Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002807.1 Hibiscus syriacus cultivar Beakdansim tig00005776_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: 70402
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:693 original size:10 final size:10
Alignment explanation
Indices: 667--703 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
657 AACTTCTAAC
667 ATCAATTTCA
1 ATCAATTTCA
677 TATCAATTTCA
1 -ATCAATTTCA
688 ATCAATTTCA
1 ATCAATTTCA
698 A-CAATT
1 ATCAATT
704 CTCCATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 5 0.19
10 11 0.42
11 10 0.38
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATCAATTTCA
Found at i:10418 original size:85 final size:85
Alignment explanation
Indices: 10275--10442 Score: 327
Period size: 85 Copynumber: 2.0 Consensus size: 85
10265 TTTCACTAGA
*
10275 TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCTGAGTCTTGATAGATG
1 TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCCGAGTCTTGATAGATG
10340 TCAAACTGGATGATACTGGC
66 TCAAACTGGATGATACTGGC
10360 TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCCGAGTCTTGATAGATG
1 TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCCGAGTCTTGATAGATG
10425 TCAAACTGGATGATACTG
66 TCAAACTGGATGATACTG
10443 AATGGGTGCA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (85 bp):
TTATGGAATGGAAGCAGTGCTGCCCATTGAAATAGAGATTTCGTCACTCCGAGTCTTGATAGATG
TCAAACTGGATGATACTGGC
Found at i:11913 original size:114 final size:110
Alignment explanation
Indices: 11767--11968 Score: 278
Period size: 114 Copynumber: 1.8 Consensus size: 110
11757 AATTTGCTCG
* * * * *
11767 AGATTAGATTTCAACTTCGCGACGGAGGATATCCAACTCAAAGCCAATTCGATAAAACTAGATTG
1 AGATTAGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAA--C--TAAAACAAGATTG
11832 GATTTCAACTTCACAACGAAGGATATCAAACTCAAAACCAACTTACTCA
62 GATTTCAACTTCACAACGAAGGATATCAAACTCAAAACCAACTTACTCA
* * **
11881 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCAAGATTGGATT
1 AGATTAGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTAAAACAAGATTGGATT
*
11946 TCAACTTCACGACGAAGGATATC
66 TCAACTTCACAACGAAGGATATC
11969 CAATTCGAGG
Statistics
Matches: 78, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
110 35 0.45
112 1 0.01
114 42 0.54
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (110 bp):
AGATTAGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTAAAACAAGATTGGATT
TCAACTTCACAACGAAGGATATCAAACTCAAAACCAACTTACTCA
Found at i:11969 original size:55 final size:55
Alignment explanation
Indices: 11767--11971 Score: 275
Period size: 55 Copynumber: 3.7 Consensus size: 55
11757 AATTTGCTCG
* * * * * * ** *
11767 AGATTAGATTTCAACTTCGCGACGGAGGATATCCAACTCAAAGCCAATTCGATAAAACT
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAA--C--TTACTCA
*
11826 AGATTGGATTTCAACTTCACAACGAAGGATATCAAACTCAAAACCAACTTACTCA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCA
11881 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCA
*
11936 AGATTGGATTTCAACTTCACGACGAAGGATATCCAA
1 AGATTGGATTTCAACTTCACAACGAAGGATATCCAA
11972 TTCGAGGCTC
Statistics
Matches: 134, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
55 92 0.69
57 1 0.01
59 41 0.31
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (55 bp):
AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAACTTACTCA
