Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003129.1 Hibiscus syriacus cultivar Beakdansim tig00006565_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: 77343
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:5504 original size:37 final size:36
Alignment explanation
Indices: 5429--5591 Score: 159
Period size: 37 Copynumber: 4.4 Consensus size: 36
5419 AATATATTCC
*
5429 AATTAAATATAAATTTGTAATAATATATTTTTATTTT
1 AATTAAATATAAATTTATAATAATATA-TTTTATTTT
* *
5466 AATTGAATATAAATTCATAAATAATATATTTGTA-TTT
1 AATTAAATATAAATTTAT-AATAATATATTT-TATTTT
* ** *
5503 AATCAAATATAAATTTATAAATAATATAATCATATTTC
1 AATTAAATATAAATTTAT-AATAATAT-ATTTTATTTT
* *
5541 AACCT-AATATAAATTTGTAATAATATATTTTCATTTT
1 AA-TTAAATATAAATTTATAATAATATATTTT-ATTTT
*
5578 AATTTAATATAAAT
1 AATTAAATATAAAT
5592 CCTTATATAA
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
36 4 0.04
37 70 0.68
38 29 0.28
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (36 bp):
AATTAAATATAAATTTATAATAATATATTTTATTTT
Found at i:20033 original size:18 final size:19
Alignment explanation
Indices: 19975--20025 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
19965 TATTTATTCT
19975 AAAT-TTTTTGGAGTATTA
1 AAATGTTTTTGGAGTATTA
19993 AAATGTTTTTGGAGTATTA
1 AAATGTTTTTGGAGTATTA
20012 AAATGTTTTTGGAG
1 AAATGTTTTTGGAG
20026 ATTGAAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.12
19 28 0.88
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (19 bp):
AAATGTTTTTGGAGTATTA
Found at i:21595 original size:10 final size:10
Alignment explanation
Indices: 21577--21655 Score: 131
Period size: 10 Copynumber: 7.9 Consensus size: 10
21567 TCTTAGGGAG
*
21577 TTTTTCCTTA
1 TTTTCCCTTA
21587 TTTTCCCTTA
1 TTTTCCCTTA
*
21597 TTTTTCCTTA
1 TTTTCCCTTA
21607 TTTTCCCTTA
1 TTTTCCCTTA
21617 TTTTCCCTTA
1 TTTTCCCTTA
*
21627 TTTTTCCTTA
1 TTTTCCCTTA
21637 TTTTCCCTTA
1 TTTTCCCTTA
21647 TTTTCCCTT
1 TTTTCCCTT
21656 CAATGGCCGA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 64 1.00
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTTCCCTTA
Found at i:21617 original size:30 final size:30
Alignment explanation
Indices: 21577--21655 Score: 149
Period size: 30 Copynumber: 2.6 Consensus size: 30
21567 TCTTAGGGAG
*
21577 TTTTTCCTTATTTTCCCTTATTTTTCCTTA
1 TTTTCCCTTATTTTCCCTTATTTTTCCTTA
21607 TTTTCCCTTATTTTCCCTTATTTTTCCTTA
1 TTTTCCCTTATTTTCCCTTATTTTTCCTTA
21637 TTTTCCCTTATTTTCCCTT
1 TTTTCCCTTATTTTCCCTT
21656 CAATGGCCGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.09, C:0.27, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTTCCCTTATTTTCCCTTATTTTTCCTTA
Found at i:23577 original size:15 final size:15
Alignment explanation
Indices: 23549--23589 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
23539 GATGGTGAAG
23549 GAAGAAGAAGAAAAT
1 GAAGAAGAAGAAAAT
23564 GAAG-AGAAGCAAAA-
1 GAAGAAGAAG-AAAAT
*
23578 CAAGAAGAAGAA
1 GAAGAAGAAGAA
23590 TGAGGTAGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.66, C:0.05, G:0.27, T:0.02
Consensus pattern (15 bp):
GAAGAAGAAGAAAAT
Found at i:31807 original size:29 final size:29
Alignment explanation
Indices: 31722--31851 Score: 172
Period size: 29 Copynumber: 4.4 Consensus size: 29
31712 AGGCCAAATT
31722 TTTTTATAAATTACAATAAATATCCA-AAC
1 TTTTTATAAATTACAATAAATA-CCATAAC
* * * *
31751 TTTCTAAAAAATTAAAATAAATAGCATAAC
1 TTT-TTATAAATTACAATAAATACCATAAC
*
31781 TTTTTATATATTACAATAAATACCATAAC
1 TTTTTATAAATTACAATAAATACCATAAC
*
31810 TTTTTATAAATTACAATAAATACCAAAAC
1 TTTTTATAAATTACAATAAATACCATAAC
*
31839 TATTTATAAATTA
1 TTTTTATAAATTA
31852 AAATCAAAGA
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
29 65 0.75
30 22 0.25
ACGTcount: A:0.50, C:0.12, G:0.01, T:0.38
Consensus pattern (29 bp):
TTTTTATAAATTACAATAAATACCATAAC
Found at i:33542 original size:20 final size:19
Alignment explanation
Indices: 33517--33558 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
33507 ATAAATCCTT
33517 TTTTTACAA-TTTTAATAATA
