Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005630.1 Hibiscus syriacus cultivar Beakdansim tig00013121_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: 86266
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:2921 original size:21 final size:22
Alignment explanation
Indices: 2890--2931 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
2880 TCAGAAAATT
*
2890 AAATAAAAAAATATATTATTAA
1 AAATAAAAAAATAAATTATTAA
2912 AAAT-AAAAAATAAATTATTA
1 AAATAAAAAAATAAATTATTA
2932 TTATTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATAAAAAAATAAATTATTAA
Found at i:3527 original size:21 final size:21
Alignment explanation
Indices: 3503--3572 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
3493 AGAAGTATTG
* *
3503 ATACTGCCTTATGCAGTACCA
1 ATACTCCCTTAGGCAGTACCA
*
3524 ATACACCCTTAGGCAGTACCA
1 ATACTCCCTTAGGCAGTACCA
* *
3545 ATACCCCCTTAGGCAATACCA
1 ATACTCCCTTAGGCAGTACCA
3566 ATACTCC
1 ATACTCC
3573 ATATTCTAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.31, C:0.34, G:0.11, T:0.23
Consensus pattern (21 bp):
ATACTCCCTTAGGCAGTACCA
Found at i:4655 original size:22 final size:24
Alignment explanation
Indices: 4620--4664 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
4610 GTTTTAACTC
4620 AATATTAATTCCTAATAA-ATAATA
1 AATATTAATTCCTAA-AAGATAATA
4644 AATA-TAA-TCCTAAAAGATAAT
1 AATATTAATTCCTAAAAGATAAT
4665 GCATCATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.10
22 11 0.55
23 3 0.15
24 4 0.20
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.33
Consensus pattern (24 bp):
AATATTAATTCCTAAAAGATAATA
Found at i:9706 original size:12 final size:12
Alignment explanation
Indices: 9689--9725 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
9679 GTTACAGTCG
9689 GAGGAGATGAAC
1 GAGGAGATGAAC
9701 GAGGAGATGAAC
1 GAGGAGATGAAC
9713 GAGGAGATGAAC
1 GAGGAGATGAAC
9725 G
1 G
9726 GGGAAGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.43, T:0.08
Consensus pattern (12 bp):
GAGGAGATGAAC
Found at i:14912 original size:12 final size:12
Alignment explanation
Indices: 14895--14919 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14885 GTTACAATTG
14895 GAGGAGATGAAC
1 GAGGAGATGAAC
14907 GAGGAGATGAAC
1 GAGGAGATGAAC
14919 G
1 G
14920 GGGAAGAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGGAGATGAAC
Found at i:36044 original size:17 final size:15
Alignment explanation
Indices: 36004--36032 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35994 GACTGTAATA
36004 TAAAATATTATAAAT
1 TAAAATATTATAAAT
36019 TAAAATATTATAAA
1 TAAAATATTATAAA
36033 AATTATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATTATAAAT
Found at i:36127 original size:37 final size:39
Alignment explanation
Indices: 36077--36155 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 39
36067 TGTCACATTT
*
36077 TTTTATAACA-TTTTCAATT-ATAATCTAAAATGTTATA
1 TTTTATAACATTTTTCAATTAATAATCGAAAATGTTATA
* **
36114 TTTTATAATATTTTTTTTATTAATAATCGAAAATGTTATA
1 TTTTATAACA-TTTTTCAATTAATAATCGAAAATGTTATA
36154 TT
1 TT
36156 ATTTGTAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 9 0.26
39 7 0.20
40 19 0.54
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.53
Consensus pattern (39 bp):
TTTTATAACATTTTTCAATTAATAATCGAAAATGTTATA
Found at i:46601 original size:43 final size:44
Alignment explanation
Indices: 46526--46664 Score: 210
Period size: 44 Copynumber: 3.2 Consensus size: 44
46516 AAATGAATGT
* *
46526 ATAATTGAAAATGCATAACAGTGCATTATTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
46570 ATAAATGAAAATGCATAA-GGTGCATTATTGGCAG-AATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATG-TGCC
* *
46613 ATAAATGAAAATGCATAACGATGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
*
