Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003967.1 Hibiscus syriacus cultivar Beakdansim tig00008594_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: 70125
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4923 original size:4 final size:4
Alignment explanation
Indices: 4914--4938 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4904 TATCATAACA
4914 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
4939 GGTAAGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:6145 original size:68 final size:68
Alignment explanation
Indices: 6031--6168 Score: 267
Period size: 68 Copynumber: 2.0 Consensus size: 68
6021 GATAGAGAAT
*
6031 TTCATGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
1 TTCAAGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
6096 GAA
66 GAA
6099 TTCAAGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
1 TTCAAGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
6164 GAA
66 GAA
6167 TT
1 TT
6169 GAAAACCTAT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.33
Consensus pattern (68 bp):
TTCAAGTAGATTAATTCTCTATCTAATACCTTAATCCAAAAATCAATCGAATAAGCTTAAAAATG
GAA
Found at i:6751 original size:29 final size:31
Alignment explanation
Indices: 6715--6803 Score: 91
Period size: 30 Copynumber: 3.0 Consensus size: 31
6705 CCAATTTTAT
6715 AACTTTTAAAAATTATATTTTTGGTCC-CTA
1 AACTTTTAAAAATTATATTTTTGGTCCACTA
* *
6745 AAC-TTTACAAAGTT-TATACTTTGG-CCACTA
1 AACTTTTA-AAAATTATAT-TTTTGGTCCACTA
*
6775 AACTTTTAAAACTTATA-TTTTGGT-CACTA
1 AACTTTTAAAAATTATATTTTTGGTCCACTA
6804 GGTAAAATTG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
29 19 0.39
30 24 0.49
31 6 0.12
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.43
Consensus pattern (31 bp):
AACTTTTAAAAATTATATTTTTGGTCCACTA
Found at i:11328 original size:13 final size:13
Alignment explanation
Indices: 11310--11341 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
11300 GATCAACAAA
*
11310 ATACATATTTAAT
1 ATACATACTTAAT
11323 ATACATACTTAAT
1 ATACATACTTAAT
11336 ATACAT
1 ATACAT
11342 TCTACTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (13 bp):
ATACATACTTAAT
Found at i:17655 original size:20 final size:20
Alignment explanation
Indices: 17630--17698 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
17620 TCGAAGTTCG
17630 CGTTGCGATTCATTCCAATT
1 CGTTGCGATTCATTCCAATT
** *
17650 CGTTGCGA--CAGGCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
17669 CGCGTTGCGATTCATTCCAATT
1 --CGTTGCGATTCATTCCAATT
17691 CGTTGCGA
1 CGTTGCGA
17699 CAGGCGAAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 16 0.42
21 8 0.21
22 2 0.05
23 5 0.13
ACGTcount: A:0.19, C:0.25, G:0.25, T:0.32
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAATT
Found at i:17666 original size:41 final size:41
Alignment explanation
Indices: 17621--17708 Score: 176
Period size: 41 Copynumber: 2.1 Consensus size: 41
17611 ACGCGGTAGT
17621 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
17662 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
17703 CGAAGT
1 CGAAGT
17709 ATTGCATTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.28
Consensus pattern (41 bp):
CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:18510 original size:6 final size:6
Alignment explanation
Indices: 18500--18544 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
18490 GGTCGGGTAG
*
18500 GGTCGG GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
18545 AATACGTGTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:18683 original size:41 final size:42
Alignment explanation
Indices: 18622--19040 Score: 728
Period size: 41 Copynumber: 10.2 Consensus size: 42
