Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007938.1 Hibiscus syriacus cultivar Beakdansim tig00110348_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2808856
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 14
Found at i:2348326 original size:22 final size:22
Alignment explanation
Indices: 2348298--2348340 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2348288 AGATCTTTAG
2348298 AGTACGTCTTGATTTATGTTAA
1 AGTACGTCTTGATTTATGTTAA
2348320 AGTACGTCTTGATTTATGTTA
1 AGTACGTCTTGATTTATGTTA
2348341 GAGGGCATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.47
Consensus pattern (22 bp):
AGTACGTCTTGATTTATGTTAA
Found at i:2348752 original size:23 final size:23
Alignment explanation
Indices: 2348725--2348779 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
2348715 AAGAAAATTA
* *
2348725 TGCCACAAAGATAGAAATACACG
1 TGCCACAAAGACAGAAATAAACG
*
2348748 TGCCACAAAGACAGATATAAACG
1 TGCCACAAAGACAGAAATAAACG
2348771 TGCCACAAA
1 TGCCACAAA
2348780 ACCATAGAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.47, C:0.24, G:0.16, T:0.13
Consensus pattern (23 bp):
TGCCACAAAGACAGAAATAAACG
Found at i:2351340 original size:3 final size:3
Alignment explanation
Indices: 2351332--2351368 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2351322 TTAAAAAATG
2351332 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2351369 TATATATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2351517 original size:69 final size:72
Alignment explanation
Indices: 2351428--2351614 Score: 207
Period size: 69 Copynumber: 2.7 Consensus size: 72
2351418 GTTTTTTCTT
* *
2351428 AAACTATAT-ATATACGAATGTTTTCAACATGTTTTCAAAA-TAT-TATATAAGTTTTCAAAAAC
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACTATATATATAAGTTTTCAAAAAC
*
2351490 GTTTTAA
66 GTTTCAA
**
2351497 AAACTATATAATATA-AAATGTTTTCAAAATGTTTTCAAAACTATAATATATGTGTTTTCAAAAA
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACTAT-ATATATAAGTTTTCAAAAA
*
2351561 TGTTTCAA
65 CGTTTCAA
* *
2351569 AAA-T-TAT-ATAT---AAT-TTTTCAAAATGATTTTAAAAATTATATATATA
1 AAACTATATAATATACAAATGTTTTCAAAATG-TTTTCAAAACTATATATATA
2351615 TTTTTTAAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
66 17 0.16
67 14 0.13
69 36 0.35
70 11 0.11
71 1 0.01
72 25 0.24
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (72 bp):
AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACTATATATATAAGTTTTCAAAAAC
GTTTCAA
Found at i:2351527 original size:11 final size:11
Alignment explanation
Indices: 2351511--2351536 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2351501 TATATAATAT
2351511 AAAATGTTTTC
1 AAAATGTTTTC
2351522 AAAATGTTTTC
1 AAAATGTTTTC
2351533 AAAA
1 AAAA
2351537 CTATAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (11 bp):
AAAATGTTTTC
Found at i:2351587 original size:32 final size:34
Alignment explanation
Indices: 2351517--2351624 Score: 118
Period size: 32 Copynumber: 3.3 Consensus size: 34
2351507 ATATAAAATG
* * *
2351517 TTTTC-AAAATGTTTTC-AAAACTATAATATATGT
1 TTTTCAAAAATGATTTCAAAAATTAT-ATATATAT
2351550 GTTTTCAAAAATG-TTTCAAAAATTATATATA-AT
1 -TTTTCAAAAATGATTTCAAAAATTATATATATAT
*
2351583 TTTTC-AAAATGATTTTAAAAATTATATATATAT
1 TTTTCAAAAATGATTTCAAAAATTATATATATAT
*
2351616 TTTTTAAAA
1 TTTTCAAAA
2351625 CGTTTTTTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
31 6 0.09
32 22 0.34
33 7 0.11
34 17 0.26
35 13 0.20
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (34 bp):
TTTTCAAAAATGATTTCAAAAATTATATATATAT
Found at i:2351587 original size:104 final size:104
Alignment explanation
Indices: 2351384--2351631 Score: 255
Period size: 104 Copynumber: 2.4 Consensus size: 104
2351374 ATACATAAAT
*
2351384 ATTTTCAAAAAC-ATATAATATAAATTTTCAAAATGTTTTTTCTTAAACTATATATATACGAATG
1 ATTTT-AAAAACTATATAATATAAATTTTCAAAATG-TTTTTCTAAAACTATATATATACG-ATG
*
2351448 TTTTCAACATGTTTTCAAAATATTATATAAGTTTTCAAAAACG
63 TTTTCAAAATGTTTTCAAAATATTATATAAGTTTTC-AAAACG
*
2351491 -TTTTAAAAACTATATAATATAAAATGTTTTCAAAATG-TTTTC-AAAACTATA-ATATATG-TG
1 ATTTTAAAAACTATATAATAT-AAA--TTTTCAAAATGTTTTTCTAAAACTATATATATACGATG
* *
2351551 TTTTCAAAAATG-TTTCAAAA-ATTATATATAATTTTTCAAAATG
63 TTTTC-AAAATGTTTTCAAAATA-T-TATATAAGTTTTCAAAACG
* * * *
2351594 ATTTTAAAAATTATAT-ATAT-ATTTTTTAAAACGTTTTT
1 ATTTTAAAAACTATATAATATAAATTTTCAAAATGTTTTT
2351632 TTTTAAAAAA
Statistics
Matches: 123, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
99 9 0.07
100 4 0.03
101 1 0.01
102 1 0.01
103 25 0.20
104 31 0.25
105 12 0.10
106 21 0.17
107 8 0.07
109 11 0.09
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (104 bp):
ATTTTAAAAACTATATAATATAAATTTTCAAAATGTTTTTCTAAAACTATATATATACGATGTTT
TCAAAATGTTTTCAAAATATTATATAAGTTTTCAAAACG
Found at i:2352467 original size:84 final size:81
Alignment explanation
Indices: 2352291--2352979 Score: 582
Period size: 81 Copynumber: 8.4 Consensus size: 81
2352281 TTATTGACAA
* * * * * * * * * * *
2352291 ATAGCCCTTCTTGCCATGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACT
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
*
2352356 CG-GGAGTC-TTTGGCAG
65 CGAAG-GTCTTTTGGCAG
* *
2352372 ATGGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
2352437 GAAGGTCTTTGATTGGCAG
66 GAAGGTC-TT--TTGGCAG
* * * *** *
2352456 ATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCAAAGCTGAGCGTAATCGAACT
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
**
2352521 CGGGGGTC-TTTGGCAG
65 CGAAGGTCTTTTGGCAG
* * *
2352537 ATAGCCCTTCTCGGCTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* **
2352602 AAAGGTCTTTTCTAACAG
66 GAAGGTC-TTT-TGGCAG
* * * * * * * * * * * *
2352620 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
*
2352685 -TAAGGGTC-TTTGGCAG
65 CGAA-GGTCTTTTGGCAG
* **
2352701 ATAGCTCTTCTTGACTTAAGCTATATTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
* **
2352766 AAAGGTCTTTTCTAACAG
66 GAAGGTC-TTT-TGGCAG
* * * * * * * * * * *
2352784 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
*
2352849 -TAAGGGTC-TTTGGCAG
65 CGAA-GGTCTTTTGGCAG
* *
2352865 ATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
2352930 GAAGGTCTTGGTGGCAG
66 GAAGGTCTT-TTGGCAG
* * * * *
2352947 GTAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAAT
2352980 AGTTTGTTTA
Statistics
Matches: 479, Mismatches: 109, Indels: 39
0.76 0.17 0.06
Matches are distributed among these distances:
80 102 0.21
81 145 0.30
82 42 0.09
83 71 0.15
84 92 0.19
85 27 0.06
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (81 bp):
ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTTTGGCAG
Found at i:2352721 original size:164 final size:164
Alignment explanation
Indices: 2352295--2352938 Score: 934
Period size: 164 Copynumber: 3.9 Consensus size: 164
2352285 TGACAAATAG
* * * * * * **
2352295 CCCTTCTTGCCATGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAAC-TCGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
* * * *
2352359 GAGTCTTTGGCAGATGGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAG
66 G-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAG
* **
2352424 CGTAGTCGAACTCGAAGGTCTTTGAT-TGGCAGATAA
130 CGTAGTCGAACTCAAAGGTCTTT--TCTAACAGATAA
* * * * ** * * ***
2352460 CCCTTCTTGACTTAAGTTATGCTGCAAATGATGCGCCCTCAAAGCTGAGCGTAATCGAACTCGGG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
*
2352525 GGTCTTTGGCAGATAGCCCTTCTCGGCTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
2352590 GTAGTCGAACTCAAAGGTCTTTTCTAACAGATAA
131 GTAGTCGAACTCAAAGGTCTTTTCTAACAGATAA
*
2352624 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
* *
2352689 GGTCTTTGGCAGATAGCTCTTCTTGACTTAAGCTATAT-TGCAAATGATGTGCCTTGGAGCTGAG
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTAT-TCTGCAAATGATGTGCCTTGGAGCTGAG
2352753 CGTAGTCGAACTCAAAGGTCTTTTCTAACAGATAA
130 CGTAGTCGAACTCAAAGGTCTTTTCTAACAGATAA
* *
2352788 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
2352853 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
*
2352918 GTAGTCGAACTCGAAGGTCTT
131 GTAGTCGAACTCAAAGGTCTT
2352939 GGTGGCAGGT
Statistics
Matches: 434, Mismatches: 41, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
163 2 0.00
164 300 0.69
165 129 0.30
166 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (164 bp):
CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTTAAG
GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCAAAGGTCTTTTCTAACAGATAA
Found at i:2359014 original size:3 final size:3
Alignment explanation
Indices: 2359006--2359049 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
2358996 TTAAAAAATG
2359006 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A
2359050 TATATATACA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2359204 original size:71 final size:71
Alignment explanation
Indices: 2359079--2359300 Score: 233
Period size: 71 Copynumber: 3.1 Consensus size: 71
2359069 TCAAAAACAT
* * ** * *
2359079 ATAATATATAAATTTTC-AAAATGTTTTTTCTTAAACTATATAATATACGAATGTTTTCAACATG
1 ATAATATATAAGTTTTCAAAAACG--TTTTCAAAAACTATATAATATA-TAATGTTTTCAAAATG
2359143 TTTTCAAAA
63 TTTTCAAAA
*
2359152 ATATTATATAAGTTTTCAAAAACGTTTT-AAAAACTATATAATATATAAATGTTTTCAAAATGTT
1 ATAATATATAAGTTTTCAAAAACGTTTTCAAAAACTATATAATATAT-AATGTTTTCAAAATGTT
2359216 TTCAAAA
65 TTCAAAA
** *
2359223 CTATAATATATGTGTTTTCAAAAATGTTTTCAAAAA-T-TAT-ATATATAAT-TTTTCAAAATGA
1 --ATAATATATAAGTTTTCAAAAACGTTTTCAAAAACTATATAATATATAATGTTTTCAAAATG-
2359284 TTTT-AAAA
63 TTTTCAAAA
*
2359292 ATTATATAT
1 ATAATATAT
2359301 TATATATATT
