Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397259.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_147.0, 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: 10737078
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 75620 characters in sequence are not A, C, G, or T
File 7 of 22
Found at i:2655255 original size:25 final size:25
Alignment explanation
Indices: 2655208--2655259 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
2655198 ATATTAATTG
2655208 TTAAATTATAAATTAATAATATTAT
1 TTAAATTATAAATTAATAATATTAT
2655233 TTAAATTATAAATT-AT--TATTAT
1 TTAAATTATAAATTAATAATATTAT
2655255 TTAAA
1 TTAAA
2655260 AAATAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.41
24 2 0.07
25 14 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAAATTATAAATTAATAATATTAT
Found at i:2655256 original size:132 final size:136
Alignment explanation
Indices: 2655110--2655364 Score: 401
Period size: 142 Copynumber: 1.9 Consensus size: 136
2655100 AATAAATTGC
2655110 AAATTATAAATA-TT-T-AA-AAAATAAAATAAAATAAAATAAAAACAAACATAATAACATTTGA
1 AAATTATAAATATTTATAAATAAAATAAAATAAAATAAAATAAAAACAAACATAATAACATTTGA
2655171 ATTATAATAAAATATTAATATTTTATAATATTAATTGTTAAATTATAAATTAATAATATTATTTA
66 ATTATAATAAAATATTAATATTTTATAATATTAATTGTTAAATTATAAATTAATAATATTATTTA
2655236 AATTAT
131 AATTAT
* * *
2655242 AAATTATTATTATTTAAAAAATAAAATAAAATAAAATAAAATAAAATAAAAACAATCATAATAAC
1 AAATTATAAATATTT-----AT-AAATAAAATAAAATAAAATAAAATAAAAACAAACATAATAAC
2655307 ATTTGAATTATAATAAAATATTAATATTTTATAATATTAATTGTTAAATTATAAATTA
60 ATTTGAATTATAATAAAATATTAATATTTTATAATATTAATTGTTAAATTATAAATTA
2655365 TTACTATTTA
Statistics
Matches: 110, Mismatches: 3, Indels: 10
0.89 0.02 0.08
Matches are distributed among these distances:
132 10 0.09
133 2 0.02
139 1 0.01
141 2 0.02
142 95 0.86
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (136 bp):
AAATTATAAATATTTATAAATAAAATAAAATAAAATAAAATAAAAACAAACATAATAACATTTGA
ATTATAATAAAATATTAATATTTTATAATATTAATTGTTAAATTATAAATTAATAATATTATTTA
AATTAT
Found at i:2655269 original size:5 final size:5
Alignment explanation
Indices: 2655259--2655292 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
2655249 TATTATTTAA
2655259 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
2655293 ACAATCATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:2655412 original size:17 final size:18
Alignment explanation
Indices: 2655390--2655432 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
2655380 AAAATAAAAA
2655390 TATAATAATAT-TTAAAT
1 TATAATAATATATTAAAT
* *
2655407 TATAATAAAATATTATAT
1 TATAATAATATATTAAAT
2655425 TAT-ATAAT
1 TATAATAAT
2655433 GCTAATTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAATAATATATTAAAT
Found at i:2655429 original size:29 final size:28
Alignment explanation
Indices: 2655359--2655429 Score: 65
Period size: 28 Copynumber: 2.5 Consensus size: 28
2655349 GTTAAATTAT
2655359 AAAT-TATTACTATTTAAAAATAAAATAA
1 AAATATATTA-TATTTAAAAATAAAATAA
* * *
2655387 AAATATAATAATATTT-AAATTATAATAA
1 AAATAT-ATTATATTTAAAAATAAAATAA
2655415 AATATTATATTATAT
1 AA-A-TATATTATAT
2655430 AATGCTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
28 16 0.46
29 13 0.37
30 6 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (28 bp):
AAATATATTATATTTAAAAATAAAATAA
Found at i:2655448 original size:91 final size:95
Alignment explanation
Indices: 2655279--2655453 Score: 250
Period size: 91 Copynumber: 1.9 Consensus size: 95
2655269 AAAATAAAAT
* * *
2655279 AAAATAAAATAAAAACAATCATAATAACATTTGAATTATAATAAAATATTAATATTTTATAATAT
1 AAAATAAAAT-AAAACAATCATAATAACATTTAAATTATAATAAAATATTAATATTATATAATAC
*
2655344 TAATTGTTAAATTATAAATTATTACTATTTA
65 TAATTATTAAATTATAAATTATTACTATTTA
* *
2655375 AAAATAAAAT-AAA-AAT-ATAATAATATTTAAATTATAATAAAATATT-ATATTATATAATGCT
1 AAAATAAAATAAAACAATCATAATAACATTTAAATTATAATAAAATATTAATATTATATAATACT
*
2655436 AATTATTCAATTATAAAT
66 AATTATTAAATTATAAAT
2655454 AAAATATTAA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
91 28 0.39
92 28 0.39
93 3 0.04
94 3 0.04
96 10 0.14
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (95 bp):
AAAATAAAATAAAACAATCATAATAACATTTAAATTATAATAAAATATTAATATTATATAATACT
AATTATTAAATTATAAATTATTACTATTTA
Found at i:2655501 original size:27 final size:25
Alignment explanation
Indices: 2655469--2655524 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 25
2655459 ATTAAAATTT
* *
2655469 AAATTATCAATTATTAATATTTTAAA
1 AAATTATAAATTACTAATA-TTTAAA
2655495 CAAATTATAAATTACTAATATTTAAA
1 -AAATTATAAATTACTAATATTTAAA
2655521 AAAT
1 AAAT
2655525 AAAAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 4 0.15
26 6 0.22
27 17 0.63
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (25 bp):
AAATTATAAATTACTAATATTTAAA
Found at i:2655530 original size:24 final size:27
Alignment explanation
Indices: 2655477--2655530 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
2655467 TTAAATTATC
* *
2655477 AATTATTAATATTTTAAACAAATTATA
1 AATTACTAATATTTTAAACAAATTAAA
2655504 AATTACTAATA-TTTAAA-AAA-TAAA
1 AATTACTAATATTTTAAACAAATTAAA
2655528 AAT
1 AAT
2655531 AAATAATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 3 0.12
26 6 0.24
27 10 0.40
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTACTAATATTTTAAACAAATTAAA
Found at i:2655537 original size:24 final size:27
Alignment explanation
Indices: 2655483--2655537 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 27
2655473 TATCAATTAT
* * *
2655483 TAATATTTTAAACAAATTATAAATTAC
1 TAATATTTTAAACAAATTAAAAATAAA
2655510 TAATA-TTTAAA-AAA-TAAAAATAAA
1 TAATATTTTAAACAAATTAAAAATAAA
2655534 TAAT
1 TAAT
2655538 CATATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 11 0.44
25 3 0.12
26 6 0.24
27 5 0.20
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (27 bp):
TAATATTTTAAACAAATTAAAAATAAA
Found at i:2670739 original size:20 final size:20
Alignment explanation
Indices: 2670702--2670765 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
2670692 AAGCTCTTAA
2670702 AAAATAATTTTTAAAAAAAT
1 AAAATAATTTTTAAAAAAAT
*
2670722 AAAATTATTTTTTTAAAAAAAAT
1 AAAA-TA-ATTTTT-AAAAAAAT
*** *
2670745 ATGTTAATTTTTCAAAAAAT
1 AAAATAATTTTTAAAAAAAT
2670765 A
1 A
2670766 TCTCTCTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 12 0.34
21 7 0.20
22 7 0.20
23 9 0.26
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AAAATAATTTTTAAAAAAAT
Found at i:2670775 original size:18 final size:18
Alignment explanation
Indices: 2670754--2670795 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2670744 TATGTTAATT
2670754 TTTCAAAAAAT-ATCTCTC
1 TTTCAAAAAATCA-CTCTC
* *
2670772 TTTCAATAAATCACTCTT
1 TTTCAAAAAATCACTCTC
2670790 TTTCAA
1 TTTCAA
2670796 GATAAATCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTCAAAAAATCACTCTC
Found at i:2671292 original size:19 final size:19
Alignment explanation
Indices: 2671241--2671297 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 19
2671231 ATATAATTTA
2671241 TTTTATCAAATAATTTTAATT
1 TTTTAT-AAA-AATTTTAATT
*
2671262 TAATTT-TAAAAATTTTTATT
1 T--TTTATAAAAATTTTAATT
2671282 TTTTATAAAAATTTTA
1 TTTTATAAAAATTTTA
2671298 TAAGGCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 10 0.32
21 4 0.13
22 1 0.03
23 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATAAAAATTTTAATT
Found at i:2675415 original size:3 final size:3
Alignment explanation
Indices: 2675407--2675444 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2675397 AAGGTAATGT
2675407 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2675445 GTCATTACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2678358 original size:2 final size:2
Alignment explanation
Indices: 2678351--2678380 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2678341 AAGACAATAA
2678351 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2678381 TGCATGTGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2680878 original size:39 final size:38
Alignment explanation
