Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006037.1 Hibiscus syriacus cultivar Beakdansim tig00014257_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: 116889
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:10721 original size:21 final size:21
Alignment explanation
Indices: 10678--10722 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
10668 GATTTCTGGG
* *
10678 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
10699 CAAGGGGAACCGATACTCC-TT
1 CAAGGGGAACCGATAC-CCATT
10720 CAA
1 CAA
10723 ACGAACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:12114 original size:14 final size:14
Alignment explanation
Indices: 12095--12122 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12085 GAAAAGAAGC
12095 TATGTGATACGTGA
1 TATGTGATACGTGA
12109 TATGTGATACGTGA
1 TATGTGATACGTGA
12123 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:12533 original size:23 final size:23
Alignment explanation
Indices: 12500--12544 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12490 ATTTTTATAT
*
12500 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
12523 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
12545 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:15838 original size:21 final size:21
Alignment explanation
Indices: 15812--15856 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
15802 GATTTTTGGG
* *
15812 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
15833 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
15854 CAA
1 CAA
15857 ACGAACAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:17663 original size:145 final size:146
Alignment explanation
Indices: 17370--17678 Score: 518
Period size: 145 Copynumber: 2.1 Consensus size: 146
17360 GAGTCGAGGG
* *
17370 TCTACGCGGTCCTTCAGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTC-GGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
17435 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
17500 TATGGCACTACGGTAAT
130 TATGGCACTACGGTAAT
*
17517 TCTACGCGGTCCTTCGG-GATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
1 TCTACGCGGTCCTTCGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
*
17581 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAAT-A-ATGTGGTCCTTATGGACATTTTTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
17644 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGT--AAT
17662 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
17679 TGCAATTATA
Statistics
Matches: 155, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
143 37 0.24
144 2 0.01
145 99 0.64
146 2 0.01
147 15 0.10
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (146 bp):
TCTACGCGGTCCTTCGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTAAT
Found at i:17679 original size:23 final size:23
Alignment explanation
Indices: 17646--17690 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17636 ATTTTTATAT
*
17646 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
17669 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
17691 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:30040 original size:18 final size:16
Alignment explanation
Indices: 30001--30048 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
29991 GACTAGACTG
30001 TTAATCATTTTTACTT
1 TTAATCATTTTTACTT
* *
30017 TAAATCACTTTTTATTAT
1 TTAATCA-TTTTTACT-T
30035 TTAATCATTTTTAC
1 TTAATCATTTTTAC
30049 CAAAACCCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 6 0.23
17 13 0.50
18 7 0.27
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATCATTTTTACTT
Found at i:30131 original size:17 final size:17
Alignment explanation
Indices: 30108--30149 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
30098 TATTTTCTTT
30108 ATTTTTACT-TTAAATC
