Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001780.1 Hibiscus syriacus cultivar Beakdansim tig00003597_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: 105030
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.34
Found at i:3413 original size:2 final size:2
Alignment explanation
Indices: 3401--3444 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3391 CTGTATTAAT
*
3401 TA TA GA 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
3443 TA
1 TA
3445 CAATTTTAGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4949 original size:2 final size:2
Alignment explanation
Indices: 4942--5006 Score: 76
Period size: 2 Copynumber: 32.5 Consensus size: 2
4932 TCATTATAAT
* * * * *
4942 TC TC TC TC TC TC TC TC TC TC CC TC TC TC CC CC TC TC CC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
4984 TC TC TC CC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
5007 ATATATATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (2 bp):
TC
Found at i:4957 original size:10 final size:10
Alignment explanation
Indices: 4943--5006 Score: 87
Period size: 10 Copynumber: 6.6 Consensus size: 10
4933 CATTATAATT
*
4943 CTCTCTCTCT
1 CTCTCTCTCC
4953 CTCTCTCTCC
1 CTCTCTCTCC
4963 CTCTCTC-CC
1 CTCTCTCTCC
*
4972 C-CTCTCCCC
1 CTCTCTCTCC
4981 CTCTCTCTCC
1 CTCTCTCTCC
*
4991 CTCTCTCTCT
1 CTCTCTCTCC
5001 CTCTCT
1 CTCTCT
5007 ATATATATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
8 5 0.10
9 6 0.12
10 38 0.78
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (10 bp):
CTCTCTCTCC
Found at i:5635 original size:21 final size:19
Alignment explanation
Indices: 5609--5651 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
5599 CATGTTTATA
5609 AAATTTTAAAAAGACAAATAT
1 AAATTTTAAAAAGA-AAAT-T
*
5630 AAATTTTAAACAGAAAATT
1 AAATTTTAAAAAGAAAATT
5649 AAA
1 AAA
5652 AAAAATATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 4 0.19
21 13 0.62
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.28
Consensus pattern (19 bp):
AAATTTTAAAAAGAAAATT
Found at i:5927 original size:17 final size:16
Alignment explanation
Indices: 5905--5941 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
5895 TTTTATATTA
5905 TTAATATATATTCACCT
1 TTAA-ATATATTCACCT
5922 TT-AATATATTCACCT
1 TTAAATATATTCACCT
5937 TTAAA
1 TTAAA
5942 ATTATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 14 0.74
16 3 0.16
17 2 0.11
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATATATTCACCT
Found at i:5930 original size:15 final size:15
Alignment explanation
Indices: 5910--5940 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5900 TATTATTAAT
5910 ATATATTCACCTTTA
1 ATATATTCACCTTTA
5925 ATATATTCACCTTTA
1 ATATATTCACCTTTA
5940 A
1 A
5941 AATTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATTCACCTTTA
Found at i:7792 original size:18 final size:18
Alignment explanation
Indices: 7769--7833 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
7759 ATGATAAACA
7769 ATATCATACATAATAGTC
1 ATATCATACATAATAGTC
* * **
7787 ATATCAAAACCATGATAAAC
1 ATATC-ATA-CATAATAGTC
7807 AATATCATACATAATAGTC
1 -ATATCATACATAATAGTC
7826 ATATCATA
1 ATATCATA
7834 TTCTTTTTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
18 13 0.36
19 9 0.25
20 9 0.25
21 5 0.14
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (18 bp):
ATATCATACATAATAGTC
Found at i:7803 original size:39 final size:39
Alignment explanation
Indices: 7749--7831 Score: 166
Period size: 39 Copynumber: 2.1 Consensus size: 39
7739 CTCATGATTT
7749 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
7788 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
1 TATCAAAACCATGATAAACAATATCATACATAATAGTCA
7827 TATCA
1 TATCA
7832 TATTCTTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.27
Consensus pattern (39 bp):
TATCAAAACCATGATAAACAATATCATACATAATAGTCA
Found at i:7899 original size:19 final size:19
Alignment explanation
Indices: 7872--7918 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
7862 CTTTCATAAC
7872 TCATTTTCACCTTTCAC-TT
1 TCATTTTCA-CTTTCACATT
*
7891 TCATATTCACTTTCACATT
1 TCATTTTCACTTTCACATT
7910 TCATTTTCA
1 TCATTTTCA
7919 TAATTCGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.21, C:0.28, G:0.00, T:0.51
Consensus pattern (19 bp):
TCATTTTCACTTTCACATT
Found at i:7901 original size:12 final size:13
Alignment explanation
Indices: 7883--7968 Score: 57
Period size: 13 Copynumber: 6.4 Consensus size: 13
7873 CATTTTCACC
7883 TTTCACTTTCATA
1 TTTCACTTTCATA
*
7896 -TTCACTTTCACA
1 TTTCACTTTCATA
*
7908 TTTCATTTTCATA
1 TTTCACTTTCATA
* * *
7921 ATTCGTTCTTTCACA
1 TTTC--ACTTTCATA
*
7936 TTTCATTTTCATA
1 TTTCACTTTCATA
* *
7949 ATTCGTACTTTCACA
1 TTTC--ACTTTCATA
7964 TTTCA
1 TTTCA
7969 AAACTCATTC
Statistics
Matches: 53, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
12 11 0.21
13 23 0.43
15 19 0.36
ACGTcount: A:0.23, C:0.23, G:0.02, T:0.51
Consensus pattern (13 bp):
TTTCACTTTCATA
Found at i:7937 original size:28 final size:28
Alignment explanation
Indices: 7876--7968 Score: 138
Period size: 28 Copynumber: 3.4 Consensus size: 28
7866 CATAACTCAT
* *
7876 TTTCACCTTTCACTTTCAT-ATTC--AC
1 TTTCACATTTCATTTTCATAATTCGTAC
*
7901 TTTCACATTTCATTTTCATAATTCGTTC
1 TTTCACATTTCATTTTCATAATTCGTAC
7929 TTTCACATTTCATTTTCATAATTCGTAC
1 TTTCACATTTCATTTTCATAATTCGTAC
7957 TTTCACATTTCA
1 TTTCACATTTCA
7969 AAACTCATTC
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
25 17 0.28
26 4 0.07
28 40 0.66
ACGTcount: A:0.23, C:0.25, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTCACATTTCATTTTCATAATTCGTAC
Found at i:8025 original size:18 final size:18
Alignment explanation
Indices: 7999--8053 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
