Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 86 of 284
Found at i:28570182 original size:19 final size:17
Alignment explanation
Indices: 28570158--28570204 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
28570148 AATTAAAGTA
*
28570158 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
28570177 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
28570194 AT-AAAAATATA
1 ATAAAAAATATA
28570205 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:28570200 original size:18 final size:19
Alignment explanation
Indices: 28570161--28570209 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
28570151 TAAAGTAATA
*
28570161 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
28570179 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
28570196 AAAAATATACACTA
1 AAAAATATATACTA
28570210 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:28570436 original size:3 final size:3
Alignment explanation
Indices: 28570423--28570508 Score: 60
Period size: 3 Copynumber: 29.3 Consensus size: 3
28570413 GAGGGCATAT
28570423 ATA AT- ATA ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA
* *
28570467 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28570509 AACAAAGCTC
Statistics
Matches: 68, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
2 13 0.19
3 46 0.68
4 7 0.10
5 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:28570449 original size:18 final size:18
Alignment explanation
Indices: 28570428--28570508 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
28570418 CATATATAAT
28570428 ATAATAATAATATAAAAA
1 ATAATAATAATATAAAAA
* *
28570446 ATAATATATACATGAGAAATA
1 ATAATA-ATA-AT-ATAAAAA
*
28570467 ATAATAATAATATAAATA
1 ATAATAATAATATAAAAA
*
28570485 ATAGTAA-AA-ATAATAAA
1 ATAATAATAATATAA-AAA
28570502 ATAATAA
1 ATAATAA
28570509 AACAAAGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
16 4 0.08
17 10 0.19
18 18 0.34
19 5 0.09
20 5 0.09
21 11 0.21
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
ATAATAATAATATAAAAA
Found at i:28570874 original size:23 final size:23
Alignment explanation
Indices: 28570839--28570911 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
28570829 CCTTTTTTAC
*
28570839 AAAAAAA-CACCTCCAAAAAACA
1 AAAAAAACCTCCTCCAAAAAACA
28570861 AAAAAAACCTCCTCC--AAAACA
1 AAAAAAACCTCCTCCAAAAAACA
* * *
28570882 AAGAACAATCCTTCTCCAAAAAACC
1 AA-AA-AAACCTCCTCCAAAAAACA
28570907 AAAAA
1 AAAAA
28570912 CCCCCCCCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 8 0.19
22 9 0.21
23 16 0.38
24 2 0.05
25 7 0.17
ACGTcount: A:0.60, C:0.29, G:0.01, T:0.10
Consensus pattern (23 bp):
AAAAAAACCTCCTCCAAAAAACA
Found at i:28570879 original size:21 final size:21
Alignment explanation
Indices: 28570837--28570902 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
28570827 AACCTTTTTT
**
28570837 ACAAAAAAACACCTCC-AAAAA
1 ACAAAAAAA-ACCTCCTCCAAA
28570858 ACAAAAAAAACCTCCTCCAAA
1 ACAAAAAAAACCTCCTCCAAA
* *
28570879 ACAAAGAACAATCCTTCTCCAAA
1 ACAAA-AA-AAACCTCCTCCAAA
28570902 A
1 A
28570903 AACCAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.16
21 17 0.45
22 2 0.05
23 13 0.34
ACGTcount: A:0.58, C:0.30, G:0.02, T:0.11
Consensus pattern (21 bp):
ACAAAAAAAACCTCCTCCAAA
Found at i:28571441 original size:40 final size:40
Alignment explanation
Indices: 28571397--28571548 Score: 191
Period size: 40 Copynumber: 3.8 Consensus size: 40
28571387 GTGTTTTTAG
*
28571397 TCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
* * * *
28571437 TCTGCTTCACTATTGCTTAGGGAAATAAGATTTG-TG-GTTTTA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCG----A
*
28571479 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
*
28571519 TCTACTCCACTACTGCTTAGGGAGATAAGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA
28571549 TTGTAATCTT
Statistics
Matches: 95, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 59 0.62
42 30 0.32
43 2 0.02
44 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGA
Found at i:28571492 original size:82 final size:83
Alignment explanation
Indices: 28571381--28571550 Score: 270
Period size: 82 Copynumber: 2.1 Consensus size: 83
28571371 TATGGGGATG
* * * *
28571381 AGATTTGTGTTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTGATGCGATCTGCTTCA
1 AGATTTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
28571446 CTATTGCTTAGGGAAATA
66 CTACTGCTTAGGGAAATA
*
28571464 AGATTTGTGGTTTTA-TCTGCTCCACTACTGCTTAGGGAGATAAGACTTAATGCGATCTACTCCA
1 AGATTTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
*
28571528 CTACTGCTTAGGGAGATA
66 CTACTGCTTAGGGAAATA
28571546 AGATT
1 AGATT
28571551 GTAATCTTCG
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
82 66 0.82
83 14 0.17
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (83 bp):
AGATTTGTGGTTTTAGTCTGCTCCACTACTACTTAGGGAGATAAGACTTAATGCGATCTACTCCA
CTACTGCTTAGGGAAATA
Found at i:28571891 original size:46 final size:46
Alignment explanation
Indices: 28571711--28572015 Score: 116
Period size: 46 Copynumber: 6.8 Consensus size: 46
28571701 ACTTCCTACC
* * *
28571711 AATATAGGAAGGCAGGATCTGCAATCTTCAATCTATTCCACTGCC-
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCT
* * * * ** * *
28571756 AGATACAGGGAGATAGAGTTAT-C-GGCTTCAATGTACTCCACTG--T
1 A-ATACAGGAAGGTA-AGATCTGCAATCTTCAATCTATTCCACTGCCT
* * * * ** * *
28571800 AGTCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTT-CGCTGCCT
1 AAT-ACAGGAAGGTAAGATCTGCAATCTTCAATCT-ATTCCACTGCCT
*
28571847 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCC-
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCT
* * * ** * *
28571892 AGATACAGTG-AGATAGAGTTAT-C-GGCTTCAATGTACTCCACTG--T
1 A-ATACAG-GAAGGTA-AGATCTGCAATCTTCAATCTATTCCACTGCCT
* * * * * * * *
28571936 AGT-CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CGCTGCCG
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCT-ATTCCACTGCCT
*
28571981 AATACAGGAAGGCAAGATCTGCAATCTTCAATCTA
1 AATACAGGAAGGTAAGATCTGCAATCTTCAATCTA
28572016 CTTCACCACC
Statistics
Matches: 178, Mismatches: 61, Indels: 42
0.63 0.22 0.15
Matches are distributed among these distances:
41 4 0.02
42 8 0.04
43 16 0.09
44 14 0.08
45 48 0.27
46 77 0.43
47 11 0.06
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (46 bp):
AATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCT
Found at i:28572096 original size:44 final size:44
Alignment explanation
Indices: 28571951--28572396 Score: 341
Period size: 44 Copynumber: 10.1 Consensus size: 44
28571941 GGGAGGTAAA
* * * * *
28571951 ATCTGCCATCTTCGATCTGCTTCGCTGCCGAATACAGGAAGGCAAG
1 ATCTGCTATCTTCGATCTACTTC-CTACC-AATATAGGAAGACAAG
* * * * *
28571997 ATCTGCAATCTTCAATCTACTTCACCACCAGTATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAAGACAAG
* * * * *
28572042 ATCTGC-ATCTTGGATCGACTTCCTATCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCCTACCAATATAGGAAGACAAG
* * * * *
28572085 ACCTGCTATCTTCGATCTGCTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAAGACAAG
* * * *
28572129 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAAGACAAG
* * * *
28572174 ATCTGC-ATCTTCGATCCACTTCCTACCAATATAGAAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCCTACCAATATAGGAAGACAAG
* *
28572217 ATCTGCTA-CATTCGATCTACTT--TACGCCAATACATGAAGACAAG
1 ATCTGCTATC-TTCGATCTACTTCCTA--CCAATATAGGAAGACAAG
* * * *
28572261 ATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAAGACAAG
* * * * * *
28572306 ATCTGC-ATATTGGATCCACTTCCTATCAATATAGGAAGATAGG
1 ATCTGCTATCTTCGATCTACTTCCTACCAATATAGGAAGACAAG
* * * * *
28572349 ACCTGCTATCTTCGATCTGCTTCAC-GCCAATACATGAAGACAAG
1 ATCTGCTATCTTCGATCTACTTC-CTACCAATATAGGAAGACAAG
28572393 ATCT
1 ATCT
28572397 ACTTTAATGA
Statistics
Matches: 307, Mismatches: 80, Indels: 28
0.74 0.19 0.07
Matches are distributed among these distances:
42 2 0.01
43 64 0.21
44 154 0.50
45 63 0.21
46 23 0.07
47 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTACTTCCTACCAATATAGGAAGACAAG
Found at i:28572223 original size:132 final size:132
Alignment explanation
Indices: 28571953--28572401 Score: 693
Period size: 132 Copynumber: 3.4 Consensus size: 132
28571943 GAGGTAAAAT
* * * * ** * *
28571953 CTGCCATCTTCGATCTGCTTCGCTGCCGAATACAGGAAGGCAAGATCTGCAATCTTCAATCTACT
1 CTGCTATCTTCGATCTGCTTCAC-GCC-AATACATGAAGACAAGATCTGCTTTCTGCGATCTACT
* * *
28572018 TCACCACCAGTATGGGAAGACAAGATCTGCATCTTGGATCGACTTCCTATCAATATAGGAAGATA
64 TCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATA
28572083 GGAC
129 GGAC
28572087 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
* * *
28572152 GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGAAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGG
*
28572217 AT
131 AC
* *
28572219 CTGCTA-CATTCGATCTACTTTACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTT
1 CTGCTATC-TTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTT
*
28572283 CGCCACCAATATGGGAAGACAAGATCTGCATATTGGATCCACTTCCTATCAATATAGGAAGATAG
65 CGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAG
28572348 GAC
130 GAC
*
28572351 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTACTTT
1 CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTT
28572402 AATGACTTCA
Statistics
Matches: 288, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
131 1 0.00
132 262 0.91
133 4 0.01
134 21 0.07
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (132 bp):
CTGCTATCTTCGATCTGCTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
GCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCACTTCCTATCAATATAGGAAGATAGG
AC
Found at i:28574920 original size:74 final size:74
Alignment explanation
Indices: 28574799--28574947 Score: 271
Period size: 74 Copynumber: 2.0 Consensus size: 74
28574789 ACAGCATCCA
**
28574799 CACACCTTAACAGTACTTGATCTTTTCCTTTTTTATTTAAAATTTCCCCATCAAGGACATAGTCA
1 CACACCTTAACAGTACTTGATCTTTTCCTTTTTTATACAAAATTTCCCCATCAAGGACATAGTCA
28574864 ATGGCTAAT
66 ATGGCTAAT
*
28574873 CACACCTTAATAGTACTTGATCTTTTCCTTTTTTATACAAAATTTCCCCATCAAGGACATAGTCA
1 CACACCTTAACAGTACTTGATCTTTTCCTTTTTTATACAAAATTTCCCCATCAAGGACATAGTCA
28574938 ATGGCTAAT
66 ATGGCTAAT
28574947 C
1 C
28574948 TCCTTAATGT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.37
Consensus pattern (74 bp):
CACACCTTAACAGTACTTGATCTTTTCCTTTTTTATACAAAATTTCCCCATCAAGGACATAGTCA
ATGGCTAAT
Found at i:28584895 original size:21 final size:21
Alignment explanation
Indices: 28584869--28584919 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
28584859 GAAGTCATTT
28584869 GGAAATGAATACGGTTTTCTC
1 GGAAATGAATACGGTTTTCTC
28584890 GGAAATGAATACGGTTTTCTC
