Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007939.1 Hibiscus syriacus cultivar Beakdansim tig00110355_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: 59423
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6675 original size:12 final size:12
Alignment explanation
Indices: 6658--6688 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
6648 TTGGCAATAG
6658 GAAGAAGGAGAA
1 GAAGAAGGAGAA
6670 GAAGAAGGAGAA
1 GAAGAAGGAGAA
*
6682 GGAGAAG
1 GAAGAAG
6689 AAAGGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (12 bp):
GAAGAAGGAGAA
Found at i:11126 original size:25 final size:25
Alignment explanation
Indices: 11092--11140 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
11082 AATGATACTA
*
11092 AAATAATTATATGTTAAATTAAATT
1 AAATAATTATATATTAAATTAAATT
*
11117 AAATACTTATATATTAAATTAAAT
1 AAATAATTATATATTAAATTAAAT
11141 ATATAAATAT
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:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (25 bp):
AAATAATTATATATTAAATTAAATT
Found at i:11132 original size:20 final size:20
Alignment explanation
Indices: 11109--11155 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
11099 TATATGTTAA
*
11109 ATTAAATTAAATACT-TATAT
1 ATTAAATTAAATA-TATAAAT
11129 ATTAAATTAAATATATAAAT
1 ATTAAATTAAATATATAAAT
11149 ATTAAAT
1 ATTAAAT
11156 ATATTATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 24 0.96
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTAAATTAAATATATAAAT
Found at i:11152 original size:15 final size:14
Alignment explanation
Indices: 11125--11159 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
11115 TTAAATACTT
*
11125 ATATATTAAATTAA
1 ATATATAAAATTAA
11139 ATATATAAATATTAA
1 ATATATAAA-ATTAA
11154 ATATAT
1 ATATAT
11160 TATTACATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATAAAATTAA
Found at i:18424 original size:27 final size:27
Alignment explanation
Indices: 18394--18494 Score: 138
Period size: 27 Copynumber: 3.9 Consensus size: 27
18384 CGGTTTTTTT
*
18394 ACCGGATTAAAAACCGATTTTTTTCAA
1 ACCGGATAAAAAACCGATTTTTTTCAA
18421 ACCGGATAAAAAACCGA-TTTTTT--A
1 ACCGGATAAAAAACCGATTTTTTTCAA
* *
18445 TCCGGATAAAAAACCGGTTTTTTTCAA
1 ACCGGATAAAAAACCGATTTTTTTCAA
18472 ACCGGATAAAAAACTC-ATTTTTT
1 ACCGGATAAAAAAC-CGATTTTTT
18495 ATCTGAAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
24 16 0.25
25 6 0.09
26 6 0.09
27 36 0.55
28 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (27 bp):
ACCGGATAAAAAACCGATTTTTTTCAA
Found at i:18517 original size:51 final size:51
Alignment explanation
Indices: 18388--18497 Score: 179
Period size: 51 Copynumber: 2.2 Consensus size: 51
18378 AACGATCGGT
* *
18388 TTTTTTA-CCGGATTAAAAACCGATTTTTTTCAAACCGGATAAAAAACCGA
1 TTTTTTATCCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAAACCGA
18438 TTTTTTATCCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAAACTC-A
1 TTTTTTATCCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAAAC-CGA
18489 TTTTTTATC
1 TTTTTTATC
18498 TGAAAAAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
50 7 0.12
51 48 0.86
52 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (51 bp):
TTTTTTATCCGGATAAAAAACCGGTTTTTTTCAAACCGGATAAAAAACCGA
Found at i:18538 original size:23 final size:21
Alignment explanation
Indices: 18512--18558 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
18502 AAAAATTCGG
18512 TTTTTT-AAAAAAACTGGATTT
1 TTTTTTAAAAAAAACT-GATTT
18533 ATTTTTTAAAAAAAACTGATTT
1 -TTTTTTAAAAAAAACTGATTT
18555 TTTT
