Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 137 of 168
Found at i:40085519 original size:11 final size:11
Alignment explanation
Indices: 40085491--40085563 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
40085481 ATTAATCCTT
*
40085491 TCTCAATTATTT
1 TCTCAATT-TTC
40085503 TCTCAATTTTC
1 TCTCAATTTTC
*
40085514 TCTCAATTTCC
1 TCTCAATTTTC
* * *
40085525 TTTCAAATTGC
1 TCTCAATTTTC
*
40085536 TCTCAATTTCC
1 TCTCAATTTTC
*
40085547 T-TCCAAATTTC
1 TCT-CAATTTTC
40085558 TCTCAA
1 TCTCAA
40085564 ATCCATATTT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
10 1 0.02
11 39 0.80
12 9 0.18
ACGTcount: A:0.23, C:0.27, G:0.01, T:0.48
Consensus pattern (11 bp):
TCTCAATTTTC
Found at i:40085538 original size:22 final size:22
Alignment explanation
Indices: 40085513--40085563 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
40085503 TCTCAATTTT
*
40085513 CTCTCAATTTCCTTTCAAATTG
1 CTCTCAATTTCCTTCCAAATTG
*
40085535 CTCTCAATTTCCTTCCAAATTT
1 CTCTCAATTTCCTTCCAAATTG
40085557 CTCTCAA
1 CTCTCAA
40085564 ATCCATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.43
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAATTG
Found at i:40085588 original size:51 final size:51
Alignment explanation
Indices: 40085527--40085624 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 51
40085517 CAATTTCCTT
40085527 TCAAATTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAATC
1 TCAAATTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAATC
* * * *
40085578 TCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
40085625 TTAATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.45
Consensus pattern (51 bp):
TCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAATC
Found at i:40085600 original size:11 final size:11
Alignment explanation
Indices: 40085503--40085600 Score: 55
Period size: 11 Copynumber: 9.3 Consensus size: 11
40085493 TCAATTATTT
*
40085503 TCTCAATTTTC
1 TCTCAATTTCC
40085514 TCTCAATTTCC
1 TCTCAATTTCC
* * *
40085525 TTTCAAATTGC
1 TCTCAATTTCC
40085536 TCTCAATTTCC
1 TCTCAATTTCC
40085547 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
40085558 TCTCAA-ATCC
1 TCTCAATTTCC
* **
40085568 -AT--ATTTAA
1 TCTCAATTTCC
*
40085576 TCTCAATTTGC
1 TCTCAATTTCC
40085587 TCTCAATTTCC
1 TCTCAATTTCC
40085598 TCT
1 TCT
40085601 TAAATTTCTC
Statistics
Matches: 63, Mismatches: 16, Indels: 16
0.66 0.17 0.17
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.06
11 48 0.76
12 6 0.10
ACGTcount: A:0.23, C:0.29, G:0.02, T:0.46
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:40087944 original size:49 final size:49
Alignment explanation
Indices: 40087890--40088148 Score: 455
Period size: 49 Copynumber: 5.3 Consensus size: 49
40087880 GTTTATATTA
*
40087890 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
40087939 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
* * *
40087988 ATTTAATAAAATACAAAATAGTTTATTTTGAATAGTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
40088037 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
* *
40088086 ATTTAGTAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
*
40088135 ATTTAATAAAATAC
1 ATGTAATAAAATAC
40088149 TGAATATTTT
Statistics
Matches: 200, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 200 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
Found at i:40089685 original size:9 final size:9
Alignment explanation
Indices: 40089671--40089701 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40089661 GTTAAACGAA
40089671 TCGAGTTAT
1 TCGAGTTAT
*
40089680 TCGAGTTAA
1 TCGAGTTAT
40089689 TCGAGTTAT
1 TCGAGTTAT
40089698 TCGA
1 TCGA
40089702 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:40090711 original size:5 final size:5
Alignment explanation
Indices: 40090701--40090731 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
40090691 GAACAAATAT
40090701 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
40090732 ATTCCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:40090831 original size:5 final size:5
Alignment explanation
Indices: 40090821--40090846 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40090811 CTCGAAAATT
40090821 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
40090847 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:40092869 original size:124 final size:124
Alignment explanation
Indices: 40092606--40093016 Score: 642
Period size: 124 Copynumber: 3.3 Consensus size: 124
40092596 CCCAAACATG
* * *
40092606 CTACTGTAGCAAAAACGTGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAACATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAATATCCTGC
* *
40092671 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAATTCGAAATTATTTTTTCAGGAC
66 TTGAAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * * *
40092731 CTACTATAGCAAAAGCGCGTCCACGTGAGAGCGATTTCAGAAATTCTTCTAATAAAGTATCCTAC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAATATCCTGC
*
40092796 TTGAAGCGTTTTTATACTATTTACTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * *
40092855 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAGAAATTTTTCTGATAAAATATCTTGG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAATATCCTGC
40092920 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
66 TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * *
40092979 TTACTGTAGCAAACGCGAGTCCACGTGGGAGGGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
40093017 CTTAATAAAT
Statistics
Matches: 260, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
124 195 0.75
125 65 0.25
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAATATCCTGC
TTGAAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:40093228 original size:6 final size:6
Alignment explanation
Indices: 40093210--40093253 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
40093200 AAAAAGCCTA
* *
40093210 AACCCT AAACCT AACCCT AACCCT AACCCT AACCCT GACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA
40093254 AAACCCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.36, C:0.45, G:0.02, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:40105609 original size:64 final size:64
Alignment explanation
Indices: 40105531--40105660 Score: 251
Period size: 64 Copynumber: 2.0 Consensus size: 64
40105521 TTTCTTCCAT
40105531 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
1 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
*
40105595 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTGCATAAATGTAAATATGC
1 TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
40105659 TT
1 TT
40105661 AAAATTTATC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.20, C:0.12, G:0.13, T:0.55
Consensus pattern (64 bp):
TTTTGTTACTTTGAATTTGGTATGAGCTTTTTCTTTTTCTTTCTTTCCATAAATGTAAATATGC
Found at i:40109035 original size:24 final size:23
Alignment explanation
Indices: 40108998--40109042 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
40108988 TTAAATCCAA
* *
40108998 AAAATAAAATGACTATATTTCTC
1 AAAATAAAAGGACTAAATTTCTC
40109021 AAAATAAAAGGGACTAAATTTC
1 AAAATAAAA-GGACTAAATTTC
40109043 AAATGTACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (23 bp):
AAAATAAAAGGACTAAATTTCTC
Found at i:40119412 original size:25 final size:26
Alignment explanation
Indices: 40119373--40119437 Score: 105
Period size: 25 Copynumber: 2.5 Consensus size: 26
40119363 ATTACTTAGG
40119373 AAGCCTTTGTGGCTAATCTTGT-GAA
1 AAGCCTTTGTGGCTAATCTTGTGGAA
**
40119398 AAGTTTTTGTGGCTAATCTTGTGGAA
1 AAGCCTTTGTGGCTAATCTTGTGGAA
40119424 AAGCCTTTGTGGCT
1 AAGCCTTTGTGGCT
40119438 TGTTATTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.22, C:0.14, G:0.26, T:0.38
Consensus pattern (26 bp):
AAGCCTTTGTGGCTAATCTTGTGGAA
Found at i:40127948 original size:30 final size:29
Alignment explanation
Indices: 40127894--40127966 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 29
40127884 TTTTTTTAAG
*
40127894 TATATTATTAT-TTTATTGTAAATTATAT
1 TATATTATTATATTTATTATAAATTATAT
40127922 TATATTATTATATTATATTATAAATTATAT
1 TATATTATTATATT-TATTATAAATTATAT
40127952 TATATTATTATATTT
1 TATATTATTATATTT
40127967 TAAATAAACA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 11 0.26
29 3 0.07
30 28 0.67
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TATATTATTATATTTATTATAAATTATAT
Found at i:40127963 original size:25 final size:25
Alignment explanation
Indices: 40127920--40127971 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
40127910 TGTAAATTAT
40127920 ATTATATTATTATATTATATTATAA
1 ATTATATTATTATATTATATTATAA
*
40127945 ATTATATTA-TATTATTATATTTTAA
1 ATTATATTATTA-TATTATATTATAA
40127970 AT
1 AT
40127972 AAACAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 2 0.08
25 23 0.92
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTATATTATTATATTATATTATAA
Found at i:40127965 original size:5 final size:5
Alignment explanation
