Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004844.1 Hibiscus syriacus cultivar Beakdansim tig00010925_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: 29805
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7247 original size:32 final size:32
Alignment explanation
Indices: 7209--7279 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
7199 GTCTGCATGT
*
7209 GCCATGCACGTCTCCAACA-CCCAACACAGGTC
1 GCCATGCAC-TCCCCAACACCCCAACACAGGTC
*
7241 GTCATGCACTCCCCAACACCCCAACACAGGTC
1 GCCATGCACTCCCCAACACCCCAACACAGGTC
7273 GCCATGC
1 GCCATGC
7280 CTACAAGGTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 8 0.23
32 27 0.77
ACGTcount: A:0.27, C:0.45, G:0.15, T:0.13
Consensus pattern (32 bp):
GCCATGCACTCCCCAACACCCCAACACAGGTC
Found at i:7571 original size:29 final size:29
Alignment explanation
Indices: 7534--7590 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
7524 GTAATGACCA
*
7534 TAGGTCGCCATGCAATCCAGGCGACCTTG
1 TAGGCCGCCATGCAATCCAGGCGACCTTG
** *
7563 TAGGCCGCCATGCCTTTCAGGCGACCTT
1 TAGGCCGCCATGCAATCCAGGCGACCTT
7591 TGTGGGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (29 bp):
TAGGCCGCCATGCAATCCAGGCGACCTTG
Found at i:7931 original size:20 final size:21
Alignment explanation
Indices: 7901--7950 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
7891 TTGCAGCAGA
7901 AGAAA-AAGAAAGTG-CAAAG
1 AGAAAGAAGAAAGTGACAAAG
*
7920 AGAAAGAAGAAAGTGAGAAAG
1 AGAAAGAAGAAAGTGACAAAG
7941 -GAAAGAAGAA
1 AGAAAGAAGAA
7951 GAGAAGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 5 0.18
20 19 0.68
21 4 0.14
ACGTcount: A:0.64, C:0.02, G:0.30, T:0.04
Consensus pattern (21 bp):
AGAAAGAAGAAAGTGACAAAG
Found at i:8309 original size:29 final size:29
Alignment explanation
Indices: 8277--8346 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
8267 TTAGTTAGTA
8277 AGTTTATTAGTATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTATAGTTAT-AT-AAAAGAAT
*
8306 AGTTTATTAGTTTTAGTTATATAAAAGAAT
1 AGTTTATTAG-TATAGTTATATAAAAGAAT
*
8336 ATTTTATTAGT
1 AGTTTATTAGT
8347 GTTTAAGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 15 0.42
30 17 0.47
31 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.47
Consensus pattern (29 bp):
AGTTTATTAGTATAGTTATATAAAAGAAT
Found at i:10624 original size:14 final size:14
Alignment explanation
Indices: 10605--10652 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
10595 TTCAAGTCGT
10605 AAATCATTACTATC
1 AAATCATTACTATC
10619 AAATCATTAC--T-
1 AAATCATTACTATC
*
10630 AAATCATTAATATC
1 AAATCATTACTATC
10644 AAATCATTA
1 AAATCATTA
10653 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:10653 original size:14 final size:14
Alignment explanation
Indices: 10605--10701 Score: 65
Period size: 14 Copynumber: 6.7 Consensus size: 14
10595 TTCAAGTCGT
*
10605 AAATCATTACTATC
1 AAATCATTAATATC
*
10619 AAATCATT-A-CT-
1 AAATCATTAATATC
10630 AAATCATTAATATC
1 AAATCATTAATATC
*
10644 AAATCATTAAATATTA
1 AAATCATT-AATA-TC
* *
10660 ATAATAAATTATTATTAC
1 A-AAT-CATTAATA-T-C
*
10678 TAATCATTAATATC
1 AAATCATTAATATC
10692 AAATCATTAA
1 AAATCATTAA
10702 ATATTAATAA
Statistics
Matches: 64, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
11 8 0.12
12 2 0.03
13 1 0.02
14 26 0.41
15 5 0.08
16 8 0.12
17 11 0.17
18 3 0.05
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:10804 original size:97 final size:94
Alignment explanation
Indices: 10622--10832 Score: 334
Period size: 96 Copynumber: 2.2 Consensus size: 94
10612 TACTATCAAA
*
