Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006259.1 Hibiscus syriacus cultivar Beakdansim tig00014934_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: 123613
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:128 original size:22 final size:22
Alignment explanation
Indices: 102--143 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
92 TAGAGAACTG
102 AAAAATTATTATAAAA-ATATCT
1 AAAAATTATT-TAAAATATATCT
124 AAAAATTATTTAAAATATAT
1 AAAAATTATTTAAAATATAT
144 AGTAATTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAATTATTTAAAATATATCT
Found at i:797 original size:23 final size:23
Alignment explanation
Indices: 761--804 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
751 ACAAGCCTAA
** *
761 TTACAAAGGTGACCCGAAGCCAG
1 TTACAAAGCAGACCCAAAGCCAG
784 TTACAAAGCAGACCCAAAGCC
1 TTACAAAGCAGACCCAAAGCC
805 CAACAAGTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.30, G:0.20, T:0.11
Consensus pattern (23 bp):
TTACAAAGCAGACCCAAAGCCAG
Found at i:1169 original size:21 final size:21
Alignment explanation
Indices: 1145--1196 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1135 GACCTCCTTT
*
1145 GGTGAGTCATAGCTCCCCCTA
1 GGTGAGTCACAGCTCCCCCTA
1166 GGTGAGTCACAGCTCCCCCTA
1 GGTGAGTCACAGCTCCCCCTA
1187 GGTGAGTCAC
1 GGTGAGTCAC
1197 TGCCAGAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.21
Consensus pattern (21 bp):
GGTGAGTCACAGCTCCCCCTA
Found at i:3756 original size:67 final size:67
Alignment explanation
Indices: 3632--3823 Score: 215
Period size: 67 Copynumber: 2.9 Consensus size: 67
3622 AAATTCAACA
* * * ** * *
3632 TGACTTTCTCGTGAAGAGAAGTTAACCTTTGTAATTCCTAACTCCCTCGTGAGGAGGAGTCAATC
1 TGACTTTCTCGTGAAGAGAAGTTAATCTTTGTTATTCCTGACTCCCTCACGAAGAGGAGTAAATC
3697 AT
66 AT
* * * *
3699 TGACTTTCTTC-TGAAGAGAAGTCAATCTTTGTTATTCATGACTTCCTCACAAAGAGGAGTAAAT
1 TGACTTTC-TCGTGAAGAGAAGTTAATCTTTGTTATTCCTGACTCCCTCACGAAGAGGAGTAAAT
*
3763 CCT
65 CAT
* * * * *
3766 TTACTTCCTCGTGAAGAAAAGTTAATCTTTTTTATCCCTGACTCCCTCACGAAGAGGA
1 TGACTTTCTCGTGAAGAGAAGTTAATCTTTGTTATTCCTGACTCCCTCACGAAGAGGA
3824 TTAATTCCTT
Statistics
Matches: 102, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
66 2 0.02
67 98 0.96
68 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (67 bp):
TGACTTTCTCGTGAAGAGAAGTTAATCTTTGTTATTCCTGACTCCCTCACGAAGAGGAGTAAATC
AT
Found at i:3833 original size:67 final size:67
Alignment explanation
Indices: 3710--3876 Score: 183
Period size: 67 Copynumber: 2.5 Consensus size: 67
3700 GACTTTCTTC
* * * * * * *
3710 TGAAGAGAAGTCAATCTTTGTTATTCATGACTTCCTCACAAAGAGGAGTAAATCCTTTACTTCCT
1 TGAAGAAAAGTCAATCTTTTTTATCCCTGACTCCCTCACAAAGAGGAGTAAATCCTTGAATTCCT
*
3775 CG
66 CA
* * * *
3777 TGAAGAAAAGTTAATCTTTTTTATCCCTGACTCCCTCACGAAGAGGATTAATTCCTTGAATTCCT
1 TGAAGAAAAGTCAATCTTTTTTATCCCTGACTCCCTCACAAAGAGGAGTAAATCCTTGAATTCCT
3842 CA
66 CA
* *
3844 TGAA-AAGAAGTCAATTTTTTTTTATCACTGACT
1 TGAAGAA-AAGTCAA-TCTTTTTTATCCCTGACT
3877 ACCCAAAAAA
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
66 2 0.02
67 65 0.78
68 16 0.19
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (67 bp):
TGAAGAAAAGTCAATCTTTTTTATCCCTGACTCCCTCACAAAGAGGAGTAAATCCTTGAATTCCT
CA
Found at i:4012 original size:81 final size:81
Alignment explanation
Indices: 3871--4863 Score: 1100
