Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001127.1 Hibiscus syriacus cultivar Beakdansim tig00002229_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: 96353
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4078 original size:90 final size:89
Alignment explanation
Indices: 3974--4139 Score: 296
Period size: 90 Copynumber: 1.9 Consensus size: 89
3964 ATTTAGTTTA
3974 AATTAATTAAATATAGATTTAATTAATTTGAAATAAAAAAATCCCTAATATGATTAGGGTAACTT
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAAAAAAA-CCCTAATATGATTAGGGTAACTT
4039 GGATATAAAAGGATTATTAAATTCT
65 GGATATAAAAGGATTATTAAATTCT
* *
4064 AATTAATTAAATATATATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGGGTAACTTG
1 AATTAATTAAATATAGATTTAATTAATTTGAAATAAAAAAACCCTAATATGATTAGGGTAACTTG
*
4129 GCTATAAAAGG
66 GATATAAAAGG
4140 GTGTGCTAGG
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 34 0.47
90 39 0.53
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.36
Consensus pattern (89 bp):
AATTAATTAAATATAGATTTAATTAATTTGAAATAAAAAAACCCTAATATGATTAGGGTAACTTG
GATATAAAAGGATTATTAAATTCT
Found at i:6941 original size:7 final size:8
Alignment explanation
Indices: 6919--6952 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
6909 GTTGGCATTT
6919 TTTTGTTTA
1 TTTT-TTTA
6928 TTTTTTTA
1 TTTTTTTA
6936 TTTTTTTA
1 TTTTTTTA
6944 TTTTTTTA
1 TTTTTTTA
6952 T
1 T
6953 ATTATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 21 0.84
9 4 0.16
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:11214 original size:24 final size:25
Alignment explanation
Indices: 11176--11223 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
11166 CATTCAAAGG
* **
11176 TCAAATCATATAAAATGATCATATT
1 TCAAATCAGATAAAACAATCATATT
11201 TCAAA-CAGATAAAACAATCATAT
1 TCAAATCAGATAAAACAATCATAT
11224 GCACATGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.29
Consensus pattern (25 bp):
TCAAATCAGATAAAACAATCATATT
Found at i:14867 original size:21 final size:21
Alignment explanation
Indices: 14843--14884 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
14833 AACCCAAGAA
14843 ATTGTAAATCTCAAAGACATT
1 ATTGTAAATCTCAAAGACATT
**
14864 ATTGTATTTCTCAAAGACATT
1 ATTGTAAATCTCAAAGACATT
14885 GTTGGGTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATTGTAAATCTCAAAGACATT
Found at i:32035 original size:21 final size:21
Alignment explanation
Indices: 32000--32118 Score: 89
Period size: 21 Copynumber: 5.4 Consensus size: 21
31990 AATATATATA
32000 ATATATATAGTTTTTGAAAAT
1 ATATATATAGTTTTTGAAAAT
*
32021 ATATAGTATAGTTTTTAAAAACAT
1 ATATA-TATAGTTTTT-GAAA-AT
* * *
32045 ATTCTTATATAATTTTTGAAAAC
1 A-T-ATATATAGTTTTTGAAAAT
* *
32068 ATAT-TATATGATTTTGAAAAC
1 ATATATATA-GTTTTTGAAAAT
*
32089 ATAT-TATATGATTTTGAAAAT
1 ATATATATA-GTTTTTGAAAAT
32110 ATAATATAT
1 AT-ATATAT
32119 TATATAGTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
20 4 0.05
21 38 0.47
22 13 0.16
23 8 0.10
24 6 0.07
25 10 0.12
26 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTTTGAAAAT
Found at i:32268 original size:19 final size:20
Alignment explanation
Indices: 32244--32294 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
32234 AATGACCAAT
32244 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
32263 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
32283 AAAATCGCAACG
1 AAAATCGCAACG
32295 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:32288 original size:20 final size:20
Alignment explanation
Indices: 32244--32541 Score: 174
Period size: 20 Copynumber: 14.6 Consensus size: 20
32234 AATGACCAAT
* *
32244 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
32263 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
32283 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