1 GGAAATGAATACGGTTTTCTC
**
28584911 CAAAATGAA
1 GGAAATGAA
28584920 AATGAAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (21 bp):
GGAAATGAATACGGTTTTCTC
Found at i:28585929 original size:39 final size:39
Alignment explanation
Indices: 28585871--28585949 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
28585861 CACCGTTACT
* *
28585871 TTCTTTGGAAGGCCAAAGCATGTGGAGATATACATGGGG
1 TTCTTCGGAAGGCCAAAGCATATGGAGATATACATGGGG
* *
28585910 TTCTTCGGAAGGTCGAAGCATATGGAGATATACATGGGG
1 TTCTTCGGAAGGCCAAAGCATATGGAGATATACATGGGG
28585949 T
1 T
28585950 CTCAGTTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.28, C:0.13, G:0.33, T:0.27
Consensus pattern (39 bp):
TTCTTCGGAAGGCCAAAGCATATGGAGATATACATGGGG
Found at i:28588367 original size:15 final size:15
Alignment explanation
Indices: 28588347--28588376 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28588337 GTTATGTTTT
28588347 CATAAAACGTTCAAC
1 CATAAAACGTTCAAC
28588362 CATAAAACGTTCAAC
1 CATAAAACGTTCAAC
28588377 TAGTGGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
CATAAAACGTTCAAC
Found at i:28589534 original size:46 final size:46
Alignment explanation
Indices: 28589481--28589621 Score: 237
Period size: 46 Copynumber: 3.1 Consensus size: 46
28589471 TGCTATAGTG
* *
28589481 TCTTTCAACTATGGTCTTATTAATTTCCTGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTA
*
28589527 TCTTTCAACCATGGTCTTATTCATTTCTTGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTA
* *
28589573 TCTTTCAACCATTGTCTTATTCATTTCCTGTCATGTTGCCATGATA
1 TCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTA
28589619 TCT
1 TCT
28589622 GTAATGGCCT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 89 1.00
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.46
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTATTCATTTCCTGTCATGTTGCCATGGTA
Found at i:28592662 original size:45 final size:45
Alignment explanation
Indices: 28592529--28592643 Score: 149
Period size: 45 Copynumber: 2.6 Consensus size: 45
28592519 GTATTACAAT
* * * * * **
28592529 ATCTTTCAACCATGGTCTTACACATTTGAATCGCAATGCCATAGC
1 ATCTTTCAGCTATGGTCTTACTCATCTAAATCGTGATGCCATAGC
* *
28592574 ATCTTTCAGCTATGGTGTTACTCGTCTAAATCGTGATGCCATAGC
1 ATCTTTCAGCTATGGTCTTACTCATCTAAATCGTGATGCCATAGC
28592619 ATCTTTCAGCTATGGTCTTACTCAT
1 ATCTTTCAGCTATGGTCTTACTCAT
28592644 TTTTGGTATG
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (45 bp):
ATCTTTCAGCTATGGTCTTACTCATCTAAATCGTGATGCCATAGC
Found at i:28592740 original size:33 final size:32
Alignment explanation
Indices: 28592703--28592780 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
28592693 AGGCCCAACC
* * *
28592703 ATGGTCTTACACTCGCGGTGCCATATCCCAGAT
1 ATGGTCTTACACTAG-GATGCCATAGCCCAGAT
* * *
28592736 ATGGTCTTATCATTAGGATGCCATAGCCTAGCT
1 ATGGTCTTA-CACTAGGATGCCATAGCCCAGAT
28592769 ATGGTCTTACAC
1 ATGGTCTTACAC
28592781 ATATATTGTC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 2 0.05
33 31 0.84
34 4 0.11
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (32 bp):
ATGGTCTTACACTAGGATGCCATAGCCCAGAT
Found at i:28595109 original size:61 final size:58
Alignment explanation
Indices: 28594954--28595117 Score: 166
Period size: 60 Copynumber: 2.7 Consensus size: 58
28594944 CATTTGGCAT
* * *** * *
28594954 CTGAACTTAACACTTTTTCTTAATTTGGTACCTAAACCTTTTTTTTTCCTAATTCGGTAC
1 CTGAACTTGACACTTTTTCCTAATTT-GTACCTAAA-CTTTTTTGGGCCCAATTCAGTAC
* *
28595014 CTGAACTTGACACTGTTTCCTAATTTTGTACCTAAACTTTTTTGGGCCCAATTTAGTAC
1 CTGAACTTGACACTTTTTCCTAA-TTTGTACCTAAACTTTTTTGGGCCCAATTCAGTAC
* * *
28595073 TTGAACTTGACATTTTTTTTCCTAATTTGATACCTAAGCTTTTTT
1 CTGAACTTGACA--CTTTTTCCTAATTTG-TACCTAAACTTTTTT
28595118 TTAGGTTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 28 0.32
60 33 0.38
61 26 0.30
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.46
Consensus pattern (58 bp):
CTGAACTTGACACTTTTTCCTAATTTGTACCTAAACTTTTTTGGGCCCAATTCAGTAC
Found at i:28595572 original size:30 final size:31
Alignment explanation
Indices: 28595524--28595598 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
28595514 CCCAAAAAGT
* *
28595524 TTTAAGTACCAACTTAAG-AAAAATGTCAAG
1 TTTAAATACCAAATTAAGAAAAAATGTCAAG
* * *
28595554 TTTAGATATCAAATTAAGAAAAAATGTTAAG
1 TTTAAATACCAAATTAAGAAAAAATGTCAAG
28595585 TTTAAATACCAAAT
1 TTTAAATACCAAAT
28595599 ATTAGGGTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 14 0.38
31 23 0.62
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (31 bp):
TTTAAATACCAAATTAAGAAAAAATGTCAAG
Found at i:28595934 original size:19 final size:19
Alignment explanation
Indices: 28595910--28595948 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
28595900 GAATTAATTC
28595910 ATAAATATTATCCGTTAAT
1 ATAAATATTATCCGTTAAT
*
28595929 ATAAATATTCTCCGTTAAT
1 ATAAATATTATCCGTTAAT
28595948 A
1 A
28595949 AGTGATAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (19 bp):
ATAAATATTATCCGTTAAT
Found at i:28605470 original size:26 final size:25
Alignment explanation
Indices: 28605433--28605538 Score: 167
Period size: 26 Copynumber: 4.1 Consensus size: 25
28605423 GTACAAATTT
28605433 ATAATGGGTTAGGTAAATGTTCCATG
1 ATAAT-GGTTAGGTAAATGTTCCATG
*
28605459 ATAATGGATTAGGTAAATATTCCATG
1 ATAATGG-TTAGGTAAATGTTCCATG
28605485 ATAATAGGTTAGGTAAATGTTCCATG
1 ATAAT-GGTTAGGTAAATGTTCCATG
28605511 ATAATGGTTTAGGTAAATGTTCCATG
1 ATAATGG-TTAGGTAAATGTTCCATG
28605537 AT
1 AT
28605539 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
25 4 0.05
26 69 0.92
27 2 0.03
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.36
Consensus pattern (25 bp):
ATAATGGTTAGGTAAATGTTCCATG
Found at i:28605495 original size:52 final size:52
Alignment explanation
Indices: 28605433--28605538 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
28605423 GTACAAATTT
*
28605433 ATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATG
1 ATAATAGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATG
* *
28605485 ATAATAGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCATG
1 ATAATAGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATG
28605537 AT
1 AT
28605539 GGGCATTTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.36
Consensus pattern (52 bp):
ATAATAGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCATG
Found at i:28607025 original size:28 final size:26
Alignment explanation
Indices: 28606983--28607057 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
28606973 AAAAGCAGCT
* * *
28606983 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGCA
*
28607011 AAATTACTGTTATACCCCTAGGTGCA
1 AAATTACTGTTATACCCCTAGATGCA
* *
28607037 AAATTACCGTTATACCTCTAG
1 AAATTACTGTTATACCCCTAG
28607058 GGTTAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 22 0.54
27 1 0.02
28 18 0.44
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGCA
Found at i:28607202 original size:27 final size:26
Alignment explanation
Indices: 28607162--28607302 Score: 183
Period size: 27 Copynumber: 5.2 Consensus size: 26
28607152 AGGAAGCGTC
28607162 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCAC-ATTATCTGAT
* *
28607189 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAT-TATCTGAT
28607216 CTGGTGGCTATGCCACGATTATCTGAT
1 CTGGTGGCTATGCCAC-ATTATCTGAT
* *
28607243 CTGGTGGCTTTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAT-TATCTGAT
* *
28607270 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTATGCCACATTATCTG-AT
28607297 CTGGTG
1 CTGGTG
28607303 ACTTCGTCAT
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
26 10 0.10
27 89 0.88
28 2 0.02
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.35
Consensus pattern (26 bp):
CTGGTGGCTATGCCACATTATCTGAT
Found at i:28607244 original size:54 final size:53
Alignment explanation
Indices: 28607162--28607302 Score: 228
Period size: 54 Copynumber: 2.6 Consensus size: 53
28607152 AGGAAGCGTC
28607162 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
28607216 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTTTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* *
28607270 CTGGTGGCTCTGCCACAATATCTGTATCTGGTG
1 CTGGTGGCTATGCCACATTATCTG-ATCTGGTG
28607303 ACTTCGTCAT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 7 0.09
54 75 0.91
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:28607316 original size:27 final size:27
Alignment explanation
Indices: 28607162--28607320 Score: 145
Period size: 27 Copynumber: 5.9 Consensus size: 27
28607152 AGGAAGCGTC
28607162 CTGGTGGCTAT-GCCACAATTATCTG-AT
1 CTGGTGGCT-TCGCCACAA-TATCTGTAT
28607189 CTGGTGGC-TCTGCCACATATATCTGT-T
1 CTGGTGGCTTC-GCCACA-ATATCTGTAT
*
28607216 CTGGTGGCTAT-GCCACGATTATCTG-AT
1 CTGGTGGCT-TCGCCAC-AATATCTGTAT
*
28607243 CTGGTGGCTTTGCCACATATATCTGT-T
1 CTGGTGGCTTCGCCACA-ATATCTGTAT
28607270 CTGGTGGC-TCTGCCACAATATCTGTAT
1 CTGGTGGCTTC-GCCACAATATCTGTAT
* * *
28607297 CTGGTGACTTCGTCATAATATCTG
1 CTGGTGGCTTCGCCACAATATCTG
28607321 GCAGCCTCGC
Statistics
Matches: 112, Mismatches: 6, Indels: 28
0.77 0.04 0.19
Matches are distributed among these distances:
25 1 0.01
26 11 0.10
27 95 0.85
28 4 0.04
29 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTTCGCCACAATATCTGTAT
Found at i:28609272 original size:12 final size:12
Alignment explanation
Indices: 28609242--28609275 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28609232 TTTTGGTCTT
* *
28609242 TTTTATATTTCT
1 TTTTATTTTTCA
28609254 TTTTATTTTTCA
1 TTTTATTTTTCA
28609266 TTTTATTTTT
1 TTTTATTTTT
28609276 TTACAAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTCA
Found at i:28610230 original size:16 final size:18
Alignment explanation
Indices: 28610191--28610231 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
28610181 TACACGTATC
28610191 TTATT-TTATCCTCATTT
1 TTATTATTATCCTCATTT
*
28610208 TTGTTATTAT-CTC-TTT
1 TTATTATTATCCTCATTT
28610224 TTATTATT
1 TTATTATT
28610232 TATTTAGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 10 0.48
17 7 0.33
18 4 0.19
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.68
Consensus pattern (18 bp):
TTATTATTATCCTCATTT
Found at i:28616737 original size:27 final size:27
Alignment explanation
Indices: 28616685--28616738 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
28616675 TAAATTGGAA
* *
28616685 AATTAAAATAATAAAAGATGATATTTT
1 AATTAAAATAAGAAAAGATCATATTTT
*
28616712 AATT-AAATAAGAAAATATCATCATTTT
1 AATTAAAATAAGAAAAGATCAT-ATTTT
28616739 CATCATCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (27 bp):
AATTAAAATAAGAAAAGATCATATTTT
Found at i:28617318 original size:74 final size:74
Alignment explanation