1 TTTTTA-AAGTTTTAATAA-A
33537 TTTTTAAAGTTTTAATAAA
1 TTTTTAAAGTTTTAATAAA
33556 TTT
1 TTT
33559 CAAGTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTTAAAGTTTTAATAAA
Found at i:34100 original size:22 final size:22
Alignment explanation
Indices: 34072--34117 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
34062 AATCTATATA
34072 CATATATAAAATATTTATTGAG
1 CATATATAAAATATTTATTGAG
34094 CATATATAAAATATTTATTGAG
1 CATATATAAAATATTTATTGAG
34116 CA
1 CA
34118 CACAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (22 bp):
CATATATAAAATATTTATTGAG
Found at i:35648 original size:31 final size:31
Alignment explanation
Indices: 35580--35639 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
35570 ACAATTTAAG
*
35580 GCAAAATGGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGGTATTTGGACTTGAATTGAATTT
35611 GCAAAAT-GTATTTGGACTT-AATTGAATTT
1 GCAAAATGGTATTTGGACTTGAATTGAATTT
35640 ATTCAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.42
Consensus pattern (31 bp):
GCAAAATGGTATTTGGACTTGAATTGAATTT
Found at i:40648 original size:41 final size:41
Alignment explanation
Indices: 40585--40697 Score: 149
Period size: 41 Copynumber: 2.8 Consensus size: 41
40575 CGTTTATACC
** *
40585 ACAAACGCCGTAATAGTGTTAATCAATAGTGGC-ATTTTTA
1 ACAAACGCCACAATAGTTTTAATCAATAGTGGCGATTTTTA
* *
40625 GATAAACGCCACAATAGTTTTAATCAATAGTGGCGTTTTTTA
1 -ACAAACGCCACAATAGTTTTAATCAATAGTGGCGATTTTTA
*
40667 ACAAACGCCACAATAG-TGTAATCAATAGTGG
1 ACAAACGCCACAATAGTTTTAATCAATAGTGG
40698 TGTTTTTTTG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
40 14 0.22
41 44 0.69
42 6 0.09
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (41 bp):
ACAAACGCCACAATAGTTTTAATCAATAGTGGCGATTTTTA
Found at i:41161 original size:41 final size:40
Alignment explanation
Indices: 41116--41229 Score: 113
Period size: 41 Copynumber: 2.7 Consensus size: 40
41106 AAGTTGTACT
**
41116 TTAGTGGCGTTTGTGACATAAACGCCGTAATAGTGT-GTCCC
1 TTAGTGGCGTTT-TGA-ATAAACGCCGTAATAGAATAGTCCC
* *
41157 TTAGTGGCATTTTCGTAATAAACGCCGTAATAGAATAGTTCC
1 TTAGTGGCGTTTT-G-AATAAACGCCGTAATAGAATAGTCCC
* *
41199 TTTGTGGCGTTTTTAATATAAACGCCGTAAT
1 TTAGTGGCG-TTTTGA-ATAAACGCCGTAAT
41230 TGTCCTTTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
40 1 0.02
41 30 0.49
42 26 0.43
43 4 0.07
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (40 bp):
TTAGTGGCGTTTTGAATAAACGCCGTAATAGAATAGTCCC
Found at i:41221 original size:42 final size:39
Alignment explanation
Indices: 41114--41229 Score: 106
Period size: 42 Copynumber: 2.8 Consensus size: 39
41104 AAAAGTTGTA
* **
41114 CTTTAGTGGCGTTTGTGACATAAACGCCGTAATAGTGTGTCC
1 CTTT-GTGGCGTTT-TTA-ATAAACGCCGTAATAGAATGTCC
* * *
41156 CTTAGTGGCATTTTCGTAATAAACGCCGTAATAGAATAGTTC
1 CTTTGTGGCGTTTT--TAATAAACGCCGTAATAGAAT-GTCC
41198 CTTTGTGGCGTTTTTAATATAAACGCCGTAAT
1 CTTTGTGGCGTTTTT-A-ATAAACGCCGTAAT
41230 TGTCCTTTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
40 2 0.03
41 26 0.43
42 33 0.54
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (39 bp):
CTTTGTGGCGTTTTTAATAAACGCCGTAATAGAATGTCC
Found at i:41573 original size:8 final size:8
Alignment explanation
Indices: 41560--41589 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
41550 TCTTGTTGCA
41560 TGGAAAAC
1 TGGAAAAC
41568 TGGAAAAC
1 TGGAAAAC
41576 TGGAAAAC
1 TGGAAAAC
41584 TGGAAA
1 TGGAAA
41590 TAAGCTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.27, T:0.13
Consensus pattern (8 bp):
TGGAAAAC
Found at i:41599 original size:8 final size:8
Alignment explanation
Indices: 41588--41617 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
41578 GAAAACTGGA
41588 AATAAGCT
1 AATAAGCT
41596 AATAAGCT
1 AATAAGCT
41604 AATAAGCT
1 AATAAGCT
41612 AATAAG
1 AATAAG
41618 TGATTCGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.23
Consensus pattern (8 bp):
AATAAGCT
Found at i:41756 original size:29 final size:29
Alignment explanation
Indices: 41707--41762 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