Indices: 40127915--40127959 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
40127905 TTTATTGTAA
40127915 ATTAT ATTAT A-T-T ATTAT ATTAT ATTAT AAATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT --ATTAT ATTAT ATTAT
40127960 TATATTTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 27 0.75
7 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:40128197 original size:13 final size:13
Alignment explanation
Indices: 40128166--40128206 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
40128156 GACGAAACAG
*
40128166 AGAAGGAAAG-AA
1 AGAAAGAAAGAAA
*
40128178 GGAAAGAAAGAAA
1 AGAAAGAAAGAAA
40128191 AGAAAGAAAGAAA
1 AGAAAGAAAGAAA
40128204 AGA
1 AGA
40128207 GAAAATTGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AGAAAGAAAGAAA
Found at i:40129441 original size:6 final size:6
Alignment explanation
Indices: 40129430--40129462 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
40129420 ATGTGCCGAC
*
40129430 TACTGT TACTGT TACTGT TACCGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TACTGT TAC
40129463 AGATTCAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.45
Consensus pattern (6 bp):
TACTGT
Found at i:40129507 original size:39 final size:38
Alignment explanation
Indices: 40129452--40129590 Score: 152
Period size: 39 Copynumber: 3.4 Consensus size: 38
40129442 TACTGTTACC
* *
40129452 GTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATACT
1 GTTACTGTTACTGATTC-GCACTTTGTGTGTCGAATACT
*
40129491 GTTACTGTTACTGATTCGATACTTTGTGTGTCGAATACT
1 GTTACTGTTACTGATTCG-CACTTTGTGTGTCGAATACT
*
40129530 GTTACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAACACT
1 GTTACTGTTA-C--T---GATTC-GCACTTTGTGTGTCGAATACT
*
40129575 GTTACCGTTACTGATT
1 GTTACTGTTACTGATT
40129591 AATGTTACTG
Statistics
Matches: 86, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
38 1 0.01
39 48 0.56
40 1 0.01
42 2 0.02
44 1 0.01
45 32 0.37
46 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.40
Consensus pattern (38 bp):
GTTACTGTTACTGATTCGCACTTTGTGTGTCGAATACT
Found at i:40129536 original size:45 final size:45
Alignment explanation
Indices: 40129443--40129587 Score: 151
Period size: 45 Copynumber: 3.4 Consensus size: 45
40129433 TGTTACTGTT
* * *
40129443 ACTGTTACCGTTACTGTTACAGATTC-AGCACTTTGTGTGTTG-A-
1 ACTGTTACTGTTACTGTTACCGATTCGA-CACTTTGTGTGTCGAAC
* * *
40129486 A----TACTGTTACTGTTACTGATTCGATACTTTGTGTGTCGAAT
1 ACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAAC
* *
40129527 ACTGTTACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAAC
1 ACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAAC
*
40129572 ACTGTTACCGTTACTG
1 ACTGTTACTGTTACTG
40129588 ATTAATGTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
39 31 0.37
40 2 0.02
41 1 0.01
43 1 0.01
45 49 0.58
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (45 bp):
ACTGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAAC
Found at i:40130466 original size:17 final size:17
Alignment explanation
Indices: 40130419--40130469 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
40130409 ACGTGGCATG
*
40130419 TACCTAAGTAATATATA
1 TACCTAAGTAATGTATA
*
40130436 TACCTAAGTAATGTTTA
1 TACCTAAGTAATGTATA
*
40130453 TACCTAAGTGATGTATA
1 TACCTAAGTAATGTATA
40130470 GGAATTAGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (17 bp):
TACCTAAGTAATGTATA
Found at i:40132942 original size:41 final size:41
Alignment explanation
Indices: 40132897--40133009 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 41
40132887 TTGTATATAA
* * *
40132897 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATT
* * * * *
40132938 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATT
*
40132979 CACCGGCACAAAGCCTGCTAGGCATAAAGCC
1 CACCGGCACAAAGCCTGCTAGGCACAAAGCC
40133010 TGAACTTACA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATT
Found at i:40134120 original size:42 final size:42
Alignment explanation
Indices: 40134057--40134155 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
40134047 CTCTCGGTAT
* *
40134057 CGCACACTTAGTGCCCGTTATTCAACATCATTATTATAATTC
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
* * *
40134099 CGCACACTTAGTGCCTATTATTCAACATCATCATTTTAATTT
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
**
40134141 TACACACTTAGTGCC
1 CGCACACTTAGTGCC
40134156 ATTCATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (42 bp):
CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
Found at i:40142349 original size:9 final size:9
Alignment explanation
Indices: 40142319--40142343 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40142309 TTTATTATCC
40142319 TTATTATTG
1 TTATTATTG
40142328 TTATTATTG
1 TTATTATTG
40142337 TTATTAT
1 TTATTAT
40142344 GATTATCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTATTATTG
Found at i:40145842 original size:29 final size:30
Alignment explanation
Indices: 40145810--40145869 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
40145800 AAAATTATAA
*
40145810 AAAAATTTGTAAAAATG-GTAAAAAA-TATT
1 AAAAATAT-TAAAAATGTGTAAAAAAGTATT
40145839 -AAAATATTAAAAATGTGTAAAAAAGTATT
1 AAAAATATTAAAAATGTGTAAAAAAGTATT
40145868 AA
1 AA
40145870 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 8 0.30
28 14 0.52
29 4 0.15
30 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (30 bp):
AAAAATATTAAAAATGTGTAAAAAAGTATT
Found at i:40149747 original size:4 final size:4
Alignment explanation
Indices: 40149738--40149764 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
40149728 TCAATGTAAA
40149738 ACTC ACTC ACTC ACTC ACTC ACTC ACT
1 ACTC ACTC ACTC ACTC ACTC ACTC ACT
40149765 TTTTTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.48, G:0.00, T:0.26
Consensus pattern (4 bp):
ACTC
Found at i:40152488 original size:25 final size:25
Alignment explanation
Indices: 40152453--40152536 Score: 125
Period size: 25 Copynumber: 3.4 Consensus size: 25
40152443 TATATATTAA
40152453 ATATATATTTTATTTTTAATCAAAT
1 ATATATATTTTATTTTTAATCAAAT
*
40152478 ATATATTTTTTATTTTTAATCAAAT
1 ATATATATTTTATTTTTAATCAAAT
* * *
40152503 ATATATATTTTATATAT-ATTAAAT
1 ATATATATTTTATTTTTAATCAAAT
40152527 ATATATATTT
1 ATATATATTT
40152537 AATATGGGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 16 0.30
25 38 0.70
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATATATATTTTATTTTTAATCAAAT
Found at i:40152529 original size:13 final size:13
Alignment explanation
Indices: 40152499--40152541 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
40152489 ATTTTTAATC
40152499 AAATATATATATT
1 AAATATATATATT
*
40152512 --TTATATATATT
1 AAATATATATATT
40152523 AAATATATATATT
1 AAATATATATATT
*
40152536 TAATAT
1 AAATAT
40152542 GGGCTGGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 10 0.40
13 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AAATATATATATT
Found at i:40155355 original size:22 final size:22
Alignment explanation
Indices: 40155327--40155479 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
40155317 TTTATTGTTC
*
40155327 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
40155349 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
40155371 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
40155393 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
40155415 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
40155437 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
40155459 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
40155480 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:40157050 original size:27 final size:28
Alignment explanation
Indices: 40157019--40157075 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
40157009 TTTTTTTTCA
* *
40157019 TTGTTTTGCTATTA-TATTGTTACTATT
1 TTGTTTTACTATTAGTATTGCTACTATT
* *
40157046 TTGTTTTATTATTAGTTTTGCTACTATT
1 TTGTTTTACTATTAGTATTGCTACTATT
40157074 TT
1 TT
40157076 AGAGATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.65
Consensus pattern (28 bp):
TTGTTTTACTATTAGTATTGCTACTATT
Found at i:40159675 original size:21 final size:20
Alignment explanation
Indices: 40159650--40159715 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 20
40159640 TGAAATATTT
40159650 TTTTTCAAAGTTTAATTAAAA
1 TTTTTCAAAG-TTAATTAAAA
*
40159671 TTTTT-ATGAAGTAAATGT-AAA
1 TTTTTCA--AAGTTAAT-TAAAA
40159692 -TTTTCAAAGATTAATT-AAA
1 TTTTTCAAAG-TTAATTAAAA
40159711 TTTTT
1 TTTTT
40159716 TTTTAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
19 7 0.19
20 13 0.35
21 13 0.35
22 4 0.11
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (20 bp):
TTTTTCAAAGTTAATTAAAA
Found at i:40163374 original size:18 final size:19
Alignment explanation
Indices: 40163346--40163385 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
40163336 ATGAAAGTAA
*
40163346 GATTGTGTTTGAAATGGAT
1 GATTGTGTTTGAAATGAAT
*
40163365 GATTGT-TTTGATATGAAT
1 GATTGTGTTTGAAATGAAT
40163383 GAT
1 GAT
40163386 ATTTATGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (19 bp):
