Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2
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: 5794061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 68655 characters in sequence are not A, C, G, or T
File 25 of 38
Found at i:3837229 original size:21 final size:21
Alignment explanation
Indices: 3837203--3837278 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3837193 ACATGTTGCA
3837203 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3837224 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3837244 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
3837265 ATGTATCGATACAT
1 ATGTATCGATACAT
3837279 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3837236 original size:41 final size:41
Alignment explanation
Indices: 3837185--3837278 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
3837175 ACAATTCAAA
*
3837185 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3837226 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3837267 GTATCGATACAT
1 GTATCGATACAT
3837279 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3837335 original size:13 final size:13
Alignment explanation
Indices: 3837317--3837342 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3837307 TACAGCAAGT
3837317 ATGTATCGATACA
1 ATGTATCGATACA
3837330 ATGTATCGATACA
1 ATGTATCGATACA
3837343 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3838439 original size:13 final size:13
Alignment explanation
Indices: 3838421--3838459 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3838411 CTCACCGAGA
3838421 TTTTTTGTTTTGT
1 TTTTTTGTTTTGT
3838434 TTTTTTGTTTT-T
1 TTTTTTGTTTTGT
*
3838446 TTCTTTTTTTTTGT
1 TT-TTTTGTTTTGT
3838460 GTTTGGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 3 0.13
13 19 0.83
14 1 0.04
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (13 bp):
TTTTTTGTTTTGT
Found at i:3838462 original size:20 final size:21
Alignment explanation
Indices: 3838421--3838463 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
3838411 CTCACCGAGA
* *
3838421 TTTTTTGTTTTGTTTTTTTGT
1 TTTTTTCTTTTGTTTTTGTGT
3838442 TTTTTTCTTTT-TTTTTGTGT
1 TTTTTTCTTTTGTTTTTGTGT
3838462 TT
1 TT
3838464 GGAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (21 bp):
TTTTTTCTTTTGTTTTTGTGT
Found at i:3845690 original size:52 final size:51
Alignment explanation
Indices: 3845620--3845739 Score: 197
Period size: 52 Copynumber: 2.3 Consensus size: 51
3845610 GAAAATTTAT
*
3845620 CTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA-TTGC
*
3845672 CTGCATGTGTCGATACATTTTAAAATGTATCGATACATCTGGGCAAATTGC
1 CTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGCAAATTGC
3845723 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
3845740 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
51 20 0.31
52 39 0.61
53 5 0.08
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGCAAATTGC
Found at i:3845766 original size:13 final size:13
Alignment explanation
Indices: 3845748--3845772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3845738 CAAAGATCAG
3845748 TGTATCGATACAA
1 TGTATCGATACAA
3845761 TGTATCGATACA
1 TGTATCGATACA
3845773 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3845850 original size:33 final size:33
Alignment explanation
Indices: 3845813--3845879 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3845803 AGTAGCTTAA
3845813 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3845846 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3845879 A
1 A
3845880 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3845853 original size:13 final size:13
Alignment explanation
Indices: 3845835--3845859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3845825 CAAAAAAATA
3845835 TGTATCGATACAT
1 TGTATCGATACAT
3845848 TGTATCGATACA
1 TGTATCGATACA
3845860 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3846093 original size:18 final size:18
Alignment explanation
Indices: 3846070--3846104 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3846060 AAACCATTTT
3846070 TAGGTCGAATCCCCCACA
1 TAGGTCGAATCCCCCACA
*
3846088 TAGGTCGAATCCTCCAC
1 TAGGTCGAATCCCCCAC
3846105 CTACTAGCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.17, T:0.20
Consensus pattern (18 bp):
TAGGTCGAATCCCCCACA
Found at i:3854623 original size:76 final size:76
Alignment explanation
Indices: 3854512--3854663 Score: 286
Period size: 76 Copynumber: 2.0 Consensus size: 76
3854502 TATCGATACA
* *
3854512 TAGGTAATTGTATCGATACATTATGGTTGATCTAGGCTAAAAATGTCAAAACCCTTGAATGTATC
1 TAGGTAATTGTATCGATACATTATGGTTGACCTAGGCTAAAAATGTAAAAACCCTTGAATGTATC
3854577 GATACACACCC
66 GATACACACCC
3854588 TAGGTAATTGTATCGATACATTATGGTTGACCTAGGCTAAAAATGTAAAAACCCTTGAATGTATC
1 TAGGTAATTGTATCGATACATTATGGTTGACCTAGGCTAAAAATGTAAAAACCCTTGAATGTATC
3854653 GATACACACCC
66 GATACACACCC
3854664 AGATGTATCG
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (76 bp):
TAGGTAATTGTATCGATACATTATGGTTGACCTAGGCTAAAAATGTAAAAACCCTTGAATGTATC
GATACACACCC
Found at i:3855638 original size:14 final size:14
Alignment explanation
Indices: 3855586--3855645 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
3855576 GATTTTTAAC
*
3855586 GATACATGAATAGT
1 GATACATGAACAGT
*
3855600 GATACGTGAACAAGGT
1 GATACATGAAC-A-GT
3855616 GA-ACAATGAACAGT
1 GATAC-ATGAACAGT
3855630 GATACATGAA-AGT
1 GATACATGAACAGT
3855643 GAT
1 GAT
3855646 GTATCGATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 6 0.15
14 18 0.46
15 6 0.15
16 9 0.23
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.22
Consensus pattern (14 bp):
GATACATGAACAGT
Found at i:3855691 original size:53 final size:53
Alignment explanation
Indices: 3855628--3855729 Score: 186
Period size: 53 Copynumber: 1.9 Consensus size: 53
3855618 ACAATGAACA
*
3855628 GTGATACATGAAAGTGATGTATCGATACATGAACAGTGATGAATAGTGACAGG
1 GTGATACATGAAAGTGATGTATCGATACATGAACAGTGATGAACAGTGACAGG
*
3855681 GTGATACATGAAAGTGATGTATCGATTCATGAACAGTGATGAACAGTGA
1 GTGATACATGAAAGTGATGTATCGATACATGAACAGTGATGAACAGTGA
3855730 AAATGAGATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.25
Consensus pattern (53 bp):
GTGATACATGAAAGTGATGTATCGATACATGAACAGTGATGAACAGTGACAGG
Found at i:3858633 original size:33 final size:33
Alignment explanation
Indices: 3858575--3858637 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
3858565 TGTTGGGCAC
*
3858575 AATGTATCGATACAATTCTTCATGTATCGAAAT
1 AATGTATCGATACAATTCCTCATGTATCGAAAT
*
3858608 AATGTATCGATACATTATCCT-ATGTATCGA
1 AATGTATCGATACAAT-TCCTCATGTATCGA
3858638 TACATTTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (33 bp):
AATGTATCGATACAATTCCTCATGTATCGAAAT
Found at i:3858715 original size:19 final size:19
Alignment explanation
Indices: 3858670--3858725 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
3858660 CTGCTAGTTT
*
3858670 CATGTATCGATAAAATTGGG
1 CATGTATCGATAAAA-TGAG
* *
3858690 TATGTATCGATACAATGAG
1 CATGTATCGATAAAATGAG
*
3858709 CATGTATCGATATAATG
1 CATGTATCGATAAAATG
3858726 TATCGATACA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
CATGTATCGATAAAATGAG
Found at i:3858744 original size:20 final size:20
Alignment explanation
Indices: 3858719--3858799 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
3858709 CATGTATCGA
3858719 TATAATGTATCGATACAAAG
1 TATAATGTATCGATACAAAG
* **
3858739 TATAATGTATTGATACATCTGGG
1 TATAATGTATCGATACA---AAG
* *
3858762 TGTGTATGTATCGATACAAAG
1 TAT-AATGTATCGATACAAAG
*
3858783 TATAATGTATTGATACA
1 TATAATGTATCGATACA
3858800 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
20 28 0.61
21 3 0.07
23 3 0.07
24 12 0.26
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (20 bp):
TATAATGTATCGATACAAAG
Found at i:3858783 original size:44 final size:44
Alignment explanation
Indices: 3858723--3858812 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
3858713 TATCGATATA
3858723 ATGTATCGATACAAAGTATAATGTATTGATACATCTGGGTGTGT
1 ATGTATCGATACAAAGTATAATGTATTGATACATCTGGGTGTGT
3858767 ATGTATCGATACAAAGTATAATGTATTGATACATCTGGGTGTGT
1 ATGTATCGATACAAAGTATAATGTATTGATACATCTGGGTGTGT
3858811 AT
1 AT
3858813 CAATACTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (44 bp):
ATGTATCGATACAAAGTATAATGTATTGATACATCTGGGTGTGT
Found at i:3858922 original size:20 final size:22
Alignment explanation
Indices: 3858897--3858937 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3858887 ACTTTGAAGT
3858897 AATTTAA-CT-TGAAAACATTC
1 AATTTAAGCTGTGAAAACATTC
*
3858917 AATTTAAGGTGTGAAAACATT
1 AATTTAAGCTGTGAAAACATT
3858938 TATACTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (22 bp):
AATTTAAGCTGTGAAAACATTC
Found at i:3866673 original size:20 final size:21
Alignment explanation
Indices: 3866648--3866688 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3866638 ACTTTGAAGT
3866648 AATTTAA-CTTGAAAACATTC
1 AATTTAAGCTTGAAAACATTC
*
3866668 AATTTAAGGTTTGAAAACATT
1 AATTTAA-GCTTGAAAACATT
3866689 TATACTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
AATTTAAGCTTGAAAACATTC
Found at i:3867671 original size:20 final size:19
Alignment explanation
Indices: 3867646--3867715 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
3867636 CCCTAAAAAA
3867646 TATCGATACACATTTAAATG
1 TATCGATACACA-TTAAATG
* **
3867666 TATCGATACAAATTGCATAG
1 TATCGATACACATTAAAT-G
**
3867686 TATCGATACACACAAATATG
1 TATCGATACACATTAA-ATG
3867706 TATCGATACA
1 TATCGATACA
3867716 GGACATTGGC
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 34 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.30
Consensus pattern (19 bp):
TATCGATACACATTAAATG
Found at i:3867768 original size:53 final size:53
Alignment explanation
Indices: 3867685--3867821 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
3867675 AAATTGCATA
3867685 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
3867739 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
3867792 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
3867822 TTTGTAGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:3867887 original size:21 final size:22
Alignment explanation
Indices: 3867853--3867907 Score: 94
Period size: 21 Copynumber: 2.5 Consensus size: 22
3867843 TTTCACTATT
*
3867853 CATCACTGTTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
3867875 CATCACT-TTCATGTATCGATA
1 CATCACTATTCATGTATCGATA
3867896 CATCACTATTCA
1 CATCACTATTCA
3867908 CACCATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 21 0.66
22 11 0.34
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (22 bp):
CATCACTATTCATGTATCGATA
Found at i:3870114 original size:84 final size:84
Alignment explanation
Indices: 3869941--3870105 Score: 210
Period size: 84 Copynumber: 2.0 Consensus size: 84
3869931 ACTCAAAGAA
* * * *
3869941 GAAAATAAATCAATAAGTGTAGAGAATGATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
3870006 TATGAAAGAGTTGCAAAAT
66 TAAGAAAGAGTTGCAAAAT
* * *
3870025 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATTAGAGGAG
1 GAAAATAAATCAATAAGTGTAGAAAATGATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
3870088 AA-AAGAAATGAGTTGCAA
64 AATAAGAAA-GAGTTGCAA
3870106 GTGGAAAATG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
82 4 0.06
83 6 0.09
84 60 0.86
ACGTcount: A:0.53, C:0.04, G:0.19, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATGATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTGCAAAAT
Found at i:3873221 original size:20 final size:19
Alignment explanation
Indices: 3873196--3873266 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
3873186 ACCCTGAAAA
3873196 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
