Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 59 of 126
Found at i:11967797 original size:10 final size:10
Alignment explanation
Indices: 11967755--11967814 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
11967745 AAAAAAAAGT
11967755 AAAAA-AAAA
1 AAAAAGAAAA
11967764 AAAAAG-AAA
1 AAAAAGAAAA
* *
11967773 AAAAGGAAAG
1 AAAAAGAAAA
11967783 AAAAAGAAAA
1 AAAAAGAAAA
11967793 AAAAAGAATGAA
1 AAAAAGAA--AA
11967805 AAATAAGAAA
1 AAA-AAGAAA
11967815 TCAAGGCGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 13 0.31
10 18 0.43
11 1 0.02
12 5 0.12
13 5 0.12
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:11967812 original size:29 final size:27
Alignment explanation
Indices: 11967744--11967814 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 27
11967734 ATGCTTAAAG
11967744 GAAAAAAAAGTAAAAAAAAAAAAAAGAA
1 GAAAAAAAAG-AAAAAAAAAAAAAAGAA
11967772 -AAAAAGGAAAGAAAAAGAAAAAAAAAGAA
1 GAAAAA--AAAGAAAAA-AAAAAAAAAGAA
*
11967801 TGAAAAATAAGAAA
1 -GAAAAAAAAGAAA
11967815 TCAAGGCGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
27 5 0.14
28 5 0.14
29 22 0.59
31 5 0.14
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (27 bp):
GAAAAAAAAGAAAAAAAAAAAAAAGAA
Found at i:11968859 original size:41 final size:41
Alignment explanation
Indices: 11968794--11968871 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
11968784 GTCAAGGAGC
11968794 ATTTACTTTCAAAGTTGTGATGCCTCTATTTA-AAGAAGCA
1 ATTTACTTTCAAAGTTGTGATGCCTCTATTTAGAAGAAGCA
*
11968834 ATTTACTTTCAAAAGTTGT-AGTGCCTCTGTTTAGAAGA
1 ATTTACTTTC-AAAGTTGTGA-TGCCTCTATTTAGAAGA
11968872 GCTTTGTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
40 11 0.32
41 19 0.56
42 4 0.12
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (41 bp):
ATTTACTTTCAAAGTTGTGATGCCTCTATTTAGAAGAAGCA
Found at i:11968987 original size:41 final size:43
Alignment explanation
Indices: 11968856--11969135 Score: 275
Period size: 43 Copynumber: 6.5 Consensus size: 43
11968846 AAGTTGTAGT
* * *
11968856 GCCTCTGTTTAGAAGAGCTTTGTTTATTTTTCTCAAAGTCATCGA
1 GCCTCTGATTAGAGGAGCTTTGTTTA-TTTT-TCAAAGTCGTCGA
* * **
11968901 GCCTTTGATTAGAGGAGCTTTGTTTATTTTTTAAAGTTATCGA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTCGA
* *
11968944 GCCTCTGATTAG-GGAAGC-TT-TCTATTTTTCAAAGTCGTTGA
1 GCCTCTGATTAGAGG-AGCTTTGTTTATTTTTCAAAGTCGTCGA
* * *
11968985 GCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTGGA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTCGA
* ** *
11969028 GCCTCTAATTAGAGGAGC--CATTTATTTTTCAAAGTCGTGGA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTCGA
* * *
11969069 GCCTCTGTTTAGAGAAGCTTTGTTTATTTTACTCAAAGTCGTTGA
1 GCCTCTGATTAGAGGAGCTTTGTTTATTTT--TCAAAGTCGTCGA
* *
11969114 GCCT-TTACTTAGAGAAGCTTTG
1 GCCTCTGA-TTAGAGGAGCTTTG
11969136 ATCAAAATTT
Statistics
Matches: 201, Mismatches: 25, Indels: 18
0.82 0.10 0.07
Matches are distributed among these distances:
41 67 0.33
42 8 0.04
43 68 0.34
44 5 0.02
45 53 0.26
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (43 bp):
GCCTCTGATTAGAGGAGCTTTGTTTATTTTTCAAAGTCGTCGA
Found at i:11968997 original size:84 final size:84
Alignment explanation
Indices: 11968878--11969127 Score: 279
Period size: 84 Copynumber: 2.9 Consensus size: 84
11968868 AAGAGCTTTG
* * * * *
11968878 TTTATTTTTCTCAAAGTCATCGAGCCTTTGATTAGAGGAGCTTTGTTTATTTTTTAAAGTTATCG
1 TTTA-TTTT-TCAAAGTCGTCGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCATCG
* *
11968943 AGCCTCTGATTAG-GGAAG-CT
64 AGCCTCTAATTAGAGG-AGCCA
* * * *
11968963 TTCTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCGTGGA
1 TT-TATTTTTCAAAGTCGTCGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCATCGA
11969028 GCCTCTAATTAGAGGAGCCA
65 GCCTCTAATTAGAGGAGCCA
* * * *
11969048 TTTATTTTTCAAAGTCGTGGAGCCTCTGTTTAGAGAAGCTTTGTTTATTTTACTCAAAGTCGTTG
1 TTTATTTTTCAAAGTCGTCGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTT--TCAAAGTCATCG
* *
11969113 AGCCTTTACTTAGAG
64 AGCCTCTAATTAGAG
11969128 AAGCTTTGAT
Statistics
Matches: 143, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
84 106 0.74
85 11 0.08
86 26 0.18
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.41
Consensus pattern (84 bp):
TTTATTTTTCAAAGTCGTCGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTCAAAGTCATCGAG
CCTCTAATTAGAGGAGCCA
Found at i:11969387 original size:10 final size:10
Alignment explanation
Indices: 11969366--11969525 Score: 55
Period size: 10 Copynumber: 15.7 Consensus size: 10
11969356 TATTTATTGC
11969366 TATTATTA-T
1 TATTATTATT
11969375 TATTATTATT
1 TATTATTATT
11969385 TATTAATATATT
1 TATT-AT-TATT
*
11969397 T-TT-TTATC
1 TATTATTATT
* *
11969405 TATTAATATA
1 TATTATTATT
*
11969415 TATTACTATT
1 TATTATTATT
*
11969425 TATCTATTAATG
1 TAT-TATT-ATT
*
11969437 TA-TATAAATT
1 TATTAT-TATT
11969447 T-TTATTATT
1 TATTATTATT
* * *
11969456 AACTATTATC
1 TATTATTATT
*
11969466 TATTAATTATC
1 TATT-ATTATT
* * *
11969477 CATTAGTATA
1 TATTATTATT
*
11969487 TA-TATGTATA
1 TATTAT-TATT
11969497 TA-TATATATT
1 TATTAT-TATT
11969507 TATTTATTATT
1 TA-TTATTATT
11969518 TATCTATT
1 TAT-TATT
11969526 TTTTTCTTTT
Statistics
Matches: 114, Mismatches: 22, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
8 4 0.04
9 16 0.14
10 56 0.49
11 26 0.23
12 12 0.11
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (10 bp):
TATTATTATT
Found at i:11969408 original size:20 final size:23
Alignment explanation
Indices: 11969372--11969489 Score: 77
Period size: 24 Copynumber: 5.1 Consensus size: 23
11969362 TTGCTATTAT
*
11969372 TATTAT-TATTATTTATTAATATA
1 TATTATAT-TTATCTATTAATATA
11969395 T-TT-T-TTTATCTATTAATATA
1 TATTATATTTATCTATTAATATA
*
11969415 TATTACTATTTATCTATTAATGTA
1 TATTA-TATTTATCTATTAATATA
* *
11969439 TATAAATTTTTAT-TATTAACTAT-
1 TAT-TATATTTATCTATTAA-TATA
* * *
11969462 TATCTATTAATTATCCATTAGTATA
1 TAT-TA-TATTTATCTATTAATATA
11969487 TAT
1 TAT
11969490 ATGTATATAT
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
20 15 0.20
21 4 0.05
22 2 0.03
23 12 0.16
24 34 0.45
25 8 0.11
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.57
Consensus pattern (23 bp):
TATTATATTTATCTATTAATATA
Found at i:11969417 original size:24 final size:24
Alignment explanation
Indices: 11969390--11969491 Score: 84
Period size: 24 Copynumber: 4.2 Consensus size: 24
11969380 TTATTTATTA
*
11969390 ATATATTTTTTTATCTATTAATAT
1 ATATATATTTTTATCTATTAATAT
* *
11969414 ATAT-TACTATTTATCTATTAATGT
1 ATATATA-TTTTTATCTATTAATAT
*
11969438 ATATAAATTTTTAT-TATTAACTAT
1 ATATATATTTTTATCTATTAA-TAT
* * * *
11969462 -TATCTATTAATTATCCATTAGTAT
1 ATATATATT-TTTATCTATTAATAT
11969486 ATATAT
1 ATATAT
11969492 GTATATATAT
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
23 13 0.22
24 38 0.63
25 9 0.15
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (24 bp):
ATATATATTTTTATCTATTAATAT
Found at i:11969476 original size:48 final size:47
Alignment explanation
Indices: 11969365--11969490 Score: 116
Period size: 48 Copynumber: 2.7 Consensus size: 47
11969355 TTATTTATTG
* **
11969365 CTATTATTATT-ATTAT-TATTTATTAATATATTTTTTTATCTATTAA
1 CTATTATTATTAATTATCTATTAATT-ATATAAATTTTTATCTATTAA
* *
11969411 -TATATATTACTATTTATCTATTAATGTATATAAATTTTTAT-TATTAA
1 CTAT-TATTATTAATTATCTATTAAT-TATATAAATTTTTATCTATTAA
* *
11969458 CTATTATCTATTAATTATCCATTAGTATATATA
1 CTATTAT-TATTAATTATCTATTAAT-TATATA
11969491 TGTATATATA
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
45 3 0.05
46 6 0.09
47 13 0.20
48 41 0.64
49 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (47 bp):
CTATTATTATTAATTATCTATTAATTATATAAATTTTTATCTATTAA
Found at i:11970233 original size:12 final size:10
Alignment explanation
Indices: 11970217--11970261 Score: 56
Period size: 9 Copynumber: 4.3 Consensus size: 10
11970207 TTCCAAAGGT
11970217 TTATTTATTTA
1 TTATTTA-TTA
11970228 TTTATTTATTA
1 -TTATTTATTA
11970239 TTA-TTATTA
1 TTATTTATTA
11970248 TTATTTATTGA
1 TTATTTATT-A
11970259 TTA
1 TTA
11970262 GATTAGAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.29
10 8 0.26
11 7 0.23
12 7 0.23
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (10 bp):
TTATTTATTA
Found at i:11970266 original size:19 final size:19
Alignment explanation
Indices: 11970229--11970266 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11970219 ATTTATTTAT
*
11970229 TTATTTATTATTATTATTA
1 TTATTTATTATTATGATTA
11970248 TTATTTATTGATTA-GATTA
1 TTATTTATT-ATTATGATTA
11970267 GAATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTATTTATTATTATGATTA
Found at i:11970454 original size:60 final size:58
Alignment explanation
Indices: 11970308--11970486 Score: 179
Period size: 60 Copynumber: 3.1 Consensus size: 58
11970298 TTTTTAAATG
* * *
11970308 ATTTTCT-TTAAAA-AAAATTCCAAAAAAAATATTTTAGAGGAAAAGTTGAAAGTATCA
1 ATTTTCTCTCAAAATAAAATTTCAAAAAAAAT-TTTTTGAGGAAAAGTTGAAAGTATCA
* * * *
11970365 ATTTTCTTTGAAAAT-AATTTTCTAAAAAAAAAGTTTTTTGAGGAAAAGTTGAAAGTATTA
1 ATTTTCTCTCAAAATAAAATTTC--AAAAAAAA-TTTTTTGAGGAAAAGTTGAAAGTATCA
* * * *
11970425 ATTTTC-CTCAAAATTAAAATTTC-AGAAAAATATTTTGGGGAAAAGTTGAAAATATCA
1 ATTTTCTCTCAAAA-TAAAATTTCAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCA
11970482 ATTTT
1 ATTTT
11970487 TCTTGTACAA
Statistics
Matches: 102, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
57 35 0.34
58 16 0.16
59 5 0.05
60 39 0.38
61 7 0.07
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (58 bp):
ATTTTCTCTCAAAATAAAATTTCAAAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCA
Found at i:11973102 original size:63 final size:63
Alignment explanation
Indices: 11973003--11973127 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
11972993 GATACAACTA
11973003 TATAATCTCAGAGTTCCGTAATTTCTTATATTGCACTCTAGTTCTTGTTGAAACCAAGCACTT
1 TATAATCTCAGAGTTCCGTAATTTCTTATATTGCACTCTAGTTCTTGTTGAAACCAAGCACTT
*
11973066 TATAATCTCAGAGTTCCGTAATTTCTTATATTGCACTCTAGTTCTTGTTGAACCCAAGCACT
1 TATAATCTCAGAGTTCCGTAATTTCTTATATTGCACTCTAGTTCTTGTTGAAACCAAGCACT
11973128 CTCAAATAGG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (63 bp):
TATAATCTCAGAGTTCCGTAATTTCTTATATTGCACTCTAGTTCTTGTTGAAACCAAGCACTT
Found at i:11980815 original size:34 final size:34
Alignment explanation
Indices: 11980777--11980860 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 34
11980767 TATTAGTATT
* * *
