Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017030.1 Corchorus olitorius cultivar O-4 contig17063, 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: 70446
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:2060 original size:21 final size:21
Alignment explanation
Indices: 2013--2062 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
2003 CTGCCCATTG
* *
2013 CCGTCCCACCACCAGTTAAGC
1 CCGTGCCACCACCAGCTAAGC
* * *
2034 CTGTGCCACCACCGGCTATGC
1 CCGTGCCACCACCAGCTAAGC
2055 CCGTGCCA
1 CCGTGCCA
2063 TCGCCATTCC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.46, G:0.20, T:0.16
Consensus pattern (21 bp):
CCGTGCCACCACCAGCTAAGC
Found at i:5741 original size:19 final size:18
Alignment explanation
Indices: 5708--5743 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5698 TTGAGATAAT
5708 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
5726 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
5744 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:7927 original size:19 final size:18
Alignment explanation
Indices: 7894--7929 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7884 TTGAGATAAT
7894 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
7912 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
7930 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:11682 original size:339 final size:339
Alignment explanation
Indices: 11062--11739 Score: 1223
Period size: 339 Copynumber: 2.0 Consensus size: 339
11052 CCTTTAGGTG
*
11062 ACTAATCACACCTTAAAAAGTATTAGTGGCGACTCCTCCTTTCCAAAGTCGTTTCAGCAGGGTTT
1 ACTAATCACACCTTAAAAAGGATTAGTGGCGACTCCTCCTTTCCAAAGTCGTTTCAGCAGGGTTT
* *
11127 CACCTGTGACTCTTTTTGATACCAGTCAGAGCAACCTTGACAAGTTGAAGAGTCTGTGGGCAAGG
66 CACCTGCGACTCATTTTGATACCAGTCAGAGCAACCTTGACAAGTTGAAGAGTCTGTGGGCAAGG
11192 TTTTCATACAAAGAACAGTTCAAGCAGAAGTATAAGCTTATTGGGTCTCTGATTGATGCCGAGGT
131 TTTTCATACAAAGAACAGTTCAAGCAGAAGTATAAGCTTATTGGGTCTCTGATTGATGCCGAGGT
11257 TGATCATTCATTGTTAACGGCCATGATACATTTCTGGGATTCCGCTCGCCGTTGTTTTGTTTTCA
196 TGATCATTCATTGTTAACGGCCATGATACATTTCTGGGATTCCGCTCGCCGTTGTTTTGTTTTCA
11322 ATGAAGTAGACATGGTGCCTACAGTGGAGGAA-AGTCGCTCCATGTTGTTTCCCTCAGACGAGTT
261 ATGAAGTAGACATGGTGCCTACAGTGGAGGAATA-TCGCTCCATGTTGTTTCCCTCAGACGAGTT
11386 TCTATTCAAGAAGCC
325 TCTATTCAAGAAGCC
* *
11401 ACTAATCACACCTTAAAAAGGATTAGTGGCGACTCCTTCTTTCCAAAGTCGTTTCGGCAGGGTTT
1 ACTAATCACACCTTAAAAAGGATTAGTGGCGACTCCTCCTTTCCAAAGTCGTTTCAGCAGGGTTT
* *
11466 CACCTGCGACTCATTTTGATACCAGTCAGAGCAACCTTGACAAGTTGAAGAGTTTGTGGGCACGG
66 CACCTGCGACTCATTTTGATACCAGTCAGAGCAACCTTGACAAGTTGAAGAGTCTGTGGGCAAGG
* ** *
11531 TTTTCATATAAAGAACAGTTCAAGCAGAAGTATGGGCTTATTGGGTCTTTGATTGATGCCGAGGT
131 TTTTCATACAAAGAACAGTTCAAGCAGAAGTATAAGCTTATTGGGTCTCTGATTGATGCCGAGGT
* *
11596 TGATCATTCATTGTTAAGGGCCATGATACATTTTTGGGATTCCGCTCGCCGTTGTTTTGTTTTCA