1 ATTTTTACTATTAAATC
* *
30124 ACTTTTTATTATTTAATC
1 A-TTTTTACTATTAAATC
30142 ATTTTTAC
1 ATTTTTAC
30150 CAAAACCCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTACTATTAAATC
Found at i:30182 original size:101 final size:101
Alignment explanation
Indices: 30007--30196 Score: 380
Period size: 101 Copynumber: 1.9 Consensus size: 101
29997 ACTGTTAATC
30007 ATTTTTACTTTAAATCACTTTTTATTATTTAATCATTTTTACCAAAACCCTCTTCTCATCTATTG
1 ATTTTTACTTTAAATCACTTTTTATTATTTAATCATTTTTACCAAAACCCTCTTCTCATCTATTG
30072 CATAACGCCTGGTCAAGACAATTCTTTATTTTCTTT
66 CATAACGCCTGGTCAAGACAATTCTTTATTTTCTTT
30108 ATTTTTACTTTAAATCACTTTTTATTATTTAATCATTTTTACCAAAACCCTCTTCTCATCTATTG
1 ATTTTTACTTTAAATCACTTTTTATTATTTAATCATTTTTACCAAAACCCTCTTCTCATCTATTG
30173 CATAACGCCTGGTCAAGACAATTC
66 CATAACGCCTGGTCAAGACAATTC
30197 AAATCGAAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 89 1.00
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (101 bp):
ATTTTTACTTTAAATCACTTTTTATTATTTAATCATTTTTACCAAAACCCTCTTCTCATCTATTG
CATAACGCCTGGTCAAGACAATTCTTTATTTTCTTT
Found at i:33327 original size:23 final size:23
Alignment explanation
Indices: 33297--33350 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
33287 GTTGCATCAT
33297 TGCCGTCTGTGGTGCTGGAGCAG
1 TGCCGTCTGTGGTGCTGGAGCAG
33320 TGCCGTCTGTGGTGCTGGAGCAG
1 TGCCGTCTGTGGTGCTGGAGCAG
*
33343 TGTCGTCT
1 TGCCGTCT
33351 TAGGCTGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.07, C:0.22, G:0.41, T:0.30
Consensus pattern (23 bp):
TGCCGTCTGTGGTGCTGGAGCAG
Found at i:36988 original size:135 final size:135
Alignment explanation
Indices: 36807--37203 Score: 668
Period size: 135 Copynumber: 2.9 Consensus size: 135
36797 TAAATAATGG
36807 AATGTGTTTCAAATAAAACATACATTATTAAGATTAAAATGAAGAAAAATAATTGATTTTCATAA
1 AATGTGTTTCAAATAAAACATACATTATTAAGATTAAAATGAAGAAAAATAATTGATTTTCATAA
*
36872 AAATAATAGTAAAGTACAAAAATAGTCCTCCGATTATAAAATATTATTTTGTTGAATGAAATGTG
66 AAATAATAGTAAAGTACAAAAATAGTCTTCCGATTATAAAATATTATTTTGTTGAATGAAATGTG
36937 TCTTT
131 TCTTT
*
36942 AATGTGTTTCAAATAAAACATACATTATTAGGATTAAAATGAAGAAAAATAATTGATTTTCATAA
1 AATGTGTTTCAAATAAAACATACATTATTAAGATTAAAATGAAGAAAAATAATTGATTTTCATAA
* *
37007 AAATATTAGTAAAGTACAAAAATAGTCTTCCGATTATAAAATATTATTTTGTTGAATGGAATGTG
66 AAATAATAGTAAAGTACAAAAATAGTCTTCCGATTATAAAATATTATTTTGTTGAATGAAATGTG
37072 TCTTT
131 TCTTT
37077 AATGTGTTTCAAATAAAACATACATTATTAAGATTAAAATGAAGAAAAATAATTGATTTTCATAA
1 AATGTGTTTCAAATAAAACATACATTATTAAGATTAAAATGAAGAAAAATAATTGATTTTCAT--
* * * * *
37142 AAAAATAATAATATTAAAGTACACAAATAGTCTTTCGATTATAATATGTTATTTTGTTGAAT
64 --AAA-AATAATAGTAAAGTACAAAAATAGTCTTCCGATTATAAAATATTATTTTGTTGAAT
37204 TCCTCAACTA
Statistics
Matches: 246, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
135 193 0.78
139 3 0.01
140 50 0.20
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (135 bp):
AATGTGTTTCAAATAAAACATACATTATTAAGATTAAAATGAAGAAAAATAATTGATTTTCATAA
AAATAATAGTAAAGTACAAAAATAGTCTTCCGATTATAAAATATTATTTTGTTGAATGAAATGTG
TCTTT
Found at i:37352 original size:2 final size:2
Alignment explanation
Indices: 37345--37371 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37335 ACCTTTTTCT
37345 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
37372 TCTTTTTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39009 original size:15 final size:15
Alignment explanation
Indices: 38989--39021 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
38979 CGTAGGACCC
38989 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
39004 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
39019 CTA
1 CTA
39022 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:39629 original size:64 final size:64
Alignment explanation
Indices: 39561--39703 Score: 191
Period size: 64 Copynumber: 2.2 Consensus size: 64
