Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2683
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: 150094
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5477 original size:19 final size:19
Alignment explanation
Indices: 5437--5479 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5427 AGAAGCTCAA
*
5437 ATTGAGCTCAAATAGGTGG
1 ATTGAGCTCAAATAGCTGG
*
5456 ATTGAGCTCAAGTGAGCT-G
1 ATTGAGCTCAAAT-AGCTGG
5475 ATTGA
1 ATTGA
5480 AAGTCTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (19 bp):
ATTGAGCTCAAATAGCTGG
Found at i:7885 original size:13 final size:13
Alignment explanation
Indices: 7867--7915 Score: 75
Period size: 13 Copynumber: 3.8 Consensus size: 13
7857 TAGCTCTCTC
7867 TTTTTTCACAATT
1 TTTTTTCACAATT
7880 TTTTTTCACAATTT
1 TTTTTTCACAA-TT
7894 TTTTTTCA-AATT
1 TTTTTTCACAATT
7906 TTTTTT-ACAA
1 TTTTTTCACAA
7916 CTGAATCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 1 0.03
12 10 0.29
13 13 0.38
14 10 0.29
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTTCACAATT
Found at i:7970 original size:11 final size:12
Alignment explanation
Indices: 7951--7998 Score: 78
Period size: 12 Copynumber: 3.9 Consensus size: 12
7941 TGGAAACCAA
7951 AATTTTTTTTTG
1 AATTTTTTTTTG
7963 AATTTTTTTTTG
1 AATTTTTTTTTG
7975 AATTTTTTTTTCG
1 AATTTTTTTTT-G
*
7988 AGTTTTTTTTT
1 AATTTTTTTTT
7999 TGAGAAACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 23 0.68
13 11 0.32
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.75
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:7971 original size:13 final size:13
Alignment explanation
Indices: 7953--8001 Score: 73
Period size: 13 Copynumber: 3.8 Consensus size: 13
7943 GAAACCAAAA
7953 TTTTTTTTTGAA-
1 TTTTTTTTTGAAT
7965 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
* *
7978 TTTTTTTTCGAGT
1 TTTTTTTTTGAAT
7991 TTTTTTTTTGA
1 TTTTTTTTTGA
8002 GAAACTACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
12 12 0.36
13 21 0.64
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:8175 original size:65 final size:66
Alignment explanation
Indices: 8070--8200 Score: 210
Period size: 65 Copynumber: 2.0 Consensus size: 66
8060 GATACCAATT
* * * *
8070 TGATACGAACTCATTTTGTGATTGATTCGAGTCGTTAGTGTTTGCTC-ATCGTGAATTTGAGTAA
1 TGATACAAACTCATTTAGTGATTGATGCGAGTCGTGAGTGTTTGCTCGATCGTGAATTTGAGTAA
8134 G
66 G
*
8135 TGATACAAACTCGTTTAGTGATTGATGCGAGTCGTGAGTGTTTGCTCGATCGTGAATTTGAGTAA
1 TGATACAAACTCATTTAGTGATTGATGCGAGTCGTGAGTGTTTGCTCGATCGTGAATTTGAGTAA
8200 G
66 G
8201 GCTAAGTTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
65 42 0.70
66 18 0.30
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (66 bp):
TGATACAAACTCATTTAGTGATTGATGCGAGTCGTGAGTGTTTGCTCGATCGTGAATTTGAGTAA
G
Found at i:11761 original size:10 final size:11
Alignment explanation
Indices: 11742--11806 Score: 105
Period size: 11 Copynumber: 6.0 Consensus size: 11
11732 AATACAACTT
11742 GAATTTTTTTC
1 GAATTTTTTTC
11753 GAATTTTTTTC
1 GAATTTTTTTC
11764 GAATTTTTTTC
1 GAATTTTTTTC
*
11775 GAATTTTTTTT
1 GAATTTTTTTC
11786 G-ATTTTTTTC
1 GAATTTTTTTC
*
11796 GATTTTTTTTC
1 GAATTTTTTTC
11807 ACCAACCTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
10 9 0.18
11 41 0.82
ACGTcount: A:0.15, C:0.08, G:0.09, T:0.68
Consensus pattern (11 bp):
GAATTTTTTTC
Found at i:17727 original size:52 final size:52
Alignment explanation
Indices: 17666--17766 Score: 177
Period size: 52 Copynumber: 1.9 Consensus size: 52
17656 CATGCACATA
*
17666 TTTGAGCTTCAACCGAGCTAGAAATGACG-TCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGA-GATCTTAAGCTGCTGTCCATTATTG
17718 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
17767 CGTTGCCTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 1 0.02
52 46 0.98
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:26311 original size:20 final size:20
Alignment explanation
Indices: 26288--26334 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