11980777 GTTTGAATCTAGAAAACGCCATTATATTAGCGAC
1 GTTTGTATCTAGAAAACACCATTATATTAACGAC
* * *
11980811 GTTTGTAT-TTGAAAAACACCGTTATATTAACGGC
1 GTTTGTATCTAG-AAAACACCATTATATTAACGAC
*
11980845 ATTTGTATCTAGAAAA
1 GTTTGTATCTAGAAAA
11980861 TGTTGCTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
33 2 0.05
34 36 0.90
35 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (34 bp):
GTTTGTATCTAGAAAACACCATTATATTAACGAC
Found at i:11981565 original size:21 final size:20
Alignment explanation
Indices: 11981535--11981591 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
11981525 AACTGTTGAA
*
11981535 ATTTTGCATGCTCTTACTTC
1 ATTTTGCATGTTCTTACTTC
* *
11981555 ATTTTAGCATGTTCTTCCTTT
1 ATTTT-GCATGTTCTTACTTC
11981576 ATTTTGGCATGTTCTT
1 ATTTT-GCATGTTCTT
11981592 GTTCTCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 5 0.16
21 27 0.84
ACGTcount: A:0.14, C:0.19, G:0.12, T:0.54
Consensus pattern (20 bp):
ATTTTGCATGTTCTTACTTC
Found at i:11984876 original size:45 final size:45
Alignment explanation
Indices: 11984800--11984894 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 45
11984790 CAAACATTAA
*
11984800 AAAAATCTTAGAAAATTCAAATCCAAGATTCAAAGGTTCACATTC
1 AAAAATCTTAGAAAATTCAAATCCAAGATTCAAAAGTTCACATTC
* * * * **
11984845 AAAAATCTTAG-ATATTGACATCTAAGAATTCAAAAGTTTGCATTC
1 AAAAATCTTAGAAAATTCAAATCCAAG-ATTCAAAAGTTCACATTC
11984890 AAAAA
1 AAAAA
11984895 CATTTATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 11 0.26
45 31 0.74
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.28
Consensus pattern (45 bp):
AAAAATCTTAGAAAATTCAAATCCAAGATTCAAAAGTTCACATTC
Found at i:11985009 original size:4 final size:4
Alignment explanation
Indices: 11985000--11985061 Score: 72
Period size: 4 Copynumber: 15.2 Consensus size: 4
11984990 AAATATTTAC
* * *
11985000 AAAT AAAT AAAT ACAT AAAT -AAT CAAAT AAAT AAAAT AAAC AAAT AAAC
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT -AAAT AAAT AAAT AAAT
11985049 AAAT AAAT AAAT A
1 AAAT AAAT AAAT A
11985062 GACAATTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.06
4 39 0.80
5 7 0.14
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:11990962 original size:29 final size:30
Alignment explanation
Indices: 11990896--11990962 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
11990886 TGAATGACTC
*
11990896 TTAAATTTTAATGAAATGTTTAATATAATGT
1 TTAAATTTTAA-GAAATGTTTAATATAATAT
* * *
11990927 CTGAATTTTAA-AAATTTTTAATATAATAT
1 TTAAATTTTAAGAAATGTTTAATATAATAT
11990956 TTAAATT
1 TTAAATT
11990963 ATGAATCTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 21 0.70
31 9 0.30
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.49
Consensus pattern (30 bp):
TTAAATTTTAAGAAATGTTTAATATAATAT
Found at i:11992666 original size:27 final size:26
Alignment explanation
Indices: 11992632--11992687 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 26
11992622 GGGCTATTAA
11992632 ATTATATTCAAAT-TTAGAAAA-AAATT
1 ATTATATT-AAATGTTA-AAAATAAATT
*
11992658 ATTACTATTAAATGTTAAAAATTAATT
1 ATTA-TATTAAATGTTAAAAATAAATT
11992685 ATT
1 ATT
11992688 TGTAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (26 bp):
ATTATATTAAATGTTAAAAATAAATT
Found at i:11993945 original size:86 final size:86
Alignment explanation
Indices: 11993834--11994003 Score: 277
Period size: 86 Copynumber: 2.0 Consensus size: 86
11993824 TTTCCTACTT
* *
11993834 AAGTCGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCGACTAGAATTATGAAAGTGTAA
1 AAGTCGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCAACTAGAATTATAAAAGTGTAA
*
11993899 TTATCGTTTTATACTTCTACA
66 TGATCGTTTTATACTTCTACA
* * *
11993920 AAGTTGAATTATAGTGTTTGTCCTTAAGGAAGTTGATTGAGTCAACTAGAATTATAAAAGTGTAA
1 AAGTCGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCAACTAGAATTATAAAAGTGTAA
*
11993985 TGATCGTTTTATATTTCTA
66 TGATCGTTTTATACTTCTA
11994004 TTATACCAGT
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (86 bp):
AAGTCGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCAACTAGAATTATAAAAGTGTAA
TGATCGTTTTATACTTCTACA
Found at i:11995527 original size:20 final size:20
Alignment explanation
Indices: 11995502--11995540 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
11995492 GTTATATTAT
11995502 TTTTAATGA-ATTTTTACTTA
1 TTTTAAT-ATATTTTTACTTA
11995522 TTTTAATATATTTTTACTT
1 TTTTAATATATTTTTACTT
11995541 TGTTAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTAATATATTTTTACTTA
Found at i:11996884 original size:86 final size:86
Alignment explanation
Indices: 11996773--11996942 Score: 268
Period size: 86 Copynumber: 2.0 Consensus size: 86
11996763 TTTCCTACTT
* *
11996773 AAGTGGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCGACTAGAATTATGAAAGTGTAA
1 AAGTGGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCAACTAGAATTATAAAAGTGTAA
* *
11996838 TTATCGTTTTATACTTCTACA
66 TGATCATTTTATACTTCTACA
* * *
11996859 AAGTTGAATTATAGTGTTTGTCCTTAAGGAAGTTGATTGAGTCAACTAGAATTATAAAAGTGTAA
1 AAGTGGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCAACTAGAATTATAAAAGTGTAA
*
11996924 TGATCATTTTATATTTCTA
66 TGATCATTTTATACTTCTA
11996943 TTATACCAGT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (86 bp):
AAGTGGAATTATAGTGTTTGTCCTTAAGAAAGTTGATTAAGTCAACTAGAATTATAAAAGTGTAA
TGATCATTTTATACTTCTACA
Found at i:12002565 original size:28 final size:30
Alignment explanation
Indices: 12002503--12002565 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
12002493 ATGACTTTTT
* *
12002503 AATTTTAATGAAATGTTTAATGTGATGTATG
1 AATTTTAA-GAAATGTTTAATGTGATATATA
*
12002534 AATTTTAA-AAAT-TTTAATGTGATATTTA
1 AATTTTAAGAAATGTTTAATGTGATATATA
12002562 AATT
1 AATT
12002566 ATGAATCTGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 4 0.14
31 8 0.28
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.48
Consensus pattern (30 bp):
AATTTTAAGAAATGTTTAATGTGATATATA
Found at i:12013376 original size:26 final size:26
Alignment explanation
Indices: 12013347--12013532 Score: 207
Period size: 26 Copynumber: 7.2 Consensus size: 26
12013337 GTTCAAACCC
*
12013347 AATTAGG-TCCATTGGTGTCCAAGCCT
1 AATTAGGCT-CATTGGTGTCCGAGCCT
*
12013373 AATTAGGCTCATTTGTGTCCGAGTCC-
1 AATTAGGCTCATTGGTGTCCGAG-CCT
* *
12013399 AACTAGGCCCATTGGTGTCCG-GCCT
1 AATTAGGCTCATTGGTGTCCGAGCCT
* ** * *
12013424 AATTAGGCTCATTTGCATCCGGGCCC
1 AATTAGGCTCATTGGTGTCCGAGCCT
*
12013450 AATTAGGCCCATTGGTGTCCGAGCCT
1 AATTAGGCTCATTGGTGTCCGAGCCT
*
12013476 AATTGGGCTCATTGGTGTCCGAGCCT
1 AATTAGGCTCATTGGTGTCCGAGCCT
* * *
12013502 AATTGGGCTCATTGGTGTTCGAGCCC
1 AATTAGGCTCATTGGTGTCCGAGCCT
12013528 AATTA
1 AATTA
12013533 AGTCCATTGA
Statistics
Matches: 134, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
24 2 0.01
25 17 0.13
26 112 0.84
27 3 0.02
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (26 bp):
AATTAGGCTCATTGGTGTCCGAGCCT
Found at i:12013515 original size:52 final size:51
Alignment explanation
Indices: 12013345--12013532 Score: 234
Period size: 52 Copynumber: 3.6 Consensus size: 51
12013335 GCGTTCAAAC
* *
12013345 CCAATTAGGTCCATTGGTGTCCAAGCCTAATTAGGCTCATTTGTGTCCGAG
1 CCAATTAGGCCCATTGGTGTCCGAGCCTAATTAGGCTCATTTGTGTCCGAG
* ** *
12013396 TCCAACTAGGCCCATTGGTGTCCG-GCCTAATTAGGCTCATTTGCATCCGGG
1 -CCAATTAGGCCCATTGGTGTCCGAGCCTAATTAGGCTCATTTGTGTCCGAG
* *
12013447 CCCAATTAGGCCCATTGGTGTCCGAGCCTAATTGGGCTCATTGGTGTCCGAG
1 -CCAATTAGGCCCATTGGTGTCCGAGCCTAATTAGGCTCATTTGTGTCCGAG
* * * *
12013499 CCTAATTGGGCTCATTGGTGTTCGAGCCCAATTA
1 CC-AATTAGGCCCATTGGTGTCCGAGCCTAATTA
12013533 AGTCCATTGA
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
51 48 0.41
52 68 0.59
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (51 bp):
CCAATTAGGCCCATTGGTGTCCGAGCCTAATTAGGCTCATTTGTGTCCGAG
Found at i:12013541 original size:52 final size:52
Alignment explanation
Indices: 12013344--12013571 Score: 205
Period size: 52 Copynumber: 4.4 Consensus size: 52
12013334 TGCGTTCAAA
* * *
12013344 CCCAATTAGGTCCATTGGTGTCCAAGCCTAATTAGGCTCATTTG-TGTCCGAG
1 CCCAATTAGGCCCATTGGTGTCCGAGCCCAATTAGGCTCA-TTGATGTCCGAG
* * * *
12013396 TCCAACTAGGCCCATTGGTGTCCG-GCCTAATTAGGCTCATT--TGCATCCGGG
1 CCCAATTAGGCCCATTGGTGTCCGAGCCCAATTAGGCTCATTGATG--TCCGAG
* * *
12013447 CCCAATTAGGCCCATTGGTGTCCGAGCCTAATTGGGCTCATTGGTGTCCGAG
1 CCCAATTAGGCCCATTGGTGTCCGAGCCCAATTAGGCTCATTGATGTCCGAG
* * * * * * *
12013499 CCTAATTGGGCTCATTGGTGTTCGAGCCCAATTAAG-TCCATTGATGTCTGGG
1 CCCAATTAGGCCCATTGGTGTCCGAGCCCAATTAGGCT-CATTGATGTCCGAG
* * *
12013551 CTCAACTAGGCCCATTTGTGT
1 CCCAATTAGGCCCATTGGTGT
12013572 TCGGGCCTAC
Statistics
Matches: 145, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
49 2 0.01
50 2 0.01
51 43 0.30
52 96 0.66
54 2 0.01
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (52 bp):
CCCAATTAGGCCCATTGGTGTCCGAGCCCAATTAGGCTCATTGATGTCCGAG
Found at i:12013580 original size:78 final size:77
Alignment explanation
Indices: 12013388--12013580 Score: 190
Period size: 78 Copynumber: 2.5 Consensus size: 77
12013378 GGCTCATTTG
* * *
12013388 TGTCCGAGTCCAACTAGGCCCATTGGTG-TCCGGCCTAATTAGGCTCATTTGCATCCGGGCCCAA
1 TGTCCGAG-CCAACTAGGCCCATTGGTGTTCGGGCCTAATTAGGCTCATTGGCATCCGAGCCCAA
* *
12013452 TTAGGCCCATTGG
65 TTAAGCCCATTGA
* * * * * * ** *
12013465 TGTCCGAGCCTAATTGGGCTCATTGGTGTCCGAGCCTAATTGGGCTCATTGGTGTTCGAGCCCAA
1 TGTCCGAGCC-AACTAGGCCCATTGGTGTTCGGGCCTAATTAGGCTCATTGGCATCCGAGCCCAA
*
12013530 TTAAGTCCATTGA
65 TTAAGCCCATTGA
* * *
12013543 TGTCTGGGCTCAACTAGGCCCATTTGTGTTCGGGCCTA
1 TGTCCGAGC-CAACTAGGCCCATTGGTGTTCGGGCCTA
12013581 CATAGGCCGA
Statistics
Matches: 90, Mismatches: 23, Indels: 5
0.76 0.19 0.04
Matches are distributed among these distances:
76 2 0.02
77 22 0.24
78 65 0.72
79 1 0.01
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.29
Consensus pattern (77 bp):
TGTCCGAGCCAACTAGGCCCATTGGTGTTCGGGCCTAATTAGGCTCATTGGCATCCGAGCCCAAT
TAAGCCCATTGA
Found at i:12013670 original size:3 final size:3
Alignment explanation
Indices: 12013662--12013697 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
12013652 TTTCTATGTA
12013662 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12013698 TTCATTTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:12020440 original size:5 final size:5
Alignment explanation
Indices: 12020432--12020471 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
12020422 TTATTTAAAG