196 TGATCATTCATTGTTAACGGCCATGATACATTTCTGGGATTCCGCTCGCCGTTGTTTTGTTTTCA
11661 ATGAAGTAGACATGGTGCCTACAGTGGAGGAATATCGCTCCATGTTGTTTCCCTCAGACGAGTTT
261 ATGAAGTAGACATGGTGCCTACAGTGGAGGAATATCGCTCCATGTTGTTTCCCTCAGACGAGTTT
11726 CTATTCAAGAAGCC
326 CTATTCAAGAAGCC
11740 TAATGACAAG
Statistics
Matches: 325, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
339 324 1.00
340 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (339 bp):
ACTAATCACACCTTAAAAAGGATTAGTGGCGACTCCTCCTTTCCAAAGTCGTTTCAGCAGGGTTT
CACCTGCGACTCATTTTGATACCAGTCAGAGCAACCTTGACAAGTTGAAGAGTCTGTGGGCAAGG
TTTTCATACAAAGAACAGTTCAAGCAGAAGTATAAGCTTATTGGGTCTCTGATTGATGCCGAGGT
TGATCATTCATTGTTAACGGCCATGATACATTTCTGGGATTCCGCTCGCCGTTGTTTTGTTTTCA
ATGAAGTAGACATGGTGCCTACAGTGGAGGAATATCGCTCCATGTTGTTTCCCTCAGACGAGTTT
CTATTCAAGAAGCC
Found at i:24112 original size:21 final size:22
Alignment explanation
Indices: 24087--24127 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
24077 GCAATTCTGT
*
24087 CATTTTCT-AATTCACTTTTGA
1 CATTTACTAAATTCACTTTTGA
*
24108 CATTTAGTAAATTCACTTTT
1 CATTTACTAAATTCACTTTT
24128 TTGCATAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (22 bp):
CATTTACTAAATTCACTTTTGA
Found at i:28459 original size:21 final size:21
Alignment explanation
Indices: 28430--28912 Score: 276
Period size: 21 Copynumber: 22.1 Consensus size: 21
28420 CCAAGAAGTA
*
28430 AAGAGTAATCAGAAAAATG-GT
1 AAGAGTAATCAGTAAAA-GAGT
*
28451 AATAGTAATCAGTAAAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
* *
28472 AAAGAATAATCAGTAAAAGAAT
1 -AAGAGTAATCAGTAAAAGAGT
*
28494 AATAGTAATCAGT-AAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
* *
28514 AAAGAGTAACCAAG-AAATG-GT
1 -AAGAGTAATC-AGTAAAAGAGT
28535 AAAGAGTAATCAGTAAAA-AGGT
1 -AAGAGTAATCAGTAAAAGA-GT
* *
28557 AATAGTAGTCAGT-AAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
* *
28577 GAGGAGTAATCAGTAAATG-GT
1 -AAGAGTAATCAGTAAAAGAGT
28598 AAGAGTAATCAGTAAAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
* **
28619 AATAACAATCAGTAAAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
28640 AAAGAGTAATCAGTAAAAGAGT
1 -AAGAGTAATCAGTAAAAGAGT
* * *
28662 AATAGTAATTAGTTAAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
* * *
28683 AATCAGTAAAT-GGTTATAGTAATCAGT
1 AA-GAGT-AATCAG-TA-A--AA-GAGT
28710 AAAAGAGTAAGAATAATCAGTAAAAGAGT
1 --AAGAGTAA------TCAGTAAAAGAGT
* * *
28739 AATAGTAGTAAGT-AAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
28759 AAAGAGTAATC-G-AGAAAGAGT
1 -AAGAGTAATCAGTA-AAAGAGT
*
28780 AATAGTAATCAGT-AAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
**
28800 AAAGAGTAAAGAGTAAAAGAGT
1 -AAGAGTAATCAGTAAAAGAGT
* * *
28822 AATAATAGTCAGTAAAGAGAAAGAGT
1 AAGAGTAATCAGT----A-AAAGAGT
*
28848 AATAGTAATCAGTAAAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
28869 AAAGAGTGAA-CAGTAAAATG-GT
1 -AAGAGT-AATCAGTAAAA-GAGT
