Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006214.1 Hibiscus syriacus cultivar Beakdansim tig00014805_pilon, whole genome shotgun sequence
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: 76439
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11982 original size:16 final size:16
Alignment explanation
Indices: 11961--11991 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11951 CTTATATATT
11961 ATTTTTTAATTAAATC
1 ATTTTTTAATTAAATC
*
11977 ATTTTTTTATTAAAT
1 ATTTTTTAATTAAAT
11992 AAAATAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTTAATTAAATC
Found at i:19134 original size:15 final size:15
Alignment explanation
Indices: 19110--19147 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
19100 AGAGGACGAT
*
19110 AATGAAGAAGAAGATG
1 AATGATGAAGAAGA-G
19126 -ATGATGAAGAAGAG
1 AATGATGAAGAAGAG
19140 AATGATGA
1 AATGATGA
19148 TGACGATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.95
ACGTcount: A:0.53, C:0.00, G:0.32, T:0.16
Consensus pattern (15 bp):
AATGATGAAGAAGAG
Found at i:19134 original size:18 final size:18
Alignment explanation
Indices: 19111--19150 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
19101 GAGGACGATA
19111 ATGAAGAAGA-AGATGATG
1 ATGAAGAAGAGA-ATGATG
19129 ATGAAGAAGAGAATGATG
1 ATGAAGAAGAGAATGATG
19147 ATGA
1 ATGA
19151 CGATGGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (18 bp):
ATGAAGAAGAGAATGATG
Found at i:30834 original size:15 final size:15
Alignment explanation
Indices: 30814--30845 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
30804 CAGATTAGTG
30814 AGAAAGCGAAATAAA
1 AGAAAGCGAAATAAA
30829 AGAAAGCGAAATAAA
1 AGAAAGCGAAATAAA
30844 AG
1 AG
30846 CGGAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.66, C:0.06, G:0.22, T:0.06
Consensus pattern (15 bp):
AGAAAGCGAAATAAA
Found at i:34262 original size:71 final size:71
Alignment explanation
Indices: 34146--34290 Score: 281
Period size: 71 Copynumber: 2.0 Consensus size: 71
34136 CATGAAACAT
34146 GATTTGCCATTGCTAGGTTAAAACATAATATTCGAAATCCTTGAAGGGTAATAGTCTGAACAGTT
1 GATTTGCCATTGCTAGGTTAAAACATAATATTCGAAATCCTTGAAGGGTAATAGTCTGAACAGTT
34211 AAAAGC
66 AAAAGC
*
34217 GATTTGTCATTGCTAGGTTAAAACATAATATTCGAAATCCTTGAAGGGTAATAGTCTGAACAGTT
1 GATTTGCCATTGCTAGGTTAAAACATAATATTCGAAATCCTTGAAGGGTAATAGTCTGAACAGTT
34282 AAAAGC
66 AAAAGC
34288 GAT
1 GAT
34291 ATAAAATGGA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (71 bp):
GATTTGCCATTGCTAGGTTAAAACATAATATTCGAAATCCTTGAAGGGTAATAGTCTGAACAGTT
AAAAGC
Found at i:35276 original size:21 final size:21
Alignment explanation
Indices: 35243--35289 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
35233 AATTTATAAA
*
35243 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
35264 TCGCGTTGTGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
35285 TCGCA
1 TCGCA
35290 ACGCGATAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:35344 original size:20 final size:20
Alignment explanation
Indices: 35280--35375 Score: 113
Period size: 20 Copynumber: 4.8 Consensus size: 20
35270 TGTGATTTTC
*
35280 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
* * *
35300 CAAAGTCTCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
35320 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * **
35340 CAAATTCGTAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
35359 CAAATTCGCAACGCGAA
1 CAAATTCGCAACGCGAA
35376 TTTAATTTCG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.23
20 49 0.77
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:35378 original size:20 final size:20
Alignment explanation
Indices: 35179--35389 Score: 103
Period size: 20 Copynumber: 10.6 Consensus size: 20
35169 AATGACCAAT
*
35179 AAATTCGTAACGCGAA-TTC
1 AAATTCGCAACGCGAATTTC
* * *
35198 TAATTTCGCAACTC-AATTTTT
1 -AAATTCGCAACGCGAA-TTTC
*
35219 AATTTCGCAACGCGAATTT-
1 AAATTCGCAACGCGAATTTC
* ** *
35238 ATAAATCGCATTGCGATTTTTC
1 A-AATTCGCAACGCGA-ATTTC
*** * *
35260 AAATTCGCGTTGTGATTTTCC
1 AAATTCGCAACGCGAATTT-C
*
