Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003746.1 Hibiscus syriacus cultivar Beakdansim tig00008016_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: 87378
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:541 original size:21 final size:21
Alignment explanation
Indices: 517--558 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
507 ATTTTATTTA
517 ATTTTAATATATAT-ATATATT
1 ATTTTAATATAT-TGATATATT
*
538 ATTTTATTATATTGATATATT
1 ATTTTAATATATTGATATATT
559 TTAACAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTTAATATATTGATATATT
Found at i:3271 original size:92 final size:96
Alignment explanation
Indices: 3110--3302 Score: 270
Period size: 93 Copynumber: 2.0 Consensus size: 96
3100 TCTGAGGTTG
** * *
3110 ACACGGTTTCCACTCTGTTGAGGAAATCTGGTCGGGGAGATGACACACTGCTCATCCGTGATGAA
1 ACACGGTTTCCACTCTACTGAGGAAATCTGGTCGGGGAGATGA-ACACTGCTCATACGCGATGAA
*
3175 GAG-TTCTAGGCCATCTTTAGGAATGATGATA
65 GAGTTTCTAGGCCATCTTTAGGAATAATGATA
3206 ACACGGTTT-CACTCTACTG-GGAAAATCTGGTCGGGG-GATG-ACACTGCTCATACGCGATGAA
1 ACACGGTTTCCACTCTACTGAGG-AAATCTGGTCGGGGAGATGAACACTGCTCATACGCGATGAA
* *
3267 GAGTTTCTCGGTCATCTTTAGGAATAATGATA
65 GAGTTTCTAGGCCATCTTTAGGAATAATGATA
3299 ACAC
1 ACAC
3303 TGCTCATATG
Statistics
Matches: 88, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
92 22 0.25
93 29 0.33
94 6 0.07
95 22 0.25
96 9 0.10
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (96 bp):
ACACGGTTTCCACTCTACTGAGGAAATCTGGTCGGGGAGATGAACACTGCTCATACGCGATGAAG
AGTTTCTAGGCCATCTTTAGGAATAATGATA
Found at i:4018 original size:41 final size:37
Alignment explanation
Indices: 3967--4047 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
3957 TTTACGAGAA
3967 ACTGTCTCCAAAGAGATAAAATTTTATTTCCAAAGAAACAG
1 ACTGTCTCC-AAGAGAT--AA-TTTATTTCCAAAGAAACAG
* * *
4008 ACTGTCTCCAATAGATAATTTGTTTCCAAAGAAATAG
1 ACTGTCTCCAAGAGATAATTTATTTCCAAAGAAACAG
4045 ACT
1 ACT
4048 CAAAGGTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 20 0.54
38 2 0.05
40 6 0.16
41 9 0.24
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (37 bp):
ACTGTCTCCAAGAGATAATTTATTTCCAAAGAAACAG
Found at i:4250 original size:33 final size:33
Alignment explanation
Indices: 4171--4259 Score: 99
Period size: 34 Copynumber: 2.7 Consensus size: 33
4161 ATAAGTTGTC
* *
4171 TCAAGCGAGACGAAATTTGTTTTGAAAAATTATA
1 TCAAGTGAGAC-AAAATTGTTTTGAAAAATTATA
* * * *
4205 TCAAGTGAGACAAACGTTGTTTTGAGAAATTGTC
1 TCAAGTGAGACAAA-ATTGTTTTGAAAAATTATA
4239 TC-AGTGAGACAAAATTGTTTT
1 TCAAGTGAGACAAAATTGTTTT
4260 AAGAGAAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
32 7 0.15
33 14 0.29
34 27 0.56
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (33 bp):
TCAAGTGAGACAAAATTGTTTTGAAAAATTATA
Found at i:4399 original size:32 final size:32
Alignment explanation
Indices: 4346--4430 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 32
4336 TTGCAACAAG
** *
4346 ATGTTGAATCCCCAAAGATGCCCCAATATCCA
1 ATGTTGAATCTTCAAAGATGCCCCAACATCCA
* * ***
4378 ATGTTGAATCTTTAAATATGCCCCAACATTTG
1 ATGTTGAATCTTCAAAGATGCCCCAACATCCA
4410 ATGTTGAATCTTCAAAGATGC
1 ATGTTGAATCTTCAAAGATGC
4431 TTTCATTGTT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (32 bp):
ATGTTGAATCTTCAAAGATGCCCCAACATCCA
Found at i:9790 original size:21 final size:21