32303 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
32323 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
32344 AAGTTCGCAACGCGATTTAAAAG
1 AAAATCGCAACGCGATTT---AG
* * *
32367 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
32387 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* *
32407 ATAATCGCAATGCGA-TT-G
1 AAAATCGCAACGCGATTTAG
32425 AAAGAGTCGCAACGCGATTTAGAAG
1 AAA-A-TCGCAACGCGATTT---AG
* * *
32450 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
32470 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
32490 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
32510 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
32530 AAAATCGCAACG
1 AAAATCGCAACG
32542 TTAAAAAGAT
Statistics
Matches: 221, Mismatches: 42, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.01
19 20 0.09
20 153 0.69
21 16 0.07
23 25 0.11
24 1 0.00
25 4 0.02
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:32422 original size:40 final size:40
Alignment explanation
Indices: 32348--32539 Score: 240
Period size: 40 Copynumber: 4.7 Consensus size: 40
32338 GCTTCCAAGT
*
32348 TCGCAACGCGATTTAAAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTT---AGAAAATCGCAATGCGATTGAGAGAA
* * * * *
32391 TCGCAATGCGATTTATATAATCGCAATGCGATTGAAAGAG
1 TCGCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAA
*
32431 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTT---AGAAAATCGCAATGCGATTGAGAGAA
* * *
32474 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAA
32514 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAAAATCGCAA
32540 CGTTAAAAAG
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
40 81 0.63
43 47 0.37
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAAAATCGCAATGCGATTGAGAGAA
Found at i:32459 original size:83 final size:83
Alignment explanation
Indices: 32348--32531 Score: 314
Period size: 83 Copynumber: 2.2 Consensus size: 83
32338 GCTTCCAAGT
* * * *
32348 TCGCAACGCGATTTAAAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATATAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
*
32413 GCAATGCGATTGAAAGAG
66 GCAATGCGATTGAAAGAA
32431 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
*
32496 GCAATGCGATTGAGAGAA
66 GCAATGCGATTGAAAGAA
32514 TCGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
32532 AATCGCAACG
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 95 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATC
GCAATGCGATTGAAAGAA
Found at i:32639 original size:6 final size:6
Alignment explanation
Indices: 32628--32727 Score: 123
Period size: 5 Copynumber: 18.5 Consensus size: 6
32618 GACACGTATT
32628 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A-CACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
32675 A-CACG A-CACG ACC-CG ACCAC- ACC-CG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
32715 ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACC
32728 CGAGACGAGA
Statistics
Matches: 91, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
4 1 0.01
5 51 0.56
6 39 0.43
ACGTcount: A:0.30, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:33433 original size:6 final size:6
Alignment explanation
Indices: 33417--33472 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
33407 TCTCGTCTCG
33417 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
33464 GGTCGT GGT
1 GGTCGT GGT
33473 AATACGTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:33570 original size:20 final size:20
Alignment explanation
Indices: 33545--33621 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
33535 ATTTTCAACG
* * *
33545 TCAATCGCGTTGCGACTCTC
1 TCAATCGCATTGCGATTCTA
*
33565 TCAATCGCATTGTGATTCTA
1 TCAATCGCATTGCGATTCTA
33585 TCAATCGCATTGCGATTCTA