12020432 AAAAT AAAAT AAAAT AAAAAT AAAGA- AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT -AAAAT AAA-AT AAAAT AAAAT AAAA
12020472 AGTATTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 1 0.03
5 25 0.78
6 6 0.19
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:12020453 original size:16 final size:14
Alignment explanation
Indices: 12020432--12020472 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 14
12020422 TTATTTAAAG
12020432 AAAATAAAATAAAAT
1 AAAATAAAA-AAAAT
12020447 AAAAATAAAGAAAAAT
1 -AAAATAAA-AAAAAT
12020463 AAAATAAAAA
1 AAAATAAAAA
12020473 GTATTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.08
15 8 0.33
16 13 0.54
17 1 0.04
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:12021096 original size:23 final size:25
Alignment explanation
Indices: 12021059--12021105 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
12021049 AAATTTTTCA
12021059 AAAATTTCTAGAAAAAATTTCACCT
1 AAAATTTCTAGAAAAAATTTCACCT
*
12021084 AAAA-TTCTA-AAAAATTTTCACC
1 AAAATTTCTAGAAAAAATTTCACC
12021106 GATTTCTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 5 0.24
25 4 0.19
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (25 bp):
AAAATTTCTAGAAAAAATTTCACCT
Found at i:12021377 original size:5 final size:5
Alignment explanation
Indices: 12021363--12021395 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
12021353 TTCAACCAAG
12021363 AAAA- AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12021396 ATATATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:12021413 original size:20 final size:20
Alignment explanation
Indices: 12021390--12021555 Score: 105
Period size: 20 Copynumber: 8.2 Consensus size: 20
12021380 ATAAAATAAA
12021390 ATAAA-AATATATATTAATAG
1 ATAAATAATA-ATATTAATAG
*
12021410 ATAAATGATAATATGTAAATAG
1 ATAAATAATAATAT-T-AATAG
*
12021432 ATAAATAATAATAATAATAG
1 ATAAATAATAATATTAATAG
*
12021452 ATAAATAATAATGTATAATAG
1 ATAAATAATAATAT-TAATAG
* *
12021473 ATATATAA-ACAGA-TAAGTA-
1 ATAAATAATA-ATATTAA-TAG
*
12021492 ATAATATAA-AATATATATTA-
1 ATAA-ATAATAATAT-TAATAG
* * *
12021512 ATAAATAGTAATAATAGATAA
1 ATAAATAATAATATTA-ATAG
*
12021533 ATAAATAATAA-A-TAATAA
1 ATAAATAATAATATTAATAG
12021551 ATAAA
1 ATAAA
12021556 ATACAAAAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
18 9 0.08
19 15 0.13
20 47 0.39
21 31 0.26
22 17 0.14
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (20 bp):
ATAAATAATAATATTAATAG
Found at i:12021436 original size:42 final size:41
Alignment explanation
Indices: 12021390--12021543 Score: 124
Period size: 40 Copynumber: 3.8 Consensus size: 41
12021380 ATAAAATAAA
* *
12021390 ATAAA-AATATATATTAATAGATAAATGATAATATGTA-AATAG
1 ATAAATAATA-ATAATAATAGATAAATAAT-A-ATGTATAATAG
12021432 ATAAATAATAATAATAATAGATAAATAATAATGTATAATAG
1 ATAAATAATAATAATAATAGATAAATAATAATGTATAATAG
* * * *
12021473 ATATATAA-ACA-GATAAGTA-ATAATATAA-AATATATATTA-
1 ATAAATAATA-ATAATAA-TAGATAA-ATAATAATGTATAATAG
* *
12021512 ATAAATAGTAATAATAGATAAATAAATAATAA
1 ATAAATAATAATAATA-ATAGATAAATAATAA
12021544 ATAATAAATA
Statistics
Matches: 93, Mismatches: 9, Indels: 21
0.76 0.07 0.17
Matches are distributed among these distances:
39 7 0.08
40 33 0.35
41 27 0.29
42 22 0.24
43 4 0.04
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (41 bp):
ATAAATAATAATAATAATAGATAAATAATAATGTATAATAG
Found at i:12021443 original size:3 final size:3
Alignment explanation
Indices: 12021435--12021550 Score: 56
Period size: 3 Copynumber: 34.7 Consensus size: 3
12021425 TAAATAGATA
* *
12021435 AAT AAT AAT AAT AAT AGAT AAAT AAT AAT GTAT AAT AGAT ATAT AAAC
1 AAT AAT AAT AAT AAT A-AT -AAT AAT AAT -AAT AAT A-AT A-AT -AAT
* *
12021483 AGAT AAGT AAT AAT -AT AA- AAT ATAT ATT AAT AAAT AGT AAT AAT AGAT
1 A-AT AA-T AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT AAT A-AT
12021531 AAAT AAAT AAT AAAT AAT AA
1 -AAT -AAT AAT -AAT AAT AA
12021551 ATAAAATACA
Statistics
Matches: 90, Mismatches: 9, Indels: 28
0.71 0.07 0.22
Matches are distributed among these distances:
2 4 0.04
3 49 0.54
4 34 0.38
5 3 0.03
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12021455 original size:7 final size:7
Alignment explanation
Indices: 12021404--12021554 Score: 52
Period size: 7 Copynumber: 21.4 Consensus size: 7
12021394 AAATATATAT
12021404 TAATAGA
1 TAATAGA
12021411 TAA-ATGA
1 TAATA-GA
12021418 TAATATG-
1 TAATA-GA
12021425 TAAATAGA
1 T-AATAGA
12021433 TAAATA-A
1 T-AATAGA
12021440 TAATA-A
1 TAATAGA
12021446 TAATAGA
1 TAATAGA
12021453 TAAATA-A
1 T-AATAGA
12021460 TAAT-GTA
1 TAATAG-A
12021467 TAATAGA
1 TAATAGA
*
12021474 T-ATATA
1 TAATAGA
*
12021480 -AACAGA
1 TAATAGA
12021486 TAAGTA-A
1 TAA-TAGA
*
12021493 TAATATA
1 TAATAGA
* *
12021500 AAATATA
1 TAATAGA
*
12021507 TATTA-A
1 TAATAGA
12021513 TAAATAGTAA
1 T-AATAG--A
12021523 TAATAGA
1 TAATAGA
*
12021530 TAAATAAA
1 T-AATAGA
*
12021538 TAATAAA
1 TAATAGA
*
12021545 TAATAAA
1 TAATAGA
12021552 TAA
1 TAA
12021555 AATACAAAAA
Statistics
Matches: 117, Mismatches: 9, Indels: 36
0.72 0.06 0.22
Matches are distributed among these distances:
6 25 0.21
7 60 0.51
8 25 0.21
9 5 0.04
10 2 0.02
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (7 bp):
TAATAGA
Found at i:12021526 original size:56 final size:55
Alignment explanation
Indices: 12021383--12021556 Score: 184
Period size: 53 Copynumber: 3.3 Consensus size: 55
12021373 AAATAAAATA
* * *
12021383 AAATAA-AATAAAAATATATATTAATAGATA--AATGATA-ATATGTAAATAGAT
1 AAATAATAATAAAAATATATATTAATAAATAGTAATAATAGATATATAAATAGAT
* * * *
12021434 AAATAATAATAATAATAGATAAATAAT-AAT-GT-ATAATAGATATATAAACAGAT
1 AAATAATAATAAAAATATAT-ATTAATAAATAGTAATAATAGATATATAAATAGAT
* *
12021487 AAGTAATAATATAAAATATATATTAATAAATAGTAATAATAGATAAATAAATA-AT
1 AAATAATAATA-AAAATATATATTAATAAATAGTAATAATAGATATATAAATAGAT
12021542 AAATAATAAATAAAA
1 AAATAAT-AATAAAA
12021557 TACAAAAATA
Statistics
Matches: 99, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
51 6 0.06
52 18 0.18
53 32 0.32
54 10 0.10
55 13 0.13
56 20 0.20
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (55 bp):
AAATAATAATAAAAATATATATTAATAAATAGTAATAATAGATATATAAATAGAT
Found at i:12021860 original size:46 final size:46
Alignment explanation
Indices: 12021794--12022048 Score: 244
Period size: 46 Copynumber: 5.7 Consensus size: 46
12021784 TCAAAGCTTT
*
12021794 TCTAAGCAGAGGCTCAACGAC-TTTGAAAAACATAAACAAAAGCTCC
1 TCTAATCAGAGGCTCAACGACTTTTGAAAAA-ATAAACAAAAGCTCC
* * *
12021840 TCTAATCAGAAGCTCTACGAC-TTTG-AAAGATAAAC-AAAGCTCC
1 TCTAATCAGAGGCTCAACGACTTTTGAAAAAATAAACAAAAGCTCC
* * *
12021883 TCTAATCAGAGGCTTTAACGACTTTTTAAAAAA-AAATAAAAGGCTCC
1 TCTAATCAGAGGC-TCAACGACTTTTGAAAAAATAAACAAAA-GCTCC
* **
12021930 TCTAATCAGAGGCTCAACGGCTTTTG-AAAAAT--A-AATTGCCTCC
1 TCTAATCAGAGGCTCAACGACTTTTGAAAAAATAAACAAAAG-CTCC
* * *
12021973 TCTAAACAGAGGCTCAACGACTGTTTGAAAACAT-AAC-AAGGCTCC
1 TCTAATCAGAGGCTCAACGACT-TTTGAAAAAATAAACAAAAGCTCC
* *
12022018 TTCTAATCAGAGGCTTAACAACTTTTGAAAA
1 -TCTAATCAGAGGCTCAACGACTTTTGAAAA
12022049 TAAATGCTCC
Statistics
Matches: 174, Mismatches: 23, Indels: 25
0.78 0.10 0.11
Matches are distributed among these distances:
42 1 0.01
43 46 0.26
44 17 0.10
45 31 0.18
46 61 0.35
47 18 0.10
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (46 bp):
TCTAATCAGAGGCTCAACGACTTTTGAAAAAATAAACAAAAGCTCC
Found at i:12021973 original size:90 final size:88
Alignment explanation
Indices: 12021794--12022059 Score: 267
Period size: 89 Copynumber: 3.0 Consensus size: 88
12021784 TCAAAGCTTT
* * * * *
12021794 TCTAAGCAGAGGCTCAACGAC-TTTGAAAAACATAAACAAAA-GCTCCTCTAATCAGAAGCTCTA
1 TCTAAACAGAGGCTCAACGACTTTTTAAAAA-A-AAATAAAAGGCTCCTCTAATCAGAGGCTCAA
* *
12021857 CGAC-TTTGAAAGATAAACAAAGCTCC
64 CGACTTTTGAAAAAT-AA-ATAGCTCC
* *
12021883 TCTAATCAGAGGCTTTAACGACTTTTTAAAAAAAAATAAAAGGCTCCTCTAATCAGAGGCTCAAC
1 TCTAAACAGAGGC-TCAACGACTTTTTAAAAAAAAATAAAAGGCTCCTCTAATCAGAGGCTCAAC
* *
12021948 GGCTTTTGAAAAATAAATTGCCTCC
65 GACTTTTGAAAAATAAATAG-CTCC
* * * *
12021973 TCTAAACAGAGGCTCAACGACTGTTT--GAAAACATAACAAGGCTCCTTCTAATCAGAGGCTTAA
1 TCTAAACAGAGGCTCAACGACTTTTTAAAAAAAAATAA-AAGGCTCC-TCTAATCAGAGGCTCAA
*
12022036 CAACTTTTG-AAAATAAAT-GCTCC
64 CGACTTTTGAAAAATAAATAGCTCC
12022059 T
1 T
12022060 TGACGACTGT
Statistics
Matches: 152, Mismatches: 18, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
86 5 0.03
87 9 0.06
88 17 0.11
89 55 0.36
90 49 0.32
91 17 0.11
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.25
Consensus pattern (88 bp):
TCTAAACAGAGGCTCAACGACTTTTTAAAAAAAAATAAAAGGCTCCTCTAATCAGAGGCTCAACG
ACTTTTGAAAAATAAATAGCTCC
Found at i:12023074 original size:16 final size:15
Alignment explanation
Indices: 12023055--12023115 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
12023045 TTCACTCTTT
12023055 TTTTTCTTTCTTTTCA
1 TTTTT-TTTCTTTTCA
12023071 TTTTTTTTTCTTTTTCA
1 -TTTTTTTTC-TTTTCA
* * *
12023088 TGTTTTTTCATTGCA
1 TTTTTTTTCTTTTCA
*
12023103 TTTTTTCTCTTTT
1 TTTTTTTTCTTTT
12023116 TTCTTTTCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
15 13 0.36
16 12 0.33
17 11 0.31
ACGTcount: A:0.07, C:0.15, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTTTTTCTTTTCA
Found at i:12032623 original size:197 final size:197
Alignment explanation
Indices: 12032288--12032684 Score: 794
Period size: 197 Copynumber: 2.0 Consensus size: 197
12032278 AGACAAGGTA
12032288 GAATCATATCCAATTGGTAAACAATCCCTCATTTTCAGTTGAATCTTTTCTGACTGGATCCTTAC
1 GAATCATATCCAATTGGTAAACAATCCCTCATTTTCAGTTGAATCTTTTCTGACTGGATCCTTAC
12032353 TTCATTGGGTGACTCACAAGGTGCTAATACAGACGAAGAACAAACTAGTCGTTCTGTGGAGTCCA
66 TTCATTGGGTGACTCACAAGGTGCTAATACAGACGAAGAACAAACTAGTCGTTCTGTGGAGTCCA
12032418 TGAAAAATTTTTGTTGAAGATCGTCTTTCAAGCAAATGTTCTTTATGCAACTTTATGATATGAGC
131 TGAAAAATTTTTGTTGAAGATCGTCTTTCAAGCAAATGTTCTTTATGCAACTTTATGATATGAGC
12032483 AT
196 AT
12032485 GAATCATATCCAATTGGTAAACAATCCCTCATTTTCAGTTGAATCTTTTCTGACTGGATCCTTAC
1 GAATCATATCCAATTGGTAAACAATCCCTCATTTTCAGTTGAATCTTTTCTGACTGGATCCTTAC
12032550 TTCATTGGGTGACTCACAAGGTGCTAATACAGACGAAGAACAAACTAGTCGTTCTGTGGAGTCCA
66 TTCATTGGGTGACTCACAAGGTGCTAATACAGACGAAGAACAAACTAGTCGTTCTGTGGAGTCCA
12032615 TGAAAAATTTTTGTTGAAGATCGTCTTTCAAGCAAATGTTCTTTATGCAACTTTATGATATGAGC
131 TGAAAAATTTTTGTTGAAGATCGTCTTTCAAGCAAATGTTCTTTATGCAACTTTATGATATGAGC
12032680 AT
196 AT
12032682 GAA
1 GAA
12032685 CCAATGCAAA