1 TTTT
18559 GCAAACCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.17
22 11 0.46
23 9 0.38
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (21 bp):
TTTTTTAAAAAAAACTGATTT
Found at i:20937 original size:13 final size:13
Alignment explanation
Indices: 20919--20951 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
20909 TTGCCAGCAC
20919 AATTTTAAAATTT
1 AATTTTAAAATTT
20932 AATTTTAAAATTT
1 AATTTTAAAATTT
20945 AATTTTA
1 AATTTTA
20952 TATATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATTTTAAAATTT
Found at i:21546 original size:14 final size:14
Alignment explanation
Indices: 21515--21552 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
21505 GACCCTTTGT
21515 ATATAGTAT-TATC
1 ATATAGTATATATC
*
21528 ATATATTATATATC
1 ATATAGTATATATC
*
21542 TTATAGTATAT
1 ATATAGTATAT
21553 TTATATTGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.50
Consensus pattern (14 bp):
ATATAGTATATATC
Found at i:21564 original size:18 final size:19
Alignment explanation
Indices: 21529--21569 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
21519 AGTATTATCA
21529 TATATTATATATCTTATAG
1 TATATTATATATCTTATAG
21548 TATATT-TATAT-TGTATAG
1 TATATTATATATCT-TATAG
21566 TATA
1 TATA
21570 AACATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.67
19 6 0.29
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (19 bp):
TATATTATATATCTTATAG
Found at i:21666 original size:24 final size:22
Alignment explanation
Indices: 21602--21690 Score: 74
Period size: 24 Copynumber: 3.9 Consensus size: 22
21592 GCATATACAT
*
21602 TATATT-TATATTATATGATATG
1 TATATTATATATTATAT-ATACG
21624 TATATTATTTATATT-TATAGTACG
1 TATATTA--TATATTATATA-TACG
*
21648 TATATTATATCATTATATATATCT
1 TATATTATAT-ATTATATATA-CG
* *
21672 TTTATTACATATTATATAT
1 TATATTATATATTATATAT
21691 TATTATTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
22 9 0.16
23 15 0.27
24 26 0.46
25 6 0.11
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (22 bp):
TATATTATATATTATATATACG
Found at i:27641 original size:31 final size:30
Alignment explanation
Indices: 27603--27698 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
27593 GTCAAAGAAC
27603 TACCTATGTCTTTCGAGACATATGGACAGT
1 TACCTATGTCTTTCGAGACATATGGACAGT
*** *
27633 ATACCTATGTTCTAAGGA-ACATATGGATAGTT
1 -TACCTATG-TCTTTCGAGACATATGGACAG-T
* * *
27665 TACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTCT-TTCGAGACATATGGACAGT
27695 TACC
1 TACC
27699 GAGGATCTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
29 1 0.02
30 7 0.14
31 36 0.72
32 6 0.12
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (30 bp):
TACCTATGTCTTTCGAGACATATGGACAGT
Found at i:27715 original size:30 final size:30
Alignment explanation
Indices: 27681--27873 Score: 368
Period size: 30 Copynumber: 6.4 Consensus size: 30
27671 GGTTCTTCGG
* *
27681 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
27711 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
27741 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
27771 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
27801 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
27831 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
27861 GACCTCTGGATAG
1 GACCTCTGGATAG
27874 GTCCTTCGGA
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 161 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:31247 original size:21 final size:21
Alignment explanation
Indices: 31205--31247 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
