Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 174 of 190
Found at i:28882951 original size:23 final size:24
Alignment explanation
Indices: 28882925--28882979 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
28882915 ATGTTAAGTT
28882925 TTAAATTTTAAATT-TATTAAA-AA
1 TTAAATTTTAAATTATA-TAAATAA
*
28882948 TTAATTTTTAAATTATATAAATTAA
1 TTAAATTTTAAATTATATAAA-TAA
28882973 TTAAATT
1 TTAAATT
28882980 AATTCTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 17 0.63
24 2 0.07
25 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTAAATTTTAAATTATATAAATAA
Found at i:28882959 original size:30 final size:30
Alignment explanation
Indices: 28882918--28882989 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
28882908 ATTATAAATG
* *
28882918 TTAAGTTTTAAATT-T-TAAATTTATTAAAAA
1 TTAATTTTTAAATTATATAAATTAATT--AAA
28882948 TTAATTTTTAAATTATATAAATTAATTAAA
1 TTAATTTTTAAATTATATAAATTAATTAAA
*
28882978 TTAATTCTTAAA
1 TTAATTTTTAAA
28882990 ATCGTTTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 27 0.73
31 1 0.03
32 9 0.24
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
TTAATTTTTAAATTATATAAATTAATTAAA
Found at i:28882963 original size:22 final size:22
Alignment explanation
Indices: 28882925--28882974 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
28882915 ATGTTAAGTT
*
28882925 TTAAATTTTAAATTTATTAAAAA
1 TTAATTTTTAAATTTA-TAAAAA
*
28882948 TTAATTTTTAAA-TTATATAAA
1 TTAATTTTTAAATTTATAAAAA
28882969 TTAATT
1 TTAATT
28882975 AAATTAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.44
22 3 0.12
23 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATTTTTAAATTTATAAAAA
Found at i:28883440 original size:20 final size:19
Alignment explanation
Indices: 28883406--28883449 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
28883396 ATTTTTATTT
* *
28883406 TATAAAAATTTTAAATATA
1 TATAAAAATTATAAAAATA
28883425 TATAAAAATTAATAAAAATA
1 TATAAAAATT-ATAAAAATA
28883445 TATAA
1 TATAA
28883450 TTTGATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TATAAAAATTATAAAAATA
Found at i:28883539 original size:26 final size:26
Alignment explanation
Indices: 28883502--28883589 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 26
28883492 CAAAAAATTA
*
28883502 ATTTAAACTTAATAAAAATATTTAAT
1 ATTTAAATTTAATAAAAATATTTAAT
28883528 ATTTAAATTTAAAATAATAAATAATTT-A-
1 ATTTAAATTT--AATAA-AAAT-ATTTAAT
28883556 ATTT-AATTTAA-ATAAAATATTATAAT
1 ATTTAAATTTAATA-AAAATATT-TAAT
28883582 -TTTAAATT
1 ATTTAAATT
28883590 AATTTTTTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 18
0.73 0.01 0.25
Matches are distributed among these distances:
23 3 0.06
24 6 0.12
25 7 0.13
26 13 0.25
27 5 0.10
28 9 0.17
29 5 0.10
30 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTAAATTTAATAAAAATATTTAAT
Found at i:28883735 original size:22 final size:22
Alignment explanation
Indices: 28883692--28883733 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
28883682 ATATGACTTA
* *
28883692 AAATTTTATAAAAATTATAAAT
1 AAATTTAATAAAAATTAAAAAT
28883714 AAATTTAAT-AAAATTAAAAA
1 AAATTTAATAAAAATTAAAAA
28883734 ATTATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTTAATAAAAATTAAAAAT
Found at i:28888873 original size:28 final size:30
Alignment explanation
Indices: 28888808--28888903 Score: 108
Period size: 28 Copynumber: 3.2 Consensus size: 30
28888798 TAAATAATTT
*
28888808 TTTAAATATTATATTAATTAATAATTTTATAA
1 TTTAAATATAATATTAA--AATAATTTTATAA
*
28888840 TATAAATATAATATTAAAA-AATTTTA-AA
1 TTTAAATATAATATTAAAATAATTTTATAA
*
28888868 TTTAAATATAATATT-AAATATTTTATTATAA
1 TTTAAATATAATATTAAAATA-ATT-TTATAA
28888899 TTTAA
1 TTTAA
28888904 GAACAATCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 3 0.05
28 17 0.30
29 9 0.16
30 5 0.09
31 7 0.12
32 15 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTAAATATAATATTAAAATAATTTTATAA
Found at i:28889831 original size:3 final size:3
Alignment explanation
Indices: 28889823--28889866 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
28889813 AAACTCTCTC
28889823 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28889867 GGCTTAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:28896747 original size:3 final size:3
Alignment explanation
Indices: 28896739--28896763 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28896729 CATCAACCAC
28896739 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
28896764 ACAGCAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28901286 original size:22 final size:22
Alignment explanation
Indices: 28901246--28901287 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28901236 TATATATTTA
*
28901246 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCTCTAAAATTAAG
28901268 TATTTGTATC-CTTAAAATTA
1 TATTTGTATCTC-TAAAATTA
28901288 GGATAGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (22 bp):
TATTTGTATCTCTAAAATTAAG
Found at i:28901545 original size:26 final size:26
Alignment explanation
Indices: 28901499--28901565 Score: 93
Period size: 25 Copynumber: 2.6 Consensus size: 26
28901489 AAAATTTTCA
* *
28901499 GCCTTCATTG-CTAACTTCTATTTTAG
1 GCCTTCATTGCCGAACTCCTA-TTTAG
28901525 GCCTTCATTGCCGAA-TCCTATTTAG
1 GCCTTCATTGCCGAACTCCTATTTAG
28901550 GCCTTCATTGCCGAAC
1 GCCTTCATTGCCGAAC
28901566 CCTTTCAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 20 0.54
26 14 0.38
27 3 0.08
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.37
Consensus pattern (26 bp):
GCCTTCATTGCCGAACTCCTATTTAG
Found at i:28905246 original size:22 final size:22
Alignment explanation
Indices: 28905206--28905247 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28905196 TGTATATTTA
*
28905206 TATTTGTACCTCTAGAATTAAG
1 TATTTGTACCTCTAAAATTAAG
28905228 TATTTGTATCC-CTAAAATTA
1 TATTTGTA-CCTCTAAAATTA
28905248 GGATAGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (22 bp):
TATTTGTACCTCTAAAATTAAG
Found at i:28907806 original size:16 final size:16
Alignment explanation
Indices: 28907780--28907829 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
28907770 TATTTAATTA
28907780 AAAATTT-AATTTAAT
1 AAAATTTAAATTTAAT
28907795 AAAATTTAAATTTAAAT
1 AAAATTTAAATTT-AAT
** *
28907812 ATTATTTAAATTAAAT
1 AAAATTTAAATTTAAT
28907828 AA
1 AA
28907830 TAATAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 7 0.24
16 9 0.31
17 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATTTAAATTTAAT
Found at i:28908156 original size:21 final size:20
Alignment explanation
Indices: 28908127--28908187 Score: 88
Period size: 19 Copynumber: 3.0 Consensus size: 20
28908117 GTAATTATCT
*
28908127 TAGTATTTTTTTTAATATTA
1 TAGTATTTTTTTAAATATTA
*
28908147 TAGTA-TTTTTTAAACATTA
1 TAGTATTTTTTTAAATATTA
28908166 TAGTATTGTTTTTAAATATTA
1 TAGTATT-TTTTTAAATATTA
28908187 T
1 T
28908188 TATTATTATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.47
20 6 0.17
21 13 0.36
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (20 bp):
TAGTATTTTTTTAAATATTA
Found at i:28908191 original size:19 final size:20
Alignment explanation
Indices: 28908153--28908191 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28908143 ATTATAGTAT
28908153 TTTTTAAACATTATAGTATTG
1 TTTTTAAACATTATA-TATTG
*
28908174 TTTTTAAATATTAT-TATT
1 TTTTTAAACATTATATATT
28908192 ATTATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTTAAACATTATATATTG
Found at i:28909203 original size:2 final size:2
Alignment explanation
Indices: 28909196--28909220 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28909186 GAGATGGCTT
28909196 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28909221 GGTTGCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28911014 original size:86 final size:88
Alignment explanation
Indices: 28910899--28911120 Score: 319
Period size: 86 Copynumber: 2.6 Consensus size: 88
28910889 GTTAAAAAAG
* * *
28910899 AAAAAAGAAAAAATCCAAACAAATCTGTATATATGGCAATAAATAACACAATACCAAAAAAAGAT
1 AAAAAAAAAAAAATCTAAACAAATATGTATATATGGCAATAAATAACACAATACCAAAAAAA-AT
*
28910964 A-A-AGAGAAATTACTCAGAAG-T
65 AGAGAGAGAAATTACTCAAAAGTT
28910985 AAAAAAAAAAAAATCTAAACAAATATGTATATATGGCAATAAAT-A-ACAATACCAAAAAAAATA
1 AAAAAAAAAAAAATCTAAACAAATATGTATATATGGCAATAAATAACACAATACCAAAAAAAATA
28911048 GAGAGAGAAATTACTCAAAAGTT
66 GAGAGAGAAATTACTCAAAAGTT
* * * * *
28911071 TAAAAAAAAAAAGTCTAAACAAATATGTATATATAGCGATAAGTAACACA
1 AAAAAAAAAAAAATCTAAACAAATATGTATATATGGCAATAAATAACACA
28911121 GAGAGAAATT
Statistics
Matches: 122, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
83 3 0.02
84 16 0.13
85 18 0.15
86 81 0.66
87 1 0.01
88 3 0.02
ACGTcount: A:0.60, C:0.11, G:0.10, T:0.19
Consensus pattern (88 bp):
AAAAAAAAAAAAATCTAAACAAATATGTATATATGGCAATAAATAACACAATACCAAAAAAAATA
GAGAGAGAAATTACTCAAAAGTT
Found at i:28915213 original size:2 final size:2
