Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003181.1 Hibiscus syriacus cultivar Beakdansim tig00006696_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: 47668
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1282 original size:14 final size:14
Alignment explanation
Indices: 1263--1291 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1253 GCCATACATC
1263 ACAGGTAAAAGAAG
1 ACAGGTAAAAGAAG
1277 ACAGGTAAAAGAAG
1 ACAGGTAAAAGAAG
1291 A
1 A
1292 TACTTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.28, T:0.07
Consensus pattern (14 bp):
ACAGGTAAAAGAAG
Found at i:6881 original size:20 final size:19
Alignment explanation
Indices: 6852--6906 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
6842 AAATGACCAA
6852 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGATCT
* *
6871 CAAATTTCGCAACTG-AATTT
1 CAAA-TTCGCAAC-GCGATCT
6891 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
6907 ATTTAATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.03
19 13 0.43
20 15 0.50
21 1 0.03
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.24
Consensus pattern (19 bp):
CAAATTCGCAACGCGATCT
Found at i:6908 original size:20 final size:20
Alignment explanation
Indices: 6852--6921 Score: 83
Period size: 19 Copynumber: 3.6 Consensus size: 20
6842 AAATGACCAA
*
6852 CAAATTCGCAACGCG-ATCT
1 CAAATTCGCAACGCGAATTT
*
6871 CAAATTTCGCAAC-TGAATTT
1 CAAA-TTCGCAACGCGAATTT
6891 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
6911 -AATTTCGCAAC
1 CAAATTCGCAAC
6922 AGGTTTTAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
19 23 0.52
20 21 0.48
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:7685 original size:12 final size:12
Alignment explanation
Indices: 7664--7697 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
7654 ACCACATTTC
*
7664 CAATACCAAACA
1 CAATATCAAACA
7676 CAATATCAAACA
1 CAATATCAAACA
*
7688 CAATCTCAAA
1 CAATATCAAA
7698 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:7850 original size:24 final size:24
Alignment explanation
Indices: 7823--7876 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
7813 GTATTCGAAA
7823 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
7847 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
7871 TTTGAT
1 TTTGAT
7877 GATGTGATGG
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:10148 original size:6 final size:6
Alignment explanation
Indices: 10137--10171 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
10127 AAGAAAAAGG
* *
10137 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
10172 CCATTCCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:10653 original size:25 final size:25
Alignment explanation
Indices: 10615--10666 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
10605 AAATCAATTA
*
10615 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
10640 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
10665 AA
1 AA
10667 AAAATAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:11072 original size:18 final size:18
Alignment explanation
Indices: 11051--11087 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11041 GTAATTGGAG
11051 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
11069 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
11087 T
1 T
11088 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:11094 original size:24 final size:24
Alignment explanation
Indices: 11043--11095 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
11033 TTTCATATGT
* * *
11043 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
11067 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
11091 AATTT
1 AATTT
11096 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:11443 original size:39 final size:39
Alignment explanation
Indices: 11400--11486 Score: 138
Period size: 39 Copynumber: 2.2 Consensus size: 39
11390 TCTGATGCTC
*
11400 ATCAAAATCCAAAGCTCATATGGTGCCAAGGAAAAGAAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
* * *
11439 ATCAAAATCCAAATCTTATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
