Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006544.1 Hibiscus syriacus cultivar Beakdansim tig00015974_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: 51916
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:4362 original size:17 final size:17
Alignment explanation
Indices: 4340--4476 Score: 159
Period size: 17 Copynumber: 7.9 Consensus size: 17
4330 ATTCTAAATG
4340 TTTACAGTTATCAGATA
1 TTTACAGTTATCAGATA
*
4357 TTTACAATTATCAGATGA
1 TTTACAGTTATCAGAT-A
*
4375 TTTTCAGTTATCAGATA
1 TTTACAGTTATCAGATA
*
4392 TTTGCAGTTATCAGATGA
1 TTTACAGTTATCAGAT-A
** *
4410 TTTTTAGTTATCATATA
1 TTTACAGTTATCAGATA
*
4427 TTTACAGTTATTAGATGA
1 TTTACAGTTATCAGAT-A
*
4445 -TTACAGTTATTAGATA
1 TTTACAGTTATCAGATA
4461 TTTTACAGTTATCAGA
1 -TTTACAGTTATCAGA
4477 CGTAGATTAA
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.01
17 59 0.57
18 43 0.42
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (17 bp):
TTTACAGTTATCAGATA
Found at i:4390 original size:35 final size:35
Alignment explanation
Indices: 4344--4476 Score: 187
Period size: 35 Copynumber: 3.8 Consensus size: 35
4334 TAAATGTTTA
*
4344 CAGTTATCAGATATTTACAATTATCAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
*
4379 CAGTTATCAGATATTTGCAGTTATCAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
* * * *
4414 TAGTTATCATATATTTACAGTTATTAGATGA-TTA
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
*
4448 CAGTTATTAGATATTTTACAGTTATCAGA
1 CAGTTATCAGATA-TTTACAGTTATCAGA
4477 CGTAGATTAA
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 12 0.14
35 74 0.86
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.44
Consensus pattern (35 bp):
CAGTTATCAGATATTTACAGTTATCAGATGATTTT
Found at i:4401 original size:52 final size:51
Alignment explanation
Indices: 4341--4476 Score: 157
Period size: 52 Copynumber: 2.6 Consensus size: 51
4331 TTCTAAATGT
* *
4341 TTACAGTTATCAGATATTTACAATTATCAGATGATTTTCAGTTATCAGAT-A
1 TTACAGTTATCAGATATTTACAGTTATCAGAT-ATTTACAGTTATCAGATGA
* ** * *
4392 TTTGCAGTTATCAGATGATTTTTAGTTATCATATATTTACAGTTATTAGATGA
1 -TTACAGTTATCAGAT-ATTTACAGTTATCAGATATTTACAGTTATCAGATGA
*
4445 TTACAGTTATTAGATATTTTACAGTTATCAGA
1 TTACAGTTATCAGATA-TTTACAGTTATCAGA
4477 CGTAGATTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
51 1 0.01
52 54 0.78
53 14 0.20
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (51 bp):
TTACAGTTATCAGATATTTACAGTTATCAGATATTTACAGTTATCAGATGA
Found at i:9839 original size:23 final size:22
Alignment explanation
Indices: 9810--9889 Score: 65
Period size: 23 Copynumber: 3.6 Consensus size: 22
9800 ATACACTAGA
9810 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCAT-CCTTGAAT
* * * *
9833 GTGCATCGATACA-CCATAAAG
1 GTGCATCGATGCATCCTTGAAT
*
9854 GTGCA-CTGATGCATTCATTGAAT
1 GTGCATC-GATGCA-TCCTTGAAT
*
9877 GTGCACCGATGCA
1 GTGCATCGATGCA
9890 CTCTGCTATG
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.02
21 15 0.34
23 27 0.61
24 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:9875 original size:44 final size:41
Alignment explanation
Indices: 9793--9891 Score: 110
Period size: 44 Copynumber: 2.3 Consensus size: 41
9783 TTGTGCATAA
* *
9793 TGCATCGATACACTAGAGTGCATCGATGCATCCCTTGAATG
1 TGCATCGATACACTAAAGTGCATCGATGCATCCATTGAATG
*
9834 TGCATCGATACACCATAAAGGTGCA-CTGATGCATTCATTGAATG
1 TGCATCGATACA-C-TAAA-GTGCATC-GATGCATCCATTGAATG
* *
9878 TGCACCGATGCACT
1 TGCATCGATACACT
9892 CTGCTATGCA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
41 12 0.24
42 2 0.04
43 5 0.10
44 30 0.61
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
TGCATCGATACACTAAAGTGCATCGATGCATCCATTGAATG
Found at i:10295 original size:9 final size:10
