Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007487.1 Hibiscus syriacus cultivar Beakdansim tig00020667_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: 70219
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:1235 original size:14 final size:14
Alignment explanation
Indices: 1216--1242 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1206 TGATCCAACG
1216 GTGCCAGACATACT
1 GTGCCAGACATACT
1230 GTGCCAGACATAC
1 GTGCCAGACATAC
1243 GGCGCTAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.19
Consensus pattern (14 bp):
GTGCCAGACATACT
Found at i:17200 original size:22 final size:22
Alignment explanation
Indices: 17172--17228 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
17162 CCAAGAGGGG
*
17172 AGTATCGATACCATAGTCTAAT
1 AGTATCGATACCATAGTATAAT
17194 AGTATCGATACCATAGTATAAT
1 AGTATCGATACCATAGTATAAT
17216 AGTATCGATACCA
1 AGTATCGATACCA
17229 GGGTGGGGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.30
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAAT
Found at i:17985 original size:68 final size:68
Alignment explanation
Indices: 17906--18496 Score: 741
Period size: 68 Copynumber: 8.7 Consensus size: 68
17896 AAGATAAATA
* * *
17906 GCCTAACTGTGCAATTGACATAAAGGTGTCAGTTATGTCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
17971 GAG
66 GAG
* * *
17974 GCCTAACTGTGCAATTGACACAAAGGTGTCAATTATACCAGTTAGATGAAAGGATAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18039 GAG
66 GAG
* * * ** * *
18042 GCCTATCTATGCAATTGATAGAAAAATGTCAATTATGCCAGTTGGATGAAAGGCTAAGTGCCTTC
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18107 GAG
66 GAG
* * * ** * *
18110 GCCTAACTGTGCATTTTACAGAAAGGTGTTAATTATGCCAACTAAATAAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18175 GAG
66 GAG
* * * *
18178 GCCTAACTGTGCAATTGACAGAAATGTGTCAATTATTCTAGTTAGATGAAAGTCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
*
18243 GCG
66 GAG
* * * * * * * **
18246 GCCTAACTGTGCATTTGACAGACATGTGTCAATTAAGCTAGTTAGATGAAAAGATAAGTGATTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18311 GAG
66 GAG
* * * **
18314 GCCTAACTGTGCAGTTGACAGAAAGGTATCAATTATGCTAGTTAGATGAAAGGAAAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18379 GAG
66 GAG
* * * * *
18382 GCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGCCAATTAAATGAAAGGCTAAGTGCATTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
18447 GAG
66 GAG
* ** * *
18450 GCTTAACTGTGCAATTGGTAAAAATGTGTCAATTATGCCAGTTAGAT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGAT
18497 AAACGGTTAA
Statistics
Matches: 446, Mismatches: 77, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 446 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (68 bp):
GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:18591 original size:81 final size:81
Alignment explanation
Indices: 18456--18878 Score: 535
Period size: 81 Copynumber: 5.2 Consensus size: 81
18446 TGAGGCTTAA
* * * * *
18456 CTGTGCAATTGGTAAAAATGTGTCAATTATGCCAGTTAGATAAACGGTTAAAGACCTTTGAGTAA
1 CTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCTTTGAGTAA
*
18521 ATGATAAATGGCCTAG
66 AAGATAAATGGCCTAG
* * * * *
18537 CTGTGTATTTGGTAGAAAGGTGTGAATTATGCCAGTTAGATGAATGGTTAAAGA-CTGTTAAGTA
1 CTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCT-TTGAGTA
*
18601 AAAGATAAATGACCTAG
65 AAAGATAAATGGCCTAG
* * * *
18618 GTGTGCATTTGGCATAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAGA-CTGTTGAGTA
1 CTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCT-TTGAGTA
18682 AAAGATAAATGGCCTAG
65 AAAGATAAATGGCCTAG
* * * * * * *
18699 CTCTGCATTTGGAAGAAAAGTGTTAATTATGCCAATTAGATGAATGGTTAAAGACCGTTGAGTAA
1 CTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCTTTGAGTAA
*
18764 AATATAAATGGCCTAG
66 AAGATAAATGGCCTAG
* * *
18780 TTGTGCATTTGGCAGAAAGGTGTCAATTATGCAAGTTAGATGAACGGTTAAAGACCGTTGAGTAA
1 CTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCTTTGAGTAA
18845 AAGATAAATGGCCTAG
66 AAGATAAATGGCCTAG
* * * *
18861 TTTTACTTTTGGCAGAAA
1 CTGTGCATTTGGCAGAAA
18879 AGGGTTATTC
Statistics
Matches: 299, Mismatches: 41, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
80 2 0.01
81 296 0.99
82 1 0.00
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.30
Consensus pattern (81 bp):
CTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCTTTGAGTAA
AAGATAAATGGCCTAG
Found at i:18740 original size:162 final size:162
Alignment explanation
Indices: 18457--18860 Score: 596
Period size: 162 Copynumber: 2.5 Consensus size: 162
18447 GAGGCTTAAC
* *
18457 TGTGCAATTGGTAAAAATGTGTCAATTATGCCAGTTAGAT-AAACGGTTAAAGACCT-TTGAGTA
1 TGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATGAAA-GGTTAAAGA-CTGTTGAGTA
* * * * * *
18520 AATGATAAATGGCCTAGCTGTGTATTTGGTAGAAAGGTGTGAATTATGCCAGTTAGATGAATGGT
64 AAAGATAAATGGCCTAGCTCTGCATTTGGAAGAAAAGTGTGAATTATGCCAATTAGATGAATGGT
*
18585 TAAAGACTGTTAAGTAAAAGATAAATGACCTAGG
129 TAAAGACCGTTAAGTAAAAGATAAATGACCTAGG
*
18619 TGTGCATTTGGCATAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAGACTGTTGAGTAAA
1 TGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAGACTGTTGAGTAAA
*
18684 AGATAAATGGCCTAGCTCTGCATTTGGAAGAAAAGTGTTAATTATGCCAATTAGATGAATGGTTA
66 AGATAAATGGCCTAGCTCTGCATTTGGAAGAAAAGTGTGAATTATGCCAATTAGATGAATGGTTA
* * * *
18749 AAGACCGTTGAGTAAAATATAAATGGCCTAGT
131 AAGACCGTTAAGTAAAAGATAAATGACCTAGG
* * * * *
18781 TGTGCATTTGGCAGAAAGGTGTCAATTATGCAAGTTAGATGAACGGTTAAAGACCGTTGAGTAAA
1 TGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAGACTGTTGAGTAAA
18846 AGATAAATGGCCTAG
66 AGATAAATGGCCTAG
18861 TTTTACTTTT
Statistics
Matches: 220, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
161 2 0.01
162 215 0.98
163 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.25, T:0.29
Consensus pattern (162 bp):
TGTGCATTTGGCAAAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAAAGACTGTTGAGTAAA
AGATAAATGGCCTAGCTCTGCATTTGGAAGAAAAGTGTGAATTATGCCAATTAGATGAATGGTTA
AAGACCGTTAAGTAAAAGATAAATGACCTAGG
Found at i:23468 original size:57 final size:55
Alignment explanation
Indices: 23405--23520 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 55
23395 ATGGCACTGA
*
23405 GTGTGCAAAAAGTTA-AGAAATTCATACTAAGTGTATGAATTTCCGTATAGG-CACTTT
1 GTGTGC-AAAA-TTAGA-AAATTCATACTAAGTGTATGAATTTCCGTAT-GGACACTAT
* * * *
23462 GTGTGCAAAATTGGAAAATTCATCCTACGTGTATGAATTTTCGTATGGACACTAT
1 GTGTGCAAAATTAGAAAATTCATACTAAGTGTATGAATTTCCGTATGGACACTAT
23517 GTGT
1 GTGT
23521 ATGAACTAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
54 2 0.04
55 39 0.75
56 5 0.10
57 6 0.12
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (55 bp):
GTGTGCAAAATTAGAAAATTCATACTAAGTGTATGAATTTCCGTATGGACACTAT
Found at i:23849 original size:68 final size:68
Alignment explanation
Indices: 23770--24363 Score: 803