1 TCAATCGCATTGCGATTCTA
33605 TCAATCGCATTGCGATT
1 TCAATCGCATTGCGATT
33622 TTCTTCTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (20 bp):
TCAATCGCATTGCGATTCTA
Found at i:33709 original size:20 final size:20
Alignment explanation
Indices: 33656--33709 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
33646 TGGAAGCTCG
* *
33656 CGTTGCGATTTTCCTTTGAC
1 CGTTGCGATTTTCTTTTGAA
* *
33676 CGTTGTGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
33696 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
33710 AAATCGCGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:33736 original size:19 final size:20
Alignment explanation
Indices: 33696--33746 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
33686 TTCTTTTTAA
*
33696 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
33716 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
33735 CGTTGCGATTTT
1 CGTTGCGATTTT
33747 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:36615 original size:22 final size:22
Alignment explanation
Indices: 36585--36626 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
36575 AGTCGAGGGT
*
36585 TTCATAGGTCCTTCGGGACATA
1 TTCACAGGTCCTTCGGGACATA
*
36607 TTCACAGGTCTTTCGGGACA
1 TTCACAGGTCCTTCGGGACA
36627 AATTTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (22 bp):
TTCACAGGTCCTTCGGGACATA
Found at i:37892 original size:25 final size:26
Alignment explanation
Indices: 37864--37915 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
37854 TTCTTGTATT
*
37864 TCTTTTTTTTTATCAATTTT-TTTTA
1 TCTTTTCTTTTATCAATTTTATTTTA
**
37889 TCTTTTCTTTTATTTATTTTATTTTA
1 TCTTTTCTTTTATCAATTTTATTTTA
37915 T
1 T
37916 TACCTAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (26 bp):
TCTTTTCTTTTATCAATTTTATTTTA
Found at i:37899 original size:13 final size:12
Alignment explanation
Indices: 37864--37915 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
37854 TTCTTGTATT
37864 TCTTTTTTTTTA
1 TCTTTTTTTTTA
*
37876 TCAATTTTTTTTA
1 TC-TTTTTTTTTA
*
37889 TCTTTTCTTTTA
1 TCTTTTTTTTTA
*
37901 TTTATTTTATTTTA
1 TCT-TTTT-TTTTA
37915 T
1 T
37916 TACCTAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
12 12 0.38
13 14 0.44
14 6 0.19
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (12 bp):
TCTTTTTTTTTA
Found at i:38391 original size:27 final size:27
Alignment explanation
Indices: 38336--38391 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
38326 GTAGTAAACA
* *
38336 ATGACTGTATTTTATCAAATATCTTAT
1 ATGACTGTATTTTATCAAATATATGAT
*
38363 ATGACTTGTATTTTATCACATA-ATGAT
1 ATGAC-TGTATTTTATCAAATATATGAT
38390 AT
1 AT
38392 TGATGGGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (27 bp):
ATGACTGTATTTTATCAAATATATGAT
Found at i:39756 original size:20 final size:20
Alignment explanation
Indices: 39731--39781 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
39721 ATCCTATTCC
39731 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
39751 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTTTATTCCCA
39771 CTGGTAATCTT
1 CTGGTAATCTT
39782 ACATTATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTTTATTCCCA
Found at i:42720 original size:21 final size:20
Alignment explanation
Indices: 42694--42759 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
42684 TTGGTATTAC
42694 ATAGTAGTATCAGTACTGGTA
1 ATAGTAGTATC-GTACTGGTA
* * *
42715 ATAGTAATACCGGTATTGGTA
1 ATAGTAGTATC-GTACTGGTA
* *
42736 ATATTAGTATCGTTACTGGAA
1 ATAGTAGTATCG-TACTGGTA
42757 ATA
1 ATA
42760 TCGGTACTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 1 0.03
21 34 0.97
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (20 bp):
ATAGTAGTATCGTACTGGTA
Found at i:43288 original size:35 final size:35
Alignment explanation
