Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 13 of 373
Found at i:3909448 original size:23 final size:23
Alignment explanation
Indices: 3909418--3909467 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3909408 AACATTAATC
*
3909418 AAATGTATGAATTGCAACCCTTT
1 AAATGTATGAAATGCAACCCTTT
*
3909441 AAATGTATGAAATGCAGCCCTTT
1 AAATGTATGAAATGCAACCCTTT
3909464 AAAT
1 AAAT
3909468 AAACTTGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (23 bp):
AAATGTATGAAATGCAACCCTTT
Found at i:3910013 original size:241 final size:241
Alignment explanation
Indices: 3909590--3910035 Score: 829
Period size: 241 Copynumber: 1.9 Consensus size: 241
3909580 ATGAATTAAT
*
3909590 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGCAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
*
3909655 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACTTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
* * * *
3909720 CTTTAAGATATAATGGATCCTCTCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATCGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATATTAAAAAATTC
3909785 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
3909831 TTTATTACCATGCAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGCAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
*
3909896 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGATGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
3909961 CTGTAAGATATAATCGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATATTAAAAAATTC
131 CTGTAAGATATAATCGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATATTAAAAAATTC
3910026 AAAAAGACTT
196 AAAAAGACTT
3910036 CAAATTACTA
Statistics
Matches: 198, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
241 198 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (241 bp):
TTTATTACCATGCAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
CTGTAAGATATAATCGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATATTAAAAAATTC
AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:3910169 original size:9 final size:9
Alignment explanation
Indices: 3910146--3910273 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
3910136 ATTGATCATT
*
3910146 ACTTAAATA
1 ACTTACATA
*
3910155 AATTACATA
1 ACTTACATA
3910164 ACTTACATA
1 ACTTACATA
* *
3910173 ACTCATATA
1 ACTTACATA
3910182 ACTTACATA
1 ACTTACATA
*
3910191 ATTTACATAACA
1 ACTTACAT---A
3910203 ACTTACATA
1 ACTTACATA
*
3910212 ACTCACATA
1 ACTTACATA
3910221 ACTTACATA
1 ACTTACATA
*
3910230 ATTTACATA
1 ACTTACATA
*
3910239 ACTCACATA
1 ACTTACATA
*
3910248 ACGTACATAACA
1 ACTTACAT---A
3910260 ACTTACATA
1 ACTTACATA
3910269 ACTTA
1 ACTTA
3910274 ACTAATACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 80 0.83
12 16 0.17
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:3910215 original size:39 final size:39
Alignment explanation
Indices: 3910163--3910240 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
3910153 TAAATTACAT
*
3910163 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
3910202 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
3910241 TCACATAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:3910240 original size:57 final size:57
Alignment explanation
Indices: 3910159--3910271 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
3910149 TAAATAAATT
* * **
3910159 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
3910216 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
3910272 TAACTAATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:3916471 original size:43 final size:43
Alignment explanation
Indices: 3916298--3916455 Score: 221
Period size: 43 Copynumber: 3.7 Consensus size: 43
3916288 TTGAAAAAAG
3916298 CGCCGCTAAAAGTCGTGACTTTTAGCGGCGCTTTACCCACAAA
1 CGCCGCTAAAAGTCGTGACTTTTAGCGGCGCTTTACCCACAAA
* * * *
3916341 CGCCGCTAAAAGCCATGACTTTTAGCGACGCTTCACCCACAAA
1 CGCCGCTAAAAGTCGTGACTTTTAGCGGCGCTTTACCCACAAA
**
3916384 CGCCTTTAAAAGTCGTG-CTTTTAGCGGCGCTTTTA-CCACAAA
1 CGCCGCTAAAAGTCGTGACTTTTAGCGGCGC-TTTACCCACAAA
* *
3916426 CGCCGCTAAAAATTGTGACTTTTAGCGGCG
1 CGCCGCTAAAAGTCGTGACTTTTAGCGGCG
3916456 TTTTTTCAAT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 32 0.32
43 67 0.68
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (43 bp):
CGCCGCTAAAAGTCGTGACTTTTAGCGGCGCTTTACCCACAAA
Found at i:3916604 original size:99 final size:100
Alignment explanation
Indices: 3916426--3916635 Score: 359
Period size: 99 Copynumber: 2.1 Consensus size: 100
3916416 TTACCACAAA
** *
3916426 CGCCGCTAAAAATTGTGACTTTTAGCGGCGTTTTTTCAATAAACGCTATAAAATTTTGGGGCGTT
1 CGCCGCTAAAAATCATGACTTTTAGCGGCGTTTTTTCAATAAACGCCATAAAATTTTGGGGCGTT
3916491 ACCTATAGCGGCATTTTTTGCGGCGTTTTAGAAAG
66 ACCTATAGCGGCATTTTTTGCGGCGTTTTAGAAAG
*
3916526 -GCCGCTAAAAATCATGACTTTTAGCGGCGTTTTTTCAATAAACGCCATAAAATTTTGTGGCGTT
1 CGCCGCTAAAAATCATGACTTTTAGCGGCGTTTTTTCAATAAACGCCATAAAATTTTGGGGCGTT
**
3916590 ACCTATAGTTGCATTTTTTGCGGCGTTTTAGAAAG
66 ACCTATAGCGGCATTTTTTGCGGCGTTTTAGAAAG
3916625 CGCCGCTAAAA
1 CGCCGCTAAAA
3916636 GTTTTAGGGG
Statistics
Matches: 103, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
99 93 0.90
100 10 0.10
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (100 bp):
CGCCGCTAAAAATCATGACTTTTAGCGGCGTTTTTTCAATAAACGCCATAAAATTTTGGGGCGTT
ACCTATAGCGGCATTTTTTGCGGCGTTTTAGAAAG
Found at i:3929912 original size:22 final size:21
Alignment explanation
Indices: 3929884--3929934 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
3929874 AACATTAAAC
3929884 ATATATTTT-TACATTAATATTA
1 ATATATTTTATA-ATTAA-ATTA
3929906 ATATATTTTATAATTAAATTA
1 ATATATTTTATAATTAAATTA
3929927 A-A-ATTTTA
1 ATATATTTTA
3929935 ATATAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.21
20 1 0.04
21 5 0.18
22 14 0.50
23 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTA
Found at i:3929927 original size:27 final size:31
Alignment explanation
Indices: 3929899--3929961 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
3929889 TTTTTACATT
3929899 AATATTAATAT-ATTT-TA-TAATTAAATTAA
1 AATATTAATATAATTTATATTAATTAAATT-A
* *
3929928 AATTTTAATATAATTTATATTAATTAAATCA
1 AATATTAATATAATTTATATTAATTAAATTA
3929959 AAT
1 AAT
3929962 TTGGGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.34
30 4 0.14
31 6 0.21
32 9 0.31
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
AATATTAATATAATTTATATTAATTAAATTA
Found at i:3933421 original size:26 final size:26
Alignment explanation
Indices: 3933345--3933428 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
3933335 CATGAAATTC
* *
3933345 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
3933371 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
*
3933397 TTATCATGGAACATTTACCTAACCTT
1 TTATCATGGAACATTTACCTAACCTA
3933423 TTATCA
1 TTATCA
3933429 ATTTGTACCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.36
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:3936857 original size:3 final size:3
Alignment explanation
Indices: 3936849--3937035 Score: 103
Period size: 3 Copynumber: 61.3 Consensus size: 3
3936839 TGCTATTACC
* *
3936849 ATT ATT ATT ATT ATT ATC ATC ATT ATT ATT ATT ATT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * *
3936896 ATT CGTT AGTT TTT ACCT -TT ATT -TT CTTT ACT ATT TTT TTT ATT ATC
1 ATT -ATT A-TT ATT A-TT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
3936943 ATT AACT ACT ATC ATT ATT ATA AAT A-T ATT ATT ATT ACT ATT TTT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
3936988 ATT ACT ATT ATT ATT ATT ATT ACT ATT ATT CTT ATT AATGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -AT-T ATT ATT
3937035 A
1 A
3937036 CTACTACTAC
Statistics
Matches: 141, Mismatches: 32, Indels: 22
0.72 0.16 0.11
Matches are distributed among these distances:
2 7 0.05
3 120 0.85
4 13 0.09
5 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:3939570 original size:16 final size:16
Alignment explanation
Indices: 3939524--3939570 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
3939514 GATTAGGTGA
3939524 ATTAATTTGAATTAAGG
1 ATTAATTTGAA-TAAGG
*
3939541 -TTAATTTGGTATAAGG
1 ATTAATTT-GAATAAGG
*
3939557 ATTAAATTGAATAA
1 ATTAATTTGAATAA
3939571 AGTGTGAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (16 bp):
ATTAATTTGAATAAGG
Found at i:3940482 original size:131 final size:130
Alignment explanation
Indices: 3940244--3940575 Score: 501
Period size: 131 Copynumber: 2.6 Consensus size: 130
3940234 AAAAACTGAG
* * * * *
3940244 ACCCAGCAC-AGTAGGGCACGATTCCTCGAATTTCTAGACATTGAACATTGCCTT-GTTTT--AG
1 ACCCAGCACGA-TAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAG
** * * *
3940305 AATTTAGAAAACATGAGTGAAATTCTAAAGGGATATTCGATTATTTTGAACAAACGGGAAATTGC
65 AATTTTTAAAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATTGC
3940370 A
130 A
* *
3940371 ACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCAAACATTTCCTTCGTTTTAAAGA
1 ACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGA
3940436 ATTTTTAAAGACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATTGC
66 ATTTTTAAA-ACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATTGC
3940501 A
130 A
*
3940502 ACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATCGCCTTCGTTTTAAAGA
1 ACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGA
3940567 ATTTTTAAA
66 ATTTTTAAA
3940576 TGGATAATTA
Statistics
Matches: 185, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
127 45 0.24
128 6 0.03
130 10 0.05
131 124 0.67
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (130 bp):
ACCCAGCACGATAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTCGTTTTAAAGA
ATTTTTAAAACATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATTGCA
Found at i:3944203 original size:131 final size:130
Alignment explanation
Indices: 3943984--3944304 Score: 468
Period size: 131 Copynumber: 2.5 Consensus size: 130
3943974 CCCCGCACAT
** * * * **
3943984 TAGGGCACGATTCATCGAATTTCTAGACATTGAACATTGCCTT-GTTTT--AGAATTTAGAAAAC
1 TAGGGCACGATTCCCCGAATTGCTAAACATCGAACATTGCCTTCGTTTTAAAGAATTTTTAAAAC
** * *
3944046 ATGAGTGAAATTTTAAAGGGATATTCGATTATTTTGAACAAACGGGAAATTGCAACCCAGCACGA
66 ATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATTGCAACCCAGCACGA
* *
3944111 TAGGGCACGATTCCCCGAATTGCCAAACATCGAACATTTCCTTCGTTTTAAAGAATTTTTAAAGA
1 TAGGGCACGATTCCCCGAATTGCTAAACATCGAACATTGCCTTCGTTTTAAAGAATTTTTAAA-A
3944176 CATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATTGCAACCCAGCACG
65 CATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATTGCAACCCAGCACG
3944241 A
130 A
* * *
3944242 TAAGGCACGATTCCCTGAATTGCTAAACATCGAACATGGCCTTCGTTTTAAAGAATTTTTAAA
1 TAGGGCACGATTCCCCGAATTGCTAAACATCGAACATTGCCTTCGTTTTAAAGAATTTTTAAA
3944305 TGGATAATTA
Statistics
Matches: 172, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
127 36 0.21
128 5 0.03
130 10 0.06
131 121 0.70
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (130 bp):
TAGGGCACGATTCCCCGAATTGCTAAACATCGAACATTGCCTTCGTTTTAAAGAATTTTTAAAAC
ATGAGTGAAATTCCAAAGGAATATTCGATTATTTTGAACAAACAGGAAATTGCAACCCAGCACGA
Found at i:3946353 original size:14 final size:15
Alignment explanation
Indices: 3946328--3946357 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3946318 CGTCTACAAT
3946328 AATAACATAAAATAA
1 AATAACATAAAATAA
3946343 AATAA-ATAAAATAA
1 AATAACATAAAATAA
3946357 A
1 A
3946358 TATAGGAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAACATAAAATAA
Found at i:3947331 original size:37 final size:38
Alignment explanation
Indices: 3947231--3947334 Score: 113
Period size: 37 Copynumber: 2.7 Consensus size: 38
3947221 CGACCACGAG
3947231 CCGATGAGACACTGGGTGTCAAACTATTACTTCGGATAAAT
1 CCGATGAGACACTGGGTGTC-AAC--TTACTTCGGATAAAT
* * * * *
3947272 TCGACGAGATACTGGGTATCAACTTACTTCGGCAT-GA-
