Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 68 of 295
Found at i:20641181 original size:59 final size:59
Alignment explanation
Indices: 20641080--20641282 Score: 291
Period size: 59 Copynumber: 3.5 Consensus size: 59
20641070 ACGACCATCA
* *
20641080 ATTATGAAAAGGGAT-GAGACGACCATTGAATTATGAAAAGGGATAGCTTTGGCTATCG
1 ATTATGAAAAGGGATGGTGACGACCATAGAATTATGAAAAGGGATAGCTTTGGCTATCG
* * * * *
20641138 ATTATGAAAAGGGATGGTGAAGACCATAAAATTATGGAAAGGGAAAGCTTTTGCTATCG
1 ATTATGAAAAGGGATGGTGACGACCATAGAATTATGAAAAGGGATAGCTTTGGCTATCG
* * * *
20641197 ATTATGAAAAGGGATGGTGATGACCATCGAATTATGAAAAGGAATAGCTTCGGCTATCG
1 ATTATGAAAAGGGATGGTGACGACCATAGAATTATGAAAAGGGATAGCTTTGGCTATCG
*
20641256 ATTATAAAAAGGGATGGTGACGACCAT
1 ATTATGAAAAGGGATGGTGACGACCAT
20641283 TAACTATGAA
Statistics
Matches: 127, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
58 15 0.12
59 112 0.88
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.25
Consensus pattern (59 bp):
ATTATGAAAAGGGATGGTGACGACCATAGAATTATGAAAAGGGATAGCTTTGGCTATCG
Found at i:20647470 original size:23 final size:23
Alignment explanation
Indices: 20647443--20647489 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20647433 ACAATATTAC
*
20647443 AATATTACTTGAATAGTTGTAAA
1 AATATTACTTGAATAGTTATAAA
**
20647466 AATATTGTTTGAATAGTTATAAA
1 AATATTACTTGAATAGTTATAAA
20647489 A
1 A
20647490 TTAAATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (23 bp):
AATATTACTTGAATAGTTATAAA
Found at i:20657360 original size:34 final size:34
Alignment explanation
Indices: 20657317--20657384 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
20657307 GCATTTTTGG
* *
20657317 CACTGTACTGAGATGGGCTAAGGCCCAA-ACTGT
1 CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
*
20657350 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTAAGGCCCAAGACTGT
20657385 TCAACTATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.67
35 5 0.17
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTAAGGCCCAAGACTGT
Found at i:20660222 original size:109 final size:109
Alignment explanation
Indices: 20660031--20660248 Score: 409
Period size: 109 Copynumber: 2.0 Consensus size: 109
20660021 AAATTGAATA
20660031 AGTTGTAAAATACATGTTCTAGAAGCTTTGAACATGAAATTGTCATGGATTTTTAATTAGAGGGT
1 AGTTGTAAAATACATGTTCTAGAAGCTTTGAACATGAAATTGTCATGGATTTTTAATTAGAGGGT
*
20660096 CTTAAATAGAAATTTGACCAATTTCTAAATTTATGGACAAAAAT
66 CTTAAATAGAAATTTGACCAATTTCTAAATTTACGGACAAAAAT
*
20660140 AGTTGTAAAATACATGTTCTAGAAGCTTTGAGCATGAAATTGTCATGGATTTTTAATTAGAGGGT
1 AGTTGTAAAATACATGTTCTAGAAGCTTTGAACATGAAATTGTCATGGATTTTTAATTAGAGGGT
*
20660205 CTTAAATAGCAATTTGACCAATTTCTAAATTTACGGACAAAAAT
66 CTTAAATAGAAATTTGACCAATTTCTAAATTTACGGACAAAAAT
20660249 GGGCATGGAT
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 106 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (109 bp):
AGTTGTAAAATACATGTTCTAGAAGCTTTGAACATGAAATTGTCATGGATTTTTAATTAGAGGGT
CTTAAATAGAAATTTGACCAATTTCTAAATTTACGGACAAAAAT
Found at i:20667197 original size:12 final size:13
Alignment explanation
Indices: 20667173--20667337 Score: 116
Period size: 12 Copynumber: 12.8 Consensus size: 13
20667163 GTAATATACC
*
20667173 ACATAACAAACAT
1 ACATAACATACAT
20667186 ACA-AACATACAT
1 ACATAACATACAT
20667198 ACA-AA-AT--AT
1 ACATAACATACAT
*
20667207 ACATAACAATATAT
1 ACATAAC-ATACAT
20667221 AACATAACATACAT
1 -ACATAACATACAT
* *
20667235 ACA-AATATACAA
1 ACATAACATACAT
20667247 ACATAACAATA-A-
1 ACATAAC-ATACAT
20667259 ACATAACATACAT
1 ACATAACATACAT
*
20667272 ATATAACAGTACAT
1 ACATAACA-TACAT
20667286 AACATAACATAACAT
1 -ACATAACAT-ACAT
* *
20667301 AACAT-ACAAATAT
1 -ACATAACATACAT
20667314 ACAT-ACATAACACT
1 ACATAACAT-ACA-T
20667328 ACATAACATA
1 ACATAACATA
20667338 ACTATAACAA
Statistics
Matches: 125, Mismatches: 11, Indels: 31
0.75 0.07 0.19
Matches are distributed among these distances:
9 5 0.04
10 2 0.02
11 5 0.04
12 40 0.32
13 21 0.17
14 25 0.20
15 27 0.22
ACGTcount: A:0.59, C:0.19, G:0.01, T:0.21
Consensus pattern (13 bp):
ACATAACATACAT
Found at i:20667207 original size:37 final size:36
Alignment explanation
Indices: 20667165--20667339 Score: 134
Period size: 37 Copynumber: 4.8 Consensus size: 36
20667155 ACATAATAGT
20667165 AATATACCACATAACAA-ACATACA-AACATACATACA
1 AATATA-CACATAACAATA-ATACATAACATACATACA
*
20667201 AA-ATATACATAACAATATATAACATAACATACATACA
1 AATATACACATAACAATA-AT-ACATAACATACATACA
*
20667238 AATATACAAACATAACAATAA-ACATAACATACATATA
1 AATATAC--ACATAACAATAATACATAACATACATACA
*
20667275 TAACAGT--ACATAAC-AT-A-ACATAACATAACATACA
1 -AATA-TACACATAACAATAATACATAACAT-ACATACA
*
20667309 AATATACATACATAACACTACATAACATAAC
1 AATATAC--ACATAACAATA-AT-ACATAAC
20667340 TATAACAACC
Statistics
Matches: 113, Mismatches: 8, Indels: 31
0.74 0.05 0.20
Matches are distributed among these distances:
32 1 0.01
33 13 0.12
34 17 0.15
35 13 0.12
36 12 0.11
37 30 0.27
38 6 0.05
39 3 0.03
40 11 0.10
41 7 0.06
ACGTcount: A:0.58, C:0.20, G:0.01, T:0.21
Consensus pattern (36 bp):
AATATACACATAACAATAATACATAACATACATACA
Found at i:20667229 original size:5 final size:5
Alignment explanation
Indices: 20667173--20667346 Score: 108
Period size: 5 Copynumber: 35.6 Consensus size: 5
20667163 GTAATATACC
20667173 ACATA ACA-A ACAT- ACA-A ACAT- ACAT- ACA-A A-ATA TACATA ACA-A
1 ACATA ACATA ACATA ACATA ACATA ACATA ACATA ACATA -ACATA ACATA
* *
20667216 TATATA ACATA ACAT- ACATA CAAATA TACA-A ACATA ACAATAA ACATA
1 -ACATA ACATA ACATA ACATA -ACATA -ACATA ACATA AC-AT-A ACATA
* *
20667264 ACAT- ACAT- ATATA ACAGT- ACATA ACATA ACATA ACATA ACATA CAAATA
1 ACATA ACATA ACATA ACA-TA ACATA ACATA ACATA ACATA ACATA -ACATA
20667313 TACAT- ACATA ACACT- ACATA ACATA ACTATA ACA
1 -ACATA ACATA ACA-TA ACATA ACATA AC-ATA ACA
20667347 ACCCATTTTT
Statistics
Matches: 137, Mismatches: 10, Indels: 44
0.72 0.05 0.23
Matches are distributed among these distances:
3 1 0.01
4 40 0.29
5 65 0.47
6 28 0.20
7 3 0.02
ACGTcount: A:0.59, C:0.20, G:0.01, T:0.21
Consensus pattern (5 bp):
ACATA
Found at i:20667247 original size:65 final size:68
Alignment explanation
Indices: 20667178--20667337 Score: 170
Period size: 70 Copynumber: 2.3 Consensus size: 68
20667168 ATACCACATA
*
20667178 ACAAACATAC-AAACAT-ACATACAAA-ATATACA-TAACA-ATATATAACATAACAT-ACATAC
1 ACAAACATACAAAACATAACATACAAATATA-ACAGT-ACATA-ACATAACATAACATAACATAC
20667237 AAATAT
63 AAATAT
*
20667243 ACAAACATAACAATAAACATAACATACATATATAACAGTACATAACATAACATAACATAACATAC
1 ACAAACAT-AC-A-AAACATAACATACAAATATAACAGTACATAACATAACATAACATAACATAC
20667308 AAATAT
63 AAATAT
* **
20667314 ACATACATAACACTACATAACATA
1 ACAAACAT-ACAAAACATAACATA
20667338 ACTATAACAA
Statistics
Matches: 81, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
65 8 0.10
66 2 0.02
69 16 0.20
70 28 0.35
71 27 0.33
ACGTcount: A:0.59, C:0.19, G:0.01, T:0.21
Consensus pattern (68 bp):
ACAAACATACAAAACATAACATACAAATATAACAGTACATAACATAACATAACATAACATACAAA
TAT
Found at i:20667331 original size:46 final size:48
Alignment explanation
Indices: 20667164--20667346 Score: 148
Period size: 46 Copynumber: 3.8 Consensus size: 48
20667154 CACATAATAG
* * *
20667164 TAATATAC-CACATAACAAACAT-ACA-AACAT-ACATACAAAATATACA
1 TAATATACATACATAACATACATAACATAACATAACATA-ACAATA-ACA
* * *
20667210 TAACAATATATAACATAACATACATACAAATATACA-AACATAACAATAAACA
1 TAA-TATACAT-ACATAACATACATA-ACATA-ACATAACATAACAAT-AACA
* *
20667262 TAACATACATATATAACAGTACATAACATAACATAACATAAC-AT-ACA
1 TAATATACATACATAACA-TACATAACATAACATAACATAACAATAACA
20667309 -AATATACATACATAACACTACATAACATAACTATAACA
1 TAATATACATACATAACA-TACATAACATAAC-ATAACA
20667347 ACCCATTTTT
Statistics
Matches: 112, Mismatches: 13, Indels: 23
0.76 0.09 0.16
Matches are distributed among these distances:
46 31 0.28
47 12 0.11
49 17 0.15
50 19 0.17
51 13 0.12
52 11 0.10
53 9 0.08
ACGTcount: A:0.58, C:0.20, G:0.01, T:0.22
Consensus pattern (48 bp):
TAATATACATACATAACATACATAACATAACATAACATAACAATAACA
Found at i:20668906 original size:13 final size:13
Alignment explanation
Indices: 20668890--20668949 Score: 86
Period size: 13 Copynumber: 4.7 Consensus size: 13
20668880 ACCAAATTTT
20668890 TCAAAAGCACTTC
1 TCAAAAGCACTTC
*
20668903 TCAAAAGCACTTT
1 TCAAAAGCACTTC
*
20668916 TC-ACAGCACTTC
1 TCAAAAGCACTTC
*
20668928 TCAAAAGCACTTT
1 TCAAAAGCACTTC
20668941 TCAAAAGCA
1 TCAAAAGCA
20668950 TTGCTAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
12 10 0.24
13 31 0.76
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.25
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:20668925 original size:25 final size:25
Alignment explanation
Indices: 20668895--20668943 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
20668885 ATTTTTCAAA
20668895 AGCACTTCTCAAAAGCACTTTTCAC
1 AGCACTTCTCAAAAGCACTTTTCAC
20668920 AGCACTTCTCAAAAGCACTTTTCA
1 AGCACTTCTCAAAAGCACTTTTCA
20668944 AAAGCATTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.31, G:0.08, T:0.29
Consensus pattern (25 bp):
AGCACTTCTCAAAAGCACTTTTCAC
Found at i:20672491 original size:43 final size:42
Alignment explanation
Indices: 20672441--20672591 Score: 187
Period size: 43 Copynumber: 3.5 Consensus size: 42
20672431 TATCCCTGAT
* * * * *
20672441 ATGGTCTTATATGTTATCACATATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACATGTAATCACATAT-AATGCCAATGTACCAGAC
* *
20672484 AAGGTCTTACACGTAATCACAATATAATGCCAATGTACCAGGA-
1 ATGGTCTTACATGTAATCAC-ATATAATGCCAATGTACCA-GAC
*
20672527 ATGGTCTTACATGTAATCACAATAAAATGCCAATGTACCAGAC
1 ATGGTCTTACATGTAATCAC-ATATAATGCCAATGTACCAGAC
20672570 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
20672592 TTCTGTAACC
Statistics
Matches: 95, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
42 4 0.04
43 85 0.89
44 6 0.06
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (42 bp):
ATGGTCTTACATGTAATCACATATAATGCCAATGTACCAGAC
Found at i:20674043 original size:10 final size:10
Alignment explanation
Indices: 20674028--20674091 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
20674018 AATAACATCC
20674028 ATACATAACA
1 ATACATAACA
20674038 ATACATAAC-
1 ATACATAACA
**
20674047 ATA-ATAGTA