31195 TTTCTGGGCT
* *
31205 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
31226 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
31247 A
1 A
31248 ACGAGTATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:32218 original size:31 final size:30
Alignment explanation
Indices: 32183--32261 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
32173 GTCTTTCGAG
*
32183 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGT-TACCTAGGTTCTAAGGA
* ** *
32214 ACATATGGATAGTTTACCTAGGTTCTTCGGG
1 ACATATGGACAG-TTACCTAGGTTCTAAGGA
*
32245 ACCTATGGACAGTTACC
1 ACATATGGACAGTTACC
32262 GAGGATCTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 5 0.12
31 34 0.85
32 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (30 bp):
ACATATGGACAGTTACCTAGGTTCTAAGGA
Found at i:32278 original size:30 final size:30
Alignment explanation
Indices: 32244--32436 Score: 368
Period size: 30 Copynumber: 6.4 Consensus size: 30
32234 GGTTCTTCGG
* *
32244 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
32274 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
32304 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
32334 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
32364 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
32394 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
32424 GACCTCTGGATAG
1 GACCTCTGGATAG
32437 GTCCTTCGGA
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 161 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:34816 original size:31 final size:31
Alignment explanation
Indices: 34781--34841 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
34771 TCGCGAGCCT
* *
34781 AAAATTTTCAAGCTCGACTCAAACTCGAAAG
1 AAAATATTCAAACTCGACTCAAACTCGAAAG
*
34812 AAAATATTGAAACTCGACTCAAACTCGAAA
1 AAAATATTCAAACTCGACTCAAACTCGAAA
34842 AGGCTCGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (31 bp):
AAAATATTCAAACTCGACTCAAACTCGAAAG
Found at i:34921 original size:29 final size:29
Alignment explanation
Indices: 34901--34959 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
34891 GAGCTCAATT
*
34901 TTGAGTTCGATTCAAGCTCGAACTCGAAC
1 TTGAGCTCGATTCAAGCTCGAACTCGAAC
* *
34930 TTGAGCTCGATTCAAGCTCAAACTCAAAC
1 TTGAGCTCGATTCAAGCTCGAACTCGAAC
34959 T
1 T
34960 CGAATTTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (29 bp):
TTGAGCTCGATTCAAGCTCGAACTCGAAC
Found at i:35093 original size:27 final size:27
Alignment explanation
Indices: 35063--35121 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
35053 CCGAGTCAAG
35063 CTCGAGTATTGCTGAGCTCGACTCGAA
1 CTCGAGTATTGCTGAGCTCGACTCGAA
*
35090 CTCGAGTATTGTTGAGCTCGACTCGAA
1 CTCGAGTATTGCTGAGCTCGACTCGAA
35117 CTCGA
1 CTCGA
35122 AAACTTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (27 bp):
CTCGAGTATTGCTGAGCTCGACTCGAA
Found at i:35244 original size:16 final size:16
Alignment explanation
Indices: 35213--35244 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
35203 ATTAAAACTC
*
35213 GACTCGAACTCGAAAA
1 GACTCGAACTCAAAAA
35229 GACTCGAACTCAAAAA
1 GACTCGAACTCAAAAA
35245 TATTTCAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
GACTCGAACTCAAAAA
Found at i:37111 original size:28 final size:28
Alignment explanation
Indices: 37067--37121 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
37057 CTCCGTTTAC
*
37067 ATTATGTTGTCGAGTCAGTTCTTGAAAT
1 ATTATGTTGTCGAGTCAGTGCTTGAAAT
*
37095 ATTATGTTGGT-GTGTCAGTGCTTGAAA
1 ATTATGTT-GTCGAGTCAGTGCTTGAAA