10622 TCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTA
1 TCATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTA
10687 ATATCAAATCATTAAATATTAATAATAAATT
65 ATATCAAATCATTAAATATTAATAAT-AATT
* **
10718 TTATTACTAATCATTACTATCAAATCATTAAA-ATTAATAATTTTATTATTTATTACTAAATCAT
1 TCATTACTAATCATTACTATCAAATCATTAAATATTAATAA-TAAATTA-TTATTACT-AATCAT
10782 TAATATCAAATCATTAAATATTAATAATAATT
63 TAATATCAAATCATTAAATATTAATAATAATT
10814 TCATTACTAATCATTACTA
1 TCATTACTAATCATTACTA
10833 AATCATTATT
Statistics
Matches: 107, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
94 8 0.07
95 28 0.26
96 37 0.35
97 34 0.32
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (94 bp):
TCATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTAA
TATCAAATCATTAAATATTAATAATAATT
Found at i:10832 original size:57 final size:50
Alignment explanation
Indices: 10622--10840 Score: 254
Period size: 48 Copynumber: 4.3 Consensus size: 50
10612 TACTATCAAA
**
10622 TCATTACTAAATCATTAATATCAAATCATTAAATATTAATAA-TAAATTAT
1 TCATTACTAAATCATTAATATCAAATCATTAAA-ATTAATAATTTTATTAT
**
10672 T-ATTACT-AATCATTAATATCAAATCATTAAATATTAATAA-TAAATT-T
1 TCATTACTAAATCATTAATATCAAATCATTAAA-ATTAATAATTTTATTAT
*
10719 T-ATTACT-AATCATTACTATCAAATCATTAAAATTAATAATTTTATTAT
1 TCATTACTAAATCATTAATATCAAATCATTAAAATTAATAATTTTATTAT
*
10767 TTATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTACT
1 TCATTACTAAATCATTAATATCAAATCATTAAA-ATTAATAAT--TTT-ATTA-T
10822 AATCATTACTAAATCATTA
1 --TCATTACTAAATCATTA
10841 TTATAATTTC
Statistics
Matches: 153, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
46 8 0.05
47 35 0.23
48 41 0.27
49 12 0.08
50 24 0.16
51 9 0.06
53 3 0.02
54 4 0.03
55 1 0.01
57 16 0.10
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (50 bp):
TCATTACTAAATCATTAATATCAAATCATTAAAATTAATAATTTTATTAT
Found at i:10933 original size:14 final size:14
Alignment explanation
Indices: 10914--10961 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
10904 TTCAAGTCGT
10914 AAATCATTACTATC
1 AAATCATTACTATC
10928 AAATCATTAC--T-
1 AAATCATTACTATC
*
10939 AAATCATTAATATC
1 AAATCATTACTATC
10953 AAATCATTA
1 AAATCATTA
10962 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:10941 original size:25 final size:25
Alignment explanation
Indices: 10913--11011 Score: 91
Period size: 25 Copynumber: 4.0 Consensus size: 25
10903 GTTCAAGTCG
*
10913 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
10938 TAAATCATTAATATCAAATCA-T--
1 TAAATCATTAATATCAAATCATTAC
*
10960 TAAAT-ATTAATAATAAATTATTTCATTAC
1 TAAATCATTAAT-ATCAA--A--TCATTAC
*
10989 T-AATCATTACTATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
11012 AAAATTAATA
Statistics
Matches: 61, Mismatches: 4, Indels: 19
0.73 0.05 0.23
Matches are distributed among these distances:
21 6 0.10
22 9 0.15
24 8 0.13
25 20 0.33
26 4 0.07
27 1 0.02
28 7 0.11
29 6 0.10
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:11160 original size:59 final size:60
Alignment explanation
Indices: 10982--11228 Score: 370
Period size: 59 Copynumber: 4.3 Consensus size: 60
10972 ATAAATTATT
* *
10982 TCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACTAA
1 TCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTACTAA
*
11041 TCATTACTAAATCATTAATATCAAATC-----ATATTAATAATAA--TT-TCATTACTAA
1 TCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTACTAA
* *
11093 TGATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAA-TTTATTATTACTAA
1 TCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTACTAA
*
