Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005086.1 Hibiscus syriacus cultivar Beakdansim tig00011426_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: 80091
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Found at i:62 original size:20 final size:22
Alignment explanation
Indices: 16--64 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
6 TCGAAACTAA
*
16 GTTGCGAATTTGTGAAATTCGC
1 GTTGCGAATTTGTGAAATTCCC
38 GTTGCGAATTTG-GAAA-TCCC
1 GTTGCGAATTTGTGAAATTCCC
58 GTTGCGA
1 GTTGCGA
65 TTTACATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 10 0.38
21 4 0.15
22 12 0.46
ACGTcount: A:0.22, C:0.16, G:0.29, T:0.33
Consensus pattern (22 bp):
GTTGCGAATTTGTGAAATTCCC
Found at i:2820 original size:5 final size:5
Alignment explanation
Indices: 2810--2835 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
2800 TCAGTTTCCC
2810 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
2836 CGGTATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:9591 original size:140 final size:141
Alignment explanation
Indices: 9320--9608 Score: 431
Period size: 140 Copynumber: 2.0 Consensus size: 141
9310 TTTGGTTGTC
*
9320 CCTTGTTCCCATATGTAATGGGGGTAAGGGGAGGTAAGATAGTAGGCTGCCCCAACACCAGGTTG
1 CCTTGTTCCCATATGTAATGGGGATAAGGGGAGGTAAGATAGTAGGCTGCCCCAACACCAGGTTG
* *
9385 AGAGCAGCTTCCGTAGAAGACCTCCAAATTATAAAATGCCCTCCGTGGGACTCGATCCTACGACC
66 AGAGCAGCTTCC--AGAAGACCTCCAAATTATAAAATGCCCTCCATGGGACTCGATCCCACGACC
* *
9450 TCAATGTTAAGAA
129 TCAAGGTTAAAAA
* * *
9463 CCTTGTTCTCATATGTAAT-GGGATAAGGGGGAGGTAAGATAGTAGGTTGCCCCCAACACTAGGT
1 CCTTGTTCCCATATGTAATGGGGATAA-GGGGAGGTAAGATAGTAGGCTG-CCCCAACACCAGGT
* *
9527 TGAGAGCAGCTTCC-G-AGACCTCCAAATTATGAAATGTCCTCCATGGGACTCGATCCCACGACC
64 TGAGAGCAGCTTCCAGAAGACCTCCAAATTATAAAATGCCCTCCATGGGACTCGATCCCACGACC
9590 TCAAGGTTAAAAA
129 TCAAGGTTAAAAA
9603 CCTTGT
1 CCTTGT
9609 GCTCTACCAA
Statistics
Matches: 134, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
140 61 0.46
141 1 0.01
142 6 0.04
143 39 0.29
144 27 0.20
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (141 bp):
CCTTGTTCCCATATGTAATGGGGATAAGGGGAGGTAAGATAGTAGGCTGCCCCAACACCAGGTTG
AGAGCAGCTTCCAGAAGACCTCCAAATTATAAAATGCCCTCCATGGGACTCGATCCCACGACCTC
AAGGTTAAAAA
Found at i:10121 original size:3 final size:3
Alignment explanation
Indices: 10113--10141 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10103 TACTTTTAAA
10113 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
10142 AAGAGTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:10176 original size:17 final size:18
Alignment explanation
Indices: 10156--10189 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
10146 GTATATTTTA
10156 ATTATTTTTAT-AAATAT
1 ATTATTTTTATCAAATAT
10173 ATTATTTTTATCAAATA
1 ATTATTTTTATCAAATA
10190 CGTTTGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTTTTATCAAATAT
Found at i:21619 original size:8 final size:8
Alignment explanation
Indices: 21590--21657 Score: 61
Period size: 8 Copynumber: 8.5 Consensus size: 8
21580 TTTTCATCAA
21590 AATATTA-
1 AATATTAT
*
21597 AATATTAAA
1 AATATT-AT
21606 ATATATTAT
1 A-ATATTAT
21615 AATATTTAT
1 AATA-TTAT
*
21624 AATAATAT
1 AATATTAT
21632 AATATTAT
