Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 138 of 143
Found at i:40878286 original size:31 final size:32
Alignment explanation
Indices: 40878239--40878318 Score: 110
Period size: 31 Copynumber: 2.5 Consensus size: 32
40878229 AATTTTAAGT
40878239 TTTATTTAGATTTAAATTTA-TCTTAAATTTAAA
1 TTTATTTA-ATTTAAATTTACT-TTAAATTTAAA
40878272 TTTATTT-ATTTAAATTTACTTTAAATTTAAA
1 TTTATTTAATTTAAATTTACTTTAAATTTAAA
*
40878303 TTTAATTAAATTTAAA
1 TTT-ATTTAATTTAAA
40878319 AATAATATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
31 25 0.58
32 4 0.09
33 14 0.33
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (32 bp):
TTTATTTAATTTAAATTTACTTTAAATTTAAA
Found at i:40878309 original size:11 final size:11
Alignment explanation
Indices: 40878215--40878318 Score: 67
Period size: 11 Copynumber: 9.5 Consensus size: 11
40878205 AACTTTGATT
*
40878215 TTTAAGTTTAA
1 TTTAAATTTAA
* *
40878226 ATTAATTTTAA
1 TTTAAATTTAA
*
40878237 GTTT-TATTTAGA
1 -TTTAAATTTA-A
40878249 TTTAAATTT-A
1 TTTAAATTTAA
40878259 TCTTAAATTTAAA
1 T-TTAAATTT-AA
40878272 TTT--ATTT-A
1 TTTAAATTTAA
*
40878280 TTTAAATTTAC
1 TTTAAATTTAA
40878291 TTTAAATTTAAA
1 TTTAAATTT-AA
*
40878303 TTT-AATTAAA
1 TTTAAATTTAA
40878313 TTTAAA
1 TTTAAA
40878319 AATAATATTA
Statistics
Matches: 73, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
8 4 0.05
10 15 0.21
11 39 0.53
12 13 0.18
13 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:40880308 original size:30 final size:30
Alignment explanation
Indices: 40880272--40880642 Score: 475
Period size: 30 Copynumber: 12.4 Consensus size: 30
40880262 AAATTGTCCA
40880272 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
40880302 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
40880332 AAAATTATATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* ** *
40880362 AAAATTACATTTCGACCTTAAAAC-TTTCTA
1 AAAATTACATTTTGACCCCAAAACTTTTC-C
40880392 AAAATTACATTTTGACCCC-AAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
40880421 AAAATTACATTTTAACCCCAAAAC-TTTCTA
1 AAAATTACATTTTGACCCCAAAACTTTTC-C
* *
40880451 AAAATTACATTTTGATCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* *
40880481 AAAATTACATTTTAACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
40880511 AAAATTACATTTTGACCCCAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
*
40880541 AAAATTACATTTTGACCCTAAAACTTTTCC
1 AAAATTACATTTTGACCCCAAAACTTTTCC
* * *
40880571 AAAATCATATTTTGACCCCAAAA--TTTCAAA
1 AAAATTACATTTTGACCCCAAAACTTTTC--C
* * * *
40880601 AAAATTGCATTTTTACCCCGAAAC-TTTCA
1 AAAATTACATTTTGACCCCAAAACTTTTCC
40880630 AAAATTACCATTT
1 AAAATTA-CATTT
40880643 CACCCTCAAA
Statistics
Matches: 299, Mismatches: 33, Indels: 18
0.85 0.09 0.05
Matches are distributed among these distances:
28 4 0.01
29 37 0.12
30 250 0.84
31 8 0.03
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCAAAACTTTTCC
Found at i:40886701 original size:30 final size:29
Alignment explanation
Indices: 40886613--40886867 Score: 281
Period size: 30 Copynumber: 8.8 Consensus size: 29
40886603 ACTCGAGGGC
*
40886613 AAAATGGTAATTTTTGTAAGTTTTGAGGT-
1 AAAAT-GTAATTTTTGGAAGTTTTGAGGTA
*
40886642 AAAAT-T--TTTTTGGGA-TTTT-AGGGTTA
1 AAAATGTAATTTTTGGAAGTTTTGA-GG-TA
40886668 AAAATGTAATTTTTGGAAGTTTTGAGGTCA
1 AAAATGTAATTTTTGGAAGTTTTGAGGT-A
*
40886698 AAAATGTAATTTTTGGAA-TTTTAGGGGTA
1 AAAATGTAATTTTTGGAAGTTTT-GAGGTA
*
40886727 AAAATGTAATTTTAGGAAGTTTTGAGGTTA
1 AAAATGTAATTTTTGGAAGTTTTGAGG-TA
* *
40886757 AAAATGTAATTTTTGGAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAGTTTTGAGGTA
*
40886786 AAAATGTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGTAATTTTTGGAAGTTTTGAGGT-A
* ** * *
40886816 AAAATGTAATTTTTAGAAGTTCAGGGGTT
1 AAAATGTAATTTTTGGAAGTTTTGAGGTA
40886845 AAAATGTAATTTTTGGATAGTTT
1 AAAATGTAATTTTTGGA-AGTTT
40886868 AGGGATCTTC
Statistics
Matches: 196, Mismatches: 16, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
23 1 0.01
24 6 0.03
25 8 0.04
26 5 0.03
27 2 0.01
29 84 0.43
30 89 0.45
31 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.24, T:0.42
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAGTTTTGAGGTA
Found at i:40886730 original size:59 final size:59
Alignment explanation
Indices: 40886613--40886867 Score: 358
Period size: 59 Copynumber: 4.4 Consensus size: 59
40886603 ACTCGAGGGC
* * * *
40886613 AAAATGGTAATTTTTGTAAGTTTTGAGGT--AAAAT-T--TTTTTGGGATTTTAGGGTTA
1 AAAAT-GTAATTTTTGGAAGTTTTGAGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGTA
*
40886668 AAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGTAATTTTTGGAATTTTAGGGGTA
1 AAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGTA
* *
40886727 AAAATGTAATTTTAGGAAGTTTTGAGGTTAAAAATGTAATTTTTGGAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGTA
* * * *
40886786 AAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGTAATTTTTAGAAGTTCAGGGGTT
1 AAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGTA
40886845 AAAATGTAATTTTTGGATAGTTT
1 AAAATGTAATTTTTGGA-AGTTT
40886868 AGGGATCTTC
Statistics
Matches: 182, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
54 22 0.12
55 5 0.03
56 5 0.03
57 1 0.01
59 144 0.79
60 5 0.03
ACGTcount: A:0.33, C:0.01, G:0.24, T:0.42
Consensus pattern (59 bp):
AAAATGTAATTTTTGGAAGTTTTGAGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGTA
Found at i:40887749 original size:12 final size:12
Alignment explanation
Indices: 40887732--40887794 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
40887722 TCAATTTCTT
40887732 TATTATTATTAA
1 TATTATTATTAA
*
40887744 TATTATTTATTAC
1 TATTA-TTATTAA
* *
40887757 TATTATTAATAC
1 TATTATTATTAA
* *
40887769 TTTTATTAAT-A
1 TATTATTATTAA
40887780 TATTCATTATTAA
1 TATT-ATTATTAA
40887793 TA
1 TA
40887795 AATATATTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
11 3 0.07
12 25 0.60
13 14 0.33
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTATTATTAA
Found at i:40888585 original size:18 final size:16
Alignment explanation
Indices: 40888549--40888629 Score: 90
Period size: 17 Copynumber: 4.8 Consensus size: 16
40888539 TAAATTTATT
* **
40888549 TTTAAGTTTAAAATTA
1 TTTAAATTTAAAAAAA
40888565 TTTCAAATTTAAAAGAAA
1 TTT-AAATTTAAAA-AAA
40888583 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAA-AAA
40888600 TTTAAATTTAAAAATTAA
1 TTTAAATTTAAAAA--AA
40888618 TTTAAATTTAAA
1 TTTAAATTTAAA
40888630 CTTAAAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
16 4 0.07
17 35 0.61
18 18 0.32
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAAAAAA
Found at i:40888591 original size:6 final size:6
Alignment explanation
Indices: 40888580--40888664 Score: 70
Period size: 6 Copynumber: 14.5 Consensus size: 6
40888570 AATTTAAAAG
** *
40888580 AAATTT AAATTT AAA-AC AAATTT AAATTT AAAAATT -AATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAATTT AAATTT
* * *
40888627 AAACTT AAA-AT AAATTT AAATTT ATAA-AT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT A-AATTT AAATTT AAA
40888665 ATCAATTTAA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
5 13 0.21
6 42 0.68
7 7 0.11
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
AAATTT
Found at i:40888626 original size:41 final size:41
Alignment explanation
Indices: 40888580--40888693 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 41
40888570 AATTTAAAAG
*
40888580 AAATTTAAATTTAAAACAAATTTAAATTTAAAAATTAATTT
1 AAATTTAAATTTAAAACAAATTTAAATTTAAAAATAAATTT
* * *
40888621 AAATTTAAACTTAAAATAAATTTAAATTTATAAATAAATTT
1 AAATTTAAATTTAAAACAAATTTAAATTTAAAAATAAATTT
* * * **
40888662 AAA-ATCAATTTAAACCAAACATAAATTTAAAA
1 AAATTTAAATTTAAAACAAATTTAAATTTAAAA
40888694 GTTGTCCCAA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
40 21 0.34
41 40 0.66
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (41 bp):
AAATTTAAATTTAAAACAAATTTAAATTTAAAAATAAATTT
Found at i:40888640 original size:17 final size:18
Alignment explanation
Indices: 40888620--40888664 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
40888610 AAAATTAATT
40888620 TAAATTTAAACTTA-AAA
1 TAAATTTAAACTTATAAA
*
40888637 TAAATTTAAATTTATAAA
1 TAAATTTAAACTTATAAA
40888655 TAAATTTAAA
1 TAAATTTAAA
40888665 ATCAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTTAAACTTATAAA
Found at i:40888658 original size:23 final size:23
Alignment explanation
Indices: 40888610--40888692 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 23
40888600 TTTAAATTTA
* *
40888610 AAAATTAATTTAAATTTAAACTT
1 AAAATAAATTTAAATTTAAACAT
40888633 AAAATAAATTTAAATTTATAA-AT
1 AAAATAAATTTAAATTTA-AACAT
* * *
40888656 AAATTTAAA-ATCAATTTAAACCA-
1 AAA-ATAAATTTAAATTTAAA-CAT
*
40888679 AACATAAATTTAAA
1 AAAATAAATTTAAA
40888693 AGTTGTCCCA
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
22 6 0.13
23 33 0.72
24 7 0.15
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAATAAATTTAAATTTAAACAT
Found at i:40888671 original size:11 final size:11
Alignment explanation
Indices: 40888602--40888675 Score: 50
Period size: 12 Copynumber: 6.9 Consensus size: 11
40888592 AAAACAAATT
40888602 TAAATTTAAAAA
1 TAAATTT-AAAA
* *
40888614 TTAATTTAAATT
1 TAAATTTAAA-A
*
40888626 TAAACTTAAAA
1 TAAATTTAAAA
40888637 TAAA-TT----
1 TAAATTTAAAA
40888643 TAAATTTATAAA
1 TAAATTTA-AAA
40888655 TAAATTTAAAA
1 TAAATTTAAAA
*
40888666 TCAATTTAAA
1 TAAATTTAAA
40888676 CCAAACATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
6 4 0.08
7 2 0.04
10 2 0.04
11 19 0.39
12 22 0.45
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:40889731 original size:17 final size:17
Alignment explanation
Indices: 40889711--40889747 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40889701 AGTTTTTCTA
* *
40889711 AAATTTAAACTTAATAT
1 AAATTTAAAATTAAAAT
40889728 AAATTTAAAATTAAAAT
1 AAATTTAAAATTAAAAT
40889745 AAA
1 AAA
40889748 AATTAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAATTTAAAATTAAAAT
Found at i:40889795 original size:13 final size:13
Alignment explanation
Indices: 40889779--40889818 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
40889769 AGTCCATTTA
40889779 TAAAGGCCCAAAT
1 TAAAGGCCCAAAT
40889792 TAAAGGCCC-AAT
1 TAAAGGCCCAAAT
40889804 TACAATGGCCCAAAT
1 TA-AA-GGCCCAAAT
40889819 AGGCCCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.21
13 11 0.46
14 5 0.21
15 3 0.12
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (13 bp):
TAAAGGCCCAAAT
Found at i:40891713 original size:88 final size:89
Alignment explanation
Indices: 40891524--40891730 Score: 212
Period size: 88 Copynumber: 2.3 Consensus size: 89
40891514 TTTTGTAGGT
* *
40891524 CCCTAAA-TTGTCCAAAAATTATATTTTAACCCCAAAACTTCAAAAAATTCCATTTTTGACCCTA
1 CCCTAAACTT-TCCAAAAATTATATTTTAACCCCAAAACTTCAAAAAATTCAATTTTTGACCCCA
** *
40891588 AATTTTCCAAAATCCCATTTTTGAC
65 AAACTTCCAAAATACCATTTTTGAC
* * * * *
40891613 CTCAAAAC-TTCCAAAAATTACTATTTTGACCTC-AAACTTTC-CAAAATTCAATTTTTGACCCC
1 CCCTAAACTTTCCAAAAATTA-TATTTTAACCCCAAAAC-TTCAAAAAATTCAATTTTTGACCCC
*
40891675 AAAACTTCCAAAATTACTA-TTTT-AC
64 AAAACTTCCAAAA-TACCATTTTTGAC
*
40891700 CCCTAAACTTTCCAAAATTTCAT-TTTTAACC
1 CCCTAAACTTTCCAAAAATT-ATATTTTAACC
40891731 TTGATTTTTC
Statistics
Matches: 97, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
87 15 0.15
88 59 0.61
89 23 0.24
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (89 bp):
CCCTAAACTTTCCAAAAATTATATTTTAACCCCAAAACTTCAAAAAATTCAATTTTTGACCCCAA