18612 AATATTTGGA
18622 CTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
18663 CTATCGCAACGAATTT-GAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
18704 CTATCGCAACGAATTT-GAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
18745 CTATCGCAACG-ATTTGGAATGAATCGCAACGCAAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
18786 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
18828 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
18869 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAATTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
18910 CTATCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
18951 CTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
18992 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
19034 CTATCGC
1 CTATCGC
19041 GTTGCGAATC
Statistics
Matches: 364, Mismatches: 9, Indels: 9
0.95 0.02 0.02
Matches are distributed among these distances:
40 5 0.01
41 279 0.77
42 80 0.22
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:18976 original size:206 final size:206
Alignment explanation
Indices: 18620--19040 Score: 761
Period size: 206 Copynumber: 2.0 Consensus size: 206
18610 GCAATATTTG
* *
18620 GACTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGAATGA
1 GACTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
* *
18685 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGAATGAATCGCAACGCGAACTTCGCCTATC
66 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACTATC
*
18750 GCAACGATTTGGAATGAATCGCAACGCAAACTTCGCCTATCGCAACGAATTTGGAATGAATCGCA
131 GCAACGATTTGGAATGAATCGCAACGCAAACTTCGCCTATCGCAACGAATTTGGAATAAATCGCA
18815 ACGCGAACTTC
196 ACGCGAACTTC
*
18826 GCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
1 GACTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
*
18891 ATCGCAACGCGAATTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACTATC
66 ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACTATC
*
18956 GCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATAAATCGCA
131 GCAACGATTTGGAATGAATCGCAACGCAAACTTCGCCTATCGCAACGAATTTGGAATAAATCGCA
*
19021 ATGCGAACTTC
196 ACGCGAACTTC
19032 GACTATCGC
1 GACTATCGC
19041 GTTGCGAATC
Statistics
Matches: 205, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
206 205 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (206 bp):
GACTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGA
ATCGCAACGCGAACTTCGCCTATCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGACTATC
GCAACGATTTGGAATGAATCGCAACGCAAACTTCGCCTATCGCAACGAATTTGGAATAAATCGCA
ACGCGAACTTC
Found at i:19701 original size:52 final size:52
Alignment explanation
Indices: 19628--19733 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
19618 ATTTGATATA
* *
19628 ATTACATTTTTTATTCCCAATACGTATATATTCTATCAATTTAATCATTATT
1 ATTACATATTTGATTCCCAATACGTATATATTCTATCAATTTAATCATTATT
* *
19680 ATTACATATTTGATTCTCAATACGTATATATTCTATCAATTTAGTCATTATT
1 ATTACATATTTGATTCCCAATACGTATATATTCTATCAATTTAATCATTATT
19732 AT
1 AT
19734 AAGTTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (52 bp):
ATTACATATTTGATTCCCAATACGTATATATTCTATCAATTTAATCATTATT
Found at i:20781 original size:14 final size:15
Alignment explanation
Indices: 20762--20790 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20752 CTTTTGGAGG
20762 ATTAAATT-TAATAA
1 ATTAAATTATAATAA
20776 ATTAAATTATAATAA
1 ATTAAATTATAATAA
20791 TGACTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAATTATAATAA
Found at i:21110 original size:331 final size:327
Alignment explanation
Indices: 20622--21245 Score: 839
Period size: 326 Copynumber: 1.9 Consensus size: 327