1 AATATTAT
*
21640 -AT-TTTT
1 AATATTAT
21646 AATATTAT
1 AATATTAT
21654 AATA
1 AATA
21658 AAATAATCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
6 3 0.06
7 10 0.20
8 21 0.42
9 11 0.22
10 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (8 bp):
AATATTAT
Found at i:21632 original size:22 final size:22
Alignment explanation
Indices: 21605--21662 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
21595 TAAATATTAA
*
21605 AATATATTATAATATTTATAAT
1 AATATAATATAATATTTATAAT
* *
21627 AATATAATATTATATTTTTAAT
1 AATATAATATAATATTTATAAT
* *
21649 ATTATAATAAAATA
1 AATATAATATAATA
21663 ATCAATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATATAATATAATATTTATAAT
Found at i:21641 original size:30 final size:30
Alignment explanation
Indices: 21607--21801 Score: 103
Period size: 30 Copynumber: 6.7 Consensus size: 30
21597 AATATTAAAA
21607 TATATTATAATATTTATAATAATATAATAT
1 TATATTATAATATTTATAATAATATAATAT
* *
21637 TATATTTTTAATA-TTATAATAAAATAATCAAT
1 TATA-TTATAATATTTATAATAATATAAT--AT
* * * *
21669 TAAATTATAATA-ATATAA-GATATTATATT
1 TATATTATAATATTTATAATAATATAATA-T
* * **
21698 TTTATTTTAATAAATAT-ATAATA-AAT-T
1 TATATTATAATATTTATAATAATATAATAT
*
21725 T-T-TTAT-ATATTTAATAATGA-ATAATAT
1 TATATTATAATATTT-ATAATAATATAATAT
*
21752 TAT-TTATATATATTTAATATTAATATAATA-
1 TATATTATA-ATATTT-ATAATAATATAATAT
* *
21782 -ATCTAATAATATTT-TAATAA
1 TATATTATAATATTTATAATAA
21802 AGATATTTAA
Statistics
Matches: 129, Mismatches: 21, Indels: 33
0.70 0.11 0.18
Matches are distributed among these distances:
24 4 0.03
25 6 0.05
26 7 0.05
27 9 0.07
28 6 0.05
29 21 0.16
30 46 0.36
31 25 0.19
32 5 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
TATATTATAATATTTATAATAATATAATAT
Found at i:21821 original size:23 final size:23
Alignment explanation
Indices: 21789--21841 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
21779 ATAATCTAAT
*
21789 AATATTTTAATAAAGATATTTAA
1 AATATATTAATAAAGATATTTAA
* * *
21812 AATATATTAATTAATATTTTTAA
1 AATATATTAATAAAGATATTTAA
21835 AATATAT
1 AATATAT
21842 AACACTATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATATATTAATAAAGATATTTAA
Found at i:22218 original size:15 final size:15
Alignment explanation
Indices: 22170--22226 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
22160 TTCCAGAAAT
*
22170 GTAATTCATTTTCCT
1 GTAATTCATTTTCCA
*
22185 G-AATTCAAATTT-CA
1 GTAATTC-ATTTTCCA
*
22199 TTAATTCATTTTCCA
1 GTAATTCATTTTCCA
22214 GTAATTCATTTTC
1 GTAATTCATTTTC
22227 TAGAAAACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.29
15 24 0.71
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:22855 original size:28 final size:28
Alignment explanation
Indices: 22818--22879 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
22808 TGACACCACC
* *
22818 ATTGCTTTCAAGCACT-GACTCGTCAACAT
1 ATTG-TTTCAAACACTAG-CTCGACAACAT
*
22847 ATTGTTTCAAACACTAGCTCGACGACAT
1 ATTGTTTCAAACACTAGCTCGACAACAT
22875 ATTGT
1 ATTGT
22880 AAACAGAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (28 bp):
ATTGTTTCAAACACTAGCTCGACAACAT
Found at i:27060 original size:2 final size:2
Alignment explanation
Indices: 27053--27078 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27043 AACACATTAA