Statistics
Matches: 131, Mismatches: 12, Indels: 18
0.81 0.07 0.11
Matches are distributed among these distances:
67 8 0.06
69 15 0.11
70 7 0.05
71 44 0.34
72 7 0.05
73 40 0.31
74 10 0.08
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (71 bp):
ATAATATATAAGTTTTCAAAAACGTTTTCAAAAACTATATAATATATAATGTTTTCAAAATGTTT
TCAAAA
Found at i:2359214 original size:11 final size:11
Alignment explanation
Indices: 2359198--2359222 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2359188 TATAATATAT
2359198 AAATGTTTTCA
1 AAATGTTTTCA
2359209 AAATGTTTTCA
1 AAATGTTTTCA
2359220 AAA
1 AAA
2359223 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2359252 original size:12 final size:12
Alignment explanation
Indices: 2359235--2359259 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2359225 ATAATATATG
2359235 TGTTTTCAAAAA
1 TGTTTTCAAAAA
2359247 TGTTTTCAAAAA
1 TGTTTTCAAAAA
2359259 T
1 T
2359260 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:2359288 original size:108 final size:108
Alignment explanation
Indices: 2359061--2359324 Score: 301
Period size: 108 Copynumber: 2.4 Consensus size: 108
2359051 ATATATACAT
*
2359061 AAAT-ATTTTCAAAAAC-ATATAATATATAAA-TTTTCAAAATGTTTTTTCTTAAACTATATAAT
1 AAATGATTTT-AAAAACTATATAATATATAAATTTTTCAAAATG--TTTTCTAAAAC-ATATAAT
*
2359123 ATACGAATGTTTTCAACATGTTTTCAAAAATATTATATAAGTTTTCAA
62 ATACG-ATGTTTTCAAAATGTTTTCAAAAATATTATATAAGTTTTCAA
*
2359171 AAACG-TTTTAAAAACTATATAATATATAAATGTTTTCAAAATGTTTTC-AAAAC-TATAATATA
1 AAATGATTTTAAAAACTATATAATATATAAAT-TTTTCAAAATGTTTTCTAAAACATATAATATA
* *
2359233 TG-TGTTTTCAAAAATGTTTTCAAAAATTATATATATAATTTTTC-A
65 CGATGTTTTC-AAAATGTTTTCAAAAA-TAT-TATATAAGTTTTCAA
* * * * *
2359278 AAATGATTTTAAAAATTATATATTATATATATTTTTTAAAACGTTTT
1 AAATGATTTTAAAAACTATATAATATATAAATTTTTCAAAATGTTTT
2359325 TTTTTAAAAA
Statistics
Matches: 135, Mismatches: 11, Indels: 19
0.82 0.07 0.12
Matches are distributed among these distances:
105 7 0.05
106 15 0.11
107 31 0.23
108 35 0.26
109 10 0.07
110 26 0.19
112 11 0.08
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (108 bp):
AAATGATTTTAAAAACTATATAATATATAAATTTTTCAAAATGTTTTCTAAAACATATAATATAC
GATGTTTTCAAAATGTTTTCAAAAATATTATATAAGTTTTCAA
Found at i:2359298 original size:34 final size:34
Alignment explanation
Indices: 2359128--2359300 Score: 176
Period size: 34 Copynumber: 4.9 Consensus size: 34
2359118 ATAATATACG
*
2359128 AATGTTTTCAACATGTTTTCAAAAA-TAT-TATAT
1 AATGTTTTCAAAATGTTTT-AAAAATTATATATAT
*
2359161 AA-GTTTTCAAAAACGTTTTAAAAACTATATAATATAT
1 AATGTTTTC-AAAATGTTTTAAAAA-T-TAT-ATATAT
* *
2359198 AAATGTTTTCAAAATGTTTTCAAAACTATA-ATAT
1 -AATGTTTTCAAAATGTTTTAAAAATTATATATAT
*
2359232 ATGTGTTTTCAAAAATGTTTTCAAAAATTATATATAT
1 A-ATGTTTTC-AAAATGTTTT-AAAAATTATATATAT
2359269 AAT-TTTTCAAAATGATTTTAAAAATTATATAT
1 AATGTTTTCAAAATG-TTTTAAAAATTATATAT
2359301 TATATATATT
Statistics
Matches: 118, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
32 11 0.09
33 11 0.09
34 30 0.25
35 23 0.19
36 12 0.10
37 10 0.08
38 15 0.13
39 6 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (34 bp):
AATGTTTTCAAAATGTTTTAAAAATTATATATAT
Found at i:2361490 original size:2 final size:2
Alignment explanation
Indices: 2361483--2361509 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2361473 AAGTATTGTA
2361483 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2361510 GTAATAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2361875 original size:24 final size:23
Alignment explanation
Indices: 2361831--2361876 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
2361821 GAATTAAATA
2361831 TTAATAAAATATTTTAATATTATT
1 TTAATAAAATA-TTTAATATTATT
2361855 TTAATCAAAATA-TTAATTATTA
1 TTAAT-AAAATATTTAA-TATTA
2361877 AAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTAATAAAATATTTAATATTATT
Found at i:2363883 original size:139 final size:139
Alignment explanation
Indices: 2363736--2364124 Score: 487
Period size: 139 Copynumber: 2.8 Consensus size: 139
2363726 AATATTCATT
* * * *
2363736 TTAGGTTTAATTTCACCTTAATCCTTTAATTTAGGAGAATTTTAAATTTAGTCTTCACTTTTATG
1 TTAGGTTTAATTTTACCTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGGTCTTCACTTTTATG
* * * *
2363801 CTCGAGCTTTCATTTTAATTATTTGATCCAATAAATTGTTAAAATTGATTAGAATTAATATTTGA
66 CCCGAGGTTTCATTTTAATTATTTGATCCAATAAATTGATAAAATTGATTAGAATTAATATTAGA
2363866 GTCTTCT-CC
131 G-CTTCTGCC
* * **
2363875 TTGGGTTTAATTTTACTTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGGT-TCTCGTTTTTAT
1 TTAGGTTTAATTTTACCTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGGTCT-TCACTTTTAT
* ** * * *
2363939 GCCCGAGGTTTCGTTTTAATTATTCAATCCAATAAATTGCTAAAATTGGTTAGGATTAATATTAG
65 GCCCGAGGTTTCATTTTAATTATTTGATCCAATAAATTGATAAAATTGATTAGAATTAATATTAG
*
2364004 AGCTTTTGCC
130 AGCTTCTGCC
** * * *
2364014 TTATATTTAATTTTGCCTTAGTCCTTTAATTTAGAATAATTTTTAATTTGGTCCTT-ACTTTTAT
1 TTAGGTTTAATTTTACCTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGGT-CTTCACTTTTAT
* * *
2364078 CCCCGGGGTTTCATTTTAATTATTTGATCCAACAAATTGATAAAATT
65 GCCCGAGGTTTCATTTTAATTATTTGATCCAATAAATTGATAAAATT
2364125 CGTTAGGTTT
Statistics
Matches: 212, Mismatches: 34, Indels: 8
0.83 0.13 0.03
Matches are distributed among these distances:
138 5 0.02
139 205 0.97
140 1 0.00
141 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (139 bp):
TTAGGTTTAATTTTACCTTAGTCCTTTAATTTAGGAGAATTTTTAATTTGGTCTTCACTTTTATG
CCCGAGGTTTCATTTTAATTATTTGATCCAATAAATTGATAAAATTGATTAGAATTAATATTAGA
GCTTCTGCC
Found at i:2364130 original size:139 final size:137
Alignment explanation
Indices: 2363654--2364142 Score: 480
Period size: 139 Copynumber: 3.5 Consensus size: 137
2363644 TTAGTTATCG
* * * * ** * * *
2363654 CTTTTATGCTCGAGG-TTCTATATTAATTGTTCGATTTAATAAATTGCTGAAATTGGTCAGGATT
1 CTTTTATGCCCGAGGTTTC-ATTTTAATTATTTGATCCAATAAATTGATAAAATT-GTTAGGATT
* * * * * * * *
2363718 AATATTATAATATTCAT-TTTAGGTTTAATTTCACCTTAATCCTTTAATTTAGGAGAATTTTAAA
64 AATATTAGAGTCTTC-TCCTTAGATTTAATTTTACCTTAGTCCTTTAATTTAGGAGAATTTTTAA
*
2363782 TTTAGTCTTCA
128 TTTGGTCTT-A
* * * *
2363793 CTTTTATGCTCGAGCTTTCATTTTAATTATTTGATCCAATAAATTGTTAAAATTGATTAGAATTA
1 CTTTTATGCCCGAGGTTTCATTTTAATTATTTGATCCAATAAATTGATAAAATTG-TTAGGATTA
* * * *
2363858 ATATTTGAGTCTTCTCCTTGGGTTTAATTTTACTTTAGTCCTTTAATTTAGGAGAATTTTTAATT
65 ATATTAGAGTCTTCTCCTTAGATTTAATTTTACCTTAGTCCTTTAATTTAGGAGAATTTTTAATT
**
2363923 TGGTTCTCG
130 TGG-TCTTA
* * ** *
2363932 TTTTTATGCCCGAGGTTTCGTTTTAATTATTCAATCCAATAAATTGCTAAAATTGGTTAGGATTA
1 CTTTTATGCCCGAGGTTTCATTTTAATTATTTGATCCAATAAATTGATAAAATT-GTTAGGATTA
* * * * *
2363997 ATATTAGAG-CTTTTGCCTTATATTTAATTTTGCCTTAGTCCTTTAATTTAGAATAATTTTTAAT
65 ATATTAGAGTCTTCT-CCTTAGATTTAATTTTACCTTAGTCCTTTAATTTAGGAGAATTTTTAAT
2364061 TTGGTCCTTA
129 TTGGT-CTTA
* * * *
2364071 CTTTTATCCCCGGGGTTTCATTTTAATTATTTGATCCAACAAATTGATAAAATTCGTTAGGTTTT
1 CTTTTATGCCCGAGGTTTCATTTTAATTATTTGATCCAATAAATTGATAAAATT-GTTAGG-ATT
2364136 AATATTA
64 AATATTA
2364143 TAGCCTACAT
Statistics
Matches: 290, Mismatches: 52, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
138 7 0.02
139 267 0.92
140 16 0.06
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (137 bp):
CTTTTATGCCCGAGGTTTCATTTTAATTATTTGATCCAATAAATTGATAAAATTGTTAGGATTAA
TATTAGAGTCTTCTCCTTAGATTTAATTTTACCTTAGTCCTTTAATTTAGGAGAATTTTTAATTT
GGTCTTA
Found at i:2377201 original size:17 final size:17
Alignment explanation
Indices: 2377179--2377223 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2377169 AGAAAAAACC
* *
2377179 CAAATCCTTACAAATAT
1 CAAATCCCTAAAAATAT
2377196 CAAATCCCTAAAAATAT
1 CAAATCCCTAAAAATAT
*
2377213 CAAATCTCTAA
1 CAAATCCCTAA
2377224 CCATAACCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (17 bp):
CAAATCCCTAAAAATAT
Found at i:2377466 original size:23 final size:23
Alignment explanation
Indices: 2377440--2377486 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2377430 GATATTTATT
2377440 ATTTTTAGAGATTTTGAATTTGA
1 ATTTTTAGAGATTTTGAATTTGA
2377463 ATTTTTAGAGATTTTGAATTTGA
1 ATTTTTAGAGATTTTGAATTTGA
2377486 A
1 A
2377487 CATCGATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (23 bp):
ATTTTTAGAGATTTTGAATTTGA
Found at i:2378778 original size:24 final size:24
Alignment explanation
Indices: 2378747--2378804 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
2378737 TATATATATA
2378747 TATATTATTTTTATTTATAATTCT
1 TATATTATTTTTATTTATAATTCT
2378771 TATATTATTTTTATTTATAATTCT
1 TATATTATTTTTATTTATAATTCT
*
2378795 TAAATTATTT
1 TATATTATTT
2378805 CACTCTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (24 bp):
TATATTATTTTTATTTATAATTCT
Found at i:2379823 original size:59 final size:59
Alignment explanation
Indices: 2379725--2379860 Score: 218
Period size: 59 Copynumber: 2.3 Consensus size: 59
2379715 TACAAAGTAC
* *
2379725 GGTTCAATAGGACACTTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTATGAG
1 GGTTCAATAGGACACTTAGAGCCATATTATCGAGTTTGCCTTTTCAATGCGACTAAGAG
** *
2379784 GGTTTGATAGGACACTTAGAGTCATATTATCGAGTTTGCCTTTTCAATGCGACTAAGAG
1 GGTTCAATAGGACACTTAGAGCCATATTATCGAGTTTGCCTTTTCAATGCGACTAAGAG
*
2379843 GGTTCAATAGGAAACTTA
1 GGTTCAATAGGACACTTA
2379861 TCCATCTATT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (59 bp):
GGTTCAATAGGACACTTAGAGCCATATTATCGAGTTTGCCTTTTCAATGCGACTAAGAG
Found at i:2383898 original size:19 final size:19
Alignment explanation
Indices: 2383871--2383936 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
2383861 AATGTTTTTA
* *
2383871 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