Indices: 43239--43305 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
43229 TAGTATTGTT
43239 TCATATATCACATTTAGA-TATTGCACAATAGTGTG
1 TCATATATCACATTTAGAGTA-TGCACAATAGTGTG
* *
43274 TCATGTATCGCATTTAGAGTATGCACAATAGT
1 TCATATATCACATTTAGAGTATGCACAATAGT
43306 TAAAGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.93
36 2 0.07
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (35 bp):
TCATATATCACATTTAGAGTATGCACAATAGTGTG
Found at i:47036 original size:31 final size:29
Alignment explanation
Indices: 46994--47061 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 29
46984 ATAATTTACT
46994 TTAAATTTTTAACTAA-TTTATAA-TTATAAA
1 TTAAATTTTTAA--AATTTTA-AATTTATAAA
47024 TTAAATCTTTTAAAATTTTAAATTTTATAAA
1 TTAAAT-TTTTAAAATTTTAAA-TTTATAAA
47055 TTAAATT
1 TTAAATT
47062 AATACTACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
29 4 0.12
30 11 0.32
31 19 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (29 bp):
TTAAATTTTTAAAATTTTAAATTTATAAA
Found at i:48407 original size:64 final size:64
Alignment explanation
Indices: 48309--48437 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
48299 GCTAACAAAC
* *
48309 ATAGCAACACTCCACTATGCTTATATAAACTACCACCATTATGCTTTTCAACTCATGGAGCTAA
1 ATAGAAACACTACACTATGCTTATATAAACTACCACCATTATGCTTTTCAACTCATGGAGCTAA
*
48373 ATAGAAACACTACACTATGCTTATATAAATTACCACCATTATGCTTTTCAACTCATGGAGCTAA
1 ATAGAAACACTACACTATGCTTATATAAACTACCACCATTATGCTTTTCAACTCATGGAGCTAA
48437 A
1 A
48438 ATGCATTAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.09, T:0.30
Consensus pattern (64 bp):
ATAGAAACACTACACTATGCTTATATAAACTACCACCATTATGCTTTTCAACTCATGGAGCTAA
Found at i:49794 original size:11 final size:11
Alignment explanation
Indices: 49778--49851 Score: 57
Period size: 10 Copynumber: 7.1 Consensus size: 11
49768 GTAAAATTAA
49778 ATTATATAAAT
1 ATTATATAAAT
49789 ATTATA-AAAT
1 ATTATATAAAT
* *
49799 CTTATAAAAAT
1 ATTATATAAAT
** *
49810 AAAAT-TTAA-
1 ATTATATAAAT
49819 ATTATATAAAT
1 ATTATATAAAT
49830 ATTATA-AAAT
1 ATTATATAAAT
* *
49840 CTTATAAAAAT
1 ATTATATAAAT
49851 A
1 A
49852 AAATTTAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
9 3 0.06
10 23 0.48
11 22 0.46
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
ATTATATAAAT
Found at i:49809 original size:21 final size:21
Alignment explanation
Indices: 49779--49851 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
49769 TAAAATTAAA
*
49779 TTATATAAATATTATAAAATC
1 TTATAAAAATATTATAAAATC
** *
49800 TTATAAAAATAAAATTTAAA--
1 TTATAAAAATATTA-TAAAATC
*
49820 TTATATAAATATTATAAAATC
1 TTATAAAAATATTATAAAATC
49841 TTATAAAAATA
1 TTATAAAAATA
49852 AAATTTAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 4 0.10
20 11 0.28
21 21 0.52
22 4 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
TTATAAAAATATTATAAAATC
Found at i:49811 original size:25 final size:23
Alignment explanation
Indices: 49783--49861 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 23
49773 ATTAAATTAT
49783 ATAAATATTATAAAATCTTATAAAA
1 ATAAA-ATT-TAAAATCTTATAAAA
*
49808 ATAAAATTT-AAA--TTATATAA
1 ATAAAATTTAAAATCTTATAAAA
49828 AT---ATTATAAAATCTTATAAAA
1 ATAAAATT-TAAAATCTTATAAAA
49849 ATAAAATTTAAAA
1 ATAAAATTTAAAA
49862 GTTCTGAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
17 3 0.07
18 1 0.02
19 3 0.07
20 9 0.20
21 9 0.20
22 3 0.07
23 6 0.13
24 6 0.13
25 5 0.11
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAAAATTTAAAATCTTATAAAA
Found at i:49821 original size:41 final size:41
Alignment explanation
Indices: 49769--49860 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
49759 TAAAATTTTG
49769 TAAAA-TTAAATTATATAAATATTATAAAATCTTATAAAAA
1 TAAAATTTAAATTATATAAATATTATAAAATCTTATAAAAA
49809 TAAAATTTAAATTATATAAATATTATAAAATCTTATAAAAA
