Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 13 of 322
Found at i:3507470 original size:18 final size:18
Alignment explanation
Indices: 3507447--3507483 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3507437 ATAAAGTCTT
3507447 AAAATAATAACT-ATAATA
1 AAAATAATAA-TAATAATA
3507465 AAAATAATAATAATAATA
1 AAAATAATAATAATAATA
3507483 A
1 A
3507484 TATAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATAATAATAATAATA
Found at i:3513083 original size:21 final size:21
Alignment explanation
Indices: 3513049--3513096 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3513039 TACTAACTTT
3513049 AAAAGTCAAATTACAAAGGAAC
1 AAAA-TCAAATTACAAAGGAAC
* * *
3513071 TAAATCAAGTTACAAATGAAC
1 AAAATCAAATTACAAAGGAAC
3513092 AAAAT
1 AAAAT
3513097 AAACAAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.58, C:0.12, G:0.10, T:0.19
Consensus pattern (21 bp):
AAAATCAAATTACAAAGGAAC
Found at i:3519227 original size:20 final size:20
Alignment explanation
Indices: 3519202--3519239 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3519192 CTAAAAACGC
*
3519202 CAGTATAGCTTAACTTTTCA
1 CAGTATAGCTTAAATTTTCA
*
3519222 CAGTATAGTTTAAATTTT
1 CAGTATAGCTTAAATTTT
3519240 TGTGGCCTTT
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:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (20 bp):
CAGTATAGCTTAAATTTTCA
Found at i:3519451 original size:104 final size:103
Alignment explanation
Indices: 3519235--3519506 Score: 467
Period size: 103 Copynumber: 2.6 Consensus size: 103
3519225 TATAGTTTAA
*
3519235 ATTTTTGTGGCCTTTTGTCTAAAAACGTCACTATTGCTTAATTTTAATTTTTTTTTATTTTTAAC
1 ATTTTTGTGGCGTTTTGTCTAAAAACGTCACTATTGCTTAATTTTAA-TTTTTTTTATTTTTAAC
*
3519300 -ATTTTTTTCTATTCTTTTTCTTTTAAAATTTTTAACAT
65 AATTTTTTTCTATTCTTTTTCTTTCAAAATTTTTAACAT
* *
3519338 ATTTTTGTGGCGTTTCGTCTAAAAACGCCACTATTGCTTAATTTTAATTTTTTTTATTTTTAACA
1 ATTTTTGTGGCGTTTTGTCTAAAAACGTCACTATTGCTTAATTTTAATTTTTTTTATTTTTAACA
3519403 TATTTTTTTCTATTCTTTTTCTTTCAAAATTTTTAACAT
66 -ATTTTTTTCTATTCTTTTTCTTTCAAAATTTTTAACAT
*
3519442 ATTTTTGTGGTGTTTTGTCT-AAAACGTCACTATTGCTTAATTTTAATTTTTTTTATTTTTAACA
1 ATTTTTGTGGCGTTTTGTCTAAAAACGTCACTATTGCTTAATTTTAATTTTTTTTATTTTTAACA
3519506 A
66 A
3519507 AAAATTAGGG
Statistics
Matches: 160, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
102 18 0.11
103 87 0.54
104 55 0.34
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.57
Consensus pattern (103 bp):
ATTTTTGTGGCGTTTTGTCTAAAAACGTCACTATTGCTTAATTTTAATTTTTTTTATTTTTAACA
ATTTTTTTCTATTCTTTTTCTTTCAAAATTTTTAACAT
Found at i:3520133 original size:7 final size:7
Alignment explanation
Indices: 3520121--3520184 Score: 56
Period size: 7 Copynumber: 9.0 Consensus size: 7
3520111 CCCATGGCCA
3520121 TTAAACC
1 TTAAACC
3520128 TTAAACC
1 TTAAACC
*
3520135 ATAAAACC
1 -TTAAACC
*
3520143 TTAAATC
1 TTAAACC
* *
3520150 ATAGACC
1 TTAAACC
3520157 TTAAACC
1 TTAAACC
**
3520164 TTAAATA
1 TTAAACC
3520171 TTAAACC
1 TTAAACC
*
3520178 GTAAACC
1 TTAAACC
3520185 AAAAAATAAA
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
7 37 0.86
8 6 0.14
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.27
Consensus pattern (7 bp):
TTAAACC
Found at i:3520141 original size:15 final size:15
Alignment explanation
Indices: 3520118--3520168 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
3520108 ATACCCATGG
*
3520118 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
3520133 CCATAAAACCTTAAA
1 CCATAAAACCTTAAA
* *
3520148 TCAT-AGACCTTAAA
1 CCATAAAACCTTAAA
*
3520162 CCTTAAA
1 CCATAAA
3520169 TATTAAACCG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.47, C:0.25, G:0.02, T:0.25
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:3520182 original size:21 final size:22
Alignment explanation
Indices: 3520128--3520184 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
3520118 CCATTAAACC
3520128 TTAAACCATAAAACCTTAAATCA
1 TTAAACCAT-AAACCTTAAATCA
* *
3520151 -TAGACCTTAAACCTTAAAT-A
1 TTAAACCATAAACCTTAAATCA
*
3520171 TTAAACCGTAAACC
1 TTAAACCATAAACC
3520185 AAAAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.26
Consensus pattern (22 bp):
TTAAACCATAAACCTTAAATCA
Found at i:3520512 original size:41 final size:39
Alignment explanation
Indices: 3520415--3520541 Score: 130
Period size: 41 Copynumber: 3.1 Consensus size: 39
3520405 GTTATATGAC
* * *
3520415 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCGAC
1 TTTTAGCGGCGTTTTACCAAAAGCG-CGCTATTGCTCTG-T
* *
3520456 TTTTAACGGTGTTTTACCAAAAGCGCTGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTACCAAAAGCGC-GCTATTGCTCTGT
**
3520496 TTTTAGCGGCGATTTTAGTAAAATGC-CGCTATTGCTCTGT
1 TTTTAGCGGCG-TTTTACCAAAA-GCGCGCTATTGCTCTGT
3520536 GTTTTA
1 -TTTTA
3520542 CAATTTTTGC
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
40 23 0.32
41 48 0.66
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.37
Consensus pattern (39 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCGCTATTGCTCTGT
Found at i:3522821 original size:153 final size:152
Alignment explanation
Indices: 3522295--3522807 Score: 694
Period size: 153 Copynumber: 3.4 Consensus size: 152
3522285 AAAGGAATGG
* * * * *
3522295 TGATGAAATTCTTACCACTAAGATCAAGACG-TATCAAAGAGGATATACCAGAAATATCACCATG
1 TGATGAAATTGTTACCACTAAGATCAAGATGCCA-CAAAGAGGATAGACCAGAAATATCACTATG
* * *
3522359 AATATCTGCTTCACTAAGAGTGCACATGTTGCAATTTGACAATATAAGATATTCAAGCTTGGATA
65 AATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAGAT-TTCAAGCTTTGAGA
3522424 GTCGAGTAAGA-ATGCAGGTATGC
129 GTCGAGTAAGAGATGCAGGTATGC
* * * *
3522447 TGATGAAATTGTTATCACTAAGATCAAGATGCCTC--AGAGGATAGATCAGAAATATAACTATGA
1 TGATGAAATTGTTACCACTAAGATCAAGATGCCACAAAGAGGATAGACCAGAAATATCACTATGA
* * * * * **
3522510 GTATTTTCTTTACCAAGAGTGCACATGTTGCAATTTGATAATGCAAGCAATTT-AAGCTTTGAGA
66 ATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAG--ATTTCAAGCTTTGAGA
3522574 GTCGAGTAAGAGATGCAGGTATGC
129 GTCGAGTAAGAGATGCAGGTATGC
* * * * *
3522598 TTATGAAATTGTTACCACTAAGATCGAGATGACTCAAAGAGGATAGATCAGAAATATCACTATGA
1 TGATGAAATTGTTACCACTAAGATCAAGATGCCACAAAGAGGATAGACCAGAAATATCACTATGA
* * *
3522663 TTATCTGCTTCACCAAGAGTGCATATGTTGCAATTTGACAATATAAGATTTCCAAGCTTTTAGAG
66 ATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAGATTT-CAAGCTTTGAGAG
3522728 TCGAGTAAGAGATGCAGGTATGC
130 TCGAGTAAGAGATGCAGGTATGC
*
3522751 TGATGAAATTGTTACCACTAAGATCAGGATGCCACAAAGAGGATAGACCAGAAATAT
1 TGATGAAATTGTTACCACTAAGATCAAGATGCCACAAAGAGGATAGACCAGAAATAT
3522808 GACGTGGAAT
Statistics
Matches: 314, Mismatches: 39, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
150 83 0.26
151 49 0.16
152 31 0.10
153 151 0.48
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (152 bp):
TGATGAAATTGTTACCACTAAGATCAAGATGCCACAAAGAGGATAGACCAGAAATATCACTATGA
ATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAGATTTCAAGCTTTGAGAGT
CGAGTAAGAGATGCAGGTATGC
Found at i:3523044 original size:25 final size:25
Alignment explanation
Indices: 3523016--3523095 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
3523006 TTACAAAGGG
** *
3523016 AAAGTCCTAATCTAATTCCTAATTT
1 AAAGTCCTAATAGAATTCTTAATTT
* *
3523041 AAAGTCCAAATAGAATTTTTAATTT
1 AAAGTCCTAATAGAATTCTTAATTT
3523066 AAAGTCCTAATAGAATTCTTAATTT
1 AAAGTCCTAATAGAATTCTTAATTT
3523091 AAAGT
1 AAAGT
3523096 TTATAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.39
Consensus pattern (25 bp):
AAAGTCCTAATAGAATTCTTAATTT
Found at i:3527637 original size:25 final size:25
Alignment explanation
Indices: 3527609--3527688 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
3527599 TTACAAAGGG
** *
3527609 AAAGTCCTAATCTAATTCCTAATTT
1 AAAGTCCTAATAGAATTCTTAATTT
*
3527634 AAAGTCCAAATAGAATTCTTAATTT
1 AAAGTCCTAATAGAATTCTTAATTT
*
3527659 AAAGTCCTAATAGAATTCTTAACTT
1 AAAGTCCTAATAGAATTCTTAATTT
3527684 AAAGT
1 AAAGT
3527689 TAGCTAAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.36
Consensus pattern (25 bp):
AAAGTCCTAATAGAATTCTTAATTT
Found at i:3532011 original size:31 final size:31
Alignment explanation
Indices: 3531973--3532032 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
3531963 GTTTTTGTTG
3531973 GTGGATGTGTTCAAAATTTGGTGAAGATAGA
1 GTGGATGTGTTCAAAATTTGGTGAAGATAGA
3532004 GTGGATGTGTTCAAAATTTGGTGAAGATA
1 GTGGATGTGTTCAAAATTTGGTGAAGATA
3532033 TTACCTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (31 bp):
GTGGATGTGTTCAAAATTTGGTGAAGATAGA
Found at i:3535301 original size:14 final size:15
Alignment explanation
Indices: 3535275--3535305 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3535265 TCCAGGTTTA
3535275 TCAACACATTTTTCT
1 TCAACACATTTTTCT
3535290 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
3535304 TC
1 TC
3535306 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:3537939 original size:12 final size:12
Alignment explanation
Indices: 3537922--3537954 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3537912 TGGTCCCAAC
3537922 GTCTTTCTTGAA
1 GTCTTTCTTGAA
3537934 GTCTTTCTTGAA
1 GTCTTTCTTGAA
*
3537946 GTATTTCTT
1 GTCTTTCTT
3537955 CGATTGAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.55
Consensus pattern (12 bp):
GTCTTTCTTGAA
Found at i:3539087 original size:30 final size:30
Alignment explanation
Indices: 3539053--3539120 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
3539043 CAACAAAATT
3539053 AACAATAAAATAAGAGTTATACAATATTCA
1 AACAATAAAATAAGAGTTATACAATATTCA
*
3539083 AACAATAAAATAAGAGTTATATAATATTCA
1 AACAATAAAATAAGAGTTATACAATATTCA
*
3539113 ACCAATAA
1 AACAATAA
3539121 CAACATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.26
