Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 38 of 204
Found at i:13306771 original size:45 final size:45
Alignment explanation
Indices: 13306708--13306794 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
13306698 TTTTATTCAT
* * * *
13306708 TTTTGTATTTTGGTAAAATACGTCATCTTGATTAATTTATTCTCA
1 TTTTGTATTCTAGCAAAATACGTCATCTTGATTAATTCATTCTCA
** *
13306753 TTTTGTATTCTAGCAAAATTTGTTATCTTGATTAATTCATTC
1 TTTTGTATTCTAGCAAAATACGTCATCTTGATTAATTCATTC
13306795 ATTCCGAGCT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.52
Consensus pattern (45 bp):
TTTTGTATTCTAGCAAAATACGTCATCTTGATTAATTCATTCTCA
Found at i:13307816 original size:100 final size:100
Alignment explanation
Indices: 13307671--13308699 Score: 1177
Period size: 100 Copynumber: 10.3 Consensus size: 100
13307661 ATTACAGTGG
* * * *
13307671 AATAGATTGAAGTTATAACGGCGAATCTTACTTCCCTAGCAGTGTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* *
13307736 CGACGTCGAATCTTGTTTCCCCGACATTACAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* *
13307771 AATAGATTGAAGTTACAACGGCGAATCTTACCTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* * * * *
13307836 TGATGGCGAATCTTGTTTTCCCGATATTGCAATTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * *
13307871 AATAGATTGAAGCTACAACCGCGAGTCTTACCTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
*
13307936 CGATGGCGAATCTTGTTTCCCCGACATTGCAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * * *
13307971 AATAGATTGAAGCTACAATGGCGAACCTTACCTCCTTGGCGGTGTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* *
13308036 CGACGACGAATCTTGTTTCCCTGACATTGCAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * *
13308071 AATAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGGTGGTGTCA-TGGAACAAATTGAAGCT
1 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGT-AGTGGAACAGATTGAAGCT
* * * * ** * **
13308135 ACGACAGCGAATCTTGCTTCCCTGGCGGTGTAGTGG
65 ACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * ** *** ** * ** *
13308171 AACAAATTGAAGCTACAACGGCGAATCTTGTTTCCCCAACATTGCAGTTAAATAGATTGAAGCTA
1 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* *** * * * * **
13308236 -GAACGGCAAATCTTACCTCCCTGGCAATGTAGTGG
66 CG-ACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * * **
13308271 AACAGACTGAAGCTACGACGGCGAATCTTGTTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* *
13308336 CGACGGTGAATCTTATTTCCCCGACATTGCAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * *
13308371 AATATATTGAAGCTATAACGGCGAATCTTACTTACCTGGCGGTGTAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* * *
13308436 CAACGGCGAATCTTATTTTCCCGACATTGCAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * * * *
13308471 AA-ATATTGAAGCTATAACGGCGAATCTTACTTACCTGGAGGTGTAGTGGAACAGATTGATGCTA
1 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
* * *
13308535 TGACGGTGAATCTTGTTTCCCCGACATTGTAGTTA
66 CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
* * **** * *
13308570 AATAGATTGAAGCTACAATGACGAATCTTA-TCTCCCTGAAATTGCAGTGGAGCAGATTGAAGCT
1 AATAGATTGAAGCTACAACGGCGAATCTTACT-TCCCTGGCGGTGTAGTGGAACAGATTGAAGCT
* *
13308634 ACGACAGCGAATCTTGTTTCCCCGACATTACAGTTA
65 ACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
*
13308670 AATAGATTGTAA-CTACAATGGCGAATCTTA
1 AATAGATTG-AAGCTACAACGGCGAATCTTA
13308700 TCTCCCTAAA
Statistics
Matches: 800, Mismatches: 122, Indels: 14
0.85 0.13 0.01
Matches are distributed among these distances:
99 94 0.12
100 702 0.88
101 4 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (100 bp):
AATAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTA
CGACGGCGAATCTTGTTTCCCCGACATTGCAGTTA
Found at i:13308079 original size:150 final size:150
Alignment explanation
Indices: 13307666--13308699 Score: 874
Period size: 150 Copynumber: 6.9 Consensus size: 150
13307656 TTGGCATTAC
* * * * * *
13307666 AGTGGAATAGATTGAAGTTATAACGGCGAATCTTACTTCCCTAGCAGTGTAGTGGAACAGATTGA
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTATTTCCCTGGCGGTGTAGTGGAACAGATTGA
* * *
13307731 AGCTACGACGTCGAATCTTGTTTCCCCGACATTACAGTTAAATAGATTGAAGTTACAACGGCGAA
66 AGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACAACGGCGAA
* *
13307796 TCTTACCTCCCTGGCGGTGT
131 TCTTACTTCCCTGGCAGTGT
** * * **** * * ** *
13307816 AGTGGAACAGATTGAAGCTATGATGGCGAATCTTGTTTTCCC-GATATTGCAATTAAATAGATTG
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTT-ATTTCCCTGGCGGTGTAGTGGAACAGATTG
* * * *** * * ** * ** * * *
13307880 AAGCTACAACCGCGAGTCTTACCTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGATGGCGA
65 AAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACAACGGCGA
** * * * *
13307945 ATCTTGTTTCCCCGACATTGC
130 ATCTTACTTCCCTGGCAGTGT
** * * * ** *
13307966 AGTTAAATAGATTGAAGCTACAATGGCGAACCTTACCTCCTTGGCGGTGTAGTGGAACAGATTGA
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTATTTCCCTGGCGGTGTAGTGGAACAGATTGA
* * *
13308031 AGCTACGACGACGAATCTTGTTTCCCTGACATTGCAGTTAAATAGATTGAAGCTACAACGGTGAA
66 AGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACAACGGCGAA
**
13308096 TCTTACTTCCCTGGTGGTGT
131 TCTTACTTCCCTGGCAGTGT
* * * ** *
13308116 CA-TGGAACAAATTGAAGCTACGACAGCGAATCTTGCTTCCCTGGCGGTGTAGTGGAACAAATTG
1 -AGTGGAACAGATTGAAGCTACAACGGCGAATCTTATTTCCCTGGCGGTGTAGTGGAACAGATTG
* * * *
13308180 AAGCTACAACGGCGAATCTTGTTTCCCCAACATTGCAGTTAAATAGATTGAAGCTAGAACGGCAA
65 AAGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACAACGGCGA
* *
13308245 ATCTTACCTCCCTGGCAATGT
130 ATCTTACTTCCCTGGCAGTGT
* * *
13308266 AGTGGAACAGACTGAAGCTACGACGGCGAATCTTGTTTCCCTGGCGGTGTAGTGGAACAGATTGA
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTATTTCCCTGGCGGTGTAGTGGAACAGATTGA
* * * *
13308331 AGCTACGACGGTGAATCTTATTTCCCCGACATTGCAGTTAAATATATTGAAGCTATAACGGCGAA
66 AGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACAACGGCGAA
* *
13308396 TCTTACTTACCTGGCGGTGT
131 TCTTACTTCCCTGGCAGTGT
* ** * * * *
13308416 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTATTTTCCC-GACATTGCAGT-TAAAATATTG
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTA-TTTCCCTGGCGGTGTAGTGGAACAGATTG
** * * ** ** * ** * * ** *
13308479 AAGCTATAACGGCGAATCTTACTTACCTGGA-GGTGTAGTGGAACAGATTGATGCTATGACGGTG
65 AAGCTACGACGGCGAATCTT-GTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACAACGGCG
** * * *
13308543 AATCTTGTTTCCCCGACATTGT
129 AATCTTACTTCCCTGGCAGTGT
** * * * * **** * *
13308565 AGTTAAATAGATTGAAGCTACAATGACGAATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTGA
1 AGTGGAACAGATTGAAGCTACAACGGCGAATCTTATTTCCCTGGCGGTGTAGTGGAACAGATTGA
* * *
13308630 AGCTACGACAGCGAATCTTGTTTCCCCGACATTACAGTTAAATAGATTGTAA-CTACAATGGCGA
66 AGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGATTG-AAGCTACAACGGCGA
13308694 ATCTTA
130 ATCTTA
13308700 TCTCCCTAAA
Statistics
Matches: 684, Mismatches: 190, Indels: 20
0.77 0.21 0.02
Matches are distributed among these distances:
148 5 0.01
149 112 0.16
150 554 0.81
151 13 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (150 bp):
AGTGGAACAGATTGAAGCTACAACGGCGAATCTTATTTCCCTGGCGGTGTAGTGGAACAGATTGA
AGCTACGACGGCGAATCTTGTTTCCCCGACATTGCAGTTAAATAGATTGAAGCTACAACGGCGAA
TCTTACTTCCCTGGCAGTGT
Found at i:13308677 original size:50 final size:50
Alignment explanation
Indices: 13307660--13308732 Score: 677
Period size: 50 Copynumber: 21.5 Consensus size: 50
13307650 ATCTCTTTGG
* * * ** *
13307660 CATTACAGTGGAATAGATTGAAGTTATAACGGCGAATCTTACTTCCCT-A
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
* * * * *
13307709 GCAGTGTAGTGGAACAGATTGAAGCTACGACGTCGAATCTTGTTTCCCCGA
1 -CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
* ** * * * ** *
13307760 CATTACAGTTAAATAGATTGAAGTTACAACGGCGAATCTTACCTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * * * *
13307810 CGGTGTAGTGGAACAGATTGAAGCTATGATGGCGAATCTTGTTTTCCC-GA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTT-ATTTCCCTGA
* * ** * * * * ** *
13307860 TATTGCAATTAAATAGATTGAAGCTACAACCGCGAGTCTTACCTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * * * *
13307910 CGGTGTAGTGGAACAGATTGAAGCTACGATGGCGAATCTTGTTTCCCCGA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * * * * ** * *
13307960 CATTGCAGTTAAATAGATTGAAGCTACAATGGCGAACCTTACCTCCTTGG
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * * *
13308010 CGGTGTAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * * * * *
13308060 CATTGCAGTTAAATAGATTGAAGCTACAACGGTGAATCTTACTTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
*** * * ** *
13308110 TGGTGTCA-TGGAACAAATTGAAGCTACGACAGCGAATCTTGCTTCCCTGG
1 CATTG-CAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * * * * **
13308160 CGGTGTAGTGGAACAAATTGAAGCTACAACGGCGAATCTTGTTTCCCCAA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * * ** *
13308210 CATTGCAGTTAAATAGATTGAAGCTA-GAACGGCAAATCTTACCTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCTACG-ACGGCGAATCTTATTTCCCTGA
* * * * *
13308260 CAATGTAGTGGAACAGACTGAAGCTACGACGGCGAATCTTGTTTCCCTGG
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * * *
13308310 CGGTGTAGTGGAACAGATTGAAGCTACGACGGTGAATCTTATTTCCCCGA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * * ** * * *
13308360 CATTGCAGTTAAATATATTGAAGCTATAACGGCGAATCTTACTTACCTGG
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
** * *
13308410 CGGTGTAGTGGAACAGATTGAAGCTACAACGGCGAATCTTATTTTCCC-GA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTA-TTTCCCTGA
* * * ** * *
13308460 CATTGCAGT-TAAAATATTGAAGCTATAACGGCGAATCTTACTTACCTGGA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCT-GA
** * * * * * *
13308510 -GGTGTAGTGGAACAGATTGATGCTATGACGGTGAATCTTGTTTCCCCGA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
* ** * * * * *