AACTTCCAAAATACCATTTTTGAC
Found at i:40891716 original size:58 final size:58
Alignment explanation
Indices: 40891524--40891902 Score: 321
Period size: 59 Copynumber: 6.4 Consensus size: 58
40891514 TTTTGTAGGT
* *
40891524 CCCTAAA-TTGTCCAAAAATT-ATATTTTAACCCCAAAACTTCAAAAAATT-CCATTTTTGA-
1 CCCTAAACTT-TCC-AAAATTCAT-TTTTAACCCCAAAACTTCCAAAAATTACTA-TTTT-AC
* * * *
40891583 CCCTAAATTTTCCAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTACTATTTTGAC
1 CCCTAAACTTTCCAAAAT-TCATTTTTAACCCCAAAACTTCCAAAAATTACTATTTT-AC
* *
40891643 CTC-AAACTTTCCAAAATTCAATTTTTGACCCCAAAACTTCC-AAAATTACTATTTTAC
1 CCCTAAACTTTCCAAAATTC-ATTTTTAACCCCAAAACTTCCAAAAATTACTATTTTAC
*** ***
40891700 CCCTAAACTTTCCAAAATTTCATTTTTAACCTTGATTTTTCC-AAAATTACTATTTTAC
1 CCCTAAACTTTCCAAAA-TTCATTTTTAACCCCAAAACTTCCAAAAATTACTATTTTAC
* * * ***
40891758 CCCTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTTTCCAAAAATTA-TCATTTTACC
1 CCCTAAACTTTCCAAAATT-CATTTTTAACCCCAAAACTTCCAAAAATTACT-ATTTTA-C
* * * *
40891818 CCCGAAA-TTTCCAAAATCTCATTTTTAACCCC--GATTTCACAAAAAATTACCATTTTAC
1 CCCTAAACTTTCCAAAAT-TCATTTTTAACCCCAAAACTTC-C-AAAAATTACTATTTTAC
40891876 CCCTAAACTTTCCAAAATTTCATTTTT
1 CCCTAAACTTTCCAAAA-TTCATTTTT
40891903 GACCTCGATT
Statistics
Matches: 276, Mismatches: 26, Indels: 36
0.82 0.08 0.11
Matches are distributed among these distances:
57 10 0.04
58 109 0.39
59 141 0.51
60 16 0.06
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (58 bp):
CCCTAAACTTTCCAAAATTCATTTTTAACCCCAAAACTTCCAAAAATTACTATTTTAC
Found at i:40891726 original size:29 final size:29
Alignment explanation
Indices: 40891524--40891902 Score: 180
Period size: 29 Copynumber: 12.9 Consensus size: 29
40891514 TTTTGTAGGT
*
40891524 CCCTAAA-TTGTCCAAAAATTAT-ATTTTAAC
1 CCCTAAACTT-TCC-AAAATT-TCATTTTTAC
* * *
40891554 CCCAAAAC-TTCAAAAAATTCCATTTTTGA-
1 CCCTAAACTTTC-CAAAATTTCATTTTT-AC
* **
40891583 CCCTAAATTTTCCAAAATCCCATTTTTGAC
1 CCCTAAACTTTCCAAAATTTCATTTTT-AC
* * * *
40891613 CTCAAAAC-TTCCAAAAATTACTATTTTGAC
1 CCCTAAACTTTCC-AAAATTTC-ATTTTTAC
*
40891643 CTC-AAACTTTCCAAAA-TTCAATTTTTGAC
1 CCCTAAACTTTCCAAAATTTC-ATTTTT-AC
* *
40891672 CCCAAAAC-TTCCAAAATTAC-TATTTTAC
1 CCCTAAACTTTCCAAAATTTCAT-TTTTAC
*
40891700 CCCTAAACTTTCCAAAATTTCATTTTTAA
1 CCCTAAACTTTCCAAAATTTCATTTTTAC
* * ** *
40891729 CCTTGATTTTTCCAAAATTAC-TATTTTAC
1 CCCTAAACTTTCCAAAATTTCAT-TTTTAC
* *
40891758 CCCTGAACTTTCCAAAATTCCATTTTTA-
1 CCCTAAACTTTCCAAAATTTCATTTTTAC
* * **
40891786 ACCTCGATTTTTCCAAAAATTATCA-TTTTACC
1 CCCT-AAACTTTCC-AAAATT-TCATTTTTA-C
* *
40891818 CCCGAAA-TTTCCAAAATCTCATTTTTAAC
1 CCCTAAACTTTCCAAAATTTCATTTTT-AC
* *
40891847 CCC--GA-TTTCACAAAAAATTACCA-TTTTAC
1 CCCTAAACTTTC-C--AAAATT-TCATTTTTAC
40891876 CCCTAAACTTTCCAAAATTTCATTTTT
1 CCCTAAACTTTCCAAAATTTCATTTTT
40891903 GACCTCGATT
Statistics
Matches: 271, Mismatches: 46, Indels: 65
0.71 0.12 0.17
Matches are distributed among these distances:
27 5 0.02
28 27 0.10
29 156 0.58
30 65 0.24
31 12 0.04
32 6 0.02
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAATTTCATTTTTAC
Found at i:40891912 original size:59 final size:57
Alignment explanation
Indices: 40891566--40891932 Score: 334
Period size: 59 Copynumber: 6.3 Consensus size: 57
40891556 CAAAACTTCA
* ** * * *
40891566 AAAAATT-CCATTTTTGA-CCCTAAATTTTCCAAAATCCCATTTTTGACCTCAAAACTTCC
1 AAAAATTACCA-TTTT-ACCCCTAAACTTTCCAAAATTTCATTTTTAACCTC--GATTTCC
* * * * * *
40891625 AAAAATTACTATTTTGACCTC-AAACTTTCCAAAA-TTCAATTTTTGACCCCAAAACTTCC
1 AAAAATTACCATTTT-ACCCCTAAACTTTCCAAAATTTC-ATTTTTAACCTC--GATTTCC
* *
40891684 -AAAATTACTATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTTGATTTTTCC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGA--TTTCC
* * *
40891742 -AAAATTACTATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTTTCC
1 AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGA--TTTCC
* * * *
40891800 AAAAATTATCATTTTACCCCCGAAA-TTTCCAAAATCTCATTTTTAACCCCGATTTCAC
1 AAAAATTACCATTTTA-CCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGATTTC-C
*
40891858 AAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTGACCTCGATTTTCC
1 -AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGA-TTTCC
40891917 TAAAAATTACCATTTT
1 -AAAAATTACCATTTT
40891933 GCCCTCGGGC
Statistics
Matches: 267, Mismatches: 28, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
56 1 0.00
57 8 0.03
58 104 0.39
59 140 0.52
60 14 0.05
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (57 bp):
AAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCATTTTTAACCTCGATTTCC
Found at i:40894232 original size:92 final size:92
Alignment explanation
Indices: 40894075--40894740 Score: 1079
Period size: 92 Copynumber: 7.4 Consensus size: 92
40894065 TTAGATCAAA
* *
40894075 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
40894140 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
* * *
40894167 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAAAATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
40894232 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
40894259 ATAACAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
* * *
40894324 ATCCTCTTGAAGCTATAGTAAAGATGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
40894351 ATAGCAAGTCTTTGTCTCTC-GAAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCC
1 ATAGCAAGTCTTTATCTCTCTG-AAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCC
40894415 TATCCTC-------T-T-G--AAGTTGG
65 TATCCTCTTGAAGTTGTAGTAAAGTTGG
* * *
40894432 ATAGCAAGTATTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAATATCAATTTCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
*
40894497 ATCCTCTTGAAGTTGTAGTAAAGATGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
40894524 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACAT-AATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
*
40894588 ATCCTCTTGAAGTTGTAGTAAAGATGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
40894615 ATAGCAAGTCTTTATCTCTCTTAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
40894680 ATCCTCTTGAAGTTGTAGTAAAGTTGG
66 ATCCTCTTGAAGTTGTAGTAAAGTTGG
*
40894707 ATAGCAAGTCTTTATCTCTCTGAAGTTATAGTAA
1 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAA
40894741 AGTTGGATAA
Statistics
Matches: 537, Mismatches: 23, Indels: 28
0.91 0.04 0.05
Matches are distributed among these distances:
81 71 0.13
82 1 0.00
83 1 0.00
84 1 0.00
85 1 0.00
88 1 0.00
89 1 0.00
90 1 0.00
91 90 0.17
92 369 0.69
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Consensus pattern (92 bp):
ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
ATCCTCTTGAAGTTGTAGTAAAGTTGG
Found at i:40894559 original size:265 final size:263
Alignment explanation
Indices: 40894075--40894694 Score: 988
Period size: 265 Copynumber: 2.3 Consensus size: 263
40894065 TTAGATCAAA
* *
40894075 ATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGTAAGATGAAGCTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTC-GAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
* *
40894140 ATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGT
65 ATCCTC-------T-T-G--AAGTTGGATAGCAAGTATTTATCTCTCTGAAGTTGTAGTAAGAGC
*
40894205 AAGATGAAGCTTCAAAAATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAACAAGTCT
119 AAGATGAAGCTTCAAAAATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAACAAGTCT
40894270 TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCTCTTGAA
184 TTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACAT-AATTCCTATCCTCTTGAA
40894335 GCTATAGTAAAGATGG
248 GCTATAGTAAAGATGG
*
40894351 ATAGCAAGTCTTTGTCTCTCGAAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTCG-AAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
*
40894416 ATCCTCTTGAAGTTGGATAGCAAGTATTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTT
65 ATCCTCTTGAAGTTGGATAGCAAGTATTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCT
* * *
40894481 TCAAATATCAATTTCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTATCTCTCTG
130 TCAAAAATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAACAAGTCTTTATCTCTCTG
* *
40894546 AAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATAATTCCTATCCTCTTGAAGTTGTAGTAAAG
195 AAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATAATTCCTATCCTCTTGAAGCTATAGTAAAG
40894611 ATGG
260 ATGG
*
40894615 ATAGCAAGTCTTTATCTCTCTTAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
1 ATAGCAAGTCTTTATCTCTC-GAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCT
40894680 ATCCTCTTGAAGTTG
65 ATCCTCTTGAAGTTG
40894695 TAGTAAAGTT
Statistics
Matches: 328, Mismatches: 14, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
264 109 0.33
265 149 0.45
267 1 0.00
268 1 0.00
269 1 0.00
275 1 0.00
276 66 0.20
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (263 bp):
ATAGCAAGTCTTTATCTCTCGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTA
TCCTCTTGAAGTTGGATAGCAAGTATTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTT
CAAAAATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAACAAGTCTTTATCTCTCTGA
AGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATAATTCCTATCCTCTTGAAGCTATAGTAAAGA
TGG
Found at i:40894647 original size:40 final size:41
Alignment explanation
Indices: 40894496--40894780 Score: 147
Period size: 40 Copynumber: 6.5 Consensus size: 41
40894486 TATCAATTTC
40894496 TATC-CTCTTGAAGTTGTAGTAAAGATGGATAGC-AAGTCTT
1 TATCTCTCTT-AAGTTGTAGTAAAGATGGATAGCAAAGTCTT
* * * *
40894536 TATCTCTCTGAAGTTGTAGTAAGAGCA-AGATGAAGTTTCAAACATAATT
1 TATCTCTCTTAAGTTGTAGTAA-AG-ATGGAT--AG---CAAA-GT-CTT
40894585 CCTATC-CTCTTGAAGTTGTAGTAAAGATGGATAGC-AAGTCTT
1 --TATCTCTCTT-AAGTTGTAGTAAAGATGGATAGCAAAGTCTT
* *
40894627 TATCTCTCTTAAGTTGTAGTAAGAGCA-AGATGAAGTTTCAAACATCAATT
1 TATCTCTCTTAAGTTGTAGTAA-AG-ATGGAT--AG---CAAA-GTC--TT
*
40894677 CCTATC-CTCTTGAAGTTGTAGTAAAGTTGGATAGC-AAGTCTT
1 --TATCTCTCTT-AAGTTGTAGTAAAGATGGATAGCAAAGTCTT
* * * * *
40894719 TATCTCTCTGAAGTTATAGTAAAGTTGGATAACGAA-TCTT
1 TATCTCTCTTAAGTTGTAGTAAAGATGGATAGCAAAGTCTT
* *
40894759 TATCTCTCTGAAGTTATAGTAA
1 TATCTCTCTTAAGTTGTAGTAA
40894781 GAGCAAGATG
Statistics
Matches: 196, Mismatches: 16, Indels: 66
0.71 0.06 0.24
Matches are distributed among these distances:
40 83 0.42
41 25 0.13
42 6 0.03
43 5 0.03
44 4 0.02
45 3 0.02
46 3 0.02
47 4 0.02
48 5 0.03
49 5 0.03
50 11 0.06
51 26 0.13
52 16 0.08
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (41 bp):
TATCTCTCTTAAGTTGTAGTAAAGATGGATAGCAAAGTCTT
Found at i:40895053 original size:183 final size:184
Alignment explanation
Indices: 40894718--40895412 Score: 1288
Period size: 183 Copynumber: 3.8 Consensus size: 184
40894708 TAGCAAGTCT
40894718 TTAT-CTCTCTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAG
1 TTATCCTCT-TGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAG
40894782 AGCAAGATGAA-TTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAA
65 AGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAA
40894846 TCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTC
130 TCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTC
40894901 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
* * *
40894966 GCAAGATGAATTTTCAAGTGTTAATTCTTATCCTCTTGAAGTTATAGTAAAGATGGATAACGAAT
66 GCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAAT
40895031 CTTTATCTCTCTGAAG-TATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTC
131 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTC
40895084 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
40895149 GCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAAT
66 GCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAAT
40895214 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTC
131 CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTC
* *
40895268 TTACCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAATTATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
* * *
40895333 GCAATATGAGTTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAGCGAAT
66 GCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAAT
40895398 CTTTATCTCTCTGAA
131 CTTTATCTCTCTGAA
40895413 AATAAAACCT
Statistics
Matches: 498, Mismatches: 11, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
183 250 0.50
184 248 0.50
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (184 bp):
TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
GCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAAT
CTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTC
Found at i:40895074 original size:275 final size:275
Alignment explanation
Indices: 40894718--40895412 Score: 1277
Period size: 275 Copynumber: 2.5 Consensus size: 275
40894708 TAGCAAGTCT
40894718 TTAT-CTCTCTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAG
1 TTATCCTCT-TGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAG-TATAGTAAG
40894782 AGCAAGATGAA-TTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAA
64 AGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAA
40894846 TCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTT
129 TCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTT
40894911 GAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAA
194 GAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAA
* *
40894976 TTTTCAAGTGTTAATTC
259 TTTTCAAATGTCAATTC
*
40894993 TTATCCTCTTGAAGTTATAGTAAAGATGGATAACGAATCTTTATCTCTCTGAAGTATAGTAAGAG
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTATAGTAAGAG
40895058 CAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATC
66 CAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATC
40895123 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGA
131 TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGA
40895188 AGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATT
196 AGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATT
40895253 TTCAAATGTCAATTC
261 TTCAAATGTCAATTC
* *
40895268 TTACCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAATTATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTG-AAGTATAGTAAGA
* * *
40895333 GCAATATGAGTTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAGCGAAT
65 GCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAAT
40895398 CTTTATCTCTCTGAA
130 CTTTATCTCTCTGAA
40895413 AATAAAACCT
Statistics
Matches: 408, Mismatches: 9, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
274 20 0.05
275 295 0.72
276 93 0.23
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (275 bp):
TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTATAGTAAGAG
CAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATC
TTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATCCTCTTGA
AGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATT
TTCAAATGTCAATTC
Found at i:40895413 original size:92 final size:92
Alignment explanation
Indices: 40894718--40895412 Score: 1288
Period size: 92 Copynumber: 7.6 Consensus size: 92
40894708 TAGCAAGTCT
40894718 TTAT-CTCTCTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAG
1 TTATCCTCT-TGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAG
40894782 AGCAAGATGAA-TTTCAAATGTCAATTC
65 AGCAAGATGAATTTTCAAATGTCAATTC
40894809 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
40894874 GCAAGATGAATTTTCAAATGTCAATTC
66 GCAAGATGAATTTTCAAATGTCAATTC
40894901 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
* *
40894966 GCAAGATGAATTTTCAAGTGTTAATTC
66 GCAAGATGAATTTTCAAATGTCAATTC
*
40894993 TTATCCTCTTGAAGTTATAGTAAAGATGGATAACGAATCTTTATCTCTCTGAAG-TATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
40895057 GCAAGATGAATTTTCAAATGTCAATTC
66 GCAAGATGAATTTTCAAATGTCAATTC
40895084 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
40895149 GCAAGATGAATTTTCAAATGTCAATTC
66 GCAAGATGAATTTTCAAATGTCAATTC
40895176 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
40895241 GCAAGATGAATTTTCAAATGTCAATTC
66 GCAAGATGAATTTTCAAATGTCAATTC
* *
40895268 TTACCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAATTATAGTAAGA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
* *
40895333 GCAATATGAGTTTTCAAATGTCAATTC
66 GCAAGATGAATTTTCAAATGTCAATTC
*
40895360 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAGCGAATCTTTATCTCTCTGAA
1 TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAA
40895413 AATAAAACCT
Statistics
Matches: 589, Mismatches: 12, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
91 158 0.27
92 431 0.73
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (92 bp):
TTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGTAAGA
GCAAGATGAATTTTCAAATGTCAATTC
Found at i:40895748 original size:17 final size:17
Alignment explanation
Indices: 40895728--40895803 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 17
40895718 ATTAAATTTT
40895728 AATTTAGTTTAAGTTTA
1 AATTTAGTTTAAGTTTA
**
40895745 AATTTTTCTTTTAAGTTTA
1 AA--TTTAGTTTAAGTTTA
*
40895764 AATTTTA-ATTAAGTTTA
1 AA-TTTAGTTTAAGTTTA
40895781 AATTT-GATTTGAA-TTTA
1 AATTTAG-TTT-AAGTTTA
40895798 AATTTA
1 AATTTA
40895804 AAATTAATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.06
17 24 0.50
18 6 0.12
19 15 0.31
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.55
Consensus pattern (17 bp):
AATTTAGTTTAAGTTTA
Found at i:40895812 original size:17 final size:17
Alignment explanation
Indices: 40895755--40895810 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
40895745 AATTTTTCTT
*
40895755 TTAAGTTTAAATTTTAA
1 TTAAGTTTAAATTTAAA
* *
40895772 TTAAGTTTAAATTTGAT
1 TTAAGTTTAAATTTAAA
40895789 TTGAA-TTTAAATTTAAAA
1 TT-AAGTTTAAATTT-AAA
40895807 TTAA
1 TTAA
40895811 TTACAGCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 28 0.85
18 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:40896170 original size:30 final size:29
Alignment explanation
Indices: 40896135--40896220 Score: 111
Period size: 31 Copynumber: 2.9 Consensus size: 29
40896125 CAGAAACTAT
*
40896135 ATTTTGACCCCAAAACTTCCTAAAAATTAC
1 ATTTTGACCCCCAAACTT-CTAAAAATTAC
*
40896165 ATTTTGACCCCTCAAACTTTTCAAAAATTAC
1 ATTTTGACCCC-CAAACTTCT-AAAAATTAC
*
40896196 ATTTTG-CCCCCGAACTTCTAAAAAT
1 ATTTTGACCCCCAAACTTCTAAAAAT
40896221 CCTATTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.12
29 7 0.14
30 16 0.32
31 21 0.42
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.33
Consensus pattern (29 bp):
ATTTTGACCCCCAAACTTCTAAAAATTAC
Found at i:40896265 original size:59 final size:58
Alignment explanation
Indices: 40896186--40896323 Score: 158
Period size: 59 Copynumber: 2.4 Consensus size: 58
40896176 TCAAACTTTT
* * *
40896186 CAAAAATTA-CATTTTGCCCCCGAAC-TTCTAAAAATCCTATTTTTAACCTCGATTT-TAC
1 CAAAAATTACCA-TTTGCCCCCGAACTTTC-AAAAATCCCATTTTTAACC-CAATTTCAAC
* * *
40896244 CAAAAATTACCATATTACCCCCGAACTTTCCAAAATCCCATTTTTGACCCAATTTCAAC
1 CAAAAATTACCAT-TTGCCCCCGAACTTTCAAAAATCCCATTTTTAACCCAATTTCAAC
40896303 C-AAAATTACCATTTGCCCCCG
1 CAAAAATTACCATTTGCCCCCG
40896324 GGTATCCAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
57 8 0.12
58 26 0.38
59 32 0.46
60 3 0.04
ACGTcount: A:0.33, C:0.30, G:0.05, T:0.31
Consensus pattern (58 bp):
CAAAAATTACCATTTGCCCCCGAACTTTCAAAAATCCCATTTTTAACCCAATTTCAAC
Found at i:40902805 original size:154 final size:154
Alignment explanation
Indices: 40902520--40902824 Score: 540
Period size: 154 Copynumber: 2.0 Consensus size: 154
40902510 ATGAGATCGA
*
40902520 CTAAAGCTTTGCATATTACCACTCGCCGTAAAGGATACACCCTACCTGAAGTGCTCATCGACAAC
1 CTAAAGCTTTGCATATTACCACTCACCGTAAAGGATACACCCTACCTGAAGTGCTCATCGACAAC
* * *
40902585 GGGTCAGCTTTAAACGTACTACCGTTGGCTACTTTGGAAAGATTACCCATCGATAGCTCATATAT
66 GGGTCAGCTTTAAACGTACTACCGTTAGCTACTTTGAAAAGATTAACCATCGATAGCTCATATAT
40902650 GACGACGTGCCACAACATAGTACC
131 GACGACGTGCCACAACATAGTACC
* *
40902674 CTAAGGCTTTGCATATTACCACTCACCGTAAAGGATACACCCTACCT-AGAGTGCTCATCGATAA
1 CTAAAGCTTTGCATATTACCACTCACCGTAAAGGATACACCCTACCTGA-AGTGCTCATCGACAA
40902738 CGGGTCAGCTTTAAACGTACTACCGTTAGCTACTTTGAAAAGATTAACCATCGATAGCTCATATA
65 CGGGTCAGCTTTAAACGTACTACCGTTAGCTACTTTGAAAAGATTAACCATCGATAGCTCATATA
40902803 TGACGACGTGCCACAACATAGT
130 TGACGACGTGCCACAACATAGT
40902825 TAGAGCTTTC
Statistics
Matches: 144, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
153 1 0.01
154 143 0.99
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (154 bp):
CTAAAGCTTTGCATATTACCACTCACCGTAAAGGATACACCCTACCTGAAGTGCTCATCGACAAC
GGGTCAGCTTTAAACGTACTACCGTTAGCTACTTTGAAAAGATTAACCATCGATAGCTCATATAT
GACGACGTGCCACAACATAGTACC
Found at i:40908739 original size:92 final size:92
Alignment explanation
Indices: 40908167--40908738 Score: 1074
Period size: 92 Copynumber: 6.2 Consensus size: 92
40908157 ATCCACGACG
40908167 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
40908232 CTCTTGAAGTTATAGTAAAGTTGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
* * *
40908259 ACGAATCTTTATCTCTCTGAAGTTATAGTAACAGCAAGATGAATTTTCAAGTGTTAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
*
40908324 CTCTTGAAGTTATAGTAAAGATGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
40908351 ACGAATCTTTATCTCTCTGAAG-TATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
40908415 CTCTTGAAGTTATAGTAAAGTTGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
40908442 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
40908507 CTCTTGAAGTTATAGTAAAGTTGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
40908534 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
40908599 CTCTTGAAGTTATAGTAAAGTTGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
* *
40908626 ACGAATCTTTATCTCTCTGAAATTATAGTAAGAGCAAGATGAGTTTTCAAATGTCAATTCTTATC
1 ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
40908691 CTCTTGAAGTTATAGTAAAGTTGGATA
66 CTCTTGAAGTTATAGTAAAGTTGGATA
*
40908718 ACAAATCTTTATCTCTCTGAA
1 ACGAATCTTTATCTCTCTGAA
40908739 AATAAAACCT
Statistics
Matches: 468, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
91 87 0.19
92 381 0.81
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (92 bp):
ACGAATCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAATTTTCAAATGTCAATTCTTATC
CTCTTGAAGTTATAGTAAAGTTGGATA
Found at i:40909137 original size:17 final size:17
Alignment explanation
Indices: 40909080--40909135 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
40909070 AAACTTCTCT
*
40909080 TTAAGTTTAAATTTTAA
1 TTAAGTTTAAATTTAAA
* *
40909097 TTAAGTTTAAATTTGAT
1 TTAAGTTTAAATTTAAA
40909114 TTGAA-TTTAAATTTAAAA
1 TT-AAGTTTAAATTT-AAA
40909132 TTAA
1 TTAA
40909136 TTACAACCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 28 0.85
18 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:40909810 original size:3 final size:3
Alignment explanation
Indices: 40909804--40909878 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
