Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1982
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: 40774
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:176 original size:41 final size:39
Alignment explanation
Indices: 112--204 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 39
102 ACAATTCAAA
112 GTATCGATACATTTGCAATGTATC-GATACATGAAAAAGAT
1 GTATCGATACATTTGCAATGTATCGGAT-CATG-AAAAGAT
152 GTATCGATACATGTTGCAATGTATCGGATCATGAAAAGAT
1 GTATCGATACAT-TTGCAATGTATCGGATCATGAAAAGAT
*
192 -TGTCGATACATTT
1 GTATCGATACATTT
205 TTGGCAGTAG
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
38 2 0.04
39 10 0.20
40 19 0.38
41 16 0.32
42 3 0.06
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.32
Consensus pattern (39 bp):
GTATCGATACATTTGCAATGTATCGGATCATGAAAAGAT
Found at i:2514 original size:21 final size:21
Alignment explanation
Indices: 2481--2525 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2471 TTGCAAGTTG
*
2481 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2503 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2523 AAA
1 AAA
2526 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:4347 original size:15 final size:15
Alignment explanation
Indices: 4327--4357 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4317 TAAAAATGTC
*
4327 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4342 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4357 C
1 C
4358 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:6439 original size:20 final size:20
Alignment explanation
Indices: 6360--6439 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
6350 AATGTCCAAA
*
6360 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
6380 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
6405 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
6425 TTGTATCGATACATT
1 ATGTATCGATACATT
6440 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:6443 original size:13 final size:13
Alignment explanation
Indices: 6425--6463 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
6415 ACATTTTTCT
6425 TTGTATCGATACA
1 TTGTATCGATACA
6438 TTGTATCGATACA
1 TTGTATCGATACA
*
6451 CTGTATCGATACA
1 TTGTATCGATACA
6464 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:8285 original size:49 final size:49
Alignment explanation
Indices: 8231--8327 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
8221 GGAGAGAAAT
8231 AGGTATGTGCAAATAAATTTTTGATGTGAATTACTTGATTAAGGGGGAG
1 AGGTATGTGCAAATAAATTTTTGATGTGAATTACTTGATTAAGGGGGAG
8280 AGGTATGTGCAAATAAATTTTTGATGTGAATTACTTGATTAAGGGGGA
1 AGGTATGTGCAAATAAATTTTTGATGTGAATTACTTGATTAAGGGGGA
8328 TTTTATTAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (49 bp):
AGGTATGTGCAAATAAATTTTTGATGTGAATTACTTGATTAAGGGGGAG
Found at i:9057 original size:13 final size:13
Alignment explanation
Indices: 9039--9064 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9029 TACAGCAAGT
9039 ATGTATCGATACA
1 ATGTATCGATACA
9052 ATGTATCGATACA
1 ATGTATCGATACA
9065 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9140 original size:18 final size:20
Alignment explanation
Indices: 9119--9155 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9109 CTATATTTTC
9119 AAAA-TGTATCGATACATCA
1 AAAATTGTATCGATACATCA
9138 AAAATTGTATCGATACAT
1 AAAATTGTATCGATACAT
9156 TTACACGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (20 bp):
AAAATTGTATCGATACATCA
Found at i:11975 original size:19 final size:16
Alignment explanation
Indices: 11940--11979 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 16
11930 AGAAATGTAA
11940 TTATTTTTTTCATTTT
1 TTATTTTTTTCATTTT
11956 TTATTTATTATTCTATTTT
1 TTATTT-TT-TTC-ATTTT
11975 TTATT
1 TTATT
11980 AGTGTAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 2 0.10
18 3 0.14
19 10 0.48
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATTTTTTTCATTTT
Found at i:13056 original size:33 final size:33
Alignment explanation
Indices: 13019--13090 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