1 TAAAATTTAAATTATATAAATATTATAAAATCTTATAAAAA
49850 TAAAATTTAAA
1 TAAAATTTAAA
49861 AGTTCTGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (41 bp):
TAAAATTTAAATTATATAAATATTATAAAATCTTATAAAAA
Found at i:50738 original size:24 final size:24
Alignment explanation
Indices: 50709--50758 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
50699 TGGTGGTTGA
*
50709 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
50733 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
50757 TT
1 TT
50759 GGGTTCTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:51265 original size:17 final size:16
Alignment explanation
Indices: 51234--51267 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
51224 CACGTGAGGA
51234 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
51250 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
51267 T
1 T
51268 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:51675 original size:16 final size:17
Alignment explanation
Indices: 51644--51676 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
51634 TTTTGCCAGA
*
51644 GCATTTTATTTTGTTTT
1 GCATTTTATATTGTTTT
51661 GCATTTT-TATTGTTTT
1 GCATTTTATATTGTTTT
51677 TGTATAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.70
Consensus pattern (17 bp):
GCATTTTATATTGTTTT
Found at i:57652 original size:19 final size:21
Alignment explanation
Indices: 57615--57657 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
57605 TAACTTTTTC
*
57615 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
57635 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
57655 TTT
1 TTT
57658 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:61495 original size:17 final size:16
Alignment explanation
Indices: 61464--61497 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
61454 CACGTGAGGA
61464 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
61480 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
61497 T
1 T
61498 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:62953 original size:17 final size:18
Alignment explanation
Indices: 62931--62969 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
62921 AATATTATAA
*
62931 TTATTTTTATAA-AATAT
1 TTATTTTAATAACAATAT
*
62948 TTATTTTAATAACTATAT
1 TTATTTTAATAACAATAT
62966 TTAT
1 TTAT
62970 ATATTATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTTTAATAACAATAT
Found at i:62968 original size:29 final size:30
Alignment explanation
Indices: 62927--62987 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
62917 TCAAAATATT
* *
62927 ATAATTATTTTTATAAAATATT-TATTTTA
1 ATAACTATATTTATAAAATATTATATTTTA
* *
62956 ATAACTATATTTATATATTATTATATTTTA
1 ATAACTATATTTATAAAATATTATATTTTA
62986 AT
1 AT
62988 TATTTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
ATAACTATATTTATAAAATATTATATTTTA
Found at i:62982 original size:16 final size:16
Alignment explanation
Indices: 62961--63039 Score: 76
Period size: 16 Copynumber: 5.0 Consensus size: 16
62951 TTTTAATAAC
62961 TATATTTATATATTAT
1 TATATTTATATATTAT
62977 TATATTT-TA-ATTATT
1 TATATTTATATATTA-T
62992 TATTATTTATTATATT-T
1 TA-TATTTA-TATATTAT
* *
63009 AATAATTA-ATATTAT
1 TATATTTATATATTAT
*
63024 TATATTTATTTATTAT
1 TATATTTATATATTAT
63040 ATTCATTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 9 0.18
15 12 0.24
16 23 0.45
17 2 0.04
18 2 0.04
19 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTATATATTAT
Found at i:62991 original size:25 final size:24
Alignment explanation
Indices: 62962--63030 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 24
62952 TTTAATAACT
62962 ATATTTATATATTATTATATTTTA
1 ATATTTATATATTATTATATTTTA
62986 ATTATTTAT-TATTTATTATA-TTTA
1 A-TATTTATATA-TTATTATATTTTA
*
63010 ATAATTA-ATATTATTATATTT
1 ATATTTATATATTATTATATTT