40909794 TAAATGTTGT
* * * * *
40909804 TAA TAA TAA TAC CAT TAA TAA TTA TAA TAA TAAA TAA TAG TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA
* * *
40909851 TAT TAA TAA CAA GAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
40909879 GGTAATAGCA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
3 50 0.89
4 6 0.11
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40910998 original size:31 final size:30
Alignment explanation
Indices: 40910924--40911027 Score: 115
Period size: 31 Copynumber: 3.5 Consensus size: 30
40910914 ATAGGTCTCT
* * *
40910924 GAACTGTTCAAAAATTATATTTTGACCCTA
1 GAACTTTTCAAAAATTACATTTTGACCCTC
* * *
40910954 GAAC-TTCCTAAAAATTACATGTTGACCCCCC
1 GAACTTTTC-AAAAATTACATTTTGA-CCCTC
40910985 GAACTTTTCAAAAATTACATTTTG-CCCTC
1 GAACTTTTCAAAAATTACATTTTGACCCTC
40911014 GAACTTTT-AAAAAT
1 GAACTTTTCAAAAAT
40911028 CCCATTTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
28 6 0.10
29 14 0.23
30 18 0.29
31 21 0.34
32 3 0.05
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.34
Consensus pattern (30 bp):
GAACTTTTCAAAAATTACATTTTGACCCTC
Found at i:40911105 original size:58 final size:59
Alignment explanation
Indices: 40910993--40911130 Score: 190
Period size: 58 Copynumber: 2.4 Consensus size: 59
40910983 CCGAACTTTT
* * * *
40910993 CAAAAATTA-CATTTTGCCCTCGAACTTTTAAAAATCCCATTTTTAACCCCAATTTTAC
1 CAAAAATTACCATTTTGCCCCCGAACTTTCAAAAATCCCATTTTTAACCCCAATTTCAA
* * * *
40911051 CAAAAATTACCATATTACCCCCGAACTTTCCAAAATCCCATTTTTGA-CCCAATTTCAA
1 CAAAAATTACCATTTTGCCCCCGAACTTTCAAAAATCCCATTTTTAACCCCAATTTCAA
40911109 CAAAAATTACCATTTTGCCCCC
1 CAAAAATTACCATTTTGCCCCC
40911131 AGGTATCCAA
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
58 38 0.55
59 31 0.45
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
CAAAAATTACCATTTTGCCCCCGAACTTTCAAAAATCCCATTTTTAACCCCAATTTCAA
Found at i:40913425 original size:11 final size:11
Alignment explanation
Indices: 40913355--40913425 Score: 52
Period size: 11 Copynumber: 5.9 Consensus size: 11
40913345 TAGCTTTGAG
*
40913355 TTTAAATTAAT
1 TTTAAATTTAT
40913366 TTTAAATTTAT
1 TTTAAATTTAT
*
40913377 TTTAAAATTTAAAA
1 TTT-AAATTT--AT
*
40913391 TTTAAAATTACTT
1 TTTAAATTTA--T
*
40913404 ATTTAAGTTTAT
1 -TTTAAATTTAT
40913416 TTTAAATTTA
1 TTTAAATTTA
40913426 AATTTGAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
11 23 0.49
12 7 0.15
13 5 0.11
14 12 0.26
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:40914106 original size:363 final size:363
Alignment explanation
Indices: 40913441--40914168 Score: 1456
Period size: 363 Copynumber: 2.0 Consensus size: 363
40913431 GAATAAATTT
40913441 AAAATAATATTAAACTTAAAAAGTCTATTTACAAGGCCCAATTGGCCCAAATACCCCTAACTCCT
1 AAAATAATATTAAACTTAAAAAGTCTATTTACAAGGCCCAATTGGCCCAAATACCCCTAACTCCT
40913506 AACCCAATTACAAAAACCCCATTTCAGCCCAACTCAGCAGTACCAAAAGTCAAAGACTGAGCCCC
66 AACCCAATTACAAAAACCCCATTTCAGCCCAACTCAGCAGTACCAAAAGTCAAAGACTGAGCCCC
40913571 CCCACGTGCCTATGCTGCTGCTGACCACCAGCTCCATCTGCCACTACCAAGCTCCACCATGCCCT
131 CCCACGTGCCTATGCTGCTGCTGACCACCAGCTCCATCTGCCACTACCAAGCTCCACCATGCCCT
40913636 GCCACCACTGCCTTAGAAGAACCTGCAACAAGCAAAGGAGATTAGAAAGACATTTAATTGTAACA
196 GCCACCACTGCCTTAGAAGAACCTGCAACAAGCAAAGGAGATTAGAAAGACATTTAATTGTAACA
40913701 AACAAAATAGAATTATAGTGTAATTGGCTATAAAAGCCTATTAGAAGTTCATAATAATGGGGGCG
261 AACAAAATAGAATTATAGTGTAATTGGCTATAAAAGCCTATTAGAAGTTCATAATAATGGGGGCG
40913766 CTGGTTCTTGAATTATCAATTAGGAACCACTTTTGAAG
326 CTGGTTCTTGAATTATCAATTAGGAACCACTTTTGAAG
40913804 AAAATAATATTAAACTTAAAAAGTCTATTTACAAGGCCCAATTGGCCCAAATACCCCTAACTCCT
1 AAAATAATATTAAACTTAAAAAGTCTATTTACAAGGCCCAATTGGCCCAAATACCCCTAACTCCT
40913869 AACCCAATTACAAAAACCCCATTTCAGCCCAACTCAGCAGTACCAAAAGTCAAAGACTGAGCCCC
66 AACCCAATTACAAAAACCCCATTTCAGCCCAACTCAGCAGTACCAAAAGTCAAAGACTGAGCCCC
40913934 CCCACGTGCCTATGCTGCTGCTGACCACCAGCTCCATCTGCCACTACCAAGCTCCACCATGCCCT
131 CCCACGTGCCTATGCTGCTGCTGACCACCAGCTCCATCTGCCACTACCAAGCTCCACCATGCCCT
40913999 GCCACCACTGCCTTAGAAGAACCTGCAACAAGCAAAGGAGATTAGAAAGACATTTAATTGTAACA
196 GCCACCACTGCCTTAGAAGAACCTGCAACAAGCAAAGGAGATTAGAAAGACATTTAATTGTAACA
40914064 AACAAAATAGAATTATAGTGTAATTGGCTATAAAAGCCTATTAGAAGTTCATAATAATGGGGGCG
261 AACAAAATAGAATTATAGTGTAATTGGCTATAAAAGCCTATTAGAAGTTCATAATAATGGGGGCG
40914129 CTGGTTCTTGAATTATCAATTAGGAACCACTTTTGAAG
326 CTGGTTCTTGAATTATCAATTAGGAACCACTTTTGAAG
40914167 AA
1 AA
40914169 CCCGTTACTG
Statistics
Matches: 365, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
363 365 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (363 bp):
AAAATAATATTAAACTTAAAAAGTCTATTTACAAGGCCCAATTGGCCCAAATACCCCTAACTCCT
AACCCAATTACAAAAACCCCATTTCAGCCCAACTCAGCAGTACCAAAAGTCAAAGACTGAGCCCC
CCCACGTGCCTATGCTGCTGCTGACCACCAGCTCCATCTGCCACTACCAAGCTCCACCATGCCCT
GCCACCACTGCCTTAGAAGAACCTGCAACAAGCAAAGGAGATTAGAAAGACATTTAATTGTAACA
AACAAAATAGAATTATAGTGTAATTGGCTATAAAAGCCTATTAGAAGTTCATAATAATGGGGGCG
CTGGTTCTTGAATTATCAATTAGGAACCACTTTTGAAG
Found at i:40915436 original size:30 final size:30
Alignment explanation
Indices: 40915402--40915859 Score: 570
Period size: 30 Copynumber: 15.4 Consensus size: 30
40915392 AATTGTCAAG
40915402 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
40915432 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
40915462 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
** * *
40915492 AAATTACATTTCAACCTCAAAAC-TTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTTC-CA
*
40915522 AAATTACATTTTGACCCCAAAAATTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
40915552 AAATTATATTTTGACCCCAAAAC-TTTCTA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
40915581 GAAATTACATTTTGACCCCAAAACTTTTCCA
1 -AAATTACATTTTGACCCCAAAACTTTTCCA
* **
40915612 AAATTACATTTTGACCCTAAAACTTTT-TG
1 AAATTACATTTTGACCCCAAAACTTTTCCA
** ** *
40915641 AAATTACATTTCAACCTTAAAAC-TTTCTAA
1 AAATTACATTTTGACCCCAAAACTTTTC-CA
40915671 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* **
40915701 AAATTACATTTTGACCCTAAAACTTTT-TG
1 AAATTACATTTTGACCCCAAAACTTTTCCA
40915730 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
40915760 AAATTACATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * * ***
40915790 AAATCATATTTTGACCCTAAAA-TTTAAAA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * * *
40915819 AAATTGCATTTTTACCCCGAAAC-TTTCAA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
40915848 AAATTACCATTT
1 AAATTA-CATTT
40915860 CACCCTCAAA
Statistics
Matches: 368, Mismatches: 50, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.01
29 84 0.23
30 268 0.73
31 13 0.04
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:40915682 original size:89 final size:90
Alignment explanation
Indices: 40915397--40915859 Score: 580
Period size: 89 Copynumber: 5.2 Consensus size: 90
40915387 CCTTAAATTG
*
40915397 TCAAGAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA
1 TCAA-AAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCA
*
40915462 AAATTATATTTTGACCCCAAAACTTT
65 AAATTACATTTTGACCCCAAAACTTT
* ** * * * *
40915488 TCCAAAATTACATTTCAACCTCAAAAC-TTTCTAAAAATTACATTTTGACCCCAAAAATTTTCCA
1 TCAAAAATTACATTTTGACCCCAAAACTTTTC-CAAAATTACATTTTGACCCTAAAACTTTTCCA
*
40915552 AAATTATATTTTGACCCCAAAAC-TT
65 AAATTACATTTTGACCCCAAAACTTT
* **
40915577 TCTAGAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTT-TG
1 TC-AAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCA
** **
40915641 AAATTACATTTCAACCTTAAAAC-TT
65 AAATTACATTTTGACCCCAAAACTTT
**
40915666 TCTAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTT-TG
1 TC-AAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCA
40915730 AAATTACATTTTGACCCCAAAACTTT
65 AAATTACATTTTGACCCCAAAACTTT
* * * ***
40915756 TCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATCATATTTTGACCCTAAAA-TTTAAAAA
1 TCAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAA
* * *
40915820 AATTGCATTTTTACCCCGAAAC-TT
66 AATTACATTTTGACCCCAAAACTTT
40915844 TCAAAAATTACCATTT
1 TCAAAAATTA-CATTT
40915860 CACCCTCAAA
Statistics
Matches: 330, Mismatches: 36, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
88 14 0.04
89 186 0.56
90 123 0.37
91 7 0.02
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (90 bp):
TCAAAAATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTGACCCTAAAACTTTTCCAA
AATTACATTTTGACCCCAAAACTTT
Found at i:40915887 original size:58 final size:54
Alignment explanation
Indices: 40915819--40915952 Score: 137
Period size: 58 Copynumber: 2.4 Consensus size: 54
40915809 AAATTTAAAA
* **
40915819 AAATTGCATTTTTACCCCGAAACTTT-CAAAAATTACCATTTCACCCTCAAACTTCCC
1 AAATTCCATTTTTACCCCG-AA-TTTACAAAAATTACCATTTCACCCT-AAA-AACCC
*
40915876 TAAATTCCATTTTTAGCCCCG-ATTTCACAAAAATTACCATTTTACCCTAAAAACCC
1 -AAATTCCATTTTTA-CCCCGAATTT-ACAAAAATTACCATTTCACCCTAAAAACCC
*
40915932 AAATTACCATTTTTCCCCCGA
1 AAATT-CCATTTTTACCCCGA
40915953 GTATCCAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
55 10 0.15
56 14 0.21
57 4 0.06
58 33 0.50
59 5 0.08
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.32
Consensus pattern (54 bp):
AAATTCCATTTTTACCCCGAATTTACAAAAATTACCATTTCACCCTAAAAACCC
Found at i:40917070 original size:17 final size:17
Alignment explanation
Indices: 40917048--40917086 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
40917038 ATAAGTTTAC
40917048 AACAACTATCTCGT-TAT
1 AACAACTATCTC-TCTAT
*
40917065 AACAACTATTTCTCTAT
1 AACAACTATCTCTCTAT
40917082 AACAA
1 AACAA
40917087 ACAAAATCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.33
Consensus pattern (17 bp):
AACAACTATCTCTCTAT
Found at i:40917541 original size:67 final size:67
Alignment explanation
Indices: 40917428--40917674 Score: 427
Period size: 67 Copynumber: 3.8 Consensus size: 67
40917418 AGGTAGGTCC
*
40917428 ATGTGATGT-TATATATATAAACAATTAGTTTATGCAAATTGATTTCAATGGAGGTGGGTCCATG
1 ATGTGATATATATATATATAAACAATTAGTTTATGCAAATTGATTTCAATGGAGGTGGGTCCATG
40917492 TA
66 TA
40917494 ATGTGATATATATATATATAAACAATTAGTTTATGCAAATTGATTTCAATGGAGGTGGGTCCATG
1 ATGTGATATATATATATATAAACAATTAGTTTATGCAAATTGATTTCAATGGAGGTGGGTCCATG
40917559 TA
66 TA
40917561 ATGTGATATATATATATATAAACAATTAGTTTATGCAAATTGATTTCAATGGAGGTGGGTCCA--
1 ATGTGATATATATATATATAAACAATTAGTTTATGCAAATTGATTTCAATGGAGGTGGGTCCATG
40917624 T-
66 TA
*
40917625 A--T-ATATATATATATATAAACAATTAGTTTATGCAAATTGATTTAAATGGA
1 ATGTGATATATATATATATAAACAATTAGTTTATGCAAATTGATTTCAATGGA
40917675 CAGTTCCGTT
Statistics
Matches: 178, Mismatches: 2, Indels: 7
0.95 0.01 0.04
Matches are distributed among these distances:
61 47 0.26
62 1 0.01
64 1 0.01
65 1 0.01
66 8 0.04
67 120 0.67
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (67 bp):
ATGTGATATATATATATATAAACAATTAGTTTATGCAAATTGATTTCAATGGAGGTGGGTCCATG
TA
Found at i:40917797 original size:23 final size:23
Alignment explanation
Indices: 40917736--40917797 Score: 54
Period size: 24 Copynumber: 2.7 Consensus size: 23
40917726 TTTAGATTTA
*
40917736 TTAAAAATTAAAAAAAAAAAATT
1 TTAAAAATTTAAAAAAAAAAATT
* ** *
40917759 TTAAAAGTTGGT-AAAAAATTACTT
1 TTAAAAATT--TAAAAAAAAAAATT
40917783 TTAAAAATTTAAAAA
1 TTAAAAATTTAAAAA
40917798 TAAATTTAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
22 1 0.03
23 12 0.40
24 17 0.57
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (23 bp):
TTAAAAATTTAAAAAAAAAAATT
Found at i:40919138 original size:6 final size:6
Alignment explanation