Found at i:12101 original size:120 final size:119
Alignment explanation
Indices: 11939--12406 Score: 639
Period size: 120 Copynumber: 3.9 Consensus size: 119
11929 TTACTCAAGA
*
11939 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * * * *
12004 CCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGCAGTAACATGCAATAC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACAT-CAATAC
* * *
12059 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAGGCTCAATTTCACAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * * ** *
12124 CCTCAATTTCAACTTCACGACGAAGGATATCGTGCCCACCAACAACTTTTATCTTTAAA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAAC----ATCAAT-AC
* * *
12183 TTGGATTTCAACTTTACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* * **
12248 CCACGATTTCAACTTCACGATGAAGGATCTCGTGCCCATAAGCAACATACAATAC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACAT-CAATAC
* *
12303 TTGGATTTCAACTTCACGTCGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
* *
12368 CCACGATTTCAACTTCACGACGAAAGATATCATGCCCAC
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCAC
12407 TTATACAATG
Statistics
Matches: 302, Mismatches: 40, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
120 197 0.65
121 2 0.01
123 2 0.01
124 101 0.33
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (119 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATCAATAC
Found at i:12314 original size:244 final size:244
Alignment explanation
Indices: 11938--12406 Score: 740
Period size: 244 Copynumber: 1.9 Consensus size: 244
11928 CTTACTCAAG
* *
11938 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCGAGGCTCAACTTCACAACGAAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCA
* * *
12003 TCCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGCAGTAACATGCAATACTTGGATTTC
66 TCCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGAAGCAACATACAATACTTGGATTTC
* * * *
12068 AACTTCACAACGAAGGATATCCAATTCAAGGCTCAATTTCACAACGAATGGGCCATCCTCAATTT
131 AACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACAATTT
* *
12133 CAACTTCACGACGAAGGATATCGTGCCCACCAACAACTTTTATCTTTAA
196 CAACTTCACGACGAAAGATATCATGCCCACCAACAACTTTTATCTTTAA
* *
12182 ATTGGATTTCAACTTTACGACGAATGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCA
* * * * * *
12247 TCCACGATTTCAACTTCACGATGAAGGATCTCGTGCCCATAAGCAACATACAATACTTGGATTTC
66 TCCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGAAGCAACATACAATACTTGGATTTC
** *
12312 AACTTCACGTCGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGATTT
131 AACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACAATTT
12377 CAACTTCACGACGAAAGATATCATGCCCAC
196 CAACTTCACGACGAAAGATATCATGCCCAC
12407 TTATACAATG
Statistics
Matches: 203, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
244 203 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (244 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACAAAGGGGCCA
TCCACGATTTCAACTTCACAACGAAGAATATCGAGCCCAGAAGCAACATACAATACTTGGATTTC
AACTTCACAACGAAAGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACAATTT
CAACTTCACGACGAAAGATATCATGCCCACCAACAACTTTTATCTTTAA
Found at i:14779 original size:36 final size:36
Alignment explanation
Indices: 14738--14825 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 36
14728 AGGAACATTA
