Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 12 of 230
Found at i:3307373 original size:22 final size:20
Alignment explanation
Indices: 3307332--3307385 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
3307322 AATATTTAAG
3307332 TTATGTAAGTT-T-TTTGTA
1 TTATGTAAGTTATGTTTGTA
3307350 TTATGTAAGTTATGTTATGTTA
1 TTATGTAAGTTATGTT-TG-TA
*
3307372 TTACGTAAGTTATG
1 TTATGTAAGTTATG
3307386 CAAGTTATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 11 0.35
19 1 0.03
20 2 0.06
21 2 0.06
22 15 0.48
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.54
Consensus pattern (20 bp):
TTATGTAAGTTATGTTTGTA
Found at i:3307391 original size:92 final size:93
Alignment explanation
Indices: 3307272--3307488 Score: 209
Period size: 92 Copynumber: 2.3 Consensus size: 93
3307262 ACGTGTATAA
* * * * *
3307272 GTTATG-TATTAAGTAAGCTATGTAAGTTGTGTATTATGTA-AGTT-GTGTCAAA-TATTTAAGT
1 GTTATGTTATTAAGTAAGTTATGCAAGTTATGT-TTAT-AACAGTTAG-GT-AAACTATGTAAGT
3307333 TATGTAAG-T-TTT-TT-GTATTATGTAAGTTAT
62 TATGTAAGTTATTTATTGGTA-TAT-TAAGTTAT
*
3307363 GTTATGTTATTACGTAAGTTATGCAAGTTATGTTTATAACGAGTTAGGTAAACTATGTAAGTTAT
1 GTTATGTTATTAAGTAAGTTATGCAAGTTATGTTTATAAC-AGTTAGGTAAACTATGTAAGTTAT
3307428 GTAAGTTATTTAATTGGTATATTAAGTTAT
65 GTAAGTTATTT-ATTGGTATATTAAGTTAT
* * *
3307458 G-GAAGTTATTATGTAAGTTATGCAAGATTAT
1 GTTATGTTATTAAGTAAGTTATGCAAG-TTAT
3307489 AATATAAGTT
Statistics
Matches: 106, Mismatches: 9, Indels: 18
0.80 0.07 0.14
Matches are distributed among these distances:
90 1 0.01
91 13 0.12
92 44 0.42
93 2 0.02
94 25 0.24
95 13 0.12
96 5 0.05
97 3 0.03
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (93 bp):
GTTATGTTATTAAGTAAGTTATGCAAGTTATGTTTATAACAGTTAGGTAAACTATGTAAGTTATG
TAAGTTATTTATTGGTATATTAAGTTAT
Found at i:3307496 original size:22 final size:21
Alignment explanation
Indices: 3307450--3307501 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
3307440 ATTGGTATAT
* * *
3307450 TAAGTTATGGAAGTTATTATG
1 TAAGTTATGCAAGTTATAATA
3307471 TAAGTTATGCAAGATTATAATA
1 TAAGTTATGCAAG-TTATAATA
3307493 TAAGTTATG
1 TAAGTTATG
3307502 TATTATGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (21 bp):
TAAGTTATGCAAGTTATAATA
Found at i:3307515 original size:8 final size:7
Alignment explanation
Indices: 3307497--3307534 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
3307487 ATAATATAAG
3307497 TTATGTA
1 TTATGTA
3307504 TTATGTTA
1 TTATG-TA
3307512 TTATGTA
1 TTATGTA
3307519 TTATGTA
1 TTATGTA
3307526 --ATGTA
1 TTATGTA
3307531 TTAT
1 TTAT
3307535 CAGATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (7 bp):
TTATGTA
Found at i:3307515 original size:27 final size:26
Alignment explanation
Indices: 3307482--3307554 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
3307472 AAGTTATGCA
*
3307482 AGATTATAATATAAGTTATGTATTATG
1 AGATTAT-ATATAAGTTATGTATTATC
** * * *
3307509 TTATTATGTATTATGTAATGTATTATC
1 AGATTATATA-TAAGTTATGTATTATC
3307536 AGATTATATATAAGTTATG
1 AGATTATATATAAGTTATG
3307555 GAAGTTATTA
Statistics
Matches: 34, Mismatches: 11, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.37, C:0.01, G:0.14, T:0.48
Consensus pattern (26 bp):
AGATTATATATAAGTTATGTATTATC
Found at i:3307571 original size:21 final size:21
Alignment explanation
Indices: 3307546--3307626 Score: 69
Period size: 21 Copynumber: 3.8 Consensus size: 21
3307536 AGATTATATA
*
3307546 TAAGTTATGGAAGTTATTATG
1 TAAGTTATGTAAGTTATTATG
** *
3307567 TAAGTTATACAAGCTTA-TATA
1 TAAGTTATGTAAG-TTATTATG
3307588 TAAGTTATGTATTACGTTATTATG
1 TAAGTTATGTA--A-GTTATTATG
3307612 T-A-TTATGTAAGTTAT
1 TAAGTTATGTAAGTTAT
3307627 GCAAGCTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
19 5 0.10
20 1 0.02
21 23 0.47
22 10 0.20
23 5 0.10
24 5 0.10
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.46
Consensus pattern (21 bp):
TAAGTTATGTAAGTTATTATG
Found at i:3307607 original size:95 final size:95
Alignment explanation
Indices: 3307445--3307621 Score: 311
Period size: 95 Copynumber: 1.9 Consensus size: 95
3307435 ATTTAATTGG
* *
3307445 TATATTAAGTTATGGAAGTTATTATGTAAGTTATGCAAGATTATAATATAAGTTATGTATTATGT
1 TATATTAAGTTATGGAAGTTATTATGTAAGTTATACAAGATTATAATATAAGTTATGTATTACGT
3307510 TATTATGTATTATGTAATGTATTATCAGAT
66 TATTATGTATTATGTAATGTATTATCAGAT
*
3307540 TATATATAAGTTATGGAAGTTATTATGTAAGTTATACAAGCTTAT-ATATAAGTTATGTATTACG
1 TATAT-TAAGTTATGGAAGTTATTATGTAAGTTATACAAGATTATAATATAAGTTATGTATTACG
3307604 TTATTATGTATTATGTAA
65 TTATTATGTATTATGTAA
3307622 GTTATGCAAG
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
95 41 0.53
96 37 0.47
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (95 bp):
TATATTAAGTTATGGAAGTTATTATGTAAGTTATACAAGATTATAATATAAGTTATGTATTACGT
TATTATGTATTATGTAATGTATTATCAGAT
Found at i:3307632 original size:52 final size:52
Alignment explanation
Indices: 3307560--3307668 Score: 166
Period size: 52 Copynumber: 2.1 Consensus size: 52
3307550 TTATGGAAGT
*
3307560 TATTATGTAAGTTATACAAGCTTATATA-TAAGTTATGTATTACGTTATTATG
1 TATTATGTAAGTTATACAAGCTTATATACCAA-TTATGTATTACGTTATTATG
* **
3307612 TATTATGTAAGTTATGCAAGCTTATATACCAATTATGTATTGTGTTATTATG
1 TATTATGTAAGTTATACAAGCTTATATACCAATTATGTATTACGTTATTATG
3307664 TATTA
1 TATTA
3307669 AGTTATATAC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 50 0.96
53 2 0.04
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.47
Consensus pattern (52 bp):
TATTATGTAAGTTATACAAGCTTATATACCAATTATGTATTACGTTATTATG
Found at i:3308975 original size:37 final size:37
Alignment explanation
Indices: 3308925--3309029 Score: 120
Period size: 46 Copynumber: 2.6 Consensus size: 37
3308915 TAGCCACGTT
3308925 TCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTC
1 TCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTC
3308962 TCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTC
1 TCTTGATCAGATAA--GT-G-T--AGC---CACTTATCACTTTGTC
*
3309008 TCTTGATCAGATAAGTATAGCC
1 TCTTGATCAGATAAGTGTAGCC
3309030 GAAGCTATCA
Statistics
Matches: 58, Mismatches: 1, Indels: 18
0.75 0.01 0.23
Matches are distributed among these distances:
37 15 0.26
39 2 0.03
40 4 0.07
41 1 0.02
42 1 0.02
43 3 0.05
44 2 0.03
46 30 0.52
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (37 bp):
TCTTGATCAGATAAGTGTAGCCACTTATCACTTTGTC
Found at i:3309065 original size:52 final size:52
Alignment explanation
Indices: 3308989--3309456 Score: 648
Period size: 52 Copynumber: 9.3 Consensus size: 52
3308979 TAGCTAAAGC
* * *
3308989 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
3309042 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
3309094 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
*
3309146 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
3309192 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
3309244 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
3309296 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
3309342 TATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* ** *
3309388 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
3309440 TATCACTTTATCACTTG
1 TATCACTTT-TCACTTG
3309457 ATCAGAAGTA
Statistics
Matches: 376, Mismatches: 23, Indels: 32
0.87 0.05 0.07
Matches are distributed among these distances:
46 126 0.34
47 2 0.01
48 2 0.01
49 1 0.00
52 227 0.60
53 18 0.05
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:3309120 original size:150 final size:150
Alignment explanation
Indices: 3308957--3309462 Score: 889
Period size: 150 Copynumber: 3.4 Consensus size: 150
3308947 ACTTATCACT
* *
3308957 TTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
3309022 GTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
66 GTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
3309087 TATCACTTATCACTTTCCAC
131 TATCACTTATCACTTTCCAC
*
3309107 TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
3309172 GTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
66 GTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
3309237 TATCACTTATCACTTTCCAC
131 TATCACTTATCACTTTCCAC
*
3309257 TTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
* *
3309322 GTATAGCCGAAGCTATAACTTATCAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGC
66 GTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
3309381 TATTACTTATCACTTTCCAC
131 TATCACTTATCACTTTCCAC
* *
3309401 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACTTGATCAGA
1 TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGA
3309463 AGTACTCAAA
Statistics
Matches: 347, Mismatches: 9, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
144 106 0.31
148 1 0.00
149 3 0.01
150 237 0.68
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (150 bp):
TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAA
GTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
TATCACTTATCACTTTCCAC
Found at i:3309457 original size:98 final size:97
Alignment explanation
Indices: 3308946--3309462 Score: 676
Period size: 98 Copynumber: 5.3 Consensus size: 97
3308936 TAAGTGTAGC
* * **
3308946 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC--T---TTG
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTG
* *
3309006 TCTCTTGATCAGATAAGTATAGCCGAAGCTAT
66 TCACTTGATCAGATAAGTGTAGCCGAAGCTAT
3309038 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CACTTATCAC-TTT-A----TCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
*
3309103 CCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTAT
60 -CACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
3309142 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTT
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC-TTTCACTT
3309207 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
65 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
3309240 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCAC--T
1 CACTTATCACTTT--A----TCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
*
3309303 ---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
60 CACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
3309338 AACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT-CACTT
** *
3309403 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
65 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
3309436 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTATCACTTGATCAGA
3309463 AGTACTCAAA
Statistics
Matches: 377, Mismatches: 23, Indels: 44
0.85 0.05 0.10
Matches are distributed among these distances:
92 49 0.13
93 3 0.01
94 1 0.00
96 1 0.00
98 233 0.62
99 3 0.01
100 1 0.00
101 1 0.00
103 3 0.01
104 82 0.22
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (97 bp):
CACTTATCACTTTATCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTCACTTG
TCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:3311818 original size:36 final size:36
Alignment explanation
Indices: 3311771--3311846 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
3311761 TTTATACCAA
3311771 AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
1 AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
3311807 AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
1 AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
3311843 AAAT
1 AAAT
3311847 TTTGAACAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (36 bp):
AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
Found at i:3312181 original size:52 final size:52
Alignment explanation
Indices: 3312119--3312217 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
3312109 GGTTATGCAA
*
