Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 17 of 187
Found at i:5930468 original size:33 final size:33
Alignment explanation
Indices: 5930266--5930468 Score: 113
Period size: 33 Copynumber: 6.0 Consensus size: 33
5930256 ACACATGCAT
* * * ** *
5930266 TGCCATGGCCCTGCCATGGTCTTACATTTGTAG
1 TGCCATAGCCCAGCTATGGTCTTACATTTAAAA
* * *
5930299 TGCCATAACCCAGTTATGGTCTTATCA-TTAGAA
1 TGCCATAGCCCAGCTATGGTCTTA-CATTTAAAA
*
5930332 TGCCATAGCCCAGCTATGGTCTTACACATGTAACTATA
1 TGCCATAGCCCAGCTATGGTCTT--ACATTTAA--A-A
* * * * * * **
5930370 CTGCCATGGTCCAACCATGGTCTTACGTTCAAGG
1 -TGCCATAGCCCAGCTATGGTCTTACATTTAAAA
* * ** *
5930404 TGTCATAACCCAATTATGGTCTTTTCA-TTAAAA
1 TGCCATAGCCCAGCTATGGTC-TTACATTTAAAA
5930437 TGCCATAGCCCAGCTATGGTCTTACATTTAAA
1 TGCCATAGCCCAGCTATGGTCTTACATTTAAA
5930469 CATTCCCATG
Statistics
Matches: 123, Mismatches: 37, Indels: 20
0.68 0.21 0.11
Matches are distributed among these distances:
32 4 0.03
33 83 0.67
34 7 0.06
35 3 0.02
37 6 0.05
38 1 0.01
39 19 0.15
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (33 bp):
TGCCATAGCCCAGCTATGGTCTTACATTTAAAA
Found at i:5940135 original size:30 final size:29
Alignment explanation
Indices: 5940092--5940184 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 29
5940082 AATGTGTATG
*
5940092 ATTAAATCAAAATTAAAGTTTCAAGTATATA
1 ATTAAA-CCAAATTAAA-TTTCAAGTATATA
* * *
5940123 TTTAAACCAAATTATAATTTCACGTGTATA
1 ATTAAACCAAATTA-AATTTCAAGTATATA
** *
5940153 ATTGTACCAAATTAAAATTCATA-TATATA
1 ATTAAACCAAATTAAATTTCA-AGTATATA
5940182 ATT
1 ATT
5940185 GCACATTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
29 14 0.28
30 29 0.58
31 7 0.14
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (29 bp):
ATTAAACCAAATTAAATTTCAAGTATATA
Found at i:5942668 original size:33 final size:33
Alignment explanation
Indices: 5942631--5942701 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
5942621 AAAACAATGT
5942631 CGTTAAAAGTTAGGAATATTATATTTCTTTACA
1 CGTTAAAAGTTAGGAATATTATATTTCTTTACA
5942664 CGTTAAAAGTTAGGAATATTATATTTCTTTACA
1 CGTTAAAAGTTAGGAATATTATATTTCTTTACA
5942697 CGTTA
1 CGTTA
5942702 GGGCCAAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (33 bp):
CGTTAAAAGTTAGGAATATTATATTTCTTTACA
Found at i:5943839 original size:28 final size:29
Alignment explanation
Indices: 5943802--5943872 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
5943792 AAAAATAAAA
5943802 ATTTACCAAAATATTA-TAACTTTTTT-TT
1 ATTTACCAAAATATTACT-ACTTTTTTATT
**
5943830 ATTTACCAAAATATTACTTTTTTTTTATT
1 ATTTACCAAAATATTACTACTTTTTTATT
5943859 ATTTACCAAAATAT
1 ATTTACCAAAATAT
5943873 AAAAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
28 22 0.56
29 17 0.44
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (29 bp):
ATTTACCAAAATATTACTACTTTTTTATT
Found at i:5944216 original size:37 final size:37
Alignment explanation
Indices: 5944171--5944359 Score: 378
Period size: 37 Copynumber: 5.1 Consensus size: 37
5944161 TCACTTTTTT
5944171 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
5944208 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
5944245 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
5944282 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
5944319 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
5944356 ATTT
1 ATTT
5944360 NNNNNNNNNN
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 152 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTCTC
Found at i:5944522 original size:37 final size:37
Alignment explanation
Indices: 5944479--5944575 Score: 185
Period size: 37 Copynumber: 2.6 Consensus size: 37
5944469 AATTTTTTTA
5944479 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
1 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
*
5944516 AAATTAAAATAGAGTTATTAAATGAGAATATTTTATT
1 AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
5944553 AAATTAAAATAGAGTTATTAAAT
1 AAATTAAAATAGAGTTATTAAAT
5944576 AAAAAAGTGA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (37 bp):
AAATTAAAATAGAGTTATTAAATGAGAATAGTTTATT
Found at i:5944580 original size:19 final size:19
Alignment explanation
Indices: 5944479--5944579 Score: 118
Period size: 18 Copynumber: 5.5 Consensus size: 19
5944469 AATTTTTTTA
5944479 AAATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
* * *
5944498 AAATGAGAATAG-TTTATT
1 AAATTAAAATAGAGTTATT
5944516 AAATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
* * **
5944535 AAATGAGAATA-TTTTATT
1 AAATTAAAATAGAGTTATT
5944553 AAATTAAAATAGAGTTATT
1 AAATTAAAATAGAGTTATT
5944572 AAA-TAAAA
1 AAATTAAAA
5944580 AAGTGAGTTG
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
18 34 0.52
19 32 0.48
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (19 bp):
AAATTAAAATAGAGTTATT
Found at i:5944890 original size:27 final size:26
Alignment explanation
Indices: 5944859--5944925 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 26
5944849 TTTTTTTGAT
5944859 ATATTTTGGTAAATAATAAAA-AAAGTA
1 ATATTTTGGTAAATAA-AAAAGAAA-TA
* **
5944886 ATATTTTAGTAAATAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAGAAATA
5944912 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
5944926 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 19 0.54
27 16 0.46
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (26 bp):
ATATTTTGGTAAATAAAAAAGAAATA
Found at i:5955029 original size:15 final size:15
Alignment explanation
Indices: 5955009--5955038 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5954999 TATTAGCAAC
5955009 TGAACTTGTATTTTT
1 TGAACTTGTATTTTT
5955024 TGAACTTGTATTTTT
1 TGAACTTGTATTTTT
5955039 AAATAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (15 bp):
TGAACTTGTATTTTT
Found at i:5963361 original size:15 final size:14
Alignment explanation
Indices: 5963324--5963368 Score: 56
Period size: 13 Copynumber: 3.1 Consensus size: 14
5963314 ACCAATATTT
*
5963324 TAATATTTTTAATA
1 TAATATTTTAAATA
5963338 TAA-ATTTTAAATA
1 TAATATTTTAAATA
5963351 TGAATATTTTAAAATA
1 T-AATATTTT-AAATA
5963367 TA
1 TA
5963369 TGATGAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 10 0.37
14 5 0.19
15 6 0.22
16 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
TAATATTTTAAATA
Found at i:5963905 original size:38 final size:38
Alignment explanation
Indices: 5963816--5963904 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
5963806 AAAAATTATA
* * * *
5963816 TTTAATACAATAAATCATTTATTATATTTATTTATGTT
1 TTTAATATAATAAAACATTTATTATATTTATGTATATT
5963854 TTTAATATAATAAAACATTTATTATATTTATGGTAGTATTT
1 TTTAATATAATAAAACATTTATTATATTTAT-GTA-TA-TT
5963895 TTTAATATAA
1 TTTAATATAA
5963905 ATATTTTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 29 0.66
39 2 0.05
40 1 0.02
41 12 0.27
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.53
Consensus pattern (38 bp):
TTTAATATAATAAAACATTTATTATATTTATGTATATT
Found at i:5963977 original size:15 final size:16
Alignment explanation
Indices: 5963959--5963988 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5963949 TGCATTATAT
5963959 TTTTTAAA-AAAAATA
1 TTTTTAAATAAAAATA
5963974 TTTTTAAATAAAAAT
1 TTTTTAAATAAAAAT
5963989 TAATCTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTTTAAATAAAAATA
Found at i:5968134 original size:61 final size:60
Alignment explanation
Indices: 5968053--5968166 Score: 165
Period size: 61 Copynumber: 1.9 Consensus size: 60
5968043 ATATATTTTT
* * * * *
5968053 TTTCTTTTTTGGTCATCCAACTATGAAAAGTTACAAAATGATCACCCAACTATTAGTAAA
1 TTTCTTTTTTGGCCACCCAACTATAAAAAATTACAAAATAATCACCCAACTATTAGTAAA
*
5968113 TTTCTTATTTTGGCCACCCAACTATAAAAAATTACAAAATAATCATCCAACTAT
1 TTTCTT-TTTTGGCCACCCAACTATAAAAAATTACAAAATAATCACCCAACTAT
5968167 ACAATTTTGT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 6 0.13
61 41 0.87
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (60 bp):
TTTCTTTTTTGGCCACCCAACTATAAAAAATTACAAAATAATCACCCAACTATTAGTAAA
Found at i:5969196 original size:18 final size:18
Alignment explanation
Indices: 5969173--5969209 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5969163 GCTTATAATT
5969173 TAGCAATTGTATATTATG
1 TAGCAATTGTATATTATG
5969191 TAGCAATTGTATATTATG
1 TAGCAATTGTATATTATG
5969209 T
1 T
5969210 TGTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (18 bp):
TAGCAATTGTATATTATG
Found at i:5970161 original size:24 final size:24
Alignment explanation
Indices: 5970134--5970179 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
5970124 AAACTTATAA
5970134 TTTTTGAAAATTTTAATTAGGCAC
1 TTTTTGAAAATTTTAATTAGGCAC
5970158 TTTTTGAAAATTTTAATTAGGC
1 TTTTTGAAAATTTTAATTAGGC
5970180 TTCTCAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (24 bp):
TTTTTGAAAATTTTAATTAGGCAC
Found at i:5970283 original size:2 final size:2
Alignment explanation
Indices: 5970276--5970301 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5970266 GGGCTTGAAA
5970276 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
5970302 TTATGAATCT
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):
AT
Found at i:5970953 original size:26 final size:22
Alignment explanation
Indices: 5970899--5970954 Score: 58
Period size: 26 Copynumber: 2.4 Consensus size: 22
5970889 CAAGTTATAA
5970899 ATATTATATTATAACAAAAAAT
1 ATATTATATTATAACAAAAAAT
* *
5970921 TTCTTATATTATTAATCCTAAAAAAT
1 ATATTATATTA-TAA--C-AAAAAAT
5970947 ATATTATA