Indices: 28617210--28617363 Score: 290
Period size: 74 Copynumber: 2.1 Consensus size: 74
28617200 ATAAGGGCAA
*
28617210 AATAGTAATTTTGCCTAAGATGTAAATTGGATTGAATTGAATTTAATTTTATTAAATTTATGTTA
1 AATAGTAATTGTGCCTAAGATGTAAATTGGATTGAATTGAATTTAATTTTATTAAATTTATGTTA
28617275 AATTCATTC
66 AATTCATTC
28617284 AATAGTAATTGTGCCTAAGATGTAAATTGGATTGAATTGAATTTAATTTTATTAAATTTATGTTA
1 AATAGTAATTGTGCCTAAGATGTAAATTGGATTGAATTGAATTTAATTTTATTAAATTTATGTTA
28617349 AATTCATTC
66 AATTCATTC
28617358 ATATAG
1 A-ATAG
28617364 ATCCAGACAG
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
74 74 0.95
75 4 0.05
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (74 bp):
AATAGTAATTGTGCCTAAGATGTAAATTGGATTGAATTGAATTTAATTTTATTAAATTTATGTTA
AATTCATTC
Found at i:28617893 original size:24 final size:25
Alignment explanation
Indices: 28617823--28617904 Score: 103
Period size: 26 Copynumber: 3.3 Consensus size: 25
28617813 GTCCCGATAT
28617823 ATGGCTCTTTGTGAGCTTCCTGATTA
1 ATGGCTCTTTGTGAGCTTCCTG-TTA
**
28617849 AAAGCTCTTTGTGAGCTTCCTGTTA
1 ATGGCTCTTTGTGAGCTTCCTGTTA
* *
28617874 ATGGCTCTTCG-GAGCTTCCTGATA
1 ATGGCTCTTTGTGAGCTTCCTGTTA
*
28617898 TTGGCTC
1 ATGGCTC
28617905 CCTTGAACCT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
24 18 0.37
25 11 0.22
26 20 0.41
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (25 bp):
ATGGCTCTTTGTGAGCTTCCTGTTA
Found at i:28623852 original size:40 final size:40
Alignment explanation
Indices: 28622849--28623834 Score: 1810
Period size: 40 Copynumber: 24.6 Consensus size: 40
28622839 GAGAATTGAG
*
28622849 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28622889 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28622929 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28622969 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623009 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623049 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623089 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623129 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623169 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623209 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623249 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623289 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623329 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623369 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623409 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623449 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623489 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623529 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623569 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623609 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
28623649 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
*
28623689 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
* * * * * *
28623729 AGTGATGTATTCGGGCTAAGTTCCAAAGAGCATTCGTGCT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
* ** * * * *
28623769 AGTGATATATCCGTGCTAAACCCCAAAGAGCATTCGTGTT
1 AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
* * *
28623809 GGTGTTATATCCGGGCTAGGTCCCGA
1 AGTGATATATCCGGGCTAAGTCCCGA
28623835 AGAGTAATCA
Statistics
Matches: 925, Mismatches: 21, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 925 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (40 bp):
AGTGATATATCCGGGCTAAGTCCCGAGGAGCATTTGTGCT
Found at i:28637524 original size:34 final size:33
Alignment explanation
Indices: 28637480--28637546 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
28637470 CTAACATTGA
*
28637480 AATGGACTAAGG-CCTACACTGATACTGATACTGT
1 AATGGACTAAGGCCCTA-ACTGAAACTGA-ACTGT
*
28637514 AATGGGCTAAGGCCCTAACTGAAACTGAACTGT
1 AATGGACTAAGGCCCTAACTGAAACTGAACTGT
28637547 TACTGATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 5 0.17
34 21 0.70
35 4 0.13
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (33 bp):
AATGGACTAAGGCCCTAACTGAAACTGAACTGT
Found at i:28645165 original size:13 final size:13
Alignment explanation
Indices: 28645143--28645175 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
28645133 AAGGGTTTGT
28645143 TTAT-TAAACTAA
1 TTATCTAAACTAA
28645155 TTATCTAAACTAA
1 TTATCTAAACTAA
*
28645168 TTAACTAA
1 TTATCTAA
28645176 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:28648227 original size:21 final size:21
Alignment explanation
Indices: 28648182--28648233 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
28648172 ACATGCAGAG
* * *
28648182 TTTTCAAAAATCAATGCGAAG
1 TTTTAAAAAATCAATGCAAAA
*
28648203 TTTTAAAAAATCAATGTAAAA
1 TTTTAAAAAATCAATGCAAAA
*
28648224 TTTTTAAAAA
1 TTTTAAAAAA
28648234 GTTCCTACCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (21 bp):
TTTTAAAAAATCAATGCAAAA
Found at i:28650980 original size:134 final size:133
Alignment explanation
Indices: 28650777--28651024 Score: 327
Period size: 134 Copynumber: 1.9 Consensus size: 133
28650767 TTCATAATCG
* * * ** * *
28650777 CAACTTTATCTAAACAGTTCATGATTTGAGATCACAACTGTAATTTTTAAAGTTCACTGATTTAT
1 CAACTCTATCTAAACAATTCATGATTTGAGATCACAACTGTAACTTTTAAAACTCACTAATTTAC
* *
28650842 GATCACAGCTTCAGTTCATTTATTTAGGATAATAAACAATTCAGTAAGAGTTTGCTGACTTCCGA
66 GATCACAGCTTCAGTTCATTGATTTACGATAATAAACAATTCAGTAAGAGTTTGCTGACTTCCGA
28650907 TTA
131 TTA
* * *
28650910 CAACTCTATTTAAACAATTCACTGATTT-ATGATCACAACTGTCACTTTTAAAACTCGCTAATTT
1 CAACTCTATCTAAACAATTCA-TGATTTGA-GATCACAACTGTAACTTTTAAAACTCACTAATTT
* * * *
28650974 ACGATCACAGCTTGAGTTCATTGATTTACGATCATGAACAATTCATTAAGA
64 ACGATCACAGCTTCAGTTCATTGATTTACGATAATAAACAATTCAGTAAGA
28651025 ATTCATCGAT
Statistics
Matches: 97, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
133 19 0.20
134 78 0.80
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (133 bp):
CAACTCTATCTAAACAATTCATGATTTGAGATCACAACTGTAACTTTTAAAACTCACTAATTTAC
GATCACAGCTTCAGTTCATTGATTTACGATAATAAACAATTCAGTAAGAGTTTGCTGACTTCCGA
TTA
Found at i:28651047 original size:134 final size:133
Alignment explanation
Indices: 28650724--28651268 Score: 477
Period size: 133 Copynumber: 4.1 Consensus size: 133
28650714 GGGTGTTTCA
* * * * * * ** *
28650724 TCATTGTTTTAAGATCACAAACAATTCATTAAGAATTTACCGATTCA-TAATCGCAACTTTATCT
1 TCATTGATTTACGATCATAAACAATTCATTAAGAATTCACCGATTTACT-ATCACAACTCCATTT
* * * * *
28650788 AAACAGTTCA-TGATTTGAGATCACAACTGTAATTTTTAAAGTTCACTGATTTATGATCACAGCT
65 AAACAGTTCACTGATTT-AGATCACAACTGTCACTTTTAAAGCTCGCTGATTTACGATCACAGCT
28650852 TCAGT
129 TCAGT
* * * * * ** * * * * * *
28650857 TCATTTATTTAGGATAATAAACAATTCAGTAAGAGTTTGCTGACTTCCGATTACAACTCTATTTA
1 TCATTGATTTACGATCATAAACAATTCATTAAGAATTCACCGATTTACTATCACAACTCCATTTA
* * *
28650922 AACAATTCACTGATTTATGATCACAACTGTCACTTTTAAAACTCGCTAATTTACGATCACAGCTT
66 AACAGTTCACTGATTTA-GATCACAACTGTCACTTTTAAAGCTCGCTGATTTACGATCACAGCTT
*
28650987 GAGT
130 CAGT
* * *
28650991 TCATTGATTTACGATCATGAACAATTCATTAAGAATTCATCGATTTACTGTCACAACTCCA-TTA
1 TCATTGATTTACGATCATAAACAATTCATTAAGAATTCACCGATTTACTATCACAACTCCATTTA
* * * * * * * * * * * *
28651055 AGCAGTTCATTGATATAAGATCATAATTGTCATTTTTAAAGTTTGTTGGTTTACGATCAGAGTTT
66 AACAGTTCACTGAT-TTAGATCACAACTGTCACTTTTAAAGCTCGCTGATTTACGATCACAGCTT
28651120 CAGT
130 CAGT
* * * *
28651124 TCATTGATTTACGATCATAAGCAATTCATTAA-ATGTTCACCGATTTACAATCGCAACTCCATTT
1 TCATTGATTTACGATCATAAACAATTCATTAAGA-ATTCACCGATTTACTATCACAACTCCATTT
* * * * * * * *
28651188 AAACAGTTCGCTGATTTACAATCACAACAGGCACTTTTAAAGCTTGCTTATTTACTATCACAACT
65 AAACAGTTCACTGATTTA-GATCACAACTGTCACTTTTAAAGCTCGCTGATTTACGATCACAGCT
28651253 TCAGT
129 TCAGT
*
28651258 TTATTGATTTA
1 TCATTGATTTA
28651269 TGATTGCATC
Statistics
Matches: 321, Mismatches: 84, Indels: 13
0.77 0.20 0.03
Matches are distributed among these distances:
132 1 0.00
133 163 0.51
134 157 0.49
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (133 bp):
TCATTGATTTACGATCATAAACAATTCATTAAGAATTCACCGATTTACTATCACAACTCCATTTA
AACAGTTCACTGATTTAGATCACAACTGTCACTTTTAAAGCTCGCTGATTTACGATCACAGCTTC
AGT
Found at i:28651339 original size:98 final size:98
Alignment explanation
Indices: 28651180--28651366 Score: 295
Period size: 98 Copynumber: 1.9 Consensus size: 98
28651170 ACAATCGCAA
* * * *
28651180 CTCCATTTAAACAGTTCGCTGATTTACAATCACAACAGGCACTTTTAAAGCTTGCTTATTTACTA
1 CTCCATTTAAACAGTTCACTGATTTACAATCACAACAGGCACTTTTAAAGCTCGCTGATTTACGA
28651245 TCACAACTTCAGTTTATTGATTTATGATTGCAT
66 TCACAACTTCAGTTTATTGATTTATGATTGCAT
** *
28651278 CTCCATTTAAACAGTTCACTGATTTATGATCACAACTA-TCACTTTTAAAGCTCGCTGATTTACG
1 CTCCATTTAAACAGTTCACTGATTTACAATCACAAC-AGGCACTTTTAAAGCTCGCTGATTTACG
28651342 ATCACAACTTCAGTTTATTGATTTA
65 ATCACAACTTCAGTTTATTGATTTA
28651367 CGATCATGAA
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 80 0.99
99 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (98 bp):
CTCCATTTAAACAGTTCACTGATTTACAATCACAACAGGCACTTTTAAAGCTCGCTGATTTACGA
TCACAACTTCAGTTTATTGATTTATGATTGCAT
Found at i:28651536 original size:134 final size:134
Alignment explanation
Indices: 28651297--28651547 Score: 394
Period size: 134 Copynumber: 1.9 Consensus size: 134
28651287 AACAGTTCAC
* * *
28651297 TGATTTATGATCACAACTATCACTTTTAAAGCTCGCTGATTTACGATCACAACTTCAGTTTATTG
1 TGATTTACGATCACAAATATCACTTTTAAAGCTCGCTGATTTACGATCACAACTTCAGTTCATTG
* *
28651362 ATTTACGATCATGAACAATTCATTAAGAGTTTGCCAATTTACAATCGCAACTCCATTTAAAAAGC
66 ATTTACGATCATGAACAATTCATTAAGAGTTCGCCAATTTACAATCACAACTCCATTTAAAAAGC
28651427 TTGT
131 TTGT
* * * *
28651431 TGATTTACGATCACAAATGTCACTTTTAAAGCTCGTTGTTTTACGATCACAGCTTCAGTTCATTG
1 TGATTTACGATCACAAATATCACTTTTAAAGCTCGCTGATTTACGATCACAACTTCAGTTCATTG
* **
28651496 ATTTATGATCATGAACAATTCATTAAGAGTTCGCTGATTTACAATCACAACT
66 ATTTACGATCATGAACAATTCATTAAGAGTTCGCCAATTTACAATCACAACT
28651548 TTATTCTCAT
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
134 105 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (134 bp):
TGATTTACGATCACAAATATCACTTTTAAAGCTCGCTGATTTACGATCACAACTTCAGTTCATTG
ATTTACGATCATGAACAATTCATTAAGAGTTCGCCAATTTACAATCACAACTCCATTTAAAAAGC
TTGT
Found at i:28653062 original size:25 final size:26
Alignment explanation
Indices: 28653017--28653069 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
28653007 AAAAAATAAA
28653017 TTAATTATTAAAATAACTAACTT-TT
1 TTAATTATTAAAATAACTAACTTATT
28653042 TTAATTATGTATAAA-AA-TAACTTATT
1 TTAATTAT-TA-AAATAACTAACTTATT
28653068 TT
1 TT
28653070 CTATAGTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 14 0.56
26 8 0.32
27 3 0.12
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAATTATTAAAATAACTAACTTATT
Found at i:28653315 original size:10 final size:10
Alignment explanation
Indices: 28653302--28653356 Score: 80
Period size: 10 Copynumber: 5.7 Consensus size: 10
28653292 GGTTCTTATA
28653302 TTTTCTTTT-C
1 TTTT-TTTTAC
28653312 TTTTTTTTAC
1 TTTTTTTTAC
28653322 TTTTTTTTAC
1 TTTTTTTTAC
28653332 TTTTTTTTAC
1 TTTTTTTTAC
28653342 --TTTTTTAC
1 TTTTTTTTAC
28653350 TTTTTTT
1 TTTTTTT
28653357 CTTATATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.19
9 4 0.10
10 30 0.71
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTTAC
Found at i:28653334 original size:20 final size:20
Alignment explanation
Indices: 28653302--28653356 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 20
28653292 GGTTCTTATA
28653302 TTTTCTTTT-CTTTTTTTTAC
1 TTTT-TTTTACTTTTTTTTAC
28653322 TTTTTTTTACTTTTTTTTAC
1 TTTTTTTTACTTTTTTTTAC
28653342 --TTTTTTACTTTTTTT
1 TTTTTTTTACTTTTTTT
28653357 CTTATATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.44
19 4 0.12
20 15 0.44
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTTACTTTTTTTTAC
Found at i:28653366 original size:20 final size:19
Alignment explanation
Indices: 28653313--28653366 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
28653303 TTTCTTTTCT
28653313 TTTTTTTACTT-TTTTTTAC
1 TTTTTTT-CTTATTTTTTAC
28653332 -TTTTTT-TTACTTTTTTAC
1 TTTTTTTCTTA-TTTTTTAC
*
28653350 TTTTTTTCTTATATTTT
1 TTTTTTTCTTATTTTTT
28653367 GTATCTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
16 2 0.07
18 14 0.47
19 11 0.37
20 3 0.10
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTTCTTATTTTTTAC
Found at i:28653420 original size:18 final size:17
Alignment explanation
Indices: 28653399--28653444 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
28653389 TTTTTTAAGT
*
28653399 TTTATATTATTTTCTTAA
1 TTTATATTATTAT-TTAA
*
28653417 TTTATTTTACTTATTTAA
1 TTTATATTA-TTATTTAA
28653435 TTTATATTAT
1 TTTATATTAT
28653445 CAATTTTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 20 0.83
19 3 0.12
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTATATTATTATTTAA
Found at i:28653441 original size:36 final size:36
Alignment explanation
Indices: 28653372--28653444 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
28653362 ATTTTGTATC
*
28653372 TTTCTTAGATTTTTTTCTTTTTTAAGTTTTATATTAT
1 TTTCTTAGATTTTTTTCTTATTTAAG-TTTATATTAT
28653409 TTTCTTA-ATTTATTTTACTTATTTAA-TTTATATTAT
1 TTTCTTAGATTT-TTTT-CTTATTTAAGTTTATATTAT
28653445 CAATTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
36 14 0.42
37 11 0.33
38 8 0.24
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.68
Consensus pattern (36 bp):
TTTCTTAGATTTTTTTCTTATTTAAGTTTATATTAT
Found at i:28653498 original size:22 final size:21
Alignment explanation
Indices: 28653462--28653520 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
28653452 GAAAAATTTG
*
28653462 TAATATATATTTAAAATGTTTTA
1 TAATAT-TTTTTAAAAT-TTTTA
28653485 TAATATTTTTTAAAATTTTTA
1 TAATATTTTTTAAAATTTTTA
*
28653506 -ATTATTATTTTAAAA
1 TAATATT-TTTTAAAA
28653521 ATATTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.15
21 13 0.39
22 9 0.27
23 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TAATATTTTTTAAAATTTTTA
Found at i:28653521 original size:22 final size:21
Alignment explanation
Indices: 28653447--28653527 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 21
28653437 TATATTATCA
28653447 ATTTTGAAAA-ATTTGTAATA-T
1 ATTTT-AAAATATTT-TAATATT
*
28653468 ATATTTAAAATGTTTTATAATATT
1 AT-TTTAAAAT-ATTT-TAATATT
28653492 -TTTTAAAAT-TTTTAATTATT
1 ATTTTAAAATATTTTAA-TATT
28653512 ATTTTAAAAATATTTT
1 ATTTT-AAAATATTTT
28653528 TTAACTTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
19 3 0.06
20 7 0.14
21 10 0.20
22 16 0.32
23 13 0.26
24 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (21 bp):
ATTTTAAAATATTTTAATATT
Found at i:28653671 original size:17 final size:16
Alignment explanation
Indices: 28653651--28653696 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 16
28653641 TTTTGAAGTC
28653651 TATTTTTTTTCCTATTT
1 TATTTTTTTT-CTATTT
28653668 TATTTTGTTTATCTATTT
1 TATTTT-TTT-TCTATTT
28653686 TATTTATTTTT
1 TATTT-TTTTT
28653697 ATTATACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 7 0.27
18 17 0.65
19 2 0.08
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (16 bp):
TATTTTTTTTCTATTT
Found at i:28653761 original size:19 final size:20
Alignment explanation
Indices: 28653739--28653780 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
28653729 TTTTCATAGA
*
28653739 TTTTGTCTT-TTTCTTTAA-
1 TTTTTTCTTCTTTCTTTAAG
*
28653757 TTTTTTTTTCTTTCTTTAAG
1 TTTTTTCTTCTTTCTTTAAG
28653777 TTTT
1 TTTT
28653781 ATATTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTTTTCTTCTTTCTTTAAG
Found at i:28654071 original size:21 final size:23
Alignment explanation
Indices: 28654047--28654089 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
28654037 TATATTTCTC
28654047 AAAT-TAATTTTTGAAA-ATTAT
1 AAATATAATTTTTGAAATATTAT
* *
28654068 AAATATTATTTTTTAAATATTA
1 AAATATAATTTTTGAAATATTA
28654090 ACCATATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
AAATATAATTTTTGAAATATTAT
Found at i:28654311 original size:10 final size:9
Alignment explanation
Indices: 28654293--28654381 Score: 63
Period size: 10 Copynumber: 9.4 Consensus size: 9
28654283 TAAAATTTAA
28654293 AAAATATTT
1 AAAATATTT
28654302 AAAATCATTT
1 AAAAT-ATTT
*
28654312 AAAATATTAA
1 AAAATATT-T
28654322 AAAATATTT
1 AAAATATTT
*
28654331 TAAATCATTT
1 AAAAT-ATTT
* *
28654341 TAAATGTTTT
1 AAAAT-ATTT
* *
28654351 ATAATATTA
1 AAAATATTT
28654360 AAAATATATT
1 AAAATAT-TT
*
28654370 -TAATATTT
1 AAAATATTT
28654378 AAAA
1 AAAA
28654382 AATAATTTGA
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
8 2 0.03
9 27 0.44
10 33 0.53
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (9 bp):
AAAATATTT
Found at i:28654317 original size:19 final size:18
Alignment explanation
Indices: 28654293--28654381 Score: 63
Period size: 19 Copynumber: 4.7 Consensus size: 18
28654283 TAAAATTTAA
28654293 AAAATATTTAAAATCATTT
1 AAAATATTTAAAAT-ATTT
*
28654312 AAAATATTAAAAAATATTT
1 AAAATATT-TAAAATATTT
* * *
28654331 TAAATCATTTTAAATGTTTT
1 AAAAT-ATTTAAAAT-ATTT
* *
28654351 ATAATATTAAAAATATATT
1 AAAATATTTAAAATAT-TT
*
28654370 -TAATATTTAAAA
1 AAAATATTTAAAA
28654382 AATAATTTGA
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
18 12 0.22
19 29 0.53
20 14 0.25
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (18 bp):
AAAATATTTAAAATATTT
Found at i:28654321 original size:29 final size:28
Alignment explanation
Indices: 28654283--28654395 Score: 109
Period size: 29 Copynumber: 3.9 Consensus size: 28
28654273 AAATTCTATG
28654283 TAAAATTTAAAAAATATTTAAAATCATT
1 TAAAATTTAAAAAATATTTAAAATCATT
*
28654311 TAAAATATTAAAAAATATTTTAAATCATT
1 TAAAAT-TTAAAAAATATTTAAAATCATT
* ** * * *
28654340 TTAAATGTTTTATAATATTAAAAATATATT
1 TAAAAT-TTAAAAAATATTTAAAAT-CATT
*
28654370 TAATATTTAAAAAATAATTTGAAAAT
1 TAAAATTTAAAAAAT-ATTT-AAAAT
28654396 ATATTTTTAA
Statistics
Matches: 66, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
28 6 0.09
29 45 0.68
30 10 0.15
31 5 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAAATTTAAAAAATATTTAAAATCATT
Found at i:28654398 original size:31 final size:34
Alignment explanation
Indices: 28654351--28654439 Score: 98
Period size: 34 Copynumber: 2.7 Consensus size: 34
28654341 TAAATGTTTT
28654351 ATAATATTAAAAATATA-TTTAATATTTA-AAAA
1 ATAATATTAAAAATATATTTTAATATTTATAAAA
*
28654383 ATAAT-TTGAAAATATATTTTTAATATTTATAAAA
1 ATAATATTAAAAATATA-TTTTAATATTTATAAAA
*
28654417 A-ATATATTATAAAACAT-TTTTAA
1 ATA-ATATTA-AAAATATATTTTAA
28654440 AAAATACATT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
31 10 0.21
32 5 0.10
33 12 0.25
34 13 0.27
35 2 0.04
36 6 0.12
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (34 bp):
ATAATATTAAAAATATATTTTAATATTTATAAAA
Found at i:28654430 original size:13 final size:13
Alignment explanation
Indices: 28654404--28654445 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
28654394 ATATATTTTT
28654404 AATATTTATAAAA
1 AATATTTATAAAA
28654417 AATATATTATAAAA
1 AATAT-TTATAAAA
*
28654431 CAT-TTT-TAAAA
1 AATATTTATAAAA
28654442 AATA
1 AATA
28654446 CATTTCAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.28
12 2 0.08
13 6 0.24
14 10 0.40
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATTTATAAAA
Found at i:28657933 original size:30 final size:30
Alignment explanation
Indices: 28657881--28657990 Score: 166
Period size: 30 Copynumber: 3.7 Consensus size: 30
28657871 GGTTAAATGG
* * *
28657881 ACTCGAACCGCCTATATCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
*
28657911 ACTCAAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
*
28657941 ACTCGAACCACCCATGTCCAGGTGATATGA
1 ACTCGAACCACCCATGTCCGGGTGATATGA
*
28657971 ACTCGAACCACCTATGTCCG
1 ACTCGAACCACCCATGTCCG
28657991 ATTTATATGA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 72 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.21
Consensus pattern (30 bp):
ACTCGAACCACCCATGTCCGGGTGATATGA
Found at i:28657999 original size:30 final size:30
Alignment explanation
Indices: 28657881--28658003 Score: 149
Period size: 30 Copynumber: 4.1 Consensus size: 30
28657871 GGTTAAATGG
* * * *
28657881 ACTCGAACCGCCTATATCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGAGTGATATGA
* *
28657911 ACTCAAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATGTCCGAGTGATATGA
28657941 ACTCGAACCACCCATGTCC-AGGTGATATGA
1 ACTCGAACCACCCATGTCCGA-GTGATATGA
* * *
28657971 ACTCGAACCACCTATGTCCGATTTATATGA
1 ACTCGAACCACCCATGTCCGAGTGATATGA
28658001 ACT
1 ACT
28658004 GCTCTGGGAC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
30 81 0.99
31 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (30 bp):
ACTCGAACCACCCATGTCCGAGTGATATGA
Found at i:28657999 original size:60 final size:60
Alignment explanation
Indices: 28657881--28658003 Score: 165
Period size: 60 Copynumber: 2.0 Consensus size: 60
28657871 GGTTAAATGG
* * * *
28657881 ACTCGAACCGCCTATATCCGGGTGATATGAACTCAAACCACCCATGTCCGGGTGATATGA
1 ACTCGAACCACCCATATCCAGGTGATATGAACTCAAACCACCCATGTCCGAGTGATATGA
* * * * *
28657941 ACTCGAACCACCCATGTCCAGGTGATATGAACTCGAACCACCTATGTCCGATTTATATGA
1 ACTCGAACCACCCATATCCAGGTGATATGAACTCAAACCACCCATGTCCGAGTGATATGA
28658001 ACT
1 ACT
28658004 GCTCTGGGAC
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (60 bp):
ACTCGAACCACCCATATCCAGGTGATATGAACTCAAACCACCCATGTCCGAGTGATATGA
Found at i:28670339 original size:29 final size:29
Alignment explanation