26278 TGGGTTAAAT
*
26288 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
26308 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
26328 TGAGCTG
1 TGAGCTG
26335 GAAAACGACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40339 original size:27 final size:27
Alignment explanation
Indices: 40298--40349 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
40288 TCATTGAAGC
* *
40298 ATCTTCATTGTTGTCCATGCATGTATT
1 ATCTTCAATGCTGTCCATGCATGTATT
40325 ATCTTCAATGCTGTCCATGCATGTA
1 ATCTTCAATGCTGTCCATGCATGTA
40350 CCTACAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (27 bp):
ATCTTCAATGCTGTCCATGCATGTATT
Found at i:42421 original size:17 final size:18
Alignment explanation
Indices: 42399--42432 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42389 TTTTTCTTTT
42399 TCAATTT-TTTCTCAATC
1 TCAATTTCTTTCTCAATC
*
42416 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTCTCAAT
42433 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.56
Consensus pattern (18 bp):
TCAATTTCTTTCTCAATC
Found at i:42450 original size:27 final size:28
Alignment explanation
Indices: 42390--42456 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
42380 TTCAACATCT
42390 TTTTCTTTTTCAATTTTTTCTCAATCTCA
1 TTTTCTTTTTCAATTTTTTCTC-ATCTCA
* *
42419 ATTTCTTTTTCAATTTTCTTTTC-T-TCA
1 TTTTCTTTTTCAATTTT-TTCTCATCTCA
42446 TTTTCTTTTTC
1 TTTTCTTTTTC
42457 TCTCACTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
29 16 0.47
30 4 0.12
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTTCTTTTTCAATTTTTTCTCATCTCA
Found at i:43833 original size:6 final size:6
Alignment explanation
Indices: 43824--43876 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
43814 TCATTTTCGA
** * *
43824 TTTCTT TTTCTT TTGT-AA TTTCTT TTTCTT TTTCGT TTTCTT TTTCAT
1 TTTCTT TTTCTT TT-TCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
43872 TTTCT
1 TTTCT
43877 CGCTCGCACT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
5 1 0.03
6 35 0.95
7 1 0.03
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:43863 original size:18 final size:17
Alignment explanation
Indices: 43817--43875 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 17
43807 GATCGCATCA
*
43817 TTTTCGATTTCTTTTTC
1 TTTTCGTTTTCTTTTTC
43834 TTTT-GTAATTTCTTTTTC
1 TTTTCGT--TTTCTTTTTC
43852 TTTTTCGTTTTCTTTTTC
1 -TTTTCGTTTTCTTTTTC
43870 ATTTTC
1 -TTTTC
43876 TCGCTCGCAC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.03
17 4 0.11
18 25 0.69
19 4 0.11
20 2 0.06
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTCGTTTTCTTTTTC
Found at i:46588 original size:56 final size:55
Alignment explanation
Indices: 46472--46589 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
46462 TGCATGCTTT
* * * *
46472 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
46526 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
46582 CATTAAAT
1 CATTAAAT
46590 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:47244 original size:20 final size:20
Alignment explanation
Indices: 47221--47267 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
47211 AATTGATCTT
*
47221 GAATGAGCTGACTTGAGCAC
1 GAATGAGCTAACTTGAGCAC
*
47241 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
47261 GAATGAG
1 GAATGAG
47268 TTGAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:48589 original size:15 final size:16
Alignment explanation
Indices: 48550--48590 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
48540 AACAACACTC
48550 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
48566 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
48580 CTTTCTTTTTC
1 CTTTCTTTTTC
48591 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:48785 original size:17 final size:15
Alignment explanation
Indices: 48748--48786 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
48738 TATCTCCCAC
48748 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