13308559 CATTGTAGTTAAATAGATTGAAGCTACAATGACGAATCTTATCTCCCTGA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
* * * * *
13308609 AATTGCAGTGGAGCAGATTGAAGCTACGACAGCGAATCTTGTTTCCCCGA
1 CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
* ** * * * * *
13308659 CATTACAGTTAAATAGATTGTAA-CTACAATGGCGAATCTTATCTCCCTAA
1 CATTGCAGTGGAACAGATTG-AAGCTACGACGGCGAATCTTATTTCCCTGA
* * *
13308709 AATTGCAGTGGAGCATATTGAAGC
1 CATTGCAGTGGAACAGATTGAAGC
13308733 CACTAATCTT
Statistics
Matches: 749, Mismatches: 260, Indels: 28
0.72 0.25 0.03
Matches are distributed among these distances:
48 4 0.01
49 41 0.05
50 690 0.92
51 14 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (50 bp):
CATTGCAGTGGAACAGATTGAAGCTACGACGGCGAATCTTATTTCCCTGA
Found at i:13308814 original size:44 final size:43
Alignment explanation
Indices: 13308693--13308865 Score: 184
Period size: 45 Copynumber: 3.9 Consensus size: 43
13308683 TACAATGGCG
* * **
13308693 AATCTTATCTCCCTAAAATTGCAGTGGAGCATATTGAAGCCAC
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGATAC
* *
13308736 TAATCTTATCCCCCCTAAAGTTGCAGTGGGGCAAATTGAAGATAC
1 -AATCTTAT-CTCCCTAAAGTTGCAGTGGAGCAAATTGAAGATAC
* * *
13308781 AAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAAACTGATGATAGAA
1 AA-TCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGAT--AC
* * * *
13308827 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAG
13308866 CTAAATAACA
Statistics
Matches: 108, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
44 39 0.36
45 66 0.61
46 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAAATTGAAGATAC
Found at i:13308863 original size:89 final size:89
Alignment explanation
Indices: 13308695--13308865 Score: 200
Period size: 89 Copynumber: 1.9 Consensus size: 89
13308685 CAATGGCGAA
* * * **
13308695 TCTTATCTCCCTAAAATTGCAGTGGAGCATATTGAAGCCACTAATCTTATCCCCCCTAAAGTTGC
1 TCTTATCTCCCTAAAATTGCAGTGGAGCAAACTGAAGACAAAAATCTTATCCCCCCTAAAGTTGC
**
13308760 AGTGGGGCAAATTGAAGATACAAG
66 AGTGGAACAAATTGAAGATACAAG
* * * ** *
13308784 TCTTATCTCCCTAAAGTTGCAGTGGAGCAAACTGATGATAGAAAATCTTAT-TTCCCTGAAGTTG
1 TCTTATCTCCCTAAAATTGCAGTGGAGCAAACTGAAGACA-AAAATCTTATCCCCCCTAAAGTTG
*
13308848 CAGTGGAACAGATTGAAG
65 CAGTGGAACAAATTGAAG
13308866 CTAAATAACA
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
89 59 0.88
90 8 0.12
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (89 bp):
TCTTATCTCCCTAAAATTGCAGTGGAGCAAACTGAAGACAAAAATCTTATCCCCCCTAAAGTTGC
AGTGGAACAAATTGAAGATACAAG
Found at i:13310552 original size:18 final size:18
Alignment explanation
Indices: 13310531--13310569 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
13310521 TTTTTTTAAA
13310531 TATTTATTAATTTTATTT
1 TATTTATTAATTTTATTT
*
13310549 TATTTATTTATTTTATTT
1 TATTTATTAATTTTATTT
13310567 TAT
1 TAT
13310570 ATTTGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTATTAATTTTATTT
Found at i:13310558 original size:13 final size:13
Alignment explanation
Indices: 13310542--13310566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13310532 ATTTATTAAT
13310542 TTTATTTTATTTA
1 TTTATTTTATTTA
13310555 TTTATTTTATTT
1 TTTATTTTATTT
13310567 TATATTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:13312069 original size:23 final size:23
Alignment explanation
Indices: 13312043--13312187 Score: 218
Period size: 23 Copynumber: 6.3 Consensus size: 23
13312033 ATAAGTGCCA
*
13312043 CACTGATATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
13312066 CACTGATACGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
13312089 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
13312112 CACTGATATGTAGCTGAATCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
13312135 CACTGATACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
13312158 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
13312181 CACTGAT
1 CACTGAT
13312188 CAATAACACT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 109 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:13312439 original size:18 final size:17
Alignment explanation
Indices: 13312413--13312451 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
13312403 ATTTTCCTTC
13312413 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
13312430 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
13312448 CACA
1 CACA
13312452 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:13318088 original size:13 final size:13
Alignment explanation
Indices: 13318070--13318133 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
13318060 ACACTCAAAT
*
13318070 TTCTCAAAAGTAC
1 TTCTCAAAAGCAC
13318083 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
13318096 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
13318109 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
13318122 TTTTCAAAAGCA
1 TTCTCAAAAGCA
13318134 ATGAAGAACT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.27
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:13322560 original size:14 final size:13
Alignment explanation
Indices: 13322537--13322578 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
13322527 TAATCTTTGA
13322537 TTTATTATTTTAT
1 TTTATTATTTTAT
13322550 TTTAGTTA-TTTAT
1 TTTA-TTATTTTAT
*
13322563 TTTAATTTTTTTAT
1 TTT-ATTATTTTAT
13322577 TT
1 TT
13322579 GATTTGGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 14 0.56
14 11 0.44
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTATTATTTTAT
Found at i:13322576 original size:18 final size:18
Alignment explanation
Indices: 13322536--13322583 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
13322526 TTAATCTTTG
13322536 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTTT
*
13322553 AGTTATTTATTTTAATTTT
1 ATTTATTTATTTT-ATTTT
13322572 -TTTATTTGATTT
1 ATTTATTT-ATTT
13322584 GGATTCAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 13 0.50
19 9 0.35
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:13323150 original size:4 final size:4
Alignment explanation
Indices: 13323141--13323239 Score: 135
Period size: 4 Copynumber: 24.8 Consensus size: 4
13323131 CACAACAAGG
* * * * * * *
13323141 ACAT ACAT ACGT ACAT ACAT GCAT GCAT GCAT GCAT GCAT GCAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
13323189 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
13323237 ACA
1 ACA
13323240 ACAATTCAAG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 91 1.00
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:13323932 original size:22 final size:22
Alignment explanation
Indices: 13323893--13323934 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
13323883 AAATCAAATC
*
13323893 TCTAAAATTATAGAATCATACT
1 TCTAAAATTATACAATCATACT
13323915 TCTAAAATT-TACATATCATA
1 TCTAAAATTATACA-ATCATA
13323935 TCTAAGATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.38
Consensus pattern (22 bp):
TCTAAAATTATACAATCATACT
Found at i:13324867 original size:4 final size:4
Alignment explanation
Indices: 13324858--13324992 Score: 270
Period size: 4 Copynumber: 33.8 Consensus size: 4
13324848 CACAACGAGG
13324858 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
13324906 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
13324954 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
13324993 GCAATTCAAA
Statistics
Matches: 131, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 131 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:13326797 original size:16 final size:16
Alignment explanation
Indices: 13326778--13326826 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
13326768 TTCGCTGTAT
*
13326778 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
13326794 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
13326810 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
13326826 T
1 T
13326827 AGTATTCTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.37, C:0.04, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:13327035 original size:18 final size:17
Alignment explanation
Indices: 13327014--13327048 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13327004 TTATTATTAA
*
13327014 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
13327032 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
13327049 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:13327193 original size:37 final size:37
Alignment explanation
Indices: 13327149--13327310 Score: 103
Period size: 37 Copynumber: 4.2 Consensus size: 37
13327139 TTTTAATTAA
13327149 AATATATGATTTAATAAAATTCTTAATATTAAATATT
1 AATATATGATTTAATAAAATTCTTAATATTAAATATT
** ** *
13327186 CTTATATGAATTTTCTAAAA-TCATAATA-TATAATACTAT
1 AATATATG-ATTTAATAAAATTCTTAATATTA-AATA-T-T
* * * * * * **
13327225 AAAATATAATTTAACATAATTATTATTATAATTTAATAAA
1 AATATATGATTTAATAAAATTCTTA--AT-ATTAAATATT
*
13327265 AATATATAATTTAATAAAATTCTTAATATTAAATATT
1 AATATATGATTTAATAAAATTCTTAATATTAAATATT
**
13327302 CTTATATGA
1 AATATATGA
13327311 ATTTTCTAAA
Statistics
Matches: 88, Mismatches: 28, Indels: 18
0.66 0.21 0.13
Matches are distributed among these distances:
36 2 0.02
37 30 0.34
38 19 0.22
39 8 0.09
40 21 0.24
41 2 0.02
42 5 0.06
43 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (37 bp):
AATATATGATTTAATAAAATTCTTAATATTAAATATT
Found at i:13327213 original size:120 final size:120
Alignment explanation
Indices: 13326994--13327395 Score: 654
Period size: 120 Copynumber: 3.4 Consensus size: 120
13326984 TTAATCATAT
*
13326994 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
* * * * *
13327059 CAATATTCTTATATGAATTTACTCAAATCGTAATATATGATACTATAAAATATAA
66 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
* *