41697 AAGTCTAATT
*
41707 ATTTTATTGTTGCATTGTTGTTAACAAAG
1 ATTTTATTGTTGCATTGTTGTGAACAAAG
41736 ATTTT-TTGGTTGCA-TGATTGTGAACAA
1 ATTTTATT-GTTGCATTG-TTGTGAACAA
41763 TGCAAATGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (29 bp):
ATTTTATTGTTGCATTGTTGTGAACAAAG
Found at i:48289 original size:21 final size:21
Alignment explanation
Indices: 48271--48377 Score: 126
Period size: 21 Copynumber: 5.1 Consensus size: 21
48261 ATGAAGCAAG
*
48271 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
48292 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
48313 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
48334 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
48355 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
48376 GG
1 GG
48378 CAGAACAGAG
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 1 0.01
21 76 0.99
ACGTcount: A:0.36, C:0.21, G:0.41, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:48375 original size:42 final size:42
Alignment explanation
Indices: 48275--48392 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
48265 AGCAAGGGAA
** *
48275 ACAGAGAGAGCAGCAGCGGAAGCAGCTAGAGCAGCAGCGGAAGC
1 ACAGAGAGAG--GCAGCGGAAGCAGAGAGAGAAGCAGCGGAAGC
* *
48319 AGCTAGAG-CA-GCAGCGGAAGCAGAGAGAGAAGCAGCGGCAGC
1 A-C-AGAGAGAGGCAGCGGAAGCAGAGAGAGAAGCAGCGGAAGC
* * *
48361 ACAGAGAGAGGCAGCGGCAGAACAGAGAGAAG
1 ACAGAGAGAGGCAGCGGAAGCAGAGAGAGAAG
48393 TAATATATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
40 4 0.07
41 2 0.03
42 48 0.79
44 1 0.02
45 2 0.03
46 4 0.07
ACGTcount: A:0.38, C:0.20, G:0.40, T:0.02
Consensus pattern (42 bp):
ACAGAGAGAGGCAGCGGAAGCAGAGAGAGAAGCAGCGGAAGC
Found at i:48378 original size:21 final size:21
Alignment explanation
Indices: 48279--48392 Score: 97
Period size: 21 Copynumber: 5.4 Consensus size: 21
48269 AGGGAAACAG
* *
48279 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * *
48301 -TAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
48322 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
48342 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
48363 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
48384 AGAGAGAAG
1 AGAGAGAAG
48393 TAATATATCA
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
21 82 1.00
ACGTcount: A:0.38, C:0.20, G:0.40, T:0.02
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:48932 original size:43 final size:43
Alignment explanation
Indices: 48833--48956 Score: 144
Period size: 43 Copynumber: 2.9 Consensus size: 43
48823 TTTTTGAAGA
* *
48833 AAACGCCGCTAAACATCAACGA-CTATTGCGGCGTTTGTCTGCC
1 AAACGCCGCTAAATATCAAC-ACCTATTGCGGCGTTTGTATGCC
* * * *
48876 AAATGCCGTTAAATATCAACACCTATTGCGGCGTTT-TAATTCT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT-ATGCC
* *
48919 AAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT
1 AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGT
48957 TGAACAATCG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
42 2 0.03
43 65 0.96
44 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (43 bp):
AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTATGCC
Found at i:48969 original size:43 final size:44
Alignment explanation
Indices: 48730--48999 Score: 134
Period size: 43 Copynumber: 6.2 Consensus size: 44
48720 CATACATTTA
* * * * *
48730 GCGGCGTTTTTG-ATAAAAACGCCGCAAAATCTCAAGACATATTCT
1 GCGGCGTTTTTGAATCAAAACGCCGCTAAATATCAACACCTA-T-T
* ** * * * * *
48775 GCGGCG--TTTGTAGGAAAACGCCGGTAAAAATAAACATCTACT
1 GCGGCGTTTTTGAATCAAAACGCCGCTAAATATCAACACCTATT
* * *
48817 GTGGCGTTTTTGAA-GAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTTTGAATCAAAACGCCGCTAAATATCAAC-ACCTATT
* * *
48860 GCGGCGTTTGTCTG---CCAAATGCCGTTAAATATCAACACCTATT
1 GCGGCGTTT-T-TGAATCAAAACGCCGCTAAATATCAACACCTATT
* * *
48903 GCGGCG-TTTT-AATTCTAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTTTGAA-TCAAAACGCCGCTAAATATCAACACCTATT
* * * **
