Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008277.1 Hibiscus syriacus cultivar Beakdansim tig00110936_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: 76893
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:6076 original size:13 final size:12
Alignment explanation
Indices: 6057--6116 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
6047 CTTTTTTGGC
6057 TTTTTTTTGTTT
1 TTTTTTTTGTTT
6069 TTTGTTTTTGTTT
1 TTT-TTTTTGTTT
**
6082 TTTTGGCTT-TTT
1 TTTT-TTTTGTTT
*
6094 TTTTGTTT-TTT
1 TTTTTTTTGTTT
*
6105 TTTGTTTTGTTT
1 TTTTTTTTGTTT
6117 GAAAAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 12 0.30
12 14 0.35
13 14 0.35
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:6089 original size:32 final size:30
Alignment explanation
Indices: 6048--6117 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 30
6038 AAATTTTGGC
*
6048 TTTTTTGGCTTTTTTTTGTTTTTTGTTTTTGT
1 TTTTTTGGCTTTTTTTT-TGTTTT-TTTTTGT
6080 TTTTTTGGCTTTTTTTTTGTTTTTTTTTGT
1 TTTTTTGGCTTTTTTTTTGTTTTTTTTTGT
6110 TTTGTTTG
1 TTT-TTTG
6118 AAAAAAATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 10 0.28
31 9 0.25
32 17 0.47
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (30 bp):
TTTTTTGGCTTTTTTTTTGTTTTTTTTTGT
Found at i:6102 original size:10 final size:10
Alignment explanation
Indices: 6057--6112 Score: 69
Period size: 10 Copynumber: 5.3 Consensus size: 10
6047 CTTTTTTGGC
6057 TTTTTTTTGT
1 TTTTTTTTGT
6067 TTTTTGTTT-T
1 TTTTT-TTTGT
6077 TGTTTTTTTGGCT
1 T-TTTTTTT-G-T
6090 TTTTTTTTGT
1 TTTTTTTTGT
6100 TTTTTTTTGT
1 TTTTTTTTGT
6110 TTT
1 TTT
6113 GTTTGAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 24 0.59
11 8 0.20
12 7 0.17
13 2 0.05
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:8565 original size:43 final size:43
Alignment explanation
Indices: 8504--8619 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
8494 AGAAAGTTAG
* * *
8504 TTTATCTTCGTTTATTTATTAAATGAACGAATACAAAAAATAT
1 TTTATGTTCGTTTATTTATTAAATGAACAAATACAAAAAAGAT
* * ** *
8547 TTTATGTTCATTTATTTATTAAACGAACAAATATGAATAAGAT
1 TTTATGTTCGTTTATTTATTAAATGAACAAATACAAAAAAGAT
* *
8590 TTTATGTTCGTTTAATTAAATAAATGAACA
1 TTTATGTTCGTTT-ATTTATTAAATGAACA
8620 TGAACAAATG
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
43 47 0.78
44 13 0.22
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (43 bp):
TTTATGTTCGTTTATTTATTAAATGAACAAATACAAAAAAGAT
Found at i:8912 original size:24 final size:24
Alignment explanation
Indices: 8884--8960 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
8874 CCCCATTAAT
*
8884 TTTATGTTCATTCATTTGTGTTTG
1 TTTATGTTCATTCGTTTGTGTTTG
* * *
8908 TTTATGTGCATTGGTTTGTGTTCG
1 TTTATGTTCATTCGTTTGTGTTTG
* * * *
8932 TTTACGTTCGTTTGTTTGTGTTTA
1 TTTATGTTCATTCGTTTGTGTTTG
8956 TTTAT
1 TTTAT
8961 CATTTTAACA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.10, C:0.08, G:0.21, T:0.61
Consensus pattern (24 bp):
TTTATGTTCATTCGTTTGTGTTTG
Found at i:9899 original size:46 final size:46
Alignment explanation
Indices: 9828--9949 Score: 145
Period size: 46 Copynumber: 2.6 Consensus size: 46
9818 TAAGGATTAA
*
9828 TCAAGTGACAAAAACGTATTATTAATAGTTTAATAAACGTCAGTGAGT
1 TCAAGTGAC--AAACGTATTATTAATAGTTTAATAAACGTCAGAGAGT
* * * * * *
9876 TTAAGTGACAAACTTATTATTAATAATTTAGTAAATGTTAGAGAGT
1 TCAAGTGACAAACGTATTATTAATAGTTTAATAAACGTCAGAGAGT
* *
9922 TCAAGTGACAAGCGTGTTATTAATAGTT
1 TCAAGTGACAAACGTATTATTAATAGTT