1 ATATTATA
5970955 AAAATTTGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 9 0.35
23 3 0.12
25 1 0.04
26 13 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATTATATTATAACAAAAAAT
Found at i:5981428 original size:84 final size:85
Alignment explanation
Indices: 5981240--5981429 Score: 233
Period size: 84 Copynumber: 2.3 Consensus size: 85
5981230 AATATAATTT
* * * *
5981240 TTTTTTATTTTTAGGGGGTTAAAGTACAATTTTACTATACATTAATTTATAATTTCTTTATTTAT
1 TTTTTCATTTTTAAGGGATCAAAGTACAATTTTACTATACATTAATTTATAATTTCTTTATTTAT
** * *
5981305 AAGAGGATTGAATTGAAAAA
66 AAGAAAACTAAATTGAAAAA
*** * *
5981325 GAATTCA-TTTTAAGAGATCAAAGTACAATTTTACTATATATTAATTTATAATATT-TTTATTTA
1 TTTTTCATTTTTAAGGGATCAAAGTACAATTTTACTATACATTAATTTATAAT-TTCTTTATTTA
5981388 TAAGAAAACTAAATT-AAAAA
65 TAAGAAAACTAAATTGAAAAA
5981408 TTTTTCATTTTTAAGGGATCAA
1 TTTTTCATTTTTAAGGGATCAA
5981430 GGTCCAAGGC
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
83 9 0.10
84 72 0.84
85 5 0.06
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (85 bp):
TTTTTCATTTTTAAGGGATCAAAGTACAATTTTACTATACATTAATTTATAATTTCTTTATTTAT
AAGAAAACTAAATTGAAAAA
Found at i:5985670 original size:11 final size:12
Alignment explanation
Indices: 5985654--5985689 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
5985644 TCATTATACA
5985654 ATATTATTATC-
1 ATATTATTATCG
5985665 ATATTATTATCG
1 ATATTATTATCG
*
5985677 ATATTATAATCG
1 ATATTATTATCG
5985689 A
1 A
5985690 ATGTGTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (12 bp):
ATATTATTATCG
Found at i:5985948 original size:2 final size:2
Alignment explanation
Indices: 5985943--5985979 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5985933 TACTTTCCTA
5985943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5985980 TTTATGCCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5996106 original size:58 final size:58
Alignment explanation
Indices: 5995985--5996096 Score: 144
Period size: 58 Copynumber: 2.0 Consensus size: 58
5995975 ATCGTCTAAT
* *
5995985 TATGTTTTT-TTT--GTCACCCACATATGAAAAGTTACAATATGATCACCTAACTATG
1 TATGTTTTTGTTTCGGTCACCCACATATGAAAAGTTACAAAATGACCACCTAACTATG
*
5996040 TTTGTTTTTGTTTCGGTCACCCA-ATTATGAAAAGTTACAAAAT-AGCCACCTAACTAT
1 TATGTTTTTGTTTCGGTCACCCACA-TATGAAAAGTTACAAAATGA-CCACCTAACTAT
5996097 TCAATTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
55 8 0.16
56 3 0.06
57 2 0.04
58 36 0.73
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.38
Consensus pattern (58 bp):
TATGTTTTTGTTTCGGTCACCCACATATGAAAAGTTACAAAATGACCACCTAACTATG
Found at i:5997417 original size:26 final size:27
Alignment explanation
Indices: 5997388--5997441 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
5997378 TACTTTAATT
*
5997388 TGATATTTT-TTTAATGTAGTA-TTGTA
1 TGAT-TTTTATTTAATATAGTATTTGTA
5997414 TGATTTTTATTTAATATAGTATTTGTA
1 TGATTTTTATTTAATATAGTATTTGTA
5997441 T
1 T
5997442 TTGATAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 4 0.16
26 15 0.60
27 6 0.24
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (27 bp):
TGATTTTTATTTAATATAGTATTTGTA
Found at i:5998198 original size:29 final size:30
Alignment explanation
Indices: 5998133--5998213 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 30
5998123 ATCAGGGTTT
5998133 TTTACCAAAAT-AT-TACAAAAAA-ATAAA
1 TTTACCAAAATAATATACAAAAAAGATAAA
** * *
5998160 AATACTAAAATAATATACAAAAAAGAT-TA
1 TTTACCAAAATAATATACAAAAAAGATAAA
*
5998189 TTTACCAAAATAATACA-AAAAAAGA
1 TTTACCAAAATAATATACAAAAAAGA
5998214 CGGCTGAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
27 8 0.19
28 10 0.23
29 23 0.53
30 2 0.05
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.23
Consensus pattern (30 bp):
TTTACCAAAATAATATACAAAAAAGATAAA
Found at i:5998204 original size:27 final size:27
Alignment explanation
Indices: 5998133--5998211 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
5998123 ATCAGGGTTT
*
5998133 TTTACCAAAATATTACAAAAAAATAAA
1 TTTACCAAAATAATACAAAAAAATAAA
** * *
5998160 AATACTAAAATAATATACAAAAAAGAT-TA
1 TTTACCAAAAT-A-ATACAAAAAA-ATAAA
5998189 TTTACCAAAATAATACAAAAAAA
1 TTTACCAAAATAATACAAAAAAA
5998212 GACGGCTGAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
26 1 0.02
27 18 0.44
28 2 0.05
29 18 0.44
30 2 0.05
ACGTcount: A:0.65, C:0.10, G:0.01, T:0.24
Consensus pattern (27 bp):
TTTACCAAAATAATACAAAAAAATAAA
Found at i:5999864 original size:18 final size:17
Alignment explanation
Indices: 5999843--5999890 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
5999833 TTATAACATT
5999843 TTTATGATTTTTATAATA
1 TTTATGATTTTTA-AATA
* *
5999861 TTTAATAATATTTAAATA
1 TTT-ATGATTTTTAAATA
5999879 TTTATTGATTTT
1 TTTA-TGATTTT
5999891 CTAGAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 1 0.04
18 15 0.62
19 8 0.33
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
TTTATGATTTTTAAATA
Found at i:6012319 original size:2 final size:2
Alignment explanation
Indices: 6012312--6012353 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6012302 TATTATTGTT
6012312 TA TA TA TA TA 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 TA TA TA TA TA
6012354 GGTTATGTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6017272 original size:56 final size:57
Alignment explanation
Indices: 6017168--6017283 Score: 164
Period size: 56 Copynumber: 2.1 Consensus size: 57
6017158 CAAGGAAATA
* * *
6017168 TCAAGGACTAATTTAGAAAAAAAAGTTTAAGCCTTAATATAGGAACAATTGTCAAGT
1 TCAAGGACTAATTTAGAAAAAAAAGTTCAAGCCTCAATATAGGAACAATTATCAAGT
* *
6017225 TCAAGGATTAATTTGGATAAAAAAAGTTCAA-CC-CAATATAGGAACAATTATCAAGT
1 TCAAGGACTAATTTAGA-AAAAAAAGTTCAAGCCTCAATATAGGAACAATTATCAAGT
6017281 TCA
1 TCA
6017284 GGAAGATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
56 24 0.45
57 17 0.32
58 12 0.23
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.28
Consensus pattern (57 bp):
TCAAGGACTAATTTAGAAAAAAAAGTTCAAGCCTCAATATAGGAACAATTATCAAGT
Found at i:6031741 original size:27 final size:25
Alignment explanation
Indices: 6031689--6031743 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 25
6031679 TTTAAATTTA
** *
6031689 AATTTTTAAATTTTAATTCTTTTAT
1 AATTTTTAAATTTTAATTAGTATAT
6031714 AATTTATTAAATTTTAAATTAGTATAT
1 AATTT-TTAAATTTT-AATTAGTATAT
6031741 AAT
1 AAT
6031744 AAAATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.20
26 9 0.36
27 11 0.44
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
AATTTTTAAATTTTAATTAGTATAT
Found at i:6031816 original size:16 final size:18
Alignment explanation
Indices: 6031793--6031835 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
6031783 TTTGGTTCTT
6031793 TAAAATTATAAAAAAT-A
1 TAAAATTATAAAAAATGA
*
6031810 T-AAATTAT-TAAAATGA
1 TAAAATTATAAAAAATGA
6031826 TAAAATTATA
1 TAAAATTATA
6031836 TTATCGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 5 0.23
16 9 0.41
17 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (18 bp):
TAAAATTATAAAAAATGA
Found at i:6031831 original size:17 final size:16
Alignment explanation
Indices: 6031793--6031834 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
6031783 TTTGGTTCTT
6031793 TAAAATTA-TAAAAAA
1 TAAAATTATTAAAAAA
*
6031808 TATAAATTATTAAAATGA
1 TA-AAATTATTAAAA-AA
6031826 TAAAATTAT
1 TAAAATTAT
6031835 ATTATCGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 6 0.26
17 12 0.52
18 3 0.13
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
TAAAATTATTAAAAAA
Found at i:6035514 original size:28 final size:28
Alignment explanation
Indices: 6035470--6035523 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
6035460 TTTTTTCAAA
*
6035470 AAAATTTGGAGATTTAATTAAAATTTTT
1 AAAATTTGGAGAATTAATTAAAATTTTT
*
6035498 AAAATTTGTGA-AATTAATTAGAATTT
1 AAAATTTG-GAGAATTAATTAAAATTT
6035524 CAAAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (28 bp):
AAAATTTGGAGAATTAATTAAAATTTTT
Found at i:6035529 original size:28 final size:28
Alignment explanation
Indices: 6035469--6035529 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
6035459 TTTTTTTCAA
* *
6035469 AAAAATTTGGAGATTTAATTAAAATTTT
1 AAAAATTTGGAGAATTAATTAAAATTTC
* *
6035497 TAAAATTTGTGA-AATTAATTAGAATTTC
1 AAAAATTTG-GAGAATTAATTAAAATTTC
6035525 AAAAA
1 AAAAA
6035530 AAATTAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (28 bp):
AAAAATTTGGAGAATTAATTAAAATTTC
Found at i:6035725 original size:17 final size:18
Alignment explanation
Indices: 6035700--6035733 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6035690 AAAATACTAG
*
6035700 ATTATAAAAT-TTATAAA
1 ATTAAAAAATGTTATAAA
6035717 ATTAAAAAATGTTATAA
1 ATTAAAAAATGTTATAA
6035734 CAAAAGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTAAAAAATGTTATAAA
Found at i:6036051 original size:98 final size:97
Alignment explanation
Indices: 6035883--6036071 Score: 281
Period size: 98 Copynumber: 1.9 Consensus size: 97
6035873 TTATTTCTAG
* * * * *
6035883 ATTTTATGTAAAAGATAAAGATACCCTTGAGTTAATATTTATTGCTTTGTTAAAATAAGAGCATT
1 ATTTTATATAAAAGATAAAAATACCCTTGAGTTAACATTTATTACTTTGTTAAAATAAAAGCATT
* *
6035948 TTAGTAATTTAACAACTGAGTTGAGATTTGAT
66 TTAGTAATTTAACAACTCAATTGAGATTTGAT
6035980 ATTTTATATAAAAGGATAAAAATACCCTTGAGTTAACATTTATTACTTTGTTAAAATAAAAGTC-
1 ATTTTATATAAAA-GATAAAAATACCCTTGAGTTAACATTTATTACTTTGTTAAAATAAAAG-CA
*
6036044 TTTTAGTAATTTAATAACTCAATTGAGA
64 TTTTAGTAATTTAACAACTCAATTGAGA
6036072 CCCGATTATA