13327114 TTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAT
1 TTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
13327178 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
65 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
*
13327234 TTTAACATAATTATTATT--ATA-A-TTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
*
13327295 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATGAAATATAA
66 AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
*
13327350 TTTAACATAATTATTATTAAATATAATTTAA-TAAAATATATAATTT
1 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTT
13327396 CAATTACTTA
Statistics
Matches: 263, Mismatches: 13, Indels: 13
0.91 0.04 0.04
Matches are distributed among these distances:
116 109 0.41
117 1 0.00
118 6 0.02
119 17 0.06
120 128 0.49
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAA
Found at i:13327293 original size:22 final size:21
Alignment explanation
Indices: 13327227--13327293 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
13327217 AATACTATAA
* *
13327227 AATATAATTTAACATAATTATT
1 AATATAATTTAATAAAATT-TT
* *
13327249 ATTATAATTTAATAAAA--AT
1 AATATAATTTAATAAAATTTT
13327268 -ATATAATTTAATAAAATTCTT
1 AATATAATTTAATAAAATT-TT
13327289 AATAT
1 AATAT
13327294 TAAATATTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 15 0.43
19 1 0.03
21 1 0.03
22 18 0.51
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AATATAATTTAATAAAATTTT
Found at i:13327329 original size:37 final size:36
Alignment explanation
Indices: 13327149--13327353 Score: 99
Period size: 38 Copynumber: 5.4 Consensus size: 36
13327139 TTTTAATTAA
* * *
13327149 AATATATGATTTAATAAAATTCTTAATATTAAATATT
1 AATATATAATTTACTAAAA-TCATAATATTAAATATT
** *
13327186 CTTATATGAATTTTCTAAAATCATAATA-TATAATACTAT
1 AATATAT-AATTTACTAAAATCATAATATTA-AATA-T-T
* * * * * **
13327225 AAAATATAATTTAACATAATTATTATTATAATTTAATAAA
1 AATATATAATTT-AC-TAA-AATCATAAT-ATTAAATATT
* *
13327265 AATATATAATTTAATAAAATTCTTAATATTAAATATT
1 AATATATAATTTACTAAAA-TCATAATATTAAATATT
** * *
13327302 CTTATATGAATTTTCTAAAATCATAATATATAATACTATG
1 AATATAT-AATTTACTAAAATCATAATAT-TAA-A-TATT
13327342 AA-ATATAATTTA
1 AATATATAATTTA
13327354 ACATAATTAT
Statistics
Matches: 120, Mismatches: 34, Indels: 27
0.66 0.19 0.15
Matches are distributed among these distances:
36 2 0.02
37 37 0.31
38 40 0.33
39 12 0.10
40 17 0.14
41 6 0.05
42 5 0.04
43 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (36 bp):
AATATATAATTTACTAAAATCATAATATTAAATATT
Found at i:13331316 original size:17 final size:17
Alignment explanation
Indices: 13331278--13331321 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
13331268 CGGCCTATTC
*
13331278 AAATATATAATGTTATA
1 AAATATATTATGTTATA
13331295 AAATATATTATGTTA-A
1 AAATATATTATGTTATA
13331311 ATAATA-ATTAT
1 A-AATATATTAT
13331322 ATATTTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (17 bp):
AAATATATTATGTTATA
Found at i:13336270 original size:20 final size:19
Alignment explanation
Indices: 13336244--13336292 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
13336234 TTACAAAAAT
13336244 ATTCAAAATAAATTTCAAA
1 ATTCAAAATAAATTTCAAA
* *
13336263 AGTTCAAAACAAATTTTAAA
1 A-TTCAAAATAAATTTCAAA
13336283 ATTCAAAATA
1 ATTCAAAATA
13336293 TTTATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATTCAAAATAAATTTCAAA
Found at i:13336311 original size:16 final size:17
Alignment explanation
Indices: 13336273--13336314 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
13336263 AGTTCAAAAC
*
13336273 AAATTT-TAAAATTCAA
1 AAATTTATAAAAATCAA
13336289 AATATTTATAAAAAT-AA
1 AA-ATTTATAAAAATCAA
13336306 AAATTTATA
1 AAATTTATA
13336315 TTTTATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTATAAAAATCAA
Found at i:13342510 original size:33 final size:33
Alignment explanation
Indices: 13342466--13342532 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
13342456 CGTAAATATT
* *
13342466 AGGGTTTGATAAATAACTAAATTAAAGAA-TCTA
1 AGGGTTGGATAAATAACCAAATTAAA-AATTCTA
*
13342499 AGGGTTGGATAACTAACCAAATTAAAAATTCTA
1 AGGGTTGGATAAATAACCAAATTAAAAATTCTA
13342532 A
1 A
13342533 TCTTAATCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (33 bp):
AGGGTTGGATAAATAACCAAATTAAAAATTCTA
Found at i:13350856 original size:30 final size:30
Alignment explanation
Indices: 13350815--13350872 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
13350805 GACCATGCCA
* *
13350815 GTCATAGCAAATTGCTACTTATGGTCTTAT
1 GTCATAACAAATTGCTACTTATGATCTTAT
*
13350845 GTCATAACAAATTGGTACTTATGATCTT
1 GTCATAACAAATTGCTACTTATGATCTT
13350873 GTACAAATGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (30 bp):
GTCATAACAAATTGCTACTTATGATCTTAT
Found at i:13352330 original size:18 final size:18
Alignment explanation
Indices: 13352307--13352364 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
13352297 GCTTCGAAAC
13352307 GGGAAAGGGAAGGGATAG
1 GGGAAAGGGAAGGGATAG
13352325 GGGAAA--G--GGG-TAG
1 GGGAAAGGGAAGGGATAG
*
13352338 GGGAAAGGGAAGGAGA-AA
1 GGGAAAGGGAAGG-GATAG
13352356 GGGAAAGGG
1 GGGAAAGGG
13352365 GAAAAGAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
13 9 0.27
14 3 0.09
15 1 0.03
16 1 0.03
17 2 0.06
18 17 0.52
ACGTcount: A:0.40, C:0.00, G:0.57, T:0.03
Consensus pattern (18 bp):
GGGAAAGGGAAGGGATAG
Found at i:13352338 original size:13 final size:13
Alignment explanation
Indices: 13352302--13352368 Score: 68
Period size: 13 Copynumber: 5.3 Consensus size: 13
13352292 TGTAGGCTTC
13352302 GAAACGGGAAA-GG
1 GAAA-GGGAAAGGG
*
13352315 G-AAGGGATAGGG
1 GAAAGGGAAAGGG
**
13352327 GAAAGGGGTAGGG
1 GAAAGGGAAAGGG
*
13352340 GAAAGGG-AAGGA
1 GAAAGGGAAAGGG
13352352 GAAAGGGAAAGGG
1 GAAAGGGAAAGGG
13352365 GAAA
1 GAAA
13352369 AGAATGGGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
11 5 0.11
12 15 0.33
13 26 0.57
ACGTcount: A:0.43, C:0.01, G:0.52, T:0.03
Consensus pattern (13 bp):
GAAAGGGAAAGGG
Found at i:13352342 original size:31 final size:31
Alignment explanation
Indices: 13352307--13352365 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
13352297 GCTTCGAAAC
*
13352307 GGGAAAGGGAAGG-GATAGGGGAAAGGGGTAG
1 GGGAAAGGGAAGGAGA-AAGGGAAAGGGGTAG
13352338 GGGAAAGGGAAGGAGAAAGGGAAAGGGG
1 GGGAAAGGGAAGGAGAAAGGGAAAGGGG
13352366 AAAAGAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.58, T:0.03
Consensus pattern (31 bp):
GGGAAAGGGAAGGAGAAAGGGAAAGGGGTAG
Found at i:13352357 original size:12 final size:12
Alignment explanation
Indices: 13352302--13352368 Score: 64
Period size: 12 Copynumber: 5.3 Consensus size: 12
13352292 TGTAGGCTTC
*
13352302 GAAACGGGAAAGG
1 GAAA-GGGAAGGG
13352315 G-AAGGGATAGGG
1 GAAAGGGA-AGGG
*
13352327 GAAAGGGGTAGGG
1 GAAA-GGGAAGGG
*
13352340 GAAAGGGAAGGA
1 GAAAGGGAAGGG
13352352 GAAAGGGAAAGGG
1 GAAAGGG-AAGGG
13352365 GAAA
1 GAAA
13352369 AGAATGGGTC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
11 4 0.09
12 19 0.42
13 19 0.42
14 3 0.07
ACGTcount: A:0.43, C:0.01, G:0.52, T:0.03
Consensus pattern (12 bp):
GAAAGGGAAGGG
Found at i:13352368 original size:25 final size:26
Alignment explanation
Indices: 13352302--13352368 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
13352292 TGTAGGCTTC
*
13352302 GAAACGGGAAA-GGG-AAGGGATAGGG
1 GAAA-GGGAAAGGGGAAAGGGATAGGA
**
13352327 GAAAGGGGTAGGGGAAAGGGA-AGGA
1 GAAAGGGAAAGGGGAAAGGGATAGGA
13352352 GAAAGGGAAAGGGGAAA
1 GAAAGGGAAAGGGGAAA
13352369 AGAATGGGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 4 0.11
25 25 0.71
26 6 0.17
ACGTcount: A:0.43, C:0.01, G:0.52, T:0.03
Consensus pattern (26 bp):
GAAAGGGAAAGGGGAAAGGGATAGGA
Found at i:13355298 original size:16 final size:16
Alignment explanation
Indices: 13355277--13355309 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
13355267 CAAAGCATTG
13355277 AAAAAACAAGACAGCA
1 AAAAAACAAGACAGCA
13355293 AAAAAACAAGACAGCA
1 AAAAAACAAGACAGCA
13355309 A
1 A
13355310 CAACTCATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.70, C:0.18, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAAAACAAGACAGCA
Found at i:13358023 original size:57 final size:58
Alignment explanation
Indices: 13357931--13358053 Score: 178
Period size: 57 Copynumber: 2.1 Consensus size: 58
13357921 ATAGAAATTG
* * *
13357931 TGAAAATGGATAAATGATAAACATTTGAAAATGAATG-TGATTTTCTCCAAAATAAAAA
1 TGAAAATGGAGAAATGAGAAACATTTGAAAATGAATGCAG-TTTTCTCCAAAATAAAAA
* *
13357989 TGAAAATGGAGAAATG-GAATCATTTGAAAATGAATGCAGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAATGAGAAACATTTGAAAATGAATGCAGTTTTCTCCAAAATAAAAA
13358046 TGAAAATG
1 TGAAAATG
13358054 ACCTGGAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
57 43 0.73
58 16 0.27
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (58 bp):
TGAAAATGGAGAAATGAGAAACATTTGAAAATGAATGCAGTTTTCTCCAAAATAAAAA
Found at i:13363940 original size:39 final size:40
Alignment explanation
Indices: 13363864--13363944 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
13363854 ATTTTCAAAG
13363864 TATGTCAAATTATTATAAAAAAACATTTTTTACATATAGA
1 TATGTCAAATTATTATAAAAAAACATTTTTTACATATAGA
*
13363904 TATGTCAAATTATTAT-AAAAAACATTTTTTAGATATAGA
1 TATGTCAAATTATTATAAAAAAACATTTTTTACATATAGA
13363943 TA
1 TA
13363945 ATGAAACATA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 24 0.60
40 16 0.40
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (40 bp):
TATGTCAAATTATTATAAAAAAACATTTTTTACATATAGA
Found at i:13369528 original size:17 final size:17
Alignment explanation
Indices: 13369502--13369535 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
13369492 TAAGAAATCT
13369502 TAAATTT-AAAATAATA
1 TAAATTTAAAAATAATA
13369518 TAAATTTTAAAAATAATA
1 TAAA-TTTAAAAATAATA