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 200 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (197 bp):
GAATCATATCCAATTGGTAAACAATCCCTCATTTTCAGTTGAATCTTTTCTGACTGGATCCTTAC
TTCATTGGGTGACTCACAAGGTGCTAATACAGACGAAGAACAAACTAGTCGTTCTGTGGAGTCCA
TGAAAAATTTTTGTTGAAGATCGTCTTTCAAGCAAATGTTCTTTATGCAACTTTATGATATGAGC
AT
Found at i:12033932 original size:59 final size:59
Alignment explanation
Indices: 12033718--12033932 Score: 276
Period size: 59 Copynumber: 3.7 Consensus size: 59
12033708 TTGTACAGGA
* *
12033718 AAAATTAATACTTTCAACTTTTCCTCAAAAAT-TCATTTTT-GAAAACTTACTTTT-AAGG
1 AAAATTAATACTTTCAACTTTTCCTCAAAAATAT-TTTTTTAGAAAGCTTA-TTTTCAAGG
* * *
12033776 AAAATTAATACTTTCAAC-TTTCCTCAAAAATATTTTGTTAGAAAGCTTATTGTCAAGA
1 AAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAGCTTATTTTCAAGG
* * * *
12033834 AAAAATGATACTTTCAACTTTTCCTTAAAAATAATTTTTTAGAAAGCTTATTTTCAAGG
1 AAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAGCTTATTTTCAAGG
* * *
12033893 AAAATTGATACTTTCTACTTTTCCTCAAAAATTTTTTTTT
1 AAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTT
12033933 TGAATTTTAT
Statistics
Matches: 136, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
57 20 0.15
58 46 0.34
59 70 0.51
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (59 bp):
AAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAGCTTATTTTCAAGG
Found at i:12033957 original size:5 final size:5
Alignment explanation
Indices: 12033949--12034020 Score: 74
Period size: 6 Copynumber: 13.2 Consensus size: 5
12033939 TTATTTAAAG
12033949 AAAAT AAAAT AAAAAT AAAAT AAAAT AAAAAT GAAAAT AAAAAT GAAAAT
1 AAAAT AAAAT -AAAAT AAAAT AAAAT -AAAAT -AAAAT -AAAAT -AAAAT
12033999 AAAAAT AAAGA- AAAAT AAAAT A
1 -AAAAT AAA-AT AAAAT AAAAT A
12034021 CAAAGTATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
4 1 0.02
5 27 0.46
6 31 0.53
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:12033987 original size:12 final size:11
Alignment explanation
Indices: 12033949--12034020 Score: 87
Period size: 12 Copynumber: 6.5 Consensus size: 11
12033939 TTATTTAAAG
12033949 AAAAT-AAAAT
1 AAAATAAAAAT
12033959 AAAA-ATAAAAT
1 AAAATA-AAAAT
12033970 AAAATAAAAAT
1 AAAATAAAAAT
12033981 GAAAATAAAAAT
1 -AAAATAAAAAT
12033993 GAAAATAAAAAT
1 -AAAATAAAAAT
*
12034005 -AAAGAAAAAT
1 AAAATAAAAAT
12034015 AAAATA
1 AAAATA
12034021 CAAAGTATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
10 13 0.24
11 18 0.33
12 24 0.44
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:12034018 original size:6 final size:6
Alignment explanation
Indices: 12033949--12034007 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
12033939 TTATTTAAAG
* *
12033949 AAAAT- AAAATA AAAAT- AAAAT- AAAATA AAAATG AAAATA AAAATG
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
12033994 AAAATA AAAATA AA
1 AAAATA AAAATA AA
12034008 GAAAAATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
5 15 0.31
6 33 0.69
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:12034588 original size:30 final size:31
Alignment explanation
Indices: 12034547--12034610 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
12034537 AGCTGGCCGA
* * *
12034547 AAAATTCAAACTTGGCCGAAAAAGTC-ACCG
1 AAAACTCAAACTTCGCCAAAAAAGTCAACCG
*
12034577 AAAACTCAAACTTCGCCAAAAAATTCAACCG
1 AAAACTCAAACTTCGCCAAAAAAGTCAACCG
12034608 AAA
1 AAA
12034611 TCTGATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.48, C:0.25, G:0.11, T:0.16
Consensus pattern (31 bp):
AAAACTCAAACTTCGCCAAAAAAGTCAACCG
Found at i:12034916 original size:5 final size:5
Alignment explanation
Indices: 12034906--12034934 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12034896 TCAACCAAGA
12034906 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
12034935 ATATATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:12034962 original size:14 final size:14
Alignment explanation
Indices: 12034921--12035153 Score: 64
Period size: 16 Copynumber: 15.2 Consensus size: 14
12034911 AAAATAAAAT
12034921 AAAATAA-AATA-A
1 AAAATAATAATATA
12034933 AAATATATATTAATATA
1 AAA-ATA-A-TAATATA
* *
12034950 AAAATGATAATATG
1 AAAATAATAATATA
*
12034964 TAAATAGATAA-ATA
1 AAAATA-ATAATATA
*
12034978 ATAATAATAATAATA
1 AAAATAATAAT-ATA
12034993 GATAAATAATAATAT-
1 -A-AAATAATAATATA
*
12035008 ATAATAGAT-ATATA
1 AAAATA-ATAATATA
12035022 AACAGATAAGTAATAATA
1 AA-A-ATAA-TAAT-ATA
*
12035040 TAAAATATATATTAATA
1 -AAAATA-ATAAT-ATA
*
12035057 AATAGTAATAATAGATAA
1 AA-AATAATAAT--AT-A
*
12035075 ATAAATAATAAATACA
1 A-AAATAAT-AATATA
* *
12035091 AAAATAAAAAAATA
1 AAAATAATAATATA
* *
12035105 CAAAATACAAAATACA
1 -AAAATA-ATAATATA
12035121 AAATATAA-AATAAATA
1 AAA-ATAATAAT--ATA
* *
12035137 AAAAAAATAAAATA
1 AAAATAATAATATA
12035151 AAA
1 AAA
12035154 TAAAACAAAT
Statistics
Matches: 167, Mismatches: 24, Indels: 58
0.67 0.10 0.23
Matches are distributed among these distances:
12 3 0.02
13 15 0.09
14 34 0.20
15 29 0.17
16 37 0.22
17 31 0.19
18 12 0.07
19 6 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (14 bp):
AAAATAATAATATA
Found at i:12034969 original size:22 final size:20
Alignment explanation
Indices: 12034925--12034983 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 20
12034915 TAAAATAAAA
12034925 TAAA-ATAAAAATAT-ATAT
1 TAAATATAAAAATATAATAT
12034943 T-AATATAAAAATGATAATAT
1 TAAATATAAAAAT-ATAATAT
* *
12034963 GTAAATAGATAAATAATAATA
1 -TAAATATAAAAAT-ATAATA
12034984 ATAATAATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 9 0.27
19 2 0.06
20 4 0.12
21 1 0.03
22 15 0.45
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAATATAAAAATATAATAT
Found at i:12034982 original size:3 final size:3
Alignment explanation
Indices: 12034974--12035085 Score: 66
Period size: 3 Copynumber: 33.7 Consensus size: 3
12034964 TAAATAGATA
12034974 AAT AAT AAT AAT AAT AAT AGAT AAAT AAT AAT ATAT AAT AGAT ATAT
1 AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT A-AT AAT A-AT A-AT
* * *
12035021 AAAC AGAT AAGT AAT AAT -AT AA- AAT ATAT ATT AAT AAAT AGT AAT
1 -AAT A-AT AA-T AAT AAT AAT AAT AAT A-AT AAT AAT -AAT AAT AAT
12035066 AAT AGAT AAAT AAAT AAT AA
1 AAT A-AT -AAT -AAT AAT AA
12035086 ATACAAAAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
2 4 0.04
3 50 0.56
4 32 0.36
5 3 0.03
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12034999 original size:31 final size:29
Alignment explanation
Indices: 12034974--12035084 Score: 93
Period size: 31 Copynumber: 3.7 Consensus size: 29
12034964 TAAATAGATA
12034974 AATAATAATAATAATAATAGATAAATAAT
1 AATAATAATAATAATAATAGATAAATAAT
* *
12035003 AATATATAATAGATATATAAACAGATAAGTAAT
1 AATA-ATAATA-ATA-AT-AATAGATAAATAAT
* *
12035036 AAT-ATAA-AATATATATTA-ATAAATAGT
1 AATAATAATAATA-ATAATAGATAAATAAT
12035063 AATAATAGATAAATAAATAATA
1 AATAATA-AT-AAT-AATAATA
12035085 AATACAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
27 10 0.15
28 5 0.08
29 11 0.17
30 7 0.11
31 15 0.23
32 3 0.05
33 15 0.23
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (29 bp):
AATAATAATAATAATAATAGATAAATAAT
Found at i:12035003 original size:56 final size:54
Alignment explanation
Indices: 12034922--12035088 Score: 130
Period size: 56 Copynumber: 3.1 Consensus size: 54
12034912 AAATAAAATA
* * * * *
12034922 AAATAA-AATA-AAAATATAT-ATTAATATAAAAATGATA-ATATGTAAATAGAT
1 AAATAATAATATAAAATAGATAAATAATA-AAAAATAATAGATATATAAACAGAT
* *
12034973 AAATAATAATAATAATAATAGATAAATAATAATATATAATAGATATATAAACAGAT
1 AAATAATAAT-ATAA-AATAGATAAATAATAAAAAATAATAGATATATAAACAGAT
* * * * *
12035029 AAGTAATAATATAAAATATAT-ATTAATAAATAGTAATAATAGATAAATAAATA-AT
1 AAATAATAATATAAAATAGATAAATAATAAA-A--AATAATAGATATATAAACAGAT
12035084 AAATA
1 AAATA
12035089 CAAAAATAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
51 6 0.07
52 3 0.03
53 8 0.09
54 9 0.10
55 23 0.25
56 43 0.47
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (54 bp):
AAATAATAATATAAAATAGATAAATAATAAAAAATAATAGATATATAAACAGAT
Found at i:12035012 original size:33 final size:34
Alignment explanation
Indices: 12034927--12035085 Score: 109
Period size: 33 Copynumber: 4.6 Consensus size: 34
12034917 AAATAAAATA
* *
12034927 AAATAAAAATATATATTAAT-ATAA-AAAT-GAT
1 AAATAATAATATATAATAATAATAATAAATAGAT
*
12034958 AATATGTAAATAGATAAATAATAATAATAAT-AATAGAT
1 AA-A--T-AATA-ATATATAATAATAATAATAAATAGAT
*
12034996 AAATAATAATATATAATAGAT-AT-ATAAACAGAT
1 AAATAATAATATATAATA-ATAATAATAAATAGAT
* * *
12035029 AAGTAATAATATAAAATATATATTAATAAATAG-T
1 AAATAATAATATATAATA-ATAATAATAAATAGAT
*
12035063 -AATAATAGATAAATAAATAATAA
1 AAATAATA-ATATAT-AATAATAA
12035086 ATACAAAAAT
Statistics
Matches: 100, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
31 2 0.02
32 3 0.03
33 41 0.41
34 16 0.16
35 15 0.15
36 10 0.10
37 8 0.08
38 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (34 bp):
AAATAATAATATATAATAATAATAATAAATAGAT
Found at i:12035084 original size:7 final size:7
Alignment explanation
Indices: 12034964--12035147 Score: 72
Period size: 7 Copynumber: 26.6 Consensus size: 7
12034954 TGATAATATG
12034964 TAAATAGA
1 TAAATA-A
12034972 TAAATAA
1 TAAATAA
12034979 T-AATAA
1 TAAATAA
12034985 T-AATAA
1 TAAATAA
*
12034991 TAGATAA
1 TAAATAA
12034998 -ATAATAA
1 TA-AATAA
*
12035005 TATATAA
1 TAAATAA
*
12035012 TAGATATA
1 TAAATA-A
*
12035020 TAAACAGA
1 TAAATA-A
*
12035028 TAAGTAA
1 TAAATAA
12035035 T-AAT-A
1 TAAATAA
12035040 TAAA-ATA
1 TAAATA-A
*
12035047 TATATTAA
1 TA-AATAA
*
12035055 TAAATAG
1 TAAATAA
12035062 T-AATAA
1 TAAATAA
*
12035068 TAGATAAA
1 TAAAT-AA
12035076 TAAATAA
1 TAAATAA
12035083 TAAATACA
1 TAAATA-A
*
12035091 AAAATAA
1 TAAATAA
12035098 -AAA-AA
1 TAAATAA
12035103 TACAA-AA
1 TA-AATAA
12035110 TACAA-AA
1 TA-AATAA
12035117 TACAA-AA
1 TA-AATAA
12035124 TATAA-AA
1 TA-AATAA
12035131 TAAATAA
1 TAAATAA
*
12035138 -AAAAAA
1 TAAATAA
12035144 TAAA
1 TAAA
12035148 ATAAAATAAA
Statistics
Matches: 141, Mismatches: 19, Indels: 33
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.03
6 33 0.23
7 70 0.50
8 33 0.23
9 1 0.01
ACGTcount: A:0.67, C:0.03, G:0.04, T:0.26
Consensus pattern (7 bp):
TAAATAA
Found at i:12035095 original size:15 final size:15
Alignment explanation
Indices: 12035063--12035147 Score: 63
Period size: 15 Copynumber: 5.6 Consensus size: 15
12035053 AATAAATAGT
*
12035063 AATAATAGATA-AATA
1 AATAATAAATACAA-A