3873216 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
3873235 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
3873256 GTATCGATACA
1 GTATCGATACA
3873267 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:3873319 original size:53 final size:53
Alignment explanation
Indices: 3873236--3873372 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
3873226 AAATTGCATA
*
3873236 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAATAGCCAAATTT
*
3873290 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAATAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAATAGCCAAATTT
*
3873343 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
3873373 TTGGTAGCAG
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 66 0.82
54 14 0.17
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAATAGCCAAATTT
Found at i:3873503 original size:13 final size:13
Alignment explanation
Indices: 3873485--3873509 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3873475 TCACTATTCA
3873485 TGTATCGATACAG
1 TGTATCGATACAG
3873498 TGTATCGATACA
1 TGTATCGATACA
3873510 TCATAAATAG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3877683 original size:23 final size:23
Alignment explanation
Indices: 3877657--3877715 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
3877647 AATATGCAAT
3877657 GTATCGATACATATATACTATTA
1 GTATCGATACATATATACTATTA
3877680 GTATCGATACATATATACTATTA
1 GTATCGATACATATATACTATTA
* *
3877703 TTATCAATACATA
1 GTATCGATACATA
3877716 AAATTGATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (23 bp):
GTATCGATACATATATACTATTA
Found at i:3879313 original size:21 final size:21
Alignment explanation
Indices: 3879273--3879314 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3879263 TAATATTCTT
* * *
3879273 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATAAATTA
3879294 GAAAAGAAAATAAATAAATTA
1 GAAAAGAAAATAAATAAATTA
3879315 TAGGAGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (21 bp):
GAAAAGAAAATAAATAAATTA
Found at i:3880548 original size:13 final size:13
Alignment explanation
Indices: 3880530--3880555 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3880520 CAATTTTTTG
3880530 TGTATCGATACAT
1 TGTATCGATACAT
3880543 TGTATCGATACAT
1 TGTATCGATACAT
3880556 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3881294 original size:21 final size:21
Alignment explanation
Indices: 3881253--3881296 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3881243 CTCTCTTTTA
* *
3881253 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
3881274 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
3881295 TC
1 TC
3881297 ATATCTTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:3883108 original size:13 final size:13
Alignment explanation
Indices: 3883090--3883128 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3883080 ATAATCACCC
*
3883090 TGTATCGATACAG
1 TGTATCGATACAA
3883103 TGTATCGATACAA
1 TGTATCGATACAA
3883116 TGTATCGATACAA
1 TGTATCGATACAA
3883129 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3883139 original size:20 final size:20
Alignment explanation
Indices: 3883114--3883192 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
3883104 GTATCGATAC
3883114 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
3883134 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
3883159 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
3883179 CATGTATCGATACA
1 AATGTATCGATACA
3883193 TTTGGACATT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:3885226 original size:15 final size:15
Alignment explanation
Indices: 3885206--3885236 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3885196 ATTTCGTTTG
*
3885206 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3885221 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3885236 G
1 G
3885237 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3888580 original size:13 final size:13
Alignment explanation
Indices: 3888562--3888587 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3888552 CAATTTTTTG
3888562 TGTATCGATACAT
1 TGTATCGATACAT
3888575 TGTATCGATACAT
1 TGTATCGATACAT
3888588 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3888684 original size:20 final size:21
Alignment explanation
Indices: 3888636--3888689 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
3888626 ATCTTAATGG
***
3888636 CATGTATCGATACATCTTTTA
1 CATGTATCGATACATCTGCAA
*
3888657 CATATATCGATACAT-TGCAA
1 CATGTATCGATACATCTGCAA
3888677 CATGTATCGATAC
1 CATGTATCGATAC
3888690 TTTGAATTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (21 bp):
CATGTATCGATACATCTGCAA
Found at i:3892404 original size:32 final size:34
Alignment explanation
Indices: 3892363--3892426 Score: 105
Period size: 32 Copynumber: 1.9 Consensus size: 34
3892353 CAAGTGATTG
3892363 AGAGGTTCTATCTTAG-CCTTG-AAAGATAGTGT
1 AGAGGTTCTATCTTAGCCCTTGAAAAGATAGTGT
3892395 AGAGGTTCTATCTTAGCCCTTGTAAAAGATAG
1 AGAGGTTCTATCTTAGCCCTTG-AAAAGATAG
3892427 GGGTGTAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 16 0.55
33 5 0.17
35 8 0.28
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.33
Consensus pattern (34 bp):
AGAGGTTCTATCTTAGCCCTTGAAAAGATAGTGT
Found at i:3894050 original size:19 final size:19
Alignment explanation
Indices: 3894013--3894052 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3894003 GAGGGGCCAC
*
3894013 TTTTTTTTATTGATTTTCA
1 TTTTTTTTATTGATATTCA
* *
3894032 TTTTTTTTCTTGCTATTCA
1 TTTTTTTTATTGATATTCA
3894051 TT
1 TT
3894053 CCCATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTTTTTATTGATATTCA
Found at i:3903775 original size:17 final size:17
Alignment explanation
Indices: 3903737--3903776 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3903727 ATACCCCAAG
*
3903737 AAAAACAAAAAATAACA
1 AAAAACAAAAAATAAAA
*
3903754 AAAAATAAAAAATAAAA
1 AAAAACAAAAAATAAAA
3903771 AAAAAC
1 AAAAAC
3903777 CAAGAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (17 bp):
AAAAACAAAAAATAAAA
Found at i:3905182 original size:86 final size:84
Alignment explanation
Indices: 3905025--3906176 Score: 1326
Period size: 86 Copynumber: 13.3 Consensus size: 84
3905015 TGTTCATCAC
* * *
3905025 TTCAAAGCCCACAAGTCAGTGGCACCTTTTTAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
3905090 CACAAGTCAGTGGCACCCT
66 CACAAGTCAGTGGCACCCT
* * * *
3905109 TTCAAAGCCTACGGAAGTCAATGGCACCCTTTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAG
1 TTCAAAGCCCAC--AAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
*
3905174 CCCACAAGTCAGTGGCACTCTT
64 CCCACAAGTCAGTGGCAC-CCT
* * *
3905196 TTCAAAGCCTACAAGTCAGTGGCACCTTTTCGAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* * *
3905261 CAGAAGTTAGTGGCATCCT
66 CACAAGTCAGTGGCACCCT
* * *
3905280 TTCAAATCCCACACAAGTCAGTGGCATCC-ATTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAA
1 TTCAAA-GCC-CACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
3905344 GCCCACGGAAGTCAGTGGCACCCT
63 GCCCAC--AAGTCAGTGGCACCCT
* * *
3905368 TTCAAAGCCCATAAGTCAGTAGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTCCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* ***
3905433 CCACAAGTCAGCGGCATTTTT
65 CCACAAGTCAGTGGCA-CCCT
* *
3905454 TTCGAAGCCCACGCAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
1 TTCAAAGCCCA--CAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * *
3905519 CCCATAAGTCGGTGGCAGCCT
64 CCCACAAGTCAGTGGCACCCT
*
3905540 TTCAAAGCCCACGAAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCACCCTCTCAAA
1 TTCAAAGCCCAC--AAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA
3905604 GCCCACGCAAGTCAGTGGCACCCT
63 GCCCA--CAAGTCAGTGGCACCCT
* * *
3905628 TTCAAAGCCCATAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCACCCTTCCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* **
3905693 CCACAAGTCAGCGGCACTTTT
65 CCACAAGTCAGTGGCAC-CCT
* *
3905714 TTCAAAGCCCACGCAAGTTAGTGGC-CC-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
1 TTCAAAGCCCA--CAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAA
* *
3905777 GCCCATAAGTCAGTGGCACCAT
63 GCCCACAAGTCAGTGGCACCCT
* * * * * *
3905799 TCCAAACCCCACCAGTCAGCGGCACTTTTCTCAAAGCCCACGCAAGTTAGTGGCACCCTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCACCTTT-TCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAA
* *
3905864 GCCCACAAGTTAGTGGCACTCTT
63 GCCCACAAGTCAGTGGCAC-CCT
* *
3905887 TTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
3905952 CCACAAGTCAGTGGCACCCT
65 CCACAAGTCAGTGGCACCCT
* *
3905972 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
* * *
3906037 CTACAAGTTAGTGGCACTCTT
65 CCACAAGTCAGTGGCAC-CCT
* * * * *
3906058 TTCAAAGCCCAGAAGTTAGTGGCATCC-TTTCAAAGCCCAAAAG-CTAGTGGTAACTCTTTTCAA
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTC-AGTGG-CAC-CCTTTCAA
* * **
3906121 AACCCACACGAGTCGGTGGCAACTATT
62 AGCCCACA--AGTCAGTGGC-AC-CCT
*
3906148 TTCAAAGCCCACACAAGTTAGTGGCACCT
1 TTCAAAG-CC-CACAAGTCAGTGGCACCT
3906177 GTTTTTTTAA
Statistics
Matches: 923, Mismatches: 103, Indels: 76
0.84 0.09 0.07
Matches are distributed among these distances:
83 9 0.01
84 21 0.02
85 225 0.24
86 330 0.36
87 185 0.20
88 112 0.12
89 11 0.01
90 12 0.01
91 4 0.00
92 14 0.02
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
CACAAGTCAGTGGCACCCT
Found at i:3905232 original size:57 final size:57
Alignment explanation
Indices: 3905025--3906174 Score: 1315
Period size: 57 Copynumber: 19.9 Consensus size: 57
3905015 TGTTCATCAC
* *
3905025 TTCAAAGCCCACAAGTCAGTGGCACCTTTTTAAAGCCCACAAGTCAGTGGCA-TCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACT-CTT
* * *
3905082 TT-AAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCTACGGAAGTCAATGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC--AAGTCAGTGGCACTCTT
*
3905139 TTCAAAGCCCACAACTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * * *
3905196 TTCAAAGCCTACAAGTCAGTGGCACCTTTTCGAAGCCCACAAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * * **
3905252 TTCAAAGCCCAGAAGTTAGTGGCATCCTTTCAAATCCCACACAAGTCAGTGGCA-TCCA
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAA-GCC-CACAAGTCAGTGGCACTCTT
* *
3905310 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACGGAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCAC--AAGTCAGTGGCACTCTT
* * * *
3905368 TTCAAAGCCCATAAGTCAGTAGCACTCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * *** * *
3905425 TCCAAAGCCCACAAGTCAGCGGCATTTTTTTCGAAGCCCACGCAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTT
* *
3905484 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCGGTGGCAGC-C-T
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCA-CTCTT
* *
3905540 TTCAAAGCCCACGAAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
3905598 CTCAAAGCCCACGCAAGTCAGTGGCACCCTTTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
3905657 TTCAAAGCCCACAAGTCAATGGCACCCTTCCAAAGCCCACAAGTCAGCGGCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
*
3905714 TTCAAAGCCCACGCAAGTTAGTGG--CCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * * * *
3905771 TTCAAAGCCCATAAGTCAGTGGCACCATTCCAAACCCCACCAGTCAGCGGCACT-TT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* *
3905827 TCTCAAAGCCCACGCAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
1 T-TCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
3905887 TTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
3905944 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * *
3906001 TTTAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCTACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