Indices: 40919127--40919158 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
40919117 CATTAAATGC
40919127 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TT
40919159 AGGCTTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:40921579 original size:28 final size:28
Alignment explanation
Indices: 40921539--40921594 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
40921529 TAATGCGGCG
40921539 AATTTTTAAAATGTTATTATATCAATTT
1 AATTTTTAAAATGTTATTATATCAATTT
40921567 AATTTTTAAAATGTTATTATATCAATTT
1 AATTTTTAAAATGTTATTATATCAATTT
40921595 TAAAAGTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (28 bp):
AATTTTTAAAATGTTATTATATCAATTT
Found at i:40921593 original size:23 final size:24
Alignment explanation
Indices: 40921539--40921603 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 24
40921529 TAATGCGGCG
40921539 AATTTTTAAAATGTTATTATATCAATTT
1 AATTTTTAAAATGTTATTATATC----T
40921567 AATTTTTAAAATGTTATTATATC-
1 AATTTTTAAAATGTTATTATATCT
40921590 AA-TTTTAAAA-GTTA
1 AATTTTTAAAATGTTA
40921604 CACCGATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.11
22 8 0.22
23 2 0.05
28 23 0.62
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (24 bp):
AATTTTTAAAATGTTATTATATCT
Found at i:40925352 original size:24 final size:22
Alignment explanation
Indices: 40925300--40925354 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
40925290 TGCTGCTGAA
*
40925300 GCTGTTGTTGCTGTGAGTTACT
1 GCTGCTGTTGCTGTGAGTTACT
* *
40925322 G-TTCTGTTGCTGTTGCAGTTGCT
1 GCTGCTGTTGCTG-TG-AGTTACT
40925345 GCTGCTGTTG
1 GCTGCTGTTG
40925355 TTGCTGCTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.35
22 3 0.12
23 7 0.27
24 7 0.27
ACGTcount: A:0.05, C:0.16, G:0.33, T:0.45
Consensus pattern (22 bp):
GCTGCTGTTGCTGTGAGTTACT
Found at i:40925354 original size:12 final size:12
Alignment explanation
Indices: 40925325--40925363 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40925315 AGTTACTGTT
*
40925325 CTGTTGCTGTTG
1 CTGTTGCTGCTG
*
40925337 CAGTTGCTGCTG
1 CTGTTGCTGCTG
*
40925349 CTGTTGTTGCTG
1 CTGTTGCTGCTG
40925361 CTG
1 CTG
40925364 ATGCAACTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.21, G:0.33, T:0.44
Consensus pattern (12 bp):
CTGTTGCTGCTG
Found at i:40926012 original size:30 final size:30
Alignment explanation
Indices: 40925976--40926035 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
40925966 ATCACATAAT
* *
40925976 TTAGATTCCAAATATACAAGTAATATGAAC
1 TTAGATTCCAAATAAACAAGTAAAATGAAC
*
40926006 TTAGATTCCAAATAAATAAGTAAAATGAAC
1 TTAGATTCCAAATAAACAAGTAAAATGAAC
40926036 CGAGTCAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (30 bp):
TTAGATTCCAAATAAACAAGTAAAATGAAC
Found at i:40927055 original size:3 final size:3
Alignment explanation
Indices: 40927049--40927199 Score: 131
Period size: 3 Copynumber: 50.3 Consensus size: 3
40927039 TGCTGTGGTG
* * *
40927049 GCT GCT GCT GCT GCT GCT GTT GTT GCT GCT GCT GCT GCT GCT GTT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * * * * * * * * * * *
40927097 GCT GTT GTT GCT GTT GTT GTT GCT GTT GTT GTT GTT GTT GTT GTT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* * * *
40927145 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GTT GCT GTT GCT GTT GTT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
40927193 GCT GCT G
1 GCT GCT G
40927200 TTGTTGTTGT
Statistics
Matches: 132, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 132 1.00
ACGTcount: A:0.00, C:0.21, G:0.34, T:0.46
Consensus pattern (3 bp):
GCT
Found at i:40927096 original size:12 final size:12
Alignment explanation
Indices: 40927049--40927202 Score: 173
Period size: 12 Copynumber: 12.8 Consensus size: 12
40927039 TGCTGTGGTG
*
40927049 GCTGCTGCTGCT
1 GCTGCTGTTGCT
*
40927061 GCTGCTGTTGTT
1 GCTGCTGTTGCT
*
40927073 GCTGCTGCTGCT
1 GCTGCTGTTGCT
40927085 GCTGCTGTTGCT
1 GCTGCTGTTGCT
*
40927097 GCTGTTGTTGCT
1 GCTGCTGTTGCT
* *
40927109 GTTGTTGTTGCT
1 GCTGCTGTTGCT
* * *
40927121 GTTGTTGTTGTT
1 GCTGCTGTTGCT
* *
40927133 GTTGTTGTTGCT
1 GCTGCTGTTGCT
*
40927145 GCTGCTGCTGCT
1 GCTGCTGTTGCT
*
40927157 GCTGCTGCTGCT
1 GCTGCTGTTGCT
40927169 GCTGCTGTTGCT
1 GCTGCTGTTGCT
* *
40927181 GTTGCTGTTGTT
1 GCTGCTGTTGCT
40927193 GCTGCTGTTG
1 GCTGCTGTTG
40927203 TTGTTGTTGG
Statistics
Matches: 126, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 126 1.00
ACGTcount: A:0.00, C:0.20, G:0.34, T:0.46
Consensus pattern (12 bp):
GCTGCTGTTGCT
Found at i:40927257 original size:12 final size:12
Alignment explanation
Indices: 40927252--40927277 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40927242 CTGCAGTTGC
40927252 TGCTGCTGCTGT
1 TGCTGCTGCTGT
40927264 TGCTGCTGCTGT
1 TGCTGCTGCTGT
40927276 TG
1 TG
40927278 ATGTTGAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.35, T:0.42
Consensus pattern (12 bp):
TGCTGCTGCTGT
Found at i:40927265 original size:15 final size:15
Alignment explanation
Indices: 40927242--40927274 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40927232 GCTGTTGCAT
40927242 CTGCAGTTGCTGCTG
1 CTGCAGTTGCTGCTG
*
40927257 CTGCTGTTGCTGCTG
1 CTGCAGTTGCTGCTG
40927272 CTG
1 CTG
40927275 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.27, G:0.33, T:0.36
Consensus pattern (15 bp):
CTGCAGTTGCTGCTG
Found at i:40927282 original size:18 final size:18
Alignment explanation
Indices: 40927249--40927324 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 18
40927239 CATCTGCAGT
* *
40927249 TGCTGCTGCTGCTGTTGC
1 TGCTGCTGTTGATGTTGC
40927267 TGCTGCTGTTGATGTTG-
1 TGCTGCTGTTGATGTTGC
* *
40927284 AG--GCTGTTGAGGTTGC
1 TGCTGCTGTTGATGTTGC
*
40927300 TGCTGCTGTTGCA-GTTGT
1 TGCTGCTGTTG-ATGTTGC
40927318 TGCTGCT
1 TGCTGCT
40927325 CCCGTGCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
15 12 0.25
16 1 0.02
17 1 0.02
18 33 0.69
19 1 0.02
ACGTcount: A:0.05, C:0.18, G:0.36, T:0.41
Consensus pattern (18 bp):
TGCTGCTGTTGATGTTGC
Found at i:40932403 original size:31 final size:30
Alignment explanation
Indices: 40932327--40932417 Score: 78
Period size: 31 Copynumber: 3.0 Consensus size: 30
40932317 TTTAAAATGG
* * * *
40932327 GTATAATTAAATCAATATTAAAGTTTCGTGT
1 GTATAATT-AACCAAAATAAAAGTTTCATGT
* *
40932358 ATATATTTGAACCAAAATAAAAGTTTCATGT
1 GTATAATT-AACCAAAATAAAAGTTTCATGT
*
40932389 GTATAATTACACC-AAATCAAAG-TTCATGT
1 GTATAATTA-ACCAAAATAAAAGTTTCATGT
40932418 ATCAAATTGC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 7 0.14
30 9 0.18
31 33 0.67
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (30 bp):
GTATAATTAACCAAAATAAAAGTTTCATGT
Found at i:40932866 original size:15 final size:15
Alignment explanation
Indices: 40932846--40932875 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40932836 TTGACGCACT
40932846 AATTACATGTTTAAC
1 AATTACATGTTTAAC
40932861 AATTACATGTTTAAC
1 AATTACATGTTTAAC
40932876 TAATATTAAG
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:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (15 bp):
AATTACATGTTTAAC
Found at i:40937652 original size:6 final size:6
Alignment explanation
Indices: 40937641--40937675 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
40937631 TATTACAGTG
40937641 AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAGAA
1 AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAGAA
40937676 GAGGAAGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.69, C:0.14, G:0.17, T:0.00
Consensus pattern (6 bp):
AAGAAC
Found at i:40938252 original size:23 final size:22
Alignment explanation
Indices: 40938205--40938255 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
40938195 AATTAGATTT
40938205 AAATATTGAAATTCAAAAAATA
1 AAATATTGAAATTCAAAAAATA
*
40938227 AAATGATT-AAATTCTAATAAATA
1 AAAT-ATTGAAATTC-AAAAAATA
40938250 AAATAT
1 AAATAT
40938256 AAAAACTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (22 bp):
AAATATTGAAATTCAAAAAATA
Found at i:40939375 original size:6 final size:6
Alignment explanation
Indices: 40939364--40939398 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
40939354 TCGTAGGGCT
*
40939364 GTAGCA GTAGCA GTAGCA GTAACA GTAGCA GTAGC
1 GTAGCA GTAGCA GTAGCA GTAGCA GTAGCA GTAGC
40939399 TTTTGTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.17
Consensus pattern (6 bp):
GTAGCA
Found at i:40944421 original size:20 final size:20
Alignment explanation
Indices: 40944383--40944422 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40944373 TAATTTATCC
*
40944383 TAAAAAAATAAAAATAAAAA
1 TAAAAAAATAAAAAGAAAAA
40944403 TAAAAAAA-AAGAAAGAAAAA
1 TAAAAAAATAA-AAAGAAAAA
40944423 GCAAACTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (20 bp):
TAAAAAAATAAAAAGAAAAA
Found at i:40946234 original size:28 final size:28
Alignment explanation
Indices: 40946180--40946236 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
40946170 AAATTTTACA
* *
40946180 TCATATGTCATTTATAACGTGTCATGAT
1 TCATATCTCATTTATAACGTGGCATGAT
* * *
40946208 TCATATCTTATTTATAATGTGGGATGAT
1 TCATATCTCATTTATAACGTGGCATGAT
40946236 T
1 T
40946237 GTGTTTTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.46
Consensus pattern (28 bp):
TCATATCTCATTTATAACGTGGCATGAT
Found at i:40965201 original size:26 final size:27
Alignment explanation
Indices: 40965158--40965219 Score: 99
Period size: 26 Copynumber: 2.3 Consensus size: 27
40965148 GGGCATTACT
40965158 TAAACCTCTCCATTCACCCATTCCAACA
1 TAAACC-CTCCATTCACCCATTCCAACA
*
40965186 TAAACCCT-CATTCACCCATTCCGACA
1 TAAACCCTCCATTCACCCATTCCAACA
40965212 TAAACCCT
1 TAAACCCT
40965220 AATCCCCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 25 0.76
27 2 0.06
28 6 0.18
ACGTcount: A:0.32, C:0.42, G:0.02, T:0.24
Consensus pattern (27 bp):
TAAACCCTCCATTCACCCATTCCAACA
Found at i:40979173 original size:11 final size:11
Alignment explanation
Indices: 40979157--40979183 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40979147 TTTTCTATAA
40979157 GAAACAGAGTT
1 GAAACAGAGTT
40979168 GAAACAGAGTT
1 GAAACAGAGTT
40979179 GAAAC
1 GAAAC
40979184 TCTTTGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.11, G:0.26, T:0.15
Consensus pattern (11 bp):
GAAACAGAGTT
Found at i:40983745 original size:19 final size:21
Alignment explanation
Indices: 40983708--40983746 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40983698 AGAAATCAAT
*
40983708 AATTTAAGAAAATATAATAAA
1 AATTTAAGAAAACATAATAAA
40983729 AATTTAA-AAAACA-AATAA
1 AATTTAAGAAAACATAATAA
40983747 TGAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (21 bp):
AATTTAAGAAAACATAATAAA
Found at i:40984893 original size:31 final size:30
Alignment explanation
Indices: 40984857--40984916 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
40984847 ATTTTTTTAA
*
40984857 ATGTATATAATTGA-ATCAAAATTAAAATTTT
1 ATGTATATAATT-ACATC-AAATAAAAATTTT
40984888 ATGTATATAATTACATCAAATAAAAATTT
1 ATGTATATAATTACATCAAATAAAAATTT
40984917 ATTATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (30 bp):
ATGTATATAATTACATCAAATAAAAATTTT
Found at i:40995941 original size:6 final size:6
Alignment explanation
Indices: 40995922--40995966 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
40995912 GGAGGATATG
* * * *
40995922 GGTAGG GGTGGA GGTAGA GGAAGA GGTAGG GGTAGA GGTAGA GGT
1 GGTAGA GGTAGA GGTAGA GGTAGA GGTAGA GGTAGA GGTAGA GGT
40995967 GCGCAACTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.58, T:0.16
Consensus pattern (6 bp):