12035078 AATAATAAATACAAA
1 AATAATAAATACAAA
*
12035093 AATAAAAAAATAC-AA
1 AAT-AATAAATACAAA
12035108 AATACA-AAATACAAA
1 AATA-ATAAATACAAA
12035123 ATATAAAATAAATA-AAA
1 A-AT--AATAAATACAAA
12035140 AA-AATAAA
1 AATAATAAA
12035148 ATAAAATAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 18
0.75 0.03 0.22
Matches are distributed among these distances:
13 6 0.10
14 7 0.12
15 23 0.38
16 13 0.22
17 5 0.08
18 6 0.10
ACGTcount: A:0.75, C:0.05, G:0.01, T:0.19
Consensus pattern (15 bp):
AATAATAAATACAAA
Found at i:12035103 original size:23 final size:23
Alignment explanation
Indices: 12035071--12035162 Score: 75
Period size: 23 Copynumber: 4.0 Consensus size: 23
12035061 GTAATAATAG
*
12035071 ATAAATAAATAATAAATACAAAA
1 ATAAAAAAATAATAAATACAAAA
12035094 ATAAAAAAATACA-AAATAC-AAA
1 ATAAAAAAATA-ATAAATACAAAA
* *
12035116 ATACAAAATATAAAATAAATAAAAAAA
1 ATA-AAAA-A-ATAATAAAT-ACAAAA
*
12035143 ATAAAATAA-AATAAA-ACAAA
1 ATAAAAAAATAATAAATACAAA
12035163 TTGAAATGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
21 4 0.07
22 6 0.11
23 26 0.46
24 4 0.07
25 7 0.12
26 4 0.07
27 6 0.11
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.17
Consensus pattern (23 bp):
ATAAAAAAATAATAAATACAAAA
Found at i:12035148 original size:5 final size:5
Alignment explanation
Indices: 12035125--12035158 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
12035115 AATACAAAAT
12035125 ATAAA AT-AA ATAAA A-AAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
12035159 CAAATTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
ATAAA
Found at i:12035163 original size:9 final size:9
Alignment explanation
Indices: 12035090--12035163 Score: 58
Period size: 9 Copynumber: 7.7 Consensus size: 9
12035080 TAATAAATAC
12035090 AAAAATAAA
1 AAAAATAAA
*
12035099 AAAATACAAAA
1 AAAA-A-TAAA
*
12035110 TACAAAATACA
1 -A-AAAATAAA
*
12035121 AAATATAAA
1 AAAAATAAA
*
12035130 ATAAATAAA
1 AAAAATAAA
12035139 AAAAATAAA
1 AAAAATAAA
12035148 ATAAAATAAA
1 A-AAAATAAA
*
12035158 ACAAAT
1 AAAAAT
12035164 TGAAATGGGC
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
9 30 0.59
10 11 0.22
11 5 0.10
12 2 0.04
13 3 0.06
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.16
Consensus pattern (9 bp):
AAAAATAAA
Found at i:12040534 original size:237 final size:236
Alignment explanation
Indices: 12040114--12040786 Score: 699
Period size: 238 Copynumber: 2.8 Consensus size: 236
12040104 CATTATCCAC
*
12040114 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCCCGATCATTTATT
1 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCTCGATCATTTATT
* * * * * *
12040179 TTCTACCTTGACTCGATCCTGATCACTTGTTTTTGACCTGTGGTTTCA-TCTCGGACATTTGATC
66 TT-TACCTCGACTCGATCCTGGTCACTTATTTTTGACCTGTGGTTTTATTC-CAGTCA-TTGATC
* * * * * ** * * *
12040243 TTGGTTCAATCTAGATCATTTCTTATAATTTATGGTTTCATTTTGATAATTTATTTTTAACCTCG
128 TTGGCTCAGTCTAAATCATTTCTTATGATTCATGGTTTCATCCTGATCATTTATTTTCAACCTTG
*** * *
12040308 ACTTGGTCATGGTCACTT-GTTTTGGCCCTTGATTTCGTCTCAG
193 ACTCAATCATGGTCACTTAGTTTTGACCCGTGATTTCGTCTCAG
* * * * *
12040351 TTATCTGATCTTGGCTGAGTTCAGATCATTTCTTATAATTCATGGTTTTATCTCGATTATTTATT
1 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCTCGATCATTTATT
* * * *
12040416 TTTGACCTCGACTCGATCTTGGT-AGCTTATTTTTTACCCGTGGTTTTGTTCCAGTCATATGATC
66 TTT-ACCTCGACTCGATCCTGGTCA-CTTATTTTTGACCTGTGGTTTTATTCCAGTCAT-TGATC
* * *
12040480 TTGGCTCAGTCTATATCATTTCTTATGATTCATGGTTTCATCCCGATCATTTATTTTCGACCTTG
128 TTGGCTCAGTCTAAATCATTTCTTATGATTCATGGTTTCATCCTGATCATTTATTTTCAACCTTG
* ** * * * *
12040545 ACTCAATCTTGGTGTCTTATTTTTGACTCGTGGTTTTGTCTCAG
193 ACTCAATCATGGTCACTTAGTTTTGACCCGTGATTTCGTCTCAG
* * * * *
12040589 TCATCTGATCTTAGCTCAGTCCAAATCACTTCTTATGATTCGTGGTTTCATCAT-GATCATTTAT
1 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATC-TCGATCATTTA-
* * * * * * * *
12040653 TTTTTACCTCGATTCAATCCTAGTCA-TTTTATTTTGACTTGTGGTTTCATCCCAATCACTTGAT
64 TTTTTACCTCGACTCGATCCTGGTCACTTAT-TTTTGACCTGTGGTTTTATTCCAGTCA-TTGAT
* * * *
12040717 ATTGGCTCAGTCCAAATCATTTCTTATGATTCATGGTTTTATCCTAATCATTTATTTTCAACCTT
127 CTTGGCTCAGTCTAAATCATTTCTTATGATTCATGGTTTCATCCTGATCATTTATTTTCAACCTT
12040782 GACTC
192 GACTC
12040787 GATCCTAGTC
Statistics
Matches: 357, Mismatches: 69, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
236 3 0.01
237 172 0.48
238 174 0.49
239 8 0.02
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (236 bp):
TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCTCGATCATTTATT
TTTACCTCGACTCGATCCTGGTCACTTATTTTTGACCTGTGGTTTTATTCCAGTCATTGATCTTG
GCTCAGTCTAAATCATTTCTTATGATTCATGGTTTCATCCTGATCATTTATTTTCAACCTTGACT
CAATCATGGTCACTTAGTTTTGACCCGTGATTTCGTCTCAG
Found at i:12040809 original size:119 final size:118
Alignment explanation
Indices: 12040114--12040818 Score: 615
Period size: 119 Copynumber: 5.9 Consensus size: 118
12040104 CATTATCCAC
*
12040114 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCCCGATCATTTATT
1 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCCTGATCATTTATT
* * * * * * * *
12040179 TTCTACCTTGACTCGATCCTGATCACTTGTTTTTGACCTGTGGTTTCATCTCGG
66 TTCAACCTCGACTCGATCCTGGTCACTT-ATTTTGACCCGTGGTTTCGTCCCAG
* * * * * * ** *
12040233 ACATTTGATCTTGGTTCAATCTAGATCATTTCTTATAATTTATGGTTTCATTTTGATAATTTATT
1 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCCTGATCATTTATT
* * * * * * * * *
12040298 TTTAACCTCGACTTGGTCATGGTCACTTGTTTTGGCCCTTGATTTCGTCTCAG
66 TTCAACCTCGACTCGATCCTGGTCACTTATTTTGACCCGTGGTTTCGTCCCAG
* * * * *
12040351 TTATCTGATCTTGGCTGAGTTCAGATCATTTCTTATAATTCATGGTTTTAT-CTCGATTATTTAT
1 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCCT-GATCATTTAT
** * * * *
12040415 TTTTGACCTCGACTCGATCTTGGT-AGCTTATTTTTTACCCGTGGTTTTGTTCCAG
65 TTTCAACCTCGACTCGATCCTGGTCA-CTTA-TTTTGACCCGTGGTTTCGTCCCAG
* * * * *
12040470 TCATATGATCTTGGCTCAGTCTATATCATTTCTTATGATTCATGGTTTCATCCCGATCATTTATT
1 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCCTGATCATTTATT
* * * * ** * * *
12040535 TTCGACCTTGACTCAATCTTGGTGTCTTATTTTTGACTCGTGGTTTTGTCTCAG
66 TTCAACCTCGACTCGATCCTGGTCACTTA-TTTTGACCCGTGGTTTCGTCCCAG
* * * * * *
12040589 TCATCTGATCTTAGCTCAGTCCAAATCACTTCTTATGATTCGTGGTTTCATCATGATCATTTATT
1 TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCCTGATCATTTATT
** * * * * ** * *
12040654 TTTTACCTCGATTCAATCCTAGTCATTTTATTTTGACTTGTGGTTTCATCCCAA
66 TTCAACCTCGACTCGATCCTGGTCA-CTTATTTTGACCCGTGGTTTCGTCCCAG
* * * * *
12040708 TCA-CTTGATATTGGCTCAGTCCAAATCATTTCTTATGATTCATGGTTTTATCCTAATCATTTAT
1 TCATC-TGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCCTGATCATTTAT
* * * * *
12040772 TTTCAACCTTGACTCGATCCTAGTCGCTTCATCTTGACTCGTGGTTT
65 TTTCAACCTCGACTCGATCCTGGTCACTT-ATTTTGACCCGTGGTTT
12040819 AGTCTCGGTC
Statistics
Matches: 474, Mismatches: 104, Indels: 16
0.80 0.18 0.03
Matches are distributed among these distances:
117 2 0.00
118 94 0.20
119 374 0.79
120 4 0.01
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.45
Consensus pattern (118 bp):
TCATCTGATCTTGGCTCAGTCCAGATCATTTCTTATAATTCATGGTTTCATCCTGATCATTTATT
TTCAACCTCGACTCGATCCTGGTCACTTATTTTGACCCGTGGTTTCGTCCCAG
Found at i:12041012 original size:26 final size:26
Alignment explanation
Indices: 12040983--12041033 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
12040973 GTCTGGGCCC
*
12040983 AATTAAGCCCATTGGTGTTCGAGCCT
1 AATTAAGCCCATTGGTGTCCGAGCCT
* *
12041009 AATTAGGCTCATTGGTGTCCGAGCC
1 AATTAAGCCCATTGGTGTCCGAGCC
12041034 CATTGATGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (26 bp):
AATTAAGCCCATTGGTGTCCGAGCCT
Found at i:12041043 original size:16 final size:16
Alignment explanation
Indices: 12041018--12041051 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12041008 TAATTAGGCT
* *
12041018 CATTGGTGTCCGAGCC
1 CATTGATGTCCAAGCC
12041034 CATTGATGTCCAAGCC
1 CATTGATGTCCAAGCC
12041050 CA
1 CA
12041052 ACTAGGTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.32, G:0.24, T:0.24
Consensus pattern (16 bp):
CATTGATGTCCAAGCC
Found at i:12041111 original size:3 final size:3
Alignment explanation
Indices: 12041103--12041134 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12041093 TTTATTAATG
12041103 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12041135 TTGTTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12041193 original size:14 final size:14
Alignment explanation
Indices: 12041176--12041213 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
12041166 GTGTATATAT
12041176 TTATATTATTATTA
1 TTATATTATTATTA
*
12041190 TTATATTATTATTC
1 TTATATTATTATTA
*
12041204 TTATTTTATT
1 TTATATTATT
12041214 TCCATTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATATTATTATTA
Found at i:12041201 original size:17 final size:17
Alignment explanation
Indices: 12041179--12041213 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12041169 TATATATTTA
12041179 TATTATTATTATTATAT
1 TATTATTATTATTATAT
* *
12041196 TATTATTCTTATTTTAT
1 TATTATTATTATTATAT
12041213 T
1 T
12041214 TCCATTTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATTATTATTATAT
Found at i:12041248 original size:13 final size:13
Alignment explanation
Indices: 12041218--12041257 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
12041208 TTTATTTCCA
*
12041218 TTTCTTTCTTTCTT
1 TTTCTTTCCTT-TT
12041232 TTTCTTTCCTTTT
1 TTTCTTTCCTTTT
12041245 TTTCTTTCCTTTT
1 TTTCTTTCCTTTT
12041258 CTATTCCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 15 0.60
14 10 0.40
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTCTTTCCTTTT
Found at i:12041248 original size:23 final size:24
Alignment explanation
Indices: 12041207--12041265 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
12041197 ATTATTCTTA
* *
12041207 TTTTATTTCCATTTCTTTCTTTCT
1 TTTTCTTTCCATTTCTTTCTTTCC
*
12041231 TTTTCTTTCC-TTTTTTTCTTTCC
1 TTTTCTTTCCATTTCTTTCTTTCC
12041254 TTTTCTATTCCA
1 TTTTCT-TTCCA
12041266 ATCCACCCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (24 bp):
TTTTCTTTCCATTTCTTTCTTTCC
Found at i:12042089 original size:19 final size:19
Alignment explanation
Indices: 12042061--12042121 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
12042051 TGATCACAAG
*
12042061 TTTTTCTTTTTCCATTTTA
1 TTTTTATTTTTCCATTTTA
**
12042080 TTTTTATTTTTTGATTTTA
1 TTTTTATTTTTCCATTTTA
*
12042099 -TTTTATTTTAACTCATTTTA
1 TTTTTATTTT-TC-CATTTTA
12042119 TTT
