Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000680.1 Hibiscus syriacus cultivar Beakdansim tig00001320_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: 55781
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:17004 original size:8 final size:8
Alignment explanation
Indices: 16991--17016 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
16981 TGAATCCTTG
16991 TTGTTTTA
1 TTGTTTTA
16999 TTGTTTTA
1 TTGTTTTA
17007 TTGTTTTA
1 TTGTTTTA
17015 TT
1 TT
17017 TTAACCACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.77
Consensus pattern (8 bp):
TTGTTTTA
Found at i:17067 original size:14 final size:14
Alignment explanation
Indices: 17028--17060 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
17018 TAACCACTTA
17028 ATTTTAAAAATTAT
1 ATTTTAAAAATTAT
17042 ATTTTAAAAATT-T
1 ATTTTAAAAATTAT
17055 ATTTTA
1 ATTTTA
17061 TCAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTTTAAAAATTAT
Found at i:21268 original size:21 final size:21
Alignment explanation
Indices: 21230--21270 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21220 ATCGATGAAT
* * *
21230 AGTTTATGTTATTGATATGAC
1 AGTTTATGATACTAATATGAC
21251 AGTTTATGATACTAATATGA
1 AGTTTATGATACTAATATGA
21271 TTGTCCATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (21 bp):
AGTTTATGATACTAATATGAC
Found at i:27106 original size:75 final size:73
Alignment explanation
Indices: 27027--27205 Score: 243
Period size: 74 Copynumber: 2.4 Consensus size: 73
27017 TTTTGACAAA
*
27027 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAA-TTTATATATTATATAGTTTTTGAAAAT
1 ATATAATATATAGTTTT--GAAAAT-ATTTT-GAAAACTTTATATATTATATAGTTTTT-AAAAT
*
27091 ATTTTTAAAATAT
61 ATTTTTAAAACAT
27104 ATATAATATATAGTTTTGAAAATATTTTGAAAACGTTTATATATTATATAGTTTTTAAAATATTT
1 ATATAATATATAGTTTTGAAAATATTTTGAAAAC-TTTATATATTATATAGTTTTTAAAATATTT
*
27169 TGAAAACAT
65 TTAAAACAT
* * *
27178 ATATAGTATATAGTTTTAAAAACATTTT
1 ATATAATATATAGTTTTGAAAATATTTT
27206 TTGTGAAATT
Statistics
Matches: 94, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
73 5 0.05
74 46 0.49
75 27 0.29
77 16 0.17
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (73 bp):
ATATAATATATAGTTTTGAAAATATTTTGAAAACTTTATATATTATATAGTTTTTAAAATATTTT
TAAAACAT
Found at i:27128 original size:36 final size:36
Alignment explanation
Indices: 27027--27374 Score: 196
Period size: 38 Copynumber: 9.4 Consensus size: 36
27017 TTTTGACAAA
* * *
27027 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAATTT
1 ATATAATATATAGTTTT--GAAAAT-ATTTT-TAAAATAT
*
27067 ATATATTATATAGTTTTTGAAAATATTTTTAAAATAT
1 ATATAATATATAG-TTTTGAAAATATTTTTAAAATAT
* *
27104 ATATAATATATAGTTTTGAAAATATTTTGAAAACGTTT
1 ATATAATATATAGTTTTGAAAATATTTTTAAAA--TAT
* * * *
27142 ATATATTATATAGTTTTTAAAATATTTTGAAAACAT
1 ATATAATATATAGTTTTGAAAATATTTTTAAAATAT
* * * *
27178 ATATAGTATATAGTTTTAAAAACATTTTTTGTGAAAT-T
1 ATATAATATATAGTTTT-GAAA-ATATTTT-TAAAATAT
* * *
27216 ATATAATATATAGTTTTAAAAACTTTTTTTTTGAAAA-CT
1 ATATAATATATAGTTTTGAAAA---TATTTTT-AAAATAT
** * *
27255 -TAT-ATA-ATAGTTTT-AAAACGTTTTGAAAA-CT
1 ATATAATATATAGTTTTGAAAATATTTTTAAAATAT
* * **
27286 ATGTAATATATAGTTTTGGAAACT-TTTTT--TTTA-
1 ATATAATATATAGTTTT-GAAAATATTTTTAAAATAT
* *