*
28891 AATAGTAATCAGT-AAAGAGT
1 AAGAGTAATCAGTAAAAGAGT
28911 AA
1 AA
28913 TCAGTAAAAT
Statistics
Matches: 360, Mismatches: 56, Indels: 93
0.71 0.11 0.18
Matches are distributed among these distances:
19 1 0.00
20 63 0.17
21 168 0.47
22 73 0.20
23 7 0.02
24 1 0.00
25 1 0.00
26 20 0.06
27 11 0.03
28 3 0.01
29 5 0.01
30 2 0.01
32 1 0.00
33 3 0.01
34 1 0.00
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.21
Consensus pattern (21 bp):
AAGAGTAATCAGTAAAAGAGT
Found at i:28490 original size:15 final size:14
Alignment explanation
Indices: 28472--28501 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28462 GTAAAAGAGT
28472 AAAGAATAATCAGTA
1 AAAGAATAAT-AGTA
28487 AAAGAATAATAGTA
1 AAAGAATAATAGTA
28501 A
1 A
28502 TCAGTAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.63, C:0.03, G:0.13, T:0.20
Consensus pattern (14 bp):
AAAGAATAATAGTA
Found at i:28593 original size:56 final size:58
Alignment explanation
Indices: 28535--28898 Score: 201
Period size: 62 Copynumber: 6.3 Consensus size: 58
28525 AAGAAATGGT
* * *
28535 AAAGAGTAATCAGTAAAAAG-GTAATAGTAGTCAGTAAAGAGTGAGGAGTAATCAGTAA
1 AAAGAGTAATCAGTAAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAATCAGT-A
**
28593 ATGGTAAGAGTAATCAGT-AAAAGAGTAATAACAATCAGTAAAAGAGTAAAGAGTAATCAGTA
1 A----AAGAGTAATCAGTAAAAAGAGTAATAGTAATCAGT-AAAGAGTAAAGAGTAATCAGTA
** * * * *
28655 AAAGAGTAAT-AGTAATTAG-TTAAAGAGTAATCAGTAAATG-GT-TATAGTAATCAGTAA
1 AAAGAGTAATCAGTAAAAAGAGT-AATAGTAATCAGTAAA-GAGTAAAGAGTAATCAGT-A
* *
28712 AAGAGTAAGAATAATCAGT-AAAAGAGTAATAGTAGTAAGTAAAGAGTAAAGAGTAATC-G-A
1 AA-AG--AG--TAATCAGTAAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAATCAGTA
** * ** *
28772 GAAAGAGTAAT-AGT--AATCAGTAAAGAGTAAAGAGTAAAGAGTAAAAGAGTAAT-AAT-
1 -AAAGAGTAATCAGTAAAAAGAGT-AATAGTAATCAGTAAAGAGT-AAAGAGTAATCAGTA
*** *
28828 AGTCAGTAA--AG-AGAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAGTGAA-CAGTA
1 AAAGAGTAATCAGTAAAAAGAGTAATAGTAATCAGT-AAAGAGTAAAGAGT-AATCAGTA
28884 AAATG-GTAAT-AGTAA
1 AAA-GAGTAATCAGTAA
28899 TCAGTAAAGA
Statistics
Matches: 232, Mismatches: 41, Indels: 66
0.68 0.12 0.19
Matches are distributed among these distances:
54 24 0.10
55 41 0.18
56 30 0.13
57 14 0.06
58 29 0.12
60 5 0.02
61 8 0.03
62 50 0.22
63 31 0.13
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.22
Consensus pattern (58 bp):
AAAGAGTAATCAGTAAAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAATCAGTA
Found at i:28618 original size:15 final size:14
Alignment explanation
Indices: 28598--28669 Score: 51
Period size: 15 Copynumber: 5.0 Consensus size: 14
28588 AGTAAATGGT
28598 AAGAGTAATCAGTAA
1 AAGAGTAAT-AGTAA
28613 AAGAGTAATA--ACA
1 AAGAGTAATAGTA-A
** *
28626 ATCAGTAAAAGAGTA-
1 AAGAGT--AATAGTAA
28641 AAGAGTAATCAGTAA
1 AAGAGTAAT-AGTAA
28656 AAGAGTAATAGTAA
1 AAGAGTAATAGTAA