1 ATACATAACA
20674056 A-ACATAACATA
1 ATACATAAC--A
20674067 CATACATAACA
1 -ATACATAACA
20674078 ATACATAAC-
1 ATACATAACA
20674087 ATACA
1 ATACA
20674092 AAATAGACAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
8 4 0.09
9 12 0.27
10 18 0.41
11 2 0.05
12 1 0.02
13 7 0.16
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.22
Consensus pattern (10 bp):
ATACATAACA
Found at i:20674043 original size:18 final size:18
Alignment explanation
Indices: 20673982--20674091 Score: 66
Period size: 18 Copynumber: 5.9 Consensus size: 18
20673972 TAGGAGTATT
20673982 ACAATAACATACATACA-A
1 ACAAT-ACATACATACATA
* *
20674000 A-TATACAAACATA-ATA
1 ACAATACATACATACATA
** *
20674016 GTAATAACATCCATACATA
1 ACAAT-ACATACATACATA
20674035 ACAATACATAACATA-ATA
1 ACAATACAT-ACATACATA
*
20674053 GTAAACATAACATACATACATA
1 --ACA-AT-ACATACATACATA
20674075 ACAATACATAACATACA
1 ACAATACAT-ACATACA
20674092 AAATAGACAA
Statistics
Matches: 70, Mismatches: 11, Indels: 21
0.69 0.11 0.21
Matches are distributed among these distances:
15 1 0.01
16 9 0.13
17 4 0.06
18 19 0.27
19 19 0.27
20 4 0.06
21 7 0.10
22 7 0.10
ACGTcount: A:0.57, C:0.19, G:0.02, T:0.22
Consensus pattern (18 bp):
ACAATACATACATACATA
Found at i:20674072 original size:40 final size:37
Alignment explanation
Indices: 20673984--20674089 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 37
20673974 GGAGTATTAC
*
20673984 AATAACATACATACA-AA-TATACA-AACATAATAGT
1 AATAACATACATACATAACAATACATAACATAATAGT
*
20674018 AATAACATCCATACATAACAATACATAACATAATAGT
1 AATAACATACATACATAACAATACATAACATAATAGT
20674055 AAACATAACATACATACATAACAATACATAACATA
1 --A-ATAACATACATACATAACAATACATAACATA
20674090 CAAAATAGAC
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
34 14 0.22
35 2 0.03
36 5 0.08
37 11 0.17
39 1 0.02
40 30 0.48
ACGTcount: A:0.58, C:0.18, G:0.02, T:0.23
Consensus pattern (37 bp):
AATAACATACATACATAACAATACATAACATAATAGT
Found at i:20674101 original size:23 final size:23
Alignment explanation
Indices: 20674019--20674101 Score: 72
Period size: 23 Copynumber: 3.9 Consensus size: 23
20674009 CATAATAGTA
* *
20674019 ATAACATCCATACATAACAATAC
1 ATAACATACATAAATAACAATAC
*
20674042 ATAACATA-AT-AGT---AA-AC
1 ATAACATACATAAATAACAATAC
*
20674059 ATAACATACATACATAACAATAC
1 ATAACATACATAAATAACAATAC
20674082 ATAACATACA-AAATAGACAA
1 ATAACATACATAAATA-ACAA
20674102 AACAATTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
17 10 0.21
18 4 0.09
19 1 0.02
21 1 0.02
22 8 0.17
23 23 0.49
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.20
Consensus pattern (23 bp):
ATAACATACATAAATAACAATAC
Found at i:20674290 original size:29 final size:29
Alignment explanation
Indices: 20674229--20674294 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 29
20674219 AATAAAAATA
* *
20674229 AAAAATAAAAGTCAAATATAATATGAATT
1 AAAAATAAAAGTCAAATATAATACGAATC
* *
20674258 AAAAATCAGAAGTCAAATATAATACGTA-C
1 AAAAAT-AAAAGTCAAATATAATACGAATC
20674287 AAAAATAA
1 AAAAATAA
20674295 TTAGTTTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 12 0.39
30 18 0.58
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (29 bp):
AAAAATAAAAGTCAAATATAATACGAATC
Found at i:20678607 original size:37 final size:37
Alignment explanation
Indices: 20678565--20678651 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
20678555 TAGTATTTTA
* *
20678565 TTAATTTAATATTAAAGTGAT-TATCTTAATATTAAAT
1 TTAATTTAATATTAAACTGATAGAT-TTAATATTAAAT
* * *
20678602 TTAATTTAATATTTACCTTATAGATTTAATATTAAAT
1 TTAATTTAATATTAAACTGATAGATTTAATATTAAAT
*
20678639 TTAATCTAATATT
1 TTAATTTAATATT
20678652 TATCTAGATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 41 0.95
38 2 0.05
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (37 bp):
TTAATTTAATATTAAACTGATAGATTTAATATTAAAT
Found at i:20678615 original size:12 final size:12
Alignment explanation
Indices: 20678565--20678653 Score: 56
Period size: 12 Copynumber: 7.2 Consensus size: 12
20678555 TAGTATTTTA
20678565 TTAATTTAATAT
1 TTAATTTAATAT
* * * *
20678577 TAAAGTGATTAT
1 TTAATTTAATAT
20678589 CTTAATATTAA-AT
1 -TTAAT-TTAATAT
20678602 TTAATTTAATAT
1 TTAATTTAATAT
** *
20678614 TTACCTTATAGAT
1 TTAATTTA-ATAT
20678627 TTAATATTAA-AT
1 TTAAT-TTAATAT
*
20678639 TTAATCTAATAT
1 TTAATTTAATAT
20678651 TTA
1 TTA
20678654 TCTAGATAAG
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
11 7 0.12
12 33 0.58
13 12 0.21
14 5 0.09
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (12 bp):
TTAATTTAATAT
Found at i:20688700 original size:305 final size:306
Alignment explanation
Indices: 20688174--20688737 Score: 796
Period size: 305 Copynumber: 1.8 Consensus size: 306
20688164 TTTGGGACTG
* * * * *
20688174 CAAAATTCGAGATATAAATAATTATTTTATGATTATTTTGAGGTCTATGATATGATTGCATGAAT
1 CAAAATCCGAGATAGAAATAATTATTTTATGATTATTTTAAGGTCTATGATATAATTACATGAAT
* *
20688239 GTGTGAAAATTTCGTGAAGAAATTCTATGCATAAAGTGCTCAATTTGAAGTTAGGGACTAAATTG
66 GTGTGAAAATTTCATGAAGAAATTCTATGCATAAAGTGCTCAATTTGAAATTAGGGACTAAATTG
* * * * ** * *
20688304 AATAAGTTGCAAAGCTTTCATTCTAGAAGTTTCTAGTATGAAATTTCTTTGAAATCTTAATTAGG
131 AATAAATTGCAAAACTTTCATTCTAGAAGTTTCTAGCATAAAATTAATTAGAAATATTAATTAGG
* *
20688369 AGGTCTTAAATAGAAATTTGACCAATTTCTAAGCG-ATTGACAAAAATTGGACATGGATGGAATG
196 AGGTCTTAAAGAGAAATTTGACCAATTTCTAAGCGTATGGACAAAAATTGGACATGGATGGAATG
20688433 TAATATCTTGATTTTGGGCCTAGTCGGAATAGTGGTTTCGTGACCA
261 TAATATCTTGATTTTGGGCCTAGTCGGAATAGTGGTTTCGTGACCA
*
20688479 CAAAATCCGAGATAGAAATAATTATTTTATGATTATTTTAAGGTCTATGATATAATTACATGATT
1 CAAAATCCGAGATAGAAATAATTATTTTATGATTATTTTAAGGTCTATGATATAATTACATGAAT
* * *
20688544 GTGTGAAAATTTCATGAAGAAATTTTATGCATAAAGTGCTTAATTTGAAATTTGGGACTAAATTG
66 GTGTGAAAATTTCATGAAGAAATTCTATGCATAAAGTGCTCAATTTGAAATTAGGGACTAAATTG
* * *
20688609 AATAAATTGCAAAACTTGT-GTTCTAGAAGTATT-TTGCATAAAATTGAATTAG-ATTATTAATT
131 AATAAATTGCAAAACTT-TCATTCTAGAAGT-TTCTAGCATAAAATT-AATTAGAAATATTAATT
** * * *
20688671 A-GAGGTCCTTAAAGATTAATTTTACCAATTTTTAAGTGTATGGACAAAAATTGGACATGGATGG
193 AGGAGGT-CTTAAAGAGAAATTTGACCAATTTCTAAGCGTATGGACAAAAATTGGACATGGATGG
20688735 AAT
257 AAT
20688738 TTTTGGAAAG
Statistics
Matches: 225, Mismatches: 29, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
304 5 0.02
305 187 0.83
306 33 0.15
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (306 bp):
CAAAATCCGAGATAGAAATAATTATTTTATGATTATTTTAAGGTCTATGATATAATTACATGAAT
GTGTGAAAATTTCATGAAGAAATTCTATGCATAAAGTGCTCAATTTGAAATTAGGGACTAAATTG
AATAAATTGCAAAACTTTCATTCTAGAAGTTTCTAGCATAAAATTAATTAGAAATATTAATTAGG
AGGTCTTAAAGAGAAATTTGACCAATTTCTAAGCGTATGGACAAAAATTGGACATGGATGGAATG
TAATATCTTGATTTTGGGCCTAGTCGGAATAGTGGTTTCGTGACCA
Found at i:20689772 original size:46 final size:48
Alignment explanation
Indices: 20689718--20689851 Score: 152
Period size: 46 Copynumber: 2.9 Consensus size: 48
20689708 TGGATATTTG
20689718 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-CGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGACGA
* * * * * *
20689765 -GCGTCCGAACTCGTTGAGTTGAGTTCAAGTTC-GTGA--GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG--ACGA
*
20689811 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20689852 GCGGGTTACA
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
43 4 0.06
45 2 0.03
46 31 0.46
47 28 0.41
48 2 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (48 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGACGA
Found at i:20691708 original size:30 final size:30
Alignment explanation
Indices: 20691674--20691732 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
20691664 CCCGAGCCTA
20691674 GGGGCAAAAGTGTAAATATGCAAAAGTTTC
1 GGGGCAAAAGTGTAAATATGCAAAAGTTTC
* * * *
20691704 GGGGCAAAATTGTAATTTTTCAAAAGTTT
1 GGGGCAAAAGTGTAAATATGCAAAAGTTT
20691733 GAGTTAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAGTGTAAATATGCAAAAGTTTC
Found at i:20703684 original size:20 final size:20
Alignment explanation
Indices: 20703639--20703685 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 20
20703629 TTTTATTAAT
*
20703639 TTAATATTAAATTGATTATC
1 TTAATATTAAAGTGATTATC
20703659 ----TATTAAAGTGATTATC
1 TTAATATTAAAGTGATTATC
20703675 TTAATATTAAA
1 TTAATATTAAA
20703686 TTAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 8
0.71 0.03 0.26
Matches are distributed among these distances:
16 15 0.68
20 7 0.32
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (20 bp):
TTAATATTAAAGTGATTATC
Found at i:20709495 original size:14 final size:15
Alignment explanation
Indices: 20709478--20709506 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20709468 AATCCTAACT
20709478 GCAAAAT-AAATTAA
1 GCAAAATAAAATTAA
20709492 GCAAAATAAAATTAA
1 GCAAAATAAAATTAA
20709507 ATGGATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (15 bp):
GCAAAATAAAATTAA
Found at i:20709782 original size:19 final size:19
Alignment explanation
Indices: 20709758--20709800 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
20709748 CTGAAAAGCC
*
20709758 CAACTCAAATCAACGGCCT
1 CAACTCAAATCAACGACCT
* *
20709777 CAACTCGAATCAATGACCT
1 CAACTCAAATCAACGACCT
20709796 CAACT
1 CAACT
20709801 GTGCGGGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.35, G:0.09, T:0.19
Consensus pattern (19 bp):
CAACTCAAATCAACGACCT
Found at i:20710534 original size:40 final size:41
Alignment explanation
Indices: 20710489--20710582 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 41
20710479 AAAAATCTTC
* * *
20710489 CAATCTTTATCCAGCT-ACTTTTTTTAAATCTCCAACCCTA
1 CAATCTTTATCCAGATCACTTTTTTAAAATCTCCAACCATA
* *
20710529 CAATCTTTATCCA-ATCACTTTTTTAAAATCTTCAACCATT
1 CAATCTTTATCCAGATCACTTTTTTAAAATCTCCAACCATA
20710569 CAATCTTTATCCAG
1 CAATCTTTATCCAG
20710583 GCAACTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
39 1 0.02
40 46 0.98
ACGTcount: A:0.30, C:0.28, G:0.02, T:0.40
Consensus pattern (41 bp):
CAATCTTTATCCAGATCACTTTTTTAAAATCTCCAACCATA
Found at i:20717306 original size:38 final size:38
Alignment explanation
Indices: 20717264--20717340 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
20717254 ACCCAACGTG
* *
20717264 TACTTTTTGAACCGAAGCGATCAACTTTAAGGGACAAA