27319 AGTATAATATATAGTTTTCTAAAACATATTTTTGAAATAT
1 A-TATAATATATAG-TTT-TGAAA-ATATTTTTAAAATAT
*
27359 ATATATTATATAGTTT
1 ATATAATATATAGTTT
27375 ATATCATATT
Statistics
Matches: 248, Mismatches: 35, Indels: 52
0.74 0.10 0.16
Matches are distributed among these distances:
31 6 0.02
32 6 0.02
33 4 0.02
34 19 0.08
35 14 0.06
36 50 0.20
37 33 0.13
38 68 0.27
39 32 0.13
40 12 0.05
41 4 0.02
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAAATATTTTTAAAATAT
Found at i:27154 original size:38 final size:36
Alignment explanation
Indices: 27027--27303 Score: 208
Period size: 38 Copynumber: 7.5 Consensus size: 36
27017 TTTTGACAAA
* *
27027 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAATTT
1 ATATAATATATAGTTTT--GAAAAT-ATTTT-GAAAATAT
* *
27067 ATATATTATATAGTTTTTGAAAATATTTTTAAAATAT
1 ATATAATATATAG-TTTTGAAAATATTTTGAAAATAT
*
27104 ATATAATATATAGTTTTGAAAATATTTTGAAAACGTTT
1 ATATAATATATAGTTTTGAAAATATTTTGAAAA--TAT
* * *
27142 ATATATTATATAGTTTTTAAAATATTTTGAAAACAT
1 ATATAATATATAGTTTTGAAAATATTTTGAAAATAT
* * * *
27178 ATATAGTATATAGTTTTAAAAACATTTTTTGTGAAAT-T
1 ATATAATATATAGTTTT-GAAA-ATATTTTG-AAAATAT
* * *
27216 ATATAATATATAGTTTTAAAAACTTTTTTTTTGAAAA-CT
1 ATATAATATATAGTTTTGAAAA----TATTTTGAAAATAT
** *
27255 -TAT-ATA-ATAGTTTT-AAAACGTTTTGAAAA-CT
1 ATATAATATATAGTTTTGAAAATATTTTGAAAATAT
*
27286 ATGTAATATATAGTTTTG
1 ATATAATATATAGTTTTG
27304 GAAACTTTTT
Statistics
Matches: 201, Mismatches: 21, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
31 11 0.05
32 2 0.01
33 3 0.01
34 8 0.04
35 4 0.02
36 45 0.22
37 28 0.14
38 65 0.32
39 13 0.06
40 18 0.09
41 4 0.02
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAAATATTTTGAAAATAT
Found at i:27218 original size:74 final size:72
Alignment explanation
Indices: 27027--27302 Score: 242
Period size: 74 Copynumber: 3.7 Consensus size: 72
27017 TTTTGACAAA
* *
27027 ATATAATATATAATTTTCAGAAAATGATTTTCGAAAATTTATATATTATATAGTTTTTGAAAATA
1 ATATAATATATAGTTTT-A-AAAAT-ATTTT-GAAAACTTATATATTATATAGTTTTT-AAAATA
* *
27092 TTTTTAAAATAT
61 TTTTGAAAACAT
*
27104 ATATAATATATAGTTTTGAAAATATTTTGAAAACGTTTATATATTATATAGTTTTTAAAATATTT
1 ATATAATATATAGTTTTAAAAATATTTTGAAAAC--TTATATATTATATAGTTTTTAAAATATTT
27169 TGAAAACAT
64 TGAAAACAT
* * * * *
27178 ATATAGTATATAGTTTTAAAAACATTTTTTGTGAAA-TTATATAATATATAGTTTTAAAAACTTT
1 ATATAATATATAGTTTT-AAAA-ATATTTTG-AAAACTTATATATTATATAGTTTTTAAAA----
*
27242 TTTTTTGAAAAC-T
59 TATTTTGAAAACAT
** * *
27255 -TAT-ATA-ATAGTTTT-AAAACGTTTTGAAAAC-TATGTAATATATAGTTTT
1 ATATAATATATAGTTTTAAAAATATTTTGAAAACTTATATATTATATAGTTTT
27303 GGAAACTTTT
Statistics
Matches: 172, Mismatches: 17, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
70 20 0.12
71 6 0.03
72 3 0.02
73 5 0.03
74 67 0.39
75 30 0.17
76 10 0.06
77 20 0.12
78 11 0.06
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (72 bp):
ATATAATATATAGTTTTAAAAATATTTTGAAAACTTATATATTATATAGTTTTTAAAATATTTTG
AAAACAT
Found at i:27405 original size:19 final size:19
Alignment explanation
Indices: 27383--27435 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
27373 TTATATCATA
27383 TTATTTATTTTATTTTATT
1 TTATTTATTTTATTTTATT
* * *
27402 TTATTAATTTAATTTAATT
1 TTATTTATTTTATTTTATT
* *
27421 TCATATATTTT-TTTT