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
97 12 0.15
98 69 0.84
99 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (97 bp):
ATTTTATATAAAAGATAAAAATACCCTTGAGTTAACATTTATTACTTTGTTAAAATAAAAGCATT
TTAGTAATTTAACAACTCAATTGAGATTTGAT
Found at i:6039262 original size:5 final size:6
Alignment explanation
Indices: 6039247--6039271 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6039237 TTCTTGCTTA
6039247 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
6039272 TGGTTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:6045104 original size:29 final size:29
Alignment explanation
Indices: 6045062--6045174 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 29
6045052 AAAAATAAAA
*
6045062 AAATTATATTTTAACCCCTAAACTTTTTG
1 AAATTACATTTTAACCCCTAAACTTTTTG
* * * *
6045091 AAATTGCATTTTAACCCTTAAA-TTTCATA
1 AAATTACATTTTAACCCCTAAACTTT-TTG
* *
6045120 AAATTACATTTTGACCCATAAACTTTTTG
1 AAATTACATTTTAACCCCTAAACTTTTTG
** *
6045149 AAATTATGTTTTGACCCCTAAACTTT
1 AAATTACATTTTAACCCCTAAACTTT
6045175 CTCAAAATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.04
29 63 0.91
30 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (29 bp):
AAATTACATTTTAACCCCTAAACTTTTTG
Found at i:6045189 original size:30 final size:29
Alignment explanation
Indices: 6045061--6045205 Score: 87
Period size: 29 Copynumber: 5.0 Consensus size: 29
6045051 AAAAAATAAA
* * *
6045061 AAAATTATATTTTAACCCCTAAACTTTTT
1 AAAATTATGTTTTGACCCCTAAACTTTTC
* *** * *
6045090 GAAATTGCATTTTAACCCTTAAA--TTTC
1 AAAATTATGTTTTGACCCCTAAACTTTTC
** * *
6045117 ATAAAATTACATTTTGACCCATAAACTTTTT
1 --AAAATTATGTTTTGACCCCTAAACTTTTC
*
6045148 GAAATTATGTTTTGACCCCTAAACTTTCTC
1 AAAATTATGTTTTGACCCCTAAACTTT-TC
* * * *
6045178 AAAATTTTGTTTTGGCCCCAAAAATTTT
1 AAAATTATGTTTTGACCCCTAAACTTTT
6045206 GCTGCATTTA
Statistics
Matches: 91, Mismatches: 20, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
27 3 0.03
29 62 0.68
30 23 0.25
31 3 0.03
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.42
Consensus pattern (29 bp):
AAAATTATGTTTTGACCCCTAAACTTTTC
Found at i:6045862 original size:14 final size:15
Alignment explanation
Indices: 6045840--6045881 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
6045830 AGCGCAACGC
6045840 CAGCAGCAGGCCCAA
1 CAGCAGCAGGCCCAA
6045855 CAGC-GCAGGCCCAA
1 CAGCAGCAGGCCCAA
*
6045869 AAGGCAGCAGGCC
1 CA-GCAGCAGGCC
6045882 AAAAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 11 0.46
15 6 0.25
16 7 0.29
ACGTcount: A:0.31, C:0.38, G:0.31, T:0.00
Consensus pattern (15 bp):
CAGCAGCAGGCCCAA
Found at i:6045902 original size:17 final size:17
Alignment explanation
Indices: 6045882--6045937 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
6045872 GCAGCAGGCC
*
6045882 AAAAA-AAAAGAAGAGA
1 AAAAAGAAAAAAAGAGA
6045898 AAAAAGAGAAAAAA-AGA
1 AAAAAGA-AAAAAAGAGA
6045915 AAAAAGAAAAAAA-AGGA
1 AAAAAGAAAAAAAGA-GA
6045932 AAAAAG
1 AAAAAG
6045938 GGTTCAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
16 12 0.33
17 19 0.53
18 5 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAGAGA
Found at i:6045906 original size:9 final size:9
Alignment explanation
Indices: 6045887--6045937 Score: 70
Period size: 9 Copynumber: 5.8 Consensus size: 9
6045877 AGGCCAAAAA
6045887 AAAAGAAGAG
1 AAAA-AAGAG
6045897 AAAAAAGAG
1 AAAAAAGAG
6045906 AAAAAA-AG
1 AAAAAAGAG
*
6045914 AAAAAAGAA
1 AAAAAAGAG
6045923 AAAAAAG-G
1 AAAAAAGAG
6045931 AAAAAAG
1 AAAAAAG
6045938 GGTTCAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 15 0.39
9 19 0.50
10 4 0.11
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:6045917 original size:15 final size:15
Alignment explanation
Indices: 6045885--6045937 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
6045875 GCAGGCCAAA
* *
6045885 AAAAAAGAAGAGAA-
1 AAAAAAGAAAAAAAG
*
6045899 AAAAGAGAAAAAAAG
1 AAAAAAGAAAAAAAG
6045914 AAAAAAGAAAAAAAAGG
1 AAAAAAG-AAAAAAA-G
6045931 AAAAAAG
1 AAAAAAG
6045938 GGTTCAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 11 0.34
15 6 0.19
16 7 0.22
17 8 0.25
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:6045922 original size:24 final size:25
Alignment explanation
Indices: 6045882--6045937 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
6045872 GCAGCAGGCC
* *
6045882 AAAAAAA-AAGAAGAGAAAAAAGAG
1 AAAAAAAGAAGAAAAGAAAAAAAAG
6045906 AAAAAAAGAA-AAAAGAAAAAAAAG
1 AAAAAAAGAAGAAAAGAAAAAAAAG
*
6045930 GAAAAAAG
1 AAAAAAAG
6045938 GGTTCAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (25 bp):
AAAAAAAGAAGAAAAGAAAAAAAAG
Found at i:6045938 original size:8 final size:8
Alignment explanation
Indices: 6045896--6045938 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
6045886 AAAAAGAAGA
6045896 GAAAAAAG
1 GAAAAAAG
*
6045904 AGAAAAAAA
1 -GAAAAAAG
6045913 GAAAAAAG
1 GAAAAAAG
*
6045921 AAAAAAAAG
1 -GAAAAAAG
6045930 GAAAAAAG
1 GAAAAAAG
6045938 G
1 G
6045939 GTTCAATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 15 0.52
9 14 0.48
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
GAAAAAAG
Found at i:6046435 original size:18 final size:18
Alignment explanation
Indices: 6046414--6046709 Score: 130
Period size: 17 Copynumber: 16.2 Consensus size: 18
6046404 AAAAATCGGG
6046414 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
6046432 TTTCAAAAATTCTCATG-
1 TTTCAAAAATTTTCGTGT
*
6046449 TTTCAAAAATCTTCGTGT
1 TTTCAAAAATTTTCGTGT
*
6046467 TTT-AAAAA-TTCCAGTG-
1 TTTCAAAAATTTTC-GTGT
6046483 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
*
6046501 TTTCAAAAAAAATTTCCCGTGT
1 TTTC---AAAAATTT-TCGTGT
* ** *
6046523 TTTTAAAAATTCCCGT-A
1 TTTCAAAAATTTTCGTGT
* * *
6046540 TATCGAAAATTTTCTTGT
1 TTTCAAAAATTTTCGTGT
* * *
6046558 TTTCAAAAAAAAAAATTCCATG-
1 TTTC-----AAAAATTTTCGTGT
*
6046580 TTTCAAAAATTTCCGTGT
1 TTTCAAAAATTTTCGTGT
*
6046598 TTTCAAAAAAAAATTCTCGT-T
1 TTTC----AAAAATTTTCGTGT
6046619 TTTCAAAAATTTTCGT-T
1 TTTCAAAAATTTTCGTGT
** *
6046636 TTAAAAAAAATTGATCGTG-
1 TT-TCAAAAATT-TTCGTGT
* *
6046655 TTTCATAAATTTCCGTG-
1 TTTCAAAAATTTTCGTGT
* *
6046672 TTTCAAAAAAATCTCGTG-
1 TTTC-AAAAATTTTCGTGT
*
6046690 TTTC-AAAATTTTCGGGT
1 TTTCAAAAATTTTCGTGT
6046707 TTT
1 TTT
6046710 TTTAAAAACA
Statistics
Matches: 209, Mismatches: 44, Indels: 51
0.69 0.14 0.17
Matches are distributed among these distances:
16 14 0.07
17 76 0.36
18 62 0.30
19 13 0.06
21 13 0.06
22 22 0.11
23 9 0.04
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:6046485 original size:34 final size:35
Alignment explanation
Indices: 6046413--6046509 Score: 162
Period size: 34 Copynumber: 2.8 Consensus size: 35
6046403 AAAAAATCGG
6046413 GTTTCAAAAATTTTCGTGTTTTCAAAAATTCTCAT
1 GTTTCAAAAATTTTCGTGTTTTCAAAAATTCTCAT
*
6046448 GTTTCAAAAATCTTCGTGTTTT-AAAAATTC-CAGT
1 GTTTCAAAAATTTTCGTGTTTTCAAAAATTCTCA-T
6046482 GTTTCAAAAATTTTCGTGTTTTCAAAAA
1 GTTTCAAAAATTTTCGTGTTTTCAAAAA
6046510 AAATTTCCCG
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
33 2 0.03
34 30 0.52
35 26 0.45
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.43
Consensus pattern (35 bp):
GTTTCAAAAATTTTCGTGTTTTCAAAAATTCTCAT
Found at i:6046513 original size:21 final size:22
Alignment explanation
Indices: 6046487--6046531 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
6046477 CCAGTGTTTC
*
6046487 AAAAATTT-TCGTGTTTTCAAA
1 AAAAATTTCCCGTGTTTTCAAA
*
6046508 AAAAATTTCCCGTGTTTTTAAA
1 AAAAATTTCCCGTGTTTTCAAA
6046530 AA
1 AA
6046532 TTCCCGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (22 bp):
AAAAATTTCCCGTGTTTTCAAA
Found at i:6046521 original size:22 final size:21
Alignment explanation
Indices: 6046487--6046627 Score: 63
Period size: 21 Copynumber: 7.1 Consensus size: 21
6046477 CCAGTGTTTC
*
6046487 AAAAATTTTCGTGTTTTCAAA
1 AAAAATTTCCGTGTTTTCAAA
*
6046508 AAAAATTTCCCGTGTTTT---T
1 AAAAATTT-CCGTGTTTTCAAA
* * *
6046527 AAAAATTCCCGT-ATATC---
1 AAAAATTTCCGTGTTTTCAAA
* * *
6046544 GAAAATTTTCTTGTTTTCAAAAA
1 AAAAATTTCCGTGTTTTC--AAA
* *
6046567 AAAAAATTCCATG-TTTC--A
1 AAAAATTTCCGTGTTTTCAAA
6046585 -AAAATTTCCGTGTTTTCAAA
1 AAAAATTTCCGTGTTTTCAAA
*
6046605 AAAAAATTCTCGT-TTTTCAAA
1 AAAAATTTC-CGTGTTTTCAAA
6046626 AA
1 AA
6046628 TTTTCGTTTT
Statistics
Matches: 89, Mismatches: 18, Indels: 26
0.67 0.14 0.20
Matches are distributed among these distances:
17 20 0.22
18 12 0.13
19 7 0.08
20 1 0.01
21 25 0.28
22 15 0.17
23 9 0.10
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (21 bp):
AAAAATTTCCGTGTTTTCAAA
Found at i:6046549 original size:57 final size:56
Alignment explanation
Indices: 6046462--6046569 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 56
6046452 CAAAAATCTT
* *
6046462 CGTGTTTTAAAAATTCCAGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTCC
1 CGTGTTTTAAAAATTCCAGTATATCAAAAATTTTCGTGTTTTCAAAAAAAATTTCC
* * *
6046518 CGTGTTTTTAAAAATTCCCGTATATCGAAAATTTTCTTGTTTTCAAAAAAAA
1 CGTG-TTTTAAAAATTCCAGTATATCAAAAATTTTCGTGTTTTCAAAAAAAA
6046570 AAATTCCATG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 4 0.09
57 42 0.91
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (56 bp):
CGTGTTTTAAAAATTCCAGTATATCAAAAATTTTCGTGTTTTCAAAAAAAATTTCC
Found at i:6046571 original size:40 final size:37
Alignment explanation
Indices: 6046527--6046645 Score: 109
Period size: 40 Copynumber: 3.1 Consensus size: 37
6046517 CCGTGTTTTT
*
6046527 AAAAATTCCCGTATATCGAAAATTTTCTTGTTTTCAAAAAA