63031 ATTTATTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 8 0.20
25 15 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATATTTATATATTATTATATTTTA
Found at i:63036 original size:42 final size:41
Alignment explanation
Indices: 62961--63039 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
62951 TTTTAATAAC
* *
62961 TATATTTATATATTATTATATTTTAATTATTTATTATTTAT
1 TATATTTATATATTAATATATTATAATTATTTATTATTTAT
*
63002 TATATTTA-ATAATTAATATTATTATATTTATTTATTAT
1 TATATTTATAT-ATTAATA-TATTATAATTATTTATTAT
63040 ATTCATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 2 0.06
41 14 0.42
42 17 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (41 bp):
TATATTTATATATTAATATATTATAATTATTTATTATTTAT
Found at i:63038 original size:13 final size:13
Alignment explanation
Indices: 62973--63048 Score: 65
Period size: 13 Copynumber: 6.2 Consensus size: 13
62963 TATTTATATA
*
62973 TTATTATATTTTAA
1 TTATTATA-TTTAT
62987 TTATT-TA-TTAT
1 TTATTATATTTAT
*
62998 TTATTATATTTAA
1 TTATTATATTTAT
*
63011 TAATTA-A--TA-
1 TTATTATATTTAT
63020 TTATTATATTTAT
1 TTATTATATTTAT
*
63033 TTATTATATTCAT
1 TTATTATATTTAT
63046 TTA
1 TTA
63049 ATTTCTACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
11 8 0.16
12 5 0.10
13 25 0.49
14 5 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (13 bp):
TTATTATATTTAT
Found at i:63511 original size:17 final size:17
Alignment explanation
Indices: 63491--63526 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
63481 CATATAAAAT
63491 ATAAGAAAATATCTAAA
1 ATAAGAAAATATCTAAA
* *
63508 ATAAGAGAATATTTAAA
1 ATAAGAAAATATCTAAA
63525 AT
1 AT
63527 TTTTAGAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (17 bp):
ATAAGAAAATATCTAAA
Found at i:65300 original size:2 final size:2
Alignment explanation
Indices: 65293--65319 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
65283 AGCACATTCT
65293 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 T
65320 TCACACAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66787 original size:2 final size:2
Alignment explanation
Indices: 66780--66804 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
66770 CTTTTAAAAC
66780 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
66805 CATACCCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66995 original size:12 final size:12
Alignment explanation
Indices: 66970--67039 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
66960 ACGGAGATAT
* *
66970 CAGAAATCAAAA
1 CAGAATTCAGAA
66982 CAGAATTCAGAA
1 CAGAATTCAGAA
*
66994 CA-ACTATCAGAA
1 CAGAAT-TCAGAA
* * *
67006 CAGAATCCATAT
1 CAGAATTCAGAA
* *
67018 TAGAAATCAGAA
1 CAGAATTCAGAA
67030 CAGAATTCAG
1 CAGAATTCAG
67040 GTCATATATC
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
11 2 0.05
12 38 0.90
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:67050 original size:24 final size:24
Alignment explanation
Indices: 66969--67076 Score: 87
Period size: 24 Copynumber: 4.5 Consensus size: 24
66959 AACGGAGATA
*
66969 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
66992 AACA-ACTATCAGAACAGAATCCATA-
1 -TCAGA-AATCAGAACAGAATTCA-AG
* *
67017 TTAGAAATCAGAACAGAATTCAGG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
67041 TCATATATCATAACAGAATTCAAG
1 TCAGAAATCAGAACAGAATTCAAG
67065 TCAGAAATCAGA
1 TCAGAAATCAGA
67077 TAAAATATTT
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
23 1 0.02
24 59 0.95
25 1 0.02
26 1 0.02
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:67050 original size:48 final size:48
Alignment explanation
Indices: 66966--67076 Score: 136
Period size: 48 Copynumber: 2.3 Consensus size: 48
66956 TTAAACGGAG
*
66966 ATATCAGAAATCAAAACAGAATTCAGAACAACTATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACAACTATCAGAACAGAATCC
* ** * *
67014 ATATTAGAAATCAGAACAGAATTCAGGTCATA-TATCATAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGAACA-ACTATCAGAACAGAATCC
67062 A-AGTCAGAAATCAGA
1 ATA-TCAGAAATCAGA
67077 TAAAATATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACAACTATCAGAACAGAATCC
Found at i:67104 original size:21 final size:21
Alignment explanation
Indices: 67078--67121 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
67068 GAAATCAGAT
67078 AAAATATTTATATGATTAGGG
1 AAAATATTTATATGATTAGGG
67099 AAAATATTTATATGATTAGGG
1 AAAATATTTATATGATTAGGG
67120 AA
1 AA
67122 CACACCAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (21 bp):
AAAATATTTATATGATTAGGG
Found at i:73071 original size:171 final size:170
Alignment explanation
Indices: 72632--73135 Score: 739
Period size: 171 Copynumber: 2.9 Consensus size: 170
72622 CAAAAGTTAA
** * *
72632 CGTTAAGTTAAAAAAAATAGAAAGTTTAGGTACTAAAACAAATCAAAACTGATAGTTTAGGTACT
1 CGTTAAGTTTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATCAAAATTGATAGTTTAGGTACT
* * *
72697 AAGCACGTTAAATTTTTAACGACAGGTACTAAAATAAAACAAAAACTAAATATTAAGTATGATTT
66 AAACACGTTAAGTTTTTAACGACAGATACTAAAATAAAACAAAAACTAAATATTAAGTATGATTT
*
72762 TGGGGAAAAAAATAAAAGTTTAAGTACTAAAACGGATCAAAAC
131 T---GAAAAAAATTAAAGTTTAAGTACTAAAACGGATCAAAAC
* *
72805 CGTTATGTTTT-AAAAATAGAAAGTTTAGGTACTAAAACAGAT-AAAATTTGATAGTTTAGGTAT
1 CGTTAAGTTTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATCAAAA-TTGATAGTTTAGGTAC
* * *
72868 TAAACATGTTAAGTTGTTAACGACAGATACTAAAATAAAATAAAAACTAAATATTAAGTATGATT
65 TAAACACGTTAAGTTTTTAACGACAGATACTAAAATAAAACAAAAACTAAATATTAAGTATGATT
72933 TTGAAAAAAATTAAAGTTTAAGTACTAAAACGGATCAAAAC
130 TTGAAAAAAATTAAAGTTTAAGTACTAAAACGGATCAAAAC
* *
72974 CGTTAAGTTTTTAAAAAATAGAAAGTTTAGCTACTAAAACAGATCAAAATTGATAGTTTATGTAC
1 CGTTAAG-TTTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATCAAAATTGATAGTTTAGGTAC
* *
73039 TAAACGA-GTTAAGTTTTTAACGGA-AAATACTAAAATAAAACAAAAACAAAATATTAAGTATGA
65 TAAAC-ACGTTAAGTTTTTAAC-GACAGATACTAAAATAAAACAAAAACTAAATATTAAGTATGA
*
73102 TTTT-AAAAAAATTAAAAGTTTGAGTACTAAAACG
128 TTTTGAAAAAAATT-AAAGTTTAAGTACTAAAACG
73136 TATTAAAATT
Statistics
Matches: 302, Mismatches: 22, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
169 44 0.15
170 13 0.04
171 125 0.41
172 112 0.37
173 8 0.03
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.29
Consensus pattern (170 bp):
CGTTAAGTTTTAAAAAATAGAAAGTTTAGGTACTAAAACAGATCAAAATTGATAGTTTAGGTACT
AAACACGTTAAGTTTTTAACGACAGATACTAAAATAAAACAAAAACTAAATATTAAGTATGATTT
TGAAAAAAATTAAAGTTTAAGTACTAAAACGGATCAAAAC
Found at i:75042 original size:21 final size:21
Alignment explanation
Indices: 75016--75085 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 21
75006 ATTTTGGACT
75016 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
75037 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
75058 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
75077 ATCGCAACG
1 ATCGCAACG
75086 CGAACTTCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
19 16 0.41
21 14 0.36
23 9 0.23
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:75090 original size:40 final size:42
Alignment explanation
Indices: 75012--75104 Score: 172
Period size: 40 Copynumber: 2.3 Consensus size: 42
75002 TGCGATTTTG
75012 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
75054 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
75094 GACTATCGCAA
1 GACTATCGCAA
75105 TGCGAATATG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 30 0.59
41 1 0.02
42 20 0.39
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:75101 original size:21 final size:21
Alignment explanation
Indices: 75037--75110 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