20612 AACAACGTAT
* * **
20622 TTTCTTTCTGATTTGTTTTCCATCCAACGAGATGATGCCACATGTCACTTTCTGGTTGGATAAAA
1 TTTCTTTCTGATTTGTTTTCCATCCAACCAGATGATGCCACATGTCACTATCTAATTGGATAAAA
* * *
20687 ATAATTAAATTAAATATATTAAATTATTAAAAAAACTTTAATTATATAGTTACACGTGTTGTTAT
66 ATAATTAAATTAAATATATTAAATTATTAAAAAAAC-TTAATTATATAATGACAC-TGTTGTCAT
20752 CTTTTGGAGGATTAAATTTAATAAATTAAATTATAATAATGACTAAATTGATAAAATATATAAGT
129 CTTTTGGAGGATTAAATTTAAT---TTAAATTATAATAATGACTAAATTGATAAAATATATAAGT
* * *** * *
20817 ATTGAGTATCAAATATGTCATTATACCAATTTTTTTAACT-ACACGTCAACTTTCCATTAAATAT
191 ATTGAGGATCAAATATGTAATTATACCAAAAATTTTAACTGACACATCAACTTCCCATTAAATAT
* **
20881 TAATGGTTAGTGGTTTAATTGAAT-GCATTTAAATAGTTGGGGTTCGAGTATGCTAAACCCCCTT
256 TAATGGCTAGTGACTTAATTGAATAG-ATTTAAATAGTTGGGGTTCGAGTATGCTAAACCCCCTT
20945 AATTTGTG
320 AATTTGTG
* * *
20953 TTTCTTTGTGGTTTGTTTTCCATCCAACCATATGATGCCACATGTCACTATCTAATTGGATAAAA
1 TTTCTTTCTGATTTGTTTTCCATCCAACCAGATGATGCCACATGTCACTATCTAATTGGAT-AAA
*
21018 AATAATTAAATTAAATATATTAAATTA-TAAAAAAA-TTAATTATATAATGATA-TG-TGTCAT-
65 AATAATTAAATTAAATATATTAAATTATTAAAAAAACTTAATTATATAATGACACTGTTGTCATC
* * *
21078 TATTTGGAGGATTAAATTTACCAATTTAAATTATAATGATGACTAATTTGATAGAATATATAAGT
130 T-TTTGGAGGATTAAATTT---AATTTAAATTATAATAATGACTAAATTGATAAAATATATAAGT
* * *
21143 ATTGAGGATCAAATATGTAATTATACCAAAAATTTTAATTGCCACATCATCTTCCCATTAAATAT
191 ATTGAGGATCAAATATGTAATTATACCAAAAATTTTAACTGACACATCAACTTCCCATTAAATAT
* *
21208 TAATTGCTAGTGACTTGATTGAATAGATTTAAATAGTT
256 TAATGGCTAGTGACTTAATTGAATAGATTTAAATAGTT
21246 AGGTTGCCTG
Statistics
Matches: 257, Mismatches: 29, Indels: 18
0.85 0.10 0.06
Matches are distributed among these distances:
325 1 0.00
326 93 0.36
327 53 0.21
328 1 0.00
329 17 0.07
331 62 0.24
332 30 0.12
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (327 bp):
TTTCTTTCTGATTTGTTTTCCATCCAACCAGATGATGCCACATGTCACTATCTAATTGGATAAAA
ATAATTAAATTAAATATATTAAATTATTAAAAAAACTTAATTATATAATGACACTGTTGTCATCT
TTTGGAGGATTAAATTTAATTTAAATTATAATAATGACTAAATTGATAAAATATATAAGTATTGA
GGATCAAATATGTAATTATACCAAAAATTTTAACTGACACATCAACTTCCCATTAAATATTAATG
GCTAGTGACTTAATTGAATAGATTTAAATAGTTGGGGTTCGAGTATGCTAAACCCCCTTAATTTG
TG
Found at i:37008 original size:21 final size:19
Alignment explanation
Indices: 36980--37025 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
36970 TCATTGAATC
36980 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
37000 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
37019 ACTTAGT
1 A-TTAGT
37026 AAGATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:47345 original size:21 final size:19
Alignment explanation
Indices: 47317--47362 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
47307 TCATTGAATC
47317 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
47337 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
47356 ACTTAGT
1 A-TTAGT
47363 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:48084 original size:32 final size:32
Alignment explanation
Indices: 48043--48112 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
48033 GTTGTGAAAA
*
48043 TCATCTTCAATCTCTTACACAACACACTCCTT
1 TCATCTTCAATCTCTTACACAACAAACTCCTT
*
48075 TCATCTTCAATCTTTTACACAACAAACTCCTT
1 TCATCTTCAATCTCTTACACAACAAACTCCTT
48107 TCATCT
1 TCATCT
48113 AACCAAAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.29, C:0.34, G:0.00, T:0.37
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACACAACAAACTCCTT
Found at i:51331 original size:32 final size:32
Alignment explanation
Indices: 51272--51332 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
51262 TTATATAATT
* * *
51272 TTAATAATTTTAAAAAATTACACTTTATTTAA
1 TTAATAATTTAAAAAAATAACAATTTATTTAA
