTTCGTGTGC-TAAAATG
66 TCGTGTGCTAAAATGTTA-AAAAATTCATACTA-AGTGTA-TGAATTTCCAT-ATA-G
* * * * * * * * * *
44854 TTAAGAAATTC--ATACT-AAGTG-TATGAATTTCCATA-TAGGGCATTTCGTGTGCTAAAATGT
1 ---GGCACTTCGTGTGCTAAAATGATAAGAAATT-CATACTA----A----GTGT-AT-GAAT-T
* *** ** * *
44914 T-AATA-AATTCATACTAAGTGTATAAAGTTCCATATTAAAATGGTAAGAAATTCATACTAAGTG
51 TCCATATAGGGC--ACTTCGTG--T---G---C----TAAAATGTTAAAAAATTCATACTAAGTG
*
44977 TATGAATTTCCATATAA
102 TATGAATTTCCATATAG
* * *
44994 GGCACTTCATGTGCTAAAATGCTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGAACT
1 GGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT
* *
45059 TCGTTTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
66 TCGTGTGCTAAAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCATATAG
** * * *
45112 GGCACTTCGTGTTTTAAAATGTTAAAAAAATCATACTAAGTGTATGAATTTCCATATAGGGCACT
1 GGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT
* *
45177 TCGTGTGCTAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATATAG
66 TCGTGTGCTAAAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCATATAG
* *
45230 GGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACT
1 GGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT
* * * *
45295 TTGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAG
66 TCGTGTGCTAAAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCATATAG
* *
45348 GGCACTTCGTGTGCTAAAATGATAAGAAAGTCATACTAAGTGTATGAATTTCCGTATAGGGCACT
1 GGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT
* * * * *
45413 TCGTGTGCTAAAAGGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
66 TCGTGTGCTAAAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCATATAG
* * * *
45466 GGCACTAT-GCGTGCTAAAAT-ATTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTGGGCA
1 GGCACT-TCGTGTGCTAAAATGA-TAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA
*** * ** *
45529 C-TCGATGTAAAAAAATGTTAATAAATTCATACTAAGTGTATGAATTTCTTTATTG
64 CTTCG-TGTGCTAAAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCATATAG
** * *
45584 GGCACTTTATGTGC-AAAAAGATAAGAAACTCATACTAAGTGTATGAATTTCCATAT
1 GGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATAT
45640 GAAAAATATA
Statistics
Matches: 754, Mismatches: 103, Indels: 99
0.79 0.11 0.10
Matches are distributed among these distances:
117 42 0.06
118 569 0.75
119 21 0.03
120 9 0.01
121 3 0.00
122 1 0.00
123 6 0.01
125 1 0.00
127 4 0.01
128 4 0.01
129 6 0.01
130 15 0.02
131 6 0.01
132 3 0.00
133 4 0.01
135 1 0.00
137 6 0.01
138 1 0.00
139 3 0.00
140 8 0.01
141 19 0.03
142 21 0.03
143 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.34
Consensus pattern (118 bp):
GGCACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT
TCGTGTGCTAAAATGTTAAAAAATTCATACTAAGTGTATGAATTTCCATATAG
Found at i:44908 original size:99 final size:99
Alignment explanation
Indices: 44732--45033 Score: 396
Period size: 99 Copynumber: 3.0 Consensus size: 99
44722 ATTTCCATAT
*
44732 AGGGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA
1 AGGGTACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA
44797 CTTCGTGTGCTAAAATGTT-ATAAAAATCATAC-A
66 CTTCGTGTGCTAAAATGTTAAT-AAAATCATACTA
44830 CAGGGTACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGC
1 -AGGGTACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGC
* *