11152 TCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTATTAA
1 TCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTACTAA
11212 TCATTACTAAATCATTA
1 TCATTACTAAATCATTA
11229 TTATAATTTC
Statistics
Matches: 170, Mismatches: 9, Indels: 17
0.87 0.05 0.09
Matches are distributed among these distances:
52 34 0.20
53 2 0.01
55 12 0.07
57 13 0.08
58 2 0.01
59 60 0.35
60 47 0.28
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (60 bp):
TCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTACTAA
Found at i:11172 original size:111 final size:109
Alignment explanation
Indices: 10929--11220 Score: 410
Period size: 111 Copynumber: 2.7 Consensus size: 109
10919 ATTACTATCA
* *
10929 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTTCATTACTAATC
1 AATCATTACTAAATCATTAATATCAAATCATTAAATAATAAT-ATAAATTATATCATTACTAATC
10994 ATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
65 ATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
* ** *
11039 AATCATTACTAAATCATTAATATCAAATCATATTAATAATAAT-TTCATTACTAATGATTACTAA
1 AATCATTACTAAATCATTAATATCAAATCAT-TAAATAATAATATAAATTA-T-ATCATTACT-A
*
11103 ATCATTACTATCAAATCATTAAATATTAATAATAA-TTTATTATTACT
62 ATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
* * * *
11150 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATA-ATAATTTTATTATTATTAATC
1 AATCATTACTAAATCATTAATATCAAATCATTAAATAATAATATA-AATTATATCATTACTAATC
11214 ATTACTA
65 ATTACTA
11221 AATCATTATT
Statistics
Matches: 162, Mismatches: 14, Indels: 14
0.85 0.07 0.07
Matches are distributed among these distances:
108 11 0.07
109 12 0.07
110 42 0.26
111 62 0.38
112 35 0.22
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (109 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATAATAATATAAATTATATCATTACTAATCA
TTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
Found at i:11323 original size:14 final size:14
Alignment explanation
Indices: 11304--11347 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
11294 AGTCGTAAAG
11304 CATTACTATCAAAT
1 CATTACTATCAAAT
11318 CATTAC--T-AAAT
1 CATTACTATCAAAT
*
11329 CATTAATATCAAAT
1 CATTACTATCAAAT
11343 CATTA
1 CATTA
11348 AATATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 9 0.35
12 1 0.04
13 1 0.04
14 15 0.58
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (14 bp):
CATTACTATCAAAT
Found at i:11327 original size:25 final size:25
Alignment explanation
Indices: 11299--11347 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
11289 GTTCAAGTCG
*
11299 TAAAGCATTACTATCAAATCATTAC
1 TAAAGCATTAATATCAAATCATTAC
*
11324 TAAATCATTAATATCAAATCATTA
1 TAAAGCATTAATATCAAATCATTA
11348 AATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAAGCATTAATATCAAATCATTAC
Found at i:11367 original size:43 final size:48
Alignment explanation
Indices: 11314--11408 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 48
11304 CATTACTATC
*
11314 AAATCATTACTAAA-T-C-ATTA-A-TATCAAATCATTAAATATTAAT
1 AAATCATTACTAAATTACAATTATACTATCAAATCATTAAAAATTAAT
*
11357 AAATTATTACTAAATTACTAATTATTACTATCAAATCATTAAAAATTAAT
1 AAATCATTACTAAATTAC-AATTA-TACTATCAAATCATTAAAAATTAAT
11407 AA
1 AA
11409 TAAATTTCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
43 13 0.30
44 1 0.02
45 1 0.02
47 4 0.09
49 1 0.02
50 23 0.53
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.38
Consensus pattern (48 bp):
AAATCATTACTAAATTACAATTATACTATCAAATCATTAAAAATTAAT
Found at i:11492 original size:56 final size:57
Alignment explanation
Indices: 11359--11549 Score: 277
Period size: 56 Copynumber: 3.4 Consensus size: 57