35281 AAATTCGCAACGCG-ATAGTC
1 AAATTCGCAACGCGAAT-TTC
* * *
35301 AAAGTCTCAACGCG-ATAGTC
1 AAATTCGCAACGCGAAT-TTC
**
35321 AAATTCGCAACGCGAAAGTC
1 AAATTCGCAACGCGAATTTC
* *
35341 AAATTCGTAAC-TGAATTTC
1 AAATTCGCAACGCGAATTTC
35360 AAATTCGCAACGCGAATTT-
1 AAATTCGCAACGCGAATTTC
*
35379 AATTTCGCAAC
1 AAATTCGCAAC
35390 AGGTTTTAGT
Statistics
Matches: 150, Mismatches: 31, Indels: 21
0.74 0.15 0.10
Matches are distributed among these distances:
19 28 0.19
20 90 0.60
21 31 0.21
22 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (20 bp):
AAATTCGCAACGCGAATTTC
Found at i:36156 original size:12 final size:12
Alignment explanation
Indices: 36135--36169 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
36125 ACCATATTTC
*
36135 CAATACCAAACA
1 CAATATCAAACA
36147 CAATATCAAACA
1 CAATATCAAACA
*
36159 CAATCTCAAAC
1 CAATATCAAAC
36170 CCCACAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.14
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:36310 original size:24 final size:24
Alignment explanation
Indices: 36280--36335 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
36270 GTGAGTACTA
**
36280 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACCCGAAATTTGATCTTG
* *
36304 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACCCGAAATTTGATCTTG
*
36328 ATCAATAC
1 GTCAATAC
36336 TCGGATTTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (24 bp):
GTCAATACCCGAAATTTGATCTTG
Found at i:36340 original size:24 final size:24
Alignment explanation
Indices: 36294--36347 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
36284 ATATTCGAAA
*
36294 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGATCAATACCCGGAC
* *
36318 TTTGATCTTGATCAATACTCGGAT
1 TTTGATCTTGATCAATACCCGGAC
36342 TTTGAT
1 TTTGAT
36348 GATATGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGATCAATACCCGGAC
Found at i:37355 original size:18 final size:18
Alignment explanation
Indices: 37334--37370 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
37324 GTAATTGGAG
37334 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
37352 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
37370 T
1 T
37371 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:37377 original size:24 final size:24
Alignment explanation
Indices: 37326--37378 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
37316 TTTCATATGT
* * *
37326 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
37350 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
37374 AATTT
1 AATTT
37379 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:38107 original size:14 final size:14
Alignment explanation
Indices: 38088--38127 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
38078 ATAATTCTTA
38088 TTTACAAATCAACT
1 TTTACAAATCAACT
38102 TTTACAAATCAACT
1 TTTACAAATCAACT
38116 TTTACAAATCAA
1 TTTACAAATCAA
38128 TTAATCAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (14 bp):
TTTACAAATCAACT
Found at i:38170 original size:61 final size:62
Alignment explanation
Indices: 38039--38178 Score: 176
Period size: 61 Copynumber: 2.2 Consensus size: 62
38029 TTTTAGAAAC
*
38039 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACAAATCAACTTT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAATAAATCTTATTTACAAATCAACTTT
* * * **
38104 TACAAATCAACTTTTACAAATCAATT-AATCAAAAAATAAATCTTATTTCCTCATCAA-TTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACAAATCAACTT-T
38165 AACAAATCAACTTT
1 AACAAATCAACTTT
38179 CAATGTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
60 2 0.03
61 40 0.60
65 25 0.37
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.33
Consensus pattern (62 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACAAATCAACTTT
Found at i:39649 original size:21 final size:21
Alignment explanation
Indices: 39596--39654 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
39586 GGCTTCTTCG
*
39596 ATGATGATAGGGGCATCTTAA
1 ATGATGATAGGTGCATCTTAA
* * * * *
39617 ACGATAAGAGGTGCCTCTTGA
1 ATGATGATAGGTGCATCTTAA