1 TACTTTTTGAACCGAAGCAATCAACTTTAAAGGACAAA
20717302 TACTTTTTGAACCGAAGCAATCAACTTTAAAGGACAAA
1 TACTTTTTGAACCGAAGCAATCAACTTTAAAGGACAAA
20717340 T
1 T
20717341 TTGTACTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (38 bp):
TACTTTTTGAACCGAAGCAATCAACTTTAAAGGACAAA
Found at i:20717918 original size:37 final size:38
Alignment explanation
Indices: 20717832--20717920 Score: 101
Period size: 37 Copynumber: 2.3 Consensus size: 38
20717822 AAATATAAAA
* *
20717832 AATCCTTCAATCTTTATCCAACCACTTTTTTTAAATCTTC
1 AATCTTTCAATCTTTATCCAACCA--TATTTTAAATCTTC
* *
20717872 AA-CTATTCAATCTTTATCCAGCCA-ATTTTAAATCTTG
1 AATCT-TTCAATCTTTATCCAACCATATTTTAAATCTTC
20717909 AATCTTTCAATC
1 AATCTTTCAATC
20717921 AAACCCTCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
37 20 0.47
38 2 0.05
39 1 0.02
40 20 0.47
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.43
Consensus pattern (38 bp):
AATCTTTCAATCTTTATCCAACCATATTTTAAATCTTC
Found at i:20721733 original size:32 final size:32
Alignment explanation
Indices: 20721686--20721788 Score: 97
Period size: 32 Copynumber: 3.3 Consensus size: 32
20721676 TAGATTTTTC
*
20721686 CCACAAAGGCATTCATTAACATTCAGTAATCG
1 CCACAAAGGTATTCATTAACATTCAGTAATCG
* * * *
20721718 CCACAAAGGTTTTCATGT-CCA--AAGT-ATTG
1 CCACAAAGGTATTCAT-TAACATTCAGTAATCG
* * *
20721747 CCACAAAGGAATTCATTAACATTCAGTACTCA
1 CCACAAAGGTATTCATTAACATTCAGTAATCG
20721779 CCACAAAGGT
1 CCACAAAGGT
20721789 TTTCTTGTCC
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
28 1 0.02
29 19 0.36
30 3 0.06
31 3 0.06
32 26 0.49
33 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (32 bp):
CCACAAAGGTATTCATTAACATTCAGTAATCG
Found at i:20721762 original size:61 final size:61
Alignment explanation
Indices: 20721686--20721821 Score: 218
Period size: 61 Copynumber: 2.2 Consensus size: 61
20721676 TAGATTTTTC
*
20721686 CCACAAAGGCATTCATTAACATTCAGTAATCGCCACAAAGGTTTTCATGTCCAAAGTATTG
1 CCACAAAGGCATTCATTAACATTCAGTAATCACCACAAAGGTTTTCATGTCCAAAGTATTG
* * * *
20721747 CCACAAAGGAATTCATTAACATTCAGTACTCACCACAAAGGTTTTCTTGTCCAGAGTATTG
1 CCACAAAGGCATTCATTAACATTCAGTAATCACCACAAAGGTTTTCATGTCCAAAGTATTG
*
20721808 TCACAAAGGCATTC
1 CCACAAAGGCATTC
20721822 CTTCCCGTGG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (61 bp):
CCACAAAGGCATTCATTAACATTCAGTAATCACCACAAAGGTTTTCATGTCCAAAGTATTG
Found at i:20728109 original size:25 final size:25
Alignment explanation
Indices: 20728027--20728110 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
20728017 CTTTCCAATA
* * *
20728027 TGCAAGCTGCAAGCTCAACAAAAATG
1 TGCAAGCTGCAAGCTTAGCAAGAA-G
* *
20728053 TGCAAACTGCAAGCTTAGCAAGATG
1 TGCAAGCTGCAAGCTTAGCAAGAAG
*
20728078 T-CAAAGCTGCAAGCTTAGCGAGAAG
1 TGC-AAGCTGCAAGCTTAGCAAGAAG
20728103 TGCAAGCT
1 TGCAAGCT
20728111 ATGAGCTCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.02
25 27 0.56
26 20 0.42
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (25 bp):
TGCAAGCTGCAAGCTTAGCAAGAAG
Found at i:20728286 original size:80 final size:79
Alignment explanation
Indices: 20728153--20728309 Score: 278
Period size: 80 Copynumber: 2.0 Consensus size: 79
20728143 GTTGCGAGCC
20728153 AAGACACCTTAAGAGACAGTAAGCAAAAATGCGAGCCTGTCAAAGGTGCAAGCTCAGCCTAGTGC
1 AAGACACCTTAAGAGACAGTAAGCAAAAATGCGAGCCTGTCAAAGGTGCAAGCTCAGCCTAGTGC
*
20728218 GAGCAGCAAAGTTG
66 GAGCAACAAAGTTG
* *
20728232 AAGACACCTTAAGAGACAGTAAGCAAAAAATGTGAGCCTGTCAAAGGTGCAAGCTCAGCCTGGTG
1 AAGACACCTTAAGAGACAGTAAGC-AAAAATGCGAGCCTGTCAAAGGTGCAAGCTCAGCCTAGTG
20728297 CGAGCAACAAAGT
65 CGAGCAACAAAGT
20728310 GCAAACCTGT
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
79 24 0.32
80 50 0.68
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (79 bp):
AAGACACCTTAAGAGACAGTAAGCAAAAATGCGAGCCTGTCAAAGGTGCAAGCTCAGCCTAGTGC
GAGCAACAAAGTTG
Found at i:20731244 original size:27 final size:27
Alignment explanation
Indices: 20731213--20731271 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
20731203 CTAATGAGAT
* *
20731213 AAGAATATTGGTTCAACAATTAATGTA
1 AAGAATATTGATTAAACAATTAATGTA
20731240 AAGAATATTGATTAAACAATTAATGTA
1 AAGAATATTGATTAAACAATTAATGTA
20731267 AAGAA
1 AAGAA
20731272 GTTTTAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.31
Consensus pattern (27 bp):
AAGAATATTGATTAAACAATTAATGTA
Found at i:20736032 original size:13 final size:13
Alignment explanation
Indices: 20736014--20736038 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20736004 AAAGAAAAAT
20736014 AAAATAAATAATA
1 AAAATAAATAATA
20736027 AAAATAAATAAT
1 AAAATAAATAAT
20736039 GACAATGATA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:20736059 original size:21 final size:20
Alignment explanation
Indices: 20736027--20736074 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 20
20736017 ATAAATAATA
20736027 AAAATAAATAATGAC-AATGAT
1 AAAAT-AATAAT-ACTAATGAT
20736048 AACAATAATAATACTAATGAT
1 AA-AATAATAATACTAATGAT
20736069 AAAATA
1 AAAATA
20736075 CGCCCATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.24
21 16 0.64
22 3 0.12
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.25
Consensus pattern (20 bp):
AAAATAATAATACTAATGAT
Found at i:20736331 original size:18 final size:18
Alignment explanation
Indices: 20736324--20736363 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20736314 TAAATAGATA
20736324 ATAATAAAACAATAATAG
1 ATAATAAAACAATAATAG
* *
20736342 ATAATAAAATAGTAATA-
1 ATAATAAAACAATAATAG
20736359 ATAAT
1 ATAAT
20736364 GAAGCCATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (18 bp):
ATAATAAAACAATAATAG
Found at i:20737351 original size:5 final size:5
Alignment explanation
Indices: 20737341--20737372 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
20737331 TTTTATGCCA
20737341 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
20737373 TAACAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:20745651 original size:16 final size:16
Alignment explanation
Indices: 20745630--20745660 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20745620 AACTTATGAT
20745630 ATATCAACAATAATTC
1 ATATCAACAATAATTC
20745646 ATATCAACAATAATT
1 ATATCAACAATAATT
20745661 ATAGATCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (16 bp):
ATATCAACAATAATTC
Found at i:20745690 original size:33 final size:32
Alignment explanation
Indices: 20745632--20745694 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 32
20745622 CTTATGATAT
20745632 ATCAACAATAATTCATATCAACAATAATTATAG
1 ATCAACAATAATTCATATCAACAAT-ATTATAG
*
20745665 ATCAATCAA-AATTCAT-TCGATCAATATTAT
1 ATCAA-CAATAATTCATATC-AACAATATTAT
20745695 GAGAAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 7 0.26
33 17 0.63
34 3 0.11
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (32 bp):
ATCAACAATAATTCATATCAACAATATTATAG
Found at i:20746187 original size:6 final size:6
Alignment explanation
Indices: 20746178--20746209 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
20746168 AATAAAATTG
*
20746178 AAATGA AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AA
20746210 GGATAGGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:20751628 original size:13 final size:13
Alignment explanation
Indices: 20751610--20751638 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
20751600 GGTTGTTTAT
20751610 TAAACTAATTAAC
1 TAAACTAATTAAC
20751623 TAAACTAATTAAC
1 TAAACTAATTAAC
20751636 TAA
1 TAA
20751639 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:20756319 original size:13 final size:13
Alignment explanation
Indices: 20756301--20756338 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
20756291 CATCAGAGTA
20756301 CTTTTAGGAAACC
1 CTTTTAGGAAACC
20756314 CTTTTAGGAAACC
1 CTTTTAGGAAACC
20756327 CTTTTAGGAAAC
1 CTTTTAGGAAAC
20756339 TTTATCAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (13 bp):
CTTTTAGGAAACC
Found at i:20762829 original size:50 final size:50
Alignment explanation
Indices: 20762763--20762894 Score: 185
Period size: 50 Copynumber: 2.6 Consensus size: 50
20762753 CACATAGTGA
* * * *
20762763 GATGCCAATGCCATGTCCCATATATGGTCTTACATTG-GTTCACACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTAC-GTGAGATCACACATATC
*
20762813 GATGCCAATGCCATGTCCCAGACATGGTCTTACGTGAGATCGCACATATC
1 GATGCCAATGCCATGTCCCAGACATGGTCTTACGTGAGATCACACATATC
* *
20762863 GATGCCAATGCCATCTCCCCGACATGGTCTTA
1 GATGCCAATGCCATGTCCCAGACATGGTCTTA
20762895 TATGGGATCA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
49 2 0.03
50 72 0.97
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (50 bp):
GATGCCAATGCCATGTCCCAGACATGGTCTTACGTGAGATCACACATATC
Found at i:20765948 original size:40 final size:40
Alignment explanation
Indices: 20765826--20765934 Score: 157
Period size: 40 Copynumber: 2.7 Consensus size: 40
20765816 TATTCGGATG
*
20765826 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
20765866 A-AATTCGGGCTAAGTCCTGAAGGCATTGGTGCGAGTTACT
1 ATAA-CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
20765906 ATAACCGGGCTATGTCCCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
20765935 AGTGAGTAGC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.03
40 55 0.93
41 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:20769419 original size:46 final size:44
Alignment explanation
Indices: 20769361--20769488 Score: 141
Period size: 46 Copynumber: 2.8 Consensus size: 44
20769351 ATATCTCGAG
*
20769361 GCCGATGCATGTCCTAGACATGTCTTACACTGGCTCTCGTCTCA-AA
1 GCCGATGCATGTCC-AGACATGTCTTACACTGGCTCTC-ACT-AGAA
* * * **
20769407 GCTGATGCATGTCCCAGAGATGTCTTACACTGGCTTTCACTATGTG
1 GCCGATGCATGT-CCAGACATGTCTTACACTGGCTCTCACTA-GAA
20769453 GCCGATGCATGTTCCAGACATGTCTTACACTGGCTC
1 GCCGATGCATG-TCCAGACATGTCTTACACTGGCTC
20769489 ACATATCACC
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
44 1 0.01
45 2 0.03
46 63 0.91
47 3 0.04
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.30
Consensus pattern (44 bp):
GCCGATGCATGTCCAGACATGTCTTACACTGGCTCTCACTAGAA
Found at i:20782667 original size:27 final size:26
Alignment explanation
Indices: 20782604--20782674 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