* * *
14738 TCAAGTTAGATAAAATTTATTTTAAGGAAAACAATC
1 TCAAGTAAGATAAAATATATTTTAAGAAAAACAATC
* * *
14774 TCAAGTGAGATAAAATATGTTTTAAGAAAAATAATC
1 TCAAGTAAGATAAAATATATTTTAAGAAAAACAATC
14810 TCAAGTAAGATAAAAT
1 TCAAGTAAGATAAAAT
14826 CATGAGTGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (36 bp):
TCAAGTAAGATAAAATATATTTTAAGAAAAACAATC
Found at i:14984 original size:78 final size:78
Alignment explanation
Indices: 14855--15027 Score: 197
Period size: 78 Copynumber: 2.2 Consensus size: 78
14845 AAGTTTGAGC
** * * * * *
14855 TTCAAGGGAAACTATCTCAAGTGAGATGATGTTAATCTAACTTCTTATGTGATAGAATCGAGCGA
1 TTCAAGGGAAAAAATCTCAAGCGAGATGATGCTAATCCAACTCCTTATGTGATAGAATCGAGCAA
14920 AATAAAATTATAT
66 AATAAAATTATAT
* * *
14933 TTCAAGGGAAAAAATCTCAAGCGAGAT-ACTGCTGATCCAACTCCTTATGTGATGGAATCTAGCA
1 TTCAAGGGAAAAAATCTCAAGCGAGATGA-TGCTAATCCAACTCCTTATGTGATAGAATCGAGCA
** *
14997 AAATGGAATTCTAT
65 AAATAAAATTATAT
15011 TTCAA-GGAAAATAATCT
1 TTCAAGGGAAAA-AATCT
15028 TAAGTAGATA
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
77 7 0.09
78 73 0.91
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (78 bp):
TTCAAGGGAAAAAATCTCAAGCGAGATGATGCTAATCCAACTCCTTATGTGATAGAATCGAGCAA
AATAAAATTATAT
Found at i:16225 original size:48 final size:47
Alignment explanation
Indices: 16115--16256 Score: 158
Period size: 48 Copynumber: 2.9 Consensus size: 47
16105 ATCATCATCA
* * *
16115 CTTAGGAATTATCGCCTTTATTGAACACACAATCACCCCTTTTACCTCAAC
1 CTTAGGAATTATCACTTTTATTGAACTCAC---CA-CCCTTTTACCTCAAC
* * * *
16166 CTTATGAATTATCACTTTTATTGGACTCACTACCCTTTGTACCTCGAC
1 CTTAGGAATTATCACTTTTATTGAACTCACCACCCTTT-TACCTCAAC
* *
16214 CTTAGGTATTATTACTTTTATTGAACTCACCACCCTTTTACCT
1 CTTAGGAATTATCACTTTTATTGAACTCACCACCCTTTTACCT
16257 TGTTTATTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
47 11 0.14
48 42 0.54
51 25 0.32
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.38
Consensus pattern (47 bp):
CTTAGGAATTATCACTTTTATTGAACTCACCACCCTTTTACCTCAAC
Found at i:25396 original size:20 final size:20
Alignment explanation
Indices: 25371--25423 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
25361 CTCGGAGGGA
25371 ACCGATTCCCCCCAGGGGGT
1 ACCGATTCCCCCCAGGGGGT
25391 ACCGATTCCCCCCAGGGGGT
1 ACCGATTCCCCCCAGGGGGT
25411 ACCGATTCCCCCC
1 ACCGATTCCCCCC
25424 TGTGTAACGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.45, G:0.25, T:0.15
Consensus pattern (20 bp):
ACCGATTCCCCCCAGGGGGT
Found at i:29617 original size:20 final size:20
Alignment explanation
Indices: 29592--29653 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
29582 TTTTGGTGCA
*
29592 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
29612 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
29633 GAAGGGGAACCGATTCCCCCA
1 G-A-GGGAACCGATACCCCCA
29654 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:39304 original size:21 final size:21
Alignment explanation
Indices: 39280--39323 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39270 AAGAATTGAA
39280 TAAATAAAAAAAATA-AAAGAT
1 TAAATAAAAAAAATACAAA-AT
* *
39301 TAAATTAAACAAATACAAAAT
1 TAAATAAAAAAAATACAAAAT
39322 TA
1 TA
39324 GAAATCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (21 bp):
TAAATAAAAAAAATACAAAAT
Found at i:40659 original size:14 final size:14
Alignment explanation