1 TTATTTATTTTATTTT
27436 CTCCAGGTCC
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTATTTTATTTTATT
Found at i:27458 original size:12 final size:12
Alignment explanation
Indices: 27441--27472 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
27431 TTTTTCTCCA
27441 GGTCCAAAAACG
1 GGTCCAAAAACG
*
27453 GGTCCAGAAACG
1 GGTCCAAAAACG
27465 GGTCCAAA
1 GGTCCAAA
27473 TCCAGTCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.38, C:0.25, G:0.28, T:0.09
Consensus pattern (12 bp):
GGTCCAAAAACG
Found at i:28538 original size:13 final size:14
Alignment explanation
Indices: 28515--28543 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
28505 TGATCCTAAG
28515 TTTTATCTTTATTT
1 TTTTATCTTTATTT
28529 TTTTAT-TTTATTT
1 TTTTATCTTTATTT
28542 TT
1 TT
28544 AAATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATCTTTATTT
Found at i:28581 original size:11 final size:11
Alignment explanation
Indices: 28565--28645 Score: 69
Period size: 11 Copynumber: 7.0 Consensus size: 11
28555 AAACTTAACC
28565 TTTTATTATTA
1 TTTTATTATTA
28576 TTTTATTATTA
1 TTTTATTATTA
*
28587 TTTCT-TTCTTTCA
1 TTT-TATT-ATT-A
28600 TTATTATTATTA
1 TT-TTATTATTA
28612 TTTT-TTATATA
1 TTTTATTAT-TA
28623 TTTTATTCATT-
1 TTTTATT-ATTA
28634 TTTTATTTATTA
1 TTTTA-TTATTA
28646 GCATTTTGTT
Statistics
Matches: 58, Mismatches: 2, Indels: 19
0.73 0.03 0.24
Matches are distributed among these distances:
10 4 0.07
11 32 0.55
12 11 0.19
13 8 0.14
14 3 0.05
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:32426 original size:36 final size:36
Alignment explanation
Indices: 32386--32503 Score: 130
Period size: 46 Copynumber: 3.0 Consensus size: 36
32376 TCCCCAATCT
32386 CCCCATGCATGAACTGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACTGATCCTTGGTCGCCCCGAGTG
*
32422 CCCCATGCATGAACCGATCCTTGGTCATCCTTGGTCGCCTCGAGTG
1 CCCCATGCATG-A---A--C-T-G--ATCCTTGGTCGCCCCGAGTG
32468 CCCCATGCATGAAC-GATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACTGATCCTTGGTCGCCCCGAGTG
32503 C
1 C
32504 ATGGCACGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
35 20 0.29
36 11 0.16
37 2 0.03
40 2 0.03
42 2 0.03
43 1 0.01
44 1 0.01
45 1 0.01
46 30 0.43
ACGTcount: A:0.16, C:0.36, G:0.25, T:0.23
Consensus pattern (36 bp):
CCCCATGCATGAACTGATCCTTGGTCGCCCCGAGTG
Found at i:32455 original size:46 final size:45
Alignment explanation
Indices: 32402--32492 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 45
32392 GCATGAACTG
32402 ATCCTTGGTCGCCCCGAGTGCCCCATGCATGAACCGATCCTTGGTC
1 ATCCTTGGTCGCCCCGAGTGCCCCATGCATGAA-CGATCCTTGGTC
*
32448 ATCCTTGGTCGCCTCGAGTGCCCCATGCATGAACGATCCTTGGTC
1 ATCCTTGGTCGCCCCGAGTGCCCCATGCATGAACGATCCTTGGTC
32493 GCCCCGAGTG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
45 12 0.27
46 32 0.73
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.25
Consensus pattern (45 bp):
ATCCTTGGTCGCCCCGAGTGCCCCATGCATGAACGATCCTTGGTC
Found at i:32514 original size:29 final size:29
Alignment explanation
Indices: 32480--32566 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
32470 CCATGCATGA
32480 ACGATCCTTGGTCGCCCCGAGTGCATGGC
1 ACGATCCTTGGTCGCCCCGAGTGCATGGC
**** * *
32509 ACGATCTCCCCAATCTCCCC-A-TGCAT-GA
1 ACGA--TCCTTGGTCGCCCCGAGTGCATGGC