20782594 AGCATAACTG
20782604 CCAGAAACAGTAAATGTGGCAGCCCA
1 CCAGAAACAGTAAATGTGGCAGCCCA
* * * *
20782630 CTAGTATCAGTAATTGTGGCATAG-CCA
1 CCAGAAACAGTAAATGTGGC--AGCCCA
20782657 CCAGAAACAGTAAATGTG
1 CCAGAAACAGTAAATGTG
20782675 ACAAAGTCAC
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
26 16 0.46
27 17 0.49
28 2 0.06
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.20
Consensus pattern (26 bp):
CCAGAAACAGTAAATGTGGCAGCCCA
Found at i:20782860 original size:27 final size:27
Alignment explanation
Indices: 20782830--20783081 Score: 339
Period size: 27 Copynumber: 9.4 Consensus size: 27
20782820 GGGCATAATT
* *
20782830 GTCATTTTACCATACAGGGGTATTGCG
1 GTCATTTTACCCTACAGGGGTATTACG
*
20782857 GTCA-TTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTACG
*
20782883 GTCATTTTACCCTACAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
*
20782910 GTCA-TTTACCCTACAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTACG
*
20782936 GTCATTTTACCCTACA-GGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* *
20782962 GTCATTTTACCCTACAAGGGTACTACG
1 GTCATTTTACCCTACAGGGGTATTACG
*
20782989 GTCATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * * *
20783016 GTCATTTTGCCCTATAAGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTACG
* * *
20783043 GTGATTTTACCCTACAGGGGTACTACA
1 GTCATTTTACCCTACAGGGGTATTACG
20783070 GTCATTTTACCC
1 GTCATTTTACCC
20783082 ACGCGACCTA
Statistics
Matches: 199, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
26 71 0.36
27 128 0.64
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACG
Found at i:20782912 original size:53 final size:54
Alignment explanation
Indices: 20782816--20783081 Score: 358
Period size: 53 Copynumber: 5.0 Consensus size: 54
20782806 CATACGAAAC
* * * * *
20782816 ACAAGGGCATAATTGTCATTTTACCATACAGGGGTATTGCGGTCA-TTTACCCT
1 ACAAGGGTATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCT
* *
20782869 ACAGGGGTATTATGGTCATTTTACCCTACAGGGGCATTACGGTCA-TTTACCCT
1 ACAAGGGTATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCT
* *
20782922 ACAGGGGTATTATGGTCATTTTACCCTACA-GGGCATTACGGTCATTTTACCCT
1 ACAAGGGTATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCT
* * * *
20782975 ACAAGGGTACTACGGTCATTTTACCCTACAAGGGTATTACGGTCATTTTGCCCT
1 ACAAGGGTATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCT
* * * *
20783029 ATAAGGGTATTATGGTGATTTTACCCTACAGGGGTACTACAGTCATTTTACCC
1 ACAAGGGTATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCC
20783082 ACGCGACCTA
Statistics
Matches: 191, Mismatches: 20, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
52 14 0.07
53 111 0.58
54 66 0.35
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (54 bp):
ACAAGGGTATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCT
Found at i:20785109 original size:35 final size:35
Alignment explanation
Indices: 20785070--20785190 Score: 136
Period size: 35 Copynumber: 3.4 Consensus size: 35
20785060 CTATTTTGGA
* *
20785070 GTGTTTCGGTTGGATTAACTCTTATAAGCATTAGT
1 GTGTTTCGGATGGATTAACTCTTATGAGCATTAGT
* *
20785105 GTGTTTCAGATGGACTAGA-TCTTATGAGCATTAGT
1 GTGTTTCGGATGGATTA-ACTCTTATGAGCATTAGT
* * *
20785140 GTGTTTCGGATGGATTAGCTCTTATGAGTATCTGGT
1 GTGTTTCGGATGGATTAACTCTTATGAGCAT-TAGT
* *
20785176 GTTTTTCGGTTGGAT
1 GTGTTTCGGATGGAT
20785191 GATCAATGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
35 55 0.76
36 17 0.24
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.42
Consensus pattern (35 bp):
GTGTTTCGGATGGATTAACTCTTATGAGCATTAGT
Found at i:20788405 original size:41 final size:41
Alignment explanation
Indices: 20788358--20788442 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
20788348 ATGAAGTAAA
20788358 CATAGTTGAGCTCATCATGCAATATTCTTTCAAGTAATTAT
1 CATAGTTGAGCTCATCATGCAATATTCTTTCAAGTAATTAT
*
20788399 CATAGTTGAGCTCATCATGCAATATTCTTTCAAGTCATTAT
1 CATAGTTGAGCTCATCATGCAATATTCTTTCAAGTAATTAT
20788440 CAT
1 CAT
20788443 TTCATCTCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (41 bp):
CATAGTTGAGCTCATCATGCAATATTCTTTCAAGTAATTAT
Found at i:20792200 original size:20 final size:20
Alignment explanation
Indices: 20792175--20792217 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
20792165 ATTTACCCAA
20792175 GAGTGATATGCTGGTATTTT
1 GAGTGATATGCTGGTATTTT
20792195 GAGTGATATGCTGGTATTTT
1 GAGTGATATGCTGGTATTTT
20792215 GAG
1 GAG
20792218 GTTTAATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.05, G:0.33, T:0.42
Consensus pattern (20 bp):
GAGTGATATGCTGGTATTTT
Found at i:20797336 original size:37 final size:42
Alignment explanation
Indices: 20797262--20797341 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
20797252 AGGGTAAATC
*
20797262 CAACAACCCAAGTTTATCTTCTCTTTTTTAAAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCTTTTTTAAAATTCTTTTTT
20797304 CAACAACCCAAGATT-TC-T-TC-TTTTT-AAATTCTTTTTT
1 CAACAACCCAAGATTATCTTCTCTTTTTTAAAATTCTTTTTT
20797341 C
1 C
20797342 TAGGATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 13 0.35
38 5 0.14
39 2 0.05
40 1 0.03
41 2 0.05
42 14 0.38
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (42 bp):
CAACAACCCAAGATTATCTTCTCTTTTTTAAAATTCTTTTTT
Found at i:20802658 original size:55 final size:53
Alignment explanation
Indices: 20802550--20802845 Score: 252
Period size: 49 Copynumber: 5.7 Consensus size: 53
20802540 ATTAGGGTTT
* * * *
20802550 AAGGATACCATGTAAGACGATGCCAAGGCATGGCAATTGGTAAGGTT-TCTAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGC-ATTGATAA-GTTCT-TAAGGC
* * *
20802605 AAGGAAATCATGTAAGACCATGTCAAGACATGTCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTT-CT-TAAGGC
* * * * *
20802660 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCTTAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTTAAGGC
* * * *
20802713 AAGGATACCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTT-TCAA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTTAAGGC
* * * * * *
20802762 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAGTT-TCAA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTTAAGGC
* *
20802811 AAGGATACCATGTAAGACCATGACAAGTCATGGCA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCA
20802846 ATGGTAAGGT
Statistics
Matches: 209, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
49 79 0.38
52 7 0.03
53 43 0.21
54 9 0.04
55 67 0.32
56 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTCTTAAGGC
Found at i:20802794 original size:49 final size:49
Alignment explanation
Indices: 20802667--20802853 Score: 257
Period size: 49 Copynumber: 3.7 Consensus size: 49
20802657 GGCAAAGGTC
* * * * *
20802667 CCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCTTAAGGCAAGGATA
1 CCATGTAAGACCATGACAAGTCATGGCAATGGTAAGTT-TCAA---AAGGATA
* * *
20802720 CCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTCAAAAGGATA
1 CCATGTAAGACCATGACAAGTCATGGCAATGGTAAGTTTCAAAAGGATA
*
20802769 CCACGTAAGACCATGACAAGTCATGGCAATGGTAAGTTTCAAAAGGATA
1 CCATGTAAGACCATGACAAGTCATGGCAATGGTAAGTTTCAAAAGGATA
20802818 CCATGTAAGACCATGACAAGTCATGGCAATGGTAAG
1 CCATGTAAGACCATGACAAGTCATGGCAATGGTAAG
20802854 GTACCCGTGT
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
49 87 0.71
52 3 0.02
53 33 0.27
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.21
Consensus pattern (49 bp):
CCATGTAAGACCATGACAAGTCATGGCAATGGTAAGTTTCAAAAGGATA
Found at i:20802815 original size:98 final size:100
Alignment explanation
Indices: 20802550--20802853 Score: 315
Period size: 108 Copynumber: 2.9 Consensus size: 100
20802540 ATTAGGGTTT
* * *
20802550 AAGGATACCATGTAAGACGATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAA-TGGTAA-GTTTC-AA-G-AAGGATACCA
* * * *
20802615 TGTAAGACCATGTCAAGACATGTCATTGATAAGTTACTAT
61 TGTAAGACCATGTCAAGACATGGCAATGGTAAGTTACTAA
* * * *
20802655 AAGGCAAAGGTCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCTTAAGGCAAGGATA
1 AAGG---A--TACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGTT-TCAA-G-AAGGATA
* *
20802720 CCATGTAAGACCATGTCGAGACATGGCAATGGTAAGTTTC-AA
58 CCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTTACTAA
* * *
20802762 AAGGATACCACGTAAGACCATGACAAGTCATGGCAATGGTAAGTTTCAA-AAGGATACCATGTAA
1 AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCAAGAAGGATACCATGTAA
* *
20802826 GACCATGACAAGTCATGGCAATGGTAAG
66 GACCATGTCAAGACATGGCAATGGTAAG
20802854 GTACCCGTGT
Statistics
Matches: 170, Mismatches: 23, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
98 40 0.24
101 3 0.02
102 34 0.20
104 1 0.01
105 4 0.02
107 5 0.03
108 49 0.29
109 6 0.04
110 28 0.16
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (100 bp):
AAGGATACCATGTAAGACCATGCCAAGGCATGGCAATGGTAAGTTTCAAGAAGGATACCATGTAA
GACCATGTCAAGACATGGCAATGGTAAGTTACTAA
Found at i:20803066 original size:16 final size:16
Alignment explanation
Indices: 20803045--20803075 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20803035 ATAAATTTGA
20803045 TTAAGTAAGTAAGTAT
1 TTAAGTAAGTAAGTAT
*
20803061 TTAAGTAAGTGAGTA
1 TTAAGTAAGTAAGTA
20803076 AGTGAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (16 bp):
TTAAGTAAGTAAGTAT
Found at i:20815679 original size:21 final size:21
Alignment explanation
Indices: 20815654--20815694 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20815644 TTATGGTTAT
*
20815654 GGTTTAATGTTTAGTATTTTG
1 GGTTTAAGGTTTAGTATTTTG
* *
20815675 GGTTTAGGGTTTAGTGTTTT
1 GGTTTAAGGTTTAGTATTTT
20815695 AAAGCTTATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (21 bp):
GGTTTAAGGTTTAGTATTTTG
Found at i:20815785 original size:22 final size:23
Alignment explanation
Indices: 20815750--20815792 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
20815740 GTCTTAGTGT
20815750 TTAGGGTTTTAAGGGTCAGGGTA
1 TTAGGGTTTTAAGGGTCAGGGTA
*
20815773 TTAGGG-TTTAAGGGTTAGGG
1 TTAGGGTTTTAAGGGTCAGGG
20815793 ATTTTGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.21, C:0.02, G:0.42, T:0.35
Consensus pattern (23 bp):
TTAGGGTTTTAAGGGTCAGGGTA
Found at i:20815917 original size:7 final size:7
Alignment explanation
Indices: 20815907--20815961 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