44895 ATTTCGTGTGCTAAAATGTTAATAAATTCATACTA
65 ACTTCGTGTGCTAAAATGTTAATAAAATCATACTA
* ** * *
44930 AGTGTA-TAAAGT-TCCATATTAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATATA
1 AGGGTACT-TCGTGTGC----TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATA
* * * * *
44993 AGGCACTTCATGTGCTAAAATGCTAAGAAATTCATACTA
61 GGGCACTTCGTGTGCTAAAATGTTAATAAAATCATACTA
45032 AG
1 AG
45034 TGTATGAATT
Statistics
Matches: 183, Mismatches: 13, Indels: 11
0.88 0.06 0.05
Matches are distributed among these distances:
98 3 0.02
99 98 0.54
100 3 0.02
102 79 0.43
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (99 bp):
AGGGTACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA
CTTCGTGTGCTAAAATGTTAATAAAATCATACTA
Found at i:44967 original size:43 final size:43
Alignment explanation
Indices: 44906--44991 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
44896 TTTCGTGTGC
* *
44906 TAAAATGTTAATAAATTCATACTAAGTGTATAAAGTTCCATAT
1 TAAAATGGTAAGAAATTCATACTAAGTGTATAAAGTTCCATAT
* *
44949 TAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATAT
1 TAAAATGGTAAGAAATTCATACTAAGTGTATAAAGTTCCATAT
44992 AAGGCACTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (43 bp):
TAAAATGGTAAGAAATTCATACTAAGTGTATAAAGTTCCATAT
Found at i:44990 original size:21 final size:21
Alignment explanation
Indices: 44918--44994 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 21
44908 AAATGTTAAT
44918 AAATT-CATACTAAGTGTAT-
1 AAATTCCATACTAAGTGTATG
* * *
44937 AAAGTTCCATATTAAAATGGTAAG
1 AAA-TTCCATACT-AAGT-GTATG
44961 AAATT-CATACTAAGTGTATG
1 AAATTCCATACTAAGTGTATG
*
44981 AATTTCCATA-TAAG
1 AAATTCCATACTAAG
44995 GCACTTCATG
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
19 3 0.07
20 14 0.31
21 12 0.27
22 8 0.18
23 5 0.11
24 3 0.07
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (21 bp):
AAATTCCATACTAAGTGTATG
Found at i:45007 original size:102 final size:102
Alignment explanation
Indices: 44747--45050 Score: 406
Period size: 102 Copynumber: 3.0 Consensus size: 102
44737 ACTTCGTGTG
44747 CTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAA
1 CTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAA
* * * *
44812 TGTT-ATAAAAATCATAC-ACAG-G-GT-ACTT-CGTGT
66 TGTTAAT-AAATTCATACTA-AGTGTATAACTTCCATAT
*
44845 GCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCATTTCGTGTGCTAAA
1 -CTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAA
*
44910 ATGTTAATAAATTCATACTAAGTGTATAAAGTTCCATAT
65 ATGTTAATAAATTCATACTAAGTGTAT-AACTTCCATAT
* * *
44949 -TAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATATAAGGCACTTCATGTGCTAAAA
1 CTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAA
* * *
45013 TGCTAAGAAATTCATACTAAGTGTATGAATTTCCATAT
66 TGTTAATAAATTCATACTAAGTGTAT-AACTTCCATAT
45051 AGGGAACTTC
Statistics
Matches: 184, Mismatches: 14, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
99 79 0.43
100 4 0.02
101 1 0.01
102 94 0.51
103 3 0.02
104 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (102 bp):
CTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAA
TGTTAATAAATTCATACTAAGTGTATAACTTCCATAT
Found at i:45022 original size:59 final size:59
Alignment explanation
Indices: 44949--45639 Score: 985
Period size: 59 Copynumber: 11.7 Consensus size: 59
44939 AGTTCCATAT
* * *
