Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001676.1 Hibiscus syriacus cultivar Beakdansim tig00003353_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: 63699
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4329 original size:26 final size:26
Alignment explanation
Indices: 4300--4349 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
4290 TGATTTTTCA
4300 TTTAATTAATTTATAACTATATAATT
1 TTTAATTAATTTATAACTATATAATT
*
4326 TTTAATTAATTTATAATTATATAA
1 TTTAATTAATTTATAACTATATAA
4350 ATTCGTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTAATTAATTTATAACTATATAATT
Found at i:14304 original size:11 final size:11
Alignment explanation
Indices: 14288--14423 Score: 90
Period size: 11 Copynumber: 12.3 Consensus size: 11
14278 TTATATTGTA
14288 AAATAAAAAAT
1 AAATAAAAAAT
14299 AAATAAAATAAT
1 AAATAAAA-AAT
14311 -AATAAAATAAT
1 AAATAAAA-AAT
14322 AATATAAAAAA-
1 AA-ATAAAAAAT
* *
14333 ATATTAATATAAT
1 A-AATAA-AAAAT
14346 -AATAATAAAAT
1 AAATAA-AAAAT
14357 AAATAAAATAGAT
1 AAATAAAA-A-AT
*
14370 AAA-AAAAACT
1 AAATAAAAAAT
* *
14380 GAGTGAAAAAAT
1 AAAT-AAAAAAT
14392 -AA-AAAAAAT
1 AAATAAAAAAT
14401 AAA-AAAAAAT
1 AAATAAAAAAT
14411 AAA-AAAAAAT
1 AAATAAAAAAT
14421 AAA
1 AAA
14424 AAAGAGTTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 25
0.75 0.07 0.18
Matches are distributed among these distances:
9 7 0.07
10 24 0.23
11 36 0.35
12 26 0.25
13 11 0.11
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.21
Consensus pattern (11 bp):
AAATAAAAAAT
Found at i:14307 original size:16 final size:16
Alignment explanation
Indices: 14288--14423 Score: 68
Period size: 18 Copynumber: 8.2 Consensus size: 16
14278 TTATATTGTA
*
14288 AAATAAAA-AATAAAT
1 AAATAAAATAAAAAAT
14303 AAAATAATAATAAAATAAT
1 -AAATAA-AATAAAA-AAT
* *
14322 AATATAAAA-AAATATT
1 AA-ATAAAATAAAAAAT
14338 AATATAATAATAATAAAAT
1 AA-ATAA-AATAA-AAAAT
*
14357 AAATAAAATAGATAAAAA
1 AAATAAAATA-A-AAAAT
* *
14375 AAACT-GAGTGAAAAAAT
1 AAA-TAAAAT-AAAAAAT
*
14392 AAAAAAAATAAAAAA-
1 AAATAAAATAAAAAAT
14407 AAAT-AAA-AAAAAAT
1 AAATAAAATAAAAAAT
14421 AAA
1 AAA
14424 AAAGAGTTTA
Statistics
Matches: 95, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
13 6 0.06
14 6 0.06
15 3 0.03
16 21 0.22
17 20 0.21
18 25 0.26
19 14 0.15
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATAAAATAAAAAAT
Found at i:14319 original size:8 final size:8
Alignment explanation
Indices: 14289--14373 Score: 72
Period size: 8 Copynumber: 10.9 Consensus size: 8
14279 TATATTGTAA
14289 AATAAAA-
1 AATAAAAT
14296 AAT-AAAT
1 AATAAAAT
14303 AA-AATAAT
1 AATAA-AAT
14311 AATAAAAT
1 AATAAAAT
*
14319 AATAATAT
1 AATAAAAT
*
14327 AAAAAAAT
1 AATAAAAT
* *
14335 ATTAATAT
1 AATAAAAT
14343 AAT--AAT
1 AATAAAAT
14349 AATAAAAT
1 AATAAAAT
14357 AAATAAAAT
1 -AATAAAAT
14366 AGATAAAA
1 A-ATAAAA
14374 AAAACTGAGT