Indices: 2680835--2680911 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 38
2680825 ATTTCTCATT
*
2680835 CCTTTTCATTCTATAAGGAA-GTAGAATTTGGTTAGTGTC
1 CCTTTTAATTCTATAA-GAATGTAGAA-TTGGTTAGTGTC
*
2680874 CCTTTTAATTCTGTAAGAATGTAGAATTGGTTAGTGTC
1 CCTTTTAATTCTATAAGAATGTAGAATTGGTTAGTGTC
2680912 GTCATTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 15 0.43
39 20 0.57
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (38 bp):
CCTTTTAATTCTATAAGAATGTAGAATTGGTTAGTGTC
Found at i:2682531 original size:15 final size:17
Alignment explanation
Indices: 2682511--2682543 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2682501 ATGAGTGAGC
2682511 AAAAA-GAAAAAA-AAA
1 AAAAAGGAAAAAAGAAA
2682526 AAAAAGGAAAAAAGAAA
1 AAAAAGGAAAAAAGAAA
2682543 A
1 A
2682544 TGTCACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAGGAAAAAAGAAA
Found at i:2700057 original size:12 final size:11
Alignment explanation
Indices: 2700040--2700073 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2700030 TTTAGTTACA
*
2700040 TTTTTCCATTT
1 TTTTTTCATTT
*
2700051 TTTTTTCTTTT
1 TTTTTTCATTT
2700062 TTTTTTCATTT
1 TTTTTTCATTT
2700073 T
1 T
2700074 GGTACAGCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:2714922 original size:5 final size:5
Alignment explanation
Indices: 2714912--2714938 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2714902 TCAAGACTTG
2714912 GGTTA GGTTA GGTTA GGTTA GGTTA GG
1 GGTTA GGTTA GGTTA GGTTA GGTTA GG
2714939 GGGGACTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (5 bp):
GGTTA
Found at i:2715185 original size:65 final size:65
Alignment explanation
Indices: 2715081--2715208 Score: 202
Period size: 65 Copynumber: 2.0 Consensus size: 65
2715071 AATCAAGTGA
* * * *
2715081 ATATCGTGAAATAGATAATTAATATGATTATGTTTCATTTCAAATCAAGAGAACCATTTATATAT
1 ATATCGTCAAACAGATAATTAATATAATTATGTTTCATTTCAAATCAAAAGAACCATTTATATAT
* *
2715146 ATATCGTCAAACAGATAATTAGTATAATTATGTTTCATTTCAAATCAAAAGAACTATTTATAT
1 ATATCGTCAAACAGATAATTAATATAATTATGTTTCATTTCAAATCAAAAGAACCATTTATAT
2715209 TAGTTGAGAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.38
Consensus pattern (65 bp):
ATATCGTCAAACAGATAATTAATATAATTATGTTTCATTTCAAATCAAAAGAACCATTTATATAT
Found at i:2716966 original size:25 final size:25
Alignment explanation
Indices: 2716920--2716967 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
2716910 TAGCTTAATT
* ** *
2716920 TTTATAAGATGTAAGTAGCTCAACA
1 TTTATAAAATGTAAACAACTCAACA
2716945 TTTATAAAATGTAAACAACTCAA
1 TTTATAAAATGTAAACAACTCAA
2716968 TTTCTATAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (25 bp):
TTTATAAAATGTAAACAACTCAACA
Found at i:2717782 original size:26 final size:26
Alignment explanation
Indices: 2717753--2717802 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
2717743 GTAAAGTTGT
2717753 TTTAACTCTAAATAAAAGTAGATTGC
1 TTTAACTCTAAATAAAAGTAGATTGC
* * *
2717779 TTTAACTTTAACTAGAAGTAGATT
1 TTTAACTCTAAATAAAAGTAGATT
2717803 TAAATCCTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (26 bp):
TTTAACTCTAAATAAAAGTAGATTGC
Found at i:2720797 original size:14 final size:14
Alignment explanation
Indices: 2720780--2720810 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
2720770 ATAAAAAAAC
2720780 AAAAAAGAAGAGAGA
1 AAAAAAG-AGAGAGA
2720795 AAAAAAGAGAGAGA
1 AAAAAAGAGAGAGA
2720809 AA
1 AA
2720811 GAGGTGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAAAAGAGAGAGA
Found at i:2721097 original size:35 final size:35
Alignment explanation
Indices: 2721051--2721122 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
2721041 TTAGAGACAC
2721051 CATGACCCTGGTTTCAATCTATACTCTATGAACTT
1 CATGACCCTGGTTTCAATCTATACTCTATGAACTT
* * *
2721086 CATGACCCTGGTTTCAATCTATTCTGTTTGAACTT
1 CATGACCCTGGTTTCAATCTATACTCTATGAACTT
2721121 CA
1 CA
2721123 GTTCTAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (35 bp):
CATGACCCTGGTTTCAATCTATACTCTATGAACTT
Found at i:2722369 original size:13 final size:13
Alignment explanation
Indices: 2722353--2722385 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2722343 ATATTAAAAA
*
2722353 AATATATTTATTT
1 AATATATTTATTG
2722366 AATATATTTATTG
1 AATATATTTATTG
2722379 AATATAT
1 AATATAT
2722386 GAAAATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (13 bp):
AATATATTTATTG
Found at i:2734249 original size:2 final size:2
Alignment explanation
Indices: 2734242--2734274 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2734232 CAAATTATTA
2734242 AT AT AT 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 AT AT AT A
2734275 CACATCTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2734371 original size:18 final size:19
Alignment explanation
Indices: 2734348--2734389 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
2734338 AGGGGAAAAA
2734348 AAACAC-AGCAATACACAT
1 AAACACAAGCAATACACAT
*
2734366 AAACACATAGTAATACACAT
1 AAACACA-AGCAATACACAT
2734386 AAAC
1 AAAC
2734390 GTGATAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.57, C:0.24, G:0.05, T:0.14
Consensus pattern (19 bp):
AAACACAAGCAATACACAT
Found at i:2737196 original size:7 final size:7
Alignment explanation
Indices: 2737184--2737208 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2737174 AAAACACAAA
2737184 CAGCAAT
1 CAGCAAT
2737191 CAGCAAT
1 CAGCAAT
2737198 CAGCAAT
1 CAGCAAT
2737205 CAGC
1 CAGC
2737209 TATGCACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.32, G:0.16, T:0.12
Consensus pattern (7 bp):
CAGCAAT
Found at i:2750517 original size:33 final size:31
Alignment explanation
Indices: 2750461--2750525 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 31
2750451 ATTATATAAA
*
2750461 TTTTAATTTTTATATTTTATTTTATTTTAAT
1 TTTTAATTCTTATATTTTATTTTATTTTAAT
*
2750492 TTTTTATTCTTATATTATATATTTTATTTTAAT
1 TTTTAATTCTTATATT-T-TATTTTATTTTAAT
2750525 T
1 T
2750526 ATAACATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 14 0.47
32 1 0.03
33 15 0.50
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTTAATTCTTATATTTTATTTTATTTTAAT
Found at i:2750528 original size:54 final size:55
Alignment explanation
Indices: 2750411--2750528 Score: 153
Period size: 54 Copynumber: 2.2 Consensus size: 55
2750401 TTTTTATAAT
2750411 TTTTTATATTATATATTTTATTTTAATTTATTTTATCTATATTATATAAATTTTAA
1 TTTTTATATTATATATTTTATTTTAATTTATTTTATCTATATTATAT-AATTTTAA
2750467 TTTTTATATT-T-TATTTTATTTTAA-TT-TTTTATTCTTATATTATAT-ATTTT-A
1 TTTTTATATTATATATTTTATTTTAATTTATTTTA-TC-TATATTATATAATTTTAA
2750518 -TTTTA-ATTATA
1 TTTTTATATTATA
2750529 ACATTATAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
49 3 0.05
50 6 0.10
51 1 0.02
52 10 0.17
53 4 0.07
54 23 0.40
55 1 0.02
56 10 0.17
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (55 bp):
TTTTTATATTATATATTTTATTTTAATTTATTTTATCTATATTATATAATTTTAA
Found at i:2751249 original size:2 final size:2
Alignment explanation
Indices: 2751244--2751276 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2751234 AGAGAGAGAG
2751244 AT AT AT 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 AT AT AT A
2751277 GTATGAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2755751 original size:14 final size:14
Alignment explanation
Indices: 2755732--2755759 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2755722 TCAATTCTTT
2755732 GGATAATTCAATTA
1 GGATAATTCAATTA
2755746 GGATAATTCAATTA
1 GGATAATTCAATTA
2755760 TTAGAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
GGATAATTCAATTA
Found at i:2757716 original size:13 final size:13
Alignment explanation
Indices: 2757698--2757722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2757688 TGCACATATG
2757698 AATGATTATATTA
1 AATGATTATATTA
2757711 AATGATTATATT
1 AATGATTATATT
2757723 TGCTAATATT
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AATGATTATATTA
Found at i:2760190 original size:31 final size:31
Alignment explanation
Indices: 2760153--2760219 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