* * * * *
3906058 TTCAAAGCCCAGAAGTTAGTGGCATCCTTTCAAAGCCCAAAAG-CTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTC-AGTGG-CACTCTT
* * ** *
3906116 TTCAAAACCCACACGAGTCGGTGGCAACTATTTTCAAAGCCCACACAAGTTAGTGGCAC
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCAAAG-CC-CACAAGTCAGTGGCAC
3906175 CTGTTTTTTT
Statistics
Matches: 945, Mismatches: 107, Indels: 76
0.84 0.09 0.07
Matches are distributed among these distances:
55 9 0.01
56 132 0.14
57 378 0.40
58 272 0.29
59 119 0.13
60 12 0.01
61 1 0.00
62 8 0.01
63 4 0.00
64 10 0.01
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
Found at i:3906107 original size:28 final size:28
Alignment explanation
Indices: 3905025--3906096 Score: 1302
Period size: 28 Copynumber: 37.4 Consensus size: 28
3905015 TGTTCATCAC
*
3905025 TTCAAAGCCCACAAGTCAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
3905053 TTTAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
3905081 TTTAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
3905109 TTCAAAGCCTACGGAAGTCAATGGCACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCT
*
3905139 TTCAAAGCCCACAACTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
3905167 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
3905196 TTCAAAGCCTACAAGTCAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
3905224 TTCGAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
3905252 TTCAAAGCCCAGAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
3905280 TTCAAATCCCACACAAGTCAGTGGCATCCA
1 TTCAAA-GCC-CACAAGTCAGTGGCACCCT
*
3905310 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
3905338 TTCAAAGCCCACGGAAGTCAGTGGCACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCT
* * *
3905368 TTCAAAGCCCATAAGTCAGTAGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
3905397 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * ***
3905425 TCCAAAGCCCACAAGTCAGCGGCATTTTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
*
3905454 TTCGAAGCCCACGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
3905484 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
3905512 TTCAAAGCCCATAAGTCGGTGGCAGCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
3905540 TTCAAAGCCCACGAAAGTCAGTGGCATCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCT
3905570 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
3905598 CTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
* *
3905628 TTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
3905657 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * **
3905685 TCCAAAGCCCACAAGTCAGCGGCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
3905714 TTCAAAGCCCACGCAAGTTAGTGG--CCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
*
3905742 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
3905771 TTCAAAGCCCATAAGTCAGTGGCACCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * **
3905799 TCCAAACCCCACCAGTCAGCGGCACTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
3905827 TCTCAAAGCCCACGCAAGTTAGTGGCACCCT
1 T-TCAAAGCCCA--CAAGTCAGTGGCACCCT
* *
3905858 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
3905887 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
3905916 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
3905944 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
3905972 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
3906001 TTTAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
3906029 TTCAAAGCCTACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
3906058 TTCAAAGCCCAGAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
3906086 TTCAAAGCCCA
1 TTCAAAGCCCA
3906097 AAAGCTAGTG
Statistics
Matches: 913, Mismatches: 103, Indels: 56
0.85 0.10 0.05
Matches are distributed among these distances:
26 10 0.01
28 480 0.53
29 241 0.26
30 148 0.16
31 34 0.04
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:3906305 original size:45 final size:46
Alignment explanation
Indices: 3906241--3906363 Score: 131
Period size: 49 Copynumber: 2.6 Consensus size: 46
3906231 CTATCTGACA
* * *
3906241 TCGCTAGCATTGAATCAGCATATTGGCACCTTT-ATTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCACCTTTCATTAGCCCAATG
* * *
3906286 TCGCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCTAATG
1 TCGCTGGCCTTGAATCAGCACATTGG--CACCTTT-CATTAGCCCAATG
* **
3906335 TCGCAGGCCTTGAATTGGCACATTGGCAC
1 TCGCTGGCCTTGAATCAGCACATTGGCAC
3906364 TCTTCTCGTC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
45 23 0.35
47 9 0.14
49 33 0.51
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (46 bp):
TCGCTGGCCTTGAATCAGCACATTGGCACCTTTCATTAGCCCAATG
Found at i:3909946 original size:21 final size:20
Alignment explanation
Indices: 3909905--3909966 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
3909895 CGATTATATC
* * *
3909905 GATACATTGTATCAATGCAT
1 GATAAATTGTATCGATACAT
*
3909925 GATTAAATTGTATTGATACAT
1 GA-TAAATTGTATCGATACAT
*
3909946 GATGAATTGTATCGATACAT
1 GATAAATTGTATCGATACAT
3909966 G
1 G
3909967 TGGCCCAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 19 0.54
21 16 0.46
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (20 bp):
GATAAATTGTATCGATACAT
Found at i:3912069 original size:21 final size:21
Alignment explanation
Indices: 3912043--3912088 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3912033 TTGCAAGAAG
*
3912043 AAAATAAAGAATTAACTAATA
1 AAAATAAAGAATTAACTAAGA
*
3912064 AAAATAATGAATTAACTAAGA
1 AAAATAAAGAATTAACTAAGA
3912085 AAAA
1 AAAA
3912089 CAAAATCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (21 bp):
AAAATAAAGAATTAACTAAGA
Found at i:3916931 original size:52 final size:52
Alignment explanation
Indices: 3916851--3916971 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
3916841 TGATTTTTTG
3916851 CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTA
1 CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTA
* * *
3916903 CCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAATTTG
1 CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTA
3916955 CCTGCATGTATCGATAC
1 CCTGCATGTATCGATAC
3916972 GAAGATCAGT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (52 bp):
CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTA
Found at i:3916983 original size:52 final size:51
Alignment explanation
Indices: 3916847--3916998 Score: 182
Period size: 52 Copynumber: 2.9 Consensus size: 51
3916837 AATATGATTT
*
3916847 TTTGCCTGCATGTATCGATAC-ATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACAATATC--AGTGTATCGATACATCTGGGCAAA
* * *
3916899 TTTACCTGTATGTATCGATACATTTTAT-AGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACA--ATATCAGTGTATCGATACATCTGGGCAAA
* * *
3916951 TTTGCCTGCATGTATCGATACGAAGATCAGTGTATCGATGCATTTGGG
1 TTTGCCTGCATGTATCGATAC-AATATCAGTGTATCGATACATCTGGG
3916999 TAATGTATCG
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
51 2 0.02
52 80 0.94
53 1 0.01
55 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (51 bp):
TTTGCCTGCATGTATCGATACAATATCAGTGTATCGATACATCTGGGCAAA
Found at i:3917100 original size:19 final size:19
Alignment explanation
Indices: 3917076--3917170 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
3917066 TTTGATACAT
3917076 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
3917095 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
3917108 GGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
3917127 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
3917140 GGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
3917159 TGTATCGATACA
1 TGTATCGATACA
3917171 TTGTATCGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 24
0.68 0.05 0.27
Matches are distributed among these distances:
13 16 0.27
14 2 0.03
16 12 0.20
18 2 0.03
19 28 0.47
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:3917105 original size:32 final size:32
Alignment explanation
Indices: 3917038--3917184 Score: 251
Period size: 32 Copynumber: 4.6 Consensus size: 32
3917028 GCTTCGTAGT
* *
3917038 GATACATTGTATCGATACAA-ACTTATGTTTT
1 GATACATTGTATCGATACAACACTTATGTATC
3917069 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
*
3917101 GATACATGGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
*
3917133 GATACATGGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
3917165 GATACATTGTATCGATACAA
1 GATACATTGTATCGATACAA
3917185 ATCGTTGAAA
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 20 0.18
32 91 0.82
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (32 bp):
GATACATTGTATCGATACAACACTTATGTATC
Found at i:3917177 original size:13 final size:13
Alignment explanation
Indices: 3917095--3917183 Score: 52
Period size: 13 Copynumber: 5.9 Consensus size: 13
3917085 ACAACACTTA
3917095 TGTATCGATACAT
1 TGTATCGATACAT
*
3917108 GGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
3917126 ATGTATCGATACAT
1 -TGTATCGATACAT
*
3917140 GGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
3917158 ATGTATCGATACAT
1 -TGTATCGATACAT
3917172 TGTATCGATACA
1 TGTATCGATACA
3917184 AATCGTTGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 24
0.68 0.05 0.27
Matches are distributed among these distances:
13 28 0.47
14 2 0.03
16 12 0.20
18 2 0.03
19 16 0.27
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3918120 original size:49 final size:49
Alignment explanation
Indices: 3918028--3918518 Score: 565
Period size: 49 Copynumber: 10.1 Consensus size: 49
3918018 CTTAGGAATG
* * * **
3918028 TTAAAGTTGAAGGTGCCAATGTGGTGATTGAAGGCCAATGACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * *
3918077 TTAAAGATGAAGGTGCCAATTTGCTGATGCAAGGTCAGCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
3918126 GTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
*
3918178 TTAAAGATGAAGGTGCCAATGTGCTGATTTAAGGCCAGCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
3918227 TTAAAGATGACAAAGATGCCAATATGCTGATTCAAGGCCAGTGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* *
3918279 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGTCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* *
3918328 TT--A-A--AA-GTGCCAATGTGCTGATTTAAGGCTAGCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * *
3918371 ATAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATG---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
* * *
3918423 TTAAAGATGAAGGTTCCAATGTGCTAATTCAAGGCCAGCAACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
*
3918472 TT--A-A--AA-GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
3918515 TTAA
1 TTAA
3918519 GGAAATGCCA
Statistics
Matches: 378, Mismatches: 47, Indels: 38
0.82 0.10 0.08
Matches are distributed among these distances:
43 69 0.18
44 4 0.01
45 1 0.00
46 3 0.01
47 2 0.01
49 169 0.45
51 2 0.01
52 128 0.34
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:3918180 original size:101 final size:100
Alignment explanation
Indices: 3918037--3918518 Score: 564
Period size: 101 Copynumber: 4.9 Consensus size: 100
3918027 GTTAAAGTTG
* * ** *
3918037 AAGGTGCCAATGTGGTGATTGAAGGCCAATGACATTGGACTTAAAGATGAAGGTGCCAATTTGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCT
* * *
3918102 GATGCAAGGTCAGCGACATTGGACGTAAAGATGACA
66 GATTCAAGGCCAGCGACATTGGACTTAAAGATGA-A
* * *
3918138 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCT
*
3918203 GATTTAAGGCCAGCGACATTGGACTTAAAGATGACA
66 GATTCAAGGCCAGCGACATTGGACTTAAAGATGA-A
* * * *
3918239 AAGATGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCT
* *