13369536 ATCTGAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 3 0.19
18 9 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTTAAAAATAATA
Found at i:13377707 original size:30 final size:30
Alignment explanation
Indices: 13377644--13377707 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
13377634 ATGTTAATGG
*
13377644 GTGATTGATTTGTCACTTTTCGATACGTTA
1 GTGATTGATTTGTCACTTTTCGATAAGTTA
* *
13377674 GTGATTGATTTGTTATTTTTCGA-AAGTTGA
1 GTGATTGATTTGTCACTTTTCGATAAGTT-A
13377704 GTGA
1 GTGA
13377708 CTAAATTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.47
Consensus pattern (30 bp):
GTGATTGATTTGTCACTTTTCGATAAGTTA
Found at i:13378014 original size:2 final size:2
Alignment explanation
Indices: 13378009--13378063 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
13377999 TTAGTAAGTT
13378009 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
13378051 TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA
13378064 AAAATATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13378129 original size:17 final size:16
Alignment explanation
Indices: 13378096--13378129 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
13378086 TATTTTTAAA
13378096 AAATATATAAAAATAT
1 AAATATATAAAAATAT
*
13378112 AAATATAGTAAGAATAT
1 AAATATA-TAAAAATAT
13378129 A
1 A
13378130 TATAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATATATAAAAATAT
Found at i:13379570 original size:10 final size:10
Alignment explanation
Indices: 13379557--13379592 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
13379547 CATGAATATA
13379557 AAATAATAAT
1 AAATAATAAT
*
13379567 AAATAATAAA
1 AAATAATAAT
13379577 AAATAATAAT
1 AAATAATAAT
13379587 -AATAAT
1 AAATAAT
13379593 GATACAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATAATAAT
Found at i:13379579 original size:20 final size:19
Alignment explanation
Indices: 13379551--13379592 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
13379541 CATGCGCATG
*
13379551 AATATAAAATAATAATAAAT
1 AATAAAAAATAATAAT-AAT
13379571 AATAAAAAATAATAATAAT
1 AATAAAAAATAATAATAAT
13379590 AAT
1 AAT
13379593 GATACAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAAAAAATAATAATAAT
Found at i:13380141 original size:19 final size:19
Alignment explanation
Indices: 13380046--13380126 Score: 108
Period size: 19 Copynumber: 4.1 Consensus size: 19
13380036 AAATTAAATC
*
13380046 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
13380066 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
13380088 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
13380107 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
13380126 T
1 T
13380127 ATAATATTGC
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 38 0.69
22 7 0.13
23 10 0.18
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:13382339 original size:29 final size:30
Alignment explanation
Indices: 13382290--13382353 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 30
13382280 AATCATAAAA
* *
13382290 TAAGGGCTTGTTTAGCTATAA-AAATAGTT
1 TAAGAGCTTGTTTAACTATAAGAAATAGTT
*
13382319 TAAGAGCTTGTTTAAAC-ATAATGTAATAGTT
1 TAAGAGCTTGTTT-AACTATAA-GAAATAGTT
13382350 TAAG
1 TAAG
13382354 GACTTTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 16 0.55
30 2 0.07
31 11 0.38
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (30 bp):
TAAGAGCTTGTTTAACTATAAGAAATAGTT
Found at i:13385124 original size:16 final size:13
Alignment explanation
Indices: 13385088--13385117 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
13385078 TTTACCGACT
13385088 TTAAT-TTTTTTA
1 TTAATATTTTTTA
13385100 TTAATATTTTTTA
1 TTAATATTTTTTA
13385113 TTAAT
1 TTAAT
13385118 CAAATTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTAATATTTTTTA
Found at i:13386071 original size:21 final size:21
Alignment explanation
Indices: 13386047--13386087 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13386037 TAATATATTC
13386047 TTTAGAAATTT-TTTAAAAAAT
1 TTTA-AAATTTCTTTAAAAAAT
*
13386068 TTTATAATTTCTTTAAAAAA
1 TTTAAAATTTCTTTAAAAAA
13386088 AATCTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTAAAATTTCTTTAAAAAAT
Found at i:13394265 original size:13 final size:13
Alignment explanation
Indices: 13394249--13394275 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13394239 TTCACAGCAC
13394249 TTTTCAAAAGTAA
1 TTTTCAAAAGTAA
13394262 TTTTCAAAAGTAA
1 TTTTCAAAAGTAA
13394275 T
1 T
13394276 GAACTAGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTTCAAAAGTAA
Found at i:13398644 original size:13 final size:13
Alignment explanation
Indices: 13398609--13398646 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
13398599 ACCCATTAAG
13398609 ATATAATTAAAAA
1 ATATAATTAAAAA
13398622 AT-T-ATGTAAAAA
1 ATATAAT-TAAAAA
13398634 ATATAATTAAAAA
1 ATATAATTAAAAA
13398647 TTATTTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.09
12 9 0.41
13 9 0.41
14 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (13 bp):
ATATAATTAAAAA
Found at i:13402862 original size:271 final size:271
Alignment explanation
Indices: 13402379--13402931 Score: 953
Period size: 271 Copynumber: 2.0 Consensus size: 271
13402369 CTGCAGCAGT
* *
13402379 AGCACTTGAACTTGTCCTATAAGAAAAATAAACAAAAGTGGAAACATTATACAGAAGTTAAACCA
1 AGCACTTGAACTCGTCCTATAAGAAAAACAAACAAAAGTGGAAACATTATACAGAAGTTAAACCA
*
13402444 AAAACTATTTCATACATTCAATAAGAAATTTAACAACATTTTTATTGAAGACTTCTTAAAGAATA
66 AAAACTATTTCATACATTCAATAAGAAATTTAACAACATTTTTATTGAAGACTGCTTAAAGAATA
* * *
13402509 TAGAAGAAATAATAACATTTTTAGTAAAGAAATACAGAGACGATAATAACATGCACAAGGGTGCT
131 TAGAAGAAACAATAACATTTTTAGTAAAGAAATACAGAGACGATAATAACAAGCACAAGGATGCT
13402574 ACCCTGTAAACAGTAAAGAGGTACAAAGGAATAGTTCCTATAGTCTAAAACATCAAAAGGCTCTA
196 ACCCTGTAAACAGTAAAGAGGTACAAAGGAATAGTTCCTATAGTCTAAAACATCAAAAGGCTCTA
13402639 AAAATGTTTCA
261 AAAATGTTTCA
* * **
13402650 AGCACTTGAACTCGTCCTGTAAGAAAAACAAACAAAAGTGGAGACATTATACAGAAGTTATGCCA
1 AGCACTTGAACTCGTCCTATAAGAAAAACAAACAAAAGTGGAAACATTATACAGAAGTTAAACCA
* * *
13402715 AAAACTATTTTATACATTCAATAAGAAATTTCACAACATTTTTATTGAAGACTGCTTAAAGAATT
66 AAAACTATTTCATACATTCAATAAGAAATTTAACAACATTTTTATTGAAGACTGCTTAAAGAATA
* * *
13402780 TAGAAGAAACAATACCATTTTTAGTAAAGAAATACAGAGACGATACTAACAAGCACATGGATGCT
131 TAGAAGAAACAATAACATTTTTAGTAAAGAAATACAGAGACGATAATAACAAGCACAAGGATGCT
13402845 ACCCTGTAAACAGTAAAGAGGTACAAAGGAATAGTTCCTATAGTCTAAAACATCAAAAGGCTCTA
196 ACCCTGTAAACAGTAAAGAGGTACAAAGGAATAGTTCCTATAGTCTAAAACATCAAAAGGCTCTA
13402910 AAAATGTTTCA
261 AAAATGTTTCA
*
13402921 AGCACTAGAAC
1 AGCACTTGAAC
13402932 CTCCAAAAAT
Statistics
Matches: 265, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
271 265 1.00
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.25
Consensus pattern (271 bp):
AGCACTTGAACTCGTCCTATAAGAAAAACAAACAAAAGTGGAAACATTATACAGAAGTTAAACCA
AAAACTATTTCATACATTCAATAAGAAATTTAACAACATTTTTATTGAAGACTGCTTAAAGAATA
TAGAAGAAACAATAACATTTTTAGTAAAGAAATACAGAGACGATAATAACAAGCACAAGGATGCT
ACCCTGTAAACAGTAAAGAGGTACAAAGGAATAGTTCCTATAGTCTAAAACATCAAAAGGCTCTA
AAAATGTTTCA
Found at i:13418424 original size:9 final size:9
Alignment explanation
Indices: 13418406--13418463 Score: 82
Period size: 9 Copynumber: 6.4 Consensus size: 9
13418396 TTTGGTTAAA
13418406 AATTAACCG
1 AATTAACCG
*
13418415 AATTATCCG
1 AATTAACCG
13418424 AATTAACCG
1 AATTAACCG
13418433 AATT-ACCTG
1 AATTAACC-G
13418442 AATTAACCG
1 AATTAACCG
*
13418451 AATTAACCT
1 AATTAACCG
13418460 AATT
1 AATT
13418464 GAATCATACA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
8 3 0.07
9 38 0.86
10 3 0.07
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:13428597 original size:30 final size:31
Alignment explanation
Indices: 13428512--13428600 Score: 80
Period size: 30 Copynumber: 2.9 Consensus size: 31
13428502 TTTTAAATAT
* *
13428512 AAATTATA-TATTCAAATTAAAAT-TTATAA
1 AAATTATATTATACATATTAAAATATTATAA
*
13428541 ATAATTAATATTA-A-TTATTTACAAATATT-TAA
1 A-AATT-ATATTATACATA-TTA-AAATATTATAA
13428573 AAATTATATTATACATATTAAAATATTA
1 AAATTATATTATACATATTAAAATATTA
13428601 ATAATAAGTT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
29 1 0.02
30 18 0.38
31 14 0.30
32 12 0.26
33 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
AAATTATATTATACATATTAAAATATTATAA
Found at i:13445404 original size:6 final size:6
Alignment explanation
Indices: 13445393--13445444 Score: 52
Period size: 6 Copynumber: 8.5 Consensus size: 6
13445383 ATTTTTTAAA
* * *
13445393 AATTTT AATTTT AATTTT AATATTAT TATTTT -ATTTT AATATT AATATT
1 AATTTT AATTTT AATTTT AAT-TT-T AATTTT AATTTT AATTTT AATTTT
13445442 AAT
1 AAT
13445445 ATAAAATTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 5 0.12
6 29 0.71
7 4 0.10
8 3 0.07
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
AATTTT
Found at i:13445430 original size:19 final size:19
Alignment explanation
Indices: 13445374--13445441 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
13445364 AATTTAAATT
*
13445374 TATTATTATATTT-TTTAAA
1 TATTATTAT-TTTATTTTAA
*
13445393 AATT-TTAATTTTAATTTTAA
1 TATTATT-ATTTT-ATTTTAA
13445413 TATTATTATTTTATTTTAA
1 TATTATTATTTTATTTTAA
*
13445432 TATTAATATT
1 TATTATTATT
13445442 AATATAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
18 5 0.12
19 21 0.51
20 13 0.32
21 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATTATTTTATTTTAA
Found at i:13445430 original size:25 final size:26
Alignment explanation
Indices: 13445394--13445442 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
13445384 TTTTTTAAAA
*
13445394 ATTTTAATTTTAATTTTAATATTATT
1 ATTTTAATTTTAATATTAATATTATT
13445420 ATTTT-ATTTTAATATTAATATTA
1 ATTTTAATTTTAATATTAATATTA
13445443 ATATAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTTAATTTTAATATTAATATTATT
Found at i:13448750 original size:9 final size:9
Alignment explanation
Indices: 13448733--13448769 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
13448723 TGAGTTTTCG
13448733 AATTCGAAT
1 AATTCGAAT
*
13448742 AACTCGAAT
1 AATTCGAAT
13448751 AATTCGAAT
1 AATTCGAAT
13448760 AATTCGAAT
1 AATTCGAAT
13448769 A
1 A
13448770 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:13449896 original size:10 final size:10
Alignment explanation
Indices: 13449878--13449907 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
13449868 AGAGGTAAAA
13449878 AAACAAATTT
1 AAACAAATTT
*
13449888 AACCAAATTT
1 AAACAAATTT
13449898 AAACAAATTT
1 AAACAAATTT
13449908 TTAACATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (10 bp):
AAACAAATTT
Found at i:13455587 original size:2 final size:2
Alignment explanation
Indices: 13455541--13455568 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13455531 GCTGCATTCA
13455541 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
13455569 TAAAGTGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13460336 original size:19 final size:20
Alignment explanation
Indices: 13460300--13460341 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
13460290 AAATGATATT
13460300 TATTTATTTATAAATATTTTA
1 TATTTATTTAT-AATATTTTA
*
13460321 TATTTATTTAT-GTATTTTA
1 TATTTATTTATAATATTTTA
13460340 TA
1 TA
13460342 AATATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
21 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TATTTATTTATAATATTTTA
Found at i:13463448 original size:19 final size:21
Alignment explanation
Indices: 13463392--13463453 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 21
13463382 TCTACGAATC
*
13463392 ATATCTCTAAGATTACATTTATT
1 ATATCTCTAAGATTACA--TAGT
*
13463415 ATATCTTCTACGATTACA-AGT
1 ATATC-TCTAAGATTACATAGT
*
13463436 -TATCTCTAAGATTGCATA
1 ATATCTCTAAGATTACATA
13463454 TATTTCACTT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 10 0.30
20 5 0.15
21 2 0.06
23 5 0.15
24 11 0.33
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (21 bp):
ATATCTCTAAGATTACATAGT
Found at i:13466615 original size:23 final size:23
Alignment explanation
Indices: 13466585--13466638 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
13466575 CACCTAAGGC
13466585 CTTCTGACTCTTCAGCCGCCGCT
1 CTTCTGACTCTTCAGCCGCCGCT
13466608 CTTCTGACTCTTCAGCCGCCGCT
1 CTTCTGACTCTTCAGCCGCCGCT
13466631 CTTCTGAC
1 CTTCTGAC
13466639 CGACGCCGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.09, C:0.43, G:0.17, T:0.31
Consensus pattern (23 bp):
CTTCTGACTCTTCAGCCGCCGCT
Found at i:13467668 original size:3 final size:3
Alignment explanation
Indices: 13467651--13467691 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
13467641 TATTTCAATG
* *
13467651 TTA TTA TCA TGA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13467692 TATACTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:13470069 original size:4 final size:4
Alignment explanation
Indices: 13470060--13470097 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
13470050 CATTAGCTTG
* *
13470060 ATTT ATTT ATTC ATTT ATTT ATTT ACTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
13470098 CCATTATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (4 bp):
ATTT
Found at i:13471144 original size:109 final size:109
Alignment explanation
Indices: 13471014--13471323 Score: 507
Period size: 109 Copynumber: 2.9 Consensus size: 109
13471004 TCAACAAAGG
* * *
13471014 CAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCTCTAATGTGCTGGGTTTCGATTTTTCTTGT
1 CAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGT
13471079 TCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATAAGA
66 TCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATAAGA
* * *
13471123 CAATGTTTTGCGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTACGATTTTTCTCAT
1 CAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGT
13471188 TCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATAAGA
66 TCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATAAGA
** *
13471232 CAATGTTTTATGTTTGGAAATTCGAGAAAACGTGCCCTAATATGCTGGGTTTCGA--TTTCTCGT
1 CAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGT
* *
13471295 TCGATCAAATAGCCAAATATCCTCTTAAA
66 TCGACCAAATAGCCAAATATCCTTTTAAA
13471324 TCTTAATCCA
Statistics
Matches: 187, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
107 34 0.18
109 153 0.82
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (109 bp):
CAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCTCGT
TCGACCAAATAGCCAAATATCCTTTTAAAAATTTCAAAATAAGA
Found at i:13483685 original size:16 final size:17
Alignment explanation
Indices: 13483651--13483690 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
13483641 CCTACTCCCT
13483651 CCCAATTTAAAACCCAG
1 CCCAATTTAAAACCCAG
*
13483668 CCCAATTT-AAATCCAG
1 CCCAATTTAAAACCCAG
13483684 -CCAATTT
1 CCCAATTT
13483691 TCTCTTAGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 8 0.36
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.25
Consensus pattern (17 bp):
CCCAATTTAAAACCCAG
Found at i:13487307 original size:24 final size:24
Alignment explanation
Indices: 13487252--13487310 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
13487242 GGTTTAATGC
* *
13487252 AAATGGAGATATTTTGGAGAGATG
1 AAATGGATATATTTTGGAAAGATG
13487276 AAATGGATATATTTTGGAAAGATG
1 AAATGGATATATTTTGGAAAGATG
13487300 AAATGGATATA
1 AAATGGATATA
13487311 AATGGAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (24 bp):
AAATGGATATATTTTGGAAAGATG
Found at i:13487382 original size:17 final size:17
Alignment explanation
Indices: 13487360--13487457 Score: 61
Period size: 17 Copynumber: 5.4 Consensus size: 17
13487350 AATTCAAGAC
13487360 TTATGTAATATTTTTAA
1 TTATGTAATATTTTTAA
* ***
13487377 TTATGTAGTGATTCAAAGA
1 TTATGTAAT-ATTTTTA-A
13487396 CTTATGTAATATTTTTAA
1 -TTATGTAATATTTTTAA
* ** *
13487414 TTATGTAGTGATTCAAATAT
1 TTATGTAAT-ATT--TTTAA
*
13487434 TTATGTAATGTTTTTAA
1 TTATGTAATATTTTTAA
13487451 TTATGTA
1 TTATGTA
13487458 GTGATTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 12
0.67 0.20 0.14
Matches are distributed among these distances:
17 25 0.43
18 8 0.14
19 7 0.12
20 18 0.31
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.51
Consensus pattern (17 bp):
TTATGTAATATTTTTAA
Found at i:13487405 original size:37 final size:37
Alignment explanation
Indices: 13487351--13487463 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
13487341 TTATGTGTTA
13487351 ATTC-AAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
13487387 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
* * *
13487424 ATTCAAATATTTATGTAATGTTTTTAATTATGTAGTG
1 ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
13487461 ATT
1 ATT
13487464 TAATTCGGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 4 0.05
37 69 0.95
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (37 bp):
ATTCAAAGACTTATGTAATATTTTTAATTATGTAGTG
Found at i:13487478 original size:9 final size:9
Alignment explanation
Indices: 13487464--13487591 Score: 132
Period size: 9 Copynumber: 13.6 Consensus size: 9
13487454 TGTAGTGATT
13487464 TAATTCGGG
1 TAATTCGGG
13487473 TAATTCGGG
1 TAATTCGGG
13487482 TAATTTTCGGG
1 TAA--TTCGGG
13487493 TAATTCGGG
1 TAATTCGGG
*
13487502 TAATTTGGG
1 TAATTCGGG
*
13487511 TAATTTTTGGG
1 TAA--TTCGGG
13487522 TAATTCGGG
1 TAATTCGGG
13487531 TAATTTTCGGG
1 TAA--TTCGGG
13487542 TAATTCGGG
1 TAATTCGGG
*
13487551 TAAGTCGGG
1 TAATTCGGG
* *
13487560 TAAGTAGGG
1 TAATTCGGG
*
13487569 TAAGTCGGG
1 TAATTCGGG
13487578 TAAGTT-GGG
1 TAA-TTCGGG
13487587 TAATT
1 TAATT
13487592 TTTAACCAAA
Statistics
Matches: 106, Mismatches: 6, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
8 2 0.02
9 76 0.72
10 1 0.01
11 27 0.25
ACGTcount: A:0.23, C:0.07, G:0.34, T:0.37
Consensus pattern (9 bp):
TAATTCGGG
Found at i:13487492 original size:20 final size:18
Alignment explanation
Indices: 13487464--13487591 Score: 132
Period size: 20 Copynumber: 6.8 Consensus size: 18
13487454 TGTAGTGATT
13487464 TAATTCGGGTAATTCGGG
1 TAATTCGGGTAATTCGGG
13487482 TAATTTTCGGGTAATTCGGG
1 TAA--TTCGGGTAATTCGGG
* *
13487502 TAATTTGGGTAATTTTTGGG
1 TAATTCGGGTAA--TTCGGG
13487522 TAATTCGGGTAATTTTCGGG
1 TAATTCGGGTAA--TTCGGG
*
13487542 TAATTCGGGTAAGTCGGG
1 TAATTCGGGTAATTCGGG
* * *
13487560 TAAGTAGGGTAAGTCGGG
1 TAATTCGGGTAATTCGGG
13487578 TAAGTT-GGGTAATT
1 TAA-TTCGGGTAATT
13487592 TTTAACCAAA
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
18 42 0.44
19 1 0.01
20 53 0.55
ACGTcount: A:0.23, C:0.07, G:0.34, T:0.37
Consensus pattern (18 bp):
TAATTCGGGTAATTCGGG
Found at i:13487506 original size:29 final size:27
Alignment explanation
Indices: 13487464--13487591 Score: 132
Period size: 29 Copynumber: 4.5 Consensus size: 27
13487454 TGTAGTGATT
13487464 TAATTCGGGTAATTCGGGTAATTTTCGGG
1 TAATTCGGGTAATTCGGGTAA--TTCGGG
* *
13487493 TAATTCGGGTAATTTGGGTAATTTTTGGG
1 TAATTCGGGTAATTCGGGTAA--TTCGGG
13487522 TAATTCGGGTAATTTTCGGGTAATTCGGG
1 TAATTCGGGTAA--TTCGGGTAATTCGGG
* * * *
13487551 TAAGTCGGGTAAGTAGGGTAAGTCGGG
1 TAATTCGGGTAATTCGGGTAATTCGGG
13487578 TAAGTT-GGGTAATT
1 TAA-TTCGGGTAATT
13487592 TTTAACCAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
27 22 0.26
28 1 0.01
29 55 0.64
31 8 0.09
ACGTcount: A:0.23, C:0.07, G:0.34, T:0.37
Consensus pattern (27 bp):
TAATTCGGGTAATTCGGGTAATTCGGG
Found at i:13488120 original size:10 final size:12
Alignment explanation
Indices: 13488090--13488130 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
13488080 ATTTTATAAA
13488090 ATTTTTTA-TAT
1 ATTTTTTAGTAT
*
13488101 ATTCTTTAGT-T
1 ATTTTTTAGTAT