GGTAGA
Found at i:41000221 original size:18 final size:18
Alignment explanation
Indices: 41000198--41000235 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41000188 GGTACTAAAC
41000198 TATATAGTAAAATAGACA
1 TATATAGTAAAATAGACA
41000216 TATATAGTAAAATAGACA
1 TATATAGTAAAATAGACA
41000234 TA
1 TA
41000236 GAATAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (18 bp):
TATATAGTAAAATAGACA
Found at i:41000246 original size:19 final size:18
Alignment explanation
Indices: 41000201--41000247 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
41000191 ACTAAACTAT
*
41000201 ATAGTAAAATAGACATAT
1 ATAGTAAAATAGACATAA
41000219 ATAGTAAAATAGACATAGA
1 ATAGTAAAATAGACATA-A
*
41000238 ATAGAAAAAT
1 ATAGTAAAAT
41000248 GACTACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (18 bp):
ATAGTAAAATAGACATAA
Found at i:41000450 original size:9 final size:9
Alignment explanation
Indices: 41000436--41000461 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41000426 TCAACTCTTG
41000436 TTCTTGTTA
1 TTCTTGTTA
41000445 TTCTTGTTA
1 TTCTTGTTA
41000454 TTCTTGTT
1 TTCTTGTT
41000462 GATGATAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.12, G:0.12, T:0.69
Consensus pattern (9 bp):
TTCTTGTTA
Found at i:41004173 original size:178 final size:178
Alignment explanation
Indices: 41003870--41004195 Score: 460
Period size: 178 Copynumber: 1.8 Consensus size: 178
41003860 TAGGCGGTGA
* * ** **
41003870 CTTTGGTTCCCCAACTTGTTTAAATTGTCCTTTTAATCCTTTTAAAATTTATGTAATTATAAATT
1 CTTTGGTTCCCCAACTTGGTAAAATAATCCTTTTAATCCTTTTAAAATTTATACAATTATAAATT
* * *
41003935 AATATAATGATATTTGAATGAGTGAAATTATACCATTGAACCAAGGGACTAAGACCCCACT-TGT
66 AATATAATGATATTTAAATGAGTGAAATTATACCATTCAACCAAGGGACTAAGACCCCACTAGGT
41003999 CCCTAGCTACGCCCAAAGGAGGAGGGGGAGACAAGGGGGCAAGCAGTGG
131 -CCTAGCTACGCCCAAAGGAGGAGGGGGAGACAAGGGGGCAAGCAGTGG
*
41004048 CTTTGG-TCCCTCAACTTGGTAAAATAATCCTTTTAGTCCTTTTAAAATTTATACAATTATAAAT
1 CTTTGGTTCCC-CAACTTGGTAAAATAATCCTTTTAATCCTTTTAAAATTTATACAATTATAAAT
* * * *
41004112 TAATATAATGATATTTAAATGAGTGAAATTATACTATTCAACTAAGGG-TTCAAGGCCCCACTAG
65 TAATATAATGATATTTAAATGAGTGAAATTATACCATTCAACCAAGGGACT-AAGACCCCACTAG
* *
41004176 GTCCTAGCTATGCTCAAAGG
129 GTCCTAGCTACGCCCAAAGG
41004196 CGAAGACAAA
Statistics
Matches: 129, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
177 5 0.04
178 122 0.95
179 2 0.02
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (178 bp):
CTTTGGTTCCCCAACTTGGTAAAATAATCCTTTTAATCCTTTTAAAATTTATACAATTATAAATT
AATATAATGATATTTAAATGAGTGAAATTATACCATTCAACCAAGGGACTAAGACCCCACTAGGT
CCTAGCTACGCCCAAAGGAGGAGGGGGAGACAAGGGGGCAAGCAGTGG
Found at i:41012106 original size:2 final size:2
Alignment explanation
Indices: 41012101--41012130 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
41012091 ACATACATAC
41012101 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41012131 CATGACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41013340 original size:1 final size:1
Alignment explanation
Indices: 41013334--41013369 Score: 54
Period size: 1 Copynumber: 36.0 Consensus size: 1
41013324 AATAAGAGAG
* *
41013334 CCCCCCCCCCCCCCCCCCCCCCCCCCTCCCCTCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
41013370 TCTCAACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.94, G:0.00, T:0.06
Consensus pattern (1 bp):
C
Found at i:41020327 original size:29 final size:29
Alignment explanation
Indices: 41020294--41020349 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
41020284 ATAAGGACTA
*
41020294 GATCAAATTAGTCACTT-TATTATTAAATG
1 GATCAAATTAGTC-CTTATACTATTAAATG
*
41020323 GATCAATTTAGTCCTTATACTATTAAA
1 GATCAAATTAGTCCTTATACTATTAAA
41020350 AAAGAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (29 bp):
GATCAAATTAGTCCTTATACTATTAAATG
Found at i:41028597 original size:170 final size:172
Alignment explanation
Indices: 41028272--41028607 Score: 489
Period size: 170 Copynumber: 2.0 Consensus size: 172
41028262 TTTTTTTGCT
* * * *
41028272 CAAGCCCATTTTTCAGGCATATATTTTTGCCTAAATCCTCTCACTTTTCGAGCGGGTCTTCGGGG
1 CAAGCCCATTTTTCAAGCATATAATTTTGCCTAAATCCTCTCACTTTTCGAGCAGATCTTCGGGG
*
41028337 TGACCCGACCCATGGATAGGTATATCACCGTCCCATAAATGAACCAATATTTTTAAAATAAAACT
66 TGACCCGAACCATGGATAGGTATATCACCGTCCCATAAATGAACCAATATTTTTAAAATAAAACT
**
41028402 GGTGGTCAAATCGGTTAGGTTATCAGTTCATCAATCTTTACC
131 GGTGGTCAAATCGGTTAAATTATCAGTTCATCAATCTTTACC
* *
41028444 CAAGCTCATTTTTCAAGTATATAATTTTG-CTCAAA-CC-CTCACTTTTCGAGCAGATCTTCGGG
1 CAAGCCCATTTTTCAAGCATATAATTTTGCCT-AAATCCTCTCACTTTTCGAGCAGATCTTCGGG
* * * * * *
41028506 GTGGCTCGAACCATGGATAGGTCTATCACTGTCCCATAAATGAACCAATGTTTTTAAAATAAAAT
65 GTGACCCGAACCATGGATAGGTATATCACCGTCCCATAAATGAACCAATATTTTTAAAATAAAAC
* *
41028571 TGGTGGTCGAATCGGTTAAATTATCAGTTCATTAATC
130 TGGTGGTCAAATCGGTTAAATTATCAGTTCATCAATC
41028608 CGATTAATTT
Statistics
Matches: 146, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
170 114 0.78
171 4 0.03
172 28 0.19
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (172 bp):
CAAGCCCATTTTTCAAGCATATAATTTTGCCTAAATCCTCTCACTTTTCGAGCAGATCTTCGGGG
TGACCCGAACCATGGATAGGTATATCACCGTCCCATAAATGAACCAATATTTTTAAAATAAAACT
GGTGGTCAAATCGGTTAAATTATCAGTTCATCAATCTTTACC
Found at i:41029175 original size:2 final size:2
Alignment explanation
Indices: 41029170--41029201 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
41029160 ACACACAGAC
*
41029170 AT AT AT 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
41029202 GCATGTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:41038411 original size:54 final size:54
Alignment explanation
Indices: 41038329--41038437 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
41038319 TTTGGATGTC
* *
41038329 CGGTGCATTTACTTGTTATTATTGTAAAAGTAATGGTAAGATTAGATACTTTAA
1 CGGTGCATTTACTTGTTATTATTGTAAAAGCAACGGTAAGATTAGATACTTTAA
41038383 CGGTGCATTTACTTGTTATTATTGTAAAAGCAACGGTAAGATTAGATACTTTAA
1 CGGTGCATTTACTTGTTATTATTGTAAAAGCAACGGTAAGATTAGATACTTTAA
41038437 C
1 C
41038438 AATACTGTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (54 bp):
CGGTGCATTTACTTGTTATTATTGTAAAAGCAACGGTAAGATTAGATACTTTAA
Found at i:41040082 original size:28 final size:27
Alignment explanation
Indices: 41040043--41040132 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 27
41040033 AATTTGACAC
* *
41040043 TTTTTTTAAATTTGGTACTTCAACTTT
1 TTTTTTTTAATTTGGTACTTAAACTTT
* *
41040070 TTTTTATTTAATTTGGTATTTGAACTTGAT
1 TTTTT-TTTAATTTGGTACTTAAACTT--T
*
41040100 ATTTTTTCTTAATTTGGTACCTAAACTTT
1 -TTTTTT-TTAATTTGGTACTTAAACTTT
41040129 TTTT
1 TTTT
41040133 GGACCTAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
27 5 0.10
28 22 0.42
29 1 0.02
30 2 0.04
31 22 0.42
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (27 bp):
TTTTTTTTAATTTGGTACTTAAACTTT
Found at i:41040092 original size:59 final size:60
Alignment explanation
Indices: 41040021--41040184 Score: 174
Period size: 59 Copynumber: 2.8 Consensus size: 60
41040011 TTAATATAAT
* * * **
41040021 ATTTGGTATTTGAATTTGACACTTTTTT-TAAATTTGGTACTTCAACTTTTTTT-TATTTA
1 ATTTGGTATTTGAATTTGACA-TTTTTTCTAAATTTGGTACCTAAACTTTTTTTGGACCTA
* * *
41040080 ATTTGGTATTTGAACTTGATATTTTTTCTTAATTTGGTACCTAAACTTTTTTTGGACCTA
1 ATTTGGTATTTGAATTTGACATTTTTTCTAAATTTGGTACCTAAACTTTTTTTGGACCTA
* * *
41040140 ATTTGGTATTTAAATTT-AGCTTTTTTTTCT-AATTTGGTATCTAAA
1 ATTTGGTATTTGAATTTGA-C-ATTTTTTCTAAATTTGGTACCTAAA
41040185 TTTATTAAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
58 6 0.07
59 42 0.48
60 32 0.36
61 8 0.09
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (60 bp):
ATTTGGTATTTGAATTTGACATTTTTTCTAAATTTGGTACCTAAACTTTTTTTGGACCTA
Found at i:41040112 original size:31 final size:30
Alignment explanation
Indices: 41040021--41040118 Score: 103
Period size: 31 Copynumber: 3.3 Consensus size: 30
41040011 TTAATATAAT
* * *
41040021 ATTTGGTATTTGAATTTGACACTTTTTTTAA
1 ATTTGGTATTTGAACTTGATA-TTTTTTTTA
* *
41040052 ATTTGGTACTTCAACTT--T-TTTTTATTTA
1 ATTTGGTATTTGAACTTGATATTTTT-TTTA
41040080 ATTTGGTATTTGAACTTGATATTTTTTCTTA
1 ATTTGGTATTTGAACTTGATATTTTTT-TTA
41040111 ATTTGGTA
1 ATTTGGTA
41040119 CCTAAACTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
27 5 0.09
28 18 0.33
30 2 0.04
31 30 0.55
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (30 bp):
ATTTGGTATTTGAACTTGATATTTTTTTTA
Found at i:41040449 original size:31 final size:32
Alignment explanation
Indices: 41040406--41040465 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
41040396 ACCAATTTTA
* * *
41040406 AAAAAAAGTGTCAAGTTTAGGTATCAAATTAG
1 AAAAAAAGTGTCAAATTCAAGTATCAAATTAG
41040438 AAAAAAA-TGTCAAATTCAAGTATCAAAT
1 AAAAAAAGTGTCAAATTCAAGTATCAAAT
41040466 GTTATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.52, C:0.08, G:0.13, T:0.27
Consensus pattern (32 bp):
AAAAAAAGTGTCAAATTCAAGTATCAAATTAG
Found at i:41041238 original size:15 final size:15
Alignment explanation
Indices: 41041218--41041261 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
41041208 ATTGATTTAG
41041218 AAATTTCAATTAATT
1 AAATTTCAATTAATT
*
41041233 AAATTT-ATTTAATT
1 AAATTTCAATTAATT
**
41041247 AAAAATCAATTAATT
1 AAATTTCAATTAATT
41041262 TTATTTGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTTCAATTAATT
Found at i:41044550 original size:15 final size:16
Alignment explanation
Indices: 41044528--41044568 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
41044518 CACAAAAACG
*
41044528 AAGG-AAAAGAAAATA
1 AAGGTAAAAGAAAAAA
*
41044543 AA-GTAAAAAAAAAAA
1 AAGGTAAAAGAAAAAA
41044558 AAGGTAAAAGA
1 AAGGTAAAAGA
41044569 TTCGATCTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 13 0.62
16 7 0.33
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (16 bp):
AAGGTAAAAGAAAAAA
Found at i:41047068 original size:37 final size:36
Alignment explanation
Indices: 41047027--41047097 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 36
41047017 TCTTGCCAAG
*
41047027 TTTGCCTTGTAAAGGCATACAA-ATGCTCTATATTCCT
1 TTTGCCTGGTAAAGGCATACAATAT-C-CTATATTCCT
41047064 TTTGCCTGGTAAAGGCATACAATATCCTATATTC
1 TTTGCCTGGTAAAGGCATACAATATCCTATATTC
41047098 TTCTCTCTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 8 0.25
37 22 0.69
38 2 0.06
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
TTTGCCTGGTAAAGGCATACAATATCCTATATTCCT
Found at i:41055078 original size:13 final size:13
Alignment explanation
Indices: 41055060--41055084 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41055050 TAATATATTT
41055060 ATTAATTAAAAAC
1 ATTAATTAAAAAC
41055073 ATTAATTAAAAA
1 ATTAATTAAAAA
41055085 TTAAAAAATA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:41059402 original size:13 final size:14
Alignment explanation
Indices: 41059379--41059407 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41059369 GAATGGGAAT
41059379 GAAGAACAAAATGG
1 GAAGAACAAAATGG
41059393 GAAGAA-AAAATGG
1 GAAGAACAAAATGG
41059406 GA
1 GA
41059408 GTAGAGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.31, T:0.07
Consensus pattern (14 bp):
GAAGAACAAAATGG
Found at i:41059847 original size:23 final size:23
Alignment explanation
Indices: 41059817--41059862 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41059807 AAACAAATAA
41059817 ACAAAGGTTTGTATTATAAGTTT
1 ACAAAGGTTTGTATTATAAGTTT
41059840 ACAAAGGTTTGTATTATAAGTTT
1 ACAAAGGTTTGTATTATAAGTTT
41059863 GATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.43
Consensus pattern (23 bp):