39638 ATGATGATAGGTGCATC
1 ATGATGATAGGTGCATC
39655 GGGCTTATTA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (21 bp):
ATGATGATAGGTGCATCTTAA
Found at i:41489 original size:14 final size:14
Alignment explanation
Indices: 41470--41505 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
41460 ATACCAAAAA
41470 ACTACAAATTATAC
1 ACTACAAATTATAC
41484 ACTACAAATTATAC
1 ACTACAAATTATAC
41498 ACTACAAA
1 ACTACAAA
41506 CAGACATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (14 bp):
ACTACAAATTATAC
Found at i:42174 original size:22 final size:22
Alignment explanation
Indices: 42146--42196 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
42136 GATGGAGATA
42146 GACGGATTTCGTCGGAAATGGG
1 GACGGATTTCGTCGGAAATGGG
*
42168 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAAATGGG
42190 GACGGAT
1 GACGGAT
42197 ATCGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAAATGGG
Found at i:46986 original size:16 final size:16
Alignment explanation
Indices: 46965--47002 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
46955 AAAAATAATT
46965 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
46981 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
46997 T-ATAAA
1 TAATAAA
47003 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:46986 original size:24 final size:21
Alignment explanation
Indices: 46935--46984 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
46925 ATATATATAT
*
46935 ATAATAATTATAATAACGAAAA
1 ATAATAATT-TAATAAAGAAAA
*
46957 A-AATAATTTAATAAAGTAAA
1 ATAATAATTTAATAAAGAAAA
46977 ATAATAAT
1 ATAATAAT
46985 AATGTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.44
21 13 0.52
22 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
ATAATAATTTAATAAAGAAAA
Found at i:47737 original size:35 final size:37
Alignment explanation
Indices: 47657--47756 Score: 107
Period size: 35 Copynumber: 2.8 Consensus size: 37
47647 GTGCTTGTGG
* * * **
47657 ATCCTATCTTTAG-GAGTTTAAAACATAGCAAAATTAT
1 ATCCTAT-TTTAGAGAGTTTGAATCCTAGCTGAATTAT
*
47694 ATCCTATTTTAG-GAG-TTGAATCCTAGCTGAATTCT
1 ATCCTATTTTAGAGAGTTTGAATCCTAGCTGAATTAT
*
47729 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAGAGAGTTTGAATCCTAG
47757 TAGGACGAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 25 0.46
36 11 0.20
37 18 0.33
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTAGAGAGTTTGAATCCTAGCTGAATTAT
Found at i:48516 original size:106 final size:102
Alignment explanation
Indices: 48217--48718 Score: 498
Period size: 106 Copynumber: 4.9 Consensus size: 102
48207 AATATTGTTC
* * *
48217 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAA-TGAGAAA-T-TTTGTTGACA
* * * * *
48282 GTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
62 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
* * * * * *
48323 CGAGTCTAATATCATTCGCTGTGAAGATGAAATTGACTCTGAA--CGAAATCTTGTTGACAATCA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAGAAATTTTGTTGACAATCA
* * *
48386 GCCGTCCCTTCATTATGAAGTTGAACTTGTGTTGTCT
66 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
* *
48423 CGAGTCCAATATCCTTCGTTGCGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AA--TGAGAAAT-TTTGTTGACA
* *
48488 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
62 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
** * * *
48529 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGTTTGGCTC-----CA-AAATTGCTTGTCGACATT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAGAAATT--TTGTTGACAAT
* * *
48588 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
64 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
* * * * * *
48627 TGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AA-TGAGAAATT-TTGTTGACAA
* *
48692 CCAGCCGTCTCTTCGTTGTGAAGTTGA
63 TCAGCCGTCCCTTCGTTGTGAAGTTGA
48719 GATTGGCTCC
Statistics
Matches: 325, Mismatches: 55, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
96 1 0.00
97 4 0.01
98 76 0.23
100 77 0.24
101 3 0.01
102 4 0.01
105 39 0.12
106 121 0.37