28670 TTAGTTAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 15
0.68 0.09 0.23
Matches are distributed among these distances:
12 1 0.02
13 7 0.16
14 10 0.23
15 25 0.57
17 1 0.02
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (14 bp):
AAGAGTAATAGTAA
Found at i:28759 original size:7 final size:7
Alignment explanation
Indices: 28749--28885 Score: 88
Period size: 7 Copynumber: 19.9 Consensus size: 7
28739 AATAGTAGTA
28749 AGTAAAG
1 AGTAAAG
28756 AGTAAAG
1 AGTAAAG
*
28763 AGTAATCG
1 AGTAA-AG
28771 AG-AAAG
1 AGTAAAG
*
28777 AGT-AAT
1 AGTAAAG
**
28783 AGTAATC
1 AGTAAAG
28790 AGTAAAG
1 AGTAAAG
28797 AGTAAAG
1 AGTAAAG
28804 AGTAAAG
1 AGTAAAG
28811 AGTAAAAG
1 AGT-AAAG
28819 AGTAATA-
1 AGTAA-AG
***
28826 A-TAGTC
1 AGTAAAG
28832 AGTAAAG
1 AGTAAAG
28839 AG-AAAG
1 AGTAAAG
*
28845 AGT-AAT
1 AGTAAAG
**
28851 AGTAATC
1 AGTAAAG
28858 AGTAAAAG
1 AGT-AAAG
28866 AGTAAAG
1 AGTAAAG
* *
28873 AGTGAAC
1 AGTAAAG
28880 AGTAAA
1 AGTAAA
28886 ATGGTAATAG
Statistics
Matches: 100, Mismatches: 20, Indels: 20
0.71 0.14 0.14
Matches are distributed among these distances:
6 22 0.22
7 62 0.62
8 16 0.16
ACGTcount: A:0.54, C:0.04, G:0.24, T:0.18
Consensus pattern (7 bp):
AGTAAAG
Found at i:28787 original size:34 final size:34
Alignment explanation
Indices: 28732--28884 Score: 113
Period size: 34 Copynumber: 4.5 Consensus size: 34
28722 ATAATCAGTA
*
28732 AAAGAGTAATAGTAGT-A-AGTAAAGAGTAAAGAGT
1 AAAGAGTAA-AG-AGTAATAGTAAACAGTAAAGAGT
* *
28766 AATCGAG-AAAGAGTAATAGTAATCAGTAAAGAGT
1 AA-AGAGTAAAGAGTAATAGTAAACAGTAAAGAGT
* *
28800 AAAGAGTAAAGAGTAAAAG-AGTA-A-TAATAGTCAGT
1 AAAGAGTAAAGAGTAATAGTA-AACAGTAA-AG--AGT
*
28835 AAAGAG-AAAGAGTAATAGTAATCAGTAAAAGAGT
1 AAAGAGTAAAGAGTAATAGTAAACAGT-AAAGAGT
* *
28869 AAAGAGTGAACAGTAA
1 AAAGAGTAAAGAGTAA
28885 AATGGTAATA
Statistics
Matches: 94, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
32 6 0.06
33 10 0.11
34 52 0.55
35 21 0.22
36 3 0.03
37 2 0.02
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (34 bp):
AAAGAGTAAAGAGTAATAGTAAACAGTAAAGAGT
Found at i:28849 original size:26 final size:27
Alignment explanation
Indices: 28804--28875 Score: 101
Period size: 26 Copynumber: 2.6 Consensus size: 27
28794 AAGAGTAAAG
*
28804 AGTAAAGAGTAAAAGAGTAATAATAGTC
1 AGTAAAGAGT-AAAGAGTAATAATAATC
*
28832 AGTAAAGAG-AAAGAGTAATAGTAATC
1 AGTAAAGAGTAAAGAGTAATAATAATC
28858 AGTAAAAGAGTAAAGAGT
1 AGT-AAAGAGTAAAGAGT
28876 GAACAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
26 18 0.45
27 6 0.15
28 16 0.40
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (27 bp):
AGTAAAGAGTAAAGAGTAATAATAATC
Found at i:28870 original size:83 final size:82
Alignment explanation
Indices: 28426--28850 Score: 298
Period size: 83 Copynumber: 5.2 Consensus size: 82
28416 TATTCCAAGA
* * *
28426 AGTAAAGAGTAATCAGAAAAATGGTAATAGTAATCAGTAAAAGAGTAAAGAATAATCAGTAAAAG