Alignment explanation
Indices: 28915208--28915240 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28915198 TACAAGTGTG
*
28915208 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28915241 GAAAAGTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28920858 original size:20 final size:20
Alignment explanation
Indices: 28920835--28920889 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
28920825 TGAAAGATTT
28920835 ATAATTTTTCAAAAAATTAC
1 ATAATTTTTCAAAAAATTAC
28920855 ATAATTTTTCAAAAAATTAC
1 ATAATTTTTCAAAAAATTAC
28920875 ATAATTTTTCAAAAA
1 ATAATTTTTCAAAAA
28920890 TTTATTTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAATTTTTCAAAAAATTAC
Found at i:28922687 original size:16 final size:16
Alignment explanation
Indices: 28922666--28922704 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
28922656 CGATATTTGA
*
28922666 TAATTATTTTAAAATT
1 TAATTAATTTAAAATT
28922682 TAATTAATTTAAAATT
1 TAATTAATTTAAAATT
*
28922698 AAATTAA
1 TAATTAA
28922705 ATCGAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTAATTTAAAATT
Found at i:28923011 original size:6 final size:6
Alignment explanation
Indices: 28922994--28923022 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28922984 TGCAAGTACA
28922994 AATTTT AA-TTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
28923023 TTCTCTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:28925039 original size:57 final size:57
Alignment explanation
Indices: 28924971--28925393 Score: 343
Period size: 56 Copynumber: 7.4 Consensus size: 57
28924961 TTTGTGTAGA
* *
28924971 AAAAATTGATACTTTCAACTTTTCTCAAAATA-TTTTATAGAAATTTTAATCTCGAG
1 AAAAATTGATACTTTCAACTTTTCTCAAAATACTTTTATAGAAACTTTAATTTCGAG
* * *
28925027 AAAAATCCGATACTTTTAACTTTTTCCCAAAATA-TCTTT-T-GAAACTTTAATTTCGAG
1 AAAAAT-TGATACTTTCAAC-TTTTCTCAAAATACT-TTTATAGAAACTTTAATTTCGAG
* * * * **
28925084 AAAAATTGATACTTTCAACTTTTTCTCAAAA-ACTTTTTTTGAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAAC-TTTTCTCAAAATACTTTTATAGAAACTTTAATTTCGAG
* * * *
28925141 AAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTTGGAAACCTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTCT-C-AAAATA-CTTTTATAGAAACTTTAATTTCGAG
* * * * **
28925201 GAAAATTGATACTTTCAATTTTTTCTCAAAAATAGTTTTA-A-AAA-TTTATTTTTAAG
1 AAAAATTGATACTTTCAA-CTTTTCTC-AAAATACTTTTATAGAAACTTTAATTTCGAG
* * ** *
28925257 GAAAATTGATACTTTCAACTTTTCCTCAAAA-ACCGTTTTA-A-AAA-TTTATTTTTAAA
1 AAAAATTGATACTTTCAACTTTT-CTCAAAATA-C-TTTTATAGAAACTTTAATTTCGAG
* * * *
28925313 AAAAATTAATACTTTCAACTTTTCTCCAAAAATA-TTTTTTGGAAACTTTAATATCGA-
1 AAAAATTGATACTTTCAACTTTTCT-C-AAAATACTTTTATAGAAACTTTAATTTCGAG
28925370 AGAAAATTGATACTTTCAACTTTT
1 A-AAAATTGATACTTTCAACTTTT
28925394 TCCAAAAATT
Statistics
Matches: 306, Mismatches: 40, Indels: 40
0.79 0.10 0.10
Matches are distributed among these distances:
54 1 0.00
55 18 0.06
56 107 0.35
57 76 0.25
58 47 0.15
59 8 0.03
60 43 0.14
61 6 0.02
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.43
Consensus pattern (57 bp):
AAAAATTGATACTTTCAACTTTTCTCAAAATACTTTTATAGAAACTTTAATTTCGAG
Found at i:28925108 original size:56 final size:56
Alignment explanation
Indices: 28924971--28925409 Score: 377
Period size: 57 Copynumber: 7.7 Consensus size: 56
28924961 TTTGTGTAGA
* * * *
28924971 AAAAATTGATACTTTCAAC-TTTTCTCAAAATATTTTATAGAAATTTTAATCTCGAG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAATATTTT-TTGAAAATTTAATTTCGAG
* * * *
28925027 AAAAATCCGATACTTTTAACTTTTTCCCAAAATATCTTTTGAAACTTTAATTTCGAG
1 AAAAAT-TGATACTTTCAACTTTTTCCCAAAATATTTTTTGAAAATTTAATTTCGAG
* * **
28925084 AAAAATTGATACTTTCAACTTTTTCTCAAAA-ACTTTTTTTGAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAATA--TTTTTTGAAAATTTAATTTCGAG
* **
28925141 AAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTTGGAAACCTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTT-TCCCAAAATA--TTTTTT-GAAAATTTAATTTCGAG
* * * * * * **
28925201 GAAAATTGATACTTTCAATTTTTTCTCAAAA-ATAGTTTTAAAAATTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTTCCCAAAATAT-TTTTTGAAAATTTAATTTCGAG
* ** * * ** *
28925257 GAAAATTGATACTTTCAAC-TTTTCCTCAAAA-ACCGTTTTAAAAATTTATTTTTAAA
1 AAAAATTGATACTTTCAACTTTTTCC-CAAAATA-TTTTTTGAAAATTTAATTTCGAG
* * * *
28925313 AAAAATTAATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAACTTTAATATCGA-
1 AAAAATTGATACTTTCAACTTTT-TCCCAAAATATTTTTT-GAAAATTTAATTTCGAG
* *
28925370 AGAAAATTGATACTTTCAACTTTTTCCAAAAATTTTTTTT
1 A-AAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTT
28925410 TGGATTTTAT
Statistics
Matches: 317, Mismatches: 51, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
55 6 0.02
56 102 0.32
57 105 0.33
58 57 0.18
59 14 0.04
60 33 0.10
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (56 bp):
AAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTGAAAATTTAATTTCGAG
Found at i:28925494 original size:41 final size:41
Alignment explanation
Indices: 28925426--28925519 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
28925416 TTATTTAAAG
* *
28925426 AAAATAAAATAATAAAACAAAATAAAAGTGAAAAGAAAAA-A
1 AAAATAAAATAATAAAACAAAAGAAAAGT-AAAACAAAAATA
*
28925467 ATAATAATAATAATAAAA-AAAAGAAAAGTAAAACAAAAATA
1 AAAATAA-AATAATAAAACAAAAGAAAAGTAAAACAAAAATA
28925508 AAAATAAAATAA
1 AAAATAAAATAA
28925520 AGATAAAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 14 0.30
41 23 0.49
42 10 0.21
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (41 bp):
AAAATAAAATAATAAAACAAAAGAAAAGTAAAACAAAAATA
Found at i:28925510 original size:17 final size:17
Alignment explanation
Indices: 28925484--28925528 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
28925474 TAATAATAAA
*
28925484 AAAAAGAAAAGTAAAAC
1 AAAAATAAAAGTAAAAC
* *
28925501 AAAAATAAAAATAAAAT
1 AAAAATAAAAGTAAAAC
*
28925518 AAAGATAAAAG
1 AAAAATAAAAG
28925529 AATATTAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.78, C:0.02, G:0.09, T:0.11
Consensus pattern (17 bp):
AAAAATAAAAGTAAAAC
Found at i:28925525 original size:6 final size:5
Alignment explanation
Indices: 28925426--28925574 Score: 64
Period size: 5 Copynumber: 29.6 Consensus size: 5
28925416 TTATTTAAAG
* *
28925426 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAA- GAAA- AAAAT AATAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AA-AAT
* *
28925475 AATAAT AAAA- AAAAG AAAAGT AAAACA AAAAT AAAAAT AAAAT AAAGAT
1 AA-AAT AAAAT AAAAT AAAA-T AAAA-T AAAAT -AAAAT AAAAT AAA-AT
* * * **
28925524 AAAAG AATAT TAAAT AAACAT AATCT AATAAT -AAAT -AAAT -AAAT -AAAT
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT
28925572 AAA
1 AAA
28925575 TTTAAAAAAA
Statistics
Matches: 113, Mismatches: 18, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
3 3 0.03
4 25 0.22
5 46 0.41
6 35 0.31
7 4 0.04
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:28925525 original size:11 final size:11
Alignment explanation
Indices: 28925426--28925527 Score: 64
Period size: 11 Copynumber: 8.8 Consensus size: 11
28925416 TTATTTAAAG
28925426 AAAATAAAATAA
1 AAAATAAAAT-A
*
28925438 TAAAACAAAATA
1 -AAAATAAAATA
* *
28925450 AAAGTGAAAAGA
1 AAAAT-AAAATA
28925462 AAAA-AATAATA
1 AAAATAA-AATA
* *
28925473 ATAATAATAAAA
1 AAAATAA-AATA
*
28925485 AAAAGAAAAGTA
1 AAAATAAAA-TA
28925497 AAACA-AAAATA
1 AAA-ATAAAATA
28925508 AAAATAAAATA
1 AAAATAAAATA
*
28925519 AAGATAAAA
1 AAAATAAAA
28925528 GAATATTAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 14
0.73 0.12 0.14
Matches are distributed among these distances:
10 3 0.04
11 30 0.42
12 28 0.39
13 10 0.14
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:28926549 original size:2 final size:2
Alignment explanation
Indices: 28926542--28926573 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28926532 GAGTTGGCTT
28926542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28926574 CGGTTGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28928428 original size:84 final size:84
Alignment explanation
Indices: 28928340--28928498 Score: 219
Period size: 84 Copynumber: 1.9 Consensus size: 84
28928330 AGAAGTAAAA
* * * *
28928340 AAAAAAAAATCTAAATAAAAAAGTATATATAGTAATAAGTAACGCAATAAAAAAAAAGATAAGAG
1 AAAAAAAAATCTAAACAAAAAAGTATATATAGCAACAAGTAACACAATAAAAAAAAAGATAAGAG
*
28928405 AGATAAATTATTCCGAAGT
66 AGAGAAATTATTCCGAAGT
* * * ** *
28928424 AAAAAAAAATCTAAACAAATAAGTATATATGGCAACAAGTAACATAATACCAACAAAGATAAGAG
1 AAAAAAAAATCTAAACAAAAAAGTATATATAGCAACAAGTAACACAATAAAAAAAAAGATAAGAG
28928489 AGAGAAATTA
66 AGAGAAATTA
28928499 CTAAAGAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
84 64 1.00
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.19
Consensus pattern (84 bp):
AAAAAAAAATCTAAACAAAAAAGTATATATAGCAACAAGTAACACAATAAAAAAAAAGATAAGAG
AGAGAAATTATTCCGAAGT