Period size: 81 Copynumber: 12.3 Consensus size: 81
3861 TTTTTTATCA
* * * *
3871 CTGACTACCCAAAAAAGAGGAACAGATCAAGTCTAATCTCCCCTAAAGAAGAGTGGAGCAGATCT
1 CTGACTACCCGAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACCC
3936 GTCTTCCAAAATTGAT
66 GTCTTCCAAAATTGAT
* * * * * * * *
3952 CTAAATACCCAAAAAAAAAGGAACAGATCAAGTCTGATCT-CCCTAAAGAAAACTGGAGCAGTCT
1 CTGACTACCC-GAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACC
*
4016 CGTCTTCTAAAATTGAT
65 CGTCTTCCAAAATTGAT
* * * * *
4033 CTGACTACCCGATAAAGAGAAACATATCAAGACTGATCTCCCCTAAAGAAGAGTGGAGCAGACTC
1 CTGACTACCCGAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACCC
*
4098 GTCCTCCAAAATTGAT
66 GTCTTCCAAAATTGAT
* * ** *
4114 CTAACTACCCGAAAAAGAGGAACATATCAAGTCTGATCTCCCAAAAAGAAGAGTGGAGCATACCC
1 CTGACTACCCGAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACCC
4179 GTCTTCCAAAATTGAT
66 GTCTTCCAAAATTGAT
* * * * * *
4195 CTAACTACTCAAAAAAGAGGAACATATCAAGTCTGATCTCCCCTAAAGAAGAGTAGAGCAGACCT
1 CTGACTACCCGAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACCC
4260 GTCTTCCAAAATTGAT
66 GTCTTCCAAAATTGAT
* * * * * **
4276 CTAACTACCTGAAAAAGAGGAAC-GTATCAAGTCTGATGTCCCCTAAAGAAAAGTGGGGCAGAAT
1 CTGACTACCCGAAAAAGAGGAACAG-ATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACC
4340 CGTCTTCCAAAATTGAT
65 CGTCTTCCAAAATTGAT
* * * * * * * * *
4357 TTGACTTCTCGAGAAAGAGGAAAAAATCATGTCTGGTCTCCCCTAAAGAAGAGTGGAACAGACCC
1 CTGACTACCCGAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACCC
*
4422 ATCTTCCAAAATTGAT
66 GTCTTCCAAAATTGAT
* * * * * * * * *
4438 CTGACTACTCGAAAAAGGGGAACAAATTAAGTATGATATCCCCTAAATAAGAGTGGAGTAGACCT
1 CTGACTACCCGAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACCC
*
4503 GTCTTCCAAAATTAAT
66 GTCTTCCAAAATTGAT
* * * * ** * * *
4519 ATGACTACCTGAAAAAGATGAACATATCAAGTCTGATCTCCTGTAAATAAGAGTGGAGCATACAC
1 CTGACTACCCGAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACCC
* *
4584 ATCTTCCAAAATTTAT
66 GTCTTCCAAAATTGAT
*
4600 CTGACTACCC--AAAAGAGGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGAAGACC
1 CTGACTACCCGAAAAAGA-GGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACC
*
4663 CATCTTCCAAAATTGAT
65 CGTCTTCCAAAATTGAT
* * * * *
4680 CCGACTACCCG-AAAAGAGGATCAAATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAACAAACCC
1 CTGACTACCCGAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACCC
*
4744 GTCTACCAAAATTGAT
66 GTCTTCCAAAATTGAT
* * * * ** ** *
4760 CTGACGACCCGAAAAAAAAGGAATAGATTAAGTCCAATCTCCCCTAAAGAAGAGTGGAATAAACC
1 CTGACTACCCG-AAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACC
* ***
4825 CATCTTCCTTCA--GAT
65 CGTCTTCCAAAATTGAT
4840 CTGACTACCCGAAAAAGAGGAACA
1 CTGACTACCCGAAAAAGAGGAACA
4864 AATAAAGTTT
Statistics
Matches: 766, Mismatches: 138, Indels: 18
0.83 0.15 0.02
Matches are distributed among these distances:
79 17 0.02
80 164 0.21
81 507 0.66
82 78 0.10
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (81 bp):
CTGACTACCCGAAAAAGAGGAACAGATCAAGTCTGATCTCCCCTAAAGAAGAGTGGAGCAGACCC
GTCTTCCAAAATTGAT
Found at i:7933 original size:74 final size:74
Alignment explanation
Indices: 7851--7993 Score: 286
Period size: 74 Copynumber: 1.9 Consensus size: 74
7841 CGAGAGAGTT
7851 TCTTAGCTTGATTTTCATTTTTCTTGTGATATGAGAAATTATTTCATTGTCTCGGCTCAACACAT
1 TCTTAGCTTGATTTTCATTTTTCTTGTGATATGAGAAATTATTTCATTGTCTCGGCTCAACACAT
