Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007154.1 Hibiscus syriacus cultivar Beakdansim tig00018721_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: 73557
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1661 original size:26 final size:26
Alignment explanation
Indices: 1627--1695 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
1617 ATGTAATTTT
* *
1627 AATGCAAAATTTAATAATTTTATTAAA
1 AATG-AAAAATTAATAACTTTATTAAA
* * *
1654 AATGAAAACTTATTAACTTTGTTAAA
1 AATGAAAAATTAATAACTTTATTAAA
*
1680 AATTAAAAATTAATAA
1 AATGAAAAATTAATAA
1696 ATAATAATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
AATGAAAAATTAATAACTTTATTAAA
Found at i:2075 original size:324 final size:321
Alignment explanation
Indices: 1380--2163 Score: 1055
Period size: 324 Copynumber: 2.4 Consensus size: 321
1370 TTAAAAACAT
* * * *
1380 TAATAATTTATTTGATCCCTCAA-TATAATTAAAA-TTGTTTTAATATTTTTATGTTTTTAAACA
1 TAATAATTCATTTGATCCCTTAATTATAATTAAAAGTTATTTTAATATTTTTATATTTTTAAACA
* * *
1443 ATTACTTTTAAAAGACAATAATTTTTTCAAAAATTTATGAAATTTATAATTTT-AAATTAT---A
66 ATTAATTTTAAAAGAAAATAATTTTTTCAAAAATATATGAAATTTATAATTTTAAAATTATAAAA
1504 A---A-TATTATCATCATCATCATTTTGTAAAAGAAATACTAGTATAAAACTTTTATAAAATTAT
131 ATTTATTATTATCATCATCATCATTTTGTAAAAGAAATACTAGTATAAAACTTTTATAAAATTAT
* * * *
1565 TCATATTTTAAAATACTTACCTCAAAGTTTTATATACTAGATTATATGTATTATGTAATTTTAAT
196 TCATA-TTTAAAATACTTACCTC--A---TCATATACTAGATTAGACGTATTATGCAATTTTAAT
** * *
1630 GCAAAATTTAATAATTTTATTAAAAATGAAAACTTATTAACTTTGTTAAAAATTAAAAATTAATA
255 GCAAAATAAAATAATTTTATTAAAAATGAAAACTTATTAACTTTATTAAAAAATAAAAATTAATA
1695 AA
320 AA
1697 TAATAATTCATTTGATCCCTTAATTATAATTAAAAGTTTATTTTAAT-TTTTTATATTTTTAAAC
1 TAATAATTCATTTGATCCCTTAATTATAATTAAAAG-TTATTTTAATATTTTTATATTTTTAAAC
** *
1761 AA-TAATTTTAAAAGGTAATAATATTTTCAAAAATATATGAAATTTATAATTTTAAAATTATAAA
65 AATTAATTTTAAAAGAAAATAATTTTTTCAAAAATATATGAAATTTATAATTTTAAAATTATAAA
* *
1825 ATATTTATTATTATCATCATTTATCATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAA
130 A-ATTTATTATTATCATCA-TCATCATTTTGTAAAAGAAATACTAG-TATAAAACTTTTATAAAA
*
1890 TTATTCATA-TTAAAATACTTACC-C-TCA-A-ACTAGATTAGACGTATTGTGCAATTTTAATGC
192 TTATTCATATTTAAAATACTTACCTCATCATATACTAGATTAGACGTATTATGCAATTTTAATGC
1950 AAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTATTAAAAAATAAAAATT
257 -AAAAT-AAAATAATTTTATTAAAAATG-A-AAAC-TTATTAACT-TTATTAAAAAATAAAAATT
*
2015 AATGAA
316 AATAAA
*
2021 TAATAATTCATTTGATCCCTTAATTGTAATTAAAAGTTATTTTAATATTTTTATATTTTTAAACA
1 TAATAATTCATTTGATCCCTTAATTATAATTAAAAGTTATTTTAATATTTTTATATTTTTAAACA
* *
2086 ATTAATTTTAAAAGAAAATATTTTTTTC-AAAATATATGAAATTTTTAATTTTTAAAATTATAAA
66 ATTAATTTTAAAAGAAAATAATTTTTTCAAAAATATATGAAATTTATAA-TTTTAAAATTAT-AA
2150 AAATTTATTATTAT
129 AAATTTATTATTAT
2164 AAAAAATAAA
Statistics
Matches: 416, Mismatches: 27, Indels: 40
0.86 0.06 0.08
Matches are distributed among these distances:
317 21 0.05
318 85 0.20
319 31 0.07
320 30 0.07
321 1 0.00
322 5 0.01
323 20 0.05
324 95 0.23
325 46 0.11
326 6 0.01
327 25 0.06
328 24 0.06
329 27 0.06
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (321 bp):
TAATAATTCATTTGATCCCTTAATTATAATTAAAAGTTATTTTAATATTTTTATATTTTTAAACA
ATTAATTTTAAAAGAAAATAATTTTTTCAAAAATATATGAAATTTATAATTTTAAAATTATAAAA
ATTTATTATTATCATCATCATCATTTTGTAAAAGAAATACTAGTATAAAACTTTTATAAAATTAT
TCATATTTAAAATACTTACCTCATCATATACTAGATTAGACGTATTATGCAATTTTAATGCAAAA
TAAAATAATTTTATTAAAAATGAAAACTTATTAACTTTATTAAAAAATAAAAATTAATAAA
Found at i:2699 original size:13 final size:12
Alignment explanation
Indices: 2683--2716 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
2673 TTGTCCAGGA
2683 TTTTTATTTATT
1 TTTTTATTTATT
2695 TTTTTATTTTATT
1 TTTTTA-TTTATT