Found at i:28932426 original size:3 final size:3
Alignment explanation
Indices: 28932377--28932411 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
28932367 TTTATAACAT
28932377 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28932412 GACTTTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28932551 original size:19 final size:18
Alignment explanation
Indices: 28932527--28932572 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
28932517 TTTTTTAGAT
28932527 TTTTTATTATTGGTTTTA
1 TTTTTATTATTGGTTTTA
*
28932545 CTTTTTATTATTTGTTTTA
1 -TTTTTATTATTGGTTTTA
28932564 TTATTTATT
1 TT-TTTATT
28932573 TACTTTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (18 bp):
TTTTTATTATTGGTTTTA
Found at i:28932819 original size:21 final size:20
Alignment explanation
Indices: 28932764--28932820 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
28932754 AATTTTATGA
*
28932764 TAAAATTATTATTATGTTTAAT
1 TAAAA-TATT-TTATGATTAAT
* *
28932786 TAAAATTTCTTTATGATTATT
1 TAAAATAT-TTTATGATTAAT
28932807 TAAAATAATTTTAT
1 TAAAAT-ATTTTAT
28932821 ACTTTAACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (20 bp):
TAAAATATTTTATGATTAAT
Found at i:28933774 original size:23 final size:23
Alignment explanation
Indices: 28933743--28933790 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
28933733 TTTATAAAGC
28933743 TTTTGGGA-TACAAATCCTAGATT
1 TTTTGGGATTA-AAATCCTAGATT
* *
28933766 TTTTTGGATTAAGATCCTAGATT
1 TTTTGGGATTAAAATCCTAGATT
28933789 TT
1 TT
28933791 CAAAGTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (23 bp):
TTTTGGGATTAAAATCCTAGATT
Found at i:28933959 original size:18 final size:16
Alignment explanation
Indices: 28933913--28933960 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
28933903 GACCTTAGGG
28933913 GAAGAAGAAAAAAATGA
1 GAAGAA-AAAAAAATGA
*
28933930 GAAGAAATAAAAATGGA
1 GAAGAAAAAAAAAT-GA
*
28933947 TAAGCAAAAAAAAA
1 GAAG-AAAAAAAAA
28933961 AAAGATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 11 0.42
18 8 0.31
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.08
Consensus pattern (16 bp):
GAAGAAAAAAAAATGA
Found at i:28934320 original size:43 final size:42
Alignment explanation
Indices: 28934231--28934651 Score: 174
Period size: 42 Copynumber: 9.8 Consensus size: 42
28934221 AAGGTTCATT
* * * *
28934231 TAAGTATAGGCTTGATAACTTTGAAAATTT-AAAAGAC-TCCC
1 TAAGTAAAGGCTTGACAACTTTAAAAATTTAAAAAG-CTTCTC
* *
28934272 TTAAGTATAGGCTTGACAATTTTAAAAAATTTAAAAAGCTTCTC
1 -TAAGTAAAGGCTTGACAACTTT-AAAAATTTAAAAAGCTTCTC
* * * *
28934316 TAAGTAAAAGCTTGACAACTTTGAAAATTAAAAAAGCTCCT-
1 TAAGTAAAGGCTTGACAACTTTAAAAATTTAAAAAGCTTCTC
* * * * *
28934357 TCACGTAAAGGCTTAACAATTTTTAAAAATTTAAAAGGCTTTTC
1 T-AAGTAAAGGCTTGACAA-CTTTAAAAATTTAAAAAGCTTCTC
** * * * *
28934401 TAAGTAGAAGTAGAGGCTCAATAACTTTTGAAAATTT-AAAAGGTTCTTT
1 TAAGT---A--A-AGGCTTGACAAC-TTTAAAAATTTAAAAAGCTTC-TC
* * * *
28934450 TAAGTAAAGGCTTTACAAACTTT-AAAATTTAAAAAACTCCTT
1 TAAGTAAAGGCTTGAC-AACTTTAAAAATTTAAAAAGCTTCTC
* * * * * * * *
28934492 TAAGTAGA-GATCGACAACTTTTGAAAATTTGAAAGGCTTTTT
1 TAAGTAAAGGCTTGACAAC-TTTAAAAATTTAAAAAGCTTCTC
** ** * *
28934534 TAAGTAAAGGCTCAACAACTTCGAAAA-TTAAAAAGGCTCCAC
1 TAAGTAAAGGCTTGACAACTTTAAAAATTTAAAAA-GCTTCTC
* ** * * * * *
28934576 TAAGTAGAGGCTAAATAAATTTTGAAAATTTGAAAATGTTTCTC
1 TAAGTAAAGGCTTGA-CAACTTTAAAAATTT-AAAAAGCTTCTC
* * *
28934620 TAAATAGAGGCTTAACAACTTT-AAAATTTAAA
1 TAAGTAAAGGCTTGACAACTTTAAAAATTTAAA
28934652 GTATTTTACT
Statistics
Matches: 290, Mismatches: 66, Indels: 47
0.72 0.16 0.12
Matches are distributed among these distances:
40 3 0.01
41 16 0.06
42 117 0.40
43 84 0.29
44 32 0.11
45 4 0.01
46 2 0.01
48 7 0.02
49 25 0.09
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (42 bp):
TAAGTAAAGGCTTGACAACTTTAAAAATTTAAAAAGCTTCTC
Found at i:28934336 original size:85 final size:85
Alignment explanation
Indices: 28934231--28934406 Score: 230
Period size: 85 Copynumber: 2.1 Consensus size: 85
28934221 AAGGTTCATT
* * * * * *
28934231 TAAGTATAGGCTTGATAACTTTGAAAATT-TAAAAGACTCCCTT-AAGTATAGGCTTGACAATTT
1 TAAGTAAAAGCTTGACAACTTTGAAAATTAAAAAAG-CT-CCTTCAAGTAAAGGCTTAACAATTT
28934294 TAAAAAATTTAAAAAGCTTCTC
64 TAAAAAATTTAAAAAGCTTCTC
* *
28934316 TAAGTAAAAGCTTGACAACTTTGAAAATTAAAAAAGCTCCTTCACGTAAAGGCTTAACAATTTTT
1 TAAGTAAAAGCTTGACAACTTTGAAAATTAAAAAAGCTCCTTCAAGTAAAGGCTTAACAATTTTA
* *
28934381 AAAAATTTAAAAGGCTTTTC
66 AAAAATTTAAAAAGCTTCTC
28934401 TAAGTA
1 TAAGTA
28934407 GAAGTAGAGG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
84 4 0.05
85 70 0.89
86 5 0.06
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (85 bp):
TAAGTAAAAGCTTGACAACTTTGAAAATTAAAAAAGCTCCTTCAAGTAAAGGCTTAACAATTTTA
AAAAATTTAAAAAGCTTCTC
Found at i:28934580 original size:84 final size:84
Alignment explanation
Indices: 28934423--28934584 Score: 213
Period size: 84 Copynumber: 1.9 Consensus size: 84
28934413 GAGGCTCAAT
** *
28934423 AACTTTTGAAAATTTAAAAGGTTCTTTTAAGTAAAGGCTTTACAAACTTTAAAATTTAAAAAACT
1 AACTTTTGAAAATTTAAAAGGTTCTTTTAAGTAAAGGCTCAACAAACTTGAAAATTTAAAAAACT
**
28934488 CCTTTAAGTAGAGATCGAC
66 CCACTAAGTAGAGATCGAC
*
28934507 AACTTTTGAAAATTTGAAAGGCTT-TTTTAAGTAAAGGCTCAAC-AACTTCGAAAA-TTAAAAAG
1 AACTTTTGAAAATTTAAAAGG-TTCTTTTAAGTAAAGGCTCAACAAACTT-GAAAATTTAAAAA-
*
28934569 GCTCCACTAAGTAGAG
63 ACTCCACTAAGTAGAG
28934585 GCTAAATAAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
83 12 0.18
84 54 0.79
85 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (84 bp):
AACTTTTGAAAATTTAAAAGGTTCTTTTAAGTAAAGGCTCAACAAACTTGAAAATTTAAAAAACT
CCACTAAGTAGAGATCGAC
Found at i:28934758 original size:78 final size:77
Alignment explanation
Indices: 28934620--28934800 Score: 190
Period size: 78 Copynumber: 2.3 Consensus size: 77
28934610 AATGTTTCTC
* * * *
28934620 TAAATAGAGGCTTAACAACTTTAAAATTTAAAGTATTTTACTCGGAAGACTTAGATATCTTGATA
1 TAAATAAAGGCTCAACAACTTTAAAATTTAAAATATTCTACTCGGAAGACTTAGATATCTT-ATA
28934685 ATAAATGTTCTTT
65 ATAAATGTTCTTT
* * *
28934698 TAAATAAAGGCTCGACAACTTTAAAATTTAAAATATTCTACT-TGAAGGACTTA-TTAATCTTAT
1 TAAATAAAGGCTCAACAACTTTAAAATTTAAAATATTCTACTCGGAA-GACTTAGAT-ATCTTAT
* ** *
28934761 AATGAATACTCTTA
64 AATAAATGTTCTTT
28934775 TAAGA-ACAA-GCTCAACAACTTTAAAA
1 TAA-ATA-AAGGCTCAACAACTTTAAAA
28934801 AGCTCCTCTA
Statistics
Matches: 87, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
77 36 0.41
78 51 0.59
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (77 bp):
TAAATAAAGGCTCAACAACTTTAAAATTTAAAATATTCTACTCGGAAGACTTAGATATCTTATAA
TAAATGTTCTTT
Found at i:28934945 original size:112 final size:111
Alignment explanation
Indices: 28934693--28934948 Score: 289
Period size: 112 Copynumber: 2.3 Consensus size: 111
28934683 TAATAAATGT
* * * ** * **
28934693 TCTTTTAAATAAAGGCTCGACAACTTTAAAATTTAAAATATTCTACTTGAAGGACTTATTAATCT
1 TCTTTTAAGTAGAGGCTCAACAACTTTAAAATTTAAAATATTCTACCCGAAAGACTTACAAATCT
* * * *
28934758 TATAATGAATACTCTTATAAGAACAAGCTCAACAACTTTAAAAAGC
66 GATAATAAATACTCCTATAAGAACAAGCTCAACAACTTTAAAAAAC
* * *
28934804 TCCTCTAAGTAGAGGTTCAACAACTTTAAAATTTAAAATATTCTACCCGAAAGACTTACAAATCT
1 TCTTTTAAGTAGAGGCTCAACAACTTTAAAATTTAAAATATTCTACCCGAAAGACTTACAAATCT
* * * *
28934869 CGATAATAAATGCTCCTCTAAGTAA-AAGCTCAATAGCTTTAAAAAAC
66 -GATAATAAATACTCCTATAAG-AACAAGCTCAACAACTTTAAAAAAC
* * *
28934916 TCTTTTAAGTAGAGGCTCTACCATTTTAAAATT
1 TCTTTTAAGTAGAGGCTCAACAACTTTAAAATT
28934949 CTCTTTTTTT
Statistics
Matches: 118, Mismatches: 25, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
111 54 0.46
112 62 0.53
113 2 0.02
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (111 bp):
TCTTTTAAGTAGAGGCTCAACAACTTTAAAATTTAAAATATTCTACCCGAAAGACTTACAAATCT
GATAATAAATACTCCTATAAGAACAAGCTCAACAACTTTAAAAAAC
Found at i:28940358 original size:21 final size:20
Alignment explanation
Indices: 28940320--28940358 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28940310 TTTGACTTCC
*
28940320 CTTTTCCTTTCTAACTTTAG
1 CTTTTCCTTTCCAACTTTAG
*
28940340 CTTTTTCTTTCCAATCTTT
1 CTTTTCCTTTCCAA-CTTT
28940359 TTTCAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.13, C:0.26, G:0.03, T:0.59
Consensus pattern (20 bp):
CTTTTCCTTTCCAACTTTAG
Found at i:28944086 original size:19 final size:19
Alignment explanation
Indices: 28944064--28944111 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
28944054 TGGTTGAATA
*
28944064 TTTCGACAAGCTTTGAGTT
1 TTTCGACAAGCTTTAAGTT
*
28944083 TTTCAACAAGCTTTAAGTT
1 TTTCGACAAGCTTTAAGTT
*
28944102 TCTCGACAAG
1 TTTCGACAAG
28944112 ATCCTTCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (19 bp):
TTTCGACAAGCTTTAAGTT
Found at i:28946952 original size:18 final size:19
Alignment explanation
Indices: 28946920--28946956 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
28946910 TACAAAAAAA
28946920 TTTTGAAAGATTTTTTTTT