2383890 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
2383909 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
*
2383928 TGAAAAGTA
1 TGAACAGTA
2383937 CCCCGAGGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:2384147 original size:21 final size:21
Alignment explanation
Indices: 2384114--2384153 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2384104 TTTTTGCATA
*
2384114 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2384136 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2384154 AGATATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2384868 original size:30 final size:32
Alignment explanation
Indices: 2384811--2384875 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 32
2384801 ATTAGATTTA
2384811 TTATTTTATTAGGAATTAAGGTTGAGTTAAAACAT
1 TTATTTTATTAGGAATTAA-G--GAGTTAAAACAT
2384846 TTATTTTATTAGGAATT-A-GAGTTAAAACAT
1 TTATTTTATTAGGAATTAAGGAGTTAAAACAT
2384876 GTTTAGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 12 0.40
34 1 0.03
35 17 0.57
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.43
Consensus pattern (32 bp):
TTATTTTATTAGGAATTAAGGAGTTAAAACAT
Found at i:2385157 original size:50 final size:52
Alignment explanation
Indices: 2385098--2385231 Score: 155
Period size: 59 Copynumber: 2.5 Consensus size: 52
2385088 CTCCAATTTG
* *
2385098 CCTTTTCATTGCGACTAGGAGGGTT-GG-TTAGAGCCATATTATTGAGTTTT
1 CCTTTTCATTTCGACTAGGAGGGTTAGGATTAGAGCCATATTATCGAGTTTT
*
2385148 CCTTTTCATTTCAACTAGGAGGGTTTGATAGGACATTTAGAGCCATATTATCGAGTTTT
1 CCTTTTCATTTCGACTAGGAGGG--T--TAGG--A-TTAGAGCCATATTATCGAGTTTT
*
2385207 CCTTTTCATTTCGAGTAGGAGGGTT
1 CCTTTTCATTTCGACTAGGAGGGTT
2385232 CGATAGGACA
Statistics
Matches: 70, Mismatches: 5, Indels: 13
0.80 0.06 0.15
Matches are distributed among these distances:
50 21 0.30
52 1 0.01
54 1 0.01
55 3 0.04
57 1 0.01
59 43 0.61
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.40
Consensus pattern (52 bp):
CCTTTTCATTTCGACTAGGAGGGTTAGGATTAGAGCCATATTATCGAGTTTT
Found at i:2385197 original size:59 final size:59
Alignment explanation
Indices: 2385125--2385241 Score: 198
Period size: 59 Copynumber: 2.0 Consensus size: 59
2385115 GGAGGGTTGG
* *
2385125 TTAGAGCCATATTATTGAGTTTTCCTTTTCATTTCAACTAGGAGGGTTTGATAGGACAT
1 TTAGAGCCATATTATCGAGTTTTCCTTTTCATTTCAACTAGGAGGGTTCGATAGGACAT
* *
2385184 TTAGAGCCATATTATCGAGTTTTCCTTTTCATTTCGAGTAGGAGGGTTCGATAGGACA
1 TTAGAGCCATATTATCGAGTTTTCCTTTTCATTTCAACTAGGAGGGTTCGATAGGACA
2385242 CTTATCCATC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTTCCTTTTCATTTCAACTAGGAGGGTTCGATAGGACAT
Found at i:2385914 original size:19 final size:19
Alignment explanation
Indices: 2385890--2385937 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
2385880 GAATTTGAAA
2385890 TTAGGATTATCTCTTATTT
1 TTAGGATTATCTCTTATTT
*
2385909 TTAGGAATTATCTTTTATTT
1 TTAGG-ATTATCTCTTATTT
2385929 TTAGGATTA
1 TTAGGATTA
2385938 AGTTTGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.56
Consensus pattern (19 bp):
TTAGGATTATCTCTTATTT
Found at i:2386119 original size:22 final size:24
Alignment explanation
Indices: 2386094--2386144 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2386084 ATTATTTTTC
2386094 TTTTTAC-TTTC-ACTTTTCTTTA
1 TTTTTACTTTTCAACTTTTCTTTA
*
2386116 TTTTT-CTTTTCAAGTTTTCTTTA
1 TTTTTACTTTTCAACTTTTCTTTA
2386139 TTTTTA
1 TTTTTA
2386145 ATATGCTAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 1 0.04
22 9 0.36
23 15 0.60
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTTTACTTTTCAACTTTTCTTTA
Found at i:2387326 original size:38 final size:39
Alignment explanation
Indices: 2387265--2387374 Score: 125
Period size: 39 Copynumber: 2.8 Consensus size: 39
2387255 ACGCGTTTGC
* *
2387265 CAAATTCGCAACACTGAATTTCAAATTTGCAA-TTGAATTT
1 CAAATTCGC-A-ACTGAATTTCAAATTCGCAACTCGAATTT
*
2387305 CAAATTCGCAACTGAATTTCAAATTCGCAACTCGATTTT
1 CAAATTCGCAACTGAATTTCAAATTCGCAACTCGAATTT
* * *
2387344 CGAATTCGCAACACGAATTT-AATTTCGCAAC
1 CAAATTCGCAAC-TGAATTTCAAATTCGCAAC
2387375 AGGTTTTAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
38 19 0.31
39 28 0.45
40 15 0.24
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (39 bp):
CAAATTCGCAACTGAATTTCAAATTCGCAACTCGAATTT
Found at i:2387349 original size:20 final size:19
Alignment explanation
Indices: 2387265--2387374 Score: 123
Period size: 19 Copynumber: 5.6 Consensus size: 19
2387255 ACGCGTTTGC
2387265 CAAATTCGCAACACTGAATTT
1 CAAATTCGC-A-ACTGAATTT
* *
2387286 CAAATTTGCAATTGAATTT
1 CAAATTCGCAACTGAATTT
2387305 CAAATTCGCAACTGAATTT
1 CAAATTCGCAACTGAATTT
*
2387324 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACT-GAATTT
* *
2387344 CGAATTCGCAACACGAATTT
1 CAAATTCGCAAC-TGAATTT
*
2387364 -AATTTCGCAAC
1 CAAATTCGCAAC
2387375 AGGTTTTAGT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 47 0.61
20 22 0.29
21 8 0.10
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (19 bp):
CAAATTCGCAACTGAATTT
Found at i:2387371 original size:39 final size:40
Alignment explanation
Indices: 2387267--2387411 Score: 142
Period size: 37 Copynumber: 3.8 Consensus size: 40
2387257 GCGTTTGCCA
* * *
2387267 AATTCGCAACACTGAATTTCAAATTT-GCAA-TTGAATTTCA
1 AATTCGCAACAC-GAATTTC-AATTTCGCAACTAGATTTTCG
* * *
2387307 AATTCGCAAC-TGAATTTCAAATTCGCAACTCGATTTTCG
1 AATTCGCAACACGAATTTCAATTTCGCAACTAGATTTTCG
* *
2387346 AATTCGCAACACGAATTT-AATTTCGCAAC-AGGTTTTAG
1 AATTCGCAACACGAATTTCAATTTCGCAACTAGATTTTCG
*
2387384 -TTTCGCAACACGAATTT-AATTTCGCAAC
1 AATTCGCAACACGAATTTCAATTTCGCAAC
2387412 AAGTTTTAGT
Statistics
Matches: 91, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
37 31 0.34
38 17 0.19
39 27 0.30
40 16 0.18
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (40 bp):
AATTCGCAACACGAATTTCAATTTCGCAACTAGATTTTCG
Found at i:2387375 original size:19 final size:20
Alignment explanation
Indices: 2387269--2387412 Score: 115
Period size: 19 Copynumber: 7.5 Consensus size: 20
2387259 GTTTGCCAAA
2387269 TTCGCAACACTGAATTTCAAAT
1 TTCGCAACAC-GAATTTC-AAT
** *
2387291 TT-GCAA-TTGAATTTCAAA
1 TTCGCAACACGAATTTCAAT
* *
2387309 TTCGCAAC-TGAATTTCAAA
1 TTCGCAACACGAATTTCAAT
* *
2387328 TTCGCAACTCGATTTTCGAA-
1 TTCGCAACACGAATTTC-AAT
2387348 TTCGCAACACGAATTT-AAT
1 TTCGCAACACGAATTTCAAT
* * *
2387367 TTCGCAACA-G-GTTTTAGT
1 TTCGCAACACGAATTTCAAT
2387385 TTCGCAACACGAATTT-AAT
1 TTCGCAACACGAATTTCAAT
2387404 TTCGCAACA
1 TTCGCAACA
2387413 AGTTTTAGTT
Statistics
Matches: 103, Mismatches: 11, Indels: 19
0.77 0.08 0.14
Matches are distributed among these distances:
17 3 0.03
18 18 0.17
19 51 0.50
20 23 0.22
21 6 0.06
22 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
TTCGCAACACGAATTTCAAT
Found at i:2387382 original size:18 final size:18
Alignment explanation
Indices: 2387361--2387430 Score: 86
Period size: 18 Copynumber: 3.8 Consensus size: 18
2387351 GCAACACGAA
2387361 TTTAATTTCGCAACAGGT
1 TTTAATTTCGCAACAGGT
* **
2387379 TTTAGTTTCGCAACACGAA
1 TTTAATTTCGCAACA-GGT
*
2387398 TTTAATTTCGCAACAAGT
1 TTTAATTTCGCAACAGGT
*
2387416 TTTAGTTTCGCAACA
1 TTTAATTTCGCAACA
2387431 CAAATCTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 28 0.65
19 15 0.35
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (18 bp):
TTTAATTTCGCAACAGGT
Found at i:2387394 original size:37 final size:37
Alignment explanation
Indices: 2387348--2387431 Score: 159
Period size: 37 Copynumber: 2.3 Consensus size: 37
2387338 GATTTTCGAA
*
2387348 TTCGCAACACGAATTTAATTTCGCAACAGGTTTTAGT
1 TTCGCAACACGAATTTAATTTCGCAACAAGTTTTAGT
2387385 TTCGCAACACGAATTTAATTTCGCAACAAGTTTTAGT
1 TTCGCAACACGAATTTAATTTCGCAACAAGTTTTAGT
2387422 TTCGCAACAC
1 TTCGCAACAC
2387432 AAATCTTTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.33
Consensus pattern (37 bp):
TTCGCAACACGAATTTAATTTCGCAACAAGTTTTAGT
Found at i:2387591 original size:15 final size:16
Alignment explanation
Indices: 2387571--2387604 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2387561 TCATCTCTAA
2387571 TTTATTT-TACATAAT
1 TTTATTTCTACATAAT
*
2387586 TTTATTTCTATATAAT
1 TTTATTTCTACATAAT
2387602 TTT
1 TTT
2387605 TCAATGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTTCTACATAAT
Found at i:2391013 original size:13 final size:15
Alignment explanation
Indices: 2390992--2391027 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
2390982 GTCAAATTCG
2390992 AAACGCG-AAATCGC
1 AAACGCGAAAATCGC
2391006 AAAC-CGAAAATCGC
1 AAACGCGAAAATCGC
2391020 -AACGCGAA
1 AAACGCGAA
2391028 TTTGACTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.47, C:0.28, G:0.19, T:0.06
Consensus pattern (15 bp):
AAACGCGAAAATCGC
Found at i:2391124 original size:20 final size:20
Alignment explanation
Indices: 2391023--2391118 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
2391013 AAATCGCAAC
*
2391023 GCGAATTTGACTTTTGCGTT
1 GCGAATTTGACTTTCGCGTT
* **
2391043 GCAAATTTGACTTTAACGTT
1 GCGAATTTGACTTTCGCGTT
**
2391063 GCGAATTTGA-TTATCGCAAT
1 GCGAATTTGACTT-TCGCGTT
* *
2391083 GTGGATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
*
2391103 GCGAATTTGATTTTCG
1 GCGAATTTGACTTTCG
2391119 TTTTGCAAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 55 0.93
21 2 0.03
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:2391280 original size:64 final size:64
Alignment explanation
Indices: 2391182--2391338 Score: 280
Period size: 64 Copynumber: 2.5 Consensus size: 64
2391172 TTGAATAAAC
2391182 AACAAATCAACTTTTA-AAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
* *
2391245 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