39551 TATTATTGGG
* *
39561 ATGCATCGATGCACCAATTGCATTCGATG-TTTCATTATT-AATGGGATGCATCGATGCACTACT
1 ATGCATCGATGCACCAATTGCATTCGATGTTTTCATT-TTAAAAGAG-TGCATCGATGCACTACT
*
39624 T
64 A
** *
39625 ATGCATCGATGCATGAATTGCATTCGATGTTTTTATTTTAAAAGAGTGCATCGATGCACTACTA
1 ATGCATCGATGCACCAATTGCATTCGATGTTTTCATTTTAAAAGAGTGCATCGATGCACTACTA
*
39689 ATGCATCGATACACC
1 ATGCATCGATGCACC
39704 TTCAAACAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 58 0.85
65 10 0.15
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTTCATTTTAAAAGAGTGCATCGATGCACTACTA
Found at i:45919 original size:15 final size:15
Alignment explanation
Indices: 45899--45931 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
45889 CGTAGGACCT
45899 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
45914 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
45929 CTA
1 CTA
45932 TTATACCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.18, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:46482 original size:64 final size:64
Alignment explanation
Indices: 46398--46615 Score: 192
Period size: 64 Copynumber: 3.4 Consensus size: 64
46388 TGAAGGTATT
* * * **
46398 CATCGATGCACTACTGATGCATCTG-TGCATAAAAGGTATTCGATGTATT-ATTATTGTTCGGAT
1 CATCGATGCACTACTTATGCATC-GATGCACAAAAGGCATTCGATGT-TTCATTATTAATCGGAT
46461 G
64 G
* * ** *
46462 CATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGATG
1 CATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATTAATCGGATG
* * ** ** * **
46526 CATCGATGCACTAATTATGCATCGATGAATGAATTGCATTCGATGTTTTTATT-TTAA-AAGAGT
1 CATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATG-TTTCATTATTAATCGGA-T
46589 G
64 G
*
46590 CATCGATGCACTACTGATGCATCGAT
1 CATCGATGCACTACTTATGCATCGAT
46616 ACACCTTCAA
Statistics
Matches: 130, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 5 0.04
64 119 0.92
65 6 0.05
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
CATCGATGCACTACTTATGCATCGATGCACAAAAGGCATTCGATGTTTCATTATTAATCGGATG
Found at i:47978 original size:2 final size:2
Alignment explanation
Indices: 47971--47996 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47961 GGTAGCAAAC
47971 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
47997 GATTACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49755 original size:14 final size:16
Alignment explanation
Indices: 49732--49768 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
49722 AGATACGTAT
49732 TAATATATATCATTGA
1 TAATATATATCATTGA
49748 TAATATATATCATTGA
1 TAATATATATCATTGA
49764 TAATA
1 TAATA
49769 CACAGAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.43
Consensus pattern (16 bp):
TAATATATATCATTGA
Found at i:57092 original size:24 final size:24
Alignment explanation
Indices: 57053--57098 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
57043 TCCAGATCCT
*
57053 CCTCCTCCACCTCCACCTCCACTC
1 CCTCCTCCACCGCCACCTCCACTC
*
57077 CCTCCTCCTCCGCCACCTCCAC
1 CCTCCTCCACCGCCACCTCCAC
57099 CGCCCCCTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.67, G:0.02, T:0.20
Consensus pattern (24 bp):
CCTCCTCCACCGCCACCTCCACTC
Found at i:57101 original size:12 final size:12
Alignment explanation
Indices: 57056--57108 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
57046 AGATCCTCCT
*
57056 CCTCCACCTCCA
1 CCTCCACCGCCA
*
57068 CCTCCACTC-CCT
1 CCTCCAC-CGCCA
*
57080 CCTCCTCCGCCA
1 CCTCCACCGCCA
*
57092 CCTCCACCGCCC
1 CCTCCACCGCCA
57104 CCTCC
1 CCTCC
57109 GGCCCCAGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.09, C:0.70, G:0.04, T:0.17
Consensus pattern (12 bp):
CCTCCACCGCCA
Found at i:57107 original size:24 final size:24
Alignment explanation
Indices: 57056--57108 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
57046 AGATCCTCCT
* *
57056 CCTCCACCTCCACCTCCACTCCCT
1 CCTCCACCGCCACCTCCACTCCCC