7989 AACTTGTTTC
*
7999 CAGACTCATAAATTATTT
1 CAGATTCATAAATTATTT
*
8017 CAGATTCATAATTTAATTT
1 CAGATTCATAAATT-ATTT
* *
8036 CATATTCATAACTTATTT
1 CAGATTCATAAATTATTT
8054 TCAAGATCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (18 bp):
CAGATTCATAAATTATTT
Found at i:8035 original size:19 final size:19
Alignment explanation
Indices: 7999--8065 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
7989 AACTTGTTTC
*
7999 CAGACTCATAAATT-ATTT
1 CAGATTCATAAATTAATTT
*
8017 CAGATTCATAATTTAATTT
1 CAGATTCATAAATTAATTT
* * *
8036 CATATTCATAACTTATTTT
1 CAGATTCATAAATTAATTT
8055 CAAGA-TCATAA
1 C-AGATTCATAA
8066 CCCAATGCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.29
19 27 0.66
20 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.04, T:0.42
Consensus pattern (19 bp):
CAGATTCATAAATTAATTT
Found at i:9626 original size:14 final size:14
Alignment explanation
Indices: 9607--9636 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9597 GTTCATTATC
9607 TTTCAGTACTTTAA
1 TTTCAGTACTTTAA
*
9621 TTTCAGTCCTTTAA
1 TTTCAGTACTTTAA
9635 TT
1 TT
9637 ATAGCACCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.17, G:0.07, T:0.53
Consensus pattern (14 bp):
TTTCAGTACTTTAA
Found at i:9744 original size:16 final size:16
Alignment explanation
Indices: 9720--9786 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 16
9710 TTTTAGGAAC
*
9720 TTTAATTTATTATTCT
1 TTTATTTTATTATTCT
* *
9736 TTTATTTTATTAACACTAACA
1 TTTATTTTATT---A-T-TCT
*
9757 TTTATTTTATTATTAT
1 TTTATTTTATTATTCT
9773 TTTATTTTATTATT
1 TTTATTTTATTATT
9787 TAATTTTATG
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
16 24 0.60
17 1 0.03
18 1 0.03
19 1 0.03
20 1 0.03
21 12 0.30
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTTTATTATTCT
Found at i:9784 original size:13 final size:13
Alignment explanation
Indices: 9758--9795 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
9748 ACACTAACAT
9758 TTATTTTA--TTA
1 TTATTTTATTTTA
9769 TTATTTTATTTTA
1 TTATTTTATTTTA
*
9782 TTATTTAATTTTA
1 TTATTTTATTTTA
9795 T
1 T
9796 GCATATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 8 0.33
13 16 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:13811 original size:11 final size:11
Alignment explanation
Indices: 13795--13819 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13785 TATATAGCAT
13795 AAAAAAGAAAA
1 AAAAAAGAAAA
13806 AAAAAAGAAAA
1 AAAAAAGAAAA
13817 AAA
1 AAA
13820 CATAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:13890 original size:14 final size:14
Alignment explanation
Indices: 13795--13903 Score: 76
Period size: 15 Copynumber: 7.2 Consensus size: 14
13785 TATATAGCAT
13795 AAAAAAGAAAAA-A
1 AAAAAAGAAAAAGA
* *
13808 AAAAGAAAAAAACATA
1 AAAA-AAGAAAA-AGA
* *
13824 AAAAAAGAGAGAGA
1 AAAAAAGAAAAAGA
13838 AAAGAAAGATAAAAGA
1 AAA-AAAGA-AAAAGA
* *
13854 AATATAGATAAAAGA
1 AAAAAAGA-AAAAGA
13869 AAGCAAAAGAGGAAAAGA
1 AA--AAAAGA--AAAAGA
13887 AAAAAAGAAAAAGA
1 AAAAAAGAAAAAGA
13901 AAA
1 AAA
13904 CATATCAACC
Statistics
Matches: 76, Mismatches: 12, Indels: 15
0.74 0.12 0.15
Matches are distributed among these distances:
13 4 0.05
14 20 0.26
15 23 0.30
16 17 0.22
17 4 0.05
18 8 0.11
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.05
Consensus pattern (14 bp):
AAAAAAGAAAAAGA
Found at i:15984 original size:55 final size:55
Alignment explanation
Indices: 15857--16887 Score: 588
Period size: 53 Copynumber: 19.1 Consensus size: 55
15847 TGTGTTTTTT
*
15857 AGAAACTAAGTCTGATTTTCAGAGGTTTCTTGAAATGCTATTTTTTAAA-GAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTG--ATG--A-TTTTTAAATGAGTTTTCAA
* * * * *
15916 AGTAACT-A---TGATTTTTATAAGTTTCTTGACGATTTTCAAATGAGTTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
15967 AGACACTAAGTCCGATTTTCGGAAGTTT-TCTGATGA-TTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCT-TGATGATTTTTAAATGAGTTTTCAA
* * * * ** * *
16021 AGAAACTAAGTGTAATTTTCATAAGTTTCTTAACAATTTTCAAATGAGTTTTTTTTTTAAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAG------TTTTCAA
* * * *
16082 AAAAACTAAGTCCGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
16137 AGAAACTAAGTATGATTTTCAGAAGTTTCTAGA-CAGTTTTTAAATGA-TATTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TTTTTAAATGAGT-TTTCAA
* * * * * * * *
16192 ATAAACTAATTTTGATTTTCATAAGTTTCTTTATTATTTTTAAATGAGCTTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
16247 AGAAACCAAGTCTGATTTTTAGAAGTTTCTTGATGA-TTTT-AACGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
16300 AGAAACTAAGTCTGATTTTCGGTAGTTCCTTGATGATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * * *
16355 TGAAATTAAGCCTGATTTTCA-AAGGTTTCTTGATG-TTTTCAAGTGAATTTAT-AA
1 AGAAACTAAGTCTGATTTTCAGAA-GTTTCTTGATGATTTTTAAATGAGTTT-TCAA
* * * * ** * * *
16409 A-AATGCTAAGCCTAATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAA-ACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
** * * ** * *
16462 AGAAGTTAAGCCTGATTTTTAGGGGTTTCTTGATG-TTTTCAAATGAATTTT-AA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * ** * * * *
16515 AGAAGCTAAGCCTGATTTTTAGGGGCTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * ** *
16568 AGAAGCTAAGCCTGATTTTCAG-GGTTTCTTGATG-TTTTCAAAT-AAATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* ** * * *
16620 AGAAGCTAAGTCTGATTTTCAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * ** * * *
16673 AGAAGCTAAG-CTTGATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * ** * ** *
16726 AGTAGCTAAG-CATGATTTTCAGGGGTTTCTTGATG-TTTTCAAAT-AAATTTGAA
1 AGAAACTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * * ** * * *
16779 AGAAGCTAAGCCTCATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
* * * *
16832 AGAAACTAAGCCTGATTTTCATG-AGTTTCTTGATG-TGTTCAAATGA-TTTTTAA