Alignment explanation
Indices: 10265--10294 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
10255 AAAACACAAG
*
10265 ATTTTTCAAA
1 ATTTTTGAAA
10275 ATTTTTGAAA
1 ATTTTTGAAA
10285 ATTTTTGAAA
1 ATTTTTGAAA
10295 TAAAAATATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (10 bp):
ATTTTTGAAA
Found at i:11865 original size:2 final size:2
Alignment explanation
Indices: 11858--11887 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11848 ATTGAACTTA
11858 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
11888 TAAGTTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13543 original size:31 final size:31
Alignment explanation
Indices: 13507--13565 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
13497 AACTTAAAAG
* * *
13507 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
13538 AGTTTTACAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
13566 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:13616 original size:22 final size:22
Alignment explanation
Indices: 13590--13680 Score: 119
Period size: 22 Copynumber: 4.0 Consensus size: 22
13580 TAATAAATTA
13590 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
13612 TTTAAAATAAATCAATCCATACAAC
1 TTTAAAATAAATCAATCCAT---AT
**
13637 TACAATAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATCCATAT
13660 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
13681 CAAATAAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
22 36 0.61
23 4 0.07
25 4 0.07
26 15 0.25
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:13699 original size:32 final size:32
Alignment explanation
Indices: 13660--13855 Score: 225
Period size: 32 Copynumber: 6.8 Consensus size: 32
13650 CAATCCATAT
13660 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
13692 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
13714 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
13746 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
13778 TATAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
13800 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
13832 TTTAAAATAAATCAATCCATACAA
1 TTTAAAATAAATCAATCCATACAA
13856 CTACAATAAT
Statistics
Matches: 140, Mismatches: 4, Indels: 40
0.76 0.02 0.22
Matches are distributed among these distances:
22 31 0.22
23 4 0.03
24 2 0.01
26 6 0.04
28 6 0.04
30 2 0.01
31 4 0.03
32 85 0.61
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:13702 original size:54 final size:53
Alignment explanation
Indices: 13581--13967 Score: 339
Period size: 54 Copynumber: 7.4 Consensus size: 53
13571 CAACTACAAT
13581 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
1 AATAAA-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
* *
13635 ACTACA-A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
1 AATAAATATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
13683 AATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
1 AATAAA-TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
** * * * **
13737 AATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATATAAAATAAAT-C-
1 AATAAA-TATTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-CAATCCATACA
**
13791 AATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACA
1 AATAAATA-TTTAAAATAAATCAAT-C---C--AT--A-T-TTTAAAATAAATCAATCCATACA
* *
13855 ACTACA-A--T--AATAAATCAATCCATATTTTAAAATAAATCAAT-C---C-
1 AATAAATATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
* *
13898 -AT--AT-TTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATACT
1 AATAAATATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
13947 AATAAATTATTTAAAATAAAT
1 AATAAA-TATTTAAAATAAAT
13968 TATTTAAAAA