Consensus pattern (30 bp):
AACAATAAAATAAGAGTTATACAATATTCA
Found at i:3540342 original size:32 final size:32
Alignment explanation
Indices: 3540277--3540348 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
3540267 TTGTTCCTTA
* *
3540277 TTGTTTGTTTGGAAAGAAAGAAACATTCATTG
1 TTGTTTGTTTGAAAAGAAAGAAACATTAATTG
3540309 TTGTTTGTTTGAAAAGAAAGAAACA-TAAGTTG
1 TTGTTTGTTTGAAAAGAAAGAAACATTAA-TTG
3540341 TT-TTTGTT
1 TTGTTTGTT
3540349 ACTATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 8 0.22
32 29 0.78
ACGTcount: A:0.33, C:0.04, G:0.21, T:0.42
Consensus pattern (32 bp):
TTGTTTGTTTGAAAAGAAAGAAACATTAATTG
Found at i:3550406 original size:39 final size:39
Alignment explanation
Indices: 3550346--3550427 Score: 128
Period size: 39 Copynumber: 2.1 Consensus size: 39
3550336 TTTGTTGGCT
*
3550346 AAACCATTCTGAGATTCCACTTCCGGGCATAATAATATC
1 AAACCATTCTGAGATTCCACTTCCAGGCATAATAATATC
* * *
3550385 AAACCATTCTGGGATTTCACTTCCAGGCATAGTAATATC
1 AAACCATTCTGAGATTCCACTTCCAGGCATAATAATATC
3550424 AAAC
1 AAAC
3550428 ATTTTCCTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.28
Consensus pattern (39 bp):
AAACCATTCTGAGATTCCACTTCCAGGCATAATAATATC
Found at i:3553506 original size:62 final size:62
Alignment explanation
Indices: 3553409--3553533 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
3553399 ATCACTATGG
3553409 AAAGCTGTCAAATTGAAAAGTTGAAGCGCATCTGTGTAATCCAATGTTGTGGGTATATACAC
1 AAAGCTGTCAAATTGAAAAGTTGAAGCGCATCTGTGTAATCCAATGTTGTGGGTATATACAC
3553471 AAAGCTGTCAAATTGAAAAGTTGAAGCGCATCTGTGTAATCCAATGTTGTGGGTATATACAC
1 AAAGCTGTCAAATTGAAAAGTTGAAGCGCATCTGTGTAATCCAATGTTGTGGGTATATACAC
3553533 A
1 A
3553534 TCATCAACTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (62 bp):
AAAGCTGTCAAATTGAAAAGTTGAAGCGCATCTGTGTAATCCAATGTTGTGGGTATATACAC
Found at i:3555589 original size:40 final size:39
Alignment explanation
Indices: 3555543--3555629 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 39
3555533 TTAATTAATT
*
3555543 TTTTAAA-TTTTAAAAAATATTTTTTTTATAATTTTTATAA
1 TTTTAAATTTTTAAAAAATATTTTTTTTAT--TTTTTAAAA
*
3555583 TTTTAAATTTTTTAAAATATATTTTTTTTATTTTTTAAAA
1 TTTTAAA-TTTTTAAAAAATATTTTTTTTATTTTTTAAAA
3555623 TTTTAAA
1 TTTTAAA
3555630 AAATTAATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 22 0.51
42 21 0.49
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTAAATTTTTAAAAAATATTTTTTTTATTTTTTAAAA
Found at i:3555608 original size:22 final size:23
Alignment explanation
Indices: 3555578--3555623 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3555568 TTATAATTTT
3555578 TATA-ATTTTAAATTTTTTAAAA
1 TATATATTTTAAATTTTTTAAAA
* **
3555600 TATATTTTTTTTATTTTTTAAAA
1 TATATATTTTAAATTTTTTAAAA
3555623 T
1 T
3555624 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TATATATTTTAAATTTTTTAAAA
Found at i:3556855 original size:19 final size:19
Alignment explanation
Indices: 3556833--3556870 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3556823 GATTTTTGAA
* *
3556833 AAATGATTTACTTTTCTGG
1 AAATAATTTACATTTCTGG
3556852 AAATAATTTACATTTCTGG
1 AAATAATTTACATTTCTGG
3556871 TGTTTAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.45
Consensus pattern (19 bp):
AAATAATTTACATTTCTGG
Found at i:3556972 original size:16 final size:16
Alignment explanation
Indices: 3556951--3556991 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
3556941 CTGTATTTAC
3556951 ATATATTAATAAATAT
1 ATATATTAATAAATAT
*
3556967 ATATATTAATAAATTT
1 ATATATTAATAAATAT
*
3556983 ATATTTTAA
1 ATATATTAA
3556992 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATATTAATAAATAT
Found at i:3558572 original size:25 final size:25
Alignment explanation
Indices: 3558521--3558573 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
3558511 TTGATCACTC
* **
3558521 AAACTCATCTTTTGAGTTGGAATAA
1 AAACTCATCCTTTGAGAGGGAATAA
3558546 AAACTCATCCTTTGAGAAGGGAA-AA
1 AAACTCATCCTTTGAG-AGGGAATAA
3558571 AAA
1 AAA
3558574 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (25 bp):
AAACTCATCCTTTGAGAGGGAATAA
Found at i:3560828 original size:40 final size:41
Alignment explanation
Indices: 3560704--3560935 Score: 287
Period size: 41 Copynumber: 5.8 Consensus size: 41
3560694 AAATATACAT
* * *
3560704 TAGCGGCG-TTTTGCCAAAAACGCCGCT-AAAAACATAGCAA
1 TAGCGGCGTTTTTGGC-AAAGCGCCGCTAAAAAACAGAGCAA
*
3560744 TAGCGGCTTTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
1 TAGCGGC-GTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
*
3560786 TAGCGGCGTTTTTGGCAAAGCGCCGCT-AAAAATAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
* *
3560826 TAGCGGCGTTTTTTGCGAAGCGCCGCTAAAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
** * * *
3560867 TAGCACCGTTTTTAGTAAA--G-CGCTAAAAAATAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
*
3560905 TAGCGGCGTTTTTGGCAGAGCGCCGCTAAAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAA
3560936 GTCATATAAC
Statistics
Matches: 165, Mismatches: 20, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
38 31 0.19
39 1 0.01
40 45 0.27
41 63 0.38
42 25 0.15
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.21
Consensus pattern (41 bp):
TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
Found at i:3560879 original size:81 final size:79
Alignment explanation
Indices: 3560721--3560935 Score: 290
Period size: 81 Copynumber: 2.7 Consensus size: 79
3560711 GTTTTGCCAA
* * *
3560721 AAACGCCGCTAAAAACATAGCAATAGCGGCTTTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
1 AAACGCCGCTAAAAATAGAGCAATAGCGGCGTTTTTT-GC-AAGCGCCGCTAAAAAACAGAGCAA
** *
3560786 TAGCGGCGTTTTTGGC
64 TAGCACCGTTTTTAGC
3560802 AAAGCGCCGCTAAAAATAGAGCAATAGCGGCGTTTTTTGCGAAGCGCCGCTAAAAAACAGAGCAA
1 AAA-CGCCGCTAAAAATAGAGCAATAGCGGCGTTTTTTGC-AAGCGCCGCTAAAAAACAGAGCAA
*
3560867 TAGCACCGTTTTTAGT
64 TAGCACCGTTTTTAGC
*
3560883 AAA-G-CGCTAAAAAATAGAGCAATAGCGGCGTTTTTGGCAGAGCGCCGCTAAAA
1 AAACGCCGCT-AAAAATAGAGCAATAGCGGCGTTTTTTGCA-AGCGCCGCTAAAA
3560936 GTCATATAAC
Statistics
Matches: 122, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
78 5 0.04
79 42 0.34
81 44 0.36
82 31 0.25
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (79 bp):
AAACGCCGCTAAAAATAGAGCAATAGCGGCGTTTTTTGCAAGCGCCGCTAAAAAACAGAGCAATA
GCACCGTTTTTAGC
Found at i:3561046 original size:46 final size:47
Alignment explanation
Indices: 3560937--3561065 Score: 143
Period size: 46 Copynumber: 2.7 Consensus size: 47
3560927 CCGCTAAAAG
* * * * * *
3560937 TCATATAACCCCTAAATCCTTAAACACCCAAAAAAATCATAGACACTAG
1 TCATATAACTCCTAAAACCCT-AA-ACCCAAAAAAACCATAAACACTAA
*
3560986 TCTATATAACTCCTAAAACCCTAAACCCAAAAAAACCCTAAACACTAA
1 TC-ATATAACTCCTAAAACCCTAAACCCAAAAAAACCATAAACACTAA
* *
3561034 TC-TATAATTCCTAAAACCCTAAACCCCAAAAA
1 TCATATAACTCCTAAAACCCTAAACCCAAAAAA
3561066 CATCATATGG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
46 28 0.40
48 22 0.31
49 4 0.06
50 16 0.23
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (47 bp):
TCATATAACTCCTAAAACCCTAAACCCAAAAAAACCATAAACACTAA
Found at i:3565189 original size:19 final size:21
Alignment explanation
Indices: 3565161--3565208 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
3565151 TTATTATTTA
3565161 TTTTAGTTTTGATTATAA-AT
1 TTTTAGTTTTGATTATAATAT
* *
3565181 TTTTA-TTTTTATTTTAATAT
1 TTTTAGTTTTGATTATAATAT
3565201 TTTTAGTT
1 TTTTAGTT
3565209 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTAGTTTTGATTATAATAT
Found at i:3565190 original size:20 final size:20
Alignment explanation
Indices: 3565149--3565208 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
3565139 TTAATCTAAT
*
3565149 TTTTATTAT-TTA-TTTTAG
1 TTTTATTATAATATTTTTAG
*
3565167 TTTTGATTATAA-ATTTTTAT
1 TTTT-ATTATAATATTTTTAG
*
3565187 TTTTATTTTAATATTTTTAG
1 TTTTATTATAATATTTTTAG
3565207 TT
1 TT
3565209 AAAATTTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.12
19 12 0.35
20 18 0.53
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTATTATAATATTTTTAG
Found at i:3569560 original size:62 final size:62
Alignment explanation
Indices: 3569463--3569586 Score: 230
Period size: 62 Copynumber: 2.0 Consensus size: 62
3569453 TGCACAGTAT
3569463 GATTGATTTTGTTGGGGTTTTGACAGTAGCAAAAGAAGATAACAAGACAGAGAACAAAAGAG
1 GATTGATTTTGTTGGGGTTTTGACAGTAGCAAAAGAAGATAACAAGACAGAGAACAAAAGAG
* *
3569525 GATTGGTTTTGTTGGGGTTTTGACAGTAGCAAAAGAAGATAACAAGACAGAGAGCAAAAGAG
1 GATTGATTTTGTTGGGGTTTTGACAGTAGCAAAAGAAGATAACAAGACAGAGAACAAAAGAG
3569587 CAAGAAGCTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.40, C:0.08, G:0.29, T:0.23
Consensus pattern (62 bp):
GATTGATTTTGTTGGGGTTTTGACAGTAGCAAAAGAAGATAACAAGACAGAGAACAAAAGAG
Found at i:3570387 original size:19 final size:19
Alignment explanation
Indices: 3570363--3570401 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3570353 TCACAATTTT
3570363 ATATAATCTTTTCTCTATC
1 ATATAATCTTTTCTCTATC
3570382 ATATAATCTTTTCTCTATC
1 ATATAATCTTTTCTCTATC
3570401 A
1 A
3570402 CTAGTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATAATCTTTTCTCTATC
Found at i:3576843 original size:30 final size:32
Alignment explanation
Indices: 3576781--3576850 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
3576771 TTAAATTTGT
* *
3576781 AATGAT-AAAATTACACTTTGACTCCCTTAAA
1 AATGATAAAAATTACAATTTGAATCCCTTAAA
*
3576812 AATGATAAAAATTA-AATTT-AATCCTTTAAA
1 AATGATAAAAATTACAATTTGAATCCCTTAAA
*
3576842 AATTATAAA
1 AATGATAAA
3576851 TATATAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.50
31 10 0.29
32 7 0.21
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.34
Consensus pattern (32 bp):
AATGATAAAAATTACAATTTGAATCCCTTAAA
Found at i:3583275 original size:9 final size:9
