Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 30 of 79
Found at i:10336975 original size:18 final size:19
Alignment explanation
Indices: 10336936--10336975 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
10336926 TTTATATTTT
* *
10336936 TAAAAAATATTAATTACCA
1 TAAAAAATATCAATTACAA
10336955 TAAAAAATATCAA-TACAA
1 TAAAAAATATCAATTACAA
10336973 TAA
1 TAA
10336976 TTTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAATATCAATTACAA
Found at i:10339798 original size:22 final size:20
Alignment explanation
Indices: 10339757--10339801 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
10339747 GCAAATCAAC
*
10339757 AAAATAAGAACAAGCCAGAG
1 AAAATAAGAACAAGACAGAG
*
10339777 AAAATAAGAACGCAAGAGAGAG
1 AAAATAAGAA--CAAGACAGAG
10339799 AAA
1 AAA
10339802 TTTGAGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.62, C:0.11, G:0.22, T:0.04
Consensus pattern (20 bp):
AAAATAAGAACAAGACAGAG
Found at i:10339963 original size:22 final size:22
Alignment explanation
Indices: 10339935--10340022 Score: 155
Period size: 22 Copynumber: 4.1 Consensus size: 22
10339925 NNNNNNNNNN
10339935 ATCATATCTTCTAAGATTGCAT
1 ATCATATCTTCTAAGATTGCAT
10339957 ATCATATCTTCTAAGATTGCAT
1 ATCATATCTTCTAAGATTGCAT
10339979 ATCATATCTTCTAAGATTGCAT
1 ATCATATCTTCTAAGATTGCAT
10340001 ATCATA---TCTAAGATTGCAT
1 ATCATATCTTCTAAGATTGCAT
10340020 ATC
1 ATC
10340023 CTTGAAGATT
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.24
22 50 0.76
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (22 bp):
ATCATATCTTCTAAGATTGCAT
Found at i:10340916 original size:100 final size:100
Alignment explanation
Indices: 10340775--10341028 Score: 420
Period size: 100 Copynumber: 2.5 Consensus size: 100
10340765 AGCTTTAATC
*
10340775 TGTTCCACTACACCG-TCAGGGAAGTAAGATTCGCTATTGTGGCTTCAATCTATTTAACTGCAAT
1 TGTTCCACTACACCGCT-AGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTATTTAACTGCAAT
* * *
10340839 GTTGGGGAAACAAGATTCGCCGTCGTAACTTCAATT
65 GTTGGAGAAACAAGATTCACCATCGTAACTTCAATT
*
10340875 TGTTCCACTACACCGCTAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTAATTAACTGCAATG
1 TGTTCCACTACACCGCTAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTATTTAACTGCAATG
*
10340940 TTGGAGAAACAAGATTCACCATCGTAGCTTCAATT
66 TTGGAGAAACAAGATTCACCATCGTAACTTCAATT
* *
10340975 TGTTCCACTACACCTCCAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTATT
1 TGTTCCACTACACCGCTAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTATT
10341029 CCACTGTAAT
Statistics
Matches: 144, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
100 143 0.99
101 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (100 bp):
TGTTCCACTACACCGCTAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTATTTAACTGCAATG
TTGGAGAAACAAGATTCACCATCGTAACTTCAATT
Found at i:10341004 original size:50 final size:50
Alignment explanation
Indices: 10340777--10341033 Score: 162
Period size: 50 Copynumber: 5.1 Consensus size: 50
10340767 CTTTAATCTG
* * * *
10340777 TTCCACTACACCGTC-AGGGAAGTAAGATTCGCTATTGTGGCTTCAATCTA
1 TTCCACTACACC-TCTAGGGAAGTAAGATTCGCCATCGTAGCTTCAATTTA
** * * * * ** * * *
10340827 TTTAACTGCA-ATGTTGGGGAAACAAGATTCGCCGTCGTAACTTCAATTTG
1 TTCCACTACACCT-CTAGGGAAGTAAGATTCGCCATCGTAGCTTCAATTTA
* * * *
10340877 TTCCACTACACCGCTAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTAA
1 TTCCACTACACCTCTAGGGAAGTAAGATTCGCCATCGTAGCTTCAAT-TTA
* * * * * ** * *
10340928 TT-AACTGCA-ATGTTGGAGAAACAAGATTCACCATCGTAGCTTCAATTTG
1 TTCCACTACACCTCTAGG-GAAGTAAGATTCGCCATCGTAGCTTCAATTTA
* * * *
10340977 TTCCACTACACCTCCAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTA
1 TTCCACTACACCTCTAGGGAAGTAAGATTCGCCATCGTAGCTTCAATTTA
10341027 TTCCACT
1 TTCCACT
10341034 GTAATGCCAA
Statistics
Matches: 144, Mismatches: 56, Indels: 14
0.67 0.26 0.07
Matches are distributed among these distances:
48 1 0.01
49 6 0.04
50 131 0.91
51 6 0.04
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (50 bp):
TTCCACTACACCTCTAGGGAAGTAAGATTCGCCATCGTAGCTTCAATTTA
Found at i:10341323 original size:128 final size:130
Alignment explanation
Indices: 10341110--10341360 Score: 425
Period size: 128 Copynumber: 1.9 Consensus size: 130
10341100 GGGATTACTA
* *
10341110 GCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTTGATCTGCTCCACTAC
1 GCTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTAC
*
10341175 TGGTTAGGGAGATAAGATCTGTAA-TTT-CCTACTCCACTGCTGCTCAGGGAGATAAAGCTAGTG
66 TGCTTAGGGAGATAAGATCTGTAATTTTACCTACTCCACTGCTGCTCAGGGAGATAAAGCTAGTG
* *
10341238 GCTTAAATCTACTTCCCTACTACCTTGGGAGGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
1 GCTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTAC
10341303 TGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGCTCAGGGAGATA
66 TGCTTAGGGAGATAAGATCTGTAATTTT--ACCTACTCCACTGCTGCTCAGGGAGATA
10341361 GGATTCACAA
Statistics
Matches: 114, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
128 84 0.74
129 3 0.03
132 27 0.24
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (130 bp):
GCTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTAC
TGCTTAGGGAGATAAGATCTGTAATTTTACCTACTCCACTGCTGCTCAGGGAGATAAAGCTAGTG
Found at i:10341377 original size:44 final size:44
Alignment explanation
Indices: 10341294--10341435 Score: 155
Period size: 44 Copynumber: 3.2 Consensus size: 44
10341284 CTTCGATCTG
* * * ** *
10341294 CTCCACTACTGCTTAGGGAGATAAGA-TCTGTAATTTTCAACCTA
1 CTCCACTGCTGCTCAGGGAGATAGGATTC-ACAATCTTCAACCTA
10341338 CTCCACTGCTGCTCAGGGAGATAGGATTCACAATCTTCAACCTA
1 CTCCACTGCTGCTCAGGGAGATAGGATTCACAATCTTCAACCTA
*
10341382 TTCCACTGCTGAC-CAGGGAGATAGGACTT-ACAATCTTCAACCTA
1 CTCCACTGCTG-CTCAGGGAGATAGGA-TTCACAATCTTCAACCTA
* *
10341426 TTCCGCTGCT
1 CTCCACTGCT
10341436 TTCCAGGGAG
Statistics
Matches: 87, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
44 82 0.94
45 5 0.06
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (44 bp):
CTCCACTGCTGCTCAGGGAGATAGGATTCACAATCTTCAACCTA
Found at i:10341442 original size:44 final size:44
Alignment explanation
Indices: 10341329--10341446 Score: 159
Period size: 44 Copynumber: 2.7 Consensus size: 44
10341319 ATCTGTAATT
* *
10341329 TTCAACCTACTCCACTGC-TGCTCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTTAC-CAGGGAGATAGGATTCACAATC
*
10341373 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTTACCAGGGAGATAGGA-TTCACAATC
* *
10341417 TTCAACCTATTCCGCTGCTTTCCAGGGAGA
1 TTCAACCTATTCCACTGCTTACCAGGGAGA
10341447 CAGTACTACT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
44 63 0.95
45 3 0.05
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTTACCAGGGAGATAGGATTCACAATC
Found at i:10354436 original size:42 final size:42
Alignment explanation
Indices: 10354381--10354673 Score: 466
Period size: 42 Copynumber: 7.0 Consensus size: 42
10354371 GTTTGTGAAA
* * **
10354381 TAAGCACCGCTAAAGAACACT-A-CTTTTAGCGGCGTTTTTGAAC
1 TAAGCGCCGCTAAAGAACA-TGATC-TTTAGAGGCGTTTTT-TTC
10354424 -AAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
10354465 TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
10354507 TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
10354549 TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
*
10354591 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
1 TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
* * *
10354633 TAAGCGCTGCTAAAGAACATGATCTTTAGCGACGTTTTTTT
1 TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTT
10354674 ATGAAAGCGC
Statistics
Matches: 240, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
41 2 0.01
42 237 0.99
43 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAGCGCCGCTAAAGAACATGATCTTTAGAGGCGTTTTTTTC
Found at i:10354798 original size:21 final size:22
Alignment explanation
Indices: 10354763--10354804 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
10354753 TAGTGGCGTT
* *
10354763 AAAAAGCGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAAACCTA
10354785 AAAAAACGCC-CTAAAAACCT
1 AAAAAACGCCGCTAAAAACCT
10354805 GTTCTGTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.50, C:0.29, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:10356281 original size:21 final size:23
Alignment explanation
Indices: 10356258--10356321 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 23
10356248 GTATATCTAC
*
10356258 AAATTAAAT-CTCTAAGATTACA
1 AAATCAAATCCTCTAAGATTACA
* *
10356280 AAATCATATCCTCTAAGATTGC-
1 AAATCAAATCCTCTAAGATTACA
* * *
10356302 ATATCATATCTTCTAAGATT
1 AAATCAAATCCTCTAAGATT
10356322 GCATATCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 25 0.69
23 11 0.31
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (23 bp):
AAATCAAATCCTCTAAGATTACA
Found at i:10356310 original size:22 final size:22
Alignment explanation
Indices: 10356267--10356347 Score: 105
Period size: 22 Copynumber: 3.8 Consensus size: 22
10356257 CAAATTAAAT
* *
10356267 CTCTAAGATTACAAAATCATATC
1 CTCTAAGATTGC-ATATCATATC
10356290 CTCTAAGATTGCATATCATATC
1 CTCTAAGATTGCATATCATATC
*
10356312 TTCTAAGATTGCATATCATA--
1 CTCTAAGATTGCATATCATATC
10356332 -TCTAAGATTGCATATC
1 CTCTAAGATTGCATATC
10356348 CTTGAAGATT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
19 16 0.29
22 28 0.51
23 11 0.20
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (22 bp):
CTCTAAGATTGCATATCATATC
Found at i:10358980 original size:108 final size:109
Alignment explanation
Indices: 10358780--10358997 Score: 429
Period size: 108 Copynumber: 2.0 Consensus size: 109
10358770 TTTTTTTCTG
10358780 ACTGAAGAAGAAAAGGGTATGAATATGATATGATTATGATTATGATTACCCTTTTACATGGCCAT
1 ACTGAAGAAGAAAAGGGTATGAATATGATATGATTATGATTATGATTACCCTTTTACATGGCCAT
10358845 ATCTTACATTAGGGTTTTTCTCACTCAAATGATTAAGTAATGTA
66 ATCTTACATTAGGGTTTTTCTCACTCAAATGATTAAGTAATGTA
10358889 ACTGAAGAAG-AAAGGGTATGAATATGATATGATTATGATTATGATTACCCTTTTACATGGCCAT
1 ACTGAAGAAGAAAAGGGTATGAATATGATATGATTATGATTATGATTACCCTTTTACATGGCCAT
10358953 ATCTTACATTAGGGTTTTTCTCACTCAAATGATTAAGTAATGTA
66 ATCTTACATTAGGGTTTTTCTCACTCAAATGATTAAGTAATGTA
10358997 A
1 A
10358998 AAGAAAAAAT
Statistics
Matches: 109, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
108 99 0.91
109 10 0.09
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (109 bp):
ACTGAAGAAGAAAAGGGTATGAATATGATATGATTATGATTATGATTACCCTTTTACATGGCCAT
ATCTTACATTAGGGTTTTTCTCACTCAAATGATTAAGTAATGTA
Found at i:10362619 original size:26 final size:28
Alignment explanation
Indices: 10362540--10362620 Score: 114
Period size: 27 Copynumber: 3.0 Consensus size: 28
10362530 TCAGGCCAAT
*
10362540 TAAATTGGCGGCACCAAAGGTGCCAAA-
1 TAAATTGGCGGCACCAATGGTGCCAAAG
*
10362567 TAAATTGGTGGCACCAATGGTGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
*
10362595 T-CATTGGCGGCACC-ATGGTGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
10362621 GAAAAAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 12 0.24