27053 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
27079 GGTTCTTGTC
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:35830 original size:16 final size:16
Alignment explanation
Indices: 35809--35869 Score: 104
Period size: 16 Copynumber: 3.8 Consensus size: 16
35799 TAATAAATAA
35809 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
35825 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
35841 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
35857 ATGAACATAAACG
1 ACGAACATAAACG
35870 TTGGATACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.56, C:0.21, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:36984 original size:14 final size:14
Alignment explanation
Indices: 36967--37006 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
36957 TGAACATAAG
36967 CGAACATAACCGAA
1 CGAACATAACCGAA
36981 CGAACAT-A---AA
1 CGAACATAACCGAA
36991 CGAACATAACCGAA
1 CGAACATAACCGAA
37005 CG
1 CG
37007 TTCACGAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
10 9 0.41
11 1 0.05
13 1 0.05
14 11 0.50
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (14 bp):
CGAACATAACCGAA
Found at i:36985 original size:24 final size:24
Alignment explanation
Indices: 36958--37006 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
36948 ATAAATGAAT
*
36958 GAACATAAGCGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
36982 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
37006 G
1 G
37007 TTCACGAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:37240 original size:30 final size:30
Alignment explanation
Indices: 37173--37259 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
37163 TACAGGCCTA
* * * * *
37173 GGTTAAACTAATAGTTTGTATAAAATTTAG
1 GGTTAAATTAATATTTTATCTAAATTTTAG
*
37203 GGATTAAATTAATATTTTATCTAAATTTTAT
1 GG-TTAAATTAATATTTTATCTAAATTTTAG
* *
37234 GGTTAAATTATTATTTCATCTTAAAT
1 GGTTAAATTAATATTTTATC-TAAAT
37260 ATAGGGGTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 18 0.38
31 29 0.62
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (30 bp):
GGTTAAATTAATATTTTATCTAAATTTTAG
Found at i:47116 original size:18 final size:18
Alignment explanation
Indices: 47085--47119 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47075 CAAGTCTCCA
* *
47085 CCACCCCCATCACCATCC
1 CCACCACCACCACCATCC
47103 CCACCACCACCACCATC
1 CCACCACCACCACCATC
47120 ACCTTCACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.66, G:0.00, T:0.09
Consensus pattern (18 bp):
CCACCACCACCACCATCC
Found at i:47130 original size:24 final size:24
Alignment explanation
Indices: 47082--47130 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
47072 TTACAAGTCT
* *
47082 CCACCACCCCCATCACCATCCCCA
1 CCACCACCACCATCACCATCACCA
*
47106 CCACCACCACCATCACCTTCACCA
1 CCACCACCACCATCACCATCACCA
47130 C
1 C
47131 TTCCTCCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.63, G:0.00, T:0.10
Consensus pattern (24 bp):
CCACCACCACCATCACCATCACCA
Found at i:47185 original size:72 final size:72
Alignment explanation
Indices: 47034--47173 Score: 208
Period size: 72 Copynumber: 1.9 Consensus size: 72
47024 TTCTCCACCT
* * * * *