20815897 GGTGTATAGC
20815907 TTAGGGT
1 TTAGGGT
20815914 TTAGGGT
1 TTAGGGT
*
20815921 TTAAGGT
1 TTAGGGT
* *
20815928 ATATGGT
1 TTAGGGT
20815935 TTAGGGT
1 TTAGGGT
* *
20815942 CTAAGGT
1 TTAGGGT
*
20815949 CTAGGGT
1 TTAGGGT
20815956 TTAGGG
1 TTAGGG
20815962 ATAAAATTTG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.20, C:0.04, G:0.38, T:0.38
Consensus pattern (7 bp):
TTAGGGT
Found at i:20815935 original size:21 final size:21
Alignment explanation
Indices: 20815885--20815961 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
20815875 TTGTAACATA
* * *
20815885 TATAGGGCTTAGGGTGTATAGC
1 TATAGGGTTTAGGGTCTA-AGG
*
20815907 T-TAGGGTTTAGGGTTTAAGG
1 TATAGGGTTTAGGGTCTAAGG
*
20815927 TATATGGTTTAGGGTCTAAGG
1 TATAGGGTTTAGGGTCTAAGG
*
20815948 TCTAGGGTTTAGGG
1 TATAGGGTTTAGGG
20815962 ATAAAATTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
20 3 0.06
21 43 0.91
22 1 0.02
ACGTcount: A:0.21, C:0.05, G:0.38, T:0.36
Consensus pattern (21 bp):
TATAGGGTTTAGGGTCTAAGG
Found at i:20819065 original size:43 final size:42
Alignment explanation
Indices: 20819008--20819283 Score: 169
Period size: 43 Copynumber: 6.5 Consensus size: 42
20818998 AAAGCGCCAT
* * * * *
20819008 TAAAGCTCACGTTCTATAGCAGCCTTTTTAGTAAAAGCATCGC
1 TAAAGGTCATGTTCTATAGCAGCGTTTGT-GTAAAAGCACCGC
* ***
20819051 TAAAGGTCATGTTCTATAGCAACGTTTGTGGGGAAGCACCGC
1 TAAAGGTCATGTTCTATAGCAGCGTTTGTGTAAAAGCACCGC
* * * * * ***
20819093 TAAAGGTTACGCTCTATAGCGGCATTTGTGTGAAAAGTGTCGC
1 TAAAGGTCATGTTCTATAGCAGCGTTTGTGT-AAAAGCACCGC
* * * * * *
20819136 TAAAGGTCATGTTCCACAACGGTGGTTGTAGTAAAAGCACCGC
1 TAAAGGTCATGTTCTATAGCAGCGTTTGT-GTAAAAGCACCGC
* *** *
20819179 TAAAGGTCATGTTCTATAGCGGCGTTTGTGGTAAAAATGCCAC
1 TAAAGGTCATGTTCTATAGCAGCGTTTGT-GTAAAAGCACCGC
* * * *
20819222 TAAAAGTCATGTTCTATTGTGACA-CTTTTGGGT-AAAGCACCGC
1 TAAAGGTCATGTTCTA-T-AG-CAGCGTTTGTGTAAAAGCACCGC
**
20819265 TAAATATCATGTTCTATAG
1 TAAAGGTCATGTTCTATAG
20819284 TGGCATTGCA
Statistics
Matches: 173, Mismatches: 55, Indels: 12
0.72 0.23 0.05
Matches are distributed among these distances:
41 1 0.01
42 34 0.20
43 126 0.73
44 5 0.03
45 6 0.03
46 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
TAAAGGTCATGTTCTATAGCAGCGTTTGTGTAAAAGCACCGC
Found at i:20820199 original size:14 final size:14
Alignment explanation
Indices: 20820180--20820212 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
20820170 ATTCAACAAG
20820180 GCATATCATTACTT
1 GCATATCATTACTT
20820194 GCATATCATTACTT
1 GCATATCATTACTT
20820208 GCATA
1 GCATA
20820213 CATGTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.39
Consensus pattern (14 bp):
GCATATCATTACTT
Found at i:20821572 original size:42 final size:45
Alignment explanation
Indices: 20821461--20821579 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 45
20821451 ATGTGTTTTT
*
20821461 TGTAAGACCACGTCTGGGACATTGGCATCG-A-CTTATGATTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGTATCTTA-GATTTACA
* * *
20821505 TGTAAGACCACATTTGGGACGTTGGCATCGTATC-TA-ATTT-CA
1 TGTAAGACCACGTCTGGGACATTGGCATCGTATCTTAGATTTACA
* *
20821547 TGTAAGACCACGTCTAGGACATTGGCATTGTAT
1 TGTAAGACCACGTCTGGGACATTGGCATCGTAT
20821580 GAGTTTTTCG
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
42 29 0.45
43 4 0.06
44 27 0.42
45 3 0.05
46 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (45 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGTATCTTAGATTTACA
Found at i:20833592 original size:29 final size:28
Alignment explanation
Indices: 20833507--20833621 Score: 115
Period size: 29 Copynumber: 4.0 Consensus size: 28
20833497 TACCTGTATT
*
20833507 TGGCCCATTAAGG-CCAATCATATTTATA
1 TGGCCCATT-AGGCCCAATCACATTTATA
* * *
20833535 TAGCCCATTAGGCCCAAATCACCTATATA
1 TGGCCCATTAGGCCC-AATCACATTTATA
20833564 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCC-AATCACATTTATA
* * * * *
20833593 TGACCCGTTGGGCCCAGTCACATTCATA
1 TGGCCCATTAGGCCCAATCACATTTATA
20833621 T
1 T
20833622 TCATGCTCAC
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
27 3 0.04
28 22 0.30
29 48 0.66
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (28 bp):
TGGCCCATTAGGCCCAATCACATTTATA
Found at i:20839450 original size:20 final size:20
Alignment explanation
Indices: 20839417--20839454 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20839407 ACTAATTGTG
*
20839417 CATGTTATGCTTAAATGTTT
1 CATGTGATGCTTAAATGTTT
*
20839437 CATGTGATGGTTAAATGT
1 CATGTGATGCTTAAATGT
20839455 GGTATATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (20 bp):
CATGTGATGCTTAAATGTTT
Found at i:20842952 original size:46 final size:46
Alignment explanation
Indices: 20842803--20843078 Score: 212
Period size: 46 Copynumber: 5.9 Consensus size: 46
20842793 TTGGGTCTTT
* * * *
20842803 TGTATGCTAG-GTAAGACATGTCTGGGACATGCATCGGCCACATTA
1 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGA
* * *
20842848 TG-AGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCAT--TGA
1 TGTA-AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGTGA
* * * *
20842894 GGCGAGAGCTAGTGTAAGACATGTCTTGGACATGCATCTGCCTCGTGA
1 TG-TA-AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGA
*
20842942 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGA
1 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGTGA
*
20842988 TGT--GTTAGTGTAAGACCATGTCTGGGACATGGCATCGG--TACG-GATA
1 TGTAAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCT-CGTG--A
* * *
20843034 TGGAGAGCAAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTC
1 TGTA-AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTC
20843079 AATTTTGATA
Statistics
Matches: 191, Mismatches: 22, Indels: 31
0.78 0.09 0.13
Matches are distributed among these distances:
44 13 0.07
45 26 0.14
46 66 0.35
47 26 0.14
48 26 0.14
49 32 0.17
50 1 0.01
51 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (46 bp):
TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGTGA
Found at i:20843057 original size:49 final size:48
Alignment explanation
Indices: 20842808--20843170 Score: 223
Period size: 49 Copynumber: 7.7 Consensus size: 48
20842798 TCTTTTGTAT
*
20842808 GCTAG-GTAAGA-CATGTCTGGGACAT-GCATCGGCCAC-ATTAT-GAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-TACGA-TATGGAGA
* * *
20842853 GCCAGTGTAAGACCATGTTTGGGACATGGCATCGG--C-ATTGAGGCGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGTACGA-T-ATG-GAGA
* * *
20842901 GCTAGTGTAAGA-CATGTCTTGGACAT-GCATCTGCCT-CG-TGATGTA-A
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC-G-GTACGAT-ATGGAGA
* *
20842947 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGAT---GT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-TACGATATGGAGA
*
20842991 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGGTACGGATATGGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGTAC-GATATGGAGA
* * * * * *
20843040 GCAAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCT-CAATTTTGATA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG--TACGATATGGAGA
* * * * *
20843089 G-TCAATGTAAGACCATGTCTGAGACATGGCATC-G-AC-TTGATGAACAA
1 GCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGTACGAT-ATGGA-GA
* *
20843136 GCCAGTGTAAGACCGTGTCTGGGACATGGCATCGG
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG
20843171 CATTATACCT
Statistics
Matches: 254, Mismatches: 36, Indels: 53
0.74 0.10 0.15
Matches are distributed among these distances:
44 11 0.04
45 28 0.11
46 61 0.24
47 56 0.22
48 28 0.11
49 68 0.27
50 1 0.00
51 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGTACGATATGGAGA
Found at i:20843057 original size:140 final size:138
Alignment explanation
Indices: 20842803--20843172 Score: 345
Period size: 140 Copynumber: 2.6 Consensus size: 138
20842793 TTGGGTCTTT
* *
20842803 TGTATGCTAGGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCCAGTGTAAGACCA
1 TGTAAGCTAGGTAAGACATGTCTGGGACATGCATCGGCCACATGAT-AGAGCCAGTGTAAGACCA
* ** * *
20842868 TGTTTGGGACATGGCATCGGCATTGAGGCGAGAGCTAGTGTAAGACATGTCTTGGACATGCATCT
65 TGTCTGGGACATGGCATCGGCACGGAGGCGAGAGCAAGTGTAAGACATGTCTGGGACATGCATCT
20842933 GCCTCGTGA
130 GCCTCGTGA
* * **
20842942 TGTAAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GAT-GTGTTAGTGTAAGACC
1 TGTAAGCTAG-GTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATAGAGCCAGTGTAAGACC
* *
20843005 ATGTCTGGGACATGGCATCGGTACGGATATG-GAGAGCAAGTGTAAGACCATGTCTGGGACATGG
64 ATGTCTGGGACATGGCATCGGCACGG--AGGCGAGAGCAAGTGTAAGA-CATGTCTGGGACAT-G
* * * **
20843069 CGTCGGCCTCAATTT
125 CATCTGCCTC-GTGA
* * * * *** *
20843084 TG-ATAGTCAATGTAAGACCATGTCTGAGACATGGCATCGACTTGATGA-ACAAGCCAGTGTAAG
1 TGTA-AG-CTAGGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATGATA-GAGCCAGTGTAAG
*
20843147 ACCGTGTCTGGGACATGGCATCGGCA
61 ACCATGTCTGGGACATGGCATCGGCA
20843173 TTATACCTTA
Statistics
Matches: 187, Mismatches: 30, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
138 35 0.19
139 24 0.13
140 47 0.25
141 11 0.06
142 11 0.06
143 16 0.09
144 10 0.05
145 33 0.18
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (138 bp):
TGTAAGCTAGGTAAGACATGTCTGGGACATGCATCGGCCACATGATAGAGCCAGTGTAAGACCAT
GTCTGGGACATGGCATCGGCACGGAGGCGAGAGCAAGTGTAAGACATGTCTGGGACATGCATCTG
CCTCGTGA
Found at i:20843066 original size:94 final size:92
Alignment explanation
Indices: 20842808--20843067 Score: 259
Period size: 94 Copynumber: 2.8 Consensus size: 92
20842798 TCTTTTGTAT
* *
20842808 GCTAG-GTAAGACATGTCTGGGACATGCATCGGCCAC-ATTAT-GAGAGCCAGTGTAAGACCATG
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGG-TACGA-TATGGAGAGCAAGTGTAAGACCATG
* * *
20842870 TTTGGGACATGGCATCGGCATTGAGGCGAGA
64 TCTGGGACAT-GCATCGGCA-TGACGAGAGA
* * * *
20842901 GCTAGTGTAAGACATGTCTTGGACATGCATCTGCCT-CG-TGATGTA-AGCTAGTGTAAGA-CAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-G-GTACGAT-ATGGAGAGCAAGTGTAAGACCAT
*
20842962 GTCTGGGACATGCATCGGC-T-ACGAGATGT
63 GTCTGGGACATGCATCGGCATGACGAGA-GA
*
20842991 GTTAGTGTAAGACCATGTCTGGGACATGGCATCGGTACGGATATGGAGAGCAAGTGTAAGACCAT
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGTAC-GATATGGAGAGCAAGTGTAAGACCAT