48946 GCGGCGTTTGTTGAA-C-AATCGCCGCTATATGTTGTA-ACCTATT
1 GCGGCGTTT-TTGAATCAAAACGCCGCTAAAT-ATCAACACCTATT
48989 GCGGCGTTTTT
1 GCGGCGTTTTT
49000 TTGTTCAAAA
Statistics
Matches: 176, Mismatches: 34, Indels: 33
0.72 0.14 0.14
Matches are distributed among these distances:
40 1 0.01
41 1 0.01
42 11 0.06
43 120 0.68
44 31 0.18
45 10 0.06
46 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
GCGGCGTTTTTGAATCAAAACGCCGCTAAATATCAACACCTATT
Found at i:52080 original size:9 final size:9
Alignment explanation
Indices: 52066--52091 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
52056 AAAAAACATG
52066 AAATTAAAT
1 AAATTAAAT
52075 AAATTAAAT
1 AAATTAAAT
52084 AAATTAAA
1 AAATTAAA
52092 CATGCATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
AAATTAAAT
Found at i:52747 original size:45 final size:48
Alignment explanation
Indices: 52671--52796 Score: 132
Period size: 45 Copynumber: 2.6 Consensus size: 48
52661 AAACATAATA
52671 TATATATATATATATATATATTAAAAGTATATAAACTATATGGTATAAGTATA-
1 TATAT-TATATA-ATATATATT---A-TATATAAACTATATGGTATAAGTATAT
* * * *
52724 TATGTT-TATAATATTTATT-TATATAAACTATGTGGTATAATTATAT
1 TATATTATATAATATATATTATATATAAACTATATGGTATAAGTATAT
*
52770 TATATTATATTATATATATTATATATA
1 TATATTATATAATATATATTATATATA
52797 TATATATATG
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
45 24 0.38
46 5 0.08
47 11 0.17
48 6 0.10
50 8 0.13
51 4 0.06
52 1 0.02
53 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (48 bp):
TATATTATATAATATATATTATATATAAACTATATGGTATAAGTATAT
Found at i:52773 original size:5 final size:5
Alignment explanation
Indices: 52763--52805 Score: 61
Period size: 5 Copynumber: 8.4 Consensus size: 5
52753 ATGTGGTATA
52763 ATTAT ATTAT ATTAT ATTAT A-TAT ATTAT ATATAT ATATAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT AT-TAT AT
52806 GCATATATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.11
5 21 0.58
6 11 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
ATTAT
Found at i:52789 original size:19 final size:17
Alignment explanation
Indices: 52765--52805 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 17
52755 GTGGTATAAT
52765 TATATTATATTATATTATA
1 TATATTATA-TATA-TATA
52784 TATATTATATATATATA
1 TATATTATATATATATA
52801 TATAT
1 TATAT
52806 GCATATATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.41
18 4 0.18
19 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATATATATATA
Found at i:53013 original size:3 final size:3
Alignment explanation
Indices: 53005--53038 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
52995 ATGCATAAGT
53005 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
53039 ATAAGTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53181 original size:2 final size:2
Alignment explanation
Indices: 52489--53166 Score: 169
Period size: 2 Copynumber: 357.5 Consensus size: 2
52479 CAAACAATTA
52489 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
52531 AT AT AT AT AT AT A- AT A- AT AT A- AT AT GT ACG AT GA- AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT AT AT
* * * * * *
52570 AT GAT A- AT AT A- AG AC AT GT AT AT AT GT -T AT A- AT GT AC AT
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
52609 -T AT ACT -T AT A- AT AT AT CT AT AT A- AT AT TT AT A- AGT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
52648 AT AT AT AA ACT AT AA AC AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
52690 AT -T A- AA AGT AT AT AA ACT AT AT GGT AT A- AGT AT AT AT GT TT
1 AT AT AT AT A-T AT AT AT A-T AT AT -AT AT AT A-T AT AT AT AT AT
* * * * *
52731 AT A- AT AT TT AT TT AT AT AA ACT AT GT GGT AT A- AT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT
**
52771 AT AT -T AT AT -T AT AT AT AT -T AT AT AT AT AT AT AT AT GC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** * * ** * * *
52810 AT AT GAT GC AT GT AT AT ACT -T AT GT GC GT CT AT AT GT AT AT AT
1 AT AT -AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