1 AGTAAAGAGTAATCAGAAACA--GTAAGAGTAATCAGTAAAAGAGT-AAGAATAAACAGTAAAAG
* * * *
28491 AATAATAGTAATCAGTAAAG
63 AGTAATAATAGTAAGTAAAG
* ** * * **
28511 AGTAAAGAGTAACCAAGAAATGGTAAAGAGTAATCAGTAAAA-AGGTAATAGTAGTCAGT-AAAG
1 AGTAAAGAGTAATC-AGAAACAGT-AAGAGTAATCAGTAAAAGA-GTAAGAATAAACAGTAAAAG
** * * *
28574 AGTGAGGAGTAATCAGTAAATG
63 AGT-AATAATAGTAAGTAAA-G
* * ** * *
28596 -GT-AAGAGTAATCAGTAAAAGAGTAATAACAATCAGTAAAAGAGTAAAGAGTAATCAGTAAAAG
1 AGTAAAGAGTAATCAG--AAACAGTAAGAGTAATCAGTAAAAGAGT-AAGAATAAACAGTAAAAG
*
28659 AG---TAATAGTAA-T-TAG
63 AGTAATAATAGTAAGTAAAG
* ** * * *
28674 -TTAAAGAGTAATCAGTAAATGGTTATAGTAATCAGTAAAAGAGTAAGAATAATCAGTAAAAGAG
1 AGTAAAGAGTAATCAG-AAACAGTAAGAGTAATCAGTAAAAGAGTAAGAATAAACAGTAAAAGAG
*
28738 TAATAGTAGTAAGTAAAG
65 TAATAATAGTAAGTAAAG
* * * *
28756 AGTAAAGAGTAATCGAGAAAGAGTAATAGTAATCAGT-AAAGAGTAAAGAGTAAAGAGTAAAAGA
1 AGTAAAGAGTAATC-AGAAACAGTAAGAGTAATCAGTAAAAGAGT-AAGAATAAACAGTAAAAGA
*
28820 GTAATAATAGTCAGTAAAG
64 GTAATAATAGTAAGTAAAG
28839 AG-AAAGAGTAAT
1 AGTAAAGAGTAAT
28851 AGTAATCAGT
Statistics
Matches: 279, Mismatches: 42, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
77 19 0.07
78 25 0.09
79 13 0.05
80 9 0.03
81 6 0.02
82 21 0.08
83 95 0.34
84 48 0.17
85 38 0.14
86 5 0.02
ACGTcount: A:0.52, C:0.04, G:0.22, T:0.21
Consensus pattern (82 bp):
AGTAAAGAGTAATCAGAAACAGTAAGAGTAATCAGTAAAAGAGTAAGAATAAACAGTAAAAGAGT
AATAATAGTAAGTAAAG
Found at i:28884 original size:69 final size:68
Alignment explanation
Indices: 28770--28909 Score: 219
Period size: 69 Copynumber: 2.0 Consensus size: 68
28760 AAGAGTAATC
* *
28770 GAGAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAAAGAGTAAAA-GAGTAATAATAGTCAG
1 GAGAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAAACAGTAAAATG-GTAATAATAATCAG
28834 TAAA
65 TAAA
* *
28838 GAGAAAGAGTAATAGTAATCAGTAAAAGAGTAAAGAGTGAACAGTAAAATGGTAATAGTAATCAG
1 GAGAAAGAGTAATAGTAATCAGT-AAAGAGTAAAGAGTAAACAGTAAAATGGTAATAATAATCAG
28903 TAAA
65 TAAA
28907 GAG
1 GAG
28910 TAATCAGTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
68 23 0.35
69 42 0.64
70 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.24, T:0.19
Consensus pattern (68 bp):
GAGAAAGAGTAATAGTAATCAGTAAAGAGTAAAGAGTAAACAGTAAAATGGTAATAATAATCAGT
AAA
Found at i:28918 original size:35 final size:35
Alignment explanation
Indices: 28797--28922 Score: 116
Period size: 35 Copynumber: 3.6 Consensus size: 35
28787 ATCAGTAAAG
* * *
28797 AGTAAAGAGTAAAGAGTAAAA-GAGTAATAATAGTC
1 AGTAAAGAGTAAACAGTAAAATG-GTAATAGTAATC
* * **
28832 AGTAAAGAG-AAAGAGT--AATAGTAATCAGTAAAAG
1 AGTAAAGAGTAAACAGTAAAATGGTAAT-AGT-AATC
*
28866 AGTAAAGAGTGAACAGTAAAATGGTAATAGTAATC
1 AGTAAAGAGTAAACAGTAAAATGGTAATAGTAATC
*
28901 AGTAAAGAGTAATCAGTAAAAT
1 AGTAAAGAGTAAACAGTAAAAT
28923 TCTCAGTAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