44949 TAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATATAAGGCACTTCATGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* * *
45008 TAAAATGCTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGAACTTCGTTTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* **
45067 TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTTT
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* * *
45126 TAAAATGTTAAAAAAATCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
*
45185 TAAAATGGTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* * *
45244 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTTCGTATAGGGCACTTTGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
*
45303 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* *
45362 TAAAATGATAAGAAAGTCATACTAAGTGTATGAATTTCCGTATAGGGCACTTCGTGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* * * *
45421 TAAAAGGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTAT-GCGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACT-TCGTGTGC
* * * **
45480 TAAAAT-ATTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTGGGCAC-TCGATGTAA
1 TAAAATGA-TAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCG-TGTGC
* * * ** * **
45539 AAAAATGTTAATAAATTCATACTAAGTGTATGAATTTCTTTATTGGGCACTTTATGTGC
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
* *
45598 -AAAAAGATAAGAAACTCATACTAAGTGTATGAATTTCCATAT
1 TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATAT
45640 GAAAAATATA
Statistics
Matches: 577, Mismatches: 49, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
57 1 0.00
58 38 0.07
59 536 0.93
60 2 0.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (59 bp):
TAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGC
Found at i:45969 original size:68 final size:69
Alignment explanation
Indices: 45860--46013 Score: 211
Period size: 68 Copynumber: 2.2 Consensus size: 69
45850 ATTAATAGGT
* * **
45860 CTAACTGTGCAATTGACAGAAAGGAGTCATTTATGCTAGTTAGAT-GAAAGGCTAAGTGCCTTTG
1 CTAACTGTGCATTTGACAGAAAGGAGTCATTTATGCTAGTTAGATAAAAAAACTAAGTGCCTTTG
45924 AGGC
66 AGGC
* * * *
45928 CTAACTGTGCATTTGATAGAAATGTGTCATTTATGCTAGTTAGATAAAAAAAACTAAGTGCGTTT
1 CTAACTGTGCATTTGACAGAAAGGAGTCATTTATGCTAGTTAGAT-AAAAAAACTAAGTGCCTTT
45993 GAGGC
65 GAGGC
*
45998 CTAACTGTGCGTTTGA
1 CTAACTGTGCATTTGA
46014 GGCCTAACTG
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
68 41 0.55
70 34 0.45
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (69 bp):
CTAACTGTGCATTTGACAGAAAGGAGTCATTTATGCTAGTTAGATAAAAAAACTAAGTGCCTTTG
AGGC
Found at i:46009 original size:19 final size:19
Alignment explanation
Indices: 45985--46032 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
45975 AAAAAACTAA
45985 GTGCGTTTGAGGCCTAACT
1 GTGCGTTTGAGGCCTAACT
46004 GTGCGTTTGAGGCCTAACT
1 GTGCGTTTGAGGCCTAACT
*
46023 GTGCATTTGA
1 GTGCGTTTGA
46033 CAGAAAGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
GTGCGTTTGAGGCCTAACT
Found at i:46118 original size:68 final size:67
Alignment explanation
Indices: 46004--46200 Score: 279
Period size: 68 Copynumber: 2.9 Consensus size: 67
45994 AGGCCTAACT
* * *
46004 GTGCGTTTGAGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGGC
1 GTGCCTTTGAGGCCTAACTGTGCATTTGA-AGAAATGTGTCATTTATGCTAGTTAGATGAAAGAC
46069 TAA
65 TAA
* *