2708 TTTATTATT
1 TTT-TTATT
2717 ATGATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 11 0.55
14 3 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:2718 original size:12 final size:12
Alignment explanation
Indices: 2682--2768 Score: 61
Period size: 12 Copynumber: 7.0 Consensus size: 12
2672 TTTGTCCAGG
2682 ATTTTTATTTATT
1 ATTTTTA-TTATT
2695 -TTTTTATT-TT
1 ATTTTTATTATT
2705 ATTTTTATTATT
1 ATTTTTATTATT
** *
2717 ATGATTATTAAAT
1 ATTTTTATT-ATT
**
2730 ATTAGATATTAATGT
1 ATT-TTTATT-AT-T
*
2745 AATTTTATTATT
1 ATTTTTATTATT
2757 ATTTTTATTATT
1 ATTTTTATTATT
2769 TTTAGGTCAT
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
10 2 0.03
11 10 0.17
12 27 0.47
13 6 0.10
14 10 0.17
15 3 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:3850 original size:2 final size:2
Alignment explanation
Indices: 3845--3908 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3835 ACATAAATAC
3845 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
3887 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3909 TCACGTGCTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6015 original size:21 final size:21
Alignment explanation
Indices: 5990--6060 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
5980 ATCTGAAGCT
*
5990 GATTGAAGACTTCCTTTAAAT
1 GATTGAAGACTTCCTTTAAAG
*
6011 GATTGAAGACTTCTTTTAAAG
1 GATTGAAGACTTCCTTTAAAG
6032 GATTGAAGACTTCCTTTAAAG
1 GATTGAAGACTTCCTTTAAAG
*
6053 GAGTGAAG
1 GATTGAAG
6061 GCCAAGATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (21 bp):
GATTGAAGACTTCCTTTAAAG
Found at i:12672 original size:22 final size:21
Alignment explanation
Indices: 12646--12712 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
12636 TTGCACTTAG
12646 TAAGTCTTTCGAGCATGATGCT
1 TAAGTCTTTCGAGCATGATG-T
* * *
12668 TAAGTCCTTCGGGTCATCA-G-
1 TAAGTCTTTCGAG-CATGATGT
*
12688 TAAGTCTTTCGAGTATGATGAT
1 TAAGTCTTTCGAGCATGATG-T
12710 TAA
1 TAA
12713 ATCCTTCGGG
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
19 3 0.09
20 12 0.35
22 15 0.44
23 4 0.12
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGT
Found at i:12706 original size:42 final size:42
Alignment explanation
Indices: 12644--13118 Score: 206
Period size: 42 Copynumber: 11.0 Consensus size: 42
12634 TTTTGCACTT
* *
12644 AGTAAGTCTTTCGAGCATGATGCTTAAGTCCTTCGGGTCATC
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATC
* * *
12686 AGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATT
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATC
** * * ** * *
12728 TTTAAGCCTTCACGAAAG-A-GTAGTGAAACAAATCCGTCAGTAAGTGCCATC
1 AGTAAGTCTT-TCG--AGCATG-A-TG-ATTAAATCCTTC-G---G-GTCATC
* * * *
12779 AATAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATT
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATC
** ** * *
12821 TTTAAG-CTTTCACGGAAG-A-GTAGTGAAGCAAATCCGTCAGTAAGTGCCATC
1 AGTAAGTCTTT--C-G-AGCATG-A-TG-ATTAAATCCTTC-G--GGT-C-ATC
* *
12872 AGTAAGTCTTTCGAGCATGATGATGAAATCCTT-TGGTCCATC
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT-CATC
*
12914 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT-AAC
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATC
* * * * * * * **
12955 TGGTAAG-CCTTC-ACCAAAGA-GTAGTGAAGCAAATC----CATC
1 -AGTAAGTCTTTCGAGC-ATGATG-ATTAAATC-CTTCGGGTCATC
* *
12994 AGTAAGTCTTTTGAGCATGATGATGAAATCCTTCGGGTCATC
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATC
*
13036 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATT
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATC
* * * * *
13078 TGTGAGTCTCTCGAGCAAGATGA-TAAATCCTTCAGGTCATC
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATC
13119 CATAAGACCT
Statistics