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (102 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAGAAATTTTGTTGACAATCA
GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
Found at i:48812 original size:160 final size:160
Alignment explanation
Indices: 48541--48878 Score: 595
Period size: 160 Copynumber: 2.1 Consensus size: 160
48531 AGTCCAATAT
* * *
48541 CCTTCGCTGTGAAGTTGAGTTTGGCTCCAAAATTGCTTGTCGACATTCAGCCGCCCCTTCGCTGT
1 CCTTCGTTGTGAAGTTGAGATTGGCTCCAAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
48606 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAA
66 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAA
*
48671 CTGGGAAATTATTGTTGACAACCAGCCGTC
131 CTGGGAAATTATTGTTGACAACCAACCGTC
* * * *
48701 TCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGTTTGTTGACAGTCAGCCGCCCCTTCGCTGT
1 CCTTCGTTGTGAAGTTGAGATTGGCTCCAAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
*
48766 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCCCTGAAA
66 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAA
48831 CTGGGAAATTATTGTTGACAACCAACCGTC
131 CTGGGAAATTATTGTTGACAACCAACCGTC
48861 CCTTCGTTGTGAAGTTGA
1 CCTTCGTTGTGAAGTTGA
48879 ACTTGTGTTG
Statistics
Matches: 168, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
160 168 1.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.33
Consensus pattern (160 bp):
CCTTCGTTGTGAAGTTGAGATTGGCTCCAAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAAATTGGCCCTGAAA
CTGGGAAATTATTGTTGACAACCAACCGTC
Found at i:48925 original size:105 final size:105
Alignment explanation
Indices: 48737--48926 Score: 272
Period size: 105 Copynumber: 1.8 Consensus size: 105
48727 CCGAAATTGT
** * * * *
48737 TTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCT
1 TTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCT
* *
48802 TCGTTGTGAAGTTAAAATTGGCCCTGAAACTGGGAAATTA
66 TCGCTGTGAAGTCAAAATTGGCCCTGAAACTGGGAAATTA
* * *
48842 TTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCT
1 TTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCT
*
48907 TCGCTGTGAAGTCGAAATTG
66 TCGCTGTGAAGTCAAAATTG
48927 ACTCTAGCTA
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
105 73 1.00
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (105 bp):
TTGTTGACAACCAACCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCT
TCGCTGTGAAGTCAAAATTGGCCCTGAAACTGGGAAATTA
Found at i:49484 original size:65 final size:65
Alignment explanation
Indices: 49380--49545 Score: 278
Period size: 65 Copynumber: 2.6 Consensus size: 65
49370 GACAAAATTT
* *
49380 TGTTTTAAGAGAAACTGTCTCAAGAGAGACGAAGTTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
49445 TGTTTCAAGAGAAACTATCTCAAGAGAGATGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
49510 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
49546 TTGTTTCGAG
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 93 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:49551 original size:102 final size:102
Alignment explanation
Indices: 49445--49884 Score: 756
Period size: 102 Copynumber: 4.3 Consensus size: 102
49435 TCAATGTTTA
* **
49445 TGTTTCAAGAGAAACTATCTCAAGAGAGATGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
49510 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
49547 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
49612 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
49649 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
49714 TGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
49751 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
49816 TGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * *
49852 TTTTTTAAGGGAAACTGTCTCAAGAGAGACAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAA
49885 GTTTGTTTTA
Statistics
Matches: 319, Mismatches: 19, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
101 35 0.11
102 284 0.89
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:49561 original size:37 final size:37
Alignment explanation