27 36 0.73
28 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (28 bp):
TAAATTGGCGGCACCAATGGTGCCAAAG
Found at i:10362724 original size:18 final size:19
Alignment explanation
Indices: 10362685--10362721 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10362675 TATTCCTCTT
* *
10362685 TAACTCTTTTTTTATTTAA
1 TAACTCTATTTTAATTTAA
10362704 TAACTCTATTTTAATTTA
1 TAACTCTATTTTAATTTA
10362722 TAAAATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (19 bp):
TAACTCTATTTTAATTTAA
Found at i:10363210 original size:29 final size:28
Alignment explanation
Indices: 10363148--10363246 Score: 146
Period size: 28 Copynumber: 3.5 Consensus size: 28
10363138 AAAAATAAAA
*
10363148 ATTTACCAAAATAGTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
*
10363176 ATTTACGAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAAC-TTTTTTTT
*
10363205 ATTTACCAAGATATATA-AACTTTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
10363233 ATTTACCAAAATAT
1 ATTTACCAAAATAT
10363247 ATCAAAAACA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
28 39 0.61
29 23 0.36
30 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.03, T:0.47
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:10363342 original size:27 final size:27
Alignment explanation
Indices: 10363312--10363389 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
10363302 CCCCAATGGT
*
10363312 ATTGGCGGCACCAAAGGTGCCAAA-TAA
1 ATTGGCGGCACCAATGGTGCCAAAGT-A
* * *
10363339 ATTGGTGGCACCATTGGTGCCAAAGTC
1 ATTGGCGGCACCAATGGTGCCAAAGTA
10363366 ATTGGCGGCACC-ATGGTGCCAAAG
1 ATTGGCGGCACCAATGGTGCCAAAG
10363390 GGAAAAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 11 0.25
27 32 0.73
28 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.29, T:0.19
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGTA
Found at i:10363493 original size:18 final size:19
Alignment explanation
Indices: 10363454--10363490 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
10363444 TATTCTCCTT
* *
10363454 TAACTCTTTTTTTATTTAA
1 TAACTCTATTTTAATTTAA
10363473 TAACTCTATTTTAATTTA
1 TAACTCTATTTTAATTTA
10363491 TAAAATATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (19 bp):
TAACTCTATTTTAATTTAA
Found at i:10363675 original size:26 final size:28
Alignment explanation
Indices: 10363596--10363676 Score: 114
Period size: 27 Copynumber: 3.0 Consensus size: 28
10363586 TCAGGCCAAT
*
10363596 TAAATTGGCGGCACCAAAGGTGCCAAA-
1 TAAATTGGCGGCACCAATGGTGCCAAAG
*
10363623 TAAATTGGTGGCACCAATGGTGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
*
10363651 T-CATTGGCGGCACC-ATGGTGCCAAAG
1 TAAATTGGCGGCACCAATGGTGCCAAAG
10363677 GAAAAAAAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 12 0.24
27 36 0.73
28 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.28, T:0.19
Consensus pattern (28 bp):
TAAATTGGCGGCACCAATGGTGCCAAAG
Found at i:10363786 original size:18 final size:19
Alignment explanation
Indices: 10363750--10363819 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
10363740 TCAACTCATT
*
10363750 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
10363769 TTTTAATTTAATAA-TCTA
1 TTTTAATTTAATAACTCTA
* *
10363787 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
10363806 TTTTAATTTAATAA
1 TTTTAATTTAATAA
10363820 ANNNNNNNNN
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
18 16 0.36
19 29 0.64
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:10364133 original size:19 final size:19
Alignment explanation
Indices: 10364078--10364140 Score: 85
Period size: 18 Copynumber: 3.4 Consensus size: 19
10364068 AGTATTACTC
10364078 AATTAAAATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
* * *
10364097 AATGAGAATAG-TTTATTA
1 AATTAAAATAGAGTTATTA
10364115 AATTAAAATAGAGTTATTA
1 AATTAAAATAGAGTTATTA
10364134 AA-TAAAA
1 AATTAAAA
10364141 AAAAGAGTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 20 0.54
19 17 0.46
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (19 bp):
AATTAAAATAGAGTTATTA
Found at i:10364141 original size:19 final size:19
Alignment explanation
Indices: 10364082--10364141 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
10364072 TTACTCAATT
*
10364082 AAAATAGAGTTATTAAATG
1 AAAATAGAGTTATTAAATA
* * *
10364101 AGAATAG-TTTATTAAATT
1 AAAATAGAGTTATTAAATA
10364119 AAAATAGAGTTATTAAATA
1 AAAATAGAGTTATTAAATA
10364138 AAAA
1 AAAA
10364142 AAAGAGTTGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (19 bp):
AAAATAGAGTTATTAAATA
Found at i:10364265 original size:27 final size:28
Alignment explanation
Indices: 10364216--10364293 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 28
10364206 TTTTTTTTTC
10364216 CTTTGGCACCA-TGGTGCCGCCAA-AGA
1 CTTTGGCACCATTGGTGCCGCCAATAGA
* **
10364242 CTTTGGCACCATTGGTGCCACCAATTTA
1 CTTTGGCACCATTGGTGCCGCCAATAGA
*
10364270 -TTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
10364294 TTAATTGGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 11 0.24
27 33 0.73
28 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.28
Consensus pattern (28 bp):
CTTTGGCACCATTGGTGCCGCCAATAGA
Found at i:10364294 original size:27 final size:26
Alignment explanation
Indices: 10364217--10364302 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
10364207 TTTTTTTTCC
* **
10364217 TTTGGCACCATGGTGCCGCCAA-AGA
1 TTTGGCACCTTGGTGCCGCCAATTTA
*
10364242 CTTTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACC-TTGGTGCCGCCAATTTA
10364270 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACC-TTGGTGCCGCCAATTTA
*
10364297 ATTGGC
1 TTTGGC
10364303 CTGATCAGGC
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 9 0.18
27 41 0.80
28 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.23, T:0.30
Consensus pattern (26 bp):
TTTGGCACCTTGGTGCCGCCAATTTA
Found at i:10366473 original size:13 final size:14
Alignment explanation
Indices: 10366452--10366500 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
10366442 CAATTTTCAA
10366452 TTTTCAATTTT-TT
1 TTTTCAATTTTATT
*
10366465 TTTTGAATTTTATT
1 TTTTCAATTTTATT
*
10366479 TTGTTCGATTTTATT
1 TT-TTCAATTTTATT
10366494 TTGTTCA
1 TT-TTCA
10366501 TTATGATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 10 0.33
14 4 0.13
15 16 0.53
ACGTcount: A:0.16, C:0.06, G:0.08, T:0.69
Consensus pattern (14 bp):
TTTTCAATTTTATT
Found at i:10366480 original size:15 final size:15
Alignment explanation
Indices: 10366471--10366499 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
10366461 TTTTTTTTGA
10366471 ATTTTATTTTGTTCG
1 ATTTTATTTTGTTCG
10366486 ATTTTATTTTGTTC
1 ATTTTATTTTGTTC
10366500 ATTATGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.10, T:0.69
Consensus pattern (15 bp):
ATTTTATTTTGTTCG
Found at i:10366628 original size:24 final size:25
Alignment explanation
Indices: 10366601--10366648 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
10366591 ATTATTTAAT
10366601 TTTAAA-TAGTTAA-TTATTATGTTG
1 TTTAAATTA-TTAACTTATTATGTTG
*
10366625 TTTAAATTATTAACTTTTTATGTT
1 TTTAAATTATTAACTTATTATGTT
10366649 TATATACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.58
Consensus pattern (25 bp):
TTTAAATTATTAACTTATTATGTTG
Found at i:10367862 original size:24 final size:23
Alignment explanation
Indices: 10367810--10367862 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
10367800 TTTTTATTCC
10367810 TTTTTTAAAAATTAGATTAAAAA
1 TTTTTTAAAAATTAGATTAAAAA
* * *
10367833 TATTTTAAAAATTACTATTCAAAA
1 TTTTTTAAAAATTA-GATTAAAAA
10367857 TTTTTT
1 TTTTTT
10367863 TCCAAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTTTTAAAAATTAGATTAAAAA
Found at i:10373619 original size:240 final size:239
Alignment explanation
Indices: 10373185--10373669 Score: 808
Period size: 240 Copynumber: 2.0 Consensus size: 239
10373175 GTGACCCTAT
*
10373185 TGTGAAAAAAGGGGTACACCCAAATAAGTACCAAGATTACTCACTTATTGAAAACCAATAGTATG
1 TGTG-AAAAAGGGGTACACCCAAATAAGTACCAAGATTACTCACTTATTGAAAACCAAGAGTATG
* * *
10373250 ATTTAAACTATCACTTAGATCGTCCTCCACGCCTTTTGAGAAATACATAATTTTTTTTCGGTTGC
65 ATTGAAACTATCACTTAGATCCTCCTCCACGCCTTTTGAGAAATACATAATTGTTTTTCGGTTGC
*
10373315 TGACCCAATGCCCTAAGACATTATAGAAGTTATCCAAAATTTCCTTAAGGACCAAACTATGTTTC
130 TGACCCAATGCCCTAAGACATTATAGAAGTTATCCAAAATTTCCTTAAGGACCAAACCATGTTTC
* * *
10373380 AAATCTGCCTTAGCAAAAAGAACCAAATCATTTGCAAAAAAACAAG
195 AAATCTGCCTTAGCAAAAAGAACCAAATCATCTAC-AAAAAACAAA
* *
10373426 TGTGAAAAAGGGGTACACCCAAATAAGTACCAAGATTACTCACTTTTTGAAAACTAAGAGTATGA
1 TGTGAAAAAGGGGTACACCCAAATAAGTACCAAGATTACTCACTTATTGAAAACCAAGAGTATGA
** *
10373491 TTGAAACTATTGCTTAGATCCTCCTCCACGCCTTTTGAGAAATACATAATTGTTTTTCGGTTGTT
66 TTGAAACTATCACTTAGATCCTCCTCCACGCCTTTTGAGAAATACATAATTGTTTTTCGGTTGCT
* * *
10373556 GACCCGATGCCTTAAGATATTATAGAAGTTATCCAAAATTTCCTTAAGGACCAAACCATGTTTCA
131 GACCCAATGCCCTAAGACATTATAGAAGTTATCCAAAATTTCCTTAAGGACCAAACCATGTTTCA
10373621 AATCTGCCTTAGCAAAAAGAACCAAATCATCTACAAAAAACAAA
196 AATCTGCCTTAGCAAAAAGAACCAAATCATCTACAAAAAACAAA
10373665 TGTGA
1 TGTGA
10373670 TAATGGATAT
Statistics
Matches: 228, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
239 14 0.06
240 210 0.92
241 4 0.02
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (239 bp):
TGTGAAAAAGGGGTACACCCAAATAAGTACCAAGATTACTCACTTATTGAAAACCAAGAGTATGA
TTGAAACTATCACTTAGATCCTCCTCCACGCCTTTTGAGAAATACATAATTGTTTTTCGGTTGCT
GACCCAATGCCCTAAGACATTATAGAAGTTATCCAAAATTTCCTTAAGGACCAAACCATGTTTCA
AATCTGCCTTAGCAAAAAGAACCAAATCATCTACAAAAAACAAA
Found at i:10382985 original size:13 final size:12
Alignment explanation
Indices: 10382953--10382996 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 12
10382943 GAATTAAAAG
10382953 AAATTAGAATATAA
1 AAATTA-AATA-AA
10382967 AAATTAAATAAA
1 AAATTAAATAAA
10382979 AATATTAAAATAAA
1 AA-ATT-AAATAAA
10382993 AAAT
1 AAAT
10382997 GGCTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.14
13 9 0.32
14 15 0.54
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AAATTAAATAAA
Found at i:10386048 original size:35 final size:35
Alignment explanation
Indices: 10385983--10386708 Score: 513
Period size: 35 Copynumber: 19.7 Consensus size: 35
10385973 AGACCTAGTC
* * **
10385983 AAGGCCAACCTTTGAAAACGGTTGGTATAGACCCGTCT
1 AAGG-CAACC-TT-AAAAAGGTTGGGATAGACTTGTCT
* * **
10386021 AAGGCAGCCTTAAAGAGGTTGGGATAGACCAGTCT
1 AAGGCAACCTTAAAAAGGTTGGGATAGACTTGTCT
** * **
10386056 AAGATAACCTTTTAAAAAAAGTTAAGATAGACTTTGTCT
1 AAGGCAACC--TT-AAAAAGGTTGGGATAGAC-TTGTCT
*
10386095 AAGGCAACCTTTAAAAAAAGTTGGGATAGACCTTGTCT
1 AAGGCAACC-TT-AAAAAGGTTGGGATAGA-CTTGTCT
* * *
10386133 AGGGTAACCTTTAAAAAACAGTTGGGATAGACCTTGTCT
1 AAGGCAACC-TT-AAAAA-GGTTGGGATAGA-CTTGTCT
* * * *
10386172 AAGGAAACCTTTAAAAAAGATTGGGATAGAATCGTCT
1 AAGGCAACC-TT-AAAAAGGTTGGGATAGACTTGTCT
*
10386209 AAGGCAACCTTAAAAAGGTTTGGATAGACATTGTCT
1 AAGGCAACCTTAAAAAGGTTGGGATAGAC-TTGTCT
* * * * * *
10386245 GAGACAACTTTTAAAAAAGGTTGAGATGGACTAGTCT