*
57080 CCTCCTCCGCCACCTCCAC-CGCCC
1 CCTCCACCGCCACCTCCACTC-CCC
57104 CCTCC
1 CCTCC
57109 GGCCCCAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.09, C:0.70, G:0.04, T:0.17
Consensus pattern (24 bp):
CCTCCACCGCCACCTCCACTCCCC
Found at i:62295 original size:39 final size:35
Alignment explanation
Indices: 62252--62350 Score: 103
Period size: 39 Copynumber: 2.7 Consensus size: 35
62242 TTTTTGGGCC
*
62252 ACCCGACCCGACCCGAGAAAA-AAGGGTTCTCCACCCGTG
1 ACCCGACCCGACCCGACAAAATAA-GGTT-T-CACCC--G
*
62291 ACCCGACCCGACCCGACAAAATTAATGTTTCACCCG
1 ACCCGACCCGACCCGACAAAA-TAAGGTTTCACCCG
62327 ACCCGACCCGACCCGA-AATAATAA
1 ACCCGACCCGACCCGACAA-AATAA
62351 AAAAAAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
35 5 0.09
36 19 0.35
38 5 0.09
39 21 0.38
40 3 0.05
41 2 0.04
ACGTcount: A:0.32, C:0.38, G:0.17, T:0.12
Consensus pattern (35 bp):
ACCCGACCCGACCCGACAAAATAAGGTTTCACCCG
Found at i:65889 original size:19 final size:19
Alignment explanation
Indices: 65862--65920 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
65852 AACCCAACTT
65862 GACCTGTTGACTTTGACTA
1 GACCTGTTGACTTTGACTA
* *
65881 GACCCGTTGGCTTTGACCT-
1 GACCTGTTGACTTTGA-CTA
*
65900 GACCTGTTGACCATTGACTA
1 GACCTGTTGA-CTTTGACTA
65920 G
1 G
65921 TCTAATTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 24 0.75
20 8 0.25
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.32
Consensus pattern (19 bp):
GACCTGTTGACTTTGACTA
Found at i:70067 original size:2 final size:2
Alignment explanation
Indices: 70060--70085 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
70050 TAACCAAACC
70060 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
70086 TAAGTTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78178 original size:65 final size:64
Alignment explanation
Indices: 77981--78181 Score: 216
Period size: 65 Copynumber: 3.1 Consensus size: 64
77971 GCACTAAGAA
* * *
77981 TGCATCGATGCATGAAATGCATTCGATGTTTCCAAATAGCCA-GAGTGCATCGATGCATGGCTGG
1 TGCATCGATGCATGAAATGCATTCGATGTTT-CAATTAACCATGAGTGCATCGATGCATGGTTGG
* * *
78045 TGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAGTGCATCGATGCATAGTA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTCAAT-TAAC-CATGAGTGCATCGATGCATGGT-
78108 T-G
62 TGG
* *
78110 TGCATCGATGCATGAAATGCATTCTATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGATT
1 TGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTA-ACCATGAGTGCATCGATGCATGG-TT
78173 GG
63 GG
78175 TGCATCG
1 TGCATCG
78182 GAGCATCACT
Statistics
Matches: 115, Mismatches: 11, Indels: 21
0.78 0.07 0.14
Matches are distributed among these distances:
63 4 0.03
64 49 0.43
65 61 0.53
66 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTCAATTAACCATGAGTGCATCGATGCATGGTTGG
Found at i:85022 original size:33 final size:33
Alignment explanation
Indices: 84980--85047 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
84970 TCCTCCAGGA
** * *
84980 GGGGTCATAAAACTCTGTGACGGTGGTGGTGGC
1 GGGGTCATAAAACTAGGTGACAGTGGTGGCGGC
85013 GGGGTCATAAAACTAGGTGACAGTGGTGGCGGC
1 GGGGTCATAAAACTAGGTGACAGTGGTGGCGGC
85046 GG
1 GG
85048 TATCAGGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.15, G:0.44, T:0.21
Consensus pattern (33 bp):
GGGGTCATAAAACTAGGTGACAGTGGTGGCGGC
Found at i:86809 original size:21 final size:20
Alignment explanation
Indices: 86780--86836 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
86770 TTTATATATA
*
86780 TAAAAAAATTAATTAAATAC
1 TAAATAAATTAATTAAATAC
86800 -AATATTAAA-TAATTTAAATAC
1 TAA-A-TAAATTAA-TTAAATAC
86821 TTAAATAAATTAATTA
1 -TAAATAAATTAATTA
86837 TTAAATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 11
0.71 0.02 0.26
Matches are distributed among these distances:
19 2 0.07
20 4 0.13
21 18 0.60
22 4 0.13
23 2 0.07