3312119 ATTATTACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
1 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
3312171 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTT
1 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTT
3312218 TCTTATTTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.44
Consensus pattern (52 bp):
ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
Found at i:3312207 original size:26 final size:26
Alignment explanation
Indices: 3312126--3312208 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 26
3312116 CAAATTATTA
3312126 CCTAAAAATGTTCTTACTTTCTTAAC
1 CCTAAAAATGTTCTTACTTTCTTAAC
** * ** * *
3312152 CCT-AATTTGAAT-TTACCGTATTAATA
1 CCTAAAAATG-TTCTTACTTTCTTAA-C
3312178 CCTAAAAATGTTCTTACTTTCTTAAC
1 CCTAAAAATGTTCTTACTTTCTTAAC
3312204 CCTAA
1 CCTAA
3312209 TTTGAATTTT
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
25 13 0.33
26 13 0.33
27 13 0.33
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (26 bp):
CCTAAAAATGTTCTTACTTTCTTAAC
Found at i:3314722 original size:112 final size:113
Alignment explanation
Indices: 3314448--3314996 Score: 673
Period size: 113 Copynumber: 4.9 Consensus size: 113
3314438 TAAATAAATT
* * * *
3314448 TAAATCCCTGAGCATTAGCGGCGCTTTATTAAAAACGCTGCTAAACCCCCTGAAAGCTAAGAAAA
1 TAAAGCCCT-AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAA
* * * * *
3314513 CGGTGTCGTTGGGTTTAATTTTATTTGCGGCGCTTTCATAAAAGCGTCGC
65 CGGCGTCGTTGGGCTTAGTTTT-TTTGCGGCGCTTTCATAAAAACGCCGC
* * * *
3314563 T--AGCCCTAGCATTAGCGGCACATTATTGAAAACGCCACTAAACCCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAAC
* *
3314626 GACGTCGTTGGGCTTAGTTTTTTTGCGGCGCTTT-ATCCAAAACGCCGC
66 GGCGTCGTTGGGCTTAGTTTTTTTGCGGCGCTTTCAT-AAAAACGCCGC
* * * * * * *
3314674 TAAAACCAC-AGCATTAGCGACGCTTTACTAAAAATGCCGCCAAA-CCCCCGAAGGCTAAGAAAA
1 TAAAGCC-CTAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAA
* * * *
3314737 CGGTGTCGTTGGGTTTAATTTTTTTTGCGGTGCTTTCATAAAAACGCCGC
65 CGGCGTCGTTGGGCTT-AGTTTTTTTGCGGCGCTTTCATAAAAACGCCGC
* *
3314787 TAAAGCCCTAGCATTAGCGGCGCATTATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAAC
* * *
3314852 GGCATCGTTGAGCTTAGTTTTTTTGCGGCGC-TTGATCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGTTTTTTTGCGGCGCTTTCAT-AAAAACGCCGC
* *
3314900 TAAAGCCCTCAGCATTAGCGACGCTTTACTAAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAA
1 TAAAGCCCT-AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAA
*
3314965 CGGCGTCGTTGGGCTTA--TTTTTTGTGGCGCTT
65 CGGCGTCGTTGGGCTTAGTTTTTTTGCGGCGCTT
3314997 CTTATTTTCA
Statistics
Matches: 368, Mismatches: 55, Indels: 24
0.82 0.12 0.05
Matches are distributed among these distances:
110 2 0.01
111 22 0.06
112 113 0.31
113 132 0.36
114 98 0.27
115 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (113 bp):
TAAAGCCCTAGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGTTTTTTTGCGGCGCTTTCATAAAAACGCCGC
Found at i:3314851 original size:226 final size:225
Alignment explanation
Indices: 3314458--3314987 Score: 812
Period size: 226 Copynumber: 2.3 Consensus size: 225
3314448 TAAATCCCTG
* * *
3314458 AGCATTAGCGGCGCTTTATTAAAAACGCTGCTAAACCCCCTGAAAGCTAAGAAAACGGTGTCGTT
1 AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAACCCCC-GAAAGCTAAGAAAACGGTGTCGTT
* * *
3314523 GGGTTTAATTTTATTTGCGGCGCTTTCATAAAAGCGTCGCTAGCCCTAGCATTAGCGGCACATTA
65 GGGTTTAATTTTTTTTGCGGCGCTTTCATAAAAACGCCGCTAGCCCTAGCATTAGCGGCACATTA
* *
3314588 TTGAAAACGCCACTAAACCCCCCGAAAGCTCAGAAAACGACGTCGTTGGGCTTAGTTTTTTTGCG
130 TTGAAAACGCCACTAAACCCCCCGAAAGCTCAGAAAACGACATCGTTGAGCTTAGTTTTTTTGCG
* *
3314653 GCGCTTTATCCAAAACGCCGCTAAA-ACCAC
195 GCGCTTGATCAAAAACGCCGCTAAAGACCAC
* * *
3314683 AGCATTAGCGACGCTTTACTAAAAATGCCGCCAAACCCCCGAAGGCTAAGAAAACGGTGTCGTTG
1 AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAACCCCCGAAAGCTAAGAAAACGGTGTCGTTG
* *
3314748 GGTTTAATTTTTTTTGCGGTGCTTTCATAAAAACGCCGCTAAAGCCCTAGCATTAGCGGCGCATT
66 GGTTTAATTTTTTTTGCGGCGCTTTCATAAAAACGCCGCT--AGCCCTAGCATTAGCGGCACATT
* *
3314813 ATTGAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCATCGTTGAGCTTAGTTTTTTTGC
129 ATTGAAAACGCCACTAAACCCCCCGAAAGCTCAGAAAACGACATCGTTGAGCTTAGTTTTTTTGC
* *
3314878 GGCGCTTGATCAAAAACGCCGCTAAAGCCCTC
194 GGCGCTTGATCAAAAACGCCGCTAAAGACCAC
* *
3314910 AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAACCCCCCGAAAGCTCAGAAAACGGCGTCGTT
1 AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAA-CCCCCGAAAGCTAAGAAAACGGTGTCGTT
*
3314975 GGGCTT-ATTTTTT
65 GGGTTTAATTTTTT
3314988 GTGGCGCTTC
Statistics
Matches: 276, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
224 60 0.22
225 35 0.13
226 107 0.39
227 43 0.16
228 31 0.11
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (225 bp):
AGCATTAGCGACGCTTTACTAAAAACGCCGCTAAACCCCCGAAAGCTAAGAAAACGGTGTCGTTG
GGTTTAATTTTTTTTGCGGCGCTTTCATAAAAACGCCGCTAGCCCTAGCATTAGCGGCACATTAT
TGAAAACGCCACTAAACCCCCCGAAAGCTCAGAAAACGACATCGTTGAGCTTAGTTTTTTTGCGG
CGCTTGATCAAAAACGCCGCTAAAGACCAC
Found at i:3319311 original size:140 final size:139
Alignment explanation
Indices: 3319049--3319332 Score: 462
Period size: 140 Copynumber: 2.0 Consensus size: 139
3319039 GAAGTCAAAG
*
3319049 AAACTTATCAAATTCATTTGTAAATGATAAATTTAAGATTTGGACATCAATTTTCCTTTAAAATT
1 AAACTTATCAAATTCATTTGTAAATGATAAATTTAAGATTTGAACATCAATTTTCCTTTAAAATT
*
3319114 TCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCTAAAG
66 TCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCAAAAG
*
3319179 ACTATCAAC
131 ACTACCAAC
* *
3319188 AAACTTATCTCAATTCATTTGTAAATGATAAATTTAAGATTTGAACATCAACTTTT-CTTTGAAA
1 AAACTTATC-AAATTCATTTGTAAATGATAAATTTAAGATTTGAACATCAA-TTTTCCTTTAAAA
** * *
3319252 TTTCGAACGGTCCTCGAAGTACAAACTCCGACATCCCTCATGTTCCGATAGTGTTCCTCCTCAAA
64 TTTCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCAAA
3319317 AGACTACCAAC
129 AGACTACCAAC
3319328 AAACT
1 AAACT
3319333 GCATAATTAT
Statistics
Matches: 134, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
139 9 0.07
140 121 0.90
141 4 0.03
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (139 bp):
AAACTTATCAAATTCATTTGTAAATGATAAATTTAAGATTTGAACATCAATTTTCCTTTAAAATT
TCGAACACTCCTCGAAGTACAAACTCCAACATCCCTCATGTTCCGATAGCGTTCCTCCTCAAAAG
ACTACCAAC
Found at i:3331132 original size:23 final size:23
Alignment explanation
Indices: 3331094--3331142 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
3331084 TAGGCTAGCT
*
3331094 TATTTTTTTTATTTAATATTAAA
1 TATTTTTTTTATTTAAAATTAAA
*
3331117 TATTTTTATTTA-TTAAAATTATA
1 TATTTTT-TTTATTTAAAATTAAA
3331140 TAT
1 TAT
3331143 ATGCAACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTTTTTTATTTAAAATTAAA
Found at i:3346826 original size:26 final size:28
Alignment explanation
Indices: 3346780--3346842 Score: 94
Period size: 26 Copynumber: 2.3 Consensus size: 28
3346770 GAGATCATGG
3346780 AAGATGATCTCATAGGAGATGATCAACT
1 AAGATGATCTCATAGGAGATGATCAACT
*
3346808 AAGATGA-C-CATAGGAGATGATCAAGT
1 AAGATGATCTCATAGGAGATGATCAACT
*
3346834 GAGATGATC
1 AAGATGATC
3346843 CAGACGAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
26 23 0.72
27 2 0.06
28 7 0.22
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (28 bp):
AAGATGATCTCATAGGAGATGATCAACT
Found at i:3346841 original size:13 final size:13
Alignment explanation
Indices: 3346795--3346842 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
3346785 GATCTCATAG
*
3346795 GAGATGATCAACT
1 GAGATGATCAAGT
* *
3346808 AAGATGACCATAG-
1 GAGATGATCA-AGT
3346821 GAGATGATCAAGT
1 GAGATGATCAAGT
3346834 GAGATGATC
1 GAGATGATC
3346843 CAGACGAGGC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
12 2 0.07
13 25 0.89
14 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.27, T:0.21
Consensus pattern (13 bp):
GAGATGATCAAGT
Found at i:3348485 original size:3 final size:3
Alignment explanation
Indices: 3348477--3348525 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
3348467 TGTACATAGC
3348477 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3348524 AA
1 AA
3348526 CGGGACTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3351713 original size:62 final size:62
Alignment explanation
Indices: 3351573--3351762 Score: 281
Period size: 62 Copynumber: 3.0 Consensus size: 62
3351563 AATTTGGATT
* *
3351573 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACTCCATATTTCCTCAAAATTGGACA
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAAC-CC-CATTTCCTCAAAATTGGACC
* *
3351637 ATATTGTGGCACATTATACTTTTAAAGCCTAAATTGCAGCCCCATTTCCTCAAAATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
* * * * *
3351699 ATATTGTGGCACATTATGCTTTTGAAGTCTAAAATGCAACCCCATCTCCTCAAGATTGGACC
1 ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
3351761 AT
1 AT
3351763 GATGGCCTTG
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
62 75 0.65
63 2 0.02
64 38 0.33
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (62 bp):
ATATTGTGGCACATTATACTTTTAAAGCCTAAAATGCAACCCCATTTCCTCAAAATTGGACC
Found at i:3352091 original size:31 final size:31
Alignment explanation
Indices: 3352053--3352114 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
3352043 TTAGAGTCAC
3352053 TATTATGACATTGATATTGAAAAAAAAAACT
1 TATTATGACATTGATATTGAAAAAAAAAACT
3352084 TATTATGACATTGATATTGAAAAAAAAAACT
1 TATTATGACATTGATATTGAAAAAAAAAACT
3352115 AACTTAGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.32
Consensus pattern (31 bp):
TATTATGACATTGATATTGAAAAAAAAAACT
Found at i:3363553 original size:12 final size:10
Alignment explanation
Indices: 3363528--3363580 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
3363518 ATTTATATTA
3363528 TAATTAAATT
1 TAATTAAATT
*
3363538 TAATTAAAAT
1 TAATTAAATT
3363548 T--TT-AATT
1 TAATTAAATT
3363555 TAATTAAATT
1 TAATTAAATT
3363565 TAATTTAAATT
1 TAA-TTAAATT
*
3363576 CAATT
1 TAATT
3363581 CTAGCCAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
7 4 0.11
8 2 0.06
9 2 0.06
10 19 0.53
11 9 0.25
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (10 bp):
TAATTAAATT
Found at i:3363554 original size:17 final size:15
Alignment explanation
Indices: 3363507--3363572 Score: 66
Period size: 15 Copynumber: 4.3 Consensus size: 15
3363497 AAAAATAAAT
3363507 TTTACATTAATATTTATA
1 TTTA-ATTAA-ATTTA-A
3363525 TTATAATTAAATTTAA
1 TT-TAATTAAATTTAA
*
3363541 -TTAA--AATTTTAA
1 TTTAATTAAATTTAA
3363553 TTTAATTAAATTTAA
1 TTTAATTAAATTTAA
3363568 TTTAA
1 TTTAA
3363573 ATTCAATTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
12 7 0.17
13 4 0.10
14 3 0.07
15 13 0.31
16 1 0.02
17 5 0.12
18 7 0.17
19 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATTAAATTTAA
Found at i:3364527 original size:22 final size:20
Alignment explanation
Indices: 3364481--3364529 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
3364471 AGCTCTGTTA
*
3364481 CCAAAAATTGTATATAAGTT
1 CCAAAAATTGTATAGAAGTT
*
3364501 CCAAAAATTGTATGTAGAATTT
1 CCAAAAATTGTA--TAGAAGTT
3364523 CCAAAAA
1 CCAAAAA
3364530 GAAAAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 12 0.48
22 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
CCAAAAATTGTATAGAAGTT
Found at i:3366885 original size:30 final size:31
Alignment explanation
Indices: 3366850--3366909 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
3366840 TTATTTGAAA
*
3366850 AATTCTTATTAAACCCTTC-AAATTTTTTTG
1 AATTCTCATTAAACCCTTCAAAATTTTTTTG
* **
3366880 AATTCTCATTAGATTCTTCAAAATTTTTTT
1 AATTCTCATTAAACCCTTCAAAATTTTTTT
3366910 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (31 bp):
AATTCTCATTAAACCCTTCAAAATTTTTTTG
Found at i:3375825 original size:34 final size:34