Alignment explanation
Indices: 3583261--3583290 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3583251 TTTCAGGAAC
3583261 TTTTTAAAA
1 TTTTTAAAA
3583270 TTTTTAAAA
1 TTTTTAAAA
3583279 -TTTTAAAA
1 TTTTTAAAA
3583287 TTTT
1 TTTT
3583291 GGATAATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:3583582 original size:16 final size:16
Alignment explanation
Indices: 3583561--3583592 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3583551 TTTACAAATG
3583561 AAAAATAATAATTATA
1 AAAAATAATAATTATA
3583577 AAAAATAATAATTATA
1 AAAAATAATAATTATA
3583593 TTAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATAATAATTATA
Found at i:3588398 original size:44 final size:45
Alignment explanation
Indices: 3588339--3588431 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 45
3588329 ATACCATCAC
* *
3588339 AAATATTGAACTAAACTGAGTAATAGAAAAATAATTTAAATATAA
1 AAATATTGAACTAAACCGAATAATAGAAAAATAATTTAAATATAA
* ** *
3588384 AAAT-TTGGACTAAACCGAATAATAGAATGATAATTTAAATATTA
1 AAATATTGAACTAAACCGAATAATAGAAAAATAATTTAAATATAA
3588428 AAAT
1 AAAT
3588432 GATAAAAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 38 0.90
45 4 0.10
ACGTcount: A:0.55, C:0.05, G:0.10, T:0.30
Consensus pattern (45 bp):
AAATATTGAACTAAACCGAATAATAGAAAAATAATTTAAATATAA
Found at i:3588619 original size:13 final size:14
Alignment explanation
Indices: 3588603--3588636 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
3588593 TTTAAAGGTT
3588603 TATTTTATAAA-TA
1 TATTTTATAAATTA
3588616 TATTTT-TAAATTA
1 TATTTTATAAATTA
3588629 TATTTTAT
1 TATTTTAT
3588637 TTTATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 14 0.74
14 1 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTTATAAATTA
Found at i:3588632 original size:26 final size:25
Alignment explanation
Indices: 3588586--3588636 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
3588576 ATGACCTGAT
3588586 AATATATTTTAAAGGTTTATTTTATA
1 AATATATTTTAAA-GTTTATTTTATA
3588612 AATATATTTTTAAA-TTATATTTTAT
1 AATATA-TTTTAAAGTT-TATTTTAT
3588637 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 2 0.09
26 14 0.61
27 7 0.30
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
AATATATTTTAAAGTTTATTTTATA
Found at i:3598142 original size:357 final size:356
Alignment explanation
Indices: 3597487--3598199 Score: 1408
Period size: 357 Copynumber: 2.0 Consensus size: 356
3597477 AGAATATTTT
3597487 GATTTTGAAAATTGAGATTCGCTTGTATCAAAATATTGACACTAAGTTAGCCCCCCCTTTTTTTA
1 GATTTTGAAAATTGAGATTCGCTTGTATCAAAATATTGACACTAAGTTAGCCCCCCCTTTTTTTA
3597552 AAAATCCCTATCTCGAAACGACAAAACGCCACATCCAATAAGTTAAGACACGATGCTTTGAAATT
66 AAAATCCCTATCTCGAAACGACAAAACGCCACATCCAATAAGTTAAGACACGATGCTTTGAAATT
3597617 CCAGGACAATTGCTCATTTTTTGAAAACCTTAAAAAATTTAAAAGGGTACTTGATTATTCGAACT
131 CCAGGACAATTGCTCATTTTTTGAAAACCTTAAAAAATTTAAAAGGGTACTTGATTATTCGAACT
*
3597682 CAACGAGAAAAGTTGCAACCCAATAAGTTAGGGCACTACTTTTTCGAAGCTTCCAAACACCTAGC
196 CAACGAGAAAAGTTGCAACCCAATAAGTTAGGGCACTACTTTTTCGAAGCTTCCAAACACCAAGC
3597747 ATTGCCTTTTTATTTTTGAAAACTTTGAAGTCTCGTTTTTAAAACTGATGCATGAAGGAGCACAT
261 ATTGCCTTTTTATTTTTGAAAACTTTGAAGTCTCGTTTTTAAAACTGATGCATGAAGGAGCACAT
3597812 TAACATAATAAAACATAACATACAAGATAGA
326 TAACATAATAAAACATAACATACAAGATAGA
3597843 NGATTTTGAAAATTGAGATTCGCTTGTATCAAAATATTGACACTAAGTTAGCCCCCCCTTTTTTT
1 -GATTTTGAAAATTGAGATTCGCTTGTATCAAAATATTGACACTAAGTTAGCCCCCCCTTTTTTT
3597908 AAAAATCCCTATCTCGAAACGACAAAACGCCACATCCAATAAGTTAAGACACGATGCTTTGAAAT
65 AAAAATCCCTATCTCGAAACGACAAAACGCCACATCCAATAAGTTAAGACACGATGCTTTGAAAT
3597973 TCCAGGACAATTGCTCATTTTTTGAAAACCTTAAAAAATTTAAAAGGGTACTTGATTATTCGAAC
130 TCCAGGACAATTGCTCATTTTTTGAAAACCTTAAAAAATTTAAAAGGGTACTTGATTATTCGAAC
3598038 TCAACGAGAAAAGTTGCAACCCAATAAGTTAGGGCACTACTTTTTCGAAGCTTCCAAACACCAAG
195 TCAACGAGAAAAGTTGCAACCCAATAAGTTAGGGCACTACTTTTTCGAAGCTTCCAAACACCAAG
3598103 CATTGCCTTTTTATTTTTGAAAACTTTGAAGTCTCGTTTTTAAAACTGATGCATGAAGGAGCACA
260 CATTGCCTTTTTATTTTTGAAAACTTTGAAGTCTCGTTTTTAAAACTGATGCATGAAGGAGCACA
3598168 TTAACATAATAAAACATAACATACAAGATAGA
325 TTAACATAATAAAACATAACATACAAGATAGA
3598200 ATATTACAGT
Statistics
Matches: 355, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
357 355 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (356 bp):
GATTTTGAAAATTGAGATTCGCTTGTATCAAAATATTGACACTAAGTTAGCCCCCCCTTTTTTTA
AAAATCCCTATCTCGAAACGACAAAACGCCACATCCAATAAGTTAAGACACGATGCTTTGAAATT
CCAGGACAATTGCTCATTTTTTGAAAACCTTAAAAAATTTAAAAGGGTACTTGATTATTCGAACT
CAACGAGAAAAGTTGCAACCCAATAAGTTAGGGCACTACTTTTTCGAAGCTTCCAAACACCAAGC
ATTGCCTTTTTATTTTTGAAAACTTTGAAGTCTCGTTTTTAAAACTGATGCATGAAGGAGCACAT
TAACATAATAAAACATAACATACAAGATAGA
Found at i:3599125 original size:13 final size:15
Alignment explanation
Indices: 3599080--3599127 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
3599070 AAGAAAAGAA
3599080 AAAGTAATATATAAT
1 AAAGTAATATATAAT
*
3599095 AACAATAATATATAAT
1 AA-AGTAATATATAAT
3599111 AAAGTAATTATATAAT
1 AAAGTAA-TATATAAT
3599127 A
1 A
3599128 TGGTATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 6 0.21
16 23 0.79
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (15 bp):
AAAGTAATATATAAT
Found at i:3601183 original size:206 final size:207
Alignment explanation
Indices: 3600829--3601255 Score: 689
Period size: 206 Copynumber: 2.1 Consensus size: 207
3600819 CAAATTTGCC
* **
3600829 TCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTTGCTTCAGTGTAATC
1 TCTTCGATTTGCTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTTGCTTCAGCCTAATC
*
3600894 GTCTGAAGGTCAGATCTGCTATGTATCTGCTCTTCATTGAAGTGGAGATGCCAGACTTCGATTTG
66 GTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTTG
* * *
3600959 TTCTCTGACACTACAGAG-ACGACAAATCATCTTAGATTTGCTTCATCGTAAGCACGTGAAAGCT
131 TTCTCTGACACTACAGAGAACGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCC
*
3601023 AAATTAGCTATG
196 AAATCAGCTATG
*
3601035 TCTTCGATTTGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTGCTTCAGCCTAATC
1 TCTTCGATTTGCTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTTGCTTCAGCCTAATC
3601100 GTCTGAAGG-CGAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTT
66 GTCTGAAGGTC-AGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTT
* * *
3601164 GTTCTTTGACAAC-ACAGAGAATGCCAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAG
130 GTTCTCTGAC-ACTACAGAGAACGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAG
3601228 CCAAATCAGCTATG
194 CCAAATCAGCTATG
* *
3601242 TTTTCGATCTGCTC
1 TCTTCGATTTGCTC
3601256 TCCGCCAATA
Statistics
Matches: 204, Mismatches: 14, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
205 1 0.00
206 137 0.67
207 66 0.32
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (207 bp):
TCTTCGATTTGCTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTTGCTTCAGCCTAATC
GTCTGAAGGTCAGATCTGCTATGTATCTGCTCTCCATTGAAGTGGAGATGCCAGACTTCGATTTG
TTCTCTGACACTACAGAGAACGACAAATCATCTTAGATTTGCTTCAACGTAAACACGTGAAAGCC
AAATCAGCTATG
Found at i:3601299 original size:44 final size:44
Alignment explanation
Indices: 3601251--3601334 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
3601241 GTTTTCGATC
* *
3601251 TGCTCTCCGCCAATACAGAGATGCCAAATCTGGTATCTTCGACA
1 TGCTCTCCGACAATACAGAGATGCCAAATCTGCTATCTTCGACA
*
3601295 TGCTCTCTGACAATACAGAGATGCCAAATCTGCTATCTTC
1 TGCTCTCCGACAATACAGAGATGCCAAATCTGCTATCTTC
3601335 AACTTGTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (44 bp):
TGCTCTCCGACAATACAGAGATGCCAAATCTGCTATCTTCGACA
Found at i:3601362 original size:44 final size:44
Alignment explanation
Indices: 3601314--3601492 Score: 161
Period size: 44 Copynumber: 4.1 Consensus size: 44
3601304 ACAATACAGA
3601314 GATGCCAAATCTGCTATCTTCAA-CTTGTTCCCTATAAACACAAG
1 GATGCCAAATCTGCTATCTTCAATC-TGTTCCCTATAAACACAAG
** * * * * * *
3601358 GATGCC--ATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCA-TAG
1 GATGCCAAAT-CTGCTATCTTCAATCTG-TTCCCTATAAACACAAG
* * * *
3601401 GAATGTCATATCTGTTATCTTCGATCTGTTCCCTATAAACACAAG
1 G-ATGCCAAATCTGCTATCTTCAATCTGTTCCCTATAAACACAAG
*
3601446 GATGCCAAATCTGCTATCTTCAA-CTTGTTCCCTATAAACACAGG
1 GATGCCAAATCTGCTATCTTCAATC-TGTTCCCTATAAACACAAG
3601490 GAT
1 GAT
3601493 ACCATGCTGA
Statistics
Matches: 106, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
42 2 0.02
43 15 0.14
44 70 0.66
45 17 0.16
46 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (44 bp):
GATGCCAAATCTGCTATCTTCAATCTGTTCCCTATAAACACAAG
Found at i:3601414 original size:132 final size:132
Alignment explanation
Indices: 3601278--3601527 Score: 380
Period size: 132 Copynumber: 1.9 Consensus size: 132
3601268 GAGATGCCAA
* *
3601278 ATCTGGTATCTTCGA-CATGCTCTCTGAC-AATAC-AGAGATGCCAAATCTGCTATCTTCAACTT
1 ATCTGGTATCTTCGATC-TGCTCCCT-ACAAACACAAG-GATGCCAAATCTGCTATCTTCAACTT
*
3601340 GTTCCCTATAAACACAAGGATGCCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCATAGGAAT
63 GTTCCCTATAAACACAAGGATACCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCATAGGAAT
3601405 GTCAT
128 GTCAT
* * *
3601410 ATCTGTTATCTTCGATCTGTTCCCTATAAACACAAGGATGCCAAATCTGCTATCTTCAACTTGTT
1 ATCTGGTATCTTCGATCTGCTCCCTACAAACACAAGGATGCCAAATCTGCTATCTTCAACTTGTT
* *
3601475 CCCTATAAACACAGGGATACCATGCTGAAATCTTCGATCTGCTTCGCTGTAAG
66 CCCTATAAACACAAGGATACCATGCTGAAATCCTCGATCTGCTTCGCTGTAAG
3601528 TCAGATCTGC
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
131 1 0.01
132 103 0.96
133 3 0.03
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (132 bp):
ATCTGGTATCTTCGATCTGCTCCCTACAAACACAAGGATGCCAAATCTGCTATCTTCAACTTGTT
CCCTATAAACACAAGGATACCATGCTGAAATCCTCGATCTGCTTCGCTGTAAGCATAGGAATGTC
AT
Found at i:3609869 original size:14 final size:16