1 AAGGCAAC-CTT-AAAAAGGTTGGGATAGACTTGTCT
10386282 AAGGCAACCTTTTAACAAA-GTTGGGATAGACCTTGTCT
1 AAGGCAACC--TTAA-AAAGGTTGGGATAGA-CTTGTCT
* ** *
10386320 AAGGCAACCTTTAAAAAAGGTTAGGATAGACCAGTTT
1 AAGGCAACC-TT-AAAAAGGTTGGGATAGACTTGTCT
** *
10386357 AAGGCAACCTTTTAAAAAAAAATTAGGATAGACCTTGTCT
1 AAGGCAACC--TT--AAAAAGGTTGGGATAGA-CTTGTCT
* *
10386397 AAGGAAACCTTCAAAAAAGGTTAGGATAGACTTGTCT
1 AAGGCAACCTT--AAAAAGGTTGGGATAGACTTGTCT
* *
10386434 AAAGCAACCTTAAAAAGGTTGGGATAGACTCGTCT
1 AAGGCAACCTTAAAAAGGTTGGGATAGACTTGTCT
* *
10386469 AAGGTAACCTTAAAAAGGTAGGGATAGACCTTTGTCT
1 AAGGCAACCTTAAAAAGGTTGGGATAGA-C-TTGTCT
* * ** *
10386506 AAGGCAACTTTTAAAAAGGTTGGGATTGACTCATTT
1 AAGGCAAC-CTTAAAAAGGTTGGGATAGACTTGTCT
* * * *
10386542 AAGACAACCTTAAAAATGTTGGGATAGACTCGTTT
1 AAGGCAACCTTAAAAAGGTTGGGATAGACTTGTCT
* ** * *
10386577 AAAGCAACCTTAAAAATATTGGGATAGACCTTTTCC
1 AAGGCAACCTTAAAAAGGTTGGGATAGA-CTTGTCT
* * * **
10386613 AAGGTAA-CTTAAAAAAAGTTGGGATAAACTCATCT
1 AAGGCAACCTT-AAAAAGGTTGGGATAGACTTGTCT
* *
10386648 AAGGCAACCTTAAAAAGGTTAGGG-TAAACTCGTCT
1 AAGGCAACCTTAAAAAGGTT-GGGATAGACTTGTCT
* *
10386683 AAGGCAAACTTAAAAAGGTTAGGATA
1 AAGGCAACCTTAAAAAGGTTGGGATA
10386709 AATCTTTGTC
Statistics
Matches: 565, Mismatches: 97, Indels: 55
0.79 0.14 0.08
Matches are distributed among these distances:
34 2 0.00
35 188 0.33
36 54 0.10
37 91 0.16
38 154 0.27
39 64 0.11
40 12 0.02
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (35 bp):
AAGGCAACCTTAAAAAGGTTGGGATAGACTTGTCT
Found at i:10386087 original size:38 final size:37
Alignment explanation
Indices: 10385973--10386663 Score: 478
Period size: 38 Copynumber: 18.7 Consensus size: 37
10385963 GGGTTGGAAA
* ** *
10385973 AGACCTAGTC-AAGGCCAACCTTTGAAAACGGTTGGTAT
1 AGACCT-GTCTAAGG-CAACCTTTAAAAAAAGTTGGGAT
* * * *
10386011 AGACCCGTCTAAGGCAGCC-TT-AAAGAGGTTGGGAT
1 AGACCTGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* ** **
10386046 AGACCAGTCTAAGATAACCTTTTAAAAAAAGTTAAGAT
1 AGACCTGTCTAAGGCAACC-TTTAAAAAAAGTTGGGAT
*
10386084 AGACTTTGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
1 AGAC-CTGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* *
10386122 AGACCTTGTCTAGGGTAACCTTTAAAAAACAGTTGGGAT
1 AGACC-TGTCTAAGGCAACCTTTAAAAAA-AGTTGGGAT
*
10386161 AGACCTTGTCTAAGGAAACCTTT-AAAAAAGATTGGGAT
1 AGACC-TGTCTAAGGCAACCTTTAAAAAAAG-TTGGGAT
* * *
10386199 AGA-ATCGTCTAAGGCAACC-TT-AAAAAGGTTTGGAT
1 AGACCT-GTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* * * * * *
10386234 AGACATTGTCTGAGACAACTTTTAAAAAAGGTTGAGAT
1 AGAC-CTGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* * *
10386272 GGA-CTAGTCTAAGGCAACCTTTTAACAAAGTTGGGAT
1 AGACCT-GTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* *
10386309 AGACCTTGTCTAAGGCAACCTTTAAAAAAGGTTAGGAT
1 AGACC-TGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* * * *
10386347 AGACCAGTTTAAGGCAACCTTTTAAAAAAAAATTAGGAT
1 AGACCTGTCTAAGGCAACC-TTT-AAAAAAAGTTGGGAT
* * * *
10386386 AGACCTTGTCTAAGGAAACCTTCAAAAAAGGTTAGGAT
1 AGACC-TGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* * *
10386424 AGACTTGTCTAAAGCAACC-TT-AAAAAGGTTGGGAT
1 AGACCTGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* * *
10386459 AGA-CTCGTCTAAGGTAACC-TT-AAAAAGGTAGGGAT
1 AGACCT-GTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* *
10386494 AGACCTTTGTCTAAGGCAA-CTTTTAAAAAGGTTGGGAT
1 AGACC--TGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* * *
10386532 TGACTCAT-T-TAAGACAACC-TT-AAAAATGTTGGGAT
1 AGAC-C-TGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* * *
10386567 AGA-CTCGTTTAAAGCAACC-TTAAAAATA-TTGGGAT
1 AGACCT-GTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* * *
10386602 AGACCTTTTCCAAGGTAA-C-TTAAAAAAAGTTGGGAT
1 AGACC-TGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
* *
10386638 A-AACTCATCTAAGGCAACC-TTAAAAA
1 AGACCT-GTCTAAGGCAACCTTTAAAAA
10386664 GGTTAGGGTA
Statistics
Matches: 529, Mismatches: 88, Indels: 74
0.77 0.13 0.11
Matches are distributed among these distances:
32 1 0.00
33 1 0.00
34 3 0.01
35 134 0.25
36 61 0.12
37 91 0.17
38 164 0.31
39 63 0.12
40 11 0.02
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
AGACCTGTCTAAGGCAACCTTTAAAAAAAGTTGGGAT
Found at i:10386144 original size:77 final size:77
Alignment explanation
Indices: 10385964--10386658 Score: 560
Period size: 73 Copynumber: 9.4 Consensus size: 77
10385954 CTTATTGAAG
* * * ** * *
10385964 GGTTGGAAAAGACCTAGTC-AAGGCCAACC-TTTGAAAACGGTTGGTATAGACC-CGTCTAAGGC
1 GGTTGGGATAGACCTAGTCTAAGG-CAACCTTTTAAAAAAAGTTGGGATAGACCTTGTCTAAGGC
* *
10386026 AGCC-TT-AAAGA
65 AACCTTTAAAAAA
** ** *
10386037 GGTTGGGATAGACC-AGTCTAAGATAACCTTTTAAAAAAAGTTAAGATAGACTTTGTCTAAGGCA
1 GGTTGGGATAGACCTAGTCTAAGGCAACCTTTTAAAAAAAGTTGGGATAGACCTTGTCTAAGGCA
10386101 ACCTTTAAAAAA
66 ACCTTTAAAAAA
* * * * *
10386113 AGTTGGGATAGACCTTGTCTAGGGTAACC-TTTAAAAAACAGTTGGGATAGACCTTGTCTAAGGA
1 GGTTGGGATAGACCTAGTCTAAGGCAACCTTTTAAAAAA-AGTTGGGATAGACCTTGTCTAAGGC
10386177 AACCTTTAAAAAA
65 AACCTTTAAAAAA
* * * * * * * *
10386190 GATTGGGATAGA-ATCGTCTAAGGCAACC--TT-AAAAAGGTTTGGATAGACATTGTCTGAGACA
1 GGTTGGGATAGACCTAGTCTAAGGCAACCTTTTAAAAAAAGTTGGGATAGACCTTGTCTAAGGCA
*
10386251 ACTTTTAAAAAA
66 ACCTTTAAAAAA
* * *
10386263 GGTTGAGATGGA-CTAGTCTAAGGCAACCTTTT-AACAAAGTTGGGATAGACCTTGTCTAAGGCA
1 GGTTGGGATAGACCTAGTCTAAGGCAACCTTTTAAAAAAAGTTGGGATAGACCTTGTCTAAGGCA
10386326 ACCTTTAAAAAA
66 ACCTTTAAAAAA
* * * * *
10386338 GGTTAGGATAGACC-AGTTTAAGGCAACCTTTTAAAAAAAAATTAGGATAGACCTTGTCTAAGGA
1 GGTTGGGATAGACCTAGTCTAAGGCAACCTTTT-AAAAAAAGTTGGGATAGACCTTGTCTAAGGC
*
10386402 AACCTTCAAAAAA
65 AACCTTTAAAAAA
* * * * * *
10386415 GGTTAGGATAGA-CTTGTCTAAAGCAACC--TT-AAAAAGGTTGGGATAGA-CTCGTCTAAGGTA
1 GGTTGGGATAGACCTAGTCTAAGGCAACCTTTTAAAAAAAGTTGGGATAGACCTTGTCTAAGGCA
10386475 ACC-TT-AAAAA
66 ACCTTTAAAAAA
* * * * * *
10386485 GGTAGGGATAGACCTTTGTCTAAGGCAA-CTTTT-AAAAAGGTTGGGATTGACTCAT-T-TAAGA
1 GGTTGGGATAGACC-TAGTCTAAGGCAACCTTTTAAAAAAAGTTGGGATAGAC-CTTGTCTAAGG
10386546 CAACC-TT-AAAAA
64 CAACCTTTAAAAAA
* * * * * * * *
10386558 TGTTGGGATAGA-CTCGTTTAAAGCAACC--TTAAAAATA-TTGGGATAGACCTTTTCCAAGGTA
1 GGTTGGGATAGACCTAGTCTAAGGCAACCTTTTAAAAAAAGTTGGGATAGACCTTGTCTAAGGCA
10386619 A-C-TTAAAAAA
66 ACCTTTAAAAAA
* *
10386629 AGTTGGGATA-AACTCA-TCTAAGGCAACCTT
1 GGTTGGGATAGACCT-AGTCTAAGGCAACCTT
10386659 AAAAAGGTTA
Statistics
Matches: 505, Mismatches: 89, Indels: 56
0.78 0.14 0.09
Matches are distributed among these distances:
69 2 0.00
70 32 0.06
71 48 0.10
72 36 0.07
73 142 0.28
74 18 0.04
75 71 0.14
76 40 0.08
77 116 0.23
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.26
Consensus pattern (77 bp):
GGTTGGGATAGACCTAGTCTAAGGCAACCTTTTAAAAAAAGTTGGGATAGACCTTGTCTAAGGCA
ACCTTTAAAAAA
Found at i:10386349 original size:225 final size:219
Alignment explanation
Indices: 10385983--10386708 Score: 729
Period size: 225 Copynumber: 3.3 Consensus size: 219
10385973 AGACCTAGTC
* * * * * *
10385983 AAGGCCAACCTTTGAAAACGGTTGGTATAGACCCGTCTAAGGCAGCCTTAAAGAGGTTGGGATAG
1 AAGG-CAACC-TT-AAAAAGGTTGGGATAGACTCGTCTAAGACAACCTTAAAAAGGTTGGGATAG
* ** ** *
10386048 ACCAGTCTAAGATAACCTTTTAAAAAAAGTTAAGATAGACTTTGTCTAAGGCAACCTTTAAAAAA
63 ACTAGTCTAAGGCAACCTTTT--AAAAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAA
* * * * *
10386113 AGTTGGGATAGACCTTGTCTAGGGTAACCTTTAAAAAACAGTTGGGATAGACCTTGTCTAAGGAA
126 AGTTGGGATAGACCTAGTTTAAGGCAACCTTTAAAAAA-AATTGGGATAGACCTTGTCTAAGGAA
*
10386178 ACCTTTAAAAAAGATTGGGATAGAATCGTCT
190 ACCTTAAAAAAAG-TTGGGATAGAATCGTCT
* * * * * *
10386209 AAGGCAACCTTAAAAAGGTTTGGATAGACATTGTCTGAGACAACTTTTAAAAAAGGTTGAGATGG
1 AAGGCAACCTTAAAAAGGTTGGGATAGAC-TCGTCTAAGACAAC-CTT-AAAAAGGTTGGGATAG
*
10386274 ACTAGTCTAAGGCAACCTTTTAACAAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAAG
63 ACTAGTCTAAGGCAACCTTTTAA-AAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAAA
* *
10386339 GTTAGGATAGACC-AGTTTAAGGCAACCTTTTAAAAAAAAATTAGGATAGACCTTGTCTAAGGAA
127 GTTGGGATAGACCTAGTTTAAGGCAACC-TTT-AAAAAAAATTGGGATAGACCTTGTCTAAGGAA
* * * *
10386403 ACCTTCAAAAAAGGTTAGGATAGACTTGTCT
190 ACCTT-AAAAAAAGTTGGGATAGAATCGTCT
* ** *
10386434 AAAGCAACCTTAAAAAGGTTGGGATAGACTCGTCTAAGGTAACCTTAAAAAGGTAGGGATAGACC
1 AAGGCAACCTTAAAAAGGTTGGGATAGACTCGTCTAAGACAACCTTAAAAAGGTTGGGATAGA-C
* * * * *
10386499 TTTGTCTAAGGCAA-CTTTTAAAAAGGTTGGGATTGACTCAT-T-TAAGACAACC-TT-AAAAAT
65 -TAGTCTAAGGCAACCTTTTAAAAA-GTTGGGATAGAC-CTTGTCTAAGGCAACCTTTAAAAAAA
* * * * * *
10386559 GTTGGGATAGA-CTCGTTTAAAGCAACC-TT-AAAAATATTGGGATAGACCTTTTCCAAGGTAA-
127 GTTGGGATAGACCTAGTTTAAGGCAACCTTTAAAAAAAATTGGGATAGACCTTGTCTAAGGAAAC
*
10386620 CTTAAAAAAAGTTGGGATA-AACTCATCT
192 CTTAAAAAAAGTTGGGATAGAA-TCGTCT
* * * *
10386648 AAGGCAACCTTAAAAAGGTTAGGG-TAAACTCGTCTAAGGCAAACTTAAAAAGGTTAGGATA
1 AAGGCAACCTTAAAAAGGTT-GGGATAGACTCGTCTAAGACAACCTTAAAAAGGTTGGGATA
10386709 AATCTTTGTC
Statistics
Matches: 421, Mismatches: 65, Indels: 40
0.80 0.12 0.08
Matches are distributed among these distances:
213 1 0.00
214 69 0.16
215 6 0.01
216 27 0.06
218 2 0.00
219 1 0.00
220 27 0.06
221 2 0.00
222 26 0.06
223 37 0.09
224 47 0.11
225 129 0.31
226 47 0.11
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (219 bp):
AAGGCAACCTTAAAAAGGTTGGGATAGACTCGTCTAAGACAACCTTAAAAAGGTTGGGATAGACT
AGTCTAAGGCAACCTTTTAAAAAGTTGGGATAGACCTTGTCTAAGGCAACCTTTAAAAAAAGTTG
GGATAGACCTAGTTTAAGGCAACCTTTAAAAAAAATTGGGATAGACCTTGTCTAAGGAAACCTTA
AAAAAAGTTGGGATAGAATCGTCT
Found at i:10397842 original size:24 final size:25
Alignment explanation
Indices: 10397815--10397862 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
10397805 ATTATATATA
* *
10397815 TATACGTACATATA-CTAAAAATAC
1 TATACATACATATATATAAAAATAC
*
10397839 TATATATACATATATATAAAAATA
1 TATACATACATATATATAAAAATA
10397863 TGAAGTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (25 bp):
TATACATACATATATATAAAAATAC
Found at i:10405910 original size:20 final size:21
Alignment explanation
Indices: 10405875--10405918 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
10405865 AAATAGTACT
*
10405875 ATTTTTATTTTGGTCACTCTA
1 ATTTTTATTTTGGTCAATCTA
10405896 ATTTTTATTTT-GTCAATCTA
1 ATTTTTATTTTGGTCAATCTA
10405916 ATT
1 ATT
10405919 GTGATAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (21 bp):
ATTTTTATTTTGGTCAATCTA
Found at i:10418279 original size:2 final size:2
Alignment explanation
Indices: 10418274--10418308 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10418264 CATATGTGTG
*
10418274 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10418309 GTCAACATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10435500 original size:309 final size:310
Alignment explanation
Indices: 10434930--10435548 Score: 1231
Period size: 309 Copynumber: 2.0 Consensus size: 310
10434920 TATAATAGAA
10434930 ATATTATATATATATATATATTATGTTGATGCATAAATTTTATGTAAACTAAATAATAAAAAGGG