Indices: 28670297--28670356 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
28670287 AAAAAAAGAT
28670297 TGAGAAAAAAGTAACCAATTATGTCTATA
1 TGAGAAAAAAGTAACCAATTATGTCTATA
28670326 TGAGAAAAAAGTAACCAATTATGTCTATA
1 TGAGAAAAAAGTAACCAATTATGTCTATA
28670355 TG
1 TG
28670357 TGACTGTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (29 bp):
TGAGAAAAAAGTAACCAATTATGTCTATA
Found at i:28671808 original size:91 final size:93
Alignment explanation
Indices: 28671651--28671818 Score: 252
Period size: 91 Copynumber: 1.8 Consensus size: 93
28671641 GGATGGTTGA
* *
28671651 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATTGATGCGAATGTCTGAACTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCTGAACTCATTGAGT
28671716 TGAGTCCGAGTTTGTGAAATGTAACTAG
66 TGAGTCCGAGTTTGTGAAATGTAACTAG
* * *
28671744 GCATCCGAACTCGTTGAG-T-AGTCCGAGTTCATTTATGGATGCGAACG-CTCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCT-GAACTCATTGAG
*
28671806 TTGAGTCTGAGTT
65 TTGAGTCCGAGTT
28671819 CACTTAGGGG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
90 2 0.03
91 47 0.69
92 1 0.01
93 18 0.26
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCTGAACTCATTGAGT
TGAGTCCGAGTTTGTGAAATGTAACTAG
Found at i:28675798 original size:23 final size:23
Alignment explanation
Indices: 28675772--28675815 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
28675762 TGTACTCCGA
*
28675772 TACTCTTATTACTTGCACTTCGG
1 TACTCTTATTACTAGCACTTCGG
* *
28675795 TACTCTTGTTCCTAGCACTTC
1 TACTCTTATTACTAGCACTTC
28675816 AATCTGATCT
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:0.16, C:0.30, G:0.11, T:0.43
Consensus pattern (23 bp):
TACTCTTATTACTAGCACTTCGG
Found at i:28676914 original size:32 final size:32
Alignment explanation
Indices: 28676873--28676936 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
28676863 AGATAACTTG
28676873 TATTAGTAGATGAACCTAATTATGTTCTTAGT
1 TATTAGTAGATGAACCTAATTATGTTCTTAGT
28676905 TATTAGTAGATGAACCTAATTATGTTCTTAGT
1 TATTAGTAGATGAACCTAATTATGTTCTTAGT
28676937 CTAATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (32 bp):
TATTAGTAGATGAACCTAATTATGTTCTTAGT
Found at i:28689894 original size:46 final size:46
Alignment explanation
Indices: 28689837--28690009 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
28689827 TGGTTGAGCA
*
28689837 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * * * *
28689883 TACGAATTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
28689930 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
28689976 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28690010 GGGGCGGGTT
Statistics
Matches: 103, Mismatches: 17, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 59 0.57
47 27 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:28689993 original size:93 final size:93
Alignment explanation
Indices: 28689834--28690004 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
28689824 GGATGGTTGA
* * *
28689834 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTACGAATTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCACGAACTCGTTGAGT
28689899 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
28689927 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCACGAACTCGTTGAGT
28689992 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
28690005 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCACGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28690056 original size:33 final size:33
Alignment explanation
Indices: 28690014--28690078 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
28690004 CACTTAGGGG
28690014 CGGGTTACATGATTTATTGATTACATATGAGGT
1 CGGGTTACATGATTTATTGATTACATATGAGGT
*
28690047 CGGGTTACATGATTTCTTGATTACATATGAGG
1 CGGGTTACATGATTTATTGATTACATATGAGG
28690079 CACTTATGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (33 bp):
CGGGTTACATGATTTATTGATTACATATGAGGT
Found at i:28690303 original size:19 final size:20
Alignment explanation
Indices: 28690266--28690303 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28690256 ATAAGGTGGT
28690266 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28690286 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28690304 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28697520 original size:46 final size:46
Alignment explanation
Indices: 28697461--28697633 Score: 163
Period size: 46 Copynumber: 3.7 Consensus size: 46
28697451 TGGTTGAGCA
* * *
28697461 TCCGACCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
28697507 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * *
28697554 TCCGAACTCGTTGATTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * **
28697600 CCCGAGCTCGTTGAGTTGAGTTTGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
28697634 GGGGCGGGTT
Statistics
Matches: 101, Mismatches: 19, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 56 0.55
47 28 0.28
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:28697895 original size:19 final size:20
Alignment explanation
Indices: 28697858--28697895 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
28697848 ATAAGGTGGT
28697858 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
28697878 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
28697896 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:28699351 original size:40 final size:41
Alignment explanation
Indices: 28699307--28699400 Score: 129
Period size: 40 Copynumber: 2.3 Consensus size: 41
28699297 CAATGGAATT
* *
28699307 TGGCACTAAGTGTGCGATTTAATATAGTTTCGGCTACA-AA
1 TGGCACTAAGTGTGCGAGTTAACATAGTTTCGGCTACATAA
** *
28699347 TGGCACTAAGTGTGCGAGTTGGCATAGTTTCGGCTATATAA
1 TGGCACTAAGTGTGCGAGTTAACATAGTTTCGGCTACATAA
28699388 -GGCACTAAGTGTG
1 TGGCACTAAGTGTG
28699401 TGATACCGAC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 46 0.96
41 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.31
Consensus pattern (41 bp):
TGGCACTAAGTGTGCGAGTTAACATAGTTTCGGCTACATAA
Found at i:28704849 original size:55 final size:54
Alignment explanation
Indices: 28704766--28704924 Score: 196
Period size: 55 Copynumber: 2.9 Consensus size: 54
28704756 TACGTGGTAT
*
28704766 CCTTGCCTTAT-GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATG-GGA
1 CCTTGCCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACATGAGGA
* * * * ***
28704818 CCTTTGCCTTATAGTAACTCATGAATGCCATGTCTTGACATGGACTTACATGATTT
1 CC-TTGCCTTATAG-AACTCATCAATGCCATGCCTTGGCATGGTCTTACATGAGGA
* *
28704874 CCTTACCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGA
1 CCTTGCCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACATGA
28704925 TATCCTTATC
Statistics
Matches: 89, Mismatches: 14, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
52 2 0.02
53 9 0.10
54 34 0.38
55 42 0.47
56 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (54 bp):
CCTTGCCTTATAGAACTCATCAATGCCATGCCTTGGCATGGTCTTACATGAGGA
Found at i:28704920 original size:54 final size:54
Alignment explanation
Indices: 28704743--28704937 Score: 214
Period size: 54 Copynumber: 3.6 Consensus size: 54
28704733 ATTGTCATAT
* * * * * *
28704743 CTTGACATGGTGTTACGTGGTATCCTTGCCTTAT-GAACTCACCAATGCCATGC
1 CTTGGCATGGTCTTACATGATATCCTTACCTTATAGAACTCATCAATGCCATGC
** * * *
28704796 CTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTCATGAATGCCATGT
1 CTTGGCATGGTCTTACATGATATCC-TTACCTTATAG-AACTCATCAATGCCATGC
* * * *
28704851 CTTGACATGGACTTACATGATTTCCTTACCTTATAGAACTTATCAATGCCATGC
1 CTTGGCATGGTCTTACATGATATCCTTACCTTATAGAACTCATCAATGCCATGC
*
28704905 CTTGGCATGGTCTTACATGATATCCTTATCTTA
1 CTTGGCATGGTCTTACATGATATCCTTACCTTA
28704938 CCAAATGCCA
Statistics
Matches: 118, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
52 2 0.02
53 27 0.23
54 45 0.38
55 42 0.36
56 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (54 bp):
CTTGGCATGGTCTTACATGATATCCTTACCTTATAGAACTCATCAATGCCATGC
Found at i:28707235 original size:27 final size:27
Alignment explanation
Indices: 28707197--28707249 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
28707187 AGTTATACAT
**
28707197 CTCATAAGGGCATAGTAGTCATTTTAC
1 CTCATAAGGGCATAACAGTCATTTTAC
*
28707224 CTCATAGGGGCATAACAGTCATTTTA
1 CTCATAAGGGCATAACAGTCATTTTA
28707250 TTAATTTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (27 bp):
CTCATAAGGGCATAACAGTCATTTTAC
Found at i:28709570 original size:18 final size:18
Alignment explanation
Indices: 28709524--28709564 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
28709514 TGGCCCATTA
*
28709524 CAGTAACAGTAATCAGTG
1 CAGTAACAGTAATCAATG
28709542 CAGTAACAGTAATCAATG
1 CAGTAACAGTAATCAATG
28709560 CAGTA
1 CAGTA
28709565 TTAGTATCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (18 bp):
CAGTAACAGTAATCAATG
Found at i:28709927 original size:22 final size:22
Alignment explanation
Indices: 28709899--28709946 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
28709889 TATAAGCATA
*
28709899 CATCACATAGAGGCAAAACAGT
1 CATCACATAGAGGCAAAACAAT
*
28709921 CATCACATAGGGGCAAAACAAT
1 CATCACATAGAGGCAAAACAAT
28709943 CATC
1 CATC
28709947 TTACCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.44, C:0.25, G:0.17, T:0.15
Consensus pattern (22 bp):
CATCACATAGAGGCAAAACAAT
Found at i:28710003 original size:52 final size:54
Alignment explanation
Indices: 28709924--28710044 Score: 192
Period size: 52 Copynumber: 2.3 Consensus size: 54
28709914 AAACAGTCAT
*
28709924 CACATAGGGGCAAAACAATCATCTTACCATATAAGGGCAAAATAGTCA-TTTAC
1 CACATAGGGGCAAAACAATCATCTTACCACATAAGGGCAAAATAGTCATTTTAC
* * *
28709977 GACATAAGGG-AAAACAATCATTTTACCACATAAGGGCAAAATAGTCATTTTAC
1 CACATAGGGGCAAAACAATCATCTTACCACATAAGGGCAAAATAGTCATTTTAC
28710030 CACATAGGGGCAAAA
1 CACATAGGGGCAAAA
28710045 TAGTTATTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
52 35 0.58
53 21 0.35
54 4 0.07
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (54 bp):
CACATAGGGGCAAAACAATCATCTTACCACATAAGGGCAAAATAGTCATTTTAC
Found at i:28710045 original size:27 final size:27
Alignment explanation
Indices: 28709924--28710055 Score: 160
Period size: 27 Copynumber: 5.0 Consensus size: 27
28709914 AAACAGTCAT
* * * *
28709924 CACATAGGGGCAAAACAATCATCTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
*
28709951 CATATAAGGGCAAAATAGTCA-TTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* * *
28709977 GACATAAGGG-AAAACAATCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
28710003 CACATAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
28710030 CACATAGGGGCAAAATAGTTATTTTA
1 CACATAAGGGCAAAATAGTCATTTTA
28710056 TCATATTGGG
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