9950 CCAGTGATTA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
46 54 0.87
48 8 0.13
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (46 bp):
TCAAGTGACAAACGTATTATTAATAGTTTAATAAACGTCAGAGAGT
Found at i:15993 original size:30 final size:30
Alignment explanation
Indices: 15918--16022 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
15908 TTCCTTTTAA
* * * *
15918 GTACTTAAAGTA-TTTGTTGGTCAAAGTAA
1 GTACTTAAAGTATTTTTTTGATCAAAATAG
*
15947 GTA-TGTAAACTTATTTTTTT-AGTCAAAATAG
1 GTACT-TAAA-GTATTTTTTTGA-TCAAAATAG
* *
15978 GTACTTAGAGTATTTTTTTGATCAAAATAT
1 GTACTTAAAGTATTTTTTTGATCAAAATAG
*
16008 GTATTTAAAGTATTT
1 GTACTTAAAGTATTT
16023 AATTATTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.02
29 7 0.12
30 32 0.53
31 19 0.32
32 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (30 bp):
GTACTTAAAGTATTTTTTTGATCAAAATAG
Found at i:16667 original size:20 final size:21
Alignment explanation
Indices: 16642--16697 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
16632 TTAATTATTA
*
16642 ATTTTTAATAATTTAT-TTTT
1 ATTTTTAATATTTTATATTTT
*
16662 ATTTTTAGTATTTTATATTTT
1 ATTTTTAATATTTTATATTTT
* *
16683 AATTTGAATATTTTA
1 ATTTTTAATATTTTA
16698 AACTTTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (21 bp):
ATTTTTAATATTTTATATTTT
Found at i:23661 original size:35 final size:35
Alignment explanation
Indices: 23615--23684 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
23605 TGTCAAGGTA
23615 GGTTGAGATTGACTTGAATTATCTAATGTAAGTTT
1 GGTTGAGATTGACTTGAATTATCTAATGTAAGTTT
23650 GGTTGAGATTGACTTGAATTATCTAATGTAAGTTT
1 GGTTGAGATTGACTTGAATTATCTAATGTAAGTTT
23685 ATAAAGCCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (35 bp):
GGTTGAGATTGACTTGAATTATCTAATGTAAGTTT
Found at i:29301 original size:30 final size:30
Alignment explanation
Indices: 29234--29302 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
29224 GGTGACGGTA
*
29234 GGAAGACATGTGAATTACCTAATATATTTG
1 GGAAGACGTGTGAATTACCTAATATATTTG
* *
29264 GGAAGACGTGTGAATTACCTAATGTCTTTG
1 GGAAGACGTGTGAATTACCTAATATATTTG
29294 GGAAGACGT
1 GGAAGACGT
29303 CTAGACCACT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (30 bp):
GGAAGACGTGTGAATTACCTAATATATTTG
Found at i:32428 original size:20 final size:21
Alignment explanation
Indices: 32395--32439 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
32385 ATCGTAGCGT
32395 GAATAATAAAAATCGCAACGC
1 GAATAATAAAAATCGCAACGC
32416 GAATAAT-AAAATCGCAACGC
1 GAATAATAAAAATCGCAACGC
32436 GAAT
1 GAAT
32440 TTAAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.16
Consensus pattern (21 bp):
GAATAATAAAAATCGCAACGC
Found at i:32449 original size:21 final size:19
Alignment explanation
Indices: 32402--32451 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
32392 CGTGAATAAT
32402 AAAAATCGCAACGCGAATA
1 AAAAATCGCAACGCGAATA
32421 ATAAAATCGCAACGCGAATTTA
1 A-AAAATCGCAACGCGAA--TA
32443 AAAAATCGC
1 AAAAATCGC
32452 GTTGCGAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 1 0.04
20 16 0.57
21 8 0.29
22 3 0.11
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (19 bp):
AAAAATCGCAACGCGAATA
Found at i:32805 original size:20 final size:20
Alignment explanation
Indices: 32780--32888 Score: 132
Period size: 20 Copynumber: 5.4 Consensus size: 20
32770 CATATATATT
32780 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
*
32800 CGTTGCGATTTCACTATTCA
1 CGTTGCGATTTTACTATTCA
32820 CGTTGCGATTTTTACTATTCA
1 CGTTGCGA-TTTTACTATTCA
* * * *