1 TTTTGAAAGATTTTTTTTT
28946939 TTTTGAAAGATTTTTTTT
1 TTTTGAAAGATTTTTTTT
28946957 CTTTCAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.68
Consensus pattern (19 bp):
TTTTGAAAGATTTTTTTTT
Found at i:28946966 original size:20 final size:19
Alignment explanation
Indices: 28946924--28946966 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
28946914 AAAAAATTTT
**
28946924 GAAAGATTTTTTTTTTTTT
1 GAAAGATTTTTTTTTTTCA
28946943 GAAAGATTTTTTTTCTTTCA
1 GAAAGATTTTTTTT-TTTCA
28946963 GAAA
1 GAAA
28946967 TACCGATGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.56
Consensus pattern (19 bp):
GAAAGATTTTTTTTTTTCA
Found at i:28947070 original size:13 final size:12
Alignment explanation
Indices: 28947052--28947095 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
28947042 AAAGTAAAAT
28947052 AAAATAAAATCAA
1 AAAATAAAAT-AA
28947065 AAAATAAAAATAA
1 AAAAT-AAAATAA
*
28947078 AATAAAAAAATAA
1 AA-AATAAAATAA
28947091 AAAAT
1 AAAAT
28947096 TTGTGATCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 2 0.07
13 18 0.67
14 7 0.26
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:28947076 original size:19 final size:19
Alignment explanation
Indices: 28947047--28947093 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
28947037 TTAAGAAAGT
*
28947047 AAAAT-AAAATAAAATCAA
1 AAAATAAAAATAAAATAAA
28947065 AAAATAAAAATAAAATAAA
1 AAAATAAAAATAAAATAAA
28947084 AAAATAAAAA
1 AAAATAAAAA
28947094 ATTTGTGATC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (19 bp):
AAAATAAAAATAAAATAAA
Found at i:28947092 original size:24 final size:24
Alignment explanation
Indices: 28947047--28947093 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
28947037 TTAAGAAAGT
*
28947047 AAAATAAAATAAAATCAAAAAATA
1 AAAATAAAATAAAATAAAAAAATA
*
28947071 AAAATAAAATAAAAAAATAAAAA
1 AAAATAAAATAAAATAA-AAAAA
28947094 ATTTGTGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (24 bp):
AAAATAAAATAAAATAAAAAAATA
Found at i:28947977 original size:3 final size:3
Alignment explanation
Indices: 28947971--28948023 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
28947961 AAAAAACATA
28947971 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28948019 AAT AA
1 AAT AA
28948024 ACTATCTAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28948103 original size:25 final size:26
Alignment explanation
Indices: 28948050--28948105 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
28948040 CGAACATTAG
*
28948050 TGGGCCTAATTGGGCCCAAACATAAA
1 TGGGTCTAATTGGGCCCAAACATAAA
* *
28948076 TGGGTCTAATTGGG-TCAGACATAAA
1 TGGGTCTAATTGGGCCCAAACATAAA
28948101 TGGGT
1 TGGGT
28948106 GTCTACGAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (26 bp):
TGGGTCTAATTGGGCCCAAACATAAA
Found at i:28949796 original size:43 final size:43
Alignment explanation
Indices: 28949744--28949825 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
28949734 CTTAGTAATC
* *
28949744 TGTGATGGACAATGATGTAAGAAACAATTTGAGAACCTTAGTT
1 TGTGATGGACAACGATGTAAGAAACAATTTAAGAACCTTAGTT
*
28949787 TGTGATGGACAACGATGTAAGAAATAATTTAAGAACCTT
1 TGTGATGGACAACGATGTAAGAAACAATTTAAGAACCTT
28949826 TAAATTTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (43 bp):
TGTGATGGACAACGATGTAAGAAACAATTTAAGAACCTTAGTT
Found at i:28954489 original size:22 final size:22
Alignment explanation
Indices: 28954446--28954492 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28954436 ATAAAAAATG
* * *
28954446 ATTTGTAAGACCTTTGAGCATA
1 ATTTGTAAGACCTCTAAACATA
*
28954468 ATTTGTAAGGCCTCTAAACATA
1 ATTTGTAAGACCTCTAAACATA
28954490 ATT
1 ATT
28954493 CTCAAGACCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
ATTTGTAAGACCTCTAAACATA
Found at i:28954592 original size:66 final size:67
Alignment explanation
Indices: 28954446--28954628 Score: 185
Period size: 66 Copynumber: 2.8 Consensus size: 67
28954436 ATAAAAAATG
* * ** * *
28954446 ATTTGTAAGACCTTTGA-GCATAATTTGTAAGGCCTCTAAACATAATTCTCAAGACCTCCAGGAA
1 ATTTGTAAAACCTTCGATGCATAATTTGTAAGGCCTCTAGGCATAATTTTTAAGACCTCCAGGAA
*
28954510 TT
66 TA
* * * *
28954512 ATTTGTAAAACCTTC-ATGCATAATTTGTAAGGCCTCTAGGTATAATTTTTAAGACGTCCGGGCA
1 ATTTGTAAAACCTTCGATGCATAATTTGTAAGGCCTCTAGGCATAATTTTTAAGACCTCCAGGAA
28954576 TA
66 TA
** * * * *
28954578 ATTTGTAATGCCTTCGAT--ATGATTTGCAAGACTTCTAGGCATAATTTTTAA
1 ATTTGTAAAACCTTCGATGCATAATTTGTAAGGCCTCTAGGCATAATTTTTAA
28954629 AAACTTTGAG
Statistics
Matches: 97, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
65 29 0.30
66 66 0.68
67 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (67 bp):
ATTTGTAAAACCTTCGATGCATAATTTGTAAGGCCTCTAGGCATAATTTTTAAGACCTCCAGGAA
TA
Found at i:28955394 original size:16 final size:16
Alignment explanation
Indices: 28955373--28955404 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
28955363 TAAGATGAGC
28955373 TTTTTATATTTTTTCA
1 TTTTTATATTTTTTCA
28955389 TTTTTATATTTTTTCA
1 TTTTTATATTTTTTCA
28955405 AAAGCTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTTATATTTTTTCA
Found at i:28955616 original size:42 final size:43
Alignment explanation
Indices: 28955442--28955621 Score: 157
Period size: 44 Copynumber: 4.2 Consensus size: 43
28955432 GCTTTTTATA
* * * * *
28955442 TATATTTTTTAAAGTTGTTAAGTCTTT-ATTGAGATGAGCCTTT
1 TATATTTTTAAAAGTTGTTGAGCCTTTGA-TGAAATGAGCATTT
* * * * *
28955485 TATATTTTTTAAAAGTTGTTGAGCCTCTGTTGAGAGGAGTATTT
1 TATA-TTTTTAAAAGTTGTTGAGCCTTTGATGAAATGAGCATTT
* * * * * **
28955529 TATATTTTTCAATAGTTGTTGAGCCTATGTTAAAAAGAGTTTTT
1 TATATTTTT-AAAAGTTGTTGAGCCTTTGATGAAATGAGCATTT
*
28955573 TATATTTTT-AAAGTTGTTGAGCCTTTGATGAAATTAGCATTT
1 TATATTTTTAAAAGTTGTTGAGCCTTTGATGAAATGAGCATTT
28955615 TATATTT
1 TATATTT
28955622 CAAAATTGTT
Statistics
Matches: 112, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
42 32 0.29
43 9 0.08
44 71 0.63
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (43 bp):
TATATTTTTAAAAGTTGTTGAGCCTTTGATGAAATGAGCATTT
Found at i:28959331 original size:20 final size:20
Alignment explanation
Indices: 28959294--28959332 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28959284 CATTTTCTAA
*
28959294 ATTTTTTATTGTTGGTTTTT
1 ATTTTTTATTATTGGTTTTT
*
28959314 ATTTTTTATTATTTGTTTT
1 ATTTTTTATTATTGGTTTT
28959333 ATTATTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (20 bp):
ATTTTTTATTATTGGTTTTT
Found at i:28959460 original size:3 final size:3
Alignment explanation
Indices: 28959452--28959505 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
28959442 TGCTTGAAAA
28959452 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
28959500 ATT ATT
1 ATT ATT
28959506 TATTCCTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28960682 original size:16 final size:15
Alignment explanation
Indices: 28960657--28960687 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
28960647 TCTGGGGGGA
28960657 AGAAAAAGAAAAATG
1 AGAAAAAGAAAAATG
28960672 AGAATAAAGAAAAATG
1 AGAA-AAAGAAAAATG
28960688 CAAGGGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (15 bp):
AGAAAAAGAAAAATG
Found at i:28961073 original size:41 final size:42
Alignment explanation
Indices: 28961006--28961093 Score: 133
Period size: 41 Copynumber: 2.1 Consensus size: 42
28960996 CTTGAAATTA
*
28961006 ATAAATTATTATTTTTTAAAATATAAAATACTATTTTTAAAT
1 ATAAAATATTATTTTTTAAAATATAAAATACTATTTTTAAAT
* * *
28961048 ATAAAATATTA-TTTTTAAAATATAAATTATTATTTTTTAAT
1 ATAAAATATTATTTTTTAAAATATAAAATACTATTTTTAAAT
28961089 ATAAA
1 ATAAA
28961094 TATAAAATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 32 0.76
42 10 0.24
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (42 bp):
ATAAAATATTATTTTTTAAAATATAAAATACTATTTTTAAAT
Found at i:28961094 original size:20 final size:20
Alignment explanation
Indices: 28961006--28961094 Score: 115
Period size: 20 Copynumber: 4.3 Consensus size: 20
28960996 CTTGAAATTA
28961006 ATAAATTATTATTTTTTAAAAT
1 ATAAATTATTA-TTTTT-AAAT
* *
28961028 ATAAAATACTATTTTTAAAT
1 ATAAATTATTATTTTTAAAT
*
28961048 ATAAAATATTATTTTTAAAAT
1 ATAAATTATTATTTTT-AAAT
*
28961069 ATAAATTATTATTTTTTAAT
1 ATAAATTATTATTTTTAAAT
28961089 ATAAAT
1 ATAAAT
28961095 ATAAAATTAA
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
20 28 0.46
21 24 0.39
22 9 0.15
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAAATTATTATTTTTAAAT
Found at i:28961125 original size:25 final size:24
Alignment explanation
Indices: 28961087--28961133 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
28961077 TTATTTTTTA
*
28961087 ATATAAATATAAAATTAAATAAAT
1 ATATAAATATAAAAATAAATAAAT
28961111 ATATAAAATATAAAAATAAATAA
1 ATAT-AAATATAAAAATAAATAA
28961134 TTAAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
ATATAAATATAAAAATAAATAAAT
Found at i:28961138 original size:21 final size:21
Alignment explanation