47034 CCACCTCCACCATCACCTTCACCCCCTCCTCCTTATGTTTACAAGTCTCCACCACCCCCATCACC
1 CCACCACCACCATCACCTTCACCACCTCCTCCCTATATCTACAAGTCTCCACCACCCCCATCACC
47099 ATCCCCA
66 ATCCCCA
* * *
47106 CCACCACCACCATCACCTTCACCACTTCCTCCCTATATCTATAAGTCTCCACCACCTCCATCACC
1 CCACCACCACCATCACCTTCACCACCTCCTCCCTATATCTACAAGTCTCCACCACCCCCATCACC
47171 ATC
66 ATC
47174 TCCGTCACCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.23, C:0.52, G:0.02, T:0.23
Consensus pattern (72 bp):
CCACCACCACCATCACCTTCACCACCTCCTCCCTATATCTACAAGTCTCCACCACCCCCATCACC
ATCCCCA
Found at i:47197 original size:48 final size:48
Alignment explanation
Indices: 47106--48512 Score: 1170
Period size: 48 Copynumber: 29.2 Consensus size: 48
47096 ACCATCCCCA
* * ** * * * * *
47106 CCACCACCACCATCACCTTCACCACTTCCTCCCTATATCTATAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * ** * * * *
47154 CCACCACCTCCATCACCATCTCCGTCACCACCTTACGTTTATAAATCA
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * * * * *
47202 CCGCCGCCACCATCACCTTCACCACCTCCTCCGTATGTCTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
47250 CCACCACCACCATCACCTTCACCACCACCTCCATATGTCTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
47298 CCACCACCTCCATCATCATCTCCCCCACCACCTTACGTTTACAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * * * * *
47346 CCTCCGCCACCATCACCTTCACCACCTCCTCCATATGTCTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
47394 ---CCACCACCATCACCTTCACCACCACCTCCATATGTCTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
47439 CCACCACCTCCATCATCATCTCCCCCACCACCTTACGTTTACAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
47487 CCTCCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * ** * * *
47535 CCACCACCTCTATCACCATCTTCCCCACCACCTTACGTTTATAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * * *
47583 CCTCCACCACCATCACCTTCACCACCACCTCCATATGTCTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * *
47631 CCACCACCTCCATCACCATCTCCCCCACCACCTTACGTTTACAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
47679 CCTCCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
47727 CCACCACCTCCATCACCATCTCCCCCACCACCTTACGTTTATAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
47775 CCTCCACCACCATCACCTTCACCCCCTCCTCCTTATTTTTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
47823 CCACCACCTCCATCACCATCTCCCCCACCACCTTACGTTTATAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * * * * *
47871 CCTCCACCACCATTACCTTCACCACCACCTCCATATGTCTACAATTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * *
47919 CCACCACCTCCATCACCATC-CCCTCCACCACCTTATGTTTATAAATCT
1 CCACCACCACCATCACCATCACCC-CCACCACCTTATGTTTACAAGTCT
* * * * *
47967 CCTCCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * ** * * *
48015 CCACCACCTCTATCACCATCTTCCCCACCACCTTACGTTTATAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * *
48063 CCTCCACCACCACCACCATCACCTTCACCACCACCTCCATATGTCTACAAGTCT
1 CCACCACCACCATCACCATCACC--C-CCACCACCT---TATGTTTACAAGTCT
* * * *
48117 CCACCACCTCCATCACCATCTCCCCCACCACCTTACGTTTACAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
48165 CCTCCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
48213 CCACCACCTCCATCACCATCTCCCCCACCACCTTACGTTTATAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