75027 TTTGGAATAA
75037 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
75058 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
75077 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
75098 ATCGCAATGCGAA
1 ATCGCAACGCGAA
75111 TATGTAAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
19 15 0.36
21 27 0.64
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:76466 original size:14 final size:14
Alignment explanation
Indices: 76447--76474 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
76437 AAGTGAAAGA
76447 ATAGTTATATAATT
1 ATAGTTATATAATT
76461 ATAGTTATATAATT
1 ATAGTTATATAATT
76475 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:78337 original size:2 final size:2
Alignment explanation
Indices: 78330--78356 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
78320 CTAAAATAAG
78330 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
78357 CTGACAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78798 original size:21 final size:22
Alignment explanation
Indices: 78766--78807 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
78756 TCTGATCAAT
*
78766 GTTTTCTTTG-TTCTTTTTGGG
1 GTTTTCTTTGTTTCGTTTTGGG
78787 GTTTT-TTATGTTTCGTTTTGG
1 GTTTTCTT-TGTTTCGTTTTGG
78808 AGTGTTGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 7 0.39
22 9 0.50
ACGTcount: A:0.02, C:0.07, G:0.24, T:0.67
Consensus pattern (22 bp):
GTTTTCTTTGTTTCGTTTTGGG
Found at i:82950 original size:2 final size:2
Alignment explanation
Indices: 82945--82972 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
82935 TTCTCTCATG
82945 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
82973 AACATTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:84857 original size:12 final size:12
Alignment explanation
Indices: 84840--84865 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
84830 TGGAGGTAGA
84840 GGTGATAGAGGT
1 GGTGATAGAGGT
84852 GGTGATAGAGGT
1 GGTGATAGAGGT
84864 GG
1 GG
84866 CTACGGAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGTGATAGAGGT
Found at i:84881 original size:30 final size:30
Alignment explanation
Indices: 84846--84940 Score: 118
Period size: 30 Copynumber: 3.2 Consensus size: 30
84836 TAGAGGTGAT
*
84846 AGAGGTGGTGATAGAGGTGGCTACGGAGGC
1 AGAGGTGGCGATAGAGGTGGCTACGGAGGC
* * *
84876 CGAGGTGGCGATAGAGGTGGCTACAGAGGT
1 AGAGGTGGCGATAGAGGTGGCTACGGAGGC
* * * *
84906 AGAGGTGGCGATAGGGGAGGCTATGGAGGT
1 AGAGGTGGCGATAGAGGTGGCTACGGAGGC
84936 AGAGG
1 AGAGG
84941 ACGTGGAAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.24, C:0.09, G:0.51, T:0.16
Consensus pattern (30 bp):
AGAGGTGGCGATAGAGGTGGCTACGGAGGC
Found at i:91990 original size:10 final size:10
Alignment explanation
Indices: 91962--91991 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
91952 ATGCACATGC
*
91962 ATATATATAT
1 ATATATATGT
91972 ATATATATGT
1 ATATATATGT
91982 ATATATATGT
1 ATATATATGT
91992 GTGTGTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:92288 original size:18 final size:18
Alignment explanation
Indices: 92265--92306 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
92255 AGGGATTATC
92265 AGTGGTCCTACGGGACAT
1 AGTGGTCCTACGGGACAT
*
92283 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTACGGGACAT
92301 AGTGGT
1 AGTGGT
92307 TATTCGGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTACGGGACAT
Found at i:92312 original size:18 final size:18
Alignment explanation
Indices: 92265--92317 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
92255 AGGGATTATC
* *
92265 AGTGGTCCTACGGGACAT
1 AGTGGTCATTCGGGACAT
*
92283 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
92301 AGTGGTTATTCGGGACA
1 AGTGGTCATTCGGGACA
92318 AATATTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Done.