1 CCGATGAGACACTGGGTGTCAACTTACTTCGG-ATAAAT
3947309 CCGATGAGACACTGGGTGTCAACTTA
1 CCGATGAGACACTGGGTGTCAACTTA
3947335 TTACTTCGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
37 22 0.42
38 10 0.19
39 2 0.04
40 3 0.06
41 16 0.30
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (38 bp):
CCGATGAGACACTGGGTGTCAACTTACTTCGGATAAAT
Found at i:3947355 original size:40 final size:39
Alignment explanation
Indices: 3947233--3947366 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 39
3947223 ACCACGAGCC
*
3947233 GATGAGACACTGGGTGTCAAACTATTACTTCGGATAAAT-T
1 GATGAGACACTGGGTGTC-AACTATTACTTCGAAT-AATCT
* * * * * *
3947273 CGACGAGATACTGGGTATCAAC--TTACTTCGGCATGA-CC
1 -GATGAGACACTGGGTGTCAACTATTACTTC-GAATAATCT
*
3947311 GATGAGACACTGGGTGTCAACTTATTACTTCGAATTATCT
1 GATGAGACACTGGGTGTCAAC-TATTACTTCGAATAATCT
*
3947351 GATGAGGCACTGGGTG
1 GATGAGACACTGGGTG
3947367 CCATACTGGT
Statistics
Matches: 74, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
37 18 0.24
38 8 0.11
39 7 0.09
40 26 0.35
41 15 0.20
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (39 bp):
GATGAGACACTGGGTGTCAACTATTACTTCGAATAATCT
Found at i:3952017 original size:13 final size:13
Alignment explanation
Indices: 3952001--3952064 Score: 62
Period size: 13 Copynumber: 5.0 Consensus size: 13
3951991 TCGTTCTCAC
3952001 ATTTTTATTTATT
1 ATTTTTATTTATT
3952014 ATTTTTATTTATT
1 ATTTTTATTTATT
*
3952027 ATTCTCT-TTTATT
1 ATT-TTTATTTATT
**
3952040 ATGCTT-TTT-TT
1 ATTTTTATTTATT
3952051 ATTTTTCATTTATT
1 ATTTTT-ATTTATT
3952065 TTGCTTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
11 6 0.15
12 4 0.10
13 27 0.66
14 4 0.10
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (13 bp):
ATTTTTATTTATT
Found at i:3955879 original size:19 final size:19
Alignment explanation
Indices: 3955855--3955899 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
3955845 ACGCCTTTTT
3955855 TGCATT-CATTTCATTCATA
1 TGCATTACATTTCA-TCATA
*
3955874 TGCATTATATTTCATCATA
1 TGCATTACATTTCATCATA
*
3955893 TACATTA
1 TGCATTA
3955900 AGTTTCATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.31, C:0.18, G:0.04, T:0.47
Consensus pattern (19 bp):
TGCATTACATTTCATCATA
Found at i:3955907 original size:19 final size:19
Alignment explanation
Indices: 3955862--3955899 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3955852 TTTTGCATTC
*
3955862 ATTTCATTCATATGCATTAT
1 ATTTCA-TCATATACATTAT
3955882 ATTTCATCATATACATTA
1 ATTTCATCATATACATTA
3955900 AGTTTCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTCATCATATACATTAT
Found at i:3959618 original size:35 final size:36
Alignment explanation
Indices: 3959572--3959641 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 36
3959562 TCTGAGTAAG
3959572 TATTATTTTATTC-TTCATTCCATTCATAACCAAAA
1 TATTATTTTATTCTTTCATTCCATTCATAACCAAAA
*
3959607 TATTATTTTATTCTTTTCATTTCATTCATAACCAA
1 TATTATTTTATTC-TTTCATTCCATTCATAACCAA
3959642 TCATATGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 13 0.41
37 19 0.59
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (36 bp):
TATTATTTTATTCTTTCATTCCATTCATAACCAAAA
Found at i:3964281 original size:11 final size:11
Alignment explanation
Indices: 3964265--3964309 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
3964255 AGATAAATAT
3964265 TATTTTATTAA
1 TATTTTATTAA
*
3964276 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
3964289 TATTTTATTAT
1 TATTTTATTAA
3964300 TATTTTATTA
1 TATTTTATTA
3964310 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:3965590 original size:51 final size:51
Alignment explanation
Indices: 3965514--3965633 Score: 204
Period size: 51 Copynumber: 2.4 Consensus size: 51
3965504 AACCAAGTTA
* *
3965514 TCCGGATGAAATATGAAACTCTTGTTGAAGCTAGAGCAATAAAGTAATAAT
1 TCCGGATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAAT
3965565 TCCGGATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAAT
1 TCCGGATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAAT
* *
3965616 TCCAGATGAAGTATGAAG
1 TCCGGATGAAATATGAAG
3965634 TAAGTTTCAG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (51 bp):
TCCGGATGAAATATGAAGCTCTTGTTGAAGCTAGAGCAACAAAGTAATAAT
Found at i:3966412 original size:21 final size:21
Alignment explanation
Indices: 3966388--3966459 Score: 58
Period size: 21 Copynumber: 3.2 Consensus size: 21
3966378 CTTTCTGAAA
3966388 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* *
3966409 TGAAA-G-ATACCATGACAACATGAT
1 TGAAATGTGTA--A-GAC--CATGGT
3966433 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
3966455 TGAAA
1 TGAAA
3966460 GATACTATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 11 0.28
22 8 0.21
24 8 0.21
25 6 0.15
26 1 0.03
27 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:3966439 original size:46 final size:46
Alignment explanation
Indices: 3966387--3966514 Score: 184
Period size: 46 Copynumber: 2.8 Consensus size: 46
3966377 GCTTTCTGAA
*
3966387 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAC
* * *
3966433 ATGAAATGTGTAAGACCATGGTTGAAAGATACTATGGCAACGTGAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAC
* ** *
3966479 ATGAAAAGAATAAAACCATGGTTGAAAGATACCATG
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATG
3966515 GCAATGCACA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAACATGAC
Found at i:3966577 original size:80 final size:80
Alignment explanation
Indices: 3966444--3966597 Score: 204
Period size: 80 Copynumber: 1.9 Consensus size: 80
3966434 TGAAATGTGT
* * *
3966444 AAGACCATGGTTGAAAGATACTATGGCAACGTGACATGAAAAGAATAAAACCATGGTTGAAAGAT
1 AAGACCATGGTTGAAAGATACTATGGCAACATGACATGAAAAGAATAAAACCATAGTTGAAAGAC
3966509 ACCATGGCAATGCAC
66 ACCATGGCAATGCAC
* * * *
3966524 AAGACCGTGGTTGAAAGATA-TCATGGCAACATGATA-GAAAATGAGTAAGACCATAGTTGAAAG
1 AAGACCATGGTTGAAAGATACT-ATGGCAACATGACATGAAAA-GAATAAAACCATAGTTGAAAG
*
3966587 ACACTATGGCA
64 ACACCATGGCA
3966598 TCATGTCGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 6 0.09
80 58 0.91
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (80 bp):
AAGACCATGGTTGAAAGATACTATGGCAACATGACATGAAAAGAATAAAACCATAGTTGAAAGAC
ACCATGGCAATGCAC
Found at i:3967527 original size:44 final size:43
Alignment explanation
Indices: 3967461--3967910 Score: 285
Period size: 44 Copynumber: 10.0 Consensus size: 43
3967451 CACCATGGTG
* * *
3967461 AATCTTATCTCCCTGAAGTTGCAGCGGAACAGATTAAAGCCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * * *
3967504 AATACTTATCTGCCTGAAGTTGCAGTGGTGTAGGTTAAAGTTAC
1 AAT-CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * ** *
3967548 AAGTCTTATCTCCCT-AATGTTGCAATGGAGCAGACTGGAGATAGC
1 AA-TCTTATCTCCCTGAA-GTTGCAGTGGAGCAGATTAAAGCTA-C
* *
3967593 AATTCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTAC
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* *
3967637 GAATTACAAAGCTTATCTCCCTGAAGTTGCAG-GGAGCAGATTGAAGCCAC
1 -AA-T------CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * * *
3967687 TAATCTTATCTCCCTAAAGTTGCAGTGGAGTAAATTGAAGTTAC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * * * * ** * *
3967731 TGATCTGATCCCCCT-AGAGTTGCAATGGAGTAGATCGAAGATAGAA
1 -AATCTTATCTCCCTGA-AGTTGCAGTGGAGCAGATTAAAGCT--AC
* * * * * * *
3967777 AAACTTATCCCCCTGAAGATGCAGTGGGGCAGGTTGAAGTTAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
* * *
3967820 GAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-C
* * * *
3967865 AAATCTTATCTCCCTGAAGTTGCACTAGAGTAGATTAAAGCAAC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
3967909 AA
1 AA
3967911 ATCATATACC
Statistics
Matches: 319, Mismatches: 69, Indels: 38
0.75 0.16 0.09
Matches are distributed among these distances:
43 29 0.09
44 145 0.45
45 103 0.32
46 4 0.01
49 1 0.00
50 17 0.05
51 20 0.06
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTAC
Found at i:3967617 original size:89 final size:89
Alignment explanation
Indices: 3967463--3967904 Score: 360
Period size: 89 Copynumber: 4.9 Consensus size: 89
3967453 CCATGGTGAA
** * * ** *
3967463 TCTTATCTCCCTGAAGTTGCAGCGGAACAGATTAAAGCCA-C-AATACTTATCTGCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGATAGCAAAT-CTTATCTCCCTGAAGTTG
* * *
3967526 CAGTGGTGTAGGTTAAAGTTACAAG
65 CAGTGGAGCAGATTAAAGTTACAAG
* * * *
3967551 TCTTATCTCCCT-AATGTTGCAATGGAGCAGACTGGAGATAGCAATTCTTATTTCCCTGAAGTTG
1 TCTTATCTCCCTGAA-GTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTG
*
3967615 CAGTGGAACAGATTAAAGCTACGAATTACAAAG
65 CAGTGGAGCAGATT-AA---A-G--TTAC-AAG
* ** * *
3967648 -CTTATCTCCCTGAAGTTGC-AGGGAGCAGATTGAAGCCA-CTAATCTTATCTCCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGC
* * * *
3967710 AGTGGAGTAAATTGAAGTTAC-TG
66 AGTGGAGCAGATTAAAGTTACAAG
* * * * * * * *
3967733 ATCTGATCCCCCT-AGAGTTGCAATGGAGTAGATCGAAGATAGAAAAACTTATCCCCCTGAAGAT
1 -TCTTATCTCCCTGA-AGTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTT
* * * *
3967797 GCAGTGGGGCAGGTTGAAGTTACGAG
64 GCAGTGGAGCAGATTAAAGTTACAAG
*
3967823 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGC
* * *
3967888 ACTAGAGTAGATTAAAG
66 AGTGGAGCAGATTAAAG
3967905 CAACAAATCA
Statistics
Matches: 273, Mismatches: 62, Indels: 37
0.73 0.17 0.10
Matches are distributed among these distances:
85 1 0.00
86 1 0.00
87 21 0.08
88 43 0.16
89 128 0.47
90 7 0.03
93 2 0.01
94 31 0.11
95 14 0.05
96 20 0.07
97 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (89 bp):
TCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGC
AGTGGAGCAGATTAAAGTTACAAG
Found at i:3967730 original size:183 final size:176
Alignment explanation
Indices: 3967463--3967904 Score: 451
Period size: 183 Copynumber: 2.5 Consensus size: 176
3967453 CCATGGTGAA
* * *
3967463 TCTTATCTCCCTGAAGTTGCAGCGGAACAGATTAAAGCCACAATACTTATCTGCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGCCACAAT-CTTATCTCCCTGAAGTTGCA
* ** * * *
3967528 GTGGTGTAGGTTAAAGTTACA-AGTCTTATCTCCCTA-ATGTTGCAATGGAGCAGA-CTGGAGAT
65 GTGGAGTAAATTAAAGTTACAGA-TCTGATCCCCCTAGA-GTTGCAATGGAGCAGATC-GAAGAT
* ** ** * *
3967590 AGCAATTCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACGAAT
127 AGAAAAACTTATCCCCCTGAAGATGCAGTGGAACAGATTAAAGCTACG-AG
*
3967641 TACAAAGCTTATCTCCCTGAAGTTGCAG-GGAGCAGATTGAAGCCACTAATCTTATCTCCCTAAA
1 T------CTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGCCAC-AATCTTATCTCCCTGAA
* * *
3967705 GTTGCAGTGGAGTAAATTGAAGTTACTGATCTGATCCCCCTAGAGTTGCAATGGAGTAGATCGAA
59 GTTGCAGTGGAGTAAATTAAAGTTACAGATCTGATCCCCCTAGAGTTGCAATGGAGCAGATCGAA
** * * *
3967770 GATAGAAAAACTTATCCCCCTGAAGATGCAGTGGGGCAGGTTGAAGTTACGAG
124 GATAGAAAAACTTATCCCCCTGAAGATGCAGTGGAACAGATTAAAGCTACGAG
* **
3967823 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGCCA-C-AATCTTATCTCCCTGAAGTTGC
* * *
3967888 ACTAGAGTAGATTAAAG
64 AGTGGAGTAAATTAAAG
3967905 CAACAAATCA
Statistics
Matches: 219, Mismatches: 33, Indels: 24
0.79 0.12 0.09
Matches are distributed among these distances:
176 21 0.10
177 15 0.07
178 36 0.16
182 2 0.01
183 118 0.54
184 27 0.12
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (176 bp):
TCTTATCTCCCTGAAGTTGCAGCGGAGCAGATTGAAGCCACAATCTTATCTCCCTGAAGTTGCAG
TGGAGTAAATTAAAGTTACAGATCTGATCCCCCTAGAGTTGCAATGGAGCAGATCGAAGATAGAA
AAACTTATCCCCCTGAAGATGCAGTGGAACAGATTAAAGCTACGAG
Found at i:3967994 original size:50 final size:50
Alignment explanation
Indices: 3967940--3968038 Score: 128
Period size: 51 Copynumber: 2.0 Consensus size: 50
3967930 GCAGAAGGTC
* * * *
3967940 AGATTAAATCTACCG-TAGCAAGTCTTATCTCCTTAAAGTTGCAGTGGAAT
1 AGATTAAAGCTACAGATA-CAAATCTTATCTCCCTAAAGTTGCAGTGGAAT
*
3967990 AGATTAAAGCTACAGATTACAAATCTTATCTCCCTAAAGTTGTAGTGGA
1 AGATTAAAGCTACAGA-TACAAATCTTATCTCCCTAAAGTTGCAGTGGA
3968039 GTGGATCGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
50 13 0.31
51 27 0.64