1 AGAAACTAAGTCTGATTTTCA-GAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
16885 AGA
1 AGA
16888 TGCTAAGCCT
Statistics
Matches: 822, Mismatches: 114, Indels: 78
0.81 0.11 0.08
Matches are distributed among these distances:
50 7 0.01
51 17 0.02
52 55 0.07
53 378 0.46
54 108 0.13
55 204 0.25
56 1 0.00
58 1 0.00
59 6 0.01
61 45 0.05
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTCAA
Found at i:16121 original size:61 final size:54
Alignment explanation
Indices: 15925--16388 Score: 290
Period size: 55 Copynumber: 8.4 Consensus size: 54
15915 AAGTAACTAT
* * ** * * *
15925 GATTTTTATAAGTTTCTTGACGATTTTCAAATGAGTTTTCAAAGACACTAAGTCC
1 GATTTTCAGAAGTTTCTTGATAATTTT-AAATGAGTTTTTAAAAAAACTAAGTCC
* * * **
15980 GATTTTCGGAAGTTT-TCTGATGATTTTAAATGAGTTTTTAAAGAAACTAAGTGT
1 GATTTTCAGAAGTTTCT-TGATAATTTTAAATGAGTTTTTAAAAAAACTAAGTCC
* * * *
16034 AATTTTCATAAGTTTCTTAACAATTTTCAAATGAGTTTTTTTTTTAAAAAAAACTAAGTCC
1 GATTTTCAGAAGTTTCTTGATAATTTT-AAATGAG-----TTTTT-AAAAAAACTAAGTCC
* * * * **
16095 GATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAACTAAGTAT
1 GATTTTCAGAAGTTTCTTGA-TAATTTTAAATGAGTTTTTAAAAAAACTAAGTCC
* * * * * **
16150 GATTTTCAGAAGTTTCTAGACAGTTTTTAAATGA-TATTTTAAATAAACTAATTTT
1 GATTTTCAGAAGTTTCTTGATA-ATTTTAAATGAGT-TTTTAAAAAAACTAAGTCC
* * * * * * * *
16205 GATTTTCATAAGTTTCTTTATTATTTTTAAATGAGCTTTGAAAGAAACCAAGTCT
1 GATTTTCAGAAGTTTCTTGA-TAATTTTAAATGAGTTTTTAAAAAAACTAAGTCC
* * * * *
16260 GATTTTTAGAAGTTTCTTGATGATTTT-AACGAGTTTTTAAAGAAACTAAGTCT
1 GATTTTCAGAAGTTTCTTGATAATTTTAAATGAGTTTTTAAAAAAACTAAGTCC
* * * * * * ** *
16313 GATTTTCGGTAGTTCCTTGATGATTTTTAAATGAGCTTTCAATGAAATTAAG-CC
1 GATTTTCAGAAGTTTCTTGAT-AATTTTAAATGAGTTTTTAAAAAAACTAAGTCC
16367 TGATTTTCA-AAGGTTTCTTGAT
1 -GATTTTCAGAA-GTTTCTTGAT
16389 GTTTTCAAGT
Statistics
Matches: 323, Mismatches: 68, Indels: 36
0.76 0.16 0.08
Matches are distributed among these distances:
53 39 0.12
54 55 0.17
55 179 0.55
56 4 0.01
60 5 0.02
61 36 0.11
62 5 0.02
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (54 bp):
GATTTTCAGAAGTTTCTTGATAATTTTAAATGAGTTTTTAAAAAAACTAAGTCC
Found at i:16249 original size:110 final size:110
Alignment explanation
Indices: 15859--16384 Score: 403
Period size: 110 Copynumber: 4.8 Consensus size: 110
15849 TGTTTTTTAG
* * * *
15859 AAACTAAGTCTGATTTTCAGAGGTTTCTTGAAATGCTATTTTTTAAA-GAGTTTTCAAAGTAACT
1 AAACTAAGTCTGATTTTCATAAGTTTCTTG--AT--TA-TTTTTAAATGAGCTTTCAAAGAAACT
* * * * * * *
15923 -A---TGATTTTTATAAGTTTCTTGAC-GATTTTCAAATGAGTTTTCAAAG
61 AAGTCTGATTTTCAGAAGTTTCTAGACAG-TTTTTAAATGATTTTTTAAAA
* * ** * * *
15969 ACACTAAGTCCGATTTTCGGAAGTTT-TCTGATGA-TTTTAAATGAGTTTTTAAAGAAACTAAGT
1 AAACTAAGTCTGATTTTCATAAGTTTCT-TGATTATTTTTAAATGAGCTTTCAAAGAAACTAAGT
* * * * *
16032 GTAATTTTCATAAGTTTCTTA-ACAATTTTCAAATGAGTTTTTTTTTTAAAAA
65 CTGATTTTCAGAAGTTTC-TAGACAGTTTTTAAATGA-----TTTTTT-AAAA
* * *
16084 AAACTAAGTCCGATTTTCAGAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAACTAAGTA
1 AAACTAAGTCTGATTTTCATAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAACTAAGTC
* *
16149 TGATTTTCAGAAGTTTCTAGACAGTTTTTAAATGATATTTTAAAT
66 TGATTTTCAGAAGTTTCTAGACAGTTTTTAAATGATTTTTTAAAA
* * * * *
16194 AAACTAATTTTGATTTTCATAAGTTTCTTTATTATTTTTAAATGAGCTTTGAAAGAAACCAAGTC
1 AAACTAAGTCTGATTTTCATAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAACTAAGTC
* * * * * * *
16259 TGATTTTTAGAAGTTTCTTGA-TGATTTT-AACGAGTTTTTAAAG
66 TGATTTTCAGAAGTTTCTAGACAGTTTTTAAATGATTTTTTAAAA
* * * * * *
16302 AAACTAAGTCTGATTTTCGGT-AGTTCCTTGATGATTTTTAAATGAGCTTTCAATGAAATTAAGC
1 AAACTAAGTCTGATTTTC-ATAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAACTAAGT
16366 CTGATTTTCA-AAGGTTTCT
65 CTGATTTTCAGAA-GTTTCT
16385 TGATGTTTTC
Statistics
Matches: 343, Mismatches: 54, Indels: 40
0.78 0.12 0.09
Matches are distributed among these distances:
104 7 0.02
105 15 0.04
106 2 0.01
107 2 0.01
108 79 0.23
109 35 0.10
110 104 0.30
111 5 0.01
114 4 0.01
115 34 0.10
116 56 0.16
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (110 bp):
AAACTAAGTCTGATTTTCATAAGTTTCTTGATTATTTTTAAATGAGCTTTCAAAGAAACTAAGTC
TGATTTTCAGAAGTTTCTAGACAGTTTTTAAATGATTTTTTAAAA
Found at i:16495 original size:53 final size:53
Alignment explanation
Indices: 16241--17025 Score: 961
Period size: 53 Copynumber: 14.8 Consensus size: 53
16231 TTAAATGAGC
* * * ** * *
16241 TTTGAAAGAAACCAAGTCTGATTTTTAGAAGTTTCTTGATGATTTT--AACGAGT
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATG-TTTTCAAATGA-A
* * * * * * * *
16294 TTTTAAAGAAACTAAGTCTGA-TTTTCGGTAGTTCCTTGATGATTTTTAAATGAGC
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGG-GGTTTCTTGATG-TTTTCAAATGA-A
* * ** * ** *
16349 TTTCAATGAAATTAAGCCTGATTTTCAAAGGTTTCTTGATGTTTTCAAGTGAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
* *
16402 TTT-ATAAAAATGCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
1 TTTGA-AAGAA-GCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
*
16456 TTTGAAAGAAGTTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
* *
16509 TTTTAAAGAAGCTAAGCCTGATTTTTAGGGGCTTCTTGATGTTTTCAAATGAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
* *
16562 TTTGAAAGAAGCTAAGCCTGATTTTCA-GGGTTTCTTGATGTTTTCAAATAAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
* *
16614 TTTGAAAGAAGCTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
*
16667 TTTGAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
* * * *
16720 TTTGAAAGTAGCTAAGCATGATTTTCAGGGGTTTCTTGATGTTTTCAAATAAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
*
16773 TTTGAAAGAAGCTAAGCCTCATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
* * * * * *
16826 TTTGAAAGAAACTAAGCCTGATTTTCATGAGTTTCTTGATGTGTTCAAATGAT
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