13009 AAATTATCCT
* *
13019 TATCAACTCTAAATGTATCATCTATCACAAATG
1 TATCAACTCTAAATATATCATCCATCACAAATG
* * * **
13052 TATCATCTTTAAATATATCCTCCATCTTAAATG
1 TATCAACTCTAAATATATCATCCATCACAAATG
13085 TATCAA
1 TATCAA
13091 TGAGAGAATG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (33 bp):
TATCAACTCTAAATATATCATCCATCACAAATG
Found at i:16960 original size:13 final size:13
Alignment explanation
Indices: 16942--16966 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16932 TTATAATATT
16942 ATATATATTTATG
1 ATATATATTTATG
16955 ATATATATTTAT
1 ATATATATTTAT
16967 TTTTAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
ATATATATTTATG
Found at i:16975 original size:17 final size:17
Alignment explanation
Indices: 16932--16976 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
16922 AATATTTGTA
16932 TTATAATATTATATATAT
1 TTATAATA-TATATATAT
* *
16950 TTATGATATATATTTAT
1 TTATAATATATATATAT
*
16967 TTTTAATATA
1 TTATAATATA
16977 AAAAATTACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTATAATATATATATAT
Found at i:17854 original size:13 final size:15
Alignment explanation
Indices: 17848--17904 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
17838 ATTAATTATT
17848 TATATTATATATATA
1 TATATTATATATATA
*
17863 TATATTTTA-ATATA
1 TATATTATATATATA
17877 TAT-TTATATTATATCA
1 TATATTATA-TATAT-A
*
17893 TATATTAAATAT
1 TATATTATATAT
17905 TTTATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 4 0.11
14 8 0.23
15 12 0.34
16 7 0.20
17 4 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:17868 original size:38 final size:39
Alignment explanation
Indices: 17803--17921 Score: 135
Period size: 38 Copynumber: 3.2 Consensus size: 39
17793 TATATATTCT
*
17803 ATTATATTATAATTATATTTA-AAATATTTTAATAAATTA
1 ATTATATTAT-ATTATATATATAAATATTTTAATAAATTA
* *
17842 ATTAT-TTATATTATATATATATATATTTTAATATA-TA
1 ATTATATTATATTATATATATAAATATTTTAATAAATTA
* *
17879 TTTATATTATATCATATAT-TAAATATTTT-ATAAA-T-
1 ATTATATTATATTATATATATAAATATTTTAATAAATTA
17914 ATTATATT
1 ATTATATT
17922 CGTATAATCA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
35 7 0.10
36 5 0.07
37 24 0.34
38 29 0.41
39 5 0.07
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.55
Consensus pattern (39 bp):
ATTATATTATATTATATATATAAATATTTTAATAAATTA
Found at i:17877 original size:18 final size:17
Alignment explanation
Indices: 17852--17921 Score: 70
Period size: 18 Copynumber: 4.0 Consensus size: 17
17842 ATTATTTATA
17852 TTATATATATATATATT
1 TTATATATATATATATT
*
17869 TTAATATATATTTATATT
1 TT-ATATATATATATATT
* *
17887 ATATCATATATTAAATATT
1 TTAT-ATATA-TATATATT
*
17906 TTATAAATAT-TATATT
1 TTATATATATATATATT
17922 CGTATAATCA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
16 5 0.12
17 5 0.12
18 24 0.56
19 9 0.21
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATATATATATATT
Found at i:17895 original size:20 final size:20
Alignment explanation
Indices: 17758--17897 Score: 65
Period size: 20 Copynumber: 6.9 Consensus size: 20
17748 AATAGTAAGA
*
17758 TTATATTTTATAATTTATATAT
1 TTATATTATATAA--TATATAT
* * **
17780 TTGTATTACATTTTATATAT
1 TTATATTATATAATATATAT
17800 TCTAT-TATATTATAAT-TATAT
1 T-TATAT-TA-TATAATATATAT
* * * * *
17821 TTAAAATATTTTAATAAATTAA
1 TTATATTA-TATAATATA-TAT
*
17843 TTAT-TTATATTATATATAT
1 TTATATTATATAATATATAT
*
17862 ATATATT-T-TAATATATAT
1 TTATATTATATAATATATAT
*
17880 TTATATTATATCATATAT
1 TTATATTATATAATATAT
17898 TAAATATTTT
Statistics
Matches: 85, Mismatches: 24, Indels: 20
0.66 0.19 0.16
Matches are distributed among these distances:
18 15 0.18
19 7 0.08
20 34 0.40
21 13 0.15
22 16 0.19
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (20 bp):
TTATATTATATAATATATAT
Found at i:18295 original size:31 final size:31
Alignment explanation
Indices: 18260--18320 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
18250 AGTTATTTTT
18260 AATTT-AGATCATTTT-TATTTGAATTAATTTA
1 AATTTGAG-TCATTTTATATTTGAA-TAATTTA
*
18291 AATTTGAGTTATTTTATATTTGAATAATTT
1 AATTTGAGTCATTTTATATTTGAATAATTT