11478 ATCAAAATC
1 ATCAAAATC
11487 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGAAA
Found at i:11867 original size:66 final size:60
Alignment explanation
Indices: 11787--11926 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 60
11777 TTTTAGAAAC
*
11787 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT----AAGC-AAAAAATAAATCTTATTTACAAATC-AATT
11852 A
60 A
* * *
11853 AACAAATCAACTTTTACAAATCAATTAATCAAAAAATAAATCTTATTTCCACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
11913 AACAAATCAACTTT
1 AACAAATCAACTTT
11927 CAATGTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 19 0.27
61 22 0.31
62 3 0.04
66 26 0.37
ACGTcount: A:0.52, C:0.17, G:0.01, T:0.30
Consensus pattern (60 bp):
AACAAATCAACTTTTACAAATCAATTAAGCAAAAAATAAATCTTATTTACAAATCAATTA
Found at i:13325 original size:21 final size:21
Alignment explanation
Indices: 13301--13396 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
13291 GACAGGACTA
*
13301 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
13322 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
* **
13343 CTTTG-ATGATGAGAGTTGCCT
1 C-TTGAACGATGAGAGGGGCCT
*
13364 CTTGAACGAT-AGGAGGTGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
13385 CTTGAATGATGA
1 CTTGAACGATGA
13397 TAGGTGCATC
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 4 0.07
21 50 0.86
22 4 0.07
ACGTcount: A:0.22, C:0.17, G:0.34, T:0.27
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:13572 original size:4 final size:4
Alignment explanation
Indices: 13540--13589 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
13530 GGGCCGCTGA
* * * *
13540 AAAT AAAT TAAT ATAT AAAT CATT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
13588 AA
1 AA
13590 TGCTGAAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:14418 original size:16 final size:16
Alignment explanation
Indices: 14397--14431 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
14387 TAAATATCCA
14397 AATCTACAAACAATAT
1 AATCTACAAACAATAT
14413 AATCTACAAACAATAT
1 AATCTACAAACAATAT
14429 AAT
1 AAT
14432 AAACAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (16 bp):
AATCTACAAACAATAT
Found at i:14437 original size:16 final size:16
Alignment explanation
Indices: 14402--14440 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
14392 ATCCAAATCT
**
14402 ACAAACAATATAATCT
1 ACAAACAATATAATAA
14418 ACAAACAATATAATAA
1 ACAAACAATATAATAA
14434 ACAAACA
1 ACAAACA
14441 TTAGTAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (16 bp):
ACAAACAATATAATAA
Found at i:16112 original size:20 final size:20
Alignment explanation
Indices: 16087--16191 Score: 108
Period size: 20 Copynumber: 5.2 Consensus size: 20
16077 GCGTAAAAAC
16087 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
16107 ATTTGACTATCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
16127 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
* * *
16146 ATTT-ACAAATTCACGTTACGA
1 ATTTGAC--TTTCGCGTTGCGA
16167 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
16187 ATTTG
1 ATTTG
16192 GAAAATCGCA
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.03
19 6 0.09
20 53 0.76
21 7 0.10
22 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:16264 original size:20 final size:20
Alignment explanation
Indices: 16215--16268 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
16205 CGGTTTACAT
*
16215 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTAGA
* *
16235 A-ACTGGGTTGCGAAATTAGA
1 ATTC-GCGTTGCGAAATTAGA
16255 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
16269 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTAGA
Found at i:18292 original size:60 final size:60
Alignment explanation
Indices: 18197--18377 Score: 197
Period size: 60 Copynumber: 3.0 Consensus size: 60
18187 ATTATATGTT
*
18197 CTCAAACTATGA-TTCTCATTTTAAATTAGTTCTTAAACTTTTGAATATTCCAATTTCATC
1 CTCAAACTATGACTT-TCATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATC
** * * * *
18257 CTCAAACTATGACTTTTGTTTTAAATTAGTCCTTAAACTTTTAAATGTTCCAATGTAATC
1 CTCAAACTATGACTTTCATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATC
** * * * *
18317 GC-CAAACTATGACCCTCATTCTAGATTGGTACC-CAAACTTTTGAATATTCCAATTTCATC
1 -CTCAAACTATGACTTTCATTTTAAATTAGT-CCTTAAACTTTTGAATATTCCAATTTCATC
18377 C
1 C
18378 CCACATTTAT
Statistics
Matches: 99, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
59 1 0.01
60 93 0.94
61 5 0.05
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (60 bp):
CTCAAACTATGACTTTCATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATC
Found at i:18587 original size:60 final size:60
Alignment explanation
Indices: 18517--18656 Score: 151
Period size: 60 Copynumber: 2.4 Consensus size: 60
18507 ATTTAGAATT
* *
18517 AAGA-TCATAGTTTGAGGATGAAAATGAAATCTTCAAAAGTTT-GAGGATTAATGTAGAAA
1 AAGAGTCATAGTTTGAGGATGAAAATGAAATATTCAAAAGTTTAG-GGATTAATATAGAAA
* * * * ** *
18576 AATAGTCATAGTTT-AGGGATGAAATTGAATTATTTAAAAGTTTAGGGATTGGTATAGAAT
1 AAGAGTCATAGTTTGA-GGATGAAAATGAAATATTCAAAAGTTTAGGGATTAATATAGAAA
*
18636 AAGAGTCATAATTTGAGGATG
1 AAGAGTCATAGTTTGAGGATG
18657 CTTTTGCAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
59 4 0.06
60 60 0.91
61 2 0.03
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.32
Consensus pattern (60 bp):
AAGAGTCATAGTTTGAGGATGAAAATGAAATATTCAAAAGTTTAGGGATTAATATAGAAA
Found at i:18814 original size:29 final size:30
Alignment explanation
Indices: 18753--18821 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
18743 ACCAAAAATA
*
18753 ATTTTTTTGTAACAATAAGGATCTAAAATT
1 ATTTTTTTGTAACAATAAGGATCTAAAAGT
* *
18783 ATTTTTTTGTCAA-AATAAGTA-CTTAAAGT
1 ATTTTTTTGT-AACAATAAGGATCTAAAAGT
*
18812 ATTATTTTGT
1 ATTTTTTTGT
18822 TGCAATAGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.44
30 17 0.50
31 2 0.06
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (30 bp):
ATTTTTTTGTAACAATAAGGATCTAAAAGT
Found at i:22413 original size:20 final size:20
Alignment explanation
Indices: 22385--22423 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
22375 CAATAAATTA
22385 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
*
22405 ATTGGTGCATCGATGCATG
1 ATTGATGCATCGATGCATG
22424 CCCTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:23103 original size:15 final size:15
Alignment explanation
Indices: 23069--23103 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
23059 AAATAAAAGT
*
23069 TCAAATATCCATCAA
1 TCAAATATCCAACAA
*
23084 ACAAATATCCAACAA
1 TCAAATATCCAACAA
23099 TCAAA
1 TCAAA
23104 GAAAGACAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (15 bp):
TCAAATATCCAACAA
Found at i:31038 original size:19 final size:20
Alignment explanation
Indices: 30995--31048 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
30985 AAAAGCCTGA
30995 GTGCATCGATGCATAGTATT
1 GTGCATCGATGCATAGTATT
*
31015 GTGCATCGATGCATGGTA-T
1 GTGCATCGATGCATAGTATT
31034 GTGCATCGATGCATA
1 GTGCATCGATGCATA
31049 AAATGCATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATAGTATT
Found at i:31084 original size:84 final size:83
Alignment explanation
Indices: 30950--31113 Score: 217
Period size: 84 Copynumber: 2.0 Consensus size: 83
30940 TGCACTAAGA
** *
30950 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAAAAGCCTGAGTGCATCGATGCATAGTATT
1 GTGCATCGATGCATAAAATGCATTCGATGTTAAGAAAAA-CCTGAGTGCATCGATGCAT-GGATT
31015 -GTGCATCGATGCATGGTAT
64 GGTGCATCGATGCATGGTAT
*
31034 GTGCATCGATGCATAAAATGCATTCGATGTTCAAGAAATTAA-TTGA-TGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTT-AAGAAA--AACCTGAGTGCATCGATGCATGGAT
*
31097 TGGTGCATCGGTGCATG
63 TGGTGCATCGATGCATG
31114 CCCTTGAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
83 4 0.06
84 58 0.82
85 7 0.10
87 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (83 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTAAGAAAAACCTGAGTGCATCGATGCATGGATTGG
TGCATCGATGCATGGTAT
Found at i:31103 original size:20 final size:20
Alignment explanation
Indices: 31075--31113 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31065 CAAGAAATTA
31075 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