1 AAAAATTCCCGT-T-TCAAAAATTTTC-TGTTTTC-AAAAA
* *
6046568 AAAAATTCCATGTTTCAAAAATTTCCGTGTTTTC-AAAA
1 AAAAATTCC-CGTTTCAAAAATTTTC-TGTTTTCAAAAA
*
6046606 AAAAATTCTCGTTTTTCAAAAATTTTC-GTTTT-AAAAA
1 AAAAATTCCCG--TTTCAAAAATTTTCTGTTTTCAAAAA
6046643 AAA
1 AAA
6046646 TTGATCGTGT
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
37 13 0.19
38 12 0.18
39 13 0.19
40 17 0.25
41 10 0.15
42 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (37 bp):
AAAAATTCCCGTTTCAAAAATTTTCTGTTTTCAAAAA
Found at i:6046588 original size:57 final size:56
Alignment explanation
Indices: 6046464--6046595 Score: 149
Period size: 57 Copynumber: 2.3 Consensus size: 56
6046454 AAAATCTTCG
* * * * *
6046464 TGTTTTAAAAATTCCAGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTCCCG
1 TGTTTTAAAAATTCCCGTATATCAAAAATTTTCGTGTTTTCAAAAAAAAATTCCCA
* *
6046520 TGTTTTTAAAAATTCCCGTATATCGAAAATTTTCTTGTTTTCAAAAAAAAAAATT-CCA
1 TG-TTTTAAAAATTCCCGTATATCAAAAATTTTCGTGTTTTC--AAAAAAAAATTCCCA
* *
6046578 TGTTTCAAAAATTTCCGT
1 TGTTTTAAAAATTCCCGT
6046596 GTTTTCAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
56 2 0.03
57 48 0.75
58 4 0.06
59 10 0.16
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (56 bp):
TGTTTTAAAAATTCCCGTATATCAAAAATTTTCGTGTTTTCAAAAAAAAATTCCCA
Found at i:6046606 original size:39 final size:38
Alignment explanation
Indices: 6046527--6046702 Score: 134
Period size: 35 Copynumber: 4.7 Consensus size: 38
6046517 CCGTGTTTTT
* * * * *
6046527 AAAAATTCCCGTATATCGAAAATTTTCTTGTTTTCAAAAAA
1 AAAAATT-CCGTGTTTCAAAAATTTCCGTGTTTTC--AAAA
*
6046568 AAAAATTCCATGTTTCAAAAATTTCCGTGTTTTCAAAA
1 AAAAATTCCGTGTTTCAAAAATTTCCGTGTTTTCAAAA
* *
6046606 AAAAATTCTCGTTTTTCAAAAATTTTC--GTTTT--AAA
1 AAAAATTC-CGTGTTTCAAAAATTTCCGTGTTTTCAAAA
* *
6046641 AAAAATTGATCGTGTTTCATAAATTTCCGTG-TTTC--AA
1 AAAAATT--CCGTGTTTCAAAAATTTCCGTGTTTTCAAAA
*
6046678 AAAAA-TCTCGTGTTTCAAAATTTTC
1 AAAAATTC-CGTGTTTCAAAAATTTC
6046703 GGGTTTTTTT
Statistics
Matches: 112, Mismatches: 16, Indels: 20
0.76 0.11 0.14
Matches are distributed among these distances:
35 25 0.22
36 16 0.14
37 15 0.13
38 13 0.12
39 15 0.13
40 21 0.19
41 7 0.06
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (38 bp):
AAAAATTCCGTGTTTCAAAAATTTCCGTGTTTTCAAAA
Found at i:6046646 original size:97 final size:98
Alignment explanation
Indices: 6046470--6046647 Score: 243
Period size: 97 Copynumber: 1.8 Consensus size: 98
6046460 TTCGTGTTTT
* * *
6046470 AAAAATTCCAGTGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTCCCGTGTTTTTAAAAATTC
1 AAAAATTCCAGTGTTTCAAAAATTTCCGTGTTTTCAAAAAAAAATTCCCGTGTTTTCAAAAATTC
***
6046535 CCGTATATCGAAAATTTTCTTGTTTTCAAAAAA
66 CCGTATAAAAAAAATTTTCTTGTTTTCAAAAAA
* *
6046568 AAAAATTCCA-TGTTTCAAAAATTTCCGTGTTTTCAAAAAAAAATTCTCGT-TTTTCAAAAATTT
1 AAAAATTCCAGTGTTTCAAAAATTTCCGTGTTTTCAAAAAAAAATTCCCGTGTTTTCAAAAATTC
* *
6046631 TCGTTTTAAAAAAAATT
66 CCG-TATAAAAAAAATT
6046648 GATCGTGTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
96 13 0.19
97 46 0.67
98 10 0.14
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (98 bp):
AAAAATTCCAGTGTTTCAAAAATTTCCGTGTTTTCAAAAAAAAATTCCCGTGTTTTCAAAAATTC
CCGTATAAAAAAAATTTTCTTGTTTTCAAAAAA
Found at i:6046758 original size:16 final size:17
Alignment explanation
Indices: 6046739--6046771 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6046729 TCTAAAATTC
6046739 TCGTATTTT-AAAAAAA
1 TCGTATTTTCAAAAAAA
*
6046755 TCGTGTTTTCAAAAAAA
1 TCGTATTTTCAAAAAAA
6046772 GAAAAAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (17 bp):
TCGTATTTTCAAAAAAA
Found at i:6054207 original size:9 final size:9
Alignment explanation
Indices: 6054193--6054251 Score: 70
Period size: 9 Copynumber: 6.8 Consensus size: 9
6054183 TATTATGCCT
6054193 AAAAAAACA
1 AAAAAAACA
6054202 AAAAAAAC-
1 AAAAAAACA
*
6054210 -AAAAAA-T
1 AAAAAAACA
6054217 AAAAAAACA
1 AAAAAAACA
6054226 AAACAAAACA
1 AAA-AAAACA
*
6054236 AAAAAAATA
1 AAAAAAACA
6054245 AAAAAAA
1 AAAAAAA
6054252 ACAGAGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 6 0.14
8 6 0.14
9 23 0.52
10 9 0.20
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.03
Consensus pattern (9 bp):
AAAAAAACA
Found at i:6054252 original size:24 final size:24
Alignment explanation
Indices: 6054192--6054254 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 24
6054182 GTATTATGCC
6054192 TAAAAAAACAAAA-AAAACAAAAAA
1 TAAAAAAA-AAAACAAAACAAAAAA
6054216 TAAAAAAACAAAACAAAACAAAAAA
1 TAAAAAAA-AAAACAAAACAAAAAA
6054241 -AATAAAAAAAAACA
1 TAA-AAAAAAAAACA
6054255 GAGAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
24 21 0.57
25 16 0.43
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.05
Consensus pattern (24 bp):
TAAAAAAAAAAACAAAACAAAAAA
Found at i:6054262 original size:29 final size:26
Alignment explanation
Indices: 6054193--6054269 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
6054183 TATTATGCCT
*
6054193 AAAAAAACAAAAAAAACAAAAAATAA
1 AAAAAAACAAAAAAAAAAAAAAATAA
*
6054219 AAAAACAA-AACAAAACAAAAAAAATAA
1 AAAAA-AACAA-AAAAAAAAAAAAATAA
* * *
6054246 AAAAAAACAGAGAAAAAGAAAAAT
1 AAAAAAACAAAAAAAAAAAAAAAT
6054270 CAAGATGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 20 0.48
27 22 0.52
ACGTcount: A:0.84, C:0.08, G:0.04, T:0.04
Consensus pattern (26 bp):
AAAAAAACAAAAAAAAAAAAAAATAA
Found at i:6054268 original size:1 final size:1
Alignment explanation
Indices: 6054193--6054252 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
6054183 TATTATGCCT
* * * * * * *
6054193 AAAAAAACAAAAAAAACAAAAAATAAAAAAACAAAACAAAACAAAAAAAATAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6054253 CAGAGAAAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.88, C:0.08, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:6055455 original size:73 final size:74
Alignment explanation
Indices: 6055182--6055974 Score: 1158
Period size: 73 Copynumber: 10.6 Consensus size: 74
6055172 GAGGTATTTC
*
6055182 TTTTTTTTT-AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACACTGAGGTA-TTT
1 TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
*
6055245 TAATTTTATG
66 TAATTTCA-G
* *
6055255 TCTTTTTTTTTTTAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACACTGAGGTAT
1 ---TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
*
6055320 TTTTAATTTCGG
63 TTTTAATTTCAG
* *
6055332 TCTTTTTTTTTTTAAATCAACTCATAATACAGAGATGAGTTGAGCCTCGGGTCACGCTGAGGTAT
1 ---TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
6055397 TTTTAATTTCAG
63 TTTTAATTTCAG
6055409 -TTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
1 TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
*
6055473 TAATTTCGG
66 TAATTTCAG
6055482 TCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 --TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
6055547 TTTAATTTCAG
64 TTTAATTTCAG
* *
6055558 -TCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGATGTATTTT
1 TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
6055622 TAATTTCAG
66 TAATTTCAG
* *
6055631 -TCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACACTGAGGTATTTT
1 TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
6055695 TAATTT-ATG
66 TAATTTCA-G
6055704 ACTTTTTTTTT-AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT--CGCTGAGGTATT
1 --TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
6055766 TTTAATTTCGG
64 TTTAATTTCAG
* *
6055777 TCTTTTTTTAAAAATCAACTCATAATACAGAGGTGAGTTGGGCCTCGGGTCACGCTGAGGTA-TT
1 T-TTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
6055841 TTAATTTCGG
65 TTAATTTCAG
*
6055851 TCTTTTTCTTAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACAGGCTGAGGTA
1 T-TTTTT-TTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCAC--GCTGAGGTA
*
6055916 TTTTCAATTT-ATG
62 TTTTTAATTTCA-G
*
6055929 TCTTTTTTTTTTAAATCAACTCATAATACAGAGGTGAGTTGAGCCT
1 --TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCT
6055975 TGGGCGACAC
Statistics
Matches: 673, Mismatches: 23, Indels: 40
0.91 0.03 0.05
Matches are distributed among these distances:
71 1 0.00
72 8 0.01
73 268 0.40
74 19 0.03
75 94 0.14
76 88 0.13
77 135 0.20
78 54 0.08
79 5 0.01
80 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (74 bp):
TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTT
TAATTTCAG
Found at i:6055533 original size:149 final size:149
Alignment explanation
Indices: 6055180--6055974 Score: 1232
Period size: 149 Copynumber: 5.3 Consensus size: 149
6055170 CTGAGGTATT
*
6055180 TCTTTTTTTTT-AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACACTGAGGTA-T
1 TCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
* *
6055243 TTTAATTTTATGTCTTTTTTTTTTTAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
66 TTTAATTTCA-G----TTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
*
6055308 ACACTGAGGTATTTTTAATTTCGG
126 ACGCTGAGGTATTTTTAATTTCGG
* *
6055332 TCTTTTTTTTTTTAAATCAACTCATAATACAGAGATGAGTTGAGCCTCGGGTCACGCTGAGGTAT
1 TC-TTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
6055397 TTTTAATTTCAGTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGC
65 TTTTAATTTCAGTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGC
6055462 TGAGGTATTTTTAATTTCGG
130 TGAGGTATTTTTAATTTCGG
6055482 TCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 TCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