46657 ACAAATGA
1 ATAAATGA
46665 CACTTAAATG
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
42 4 0.05
43 37 0.43
44 43 0.49
45 3 0.03
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
Found at i:47061 original size:44 final size:44
Alignment explanation
Indices: 47011--47275 Score: 379
Period size: 44 Copynumber: 6.0 Consensus size: 44
47001 AAATGAATGA
* * *
47011 ATAAATGAAAATGCATAACGGTGCATTATTGGCAAAAAAGTACT
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGCC
* * *
47055 ATAAATGAAAATGCATAACGGTGCATTTTTGGCAGAAATGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGCC
* *
47099 ATAAATGAAAATGCTTAACGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGCC
* * *
47143 GTAAATGAAAATGCATAATGGTGCATTATTGGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGCC
* * * *
47187 ATAAATGAAAATGCATAACAGTACATTATTGGTAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGCC
47231 ATAAATGAAAATGCATAACGGTGCATT-TTGGCAGAAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAA-GTGCC
47275 A
1 A
47276 CCCCTGGTTT
Statistics
Matches: 197, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
43 9 0.05
44 188 0.95
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAAGTGCC
Found at i:52635 original size:8 final size:8
Alignment explanation
Indices: 52622--52648 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
52612 ACCAATTAGT
52622 AAGAATGA
1 AAGAATGA
52630 AAGAATGA
1 AAGAATGA
52638 AAGAATGA
1 AAGAATGA
52646 AAG
1 AAG
52649 GGTTATTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (8 bp):
AAGAATGA
Found at i:53977 original size:44 final size:44
Alignment explanation
Indices: 53864--54122 Score: 303
Period size: 44 Copynumber: 5.9 Consensus size: 44
53854 AAATGAATGA
** *
53864 ATAAATGAAAATGCATAACATTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
* * *
53908 ATAAA--AAAATGCATAACGTTGCATTATCGGCAGAAATGTACC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
* * *
53950 ATAAATGAAAATGCATAACGGTACATTATTGGCAAAAATGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
* *
53994 ATAAATGAAAATGCATAATGGTGCATTATTAGG-AGAAATGTGCT
1 ATAAATGAAAATGCATAACGGTGCATTATT-GGCAGAAATGTGCC
*
54038 ATAAATGAAAATGCATAACGGTGCATT-TTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
* *
54081 ACAAATGAAACTTAAATGCATAACGGTGTATT-TTGGCAGAAA
1 ATAAATG--A---AAATGCATAACGGTGCATTATTGGCAGAAA
54123 GTTTAACTGA
Statistics
Matches: 186, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
42 40 0.22
43 17 0.09
44 98 0.53
45 3 0.02
48 28 0.15
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAATGTGCC
Found at i:61309 original size:7 final size:7
Alignment explanation
Indices: 61299--61336 Score: 53
Period size: 6 Copynumber: 5.6 Consensus size: 7
61289 CTAAAAAAAT
61299 AAAAAG-
1 AAAAAGA
61305 AAAAAG-
1 AAAAAGA
61311 AAAAAGA
1 AAAAAGA
61318 AAAAAGAA
1 AAAAAG-A
61326 AAAAAGA
1 AAAAAGA
61333 AAAA
1 AAAA
61337 TACTAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.40
7 11 0.37
8 7 0.23
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:61336 original size:6 final size:6
Alignment explanation
Indices: 61293--61328 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
61283 AAGGAACTAA
*
61293 AAAAAT AAAAAG AAAAAG AAAAAG AAAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAA
61329 AAGAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:61493 original size:23 final size:23
Alignment explanation
Indices: 61447--61528 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 23
61437 ATGAAAAAAT
61447 AATAAAATTAAAAACTAAAA-AATAG
1 AATAAAA-T-AAAA-TAAAATAATAG
61472 AATAAAATAAAATAAAATAATAG
1 AATAAAATAAAATAAAATAATAG
* * *
61495 AATTAAATTAAATTAAATAAATA-
1 AATAAAATAAAATAAAAT-AATAG
61518 AA-AAAATAAAA