37122 ACAATGACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.24, C:0.09, G:0.25, T:0.42
Consensus pattern (28 bp):
ATTATGTTGTCGAGTCAGTGCTTGAAAT
Found at i:37358 original size:11 final size:11
Alignment explanation
Indices: 37342--37404 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
37332 GTATTATAGA
37342 ATTTTTAATAT
1 ATTTTTAATAT
37353 ATTTTTAA-A-
1 ATTTTTAATAT
37362 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
37373 ATCAATAATGT
1 ATTTTTAATAT
37384 ATTTTTAATAT
1 ATTTTTAATAT
37395 ATTTTTAATA
1 ATTTTTAATA
37405 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:44009 original size:43 final size:41
Alignment explanation
Indices: 43962--44151 Score: 193
Period size: 42 Copynumber: 4.5 Consensus size: 41
43952 TAATAGGTTA
*
43962 TGATGTTTAGCGGCATTTTTCTCTA-AAACGCCGCAGTAGTTGT
1 TGATGTTTTGCGGC-TTTTTCTC-ACAAACGCCGCAGTAGTT-T
* *
44005 TGATGTTTTGCGGCGTTTTCACACAAACGCCGCAGTAGGTTT
1 TGATGTTTTGCGGCTTTTTCTCACAAACGCCGCAGTA-GTTT
* *
44047 TGATGTTTTGCGGTGTTTTTCTCACAAACGCCGCAGTAGGTAT
1 TGATGTTTTGCGG-CTTTTTCTCACAAACGCCGCAGTA-GTTT
*** * * *
44090 TGATGTTTTTTAGCGTTTTCTTACAAACGCCGTAGTAGGTTT
1 TGATGTTTTGCGGCTTTTTCTCACAAACGCCGCAGTA-GTTT
*
44132 TGATGTTTTGTGGCGTTTTT
1 TGATGTTTTGCGGC-TTTTT
44152 ACTAAAAATG
Statistics
Matches: 125, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 69 0.55
43 55 0.44
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.41
Consensus pattern (41 bp):
TGATGTTTTGCGGCTTTTTCTCACAAACGCCGCAGTAGTTT
Found at i:44036 original size:42 final size:42
Alignment explanation
Indices: 43907--44150 Score: 240
Period size: 43 Copynumber: 5.7 Consensus size: 42
43897 ACAAAAATGT
* * * * * * *
43907 CGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGACAAACAC
1 CGCAGTAGGTTTTGATGTTTTGCGGCGTTTTCT-CACAAACGC
* * * * *
43950 CGTAATAGGTTATGATGTTTAGCGGCATTTTTCTCTA-AAACGC
1 CGCAGTAGGTTTTGATGTTTTGCGGC-GTTTTCTC-ACAAACGC
*
43993 CGCAGTA-GTTGTTGATGTTTTGCGGCGTTTTCACACAAACGC
1 CGCAGTAGGTT-TTGATGTTTTGCGGCGTTTTCTCACAAACGC
*
44035 CGCAGTAGGTTTTGATGTTTTGCGGTGTTTTTCTCACAAACGC
1 CGCAGTAGGTTTTGATGTTTTGCGGCG-TTTTCTCACAAACGC
* *** *
44078 CGCAGTAGGTATTGATGTTTTTTAGCGTTTTCTTACAAACGC
1 CGCAGTAGGTTTTGATGTTTTGCGGCGTTTTCTCACAAACGC
* *
44120 CGTAGTAGGTTTTGATGTTTTGTGGCGTTTT
1 CGCAGTAGGTTTTGATGTTTTGCGGCGTTTT
44151 TACTAAAAAT
Statistics
Matches: 169, Mismatches: 26, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
41 1 0.01
42 78 0.46
43 84 0.50
44 6 0.04
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (42 bp):
CGCAGTAGGTTTTGATGTTTTGCGGCGTTTTCTCACAAACGC
Found at i:44051 original size:85 final size:85
Alignment explanation
Indices: 43907--44139 Score: 270
Period size: 85 Copynumber: 2.7 Consensus size: 85
43897 ACAAAAATGT
* * * * * * * *
43907 CGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGACAAACACCGTAATAGGTTATGATGTTTAG
1 CGCAGTAGGTGTTGATGTTTTGCGGCG-TTTTCACACAAACGCCGTAGTAGGTTTTGATGTTTAG
43972 CGGCATTTTTCTCTA-AAACGC
65 CGGCATTTTTCTC-ACAAACGC
* * *
43993 CGCAGTAGTTGTTGATGTTTTGCGGCGTTTTCACACAAACGCCGCAGTAGGTTTTGATGTTTTGC
1 CGCAGTAGGTGTTGATGTTTTGCGGCGTTTTCACACAAACGCCGTAGTAGGTTTTGATGTTTAGC
**
44058 GGTGTTTTTCTCACAAACGC
66 GGCATTTTTCTCACAAACGC
* *** **
44078 CGCAGTAGGTATTGATGTTTTTTAGCGTTTTCTTACAAACGCCGTAGTAGGTTTTGATGTTT
1 CGCAGTAGGTGTTGATGTTTTGCGGCGTTTTCACACAAACGCCGTAGTAGGTTTTGATGTTT
44140 TGTGGCGTTT
Statistics
Matches: 125, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
84 1 0.01
85 101 0.81
86 23 0.18
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (85 bp):