48261 CCTCCACCACCATCACCTTCACCCCCTCCTCCTTATTTTTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * *
48309 CCACCACCTCCATCACCATCTCCCCCACCACCTTACGTTTATAAATCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * * * * *
48357 CCTCCACCACCAACACCCTCACCACCACCTCCATATATCTACAAGTCT
1 CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
* * * * * * *
48405 CCACCACCTCCATCTCCATCACCTCCTCCTA-GTTATGTCTACAAGTCC
1 CCACCACCACCATCACCATCACCCCCACC-ACCTTATGTTTACAAGTCT
* * * * * * **
48453 CCTCCTCCACGATCA-CATCCACCACCTCCTCCTTACATTTACAAGTCT
1 CCACCACCACCATCACCAT-CACCCCCACCACCTTATGTTTACAAGTCT
*
48501 CCACCGCCACCA
1 CCACCACCACCA
48513 ATTCACTCCC
Statistics
Matches: 1055, Mismatches: 290, Indels: 28
0.77 0.21 0.02
Matches are distributed among these distances:
45 43 0.04
47 5 0.00
48 954 0.90
49 3 0.00
50 1 0.00
51 18 0.02
52 1 0.00
54 30 0.03
ACGTcount: A:0.24, C:0.48, G:0.03, T:0.25
Consensus pattern (48 bp):
CCACCACCACCATCACCATCACCCCCACCACCTTATGTTTACAAGTCT
Found at i:47302 original size:27 final size:27
Alignment explanation
Indices: 47223--47310 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 27
47213 ATCACCTTCA
* *
47223 CCACCTCCTCCGTATGTCTACAAGTCT
1 CCACCACCTCCATATGTCTACAAGTCT
* ** *
47250 CCACCACCACC--A--TC-AC-CTTCA
1 CCACCACCTCCATATGTCTACAAGTCT
47271 CCACCACCTCCATATGTCTACAAGTCT
1 CCACCACCTCCATATGTCTACAAGTCT
47298 CCACCACCTCCAT
1 CCACCACCTCCAT
47311 CATCATCTCC
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
21 12 0.26
22 2 0.04
23 3 0.07
25 3 0.07
26 2 0.04
27 24 0.52
ACGTcount: A:0.24, C:0.48, G:0.06, T:0.23
Consensus pattern (27 bp):
CCACCACCTCCATATGTCTACAAGTCT
Found at i:48457 original size:96 final size:96
Alignment explanation
Indices: 47109--48505 Score: 1814
Period size: 96 Copynumber: 14.5 Consensus size: 96
47099 ATCCCCACCA
* * * * *
47109 CCACCACCATCACCTTCACCACTTCCTCCCTATATCTATAAGTCTCCACCACCTCCATCACCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
** * *
47174 TCCGTCACCACCTTACGTTTATAAATCACCG
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* * * * *
47205 CCGCCACCATCACCTTCACCACCTCCTCCGTATGTCTACAAGTCTCCACCACCACCATCACCTTC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
* * * * * * * * *
47270 ACCACCACCTCCATATGTCTACAAGTCTCCA
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* * * * * * * * * * * * * *
47301 CCACCTCCATCATCATCTCCCCCACCACCTTACGTTTACAAATCTCCTCCGCCACCATCACCTTC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
* * * * * * * * *
47366 ACCACCTCCTCCATATGTCTA-CAA-GT-CT
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* * *
47394 CCACCACCATCACCTTCACCACCACCTCCATATGTCTACAAGTCTCCACCACCTCCATCATCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
*
47459 TCCCCCACCACCTTACGTTTACAAATCTCCT
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* *
47490 CCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCTATCACCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
*
47555 TTCCCCACCACCTTACGTTTATAAATCTCCT
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* *
47586 CCACCACCATCACCTTCACCACCACCTCCATATGTCTACAAGTCTCCACCACCTCCATCACCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