* * * **
16879 TTTTAAAGATGCTAAGCCTAATAATTAGGGGTTT-TTGATGTTTTCAAATGAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
* * *
16931 TTTGAAGGAAGCTAAGCTTGATTTATAGGGGTTTCTTGATGTTTTCAAATGAA
1 TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
* * *
16984 TTTTTAAAGAAGCTAATCCTAATTTTTAGGGGTTTCTTGATG
1 -TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATG
17026 ATAACTGTAA
Statistics
Matches: 637, Mismatches: 85, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
52 97 0.15
53 417 0.65
54 87 0.14
55 33 0.05
56 3 0.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.41
Consensus pattern (53 bp):
TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTCAAATGAA
Found at i:16715 original size:264 final size:265
Alignment explanation
Indices: 16361--17025 Score: 1005
Period size: 264 Copynumber: 2.5 Consensus size: 265
16351 TCAATGAAAT
** * * * *
16361 TAAGCCTGATTTTCAAAGGTTTCTTGATGTTTTCAAGTGAATTT-ATAAAAATGCTAAGCCTAAT
1 TAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGA-AAGAA-GCTAAGCTTGAT
*
16425 TTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGTTAAGCCTGATTTTTAGGGGTTT
64 TTTTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTT
* * *
16490 CTTGATGTTTTCAAATGAATTTTAAAGAAGCTAAGCCTGATTTTTAGGGGCTTCTTGATGTTTTC
129 CTTGATGTTTTCAAATAAATTTGAAAGAAGCTAAGCCTCATTTTTAGGGGCTTCTTGATGTTTTC
* * *
16555 AAATGAATTTGAAAGAAGCTAAGCCTGATTTTCA-GGGTTTCTTGATGTTTTCAAATAAATTTGA
194 AAATGAATTTGAAAGAAACTAAGCCTGATTTTCATGAGTTTCTTGATGTGTTCAAATAAATTTGA
16619 AAGAAGC
259 AAGAAGC
*
16626 TAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCTTGATTT
1 TAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCTTGATTT
* * *
16691 TTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGTAGCTAAGCATGATTTTCAGGGGTTTCT
66 TTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT
*
16756 TGATGTTTTCAAATAAATTTGAAAGAAGCTAAGCCTCATTTTTAGGGGTTTCTTGATGTTTTCAA
131 TGATGTTTTCAAATAAATTTGAAAGAAGCTAAGCCTCATTTTTAGGGGCTTCTTGATGTTTTCAA
* * *
16821 ATGAATTTGAAAGAAACTAAGCCTGATTTTCATGAGTTTCTTGATGTGTTCAAATGATTTTTAAA
196 ATGAATTTGAAAGAAACTAAGCCTGATTTTCATGAGTTTCTTGATGTGTTCAAATAAATTTGAAA
*
16886 GATGC
261 GAAGC
* * *
16891 TAAGCCTAATAATT-AGGGGTTT-TTGATGTTTTCAAATGAATTTGAAGGAAGCTAAGCTTGATT
1 TAAGCCTGAT-TTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCTTGATT
* * * *
16954 TATAGGGGTTTCTTGATGTTTTCAAATGAATTTTTAAAGAAGCTAATCCTAATTTTTAGGGGTTT
65 TTTAGGGGTTTCTTGATGTTTTCAAATGAA-TTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTT
17019 CTTGATG
129 CTTGATG
17026 ATAACTGTAA
Statistics
Matches: 363, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
264 234 0.64
265 126 0.35
266 3 0.01
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (265 bp):
TAAGCCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCTTGATTT
TTAGGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAGCTAAGCCTGATTTTTAGGGGTTTCT
TGATGTTTTCAAATAAATTTGAAAGAAGCTAAGCCTCATTTTTAGGGGCTTCTTGATGTTTTCAA
ATGAATTTGAAAGAAACTAAGCCTGATTTTCATGAGTTTCTTGATGTGTTCAAATAAATTTGAAA
GAAGC
Found at i:26677 original size:21 final size:21
Alignment explanation
Indices: 26651--26698 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
26641 AAACTTGGGA
26651 AAGCTCTATATGGTCTTAAGC
1 AAGCTCTATATGGTCTTAAGC
26672 AAGCTCTATATGGTCTTAAGC
1 AAGCTCTATATGGTCTTAAGC
26693 AAGCTC
1 AAGCTC
26699 CTTGCAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (21 bp):
AAGCTCTATATGGTCTTAAGC
Found at i:35809 original size:90 final size:88
Alignment explanation
Indices: 35657--35826 Score: 286
Period size: 90 Copynumber: 1.9 Consensus size: 88
35647 GCACACCCTT
* *
35657 TTATAGCCAATTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
*
35722 ATTAATTAGAATTTAATAATCCTC
66 ATTAATT-GAAATTAATAATCCTC
*
35746 TTATATCCAAGTTACCCTAATCATATTGAGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATT-AGGATTTTATTATTTCAAATTAATTAAATCTATATTT
35811 AATTAATTGAAATTAA
65 AATTAATTGAAATTAA
35827 ATATTCAGGA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 32 0.42
90 44 0.58
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:36901 original size:14 final size:14
Alignment explanation
Indices: 36882--36908 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36872 CAGTGTGACT
36882 ATCATGCCTCTGCG
1 ATCATGCCTCTGCG
36896 ATCATGCCTCTGC
1 ATCATGCCTCTGC
36909 TGTGTAAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.37, G:0.19, T:0.30
Consensus pattern (14 bp):
ATCATGCCTCTGCG
Found at i:42649 original size:90 final size:88
Alignment explanation
Indices: 42497--42666 Score: 295
Period size: 90 Copynumber: 1.9 Consensus size: 88
42487 ACACACCCTT
42497 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
42562 ATTAATTAGAATTTAATAATCCTC
66 ATTAATT-GAAATTAATAATCCTC
* *
42586 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
42651 AATTAATTGAAATTAA
65 AATTAATTGAAATTAA
42667 ATATTCGAGA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 36 0.47
90 41 0.53
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAATAATCCTC
Found at i:48254 original size:16 final size:16
Alignment explanation
Indices: 48230--48260 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48220 ATTGACTCCT
48230 TGTTCTTGACTTGGTG
1 TGTTCTTGACTTGGTG
*
48246 TGTTGTTGACTTGGT
1 TGTTCTTGACTTGGT
48261 TTAACGGTAA
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:0.06, C:0.10, G:0.32, T:0.52
Consensus pattern (16 bp):
TGTTCTTGACTTGGTG
Found at i:49191 original size:53 final size:53
Alignment explanation
Indices: 49133--49237 Score: 165
Period size: 53 Copynumber: 2.0 Consensus size: 53
49123 TCTGGGTAAC
* * * *
49133 TACAAGATAGTACATGTTCATAGATAATTCTTAATCTTTTAACATTGAACGCG