18321 GAGTTTGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 17 0.63
32 10 0.37
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (31 bp):
AATTTGAGTCATTTTATATTTGAATAATTTA
Found at i:18306 original size:16 final size:16
Alignment explanation
Indices: 18230--18313 Score: 64
Period size: 16 Copynumber: 5.3 Consensus size: 16
18220 TTATTTTGTG
* *
18230 TTTGATTTATTTAAAA
1 TTTGAGTTATTTTAAA
* *
18246 TTTAAGTTATTTTTAA
1 TTTGAGTTATTTTAAA
* *
18262 TTT-AGATCATTTT-TA
1 TTTGAG-TTATTTTAAA
* *
18277 TTTGAATTAATTTAAA
1 TTTGAGTTATTTTAAA
*
18293 TTTGAGTTATTTTATA
1 TTTGAGTTATTTTAAA
18309 TTTGA
1 TTTGA
18314 ATAATTTGAG
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
15 11 0.21
16 41 0.79
ACGTcount: A:0.32, C:0.01, G:0.08, T:0.58
Consensus pattern (16 bp):
TTTGAGTTATTTTAAA
Found at i:18320 original size:16 final size:16
Alignment explanation
Indices: 18270--18320 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
18260 AATTTAGATC
18270 ATTTT-TATTTGAATTA
1 ATTTTATATTTGAA-TA
* * *
18286 A-TTTAAATTTGAGTT
1 ATTTTATATTTGAATA
18301 ATTTTATATTTGAATA
1 ATTTTATATTTGAATA
18317 ATTT
1 ATTT
18321 GAGTTTGACA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (16 bp):
ATTTTATATTTGAATA
Found at i:18471 original size:17 final size:17
Alignment explanation
Indices: 18449--18481 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18439 CTTATTCAAA
18449 AATAA-TAAAATAATAAT
1 AATAATTAAAA-AATAAT
18466 AATAATTAAAAAATAA
1 AATAATTAAAAAATAA
18482 ATACATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATTAAAAAATAAT
Found at i:19035 original size:15 final size:15
Alignment explanation
Indices: 19015--19044 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19005 TTTTCGTGTA
19015 AATAATAAATTAATT
1 AATAATAAATTAATT
*
19030 AATAATAATTTAATT
1 AATAATAAATTAATT
19045 CCAAAAACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATAATAAATTAATT
Found at i:19390 original size:20 final size:20
Alignment explanation
Indices: 19361--19446 Score: 111
Period size: 20 Copynumber: 4.2 Consensus size: 20
19351 ATATAAGAAT
19361 CAAGAAACAATATTCAAAAG
1 CAAGAAACAATATTCAAAAG
* *
19381 CAAAAAACAATGGTT-AAACTAG
1 CAAGAAACAAT-ATTCAAA--AG
19403 CAAGAAACAATATTCAAAAG
1 CAAGAAACAATATTCAAAAG
*
19423 CAAGAAATAATATTCAAAAG
1 CAAGAAACAATATTCAAAAG
19443 CAAG
1 CAAG
19447 GCATTTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
20 38 0.67
21 4 0.07
22 15 0.26
ACGTcount: A:0.58, C:0.14, G:0.12, T:0.16
Consensus pattern (20 bp):
CAAGAAACAATATTCAAAAG
Found at i:22323 original size:20 final size:20
Alignment explanation
Indices: 22298--22471 Score: 123
Period size: 20 Copynumber: 8.8 Consensus size: 20
22288 TTTTCACAAT
22298 TTGTATCGATACATTGTACA
1 TTGTATCGATACATTGTACA
* *
22318 TTGTATCGATATATTGTTCA
1 TTGTATCGATACATTGTACA
* *
22338 TTGTATCGATATATTGTTCA
1 TTGTATCGATACATTGTACA
22358 TTGTATCGATACATTGT--A
1 TTGTATCGATACATTGTACA
* * *
22376 TCG-ATAC-ATTC-TGGGTTTACCCA
1 TTGTAT-CGATACAT---TGTA--CA
* * *
22399 GATGTATCGATACATTTTGCA
1 -TTGTATCGATACATTGTACA
22420 TTGTATCGATACATTGCT-CA
1 TTGTATCGATACATTG-TACA
22440 TT-TATCGATACATTGTA-A
1 TTGTATCGATACATTGTACA
22458 -TGTATCGATACATT
1 TTGTATCGATACATT
22472 CAGACATTTT
Statistics
Matches: 127, Mismatches: 12, Indels: 32
0.74 0.07 0.19
Matches are distributed among these distances:
16 1 0.01
17 6 0.05
18 18 0.14
19 15 0.12
20 72 0.57
21 3 0.02
23 4 0.03
24 2 0.02
25 5 0.04
26 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTGTACA
Found at i:22382 original size:13 final size:13
Alignment explanation
Indices: 22356--22385 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
22346 ATATATTGTT
22356 CATTGTATCGATA
1 CATTGTATCGATA
22369 CATTGTATCGATA
1 CATTGTATCGATA
22382 CATT
1 CATT
22386 CTGGGTTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:24908 original size:79 final size:79
Alignment explanation
Indices: 24761--25057 Score: 368
Period size: 79 Copynumber: 3.8 Consensus size: 79
24751 TTTGTCTCGA
* * ** * *