Indices: 28961103--28961144 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28961093 ATATAAAATT
*
28961103 AAATAAATATATAAAATATAA
1 AAATAAATATATAAAAAATAA
28961124 AAATAAATA-ATTAAAAAATAA
1 AAATAAATATA-TAAAAAATAA
28961145 TTTTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATAAATATATAAAAAATAA
Found at i:28961140 original size:15 final size:16
Alignment explanation
Indices: 28961098--28961144 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
28961088 TATAAATATA
*
28961098 AAATTAAATAAATATAT
1 AAATTAAA-AAATAAAT
*
28961115 AAAATATAAAAATAAAT
1 AAATTA-AAAAATAAAT
28961132 -AATTAAAAAATAA
1 AAATTAAAAAATAA
28961145 TTTTATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 8 0.31
16 4 0.15
17 12 0.46
18 2 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAATTAAAAAATAAAT
Found at i:28965113 original size:17 final size:17
Alignment explanation
Indices: 28965091--28965124 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28965081 ATTTAATTAT
28965091 TTTTATAAGTTTTTAAA
1 TTTTATAAGTTTTTAAA
*
28965108 TTTTATAATTTTTTAAA
1 TTTTATAAGTTTTTAAA
28965125 AATAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTATAAGTTTTTAAA
Found at i:28965132 original size:15 final size:15
Alignment explanation
Indices: 28965114--28965162 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
28965104 TAAATTTTAT
*
28965114 AATTTTTTAAAAATA
1 AATTTTTAAAAAATA
*
28965129 AATTTTCAAAAAATCA
1 AATTTTTAAAAAAT-A
*
28965145 TAATTTTTCAAAAATA
1 -AATTTTTAAAAAATA
28965161 AA
1 AA
28965163 ATTTCGAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 14 0.50
16 2 0.07
17 12 0.43
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
AATTTTTAAAAAATA
Found at i:28965167 original size:14 final size:15
Alignment explanation
Indices: 28965122--28965172 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
28965112 ATAATTTTTT
28965122 AAAAATAAATTTTCA
1 AAAAATAAATTTTCA
28965137 AAAAATCATAATTTTTC-
1 AAAAAT-A-AA-TTTTCA
*
28965154 AAAAATAAAATTTCGA
1 AAAAATAAATTTTC-A
28965170 AAA
1 AAA
28965173 CTTATAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
14 4 0.13
15 8 0.27
16 5 0.17
17 8 0.27
18 5 0.17
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (15 bp):
AAAAATAAATTTTCA
Found at i:28965183 original size:33 final size:32
Alignment explanation
Indices: 28965110--28965185 Score: 98
Period size: 32 Copynumber: 2.3 Consensus size: 32
28965100 TTTTTAAATT
* *
28965110 TTATAATTTTTTAAAAATAAATTTTCAAAAAA
1 TTATAATTTTTCAAAAATAAAATTTCAAAAAA
* * *
28965142 TCATAATTTTTCAAAAATAAAATTTCGAAAAC
1 TTATAATTTTTCAAAAATAAAATTTCAAAAAA
28965174 TTATAAATTTTT
1 TTAT-AATTTTT
28965186 GATAAATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 30 0.81
33 7 0.19
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.43
Consensus pattern (32 bp):
TTATAATTTTTCAAAAATAAAATTTCAAAAAA
Found at i:28965202 original size:17 final size:17
Alignment explanation
Indices: 28965161--28965202 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28965151 TTCAAAAATA
*
28965161 AAATTTCGAAAACTTAT
1 AAATTTTGAAAACTTAT
28965178 AAATTTTTGATAAA-TTAT
1 AAA-TTTTGA-AAACTTAT
28965196 AAATTTT
1 AAATTTT
28965203 TTTAGAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 12 0.55
19 3 0.14
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (17 bp):
AAATTTTGAAAACTTAT
Found at i:28965277 original size:33 final size:32
Alignment explanation
Indices: 28965240--28965356 Score: 119
Period size: 34 Copynumber: 3.5 Consensus size: 32
28965230 ATAACTTTTC
*
28965240 ATTTTCAAAAAGATTTATGATTTTTAAAAATTT
1 ATTTTCAAAAA-ATTTATGATTTTTGAAAATTT
**
28965273 ATTTTTGAAAAATTATATGATTTTTTGAAAATTT
1 ATTTTCAAAAAATT-TATGA-TTTTTGAAAATTT
* * *
28965307 ATTTCCAAAAAAGTTTATAAATTTTTGAAAATTC
1 ATTTTCAAAAAA-TTTAT-GATTTTTGAAAATTT
*
28965341 ATTTT-TAAAAATTTAT
1 ATTTTCAAAAAATTTAT
28965357 ATAAAAAAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
32 8 0.11
33 19 0.27
34 40 0.57
35 3 0.04
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (32 bp):
ATTTTCAAAAAATTTATGATTTTTGAAAATTT
Found at i:28967176 original size:20 final size:20
Alignment explanation
Indices: 28967151--28967192 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
28967141 TTTATATAGT
28967151 ATTTAAAATTAACAAGTTTA
1 ATTTAAAATTAACAAGTTTA
28967171 ATTTAAAATTAACAAGTTTA
1 ATTTAAAATTAACAAGTTTA
28967191 AT
1 AT
28967193 ACCATTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (20 bp):
ATTTAAAATTAACAAGTTTA
Found at i:28969002 original size:2 final size:2
Alignment explanation
Indices: 28968995--28969025 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28968985 CATATTGGGA
28968995 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28969026 AATAGAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28969274 original size:20 final size:21
Alignment explanation
Indices: 28969249--28969288 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
28969239 ATCTAAAAAA
28969249 TTGAAAAATAAATAT-AATTG
1 TTGAAAAATAAATATGAATTG
28969269 TTGAAAAATAAATATGAATT
1 TTGAAAAATAAATATGAATT
28969289 TTACAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (21 bp):
TTGAAAAATAAATATGAATTG
Found at i:28969296 original size:21 final size:20
Alignment explanation
Indices: 28969252--28969298 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
28969242 TAAAAAATTG
*
28969252 AAAAATAAATATAATTGTTG
1 AAAAATAAATATAATTGTTC
28969272 AAAAATAAATATGAATT-TTAC
1 AAAAATAAATAT-AATTGTT-C
28969293 AAAAAT
1 AAAAAT
28969299 TCATCTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (20 bp):
AAAAATAAATATAATTGTTC
Found at i:28969763 original size:17 final size:18
Alignment explanation
Indices: 28969738--28969773 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28969728 TGATATTATT
*
28969738 TAATTTTATTTTAT-TTA
1 TAATATTATTTTATCTTA
28969755 TAATATTATTTTATCTTA
1 TAATATTATTTTATCTTA
28969773 T
1 T
28969774 CCTATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATATTATTTTATCTTA
Found at i:28969779 original size:27 final size:26
Alignment explanation
Indices: 28969730--28969784 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
28969720 AGATAAAATG
* **
28969730 ATATTATTTAATTTTATTTTATTTATA
1 ATATTATTTAATCTTATCCTA-TTATA
*
28969757 ATATTATTTTATCTTATCCTATTATA
1 ATATTATTTAATCTTATCCTATTATA
28969783 AT
1 AT
28969785 TTTGTATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (26 bp):
ATATTATTTAATCTTATCCTATTATA
Found at i:28970596 original size:13 final size:13
Alignment explanation
Indices: 28970573--28970610 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
28970563 ATCAGTTTTT
*
28970573 AATTTTTATATAA
1 AATTTTAATATAA
*
28970586 TATTTTAATATAA
1 AATTTTAATATAA
28970599 AATTTTAATATA
1 AATTTTAATATA
28970611 TTTAAATAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATTTTAATATAA
Found at i:28970844 original size:3 final size:3
Alignment explanation
Indices: 28970831--28970862 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
28970821 ACCCATTTTG
*
28970831 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
28970863 ATTTTTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:28970877 original size:5 final size:5
Alignment explanation
Indices: 28970867--28970905 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
28970857 TTATTAATTT
* *
28970867 TTTTC TTTTC TTTTT TTTTC TTTTC TTTTT TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
28970906 TTGATATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (5 bp):
TTTTC
Found at i:28970884 original size:15 final size:15
Alignment explanation
Indices: 28970864--28970905 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
28970854 TTATTATTAA
28970864 TTTTTTTCTTTTCTT
1 TTTTTTTCTTTTCTT
28970879 TTTTTTTCTTTTCTT
1 TTTTTTTCTTTTCTT
28970894 TTTTTTTCTTTT
1 TTTTTTTCTTTT
28970906 TTGATATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTCTTTTCTT
Found at i:28970885 original size:10 final size:10
Alignment explanation
Indices: 28970864--28970907 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
28970854 TTATTATTAA
28970864 TTTTTTTCTT
1 TTTTTTTCTT
28970874 TTCTTTTT-TT
1 TT-TTTTTCTT
*
28970884 TTCTTTTCTT
1 TTTTTTTCTT
28970894 TTTTTTTCTT
1 TTTTTTTCTT
28970904 TTTT
1 TTTT
28970908 GATATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 4 0.13
10 21 0.70
11 5 0.17
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:28972214 original size:21 final size:21
Alignment explanation
Indices: 28972188--28972228 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28972178 TCTTTCAAGC
28972188 AAAAAA-TAATAATAATAAATT
1 AAAAAATTAATAATAA-AAATT
*
28972209 AAAAAATTATTAATAAAAAT
1 AAAAAATTAATAATAAAAAT
28972229 GAAATCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAATTAATAATAAAAATT
Found at i:28972377 original size:17 final size:18
Alignment explanation
Indices: 28972344--28972377 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28972334 TTATTTCAAG
*
28972344 TAAATAGCAAGAATTAAA
1 TAAATAACAAGAATTAAA
28972362 TAAATAACAA-AATTAA
1 TAAATAACAAGAATTAA
28972378 TAACAACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (18 bp):
TAAATAACAAGAATTAAA
Found at i:28984221 original size:50 final size:50
Alignment explanation
Indices: 28984088--28984254 Score: 160
Period size: 50 Copynumber: 3.4 Consensus size: 50
28984078 GTTTCAAGAA
* * * *
28984088 AAGAT-AAATTTTTAAAGTAGTTAAGCTTTTATTTAAATGAA-CTTTTTTC
1 AAGATAAAATTTTTAAAGTAATTGAGCTTTTACTTAAA-GAAGCCTTTTTC
* * * * * * * *
28984137 GAGATGAGATTTTTAGAGTCATTGAGCCTCTACTTATAGAAGCCTTTTTC
1 AAGATAAAATTTTTAAAGTAATTGAGCTTTTACTTAAAGAAGCCTTTTTC
* * *
28984187 AAGATAAAATTTTTAAAGTAATTGAGATTTTACTTAAAGGAG-CTTTTTT
1 AAGATAAAATTTTTAAAGTAATTGAGCTTTTACTTAAAGAAGCCTTTTTC
*
28984236 TAGATAAAATTTTTAAAGT
1 AAGATAAAATTTTTAAAGT
28984255 TGTTAAGCTT
Statistics
Matches: 93, Mismatches: 23, Indels: 4
0.77 0.19 0.03
Matches are distributed among these distances:
49 31 0.33
50 62 0.67
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (50 bp):
AAGATAAAATTTTTAAAGTAATTGAGCTTTTACTTAAAGAAGCCTTTTTC
Found at i:28984272 original size:49 final size:49
Alignment explanation
Indices: 28984088--28984278 Score: 150
Period size: 50 Copynumber: 3.9 Consensus size: 49
28984078 GTTTCAAGAA
* * * * *
28984088 AAGAT-AAATTTTTAAAGTAGTTAAGCTTTTATTTAAATGAACTTTTTT
1 AAGATAAAATTTTTAAAGTAATTAAGCTTCTACTTAAAGGAGCTTTTTT
* * * * * * * * * *
28984136 CGAGATGAGATTTTTAGAGTCATTGAGCCTCTACTTATAGAAGCCTTTTTC
1 -AAGATAAAATTTTTAAAGTAATTAAGCTTCTACTTAAAGGAG-CTTTTTT
* * *
28984187 AAGATAAAATTTTTAAAGTAATTGAGATTTTACTTAAAGGAGCTTTTTT
1 AAGATAAAATTTTTAAAGTAATTAAGCTTCTACTTAAAGGAGCTTTTTT
* ** * *
28984236 TAGATAAAATTTTTAAAGTTGTTAAGCTTCTGCTTAAATGAGC
1 AAGATAAAATTTTTAAAGTAATTAAGCTTCTACTTAAAGGAGC
28984279 ATTCATTATC
Statistics
Matches: 107, Mismatches: 33, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
49 45 0.42
50 56 0.52
51 6 0.06
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (49 bp):
AAGATAAAATTTTTAAAGTAATTAAGCTTCTACTTAAAGGAGCTTTTTT
Found at i:28984508 original size:44 final size:43
Alignment explanation
Indices: 28984317--28984544 Score: 208
Period size: 44 Copynumber: 5.2 Consensus size: 43
28984307 GAGTAAAATA
* * * * *
28984317 TTTTAAATTTTTAAAAGTTATTAAACTTTTACTTAGATGAGGC
1 TTTTAAATTTTTAAAAGTCATTAAACCTCTACTTAGAAGAGCC
* *
28984360 TTTTAAATTTTTAAAAGTCATTGAACCTCTGCTTA-AAGAAGGCC
1 TTTTAAATTTTTAAAAGTCATTAAACCTCTACTTAGAAG-A-GCC
* * * * * ** *
28984404 TTTTAAATTTTTAAAAATCGTTAAGCTTATGTTTAGAATAGCCC
1 TTTTAAATTTTTAAAAGTCATTAAACCTCTACTTAGAAGAG-CC
* * *
28984448 TTTTAAGTTTTCAAAAGTCATTAAACATCTACTTAGAAGAGCTC
1 TTTTAAATTTTTAAAAGTCATTAAACCTCTACTTAGAAGAGC-C
* * *
28984492 TTTTAAATTTTTAAAAG-CAATTAAGCCTCTATTTAGATGAGCC
1 TTTTAAATTTTTAAAAGTC-ATTAAACCTCTACTTAGAAGAGCC
28984535 TTTTAAATTT
1 TTTTAAATTT
28984545 AAAAAAAAAA
Statistics
Matches: 148, Mismatches: 31, Indels: 12
0.77 0.16 0.06
Matches are distributed among these distances:
42 2 0.01
43 45 0.30
44 99 0.67
45 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (43 bp):
TTTTAAATTTTTAAAAGTCATTAAACCTCTACTTAGAAGAGCC
Found at i:28985805 original size:13 final size:14
Alignment explanation
Indices: 28985787--28985817 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28985777 AATAATTTTA
28985787 AAATAAT-AAAATT
1 AAATAATGAAAATT
28985800 AAATAATGAAAATT
1 AAATAATGAAAATT
28985814 AAAT
1 AAAT
28985818 TTTTAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAATAATGAAAATT
Found at i:28990341 original size:30 final size:29
Alignment explanation
Indices: 28990286--28990390 Score: 99
Period size: 30 Copynumber: 3.6 Consensus size: 29
28990276 TTATTTCTTT
28990286 AAATATAAATA-AAAAATTAATTTAAATACA
1 AAATA-AAATATAAAAATT-ATTTAAATACA
* * * *
28990316 AATTAAAGTATAAATATTTATTTAAATATA
1 AAATAAAATATAAA-AATTATTTAAATACA
*
28990346 AAATAAAATATAAAAATTATTTAAGTA-A
1 AAATAAAATATAAAAATTATTTAAATACA
*
28990374 AAGA-AAATTATAAAAAT
1 AA-ATAAAATATAAAAAT
28990391 ATCAAATTTA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
28 15 0.24
29 16 0.25
30 29 0.46
31 3 0.05
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (29 bp):
AAATAAAATATAAAAATTATTTAAATACA
Found at i:28994426 original size:106 final size:106
Alignment explanation
Indices: 28994240--28994453 Score: 374
Period size: 106 Copynumber: 2.0 Consensus size: 106
28994230 TTTTAACAAC
* * * *
28994240 ATTTGTAATAAGCTGGTGCAAACTACTTTGTATAAAGCAGTACTAGGCCTAGCAAATGAATAGTA
1 ATTTGTAATAAGCTGCTGCAAACTACTTCGTACAAACCAGTACTAGGCCTAGCAAATGAATAGTA
*
28994305 AAATATTCACCAGAGATTTAATATTGACAAAAGAAAAATGT
66 AAATATTCACCAGAGATTTAATACTGACAAAAGAAAAATGT
28994346 ATTTGTAATAAGCTGCTGCAAACTACTTCGTACAAACCAGTACTAGGCCTAGCAAATGAATAGTA
1 ATTTGTAATAAGCTGCTGCAAACTACTTCGTACAAACCAGTACTAGGCCTAGCAAATGAATAGTA
*
28994411 AAATATTCACGAGAGATTTAATACTGACAAAAGAAAAATGT
66 AAATATTCACCAGAGATTTAATACTGACAAAAGAAAAATGT
28994452 AT
1 AT
28994454 AACTAGGAAA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
106 102 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (106 bp):
ATTTGTAATAAGCTGCTGCAAACTACTTCGTACAAACCAGTACTAGGCCTAGCAAATGAATAGTA
AAATATTCACCAGAGATTTAATACTGACAAAAGAAAAATGT
Found at i:28997468 original size:17 final size:17
Alignment explanation
Indices: 28997446--28997560 Score: 64
Period size: 17 Copynumber: 6.9 Consensus size: 17
28997436 AATTAAAGAT
28997446 ATTAAAATTAATAAATA
1 ATTAAAATTAATAAATA
28997463 ATTAAAATTTAAT-AA-A
1 ATTAAAA-TTAATAAATA
***
28997479 ATTATTTTTATATAAA-A
1 ATTAAAATTA-ATAAATA
* * *
28997496 A-TATAA-TAAGAAAGAA
1 ATTAAAATTAATAAA-TA
*
28997512 AATAATAATTAA-AAAT-
1 ATTAA-AATTAATAAATA
*
28997528 ATTAAATTTAATAAATA
1 ATTAAAATTAATAAATA
28997545 ATTAAAATTTAATAAA
1 ATTAAAA-TTAATAAA
28997561 ATTATTTTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 21
0.70 0.10 0.19
Matches are distributed among these distances:
14 4 0.05
15 10 0.13
16 20 0.26
17 21 0.28
18 18 0.24
19 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
ATTAAAATTAATAAATA
Found at i:28997474 original size:18 final size:18
Alignment explanation
Indices: 28997446--28997560 Score: 65
Period size: 18 Copynumber: 6.9 Consensus size: 18
28997436 AATTAAAGAT
28997446 ATTAAAA-TTAATAAATA
1 ATTAAAATTTAATAAATA
28997463 ATTAAAATTTAAT-AA-A
1 ATTAAAATTTAATAAATA
**
28997479 ATT-ATTTTTATATAAA-A
1 ATTAAAATTTA-ATAAATA
* * *
28997496 A-TATAA--TAAGAAAGAA
1 ATTAAAATTTAATAAA-TA
*
28997512 AATAATAA-TTAA-AAAT-
1 ATTAA-AATTTAATAAATA
28997528 ATT-AAATTTAATAAATA
1 ATTAAAATTTAATAAATA
28997545 ATTAAAATTTAATAAA
1 ATTAAAATTTAATAAA
28997561 ATTATTTTTA
Statistics
Matches: 76, Mismatches: 9, Indels: 25
0.69 0.08 0.23
Matches are distributed among these distances:
14 6 0.08
15 12 0.16
16 15 0.20
17 18 0.24
18 22 0.29
19 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
ATTAAAATTTAATAAATA
Found at i:28997620 original size:82 final size:82
Alignment explanation
Indices: 28997411--28997576 Score: 296
Period size: 82 Copynumber: 2.0 Consensus size: 82
28997401 AGGGTGAGAT
* * * *
28997411 AAAATATAATGAGAAATAAAATAATAATTAAAGATATTAAAATTAATAAATAATTAAAATTTAAT
1 AAAATATAATAAGAAAGAAAATAATAATTAAAAATATTAAATTTAATAAATAATTAAAATTTAAT
28997476 AAAATTATTTTTATATA
66 AAAATTATTTTTATATA
28997493 AAAATATAATAAGAAAGAAAATAATAATTAAAAATATTAAATTTAATAAATAATTAAAATTTAAT
1 AAAATATAATAAGAAAGAAAATAATAATTAAAAATATTAAATTTAATAAATAATTAAAATTTAAT
28997558 AAAATTATTTTTATATA
66 AAAATTATTTTTATATA
28997575 AA
1 AA
28997577 TTAATAATTG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (82 bp):
AAAATATAATAAGAAAGAAAATAATAATTAAAAATATTAAATTTAATAAATAATTAAAATTTAAT
AAAATTATTTTTATATA
Found at i:29006831 original size:2 final size:2
Alignment explanation
Indices: 29006826--29006850 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29006816 TAAATCACGG
29006826 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29006851 CACACATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29007671 original size:12 final size:12
Alignment explanation
Indices: 29007616--29007680 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
29007606 AAAAATTATT
29007616 TTTAATTA-ATTA
1 TTTAATTATA-TA
* *
29007628 ATTAATTTTATA
1 TTTAATTATATA
29007640 TTT-A-TATATA
1 TTTAATTATATA
29007650 TTT--TTATATA
1 TTTAATTATATA
*
29007660 TTTAATTTTATA
1 TTTAATTATATA
29007672 TTTATATTA
1 TTTA-ATTA
29007681 AAAAATAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
10 17 0.40
11 1 0.02
12 20 0.48
13 4 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
TTTAATTATATA