2391309 AACAAATCAACTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
2391339 ATTCAATTAA
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
63 16 0.18
64 70 0.78
65 4 0.04
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTA
Found at i:2392697 original size:21 final size:20
Alignment explanation
Indices: 2392673--2392791 Score: 139
Period size: 21 Copynumber: 5.7 Consensus size: 20
2392663 GTGAATCGGG
*
2392673 CTCTTGAACGGTGAGAGGGAC
1 CTCTTGAACGATGAGAGGG-C
*
2392694 CTCTTGAACGATGACATGGGC
1 CTCTTGAACGATGAGA-GGGC
* * *
2392715 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGATGAGA-GGGC
2392736 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGA-GGGC
*
2392757 CTCTTGAATGATGAGAGAGGC
1 CTCTTGAACGATGAGAG-GGC
2392778 CTCTTGAACGATGA
1 CTCTTGAACGATGA
2392792 CAGGTGTATC
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
20 1 0.01
21 80 0.95
22 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.22
Consensus pattern (20 bp):
CTCTTGAACGATGAGAGGGC
Found at i:2392733 original size:42 final size:42
Alignment explanation
Indices: 2392673--2392795 Score: 169
Period size: 42 Copynumber: 2.9 Consensus size: 42
2392663 GTGAATCGGG
*
2392673 CTCTTGAACGGTGAGAGGGACCTCTTGAACGATGACATGGGC
1 CTCTTGAACGGTGAGAGGGACCTCTTGAACGATGACAGGGGC
* *
2392715 CTCTTGAACGGTGGGAGGGGA-CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTGAGA-GGGACCTCTTGAACGATGACAGGGGC
* *
2392757 CTCTTGAATGATGAGAGAGG-CCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGAGAG-GGACCTCTTGAACGATGACAGG
2392796 TGTATCGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
41 1 0.01
42 66 0.93
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGAGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:2394930 original size:20 final size:20
Alignment explanation
Indices: 2394908--2395006 Score: 189
Period size: 20 Copynumber: 5.0 Consensus size: 20
2394898 TCACAATGCG
*
2394908 AAAATGAAAATCGCAACGCG
1 AAAATGAAAATCGCAACGCA
2394928 AAAATGAAAATCGCAACGCA
1 AAAATGAAAATCGCAACGCA
2394948 AAAATGAAAATCGCAACGCA
1 AAAATGAAAATCGCAACGCA
2394968 AAAATGAAAATCGCAACGCA
1 AAAATGAAAATCGCAACGCA
2394988 AAAATGAAAATCGCAACGC
1 AAAATGAAAATCGCAACGC
2395007 GAAACTAAAT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.54, C:0.20, G:0.16, T:0.10
Consensus pattern (20 bp):
AAAATGAAAATCGCAACGCA
Found at i:2395058 original size:20 final size:20
Alignment explanation
Indices: 2395016--2395058 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2395006 CGAAACTAAA
* * *
2395016 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGAATTTAAGT
*
2395036 TTCGTGTTGCGAATTTAAGT
1 TTCGCGTTGCGAATTTAAGT
2395056 TTC
1 TTC
2395059 AAAAACTATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.16, G:0.21, T:0.49
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTAAGT
Found at i:2395395 original size:20 final size:21
Alignment explanation
Indices: 2395370--2395428 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
2395360 CTATGAGAGA
2395370 TGGAGAT-AGACGGATTTCGT
1 TGGAGATGAGACGGATTTCGT
*
2395390 TGGAGATGGGGACGGATTTCGT
1 TGGAGAT-GAGACGGATTTCGT
**
2395412 CAGAGATGAGGACGGAT
1 TGGAGATGA-GACGGAT
2395429 GTCGCCGTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 7 0.22
21 1 0.03
22 24 0.75
ACGTcount: A:0.25, C:0.10, G:0.41, T:0.24
Consensus pattern (21 bp):
TGGAGATGAGACGGATTTCGT
Found at i:2395406 original size:22 final size:22
Alignment explanation
Indices: 2395378--2395428 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2395368 GATGGAGATA
** *
2395378 GACGGATTTCGTTGGAGATGGG
1 GACGGATTTCGTCAGAGATGAG
2395400 GACGGATTTCGTCAGAGATGAG
1 GACGGATTTCGTCAGAGATGAG
2395422 GACGGAT
1 GACGGAT
2395429 GTCGCCGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCAGAGATGAG
Found at i:2395571 original size:20 final size:20
Alignment explanation
Indices: 2395546--2395647 Score: 161
Period size: 20 Copynumber: 5.2 Consensus size: 20
2395536 ATAAACGTGC
2395546 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
2395566 TTTGACTTCTATGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
2395586 TTTGACTTATGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
2395606 TTTGACTTCTGTATTGCGAA
1 TTTGACTTCTGTGTTGCGAA
*
2395626 TTTGACTTATGTGTTGC-AA
1 TTTGACTTCTGTGTTGCGAA
2395645 TTT
1 TTT
2395648 ATAAATTCGC
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
19 5 0.07
20 70 0.93
ACGTcount: A:0.19, C:0.13, G:0.22, T:0.47
Consensus pattern (20 bp):
TTTGACTTCTGTGTTGCGAA
Found at i:2395662 original size:40 final size:40
Alignment explanation
Indices: 2395546--2395669 Score: 135
Period size: 40 Copynumber: 3.1 Consensus size: 40
2395536 ATAAACGTGC
* * * ***
2395546 TTTGACTTCTGTGTTGCGAATTTGACTTCTATGTTGCGAA
1 TTTGACTTATGTGTTGCGAATTTAAATTCTGCATTGCGAA
* * *
2395586 TTTGACTTATGTGTTGCGAATTTGACTTCTGTATTGCGAA
1 TTTGACTTATGTGTTGCGAATTTAAATTCTGCATTGCGAA
2395626 TTTGACTTATGTGTTGC-AATTTATAAATTC-GCATTGCGAA
1 TTTGACTTATGTGTTGCGAA-TT-TAAATTCTGCATTGCGAA
2395666 TTTG
1 TTTG
2395670 GAAACTGGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.03
40 69 0.91
41 5 0.07
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.45
Consensus pattern (40 bp):
TTTGACTTATGTGTTGCGAATTTAAATTCTGCATTGCGAA
Found at i:2396705 original size:27 final size:28
Alignment explanation
Indices: 2396661--2396716 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
2396651 TGCTTAGCAA
*
2396661 TATTAAAAAATAACATAAATGTTAGTAG
1 TATTAAAAAATAAAATAAATGTTAGTAG
2396689 TATT-AAAAATAAAATAAATGTTAGTAG
1 TATTAAAAAATAAAATAAATGTTAGTAG
2396716 T
1 T
2396717 TAGAGATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.54, C:0.02, G:0.11, T:0.34
Consensus pattern (28 bp):
TATTAAAAAATAAAATAAATGTTAGTAG
Found at i:2396739 original size:41 final size:41
Alignment explanation
Indices: 2396682--2396760 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
2396672 AACATAAATG
*
2396682 TTAGTAGTATTAAAAATAAAATAAATGTTAGTAGTTAGAGA
1 TTAGTAGTATTAAAAATAAAATAAATATTAGTAGTTAGAGA
*
2396723 TTAGTAGTATTAAAAATAAAATAAATATTAGTATTTAG
1 TTAGTAGTATTAAAAATAAAATAAATATTAGTAGTTAG
2396761 CGGATAATAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (41 bp):
TTAGTAGTATTAAAAATAAAATAAATATTAGTAGTTAGAGA
Found at i:2403702 original size:69 final size:69
Alignment explanation
Indices: 2403623--2403755 Score: 257
Period size: 69 Copynumber: 1.9 Consensus size: 69
2403613 AGGCGAGGAA
2403623 AATATTTTAGGACGTTGAAATGGGTTAAAATGATTATCTTATTAAGCTGAAAAATAACAATAATT
1 AATATTTTAGGACGTTGAAATGGGTTAAAATGATTATCTTATTAAGCTGAAAAATAACAATAATT
2403688 GTGC
66 GTGC
*
2403692 AATATTTTAGGGCGTTGAAATGGGTTAAAATGATTATCTTATTAAGCTGAAAAATAACAATAAT
1 AATATTTTAGGACGTTGAAATGGGTTAAAATGATTATCTTATTAAGCTGAAAAATAACAATAAT
2403756 GTGTACATAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (69 bp):
AATATTTTAGGACGTTGAAATGGGTTAAAATGATTATCTTATTAAGCTGAAAAATAACAATAATT
GTGC
Found at i:2404023 original size:17 final size:17
Alignment explanation
Indices: 2403992--2404024 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2403982 AAATATTATT
2403992 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
2404009 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
2404025 TAATACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:2405681 original size:20 final size:19
Alignment explanation
Indices: 2405645--2405697 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
2405635 TGATTTAATT
* *
2405645 AGTATCGATACCGAAGGGGG
1 AGTATCGATACC-AAAGGGA
*
2405665 AGTATCGATACTAAAGGGA
1 AGTATCGATACCAAAGGGA
2405684 AGGTATCGATACCA
1 A-GTATCGATACCA
2405698 TTTCAAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.36, C:0.15, G:0.30, T:0.19
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:2406631 original size:58 final size:58
Alignment explanation
Indices: 2406125--2406632 Score: 781
Period size: 58 Copynumber: 8.8 Consensus size: 58
2406115 ATGACACTAA
2406125 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTT-TCGTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCACTTC
2406183 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * *
2406241 GTGTGCAAAAAGTTAATAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * *
2406299 GTGTGCAAAAAGTTAAGAAACTCATAGTAAGCGTATGAATTTAC-GTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTT-CTGTATTGGGCACTTC
*
2406357 GTGTGCAAAAAGTTAAGAAATTCATAGTAAGTGTATGAATTT-TCGTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCACTTC
* *
2406415 GTGTGCAACAAGTTAATAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * *
2406473 GTGTGCAACAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTACTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
** * *
2406531 GTGTGCAAACTGTTAAGAGATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
* * *
2406589 GTGTGCAAACTA-TTAAGAGATTTATACTAAGTGTATGAATTTCT
1 GTGTGCAAA-AAGTTAAGAAATTCATACTAAGTGTATGAATTTCT
2406633 ATATGGGAAA
Statistics
Matches: 420, Mismatches: 24, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
58 417 0.99
59 3 0.01
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACTTC
Found at i:2407589 original size:64 final size:64
Alignment explanation
Indices: 2407521--2407680 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
2407511 TTCAAGGTGC
* ** * *
2407521 GTATCGATGCACATGAAGTGCATCGATGCACTTCTTTAAAATAAAAACATCGAATGCCATCGGT
1 GTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCAAATGCCATCGGT
* * ** ***