11349 ATATTAATAA
*
11359 ATTATTACTAA--ATTACTAATTATTACTATCAAATCATTAAAAATTAATAATAAATTTC
1 ATTATTACTAATCATTACTAA-TATTACTATCAAATCATTAAATATTAATAAT--ATTTC
*
11417 ATTATTACTAATCATTACTAA-ATTAATATCAAATCATTAAATATTAATAATATTTC
1 ATTATTACTAATCATTACTAATATTACTATCAAATCATTAAATATTAATAATATTTC
11473 ATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAAT-A-A-TTC
1 ATTATTACTAATCATTACT-AAT-ATTACTATCAAATCATTAAATATTAATAATATTTC
11529 ATTATTACTAATCATTACTAA
1 ATTATTACTAATCATTACTAA
11550 ATCTTAGAAA
Statistics
Matches: 125, Mismatches: 3, Indels: 13
0.89 0.02 0.09
Matches are distributed among these distances:
55 2 0.02
56 46 0.37
57 3 0.02
58 40 0.32
59 26 0.21
60 8 0.06
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (57 bp):
ATTATTACTAATCATTACTAATATTACTATCAAATCATTAAATATTAATAATATTTC
Found at i:14552 original size:119 final size:120
Alignment explanation
Indices: 14401--14756 Score: 600
Period size: 119 Copynumber: 3.0 Consensus size: 120
14391 CGAGGGTCTA
14401 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
14466 GATCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
14521 TGTGGTCCTTCGGGAC-TATATGTATTCTTTGGAACATGTGGGAAGTCTGGTGAGACAC-TACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
14584 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GAT-CCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
* *
14640 TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
**
14705 GATCC---CTATATG--TATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCTAGC-ATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
14756 T
1 T
14757 ATTATATGGC
Statistics
Matches: 226, Mismatches: 6, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
116 38 0.17
117 1 0.00
118 13 0.06
119 108 0.48
120 58 0.26
121 8 0.04
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (120 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:14645 original size:18 final size:18
Alignment explanation
Indices: 14622--14657 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
14612 AGGAATGATA
14622 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
14640 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
14658 ATATGTATTC
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:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:14815 original size:23 final size:23
Alignment explanation
Indices: 14766--14823 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
14756 TATTATATGG
*
14766 CACTACGGTGCAATTCTACGCGG
1 CACTACGGTGCAATTCTACGCGA
* *
14789 CACTACGGTGCAATTCTATGTGA
1 CACTACGGTGCAATTCTACGCGA
*
14812 CACTTCGGTGCA
1 CACTACGGTGCA
14824 TTTATATGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGA
Found at i:14962 original size:17 final size:18
Alignment explanation
Indices: 14929--14962 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
14919 GAACAAATAT
*
14929 ATGTTAGTGGTATGATAA
1 ATGTTAGTGGAATGATAA
14947 ATGTTA-TGGAATGATA
1 ATGTTAGTGGAATGATA
14963 TGATGTTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.38
Consensus pattern (18 bp):
ATGTTAGTGGAATGATAA
Found at i:14968 original size:18 final size:18
Alignment explanation
Indices: 14925--14969 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
14915 ATATGAACAA
*
14925 ATATATGTTAGTGGTATG
1 ATATATGTTAGTGGAATG
*
14943 ATAAATGTTA-TGGAATG
1 ATATATGTTAGTGGAATG
14960 ATATGATGTT
1 ATAT-ATGTT
14970 GTGTGTGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (18 bp):
ATATATGTTAGTGGAATG
Found at i:17968 original size:17 final size:17