Indices: 40642--40668 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40632 AAAAATGTTA
40642 GAATTAAAAATCTC
1 GAATTAAAAATCTC
40656 GAATTAAAAATCT
1 GAATTAAAAATCT
40669 ACCACATTGA
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:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (14 bp):
GAATTAAAAATCTC
Found at i:50313 original size:15 final size:15
Alignment explanation
Indices: 50281--50309 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
50271 ATTAGTAATA
50281 AAAAAATAACCTCAC
1 AAAAAATAACCTCAC
50296 AAAAAA-AACCTCAC
1 AAAAAATAACCTCAC
50310 CAAACACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAACCTCAC
Found at i:51747 original size:42 final size:40
Alignment explanation
Indices: 51700--51839 Score: 151
Period size: 42 Copynumber: 3.4 Consensus size: 40
51690 ATTTTTTAAC
51700 AAACGCCGCAATAGAGTGGTAAATTAGCGGCGTTTATACCA
1 AAACGCCGCAATAGA-TGGTAAATTAGCGGCGTTTATACCA
* * *
51741 GAAACGCCGCAATAGAT--TAACATATAGTGGCATTT-TAGTCA
1 -AAACGCCGCAATAGATGGTAA-AT-TAGCGGCGTTTATA-CCA
*
51782 AAACACCGCAATAGATCGGTAAATTAGCGGCGTTTATACCA
1 AAACGCCGCAATAGAT-GGTAAATTAGCGGCGTTTATACCA
*
51823 CAAACGCCGTAATAGAT
1 -AAACGCCGCAATAGAT
51840 TACACATATA
Statistics
Matches: 81, Mismatches: 9, Indels: 16
0.76 0.08 0.15
Matches are distributed among these distances:
39 3 0.04
40 19 0.23
41 23 0.28
42 33 0.41
43 3 0.04
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (40 bp):
AAACGCCGCAATAGATGGTAAATTAGCGGCGTTTATACCA
Found at i:51775 original size:82 final size:82
Alignment explanation
Indices: 51689--51879 Score: 269
Period size: 82 Copynumber: 2.3 Consensus size: 82
51679 TTTATTACGA
*
51689 CATTTTTTAACAAACGCCGCAATAGAGT-GGTAAATTAGCGGCGTTTATACCAGAAACGCCGCAA
1 CATTTTTTAA-AAACGCCGCAATAGA-TCGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAA
51753 TAGATTA-ACATATAGTGG
64 TAGATTACACATATAGTGG
* * * *
51771 CATTTTAGTCAAAACACCGCAATAGATCGGTAAATTAGCGGCGTTTATACCACAAACGCCGTAAT
1 CATTTT-TTAAAAACGCCGCAATAGATCGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAAT
51836 AGATTACACATATAGTGG
65 AGATTACACATATAGTGG
*
51854 CATTTATTCTTAAAACGCCGCAATAG
1 CATTT-TT-TAAAAACGCCGCAATAG
51880 TGATAATTAA
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
81 1 0.01
82 61 0.64
83 18 0.19
84 16 0.17
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (82 bp):
CATTTTTTAAAAACGCCGCAATAGATCGGTAAATTAGCGGCGTTTATACCACAAACGCCGCAATA
GATTACACATATAGTGG
Found at i:51860 original size:42 final size:40
Alignment explanation
Indices: 51700--51879 Score: 145
Period size: 42 Copynumber: 4.3 Consensus size: 40
51690 ATTTTTTAAC
* *
51700 AAACGCCGCAATAGAGTGGTAA-AT-TAGCGGCGTTTATACCA
1 AAACGCCGCAATAGA-T--TAACATATAGTGGCATTTATACCA
*
51741 GAAACGCCGCAATAGATTAACATATAGTGGCATTT-TAGTCA
1 -AAACGCCGCAATAGATTAACATATAGTGGCATTTATA-CCA
* * *
51782 AAACACCGCAATAGATCGGTAA-AT-TAGCGGCGTTTATACCA
1 AAACGCCGCAATAGAT---TAACATATAGTGGCATTTATACCA
* * *
51823 CAAACGCCGTAATAGATTACACATATAGTGGCATTTATTCTTA
1 -AAACGCCGCAATAGATTA-ACATATAGTGGCATTTATAC-CA
51866 AAACGCCGCAATAG
1 AAACGCCGCAATAG
51880 TGATAATTAA
Statistics
Matches: 112, Mismatches: 14, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
39 5 0.04
40 20 0.18
41 25 0.22
42 58 0.52
43 4 0.04
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (40 bp):
AAACGCCGCAATAGATTAACATATAGTGGCATTTATACCA