GATTGTGTTTGAAATGAAT
Found at i:40167435 original size:2 final size:2
Alignment explanation
Indices: 40167428--40167466 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
40167418 GTCCTACCAT
40167428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40167467 TATTATTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40168388 original size:17 final size:19
Alignment explanation
Indices: 40168352--40168396 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
40168342 GTTTAACTAA
40168352 TATTTTATATTTAATATAT
1 TATTTTATATTTAATATAT
*
40168371 TATTTT-TA-TTAATTTA-
1 TATTTTATATTTAATATAT
40168387 T-TTTTATATT
1 TATTTTATATT
40168397 GCTTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
15 4 0.17
16 3 0.13
17 8 0.35
18 2 0.09
19 6 0.26
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TATTTTATATTTAATATAT
Found at i:40168991 original size:83 final size:81
Alignment explanation
Indices: 40168904--40169163 Score: 290
Period size: 80 Copynumber: 3.2 Consensus size: 81
40168894 AAATAAATTC
* * *
40168904 ATTTTAAAGGGACTAAAGTGTAATTTTACTATATATTAAATTATGATTTCTTTATTTATAAGAGG
1 ATTTT-AAGGGAC-AAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGG
* *
40168969 ACTGAATTGAAAATTTTT
64 ATTAAATTGAAAATTTTT
* * * * **
40168987 ATTTTAAGAGGTCAAAGTGCAATTTTATTATAATATTAATTTGTAATTTATCCATTTATAAGAGG
1 ATTTTAAG-GGACAAAGTGCAATTTTACTAT-ATATTAATTTATAATTTCTTTATTTATAAGAGG
*
40169052 ATTAAATTG-AAATTATT
64 ATTAAATTGAAAATTTTT
* * * * *
40169069 ATTGTGAGGGACAAAATACAAATTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGAT
1 ATTTTAAGGGACAAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGAT
* *
40169134 TAAATTTAAAATTTTC
66 TAAATTGAAAATTTTT
*
40169150 ATTTT-CGGGACAAA
1 ATTTTAAGGGACAAA
40169164 TCGTTTGTGT
Statistics
Matches: 146, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
80 45 0.31
81 27 0.18
82 32 0.22
83 42 0.29
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (81 bp):
ATTTTAAGGGACAAAGTGCAATTTTACTATATATTAATTTATAATTTCTTTATTTATAAGAGGAT
TAAATTGAAAATTTTT
Found at i:40170088 original size:12 final size:12
Alignment explanation
Indices: 40170071--40170102 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
40170061 ATTTCCTCTT
40170071 ATCATCATCACC
1 ATCATCATCACC
40170083 ATCATCATCACC
1 ATCATCATCACC
*
40170095 ACCATCAT
1 ATCATCAT
40170103 GACTCAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (12 bp):
ATCATCATCACC
Found at i:40170091 original size:15 final size:15
Alignment explanation
Indices: 40170071--40170102 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40170061 ATTTCCTCTT
*
40170071 ATCATCATCACCATC
1 ATCATCACCACCATC
40170086 ATCATCACCACCATC
1 ATCATCACCACCATC
40170101 AT
1 AT
40170103 GACTCAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (15 bp):
ATCATCACCACCATC
Found at i:40172941 original size:16 final size:17
Alignment explanation
Indices: 40172911--40172943 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40172901 TCGGAAAATT
*
40172911 TTTTAAAATTTATAAAG
1 TTTTAAAATTAATAAAG
40172928 TTTT-AAATTAATAAAG
1 TTTTAAAATTAATAAAG
40172944 GTAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TTTTAAAATTAATAAAG
Found at i:40173043 original size:55 final size:54
Alignment explanation
Indices: 40172995--40173111 Score: 198
Period size: 55 Copynumber: 2.1 Consensus size: 54
40172985 TTTAATCATT
*
40172995 TAAAAGTTATTAAGATATAGTCTATTAAAATAGTAAAATTATATATTTATTATCA
1 TAAAAATTATTAAGATATAGTCTATTAAAATAGTAAAATTATATATTTA-TATCA
*
40173050 TAAAAATTATTAAGATATAGTCTATTAAAATAGTAAAATTATATTTTTATTATCA
1 TAAAAATTATTAAGATATAGTCTATTAAAATAGTAAAATTATATATTTA-TATCA
40173105 TAAAAAT
1 TAAAAAT
40173112 AGTAGGGTGT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 60 1.00
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (54 bp):
TAAAAATTATTAAGATATAGTCTATTAAAATAGTAAAATTATATATTTATATCA
Found at i:40173045 original size:25 final size:25
Alignment explanation
Indices: 40173017--40173101 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 25
40173007 AGATATAGTC
40173017 TATTAAAATAGTAAAATTATATATT
1 TATTAAAATAGTAAAATTATATATT
**
40173042 TATTATCATA--AAAATTATTAAGATATAGT
1 TATTAAAATAGTAAAATTA-T---ATAT--T
*
40173071 CTATTAAAATAGTAAAATTATATTTT
1 -TATTAAAATAGTAAAATTATATATT
40173097 TATTA
1 TATTA
40173102 TCATAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 18
0.67 0.07 0.26
Matches are distributed among these distances:
23 7 0.15
24 1 0.02
25 13 0.28
26 1 0.02
27 4 0.09
28 3 0.07
29 1 0.02
30 8 0.17
31 1 0.02
32 7 0.15
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (25 bp):
TATTAAAATAGTAAAATTATATATT
Found at i:40173056 original size:31 final size:31
Alignment explanation
Indices: 40173021--40173115 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 31
40173011 ATAGTCTATT
40173021 AAAATAGTAAAATTATATATTTATTATCATA
1 AAAATAGTAAAATTATATATTTATTATCATA
* * * * *
40173052 AAAAT--T---ATTA-AGATATAGTCT-ATT
1 AAAATAGTAAAATTATATATTTATTATCATA
*
40173076 AAAATAGTAAAATTATATTTTTATTATCATA
1 AAAATAGTAAAATTATATATTTATTATCATA
40173107 AAAATAGTA
1 AAAATAGTA
40173116 GGGTGTGAGT
Statistics
Matches: 46, Mismatches: 11, Indels: 14
0.65 0.15 0.20
Matches are distributed among these distances:
24 7 0.15
25 7 0.15
26 5 0.11
29 5 0.11
30 6 0.13
31 16 0.35
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (31 bp):
AAAATAGTAAAATTATATATTTATTATCATA
Found at i:40173088 original size:32 final size:32
Alignment explanation
Indices: 40172995--40173091 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 32
40172985 TTTAATCATT
40172995 TAAAAGTTATTAAGATATAGTCTATTAAAATAG
1 TAAAA-TTATTAAGATATAGTCTATTAAAATAG
**
40173028 TAAAATTA-T---ATAT--T-TATTATCATA-
1 TAAAATTATTAAGATATAGTCTATTAAAATAG
40173052 -AAAATTATTAAGATATAGTCTATTAAAATAG
1 TAAAATTATTAAGATATAGTCTATTAAAATAG
40173083 TAAAATTAT
1 TAAAATTAT
40173092 ATTTTTATTA
Statistics
Matches: 51, Mismatches: 4, Indels: 19
0.69 0.05 0.26
Matches are distributed among these distances:
23 7 0.14
24 1 0.02
25 8 0.16
26 1 0.02
27 4 0.08
28 4 0.08
29 1 0.02
30 8 0.16
31 1 0.02
32 11 0.22
33 5 0.10
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.40
Consensus pattern (32 bp):
TAAAATTATTAAGATATAGTCTATTAAAATAG
Found at i:40174100 original size:5 final size:5
Alignment explanation
Indices: 40174090--40174117 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
40174080 AAACCCACCC
40174090 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
40174118 TTCAAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:40175180 original size:34 final size:34
Alignment explanation
Indices: 40175142--40175209 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
40175132 CTAAGAAAGA
40175142 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
1 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
40175176 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
1 GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
40175210 TCATTGCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (34 bp):
GCAATGCTTTTTATTATAGTTCTGGAGTGAGCTG
Found at i:40184386 original size:19 final size:18
Alignment explanation
Indices: 40184362--40184415 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
40184352 TGCCAGAAGT
40184362 AAATAAAAGAAAAATTAGA
1 AAATAAAAGAAAAATTA-A
** *
40184381 AAATAAAAGTTAAACTAA
1 AAATAAAAGAAAAATTAA
*
40184399 AAATAAAATAAAAATTA
1 AAATAAAAGAAAAATTA
40184416 TAATAGAAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (18 bp):
AAATAAAAGAAAAATTAA
Found at i:40184406 original size:23 final size:23
Alignment explanation
Indices: 40184380--40184429 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
40184370 GAAAAATTAG
*
40184380 AAAATAAAAGTTA-AACTAAAAAT
1 AAAATAAAAATTATAA-TAAAAAT
*
40184403 AAAATAAAAATTATAATAGAAAT
1 AAAATAAAAATTATAATAAAAAT
40184426 AAAA
1 AAAA
40184430 ATGGCTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAATAAAAATTATAATAAAAAT
Found at i:40184909 original size:25 final size:25
Alignment explanation
Indices: 40184872--40184920 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
40184862 TTGCTTAGGG
40184872 ATTTTATTGTATTCAATATTAATAT
1 ATTTTATTGTATTCAATATTAATAT
*
40184897 ATTTATATT-TATTTAATATTAATA
1 ATTT-TATTGTATTCAATATTAATA
40184921 CAAAATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTATTGTATTCAATATTAATAT
Found at i:40187683 original size:3 final size:3
Alignment explanation
Indices: 40187675--40187709 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
40187665 TCAGTCCCAG
40187675 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
40187710 TGAAGAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:40188410 original size:22 final size:23
Alignment explanation
Indices: 40188382--40188434 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
40188372 CGTACTCCCG
40188382 TCCCCCCTCCCT-CCCCTCCCCC
1 TCCCCCCTCCCTCCCCCTCCCCC
*
40188404 TCCCCCCT-CCTCCCCCTCCCCT
1 TCCCCCCTCCCTCCCCCTCCCCC