1 AATAAAATAAAA
61529 AACATAAACA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
22 12 0.24
23 26 0.52
24 5 0.10
25 7 0.14
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.23
Consensus pattern (23 bp):
AATAAAATAAAATAAAATAATAG
Found at i:62658 original size:65 final size:64
Alignment explanation
Indices: 62517--62672 Score: 197
Period size: 65 Copynumber: 2.4 Consensus size: 64
62507 TACACTAGGG
* * * * *
62517 GTGCATTGGTACACTAATTACATTCGATGTTTCAAAGAGCCAGGAGTTCATCGATGCATGGTCT
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAGAGCCAAGAGTGCATCGATGCATGGTCT
* * * **
62581 GTGCATCAGTACACAAAATGCATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGG-CT
1 GTGCATCGGTACACTAAATGCATTCGATGTTTC-AAAGAGCCAAGAGTGCATCGATGCATGGTC-
62645 T
64 T
62646 GTGCATCGGTACACTAAATGCATTCGA
1 GTGCATCGGTACACTAAATGCATTCGA
62673 AATGGAGTGC
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 29 0.37
65 49 0.63
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAGAGCCAAGAGTGCATCGATGCATGGTCT
Found at i:62713 original size:20 final size:20
Alignment explanation
Indices: 62674--62713 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
62664 TGCATTCGAA
*
62674 ATGGAGTGCATCGATGCATC
1 ATGGAGTGCATCGATACATC
*
62694 ATGGAGTGCATCGGTACATC
1 ATGGAGTGCATCGATACATC
62714 CCTACATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (20 bp):
ATGGAGTGCATCGATACATC
Found at i:63363 original size:13 final size:13
Alignment explanation
Indices: 63345--63370 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63335 AGCATTTAAG
63345 TTCAAACATCCAA
1 TTCAAACATCCAA
63358 TTCAAACATCCAA
1 TTCAAACATCCAA
63371 ATCATCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (13 bp):
TTCAAACATCCAA
Found at i:63386 original size:69 final size:69
Alignment explanation
Indices: 63308--63455 Score: 296
Period size: 69 Copynumber: 2.1 Consensus size: 69
63298 GTCAAGTTGA
63308 AAATTCAAACCAAACCAAATATATATAAGCATTTAAGTTCAAACATCCAATTCAAACATCCAAAT
1 AAATTCAAACCAAACCAAATATATATAAGCATTTAAGTTCAAACATCCAATTCAAACATCCAAAT
63373 CATC
66 CATC
63377 AAATTCAAACCAAACCAAATATATATAAGCATTTAAGTTCAAACATCCAATTCAAACATCCAAAT
1 AAATTCAAACCAAACCAAATATATATAAGCATTTAAGTTCAAACATCCAATTCAAACATCCAAAT
63442 CATC
66 CATC
63446 AAATTCAAAC
1 AAATTCAAAC
63456 AATCTAAAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 79 1.00
ACGTcount: A:0.50, C:0.23, G:0.03, T:0.24
Consensus pattern (69 bp):
AAATTCAAACCAAACCAAATATATATAAGCATTTAAGTTCAAACATCCAATTCAAACATCCAAAT
CATC
Found at i:63432 original size:13 final size:13
Alignment explanation
Indices: 63414--63439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63404 AGCATTTAAG
63414 TTCAAACATCCAA
1 TTCAAACATCCAA
63427 TTCAAACATCCAA
1 TTCAAACATCCAA
63440 ATCATCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (13 bp):
TTCAAACATCCAA
Found at i:63445 original size:22 final size:21
Alignment explanation
Indices: 63416--63456 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
63406 CATTTAAGTT
*
63416 CAAACATCCAATTCAAACATC
1 CAAACATCAAATTCAAACATC
63437 CAAATCATCAAATTCAAACA
1 CAAA-CATCAAATTCAAACA
63457 ATCTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (21 bp):
CAAACATCAAATTCAAACATC
Found at i:65464 original size:23 final size:22
Alignment explanation
Indices: 65374--65464 Score: 73
Period size: 23 Copynumber: 4.2 Consensus size: 22
65364 CGACGAGGGT
*
65374 ATCGATGCACA-TCAGAG-TGC
1 ATCGATGCACATTCAGGGATGC
* *
65394 ATCGATGCACATTCAAGGAATAC
1 ATCGATGCACATTC-AGGGATGC
* * *
65417 ATCGGTGCATC-TTCA-TGATGT
1 ATCGATGCA-CATTCAGGGATGC
65438 ATCGATGCACATTCAAGGGATGC
1 ATCGATGCACATTC-AGGGATGC
65461 ATCG
1 ATCG
65465 GTATACTGTC
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
20 12 0.23
21 15 0.28
22 4 0.08