51304 TTAA-AATTTAAAAAAATAACAAATTTATT
1 TTAATAATTTAAAAAAATAAC-AATTTATT
51333 ACTTAGCAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.56
32 11 0.44
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (32 bp):
TTAATAATTTAAAAAAATAACAATTTATTTAA
Found at i:52296 original size:5 final size:5
Alignment explanation
Indices: 52286--52332 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
52276 AAAGATATAT
*
52286 TAAAA TAAAA T-AAA TAAAA -AAGA -AAAA TAAAA TAAAA TAATAA TAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAA
52333 TATTAATAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
4 10 0.27
5 22 0.59
6 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (5 bp):
TAAAA
Found at i:52330 original size:11 final size:10
Alignment explanation
Indices: 52286--52332 Score: 55
Period size: 9 Copynumber: 4.9 Consensus size: 10
52276 AAAGATATAT
52286 TAAAATAAAA
1 TAAAATAAAA
52296 T-AAATAAAA
1 TAAAATAAAA
*
52305 -AAGA-AAAA
1 TAAAATAAAA
52313 TAAAATAAAA
1 TAAAATAAAA
52323 TAATAATAAA
1 TAA-AATAAA
52333 TATTAATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
8 4 0.13
9 13 0.42
10 8 0.26
11 6 0.19
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:52330 original size:16 final size:17
Alignment explanation
Indices: 52286--52356 Score: 76
Period size: 16 Copynumber: 4.4 Consensus size: 17
52276 AAAGATATAT
52286 TAAAATAA-AATAAATA
1 TAAAATAATAATAAATA
* * *
52302 AAAAAGAAAAATAAA-A
1 TAAAATAATAATAAATA
52318 TAAAATAATAATAAATA
1 TAAAATAATAATAAATA
* *
52335 T-TAATAGTAATAAATA
1 TAAAATAATAATAAATA
52351 TAAAAT
1 TAAAAT
52357 GGGGATTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
16 33 0.75
17 11 0.25
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
TAAAATAATAATAAATA
Found at i:52401 original size:19 final size:18
Alignment explanation
Indices: 52382--52430 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
52372 GTTATTTTTA
52382 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
52400 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
52419 AAATAAACAAAT
1 AAATAAA-AAAT
52431 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:54911 original size:4 final size:5
Alignment explanation
Indices: 54899--54957 Score: 56
Period size: 5 Copynumber: 12.8 Consensus size: 5
54889 AAAAAATTAA
* *
54899 AAATA AAAT- AAATG GAATG AAATG AAATG AAATG AAAT- AAAT- AAAT-
1 AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG AAATG
*
54945 AAAT- AAATA AAAT
1 AAATG AAATG AAAT
54958 AAAAATAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
4 20 0.40
5 30 0.60
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.22
Consensus pattern (5 bp):
AAATG
Found at i:54927 original size:10 final size:9
Alignment explanation
Indices: 54899--54955 Score: 64
Period size: 10 Copynumber: 6.3 Consensus size: 9
54889 AAAAAATTAA
*
54899 AAATAAAAT
1 AAATGAAAT
*
54908 AAATGGAAT
1 AAATGAAAT
54917 GAAATGAAAT
1 -AAATGAAAT
54927 GAAATGAAAT
1 -AAATGAAAT
54937 AAAT-AAAT
1 AAATGAAAT
54945 AAAT-AAAT
1 AAATGAAAT
54953 AAA
1 AAA
54956 ATAAAAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
8 15 0.34
9 11 0.25
10 18 0.41
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (9 bp):
AAATGAAAT
Found at i:55521 original size:21 final size:21
Alignment explanation
Indices: 55497--55548 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
55487 ATTTTGTAAA
55497 CATCAAATTCAACGATCTAAC
1 CATCAAATTCAACGATCTAAC
55518 CATCAAATTCAACGATCTAAC
1 CATCAAATTCAACGATCTAAC
55539 CATCAAATTC
1 CATCAAATTC
55549 CATTGTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.29, G:0.04, T:0.25
Consensus pattern (21 bp):
CATCAAATTCAACGATCTAAC