3918304 GATTCAAGTCCAGCGATATTGGAC-T-----T-AA
66 GATTCAAGGCCAGCGACATTGGACTTAAAGATGAA
* * * *
3918332 AA-GTGCCAATGTGCTGATTTAAGGCTAGCGACATTGGACATAAAGATGACAAAGGTGCCAATAT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTGCCAATGT
*
3918396 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG--
63 GCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAA
* * *
3918432 AAGGTTCCAATGTGCTAATTCAAGGCCAGCAACATTGGACTT--A-A--AA-GTGCCAATGTGCT
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCT
*
3918491 GATTCAAGGCCAACGACATTGGACTTAA
66 GATTCAAGGCCAGCGACATTGGACTTAA
3918519 GGAAATGCCA
Statistics
Matches: 334, Mismatches: 36, Indels: 31
0.83 0.09 0.08
Matches are distributed among these distances:
92 77 0.23
93 5 0.01
94 1 0.00
95 39 0.12
96 1 0.00
98 1 0.00
99 1 0.00
100 3 0.01
101 206 0.62
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (100 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATGTGCT
GATTCAAGGCCAGCGACATTGGACTTAAAGATGAA
Found at i:3918409 original size:144 final size:144
Alignment explanation
Indices: 3918040--3918518 Score: 658
Period size: 144 Copynumber: 3.3 Consensus size: 144
3918030 AAAGTTGAAG
* * * *
3918040 GTGCCAATGTGGTGATTGAAGGCCAATGACATTGGACTTAAAGATG---AAGGTGCCAATTTGCT
1 GTGCCAATGTGCTGATTTAAGGCCAACGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCT
* * * * * *
3918102 GATGCAAGGTCAGCGACATTGGACGTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAG
66 GATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGCCAATGTGCTGATTCAAGGCCAG
3918167 CGATATTGGACTTAAAGATGAA
128 CGATATTGGACTT--A-A--AA
* *
3918189 GGTGCCAATGTGCTGATTTAAGGCCAGCGACATTGGACTTAAAGATGACAAAGATGCCAATATGC
1 -GTGCCAATGTGCTGATTTAAGGCCAACGACATTGGACTTAAAGATGACAAAGGTGCCAATATGC
* *
3918254 TGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGTCCAGCG
65 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCG
3918319 ATATTGGACTTAAAA
130 ATATTGGACTTAAAA
* * *
3918334 GTGCCAATGTGCTGATTTAAGGCTAGCGACATTGGACATAAAGATGACAAAGGTGCCAATATGCT
1 GTGCCAATGTGCTGATTTAAGGCCAACGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCT
* * *
3918399 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTTCCAATGTGCTAATTCAAGGCCAGCAA
66 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
*
3918464 CATTGGACTTAAAA
131 TATTGGACTTAAAA
*
3918478 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGACTTAA
1 GTGCCAATGTGCTGATTTAAGGCCAACGACATTGGACTTAA
3918519 GGAAATGCCA
Statistics
Matches: 299, Mismatches: 27, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
144 172 0.58
145 2 0.01
147 1 0.00
148 1 0.00
150 81 0.27
153 42 0.14
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (144 bp):
GTGCCAATGTGCTGATTTAAGGCCAACGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCT
GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
TATTGGACTTAAAA
Found at i:3918420 original size:95 final size:93
Alignment explanation
Indices: 3918238--3918518 Score: 297
Period size: 92 Copynumber: 3.0 Consensus size: 93
3918228 TAAAGATGAC
* * * *
3918238 AAAGATGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACATAAAGATGAAGGTGCCAATATGC
*
3918303 TGATTCAAGTCCAGCGATATTGGACTTA
66 TGATTCAAGGCCAGCGATATTGGACTTA
* * *
3918331 AAAG-TGCCAATGTGCTGATTTAAGGCTAGCGACATTGGACATAAAGATGACAAAGGTGCCAATA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACATAAAGATG---AAGGTGCCAATA
3918395 TGCTGATTCAAGGCCAGCGATATTGGACTTA
63 TGCTGATTCAAGGCCAGCGATATTGGACTTA
* * * * *
3918426 AAGATGAAGGTTCCAATGTGCTAATTCAAGGCCAGCAACATTGGAC-T-TA-A--AA-GTGCCAA
1 AA-A-G-A--TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACATAAAGATGAAGGTGCCAA
* * *
3918485 TGTGCTGATTCAAGGCCAACGACATTGGACTTA
61 TATGCTGATTCAAGGCCAGCGATATTGGACTTA
3918518 A
1 A
3918519 GGAAATGCCA
Statistics
Matches: 162, Mismatches: 17, Indels: 19
0.82 0.09 0.10
Matches are distributed among these distances:
92 77 0.48
93 6 0.04
95 43 0.27
96 1 0.01
97 1 0.01
98 1 0.01
99 1 0.01
100 1 0.01
101 31 0.19
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (93 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACATAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTTA
Found at i:3918569 original size:33 final size:33
Alignment explanation
Indices: 3918532--3918717 Score: 225
Period size: 33 Copynumber: 5.7 Consensus size: 33
3918522 AATGCCACTA
*
3918532 ACTTGTGTGGGCTTTTGAGAAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTTGAAAAGGGTTGCCACCG
* ** * * *
3918565 ACTTGTGTGGGC-TTTGGAGGGGGTTACGACCA
1 ACTTGTGTGGGCTTTTGAAAAGGGTTGCCACCG
** *
3918597 ACTTGTGTGGGCTTTAAAAAAAGGTTGCCACCG
1 ACTTGTGTGGGCTTTTGAAAAGGGTTGCCACCG
* *
3918630 ACTTGTGTGCGC-TTTGAAAAGGCTTGCCACCG
1 ACTTGTGTGGGCTTTTGAAAAGGGTTGCCACCG
* *
3918662 ACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCG
1 ACTTGTGTGGGCTTTTGAAAAGGGTTGCCACCG
3918695 ACTTGTGTGGGC-TTTGAAAAGGG
1 ACTTGTGTGGGCTTTTGAAAAGGG
3918718 GAAAGATGCC
Statistics
Matches: 124, Mismatches: 27, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
32 61 0.49
33 63 0.51
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.28
Consensus pattern (33 bp):
ACTTGTGTGGGCTTTTGAAAAGGGTTGCCACCG
Found at i:3918635 original size:65 final size:65
Alignment explanation
Indices: 3918526--3918716 Score: 265
Period size: 65 Copynumber: 2.9 Consensus size: 65
3918516 TAAGGAAATG
* * * * * ** *
3918526 CCACTAACTTGTGTGGGCTTTTGAGAAGGGTTGCCACCGACTTGTGTGGGCTTTGGAGGGGGTTA
1 CCACCAACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGCTTA
* * * *
3918591 CGACCAACTTGTGTGGGCTTTAAAAAAAGGTTGCCACCGACTTGTGTGCGCTTTGAAAAGGCTTG
1 CCACCAACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGCTTA
*
3918656 CCACCGACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGG
1 CCACCAACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGG
3918717 GGAAAGATGC
Statistics
Matches: 110, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
65 110 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (65 bp):
CCACCAACTTGTGTGGGCTTTAGAAAAAGGTTGCCACCGACTTGTGTGGGCTTTGAAAAGGCTTA
Found at i:3918822 original size:68 final size:68
Alignment explanation
Indices: 3918747--3919065 Score: 326
Period size: 68 Copynumber: 4.9 Consensus size: 68
3918737 TGGACTTAAA
*
3918747 AAGGTGCCAGGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCACGCAGTTGTGGGCTTAAAAGG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCACGCAGTTGTGGGCTTAAAAGG
3918812 AAC
66 AAC
** * * *
3918815 AAGGTGCCATAGAGTTGTGGACTTT------AAAAAG-GTGCCACGGAGTTGTGGACTTTAAAAG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCACGCAGTTGTGGGC-TTAAAAG
* *
3918873 AAAA
65 GAAC
* * * * ** ** *
3918877 AAGAATGCCATGCAGTTGTGGGC-TTAAAAGGAAAAA-AGCGCCACAAAGTTGTGGACTTTAAAA
1 AAG-GTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCACGCAGTTGTGGGC-TTAAAA
3918940 -G---
64 GGAAC
*
3918941 --GGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCATGCAGTTGTGGGCTTAAAAGG
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCACGCAGTTGTGGGCTTAAAAGG
3919004 AAC
66 AAC
* *
3919007 AAGGTGCCACAGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCACGGAGTTGTGGGCTT
1 AAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCACGCAGTTGTGGGCTT
3919066 TTGAAGGTTG
Statistics
Matches: 206, Mismatches: 28, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
61 31 0.15
62 40 0.19
63 30 0.15
68 105 0.51
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.21
Consensus pattern (68 bp):
AAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCACGCAGTTGTGGGCTTAAAAGG
AAC
Found at i:3918857 original size:28 final size:28
Alignment explanation
Indices: 3918730--3918871 Score: 106
Period size: 28 Copynumber: 4.7 Consensus size: 28
3918720 AAGATGCCTT
*
3918730 GGAGTTGTGGAC-TTAAAAAGGTGCCAG
1 GGAGTTGTGGACTTTAAAAAGGTGCCAC
*
3918757 GGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCAC
1 GGAGTTGTGGACTTT------AAAAAG-GTGCCAC
* * * *
3918792 GCAGTTGTGGGCTTAAAAGGAACAAGGTGCCAT
1 GGAGTTGTGGACTT--TA--AA-AAGGTGCCAC
*
3918825 AGAGTTGTGGACTTTAAAAAGGTGCCAC
1 GGAGTTGTGGACTTTAAAAAGGTGCCAC
3918853 GGAGTTGTGGACTTTAAAA
1 GGAGTTGTGGACTTTAAAA
3918872 GAAAAAAGAA
Statistics
Matches: 89, Mismatches: 13, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
27 12 0.13
28 29 0.33
29 2 0.02
31 2 0.02
33 18 0.20
34 9 0.10
35 17 0.19
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.23
Consensus pattern (28 bp):
GGAGTTGTGGACTTTAAAAAGGTGCCAC
Found at i:3918948 original size:28 final size:28
Alignment explanation
Indices: 3918916--3918969 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
3918906 GGAAAAAAGC
3918916 GCCACAAAGTTGTGGACTTTAAAAGGGT
1 GCCACAAAGTTGTGGACTTTAAAAGGGT
**
3918944 GCCACGGAGTTGTGGACTTTAAAAGG
1 GCCACAAAGTTGTGGACTTTAAAAGG
3918970 AAAAAGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (28 bp):
GCCACAAAGTTGTGGACTTTAAAAGGGT
Found at i:3919037 original size:96 final size:96
Alignment explanation
Indices: 3918731--3919035 Score: 522
Period size: 96 Copynumber: 3.2 Consensus size: 96
3918721 AGATGCCTTG
* *
3918731 GAGTTGTGGAC-TTAAAAAGGTGCCAGGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCACGCA
1 GAGTTGTGGACTTTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCATGCA
*
3918795 GTTGTGGGCTTAAAAGGAACAAGGTGCCATA
66 GTTGTGGGCTTAAAAGGAACAAGGTGCCACA
*
3918826 GAGTTGTGGACTTTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAAAAAAGAATGCCATGCA
1 GAGTTGTGGACTTTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCATGCA
* * *
3918891 GTTGTGGGCTTAAAAGGAAAAAAGCGCCACA
66 GTTGTGGGCTTAAAAGGAACAAGGTGCCACA
* *
3918922 AAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCATGCA
1 GAGTTGTGGACTTTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCATGCA
3918987 GTTGTGGGCTTAAAAGGAACAAGGTGCCACA
66 GTTGTGGGCTTAAAAGGAACAAGGTGCCACA
3919018 GAGTTGTGGACTTTAAAA
1 GAGTTGTGGACTTTAAAA
3919036 GGAAAAAGAA
Statistics
Matches: 195, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
95 11 0.06
96 184 0.94
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.22
Consensus pattern (96 bp):
GAGTTGTGGACTTTAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAAAGAATGCCATGCA
GTTGTGGGCTTAAAAGGAACAAGGTGCCACA
Found at i:3919108 original size:58 final size:58
Alignment explanation
Indices: 3919046--3919355 Score: 430
Period size: 58 Copynumber: 5.3 Consensus size: 58
3919036 GGAAAAAGAA
* * * *
3919046 TGCCACGGAGTTGTGGGCTTTTGAAGGTTGCCACTGATTTGTGGGCTTTGAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGG
*
3919104 TGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGG
*
3919162 TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTAACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGG
* * *
3919220 TGCCACTGACTTGTGGGCTTTGGAAAAAGG-TGCCACTGACTTGTGGGCTTTGGATAA-GC
1 TGCCACTGACTTGTGGGCTTTTG---AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGG
* * * * *
3919279 TGCCACTGACTTGTGGGCTTTGGAAAGGATGCCACTAACTTGTGGGCTTTTG--AAGGT
1 TGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGG
3919336 TGCCACTGACTTGTGGGCTT
1 TGCCACTGACTTGTGGGCTT
3919356 AAAAAGAAAC
Statistics
Matches: 233, Mismatches: 14, Indels: 11
0.90 0.05 0.04
Matches are distributed among these distances:
56 2 0.01
57 26 0.11
58 152 0.65
59 24 0.10
60 25 0.11
61 4 0.02
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (58 bp):
TGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGG
Found at i:3919110 original size:30 final size:29
Alignment explanation
Indices: 3919046--3919355 Score: 341
Period size: 30 Copynumber: 10.7 Consensus size: 29
3919036 GGAAAAAGAA
* * *