Alignment explanation
Indices: 9745--9803 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
9735 CCCCTGTGGT
9745 GGGAATCGGTTCCCCTTCAAAGG
1 GGGAATCGGTT-CCC-TCAAAGG
9768 GGGAATCGGTTCCCTC-AAGG
1 GGGAATCGGTTCCCTCAAAGG
* *
9788 GGGGATCGATTCCCTC
1 GGGAATCGGTTCCCTC
9804 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 18 0.53
21 2 0.06
22 3 0.09
23 11 0.32
ACGTcount: A:0.19, C:0.27, G:0.32, T:0.22
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCAAAGG
Found at i:21733 original size:28 final size:29
Alignment explanation
Indices: 21664--21737 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 29
21654 TAAAAAATTT
* *
21664 AAATATTTTAAATACTTATTTTGACAAAA
1 AAATAATTTAAGTACTTATTTTGACAAAA
* *
21693 AGATATAACTTTAAGTATTTATTTTGA-ATAA
1 A-A-ATAA-TTTAAGTACTTATTTTGACAAAA
21724 AAATAATTTAAGTA
1 AAATAATTTAAGTA
21738 GTTAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 8 0.21
29 5 0.13
30 2 0.05
31 7 0.18
32 16 0.42
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (29 bp):
AAATAATTTAAGTACTTATTTTGACAAAA
Found at i:21746 original size:17 final size:17
Alignment explanation
Indices: 21724--21779 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
21714 TTTTGAATAA
21724 AAATAATTTAAGTAGTT
1 AAATAATTTAAGTAGTT
* *
21741 AAATAA--AAAATA-TAT
1 AAATAATTTAAGTAGT-T
21756 AAAATAATTTAAGTAGTT
1 -AAATAATTTAAGTAGTT
21774 AAATAA
1 AAATAA
21780 AAATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 1 0.03
15 5 0.17
16 6 0.20
17 12 0.40
18 5 0.17
19 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (17 bp):
AAATAATTTAAGTAGTT
Found at i:21763 original size:33 final size:34
Alignment explanation
Indices: 21723--21791 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
21713 ATTTTGAATA
21723 AAAATAATTTAAGTAGTTAAATAAAAA-ATATAT
1 AAAATAATTTAAGTAGTTAAATAAAAATATATAT
21756 AAAATAATTTAAGTAGTTAAATAAAAATATATAT
1 AAAATAATTTAAGTAGTTAAATAAAAATATATAT
21790 AA
1 AA
21792 TTTAGATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (34 bp):
AAAATAATTTAAGTAGTTAAATAAAAATATATAT
Found at i:40088 original size:3 final size:3
Alignment explanation
Indices: 40080--40160 Score: 144
Period size: 3 Copynumber: 27.0 Consensus size: 3
40070 CCATATTGAT
*
40080 TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
40128 TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40161 AATATATTAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41551 original size:16 final size:15
Alignment explanation
Indices: 41510--41551 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
41500 ATCGTTTTAG
41510 TTATATTTTTATTGT
1 TTATATTTTTATTGT
41525 TT-TAATTTTTACTTGT
1 TTAT-ATTTTTA-TTGT
*
41541 TTATATATTTA
1 TTATATTTTTA
41552 AATATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 9 0.39
16 12 0.52
17 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (15 bp):
TTATATTTTTATTGT
Found at i:53002 original size:12 final size:12
Alignment explanation
Indices: 52985--53009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52975 TATTATGCTT
52985 GAAAAAAAAAAA
1 GAAAAAAAAAAA
52997 GAAAAAAAAAAA
1 GAAAAAAAAAAA
53009 G
1 G
53010 GGGTCAAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:54416 original size:82 final size:82
Alignment explanation