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
6 8 0.13
7 6 0.10
8 32 0.52
9 16 0.26
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (8 bp):
AATAAAAT
Found at i:14399 original size:9 final size:10
Alignment explanation
Indices: 14385--14426 Score: 77
Period size: 10 Copynumber: 4.3 Consensus size: 10
14375 AAACTGAGTG
14385 AAAAAAT-AA
1 AAAAAATAAA
14394 AAAAAATAAA
1 AAAAAATAAA
14404 AAAAAATAAA
1 AAAAAATAAA
14414 AAAAAATAAA
1 AAAAAATAAA
14424 AAA
1 AAA
14427 GAGTTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:14424 original size:16 final size:16
Alignment explanation
Indices: 14287--14425 Score: 54
Period size: 16 Copynumber: 8.2 Consensus size: 16
14277 GTTATATTGT
14287 AAAATAAAAAATAAAT-
1 AAAATAAAAAA-AAATA
*
14303 AAAATAATAATAAAATA
1 AAAATAA-AAAAAAATA
* *
14320 ATAATATAAAAAAATA
1 AAAATAAAAAAAAATA
** * *
14336 TTAATATAATAATAAT-
1 AAAATA-AAAAAAAATA
14352 AAAATAAATAAAATAGATA
1 AAAATAAA-AAAA-A-ATA
*
14371 AAAAAAACTGAGTGAAAAAAT-
1 AAAATAA---A---AAAAAATA
*
14392 AAAA-AAAATAAAA-A
1 AAAATAAAAAAAAATA
14406 AAAATAAAAAAAAATA
1 AAAATAAAAAAAAATA
14422 AAAA
1 AAAA
14426 AGAGTTTAAA
Statistics
Matches: 92, Mismatches: 16, Indels: 30
0.67 0.12 0.22
Matches are distributed among these distances:
14 9 0.10
15 10 0.11
16 35 0.38
17 16 0.17
18 2 0.02
19 6 0.07
20 2 0.02
21 4 0.04
22 3 0.03
23 1 0.01
24 4 0.04
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAATAAAAAAAAATA
Found at i:15755 original size:38 final size:37
Alignment explanation
Indices: 15699--15968 Score: 247
Period size: 38 Copynumber: 7.6 Consensus size: 37
15689 TTCAAAAACA
15699 TTTTAAAAACTATATATTATATATATGTTTTCAAAATG
1 TTTTAAAAACTATATA-TATATATATGTTTTCAAAATG
*
15737 TTTTTAAAACTATATATTATATATATGTTTTCAAAATG
1 TTTTAAAAACTATATA-TATATATATGTTTTCAAAATG
*
15775 TTTTCAAAACTATATA-ATATATATGTTTTC------
1 TTTTAAAAACTATATATATATATATGTTTTCAAAATG
*
15805 ----AAAAACTATATAT-TATATATATTTTCAAAAATG
1 TTTTAAAAACTATATATATATATATGTTTTC-AAAATG
*
15838 TTTTCAAAAACTATATAT-TATATATGTTTTC--AATT
1 TTTT-AAAAACTATATATATATATATGTTTTCAAAATG
* *
15873 TTTTTAAAACT-T-TATA-ATATATATTTTCAAAATG
1 TTTTAAAAACTATATATATATATATGTTTTCAAAATG
* *
15907 TTTTCAAAACTATATA-ATATATATATTTTCGAAAATTG
1 TTTTAAAAACTATATATATATATATGTTTTC-AAAA-TG
*
15945 CTTTCTAAAAATTATATAT-TATAT
1 -TTT-TAAAAACTATATATATATAT
15969 TTTTCCAAAA
Statistics
Matches: 196, Mismatches: 12, Indels: 46
0.77 0.05 0.18
Matches are distributed among these distances:
26 23 0.12
32 14 0.07
33 1 0.01
34 19 0.10
35 9 0.05
36 28 0.14
37 4 0.02
38 79 0.40
39 3 0.02
40 16 0.08
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTTAAAAACTATATATATATATATGTTTTCAAAATG
Found at i:15816 original size:26 final size:26
Alignment explanation
Indices: 15772--15835 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
15762 TGTTTTCAAA
15772 ATGTTTTC-AAAACTATATAATATAT