2760143 TTTAACTTAA
2760153 TTTTTTTAATATATTTGAAGCTAATGATCTT
1 TTTTTTTAATATATTTGAAGCTAATGATCTT
2760184 TTTTTTTAATATATTTGAAGCTAATGATCTT
1 TTTTTTTAATATATTTGAAGCTAATGATCTT
2760215 TTTTT
1 TTTTT
2760220 ATTTTTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (31 bp):
TTTTTTTAATATATTTGAAGCTAATGATCTT
Found at i:2760396 original size:14 final size:14
Alignment explanation
Indices: 2760377--2760410 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2760367 TGATTTGATG
2760377 TTATTTGTTCAAAA
1 TTATTTGTTCAAAA
*
2760391 TTATTTGTTGAAAA
1 TTATTTGTTCAAAA
*
2760405 CTATTT
1 TTATTT
2760411 ATTGTTGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (14 bp):
TTATTTGTTCAAAA
Found at i:2760474 original size:78 final size:78
Alignment explanation
Indices: 2760326--2760474 Score: 217
Period size: 78 Copynumber: 1.9 Consensus size: 78
2760316 TGCGTTCAAG
* * * *
2760326 ACTATTTATTGTTGTTTTTATCCATTGTTGGAGATTATTAATGATTTGATGTTATTTGTTCAAAA
1 ACTATTTATTGTTGTTTTTATCCATGGTTGAAGACTATTAATGATTTGATGTTATTTGCTCAAAA
*
2760391 TTATTTGTTGAAA
66 CTATTTGTTGAAA
* * * *
2760404 ACTATTTATTGTTGTTTTTATCCATGGTTGAATACTGTTAATGATTTGTTGTTATTTGCTCAAGA
1 ACTATTTATTGTTGTTTTTATCCATGGTTGAAGACTATTAATGATTTGATGTTATTTGCTCAAAA
2760469 CTATTT
66 CTATTT
2760475 ATTTTTGTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 62 1.00
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.52
Consensus pattern (78 bp):
ACTATTTATTGTTGTTTTTATCCATGGTTGAAGACTATTAATGATTTGATGTTATTTGCTCAAAA
CTATTTGTTGAAA
Found at i:2760925 original size:17 final size:18
Alignment explanation
Indices: 2760888--2760935 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2760878 AAAAATAAAT
*
2760888 AAAAAGACAAAAGAGAAG
1 AAAAAGAAAAAAGAGAAG
* *
2760906 AAAAAGAGAAAAG-GAGG
1 AAAAAGAAAAAAGAGAAG
*
2760923 AAATAGAAAAAAG
1 AAAAAGAAAAAAG
2760936 TGTAGAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.71, C:0.02, G:0.25, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAAGAGAAG
Found at i:2761112 original size:16 final size:15
Alignment explanation
Indices: 2761087--2761116 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2761077 TTAGCGGTGC
2761087 ATTTTATTATTATTT
1 ATTTTATTATTATTT
2761102 ATTTATATTATTATT
1 ATTT-TATTATTATT
2761117 AAATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATTATTATTT
Found at i:2768501 original size:2 final size:2
Alignment explanation
Indices: 2768496--2768531 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2768486 ACACACATAC
* *
2768496 AT AT AT AT AC AT AC 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
2768532 TCTCATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2768507 original size:14 final size:14
Alignment explanation
Indices: 2768490--2768531 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
2768480 ATACATACAC
2768490 ACATACATATATAT
1 ACATACATATATAT
2768504 ACATACATATATAT
1 ACATACATATATAT
* *
2768518 ATATATATATATAT
1 ACATACATATATAT
2768532 TCTCATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
ACATACATATATAT
Found at i:2768519 original size:18 final size:18
Alignment explanation
Indices: 2768477--2768522 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2768467 GCTTTCTTTT
*
2768477 CATATACATACACACATA
1 CATATATATACACACATA
*
2768495 CATATATATACATACATA
1 CATATATATACACACATA
*
2768513 TATATATATA
1 CATATATATA
2768523 TATATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (18 bp):
CATATATATACACACATA
Found at i:2771150 original size:35 final size:35
Alignment explanation
Indices: 2771051--2771165 Score: 101
Period size: 35 Copynumber: 3.3 Consensus size: 35
2771041 TCTACTTGTA
**
2771051 TTAGTTGTTCCATATAGAA-TAATGCTTCA-TTTATT
1 TTAGTTGTTCCACGT-GAAGTAATGCTTCACTTTA-T
* * **
2771086 TTAATTGTTCCATGTGAAGTAATAATTCACTTTAT
1 TTAGTTGTTCCACGTGAAGTAATGCTTCACTTTAT
* *
2771121 TTAGTTGTTCCGCGTGAAGTAGTGCTTCACTTGTA-
1 TTAGTTGTTCCACGTGAAGTAATGCTTCACTT-TAT
*
2771156 ATAGTTGTTC
1 TTAGTTGTTC
2771166 TCATTATTCT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 3 0.05
35 57 0.86
36 6 0.09
ACGTcount: A:0.25, C:0.13, G:0.17, T:0.45
Consensus pattern (35 bp):
TTAGTTGTTCCACGTGAAGTAATGCTTCACTTTAT
Found at i:2773876 original size:4 final size:4
Alignment explanation
Indices: 2773867--2773897 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2773857 TTAAGGGATG
2773867 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTT
2773898 CACCGGTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
CTTT
Found at i:2775000 original size:6 final size:7
Alignment explanation
Indices: 2774984--2775008 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2774974 TTAATCATCC
2774984 AAAAATA
1 AAAAATA
2774991 AAAAATA
1 AAAAATA
2774998 AAAAATA
1 AAAAATA
2775005 AAAA
1 AAAA
2775009 GAATTCTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2781484 original size:16 final size:16
Alignment explanation
Indices: 2781459--2781505 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
2781449 GAATCAAGTT
2781459 ATTTTGAATTTAAATC
1 ATTTTGAATTTAAATC
* *
2781475 ATTTTAAATTTCAATC
1 ATTTTGAATTTAAATC
*
2781491 ATTTCGAATTTAAAT
1 ATTTTGAATTTAAAT
2781506 TCAAATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (16 bp):
ATTTTGAATTTAAATC
Found at i:2782608 original size:20 final size:20
Alignment explanation
Indices: 2782572--2782609 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2782562 GTAAATGAAA
*
2782572 AGATTAAATATAGAAAAAGG
1 AGATTAAATATAAAAAAAGG
2782592 AGATATAAA-ATAAAAAAA
1 AGAT-TAAATATAAAAAAA
2782610 TTAATAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.18
Consensus pattern (20 bp):
AGATTAAATATAAAAAAAGG
Found at i:2785959 original size:2 final size:2
Alignment explanation
Indices: 2785952--2785992 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2785942 CCACTAGCAC
*
2785952 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2785993 CACATTGATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2785997 original size:10 final size:10
Alignment explanation
Indices: 2785956--2785997 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
2785946 TAGCACATAT
*
2785956 ATATATATAT
1 ATATATATAC
*
2785966 ATATATATAT
1 ATATATATAC
2785976 ATATATATAC
1 ATATATATAC
*
2785986 ATATATACAC
1 ATATATATAC
2785996 AT
1 AT
2785998 TGATGATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATAC
Found at i:2787631 original size:22 final size:22
Alignment explanation
Indices: 2787596--2787639 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2787586 ATTTATAATT
*
2787596 TAATTAAAATATTAATAATTTA
1 TAATTAAAACATTAATAATTTA
* *
2787618 TAATTTAAACATTAATATTTTA
1 TAATTAAAACATTAATAATTTA
2787640 GTATAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TAATTAAAACATTAATAATTTA
Found at i:2787650 original size:25 final size:25
Alignment explanation
Indices: 2787616--2787664 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2787606 ATTAATAATT
2787616 TATAATTTAAACATTAATATTTTAG
1 TATAATTTAAACATTAATATTTTAG
**
2787641 TATAATTTAATTATTAATATTTTA
1 TATAATTTAAACATTAATATTTTA
2787665 AATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (25 bp):
TATAATTTAAACATTAATATTTTAG
Found at i:2787675 original size:15 final size:15
Alignment explanation
Indices: 2787646--2787679 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2787636 TTTAGTATAA
*
2787646 TTTAATTATTAATAT
1 TTTAAATATTAATAT
2787661 TTTAAATATTAATAT
1 TTTAAATATTAATAT
2787676 TTTA
1 TTTA
2787680 TTTATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTAAATATTAATAT
Found at i:2787863 original size:16 final size:16
Alignment explanation
Indices: 2787775--2787863 Score: 56
Period size: 16 Copynumber: 5.3 Consensus size: 16
2787765 TTTAATAAAG
*
2787775 AAAACATTAATATTTT
1 AAAATATTAATATTTT
*
2787791 AAAATACTAATATTTT
1 AAAATATTAATATTTT
* *
2787807 AATCATATTAGTA--TT
1 AA-AATATTAATATTTT
* *
2787822 AATAATGTTTAAATTATATAT
1 AA-AAT-ATT-AA-TAT-TTT
2787843 AAAATATTAATATTTT
1 AAAATATTAATATTTT