Found at i:57907 original size:18 final size:19
Alignment explanation
Indices: 57884--57937 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
57874 TAAGTTGAAA
*
57884 AATATATTAAAAT-AAAAT
1 AATATATAAAAATAAAAAT
57902 AATATAATAAAAATAAAAAT
1 AATAT-ATAAAAATAAAAAT
57922 AATATAATAATAAATA
1 AATAT-ATAA-AAATA
57938 TTAATAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 5 0.16
19 7 0.22
20 15 0.47
21 5 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATATAAAAATAAAAAT
Found at i:57922 original size:20 final size:20
Alignment explanation
Indices: 57892--57937 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
57882 AAAATATATT
57892 AAAAT-AAAATAATATAATA
1 AAAATAAAAATAATATAATA
57911 AAAATAAAAATAATATAATA
1 AAAATAAAAATAATATAATA
57931 ATAAATA
1 A-AAATA
57938 TTAATAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 5 0.20
20 15 0.60
21 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAATAAAAATAATATAATA
Found at i:57949 original size:12 final size:11
Alignment explanation
Indices: 57895--57953 Score: 54
Period size: 10 Copynumber: 5.5 Consensus size: 11
57885 ATATATTAAA
57895 ATAA-AATAAT
1 ATAATAATAAT
57905 ATAATAA-AA-
1 ATAATAATAAT
*
57914 ATAAAAATAAT
1 ATAATAATAAT
57925 ATAATAATAAAT
1 ATAATAAT-AAT
*
57937 ATTAATAGTAAT
1 A-TAATAATAAT
57949 A-AATA
1 ATAATA
57954 TAAAAGGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
9 6 0.15
10 12 0.29
11 9 0.22
12 8 0.20
13 6 0.15
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:57953 original size:23 final size:22
Alignment explanation
Indices: 57883--57958 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 22
57873 TTAAGTTGAA
*
57883 AAATATATTAAAAT-AAAATAAT
1 AAATA-ATAAAAATAAAAATAAT
57905 --ATAATAAAAATAAAAATAAT
1 AAATAATAAAAATAAAAATAAT
* * *
57925 ATAATAATAAATATTAATAGTAAT
1 A-AATAATAAA-AATAAAAATAAT
57949 AAAT-ATAAAA
1 AAATAATAAAA
57959 GGGGGATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 7 0.16
20 11 0.24
21 1 0.02
22 5 0.11
23 11 0.24
24 10 0.22
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (22 bp):
AAATAATAAAAATAAAAATAAT
Found at i:60188 original size:30 final size:30
Alignment explanation
Indices: 60154--60217 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
60144 GTACTCTATA
*
60154 GGTCGTCATGTGCTCCTGGAGACCTATGGT
1 GGTCGCCATGTGCTCCTGGAGACCTATGGT
*
60184 GGTCGCCGTGTGCTCCTGGAGACCTATGGT
1 GGTCGCCATGTGCTCCTGGAGACCTATGGT
60214 GGTC
1 GGTC
60218 ACTGTAGCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.11, C:0.25, G:0.36, T:0.28
Consensus pattern (30 bp):
GGTCGCCATGTGCTCCTGGAGACCTATGGT
Found at i:61268 original size:19 final size:19
Alignment explanation
Indices: 61244--61282 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
61234 TATATTTTAA
61244 ATTTTT-AGTAAAAAAGATT
1 ATTTTTAAGTAAAAAA-ATT
*
61263 ATTTTTAATTAAAAAAATT
1 ATTTTTAAGTAAAAAAATT
61282 A
1 A
61283 AAAATTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (19 bp):
ATTTTTAAGTAAAAAAATT
Found at i:61294 original size:28 final size:28
Alignment explanation
Indices: 61263--61320 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
61253 AAAAAAGATT
*
61263 ATTT-TTAATTAAAAAAATTAAAAATTTA
1 ATTTATTAA-TAAAAAAACTAAAAATTTA
* * *
61291 ATTTATTTATAAAAAACCTCAAAATTTA
1 ATTTATTAATAAAAAAACTAAAAATTTA
61319 AT
1 AT
61321 GAAATTGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (28 bp):
ATTTATTAATAAAAAAACTAAAAATTTA
Found at i:65351 original size:22 final size:24
Alignment explanation
Indices: 65326--65372 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
65316 AGTTGTGGTA
65326 TTTTG-ATTAACTGC-TTATTTCT
1 TTTTGAATTAACTGCTTTATTTCT