25 8 0.09
26 26 0.29
27 55 0.62
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (27 bp):
CACATAAGGGCAAAATAGTCATTTTAC
Found at i:28719004 original size:41 final size:41
Alignment explanation
Indices: 28718947--28719173 Score: 323
Period size: 41 Copynumber: 5.5 Consensus size: 41
28718937 TCATAAAATT
* *
28718947 TGCTAGGC-ATAAAGCCT-AGTATAATACACTGGCACAGAGCC
1 TGCTAGGCAAT-AAGCCTGA-TATAATACACCGGCACAAAGCC
*
28718988 TGCTAGGCAATAAGCCTGATATAATACACCGGCATATAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGC--ACAAAGCC
28719031 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* *
28719072 TGCTAGGCAATAAGCCTGATTTAAAACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* *
28719113 TGCTAGGCAATAAGCCTGATATAATACGCCGGCGCAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
*
28719154 TACTAGGCAATAAAGCCTGA
1 TGCTAGGCAAT-AAGCCTGA
28719174 ATATCACTGA
Statistics
Matches: 170, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
41 120 0.71
42 11 0.06
43 39 0.23
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (41 bp):
TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
Found at i:28719080 original size:84 final size:82
Alignment explanation
Indices: 28718947--28719173 Score: 323
Period size: 84 Copynumber: 2.7 Consensus size: 82
28718937 TCATAAAATT
* *
28718947 TGCTAGGC-ATAAAGCCT-AGTATAATACACTGGCACAGAGCCTGCTAGGCAATAAGCCTGATAT
1 TGCTAGGCAAT-AAGCCTGA-TATAATACACCGGCACAAAGCCTGCTAGGCAATAAGCCTGATAT
* *
28719010 AATACACCGGCATATAAAGCC
64 AAAACACCGGC--ACAAAGCC
*
28719031 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTGCTAGGCAATAAGCCTGATTTAA
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTGCTAGGCAATAAGCCTGATATAA
28719096 AACACCGGCACAAAGCC
66 AACACCGGCACAAAGCC
* * *
28719113 TGCTAGGCAATAAGCCTGATATAATACGCCGGCGCAAAGCCTACTAGGCAATAAAGCCTGA
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTGCTAGGCAAT-AAGCCTGA
28719174 ATATCACTGA
Statistics
Matches: 132, Mismatches: 8, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
82 56 0.42
83 8 0.06
84 65 0.49
85 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.19
Consensus pattern (82 bp):
TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCCTGCTAGGCAATAAGCCTGATATAA
AACACCGGCACAAAGCC
Found at i:28725802 original size:41 final size:41
Alignment explanation
Indices: 28725668--28725968 Score: 437
Period size: 41 Copynumber: 7.3 Consensus size: 41
28725658 ACATAAAATT
*
28725668 TGCTAGGC-ATAAAGCCT-AGTAT-ATACACCGGCACAGAGCC
1 TGCTAGGCAAT-AAGCCTGA-TATAATACACCGGCACAAAGCC
*
28725708 TGCTAGGCAATAAGCCTGATATAATACACCGGCATATAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGC--ACAAAGCC
*
28725751 TGCTAGGCAATAAGCCTGATATAATACACTGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* *
28725792 TGCTAGGCAATAAGCTTGATTTAATACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* * *
28725833 TACTAGGCAATAAGCCTGATTTAATACACTGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
* * *
28725874 TGCTAGGCAATAAGTCTGATTTAAAACACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
*
28725915 TGCTAGGCAATAAGCCTGATATAATATACCGGCACAAAGCC
1 TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
28725956 TGCTAGGCAATAA
1 TGCTAGGCAATAA
28725969 AGCCCGAATA
Statistics
Matches: 238, Mismatches: 18, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
40 17 0.07
41 183 0.77
43 38 0.16
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (41 bp):
TGCTAGGCAATAAGCCTGATATAATACACCGGCACAAAGCC
Found at i:28730797 original size:19 final size:18
Alignment explanation
Indices: 28730757--28730800 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
28730747 CTTTGGCCGA
*
28730757 ATATACTTTTCATATGCAC
1 ATATA-TTTTCATATACAC
*
28730776 ATATATTTTCATTTACATC
1 ATATATTTTCATATACA-C
28730795 ATATAT
1 ATATAT
28730801 AATTAGTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATATTTTCATATACAC
Found at i:28731025 original size:43 final size:43
Alignment explanation
Indices: 28730970--28731124 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 43
28730960 ATATCGTACA
*
28730970 ATGCCAACGTCCCAGACGTGGTTTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
** *
28731013 ATGCC-ACTGTCCCAGACAG-GGTCTTACA-CAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
* * * * ** *
28731054 ATGTCGATGTCCCAAACAAGGTCTTACATGTAATCACATATTG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
*
28731097 ATGCCAACATCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
28731125 CGAGAACACA
Statistics
Matches: 87, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
41 23 0.26
42 19 0.22
43 44 0.51
44 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
Found at i:28734505 original size:8 final size:8
Alignment explanation
Indices: 28734492--28734520 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
28734482 CTAGATGTGC
28734492 AAAAGCCG
1 AAAAGCCG
28734500 AAAAGCCG
1 AAAAGCCG
28734508 AAAAGCCG
1 AAAAGCCG
28734516 AAAAG
1 AAAAG
28734521 TTGGCATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.55, C:0.21, G:0.24, T:0.00
Consensus pattern (8 bp):
AAAAGCCG
Found at i:28735248 original size:60 final size:59
Alignment explanation
Indices: 28735172--28735308 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 59
28735162 AACTATGTTA
* *
28735172 ATATGGGCAAGGCCCAATATA-TCTCGACT-TGTAATAGGGCTACGGCCCAGATTGATACTG
1 ATATGGGCTAGGCCCAATATACTCT-GA-TATGTAA-AGGGCTACGGCCCAGATTAATACTG
* * *
28735232 ATATGGGCTAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATACTCTGATA-TGTAAAGGGCTACGGCCCAGATTAATACTG
28735292 ATATGGGCTAAGGCCCA
1 ATATGGGCT-AGGCCCA
28735309 GTTAACACTG
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 1 0.01
60 52 0.76
61 15 0.22
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (59 bp):
ATATGGGCTAGGCCCAATATACTCTGATATGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:28736272 original size:19 final size:19
Alignment explanation
Indices: 28736245--28736287 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
28736235 GCAAATTCGA
*
28736245 CCAATGGTAGATATTTCTC
1 CCAACGGTAGATATTTCTC
28736264 CCAACGGTAGATATTTCTC
1 CCAACGGTAGATATTTCTC
28736283 CCAAC
1 CCAAC
28736288 TACCTTCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (19 bp):
CCAACGGTAGATATTTCTC
Found at i:28741758 original size:10 final size:10
Alignment explanation
Indices: 28741740--28741791 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
28741730 ATTATTAACA
*
28741740 TAATGAATTT
1 TAATTAATTT
28741750 TAATTAATTT
1 TAATTAATTT
*
28741760 TATTGTAAATTT
1 TAAT-T-AATTT
28741772 TAATTAATTT
1 TAATTAATTT
*
28741782 TGATT-ATTT
1 TAATTAATTT
28741791 T
1 T
28741792 CGACAGAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 5 0.14
10 21 0.58
11 2 0.06
12 8 0.22
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (10 bp):
TAATTAATTT
Found at i:28743363 original size:27 final size:27
Alignment explanation
Indices: 28743343--28743701 Score: 222
Period size: 27 Copynumber: 13.3 Consensus size: 27
28743333 ATTACTAAAG
* * *
28743343 TACCCCCGATTTATAGAATTATC-GTT
1 TACCCTCGATTTATAGAATTACCAATT
*
28743369 CTACCCTCGATTTATAGAATTACCATTT
1 -TACCCTCGATTTATAGAATTACCAATT
* *
28743397 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCAATT
* *
28743424 TACACTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCAATT
* *
28743451 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCAATT
* *
28743478 TACACTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCAATT
** * * * **
28743505 TACCCTTAATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAGAATTACCAATT
* * * * * **
28743532 TACCCTTGGTTTGTAAAATTACTAAAA
1 TACCCTCGATTTATAGAATTACCAATT
* * * * *
28743559 TACCCCCTGATTTCTAAAATTACTGAA-A
1 TACCCTC-GATTTATAGAATTAC-CAATT
* **
28743587 TACCCTCGACTTGTA-AAAATTACCAAAG
1 TACCCTCGA-TT-TATAGAATTACCAATT
* * ***
28743615 TACCCTCGGTTTATAAAATTACTGCTT
1 TACCCTCGATTTATAGAATTACCAATT
* * * *
28743642 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACCAATT
** * *
28743669 TACCCTTAATTTACA-AATTACCATTT
1 TACCCTCGATTTATAGAATTACCAATT
28743695 TACCCTC
1 TACCCTC
28743702 AATTGTGAAA
Statistics
Matches: 278, Mismatches: 47, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
26 18 0.06
27 217 0.78
28 40 0.14
29 3 0.01
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.38
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCAATT
Found at i:28743467 original size:81 final size:81
Alignment explanation
Indices: 28743349--28743507 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 81
28743339 AAAGTACCCC
* * * *
28743349 CGATTTATAGAATTATCGTTCTACCCTCGATTTATAGAATTACCATTTTACCCTTGATTTATAGA
1 CGATTTATAGAATTACCATTCTACCCTCGATTTATAGAATTACCATTTTACACTCGATTTATAGA
28743414 ATTACCATTTTACACT
66 ATTACCATTTTACACT
* *
28743430 CGATTTATAGAATTACCATTTTACCCTTGATTTATAGAATTACCATTTTACACTCGATTTATAGA
1 CGATTTATAGAATTACCATTCTACCCTCGATTTATAGAATTACCATTTTACACTCGATTTATAGA
28743495 ATTACCATTTTAC
66 ATTACCATTTTAC
28743508 CCTTAATTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (81 bp):
CGATTTATAGAATTACCATTCTACCCTCGATTTATAGAATTACCATTTTACACTCGATTTATAGA
ATTACCATTTTACACT
Found at i:28743517 original size:81 final size:81
Alignment explanation
Indices: 28743351--28743526 Score: 253
Period size: 81 Copynumber: 2.2 Consensus size: 81
28743341 AGTACCCCCG
* * * *
28743351 ATTTATAGAATTATCGTTCTACCCTCGATTTATAGAATTACCATTTTACCCTTGATTTATAGAAT
1 ATTTATAGAATTACCATTCTACCCTCGATTTATAGAATTACCATTTTACACTCGATTTATAGAAT
*
28743416 TACCATTTTACACTCG
66 TACCATTTTACACTCA
* *
28743432 ATTTATAGAATTACCATTTTACCCTTGATTTATAGAATTACCATTTTACACTCGATTTATAGAAT
1 ATTTATAGAATTACCATTCTACCCTCGATTTATAGAATTACCATTTTACACTCGATTTATAGAAT
* *
28743497 TACCATTTTACCCTTA
66 TACCATTTTACACTCA
* *
28743513 ATTTACAAAATTAC
1 ATTTATAGAATTAC
28743527 TAAAATACCC
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (81 bp):
ATTTATAGAATTACCATTCTACCCTCGATTTATAGAATTACCATTTTACACTCGATTTATAGAAT
TACCATTTTACACTCA
Found at i:28743553 original size:54 final size:54
Alignment explanation
Indices: 28743350--28743526 Score: 291
Period size: 54 Copynumber: 3.3 Consensus size: 54
28743340 AAGTACCCCC
* * * *
28743350 GATTTATAGAATTATCGTTCTACCCTCGATTTATAGAATTACCATTTTACCCTT
1 GATTTATAGAATTACCATTTTACACTCGATTTATAGAATTACCATTTTACCCTT
28743404 GATTTATAGAATTACCATTTTACACTCGATTTATAGAATTACCATTTTACCCTT
1 GATTTATAGAATTACCATTTTACACTCGATTTATAGAATTACCATTTTACCCTT
28743458 GATTTATAGAATTACCATTTTACACTCGATTTATAGAATTACCATTTTACCCTT
1 GATTTATAGAATTACCATTTTACACTCGATTTATAGAATTACCATTTTACCCTT
* * *
28743512 AATTTACAAAATTAC