Indices: 54139--54797 Score: 1023
Period size: 82 Copynumber: 8.2 Consensus size: 82
54129 ACATTAACTG
* *
54139 GAAGATGAATGTGCTC-ATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAG
1 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAG
54203 AACCAATCATTGAATTTA
65 AACCAATCATTGAATTTA
54221 GAAGATGAA-TTGCC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAGA
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAGA
54284 ACCAATCATTGAATTTA
66 ACCAATCATTGAATTTA
*
54301 GAAGATGAATTTGCCAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-CAG
54366 AACCAATCATTGAATTTA
65 AACCAATCATTGAATTTA
*
54384 GAAGATGAATTTGCCAATAGCATCTTCT-GAAGTGTTTCTTTGAGTTATC-AATCTGGTTGGACA
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTG-TTCTTTGAGTTATCTGATCTGGTTGG-CA
54447 GAACCAATCATTG-ATTTA
64 GAACCAATCATTGAATTTA
*
54465 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGG-TGGACAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-CAG
54529 AACCAATCATTGAATTTA
65 AACCAATCATTGAATTTA
54547 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC-GATCTGGTTGGACAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-CAG
54611 AACCAATCATTGAATTT-
65 AACCAATCATTGAATTTA
* * *
54628 GAAGATGAATGTGCTC-ATAGCATCTTTTGGAAGTG-T-TTTGAG-T-TCTGATCTGGTTTGCAG
1 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAG
*
54688 AACCAATCATAGAA-TTA
65 AACCAATCATTGAATTTA
54705 GAAGATGAATTTGCCAATAGCATCTTCTGG-A---TTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGCAG
*
54766 AACCAATCATTGAATTTG
65 AACCAATCATTGAATTTA
54784 GAAGATGAATTTGC
1 GAAGATGAATTTGC
54798 TCATATAGAA
Statistics
Matches: 542, Mismatches: 17, Indels: 39
0.91 0.03 0.07
Matches are distributed among these distances:
74 1 0.00
75 6 0.01
76 5 0.01
77 54 0.10
78 30 0.06
79 22 0.04
80 76 0.14
81 111 0.20
82 175 0.32
83 62 0.11
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (82 bp):
GAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAGA
ACCAATCATTGAATTTA
Found at i:54533 original size:163 final size:164
Alignment explanation
Indices: 54139--54802 Score: 1042
Period size: 163 Copynumber: 4.1 Consensus size: 164
54129 ACATTAACTG
*
54139 GAAGATGAATGTGCTCATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAGA
1 GAAGATGAATTTGCTCATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAGA
54204 ACCAATCATTGAATTTAGAAGATGAA-TTGCC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 ACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
54267 CTGATCTGGTTGGCAGAACCAATCATTGAATTTA
131 CTGATCTGGTTGGCAGAACCAATCATTGAATTTA
54301 GAAGATGAATTTGC-CAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
1 GAAGATGAATTTGCTC-ATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-CA
54365 GAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCT-GAAGTGTTTCTTTGAGT
64 GAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTG-TTCTTTGAGT
*
54429 TATC-AATCTGGTTGGACAGAACCAATCATTG-ATTTA
128 TATCTGATCTGGTTGG-CAGAACCAATCATTGAATTTA
* *
54465 GAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGG-TGGACA
1 GAAGATGAATTTGCTC-ATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG-CA
54528 GAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
64 GAACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