Alignment explanation
Indices: 3609834--3609870 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3609824 CAAACGATAT
3609834 GATG-AAATGCTATGA
1 GATGCAAATGCTATGA
3609849 GATGCAAATGC-ATGA
1 GATGCAAATGCTATGA
3609864 -ATGCAAA
1 GATGCAAA
3609871 AAAGGATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.33
15 8 0.38
16 6 0.29
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (16 bp):
GATGCAAATGCTATGA
Found at i:3613302 original size:16 final size:15
Alignment explanation
Indices: 3613276--3613324 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 15
3613266 AAAGAAAAGA
3613276 AAAAGTAATATATAAT
1 AAAA-TAATATATAAT
3613292 AACAATAATATATAAT
1 AA-AATAATATATAAT
3613308 AAAATAATTATATAAT
1 AAAATAA-TATATAAT
3613324 A
1 A
3613325 TGGTATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.16
16 24 0.77
17 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAATAATATATAAT
Found at i:3613320 original size:18 final size:16
Alignment explanation
Indices: 3613281--3613324 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
3613271 AAAGAAAAAG
3613281 TAATATATAATAACAA
1 TAATATATAATAACAA
3613297 TAATATATAATAA-AA
1 TAATATATAATAACAA
3613312 TAATTATATAATA
1 TAA-TATATAATA
3613325 TGGTATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATATATAATAACAA
Found at i:3626020 original size:32 final size:32
Alignment explanation
Indices: 3625979--3626042 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
3625969 AGTTAGGATG
3625979 ATAGCAATTCTGATTTAGAGCGACCTTGAGAA
1 ATAGCAATTCTGATTTAGAGCGACCTTGAGAA
*
3626011 ATAGCAATTCTGATTTAGAGCGATCTTGAGAA
1 ATAGCAATTCTGATTTAGAGCGACCTTGAGAA
3626043 GGTTCTTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (32 bp):
ATAGCAATTCTGATTTAGAGCGACCTTGAGAA
Found at i:3632234 original size:25 final size:25
Alignment explanation
Indices: 3632206--3632253 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
3632196 ATATTAATCA
3632206 AAATTCAAATAAAGA-GTACAATTAG
1 AAATTCAAATAAA-ATGTACAATTAG
3632231 AAATTCAAATAAAATGTACAATT
1 AAATTCAAATAAAATGTACAATT
3632254 GGTTCTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (25 bp):
AAATTCAAATAAAATGTACAATTAG
Found at i:3632905 original size:21 final size:21
Alignment explanation
Indices: 3632879--3632934 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
3632869 GACATTATTC
*
3632879 AAAAATATATATTAAAAAAAT
1 AAAAATATAAATTAAAAAAAT
* *
3632900 AAAAATAAAAATTAAAAAATT
1 AAAAATATAAATTAAAAAAAT
*
3632921 AAAATTATAAATTA
1 AAAAATATAAATTA
3632935 TAATTGGTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATATAAATTAAAAAAAT
Found at i:3633103 original size:15 final size:14
Alignment explanation
Indices: 3633072--3633106 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3633062 AAGTAAGTTA
3633072 TTTATAATTTTTAT
1 TTTATAATTTTTAT
*
3633086 TTTATATTTTTATAT
1 TTTATAATTTT-TAT
3633101 TTTATA
1 TTTATA
3633107 GTTATTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATAATTTTTAT
Found at i:3639743 original size:44 final size:44
Alignment explanation
Indices: 3639693--3639779 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
3639683 GTTTAGTAAT
3639693 TAAAACCATAAATCTCAAGTATGAGATTTTGTAAGGGAGAAAAC
1 TAAAACCATAAATCTCAAGTATGAGATTTTGTAAGGGAGAAAAC
3639737 TAAAACCATAAATCTCAAGTATGAGATTTTGTAAGGGAGAAAA
1 TAAAACCATAAATCTCAAGTATGAGATTTTGTAAGGGAGAAAA
3639780 TAGAGATTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (44 bp):
TAAAACCATAAATCTCAAGTATGAGATTTTGTAAGGGAGAAAAC
Found at i:3646021 original size:16 final size:17
Alignment explanation
Indices: 3646000--3646032 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3645990 TTGAAACTTT
3646000 ATTTTAAT-ATTTTTAA
1 ATTTTAATAATTTTTAA
*
3646016 ATTTTAGTAATTTTTAA
1 ATTTTAATAATTTTTAA
3646033 TCATTGGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTTTAATAATTTTTAA
Found at i:3646534 original size:21 final size:22
Alignment explanation
Indices: 3646483--3646534 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
3646473 TTTTTAAATT
* *
3646483 TATCATATATTATTTTTCATTTA
1 TATCATATATTA-TTATAATTTA
* *
3646506 TTTTATATATTA-TATAATTTA
1 TATCATATATTATTATAATTTA
3646527 TATCATAT
1 TATCATAT
3646535 GAAGAAAAGT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 13 0.57
23 10 0.43
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (22 bp):
TATCATATATTATTATAATTTA
Found at i:3648598 original size:22 final size:21
Alignment explanation
Indices: 3648554--3648612 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
3648544 ATTTGGATAT
3648554 AAAAAATTTTAAATAATAATTG
1 AAAAAATTTTAAATAAT-ATTG
3648576 AAAAATATTTTAACATAAT-TTG
1 AAAAA-ATTTTAA-ATAATATTG
**
3648598 ATTAAATTTCTAAAT
1 AAAAAATTT-TAAAT
3648613 TAACTCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 6 0.19
22 14 0.44
23 7 0.22
24 5 0.16
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (21 bp):
AAAAAATTTTAAATAATATTG
Found at i:3667605 original size:108 final size:102
Alignment explanation
Indices: 3667479--3667685 Score: 342
Period size: 102 Copynumber: 2.0 Consensus size: 102
3667469 AGTAGACCTA
*
3667479 ATATATATATATATTATAATAGACTTAACTATCAAGTTCGGGAATAAAAAATATATTTGTAATTG
1 ATATATATATATATTATAATAGACTTAACTATC-A-----GGAATAAAAAATACATTTGTAATTG
3667544 TATAAAATGCAATATATATAAAAGAGATTAATATTTTATATAT
60 TATAAAATGCAATATATATAAAAGAGATTAATATTTTATATAT
3667587 ATATATATATATATTATAATAGACTTAACTATCAGGAATAAAAAATACATTTGTAATTGTATAAA
1 ATATATATATATATTATAATAGACTTAACTATCAGGAATAAAAAATACATTTGTAATTGTATAAA
*
3667652 ATGCAATATATATAAAAGAGATTGATATTTTATA
66 ATGCAATATATATAAAAGAGATTAATATTTTATA
3667686 CAAATTTGAA
Statistics
Matches: 97, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
102 63 0.65
107 1 0.01
108 33 0.34
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (102 bp):
ATATATATATATATTATAATAGACTTAACTATCAGGAATAAAAAATACATTTGTAATTGTATAAA
ATGCAATATATATAAAAGAGATTAATATTTTATATAT
Found at i:3670871 original size:18 final size:19
Alignment explanation
Indices: 3670844--3670881 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3670834 ATTTAAAATA
*
3670844 TATTTTTATTTTTAT-ATT
1 TATTTATATTTTTATGATT
3670862 TATTTATATTTTTATGATT
1 TATTTATATTTTTATGATT
3670881 T
1 T
3670882 TCAAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (19 bp):
TATTTATATTTTTATGATT
Found at i:3674397 original size:175 final size:176
Alignment explanation
Indices: 3674102--3674452 Score: 560
Period size: 175 Copynumber: 2.0 Consensus size: 176
3674092 AAGAAAAAGT
* * * *
3674102 TAGTTTTGTAAAAGTTATACCTTCTCCTTGAAATGTATTAATTCTAATTGTGAATTGGGAAGTCC
1 TAGTTTTGTAAAAGTTATACCTTCTCCTTGAAATGTATTAATTCTAATAGTAAATTGAGAAATCC
* * * *
3674167 TTAATGGTGGAAAGCTAAGGTAGTGGAGATATGCAATTAGTGCCGAACGATTATAAACCGAAGTG
66 TTAATGGTGGAAAGCTAAGGTAGTGGAGATAGGCAATTAGGGCCGAACCATTATAAACCAAAGTG
*
3674232 TTCAAGCTTTTCTTTCATTTTCTTATCATTTAGAAAAGTTTGTAGA
131 TTCAAGCTTTACTTTCATTTTCTTATCATTTAGAAAAGTTTGTAGA
*
3674278 TAGTTTTGTAAAAGTTATACCTTCTCCTTGAAATGTATTAATT-TTATAGTAAATTGAGAAATCC
1 TAGTTTTGTAAAAGTTATACCTTCTCCTTGAAATGTATTAATTCTAATAGTAAATTGAGAAATCC
* * * *
3674342 TTAATGGTGGAAAGCTAAGGTAGTGGAGATAGGTAATTGGGGCCGAACCATTATAAACTAAAGTT
66 TTAATGGTGGAAAGCTAAGGTAGTGGAGATAGGCAATTAGGGCCGAACCATTATAAACCAAAGTG
*
3674407 TTCAATCTTTACTTTCATTTTCTTATCATTTAGAAAAGTTTGTAGA
131 TTCAAGCTTTACTTTCATTTTCTTATCATTTAGAAAAGTTTGTAGA
3674453 ATTTTTTAAA
Statistics
Matches: 160, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
175 117 0.73
176 43 0.27
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (176 bp):
TAGTTTTGTAAAAGTTATACCTTCTCCTTGAAATGTATTAATTCTAATAGTAAATTGAGAAATCC
TTAATGGTGGAAAGCTAAGGTAGTGGAGATAGGCAATTAGGGCCGAACCATTATAAACCAAAGTG
TTCAAGCTTTACTTTCATTTTCTTATCATTTAGAAAAGTTTGTAGA
Found at i:3676083 original size:28 final size:28
Alignment explanation
Indices: 3676043--3676121 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
3676033 GCAATCAAAT
* * *
3676043 ATGGTACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
*
3676071 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTGCGAAATATTGAGA
* *
3676099 ATGACACTTAGTGTGCAAAATAT
1 ATGGCACTTAGTGTGCGAAATAT
3676122 CGAATGATTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTGCGAAATATTGAGA
Found at i:3680019 original size:460 final size:460
Alignment explanation
Indices: 3679159--3680078 Score: 1831
Period size: 460 Copynumber: 2.0 Consensus size: 460
3679149 ATGTATGAAG
3679159 GTATTGAATATATAATAATTTGCTATAAGCTTTGTCACACACGGTTTACTTTAAACCCATAAATT
1 GTATTGAATATATAATAATTTGCTATAAGCTTTGTCACACACGGTTTACTTTAAACCCATAAATT
3679224 AAGGATGATTTAGGGGTTAAATTGAAAGATATCATAAGCTAGCGGCCTTTTTTGGAAAATCAGGA
66 AAGGATGATTTAGGGGTTAAATTGAAAGATATCATAAGCTAGCGGCCTTTTTTGGAAAATCAGGA
*
3679289 AAAGTTAGAAACAAAATTGGACAAGGTTGAGAATTGATTATGGTTCAGTTTAATCTAGATTAGCC
131 AAAGTTAGAAACAAAATTGGACAAGGTTGAGAATTGATTATGGTTCAGTTTAATCTAGACTAGCC
3679354 AGTCTTTTACTGGGGGACAAAATGATTGTCAATGGATGGTTCCTAAATGGTTGGAGACCGTGAGA
196 AGTCTTTTACTGGGGGACAAAATGATTGTCAATGGATGGTTCCTAAATGGTTGGAGACCGTGAGA
3679419 GAGGGGGTATATTGATAAACCGTAATTTATACATATTTTTACCCCATGCTTAACGCATTTTATGG
261 GAGGGGGTATATTGATAAACCGTAATTTATACATATTTTTACCCCATGCTTAACGCATTTTATGG
3679484 ATGATTTTCCATTAGAATTGGTGGATTCGATGCTCCTAATGCTTTAATTTCATGTTTTATACTTA
326 ATGATTTTCCATTAGAATTGGTGGATTCGATGCTCCTAATGCTTTAATTTCATGTTTTATACTTA
3679549 GGAGATAATAGGAGAGCGAAAAGAACCATAAACGGGCCAAAAACAGAGAAAAATGGGCCAAAGTA
391 GGAGATAATAGGAGAGCGAAAAGAACCATAAACGGGCCAAAAACAGAGAAAAATGGGCCAAAGTA
3679614 CGAAT
456 CGAAT
3679619 GTATTGAATATATAATAATTTGCTATAAGCTTTGTCACACACGGTTTACTTTAAACCCATAAATT