*
40188426 TCCCTCCTC
1 TCCCCCCTC
40188435 TCTCTGTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.00, C:0.77, G:0.00, T:0.23
Consensus pattern (23 bp):
TCCCCCCTCCCTCCCCCTCCCCC
Found at i:40188431 original size:16 final size:16
Alignment explanation
Indices: 40188384--40188432 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
40188374 TACTCCCGTC
40188384 CCCCCT-CCCTCCCCT
1 CCCCCTCCCCTCCCCT
40188399 CCCCCTCCCC-CCTCCT
1 CCCCCTCCCCTCC-CCT
*
40188415 CCCCCTCCCCTTCCCT
1 CCCCCTCCCCTCCCCT
40188431 CC
1 CC
40188433 TCTCTCTGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 8 0.27
16 21 0.70
17 1 0.03
ACGTcount: A:0.00, C:0.80, G:0.00, T:0.20
Consensus pattern (16 bp):
CCCCCTCCCCTCCCCT
Found at i:40188439 original size:2 final size:2
Alignment explanation
Indices: 40188432--40188489 Score: 50
Period size: 2 Copynumber: 29.5 Consensus size: 2
40188422 CCCTTCCCTC
* *
40188432 CT CT CT CT GT C- CT C- CT ACT CT CT CT CT CT CT CT CT C- CC CGT
1 CT CT CT CT CT CT CT CT CT -CT CT CT CT CT CT CT CT CT CT CT C-T
*
40188473 CT CT CT CT CC CT CT CT C
1 CT CT CT CT CT CT CT CT C
40188490 CATATATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
1 3 0.07
2 40 0.87
3 3 0.07
ACGTcount: A:0.02, C:0.53, G:0.03, T:0.41
Consensus pattern (2 bp):
CT
Found at i:40192749 original size:27 final size:27
Alignment explanation
Indices: 40192719--40192774 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
40192709 CCCAGAAAGA
40192719 GATGTTACTTGCAAGGCATGAGTGTGG
1 GATGTTACTTGCAAGGCATGAGTGTGG
40192746 GATGTTACTTGCAAGGCATGAGTGTGG
1 GATGTTACTTGCAAGGCATGAGTGTGG
40192773 GA
1 GA
40192775 CAATTATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.23, C:0.11, G:0.38, T:0.29
Consensus pattern (27 bp):
GATGTTACTTGCAAGGCATGAGTGTGG
Found at i:40196584 original size:41 final size:41
Alignment explanation
Indices: 40196536--40196617 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
40196526 ATAGCAAAAT
40196536 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
1 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
40196577 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
1 CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
40196618 TAAAGCTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (41 bp):
CAAAATGACTGATTATTATGCAAAAGATTACTCAAAACACA
Found at i:40197243 original size:7 final size:7
Alignment explanation
Indices: 40197225--40197258 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
40197215 ATATTTGTAA
40197225 GTGTGT-
1 GTGTGTG
40197231 GTGTGTG
1 GTGTGTG
40197238 GTGTGTG
1 GTGTGTG
40197245 GTGTGTG
1 GTGTGTG
40197252 GTGTGTG
1 GTGTGTG
40197259 CATCATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.00, C:0.00, G:0.56, T:0.44
Consensus pattern (7 bp):
GTGTGTG
Found at i:40198881 original size:365 final size:365
Alignment explanation
Indices: 40198211--40198929 Score: 1332
Period size: 365 Copynumber: 2.0 Consensus size: 365
40198201 ATGAGTTTCC
40198211 ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATCTCA
1 ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATCTCA
* * *
40198276 GCAAGCATATTTTGGAAGAAGAAATTTAAAATCATACCATATATTATACTAGTTTTAGTCAACAG
66 GCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAGTCAACAG
40198341 CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
131 CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
*
40198406 AAGAAAAAGATAACAGGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTACTCAGCTC
196 AAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTACTCAGCTC
40198471 TGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACTG
261 TGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACTG
40198536 TATACACAGACAGTCAGAGGCGAATCTAGTGAGTTTATCG
326 TATACACAGACAGTCAGAGGCGAATCTAGTGAGTTTATCG
*
40198576 ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTTTTAACAATTTAAGAAACCAACATCTCA
1 ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATCTCA
40198641 GCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAGTCAACAG
66 GCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAGTCAACAG
40198706 CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
131 CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
* * *
40198771 AGGAAAAAGATAACACGCATGACAGAAAATATTAAATAGGAAGTTTGTTTGATGTTA-TCCTGCT
196 AAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTACT-CAGCT
*
40198835 TTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACT
260 CTGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACT
*
40198900 GTATTCACAGACAGTCAGAGGCGAATCTAG
325 GTATACACAGACAGTCAGAGGCGAATCTAG
40198930 GGGGCAGGCA
Statistics
Matches: 343, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
364 1 0.00
365 342 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (365 bp):
ATGATGAGTTTGAAAATTGTGCTTCTTACAAACTTGTCTTAACAATTTAAGAAACCAACATCTCA
GCAAGCATATTTTGGAAAAAGAAATTTAAAATCATACCATACATTATACTAGTTTCAGTCAACAG
CTACACTAGTAACATAAGAAAAACACTTTTGGTGTATCCCTTTAAAATTTAACAATATTTTGAGC
AAGAAAAAGATAACACGCATGACAAAAAATATTAAATAGGAAGTTTGTTTGATGTTACTCAGCTC
TGTAATTGCATATATTCTCTCCAAATGCTTTGTTAAAGTTACCATATAGTTAAATAACCTAACTG
TATACACAGACAGTCAGAGGCGAATCTAGTGAGTTTATCG
Found at i:40207182 original size:222 final size:225
Alignment explanation
Indices: 40206723--40207210 Score: 565
Period size: 222 Copynumber: 2.2 Consensus size: 225
40206713 TTAAATATCT
* * * * * *
40206723 TTTGTTTCTTTCTTATAATA-CTCTTTTTTGATGCCATAAGTGATCTTTAAAAAATATTATCAAC
1 TTTGTTTCTTTCTTATAA-AGCTCTTCTTTGATGCC-T---T-AGCATTAATAAATCTCATCAAC
* *
40206787 CAAGCAAATATTTCTCAAAATCAACAATTACCAAGTACACAACAATACTCGTTTCTCAAGAAAAA
60 CAAGCAAATATTTCCCAAAATCAACAATTACCAAGTACACAACAATACTCATTTCT-AAGAAAAA
* * * *
40206852 GAAATGCAAGAATATTACCAATGGAGCAAATAGCCATAATATTCTTTCACCAACAAGGGTAATTC
124 GAAATGCAAGAATATTACCAATGGAACAAATAACCATAATATTCTTGCACCAACAAAGGTAATTC
** ***
40206917 TGATCAAATGATAATCAAGTATTGCACTCAATTGTCA
189 TGATCAAATGATAATCAAGTATCACACTCAACCCTCA
* * * *
40206954 TTTGTTTCTTTTTTATAATGC-CTTTCTTTGATGCCTTAGCATTAATAAATCTCATCAATCAAGT
1 TTTGTTTCTTTCTTATAAAGCTC-TTCTTTGATGCCTTAGCATTAATAAATCTCATCAACCAAGC
* **
40207018 AAATATTTCCCAAAATCAACAATTA-CAAGTACACAACAATATTCATTTCT-TTAAAAA-AAATG
65 AAATATTTCCCAAAATCAACAATTACCAAGTACACAACAATACTCATTTCTAAGAAAAAGAAATG
* * * *
40207080 -AAGAATCTTACCAATGGAAACAAATAATCATAATCTTCTTGCACCAACAAAGGTAATTTTGATC
130 CAAGAATATTACCAATGG-AACAAATAACCATAATATTCTTGCACCAACAAAGGTAATTCTGATC
* * * *
40207144 AAATGGTAATTAAGTATCACACTCAGCCCTCT
194 AAATGATAATCAAGTATCACACTCAACCCTCA
40207176 TTTGTTTCTTTCTTATAAAGCTCTTCTTTGATGCC
1 TTTGTTTCTTTCTTATAAAGCTCTTCTTTGATGCC
40207211 ATAAGTAATA
Statistics
Matches: 219, Mismatches: 34, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
221 16 0.07
222 98 0.45
223 6 0.03
225 23 0.11
226 44 0.20
227 1 0.00
230 2 0.01
231 29 0.13
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (225 bp):
TTTGTTTCTTTCTTATAAAGCTCTTCTTTGATGCCTTAGCATTAATAAATCTCATCAACCAAGCA
AATATTTCCCAAAATCAACAATTACCAAGTACACAACAATACTCATTTCTAAGAAAAAGAAATGC
AAGAATATTACCAATGGAACAAATAACCATAATATTCTTGCACCAACAAAGGTAATTCTGATCAA
ATGATAATCAAGTATCACACTCAACCCTCA
Found at i:40212503 original size:326 final size:329
Alignment explanation
Indices: 40211905--40212535 Score: 858
Period size: 326 Copynumber: 1.9 Consensus size: 329
40211895 TCTTTTGAGC
* * * **
40211905 TAAAAATATTTATTTTATTGTTGTTTATTTATATACACATTGCTAATGATCACTTCTCCATTTAT
1 TAAAAATATTTATTTTATTGATATTTATTTATATACACATTGCTAACGATCACTTCTCCACCTAT
* * * * * *
40211970 AAATACCTTATCCTCCAAGAAAAATAGGATAAGCAAGAACAAATGACGAAAACTTAGCTCGAGTG
66 AAATACCTCATCCTCCAAAAAAAATAGGATAAGCAAGAACAAATGACAAAAACGTAGCTCAAGTA
* * * * * * *
40212035 TAACCTTGACCTTCTAAAACCATCGAGTCTAGTAACTCTCCAAACCATCTATAGTGTGAACTGTT
131 TAACCTCGACCTTCTAAAACCACCAAATCTAGCAACTCTCCAAACCATCTATAGTGTGAACCGCT
* ** * *
40212100 CTCATTTTAGTGGCTATCCATACCTCATACGATGTGAACTACCCTCATTGTATTATTCGGCATAT
196 CCCATTTTAGCAGCTATCCACACCTCATACGATGTGAACTACCCTCATTGTATTATTCGACATAT
* *
40212165 TGTGTTACTTAATTGTTAT-AT-TAAA-AATAAGATGAATATTTATTTTATTGTTATTTATCGTT
261 TGTGTAACTTAATTGTTATCATATAAATAAAAAGATGAATATTTATTTTATTGTTATTTATCGTT
40212227 ATAA
326 ATAA
* **
40212231 TAAAAATATTTATTTTATTGATATTTATTTATATACACTTTGCTCGCGATCACTTCTCCACCTAT
1 TAAAAATATTTATTTTATTGATATTTATTTATATACACATTGCTAACGATCACTTCTCCACCTAT
* * * *
40212296 AAATACCTCATCCTCCAAAAAAAATGGGCTAAGCAATAAGAAA-GTACAAAAACGTAGCTCAAGT
66 AAATACCTCATCCTCCAAAAAAAATAGGATAAGCAAGAACAAATG-ACAAAAACGTAGCTCAAGT
* * *
40212360 ATAACCTCGTCCTTCTAAAACCACCAAATCTAGCGACTCTCCACACCATCTATAGTGTGAACCGC
130 ATAACCTCGACCTTCTAAAACCACCAAATCTAGCAACTCTCCAAACCATCTATAGTGTGAACCGC
* *
40212425 TCCCATTTTAGCAGCTCTCCACACCTCATATGATGTGAACTACTCC-CATTGTATTATTCGACAT
195 TCCCATTTTAGCAGCTATCCACACCTCATACGATGTGAACTAC-CCTCATTGTATTATTCGACAT
*
40212489 CTTGTGTAACTTAATTGTTATCATAATAAATAAAAAGATGAATATTT
259 ATTGTGTAACTTAATTGTTATCAT-ATAAATAAAAAGATGAATATTT
40212536 GATACATTGT
Statistics