Period size: 68 Copynumber: 8.7 Consensus size: 68
23760 AAGAAAAATA
* * *
23770 GCCTAACTGTGCAATTGACATAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTACCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
23835 GAG
66 GAG
* * * *
23838 GGCTAATTGTGCAATTGATAGAAAGGTGTCAATTATGCCCGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
23903 GAG
66 GAG
* *** * * *
23906 GCCTAACTATTTGATTGACAGAAATGTGTTAATTATGCCA-TATAGATGAAAGGCTAAGTGTCTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGT-TAGATGAAAGGCTAAGTGCCTT
*
23970 TAAG
65 TGAG
* *
23974 GCATAATTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
*
24039 AAG
66 GAG
* * * * **
24042 GCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAATTAGATGTAATTCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
24107 GAG
66 GAG
* * *
24110 GCCTAACTGTGCAGTTGACAGAAAGGTGTCAATTATGCTAGTTAGATTAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
24175 GAG
66 GAG
* * * * ** *
24178 GCCGAACTGTGCATTTGACATAAACGTGTCAATTATGTGAGTTAGATAAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
*
24243 AAG
66 GAG
* * *
24246 GCCTAACTGTGCAATTGGCAGGAAGGTGTCAATTATGCCAGTTAGATAAAAGGCTAAGTGCCTTT
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
24311 GAG
66 GAG
* * *
24314 GCCTAACTGTGCAATTGACAAAAAGGTGCCAATTATACCAGTTAGATGAA
1 GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
24364 CGGTTAAAGA
Statistics
Matches: 456, Mismatches: 68, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
67 1 0.00
68 454 1.00
69 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (68 bp):
GCCTAACTGTGCAATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:24448 original size:81 final size:81
Alignment explanation
Indices: 24313--24752 Score: 562
Period size: 81 Copynumber: 5.4 Consensus size: 81
24303 GTGCCTTTGA
* * * *
24313 GGCCTAACTGTGCAATTGACA-AAAAGGTGCCAATTATACCAGTTAGATGAACGGTTAAAGACCG
1 GGCCTAGCTGTGCATTTGGCAGAAAA-GTGTCAATTATACCAGTTAGATGAACGGTTAAAGACCG
* *
24377 TTAAGTAAATGATAAAT
65 TTGAGTAAAAGATAAAT
*
24394 GGCCTAGCTGTGCATTTGGCAGAAAAGTGTTAATTATACCAGTTAGATGAACGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATACCAGTTAGATGAACGGTTAAAGACCGT
24459 TGAGTAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * * *
24475 GGCCTAGTTGTGCATTTGGTATAAATGTATCAATTATACCAGTTAGATGAATGGTTAAAGACAGT
1 GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATACCAGTTAGATGAACGGTTAAAGACCGT
*
24540 TGAGAAAAAGATAAAT
66 TGAGTAAAAGATAAAT
* * * * * *
24556 GG-ATAGCTGTGTATTTGGAAG-AAAGTTGATCAAATTATGCCAGTTAGATTAATGGTTAAAGAC
1 GGCCTAGCTGTGCATTTGGCAGAAAAG-TG-TC-AATTATACCAGTTAGATGAACGGTTAAAGAC
24619 CGTTGAGTAAAAGATAAAT
63 CGTTGAGTAAAAGATAAAT
* * * * *
24638 GGCCTAGCTATACATTTGGCAGAAATGTGTCAATTATGCCAGTTGGATGAACGGTTAAAGACCGT
1 GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATACCAGTTAGATGAACGGTTAAAGACCGT
*
24703 TGAGTAAACGATAAAT
66 TGAGTAAAAGATAAAT
* *
24719 GGCCTAGCTGTGCTTTTGGCAGAAAAGGGTCAAT
1 GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAAT
24753 CATGCAAGTT
Statistics
Matches: 311, Mismatches: 42, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
79 3 0.01
80 15 0.05
81 220 0.71
82 54 0.17
83 16 0.05
84 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATACCAGTTAGATGAACGGTTAAAGACCGT
TGAGTAAAAGATAAAT
Found at i:24638 original size:163 final size:161
Alignment explanation
Indices: 24343--24743 Score: 554