7916 CATTCATAG
66 CATTCATAG
7925 TCTTAGCTTGATTTTCATTTTTCTTGTGATATGAGAAATTATTTCATTGTCTCGGCTCAACACAT
1 TCTTAGCTTGATTTTCATTTTTCTTGTGATATGAGAAATTATTTCATTGTCTCGGCTCAACACAT
7990 CATT
66 CATT
7994 TATGGTCTCA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.45
Consensus pattern (74 bp):
TCTTAGCTTGATTTTCATTTTTCTTGTGATATGAGAAATTATTTCATTGTCTCGGCTCAACACAT
CATTCATAG
Found at i:11397 original size:27 final size:29
Alignment explanation
Indices: 11340--11398 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
11330 AAAAAGATTG
11340 AATACTTTAAATATATATTTTGATCCGAA
1 AATACTTTAAATATATATTTTGATCCGAA
*
11369 AATACTTTAAATATCTATTTTGA-CC-AA
1 AATACTTTAAATATATATTTTGATCCGAA
11396 AAT
1 AAT
11399 TGTTACTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 5 0.17
28 2 0.07
29 22 0.76
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.41
Consensus pattern (29 bp):
AATACTTTAAATATATATTTTGATCCGAA
Found at i:11764 original size:2 final size:2
Alignment explanation
Indices: 11751--11825 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
11741 TAACCTGTCA
*
11751 AT AT AC 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
11793 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
11826 ATTGGCTCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16312 original size:36 final size:36
Alignment explanation
Indices: 16271--16346 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
16261 ATTTTCGGGA
*
16271 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
16307 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
16343 TTTT
1 TTTT
16347 TTAGCTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:23975 original size:20 final size:20
Alignment explanation
Indices: 23938--23976 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23928 GAGCCCGTTA
* *
23938 GTATCAATACTGGTCTTAGG
1 GTATCAATACTCGCCTTAGG
*
23958 GTATCATTACTCGCCTTAG
1 GTATCAATACTCGCCTTAG
23977 TATCGATACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
GTATCAATACTCGCCTTAGG
Found at i:27557 original size:22 final size:22
Alignment explanation
Indices: 27532--27618 Score: 129
Period size: 22 Copynumber: 4.0 Consensus size: 22
27522 TAGCGAACAG
* *
27532 TAACTGCTACAATAAACTACAA
1 TAACTGCTACAGTAAGCTACAA
27554 TAACTGCTACAGTAAGCTACAA
1 TAACTGCTACAGTAAGCTACAA
* * *
27576 TAATTGCTATAGTAAGCTATAA
1 TAACTGCTACAGTAAGCTACAA
27598 TAACTGCTACAGTAAGCTACA
1 TAACTGCTACAGTAAGCTACA
27619 GTACCTCCGA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (22 bp):
TAACTGCTACAGTAAGCTACAA
Found at i:27572 original size:10 final size:10
Alignment explanation
Indices: 27559--27621 Score: 54
Period size: 10 Copynumber: 5.9 Consensus size: 10
27549 TACAATAACT
27559 GCTACAGTAA
1 GCTACAGTAA
*
27569 GCTACAATAA
1 GCTACAGTAA
*
27579 TTGCTATAGTAA
1 --GCTACAGTAA
* *
27591 GCTATAATAA
1 GCTACAGTAA
27601 CTGCTACAGTAA
1 --GCTACAGTAA
27613 GCTACAGTA
1 GCTACAGTA
27622 CCTCCGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
10 27 0.63
12 16 0.37
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.27
Consensus pattern (10 bp):
GCTACAGTAA
Found at i:28029 original size:45 final size:45
Alignment explanation
Indices: 27956--28080 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
27946 ATTCAATATT
*
27956 TTACCATTTATTAACCACAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTA-T-ACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * **
28003 TTACCATTTATCCCATAAGCTCGTAAGCTTATCTTACCATTATAC
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * *
28048 TTTCCA-TTATTCCATAAGCTCGTAAACTTATTT
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTT
28081 ACATGGTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 24 0.35
45 34 0.49
46 1 0.01
47 10 0.14
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.38
Consensus pattern (45 bp):
TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:35016 original size:13 final size:13
Alignment explanation
Indices: 35000--35029 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34990 GTGAACAGTG
35000 AACAGTAACAACA
1 AACAGTAACAACA
*
35013 AACAGTAACAACG
1 AACAGTAACAACA
35026 AACA
1 AACA
35030 ATGGGGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.23, G:0.10, T:0.07
Consensus pattern (13 bp):
AACAGTAACAACA
Found at i:39810 original size:22 final size:22
Alignment explanation
Indices: 39782--39866 Score: 170
Period size: 22 Copynumber: 3.9 Consensus size: 22
39772 CTATTCATTT
39782 CTACAGTAAGCTACAATAAATG
1 CTACAGTAAGCTACAATAAATG
39804 CTACAGTAAGCTACAATAAATG
1 CTACAGTAAGCTACAATAAATG
39826 CTACAGTAAGCTACAATAAATG
1 CTACAGTAAGCTACAATAAATG
39848 CTACAGTAAGCTACAATAA
1 CTACAGTAAGCTACAATAA
39867 GCTACAATAC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (22 bp):
CTACAGTAAGCTACAATAAATG
Found at i:39818 original size:10 final size:10
Alignment explanation
Indices: 39782--39875 Score: 98
Period size: 10 Copynumber: 8.8 Consensus size: 10
39772 CTATTCATTT
*
39782 CTACAGTAAG
1 CTACAATAAG
39792 CTACAATAAATG
1 CTACAAT-AA-G
*
39804 CTACAGTAAG
1 CTACAATAAG
39814 CTACAATAAATG
1 CTACAAT-AA-G
*
39826 CTACAGTAAG
1 CTACAATAAG
39836 CTACAATAAATG
1 CTACAAT-AA-G
*
39848 CTACAGTAAG
1 CTACAATAAG
39858 CTACAATAAG
1 CTACAATAAG
39868 CTACAATA
1 CTACAATA
39876 CCTCCGAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
10 38 0.54
11 12 0.17
12 21 0.30
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (10 bp):
CTACAATAAG
Found at i:40278 original size:45 final size:45
Alignment explanation
Indices: 40209--40333 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
40199 ATTCAATATT
*
40209 TTACCATTTATTAACCATAAGCTCGTAAGATTATTTTACCAAAATAC
1 TTACCATTTA-T-ACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * ** *
40256 TTACCATTTATCCCATAAGCTCGTAAGCTTATCTTACCATTATAT
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* *
40301 TTGCCA-TTATTCCATAAGCTCGTAAGCTTATTT
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTT
40334 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 25 0.36
45 33 0.48
46 1 0.01
47 10 0.14
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (45 bp):
TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:46354 original size:40 final size:40
Alignment explanation
Indices: 46298--46379 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
46288 TGCAAGTTTA
*
46298 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCAGTGTATATGGTGGGCACGACCTTATGTG
*
46338 TAATACACTTTAGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCAGTGTATATGGTGGGCACGACCTTATGTG
46378 TA
1 TA
46380 GCACTACAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCAGTGTATATGGTGGGCACGACCTTATGTG