13488112 -TTTTTTAGTAT
1 ATTTTTTAGTAT
13488123 ATTTTTTA
1 ATTTTTTA
13488131 AAATTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (12 bp):
ATTTTTTAGTAT
Found at i:13488177 original size:18 final size:18
Alignment explanation
Indices: 13488156--13488194 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
13488146 TTTTAAAAAA
*
13488156 TATAAATTTTGAAAGTTT
1 TATAAATATTGAAAGTTT
* *
13488174 TATAAATATTGTAATTTT
1 TATAAATATTGAAAGTTT
13488192 TAT
1 TAT
13488195 TGAGAGAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (18 bp):
TATAAATATTGAAAGTTT
Found at i:13488509 original size:11 final size:11
Alignment explanation
Indices: 13488493--13488532 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
13488483 GTTGTTGCGG
*
13488493 AAAAGAAAAGA
1 AAAAGAAGAGA
13488504 AAAAG-AGAGA
1 AAAAGAAGAGA
*
13488514 AAAAGAGGAGA
1 AAAAGAAGAGA
13488525 AAAAGAAG
1 AAAAGAAG
13488533 GTATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:13488595 original size:19 final size:21
Alignment explanation
Indices: 13488557--13488595 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
13488547 AATAATTGAT
*
13488557 TATATTGTTGTTACTATTTTG
1 TATATTGTTGTTAATATTTTG
13488578 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
13488596 TTGTTTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.64
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:13488657 original size:3 final size:3
Alignment explanation
Indices: 13488641--13488675 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
13488631 AAAATAATAG
*
13488641 TAT TAGT TAG TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT T
13488676 GTTGTTGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:13488680 original size:3 final size:3
Alignment explanation
Indices: 13488674--13488720 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
13488664 ATTATTATTA
13488674 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
13488721 AGTATTAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:13489570 original size:14 final size:15
Alignment explanation
Indices: 13489548--13489624 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
13489538 CAATCAAACA
13489548 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
13489562 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
13489577 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
13489597 CCA-AAAATCATTTT
1 CCAGAAAATCATTTT
* *
13489611 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
13489625 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.40
15 16 0.32
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:13489608 original size:34 final size:35
Alignment explanation
Indices: 13489552--13489618 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
13489542 CAAACACCAG
* *
13489552 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
*
13489587 AAAACATTTTCCA-AAAATCATTTTACGGAAAA
1 AAAACATTTTCCAGAAAATCATTTTACAGAAAA
13489619 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGAAAATCATTTTACAGAAAAGT
Found at i:13490152 original size:18 final size:18
Alignment explanation
Indices: 13490129--13490166 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
13490119 GGTTGGTGGT
*
13490129 GAAGAAGAATGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
13490147 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
13490165 GA
1 GA
13490167 TCATTGGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.08, G:0.45, T:0.13
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:13492295 original size:21 final size:21
Alignment explanation
Indices: 13492269--13492311 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
13492259 ATAGCCGAAA
13492269 TAAATGCCCTAACCGAAACTT
1 TAAATGCCCTAACCGAAACTT
13492290 TAAATGCCCTAACCGAAACTT
1 TAAATGCCCTAACCGAAACTT
13492311 T
1 T
13492312 CATGCTGGTC
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:0.37, C:0.28, G:0.09, T:0.26
Consensus pattern (21 bp):
TAAATGCCCTAACCGAAACTT
Found at i:13494879 original size:24 final size:22
Alignment explanation
Indices: 13494835--13494877 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
13494825 GTTTTTTTTG
*
13494835 ATATATTTTGGTAAATAAAAAT
1 ATATATATTGGTAAATAAAAAT
13494857 ATATATATTGGTAAATAAAAA
1 ATATATATTGGTAAATAAAAA
13494878 AAACTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (22 bp):
ATATATATTGGTAAATAAAAAT
Found at i:13495677 original size:34 final size:35
Alignment explanation
Indices: 13495629--13495758 Score: 97
Period size: 37 Copynumber: 3.6 Consensus size: 35
13495619 AAAATACCTT
13495629 TTCTT-TTCTTTTCTTTTTTTTTCCTTCC-TTCCATC
1 TTCTTCTTC-TTTCTTTTTTTTTCCTTCCATTCC-TC
* * *
13495664 TTCTTCTTC-TTC-TTCTTTTTCTCTTCTCATTTCTTT
1 TTCTTCTTCTTTCTTTTTTTTTC-CTTC-CA-TTCCTC
* * *
13495700 TTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTT
1 TTC-TT-CTTCTTTCTTT-TTTTTTCCT-TCCATTCCTC
13495739 TTCTTCTTCTTTCTTTTTTT
1 TTCTTCTTCTTTCTTTTTTT
13495759 CTCTTCTCCT
Statistics
Matches: 77, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
33 8 0.10
34 7 0.09
35 6 0.08
36 11 0.14
37 16 0.21
38 6 0.08
39 11 0.14
40 4 0.05
41 8 0.10
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.71
Consensus pattern (35 bp):
TTCTTCTTCTTTCTTTTTTTTTCCTTCCATTCCTC
Found at i:13495697 original size:18 final size:17
Alignment explanation
Indices: 13495676--13495796 Score: 83
Period size: 18 Copynumber: 6.9 Consensus size: 17
13495666 CTTCTTCTTC
13495676 TTCTTTTTCTCTTCTCAT
1 TTCTTTTTCTCTTCTC-T
13495694 TTCTTTTTCTTTCCTTCTTTCT
1 TTCTTTTTC--T-CTTC--TCT
13495716 TTCTTTTT-TCTTCTCCT
1 TTCTTTTTCTCTTCT-CT
*
13495733 TTCCTTTTCTTCTTCT-T
1 TTCTTTTTC-TCTTCTCT
*
13495750 TCTTTTTTTCTCTTCTCCT
1 T-TCTTTTTCTCTTCT-CT
*
13495769 TTCCTTTTCT-TTC-C-
1 TTCTTTTTCTCTTCTCT
13495783 TTCTTTTTCT-TTCT
1 TTCTTTTTCTCTTCT
13495797 TTCCCTCTCC
Statistics
Matches: 85, Mismatches: 6, Indels: 27
0.72 0.05 0.23
Matches are distributed among these distances:
14 12 0.14
15 1 0.01
16 1 0.01
17 20 0.24
18 26 0.31
19 9 0.11
20 1 0.01
21 4 0.05
22 9 0.11
23 2 0.02
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (17 bp):
TTCTTTTTCTCTTCTCT
Found at i:13495704 original size:36 final size:39
Alignment explanation
Indices: 13495669--13495794 Score: 183
Period size: 36 Copynumber: 3.4 Consensus size: 39
13495659 CCATCTTCTT
* *
13495669 CTTC-TTCTTCTTTTTCTCTTCTCATTTCTTTTTCTTTC
1 CTTCTTTCTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTC
13495707 CTTCTTTCTTTCTTTTT-TCTTCTCCTTTCCTTTTC-TT-
1 CTTCTTTC-TTCTTTTTCTCTTCTCCTTTCCTTTTCTTTC
13495744 CTTCTTTCTT-TTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTC
13495782 CTTCTTT-TTCTTT
1 CTTCTTTCTTCTTT
13495795 CTTTCCCTCT
Statistics
Matches: 80, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
35 5 0.06
36 20 0.25
37 12 0.15
38 16 0.20
39 19 0.24
40 8 0.10
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (39 bp):
CTTCTTTCTTCTTTTTCTCTTCTCCTTTCCTTTTCTTTC
Found at i:13495744 original size:55 final size:56
Alignment explanation
Indices: 13495625--13495756 Score: 146
Period size: 55 Copynumber: 2.4 Consensus size: 56
13495615 AAAAAAAATA
* * *
13495625 CCTTTTCTTTTCTTTTCTTTTTTTTTCCTTCCTTCCATCTTCTTCTTCTTCTTCTTT
1 CCTTTTCTTCTC-TTTCTTTTTCTTTCCTTCCTTCCATCTTCTTCTTCTTCTCCTTT
* * **
13495682 --TTCTCTTCTCATTTCTTTTTCTTTCCTTCTTTCTTTCTT-TT-TTCTTCTCCTTT
1 CCTTTTCTTCTC-TTTCTTTTTCTTTCCTTCCTTCCATCTTCTTCTTCTTCTCCTTT
13495735 CCTTTTCTTCTTCTTTCTTTTT
1 CCTTTTCTTC-TCTTTCTTTTT
13495757 TTCTCTTCTC
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
53 11 0.17
54 2 0.03
55 48 0.76
56 2 0.03
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70
Consensus pattern (56 bp):
CCTTTTCTTCTCTTTCTTTTTCTTTCCTTCCTTCCATCTTCTTCTTCTTCTCCTTT
Found at i:13495806 original size:75 final size:75
Alignment explanation
Indices: 13495625--13495808 Score: 238
Period size: 75 Copynumber: 2.5 Consensus size: 75
13495615 AAAAAAAATA
*
13495625 CCTTTTCTTTTCTT-TTCTTT-TTTTTTCCT-TCC-TTCCATCTTCTTCTTCTTCTTCTTTTTCT
1 CCTTTTCTTTCCTTCTTCTTTCTTTTTTCCTCTCCTTTCCATCTTCTTCTTCTTCTTCTTTTTCT
13495686 CTTCTCATTT
66 CTTCTCATTT
* * *
13495696 CTTTTTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCCTTTCC-TTTTCTTCTTCTTTCTT-TTTTT
1 CCTTTTCTTTCCTTC-TTCTTTCTTTTTTCCTCTCCTTTCCATCTTCTTCTTC-TTCTTCTTTTT
*
13495759 CTCTTCTCCTTT
64 CTCTTCTCATTT
13495771 CCTTTTCTTTCCTTCTT-TTTCTTTCTTTCCCTCTCCTT
1 CCTTTTCTTTCCTTCTTCTTTCTTT-TTT-CCTCTCCTT
13495809 CTGGTCCCCC
Statistics
Matches: 98, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
71 12 0.12
73 13 0.13
74 13 0.13
75 51 0.52
76 9 0.09
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (75 bp):
CCTTTTCTTTCCTTCTTCTTTCTTTTTTCCTCTCCTTTCCATCTTCTTCTTCTTCTTCTTTTTCT
CTTCTCATTT
Found at i:13495808 original size:34 final size:36
Alignment explanation
Indices: 13495698--13495808 Score: 113
Period size: 37 Copynumber: 3.1 Consensus size: 36
13495688 TCTCATTTCT
*
13495698 TTTTCTTTCCTTCTTTCTTTCTTT-TTT-CTTCTCC
1 TTTTCTTTCCTTCTTTCTTTCTTTCTTTCCCTCTCC
* * *
13495732 TTTCCTTTTCTTCTTCTTTCTTTTTTTCTCTTCTCCTTTCC
1 TTTTC-TTTC--CTTCTTTCTTTCTTTCT-TTC-CCTCTCC
13495773 TTTTCTTTCCTTC-TT-TTTCTTTCTTTCCCTCTCC
1 TTTTCTTTCCTTCTTTCTTTCTTTCTTTCCCTCTCC
13495807 TT
1 TT
13495809 CTGGTCCCCC
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
34 12 0.19
35 7 0.11
36 8 0.13
37 16 0.25
38 5 0.08
39 2 0.03
40 4 0.06
41 9 0.14
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTTCTTTCCTTCTTTCTTTCTTTCTTTCCCTCTCC
Found at i:13495880 original size:27 final size:27
Alignment explanation
Indices: 13495842--13495911 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
13495832 CCCTAATAAA