52853 AT AT GT -T AT AC AT AT A- AGT AT AT AT GT A- AT -T AT GT AT GAT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT -AT
** * * * * * * *
52893 GC AT GT AT GT AT AT AT AT AT AT TT AT AC AT GT -T AG A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
52933 AT -T A- AA AA AT AA AA AA AA AT AT GT AT AT AT AT -T A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** *
52971 -T AT AT AT AT AT AT AA AT AT AT AT -T AT GC AT A- AGT TT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
53010 AT -T AT -T AT -T AT -T AT -T AT -T AT -T AT -T AT -T AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
53042 AGT AT AT AC A- AA AGT GT GT GT AT AT AT AT A- AG A- AT ACT -T
1 A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT
53081 A- AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53123 AT AT AT AT AT AT AT A- AGT AT AT A- AT AT AT A- AT AT AT A- AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
53162 AT AT A
1 AT AT A
53167 AGTATAAAAT
Statistics
Matches: 500, Mismatches: 95, Indels: 162
0.66 0.13 0.21
Matches are distributed among these distances:
1 59 0.12
2 417 0.83
3 24 0.05
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (2 bp):
AT
Found at i:53642 original size:2 final size:2
Alignment explanation
Indices: 53637--53678 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
53627 AAAAAAATCT
53637 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53679 ATGTCAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54303 original size:149 final size:149
Alignment explanation
Indices: 54114--54412 Score: 465
Period size: 149 Copynumber: 2.0 Consensus size: 149
54104 AGATCAGAAA
* * *
54114 AATAATAAGTCGGATTACTTACCGGTTGAGTCAATTACAAGTCGGGTAATACCAGTTATTTAGCA
1 AATAATAAGTCAGATTACTTACAGGTTGAGTCAATTACAAGTCGGGTAATACCAGTTATTTACCA
* *
54179 GATTAATCACGGGTTCGGGTTCATATCAATC-GAATGTAGGTCGGGTTCGGTTATCGTATTATCG
66 GATTAATCACGAGTTCGGGTTCATATCAATCAG-ATGTAGGTCGGGTTCGGTTATCATATTATCG
* *
54243 ATTTAATCCGGTTTCAGGTC
130 ATTCAATCCGGTTTCAAGTC
*
54263 AATAATAAGTTAGATTACTTACAGGTTGAGTCAATTACAAGTCGGGTAATACCAGTTATTTACCA
1 AATAATAAGTCAGATTACTTACAGGTTGAGTCAATTACAAGTCGGGTAATACCAGTTATTTACCA
* * *
54328 GGTTAGTCACGAGTTCGGGTTCATATCAGTCAGATGTAGGTCGGGTTCGGTTATCATATTATCGA
66 GATTAATCACGAGTTCGGGTTCATATCAATCAGATGTAGGTCGGGTTCGGTTATCATATTATCGA
**
54393 TTCAATTTGGTTTCAAGTC
131 TTCAATCCGGTTTCAAGTC
54412 A
1 A
54413 TTTCTCAGAT
Statistics
Matches: 136, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
149 135 0.99
150 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (149 bp):
AATAATAAGTCAGATTACTTACAGGTTGAGTCAATTACAAGTCGGGTAATACCAGTTATTTACCA
GATTAATCACGAGTTCGGGTTCATATCAATCAGATGTAGGTCGGGTTCGGTTATCATATTATCGA
TTCAATCCGGTTTCAAGTC
Found at i:59092 original size:16 final size:16
Alignment explanation
Indices: 59066--59110 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
59056 TAAGCTCCAA
*
59066 TCAATCTAAAACAAA-
1 TCAAGCTAAAACAAAG
59081 TGCAAGCTAAAACAAAG
1 T-CAAGCTAAAACAAAG
*
59098 TCAATCTAAAACA
1 TCAAGCTAAAACA
59111 TACTGGCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.56, C:0.20, G:0.07, T:0.18
Consensus pattern (16 bp):
TCAAGCTAAAACAAAG
Found at i:59802 original size:13 final size:13
Alignment explanation
Indices: 59784--59867 Score: 73
Period size: 13 Copynumber: 6.5 Consensus size: 13
59774 TCAATTATTC
59784 CAATATGCAATAA
1 CAATATGCAATAA
59797 CAATATGC-ATGAA
1 CAATATGCAAT-AA
*
59810 CAATATGTAATAA
1 CAATATGCAATAA
* *
59823 CATTATTC-ATGAA
1 CAATATGCAAT-AA
*
59836 CAATATGAAATAA
1 CAATATGCAATAA
* **
59849 CATTATGCTGTAA
1 CAATATGCAATAA
59862 CAATAT
1 CAATAT
59868 ATAATTACAG
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
12 4 0.07
13 47 0.85
14 4 0.07
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.30
Consensus pattern (13 bp):
CAATATGCAATAA
Found at i:59821 original size:26 final size:26
Alignment explanation