1 GTATTGAATATATAATAATTTGCTATAAGCTTTGTCACACACGGTTTACTTTAAACCCATAAATT
3679684 AAGGATGATTTAGGGGTTAAATTGAAAGATATCATAAGCTAGCGGCCTTTTTTGGAAAATCAGGA
66 AAGGATGATTTAGGGGTTAAATTGAAAGATATCATAAGCTAGCGGCCTTTTTTGGAAAATCAGGA
3679749 AAAGTTAGAAACAAAATTGGACAAGGTTGAGAATTGATTATGGTTCAGTTTAATCTAGACTAGCC
131 AAAGTTAGAAACAAAATTGGACAAGGTTGAGAATTGATTATGGTTCAGTTTAATCTAGACTAGCC
3679814 AGTCTTTTACTGGGGGACAAAATGATTGTCAATGGATGGTTCCTAAATGGTTGGAGACCGTGAGA
196 AGTCTTTTACTGGGGGACAAAATGATTGTCAATGGATGGTTCCTAAATGGTTGGAGACCGTGAGA
3679879 GAGGGGGTATATTGATAAACCGTAATTTATACATATTTTTACCCCATGCTTAACGCATTTTATGG
261 GAGGGGGTATATTGATAAACCGTAATTTATACATATTTTTACCCCATGCTTAACGCATTTTATGG
3679944 ATGATTTTCCATTAGAATTGGTGGATTCGATGCTCCTAATGCTTTAATTTCATGTTTTATACTTA
326 ATGATTTTCCATTAGAATTGGTGGATTCGATGCTCCTAATGCTTTAATTTCATGTTTTATACTTA
3680009 GGAGATAATAGGAGAGCGAAAAGAACCATAAACGGGCCAAAAACAGAGAAAAATGGGCCAAAGTA
391 GGAGATAATAGGAGAGCGAAAAGAACCATAAACGGGCCAAAAACAGAGAAAAATGGGCCAAAGTA
3680074 CGAAT
456 CGAAT
3680079 TCAACACGTC
Statistics
Matches: 459, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
460 459 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (460 bp):
GTATTGAATATATAATAATTTGCTATAAGCTTTGTCACACACGGTTTACTTTAAACCCATAAATT
AAGGATGATTTAGGGGTTAAATTGAAAGATATCATAAGCTAGCGGCCTTTTTTGGAAAATCAGGA
AAAGTTAGAAACAAAATTGGACAAGGTTGAGAATTGATTATGGTTCAGTTTAATCTAGACTAGCC
AGTCTTTTACTGGGGGACAAAATGATTGTCAATGGATGGTTCCTAAATGGTTGGAGACCGTGAGA
GAGGGGGTATATTGATAAACCGTAATTTATACATATTTTTACCCCATGCTTAACGCATTTTATGG
ATGATTTTCCATTAGAATTGGTGGATTCGATGCTCCTAATGCTTTAATTTCATGTTTTATACTTA
GGAGATAATAGGAGAGCGAAAAGAACCATAAACGGGCCAAAAACAGAGAAAAATGGGCCAAAGTA
CGAAT
Found at i:3682337 original size:17 final size:16
Alignment explanation
Indices: 3682302--3682353 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
3682292 GGGAAAAAAC
*
3682302 AAAGGAAAGAGAAATG
1 AAAGGAAAAAGAAATG
*
3682318 AAATGAAAAAGAATATG
1 AAAGGAAAAAGAA-ATG
*
3682335 AAAGGAAAAAGAAGTG
1 AAAGGAAAAAGAAATG
3682351 AAA
1 AAA
3682354 AATTAAGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (16 bp):
AAAGGAAAAAGAAATG
Found at i:3694387 original size:15 final size:16
Alignment explanation
Indices: 3694367--3694399 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3694357 TATGTATATG
3694367 TTGATAA-TATGACTA
1 TTGATAAGTATGACTA
*
3694382 TTGATAAGTATGTCTA
1 TTGATAAGTATGACTA
3694398 TT
1 TT
3694400 TTTCAGGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.45
Consensus pattern (16 bp):
TTGATAAGTATGACTA
Found at i:3696327 original size:5 final size:5
Alignment explanation
Indices: 3696317--3696367 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
3696307 TAGGACATGT
* * * *
3696317 TATGA TATGA TATGA TATGT TATAA TA-CA TTATGA TATGA TAAGA TATGA
1 TATGA TATGA TATGA TATGA TATGA TATGA -TATGA TATGA TATGA TATGA
3696367 T
1 T
3696368 CAGAATGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
4 1 0.03
5 35 0.95
6 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (5 bp):
TATGA
Found at i:3698012 original size:6 final size:6
Alignment explanation
Indices: 3698001--3698026 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3697991 GTAATCAGCT
3698001 ATCTAC ATCTAC ATCTAC ATCTAC AT
1 ATCTAC ATCTAC ATCTAC ATCTAC AT
3698027 ACACATACAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (6 bp):
ATCTAC
Found at i:3699306 original size:74 final size:74
Alignment explanation
Indices: 3699161--3699308 Score: 185
Period size: 74 Copynumber: 2.0 Consensus size: 74
3699151 TAAATAATGA
** * *** *
3699161 GGTGAATTTATTATTTACTTTTTAAAGGAAAATATATAGTTATGTATTTGGTATTAGTATTTATG
1 GGTGAATTTATTATTTACTTTTTAAAGGAAAATATATAAATATGAATCAAGTAATAGTATTTATG
3699226 TATATTTAT
66 TATATTTAT
3699235 GGTGAATTTATTATTTACTTTTTAAAGGAAAATCATATAAATAT-AATCAAGTAATAGGTA-TTA
1 GGTGAATTTATTATTTACTTTTTAAAGGAAAAT-ATATAAATATGAATCAAGTAATA-GTATTTA
3699298 T-TAGTATTTAT
64 TGTA-TATTTAT
3699309 TTCACCTGCT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
73 2 0.03
74 51 0.80
75 11 0.17
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (74 bp):
GGTGAATTTATTATTTACTTTTTAAAGGAAAATATATAAATATGAATCAAGTAATAGTATTTATG
TATATTTAT
Found at i:3701694 original size:24 final size:24
Alignment explanation
Indices: 3701667--3701718 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3701657 TTAGTAAGTC
*
3701667 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3701691 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3701715 AAAT
1 AAAT
3701719 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3702911 original size:24 final size:24
Alignment explanation
Indices: 3702884--3702935 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3702874 TTAGTAAGTC
*
3702884 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3702908 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3702932 AAAT
1 AAAT
3702936 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3704882 original size:24 final size:24
Alignment explanation
Indices: 3704855--3704906 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3704845 TTAGTAAGTC
*
3704855 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
3704879 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
3704903 AAAT
1 AAAT
3704907 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:3708843 original size:4 final size:4
Alignment explanation
Indices: 3708824--3708860 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
3708814 AGCCCCAGCC
3708824 TTTA TTCTA TTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TT-TA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
3708861 CCCATTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 25 0.81
5 4 0.13
6 2 0.06
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:3712031 original size:129 final size:129
Alignment explanation
Indices: 3711801--3712044 Score: 479
Period size: 129 Copynumber: 1.9 Consensus size: 129
3711791 TAATATCAAT
*
3711801 ATATTAATGGCTTAATACATCACTTAATGCTTAAGTTTGACATTTTTTTTAACGAGGTATTTGGG
1 ATATTAATGGCTTAATACATCACTTAATGCTTAAGTTTGACATTTTTTTAAACGAGGTATTTGGG
3711866 GTTTTTTTTTTCAATGTGATACTTGTATTTAGAAAAAGTTATATATTTCGAACATATGCTTAAG
66 GTTTTTTTTTTCAATGTGATACTTGTATTTAGAAAAAGTTATATATTTCGAACATATGCTTAAG
3711930 ATATTAATGGCTTAATACATCACTTAATGCTTAAGTTTGACATTTTTTTAAACGAGGTATTTGGG
1 ATATTAATGGCTTAATACATCACTTAATGCTTAAGTTTGACATTTTTTTAAACGAGGTATTTGGG
3711995 GTTTTTTTTTTCAATGTGATACTTGTATTTAGAAAAAGTTATATATTTCG
66 GTTTTTTTTTTCAATGTGATACTTGTATTTAGAAAAAGTTATATATTTCG
3712045 GTACCCAAAA
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 114 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (129 bp):
ATATTAATGGCTTAATACATCACTTAATGCTTAAGTTTGACATTTTTTTAAACGAGGTATTTGGG
GTTTTTTTTTTCAATGTGATACTTGTATTTAGAAAAAGTTATATATTTCGAACATATGCTTAAG
Found at i:3712648 original size:14 final size:14
Alignment explanation
Indices: 3712631--3712671 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
3712621 AAAAAATATT
3712631 TTTTAATTATTTTA
1 TTTTAATTATTTTA
3712645 TTTTAATTATTTTA
1 TTTTAATTATTTTA
3712659 TTTTATATTATTT
1 TTTTA-ATTATTT
3712672 CTCTTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTAATTATTTTA
Found at i:3712682 original size:15 final size:14
Alignment explanation
Indices: 3712630--3712691 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
3712620 TAAAAAATAT
3712630 TTTTTAATTATTTTA
1 TTTTT-ATTATTTTA
*
3712645 TTTTAATTATTTTA
1 TTTTTATTATTTTA
*
3712659 TTTTATATTATTTCTC
1 TTTT-TATTATTT-TA
3712675 TTTTTA-T-TTTTA
1 TTTTTATTATTTTA
3712687 TTTTT
1 TTTTT
3712692 CTATTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 6 0.15
13 3 0.07
14 14 0.34
15 13 0.32
16 5 0.12
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTATTATTTTA
Found at i:3712698 original size:8 final size:7
Alignment explanation
Indices: 3712627--3712700 Score: 53
Period size: 8 Copynumber: 10.1 Consensus size: 7
3712617 CTTTAAAAAA
3712627 TATTTTT
1 TATTTTT
3712634 TAATTATTT
1 T-ATT-TTT
3712643 TA-TTTT
1 TATTTTT
*
3712649 AATTATTT
1 TATT-TTT
*
3712657 TATTTTA
1 TATTTTT
*
3712664 TATTATT
1 TATTTTT
*
3712671 TCTCTTTT
1 TAT-TTTT
3712679 TA-TTTT
1 TATTTTT
3712685 TATTTTT
1 TATTTTT
3712692 CTATTTTT
1 -TATTTTT
3712700 T
1 T
3712701 TTCTCTTCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
6 10 0.19
7 17 0.33
8 21 0.40
9 4 0.08
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (7 bp):
TATTTTT
Found at i:3712701 original size:22 final size:22
Alignment explanation
Indices: 3712654--3712699 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
3712644 ATTTTAATTA
3712654 TTTTATTTTATATTATTTCTCT
1 TTTTATTTTATATTATTTCTCT
*
3712676 TTTTATTTT-TATT-TTTCTAT
1 TTTTATTTTATATTATTTCTCT
3712696 TTTT
1 TTTT
3712700 TTTCTCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 4 0.17
22 9 0.39
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTATTTTATATTATTTCTCT
Found at i:3714057 original size:3 final size:3
Alignment explanation
Indices: 3714042--3714077 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3714032 AAGCATAAAC
* *
3714042 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3714078 CATTGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3714209 original size:3 final size:3
Alignment explanation
Indices: 3714177--3714251 Score: 57
Period size: 3 Copynumber: 25.3 Consensus size: 3
3714167 ATACACGTAC
* * *
3714177 ATA ATA A-A A-A ATA TATA CTA ATA CATA ATA ATA ATA ATA ATG GTA
1 ATA ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA
* * *
3714222 ATA CTA ATA ATA CTA ATA AT- ATA AAA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3714252 CAAGGATATT