1 TACAAGATAATACATGTTCATAGATAACTCTCAATCTTTCAACATTGAACGCG
*
49186 TACAAGATAATATATGTTCATAGATAACTCTCAATCTTTCAACATTGAACGC
1 TACAAGATAATACATGTTCATAGATAACTCTCAATCTTTCAACATTGAACGC
49238 TCACATTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (53 bp):
TACAAGATAATACATGTTCATAGATAACTCTCAATCTTTCAACATTGAACGCG
Found at i:57687 original size:16 final size:16
Alignment explanation
Indices: 57668--57698 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
57658 TGAATTGATA
57668 TGATATTTACCTGACC
1 TGATATTTACCTGACC
*
57684 TGATATTTATCTGAC
1 TGATATTTACCTGAC
57699 TTATAAATTA
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:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (16 bp):
TGATATTTACCTGACC
Found at i:57739 original size:19 final size:19
Alignment explanation
Indices: 57715--57751 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
57705 ATTATAATTG
57715 ATGAAATTGTGAGATTTTA
1 ATGAAATTGTGAGATTTTA
57734 ATGAAATTGTGAGATTTT
1 ATGAAATTGTGAGATTTT
57752 GAATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (19 bp):
ATGAAATTGTGAGATTTTA
Found at i:58034 original size:24 final size:24
Alignment explanation
Indices: 57974--58034 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
57964 TTTATGTTTT
* *
57974 ATGTAATAATTAATTAATAATTTAA
1 ATGTAAT-ATAAATTAACAATTTAA
*
57999 ATGTAATTTAAATTAACAATTTAA
1 ATGTAATATAAATTAACAATTTAA
58023 A-GTATATATAAA
1 ATGTA-ATATAAA
58035 AGATGAGTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 3 0.10
24 21 0.68
25 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (24 bp):
ATGTAATATAAATTAACAATTTAA
Found at i:59145 original size:23 final size:23
Alignment explanation
Indices: 59113--59174 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
59103 AGTTGACATC
*
59113 AAAATTATAAAATAAATAAAGAA
1 AAAATAATAAAATAAATAAAGAA
* * *
59136 AAAATAAT-AATTAAATTATGAA
1 AAAATAATAAAATAAATAAAGAA
* *
59158 AAAAGAATAAAGTAAAT
1 AAAATAATAAAATAAAT
59175 TGAAATAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 18 0.56
23 14 0.44
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (23 bp):
AAAATAATAAAATAAATAAAGAA
Found at i:59994 original size:42 final size:42
Alignment explanation
Indices: 59893--59986 Score: 152
Period size: 42 Copynumber: 2.2 Consensus size: 42
59883 CGAAAATCAG
* *
59893 AAGAATCAATAAACTTAACAATTTCATGAAATTTAATAATAA
1 AAGAATCAATAAACTTAACAATTTCACGAAATTTAATAACAA
* *
59935 AAGAATCAATAAACTTAACTATTTCACGCAATTTAATAACAA
1 AAGAATCAATAAACTTAACAATTTCACGAAATTTAATAACAA
59977 AAGAATCAAT
1 AAGAATCAAT
59987 TACCTTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (42 bp):
AAGAATCAATAAACTTAACAATTTCACGAAATTTAATAACAA
Found at i:61233 original size:43 final size:43
Alignment explanation
Indices: 61186--61306 Score: 142
Period size: 40 Copynumber: 2.9 Consensus size: 43
61176 GAAAAGTCTC
*
61186 AATTAGAGAAGAGGAACATAAGAAGAAGAAGGGGAAGAATCTA
1 AATTAGAGAAGAGGAACATAAGAATAAGAAGGGGAAGAATCTA
* *
61229 AATTAGAG-A-A-TAAC-TGAAGAATAAGAAGGGGAAGAATCTT
1 AATTAGAGAAGAGGAACAT-AAGAATAAGAAGGGGAAGAATCTA
* * * *
61269 GATTAGAGAAGAGGAATAGAAGAATAAGAAGTGGAAGA
1 AATTAGAGAAGAGGAACATAAGAATAAGAAGGGGAAGA
61307 GACCCGGTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
39 1 0.02
40 32 0.49
41 2 0.03
42 2 0.03
43 28 0.43
ACGTcount: A:0.52, C:0.03, G:0.30, T:0.15
Consensus pattern (43 bp):
AATTAGAGAAGAGGAACATAAGAATAAGAAGGGGAAGAATCTA
Found at i:61318 original size:43 final size:43
Alignment explanation
Indices: 61187--61331 Score: 145
Period size: 43 Copynumber: 3.4 Consensus size: 43
61177 AAAAGTCTCA
* * * ***
61187 ATTAGAGAAGAGGAACATAAGAAGAAGAAGGGGAAGAATCTAA
1 ATTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGAATCCCG
* * **
61230 ATTAGAGAATA--ACT-GAAGAATAAGAAGGGGAAGAATCTTG
1 ATTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGAATCCCG
*
61270 ATTAGAGAAGAGGAATAGAAGAATAAGAAGTGGAAGAGA-CCCG
1 ATTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGA-ATCCCG
*
61313 GTTAGAGAAGAGGAATAGA
1 ATTAGAGAAGAGGAATAGA
61332 GATAGAAGAA
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
40 32 0.38
41 1 0.01
42 2 0.02
43 49 0.58
44 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.31, T:0.14
Consensus pattern (43 bp):
ATTAGAGAAGAGGAATAGAAGAATAAGAAGGGGAAGAATCCCG
Found at i:65092 original size:26 final size:26
Alignment explanation
Indices: 65056--65115 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
65046 ATCGAAGTGC
65056 TAATACACATAAGGACGTGCCCACCA
1 TAATACACATAAGGACGTGCCCACCA
* **
65082 TAATACACATATGGTTGTGCCCACCA
1 TAATACACATAAGGACGTGCCCACCA
65108 TAATACAC
1 TAATACAC
65116 TTAGTGCCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.28, G:0.13, T:0.22
Consensus pattern (26 bp):
TAATACACATAAGGACGTGCCCACCA
Found at i:66044 original size:29 final size:30
Alignment explanation
Indices: 65989--66055 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
65979 CAACTATTCA
* * *
65989 CAACTTTTCCAAAATTATTGATTTGGTCCT
1 CAACTTTTCCAAAATTATAGATATGGTCCC
66019 CAACTTTT-CAAAATATATAGA-ATGGTCCC
1 CAACTTTTCCAAAAT-TATAGATATGGTCCC
*
66048 CAAATTTT
1 CAACTTTT
66056 TCTAAGGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 19 0.59
30 13 0.41
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (30 bp):
CAACTTTTCCAAAATTATAGATATGGTCCC
Found at i:80289 original size:30 final size:32
Alignment explanation
Indices: 80244--80303 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
80234 TGCAAATAAA
*
80244 ATGAAATATTAATAAGAAAATATATAAATACT
1 ATGAAATATTAATAAGAAAATATAAAAATACT
* *
80276 ATGAAA-A-TAATAAGTATATATAAAAATA
1 ATGAAATATTAATAAGAAAATATAAAAATA
80304 ATTTTGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 18 0.72
31 1 0.04
32 6 0.24
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.30