2407585 GTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAAATACAAACATCAAATGGAATTTAT
1 GTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCAAATGCCATCGGT
* *
2407649 GTACCGATGCA-TAGATAGTGCATCGATGCACC
1 GTATCGATGCACAAGA-AGTGCATCGATGCACC
2407681 TGTCAAGGGA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
63 2 0.03
64 78 0.98
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (64 bp):
GTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAAATAAAAACATCAAATGCCATCGGT
Found at i:2408355 original size:23 final size:23
Alignment explanation
Indices: 2408324--2408381 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2408314 TCTTATATGG
*
2408324 CACTACGGTGCAATTCTACGCGA
1 CACTTCGGTGCAATTCTACGCGA
* * *
2408347 CACTTCGGTGTAATTCTACGTGG
1 CACTTCGGTGCAATTCTACGCGA
*
2408370 CATTTCGGTGCA
1 CACTTCGGTGCA
2408382 TTTATACGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGA
Found at i:2409970 original size:2 final size:2
Alignment explanation
Indices: 2409963--2410004 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2409953 TCATTGTTGC
2409963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2410005 TTTAGGATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2410058 original size:12 final size:12
Alignment explanation
Indices: 2410041--2410074 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2410031 TTAATATTTT
2410041 TAATAATTTATA
1 TAATAATTTATA
* *
2410053 TTATAACTTATA
1 TAATAATTTATA
2410065 TAATAATTTA
1 TAATAATTTA
2410075 GGGTAAATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATAATTTATA
Found at i:2411882 original size:28 final size:28
Alignment explanation
Indices: 2411834--2411931 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 28
2411824 TTAGAAATTA
* * * *
2411834 AAAGGGCTAAACAGTAAATACATAAAGTT
1 AAAGGGCCAAA-AATAAATACAAAAACTT
*
2411863 AAAGGGCCAAAAATAAATACAGAAACTT
1 AAAGGGCCAAAAATAAATACAAAAACTT
* *
2411891 AAAGGACCAAAAATCAACA-ACAAAAATTT
1 AAAGGGCCAAAAAT-AA-ATACAAAAACTT
*
2411920 AAAGGTCCAAAA
1 AAAGGGCCAAAA
2411932 TAGTAAAAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 27 0.46
29 31 0.53
30 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.13, T:0.15
Consensus pattern (28 bp):
AAAGGGCCAAAAATAAATACAAAAACTT
Found at i:2411962 original size:30 final size:30
Alignment explanation
Indices: 2411916--2412000 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
2411906 AACAACAAAA
* *
2411916 ATTTAAAGGTCCAAAATAGTAAAAACAGAC
1 ATTTAAAGGACTAAAATAGTAAAAACAGAC
* * * * *
2411946 ATTTAAGGGATTAAAATAGCAAAAACATAT
1 ATTTAAAGGACTAAAATAGTAAAAACAGAC
*
2411976 ATTTAAAGGACTGAAATAGTAAAAA
1 ATTTAAAGGACTAAAATAGTAAAAA
2412001 TGTGATCTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAGTAAAAACAGAC
Found at i:2413561 original size:3 final size:3
Alignment explanation
Indices: 2413548--2413591 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
2413538 ATATATATTT
*
2413548 ATA ATTA ATA ATA ATA ATA ATA ATA ATA AT- ATA TTA ATA ATA AT
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2413592 TTTATAGATC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:2413597 original size:17 final size:17
Alignment explanation
Indices: 2413540--2413591 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 17
2413530 TGCATCAAAT
*
2413540 ATATATTTATAATTAATA
1 ATATATTAATAA-TAATA
*
2413558 ATAATAATAATAATAATA
1 AT-ATATTAATAATAATA
2413576 ATATATTAATAATAAT
1 ATATATTAATAATAAT
2413592 TTTATAGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
17 13 0.43
18 9 0.30
19 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATATTAATAATAATA
Found at i:2422769 original size:21 final size:20
Alignment explanation
Indices: 2422682--2422820 Score: 78
Period size: 19 Copynumber: 7.0 Consensus size: 20
2422672 ATTTTATTAA
2422682 TTTAATAT-TAATAA-AATAT
1 TTTAATATAT-ATAATAATAT
* *
2422701 TTTAATATCATTTTAATTAAAAT
1 TTTAATAT-A-TATAA-TAATAT
*
2422724 ATTAAT-TAT-TAA-AATAT
1 TTTAATATATATAATAATAT
* * *
2422741 TTAAAATATATTTATTAATAT
1 TT-TAATATATATAATAATAT
2422762 TTCTAATA-ATATAATAATAT
1 TT-TAATATATATAATAATAT
*
2422782 TTTAATAT-TATAATAAAAT
1 TTTAATATATATAATAATAT
* *
2422801 AATCAAT-TATATAATAATAT
1 -TTTAATATATATAATAATAT
2422821 AAGATATTAT
Statistics
Matches: 93, Mismatches: 15, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
17 5 0.05
18 3 0.03
19 30 0.32
20 29 0.31
21 15 0.16
22 2 0.02
23 9 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAATATATATAATAATAT
Found at i:2422778 original size:8 final size:8
Alignment explanation
Indices: 2422765--2422822 Score: 55
Period size: 8 Copynumber: 7.4 Consensus size: 8
2422755 TTAATATTTC
2422765 TAATAATA
1 TAATAATA
2422773 TAATAATA
1 TAATAATA
**
2422781 TTTTAATA
1 TAATAATA
*
2422789 TTATAATA
1 TAATAATA
*
2422797 AAATAAT-
1 TAATAATA
* *
2422804 CAATTATA
1 TAATAATA
2422812 TAATAATA
1 TAATAATA
2422820 TAA
1 TAA
2422823 GATATTATAT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
7 5 0.12
8 35 0.88
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (8 bp):
TAATAATA
Found at i:2422793 original size:19 final size:20
Alignment explanation
Indices: 2422756--2422820 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
2422746 ATATATTTAT
2422756 TAATATTTCTAATAATATAA
1 TAATATTTCTAATAATATAA
*
2422776 TAATATTT-TAATATTATAA
1 TAATATTTCTAATAATATAA
* * *
2422795 TAAAATAATC-AATTATATAA
1 TAATAT-TTCTAATAATATAA
2422815 TAATAT
1 TAATAT
2422821 AAGATATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
19 15 0.41
20 22 0.59
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATTTCTAATAATATAA
Found at i:2422939 original size:27 final size:26
Alignment explanation
Indices: 2422896--2422951 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
2422886 TCATAGAAAA
2422896 AATATTATTAAATTA-TTAATAATGAAT
1 AATATTATTAAATTATTTAAT-AT-AAT
*
2422923 AATATTATT-TATATATTTAATATAAT
1 AATATTATTAAAT-TATTTAATATAAT
2422949 AAT
1 AAT
2422952 CTAATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 8 0.31
27 13 0.50
28 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
AATATTATTAAATTATTTAATATAAT
Found at i:2422983 original size:23 final size:23
Alignment explanation
Indices: 2422933--2423007 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
2422923 AATATTATTT
*
2422933 ATATATTTAATATAATA-ATCTAATA
1 ATAT-TTTAATA-AATATATTTAA-A
2422958 ATATTTTAATAAATATATTTAAA
1 ATATTTTAATAAATATATTTAAA
** * *
2422981 ATATACTAATTAATATTTTTAAA
1 ATATTTTAATAAATATATTTAAA
2423004 ATAT
1 ATAT
2423008 AATATAACAC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 28 0.64
24 12 0.27
25 4 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTTTAATAAATATATTTAAA
Found at i:2422990 original size:34 final size:37
Alignment explanation
Indices: 2422933--2423008 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
2422923 AATATTATTT
*
2422933 ATATATTTAATATAATAATCTAA-TAATATTTTAATAA
1 ATATATTTAAAATAATAATCTAATTAATATTTTAA-AA
*
2422970 ATATATTTAAAAT-AT-A-CTAATTAATATTTTTAAA
1 ATATATTTAAAATAATAATCTAATTAATATTTTAAAA
2423004 ATATA
1 ATATA
2423009 ATATAACACT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
34 11 0.31
35 11 0.31
36 2 0.06
37 12 0.33
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (37 bp):
ATATATTTAAAATAATAATCTAATTAATATTTTAAAA
Found at i:2423008 original size:23 final size:23
Alignment explanation
Indices: 2422964--2423008 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2422954 AATAATATTT
2422964 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
2422987 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
2423009 ATATAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:2423126 original size:91 final size:87
Alignment explanation
Indices: 2422977--2423146 Score: 200
Period size: 91 Copynumber: 1.9 Consensus size: 87
2422967 TAAATATATT
* * * * * *
2422977 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAA-A
2423042 TAATTTATAATATTTTTGTTTCAA
65 TAATTT-TAATATTTTTGTTTCAA
*
2423066 TAAAATATACCAACATTAATATTTTTATTAATAAAATTATAAAAATAATA-TTTAAT-AATAAAT
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
*
2423129 AAATTATTTTAATATTTT
62 AAATAATTTTAATATTTT
2423147 AAAAATAATA
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
89 18 0.26
90 8 0.12
91 21 0.30
92 12 0.17
93 10 0.14
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (87 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAAAT
AATTTTAATATTTTTGTTTCAA
Found at i:2423141 original size:27 final size:26
Alignment explanation
Indices: 2423111--2423187 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 26
2423101 ATTATAAAAA
2423111 TAATATTTAATAATAAATAAATTATTT
1 TAATATTT-ATAATAAATAAATTATTT
* *
2423138 TAATATTT-TAA-AAAT-AATAATAT
1 TAATATTTATAATAAATAAATTATTT
* *
2423161 TAATTTTTATGATAAATAATATTATTT
1 TAATATTTATAATAAATAA-ATTATTT
2423188 CTTGTATTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
23 13 0.32
24 6 0.15
25 7 0.17
26 1 0.03
27 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
TAATATTTATAATAAATAAATTATTT
Found at i:2423154 original size:28 final size:28
Alignment explanation
Indices: 2423111--2423167 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
2423101 ATTATAAAAA
*
2423111 TAATATTTAATAATAAATAA-ATT-ATTT
1 TAATATTTAAAAAT-AATAATATTAATTT
2423138 TAATATTTTAAAAATAATAATATTAATTT
1 TAATA-TTTAAAAATAATAATATTAATTT
2423167 T
1 T
2423168 TATGATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
28 11 0.42