*
47651 TCCCCCACCACCTTACGTTTACAAATCTCCT
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
*
47682 CCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
47747 TCCCCCACCACCTTACGTTTATAAATCTCCT
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* * *
47778 CCACCACCATCACCTTCACCCCCTCCTCCTTATTTTTACAAGTCTCCACCACCTCCATCACCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
47843 TCCCCCACCACCTTACGTTTATAAATCTCCT
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* * * *
47874 CCACCACCATTACCTTCACCACCACCTCCATATGTCTACAATTCTCCACCACCTCCATCACCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
*
47939 -CCCTCCACCACCTTATGTTTATAAATCTCCT
66 TCCC-CCACCACCTTACGTTTATAAATCTCCT
* *
47970 CCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCTATCACCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
*
48035 TTCCCCACCACCTTACGTTTATAAATCTCCT
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* *
48066 CCACCACCACCACCATCACCTTCACCACCACCTCCATATGTCTACAAGTCTCCACCACCTCCATC
1 ------CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATC
*
48131 ACCATCTCCCCCACCACCTTACGTTTACAAATCTCCT
60 ACCATCTCCCCCACCACCTTACGTTTATAAATCTCCT
*
48168 CCACCACCATCACCTTCACCCCCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
48233 TCCCCCACCACCTTACGTTTATAAATCTCCT
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* * *
48264 CCACCACCATCACCTTCACCCCCTCCTCCTTATTTTTACAAGTCTCCACCACCTCCATCACCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
48329 TCCCCCACCACCTTACGTTTATAAATCTCCT
66 TCCCCCACCACCTTACGTTTATAAATCTCCT
* * * * * *
48360 CCACCACCAACACCCTCACCACCACCTCCATATATCTACAAGTCTCCACCACCTCCATCTCCATC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
* * * * * * * * *
48425 ACCTCCTCCTA-GTTATGTCTACAAGTCCCCT
66 TCCCCCACC-ACCTTACGTTTATAAATCTCCT
* * * * * **
48456 CCTCCACGATCACATCCACCACCTCCTCCTTACATTTACAAGTCTCCACC
1 CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACC
48506 GCCACCAATT
Statistics
Matches: 1154, Mismatches: 135, Indels: 24
0.88 0.10 0.02
Matches are distributed among these distances:
93 65 0.06
94 3 0.00
95 5 0.00
96 988 0.86
97 3 0.00
102 90 0.08
ACGTcount: A:0.24, C:0.47, G:0.03, T:0.25
Consensus pattern (96 bp):
CCACCACCATCACCTTCACCACCTCCTCCATATGTTTACAAGTCTCCACCACCTCCATCACCATC
TCCCCCACCACCTTACGTTTATAAATCTCCT
Found at i:48568 original size:48 final size:47
Alignment explanation
Indices: 48495--48795 Score: 226
Period size: 48 Copynumber: 6.3 Consensus size: 47
48485 TTACATTTAC
* * * * * * * *
48495 AAGTCTCCACCGCCACCAATTCACTCCCCATCTCCTTCTTATGTGTAT
1 AAGTCTCCACCACCACCAGTCCACTCCCGA-CTCGTCCCTATGTATAT
* * *
48543 AAGTCTCCACCACCACCAGTCCACTCTCGACTTAGTCCCTATGTTTAT
1 AAGTCTCCACCACCACCAGTCCACTCCCGAC-TCGTCCCTATGTATAT
* * * *
48591 AAGTCTCCACCACCTCCATTTCACTCCCGACCTCGTCCCTATGTACAT
1 AAGTCTCCACCACCACCAGTCCACTCCCGA-CTCGTCCCTATGTATAT
* ** *
48639 AAGTCTCCACCACCACCAGCCCACTTTCGACCTCGTCCCTATGTTTAT
1 AAGTCTCCACCACCACCAGTCCACTCCCGA-CTCGTCCCTATGTATAT
* * * ** * *
48687 AGGTCTCCACCACCTCCATTCCACT-ATGAACCTCGTCCCTATATCTAT
1 AAGTCTCCACCACCACCAGTCCACTCCCG-A-CTCGTCCCTATGTATAT
* * * * * * * *
48735 AAGTCTCCACCGCCACCAGTTCACTTCTGACCCCCTTCCTATGTCTAT
1 AAGTCTCCACCACCACCAGTCCACTCCCGA-CTCGTCCCTATGTATAT