23 21 0.40
24 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (22 bp):
ATCGATGCACATTCAGGGATGC
Found at i:68136 original size:22 final size:22
Alignment explanation
Indices: 68111--68161 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
68101 TTAGTACTTA
68111 AAAATAGAACCCAAGTATATCT
1 AAAATAGAACCCAAGTATATCT
68133 AAAATAGAACCCAAGTATATCT
1 AAAATAGAACCCAAGTATATCT
*
68155 AGAATAG
1 AAAATAG
68162 TCATCTACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.22
Consensus pattern (22 bp):
AAAATAGAACCCAAGTATATCT
Found at i:71332 original size:64 final size:65
Alignment explanation
Indices: 71243--71398 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
71233 TACACTAGGG
* * *
71243 GTGCATCGGTACACTAATTACATTCGATGTTTC-AAAGAGCCAGGAGTGCATCGATGCATGG-TC
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCT-
71306 T
65 T
* * * **
71307 GTGCATCGGTACACAAAATGTATTCGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
71372 GTGCATCGGTACACTAAATGCATTCGA
1 GTGCATCGGTACACTAAATGCATTCGA
71399 AATGGAGTGA
Statistics
Matches: 80, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 29 0.36
65 50 0.62
66 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTT
Found at i:72056 original size:22 final size:22
Alignment explanation
Indices: 72028--72069 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
72018 ATGACTCGGG
72028 GAGGCTAGATTTAGGATCGACC
1 GAGGCTAGATTTAGGATCGACC
72050 GAGGCTAGATTTAGGATCGA
1 GAGGCTAGATTTAGGATCGA
72070 AAACCTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.14, G:0.33, T:0.24
Consensus pattern (22 bp):
GAGGCTAGATTTAGGATCGACC
Found at i:72821 original size:23 final size:23
Alignment explanation
Indices: 72779--72836 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
72769 ATAATTAAAG
* *
72779 TATATAACATAGTACATATACAC
1 TATATAATATAATACATATACAC
* *
72802 TATATAATATAATACGTATATAC
1 TATATAATATAATACATATACAC
*
72825 TATATACTATAA
1 TATATAATATAA
72837 ATAATAACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (23 bp):
TATATAATATAATACATATACAC
Found at i:85072 original size:5 final size:5
Alignment explanation
Indices: 85051--85093 Score: 54
Period size: 5 Copynumber: 9.0 Consensus size: 5
85041 TAAAAACTGA
* *
85051 AAAAT AGAAT CAAAT AAAAT --AAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
85094 TATAACATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
5 29 0.91
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:85077 original size:23 final size:23
Alignment explanation
Indices: 85051--85104 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
85041 TAAAAACTGA
* *
85051 AAAATAGAATCAAATAAAATAAT
1 AAAATAAAATAAAATAAAATAAT
*
85074 AAAATAAAATAAAATAAAATTAT
1 AAAATAAAATAAAATAAAATAAT
*
85097 AACATAAA
1 AAAATAAA
85105 CAAAACACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAAAATAAAATAAAATAAT
Found at i:85104 original size:18 final size:18
Alignment explanation
Indices: 85025--85090 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 18
85015 GATAGAAAAT
85025 ATAAATATAATAAAAGTAAAA
1 ATAAA-ATAATAAAA-T-AAA
* * *
85046 ACTGAAA-AATAGAATCAA
1 A-TAAAATAATAAAATAAA
85064 ATAAAATAATAAAATAAA
1 ATAAAATAATAAAATAAA
85082 ATAAAATAA
1 ATAAAATAA
85091 AATTATAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
17 4 0.11
18 21 0.57
19 1 0.03
20 6 0.16
21 2 0.05
22 3 0.08
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (18 bp):
ATAAAATAATAAAATAAA
Found at i:85140 original size:2 final size:2
Alignment explanation
Indices: 85135--85167 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
85125 AAATGAGATA
85135 AT 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 AT A
85168 AATAAAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.