2787859 AAAAT
1 AAAAT
2787864 TTATAACTAA
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
15 7 0.13
16 25 0.45
17 11 0.20
18 4 0.07
19 2 0.04
20 3 0.05
21 3 0.05
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (16 bp):
AAAATATTAATATTTT
Found at i:2789068 original size:19 final size:20
Alignment explanation
Indices: 2789030--2789091 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 20
2789020 AATGTATATC
*
2789030 ATTAATAAATAATCAAATTAA
1 ATTAATAAAT-ATAAAATTAA
2789051 ATTAATAAAT-TAAAATT-A
1 ATTAATAAATATAAAATTAA
* *
2789069 ATTTATAAAATGTAAAA-TAA
1 ATTAAT-AAATATAAAATTAA
2789089 ATT
1 ATT
2789092 TTAAAATCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 6 0.17
19 11 0.31
20 9 0.25
21 10 0.28
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
ATTAATAAATATAAAATTAA
Found at i:2789096 original size:19 final size:19
Alignment explanation
Indices: 2789048--2789098 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
2789038 ATAATCAAAT
*
2789048 TAAATTAAT-AAATTAAAA
1 TAAATTTATAAAATTAAAA
*
2789066 TTAATTTATAAAATGTAAAA
1 TAAATTTATAAAAT-TAAAA
2789086 TAAATTT-TAAAAT
1 TAAATTTATAAAAT
2789099 CATATGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.25
19 10 0.36
20 11 0.39
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAATTTATAAAATTAAAA
Found at i:2794916 original size:12 final size:12
Alignment explanation
Indices: 2794883--2794916 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2794873 GGTTTGAGGG
2794883 AGAAAGGGAGCA
1 AGAAAGGGAGCA
*
2794895 AAAAAGGGAGCA
1 AGAAAGGGAGCA
*
2794907 AGAAATGGAG
1 AGAAAGGGAG
2794917 ATCGGATAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.38, T:0.03
Consensus pattern (12 bp):
AGAAAGGGAGCA
Found at i:2810016 original size:28 final size:29
Alignment explanation
Indices: 2809970--2810029 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 29
2809960 GTTGTGTAAT
* * *
2809970 AATTTTTTCATTATGACGTGTAAAAACTA
1 AATTTTTTCAATATAACGTATAAAAACTA
*
2809999 AATTTTTT-AATATAACGTATAACAACTA
1 AATTTTTTCAATATAACGTATAAAAACTA
2810027 AAT
1 AAT
2810030 CTTCAACATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (29 bp):
AATTTTTTCAATATAACGTATAAAAACTA
Found at i:2810166 original size:27 final size:28
Alignment explanation
Indices: 2810109--2810185 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
2810099 TGTAACAACG
* **
2810109 TATAATAATTACATTTTTCAATGTGACA
1 TATAATAACTACATTTTTCAACATGACA
* *
2810137 TATAATAACTAAATTTTT-AACATGATA
1 TATAATAACTACATTTTTCAACATGACA
2810164 TATAATAACTACATTTTTCAAC
1 TATAATAACTACATTTTTCAAC
2810186 CAGCCATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.43, C:0.12, G:0.04, T:0.42
Consensus pattern (28 bp):
TATAATAACTACATTTTTCAACATGACA
Found at i:2810276 original size:21 final size:21
Alignment explanation
Indices: 2810246--2810285 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2810236 GAAAAGGAGG
*
2810246 AAAAAGAAAAAACAATAAAGA
1 AAAAAGAAAAAAAAATAAAGA
*
2810267 AAAAATAAAAAAAAATAAA
1 AAAAAGAAAAAAAAATAAA
2810286 AATAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.85, C:0.03, G:0.05, T:0.07
Consensus pattern (21 bp):
AAAAAGAAAAAAAAATAAAGA
Found at i:2810281 original size:10 final size:10
Alignment explanation
Indices: 2810246--2810292 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
2810236 GAAAAGGAGG
*
2810246 AAAAAGAAAA
1 AAAAATAAAA
*
2810256 AACAATAAAGA
1 AAAAATAAA-A
2810267 AAAAATAAAA
1 AAAAATAAAA
2810277 AAAAATAAAA
1 AAAAATAAAA
*
2810287 ATAAAT
1 AAAAAT
2810293 TATATTGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.11
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:2810470 original size:133 final size:136
Alignment explanation
Indices: 2810302--2810576 Score: 398
Period size: 135 Copynumber: 2.0 Consensus size: 136
2810292 TTATATTGAT
* *
2810302 TAATAAATTATTGATGTTTAATAAAAATAAAAATT-AAATATTAA-AAATAAAAAATACAAATGG
1 TAATAAATTATTGATGTTTAATAAAAATAAAAATTAAAAGATTAAGAAATAAAAAATACAAATAG
* * * *
2810365 AGAAAAATTATTCAAAT-ATTAGAATAAAAAATTATATAACTAATTTAAT-ATAACTTACTT-AA
66 AGAAAAATAATCCAAATAATTAAAATAAAAAA-TATATAACTAATTTAATAATAAATTA-TTCAA
2810427 TAATTTAA
129 TAATTTAA
* * *
2810435 TAATAAATTATTGATGTTTAATGAAAATATAAATTAAAAGATTAAGAAATGAAAAATACAAATAG
1 TAATAAATTATTGATGTTTAATAAAAATAAAAATTAAAAGATTAAGAAATAAAAAATACAAATAG
* *
2810500 AGAAAAATAATCCAAATAATTAAAATTAAATATATATAACTAATTTAATAATAAATTATTCAATA
66 AGAAAAATAATCCAAATAATTAAAATAAAAAATATATAACTAATTTAATAATAAATTATTCAATA
2810565 ATTTAA
131 ATTTAA
2810571 TAATAA
1 TAATAA
2810577 CTTAAAAATA
Statistics
Matches: 126, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
133 33 0.26
134 8 0.06
135 51 0.40
136 34 0.27
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (136 bp):
TAATAAATTATTGATGTTTAATAAAAATAAAAATTAAAAGATTAAGAAATAAAAAATACAAATAG
AGAAAAATAATCCAAATAATTAAAATAAAAAATATATAACTAATTTAATAATAAATTATTCAATA
ATTTAA
Found at i:2810574 original size:8 final size:8
Alignment explanation
Indices: 2810514--2810615 Score: 54
Period size: 8 Copynumber: 12.8 Consensus size: 8
2810504 AAATAATCCA
2810514 AATAA-TT
1 AATAATTT
*
2810521 AA-AATTA
1 AATAATTT
*
2810528 AATATATAT
1 AATA-ATTT
2810537 AACTAATTT
1 AA-TAATTT
*
2810546 AATAA-TA
1 AATAATTT
* *
2810553 AATTATTC
1 AATAATTT
2810561 AATAATTT
1 AATAATTT
2810569 AATAATAACTT
1 AATAAT---TT
*
2810580 AAAAATATT
1 AATAAT-TT
2810589 AATAATTT
1 AATAATTT
2810597 -AT-A-TT
1 AATAATTT
2810602 AATAATTT
1 AATAATTT
2810610 AATAAT
1 AATAAT
2810616 AAATTATCGA
Statistics
Matches: 72, Mismatches: 12, Indels: 21
0.69 0.11 0.20
Matches are distributed among these distances:
5 2 0.03
6 5 0.07
7 13 0.18
8 27 0.38
9 16 0.22
10 2 0.03
11 7 0.10
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (8 bp):
AATAATTT
Found at i:2810575 original size:11 final size:11
Alignment explanation
Indices: 2810535--2810617 Score: 66
Period size: 11 Copynumber: 7.6 Consensus size: 11
2810525 TTAAATATAT
2810535 ATAACTAATTTA
1 ATAA-TAATTTA
*
2810547 ATAATAAATTA
1 ATAATAATTTA
*
2810558 TTCAATAATTTA
1 AT-AATAATTTA
*
2810570 ATAATAACTTA
1 ATAATAATTTA
*
2810581 AAAAT-A-TTA
1 ATAATAATTTA
2810590 ATAAT--TTATA
1 ATAATAATT-TA
*
2810600 TTAATAATTTA
1 ATAATAATTTA
2810611 ATAATAA
1 ATAATAA
2810618 ATTATCGATG
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
9 8 0.14
10 7 0.12
11 27 0.47
12 15 0.26
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAATAATTTA
Found at i:2810602 original size:13 final size:13
Alignment explanation
Indices: 2810584--2810622 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2810574 TAACTTAAAA
2810584 ATATTAATAATTT
1 ATATTAATAATTT
2810597 ATATTAATAATTT
1 ATATTAATAATTT
*
2810610 A-A-TAATAAATT
1 ATATTAATAATTT
2810621 AT
1 AT
2810623 CGATGTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 14 0.58
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATTAATAATTT
Found at i:2810835 original size:15 final size:15
Alignment explanation
Indices: 2810806--2810843 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
2810796 ATAAAACTAC
*
2810806 ATATTAATT-TTTTT
1 ATATTATTTATTTTT
*
2810820 ATTTTATTTATTTTT
1 ATATTATTTATTTTT
2810835 ATATTATTT
1 ATATTATTT
2810844 TCACAAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
ATATTATTTATTTTT
Found at i:2811464 original size:16 final size:16
Alignment explanation
Indices: 2811422--2811464 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
2811412 GCTTAAACTT
*
2811422 TTTTATTTTAAATTTA
1 TTTTATTTTAAATTCA
2811438 TTTTAATTTTAAATTCA
1 TTTT-ATTTTAAATTCA
2811455 TTTTATTTTA
1 TTTTATTTTA
2811465 GTAAGAGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTATTTTAAATTCA
Found at i:2816682 original size:4 final size:4
Alignment explanation
Indices: 2816673--2816698 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2816663 CATGTGCATA
2816673 TGGG TGGG TGGG TGGG TGGG TGGG TG
1 TGGG TGGG TGGG TGGG TGGG TGGG TG