24761 GGATACTCCAATCCCGGTTCCATTTCCAAAACATCAATTT-T--TTATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTCTCATAATCGGGGATACTCCAACCC
*
24823 CGTTATTTCCAAGG
66 CGTTATTTCCGAGG
* ** * *
24837 GGATACTCCAACCTCGGCTTTATTTCTAAAATATAAATTTCTCATAATCGGGGATACTCCAACCC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTCTCATAATCGGGGATACTCCAACCC
* *
24902 CATTATTTTCGAGG
66 CGTTATTTCCGAGG
* * *
24916 GGATACTCTAACCCCGATTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAATCC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTCTCATAATCGGGGATACTCCAACCC
*
24981 CGTTATTTCTGAGG
66 CGTTATTTCCGAGG
* * *
24995 GGATACTCCAACCCCGATTTTATTTCTAAAACACCAA-TTCTCCACAATCGAGGATACTCCAAC
1 GGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTCT-CATAATCGGGGATACTCCAAC
25058 TCCGATTTTA
Statistics
Matches: 188, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
76 32 0.17
77 1 0.01
78 3 0.02
79 152 0.81
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (79 bp):
GGATACTCCAACCCCGATTTTATTTCTAAAACATCAATTTCTCATAATCGGGGATACTCCAACCC
CGTTATTTCCGAGG
Found at i:25055 original size:51 final size:51
Alignment explanation
Indices: 24995--25110 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
24985 ATTTCTGAGG
24995 GGATACTCCAACCCCGATTTTATTTCTAAAACACCAA-TTCTCCACAATCGA
1 GGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTCTCC-CAATCGA
* * *
25046 GGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCCCAATCGG
1 GGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTCTCCCAATCGA
*
25097 GGATACTCTAACCC
1 GGATACTCCAACCC
25111 TATTATTTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 54 0.92
52 5 0.08
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.29
Consensus pattern (51 bp):
GGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTCTCCCAATCGA
Found at i:25124 original size:158 final size:157
Alignment explanation
Indices: 24962--25298 Score: 383
Period size: 158 Copynumber: 2.1 Consensus size: 157
24952 ATTTTTCATA
* * * * * *
24962 ATCGGGGATACTCCAATCCCGTTATTTCTGAGGGGATACTCCAACCCC-GATTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTACCGAAGGGATACTCCAACCCCTG-CTTTATTTCCAAAA
* ** * *
25026 CACCAA-TTCTCCACAATCGAGGATACTCCAACTCCGATTTTATTTCTAAAACACCAATTTTTCC
65 CACCAATTTCT-CACAATCGAGGATACTCCAACCCCGACCTTATTTCTAAAACACCAATTTCTCA
* *
25090 CAATCGGGGATACTCTAACCCTATTATTT
129 CAATCGGGGATACTCCAACCCCATTATTT
25119 CATCGGGGATACTCCAACCCCGTTATTACCGAAGGGATACTCCAACCCCTGCTTTATTTCCAAAA
1 -ATCGGGGATACTCCAACCCCGTTATTACCGAAGGGATACTCCAACCCCTGCTTTATTTCCAAAA
* *** * ** * ***
25184 TATTGATTTCTCACAATCGGGGATACTTTAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
65 CACCAATTTCTCACAATCGAGGATACTCCAACCCCGACCTTATTTCTAAAACACCAATTTCTCAC
*
25249 AATCGGGGATACTCCAACCCCGTTATTT
130 AATCGGGGATACTCCAACCCCATTATTT
25277 -TCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
25299 GCTTTATTTC
Statistics
Matches: 150, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
156 2 0.01
158 143 0.95
159 5 0.03
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (157 bp):
ATCGGGGATACTCCAACCCCGTTATTACCGAAGGGATACTCCAACCCCTGCTTTATTTCCAAAAC
ACCAATTTCTCACAATCGAGGATACTCCAACCCCGACCTTATTTCTAAAACACCAATTTCTCACA
ATCGGGGATACTCCAACCCCATTATTT
Found at i:25144 original size:28 final size:26
Alignment explanation
Indices: 25092--25167 Score: 80
Period size: 28 Copynumber: 2.8 Consensus size: 26
25082 ATTTTTCCCA
* *
25092 ATCGGGGATACTCTAACCCTATTATTT
1 ATCGGGGATACTCCAACCCCATTA-TT
*
25119 CATCGGGGATACTCCAACCCCGTTATT
1 -ATCGGGGATACTCCAACCCCATTATT
*
25146 ACCGAAGGGATACTCCAACCCC
1 ATCG--GGGATACTCCAACCCC
25168 TGCTTTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
26 3 0.07
27 2 0.05
28 37 0.88
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (26 bp):
ATCGGGGATACTCCAACCCCATTATT
Found at i:25217 original size:51 final size:51
Alignment explanation
Indices: 25152--25270 Score: 186
Period size: 51 Copynumber: 2.3 Consensus size: 51
25142 TATTACCGAA
*
25152 GGGATACTCCAACCCCTG-CTTTATTTCCAAAATATTGATTTCTCACAATCG