54593 ATC-GATCTGGTTGGACAGAACCAATCATTGAATTT-
129 ATCTGATCTGGTTGG-CAGAACCAATCATTGAATTTA
* * *
54628 GAAGATGAATGTGCTCATAGCATCTTTTGGAAGTG-T-TTTGAG-T-TCTGATCTGGTTTGCAGA
1 GAAGATGAATTTGCTCATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAGA
*
54689 ACCAATCATAGAA-TTAGAAGATGAATTTGCCAATAGCATCTTCTGG-A---TTCTTTGAGTTAT
66 ACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
54749 CTGATCTGGTTTGGCAGAACCAATCATTGAATTTG
131 CTGATCTGG-TTGGCAGAACCAATCATTGAATTTA
54784 GAAGATGAATTTGCTCATA
1 GAAGATGAATTTGCTCATA
54803 TAGAAATAAG
Statistics
Matches: 478, Mismatches: 11, Indels: 32
0.92 0.02 0.06
Matches are distributed among these distances:
154 14 0.03
155 27 0.06
156 22 0.05
157 1 0.00
158 33 0.07
159 25 0.05
160 3 0.01
161 7 0.01
162 59 0.12
163 154 0.32
164 92 0.19
165 41 0.09
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (164 bp):
GAAGATGAATTTGCTCATAGCATCTTATGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGCAGA
ACCAATCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTGGCAGAACCAATCATTGAATTTA
Found at i:55890 original size:113 final size:113
Alignment explanation
Indices: 55600--56123 Score: 668
Period size: 113 Copynumber: 4.7 Consensus size: 113
55590 ATGATTGACA
*
55600 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAGGAATAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
55662 AGAATTTGTTC-ACCTTTTGCCTGAATTCATCACTTGATGGATTATC-
66 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATTATCT
*
55708 TTTCCAGAG--AGTTCATAAT----AGAACTCATTTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
55767 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATTATCT
66 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATTATCT
* * **
55815 TTTCCAGAGAAAGTTCATAATGAGAAGAACTAATCTAAAGAAGGAAGAAGAAACTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * * *
55880 AGAATTTGTTCAACCTTTTG-CTCAAATCTATTACTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCCTGAATTC-ATCACTTGATGGATTATCT
55928 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* ** * * *
55993 AGAACTTGTTCAACTTTTTGTTTGAATTCATCATTTGATGGATCGA-CA
66 AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGAT-TATCT
* *
56041 TTTCCAG-GTAGAGTTCATAATGAGAGGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 TTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAAT
56105 GAGAAGAA---GTTCAACCTTT
62 GAGAAGAACTTGTTCAACCTTT
56124 GCTCAAATCC
Statistics
Matches: 364, Mismatches: 34, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
102 10 0.03
105 35 0.10
106 43 0.12
107 9 0.02
108 9 0.02
109 10 0.03
112 7 0.02
113 195 0.54
114 6 0.02
115 1 0.00
116 39 0.11
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATTATCT
Found at i:56400 original size:3 final size:3
Alignment explanation
Indices: 56392--56488 Score: 144
Period size: 3 Copynumber: 33.0 Consensus size: 3
56382 CCATATTGAT
* *
56392 TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
56440 TTA TTA TCA TTA -TA TTA TTA TT- TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
56486 TTA
1 TTA
56489 AATATATAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 4 0.05
3 80 0.95
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:56524 original size:12 final size:12
Alignment explanation