Alignment explanation
Indices: 17915--17977 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
17905 ATAATATAAA
17915 TTAAACAAAATA-TTTT
1 TTAAACAAAATATTTTT
* * *
17931 TAAAACAACACTAAATATTT
1 TTAAACAA-A--ATATTTTT
17951 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
17968 TTAAACAAAA
1 TTAAACAAAA
17978 ATTATATCGC
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
16 7 0.19
17 17 0.46
19 3 0.08
20 10 0.27
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:18768 original size:22 final size:23
Alignment explanation
Indices: 18743--18792 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
18733 AATTTGACTG
18743 TTGAAGCAAATAA-TATTGAGCA
1 TTGAAGCAAATAACTATTGAGCA
* ** *
18765 TTGAATCATGTAACTATTGAGCG
1 TTGAAGCAAATAACTATTGAGCA
18788 TTGAA
1 TTGAA
18793 AGGCTGCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (23 bp):
TTGAAGCAAATAACTATTGAGCA
Found at i:18947 original size:23 final size:23
Alignment explanation
Indices: 18917--18960 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
18907 GATTGGCTAC
*
18917 AATCTCCCAGCTATGGATGCAGG
1 AATCTCCCAGCTATAGATGCAGG
18940 AATCTCCCAGCTATAGATGCA
1 AATCTCCCAGCTATAGATGCA
18961 ACGCATGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (23 bp):
AATCTCCCAGCTATAGATGCAGG
Found at i:19130 original size:32 final size:32
Alignment explanation
Indices: 19065--19142 Score: 131
Period size: 32 Copynumber: 2.4 Consensus size: 32
19055 GTAGGTCGCT
19065 GGGAGTGCATGGCGACCTGTGTTGGGGTGTTG
1 GGGAGTGCATGGCGACCTGTGTTGGGGTGTTG
19097 GGGACGTGCATGGCGACCTGTGTT-GGGTGTTG
1 GGGA-GTGCATGGCGACCTGTGTTGGGGTGTTG
19129 GGGATGTGCATGGC
1 GGGA-GTGCATGGC
19143 ATATGCAGAC
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 25 0.57
33 19 0.43
ACGTcount: A:0.10, C:0.14, G:0.49, T:0.27
Consensus pattern (32 bp):
GGGAGTGCATGGCGACCTGTGTTGGGGTGTTG
Found at i:20427 original size:41 final size:41
Alignment explanation
Indices: 20271--20509 Score: 143
Period size: 41 Copynumber: 5.8 Consensus size: 41
20261 AAAATAAAAC
* *
20271 TTTAGCGGAGTTTTT-TAAACAAACGCCGCAATAGGGT-GTTAA
1 TTTAGCGGCGTTTTTAT-AA-AAACGCCGCAATAGAGTAG-TAA
* * * * * *
20313 GTTAGCGGCGTTTATAGCT-CAAACGCCGGAATATAGTTGT--
1 TTTAGCGGCGTTTTTA--TAAAAACGCCGCAATAGAGTAGTAA
* * *
20353 TTATAGTGGCGTTTTCTAAAAAAACACCGCAATAGAGTAGTAA
1 TT-TAGCGGCGTTTT-TATAAAAACGCCGCAATAGAGTAGTAA
* *
20396 TTTAGCGGCGTTTTTATATAAACGCCGCAATAGAGTTGT--
1 TTTAGCGGCGTTTTTATAAAAACGCCGCAATAGAGTAGTAA
* ** * *
20435 TTATAGTGGCGTTTGTGCTAAAAATGCCGCAA-AGAGTAATAA
1 TT-TAGCGGCGTTT-TTATAAAAACGCCGCAATAGAGTAGTAA
** *
20477 TTTAGCGGCGATTTTCCTACAAACGCCGCAATA
1 TTTAGCGGCG-TTTTTATAAAAACGCCGCAATA
20510 TGTTTGTCTG
Statistics
Matches: 150, Mismatches: 32, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
39 2 0.01
40 17 0.11
41 81 0.54
42 46 0.31
43 3 0.02
45 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTATAAAAACGCCGCAATAGAGTAGTAA
Found at i:20446 original size:82 final size:82
Alignment explanation
Indices: 20280--20543 Score: 252
Period size: 82 Copynumber: 3.2 Consensus size: 82
20270 CTTTAGCGGA
* * * * * ** *
20280 GTTTTTTAAACAAACGCCGCAATAGGGT-GTTAAGTTAGCGGCGTTTATAGCTCAAACGCCGGAA
1 GTTTTCTAAAAAAACGCCGCAATAGAGTAG-TAATTTAGCGGCGTTTTTATAT-AAACGCCGCAA
*
20344 TATAGTTGTTTATAGTGGC
64 TAGAGTTGTTTATAGTGGC
*
20363 GTTTTCTAAAAAAACACCGCAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGCAATA
1 GTTTTCTAAAAAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGCAATA
20428 GAGTTGTTTATAGTGGC
66 GAGTTGTTTATAGTGGC