Found at i:47150 original size:40 final size:40
Alignment explanation
Indices: 47095--47172 Score: 113
Period size: 40 Copynumber: 1.9 Consensus size: 40
47085 AAGATTTTTT
*
47095 TGAACAGTGTACAGTGTACCAATC-CACTACTACAGTAAAG
1 TGAACAATGTACAGTGTACCAA-CGCACTACTACAGTAAAG
* *
47135 TGAACAATGTACAGTGTACCGACGCACTGCTACAGTAA
1 TGAACAATGTACAGTGTACCAACGCACTACTACAGTAA
47173 CGTCAGCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.03
40 33 0.97
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (40 bp):
TGAACAATGTACAGTGTACCAACGCACTACTACAGTAAAG
Found at i:47736 original size:40 final size:40
Alignment explanation
Indices: 47692--47773 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
47682 ACCGTAGTGC
* * *
47692 TACACATAAGGTCGTGCCCGCCATATACACCGAAGTGTAT
1 TACACATAAGCTCGTGCCCACCATATACACCAAAGTGTAT
47732 TACACATAAGCTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGCTCGTGCCCACCATATACACCAAAGTGTAT
47772 TA
1 TA
47774 TAAACCTACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGCTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:51465 original size:21 final size:21
Alignment explanation
Indices: 51439--51493 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
51429 AAAATAGTTC
* * *
51439 GTCAGTATCGATATTGTGCCT
1 GTCAGTATCGATACTGAGCAT
51460 GTCAGTATCGATACTGAGCAT
1 GTCAGTATCGATACTGAGCAT
*
51481 ATCAGTATCGATA
1 GTCAGTATCGATA
51494 ATGGCCTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (21 bp):
GTCAGTATCGATACTGAGCAT
Found at i:56588 original size:44 final size:44
Alignment explanation
Indices: 56536--56623 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
56526 ACTATAAAAT
56536 CATAACCTCTTTAAAAACATAACAATAATAATAAAACCCAGATC
1 CATAACCTCTTTAAAAACATAACAATAATAATAAAACCCAGATC
56580 CATAACCTCTTTAAAAACATAACAATAATAATAAAACCCAGATC
1 CATAACCTCTTTAAAAACATAACAATAATAATAAAACCCAGATC
56624 GAGTAATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.52, C:0.23, G:0.02, T:0.23
Consensus pattern (44 bp):
CATAACCTCTTTAAAAACATAACAATAATAATAAAACCCAGATC
Found at i:58753 original size:25 final size:26
Alignment explanation
Indices: 58690--58753 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
58680 AGTTTTATTA
*
58690 AAGCTTTCTCTTTTATTTTATTTTTC
1 AAGCTTTCTTTTTTATTTTATTTTTC
* *
58716 AAGTTTTCATTTTTATTTTA-TTTTC
1 AAGCTTTCTTTTTTATTTTATTTTTC
*
58741 AAGCTTTGTTTTT
1 AAGCTTTCTTTTT
58754 AAATATGCTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 15 0.47
26 17 0.53
ACGTcount: A:0.17, C:0.11, G:0.06, T:0.66
Consensus pattern (26 bp):
AAGCTTTCTTTTTTATTTTATTTTTC
Found at i:62389 original size:36 final size:36
Alignment explanation
Indices: 62342--62412 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
62332 CTGAAGGAGG
62342 ATTTGTACCAACACGAGTTCAGAATGGATGGAGAGA
1 ATTTGTACCAACACGAGTTCAGAATGGATGGAGAGA
*
62378 ATTTGTACCAACAGGAGTTCAGAATGGATGGAGAG
1 ATTTGTACCAACACGAGTTCAGAATGGATGGAGAG
62413 TCTGCATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.30, T:0.23
Consensus pattern (36 bp):
ATTTGTACCAACACGAGTTCAGAATGGATGGAGAGA
Found at i:64825 original size:6 final size:6
Alignment explanation
Indices: 64814--64846 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
64804 ATTCTGTTAC