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAATAAATTAATTAAATAC
Found at i:86826 original size:17 final size:16
Alignment explanation
Indices: 86787--86854 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 16
86777 ATATAAAAAA
*
86787 ATTAATTAAA-TACAAT
1 ATTAAATAAATTA-AAT
*
86803 ATTAAATAATTTAAAT
1 ATTAAATAAATTAAAT
*
86819 ACTTAAATAAATTAATT
1 A-TTAAATAAATTAAAT
*
86836 ATTAAATATAATAAAAT
1 ATTAAATA-AATTAAAT
86853 AT
1 AT
86855 ACCTTAAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
16 19 0.44
17 24 0.56
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAAATAAATTAAAT
Found at i:88324 original size:23 final size:23
Alignment explanation
Indices: 88298--88347 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
88288 AAAAAATGAA
88298 AAACATGCCAC-AAAGACGGAGAT
1 AAACATGCCACAAAAG-CGGAGAT
* * *
88321 AAACGTGCGATAAAAGCGGAGAT
1 AAACATGCCACAAAAGCGGAGAT
88344 AAAC
1 AAAC
88348 GTACAACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (23 bp):
AAACATGCCACAAAAGCGGAGAT
Found at i:88402 original size:16 final size:16
Alignment explanation
Indices: 88377--88407 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
88367 ATTCTTATTA
*
88377 AAAAATAAAAGAAAAT
1 AAAAAGAAAAGAAAAT
88393 AAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA
88408 CCGACGGTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAT
Found at i:94796 original size:37 final size:37
Alignment explanation
Indices: 94755--94828 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
94745 TCAATGTGGA
94755 TTGAGCATGTAGTACCTCTTGTAACATTGCGGCCATT
1 TTGAGCATGTAGTACCTCTTGTAACATTGCGGCCATT
94792 TTGAGCATGTAGTACCTCTTGTAACATTGCGGCCATT
1 TTGAGCATGTAGTACCTCTTGTAACATTGCGGCCATT
94829 GGAGTTGTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (37 bp):
TTGAGCATGTAGTACCTCTTGTAACATTGCGGCCATT
Found at i:96772 original size:87 final size:87
Alignment explanation
Indices: 96604--96773 Score: 245
Period size: 88 Copynumber: 1.9 Consensus size: 87
96594 TACTACTTTA
* * * *
96604 TTAAGTCTCTCGACTATTAAAAATTACAAAATAGTCCTCTACTATTCATTATGTTCTAAACTAGT
1 TTAAGTCCCTCAACTATTAAAAATTACAAAATAGCCCTCCACTATTCATTATGTTCTAAACTAGT
*
96669 ATTTTTCTATTAAAAAATAGCT
66 ATTTTTCCATTAAAAAATAGCT
96691 TTAAGTCCCTCAACTATTAAAAGA-TACAAAATAGCCCTCCACCTATTCATTATGTT-TCAAACT
1 TTAAGTCCCTCAACTATTAAAA-ATTACAAAATAGCCCTCCA-CTATTCATTATGTTCT-AAACT
*
96754 AGTCTTTTTCCATTAAAAAA
63 AGTATTTTTCCATTAAAAAA
96774 ATTAGTGATT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
87 36 0.49
88 38 0.51
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.37
Consensus pattern (87 bp):
TTAAGTCCCTCAACTATTAAAAATTACAAAATAGCCCTCCACTATTCATTATGTTCTAAACTAGT
ATTTTTCCATTAAAAAATAGCT
Found at i:98310 original size:15 final size:14
Alignment explanation
Indices: 98281--98313 Score: 57
Period size: 14 Copynumber: 2.3 Consensus size: 14
98271 AAAATGATAA
98281 ATATATACTATATC
1 ATATATACTATATC
98295 ATATATACTCATATC
1 ATATATACT-ATATC
98310 ATAT
1 ATAT
98314 GATTCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATATACTATATC
Found at i:103193 original size:18 final size:18
Alignment explanation
Indices: 103172--103206 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
103162 ATTGCTCGGA
103172 GGGTACCGATTCCCCCAG
1 GGGTACCGATTCCCCCAG
103190 GGGTACCGATTCCCCCA
1 GGGTACCGATTCCCCCA
103207 TCTCATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (18 bp):
GGGTACCGATTCCCCCAG
Found at i:106269 original size:16 final size:16
Alignment explanation
Indices: 106248--106284 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
106238 TGTGTAACAC
*
106248 CTTTAATTTTAATTTA
1 CTTTAATTTGAATTTA
106264 CTTTAATTTGAATTTA
1 CTTTAATTTGAATTTA
106280 -TTTAA
1 CTTTAA
106285 GTATTTTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (16 bp):
CTTTAATTTGAATTTA
Done.