* * ** *
20445 GTTTGTGCT--AAAAATGCCGCAA-AGAGTAATAATTTAGCGGCGATTTTCCTACAAACGCCGCA
1 GTTT-T-CTAAAAAAACGCCGCAATAGAGTAGTAATTTAGCGGCG-TTTTTATATAAACGCCGCA
* * *
20507 ATATG-TTTGTCTGTAGTGGC
63 ATA-GAGTTGTTTATAGTGGC
* *
20527 GCTTT-TATAAAAACGCC
1 GTTTTCTAAAAAAACGCC
20544 ACAAAAAATG
Statistics
Matches: 153, Mismatches: 21, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
79 1 0.01
81 28 0.18
82 77 0.50
83 44 0.29
84 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (82 bp):
GTTTTCTAAAAAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTTTATATAAACGCCGCAATA
GAGTTGTTTATAGTGGC
Found at i:22034 original size:18 final size:18
Alignment explanation
Indices: 22011--22046 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
22001 TAGCGCGTTT
22011 GTAGCTAAAACGCCGCAA
1 GTAGCTAAAACGCCGCAA
22029 GTAGCTAAAACGCCGCAA
1 GTAGCTAAAACGCCGCAA
22047 TAGAGTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.22, T:0.11
Consensus pattern (18 bp):
GTAGCTAAAACGCCGCAA
Found at i:22052 original size:59 final size:60
Alignment explanation
Indices: 21970--22088 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 60
21960 AGCGGCGTTT
* * * *
21970 GTAGCTCAAATGCCGTAATAGAGTAGTAATATAGC-GCGTTTGTAGCTAAAACGCCGCAA
1 GTAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAACGCCGCAA
*
22029 GTAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAATGCCGCAA
1 GTAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAACGCCGCAA
22089 TAGAGTAGTA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
59 32 0.59
60 22 0.41
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (60 bp):
GTAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAACGCCGCAA
Found at i:22304 original size:124 final size:125
Alignment explanation
Indices: 22034--22379 Score: 486
Period size: 124 Copynumber: 2.8 Consensus size: 125
22024 CGCAAGTAGC
* * * * * *
22034 TAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAATGCCGCAATAGAGTAGTA
1 TAAAACGCCACAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
* * **
22099 ATATAGCGGCGTTT-GAGCTACAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTATGA
66 ATATAGCGGCGTTTATAGCT-CAAACGCCGCAATAGAGTAGTAATATAGCACCGTTTATGA
* * * * *
22159 TCAAACACCATAATAGA-TTGTAATATAGCGGCGTTTATAGCTCAAACGTCATAATAGAGTTGTA
1 TAAAACGCCACAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
22223 ATATAGCGGCGTTTATAGCTCAAACGCCGCAATAGAGTAGTAATATAGCACCG-TTATAGA
66 ATATAGCGGCGTTTATAGCTCAAACGCCGCAATAGAGTAGTAATATAGCACCGTTTAT-GA
*
22283 TAAAACGCC-CAATAGAGTTGTAATATAAC-GCGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
1 TAAAACGCCACAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
*
22346 ATATAGCGGCTTTTATAGCTCAAACGCCGCAATA
66 ATATAGCGGCGTTTATAGCTCAAACGCCGCAATA
22380 TGGTTAACAT
Statistics
Matches: 196, Mismatches: 22, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
123 75 0.38
124 104 0.53
125 17 0.09
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (125 bp):
TAAAACGCCACAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGCCGTAATAGAGTTGTA
ATATAGCGGCGTTTATAGCTCAAACGCCGCAATAGAGTAGTAATATAGCACCGTTTATGA
Found at i:22373 original size:82 final size:84
Alignment explanation
Indices: 22030--22379 Score: 442
Period size: 82 Copynumber: 4.2 Consensus size: 84
22020 ACGCCGCAAG
* * *
22030 TAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTAAAATGCCGCAATAGAGT
1 TAGCTCAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGCAATAGAGT
22095 AGTAATATAGCGGCGTTT-
66 AGTAATATAGCGGCGTTTA
* * * * **