1 GGGATACTCCAACCCC-GACCTTATTTCCAAAATATTGATTTCTCACAATCG
** *
25203 GGGATACTTTAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATCG
1 GGGATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCG
25254 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
25271 TTATTTTCGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 1 0.02
51 60 0.98
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCG
Found at i:25254 original size:130 final size:131
Alignment explanation
Indices: 25120--25400 Score: 483
Period size: 130 Copynumber: 2.2 Consensus size: 131
25110 CTATTATTTC
*
25120 ATCGGGGATACTCCAACCCCGTTATTACCGAAGGGATACTCCAACCCCTGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTACCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
* *
25185 ATTGATTTCTCACAATC-GGGGATACTTTAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
66 ATCGATTTCTCACAATCGGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
25249 A
131 A
** *
25250 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTACCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
**
25315 ATCGATTTCTCACAATCGGGGGATACTTCAACCCCGGTCTTATTTCTAAAATATTGATTTCTCAC
66 ATCGATTTCTCACAATCGGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
25380 A
131 A
25381 ATCGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
25401 ATTACTTTCA
Statistics
Matches: 142, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
130 77 0.54
131 65 0.46
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (131 bp):
ATCGGGGATACTCCAACCCCGTTATTACCGAAGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
ATCGATTTCTCACAATCGGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
A
Found at i:25285 original size:79 final size:80
Alignment explanation
Indices: 25202--25350 Score: 228
Period size: 79 Copynumber: 1.9 Consensus size: 80
25192 TCTCACAATC
** * *
25202 GGGGATACTTTAACCCCGACCTTATTTCTAAAATATTGATTTCTCACAATC-GGGGATACTCCAA
1 GGGGATACTCCAACCCCGACCTTATTTCCAAAATATCGATTTCTCACAATCGGGGGATACTCCAA
25266 CCCCGTTATTTTCGA
66 CCCCGTTATTTTCGA
* * *
25281 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATCGATTTCTCACAATCGGGGGATACTTCAA
1 GGGGATACTCCAACCCCGACCTTATTTCCAAAATATCGATTTCTCACAATCGGGGGATACTCCAA
25346 CCCCG
66 CCCCG
25351 GTCTTATTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 45 0.73
80 17 0.27
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (80 bp):
GGGGATACTCCAACCCCGACCTTATTTCCAAAATATCGATTTCTCACAATCGGGGGATACTCCAA
CCCCGTTATTTTCGA
Found at i:25359 original size:52 final size:51
Alignment explanation
Indices: 25281--25400 Score: 188
Period size: 52 Copynumber: 2.3 Consensus size: 51
25271 TTATTTTCGA
25281 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATCGATTTCTCACAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATCGATTTCTCACAATC
* * *
25332 GGGGGATACTTCAACCCCGG-TCTTATTTCTAAAATATTGATTTCTCACAATC
1 -GGGGATACTCCAACCCCGGCT-TTATTTCCAAAATATCGATTTCTCACAATC
25384 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
25401 ATTACTTTCA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 17 0.27
52 46 0.73
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCTTTATTTCCAAAATATCGATTTCTCACAATC
Found at i:25417 original size:131 final size:129
Alignment explanation
Indices: 25120--25424 Score: 470
Period size: 131 Copynumber: 2.3 Consensus size: 129
25110 CTATTATTTC
* *
25120 ATCGGGGATACTCCAACCCCGTTATTAC-CGAAGGGATACTCCAACCCCTGCTTTATTTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTCAC--AGGGATACTCCAACCCCGGCTTTATTTCCAAAA
* *
25184 TATTGATTTCTCACAATCGGGGATACTTTAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
64 TATCGATTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
25249 A
129 A
*
25250 ATCGGGGATACTCCAACCCCGTTATTTTCGA-GGGGATACTCCAACCCCGGCTTTATTTCCAAAA
1 ATCGGGGATACTCCAACCCCGTTA-TTTC-ACAGGGATACTCCAACCCCGGCTTTATTTCCAAAA
**
25314 TATCGATTTCTCACAATCGGGGGATACTTCAACCCCGGTCTTATTTCTAAAATATTGATTTCTCA
64 TATCGATTTCTCACAATC-GGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCA
25379 CA
128 CA
*