1 ATATTATATATATATATATATTATGTTGATGCATAAATTTTATGTAAACTAAATAATAAAAAGGG
10434995 AAAGAATCCATTTATACTGGTGTAATAGTTTTACACTCTTCCATATATTTTTTTACGATTAATAA
66 AAAGAATCCATTTATACTGGTGTAATAGTTTTACACTCTTCCATATATTTTTTTACGATTAATAA
10435060 TTTAATAATCTAACGTTAAATTTATCGATATAATTGCACTTGTCATGCATGTAAATTTTATAATC
131 TTTAATAATCTAACGTTAAATTTATCGATATAATTGCACTTGTCATGCATGTAAATTTTATAATC
10435125 GATTTGATATCTCTAGTATATTGATTTAAAATATTGTCTATATTAGTAATTATTGAACTGTTCAA
196 GATTTGATATCTCTAGTATATTGATTTAAAATATTGTCTATATTAGTAATTATTGAACTGTTCAA
10435190 AGATTTTTTATATAAATTAAATAATTAAAAAATTAATTTATATTAAATTT
261 AGATTTTTTATATAAATTAAATAATTAAAAAATTAATTTATATTAAATTT
10435240 ATATTATATA-ATATATATATTATGTTGATGCATAAATTTTATGTAAACTAAATAATAAAAAGGG
1 ATATTATATATATATATATATTATGTTGATGCATAAATTTTATGTAAACTAAATAATAAAAAGGG
10435304 AAAGAATCCATTTATACTGGTGTAATAGTTTTACACTCTTCCATATATTTTTTTACGATTAATAA
66 AAAGAATCCATTTATACTGGTGTAATAGTTTTACACTCTTCCATATATTTTTTTACGATTAATAA
10435369 TTTAATAATCTAACGTTAAATTTATCGATATAATTGCACTTGTCATGCATGTAAATTTTATAATC
131 TTTAATAATCTAACGTTAAATTTATCGATATAATTGCACTTGTCATGCATGTAAATTTTATAATC
10435434 GATTTGATATCTCTAGTATATTGATTTAAAATATTGTCTATATTAGTAATTATTGAACTGTTCAA
196 GATTTGATATCTCTAGTATATTGATTTAAAATATTGTCTATATTAGTAATTATTGAACTGTTCAA
10435499 AGATTTTTTATATAAATTAAATAATTAAAAAATTAATTTATATTAAATTT
261 AGATTTTTTATATAAATTAAATAATTAAAAAATTAATTTATATTAAATTT
10435549 GACATGCATG
Statistics
Matches: 309, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
309 299 0.97
310 10 0.03
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (310 bp):
ATATTATATATATATATATATTATGTTGATGCATAAATTTTATGTAAACTAAATAATAAAAAGGG
AAAGAATCCATTTATACTGGTGTAATAGTTTTACACTCTTCCATATATTTTTTTACGATTAATAA
TTTAATAATCTAACGTTAAATTTATCGATATAATTGCACTTGTCATGCATGTAAATTTTATAATC
GATTTGATATCTCTAGTATATTGATTTAAAATATTGTCTATATTAGTAATTATTGAACTGTTCAA
AGATTTTTTATATAAATTAAATAATTAAAAAATTAATTTATATTAAATTT
Found at i:10449627 original size:43 final size:43
Alignment explanation
Indices: 10449566--10449655 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
10449556 AATGCAAAAA
10449566 AAAAAAAAAAAAACTCTAAACTAAGGTAGAAGAAGAGAAAATG
1 AAAAAAAAAAAAACTCTAAACTAAGGTAGAAGAAGAGAAAATG
10449609 AAAAAAAAAAAAACTCTAAACTAAGGTAGAAGAAGAGAAAATG
1 AAAAAAAAAAAAACTCTAAACTAAGGTAGAAGAAGAGAAAATG
10449652 AAAA
1 AAAA
10449656 CCGTAGAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.67, C:0.07, G:0.16, T:0.11
Consensus pattern (43 bp):
AAAAAAAAAAAAACTCTAAACTAAGGTAGAAGAAGAGAAAATG
Found at i:10454730 original size:161 final size:159
Alignment explanation
Indices: 10454450--10454754 Score: 414
Period size: 161 Copynumber: 1.9 Consensus size: 159
10454440 CATACCATCC
* * * * * * * *
10454450 TTTTTTGGCTTCTAGTTCTTGTACTCGTACTAGACTGTGGAAAAAAAATCACAACCTCAAATTAT
1 TTTTTTGGATTCTAGTTCTTGTACTCGTACCAGAATGAGCAAAAAAAATAACAACCCCAAATTAG
* *
10454515 ATTTAAGTATTTCGAAACTTGACAGTAAAAAAGTGTTTACAATATACCTATGATCCAGTTGTGTT
66 ATATAAATATTTCGAAACTTGACAGTAAAAAAGTGTTTACAATATACCTATGATCCAGTTGTGTT
* *
10454580 AGGTTGAATGCATGGTCTTCTATTGTTCT
131 AGCTTGAAAGCATGGTCTTCTATTGTTCT
*
10454609 TTTTTTGGATTCTAGTTCTTGTACTCGTGCCAGAATGAGACAATAAAAAATAACAACCCCAAATT
1 TTTTTTGGATTCTAGTTCTTGTACTCGTACCAGAATGAG-CAA-AAAAAATAACAACCCCAAATT
* * ** *
10454674 AGATATAAATATTTTGGAACTTGACAGTGAAAAAA-TGTTTATGATATACGTATGATCCAGTTGT
64 AGATATAAATATTTCGAAACTTGACAGT-AAAAAAGTGTTTACAATATACCTATGATCCAGTTGT
10454738 GTTAGCTTGAAAGCATG
128 GTTAGCTTGAAAGCATG
10454755 ATTTTCTGTT
Statistics
Matches: 125, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
159 34 0.27
160 2 0.02
161 83 0.66
162 6 0.05
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (159 bp):
TTTTTTGGATTCTAGTTCTTGTACTCGTACCAGAATGAGCAAAAAAAATAACAACCCCAAATTAG
ATATAAATATTTCGAAACTTGACAGTAAAAAAGTGTTTACAATATACCTATGATCCAGTTGTGTT
AGCTTGAAAGCATGGTCTTCTATTGTTCT
Found at i:10455712 original size:31 final size:31
Alignment explanation
Indices: 10455674--10455738 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
10455664 ATAAGTAAAA
* *
10455674 CATCAGTAATAAATTCGTGCAAAATAAATAG
1 CATCAGTAAAAAATTCGTGAAAAATAAATAG
*
10455705 CATCAGTAAAAAATTGGTGAAAAATAAATAG
1 CATCAGTAAAAAATTCGTGAAAAATAAATAG
10455736 CAT
1 CAT
10455739 TATTTACCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.25
Consensus pattern (31 bp):
CATCAGTAAAAAATTCGTGAAAAATAAATAG
Found at i:10457300 original size:15 final size:17
Alignment explanation
Indices: 10457263--10457304 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
10457253 TATTTAAATA
*
10457263 TTCAACACCCTCACCACC
1 TTCACCACCCTCA-CACC
10457281 TTCACCACCCTCA-ACC
1 TTCACCACCCTCACACC
10457297 -TCACCACC
1 TTCACCACC
10457305 TTACCATCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 3 0.13
18 12 0.52
ACGTcount: A:0.26, C:0.57, G:0.00, T:0.17
Consensus pattern (17 bp):
TTCACCACCCTCACACC
Found at i:10457368 original size:88 final size:90
Alignment explanation
Indices: 10457168--10457387 Score: 239
Period size: 88 Copynumber: 2.5 Consensus size: 90
10457158 CATCCCGATT
* * ** *
10457168 TAAAC-TTCAGCACCCTTACCATTTTCACCACCCTCAACCTCATCACCCTCACCACCTTTACTAC
1 TAAACATTCAACACCCTCACCACCTTCACCACCCTCAACCTCACCACCCTCACCACCTTTACTAC
** * * * **
10457232 TAGTAACCTCAGCACCCTTCCTATT
66 TAACAACCTCAACACCCTCCCCACC
* * * *
10457257 TAAATATTCAACACCCTCACCACCTTCACCACCCTCAACCTCACCA-CCTTACCATCTTTACTGC
1 TAAACATTCAACACCCTCACCACCTTCACCACCCTCAACCTCACCACCCTCACCACCTTTACTAC
10457321 TAACAA-CTCAACACCCTCCCCACC
66 TAACAACCTCAACACCCTCCCCACC
* * **
10457345 TAAACATTCACCACCCTCCCCACCTTCACCACCAGCAACCTCA
1 TAAACATTCAACACCCTCACCACCTTCACCACCCTCAACCTCA
10457388 ACACTGTCTC
Statistics
Matches: 109, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
88 51 0.47
89 23 0.21
90 35 0.32
ACGTcount: A:0.28, C:0.46, G:0.02, T:0.23
Consensus pattern (90 bp):
TAAACATTCAACACCCTCACCACCTTCACCACCCTCAACCTCACCACCCTCACCACCTTTACTAC
TAACAACCTCAACACCCTCCCCACC
Found at i:10458376 original size:29 final size:28
Alignment explanation
Indices: 10458336--10458413 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 28
10458326 AAAACAATAA
*
10458336 AAAAAT-CCCAAAATCGAAAACCCTAAAC
1 AAAAATCCCCAAAATC-AAAACCATAAAC
* * * *
10458364 TAAAATCCCCAAAATAAAAAAATCATAAAG
1 AAAAATCCCCAAAAT--CAAAACCATAAAC
10458394 AAAAATCCCCAAAATCAAAA
1 AAAAATCCCCAAAATCAAAA
10458414 TAACCTAACC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
28 9 0.22
29 8 0.20
30 23 0.57
ACGTcount: A:0.62, C:0.23, G:0.03, T:0.13
Consensus pattern (28 bp):
AAAAATCCCCAAAATCAAAACCATAAAC
Found at i:10459106 original size:18 final size:18
Alignment explanation
Indices: 10459078--10459131 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
10459068 CAACACCTGC
10459078 AAAAG-AAGAAAATGAAA
1 AAAAGAAAGAAAATGAAA
*
10459095 AAAAGAAAGAAAAAG-AA
1 AAAAGAAAGAAAATGAAA
*
10459112 AAGAGAAAAGAAAATTGAAA
1 AAAAG-AAAGAAAA-TGAAA
10459132 GAGATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 11 0.37
18 16 0.53
19 1 0.03
20 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.06
Consensus pattern (18 bp):
AAAAGAAAGAAAATGAAA
Found at i:10462061 original size:11 final size:11
Alignment explanation
Indices: 10462045--10462075 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
10462035 CATCGCGTAG
10462045 TCGCGCAAAGT
1 TCGCGCAAAGT
10462056 TCGCGCAAAGT
1 TCGCGCAAAGT
10462067 TCGCGCAAA
1 TCGCGCAAA
10462076 ATTCTCGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (11 bp):
TCGCGCAAAGT
Found at i:10476768 original size:28 final size:28
Alignment explanation
Indices: 10476736--10476795 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
10476726 AAGCCGACCA
* *
10476736 TATGAATTTCCTCACACAAGCATTAGGT
1 TATGAAATGCCTCACACAAGCATTAGGT
* * *
10476764 TATGAAATGGCTCACACAAGCCTTCGGT
1 TATGAAATGCCTCACACAAGCATTAGGT
10476792 TATG
1 TATG
10476796 GTGATTGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (28 bp):
TATGAAATGCCTCACACAAGCATTAGGT
Found at i:10477725 original size:20 final size:21
Alignment explanation
Indices: 10477686--10477735 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
10477676 GCTTATATAC
* *
10477686 TTTATTTAACTTATACTTAAA
1 TTTAATTAACTTAAACTTAAA
10477707 TTTAATTAA-TTAAACTTAAA
1 TTTAATTAACTTAAACTTAAA
*
10477727 CTTAATTAA
1 TTTAATTAA
10477736 AAAAGTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTAATTAACTTAAACTTAAA
Found at i:10481159 original size:17 final size:17
Alignment explanation
Indices: 10481137--10481171 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
10481127 GAACGCGAAG
10481137 ATAAACACAATAGATTA
1 ATAAACACAATAGATTA
10481154 ATAAACACAATAGATTA
1 ATAAACACAATAGATTA
10481171 A
1 A
10481172 CCTACTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (17 bp):
ATAAACACAATAGATTA
Found at i:10484416 original size:11 final size:11
Alignment explanation
Indices: 10484373--10484426 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
10484363 ATTGACAGCG
*
10484373 AAACAACACTA
1 AAACAACACCA
* *
10484384 AAATACCACCCA
1 AAACAACA-CCA
10484396 AAATCAACACCA
1 AAA-CAACACCA
10484408 AAACAACACCAA
1 AAACAACACC-A
10484420 AAACAAC
1 AAACAAC
10484427 CTGCAAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 13 0.37
12 19 0.54
13 3 0.09
ACGTcount: A:0.61, C:0.33, G:0.00, T:0.06
Consensus pattern (11 bp):
AAACAACACCA
Found at i:10484417 original size:24 final size:23
Alignment explanation
Indices: 10484373--10484426 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
10484363 ATTGACAGCG
* * *
10484373 AAACAACACTAAAATACCACCCAA
1 AAACAACACCAAAACAACA-CCAA
*
10484397 AATCAACACCAAAACAACACCAA
1 AAACAACACCAAAACAACACCAA
10484420 AAACAAC
1 AAACAAC
10484427 CTGCAAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.61, C:0.33, G:0.00, T:0.06
Consensus pattern (23 bp):
AAACAACACCAAAACAACACCAA
Found at i:10487258 original size:18 final size:19
Alignment explanation
Indices: 10487217--10487258 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
10487207 ATAAGTTAAT
*
10487217 CATCATGTATTTTCCATCA
1 CATCATGAATTTTCCATCA
*
10487236 -TTCATGAATTTT-CATCA
1 CATCATGAATTTTCCATCA
10487253 CATCAT
1 CATCAT
10487259 ACCAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.43
Consensus pattern (19 bp):
CATCATGAATTTTCCATCA
Found at i:10489811 original size:62 final size:62
Alignment explanation
Indices: 10489714--10489837 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
10489704 TAGGAGAGAG
10489714 GTCTAATATGGTGAGTGTTAAAAGTTACGGTTACTTATTGTACAAATGCTAAGATAGTAGAT
1 GTCTAATATGGTGAGTGTTAAAAGTTACGGTTACTTATTGTACAAATGCTAAGATAGTAGAT
10489776 GTCTAATATGGTGAGTGTTAAAAGTTACGGTTACTTATTGTACAAATGCTAAGATAGTAGAT
1 GTCTAATATGGTGAGTGTTAAAAGTTACGGTTACTTATTGTACAAATGCTAAGATAGTAGAT
10489838 TATCTCTCTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.35
Consensus pattern (62 bp):
GTCTAATATGGTGAGTGTTAAAAGTTACGGTTACTTATTGTACAAATGCTAAGATAGTAGAT
Found at i:10491369 original size:6 final size:6