Found at i:51921 original size:41 final size:41
Alignment explanation
Indices: 51870--52024 Score: 197
Period size: 41 Copynumber: 3.8 Consensus size: 41
51860 TTCTTAAAAC
* *
51870 GCCGCAATAGTGATAATTAATAGTGGCGTTTTTAGACAAAT
1 GCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGACAAAT
*
51911 GCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGAAAAAT
1 GCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGACAAAT
* * *
51952 GCCGCAATAGTTTTAATCAATAGTGGCATTTTTTA-ACAAAC
1 GCCGCAATAGTGTTAATCAATAGTGGC-GTTTTTAGACAAAT
* ** *
51993 ACCATAATAGTG-TAATCAATAGTGGCATTTTT
1 GCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
52025 TTGTATAAAC
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
39 5 0.05
40 14 0.14
41 76 0.75
42 6 0.06
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (41 bp):
GCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGACAAAT
Found at i:52025 original size:41 final size:40
Alignment explanation
Indices: 51847--52026 Score: 130
Period size: 41 Copynumber: 4.4 Consensus size: 40
51837 GATTACACAT
* * *
51847 ATAGTGGCATTTATTCTT-AAAACGCCGCAATAGTGATAATTA
1 ATAGTGGCATTT-TT-TTAAAAACACCACAATAGTG-TAATCA
* ** * ** *
51889 ATAGTGGCGTTTTTAGACAAATGCCGCAATAGTGTTAATCA
1 ATAGTGGCATTTTTTTAAAAACACCACAATAGTG-TAATCA
* ** ** * *
51930 ATAGTGGCGTTTTTAGAAAAATGCCGCAATAGTTTTAATCA
1 ATAGTGGCATTTTTTTAAAAACACCACAATAG-TGTAATCA
*
51971 ATAGTGGCA-TTTTTTAACAAACACCATAATAGTGTAATCA
1 ATAGTGGCATTTTTTTAA-AAACACCACAATAGTGTAATCA
52011 ATAGTGGCATTTTTTT
1 ATAGTGGCATTTTTTT
52027 GTATAAACGC
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
40 22 0.19
41 83 0.71
42 12 0.10
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (40 bp):
ATAGTGGCATTTTTTTAAAAACACCACAATAGTGTAATCA
Found at i:52025 original size:82 final size:83
Alignment explanation
Indices: 51847--52041 Score: 207
Period size: 82 Copynumber: 2.4 Consensus size: 83
51837 GATTACACAT
* *** * **
51847 ATAGTGGCATTTATTCTTAAAACGCCGCAATAGTGATAATTAATAGTGGCGTTTTTAGACAAATG
1 ATAGTGGCATTTTTTAGAAAAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTAGACAAACA
*
51912 CCGCAATAGTGTTAATCA
66 CCACAATAGTGTTAATCA
* * ** *
51930 ATAGTGGC-GTTTTTAGAAAAATGCCGCAATAGTTTTAATCAATAGTGGCATTTTTTA-ACAAAC
1 ATAGTGGCATTTTTTAGAAAAACGCCGCAATAGTGATAATCAATAGTGGC-GTTTTTAGACAAAC
*
51993 ACCATAATAGTG-TAATCA
65 ACCACAATAGTGTTAATCA
* *
52011 ATAGTGGCATTTTTTTGTATAAACGCCGCAA
1 ATAGTGGCATTTTTTAG-AAAAACGCCGCAA
52042 AATGTTAAAT
Statistics
Matches: 91, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
81 14 0.15
82 52 0.57
83 25 0.27
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (83 bp):
ATAGTGGCATTTTTTAGAAAAACGCCGCAATAGTGATAATCAATAGTGGCGTTTTTAGACAAACA
CCACAATAGTGTTAATCA
Found at i:53367 original size:43 final size:43
Alignment explanation
Indices: 53274--53371 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 43
53264 TAAAAGGTAA
* *
53274 TTAGCGGCGTTTGTATCCAGAAACGCCGCTATAAATATGACAT
1 TTAGTGGCGTTTGTATCCAAAAACGCCGCTATAAATATGACAT
* *
53317 TTTGTGGCGTTTGTATCCAAAAATGCCGCTA-AAGAGTAAT-AC-T
1 TTAGTGGCGTTTGTATCCAAAAACGCCGCTATAA-A-T-ATGACAT
53360 TTAGTGGCGTTT
1 TTAGTGGCGTTT
53372 TTGAAACAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.04
43 40 0.85
44 3 0.06
45 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (43 bp):