2816699 CAGGGATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.73, T:0.27
Consensus pattern (4 bp):
TGGG
Found at i:2829187 original size:37 final size:37
Alignment explanation
Indices: 2829146--2829219 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
2829136 ACCTTGTCGC
* *
2829146 CATGGACCACCCTGCCT-TCTCCTCCGAAGGTGCTTGA
1 CATGGACCACCCTG-CTGTCTCCTCCAAAAGTGCTTGA
* *
2829183 CATGGACCACGCTGCTGTCTTCTCCAAAAGTGCTTGA
1 CATGGACCACCCTGCTGTCTCCTCCAAAAGTGCTTGA
2829220 TATTACTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.06
37 30 0.94
ACGTcount: A:0.19, C:0.34, G:0.22, T:0.26
Consensus pattern (37 bp):
CATGGACCACCCTGCTGTCTCCTCCAAAAGTGCTTGA
Found at i:2829405 original size:333 final size:338
Alignment explanation
Indices: 2828680--2829684 Score: 1420
Period size: 333 Copynumber: 3.0 Consensus size: 338
2828670 CTATATATCC
* * * *
2828680 CTTGCACTGTCCCTAAAATGCTAATCAACACG-CCCTTGTCGCCATGGACCACCTTGCTTCTCTT
1 CTTGCACTCTCCCTAAAACGCTAATCCA-ACGACCCTTGTCGCCATGGACCACCTTGCTTCCCTT
*
2828744 CT-CGAAGGTGCTTGGCATAAACA-CCTACCTGACATCTTCACCCAACCAATTCGATGACGACCT
65 CTCCGAAGGTGCTTGGCATAACCACCCTA-CTGACATCTTCACCCAACCAATTCGATGACGACCT
2828807 TGTCGCCAT-GAGCCACCCTGCC-T-TCCTCCGAAGGTGCTTTGACATGGACCACGCTGCTGTCT
129 TGTCGCCATGGA-CCACCCTGCCTTCTCCTCCGAAGGTGC-TTGACATGGACCACGCTGCTGTCT
2828869 TCTCCAAAAGTGCTTGATA-TACTTGTCACAGAACCATTACTTTCTTTCTCAAAAACTAATTTGG
192 TCTCCAAAAGTGCTTGATATTACTTGTCACAGAACCATTACTTTCTTTCTCAAAAACTAATTT-G
*
2828933 AAAATTGTATGTCATCATTTATAAATTTATTAAGATTTCTCTACTTGTTCGATCAAAGATTTTTA
256 AAAATTGTACGTCATCATTTATAAATTTA-TAAGATTTCTCTACTTGTTCGAT-AAAGATTTTTA
2828998 GATACATTTTAAATTCTCTA
319 GATACATTTTAAATTCTCTA
*
2829018 CTTGCACTCT-CCTTAAACGCTAATCCAACGACGCCTTGTCGCCA-GGA-C-CCTTGCTTCCCTT
1 CTTGCACTCTCCCTAAAACGCTAATCCAACGAC-CCTTGTCGCCATGGACCACCTTGCTTCCCTT
*
2829079 CTCCGATGGTGCTT-GCA-AACCACCCTA-TGACATCTTCACCCAACCAATTCGATGACGACCTT
65 CTCCGAAGGTGCTTGGCATAACCACCCTACTGACATCTTCACCCAACCAATTCGATGACGACCTT
2829141 GTCGCCATGGACCACCCTGCCTTCTCCTCCGAAGGTGCTTGACATGGACCACGCTGCTGTCTTCT
130 GTCGCCATGGACCACCCTGCCTTCTCCTCCGAAGGTGCTTGACATGGACCACGCTGCTGTCTTCT
2829206 CCAAAAGTGCTTGATATTACTTGTCACAGAACCATTACTTTCTTTCTCAAAAACTAATTTGAAAA
195 CCAAAAGTGCTTGATATTACTTGTCACAGAACCATTACTTTCTTTCTCAAAAACTAATTTGAAAA
*
2829271 TTGTACGTCATGATTTATAAATTTATAAGATTTCTCTACTTGTTCGATAACAGATTTTTA-ATAC
260 TTGTACGTCATCATTTATAAATTTATAAGATTTCTCTACTTGTTCGATAA-AGATTTTTAGATAC
**
2829335 ATTTTATTTTCT-TA
324 ATTTTAAATTCTCTA
2829349 CTTGCACTCTCCCTAAAACGCTAATCCAACGACCCTT-TCGCCATGGACCACCTTGCTTCCCTTC
1 CTTGCACTCTCCCTAAAACGCTAATCCAACGACCCTTGTCGCCATGGACCACCTTGCTTCCCTTC
* * *
2829413 TCCGAAGGTGCTTGGCATGAACCACCTTACTGACATCTTCACCCAACCAATTCAACGACGA-CTT
66 TCCGAAGGTGCTTGGCAT-AACCACCCTACTGACATCTTCACCCAACCAATTCGATGACGACCTT
* ** * *
2829477 GTCGCCATGGACC-CCTTGCCTTCCTCCTTTGAAGGTGCTTGACATGGACCACCCTGCTATCTTC
130 GTCGCCATGGACCACCCTGCCTT-CTCCTCCGAAGGTGCTTGACATGGACCACGCTGCTGTCTTC
* * ** * * * *
2829541 TCCAAAAGTGCTTGATATTATTTATCGTAGAATCATTACTTTTTTTTTTCAAAAATTAATTTGAG
194 TCCAAAAGTGCTTGATATTACTTGTCACAGAACCATTAC-TTTCTTTCTCAAAAACTAATTTGA-
* * * *
2829606 AAATTGTACAACATCATCATTTATAAATTTTTTAAAATTTTTCTACTTGTTCGATATATA-ATTT
257 AAATTGT---ACGTCATCATTTATAAA-TTTATAAGATTTCTCTACTTGTTCGATA-A-AGATTT
2829670 TTAGATACATTTTAA
316 TTAGATACATTTTAA
2829685 TTACTTCTTT
Statistics
Matches: 605, Mismatches: 36, Indels: 47
0.88 0.05 0.07
Matches are distributed among these distances:
330 6 0.01
331 19 0.03
332 38 0.06
333 111 0.18
334 81 0.13
335 86 0.14
336 110 0.18
337 68 0.11
338 27 0.04
341 15 0.02
342 32 0.05
343 12 0.02
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (338 bp):
CTTGCACTCTCCCTAAAACGCTAATCCAACGACCCTTGTCGCCATGGACCACCTTGCTTCCCTTC
TCCGAAGGTGCTTGGCATAACCACCCTACTGACATCTTCACCCAACCAATTCGATGACGACCTTG
TCGCCATGGACCACCCTGCCTTCTCCTCCGAAGGTGCTTGACATGGACCACGCTGCTGTCTTCTC
CAAAAGTGCTTGATATTACTTGTCACAGAACCATTACTTTCTTTCTCAAAAACTAATTTGAAAAT
TGTACGTCATCATTTATAAATTTATAAGATTTCTCTACTTGTTCGATAAAGATTTTTAGATACAT
TTTAAATTCTCTA
Found at i:2830176 original size:24 final size:24
Alignment explanation
Indices: 2830149--2830210 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
2830139 ATGCGTGTGA
2830149 GTGCCAGTTGCCGTGTAGGCATGT
1 GTGCCAGTTGCCGTGTAGGCATGT
2830173 GTGCCAGTTGCCGTGTAGGCATGT
1 GTGCCAGTTGCCGTGTAGGCATGT
*
2830197 GTGCCTGTTGCCGT
1 GTGCCAGTTGCCGT
2830211 ATAGCCGTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.10, C:0.23, G:0.37, T:0.31
Consensus pattern (24 bp):
GTGCCAGTTGCCGTGTAGGCATGT
Found at i:2832427 original size:23 final size:24
Alignment explanation
Indices: 2832376--2832427 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
2832366 ATTCAACCTC
*
2832376 AACAAAAGGAGGAAGCCAAAATGAG
1 AACAAAAGGA-GAAGCCAAAATGAA
**
2832401 AACAAAAGGA-AAGCCAAGCTGAA
1 AACAAAAGGAGAAGCCAAAATGAA
2832424 AACA
1 AACA
2832428 CATCCTTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 14 0.58
25 10 0.42
ACGTcount: A:0.58, C:0.15, G:0.23, T:0.04
Consensus pattern (24 bp):
AACAAAAGGAGAAGCCAAAATGAA
Found at i:2832779 original size:18 final size:18
Alignment explanation
Indices: 2832732--2832780 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
2832722 GTGTCTCCAG
* *
2832732 CATAGCCAACATTGCCAT
1 CATAGCCAACGTTGCCAC
*
2832750 CATAGCCGACGTTGCCAC
1 CATAGCCAACGTTGCCAC
*
2832768 CGTAGCCAACGTT
1 CATAGCCAACGTT
2832781 CCTGCCCTCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.35, G:0.18, T:0.20
Consensus pattern (18 bp):
CATAGCCAACGTTGCCAC
Found at i:2835861 original size:2 final size:2
Alignment explanation
Indices: 2835854--2835897 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2835844 ATGTCTTTGA
2835854 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
2835896 AT
1 AT
2835898 TACTAAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2840699 original size:16 final size:16
Alignment explanation
Indices: 2840678--2840711 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2840668 TTGAACTTTG
*
2840678 AAAATAAAAAATAAAA
1 AAAATAAAAAACAAAA
2840694 AAAATAAAAAACAAAA
1 AAAATAAAAAACAAAA
2840710 AA
1 AA
2840712 GAAAGAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAATAAAAAACAAAA
Found at i:2842904 original size:24 final size:25
Alignment explanation
Indices: 2842858--2842921 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
2842848 TATTAAAAAA
*
2842858 TAATATCTAGTAATT-TTATATATTT
1 TAATAT-TAATAATTATTATATATTT
2842883 TAATATTAATAATTATTA-ATATTT
1 TAATATTAATAATTATTATATATTT
*
2842907 AAATATT-AT-ATTATT
1 TAATATTAATAATTATT
2842922 TTTTATCATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 6 0.17
23 2 0.06
24 19 0.53
25 9 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TAATATTAATAATTATTATATATTT
Found at i:2849199 original size:41 final size:41
Alignment explanation
Indices: 2849152--2849246 Score: 190
Period size: 41 Copynumber: 2.3 Consensus size: 41
2849142 AAAATATCAA
2849152 AGTATGAACACGATTCGATTATCCGAAACCCCAAAAAAATT
1 AGTATGAACACGATTCGATTATCCGAAACCCCAAAAAAATT
2849193 AGTATGAACACGATTCGATTATCCGAAACCCCAAAAAAATT
1 AGTATGAACACGATTCGATTATCCGAAACCCCAAAAAAATT
2849234 AGTATGAACACGA
1 AGTATGAACACGA
2849247 CTATATGTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (41 bp):
AGTATGAACACGATTCGATTATCCGAAACCCCAAAAAAATT
Found at i:2850933 original size:4 final size:4
Alignment explanation
Indices: 2850924--2850952 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2850914 TTTGGGTGAT
2850924 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
2850953 AAAAATGATA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2852948 original size:2 final size:2
Alignment explanation
Indices: 2852943--2852978 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2852933 TAAAAAAACT
* *
2852943 TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA GA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2852979 GAACATGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2855138 original size:2 final size:2