Alignment explanation
Indices: 10491358--10491386 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
10491348 TATATTGAGA
10491358 ATGTAT ATGTAT ATGTAT ATGTAT ATGTA
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTA
10491387 ATATTAATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (6 bp):
ATGTAT
Found at i:10493551 original size:14 final size:17
Alignment explanation
Indices: 10493518--10493558 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
10493508 TCCTACTTTT
10493518 TTTATTATAATATTTAA
1 TTTATTATAATATTTAA
*
10493535 TTTA-TATAA-ATTTAT
1 TTTATTATAATATTTAA
10493550 TTTCATTAT
1 TTT-ATTAT
10493559 TCTTATCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 8 0.38
16 6 0.29
17 7 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATTATAATATTTAA
Found at i:10494274 original size:16 final size:15
Alignment explanation
Indices: 10494253--10494303 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 15
10494243 CCAGTTTACT
10494253 ATGTATGTTTTTTTTA
1 ATGTAT-TTTTTTTTA
10494269 ATGTATTATTTTTTTAAA
1 ATGTATT-TTTTTTT--A
*
10494287 ATGTATTATTTTTTA
1 ATGTATTTTTTTTTA
10494302 AT
1 AT
10494304 TTAAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 13 0.42
17 6 0.19
18 8 0.26
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (15 bp):
ATGTATTTTTTTTTA
Found at i:10494282 original size:15 final size:16
Alignment explanation
Indices: 10494261--10494300 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
10494251 CTATGTATGT
10494261 TTTTTTTAATGTATTA
1 TTTTTTTAATGTATTA
10494277 TTTTTTTAAAATGTATTA
1 TTTTTTT--AATGTATTA
10494295 TTTTTT
1 TTTTTT
10494301 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.32
18 15 0.68
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (16 bp):
TTTTTTTAATGTATTA
Found at i:10503473 original size:21 final size:21
Alignment explanation
Indices: 10503447--10503488 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
10503437 TTTTTTTATT
*
10503447 TGAATCTAATAAA-AAAACATA
1 TGAATC-AAAAAATAAAACATA
10503468 TGAATCAAAAAATAAAACATA
1 TGAATCAAAAAATAAAACATA
10503489 AACATACCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.64, C:0.10, G:0.05, T:0.21
Consensus pattern (21 bp):
TGAATCAAAAAATAAAACATA
Found at i:10503513 original size:16 final size:16
Alignment explanation
Indices: 10503492--10503524 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10503482 AAACATAAAC
*
10503492 ATACCTTACCAAAATA
1 ATACCTTACAAAAATA
10503508 ATACCTTACAAAAATA
1 ATACCTTACAAAAATA
10503524 A
1 A
10503525 ATAAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (16 bp):
ATACCTTACAAAAATA
Found at i:10503843 original size:32 final size:30
Alignment explanation
Indices: 10503785--10503849 Score: 76
Period size: 32 Copynumber: 2.1 Consensus size: 30
10503775 ATGTTTTCCC
* *
10503785 TTTTTTCTTTCCTTCTCTTCTATTCTCTTT
1 TTTTTTCTTTCCTTCTCATCTATTCTCTAT
* *
10503815 TTTTTTCCTTCTCCTTTTCATCTCTTCTCTAT
1 TTTTTT-CTT-TCCTTCTCATCTATTCTCTAT
10503847 TTT
1 TTT
10503850 GCTCCTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 6 0.21
31 3 0.10
32 20 0.69
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTTTTCTTTCCTTCTCATCTATTCTCTAT
Found at i:10515885 original size:15 final size:15
Alignment explanation
Indices: 10515865--10515898 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
10515855 TTTGTTCGGT
10515865 TCTATTCTACTCTAC
1 TCTATTCTACTCTAC
* *
10515880 TCTATTTTACTCTGC
1 TCTATTCTACTCTAC
10515895 TCTA
1 TCTA
10515899 CTTGATTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.29, G:0.03, T:0.50
Consensus pattern (15 bp):
TCTATTCTACTCTAC
Found at i:10517188 original size:21 final size:21
Alignment explanation
Indices: 10517139--10517179 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
10517129 TTATCATAGT
*
10517139 TATCATATTATAGATCATACA
1 TATCATATTACAGATCATACA
10517160 TATCATATTACAGATCATAC
1 TATCATATTACAGATCATAC
10517180 TGACTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (21 bp):
TATCATATTACAGATCATACA
Found at i:10530989 original size:5 final size:5
Alignment explanation
Indices: 10530969--10531002 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
10530959 GATGGAATTT
* *
10530969 GAATC AAATA GAATC GAATC GAATC GAATC GAAT
1 GAATC GAATC GAATC GAATC GAATC GAATC GAAT
10531003 ATATTTGTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (5 bp):
GAATC
Found at i:10531288 original size:30 final size:29
Alignment explanation
Indices: 10531254--10531311 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
10531244 AGAGGTGGGA
*
10531254 TGGGAAAGGAATAAAAGTTTTAGGGGAAAG
1 TGGGAAA-GAATAAAAATTTTAGGGGAAAG
* * *
10531284 TGGGAGAGAGTAAAAATTTTGGGGGAAA
1 TGGGAAAGAATAAAAATTTTAGGGGAAA
10531312 ATAAAAGGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (29 bp):
TGGGAAAGAATAAAAATTTTAGGGGAAAG
Found at i:10531684 original size:9 final size:9
Alignment explanation
Indices: 10531670--10531706 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
10531660 TATAGTTTGA
10531670 TATTCGAAT
1 TATTCGAAT
10531679 TATTCGAAT
1 TATTCGAAT
*
10531688 TATTCGAGT
1 TATTCGAAT
10531697 TATTCGAAT
1 TATTCGAAT
10531706 T
1 T
10531707 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:10533782 original size:11 final size:11
Alignment explanation
Indices: 10533766--10533790 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10533756 AACAAAATTA
10533766 AAATTAAAACC
1 AAATTAAAACC
10533777 AAATTAAAACC
1 AAATTAAAACC
10533788 AAA
1 AAA
10533791 AGAAAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATTAAAACC
Found at i:10543861 original size:62 final size:63
Alignment explanation
Indices: 10543750--10543893 Score: 161
Period size: 62 Copynumber: 2.3 Consensus size: 63
10543740 TAAGTGAGCT
* * *
10543750 TAATTAAAAATTTCAAAAAACATTAAAAGGTAAAATGAGAAATTTCAAAAAAATT-GAGGAGTC
1 TAATTAAAATTTTCTAAAAACATTAAAAGGTAAAATGAGAAATTTCAAAAAAATTGGAGG-GCC
* * **
10543813 TAATTAAAATTTTCTAAAAAC-TTTAAAGG-AGAAATGA-AATTTTCCAAAAATTTTGGAGGGCC
1 TAATTAAAATTTTCTAAAAACATTAAAAGGTA-AAATGAGAAATTT-CAAAAAAATTGGAGGGCC
*
10543875 TAATTAAAATTTACTAAAA
1 TAATTAAAATTTTCTAAAA
10543894 CTTCAAGGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
61 6 0.09
62 41 0.59
63 23 0.33
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.30
Consensus pattern (63 bp):
TAATTAAAATTTTCTAAAAACATTAAAAGGTAAAATGAGAAATTTCAAAAAAATTGGAGGGCC
Found at i:10543902 original size:60 final size:62
Alignment explanation
Indices: 10543812--10543927 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 62
10543802 ATTGAGGAGT
* * *
10543812 CTAATTAAAATTTTCTAAAAACTTTAAAGGAGAAATGA-AATTTTCCAAAAATTTTGGAGGGC
1 CTAATTAAAATTTACTAAAAACTTTAAAGGAAAAATCATAA-TTTCCAAAAATTTTGGAGGGC
* *
10543874 CTAATTAAAATTTACT-AAAAC-TTCAAGGAAAAATCATAATTTCCCAAAATTTTG
1 CTAATTAAAATTTACTAAAAACTTTAAAGGAAAAATCATAATTTCCAAAAATTTTG
10543928 ATAGGCCCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 26 0.54
61 7 0.15
62 15 0.31
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (62 bp):
CTAATTAAAATTTACTAAAAACTTTAAAGGAAAAATCATAATTTCCAAAAATTTTGGAGGGC
Found at i:10550994 original size:23 final size:23
Alignment explanation
Indices: 10550968--10551011 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
10550958 CCCAATTCTT
* *
10550968 CTTTCCCTCTTTTTTTTTTTTTA
1 CTTTCCCTCTCTTTTTGTTTTTA
*
10550991 CTTTCTCTCTCTTTTTGTTTT
1 CTTTCCCTCTCTTTTTGTTTT
10551012 GGGTTTCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (23 bp):
CTTTCCCTCTCTTTTTGTTTTTA
Found at i:10553877 original size:24 final size:23
Alignment explanation
Indices: 10553840--10553886 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
10553830 AATTTAACTA
10553840 AAAAAAGAGAAAAAA-ATTAAATT
1 AAAAAAGAGAAAAAACA-TAAATT
*
10553863 AAAAAAGATGTAAAAACATAAATT
1 AAAAAAGA-GAAAAAACATAAATT
10553887 TATAATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (23 bp):
AAAAAAGAGAAAAAACATAAATT
Found at i:10563024 original size:59 final size:59
Alignment explanation
Indices: 10562891--10563016 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 59
10562881 CTACAGAATT
* ** * * * * * *
10562891 AAAATTATGAAACAAAATCAAAATCAATTTTGTTAAACGGCAAGATTAAATCCCTAAAC
1 AAAATTATGTAATTAAATCAAAATAAAGTTTATTAAACGACAAGAATAAATCCCGAAAC
**
10562950 AAAATTATGTAATTAAATCAAAATAAAGTTTATTAAACGACGTGAATAAATCCCGAAAC
1 AAAATTATGTAATTAAATCAAAATAAAGTTTATTAAACGACAAGAATAAATCCCGAAAC
*
10563009 AGAATTAT
1 AAAATTAT
10563017 TTGATTAAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.27
Consensus pattern (59 bp):
AAAATTATGTAATTAAATCAAAATAAAGTTTATTAAACGACAAGAATAAATCCCGAAAC
Found at i:10563171 original size:88 final size:86
Alignment explanation
Indices: 10562982--10563260 Score: 318
Period size: 88 Copynumber: 3.3 Consensus size: 86
10562972 ATAAAGTTTA
* * * * *
10562982 TTAAACGACGTGAATAAATCCCGAAACAGA-ATTATTTGA--TTAA-GTCTTCGTTTGGAAAC-A
1 TTAAACGACGGGAATAAATCCCAAAACAGATTTTATTTAACTTTAATTTC-TCGTTTGGAAACAA
* * *
10563042 AAT-CAATATCGAATAAAATCTTG
65 AATAAAAAAT-GAATAAAATC-CG
* * *
10563065 TTAAATGGCGGGAATAAATCCCAAAACAGATTTTATTTAACTTTAATTTCTCGTTTTGGCAACAA
1 TTAAACGACGGGAATAAATCCCAAAACAGATTTTATTTAACTTTAATTTCTCG-TTTGGAAACAA
10563130 AATAAAAAATGTAATAAAATCCG
65 AATAAAAAATG-AATAAAATCCG
* * * *
10563153 TTGAACGACGGGAATAAATCTCGAAACAGATTTTATTTAACTTTAATTTCTCGTTTGGAAATAAA
1 TTAAACGACGGGAATAAATCCCAAAACAGATTTTATTTAACTTTAATTTCTCGTTTGGAAACAAA
*
10563218 ATAAAAAATGAATAAAATCTG
66 ATAAAAAATGAATAAAATCCG
*
10563239 TTAAACGGCGGGAATAAATCCC
1 TTAAACGACGGGAATAAATCCC
10563261 GAAATAAAGT
Statistics
Matches: 166, Mismatches: 22, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
83 26 0.16
84 7 0.04
86 36 0.22
87 30 0.18
88 54 0.33
89 13 0.08
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (86 bp):
TTAAACGACGGGAATAAATCCCAAAACAGATTTTATTTAACTTTAATTTCTCGTTTGGAAACAAA
ATAAAAAATGAATAAAATCCG
Found at i:10563268 original size:35 final size:35
Alignment explanation
Indices: 10563228--10563299 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
10563218 ATAAAAAATG
10563228 AATAAAATCTGTTAAAC-GGCGGGAATAAATCCCGA
1 AATAAAATCTGTTAAACGGGC-GGAATAAATCCCGA
* * *
10563263 AATAAAGTTTGTTAAACGGGCGGAATAAATCCTGA
1 AATAAAATCTGTTAAACGGGCGGAATAAATCCCGA
10563298 AA
1 AA
10563300 CATAACTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 30 0.91
36 3 0.09
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (35 bp):
AATAAAATCTGTTAAACGGGCGGAATAAATCCCGA
Found at i:10563451 original size:87 final size:86
Alignment explanation
Indices: 10563323--10563557 Score: 267
Period size: 87 Copynumber: 2.7 Consensus size: 86
10563313 TGAAGTCATC
* * * **
10563323 ATTTGGAAAC-AAATCAATATCGAATAAAATCTAGTTAAACGGCAAGAATAAATCCCAAAACAGA
1 ATTTGGAAACAAAATCAAAAT-GAATAAAATC-CGTTGAACGGCGGGAATAAATCCCAAAACAGA
10563387 TTTTATTTAATTTTAATTTCTCG