Indices: 59784--59896 Score: 138
Period size: 26 Copynumber: 4.3 Consensus size: 26
59774 TCAATTATTC
* *
59784 CAATATGCAATAACAATATGCATGAA
1 CAATATGTAATAACATTATGCATGAA
*
59810 CAATATGTAATAACATTATTCATGAA
1 CAATATGTAATAACATTATGCATGAA
*
59836 CAATATGAAATAACATTATGC-TGTAA
1 CAATATGTAATAACATTATGCATG-AA
* * *
59862 CAATATATAATTACAGTATGCATGAA
1 CAATATGTAATAACATTATGCATGAA
*
59888 GAATATGTA
1 CAATATGTA
59897 TTAGCAAGTT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
25 2 0.03
26 70 0.95
27 2 0.03
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (26 bp):
CAATATGTAATAACATTATGCATGAA
Found at i:61824 original size:15 final size:15
Alignment explanation
Indices: 61806--61918 Score: 72
Period size: 15 Copynumber: 7.5 Consensus size: 15
61796 TCTCAGATGG
*
61806 TTCTGGTTTATTAAT
1 TTCTGGTTCATTAAT
* *
61821 TTCTGGCTCA--ACT
1 TTCTGGTTCATTAAT
61834 GGTTCTGGTTCATTAAT
1 --TTCTGGTTCATTAAT
*
61851 TTCAGGTTCATTAAT
1 TTCTGGTTCATTAAT
* **
61866 TTCT-GTCTCAGCT-GG
1 TTCTGGT-TCA-TTAAT
61881 TTCTGGTTCATTAAT
1 TTCTGGTTCATTAAT
* * *
61896 TTCGGGCTCACTAAT
1 TTCTGGTTCATTAAT
61911 TTCTGGTT
1 TTCTGGTT
61919 TCAACTGGTT
Statistics
Matches: 72, Mismatches: 18, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
13 2 0.03
14 3 0.04
15 62 0.86
16 3 0.04
17 2 0.03
ACGTcount: A:0.17, C:0.18, G:0.19, T:0.47
Consensus pattern (15 bp):
TTCTGGTTCATTAAT
Found at i:61851 original size:30 final size:30
Alignment explanation
Indices: 61781--61853 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
61771 TCAATTTCAA
* *
61781 GTTCATTAATGTCTGTCTCAGATGGTTCTG
1 GTTCATTAATTTCTGGCTCAGATGGTTCTG
*
61811 GTTTATTAATTTCTGGCTCA-ACTGGTTCTG
1 GTTCATTAATTTCTGGCTCAGA-TGGTTCTG
61841 GTTCATTAATTTC
1 GTTCATTAATTTC
61854 AGGTTCATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 1 0.03
30 37 0.97
ACGTcount: A:0.18, C:0.16, G:0.19, T:0.47
Consensus pattern (30 bp):
GTTCATTAATTTCTGGCTCAGATGGTTCTG
Found at i:61860 original size:75 final size:75
Alignment explanation
Indices: 61763--61905 Score: 232
Period size: 75 Copynumber: 1.9 Consensus size: 75
61753 TCAGCATGTC
* *
61763 CTGGTTCATCAATTTCAAGTTCATTAATGTCTGTCTCAGATGGTTCTGGTTTATTAATTTCTGGC
1 CTGGTTCATCAATTTCAAGTTCATTAATGTCTGTCTCAGATGGTTCTGGTTCATTAATTTCGGGC
61828 TCAACTGGTT
66 TCAACTGGTT
* * * *
61838 CTGGTTCATTAATTTCAGGTTCATTAATTTCTGTCTCAGCTGGTTCTGGTTCATTAATTTCGGGC
1 CTGGTTCATCAATTTCAAGTTCATTAATGTCTGTCTCAGATGGTTCTGGTTCATTAATTTCGGGC
61903 TCA
66 TCA
61906 CTAATTTCTG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (75 bp):
CTGGTTCATCAATTTCAAGTTCATTAATGTCTGTCTCAGATGGTTCTGGTTCATTAATTTCGGGC
TCAACTGGTT
Found at i:61865 original size:45 final size:45
Alignment explanation
Indices: 61810--61954 Score: 182
Period size: 45 Copynumber: 3.2 Consensus size: 45
61800 AGATGGTTCT
*
61810 GGTTTATTAATTTCTGGCTCAACTGGTTCTGGTTCATTAATTTCA
1 GGTTCATTAATTTCTGGCTCAACTGGTTCTGGTTCATTAATTTCA
* * *
61855 GGTTCATTAATTTCTGTCTCAGCTGGTTCTGGTTCATTAATTTCG
1 GGTTCATTAATTTCTGGCTCAACTGGTTCTGGTTCATTAATTTCA
* * * * * *
61900 GGCTCACTAATTTCTGGTTTCAACTGGTTATGCTTCATCAATTTCA
1 GGTTCATTAATTTCTGG-CTCAACTGGTTCTGGTTCATTAATTTCA
*
61946 GGTTGATTA
1 GGTTCATTA
61955 TGTTCAGACC
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
45 55 0.66
46 28 0.34
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (45 bp):
GGTTCATTAATTTCTGGCTCAACTGGTTCTGGTTCATTAATTTCA
Found at i:61915 original size:30 final size:31
Alignment explanation
Indices: 61847--61918 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
61837 TCTGGTTCAT
* * *
61847 TAATTTCAGGTTCATTAATTTCTGTCTCAGC
1 TAATTTCTGGTTCATTAATTTCGGGCTCAGC
**
61878 T-GGTTCTGGTTCATTAATTTCGGGCTCA-C
1 TAATTTCTGGTTCATTAATTTCGGGCTCAGC
61907 TAATTTCTGGTT
1 TAATTTCTGGTT
61919 TCAACTGGTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
29 2 0.06
30 30 0.91
31 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (31 bp):
TAATTTCTGGTTCATTAATTTCGGGCTCAGC
Found at i:62792 original size:68 final size:68