1 ATGTTTTCAAAAACTATATAATATAT
*
15797 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATAATATAT
*
15823 ATATTTTCAAAAA
1 ATGTTTTCAAAAA
15836 TGTTTTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
25 8 0.22
26 28 0.78
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (26 bp):
ATGTTTTCAAAAACTATATAATATAT
Found at i:15900 original size:32 final size:33
Alignment explanation
Indices: 15797--15930 Score: 144
Period size: 34 Copynumber: 3.8 Consensus size: 33
15787 TATAATATAT
15797 ATGTTTTCAAAAACTATATATTATATATATTTTCAAAA
1 ATGTTTTC-AAAACTATATA--ATATATATTTTC--AA
*
15835 ATGTTTTCAAAAACTATATATTATATATGTTTTC-A
1 ATGTTTTC-AAAACTATATA--ATATATATTTTCAA
* * *
15870 ATTTTTTTAAAACTTTATAATATATATTTTCAAA
1 ATGTTTTCAAAACTATATAATATATATTTTC-AA
15904 ATGTTTTCAAAACTATATAATATATAT
1 ATGTTTTCAAAACTATATAATATATAT
15931 ATTTTCGAAA
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
32 11 0.13
34 35 0.41
35 7 0.08
38 33 0.38
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (33 bp):
ATGTTTTCAAAACTATATAATATATATTTTCAA
Found at i:17220 original size:82 final size:82
Alignment explanation
Indices: 17095--17345 Score: 297
Period size: 82 Copynumber: 3.0 Consensus size: 82
17085 TCGACAATTT
* * * *
17095 TTGTTGATAGATAACCCTTCTCTCCTTAAGCTATGTTGTAAATTTGATATGCCCTTGAGTTGAAT
1 TTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAAT
17160 GTAATCAAACTCGAAGG
66 GTAATCAAACTCGAAGG
* * *
17177 TTGTTGACATATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAAT
1 TTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAAT
* *
17242 GTAATCGAACTCGAAGATTT
66 GTAATCAAACTCGAAG---G
* * * * * * *
17262 TTATTGACAGATAACCTTTCTCGCCTTAAGTTATGCTGTAAACTTGTTATGTCTTTGAGCTGAAT
1 TTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAAT
* *
17327 AG-AATCGAACTCAAAGG
66 -GTAATCAAACTCGAAGG
17344 TT
1 TT
17346 TCTGTTGATA
Statistics
Matches: 144, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
82 75 0.52
85 68 0.47
86 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (82 bp):
TTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAAT
GTAATCAAACTCGAAGG
Found at i:17320 original size:85 final size:85
Alignment explanation
Indices: 17070--17362 Score: 335
Period size: 85 Copynumber: 3.5 Consensus size: 85
17060 GTCATCGAGT
* * * *
17070 TGAATGGAATCAAACTCGACA-ATTTTTGTTGATAGATAACCCTTCTCTCCTTAAGCTATGTTGT
1 TGAATGTAATCAAACTCGA-AGATTTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGT
*
17134 AAATTTGATATGCCCTTGAGT
65 AAATTTGATATGCCCTTGAGC
* * * *
17155 TGAATGTAATCAAACTCGAAG---GTTGTTGACATATAGCCCTTCTCGCCTTGAGCTATGCTGTA
1 TGAATGTAATCAAACTCGAAGATTTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGTA
17217 AATTTGATATGCCCTTGAGC
66 AATTTGATATGCCCTTGAGC
* * * *
17237 TGAATGTAATCGAACTCGAAGATTTTTATTGACAGATAACCTTTCTCGCCTTAAGTTATGCTGTA