65348 TTTTGAAAATTAACTGCTTTATTTC
1 TTTTG--AATTAACTGCTTTATTTC
65373 ACTGATGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.23, C:0.13, G:0.09, T:0.55
Consensus pattern (24 bp):
TTTTGAATTAACTGCTTTATTTCT
Found at i:65513 original size:19 final size:19
Alignment explanation
Indices: 65489--65525 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
65479 ACGACCAACA
*
65489 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
65508 AAATCGTAACGCGATCTC
1 AAATCGCAACGCGATCTC
65526 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:65678 original size:41 final size:41
Alignment explanation
Indices: 65632--65726 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
65622 GAATATGTAA
* *
65632 ATCGCAACGCGATAATATATAATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAATACATAACCGCAACGAGATTCTGACT
* *
65673 TTCGCAACGCGATAATACATAACCGCAACGTGATTCTGACT
1 ATCGCAACGCGATAATACATAACCGCAACGAGATTCTGACT
*
65714 ATCGCAATGCGAT
1 ATCGCAACGCGAT
65727 TCTGACTGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (41 bp):
ATCGCAACGCGATAATACATAACCGCAACGAGATTCTGACT
Found at i:65679 original size:20 final size:20
Alignment explanation
Indices: 65653--65743 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
65643 ATAATATATA
*
65653 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
65673 TTCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* *
65693 AACCGCAACGTGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
65714 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
65734 GTCGCAACGC
1 ATCGCAACGC
65744 TGAATTTCAA
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 2 0.04
20 38 0.70
21 12 0.22
22 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:66585 original size:24 final size:24
Alignment explanation
Indices: 66558--66611 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
66548 GTATTCTAAA
66558 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
66582 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
66606 TTTGAT
1 TTTGAT
66612 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:68889 original size:17 final size:18
Alignment explanation
Indices: 68858--68891 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
68848 AGAAAAAGGT
*
68858 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
68876 AATC-AAATCCCAATCA
1 AATCAAAATCCCAATCA
68892 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.53, C:0.26, G:0.03, T:0.18
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:69200 original size:140 final size:139
Alignment explanation
Indices: 68949--69230 Score: 528
Period size: 140 Copynumber: 2.0 Consensus size: 139
68939 GCAAACGTTG
68949 TATTATGTGTATTTTATGTGTAACGTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTT
1 TATTATGTGTATTTTATGTGTAACGTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTT
*
69014 TGAACATTGCTATGATTTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGC
66 TGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGC
69079 GAATTTGAC
131 GAATTTGAC
* *
69088 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAGCTTGAGT
1 TATTATGTGTATTTTATGTGT-AACGTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
69153 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
65 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
69218 CGAATTTGAC
130 CGAATTTGAC
69228 TAT
1 TAT
69231 CGCAACGCAA
Statistics
Matches: 139, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
139 21 0.15
140 118 0.85
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.43
Consensus pattern (139 bp):
TATTATGTGTATTTTATGTGTAACGTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTT
TGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGC
GAATTTGAC
Found at i:69226 original size:20 final size:20
Alignment explanation
Indices: 69201--69331 Score: 148
Period size: 20 Copynumber: 6.8 Consensus size: 20
69191 TTACACATTC
*
69201 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
69221 ATTTGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
* *
69240 A----A-AATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
69255 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
69275 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * * *
69295 ATTTTATTATCGCAATGGGA
1 ATTTGACTATCGCAACGCGA
69315 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
69332 AGAAAATCGC
Statistics
Matches: 93, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
14 10 0.11
15 3 0.03
19 3 0.03
20 77 0.83
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:69248 original size:14 final size:14
Alignment explanation
Indices: 69229--69255 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
69219 GAATTTGACT
69229 ATCGCAACGCAAAA
1 ATCGCAACGCAAAA
69243 ATCGCAACGCAAA
1 ATCGCAACGCAAA
69256 TTTGACTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
ATCGCAACGCAAAA
Found at i:69543 original size:27 final size:27
Alignment explanation
Indices: 69511--69610 Score: 101
Period size: 27 Copynumber: 3.4 Consensus size: 27
69501 ATAAGAATTA
*
69511 TTTACACATCAATTAAACAAATCAACT
1 TTTACAAATCAATTAAACAAATCAACT
* *
69538 TTTACAAATCAATTAAAAGCACAAATAAGAATT
1 TTTACAAATCAATT--AA--ACAAAT--CAACT
*
69571 ATTTACACATCAATTAAACAAATCAACT
1 -TTTACAAATCAATTAAACAAATCAACT
69599 TTTACAAATCAA
1 TTTACAAATCAA
69611 CTTTTACAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
27 24 0.41
28 3 0.05
29 2 0.03
30 6 0.10
31 6 0.10
32 2 0.03
33 3 0.05
34 13 0.22
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (27 bp):
TTTACAAATCAATTAAACAAATCAACT
Found at i:69564 original size:61 final size:63
Alignment explanation
Indices: 69459--69610 Score: 254
Period size: 61 Copynumber: 2.4 Consensus size: 63
69449 GATTGAAATC
69459 AACAAATCAACTTTTACATTTCAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAAT
1 AACAAATCAACTTTTACA----AATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAAT
69524 TA
62 TA
69526 AACAAATCAACTTTTACAAATCAATT-AA-AAGCACAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAATTA
69587 AACAAATCAACTTTTACAAATCAA
1 AACAAATCAACTTTTACAAATCAA
69611 CTTTTACAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
61 57 0.67
62 2 0.02
63 8 0.09
67 18 0.21
ACGTcount: A:0.51, C:0.17, G:0.03, T:0.29
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAATAAGCACAAATAAGAATTATTTACACATCAATTA
Found at i:69593 original size:30 final size:30
Alignment explanation
Indices: 69497--69593 Score: 110
Period size: 27 Copynumber: 3.2 Consensus size: 30
69487 TTAAATAAGC
69497 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
* * *
69527 ACAAAT--CAACT-TTTACAAATCAATTAAAA
1 ACAAATAAGAATTATTTACACATCAATT--AA
69556 GCACAAATAAGAATTATTTACACATCAATTAA
1 --ACAAATAAGAATTATTTACACATCAATTAA
69588 ACAAAT
1 ACAAAT
69594 CAACTTTTAC
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
27 13 0.24
28 3 0.06
29 2 0.04
30 12 0.22
31 6 0.11
32 2 0.04
33 3 0.06
34 13 0.24
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:69607 original size:14 final size:14
Alignment explanation
Indices: 69588--69623 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
69578 CATCAATTAA
69588 ACAAATCAACTTTT
1 ACAAATCAACTTTT
69602 ACAAATCAACTTTT
1 ACAAATCAACTTTT
69616 ACAAATCA
1 ACAAATCA
69624 TTAAACAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Done.