Alignment explanation
Indices: 62704--62874 Score: 261
Period size: 68 Copynumber: 2.5 Consensus size: 68
62694 GCATGAAAAC
* * * *
62704 CATTAATACTAACAGTAAACCCCCAAAACTCATATTAACTCATATAAACTCCCTAACATATATAC
1 CATTTATACTAACAGTAAACCCACAAAACTCATATGAACTCATATAAACTCCCTAACATAAATAC
62769 TAA
66 TAA
* *
62772 CATTTATACAAACAGTAAACCCACAAAACTCATATGAACTCATATAAACTCCCTAACATAAATGC
1 CATTTATACTAACAGTAAACCCACAAAACTCATATGAACTCATATAAACTCCCTAACATAAATAC
62837 TAA
66 TAA
* * *
62840 CATGTATACTAATAGTAAACCCACTAAACTCATAT
1 CATTTATACTAACAGTAAACCCACAAAACTCATAT
62875 AATCTCAGTA
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 93 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.26
Consensus pattern (68 bp):
CATTTATACTAACAGTAAACCCACAAAACTCATATGAACTCATATAAACTCCCTAACATAAATAC
TAA
Found at i:70364 original size:81 final size:81
Alignment explanation
Indices: 70256--70845 Score: 664
Period size: 81 Copynumber: 7.4 Consensus size: 81
70246 TGTTTTAAAA
* * *
70256 TTAAAGATTAAATGCCTAACTGTGCATTTGGCA-AAATTGTGCCAATCATGCTTGTTAGATGAAA
1 TTAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAA-GGTGCCAATCATGCATGTTAGATGAAA
* **
70320 ACTTAAATATTTTTGAG
65 AGTTAAATACCTTTGAG
* * * * * * *
70337 TTAAAAACTAAATGTCTAATTGTGCATTTGGAAGAAATGTGCCAATCATGCCTGTTAGATGAAAG
1 TTAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCATGTTAGATGAAAA
* *
70402 GTTAATTGCCTTTGAG
66 GTTAAATACCTTTGAG
* *
70418 ATAAAGACTAAATGCCTAACTGTGCATTTGGCGGAAAGGTGCCAATCATGCATGTTAGATGAAAA
1 TTAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCATGTTAGATGAAAA
70483 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
70499 ATAAAGACTAAATGCCTAACTGTGCATTTGGTAGAAATGTGTCAATCATGCATGTTAGATGAAAG
1 TTAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCATGTTAGATGAAAA
70564 GTTAAATGA-CTTTGAG
66 GTTAAAT-ACCTTTGAG
* * * *
70580 TTAAAGACTAAATGCCTAACTGTGCATTCGGTAGAAAGGTGCTAATCATGCCTGTTAGATG-AAA
1 TTAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCATGTTAGATGAAAA
*
70644 GATTAAATGCCTTTGAG
66 G-TTAAATACCTTTGAG
*
70661 TTAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGTCAATCATGGC-TGTTAGATGAAA
1 TTAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCAT-GCATGTTAGATGAAA
* * *
70725 GGTT-AATGCCTTTTAG
65 AGTTAAATACCTTTGAG
* * * * *
70741 TTAAAAACT-AAT--CTAACTATGTATTTGGCAAAAAGGTGCCAATCGTGCCA-GTT--ATGAAA
1 TTAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATG-CATGTTAGATGAAA
* *
70800 GGTTAAATGCCTTTAGAG
65 AGTTAAATACCTTT-GAG
* * * *
70818 -GAAAGACTGAATGCTTAACAGTGCATTT
1 TTAAAGACTAAATGCCTAACTGTGCATTT
70846 TGACATAAAC
Statistics
Matches: 441, Mismatches: 55, Indels: 28
0.84 0.10 0.05
Matches are distributed among these distances:
75 10 0.02
76 16 0.04
77 38 0.09
79 13 0.03
80 22 0.05
81 333 0.76
82 9 0.02
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (81 bp):
TTAAAGACTAAATGCCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCATGTTAGATGAAAA
GTTAAATACCTTTGAG
Found at i:70692 original size:243 final size:241
Alignment explanation
Indices: 70257--70844 Score: 744
Period size: 243 Copynumber: 2.4 Consensus size: 241
70247 GTTTTAAAAT
* * **
70257 TAAAGATTAAATGCCTAACTGTGCATTTGGCAAAATTGTGCCAATCATGCTTGTTAGATGAAAAC
1 TAAAGACTAAATGCCTAACTGTGCATTTGGCAAAA-TGTGCCAATCATGCATGTTAGATGAAAGG
* * * * * *
70322 TTAAAT-ATTTTTGAGTTAAAAACTAAATGTCTAATTGTGCATTTGGAAGAAATGTGCCAATCAT
65 TTAAATGA-CTTTGAGTTAAAGACTAAATGCCTAACTGTGCATTCGGAAGAAAGGTGCCAATCAT
* * *
70386 GCCTGTTAGATGAAAGGTTAATTGCCTTTGAGATAAAGACTAAATGCCTAACTGTGCATTTGGCG
129 GCCTGTTAGATGAAAGATTAAATGCCTTTGAGATAAAGACTAAATGCCTAACTGTGCATTTGGCA
70451 GAAAGGTGCCAATCAT-GCATGTTAGATGAAAAGTTAAATACCTTTGAGA
194 GAAAGGTGCCAATCATGGC-TGTTAGATGAAAAGTT-AATACCTTTGAGA
* *
70500 TAAAGACTAAATGCCTAACTGTGCATTTGGTAGAAATGTGTCAATCATGCATGTTAGATGAAAGG
1 TAAAGACTAAATGCCTAACTGTGCATTTGGCA-AAATGTGCCAATCATGCATGTTAGATGAAAGG
* *
70565 TTAAATGACTTTGAGTTAAAGACTAAATGCCTAACTGTGCATTCGGTAGAAAGGTGCTAATCATG