20843056 GTCTGGGACATG
63 GTCTGGGACATG
20843068 GCGTCGGCCT
Statistics
Matches: 139, Mismatches: 14, Indels: 27
0.77 0.08 0.15
Matches are distributed among these distances:
89 4 0.03
90 14 0.10
91 15 0.11
92 18 0.13
93 32 0.23
94 54 0.39
95 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (92 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGTACGATATGGAGAGCAAGTGTAAGACCATGTC
TGGGACATGCATCGGCATGACGAGAGA
Found at i:20846977 original size:28 final size:28
Alignment explanation
Indices: 20846934--20847003 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
20846924 ATGAAAATTT
* * * *
20846934 CACTAAGCGTGCGAGTTTGGTTAACGAG
1 CACTAAGTGTGTGAGTTTGATTAACGAC
*
20846962 CACTAAGTGTGTGAGTTTGATTATCGAC
1 CACTAAGTGTGTGAGTTTGATTAACGAC
*
20846990 CACTAAGTATGTGA
1 CACTAAGTGTGTGA
20847004 AGGAAAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGTGAGTTTGATTAACGAC
Found at i:20852714 original size:21 final size:21
Alignment explanation
Indices: 20852687--20852748 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
20852677 TATAATGAGT
20852687 ATATCATAGCATATCATGTAC
1 ATATCATAGCATATCATGTAC
* * * *
20852708 ATCTCATAACAGATCATGTGC
1 ATATCATAGCATATCATGTAC
20852729 ATATCAT-GTCATATCATGTA
1 ATATCATAG-CATATCATGTA
20852749 TAATAATATC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.34
Consensus pattern (21 bp):
ATATCATAGCATATCATGTAC
Found at i:20852741 original size:10 final size:10
Alignment explanation
Indices: 20852687--20852747 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
20852677 TATAATGAGT
20852687 ATATCATAG-C
1 ATATCAT-GTC
20852697 ATATCATGTAC
1 ATATCATGT-C
* **
20852708 ATCTCATAAC
1 ATATCATGTC
*
20852718 AGATCATGTGC
1 ATATCATGT-C
20852729 ATATCATGTC
1 ATATCATGTC
20852739 ATATCATGT
1 ATATCATGT
20852748 ATAATAATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
9 1 0.03
10 23 0.57
11 16 0.40
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (10 bp):
ATATCATGTC
Found at i:20853451 original size:27 final size:27
Alignment explanation
Indices: 20853391--20853453 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
20853381 GCATATTCGA
20853391 CATTTTACCATACAAGGGTATTACGGT
1 CATTTTACCATACAAGGGTATTACGGT
* * *
20853418 CACTTTACCCTACAGGGGCT-TTACGGT
1 CATTTTACCATACAAGGG-TATTACGGT
*
20853445 CTTTTTACC
1 CATTTTACC
20853454 TATTAGGGGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 29 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.35
Consensus pattern (27 bp):
CATTTTACCATACAAGGGTATTACGGT
Found at i:20853537 original size:27 final size:27
Alignment explanation
Indices: 20853507--20853604 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
20853497 GTAAATCTAC
20853507 AAACCAAGGGTATTTC-AGTAATTTTGT
1 AAACCAAGGGTATTTCTA-TAATTTTGT
*
20853534 AAACCAATGGTATTTCTATAATTTT-T
1 AAACCAAGGGTATTTCTATAATTTTGT
* *
20853560 AGAAAGTCAAAGGTATTTCTATAATTTTGT
1 --AAA-CCAAGGGTATTTCTATAATTTTGT
* *
20853590 AAATCAGGGGTATTT
1 AAACCAAGGGTATTT
20853605 TGGTAATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
26 1 0.02
27 32 0.52
28 7 0.11
29 20 0.33
30 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.16, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTCTATAATTTTGT
Found at i:20853611 original size:27 final size:27
Alignment explanation
Indices: 20853595--20853726 Score: 142
Period size: 27 Copynumber: 4.9 Consensus size: 27
20853585 TTTGTAAATC
20853595 AGGGGTATTTTGGTAATTTTACAAA-T
1 AGGGGTATTTTGGTAATTTTACAAACT
* * * *
20853621 TGACGGTATTTCGGTAATTTCACAAACT
1 AG-GGGTATTTTGGTAATTTTACAAACT
*
20853649 AGTGGTATTTTGGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
* **
20853676 AGGGGTATTTTGGTAATTCTACCCTA-T
1 AGGGGTATTTTGGTAATTTTA-CAAACT
* *
20853703 AGGGGTATTTTAGTAATTTCACAA
1 AGGGGTATTTTGGTAATTTTACAA
20853727 TCGAGGGTAA
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 80 0.93
28 4 0.05
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACT
Found at i:20853755 original size:27 final size:27
Alignment explanation
Indices: 20853725--20853843 Score: 159
Period size: 27 Copynumber: 4.4 Consensus size: 27
20853715 GTAATTTCAC
*
20853725 AATCGAGGGTAAAACGATAATTCTGTA
1 AATCGAGGGTAAAACGATAATTCTATA
20853752 AATCGAGGGTAAAAC-AGTAATTCTATA
1 AATCGAGGGTAAAACGA-TAATTCTATA
* *
20853779 AATTGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGATAATTCTATA
* * *
20853806 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAACGATAATTCTATA
*
20853833 AATCGAAGGTA
1 AATCGAGGGTA
20853844 CTTTGGTAAT
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
26 1 0.01
27 82 0.99
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
AATCGAGGGTAAAACGATAATTCTATA
Found at i:20855165 original size:37 final size:37
Alignment explanation
Indices: 20855115--20855193 Score: 158
Period size: 37 Copynumber: 2.1 Consensus size: 37
20855105 TATGAGAAAA
20855115 TATGTTGTATGAGTAAATGGTTTAGAAATTTGTGAAC
1 TATGTTGTATGAGTAAATGGTTTAGAAATTTGTGAAC
20855152 TATGTTGTATGAGTAAATGGTTTAGAAATTTGTGAAC
1 TATGTTGTATGAGTAAATGGTTTAGAAATTTGTGAAC
20855189 TATGT
1 TATGT
20855194 AATATATGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.32, C:0.03, G:0.24, T:0.42
Consensus pattern (37 bp):
TATGTTGTATGAGTAAATGGTTTAGAAATTTGTGAAC
Found at i:20864590 original size:40 final size:39
Alignment explanation
Indices: 20864546--20864678 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 39
20864536 CGATTATTTG
* * *
20864546 TGGCACTTAATGTGCAATATGACCTAGCTTCAGCTATATA
1 TGGCACTTAGTGTGCGAT-TGACATAGCTTCAGCTATATA
*
20864586 TGGCACTTAGTGTTCGATTCGACATAGCTTCAGCTATATA
1 TGGCACTTAGTGTGCGATT-GACATAGCTTCAGCTATATA
* *
20864626 TGGCACTTAGTGTGCGATTTGAGATAGCTTCAGCTATGTA
1 TGGCACTTAGTGTGCGA-TTGACATAGCTTCAGCTATATA
*
20864666 CGGCACTTAGTGT
1 TGGCACTTAGTGT
20864679 ACGAGATATC
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
39 1 0.01
40 80 0.96
41 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (39 bp):
TGGCACTTAGTGTGCGATTGACATAGCTTCAGCTATATA
Found at i:20864712 original size:28 final size:28
Alignment explanation
Indices: 20864667--20864722 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
20864657 AGCTATGTAC
*
20864667 GGCACTTAGTGTACGAGATATCGAGTAT
1 GGCACTTAGTGTACGAGACATCGAGTAT
*
20864695 GGCACTTAGTGTGA-GAGACATTGAGTAT
1 GGCACTTAGTGT-ACGAGACATCGAGTAT
20864723 TCAACAGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.29
Consensus pattern (28 bp):
GGCACTTAGTGTACGAGACATCGAGTAT
Found at i:20881804 original size:12 final size:12
Alignment explanation
Indices: 20881787--20881820 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20881777 AGGCAATCCA
*
20881787 GGAAATTCCTCT
1 GGAAATTCATCT
*
20881799 GGAAATACATCT
1 GGAAATTCATCT
20881811 GGAAATTCAT
1 GGAAATTCAT
20881821 AGACTATCGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (12 bp):
GGAAATTCATCT
Found at i:20887153 original size:2 final size:2
Alignment explanation
Indices: 20887148--20887172 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20887138 TTCATATATA
20887148 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
20887173 TTTGGTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:20888249 original size:10 final size:10
Alignment explanation
Indices: 20888234--20888285 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
20888224 AAAATTTAGG
20888234 ATTTATTTTT
1 ATTTATTTTT
*
20888244 ATTTATCTTT
1 ATTTATTTTT
* *
20888254 AATTATCTTT
1 ATTTATTTTT
* *
20888264 AATTATTTGT
1 ATTTATTTTT
20888274 ATTTATCTTTT
1 ATTTAT-TTTT
20888285 A
1 A
20888286 GAATTTAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
10 31 0.89
11 4 0.11
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:20893305 original size:11 final size:11
Alignment explanation
Indices: 20893290--20893320 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
20893280 TTTAATTTTA
20893290 AAAAAAAAAGAG
1 AAAAAAAAA-AG
20893302 AAAAAAAAAAG
1 AAAAAAAAAAG
20893313 AAAAAAAA
1 AAAAAAAA
20893321 TATTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:20893307 original size:13 final size:12
Alignment explanation
Indices: 20893289--20893320 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
20893279 ATTTAATTTT
20893289 AAAAAAAAAAGA
1 AAAAAAAAAAGA
20893301 GAAAAAAAAAAGA
1 -AAAAAAAAAAGA
20893314 AAAAAAA
1 AAAAAAA
20893321 TATTAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:20893955 original size:10 final size:10
Alignment explanation
Indices: 20893942--20893984 Score: 61
Period size: 10 Copynumber: 4.3 Consensus size: 10
20893932 AGGATTTACT
20893942 TTTATTTATC
1 TTTATTTATC
*
20893952 TTTAATTATC
1 TTTATTTATC
20893962 TTTATTTAT-
1 TTTATTTATC
20893971 TTGTATTTATC
1 TT-TATTTATC
20893982 TTT
1 TTT
20893985 TAGAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 2 0.07
10 25 0.86
11 2 0.07
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTATTTATC
Found at i:20897426 original size:79 final size:81
Alignment explanation
Indices: 20897290--20897474 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
20897280 TTGAATGATG
*
20897290 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
20897354 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
20897369 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
20897431 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
20897449 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20897475 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:20897488 original size:40 final size:40
Alignment explanation
Indices: 20897291--20897474 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
20897281 TGAATGATGT
* * * *
20897291 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
20897331 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
20897371 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
20897409 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
20897450 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
20897475 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:20897496 original size:79 final size:79
Alignment explanation