32 7 0.10
33 2 0.03
34 17 0.23
35 36 0.49
36 3 0.04
37 8 0.11
ACGTcount: A:0.53, C:0.04, G:0.22, T:0.21
Consensus pattern (35 bp):
AGTAAAGAGTAAACAGTAAAATGGTAATAGTAATC
Found at i:33156 original size:6 final size:6
Alignment explanation
Indices: 33145--33169 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33135 CAAATCAAAT
33145 AGAAAA AGAAAA AGAAAA AGAAAA A
1 AGAAAA AGAAAA AGAAAA AGAAAA A
33170 TAATTCACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:44619 original size:19 final size:19
Alignment explanation
Indices: 44595--44639 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
44585 TGTAGGATAA
44595 ATTTCGAATTCATAATACC
1 ATTTCGAATTCATAATACC
*
44614 ATTTCGAATTCGTAATACC
1 ATTTCGAATTCATAATACC
*
44633 CTTTCGA
1 ATTTCGA
44640 GAGTTCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (19 bp):
ATTTCGAATTCATAATACC
Found at i:44724 original size:27 final size:27
Alignment explanation
Indices: 44669--44724 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
44659 CGACGTTTAA
* *
44669 GGGCAAAACTGTAATTTAGTCAACCAG
1 GGGCAAAACTGTAATTTAGACAACAAG
44696 GGGCAAAA-TGGTAATTTA-ACATACAAG
1 GGGCAAAACT-GTAATTTAGACA-ACAAG
44723 GG
1 GG
44725 CTGTTACGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.21
Consensus pattern (27 bp):
GGGCAAAACTGTAATTTAGACAACAAG
Found at i:45498 original size:17 final size:18
Alignment explanation
Indices: 45478--45536 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
45468 TTTTATTTTC
45478 CTTTCCTTTT-TTTTCTT
1 CTTTCCTTTTCTTTTCTT
45495 CTTTTCTCCTTTTCTTTTCTT
1 C--TT-TCCTTTTCTTTTCTT
**
45516 -TTTCCTTCTTCACTTCTT
1 CTTTCCTT-TTCTTTTCTT
45534 CTT
1 CTT
45537 CTTTTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
17 6 0.18
18 10 0.29
19 4 0.12
20 7 0.21
21 7 0.21
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (18 bp):
CTTTCCTTTTCTTTTCTT
Found at i:45532 original size:18 final size:18
Alignment explanation
Indices: 45492--45538 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
45482 CCTTTTTTTT
*
45492 CTTCTTTTCTCCTTTTCT
1 CTTCTTTTCTCCTTTTCA
*
45510 TTTCTTTT-TCCTTCTTCA
1 CTTCTTTTCTCCTT-TTCA
45528 CTTCTTCTTCT
1 CTTCTT-TTCT
45539 TTTATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 5 0.22
18 15 0.65
19 2 0.09
20 1 0.04
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (18 bp):
CTTCTTTTCTCCTTTTCA
Found at i:52664 original size:15 final size:14
Alignment explanation
Indices: 52646--52687 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
52636 TTCCTCTTCT
52646 TTTATTTTATCTTAA
1 TTTATTTTAT-TTAA
*
52661 TTTATTTTTATTTAT
1 TTTA-TTTTATTTAA
52676 TTTA-TTTATTTA
1 TTTATTTTATTTA
52688 TTTTTTAAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
15 11 0.44
16 6 0.24
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTTATTTAA
Found at i:52673 original size:10 final size:10
Alignment explanation
Indices: 52645--52686 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
52635 CTTCCTCTTC
52645 TTTTATTTTAT
1 TTTTA-TTTAT
* *
52656 CTTAATTTAT
1 TTTTATTTAT
52666 TTTTATTTA-
1 TTTTATTTAT
52675 TTTTATTTAT
1 TTTTATTTAT
52685 TT
1 TT
52687 ATTTTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
9 9 0.35
10 14 0.54
11 3 0.12
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:55661 original size:48 final size:48
Alignment explanation
Indices: 55605--55697 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
55595 AAGCATTCAC
*
55605 TTATCTCCTCCCCCACACTTAAACTCAACATTGTCCTTAATGTGAAAG
1 TTATCTCCTCCCCCACACTTAAACTCAACATTGTCCTCAATGTGAAAG
55653 TTATCTCCTCCCCCACACTTAAACTCAACATTGTCCTCAATGTGA
1 TTATCTCCTCCCCCACACTTAAACTCAACATTGTCCTCAATGTGA
55698 GAGTAAACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.28, C:0.33, G:0.08, T:0.31
Consensus pattern (48 bp):
TTATCTCCTCCCCCACACTTAAACTCAACATTGTCCTCAATGTGAAAG
Found at i:60609 original size:50 final size:50
Alignment explanation
Indices: 60555--60658 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
60545 ATACTAAGCT
60555 CAAATAAGCCCATAATTGGAGTTAAAATCCCAATTAATGCCTGATTGAGC
1 CAAATAAGCCCATAATTGGAGTTAAAATCCCAATTAATGCCTGATTGAGC
60605 CAAATAAGCCCATAATTGGAGTTAAAATCCCAATTAATGCCTGATTGAGC
1 CAAATAAGCCCATAATTGGAGTTAAAATCCCAATTAATGCCTGATTGAGC
60655 CAAA
1 CAAA
60659 AACAACCCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (50 bp):
CAAATAAGCCCATAATTGGAGTTAAAATCCCAATTAATGCCTGATTGAGC
Found at i:63683 original size:15 final size:15
Alignment explanation
Indices: 63665--63693 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
63655 GTTTCTAGTA
63665 TAATTGTTTTCTTTT
1 TAATTGTTTTCTTTT
63680 TAATTGTTTTCTTT
1 TAATTGTTTTCTTT
63694 CAACCTCTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TAATTGTTTTCTTTT
Found at i:65364 original size:18 final size:18
Alignment explanation
Indices: 65343--65377 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65333 GGGTAATTAC
*
65343 AAAAAAATTGTTTTCATA
1 AAAAAAAGTGTTTTCATA
*
65361 AAAAGAAGTGTTTTCAT
1 AAAAAAAGTGTTTTCAT
65378 GCAAGAGGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (18 bp):
AAAAAAAGTGTTTTCATA
Found at i:69067 original size:2 final size:2
Alignment explanation
Indices: 69062--69089 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69052 TGTGTGTGTG
69062 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
69090 GAGAGAGAGA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:69094 original size:2 final size:2
Alignment explanation
Indices: 69089--69130 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
69079 ATATATATAT
*
69089 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
69131 GAACATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.