1 TGAATGTAATCAAACTCGAAGATTTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGTA
* * * *
17302 AACTTGTTATGTCTTTGAGC
66 AATTTGATATGCCCTTGAGC
* * * * *
17322 TGAATAG-AATCGAACTCAAAGGTTTCTGTTGATAGATAACC
1 TGAAT-GTAATCAAACTCGAAGATTTTTGTTGACAGATAACC
17363 TTTATCACCT
Statistics
Matches: 177, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
82 73 0.41
84 1 0.01
85 102 0.58
86 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (85 bp):
TGAATGTAATCAAACTCGAAGATTTTTGTTGACAGATAACCCTTCTCGCCTTAAGCTATGCTGTA
AATTTGATATGCCCTTGAGC
Found at i:18944 original size:99 final size:99
Alignment explanation
Indices: 18772--18973 Score: 323
Period size: 99 Copynumber: 2.0 Consensus size: 99
18762 GGACATCTCA
* * **
18772 ATATTATAATCACCTTTATTAGGCTAGCTCAATCTTATCCATAAATCTGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTGATTAGGCTAGCTCAATCTTATCCATAAAGCCAGGGCGTTTAACCAATT
*
18837 GCTTTAGAGGGACAACTCAAGCTTTATTGTATAG
66 GCTCTAGAGGGACAACTCAAGCTTTATTGTATAG
* *
18871 ATATTATAATCACCTTGATTAGGCTAGCTGAATCTTATCCATAAAGCCAGGGTGTTTAACCAATT
1 ATATTATAATCACCTTGATTAGGCTAGCTCAATCTTATCCATAAAGCCAGGGCGTTTAACCAATT
* *
18936 GCTCTAGAGGGACAGCTCAAGCTTTATTGTATAT
66 GCTCTAGAGGGACAACTCAAGCTTTATTGTATAG
18970 ATAT
1 ATAT
18974 AATATTATAA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 94 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (99 bp):
ATATTATAATCACCTTGATTAGGCTAGCTCAATCTTATCCATAAAGCCAGGGCGTTTAACCAATT
GCTCTAGAGGGACAACTCAAGCTTTATTGTATAG
Found at i:20931 original size:39 final size:39
Alignment explanation
Indices: 20849--21081 Score: 258
Period size: 40 Copynumber: 5.9 Consensus size: 39
20839 TTCAAAAACA
*
20849 TTTTAAAAACTATATATTATATATATTTTTTTCAAAATGT
1 TTTTAAAAACTATATATTATATATA-TGTTTTCAAAATGT
*
20889 TTTTAGAAACTATATATTATATATATGTTTTCAAAATGT
1 TTTTAAAAACTATATATTATATATATGTTTTCAAAATGT
20928 TTTTAAAAACTATATATTATATATATGTTTTCAAAAATGT
1 TTTTAAAAACTATATATTATATATATGTTTTC-AAAATGT
* *** * * *
20968 TTTCAATTTCTATATATTATATATATATTTTAAAAATAT
1 TTTTAAAAACTATATATTATATATATGTTTTCAAAATGT
* * * *
21007 TTTCAATATA-TATATATATATATTATATTTTTTC-AAATTT
1 TTTTAA-AAACTATATAT-TATA-TATATGTTTTCAAAATGT
*
21047 TTTTGAAAAACTATATA-T-CATATATGTTTTCAAAA
1 TTTT-AAAAACTATATATTATATATATGTTTTCAAAA
21082 AAATTTCAAA
Statistics
Matches: 167, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
37 10 0.06
38 4 0.02
39 64 0.38
40 72 0.43
41 17 0.10
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (39 bp):
TTTTAAAAACTATATATTATATATATGTTTTCAAAATGT
Found at i:20951 original size:79 final size:77
Alignment explanation
Indices: 20838--21141 Score: 270
Period size: 79 Copynumber: 3.9 Consensus size: 77
20828 GTTTTCAAAA
*
20838 TTTCAAAAACATTTTAAAAACTATATATTATATATATTTTTTTCAAAATGTTTTTAGAAACTATA
1 TTTC-AAAATATTTTAAAAACTATATATTATATATATTTTTTTCAAAATGTTTTTA-AAACTATA
20903 TATTATATATATGT
64 TATTATATATATGT