Alignment explanation
Indices: 3375778--3375875 Score: 96
Period size: 31 Copynumber: 3.0 Consensus size: 34
3375768 CCAAAATTCA
** *
3375778 TATATAAAATTGAACATTAAAGTATCTTTATTGG
1 TATATAATTTTGAACATTATAGTATCTTTATTGG
*** *
3375812 TATATAATTTTGAACA-TATA-TAT-AAAATTCG
1 TATATAATTTTGAACATTATAGTATCTTTATTGG
*
3375843 TATATAATTTTG-AGATTATAGTATCTTTATTGG
1 TATATAATTTTGAACATTATAGTATCTTTATTGG
3375876 CATAGACATT
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
30 2 0.04
31 20 0.41
32 6 0.12
33 7 0.14
34 14 0.29
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (34 bp):
TATATAATTTTGAACATTATAGTATCTTTATTGG
Found at i:3377003 original size:22 final size:22
Alignment explanation
Indices: 3376954--3377004 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3376944 GTTAGTGAAT
3376954 AAAAATATATAAATATAAATAA
1 AAAAATATATAAATATAAATAA
* * *
3376976 ACAAATATTTATATATAAA-AA
1 AAAAATATATAAATATAAATAA
3376997 ATAAAATA
1 A-AAAATA
3377005 AATTGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAATATATAAATATAAATAA
Found at i:3377993 original size:125 final size:125
Alignment explanation
Indices: 3377778--3378311 Score: 648
Period size: 125 Copynumber: 4.3 Consensus size: 125
3377768 ATTATTGCAG
* * * **
3377778 TCGCGACCA-CGTGAACGCGCTTTTGGTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGATTTT
1 TCGCG-CCATCGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTT
* *
3377842 TCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGGTGCTATATGCGAAGAATTTGTGAAA
65 TCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAA
* * ** *
3377903 TCGCGCCATCGTGGACGCGCTTTTGCTACAGTTGGTCTTGGAAGGAATAATTTTGAGTTGACGTT
1 TCGCGCCATCGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATAATTTCGAGTTGACGTT
* * *** * *
3377968 TTTGAGCAAATAGTAT-AAAATCGCTTCTCCCAGGATGTTTTATGAGAAGAATTTGTGAAA
65 TCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAA
* * *
3378028 TCGTGGC-TACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTT
1 TCGCGCCAT-CGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTT
* * * *
3378092 TCTGAGCAAATAGTATAAAAAAAGGCTTCAAGCAGGCTGCTATTTGCGAAGAATTTGTGAAA
65 TCTGAGCAAATAGTAT-AAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAA
* * *
3378154 TCGCGGCC-TCATGGACGCGCTTTTGCTACAGTTGGTCCTAGAAGAAATAATTTCGAGTTGACGT
1 TCGC-GCCATCGTGGACGCGCTTTTGCTACAGTAGGTCCT-GAAAAAATAATTTCGAGTTGACGT
* * * * **
3378218 TTCTGAGCAAATAGTAT-AAAATCGCTTCTATCAGGATGCTTTATGAGGGGAATTTGTGAAA
64 TTCTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAA
3378279 TCGCGCCCA-CGTGGACGCGCTTTTGCTACAGTA
1 TCGCG-CCATCGTGGACGCGCTTTTGCTACAGTA
3378312 ACATGTTTGG
Statistics
Matches: 344, Mismatches: 56, Indels: 18
0.82 0.13 0.04
Matches are distributed among these distances:
124 41 0.12
125 162 0.47
126 99 0.29
127 42 0.12
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (125 bp):
TCGCGCCATCGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTTGACGTTT
CTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATATGAGAAGAATTTGTGAAA
Found at i:3378234 original size:251 final size:250
Alignment explanation
Indices: 3377778--3378311 Score: 845
Period size: 251 Copynumber: 2.1 Consensus size: 250
3377768 ATTATTGCAG
* * * **
3377778 TCGCGACCACGTGAACGCGCTTTTGGTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGATTTTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTT
*
3377843 CTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGGTGCTATATGCGAAGAATTTGTGAAATCGCG
66 CTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGCTGCTATATGCGAAGAATTTGTGAAATCGCG
* * * * * *
3377908 CCATCGTGGACGCGCTTTTGCTACAGTTGGTCTTGGAAGGAATAATTTTGAGTTGACGTTTTTGA
131 CCATCATGGACGCGCTTTTGCTACAGTTGGTCCTAGAAGAAATAATTTCGAGTTGACGTTTCTGA
* *
3377973 GCAAATAGTATAAAATCGCTTCTCCCAGGATGTTTTATGAGAAGAATTTGTGAAA
196 GCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
* * *
3378028 TCGTGGCTACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTT
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTT
* *
3378093 CTGAGCAAATAGTATAAAAAAAGGCTTCAAGCAGGCTGCTATTTGCGAAGAATTTGTGAAATCGC
66 CTGAGCAAATAGTAT-AAAAAACGCTTCAAGCAGGCTGCTATATGCGAAGAATTTGTGAAATCGC
3378158 GGCC-TCATGGACGCGCTTTTGCTACAGTTGGTCCTAGAAGAAATAATTTCGAGTTGACGTTTCT
130 -GCCATCATGGACGCGCTTTTGCTACAGTTGGTCCTAGAAGAAATAATTTCGAGTTGACGTTTCT
* **
3378222 GAGCAAATAGTATAAAATCGCTTCTATCAGGATGCTTTATGAGGGGAATTTGTGAAA
194 GAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
3378279 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
1 TCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
3378312 ACATGTTTGG
Statistics
Matches: 258, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
250 73 0.28
251 182 0.71
252 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (250 bp):
TCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGAAAAAATTATTTCGAGTTGACGTTT
CTGAGCAAATAGTATAAAAAACGCTTCAAGCAGGCTGCTATATGCGAAGAATTTGTGAAATCGCG
CCATCATGGACGCGCTTTTGCTACAGTTGGTCCTAGAAGAAATAATTTCGAGTTGACGTTTCTGA
GCAAATAGTATAAAATCGCTTCTACCAGGATGCTTTATGAGAAGAATTTGTGAAA
Found at i:3380949 original size:22 final size:22
Alignment explanation
Indices: 3380868--3380952 Score: 102
Period size: 22 Copynumber: 3.9 Consensus size: 22
3380858 ACTTGTGAAA
*
3380868 TAGGGTTTTTAAGGTT-AGGGTT
1 TAGGG-TTTTAAGGTTAAGGTTT
*
3380890 TGGGGTGTTT-AGGTTAAGGTTT
1 TAGGGT-TTTAAGGTTAAGGTTT
*
3380912 TAGGGTTTTTAGGTTAAGGTTT
1 TAGGGTTTTAAGGTTAAGGTTT
*
3380934 TAGGGTTTTAAAGTTAAGG
1 TAGGGTTTTAAGGTTAAGG
3380953 GTCATGGTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
21 9 0.16
22 46 0.84
ACGTcount: A:0.20, C:0.00, G:0.35, T:0.45
Consensus pattern (22 bp):
TAGGGTTTTAAGGTTAAGGTTT
Found at i:3381550 original size:18 final size:18
Alignment explanation
Indices: 3381518--3381557 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3381508 GACTCAGAAA
** *
3381518 AGGATACATGTAAGGGTT
1 AGGATACATAAAAGGGCT
3381536 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
3381554 AGGA
1 AGGA
3381558 AACGCACCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:3384409 original size:30 final size:30
Alignment explanation
Indices: 3384375--3384436 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
3384365 CTTAACAAGT
3384375 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
*
3384405 AAATGCCTTTAAATTAATAACAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
3384435 AA
1 AA
3384437 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.03, T:0.27
Consensus pattern (30 bp):
AAATGCCTTTAAAATAATAACAAAATTAAC
Found at i:3384513 original size:22 final size:22
Alignment explanation
Indices: 3384465--3384513 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
3384455 ATATCCAAAC
* *
3384465 AATAACAATAAAATAGTAGCAA
1 AATAACAACAAAATAGTAACAA
* * *
3384487 CATAATAACAAAATGGTAACAA
1 AATAACAACAAAATAGTAACAA
3384509 AATAA
1 AATAA
3384514 GGAGAAAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAACAA
Found at i:3385099 original size:14 final size:15
Alignment explanation
Indices: 3385080--3385109 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3385070 CAACCCAAAA
3385080 ATCAAACCC-ATTAC
1 ATCAAACCCAATTAC
3385094 ATCAAACCCAATTAC
1 ATCAAACCCAATTAC
3385109 A
1 A
3385110 GGCCCAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (15 bp):
ATCAAACCCAATTAC
Found at i:3386246 original size:23 final size:22
Alignment explanation
Indices: 3386219--3386336 Score: 76
Period size: 23 Copynumber: 5.0 Consensus size: 22
3386209 ACATTGTTTA
*
3386219 AATTTATCGTATATTATTATTTT
1 AATTT-TCATATATTATTATTTT
*
3386242 AATTTTGCATGTATTATT-TTTCT
1 AATTTT-CATATATTATTATTT-T
* *
3386265 AAGCTTTTCATGTATTAATATTTTTTT
1 AA--TTTTCA--TA-TATTATTATTTT
*
3386292 AATTTATTATATATTATTATTTT
1 AATTT-TCATATATTATTATTTT
* *
3386315 AATTTCCACATATATATTATTT
1 AATTTTCATATAT-TATTATTT
3386337 CATATGTTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
22 9 0.12
23 40 0.53
24 4 0.05
25 7 0.09
26 3 0.04
27 9 0.12
28 3 0.04
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (22 bp):
AATTTTCATATATTATTATTTT
Found at i:3390842 original size:4 final size:4
Alignment explanation
Indices: 3390828--3390861 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
3390818 AAAAAATAGT
3390828 TTAA TTAAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TT-AA TTAA TTAA TTAA TTAA TTAA TTAA T
3390862 ATTTGGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:3392597 original size:6 final size:6
Alignment explanation
Indices: 3392586--3392624 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
3392576 CTAATAATAA
3392586 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATAG ATA
3392625 GGCTAACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
ATATAG
Found at i:3398859 original size:19 final size:17
Alignment explanation
Indices: 3398835--3398951 Score: 59
Period size: 16 Copynumber: 6.9 Consensus size: 17
3398825 TAATATTAGA
3398835 AAAATATATATAATAGTGT
1 AAAATATATATAATA-T-T
3398854 AAAATATAACTAATAATATT
1 AAAATAT-A-T-ATAATATT
*
3398874 AAAATATATACAATGA-T
1 AAAATATATATAAT-ATT
* * *
3398891 AATATATATAAAAGA-T
1 AAAATATATATAATATT
* *
3398907 -ATATGTATAT-ATAATT
1 AAAATATATATAAT-ATT
*
3398923 -ATATA-ATATAATATT
1 AAAATATATATAATATT
3398938 AAAATATA-ATAATA
1 AAAATATATATAATA
3398952 CAACATAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 21
0.73 0.08 0.19
Matches are distributed among these distances:
14 1 0.01
15 16 0.20
16 19 0.24
17 17 0.21
18 2 0.03
19 8 0.10
20 9 0.11
21 2 0.03
22 6 0.08
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:3399316 original size:3 final size:3
Alignment explanation
Indices: 3399285--3399352 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
3399275 ATACACGTAC
* * * *
3399285 ATA ATA AAA ATA TATA CTA ATA CATA ATA ATA ATA CTA ATA CTA ATA
1 ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
* *
3399332 ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
3399353 CAAGGATATT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3399827 original size:11 final size:12
Alignment explanation
Indices: 3399811--3399846 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
3399801 AGAAAAAAAA
3399811 GAAGAGAG-AGG
1 GAAGAGAGAAGG
3399822 GAAGAGAGAAGG
1 GAAGAGAGAAGG
3399834 G-AGAGAGAAGG
1 GAAGAGAGAAGG
3399845 GA
1 GA
3399847 GGGGGGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
GAAGAGAGAAGG
Found at i:3400912 original size:44 final size:44
Alignment explanation
Indices: 3400883--3401811 Score: 322
Period size: 44 Copynumber: 20.8 Consensus size: 44
3400873 CCTTTATTTT
* * *
3400883 AATCCACTCCACTGTAATCTCAGGCAGATAGGATTACTATCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTC
*
3400927 AATCTACTCCGCTGTAATCTCAGGGAGATAAGATTACTATCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * * *
3400971 AATCTGCTCCATTGTAATCTCAGGGAGATAAGATCTGA-AATTTTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTC
** ** * **
3401017 GGTCTGTTCCACTGAAATCTCAGGGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * * *
3401061 AATCTGATGTGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCATTTAT-TTT
1 AATC-----T-A-CT-C-C-ACTGTAATC-TCAGGGAGATAAGATTA-CTATCTTC
* * * *
3401115 AATCTGCTCCACTGTAA-CTTCAGAGAGATAGGATTACTAGCTTC
1 AATCTACTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTC
* * **
3401159 AATCTACTCCGCTGTAATCTCAGAGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * *
3401203 AATCTGATGTGATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTAT-TTT
1 AATC-----T-A-CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTATCTTC
** * * * *
3401257 AATCCGCTCCACTGTAATTTCAGAGAGATAGGATTACTAGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * **
3401301 AATCTACTCCGCTGTAATCTCAGAGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * *
3401345 AATCTGCTCTACTGTAACCTCAGGGAGATAAGA-T-CTGA-CTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTC
* * *
3401387 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTC
** * * * * *
3401433 GGTCTACTCCCCTGTAACCTCAGGGTGATAAGA--CCTGA--TGC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTC
* ** * * *
3401474 GATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCT-TTAT-TTT
1 AATCTACTCCACTGTAATC-TCAGGGAGATAAGAT--TACTATCTTC
** * * *
3401518 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATCTGA-AATTCTTT
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTC
** ** * * *
3401564 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCT-GTAT-GT-
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGA-TTACTATCTTC
* * * *
3401606 GATCTTCTCTACTGTAA-CTTCAGAGAGATAAGA-T-CT-T-TT-
1 AATCTACTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTC
** * * * * *
3401645 AATCCGCTCCATTGTAATTTCAAGGAGATAGGATTACTATCTTT
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTC
* * * * **
3401689 GATCTGCTCCGCTGTAATCTTAGGGAGATAAGATCT-CTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTC
* * * *
3401733 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTT
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTC
** **
3401779 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGA
3401812 CCTGTATAAT
Statistics
Matches: 680, Mismatches: 136, Indels: 136
0.71 0.14 0.14
Matches are distributed among these distances:
39 25 0.04
40 4 0.01
41 31 0.05
42 67 0.10
43 10 0.01
44 324 0.48
45 11 0.02
46 134 0.20
47 4 0.01
49 3 0.00
50 1 0.00
51 3 0.00
52 2 0.00
53 4 0.01
54 53 0.08
55 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
AATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTC
Found at i:3401220 original size:142 final size:141
Alignment explanation
Indices: 3401032--3401738 Score: 674
Period size: 142 Copynumber: 5.2 Consensus size: 141
3401022 GTTCCACTGA
3401032 AATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGA
1 AATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGA
* * *
3401097 GATAAGATCATTTATTTTAATCTGCTCCACTGTAACTTCAGAGAGATAGGATTACTAGCTTCAAT
66 GATAAGATC-TTTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTATCTTCGAT
3401162 CTACTCCGCTGT
130 CTACTCCGCTGT
*
3401174 AATCTCAGAGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGA
1 AATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGA
* * *
3401239 GATAAGATCCTTTATTTTAATCCGCTCCACTGTAATTTCAGAGAGATAGGATTACTAGCTTCAAT
66 GATAAGAT-CTTTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTATCTTCGAT
3401304 CTACTCCGCTGT
130 CTACTCCGCTGT
* * *
3401316 AATCTCAGAGAGATAAGATCTCTGGCTTCAATC-----TG-----CTCTACTGTAACCTCAGGGA
1 AATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGA
* * * * * * * *
3401371 GATAAGATC-TGACTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA-AATTCTTCG
66 GATAAGATCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGAT-T-ACTA-TCTTCG
* *
3401434 GTCTACTCCCCTGT
128 ATCTACTCCGCTGT
* * * *
3401448 AACCTCAGGGTGATAAGA----------C---CTGATGCGATCTACTCTGCTGTAACTTCAGAGA
1 AATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGA
* *
3401500 GATAAGATCCTTTATTTTAATCCGCTCCACTGTAA-TCTCAGGGAGATAGGATCTGA-AATTCTT
66 GATAAGAT-CTTTATTTTAATCCGCTCCACTGTAACT-TCAGAGAGATAGGAT-T-ACTA-TCTT
* * ** *
3401563 TGGTCTGTTCCACTGT
126 CGATCTACTCCGCTGT
*
3401579 AATCTCAGGGAGATAAGA-C-CT-G--------T-ATGTGATCTTCTCTACTGTAACTTCAGAGA
1 AATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGA
* * *
3401632 GATAAGATC----TTTTAATCCGCTCCATTGTAATTTCA-AGGAGATAGGATTACTATCTTTGAT
66 GATAAGATCTTTATTTTAATCCGCTCCACTGTAACTTCAGA-GAGATAGGATTACTATCTTCGAT
*
3401692 CTGCTCCGCTGT
130 CTACTCCGCTGT
*
3401704 AATCTTAGGGAGATAAGATCTCTGGCTTCAATCTG
1 AATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
3401739 CTCCACTGTA
Statistics
Matches: 482, Mismatches: 47, Indels: 77
0.80 0.08 0.13
Matches are distributed among these distances:
119 1 0.00
122 1 0.00
124 1 0.00
125 35 0.07
126 3 0.01
127 35 0.07
128 2 0.00
129 25 0.05
130 34 0.07
131 77 0.16
132 93 0.19
133 1 0.00
136 1 0.00
137 2 0.00
142 170 0.35
143 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (141 bp):
AATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGATGTGATCTACTCTACTGTAACTTCAGAGA
GATAAGATCTTTATTTTAATCCGCTCCACTGTAACTTCAGAGAGATAGGATTACTATCTTCGATC
TACTCCGCTGT
Found at i:3401534 original size:173 final size:170
Alignment explanation
Indices: 3401300--3401816 Score: 472
Period size: 173 Copynumber: 3.0 Consensus size: 170
3401290 TTACTAGCTT
* *** * * *
3401300 CAATCTACTCCGCTGTAATCTCAGAGAGATAAGATCTCTGGCTTCAATCTGCTCTACTGTAACCT
1 CAATCTACTCCGCTGTAAT-TCAGAGAGATAAGATCTATTATTTTAATCTGCTCCACTGTAATCT
3401365 CAGGGAGATAAGATCTGACTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTC
65 CAGGGAGATAAGATCTGACTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTC
* *
3401430 TTCGGTCTACTCCCCTGTAACCTCAGGGTGATAAGACCTGATG
130 TT-GGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTG-TG
* * *
3401473 CGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCACTGTAATC
1 CAATCTACTCCGCTGTAA-TTCAGAGAGATAAGAT-CTATTATTTTAATCTGCTCCACTGTAATC
* *** * * *
3401537 TCAGGGAGATAGGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG-
64 TCAGGGAGATAAGATCTG--A--CTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA
* * * * * * * * *
3401601 TA-T-GTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCT-TT
125 AATTCTTGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGTG
* ** ** * * * *
3401644 TAATCCGCTCCATTGTAATTTCA-AGGAGATAGGAT-TACTATCTTTGATCTGCTCCGCTGTAAT
1 CAATCTACTCCGCTGTAA-TTCAGA-GAGATAAGATCTATTAT-TTTAATCTGCTCCACTGTAAT
* *
3401707 CTTAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAA
63 CTCAGGGAGATAAGA--TCTGACTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAA
** *
3401772 ATTCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTGT
126 ATTC-TTGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGT
3401817 ATAATAAACC
Statistics
Matches: 269, Mismatches: 59, Indels: 31
0.75 0.16 0.09
Matches are distributed among these distances:
169 36 0.13
170 5 0.02
171 57 0.21
173 128 0.48
174 5 0.02
175 2 0.01
176 1 0.00
177 35 0.13
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (170 bp):
CAATCTACTCCGCTGTAATTCAGAGAGATAAGATCTATTATTTTAATCTGCTCCACTGTAATCTC
AGGGAGATAAGATCTGACTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCT
TGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGTG
Found at i:3411734 original size:4 final size:4
Alignment explanation
Indices: 3411725--3411755 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3411715 CAAACACAAA
3411725 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3411756 AACCTTGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3411836 original size:22 final size:22
Alignment explanation
Indices: 3411796--3411837 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3411786 TGGCCACCTA
*
3411796 CCTTGGCCACCAACTCCACCAC
1 CCTTGGCCACCAACACCACCAC
3411818 CCTTGGCCACCTAA-ACCACC
1 CCTTGGCCACC-AACACCACC
3411838 CCAACCACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.24, C:0.52, G:0.10, T:0.14
Consensus pattern (22 bp):
CCTTGGCCACCAACACCACCAC
Found at i:3412256 original size:19 final size:19
Alignment explanation
Indices: 3412212--3412265 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
3412202 TATATATACT
3412212 AAAAA-AATATAAAAATAA
1 AAAAATAATATAAAAATAA
* * *
3412230 CAACATAATATAAACATAA
1 AAAAATAATATAAAAATAA
*
3412249 AAAAATAA-AAAAAAATA
1 AAAAATAATATAAAAATA
3412266 TTTTTTTACC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
18 10 0.36
19 18 0.64
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAATAATATAAAAATAA
Found at i:3412381 original size:11 final size:11
Alignment explanation
Indices: 3412365--3412399 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
3412355 TCCTTCCCCC
3412365 CTCCCTTCTCT
1 CTCCCTTCTCT
3412376 CTCCCTTCTCT
1 CTCCCTTCTCT
3412387 CTTCCC-TCTCT
1 C-TCCCTTCTCT
3412398 CT
1 CT
3412400 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 18 0.78
12 4 0.17
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:3412888 original size:3 final size:3
Alignment explanation
Indices: 3412864--3412931 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
3412854 AATATCCTTG
* * * *
3412864 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA GTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
3412912 TTA GTA TATA TTT TTA TTA T
1 TTA TTA T-TA TTA TTA TTA T
3412932 GTACGTGTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3412941 original size:23 final size:23
Alignment explanation
Indices: 3412871--3412942 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
3412861 TTGTTATTTT
* *
3412871 TATATTATTAGTAT-TATTAGTA
1 TATATTATTATTATGTAGTAGTA
*
3412893 TTAGTATTATTATTATGTATTAGTA
1 -TA-TATTATTATTATGTAGTAGTA
*
3412918 TATATTTTTATTATGTACGT-GTA
1 TATATTATTATTATGTA-GTAGTA
3412941 TA
1 TA
3412943 CATATATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
23 21 0.49
24 14 0.33
25 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (23 bp):
TATATTATTATTATGTAGTAGTA
Found at i:3413342 original size:64 final size:64
Alignment explanation
Indices: 3413268--3413399 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 64
3413258 GTCGTATTAT
*
3413268 TATATTTTAATATTA-TA-TTATATAATTATA-TA-TACATATATCTTTTATATATATTATCATT
1 TATATTTTAATATTATTAGTTATAT-ATTACACTATTACATATAT-TTTTATA-ATATTAT-ATT
3413329 GTA
62 GTA
* * *
3413332 TATATTTTAATATTATTAGTTATATTTTACACTATTATATATATTTTTCTAATATTATATTGTA
1 TATATTTTAATATTATTAGTTATATATTACACTATTACATATATTTTTATAATATTATATTGTA
3413396 TATA
1 TATA
3413400 CTGTTGTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
64 25 0.42
65 13 0.22
66 14 0.23
67 8 0.13
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (64 bp):
TATATTTTAATATTATTAGTTATATATTACACTATTACATATATTTTTATAATATTATATTGTA
Found at i:3413374 original size:19 final size:18
Alignment explanation
Indices: 3413330--3413389 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 18
3413320 ATTATCATTG
3413330 TATATATTTTAATATTAT
1 TATATATTTTAATATTAT
3413348 TAGTTATATTTTACACTATTAT
1 TA--TATATTTTA-A-TATTAT
*
3413370 ATATATTTTTCTAATATTAT
1 -TATATATTT-TAATATTAT
3413390 ATTGTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.06
20 15 0.43
21 8 0.23
22 8 0.23
23 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (18 bp):
TATATATTTTAATATTAT
Found at i:3424941 original size:30 final size:30
Alignment explanation
Indices: 3424895--3424961 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
3424885 CACATGGCCA
* * *
3424895 TGTGGCTCACACGGCTTGGACCCACACCCG
1 TGTGCCTCACACGGCTTAGACACACACCCG
* *
3424925 TGTGCCTCATACGGCTTAGACACACGCCCG
1 TGTGCCTCACACGGCTTAGACACACACCCG
3424955 TGTGCCT
1 TGTGCCT
3424962 AGGCTTGTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.16, C:0.37, G:0.25, T:0.21
Consensus pattern (30 bp):
TGTGCCTCACACGGCTTAGACACACACCCG
Found at i:3428411 original size:21 final size:21
Alignment explanation
Indices: 3428366--3428411 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
3428356 ATTATTGAAC
*
3428366 TAAAACACTATTATCAAGGAAT
1 TAAAACACTATTAT-AAGAAAT