Matches: 318, Mismatches: 74, Indels: 83
0.67 0.16 0.17
Matches are distributed among these distances:
38 7 0.02
39 12 0.04
40 6 0.02
41 34 0.11
42 155 0.49
43 12 0.04
44 5 0.02
45 8 0.03
46 19 0.06
47 19 0.06
48 8 0.03
49 7 0.02
50 6 0.02
51 16 0.05
52 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (42 bp):
AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATC
Found at i:12841 original size:93 final size:93
Alignment explanation
Indices: 12682--12904 Score: 392
Period size: 93 Copynumber: 2.4 Consensus size: 93
12672 TCCTTCGGGT
12682 CATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGAAAGA
1 CATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGAAAGA
12747 GTAGTGAAACAAATCCGTCAGTAAGTGC
66 GTAGTGAAACAAATCCGTCAGTAAGTGC
* * *
12775 CATCAATAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTTTTAAGCTTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGAAAGA
*
12840 GTAGTGAAGCAAATCCGTCAGTAAGTGC
66 GTAGTGAAACAAATCCGTCAGTAAGTGC
* *
12868 CATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTT
1 CATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTT
12905 TGGTCCATCA
Statistics
Matches: 123, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 123 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (93 bp):
CATCAGTAAGTCTTTCGAGTATGATGATTAAATCCTTCGGGTAATTTTTAAGCCTTCACGAAAGA
GTAGTGAAACAAATCCGTCAGTAAGTGC
Found at i:13554 original size:53 final size:53
Alignment explanation
Indices: 13496--13769 Score: 410
Period size: 53 Copynumber: 5.2 Consensus size: 53
13486 ATCACACCAT
*
13496 AAGATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* *
13549 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * *
13602 AAGATTATTCAAATTCTACTCCCCG-AGCAAGAGGGAGCGAACCCGTAGGTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
13654 AAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGAAGCGAACCCGTAGGAAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
13707 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGCT-GGTC-G
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGG-CAG
13760 AAGATTGTTC
1 AAGATTGTTC
13770 AAAGAAGAGA
Statistics
Matches: 202, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
52 48 0.24
53 153 0.76
54 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:13679 original size:105 final size:106
Alignment explanation
Indices: 13509--13765 Score: 392
Period size: 105 Copynumber: 2.4 Consensus size: 106
13499 ATTGTTCGAG
* * *
13509 TTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTAGGCAGAAGATTGTTCGAGTTCTACTCCCTG
1 TTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGTAGAAGATTATTCGAGTTCTACTCCCTG
* *
13574 AAGCAAGAGGGAGCGAACCCGTAAGTAGAAGATTATTCAAA
66 AAGCAAGAGGAAGCGAACCCGTAAGAAGAAGATTATTCAAA
*
13615 TTCTACTCCCCG-AGCAAGAGGGAGCGAACCCGTAGGTAGAAGATTATTCGAGTTCTACTCCCTG
1 TTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGTAGAAGATTATTCGAGTTCTACTCCCTG
* * * *
13679 AAGCAAGAGGAAGCGAACCCGTAGGAAGAAGATTGTTCGAG
66 AAGCAAGAGGAAGCGAACCCGTAAGAAGAAGATTATTCAAA
*
13720 TTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGCT-GGTCGAAGATT
1 TTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGGTAGAAGATT
13766 GTTCAAAGAA
Statistics
Matches: 137, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
105 95 0.69
106 41 0.30
107 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (106 bp):
TTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGTAGAAGATTATTCGAGTTCTACTCCCTG
AAGCAAGAGGAAGCGAACCCGTAAGAAGAAGATTATTCAAA
Found at i:13950 original size:5 final size:5
Alignment explanation
Indices: 13929--13963 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