Indices: 56487--56521 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
56477 TTATTATTAT
56487 TAAATATATAAA
1 TAAATATATAAA
*
56499 TACATATATAAA
1 TAAATATATAAA
56511 TAAATAT-TAAA
1 TAAATATATAAA
56522 ATATATACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATATATAAA
Found at i:57847 original size:14 final size:15
Alignment explanation
Indices: 57830--57858 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57820 TTTTAGTTAT
57830 ATTTTTA-TTGTTTA
1 ATTTTTACTTGTTTA
57844 ATTTTTACTTGTTTA
1 ATTTTTACTTGTTTA
57859 TATATTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (15 bp):
ATTTTTACTTGTTTA
Found at i:60864 original size:18 final size:18
Alignment explanation
Indices: 60838--60872 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
60828 ATGTTCTGAA
* *
60838 TTTACTTTTTTTAATAAT
1 TTTAATTTTATTAATAAT
60856 TTTAATTTTATTAATAA
1 TTTAATTTTATTAATAA
60873 AAAATTAAAA
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:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAATTTTATTAATAAT
Found at i:61440 original size:23 final size:22
Alignment explanation
Indices: 61394--61440 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
61384 AATCTGACAG
**
61394 AAAATGTCACAAAAGTAAAGAA
1 AAAATGTCACAAAAACAAAGAA
*
61416 AAAATTGTCACAAAAACAAATAA
1 AAAA-TGTCACAAAAACAAAGAA
61439 AA
1 AA
61441 CGTGTTACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.15
Consensus pattern (22 bp):
AAAATGTCACAAAAACAAAGAA
Found at i:61826 original size:18 final size:18
Alignment explanation
Indices: 61803--61837 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
61793 AAATTCAACG
61803 TTGAATTGAATAAAATAA
1 TTGAATTGAATAAAATAA
* *
61821 TTGAATTTATTAAAATA
1 TTGAATTGAATAAAATA
61838 GAGTAAATTA
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:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
TTGAATTGAATAAAATAA
Found at i:67798 original size:61 final size:60
Alignment explanation
Indices: 67728--68123 Score: 300
Period size: 61 Copynumber: 6.6 Consensus size: 60
67718 TACGTTAGTC
*
67728 TAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTTGAAGTTCGTGTTGTGATTTT
1 TAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTTGAAGTTCGTGTTGCGATTTT
67788 CTAAATTCGTTGCGATAGTCCAAGTTCACGTT-C-------GAAGTTCGTGTTGCGATTTTT
1 -TAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTTGAAGTTCGTGTTGCGA-TTTT
* ** * * * *
67842 TAAATTCGTTGTGATAGTCCAAGTTCACGTTGCGATTTTTCAAATTC--GTTGCGATAGTC
1 TAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTTGAAGTTCGTGTTGCGAT-TTT
* * * * *
67901 CAAGTTTACATTGCGATAGTCGAAGTTCGCGTTGCGATAGTTGAAGTTCGTGTTGCGATTTT
1 TAA-ATT-CGTTGCGATAGTCCAAGTTCACGTTGCGATAGTTGAAGTTCGTGTTGCGATTTT
* * * * * * *
67963 TCAAATTCGTTGCGATAGTCTAAGTTCACGTTGTGAT-TTTCCAAATTC--GTTGTGATAGTT
1 T-AAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTT-GAAGTTCGTGTTGCGAT-TTT
* ** * *
68023 TAAGTTCACGTTGCGATTTTTCAAATT--CGTTGCGATAGTTAGTCGAAGTTCGTGTTGCGATTT
1 TAAATT--CGTTGCGATAGTCCAAGTTCACGTTGCGATAG-T--T-GAAGTTCGTGTTGCGATTT
68086 T
60 T
* * *
68087 TCAAATTTGTTGCGATAGTTCAAGTTCGCGTTGCGAT
1 T-AAATTCGTTGCGATAGTCCAAGTTCACGTTGCGAT
68124 TTTTCAAATT
Statistics
Matches: 261, Mismatches: 46, Indels: 52
0.73 0.13 0.14
Matches are distributed among these distances:
53 45 0.17
54 5 0.02
58 1 0.00
59 29 0.11
60 8 0.03
61 115 0.44
62 3 0.01
63 32 0.12
64 3 0.01
65 20 0.08
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (60 bp):
TAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTTGAAGTTCGTGTTGCGATTTT
Found at i:67848 original size:53 final size:53
Alignment explanation
Indices: 67768--67872 Score: 183
Period size: 53 Copynumber: 2.0 Consensus size: 53
67758 TGCGATAGTT
*
67768 GAAGTTCGTGTTGTGATTTTCTAAATTCGTTGCGATAGTCCAAGTTCACGTTC
1 GAAGTTCGTGTTGCGATTTTCTAAATTCGTTGCGATAGTCCAAGTTCACGTTC
* *
67821 GAAGTTCGTGTTGCGATTTTTTAAATTCGTTGTGATAGTCCAAGTTCACGTT
1 GAAGTTCGTGTTGCGATTTTCTAAATTCGTTGCGATAGTCCAAGTTCACGTT
67873 GCGATTTTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (53 bp):
GAAGTTCGTGTTGCGATTTTCTAAATTCGTTGCGATAGTCCAAGTTCACGTTC
Found at i:67877 original size:40 final size:40
Alignment explanation
Indices: 67830--68171 Score: 389
Period size: 40 Copynumber: 8.4 Consensus size: 40
67820 CGAAGTTCGT
* *
67830 GTTGCGATTTTTTAAATTCGTTGTGATAGTCCAAGTTCAC
1 GTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTCAC
*
67870 GTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTTAC
1 GTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTCAC
* ** * ** **
67910 ATTGCGA-TAGTCGAAGTTCGCGTTGCGATAGTTGAAGTTCGT
1 GTTGCGATTTTTC-AAATT--CGTTGCGATAGTCCAAGTTCAC
*
67952 GTTGCGATTTTTCAAATTCGTTGCGATAGTCTAAGTTCAC
1 GTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTCAC
* * * **
67992 GTTGTGATTTTCCAAATTCGTTGTGATAGTTTAAGTTCAC
1 GTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTCAC
* **
68032 GTTGCGATTTTTCAAATTCGTTGCGATAGTTAGTCGAAGTTCGT
1 GTTGCGATTTTTCAAATTCGTTGCG--A--TAGTCCAAGTTCAC
* * *
68076 GTTGCGATTTTTCAAATTTGTTGCGATAGTTCAAGTTCGC
1 GTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTCAC
*
68116 GTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTCGC
1 GTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTCAC
*
68156 GTTGCGATTTTCCAAA
1 GTTGCGATTTTTCAAA
68172 ATCGCAACGA
Statistics
Matches: 256, Mismatches: 38, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.01
40 187 0.73
42 29 0.11
43 3 0.01
44 34 0.13
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.40
Consensus pattern (40 bp):
GTTGCGATTTTTCAAATTCGTTGCGATAGTCCAAGTTCAC
Found at i:67893 original size:19 final size:19
Alignment explanation
Indices: 67830--67896 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
67820 CGAAGTTCGT
*
67830 GTTGCGATTTTTTAAATTC
1 GTTGCGATTTTTCAAATTC
* ** * *
67849 GTTGTGATAGTCCAAGTTCAC
1 GTTGCGATTTTTCAAATT--C
67870 GTTGCGATTTTTCAAATTC
1 GTTGCGATTTTTCAAATTC
67889 GTTGCGAT
1 GTTGCGAT
67897 AGTCCAAGTT
Statistics
Matches: 35, Mismatches: 11, Indels: 4
0.70 0.22 0.08
Matches are distributed among these distances:
19 21 0.60
21 14 0.40
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (19 bp):
GTTGCGATTTTTCAAATTC
Found at i:67946 original size:21 final size:20
Alignment explanation
Indices: 67734--68163 Score: 178
Period size: 21 Copynumber: 21.4 Consensus size: 20
67724 AGTCTAAATT
*
67734 CGTTGCGATAGTCCAAGTTC
1 CGTTGCGATAGTTCAAGTTC
*
67754 ACGTTGCGATAGTTGAAGTTC
1 -CGTTGCGATAGTTCAAGTTC
* * * *
67775 GTGTTGTGAT-TTTCTAAATT-
1 -CGTTGCGATAGTTC-AAGTTC
*
67795 CGTTGCGATAGTCCAAGTTC