Consensus pattern (32 bp):
ATGAAATATTAATAAGAAAATATAAAAATACT
Found at i:82359 original size:3 final size:3
Alignment explanation
Indices: 82351--82410 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
82341 AATTATTTTT
*
82351 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
82399 TAA TAA TAA TAA
1 TAA TAA TAA TAA
82411 AATGAGTAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:85425 original size:23 final size:22
Alignment explanation
Indices: 85344--85440 Score: 108
Period size: 23 Copynumber: 4.4 Consensus size: 22
85334 GTCGAGGGTT
*
85344 CTATGTGGTCCTTAGGGAAAAAA
1 CTATGTGGTCCTTCGGG-AAAAA
85367 CTATGTGGTCCTTCAGGG-AAAA
1 CTATGTGGTCCTTC-GGGAAAAA
*
85389 TTATGTGGTCCTTCGGGATAAAA
1 CTATGTGGTCCTTCGGGA-AAAA
* * *
85412 CTATGTAGTCCTTCGAGACAAA
1 CTATGTGGTCCTTCGGGAAAAA
85434 -TATGTGG
1 CTATGTGG
85441 CACTTTGGTG
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
21 9 0.14
22 20 0.31
23 32 0.50
24 3 0.05
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (22 bp):
CTATGTGGTCCTTCGGGAAAAA
Found at i:86108 original size:23 final size:24
Alignment explanation
Indices: 86064--86110 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
86054 CACTGAAGTG
* *
86064 CCACGTAGAATTTTTCCCGAAGGA
1 CCACGTAGAATATGTCCCGAAGGA
86088 CCACGTAGAA-ATGTCCCGAAGGA
1 CCACGTAGAATATGTCCCGAAGGA
86111 TCACATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (24 bp):
CCACGTAGAATATGTCCCGAAGGA
Found at i:86542 original size:13 final size:13
Alignment explanation
Indices: 86524--86553 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
86514 CCTTTTAGCT
86524 TTTGTTAAATCTC
1 TTTGTTAAATCTC
*
86537 TTTGTTATATCTC
1 TTTGTTAAATCTC
86550 TTTG
1 TTTG
86554 ATCAATACGT
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:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (13 bp):
TTTGTTAAATCTC
Found at i:87985 original size:26 final size:26
Alignment explanation
Indices: 87956--88015 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
87946 ACCGAAGTGC
* *
87956 TAATACACGTAAATTCGTGCCCACCA
1 TAATACACATAAAGTCGTGCCCACCA
*
87982 TAATACACATAAGGTCGTGCCCACCA
1 TAATACACATAAAGTCGTGCCCACCA
88008 TAATACAC
1 TAATACAC
88016 TTAGTTCCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.37, C:0.30, G:0.12, T:0.22
Consensus pattern (26 bp):
TAATACACATAAAGTCGTGCCCACCA
Found at i:91391 original size:31 final size:31
Alignment explanation
Indices: 91356--91428 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
91346 TGGGACTCCA
**
91356 AATCAAGCAAAGAAAAGGTGACATCTTCATC
1 AATCAAGCAAAGAAAAGACGACATCTTCATC
91387 AATCAAGCAAAGAAAAGACGACATCTTCATC
1 AATCAAGCAAAGAAAAGACGACATCTTCATC
91418 AATCAAGCAAA
1 AATCAAGCAAA
91429 ATACGTCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (31 bp):
AATCAAGCAAAGAAAAGACGACATCTTCATC
Found at i:92071 original size:15 final size:15
Alignment explanation
Indices: 92051--92081 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
92041 GGACATTGAA
92051 ATTAGACATCATTTC
1 ATTAGACATCATTTC
*
92066 ATTAGAGATCATTTC
1 ATTAGACATCATTTC
92081 A
1 A
92082 CAAAAGGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (15 bp):
ATTAGACATCATTTC
Found at i:92531 original size:23 final size:22
Alignment explanation
Indices: 92500--92573 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
92490 GAAAGTGTAC
92500 CGATGCATCCCTTGAATGTGCAT
1 CGATGCAT-CCTTGAATGTGCAT
* * *
92523 CGATACAT-CATGAA-GATGCAC
1 CGATGCATCCTTGAATG-TGCAT
92544 CGATGCATTCCTTGAATGTGCAT
1 CGATGCA-TCCTTGAATGTGCAT
92567 CGATGCA
1 CGATGCA
92574 CTATGCTATG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 1 0.02
21 15 0.37
22 1 0.02
23 23 0.56
24 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (22 bp):
CGATGCATCCTTGAATGTGCAT
Found at i:93054 original size:13 final size:13
Alignment explanation
Indices: 93036--93069 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
93026 TTCATATTGA
*
93036 TTTTCAAACATCG
1 TTTTCAAACATAG
93049 TTTTCAAACATAG
1 TTTTCAAACATAG
*
93062 CTTTCAAA
1 TTTTCAAA
93070 ATTGCCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:97449 original size:21 final size:20
Alignment explanation
Indices: 97402--97456 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 20
97392 AGTACTCAAG
97402 GGAGTATCGATACCTAGGGTA
1 GGAGTATCGATACCTA-GGTA
97423 -GAGTATCGATACTCTCA-GTA
1 GGAGTATCGATAC-CT-AGGTA
*
97443 GGAGTATTGATACC
1 GGAGTATCGATACC
97457 GAGCTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 16 0.53
21 13 0.43
22 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.27
Consensus pattern (20 bp):
GGAGTATCGATACCTAGGTA
Found at i:98681 original size:40 final size:40
Alignment explanation
Indices: 98584--98687 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
98574 TACGATTTCC
* *
98584 TTTTTCAAAATAGGAAAATAAAATTCAACGATTTATTTTCT
1 TTTTTCAAAATAGGAAAAT-AAATTAAACGATTTATTTTAT
* * **
98625 TTTAT-GAACCAGGAAAATAAATTAAACGATTTATTTTAT
1 TTTTTCAAAATAGGAAAATAAATTAAACGATTTATTTTAT
*
98664 TTTTTCAAAATAAGAAAATAAATT
1 TTTTTCAAAATAGGAAAATAAATT
98688 CAACAATTCA
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
39 23 0.45
40 24 0.47
41 4 0.08
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (40 bp):
TTTTTCAAAATAGGAAAATAAATTAAACGATTTATTTTAT
Found at i:98745 original size:79 final size:80
Alignment explanation
Indices: 98584--98745 Score: 191
Period size: 79 Copynumber: 2.0 Consensus size: 80
98574 TACGATTTCC
* * * ** ** *
98584 TTTTTCAAAATAGGAAAATAAAATTCAACGATTTATTTTCTTTTATGAACCAGGAAAATAAATTA
1 TTTTTCAAAATAAGAAAATAAAATTCAACAATTCATTACCTTTTACAAAACAGGAAAATAAATTA
*
98649 AACGATTTATTTTAT
66 AACGATTTATTTCAT
* *
98664 TTTTTCAAAATAAGAAAAT-AAATTCAACAATTCATTACCTTTTACAAAACATGAAAATAAATTC