Statistics
Matches: 273, Mismatches: 25, Indels: 70
0.74 0.07 0.19
Matches are distributed among these distances:
40 1 0.00
42 2 0.01
44 33 0.12
45 1 0.00
47 1 0.00
48 61 0.22
49 1 0.00
50 5 0.02
52 5 0.02
53 3 0.01
54 107 0.39
55 11 0.04
56 5 0.02
57 1 0.00
58 12 0.04
60 3 0.01
62 7 0.03
63 10 0.04
64 4 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (53 bp):
AATAAATATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACA
Found at i:13718 original size:22 final size:22
Alignment explanation
Indices: 13692--13734 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
13682 AAATAAATTA
13692 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
13714 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
13735 CAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:13766 original size:86 final size:85
Alignment explanation
Indices: 13660--13900 Score: 393
Period size: 86 Copynumber: 2.9 Consensus size: 85
13650 CAATCCATAT
13660 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACAAATAAATTA-TTAAAATAAATCAATCCATATTTTAAAATAAA
13725 TCAATCCATACAAATAAATTA
65 TCAATCCATACAAATAAATTA
*
13746 TTTAAAATAAATCAATCCATACTAATAAATTATATAAAATAAATCAATCCATATTTTAAAATAAA
1 TTTAAAATAAATCAATCCATACAAATAAATTAT-TAAAATAAATCAATCCATATTTTAAAATAAA
*
13811 TCAATCCATACTAATAAATTA
65 TCAATCCATACAAATAAATTA
* *
13832 TTTAAAATAAATCAATCCATACAACTACA--A-T--AATAAATCAATCCATATTTTAAAATAAAT
1 TTTAAAATAAATCAATCCATACAAATAAATTATTAAAATAAATCAATCCATATTTTAAAATAAAT
13892 CAATCCATA
66 CAATCCATA
13901 TTTTAAAATA
Statistics
Matches: 149, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
80 38 0.26
82 1 0.01
84 1 0.01
85 1 0.01
86 108 0.72
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (85 bp):
TTTAAAATAAATCAATCCATACAAATAAATTATTAAAATAAATCAATCCATATTTTAAAATAAAT
CAATCCATACAAATAAATTA
Found at i:13829 original size:22 final size:22
Alignment explanation
Indices: 13779--13828 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
13769 AATAAATTAT
*
13779 ATAAAATAAATCAATCCATATT
1 ATAAAATAAATCAATCCATATA
*
13801 TTAAAATAAATCAATCCATACTA
1 ATAAAATAAATCAATCCATA-TA
13824 ATAAA
1 ATAAA
13829 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAAATAAATCAATCCATATA
Found at i:13888 original size:22 final size:22
Alignment explanation
Indices: 13863--14004 Score: 158
Period size: 22 Copynumber: 6.3 Consensus size: 22
13853 CAACTACAAT
13863 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
13885 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
*
13907 AATAAATCAATTCATATTTTAA
1 AATAAATCAATCCATATTTTAA
**
13929 AATAAATCAATCCATACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * ** *
13952 ATTATTTAAAATAAATTATTTAAA
1 AATAAAT-CAATCCA-TATTTTAA
*
13976 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
13998 AATAAAT
1 AATAAAT
14005 TATTTAAAAA
Statistics
Matches: 96, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
22 71 0.74
23 12 0.12
24 11 0.11
25 2 0.02
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:13966 original size:14 final size:15
Alignment explanation
Indices: 13947--13982 Score: 65
Period size: 14 Copynumber: 2.5 Consensus size: 15
13937 AATCCATACT
13947 AATAAATTATTT-AA
1 AATAAATTATTTAAA
13961 AATAAATTATTTAAA
1 AATAAATTATTTAAA
13976 AATAAAT
1 AATAAAT
13983 CAATCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AATAAATTATTTAAA
Found at i:15472 original size:20 final size:21
Alignment explanation
Indices: 15447--15485 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
15437 CAGACTTTAT
*
15447 TTTCAAAA-TACAAAATGATA
1 TTTCAAAATTAAAAAATGATA
15467 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