29 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TAATATTTAAAAATAATAATATTAATTT
Found at i:2424738 original size:31 final size:32
Alignment explanation
Indices: 2424702--2424790 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
2424692 ATTATTTTAT
* **
2424702 TTTTTATTAATTAATTTAGATCAAGTT-TGTG
1 TTTTTATTGATTAATTTAGATCAAGTTATGAA
* *
2424733 TTTTTATTGATTAATTCAGATCGA-TTACTGAA
1 TTTTTATTGATTAATTTAGATCAAGTTA-TGAA
*
2424765 TTCTTATTGATTAATTTAGATCAAGT
1 TTTTTATTGATTAATTTAGATCAAGT
2424791 ACTATATAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
30 2 0.04
31 21 0.45
32 23 0.49
33 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (32 bp):
TTTTTATTGATTAATTTAGATCAAGTTATGAA
Found at i:2433161 original size:19 final size:19
Alignment explanation
Indices: 2433137--2433173 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2433127 ATTACCCGGA
2433137 GGGTACCGATTCCCCCCAG
1 GGGTACCGATTCCCCCCAG
*
2433156 GGGTACCGATTCCTCCCA
1 GGGTACCGATTCCCCCCA
2433174 ACTCATAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.41, G:0.24, T:0.19
Consensus pattern (19 bp):
GGGTACCGATTCCCCCCAG
Found at i:2433986 original size:32 final size:32
Alignment explanation
Indices: 2433950--2434023 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
2433940 ATTCAGAACG
2433950 AGTATTGCATTATTATTGATGAATTCAAATCA
1 AGTATTGCATTATTATTGATGAATTCAAATCA
* * * * * *
2433982 AGTATTGTATTTTTATTGATTAGTTTAGATCA
1 AGTATTGCATTATTATTGATGAATTCAAATCA
2434014 AGTATTGCAT
1 AGTATTGCAT
2434024 AAATATATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (32 bp):
AGTATTGCATTATTATTGATGAATTCAAATCA
Found at i:2434470 original size:43 final size:42
Alignment explanation
Indices: 2434394--2434496 Score: 136
Period size: 43 Copynumber: 2.5 Consensus size: 42
2434384 ATATAAAAAA
* *
2434394 TATTAAATAATATA-TTTATAATCATTTATTATATTTTAAAT
1 TATTAAATAATATATTTTATAATAATTTACTATATTTTAAAT
* *
2434435 TATTAAAATAATATATTTTATCATAATTTACTATATTTTTAAT
1 TATT-AAATAATATATTTTATAATAATTTACTATATTTTAAAT
* *
2434478 AATTAAATAACATATTTTA
1 TATTAAATAATATATTTTA
2434497 ACATTATAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
41 4 0.07
42 24 0.44
43 26 0.48
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (42 bp):
TATTAAATAATATATTTTATAATAATTTACTATATTTTAAAT
Found at i:2446229 original size:8 final size:8
Alignment explanation
Indices: 2446218--2446249 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
2446208 AATTTAGATT
2446218 AAATTTTA
1 AAATTTTA
2446226 AAATTTTTA
1 AAA-TTTTA
2446235 AAATTTTA
1 AAATTTTA
2446243 AAATTTT
1 AAATTTT
2446250 GGAGGGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
AAATTTTA
Found at i:2446235 original size:9 final size:9
Alignment explanation
Indices: 2446221--2446249 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2446211 TTAGATTAAA
2446221 TTTTAAAAT
1 TTTTAAAAT
2446230 TTTTAAAA-
1 TTTTAAAAT
2446238 TTTTAAAAT
1 TTTTAAAAT
2446247 TTT
1 TTT
2446250 GGAGGGACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:2446429 original size:2 final size:2
Alignment explanation
Indices: 2446422--2446455 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2446412 ATCATTAATC
2446422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2446456 TGAATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2448940 original size:40 final size:40
Alignment explanation
Indices: 2448896--2448975 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
2448886 TATATGTATA
2448896 TGCAAACACAACATCACATCTTATACGGAATATACATATT
1 TGCAAACACAACATCACATCTTATACGGAATATACATATT
* * *
2448936 TGCAAACACAGCATCATATCTTATACGGAATATATATATT
1 TGCAAACACAACATCACATCTTATACGGAATATACATATT
2448976 AGACGTATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (40 bp):
TGCAAACACAACATCACATCTTATACGGAATATACATATT
Found at i:2449808 original size:12 final size:12
Alignment explanation
Indices: 2449791--2449859 Score: 84
Period size: 12 Copynumber: 5.6 Consensus size: 12
2449781 GAGTGTTATG
2449791 TTATTATATATA
1 TTATTATATATA
*
2449803 TTATTATATAGA
1 TTATTATATATA
*
2449815 TAGATATATATATA
1 T-TAT-TATATATA
* *
2449829 TTAATATATAAA
1 TTATTATATATA
2449841 TTATTATATATA
1 TTATTATATATA
2449853 TTATTAT
1 TTATTAT
2449860 TACAAATGGA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
12 36 0.77
13 3 0.06
14 8 0.17
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (12 bp):
TTATTATATATA
Found at i:2449829 original size:26 final size:24
Alignment explanation
Indices: 2449793--2449859 Score: 89
Period size: 26 Copynumber: 2.7 Consensus size: 24
2449783 GTGTTATGTT
*
2449793 ATTATATATATTATTATATAGATAG
1 ATTATATATATTATTATATAAAT-G
* *
2449818 ATATATATATATTAATATATAAATT
1 AT-TATATATATTATTATATAAATG
2449843 ATTATATATATTATTAT
1 ATTATATATATTATTAT
2449860 TACAAATGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 14 0.38
25 4 0.11
26 19 0.51
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (24 bp):
ATTATATATATTATTATATAAATG
Found at i:2451229 original size:16 final size:17
Alignment explanation
Indices: 2451200--2451235 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2451190 ATTTTAAGAC
*
2451200 TAATTATAATATTAGTA
1 TAATTATAATATTAGGA
2451217 TAATTAT-ATATTAGGA
1 TAATTATAATATTAGGA
2451233 TAA
1 TAA
2451236 CTTTATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (17 bp):
TAATTATAATATTAGGA
Found at i:2451288 original size:26 final size:24
Alignment explanation
Indices: 2451263--2451339 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 24
2451253 TATCGTTTTA
2451263 ATATTAAAATATTATAATAATATTT
1 ATATTAAAATATTA-AATAATATTT
*
2451288 ATATTACACACTATTAAATAATATTT
1 ATATTA-A-AATATTAAATAATATTT
* * *
2451314 -TATTTAAATTTTAAATACAAATTT
1 ATATTAAAATATTAAATA-ATATTT
2451338 AT
1 AT
2451340 CAATTATAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
23 9 0.21
24 6 0.14
25 11 0.26
26 11 0.26
27 6 0.14
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATTAAAATATTAAATAATATTT
Found at i:2452583 original size:2 final size:2
Alignment explanation
Indices: 2452578--2452635 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2452568 TATTCGCGCC
2452578 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2452620 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
2452636 GCGCACCTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2452762 original size:16 final size:17
Alignment explanation
Indices: 2452743--2452784 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
2452733 ACACTTGCAA
*
2452743 TAATATAAATA-AATCC
1 TAATATAAATATAATAC
*
2452759 TAATA-CAATATAATAC
1 TAATATAAATATAATAC
2452775 TAATATAAAT
1 TAATATAAAT
2452785 GAACACACGC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 4 0.19
16 14 0.67
17 3 0.14
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATATAAATATAATAC
Found at i:2453037 original size:18 final size:18
Alignment explanation
Indices: 2452989--2453037 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
2452979 TACAATTATT
*
2452989 ATTTTATAAATAACAAATA
1 ATTTTAT-AATAAAAAATA
* * *
2453008 GTTTTTTTATAAAAAATA
1 ATTTTATAATAAAAAATA
2453026 ATTTTATAATAA
1 ATTTTATAATAA
2453038 TATGACATCA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTTTATAATAAAAAATA
Found at i:2453364 original size:14 final size:14
Alignment explanation
Indices: 2453341--2453371 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2453331 CAGTAAAGCA
*
2453341 CGCCCCCTGCAGCG
1 CGCCCACTGCAGCG
2453355 CGCCCACTGCAGCG
1 CGCCCACTGCAGCG
2453369 CGC
1 CGC
2453372 TTTACGCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.55, G:0.29, T:0.06
Consensus pattern (14 bp):
CGCCCACTGCAGCG
Found at i:2453801 original size:14 final size:15
Alignment explanation
Indices: 2453782--2453828 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2453772 TATAAGGTAA
2453782 TTTTATTATAATT-T
1 TTTTATTATAATTAT
*
2453796 TTTTATTATACTTAT
1 TTTTATTATAATTAT
*
2453811 TGTTTATTATGATTAT
1 T-TTTATTATAATTAT
2453827 TT
1 TT
2453829 GAAAAAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.43
15 3 0.11
16 13 0.46
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (15 bp):
TTTTATTATAATTAT
Found at i:2453872 original size:23 final size:24
Alignment explanation
Indices: 2453813--2453872 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 24
2453803 ATACTTATTG
*
2453813 TTTATTATGATTATTTGAAAAAAT
1 TTTATTATGATTATGTGAAAAAAT
* * * *
2453837 ATTA-TACGTTTATGTGTAAAAAT
1 TTTATTATGATTATGTGAAAAAAT
2453860 TTTATTATG-TTAT
1 TTTATTATGATTAT
2453873 ATTTTCGTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (24 bp):
TTTATTATGATTATGTGAAAAAAT
Found at i:2455090 original size:4 final size:4
Alignment explanation
Indices: 2455081--2455109 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2455071 AATCATGCAT
2455081 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA T
2455110 TATTACTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:2455217 original size:25 final size:25
Alignment explanation
Indices: 2455181--2455238 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
2455171 AGATATATGA
* *
2455181 TTTCCATCCAAGCGAAGCATACCGC
1 TTTCCATTCAAGCGAAGCAGACCGC
2455206 TTTCCATTCAAGCGAAGCAGACCGC
1 TTTCCATTCAAGCGAAGCAGACCGC
2455231 TTTCCATT
1 TTTCCATT
2455239 TTATATCTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.26
Consensus pattern (25 bp):
TTTCCATTCAAGCGAAGCAGACCGC
Found at i:2455294 original size:17 final size:17
Alignment explanation