48783 AAGTCTCCACCAC
1 AAGTCTCCACCAC
48796 ATCCAACCAC
Statistics
Matches: 205, Mismatches: 44, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
47 2 0.01
48 200 0.98
49 3 0.01
ACGTcount: A:0.22, C:0.41, G:0.09, T:0.28
Consensus pattern (47 bp):
AAGTCTCCACCACCACCAGTCCACTCCCGACTCGTCCCTATGTATAT
Found at i:48595 original size:96 final size:96
Alignment explanation
Indices: 48490--48795 Score: 285
Period size: 96 Copynumber: 3.2 Consensus size: 96
48480 CCTCCTTACA
* * * * * **
48490 TTTACAAGTCTCCACCGCCACCAATTCACTCCCCATCTCCTTCTTATGTGTATAAGTCTCCACCA
1 TTTATAAGTCTCCACCACCACCAATTCACTCCCCACCTCCTCCCTATGTACATAAGTCTCCACCA
* *
48555 CCACCAGTCCACTCTCGACTTAGTCCCTATG
66 CCACCAGCCCACTCTCGACCTAGTCCCTATG
* * * *
48586 TTTATAAGTCTCCACCACCTCCATTTCACTCCCGACCTCGTCCCTATGTACATAAGTCTCCACCA
1 TTTATAAGTCTCCACCACCACCAATTCACTCCCCACCTCCTCCCTATGTACATAAGTCTCCACCA
* *
48651 CCACCAGCCCACTTTCGACCTCGTCCCTATG
66 CCACCAGCCCACTCTCGACCTAGTCCCTATG
* * **** * *
48682 TTTATAGGTCTCCACCACCTCC-ATTCCACTATGAACCTCGTCCCTATAT-CTATAAGTCTCCAC
1 TTTATAAGTCTCCACCACCACCAATT-CACTCCCCACCTCCTCCCTATGTAC-ATAAGTCTCCAC
* ** *** *
48745 CGCCACCAGTTCACT-TCTGACCCCCTTCCTATG
64 CACCACCAGCCCACTCTC-GACCTAGTCCCTATG
*
48778 TCTATAAGTCTCCACCAC
1 TTTATAAGTCTCCACCAC
48796 ATCCAACCAC
Statistics
Matches: 177, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
95 5 0.03
96 172 0.97
ACGTcount: A:0.22, C:0.41, G:0.09, T:0.29
Consensus pattern (96 bp):
TTTATAAGTCTCCACCACCACCAATTCACTCCCCACCTCCTCCCTATGTACATAAGTCTCCACCA
CCACCAGCCCACTCTCGACCTAGTCCCTATG
Found at i:48682 original size:144 final size:144
Alignment explanation
Indices: 48534--48795 Score: 339
Period size: 144 Copynumber: 1.8 Consensus size: 144
48524 ATCTCCTTCT
* * * *
48534 TATGTGTATAAGTCTCCACCACCACCAGTCCACTCTCG-ACTTAGTCCCTATGTTTATAAGTCTC
1 TATGTGTATAAGTCTCCACCACCACCAGTCCACTAT-GAACCTAGTCCCTATATCTATAAGTCTC
* * * *
48598 CACCACCTCCATTTCACTCCCGACCTCGTCCCTATGTAC-ATAAGTCTCCACCACCACCAGCCCA
65 CACCACCACCAGTTCACTCCCGACCCCCTCCCTATGT-CTATAAGTCTCCACCACCACCAGCCCA
48662 CTTTCGACCTCGTCCC
129 CTTTCGACCTCGTCCC
* * * * *
48678 TATGTTTATAGGTCTCCACCACCTCCATTCCACTATGAACCTCGTCCCTATATCTATAAGTCTCC
1 TATGTGTATAAGTCTCCACCACCACCAGTCCACTATGAACCTAGTCCCTATATCTATAAGTCTCC
* * * *
48743 ACCGCCACCAGTTCACTTCTGACCCCCTTCCTATGTCTATAAGTCTCCACCAC
66 ACCACCACCAGTTCACTCCCGACCCCCTCCCTATGTCTATAAGTCTCCACCAC
48796 ATCCAACCAC
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
143 2 0.02
144 97 0.98
ACGTcount: A:0.22, C:0.40, G:0.10, T:0.29
Consensus pattern (144 bp):
TATGTGTATAAGTCTCCACCACCACCAGTCCACTATGAACCTAGTCCCTATATCTATAAGTCTCC
ACCACCACCAGTTCACTCCCGACCCCCTCCCTATGTCTATAAGTCTCCACCACCACCAGCCCACT
TTCGACCTCGTCCC
Found at i:58690 original size:20 final size:21
Alignment explanation
Indices: 58661--58700 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
58651 TAATAGAATA
*
58661 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
58682 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
58701 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:58690 original size:53 final size:52
Alignment explanation
Indices: 58628--58754 Score: 220