Indices: 49510--49919 Score: 242
Period size: 36 Copynumber: 11.9 Consensus size: 37
49500 TCAATGTTTA
* *
49510 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
49547 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
49583 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
49611 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
49649 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * **
49685 TATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* **
49713 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACGGAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAAAATTT
* *
49751 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
49787 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
49815 ATGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* * *
49852 TTTTTTAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
49888 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
49920 TGGTGAGCAC
Statistics
Matches: 279, Mismatches: 55, Indels: 78
0.68 0.13 0.19
Matches are distributed among these distances:
27 3 0.01
28 5 0.02
29 40 0.14
30 11 0.04
32 2 0.01
33 2 0.01
34 2 0.01
35 8 0.03
36 106 0.38
37 93 0.33
38 7 0.03
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:50803 original size:22 final size:22
Alignment explanation
Indices: 50777--50827 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
50767 TTGTGTTTGG
50777 TCAAAGGTTTGGCATTTAATGC
1 TCAAAGGTTTGGCATTTAATGC
* *
50799 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTAATGC
50821 TCAAAGG
1 TCAAAGG
50828 ATTGATGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTAATGC
Found at i:51460 original size:20 final size:21
Alignment explanation
Indices: 51437--51496 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
51427 TTTGTCCCTT
*
51437 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
51457 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
*
51478 TTTTTTGCTTCTT-TTCTTT
1 TTTTTT-ATTCTTGTTCTTT
51497 TTTCTTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 16 0.48
21 12 0.36
22 5 0.15
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:51507 original size:22 final size:22
Alignment explanation
Indices: 51453--51505 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
51443 ATTTTTGTTC
51453 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
51474 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
51497 TTTCTTTTT
1 TTTCTTTTT
51506 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:53417 original size:5 final size:5
Alignment explanation
Indices: 53407--53434 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
53397 GCAAGTGATG
53407 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
53435 GATGAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:54873 original size:24 final size:22
Alignment explanation
Indices: 54823--54881 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
54813 ATATATATAT
*
54823 ATAATAATATAATAACGAAAAA
1 ATAATAATATAATAAAGAAAAA
*
54845 A-AATAATTTAATAAAGTAAAATA
1 ATAATAATATAATAAAG-AAAA-A
*
54868 ATAATAATGTAATA
1 ATAATAATATAATA
54882 TAATATAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 5 0.16
23 2 0.06
24 11 0.35
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (22 bp):
ATAATAATATAATAAAGAAAAA
Found at i:54874 original size:16 final size:16
Alignment explanation
Indices: 54853--54890 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
54843 AAAAATAATT
54853 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
54869 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
54885 T-ATAAA
1 TAATAAA
54891 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:55079 original size:15 final size:15
Alignment explanation
Indices: 55059--55101 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
55049 TTAATAGTAC
55059 AATAATAATAAATAT
1 AATAATAATAAATAT
*
55074 AATAATTATAAATAT
1 AATAATAATAAATAT
55089 ATATATATAATAA
1 A-ATA-ATAATAA
55102 CTTTAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 15 0.62