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
2 6 0.11
3 44 0.79
4 6 0.11
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3715378 original size:22 final size:21
Alignment explanation
Indices: 3715353--3715404 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
3715343 AGTGTCAGAC
3715353 GGTATGGGACTGTTGTAGTGGA
1 GGTATGGG-CTGTTGTAGTGGA
*
3715375 GGTATAGGGCTGTTGTAGTGGG
1 GGTAT-GGGCTGTTGTAGTGGA
3715397 GGTATGGG
1 GGTATGGG
3715405 GTTGCTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 3 0.11
22 22 0.79
23 3 0.11
ACGTcount: A:0.15, C:0.04, G:0.50, T:0.31
Consensus pattern (21 bp):
GGTATGGGCTGTTGTAGTGGA
Found at i:3716485 original size:217 final size:215
Alignment explanation
Indices: 3716148--3716633 Score: 658
Period size: 217 Copynumber: 2.2 Consensus size: 215
3716138 GATATCTCAA
* * * ** *** *
3716148 CATGTGAACTGAGGCTCAACTCACTTTTCGCAATATGAGTTGATTTTTTTGACAACAGAAATTGA
1 CATGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-AATTAAAACAACAAAAATTGA
* * * * * *
3716213 AATTACCTCAGCGTGTCCTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAAGTA
65 AAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGCTGATTTTGAAAAAGTA
3716278 GAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAACA-AAATTTGCC
130 GAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAA-TT---
3716340 AAACA-GATT-TTGAAAATACCTCGG
191 AAA-AGGATTATTGAAAATACCTCGG
*
3716364 CATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACACACAAAAAATTG
1 CATGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACA-AC-AAAAATTG
3716429 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGCTGATTTTGAAAAAGT
64 AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGCTGATTTTGAAAAAGT
*
3716494 AGAAATTAAAAGGTTCAACCTACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACATAAATTA
129 AGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGA--TTTTTTGAAAAACATAAATTA
*
3716559 AAAGGCTTAATTGAAAATACCTCGG
192 AAAGGATT-ATTGAAAATACCTCGG
* *
3716584 CGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAA
1 CATGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAA
3716634 NNNNNNNNNN
Statistics
Matches: 239, Mismatches: 21, Indels: 16
0.87 0.08 0.06
Matches are distributed among these distances:
215 5 0.02
216 41 0.17
217 108 0.45
218 6 0.03
220 68 0.28
221 8 0.03
222 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (215 bp):
CATGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACAACAAAAATTGAA
AATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGCTGATTTTGAAAAAGTAG
AAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACATAAATTAAAAG
GATTATTGAAAATACCTCGG
Found at i:3719722 original size:25 final size:24
Alignment explanation
Indices: 3719681--3719747 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
3719671 TGGCATTTGA
*
3719681 TTTTTT-TTTTGTTTTTTTCTTGTCC
1 TTTTTTCTTTT-TCTTTTTCTTGT-C
* * *
3719706 TTTTTTCTTTTTGTTTTTTTTGTT
1 TTTTTTCTTTTTCTTTTTCTTGTC
3719730 TTGTTTTCTTTTTCTTTT
1 TT-TTTTCTTTTTCTTTT
3719748 CATGACTGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 2 0.06
25 30 0.83
26 4 0.11
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (24 bp):
TTTTTTCTTTTTCTTTTTCTTGTC
Found at i:3725431 original size:26 final size:27
Alignment explanation
Indices: 3725383--3725444 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
3725373 NNNNNNNNNN
*
3725383 ATAATAATATAAAAAGTAGATAA-AAT
1 ATAATAATATAAAAAGTAAATAAGAAT
*
3725409 ATAATGATATAAAAA-TAAAATAAGAAT
1 ATAATAATATAAAAAGT-AAATAAGAAT
3725436 A-AAGTAATA
1 ATAA-TAATA
3725445 GGTAATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 1 0.03
26 21 0.70
27 8 0.27
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (27 bp):
ATAATAATATAAAAAGTAAATAAGAAT
Found at i:3726749 original size:13 final size:13
Alignment explanation
Indices: 3726733--3726758 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3726723 TTTATTTGGT
3726733 TTATTGGGTTTTG
1 TTATTGGGTTTTG
3726746 TTATTGGGTTTTG
1 TTATTGGGTTTTG
3726759 GGGGTGGCCC
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:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TTATTGGGTTTTG
Found at i:3728145 original size:7 final size:7
Alignment explanation
Indices: 3728133--3728162 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3728123 TTCCAATTAA
3728133 TTTTTTG
1 TTTTTTG
3728140 TTTTTT-
1 TTTTTTG
3728146 TTTTTTG
1 TTTTTTG
3728153 TTTTTTG
1 TTTTTTG
3728160 TTT
1 TTT
3728163 GTGACAGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (7 bp):
TTTTTTG
Found at i:3728151 original size:13 final size:13
Alignment explanation
Indices: 3728133--3728158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3728123 TTCCAATTAA
3728133 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
3728146 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
3728159 GTTTGTGACA
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:3728332 original size:5 final size:5
Alignment explanation
Indices: 3728322--3728351 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3728312 CTTCCATCAA
*
3728322 TTTTC TTTTC TTTTC TTTTC CTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC
3728352 CCTTTAGCCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:3730114 original size:9 final size:9
Alignment explanation
Indices: 3730076--3730120 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
3730066 AAAACTAGGG
3730076 AATTTATTAT
1 AATTT-TTAT
3730086 -ATTTTTA-
1 AATTTTTAT
3730093 AA-TTTTA-
1 AATTTTTAT
3730100 AATTTTTAT
1 AATTTTTAT
3730109 AATTTTTAT
1 AATTTTTAT
3730118 AAT
1 AAT
3730121 AAATAACATT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.22
8 9 0.28
9 16 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
AATTTTTAT
Found at i:3730115 original size:17 final size:18
Alignment explanation
Indices: 3730076--3730120 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 18
3730066 AAAACTAGGG
3730076 AATTTATTAT-ATTTTTA-
1 AATTT-TTATAATTTTTAT
3730093 AA-TTTTA-AATTTTTAT
1 AATTTTTATAATTTTTAT
3730109 AATTTTTATAAT
1 AATTTTTATAAT
3730121 AAATAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 10 0.42
16 4 0.17
17 7 0.29
18 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTTTATAATTTTTAT
Found at i:3731970 original size:45 final size:45
Alignment explanation
Indices: 3731899--3732004 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 45
3731889 TAGCAGTAGT
* *
3731899 AGTAACAGTAACAGTATTCAATACACAAAGTG-CTGAATCTG-TAAC
1 AGTAACGGTAACAGTATTCAACACACAAAGTGTC-GAATC-GATAAC
*
3731944 AGTAACGGTAACAGTATTCGACACACAAAGTGTCGAATCGATAAC
1 AGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATCGATAAC
3731989 AGTAACGGTAACAGTA
1 AGTAACGGTAACAGTA
3732005 ACAGTAGTCG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
44 1 0.02
45 54 0.96
46 1 0.02
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.22
Consensus pattern (45 bp):
AGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATCGATAAC
Found at i:3732570 original size:6 final size:6
Alignment explanation
Indices: 3732555--3732598 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
3732545 AAATCTCTAG
** *
3732555 TTTTTCC TTTTTC TTTTTC TTTCCC TTTTTC TTTCTC TTTTTC T
1 TTTTT-C TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T
3732599 CCCCTGTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:3732576 original size:12 final size:12
Alignment explanation
Indices: 3732555--3732598 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
3732545 AAATCTCTAG
*
3732555 TTTTTCCTTTTTC
1 TTTTT-CTTTCTC
*
3732568 TTTTTCTTTCCC
1 TTTTTCTTTCTC
3732580 TTTTTCTTTCTC
1 TTTTTCTTTCTC
3732592 TTTTTCT
1 TTTTTCT
3732599 CCCCTGTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 23 0.82
13 5 0.18
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTCTTTCTC
Found at i:3732583 original size:18 final size:18
Alignment explanation
Indices: 3732560--3732594 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3732550 TCTAGTTTTT
*
3732560 CCTTTTTCTTTTTCTTTC
1 CCTTTTTCTTTCTCTTTC
3732578 CCTTTTTCTTTCTCTTT
1 CCTTTTTCTTTCTCTTT
3732595 TTCTCCCCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
CCTTTTTCTTTCTCTTTC
Found at i:3732608 original size:24 final size:24
Alignment explanation
Indices: 3732555--3732609 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
3732545 AAATCTCTAG
* *
3732555 TTTTTCCTTTTTCTTTTTCTTTCCC
1 TTTTT-CTTTCTCTTTTTCTTCCCC
3732580 TTTTTCTTTCTCTTTTTC-TCCCC
1 TTTTTCTTTCTCTTTTTCTTCCCC
3732603 TGTTTTC
1 T-TTTTC
3732610 GAATGTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 17 0.63
25 5 0.19
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTTCTTTCTCTTTTTCTTCCCC
Found at i:3732902 original size:33 final size:32
Alignment explanation
Indices: 3732844--3732906 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
3732834 ATTATTCAAT
3732844 TAATAAATATCTCTTAATTATAATAATAATAAA
1 TAATAAATATCTCTTAATTATAATAA-AATAAA
3732877 TAATAAATATCTAC-TAATT-TAAATAAAATA
1 TAATAAATATCT-CTTAATTAT-AATAAAATA
3732907 TTATAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
32 5 0.18
33 22 0.79
34 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (32 bp):
TAATAAATATCTCTTAATTATAATAAAATAAA
Found at i:3734503 original size:8 final size:8
Alignment explanation
Indices: 3734490--3734514 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3734480 AAGAGTTTTA
3734490 AGCTTGAC
1 AGCTTGAC
3734498 AGCTTGAC
1 AGCTTGAC
3734506 AGCTTGAC
1 AGCTTGAC
3734514 A