CGCAGTAGGTGTTGATGTTTTGCGGCGTTTTCACACAAACGCCGTAGTAGGTTTTGATGTTTAGC
GGCATTTTTCTCACAAACGC
Found at i:47685 original size:35 final size:36
Alignment explanation
Indices: 47568--47707 Score: 230
Period size: 36 Copynumber: 3.9 Consensus size: 36
47558 TGAATAAGAA
*
47568 GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
*
47604 GAACGGAAGGAAGCATCGACACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
47640 GAACGAAAGGAAGCATCGACACTTTCGATTC-AAGT
1 GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
*
47675 GAACGGAAGGAAGCATC-AGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGA-CACTTTCGATTCAA
47708 TTGTTCATCT
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
34 1 0.01
35 32 0.33
36 65 0.66
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGACACTTTCGATTCAAAGT
Found at i:47704 original size:71 final size:72
Alignment explanation
Indices: 47568--47707 Score: 248
Period size: 71 Copynumber: 2.0 Consensus size: 72
47558 TGAATAAGAA
47568 GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTTTCGAT
1 GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTTTCGAT
47633 TCAAAGT
66 TCAAAGT
*
47640 GAACGAAAGGAAGCATCGACACTTTCGATTC-AAGTGAACGGAAGGAAGCATC-AGCACTTTCGA
1 GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGA-CACTTTCGA
47703 TTCAA
65 TTCAA
47708 TTGTTCATCT
Statistics
Matches: 66, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
70 1 0.02
71 35 0.53
72 30 0.45
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (72 bp):
GAACGAAAGGAAGCATCAACACTTTCGATTCAAAGTGAACGGAAGGAAGCATCGACACTTTCGAT
TCAAAGT
Found at i:52713 original size:2 final size:2
Alignment explanation
Indices: 52702--52765 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
52692 ATTGTAAATT
52702 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52743 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
52766 TACCGTTTAC
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52984 original size:31 final size:31
Alignment explanation
Indices: 52942--53025 Score: 114
Period size: 31 Copynumber: 2.7 Consensus size: 31
52932 GCTTAGCTCG
* *
52942 ACTCGACTCGACTCGAAAACTCTGAAATTGA
1 ACTCGACTCGACTCGAAAACTCTAAAATGGA
* * * *
52973 ATTTGACTCGACTCGAAAATTTTAAAATGGA
1 ACTCGACTCGACTCGAAAACTCTAAAATGGA
53004 ACTCGACTCGACTCGAAAACTC
1 ACTCGACTCGACTCGAAAACTC
53026 GCGAGCTTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (31 bp):
ACTCGACTCGACTCGAAAACTCTAAAATGGA
Found at i:54314 original size:17 final size:17
Alignment explanation
Indices: 54292--54346 Score: 69
Period size: 17 Copynumber: 3.3 Consensus size: 17
54282 TTTCCAAAAG
54292 AAATTTTATTTTTTTAA
1 AAATTTTATTTTTTTAA
54309 AAATTTTA--TTTTTAA
1 AAATTTTATTTTTTTAA
* *
54324 ATGATTTTATTTTTTAAA
1 A-AATTTTATTTTTTTAA
54342 AAATT
1 AAATT
54347 CTAAATTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 8 0.25
16 6 0.19
17 11 0.34
18 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
AAATTTTATTTTTTTAA
Found at i:55690 original size:20 final size:23
Alignment explanation
Indices: 55638--55690 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
55628 TCTAAGAAGA
55638 TGAACGATAAAATGTTTTTCCTT
1 TGAACGATAAAATGTTTTTCCTT
*
55661 TG-ACGGTAAAATG-TTTT-CTT
1 TGAACGATAAAATGTTTTTCCTT
55681 TGAAC-ATAAA
1 TGAACGATAAA
55691 CTTTCTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.33
21 6 0.22
22 10 0.37
23 2 0.07
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (23 bp):
TGAACGATAAAATGTTTTTCCTT
Done.