1 TTTTTCAAAATAAGAAAATAAAATTCAACAATTCATTACCTTTTACAAAACAGGAAAATAAATTA
* * *
98728 GACGGTTTGTTTCAT
66 AACGATTTATTTCAT
98743 TTT
1 TTT
98746 ACAAGATAGA
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
79 50 0.74
80 18 0.26
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (80 bp):
TTTTTCAAAATAAGAAAATAAAATTCAACAATTCATTACCTTTTACAAAACAGGAAAATAAATTA
AACGATTTATTTCAT
Found at i:99026 original size:115 final size:113
Alignment explanation
Indices: 98850--99255 Score: 430
Period size: 115 Copynumber: 3.5 Consensus size: 113
98840 CCTTTTATAA
* * * * * *
98850 AATCATTTAAAATTATCAAGAAAATAAATTTAACAATTT-CTTTCTTTCTAAAAGAT-GAATCAT
1 AATCATTCAAGATTCTCAAGAAAATAAA-TTAACAATTTATTTTCTTAC--AAAGTTAGAATCAT
* * * * *
98913 CCACGATTCTTAAGAAAATAAATTCAACGATTTATTTTTCATACAAATTTAG
63 TCAAGATTCTAAAG-AAATAAATTCAACAATTTATTTTTCATACAAAATTAG
*
98965 AATCATTCAAGATTCTCAAGAAAATAAATTAAACAATTTATTTTCTTACAAAGTTACAATCATTC
1 AATCATTCAAGATTCTCAAGAAAATAAATT-AACAATTTATTTTCTTACAAAGTTAGAATCATTC
* * * *
99030 AAGATTCTCAAGGAAAT-AATTCAAACTATTTA-TTTTCATTATAAAGTTAG
65 AAGATTCT-AAAGAAATAAATTC-AACAATTTATTTTTCA-TACAAAATTAG
* * * **
99080 AATCATTTAAGATTCTCAAGGAAATAAATCTAACTATACATTTTTCTTACAAAGTTAGAATCATT
1 AATCATTCAAGATTCTCAAGAAAATAAAT-TAACAATTTA-TTTTCTTACAAAGTTAGAATCATT
*
99145 CAAGATTCTAAATGAAATAAATTCAACAATTT-TTTTTCTTACAAAATTAG
64 CAAGATTCTAAA-GAAATAAATTCAACAATTTATTTTTCATACAAAATTAG
* *
99195 AATCATTCAAGATTCTC-AGGAAATAAATTCAACAATTAATTTTCCTTACAAAGTTA-AATCA
1 AATCATTCAAGATTCTCAAGAAAATAAATT-AACAATTTATTTT-CTTACAAAGTTAGAATCA
99256 ACACAAGATT
Statistics
Matches: 249, Mismatches: 29, Indels: 28
0.81 0.09 0.09
Matches are distributed among these distances:
113 10 0.04
114 47 0.19
115 128 0.51
116 59 0.24
117 5 0.02
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (113 bp):
AATCATTCAAGATTCTCAAGAAAATAAATTAACAATTTATTTTCTTACAAAGTTAGAATCATTCA
AGATTCTAAAGAAATAAATTCAACAATTTATTTTTCATACAAAATTAG
Found at i:99141 original size:173 final size:171
Alignment explanation
Indices: 98946--99255 Score: 471
Period size: 173 Copynumber: 1.8 Consensus size: 171
98936 TCAACGATTT
* *
98946 ATTTTTCATACAAATTTAGAATCATTCAAGATTCTCAA-GAAAATAAATTAAACAATTTATTTTC
1 ATTTTTCATACAAAGTTAGAATCATTCAAGATTCTAAATG-AAATAAATTAAACAATTTATTTTC
* * * *
99010 TTACAAAGTTACAATCATTCAAGATTCTCAAGGAAAT-AATTCAAACTATTTATTTTCATTATAA
65 TTACAAAATTACAATCATTCAAGATTCTC-AGGAAATAAATTC-AACAATTAATTTTCATTACAA
99074 AGTTAGAATCATTTAAGATTCTCAAGGAAATAAATCTAACTATAC
128 AGTTA-AATCATTTAAGATTCTCAAGGAAATAAATCTAACTATAC
* * *
99119 ATTTTTCTTACAAAGTTAGAATCATTCAAGATTCTAAATGAAATAAATTCAACAATTTTTTTTCT
1 ATTTTTCATACAAAGTTAGAATCATTCAAGATTCTAAATGAAATAAATTAAACAATTTATTTTCT
* *
99184 TACAAAATTAGAATCATTCAAGATTCTCAGGAAATAAATTCAACAATTAATTTTCCTTACAAAGT
66 TACAAAATTACAATCATTCAAGATTCTCAGGAAATAAATTCAACAATTAATTTTCATTACAAAGT
99249 TAAATCA
131 TAAATCA
99256 ACACAAGATT
Statistics
Matches: 124, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
171 5 0.04
172 29 0.23
173 89 0.72
174 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.37
Consensus pattern (171 bp):
ATTTTTCATACAAAGTTAGAATCATTCAAGATTCTAAATGAAATAAATTAAACAATTTATTTTCT
TACAAAATTACAATCATTCAAGATTCTCAGGAAATAAATTCAACAATTAATTTTCATTACAAAGT
TAAATCATTTAAGATTCTCAAGGAAATAAATCTAACTATAC
Found at i:99265 original size:57 final size:58
Alignment explanation
Indices: 98850--99255 Score: 445
Period size: 57 Copynumber: 7.1 Consensus size: 58
98840 CCTTTTATAA
* * * * * * *
98850 AATCATTTAAAATTATCAAGAAAATAAATTTAACAATTTCTTTCTT-TCTA-AAAGAT-G
1 AATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTT-TTCT-TACAAAGTTAG
* * * * * * *
98907 AATCATCCACGATTCTTAAGAAAATAAATTCAACGATTTATTTTTCATACAAATTTAG
1 AATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
* * *
98965 AATCATTCAAGATTCTCAAGAAAATAAATTAAACAATTTA-TTTTCTTACAAAGTTAC
1 AATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
* *
99022 AATCATTCAAGATTCTCAAGGAAAT-AATTCAAACTATTTA-TTTTCATTATAAAGTTAG
1 AATCATTCAAGATTCTCAAGGAAATAAATTC-AACAATTTATTTTTC-TTACAAAGTTAG
* * **
99080 AATCATTTAAGATTCTCAAGGAAATAAA-TCTAACTATACATTTTTCTTACAAAGTTAG
1 AATCATTCAAGATTCTCAAGGAAATAAATTC-AACAATTTATTTTTCTTACAAAGTTAG
* * *
99138 AATCATTCAAGATTCTAAATGAAATAAATTCAACAATTT-TTTTTCTTACAAAATTAG
1 AATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
* *
99195 AATCATTCAAGATTCTC-AGGAAATAAATTCAACAATTAATTTTCCTTACAAAGTTA-
1 AATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
99251 AATCA
1 AATCA
99256 ACACAAGATT
Statistics
Matches: 298, Mismatches: 42, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
56 32 0.11
57 137 0.46
58 120 0.40
59 9 0.03
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (58 bp):
AATCATTCAAGATTCTCAAGGAAATAAATTCAACAATTTATTTTTCTTACAAAGTTAG
Found at i:99470 original size:42 final size:44
Alignment explanation
Indices: 99423--99545 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 44
99413 TTTAGCAACT
99423 CAATAATCAGAATGAACTAATTCTTTGATTTTT-TTTACA-AT-C
1 CAATAATCAGAATGAACTAA-TCTTTGATTTTTATTTACACATCC
* * * * *
99465 CAATAATAAAAATGAGCTAATCATTTGATTTTTAATTTTCACTTCC
1 CAATAATCAGAATGAACTAATC-TTTGATTTTT-ATTTACACATCC
* * *
99511 CAATAATC-GAAAGAATTAATCTTTGATTTTAATTT
1 CAATAATCAGAATGAACTAATCTTTGATTTTTATTT
99546 CCGCAACTCA
Statistics
Matches: 65, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
41 2 0.03
42 27 0.42
43 4 0.06
44 14 0.22
45 10 0.15
46 8 0.12
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.42
Consensus pattern (44 bp):
CAATAATCAGAATGAACTAATCTTTGATTTTTATTTACACATCC
Found at i:100157 original size:42 final size:42
Alignment explanation
Indices: 100097--100206 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
100087 TATGAAATCT
*