6055547 TTTAATTTCAGTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCT
66 TTTAATTTCAGTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCT
* *
6055612 GATGTATTTTTAATTTCAG
131 GAGGTATTTTTAATTTCGG
*
6055631 TC---TTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACACTGAGGTATT
1 TCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
6055693 TTTAATTT-ATGACTTTTTTTTTAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT--C
66 TTTAATTTCA-G--TTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCAC
6055755 GCTGAGGTATTTTTAATTTCGG
128 GCTGAGGTATTTTTAATTTCGG
* *
6055777 TC-TTTTTTTAAAAATCAACTCATAATACAGAGGTGAGTTGGGCCTCGGGTCACGCTGAGGTA-T
1 TCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
6055840 TTTAATTTCGGTCTTTTTCTTAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCAC
66 TTTAATTTCAGT-TTTTT-TT-AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCAC
* **
6055905 AGGCTGAGGTATTTTCAATTTATG
128 --GCTGAGGTATTTTTAATTTCGG
*
6055929 TCTTTTTTTTTTAAATCAACTCATAATACAGAGGTGAGTTGAGCCT
1 TCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCT
6055975 TGGGCGACAC
Statistics
Matches: 600, Mismatches: 26, Indels: 33
0.91 0.04 0.05
Matches are distributed among these distances:
145 2 0.00
146 96 0.16
147 12 0.02
148 140 0.23
149 144 0.24
150 74 0.12
152 23 0.04
153 49 0.08
154 50 0.08
155 10 0.02
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (149 bp):
TCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
TTTAATTTCAGTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCT
GAGGTATTTTTAATTTCGG
Found at i:6056211 original size:29 final size:29
Alignment explanation
Indices: 6056178--6056290 Score: 138
Period size: 29 Copynumber: 3.9 Consensus size: 29
6056168 TAAAAATAAA
6056178 AAATTACATTTTAACCCCTAAACTTTTTG
1 AAATTACATTTTAACCCCTAAACTTTTTG
* * *
6056207 AAATTGCATTTTAACCCCTAAA-TTTCATA
1 AAATTACATTTTAACCCCTAAACTTT-TTG
* *
6056236 AAATTACATTTTGACCCATAAACTTTTTG
1 AAATTACATTTTAACCCCTAAACTTTTTG
** *
6056265 AAATTATGTTTTGACCCCTAAACTTT
1 AAATTACATTTTAACCCCTAAACTTT
6056291 CTCAAGGCCC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
28 3 0.04
29 65 0.92
30 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (29 bp):
AAATTACATTTTAACCCCTAAACTTTTTG
Found at i:6056282 original size:58 final size:59
Alignment explanation
Indices: 6056177--6056291 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 59
6056167 ATAAAAATAA
* *
6056177 AAAATTACATTTTAACCCCTAAACTTTTTGAAATTGCATTTTAACCCCTAAA-TTTCAT
1 AAAATTACATTTTAACCCATAAACTTTTTGAAATTACATTTTAACCCCTAAACTTTCAT
* ** *
6056235 AAAATTACATTTTGACCCATAAACTTTTTGAAATTATGTTTTGACCCCTAAACTTTC
1 AAAATTACATTTTAACCCATAAACTTTTTGAAATTACATTTTAACCCCTAAACTTTC
6056292 TCAAGGCCCC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 46 0.92
59 4 0.08
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (59 bp):
AAAATTACATTTTAACCCATAAACTTTTTGAAATTACATTTTAACCCCTAAACTTTCAT
Found at i:6056723 original size:17 final size:17
Alignment explanation
Indices: 6056655--6056722 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
6056645 AGAAGAAGGA
*
6056655 GAAAAAAGAAGAAAAAG
1 GAAAAAGGAAGAAAAAG
*
6056672 AGAAAGAAGGAAGGAAGAA-
1 -GAAA-AAGGAA-GAAAAAG
*
6056691 GAAGAAGGAAGAAAAAG
1 GAAAAAGGAAGAAAAAG
6056708 GAAAAAGGAA-AAAAA
1 GAAAAAGGAAGAAAAA
6056723 AAAATTTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 10 0.24
17 15 0.36
18 7 0.17
19 5 0.12
20 5 0.12
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAAAAGGAAGAAAAAG
Found at i:6056878 original size:29 final size:26
Alignment explanation
Indices: 6056822--6056879 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 26
6056812 CCAGCAGCCC
* *
6056822 AAAGAAAAAAAAACAAAAAAAGGGCA
1 AAAGAAAAAAAAAAAAAAAAAGGCCA
6056848 AAAGCAAAAAAAAAAAAAGAAACAGGCCA
1 AAAG-AAAAAAAAAAAAA-AAA-AGGCCA
6056877 AAA
1 AAA
6056880 ACAGCCCAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 4 0.15
27 12 0.44
28 3 0.11
29 8 0.30
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (26 bp):
AAAGAAAAAAAAAAAAAAAAAGGCCA
Found at i:6057011 original size:12 final size:12
Alignment explanation
Indices: 6056994--6057034 Score: 54
Period size: 10 Copynumber: 3.8 Consensus size: 12
6056984 AGCAGGCCAA
6056994 AAAAAAGAAGAG
1 AAAAAAGAAGAG
6057006 AAAAAAG-AGA-
1 AAAAAAGAAGAG
6057016 AAAAAA-AA-AG
1 AAAAAAGAAGAG
6057026 AAAAAAGAA
1 AAAAAAGAA
6057035 AAAAAGGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.04
10 13 0.50
11 5 0.19
12 7 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAGAG
Found at i:6057015 original size:9 final size:9
Alignment explanation
Indices: 6056996--6057048 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 9
6056986 CAGGCCAAAA
6056996 AAAAGAAGAG
1 AAAA-AAGAG
6057006 AAAAAAGAG
1 AAAAAAGAG
*
6057015 AAAAAAAAAAG
1 --AAAAAAGAG
6057026 AAAAAAGA-
1 AAAAAAGAG
6057034 AAAAAAG-G
1 AAAAAAGAG
6057042 AAAAAAG
1 AAAAAAG
6057049 GGTTCAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 14 0.37
9 12 0.32
10 4 0.11
11 8 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:6057020 original size:11 final size:11
Alignment explanation
Indices: 6056992--6057031 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
6056982 GCAGCAGGCC
6056992 AAAAAAAAGAAG
1 AAAAAAAAG-AG
*
6057004 AGAAAAAAGAG
1 AAAAAAAAGAG
*
6057015 AAAAAAAAAAG
1 AAAAAAAAGAG
6057026 AAAAAA
1 AAAAAA
6057032 GAAAAAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:6057027 original size:20 final size:21
Alignment explanation
Indices: 6056992--6057039 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
6056982 GCAGCAGGCC
6056992 AAAAAAAAGAAGAGAAAAAAG
1 AAAAAAAAGAAGAGAAAAAAG
6057013 AGAAAAAAA-AA-AGAAAAAAG
1 A-AAAAAAAGAAGAGAAAAAAG
6057033 AAAAAAA
1 AAAAAAA
6057040 GGAAAAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.23
20 10 0.38
21 3 0.12
22 7 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAAAGAAGAGAAAAAAG
Found at i:6057029 original size:7 final size:7
Alignment explanation
Indices: 6057004--6057048 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
6056994 AAAAAAGAAG
6057004 AGAAAAA
1 AGAAAAA
*
6057011 AGAGAAA
1 AGAAAAA
6057018 A-AAAAA
1 AGAAAAA
6057024 AGAAAAA
1 AGAAAAA
6057031 AGAAAAAA
1 AG-AAAAA
6057039 AGGAAAAA
1 A-GAAAAA
6057047 AG
1 AG
6057049 GGTTCAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 5 0.15
7 15 0.45
8 12 0.36
9 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
AGAAAAA
Found at i:6057034 original size:27 final size:24
Alignment explanation
Indices: 6056992--6057047 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 24
6056982 GCAGCAGGCC
*
6056992 AAAAAAAAGAAGAGAAAAAAGAGAA
1 AAAAAAAAGAAAAGAAAAAA-AGAA
*
6057017 AAAAAAAAGAAAAAAGAAAAAAAGGA
1 AAAAAAAAG--AAAAGAAAAAAAGAA
6057043 AAAAA
1 AAAAA
6057048 GGGTTCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 9 0.33
26 8 0.30
27 10 0.37
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAAAAAAGAAAAGAAAAAAAGAA
Found at i:6057047 original size:11 final size:10
Alignment explanation
Indices: 6056992--6057039 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 10
6056982 GCAGCAGGCC
6056992 AAAAAAAAGA
1 AAAAAAAAGA
6057002 AGAGAAAAAAGA
1 A-A-AAAAAAGA
6057014 GAAAAAAAA-A
1 -AAAAAAAAGA
*
6057024 AGAAAAAAGA
1 AAAAAAAAGA
6057034 AAAAAA
1 AAAAAA
6057040 GGAAAAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
9 7 0.22
10 8 0.25
11 7 0.22
12 9 0.28
13 1 0.03
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:6057242 original size:6 final size:5
Alignment explanation
Indices: 6057204--6057231 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
6057194 TATTTATATT
6057204 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
6057232 TAAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:6057402 original size:16 final size:16
Alignment explanation
Indices: 6057370--6057404 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6057360 GAAAATATTC
*
6057370 TAAAATTCTCATTTTT
1 TAAAATTCTCATGTTT
*
6057386 TAAAATTCTCGTGTTT
1 TAAAATTCTCATGTTT
6057402 TAA
1 TAA
6057405 TAGAATCACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (16 bp):
TAAAATTCTCATGTTT
Found at i:6057595 original size:34 final size:34
Alignment explanation
Indices: 6057523--6057619 Score: 151
Period size: 34 Copynumber: 2.8 Consensus size: 34
6057513 AAAAAATCGG
6057523 GTTTCAAAAATTTTCGTGTTTTCAAAAATTCTCAT
1 GTTTCAAAAATTTTCGTGTTTT-AAAAATTCTCAT
*
6057558 GTTTCAAAAATCTTCGTGTTTTAAAAATTC-CAGT
1 GTTTCAAAAATTTTCGTGTTTTAAAAATTCTCA-T
*
6057592 GTTTCAAAAATTTTCGTGTTTTCAAAAT
1 GTTTCAAAAATTTTCGTGTTTTAAAAAT
6057620 AAATTTCCCG
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
33 2 0.03
34 35 0.60
35 21 0.36
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (34 bp):
GTTTCAAAAATTTTCGTGTTTTAAAAATTCTCAT
Found at i:6057619 original size:17 final size:18
Alignment explanation
Indices: 6057524--6057676 Score: 118
Period size: 17 Copynumber: 8.5 Consensus size: 18
6057514 AAAAATCGGG
6057524 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
6057542 TTTCAAAAATTCTCATG-
1 TTTCAAAAATTTTCGTGT
*
6057559 TTTCAAAAATCTTCGTGT
1 TTTCAAAAATTTTCGTGT
*
6057577 TTT-AAAAA-TTCCAGTG-
1 TTTCAAAAATTTTC-GTGT
6057593 TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
*
6057611 TTTCAAAATAAATTTCCCGTGT
1 TTTC--AA-AAATTT-TCGTGT