ACAAAGGTTTGTATTATAAGTTT
Found at i:41074825 original size:31 final size:30
Alignment explanation
Indices: 41074782--41074856 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
41074772 ATTTAAATTC
*
41074782 AAAAAATAGAAAGATTAAAATTTTAATA-AT
1 AAAAAATAGAAAGATT-AAATTTAAATATAT
*
41074812 AAAAAATGTGAAAGATTAAATTTAAATATAT
1 AAAAAAT-AGAAAGATTAAATTTAAATATAT
41074843 AAAAAGTATAGAAA
1 AAAAA--ATAGAAA
41074857 TTTAAAGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 17 0.45
31 15 0.39
32 4 0.11
33 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (30 bp):
AAAAAATAGAAAGATTAAATTTAAATATAT
Found at i:41078983 original size:5 final size:6
Alignment explanation
Indices: 41078968--41078993 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41078958 TTCATCTATA
41078968 CCCCCT CCCCCT CCCCCT CCCCCT CC
1 CCCCCT CCCCCT CCCCCT CCCCCT CC
41078994 ATTTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCCCT
Found at i:41082560 original size:2 final size:2
Alignment explanation
Indices: 41082553--41082578 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41082543 TTCCTATCTT
41082553 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
41082579 ACATACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:41087948 original size:16 final size:17
Alignment explanation
Indices: 41087917--41087949 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41087907 AACTAAAATG
*
41087917 TAATTTCATCATTTTAT
1 TAATTTCATAATTTTAT
41087934 TAATTT-ATAATTTTAT
1 TAATTTCATAATTTTAT
41087950 ATCTTTAAAA
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:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTCATAATTTTAT
Found at i:41088052 original size:31 final size:31
Alignment explanation
Indices: 41088014--41088117 Score: 140
Period size: 31 Copynumber: 3.4 Consensus size: 31
41088004 GAGGGATCAG
41088014 ACATATAATTTTATAAAATTTATATGACCAA
1 ACATATAATTTTATAAAATTTATATGACCAA
* **
41088045 ACATATAATTTTATAAAATTTA-GTGTA-TTA
1 ACATATAATTTTATAAAATTTATATG-ACCAA
* *
41088075 ACTTCTAATTTTATAAAATTTATATGACCAA
1 ACATATAATTTTATAAAATTTATATGACCAA
41088106 ACATATAATTTT
1 ACATATAATTTT
41088118 TCATTTTAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
30 24 0.40
31 36 0.60
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (31 bp):
ACATATAATTTTATAAAATTTATATGACCAA
Found at i:41105660 original size:16 final size:17
Alignment explanation
Indices: 41105631--41105662 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41105621 TACAAAATTG
41105631 TTTTTAAATCTTTTTAT
1 TTTTTAAATCTTTTTAT
41105648 TTTTTAAAT-TTTTTA
1 TTTTTAAATCTTTTTA
41105663 GTATTTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTAAATCTTTTTAT
Found at i:41105669 original size:17 final size:17
Alignment explanation
Indices: 41105632--41105671 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
41105622 ACAAAATTGT
*
41105632 TTTTAAATCTTTTTATT
1 TTTTAAATCTTTTTATA
41105649 TTTTAAAT-TTTTTAGTA
1 TTTTAAATCTTTTTA-TA
41105666 TTTTAA
1 TTTTAA
41105672 TGATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTAAATCTTTTTATA
Found at i:41111313 original size:25 final size:25
Alignment explanation
Indices: 41111258--41111313 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
41111248 TTCGGAAAAA
*
41111258 AAAAATTTACAAGTCAAAATAAGAT
1 AAAAATTTACAACTCAAAATAAGAT
*
41111283 ACAAAATTTA-AACTCAAAATCAGCAT
1 A-AAAATTTACAACTCAAAATAAG-AT
41111309 AAAAA
1 AAAAA
41111314 AATTTGGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.21
Consensus pattern (25 bp):
AAAAATTTACAACTCAAAATAAGAT
Found at i:41111314 original size:26 final size:26
Alignment explanation
Indices: 41111257--41111314 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
41111247 ATTCGGAAAA
*
41111257 AAAAAATTTACAAGTCAAAATAAGAT
1 AAAAAATTTACAACTCAAAATAAGAT
* *
41111283 ACAAAATTTA-AACTCAAAATCAGCAT
1 AAAAAATTTACAACTCAAAATAAG-AT
41111309 AAAAAA
1 AAAAAA
41111315 ATTTGGCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (26 bp):
AAAAAATTTACAACTCAAAATAAGAT
Found at i:41117262 original size:30 final size:31
Alignment explanation
Indices: 41117218--41117283 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
41117208 GTCAAAAAAG
*
41117218 TTTTT-TGAGGGTTAAAAT-TAAATTATTTA
1 TTTTTATGAGAGTTAAAATATAAATTATTTA
* *
41117247 TTTTTATGAGAGTTAAAATATAATTTTTTTA
1 TTTTTATGAGAGTTAAAATATAAATTATTTA
*
41117278 ATTTTA
1 TTTTTA
41117284 ATAGCTTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 5 0.16
30 12 0.39
31 14 0.45
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.55
Consensus pattern (31 bp):
TTTTTATGAGAGTTAAAATATAAATTATTTA
Found at i:41123925 original size:3 final size:3
Alignment explanation
Indices: 41123917--41123947 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
41123907 CCTTTAGTCC
41123917 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
41123948 TTGTAAAATA
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:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:41130743 original size:15 final size:15
Alignment explanation
Indices: 41130717--41130761 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
41130707 TTTTACTCAA
41130717 AACTTGAAAAATAAAT
1 AACTT-AAAAATAAAT
*
41130733 AACTTAAAAATAATT
1 AACTTAAAAATAAAT
*
41130748 AAATTAAAAATAAA
1 AACTTAAAAATAAA
41130762 GACTAAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (15 bp):
AACTTAAAAATAAAT
Found at i:41131119 original size:36 final size:37
Alignment explanation
Indices: 41131068--41131137 Score: 115
Period size: 36 Copynumber: 1.9 Consensus size: 37
41131058 AATCTTGAAA
*
41131068 CGATCACTAATAAAAATGTTTTACTTGAATAGTAGCT
1 CGATCACTAATAAAAAAGTTTTACTTGAATAGTAGCT
*
41131105 CGAT-ACTATTAAAAAAGTTTTACTTGAATAGTA
1 CGATCACTAATAAAAAAGTTTTACTTGAATAGTA
41131138 TCTTGACCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 27 0.87
37 4 0.13
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (37 bp):
CGATCACTAATAAAAAAGTTTTACTTGAATAGTAGCT
Found at i:41182137 original size:12 final size:11
Alignment explanation
Indices: 41182118--41182147 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
41182108 CCTTACTAGG
41182118 TTTTTATTTAT
1 TTTTTATTTAT
41182129 TTATTTATTTAT
1 TT-TTTATTTAT
41182141 TTTTTAT
1 TTTTTAT
41182148 AGTGTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:41187740 original size:16 final size:16
Alignment explanation
Indices: 41187705--41187749 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
41187695 TTTTAAAATT
41187705 TTAAAAAAT-ATAAAA
1 TTAAAAAATAATAAAA
* *
41187720 ATAAAAAATAATCAAA
1 TTAAAAAATAATAAAA
*
41187736 TTAAAATATAATAA
1 TTAAAAAATAATAA
41187750 CTAAATCCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
TTAAAAAATAATAAAA
Found at i:41188561 original size:142 final size:142
Alignment explanation
Indices: 41188400--41188658 Score: 360
Period size: 142 Copynumber: 1.8 Consensus size: 142
41188390 TTCATGGATC
* *
41188400 AATCGATCTGATCCTTTATT-TCGAAACAGTA-CCTTAATCGGTTTTTGGTTCGATCGATCAGTC
1 AATCAATCTGACCCTTTATTCT-GAAACAGTATCC-TAATCGGTTTTTGGTTCGATCGATCAGTC
* * *
41188463 CAGTTCTGAAAGCACTAATTTTAGATCTAGTTTAAGGCGTAAGTTGGATTTGACCCTTTCAAGTT
64 CAGTTCTGAAAGCACTAATCTTAGATCTAGTTTAAGGCGTAAGCTGAATTTGACCCTTTCAAGTT
41188528 TAAGGTGTGAGTTG
129 TAAGGTGTGAGTTG
* * *
41188542 AATCAATCTGACCCTTTATTCTGGAACAGTATCCTAATCGGTTTTTGGTTCGATCGATCGGTCTA
1 AATCAATCTGACCCTTTATTCTGAAACAGTATCCTAATCGGTTTTTGGTTCGATCGATCAGTCCA
* * * * * *
41188607 TTTCTGAAAGCAGTGATCTTAGGTCTGGTTTAAGGCGTGAGCTGAATTTGAC
66 GTTCTGAAAGCACTAATCTTAGATCTAGTTTAAGGCGTAAGCTGAATTTGAC
41188659 GTTTTCAGAG
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
142 98 0.97
143 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (142 bp):
AATCAATCTGACCCTTTATTCTGAAACAGTATCCTAATCGGTTTTTGGTTCGATCGATCAGTCCA
GTTCTGAAAGCACTAATCTTAGATCTAGTTTAAGGCGTAAGCTGAATTTGACCCTTTCAAGTTTA
AGGTGTGAGTTG
Found at i:41189694 original size:28 final size:29
Alignment explanation
Indices: 41189636--41189696 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
41189626 AAAATCACAG
*
41189636 TTATTTAAAATCAAATTGAATTCTACTTT
1 TTATTTAAAATCAAATTGAATTCTAATTT
* *
41189665 TTATTTAATAT-ATAATT-AATTTTAATTT
1 TTATTTAAAATCA-AATTGAATTCTAATTT
41189693 TTAT
1 TTAT
41189697 GATATAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (29 bp):
TTATTTAAAATCAAATTGAATTCTAATTT
Found at i:41190080 original size:237 final size:225
Alignment explanation
Indices: 41189780--41190228 Score: 745
Period size: 225 Copynumber: 1.9 Consensus size: 225
41189770 ATTAAATATA
*
41189780 AAATGATGCTATATTAATGTATTAATAATTTATAAGGATTGGATCAAATCAAATCAAAATTTCAT
1 AAATGATGCTATATTAATGTATTAATAATTTATAAAGATTGGATCAAATCAAATC-AAA----A-
41189845 GTCAAAGTTCATGCATAGTTTTAACGATTTATCCCTAATATATATTATATATATGACTTATTTAA
60 -T-----TTCATGCATAGTTTTAACGATTTATCCCTAATATATATTATATATATGACTTATTTAA
*
41189910 TAATTGAAATAACATATGATCTAGTTGAAATCGTGATTCATCTATCATGTAAGAACAGAAAGTGA
119 TAATTGAAATAACATATGACCTAGTTGAAATCGTGATTCATCTATCATGTAAGAACAGAAAGTGA
41189975 AACTGAGCCCGGACAACTCACGGCATCAAATCAAATCAAATC
184 AACTGAGCCCGGACAACTCACGGCATCAAATCAAATCAAATC
*
41190017 AAATGATGCTATATTAATGTATTAATAATTTGTAAAGATTGGATCAAATCAAATCAAAATTTCAT
1 AAATGATGCTATATTAATGTATTAATAATTTATAAAGATTGGATCAAATCAAATCAAAATTTCAT
*
41190082 GCATAGTTTTAACGATTTATCCCTAATATATATTATATATATGACTTATTTAGTAATTGAAATAA
66 GCATAGTTTTAACGATTTATCCCTAATATATATTATATATATGACTTATTTAATAATTGAAATAA
*
41190147 CATATGACCTAGTTGAAATCGTGATTCATCTATCATGTAAGAACAGAAAGTGAAATTGAGCCCGG
131 CATATGACCTAGTTGAAATCGTGATTCATCTATCATGTAAGAACAGAAAGTGAAACTGAGCCCGG
41190212 ACAACTCACGGCATCAA
196 ACAACTCACGGCATCAA
41190229 CACAATTAAG
Statistics
Matches: 207, Mismatches: 5, Indels: 12
0.92 0.02 0.05
Matches are distributed among these distances:
225 149 0.72
230 1 0.00
232 1 0.00
236 3 0.01
237 53 0.26
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (225 bp):
AAATGATGCTATATTAATGTATTAATAATTTATAAAGATTGGATCAAATCAAATCAAAATTTCAT
GCATAGTTTTAACGATTTATCCCTAATATATATTATATATATGACTTATTTAATAATTGAAATAA
CATATGACCTAGTTGAAATCGTGATTCATCTATCATGTAAGAACAGAAAGTGAAACTGAGCCCGG
ACAACTCACGGCATCAAATCAAATCAAATC
Found at i:41190418 original size:2 final size:2
Alignment explanation
Indices: 41190413--41190442 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41190403 TAGCAGAGAG
41190413 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
41190443 AGAGAGCAGC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41198151 original size:17 final size:19
Alignment explanation
Indices: 41198116--41198151 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41198106 AAATTTATCT
41198116 TTCTCTTTTTTTTCTATAA
1 TTCTCTTTTTTTTCTATAA
41198135 TTCT-TTTTTTTTC-ATAA
1 TTCTCTTTTTTTTCTATAA
41198152 AACAACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 9 0.53
19 4 0.24
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (19 bp):
TTCTCTTTTTTTTCTATAA
Found at i:41203404 original size:5 final size:5
Alignment explanation
Indices: 41203394--41203435 Score: 57
Period size: 5 Copynumber: 7.8 Consensus size: 5
41203384 ACATGACACT
41203394 TTTTA TTTTA TTTTA TTTTA TTTTA TTTATAA TTTTCA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTT-T-A TTTT-A TTTT
41203436 CCAATTTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
5 23 0.68
6 7 0.21
7 4 0.12
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:41218880 original size:26 final size:26