1 TTT
12042122 CCCTTATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 9 0.27
19 16 0.48
20 6 0.18
21 2 0.06
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTATTTTTCCATTTTA
Found at i:12042090 original size:20 final size:20
Alignment explanation
Indices: 12042067--12042121 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
12042057 CAAGTTTTTC
12042067 TTTTTCCATTTTATTTTTAT
1 TTTTTCCATTTTATTTTTAT
*
12042087 TTTTT-GATTTTA-TTTTAT
1 TTTTTCCATTTTATTTTTAT
**
12042105 TTTAACTCATTTTATTT
1 TTTTTC-CATTTTATTT
12042122 CCCTTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 9 0.32
19 6 0.21
20 11 0.39
21 2 0.07
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTTTCCATTTTATTTTTAT
Found at i:12059047 original size:88 final size:88
Alignment explanation
Indices: 12058939--12059110 Score: 254
Period size: 88 Copynumber: 2.0 Consensus size: 88
12058929 TCTTTGAGTA
* *
12058939 GCACAAGCCTGGAGCTTGAGTCTCAACCCATGACAAGTTGTATCAGAGCCAGCTGTAAGGGTACT
1 GCACAAGCCTGGAGCTTGAGTCTCAACCCATGACAAGTTGTACCAGAACCAGCTGTAAGGGTACT
12059004 AGTGATGTGCCACTGAGGACGTC
66 AGTGATGTGCCACTGAGGACGTC
* *** * * **
12059027 GCACAAGCCTTGAGCTTGAGTCTTGGCCCGTGATAAGTTGTACCAGAACCAGCTGTGGGGGTACT
1 GCACAAGCCTGGAGCTTGAGTCTCAACCCATGACAAGTTGTACCAGAACCAGCTGTAAGGGTACT
12059092 AGTGATGTGCCACTGAGGA
66 AGTGATGTGCCACTGAGGA
12059111 TAGTGAGCCT
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.23
Consensus pattern (88 bp):
GCACAAGCCTGGAGCTTGAGTCTCAACCCATGACAAGTTGTACCAGAACCAGCTGTAAGGGTACT
AGTGATGTGCCACTGAGGACGTC
Found at i:12059403 original size:63 final size:62
Alignment explanation
Indices: 12059299--12059493 Score: 210
Period size: 63 Copynumber: 3.0 Consensus size: 62
12059289 CCTTCAACTG
* *
12059299 TGTACTATTAGTTATGGGATATAAGTATTCACACCATTTTCAATTGTGTACTAGAGTTGGTCA
1 TGTACTATTGGTTATGGGATATAAGTGTTCACACCA-TTTCAATTGTGTACTAGAGTTGGTCA
** * * * * *
12059362 TGTACTATTGGTTATAAGATATAAGTGTTCATACCACTTTCAACTTGTGAAACTTGTGAGGTGCT
1 TGTACTATTGGTTATGGGATATAAGTGTTCACACCA-TTTCAA-TTGTG-TAC-T-AGAGTTGGT
**
12059427 TG
61 CA
* *
12059429 TGTACTATTGGTTATGGGATATAAGTGTTCACACCATCTTCAACTGTGTATTAGAGTTGGTCA
1 TGTACTATTGGTTATGGGATATAAGTGTTCACACCAT-TTCAATTGTGTACTAGAGTTGGTCA
12059492 TG
1 TG
12059494 AGATATAAGT
Statistics
Matches: 104, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
63 45 0.43
64 6 0.06
65 3 0.03
66 6 0.06
67 44 0.42
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (62 bp):
TGTACTATTGGTTATGGGATATAAGTGTTCACACCATTTCAATTGTGTACTAGAGTTGGTCA
Found at i:12059815 original size:85 final size:85
Alignment explanation
Indices: 12059655--12059817 Score: 215
Period size: 85 Copynumber: 1.9 Consensus size: 85
12059645 TCTCACATCG
** *
12059655 ATTGTGTACTAGAGTTGGTTATGGGATATAAGTGTTCACACCATCTTCAATTTGTGAAGTGCCTT
1 ATTGTGTACTAGAGTTGGTTATGAAATATAAGTGTTCACACCATCTTCAATTTGTGAAGTACCTT
*
12059720 TTGTAGGACAAAGTCCTTTA
66 TTATAGGACAAAGTCCTTTA
* * *
12059740 ATTGTGTACTAGAGTTGGTTATGAAATATAGGTGTTCATACCA-CATTCAATTTGTG-AGATATC
1 ATTGTGTACTAGAGTTGGTTATGAAATATAAGTGTTCACACCATC-TTCAATTTGTGAAG-TACC
12059803 TTTTAT-GAGACAAAG
64 TTTTATAG-GACAAAG
12059818 CCATGAGACT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
84 4 0.06
85 64 0.94
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.37
Consensus pattern (85 bp):
ATTGTGTACTAGAGTTGGTTATGAAATATAAGTGTTCACACCATCTTCAATTTGTGAAGTACCTT
TTATAGGACAAAGTCCTTTA
Found at i:12060544 original size:21 final size:22
Alignment explanation
Indices: 12060503--12060545 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
12060493 GGCCCTACCG
12060503 TGTAGCACTTAGCTATTCTCACGA
1 TGTAGCACTTAG--ATTCTCACGA
12060527 TGTAGCACTTAG-TTCTCAC
1 TGTAGCACTTAGATTCTCAC
12060546 CAACTGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
24 12 0.63
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (22 bp):
TGTAGCACTTAGATTCTCACGA
Found at i:12062415 original size:298 final size:298
Alignment explanation
Indices: 12061879--12062467 Score: 973
Period size: 298 Copynumber: 2.0 Consensus size: 298
12061869 AAAAAAAAGT
* *
12061879 GTCTTTTAAGAAAGAAAGATGTTTTTATATCTTTTCAAATTTGTATGAAAGAATGAATGTTAGTT
1 GTCTTTTAACAAAGAAAGATATTTTTATATCTTTTCAAATTTGTATGAAAGAATGAATGTTAGTT
*
12061944 TCTGAAAAAGTTTTTAAACTTCCATGGACTTTGAAACAAAATATAGAACTTTTAAGATTTTTTTG
66 TCTGAAAAAGTTTTTAAACTTCCATGGACTTTGAAACAAAATATAGAACTTTTAAGATTTTTTTA
* * *
12062009 AAGAAAAACATCCAATAATTTTGAGTTGCAGAACAAAAGATGGTCTTTTCCTCAATATTCAACAT
131 AAGAAAAACATCCAATAAATTTGAGTCGCAAAACAAAAGATGGTCTTTTCCTCAATATTCAACAT
* *
12062074 AGAAATTTATAGATTGAAAATTCAAGATTGATAGTCTAAAGTTGTCTTGACATTTTCCTTGATTG
196 AGAAATTTACAGATTGAAAATTCAAGATTGATAGCCTAAAGTTGTCTTGACATTTTCCTTGATTG
***
12062139 TTGATAAATCTGAAAATTTAAAATACGACATAGGAAGA
261 CAAATAAATCTGAAAATTTAAAATACGACATAGGAAGA
* *
12062177 GTCTTTTAACAAAGAAAGATATTTTTATATCTTTTCAAATTTGTATGGAAGAATGAATGTTGGTT
1 GTCTTTTAACAAAGAAAGATATTTTTATATCTTTTCAAATTTGTATGAAAGAATGAATGTTAGTT
12062242 TCTG-AAAAGTTTTTAAACTTCCATGGACTTTGAAACAAAATATAGAACTTTTAAGATTTTTTTT
66 TCTGAAAAAGTTTTTAAACTTCCATGGACTTTGAAACAAAATATAGAACTTTTAAGA-TTTTTTT
* * * * *
12062306 AAAGAATAATATCCAATAAATTTGAGTCGTAAAACAAAAGATGGTGTTTTTCTCAATATTCAACA
130 AAAGAAAAACATCCAATAAATTTGAGTCGCAAAACAAAAGATGGTCTTTTCCTCAATATTCAACA
*
12062371 TTGAAATTTACAGATTGAAAATTCAAGATTGATAGCCTAAAGTTGTCTTGACATTTTCCTTGATT
195 TAGAAATTTACAGATTGAAAATTCAAGATTGATAGCCTAAAGTTGTCTTGACATTTTCCTTGATT
* *
12062436 GCAAATAAATTTGAAATTTTAAAATACGACAT
260 GCAAATAAATCTGAAAATTTAAAATACGACAT
12062468 GATAATATGA
Statistics
Matches: 269, Mismatches: 21, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
297 52 0.19
298 217 0.81
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (298 bp):
GTCTTTTAACAAAGAAAGATATTTTTATATCTTTTCAAATTTGTATGAAAGAATGAATGTTAGTT
TCTGAAAAAGTTTTTAAACTTCCATGGACTTTGAAACAAAATATAGAACTTTTAAGATTTTTTTA
AAGAAAAACATCCAATAAATTTGAGTCGCAAAACAAAAGATGGTCTTTTCCTCAATATTCAACAT
AGAAATTTACAGATTGAAAATTCAAGATTGATAGCCTAAAGTTGTCTTGACATTTTCCTTGATTG
CAAATAAATCTGAAAATTTAAAATACGACATAGGAAGA
Found at i:12062721 original size:15 final size:13
Alignment explanation
Indices: 12062699--12062732 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
12062689 ATTTGTAGTG
12062699 ATATGATATTAATT
1 ATATGATATT-ATT
12062713 ATCATGATATTATT
1 AT-ATGATATTATT
12062727 ATATGA
1 ATATGA
12062733 ATATGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 7 0.37
15 8 0.42
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (13 bp):
ATATGATATTATT
Found at i:12063419 original size:22 final size:23
Alignment explanation
Indices: 12063371--12063420 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
12063361 TAAGTCAAAT
* * *
12063371 TAGTTAATCGTTGATAATTTTAA
1 TAGTAAATCATTGATAATATTAA
12063394 -AGTAAATCATTGATAA-ATTAA
1 TAGTAAATCATTGATAATATTAA
12063415 TAGTAA
1 TAGTAA
12063421 GTTATAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.40
Consensus pattern (23 bp):
TAGTAAATCATTGATAATATTAA
Found at i:12065829 original size:12 final size:13
Alignment explanation
Indices: 12065807--12065854 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 13
12065797 TAATCATGCA
12065807 AAAATAC-TAAA-
1 AAAATACATAAAT
*
12065818 AAAACACATAAAT
1 AAAATACATAAAT
12065831 AAAATAC-TAAAT
1 AAAATACATAAAT
*
12065843 AAAATAAATAAA
1 AAAATACATAAA
12065855 AATATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
11 6 0.19
12 15 0.48
13 10 0.32
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (13 bp):
AAAATACATAAAT
Found at i:12065839 original size:24 final size:23
Alignment explanation
Indices: 12065806--12065866 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
12065796 TTAATCATGC
12065806 AAAAATACTAAAAAAACACATAAAT
1 AAAAATACTAAAAAAA-A-ATAAAT
*
12065831 -AAAATACT-AAATAAAATAAAT
1 AAAAATACTAAAAAAAAATAAAT
12065852 AAAAATA-TAAAAAAA
1 AAAAATACTAAAAAAA
12065867 TAGAAATGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 7 0.22
22 12 0.38
23 5 0.16
24 8 0.25
ACGTcount: A:0.75, C:0.07, G:0.00, T:0.18
Consensus pattern (23 bp):
AAAAATACTAAAAAAAAATAAAT
Found at i:12065851 original size:21 final size:21
Alignment explanation
Indices: 12065806--12065868 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 21
12065796 TTAATCATGC
12065806 AAAAATACTAAAAAAACACATAAAT
1 AAAAATACT--AAAAA-A-ATAAAT
12065831 -AAAATACTAAATAAAATAAAT
1 AAAAATACTAAA-AAAATAAAT
12065852 AAAAATA-TAAAAAAATA
1 AAAAATACTAAAAAAATA
12065869 GAAATGGCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 6 0.17
21 10 0.28
22 10 0.28
23 2 0.06
24 8 0.22
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (21 bp):
AAAAATACTAAAAAAATAAAT
Found at i:12065867 original size:16 final size:17
Alignment explanation
Indices: 12065841--12065873 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12065831 AAAATACTAA
12065841 ATAAAATAAATAAAAAT
1 ATAAAATAAATAAAAAT
*
12065858 ATAAAA-AAATAGAAAT
1 ATAAAATAAATAAAAAT
12065874 GGCTCTGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
ATAAAATAAATAAAAAT
Found at i:12066767 original size:3 final size:3
Alignment explanation
Indices: 12066761--12066829 Score: 75
Period size: 3 Copynumber: 21.3 Consensus size: 3
12066751 AAAAAAGTAA
* *
12066761 AAT AAT AAT AAAT AAAT AAAT AAT GAAA AACA AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT -AAT -AAT AAT -AAT AA-T AAT AAT AAT AAT AAT
12066808 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
12066830 TATACTTGGG
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
3 45 0.74
4 16 0.26
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:12066773 original size:35 final size:38
Alignment explanation
Indices: 12066723--12066809 Score: 112
Period size: 35 Copynumber: 2.4 Consensus size: 38
12066713 CAACAAAACA
*
12066723 AATAATCAA-AATAAATAAATAAA-ACT-AAAAA-AAAGT
1 AATAAT-AATAATAAATAAATAAATAATGAAAAACAAA-T
12066759 AA-AATAATAATAAATAAATAAATAATGAAAAACAAAT
1 AATAATAATAATAAATAAATAAATAATGAAAAACAAAT
12066796 AATAATAATAATAA
1 AATAATAATAATAA
12066810 TAATAATAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
34 2 0.04
35 17 0.38
36 4 0.09
37 8 0.18
38 14 0.31
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.22
Consensus pattern (38 bp):
AATAATAATAATAAATAAATAAATAATGAAAAACAAAT
Found at i:12066803 original size:38 final size:36
Alignment explanation