65 TTAAATGACTTTGAGTTAAAGACTAAATGCCTAACTGTGCATTCGGAAGAAAGGTGCCAATCATG
*
70630 CCTGTTAGATGAAAGATTAAATGCCTTTGAGTTAAAGACTAAATGCCTAACTGTGCATTTGGCAG
130 CCTGTTAGATGAAAGATTAAATGCCTTTGAGATAAAGACTAAATGCCTAACTGTGCATTTGGCAG
* * * * *
70695 AAAGGTGTCAATCATGGCTGTTAGATGAAAGGTTAATGCCTTTTAGT
195 AAAGGTGCCAATCATGGCTGTTAGATGAAAAGTTAATACCTTTGAGA
* * * * *
70742 TAAAAACT-AAT--CTAACTATGTATTTGGCAAAAAGGTGCCAATCGTGCCA-GTT--ATGAAAG
1 TAAAGACTAAATGCCTAACTGTGCATTTGGC-AAAATGTGCCAATCATG-CATGTTAGATGAAAG
* * * * *
70801 GTTAAATGCCTTTAGAG-GAAAGACTGAATGCTTAACAGTGCATT
64 GTTAAATGACTTT-GAGTTAAAGACTAAATGCCTAACTGTGCATT
70845 TTGACATAAA
Statistics
Matches: 304, Mismatches: 35, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
237 42 0.14
238 3 0.01
239 30 0.10
240 3 0.01
241 3 0.01
242 17 0.06
243 200 0.66
244 6 0.02
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (241 bp):
TAAAGACTAAATGCCTAACTGTGCATTTGGCAAAATGTGCCAATCATGCATGTTAGATGAAAGGT
TAAATGACTTTGAGTTAAAGACTAAATGCCTAACTGTGCATTCGGAAGAAAGGTGCCAATCATGC
CTGTTAGATGAAAGATTAAATGCCTTTGAGATAAAGACTAAATGCCTAACTGTGCATTTGGCAGA
AAGGTGCCAATCATGGCTGTTAGATGAAAAGTTAATACCTTTGAGA
Found at i:72219 original size:12 final size:12
Alignment explanation
Indices: 72202--72238 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
72192 ATTACATATA
72202 AATTTAACTATT
1 AATTTAACTATT
72214 AATTTAACTATT
1 AATTTAACTATT
72226 AATTTAACTATT
1 AATTTAACTATT
72238 A
1 A
72239 GGTAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTTAACTATT
Found at i:73015 original size:24 final size:24
Alignment explanation
Indices: 72988--73042 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
72978 CTTCGGTTTA
72988 GGGAATGTTTCCCAAAATTACCAG
1 GGGAATGTTTCCCAAAATTACCAG
73012 GGGAATGTTTCCCAAAATTACCAG
1 GGGAATGTTTCCCAAAATTACCAG
*
73036 GAGAATG
1 GGGAATG
73043 CTTTATGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (24 bp):
GGGAATGTTTCCCAAAATTACCAG
Found at i:74141 original size:21 final size:22
Alignment explanation
Indices: 74102--74142 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
74092 AAAAACCTTC
**
74102 AATTAAATAATTTTTAAATATA
1 AATTAAATAATTTAAAAATATA
74124 AATTAAAT-ATTTAAAAATA
1 AATTAAATAATTTAAAAATA
74143 ATTTTGGTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATTAAATAATTTAAAAATATA
Found at i:74282 original size:2 final size:2
Alignment explanation
Indices: 74231--74267 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
74221 TTTTCAAAAC
74231 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
74268 TCGAAAACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74288 original size:30 final size:28
Alignment explanation
Indices: 74247--74326 Score: 99
Period size: 30 Copynumber: 2.8 Consensus size: 28
74237 TATATATATA
74247 TATATATATATATATATATATTCGAAAAC
1 TATATATATATATATATATATTCG-AAAC
*
74276 TATATATCATATATATATACTTTTCGAAAC
1 TATATAT-ATATATATATA-TATTCGAAAC
* *
74306 CATATAT-TATGTATATATATT
1 TATATATATATATATATATATT
74327 ATATATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.07
28 9 0.20
29 7 0.16
30 21 0.47
31 5 0.11
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (28 bp):
TATATATATATATATATATATTCGAAAC
Found at i:74325 original size:13 final size:13
Alignment explanation
Indices: 74307--74336 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
74297 TTTCGAAACC
*
74307 ATATATTATGTAT
1 ATATATTATATAT
74320 ATATATTATATAT
1 ATATATTATATAT
74333 ATAT
1 ATAT
74337 TAGAAACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
ATATATTATATAT
Found at i:74333 original size:11 final size:12
Alignment explanation
Indices: 74307--74339 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
74297 TTTCGAAACC
74307 ATATATTATGTAT
1 ATATATTA-GTAT
74320 ATATATTA-TAT
1 ATATATTAGTAT
74331 ATATATTAG
1 ATATATTAG
74340 AAACTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
13 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (12 bp):
ATATATTAGTAT
Done.