Found at i:29008787 original size:430 final size:430
Alignment explanation
Indices: 29007987--29008852 Score: 1615
Period size: 430 Copynumber: 2.0 Consensus size: 430
29007977 TTGCATTTAT
* *
29007987 AAAAATACTCTTACGCCAAAGCTTGACACCAACATTTGGAGCATCAAGTAAGGAAAAATTCTTAT
1 AAAAATACTCTTACACCAAAGCTTGACACCAACATTTGAAGCATCAAGTAAGGAAAAATTCTTAT
* * * *
29008052 ATTAGCCGTACACAAAATAATACCACCAAGAAAAAAAAATCTAATAAGAAAAAGAGATAGTCGGC
66 ATTAGCCGTACACAAAATAATACCACCAAGAAAAAAAAACCTAATAAAAAAAAGAGATAGCCGAC
29008117 CTAGCTAAAATAAAAACTCACCTAAGCCAGCACTCTATCCACTTAGCTTAACCACAGATGAGACC
131 CTAGCTAAAATAAAAACTCACCTAAGCCAGCACTCTATCCACTTAGCTTAACCACAGATGAGACC
*
29008182 AACCATGAAACAATTTCAAGCCCTGATAGAACAAATACAAGCTCTCAAACAGATGCTGCAAACTA
196 AACCATGAAACAATTTCAAGCCCTGATAGAACAAATACAAGCACTCAAACAGATGCTGCAAACTA
29008247 TAACCCCACCACAAGTCTTCAAAGTGACGGATTTAGTCACACTTGGTCGAGAAGCTGTTATCGGG
261 TAACCCCACCACAAGTCTTCAAAGTGACGGATTTAGTCACACTTGGTCGAGAAGCTGTTATCGGG
29008312 TAACCAAGTTACGAAGAGGCAGAAGTTTTCTTGGCCTCTAGAGAAAAAGAACACGCCAACCTAAC
326 TAACCAAGTTACGAAGAGGCAGAAGTTTTCTTGGCCTCTAGAGAAAAAGAACACGCCAACCTAAC
*
29008377 TTGTCATGCCCCAACCACAATTTCATACATGCCACAACCC
391 TCGTCATGCCCCAACCACAATTTCATACATGCCACAACCC
* *
29008417 AAAAATACTCTTACATCAGAGCTTGACACCAACATTTGAAGCATCAAGTAAGGAAAAATTCTTAT
1 AAAAATACTCTTACACCAAAGCTTGACACCAACATTTGAAGCATCAAGTAAGGAAAAATTCTTAT
29008482 ATTAGCCGTACACAAAATAATACCACCAAGAAAAAAAAACCTAATAAAAAAAAGAGATAGCCGAC
66 ATTAGCCGTACACAAAATAATACCACCAAGAAAAAAAAACCTAATAAAAAAAAGAGATAGCCGAC
29008547 CTAGCTAAAATAAAAACTCACCTAAGCCAGCACTCTATCCACTTAGCTTAACCACAGATGAGACC
131 CTAGCTAAAATAAAAACTCACCTAAGCCAGCACTCTATCCACTTAGCTTAACCACAGATGAGACC
*
29008612 GACCATGAAACAATTTCAAGCCCTGATAGAACAAATACAAGCACTCAAACAGATGCTGCAAACTA
196 AACCATGAAACAATTTCAAGCCCTGATAGAACAAATACAAGCACTCAAACAGATGCTGCAAACTA
*
29008677 TAATCCCACCACAAGTCTTCAAAGTGACGGATTTAGTCACACTTGGTCGAGAAGCTGTTATCGGG
261 TAACCCCACCACAAGTCTTCAAAGTGACGGATTTAGTCACACTTGGTCGAGAAGCTGTTATCGGG
29008742 TAACCAAGTTACGAAGAGGCAGAAGTTTTCTTGGCCTCTAGAGAAAAAGAACACGCCAACCTAAC
326 TAACCAAGTTACGAAGAGGCAGAAGTTTTCTTGGCCTCTAGAGAAAAAGAACACGCCAACCTAAC
*
29008807 TCGTCATGCCCCAACCATAATTTCATACATGCCACAACCC
391 TCGTCATGCCCCAACCACAATTTCATACATGCCACAACCC
29008847 AAAAAT
1 AAAAAT
29008853 CCAAACAAAC
Statistics
Matches: 423, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
430 423 1.00
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (430 bp):
AAAAATACTCTTACACCAAAGCTTGACACCAACATTTGAAGCATCAAGTAAGGAAAAATTCTTAT
ATTAGCCGTACACAAAATAATACCACCAAGAAAAAAAAACCTAATAAAAAAAAGAGATAGCCGAC
CTAGCTAAAATAAAAACTCACCTAAGCCAGCACTCTATCCACTTAGCTTAACCACAGATGAGACC
AACCATGAAACAATTTCAAGCCCTGATAGAACAAATACAAGCACTCAAACAGATGCTGCAAACTA
TAACCCCACCACAAGTCTTCAAAGTGACGGATTTAGTCACACTTGGTCGAGAAGCTGTTATCGGG
TAACCAAGTTACGAAGAGGCAGAAGTTTTCTTGGCCTCTAGAGAAAAAGAACACGCCAACCTAAC
TCGTCATGCCCCAACCACAATTTCATACATGCCACAACCC
Found at i:29018718 original size:50 final size:51
Alignment explanation
Indices: 29018661--29018768 Score: 155
Period size: 51 Copynumber: 2.1 Consensus size: 51
29018651 AATTCAAAAA
*
29018661 TTATTTTATTTA-TTTATATACATTCCTTTAAATAATAAATTATTCATGTT
1 TTATTTTATTTATTTTATATACATTCATTTAAATAATAAATTATTCATGTT
* * * *
29018711 TTATTTTATTTATTTTTTATACATTTATTTAAATAATAAATTGTTTATGTT
1 TTATTTTATTTATTTTATATACATTCATTTAAATAATAAATTATTCATGTT
*
29018762 TAATTTT
1 TTATTTT
29018769 TTGATCATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 12 0.24
51 39 0.76
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (51 bp):
TTATTTTATTTATTTTATATACATTCATTTAAATAATAAATTATTCATGTT
Found at i:29018877 original size:14 final size:14
Alignment explanation
Indices: 29018846--29018887 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
29018836 CATAAAAAAT
*
29018846 AAATAAATCATAATC
1 AAATAAAT-ATAAAC
29018861 AAATAAATATAAAC
1 AAATAAATATAAAC
*
29018875 AAACAAATATAAA
1 AAATAAATATAAA
29018888 TGAATTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAATATAAAC
Found at i:29019012 original size:21 final size:22
Alignment explanation
Indices: 29018975--29019016 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
29018965 TAAACTAACT
*
29018975 ATAAATAAATCAAATTTAAATA
1 ATAAAAAAATCAAATTTAAATA
29018997 ATAAAAAAAT-AAATTTAAAT
1 ATAAAAAAATCAAATTTAAAT
29019017 CAAATTTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAAAAAAATCAAATTTAAATA
Found at i:29021166 original size:1 final size:1
Alignment explanation
Indices: 29021160--29021186 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
29021150 TGGTGTTCAG
29021160 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
29021187 AACTTGATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:29031521 original size:16 final size:15
Alignment explanation
Indices: 29031500--29031558 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
29031490 ATTATTTATT
29031500 AAAAATGAAAAGAAGA
1 AAAAATGAAAAGAA-A
29031516 AAAAATAGAAAAGGAAA
1 AAAAAT-GAAAA-GAAA
** *
29031533 AAAAACAAAAACAAA
1 AAAAATGAAAAGAAA
29031548 AAAAATGAAAA
1 AAAAATGAAAA
29031559 ACAAAATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.33
16 10 0.28
17 11 0.31
18 3 0.08
ACGTcount: A:0.80, C:0.03, G:0.12, T:0.05
Consensus pattern (15 bp):
AAAAATGAAAAGAAA
Found at i:29031559 original size:16 final size:16
Alignment explanation
Indices: 29031500--29031564 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
29031490 ATTATTTATT
*
29031500 AAAAATGAAAAGA-AGA
1 AAAAATGAAAA-ACAAA
**
29031516 AAAAATAGAAAAGGAAA
1 AAAAAT-GAAAAACAAA
*
29031533 AAAAA-CAAAAACAAA
1 AAAAATGAAAAACAAA
29031548 AAAAATGAAAAACAAA
1 AAAAATGAAAAACAAA
29031564 A
1 A
29031565 TTTAGTGAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
15 12 0.30
16 16 0.40
17 12 0.30
ACGTcount: A:0.80, C:0.05, G:0.11, T:0.05
Consensus pattern (16 bp):
AAAAATGAAAAACAAA
Found at i:29036608 original size:16 final size:19
Alignment explanation
Indices: 29036580--29036624 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
29036570 TAAACACCAT
*
29036580 TTTTTTGTTT-TTATAATA-
1 TTTTTTATTTATTAT-ATAC
29036598 TTTTTTATTTATTATATAC
1 TTTTTTATTTATTATATAC
29036617 TTTTTTAT
1 TTTTTTAT
29036625 CATTGGACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTTATTTATTATATAC
Found at i:29041529 original size:2 final size:2
Alignment explanation
Indices: 29041522--29041557 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
29041512 TTTACAGTTC
29041522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29041558 TCTTAACACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29050016 original size:11 final size:11
Alignment explanation
Indices: 29050000--29050024 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29049990 TTTAAAAATG
29050000 TAAATTTTATA
1 TAAATTTTATA
29050011 TAAATTTTATA
1 TAAATTTTATA
29050022 TAA
1 TAA
29050025 TACTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TAAATTTTATA
Found at i:29050545 original size:2 final size:2
Alignment explanation
Indices: 29050538--29050563 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29050528 GATCAATCAT
29050538 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
29050564 AAGACAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29050783 original size:33 final size:33
Alignment explanation
Indices: 29050724--29050793 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
29050714 GTAAAAAAAA
* *
29050724 ATTT-TATTTTATCAAAATTTAGTAATTTATAT
1 ATTTATATTATATCAAAATTTAATAATTTATAT
*
29050756 ATTTATATTATAT-AAAATATTAATAATTTATGT
1 ATTTATATTATATCAAAAT-TTAATAATTTATAT
29050789 ATTTA
1 ATTTA
29050794 AAAATGTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 9 0.27
33 24 0.73
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (33 bp):
ATTTATATTATATCAAAATTTAATAATTTATAT
Found at i:29052007 original size:33 final size:32
Alignment explanation
Indices: 29051968--29052029 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
29051958 AAATTTTTTT
* *
29051968 TTAATTTTTGTTAAATTTATATATTTTTTAATG
1 TTAATTTGTATTAAATTTATAT-TTTTTTAATG
*
29052001 TTAATTTGTATTATATTTATATTTTTTTA
1 TTAATTTGTATTAAATTTATATTTTTTTA
29052030 TATCAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 7 0.27
33 19 0.73
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (32 bp):
TTAATTTGTATTAAATTTATATTTTTTTAATG
Found at i:29052045 original size:32 final size:33
Alignment explanation
Indices: 29051982--29052048 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
29051972 TTTTTGTTAA
* * *
29051982 ATTTATATATTTTTTAATGTTAATTTGTATTAT
1 ATTTATATATTTTTTAATATCAATTTATATTAT
29052015 ATTTATAT-TTTTTT-ATATCAATTTTATATTAT
1 ATTTATATATTTTTTAATATCAA-TTTATATTAT
29052047 AT
1 AT
29052049 CATCGTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 5 0.17
32 17 0.57
33 8 0.27