Matches: 261, Mismatches: 38, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
325 1 0.00
326 237 0.91
327 4 0.02
329 4 0.02
330 15 0.06
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (329 bp):
TAAAAATATTTATTTTATTGATATTTATTTATATACACATTGCTAACGATCACTTCTCCACCTAT
AAATACCTCATCCTCCAAAAAAAATAGGATAAGCAAGAACAAATGACAAAAACGTAGCTCAAGTA
TAACCTCGACCTTCTAAAACCACCAAATCTAGCAACTCTCCAAACCATCTATAGTGTGAACCGCT
CCCATTTTAGCAGCTATCCACACCTCATACGATGTGAACTACCCTCATTGTATTATTCGACATAT
TGTGTAACTTAATTGTTATCATATAAATAAAAAGATGAATATTTATTTTATTGTTATTTATCGTT
ATAA
Found at i:40212758 original size:14 final size:13
Alignment explanation
Indices: 40212736--40212792 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
40212726 CAACATCAAA
40212736 AAACT-AAAACCTT
1 AAACTCAAAA-CTT
*
40212749 AAAC-CTAAAATCTG
1 AAACTC-AAAA-CTT
40212763 AAACTCAAAACTT
1 AAACTCAAAACTT
40212776 AAAACTCAAAACTT
1 -AAACTCAAAACTT
40212790 AAA
1 AAA
40212793 AAAGAGGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 9 0.24
14 27 0.73
15 1 0.03
ACGTcount: A:0.56, C:0.21, G:0.02, T:0.21
Consensus pattern (13 bp):
AAACTCAAAACTT
Found at i:40212758 original size:21 final size:20
Alignment explanation
Indices: 40212734--40212793 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
40212724 CCCAACATCA
*
40212734 AAAAACTAAAACCTTAAACCT
1 AAAAACTAAAA-CTTAAAACT
* * *
40212755 AAAATCTGAAACTCAAAACT
1 AAAAACTAAAACTTAAAACT
*
40212775 TAAAACTCAAAACTTAAAA
1 AAAAACT-AAAACTTAAAA
40212794 AAGAGGCAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAACTAAAACTTAAAACT
Found at i:40212793 original size:14 final size:14
Alignment explanation
Indices: 40212763--40212793 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40212753 CTAAAATCTG
40212763 AAACTCAAAACTTA
1 AAACTCAAAACTTA
40212777 AAACTCAAAACTTA
1 AAACTCAAAACTTA
40212791 AAA
1 AAA
40212794 AAGAGGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACTCAAAACTTA
Found at i:40213053 original size:17 final size:17
Alignment explanation
Indices: 40213027--40213068 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
40213017 GTCTAACAAA
*
40213027 ATTTTGTAAAAAAAATT
1 ATTTTATAAAAAAAATT
40213044 ATTTTATAAAAAAAATT
1 ATTTTATAAAAAAAATT
40213061 ATTTTATA
1 ATTTTATA
40213069 TGAAAGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTTTATAAAAAAAATT
Found at i:40215101 original size:26 final size:24
Alignment explanation
Indices: 40215057--40215109 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
40215047 AAGTTCAAGC
*
40215057 GAGCCATAACGGGTAGCTCATGAA
1 GAGCCATAACGGGTAGCTCATAAA
40215081 GAGCCATATATCGGG-ACGCTCATAAA
1 GAGCCATA-A-CGGGTA-GCTCATAAA
40215107 GAG
1 GAG
40215110 ATGTGGTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 8 0.32
25 2 0.08
26 15 0.60
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (24 bp):
GAGCCATAACGGGTAGCTCATAAA
Found at i:40217667 original size:14 final size:15
Alignment explanation
Indices: 40217638--40217674 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
40217628 CTCACTTTCG
40217638 AAATTAATAGAAATT
1 AAATTAATAGAAATT
*
40217653 AAATTAGTA-AAATT
1 AAATTAATAGAAATT
40217667 AAA-TAATA
1 AAATTAATA
40217675 TAGGTTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 4 0.20
14 8 0.40
15 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
AAATTAATAGAAATT
Found at i:40221476 original size:91 final size:92
Alignment explanation
Indices: 40221305--40221491 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 92
40221295 CAAAACTCAA
*
40221305 AACAAGTTTCAAAATATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTCG
1 AACAAGTTTCAAAATATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTAG
*
40221370 ACAAGATTTATTAAGTAGTGAAATCGC
66 ACAAGATTTATTAAGTAGTGAAATCAC
* * * * *
40221397 AACAAGTTTCCAAA-GTCAAAATAACTTAAAATAGTGCAATGCTAAAAATAAGTGCTACTTCTAG
1 AACAAGTTTCAAAATATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTAG
40221461 ACAAGATTTATTAAGTAGTGAAATCAC
66 ACAAGATTTATTAAGTAGTGAAATCAC
40221488 AACA
1 AACA
40221492 TAAATTATGC
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 75 0.85
92 13 0.15
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.26
Consensus pattern (92 bp):
AACAAGTTTCAAAATATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTAG
ACAAGATTTATTAAGTAGTGAAATCAC
Found at i:40224418 original size:16 final size:17
Alignment explanation
Indices: 40224397--40224433 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
40224387 TAGTTTTTTT
*
40224397 TAAAAATAAAA-AAAAG
1 TAAAAATAAAATAAAAA
40224413 TAAAAATAAAATAAAAA
1 TAAAAATAAAATAAAAA
40224430 TAAA
1 TAAA
40224434 GAAAGCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
TAAAAATAAAATAAAAA
Found at i:40224427 original size:11 final size:11
Alignment explanation
Indices: 40224399--40224433 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
40224389 GTTTTTTTTA
40224399 AAAATAAAAA-
1 AAAATAAAAAT
*
40224409 AAAGTAAAAAT
1 AAAATAAAAAT
40224420 AAAATAAAAAT
1 AAAATAAAAAT
40224431 AAA
1 AAA
40224434 GAAAGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:40225707 original size:88 final size:88
Alignment explanation
Indices: 40225555--40226036 Score: 815
Period size: 88 Copynumber: 5.5 Consensus size: 88
40225545 NNNNNNNNNN
* *
40225555 CTGCTTCGCTGTC-ATGCAGGAAGGCAAGATCTTTTGTCCTCAACCAGCTCCATCACAACTGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
*
40225619 GAGGCAAGGTTTGTGTCTTCGAT
66 GAGGCAAGGTTTGTGTCTTCGAC
*
40225642 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTATTGTCTTCAACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
40225707 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
*
40225730 CTGCTTCGCTGTCAATGTAGGAAGGCAAGAT-TTGTTGTCTTCAACCAGCTCCATCACAACCGAG
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTT-TTGTCTTCAACCAGCTCCATCACAACCGAG
*
40225794 AGAGGCAAGGTTTATGTCTTCGAC
65 AGAGGCAAGGTTTGTGTCTTCGAC
* *
40225818 CTGCTTCGTTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCGACCAGCTCCATCACAACCGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
40225883 GAGGCAAGGTTTGTGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
* * * *
40225906 CTACTTAGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCGACCAGCTCCATCACAACTGAGA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
*
40225971 GAGGCAAGGTTTGAGTCTTCGAC
66 GAGGCAAGGTTTGTGTCTTCGAC
*
40225994 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCA
1 CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCA
40226037 CTGATCTGTT
Statistics
Matches: 372, Mismatches: 20, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
87 14 0.04
88 356 0.96
89 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (88 bp):
CTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGA
GAGGCAAGGTTTGTGTCTTCGAC
Found at i:40227245 original size:7 final size:7
Alignment explanation
Indices: 40227226--40227269 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
40227216 TTAGCCTCTC
40227226 CATTTTT
1 CATTTTT
40227233 -ACTTTTT
1 CA-TTTTT
40227240 CATTTTTTT
1 CA--TTTTT
40227249 CATTTTT
1 CATTTTT
40227256 CATTTTT
1 CATTTTT
40227263 CATTTTT
1 CATTTTT
40227270 TTCATCTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 1 0.03
7 24 0.73
8 1 0.03
9 7 0.21
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (7 bp):
CATTTTT
Found at i:40227249 original size:9 final size:9
Alignment explanation
Indices: 40227235--40227281 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
40227225 CCATTTTTAC
40227235 TTTTTCATT
1 TTTTTCATT
40227244 TTTTTCA--
1 TTTTTCATT
40227251 TTTTTCA--
1 TTTTTCATT
40227258 TTTTTCATT
1 TTTTTCATT
40227267 TTTTTCATCT
1 TTTTTCAT-T
40227277 TTTTT
1 TTTTT
40227282 TTTACTCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 14 0.40
9 15 0.43
10 6 0.17
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTCATT
Found at i:40227284 original size:16 final size:15
Alignment explanation
Indices: 40227235--40227284 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
40227225 CCATTTTTAC
*
40227235 TTTTTCATTTTTTTCA
1 TTTTTCATTTTTTT-T
*
40227251 TTTTTCATTTTTCATT
1 TTTTTCATTTTT-TTT
*
40227267 TTTTTCATCTTTTTT
1 TTTTTCATTTTTTTT
40227282 TTT
1 TTT
40227285 ACTCGAAGTG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 5 0.17
16 23 0.79
17 1 0.03
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCATTTTTTTT
Found at i:40227284 original size:23 final size:23
Alignment explanation
Indices: 40227226--40227279 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
40227216 TTAGCCTCTC
40227226 CATTTTT-ACTTTTTCATTTTTTT
1 CATTTTTCA-TTTTTCATTTTTTT
40227249 CATTTTTCATTTTTCATTTTTTT
1 CATTTTTCATTTTTCATTTTTTT
40227272 CATCTTTT
1 CAT-TTTT
40227280 TTTTTACTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
23 24 0.83
24 5 0.17
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (23 bp):
CATTTTTCATTTTTCATTTTTTT
Found at i:40228106 original size:6 final size:6
Alignment explanation