22113 GAGCTACAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTAT-GATCAAACACCATAATAGA-
1 TAGCT-CAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGCAATAGAG
*
22176 TTGTAATATAGCGGCGTTTA
65 TAGTAATATAGCGGCGTTTA
* ** *
22196 TAGCTCAAACGTCATAATAGAGTTGTAATATAGCGGCGTTTATAGCTCAAACGCCGCAATAGAGT
1 TAGCTCAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGCAATAGAGT
**
22261 AGTAATATAGCACCG-TTA
66 AGTAATATAGCGGCGTTTA
* * * * *
22279 TAGATAAAACGCC-CAATAGAGTTGTAATATAAC-GCGTTTATAGCTCAAACGCCGTAATAGAGT
1 TAGCTCAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGCAATAGAGT
* *
22342 TGTAATATAGCGGCTTTTA
66 AGTAATATAGCGGCGTTTA
22361 TAGCTCAAACGCCGCAATA
1 TAGCTCAAACGCCGCAATA
22380 TGGTTAACAT
Statistics
Matches: 228, Mismatches: 33, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
81 40 0.18
82 85 0.37
83 54 0.24
84 49 0.21
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (84 bp):
TAGCTCAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTATAGCTCAAACGCCGCAATAGAGT
AGTAATATAGCGGCGTTTA
Found at i:22393 original size:42 final size:42
Alignment explanation
Indices: 22030--22379 Score: 442
Period size: 42 Copynumber: 8.5 Consensus size: 42
22020 ACGCCGCAAG
* *
22030 TAGCTAAAACGCCGCAATAGAGTAGTAATATAGCGGCGTTTA
1 TAGCTCAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTA
* * *
22072 TAGCTAAAATGCCGCAATAGAGTAGTAATATAGCGGCGTTT-
1 TAGCTCAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTA
* * *
22113 GAGCTACAAACGCCGTAATAGAGTAGTAATATAGCGGCGTTTA
1 TAGCT-CAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTA
* * **
22156 T-GATCAAACACCATAATAGA-TTGTAATATAGCGGCGTTTA
1 TAGCTCAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTA
* **
22196 TAGCTCAAACGTCATAATAGAGTTGTAATATAGCGGCGTTTA
1 TAGCTCAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTA
* **
22238 TAGCTCAAACGCCGCAATAGAGTAGTAATATAGCACCG-TTA
1 TAGCTCAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTA
* * *
22279 TAGATAAAACGCC-CAATAGAGTTGTAATATAAC-GCGTTTA
1 TAGCTCAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTA
* *
22319 TAGCTCAAACGCCGTAATAGAGTTGTAATATAGCGGCTTTTA
1 TAGCTCAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTA
22361 TAGCTCAAACGCCGCAATA
1 TAGCTCAAACGCCGCAATA
22380 TGGTTAACAT
Statistics
Matches: 271, Mismatches: 30, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
39 2 0.01
40 52 0.19
41 66 0.24
42 151 0.56
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (42 bp):
TAGCTCAAACGCCGCAATAGAGTTGTAATATAGCGGCGTTTA
Found at i:22784 original size:23 final size:23
Alignment explanation
Indices: 22736--22784 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
22726 TTCACTGCGC
* *
22736 CGTGCCTTCTTCGTCTCCGGCGT
1 CGTGCCTTCTTCGTCTCCGACAT
*
22759 CGTGCCTTCTTTGTCTCCGACAT
1 CGTGCCTTCTTCGTCTCCGACAT
22782 CGT
1 CGT
22785 CGCATTTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.04, C:0.37, G:0.22, T:0.37
Consensus pattern (23 bp):
CGTGCCTTCTTCGTCTCCGACAT
Found at i:29761 original size:20 final size:21
Alignment explanation
Indices: 29735--29797 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
29725 AATGAAGCAA
*
29735 GGAAGCAAAGAGAGCAGCAGT
1 GGAAGCAGAGAGAGCAGCAGT
**
29756 GG-AGCAGCTAGAGCAGCAGT
1 GGAAGCAGAGAGAGCAGCAGT
*
29776 GGAAGCAGAGAGAGAAGCAGT
1 GGAAGCAGAGAGAGCAGCAGT
29797 G
1 G
29798 TGACAGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 17 0.49
21 18 0.51
ACGTcount: A:0.38, C:0.14, G:0.41, T:0.06
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGT
Done.