1 GATTTATAGAATTAC
28743527 TAAAATACCC
Statistics
Matches: 116, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 116 1.00
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (54 bp):
GATTTATAGAATTACCATTTTACACTCGATTTATAGAATTACCATTTTACCCTT
Found at i:28743563 original size:54 final size:54
Alignment explanation
Indices: 28743505--28743890 Score: 176
Period size: 54 Copynumber: 7.1 Consensus size: 54
28743495 ATTACCATTT
*
28743505 TACCCTTAATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACTAAAA
1 TACCCTTAATTTACAAAATTACTAAAATACCCTTGATTTGTAAAATTACTAAAA
* * * * * * *
28743559 TACCCCCTGATTT-CTAAAATTACTGAAATACCCTCGACTTGTAAAAATTACCAAAG
1 TA-CCCTTAATTTAC-AAAATTACTAAAATACCCTTGATTTGT-AAAATTACTAAAA
*** * **** ** * ***
28743615 TACCCTCGGTTTATAAAATTACTGCTTTACCCTTGATTTACAGAATTACTATTT
1 TACCCTTAATTTACAAAATTACTAAAATACCCTTGATTTGTAAAATTACTAAAA
* *** * * *
28743669 TACCCTTAATTTAC-AAATTACCATTTTACCC-TCAATTGTGAAATTACTAAAA
1 TACCCTTAATTTACAAAATTACTAAAATACCCTTGATTTGTAAAATTACTAAAA
** * * *
28743721 TACCCTTATAGGGT--AAAATTACCAAAACACCCCT-AGTTTGTAAAATTA-TCAAAA
1 TACCCTTA-A-TTTACAAAATTACTAAAATACCCTTGA-TTTGTAAAATTACT-AAAA
** ** *** ** ** *
28743775 TACCAGTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTAATTTACAAAATTACTAAAATACCCTTGATTTGTAAAATTACTAAAA
* * * * *
28743829 TACCCCTGATTTACAAAATTA-TAGAAATACCCTTGATTTGTAGATTTACCAAAA
1 TACCCTTAATTTACAAAATTACTA-AAATACCCTTGATTTGTAAAATTACTAAAA
*
28743883 CACCCTTA
1 TACCCTTA
28743891 TAGGATGAAA
Statistics
Matches: 242, Mismatches: 75, Indels: 30
0.70 0.22 0.09
Matches are distributed among these distances:
52 21 0.09
53 30 0.12
54 119 0.49
55 59 0.24
56 13 0.05
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (54 bp):
TACCCTTAATTTACAAAATTACTAAAATACCCTTGATTTGTAAAATTACTAAAA
Found at i:28743587 original size:28 final size:28
Alignment explanation
Indices: 28743519--28743591 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
28743509 CTTAATTTAC
* * *
28743519 AAAATTACTAAAATA-CCCTTGGTTTGT
1 AAAATTACTAAAATACCCCCTGATTTCT
28743546 AAAATTACTAAAATACCCCCTGATTTCT
1 AAAATTACTAAAATACCCCCTGATTTCT
*
28743574 AAAATTACTGAAATACCC
1 AAAATTACTAAAATACCC
28743592 TCGACTTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 15 0.37
28 26 0.63
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.32
Consensus pattern (28 bp):
AAAATTACTAAAATACCCCCTGATTTCT
Found at i:28743605 original size:28 final size:27
Alignment explanation
Indices: 28743519--28743888 Score: 155
Period size: 27 Copynumber: 13.7 Consensus size: 27
28743509 CTTAATTTAC
* *
28743519 AAAATTACTAAAATACCCTTGGTTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* *
28743546 AAAATTACTAAAATACCCCCTGATTTCT
1 AAAATTACTAAAATACCCTC-GATTTGT
* *
28743574 AAAATTACTGAAATACCCTCGACTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* * * *
28743601 AAAAATTACCAAAGTACCCTCGGTTTAT
1 -AAAATTACTAAAATACCCTCGATTTGT
**** * **
28743629 AAAATTACTGCTTTACCCTTGATTTAC
1 AAAATTACTAAAATACCCTCGATTTGT
* *** * *
28743656 AGAATTACTATTTTACCCT-TAATT-T
1 AAAATTACTAAAATACCCTCGATTTGT
* *** *
28743681 ACAAATTACCATTTTACCCTC-AATTGT
1 A-AAATTACTAAAATACCCTCGATTTGT
* * **
28743708 GAAATTACTAAAATACCCT-TATAGGGT
1 AAAATTACTAAAATACCCTCGAT-TTGT
* * *
28743735 AAAATTACCAAAACACCC-CTAGTTTGT
1 AAAATTACTAAAATACCCTCGA-TTTGT
* *
28743762 AAAATTA-TCAAAATACCAGT-GGTTTGT
1 AAAATTACT-AAAATACC-CTCGATTTGT
* ** *
28743789 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* **
28743816 AAAATTACCAAAATACCC-CTGATTTAC
1 AAAATTACTAAAATACCCTC-GATTTGT
*
28743843 AAAATTA-TAGAAATACCCTTGATTTGT
1 AAAATTACTA-AAATACCCTCGATTTGT
* * * *
28743870 AGATTTACCAAAACACCCT
1 AAAATTACTAAAATACCCT
28743889 TATAGGATGA
Statistics
Matches: 258, Mismatches: 67, Indels: 36
0.71 0.19 0.10
Matches are distributed among these distances:
25 1 0.00
26 41 0.16
27 170 0.66
28 46 0.18
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTCGATTTGT
Found at i:28743647 original size:55 final size:55
Alignment explanation
Indices: 28743513--28743638 Score: 146
Period size: 55 Copynumber: 2.3 Consensus size: 55
28743503 TTTACCCTTA
* * * ** *
28743513 ATTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCCCTG
1 ATTTATAAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAATACCCCCTG
* * *
28743568 ATTTCTAAAATTACTGAAATACCCTCGACTTGTAAAAATTACCAAAGTACCCTC-G
1 ATTTATAAAATTACTGAAATACCCTCGACTTGT-AAAATTACCAAAATACCCCCTG
*
28743623 GTTTATAAAATTACTG
1 ATTTATAAAATTACTG
28743639 CTTTACCCTT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 42 0.71
56 17 0.29
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (55 bp):
ATTTATAAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAATACCCCCTG
Found at i:28743694 original size:26 final size:27
Alignment explanation
Indices: 28743640--28743705 Score: 98
Period size: 26 Copynumber: 2.5 Consensus size: 27
28743630 AAATTACTGC
* *
28743640 TTTACCCTTGATTTACAGAATTACTAT
1 TTTACCCTTAATTTACAGAATTACCAT
28743667 TTTACCCTTAATTTACA-AATTACCAT
1 TTTACCCTTAATTTACAGAATTACCAT
*
28743693 TTTACCCTCAATT
1 TTTACCCTTAATT
28743706 GTGAAATTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 20 0.56
27 16 0.44
ACGTcount: A:0.30, C:0.23, G:0.03, T:0.44
Consensus pattern (27 bp):
TTTACCCTTAATTTACAGAATTACCAT
Found at i:28743878 original size:81 final size:81
Alignment explanation
Indices: 28743733--28743888 Score: 183
Period size: 81 Copynumber: 1.9 Consensus size: 81
28743723 CCCTTATAGG
** *
28743733 GTAAAATTACCAAAACACCCCTAGTTTGTAAAATTATCAAAATACCAGTGGTTTGTGAAATTACC
1 GTAAAATTACCAAAACACCCCTAGTTTACAAAATTATCAAAATACCAGTGATTTGTGAAATTACC
* *
28743798 GAAATACCCTCAATTT
66 AAAACACCCTCAATTT
* ** *
28743814 GTAAAATTACCAAAATACCCCT-GATTTACAAAATTAT-AGAAATACCCTTGATTTGT-AGATTT
1 GTAAAATTACCAAAACACCCCTAG-TTTACAAAATTATCA-AAATACCAGTGATTTGTGA-AATT
28743876 ACCAAAACACCCT
63 ACCAAAACACCCT
28743889 TATAGGATGA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
80 3 0.05
81 60 0.95
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (81 bp):
GTAAAATTACCAAAACACCCCTAGTTTACAAAATTATCAAAATACCAGTGATTTGTGAAATTACC
AAAACACCCTCAATTT
Found at i:28744717 original size:20 final size:20
Alignment explanation
Indices: 28744692--28744778 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
28744682 GATATGATAT
*
28744692 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
28744712 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
*
28744732 ATATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
28744752 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
28744772 ACATGAT
1 ACATGAT
28744779 GTATTCATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:28744906 original size:52 final size:51
Alignment explanation
Indices: 28744828--28744963 Score: 206
Period size: 52 Copynumber: 2.7 Consensus size: 51
28744818 GAGGAAGTGC
28744828 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
* *
28744880 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCTAGTTTCCCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
*
28744931 AAAAAGGCTT-TGCCCCAG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAG-GGCT
28744964 AGGCCTCCAG
Statistics
Matches: 80, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
48 5 0.06
49 9 0.11
50 8 0.10
51 22 0.28
52 36 0.45
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCG
Found at i:28744925 original size:25 final size:26
Alignment explanation
Indices: 28744828--28744963 Score: 172
Period size: 26 Copynumber: 5.3 Consensus size: 26
28744818 GAGGAAGTGC
28744828 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
28744854 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
28744880 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* ***
28744906 AAAAGGGCTT-TGCCCTAGTTTCCCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
28744931 AAAAAGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
28744954 AAAAGAGGCT
1 AAAAG-GGCT
28744964 AGGCCTCCAG
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
23 4 0.04
24 6 0.06
25 27 0.28
26 58 0.61
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:28745155 original size:42 final size:42
Alignment explanation
Indices: 28745096--28745183 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
28745086 TAGTCTCCCC
* ** *
28745096 AAATAGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATAGGCTTGCATACATCCATTGACATTACATATGATATTG
*
28745138 AAATAGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATAGGCTTGCATACATCCATTGACATTACATATGATATTG
28745180 AAAT
1 AAAT
28745184 GGGCCTATGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (42 bp):
AAATAGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:28745246 original size:31 final size:31
Alignment explanation
Indices: 28745211--28745289 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
28745201 CGTTTACAGT
28745211 AAAGGCTTCGGCCCAGTGAAATCATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATCATTTATGA
* *
28745242 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATCATTTATGA
28745273 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
28745290 AACCGTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATCATTTATGA
Found at i:28751671 original size:7 final size:7
Alignment explanation
Indices: 28751656--28751689 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
28751646 TCAAGTAATT
*
28751656 CATTGAA
1 CATTTAA
28751663 CATTTAA
1 CATTTAA
28751670 CATTTAA
1 CATTTAA
28751677 CATTTAA
1 CATTTAA
28751684 CATTTA
1 CATTTA
28751690 CTAATATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (7 bp):
CATTTAA
Found at i:28757693 original size:25 final size:25
Alignment explanation
Indices: 28757650--28757697 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28757640 TTATAACATG
* * *
28757650 AAAATGACCATTTTGCCCCTAGGTA
1 AAAATGACCAATATACCCCTAGGTA
28757675 AAAATGACCAATATACCCCTAGG
1 AAAATGACCAATATACCCCTAGG
28757698 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (25 bp):
AAAATGACCAATATACCCCTAGGTA
Found at i:28757781 original size:11 final size:11
Alignment explanation
Indices: 28757745--28757800 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
28757735 CATGGTATGT
28757745 ATGATATGCAC
1 ATGATATGCAC
* *
28757756 ATGACATG--T
1 ATGATATGCAC
28757765 ATGATATGCAC
1 ATGATATGCAC
*
28757776 ATGATATG--T
1 ATGATATGCAC
28757785 ATGATATGCAC
1 ATGATATGCAC
28757796 ATGAT
1 ATGAT
28757801 GTATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:28757800 original size:20 final size:20
Alignment explanation