Indices: 40228090--40228128 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
40228080 TTGACCTCTC
* *
40228090 CTTTTT ATTTTT CTTTTT ATTTTT CTTTTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT CTTTTT CT
40228129 CCTATTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:40228125 original size:12 final size:12
Alignment explanation
Indices: 40228090--40228119 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
40228080 TTGACCTCTC
40228090 CTTTTTATTTTT
1 CTTTTTATTTTT
40228102 CTTTTTATTTTT
1 CTTTTTATTTTT
40228114 CTTTTT
1 CTTTTT
40228120 TCTTTTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (12 bp):
CTTTTTATTTTT
Found at i:40228154 original size:18 final size:16
Alignment explanation
Indices: 40228133--40228221 Score: 106
Period size: 16 Copynumber: 5.3 Consensus size: 16
40228123 TTTTCTCCTA
*
40228133 TTTTCTTTGATTTTTT
1 TTTTTTTTGATTTTTT
*
40228149 ATTTTTTTGATTTTTT
1 TTTTTTTTGATTTTTT
*
40228165 TTGATTTTTTAATTTTTT
1 TT--TTTTTTGATTTTTT
*
40228183 TTATTTTTGATTTTTTT
1 TTTTTTTTGA-TTTTTT
40228200 TATTTTTTTGATTTTTT
1 T-TTTTTTTGATTTTTT
40228217 TTTTT
1 TTTTT
40228222 AGTCTGAACT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
16 25 0.40
17 14 0.23
18 23 0.37
ACGTcount: A:0.11, C:0.01, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTTTTTGATTTTTT
Found at i:40228161 original size:9 final size:9
Alignment explanation
Indices: 40228132--40228217 Score: 92
Period size: 9 Copynumber: 9.9 Consensus size: 9
40228122 TTTTTCTCCT
40228132 ATTTTCTTTG
1 ATTTT-TTTG
40228142 A-TTTTTT-
1 ATTTTTTTG
40228149 ATTTTTTTG
1 ATTTTTTTG
40228158 ATTTTTTTTG
1 A-TTTTTTTG
*
40228168 A-TTTTTTA
1 ATTTTTTTG
40228176 ATTTTTTT-
1 ATTTTTTTG
*
40228184 -TATTTTTG
1 ATTTTTTTG
*
40228192 ATTTTTTTT
1 ATTTTTTTG
40228201 ATTTTTTTG
1 ATTTTTTTG
40228210 ATTTTTTT
1 ATTTTTTT
40228218 TTTTAGTCTG
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
7 7 0.11
8 16 0.25
9 32 0.49
10 10 0.15
ACGTcount: A:0.13, C:0.01, G:0.06, T:0.80
Consensus pattern (9 bp):
ATTTTTTTG
Found at i:40228161 original size:26 final size:25
Alignment explanation
Indices: 40228132--40228217 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 25
40228122 TTTTTCTCCT
40228132 ATTTTCTTTGATTTTTTATTTTTTTG
1 ATTTT-TTTGATTTTTTATTTTTTTG
40228158 ATTTTTTTTGATTTTTTAATTTTTTT-
1 A-TTTTTTTGATTTTTT-ATTTTTTTG
*
40228184 -TATTTTTGATTTTTTTTATTTTTTTG
1 ATTTTTTTGA--TTTTTTATTTTTTTG
40228210 ATTTTTTT
1 ATTTTTTT
40228218 TTTTAGTCTG
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
24 8 0.15
25 8 0.15
26 18 0.35
27 18 0.35
ACGTcount: A:0.13, C:0.01, G:0.06, T:0.80
Consensus pattern (25 bp):
ATTTTTTTGATTTTTTATTTTTTTG
Found at i:40228180 original size:34 final size:33
Alignment explanation
Indices: 40228131--40228221 Score: 121
Period size: 34 Copynumber: 2.7 Consensus size: 33
40228121 CTTTTTCTCC
*
40228131 TATTTTCTTTGATTTTTTATTTTTTTGATTTTTTT
1 TATTTT-TTTAATTTTTT-TTTTTTTGATTTTTTT
40228166 TGA-TTTTTTAATTTTTTTTATTTTTGATTTTTTT
1 T-ATTTTTTTAATTTTTTTT-TTTTTGATTTTTTT
*
40228200 TATTTTTTTGATTTTTTTTTTT
1 TATTTTTTTAATTTTTTTTTTT
40228222 AGTCTGAACT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
33 6 0.12
34 40 0.78
35 4 0.08
36 1 0.02
ACGTcount: A:0.12, C:0.01, G:0.05, T:0.81
Consensus pattern (33 bp):
TATTTTTTTAATTTTTTTTTTTTTGATTTTTTT
Found at i:40228215 original size:10 final size:10
Alignment explanation
Indices: 40228150--40228218 Score: 73
Period size: 10 Copynumber: 7.7 Consensus size: 10
40228140 TGATTTTTTA
40228150 TTTTTTTGAT
1 TTTTTTTGAT
40228160 TTTTTTTGA-
1 TTTTTTTGAT
*
40228169 -TTTTTTAAT
1 TTTTTTTGAT
40228178 TTTTTTT-A-
1 TTTTTTTGAT
40228186 --TTTTTGAT
1 TTTTTTTGAT
40228194 TTTTTTT-A-
1 TTTTTTTGAT
40228202 TTTTTTTGAT
1 TTTTTTTGAT
40228212 TTTTTTT
1 TTTTTTT
40228219 TTTAGTCTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
6 5 0.10
7 1 0.02
8 14 0.28
9 3 0.06
10 27 0.54
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.83
Consensus pattern (10 bp):
TTTTTTTGAT
Found at i:40231878 original size:28 final size:28
Alignment explanation
Indices: 40231847--40231940 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 28
40231837 AATGTCTGCT
*
40231847 TATATATATATATCATAAAATATGTATG
1 TATATATATAGATCATAAAATATGTATG
* *
40231875 TATAT-TA-AGATAAT-AAA-ATGCATG
1 TATATATATAGATCATAAAATATGTATG
*
40231899 CATATATACATAGATCATAAAATATAGATATG
1 --TATATATATAGATCATAAAATAT-G-TATG
40231931 TATATATATA
1 TATATATATA
40231941 TATATATGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
24 6 0.12
25 3 0.06
26 10 0.20
27 3 0.06
28 11 0.22
29 3 0.06
30 11 0.22
31 1 0.02
32 3 0.06
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (28 bp):
TATATATATAGATCATAAAATATGTATG
Found at i:40238783 original size:9 final size:9
Alignment explanation
Indices: 40238769--40238871 Score: 138
Period size: 9 Copynumber: 11.4 Consensus size: 9
40238759 GTAGTGATTC
*
40238769 AATTCGGAT
1 AATTCGGTT
40238778 AATTC-GTGT
1 AATTCGGT-T
*
40238787 AATTCGGGT
1 AATTCGGTT
40238796 AATTCGGTT
1 AATTCGGTT
*
40238805 AATTCGGGT
1 AATTCGGTT
*
40238814 AATTTGGTT
1 AATTCGGTT
40238823 AATTCGGTT
1 AATTCGGTT
40238832 AATTCGGTT
1 AATTCGGTT
40238841 AATTCAGG-T
1 AATTC-GGTT
40238850 AATTCGGTT
1 AATTCGGTT
40238859 AATTCGGTT
1 AATTCGGTT
40238868 AATT
1 AATT
40238872 TTTAACCAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
8 3 0.04
9 77 0.93
10 3 0.04
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:40241191 original size:13 final size:13
Alignment explanation
Indices: 40241173--40241204 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40241163 TTTCCAGCAA
40241173 TTATGAATTTATT
1 TTATGAATTTATT
40241186 TTATGAATTTATT
1 TTATGAATTTATT
*
40241199 TGATGA
1 TTATGA
40241205 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:40241412 original size:50 final size:50
Alignment explanation
Indices: 40241299--40241540 Score: 286
Period size: 50 Copynumber: 4.7 Consensus size: 50
40241289 ATTTGGGTAA
* * *
40241299 AGAGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* * *
40241355 AGAGGTCCCCTGTAAGACCATGTTTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * *
40241405 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
40241455 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
40241505 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
40241541 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 94 0.57
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 37 0.22
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:40241483 original size:100 final size:103
Alignment explanation
Indices: 40241299--40241548 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 103
40241289 ATTTGGGTAA
*
40241299 AGAGATCCCATGTAAGACCATATCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* * * *
40241364 CTGTAAGACCATGTTTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
40241405 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
*
40241467 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
40241505 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
40241549 GTTATTATCA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 40 0.31
ACGTcount: A:0.27, C:0.23, G:0.28, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:40253256 original size:9 final size:9
Alignment explanation
Indices: 40253225--40253267 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
40253215 GTTCAAGGTG
40253225 TAATTAATT
1 TAATTAATT
40253234 TAA-TAATTT
1 TAATTAA-TT
40253243 TAATTAATT
1 TAATTAATT
* *
40253252 AAATTTATT
1 TAATTAATT
40253261 TAATTAA
1 TAATTAA
40253268 AAATCTATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 3 0.11
9 22 0.79
10 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TAATTAATT
Found at i:40253265 original size:14 final size:14
Alignment explanation
Indices: 40253226--40253268 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
40253216 TTCAAGGTGT
*
40253226 AATTAATTTAA-TA
1 AATTTATTTAATTA
* *
40253239 ATTTTAATTAATTA
1 AATTTATTTAATTA
40253253 AATTTATTTAATTA
1 AATTTATTTAATTA
40253267 AA
1 AA
40253269 AATCTATTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTATTTAATTA
Found at i:40259075 original size:13 final size:13
Alignment explanation
Indices: 40259059--40259111 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
40259049 TTTAAACCAA
40259059 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
40259072 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* * *
40259085 ACTTTTCCACAGT
1 ACTTTTCAAAAGC
*
40259098 AATTTTCAAAAGC
1 ACTTTTCAAAAGC
40259111 A
1 A
40259112 TTGCCAAACT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:40263490 original size:2 final size:2
Alignment explanation
Indices: 40263483--40263524 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
40263473 TGGATATGTG
40263483 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40263525 GTAATGACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40264258 original size:13 final size:13