Period size: 163 Copynumber: 2.5 Consensus size: 161
24333 AAAAAGGTGC
* * *
24343 CAATTATACCAGTTAGATGAACGGTTAAAGACCGTTAAGTAAATGATAAATGGCCTAGCTGTGCA
1 CAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTGTGTA
*
24408 TTTGGCAGAAAAGTGTTAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAA
66 TTTGGCAG-AAAGTGTAAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAA
* * * * *
24473 ATGGCCTAGTTGTGCATTTGGTATAAATGTAT
130 ATGGCCTAGCTATACATTTGGCAGAAATGTAT
* * * *
24505 CAATTATACCAGTTAGATGAATGGTTAAAGACAGTTGAGAAAAAGATAAATGG-ATAGCTGTGTA
1 CAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTGTGTA
* * * *
24569 TTTGGAAGAAAGTTGATCAAATTATGCCAGTTAGATTAATGGTTAAAGACCGTTGAGTAAAAGAT
66 TTTGGCAGAAAG-TG-T-AAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
24634 AAATGGCCTAGCTATACATTTGGCAGAAATGTGT
128 AAATGGCCTAGCTATACATTTGGCAGAAATGTAT
* * *
24668 CAATTATGCCAGTTGGATGAACGGTTAAAGACCGTTGAGTAAACGATAAATGGCCTAGCTGTGCT
1 CAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTGTG-T
24733 -TTTGGCAGAAA
65 ATTTGGCAGAAA
24744 AGGGTCAATC
Statistics
Matches: 208, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
160 4 0.02
161 18 0.09
162 49 0.24
163 118 0.57
164 18 0.09
165 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (161 bp):
CAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTGTGTA
TTTGGCAGAAAGTGTAAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAA
TGGCCTAGCTATACATTTGGCAGAAATGTAT
Found at i:32892 original size:18 final size:18
Alignment explanation
Indices: 32869--32913 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
32859 TTGAAACATA
32869 TGATAATTGTATAATTTT
1 TGATAATTGTATAATTTT
32887 TGATAATTGTATAATTTT
1 TGATAATTGTATAATTTT
*
32905 TTATAATTG
1 TGATAATTG
32914 AGTGACTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
TGATAATTGTATAATTTT
Found at i:33404 original size:47 final size:47
Alignment explanation
Indices: 33335--33427 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
33325 TACATTCATG
*
33335 CCGTTTCACGTGTTGCAGAATAGCTTTTGCTTATCCACCAGCTCTTT
1 CCGTTTCACGTGTTGCAGAATAGCTTTCGCTTATCCACCAGCTCTTT
33382 CCGTTTCACGTGTTG-AGGAATAGCTTTCGCTTATCCACCAGCTCTT
1 CCGTTTCACGTGTTGCA-GAATAGCTTTCGCTTATCCACCAGCTCTT
33428 CTGTGTCAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
46 1 0.02
47 43 0.98
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37
Consensus pattern (47 bp):
CCGTTTCACGTGTTGCAGAATAGCTTTCGCTTATCCACCAGCTCTTT
Found at i:44826 original size:49 final size:50
Alignment explanation
Indices: 44754--44866 Score: 183
Period size: 49 Copynumber: 2.2 Consensus size: 50
44744 AAGCTAATAC
*
44754 AAAGGGTGTGCACAAATTTCAACAAGTACAGAAAAGTC-AAAAAAATTAA
1 AAAGGGTGTGCACAAATTTCAACAAGTACAGAAAAGTCAAAAAAAATAAA
*
44803 AAAGGGTGTGCACAAATTTCAACAAGTGCAGAAAAGTCAAAAAAAAAATAAA
1 AAAGGGTGTGCACAAATTTCAACAAGTACAGAAAAGTC--AAAAAAAATAAA
44855 AAAGGGTGTGCA
1 AAAGGGTGTGCA
44867 GAATTTTTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
49 37 0.63
52 22 0.37
ACGTcount: A:0.52, C:0.12, G:0.19, T:0.17
Consensus pattern (50 bp):
AAAGGGTGTGCACAAATTTCAACAAGTACAGAAAAGTCAAAAAAAATAAA
Found at i:46137 original size:75 final size:71
Alignment explanation
Indices: 46018--46165 Score: 233
Period size: 75 Copynumber: 2.0 Consensus size: 71
46008 GTAACCTAGC
*
46018 TGTCAATGAATCTTTCAGGTTCGAGTGTCAGCTGTACTTACTAATGAACCTTTCTTGTTGAATCC