32841 CATTGCGAAATTGA--AGTTCG
1 CGTTGCG-ATTTTACTA-TTCA
32861 CGTTGCGATTTTACTATTCA
1 CGTTGCGATTTTACTATTCA
32881 CGTTGCGA
1 CGTTGCGA
32889 AATTGGAGTT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.07
20 47 0.64
21 21 0.28
22 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTACTATTCA
Found at i:32889 original size:40 final size:40
Alignment explanation
Indices: 32780--32908 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
32770 CATATATATT
* *
32780 CGTTGCGATTTTACTATTCACGTTGCG-ATTTCACTA-TTCA
1 CGTTGCGATTTTACTATTCACGTTGCGAAATTGA--AGTTCA
* *
32820 CGTTGCGATTTTTACTATTCACATTGCGAAATTGAAGTTCG
1 CGTTGCGA-TTTTACTATTCACGTTGCGAAATTGAAGTTCA
*
32861 CGTTGCGATTTTACTATTCACGTTGCGAAATTGGAGTTCA
1 CGTTGCGATTTTACTATTCACGTTGCGAAATTGAAGTTCA
32901 CGTTGCGA
1 CGTTGCGA
32909 ATTTGACTTT
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
40 46 0.58
41 29 0.37
42 4 0.05
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTTACTATTCACGTTGCGAAATTGAAGTTCA
Found at i:32924 original size:20 final size:20
Alignment explanation
Indices: 32780--33019 Score: 103
Period size: 20 Copynumber: 11.7 Consensus size: 20
32770 CATATATATT
*
32780 CGTTGCG-ATTTTACTATTCA
1 CGTTGCGAATTTGACT-TTCA
*
32800 CGTTGCG-ATTTCACTATTCA
1 CGTTGCGAATTTGACT-TTCA
* *
32820 CGTTGCGATTTTTACTATTCA
1 CGTTGCGAATTTGACT-TTCA
* * ** *
32841 CATTGCGAAATTGAAGTTCG
1 CGTTGCGAATTTGACTTTCA
*
32861 CGTTGCG-ATTTTACTATTCA
1 CGTTGCGAATTTGACT-TTCA
* *
32881 CGTTGCGAAATTGGA-GTTCA
1 CGTTGCG-AATTTGACTTTCA
*
32901 CGTTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGACTTTCA
* * **
32921 CGTTTGCGTTGTGAATTTAATTTTTG
1 CG-TTGC-----GAATTTGACTTTCA
** * * *
32947 TATTGCAAATTTGACTATCG
1 CGTTGCGAATTTGACTTTCA
* *
32967 CGTTACGAATTTGAC-TTCTG
1 CGTTGCGAATTTGACTTTC-A
* *
32987 TGTTGCGAATTTGACTATCA
1 CGTTGCGAATTTGACTTTCA
33007 CGTTGCGAATTTG
1 CGTTGCGAATTTG
33020 TTGGTCATTT
Statistics
Matches: 165, Mismatches: 42, Indels: 26
0.71 0.18 0.11
Matches are distributed among these distances:
19 12 0.07
20 107 0.65
21 27 0.16
22 4 0.02
25 4 0.02
26 11 0.07
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.41
Consensus pattern (20 bp):
CGTTGCGAATTTGACTTTCA
Found at i:33755 original size:14 final size:14
Alignment explanation
Indices: 33736--33788 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
33726 CATCTACAAT
33736 AATAAATTATTTAA
1 AATAAATTATTTAA
* *
33750 AATAAATCAATTCATACT
1 AATAAAT-TATT--TA-A
33768 AATAAATTATTTAA
1 AATAAATTATTTAA
33782 AATAAAT
1 AATAAAT
33789 CAATCCATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 14 0.45
15 5 0.16
17 5 0.16
18 7 0.23
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.38
Consensus pattern (14 bp):
AATAAATTATTTAA
Found at i:33776 original size:32 final size:32
Alignment explanation
Indices: 33735--33984 Score: 134
Period size: 32 Copynumber: 7.8 Consensus size: 32
33725 ACATCTACAA
33735 TAATAAATTATTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATTCATAC
*
33767 TAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATTCATAC
* * *
33799 -AACTACAA-TA-AT-AAATCAATCCATATT-TTA-
1 TAA-TA-AATTATTTAAAATAAAT-CA-ATTCATAC
* * * * * *
33829 AAATAAATCAATTTATACTAATAAAT-TATTTAAAA
1 TAATAAAT-TATTTA-A--AATAAATCAATTCATAC
*
33864 TAAATTAATCTATATTTTAAAATAAATCAA-TCTATAC
1 T-AA-TAA-AT-TA-TTTAAAATAAATCAATTC-ATAC
*
33901 TAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATTCATAC
* *
33933 -AACTACA--A--T--AATAAATCAATCCATAC