3919046 TGCCACGGAGTTGTGGGCTTTTG--AAGGT
1 TGCCACTGACTTGTGGGC-TTTGAAAAGGG
*
3919074 TGCCACTGATTTGTGGGCTTTGAAAAAGGG
1 TGCCACTGACTTGTGGGCTTTG-AAAAGGG
* *
3919104 TGCCACTAACTTGTGGGCTTTTG--AAGGT
1 TGCCACTGACTTGTGGGC-TTTGAAAAGGG
3919132 TGCCACTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-GAAAAGGG
*
3919162 TGCCACTGACTTGTGGGCTTTTG--AAGGT
1 TGCCACTGACTTGTGGGC-TTTGAAAAGGG
*
3919190 TGCCACTAACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTT-GAAAAGGG
*
3919220 TGCCACTGACTTGTGGGCTTTGGAAAAAGG
1 TGCCACTGACTTGTGGGCTTT-GAAAAGGG
* *
3919250 TGCCACTGACTTGTGGGCTTTGGATAA-GC
1 TGCCACTGACTTGTGGGCTTT-GAAAAGGG
* *
3919279 TGCCACTGACTTGTGGGCTTTGGAAAGGA
1 TGCCACTGACTTGTGGGCTTTGAAAAGGG
* *
3919308 TGCCACTAACTTGTGGGCTTTTG--AAGGT
1 TGCCACTGACTTGTGGGC-TTTGAAAAGGG
3919336 TGCCACTGACTTGTGGGCTT
1 TGCCACTGACTTGTGGGCTT
3919356 AAAAAGAAAC
Statistics
Matches: 248, Mismatches: 21, Indels: 27
0.84 0.07 0.09
Matches are distributed among these distances:
27 12 0.05
28 84 0.34
29 40 0.16
30 105 0.42
31 7 0.03
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAAGGG
Found at i:3919181 original size:88 final size:85
Alignment explanation
Indices: 3919040--3919355 Score: 377
Period size: 88 Copynumber: 3.6 Consensus size: 85
3919030 TTAAAAGGAA
* * * * * * *
3919040 AAAGAATGCCACGGAGTTGTGGGCTTTTGAAGGTTGCCACTGATTTGTGGGCTTTGAAAAAGGGT
1 AAAGGATGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTTTG--AAAGGCT
*
3919105 GCCACTAACTTGTGGGCTTTTG
64 GCCACTAACTTGTGGGCTTTGG
* *
3919127 -AAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTTG-AAGGT
1 AAAGGATGCCACTGACTTGTGGGCTTTGG--AAGGGTGCCACTGACTTGTGGGC-TTTGAAAGGC
3919190 TGCCACTAACTTGTGGGCTTTGG
63 TGCCACTAACTTGTGGGCTTTGG
* *
3919213 AAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAAGGTGCCACTGACTTGTGGGCTTTGGATAA-
1 -AAAGGATGCCACTGACTTGTGGGCTTTGG--AAGGGTGCCACTGACTTGTGGGCTTT-GA-AAG
*
3919277 GCTGCCACTGACTTGTGGGCTTTGG
61 GCTGCCACTAACTTGTGGGCTTTGG
* * *
3919302 AAAGGATGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTT
1 AAAGGATGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTT
3919356 AAAAAGAAAC
Statistics
Matches: 203, Mismatches: 18, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
86 72 0.35
87 3 0.01
88 99 0.49
89 27 0.13
90 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (85 bp):
AAAGGATGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGCTGC
CACTAACTTGTGGGCTTTGG
Found at i:3920582 original size:14 final size:13
Alignment explanation
Indices: 3920560--3920603 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
3920550 CCTTTGCACC
3920560 TTTTTTGTTTTGT
1 TTTTTTGTTTTGT
3920573 TTTTTGTGTTTTGT
1 TTTTT-TGTTTTGT
3920587 TTTTTTGACTTTTGT
1 TTTTTTG--TTTTGT
3920602 TT
1 TT
3920604 GTGTGTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.25
14 13 0.46
15 8 0.29
ACGTcount: A:0.02, C:0.02, G:0.16, T:0.80
Consensus pattern (13 bp):
TTTTTTGTTTTGT
Found at i:3920592 original size:15 final size:15
Alignment explanation
Indices: 3920560--3920603 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
3920550 CCTTTGCACC
3920560 TTTTT-TGTTTTG-T
1 TTTTTGTGTTTTGTT
3920573 TTTTTGTGTTTTGTT
1 TTTTTGTGTTTTGTT
**
3920588 TTTTTGACTTTTGTT
1 TTTTTGTGTTTTGTT
3920603 T
1 T
3920604 GTGTGTTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
15 15 0.56
ACGTcount: A:0.02, C:0.02, G:0.16, T:0.80
Consensus pattern (15 bp):
TTTTTGTGTTTTGTT
Found at i:3920617 original size:28 final size:27
Alignment explanation
Indices: 3920560--3920617 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
3920550 CCTTTGCACC
* **
3920560 TTTTTTGTTTTGTTTTTTGTGTTTTGT
1 TTTTTTGTTTTGTTTTGTGTGTTTACT
3920587 TTTTTTGACTTTTG-TTTGTGTGTTTACT
1 TTTTTTG--TTTTGTTTTGTGTGTTTACT
3920615 TTT
1 TTT
3920618 GACTTTTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 7 0.27
28 14 0.54
29 5 0.19
ACGTcount: A:0.03, C:0.03, G:0.17, T:0.76
Consensus pattern (27 bp):
TTTTTTGTTTTGTTTTGTGTGTTTACT
Found at i:3924936 original size:27 final size:27
Alignment explanation
Indices: 3924898--3924971 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
3924888 TTTGGTTGAA
3924898 AATGGGGTTGGAGTGTCCCCTCAGAGG
1 AATGGGGTTGGAGTGTCCCCTCAGAGG
3924925 AATGGGGTTGGAGTGTCCCCTCAGAGG
1 AATGGGGTTGGAGTGTCCCCTCAGAGG
*
3924952 AATGGGGTTAGAGTGTCCCC
1 AATGGGGTTGGAGTGTCCCC
3924972 GATGAATAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.19, C:0.19, G:0.39, T:0.23
Consensus pattern (27 bp):
AATGGGGTTGGAGTGTCCCCTCAGAGG
Found at i:3927099 original size:51 final size:52
Alignment explanation
Indices: 3926974--3927100 Score: 211
Period size: 52 Copynumber: 2.5 Consensus size: 52
3926964 CGAAATATGA
*
3926974 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATATATTTCATAGTGTATCGATACATCTAGGC
* *
3927026 AAATTTGCCTGTATGTATCGATATATTTTATAGTGTATCGATACATCT-GGC
1 AAATTTGCCTGCATGTATCGATATATTTCATAGTGTATCGATACATCTAGGC
*
3927077 AAATTTGCTTGCATGTATCGATAT
1 AAATTTGCCTGCATGTATCGATAT
3927101 GAAAATCAGT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
51 25 0.36
52 45 0.64
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATATATTTCATAGTGTATCGATACATCTAGGC
Found at i:3927112 original size:51 final size:51
Alignment explanation
Indices: 3926974--3927121 Score: 183
Period size: 52 Copynumber: 2.9 Consensus size: 51
3926964 CGAAATATGA
* **
3926974 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATATA-TAAATAGTGTATCGATACATCTAGGC
* **
3927026 AAATTTGCCTGTATGTATCGATATATTTTATAGTGTATCGATACATCT-GGC
1 AAATTTGCCTGCATGTATCGATATA-TAAATAGTGTATCGATACATCTAGGC
*
3927077 AAATTTGCTTGCATGTATCGATATGA-AAATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATAT-ATAAAT-AGTGTATCGATACA
3927122 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
50 2 0.02
51 39 0.45
52 46 0.53
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATATATAAATAGTGTATCGATACATCTAGGC
Found at i:3927128 original size:13 final size:13
Alignment explanation
Indices: 3927110--3927134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3927100 TGAAAATCAG
3927110 TGTATCGATACAA
1 TGTATCGATACAA
3927123 TGTATCGATACA
1 TGTATCGATACA
3927135 TTTGGGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3927210 original size:18 final size:19
Alignment explanation
Indices: 3927187--3927235 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
3927177 AGCGATACAT
3927187 TGTATCGATACAA-ACTCA
1 TGTATCGATACAACACTCA
*
3927205 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTCA
3927224 TGTATCGATACA
1 TGTATCGATACA
3927236 TTATATTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAACACTCA
Found at i:3929707 original size:20 final size:20
Alignment explanation
Indices: 3929682--3929719 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3929672 TAGATTTTTC
3929682 CAAAATGCATCGATACATTG
1 CAAAATGCATCGATACATTG
*
3929702 CAAAATGTATCGATACAT
1 CAAAATGCATCGATACAT
3929720 CTAGGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (20 bp):
CAAAATGCATCGATACATTG
Found at i:3931646 original size:17 final size:17
Alignment explanation
Indices: 3931609--3931646 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
3931599 GGCTTATAAC
3931609 ATAAAGGGGAGAACGTT
1 ATAAAGGGGAGAACGTT
3931626 -TAAAGGGAGAGAA-GTT
1 ATAAAGGG-GAGAACGTT
3931642 ATAAA
1 ATAAA
3931647 CTTGAGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.47, C:0.03, G:0.32, T:0.18
Consensus pattern (17 bp):
ATAAAGGGGAGAACGTT
Found at i:3932418 original size:13 final size:13
Alignment explanation
Indices: 3932400--3932427 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3932390 ATAAATAATG
3932400 CATTGTATCGATA
1 CATTGTATCGATA
3932413 CATTGTATCGATA
1 CATTGTATCGATA
3932426 CA
1 CA
3932428 ACTTGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:3932550 original size:20 final size:21
Alignment explanation
Indices: 3932505--3932561 Score: 98
Period size: 20 Copynumber: 2.8 Consensus size: 21
3932495 GTATCAATAC
3932505 ATTGTATCGATACATGATTAA
1 ATTGTATCGATACATGATTAA
*
3932526 ATTGTATCGATACATGA-TGA
1 ATTGTATCGATACATGATTAA
3932546 ATTGTATCGATACATG
1 ATTGTATCGATACATG
3932562 TGGCCCAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
20 18 0.51
21 17 0.49
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (21 bp):
ATTGTATCGATACATGATTAA
Found at i:3934323 original size:20 final size:20
Alignment explanation
Indices: 3934300--3934372 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
3934290 TCAATTCAAA
*
3934300 GTATCGATACACGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
3934320 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3934341 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3934361 GTATCGATACAT
1 GTATCGATACAT
3934373 AAAAAAGATG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3934344 original size:21 final size:21
Alignment explanation
Indices: 3934318--3934393 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
3934308 ACACGTTGCA
3934318 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
3934339 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
3934359 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
3934380 ATGTATCGATACAT
1 ATGTATCGATACAT
3934394 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:3934393 original size:41 final size:41
Alignment explanation
Indices: 3934300--3934393 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
3934290 TCAATTCAAA
* *
3934300 GTATCGATACACGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3934341 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
3934382 GTATCGATACAT
1 GTATCGATACAT
3934394 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:3934450 original size:13 final size:13
Alignment explanation
Indices: 3934432--3934457 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3934422 TACAGCAAGT
3934432 ATGTATCGATACA
1 ATGTATCGATACA
3934445 ATGTATCGATACA
1 ATGTATCGATACA
3934458 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3935679 original size:151 final size:147
Alignment explanation
Indices: 3935479--3935823 Score: 454
Period size: 142 Copynumber: 2.4 Consensus size: 147
3935469 GGATACTTAT
*
3935479 AGGAATATTAG-AAT-TTGAAAAATTAAGATGATAAGTTTTATTTAATTTTTATTTAAATTTTAA
1 AGGAATATTAGAAATCTTGAAAAATTAAGATGATAATTTTTATTTAA-TTTT-TTT---TTTTAA
* * * *
3935542 TTTCT-AAAAATTCATTTCATTCCTGAATGGAAAACCTAAAAAATACAAAAAGTTTTGAAGATTT
61 TTTCTAAAAAATTCATTTCATACCTGAATAGAAAACCGAAAAAATACAAAAAGTTTTGAAAATTT
*
3935606 CTATACCCCTACGAAAAACTAA
126 CTATACCCCTACGAAAAACCAA
*
3935628 AGGAATATTAGAAATCTTGAAAAATTAAGATGATAATTTTTATTT-A----CTTTTTTAATTTCT
1 AGGAATATTAGAAATCTTGAAAAATTAAGATGATAATTTTTATTTAATTTTTTTTTTTAATTTCT
* * * **
3935688 AAAAAATTCATTTCGTACCTTAATAGAGAACCGAAAAAATATGAAAAGTTTTGAAAATTTCTATA
66 AAAAAATTCATTTCATACCTGAATAGAAAACCGAAAAAATACAAAAAGTTTTGAAAATTTCTATA
*
3935753 CCCCTACGAAAAACCAT
131 CCCCTACGAAAAACCAA
* *
3935770 AGCAATATTAGAAATCTTGAAAAATTAAGATAATAATTTTTATTTAATTTTTTT
1 AGGAATATTAGAAATCTTGAAAAATTAAGATGATAATTTTTATTTAATTTTTTT
3935824 CAAAAATTTT
Statistics
Matches: 172, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
141 11 0.06
142 113 0.66
143 1 0.01
144 2 0.01
147 2 0.01
149 11 0.06
150 4 0.02
151 28 0.16
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (147 bp):
AGGAATATTAGAAATCTTGAAAAATTAAGATGATAATTTTTATTTAATTTTTTTTTTTAATTTCT
AAAAAATTCATTTCATACCTGAATAGAAAACCGAAAAAATACAAAAAGTTTTGAAAATTTCTATA
CCCCTACGAAAAACCAA
Found at i:3935740 original size:142 final size:140
Alignment explanation
Indices: 3935521--3935876 Score: 477
Period size: 142 Copynumber: 2.5 Consensus size: 140