25381 ATCGGGGATACTCCAACCCCATTACTTTCACAGGGATACTCCAA
1 ATCGGGGATACTCCAACCCCGTTA-TTTCACAGGGATACTCCAA
25425 TCTCAATTTT
Statistics
Matches: 160, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
130 73 0.46
131 87 0.54
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (129 bp):
ATCGGGGATACTCCAACCCCGTTATTTCACAGGGATACTCCAACCCCGGCTTTATTTCCAAAATA
TCGATTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACA
Found at i:25452 original size:131 final size:130
Alignment explanation
Indices: 25120--25480 Score: 429
Period size: 131 Copynumber: 2.8 Consensus size: 130
25110 CTATTATTTC
* * **
25120 ATCGGGGATACTCCAACCCCGTTA-TTACCGAAGGGATACTCCAACCCCTGCTTTATTTCCAAAA
1 ATCGGGGATACTCCAACCCCATTACTT-TCGAAGGGATACTCCAACCCCAACTTTATTTCCAAAA
* ** *
25184 TATTGATTTCTCACAATCGGGGATACTTTAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
65 CACCGATTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
25249 A
130 A
* * * ** *
25250 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCATTACTTTCGAAGGGATACTCCAACCCCAACTTTATTTCCAAAAC
* **
25315 ATCGATTTCTCACAATCGGGGGATACTTCAACCCCGGTCTTATTTCTAAAATATTGATTTCTCAC
66 ACCGATTTCTCACAATC-GGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCAC
25380 A
130 A
* * * * *
25381 ATCGGGGATACTCCAACCCCATTACTTTC-ACAGGGATACTCCAATCTCAATTTTATTTTCAGAA
1 ATCGGGGATACTCCAACCCCATTACTTTCGA-AGGGATACTCCAACCCCAACTTTATTTCCAAAA
* ** * * *
25445 CACCGATTTTTCATGATTGGGGATACTCCAGCCCCG
65 CACCGATTTCTCACAATCGGGGATACTTCAACCCCG
25481 TTGTTATCTC
Statistics
Matches: 203, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
130 92 0.45
131 111 0.55
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (130 bp):
ATCGGGGATACTCCAACCCCATTACTTTCGAAGGGATACTCCAACCCCAACTTTATTTCCAAAAC
ACCGATTTCTCACAATCGGGGATACTTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCACA
Found at i:31856 original size:61 final size:61
Alignment explanation
Indices: 31635--32201 Score: 724
Period size: 62 Copynumber: 9.2 Consensus size: 61
31625 CTCTTTTAGC
* *
31635 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGACA
1 CCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
31696 CCTTGCTAGTCCTCAAAGAGCAAGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTT-CCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
31758 CCTTTCTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CC-TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
31820 CCTTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
31881 CATTCCAATCCTCAAAGAGCAGGATGCCTTTTTTCTTTTTAAAGCCCA-A-AAGTTGGTGGCA
1 CCTTCCAGTCCTCAAAGAGCAGGACGCC--TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** * * *
31942 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* ** *
32003 CCCTCCAGTCCTCAAAGAGCAGGACGCCTTTTTTATTTTTAAAGCCCACACATGTTGGTGGCA
1 CCTTCCAGTCCTCAAAGAGCAGGACGCC--TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
32066 CTTTTCCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 C-CTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
32128 CCTTGCTAGTCCTCAAAGAGTAAGACACCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTT-CCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
32190 CATTCCAATCCT
1 CCTTCCAGTCCT
32202 GTCCCTTCCG
Statistics
Matches: 443, Mismatches: 53, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
59 15 0.03
60 1 0.00
61 162 0.37
62 194 0.44
63 47 0.11
64 24 0.05
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (61 bp):
CCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:31963 original size:122 final size:123
Alignment explanation
Indices: 31635--32190 Score: 742
Period size: 122 Copynumber: 4.5 Consensus size: 123
31625 CTCTTTTAGC
* *
31635 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGACACCTT
1 CCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * *
31700 GCTAGTCCTCAAAGAGCAAGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
66 TCCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
31758 CCTTTCTAGTCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC-
