Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004703.1 Hibiscus syriacus cultivar Beakdansim tig00010570_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: 62881
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1929 original size:14 final size:13
Alignment explanation
Indices: 1906--1940 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
1896 AATTATTTCC
1906 TATTTATTAGGATT
1 TATTT-TTAGGATT
1920 TATCTTTTAGGATT
1 TAT-TTTTAGGATT
1934 TATTTTT
1 TATTTTT
1941 CTTGTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 14 0.70
15 2 0.10
ACGTcount: A:0.23, C:0.03, G:0.11, T:0.63
Consensus pattern (13 bp):
TATTTTTAGGATT
Found at i:4543 original size:23 final size:21
Alignment explanation
Indices: 4516--4574 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
4506 TTATTTTCAA
4516 TTTTAGTAATTTTATAAAAATAT
1 TTTTA-TAATTTT-TAAAAATAT
** *
4539 TTTTAATAAAACTTTAAATATAT
1 TTTT-AT-AATTTTTAAAAATAT
4562 TTTTATAATTTTT
1 TTTTATAATTTTT
4575 CTTATTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 5 0.17
22 2 0.07
23 17 0.59
24 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTATAATTTTTAAAAATAT
Found at i:11358 original size:45 final size:45
Alignment explanation
Indices: 11294--11383 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
11284 TGAACCTGAA
*
11294 AATTTTATGAAACTCATGATGAGGATGACTTCCAAAATTGAGTTT
1 AATTTTATGAAACCCATGATGAGGATGACTTCCAAAATTGAGTTT
11339 AATTTTATGAAACCCATGATGAGGATGACTTCCAAAATTGAGTTT
1 AATTTTATGAAACCCATGATGAGGATGACTTCCAAAATTGAGTTT
11384 TGTATTGATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (45 bp):
AATTTTATGAAACCCATGATGAGGATGACTTCCAAAATTGAGTTT
Found at i:12176 original size:15 final size:16
Alignment explanation
Indices: 12148--12179 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
12138 CAACACGACA
12148 ATATAATGTTTTATGT
1 ATATAATGTTTTATGT
12164 ATATAAT-TTTTATGT
1 ATATAATGTTTTATGT
12179 A
1 A
12180 CTAGCTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
ATATAATGTTTTATGT
Found at i:12476 original size:24 final size:25
Alignment explanation
Indices: 12449--12509 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
12439 CATAACAGAG
* *
12449 TTTATATTATTTTTA-AATTTAATT
1 TTTATATTATTTTTACAAATTAAAT
12473 TTTATATT-TTTTTACAAATTAAAT
1 TTTATATTATTTTTACAAATTAAAT
* *
12497 GTCATATTATTTT
1 TTTATATTATTTT
12510 AATTTGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 6 0.19
24 21 0.68
25 4 0.13
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTATATTATTTTTACAAATTAAAT
Found at i:13300 original size:16 final size:17
Alignment explanation
Indices: 13264--13298 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
13254 CATGAACATG
13264 ATGTTATATATTAATAT
1 ATGTTATATATTAATAT
13281 ATGTATATATATTAATAT
1 ATGT-TATATATTAATAT
13299 GTGTGTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
ATGTTATATATTAATAT
Found at i:18280 original size:22 final size:22
Alignment explanation
Indices: 18255--18309 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
18245 TATAGCTCAC
*
18255 AACTAAAGTCTTACTACTAACA
1 AACTAAAGCCTTACTACTAACA
* *
18277 AACTCAAGCCTTACTGCTAACA
1 AACTAAAGCCTTACTACTAACA
*
18299 AACTCAAGCCT
1 AACTAAAGCCT
18310 AACTGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (22 bp):
AACTAAAGCCTTACTACTAACA
Found at i:18314 original size:22 final size:22
Alignment explanation
Indices: 18271--18317 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
18261 AGTCTTACTA
*
18271 CTAACAAACTCAAGCCTTACTG
1 CTAACAAACTCAAGCCTAACTG
18293 CTAACAAACTCAAGCCTAACTG
1 CTAACAAACTCAAGCCTAACTG
18315 CTA
1 CTA
18318 CTAACAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.38, C:0.32, G:0.09, T:0.21
Consensus pattern (22 bp):
CTAACAAACTCAAGCCTAACTG
Found at i:18649 original size:17 final size:17
Alignment explanation