64 TTTTATTTAATTTTAATTTCTCG
* * * * *
10563410 ATTTGGCAACAAAATCAAAATGTAATAAAATCCGTTGAACGGCGGGAATAAGTCTCGAAATAGAT
1 ATTTGGAAACAAAATCAAAATG-AATAAAATCCGTTGAACGGCGGGAATAAATCCCAAAACAGAT
10563475 TTTATTTAATTTTAATTTCTCG
65 TTTATTTAATTTTAATTTCTCG
* ** * *
10563497 -TTTGGAAATAAAGTAAAAAAAAGGAATAAAATCCGTTGAACAGCGGGAATAAATCCCAAAA
1 ATTTGGAAA-CAA--AATCAAAATGAATAAAATCCGTTGAACGGCGGGAATAAATCCCAAAA
10563558 TAAAGTATGT
Statistics
Matches: 124, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
86 7 0.06
87 59 0.48
88 51 0.41
89 7 0.06
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (86 bp):
ATTTGGAAACAAAATCAAAATGAATAAAATCCGTTGAACGGCGGGAATAAATCCCAAAACAGATT
TTATTTAATTTTAATTTCTCG
Found at i:10563559 original size:88 final size:87
Alignment explanation
Indices: 10563368--10563559 Score: 260
Period size: 88 Copynumber: 2.2 Consensus size: 87
10563358 TAAACGGCAA
* * ** * *
10563368 GAATAAATCCCAAAACAGATTTTATTTAATTTTAATTTCTCGATTTGGCAACAAAATCAAAATGT
1 GAATAAATCCCAAAATAGATTTTATTTAATTTTAATTTCTCGATTTGGAAACAAAAAAAAAAAGG
*
10563433 AATAAAATCCGTTGAACGGCGG
66 AATAAAATCCGTTGAACAGCGG
* * * *
10563455 GAATAAGTCTCGAAATAGATTTTATTTAATTTTAATTTCTCG-TTTGGAAATAAAGTAAAAAAAA
1 GAATAAATCCCAAAATAGATTTTATTTAATTTTAATTTCTCGATTTGGAAACAAA--AAAAAAAA
10563519 GGAATAAAATCCGTTGAACAGCGG
64 GGAATAAAATCCGTTGAACAGCGG
10563543 GAATAAATCCCAAAATA
1 GAATAAATCCCAAAATA
10563560 AAGTATGTTA
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
86 10 0.11
87 38 0.43
88 41 0.46
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (87 bp):
GAATAAATCCCAAAATAGATTTTATTTAATTTTAATTTCTCGATTTGGAAACAAAAAAAAAAAGG
AATAAAATCCGTTGAACAGCGG
Found at i:10563647 original size:293 final size:291
Alignment explanation
Indices: 10562968--10563692 Score: 1110
Period size: 293 Copynumber: 2.5 Consensus size: 291
10562958 GTAATTAAAT
* *
10562968 CAAAATAAAGTTTATTAAACGACGTGAATAAATCCCGAAACAGAATTATTTGATTAAGTCTTCGT
1 CAAAATAAAGTTTGTTAAACG-CGGGAATAAATCCCGAAACAGAATTATTTGATTAAGTCTTCGT
10563033 TTGGAAACAAATCAATATCGAATAAAATCTTGTTAAATGGCGGGAATAAATCCCAAAACAGATTT
65 TTGGAAACAAATCAATATCGAATAAAATCTTGTTAAATGGCGGGAATAAATCCCAAAACAGATTT
* *
10563098 TATTTAACTTTAATTTCTCGTTTTGGCAACAAAATAAAAAATGTAATAAAATCCGTTGAACGACG
130 TATTTAATTTTAATTTCTCGATTTGGCAACAAAATAAAAAATGTAATAAAATCCGTTGAACGACG
* *
10563163 GGAATAAATCTCGAAACAGATTTTATTTAACTTTAATTTCTCGTTTGGAAATAAAATAAAAAATG
195 GGAATAAATCTCGAAACAGATTTTATTTAACTTTAATTTCTCGTTTGGAAATAAAAAAAAAAAGG
* *
10563228 AATAAAATCTGTTAAACGGCGGGAATAAATCC
260 AATAAAATCCGTTAAACAGCGGGAATAAATCC
* * * * * * * *
10563260 CGAAATAAAGTTTGTTAAACGGGCGGAATAAATCCTGAAACATAACTATTTGATGAAGTCATCAT
1 CAAAATAAAGTTTGTTAAACGCG-GGAATAAATCCCGAAACAGAATTATTTGATTAAGTCTTCGT
* * **
10563325 TTGGAAACAAATCAATATCGAATAAAATCTAGTTAAACGGCAAGAATAAATCCCAAAACAGATTT
65 TTGGAAACAAATCAATATCGAATAAAATCTTGTTAAATGGCGGGAATAAATCCCAAAACAGATTT
* *
10563390 TATTTAATTTTAATTTCTCGATTTGGCAACAAAAT-CAAAATGTAATAAAATCCGTTGAACGGCG
130 TATTTAATTTTAATTTCTCGATTTGGCAACAAAATAAAAAATGTAATAAAATCCGTTGAACGACG
* * *
10563454 GGAATAAGTCTCGAAATAGATTTTATTTAATTTTAATTTCTCGTTTGGAAATAAAGTAAAAAAAA
195 GGAATAAATCTCGAAACAGATTTTATTTAACTTTAATTTCTCGTTTGGAAATAAA--AAAAAAAA
*
10563519 GGAATAAAATCCGTTGAACAGCGGGAATAAATCC
258 GGAATAAAATCCGTTAAACAGCGGGAATAAATCC
* *
10563553 CAAAATAAAGTATGTTAAACAGCGGGAATAAATCCCGAAATAGAATTATTTGATTAAGTCTTCGT
1 CAAAATAAAGTTTGTTAAAC-GCGGGAATAAATCCCGAAACAGAATTATTTGATTAAGTCTTCGT
* * * *
10563618 TTGTAAACAAACCAATATCGAATAAAATCTTGTTAAATAGCGGGAATAAATCCCAAAATAGATTT
65 TTGGAAACAAATCAATATCGAATAAAATCTTGTTAAATGGCGGGAATAAATCCCAAAACAGATTT
10563683 TATTTAATTT
130 TATTTAATTT
10563693 GAAAACAAAA
Statistics
Matches: 385, Mismatches: 44, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
291 80 0.21
292 147 0.38
293 156 0.41
294 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (291 bp):
CAAAATAAAGTTTGTTAAACGCGGGAATAAATCCCGAAACAGAATTATTTGATTAAGTCTTCGTT
TGGAAACAAATCAATATCGAATAAAATCTTGTTAAATGGCGGGAATAAATCCCAAAACAGATTTT
ATTTAATTTTAATTTCTCGATTTGGCAACAAAATAAAAAATGTAATAAAATCCGTTGAACGACGG
GAATAAATCTCGAAACAGATTTTATTTAACTTTAATTTCTCGTTTGGAAATAAAAAAAAAAAGGA
ATAAAATCCGTTAAACAGCGGGAATAAATCC
Found at i:10564017 original size:88 final size:86
Alignment explanation
Indices: 10563727--10564028 Score: 330
Period size: 86 Copynumber: 3.5 Consensus size: 86
10563717 AATATTGTTA
* * * *
10563727 AACGGCGAGAATAAAGC-CTGAAATAGA-TTTATTTAATTTTAATTTCTCGTTTTGGAAACAAAA
1 AACGGCGGGAATAAATCTC-GAAACAGATTTTATTTAATTTTAATTTCTCGTTTTGGAAATAAAA
10563790 TC-AAATGTAATAAAATTCGTTG
65 TCAAAATG-AATAAAATTCGTTG
* *
10563812 AACGGCGGGAATAAATC-CAGAAACATATTTTATTTAACTTTAATTTCTCG-TTTGGAAATAAAA
1 AACGGCGGGAATAAATCTC-GAAACAGATTTTATTTAATTTTAATTTCTCGTTTTGGAAATAAAA
*
10563875 TAAAAAATGAATAAAATTCGTTG
65 T-CAAAATGAATAAAATTCGTTG
* * * *
10563898 AACGGCGGGAATAAAT-TCCGAGACAGTTTTTATTTTAATTTTAA-TACTTGTTTTGGAAATAAA
1 AACGGCGGGAATAAATCT-CGAAACAGATTTTA-TTTAATTTTAATTTCTCGTTTTGGAAATAAA
*
10563961 ATCAAAATTAGAATAAAATCCGTTG
64 ATCAAAA-T-GAATAAAATTCGTTG
* * * * *
10563986 AATGGCGGGAATAGATCTCGAAATAGATTTTATTGACTTTTAA
1 AACGGCGGGAATAAATCTCGAAACAGATTTTATTTAATTTTAA
10564029 AATATATATT
Statistics
Matches: 184, Mismatches: 23, Indels: 18
0.82 0.10 0.08
Matches are distributed among these distances:
85 35 0.19
86 69 0.38
87 40 0.22
88 39 0.21
89 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (86 bp):
AACGGCGGGAATAAATCTCGAAACAGATTTTATTTAATTTTAATTTCTCGTTTTGGAAATAAAAT
CAAAATGAATAAAATTCGTTG
Found at i:10564174 original size:18 final size:19
Alignment explanation
Indices: 10564151--10564198 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
10564141 TTAGTGAACA
10564151 AAATATATAAATAT-AAAT
1 AAATATATAAATATAAAAT
* *
10564169 AAATATTTATATATAAAAT
1 AAATATATAAATATAAAAT
10564188 AAA-ATATAAAT
1 AAATATATAAAT
10564199 GAAATAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATATATAAATATAAAAT
Found at i:10565578 original size:2 final size:2
Alignment explanation
Indices: 10565571--10565604 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
10565561 ATTTTAAGAA
10565571 AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
10565605 TAATGTCGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 27 0.90
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:10567515 original size:13 final size:13
Alignment explanation
Indices: 10567497--10567524 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10567487 CTGAATTAGT
10567497 TTTACTAACCACC
1 TTTACTAACCACC
10567510 TTTACTAACCACC
1 TTTACTAACCACC
10567523 TT
1 TT
10567525 ATCATGGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTACTAACCACC
Found at i:10572336 original size:14 final size:14
Alignment explanation
Indices: 10572317--10572345 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10572307 TTTTGCGTTA
10572317 TATATGTGTGAAAT
1 TATATGTGTGAAAT
10572331 TATATGTGTGAAAT
1 TATATGTGTGAAAT
10572345 T
1 T
10572346 TTTGTGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (14 bp):
TATATGTGTGAAAT
Found at i:10573491 original size:41 final size:41
Alignment explanation
Indices: 10573446--10573557 Score: 152
Period size: 41 Copynumber: 2.7 Consensus size: 41
10573436 ACTTTATATT
*
10573446 AATGTATCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGA
1 AATGTATCAGGCTTTATGCCTAGCAGGCTTCATGCCGGTGA
* * * *
10573487 AATGTATCAGGCTTTAAGCCTAACAAGCTTCATGCCGGTGT
1 AATGTATCAGGCTTTATGCCTAGCAGGCTTCATGCCGGTGA
***
10573528 ACCCTATCAGGCTTTATGCCTAGCAGGCTT
1 AATGTATCAGGCTTTATGCCTAGCAGGCTT
10573558 GGTGCCAGTG
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (41 bp):
AATGTATCAGGCTTTATGCCTAGCAGGCTTCATGCCGGTGA
Found at i:10576977 original size:2 final size:2
Alignment explanation
Indices: 10576972--10576996 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10576962 ATAAGTTATG
10576972 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10576997 TAATTAGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10577317 original size:7 final size:6
Alignment explanation
Indices: 10577282--10577316 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
10577272 TGGGTTTTAA
10577282 GGTTAG GGTTAG GGTTAG GGTTAG GGTTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GG-TTAG GGTT
10577317 TTTAGGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.14, C:0.00, G:0.49, T:0.37
Consensus pattern (6 bp):
GGTTAG
Found at i:10578130 original size:2 final size:2
Alignment explanation
Indices: 10578125--10578149 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
10578115 ATAAGTTATG
10578125 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
10578150 TAATTAGTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10578470 original size:7 final size:6
Alignment explanation
Indices: 10578435--10578469 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
10578425 TGGGTTTTAA
10578435 GGTTAG GGTTAG GGTTAG GGTTAG GGTTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GG-TTAG GGTT
10578470 TTTAGGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.14, C:0.00, G:0.49, T:0.37
Consensus pattern (6 bp):
GGTTAG
Found at i:10581626 original size:49 final size:49
Alignment explanation
Indices: 10581571--10581748 Score: 329
Period size: 49 Copynumber: 3.6 Consensus size: 49
10581561 TAAGAATATT
* *
10581571 AACTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
10581620 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
10581669 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
1 AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
10581718 AACTATTTTGTATTTTATTACATCAATATAA
1 AACTATTTTGTATTTTATTACATCAA-ATAA
10581749 ACTATTTTGT
Statistics
Matches: 126, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
49 122 0.97
50 4 0.03
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (49 bp):
AACTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATA
Found at i:10582193 original size:18 final size:18
Alignment explanation
Indices: 10582166--10582203 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
10582156 GGAAAAGTAA
* *
10582166 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
10582184 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTAGGAT
10582202 AC
1 AC
10582204 GCACCTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:10584033 original size:11 final size:11
Alignment explanation
Indices: 10584017--10584062 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
10584007 TCTTTCAAAT
10584017 AGGAATTTGAG
1 AGGAATTTGAG
10584028 AGGAATTTGAG
1 AGGAATTTGAG
10584039 A-GAATATT-AG
1 AGGAAT-TTGAG
*
10584049 AGAGAAATTGAG
1 AG-GAATTTGAG
10584061 AG
1 AG
10584063 AAAGGATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.23
11 16 0.53
12 7 0.23
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (11 bp):
AGGAATTTGAG
Found at i:10584061 original size:10 final size:10