15486 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:19302 original size:23 final size:23
Alignment explanation
Indices: 19272--19347 Score: 75
Period size: 23 Copynumber: 3.4 Consensus size: 23
19262 TTGTGCATAA
19272 TGCATCGATACATCCCTTGAATG
1 TGCATCGATACATCCCTTGAATG
* * *
19295 TGCGTCGATAC--CCCATGAAGG
1 TGCATCGATACATCCCTTGAATG
* * *
19316 TGCACCGATGCATTCCTTGAATG
1 TGCATCGATACATCCCTTGAATG
*
19339 TGCACCGAT
1 TGCATCGAT
19348 GCACTCTGCT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
21 16 0.38
23 26 0.62
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (23 bp):
TGCATCGATACATCCCTTGAATG
Found at i:21334 original size:2 final size:2
Alignment explanation
Indices: 21327--21406 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
21317 ATTGAACTTA
21327 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
21369 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
21407 GTTTTGGTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22104 original size:19 final size:19
Alignment explanation
Indices: 22080--22133 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
22070 CAAATGTAAT
22080 TAGTGTACCGATGCACCCC
1 TAGTGTACCGATGCACCCC
* *
22099 TAGTGTACCGATGAACTCC
1 TAGTGTACCGATGCACCCC
22118 TAGTGTACCGATGCAC
1 TAGTGTACCGATGCAC
22134 TAAGTCTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (19 bp):
TAGTGTACCGATGCACCCC
Found at i:22370 original size:14 final size:14
Alignment explanation
Indices: 22353--22385 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
22343 TAAGAAGAAT
22353 TGAGAGAGAATCAA
1 TGAGAGAGAATCAA
22367 TGAGAGAGAATCAA
1 TGAGAGAGAATCAA
*
22381 AGAGA
1 TGAGA
22386 AAGCATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.30, T:0.12
Consensus pattern (14 bp):
TGAGAGAGAATCAA
Found at i:28255 original size:15 final size:16
Alignment explanation
Indices: 28227--28256 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28217 ATCAGTTATA
28227 TGTTTTACTTTATTTC
1 TGTTTTACTTTATTTC
28243 TGTTTTA-TTTATTT
1 TGTTTTACTTTATTT
28257 ATTGTAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (16 bp):
TGTTTTACTTTATTTC
Found at i:35986 original size:28 final size:27
Alignment explanation
Indices: 35940--36006 Score: 100
Period size: 28 Copynumber: 2.5 Consensus size: 27
35930 ACTGAAATGT
35940 TCCTCTATCAATTTCCTTTGCAATTGC
1 TCCTCTATCAATTTCCTTTGCAATTGC
* *
35967 TCGCTCTATCAATTTTCTTTGCAATTTC
1 TC-CTCTATCAATTTCCTTTGCAATTGC
35995 TCC-CTATCAATT
1 TCCTCTATCAATT
36007 GCACTCTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
26 9 0.24
27 3 0.08
28 25 0.68
ACGTcount: A:0.19, C:0.28, G:0.06, T:0.46
Consensus pattern (27 bp):
TCCTCTATCAATTTCCTTTGCAATTGC
Found at i:42136 original size:21 final size:21
Alignment explanation
Indices: 42103--42157 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
42093 ACGTAAATAC
* *
42103 TATTTAATTTAATAT-TTTAT
1 TATTTAAATTAATATATATAT
42123 TATTTCAAATTAATTATATATAT
1 TATTT-AAATTAA-TATATATAT
42146 TA-TTAAATTAAT
1 TATTTAAATTAAT
42158 TAATTAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 6 0.20
21 13 0.43
22 5 0.17
23 6 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTAAATTAATATATATAT
Found at i:42415 original size:24 final size:24
Alignment explanation
Indices: 42360--42415 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
42350 GAAATAAAGT
* *
42360 GCCATTCTCTTCAACCTTTCTGCT
1 GCCATTCTCTTCAACCTTTCCGCC
*
42384 GCCATTCTCTTCAACTTTTCCGCC
1 GCCATTCTCTTCAACCTTTCCGCC
*
42408 GCCGTTCT
1 GCCATTCT
42416 ACTGCACCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.11, C:0.39, G:0.11, T:0.39
Consensus pattern (24 bp):
GCCATTCTCTTCAACCTTTCCGCC
Done.