3935511 AAGTTTTATT
* * * * *
3935521 TAATTTTTATTTAAATTTTAATTTCT-AAAAATTCATTTCATTCCTGAATGGAAAACCTAAAAAA
1 TAATTTTTATTT-AATTTTAATTTCTAAAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAAA
** * * *
3935585 TACAAAAAGTTTTGAAGATTTCTATACCCCTACGAAAAACTAAAGGAATATTAGAAATCTTGAAA
65 TATGAAAAGTTTTGAAAATTTCTATACCCCTACGAAAAACCAAAGCAATATTAGAAATCTTGAAA
*
3935650 AATTAAGATGA
130 AATTAAGATAA
* *
3935661 TAATTTTTATTTACTTTTTTAATTTCTAAAAAATTCATTTCGTACCTTAATAGAGAACCGAAAAA
1 TAATTTTTATTTA--ATTTTAATTTCTAAAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAA
*
3935726 ATATGAAAAGTTTTGAAAATTTCTATACCCCTACGAAAAACCATAGCAATATTAGAAATCTTGAA
64 ATATGAAAAGTTTTGAAAATTTCTATACCCCTACGAAAAACCAAAGCAATATTAGAAATCTTGAA
3935791 AAATTAAGATAA
129 AAATTAAGATAA
* * * * * *
3935803 TAATTTTTATTTAATTTT--TTTC-AAAAATTTTATTTTGCACCTTAATGGAGACCCGAAAAGAT
1 TAATTTTTATTTAATTTTAATTTCTAAAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAAAT
3935865 ATGAAAAGTTTT
66 ATGAAAAGTTTT
3935877 TCGAGACTTT
Statistics
Matches: 191, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
137 45 0.24
138 4 0.02
139 1 0.01
140 16 0.08
141 11 0.06
142 114 0.60
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (140 bp):
TAATTTTTATTTAATTTTAATTTCTAAAAAATTCATTTCGTACCTTAATGGAGAACCGAAAAAAT
ATGAAAAGTTTTGAAAATTTCTATACCCCTACGAAAAACCAAAGCAATATTAGAAATCTTGAAAA
ATTAAGATAA
Found at i:3936730 original size:10 final size:10
Alignment explanation
Indices: 3936698--3936748 Score: 59
Period size: 10 Copynumber: 4.9 Consensus size: 10
3936688 TGGCTTAATT
3936698 TTTCTATTTTC
1 TTTCT-TTTTC
*
3936709 TCTCTATTTTC
1 TTTCT-TTTTC
3936720 TTTCTTTTTC
1 TTTCTTTTTC
3936730 TTTCTTTTT-
1 TTTCTTTTTC
3936739 TTCTCTTTTT
1 TT-TCTTTTT
3936749 TTTTTCTTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
9 2 0.05
10 21 0.57
11 14 0.38
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:3936735 original size:14 final size:14
Alignment explanation
Indices: 3936716--3936755 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
3936706 TTCTCTCTAT
3936716 TTTCTTTCTTTT-TC
1 TTTCTTT-TTTTCTC
3936730 TTTCTTTTTTTCTC
1 TTTCTTTTTTTCTC
3936744 TTT-TTTTTTTCT
1 TTTCTTTTTTTCT
3936756 TACTTGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTCTTTTTTTCTC
Found at i:3937316 original size:165 final size:163
Alignment explanation
Indices: 3937145--3937976 Score: 700
Period size: 165 Copynumber: 5.0 Consensus size: 163
3937135 AAATTAGATA
** * * *
3937145 AATTTTAAAAATTTTAAACCCAGGAAAATCCCCCTAAAACATTTATGGACTAGAAAATTCGATAT
1 AATTTTAAAAATTAAAAACCAAGAAAAATCCCCCTAAAACATTTATGGAGTAGAAAATTCG-TAT
*** * *
3937210 TTCGGTAATAGGAAAATTTCAAAGAAAAAATTCAAAATTCATGAAAATAAATGAATTTTTGAAAA
65 TTCAAAAATAGGAAAATTTCAAAGAAAAAATT-AAAACTCATGAAAATGAATGAATTTTTGAAAA
*
3937275 TTGATTTAATA-AGAATTAAATAATAATACTTTATG
129 TTGATTTAATATA-AATTAAATAATAATATTTTATG
* * * * * *
3937310 AATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAATATTTTTGGAGAACCAAAATCCGTA
1 AATTTTAAAAATTAAAAACCAAGAAAAAT-CCCCCTAAAACATTTATGGAGTA-GAAAATTCGTA
* * ** *
3937375 TTTCAAAAATAGGAGAATTTCAAGAAAAAAAAGAAAAACTCATGAAATTGAATGAATTTTTGAAA
64 TTTCAAAAATAGGAAAATTTCAA-AGAAAAAATTAAAACTCATGAAAATGAATGAATTTTTGAAA
* *
3937440 ATTGATTTTATATAAATTAAATAATAATATTTTATA
128 ATTGATTTAATATAAATTAAATAATAATATTTTATG
** ** * * * * *
3937476 AATTTTAAATCTTAAAAACCAAGAAAAATCTTCCGAAAACATTTACGAAGTAAAAAACTTTGTAT
1 AATTTTAAAAATTAAAAACCAAGAAAAATCCCCCTAAAACATTTATGGAGTAGAAAA-TTCGTAT
** * *
3937541 TTCAAAAATAGGAGAGCTTT-AAGGGAAAAATGTAAAACTCATGAAAATGAATGAATTTTTGAAA
65 TTCAAAAATAGGA-AAATTTCAAAGAAAAAAT-TAAAACTCATGAAAATGAATGAATTTTTGAAA
*
3937605 ATTGATTTAATATAAATTAAATAATAATATTTCATG
128 ATTGATTTAATATAAATTAAATAATAATATTTTATG
* ** * * *
3937641 AATTTTAAAAATTATAAACTGAGAAAAATCCCTCTAAAAACATTTA-CGAGGTAGAAAACTC-TA
1 AATTTTAAAAATTAAAAACCAAGAAAAATCCCCCT-AAAACATTTATGGA-GTAGAAAATTCGT-
* * * * *
3937704 CACTTT-AGAAATA-GAGAGTTTCAAGGAAAAAACTGAAAAGCTCATGAAAATGAATGAATTTTT
63 -A-TTTCAAAAATAGGAAAATTTCAAAGAAAAAA-TTAAAA-CTCATGAAAATGAATGAATTTTT
* * * **
3937767 GAAAACTAATTTAAT-TGAATTAAATAACGATATTTTATG
124 GAAAATTGATTTAATATAAATTAAATAATAATATTTTATG
* * * *** * *
3937806 AATTTTAAAAATTAAAAACCAAAAAAAATCCCTCCAAAAATATTTGCAGAGTAGAAAACTCCATA
1 AATTTTAAAAATTAAAAACCAAGAAAAATCCC-CCTAAAACATTTATGGAGTAGAAAA-TTCGTA
* * *
3937871 TTT-TAAAATAAGAAGAA-TTCTAAA-AGAAAATTAATAACTCAT-AAAAT-AATAGAAATTTTT
64 TTTCAAAAATAGGAA-AATTTC-AAAGAAAAAATTAA-AACTCATGAAAATGAAT-G-AATTTTT
* * * ** * * *
3937931 CAAAACTAATTTAAT-TGTGATTAAATGATAATATTTAAAG
124 GAAAATTGATTTAATAT-AAATTAAATAATAATATTTTATG
3937971 AATTTT
1 AATTTT
3937977 GATGCTTGAA
Statistics
Matches: 540, Mismatches: 101, Indels: 52
0.78 0.15 0.08
Matches are distributed among these distances:
162 3 0.01
163 6 0.01
164 51 0.09
165 265 0.49
166 196 0.36
167 19 0.04
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (163 bp):
AATTTTAAAAATTAAAAACCAAGAAAAATCCCCCTAAAACATTTATGGAGTAGAAAATTCGTATT
TCAAAAATAGGAAAATTTCAAAGAAAAAATTAAAACTCATGAAAATGAATGAATTTTTGAAAATT
GATTTAATATAAATTAAATAATAATATTTTATG
Found at i:3937440 original size:166 final size:165
Alignment explanation
Indices: 3937216--3937850 Score: 705
Period size: 165 Copynumber: 3.8 Consensus size: 165
3937206 ATATTTCGGT
* ** * *
3937216 AATAGGAAAATTTCAA-AGAAAAAATTCAAAATTCATGAAAATAAATGAATTTTTGAAAATTGAT
1 AATAGGAGAATTTCAAGA-AAAAAATGAAAAACTCATGAAAATGAATGAATTTTTGAAAATTGAT
* *
3937280 TTAATA-AGAATTAAATAATAATACTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCC
65 TTAATATA-AATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTC
* * *
3937344 CAAAAATATTTTTGGAGAACCAAAA-TCCGTATTTCAAA
129 CAAAAACATTTTAGGAGAA--AAAACTCTGTATTTCAAA
* *
3937382 AATAGGAGAATTTCAAGAAAAAAAAGAAAAACTCATGAAATTGAATGAATTTTTGAAAATTGATT
1 AATAGGAGAATTTCAAGAAAAAAATGAAAAACTCATGAAAATGAATGAATTTTTGAAAATTGATT
* * ** * *
3937447 TTATATAAATTAAATAATAATATTTTATAAATTTTAAATCTTAAAAACCAAGAAAAAT-CTTCCG
66 TAATATAAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCA
* *
3937511 AAAACA-TTTACGAAGTAAAAAACTTTGTATTTCAAA
131 AAAACATTTTA-GGAG-AAAAAACTCTGTATTTCAAA
* ** *
3937547 AATAGGAGAGCTTT-AAGGGAAAAATGTAAAACTCATGAAAATGAATGAATTTTTGAAAATTGAT
1 AATAGGAGA-ATTTCAAGAAAAAAATGAAAAACTCATGAAAATGAATGAATTTTTGAAAATTGAT
* * ** *
3937611 TTAATATAAATTAAATAATAATATTTCATGAATTTTAAAAATTATAAACTGAGAAAAATCCCTCT
65 TTAATATAAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCC
* * ** *
3937676 AAAAACA-TTTACGAGGTAGAAAACTCTACACTTT-AGA
130 AAAAACATTTTAGGA-G-AAAAAACTCTGTA-TTTCAAA
* * * * *
3937713 AATA-GAGAGTTTCAAGGAAAAAACTGAAAAGCTCATGAAAATGAATGAATTTTTGAAAACTAAT
1 AATAGGAGAATTTCAA-GAAAAAAATGAAAAACTCATGAAAATGAATGAATTTTTGAAAATTGAT
* ** *
3937777 TTAAT-TGAATTAAATAACGATATTTTATGAATTTTAAAAATTAAAAACCAAAAAAAATCCCTCC
65 TTAATATAAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCC
*
3937841 AAAAATATTT
130 AAAAACATTT
3937851 GCAGAGTAGA
Statistics
Matches: 395, Mismatches: 62, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
164 10 0.03
165 190 0.48
166 190 0.48
167 5 0.01
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (165 bp):
AATAGGAGAATTTCAAGAAAAAAATGAAAAACTCATGAAAATGAATGAATTTTTGAAAATTGATT
TAATATAAATTAAATAATAATATTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCCA
AAAACATTTTAGGAGAAAAAACTCTGTATTTCAAA
Found at i:3937670 original size:331 final size:330
Alignment explanation
Indices: 3937235--3937835 Score: 802
Period size: 331 Copynumber: 1.8 Consensus size: 330
3937225 ATTTCAAAGA
*
3937235 AAAAATTCAAAATTCATGAAAATAAATGAATTTTTGAAAATTGATTTAATAAGAATTAAATAATA
1 AAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAATTGATTTAATAAGAATTAAATAATA
* **
3937300 ATACTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAATATTTTTG-GAGAAC
66 ATACTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTACGAG-GAA-
** *
3937364 CAAAA-TCCGTA-TTTCAAAAATAGGAGAATTTCAA-GAAAAAAAAGAAAAACTCATGAAATTGA
129 CAAAACTCCACACTTT-AAAAATA-GAGAATTTCAAGGAAAAAAAAGAAAAACTCATGAAAATGA
* * * * **
3937426 ATGAATTTTTGAAAATTGATTTTATATAAATTAAATAATAATATTTTATAAATTTTAAATCTTAA
192 ATGAATTTTTGAAAACTAATTTAAT-TAAATTAAATAACAATATTTTATAAATTTTAAAAATTAA
*
3937491 AAACCAAGAAAAATCTTCCGAAAACATTTACGAAGTAAAAAACTTTGTATTTCAAAAATAGGAGA
256 AAACCAAAAAAAATCTTCCGAAAACATTTACGAAGTAAAAAACTTTGTATTTCAAAAATAGGAGA
3937556 GCTTTAAGGG
321 GCTTTAAGGG
*
3937566 AAAAATGT-AAAACTCATGAAAATGAATGAATTTTTGAAAATTGATTTAATATA-AATTAAATAA
1 AAAAAT-TCAAAACTCATGAAAATAAATGAATTTTTGAAAATTGATTTAATA-AGAATTAAATAA
* ** * * *
3937629 TAATA-TTTCATGAATTTTAAAAATTATAAACTGAGAAAAATCCCTCTAAAAACATTTACGAGGT
64 TAATACTTT-ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTACGAGGA
* * * * ** *
3937693 AGAAAACTCTACACTTTAGAAATAGAGAGTTTCAAGGAAAAAACTGAAAAGCTCATGAAAATGAA
128 ACAAAACTCCACACTTTAAAAATAGAGAATTTCAAGGAAAAAAAAGAAAAACTCATGAAAATGAA
* * *
3937758 TGAATTTTTGAAAACTAATTTAATTGAATTAAATAACGATATTTTATGAATTTTAAAAATTAAAA
193 TGAATTTTTGAAAACTAATTTAATTAAATTAAATAACAATATTTTATAAATTTTAAAAATTAAAA
3937823 ACCAAAAAAAATC
258 ACCAAAAAAAATC
3937836 CCTCCAAAAA
Statistics
Matches: 232, Mismatches: 31, Indels: 15
0.83 0.11 0.05
Matches are distributed among these distances:
330 64 0.28
331 162 0.70
332 6 0.03
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (330 bp):
AAAAATTCAAAACTCATGAAAATAAATGAATTTTTGAAAATTGATTTAATAAGAATTAAATAATA
ATACTTTATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAACATTTACGAGGAACA
AAACTCCACACTTTAAAAATAGAGAATTTCAAGGAAAAAAAAGAAAAACTCATGAAAATGAATGA
ATTTTTGAAAACTAATTTAATTAAATTAAATAACAATATTTTATAAATTTTAAAAATTAAAAACC
AAAAAAAATCTTCCGAAAACATTTACGAAGTAAAAAACTTTGTATTTCAAAAATAGGAGAGCTTT
AAGGG
Found at i:3937956 original size:330 final size:331
Alignment explanation
Indices: 3937106--3937976 Score: 743
Period size: 331 Copynumber: 2.6 Consensus size: 331
3937096 TGAAAATTTC
* * * * * ** ** * **
3937106 AAAACTAATTTAATGTGAATTTAATGACAAAATTAGATAAATTTTAAAAATTTTAAACCCAGGAA
1 AAAACTAATTTAATATAAATTAAATAACAATATTTTATAAATTTTAAAAATTAAAAACCAAAAAA
* * * * * * * * *** *
3937171 AATCCCCCTAAAACATTTATGGACTAGAAAATTCGATATTTCGGTAATAGGAA-A-ATTTCAAAG
66 AATCCTCCAAAAACATTTACGAAGTAAAAAACTCCATATTTCAAAAATA-GAAGAGATTTAAAAG
* * * * *
3937234 AAAAAAT-TCAAAATTCATGAAAATAAATGAATTTTTGAAAATTGATTTAATA-AGAATTAAATA
130 -AAAAATGT-AAAACTCATGAAAATGAATGAATTTTTCAAAACTAATTTAATATA-AATTAAATA
* * ** * * * **
3937297 ATAATACTTT-ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCCAAAAATATTTTTG-GA
192 ATAATA-TTTAAAGAATTTTAAAAATTATAAACTGAGAAAAATCCCTCTAAAAACATTTACGAG-
* * *** * *
3937360 GAACCAAAA-TCCGTA-TTTCAAAAATAGGAGAATTTCAAGAAAAAAAAGAAAAACTCATGAAAT
255 GTA-GAAAACTCTACACTTT-AGAAATAGGAGAATTTCAAGAAAAAAAAGAAAAACTCATGAAAA
3937423 TGAATGAATTTTTG
318 TGAATGAATTTTTG
* * * * ** *
3937437 AAAATTGATTTTATATAAATTAAATAATAATATTTTATAAATTTTAAATCTTAAAAACCAAGAAA
1 AAAACTAATTTAATATAAATTAAATAACAATATTTTATAAATTTTAAAAATTAAAAACCAAAAAA
* * *** * * **
3937502 AATCTTCCGAAAACATTTACGAAGTAAAAAACTTTGTATTTCAAAAATAGGAGAGCTTTAAGGGA
66 AATCCTCCAAAAACATTTACGAAGTAAAAAACTCCATATTTCAAAAATAGAAGAGATTTAAAAGA
* * *
3937567 AAAATGTAAAACTCATGAAAATGAATGAATTTTTGAAAATTGATTTAATATAAATTAAATAATAA
131 AAAATGTAAAACTCATGAAAATGAATGAATTTTTCAAAACTAATTTAATATAAATTAAATAATAA
* *
3937632 TATTTCATGAATTTTAAAAATTATAAACTGAGAAAAATCCCTCTAAAAACATTTACGAGGTAGAA
196 TATTTAAAGAATTTTAAAAATTATAAACTGAGAAAAATCCCTCTAAAAACATTTACGAGGTAGAA
* ** *
3937697 AACTCTACACTTTAGAAATA-GAGAGTTTCAAGGAAAAAACTGAAAAGCTCATGAAAATGAATGA
261 AACTCTACACTTTAGAAATAGGAGAATTTCAA-GAAAAAAAAGAAAAACTCATGAAAATGAATGA
3937761 ATTTTTG
325 ATTTTTG
* * *
3937768 AAAACTAATTTAAT-TGAATTAAATAACGATATTTTATGAATTTTAAAAATTAAAAACCAAAAAA