Indices: 20897343--20897507 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
20897333 GGACTAAGAT
* **
20897343 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
20897408 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
20897422 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
20897485 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
20897501 CCGAAGG
1 CCGAAGG
20897508 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:20905386 original size:79 final size:81
Alignment explanation
Indices: 20905250--20905434 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
20905240 TTGAATGATG
* *
20905250 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
20905314 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
20905329 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
20905391 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
20905409 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
20905435 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:20905448 original size:40 final size:40
Alignment explanation
Indices: 20905251--20905434 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
20905241 TGAATGATGT
* * * *
20905251 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
20905291 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
20905331 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
20905369 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
20905410 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
20905435 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:20905456 original size:79 final size:79
Alignment explanation
Indices: 20905303--20905467 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
20905293 GGACTAAGAT
* * **
20905303 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
20905368 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
20905382 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
20905445 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
20905461 CCGAAGG
1 CCGAAGG
20905468 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:20907702 original size:25 final size:23
Alignment explanation
Indices: 20907674--20907719 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
20907664 AAGCTCCTCA
20907674 TGAGCTGATGAACAATAAGCTCTAT
1 TGAGCTGA--AACAATAAGCTCTAT
* *
20907699 TGAGTTGAAACAGTAAGCTCT
1 TGAGCTGAAACAATAAGCTCT
20907720 TACGAGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
25 7 0.37
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (23 bp):
TGAGCTGAAACAATAAGCTCTAT
Found at i:20911256 original size:35 final size:35
Alignment explanation
Indices: 20911217--20911333 Score: 89
Period size: 35 Copynumber: 3.3 Consensus size: 35
20911207 ACACATACAC
*
20911217 TTATATGCATACACTCATAAGTCAAAGTATAACAA
1 TTATATACATACACTCATAAGTCAAAGTATAACAA
* ** * *
20911252 TTATATACAT-CTTTA-TCAT-ACT-AAACACACATACAC
1 TTATATACATAC---ACTCATAAGTCAAA-GTATA-ACAA
* *
20911288 TTATGTGCATACACTCATAAGTCAAAGTATAACAA
1 TTATATACATACACTCATAAGTCAAAGTATAACAA
20911323 TTATATACATA
1 TTATATACATA
20911334 TTTATATCAA
Statistics
Matches: 58, Mismatches: 15, Indels: 18
0.64 0.16 0.20
Matches are distributed among these distances:
34 5 0.09
35 29 0.50
36 19 0.33
37 5 0.09
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.32
Consensus pattern (35 bp):
TTATATACATACACTCATAAGTCAAAGTATAACAA
Found at i:20911271 original size:71 final size:71
Alignment explanation
Indices: 20911187--20911338 Score: 277
Period size: 71 Copynumber: 2.1 Consensus size: 71
20911177 CCAAGCCAAA
*
20911187 ACATCTTTATCATACTAAATACACATACACTTATATGCATACACTCATAAGTCAAAGTATAACAA
1 ACATCTTTATCATACTAAACACACATACACTTATATGCATACACTCATAAGTCAAAGTATAACAA
20911252 TTATAT
66 TTATAT
*
20911258 ACATCTTTATCATACTAAACACACATACACTTATGTGCATACACTCATAAGTCAAAGTATAACAA
1 ACATCTTTATCATACTAAACACACATACACTTATATGCATACACTCATAAGTCAAAGTATAACAA
20911323 TTATAT
66 TTATAT
*
20911329 ACATATTTAT
1 ACATCTTTAT
20911339 ATCAACGGTC
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (71 bp):
ACATCTTTATCATACTAAACACACATACACTTATATGCATACACTCATAAGTCAAAGTATAACAA
TTATAT
Found at i:20914603 original size:53 final size:53
Alignment explanation
Indices: 20914499--20914606 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
20914489 ACTTGTATAA
** *
20914499 GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCGGTGTAAACT
1 GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCAATATAAACT
20914552 GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCAATATAAACT
1 GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCAATATAAACT
20914605 GC
1 GC
20914607 CATCAAACTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (53 bp):
GCTATTTTGAGGTCTTAAATCCAAGGATGGCACATTGATATTCAATATAAACT
Found at i:20915091 original size:26 final size:26
Alignment explanation
Indices: 20915062--20915112 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
20915052 GGTTTAAATT
* * * *
20915062 CTTACAAAATTAAAATTAGAGATTAC
1 CTTAAAAAACTAAAATCAGAAATTAC
20915088 CTTAAAAAACTAAAATCAGAAATTA
1 CTTAAAAAACTAAAATCAGAAATTA
20915113 AATTCATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (26 bp):
CTTAAAAAACTAAAATCAGAAATTAC
Found at i:20915295 original size:52 final size:51
Alignment explanation
Indices: 20915217--20915317 Score: 193
Period size: 52 Copynumber: 2.0 Consensus size: 51
20915207 GAATCATGAC
20915217 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTTCCAACAACT
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAA-TTTTTTTTCCAACAACT
20915269 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAA
1 GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAA
20915318 ATAGTTGTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 15 0.31
52 34 0.69
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (51 bp):
GATATTCATTCTTCCAAAAATTGTTATTTTTTAATTTTTTTTCCAACAACT
Found at i:20917156 original size:20 final size:21
Alignment explanation
Indices: 20917131--20917171 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
20917121 AGTTCTTTTA
20917131 AATTTAATATATTTA-AAAAT
1 AATTTAATATATTTATAAAAT
*
20917151 AATTTAATATTTTTATAAAAT
1 AATTTAATATATTTATAAAAT
20917172 TTTAAAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTTAATATATTTATAAAAT
Found at i:20917172 original size:18 final size:19
Alignment explanation
Indices: 20917130--20917176 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
20917120 AAGTTCTTTT
20917130 AAATTTAATATATTTAAAA
1 AAATTTAATATATTTAAAA
* *
20917149 ATAATTTAATATTTTTATAA
1 A-AATTTAATATATTTAAAA
*
20917169 AATTTTAA
1 AAATTTAA
20917177 AATCCGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTAATATATTTAAAA
Found at i:20919166 original size:21 final size:21
Alignment explanation
Indices: 20919105--20919169 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
20919095 AGATCCTGAA
* *
20919105 TTTTCGTAATATTGTCAAAAC
1 TTTTAGTAATATTGTCAAATC
* *
20919126 TTTTACG-ATTATTGCCAAATC
1 TTTTA-GTAATATTGTCAAATC
*
20919147 TTTTAGTAATCTTGTCAAATC
1 TTTTAGTAATATTGTCAAATC
20919168 TT
1 TT
20919170 GAAACCAACC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (21 bp):
TTTTAGTAATATTGTCAAATC
Found at i:20922179 original size:26 final size:26
Alignment explanation
Indices: 20922149--20922201 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
20922139 TATCTATGAA
20922149 TAACTTTTCATTTTTCTACCATAAAT
1 TAACTTTTCATTTTTCTACCATAAAT
20922175 TAACTTTTCATTTTTCTACCATAAAT
1 TAACTTTTCATTTTTCTACCATAAAT
20922201 T
1 T
20922202 TCTAATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (26 bp):
TAACTTTTCATTTTTCTACCATAAAT
Found at i:20922970 original size:90 final size:90
Alignment explanation
Indices: 20922807--20922997 Score: 222
Period size: 90 Copynumber: 2.1 Consensus size: 90
20922797 GGCTATTACA
* ** * ** * * * *
20922807 TAACCTGCAACACTGGTGGTTCATCCACCTATTTTCTGGCTGCTCTTATCTGCAATTTTGTTGTG
1 TAACCTGCAACACTGGTGGTTCATCCACCCACATTCTGACAACTCTCATCTACAATTATGTTATG
** *
20922872 TGTCCACAACCATCTGGCAACATTT
66 ACTCCACAACCATCTGGCAACATAT
*
20922897 TAACCTGCAACATTGGTGGTTCATCCACCCACATTCTGACAACTCTCATCTACAATTATGTTATG
1 TAACCTGCAACACTGGTGGTTCATCCACCCACATTCTGACAACTCTCATCTACAATTATGTTATG
*
20922962 CACT-CACAACCATCTGGCAACGTAT
66 -ACTCCACAACCATCTGGCAACATAT
*
20922987 TAAACTGCAAC
1 TAACCTGCAAC
20922998 TTTTGTGGCT
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
90 83 0.99
91 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (90 bp):
TAACCTGCAACACTGGTGGTTCATCCACCCACATTCTGACAACTCTCATCTACAATTATGTTATG
ACTCCACAACCATCTGGCAACATAT
Found at i:20928534 original size:11 final size:11
Alignment explanation
Indices: 20928519--20928552 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
20928509 AATTGATTAC
*
20928519 AAGGTGATATT
1 AAGGTGAAATT
*
20928530 TAGGTGAAATT
1 AAGGTGAAATT
20928541 AAGGTGAAATT
1 AAGGTGAAATT
20928552 A
1 A
20928553 TAGTAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (11 bp):
AAGGTGAAATT
Found at i:20934075 original size:42 final size:42
Alignment explanation
Indices: 20934016--20934174 Score: 212
Period size: 42 Copynumber: 3.8 Consensus size: 42
20934006 TTAGGGCTAC
*
20934016 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCTATA
1 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
* *
20934058 TGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCGATA
1 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
* * * *
20934100 TGAGACTT-CGTGTAAGACCATAGCTGAGCTATTAGCATCGATA
1 TGAGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* *
20934143 CGAGATTACATGTAAGACCATATCTGGGATAT
1 TGAGATTACGTGTAAGACCATATCTGGGATAT
20934175 AACATTGGTA
Statistics
Matches: 101, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
42 66 0.65
43 35 0.35
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (42 bp):
TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:20934160 original size:85 final size:84
Alignment explanation
Indices: 20934016--20934174 Score: 212
Period size: 85 Copynumber: 1.9 Consensus size: 84