16 3 0.12
17 6 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATAATAATAAATAT
Found at i:55615 original size:35 final size:36
Alignment explanation
Indices: 55545--55644 Score: 121
Period size: 35 Copynumber: 2.8 Consensus size: 36
55535 GTGCTTGTGG
* * *
55545 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
55582 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
* *
55617 ATCATATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
55645 TAAGACGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 26 0.47
36 11 0.20
37 18 0.33
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:55819 original size:15 final size:15
Alignment explanation
Indices: 55801--55843 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
55791 ATTAGAAGAG
**
55801 ATAAAATTTATTTTA
1 ATAAAATTTAAATTA
*
55816 ATAATATTTAAATTA
1 ATAAAATTTAAATTA
55831 ATAAAAATTTAAA
1 AT-AAAATTTAAA
55844 ATGTTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAAATTTAAATTA
Found at i:61206 original size:15 final size:15
Alignment explanation
Indices: 61186--61218 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
61176 CGTAGGACCC
61186 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
61201 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
61216 CTA
1 CTA
61219 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:61367 original size:23 final size:26
Alignment explanation
Indices: 61330--61398 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
61320 TTCTCTTGTG
61330 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
61354 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
61379 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
61399 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:61380 original size:12 final size:12
Alignment explanation
Indices: 61363--61398 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
61353 TATCATGTTC
61363 TCATATCACATG
1 TCATATCACATG
*
61375 TCATATCACATA
1 TCATATCACATG
61387 TCATATCACATG
1 TCATATCACATG
61399 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:61818 original size:64 final size:63
Alignment explanation
Indices: 61748--61891 Score: 191
Period size: 64 Copynumber: 2.3 Consensus size: 63
61738 CATAAAAGGT
** * * *
61748 ATTCGATGTATTATTATTGCTGGGATGCATCGATGTACTCCTTATGCATCGATGCACCAATTGC
1 ATTCGATGT-TTATTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
* **
61812 ATTCGATGTTTCATTATTAATGGGATGCATCGATGCACTACTTATATATCGATGCATGAATTGC
1 ATTCGATGTTT-ATTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
61876 ATTCGATGTTT-TTATT
1 ATTCGATGTTTATTATT
61892 TTAAAAGAGT
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
62 5 0.07
63 2 0.03
64 64 0.90
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (63 bp):
ATTCGATGTTTATTATTAATGGGATGCATCGATGCACTACTTATACATCGATGCACCAATTGC
Found at i:61927 original size:64 final size:64
Alignment explanation
Indices: 61771--61933 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 64
61761 TTATTGCTGG
* * *
61771 GATGCATCGATGTACT-CCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGG
1 GATGCATCGATGCACTACC-TATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
* ** ** *
61835 GATGCATCGATGCACTACTTATATATCGATGCATGAATTGCATTCGATGTTTTTATT-TTAAA-A
1 GATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATTAAAGA
* *
61898 GAGTGCATCGATGCACTACCAATGCATCGATACACC
1 GA-TGCATCGATGCACTACCTATGCATCGATGCACC
61934 TTCAAACAAT
Statistics
Matches: 80, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
63 2 0.03
64 71 0.89
65 7 0.09
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (64 bp):
GATGCATCGATGCACTACCTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGA
Found at i:65107 original size:21 final size:21
Alignment explanation
Indices: 65081--65136 Score: 70
Period size: 15 Copynumber: 3.0 Consensus size: 21
65071 ACGGTGAAAA
65081 GTGCATTCGTAAAAGCAGCTG
1 GTGCATTCGTAAAAGCAGCTG
65102 GTGCATTCGT---A--A-CTG
1 GTGCATTCGTAAAAGCAGCTG