1 TAA-TAAATTATTTAAAATAAATCAATTCATAC
33959 TAATAAATTATTTAAAATAAATCAAT
1 TAATAAATTATTTAAAATAAATCAAT
33985 CAATATTTTA
Statistics
Matches: 166, Mismatches: 23, Indels: 58
0.67 0.09 0.23
Matches are distributed among these distances:
26 20 0.12
27 2 0.01
28 2 0.01
29 2 0.01
30 11 0.07
31 12 0.07
32 71 0.43
33 8 0.05
34 3 0.02
35 3 0.02
36 18 0.11
37 7 0.04
38 3 0.02
39 4 0.02
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TAATAAATTATTTAAAATAAATCAATTCATAC
Found at i:33851 original size:18 final size:18
Alignment explanation
Indices: 33830--33908 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
33820 CATATTTTAA
33830 AATAAATCAATTTATACT
1 AATAAATCAATTTATACT
* * *
33848 AATAAAT-TATTTAAAAT
1 AATAAATCAATTTATACT
* *
33865 AAATTAATCTATATTT-TA-A
1 -AATAAATC-A-ATTTATACT
*
33884 AATAAATCAATCTATACT
1 AATAAATCAATTTATACT
33902 AATAAAT
1 AATAAAT
33909 TATTTAAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
16 3 0.07
17 10 0.22
18 27 0.60
20 1 0.02
21 4 0.09
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (18 bp):
AATAAATCAATTTATACT
Found at i:33872 original size:22 final size:22
Alignment explanation
Indices: 33847--33890 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
33837 CAATTTATAC
33847 TAATAAAT-TATTTAAAATAAAT
1 TAATAAATAT-TTTAAAATAAAT
**
33869 TAATCTATATTTTAAAATAAAT
1 TAATAAATATTTTAAAATAAAT
33891 CAATCTATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAATAAATATTTTAAAATAAAT
Found at i:33890 original size:54 final size:54
Alignment explanation
Indices: 33808--34086 Score: 329
Period size: 54 Copynumber: 5.1 Consensus size: 54
33798 CAACTACAAT
* **
33808 AATAAATCAATCCATATTTTAAAATAAATCAATTTATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
33862 AATAAATTAATCTATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * **
33916 AATAAATCAATCCATACAACTACAATAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAAT-C-TA-TATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAA
*
33974 AATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
34028 AAT--A--AA--T-TATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATA----CTAATAAATTA-TTTAA
34080 AATAAAT
1 AATAAAT
34087 TATTTTATAA
Statistics
Matches: 197, Mismatches: 16, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
47 24 0.12
50 2 0.01
51 10 0.05
52 9 0.05
54 97 0.49
55 5 0.03
56 3 0.02
57 5 0.03
58 42 0.21
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (54 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:33895 original size:22 final size:22
Alignment explanation
Indices: 33857--33899 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
33847 TAATAAATTA
*
33857 TTTAAAATAAATTAATCTATAT
1 TTTAAAATAAATCAATCTATAT
33879 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATCTATA
33900 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:33908 original size:22 final size:22
Alignment explanation
Indices: 33859--33907 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
33849 ATAAATTATT
* **
33859 TAAAATAAATTAATCTATATTT
1 TAAAATAAATCAATCTATATAA
33881 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATA-TAA
33904 TAAA
1 TAAA
33908 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAATAAATCAATCTATATAA
Found at i:33946 original size:112 final size:112
Alignment explanation
Indices: 33830--34034 Score: 365
Period size: 112 Copynumber: 1.8 Consensus size: 112
33820 CATATTTTAA