3428388 TAAAACATCTATTAT-AGAAAT
1 TAAAACA-CTATTATAAGAAAT
3428409 TAA
1 TAA
3428412 TTAGTGAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 7 0.32
23 7 0.32
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (21 bp):
TAAAACACTATTATAAGAAAT
Found at i:3429924 original size:30 final size:30
Alignment explanation
Indices: 3429881--3429939 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
3429871 TTGGTTACAC
* * *
3429881 GTAATCAGTAGCCATCATATCCTGTCGCAT
1 GTAATCAGCAGCCACCATATCCTATCGCAT
* *
3429911 GTAATCTGCAGCCACCGTATCCTATCGCA
1 GTAATCAGCAGCCACCATATCCTATCGCA
3429940 CCCTGTGCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (30 bp):
GTAATCAGCAGCCACCATATCCTATCGCAT
Found at i:3433692 original size:31 final size:31
Alignment explanation
Indices: 3433655--3433788 Score: 125
Period size: 29 Copynumber: 4.5 Consensus size: 31
3433645 TTAATGGCTC
3433655 AGTGACTAAAATGTTACAACACGATAACAT-
1 AGTGACTAAAATGTTACAACACGATAACATA
** * ***
3433685 AGTTGACTAAAACATAACATTTC-A-AACATA
1 AG-TGACTAAAATGTTACAACACGATAACATA
3433715 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTTACAACACGATAACATA
* * ***
3433746 AGTGACTAAAACGTAACATTTC-A-AACATA
1 AGTGACTAAAATGTTACAACACGATAACATA
3433775 AGTGACTAAAATGT
1 AGTGACTAAAATGT
3433789 AACCTGAGGC
Statistics
Matches: 82, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
29 38 0.46
30 7 0.09
31 37 0.45
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.25
Consensus pattern (31 bp):
AGTGACTAAAATGTTACAACACGATAACATA
Found at i:3433720 original size:29 final size:29
Alignment explanation
Indices: 3433680--3433791 Score: 127
Period size: 29 Copynumber: 3.8 Consensus size: 29
3433670 ACAACACGAT
*
3433680 AACAT-AGTTGACTAAAACATAACATTTCA
1 AACATAAG-TGACTAAAACGTAACATTTCA
* * ***
3433709 AACATAAGTGACTAAAATGTTACAACACGA
1 AACATAAGTGACTAAAACGTAACATTTC-A
3433739 TAACATAAGTGACTAAAACGTAACATTTCA
1 -AACATAAGTGACTAAAACGTAACATTTCA
*
3433769 AACATAAGTGACTAAAATGTAAC
1 AACATAAGTGACTAAAACGTAAC
3433792 CTGAGGCAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
29 41 0.60
30 4 0.06
31 23 0.34
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATTTCA
Found at i:3433723 original size:60 final size:60
Alignment explanation
Indices: 3433655--3433788 Score: 243
Period size: 60 Copynumber: 2.2 Consensus size: 60
3433645 TTAATGGCTC
3433655 AGTGACTAAAATGTTACAACACGATAACAT-AGTTGACTAAAACATAACATTTCAAACATA
1 AGTGACTAAAATGTTACAACACGATAACATAAG-TGACTAAAACATAACATTTCAAACATA
*
3433715 AGTGACTAAAATGTTACAACACGATAACATAAGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTTACAACACGATAACATAAGTGACTAAAACATAACATTTCAAACATA
3433775 AGTGACTAAAATGT
1 AGTGACTAAAATGT
3433789 AACCTGAGGC
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
60 70 0.97
61 2 0.03
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.25
Consensus pattern (60 bp):
AGTGACTAAAATGTTACAACACGATAACATAAGTGACTAAAACATAACATTTCAAACATA
Found at i:3435594 original size:21 final size:20
Alignment explanation
Indices: 3435564--3435625 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
3435554 AAAAATTAAT
3435564 TTTG-GAAAATCTCAATTATG-
1 TTTGAGAAAAT-T-AATTATGA
*
3435584 TTTGAGAAAATTAATTTTGA
1 TTTGAGAAAATTAATTATGA
*
3435604 TTTTGAGAAAATTAATTTTGA
1 -TTTGAGAAAATTAATTATGA
3435625 T
1 T
3435626 CAAGTAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 6 0.16
20 6 0.16
21 26 0.68
ACGTcount: A:0.37, C:0.03, G:0.15, T:0.45
Consensus pattern (20 bp):
TTTGAGAAAATTAATTATGA
Found at i:3435768 original size:20 final size:19
Alignment explanation
Indices: 3435725--3435768 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3435715 ATTGAATTTG
*
3435725 AAAATTGGACTTGAGATAA
1 AAAATTGGACTTGAGAAAA
3435744 AAAATTGGAAC-TGAGAAACA
1 AAAATTGG-ACTTGAGAAA-A
3435764 AAAAT
1 AAAAT
3435769 CGAGATTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.55, C:0.07, G:0.18, T:0.20
Consensus pattern (19 bp):
AAAATTGGACTTGAGAAAA
Found at i:3442969 original size:17 final size:18
Alignment explanation
Indices: 3442947--3442982 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3442937 CAATTTGGGT
3442947 CATGTGGG-CCACACGGG
1 CATGTGGGCCCACACGGG
3442964 CATGTGGGCCCACACGGG
1 CATGTGGGCCCACACGGG
3442982 C
1 C
3442983 GAACATCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.17, C:0.33, G:0.39, T:0.11
Consensus pattern (18 bp):
CATGTGGGCCCACACGGG
Found at i:3446230 original size:18 final size:17
Alignment explanation
Indices: 3446208--3446251 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
3446198 TAAAAATACG
3446208 TTTTGAAATTGAATAATGA
1 TTTTGAAA-TGAATAAT-A
3446227 -TTTGTAAATGAATAATA
1 TTTTG-AAATGAATAATA
3446244 TTTTGAAA
1 TTTTGAAA
3446252 ACAAACAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.17
18 16 0.70
19 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (17 bp):
TTTTGAAATGAATAATA
Found at i:3451244 original size:71 final size:71
Alignment explanation
Indices: 3451129--3451267 Score: 244
Period size: 72 Copynumber: 2.0 Consensus size: 71
3451119 ACCAACACCA
* *
3451129 TGATAAAGAATTGTACTCATTTTTTATTTTTAATTTGATGTA-TTTTTTGTGTTTAAATTTCGTT
1 TGATAAAGAATTGCACTCATTTTTTATTTTTAATATGATGTATTTTTTTGTGTTTAAATTTCGTT
3451193 TTAATT
66 TTAATT
3451199 TGATAAAGAATTGCACTCATTTTTTTATTTTTAATATGATGTATTTTTTTGTGTTTAAATTTCGT
1 TGATAAAGAATTGCACTCA-TTTTTTATTTTTAATATGATGTATTTTTTTGTGTTTAAATTTCGT
3451264 TTTA
65 TTTA
3451268 CTTACAATTT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
70 18 0.28
71 22 0.34
72 25 0.38
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.58
Consensus pattern (71 bp):
TGATAAAGAATTGCACTCATTTTTTATTTTTAATATGATGTATTTTTTTGTGTTTAAATTTCGTT
TTAATT
Found at i:3451291 original size:71 final size:71
Alignment explanation
Indices: 3451133--3451274 Score: 218
Period size: 71 Copynumber: 2.0 Consensus size: 71
3451123 ACACCATGAT
* *
3451133 AAAGAATTGTACTCA-TTTTTTATTTTTAATTTGATGTATTTTTTGTGTTTAAATTTCGTTTTAA
1 AAAGAATTGCACTCATTTTTTTATTTTTAATATGATGTATTTTTTGTGTTTAAATTTCGTTTTAA
* *
3451197 TTTGAT
66 CTTGAC
3451203 AAAGAATTGCACTCATTTTTTTATTTTTAATATGATGTATTTTTTTGTGTTTAAATTTCGTTTT-
1 AAAGAATTGCACTCATTTTTTTATTTTTAATATGATGTA-TTTTTTGTGTTTAAATTTCGTTTTA
3451267 ACTT-AC
65 ACTTGAC
3451273 AA
1 AA
3451275 TTTATTTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
70 17 0.26
71 25 0.38
72 24 0.36
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (71 bp):
AAAGAATTGCACTCATTTTTTTATTTTTAATATGATGTATTTTTTGTGTTTAAATTTCGTTTTAA
CTTGAC
Found at i:3452070 original size:116 final size:110
Alignment explanation
Indices: 3451829--3452125 Score: 306
Period size: 113 Copynumber: 2.6 Consensus size: 110
3451819 CCACAAAATC
* * * *
3451829 TCTTAACCAAAACGCAGCGTTTTCGTCTTGATGTATACAAGAATTAGTGGCGCTTAGGAGAAAAC
1 TCTTAACCAAAACGCA-CATTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTAAG-GAAAAC
* * * * * * * *
3451894 GCCGTTAAAGCGTATTAGTGGCGTTTTGCGAGATGCGCCGCAAAATA
64 GCCGCTAAAGCGTATTAGCGGCGCTTTGCAAAAAGCACCGCAAAAGA
* * * *
3451941 TCTTAACCAAAACGCATCATTTTTGGTGTTGATGTATCCTAGAATTAGTGACGCTTACCGGAAAA
1 TCTTAACCAAAACGCA-CA-TTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTA-AGGAAAA
*
3452006 CGCCGCTAACGCATAGTATTAGCGGCGCTTTGCAAAAAGCACCGCAAAAGA
63 CGCCGCTAAAGC---GTATTAGCGGCGCTTTGCAAAAAGCACCGCAAAAGA
* * * * **
3452057 TCTTAACCAAAACGCAGAGTTCGGTCTTGAGGTATGTTAGAATTAGTGGCGCTTATAGGAAAACG
1 TCTTAACCAAAACGCACATTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTA-AGGAAAACG
3452122 CCGC
65 CCGC
3452126 AAACAGATAG
Statistics
Matches: 153, Mismatches: 27, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
112 17 0.11
113 47 0.31
114 43 0.28
115 1 0.01
116 45 0.29
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (110 bp):
TCTTAACCAAAACGCACATTTTGGTCTTGATGTATACTAGAATTAGTGGCGCTTAAGGAAAACGC
CGCTAAAGCGTATTAGCGGCGCTTTGCAAAAAGCACCGCAAAAGA
Found at i:3452677 original size:115 final size:115
Alignment explanation
Indices: 3452138--3452678 Score: 543
Period size: 115 Copynumber: 4.7 Consensus size: 115
3452128 ACAGATAGTG
* * *
3452138 AAAAGCGCCGCAAAATATTTGAACCAAAACACATCGTTTTGGTATTGATGTATACTAGAATTAGT
1 AAAAGCGCCGCAAAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGT
* * * *
3452203 GGCGTTTACAGT-AAAATGCCGCTAAAGCATAGTATTAGCGGCGATTCTTTGC
66 GGCGCTTAC-GTGGAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTC--TGC
* * * *
3452255 --TAGCGCCGCAAAATATCCT-AACTAAAACGCAGCGTTTTGGTCTTGATGTATACTAAAATTAG
1 AAAAGCGCCGCAAAATAT-CTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAG
*
3452317 TGGCGCTTACG-GGAAACGCCGCTAAAGAATAGTATTAGCGGCGCTTACTG-
65 TGGCGCTTACGTGGAAACGCCGCTAAAGCATAGTATTAGCGGCGCTT-CTGC
* * * **
3452367 AAAAGCGCCACAAAATATCTTAACCAAAACGCATAGTTTTAATCTTGATGTATACTAGAATTAGT
1 AAAAGCGCCGCAAAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGT
* * * *
3452432 GGCGCTTAC-TAGAAAACACCGTTAAATCATAGTATTAGCGGCGCTT-TGC
66 GGCGCTTACGT-GGAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTCTGC
* * * ** * **
3452481 AAAAAGCACCGCAACATATCTTAA-CAAAACGCAGAG-TTTGGTCTTGAGGTATGTTAGAATTAG
1 -AAAAGCGCCGCAAAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAG
* *
3452544 TGGCGCTTA--TAGGAAAACGCCGC-AACTGGATAGTATTAGCGGCGCTTC-GC
65 TGGCGCTTACGT-GG-AAACGCCGCTAA-AGCATAGTATTAGCGGCGCTTCTGC
** * * **
3452594 GGAAGCGCCGCAAAAATATCTGAACCAAAACGCATCGCTTTGGTCTCGATGTATACTTCAATTAG
1 AAAAGCGCCGC-AAAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAG
*
3452659 TGGCGCTTACGTTGAAACGC
65 TGGCGCTTACGTGGAAACGC
3452679 AGCGTTTTGG
Statistics
Matches: 352, Mismatches: 54, Indels: 38
0.79 0.12 0.09
Matches are distributed among these distances:
112 13 0.04
113 74 0.21
114 113 0.32
115 149 0.42
116 2 0.01
117 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (115 bp):
AAAAGCGCCGCAAAATATCTGAACCAAAACGCATCGTTTTGGTCTTGATGTATACTAGAATTAGT
GGCGCTTACGTGGAAACGCCGCTAAAGCATAGTATTAGCGGCGCTTCTGC
Found at i:3452699 original size:52 final size:52
Alignment explanation
Indices: 3452621--3452719 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 52
3452611 ATCTGAACCA
* **
3452621 AAACGCATCGCTTTGGTCTCGATGTATACTTCAATTAGTGGCGCTTACGTTG
1 AAACGCAGCGCTTTGGTCTCGATGTATACTAAAATTAGTGGCGCTTACGTTG
*
3452673 AAACGCAGCGTTTTGGTCGT-GATGTATACTAAAATTAGTGGCGCTTA
1 AAACGCAGCGCTTTGGTC-TCGATGTATACTAAAATTAGTGGCGCTTA
3452720 GGGTAAACCG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 41 0.98
53 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (52 bp):
AAACGCAGCGCTTTGGTCTCGATGTATACTAAAATTAGTGGCGCTTACGTTG
Found at i:3452901 original size:49 final size:47
Alignment explanation
Indices: 3452848--3452955 Score: 110
Period size: 49 Copynumber: 2.2 Consensus size: 47
3452838 GTTTATCATA
* ** *
3452848 TTTGGTTTAGGTTTAGGGTATTAGGGTTCATTATATAATGTTTAGTATT
1 TTTGGTTTAGGTTTAGGGT-TTAAGGTTCACAATAT-AGGTTTAGTATT
* * *
3452897 TTTGGATTATA-ATTTAGGGTTTAAGGTTTACAATATAGGTTTAGTGTT
1 TTTGG-TT-TAGGTTTAGGGTTTAAGGTTCACAATATAGGTTTAGTATT
3452945 TTTGGTTTAGG
1 TTTGGTTTAGG
3452956 GTTTGAGAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
46 2 0.04
47 2 0.04
48 15 0.31
49 17 0.35
50 10 0.21
51 2 0.04
ACGTcount: A:0.23, C:0.02, G:0.25, T:0.50
Consensus pattern (47 bp):
TTTGGTTTAGGTTTAGGGTTTAAGGTTCACAATATAGGTTTAGTATT
Found at i:3453290 original size:21 final size:21
Alignment explanation
Indices: 3453260--3453299 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3453250 TACAATGCAT
*
3453260 GGTTTTGAGTGTAAGGTTTCG
1 GGTTTAGAGTGTAAGGTTTCG
3453281 GGTTTAGAGTGTAAGGTTT
1 GGTTTAGAGTGTAAGGTTT
3453300 GCAGTTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTTAGAGTGTAAGGTTTCG
Found at i:3453306 original size:21 final size:21
Alignment explanation
Indices: 3453261--3453308 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3453251 ACAATGCATG
* *
3453261 GTTTTGAGTGTAAGGTTTCGG
1 GTTTAGAGTGTAAGGTTTCGA
3453282 GTTTAGAGTGTAAGGTTT-GCA
1 GTTTAGAGTGTAAGGTTTCG-A
3453303 GTTTAG
1 GTTTAG
3453309 GGTTTAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.19, C:0.04, G:0.35, T:0.42
Consensus pattern (21 bp):
GTTTAGAGTGTAAGGTTTCGA
Found at i:3453347 original size:29 final size:30
Alignment explanation
Indices: 3453272--3453352 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 30
3453262 TTTTGAGTGT
* * *
3453272 AAGGTTTCGGGTTTAGA-GTGTAAGGTTTG
1 AAGGTTACGGGTTTAGAGGTGTAAAGTTTA
* *
3453301 CAGTTTA-GGGTTTAAGAGGT-TAAAGTTTA
1 AAGGTTACGGGTTT-AGAGGTGTAAAGTTTA
3453330 AAGGTTACGGGTTTAGA-GTGTAA
1 AAGGTTACGGGTTTAGAGGTGTAA
3453353 GGTTAGGAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
28 8 0.20
29 25 0.61
30 8 0.20
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.36
Consensus pattern (30 bp):
AAGGTTACGGGTTTAGAGGTGTAAAGTTTA
Found at i:3454132 original size:22 final size:22
Alignment explanation
Indices: 3454107--3454172 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 22
3454097 CCACTCTGAT
*
3454107 TTTCCCAATTTCATTTCCCGAA-
1 TTTCCC-ATTTCATTTCCCCAAC
*
3454129 TTTCCCATTTCCTATTCCCCCAAC
1 TTTCCCATTT-C-ATTTCCCCAAC
*
3454153 TTCCCCGATTTCATTTCCCC
1 TTTCCC-ATTTCATTTCCCC
3454173 CCAATTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 15 0.42
24 6 0.17
25 4 0.11
ACGTcount: A:0.17, C:0.41, G:0.03, T:0.39
Consensus pattern (22 bp):
TTTCCCATTTCATTTCCCCAAC
Found at i:3454188 original size:40 final size:40
Alignment explanation
Indices: 3454132--3454211 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
3454122 TCCCGAATTT
* * *
3454132 CCCATTTCCTATTCCCCCAACTTCCCCGATTTCATTTCCC
1 CCCAATTCCTATTCCCCCAACTTCCCCAATTTAATTTCCC
* *
3454172 CCCAATTCCTTTTCCCCCAATTTCCCCAATTTAATTTCCC
1 CCCAATTCCTATTCCCCCAACTTCCCCAATTTAATTTCCC
3454212 TAAATCCCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.17, C:0.45, G:0.01, T:0.36
Consensus pattern (40 bp):
CCCAATTCCTATTCCCCCAACTTCCCCAATTTAATTTCCC
Found at i:3454196 original size:16 final size:16
Alignment explanation
Indices: 3454155--3454196 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3454145 CCCCCAACTT
* *
3454155 CCCCGATTTCATTTCC
1 CCCCAATTTCCTTTCC
*
3454171 CCCCAA-TTCCTTTTC
1 CCCCAATTTCCTTTCC
3454186 CCCCAATTTCC
1 CCCCAATTTCC
3454197 CCAATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.14, C:0.48, G:0.02, T:0.36
Consensus pattern (16 bp):
CCCCAATTTCCTTTCC
Found at i:3455676 original size:17 final size:17
Alignment explanation
Indices: 3455656--3455716 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
3455646 TTAATATCTA
3455656 TATAAGTTTTCTAAATT
1 TATAAGTTTTCTAAATT
3455673 TATAAGTTTTCT--A--
1 TATAAGTTTTCTAAATT
* *
3455686 TATTAG-TAT-TAAATT
1 TATAAGTTTTCTAAATT
3455701 TATAAGTTTTCTAAAT
1 TATAAGTTTTCTAAAT
3455717 AAGTGTTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
11 1 0.03
12 2 0.06
13 6 0.18
15 6 0.18
16 2 0.06
17 17 0.50
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTCTAAATT
Found at i:3455686 original size:30 final size:30
Alignment explanation
Indices: 3455652--3455733 Score: 114
Period size: 28 Copynumber: 2.8 Consensus size: 30
3455642 TGTTTTAATA
3455652 TCTATATAAGTTTTCTAAATTTATAAGTTT
1 TCTATATAAGTTTTCTAAATTTATAAGTTT
* *
3455682 TCTATATTAG-TAT-TAAATTTATAAGTTT
1 TCTATATAAGTTTTCTAAATTTATAAGTTT
* *
3455710 TCTAAATAAGTGTTCTAAATTTAT
1 TCTATATAAGTTTTCTAAATTTAT
3455734 TAGTAATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 23 0.52
29 3 0.07
30 18 0.41
ACGTcount: A:0.35, C:0.06, G:0.07, T:0.51
Consensus pattern (30 bp):
TCTATATAAGTTTTCTAAATTTATAAGTTT
Found at i:3455825 original size:27 final size:27
Alignment explanation
Indices: 3455784--3455874 Score: 164
Period size: 27 Copynumber: 3.4 Consensus size: 27
3455774 AAATAATTAT
3455784 ATAACTTACACAACTTACACAACTTAC
1 ATAACTTACACAACTTACACAACTTAC
* *
3455811 ATAACATACATAACTTACACAACTTAC
1 ATAACTTACACAACTTACACAACTTAC
3455838 ATAACTTACACAACTTACACAACTTAC
1 ATAACTTACACAACTTACACAACTTAC
3455865 ATAACTTACA
1 ATAACTTACA
3455875 TAATAAATAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 60 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.26
Consensus pattern (27 bp):
ATAACTTACACAACTTACACAACTTAC
Found at i:3455875 original size:9 final size:9
Alignment explanation
Indices: 3455784--3455877 Score: 134
Period size: 9 Copynumber: 10.4 Consensus size: 9
3455774 AAATAATTAT
3455784 ATAACTTAC
1 ATAACTTAC
*
3455793 ACAACTTAC
1 ATAACTTAC
*
3455802 ACAACTTAC
1 ATAACTTAC
*
3455811 ATAACATAC
1 ATAACTTAC
3455820 ATAACTTAC
1 ATAACTTAC
*
3455829 ACAACTTAC
1 ATAACTTAC
3455838 ATAACTTAC
1 ATAACTTAC
*
3455847 ACAACTTAC
1 ATAACTTAC
*
3455856 ACAACTTAC
1 ATAACTTAC
3455865 ATAACTTAC
1 ATAACTTAC
3455874 ATAA
1 ATAA
3455878 TAAATAACTT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 77 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (9 bp):
ATAACTTAC
Found at i:3459236 original size:21 final size:21
Alignment explanation
Indices: 3459211--3459279 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
3459201 CAACTTAAAA
*
3459211 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCAGCAGCGAGAGAAG
*
3459232 CAGAGGCTGCAGCGAGAGAAG
1 CAGAGGCAGCAGCGAGAGAAG
*
3459253 CAGAGGCCGCAGCGAGAGAAG
1 CAGAGGCAGCAGCGAGAGAAG
3459274 CAGAGG
1 CAGAGG
3459280 TTCAAAAGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.33, C:0.20, G:0.45, T:0.01
Consensus pattern (21 bp):
CAGAGGCAGCAGCGAGAGAAG
Found at i:3459831 original size:42 final size:42
Alignment explanation
Indices: 3459779--3459919 Score: 147
Period size: 43 Copynumber: 3.3 Consensus size: 42
3459769 AACATTACTT
* **
3459779 TTAGCAGCGTTTTCTCCCAAGCATTGCTAAAGAACATGATCA
1 TTAGCGGCGTTTTCTCCCAAGCACCGCTAAAGAACATGATCA
* * *
3459821 TTAGCGGCGTTTTTTTCCTAAGCGCCGCTAAAGAACATGATCA
1 TTAGCGGCG-TTTTCTCCCAAGCACCGCTAAAGAACATGATCA
* ** * * *
3459864 TTAGCGGCGTTTTTTTCTTAAGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCG-TTTTCTCCCAAGCACCGCTAAAGAACATGATCA
*
3459907 TTAGCGGCTTTTT
1 TTAGCGGCGTTTT
3459920 TTCTGTAAGC
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 12 0.14
43 76 0.86
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (42 bp):
TTAGCGGCGTTTTCTCCCAAGCACCGCTAAAGAACATGATCA
Found at i:3459858 original size:43 final size:43
Alignment explanation
Indices: 3459804--3459939 Score: 211
Period size: 43 Copynumber: 3.2 Consensus size: 43
3459794 CCCAAGCATT
3459804 GCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCTAAGCGCC
1 GCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCTAAGCGCC
*
3459847 GCTAAAGAACATGATCATTAGCGGCGTTTTTTTCTTAAGCGCC
1 GCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCTAAGCGCC
* * *
3459890 GCTAAAGAACATGACCTTTAGCGGC-TTTTTTTCTGTAAGCGCC
1 GCTAAAGAACATGATCATTAGCGGCGTTTTTTTC-CTAAGCGCC
*
3459933 GCAAAAG
1 GCTAAAG
3459940 TTAGCGACGT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 8 0.09
43 79 0.91
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (43 bp):
GCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCTAAGCGCC
Found at i:3460286 original size:22 final size:22
Alignment explanation
Indices: 3460261--3460302 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3460251 TTTAATATTG
*
3460261 TTAAATATGTAATTATTAATCC
1 TTAAATATATAATTATTAATCC
* *
3460283 TTAAATTTATAATTCTTAAT
1 TTAAATATATAATTATTAAT
3460303 TTTTTATTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAAATATATAATTATTAATCC
Found at i:3460900 original size:55 final size:53
Alignment explanation
Indices: 3460837--3461000 Score: 139
Period size: 55 Copynumber: 3.2 Consensus size: 53
3460827 CATATATTAA
*
3460837 AATATTAACAAAAAATTATAATAAATTGTGTTTTATATTCTTACTAAGATATCAT
1 AATATTAACAACAAATTATAATAAATT-T-TTTTATATTCTTACTAAGATATCAT
** ** * * * *
3460892 AATATTAACTAACTTATT-TTTTAAA---ATTTATATTC---C--ATATATTAA
1 AATATTAAC-AACAAATTATAATAAATTTTTTTATATTCTTACTAAGATATCAT
3460937 AATATTAACAACAAATTATAATAAATTATTTTTTATATTCTTACTAAGATATCAT
1 AATATTAACAACAAATTATAATAAA-T-TTTTTTATATTCTTACTAAGATATCAT
3460992 AATATTAAC
1 AATATTAAC
3461001 TAATTTGAAT
Statistics
Matches: 80, Mismatches: 17, Indels: 24
0.66 0.14 0.20
Matches are distributed among these distances:
44 6 0.08
45 20 0.25
47 1 0.01
50 18 0.22
53 1 0.01
55 29 0.36
56 5 0.06
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (53 bp):
AATATTAACAACAAATTATAATAAATTTTTTTATATTCTTACTAAGATATCAT
Found at i:3460919 original size:100 final size:100
Alignment explanation
Indices: 3460811--3461003 Score: 350
Period size: 100 Copynumber: 1.9 Consensus size: 100
3460801 TTAAAAAATA
* *
3460811 TTTAAAATTTATATTTCATATATTAAAATATTAACAAAAAATTATAATAAATTGTGTTTTATATT
1 TTTAAAATTTATATTCCATATATTAAAATATTAACAAAAAATTATAATAAATTATGTTTTATATT
3460876 CTTACTAAGATATCATAATATTAACTAACTTATTT
66 CTTACTAAGATATCATAATATTAACTAACTTATTT
* *
3460911 TTTAAAATTTATATTCCATATATTAAAATATTAACAACAAATTATAATAAATTATTTTTTATATT
1 TTTAAAATTTATATTCCATATATTAAAATATTAACAAAAAATTATAATAAATTATGTTTTATATT
3460976 CTTACTAAGATATCATAATATTAACTAA
66 CTTACTAAGATATCATAATATTAACTAA
3461004 TTTGAATATT
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (100 bp):
TTTAAAATTTATATTCCATATATTAAAATATTAACAAAAAATTATAATAAATTATGTTTTATATT
CTTACTAAGATATCATAATATTAACTAACTTATTT
Found at i:3460972 original size:50 final size:49
Alignment explanation
Indices: 3460818--3460976 Score: 121
Period size: 50 Copynumber: 3.2 Consensus size: 49
3460808 ATATTTAAAA
* * *
3460818 TTTATATTTCATATATTAAAATATTAACAAAAAATTATAATAAATTGTGT
1 TTTATATTCCATATATTAAAATATTAACAACAAATTATAATAAATTAT-T
* * * ** **
3460868 TTTATATTCTTACTAAGATATCATAATATTAACTAACTTATT-TTTTAAA--A--
1 TTTATATTC---C--ATATATTAAAATATTAAC-AACAAATTATAATAAATTATT
3460918 TTTATATTCCATATATTAAAATATTAACAACAAATTATAATAAATTATTT
1 TTTATATTCCATATATTAAAATATTAACAACAAATTATAATAAATTA-TT
3460968 TTTATATTC
1 TTTATATTC
3460977 TTACTAAGAT
Statistics
Matches: 80, Mismatches: 17, Indels: 24
0.66 0.14 0.20
Matches are distributed among these distances:
44 6 0.08
45 20 0.25
47 2 0.03
50 26 0.32
53 1 0.01
55 20 0.25
56 5 0.06
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (49 bp):
TTTATATTCCATATATTAAAATATTAACAACAAATTATAATAAATTATT
Found at i:3462330 original size:11 final size:11
Alignment explanation
Indices: 3462316--3462349 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3462306 AAAAATAAAC
3462316 TTTTAATATTT
1 TTTTAATATTT
3462327 TTTTAATATTT
1 TTTTAATATTT
**
3462338 TTAGAATATTT
1 TTTTAATATTT
3462349 T
1 T
3462350 AAGATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTTAATATTT
Found at i:3462338 original size:9 final size:9
Alignment explanation
Indices: 3462316--3462368 Score: 54
Period size: 9 Copynumber: 5.6 Consensus size: 9
3462306 AAAAATAAAC
3462316 TTTTAATATTT
1 TTTTAATA--T
3462327 TTTTAATAT
1 TTTTAATAT
3462336 TTTTAGA-AT
1 TTTTA-ATAT
*
3462345 ATTTTAAGAT
1 -TTTTAATAT
3462355 TTTTAATAT
1 TTTTAATAT
3462364 TTTTA
1 TTTTA
3462369 TAATTTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 22 0.58
10 8 0.21
11 8 0.21
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (9 bp):
TTTTAATAT
Found at i:3462349 original size:19 final size:17
Alignment explanation
Indices: 3462327--3462376 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
3462317 TTTAATATTT