65117 GTGCATTCGTAAAAGCAGCT
1 GTGCATTCGTAAAAGCAGCT
65137 CGAGTGTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
15 13 0.45
16 1 0.03
18 2 0.07
20 1 0.03
21 12 0.41
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (21 bp):
GTGCATTCGTAAAAGCAGCTG
Found at i:68162 original size:15 final size:15
Alignment explanation
Indices: 68142--68174 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
68132 CGTAGGACCC
68142 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
68157 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
68172 CTA
1 CTA
68175 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:68323 original size:23 final size:26
Alignment explanation
Indices: 68286--68354 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
68276 TTCTCTTGTG
68286 ATCATGTATCTCATATCAC-T-TCAT
1 ATCATGTATCTCATATCACATGTCAT
68310 ATCATGT-TCTCATATCACATGTCAT
1 ATCATGTATCTCATATCACATGTCAT
* *
68335 ATCA--CATATCATATCACATG
1 ATCATGTATCTCATATCACATG
68355 AACATATATA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 21 0.52
25 8 0.20
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.38
Consensus pattern (26 bp):
ATCATGTATCTCATATCACATGTCAT
Found at i:68336 original size:12 final size:12
Alignment explanation
Indices: 68319--68354 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
68309 TATCATGTTC
68319 TCATATCACATG
1 TCATATCACATG
*
68331 TCATATCACATA
1 TCATATCACATG
68343 TCATATCACATG
1 TCATATCACATG
68355 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:68794 original size:64 final size:63
Alignment explanation
Indices: 68662--68883 Score: 214
Period size: 64 Copynumber: 3.5 Consensus size: 63
68652 TAATGAAGGT
* * ** * **
68662 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-AAAATTGCATTCGATGT-TTATTATTAATGGG
* **
68727 ATGCATCGATGCACTTCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTGCATTCGATGTTT-ATTATTAATGGG
* ** * **
68791 ATGCATCGATGCACTACTTATGGATCGATGCATGAATTACATTCGATGTTT-TTATTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTGCATTCGATGTTTATTA--TTAATGGG
**
68854 AGTGCATCGATGCACTACCAATGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
68884 ACACCTTCAA
Statistics
Matches: 133, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
62 3 0.02
63 4 0.03
64 97 0.73
65 29 0.22
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTGCATTCGATGTTTATTATTAATGGG
Found at i:69784 original size:42 final size:42
Alignment explanation
Indices: 69722--69803 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
69712 GAATATATGA
** * * * *
69722 GAACAAGATATAAGTTATGTGATATGATCTACGTGTTTACAT
1 GAACAAGATATAAGCCATGTGACATAACCTACGTGATTACAT
*
69764 GAACATGATATAAGCCATGTGACATAACCTACGTGATTAC
1 GAACAAGATATAAGCCATGTGACATAACCTACGTGATTAC
69804 TTGTCTATGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (42 bp):
GAACAAGATATAAGCCATGTGACATAACCTACGTGATTACAT
Found at i:69953 original size:23 final size:23
Alignment explanation
Indices: 69915--69979 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
69905 CTACGCGATC
**
69915 CTTCGGGACAAATCTACGTGGTCA
1 CTTCGGGACATTTCTACGTGG-CA
*
69939 -TTCGGGACATTTCTATGTGGCA
1 CTTCGGGACATTTCTACGTGGCA
69961 CTTCGGTG-CAATTTCTACG
1 CTTCGG-GAC-ATTTCTACG
69980 CGACACTTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 2 0.06
23 23 0.68
24 9 0.26
ACGTcount: A:0.20, C:0.23, G:0.25, T:0.32
Consensus pattern (23 bp):
CTTCGGGACATTTCTACGTGGCA
Found at i:74017 original size:58 final size:58
Alignment explanation
Indices: 73954--74073 Score: 222
Period size: 58 Copynumber: 2.1 Consensus size: 58
73944 CTCGAAGCAG
73954 TATGTCTCTAAAACTATCTTTAGCTCAAATAGGCTGCCAAAGAACTCTATTACCATAT
1 TATGTCTCTAAAACTATCTTTAGCTCAAATAGGCTGCCAAAGAACTCTATTACCATAT
* *
74012 TATGTCTCTAAAACTATCTTTAGCTCAAGTAGGCTGCCAAAGAACTCTATTACCATTT
1 TATGTCTCTAAAACTATCTTTAGCTCAAATAGGCTGCCAAAGAACTCTATTACCATAT
74070 TATG
1 TATG
74074 GTACATTCAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (58 bp):
TATGTCTCTAAAACTATCTTTAGCTCAAATAGGCTGCCAAAGAACTCTATTACCATAT
Done.