48764 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
48781 TCATTT
1 TCATTT
48787 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:49812 original size:12 final size:13
Alignment explanation
Indices: 49792--49826 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
49782 ATTGAATACA
*
49792 AATTTTTTTTTTG
1 AATTTTTTTTTCG
49805 AATTTTTTTTTCG
1 AATTTTTTTTTCG
49818 AATTTTTTT
1 AATTTTTTT
49827 CCTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (13 bp):
AATTTTTTTTTCG
Found at i:50996 original size:56 final size:56
Alignment explanation
Indices: 50891--50997 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
50881 ATTAATGTCG
* * * * *
50891 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCAT
50947 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
50998 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCAT
Found at i:51652 original size:20 final size:20
Alignment explanation
Indices: 51629--51675 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
51619 AATTGATCTT
*
51629 GAATGAGCTGACTTGAGCAC
1 GAATGAGCTAACTTGAGCAC
*
51649 GAATGAGCTAACTTGAGCTC
1 GAATGAGCTAACTTGAGCAC
51669 GAATGAG
1 GAATGAG
51676 TTGAACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (20 bp):
GAATGAGCTAACTTGAGCAC
Found at i:53691 original size:23 final size:22
Alignment explanation
Indices: 53639--53692 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
53629 TCCACGTCTT
*
53639 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
53661 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
53684 TTTCTTTTC
1 TTTCTTTTC
53693 ACTCTCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 3 0.11
22 5 0.19
23 13 0.48
24 6 0.22
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:57616 original size:10 final size:10
Alignment explanation
Indices: 57603--57654 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
57593 TTTTTGAATC
57603 TTTTTTTCGA
1 TTTTTTTCGA
57613 TTTTTTT--A
1 TTTTTTTCGA
57621 TTTTTTTCGA
1 TTTTTTTCGA
**
57631 TTTTCCTC--
1 TTTTTTTCGA
57639 TTTTTTT-GA
1 TTTTTTTCGA
57648 TTTTTTT
1 TTTTTTT
57655 GTTCAATTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
8 13 0.38
9 7 0.21
10 14 0.41
ACGTcount: A:0.08, C:0.10, G:0.06, T:0.77
Consensus pattern (10 bp):
TTTTTTTCGA
Found at i:57626 original size:18 final size:18
Alignment explanation
Indices: 57603--57654 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
57593 TTTTTGAATC
57603 TTTTTTTCGATTTTTTTA
1 TTTTTTTCGATTTTTTTA
** *
57621 TTTTTTTCGATTTTCCTC
1 TTTTTTTCGATTTTTTTA
57639 TTTTTTT-GATTTTTTT
1 TTTTTTTCGATTTTTTT
57655 GTTCAATTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 7 0.24
18 22 0.76
ACGTcount: A:0.08, C:0.10, G:0.06, T:0.77
Consensus pattern (18 bp):
TTTTTTTCGATTTTTTTA
Found at i:60623 original size:23 final size:22
Alignment explanation
Indices: 60571--60623 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
60561 TCCACGTCTT
*
60571 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
60593 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
60616 TTTCTTTT
1 TTTCTTTT
60624 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:63551 original size:15 final size:14
Alignment explanation
Indices: 63531--63582 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
63521 AAATTGTAGT
63531 TTCGAAAAAAAAGAA
1 TTCGAAAAAAAA-AA
63546 TTCG-AAAAAAAAA
1 TTCGAAAAAAAAAA
*
63559 TTTG--AAAAAAAA
1 TTCGAAAAAAAAAA
63571 TT-GAAAAAAAAA
1 TTCGAAAAAAAAA
63583 TTGTATACGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 1 0.03
12 10 0.29
13 12 0.35
14 7 0.21
15 4 0.12
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (14 bp):
TTCGAAAAAAAAAA
Found at i:63566 original size:12 final size:12
Alignment explanation
Indices: 63537--63581 Score: 56
Period size: 11 Copynumber: 3.7 Consensus size: 12
63527 TAGTTTCGAA
*
63537 AAAAAAGAATTCG
1 AAAAAA-AATTTG
63550 AAAAAAAAATTTG
1 -AAAAAAAATTTG
63563 AAAAAAAA-TTG