1 AAAACTAATTTAATATAAATTAAATAACAATATTTTATAAATTTTAAAAATTAAAAACCAAAAAA
* * * *
3937832 AATCCCTCCAAAAATATTTGC-AGAGTAGAAAACTCCATATTT-TAAAATAAGAAGA-ATTCTAA
66 AAT-CCTCCAAAAACATTTACGA-AGTAAAAAACTCCATATTTCAAAAAT-AGAAGAGATT-TAA
**
3937894 AAG-AAAAT-TAATAACTCAT-AAAAT-AATAGAAATTTTTCAAAACTAATTTAAT-TGTGATTA
127 AAGAAAAATGTAA-AACTCATGAAAATGAAT-G-AATTTTTCAAAACTAATTTAATAT-AAATTA
*
3937954 AATGATAATATTTAAAGAATTTT
188 AATAATAATATTTAAAGAATTTT
3937977 GATGCTTGAA
Statistics
Matches: 435, Mismatches: 88, Indels: 35
0.78 0.16 0.06
Matches are distributed among these distances:
328 3 0.01
329 10 0.02
330 128 0.29
331 283 0.65
332 11 0.03
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (331 bp):
AAAACTAATTTAATATAAATTAAATAACAATATTTTATAAATTTTAAAAATTAAAAACCAAAAAA
AATCCTCCAAAAACATTTACGAAGTAAAAAACTCCATATTTCAAAAATAGAAGAGATTTAAAAGA
AAAATGTAAAACTCATGAAAATGAATGAATTTTTCAAAACTAATTTAATATAAATTAAATAATAA
TATTTAAAGAATTTTAAAAATTATAAACTGAGAAAAATCCCTCTAAAAACATTTACGAGGTAGAA
AACTCTACACTTTAGAAATAGGAGAATTTCAAGAAAAAAAAGAAAAACTCATGAAAATGAATGAA
TTTTTG
Found at i:3939275 original size:34 final size:35
Alignment explanation
Indices: 3939223--3939355 Score: 133
Period size: 35 Copynumber: 3.8 Consensus size: 35
3939213 AAATGAAAAC
* *
3939223 GAAAAGGGTTTGACCAGATACAATCAAACAATAAT
1 GAAAAGAGTTTGACCAGATACAACCAAACAATAAT
** *
3939258 GAAAAGAG-TTGACCAGATACAACCAAATGATGAT
1 GAAAAGAGTTTGACCAGATACAACCAAACAATAAT
* * * * * *
3939292 GAAAAGAGTTTGACCAAATATAGCTAAACGATGAT
1 GAAAAGAGTTTGACCAGATACAACCAAACAATAAT
* * *
3939327 GAAAATAGTTTGACCAGATATAGCCAAAC
1 GAAAAGAGTTTGACCAGATACAACCAAAC
3939356 TGTTAGGATC
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 30 0.36
35 54 0.64
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (35 bp):
GAAAAGAGTTTGACCAGATACAACCAAACAATAAT
Found at i:3942751 original size:1 final size:1
Alignment explanation
Indices: 3942745--3942778 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
3942735 AAAGTGTTTG
**
3942745 AAAAAAAAAAAAAATGAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3942779 TTTTAAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.00, G:0.03, T:0.03
Consensus pattern (1 bp):
A
Found at i:3942764 original size:16 final size:16
Alignment explanation
Indices: 3942743--3942774 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3942733 ATAAAGTGTT
3942743 TGAAAAAAAAAAAAAA
1 TGAAAAAAAAAAAAAA
3942759 TGAAAAAAAAAAAAAA
1 TGAAAAAAAAAAAAAA
3942775 AAAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.06, T:0.06
Consensus pattern (16 bp):
TGAAAAAAAAAAAAAA
Found at i:3942808 original size:21 final size:21
Alignment explanation
Indices: 3942784--3942840 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3942774 AAAAATTTTA
3942784 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3942805 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3942826 AATGTATCGATACAT
1 AATGTATCGATACAT
3942841 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3942920 original size:19 final size:19
Alignment explanation
Indices: 3942896--3942963 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3942886 AATTCAACAA
3942896 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3942915 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3942930 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3942947 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3942964 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3942935 original size:13 final size:13
Alignment explanation
Indices: 3942917--3942941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3942907 ACATAAGTTT
3942917 TGTATCGATACAA
1 TGTATCGATACAA
3942930 TGTATCGATACA
1 TGTATCGATACA
3942942 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3942939 original size:32 final size:32
Alignment explanation
Indices: 3942898--3942960 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3942888 TTCAACAATT
*
3942898 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3942930 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3942961 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3943021 original size:13 final size:13
Alignment explanation
Indices: 3943003--3943028 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3942993 CATTTTTCTG
3943003 TGTATCGATACAT
1 TGTATCGATACAT
3943016 TGTATCGATACAT
1 TGTATCGATACAT
3943029 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3943025 original size:33 final size:33
Alignment explanation
Indices: 3942983--3943049 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3942973 GCCAAGGAAA
***
3942983 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3943016 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3943049 T
1 T
3943050 TGTAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3945575 original size:28 final size:27
Alignment explanation
Indices: 3945508--3945580 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
3945498 CTTCACAATC
* *
3945508 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
3945535 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
3945563 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
3945581 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:3945625 original size:51 final size:51
Alignment explanation
Indices: 3945563--3945733 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
3945553 TTATTTCTGA
* * *
3945563 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
3945614 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * * *
3945667 GGGGATACTCCAATTCTGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
3945719 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3945734 TCGTTATTTC
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 36 0.38
52 18 0.19
53 31 0.32
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:3945752 original size:28 final size:28
Alignment explanation
Indices: 3945716--3945797 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
3945706 ATTTTTCACA
*
3945716 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3945744 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
3945772 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
3945798 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:3955956 original size:55 final size:55
Alignment explanation
Indices: 3955871--3956924 Score: 1561
Period size: 55 Copynumber: 19.1 Consensus size: 55
3955861 CAAAGCCCTG
*
3955871 GAGCATGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAA
1 GAGCA-GGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAA
* *
3955927 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAC
1 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAA
*
3955982 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
1 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
3956037 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
1 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
*
3956092 GAGCAGGACACCTTTCAAAGCCCACACAAATTGGTGGCA--TTGTCCAGTCCTCAAA
1 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-T-CAGTCCTCAAA
*
3956147 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
1 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
3956202 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
1 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
*
3956257 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAA
1 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAA
* *
3956312 GAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAA
1 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAA
*
3956367 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
1 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
3956422 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
1 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
*
3956477 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTGTCCAGTCCTTAAA
1 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-T-CAGTCCTCAAA
*
3956532 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAA
1 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
3956587 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
1 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
*
3956642 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAA
1 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAA
* *
3956697 GAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAA
1 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAA
* *
3956752 GAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCATTCCCCAAA
1 GAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
* * *
3956807 GAGCAGGACACTTTTCAAATCCCACACAAGTGGGTGGCACCTTTCAGTCCTCAAA
1 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
* * * * * *
3956862 GAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAAT
1 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
3956917 GAGCAGGA
1 GAGCAGGA
3956925 TACAATTTAT
Statistics
Matches: 936, Mismatches: 39, Indels: 47
0.92 0.04 0.05
Matches are distributed among these distances:
53 4 0.00
54 18 0.02
55 884 0.94
56 26 0.03
57 4 0.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
Found at i:3956104 original size:26 final size:26
Alignment explanation
Indices: 3956019--3956658 Score: 101
Period size: 26 Copynumber: 23.3 Consensus size: 26
3956009 AAGTTGGTGG
*
3956019 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3956045 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3956074 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* **
3956100 CACCTTTCAAAGCCCACACAA-ATTGGTGG-
1 CACCTTTC--AGTCCACA-AAGA--GCAGGA
*
3956129 CA--TTGTCCAGTCCTCAAAGAGCAGGA
1 CACCTT-T-CAGTCCACAAAGAGCAGGA
* * * **
3956155 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3956184 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3956210 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3956239 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
3956265 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* * *
3956294 CA-TTTTCCAGTCCTCAAAGAACAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * **
3956320 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* *
3956349 CA-TTTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * * **
3956375 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3956404 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3956430 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3956459 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
3956485 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
**
3956514 CA--TTGTCCAGTCCTTAAAGAGCAGGA
1 CACCTT-T-CAGTCCACAAAGAGCAGGA
* * * **
3956540 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3956569 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3956595 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3956624 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
3956650 CACCTTTCA
1 CACCTTTCA
3956659 AAGCCCACAC
Statistics
Matches: 415, Mismatches: 133, Indels: 132
0.61 0.20 0.19
Matches are distributed among these distances:
25 32 0.08
26 94 0.23
27 82 0.20
28 94 0.23
29 81 0.20
30 32 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:3956851 original size:29 final size:29
Alignment explanation
Indices: 3956772--3956852 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 29
3956762 CCTCTTAAAG
* *
3956772 CCCACACAAGTTGGTGGCACCTTTC-ATT
1 CCCACACAAGTGGGTGGCACCTTTCAAAT
* * * *
3956800 CCC-CA-AAGAGCAG-GACACTTTTCAAAT
1 CCCACACAAGTG-GGTGGCACCTTTCAAAT