1 CC-TTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* *
31822 TTCTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCA
65 TTCCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
31881 CATTCCAATCCTCAAAGAGCAGGATGCCTTTTTTCTTTTTAAAGCCCA-A-AAGTTGGTGGCA-T
1 CCTTCCAGTCCTCAAAGAGCAGGACGCC--TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
31943 TTTCCAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTCAAAGCCCACACGAGTTGGTGGCA
64 TTTCCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* ** * *
32003 CCCTCCAGTCCTCAAAGAGCAGGACGCCTTTTTTATTTTTAAAGCCCACACATGTTGGTGGCACT
1 CCTTCCAGTCCTCAAAGAGCAGGACGCC--TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACC
** *
32068 TTTCCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
64 TTTCCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * * *
32128 CCTTGCTAGTCCTCAAAGAGTAAGACACCTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCAC
1 CCTT-CCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC
32191 ATTCCAATCC
Statistics
Matches: 386, Mismatches: 39, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
122 132 0.34
123 61 0.16
124 113 0.29
125 60 0.16
126 20 0.05
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.27
Consensus pattern (123 bp):
CCTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
TCCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:34145 original size:161 final size:162
Alignment explanation
Indices: 33959--34415 Score: 702
Period size: 161 Copynumber: 2.8 Consensus size: 162
33949 TTAATTCAAT
* * * *
33959 TTAATTTTATTTACTTTTAAAAATACCATTTCGTACCCTAATGGAAGCCCGAAAGAATATAAAAG
1 TTAATTTTATTTATTTTTGAAAATACTATTTCATACCCTAATGGAAGCCCGAAAGAATATAAAAG
* * * *
34024 GGTTTTGAAATCTTTTATACCTCTACGGATGCCCATAGGAATATAAAAAAATAGAAAAAATAAAT
66 GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAAGAATATAAAAGATTAGAAAAAATAAAT
34089 ATTAGAATTTATCCCAATAACACCAATTTAAA
131 ATTAGAATTTATCCCAATAACACCAATTTAAA
* *
34121 TTAA-TTTATTTATTTTTGAAAATACTATTTCATACCCTAATGGAAGCTCGAAAGAATATGAAAG
1 TTAATTTTATTTATTTTTGAAAATACTATTTCATACCCTAATGGAAGCCCGAAAGAATATAAAAG
* *
34185 GTTTTTGAAATCTTTTATACCCCTACAGATGCCCATAAGAATATAAAAGATTAG-AAAAATAAAA
66 GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAAGAATATAAAAGATTAGAAAAAAT-AAA
* * * *
34249 TATTGGAATTTATCTCAATAATACCAATTTAAG
130 TATTAGAATTTATCCCAATAACACCAATTTAAA
* * * * *
34282 TTAATTTTATTTATTTTTGAAAATATTATTTCATATCCTAACGGAAGCCTGAAAGAATACAAAAG
1 TTAATTTTATTTATTTTTGAAAATACTATTTCATACCCTAATGGAAGCCCGAAAGAATATAAAAG
34347 GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAAGAATATAAAAGATTAGAAAAAATAAAT
66 GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAAGAATATAAAAGATTAGAAAAAATAAAT
34412 ATTA
131 ATTA
34416 TTTAATTTTA
Statistics
Matches: 266, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
160 6 0.02
161 138 0.52
162 116 0.44
163 6 0.02
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (162 bp):
TTAATTTTATTTATTTTTGAAAATACTATTTCATACCCTAATGGAAGCCCGAAAGAATATAAAAG
GTTTTTGAAATCTTTTATACCTCTACGGATGCCCATAAGAATATAAAAGATTAGAAAAAATAAAT
ATTAGAATTTATCCCAATAACACCAATTTAAA
Found at i:38675 original size:35 final size:33
Alignment explanation
Indices: 38631--38711 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 33
38621 ATTCTCCTTC
* * *
38631 TTTTTAAAGTCCATGACTCCATGGGACCCTTTTT
1 TTTTTAAAGTCCATAACTCCATGGCA-CCTTTCT
*
38665 TTTTTAAAAGTCCATAACTCCGTGGCACCTTTCT
1 TTTTT-AAAGTCCATAACTCCATGGCACCTTTCT
*
38699 CTTTTAAAGTCCA
1 TTTTTAAAGTCCA
38712 CAAATCCGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 8 0.20
34 15 0.37
35 18 0.44
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (33 bp):
TTTTTAAAGTCCATAACTCCATGGCACCTTTCT
Found at i:38720 original size:33 final size:32
Alignment explanation
Indices: 38632--38949 Score: 118
Period size: 33 Copynumber: 10.1 Consensus size: 32
38622 TTCTCCTTCT
** * * *
38632 TTTTAAAGTCCATGACTCCATGGGACCCTTTTTT
1 TTTTAAAGTCCACAACTCCGTGGCA-CC-TTTTC
*
38666 TTTTAAAAGTCCATAACTCCGTGGCACCTTTCTC