1 AAAAAAAATTTG
63574 AAAAAAAA
1 AAAAAAAA
63582 ATTGTATACG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.37
12 8 0.27
13 5 0.17
14 6 0.20
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (12 bp):
AAAAAAAATTTG
Found at i:63582 original size:12 final size:12
Alignment explanation
Indices: 63536--63585 Score: 66
Period size: 12 Copynumber: 4.0 Consensus size: 12
63526 GTAGTTTCGA
63536 AAAAAAAGAATTCG
1 AAAAAAA-AATT-G
63550 AAAAAAAAATTTG
1 AAAAAAAAA-TTG
63563 -AAAAAAAATTG
1 AAAAAAAAATTG
63574 AAAAAAAAATTG
1 AAAAAAAAATTG
63586 TATACGGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.09
12 19 0.56
13 3 0.09
14 9 0.26
ACGTcount: A:0.70, C:0.02, G:0.10, T:0.18
Consensus pattern (12 bp):
AAAAAAAAATTG
Found at i:66708 original size:14 final size:14
Alignment explanation
Indices: 66689--66723 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
66679 TCAAGTTGAA
66689 AAAAAAAATTCATG
1 AAAAAAAATTCATG
*
66703 AAAAAAAATTCGTG
1 AAAAAAAATTCATG
66717 AAAAAAA
1 AAAAAAA
66724 GAAGAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.69, C:0.06, G:0.09, T:0.17
Consensus pattern (14 bp):
AAAAAAAATTCATG
Found at i:68299 original size:30 final size:30
Alignment explanation
Indices: 68264--68327 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
68254 AGCTCGATTT
68264 AGCTCACA-TGAGCTTAATTTAGCT-TGTTTG
1 AGCTCA-ATTGAGCTTAATTTAGCTCT-TTTG
* *
68294 AGCTCAATTTAGCTTACTTTAGCTCTTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCTTTTG
68324 AGCT
1 AGCT
68328 TGGCTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 28 0.93
31 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAGCTCTTTTG
Found at i:68317 original size:20 final size:20
Alignment explanation
Indices: 68254--68318 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
68244 AGTTTTTCCC
* * * *
68254 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
* *
68274 AGCTTAATTTAGCTT-GTTT
1 AGCTCAATTTAGCTTACTTT
68293 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
68314 AGCTC
1 AGCTC
68319 TTTTGAGCTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.03
20 31 0.89
21 3 0.09
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:71040 original size:12 final size:12
Alignment explanation
Indices: 71019--71174 Score: 64
Period size: 12 Copynumber: 13.6 Consensus size: 12
71009 AGAAAAGGAG
*
71019 AAAGAGATTGAA
1 AAAGAAATTGAA
71031 AAAGAAATTG--
1 AAAGAAATTGAA
71041 AAAGAAATTG--
1 AAAGAAATTGAA
**
71051 AAAGAAAACGAA
1 AAAGAAATTGAA
**
71063 AAAGAAAAAGAA
1 AAAGAAATTGAA
* * *
71075 ATTACAAA-AGAA
1 A-AAGAAATTGAA
*
71087 AAAGAAATCGAA
1 AAAGAAATTGAA
** **
71099 AAAGTGAGAGAA
1 AAAGAAATTGAA
*
71111 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
71125 AAAGAAAATTGAA
1 AAAG-AAATTGAA
71138 AAAGAAATTG--
1 AAAGAAATTGAA
71148 --AG-AA-TGAA
1 AAAGAAATTGAA
*
71156 AAAAAAATTGAA
1 AAAGAAATTGAA
71168 AAAGAAA
1 AAAGAAA
71175 AAGCGAAAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 26
0.71 0.13 0.17
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 2 0.02
10 19 0.17
11 6 0.05
12 59 0.53
13 10 0.09
14 6 0.05
15 5 0.05
ACGTcount: A:0.68, C:0.02, G:0.19, T:0.12
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:71044 original size:10 final size:10
Alignment explanation
Indices: 71031--71057 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
71021 AGAGATTGAA
71031 AAAGAAATTG
1 AAAGAAATTG
71041 AAAGAAATTG
1 AAAGAAATTG
71051 AAAGAAA
1 AAAGAAA
71058 ACGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (10 bp):
AAAGAAATTG
Found at i:71063 original size:6 final size:6
Alignment explanation
Indices: 71051--71177 Score: 60
Period size: 6 Copynumber: 20.7 Consensus size: 6
71041 AAAGAAATTG
* * * **
71051 AAAGAA AACGAA AAAGAA AAAGAA ATTA-CA AAAGAA AAAGAA ATCGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA
** * * * ** *
71099 AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA AAAGAA ATTGAG