3956827 CCCACACAAGTGGGTGGCACCTTTCA
1 CCCACACAAGTGGGTGGCACCTTTCA
3956853 GTCCTCAAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 9
0.67 0.18 0.16
Matches are distributed among these distances:
26 11 0.29
27 8 0.21
28 6 0.16
29 13 0.34
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (29 bp):
CCCACACAAGTGGGTGGCACCTTTCAAAT
Found at i:3958207 original size:21 final size:21
Alignment explanation
Indices: 3958183--3958239 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3958173 AAAAAATTTA
3958183 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3958204 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3958225 AATGTATCGATACAT
1 AATGTATCGATACAT
3958240 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3958319 original size:19 final size:19
Alignment explanation
Indices: 3958295--3958362 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3958285 AATTCAACAA
3958295 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3958314 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3958329 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3958346 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3958363 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3958334 original size:13 final size:13
Alignment explanation
Indices: 3958316--3958340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3958306 ACATAAGTTT
3958316 TGTATCGATACAA
1 TGTATCGATACAA
3958329 TGTATCGATACA
1 TGTATCGATACA
3958341 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3958338 original size:32 final size:32
Alignment explanation
Indices: 3958297--3958359 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3958287 TTCAACAATT
*
3958297 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3958329 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3958360 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3958420 original size:13 final size:13
Alignment explanation
Indices: 3958402--3958427 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3958392 CATTTTTCTG
3958402 TGTATCGATACAT
1 TGTATCGATACAT
3958415 TGTATCGATACAT
1 TGTATCGATACAT
3958428 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3958424 original size:33 final size:33
Alignment explanation
Indices: 3958382--3958448 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3958372 GCCAAGGAAA
***
3958382 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3958415 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
3958448 T
1 T
3958449 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3961016 original size:51 final size:51
Alignment explanation
Indices: 3960954--3961124 Score: 207
Period size: 51 Copynumber: 3.3 Consensus size: 51
3960944 TTATTTCTGA
* * *
3960954 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
3961005 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** *
3961058 GGGGATACTCCAATTCCGATTTTATTTTCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
3961110 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3961125 TCGTTATTTC
Statistics
Matches: 98, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.18
53 33 0.34
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:3961143 original size:28 final size:28
Alignment explanation
Indices: 3961107--3961188 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
3961097 ATTTTTCACA
*
3961107 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
3961135 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
3961163 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
3961189 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:3973552 original size:1 final size:1
Alignment explanation
Indices: 3973546--3973623 Score: 93
Period size: 1 Copynumber: 78.0 Consensus size: 1
3973536 CCTTCTCTTC
* * * * *
3973546 AAAAAAAAAAAAAAAACAAAAAAAAAAACAAAAAAAAAAAACAAAAAAAACAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
3973611 AGAAAAGAAAAAA
1 AAAAAAAAAAAAA
3973624 CCTACTTAAG
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.91, C:0.05, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:3973578 original size:22 final size:21
Alignment explanation
Indices: 3973546--3973623 Score: 104
Period size: 21 Copynumber: 3.7 Consensus size: 21
3973536 CCTTCTCTTC
*
3973546 AAAAAAAA-AAAAAAAACAAA
1 AAAAAAAACAAAAAAAAAAAA
3973566 AAAAAAAACAAAAAAAAAAAA
1 AAAAAAAACAAAAAAAAAAAA
3973587 CAAAAAAAACAAAAAAAAAAAA
1 -AAAAAAAACAAAAAAAAAAAA
* * *
3973609 AGAGAAAAGAAAAAA
1 AAAAAAAACAAAAAA
3973624 CCTACTTAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
20 8 0.15
21 23 0.44
22 21 0.40
ACGTcount: A:0.91, C:0.05, G:0.04, T:0.00
Consensus pattern (21 bp):
AAAAAAAACAAAAAAAAAAAA
Found at i:3974674 original size:55 final size:55
Alignment explanation
Indices: 3974589--3975706 Score: 1682
Period size: 55 Copynumber: 20.3 Consensus size: 55
3974579 TCCGCTTTTT
*
3974589 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3974644 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
*
3974699 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
*
3974754 AGTCCTCAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3974809 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3974864 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAATTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-C
3974919 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3974974 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3975029 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
3975084 AGTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
3975139 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3975194 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
3975249 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-C
3975304 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3975359 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
3975414 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
* *
3975469 AGTCCTCAAAGAACAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
3975524 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
3975579 ATTCCCCAAAGAGCAGGACA-CTTTTCAAATCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
3975634 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* *
3975689 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
3975707 TACAATTTAT
Statistics
Matches: 999, Mismatches: 38, Indels: 52
0.92 0.03 0.05
Matches are distributed among these distances:
53 4 0.00
54 25 0.03
55 943 0.94
56 23 0.02
57 4 0.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:3974886 original size:26 final size:26
Alignment explanation
Indices: 3974801--3975440 Score: 110
Period size: 28 Copynumber: 23.3 Consensus size: 26
3974791 AAGTTGGTGG
*
3974801 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3974827 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3974856 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* **
3974882 CACCTTTCAAAGCCCACACAA-ATTGGTGG-
1 CACCTTTC--AGTCCACA-AAGA--GCAGGA
*
3974911 CA--TTGTCCAGTCCTCAAAGAGCAGGA
1 CACCTT-T-CAGTCCACAAAGAGCAGGA
* * * **
3974937 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3974966 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3974992 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3975021 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
3975047 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* * *
3975076 CA-TTTTCCAGTCCTCAAAGAACAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * **
3975102 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* *
3975131 CA-TTTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * * **
3975157 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3975186 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3975212 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3975241 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
3975267 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
*
3975296 CA--TTGTCCAGTCCTCAAAGAGCAGGA
1 CACCTT-T-CAGTCCACAAAGAGCAGGA
* * * **
3975322 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3975351 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
3975377 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
3975406 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
3975432 CACCTTTCA
1 CACCTTTCA
3975441 AAGCCCACAC
Statistics
Matches: 417, Mismatches: 131, Indels: 132
0.61 0.19 0.19
Matches are distributed among these distances:
25 32 0.08
26 94 0.23
27 83 0.20
28 95 0.23
29 81 0.19
30 32 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:3975633 original size:29 final size:29
Alignment explanation
Indices: 3975554--3975634 Score: 71
Period size: 29 Copynumber: 2.9 Consensus size: 29
3975544 CCTCTTAAAG
* *
3975554 CCCACACAAGTTGGTGGCACCTTTC-ATT
1 CCCACACAAGTGGGTGGCACCTTTCAAAT
* * * *
3975582 CCC-CA-AAGAGCAG-GACACTTTTCAAAT
1 CCCACACAAGTG-GGTGGCACCTTTCAAAT
3975609 CCCACACAAGTGGGTGGCACCTTTCA
1 CCCACACAAGTGGGTGGCACCTTTCA
3975635 GTCCTCAAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 9
0.67 0.18 0.16
Matches are distributed among these distances:
26 11 0.29
27 8 0.21
28 6 0.16
29 13 0.34
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (29 bp):
CCCACACAAGTGGGTGGCACCTTTCAAAT
Found at i:3976712 original size:13 final size:13
Alignment explanation
Indices: 3976694--3976719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3976684 GATAAAGTGT
3976694 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
3976707 TTGAAAAAAAAAA
1 TTGAAAAAAAAAA
3976720 AAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
TTGAAAAAAAAAA
Found at i:3976756 original size:21 final size:21
Alignment explanation
Indices: 3976732--3976788 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3976722 AAAAAATTTA
3976732 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
3976753 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
3976774 AATGTATCGATACAT
1 AATGTATCGATACAT
3976789 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:3976868 original size:19 final size:19
Alignment explanation
Indices: 3976844--3976911 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3976834 AATTCAACAA
3976844 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3976863 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3976878 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3976895 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3976912 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3976883 original size:13 final size:13
Alignment explanation
Indices: 3976865--3976889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3976855 ACATAAGTTT
3976865 TGTATCGATACAA
1 TGTATCGATACAA
3976878 TGTATCGATACA
1 TGTATCGATACA
3976890 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3976887 original size:32 final size:32
Alignment explanation
Indices: 3976846--3976908 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3976836 TTCAACAATT
*
3976846 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3976878 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3976909 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3976969 original size:13 final size:13
Alignment explanation
Indices: 3976951--3976976 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3976941 CATTTTTCTG
3976951 TGTATCGATACAT
1 TGTATCGATACAT
3976964 TGTATCGATACAT
1 TGTATCGATACAT
3976977 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.