52 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (50 bp):
AGATTAAAGCTACAGATACAAATCTTATCTCCCTAAAGTTGCAGTGGAAT
Found at i:3968900 original size:467 final size:467
Alignment explanation
Indices: 3968021--3968959 Score: 1761
Period size: 467 Copynumber: 2.0 Consensus size: 467
3968011 AATCTTATCT
*
3968021 CCCTAAAGTTGTAGTGGAGTGGATCGAAGCAACAATTCCTATACCCTTGAAGATGCAGTGGGATG
1 CCCTAAAGTTGTAGTGGAGTGGATCGAAGCAACAATTCCTATACCCTTAAAGATGCAGTGGGATG
*
3968086 AAATAAGGCTACTTTAAGAAAAGAAGCACCAAAAAATCAAGATTCGGCAAAACCAGGCAAAATTG
66 AAATAAGGCTACTTTAAGAAAAAAAGCACCAAAAAATCAAGATTCGGCAAAACCAGGCAAAATTG
3968151 ACCCTTTTAAAAGTCTTTGCTCCATTCACGCTACACGTCAACGAGCAAAAAAGGGAAACTATAAT
131 ACCCTTTTAAAAGTCTTTGCTCCATTCACGCTACACGTCAACGAGCAAAAAAGGGAAACTATAAT
*
3968216 AGGCCAATTTTGGCCTGGGCCAGATTACAAAACTAAACCCAAACCAAATAAATAAAAAATAGTCC
196 AGGCCAATTTTGGCCTAGGCCAGATTACAAAACTAAACCCAAACCAAATAAATAAAAAATAGTCC
*
3968281 AAAATTAATGGTCCATTTACAAACCAAATAACGTAAACTAAGACCCATTACATACCAAGCCTAAA
261 AAAATTAATGGTCCATTTACAAACCAAATAACATAAACTAAGACCCATTACATACCAAGCCTAAA
* *
3968346 GGAAGCCCAAGCAGATGACCCCAACTAAAATCCAAACCAAAACTAAACCAGCCCAAAGTTAAAAC
326 GGAAGCCCAAGCAGATGACCCAAACTAAAACCCAAACCAAAACTAAACCAGCCCAAAGTTAAAAC
3968411 CCAATTACAAACCCAATAACCTAAACCCTAATAGCCCAATACAACCCAAAACAAAAGTAAGCAGA
391 CCAATTACAAACCCAATAACCTAAACCCTAATAGCCCAATACAACCCAAAACAAAAGTAAGCAGA
3968476 AGAAAGAAAAAA
456 AGAAAGAAAAAA
* *
3968488 CCCTGAAGTTGTAGTGGAGTGGATTGAAGCAACAATTCCTATACCCTTAAAGATGCAGTGGGATG
1 CCCTAAAGTTGTAGTGGAGTGGATCGAAGCAACAATTCCTATACCCTTAAAGATGCAGTGGGATG
*
3968553 AAATAAGGCTACTTTAAGAAAAAAAGCACCAAAAAGTCAAGATTCGGCAAAACCAGGCAAAATTG
66 AAATAAGGCTACTTTAAGAAAAAAAGCACCAAAAAATCAAGATTCGGCAAAACCAGGCAAAATTG
*
3968618 ACCCTTTTAAAAGTCTTTGCTCCATTCACGCTACACGTCAACGAGCAAAAAAGGGCAACTATAAT
131 ACCCTTTTAAAAGTCTTTGCTCCATTCACGCTACACGTCAACGAGCAAAAAAGGGAAACTATAAT
*
3968683 AGGCCAATTTTGGGCTAGGCCAGATTACAAAACTAAACCCAAACCAAATAAATAAAAAATAGTCC
196 AGGCCAATTTTGGCCTAGGCCAGATTACAAAACTAAACCCAAACCAAATAAATAAAAAATAGTCC
3968748 AAAATTAATGGTCCATTTACAAACCAAATAACATAAACTAAGACCCATTACATACCAAGCCTAAA
261 AAAATTAATGGTCCATTTACAAACCAAATAACATAAACTAAGACCCATTACATACCAAGCCTAAA
3968813 GGAAGCCCAAGCAGATGACCCAAACTAAAACCCAAACCAAAACTAAACCAGCCCAAAGTTAAAAC
326 GGAAGCCCAAGCAGATGACCCAAACTAAAACCCAAACCAAAACTAAACCAGCCCAAAGTTAAAAC
* *
3968878 CCAATTACAAACCTATTAACCTAAACCCTAATAGCCCAATACAACCCAAAACAAAAGTAAGCAGA
391 CCAATTACAAACCCAATAACCTAAACCCTAATAGCCCAATACAACCCAAAACAAAAGTAAGCAGA
3968943 AGAAAGAAAAAA
456 AGAAAGAAAAAA
3968955 CCCTA
1 CCCTA
3968960 GGTGTGCCGC
Statistics
Matches: 458, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
467 458 1.00
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (467 bp):
CCCTAAAGTTGTAGTGGAGTGGATCGAAGCAACAATTCCTATACCCTTAAAGATGCAGTGGGATG
AAATAAGGCTACTTTAAGAAAAAAAGCACCAAAAAATCAAGATTCGGCAAAACCAGGCAAAATTG
ACCCTTTTAAAAGTCTTTGCTCCATTCACGCTACACGTCAACGAGCAAAAAAGGGAAACTATAAT
AGGCCAATTTTGGCCTAGGCCAGATTACAAAACTAAACCCAAACCAAATAAATAAAAAATAGTCC
AAAATTAATGGTCCATTTACAAACCAAATAACATAAACTAAGACCCATTACATACCAAGCCTAAA
GGAAGCCCAAGCAGATGACCCAAACTAAAACCCAAACCAAAACTAAACCAGCCCAAAGTTAAAAC
CCAATTACAAACCCAATAACCTAAACCCTAATAGCCCAATACAACCCAAAACAAAAGTAAGCAGA
AGAAAGAAAAAA
Found at i:3972564 original size:35 final size:35
Alignment explanation
Indices: 3972466--3972975 Score: 461
Period size: 35 Copynumber: 14.5 Consensus size: 35
3972456 TGGCAAAGTG
* * * *
3972466 TGAAATGTAGGTATGGTAT-TTCCATACAGAGCTA
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* *
3972500 TGAAACGTAGGTATGGTATTATCAAATCCAAACTGAGTTA
1 TGAAACGTAGGTATGG---TATC--ATCCATACCGAGTTA
* *
3972540 AGAAACGTAGGTATGGTATCATCCATACCGAGTTG
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* * * * *
3972575 TGAAATGTAGGTATGGTATTAACCATACTGAGTTG
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* * *
3972610 TGAAATGTAGGTATGGTATCATCCATACGGAGTTG
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* * * *
3972645 TGAAACATAGGTATGGTATTAACCATACCGAGTTG
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* * *
3972680 TGAAACGTAGGTATGGTATTAACCATACCGAGTTG
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* * * * * *
3972715 TGAAACATAGGTATGGTATTAACCATACTGAGCTG
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* *
3972750 TGAAACGTAGGTATGGTAT-TTCCATACCGAGCTA
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* *
3972784 TGAAACGTAGGTATGGTAT-TTCCATACCGAGCTA
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* ** * * *
3972818 TGAAACGTAAGTATGGCGTCGTCCATACTGAGCTA
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* * * *
3972853 TGATACGTAGGTATGGCATCGTCCATACTGAGTTA
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
** ** *
3972888 TGAAATATAGGTATGGTATTTTCCATACCGAG-CA
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
* * ** * *
3972922 TGAAAAGTAGGTATGGTGTTTTCCATATCGAGTTG
1 TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
3972957 TGAAACGTAGGTATGGTAT
1 TGAAACGTAGGTATGGTAT
3972976 TTCAATGAGG
Statistics
Matches: 412, Mismatches: 56, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
34 105 0.25
35 274 0.67
37 7 0.02
40 26 0.06
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (35 bp):
TGAAACGTAGGTATGGTATCATCCATACCGAGTTA
Found at i:3972627 original size:70 final size:70
Alignment explanation
Indices: 3972464--3972975 Score: 530
Period size: 70 Copynumber: 7.3 Consensus size: 70
3972454 CATGGCAAAG
* * *
3972464 TGTGAAATGTAGGTATGGTAT-TTCCATACAGAGCTATGAAACGTAGGTATGGTATTATCAAATC
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGCTATGAAACGTAGGTATGGTA-T-T--AA-C
*
3972528 CAAACTGAGT
61 CATACTGAGT
** * * *
3972538 TAAGAAACGTAGGTATGGTATCATCCATACCGAGTTGTGAAATGTAGGTATGGTATTAACCATAC
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGCTATGAAACGTAGGTATGGTATTAACCATAC
3972603 TGAGT
66 TGAGT
* * * * *
3972608 TGTGAAATGTAGGTATGGTATCATCCATACGGAGTTGTGAAACATAGGTATGGTATTAACCATAC
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGCTATGAAACGTAGGTATGGTATTAACCATAC
*
3972673 CGAGT
66 TGAGT
* * * * *
3972678 TGTGAAACGTAGGTATGGTATTAACCATACCGAGTTGTGAAACATAGGTATGGTATTAACCATAC
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGCTATGAAACGTAGGTATGGTATTAACCATAC
*
3972743 TGAGC
66 TGAGT
* *
3972748 TGTGAAACGTAGGTATGGTAT-TTCCATACCGAGCTATGAAACGTAGGTATGGTATT-TCCATAC
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGCTATGAAACGTAGGTATGGTATTAACCATAC
* *
3972811 CGAGC
66 TGAGT
* * ** * * * * ***
3972816 TATGAAACGTAAGTATGGCGTCGTCCATACTGAGCTATGATACGTAGGTATGGCATCGTCCATAC
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGCTATGAAACGTAGGTATGGTATTAACCATAC
3972881 TGAGT
66 TGAGT
* ** ** * * **
3972886 TATGAAATATAGGTATGGTATTTTCCATACCGAGC-ATGAAAAGTAGGTATGGTGTTTTCCATA-
1 TGTGAAACGTAGGTATGGTATCATCCATACCGAGCTATGAAACGTAGGTATGGTATTAACCATAC
3972949 TCGAGT
66 T-GAGT
3972955 TGTGAAACGTAGGTATGGTAT
1 TGTGAAACGTAGGTATGGTAT
3972976 TTCAATGAGG
Statistics
Matches: 377, Mismatches: 57, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
68 28 0.07
69 104 0.28
70 195 0.52
71 2 0.01
73 1 0.00
74 19 0.05
75 28 0.07
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (70 bp):
TGTGAAACGTAGGTATGGTATCATCCATACCGAGCTATGAAACGTAGGTATGGTATTAACCATAC
TGAGT
Found at i:3972658 original size:105 final size:104
Alignment explanation
Indices: 3972464--3972975 Score: 553
Period size: 105 Copynumber: 4.9 Consensus size: 104
3972454 CATGGCAAAG
*
3972464 TGTGAAATGTAGGTATGGTATTTCCATACAGAGCTATGAAACGTAGGTATGGTATTATCAAATCC
1 TGTGAAATGTAGGTATGGTATTTCCATACCGAGCTATGAAACGTAGGTATGG---TATC--ATCC
* **
3972529 AAACTGAGTTAAGAAACGTAGGTATGGTATCATCCATACCGAGT
61 ATACTGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* * * * *
3972573 TGTGAAATGTAGGTATGGTATTAACCATACTGAGTTGTGAAATGTAGGTATGGTATCATCCATAC
1 TGTGAAATGTAGGTATGGTATT-TCCATACCGAGCTATGAAACGTAGGTATGGTATCATCCATAC
* * * *
3972638 GGAGTTGTGAAACATAGGTATGGTATTAACCATACCGAGT
65 TGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* * * * * * *
3972678 TGTGAAACGTAGGTATGGTATTAACCATACCGAGTTGTGAAACATAGGTATGGTATTAACCATAC
1 TGTGAAATGTAGGTATGGTATT-TCCATACCGAGCTATGAAACGTAGGTATGGTATCATCCATAC
* * *
3972743 TGAGCTGTGAAACGTAGGTATGGTAT-TTCCATACCGAGC
65 TGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* * * ** *
3972782 TATGAAACGTAGGTATGGTATTTCCATACCGAGCTATGAAACGTAAGTATGGCGTCGTCCATACT
1 TGTGAAATGTAGGTATGGTATTTCCATACCGAGCTATGAAACGTAGGTATGGTATCATCCATACT
* * * * * *
3972847 GAGCTATGATACGTAGGTATGGCATCGTCCATACTGAGT
66 GAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAGT
* * * * **
3972886 TATGAAATATAGGTATGGTATTTTCCATACCGAGC-ATGAAAAGTAGGTATGGTGTTTTCCATA-
1 TGTGAAATGTAGGTATGGTA-TTTCCATACCGAGCTATGAAACGTAGGTATGGTATCATCCATAC
3972949 TCGAGTTGTGAAACGTAGGTATGGTAT
65 T-GAGTTGTGAAACGTAGGTATGGTAT
3972976 TTCAATGAGG
Statistics
Matches: 347, Mismatches: 52, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
103 56 0.16
104 103 0.30
105 137 0.39
107 4 0.01
109 22 0.06
110 25 0.07
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (104 bp):
TGTGAAATGTAGGTATGGTATTTCCATACCGAGCTATGAAACGTAGGTATGGTATCATCCATACT
GAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAGT
Found at i:3973121 original size:31 final size:31
Alignment explanation
Indices: 3973072--3973132 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3973062 ATAAGTAATT
*
3973072 TGATTAGTGAAAAATGGTAGCTCCGGCTACC
1 TGATCAGTGAAAAATGGTAGCTCCGGCTACC
* * *
3973103 TGATCAGTGAATAGTGGTAGCTTCGGCTAC
1 TGATCAGTGAAAAATGGTAGCTCCGGCTAC
3973133 AAGTGACAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (31 bp):
TGATCAGTGAAAAATGGTAGCTCCGGCTACC
Found at i:3979419 original size:2 final size:2
Alignment explanation
Indices: 3979414--3979453 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3979404 CCTAGATGAC
3979414 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3979454 CGTGTTTAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3981242 original size:22 final size:22
Alignment explanation
Indices: 3981204--3981257 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
3981194 CCATGCCAAA
3981204 TTTCAAAA-AA-TT-AAATTAAG
1 TTTCAAAATAATTTAAAATT-AG
3981224 TTT-AAAATAATTTAAAATTAG
1 TTTCAAAATAATTTAAAATTAG
*
3981245 TTTCAAATTAATT
1 TTTCAAAATAATT
3981258 GAAACAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 5 0.17
21 7 0.24
22 13 0.45
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
TTTCAAAATAATTTAAAATTAG
Found at i:3983956 original size:80 final size:80
Alignment explanation
Indices: 3983818--3983977 Score: 284
Period size: 80 Copynumber: 2.0 Consensus size: 80
3983808 CTATTTTCGA
*
3983818 GGCTAACATTTTTACTCAAACATTATCAAATTTTAGACAAACTTTCGAGCCTCGATAAATAACTC
1 GGCTAACATTTTTACTCAAACATTATCAAATTTTAGACAAACTTTCGAGCCTCAATAAATAACTC
*
3983883 GACCCATAAATAATT
66 CACCCATAAATAATT
* *
3983898 GGCTAACATTTTTACTCAAACATTCTCAAATTTTAGATAAACTTTCGAGCCTCAATAAATAACTC
1 GGCTAACATTTTTACTCAAACATTATCAAATTTTAGACAAACTTTCGAGCCTCAATAAATAACTC
3983963 CACCCATAAATAATT
66 CACCCATAAATAATT
3983978 CTAGAATGAC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.39, C:0.22, G:0.07, T:0.32
Consensus pattern (80 bp):
GGCTAACATTTTTACTCAAACATTATCAAATTTTAGACAAACTTTCGAGCCTCAATAAATAACTC
CACCCATAAATAATT
Found at i:3984748 original size:9 final size:9
Alignment explanation
Indices: 3984725--3984772 Score: 57
Period size: 9 Copynumber: 5.6 Consensus size: 9
3984715 TACCAATTCA
3984725 GTTAATTTGG
1 GTTAATTT-G
3984735 GTTAATTTG
1 GTTAATTTG
*
3984744 ATTAA-TT-
1 GTTAATTTG
3984751 -TTAATTTG
1 GTTAATTTG
3984759 GTTAATTTG
1 GTTAATTTG
3984768 GTTAA
1 GTTAA
3984773 ATGAACATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
6 4 0.12
7 2 0.06
8 2 0.06
9 18 0.53
10 8 0.24
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (9 bp):