1 TGTCAATGAATCTTTCAGGTTCGAGTGTCAGCTGTACTTACTAATGAACCTCTCTTGTTGAATCC
46083 TGATTG
66 TGATTG
*
46089 TGTCAATGAATCTTTCTCTCAGGTTCGAGTGTCAGCTGTACTTACTAATGGACCTCTCTTGTTGA
1 TGTCAATGAATC--T-T-TCAGGTTCGAGTGTCAGCTGTACTTACTAATGAACCTCTCTTGTTGA
*
46154 ATCTTGATTG
62 ATCCTGATTG
46164 TG
1 TG
46166 ATCGCTACAT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
71 12 0.17
73 1 0.01
74 1 0.01
75 56 0.80
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (71 bp):
TGTCAATGAATCTTTCAGGTTCGAGTGTCAGCTGTACTTACTAATGAACCTCTCTTGTTGAATCC
TGATTG
Found at i:52709 original size:24 final size:24
Alignment explanation
Indices: 52685--52742 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
52675 TCTATGCGGT
52685 CTTTCGGGACAAATTCTACGTGGTC
1 CTTT-GGGACAAATTCTACGTGGTC
52710 CTTTGGGACAAATTCTACGTGGTC
1 CTTTGGGACAAATTCTACGTGGTC
52734 CTTTGGGAC
1 CTTTGGGAC
52743 GTATATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 29 0.88
25 4 0.12
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (24 bp):
CTTTGGGACAAATTCTACGTGGTC
Found at i:52926 original size:24 final size:24
Alignment explanation
Indices: 52856--52926 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
52846 CAATCTTATA
*
52856 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
52879 CGGCACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
52903 TGGCACTTTGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
52927 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 12 0.30
24 28 0.70
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:53241 original size:18 final size:17
Alignment explanation
Indices: 53205--53243 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
53195 TAAAAGGTAT
* *
53205 TAATGATAATAATACGA
1 TAATGATAAGAATAAGA
53222 TAATGATAAGGAATAAGA
1 TAATGATAA-GAATAAGA
53240 TAAT
1 TAAT
53244 CATATATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.03, G:0.15, T:0.28
Consensus pattern (17 bp):
TAATGATAAGAATAAGA
Found at i:55459 original size:22 final size:22
Alignment explanation
Indices: 55433--55485 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
55423 CCGTTTAACA
55433 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
55455 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
55477 GGGGGAATC
1 GGGGGAATC
55486 AGTTCCCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.15, C:0.25, G:0.43, T:0.17
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCTTGG
Found at i:62073 original size:6 final size:6
Alignment explanation
Indices: 62062--62086 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
62052 TGCCATTTCC
62062 TCGTCA TCGTCA TCGTCA TCGTCA T
1 TCGTCA TCGTCA TCGTCA TCGTCA T
62087 ATTCATCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (6 bp):
TCGTCA
Found at i:67631 original size:24 final size:23
Alignment explanation
Indices: 67586--67670 Score: 127
Period size: 23 Copynumber: 3.7 Consensus size: 23
67576 TCGGAAAAAA
*
67586 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTTTGGTGCAAACC
67609 TATGTGGCACTTTTGGTGCAAACC
1 TATGTGGCAC-TTTGGTGCAAACC
*
67633 TATGTGACACTTTGGTGCAAACC
1 TATGTGGCACTTTGGTGCAAACC
67656 TATGTGGTC-CTTTGG
1 TATGTGG-CACTTTGG
67671 GACAATTATG
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
23 35 0.61
24 22 0.39
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (23 bp):
TATGTGGCACTTTGGTGCAAACC
Done.