** * *
33830 AATAAATCAATTTATACTAATAAATTATTTAAAATAAATTAATCTATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAAT
*
33895 CTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
66 CCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
33942 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAAT
34007 CCATACTAATAAATTATTTAAAATAAAT
66 CCATACTAATAAATTATTTAAAATAAAT
34035 TATTTTAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 88 1.00
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.36
Consensus pattern (112 bp):
AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCAATATTTTAAAATAAATCAAT
CCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
Found at i:33995 original size:22 final size:22
Alignment explanation
Indices: 33969--34071 Score: 89
Period size: 22 Copynumber: 4.5 Consensus size: 22
33959 TAATAAATTA
33969 TTTAAAATAAATCAATCAATAT
1 TTTAAAATAAATCAATCAATAT
*
33991 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCAATA-T
** * ** * *
34014 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCAA-TAT
*
34038 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCAATAT
*
34060 TTTATAATAAAT
1 TTTAAAATAAAT
34072 TATTTTAAAA
Statistics
Matches: 60, Mismatches: 18, Indels: 6
0.71 0.21 0.07
Matches are distributed among these distances:
22 34 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCAATAT
Found at i:33995 original size:134 final size:130
Alignment explanation
Indices: 33743--34058 Score: 380
Period size: 134 Copynumber: 2.4 Consensus size: 130
33733 AATAATAAAT
33743 TATTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
1 TATTTAAAATAAATCAATT-ATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
* * * * *
33808 AATAAATCAATCCATATTTTAAAATAAATCAATTTATACTAATAAATTATTTAAAATAAATTAAT
65 AATAAATCAATCCATA-TCT-AAATAAATCAATTTAAAATAATAAAATATTTAAAATAAATCAAT
*
33873 CTA
128 CCA
33876 TATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
1 TA-TTTAAAATAAATCAAT-TATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAA
*
33941 TAATAAATCAATCCATA-CT-AATAAAT-TATTTAAAATAAATCAATCAATATTTTAAAATAAAT
64 TAATAAATCAATCCATATCTAAATAAATCAATTTAAAAT-AAT-AA--AATA-TTTAAAATAAAT
34003 CAATCCA
124 CAATCCA
* * *
34010 TA-CT--AATAAAT-TATT-TA-AAATAAATTATTTTAAAATAAATCAATCCATA
1 TATTTAAAATAAATCAATTATACTAATAAATTA-TTTAAAATAAATCAATCCATA
34059 TTTTATAATA
Statistics
Matches: 165, Mismatches: 10, Indels: 22
0.84 0.05 0.11
Matches are distributed among these distances:
126 9 0.05
127 23 0.14
128 1 0.01
129 9 0.05
130 17 0.10
131 2 0.01
132 2 0.01
133 5 0.03
134 96 0.58
135 1 0.01
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (130 bp):
TATTTAAAATAAATCAATTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATA
ATAAATCAATCCATATCTAAATAAATCAATTTAAAATAATAAAATATTTAAAATAAATCAATCCA
Found at i:34057 original size:47 final size:49
Alignment explanation
Indices: 33942--34131 Score: 180
Period size: 54 Copynumber: 3.8 Consensus size: 49
33932 CAACTACAAT
*
33942 AATAAATCAATCCATA-CTAATAAATTA-TTTAAAATAAATCAATCAATATTTTAA
1 AATAAATCAATCCATATATAATAAATTATTTTAAAAT--A--AAT---TATTTTAA
*
33996 AATAAATCAATCCATA-CTAATAAATTA-TTTAAAATAAATTATTTTAA
1 AATAAATCAATCCATATATAATAAATTATTTTAAAATAAATTATTTTAA
*
34043 AATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTTAT
1 AATAAATCAATCCATA---TATAATAAATTATTTTAAAATAAATTATTTTAA
* * *
34095 AATAAAT-TAT---TTTAAAATAAATTATTTTAAAATAAAT
1 AATAAATCAATCCATATATAATAAATTATTTTAAAATAAAT
34132 AACTTTATTA