Alignment explanation
Indices: 10584023--10584065 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
10584013 AAATAGGAAT
*
10584023 TTGAGAGGAAT
1 TTGAGA-GAAA
10584034 TTGAGAGAATA
1 TTGAGAGAA-A
10584045 TTAGAGAGAAA
1 TT-GAGAGAAA
10584056 TTGAGAGAAA
1 TTGAGAGAAA
10584066 GGATTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 11 0.38
11 11 0.38
12 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (10 bp):
TTGAGAGAAA
Found at i:10586593 original size:71 final size:69
Alignment explanation
Indices: 10586518--10586681 Score: 235
Period size: 71 Copynumber: 2.3 Consensus size: 69
10586508 ATTTTTTATG
*
10586518 TTTTTTTTG-TTATTAATTATTATAAATTGTTTGTGTTTAGTTTAGTGTTTTGTG-TGTTTTTAT
1 TTTTTTTTGTTTTTTAATTATT-T-AATTGTTTGT-TTTAGTTTAGTGTTTTGTGAT-TTTTTAT
*
10586581 GAATGTAA
62 GAATATAA
10586589 TTTTTTTTGTATTTTTAAATTATTTAATTGTTTGTTTTAGTTTAGTGTTTTGTGATTTTTTATGA
1 TTTTTTTTGT-TTTTT-AATTATTTAATTGTTTGTTTTAGTTTAGTGTTTTGTGATTTTTTATGA
10586654 ATATAA
64 ATATAA
10586660 -TTTTTTTGTTTTTTAATTATTT
1 TTTTTTTTGTTTTTTAATTATTT
10586682 TATAGTTATT
Statistics
Matches: 87, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
68 8 0.09
69 5 0.06
70 9 0.10
71 42 0.48
72 11 0.13
73 5 0.06
74 7 0.08
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (69 bp):
TTTTTTTTGTTTTTTAATTATTTAATTGTTTGTTTTAGTTTAGTGTTTTGTGATTTTTTATGAAT
ATAA
Found at i:10586939 original size:102 final size:101
Alignment explanation
Indices: 10586668--10587183 Score: 536
Period size: 102 Copynumber: 4.9 Consensus size: 101
10586658 AATTTTTTTG
* * * *
10586668 TTTTTTAATTATTTTATAGTTATTTTGTTAGTAATTTCTAATTAGGTTATAAATTGTTTGTGTTT
1 TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTT
* * **
10586733 AGTTTAGTG-TT-TTGTGATTTTCTATTAATGTAAAAATTTTTA
66 AGTTTAATGTTTATTGTGA-TTT-T-TT-A--T--AAATGTGCA
* * * *
10586775 TTTTTTAAATTATTTTAAAGTCAATTTTTTTAGTAATTTATGGTTAGGTTATTAATTGTTTGTGT
1 -TTTTTAAATTATTTTAAAGT-TATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGT
10586840 TTAGTTTAATGTTTATTGTGATTTTTTATAAATGTGCA
64 TTAGTTTAATGTTTATTGTGATTTTTTATAAATGTGCA
* * * *
10586878 TTTTTAAAATTATTTGAAAGTTATTTTGCTAGTAATTTATGATTAGGTCATAAATTTTTTGTGTT
1 TTTTT-AAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTT
* **
10586943 TAGTTTAATGTTTATTGTGATTTTTTATGAATGTAAAA
65 TAGTTTAATGTTTATTGTGATTTTTTATAAATGT-GCA
* * *
10586981 TTTTTTAATTATTTTAAAGTTATTTTGTTAGTAATTTATTATTAGGTCATAAATTGTTTGTGTTT
1 TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTT
* * * *
10587046 AGTTTAGTGTTTATTGTGACTTGTTATAAATGTAAATTTTTTGCG
66 AGTTTAATGTTTATTGTGA-TT-TT-T---TATAAA---TGTGCA
*
10587091 TTCTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATT-ATT-TGTT
1 TT-TTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTT
* * *
10587154 TAGTTTAATGTGTATTATGATTTGTTATAA
65 TAGTTTAATGTTTATTGTGATTTTTTATAA
10587184 TGTATTTTTT
Statistics
Matches: 349, Mismatches: 44, Indels: 35
0.82 0.10 0.08
Matches are distributed among these distances:
102 148 0.42
103 32 0.09
104 2 0.01
105 2 0.01
106 1 0.00
107 2 0.01
108 26 0.07
109 69 0.20
110 9 0.03
111 58 0.17
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (101 bp):
TTTTTAAATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTGTTTGTGTTT
AGTTTAATGTTTATTGTGATTTTTTATAAATGTGCA
Found at i:10587124 original size:111 final size:108
Alignment explanation
Indices: 10586987--10587196 Score: 312
Period size: 111 Copynumber: 1.9 Consensus size: 108
10586977 AAAATTTTTT
* *
10586987 AATTATTTTAAAGTTATTTTGTTAGTAATTTATTATTAGGTCATAAATTGTTTGTGTTTAGTTTA
1 AATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTCATAAATT-ATT-TGTTTAGTTTA
* * *
10587052 GTGTTTATTGTGACTTGTTATAAATGTAAATTTTTTGCGTTCTTTA
64 ATGTGTATTATGACTTGTTAT-AATGTAAATTTTTTGCGTTCTTTA
*
10587098 AATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTTATAAATTATTTGTTTAGTTTAAT
1 AATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTCATAAATTATTTGTTTAGTTTAAT
* **
10587163 GTGTATTATGATTTGTTATAATGTATTTTTTTTG
66 GTGTATTATGACTTGTTATAATGTAAATTTTTTG
10587197 ATTTATTTGA
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 13 0.14
109 28 0.31
110 2 0.02
111 47 0.52
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (108 bp):
AATTATTTTAAAGTTATTTTGTTAGTAATTTATGATTAGGTCATAAATTATTTGTTTAGTTTAAT
GTGTATTATGACTTGTTATAATGTAAATTTTTTGCGTTCTTTA
Found at i:10592977 original size:37 final size:37
Alignment explanation
Indices: 10592936--10593010 Score: 125
Period size: 37 Copynumber: 2.0 Consensus size: 37
10592926 TGTTAATTTC
*
10592936 AAGACTTATGTAATGTTGTTT-TTTATGTAGTGATTCA
1 AAGACTTATGTAATGTT-TTTAATTATGTAGTGATTCA
10592973 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
10593010 A
1 A
10593011 TTCAGTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 3 0.08
37 33 0.92
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTCA
Found at i:10601569 original size:14 final size:15
Alignment explanation
Indices: 10601518--10601566 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
10601508 CTATAAAAGA
*
10601518 TAATTTAACATA-AT
1 TAATTAAACATATAT
10601532 TATTATTAAACATATAT
1 TA--ATTAAACATATAT
10601549 TAATTAAA-ATATA-
1 TAATTAAACATATAT
10601562 TAATT
1 TAATT
10601567 TAATAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.16
14 7 0.23
15 6 0.19
16 9 0.29
17 4 0.13
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTAAACATATAT
Found at i:10608917 original size:18 final size:18
Alignment explanation
Indices: 10608890--10608938 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
10608880 TGTATTAGAT
10608890 TATAAATATATTAATTAA
1 TATAAATATATTAATTAA
* *
10608908 TATAATTATATTTATTAA
1 TATAAATATATTAATTAA
*
10608926 AATATAATA-ATTA
1 TATA-AATATATTA
10608939 TATGTAGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAAATATATTAATTAA
Found at i:10609010 original size:39 final size:39
Alignment explanation
Indices: 10608958--10609076 Score: 113
Period size: 39 Copynumber: 3.1 Consensus size: 39
10608948 AACTATTAAT
10608958 TTTAAAACAATTAAATTCATTATCTAAAACCTAAATAAA
1 TTTAAAACAATTAAATTCATTATCTAAAACCTAAATAAA
* * * * *
10608997 TTTATTAA-AATTAATAATT-A-TATGTAGTTAA-CT-ATTAAT
1 TTTA-AAACAATT-A-AATTCATTATCTA--AAACCTAAATAAA
10609036 TTTAAAACAATTAAATTCATTATCTAAAACCTAAATAAA
1 TTTAAAACAATTAAATTCATTATCTAAAACCTAAATAAA
10609075 TT
1 TT
10609077 ATCCAAGTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
37 6 0.10
38 6 0.10
39 36 0.60
40 6 0.10
41 6 0.10
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (39 bp):
TTTAAAACAATTAAATTCATTATCTAAAACCTAAATAAA
Found at i:10609019 original size:78 final size:79
Alignment explanation
Indices: 10608917--10609076 Score: 313
Period size: 78 Copynumber: 2.0 Consensus size: 79
10608907 ATATAATTAT
10608917 ATTTATTAAAATATAATAATTATATGTAGTTAACTATTAATTTTAAAACAATTAAATTCATTATC
1 ATTTATTAAAATATAATAATTATATGTAGTTAACTATTAATTTTAAAACAATTAAATTCATTATC
10608982 TAAAACCTAAATAA
66 TAAAACCTAAATAA
10608996 ATTTATTAAAAT-TAATAATTATATGTAGTTAACTATTAATTTTAAAACAATTAAATTCATTATC
1 ATTTATTAAAATATAATAATTATATGTAGTTAACTATTAATTTTAAAACAATTAAATTCATTATC
10609060 TAAAACCTAAATAA
66 TAAAACCTAAATAA
10609074 ATT
1 ATT
10609077 ATCCAAGTAA
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 69 0.85
79 12 0.15
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (79 bp):
ATTTATTAAAATATAATAATTATATGTAGTTAACTATTAATTTTAAAACAATTAAATTCATTATC
TAAAACCTAAATAA
Found at i:10613385 original size:6 final size:6
Alignment explanation
Indices: 10613374--10613412 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
10613364 CAGACTTTTG
*
10613374 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAATA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA
10613413 TTTCTAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:10615543 original size:9 final size:9
Alignment explanation
Indices: 10615529--10616249 Score: 1442
Period size: 9 Copynumber: 80.1 Consensus size: 9
10615519 TGAGTTTTCG
10615529 AATTCGAAT
1 AATTCGAAT
10615538 AATTCGAAT
1 AATTCGAAT
10615547 AATTCGAAT
1 AATTCGAAT
10615556 AATTCGAAT
1 AATTCGAAT
10615565 AATTCGAAT
1 AATTCGAAT
10615574 AATTCGAAT
1 AATTCGAAT
10615583 AATTCGAAT
1 AATTCGAAT
10615592 AATTCGAAT
1 AATTCGAAT
10615601 AATTCGAAT
1 AATTCGAAT
10615610 AATTCGAAT
1 AATTCGAAT
10615619 AATTCGAAT
1 AATTCGAAT
10615628 AATTCGAAT
1 AATTCGAAT
10615637 AATTCGAAT
1 AATTCGAAT
10615646 AATTCGAAT
1 AATTCGAAT
10615655 AATTCGAAT
1 AATTCGAAT
10615664 AATTCGAAT
1 AATTCGAAT
10615673 AATTCGAAT
1 AATTCGAAT
10615682 AATTCGAAT
1 AATTCGAAT
10615691 AATTCGAAT
1 AATTCGAAT
10615700 AATTCGAAT
1 AATTCGAAT
10615709 AATTCGAAT
1 AATTCGAAT
10615718 AATTCGAAT
1 AATTCGAAT
10615727 AATTCGAAT
1 AATTCGAAT
10615736 AATTCGAAT
1 AATTCGAAT
10615745 AATTCGAAT
1 AATTCGAAT
10615754 AATTCGAAT
1 AATTCGAAT
10615763 AATTCGAAT
1 AATTCGAAT
10615772 AATTCGAAT
1 AATTCGAAT
10615781 AATTCGAAT
1 AATTCGAAT
10615790 AATTCGAAT
1 AATTCGAAT
10615799 AATTCGAAT
1 AATTCGAAT
10615808 AATTCGAAT
1 AATTCGAAT
10615817 AATTCGAAT
1 AATTCGAAT
10615826 AATTCGAAT
1 AATTCGAAT
10615835 AATTCGAAT
1 AATTCGAAT
10615844 AATTCGAAT
1 AATTCGAAT
10615853 AATTCGAAT
1 AATTCGAAT
10615862 AATTCGAAT
1 AATTCGAAT
10615871 AATTCGAAT
1 AATTCGAAT
10615880 AATTCGAAT
1 AATTCGAAT
10615889 AATTCGAAT
1 AATTCGAAT
10615898 AATTCGAAT
1 AATTCGAAT
10615907 AATTCGAAT
1 AATTCGAAT
10615916 AATTCGAAT
1 AATTCGAAT
10615925 AATTCGAAT
1 AATTCGAAT
10615934 AATTCGAAT
1 AATTCGAAT
10615943 AATTCGAAT
1 AATTCGAAT
10615952 AATTCGAAT
1 AATTCGAAT
10615961 AATTCGAAT
1 AATTCGAAT
10615970 AATTCGAAT
1 AATTCGAAT
10615979 AATTCGAAT
1 AATTCGAAT
10615988 AATTCGAAT
1 AATTCGAAT
10615997 AATTCGAAT
1 AATTCGAAT
10616006 AATTCGAAT
1 AATTCGAAT
10616015 AATTCGAAT
1 AATTCGAAT
10616024 AATTCGAAT
1 AATTCGAAT
10616033 AATTCGAAT
1 AATTCGAAT
10616042 AATTCGAAT
1 AATTCGAAT
10616051 AATTCGAAT
1 AATTCGAAT
10616060 AATTCGAAT
1 AATTCGAAT
10616069 AATTCGAAT
1 AATTCGAAT
10616078 AATTCGAAT
1 AATTCGAAT
10616087 AATTCGAAT
1 AATTCGAAT
10616096 AATTCGAAT
1 AATTCGAAT
10616105 AATTCGAAT
1 AATTCGAAT
10616114 AATTCGAAT
1 AATTCGAAT
10616123 AATTCGAAT
1 AATTCGAAT
10616132 AATTCGAAT
1 AATTCGAAT
10616141 AATTCGAAT
1 AATTCGAAT
10616150 AATTCGAAT
1 AATTCGAAT
10616159 AATTCGAAT
1 AATTCGAAT
10616168 AATTCGAAT
1 AATTCGAAT
10616177 AATTCGAAT
1 AATTCGAAT
10616186 AATTCGAAT
1 AATTCGAAT
10616195 AATTCGAAT
1 AATTCGAAT
10616204 AATTCGAAT
1 AATTCGAAT
10616213 AATTCGAAT
1 AATTCGAAT
10616222 AATTCGAAT
1 AATTCGAAT
10616231 AATTCGAAT
1 AATTCGAAT
10616240 AATTCGAAT
1 AATTCGAAT
10616249 A
1 A
10616250 TGATGGGTGA
Statistics
Matches: 712, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 712 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:10617649 original size:9 final size:9
Alignment explanation
Indices: 10617637--10617662 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