Alignment explanation
Indices: 2855131--2855157 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2855121 TTCTCATTGG
2855131 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
2855158 ATCTCTTTAA
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:2860235 original size:28 final size:26
Alignment explanation
Indices: 2860174--2860245 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 26
2860164 TTTTTTAAAA
*
2860174 AATTAAATTTATTTTTATTTTTTATTAC
1 AATT-AATTAATTTTT-TTTTTTATTAC
* *
2860202 ATTTAATTAATTTTTTTATTTTATTTC
1 AATTAATTAATTTTTTT-TTTTATTAC
* *
2860229 GAATTAAATAAATTTTT
1 -AATTAATTAATTTTTT
2860246 ATAATTAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 2 0.06
27 18 0.50
28 16 0.44
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (26 bp):
AATTAATTAATTTTTTTTTTTATTAC
Found at i:2869294 original size:16 final size:15
Alignment explanation
Indices: 2869268--2869306 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
2869258 TTTTATGTTA
2869268 TTTTCTTTTTCCCTT-
1 TTTTCTTTTT-CCTTC
2869283 TTTTCTTATTTCCTTC
1 TTTTCTT-TTTCCTTC
2869299 TTTTCTTT
1 TTTTCTTT
2869307 AGTAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTCTTTTTCCTTC
Found at i:2870446 original size:15 final size:15
Alignment explanation
Indices: 2870428--2870457 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2870418 CTTTGGATAA
2870428 GAGTCCTTTAAATTT
1 GAGTCCTTTAAATTT
2870443 GAGTCCTTTAAATTT
1 GAGTCCTTTAAATTT
2870458 AGAATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
GAGTCCTTTAAATTT
Found at i:2875750 original size:192 final size:197
Alignment explanation
Indices: 2875381--2875934 Score: 744
Period size: 192 Copynumber: 2.8 Consensus size: 197
2875371 ACTTAGCAAA
** * *
2875381 ATATTTCCAGCAAAAGGTCTTGCTGTTGAAGTATTTCCCTATGATGTTAACAATATAAAATCATC
1 ATATTTCTGGCAAAAGGTCTTGCTGTTGAAGTATTTCCATATGATGTTGACAATA-AAAATCATC
2875446 ATTATTTATTATCACATGAAATACC-AATGTGGAGAGGTGATATTTTATAAAATCCTGAAGGCAT
65 ATTATTTATTATCACATGAAATACCAAATGTGGAGAGGTGATATTTTATAAAATCCTGAAGGCAT
* *
2875510 CTACCTGATATTTGAATGATGTTGCCTTTCTCTTCCCCACAACAACAACAAAGAATTGAA-C-TT
130 CTACCTGATATTTGAGTGATGTTGCCTTTCTCTCCCCCACAACAACAACAAAGAATTGAATCATT
2875573 T-C
195 TAC
**
2875575 -TA-TT-TGGCAAAAGGTCTTGCCATTGAAGTATTTCCATATGATGTTGACAATAAAAATTCATC
1 ATATTTCTGGCAAAAGGTCTTGCTGTTGAAGTATTTCCATATGATGTTGACAATAAAAA-TCATC
* * * *
2875637 ATTATTTATTATCACATGAAATACCAAACGTGGAGAGGTGATAATATATAAAATCCTGAGGGCAT
65 ATTATTTATTATCACATGAAATACCAAATGTGGAGAGGTGATATTTTATAAAATCCTGAAGGCAT
* * *
2875702 CTGCCTGCTATTTGAGTGATGTTGCCTTTCTCTCCCCCACAGCAACAACAAAGAATTGAACTTTC
130 CTACCTGATATTTGAGTGATGTTGCCTTTCTCTCCCCCACAACAACAACAAAGAATTGAA---TC
2875767 TATTTAGC
192 -ATTTA-C
*
2875775 AAAATATTTCTGGCAAAAGGTCTTGCTGTTGAAGTATTTCCATATAATGTTGACAATAAAAAATC
1 ---ATATTTCTGGCAAAAGGTCTTGCTGTTGAAGTATTTCCATATGATGTTGACAAT-AAAAATC
* * * *
2875840 AGCATTATTTTTATTATCACCTGAAATACCAAAATGTGGAGAGGTGATATTTTAGAAAGTCCTGA
62 ATCATTA--TTTATTATCACATGAAATACC-AAATGTGGAGAGGTGATATTTTATAAAATCCTGA
*
2875905 AGGCATCTACCTGATATTTGAGTCATGTTG
124 AGGCATCTACCTGATATTTGAGTGATGTTG
2875935 TTTGGGCAGA
Statistics
Matches: 311, Mismatches: 29, Indels: 25
0.85 0.08 0.07
Matches are distributed among these distances:
190 4 0.01
191 72 0.23
192 92 0.30
193 2 0.01
196 1 0.00
198 3 0.01
200 1 0.00
204 2 0.01
205 2 0.01
206 52 0.17
207 5 0.02
208 20 0.06
209 55 0.18
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (197 bp):
ATATTTCTGGCAAAAGGTCTTGCTGTTGAAGTATTTCCATATGATGTTGACAATAAAAATCATCA
TTATTTATTATCACATGAAATACCAAATGTGGAGAGGTGATATTTTATAAAATCCTGAAGGCATC
TACCTGATATTTGAGTGATGTTGCCTTTCTCTCCCCCACAACAACAACAAAGAATTGAATCATTT
AC
Found at i:2884569 original size:13 final size:13
Alignment explanation
Indices: 2884551--2884575 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2884541 AAATTACCTA
2884551 TTTTCTTTATTTC
1 TTTTCTTTATTTC
2884564 TTTTCTTTATTT
1 TTTTCTTTATTT
2884576 TTGTTTTTTC
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTATTTC
Found at i:2896327 original size:17 final size:18
Alignment explanation
Indices: 2896293--2896329 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2896283 CTCATTTCTC
*
2896293 ATTAGTATAAATTAAAAT
1 ATTAGAATAAATTAAAAT
2896311 ATTAGAATAAA-TAAAAT
1 ATTAGAATAAATTAAAAT
2896328 AT
1 AT
2896330 GATCTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
ATTAGAATAAATTAAAAT
Found at i:2898892 original size:17 final size:18
Alignment explanation
Indices: 2898855--2898892 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2898845 AACAATATAA
*
2898855 TCTTTTCAATAATTACAT
1 TCTTTACAATAATTACAT
*
2898873 TCTTTACAAT-ATTACTT
1 TCTTTACAATAATTACAT
2898890 TCT
1 TCT
2898893 CATATTATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (18 bp):
TCTTTACAATAATTACAT
Found at i:2898989 original size:15 final size:15
Alignment explanation
Indices: 2898922--2898990 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
2898912 CAAAGTTACC
2898922 TTTCTAATAATCACA
1 TTTCTAATAATCACA
* ** *
2898937 -TACTTGTAATCATA
1 TTTCTAATAATCACA
*
2898951 TTT-TCAACAATCACA
1 TTTCT-AATAATCACA
2898966 -TTCTCAATAATCACA
1 TTTCT-AATAATCACA
2898981 TTTCTAATAA
1 TTTCTAATAA
2898991 AATACCAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
14 13 0.32
15 23 0.57
16 4 0.10
ACGTcount: A:0.39, C:0.20, G:0.01, T:0.39
Consensus pattern (15 bp):
TTTCTAATAATCACA
Found at i:2917245 original size:15 final size:15
Alignment explanation
Indices: 2917225--2917274 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 15
2917215 ATTTAGAAAG
2917225 TAAAATTAATATTTA
1 TAAAATTAATATTTA
*
2917240 TAAAA-TAAT-TATA
1 TAAAATTAATATTTA
2917253 TTAAAATTAAATATTTA
1 -TAAAATT-AATATTTA
2917270 TAAAA
1 TAAAA
2917275 ATAAAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 3 0.10
14 9 0.31
15 6 0.21
16 8 0.28
17 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATTAATATTTA
Found at i:2917279 original size:16 final size:16
Alignment explanation
Indices: 2917226--2917295 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
2917216 TTTAGAAAGT
*
2917226 AAAATTAATATTTAT-
1 AAAATAAATATTTATA
* *
2917241 AAAATAATTATAT-TA
1 AAAATAAATATTTATA
*
2917256 AAATTAAATATTTATA
1 AAAATAAATATTTATA
*
2917272 AAAATAAA-ATTTTTTA
1 AAAATAAATA-TTTATA
2917288 AAAATAAA
1 AAAATAAA
2917296 AAATATATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
14 1 0.02
15 21 0.48
16 22 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATAAATATTTATA
Found at i:2917296 original size:16 final size:17
Alignment explanation
Indices: 2917239--2917310 Score: 65
Period size: 17 Copynumber: 4.0 Consensus size: 17
2917229 ATTAATATTT
*
2917239 ATAAAATAATTATATTAAA
1 ATAAAAT-ATT-TATAAAA
*
2917258 ATTAAATATTTATAAAA
1 ATAAAATATTTATAAAA
*
2917275 ATAAAAT-TTTTTAAAA
1 ATAAAATATTTATAAAA
2917291 ATAAAAAATATATTATAAAA
1 AT--AAAATAT-TTATAAAA
2917311 TTTTAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
16 10 0.23
17 12 0.27
18 8 0.18
19 7 0.16
20 7 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAATATTTATAAAA
Found at i:2921158 original size:12 final size:12
Alignment explanation
Indices: 2921136--2921169 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2921126 AATAAATTGG
*
2921136 ATATATATGTAT
1 ATATGTATGTAT
*
2921148 GTATGTATGTAT
1 ATATGTATGTAT
2921160 ATATGTATGT
1 ATATGTATGT
2921170 TACAGCACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (12 bp):
ATATGTATGTAT
Found at i:2921446 original size:90 final size:89
Alignment explanation
Indices: 2921326--2921495 Score: 205
Period size: 89 Copynumber: 1.9 Consensus size: 89
2921316 ATTGACTATG
* * * * ** *
2921326 ATGATAAGGGAATAGAAAATCCTTGAAAGAATTTGTAAGGGTTGCCAATTTTGTCTTAAAAAGTA
1 ATGATAAGGAAATAAAAAATCCATGAAAGAAATTGTAA-GAATGCCAATTATGTCTTAAAAAGTA
* *
2921391 ATTGTTGGCTTGCTTTTTGTTTTTA
65 ATTGCTGGCTGGCTTTTTGTTTTTA
** * * *
2921416 ATGATAAGGAAATAAAAAATTGATGAAAGAAATTGTAAGAATGCTAATTATGTCTTTATAAGTAA