1 A
3734515 AATTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (8 bp):
AGCTTGAC
Found at i:3736051 original size:31 final size:30
Alignment explanation
Indices: 3736008--3736070 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
3735998 ATATGAGATA
3736008 AGTCTTTGTATTTTTTTCAAATTT-GAAATTT
1 AGTCTTTGTA-TTTTTT-AAATTTCGAAATTT
* *
3736039 AGTCTTTTTATTTTTTAAATTTCGAGATTT
1 AGTCTTTGTATTTTTTAAATTTCGAAATTT
3736069 AG
1 AG
3736071 GTTCAATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 6 0.21
30 14 0.48
31 9 0.31
ACGTcount: A:0.25, C:0.06, G:0.11, T:0.57
Consensus pattern (30 bp):
AGTCTTTGTATTTTTTAAATTTCGAAATTT
Found at i:3746012 original size:300 final size:293
Alignment explanation
Indices: 3745418--3746394 Score: 1019
Period size: 300 Copynumber: 3.3 Consensus size: 293
3745408 TAAAAGTAAC
* * * * * *
3745418 GGAGATAATAACTTATGCATATTAAAAATGAAAATGTATAAATTAGAATAAAATGAAGCTTTGGT
1 GGAGATAATAACTTGTGCATATT-AAAAT-AAAATGTATAAAATATATTAAAATAAAGTTTTGGT
* ** * *
3745483 TGATTGGTAAAAGTAA-AGTTTTGCTAACTC-AATTAGTGTG-GGTTCAAATCCTACTATATGCA
64 TGAGTGGTAAATTTAATA--TTT--TAA-TCAAATTTGTGGGAGGTTCAAATCC-ACTATATGCA
* * * *
3745545 TATTTTAATTTGTTTTTGTTAAAAAGAAAATACTAAAATACTCTTAAATAGTATAACTTATTTTA
123 TATTTTAATTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAATAGTATAACTTATTTTA
* * * ** * *
3745610 ATTATGAAAAGGTATTTTTGTAATTTTTTAACCGAGTTGGTGACCCAATTGAATGTGACAGCAAT
188 ATTA-CAAAAGGCATTTTTGTAATTTCTTAACCGAGTTGGTGA-CCAATTGAGGGTGACACCAAC
* *
3745675 TTAGTAAAACGCTTAAT-AATATTAACTATAGATATACAACTATG
251 TTAGTAAAACACTTAATAAATAGTAA-TATA-ATATACAACTATG
* *
3745719 GGAGATAATAACTTGTGTAAATTAAAATAAAATTGTATAAAATATATTAAAATAAAGTTTTGGTT
1 GGAGATAATAACTTGTGCATATTAAAATAAAA-TGTATAAAATATATTAAAATAAAGTTTTGGTT
* *
3745784 AAGTGGTAAATTTAATATTTT-A-CAAATTTAGTTGGGGTAGGTTCAAATTCCACTATGTGCATA
65 GAGTGGTAAATTTAATATTTTAATCAAATTT-G-T-GGG-AGGTTCAAA-TCCACTATATGCATA
* * *
3745847 TTTTAATTTATTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAATAGTATTAGTTATTTTAAT
125 TTTTAATTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAATAGTATAACTTATTTTAAT
* ** * * * *
3745912 TACAAAATGCATTTTTGTAATTTCTTAATTGATTTGGTGACTCGATCGAGGGTGACACCAACATA
190 TACAAAAGGCATTTTTGTAATTTCTTAACCGAGTTGGTGAC-CAATTGAGGGTGACACCAACTTA
*
3745977 ATAAAACACTTAATAAATAGTAAGTATAAATATACAACTA-G
254 GTAAAACACTTAATAAATAGTAA-TAT-AATATACAACTATG
* * *
3746018 TGGAGATAGTAATTTGTGCATTTTAAAATAAAAATGTATAAAATATATTAAAATGAAA-TTTTGG
1 -GGAGATAATAACTTGTGCATATTAAAAT-AAAATGTATAAAATATATTAAAAT-AAAGTTTTGG
* * * *
3746082 TTGAGTGATAAATTTAAGGTTTTTTAATCCAATTTGTGTGA-GTTCAAATCTCAC-ATATGCATA
63 TTGAGTGGTAAATTTAA--TATTTTAATCAAATTTGTGGGAGGTTCAAATC-CACTATATGCATA
*
3746145 TTTTAATTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAACAGTATAACTTATTTTAAT
125 TTTTAATTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAATAGTATAACTTATTTTAAT
* * * *
3746210 TACGAAAGGACATTTTTATAATTTCCTAACCGAGTTGGTGACCTAGTTGAGGGTGACACCAACTT
190 TACAAAAGG-CATTTTTGTAATTTCTTAACCGAGTTGGTGACC-AATTGAGGGTGACACCAACTT
* *
3746275 AGCAAAATACTTAATAAATAGT-ATAGT--TATACAACTAAT-
253 AGTAAAACACTTAATAAATAGTAATA-TAATATACAACT-ATG
* * * * * * * *
3746314 GAAGAGAACAACTCGTGCCTATTAAAATACAAAAGTATAAAATATATTAAAATAAGGCTTTGGTT
1 GGAGATAATAACTTGTGCATATTAAAATA-AAATGTATAAAATATATTAAAATAAAGTTTTGGTT
3746379 GAGTGGTAAATTTAAT
65 GAGTGGTAAATTTAAT
3746395 GTAACACCCC
Statistics
Matches: 568, Mismatches: 81, Indels: 62
0.80 0.11 0.09
Matches are distributed among these distances:
293 1 0.00
294 4 0.01
295 76 0.13
296 3 0.01
297 4 0.01
298 84 0.15
299 140 0.25
300 208 0.37
301 34 0.06
302 6 0.01
303 2 0.00
304 6 0.01
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (293 bp):
GGAGATAATAACTTGTGCATATTAAAATAAAATGTATAAAATATATTAAAATAAAGTTTTGGTTG
AGTGGTAAATTTAATATTTTAATCAAATTTGTGGGAGGTTCAAATCCACTATATGCATATTTTAA
TTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAATAGTATAACTTATTTTAATTACAAA
AGGCATTTTTGTAATTTCTTAACCGAGTTGGTGACCAATTGAGGGTGACACCAACTTAGTAAAAC
ACTTAATAAATAGTAATATAATATACAACTATG
Found at i:3746723 original size:18 final size:19
Alignment explanation
Indices: 3746702--3746743 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3746692 GGAAGTTCCC
3746702 TTTTCTTCT-TTTC-TTTCT
1 TTTTC-TCTGTTTCTTTTCT
3746720 TTTTCTCTGTTTCTTTTCT
1 TTTTCTCTGTTTCTTTTCT
3746739 TTTTC
1 TTTTC
3746744 CTTTGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 9 0.41
19 10 0.45
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTCTCTGTTTCTTTTCT
Found at i:3747809 original size:181 final size:181
Alignment explanation
Indices: 3747505--3747866 Score: 670
Period size: 181 Copynumber: 2.0 Consensus size: 181
3747495 TTCTATTCAG
3747505 CTGTTTGGTCCTAAGTCACCAATTTTAGTTTGTGTATGTTTTTTATCTGAAAATGCGTCTGTGTA
1 CTGTTTGGTCCTAAGTCACCAATTTTAGTTTGTGTATGTTTTTTATCTGAAAATGCGTCTGTGTA
* * *
3747570 TTCCGACCCTTGGCTAGACTTTAGTGAGGGTAACTAAGTCTCTATATCTATGGCTATGTGTTCTG
66 TTCCGACCCTTAGCTAGAATTTAGTGAGGGTAACTAAGTCTCTATATATATGGCTATGTGTTCTG
3747635 TTAATGTGTAATTCGTGACTGTTGTGGGTGAGATGTCTGTTTTCTGAACCC
131 TTAATGTGTAATTCGTGACTGTTGTGGGTGAGATGTCTGTTTTCTGAACCC
* *
3747686 CTGTTTGGTCCTAAGTCACCACTTTTAGTTTGTGTATGTTTTTTATCTGAAAATGCGTCTTTGTA
1 CTGTTTGGTCCTAAGTCACCAATTTTAGTTTGTGTATGTTTTTTATCTGAAAATGCGTCTGTGTA
3747751 TTCCGACCCTTAGCTAGAATTTAGTGAGGGTAACTAAGTCTCTATATATATGGCTATGTGTTCTG
66 TTCCGACCCTTAGCTAGAATTTAGTGAGGGTAACTAAGTCTCTATATATATGGCTATGTGTTCTG
*
3747816 TTAATGTGTAATTCGTGACTGTTGTGGGTGGGATGTCTGTTTTCTGAACCC
131 TTAATGTGTAATTCGTGACTGTTGTGGGTGAGATGTCTGTTTTCTGAACCC
3747867 GATTAGCTGG
Statistics
Matches: 175, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
181 175 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.42
Consensus pattern (181 bp):
CTGTTTGGTCCTAAGTCACCAATTTTAGTTTGTGTATGTTTTTTATCTGAAAATGCGTCTGTGTA
TTCCGACCCTTAGCTAGAATTTAGTGAGGGTAACTAAGTCTCTATATATATGGCTATGTGTTCTG
TTAATGTGTAATTCGTGACTGTTGTGGGTGAGATGTCTGTTTTCTGAACCC
Found at i:3754121 original size:19 final size:20
Alignment explanation
Indices: 3754097--3754135 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
3754087 TCCCATTATT
3754097 TATTTATTTTT-TGTTTTAA
1 TATTTATTTTTATGTTTTAA
3754116 TATTTATTTTTATGTTTTAA
1 TATTTATTTTTATGTTTTAA
3754136 ATGTATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (20 bp):
TATTTATTTTTATGTTTTAA
Found at i:3754153 original size:25 final size:23
Alignment explanation
Indices: 3754097--3754161 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 23
3754087 TCCCATTATT
*
3754097 TATTTATTTTT-TGTTTT-AA--
1 TATTTATTTTTATATTTTAAATG
*
3754116 TATTTATTTTTATGTTTTAAATG
1 TATTTATTTTTATATTTTAAATG
3754139 TATTTGATTTATTATATTTTAAA
1 TATTT-ATTT-TTATATTTTAAA
3754162 GTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
21 2 0.05
23 5 0.13
24 4 0.10
25 11 0.28
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (23 bp):
TATTTATTTTTATATTTTAAATG
Found at i:3755867 original size:36 final size:38
Alignment explanation
Indices: 3755816--3755894 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 38
3755806 AATACAACTC
* * *
3755816 TTTTT-AACTAATAATTGTAATTTAAA-A-TCTAATTA
1 TTTTTAAACAAATAATTGTAAATTAAATATTATAATTA
*
3755851 TTTTTAAACAAATAATTTTAAATTAAATATTATAATTA
1 TTTTTAAACAAATAATTGTAAATTAAATATTATAATTA
3755889 TTTTTA
1 TTTTTA
3755895 TATGTAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 5 0.14
36 18 0.49
37 1 0.03
38 13 0.35
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (38 bp):
TTTTTAAACAAATAATTGTAAATTAAATATTATAATTA
Found at i:3763467 original size:30 final size:30
Alignment explanation
Indices: 3763426--3763484 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
3763416 TAAATCCATG
3763426 TTATTTTATACAT-ATAATTTCTTTTAAAT
1 TTATTTTATACATCATAATTTCTTTTAAAT
* *
3763455 TTATTTGTATACATCATTATTTTTTTTAAA
1 TTATTT-TATACATCATAATTTCTTTTAAA
3763485 ATCTATTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 7 0.27
31 13 0.50
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (30 bp):
TTATTTTATACATCATAATTTCTTTTAAAT
Found at i:3766293 original size:28 final size:27
Alignment explanation
Indices: 3766241--3766293 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
3766231 AACACAATTT
**
3766241 GGGCCTAAGCCCTTTCAGTTTCAGTTA
1 GGGCCTAAGCCCTTTCAGTAACAGTTA
*
3766268 GGGCCTTAGCCCATTTCAGTAACAGT
1 GGGCCTAAGCCC-TTTCAGTAACAGT
3766294 AGCAGTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (27 bp):
GGGCCTAAGCCCTTTCAGTAACAGTTA
Found at i:3766365 original size:34 final size:34
Alignment explanation
Indices: 3766268--3766367 Score: 146
Period size: 34 Copynumber: 2.9 Consensus size: 34
3766258 GTTTCAGTTA
* * *
3766268 GGGCCTTAGCCCATTTCAGTAACAGTAGCAGTTT
1 GGGCCTGAGCCCATTTCAGTAACAGTATCAGTCT
* *
3766302 GGGCCTGAGCCTATTTTAGTAACAGTATCAGTCT
1 GGGCCTGAGCCCATTTCAGTAACAGTATCAGTCT
*
3766336 GGGCCTGAGCCCATTTCAGTAACAATATCAGT
1 GGGCCTGAGCCCATTTCAGTAACAGTATCAGT
3766368 GAGGCCTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 58 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (34 bp):
GGGCCTGAGCCCATTTCAGTAACAGTATCAGTCT
Found at i:3773082 original size:22 final size:22
Alignment explanation
Indices: 3773055--3773123 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
3773045 TCTCCGATTA
3773055 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
3773077 TTAGCACATTCGTGTTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* * *
3773099 ATAGCACTTTAGTGCTCTTTGT
1 TTAGCACATTAGTGCTCTCTGT
3773121 TTA
1 TTA
3773124 ATAGTGCATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.45