* * * **
20917 TTTCAAAATGTTTTTAAAAACTATATATTATATATA-TGTTTTCAAAAATGTTTTCAATTTCTAT
1 TTTCAAAAT-ATTTTAAAAACTATATATTATATATATTTTTTTC-AAAATGTTTTTAA-AACTAT
*
20981 ATATTATATATATAT
63 ATATTATATATATGT
* * * *
20996 TTTAAAAATATTTTCAATA-TATATATATATATATTATATTTTTTC-AAATTTTTTTGAAAAACT
1 TTTCAAAATATTTTAAAAACTATATAT-TATATA-TAT-TTTTTTCAAAATGTTTTT--AAAACT
*
21059 ATATA-T-CATATATGT
61 ATATATTATATATATGT
* * * * *
21074 TTTCAAAAAAATTTCAAAACTATATA--ATACATA---TTTT-AAAATTGTTTTCAAAACTATAT
1 TTTCAAAATATTTTAAAAACTATATATTATATATATTTTTTTCAAAA-TGTTTTTAAAACTATAT
*
21133 AATATATAT
65 ATTATATAT
21142 TTTCAAAAAC
Statistics
Matches: 185, Mismatches: 26, Indels: 35
0.75 0.11 0.14
Matches are distributed among these distances:
70 11 0.06
71 8 0.04
72 9 0.05
75 2 0.01
76 4 0.02
77 7 0.04
78 46 0.25
79 83 0.45
80 7 0.04
81 8 0.04
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.48
Consensus pattern (77 bp):
TTTCAAAATATTTTAAAAACTATATATTATATATATTTTTTTCAAAATGTTTTTAAAACTATATA
TTATATATATGT
Found at i:20994 original size:11 final size:11
Alignment explanation
Indices: 20978--21034 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
20968 TTTCAATTTC
20978 TATATATTATA
1 TATATATTATA
*
20989 TATATATTTTA
1 TATATATTATA
* * *
21000 AAAATATTTTCA
1 TATATATTAT-A
21012 -ATATATATATA
1 TATATAT-TATA
21023 TATATATTATA
1 TATATATTATA
21034 T
1 T
21035 TTTTTCAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 29 0.76
12 9 0.24
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATATTATA
Found at i:21193 original size:15 final size:16
Alignment explanation
Indices: 21171--21208 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
21161 AAAATTATAT
*
21171 ATTATATTTTTCCAAA
1 ATTATATTTTTCAAAA
21187 A-TATA-TTTTCAAAA
1 ATTATATTTTTCAAAA
21201 ATTATATT
1 ATTATATT
21209 ACATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
14 9 0.47
15 8 0.42
16 2 0.11
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTATATTTTTCAAAA
Found at i:28979 original size:19 final size:21
Alignment explanation
Indices: 28942--28984 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
28932 CACTCACTAT
*
28942 TGTATTACTTGCATCGA-TTG
1 TGTATTACTTGCATAGATTTG
*
28962 TGTA-TACTTGTATAGATTTG
1 TGTATTACTTGCATAGATTTG
28982 TGT
1 TGT
28985 GCCATATCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.49
Consensus pattern (21 bp):
TGTATTACTTGCATAGATTTG
Found at i:30566 original size:2 final size:2
Alignment explanation
Indices: 30559--30621 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
30549 ACTAAAACAA
30559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
30601 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
30622 GAAGCGGCTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40570 original size:50 final size:51
Alignment explanation
Indices: 40506--40632 Score: 229