1 AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA AAAGAA AAAGAA
* *
71150 AATGAA AAA-AA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AA-AGAA AAAGAA AAAG
71178 CGAAAAAAGA
Statistics
Matches: 86, Mismatches: 28, Indels: 14
0.67 0.22 0.11
Matches are distributed among these distances:
5 5 0.06
6 65 0.76
7 12 0.14
8 4 0.05
ACGTcount: A:0.70, C:0.02, G:0.18, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:71157 original size:69 final size:70
Alignment explanation
Indices: 71041--71171 Score: 169
Period size: 69 Copynumber: 1.9 Consensus size: 70
71031 AAAGAAATTG
* *
71041 AAAGAAATTGAAAGAAAACGAAAAAGAAAAAGAAATTACAAAAGAAAAAGAAATCGAAAAAGTGA
1 AAAGAAAATGAAAGAAAACGAAAAAGAAAAAGAAATTACAAAAGAAAAAAAAATCGAAAAAGTGA
71106 GAGAA
66 GAGAA
* * * *
71111 AAAGAAAATG-AAGAAAA-GAAAATTGAAAAAGAAATTGA-GAATGAAAAAAAAATTGAAAAAG
1 AAAGAAAATGAAAGAAAACGAAAA-AGAAAAAGAAATT-ACAAAAGAAAAAAAAATCGAAAAAG
71172 AAAAAGCGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
68 5 0.09
69 38 0.72
70 10 0.19
ACGTcount: A:0.69, C:0.02, G:0.18, T:0.11
Consensus pattern (70 bp):
AAAGAAAATGAAAGAAAACGAAAAAGAAAAAGAAATTACAAAAGAAAAAAAAATCGAAAAAGTGA
GAGAA
Found at i:71163 original size:30 final size:27
Alignment explanation
Indices: 71108--71195 Score: 97
Period size: 30 Copynumber: 3.1 Consensus size: 27
71098 AAAAGTGAGA
*
71108 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAAAAAATT
*
71135 GAAAAAGAAATTGAGAATGAAAAAAAAATT
1 GAAAAAGAAAAT--GAA-GAAAAAAAAATT
* *
71165 GAAAAAGAAAAAG-CGAAAAAAGAAATT
1 GAAAAAGAAAATGAAGAAAAAA-AAATT
71192 GAAA
1 GAAA
71196 GAGAGCTTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 7 0.13
27 20 0.38
28 1 0.02
29 3 0.06
30 21 0.40
ACGTcount: A:0.69, C:0.01, G:0.18, T:0.11
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAAAAAATT
Found at i:71229 original size:33 final size:33
Alignment explanation
Indices: 71192--71254 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
71182 AAAAGAAATT
71192 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
71225 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
71255 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:83226 original size:19 final size:18
Alignment explanation
Indices: 83190--83229 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
83180 TTTCCACTCG
*
83190 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
83208 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
83227 TTT
1 TTT
83230 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:84304 original size:15 final size:15
Alignment explanation
Indices: 84284--84337 Score: 76
Period size: 14 Copynumber: 3.7 Consensus size: 15
84274 TAGCTTCTTC
84284 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
*
84299 TTTTTTTTTCAC-AAT
1 -TTTTTTTTCACGAAA
84314 TTTTTTTTCACG-AA
1 TTTTTTTTCACGAAA
84328 TTTTTTTTCA
1 TTTTTTTTCA
84338 ACTTGATATC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 22 0.63
15 2 0.06
16 11 0.31
ACGTcount: A:0.20, C:0.13, G:0.04, T:0.63
Consensus pattern (15 bp):
TTTTTTTTCACGAAA
Found at i:84392 original size:12 final size:12
Alignment explanation
Indices: 84375--84420 Score: 76
Period size: 11 Copynumber: 3.8 Consensus size: 12
84365 ATGGAAACCA
84375 AATTTTTTTTTG
1 AATTTTTTTTTG
84387 AA-TTTTTTTTG
1 AATTTTTTTTTG
84398 AATTTTTTTTTCG
1 AATTTTTTTTT-G
84411 AATTTTTTTT
1 AATTTTTTTT
84421 GAAGAAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.34
12 10 0.31
13 11 0.34
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:84394 original size:11 final size:11
Alignment explanation
Indices: 84378--84423 Score: 74
Period size: 12 Copynumber: 4.0 Consensus size: 11
84368 GAAACCAAAT
84378 TTTTTTTTGAA
1 TTTTTTTTGAA
84389 TTTTTTTTGAA
1 TTTTTTTTGAA
84400 TTTTTTTTTCGAA
1 -TTTTTTTT-GAA
84413 TTTTTTTTGAA
1 TTTTTTTTGAA
84424 GAAACTACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 14 0.42
12 16 0.48
13 3 0.09