Indices: 18627--18663 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
18617 TTGGCCACTG
18627 CACTGCTATTGTCACAC
1 CACTGCTATTGTCACAC
18644 CACTGCTATTGTCACAC
1 CACTGCTATTGTCACAC
18661 CAC
1 CAC
18664 ACCACTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.38, G:0.11, T:0.27
Consensus pattern (17 bp):
CACTGCTATTGTCACAC
Found at i:22848 original size:22 final size:22
Alignment explanation
Indices: 22823--22885 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
22813 TATAGCTCAC
*
22823 AACTAAAGCCTTATTGCTAACA
1 AACTCAAGCCTTATTGCTAACA
*
22845 AACTCAAGCCTTACTGCTAACA
1 AACTCAAGCCTTATTGCTAACA
*
22867 AACTCAAGCCTAATTGCTA
1 AACTCAAGCCTTATTGCTA
22886 CTAACAAATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (22 bp):
AACTCAAGCCTTATTGCTAACA
Found at i:24475 original size:2 final size:2
Alignment explanation
Indices: 24468--24497 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24458 AGATAATAAC
24468 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24498 CAAAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26090 original size:82 final size:84
Alignment explanation
Indices: 25943--26115 Score: 278
Period size: 82 Copynumber: 2.0 Consensus size: 84
25933 AAACTCATGT
* *
25943 TTTAGGATATTATTTTAAATATTTTATCTTATCTTATCTTTGTTTTAGGTATTTTAGTTTAAATA
1 TTTAGGATATTATTTTAAATATTTTA--TTA-CTTATATTTGTTTTAGGTATTATAGTTTAAATA
26008 GTTTTAAGTATTTTAATTAGGA
63 GTTTTAAGTATTTTAATTAGGA
26030 TTTAGGATATTATTTTAAATATTTTA-TA-TTATATTTGTTTTAGGTATTATAGTTTAAATAGTT
1 TTTAGGATATTATTTTAAATATTTTATTACTTATATTTGTTTTAGGTATTATAGTTTAAATAGTT
*
26093 TTAAGTATTTTAATTAGTA
66 TTAAGTATTTTAATTAGGA
26112 TTTA
1 TTTA
26116 TTTTCTTTAT
Statistics
Matches: 83, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
82 55 0.66
84 2 0.02
87 26 0.31
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.57
Consensus pattern (84 bp):
TTTAGGATATTATTTTAAATATTTTATTACTTATATTTGTTTTAGGTATTATAGTTTAAATAGTT
TTAAGTATTTTAATTAGGA
Found at i:26990 original size:21 final size:20
Alignment explanation
Indices: 26961--27014 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
26951 CCTTCTTATC
26961 TTTA-TTATTATCTTATAAT
1 TTTATTTATTATCTTATAAT
* *
26980 TATTATTTATTATTTTATTAT
1 T-TTATTTATTATCTTATAAT
*
27001 TTTATCT-TTATCTT
1 TTTATTTATTATCTT
27015 CCATTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 7 0.24
20 8 0.28
21 14 0.48
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTATTTATTATCTTATAAT
Found at i:27049 original size:12 final size:12
Alignment explanation
Indices: 27032--27056 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27022 AAACAATTTA
27032 TATTTAATTATT
1 TATTTAATTATT
27044 TATTTAATTATT
1 TATTTAATTATT
27056 T
1 T
27057 TTCTTGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTAATTATT
Found at i:27848 original size:14 final size:15
Alignment explanation
Indices: 27825--27857 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
27815 AACATTGAAA
27825 AAAAACAAGAAAAAG
1 AAAAACAAGAAAAAG
*
27840 AAAAA-AAGAAGAAG
1 AAAAACAAGAAAAAG
27854 AAAA
1 AAAA
27858 GGGTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAACAAGAAAAAG
Found at i:30061 original size:21 final size:21
Alignment explanation
Indices: 30021--30077 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
30011 TCGGTAATTA
30021 GCGTTGCGAATTT-AAGAATC
1 GCGTTGCGAATTTGAAGAATC
* *
30041 GCGTTGCGATTTTGGAGAATC
1 GCGTTGCGAATTTGAAGAATC
30062 GCGTTGCGAATTTGAA
1 GCGTTGCGAATTTGAA
30078 AACTGAGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 12 0.38
21 20 0.62
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.32
Consensus pattern (21 bp):
GCGTTGCGAATTTGAAGAATC
Found at i:30134 original size:99 final size:99
Alignment explanation
Indices: 29963--30170 Score: 380
Period size: 99 Copynumber: 2.1 Consensus size: 99
29953 ACAGTAATTA