13495842 CATTGGTGCCGCCAATGG-TATTGGCAC
1 CATTGGTGCCGCCAATGGCT-TTGGCAC
13495869 CATTGGTGCCGCCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCTTTGGCAC
*
13495896 CTTTGGTGCCGCCAAT
1 CATTGGTGCCGCCAAT
13495912 CCCATTGGCG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCTTTGGCAC
Found at i:13495919 original size:27 final size:27
Alignment explanation
Indices: 13495842--13495920 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
13495832 CCCTAATAAA
*
13495842 CATTGGTGCCGCCAATGGTATTGGCAC
1 CATTGGTGCCGCCAATGGCATTGGCAC
*
13495869 CATTGGTGCCGCCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCATTGGCAC
* **
13495896 CTTTGGTGCCGCCAATCCCATTGGC
1 CATTGGTGCCGCCAATGGCATTGGC
13495921 GTGACCAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.27
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCATTGGCAC
Found at i:13496025 original size:21 final size:20
Alignment explanation
Indices: 13495984--13496024 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13495974 TTTTTTTGAT
13495984 ATATTTTGGTAAATAAAAAA
1 ATATTTTGGTAAATAAAAAA
13496004 ATATTTTGGTAAATAAAAAA
1 ATATTTTGGTAAATAAAAAA
13496024 A
1 A
13496025 AGTTATAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (20 bp):
ATATTTTGGTAAATAAAAAA
Found at i:13501005 original size:34 final size:35
Alignment explanation
Indices: 13500961--13501045 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 35
13500951 ATACTGTGCC
* * *
13500961 TTGGTATGGTGTAGTTATCGCTCTGTCGAGTTAT-
1 TTGGTGTGGTGTAGTTATCGCTCTGTCAAGCTATA
13500995 TTGGTGTGGTGTAGTTATCGCTCTGTCAAGCTATA
1 TTGGTGTGGTGTAGTTATCGCTCTGTCAAGCTATA
*
13501030 TT-GTGTAGTGTAGTTA
1 TTGGTGTGGTGTAGTTA
13501046 CCTGTGTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 44 0.96
35 2 0.04
ACGTcount: A:0.16, C:0.11, G:0.29, T:0.44
Consensus pattern (35 bp):
TTGGTGTGGTGTAGTTATCGCTCTGTCAAGCTATA
Found at i:13501861 original size:15 final size:17
Alignment explanation
Indices: 13501829--13501862 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13501819 TTAAACTTAT
13501829 AGATGGTTATATTGGTA
1 AGATGGTTATATTGGTA
13501846 AGATGGTTA-A-TGGTA
1 AGATGGTTATATTGGTA
13501861 AG
1 AG
13501863 TGATAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (17 bp):
AGATGGTTATATTGGTA
Found at i:13506126 original size:2 final size:2
Alignment explanation
Indices: 13506115--13506147 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13506105 ATATGTGAAT
13506115 TA TA -A 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
13506148 AAATACCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13506164 original size:15 final size:12
Alignment explanation
Indices: 13506113--13506181 Score: 57
Period size: 15 Copynumber: 5.1 Consensus size: 12
13506103 GCATATGTGA
13506113 ATTATAATATATAT
1 ATTATAA-A-ATAT
*
13506127 ATATATATATATAT
1 AT-TATA-AAATAT
13506141 ATATATAAAATACCT
1 AT-TATAAAATA--T
13506156 ATGTATAAAATAT
1 AT-TATAAAATAT
13506169 ATTATAAAATAT
1 ATTATAAAATAT
13506181 A
1 A
13506182 AAGAATATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
12 11 0.23
13 7 0.15
14 13 0.27
15 16 0.33
16 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (12 bp):
ATTATAAAATAT
Found at i:13506176 original size:12 final size:13
Alignment explanation
Indices: 13506123--13506181 Score: 66
Period size: 15 Copynumber: 4.4 Consensus size: 13
13506113 ATTATAATAT
*
13506123 ATATATATATATAT
1 ATATATATATA-AA
13506137 ATATATATATAAA
1 ATATATATATAAA
*
13506150 ATACCTATGTATAAA
1 ATA--TATATATAAA
13506165 ATATAT-TATAAA
1 ATATATATATAAA
13506177 ATATA
1 ATATA
13506182 AAGAATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
12 11 0.27
13 7 0.17
14 11 0.27
15 12 0.29
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (13 bp):
ATATATATATAAA
Found at i:13506339 original size:2 final size:2
Alignment explanation
Indices: 13506286--13506323 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
13506276 ATTTTAAAAA
* *
13506286 AT AT AT AT AT AT AT AT AT AT AA AT AG 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
13506324 GGGTGCGCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13506557 original size:3 final size:3
Alignment explanation
Indices: 13506535--13506597 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
13506525 AAAATAAAAC
* *
13506535 TAA TAA TATT TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
13506581 TAA TAA TTA TCA TAA TA
1 TAA TAA TAA TAA TAA TA
13506598 CAAAAATAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
3 50 0.96
4 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:13507745 original size:24 final size:24
Alignment explanation
Indices: 13507712--13507758 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
13507702 ATTTGTAAAT
13507712 GGGCTAATTGGGTTTAGTTTGTTG
1 GGGCTAATTGGGTTTAGTTTGTTG
*
13507736 GGGCTGATTGGGTTTAGTTTGTT
1 GGGCTAATTGGGTTTAGTTTGTT
13507759 TGGGTTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.11, C:0.04, G:0.38, T:0.47
Consensus pattern (24 bp):
GGGCTAATTGGGTTTAGTTTGTTG
Found at i:13507916 original size:31 final size:29
Alignment explanation
Indices: 13507881--13507955 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
13507871 TTAATAGCTC
*
13507881 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* * ***
13507912 AGTGACAAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
13507941 AGTGACTAAAATGTA
1 AGTGACTAAAATGTA
13507956 GCCTAAGGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
29 19 0.53
30 1 0.03
31 16 0.44
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:13511604 original size:16 final size:16
Alignment explanation
Indices: 13511582--13511620 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
13511572 CCAATTTAAG
13511582 ATTTAATTTAT-ACATA
1 ATTTAATTT-TGACATA
*
13511598 TTTTAATTTTGACATA
1 ATTTAATTTTGACATA
13511614 ATTTAAT
1 ATTTAAT
13511621 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTAATTTTGACATA
Found at i:13512898 original size:43 final size:43
Alignment explanation
Indices: 13512801--13512912 Score: 147
Period size: 43 Copynumber: 2.6 Consensus size: 43
13512791 ATGCAGGGAC
13512801 ACACGCTCGTGTGGCCAGGCCGTGTGACTCACACGGTCAAAAG
1 ACACGCTCGTGTGGCCAGGCCGTGTGACTCACACGGTCAAAAG
** * * *
13512844 ACACATTCGTGTGGCCAGGTCGTGTGACTCACATGGTCAAGAG
1 ACACGCTCGTGTGGCCAGGCCGTGTGACTCACACGGTCAAAAG
*
13512887 ACACGCCCGTGT--CTCAGGCCGTGTGA
1 ACACGCTCGTGTGGC-CAGGCCGTGTGA
13512913 GCATTTGAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.02
42 11 0.19
43 47 0.80
ACGTcount: A:0.21, C:0.29, G:0.30, T:0.20
Consensus pattern (43 bp):
ACACGCTCGTGTGGCCAGGCCGTGTGACTCACACGGTCAAAAG
Found at i:13516942 original size:71 final size:70
Alignment explanation
Indices: 13516816--13516967 Score: 198
Period size: 71 Copynumber: 2.1 Consensus size: 70
13516806 CTTAAAACTG
* * *
13516816 AATGTATATTCACTATAAACATGAATAGCCGAATGCTTATATACATATATGCTTAACAGATATTA
1 AATGTATATACACTATAAACATGAATAACCGAATGCTTATATACATATA-GCTTAACAAATATTA
**
13516881 GCTCCA
65 GAACCA
* *
13516887 AATGTATATACACTTTGAACATGAATAACCGAATGCATATATATACATATA-CTTAACAAATATT
1 AATGTATATACACTATAAACATGAATAACCGAATGC-T-TATATACATATAGCTTAACAAATATT
*
13516951 ATAACCA
64 AGAACCA
13516958 AATGTATATA
1 AATGTATATA
13516968 TGTATTTATC
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
71 58 0.82
72 1 0.01
73 12 0.17
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.32
Consensus pattern (70 bp):
AATGTATATACACTATAAACATGAATAACCGAATGCTTATATACATATAGCTTAACAAATATTAG
AACCA
Found at i:13517498 original size:41 final size:41
Alignment explanation
Indices: 13517427--13517614 Score: 268
Period size: 41 Copynumber: 4.6 Consensus size: 41
13517417 GCCGGTAATT
* * *
13517427 AGCCTGTTAGACGTAAAGTCCGAAATATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
* * *
13517468 AGCTTGCTAGACATAAAGTCTGAAACATTTCACCTGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
* * *
13517509 AGCCTGCTAGACATAAAGTCCGAAATATTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
* *
13517550 AGCCTGCTAGATGTAAAGTCTGAAACATTTCACCAGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
*
13517591 AGCCTACTAGACGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCTGAA
13517615 TCATCTTTAT
Statistics
Matches: 130, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 130 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAAACATTTCACCGGCATCA
Found at i:13517520 original size:82 final size:82
Alignment explanation
Indices: 13517427--13517610 Score: 305
Period size: 82 Copynumber: 2.2 Consensus size: 82
13517417 GCCGGTAATT
* *
13517427 AGCCTGTTAGACGTAAAGTCCGAAATATTTCACCGGCATCAAGCTTGCTAGACATAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAA
*
13517492 ACATTTCACCTGCATCA
66 ACATTTCACCAGCATCA
* **
13517509 AGCCTGCTAGACATAAAGTCCGAAATATTTCACCGGCATCAAGCCTGCTAGATGTAAAGTCTGAA
1 AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAA
13517574 ACATTTCACCAGCATCA
66 ACATTTCACCAGCATCA
*
13517591 AGCCTACTAGACGTAAAGTC
1 AGCCTGCTAGACGTAAAGTC
13517611 TGAATCATCT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 94 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (82 bp):
AGCCTGCTAGACGTAAAGTCCGAAATATTTCACCGGCATCAAGCCTGCTAGACATAAAGTCTGAA
ACATTTCACCAGCATCA
Found at i:13523431 original size:23 final size:24
Alignment explanation
Indices: 13523399--13523457 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
13523389 TATGTATACT
* *
13523399 AAAATAA-ATATATACATTTAGATA
1 AAAATAATATAT-TACATATAAATA
13523423 AAAATAATA-ATTACATATAAATA
1 AAAATAATATATTACATATAAATA
*
13523446 AATAAAAATATA
1 AA-AATAATATA
13523458 ATTATATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 12 0.41