1 ATGATAAGGAAATAAAAAATCCATGAAAGAAATTGTAAGAATGCCAATTATGTCTTAAAAAGTAA
2921481 TTGCTGGCTGGCTTT
66 TTGCTGGCTGGCTTT
2921496 GTTTTGTTTA
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
89 34 0.52
90 32 0.48
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.37
Consensus pattern (89 bp):
ATGATAAGGAAATAAAAAATCCATGAAAGAAATTGTAAGAATGCCAATTATGTCTTAAAAAGTAA
TTGCTGGCTGGCTTTTTGTTTTTA
Found at i:2927034 original size:30 final size:29
Alignment explanation
Indices: 2926968--2927041 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 29
2926958 AAAAAAATTT
* **
2926968 TAAATAAAATTTTAT-TTTTTATTATATT
1 TAAATAAATTTTTATATTTTTATTATAAA
* *
2926996 TAATTAAATTTTTATATTTTTATTTTAAAA
1 TAAATAAATTTTTATATTTTTATTAT-AAA
2927026 TAAATAAATTTTTATA
1 TAAATAAATTTTTATA
2927042 ATTAATGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 13 0.34
29 9 0.24
30 16 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TAAATAAATTTTTATATTTTTATTATAAA
Found at i:2927347 original size:30 final size:28
Alignment explanation
Indices: 2927310--2927396 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 28
2927300 TTATTTGATT
* *
2927310 TAAAATAAAAATTTAAAAATTAATTTAA
1 TAAAATAAAAATATAAAAATTTATTTAA
2927338 CTCAAAATAAAAATATAAAAATTTATTTGAA
1 -T-AAAATAAAAATATAAAAATTTATTT-AA
*
2927369 TATAATAAAAATATAAAAATTTATTTAA
1 TAAAATAAAAATATAAAAATTTATTTAA
2927397 ATTTTTTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
28 2 0.04
29 25 0.47
30 24 0.45
31 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (28 bp):
TAAAATAAAAATATAAAAATTTATTTAA
Found at i:2927375 original size:29 final size:29
Alignment explanation
Indices: 2927298--2927394 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 29
2927288 ACTTACGAAT
* *
2927298 ATTTATTTGATTTAAAATAAAAATTTAAAA
1 ATTTATTTGA-ATAAAATAAAAATATAAAA
*
2927328 ATTAATTT-AACTCAAAATAAAAATATAAAA
1 ATTTATTTGAA-T-AAAATAAAAATATAAAA
*
2927358 ATTTATTTGAATATAATAAAAATATAAAA
1 ATTTATTTGAATAAAATAAAAATATAAAA
2927387 ATTTATTT
1 ATTTATTT
2927395 AAATTTTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
29 26 0.44
30 31 0.53
31 2 0.03
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (29 bp):
ATTTATTTGAATAAAATAAAAATATAAAA
Found at i:2933947 original size:37 final size:37
Alignment explanation
Indices: 2933906--2933980 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
2933896 TATAGATTTT
*
2933906 TCCATTATTAAAATTCTTGAGTCTTTGGGAATTTAAA
1 TCCATTATTAAAATTCTTGAGCCTTTGGGAATTTAAA
*
2933943 TCCATTATTAAAGTTCTTGAGCCTTTGGGAATTTAAA
1 TCCATTATTAAAATTCTTGAGCCTTTGGGAATTTAAA
2933980 T
1 T
2933981 GTCTGTGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (37 bp):
TCCATTATTAAAATTCTTGAGCCTTTGGGAATTTAAA
Found at i:2947392 original size:2 final size:2
Alignment explanation
Indices: 2947385--2947415 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2947375 ACATATAAAT
*
2947385 AC AC AC AC AC AC GC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2947416 TATGTATGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2961541 original size:25 final size:27
Alignment explanation
Indices: 2961506--2961555 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
2961496 TAAAAATAAT
2961506 TTTTTCTTAA-CACGGCATGTAACAAC
1 TTTTTCTTAACCACGGCATGTAACAAC
* *
2961532 TTTTT-TTAACCATGTCATGTAACA
1 TTTTTCTTAACCACGGCATGTAACA
2961556 TGCTTTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (27 bp):
TTTTTCTTAACCACGGCATGTAACAAC
Found at i:2961568 original size:79 final size:82
Alignment explanation
Indices: 2961412--2961568 Score: 178
Period size: 79 Copynumber: 2.0 Consensus size: 82
2961402 TTACATGGTA
* * * * * * *
2961412 TGTAACAATAATATTTTTTTTCAACATGGTACGTAATAACTTTTTTTTAACAATAGCGTGTAACT
1 TGTAAAAATAATATTTTTCTTCAACACGGCACGTAACAACTTTTTTTTAACAATAGCATGTAACA
*
2961477 TGTTTTTATACATGACG
66 TGCTTTTATACATGACG
* *
2961494 TGTAAAAATAAT-TTTTTCTT-AACACGGCATGTAACAAC-TTTTTTTAACCAT-GTCATGTAAC
1 TGTAAAAATAATATTTTTCTTCAACACGGCACGTAACAACTTTTTTTTAACAATAG-CATGTAAC
*
2961555 ATGCTTTTGTACAT
65 ATGCTTTTATACAT
2961569 AGCATGCACC
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
78 1 0.02
79 30 0.48
80 14 0.22
81 7 0.11
82 11 0.17
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (82 bp):
TGTAAAAATAATATTTTTCTTCAACACGGCACGTAACAACTTTTTTTTAACAATAGCATGTAACA
TGCTTTTATACATGACG
Found at i:2965629 original size:30 final size:30
Alignment explanation
Indices: 2965593--2965653 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2965583 ATATTTACGG
* * *
2965593 TGTCCAGCTTGTACCGGCAAAACTCAGGAA
1 TGTCCAGCTTGCAACGGCAAAACGCAGGAA
*
2965623 TGTCCAGCTTGCAATGGCAAAACGCAGGAA
1 TGTCCAGCTTGCAACGGCAAAACGCAGGAA
2965653 T
1 T
2965654 CATAATTCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.20
Consensus pattern (30 bp):
TGTCCAGCTTGCAACGGCAAAACGCAGGAA
Found at i:2975032 original size:27 final size:27
Alignment explanation
Indices: 2975002--2975056 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
2974992 TTCAAATTAG
2975002 TAATCATTATTTAG-CTAAAATATAATA
1 TAAT-ATTATTTAGACTAAAATATAATA
* *
2975029 TAATATTTTTTAGACTAATATATAATA
1 TAATATTATTTAGACTAAAATATAATA
2975056 T
1 T
2975057 GTACACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (27 bp):
TAATATTATTTAGACTAAAATATAATA
Found at i:2975359 original size:66 final size:62
Alignment explanation
Indices: 2975286--2975478 Score: 200
Period size: 57 Copynumber: 3.0 Consensus size: 62
2975276 AGAGAAAAAA
2975286 AATTATTTGATTGATTCACGGAAAAAAAGAATATAGAAGAAGAGTTTTTCTAATTTGATGAATGA
1 AATTATTTGATTGATTCAC--AAAAAAAGAA-ATAGAA-AAGAGTTTTTCTAATTTGATGAATGA
2975351 T
62 T
* *
2975352 AATTATTTGATTGATT--C-AAAAAA-AAAGAG-AAAGAGTTTTTCTAATTT-ACTAAATGAT
1 AATTATTTGATTGATTCACAAAAAAAGAAATAGAAAAGAGTTTTTCTAATTTGA-TGAATGAT
* * * *
2975409 AATTATTTGATTGGTTCACACAAAAAAAGAGAATGAGAAAAAAGGTATTTCCAATTTGATGAATG
1 AATTATTTGATTGATT--CACAAAAAAAGA-AAT-AGAAAAGA-GTTTTTCTAATTTGATGAATG
2975474 AT
61 AT
2975476 AAT
1 AAT
2975479 CTTTATTCTT
Statistics
Matches: 107, Mismatches: 8, Indels: 23
0.78 0.06 0.17
Matches are distributed among these distances:
56 1 0.01
57 39 0.36
58 1 0.01
59 3 0.03
60 2 0.02
61 7 0.07
62 6 0.06
63 1 0.01
64 3 0.03
65 2 0.02
66 20 0.19
67 21 0.20
68 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.34
Consensus pattern (62 bp):
AATTATTTGATTGATTCACAAAAAAAGAAATAGAAAAGAGTTTTTCTAATTTGATGAATGAT
Found at i:2986873 original size:11 final size:11
Alignment explanation
Indices: 2986836--2986871 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
2986826 CATTACTCTT
2986836 CTCCCCTTCTC
1 CTCCCCTTCTC
2986847 CTCCCCTT-TC
1 CTCCCCTTCTC
*
2986857 CTCCTCTTCTC
1 CTCCCCTTCTC
2986868 CTCC
1 CTCC
2986872 TCCTCCTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (11 bp):
CTCCCCTTCTC
Found at i:2995071 original size:19 final size:19
Alignment explanation
Indices: 2995035--2995072 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2995025 ATATCTCAAA
*
2995035 AAAATTGTTAAATTATTTT
1 AAAATTGTTAAATAATTTT
2995054 AAAATT-TTAAATAAATTTT
1 AAAATTGTTAAAT-AATTTT
2995073 TATTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
AAAATTGTTAAATAATTTT
Found at i:2996259 original size:20 final size:21
Alignment explanation
Indices: 2996236--2996276 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2996226 GTTTAACTAT
*
2996236 TTAAATT-TAATATGATTTTA
1 TTAAATTATAATATAATTTTA
2996256 TTAAATTATAATATAATTTTA
1 TTAAATTATAATATAATTTTA
2996277 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTAAATTATAATATAATTTTA
Found at i:3032484 original size:23 final size:23
Alignment explanation
Indices: 3032458--3032528 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
3032448 TGCAATAGCT
3032458 TCTTTCCTATTAATTCAATAATA
1 TCTTTCCTATTAATTCAATAATA
* * *
3032481 TCTTT--TAGTGAGT-AA-AACCT-
1 TCTTTCCTATTAATTCAATAA--TA
3032501 TCTTTCCTATTAATTCAATAATA
1 TCTTTCCTATTAATTCAATAATA
3032524 TCTTT
1 TCTTT