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:3777756 original size:42 final size:42
Alignment explanation
Indices: 3777709--3777795 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
3777699 GATTTTTCTA
*
3777709 TTAATAACAAGTAAATATGACAATGCACATGTGATAATTTAT
1 TTAATAACAAGTAAATATAACAATGCACATGTGATAATTTAT
*
3777751 TTAATAACAAGTTAATATAACAATGCACATGTGATAATTTAT
1 TTAATAACAAGTAAATATAACAATGCACATGTGATAATTTAT
3777793 TTA
1 TTA
3777796 TCGTGCAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (42 bp):
TTAATAACAAGTAAATATAACAATGCACATGTGATAATTTAT
Found at i:3783767 original size:14 final size:14
Alignment explanation
Indices: 3783750--3783786 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
3783740 TATTAAATTC
3783750 AAAAAATGA-ATTTT
1 AAAAAAT-ATATTTT
3783764 AAAAAA-ATATTTT
1 AAAAAATATATTTT
3783777 AAAAAATATA
1 AAAAAATATA
3783787 CCCATACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.05
13 11 0.52
14 9 0.43
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (14 bp):
AAAAAATATATTTT
Found at i:3787422 original size:126 final size:126
Alignment explanation
Indices: 3787197--3787448 Score: 441
Period size: 126 Copynumber: 2.0 Consensus size: 126
3787187 CATGAGGTAC
*
3787197 ACGTGTAGTTGTCTAGTTATTTCGTCACCCACACTAGTTTTTAACTGTAAAAATGGATGAAATTT
1 ACGTGTAGTTGTCTAGTTATTTCGTCACCCACACTAGTTTTTAACTGTAAAAATAGATGAAATTT
*
3787262 TAAATAGAAATAATCAATTTGCTTTTTAATCTAATATATATTAACTAATTTGTCTATTTTT
66 TAAATAGAAATAATCAATTTGCTTTTTAATCTAATATACATTAACTAATTTGTCTATTTTT
* *
3787323 ACGTGTAGTTGTCTAGTTATTTTGTCACCCACGCTAGTTTTTAACTGTAAAAATAGATGAAATTT
1 ACGTGTAGTTGTCTAGTTATTTCGTCACCCACACTAGTTTTTAACTGTAAAAATAGATGAAATTT
* * *
3787388 TTAATAGAAATGATCAATTTGCTTTTTAATCTAATGTACATTAACTAATTTGTCTATTTTT
66 TAAATAGAAATAATCAATTTGCTTTTTAATCTAATATACATTAACTAATTTGTCTATTTTT
3787449 TAGTAAAAGT
Statistics
Matches: 119, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 119 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (126 bp):
ACGTGTAGTTGTCTAGTTATTTCGTCACCCACACTAGTTTTTAACTGTAAAAATAGATGAAATTT
TAAATAGAAATAATCAATTTGCTTTTTAATCTAATATACATTAACTAATTTGTCTATTTTT
Found at i:3788849 original size:11 final size:11
Alignment explanation
Indices: 3788835--3788877 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
3788825 AAATAATAAC
3788835 AATAAAATAGT
1 AATAAAATAGT
*
3788846 AATAACATAGT
1 AATAAAATAGT
* *
3788857 AATAAAACAAT
1 AATAAAATAGT
*
3788868 AAGAAAATAG
1 AATAAAATAG
3788878 CAGCAAAACA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.65, C:0.05, G:0.09, T:0.21
Consensus pattern (11 bp):
AATAAAATAGT
Found at i:3788907 original size:22 final size:22
Alignment explanation
Indices: 3788860--3788906 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
3788850 ACATAGTAAT
* * *
3788860 AAAACAATAAGAAAATAGCAGC
1 AAAACAATAAGAAAACAACAAC
3788882 AAAACAATAA-AAAACAACAAC
1 AAAACAATAAGAAAACAACAAC
3788903 AAAA
1 AAAA
3788907 ATAACAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.72, C:0.15, G:0.06, T:0.06
Consensus pattern (22 bp):
AAAACAATAAGAAAACAACAAC
Found at i:3795494 original size:35 final size:35
Alignment explanation
Indices: 3795455--3795522 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
3795445 TACATAAGTG
*
3795455 CACTTATATATGGTCAAGTGGCAACATATAATTGC
1 CACTTATATATGGTCAAATGGCAACATATAATTGC
* * *
3795490 CACTTATGTATGGTGAAATGGTAACATATAATT
1 CACTTATATATGGTCAAATGGCAACATATAATT
3795523 TTAAGCTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (35 bp):
CACTTATATATGGTCAAATGGCAACATATAATTGC
Found at i:3801501 original size:18 final size:18
Alignment explanation
Indices: 3801478--3801531 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
3801468 AATGTGTTAT
3801478 AAATTATATAATATATAA
1 AAATTATATAATATATAA
*
3801496 AAATTACATAATATA-AA
1 AAATTATATAATATATAA
*
3801513 ATATTATA-AAT-T-TAA
1 AAATTATATAATATATAA
3801528 AAAT
1 AAAT
3801532 AGGTTAAGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 6 0.19
16 3 0.10
17 8 0.26
18 14 0.45
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATTATATAATATATAA
Found at i:3803364 original size:58 final size:55
Alignment explanation
Indices: 3803296--3803405 Score: 134
Period size: 55 Copynumber: 1.9 Consensus size: 55
3803286 TATCGATATT
* * *
3803296 TTTAAATATTTTTCATATATATAGTTTTATTTTT-AATTTCTTGAT-AATTATATATAAA
1 TTTAAATA-TTTT-ATATATA-A-TATAATTTTTAAATTT-TTAATAAATTATATATAAA
3803354 TTTAAATATTTTATATATAATATAATTTTTAAATTTTTAATAAATTATATAT
1 TTTAAATATTTTATATATAATATAATTTTTAAATTTTTAATAAATTATATAT
3803406 TGTTTTAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
54 12 0.26
55 16 0.34
56 7 0.15
57 4 0.09
58 8 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (55 bp):
TTTAAATATTTTATATATAATATAATTTTTAAATTTTTAATAAATTATATATAAA
Found at i:3803403 original size:27 final size:26
Alignment explanation
Indices: 3803324--3803413 Score: 67
Period size: 27 Copynumber: 3.3 Consensus size: 26
3803314 ATATAGTTTT
3803324 ATTTTT-AATTTCTTGAT-AATTATATA
1 ATTTTTAAATTT-TT-ATAAATTATATA
** * *
3803350 TAAATTTAAATATTTTATATATAATATA
1 -ATTTTTAAAT-TTTTATAAATTATATA
3803378 ATTTTTAAATTTTTAATAAATTATATA
1 ATTTTTAAATTTTT-ATAAATTATATA
*
3803405 TTGTTTTAA
1 AT-TTTTAA
3803414 TAAAAAATTA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
26 4 0.08
27 25 0.51
28 18 0.37
29 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (26 bp):
ATTTTTAAATTTTTATAAATTATATA
Found at i:3808628 original size:39 final size:39
Alignment explanation
Indices: 3808585--3808660 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
3808575 ACCTGCTAAA
3808585 CAGTTCCTCGATCCAAACTCGAAACTCAGTTAAACTCAG
1 CAGTTCCTCGATCCAAACTCGAAACTCAGTTAAACTCAG
* * *
3808624 CAGTTCCTCGATCCGAACTTGAAACTCTGTTAAACTC
1 CAGTTCCTCGATCCAAACTCGAAACTCAGTTAAACTC
3808661 GTTACCTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.26
Consensus pattern (39 bp):
CAGTTCCTCGATCCAAACTCGAAACTCAGTTAAACTCAG
Found at i:3810195 original size:21 final size:20
Alignment explanation
Indices: 3810166--3810204 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3810156 AACACAAAGT
*
3810166 ACATCATTCAATACTCAATGC
1 ACATAATTCAATAC-CAATGC
*
3810187 ACATAATTCCATACCAAT
1 ACATAATTCAATACCAAT
3810205 CAACCCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (20 bp):
ACATAATTCAATACCAATGC
Found at i:3811956 original size:9 final size:9
Alignment explanation
Indices: 3811942--3811972 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3811932 AAAATTAGAT
3811942 AATTAATCA
1 AATTAATCA
*
3811951 AATTAATCG
1 AATTAATCA
3811960 AATTAATCA
1 AATTAATCA
3811969 AATT
1 AATT
3811973 TAATAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (9 bp):
AATTAATCA
Found at i:3812042 original size:44 final size:44
Alignment explanation
Indices: 3811993--3812081 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
3811983 TATTATGTGT
3811993 TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
1 TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
3812037 TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
1 TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
3812081 T
1 T
3812082 GACATAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (44 bp):
TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
Found at i:3815405 original size:4 final size:4
Alignment explanation
Indices: 3815396--3815424 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3815386 AGTTAGAATC
3815396 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
3815425 AACCTCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:3815730 original size:67 final size:68
Alignment explanation
Indices: 3815622--3815759 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 68
3815612 GTATCCAACC
* *
3815622 TGGGGAGTACATTCGTAAGAATGAAACTAAAAGGAATTGAC-AGGGGCTGCACAAGTAGTGGAGC
1 TGGGGAGTACATTCGCAAGAATGAAACTAAAAGGAATTGACAAGGGGCCGCACAAGTAGTGGAGC
3815686 ATG
66 ATG
* *
3815689 TGGGGAGTACA-TCTGCAAGAATGAAACTTAAAGGAATTGACAAGGGGCCGCACAAGTGGTGGAG
1 TGGGGAGTACATTC-GCAAGAATGAAACTAAAAGGAATTGACAAGGGGCCGCACAAGTAGTGGAG
3815753 CATG
65 CATG
3815757 TGG
1 TGG
3815760 TTTAATTTGA
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
66 2 0.03
67 36 0.55
68 27 0.42
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.19
Consensus pattern (68 bp):
TGGGGAGTACATTCGCAAGAATGAAACTAAAAGGAATTGACAAGGGGCCGCACAAGTAGTGGAGC
ATG
Found at i:3818926 original size:6 final size:6
Alignment explanation
Indices: 3818915--3818962 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
3818905 CTATGGAGTT
*
3818915 GGATTA GAATTA GGATTA GGATTA GGATTA GGATTA GGATTA GGATTA
1 GGATTA GGATTA GGATTA GGATTA GGATTA GGATTA GGATTA GGATTA
3818963 ATCAAAATCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.33
Consensus pattern (6 bp):
GGATTA
Found at i:3818997 original size:25 final size:24
Alignment explanation
Indices: 3818964--3819013 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
3818954 TTAGGATTAA
3818964 TCAAAATCCTATTTCTATTTATAT
1 TCAAAATCCTATTTCTATTTATAT
*
3818988 TCAATAATCCTATTTCTATTTGTAT
1 TCAA-AATCCTATTTCTATTTATAT
3819013 T
1 T
3819014 TGGATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (24 bp):
TCAAAATCCTATTTCTATTTATAT
Found at i:3820399 original size:19 final size:20
Alignment explanation
Indices: 3820377--3820420 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3820367 AAAAATTAAA
3820377 AAAAATT-AAAATAATTTTC
1 AAAAATTCAAAATAATTTTC
3820396 AAAAATTCAAAATAATTTTC
1 AAAAATTCAAAATAATTTTC
3820416 AAAAA
1 AAAAA
3820421 CAAATTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTC
Done.