3462327 TTTTAATATTTTTAGAATA
1 TTTTAATATTTTT--AATA
*
3462346 TTTTAAGATTTTTAATA
1 TTTTAATATTTTTAATA
*
3462363 TTTTTATAATTTTT
1 TTTTAAT-ATTTTT
3462377 TTACAATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.33
18 6 0.22
19 12 0.44
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TTTTAATATTTTTAATA
Found at i:3467474 original size:34 final size:33
Alignment explanation
Indices: 3467428--3467492 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
3467418 AAATGAATAT
* *
3467428 TATTTTATCTATTTGA-TGTTGATTAGGATAAAA
1 TATTTTATCTATTCGACT-TTGATTAGAATAAAA
3467461 TATTTTAATCTATTCGACTTTGATTAGAATAA
1 TATTTT-ATCTATTCGACTTTGATTAGAATAA
3467493 GGGTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
34 21 0.75
35 1 0.04
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (33 bp):
TATTTTATCTATTCGACTTTGATTAGAATAAAA
Found at i:3468417 original size:40 final size:40
Alignment explanation
Indices: 3468352--3468506 Score: 253
Period size: 39 Copynumber: 3.9 Consensus size: 40
3468342 AAATATATTT
* *
3468352 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
3468392 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 A-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
3468433 A-TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT-A
3468473 ATTTTTTT-ATTTTAAAATA-TTTTAAAATACTTTT
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
3468507 AAAATACTTT
Statistics
Matches: 110, Mismatches: 2, Indels: 7
0.92 0.02 0.06
Matches are distributed among these distances:
39 52 0.47
40 14 0.13
41 44 0.40
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:3468461 original size:50 final size:50
Alignment explanation
Indices: 3468403--3468530 Score: 113
Period size: 50 Copynumber: 2.5 Consensus size: 50
3468393 TTTTTTTTAA
** *
3468403 TTTTAAAATA-TTTTTAAAATACTTTTTTTAATTTT-TTA-ATTTTAAAATAT
1 TTTTAAAATACTTTTTAAAA-A-TTTTTTT-ATTTTAAAATATTTTAAAATAC
**
3468453 TTTTAAAATACTTTTTTTAAATTTTTTT--ATTTTAAAATATTTTAAAATAC
1 TTTTAAAATAC--TTTTTAAAAATTTTTTTATTTTAAAATATTTTAAAATAC
*
3468503 TTTTAAAATACTTTTTTTAAAATTTTTT
1 TTTTAAAATAC-TTTTTAAAAATTTTTT
3468531 AAAATTTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
48 5 0.08
49 14 0.22
50 32 0.50
51 5 0.08
53 8 0.12
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (50 bp):
TTTTAAAATACTTTTTAAAAATTTTTTTATTTTAAAATATTTTAAAATAC
Found at i:3468467 original size:28 final size:28
Alignment explanation
Indices: 3468414--3468467 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
3468404 TTTAAAATAT
** *
3468414 TTTTAAAATACTTTTTTTAATTTTTTAA
1 TTTTAAAATACTTTTTAAAATCTTTTAA
3468442 TTTTAAAATA-TTTTTAAAATACTTTT
1 TTTTAAAATACTTTTTAAAAT-CTTTT
3468468 TTTAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAAATACTTTTTAAAATCTTTTAA
Found at i:3468493 original size:10 final size:10
Alignment explanation
Indices: 3468480--3468545 Score: 71
Period size: 10 Copynumber: 6.2 Consensus size: 10
3468470 TAAATTTTTT
3468480 TATTTTAAAA
1 TATTTTAAAA
3468490 TATTTTAAAA
1 TATTTTAAAA
3468500 TACTTTTAAAA
1 TA-TTTTAAAA
3468511 TACTTTTTTTAAAA
1 TA----TTTTAAAA
*
3468525 TTTTTTAAAA
1 TATTTTAAAA
3468535 T-TTTTAAAA
1 TATTTTAAAA
3468544 TA
1 TA
3468546 AAAATGGGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
9 9 0.18
10 21 0.43
11 10 0.20
14 9 0.18
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:3468518 original size:39 final size:39
Alignment explanation
Indices: 3468352--3468535 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 39
3468342 AAATATATTT
* *
3468352 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTAA
1 ATTTTTTT-ATTTTAAAATATTTTTAAAATAC-TTTTTTAA
* *
3468393 TTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTT-ATTTTAAAATATTTTTAAAATACTTTTTTAA
*
3468433 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 ATTTTTTTATTTTAAAATATTTTTAAAATAC-TTTTTTAA
3468473 ATTTTTTTATTTTAAAATA-TTTTAAAATAC--TTTTAA
1 ATTTTTTTATTTTAAAATATTTTTAAAATACTTTTTTAA
* **
3468509 AATACTTT-TTTTAAAAT-TTTTTAAAAT
1 ATTTTTTTATTTTAAAATATTTTTAAAAT
3468536 TTTTAAAATA
Statistics
Matches: 130, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
35 18 0.14
36 11 0.08
39 34 0.26
40 38 0.29
41 29 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (39 bp):
ATTTTTTTATTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:3468519 original size:41 final size:42
Alignment explanation
Indices: 3468351--3468545 Score: 246
Period size: 39 Copynumber: 4.8 Consensus size: 42
3468341 TAAATATATT
* *
3468351 TATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTTTAA
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
3468393 T-TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT-A
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
3468433 -A-TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
**
3468473 -ATTTTTTT-ATTTTAAAATA-TTTTAAAATAC-TTTTAAAA
1 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
*
3468511 TACTTTTTTTAAAATTTTTTAAA-ATTTTTAAAATA
1 TA-TTTTTTT--AA-TTTTAAAATATTTTTAAAATA
3468546 AAAATGGGCC
Statistics
Matches: 138, Mismatches: 5, Indels: 18
0.86 0.03 0.11
Matches are distributed among these distances:
38 6 0.04
39 49 0.36
40 21 0.15
41 42 0.30
42 1 0.01
43 2 0.01
44 17 0.12
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (42 bp):
TATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAA
Found at i:3469155 original size:61 final size:61
Alignment explanation
Indices: 3469060--3469181 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
3469050 CCAACAATAT
3469060 TTGTACCTAAACTTGGACATTATCAAAGGTAAATGAATAGTCACTGCTTAAAATTAAGAGC
1 TTGTACCTAAACTTGGACATTATCAAAGGTAAATGAATAGTCACTGCTTAAAATTAAGAGC
3469121 TTGTACCTAAACTTGGACATTATCAAAGGTAAATGAATAGTCACTGCTTAAAATTAAGAGC
1 TTGTACCTAAACTTGGACATTATCAAAGGTAAATGAATAGTCACTGCTTAAAATTAAGAGC
3469182 AGGTACAAGT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (61 bp):
TTGTACCTAAACTTGGACATTATCAAAGGTAAATGAATAGTCACTGCTTAAAATTAAGAGC
Found at i:3493056 original size:30 final size:29
Alignment explanation
Indices: 3492977--3493065 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
3492967 ATACTAAAAC
3492977 TATACATG-AACTATGATTTCATGTACAATTG
1 TATACATGAAACT-TGATTT--TGTACAATTG
* *
3493008 TATACAT-AAACTTTGATTTTGTGCAATTT
1 TATACATGAAAC-TTGATTTTGTACAATTG
* *
3493037 TATACATGAAATCTTGATTTGGTCCAATT
1 TATACATGAAA-CTTGATTTTGTACAATT
3493066 CTTGTAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
29 15 0.30
30 17 0.34
31 17 0.34
32 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (29 bp):
TATACATGAAACTTGATTTTGTACAATTG
Found at i:3494478 original size:14 final size:14
Alignment explanation
Indices: 3494461--3494522 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
3494451 ATAAAATATT
3494461 TTTATTTAAATTTA
1 TTTATTTAAATTTA
* *
3494475 TTTATTAAAAATTA
1 TTTATTTAAATTTA
*
3494489 TTAATTTAATATTTA
1 TTTATTTAA-ATTTA
*
3494504 TATATTT-AATTTAA
1 TTTATTTAAATTT-A
3494518 TTTAT
1 TTTAT
3494523 CTCAATCTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 4 0.11
14 25 0.66
15 9 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATTTAAATTTA
Found at i:3494510 original size:15 final size:14
Alignment explanation
Indices: 3494455--3494513 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
3494445 AATAATATAA
3494455 AATATTT-TTATTT
1 AATATTTATTATTT
3494468 AA-ATTTATT-TATT
1 AATATTTATTAT-TT
* *
3494481 AAAAATTATTAATTT
1 AATATTTATT-ATTT
3494496 AATATTTATATATTT
1 AATATTTAT-TATTT
3494511 AAT
1 AAT
3494514 TTAATTTATC
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
12 5 0.14
13 8 0.22
14 6 0.16
15 16 0.43
16 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AATATTTATTATTT
Found at i:3495483 original size:3 final size:3
Alignment explanation
Indices: 3495477--3495511 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3495467 ATTGTTGTAC
3495477 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3495512 TTATTATCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3498013 original size:19 final size:18
Alignment explanation
Indices: 3497981--3498018 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3497971 ATATATATTT
3497981 TATTTTTTAATTTAAAAA
1 TATTTTTTAATTTAAAAA
* *
3497999 TATTTTTTATTTTTAAAA
1 TATTTTTTAATTTAAAAA
3498017 TA
1 TA
3498019 AAATTTTGGT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTTTTTAATTTAAAAA
Found at i:3498020 original size:24 final size:25
Alignment explanation
Indices: 3497966--3498021 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
3497956 GCTCGAATAT
*
3497966 AATAAATATATATTTTATTTTTTAA
1 AATAAAAATATATTTTATTTTTTAA
** *
3497991 TTTAAAAATATTTTTTA-TTTTTAA
1 AATAAAAATATATTTTATTTTTTAA
3498015 AATAAAA
1 AATAAAA
3498022 TTTTGGTGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
AATAAAAATATATTTTATTTTTTAA
Found at i:3498021 original size:23 final size:24
Alignment explanation
Indices: 3497966--3498022 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
3497956 GCTCGAATAT
3497966 AATAAATATATATTTTATTTTTTAA
1 AATAAA-ATATATTTTATTTTTTAA
** *
3497991 TTTAAAA-ATATTTTTTATTTTTAA
1 AATAAAATATATTTTAT-TTTTTAA
3498015 AATAAAAT
1 AATAAAAT
3498023 TTTGGTGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
23 8 0.32
24 13 0.52
25 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATAAAATATATTTTATTTTTTAA
Found at i:3504120 original size:78 final size:78
Alignment explanation
Indices: 3503991--3504152 Score: 324
Period size: 78 Copynumber: 2.1 Consensus size: 78
3503981 GGCCTTTCCT
3503991 AACATAGGTTCAACCCATAACATTACCCCCTCTTGCCATATGAGCTTATCCTTAAGTTCGAAGTC
1 AACATAGGTTCAACCCATAACATTACCCCCTCTTGCCATATGAGCTTATCCTTAAGTTCGAAGTC
3504056 AAGATTACTTGAC
66 AAGATTACTTGAC
3504069 AACATAGGTTCAACCCATAACATTACCCCCTCTTGCCATATGAGCTTATCCTTAAGTTCGAAGTC
1 AACATAGGTTCAACCCATAACATTACCCCCTCTTGCCATATGAGCTTATCCTTAAGTTCGAAGTC
3504134 AAGATTACTTGAC
66 AAGATTACTTGAC
3504147 AACATA
1 AACATA
3504153 AATCAACCTA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 84 1.00
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (78 bp):
AACATAGGTTCAACCCATAACATTACCCCCTCTTGCCATATGAGCTTATCCTTAAGTTCGAAGTC
AAGATTACTTGAC
Found at i:3506055 original size:17 final size:17
Alignment explanation
Indices: 3506033--3506075 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3506023 AAACAATTAA
*
3506033 TATTAATTGCTTAAATG
1 TATTAATTACTTAAATG
3506050 TATTAATTACTTAAATG
1 TATTAATTACTTAAATG
3506067 TATTAATTA
1 TATTAATTA
3506076 TTGATATTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.49
Consensus pattern (17 bp):
TATTAATTACTTAAATG
Found at i:3512777 original size:12 final size:13
Alignment explanation
Indices: 3512754--3512785 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
3512744 AAACTGATGC
3512754 TTTACGATAAAAT
1 TTTACGATAAAAT
3512767 TTTAC-ATAAAAT
1 TTTACGATAAAAT
3512779 TTTACGA
1 TTTACGA
3512786 GCATTTTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
TTTACGATAAAAT
Found at i:3512887 original size:67 final size:67
Alignment explanation
Indices: 3512779--3512908 Score: 181
Period size: 66 Copynumber: 1.9 Consensus size: 67
3512769 TACATAAAAT
* ** * **
3512779 TTTACGAGCATTTTGTCTCAGTAACTTAGCCTGCTGCCAACCTGA-ACTGATGCTTAGCTATATA
1 TTTACAAGCATTTTGTAACAGTAACCTAGCCTGCTGCCAACCTGAGACCCATGCTTAGCTATATA
3512843 AA
66 AA
*
3512845 TTTACAAGCATTTTGTAACAGTAGCCTATGCCTGCTGCCAACCTGAGACCCATGCTTAGCTATA
1 TTTACAAGCATTTTGTAACAGTAACCTA-GCCTGCTGCCAACCTGAGACCCATGCTTAGCTATA
3512909 AAAAATTTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 23 0.42