GTTAATTTG
Found at i:3984756 original size:15 final size:15
Alignment explanation
Indices: 3984736--3984766 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3984726 TTAATTTGGG
3984736 TTAATTTGATTAATT
1 TTAATTTGATTAATT
*
3984751 TTAATTTGGTTAATT
1 TTAATTTGATTAATT
3984766 T
1 T
3984767 GGTTAAATGA
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:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (15 bp):
TTAATTTGATTAATT
Found at i:3984766 original size:24 final size:25
Alignment explanation
Indices: 3984726--3984772 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
3984716 ACCAATTCAG
3984726 TTAATTTGGGTTAATTTGATTAATT
1 TTAATTTGGGTTAATTTGATTAATT
*
3984751 TTAATTT-GGTTAATTTGGTTAA
1 TTAATTTGGGTTAATTTGATTAA
3984773 ATGAACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (25 bp):
TTAATTTGGGTTAATTTGATTAATT
Found at i:3985810 original size:16 final size:18
Alignment explanation
Indices: 3985773--3985806 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3985763 AAATTTTAAC
*
3985773 TTTT-TTAATTTATATAA
1 TTTTATTAATATATATAA
3985790 TTTTATTAATATATATA
1 TTTTATTAATATATATA
3985807 TTTACCTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATTAATATATATAA
Found at i:3993547 original size:89 final size:88
Alignment explanation
Indices: 3993428--3993596 Score: 221
Period size: 89 Copynumber: 1.9 Consensus size: 88
3993418 TCTTGCTGCT
* * * * * * * **
3993428 TTTTTTTTTACTCATTTGGGTACTTGAACTTTCAAAATGTATCAAAAATATCCTTAAACTTTTCA
1 TTTTTTTGTACTCAATTGGATACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAAC-TTAAA
3993493 AAAAAAGCAATTAAGCCCCTACTA
65 AAAAAAGCAATTAAGCCCCTACTA
* * *
3993517 TTTTTTTGTACTTAATTGGATACTTTAACTTTCAAAATGCATCAAAGAGACCCTCAAACTTAAAA
1 TTTTTTTGTACTCAATTGGATACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTAAAA
3993582 AAAAAGCAATTAAGC
66 AAAAAGCAATTAAGC
3993597 TCATGCTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
88 19 0.28
89 49 0.72
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (88 bp):
TTTTTTTGTACTCAATTGGATACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTAAAA
AAAAAGCAATTAAGCCCCTACTA
Found at i:3993708 original size:20 final size:19
Alignment explanation
Indices: 3993683--3993731 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
3993673 TTAAAAATTT
3993683 AAATATTAAAAATTAGAAAA
1 AAATATTAAAAA-TAGAAAA
* *
3993703 AAATATT-AATATAGTAAA
1 AAATATTAAAAATAGAAAA
3993721 AAATA-TAAAAA
1 AAATATTAAAAA
3993732 AAAATATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 14 0.56
19 3 0.12
20 7 0.28
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AAATATTAAAAATAGAAAA
Found at i:3993720 original size:28 final size:29
Alignment explanation
Indices: 3993675--3993743 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
3993665 AATTTTAATT
* *
3993675 AAAAAT-TTAAATA-TTAAAAAT-TAGAA
1 AAAAATATTAAATAGTAAAAAATATAAAA
3993701 AAAAATATTAATATAGTAAAAAATATAAAA
1 AAAAATATTAA-ATAGTAAAAAATATAAAA
*
3993731 AAAAATATAAAAT
1 AAAAATATTAAAT
3993744 TTTATAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.17
27 4 0.11
28 3 0.08
29 9 0.25
30 14 0.39
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (29 bp):
AAAAATATTAAATAGTAAAAAATATAAAA
Found at i:3993727 original size:12 final size:12
Alignment explanation
Indices: 3993718--3993742 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3993708 TTAATATAGT
3993718 AAAAAATATAAA
1 AAAAAATATAAA
3993730 AAAAAATATAAA
1 AAAAAATATAAA
3993742 A
1 A
3993743 TTTTATAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAATATAAA
Found at i:3994030 original size:18 final size:19
Alignment explanation
Indices: 3993986--3994036 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
3993976 AATTTTTCTA
3993986 TATTTTTATTAAAATTTAAT
1 TATTTTT-TTAAAATTTAAT
*
3994006 AATTTTTTTAAAATTT-AT
1 TATTTTTTTAAAATTTAAT
3994024 TATTTTTTATAAA
1 TATTTTTT-TAAA
3994037 TTATTTTCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTTTTAAAATTTAAT
Found at i:3994780 original size:3 final size:3
Alignment explanation
Indices: 3994772--3994798 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3994762 ATACAAGATC
3994772 GTT GTT GTT GTT GTT GTT GTT GTT GTT
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT
3994799 AAGGGGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
GTT
Found at i:3997929 original size:22 final size:21
Alignment explanation
Indices: 3997904--3997949 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
3997894 TGGTATAGTC
3997904 TTAAATTAAGTACG-AAATATAA
1 TTAAATT-AGT-CGAAAATATAA
3997926 TTAAATTAGTCGATAAATATAA
1 TTAAATTAGTCGA-AAATATAA
3997948 TT
1 TT
3997950 TTTAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 3 0.14
22 17 0.77
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (21 bp):
TTAAATTAGTCGAAAATATAA
Found at i:4004484 original size:31 final size:31
Alignment explanation
Indices: 4004443--4004501 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4004433 GTGGAGGTTT
*
4004443 TTTTTTTTTAA-ATTTAAATTTAATATAATTG
1 TTTTTATTTAATA-TTAAATTTAATATAATTG
4004474 TTTTTATTTAATATTAAATTTAATATAA
1 TTTTTATTTAATATTAAATTTAATATAA
4004502 AATTGAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (31 bp):
TTTTTATTTAATATTAAATTTAATATAATTG
Found at i:4005282 original size:18 final size:18
Alignment explanation
Indices: 4005255--4005332 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
4005245 TTTATTTTCT
* *
4005255 ATATTCTTTAGATTTTTTA
1 ATATT-TTTAAATTTTATA
4005274 ATATTTTTAAATTTTATA
1 ATATTTTTAAATTTTATA
**
4005292 A-A-TTTTAAA-AATATA
1 ATATTTTTAAATTTTATA
*
4005307 A-ATTTTGAAATTTTTATAA
1 ATATTTTTAAA-TTTTAT-A
4005326 ATATTTT
1 ATATTTT
4005333 GAATTTATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
15 6 0.13
16 13 0.28
17 1 0.02
18 15 0.32
19 7 0.15
20 5 0.11
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (18 bp):
ATATTTTTAAATTTTATA
Found at i:4005321 original size:24 final size:24
Alignment explanation
Indices: 4005281--4005329 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4005271 TTAATATTTT
4005281 TAAATTTTATAAATTTTAAAAATA
1 TAAATTTTATAAATTTTAAAAATA
* *
4005305 TAAATTTTGA-AATTTTTATAAATA
1 TAAATTTT-ATAAATTTTAAAAATA
4005329 T
1 T
4005330 TTTGAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
TAAATTTTATAAATTTTAAAAATA
Found at i:4007023 original size:29 final size:28
Alignment explanation
Indices: 4006981--4007035 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 28
4006971 ATTTAAAATT
4006981 TAAAAAGTAAAAAACTAAATTCCTAAAAA
1 TAAAAAGTAAAAAACTAAATT-CTAAAAA
4007010 TAAAAA-TATAAAAACTAAATTCTAAA
1 TAAAAAGTA-AAAAACTAAATTCTAAA
4007036 TTTATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.24
Consensus pattern (28 bp):
TAAAAAGTAAAAAACTAAATTCTAAAAA
Found at i:4017433 original size:40 final size:40
Alignment explanation
Indices: 4017192--4017419 Score: 370
Period size: 40 Copynumber: 5.7 Consensus size: 40
4017182 TATTCGAATG
* *
4017192 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
4017232 A-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACT
1 ATA-ACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
4017271 ATATCTGGGCTAAGTCCCGAAGGCACTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
4017311 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGTGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
4017351 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
4017391 ATAACCGGGCTAAGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
4017420 AGCAAGTAGC
Statistics
Matches: 175, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
39 35 0.20
40 140 0.80
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:4026085 original size:23 final size:23
Alignment explanation
Indices: 4026025--4026089 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
4026015 CTGATCAAAG
4026025 TACGACACATAAAGTGCCT-AAA
1 TACGACACATAAAGTGCCTGAAA
** *
4026047 -ACGACACACGAGGTGCCTGAAA
1 TACGACACATAAAGTGCCTGAAA
4026069 TACGACACATAAAGTGCCTGA
1 TACGACACATAAAGTGCCTGA
4026090 TCAGTAAAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
21 15 0.43
22 3 0.09
23 17 0.49
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (23 bp):
TACGACACATAAAGTGCCTGAAA
Found at i:4026485 original size:15 final size:15
Alignment explanation
Indices: 4026460--4026517 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
4026450 TCATATATAT
4026460 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
4026476 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
4026491 AATAATTTCAATCAA
1 TATAAATTCAATCAA
4026506 TATAAATTCAAT
1 TATAAATTCAAT
4026518 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:4028588 original size:40 final size:40
Alignment explanation
Indices: 4028486--4028729 Score: 361
Period size: 40 Copynumber: 6.2 Consensus size: 40
4028476 ATGATAACCA
* *
4028486 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCG
4028526 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
* *
4028565 GGCTAAGTCCCGAAGGCACTTGTGCGAGTTACTATATCTG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
*
4028605 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
* *
4028645 GGCTAAGTCCCGAAAGCATTTGTGCGAGTTACTATAACCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
* *
4028685 GGCTAAGTCCCGAAGGCATTTGAGCAAG-TAGCTATATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCG
4028724 GGCTAA
1 GGCTAA
4028730 ATTCTGAAGG
Statistics
Matches: 189, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
39 43 0.23
40 146 0.77
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCG
Found at i:4030795 original size:13 final size:13
Alignment explanation
Indices: 4030779--4030811 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
4030769 CAGACACACA
4030779 CCCGTGTCAATTG
1 CCCGTGTCAATTG
4030792 CCCGTGTCAATTG
1 CCCGTGTCAATTG
4030805 CCCGTGT
1 CCCGTGT
4030812 GAACCCTCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.30
Consensus pattern (13 bp):
CCCGTGTCAATTG
Found at i:4030952 original size:30 final size:30
Alignment explanation
Indices: 4030907--4030982 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
4030897 TACACAGCTT
*
4030907 GTCACACGCCCGTGTGGCTCACACGGCCTA
1 GTCAAACGCCCGTGTGGCTCACACGGCCTA
* * *
4030937 GTCAAATGCCTGTGTGGCTCACACGGTCTA
1 GTCAAACGCCCGTGTGGCTCACACGGCCTA
4030967 GTCAAACGCCCGTGTG
1 GTCAAACGCCCGTGTG
4030983 CCTGGCTGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (30 bp):
GTCAAACGCCCGTGTGGCTCACACGGCCTA
Found at i:4032111 original size:6 final size:6
Alignment explanation
Indices: 4032100--4032124 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4032090 AATGAAGAAG
4032100 AATTTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA A
4032125 TTATAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:4032509 original size:19 final size:19
Alignment explanation
Indices: 4032469--4032510 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
4032459 TTAAATTTTG
* *
4032469 TTATTACCCTTAGTTTATA
1 TTATTACCCTAAGCTTATA
4032488 TTATTAACCCTAAGCTTA-A
1 TTATT-ACCCTAAGCTTATA
4032507 TTAT
1 TTAT
4032511 CTAGCCAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.31, C:0.17, G:0.05, T:0.48
Consensus pattern (19 bp):
TTATTACCCTAAGCTTATA
Found at i:4038085 original size:97 final size:95
Alignment explanation
Indices: 4037847--4038171 Score: 587
Period size: 95 Copynumber: 3.4 Consensus size: 95
4037837 AAGATCTGTA
4037847 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
4037912 TAGTCAGGGAGGTAAAATCTGCCCTCTTCG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
4037942 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
4038007 TAGTCACATGGAGGTAAAATCTGCCATCTTCG