24 15 0.52
25 2 0.07
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (24 bp):
AAAATAATATATTACATATAAATA
Found at i:13524109 original size:23 final size:22
Alignment explanation
Indices: 13524066--13524123 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
13524056 AAAGGGTATC
* *
13524066 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
13524087 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
13524110 TACATATCATATCT
1 TACAAATCATATCT
13524124 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:13524126 original size:19 final size:19
Alignment explanation
Indices: 13524079--13524168 Score: 99
Period size: 19 Copynumber: 4.4 Consensus size: 19
13524069 AAATTAAATC
*
13524079 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
13524099 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
13524121 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
13524142 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
13524161 TCTAAGAT
1 TCTAAGAT
13524169 AAAAAATTAT
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
19 25 0.41
21 18 0.30
22 7 0.11
23 11 0.18
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:13524139 original size:21 final size:19
Alignment explanation
Indices: 13524102--13524168 Score: 107
Period size: 19 Copynumber: 3.4 Consensus size: 19
13524092 AATCATATCT
*
13524102 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
13524121 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
13524142 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
13524161 TCTAAGAT
1 TCTAAGAT
13524169 AAAAAATTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
19 26 0.58
21 19 0.42
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:13524592 original size:132 final size:132
Alignment explanation
Indices: 13524451--13524861 Score: 678
Period size: 132 Copynumber: 3.1 Consensus size: 132
13524441 GAGGATAAGA
* *
13524451 CTTGCTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* * *
13524516 CACTACTGCTTAGGGAGATAAGATCTACAATCTTTAGCTTACTCCGCTGCTGCTCAGGGAGGCAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
13524581 GG
131 GG
* *
13524583 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAATATAAGATTTGCCGTCTTTGATCTGTTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* *
13524648 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCTGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
13524713 GG
131 GG
* * *
13524715 CTTGATGGCTTAAATCTACTTTCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
* * *
13524780 CACTATTGCTTAGGAAGATAAGATCTACAATCTTCAGCCTACTCCGCTGTTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
13524845 GG
131 GG
*
13524847 CTTGGTGCCTTAAAT
1 CTTGGTGGCTTAAAT
13524862 NNNNNNNNNN
Statistics
Matches: 258, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 258 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTCTTTGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAGCCTACTCCGCTGCTGCTCAGGGAGACAA
GG
Found at i:13528776 original size:15 final size:14
Alignment explanation
Indices: 13528752--13528784 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
13528742 AGCCTCTCCA
13528752 TTTTACTTTTTCAT
1 TTTTACTTTTTCAT
13528766 TTTTCACTTTTTCAT
1 TTTT-ACTTTTTCAT
13528781 TTTT
1 TTTT
13528785 TTCATTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTACTTTTTCAT
Found at i:13528787 original size:17 final size:17
Alignment explanation
Indices: 13528752--13528803 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
13528742 AGCCTCTCCA
13528752 TTTT-ACTTTTTCA--T
1 TTTTCACTTTTTCATTT
13528766 TTTTCACTTTTTCATTT
1 TTTTCACTTTTTCATTT
*
13528783 TTTTCA-TTTCATCATTT
1 TTTTCACTTT-TTCATTT
13528800 TTTT
1 TTTT
13528804 TCGACTCAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 4 0.12
15 9 0.27
16 3 0.09
17 17 0.52
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCACTTTTTCATTT
Found at i:13532781 original size:21 final size:22
Alignment explanation
Indices: 13532752--13532804 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
13532742 ATGTATACTA
*
13532752 AAATAAAT-ATATACATATAGAT
1 AAATAAATAAT-TACATACAGAT
*
13532774 AAA-AAATAATTACATACATAT
1 AAATAAATAATTACATACAGAT
13532795 AAATAAATAA
1 AAATAAATAA
13532805 AAAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATAAATAATTACATACAGAT
Found at i:13532790 original size:25 final size:25
Alignment explanation
Indices: 13532733--13532811 Score: 79
Period size: 25 Copynumber: 3.1 Consensus size: 25
13532723 TTAATATGTG
*
13532733 TACATACATAT-GTATACTAAAATAAA
1 TACATACATATAG-ATA-AAAAATAAA
* *
13532759 TATATACATATAGATAAAAAATAAT
1 TACATACATATAGATAAAAAATAAA
* *
13532784 TACATACATATAAATAAATAAAAAAA
1 TACATACATATAGATAAA-AAATAAA
13532810 TA
1 TA
13532812 ATTATATTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 23 0.52
26 20 0.45
27 1 0.02
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.29
Consensus pattern (25 bp):
TACATACATATAGATAAAAAATAAA
Found at i:13532932 original size:28 final size:27
Alignment explanation
Indices: 13532875--13532932 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
13532865 TATTTTTTTT
* * *
13532875 AAAAATAATTAAATATAAAAAAGAATA
1 AAAAATAATTAAATAAAAAAAAAAAGA
13532902 AAAAACTAATT-AATAAAAAAAATAAAGA
1 AAAAA-TAATTAAATAAAAAAAA-AAAGA
13532930 AAA
1 AAA
13532933 TGAAAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (27 bp):
AAAAATAATTAAATAAAAAAAAAAAGA
Found at i:13533494 original size:21 final size:21
Alignment explanation
Indices: 13533459--13533532 Score: 120
Period size: 19 Copynumber: 3.7 Consensus size: 21
13533449 AATCATATCT
13533459 TCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATATCATA
13533478 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
13533499 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
13533518 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
13533533 CCTCAAAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
19 28 0.55
21 23 0.45
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:13535739 original size:25 final size:25
Alignment explanation
Indices: 13535711--13535832 Score: 147
Period size: 25 Copynumber: 4.9 Consensus size: 25
13535701 ACGAGTTGTA
13535711 AACGGGAAGCTC-TGCTGAGCTGAAT
1 AACGGGAAGCTCATGC-GAGCTGAAT
*
13535736 AACGGGAAGCTCATGCGAGCTGTAT
1 AACGGGAAGCTCATGCGAGCTGAAT
* *
13535761 AACGGGAAGCTCATGCGAGTTGTAT
1 AACGGGAAGCTCATGCGAGCTGAAT
** * *
13535786 AATAGGAAGCTCATGCCAGCTAAAT
1 AACGGGAAGCTCATGCGAGCTGAAT
* *
13535811 AATGGGAAGCTCATGAGAGCTG
1 AACGGGAAGCTCATGCGAGCTG
13535833 TGGTGTGTCT
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
25 81 0.96
26 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.20
Consensus pattern (25 bp):
AACGGGAAGCTCATGCGAGCTGAAT
Found at i:13535769 original size:50 final size:50
Alignment explanation
Indices: 13535695--13535832 Score: 154
Period size: 50 Copynumber: 2.8 Consensus size: 50
13535685 ATTCATATAT
* * *
13535695 GCTCATACGAGTTGTA-AACGGGAAGCTC-TGCTGAGCTGAATAACGGGAA
1 GCTCATGCGAGCTGTATAACGGGAAGCTCATGC-GAGCTGAATAACAGGAA
* * *
13535744 GCTCATGCGAGCTGTATAACGGGAAGCTCATGCGAGTTGTATAATAGGAA
1 GCTCATGCGAGCTGTATAACGGGAAGCTCATGCGAGCTGAATAACAGGAA
* ** * *
13535794 GCTCATGCCAGCTAAATAATGGGAAGCTCATGAGAGCTG
1 GCTCATGCGAGCTGTATAACGGGAAGCTCATGCGAGCTG
13535833 TGGTGTGTCT
Statistics
Matches: 75, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
49 14 0.19
50 58 0.77
51 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.30, T:0.22
Consensus pattern (50 bp):
GCTCATGCGAGCTGTATAACGGGAAGCTCATGCGAGCTGAATAACAGGAA
Found at i:13535818 original size:75 final size:74
Alignment explanation
Indices: 13535695--13535833 Score: 190
Period size: 75 Copynumber: 1.9 Consensus size: 74
13535685 ATTCATATAT
* * * *
13535695 GCTCATACGAGTTGTAAACGGGAAGCTCTGCTGAGCTGAATAACGGGAAGCTCATGCGAGCTGTA
1 GCTCATACGAGTTGTAAACAGGAAGCTCTGCTCAGCTAAATAACGGGAAGCTCATGAGAGCTGTA
13535760 TAACGGGAA
66 TAACGGGAA
* * *
13535769 GCTCATGCGAGTTGTATAATAGGAAGCTCATGC-CAGCTAAATAATGGGAAGCTCATGAGAGCTG
1 GCTCATACGAGTTGTA-AACAGGAAGCTC-TGCTCAGCTAAATAACGGGAAGCTCATGAGAGCTG
13535833 T
64 T
13535834 GGTGTGTCTG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
74 15 0.27
75 38 0.68
76 3 0.05
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.22
Consensus pattern (74 bp):
GCTCATACGAGTTGTAAACAGGAAGCTCTGCTCAGCTAAATAACGGGAAGCTCATGAGAGCTGTA
TAACGGGAA
Found at i:13542068 original size:24 final size:24
Alignment explanation
Indices: 13542047--13542093 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
13542037 AATTCTAATC
*
13542047 AATGTAAAATATATTATGCTAAAA
1 AATGTAAAATATATTATACTAAAA
*
13542071 AATGTTAAATATATTATACTAAA
1 AATGTAAAATATATTATACTAAA
13542094 TCTTCTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.36
Consensus pattern (24 bp):
AATGTAAAATATATTATACTAAAA
Found at i:13542159 original size:35 final size:35
Alignment explanation
Indices: 13542113--13542181 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
13542103 AAGAAAATAT
*
13542113 ATTTTGTTTAACTT-AGCTTGCAAGCAATCTCTTAG
1 ATTTTGTTTAACTTGA-CTTGCAAACAATCTCTTAG
13542148 ATTTTGTTTAACTTGACTTGCAAACAATCTCTTA
1 ATTTTGTTTAACTTGACTTGCAAACAATCTCTTA
13542182 AAATTTGGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (35 bp):
ATTTTGTTTAACTTGACTTGCAAACAATCTCTTAG
Found at i:13547092 original size:2 final size:2
Alignment explanation
Indices: 13547085--13547125 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
13547075 ACATTTCTTT
*
13547085 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13547126 GCACATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.