1 TTTT-AAAGTCCACAACTCCGTGGCACCTTT-TC
* * *
38700 TTTTAAAGTCCACAAATCCGTGACACTTTTTTC
1 TTTTAAAGTCCACAACTCCGTGGCAC-CTTTTC
***
38733 TCCAAAAGTCCACAACTCCGTGGCA-C-TTT-
1 TTTTAAAGTCCACAACTCCGTGGCACCTTTTC
* ** *
38762 TTTTAAAGTCCACGACTCAATGGCATCTTTTC
1 TTTTAAAGTCCACAACTCCGTGGCACCTTTTC
** ** * * * *
38794 --CCAAAGTCCATGACTCAGTCGCTCC-CTTC
1 TTTTAAAGTCCACAACTCCGTGGCACCTTTTC
* * ** * *
38823 --TCAAAGTCCACGACTTAGTGGCATCTCTTC
1 TTTTAAAGTCCACAACTCCGTGGCACCTTTTC
** * *
38853 --CCAAAGTCCACAACTCCGTAGCACCCTTTTTA
1 TTTTAAAGTCCACAACTCCGTGGCA-CC-TTTTC
* * * *
38885 TTTTTAAGTCTATAACTCCGTTGCACCTTTTC
1 TTTTAAAGTCCACAACTCCGTGGCACCTTTTC
** * *
38917 TTTT-AAGTCTGCAACTCCATGGCACCCTTTC
1 TTTTAAAGTCCACAACTCCGTGGCACCTTTTC
38948 TT
1 TT
38950 AAACTCCACA
Statistics
Matches: 219, Mismatches: 54, Indels: 25
0.73 0.18 0.08
Matches are distributed among these distances:
29 41 0.19
30 44 0.20
31 28 0.13
32 11 0.05
33 46 0.21
34 31 0.14
35 18 0.08
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (32 bp):
TTTTAAAGTCCACAACTCCGTGGCACCTTTTC
Found at i:38800 original size:30 final size:30
Alignment explanation
Indices: 38766--38868 Score: 127
Period size: 30 Copynumber: 3.5 Consensus size: 30
38756 CACTTTTTTT
* *
38766 AAAGTCCACGACTCAATGGCATCTTTTCCC
1 AAAGTCCACGACTCAGTGGCATCTCTTCCC
* * * *
38796 AAAGTCCATGACTCAGTCGC-TCCCTTCTC
1 AAAGTCCACGACTCAGTGGCATCTCTTCCC
*
38825 AAAGTCCACGACTTAGTGGCATCTCTTCCC
1 AAAGTCCACGACTCAGTGGCATCTCTTCCC
*
38855 AAAGTCCACAACTC
1 AAAGTCCACGACTC
38869 CGTAGCACCC
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
29 23 0.39
30 36 0.61
ACGTcount: A:0.26, C:0.35, G:0.14, T:0.25
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTCTTCCC
Found at i:38803 original size:59 final size:59
Alignment explanation
Indices: 38671--38876 Score: 178
Period size: 59 Copynumber: 3.4 Consensus size: 59
38661 TTTTTTTTTA
* * * * * *
38671 AAAGTCCATAACTCCGTGGCACCTTTCTCTTTTAAAGTCCACAAATCCGTGACACTTTTTTCTCC
1 AAAGTCCACAACTCCGTGGCA-C-TT-T-TTTTAAAGTCCACGACTCAGTGGCA-TCTTTTC-CC
*
38736 AAAAGTCCACAACTCCGTGGCACTTTTTTTAAAGTCCACGACTCAATGGCATCTTTTCCC
1 -AAAGTCCACAACTCCGTGGCACTTTTTTTAAAGTCCACGACTCAGTGGCATCTTTTCCC
** * * * ** * * * *
38796 AAAGTCCATGACTCAGTCGCTCCCTTCTCAAAGTCCACGACTTAGTGGCATCTCTTCCC
1 AAAGTCCACAACTCCGTGGCACTTTTTTTAAAGTCCACGACTCAGTGGCATCTTTTCCC
*
38855 AAAGTCCACAACTCCGTAGCAC
1 AAAGTCCACAACTCCGTGGCAC
38877 CCTTTTTATT
Statistics
Matches: 116, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
59 64 0.55
60 2 0.02
61 6 0.05
62 20 0.17
63 1 0.01
64 2 0.02
65 1 0.01
66 20 0.17
ACGTcount: A:0.26, C:0.33, G:0.13, T:0.29
Consensus pattern (59 bp):
AAAGTCCACAACTCCGTGGCACTTTTTTTAAAGTCCACGACTCAGTGGCATCTTTTCCC
Found at i:38902 original size:34 final size:33
Alignment explanation
Indices: 38856--38946 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 33
38846 TCTCTTCCCA
* *
38856 AAGTCCACAACTCCGTAGCACCCTTTTTATTTTT
1 AAGTCTACAACTCCGTAGCACCCTTTTT-CTTTT
* *
38890 AAGTCTATAACTCCGTTGCA-CC-TTTTCTTTT
1 AAGTCTACAACTCCGTAGCACCCTTTTTCTTTT
* * *
38921 AAGTCTGCAACTCCATGGCACCCTTT
1 AAGTCTACAACTCCGTAGCACCCTTT
38947 CTTAAACTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
31 20 0.43
32 6 0.13
33 4 0.09
34 17 0.36
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.37
Consensus pattern (33 bp):
AAGTCTACAACTCCGTAGCACCCTTTTTCTTTT
Found at i:40518 original size:34 final size:35
Alignment explanation
Indices: 40428--40526 Score: 118
Period size: 34 Copynumber: 2.9 Consensus size: 35
40418 TAAAAGGAGA
*
40428 TGCCAC-GACTTGTGTGGGCTTTTGAGA-GGGTTG
1 TGCCACAGACTTGTGTGGGCTTTTGAAAGGGGTTG
40461 TGCCACA-ACGTTGTGGTGGGCTTTTGAAAGGGGTTG
1 TGCCACAGAC-TTGT-GTGGGCTTTTGAAAGGGGTTG
*
40497 -G-CACAGACTTGTGTGGCGCTTTAGAAAGGG
1 TGCCACAGACTTGTGTGG-GCTTTTGAAAGGG
40527 TTACCCCGCT
Statistics
Matches: 58, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
33 12 0.21
34 24 0.41
35 16 0.28
36 6 0.10
ACGTcount: A:0.17, C:0.15, G:0.38, T:0.29
Consensus pattern (35 bp):
TGCCACAGACTTGTGTGGGCTTTTGAAAGGGGTTG
Done.