Alignment explanation
Indices: 40264240--40264271 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40264230 TTTCCAGCAA
40264240 TTATGAATTTATT
1 TTATGAATTTATT
40264253 TTATGAATTTATT
1 TTATGAATTTATT
*
40264266 TGATGA
1 TTATGA
40264272 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:40264477 original size:50 final size:50
Alignment explanation
Indices: 40264366--40264564 Score: 245
Period size: 50 Copynumber: 3.8 Consensus size: 50
40264356 ATTTGGGTAA
*
40264366 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCCTTGAGATCATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAG---ATG
* *
40264422 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
40264472 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCGACATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
40264522 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40264565 TGTTATTATC
Statistics
Matches: 128, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
50 50 0.39
51 34 0.27
53 3 0.02
55 2 0.02
56 39 0.30
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:40264563 original size:101 final size:103
Alignment explanation
Indices: 40264378--40264564 Score: 272
Period size: 101 Copynumber: 1.8 Consensus size: 103
40264368 AGATCCCATG
* **
40264378 TAAGACCATGTCTGGGACATGGCATTAGCATCCTTGAGATCATGAGAGGTCCCATGTAAGACCAT
1 TAAGACCATGTCTGGGACATGGCATGAGCATCC-T--GATCATGAGACATCCCATGTAAGACCAT
40264443 GTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTA
63 GTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTA
*
40264484 TAAGACCATGTCTGGGACATGGCATGGGCA-CC-GA-CATGAGAACATCCCATGTAAGACCATGT
1 TAAGACCATGTCTGGGACATGGCATGAGCATCCTGATCATGAG-ACATCCCATGTAAGACCATGT
*
40264546 CTGGGACATGGCTTTGGCA
65 CTGGGACATGGCGTTGGCA
40264565 TGTTATTATC
Statistics
Matches: 75, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
100 6 0.08
101 39 0.52
105 2 0.03
106 28 0.37
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (103 bp):
TAAGACCATGTCTGGGACATGGCATGAGCATCCTGATCATGAGACATCCCATGTAAGACCATGTC
TGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTA
Found at i:40271164 original size:22 final size:22
Alignment explanation
Indices: 40271139--40271186 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
40271129 TGGTAGTTAC
40271139 CATATTTTTCATCACAAAAGTT
1 CATATTTTTCATCACAAAAGTT
40271161 CATATTTTTCATCACAAAAGTT
1 CATATTTTTCATCACAAAAGTT
40271183 CATA
1 CATA
40271187 GAACTCTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.40
Consensus pattern (22 bp):
CATATTTTTCATCACAAAAGTT
Found at i:40276844 original size:18 final size:18
Alignment explanation
Indices: 40276821--40276862 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40276811 ATTCTCAAGT
40276821 TTTTAAGAA-AAATAACAA
1 TTTTAAGAAGAAATAA-AA
*
40276839 TTTTAA-AAGAAATCAAA
1 TTTTAAGAAGAAATAAAA
40276856 TTTTAAG
1 TTTTAAG
40276863 GAAACACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (18 bp):
TTTTAAGAAGAAATAAAA
Found at i:40283786 original size:37 final size:38
Alignment explanation
Indices: 40283735--40283840 Score: 115
Period size: 37 Copynumber: 2.7 Consensus size: 38
40283725 AATTCGAAGC
* *
40283735 AATAAGTTGACACCCAGTGTCTCATCG-GCTAAACCGA
1 AATAATTTGACACCCAGTGTCTCATCGAACTAAACCGA
* * * *
40283772 AATAATTTGGCACCCAGTGCCTCATCGAATTAATCCGA
1 AATAATTTGACACCCAGTGTCTCATCGAACTAAACCGA
*
40283810 AGTAAATAATTGACACCCAGTGTCTCATCGA
1 AAT-AAT--TTGACACCCAGTGTCTCATCGA
40283841 CTCGAAGTCG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 24 0.43
38 9 0.16
39 3 0.05
41 20 0.36
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (38 bp):
AATAATTTGACACCCAGTGTCTCATCGAACTAAACCGA
Found at i:40284677 original size:11 final size:11
Alignment explanation
Indices: 40284661--40284697 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40284651 ATCCTAACTT
40284661 TTTCTCTTTTC
1 TTTCTCTTTTC
40284672 TTTCTCTTTTCC
1 TTTCTCTTTT-C
40284684 TTT-TC-TTTC
1 TTTCTCTTTTC
40284693 TTTCT
1 TTTCT
40284698 TTCTCTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.17
10 4 0.17
11 12 0.50
12 4 0.17
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTCTCTTTTC
Found at i:40284688 original size:17 final size:18
Alignment explanation
Indices: 40284660--40284703 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
40284650 AATCCTAACT
40284660 TTTTCTCTTTTCTTTCTC
1 TTTTCTCTTTTCTTTCTC
*
40284678 TTTTC-CTTTTCTTTCTT
1 TTTTCTCTTTTCTTTCTC
40284695 TCTTTCTCT
1 T-TTTCTCT
40284704 GTTTTCGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 9 0.39
19 2 0.09
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTCTCTTTTCTTTCTC
Found at i:40292017 original size:26 final size:28
Alignment explanation
Indices: 40291958--40292017 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
40291948 ATTAATTAAT
* *
40291958 TTTTTTCACTTTTTACTAGATAATATCA
1 TTTTTTCACTTTTTACAACATAATATCA
* *
40291986 TATTTTCA-TTTTT-CAACATAATATTA
1 TTTTTTCACTTTTTACAACATAATATCA
40292012 TTTTTT
1 TTTTTT
40292018 TAAAAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 5 0.19
28 7 0.26
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTTTCACTTTTTACAACATAATATCA
Found at i:40299022 original size:9 final size:9
Alignment explanation
Indices: 40298997--40299038 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
40298987 ATAGAAACTA
40298997 TAAAATATTG
1 TAAAA-ATTG
*
40299007 T-AAAATTT
1 TAAAAATTG
40299015 TAAAAATTG
1 TAAAAATTG
*
40299024 TAAAAATAG
1 TAAAAATTG
40299033 TAAAAA
1 TAAAAA
40299039 AATTTGTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
8 4 0.14
9 23 0.82
10 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (9 bp):
TAAAAATTG
Found at i:40302366 original size:16 final size:16
Alignment explanation
Indices: 40302345--40302380 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
40302335 TATATATGGA
40302345 TCAAGATAGAATGATC
1 TCAAGATAGAATGATC
*
40302361 TCAAGATAGGATGATC
1 TCAAGATAGAATGATC
40302377 TCAA
1 TCAA
40302381 AAAGAGTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (16 bp):
TCAAGATAGAATGATC
Found at i:40310298 original size:7 final size:7
Alignment explanation
Indices: 40310288--40310320 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
40310278 TATTATATAC
40310288 TCAATTT
1 TCAATTT
40310295 TCAATTT
1 TCAATTT
40310302 TCAATTT
1 TCAATTT
40310309 TCAATTT
1 TCAATTT
40310316 TCAAT
1 TCAAT
40310321 CTAAACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (7 bp):
TCAATTT
Found at i:40312536 original size:20 final size:20
Alignment explanation
Indices: 40312513--40312565 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
40312503 AAGCTCTTTT
*
40312513 AAAATTTTAAAATTATTAAA-
1 AAAATTATAAAATTA-TAAAC
**
40312533 AAAACCATAAAATTATAAAC
1 AAAATTATAAAATTATAAAC
40312553 AAAATTCATAAAA
1 AAAATT-ATAAAA
40312566 AAGCTTCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.15
20 16 0.62
21 6 0.23
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATTATAAAATTATAAAC
Found at i:40316213 original size:30 final size:29
Alignment explanation
Indices: 40316157--40316213 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
40316147 TATTATAAAC
* *
40316157 TGAAAAATTAACTACTAAAACATAAGTGT
1 TGAAAAAATAACTACTAAAAAATAAGTGT
*
40316186 TGAAAAAATAAGTACTAAAAAATTAAGT
1 TGAAAAAATAACTACTAAAAAA-TAAGT
40316214 ATTTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.26
Consensus pattern (29 bp):
TGAAAAAATAACTACTAAAAAATAAGTGT
Found at i:40316947 original size:9 final size:9
Alignment explanation
Indices: 40316933--40316972 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
40316923 GTAGTGATTC
*
40316933 AATTCGGTT
1 AATTCGGGT
*
40316942 AATTCGGTT
1 AATTCGGGT
40316951 AATTCGGGT
1 AATTCGGGT
40316960 AATTCGGGT
1 AATTCGGGT
40316969 AATT
1 AATT
40316973 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:40320078 original size:2 final size:2
Alignment explanation
Indices: 40320071--40320103 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40320061 AATTGGAATG
40320071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40320104 GTGGCTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40322894 original size:62 final size:62
Alignment explanation
Indices: 40322780--40322899 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 62
40322770 TCTTAAATAT
* ** * ** *
40322780 AAAAAATTTAACAAATTTAACCCTTAATATTTACAAATTTTTGTCATTTTAGTTCTAATTCC
1 AAAAAATTTAACAAATTTAACCCTCAATATTTACAAAAATCTGTCAAATTAGTCCTAATTCC
*
40322842 AAAAAATTTAATAAA-TTAGACCCTCAATATTTACAAAAATCTGTCAAATTAGTCCTAA
1 AAAAAATTTAACAAATTTA-ACCCTCAATATTTACAAAAATCTGTCAAATTAGTCCTAA
40322900 CTCTAAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 3 0.06
62 46 0.94
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (62 bp):
AAAAAATTTAACAAATTTAACCCTCAATATTTACAAAAATCTGTCAAATTAGTCCTAATTCC
Found at i:40324954 original size:26 final size:27