* ** *
6057633 TTTTAAAAATTCCCGT-A
1 TTTCAAAAATTTTCGTGT
* * *
6057650 TATCGAAAATTTTCTTGT
1 TTTCAAAAATTTTCGTGT
6057668 TTTCAAAAA
1 TTTCAAAAA
6057677 AAAAATTTCC
Statistics
Matches: 104, Mismatches: 21, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
16 5 0.05
17 40 0.38
18 36 0.35
19 5 0.05
20 4 0.04
21 6 0.06
22 8 0.08
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:6057680 original size:22 final size:22
Alignment explanation
Indices: 6057655--6057738 Score: 65
Period size: 20 Copynumber: 4.1 Consensus size: 22
6057645 CCGTATATCG
*
6057655 AAAATTTTCTTGTTTTCAAAAAA
1 AAAATTTCCTTGTTTTC-AAAAA
*
6057678 AAAATTTCCATG-TTTC----A
1 AAAATTTCCTTGTTTTCAAAAA
*
6057695 TAAATTTCCTTGTTTTCAAAAA
1 AAAATTTCCTTGTTTTCAAAAA
* *
6057717 AAAA-TT-CTCGTTTTTAAAAA
1 AAAATTTCCTTGTTTTCAAAAA
6057737 AA
1 AA
6057739 TTNNNNNNNN
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
17 11 0.22
18 4 0.08
20 14 0.29
21 2 0.04
22 8 0.16
23 10 0.20
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.42
Consensus pattern (22 bp):
AAAATTTCCTTGTTTTCAAAAA
Found at i:6057681 original size:40 final size:40
Alignment explanation
Indices: 6057637--6057720 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
6057627 CCGTGTTTTT
* *
6057637 AAAAATTCCCGTATATCGA-AAATTTTCTTGTTTTCAAAAA
1 AAAAATTCCCATATATC-ATAAATTTCCTTGTTTTCAAAAA
* * *
6057677 AAAAATTTCCATGTTTCATAAATTTCCTTGTTTTCAAAAA
1 AAAAATTCCCATATATCATAAATTTCCTTGTTTTCAAAAA
6057717 AAAA
1 AAAA
6057721 TTCTCGTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 1 0.03
40 37 0.97
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (40 bp):
AAAAATTCCCATATATCATAAATTTCCTTGTTTTCAAAAA
Found at i:6065008 original size:42 final size:42
Alignment explanation
Indices: 6064955--6065122 Score: 178
Period size: 42 Copynumber: 3.8 Consensus size: 42
6064945 TAATAAATAT
* *
6064955 ATTTATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTT-TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
6064998 ATTTTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
1 ATTTTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
* *
6065040 ATTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATA-TTTTTAAA
1 A-----TTT--TTTTTTAAATTTTAAAATATTTTTAAAATACTTTTT-TA
* *
6065089 ATACTTTTTTTAATTTTTAAAA-ATTTTTAAAATA
1 AT-TTTTTTTTAAATTTTAAAATATTTTTAAAATA
6065123 AAAATGGGCC
Statistics
Matches: 109, Mismatches: 7, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
42 49 0.45
43 19 0.17
44 1 0.01
45 1 0.01
47 3 0.03
48 5 0.05
49 31 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (42 bp):
ATTTTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:6065117 original size:10 final size:11
Alignment explanation
Indices: 6065011--6065122 Score: 82
Period size: 11 Copynumber: 10.9 Consensus size: 11
6065001 TTTTTTTAAA
6065011 TTTTAAAATAT
1 TTTTAAAATAT
6065022 TTTTAAAATACT
1 TTTTAAAATA-T
*
6065034 TTTT-TAAT-T
1 TTTTAAAATAT
**
6065043 TTTTTTAAT-T
1 TTTTAAAATAT
*
6065053 TTTT----TAA
1 TTTTAAAATAT
6065060 TTTTAAAATAT
1 TTTTAAAATAT
6065071 TTTTAAAATAT
1 TTTTAAAATAT
6065082 TTTTAAAATACT
1 TTTTAAAATA-T
**
6065094 TTTT-TTA-AT
1 TTTTAAAATAT
6065103 TTTTAAAA-AT
1 TTTTAAAATAT
6065113 TTTTAAAATA
1 TTTTAAAATA
6065123 AAAATGGGCC
Statistics
Matches: 84, Mismatches: 7, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
9 10 0.12
10 21 0.25
11 38 0.45
12 10 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:6066573 original size:27 final size:25
Alignment explanation
Indices: 6066535--6066599 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 25
6066525 TTCACAAACC
*
6066535 AAATAAA-ATTAATTATTAACTTTT
1 AAATAAATATTAATTATTAAATTTT
* *
6066559 AAATATAAATATTAAATCTTAAATTTT
1 -AA-ATAAATATTAATTATTAAATTTT
*
6066586 GAATAAATATTAAT
1 AAATAAATATTAAT
6066600 AACATGTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
25 13 0.39
26 6 0.18
27 14 0.42
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (25 bp):
AAATAAATATTAATTATTAAATTTT
Found at i:6074817 original size:2 final size:2
Alignment explanation
Indices: 6074810--6074851 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6074800 CGTACATCAA
6074810 AT AT AT 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 AT AT AT
6074852 TATTNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6075291 original size:32 final size:33
Alignment explanation
Indices: 6075255--6075326 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 33
6075245 ATTTTTTAAA
* *
6075255 CGGGCCTCATTTTTTTGCCC-AA-TCCCATATTT
1 CGGGCCT-ATGTTTTTACCCGAACTCCCATATTT
6075287 CGGGCCTATGTTTTTACCCGAACCCTCCCATATTT
1 CGGGCCTATGTTTTTACCCGAA--CTCCCATATTT
6075322 CGGGC
1 CGGGC
6075327 GGGCCGTCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 10 0.29
32 9 0.26
35 15 0.44
ACGTcount: A:0.15, C:0.33, G:0.17, T:0.35
Consensus pattern (33 bp):
CGGGCCTATGTTTTTACCCGAACTCCCATATTT
Found at i:6076898 original size:10 final size:9
Alignment explanation
Indices: 6076886--6076981 Score: 81
Period size: 9 Copynumber: 10.4 Consensus size: 9
6076876 ACATGTGGAA
6076886 AAAAATTAT
1 AAAAATTAT
6076895 AAAAA--AT
1 AAAAATTAT
*
6076902 AAAAATCAAT
1 AAAAAT-TAT
6076912 AAAAATTAT
1 AAAAATTAT
*
6076921 AACAATTAT
1 AAAAATTAT
*
6076930 -TAAATTAT
1 AAAAATTAT
6076938 AATAAAATTAT
1 -A-AAAATTAT
*
6076949 AAAATTTATT
1 AAAAATTA-T
*
6076959 AAAAATTAA
1 AAAAATTAT
6076968 AAAAATATAT
1 AAAAAT-TAT
6076978 AAAA
1 AAAA
6076982 TGCATAAAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
7 7 0.10
8 6 0.09
9 27 0.39
10 23 0.33
11 7 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6076957 original size:28 final size:27
Alignment explanation
Indices: 6076884--6076982 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 27
6076874 TGACATGTGG
* * *
6076884 AAAAAAATTATAAAA--AATAAAAATC
1 AAAAAAATTATAAAATTTATTAAAATT
6076909 AATAAAAATTATAACAA-TTATT-AAATT
1 AA-AAAAATTATAA-AATTTATTAAAATT
6076936 ATAATAAAATTATAAAATTTATTAAAAATT
1 A-AA-AAAATTATAAAATTTATT-AAAATT
6076966 AAAAAAATATATAAAAT
1 AAAAAAAT-TATAAAAT
6076983 GCATAAAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
25 2 0.03
26 11 0.18
27 10 0.16
28 23 0.37
29 10 0.16
30 6 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAAAAATTATAAAATTTATTAAAATT
Found at i:6076963 original size:19 final size:18
Alignment explanation
Indices: 6076886--6076981 Score: 63
Period size: 19 Copynumber: 5.2 Consensus size: 18
6076876 ACATGTGGAA
*
6076886 AAAAATTATAAAA--AAT
1 AAAAATTATAAAATTATT
*
6076902 AAAAATCAATAAAAATTA-T
1 AAAAAT-TAT-AAAATTATT
* * *
6076921 AACAATTATTAAATTATA
1 AAAAATTATAAAATTATT
6076939 ATAAAATTATAAAATTTATT
1 A-AAAATTATAAAA-TTATT
* *
6076959 AAAAATTAAAAAAATATAT
1 AAAAATTATAAAATTAT-T
6076978 AAAA
1 AAAA
6076982 TGCATAAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
16 6 0.10
17 8 0.13
18 10 0.16
19 32 0.52
20 6 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATTATAAAATTATT
Found at i:6077240 original size:29 final size:30
Alignment explanation
Indices: 6077205--6077268 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
6077195 TCTTTAAATT
*
6077205 TTTTATAATCTTCTTACGA-CTTTATAAAA
1 TTTTATAATCTTCTTACGATCTTAATAAAA
* * *
6077234 TTTTATAATTTTTTTATGATCTTAATAAAA
1 TTTTATAATCTTCTTACGATCTTAATAAAA
6077264 TTTTA
1 TTTTA
6077269 GAATTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (30 bp):
TTTTATAATCTTCTTACGATCTTAATAAAA
Found at i:6077264 original size:30 final size:29
Alignment explanation
Indices: 6077205--6077276 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
6077195 TCTTTAAATT
* * *
6077205 TTTTATAATCTTCTTACGACTTTATAAAA
1 TTTTATAATTTTTTTACGACTTAATAAAA
*
6077234 TTTTATAATTTTTTTATGATCTTAATAAAA
1 TTTTATAATTTTTTTACGA-CTTAATAAAA
*
6077264 TTTTAGAATTTTT
1 TTTTATAATTTTT
6077277 ATAATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 16 0.43
30 21 0.57
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (29 bp):
TTTTATAATTTTTTTACGACTTAATAAAA
Found at i:6077339 original size:8 final size:8
Alignment explanation
Indices: 6077326--6077402 Score: 57
Period size: 8 Copynumber: 9.0 Consensus size: 8
6077316 TAAACTTTAA
6077326 ATATTTTT
1 ATATTTTT
6077334 ATATTTTT
1 ATATTTTT
6077342 ATATTTTT
1 ATATTTTT
* *
6077350 ATTAAAATTTA
1 A-T--ATTTTT
6077361 ATATTTTT
1 ATATTTTT
*
6077369 ATAACTTTT
1 AT-ATTTTT
*
6077378 ATTAATTTT
1 A-TATTTTT
6077387 -TATTTTT
1 ATATTTTT
6077394 ATCATTTTT
1 AT-ATTTTT
6077403 TTGCCACATG
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
7 6 0.11
8 24 0.44
9 18 0.33
10 2 0.04
11 5 0.09
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (8 bp):
ATATTTTT
Found at i:6077377 original size:10 final size:9
Alignment explanation
Indices: 6077264--6077389 Score: 53
Period size: 9 Copynumber: 13.7 Consensus size: 9
6077254 CTTAATAAAA
*
6077264 TTTTAGAAT
1 TTTTATAAT
6077273 TTTTATAATTT
1 TTTTATAA--T
*
6077284 TTTTACAAT
1 TTTTATAAT
* *
6077293 TTGTA-ATT
1 TTTTATAAT
*
6077301 TTTTCTAAT
1 TTTTATAAT
* *
6077310 TTTAGATAAA
1 TTT-TATAAT
* *
6077320 CTTTAAATAT
1 TTTTATA-AT
6077330 TTTTAT-AT
1 TTTTATAAT
6077338 TTTTAT-AT
1 TTTTATAAT
*
6077346 TTTTATTAAA
1 TTTTA-TAAT
*
6077356 ATTTA-ATAT
1 TTTTATA-AT
*
6077365 TTTTATAAC
1 TTTTATAAT
6077374 TTTTATTAAT
1 TTTTA-TAAT
6077384 TTTTAT
1 TTTTAT
6077390 TTTTATCATT
Statistics