46072 GTGCCTTTGAGGCCTAAATGTGCATTTGATAGAAATGTATCATTTATGCTAGTTAGATGAAAGAC
1 GTGCCTTTGAGGCCTAACTGTGCATTTGA-AGAAATGTGTCATTTATGCTAGTTAGATGAAAGAC
46137 TAA
65 TAA
* * *
46140 GTGCCTTTGAGGCCTAACTGTGCAATTGGCAAG-AATGTGTCAATTACGCTAGTTAGATGAA
1 GTGCCTTTGAGGCCTAACTGTGC-ATTTG-AAGAAATGTGTCATTTATGCTAGTTAGATGAA
46201 GGGTTAAATA
Statistics
Matches: 116, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
68 109 0.94
69 6 0.05
70 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (67 bp):
GTGCCTTTGAGGCCTAACTGTGCATTTGAAGAAATGTGTCATTTATGCTAGTTAGATGAAAGACT
AA
Found at i:56443 original size:43 final size:43
Alignment explanation
Indices: 56363--56446 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
56353 AACATATTCG
* ** *
56363 ATATTTAGCGGCATTTGTAGTCACAAACGTCGTAATAGATTAA
1 ATATTTAGCGACATTTGTAGTCACAAACACCGCAATAGATTAA
* *
56406 ATATTTAGCGACGTTTGTAGTCAGAAACACCGCAATAGATT
1 ATATTTAGCGACATTTGTAGTCACAAACACCGCAATAGATT
56447 TGATATGTAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (43 bp):
ATATTTAGCGACATTTGTAGTCACAAACACCGCAATAGATTAA
Found at i:56458 original size:43 final size:43
Alignment explanation
Indices: 56362--56458 Score: 113
Period size: 43 Copynumber: 2.3 Consensus size: 43
56352 AAACATATTC
* ** *
56362 GATATTTAGCGGCATTTGTAGTCACAAACGTCGTAATAGATTA
1 GATATTTAGCGACATTTGTAGTCACAAACACCGCAATAGATTA
* * * *
56405 AATATTTAGCGACGTTTGTAGTCAGAAACACCGCAATAGATTT
1 GATATTTAGCGACATTTGTAGTCACAAACACCGCAATAGATTA
*
56448 GATATGTAGCG
1 GATATTTAGCG
56459 GCGTGTCTGG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (43 bp):
GATATTTAGCGACATTTGTAGTCACAAACACCGCAATAGATTA
Found at i:56913 original size:21 final size:21
Alignment explanation
Indices: 56884--56948 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
56874 AATGCTACTT
* * *
56884 CTCTTTCTGTTTCTCTCGTTG
1 CTCTCTCTGCTTCTCTCGCTG
56905 CTCTCTCTGCTTCTCTCGCTG
1 CTCTCTCTGCTTCTCTCGCTG
* *
56926 CTCTCTCTACTTCTCTCTCTG
1 CTCTCTCTGCTTCTCTCGCTG
56947 CT
1 CT
56949 TTTTTCGTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.02, C:0.38, G:0.11, T:0.49
Consensus pattern (21 bp):
CTCTCTCTGCTTCTCTCGCTG
Found at i:63894 original size:41 final size:42
Alignment explanation
Indices: 63837--63948 Score: 126
Period size: 41 Copynumber: 2.7 Consensus size: 42
63827 CCTATTGCGG
63837 CGTTTGTATAAAAACGCCGCTAAAGTACTACTCAATTGT-GT
1 CGTTTGTATAAAAACGCCGCTAAAGTACTACTCAATTGTGGT
* * *
63878 CGTTTGT-TGAAAAACGCCACTATAG-A-TGAACTCTATTGTGGT
1 CGTTTGTAT-AAAAACGCCGCTAAAGTACT--ACTCAATTGTGGT
*
63920 -ATTTGTATAAAAACGCCGCTAAAGTACTA
1 CGTTTGTATAAAAACGCCGCTAAAGTACTA
63949 TTTATCACGG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
39 1 0.02
40 2 0.03
41 50 0.86
42 4 0.07
43 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (42 bp):
CGTTTGTATAAAAACGCCGCTAAAGTACTACTCAATTGTGGT
Found at i:64090 original size:83 final size:83
Alignment explanation
Indices: 63811--64113 Score: 299
Period size: 82 Copynumber: 3.7 Consensus size: 83
63801 TTTGAAAATA
* * * * * *
63811 GCCACTATAGATGAACCCTATTGCGGCGTTTGTATAAAAACGCCGCTAAAGTACTACTCAATTGT
1 GCCACTATAAACGAATCCTATTGCGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTATCGT
*
63876 GTCGTTTGTT-GAAAAAC
66 GGCGTTTGTTGGAAAAAC
* * * * * *
63893 GCCACTATAGATGAA-CTCTATTGTGGTATTTGTATAAAAACGCCGCTAAAGTACTA-TTTATCA