Alignment explanation
Indices: 41218851--41218909 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
41218841 TATATTTATA
41218851 AAAAAATC-TAAAATTAAAAAAAAAAT
1 AAAAAATCATAAAA-TAAAAAAAAAAT
**
41218877 AAAAAATCATAAAATAAAGGAAAAAT
1 AAAAAATCATAAAATAAAAAAAAAAT
*
41218903 AATAAAT
1 AAAAAAT
41218910 ACAAGTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (26 bp):
AAAAAATCATAAAATAAAAAAAAAAT
Found at i:41221132 original size:348 final size:348
Alignment explanation
Indices: 41220494--41221142 Score: 806
Period size: 348 Copynumber: 1.9 Consensus size: 348
41220484 TTCCTAGGTC
* * *
41220494 AAATTTTGTTATTAGTCCCTATACTATGTCTAGGTTGTTAATTTAGTACTTATGCTCTAGTTCAG
1 AAATTTTGTTAGTAGTCCCTATACTATGGCTAGGTTGTTAATTTAGTACTTATGCTCTAATTCAG
* * * * *** *
41220559 TTAAATTTTAGTCCGTGTACTTTTTGAATTTTGAAGTTTTAAGTCTTTTCCCAAACAGTACAGTT
66 GTAAATCTTAGTACGTGTACTTTTTGAATATTGAAGTTTTAAGTCTTAAACCAAACAGAACAGTT
* * * * * * *
41220624 GAAATCATTTGGTTAAATTTTGTTATTAGTCTCTATACTATGTGCAAATTGCTAATTTAGTTCAT
131 GAAATCATCTGGTTAAATTTTGTTATTAGACTCTATACTATATGCAAACTGCGAATTTAATCCAT
*
41220689 GTTCTCTAATTTAATCAAGTTTAGTCGGTGTACTTTTTGAATTTTGGAGTTTAAATCTTGACCCA
196 GTTCTATAATTTAATCAAGTTTAGTCGGTGTACTTTTTGAATTTTGGAGTTTAAATCTTGACCCA
* * * *
41220754 AATGTTAATAGTTAAATGTGCTCGATCAAATTCTATTATTATTCTTGTACTATTCGTAAGTTGTG
261 AATGGTAATAGTTAAATCTACTCAATCAAATTCTATTATTATTCTTGTACTATTCGTAAGTTGTG
41220819 GATTTAATCTCTAATTTTCTAAT
326 GATTTAATCTCTAATTTTCTAAT
* *
41220842 AAATTTTGTTAGTAGTCCCTATACTATGGCTAGGTTGTTAGTTTAGT-CTTTATGCTCTAATT-T
1 AAATTTTGTTAGTAGTCCCTATACTATGGCTAGGTTGTTAATTTAGTAC-TTATGCTCTAATTCA
* * * * *
41220905 GGTCAATCTTAGTATGTGTAGTTTTTGAATATTGAAG-TTTAAGTCTTGAAACCAAACGGAAATA
65 GGTAAATCTTAGTACGTGTACTTTTTGAATATTGAAGTTTTAAGTCTT-AAACCAAACAG-AACA
* * *
41220969 GTT-AAATTCATCTGGTTAAATTTTGTTATTAGAC-CATGTACTATATGTAAGCTGCGAATTTAA
128 GTTGAAA-TCATCTGGTTAAATTTTGTTATTAGACTC-TATACTATATGCAAACTGCGAATTTAA
* ** ** * ** *
41221032 TCCTTGTAT-TATAATTTGGTTTATTTTAGTTTGTGTATTTTTTGAATTTTGGAGTTTAAATCTT
191 TCCATGT-TCTATAATTTAATCAAGTTTAGTCGGTGTACTTTTTGAATTTTGGAGTTTAAATCTT
* *
41221096 GATCCAAATGGTAATAGTTAAATCTATTCAATCAAATTCTATTATTA
255 GACCCAAATGGTAATAGTTAAATCTACTCAATCAAATTCTATTATTA
41221143 GTCTCGTATT
Statistics
Matches: 251, Mismatches: 44, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
346 10 0.04
347 42 0.17
348 198 0.79
349 1 0.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (348 bp):
AAATTTTGTTAGTAGTCCCTATACTATGGCTAGGTTGTTAATTTAGTACTTATGCTCTAATTCAG
GTAAATCTTAGTACGTGTACTTTTTGAATATTGAAGTTTTAAGTCTTAAACCAAACAGAACAGTT
GAAATCATCTGGTTAAATTTTGTTATTAGACTCTATACTATATGCAAACTGCGAATTTAATCCAT
GTTCTATAATTTAATCAAGTTTAGTCGGTGTACTTTTTGAATTTTGGAGTTTAAATCTTGACCCA
AATGGTAATAGTTAAATCTACTCAATCAAATTCTATTATTATTCTTGTACTATTCGTAAGTTGTG
GATTTAATCTCTAATTTTCTAAT
Found at i:41229393 original size:31 final size:31
Alignment explanation
Indices: 41229358--41229422 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
41229348 TTACAAAATG
* *
41229358 GTCGTTGAATTATTCGAAACTTTTTATTTAA
1 GTCGTTGAACTATTCAAAACTTTTTATTTAA
*
41229389 GTCGTTGAACTATTCAAAAGTTTTTATTTAA
1 GTCGTTGAACTATTCAAAACTTTTTATTTAA
41229420 GTC
1 GTC
41229423 TATGGGCTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (31 bp):
GTCGTTGAACTATTCAAAACTTTTTATTTAA
Found at i:41231566 original size:29 final size:30
Alignment explanation
Indices: 41231455--41231753 Score: 159
Period size: 29 Copynumber: 10.2 Consensus size: 30
41231445 CAAGAGGTCC
*
41231455 CTAAACTTTTCAAAAATTTG-ATTTTAA-CT
1 CTAAACTTTTCTAAAA-TTGCATTTTAACCT
41231484 CTTAAACTTTTCTAAAATTGCATTTTAACCT
1 C-TAAACTTTTCTAAAATTGCATTTTAACCT
*
41231515 CTAAACTTTTCTAAAATTGCATTTTGACCT
1 CTAAACTTTTCTAAAATTGCATTTTAACCT
* * * *
41231545 -TGAAGTTTTCCAAAATTACATTTTAA-CT
1 CTAAACTTTTCTAAAATTGCATTTTAACCT
* * ***
41231573 CTTAAAC-TTCCCAAAATCATATTTTAA-CT
1 C-TAAACTTTTCTAAAATTGCATTTTAACCT
* * * * *
41231602 CTTAAAC-TTCCCAAAATTGTATTTTGACCC
1 C-TAAACTTTTCTAAAATTGCATTTTAACCT
* * * * *** *
41231632 CCAAACATTCCCAAAACCACATTTTGACC-
1 CTAAACTTTTCTAAAATTGCATTTTAACCT
* *** *
41231661 CTAAACTTTCCTAAAATCATATTTTGACC-
1 CTAAACTTTTCTAAAATTGCATTTTAACCT
* ** * *
41231690 CTAAACTTTCCTAAAATTATATTTTTACCC
1 CTAAACTTTTCTAAAATTGCATTTTAACCT
* * *
41231720 CTAAAATTTTCCAAATTTGCATTTTAACCT
1 CTAAACTTTTCTAAAATTGCATTTTAACCT
41231750 -TAAA
1 CTAAA
41231754 TTCTCCGAAA
Statistics
Matches: 226, Mismatches: 36, Indels: 16
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.01
29 127 0.56
30 94 0.42
31 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (30 bp):
CTAAACTTTTCTAAAATTGCATTTTAACCT
Found at i:41231646 original size:88 final size:88
Alignment explanation
Indices: 41231475--41231753 Score: 233
Period size: 88 Copynumber: 3.2 Consensus size: 88
41231465 CAAAAATTTG
* * *** * * **
41231475 ATTTTAACTCTTAAACTTTTCTAAAATTGCATTTTAACCTCTAAACTTTTCTAAAATTGCATTTT
1 ATTTTAAC-CTTAAACTTTCCCAAAATCATATTTTAACC-CTAAACTTTCCCAAAATTATATTTT
*** * *
41231540 GA-CCTTGAAGTTTTCCAAAATTAC
64 GACCCCCAAAATTTCCCAAAATTAC
* *
41231564 ATTTTAACTCTTAAAC-TTCCCAAAATCATATTTTAACTCTTAAAC-TTCCCAAAATTGTATTTT
1 ATTTTAAC-CTTAAACTTTCCCAAAATCATATTTTAAC-CCTAAACTTTCCCAAAATTATATTTT
**
41231627 GACCCCCAAACA-TTCCCAAAACCAC
64 GACCCCCAAA-ATTTCCCAAAATTAC
* * * * * *
41231652 ATTTTGACCCTAAACTTTCCTAAAATCATATTTTGACCCTAAACTTTCCTAAAATTATATTTTTA
1 ATTTTAACCTTAAACTTTCCCAAAATCATATTTTAACCCTAAACTTTCCCAAAATTATATTTTGA
* * * *
41231717 CCCCTAAAATTTTCCAAATTTGC
66 CCCCCAAAATTTCCCAAAATTAC
41231740 ATTTTAACCTTAAA
1 ATTTTAACCTTAAA
41231754 TTCTCCGAAA
Statistics
Matches: 152, Mismatches: 32, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
87 30 0.20
88 105 0.69
89 17 0.11
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (88 bp):
ATTTTAACCTTAAACTTTCCCAAAATCATATTTTAACCCTAAACTTTCCCAAAATTATATTTTGA
CCCCCAAAATTTCCCAAAATTAC
Found at i:41231744 original size:59 final size:58
Alignment explanation
Indices: 41231453--41231753 Score: 185
Period size: 59 Copynumber: 5.1 Consensus size: 58
41231443 CTCAAGAGGT
* * * * * *
41231453 CCCTAAACTTTTCAAAAATT-TGATTTTAACTCTTAAACTTTTCTAAAATTGCATTTTAA
1 CCCTAAACTTTCCCAAAATTAT-ATTTTGAC-CCTAAAATTTTCCAAAATTGCATTTTAA
* * ** * * * *
41231512 CCTCTAAACTTTTCTAAAATTGCATTTTGACCTTGAAGTTTTCCAAAATTACATTTTAA
1 CC-CTAAACTTTCCCAAAATTATATTTTGACCCTAAAATTTTCCAAAATTGCATTTTAA
* * * * * * * * *
41231571 CTCTTAAAC-TTCCCAAAATCATATTTTAACTCTTAAACTTCCCAAAATTGTATTTTGAC
1 C-CCTAAACTTTCCCAAAATTATATTTTGACCCTAAAATTTTCCAAAATTGCATTTT-AA
* * ** * * *** *
41231630 CCCCAAACATTCCCAAAACCACATTTTGACCCT-AAACTTTCCTAAAATCATATTTTGA
1 CCCTAAACTTTCCCAAAATTATATTTTGACCCTAAAATTTTCC-AAAATTGCATTTTAA
* * *
41231688 CCCTAAACTTTCCTAAAATTATATTTTTACCCCTAAAATTTTCCAAATTTGCATTTTAA
1 CCCTAAACTTTCCCAAAATTATATTTTGA-CCCTAAAATTTTCCAAAATTGCATTTTAA
*
41231747 CCTTAAA
1 CCCTAAA
41231754 TTCTCCGAAA
Statistics
Matches: 186, Mismatches: 48, Indels: 16
0.74 0.19 0.06
Matches are distributed among these distances:
58 68 0.37
59 85 0.46
60 33 0.18
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (58 bp):
CCCTAAACTTTCCCAAAATTATATTTTGACCCTAAAATTTTCCAAAATTGCATTTTAA
Found at i:41232727 original size:18 final size:19
Alignment explanation
Indices: 41232706--41232744 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41232696 GTTCGGTTTT
41232706 AATTAAAT-AAAATATTAA
1 AATTAAATAAAAATATTAA
**
41232724 AATTTTATAAAAATATTAA
1 AATTAAATAAAAATATTAA
41232743 AA
1 AA
41232745 ATTATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTAAATAAAAATATTAA
Found at i:41232749 original size:18 final size:19
Alignment explanation
Indices: 41232714--41232753 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
41232704 TTAATTAAAT
*
41232714 AAAATATTAAAATTTTATA
1 AAAATATTAAAATATTATA
41232733 AAAATATTAAAA-ATTATA
1 AAAATATTAAAATATTATA
41232751 AAA
1 AAA
41232754 TTTGATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATATTAAAATATTATA
Found at i:41235857 original size:134 final size:135
Alignment explanation
Indices: 41235680--41235937 Score: 419
Period size: 134 Copynumber: 1.9 Consensus size: 135
41235670 TTTGATTGAC
* *
41235680 GTACAAGGATTAATTTACTTATTTTTTAAGCATAGGGAGGTAAAATGCAATCTGACTCCTAATAA
1 GTACAAGGATTAATTTACTTATTTTTTAAGCACAGGGAGGTAAAATACAATCTGACTCCTAATAA
* * * *
41235745 AGGGATCTCGGTAGTACTTTTACCACTGTCATGTCTTTGCAATAAGCACGGGC-ATGGGATATTT
66 AGAGATCTCAGTAGTACTTTTACCACTGTCATGCCTTTGCAATAAACACGGGCAATGGGATATTT
41235809 TAATA
131 TAATA
* * *
41235814 GTACAATGATTAATTTACTTATTTTTTAAGTACAGGGATGTAAAATACAATCTGACTCCTAATAA
1 GTACAAGGATTAATTTACTTATTTTTTAAGCACAGGGAGGTAAAATACAATCTGACTCCTAATAA
*
41235879 AGAGATCTCAGTAGTACTTTTACCATTGTCATGCCTTTGCAATAAACACGGGCAATGGG
66 AGAGATCTCAGTAGTACTTTTACCACTGTCATGCCTTTGCAATAAACACGGGCAATGGG
41235938 TGATTATTTT
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
134 108 0.96
135 5 0.04
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (135 bp):
GTACAAGGATTAATTTACTTATTTTTTAAGCACAGGGAGGTAAAATACAATCTGACTCCTAATAA
AGAGATCTCAGTAGTACTTTTACCACTGTCATGCCTTTGCAATAAACACGGGCAATGGGATATTT
TAATA
Found at i:41237762 original size:3 final size:3
Alignment explanation
Indices: 41237754--41237783 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41237744 CGTAATCCAT
41237754 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
41237784 AATGTGAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:41239472 original size:31 final size:31
Alignment explanation
Indices: 41239424--41239518 Score: 145
Period size: 31 Copynumber: 3.1 Consensus size: 31
41239414 CAAAATGCAC
* * *
41239424 TGAATTATTTGAAAGTTTTCATTTAAGTTAT
1 TGAACTATTTGAAAGTTTTTATTCAAGTTAT
* *
41239455 TGAACTATTCGAAAGTTTTTATTCAAGTTGT
1 TGAACTATTTGAAAGTTTTTATTCAAGTTAT
41239486 TGAACTATTTGAAAGTTTTTATTCAAGTTAT
1 TGAACTATTTGAAAGTTTTTATTCAAGTTAT
41239517 TG
1 TG
41239519 GGTTGTTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (31 bp):
TGAACTATTTGAAAGTTTTTATTCAAGTTAT
Found at i:41250617 original size:35 final size:35
Alignment explanation
Indices: 41250576--41250645 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
41250566 GGGTAAATTA
*
41250576 TACAAAATATCACTAAAATTACTAGTAAATTTATG
1 TACAAAATATCACTAAAATTACTAATAAATTTATG
* *
41250611 TACAAAATATCATTAAAATTATTAATAAATTTATG
1 TACAAAATATCACTAAAATTACTAATAAATTTATG
41250646 CTTCGATCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (35 bp):
TACAAAATATCACTAAAATTACTAATAAATTTATG
Found at i:41254773 original size:40 final size:40
Alignment explanation
Indices: 41254718--41254797 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
41254708 ATAATAAGAT
*
41254718 AAATTCCCCTGCATCACTTATCAAAATACAATACTTCAAA
1 AAATTCCCCTGCATCACTTATCAAAATACAATACATCAAA
** * *
41254758 AAATTCCGTTGCATCATTTGTCAAAATACAATACATCAAA
1 AAATTCCCCTGCATCACTTATCAAAATACAATACATCAAA
41254798 TCAACACAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (40 bp):
AAATTCCCCTGCATCACTTATCAAAATACAATACATCAAA
Found at i:41258007 original size:16 final size:16
Alignment explanation
Indices: 41257986--41258018 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41257976 CATAAAACAG
41257986 AAGATAGAAGTGAGTT
1 AAGATAGAAGTGAGTT
41258002 AAGATAGAAGTGAGTT
1 AAGATAGAAGTGAGTT
41258018 A
1 A
41258019 GGCTATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.30, T:0.24
Consensus pattern (16 bp):
AAGATAGAAGTGAGTT
Done.