Matches: 85, Mismatches: 22, Indels: 20
0.67 0.17 0.16
Matches are distributed among these distances:
8 21 0.25
9 32 0.38
10 24 0.28
11 8 0.09
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:6077639 original size:93 final size:94
Alignment explanation
Indices: 6077498--6077680 Score: 253
Period size: 93 Copynumber: 2.0 Consensus size: 94
6077488 AAAAGGGCAG
* * *
6077498 GGGCTTAATTGTGTTTTTTTGAAAAAAATTTGAGAGCCTTTTTAATACATTTTGAAAGTTCAAGT
1 GGGCTTAATTGTGTTTTTTTGAAAAAAATTTAAGAGCCTTTTTAATACATTATAAAAGTTCAAGT
* * *
6077563 GCCTAATTGAGTGCAAAAAAAAAAAGTAA
66 GCCCAAGTGAATGCAAAAAAAAAAAGTAA
* * * *
6077592 GGGCTTAATTGCT-TTTTTTTG-TAAAAATTTAAGGGTCTTTTTGATACATTATAAAAGTTCAAG
1 GGGCTTAATTG-TGTTTTTTTGAAAAAAATTTAAGAGCCTTTTTAATACATTATAAAAGTTCAAG
6077655 TGCCCAAGTGAATGCAAAAAAAAAAA
65 TGCCCAAGTGAATGCAAAAAAAAAAA
6077681 CAGGGACTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
93 58 0.74
94 19 0.24
95 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (94 bp):
GGGCTTAATTGTGTTTTTTTGAAAAAAATTTAAGAGCCTTTTTAATACATTATAAAAGTTCAAGT
GCCCAAGTGAATGCAAAAAAAAAAAGTAA
Found at i:6077852 original size:4 final size:4
Alignment explanation
Indices: 6077843--6077885 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
6077833 TCTGTTTGTC
6077843 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
6077886 GGGGAGTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:6090384 original size:21 final size:21
Alignment explanation
Indices: 6090360--6090400 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6090350 CATAAAGTAA
*
6090360 AAGCACATCTTTAAATAGCAG
1 AAGCACATCATTAAATAGCAG
6090381 AAGCACATCATTAAATAGCA
1 AAGCACATCATTAAATAGCA
6090401 AACTCTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.20, G:0.12, T:0.22
Consensus pattern (21 bp):
AAGCACATCATTAAATAGCAG
Found at i:6094388 original size:18 final size:19
Alignment explanation
Indices: 6094367--6094402 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
6094357 TTTGAAATTC
6094367 TTCATCTCT-CAATTCTAT
1 TTCATCTCTGCAATTCTAT
*
6094385 TTCATCTTTGCAATTCTA
1 TTCATCTCTGCAATTCTA
6094403 CAGAAAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (19 bp):
TTCATCTCTGCAATTCTAT
Found at i:6097333 original size:135 final size:128
Alignment explanation
Indices: 6097131--6097461 Score: 391
Period size: 135 Copynumber: 2.5 Consensus size: 128
6097121 TTCAGTCTTT
* * *
6097131 AATTGAACTGAAAGAACACAAAAAGCAAATGCTGTGCAGTTTGCCAATAGCTAAGAACAGTAAAA
1 AATTGAACTGAAAGAACACAAAAAGCAAA-GCTGT--AGTTTGCAAAGAGCTAAGAACAG-CAAA
6097196 TCAACAAAAGGAG-CAATCAATAAAAATCAAACAATACAAAAAAAAAAAGTAAAAACAGACAAAC
62 TCAACAAAAGG-GTCAATCAATAAAAATCAAACAATAC----AAAAAAAGTAAAAACAGACAAAC
*
6097260 CCGTTTA
122 CCATTTA
* *
6097267 AATTTGAACTGAAAGAACACAAAAATCAAAGACTGTAATTTGCAAAGAGCTAAGAACAGCAGAAT
1 AA-TTGAACTGAAAGAACACAAAAAGCAAAG-CTGTAGTTTGCAAAGAGCTAAGAACAGCA-AAT
* * * *
6097332 CAACAAAAGGGTCAGTCAATAAGAATCAAACAGTACAGAAAAAGTAAAAACAGACAAACCCATTT
63 CAACAAAAGGGTCAATCAATAAAAATCAAACAATACAAAAAAAGTAAAAACAGACAAACCCATTT
*
6097397 T
128 A
* *
6097398 AATTGAACTGAAAGAACAC-GAAAGCAAAGGCTGTAGTTT--AAAGAACTAAGAACAGCTAAATC
1 AATTGAACTGAAAGAACACAAAAAGCAAA-GCTGTAGTTTGCAAAGAGCTAAGAACAGC-AAATC
6097460 AA
64 AA
6097462 TCAATAAGAA
Statistics
Matches: 174, Mismatches: 15, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
127 22 0.13
128 1 0.01
129 15 0.09
130 18 0.10
131 29 0.17
134 2 0.01
135 54 0.31
136 3 0.02
137 30 0.17
ACGTcount: A:0.53, C:0.16, G:0.15, T:0.16
Consensus pattern (128 bp):
AATTGAACTGAAAGAACACAAAAAGCAAAGCTGTAGTTTGCAAAGAGCTAAGAACAGCAAATCAA
CAAAAGGGTCAATCAATAAAAATCAAACAATACAAAAAAAGTAAAAACAGACAAACCCATTTA
Found at i:6097502 original size:130 final size:130
Alignment explanation
Indices: 6097133--6097502 Score: 324
Period size: 135 Copynumber: 2.8 Consensus size: 130
6097123 CAGTCTTTAA
* * * * * *
6097133 TTGAACTGAAAGAACACAAAAAGCAAATG-CTGTGCAGTTTGCCAATAGCTAAGAACAGTAAAAT
1 TTGAACTGAAAGAACACAAAAAGCAAA-GACTGT--AATTT-CAAAGAACTAAGAACAGCAGAAT
* * * *
6097197 CAACAAAAGGAGCAATCAATAA-AAATCAAACAATACAAAAAAAAAAAGTAAAAACAGACAAACC
62 CAACAAAAGAATCAATCAATAAGAAA-CAAAC---A-AAACAGAAAAAGTAAAAACAGACAAACC
*
6097261 CGTTTAAAT
122 CATTTAAAT
* *
6097270 TTGAACTGAAAGAACACAAAAATCAAAGACTGTAATTTGCAAAGAGCTAAGAACAGCAGAATCAA
1 TTGAACTGAAAGAACACAAAAAGCAAAGACTGTAATTT-CAAAGAACTAAGAACAGCAGAATCAA
** * * ** *
6097335 CAAAAGGGTCAGTCAATAAGAATCAAACAGTACAGAAAAAGTAAAAACAGACAAACCCATTTTAA
65 CAAAAGAATCAATCAATAAGAAACAAACAAAACAGAAAAAGTAAAAACAGACAAACCCATTTAAA
6097400 -
130 T
* * *
6097400 TTGAACTGAAAGAACAC-GAAAGCAAAGGCTGTAGTTT-AAAGAACTAAGAACAGCTA-AATCAA
1 TTGAACTGAAAGAACACAAAAAGCAAAGACTGTAATTTCAAAGAACTAAGAACAGC-AGAATCAA
*
6097462 TCAATAAGAATCAAAT-AGTAAAGAAACTAAA-AAAACAGAAA
65 -CAA-AAGAATC-AATCAAT-AAGAAAC-AAACAAAACAGAAA
6097503 GAAACCCATT
Statistics
Matches: 197, Mismatches: 28, Indels: 23
0.79 0.11 0.09
Matches are distributed among these distances:
127 22 0.11
128 4 0.02
129 23 0.12
130 33 0.17
131 33 0.17
132 1 0.01
135 48 0.24
136 3 0.02
137 30 0.15
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.16
Consensus pattern (130 bp):
TTGAACTGAAAGAACACAAAAAGCAAAGACTGTAATTTCAAAGAACTAAGAACAGCAGAATCAAC
AAAAGAATCAATCAATAAGAAACAAACAAAACAGAAAAAGTAAAAACAGACAAACCCATTTAAAT
Found at i:6097734 original size:3 final size:3
Alignment explanation
Indices: 6097726--6097756 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6097716 TCAAATTAAC
6097726 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
6097757 TAAAGAAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6100576 original size:2 final size:2
Alignment explanation
Indices: 6100571--6100595 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6100561 TTAAGTGTGT
6100571 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
6100596 GAGCACTTTC
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:6108859 original size:46 final size:46
Alignment explanation
Indices: 6108806--6108895 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
6108796 ATGAACGTAA
* *
6108806 TCTTTTAGTTTATATAAAAATTTAAAGCCGATGGTTCTTGCTTTAG
1 TCTTTTAGATTATATAAAAATTTAAAGACGATGGTTCTTGCTTTAG
6108852 TCTTTTAGATTATATAAAAATTTAAAGACGATGGTTCTTGCTTT
1 TCTTTTAGATTATATAAAAATTTAAAGACGATGGTTCTTGCTTT
6108896 TGTTGCTATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (46 bp):
TCTTTTAGATTATATAAAAATTTAAAGACGATGGTTCTTGCTTTAG
Found at i:6109322 original size:30 final size:30
Alignment explanation
Indices: 6109286--6109347 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
6109276 ATTTTCGTAA
* *
6109286 TTTTTATAATG-TTTTATAATTTTTTATAAT
1 TTTTTAT-ATGTTTTTAAAATTTGTTATAAT
*
6109316 TTTTTATATGTTTTTAAAATTTGTTGTAAT
1 TTTTTATATGTTTTTAAAATTTGTTATAAT
6109346 TT
1 TT
6109348 AAAAAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.66
Consensus pattern (30 bp):
TTTTTATATGTTTTTAAAATTTGTTATAAT
Found at i:6109330 original size:10 final size:10
Alignment explanation
Indices: 6109286--6109347 Score: 72
Period size: 10 Copynumber: 6.2 Consensus size: 10
6109276 ATTTTCGTAA
6109286 TTTTTATAAT
1 TTTTTATAAT
*
6109296 GTTTTATAAT
1 TTTTTATAAT
6109306 TTTTTATAAT
1 TTTTTATAAT
6109316 TTTTTAT-AT
1 TTTTTATAAT
*
6109325 GTTTTTAAAAT
1 -TTTTTATAAT
* *
6109336 TTGTTGTAAT
1 TTTTTATAAT
6109346 TT
1 TT
6109348 AAAAAACTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
9 2 0.05
10 40 0.91
11 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.66
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:6114220 original size:15 final size:15
Alignment explanation
Indices: 6114197--6114227 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6114187 AGGGTTTGAC
6114197 TCAAATACATCAGTG
1 TCAAATACATCAGTG
*
6114212 TCAACTACATCAGTG
1 TCAAATACATCAGTG
6114227 T
1 T
6114228 TTGAAGATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (15 bp):
TCAAATACATCAGTG
Found at i:6117036 original size:31 final size:29
Alignment explanation
Indices: 6116966--6117039 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
6116956 GGCTCAGGTT
* *
6116966 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
6116995 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
6117026 ACATTTTAGTCACT
1 ACATTTTAGTCACT
6117040 GAGCCGTTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 19 0.51
30 2 0.05
31 16 0.43
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:6117935 original size:26 final size:26
Alignment explanation
Indices: 6117898--6117976 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
6117888 TTTGAATTTT
*
6117898 AATTAGAA-TAATTAATGATATTAGT-
1 AATTTGAATTAATTAATGATATTA-TA
* * * *
6117923 TATTTGAATTAATTACTGTTTTTATCA
1 AATTTGAATTAATTAATGATATTAT-A
6117950 AATTTGAATTAATT-ATGATATTATA
1 AATTTGAATTAATTAATGATATTATA
6117975 AA
1 AA
6117977 AATAGGGATC
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
25 10 0.24
26 19 0.45
27 13 0.31
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.47
Consensus pattern (26 bp):
AATTTGAATTAATTAATGATATTATA
Found at i:6117979 original size:27 final size:27
Alignment explanation
Indices: 6117924--6117977 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
6117914 GATATTAGTT
* * *
6117924 ATTTGAATTAATTACTGTTTTTATCAA
1 ATTTGAATTAATTACTGATATTATAAA
6117951 ATTTGAATTAATTA-TGATATTATAAA
1 ATTTGAATTAATTACTGATATTATAAA
6117977 A
1 A