ACGTcount: A:0.17, C:0.02, G:0.09, T:0.72
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:84395 original size:13 final size:13
Alignment explanation
Indices: 84377--84420 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
84367 GGAAACCAAA
84377 TTTTTTTTTGAA-
1 TTTTTTTTTGAAT
84389 -TTTTTTTTGAAT
1 TTTTTTTTTGAAT
*
84401 TTTTTTTTCGAAT
1 TTTTTTTTTGAAT
84414 TTTTTTT
1 TTTTTTT
84421 GAAGAAACTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.38
13 18 0.62
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:84413 original size:24 final size:23
Alignment explanation
Indices: 84375--84423 Score: 89
Period size: 24 Copynumber: 2.1 Consensus size: 23
84365 ATGGAAACCA
84375 AATTTTTTTTTGAATTTTTTTTG
1 AATTTTTTTTTGAATTTTTTTTG
84398 AATTTTTTTTTCGAATTTTTTTTG
1 AATTTTTTTTT-GAATTTTTTTTG
84422 AA
1 AA
84424 GAAACTACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.20, C:0.02, G:0.08, T:0.69
Consensus pattern (23 bp):
AATTTTTTTTTGAATTTTTTTTG
Found at i:87232 original size:11 final size:11
Alignment explanation
Indices: 87214--87242 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
87204 AAAAAATTAA
87214 AAAAAAATCCG
1 AAAAAAATCCG
87225 AAAAAAATCCG
1 AAAAAAATCCG
87236 AAAAAAA
1 AAAAAAA
87243 AAAGTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.72, C:0.14, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAAAAATCCG
Found at i:87326 original size:19 final size:18
Alignment explanation
Indices: 87308--87343 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
87298 TGAGAGAAAT
87308 TCAAAATTAAAAAAAAAA
1 TCAAAATTAAAAAAAAAA
*
87326 TCAGAATTAAAAAAAAAA
1 TCAAAATTAAAAAAAAAA
87344 AGAAAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.06, G:0.03, T:0.17
Consensus pattern (18 bp):
TCAAAATTAAAAAAAAAA
Found at i:88275 original size:21 final size:21
Alignment explanation
Indices: 88235--88293 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
88225 AATCTTGAAT
*
88235 GAAATTGAGAGAAGAA-AAAAA
1 GAAA-TGAGAGAAAAAGAAAAA
88256 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* *
88277 GAAATAAAAGAAAAAGA
1 GAAATGAGAGAAAAAGA
88294 TGAAAATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 10 0.29
21 24 0.71
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:88285 original size:15 final size:14
Alignment explanation
Indices: 88246--88293 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
88236 AAATTGAGAG
88246 AAGAAAAAAAGAAA
1 AAGAAAAAAAGAAA
* *
88260 TGAGAGAAAAAGAAA
1 -AAGAAAAAAAGAAA
88275 AAGAAATAAAAGAAA
1 AAGAAA-AAAAGAAA
88290 AAGA
1 AAGA
88294 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (14 bp):
AAGAAAAAAAGAAA
Found at i:93740 original size:19 final size:18
Alignment explanation
Indices: 93704--93743 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
93694 TTTCCACTCG
*
93704 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
93722 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
93741 TTT
1 TTT
93744 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:93867 original size:12 final size:12
Alignment explanation
Indices: 93848--93876 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
93838 TCTTTTTCAA
93848 TTTT-TGTTTCT
1 TTTTCTGTTTCT
93859 TTTTCTGTTTCT
1 TTTTCTGTTTCT
93871 TTTTCT
1 TTTTCT
93877 CTCGTCACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTCTGTTTCT
Found at i:94818 original size:12 final size:13
Alignment explanation
Indices: 94800--94837 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
94790 ACTAGCTCTC
94800 TTTTTTTTCACAA
1 TTTTTTTTCACAA
94813 TTTTTTTTTCA-AA
1 -TTTTTTTTCACAA
94826 TTTTTTTT-ACAA
1 TTTTTTTTCACAA
94838 CTTGATATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.04
12 10 0.43
13 2 0.09
14 10 0.43
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTTTTTTCACAA
Found at i:94818 original size:13 final size:14
Alignment explanation
Indices: 94800--94833 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