TTAGTGGCGTTTGTATCCAAAAACGCCGCTATAAATATGACAT
Found at i:53700 original size:41 final size:41
Alignment explanation
Indices: 53655--53775 Score: 129
Period size: 41 Copynumber: 3.0 Consensus size: 41
53645 TTTGCAGCAT
*
53655 TTTTTATACAAACACCGTAATAGGGTTAATATATAGTGGCG
1 TTTTTATACAAACGCCGTAATAGGGTTAATATATAGTGGCG
* * * *
53696 TTTTTCA-ACAAACGCCATAATAGAG-TAGTACTTTAGTGGCG
1 TTTTT-ATACAAACGCCGTAATAGGGTTAATA-TATAGTGGCG
* * * *
53737 TTTTTATACAAATGCCGTAATAAGGTTCATCTATAGTGG
1 TTTTTATACAAACGCCGTAATAGGGTTAATATATAGTGG
53776 TATTTTTCAA
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
40 5 0.08
41 55 0.87
42 3 0.05
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (41 bp):
TTTTTATACAAACGCCGTAATAGGGTTAATATATAGTGGCG
Found at i:53721 original size:82 final size:82
Alignment explanation
Indices: 53632--53821 Score: 204
Period size: 82 Copynumber: 2.3 Consensus size: 82
53622 ACTCTAATTC
* *
53632 AATAGAGTAGT-CATTT-GCAGCATTTTTTATACAAACACCGTAATAGGGTTAATATATAGTGGC
1 AATAGAGTAGTAC-TTTAGCAGC-GTTTTTATACAAACACCGTAATAAGGTTAATATATAGTGGC
* *
53695 GTTTTTCAACAAACGCCAT
64 ATTTTTCAAAAAACGCCAT
** ** * * *
53714 AATAGAGTAGTACTTTAGTGGCGTTTTTATACAAATGCCGTAATAAGGTTCATCTATAGTGGTAT
1 AATAGAGTAGTACTTTAGCAGCGTTTTTATACAAACACCGTAATAAGGTTAATATATAGTGGCAT
** **
53779 TTTTCAAAAAACATCGC
66 TTTTCAAAAAACGCCAT
*
53796 AATAGAGTAGTACTTTAGCGGCGTTT
1 AATAGAGTAGTACTTTAGCAGCGTTT
53822 ATAGAAAAAC
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
82 86 0.96
83 4 0.04
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (82 bp):
AATAGAGTAGTACTTTAGCAGCGTTTTTATACAAACACCGTAATAAGGTTAATATATAGTGGCAT
TTTTCAAAAAACGCCAT
Found at i:61915 original size:21 final size:21
Alignment explanation
Indices: 61897--62001 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
61887 ATGAAGCAAG
61897 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* ** *
61918 AGAAGCAGCCATAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
61939 GGAAGCAGAGAAAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* * *
61960 GGTAGCACAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
61981 -GACAGCACAGAGAGAAGCAGC
1 GGA-AGCAGAGAGAGCAGCAGC
62002 ATATCAGCAG
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
20 1 0.01
21 69 0.99
ACGTcount: A:0.41, C:0.21, G:0.36, T:0.02
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:62013 original size:42 final size:42
Alignment explanation
Indices: 61933--62014 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
61923 CAGCCATAGC
* *
61933 AGCAGCGGAAGCAGAGAAAGAAGCAGCGGTAGCACAGAGAGA
1 AGCAGCGGAAGCACAGAAAGAAGCAGCGATAGCACAGAGAGA
* *
61975 AGCAGC-GACAGCACAGAGAGAAGCAGC-ATATCAGCAGAGA
1 AGCAGCGGA-AGCACAGAAAGAAGCAGCGATAGCA-CAGAGA
62015 TGTGAAGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
41 6 0.18
42 28 0.82
ACGTcount: A:0.43, C:0.20, G:0.34, T:0.04
Consensus pattern (42 bp):
AGCAGCGGAAGCACAGAAAGAAGCAGCGATAGCACAGAGAGA
Found at i:62507 original size:85 final size:85
Alignment explanation
Indices: 62418--62582 Score: 215
Period size: 85 Copynumber: 1.9 Consensus size: 85
62408 TTTTAGCAAC
**
62418 AACGCCACAAAACATCAATGCCTACTACGACGTTTGT-GAGAAAAACGCCGCAAAACATCAAAAC
1 AACGCCACAAAACATCAACACCTACTACGACGTTT-TAGAGAAAAACGCCGCAAAACATCAAAAC
*
62482 CTACTGCGGCGTTTGTGGGAA