6117978 ATAGGGATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 10 0.42
27 14 0.58
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (27 bp):
ATTTGAATTAATTACTGATATTATAAA
Found at i:6120699 original size:30 final size:29
Alignment explanation
Indices: 6120665--6120722 Score: 107
Period size: 30 Copynumber: 2.0 Consensus size: 29
6120655 GAAACTAATC
6120665 TCAATTACTGATTCTTAGGAAATTAGGATA
1 TCAATTACTGATTCTTAGG-AATTAGGATA
6120695 TCAATTACTGATTCTTAGGAATTAGGAT
1 TCAATTACTGATTCTTAGGAATTAGGAT
6120723 TTATTTCCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (29 bp):
TCAATTACTGATTCTTAGGAATTAGGATA
Found at i:6134474 original size:29 final size:31
Alignment explanation
Indices: 6134441--6134499 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
6134431 ATCTAAGGTA
6134441 TAATT-TGATACAT-GAACTTTGA-TGTGGTG
1 TAATTATGA-ACATAGAACTTTGATTGTGGTG
6134470 TAATTATGAACATAGAACTTTGATTGTGGT
1 TAATTATGAACATAGAACTTTGATTGTGGT
6134500 TCAAATACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 9 0.33
30 12 0.44
31 6 0.22
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (31 bp):
TAATTATGAACATAGAACTTTGATTGTGGTG
Found at i:6137955 original size:27 final size:27
Alignment explanation
Indices: 6137887--6137956 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
6137877 CGCCAATGGG
*
6137887 ATTGGCGGCACCAAAGGTGCCAAAGCC
1 ATTGGCGGCACCAATGGTGCCAAAGCC
*
6137914 ATTGGCAGCACCAATGGTGCCAATA-CC
1 ATTGGCGGCACCAATGGTGCCAA-AGCC
6137941 ATTGGCGGCACCAATG
1 ATTGGCGGCACCAATG
6137957 TTTATTAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.29, C:0.29, G:0.27, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGCC
Found at i:6138007 original size:4 final size:4
Alignment explanation
Indices: 6137998--6138151 Score: 119
Period size: 4 Copynumber: 38.8 Consensus size: 4
6137988 GAAGGAGAGG
*
6137998 GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AA -AAA GAAT GAAA GAAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
* *
6138045 GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA GAAA G-AA -AAA GAAAA GGAAA
1 -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA
* *
6138094 GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA G-AA -AAA GAAA -AGA GAAGA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA-A
*
6138141 GAAA AAAA GAA
1 GAAA GAAA GAA
6138152 GAAGAAGAAG
Statistics
Matches: 122, Mismatches: 12, Indels: 32
0.73 0.07 0.19
Matches are distributed among these distances:
3 19 0.16
4 74 0.61
5 25 0.20
6 4 0.03
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:6138067 original size:44 final size:42
Alignment explanation
Indices: 6138009--6138162 Score: 176
Period size: 44 Copynumber: 3.7 Consensus size: 42
6137999 AAAGAAAGAA
*
6138009 AGAAAGAAAGAAAGAAAGAAAAAGAATGAAAGAAAAGGAAAGG
1 AGAAAGAAAAAAAGAAAGAAAAAGAA-GAAAGAAAAGGAAAGG
6138052 AGAAGAGAAAAAAAGAAAGAAAGAAAGAA-AAAGAAAAGGAAAGG
1 AGAA-AGAAAAAAAGAAAG-AA-AAAGAAGAAAGAAAAGGAAAGG
* *
6138096 AG-AAG-AAAAAAGAAAG--AAAGAAGGAAAGAAAAAGAAAAG
1 AGAAAGAAAAAAAGAAAGAAAAAGAA-GAAAGAAAAGGAAAGG
*
6138135 AGAAGAGAAAAAAAG-AAGAAGAAGAAGA
1 AGAA-AGAAAAAAAGAAAGAAAAAGAAGA
6138163 GGGAAGGAAG
Statistics
Matches: 97, Mismatches: 4, Indels: 21
0.80 0.03 0.17
Matches are distributed among these distances:
37 6 0.06
39 15 0.15
40 1 0.01
41 16 0.16
42 11 0.11
43 10 0.10
44 30 0.31
45 2 0.02
46 6 0.06
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (42 bp):
AGAAAGAAAAAAAGAAAGAAAAAGAAGAAAGAAAAGGAAAGG
Found at i:6138174 original size:83 final size:84
Alignment explanation
Indices: 6137987--6138192 Score: 228
Period size: 83 Copynumber: 2.5 Consensus size: 84
6137977 TGGGGGGACC
* * * * *
6137987 AGAAGGAGAGGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAAAGAATGAAAGAAAAGGAAAGG
1 AGAAGAAGAGGG-AAGAAGGAAAGAAAGAAAGAAAGAAAG-AAAAGAAGGAAAGAAAAAGAAAAG
6138052 AGAAGAGAAAAAAAGAAAGAA
64 AGAAGAGAAAAAAAGAAAGAA
**
6138073 AGAAAGAA-AAAGAA-AAGGAAAGGAGAAGAAA-AAAGAAAG-AAAGAAGGAAAGAAAAAGAAAA
1 AG-AAGAAGAGGGAAGAAGGAAA-GA-AAGAAAGAAAGAAAGAAAAGAAGGAAAGAAAAAGAAAA
6138134 GAGAAGAGAAAAAAAG-AAG-A
63 GAGAAGAGAAAAAAAGAAAGAA
*
6138154 AGAAGAAGAGGGAAGGAAGGAAA-AAAAAAAGAAAAGAAA
1 AGAAGAAGAGGGAA-GAAGGAAAGAAAGAAAG-AAAGAAA
6138193 AGGTATTTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
80 10 0.10
81 8 0.08
82 10 0.10
83 42 0.41
84 6 0.06
85 12 0.12
86 10 0.10
87 4 0.04
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.00
Consensus pattern (84 bp):
AGAAGAAGAGGGAAGAAGGAAAGAAAGAAAGAAAGAAAGAAAAGAAGGAAAGAAAAAGAAAAGAG
AAGAGAAAAAAAGAAAGAA
Found at i:6139696 original size:14 final size:14
Alignment explanation
Indices: 6139677--6139705 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6139667 CTCCCAATTG
6139677 ACGGGAGTCCCGTA
1 ACGGGAGTCCCGTA
6139691 ACGGGAGTCCCGTA
1 ACGGGAGTCCCGTA
6139705 A
1 A
6139706 TGGAAGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (14 bp):
ACGGGAGTCCCGTA
Found at i:6143551 original size:18 final size:18
Alignment explanation
Indices: 6143525--6143567 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
6143515 CACAATGATT
6143525 GCCACCACCTTCTTCTTC
1 GCCACCACCTTCTTCTTC
*
6143543 GCCAGCACCTTCTTCTTC
1 GCCACCACCTTCTTCTTC
*
6143561 ACCACCA
1 GCCACCA
6143568 ACCATGTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.28
Consensus pattern (18 bp):
GCCACCACCTTCTTCTTC
Found at i:6144360 original size:3 final size:3
Alignment explanation
Indices: 6144352--6144435 Score: 159
Period size: 3 Copynumber: 28.0 Consensus size: 3
6144342 TCTTAATACT
*
6144352 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC GAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
6144400 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
6144436 NNNNNNNNNN
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.65, C:0.33, G:0.01, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:6144549 original size:3 final size:3
Alignment explanation
Indices: 6144536--6144580 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
6144526 NNNNNNNNNN
*
6144536 CAA CGA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
6144581 TAATAATAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.33, G:0.02, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:6144674 original size:19 final size:21
Alignment explanation
Indices: 6144650--6144688 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
6144640 AGTAAAACAA
*
6144650 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
6144669 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
6144689 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:6144743 original size:10 final size:11
Alignment explanation
Indices: 6144713--6144742 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6144703 TAAAAAACAC
6144713 CTTCTTTTTCT
1 CTTCTTTTTCT
*
6144724 CCTCTTTTTCT
1 CTTCTTTTTCT
6144735 CTTCTTTT
1 CTTCTTTT
6144743 CCGCAACAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:6144877 original size:27 final size:27
Alignment explanation
Indices: 6144847--6144921 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
6144837 CAATCAATAC
6144847 GGCACCATTGGTGCCGCCAATGG-TATT
1 GGCACCATTGGTGCCGCCAATGGCT-TT
6144874 GGCACCATTGGTGCCGCCAATGGCTTT
1 GGCACCATTGGTGCCGCCAATGGCTTT
*
6144901 GGCACCTTTGGTGCCGCCAAT
1 GGCACCATTGGTGCCGCCAAT
6144922 CCCATTAGCG
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 45 0.98
28 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.25
Consensus pattern (27 bp):
GGCACCATTGGTGCCGCCAATGGCTTT
Found at i:6145026 original size:21 final size:21
Alignment explanation
Indices: 6145002--6145044 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6144992 TATTTTTTTG
6145002 ATATATTTTGGTAAATAAAAA
1 ATATATTTTGGTAAATAAAAA
6145023 ATATATTTTGGTAAATAAAAA
1 ATATATTTTGGTAAATAAAAA
6145044 A
1 A
6145045 AGTTATAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (21 bp):
ATATATTTTGGTAAATAAAAA
Found at i:6145910 original size:20 final size:20
Alignment explanation
Indices: 6145885--6145924 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
6145875 AGACTTTATC
*
6145885 TAATAAACCATTGAAAAAAT
1 TAATAAACCATTAAAAAAAT
6145905 TAATAAACCATTAAAAAAAT
1 TAATAAACCATTAAAAAAAT
6145925 ATTTTCAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (20 bp):
TAATAAACCATTAAAAAAAT
Found at i:6146800 original size:19 final size:19
Alignment explanation
Indices: 6146754--6146804 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
6146744 TTACTTTCAA
*
6146754 AAAATTATATTT--TATTT
1 AAAATTATATTTAATTTTT
*
6146771 AAATTTA-ATTTAATTTTT
1 AAAATTATATTTAATTTTT
6146789 AAAATTATATTTAATT
1 AAAATTATATTTAATT
6146805 CAATTACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 4 0.14
17 6 0.21
18 10 0.36
19 8 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AAAATTATATTTAATTTTT
Found at i:6148948 original size:31 final size:31
Alignment explanation
Indices: 6148913--6148976 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
6148903 CAATCCATTA
*
6148913 ACTTAAATAAAAAATTTTGAATAATTCAGTG
1 ACTTAAATAAAAAATTTTAAATAATTCAGTG
* * * *
6148944 ACTTAAATGAAAACTTTTAAATAGTTTAGTG
1 ACTTAAATAAAAAATTTTAAATAATTCAGTG
6148975 AC
1 AC
6148977 CATTTTGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (31 bp):
ACTTAAATAAAAAATTTTAAATAATTCAGTG
Done.