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (33 bp):
ATTTATATATTTTTTAATATCAATTTATATTAT
Found at i:29053058 original size:3 final size:3
Alignment explanation
Indices: 29053050--29053075 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29053040 CAATAAAAAT
29053050 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
29053076 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29054538 original size:13 final size:13
Alignment explanation
Indices: 29054520--29054548 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29054510 GAATTATGTG
29054520 TTTCATATATTAA
1 TTTCATATATTAA
29054533 TTTCATATATTAA
1 TTTCATATATTAA
29054546 TTT
1 TTT
29054549 TTAAAAATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTCATATATTAA
Found at i:29055075 original size:62 final size:61
Alignment explanation
Indices: 29054811--29055078 Score: 179
Period size: 62 Copynumber: 4.3 Consensus size: 61
29054801 TTTTATAAAA
* * * * * **
29054811 GGATTA-TCAAAGGCGTTTTTGATCAAAAATACCTTGAGTAATTCCTTTTAATTTTTTATACT
1 GGATTATTCAAA-GCGTTTTTGAT-AAAAATACCTTGAATAATCCCCTCTAATTTTTTAGAGG
* * * * *
29054873 GAATTATTCAAGGCGTTTTTGACAAAAAATACCTTGAATAA-CCCCTTTCA-TTTTTATGAGG
1 GGATTATTCAAAGCGTTTTTGA-TAAAAATACCTTGAATAATCCCCTCTAATTTTTTA-GAGG
* * ** * * ** * *
29054934 GGATTATTGAAGGTATTTTTGATCAAAA-ACGCTTTGAATAACCCCCTCCCATTTGTATA-AAG
1 GGATTATTCAAAGCGTTTTTGATAAAAATAC-C-TTGAATAATCCCCTCTAATTT-TTTAGAGG
* * * *
29054996 TGATTATT-GAAGACGTTTTTTACTAAAAATACCTTCAATAATCCCCTCTAATTTTTTAGAGG
1 GGATTATTCAAAG-CGTTTTTGA-TAAAAATACCTTGAATAATCCCCTCTAATTTTTTAGAGG
29055058 GGATTATTCAAAGCGTTTTTG
1 GGATTATTCAAAGCGTTTTTG
29055079 GCCAACAATG
Statistics
Matches: 157, Mismatches: 36, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
59 2 0.01
60 11 0.07
61 38 0.24
62 86 0.55
63 15 0.10
64 5 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (61 bp):
GGATTATTCAAAGCGTTTTTGATAAAAATACCTTGAATAATCCCCTCTAATTTTTTAGAGG
Found at i:29055094 original size:62 final size:62
Alignment explanation
Indices: 29055027--29055193 Score: 160
Period size: 62 Copynumber: 2.7 Consensus size: 62
29055017 ACTAAAAATA
* *
29055027 CCTTCAATAATCCCCTCTAATTTTTTAGAGGGGATTATTCAAAGCGTTTTTGGCCAACAA-TG
1 CCTTCAATAATCCCCTCTAATTTTTTAGAGGGAATTATTCAAAGCGTTATTGGCCAA-AACTG
* ** * * *** * *
29055089 TCTTCAATAATCCATTTTCA-TTTTTATGAACAAATTATTCAAGGTGTTATTGGCCAAAACTG
1 CCTTCAATAATCCCCTCTAATTTTTTA-GAGGGAATTATTCAAAGCGTTATTGGCCAAAACTG
* * *
29055151 CCTTTAATAATCCCCTCTAGTTTTATAGAGGGAATTATT-AAAG
1 CCTTCAATAATCCCCTCTAATTTTTTAGAGGGAATTATTCAAAG
29055194 GCGGTTGGTT
Statistics
Matches: 78, Mismatches: 24, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
61 11 0.14
62 62 0.79
63 5 0.06
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (62 bp):
CCTTCAATAATCCCCTCTAATTTTTTAGAGGGAATTATTCAAAGCGTTATTGGCCAAAACTG
Found at i:29059863 original size:45 final size:46
Alignment explanation
Indices: 29059796--29059883 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 46
29059786 AAATATCTTC
** * * *
29059796 TTTTTTTAATTTCTATTTTTTTTTACCATTTGGGTCTATTTAGTAT
1 TTTTTTTAATTTCTATAATTTTTCACCATTTGAGTCAATTTAGTAT
* *
29059842 TTTTTTTAATTTTTA-AATTTTTCACTATTTGAGTCAATTTAG
1 TTTTTTTAATTTCTATAATTTTTCACCATTTGAGTCAATTTAG
29059884 AAAAATATGA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
45 21 0.60
46 14 0.40
ACGTcount: A:0.22, C:0.08, G:0.08, T:0.62
Consensus pattern (46 bp):
TTTTTTTAATTTCTATAATTTTTCACCATTTGAGTCAATTTAGTAT
Found at i:29064635 original size:22 final size:21
Alignment explanation
Indices: 29064597--29064640 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
29064587 AATAATTTTA
*
29064597 ATCATAAAACATATAATATAT
1 ATCAGAAAACATATAATATAT
* *
29064618 ATCAGAAACACATTTAATCTAT
1 ATCAGAAA-ACATATAATATAT
29064640 A
1 A
29064641 GCTAAACAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (21 bp):
ATCAGAAAACATATAATATAT
Found at i:29065313 original size:26 final size:26
Alignment explanation
Indices: 29065259--29065314 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
29065249 CCCGATTCAA
*
29065259 TTTTATGAGTAGATTGTTCAAGGTAT
1 TTTTATGAGTAGATTATTCAAGGTAT
* *
29065285 TTTTA-GAGTGGATTATTCAAGGTGT
1 TTTTATGAGTAGATTATTCAAGGTAT
29065310 TTTTA
1 TTTTA
29065315 GTCATAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (26 bp):
TTTTATGAGTAGATTATTCAAGGTAT
Found at i:29065802 original size:63 final size:63
Alignment explanation
Indices: 29065670--29065806 Score: 161
Period size: 63 Copynumber: 2.2 Consensus size: 63
29065660 AATGGCAGAG
* * *
29065670 GATTATTGAAGGTGTTTTTGGCTAAAAACACCTTGAATAATCCCTTACAAAAAAATTAATAAA
1 GATTATTCAAGGTGTTTTTGGCTAAAAACACATTCAATAATCCCTTACAAAAAAATTAATAAA
* ** * * *
29065733 GGTTATTCAAGGTGTTTTTGG-TCAAAAATGCATTCAATAATCCCCTTATAAAAAAATT-TTGAA
1 GATTATTCAAGGTGTTTTTGGCT-AAAAACACATTCAATAAT-CCCTTACAAAAAAATTAATAAA
29065796 GATTATTCAAG
1 GATTATTCAAG
29065807 ACATTTTTAG
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
62 1 0.02
63 46 0.74
64 15 0.24
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (63 bp):
GATTATTCAAGGTGTTTTTGGCTAAAAACACATTCAATAATCCCTTACAAAAAAATTAATAAA
Found at i:29065814 original size:63 final size:63
Alignment explanation
Indices: 29065705--29065823 Score: 141
Period size: 63 Copynumber: 1.9 Consensus size: 63
29065695 AAACACCTTG
* *** *
29065705 AATAATCCCTTACAAAAAAATTAATAAAGGTTATTCAAGGTGTTTTTGGTCAAAAATGCATTC
1 AATAATCCCTTACAAAAAAATTAATAAAGATTATTCAAGACATTTTTAGTCAAAAATGCATTC
* * * *
29065768 AATAATCCCCTTATAAAAAAATT-TTGAAGATTATTCAAGACATTTTTAGTTAAAAA
1 AATAAT-CCCTTACAAAAAAATTAATAAAGATTATTCAAGACATTTTTAGTCAAAAA
29065824 CGTCATGAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
63 31 0.67
64 15 0.33
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (63 bp):
AATAATCCCTTACAAAAAAATTAATAAAGATTATTCAAGACATTTTTAGTCAAAAATGCATTC
Found at i:29067701 original size:31 final size:31
Alignment explanation
Indices: 29067658--29067716 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
29067648 GTAGATCATG
29067658 CATACAAGATAAT-TCTAACAAATAATCAATA
1 CATACAAGATAATCTC-AACAAATAATCAATA
29067689 CATACGAA-ATAATCTCAACAAATAATCA
1 CATAC-AAGATAATCTCAACAAATAATCA
29067717 CCGACAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.54, C:0.19, G:0.03, T:0.24
Consensus pattern (31 bp):
CATACAAGATAATCTCAACAAATAATCAATA
Found at i:29078856 original size:20 final size:21
Alignment explanation
Indices: 29078819--29078868 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
29078809 TCCGAAATTA
29078819 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
29078840 ATAAAATATTA-TTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
29078860 AT-AAATATT
1 ATAAAATATT
29078869 TAAATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 7 0.24
20 11 0.38
21 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:29078870 original size:14 final size:16
Alignment explanation
Indices: 29078841--29078895 Score: 64
Period size: 14 Copynumber: 3.7 Consensus size: 16
29078831 TTTTTAAATA
*
29078841 TAAA-ATATTATT-TT
1 TAAATATATAATTATT
29078855 TAAATATA-AA-TATT
1 TAAATATATAATTATT
*
29078869 TAAATATATAATTATA
1 TAAATATATAATTATT
29078885 TAAATATATAA
1 TAAATATATAA
29078896 ATAAAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 1 0.03
14 15 0.43
15 5 0.14
16 14 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATATATAATTATT
Found at i:29078874 original size:8 final size:8
Alignment explanation
Indices: 29078858--29078898 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
29078848 TTATTTTTAA
29078858 ATATAAAT
1 ATATAAAT
*
29078866 ATTTAAAT
1 ATATAAAT
*
29078874 ATATAATT
1 ATATAAAT
29078882 ATATAAAT
1 ATATAAAT
29078890 ATATAAAT
1 ATATAAAT
29078898 A
1 A
29078899 AAAAATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:29078905 original size:24 final size:24
Alignment explanation
Indices: 29078858--29078906 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
29078848 TTATTTTTAA
* * *
29078858 ATATAAATATTTAAATATATAATT
1 ATATAAATATATAAATAAAAAATT
29078882 ATATAAATATATAAATAAAAAATT
1 ATATAAATATATAAATAAAAAATT
29078906 A
1 A
29078907 ATTTAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
ATATAAATATATAAATAAAAAATT
Found at i:29081606 original size:21 final size:20
Alignment explanation
Indices: 29081558--29081606 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
29081548 AAAGTATTTA
*
29081558 AAAAAATAAATAAAAAAACT
1 AAAAAATAAATAAAAAAACC
* *
29081578 AACTAAATAAATAAATAATACC
1 AA-AAAATAAATAAA-AAAACC
29081600 AAAAAAT
1 AAAAAAT
29081607 TAGCTTAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 2 0.09
21 15 0.65
22 6 0.26
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.18
Consensus pattern (20 bp):
AAAAAATAAATAAAAAAACC
Done.