20934006 TTAGGGCTAC
* * * * * * *
20934016 TGAGATTACGTGTAAGACCATATCTGGGATATGGCATCTATATGAGATTTCGTGTAAGACCATAT
1 TGAGATTACGTGTAAGACCATAGCTGAGATATAGCATCGATACGAGATTACATGTAAGACCATAT
20934081 CTAGGATATGGCATCGATA
66 CTAGGATATGGCATCGATA
*
20934100 TGAGACTT-CGTGTAAGACCATAGCTGAGCTATTAGCATCGATACGAGATTACATGTAAGACCAT
1 TGAGA-TTACGTGTAAGACCATAGCTGAGATA-TAGCATCGATACGAGATTACATGTAAGACCAT
*
20934164 ATCTGGGATAT
64 ATCTAGGATAT
20934175 AACATTGGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 25 0.39
85 39 0.61
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (84 bp):
TGAGATTACGTGTAAGACCATAGCTGAGATATAGCATCGATACGAGATTACATGTAAGACCATAT
CTAGGATATGGCATCGATA
Found at i:20934775 original size:20 final size:21
Alignment explanation
Indices: 20934750--20934807 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
20934740 TGATTTTAGG
20934750 ATTTATTTTCATTTATCTA-T
1 ATTTATTTTCATTTATCTATT
*
20934770 ATTTATCTTT-AATTATC-ATT
1 ATTTAT-TTTCATTTATCTATT
*
20934790 ATTTATTTGCATTTATCT
1 ATTTATTTTCATTTATCT
20934808 TTTAGAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.26, C:0.10, G:0.02, T:0.62
Consensus pattern (21 bp):
ATTTATTTTCATTTATCTATT
Found at i:20938522 original size:15 final size:14
Alignment explanation
Indices: 20938502--20938609 Score: 65
Period size: 15 Copynumber: 7.0 Consensus size: 14
20938492 CAACCCAACC
20938502 TTTACTTTTATTTTT
1 TTTA-TTTTATTTTT
* *
20938517 TTTACTTTTCTTAATT
1 TTTA-TTTTATT-TTT
*
20938533 TTTATTCATTA-TTAT
1 TTTATT--TTATTTTT
20938548 TTTATTTTATTTTAT
1 TTTATTTTATTTT-T
*
20938563 TATTATTATTTATTTTAC
1 T-TTA-T-TTTATTTT-T
20938581 TTTATTTTATTATTT
1 TTTATTTTATT-TTT
*
20938596 ATTATTTTATTTTT
1 TTTATTTTATTTTT
20938610 GGATATTAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
13 3 0.04
14 5 0.07
15 38 0.51
16 13 0.17
17 6 0.08
18 10 0.13
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTATTTTT
Found at i:20938547 original size:10 final size:9
Alignment explanation
Indices: 20938534--20938606 Score: 61
Period size: 8 Copynumber: 8.6 Consensus size: 9
20938524 TTCTTAATTT
20938534 TTATTCATTA
1 TTATT-ATTA
20938544 TTATT-TTA
1 TTATTATTA
20938552 TT-TTATT-
1 TTATTATTA
20938559 TTATTATTA
1 TTATTATTA
20938568 TTATTTATT-
1 TTA-TTATTA
*
20938577 TTACT-TTA
1 TTATTATTA
20938585 TT-TTATTA
1 TTATTATTA
20938593 TTTATTATT-
1 -TTATTATTA
20938602 TTATT
1 TTATT
20938607 TTTGGATATT
Statistics
Matches: 53, Mismatches: 2, Indels: 18
0.73 0.03 0.25
Matches are distributed among these distances:
7 7 0.13
8 23 0.43
9 8 0.15
10 15 0.28
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.73
Consensus pattern (9 bp):
TTATTATTA
Found at i:20938554 original size:5 final size:5
Alignment explanation
Indices: 20938544--20938608 Score: 69
Period size: 5 Copynumber: 12.4 Consensus size: 5
20938534 TTATTCATTA
*
20938544 TTATT TTATT TTATT TTATT ATTATTAT TTATT TTACT TTATT TTATT
1 TTATT TTATT TTATT TTATT -TTA-T-T TTATT TTATT TTATT TTATT
*
20938592 ATT-TA TTATT TTATT TT
1 -TTATT TTATT TTATT TT
20938609 TGGATATTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
4 2 0.04
5 38 0.75
6 6 0.12
7 4 0.08
8 1 0.02
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:20938575 original size:28 final size:28
Alignment explanation
Indices: 20938534--20938608 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
20938524 TTCTTAATTT
*
20938534 TTATTCATTA-TTATTTTATTTTATTTTA
1 TTATT-ATTATTTATTTTACTTTATTTTA
20938562 TTATTATTATTTATTTTACTTTATTTTA
1 TTATTATTATTTATTTTACTTTATTTTA
20938590 TTATTTATTATTTTATTTT
1 TTA-TTATTA-TTTATTTT
20938609 TGGATATTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
27 4 0.09
28 25 0.58
29 6 0.14
30 8 0.19
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (28 bp):
TTATTATTATTTATTTTACTTTATTTTA
Found at i:20938600 original size:25 final size:26
Alignment explanation
Indices: 20938501--20938604 Score: 92
Period size: 25 Copynumber: 4.0 Consensus size: 26
20938491 GCAACCCAAC
*
20938501 CTTTACTTTTATT-TTTTTTACTTTT-
1 CTTTACTTTTATTATTTATTA-TTTTA
* *
20938526 CTTAATTTTTATTCA-TTATTATTTTA
1 CTTTACTTTTATT-ATTTATTATTTTA
*
20938552 TTTTA-TTTTATTATTATTATTTATTTTA
1 CTTTACTTTTATTA-T-TTA-TTATTTTA
20938580 CTTTA-TTTTATTATTTATTATTTTA
1 CTTTACTTTTATTATTTATTATTTTA
20938605 TTTTTGGATA
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
24 1 0.02
25 30 0.45
26 11 0.17
27 4 0.06
28 20 0.30
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (26 bp):
CTTTACTTTTATTATTTATTATTTTA
Found at i:20938617 original size:53 final size:51
Alignment explanation
Indices: 20938517--20938634 Score: 123
Period size: 53 Copynumber: 2.2 Consensus size: 51
20938507 TTTTATTTTT
* ** * *
20938517 TTTACTTTTCTTAATTTTTATTCATTATTATTTTATTTTATTTTATTATTATTA
1 TTTA-TTTTCTTTA-TTTTATTCATTATTATTTTATTTTATGATATTAATA-AA
20938571 TTTATTTTACTTTATTTTATT-ATTTATTATTTTATTTT-TGGATATTAATAAA
1 TTTATTTT-CTTTATTTTATTCA-TTATTATTTTATTTTAT-GATATTAATAAA
20938623 TTTATTTTCTTT
1 TTTATTTTCTTT
20938635 TATCTAGGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
51 4 0.07
52 11 0.20
53 33 0.59
54 8 0.14
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (51 bp):
TTTATTTTCTTTATTTTATTCATTATTATTTTATTTTATGATATTAATAAA
Found at i:20943046 original size:10 final size:10
Alignment explanation
Indices: 20943031--20943090 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
20943021 TAATTTTAGG
20943031 ATTTAT-TTT
1 ATTTATCTTT
20943040 CATTTATCTTT
1 -ATTTATCTTT
20943051 ATTTATCTTT
1 ATTTATCTTT
*
20943061 AATTATCTTT
1 ATTTATCTTT
20943071 ATTTAT-TTGT
1 ATTTATCTT-T
20943081 ATTTATCTTT
1 ATTTATCTTT
20943091 TAGAATTTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:20947396 original size:46 final size:46
Alignment explanation
Indices: 20947334--20947654 Score: 430
Period size: 46 Copynumber: 7.0 Consensus size: 46
20947324 AGTGTGCTCT
20947334 CTGATA-GAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
20947380 CTGATATGAAACGTGTAAGACCATGGTTGAAACATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
20947426 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
20947472 CTGATATGAAATGTGTAAGACCAAGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
20947518 ATGACATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * ** * * *
20947564 GTGACGAGGAAATGAATAAGATCATGGTTGAATGATAACATGGCAAC
1 CTGA-TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
20947611 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
20947655 TCATGTCGAA
Statistics
Matches: 247, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.00
46 207 0.84
47 39 0.16
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:20953160 original size:42 final size:42
Alignment explanation
Indices: 20953107--20953259 Score: 182
Period size: 42 Copynumber: 3.6 Consensus size: 42
20953097 CTGAGATTAC
* * *
20953107 GTAAGACCATATCTGGGATATGGCATCTATATAAGATTTCTT
1 GTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCAT
* * * *
20953149 GTAAGATCATATCTAGGATATGGCATCGATATGAGACTTCGT
1 GTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCAT
* * * *
20953191 GTAAGACCATAGCT-GGACTATTAGCATCGATACGAGATTACAT
1 GTAAGACCATATCTGGGA-TA-TGGCATCGATATGAGATTTCAT
20953234 GTAAGACCATATCTGGGATATGGCAT
1 GTAAGACCATATCTGGGATATGGCAT
20953260 TGGTATGGTA
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.03
42 55 0.59
43 32 0.34
44 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (42 bp):
GTAAGACCATATCTGGGATATGGCATCGATATGAGATTTCAT
Found at i:20954204 original size:17 final size:18
Alignment explanation
Indices: 20954172--20954205 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20954162 TGATCATGGT
*
20954172 ATGCTTGGTGAATGTGAA
1 ATGCTTGGTAAATGTGAA
20954190 ATGCTTGG-AAATGTGA
1 ATGCTTGGTAAATGTGA
20954206 TTTATGGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (18 bp):
ATGCTTGGTAAATGTGAA
Found at i:20955350 original size:4 final size:5
Alignment explanation
Indices: 20955318--20955394 Score: 50
Period size: 6 Copynumber: 14.2 Consensus size: 5
20955308 AAACAAGCAA
*
20955318 AAAAG AAAAAG AACAAG -GAAG TAAAAG -AAAG AAAAG AAAAG AAAAG
1 AAAAG -AAAAG AA-AAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG
*
20955364 AGGAAG AAGAAG AAGAAG AAGAAG AATAAG A
1 A-AAAG AA-AAG AA-AAG AA-AAG AA-AAG A
20955395 GAACTAATGT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
4 7 0.12
5 17 0.28
6 36 0.60
ACGTcount: A:0.70, C:0.01, G:0.26, T:0.03
Consensus pattern (5 bp):
AAAAG
Found at i:20955356 original size:31 final size:31
Alignment explanation
Indices: 20955318--20955386 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 31
20955308 AAACAAGCAA
*
20955318 AAAAGAAAAAGAACA-AGGAAGTAA-AAGAAAG
1 AAAAGAAAAAGAAAAGAGGAAG-AAGAAG-AAG
20955349 AAAAG-AAAAGAAAAGAGGAAGAAGAAGAAG
1 AAAAGAAAAAGAAAAGAGGAAGAAGAAGAAG
20955379 AAGAAGAA
1 AA-AAGAA
20955387 GAATAAGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
30 15 0.45
31 17 0.52
32 1 0.03
ACGTcount: A:0.71, C:0.01, G:0.26, T:0.01
Consensus pattern (31 bp):
AAAAGAAAAAGAAAAGAGGAAGAAGAAGAAG
Found at i:20955374 original size:3 final size:3
Alignment explanation
Indices: 20955346--20955394 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
20955336 AAGTAAAAGA
* *
20955346 AAG AA- AAG AA- AAG AA- AAG AGG AAG AAG AAG AAG AAG AAG AAG AAT
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
20955391 AAG A
1 AAG A
20955395 GAACTAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:20956349 original size:38 final size:37
Alignment explanation
Indices: 20956267--20956348 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 37
20956257 TTGTCTAAAA
20956267 ACATTTTTACTAATTCTCTTTATAAAATATGTTTATT
1 ACATTTTTACTAATTCTCTTTATAAAATATGTTTATT
20956304 ACATTTTTACTAACTTCTCTTTATAAAATATGTTTA-T
1 ACATTTTTACTAA-TTCTCTTTATAAAATATGTTTATT
*
20956341 ACTTTTTT
1 ACATTTTT
20956349 TTATTTACTA
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
37 21 0.49
38 22 0.51
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.55
Consensus pattern (37 bp):
ACATTTTTACTAATTCTCTTTATAAAATATGTTTATT
Done.