Indices: 12066723--12066821 Score: 109
Period size: 35 Copynumber: 2.8 Consensus size: 36
12066713 CAACAAAACA
*
12066723 AATAATCAA-AATAAATAAATAAAACTAAAAAAAAGT
1 AATAAT-AATAATAAATAAATAAAAATAAAAAAAAGT
12066759 AA-AATAATAATAAATAAATAAATAATGAAAAACAAA-T
1 AATAATAATAATAAATAAATAAA-AAT-AAAAA-AAAGT
*
12066796 AATAATAATAAT-AAT-AATAATAATAA
1 AATAATAATAATAAATAAATAAAAATAA
12066822 TAATAATATA
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
34 4 0.07
35 20 0.36
36 9 0.16
37 11 0.20
38 12 0.21
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (36 bp):
AATAATAATAATAAATAAATAAAAATAAAAAAAAGT
Found at i:12067139 original size:41 final size:42
Alignment explanation
Indices: 12067060--12067139 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
12067050 TTTTTGAAAA
* * *
12067060 AAATAAATATGGCTCATCTAAACAGAGGCTCAATGACTTGAG
1 AAATAAATATAGCTCATCTAAACAGAAGCTCAACGACTTGAG
* *
12067102 AAATAAATA-AGCTCCTCTAAACAGAAGCTTAACGACTT
1 AAATAAATATAGCTCATCTAAACAGAAGCTCAACGACTT
12067140 AGTTTCACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 24 0.73
42 9 0.27
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (42 bp):
AAATAAATATAGCTCATCTAAACAGAAGCTCAACGACTTGAG
Found at i:12067195 original size:16 final size:17
Alignment explanation
Indices: 12067171--12067209 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
12067161 GTAAAATTTT
*
12067171 AGATATGCAAGAATTC-
1 AGATTTGCAAGAATTCA
*
12067187 AGATTTGCAAGATTTCA
1 AGATTTGCAAGAATTCA
12067204 AGATTT
1 AGATTT
12067210 ACATTTGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (17 bp):
AGATTTGCAAGAATTCA
Found at i:12067411 original size:21 final size:21
Alignment explanation
Indices: 12067385--12067425 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12067375 GTTTCACATC
12067385 TCAAAGA-TTCTCATTTGAAAT
1 TCAAAGACTT-TCATTTGAAAT
12067406 TCAAAGACTTTCATTTGAAA
1 TCAAAGACTTTCATTTGAAA
12067426 ACTTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.37
Consensus pattern (21 bp):
TCAAAGACTTTCATTTGAAAT
Found at i:12068580 original size:27 final size:27
Alignment explanation
Indices: 12068547--12068636 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
12068537 AATTTGAGTC
*
12068547 TTCATTTTCTCTCATTTTTATTTTTTT
1 TTCATTTTTTCTCATTTTTATTTTTTT
* *
12068574 TTCATTTTTTTTTCA-TTTTA-TATTTT
1 TTCA-TTTTTTCTCATTTTTATTTTTTT
*
12068600 TTCATTTTTTCCTCA-TTTTATATTTTT
1 TTCATTTTTT-CTCATTTTTATTTTTTT
*
12068627 TTCTTTTTTT
1 TTCATTTTTT
12068637 TTACTATTGA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
25 6 0.11
26 17 0.32
27 22 0.42
28 8 0.15
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (27 bp):
TTCATTTTTTCTCATTTTTATTTTTTT
Found at i:12068606 original size:26 final size:27
Alignment explanation
Indices: 12068562--12068638 Score: 113
Period size: 26 Copynumber: 2.9 Consensus size: 27
12068552 TTTCTCTCAT
*
12068562 TTTTATTTTTTTTTCATTTTTTTTTCA
1 TTTTATATTTTTTTCATTTTTTTTTCA
**
12068589 TTTTATA-TTTTTTCATTTTTTCCTCA
1 TTTTATATTTTTTTCATTTTTTTTTCA
12068615 TTTTATATTTTTTTC-TTTTTTTTT
1 TTTTATATTTTTTTCATTTTTTTTT
12068639 ACTATTGATA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
26 31 0.70
27 13 0.30
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTATATTTTTTTCATTTTTTTTTCA
Found at i:12068609 original size:10 final size:11
Alignment explanation
Indices: 12068561--12068592 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
12068551 TTTTCTCTCA
12068561 TTTTT-ATTTT
1 TTTTTCATTTT
12068571 TTTTTCATTTT
1 TTTTTCATTTT
12068582 TTTTTCATTTT
1 TTTTTCATTTT
12068593 ATATTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCATTTT
Found at i:12073189 original size:11 final size:11
Alignment explanation
Indices: 12073173--12073239 Score: 64
Period size: 11 Copynumber: 5.8 Consensus size: 11
12073163 TTAAATCATG
12073173 AAAAAAATACT
1 AAAAAAATACT
*
12073184 AAAAAAACACAT
1 AAAAAAATAC-T
*
12073196 AAATAAAACACT
1 AAA-AAAATACT
*
12073208 AAATAAAATA-A
1 AAA-AAAATACT
12073219 ATAAAAAATACT
1 A-AAAAAATACT
12073231 AAAAAAATA
1 AAAAAAATA
12073240 AAAATGACTC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
11 24 0.50
12 17 0.35
13 7 0.15
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAAAAATACT
Found at i:12073203 original size:13 final size:12
Alignment explanation
Indices: 12073176--12073215 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
12073166 AATCATGAAA
*
12073176 AAAATACTAAA-
1 AAAACACTAAAT
12073187 AAAACACATAAAT
1 AAAACAC-TAAAT
12073200 AAAACACTAAAT
1 AAAACACTAAAT
12073212 AAAA
1 AAAA
12073216 TAAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.23
12 13 0.50
13 7 0.27
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAACACTAAAT
Found at i:12073220 original size:21 final size:21
Alignment explanation
Indices: 12073194--12073241 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
12073184 AAAAAAACAC
12073194 ATAAAT-AAAACACTAAATAAA
1 ATAAATAAAAACACTAAA-AAA
*
12073215 ATAAATAAAAAATACTAAAAAA
1 ATAAAT-AAAAACACTAAAAAA
12073237 ATAAA
1 ATAAA
12073242 AATGACTCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 6 0.25
22 8 0.33
23 10 0.42
ACGTcount: A:0.75, C:0.06, G:0.00, T:0.19
Consensus pattern (21 bp):
ATAAATAAAAACACTAAAAAA
Found at i:12073765 original size:31 final size:31
Alignment explanation
Indices: 12073698--12073765 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
12073688 AAAACTCATT
* *
12073698 GAAAAATTCAATCAACGCCGAAAAATTCATC
1 GAAAAATTCAACCAACGCCGAAAAATTCAAC
* * **
12073729 AAAAAATTCAACCACCGTTGAAAAATTCAAC
1 GAAAAATTCAACCAACGCCGAAAAATTCAAC
12073760 GAAAAA
1 GAAAAA
12073766 CTGAAAATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (31 bp):
GAAAAATTCAACCAACGCCGAAAAATTCAAC
Found at i:12074143 original size:9 final size:9
Alignment explanation
Indices: 12074131--12074230 Score: 50
Period size: 9 Copynumber: 10.8 Consensus size: 9
12074121 ACAAATAATC
12074131 AAAATAAAT
1 AAAATAAAT
12074140 AAAAGTAAA-
1 AAAA-TAAAT
12074149 AAAAGT-AA-
1 AAAA-TAAAT
*
12074157 AAAA-AAGT
1 AAAATAAAT
12074165 AAAATAACA-
1 AAAATAA-AT
*
12074174 ATACATAAAT
1 A-AAATAAAT
12074184 AAAATAAAT
1 AAAATAAAT
12074193 -AAATAAAT
1 AAAATAAAT
*
12074201 GAAAAATGAAAA
1 --AAAAT-AAAT
12074213 ACAAATAAAT
1 A-AAATAAAT
12074223 AATAATAA
1 AA-AATAA
12074231 TAATAATATA
Statistics
Matches: 72, Mismatches: 6, Indels: 25
0.70 0.06 0.24
Matches are distributed among these distances:
7 1 0.01
8 18 0.25
9 22 0.31
10 20 0.28
11 8 0.11
12 3 0.04
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (9 bp):
AAAATAAAT
Found at i:12074151 original size:8 final size:9
Alignment explanation
Indices: 12074131--12074168 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
12074121 ACAAATAATC
12074131 AAAA-TAAA
1 AAAAGTAAA
12074139 TAAAAGTAAA
1 -AAAAGTAAA
12074149 AAAAGTAAAA
1 AAAAGT-AAA
12074159 AAAAGTAAA
1 AAAAGTAAA
12074168 A
1 A
12074169 TAACAATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 14 0.52
10 13 0.48
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (9 bp):
AAAAGTAAA
Found at i:12074159 original size:10 final size:10
Alignment explanation
Indices: 12074131--12074168 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
12074121 ACAAATAATC
*
12074131 AAAA-TAAAT
1 AAAAGTAAAA
12074140 AAAAGT-AAA
1 AAAAGTAAAA
12074149 AAAAGTAAAA
1 AAAAGTAAAA
12074159 AAAAGTAAAA
1 AAAAGTAAAA
12074169 TAACAATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 12 0.46
10 14 0.54
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (10 bp):
AAAAGTAAAA
Found at i:12074162 original size:19 final size:18
Alignment explanation
Indices: 12074131--12074168 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
12074121 ACAAATAATC
*
12074131 AAAATAAATAAAAGTAAA
1 AAAATAAAAAAAAGTAAA
12074149 AAAAGTAAAAAAAAGTAAA
1 AAAA-TAAAAAAAAGTAAA
12074168 A
1 A
12074169 TAACAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAATAAAAAAAAGTAAA
Found at i:12074206 original size:19 final size:19
Alignment explanation
Indices: 12074132--12074224 Score: 53
Period size: 22 Copynumber: 4.5 Consensus size: 19
12074122 CAAATAATCA
12074132 AAATAAATAAAAGTAAAAA-
1 AAATAAATAAAAG-AAAAAT
* * *
12074151 AAGTAAAAAAAAGTAAAAT
1 AAATAAATAAAAGAAAAAT
* *
12074170 AACAATACATAAATAAAATAAAT
1 -A-AATAAATAAA-AGAA-AAAT
*
12074193 AAATAAATGAAAAATGAAAAAC
1 AAATAAAT--AAAA-GAAAAAT
12074215 AAATAAATAA
1 AAATAAATAA
12074225 TAATAATAAT
Statistics
Matches: 55, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
18 4 0.07
19 11 0.20
20 3 0.05
21 13 0.24
22 15 0.27
23 9 0.16
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.17
Consensus pattern (19 bp):
AAATAAATAAAAGAAAAAT
Found at i:12077397 original size:5 final size:5
Alignment explanation
Indices: 12077384--12077480 Score: 63
Period size: 5 Copynumber: 18.8 Consensus size: 5
12077374 TGGTTGTGTT
* ** *
12077384 TTATG TTATA TTATA GAATTA TTATA TTATA TTATA GTATCA TTATCA
1 TTATA TTATA TTATA TTA-TA TTATA TTATA TTATA TTAT-A TTAT-A
* * * *
12077432 -TATTA TTATA AT-TA GTATA TTATA TGATA TTATA TGATA TTATTA TTAT
1 TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA TTAT
12077481 TATTTTATTT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
4 3 0.04
5 52 0.72
6 17 0.24
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (5 bp):
TTATA
Found at i:12077408 original size:21 final size:21
Alignment explanation
Indices: 12077384--12077429 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
12077374 TGGTTGTGTT
* *
12077384 TTATGTTATATTATAGAATTA
1 TTATATTATATTATAGAATCA
*
12077405 TTATATTATATTATAGTATCA
1 TTATATTATATTATAGAATCA
12077426 TTAT
1 TTAT
12077430 CATATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (21 bp):
TTATATTATATTATAGAATCA
Found at i:12077868 original size:19 final size:20
Alignment explanation
Indices: 12077828--12077871 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
12077818 AAATTTTGGT
12077828 TTTTAAGATTTTAGGATTGA
1 TTTTAAGATTTTAGGATTGA
*
12077848 TTTTAAG-TTTT-GGGTTCGA
1 TTTTAAGATTTTAGGATT-GA
12077867 TTTTA
1 TTTTA
12077872 GGTTGCTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 11 0.50
20 7 0.32
ACGTcount: A:0.23, C:0.02, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTTAAGATTTTAGGATTGA
Found at i:12077970 original size:20 final size:20
Alignment explanation