66 TAGT--CAGGGAGGTAAAATCTGCCATCTTCG
*
4038039 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCATTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
* *
4038104 TAGTCAGGGAGGTAAAATCTGCCATATTTG
66 TAGTCAGGGAGGTAAAATCTGCCATCTTCG
4038134 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG
4038172 GATCTGTTTT
Statistics
Matches: 222, Mismatches: 6, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
95 130 0.59
97 92 0.41
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TAGTCAGGGAGGTAAAATCTGCCATCTTCG
Found at i:4038232 original size:95 final size:94
Alignment explanation
Indices: 4037847--4038232 Score: 404
Period size: 95 Copynumber: 4.0 Consensus size: 94
4037837 AAGATCTGTA
** **
4037847 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAG-TATCGGCTTCAATCCACTCCACAA
* * *
4037912 TAGTCAGGGAGGTAAAATCTGCCCTCTTCG
65 TAGTCAGGAAGGCAAAATCTGCCATCTTCG
** **
4037942 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAG-TATCGGCTTCAATCCACTCCACAA
*
4038007 TAGTCACATGG-AGGTAAAATCTGCCATCTTCG
65 TAGT--CA-GGAAGGCAAAATCTGCCATCTTCG
** ***
4038039 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCATTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAG-TATCGGCTTCAATCCACTCCACAA
* * * *
4038104 TAGTCAGGGAGGTAAAATCTGCCATATTTG
65 TAGTCAGGAAGGCAAAATCTGCCATCTTCG
**
4038134 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAG-G-ATCTGTTTTTCAATCCACTTCCTA
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTATC-G-GCTTCAATCCAC-TCC-A
** *
4038197 CCAATA-T-AGGAAGGCAGGATCTGCTATCTTCG
62 -CAATAGTCAGGAAGGCAAAATCTGCCATCTTCG
4038229 ATCT
1 ATCT
4038233 ACTTGACACC
Statistics
Matches: 264, Mismatches: 18, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
92 3 0.01
93 1 0.00
94 11 0.04
95 153 0.58
96 2 0.01
97 92 0.35
98 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (94 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTATCGGCTTCAATCCACTCCACAAT
AGTCAGGAAGGCAAAATCTGCCATCTTCG
Found at i:4038247 original size:44 final size:44
Alignment explanation
Indices: 4038189--4038723 Score: 513
Period size: 44 Copynumber: 12.1 Consensus size: 44
4038179 TTTTCAATCC
* * *
4038189 ACTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCT
1 ACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
** * * * *
4038233 ACTTGACACCAATATATGAATACAAGATCTGCTTTTTTGCGATCT
1 ACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTT-CGATCT
* * *
4038278 ACTTCACCACCAGTATGGGAAGACAAGATCTGC-ATCTT-GAATCC
1 ACTTC-CCACCAATATAGGAAGACAAGATCTGCTATCTTCG-ATCT
* * * * *
4038322 ACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCT
1 ACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * * * * * *
4038366 ACTTCACGCCAATACATGAAGACAAGATCTACTTTCTGCGATCT
1 ACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * *
4038410 ACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCGTCGATCC
1 ACTTC-CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * * *
4038454 ACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCT
1 ACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * * * * *
4038498 ACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCT
1 ACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* *
4038542 ACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCC
1 ACTTC-CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * *
4038586 ACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCT
1 ACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * * * * * *
4038630 ACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTGCGATCT
1 ACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
* * *
4038674 ACTTCGCCACCAATATGGGAAGACAAGATCTGCAATCTTCAATCT
1 ACTTC-CCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
4038719 A-TTCC
1 ACTTCC
4038724 TGCCAATACA
Statistics
Matches: 385, Mismatches: 96, Indels: 21
0.77 0.19 0.04
Matches are distributed among these distances:
43 67 0.17
44 209 0.54
45 87 0.23
46 22 0.06
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (44 bp):
ACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTTCGATCT
Found at i:4038467 original size:132 final size:132
Alignment explanation
Indices: 4038185--4038742 Score: 895
Period size: 132 Copynumber: 4.2 Consensus size: 132
4038175 CTGTTTTTCA
** * * * *
4038185 ATCCACTTCCTACCAATATAGGAAGGCAGGATCTGCTATCTTCGATCTACTTGACACCAATATAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * *
4038250 GAATACAAGATCTGCTTTTTTGCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCATCT
66 GAAGACAAGATCTGC-TTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCT
4038315 T-G
130 TCG
*
4038317 AATCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACA
1 -ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACA
* *
4038382 TGAAGACAAGATCTACTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCG
65 TGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCT
4038447 TCG
130 TCG
4038450 ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
4038515 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
4038580 CG
131 CG
*
4038582 ATCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
4038647 GAAGATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCAATCT
66 GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCT
*
4038712 TCA
130 TCG
* * * *
4038715 ATCTA-TTCCTGCCAATACAGGGAGATAG
1 ATCCACTTCCTACCAATATAGGAAGATAG
4038743 ATTACCTTCA
Statistics
Matches: 400, Mismatches: 23, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
132 318 0.80
133 82 0.20
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (132 bp):
ATCCACTTCCTACCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
GAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTT
CG
Found at i:4038861 original size:121 final size:125
Alignment explanation
Indices: 4038656--4038972 Score: 421
Period size: 135 Copynumber: 2.5 Consensus size: 125
4038646 TGAAGATAAG
* * ** *
4038656 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCAATCTTCAATCTAT
1 ATCTGCCTTCT-CGATCTGCTTCGCCA--AATACAGGAAGGCAAGATCTGCAATCTTCAATCTAT
4038721 TCCTGCCAATACAGGGAGATAGA-TTA-C-CTTCAATCTACT-CAC-GT-ACAGGGAGGTAAA
63 TCCTGCCAATACAGGGAGATAGAGTTATCGCTTCAATCTACTCCACTGTCACAGGGAGGTAAA
4038778 ATCTGCCTTCTCGATCTGCTTCGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCC
1 ATCTGCCTTCTCGATCTGCTTCGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATT-C
4038843 ACTGCCAATACAGGGAGATAGAGTTATCGGCTTCAATCTACTCCACTGTAGTCACAGGGAGGTAA
65 -CTGCCAATACAGGGAGATAGAGTTATC-GCTTCAATCTACTCCAC--T-GTCACAGGGAGGTAA
4038908 A
125 A
*
4038909 ATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCT
1 ATCTGCCTTC-TCGATCTGCTT--C-GCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCT
4038973 GCTCTGCTAC
Statistics
Matches: 173, Mismatches: 6, Indels: 19
0.87 0.03 0.10
Matches are distributed among these distances:
119 34 0.20
120 1 0.01
121 35 0.20
122 13 0.08
123 1 0.01
125 12 0.07
126 3 0.02
130 2 0.01
131 22 0.13
132 11 0.06
134 1 0.01
135 38 0.22
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (125 bp):
ATCTGCCTTCTCGATCTGCTTCGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCC
TGCCAATACAGGGAGATAGAGTTATCGCTTCAATCTACTCCACTGTCACAGGGAGGTAAA
Found at i:4039042 original size:86 final size:86
Alignment explanation
Indices: 4038917--4039266 Score: 524
Period size: 86 Copynumber: 4.1 Consensus size: 86
4038907 AAATCTGCCA
* * * * *
4038917 TCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTACTA
4038982 CAAACGAGAGAGGCAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* * *
4039004 TCTTTGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTACTAC
*
4039069 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
*
4039090 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTACTAC
*
4039155 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* *
4039176 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTG-ATAACTTCAACCAGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCA-ATCTTCAACCAGCTCTACTA
* *
4039240 C-GACTGAGAGAGGCAAGGTTTA
65 CAAAC-GAGAGAGGCAAGGTTTG
4039262 TCTTC
1 TCTTC
4039267 AATTTTCACT
Statistics
Matches: 244, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
85 2 0.01
86 223 0.91
87 19 0.08
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCAATCTTCAACCAGCTCTACTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:4039126 original size:42 final size:42
Alignment explanation
Indices: 4039079--4039212 Score: 105
Period size: 42 Copynumber: 3.1 Consensus size: 42
4039069 AAACGAGAGT
4039079 GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
1 GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
* * * * * * * * *
4039121 GGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGAGT
1 GGCAAGGT-T--TGTCTTCGATCTGCTTC-GCTGTCAATGCAG-GA-A
4039165 GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
1 GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
4039207 GGCAAG
1 GGCAAG
4039213 ATCTGATAAC
Statistics
Matches: 64, Mismatches: 18, Indels: 20
0.63 0.18 0.20
Matches are distributed among these distances:
41 12 0.19
42 19 0.30
43 8 0.12
44 13 0.20
45 12 0.19
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (42 bp):
GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
Found at i:4043377 original size:19 final size:20
Alignment explanation
Indices: 4043353--4043396 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
4043343 CGTGAAAGTC
* *
4043353 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
4043372 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
4043392 -AATGC
1 TAATGC
4043397 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:4050942 original size:55 final size:53
Alignment explanation
Indices: 4050782--4050949 Score: 180
Period size: 53 Copynumber: 3.2 Consensus size: 53
4050772 TTTTTCTTTT
* * * * *
4050782 TGAACTTACCATTGCCATGTCTCGACATGGTCTTACGTGGTATCCTTGCCTTA
1 TGAACTCACCAATGCCATGTCTTGACATAGTCTTACATGGTATCCTTGCCTTA
* * *
4050835 TGAACTCACCAATGCCATGCCTTGGCATAGTCTTACATGAG-A-CCTTTTCCTTA
1 TGAACTCACCAATGCCATGTCTTGACATAGTCTTACATG-GTATCC-TTGCCTTA
* * *
4050888 TAGTAACTCATCAATGCCATGTCTTGACATTGTCTTACATGGTATCCTAGCCTTA
1 T-G-AACTCACCAATGCCATGTCTTGACATAGTCTTACATGGTATCCTTGCCTTA
4050943 TG-ACTCA
1 TGAACTCA
4050950 TGATCTTGCA
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
52 7 0.07
53 41 0.43
54 4 0.04
55 41 0.43
56 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.35
Consensus pattern (53 bp):
TGAACTCACCAATGCCATGTCTTGACATAGTCTTACATGGTATCCTTGCCTTA
Found at i:4051036 original size:93 final size:97
Alignment explanation
Indices: 4050859--4051036 Score: 249
Period size: 93 Copynumber: 1.9 Consensus size: 97
4050849 CCATGCCTTG
* *
4050859 GCATAGTCTTACATGAGACCTTTTCCTTATAGTAACTCATCAATGCCATGTCTTGACATTGTCTT
1 GCATAGTCTTACAT-AGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTT
* *
4050924 ACATGGTATCCTAGCCTTATGACTCATGATCTT
65 ACATGATATCCTAGACTTATGACTCATGATCTT
*
4050957 GCATGGTCTTACAT-GACC-TTGCCTTATAG-AACTCATCAATGCCATG-CTTGACATGGTCTTA
1 GCATAGTCTTACATAGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTA
*
4051018 CATGAT-TCCTTATACTTAT
66 CATGATATCC-TAGACTTAT
4051037 CAATGCCATG
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
92 3 0.04
93 26 0.36
94 17 0.23
95 10 0.14
96 4 0.05
98 13 0.18
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (97 bp):
GCATAGTCTTACATAGACCTTTGCCTTATAGTAACTCATCAATGCCATGTCTTGACATGGTCTTA
CATGATATCCTAGACTTATGACTCATGATCTT
Found at i:4051060 original size:41 final size:41
Alignment explanation
Indices: 4050958--4051091 Score: 144
Period size: 41 Copynumber: 3.0 Consensus size: 41
4050948 CATGATCTTG
*