65 CTACTGCAGCGTTTGTGGGAA
* * ** * * *
62503 AACGCCACAACACATCAACACCTACTGCGGTGTTTTAGATAAAAACGCCGCTAAACATCATAACC
1 AACGCCACAAAACATCAACACCTACTACGACGTTTTAGAGAAAAACGCCGCAAAACATCAAAACC
*
62568 TATTGCAGCGTTTGT
66 TACTGCAGCGTTTGT
62583 CTATAAAACA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 1 0.01
85 67 0.99
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.21
Consensus pattern (85 bp):
AACGCCACAAAACATCAACACCTACTACGACGTTTTAGAGAAAAACGCCGCAAAACATCAAAACC
TACTGCAGCGTTTGTGGGAA
Found at i:62518 original size:42 final size:43
Alignment explanation
Indices: 62418--62582 Score: 172
Period size: 43 Copynumber: 3.9 Consensus size: 43
62408 TTTTAGCAAC
** * *
62418 AACGCCACAAAACATCAATGCCTACTACGACGTTTGTGAGAAA
1 AACGCCACAAAACATCAAAACCTACTGCGGCGTTTGTGAGAAA
* *
62461 AACGCCGCAAAACATCAAAACCTACTGCGGCGTTTGTG-GGAA
1 AACGCCACAAAACATCAAAACCTACTGCGGCGTTTGTGAGAAA
* * * *
62503 AACGCCACAACACATCAACACCTACTGCGGTGTTT-TAGATAAA
1 AACGCCACAAAACATCAAAACCTACTGCGGCGTTTGT-GAGAAA
* * * * *
62546 AACGCCGCTAAACATCATAACCTATTGCAGCGTTTGT
1 AACGCCACAAAACATCAAAACCTACTGCGGCGTTTGT
62583 CTATAAAACA
Statistics
Matches: 99, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 35 0.35
43 62 0.63
44 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.21
Consensus pattern (43 bp):
AACGCCACAAAACATCAAAACCTACTGCGGCGTTTGTGAGAAA
Found at i:62591 original size:43 final size:43
Alignment explanation
Indices: 62459--62788 Score: 289
Period size: 43 Copynumber: 7.7 Consensus size: 43
62449 GTTTGTGAGA
* * * * ***
62459 AAAACGCCGCAAAACATCAAAACCTACTGCGGCGTTTGT-GGG
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTAC
* * * * *
62501 AAAACGCCAC-AACACATCAACACCTACTGCGGTGTTT-TAGATA-
1 AAAACGCCGCTAA-ATATCAACACCTATTGCGGCGTTTGT--CTAC
* * *
62544 AAAACGCCGCTAAACATCATA-ACCTATTGCAGCGTTTGTCTAT
1 AAAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTGTCTAC
* * *
62587 AAAACACTGCTAAATATCAATACCTATTGCGGCGTTTGTCTGA-
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCT-AC
* * * *
62630 AAAATGCCGCTAAATATCAACACCTATTGCAGTGTTTGTCTAAA
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCT-AC
* **
62674 AAAACACCGCTAAATATCAACATTTATTGCGGCGTTTGTC-AC
1 AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTAC
62716 ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTC-AC
1 A-AAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTAC
* *
62759 ACAAACGCCGCTAAATATTAATACCTATTG
1 A-AAACGCCGCTAAATATCAACACCTATTG
62789 TGGCATTTTT
Statistics
Matches: 243, Mismatches: 33, Indels: 23
0.81 0.11 0.08
Matches are distributed among these distances:
41 3 0.01
42 36 0.15
43 165 0.68
44 39 0.16
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (43 bp):
AAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCTAC
Found at i:62729 original size:130 final size:129
Alignment explanation
Indices: 62459--62788 Score: 344
Period size: 130 Copynumber: 2.6 Consensus size: 129
62449 GTTTGTGAGA
* * * * * * *
62459 AAAACGCCGCAAAACATCAAAACCTACTGCGGCGTTTGT-GGGAAAACGCCAC-AACACATCAAC
1 AAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTGTCAGAAAAACGCCGCTAA-ATATCAAC
* * * * *
62522 ACCTACTGCGGTGTTTTAGATAAAAACGCCGCTAAACATCATAACCTATTGCAGCGTTTGTCTAT
65 ACCTATTGCAGTGTTTTAGAAAAAAACACCGCTAAACATCATAACCTATTGCAGCGTTTGTCTAC
* * * * *