10617627 TCTCTTTTAA
10617637 ATATTTTGC
1 ATATTTTGC
10617646 ATATTTTGC
1 ATATTTTGC
10617655 ATATTTTG
1 ATATTTTG
10617663 AACTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.58
Consensus pattern (9 bp):
ATATTTTGC
Found at i:10619196 original size:50 final size:50
Alignment explanation
Indices: 10619087--10619286 Score: 192
Period size: 56 Copynumber: 3.9 Consensus size: 50
10619077 TAAATATAAC
* * * * * * *
10619087 ATGCCAAAGCTATGTCCCAGACATAGTCTTACATGAGATGTTTCTTGT-A-
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT-TCTCATCTCAG
* * *
10619136 ATGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATCTC-G
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-TTCTCATCTCAG
* *
10619186 GTGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA--T-TC-TCATCTC-A-G
10619242 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATT-TCATC
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATTCTCATC
10619287 CTCTTAATGT
Statistics
Matches: 124, Mismatches: 18, Indels: 16
0.78 0.11 0.10
Matches are distributed among these distances:
49 36 0.29
50 35 0.28
51 5 0.04
52 2 0.02
53 7 0.06
54 1 0.01
56 38 0.31
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATTCTCATCTCAG
Found at i:10623224 original size:18 final size:18
Alignment explanation
Indices: 10623203--10623239 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10623193 TCTTCTCTTT
10623203 CTTTTTCATTTTCAGCAA
1 CTTTTTCATTTTCAGCAA
* *
10623221 CTTTTTCTTTTTTAGCAA
1 CTTTTTCATTTTCAGCAA
10623239 C
1 C
10623240 AACTTCCGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.54
Consensus pattern (18 bp):
CTTTTTCATTTTCAGCAA
Found at i:10635685 original size:21 final size:22
Alignment explanation
Indices: 10635661--10635704 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
10635651 AAAAAAAATT
10635661 ACTT-GGAATTTTATAAAGAAA
1 ACTTGGGAATTTTATAAAGAAA
* *
10635682 ACTTGGGATTTTTATAGAGAAA
1 ACTTGGGAATTTTATAAAGAAA
10635704 A
1 A
10635705 ATCATTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (22 bp):
ACTTGGGAATTTTATAAAGAAA
Found at i:10643544 original size:25 final size:25
Alignment explanation
Indices: 10643515--10643585 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
10643505 CAAACGTTCT
*
10643515 AGATAATACATCACAAAGGCTCTTC
1 AGATAATTCATCACAAAGGCTCTTC
* *
10643540 AGATAATTCACCACAAAGGCTCTTT
1 AGATAATTCATCACAAAGGCTCTTC
**
10643565 AGATAATTTGTCACAAAGGCT
1 AGATAATTCATCACAAAGGCT
10643586 TGGCTTGGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (25 bp):
AGATAATTCATCACAAAGGCTCTTC
Found at i:10648684 original size:21 final size:21
Alignment explanation
Indices: 10648660--10648700 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
10648650 GGTCGTATGG
* *
10648660 CTACTCCACATGCCCGTGTAA
1 CTACTCCACATACCCATGTAA
*
10648681 CTACTTCACATACCCATGTA
1 CTACTCCACATACCCATGTA
10648701 TGTAGACCAT
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:0.27, C:0.37, G:0.10, T:0.27
Consensus pattern (21 bp):
CTACTCCACATACCCATGTAA
Found at i:10657607 original size:19 final size:17
Alignment explanation
Indices: 10657558--10657608 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
10657548 TTTTAATGGT
10657558 TAAA-TAAGTAAATTAG
1 TAAATTAAGTAAATTAG
*
10657574 TAAATAAATGATAAATTAAG
1 TAAATTAA-G-TAAATT-AG
10657594 TAAAATTAAGTAAAT
1 T-AAATTAAGTAAAT
10657609 GTATCATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 1 0.04
19 11 0.39
20 4 0.14
21 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (17 bp):
TAAATTAAGTAAATTAG
Found at i:10658495 original size:42 final size:43
Alignment explanation
Indices: 10658448--10658567 Score: 136
Period size: 42 Copynumber: 2.8 Consensus size: 43
10658438 TTTCAAGGCG
* * *
10658448 TGATTTTGTGTAAGACCATGTCTGGGACATTGGCATC-GTATA
1 TGATTTCGTGTAAGACCATATCTGGGACAGTGGCATCGGTATA
*
10658490 TGATTTCGTGTAAGACCCTATCTGGGACAGTGGCATCGGTATA
1 TGATTTCGTGTAAGACCATATCTGGGACAGTGGCATCGGTATA
* ** * * *
10658533 TTATAACATGTAAGACCTTATCTGGGATA-TGGCAT
1 TGATTTCGTGTAAGACCATATCTGGGACAGTGGCAT
10658568 TGTTTGAGCT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 39 0.58
43 28 0.42
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (43 bp):
TGATTTCGTGTAAGACCATATCTGGGACAGTGGCATCGGTATA
Found at i:10659216 original size:48 final size:48
Alignment explanation
Indices: 10659112--10659216 Score: 131
Period size: 48 Copynumber: 2.2 Consensus size: 48
10659102 TGATGATATG
* * * * *
10659112 ATGCTGTCCAAATTGATGCTTAATTGCTGTCCATTTTTTAGTATATTA
1 ATGCTGTCCAAATTGATGCTTAAGTGCTATCCATTTTTTAGCAAATCA
* *
10659160 ATGTTGTCCAAATTGGTGCTTAAGTGCTATCCATTTTTTTA-CAAATCA
1 ATGCTGTCCAAATTGATGCTTAAGTGCTATCCA-TTTTTTAGCAAATCA
10659208 ATGCTGTCC
1 ATGCTGTCC
10659217 GAATGTTGTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
48 41 0.85
49 7 0.15
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (48 bp):
ATGCTGTCCAAATTGATGCTTAAGTGCTATCCATTTTTTAGCAAATCA
Found at i:10664254 original size:33 final size:33
Alignment explanation
Indices: 10664212--10664336 Score: 133
Period size: 33 Copynumber: 3.5 Consensus size: 33
10664202 ATACGGTGGG
10664212 ATCAGCACTTAGCAACCACCAATGATTCGGGGA
1 ATCAGCACTTAGCAACCACCAATGATTCGGGGA
* *
10664245 ATCAGCACTTAGCAACCCCCTTTACATTTAAGATACGGTGGA
1 ATCAGCACTTAGCAACCACC---A-A--T--GATTCGG-GGA
* *
10664287 ATCAGCACTTAACAACCACCAATGAATCGGGGA
1 ATCAGCACTTAGCAACCACCAATGATTCGGGGA
10664320 ATCAGCACTTAGCAACC
1 ATCAGCACTTAGCAACC
10664337 CCTTGGGGGA
Statistics
Matches: 76, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
33 38 0.50
34 5 0.07
36 2 0.03
37 1 0.01
38 1 0.01
39 2 0.03
41 6 0.08
42 21 0.28
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATGATTCGGGGA
Found at i:10664254 original size:75 final size:74
Alignment explanation
Indices: 10664130--10664340 Score: 325
Period size: 75 Copynumber: 2.8 Consensus size: 74
10664120 TATCTATTAT
* * * *
10664130 CGGT-GGATTCAGTACTTAGCAACCACCAATGAGTCGGGAAATCAACACTTAGCAACCCCTTTCA
1 CGGTGGGA-TCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTT-A
10664194 CATTTAAGATA
64 CATTTAAGATA
*
10664205 CGGTGGGATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCCTTTAC
1 CGGTGGGATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCCTTTAC
10664270 ATTTAAGATA
65 ATTTAAGATA
* *
10664280 CGGTGGAATCAGCACTTAACAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
1 CGGTGGGATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTT
10664341 GGGGGAATTA
Statistics
Matches: 127, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
74 6 0.05
75 111 0.87
76 10 0.08
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (74 bp):
CGGTGGGATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTACA
TTTAAGATA
Found at i:10664353 original size:27 final size:27
Alignment explanation
Indices: 10664315--10664367 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
10664305 CCAATGAATC
10664315 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTTG
*
10664342 GGGGAATTAGCACTTAGCAACCCCTT
1 GGGGAATCAGCACTTAGCAACCCCTT
10664368 TTATATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.21
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTTG
Found at i:10667344 original size:36 final size:35
Alignment explanation
Indices: 10667304--10667381 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 35
10667294 ACAATCTACA
*
10667304 AGTAAGGAAGGACAACGGTAAGCATATCAAAGGCTT
1 AGTAAGGAA-GACAACAGTAAGCATATCAAAGGCTT
10667340 AGTAAGGGAAGACAACAGTAAGCATATCAAAGGCTT
1 AGTAA-GGAAGACAACAGTAAGCATATCAAAGGCTT
10667376 AGTAAG
1 AGTAAG
10667382 TTCATACAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 1 0.03
36 35 0.88
37 4 0.10
ACGTcount: A:0.44, C:0.13, G:0.27, T:0.17
Consensus pattern (35 bp):
AGTAAGGAAGACAACAGTAAGCATATCAAAGGCTT
Found at i:10674877 original size:15 final size:15
Alignment explanation
Indices: 10674847--10674875 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10674837 ACTATTAGTA
10674847 ATTTTTTAAATATTT
1 ATTTTTTAAATATTT
10674862 ATTTTTT-AATATTT
1 ATTTTTTAAATATTT
10674876 TACTATACTC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTAAATATTT
Found at i:10685660 original size:21 final size:20
Alignment explanation
Indices: 10685635--10685684 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
10685625 AATTTTCTTA
*
10685635 TTTCTCTTTTCTTCTTTTTCC
1 TTTCTCTTTTCTTCTCTTT-C
* *
10685656 TTTCTTTTTTTTTCTCTTTC
1 TTTCTCTTTTCTTCTCTTTC
*
10685676 TTTGTCTTT
1 TTTCTCTTT
10685685 AGAGATAACT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTTTCTTCTCTTTC
Found at i:10700475 original size:22 final size:20
Alignment explanation
Indices: 10700432--10700470 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
10700422 TAATTTAAAA
10700432 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
10700452 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
10700471 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:10700532 original size:32 final size:32
Alignment explanation
Indices: 10700491--10700577 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
10700481 AACTTTTCCG
** *
10700491 GAAAATATTTTCAAGAAATCTGTCAAACAGCA
1 GAAAATATTTTCAAGAAATCAATCAAACACCA
*
10700523 GAAAATATTTTACACAG-ATTCAATCAAACACCA
1 GAAAATATTTT-CA-AGAAATCAATCAAACACCA
*
10700556 GAAAATATTTTCCAGTAAATCA
1 GAAAATATTTTCAAG-AAATCA
10700578 TTTTACAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 2 0.04
32 12 0.27
33 29 0.64
34 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCAAGAAATCAATCAAACACCA
Found at i:10700575 original size:14 final size:15
Alignment explanation
Indices: 10700553--10700629 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
10700543 CAATCAAACA
10700553 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
10700567 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
10700582 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
10700602 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
10700616 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
10700630 ACTGCCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:10700594 original size:20 final size:20
Alignment explanation
Indices: 10700569--10700608 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
10700559 AATATTTTCC
*
10700569 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
10700589 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
10700609 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:10700614 original size:34 final size:35
Alignment explanation
Indices: 10700557--10700623 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
10700547 CAAACACCAG
*
10700557 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
10700592 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
10700624 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Done.