4050958 CATGGTCTTACATGACCTTGCCTTATAGAACTCATCAATGCCATGCTT
1 CATGGTCTTACATGA--TT-CCTTAT---ACTTATCAATGCCATG-TT
4051006 GACATGGTCTTACATGATTCCTTATACTTATCAATGCCATGTT
1 --CATGGTCTTACATGATTCCTTATACTTATCAATGCCATGTT
*
4051049 CATGGTCTTACATGATATCCTTAT-CTTACCAAATGCCATGTT
1 CATGGTCTTACATGAT-TCCTTATACTTATC-AATGCCATGTT
4051091 C
1 C
4051092 CAAACATGGT
Statistics
Matches: 80, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
41 21 0.26
42 19 0.24
43 2 0.03
44 15 0.19
47 6 0.08
48 2 0.03
50 15 0.19
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (41 bp):
CATGGTCTTACATGATTCCTTATACTTATCAATGCCATGTT
Found at i:4051103 original size:47 final size:42
Alignment explanation
Indices: 4050993--4051258 Score: 160
Period size: 47 Copynumber: 5.9 Consensus size: 42
4050983 TAGAACTCAT
*
4050993 CAATGCCATGCTTGACATGGTCTTACATGAT-TCCTTATACTTAT
1 CAATGCCATG-TT-ACATGGTCTTACATGATATCCTTAT-CTTAC
4051037 CAATGCCATGTT-CATGGTCTTACATGATATCCTTATCTTAC
1 CAATGCCATGTTACATGGTCTTACATGATATCCTTATCTTAC
* *
4051078 CAAATGCCATGTTCCAAACATGGTCTTACATGGTATCCTTGTCTTAGTGC
1 C-AATGCCATGTT----ACATGGTCTTACATGATATCCTTATCTTA---C
* ** * * *
4051128 CAATGTCACATCTTGATGTGGTCTTACATGGA-GTCCTTAATCAATGC
1 CAATG-C-CATGTT-ACATGGTCTTACAT-GATATCCTT-ATC-TTAC
* * ** **
4051175 CGATGCCATGTCTTGACATGGTCTTACACGGGATCCTTGCCTTAC
1 CAATGCCATG--TT-ACATGGTCTTACATGATATCCTTATCTTAC
*
4051220 CAATGCCATGTATTGACATGGTCTTACATGGTATCCTTA
1 CAATGCCATG--TT-ACATGGTCTTACATGATATCCTTA
4051259 ACCGTCAATT
Statistics
Matches: 176, Mismatches: 28, Indels: 35
0.74 0.12 0.15
Matches are distributed among these distances:
41 21 0.12
42 18 0.10
43 2 0.01
44 10 0.06
45 39 0.22
46 3 0.02
47 50 0.28
48 17 0.10
49 7 0.04
50 4 0.02
51 5 0.03
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (42 bp):
CAATGCCATGTTACATGGTCTTACATGATATCCTTATCTTAC
Found at i:4055090 original size:48 final size:46
Alignment explanation
Indices: 4055033--4055136 Score: 136
Period size: 48 Copynumber: 2.2 Consensus size: 46
4055023 CTTCGACATA
* *
4055033 GACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAATATG
1 GACTTACATGAATCATTCCTGTCTCCAAAGCC--ATATATATAATATG
** * *
4055081 GACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATCTGATATG
1 GACTTACATGAATCATTCCTGTCTCCAAAGCCATATATATAATATG
4055127 GACTTACATG
1 GACTTACATG
4055137 GCTCATTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
46 22 0.44
48 28 0.56
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (46 bp):
GACTTACATGAATCATTCCTGTCTCCAAAGCCATATATATAATATG
Found at i:4055134 original size:46 final size:47
Alignment explanation
Indices: 4055033--4055149 Score: 155
Period size: 46 Copynumber: 2.5 Consensus size: 47
4055023 CTTCGACATA
** * *
4055033 GACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAATATG
1 GACTTACATGGCTCATTCCTGTCTCCAAAGCCA-ATATATATAATATG
* *
4055081 GACTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATATCTGATATG
1 GACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATAATATG
*
4055127 GACTTACATGGCTCATTTCTGTC
1 GACTTACATGGCTCATTCCTGTC
4055150 CTGTCCTGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
46 34 0.55
48 28 0.45
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (47 bp):
GACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATATAATATG
Found at i:4055521 original size:30 final size:30
Alignment explanation
Indices: 4055485--4055545 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4055475 TCTTTTACTC
*
4055485 AAACTTTT-CAAAAATTACATTTTTGCCCCT
1 AAACTTTTGC-AAAATTACACTTTTGCCCCT
* *
4055515 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACACTTTTGCCCCT
4055545 A
1 A
4055546 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACACTTTTGCCCCT
Found at i:4062518 original size:46 final size:48
Alignment explanation
Indices: 4062413--4062532 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 48
4062403 TGTCTTCGAC
** * * *
4062413 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCA-ATATATACTAAT
*
4062462 ATGG-CTTACATGGCTCATTCCTGTCTCCAAAGCC-ATATAT-CTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATACTAAT
*
4062507 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
4062533 CTGTCCTGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
45 7 0.11
46 26 0.41
48 26 0.41
49 4 0.06
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAATATATACTAAT
Found at i:4062902 original size:30 final size:30
Alignment explanation
Indices: 4062868--4062928 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4062858 TCCTTTACTC
*
4062868 AAACTTTT-CAAAAATTACATTTTTGCCCCT
1 AAACTTTTGC-AAAATTACACTTTTGCCCCT
* *
4062898 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACACTTTTGCCCCT
4062928 A
1 A
4062929 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACACTTTTGCCCCT
Found at i:4065973 original size:19 final size:18
Alignment explanation
Indices: 4065931--4065978 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
4065921 AAACAAAACC
* *
4065931 ACATATAAATATATATAT
1 ACATAAAAATATACATAT
4065949 ACATAAAAATATACACTAT
1 ACATAAAAATATACA-TAT
* *
4065968 ATATAATAATA
1 ACATAAAAATA
4065979 ATAGTAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 13 0.52
19 12 0.48
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
ACATAAAAATATACATAT
Found at i:4066216 original size:12 final size:12
Alignment explanation
Indices: 4066192--4066222 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
4066182 GAGGGTATAT
4066192 ATAATAT-AATA
1 ATAATATAAATA
4066203 ATAATATAAATA
1 ATAATATAAATA
4066215 ATAATATA
1 ATAATATA
4066223 TACATGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATATAAATA
Found at i:4066786 original size:30 final size:30
Alignment explanation
Indices: 4066752--4066867 Score: 214
Period size: 30 Copynumber: 3.9 Consensus size: 30
4066742 ATTTGATGGT
*
4066752 GTAGGTGCAAGTGGGAGACAAGGTGGTGGA
1 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
*
4066782 GTAGGTGCAAGTGGGAGGCAAGGTGATGGA
1 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
4066812 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
1 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
4066842 GTAGGTGCAAGTGGGAGGCAAGGTGG
1 GTAGGTGCAAGTGGGAGGCAAGGTGG
4066868 CTAGGGTTTT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.25, C:0.07, G:0.52, T:0.16
Consensus pattern (30 bp):
GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
Found at i:4066805 original size:18 final size:18
Alignment explanation
Indices: 4066784--4066866 Score: 64
Period size: 18 Copynumber: 5.3 Consensus size: 18
4066774 GTGGTGGAGT
4066784 AGGTGCAAGTGGGAGGCA
1 AGGTGCAAGTGGGAGGCA
*
4066802 AGGTG--A-T-GGA-G-T
1 AGGTGCAAGTGGGAGGCA
4066814 AGGTGCAAGTGGGAGGCA
1 AGGTGCAAGTGGGAGGCA
*
4066832 AGGTG---GT-GGA-G-T
1 AGGTGCAAGTGGGAGGCA
4066844 AGGTGCAAGTGGGAGGCA
1 AGGTGCAAGTGGGAGGCA
4066862 AGGTG
1 AGGTG
4066867 GCTAGGGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 24
0.64 0.05 0.31
Matches are distributed among these distances:
12 10 0.20
13 2 0.04
14 7 0.14
15 6 0.12
16 7 0.14
17 2 0.04
18 15 0.31
ACGTcount: A:0.25, C:0.07, G:0.52, T:0.16
Consensus pattern (18 bp):
AGGTGCAAGTGGGAGGCA
Found at i:4067624 original size:44 final size:43
Alignment explanation
Indices: 4067397--4067891 Score: 196
Period size: 44 Copynumber: 11.5 Consensus size: 43
4067387 CAGCTTGGTA
*** **
4067397 CCCTACTGCTTAGGGGTTTAAGGCCCATCGTCTTCGATCTGTTT
1 CCCTACTGCTTAGGGGTTTAA-GCTTGTCACCTTCGATCTGTTT
* * ** * *
4067441 CCCTATTGCTTA-GGGTGTTAAGATCTGT-AAATT-TATCCTGTTA
1 CCCTACTGCTTAGGGGT-TTAAGCT-TGTCACCTTCGAT-CTGTTT
* * *
4067484 CCCTACTGTTTAGTGG-TTAAGGCTTGTCACCTTCGATCTATTT
1 CCCTACTGCTTAGGGGTTTAA-GCTTGTCACCTTCGATCTGTTT
* * * * * * *
4067527 CCCTAGTGCTTAAGGGGTTTAAGGTCTGTAAATCTT-TAGCCTGTTA
1 CCCTACTGCTT-AGGGGTTTAAGCT-TGT-CACCTTCGA-TCTGTTT
4067573 CCCTACTGCTTAGGGGTTTAAGCCTTGTCACCTTCGATCTGTTT
1 CCCTACTGCTTAGGGGTTTAAG-CTTGTCACCTTCGATCTGTTT
* * ** ** * *
4067617 CTCTACTGTTTA-GGG--T---C-TGT-AAATTTAACCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGCTTGTCACCTTCGATCTGTTT
* ** *
4067652 CCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTTGATCTGTTT
1 CCCTACTGCTTAGGGGTTTAA-GCTTGTCACCTTCGATCTGTTT
* * ** * * *
4067696 CCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTC-AGCCTATTA
1 CCCTACTGCTTAGGGGTTTAAGCT-TGTCACCTTCGA-TCTGTTT
*** * *
4067739 CCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTATTT
1 CCCTACTGCTTAGGGGTTTAA-GCTTGTCACCTTCGATCTGTTT
* * ** * *
4067783 CCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTC-AGCCTGTTA
1 CCCTACTGCTTAGGGGTTTAAGCT-TGTCACCTTCGA-TCTGTTT
* * ** **
4067826 CCCTACTGCTTAGGGGGTTAAGGTCCATTGCCTTCGATCTGTTT
1 CCCTACTGCTTAGGGGTTTAAGCT-TGTCACCTTCGATCTGTTT
*
4067870 CCCTACTGCTTAGGGGGTTAAG
1 CCCTACTGCTTAGGGGTTTAAG
4067892 ATCTGTAAAT
Statistics
Matches: 327, Mismatches: 92, Indels: 64
0.68 0.19 0.13
Matches are distributed among these distances:
35 19 0.06
36 6 0.02
37 1 0.00
38 1 0.00
41 1 0.00
42 12 0.04
43 107 0.33
44 136 0.42
45 25 0.08
46 19 0.06
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (43 bp):
CCCTACTGCTTAGGGGTTTAAGCTTGTCACCTTCGATCTGTTT
Found at i:4067760 original size:43 final size:43
Alignment explanation
Indices: 4067690--4068150 Score: 278
Period size: 43 Copynumber: 10.7 Consensus size: 43
4067680 CGTCTTTGAT
*
4067690 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* * ** ** *** *
4067733 CTATTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGT-AAATTCAG-C
* *
4067777 CTATTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* *** *
4067820 CTGTTACCCTACTGCTTAGGGGGTTAAGGTCCAT-TGCCTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGAT-C-TGTAAATTCAG-C
* *
4067864 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAAC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* * * ** ** * *
4067907 CTATTACTCTACTGCTTAGGGGTTTAAGGCCCTTCGT-CTTTGA-T
1 CTGTTACCCTACTGCTTAGGGGGTTAA-GATC-T-GTAAATTCAGC
** * * * ** *
4067951 CTACT-CCACTACTGCTTAGGGAGATAAGATCTG-CAATTTGGT
1 CTGTTACC-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
* * * * *
4067993 CTGTTACCCTACTGCTTAAGGGTTTAAGACCCTTCGT--CTTC-GAT
1 CTGTTACCCTACTGCTTAGGGGGTTAAGA-TC-T-GTAAATTCAG-C
**** *
4068037 CTGTTTTTTTACTG-TATAGGGGGTTAAGATCTGGAAATTCAGC
1 CTGTTACCCTACTGCT-TAGGGGGTTAAGATCTGTAAATTCAGC
* *
4068080 CTGTTACCCTACTGCTTAGGGGTTTAAGATCTGTAAATTTAGC
1 CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
4068123 CTGTTACCCTACTGCTTAGGGGGTTAAG
1 CTGTTACCCTACTGCTTAGGGGGTTAAG
4068151 GCTTGTGGAT
Statistics
Matches: 310, Mismatches: 83, Indels: 50
0.70 0.19 0.11
Matches are distributed among these distances:
41 4 0.01
42 24 0.08
43 160 0.52
44 114 0.37
45 6 0.02
46 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (43 bp):
CTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGC
Found at i:4067778 original size:87 final size:87
Alignment explanation
Indices: 4067632--4068107 Score: 625
Period size: 87 Copynumber: 5.5 Consensus size: 87
4067622 CTGTTTAGGG
* * ** *
4067632 TCTGTAAATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTTGATCTGTTTC
1 TCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGTCTTCGATCTGTTTC
4067697 CCTACTGCTTAGGGGGTTAAGA
66 CCTACTGCTTAGGGGGTTAAGA
* * *
4067719 TCTGTAAATTCAGCCTATTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTATTTC
1 TCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGTCTTCGATCTGTTTC
4067784 CCTACTGCTTAGGGGGTTAAGA
66 CCTACTGCTTAGGGGGTTAAGA
* * * *
4067806 TCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCCATTGCCTTCGATCTGTTTC
1 TCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGTCTTCGATCTGTTTC
4067871 CCTACTGCTTAGGGGGTTAAGA
66 CCTACTGCTTAGGGGGTTAAGA
* * * * * **