100097 CGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATGTTTTAC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTAC
*
100139 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCC
1 CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTAC
*
100181 CGTGTTTGTTTCACGTAATTCATTTT
1 CGTGTTTGTTTCACGTAATTCGTTTT
100207 TCCAGAATGT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.17, C:0.16, G:0.18, T:0.48
Consensus pattern (42 bp):
CGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTAC
Found at i:100443 original size:52 final size:48
Alignment explanation
Indices: 100387--100499 Score: 129
Period size: 52 Copynumber: 2.2 Consensus size: 48
100377 TTTTCATCAA
* **
100387 AATATTATTATTAA-AATATTTAAAATATATTTATTAATATTTATAATAATAT
1 AATATTATT-TTAATAATATATAAAATA-ATCAATT-ATA--TATAATAATAT
*
100439 AATATTATTTTAATATTATATAAAATAATCAATTATATATAATAATAT
1 AATATTATTTTAATAATATATAAAATAATCAATTATATATAATAATAT
100487 AGATATTATTTTA
1 A-ATATTATTTTA
100500 TTTTAATAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
48 12 0.22
49 11 0.20
50 3 0.05
51 9 0.16
52 20 0.36
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (48 bp):
AATATTATTTTAATAATATATAAAATAATCAATTATATATAATAATAT
Found at i:100473 original size:28 final size:28
Alignment explanation
Indices: 100420--100570 Score: 82
Period size: 26 Copynumber: 5.7 Consensus size: 28
100410 AATATATTTA
100420 TTAATATTTATAATAATATAATATTATT
1 TTAATATTTATAATAATATAATATTATT
*
100448 TTAATA-TTAT-ATAAAATAATCA--A--
1 TTAATATTTATAATAATATAAT-ATTATT
100471 TT-ATA--TATAATAATATAGATATTA-T
1 TTAATATTTATAATAATATA-ATATTATT
*
100496 TT--TATTT-TAATAAATATAATAAATTTTT
1 TTAATATTTATAAT-AATATAAT--ATTATT
* *
100524 TTATATATTGAATAATGA-ATAATATTA-T
1 TTA-ATATT-TATAATAATATAATATTATT
100552 TTATATATTTA-AATAATAT
1 TTA-ATATTTATAATAATAT
100571 TTTAGTAAAG
Statistics
Matches: 97, Mismatches: 8, Indels: 37
0.68 0.06 0.26
Matches are distributed among these distances:
21 3 0.03
22 11 0.11
23 4 0.04
24 3 0.03
25 9 0.09
26 20 0.21
27 11 0.11
28 19 0.20
29 3 0.03
31 9 0.09
32 1 0.01
33 4 0.04
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (28 bp):
TTAATATTTATAATAATATAATATTATT
Found at i:100515 original size:48 final size:48
Alignment explanation
Indices: 100428--100520 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 48
100418 TATTAATATT
*
100428 TATAATAATATAATATTATTTTAATATTATATAAAATAATCAATTATA
1 TATAATAATATAATATTATTTTAATATTATATAAAATAATAAATTATA
*
100476 TATAATAATATAGATATTATTTT-ATTTTA-ATAAATATAATAAATT
1 TATAATAATATA-ATATTATTTTAATATTATATAAA-ATAATAAATT
100521 TTTTTATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
47 5 0.12
48 26 0.63
49 10 0.24
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (48 bp):
TATAATAATATAATATTATTTTAATATTATATAAAATAATAAATTATA
Found at i:101010 original size:20 final size:20
Alignment explanation
Indices: 100892--101001 Score: 211
Period size: 20 Copynumber: 5.5 Consensus size: 20
100882 TTTCCAGATG
100892 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
100912 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
100932 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
100952 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
100972 TTTTCCAAAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
100992 TTTTCCAGAA
1 TTTTCCAGAA
101002 TTCAAATTCC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:101017 original size:29 final size:30
Alignment explanation
Indices: 100984--101055 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
100974 TTCCAAAAAT
100984 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* *
101013 GTAATTTATTTTCCAGTAATTCAAATTCTA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
101043 GTAATTCATTTTC
1 GTAATTCATTTTC
101056 TGGAAAATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 15 0.38
30 24 0.62
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:101056 original size:15 final size:15
Alignment explanation
Indices: 100984--101055 Score: 83
Period size: 15 Copynumber: 4.9 Consensus size: 15
100974 TTCCAAAAAT
100984 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
100999 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
101013 GTAATTTATTTTCCA
1 GTAATTCATTTTCCA
** *
101028 GTAATTCAAATTCTA
1 GTAATTCATTTTCCA
101043 GTAATTCATTTTC
1 GTAATTCATTTTC
101056 TGGAAAATCA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
14 12 0.27
15 33 0.73
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:103011 original size:23 final size:22
Alignment explanation
Indices: 102985--103042 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
102975 ATTAAATAAT
* *
102985 TATTTATATATTTATAAAATT-
1 TATTTATATATTCAAAAAATTA
*
103006 TATATTAAATTATTCAAAAAATTA
1 TAT-TTATA-TATTCAAAAAATTA
103030 TATTTATAATATT
1 TATTTAT-ATATT
103043 ATTTTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 3 0.10
22 4 0.14
23 18 0.62
24 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TATTTATATATTCAAAAAATTA
Found at i:104138 original size:2 final size:2
Alignment explanation
Indices: 104131--104200 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
104121 CTGATTCGTG
104131 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
104173 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
104201 CTTTTTTTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:104307 original size:20 final size:20
Alignment explanation
Indices: 104269--104307 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
104259 CTTTCAGCCA
* * *
104269 AGTATCGGTACTCCCATAGG
1 AGTATCGATACTACAATAGG
104289 AGTATCGATACTACAATAG
1 AGTATCGATACTACAATAG
104308 CTTGGTATCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
AGTATCGATACTACAATAGG
Done.