Indices: 2455268--2455305 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2455258 AATTAAATAC
*
2455268 AATA-TTAAATAATTTA
1 AATACTTAAATAAATTA
2455284 AATACTTAAATAAATTA
1 AATACTTAAATAAATTA
2455301 AATAC
1 AATAC
2455306 ACAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
AATACTTAAATAAATTA
Found at i:2456132 original size:2 final size:2
Alignment explanation
Indices: 2456125--2456151 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2456115 TTCCTAACGT
2456125 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2456152 CTTACTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2456250 original size:23 final size:24
Alignment explanation
Indices: 2456224--2456340 Score: 81
Period size: 25 Copynumber: 4.9 Consensus size: 24
2456214 TTTATTTTTC
2456224 ATTTATTTATTATTATTAT-TACT
1 ATTTATTTATTATTATTATATACT
2456247 ATTTAGTATT-TTATTA-TATTATACAT
1 ATTTA-T-TTATTATTATTA-TATAC-T
*
2456273 ACATTT-TTTA-TATTTTTATATA-T
1 --ATTTATTTATTATTATTATATACT
2456296 ATTT-TTTATTATT-TTATTTATACT
1 ATTTATTTATTATTATTA--TATACT
2456320 ATTTATTTATT-TTCATTATAT
1 ATTTATTTATTATT-ATTATAT
2456341 TTTTAGTTTC
Statistics
Matches: 77, Mismatches: 1, Indels: 31
0.71 0.01 0.28
Matches are distributed among these distances:
21 11 0.14
22 4 0.05
23 12 0.16
24 18 0.23
25 21 0.27
26 7 0.09
28 4 0.05
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (24 bp):
ATTTATTTATTATTATTATATACT
Found at i:2456299 original size:21 final size:21
Alignment explanation
Indices: 2456253--2456344 Score: 73
Period size: 21 Copynumber: 4.3 Consensus size: 21
2456243 TACTATTTAG
* *
2456253 TATTTTATTATA-TTATACATA
1 TATTTT-TTATATTTTTATATA
*
2456274 CATTTTTTATATTTTTATATA
1 TATTTTTTATATTTTTATATA
*
2456295 TATTTTTTATTATTTTATTTATA
1 TATTTTTTA-TATTTT-TATATA
* *
2456318 CTATTTATT-TATTTTCAT-TA
1 -TATTTTTTATATTTTTATATA
2456338 TATTTTT
1 TATTTTT
2456345 AGTTTCTTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
19 6 0.10
20 7 0.12
21 21 0.36
22 12 0.21
23 5 0.09
24 7 0.12
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTTTTATATTTTTATATA
Found at i:2456331 original size:44 final size:43
Alignment explanation
Indices: 2456255--2456344 Score: 110
Period size: 44 Copynumber: 2.1 Consensus size: 43
2456245 CTATTTAGTA
* *
2456255 TTTTATTATATTATACATACATTTTTTATATTTTTATATATATT
1 TTTTATTATATTATACATACATTTATTATATTTTCAT-TATATT
* **
2456299 TTTTATTATTTTATTTATACTATTTATT-TATTTTCATTATATT
1 TTTTATTATATTATACATAC-ATTTATTATATTTTCATTATATT
2456342 TTT
1 TTT
2456345 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
43 9 0.22
44 25 0.62
45 6 0.15
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (43 bp):
TTTTATTATATTATACATACATTTATTATATTTTCATTATATT
Found at i:2456450 original size:20 final size:19
Alignment explanation
Indices: 2456423--2456478 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2456413 TTTTGTCTTC
2456423 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
2456442 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
2456462 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
2456479 ATTATTTGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:2459804 original size:31 final size:31
Alignment explanation
Indices: 2459766--2459884 Score: 136
Period size: 31 Copynumber: 3.8 Consensus size: 31
2459756 TCCTTGGCAA
* *
2459766 CTGTCCATAGGTTCCGAAGAACCTAGGTAAT
1 CTGTCCATATGTTCCGAAGAACATAGGTAAT
**
2459797 CTGTCCATATGTTCCTTAGAACATAGGTATAT
1 CTGTCCATATGTTCCGAAGAACATAGGTA-AT
2459829 -TGTCCATATG-TCTCGAA-AGACATAGGTAATT
1 CTGTCCATATGTTC-CGAAGA-ACATAGGTAA-T
*
2459860 CTGTCCATATGTTCCGTAGAACATA
1 CTGTCCATATGTTCCGAAGAACATA
2459885 AGTATAGCCT
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
30 4 0.05
31 47 0.64
32 20 0.27
33 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (31 bp):
CTGTCCATATGTTCCGAAGAACATAGGTAAT
Found at i:2461160 original size:64 final size:64
Alignment explanation
Indices: 2461008--2461164 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 64
2460998 CAATAAGGGT
* * ** *
2461008 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATACATTCGATGTTCTATTATTAAAGAG
* * * *
2461072 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTATATTCGATGTTTCTATT-TTAAA-
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATACATTCGATG-TTCTATTATTAAAG
2461133 AG
63 AG
2461135 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
2461165 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
63 3 0.04
64 62 0.82
65 11 0.14
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCGATGTTCTATTATTAAAGAG
Found at i:2464411 original size:22 final size:22
Alignment explanation
Indices: 2464383--2464433 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
2464373 CCCCATCAAG
2464383 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATGCCAAA
2464405 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATGCCAAA
2464427 CCTTTGA
1 CCTTTGA
2464434 CCAAACACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATGCCAAA
Found at i:2465471 original size:106 final size:106
Alignment explanation
Indices: 2465344--2466832 Score: 2289
Period size: 106 Copynumber: 14.0 Consensus size: 106
2465334 ATATCGTTCC
* * * * *
2465344 ACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2465409 AAGTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2465450 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2465515 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2465556 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCGGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2465621 AATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2465662 ATTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGTCCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
2465727 AATTTTGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
2465768 ACTCCAGAAAACGTAAGCTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
2465833 AATTTTGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2465874 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGAGCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2465939 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2465980 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2466045 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2466086 ACTCGAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2466151 ATTTTCAGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2466192 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2466257 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
2466298 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2466363 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
2466404 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2466469 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
2466510 ACTCGAGACAACGCAAGTTCAACTTCAAGACGAAGGGATCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
2466575 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
2466616 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** * * *
2466681 AATTTTGGAGCCAATTTTAACTTCACAATCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCAC-AGCGAAGGATATTGG
* * * * *
2466723 ACTCGAGACAACACAAGTTCAACTTCACAACAAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* * * *
2466787 CGATTCCAGAGTCAATTTCAACTTCAC-GACGGAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
2466829 ACTC
1 ACTC
2466833 GGAACAATGC
Statistics
Matches: 1279, Mismatches: 101, Indels: 6
0.92 0.07 0.00
Matches are distributed among these distances:
106 1188 0.93
107 91 0.07
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:2467672 original size:37 final size:37
Alignment explanation
Indices: 2467585--2467686 Score: 125
Period size: 37 Copynumber: 2.8 Consensus size: 37
2467575 TTTCGTCCTA
* *
2467585 CTAGGATTCAAACTCCTAAAAATAAGATATAATTTAG
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTAG
*
2467622 CTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTA-
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATT-TAG
** * *
2467659 CTATTATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
2467687 CCATGAGCAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
37 55 0.96
38 2 0.04
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (37 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTAG
Found at i:2468650 original size:21 final size:21
Alignment explanation
Indices: 2468608--2468650 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2468598 TTTCTGGGGT
*
2468608 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
2468629 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
2468650 A
1 A
2468651 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2468703 original size:20 final size:20
Alignment explanation
Indices: 2468678--2468715 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2468668 GAACGCTAGA
*
2468678 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
2468698 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
2468716 TAATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:2469382 original size:103 final size:103
Alignment explanation
Indices: 2469198--2469423 Score: 355
Period size: 103 Copynumber: 2.2 Consensus size: 103
2469188 GTAGAGGGTC
* * *
2469198 TATGTGGTCATTCGGGACATATATGTATTCTTTGAAACATGTGTGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGAAACATGTGTGAGGTCTGGTGAGACACATAC
* * *