4067893 TCTGTAAATTCAACCTATTACTCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTTGATCT-ACTC
1 TCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGTCTTCGATCTGTTTC
* *
4067957 CACTACTGCTTAGGGAGATAAGA
66 C-CTACTGCTTAGGGGGTTAAGA
* ** * * * * *
4067980 TCTG-CAATTTGGTCTGTTACCCTACTGCTTAAGGGTTTAAGACCCTTCGTCTTCGATCTGTTTT
1 TCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGTCTTCGATCTGTTTC
**
4068044 TTTACTG-TATAGGGGGTTAAGA
66 CCTACTGCT-TAGGGGGTTAAGA
*
4068066 TCTGGAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
1 TCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAG
4068108 ATCTGTAAAT
Statistics
Matches: 337, Mismatches: 48, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
85 1 0.00
86 68 0.20
87 268 0.80
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.36
Consensus pattern (87 bp):
TCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGTCTTCGATCTGTTTC
CCTACTGCTTAGGGGGTTAAGA
Found at i:4067867 original size:174 final size:173
Alignment explanation
Indices: 4067395--4068107 Score: 790
Period size: 174 Copynumber: 4.1 Consensus size: 173
4067385 TTCAGCTTGG
* * * *
4067395 TACCCTACTGCTTAGGGGTTTAAGGCCCATCGTCTTCGATCTGTTTCCCTATTGCTTAGGGTGTT
1 TACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTATTTCCCTACTGCTTAGGGGGTT
* * *
4067460 AAGATCTGTAAATTTATCCTGTTACCCTACTGTTTA-GTGGTTAAGG-C-TTGTCACCTTCGATC
66 AAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCATTG---CCTTCGATC
* * * * * *
4067522 TATTTCCCTAGTGCTTAAGGGGTTTAAGGTCTGTAAATCTTTAGCCTGT
128 TGTTTCCCTACTGCTT-AGGGGGTTAAGATCTGTAAA--TTCAGCCTAT
** * * * *
4067571 TACCCTACTGCTTAGGGGTTTAA-GCCTTGTCACCTTCGATCTGTTTCTCTACTGTTTA---GG-
1 TACCCTACTGCTTAGGGGTTTAAGGCC-CATCGCCTTCGATCTATTTCCCTACTGCTTAGGGGGT
* * * * * *
4067631 ---G-TCTGTAAATTTAACCTGTTACCCTACTGCTTAGGGGTTTAAGGCTTATCGTCTTTGATCT
65 TAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC-CATTGCCTTCGATCT
4067692 GTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTAT
129 GTTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTAT
4067737 TACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTATTTCCCTACTGCTTAGGGGGTT
1 TACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTATTTCCCTACTGCTTAGGGGGTT
*
4067802 AAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGTCCATTGCCTTCGATCTG
66 AAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG-CCATTGCCTTCGATCTG
*
4067867 TTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAACCTAT
130 TTTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTAT
* * * * * * *
4067911 TACTCTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTTGATCTA-CTCCACTACTGCTTAGGGAGA
1 TACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTATTTCC-CTACTGCTTAGGGGGT
* * * * * * * *
4067975 TAAGATCTG-CAATTTGGTCTGTTACCCTACTGCTTAAGGGTTTAAGACCCTTCGTCTTCGATCT
65 TAAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCATT-GCCTTCGATCT
*** * *
4068039 GTTTTTTTACTG-TATAGGGGGTTAAGATCTGGAAATTCAGCCTGT
129 GTTTCCCTACTGCT-TAGGGGGTTAAGATCTGTAAATTCAGCCTAT
4068084 TACCCTACTGCTTAGGGGTTTAAG
1 TACCCTACTGCTTAGGGGTTTAAG
4068108 ATCTGTAAAT
Statistics
Matches: 460, Mismatches: 59, Indels: 39
0.82 0.11 0.07
Matches are distributed among these distances:
166 56 0.12
167 3 0.01
168 48 0.10
169 32 0.07
172 7 0.02
173 106 0.23
174 157 0.34
175 4 0.01
176 47 0.10
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.37
Consensus pattern (173 bp):
TACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTCGATCTATTTCCCTACTGCTTAGGGGGTT
AAGATCTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCATTGCCTTCGATCTGT
TTCCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAGCCTAT
Found at i:4068328 original size:64 final size:64
Alignment explanation
Indices: 4068227--4068350 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
4068217 GTATCCATGC
** *
4068227 TTATGCCAAATAATTAGGACGTTATGACTGAAATGAATCAAATGCTCCTAATTAAATGTGATGT
1 TTATGCCAAATAATTAGGACACTATGACTGAAATGAATCAAATGCTCCTAACTAAATGTGATGT
* * * *
4068291 TTATGTCAAATAATTAGGATACTATGA-TCGAAATGAATCAAATGTTCCTAACTAGATGTG
1 TTATGCCAAATAATTAGGACACTATGACT-GAAATGAATCAAATGCTCCTAACTAAATGTG
4068351 TTATTATAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
63 1 0.02
64 51 0.98
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (64 bp):
TTATGCCAAATAATTAGGACACTATGACTGAAATGAATCAAATGCTCCTAACTAAATGTGATGT
Found at i:4069118 original size:52 final size:53
Alignment explanation
Indices: 4069016--4069129 Score: 185
Period size: 52 Copynumber: 2.2 Consensus size: 53
4069006 GCATAGCTCG
* *
4069016 AAATGAATAAATTAATCAAAGATTGCAAATGCCATAAGAAAGAAATTAACTCA
1 AAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAAGAAATTAACTCA
* *
4069069 AAATGAATAAGTTAATCAAAGATAGC-AATGCAATAAGAAGGAAATTAACTCA
1 AAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAAGAAATTAACTCA
4069121 AAATGAATA
1 AAATGAATA
4069130 TAGCAAATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 33 0.58
53 24 0.42
ACGTcount: A:0.55, C:0.10, G:0.13, T:0.22
Consensus pattern (53 bp):
AAATGAATAAATTAATCAAAGATAGCAAATGCAATAAGAAAGAAATTAACTCA
Found at i:4069439 original size:4 final size:4
Alignment explanation
Indices: 4069423--4069466 Score: 79
Period size: 4 Copynumber: 10.8 Consensus size: 4
4069413 GCCTCTCCTT
4069423 TTTC TTCTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TT-TC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
4069467 TTTTTTTAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 35 0.90
5 4 0.10
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:4070858 original size:25 final size:27
Alignment explanation
Indices: 4070821--4070873 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
4070811 TCAAACATGC
*
4070821 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTACTAGGGGT
*
4070847 ATTTCGGT-AATTTAACTACTAGGGGT
1 ATTTAGGTCAATTTAACTACTAGGGGT
4070873 A
1 A
4070874 AAACTGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTACTAGGGGT
Found at i:4072396 original size:26 final size:26
Alignment explanation
Indices: 4072367--4072442 Score: 134
Period size: 26 Copynumber: 2.9 Consensus size: 26
4072357 CCCATCATGG
4072367 AACATTTACCTAACCCATTATCAAGA
1 AACATTTACCTAACCCATTATCAAGA
* *
4072393 AACATTTACCTAACCCATTATCATGG
1 AACATTTACCTAACCCATTATCAAGA
4072419 AACATTTACCTAACCCATTATCAA
1 AACATTTACCTAACCCATTATCAA
4072443 TTTGTATCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.39, C:0.28, G:0.04, T:0.29
Consensus pattern (26 bp):
AACATTTACCTAACCCATTATCAAGA
Found at i:4075168 original size:5 final size:5
Alignment explanation
Indices: 4075158--4075198 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
4075148 TAATGCAAAT
*
4075158 AATGC AATGC AATGC AATGC AAATGC -ATGA AATG- AATGC AA
1 AATGC AATGC AATGC AATGC -AATGC AATGC AATGC AATGC AA
4075199 AAGAAAGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
4 7 0.22
5 20 0.62
6 5 0.16
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (5 bp):
AATGC
Found at i:4075181 original size:24 final size:24
Alignment explanation
Indices: 4075149--4075198 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4075139 GGGAAAGTCT
*
4075149 AATGCAAAT-AATGCAATGCAATGC
1 AATGCAAATGAATGAAATG-AATGC
*
4075173 AATGCAAATGCATGAAATGAATGC
1 AATGCAAATGAATGAAATGAATGC
4075197 AA
1 AA
4075199 AAGAAAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (24 bp):
AATGCAAATGAATGAAATGAATGC
Found at i:4077283 original size:12 final size:13
Alignment explanation
Indices: 4077259--4077316 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
4077249 GAGAGGGTAT
4077259 ATATAATATAATA
1 ATATAATATAATA
4077272 ATATAA-ATAATA
1 ATATAATATAATA
* * *
4077284 ATATATACATGAGA
1 ATATA-ATATAATA
4077298 A-ATAATAATAATA
1 ATATAAT-ATAATA
4077311 ATATAA
1 ATATAA
4077317 AAAAAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
12 12 0.33
13 15 0.42
14 9 0.25
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:4077860 original size:30 final size:30
Alignment explanation
Indices: 4077824--4077909 Score: 172
Period size: 30 Copynumber: 2.9 Consensus size: 30
4077814 ATTTGATGAT
4077824 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
1 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
4077854 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
1 GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
4077884 GTAGGTGCAAGTGGGAGGCAAGGTGG
1 GTAGGTGCAAGTGGGAGGCAAGGTGG
4077910 CTAGGGTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.23, C:0.07, G:0.53, T:0.16
Consensus pattern (30 bp):
GTAGGTGCAAGTGGGAGGCAAGGTGGTGGA
Found at i:4077907 original size:18 final size:18
Alignment explanation
Indices: 4077826--4077908 Score: 64
Period size: 18 Copynumber: 5.3 Consensus size: 18
4077816 TTGATGATGT
4077826 AGGTGCAAGTGGGAGGCA
1 AGGTGCAAGTGGGAGGCA
*
4077844 AGGTG---GT-GGA-G-T
1 AGGTGCAAGTGGGAGGCA
4077856 AGGTGCAAGTGGGAGGCA
1 AGGTGCAAGTGGGAGGCA
*
4077874 AGGTG---GT-GGA-G-T
1 AGGTGCAAGTGGGAGGCA
4077886 AGGTGCAAGTGGGAGGCA
1 AGGTGCAAGTGGGAGGCA
4077904 AGGTG
1 AGGTG
4077909 GCTAGGGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 24
0.64 0.05 0.31
Matches are distributed among these distances:
12 10 0.20
13 2 0.04
14 6 0.12
15 8 0.16
16 6 0.12
17 2 0.04
18 15 0.31
ACGTcount: A:0.24, C:0.07, G:0.53, T:0.16
Consensus pattern (18 bp):
AGGTGCAAGTGGGAGGCA
Found at i:4079176 original size:84 final size:84
Alignment explanation
Indices: 4079035--4079191 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 84
4079025 ATTCATTCCT
* * *
4079035 TTTGCATTGACTTCTCAAGGTAAAAATCTGTATCTTCCTTTATTTTCTGGCATTGGGTTCCTTAG
1 TTTGCATTGAATTCTCAAGGGAAAAATCTGTATCTTCCTTTATTTTCTGGAATTGGGTTCCTTAG
4079100 AATCTTGAATTTTATTCTC
66 AATCTTGAATTTTATTCTC
* * *
4079119 TTTGCATTGAATTTTCAAGGGAAAAA-GTGTATTTTTCCTTTATTTTCTGGAATTGGGTTCCTTA
1 TTTGCATTGAATTCTCAAGGGAAAAATCTGTA-TCTTCCTTTATTTTCTGGAATTGGGTTCCTTA
*
4079183 GAATTTTGA
65 GAATCTTGA
4079192 GAGAAAAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
83 4 0.06
84 61 0.94
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (84 bp):
TTTGCATTGAATTCTCAAGGGAAAAATCTGTATCTTCCTTTATTTTCTGGAATTGGGTTCCTTAG
AATCTTGAATTTTATTCTC
Found at i:4081768 original size:16 final size:16
Alignment explanation
Indices: 4081747--4081778 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4081737 GTTGACTGAT
4081747 TGGAAATCAGTGGATG
1 TGGAAATCAGTGGATG
4081763 TGGAAATCAGTGGATG
1 TGGAAATCAGTGGATG
4081779 CTATTTATCT
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:0.31, C:0.06, G:0.38, T:0.25
Consensus pattern (16 bp):
TGGAAATCAGTGGATG
Found at i:4094352 original size:21 final size:22
Alignment explanation
Indices: 4094309--4094367 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
4094299 AATTGAAATG
4094309 TATATTTAAAATGTTTTATAATATA
1 TATATTTAAAA---TTTATAATATA
* *
4094334 TTTTTTTAAAATTTA-AATATA
1 TATATTTAAAATTTATAATATA
4094355 TATATTTAAAATT
1 TATATTTAAAATT
4094368 ATTTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
21 17 0.57
22 4 0.13
25 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TATATTTAAAATTTATAATATA
Found at i:4094373 original size:35 final size:34
Alignment explanation
Indices: 4094323--4094403 Score: 110
Period size: 34 Copynumber: 2.3 Consensus size: 34
4094313 TTTAAAATGT
*
4094323 TTTATAATATATTTTTTTAAAATTTAAATATATATA
1 TTTAAAATATA-TTTTTTAAAATTTAAA-ATATATA
*
4094359 TTTAAAAT-TATTTTTTAAAATTTTAAATATATA
1 TTTAAAATATATTTTTTAAAATTTAAAATATATA
4094392 TTTAATAATATA
1 TTTAA-AATATA
4094404 AAACATTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
33 12 0.29
34 18 0.44
35 4 0.10
36 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (34 bp):
TTTAAAATATATTTTTTAAAATTTAAAATATATA