Indices: 28757734--28757800 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
28757724 ATTTTGATAA
*
28757734 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
28757754 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
28757774 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
28757794 ACATGAT
1 ACATGAT
28757801 GTATTCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:28757877 original size:24 final size:23
Alignment explanation
Indices: 28757850--28758040 Score: 233
Period size: 24 Copynumber: 8.0 Consensus size: 23
28757840 GAGGAAGTGG
28757850 AAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
* *
28757873 CAAAAGGGCTTACGCCCTAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
28757897 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
28757920 AAAAAGGGCTTATGCCCCAATTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
28757944 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
28757968 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
28757991 AAAAAGGGC-TATTGCCCCAGTTATT
1 -AAAAGGGCTTA-TGCCCCAGTTA-T
*
28758016 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
28758040 A
1 A
28758041 TGATAAAGCA
Statistics
Matches: 147, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
23 43 0.29
24 91 0.62
25 13 0.09
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:28757925 original size:47 final size:47
Alignment explanation
Indices: 28757850--28758040 Score: 235
Period size: 47 Copynumber: 4.0 Consensus size: 47
28757840 GAGGAAGTGG
* *
28757850 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCTAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATA
* * *
28757897 TAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAATTATC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATA
* *
28757945 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATA
*
28757992 AAAAGGGC-TATTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAGGGCTTA-TGCCCCAGTTA-TAAAAG-GGCTTATGCC-CCAGTTATA
28758041 TGATAAAGCA
Statistics
Matches: 126, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
46 2 0.02
47 81 0.64
48 31 0.25
49 12 0.10
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATA
Found at i:28757966 original size:71 final size:71
Alignment explanation
Indices: 28757850--28758039 Score: 303
Period size: 71 Copynumber: 2.7 Consensus size: 71
28757840 GAGGAAGTGG
*
28757850 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCTAGTTATTAAAGGGCTTATGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCA
28757915 GTTATA
66 GTTATA
*
28757921 AAAAGGGCTTATGCCCCAATTATCAAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCA
28757986 GTTATA
66 GTTATA
* *
28757992 AAAAGGGC-TATTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAGGGCTTA-TGCCCCAGTTATCAAAAG-GGCTTACGCC-CCAGTTAT
28758040 ATGATAAAGC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
70 2 0.02
71 98 0.88
72 11 0.10
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCA
GTTATA
Found at i:28758268 original size:31 final size:31
Alignment explanation
Indices: 28758233--28758296 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
28758223 CGTTTACAGT
*
28758233 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
28758264 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
28758295 AA
1 AA
28758297 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:28765941 original size:20 final size:20
Alignment explanation
Indices: 28765916--28765973 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
28765906 AAACACGGTT
28765916 TGTATGATATGCACATGACA
1 TGTATGATATGCACATGACA
* *
28765936 TGTATGATATGCACATAATA
1 TGTATGATATGCACATGACA
28765956 TGTATGATATGCACATGA
1 TGTATGATATGCACATGA
28765974 TGTATTCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
TGTATGATATGCACATGACA
Found at i:28766051 original size:24 final size:24
Alignment explanation
Indices: 28766024--28766117 Score: 118
Period size: 24 Copynumber: 4.0 Consensus size: 24
28766014 GAGGAAGTGG
*
28766024 AAAAGGGATTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
28766048 AAAAGGGCTTACGCCCTAGATAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
28766071 TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
* *
28766095 AAAAAGGCTTATGCCCCATTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
28766118 ATGAAAGGAG
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 19 0.33
24 39 0.67
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:28766124 original size:24 final size:24
Alignment explanation
Indices: 28766032--28766234 Score: 112
Period size: 24 Copynumber: 8.9 Consensus size: 24
28766022 GGAAAAGGGA
*
28766032 TTATGCCCCAGTTATCA-AAAGGGC
1 TTATGCCCCAGTTAT-ATAAAAGGC
* * * *
28766056 TTACGCCCTAGATAT-TAAAGGGC
1 TTATGCCCCAGTTATATAAAAGGC
28766079 TTATGCCCCAGTTATCA-AAAAGGC
1 TTATGCCCCAGTTAT-ATAAAAGGC
* *
28766103 TTATGCCCCATTTATATGAAAGG-
1 TTATGCCCCAGTTATATAAAAGGC
** ** * *
28766126 --A-G--GAAG-TGGA-AAAGGGA
1 TTATGCCCCAGTTATATAAAAGGC
*
28766143 TTATGCCCCAGTTATCA-AAAGGGC
1 TTATGCCCCAGTTAT-ATAAAAGGC
* *
28766167 TTACGCCCCAGTTAT-TAAAGGGC
1 TTATGCCCCAGTTATATAAAAGGC
28766190 TTATGCCCCAGTTATA-AAAAGGGC
1 TTATGCCCCAGTTATATAAAA-GGC
*
28766214 TTTTGCCCCAGTTAT-TAAAAG
1 TTATGCCCCAGTTATATAAAAG
28766235 AGGCTAGGCC
Statistics
Matches: 138, Mismatches: 25, Indels: 33
0.70 0.13 0.17
Matches are distributed among these distances:
16 4 0.03
17 2 0.01
18 1 0.01
19 1 0.01
20 2 0.01
21 1 0.01
22 2 0.01
23 46 0.33
24 79 0.57
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (24 bp):
TTATGCCCCAGTTATATAAAAGGC
Found at i:28766190 original size:23 final size:24
Alignment explanation
Indices: 28766135--28766254 Score: 145
Period size: 24 Copynumber: 5.0 Consensus size: 24
28766125 GAGGAAGTGG
* *
28766135 AAAAGGGATTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATA
*
28766159 AAAAGGGCTTACGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATA
*
28766182 TAAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATA
* *
28766206 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATA
*
28766230 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
28766255 TGATAAAGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
23 21 0.25
24 51 0.61
25 11 0.13
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATA
Found at i:28766196 original size:111 final size:111
Alignment explanation
Indices: 28766002--28766228 Score: 402
Period size: 111 Copynumber: 2.0 Consensus size: 111
28765992 GGGTTGGGTT
*
28766002 TTTATATGAAAGGAGGAAGTGGAAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTACGCCCTAG
1 TTTATATGAAAGGAGGAAGTGGAAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAG
28766067 ATATTAAAGGGCTTATGCCCCAGTTATCAAAAA-GGCTTATGCCCCA
66 ATATTAAAGGGCTTATGCCCCAGTTAT-AAAAAGGGCTTATGCCCCA
28766113 TTTATATGAAAGGAGGAAGTGGAAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAG
1 TTTATATGAAAGGAGGAAGTGGAAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAG
* *
28766178 TTATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCA
66 ATATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
*
28766224 GTTAT
1 TTTAT
28766229 TAAAAGAGGC
Statistics
Matches: 111, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
110 5 0.05
111 106 0.95
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (111 bp):
TTTATATGAAAGGAGGAAGTGGAAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAG
ATATTAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCA
Found at i:28766210 original size:47 final size:48
Alignment explanation
Indices: 28766135--28766254 Score: 163
Period size: 47 Copynumber: 2.5 Consensus size: 48
28766125 GAGGAAGTGG
* *
28766135 AAAAGGGATTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTACGCCCCAGTTATT
**
28766183 -AAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTACGCCCCAGTTATT
*
28766230 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
28766255 TGATAAAGCA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
47 43 0.67
48 9 0.14
49 12 0.19
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTACGCCCCAGTTATT
Found at i:28766503 original size:31 final size:31
Alignment explanation
Indices: 28766447--28766510 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
28766437 CATTTACAGT
*
28766447 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
** *
28766478 AAAGGCTTCGGCCCAGTGTTGTGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
28766509 AA
1 AA
28766511 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:28768815 original size:15 final size:16
Alignment explanation
Indices: 28768785--28768816 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28768775 CACCTAAATG
28768785 ACATAATGATTTGCCA
1 ACATAATGATTTGCCA
28768801 ACATAATGA-TTGCCA
1 ACATAATGATTTGCCA
28768816 A
1 A
28768817 TAGAGCAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (16 bp):
ACATAATGATTTGCCA
Found at i:28771874 original size:43 final size:43
Alignment explanation
Indices: 28771826--28771966 Score: 137
Period size: 43 Copynumber: 3.3 Consensus size: 43
28771816 GTCCCAGGTG
*
28771826 TGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGACA
1 TGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACA
* * * * *
28771869 AGGTCTTACACGAAATCAAATAT-GATGTCGA-TGTCCCAAACT
1 TGGTCTTACACGTAATCAAATATCGATG-CCACTGTCCCAGACA
* * *
28771911 TGGTCTTACACGTAAATCATAA-GTCAATGCCAAC-GTCCCAGACG
1 TGGTCTTACACGT-AATCA-AATATCGATGCC-ACTGTCCCAGACA
28771955 TGGTCTTACACG
1 TGGTCTTACACG
28771967 AAAACACATA
Statistics
Matches: 79, Mismatches: 13, Indels: 11
0.77 0.13 0.11
Matches are distributed among these distances:
42 24 0.30
43 29 0.37
44 26 0.33
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
TGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACA
Found at i:28772356 original size:8 final size:8
Alignment explanation
Indices: 28772343--28772367 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28772333 AAATTTGCCC
28772343 TCACATTT
1 TCACATTT
28772351 TCACATTT
1 TCACATTT
28772359 TCACATTT
1 TCACATTT
28772367 T
1 T
28772368 TGCACTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCACATTT
Found at i:28780261 original size:21 final size:19
Alignment explanation
Indices: 28780232--28780270 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
28780222 TTATAACCCA
*
28780232 TAATTATTTTCACGAAATTTT
1 TAATGATTTTC-C-AAATTTT
28780253 TAATGATTTTCCAAATTT
1 TAATGATTTTCCAAATTT
28780271 AAGACAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (19 bp):
TAATGATTTTCCAAATTTT
Done.