64814 ATTTTT ATTTTT A-TTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTT
64847 CGATTGAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:64830 original size:11 final size:12
Alignment explanation
Indices: 64814--64846 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
64804 ATTCTGTTAC
64814 ATTTTTATTTTT
1 ATTTTTATTTTT
64826 A-TTTTATTTTT
1 ATTTTTATTTTT
64837 ATTTTTATTT
1 ATTTTTATTT
64847 CGATTGAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:64834 original size:17 final size:17
Alignment explanation
Indices: 64814--64846 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
64804 ATTCTGTTAC
64814 ATTTTTATTTTTATTTT
1 ATTTTTATTTTTATTTT
64831 ATTTTTATTTTTATTT
1 ATTTTTATTTTTATTT
64847 CGATTGAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
ATTTTTATTTTTATTTT
Found at i:66841 original size:12 final size:12
Alignment explanation
Indices: 66824--66873 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
66814 TGCCTCCTAC
*
66824 CGTGGCTGAGGT
1 CGTGGCTGTGGT
66836 CGTGGCTGTGGT
1 CGTGGCTGTGGT
*
66848 CATGG-TCGTGGT
1 CGTGGCT-GTGGT
66860 CGTGGCTGTGGT
1 CGTGGCTGTGGT
66872 CG
1 CG
66874 ACATTAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 1 0.03
12 31 0.94
13 1 0.03
ACGTcount: A:0.04, C:0.18, G:0.48, T:0.30
Consensus pattern (12 bp):
CGTGGCTGTGGT
Found at i:81834 original size:13 final size:13
Alignment explanation
Indices: 81816--81840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
81806 CAAAAGTAGT
81816 GGTACTGTTCACG
1 GGTACTGTTCACG
81829 GGTACTGTTCAC
1 GGTACTGTTCAC
81841 TGTATTTCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (13 bp):
GGTACTGTTCACG
Found at i:86766 original size:5 final size:6
Alignment explanation
Indices: 86748--86777 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
86738 AATTTCGTTA
86748 TATTTT TATTTTT TATTTT TATTTT TATTT
1 TATTTT TA-TTTT TATTTT TATTTT TATTT
86778 CGATTAAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TATTTT
Found at i:98219 original size:24 final size:24
Alignment explanation
Indices: 98175--98221 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
98165 ATAAAGAACC
*
98175 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
98199 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
98222 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:101544 original size:19 final size:20
Alignment explanation
Indices: 101522--101565 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
101512 GAGAAAAGGT
101522 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
101541 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
101561 AAAAG
1 AAAAG
101566 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:108303 original size:24 final size:24
Alignment explanation
Indices: 108259--108305 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
108249 ATAAAGAACC
*
108259 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
108283 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
108306 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:111172 original size:21 final size:21
Alignment explanation
Indices: 111138--111178 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
111128 GTACCGATAC
*
111138 TGAGCCTATCAGTATCAATAT
1 TGAGCATATCAGTATCAATAT
*
111159 TGAGCATATTAGTATCAATA
1 TGAGCATATCAGTATCAATA