32537 ACCGATCCTTGGTCGCCCCGAGTGCATGGC
1 A-CGATCCTTGGTCGCCCCGAGTGCATGGC
32567 GACCTCCTTA
Statistics
Matches: 40, Mismatches: 12, Indels: 11
0.63 0.19 0.17
Matches are distributed among these distances:
27 9 0.22
28 3 0.08
29 17 0.43
30 2 0.05
31 9 0.22
ACGTcount: A:0.17, C:0.38, G:0.24, T:0.21
Consensus pattern (29 bp):
ACGATCCTTGGTCGCCCCGAGTGCATGGC
Found at i:32631 original size:29 final size:29
Alignment explanation
Indices: 32558--32636 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
32548 GTCGCCCCGA
* * *
32558 GTGCATGGCGACCTCCTTAGTCGTTGGGC
1 GTGCATGACGACCTCTTTGGTCGTTGGGC
*
32587 GTGCATGTCGACCTCTTTGGTCGTTGGGC
1 GTGCATGACGACCTCTTTGGTCGTTGGGC
32616 GTGCATGACGACCTCTTTGGT
1 GTGCATGACGACCTCTTTGGT
32637 TACTGTACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.10, C:0.25, G:0.33, T:0.32
Consensus pattern (29 bp):
GTGCATGACGACCTCTTTGGTCGTTGGGC
Found at i:35101 original size:15 final size:14
Alignment explanation
Indices: 35078--35125 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
35068 AATTTGAAAG
35078 TTAGAGTAATTAAA
1 TTAGAGTAATTAAA
35092 TTAGGAGTAATTTGAAA
1 TTA-GAGTAA-TT-AAA
35109 GTTA-AGTAATTAAA
1 -TTAGAGTAATTAAA
35123 TTA
1 TTA
35126 AATAAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 6 0.20
15 8 0.27
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.38
Consensus pattern (14 bp):
TTAGAGTAATTAAA
Found at i:35118 original size:16 final size:17
Alignment explanation
Indices: 35068--35119 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
35058 ATAAAAAATA
35068 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
35085 AA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
35100 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
35116 AATT
1 AATT
35120 AAATTAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 3 0.10
15 9 0.29
16 11 0.35
17 5 0.16
18 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:46018 original size:23 final size:24
Alignment explanation
Indices: 45992--46037 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
45982 GTTATATTCT
45992 AATTAT-TTAATTATT-TTTTTTGG
1 AATTATATTAATT-TTATTTTTTGG
46015 AATTATACTTAATTTTATTTTTT
1 AATTATA-TTAATTTTATTTTTT
46038 AATTCCGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 12 0.60
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (24 bp):
AATTATATTAATTTTATTTTTTGG
Found at i:54686 original size:2 final size:2
Alignment explanation
Indices: 54679--54709 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54669 AATTAAATTA
54679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
54710 AACTATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55184 original size:43 final size:42
Alignment explanation
Indices: 55138--55217 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
55128 TATTTTTGAT
55138 TTTTTAATA-ATTTATATTTTATTA-TATATTTAATTTTTTTAA
1 TTTTTAATATATTTA-ATTTTATTAGTAT-TTTAATTTTTTTAA
* *
55180 TTTTTAATATATTTAATTTTTTTAGTATTTTTATTTTT
1 TTTTTAATATATTTAATTTTATTAGTATTTTAATTTTT
55218 AGTATTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 26 0.76
43 8 0.24
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (42 bp):
TTTTTAATATATTTAATTTTATTAGTATTTTAATTTTTTTAA