Found at i:4094481 original size:9 final size:9
Alignment explanation
Indices: 4094451--4094526 Score: 66
Period size: 9 Copynumber: 8.1 Consensus size: 9
4094441 TTATTATTAG
4094451 TTTTATAATA
1 TTTTA-AATA
4094461 TTTT-AA-A
1 TTTTAAATA
4094468 TTTTAAATA
1 TTTTAAATA
*
4094477 TTTTAAATTTG
1 TTTTAAA--TA
4094488 TTTTATAATA
1 TTTTA-AATA
4094498 TTTTAAATA
1 TTTTAAATA
* *
4094507 TTCTTAATTT
1 TT-TTAAATA
4094517 TTTTAAATA
1 TTTTAAATA
4094526 T
1 T
4094527 ATTATTTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
7 5 0.09
8 4 0.07
9 20 0.37
10 17 0.31
11 6 0.11
12 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (9 bp):
TTTTAAATA
Found at i:4094498 original size:21 final size:19
Alignment explanation
Indices: 4094450--4094505 Score: 73
Period size: 16 Copynumber: 3.0 Consensus size: 19
4094440 TTTATTATTA
4094450 GTTTTATAATATTTTAAA-
1 GTTTTATAATATTTTAAAT
4094468 -TTTTA-AATATTTTAAATTT
1 GTTTTATAATATTTTAAA--T
4094487 GTTTTATAATATTTTAAAT
1 GTTTTATAATATTTTAAAT
4094506 ATTCTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 11 0.33
17 5 0.15
19 1 0.03
20 5 0.15
21 11 0.33
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (19 bp):
GTTTTATAATATTTTAAAT
Found at i:4094501 original size:30 final size:28
Alignment explanation
Indices: 4094467--4094526 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 28
4094457 AATATTTTAA
4094467 ATTTTAAATATT-TTAAATTTGTTTTATAAT
1 ATTTTAAATATTCTT-AATTT-TTTTA-AAT
4094497 ATTTTAAATATTCTTAATTTTTTTAAAT
1 ATTTTAAATATTCTTAATTTTTTTAAAT
4094525 AT
1 AT
4094527 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 5 0.17
29 5 0.17
30 17 0.59
31 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTTAAATATTCTTAATTTTTTTAAAT
Found at i:4094535 original size:18 final size:19
Alignment explanation
Indices: 4094498--4094535 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4094488 TTTTATAATA
*
4094498 TTTTAAATATTCTTAATTT
1 TTTTAAATATTATTAATTT
4094517 TTTTAAATA-TATT-ATTT
1 TTTTAAATATTATTAATTT
4094534 TT
1 TT
4094536 AAAGATATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTTAAATATTATTAATTT
Found at i:4094548 original size:115 final size:105
Alignment explanation
Indices: 4094417--4094643 Score: 312
Period size: 115 Copynumber: 2.1 Consensus size: 105
4094407 CATTTAAATA
*
4094417 TTTTAAAGATATGACCTTTCAAATTTATTATTAGTTTTATAATATTTTAAATTTTAAATATTTTA
1 TTTTAAAGATATGACCTTTCAAATTTATTATTAGTTTTATAATATTTTAAA-TGT--ATATTTTA
* *
4094482 AATTTGTTTTATAATATTTTAAATATTCTTAATTTTTTTAAATATATT-AT
63 AATAT-TTTTA-AA-ATTTTAAATA----TAATTTTTATAAAT-TATTAAT
*
4094532 TTTTAAAGATATGACCTTTCAAATTTATTATTTGTTTTATAATATTTTAAATGTATATTTTAAAT
1 TTTTAAAGATATGACCTTTCAAATTTATTATTAGTTTTATAATATTTTAAATGTATATTTTAAAT
4094597 ATTTTTAAAATTTTAAATATAATTTTTATAAATTATTAAT
66 ATTTTTAAAATTTTAAATATAATTTTTATAAATTATTAAT
4094637 TTTTAAA
1 TTTTAAA
4094644 CTAAATTTAA
Statistics
Matches: 107, Mismatches: 4, Indels: 12
0.87 0.03 0.10
Matches are distributed among these distances:
104 4 0.04
105 22 0.21
109 10 0.09
110 2 0.02
111 5 0.05
112 12 0.11
114 2 0.02
115 50 0.47
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.56
Consensus pattern (105 bp):
TTTTAAAGATATGACCTTTCAAATTTATTATTAGTTTTATAATATTTTAAATGTATATTTTAAAT
ATTTTTAAAATTTTAAATATAATTTTTATAAATTATTAAT
Found at i:4098055 original size:30 final size:30
Alignment explanation
Indices: 4098014--4098086 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
4098004 GTTGCTCTGG
* * *
4098014 GTGAAATGAACTTGAACTGCCTATATCCGA
1 GTGATATGAACTTGAACCGCCCATATCCGA
*
4098044 GTGATATGAACTTGAACCGCCCATGTCCGA
1 GTGATATGAACTTGAACCGCCCATATCCGA
4098074 GTGATATGAACTT
1 GTGATATGAACTT
4098087 TAATTGCTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (30 bp):
GTGATATGAACTTGAACCGCCCATATCCGA
Found at i:4101283 original size:21 final size:21
Alignment explanation
Indices: 4101228--4101285 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
4101218 TGATAAGTTA
4101228 TAATATATAT-TTTTAATTTT
1 TAATATATATATTTTAATTTT
* * *
4101248 TAA-ATTTAAATTTTTACTTTT
1 TAATATATATA-TTTTAATTTT
4101269 TAATATATATATTTTAA
1 TAATATATATATTTTAA
4101286 ATAAAGTCAT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.14
20 3 0.10
21 17 0.59
22 5 0.17
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATATATATATTTTAATTTT
Found at i:4101421 original size:23 final size:21
Alignment explanation
Indices: 4101391--4101461 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 21
4101381 ATTATTTTTT
4101391 AAAATTTTAAATAGAATTTAAA
1 AAAATTTTAAATA-AATTTAAA
* *
4101413 AAAAGTTTTGAATATATTTAAA
1 AAAA-TTTTAAATAAATTTAAA
*
4101435 AATAATTTAAAAATCATAATTTAAA
1 AA-AATTT-TAAAT-A-AATTTAAA
4101460 AA
1 AA
4101462 TTTATATGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 16 0.41
23 13 0.33
24 1 0.03
25 9 0.23
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (21 bp):
AAAATTTTAAATAAATTTAAA
Found at i:4101455 original size:14 final size:14
Alignment explanation
Indices: 4101436--4101462 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4101426 ATATTTAAAA
4101436 ATAATTTAAAAATC
1 ATAATTTAAAAATC
4101450 ATAATTTAAAAAT
1 ATAATTTAAAAAT
4101463 TTATATGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATTTAAAAATC
Found at i:4101626 original size:22 final size:23
Alignment explanation
Indices: 4101595--4101657 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 23
4101585 AAAATTTAAA
4101595 AAAATAATTTCAAATATATA-TATT
1 AAAA-AATTTCAAATATATATTA-T
* * * *
4101619 TAAAATTTTTAAA-AAATATTAT
1 AAAAAATTTCAAATATATATTAT
4101641 AAAAAATTTCAAATATA
1 AAAAAATTTCAAATATA
4101658 CCTTTCAAGT
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
22 15 0.52
23 11 0.38
24 3 0.10
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
AAAAAATTTCAAATATATATTAT
Found at i:4103297 original size:29 final size:30
Alignment explanation
Indices: 4103238--4103318 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
4103228 AAATTGAATC
*
4103238 AAATTAAAATTTCTATGTATAAAATTACACA-
1 AAATCAAAA-TTC-ATGTATAAAATTACACAT
* *
4103269 AAATCAAAATTCATGTATACAATTGCACATT
1 AAATCAAAATTCATGTATAAAATTACACA-T
* *
4103300 AAATCATAGTTCATGTATA
1 AAATCAAAATTCATGTATA
4103319 GTTTTGGGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 15 0.35
30 3 0.07
31 25 0.58
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTCATGTATAAAATTACACAT
Found at i:4116535 original size:5 final size:6
Alignment explanation
Indices: 4116518--4116542 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4116508 GAGTATTAGG
4116518 ATAAAA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA A
4116543 CAATATTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:4116984 original size:15 final size:13
Alignment explanation
Indices: 4116952--4117018 Score: 50
Period size: 15 Copynumber: 5.1 Consensus size: 13
4116942 TACAAAGTTA
4116952 AAAATA-ATATAT
1 AAAATATATATAT
4116964 AAAATATATATAT
1 AAAATATATATAT
*
4116977 ACACAATATCTAT-T
1 A-A-AATATATATAT
* *
4116991 AAAAGA-ATATAC
1 AAAATATATATAT
4117003 ACATAATATATATAT
1 A-A-AATATATATAT
4117018 A
1 A
4117019 TATGCATGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
11 3 0.07
12 10 0.24
13 9 0.21
14 6 0.14
15 14 0.33
ACGTcount: A:0.58, C:0.07, G:0.01, T:0.33
Consensus pattern (13 bp):
AAAATATATATAT
Found at i:4117502 original size:19 final size:19
Alignment explanation
Indices: 4117478--4117514 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
4117468 CATAAGTAAA
4117478 TAAAATAAAATAATAATAC
1 TAAAATAAAATAATAATAC
*
4117497 TAAAATAAAGTAATAATA
1 TAAAATAAAATAATAATA
4117515 AAAAATACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (19 bp):
TAAAATAAAATAATAATAC
Found at i:4117510 original size:16 final size:14
Alignment explanation
Indices: 4117476--4117521 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 14
4117466 CACATAAGTA
4117476 AATAA-AATAAAAT
1 AATAATAATAAAAT
*
4117489 AATAATACTAAAAT
1 AATAATAATAAAAT
4117503 AAAGTAATAATAAAA-
1 -AA-TAATAATAAAAT
4117518 AATA
1 AATA
4117522 CTATATATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 7 0.25
14 9 0.32
15 2 0.07
16 10 0.36
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:4117709 original size:15 final size:15
Alignment explanation
Indices: 4117686--4117729 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4117676 TAATACTTCA
*
4117686 TAAATATATATATAC
1 TAAAAATATATATAC
* *
4117701 TAAAAATATACATAG
1 TAAAAATATATATAC
*
4117716 TAATAATATATATA
1 TAAAAATATATATA
4117730 TATAACAGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (15 bp):
TAAAAATATATATAC
Found at i:4117709 original size:17 final size:16
Alignment explanation
Indices: 4117687--4117734 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
4117677 AATACTTCAT
*
4117687 AAATATATATATACTAA
1 AAATATATATATAAT-A
*
4117704 AAATATACATAGTAATA
1 AAATATATATA-TAATA
*
4117721 ATATATATATATAA
1 AAATATATATATAA
4117735 CAGTAAGACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (16 bp):
AAATATATATATAATA
Found at i:4120065 original size:130 final size:129
Alignment explanation
Indices: 4119886--4120393 Score: 576
Period size: 130 Copynumber: 3.9 Consensus size: 129
4119876 ACCTAAAGGA
* * * ** * * *
4119886 ATATTCGATTGTTTTGACCAAACGAGAAATCACAACCCAGCGCGATAGGGCATGATTCC-CGAAT
1 ATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAAT
* * * * * * * * *
4119950 CGTCAAACA-CTGAGTATT-GCCTTCGTTTTAAGGGATTTTTAGAAGATACGAGTGAAATTTGAA
66 TGCCAAATATC-AAAT-TTCGTCTTCGTTTTAAAGAATTTTTAGAAGA-ATGA-TGAAATTTGAA
4120013 GTG
127 GTG
* *
4120016 ATATTCGATTATTTTGAGCGAACGCGAAATTGTAACCCAGCACGTTAGGGCACGATTCCGCGAAT
1 ATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAAT
* *
4120081 TGCCAATTATCAAATTTCGTCTTCGTTTTAAAGAATTTTT-GAATGAATGATGAAATCTTGAAGG
66 TGCCAAATATCAAATTTCGTCTTCGTTTTAAAGAATTTTTAGAA-GAATGATGAAAT-TTGAAGT
4120145 G
129 G
* * * * *
4120146 ATATTTGATTATTTTGAGCAAACTCGGAATTGCAACCCAGCACGTTAGGGTACGATTCCGTGAAT
1 ATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAAT
* *
4120211 TGCCAAATATCAAATTTCGTCTTCATTTTAAAGAATTTTTAAAAGACATGAATGAAATTTTGAAG
66 TGCCAAATATCAAATTTCGTCTTCGTTTTAAAGAATTTTTAGAAGA-ATG-ATGAAA-TTTGAAG
4120276 TG
128 TG
* * *
4120278 ATATTCGGTTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCTGCGAAT
1 ATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAAT
* * * *
4120343 TGCCAAACATCGAATGTCGTCTTCGTTTTGAAGAATTTTT-GAATGAATGAT
66 TGCCAAATATCAAATTTCGTCTTCGTTTTAAAGAATTTTTAGAA-GAATGAT
4120394 TATAAAGCTA
Statistics
Matches: 322, Mismatches: 46, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
129 6 0.02
130 164 0.51
131 43 0.13
132 108 0.34
133 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (129 bp):
ATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAGCACGTTAGGGCACGATTCCGCGAAT
TGCCAAATATCAAATTTCGTCTTCGTTTTAAAGAATTTTTAGAAGAATGATGAAATTTGAAGTG
Found at i:4120859 original size:24 final size:24
Alignment explanation
Indices: 4120828--4120874 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
4120818 AAGTTATATG
4120828 AAAATAA-TAACATGTACCATAGT
1 AAAATAATTAACATGTACCATAGT
*
4120851 AAAACTAATTTAATATGTACCATA
1 AAAA-TAA-TTAACATGTACCATA
4120875 TACATGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
26 13 0.65
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (24 bp):
AAAATAATTAACATGTACCATAGT
Found at i:4121480 original size:18 final size:18
Alignment explanation
Indices: 4121457--4121495 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4121447 GATACAAATG
* *
4121457 ATACAATTAATATTAACA
1 ATACAACTAATATAAACA
4121475 ATACAACTAATATAAACA
1 ATACAACTAATATAAACA
4121493 ATA
1 ATA
4121496 AAAAAACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (18 bp):
ATACAACTAATATAAACA
Done.