Indices: 12077929--12077971 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12077919 AAATTTAAGG
* *
12077929 AAAATCTATGATTTTTTTGA
1 AAAATCTAAGATTTTTTAGA
12077949 AAAATCTAAG-TTTTTCTAGA
1 AAAATCTAAGATTTTT-TAGA
12077969 AAA
1 AAA
12077972 TATGAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (20 bp):
AAAATCTAAGATTTTTTAGA
Found at i:12078305 original size:13 final size:13
Alignment explanation
Indices: 12078289--12078313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12078279 TTCTTTTTCC
12078289 ATTTTATTTTTTG
1 ATTTTATTTTTTG
12078302 ATTTTATTTTTT
1 ATTTTATTTTTT
12078314 TAACTCACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
ATTTTATTTTTTG
Found at i:12078370 original size:16 final size:16
Alignment explanation
Indices: 12078351--12078397 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
12078341 TATTTTTTGG
12078351 TTTTATTTTTAAGAGA
1 TTTTATTTTTAAGAGA
**
12078367 TTTTATTTTT--GCTA
1 TTTTATTTTTAAGAGA
12078381 TTTTATTTTTAAGAGA
1 TTTTATTTTTAAGAGA
12078397 T
1 T
12078398 CTTAAGGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
16 13 0.52
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.62
Consensus pattern (16 bp):
TTTTATTTTTAAGAGA
Found at i:12091556 original size:153 final size:153
Alignment explanation
Indices: 12091278--12091559 Score: 458
Period size: 153 Copynumber: 1.8 Consensus size: 153
12091268 GAGTACGAAC
* * * * *
12091278 TCTAAAAGTATTAAAAGTGAATGACATAAATACTCTTATAAATTTTAAGAAATAACAAATTTACC
1 TCTAAAAGTATTAAAAATGAATAACATAAATACTCTTATAAATTTTAAAAAATAAAAAATTTACA
*
12091343 TTTAAATTTCTAGCATTTTTTATTTATTTAATAAAGATTATTTGTCATTAAATATATAGCTTTTA
66 TTTAAATTTCTAGCATTATTTATTTATTTAATAAAGATTATTTGTCATTAAATATATAGCTTTTA
12091408 TTAGTTAGTTATTTAAATTTAAA
131 TTAGTTAGTTATTTAAATTTAAA
* * *
12091431 TCTAAAAGTGTTAAAAATGAATAACATAAATGC-CGTTATAAATTTTAAAAAATAAAAAATTTAT
1 TCTAAAAGTATTAAAAATGAATAACATAAATACTC-TTATAAATTTTAAAAAATAAAAAATTTAC
*
12091495 ATTTCAATTTCTAGCATTATTTATTTATTTAATAAAGATTATTTGTCATTAAATATATAGCTTTT
65 ATTTAAATTTCTAGCATTATTTATTTATTTAATAAAGATTATTTGTCATTAAATATATAGCTTTT
12091560 TATTTATTTA
Statistics
Matches: 118, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
152 1 0.01
153 117 0.99
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (153 bp):
TCTAAAAGTATTAAAAATGAATAACATAAATACTCTTATAAATTTTAAAAAATAAAAAATTTACA
TTTAAATTTCTAGCATTATTTATTTATTTAATAAAGATTATTTGTCATTAAATATATAGCTTTTA
TTAGTTAGTTATTTAAATTTAAA
Found at i:12094111 original size:22 final size:22
Alignment explanation
Indices: 12094053--12094100 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12094043 AATTTAGACA
*
12094053 AAATCAAT-ATTAACTTTATATT
1 AAATCAATGA-TAACTGTATATT
12094075 AAATCAATGATAACTGTATATT
1 AAATCAATGATAACTGTATATT
12094097 AAAT
1 AAAT
12094101 TATAGATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (22 bp):
AAATCAATGATAACTGTATATT
Found at i:12094121 original size:22 final size:22
Alignment explanation
Indices: 12094063--12094153 Score: 71
Period size: 22 Copynumber: 4.1 Consensus size: 22
12094053 AAATCAATAT
* *
12094063 TAACTTTATATTAAATCAAT-GA
1 TAACTTAATAATAAAT-AATAGA
* *
12094085 TAACTGT-ATATTAAATTATAGA
1 TAACT-TAATAATAAATAATAGA
*
12094107 TAACTTAATAGTAAATAAATA-A
1 TAACTTAATAATAAAT-AATAGA
* *
12094129 TAATTTAATAATAAATAATTGA
1 TAACTTAATAATAAATAATAGA
12094151 TAA
1 TAA
12094154 GATAGTTGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
21 6 0.10
22 48 0.83
23 4 0.07
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.38
Consensus pattern (22 bp):
TAACTTAATAATAAATAATAGA
Found at i:12094196 original size:14 final size:14
Alignment explanation
Indices: 12094172--12094208 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
12094162 TATGCCAGTG
12094172 ATAAT-ATAATAAT
1 ATAATCATAATAAT
12094185 A-AATACATAATAAT
1 ATAAT-CATAATAAT
12094199 ATAATCATAA
1 ATAATCATAA
12094209 ATTACAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.14
13 1 0.05
14 14 0.67
15 3 0.14
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (14 bp):
ATAATCATAATAAT
Found at i:12094225 original size:22 final size:22
Alignment explanation
Indices: 12094172--12094219 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
12094162 TATGCCAGTG
12094172 ATAATATAATAATAAATACATA
1 ATAATATAATAATAAATACATA
*
12094194 ATAATATAATCATAAATTACA-A
1 ATAATATAATAATAAA-TACATA
12094216 ATAA
1 ATAA
12094220 CTTAATAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAATATAATAATAAATACATA
Found at i:12094332 original size:22 final size:22
Alignment explanation
Indices: 12094302--12094362 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
12094292 AAAATAAGTG
* *
12094302 ATAATTTAATAGTAAATTAATGG
1 ATAACTTAATAGTAAATTAAT-A
12094325 A-AACTTAATAGTAAATTAATA
1 ATAACTTAATAGTAAATTAATA
*
12094346 ATAATTTAATAGTAAAT
1 ATAACTTAATAGTAAAT
12094363 AAGATTCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (22 bp):
ATAACTTAATAGTAAATTAATA
Found at i:12094343 original size:11 final size:11
Alignment explanation
Indices: 12094307--12094362 Score: 69
Period size: 11 Copynumber: 5.1 Consensus size: 11
12094297 AAGTGATAAT
12094307 TTAATAGTAAA
1 TTAATAGTAAA
*
12094318 TTAAT-GGAAA
1 TTAATAGTAAA
12094328 CTTAATAGTAAA
1 -TTAATAGTAAA
* *
12094340 TTAATAATAAT
1 TTAATAGTAAA
12094351 TTAATAGTAAA
1 TTAATAGTAAA
12094362 T
1 T
12094363 AAGATTCAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
10 4 0.11
11 29 0.78
12 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (11 bp):
TTAATAGTAAA
Found at i:12096844 original size:22 final size:21
Alignment explanation
Indices: 12096819--12096866 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12096809 ATAAATTACC
12096819 AAATTAACATCCAAAGTTACTA
1 AAATT-ACATCCAAAGTTACTA
** *
12096841 AAATTGTATCGAAAGTTACTA
1 AAATTACATCCAAAGTTACTA
12096862 AAATT
1 AAATT
12096867 TTATCAAAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.31
Consensus pattern (21 bp):
AAATTACATCCAAAGTTACTA
Found at i:12096855 original size:21 final size:20
Alignment explanation
Indices: 12096830--12096875 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
12096820 AATTAACATC
12096830 CAAAGTTACTAAAATTGTAT
1 CAAAGTTACTAAAATTGTAT
*
12096850 CGAAAGTTACTAAAATTTTAT
1 C-AAAGTTACTAAAATTGTAT
12096871 CAAAG
1 CAAAG
12096876 GCTATGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (20 bp):
CAAAGTTACTAAAATTGTAT
Found at i:12104350 original size:22 final size:21
Alignment explanation
Indices: 12104325--12104371 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
12104315 AATTGAATCT
*
12104325 AATTATGA-AAAAGAATTTTATA
1 AATT-TGAGAAAA-AATTTTAAA
12104347 AATTTGAGGAAAAAATTTTAAA
1 AATTTGA-GAAAAAATTTTAAA
12104369 AAT
1 AAT
12104372 AGATAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 3 0.14
22 15 0.68
23 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (21 bp):
AATTTGAGAAAAAATTTTAAA
Found at i:12110444 original size:112 final size:111
Alignment explanation
Indices: 12110235--12110459 Score: 330
Period size: 112 Copynumber: 2.0 Consensus size: 111
12110225 TGGAGTTTGG
* *
12110235 AAAAAAAAAAGAGTTCACACCAAAGAATCAGGTCCAGGTAAATGCAAAATGCAGCAGACCCACTT
1 AAAAAAAAAAGAGTTCACACCAAAGAATCAGGTCAAGGTAAATGCAAAATGCAACAGACCCACTT
* *
12110300 TTTTATTTTCCATTGTCATTATCTAGTTAGATTCCCCCACCAAAAAA
66 CTTTATATTCCATTGTCATTATCTAGTTAGATT-CCCCACCAAAAAA
**
12110347 AAAAAAAAAATTG-GTTCACACCAAAGAAATCAGGTCAAGGTAAATGC-AAATGCAACAGACTTA
1 AAAAAAAAAA--GAGTTCACACCAAAG-AATCAGGTCAAGGTAAATGCAAAATGCAACAGACCCA
*
12110410 CTTCTTTA-ATTCCATTGTCATTATCTAGTTAGATTCCCCACCCAAAAA
63 CTTCTTTATATTCCATTGTCATTATCTAGTTAGATTCCCCACCAAAAAA
12110458 AA
1 AA
12110460 TGACTTCACA
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
111 14 0.14
112 36 0.35
113 33 0.32
114 20 0.19
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.25
Consensus pattern (111 bp):
AAAAAAAAAAGAGTTCACACCAAAGAATCAGGTCAAGGTAAATGCAAAATGCAACAGACCCACTT
CTTTATATTCCATTGTCATTATCTAGTTAGATTCCCCACCAAAAAA
Found at i:12116680 original size:29 final size:30
Alignment explanation
Indices: 12116627--12116694 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
12116617 ATGAATGACT
* * *
12116627 TTTAAATTTTAGTGAAATGTTTAATCTAATG
1 TTTAAATTTTA-TAAAATGTTTAATATAATA
* *
12116658 TTTAAATTTT-TAAAATTTTTAATATGATA
1 TTTAAATTTTATAAAATGTTTAATATAATA
12116687 TTTAAATT
1 TTTAAATT
12116695 ATAAACTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 22 0.69
31 10 0.31
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.53
Consensus pattern (30 bp):
TTTAAATTTTATAAAATGTTTAATATAATA
Found at i:12138286 original size:26 final size:26
Alignment explanation
Indices: 12138214--12138286 Score: 60
Period size: 26 Copynumber: 2.8 Consensus size: 26
12138204 TAAATTTAAA
* * *
12138214 AAAATTTCTCACTTAGAGATTTCATAG
1 AAAATTTATCA-TTGGAAATTTCATAG
* *
12138241 AAAATTTATTATTTGAAATTTC-TA-
1 AAAATTTATCATTGGAAATTTCATAG
12138265 AAAATCTTATCATTGGATAATT
1 AAAAT-TTATCATTGGA-AATT
12138287 ATCAAATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 5 0.13
25 11 0.29
26 13 0.34
27 9 0.24
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (26 bp):
AAAATTTATCATTGGAAATTTCATAG
Found at i:12138682 original size:7 final size:7
Alignment explanation
Indices: 12138670--12138702 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
12138660 TAAAAATATA
12138670 TTTTTTC
1 TTTTTTC
12138677 TTTTTTC
1 TTTTTTC
12138684 TTTTTTC
1 TTTTTTC
12138691 TTTTTTC
1 TTTTTTC
12138698 TTTTT
1 TTTTT
12138703 ACTAAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:12139535 original size:13 final size:13
Alignment explanation
Indices: 12139519--12139544 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12139509 ATCATAAATC
12139519 ATCATCATTATAA
1 ATCATCATTATAA
12139532 ATCATCATTATAA
1 ATCATCATTATAA
12139545 TTCGTTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
ATCATCATTATAA
Found at i:12139562 original size:24 final size:24
Alignment explanation
Indices: 12139535--12139582 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
12139525 ATTATAAATC
12139535 ATCATTATAATTCGTTTATCGTTA
1 ATCATTATAATTCGTTTATCGTTA
12139559 ATCATTATAATTCGTTTATCGTTA
1 ATCATTATAATTCGTTTATCGTTA
12139583 GCTACGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (24 bp):
ATCATTATAATTCGTTTATCGTTA
Done.