Statistics
Matches: 126, Mismatches: 5, Indels: 19
0.84 0.03 0.13
Matches are distributed among these distances:
45 24 0.19
47 24 0.19
48 1 0.01
50 3 0.02
51 12 0.10
52 27 0.21
54 35 0.28
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.41
Consensus pattern (49 bp):
AATAAATCAATCCATATATAATAAATTATTTTAAAATAAATTATTTTAA
Found at i:34060 original size:69 final size:67
Alignment explanation
Indices: 33960--34116 Score: 210
Period size: 69 Copynumber: 2.3 Consensus size: 67
33950 AATCCATACT
*
33960 AATAAATTA-TTTAAAATAAATCAATCAATATTTTAAAATAAATCAATCCATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCAATATTTTAAAATAAAT-AAT-CATA-AAATAAATTAT
34023 TTTAA
63 TTTAA
* * * **
34028 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAAATTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCAATATTTTAAAATAAATAATCATAAAATAAATTATTTT
*
34093 AT
66 AA
34095 AATAAATTATTTTAAAATAAAT
1 AATAAATTATTTTAAAATAAAT
34117 TATTTTAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
66 9 0.11
67 28 0.35
68 11 0.14
69 32 0.40
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCAATATTTTAAAATAAATAATCATAAAATAAATTATTTT
AA
Found at i:34121 original size:45 final size:43
Alignment explanation
Indices: 34016--34154 Score: 150
Period size: 45 Copynumber: 3.4 Consensus size: 43
34006 TCCATACTAA
*
34016 TAAATTA-TTTAAAATAAATTATTTTAAAATAAAT--C---AA
1 TAAATTATTTTAAAATAAATTATTTTAAAATAAATAACTTTAT
** * * *
34053 TCCA-TATTTTATAATAAATTATTTTAAAATAAATTATTTTAT
1 TAAATTATTTTAAAATAAATTATTTTAAAATAAATAACTTTAT
34095 AATAAATTATTTTAAAATAAATTATTTTAAAATAAATAACTTTAT
1 --TAAATTATTTTAAAATAAATTATTTTAAAATAAATAACTTTAT
34140 TAAATTA-TTTAAAAT
1 TAAATTATTTTAAAAT
34155 TATTTTAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 13
0.78 0.09 0.12
Matches are distributed among these distances:
36 2 0.02
37 28 0.34
42 9 0.11
43 7 0.08
44 2 0.02
45 35 0.42
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (43 bp):
TAAATTATTTTAAAATAAATTATTTTAAAATAAATAACTTTAT
Found at i:34138 original size:15 final size:15
Alignment explanation
Indices: 34014--34131 Score: 148
Period size: 15 Copynumber: 7.5 Consensus size: 15
34004 AATCCATACT
34014 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
34028 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
34043 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
34065 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
34080 AATAAATTATTTTAT
1 AATAAATTATTTTAA
34095 AATAAATTATTTTAA
1 AATAAATTATTTTAA
34110 AATAAATTATTTTAA
1 AATAAATTATTTTAA
34125 AATAAAT
1 AATAAAT
34132 AACTTTATTA
Statistics
Matches: 92, Mismatches: 4, Indels: 15
0.83 0.04 0.14
Matches are distributed among these distances:
14 9 0.10
15 65 0.71
17 1 0.01
18 3 0.03
19 3 0.03
20 1 0.01
22 10 0.11
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:35437 original size:3 final size:3
Alignment explanation
Indices: 35429--35463 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
35419 ACTCAATTGA
35429 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35464 ATAGGAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:39344 original size:23 final size:23
Alignment explanation
Indices: 39318--39362 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
39308 ACCAAAATAA
39318 TTACGTGAAAGGAGAAAGTTCAC
1 TTACGTGAAAGGAGAAAGTTCAC
*
39341 TTACGTGAGAGGAGAAAGTTCA
1 TTACGTGAAAGGAGAAAGTTCA
39363 GTGTTCGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (23 bp):