62587 AAAACACTGCTAAATATCAATACCTATTGCGGCGTTTGTCTGAAAAATGCCGCTAAATATCAACA
1 AAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTGTCAGAAAAACGCCGCTAAATATCAACA
** * ** *
62652 CCTATTGCAGTGTTTGTCTAAAAAAACACCGCTAAATATCA-ACATTTATTGCGGCGTTTGTC-A
66 CCTATTGCAGTGTTT-TAGAAAAAAACACCGCTAAACATCATA-ACCTATTGCAGCGTTTGTCTA
62715 C
129 C
* * * * *
62716 ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCACACAAACGCCGCTAAATATTAAT
1 A-AAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTGTCAGAAAAACGCCGCTAAATATCAAC
62781 ACCTATTG
65 ACCTATTG
62789 TGGCATTTTT
Statistics
Matches: 166, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
128 33 0.20
129 33 0.20
130 100 0.60
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (129 bp):
AAAACGCCGCTAAATATCAAAACCTATTGCGGCGTTTGTCAGAAAAACGCCGCTAAATATCAACA
CCTATTGCAGTGTTTTAGAAAAAAACACCGCTAAACATCATAACCTATTGCAGCGTTTGTCTAC
Found at i:62809 original size:87 final size:85
Alignment explanation
Indices: 62543--62813 Score: 312
Period size: 87 Copynumber: 3.1 Consensus size: 85
62533 TGTTTTAGAT
* * *
62543 AAAAACGCCGCTAAACATCATA-ACCTATTGCAGCGTTTGTCTATAAAACACTGCTAAATATCAA
1 AAAAACGCCGCTAAATATCA-ACACCTATTGCAGCGTTTGTCTAAAAAACACCGCTAAATATCAA
*
62607 TACCTATTGCGGCGTTTGTCTG
65 TACCTATTGCGGCGTTTGT-TA
* *
62629 AAAAATGCCGCTAAATATCAACACCTATTGCAGTGTTTGTCTAAAAAAACACCGCTAAATATCAA
1 AAAAACGCCGCTAAATATCAACACCTATTGCAGCGTTTGTCT-AAAAAACACCGCTAAATATCAA
* ** *
62694 CATTTATTGCGGCGTTTGTCA
65 TACCTATTGCGGCGTTTGTTA
* * * * *
62715 CACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTC-ACACAAACGCCGCTAAATATTA
1 -AAAAACGCCGCTAAATATCAACACCTATTGCAGCGTTTGTCTA-AAAAACACCGCTAAATATCA
* *
62779 ATACCTATTGTGGCATTTTTGTTA
64 ATACCTATTGCGGC--GTTTGTTA
62803 AAAAACGCCGC
1 AAAAACGCCGC
62814 GAACTTTAGC
Statistics
Matches: 155, Mismatches: 24, Indels: 11
0.82 0.13 0.06
Matches are distributed among these distances:
85 2 0.01
86 64 0.41
87 83 0.54
88 6 0.04
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.28
Consensus pattern (85 bp):
AAAAACGCCGCTAAATATCAACACCTATTGCAGCGTTTGTCTAAAAAACACCGCTAAATATCAAT
ACCTATTGCGGCGTTTGTTA
Found at i:68455 original size:10 final size:10
Alignment explanation
Indices: 68428--68461 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
68418 TCTTTCTTTC
68428 TTTTTTTTAT
1 TTTTTTTTAT
*
68438 TTGATTTTTAT
1 TT-TTTTTTAT
68449 TTTTTTTTAT
1 TTTTTTTTAT
68459 TTT
1 TTT
68462 GTACTAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:68780 original size:17 final size:17
Alignment explanation
Indices: 68758--68790 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
68748 GGTGAAGTAG
68758 AATGGTGTTGTCGTGGC
1 AATGGTGTTGTCGTGGC
68775 AATGGTGTTGTCGTGG
1 AATGGTGTTGTCGTGG
68791 TAGTGTAAGG
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:0.12, C:0.09, G:0.42, T:0.36
Consensus pattern (17 bp):
AATGGTGTTGTCGTGGC
Found at i:70291 original size:25 final size:25
Alignment explanation
Indices: 70262--70312 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
70252 TTTTGGAAAT
70262 ACTAAGATGAATTCTAAAAGAATTC
1 ACTAAGATGAATTCTAAAAGAATTC
70287 ACTAAGATGAATTCTAAAAGAATTC
1 ACTAAGATGAATTCTAAAAGAATTC
70312 A
1 A
70313 TTTTTTTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.27
Consensus pattern (25 bp):
ACTAAGATGAATTCTAAAAGAATTC
Done.