67 17 0.31
68 15 0.27
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (67 bp):
TTTACAAGCATTTTGTAACAGTAACCTAGCCTGCTGCCAACCTGAGACCCATGCTTAGCTATATA
AA
Found at i:3519037 original size:216 final size:216
Alignment explanation
Indices: 3518664--3519466 Score: 1139
Period size: 216 Copynumber: 3.7 Consensus size: 216
3518654 CTCAGTTAAT
* * *
3518664 GAGTTGTAATGGCTAAAGATACTAACAATGTCACGCTAGCATGCAGAAAGATTATCGCCAA-TTA
1 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATTATCGCCAACTTG
* * * *
3518728 AAAATTCAAGCTAGGATTATTTTCATTTGACGAACCCTTCTTTTGATGAACAAACAGGGATTGAC
66 AGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTAATGAACAAACAGGGATTGAC
* *
3518793 TCATGCAAAAGGAGGTCAAGATTTAAGCAACATCTGTTGCTTGGTAGACA-CATTTTTTAGCTAG
131 TCATGCAAAAGGAGGTCAACATTTAAGCAACATCTATTGCTTGGTAGACATC-TTTTTTAGCTAG
*
3518857 CCATAATTCCTCACTTGTCAAG
195 CCATAATTCCTTACTTGTCAAG
3518879 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATTATCGCCAACTTG
1 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATTATCGCCAACTTG
* * *
3518944 AGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTGATGCACAAAGAGGGATTGAC
66 AGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTAATGAACAAACAGGGATTGAC
* *
3519009 TCATGCAAAAGGAGGTTAACAATTAAGCAACAT-TCATTGCTTGGTAGACATCTTTTTTAGCTAG
131 TCATGCAAAAGGAGGTCAACATTTAAGCAACATCT-ATTGCTTGGTAGACATCTTTTTTAGCTAG
* *
3519073 CCATAATTCTTTGCTTGTCAAG
195 CCATAATTCCTTACTTGTCAAG
* *
3519095 GAGTTGTAATGGATAAAGATATTAACAATGTCACGTTAGCTTGCAGAAAGATTATCGCCAACTTG
1 GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATTATCGCCAACTTG
* * * * * * ** *
3519160 AGAATTCAAGCTAAGATTATTCACATTCGATGAACCCTTGTTTTAATGAAAAAACAAGGACCGGC
66 AGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTAATGAACAAACAGGGATTGAC
* * * * * *
3519225 TAATGCCAAATGAAGTCAACATTTAAGCAACATCCATTGCTTGGTAGACATCTTTTTTAGTTAGC
131 TCATGCAAAAGGAGGTCAACATTTAAGCAACATCTATTGCTTGGTAGACATCTTTTTTAGCTAGC
*
3519290 CATAATTCCTTACTTGTCAGG
196 CATAATTCCTTACTTGTCAAG
* * * *
3519311 GAGTTGCAATGGCTAAAGATATTAA-AGATGTTACACTAGCTTGTAGAAAGATTATCGCCAACTT
1 GAGTTGTAATGGCTAAAGATATTAACA-ATGTCACGCTAGCTTGCAGAAAGATTATCGCCAACTT
* * * *
3519375 GAGAATTCGAGCTAGGATTATTCTCATTCGACAAACCCTTCTTTTAATGAACTAACAGGGA-TCA
65 GAGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTAATGAACAAACAGGGATTGA
*
3519439 GCTCATGCAAAAGGAAGTCAACATTTAA
130 -CTCATGCAAAAGGAGGTCAACATTTAA
3519467 CATTTTTTAG
Statistics
Matches: 521, Mismatches: 61, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
215 61 0.12
216 459 0.88
217 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (216 bp):
GAGTTGTAATGGCTAAAGATATTAACAATGTCACGCTAGCTTGCAGAAAGATTATCGCCAACTTG
AGAATTCAAGCTAGGATTATTCTCATTCGACGAACCCTTCTTTTAATGAACAAACAGGGATTGAC
TCATGCAAAAGGAGGTCAACATTTAAGCAACATCTATTGCTTGGTAGACATCTTTTTTAGCTAGC
CATAATTCCTTACTTGTCAAG
Found at i:3519606 original size:192 final size:192
Alignment explanation
Indices: 3519277--3519653 Score: 560
Period size: 192 Copynumber: 2.0 Consensus size: 192
3519267 GGTAGACATC
* * *
3519277 TTTTTTAGTTAGCCATAATTCCTTACTTGTCAGGGAGTTGCAATGGCTAAAGATATTAAAGATGT
1 TTTTTTAGCTAGCCATAATTCCTCACTTGTCAAGGAGTTGCAATGGCTAAAGATATTAAAGATGT
* * *
3519342 TACACTAGCTTGTAGAAAGATTATCGCCAACTTGAGAATTCGAGCTAGGATTATTCTCATTCGAC
66 CACACTAGCTTGCAGAAAGATTATCGCCAACTTGAGAATTCAAGCTAGGATTATTCTCATTCGAC
*
3519407 AAACCCTTCTTTTAATGAACTAA-CAGGGATCAGCTCATGCAAAAGGAAGTCAACATTTAACA
131 AAACCCTTCTTTTAATGAAC-AAGCAGGGATCAGCTCATGCAAAAGGAAGTAAACATTTAACA
*
3519469 TTTTTTAGCTAGCCATAATTCCTCACTTGTCAAGGAGTTGTAATGGCTAAAGATATTAACA-ATG
1 TTTTTTAGCTAGCCATAATTCCTCACTTGTCAAGGAGTTGCAATGGCTAAAGATATTAA-AGATG
* * * * *
3519533 TCACGCTAGCTTGCAGAAAGATTATTGCCAACTTGAGAGTTCAATCTAGGATTATTCTTATTCGA
65 TCACACTAGCTTGCAGAAAGATTATCGCCAACTTGAGAATTCAAGCTAGGATTATTCTCATTCGA
* * * * *
3519598 CGAACCCTTCTTTTGATGCACAAGCAGGGATTAGCTCATGTAAAAGGAAGTAAACA
130 CAAACCCTTCTTTTAATGAACAAGCAGGGATCAGCTCATGCAAAAGGAAGTAAACA
3519654 ATGAAGCAAC
Statistics
Matches: 165, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
191 2 0.01
192 162 0.98
193 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (192 bp):
TTTTTTAGCTAGCCATAATTCCTCACTTGTCAAGGAGTTGCAATGGCTAAAGATATTAAAGATGT
CACACTAGCTTGCAGAAAGATTATCGCCAACTTGAGAATTCAAGCTAGGATTATTCTCATTCGAC
AAACCCTTCTTTTAATGAACAAGCAGGGATCAGCTCATGCAAAAGGAAGTAAACATTTAACA
Found at i:3519832 original size:83 final size:83
Alignment explanation
Indices: 3519693--3519856 Score: 310
Period size: 83 Copynumber: 2.0 Consensus size: 83
3519683 TCTTTTTAGC
3519693 TAGCCATAATTCCTCACTTGGTGTTTTTATTTGTTCGATCACTTGTATCAAAAGAATGTTTGAAC
1 TAGCCATAATTCCTCACTTGGTGTTTTTATTTGTTCGATCACTTGTATCAAAAGAATGTTTGAAC
3519758 AACTTTAAATAGAATAGG
66 AACTTTAAATAGAATAGG
*
3519776 TAGCCATAATTCCTCACTTGGTGTTTTTATTTGTTCGATCACTTGTATCGAAAGAATGTTTGAAC
1 TAGCCATAATTCCTCACTTGGTGTTTTTATTTGTTCGATCACTTGTATCAAAAGAATGTTTGAAC
*
3519841 AACTTTAATTAGAATA
66 AACTTTAAATAGAATA
3519857 CGTTTAAGCA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (83 bp):
TAGCCATAATTCCTCACTTGGTGTTTTTATTTGTTCGATCACTTGTATCAAAAGAATGTTTGAAC
AACTTTAAATAGAATAGG
Found at i:3527419 original size:11 final size:11
Alignment explanation
Indices: 3527403--3527448 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
3527393 TGGCGTCTTC
3527403 TACAAAAATAA
1 TACAAAAATAA
3527414 TACAAAAATAA
1 TACAAAAATAA
* * *
3527425 AATAAAAAAAA
1 TACAAAAATAA
*
3527436 TACTAAAATAA
1 TACAAAAATAA
3527447 TA
1 TA
3527449 TATTTTTTTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.20
Consensus pattern (11 bp):
TACAAAAATAA
Found at i:3527911 original size:144 final size:149
Alignment explanation
Indices: 3527678--3528158 Score: 558
Period size: 144 Copynumber: 3.2 Consensus size: 149
3527668 TTTAGTGTGT
* * * * *
3527678 TTTTTATTGAAAGTAATAAAATTCGAAAAAAAAATACGAACAAAGGGCCGAAATAAGAG-TTTTT
1 TTTTTATTGAAAGTAATAAAATCCTAGAAAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTT
*
3527742 TTAATTTATTTAAAAAACACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATA-AAA
66 TTAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAA
* *
3527806 -T-T-A-GAAAATATTATA
131 TTATAACAAAAATAATATA
* * *
3527821 -TTTT-TT-AAAGTAATAAACT-CTGGGGAAAAAAATACGAATAAAGGGCCAAAATAAGGGTTTT
1 TTTTTATTGAAAGTAATAAAATCCT--AGAAAAAAATACGAATAAAGGGCCGAAATAAGGG-TTT
* *
3527882 TTTTTAAATTTATTTAAAAAATACACTAAATTAATACATTTTAAACATAATGTACTAAAATAATA
63 TTTTT-AATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATA
3527947 TAAATTAATAAAAAACAAAAATAATATA
127 TAAATT-AT----AACAAAAATAATATA
* *
3527975 TTTTTATTGAAAGTAATAAAATCCTAG-AAAAAATACGAATAAAGGACTGAAATAAGGGTTTTTT
1 TTTTTATTGAAAGTAATAAAATCCTAGAAAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTT
*
3528039 TTAATTTATTT-AAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAA
66 TTAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAA
* * * *
3528103 ATAAAAAAATAAAAAATAATA
131 TTATAACAA-AAATAAT-ATA
* *
3528124 TATTTT-TTAAAAGTAATAAAATTC-AGAAAAAAATA
1 T-TTTTATTGAAAGTAATAAAATCCTAGAAAAAAATA
3528159 TAAACAAATG
Statistics
Matches: 289, Mismatches: 26, Indels: 40
0.81 0.07 0.11
Matches are distributed among these distances:
139 1 0.00
140 12 0.04
141 31 0.11
142 4 0.01
143 7 0.02
144 56 0.19
145 3 0.01
146 1 0.00
147 4 0.01
148 9 0.03
149 28 0.10
150 4 0.01
151 1 0.00
152 51 0.18
153 10 0.03
154 18 0.06
155 32 0.11
156 3 0.01
157 12 0.04
158 2 0.01
ACGTcount: A:0.53, C:0.07, G:0.08, T:0.32
Consensus pattern (149 bp):
TTTTTATTGAAAGTAATAAAATCCTAGAAAAAAATACGAATAAAGGGCCGAAATAAGGGTTTTTT
TTAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAA
TTATAACAAAAATAATATA
Found at i:3528087 original size:152 final size:151
Alignment explanation
Indices: 3527793--3528155 Score: 475
Period size: 152 Copynumber: 2.4 Consensus size: 151
3527783 CATAATGTAC
* * * * **
3527793 TAAAATAATAAAATTAGAAAATATTATATTTTTT-AAAGTAATAAACTCTGGGGAAAAAAATACG
1 TAAAATAA-AAAAATAAAAAATAATATATTTTTTAAAAGTAATAAAATC--CAG-AAAAAATACG
* *
3527857 AATAAAGGGCCAAAATAAGGGTTTTTTTTTAAATTTATTTAAAAAATACACTAAATTAATACATT
62 AATAAAGGACCAAAATAAGGGTTTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATT
*
3527922 TTAAACATAATGTACTAAAATAATA
127 TCAAACATAATGTACTAAAATAATA
* *
3527947 TAAATTAATAAAAA-ACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCTAGAAAAAATAC
1 TAAAATAA-AAAAATA-AAAAATAATATA-TTTT-TTAAAAGTAATAAAATCC-AGAAAAAATAC
**
3528011 GAATAAAGGACTGAAATAAGGG-TTTTTTTT-AATTTATTT-AAAAACACACTAAATTAATACAT
61 GAATAAAGGACCAAAATAAGGGTTTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACAT
*
3528073 TTCAAACATAATGTACTAAAATAATG
126 TTCAAACATAATGTACTAAAATAATA
*
3528099 TAAAATAAAAAAATAAAAAATAATATATTTTTTAAAAGTAATAAAATTCAGAAAAAA
1 TAAAATAAAAAAATAAAAAATAATATATTTTTTAAAAGTAATAAAATCCAGAAAAAA
3528156 ATATAAACAA
Statistics
Matches: 187, Mismatches: 16, Indels: 18
0.85 0.07 0.08
Matches are distributed among these distances:
148 8 0.04
149 16 0.09
150 4 0.02
151 17 0.09
152 54 0.29
153 10 0.05
154 30 0.16
155 32 0.17
156 3 0.02
157 13 0.07
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (151 bp):
TAAAATAAAAAAATAAAAAATAATATATTTTTTAAAAGTAATAAAATCCAGAAAAAATACGAATA
AAGGACCAAAATAAGGGTTTTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAA
ACATAATGTACTAAAATAATA
Found at i:3528315 original size:16 final size:19
Alignment explanation
Indices: 3528286--3528321 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
3528276 AAAAAAATTA
3528286 TATTATTTTAGTATT-TTT
1 TATTATTTTAGTATTATTT
3528304 TATT-TTTT-GTATTATTT
1 TATTATTTTAGTATTATTT
3528321 T
1 T
3528322 TATAAAACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.29
17 8 0.47
18 4 0.24
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (19 bp):
TATTATTTTAGTATTATTT
Found at i:3528542 original size:18 final size:18
Alignment explanation
Indices: 3528507--3528549 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3528497 AATCGCCTTG
3528507 TATTTT-ATTTTTTCAAA
1 TATTTTAATTTTTTCAAA
*
3528524 TTTTTTAATTTTATT-AAA
1 TATTTTAATTTT-TTCAAA
3528542 TATTTTAA
1 TATTTTAA
3528550 GACTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 5 0.23
18 15 0.68
19 2 0.09
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTTTAATTTTTTCAAA
Found at i:3529851 original size:25 final size:25
Alignment explanation
Indices: 3529817--3529873 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
3529807 TTACTAATAG
*
3529817 ATAG-TTAGTTTAGTGACCTTGGGT
1 ATAGTTTAGTTTAGTGACATTGGGT
3529841 ATAGTTTAGTTTAGTGACATTGGGT
1 ATAGTTTAGTTTAGTGACATTGGGT
*
3529866 GTAGTTTA
1 ATAGTTTA
3529874 CCCTTACAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.44
Consensus pattern (25 bp):
ATAGTTTAGTTTAGTGACATTGGGT
Found at i:3532515 original size:15 final size:17
Alignment explanation
Indices: 3532495--3532527 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3532485 ATGAAAATTT
3532495 TAGT-AAAATAAA-AAA
1 TAGTAAAAATAAATAAA
3532510 TAGTAAAAATAAATAAA
1 TAGTAAAAATAAATAAA
3532527 T
1 T
3532528 GGCTAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
TAGTAAAAATAAATAAA
Found at i:3533812 original size:23 final size:24
Alignment explanation
Indices: 3533760--3533814 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
3533750 TTTGATGGGT
* *
3533760 AAAATTAATAATAGTATAGTATTG
1 AAAAATAATAATAGTATAGTAGTG
*
3533784 AAAAATAATAATAGTA-ATTAGTG
1 AAAAATAATAATAGTATAGTAGTG
3533807 AAAAATAA
1 AAAAATAA
3533815 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 13 0.46
24 15 0.54
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (24 bp):
AAAAATAATAATAGTATAGTAGTG
Done.