Period size: 53 Copynumber: 2.4 Consensus size: 52
58618 AGCAACAGAA
58628 TAAAAATGATTCC-ATCTAATAACTAATAGAATAAAAAACTGATTCTATCTAAT
1 TAAAAATGA-TCCTATCTAATAACTAATAGAAT-AAAAACTGATTCTATCTAAT
58681 TAAAAATGATCCTATCTAATAACTAATAGAATAAAAACTGATTCTATCTAAT
1 TAAAAATGATCCTATCTAATAACTAATAGAATAAAAACTGATTCTATCTAAT
58733 TAAAAACTGATCCTATCTAATA
1 TAAAAA-TGATCCTATCTAATA
58755 TTTTAATTTA
Statistics
Matches: 72, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
52 29 0.40
53 43 0.60
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (52 bp):
TAAAAATGATCCTATCTAATAACTAATAGAATAAAAACTGATTCTATCTAAT
Found at i:58760 original size:25 final size:21
Alignment explanation
Indices: 58712--58753 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
58702 ACTAATAGAA
*
58712 TAAAAACTGATTCTATCTAAT
1 TAAAAACTGATCCTATCTAAT
58733 TAAAAACTGATCCTATCTAAT
1 TAAAAACTGATCCTATCTAAT
58754 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
TAAAAACTGATCCTATCTAAT
Found at i:63386 original size:20 final size:21
Alignment explanation
Indices: 63357--63396 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
63347 TAATAGAATA
*
63357 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
63378 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
63397 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:63386 original size:53 final size:52
Alignment explanation
Indices: 63324--63450 Score: 227
Period size: 53 Copynumber: 2.4 Consensus size: 52
63314 AGCAACATAA
*
63324 TAAAAATGATTCTATCTAATAACTAATAGAATAAAAAACTGATTCTATCTAAT
1 TAAAAATGATCCTATCTAATAACTAATAGAAT-AAAAACTGATTCTATCTAAT
63377 TAAAAATGATCCTATCTAATAACTAATAGAATAAAAACTGATTCTATCTAAT
1 TAAAAATGATCCTATCTAATAACTAATAGAATAAAAACTGATTCTATCTAAT
63429 TAAAAACTGATCCTATCTAATA
1 TAAAAA-TGATCCTATCTAATA
63451 TTTAATTTAG
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
52 26 0.36
53 46 0.64
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (52 bp):
TAAAAATGATCCTATCTAATAACTAATAGAATAAAAACTGATTCTATCTAAT
Found at i:63434 original size:21 final size:21
Alignment explanation
Indices: 63408--63449 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
63398 ACTAATAGAA
*
63408 TAAAAACTGATTCTATCTAAT
1 TAAAAACTGATCCTATCTAAT
63429 TAAAAACTGATCCTATCTAAT
1 TAAAAACTGATCCTATCTAAT
63450 ATTTAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
TAAAAACTGATCCTATCTAAT
Found at i:65830 original size:21 final size:20
Alignment explanation
Indices: 65791--65831 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
65781 CCTCGACAGA
**
65791 ACTAGAATACCCCTTTCTTG
1 ACTAGAATACCCCCATCTTG
65811 ACTAGAGATACCCCCATCTTG
1 ACTAGA-ATACCCCCATCTTG
65832 TGACTTCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (20 bp):
ACTAGAATACCCCCATCTTG
Found at i:69316 original size:22 final size:22
Alignment explanation
Indices: 69291--69341 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
69281 CTGTTAGCGC
69291 CCGGCGATGGAAGCTGTGACTG
1 CCGGCGATGGAAGCTGTGACTG
*
69313 CCGGCGATGGAGGCTGTGACTG
1 CCGGCGATGGAAGCTGTGACTG
69335 CCGGCGA
1 CCGGCGA
69342 AAAAAGAAGG
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:0.16, C:0.25, G:0.43, T:0.16
Consensus pattern (22 bp):
CCGGCGATGGAAGCTGTGACTG
Done.