Alignment explanation
Indices: 40324918--40324980 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
40324908 GGGCTGGCCC
* * *
40324918 ATTTTAAAAAT-AAACATTAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAAAAT
40324944 ATTTTAAAAATAAAAAATAAAAAAAAT
1 ATTTTAAAAATAAAAAATAAAAAAAAT
40324971 ATTTTAAAAA
1 ATTTTAAAAA
40324981 GTATTTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 11 0.33
27 22 0.67
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
ATTTTAAAAATAAAAAATAAAAAAAAT
Found at i:40324966 original size:39 final size:40
Alignment explanation
Indices: 40324922--40325009 Score: 126
Period size: 39 Copynumber: 2.2 Consensus size: 40
40324912 TGGCCCATTT
*
40324922 TAAAAATAAACA-TTAAAAAATTATTTTAAAAATAAAAAA
1 TAAAAATAAACATTTAAAAAAGTATTTTAAAAATAAAAAA
* * *
40324961 TAAAAA-AAATATTTTAAAAAGTATTTTAAAATTAAAAAA
1 TAAAAATAAACATTTAAAAAAGTATTTTAAAAATAAAAAA
40325000 TAAAAATAAA
1 TAAAAATAAA
40325010 AAATATATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
38 4 0.09
39 36 0.84
40 3 0.07
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (40 bp):
TAAAAATAAACATTTAAAAAAGTATTTTAAAAATAAAAAA
Found at i:40335611 original size:33 final size:34
Alignment explanation
Indices: 40335572--40335648 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
40335562 TAACTTGAAA
40335572 GTGTCTTCAACAGAGT-ACTC-TAATACTTCATTG
1 GTGTCTTCAACAGA-TAACTCTTAATACTTCATTG
* * *
40335605 GTGTCTTCAACATATAAGTCTTATTACTTCATTG
1 GTGTCTTCAACAGATAACTCTTAATACTTCATTG
40335639 GTGTCTTCAA
1 GTGTCTTCAA
40335649 AACTTTCAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 16 0.41
34 22 0.56
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (34 bp):
GTGTCTTCAACAGATAACTCTTAATACTTCATTG
Found at i:40340762 original size:16 final size:17
Alignment explanation
Indices: 40340736--40340768 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40340726 GCACGCTGAT
*
40340736 TTTTCCATGTTTTTGCA
1 TTTTCCATGTTTCTGCA
40340753 TTTT-CATGTTTCTGCA
1 TTTTCCATGTTTCTGCA
40340769 ATTGCAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.58
Consensus pattern (17 bp):
TTTTCCATGTTTCTGCA
Found at i:40358657 original size:8 final size:8
Alignment explanation
Indices: 40358644--40358670 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40358634 AGGAGGATTG
40358644 AATTTTAA
1 AATTTTAA
40358652 AATTTTAA
1 AATTTTAA
40358660 AATTTTAA
1 AATTTTAA
40358668 AAT
1 AAT
40358671 ATAACAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:40359149 original size:38 final size:39
Alignment explanation
Indices: 40359093--40359171 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 39
40359083 ACCCTTCAAT
* *
40359093 ATTTATAGATTCTATCAATTTGGTCCTAATTC-TAAAAA
1 ATTTATAGATTATATCAATTTAGTCCTAATTCTTAAAAA
* * * *
40359131 ATTTATATATTATGTCAATTTAGTCTTGATTCTTAAAAA
1 ATTTATAGATTATATCAATTTAGTCCTAATTCTTAAAAA
40359170 AT
1 AT
40359172 CAAAATTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (39 bp):
ATTTATAGATTATATCAATTTAGTCCTAATTCTTAAAAA
Found at i:40361045 original size:2 final size:2
Alignment explanation
Indices: 40361040--40361064 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40361030 AATCTGGTTG
40361040 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
40361065 CAGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40363066 original size:3 final size:3
Alignment explanation
Indices: 40363058--40363089 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40363048 CTTTTTAAAA
40363058 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40363090 ACAAGAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40365840 original size:128 final size:128
Alignment explanation
Indices: 40365459--40365842 Score: 612
Period size: 128 Copynumber: 3.0 Consensus size: 128
40365449 TTATATTGAT
40365459 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGA---TTATTTGACCTTCAATTG
1 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
* * *
40365521 GCTAGCATGATCTCATAAAACCTAAGGCACATTACAATATCATTGATAATGATGAACTGCAAC
66 GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
* * * * *
40365584 AATACTAAATAGAATGATGCTGATAATATCACCAAGGCTAATGATCTCTATTTGACTTTCAATTG
1 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
* *
40365649 GCTAGCATGATCTCATAAAAACCAAGGCACATTACAATATCACTGATAATCATGAGCTGCAAC
66 GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
* *
40365712 GATACTAAATAGAAAAATGTTGATAATATCACCAAGGCCAATGATCTTTATTTGACCTTCAATTG
1 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
* * *
40365777 GCTAGCCTGATCTCATAAAACCCAAGGCACATTATAATATCACCGATAATGATGAGCTGCAAC
66 GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
40365840 GAT
1 GAT
40365843 TTACCTTCTT
Statistics
Matches: 234, Mismatches: 22, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
125 41 0.18
128 193 0.82
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (128 bp):
GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
Found at i:40368267 original size:181 final size:181
Alignment explanation
Indices: 40367963--40368325 Score: 708
Period size: 181 Copynumber: 2.0 Consensus size: 181
40367953 AATAGGTAAA
*
40367963 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATTACCCCAAAAGTCATGGTGATCTA
1 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
40368028 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
66 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
*
40368093 CTCAGAAGGTGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
131 CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
40368144 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
1 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
40368209 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
66 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
40368274 CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
131 CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
40368325 A
1 A
40368326 AAATTAACTA
Statistics
Matches: 180, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 180 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (181 bp):
AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
Found at i:40376605 original size:6 final size:6
Alignment explanation
Indices: 40376594--40376628 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
40376584 GAGTCTGCAA
40376594 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
40376629 TCTTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:40387012 original size:3 final size:3
Alignment explanation
Indices: 40387006--40387049 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
40386996 CTCCCTAAAC
* *
40387006 TAT TAT TAT TAT TAT TAC TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
40387050 ACACCAACCG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:40389205 original size:70 final size:71
Alignment explanation
Indices: 40389080--40389223 Score: 263
Period size: 70 Copynumber: 2.0 Consensus size: 71
40389070 TTCTCATTGC
40389080 TCATAGGCTTAATGATTTTAAGTCTACTACTCTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCA
1 TCATAGGCTTAATGATTTTAAGTCTACTA--CTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCA
40389145 GGTAATGA
64 GGTAATGA
40389153 TCATAGGCTTAATGATTTTAAGTCTACTA-TTTTTGGTTGTCAGGGTAGTTTTTATCAAACCAGG
1 TCATAGGCTTAATGATTTTAAGTCTACTACTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCAGG
40389217 TAATGA
66 TAATGA
40389223 T
1 T
40389224 GTGTTGTAGG
Statistics
Matches: 71, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
70 42 0.59
73 29 0.41
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (71 bp):
TCATAGGCTTAATGATTTTAAGTCTACTACTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCAGG
TAATGA
Found at i:40392166 original size:2 final size:2
Alignment explanation
Indices: 40392159--40392191 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40392149 TAAAGCGTAG
40392159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40392192 AATTAGAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40394344 original size:14 final size:14
Alignment explanation
Indices: 40394325--40394355 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40394315 AATCTTGCAC
40394325 GAGCAGTTGAACAT
1 GAGCAGTTGAACAT
40394339 GAGCAGTTGAACAT
1 GAGCAGTTGAACAT
40394353 GAG
1 GAG
40394356 TCATGAGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.19
Consensus pattern (14 bp):
GAGCAGTTGAACAT
Found at i:40396040 original size:14 final size:14
Alignment explanation
Indices: 40396021--40396062 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
40396011 TTAAGAATTT
40396021 TATTAAATTAT-ATA
1 TATT-AATTATAATA
40396035 TATTAATTATAATA
1 TATTAATTATAATA
*
40396049 TATTTAATAATAAT
1 TA-TTAATTATAAT
40396063 TATGTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 6 0.24
14 9 0.36
15 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTAATTATAATA
Done.