Period size: 50 Copynumber: 2.5 Consensus size: 51
40496 TGTTATAAAA
*
40506 ATATTAGATTTATAATAAAAATAATAGAAAACAACTAAAA-AAATAAAATT
1 ATATTAGATTTATAATAAAAATAATAGAAAACAACTAAAATAAATAAAATG
*
40556 ATATTAGATTTATAATAAAAATAATAGAAAACAACTAAAATAAATGAAATG
1 ATATTAGATTTATAATAAAAATAATAGAAAACAACTAAAATAAATAAAATG
40607 ATATTAGATTTATAATAAAAATAATA
1 ATATTAGATTTATAATAAAAATAATA
40633 TAAAGTTTAC
Statistics
Matches: 74, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
50 40 0.54
51 34 0.46
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (51 bp):
ATATTAGATTTATAATAAAAATAATAGAAAACAACTAAAATAAATAAAATG
Found at i:42207 original size:31 final size:31
Alignment explanation
Indices: 42169--42228 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
42159 CATAGAGTTT
*
42169 AAAAACATCCAATTACGTATCAAAATTATCG
1 AAAAACATCCAATAACGTATCAAAATTATCG
42200 AAAAACATCCAATAACGTATCAAAATTAT
1 AAAAACATCCAATAACGTATCAAAATTAT
42229 TGAACTGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (31 bp):
AAAAACATCCAATAACGTATCAAAATTATCG
Found at i:43695 original size:21 final size:21
Alignment explanation
Indices: 43671--43710 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43661 CACAGTGTAG
*
43671 ATGAAAGCATGTCTAACATGT
1 ATGAAAGCATGTCCAACATGT
*
43692 ATGAGAGCATGTCCAACAT
1 ATGAAAGCATGTCCAACAT
43711 TTGGTATCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (21 bp):
ATGAAAGCATGTCCAACATGT
Found at i:56778 original size:15 final size:17
Alignment explanation
Indices: 56744--56780 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
56734 TAAAAATAGT
56744 ATAATAAAATTTAATAA
1 ATAATAAAATTTAATAA
*
56761 ATAAT-AAA-TTATTAA
1 ATAATAAAATTTAATAA
56776 ATAAT
1 ATAAT
56781 TCTAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATAAAATTTAATAA
Found at i:56966 original size:51 final size:51
Alignment explanation
Indices: 56896--57008 Score: 199
Period size: 51 Copynumber: 2.2 Consensus size: 51
56886 GTATTTATAG
* * *
56896 GAAGATGGGAGGGGGAGACGAGTGGTAATTAATGTGGGAGACGGATATTTT
1 GAAGATGGGAGGGGGAGACGAGTGATAATTAATGTGGGAGACCGATAGTTT
56947 GAAGATGGGAGGGGGAGACGAGTGATAATTAATGTGGGAGACCGATAGTTT
1 GAAGATGGGAGGGGGAGACGAGTGATAATTAATGTGGGAGACCGATAGTTT
56998 GAAGATGGGAG
1 GAAGATGGGAG
57009 CAGATCATGA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.31, C:0.04, G:0.43, T:0.21
Consensus pattern (51 bp):
GAAGATGGGAGGGGGAGACGAGTGATAATTAATGTGGGAGACCGATAGTTT
Found at i:62103 original size:32 final size:32
Alignment explanation
Indices: 62067--62127 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
62057 CAATTATAAC
62067 ACTAAAGCAATCGATTTTAACTGAATTAACCG
1 ACTAAAGCAATCGATTTTAACTGAATTAACCG
62099 ACTAAAGCAATCGATTTTAACTGAATTAA
1 ACTAAAGCAATCGATTTTAACTGAATTAA
62128 TAAGTCGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (32 bp):
ACTAAAGCAATCGATTTTAACTGAATTAACCG
Done.