* *
29963 GCGTTGCGAATTTGAAAACTGAGTTGTGAATAGTTGTGTTTACTTATATCGGTAATTAGCGTTGC
1 GCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGC
30028 GAATTTAAGAATCGCGTTGCGATTTTGGAGAATC
66 GAATTTAAGAATCGCGTTGCGATTTTGGAGAATC
30062 GCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGC
1 GCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGC
*
30127 GAATTTAATAATCGCGTTGCGATTTTGGAGAATC
66 GAATTTAAGAATCGCGTTGCGATTTTGGAGAATC
*
30161 GCGTTACGAA
1 GCGTTGCGAA
30171 ACTGGAGTTC
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 105 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (99 bp):
GCGTTGCGAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATTAGCGTTGC
GAATTTAAGAATCGCGTTGCGATTTTGGAGAATC
Found at i:30176 original size:21 final size:20
Alignment explanation
Indices: 30152--30190 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30142 GTTGCGATTT
30152 TGGAGAATCGCGTTACGAAAC
1 TGGAG-ATCGCGTTACGAAAC
* *
30173 TGGAGTTCGCGTTGCGAA
1 TGGAGATCGCGTTACGAA
30191 TTTGTTGGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (20 bp):
TGGAGATCGCGTTACGAAAC
Found at i:31450 original size:19 final size:18
Alignment explanation
Indices: 31423--31461 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
31413 TATCTAATCT
*
31423 TAATTAATATAAACCTTAA
1 TAATAAATATAAACC-TAA
*
31442 TAATAAATATTAACCTAA
1 TAATAAATATAAACCTAA
31460 TA
1 TA
31462 TAATTTAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAAATATAAACCTAA
Found at i:39670 original size:2 final size:2
Alignment explanation
Indices: 39663--39704 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
39653 TATTTTTCAA
*
39663 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39705 TTAATATTAA
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:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47320 original size:21 final size:20
Alignment explanation
Indices: 47276--47329 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
47266 AATACAATTA
* * *
47276 GTGCATCGATGAATCCTTCT
1 GTGCATCGATGCATCATGCT
47296 GTGCATCGATGCATCATGGCT
1 GTGCATCGATGCATCAT-GCT
*
47317 GTGCATCCATGCA
1 GTGCATCGATGCA
47330 CGAAGGCTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.20, C:0.26, G:0.24, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCATGCT
Found at i:47337 original size:21 final size:21
Alignment explanation
Indices: 47294--47337 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
47284 ATGAATCCTT
* *
47294 CTGTGCATCGATGCATCATGG
1 CTGTGCATCCATGCATCAAGG
47315 CTGTGCATCCATGCA-CGAAGG
1 CTGTGCATCCATGCATC-AAGG
47336 CT
1 CT
47338 ACAACGGCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (21 bp):
CTGTGCATCCATGCATCAAGG
Found at i:47756 original size:29 final size:30
Alignment explanation
Indices: 47686--47745 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
47676 TAATTTAAGG
47686 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
47717 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
47746 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:47851 original size:21 final size:20
Alignment explanation
Indices: 47825--47920 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 20
47815 AGGGTGTCAA
47825 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
47846 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
47867 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
47888 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
47909 AGTGCATCCATG
1 AGTGCATCCATG
47921 TACTCAAACA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.06
20 11 0.16
21 36 0.54
22 13 0.19
23 3 0.04
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:47973 original size:20 final size:20
Alignment explanation
Indices: 47948--48017 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
47938 CAATTAGTGT
* *