1 CGTTGCGATAGTTCAAGTTC
67815 ACGTT-CGA-AGTTC--G-T-
1 -CGTTGCGATAGTTCAAGTTC
** * *
67830 -GTTGCGATTTTTTAAATT-
1 CGTTGCGATAGTTCAAGTTC
* *
67848 CGTTGTGATAGTCCAAGTTC
1 CGTTGCGATAGTTCAAGTTC
** *
67868 ACGTTGCGATTTTTCAAATT-
1 -CGTTGCGATAGTTCAAGTTC
* *
67888 CGTTGCGATAGTCCAAGTTTA
1 CGTTGCGATAGTTCAAG-TTC
*
67909 CATTGCGATAG-TCGAAGTTC
1 CGTTGCGATAGTTC-AAGTTC
*
67929 GCGTTGCGATAGTTGAAGTTC
1 -CGTTGCGATAGTTCAAGTTC
* ** *
67950 GTGTTGCGATTTTTCAAATT-
1 -CGTTGCGATAGTTCAAGTTC
67970 CGTTGCGATAG-TCTAAGTTC
1 CGTTGCGATAGTTC-AAGTTC
* * *
67990 ACGTTGTGAT-TTTCCAAATT-
1 -CGTTGCGATAGTT-CAAGTTC
* *
68010 CGTTGTGATAGTTTAAGTTC
1 CGTTGCGATAGTTCAAGTTC
** *
68030 ACGTTGCGATTTTTCAAATT-
1 -CGTTGCGATAGTTCAAGTTC
68050 CGTTGCGATAGTTAGTCGAAGTTC
1 CGTTGCGATAG-T--TC-AAGTTC
* ** *
68074 GTGTTGCGATTTTTCAAATT-
1 -CGTTGCGATAGTTCAAGTTC
*
68094 TGTTGCGATAGTTCAAGTTC
1 CGTTGCGATAGTTCAAGTTC
** *
68114 GCGTTGCGATTTTTCAAATT-
1 -CGTTGCGATAGTTCAAGTTC
*
68134 CGTTGCGATAGTCCAAGTTC
1 CGTTGCGATAGTTCAAGTTC
68154 GCGTTGCGAT
1 -CGTTGCGAT
68164 TTTCCAAAAT
Statistics
Matches: 298, Mismatches: 76, Indels: 70
0.67 0.17 0.16
Matches are distributed among these distances:
13 3 0.01
14 3 0.01
15 2 0.01
16 1 0.00
17 1 0.00
18 3 0.01
19 105 0.35
20 15 0.05
21 146 0.49
22 6 0.02
23 4 0.01
24 1 0.00
25 8 0.03
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTTCAAGTTC
Found at i:67991 original size:122 final size:123
Alignment explanation
Indices: 67819--68164 Score: 459
Period size: 122 Copynumber: 2.8 Consensus size: 123
67809 AAGTTCACGT
* * *
67819 TCGAAGTTCGTGTTGCGATTTTTTAAATTCGTTGTGATAGTCCAAGTTCACGTTGCGATTTTTCA
1 TCGAAGTTCGTGTTGCGATTTTTCAAATTCGTTGCGATAGTCTAAGTTCACGTTGCGATTTTTCA
* *
67884 AATTCGTTGCGATAGTCCAAGTTTACATTGCGA-TAGTCGAAGTTCGCGTTGCGATAG-T-
66 AATTCGTTGCGATAGTCCAAGTTCACATTGCGATTAGTC-AAATT--CGTTGCGATAGTTA
* *
67942 T-GAAGTTCGTGTTGCGATTTTTCAAATTCGTTGCGATAGTCTAAGTTCACGTTGTGATTTTCCA
1 TCGAAGTTCGTGTTGCGATTTTTCAAATTCGTTGCGATAGTCTAAGTTCACGTTGCGATTTTTCA
* ** * **
68006 AATTCGTTGTGATAGTTTAAGTTCACGTTGCGATTTTTCAAATTCGTTGCGATAGTTA
66 AATTCGTTGCGATAGTCCAAGTTCACATTGCGATTAGTCAAATTCGTTGCGATAGTTA
* *
68064 GTCGAAGTTCGTGTTGCGATTTTTCAAATTTGTTGCGATAGT-TCAAGTTCGCGTTGCGATTTTT
1 -TCGAAGTTCGTGTTGCGATTTTTCAAATTCGTTGCGATAGTCT-AAGTTCACGTTGCGATTTTT
* *
68128 CAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATT
64 CAAATTCGTTGCGATAGTCCAAGTTCACATTGCGATT
68165 TTCCAAAATC
Statistics
Matches: 196, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
120 11 0.06
121 1 0.01
122 90 0.46
123 6 0.03
124 88 0.45
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (123 bp):
TCGAAGTTCGTGTTGCGATTTTTCAAATTCGTTGCGATAGTCTAAGTTCACGTTGCGATTTTTCA
AATTCGTTGCGATAGTCCAAGTTCACATTGCGATTAGTCAAATTCGTTGCGATAGTTA
Found at i:68176 original size:21 final size:21
Alignment explanation
Indices: 68112--68176 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
68102 TAGTTCAAGT
*
68112 TCGCGTTGCGATTTTTC-AAA
1 TCGCGTTGCGATTTTCCAAAA
* ** **
68132 T-TCGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTTCCAAAA
68152 TCGCGTTGCGATTTTCCAAAA
1 TCGCGTTGCGATTTTCCAAAA
68173 TCGC
1 TCGC
68177 AACGACTGGT
Statistics
Matches: 32, Mismatches: 11, Indels: 3
0.70 0.24 0.07
Matches are distributed among these distances:
19 11 0.34
20 3 0.09
21 18 0.56
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCAAAA
Found at i:68606 original size:22 final size:21
Alignment explanation
Indices: 68581--68638 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
68571 CACTATCGCA
*
68581 ACAACACGTTTTTCAAACTCTC
1 ACAACAC-TTTTTCAAACTATC
*
68603 ACAACACATTTT--AACTATC
1 ACAACACTTTTTCAAACTATC
*
68622 GCAACACATTTTTCAAA
1 ACAACAC-TTTTTCAAA
68639 ATCGCGTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 4 0.14
22 9 0.31
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (21 bp):
ACAACACTTTTTCAAACTATC
Found at i:70535 original size:9 final size:9
Alignment explanation
Indices: 70521--70556 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
70511 TATGGAAATC
*
70521 GAGGAGGAG
1 GAGGAGAAG
70530 GAGGAGAAG
1 GAGGAGAAG
70539 GAGGAGAAG
1 GAGGAGAAG
*
70548 AAGGAGAAG
1 GAGGAGAAG
70557 TATGAAGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (9 bp):
GAGGAGAAG
Found at i:74349 original size:24 final size:24
Alignment explanation
Indices: 74321--74370 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
74311 CCCATGGTAT
* *
74321 AGGTTTTACTACTCCCGTTAATAG
1 AGGTTTGACTACTCCCATTAATAG
*
74345 AGGTTTGACTACTCCCATTAGTAG
1 AGGTTTGACTACTCCCATTAATAG
74369 AG
1 AG
74371 CAACCATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (24 bp):
AGGTTTGACTACTCCCATTAATAG
Found at i:76088 original size:23 final size:23
Alignment explanation
Indices: 76058--76101 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
76048 GGTGACTTAG
76058 AAAGCTTAATCT-TGAAAACATTC
1 AAAGCTT-ATCTGTGAAAACATTC
*
76081 AAAGCTTATTTGTGAAAACAT
1 AAAGCTTATCTGTGAAAACAT
76102 GGCCTCTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (23 bp):
AAAGCTTATCTGTGAAAACATTC
Found at i:78099 original size:29 final size:30
Alignment explanation
Indices: 78046--78102 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
78036 AAACAAAAAC
*
78046 TTAAAGGATCAAAATAGTACAAATAGAAAT
1 TTAAAGGATCAAAATAGTAAAAATAGAAAT
78076 TTAAA-GATCCAAAATAG-AAAAATAGAA
1 TTAAAGGAT-CAAAATAGTAAAAATAGAA
78103 GCTTAAGGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.21
Consensus pattern (30 bp):
TTAAAGGATCAAAATAGTAAAAATAGAAAT
Found at i:78108 original size:29 final size:30
Alignment explanation
Indices: 78042--78121 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
78032 GGAAAAACAA
*
78042 AAACTTAAAGGATCAAAATAGTACAAATAG
1 AAACTTAAAGGATCAAAATAGTAAAAATAG
*
78072 AAATTTAAA-GATCCAAAATAG-AAAAATAG
1 AAACTTAAAGGAT-CAAAATAGTAAAAATAG
* *
78101 AAGCTTAAGGGA-CTAAAATAG
1 AAACTTAAAGGATC-AAAATAG
78122 AAATAACAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 1 0.02
29 23 0.55
30 18 0.43
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.20
Consensus pattern (30 bp):
AAACTTAAAGGATCAAAATAGTAAAAATAG
Found at i:79086 original size:21 final size:21
Alignment explanation
Indices: 79046--79087 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
79036 GGGTTTGAAA
**
79046 CTCTTGTGTTTTTTCTTTTTC
1 CTCTTGTGTTTTTTAATTTTC
*
79067 CTCTTGTTTTTTTTAATTTTC
1 CTCTTGTGTTTTTTAATTTTC
79088 TGGAAACTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.17, G:0.07, T:0.71
Consensus pattern (21 bp):
CTCTTGTGTTTTTTAATTTTC
Done.