94790 ACTAGCTCTC
94800 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
94814 TTTTTTTTCA-AAT
1 TTTTTTTTCACAAT
94827 TTTTTTT
1 TTTTTTT
94834 ACAACTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:94893 original size:12 final size:12
Alignment explanation
Indices: 94876--94922 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 12
94866 GGAAACTAGT
94876 TTTTTTTTCGAA
1 TTTTTTTTCGAA
*
94888 TTTTTTTTTTGAA
1 -TTTTTTTTCGAA
*
94901 -TTTTTTTCGAG
1 TTTTTTTTCGAA
94912 TTTTTTTTCGA
1 TTTTTTTTCGA
94923 GAAACTACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 9 0.30
12 10 0.33
13 11 0.37
ACGTcount: A:0.13, C:0.06, G:0.11, T:0.70
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:94923 original size:12 final size:12
Alignment explanation
Indices: 94876--94923 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
94866 GGAAACTAGT
*
94876 TTTTTTTTCGAAT
1 TTTTTTTTCG-AG
*
94889 TTTTTTTTTGA-
1 TTTTTTTTCGAG
*
94900 ATTTTTTTCGAG
1 TTTTTTTTCGAG
94912 TTTTTTTTCGAG
1 TTTTTTTTCGAG
94924 AAACTACTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 9 0.30
12 12 0.40
13 9 0.30
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCGAG
Found at i:104042 original size:21 final size:23
Alignment explanation
Indices: 103997--104043 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
103987 TCACCTGCAA
* *
103997 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
104020 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
104041 TAA
1 TAA
104044 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:106517 original size:13 final size:13
Alignment explanation
Indices: 106499--106549 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
106489 TAGTTTCTCG
106499 AAAAAAAAACTCA
1 AAAAAAAAACTCA
** *
106512 AAAAAAAATTTGA
1 AAAAAAAAACTCA
*
106525 AAAAAAAAATTCGA
1 AAAAAAAAACTC-A
106539 AAAAAAAAACT
1 AAAAAAAAACT
106550 AGTTTCCATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
13 20 0.65
14 11 0.35
ACGTcount: A:0.75, C:0.08, G:0.04, T:0.14
Consensus pattern (13 bp):
AAAAAAAAACTCA
Found at i:106518 original size:14 final size:14
Alignment explanation
Indices: 106495--106549 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
106485 ATAGTAGTTT
106495 CTCG-AAAAAAAAA
1 CTCGAAAAAAAAAA
106508 CTC--AAAAAAAAA
1 CTCGAAAAAAAAAA
* *
106520 TTTGAAAAAAAAAA
1 CTCGAAAAAAAAAA
*
106534 TTCGAAAAAAAAAA
1 CTCGAAAAAAAAAA
106548 CT
1 CT
106550 AGTTTCCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
12 10 0.28
13 3 0.08
14 23 0.64
ACGTcount: A:0.69, C:0.11, G:0.05, T:0.15
Consensus pattern (14 bp):
CTCGAAAAAAAAAA
Found at i:106609 original size:14 final size:13
Alignment explanation
Indices: 106588--106637 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
106578 TATCAAGTTG
*
106588 TGAAAAAAACTTT
1 TGAAAAAAAATTT
*
106601 TGAAAAAAAAATTG
1 TG-AAAAAAAATTT
*
106615 TGAAAAAAAAATT
1 TGAAAAAAAATTT
106628 TGAAAAAAAA
1 TGAAAAAAAA
106638 GAGAGCTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 21 0.66
14 11 0.34
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (13 bp):
TGAAAAAAAATTT
Found at i:106615 original size:27 final size:27
Alignment explanation
Indices: 106585--106637 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
106575 GGATATCAAG
**
106585 TTGTGAAAAAAACTTTTGAAAAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAAAAA
106612 TTGTGAAAAAAAAATTTGAAAAAAAA
1 TTGTGAAAAAAAAATTTGAAAAAAAA
106638 GAGAGCTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (27 bp):
TTGTGAAAAAAAAATTTGAAAAAAAAA
Found at i:116150 original size:24 final size:22
Alignment explanation
Indices: 116098--116152 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
116088 TTCGGCTACT
*
116098 GATGTGTTCACACAACAATTAAA
1 GATG-GTTCACACAAAAATTAAA
*
116121 -AGGGTTCACACTAAAACATTAAA
1 GATGGTTCACAC-AAAA-ATTAAA
116144 GATGGTTCA
1 GATGGTTCA
116153 TGAATTCGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 6 0.23