Found at i:55195 original size:25 final size:26
Alignment explanation
Indices: 55161--55212 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
55151 ATATTTTATT
55161 ATATATTTAATTTTTTTA-ATTTTTA
1 ATATATTTAATTTTTTTAGATTTTTA
55186 ATATATTTAATTTTTTTAGTATTTTTA
1 ATATATTTAATTTTTTTAG-ATTTTTA
55213 TTTTTAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 18 0.72
27 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
ATATATTTAATTTTTTTAGATTTTTA
Found at i:55203 original size:18 final size:17
Alignment explanation
Indices: 55137--55200 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 17
55127 ATATTTTTGA
*
55137 TTTTTTAATAATTTATAT
1 TTTTTTAATATTTTA-AT
*
55155 TTTATT-ATATATTTAAT
1 TTTTTTAATAT-TTTAAT
55172 TTTTTTAAT-TTTTAAT
1 TTTTTTAATATTTTAAT
* *
55188 ATATTTAAT-TTTT
1 TTTTTTAATATTTT
55201 TTAGTATTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 17 0.44
17 11 0.28
18 11 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTTAATATTTTAAT
Found at i:55208 original size:16 final size:16
Alignment explanation
Indices: 55175--55224 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
55165 ATTTAATTTT
*
55175 TTTAATTTTTAATA-TA
1 TTTAATTTTT-TTAGTA
55191 TTTAATTTTTTTAGTA
1 TTTAATTTTTTTAGTA
55207 TTT--TTATTTTTAGTA
1 TTTAATT-TTTTTAGTA
55222 TTT
1 TTT
55225 TATATAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 2 0.06
15 14 0.45
16 15 0.48
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (16 bp):
TTTAATTTTTTTAGTA
Found at i:55225 original size:9 final size:9
Alignment explanation
Indices: 55126--55212 Score: 58
Period size: 9 Copynumber: 10.1 Consensus size: 9
55116 TGTTTTTAAA
55126 AATATTTTT
1 AATATTTTT
*
55135 GAT-TTTTT
1 AATATTTTT
*
55143 AATA-ATTT
1 AATATTTTT
55151 -ATATTTTAT
1 AATATTTT-T
* *
55160 TATATATTT
1 AATATTTTT
55169 AAT-TTTTT
1 AATATTTTT
*
55177 TA-ATTTTT
1 AATATTTTT
*
55185 AATATATTT
1 AATATTTTT
*
55194 AATTTTTTT
1 AATATTTTT
*
55203 AGTATTTTT
1 AATATTTTT
55212 A
1 A
55213 TTTTTAGTAT
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
7 3 0.05
8 23 0.40
9 26 0.45
10 6 0.10
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (9 bp):
AATATTTTT
Found at i:55225 original size:42 final size:42
Alignment explanation
Indices: 55129--55234 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 42
55119 TTTTAAAAAT
*
55129 ATTTTTG-ATTTTTTAATAATTTATATTTTATTATATATTTA
1 ATTTTTGTAATTTTTAATAATTTATATTTTATTATATATTTA
* * *
55170 ATTTTTTTAATTTTTAATATATTTA-ATTTTTTTAGTAT-TTTT
1 ATTTTTGTAATTTTTAATA-ATTTATATTTTATTA-TATATTTA
55212 ATTTTTAGT-A-TTTTATATAATTT
1 ATTTTT-GTAATTTTTA-ATAATTT
55235 TTTGAATAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
41 15 0.27
42 31 0.56
43 9 0.16
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (42 bp):
ATTTTTGTAATTTTTAATAATTTATATTTTATTATATATTTA
Found at i:55255 original size:15 final size:16
Alignment explanation
Indices: 55235--55268 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
55225 TATATAATTT
55235 TTTG-AATAATTTTAA
1 TTTGAAATAATTTTAA
*
55250 TTTGAAATATTTTTAA
1 TTTGAAATAATTTTAA
55266 TTT
1 TTT
55269 TCTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
TTTGAAATAATTTTAA
Done.