111179 ATGCCCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TGAGCATATCAGTATCAATAT
Found at i:113894 original size:3 final size:3
Alignment explanation
Indices: 113878--113952 Score: 96
Period size: 3 Copynumber: 25.0 Consensus size: 3
113868 ATTTTTACTT
* * * *
113878 TTA TTA TAA ATA TTA TTA TTA ATA CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
113926 TTA TTA TTA TTA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
113953 CAGGCCTGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:122006 original size:75 final size:75
Alignment explanation
Indices: 121883--122058 Score: 246
Period size: 75 Copynumber: 2.4 Consensus size: 75
121873 AACAAGAAGA
* * * * * *
121883 AAATGTCGGGGCATGCTGAGAGCCCAATTCAATCAGAAATAAGAATGTTGATGCGTTTTGAATGT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAACAAGAATGTTGATGCATTTTGAACGT
*
121948 TTTTATCAGC
66 TTGTATCAGC
* *
121958 AAATGTTGGGGCATGCTGAAAGCCCATTTTAATCAGAAACATGAATGTTGATGCATTTTGAACGT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAACAAGAATGTTGATGCATTTTGAACGT
* *
122023 TTGTATTAGT
66 TTGTATCAGC
122033 AAATGTTGGGG-ATGCTGAAAGCCCAT
1 AAATGTTGGGGCATGCTGAAAGCCCAT
122059 ATCATCTTGT
Statistics
Matches: 90, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
74 15 0.17
75 75 0.83
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (75 bp):
AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAACAAGAATGTTGATGCATTTTGAACGT
TTGTATCAGC
Found at i:123504 original size:42 final size:43
Alignment explanation
Indices: 123402--123591 Score: 273
Period size: 41 Copynumber: 4.5 Consensus size: 43
123392 GGGTTATTTG
123402 TAAGACCTTCAGTGCAAGATGTTAAAGTCCTTCGGGCC--CCA
1 TAAGACCTTCAGTGCAAGATGTTAAAGTCCTTCGGGCCATCCA
*
123443 TAAGACCTTCAGTGCAAGATGTTAAAGTCCTT-GGGCCATCCG
1 TAAGACCTTCAGTGCAAGATGTTAAAGTCCTTCGGGCCATCCA
* * **
123485 TAAGACCTTCAATGTAAGATGTTAAAGTCCTTCGGAACATCCA
1 TAAGACCTTCAGTGCAAGATGTTAAAGTCCTTCGGGCCATCCA
**
123528 TAAGACCTTCAGTGC-AGATGTT-AAGTCCTTTAGGCCATCCA
1 TAAGACCTTCAGTGCAAGATGTTAAAGTCCTTCGGGCCATCCA
*
123569 TAAGACCTTCAGTGCAGGATGTT
1 TAAGACCTTCAGTGCAAGATGTT
123592 TTCAAATGAG
Statistics
Matches: 132, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
40 5 0.04
41 62 0.47
42 45 0.34
43 20 0.15
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (43 bp):
TAAGACCTTCAGTGCAAGATGTTAAAGTCCTTCGGGCCATCCA
Found at i:123554 original size:83 final size:84
Alignment explanation
Indices: 123401--123591 Score: 271
Period size: 83 Copynumber: 2.3 Consensus size: 84
123391 CGGGTTATTT
* *
123401 GTAAGACCTTCAGTGCAAGATGTTAAAGTCCTTCGGGCCCCATAAGACCTTCAGTGCAAGATGTT
1 GTAAGACCTTCAATGCAAGATGTTAAAGTCCTTCGGACCCCATAAGACCTTCAGTGCAAGATGTT
*
123466 AAAGTCC-TTGGGCCATCC
66 AAAGTCCTTTAGGCCATCC
* *
123484 GTAAGACCTTCAATGTAAGATGTTAAAGTCCTTCGGAACATCCATAAGACCTTCAGTGC-AGATG
1 GTAAGACCTTCAATGCAAGATGTTAAAGTCCTTCGG-AC-CCCATAAGACCTTCAGTGCAAGATG
123548 TT-AAGTCCTTTAGGCCATCC
64 TTAAAGTCCTTTAGGCCATCC
* * *
123568 ATAAGACCTTCAGTGCAGGATGTT
1 GTAAGACCTTCAATGCAAGATGTT
123592 TTCAAATGAG
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
83 40 0.42
84 38 0.40
85 18 0.19
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (84 bp):
GTAAGACCTTCAATGCAAGATGTTAAAGTCCTTCGGACCCCATAAGACCTTCAGTGCAAGATGTT
AAAGTCCTTTAGGCCATCC
Done.