TTACGTGAAAGGAGAAAGTTCAC
Found at i:48706 original size:2 final size:2
Alignment explanation
Indices: 48699--48726 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48689 ATTATTTTTA
48699 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
48727 GCCTTCACAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:53370 original size:73 final size:73
Alignment explanation
Indices: 53283--53428 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
53273 TTGCAACAAA
53283 GTCATCAAACATTTAGTTCGTTTAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAGTAGA
1 GTCATCAAACATTTAGTTCGTTTAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAGTAGA
53348 AGATGATG
66 AGATGATG
53356 GTCATCAAACATTTAGTTCGTTTAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAGTAGA
1 GTCATCAAACATTTAGTTCGTTTAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAGTAGA
53421 AGATGATG
66 AGATGATG
53429 TGGCATGTGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (73 bp):
GTCATCAAACATTTAGTTCGTTTAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAGTAGA
AGATGATG
Found at i:53421 original size:39 final size:39
Alignment explanation
Indices: 53305--53421 Score: 95
Period size: 36 Copynumber: 3.1 Consensus size: 39
53295 TTAGTTCGTT
53305 TAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAG
1 TAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAG
* * * *** * *
53344 TAGAA-G-ATGATGGTCATCAAAC-ATTTAGTT--CGT--T
1 TAGAATGTGTGAT-GTAACCGTCCGTTTTA-TTGCCGTCAG
53378 TAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAG
1 TAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAG
53417 TAGAA
1 TAGAA
53422 GATGATGTGG
Statistics
Matches: 53, Mismatches: 16, Indels: 18
0.61 0.18 0.21
Matches are distributed among these distances:
34 5 0.09
35 8 0.15
36 11 0.21
37 11 0.21
38 8 0.15
39 10 0.19
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (39 bp):
TAGAATGTGTGATGTAACCGTCCGTTTTATTGCCGTCAG
Found at i:54031 original size:35 final size:36
Alignment explanation
Indices: 53948--54044 Score: 126
Period size: 35 Copynumber: 2.7 Consensus size: 36
53938 AATAGATTAT
* * * *
53948 GAATTTGGGGTTGAGCATGTAATTGATGTATTTTTG
1 GAATTTAGGGTTTAGAATGTAATTGAAGTATTTTTG
*
53984 GAATTTTA-GGTTTAGAATGTAATTTAAGTA-TTTTG
1 GAA-TTTAGGGTTTAGAATGTAATTGAAGTATTTTTG
54019 GAATTTAGGGTTTAGAATGTAATTGA
1 GAATTTAGGGTTTAGAATGTAATTGA
54045 TGACTATGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
34 4 0.08
35 25 0.47
36 21 0.40
37 3 0.06
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.44
Consensus pattern (36 bp):
GAATTTAGGGTTTAGAATGTAATTGAAGTATTTTTG
Found at i:69225 original size:18 final size:18
Alignment explanation
Indices: 69204--69245 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
69194 GGAGGAGGGA
*
69204 GATCGACGATAGGTTCAG
1 GATCGACGACAGGTTCAG
69222 GATCGACGACAGGTTCAG
1 GATCGACGACAGGTTCAG
69240 GATCGA
1 GATCGA
69246 TGGGAGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.19, G:0.33, T:0.19
Consensus pattern (18 bp):
GATCGACGACAGGTTCAG
Found at i:69732 original size:15 final size:16
Alignment explanation
Indices: 69699--69736 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
69689 GCGACTTTAT
69699 AAAATATTAGGAATGA
1 AAAATATTAGGAATGA
**
69715 AAAATATTATTAAT-A
1 AAAATATTAGGAATGA
69730 AAAATAT
1 AAAATAT
69737 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (16 bp):
AAAATATTAGGAATGA
Done.