47948 ATCGATGCATCCTTCTATGC
1 ATCGATGCATCCTGCTGTGC
**
47968 ATCGATGCATCAAGGCTGTGC
1 ATCGATGCATC-CTGCTGTGC
47989 ATCGATGCATCCTGCTGTGC
1 ATCGATGCATCCTGCTGTGC
*
48009 ATCCATGCA
1 ATCGATGCA
48018 CGAAGGCTGC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (20 bp):
ATCGATGCATCCTGCTGTGC
Found at i:47991 original size:21 final size:21
Alignment explanation
Indices: 47965--48026 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
47955 CATCCTTCTA
47965 TGCATCGATGCATCAAGGCTG
1 TGCATCGATGCATCAAGGCTG
**
47986 TGCATCGATGCATC-CTGCTG
1 TGCATCGATGCATCAAGGCTG
*
48006 TGCATCCATGCA-CGAAGGCTG
1 TGCATCGATGCATC-AAGGCTG
48027 CAACGACTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
21 18 0.53
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCATCAAGGCTG
Found at i:47995 original size:41 final size:41
Alignment explanation
Indices: 47948--48026 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
47938 CAATTAGTGT
* *
47948 ATCGATGCATCCTTCTATGCATCGATGCATC-AAGGCTGTGC
1 ATCGATGCATCCTGCTATGCATCCATGCA-CGAAGGCTGTGC
*
47989 ATCGATGCATCCTGCTGTGCATCCATGCACGAAGGCTG
1 ATCGATGCATCCTGCTATGCATCCATGCACGAAGGCTG
48027 CAACGACTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.27
Consensus pattern (41 bp):
ATCGATGCATCCTGCTATGCATCCATGCACGAAGGCTGTGC
Found at i:49314 original size:19 final size:20
Alignment explanation
Indices: 49290--49337 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
49280 AAACGATTTC
* *
49290 TTTTGAAAGCAAAAATG-GA
1 TTTTGAAAACAAAAATGAAA
*
49309 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
49329 TTTTGAAAA
1 TTTTGAAAA
49338 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:50550 original size:29 final size:31
Alignment explanation
Indices: 50499--50557 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
50489 AATTTAAGGC
50499 AAAATGGTTTCTGGACTTGAATTGAATTTAA
1 AAAATGGTTTCTGGACTTGAATTGAATTTAA
*
50530 AAAAT-GTTTTTGGACTT-AATTGAATTTA
1 AAAATGGTTTCTGGACTTGAATTGAATTTA
50558 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (31 bp):
AAAATGGTTTCTGGACTTGAATTGAATTTAA
Found at i:50663 original size:21 final size:20
Alignment explanation
Indices: 50637--50735 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
50627 AGGGTGTCAA
*
50637 AGTGCATCTATGCACCCATGC
1 AGTGCATCCATGCACCC-TGC
50658 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
50679 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
50700 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
50721 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
50736 TCAAACACCG
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 32 0.46
22 16 0.23
23 3 0.04
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.22
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:50726 original size:20 final size:20
Alignment explanation
Indices: 50637--50848 Score: 147
Period size: 20 Copynumber: 10.7 Consensus size: 20
50627 AGGGTGTCAA
* *
50637 AGTGCATCTATGCACCCATGC
1 AGTGCATCGATGCATCC-TGC
*
50658 AGTGCATCCATGCATCCCTGC
1 AGTGCATCGATGCAT-CCTGC
*
50679 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCGATGCATCCTG--C
50700 TAGTGCATCGATGCA-CCATGC
1 -AGTGCATCGATGCATCC-TGC
*
50721 AGTGCATCCATGCA--CT-C
1 AGTGCATCGATGCATCCTGC
** *
50738 A-AACACCGAATGCAAT--T--
1 AGTGCATCG-ATGC-ATCCTGC
50755 AGTGCATCGATGCATCCTGC
1 AGTGCATCGATGCATCCTGC
* *
50775 TGTGCATCGATGCATCCTGT
1 AGTGCATCGATGCATCCTGC
*
50795 TGTGCATCGATGCATCCTGC
1 AGTGCATCGATGCATCCTGC
* *
50815 TGTGCATCGATGCATCCTAC
1 AGTGCATCGATGCATCCTGC
* *
50835 TGTGCATCCATGCA
1 AGTGCATCGATGCA
50849 CGAAGGCTGC
Statistics
Matches: 162, Mismatches: 16, Indels: 27
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.03
17 11 0.07
18 8 0.05
19 5 0.03
20 82 0.51
21 32 0.20
22 17 0.10
23 2 0.01
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTGC
Done.