3032529 TAGTGAGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 2 0.06
20 7 0.20
21 6 0.17
22 6 0.17
23 12 0.34
24 2 0.06
ACGTcount: A:0.31, C:0.17, G:0.04, T:0.48
Consensus pattern (23 bp):
TCTTTCCTATTAATTCAATAATA
Found at i:3032503 original size:43 final size:43
Alignment explanation
Indices: 3032456--3032544 Score: 178
Period size: 43 Copynumber: 2.1 Consensus size: 43
3032446 TCTGCAATAG
3032456 CTTCTTTCCTATTAATTCAATAATATCTTTTAGTGAGTAAAAC
1 CTTCTTTCCTATTAATTCAATAATATCTTTTAGTGAGTAAAAC
3032499 CTTCTTTCCTATTAATTCAATAATATCTTTTAGTGAGTAAAAC
1 CTTCTTTCCTATTAATTCAATAATATCTTTTAGTGAGTAAAAC
3032542 CTT
1 CTT
3032545 TCTTATGTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (43 bp):
CTTCTTTCCTATTAATTCAATAATATCTTTTAGTGAGTAAAAC
Found at i:3037055 original size:15 final size:14
Alignment explanation
Indices: 3037035--3037080 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
3037025 TAATTTTTAT
3037035 TAAAAAGATTAAAAA
1 TAAAAA-ATTAAAAA
3037050 TAAAAAATTAAAAA
1 TAAAAAATTAAAAA
3037064 TTAAAAAATTTAAAAA
1 -TAAAAAA-TTAAAAA
3037080 T
1 T
3037081 TAATATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.28
15 14 0.48
16 7 0.24
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (14 bp):
TAAAAAATTAAAAA
Found at i:3037070 original size:16 final size:16
Alignment explanation
Indices: 3037033--3037083 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
3037023 GTTAATTTTT
*
3037033 ATTAAAAAGATTAAAA
1 ATTAAAAAAATTAAAA
3037049 A-T-AAAAAATTAAAA
1 ATTAAAAAAATTAAAA
*
3037063 ATTAAAAAATTTAAAA
1 ATTAAAAAAATTAAAA
3037079 ATTAA
1 ATTAA
3037084 TATATTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.39
15 2 0.06
16 17 0.55
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
ATTAAAAAAATTAAAA
Found at i:3037078 original size:7 final size:7
Alignment explanation
Indices: 3037037--3037083 Score: 58
Period size: 7 Copynumber: 6.3 Consensus size: 7
3037027 ATTTTTATTA
3037037 AAAAGATT
1 AAAA-ATT
*
3037045 AAAAATA
1 AAAAATT
3037052 AAAAATT
1 AAAAATT
3037059 AAAAATT
1 AAAAATT
3037066 AAAAAATTT
1 -AAAAA-TT
3037075 AAAAATT
1 AAAAATT
3037082 AA
1 AA
3037084 TATATTAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 19 0.54
8 14 0.40
9 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:3037893 original size:14 final size:14
Alignment explanation
Indices: 3037874--3037920 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3037864 GATGGTTCGT
3037874 AAAAATTTAAAGAA
1 AAAAATTTAAAGAA
*
3037888 AAAAATTT----AT
1 AAAAATTTAAAGAA
3037898 AAAAATTTAAAGAA
1 AAAAATTTAAAGAA
3037912 AAAAATTTA
1 AAAAATTTA
3037921 TAAAAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
10 9 0.33
14 18 0.67
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (14 bp):
AAAAATTTAAAGAA
Found at i:3037905 original size:24 final size:24
Alignment explanation
Indices: 3037873--3037932 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
3037863 TGATGGTTCG
3037873 TAAAAATTTAAAGAAAAAAATTTA
1 TAAAAATTTAAAGAAAAAAATTTA
3037897 TAAAAATTTAAAGAAAAAAATTTA
1 TAAAAATTTAAAGAAAAAAATTTA
3037921 TAAAAATTTAAA
1 TAAAAATTTAAA
3037933 ATATATAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (24 bp):
TAAAAATTTAAAGAAAAAAATTTA
Found at i:3049976 original size:72 final size:72
Alignment explanation
Indices: 3049859--3050000 Score: 248
Period size: 72 Copynumber: 2.0 Consensus size: 72
3049849 ATCTTCTTAC
* *
3049859 GTCCACCACTGAGCGTACTTCATTTGTACATCTAGTTGATCATCCCATCAACATAACCACCTAAA
1 GTCCACCACTGAGCCTACTTCATTTATACATCTAGTTGATCATCCCATCAACATAACCACCTAAA
3049924 GCTACAT
66 GCTACAT
* *
3049931 GTCCACTACTGAGCCTACTTCATTTATACATCTAGTTGATCATCCCATTAACATAACCACCTAAA
1 GTCCACCACTGAGCCTACTTCATTTATACATCTAGTTGATCATCCCATCAACATAACCACCTAAA
3049996 GCTAC
66 GCTAC
3050001 TTCACCTGCC
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.31, C:0.30, G:0.10, T:0.29
Consensus pattern (72 bp):
GTCCACCACTGAGCCTACTTCATTTATACATCTAGTTGATCATCCCATCAACATAACCACCTAAA
GCTACAT
Found at i:3053673 original size:16 final size:17
Alignment explanation
Indices: 3053654--3053688 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3053644 ATGAATAAAA
3053654 AATAAAATTATTTT-TT
1 AATAAAATTATTTTATT
*
3053670 AATAATATTATTTTATT
1 AATAAAATTATTTTATT
3053687 AA
1 AA
3053689 ATTAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATAAAATTATTTTATT
Found at i:3057369 original size:3 final size:3
Alignment explanation
Indices: 3057361--3057391 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3057351 TTTTACTACA
3057361 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3057392 TGCTCTGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3060548 original size:2 final size:2
Alignment explanation
Indices: 3060504--3060531 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3060494 ACAAATTAGG
3060504 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
3060532 GTCACTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3061624 original size:2 final size:2
Alignment explanation
Indices: 3061617--3061652 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3061607 CTGTATTCTT
3061617 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
3061653 AACGTTGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3062026 original size:21 final size:22
Alignment explanation
Indices: 3062002--3062073 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 22
3061992 CACGTTGTAC
3062002 ACTA-TCAAATGTTACTACTCT
1 ACTATTCAAATGTTACTACTCT
** *
3062023 ACTATTCAAAACTTAC-AC-CC
1 ACTATTCAAATGTTACTACTCT
*
3062043 ACTACTC-AATGTTACTACTCT
1 ACTATTCAAATGTTACTACTCT
3062064 ACTATTCAAA
1 ACTATTCAAA
3062074 ATTTACACCC
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 6 0.15
20 9 0.23
21 13 0.33
22 11 0.28
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (22 bp):
ACTATTCAAATGTTACTACTCT
Found at i:3062051 original size:20 final size:20
Alignment explanation
Indices: 3062023--3062092 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
3062013 TTACTACTCT
*
3062023 ACTATTCAAAACTTACACCC
1 ACTACTCAAAACTTACACCC
** *
3062043 ACTACTC-AATGTTACTACTCT
1 ACTACTCAAAACTTAC-AC-CC
* *
3062064 ACTATTCAAAATTTACACCC
1 ACTACTCAAAACTTACACCC
3062084 ACTACTCAA
1 ACTACTCAA
3062093 TTATATGATC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 6 0.16
20 17 0.45
21 9 0.24
22 6 0.16
ACGTcount: A:0.37, C:0.31, G:0.01, T:0.30
Consensus pattern (20 bp):
ACTACTCAAAACTTACACCC
Found at i:3062054 original size:41 final size:41
Alignment explanation
Indices: 3062001--3062093 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
3061991 ACACGTTGTA
3062001 CACTA-TCAAATGTTACTACTCTACTATTCAAAACTTACACC
1 CACTACTC-AATGTTACTACTCTACTATTCAAAACTTACACC
*
3062042 CACTACTCAATGTTACTACTCTACTATTCAAAATTTACACC
1 CACTACTCAATGTTACTACTCTACTATTCAAAACTTACACC
3062083 CACTACTCAAT
1 CACTACTCAAT
3062094 TATATGATCA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 48 0.96
42 2 0.04
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.32
Consensus pattern (41 bp):
CACTACTCAATGTTACTACTCTACTATTCAAAACTTACACC
Found at i:3071395 original size:12 final size:12
Alignment explanation
Indices: 3071361--3071395 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3071351 ATTTTTTTTG
*
3071361 TATATATTAGTA
1 TATATATTATTA
*
3071373 TATATAATATTA
1 TATATATTATTA
3071385 TATATATTATT
1 TATATATTATT
3071396 TTTAAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (12 bp):
TATATATTATTA
Found at i:3071729 original size:22 final size:22
Alignment explanation
Indices: 3071704--3071763 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
3071694 TAGGTAATTA
3071704 TAATTTTTATTTTATTATTTTT
1 TAATTTTTATTTTATTATTTTT
* *
3071726 TAATTCTTATTTTTTTATTTTT
1 TAATTTTTATTTTATTATTTTT
*
3071748 TTATTTATATATTTTA
1 TAATTT-T-TATTTTA
3071764 GAGATGTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 24 0.77
23 1 0.03
24 6 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
TAATTTTTATTTTATTATTTTT
Done.