1 GCCACTATAAACGAATC-CTATTGCGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTATCG
* * *
63956 CGGCGTTTGCTGGAAAAAT
65 TGGCGTTTGTTGGAAAAAC
* * * * * * *
63975 GCCATTA-AGAACGATTCATATTGCGGCATTTGTACAAAAACACAGCTAAATTACTACTCTATCG
1 GCCACTATA-AACGAATCCTATTGCGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTATCG
*
64039 TGGCGTTTATTGGAAAAAC
65 TGGCGTTTGTTGGAAAAAC
** * * *
64058 GCCACTATAAACGAATCCTATTATGGCGTTTGTTTAAAAACTCCGCTAAAGTACTA
1 GCCACTATAAACGAATCCTATTGCGGCATTTGTATAAAAACGCCGCTAAAGTACTA
64114 GTCTTCACGG
Statistics
Matches: 176, Mismatches: 39, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
81 13 0.07
82 98 0.56
83 64 0.36
84 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (83 bp):
GCCACTATAAACGAATCCTATTGCGGCATTTGTATAAAAACGCCGCTAAAGTACTACTCTATCGT
GGCGTTTGTTGGAAAAAC
Found at i:73179 original size:43 final size:43
Alignment explanation
Indices: 73132--73271 Score: 138
Period size: 43 Copynumber: 3.3 Consensus size: 43
73122 TGACGACATA
*
73132 TAGCGGCATTTGTTAAACAAACGCCGCAATAGGTGTTGATCTT
1 TAGCGGCATTTGTTAAACAAACGCCGCAATAGGTGTTGATGTT
** ** * *
73175 TAGCGGTGTTTGGCAGATAAACGCCGCAATAGGTGTTGATGTT
1 TAGCGGCATTTGTTAAACAAACGCCGCAATAGGTGTTGATGTT
* ** * * *
73218 TAGCGGCGTTT-TTCCCACAAACGTCACAGTAGGTGTTGATGTT
1 TAGCGGCATTTGTT-AAACAAACGCCGCAATAGGTGTTGATGTT
*
73261 TAGCGGTATTT
1 TAGCGGCATTT
73272 TTATCGCAAA
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TAGCGGCATTTGTTAAACAAACGCCGCAATAGGTGTTGATGTT
Found at i:73294 original size:43 final size:43
Alignment explanation
Indices: 73132--73295 Score: 136
Period size: 43 Copynumber: 3.8 Consensus size: 43
73122 TGACGACATA
* *
73132 TAGCGGCATTTGTTA-AACAAACGCCGCAATAGGTGTTGATCTT
1 TAGCGGCATTT-TTACCACAAACGCCGCAATAGGTGTTGATGTT
** * *
73175 TAGCGG--TGTTTGGCAGATAAACGCCGCAATAGGTGTTGATGTT
1 TAGCGGCAT-TTTTAC-CACAAACGCCGCAATAGGTGTTGATGTT
* * * * *
73218 TAGCGGCGTTTTTCCCACAAACGTCACAGTAGGTGTTGATGTT
1 TAGCGGCATTTTTACCACAAACGCCGCAATAGGTGTTGATGTT
* * * * *
73261 TAGCGGTATTTTTATCGCAAATGCCGTAATAGGTG
1 TAGCGGCATTTTTACCACAAACGCCGCAATAGGTG
73296 CGGTATATAG
Statistics
Matches: 94, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 85 0.90
44 4 0.04
45 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
TAGCGGCATTTTTACCACAAACGCCGCAATAGGTGTTGATGTT
Found at i:73376 original size:43 final size:43
Alignment explanation
Indices: 73297--73379 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
73287 TAATAGGTGC
*
73297 GGTATATAGCGGCGTTTTTAGGATACAAATGCCGCTAAATGTAT
1 GGTATATAGCGGCGTTTTTA-GATACAAACGCCGCTAAATGTAT
* *
73341 GGTATATTGCGGCGGTTTTT-GTTACAAACGCCGCTAAAT
1 GGTATATAGCGGC-GTTTTTAGATACAAACGCCGCTAAAT
73380 AACACAGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 17 0.49
44 12 0.34
45 6 0.17
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (43 bp):
GGTATATAGCGGCGTTTTTAGATACAAACGCCGCTAAATGTAT
Found at i:73804 original size:21 final size:21
Alignment explanation
Indices: 73744--73798 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
73734 CCACTGCTTT
73744 TCTCTCTGCTTCCGCTGCTGC
1 TCTCTCTGCTTCCGCTGCTGC
**
73765 TCTGGCTGCTTCCGCTGCTGC
1 TCTCTCTGCTTCCGCTGCTGC
73786 TCTCTCTGCTTCC
1 TCTCTCTGCTTCC
73799 CTTGCTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.00, C:0.42, G:0.20, T:0.38
Consensus pattern (21 bp):
TCTCTCTGCTTCCGCTGCTGC
Done.