31095 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
31114 CCCTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:32548 original size:30 final size:31
Alignment explanation
Indices: 32514--32593 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
32504 CATCGTTAGA
*
32514 TTTTAATAATTGTAATAT-TTTTATGTAATG
1 TTTTAATAATTGTAATATGTTTAATGTAATG
* * *
32544 TTTTAATATTTCT-TTATGTTTAATGTAATG
1 TTTTAATAATTGTAATATGTTTAATGTAATG
32574 TTTT--TAATTG-AATATAGTTT
1 TTTTAATAATTGTAATAT-GTTT
32594 TTTATTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
28 7 0.17
29 7 0.17
30 26 0.65
ACGTcount: A:0.30, C:0.01, G:0.10, T:0.59
Consensus pattern (31 bp):
TTTTAATAATTGTAATATGTTTAATGTAATG
Found at i:33501 original size:33 final size:35
Alignment explanation
Indices: 33464--33542 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 35
33454 AGATTTTATT
*
33464 TAATGTTTAAGG-T-TTGTTTTTATCTCCTTAACG
1 TAATGTGTAAGGTTGTTGTTTTTATCTCCTTAACG
*
33497 TAATGTGTAAGGTTTGTTGTTTTTATCTCCTTAATG
1 TAATGTGTAAGG-TTGTTGTTTTTATCTCCTTAACG
*
33533 TAATATGTAA
1 TAATGTGTAA
33543 TATGGTAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
33 11 0.28
35 1 0.03
36 28 0.70
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (35 bp):
TAATGTGTAAGGTTGTTGTTTTTATCTCCTTAACG
Found at i:35772 original size:19 final size:18
Alignment explanation
Indices: 35736--35774 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
35726 TCTTAACCTA
* *
35736 AAAAACCCTAAGTTGCTC
1 AAAAACCCTAAATGGCTC
35754 AAAAACCCTAAAATGGCTC
1 AAAAACCCT-AAATGGCTC
35773 AA
1 AA
35775 CCAACCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.18
Consensus pattern (18 bp):
AAAAACCCTAAATGGCTC
Found at i:42906 original size:80 final size:81
Alignment explanation
Indices: 42772--42933 Score: 281
Period size: 80 Copynumber: 2.0 Consensus size: 81
42762 AGAGCGGCGG
42772 CAAAGGCGTAGAGGGCCATAAAAGCCGAGTTGACAGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
1 CAAAGGCGTAGAGGGCCATAAAAGCCGAGTTGACAGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
42837 AGTATCACAACCGGAA
66 AGTATCACAACCGGAA
* * *
42853 CAAAGGCGTAGAGGGCCAT-GAAGCCTAGTTGACGGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
1 CAAAGGCGTAGAGGGCCATAAAAGCCGAGTTGACAGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
*
42917 AGTATCACAACTGGAA
66 AGTATCACAACCGGAA
42933 C
1 C
42934 GCATTGGAGG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
80 58 0.75
81 19 0.25
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.23
Consensus pattern (81 bp):
CAAAGGCGTAGAGGGCCATAAAAGCCGAGTTGACAGCCCGTTTCTTCTTTACCGTGCTCCTGTAC
AGTATCACAACCGGAA
Found at i:46116 original size:23 final size:25
Alignment explanation
Indices: 46086--46135 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 25
46076 GTTTGTATTT
46086 TTTTTTTTTA-AATT-ATTTAATTA
1 TTTTTTTTTATAATTAATTTAATTA
*
46109 -TTTTTTTTATAATTAATTTTATTA
1 TTTTTTTTTATAATTAATTTAATTA
46133 TTT
1 TTT
46136 AGTGGACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 9 0.39
23 4 0.17
24 8 0.35
25 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTTTTTTTATAATTAATTTAATTA
Found at i:46127 original size:24 final size:22
Alignment explanation
Indices: 46087--46135 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 22
46077 TTTGTATTTT
46087 TTTTTTTTAAATTATTTAATTA
1 TTTTTTTTAAATTATTTAATTA
*
46109 TTTTTTTTATAATTAATTTTATTA
1 TTTTTTTTA-AATT-ATTTAATTA
46133 TTT
1 TTT
46136 AGTGGACAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.38
23 4 0.17
24 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTTAAATTATTTAATTA
Found at i:46252 original size:20 final size:21
Alignment explanation
Indices: 46209--46252 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
46199 TTCCGTAGAC
46209 TTTTTATTTTTTAATATTATAA
1 TTTTTATTTTTTAATA-TATAA
46231 TTTTTATTTATTTAA-A-ATAA
1 TTTTTATTT-TTTAATATATAA
46251 TT
1 TT
46253 ATTCTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.29
22 10 0.48
23 5 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTTATTTTTTAATATATAA
Done.