24 7 0.27
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (22 bp):
GATGGTTCACACAAAAATTAAA
Found at i:124080 original size:22 final size:21
Alignment explanation
Indices: 124048--124111 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
124038 TTGGTATTTA
124048 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
124069 GGAAGTTGGTACGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
124091 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
124112 ATGGTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:130685 original size:17 final size:18
Alignment explanation
Indices: 130663--130703 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
130653 CGTTTCTTTT
130663 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
130680 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
130698 T-TTTTG
1 TCTTTTG
130704 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:130687 original size:24 final size:25
Alignment explanation
Indices: 130634--130687 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
130624 AACAAATTCT
* *
130634 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
130659 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
130682 TTTTTT
1 TTTTTT
130688 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:136342 original size:15 final size:16
Alignment explanation
Indices: 136322--136357 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
136312 TTTTCACTTG
136322 CTTTTTCTTTT-TCAT
1 CTTTTTCTTTTCTCAT
136337 CTTTTTCTTTTCTCAT
1 CTTTTTCTTTTCTCAT
136353 -TTTTT
1 CTTTTT
136358 TTCACTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (16 bp):
CTTTTTCTTTTCTCAT
Found at i:136389 original size:19 final size:19
Alignment explanation
Indices: 136365--136410 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
136355 TTTTTCACTC
136365 TCTTTTTTCGAATTTTC-TT
1 TCTTTTTTC-AATTTTCTTT
*
136384 TCTTTTTTTCATTTTTCTTT
1 TC-TTTTTTCAATTTTCTTT
136404 TCTTTTT
1 TCTTTTT
136411 CTCTCATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (19 bp):
TCTTTTTTCAATTTTCTTT
Found at i:136392 original size:20 final size:20
Alignment explanation
Indices: 136367--136410 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
136357 TTTCACTCTC
136367 TTTTTTCGAATTTTC-TTTCT
1 TTTTTTC-AATTTTCTTTTCT
*
136387 TTTTTTCATTTTTCTTTTCT
1 TTTTTTCAATTTTCTTTTCT
136407 TTTT
1 TTTT
136411 CTCTCATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.77
Consensus pattern (20 bp):
TTTTTTCAATTTTCTTTTCT
Found at i:138631 original size:12 final size:11
Alignment explanation
Indices: 138604--138646 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
138594 ACCGTATACA
*
138604 ATTTTTTTTTG
1 ATTTTTTTTCG
138615 A-TTTTTTTCG
1 ATTTTTTTTCG
*
138625 ATTTTTTTTCAA
1 ATTTTTTTTC-G
138637 ATTTTTTTTC
1 ATTTTTTTTC
138647 ACGAATCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 9 0.32
11 9 0.32
12 10 0.36
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (11 bp):
ATTTTTTTTCG
Found at i:138981 original size:22 final size:21
Alignment explanation
Indices: 138949--139012 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
138939 TTGGTATTTA
138949 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
138970 GGAAGTTGGTACGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
138992 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
139013 ATGGTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:144481 original size:20 final size:20
Alignment explanation
Indices: 144456--144504 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
144446 AAACGAATTA
144456 AATTTCCAAA-ATAGCAAACC
1 AATTT-CAAATATAGCAAACC
*
144476 AATTTCAAATTCTAGCAAACC
1 AATTTCAAA-TATAGCAAACC
*
144497 AATCTCAA
1 AATTTCAA
144505 CCTGTATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 5 0.20
21 16 0.64
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (20 bp):
AATTTCAAATATAGCAAACC
Done.