2469263 TTGATCTTTGATATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGACATATGTATATGATTCTTAAAGAATGA
* *
2469301 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGAAACATGTGTGAGGTCTGGTGAGACACATAC
*
2469366 TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
66 TTGATCCTTGACATATGTATATGATTCTTAAAGAATGA
2469404 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
2469424 TATTATATGA
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
102 1 0.01
103 112 0.99
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGAAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGACATATGTATATGATTCTTAAAGAATGA
Found at i:2469460 original size:23 final size:23
Alignment explanation
Indices: 2469434--2469494 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
2469424 TATTATATGA
*
2469434 CACTACGGTGCAATTCTATGCGG
1 CACTACGGTGCAATTCTAAGCGG
* *
2469457 CACTCCGGTGCAATTCTAAGTGG
1 CACTACGGTGCAATTCTAAGCGG
2469480 CACTTA-GGTGCAATT
1 CAC-TACGGTGCAATT
2469495 ATACGAGCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (23 bp):
CACTACGGTGCAATTCTAAGCGG
Found at i:2475579 original size:21 final size:21
Alignment explanation
Indices: 2475537--2475579 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2475527 TTTCTGGGCT
*
2475537 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
2475558 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
2475579 A
1 A
2475580 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:2475632 original size:20 final size:20
Alignment explanation
Indices: 2475607--2475644 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2475597 TAACGCTAGA
*
2475607 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
2475627 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
2475645 TAATAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:2476352 original size:103 final size:103
Alignment explanation
Indices: 2476127--2476344 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
2476117 GTAGAGGGTC
* *
2476127 TATGTGGTCCTTCGGGACATATACGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTAC
1 TATGTGGTCCTTCGGGACATATACGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
* *
2476192 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
* *
2476230 TATGTGGTCATTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATACGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
2476295 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
2476333 TATGTGGTCCTT
1 TATGTGGTCCTT
2476345 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATACGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTATTAAGGAATGA
Found at i:2477359 original size:101 final size:98
Alignment explanation
Indices: 2477174--2477360 Score: 211
Period size: 101 Copynumber: 1.9 Consensus size: 98
2477164 ATTTACCCCT
* * *
2477174 TATTATTATATATATATATATGTATATATTTAATTATATTTTATTTATTTATTATAATTTTTTTT
1 TATTATTATATATATATATATGTATATATTT-ATTATATTTTACTTATTTACTATAATTTTTTTC
**
2477239 TCATTTTTCTTTGCATTATATTATATTATTTTCC
65 TCATTTTTCTTAACATTATATTATATTATTTTCC
*
2477273 TATTATTATATATATATATAT-TATTATCATTT-TTATCTATGTTTACTTATTTACTAT-GTTTT
1 TATTATTATATATATATATATGTA-TAT-ATTTATTA--TAT-TTTACTTATTTACTATAATTTT
*
2477335 TTTACT-ATATTTTCTTAACGTTATAT
61 TTT-CTCAT-TTTTCTTAACATTATAT
2477361 ATTTATATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
98 5 0.07
99 24 0.32
100 16 0.22
101 29 0.39
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (98 bp):
TATTATTATATATATATATATGTATATATTTATTATATTTTACTTATTTACTATAATTTTTTTCT
CATTTTTCTTAACATTATATTATATTATTTTCC
Found at i:2477436 original size:11 final size:11
Alignment explanation
Indices: 2477420--2477446 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2477410 TTTTTAGTTA
2477420 ATATTATATGT
1 ATATTATATGT
2477431 ATATTATATGT
1 ATATTATATGT
2477442 ATATT
1 ATATT
2477447 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (11 bp):
ATATTATATGT
Found at i:2477444 original size:6 final size:5
Alignment explanation
Indices: 2477420--2477574 Score: 61
Period size: 5 Copynumber: 32.0 Consensus size: 5
2477410 TTTTTAGTTA
* *
2477420 ATATT ATATGT ATATT ATATGT ATATTT ATTTT TTATT -TATT -TATT
1 ATATT ATAT-T ATATT ATAT-T ATA-TT ATATT ATATT ATATT ATATT
* * *
2477466 -TATT ATTATT ACTATTT AGTATT TTATT ATATT ATACAT ACATT -T-TT
1 ATATT A-TATT A-TA-TT A-TATT ATATT ATATT ATA-TT ATATT ATATT
*
2477513 ATATT -T-TT ATATAT ATATT -T-TT -TATT ATTTT AT-TT ATATT AT-TT
1 ATATT ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT
2477557 AT-TT AT-TT -TCATT ATATT
1 ATATT ATATT AT-ATT ATATT
2477575 TTTAGTTTCT
Statistics
Matches: 120, Mismatches: 12, Indels: 36
0.71 0.07 0.21
Matches are distributed among these distances:
3 8 0.07
4 32 0.27
5 44 0.37
6 30 0.25
7 6 0.05
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (5 bp):
ATATT
Found at i:2477459 original size:4 final size:4
Alignment explanation
Indices: 2477443--2477564 Score: 53
Period size: 4 Copynumber: 30.2 Consensus size: 4
2477433 ATTATATGTA
*
2477443 TATT TATT T-TT TATT TATT TATT TA-T TA-T TATT ACTATT TA-G TATTT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT --TATT TATT TA-TT
** * * *
2477490 TATT ATATT ATACA TACAT T-TT TATAT T-TT TATA TATA TATT T-TT
1 TATT -TATT -TATT TA-TT TATT TAT-T TATT TATT TATT TATT TATT
2477535 TA-T TATTT TATT TATAT TATT TATT TATT T
1 TATT TA-TT TATT TAT-T TATT TATT TATT T
2477565 TCATTATATT
Statistics
Matches: 94, Mismatches: 9, Indels: 30
0.71 0.07 0.23
Matches are distributed among these distances:
3 21 0.22
4 50 0.53
5 19 0.20
6 4 0.04
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (4 bp):
TATT
Found at i:2477517 original size:29 final size:27
Alignment explanation
Indices: 2477480--2477554 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 27
2477470 ATTATTACTA
2477480 TTTAGTATTTTATTATATTATACATACATT
1 TTTAGTATTTTATTATATTAT--ATA-ATT
*
2477510 TTTA-TA-TTT-TTATA-TATATATTT
1 TTTAGTATTTTATTATATTATATAATT
*
2477533 TTTATTATTTTATTTATATTAT
1 TTTAGTATTTTA-TTATATTAT
2477555 TTATTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
23 6 0.15
24 5 0.13
25 3 0.08
26 3 0.08
27 10 0.26
28 6 0.15
29 2 0.05
30 4 0.10
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTAGTATTTTATTATATTATATAATT
Found at i:2477529 original size:14 final size:13
Alignment explanation
Indices: 2477511--2477578 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 13
2477501 ACATACATTT
2477511 TTATATTTTTATA
1 TTATATTTTTATA
2477524 TATATATTTTT-TA
1 T-TATATTTTTATA
*
2477537 TTATTTTATTTATA
1 TTATATT-TTTATA
*
2477551 TTATTTATTTATTTTCA
1 TTA--TATTT-TTAT-A
2477568 TTATATTTTTA
1 TTATATTTTTA
2477579 GTTTCTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
12 5 0.11
13 7 0.16
14 16 0.36
15 6 0.14
16 6 0.14
17 4 0.09
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATATTTTTATA
Found at i:2477571 original size:13 final size:13
Alignment explanation
Indices: 2477441--2477562 Score: 62
Period size: 13 Copynumber: 9.2 Consensus size: 13
2477431 ATATTATATG
2477441 TATATTTATTT-TT
1 TATA-TTATTTATT
2477454 TAT-TTATTTATT
1 TATATTATTTATT
2477466 TATTATTATTACTATT
1 TA-TATTATT--TATT
*
2477482 TAGTATTTTATTATAT
1 TA-TATTAT-TTAT-T
* *
2477498 TATACATACATT-TT
1 TATA-TTA-TTTATT
*
2477512 TATATT-TTTATA
1 TATATTATTTATT
2477524 TATA-TA-TT-TT
1 TATATTATTTATT
2477534 T-TATTATTTTATT
1 TATATTA-TTTATT
2477547 TATATTATTTATT
1 TATATTATTTATT
2477560 TAT
1 TAT
2477563 TTTCATTATA
Statistics
Matches: 84, Mismatches: 9, Indels: 32
0.67 0.07 0.26
Matches are distributed among these distances:
9 2 0.02
10 4 0.05
11 11 0.13
12 11 0.13
13 17 0.20
14 15 0.18
15 6 0.07
16 17 0.20
17 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (13 bp):
TATATTATTTATT
Found at i:2477571 original size:22 final size:20
Alignment explanation
Indices: 2477445--2477578 Score: 78
Period size: 22 Copynumber: 6.2 Consensus size: 20
2477435 TATATGTATA
2477445 TTTATT-TTTTATTTATTTATT
1 TTTATTATTTTATTTA--TATT
*
2477466 TATTATTATTACTATTTAGTA-T
1 T-TTATTATT-TTATTTA-TATT
** *
2477488 TTTATTATATTATACATACATT
1 TTTATTAT-TT-TATTTATATT
2477510 TTTA-TATTTTTATATATATATTT
1 TTTATTA-TTTTAT-T-TATA-TT
2477533 TTTATTATTTTATTTATATT
1 TTTATTATTTTATTTATATT
2477553 ATTTATTTATTTTCA-TTATATT
1 -TTTA-TTATTTT-ATTTATATT
2477575 TTTA
1 TTTA
2477579 GTTTCTTTGT
Statistics
Matches: 90, Mismatches: 9, Indels: 28
0.71 0.07 0.22
Matches are distributed among these distances:
20 4 0.04
21 25 0.28
22 36 0.40
23 17 0.19
24 8 0.09
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (20 bp):
TTTATTATTTTATTTATATT
Found at i:2479130 original size:16 final size:16
Alignment explanation
Indices: 2479109--2479140 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2479099 ACATTGATAC
2479109 CAATAATTTTGGAGAT
1 CAATAATTTTGGAGAT
2479125 CAATAATTTTGGAGAT
1 CAATAATTTTGGAGAT
2479141 ACTACCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (16 bp):
CAATAATTTTGGAGAT
Found at i:2481606 original size:36 final size:36
Alignment explanation
Indices: 2481559--2481629 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
2481549 TATTATTTTT
*
2481559 ATAAATAAAATTCGGACG-ATATCATATTCATAAACC
1 ATAAATAAAATTCGGA-GAAGATCATATTCATAAACC
* *
2481595 ATAAATAAAATTTGGAGAAGATCATATTTATAAAC
1 ATAAATAAAATTCGGAGAAGATCATATTCATAAAC
2481630 AATATAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 1 0.03
36 30 0.97
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (36 bp):
ATAAATAAAATTCGGAGAAGATCATATTCATAAACC
Done.