13919 TGTCTGGGAT
*
13929 TTTTA TTTATT TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTT
13964 TATTATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:13955 original size:21 final size:22
Alignment explanation
Indices: 13929--13972 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
13919 TGTCTGGGAT
13929 TTTTA-TTTATTTTTTATT-TTA
1 TTTTATTTTA-TTTTTATTATTA
13950 TTTTATTTTATTTTTATTATTA
1 TTTTATTTTATTTTTATTATTA
13972 T
1 T
13973 AATTATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTTATTTTATTTTTATTATTA
Found at i:15119 original size:2 final size:2
Alignment explanation
Indices: 15114--15139 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15104 TTTACATAAA
15114 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
15140 GCACGTGCTT
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:21030 original size:20 final size:21
Alignment explanation
Indices: 20992--21031 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20982 GATGTCTATC
* *
20992 ATTATTTTTAATAATAAAAAT
1 ATTATTTTTAAAAAGAAAAAT
21013 ATTA-TTTTAAAAAGAAAAA
1 ATTATTTTTAAAAAGAAAAA
21032 AATTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
ATTATTTTTAAAAAGAAAAAT
Found at i:33206 original size:25 final size:25
Alignment explanation
Indices: 33176--33301 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 25
33166 AGTCCATAAT
33176 TAAATAAAAACATTAAGAAACAAAA
1 TAAATAAAAACATTAAGAAACAAAA
* *
33201 TAAATAAAAA-GTT------CATAAT
1 TAAATAAAAACATTAAGAAACA-AAA
*
33220 TAAATAAAAATATTAAGAAACAAAA
1 TAAATAAAAACATTAAGAAACAAAA
* *
33245 TAAATAAAAA-GTT------CATAAT
1 TAAATAAAAACATTAAGAAACA-AAA
33264 TAAATAAAAACATTAAGAAACAAAAA
1 TAAATAAAAACATTAAGAAAC-AAAA
33290 TAAATAAAAACA
1 TAAATAAAAACA
33302 AGTCTATCGA
Statistics
Matches: 76, Mismatches: 8, Indels: 33
0.65 0.07 0.28
Matches are distributed among these distances:
18 4 0.05
19 24 0.32
20 4 0.05
24 4 0.05
25 22 0.29
26 17 0.22
27 1 0.01
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.21
Consensus pattern (25 bp):
TAAATAAAAACATTAAGAAACAAAA
Found at i:33206 original size:44 final size:44
Alignment explanation
Indices: 33136--33299 Score: 287
Period size: 44 Copynumber: 3.8 Consensus size: 44
33126 ACCATTAAAT
*
33136 AATAAAAACATT-A-AAACAAAATAAATAAAAAGTCCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTTCATAATTA
33178 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTTCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTTCATAATTA
*
33222 AATAAAAATATTAAGAAACAAAATAAATAAAAAGTTCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTTCATAATTA
33266 AATAAAAACATTAAGAAACAAAAATAAATAAAAA
1 AATAAAAACATTAAGAAAC-AAAATAAATAAAAA
33300 CAAGTCTATC
Statistics
Matches: 116, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
42 12 0.10
43 1 0.01
44 89 0.77
45 14 0.12
ACGTcount: A:0.68, C:0.07, G:0.04, T:0.21
Consensus pattern (44 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAGTTCATAATTA
Found at i:41805 original size:157 final size:157
Alignment explanation
Indices: 41519--41835 Score: 625
Period size: 157 Copynumber: 2.0 Consensus size: 157
41509 TAAAATAAAC
*
41519 AAAAATGCCAAACTAATGAAACATGAGAGATAAAAAAAACCCTTAAAATGATAAACAGGTGAATG
1 AAAAATGCCAAACTAATGAAACATGAGACATAAAAAAAACCCTTAAAATGATAAACAGGTGAATG
41584 AACTTCTAAAAAGCTCCTTACATGACTCCAGTTGGTTTCGGCCAACGATCTCGAGCACAGATCAC
66 AACTTCTAAAAAGCTCCTTACATGACTCCAGTTGGTTTCGGCCAACGATCTCGAGCACAGATCAC
41649 AGAGTTAAATATAGACTAACGCAAGAG
131 AGAGTTAAATATAGACTAACGCAAGAG
41676 AAAAATGCCAAACTAATGAAACATGAGACATAAAAAAAACCCTTAAAATGATAAACAGGTGAATG
1 AAAAATGCCAAACTAATGAAACATGAGACATAAAAAAAACCCTTAAAATGATAAACAGGTGAATG
41741 AACTTCTAAAAAGCTCCTTACATGACTCCAGTTGGTTTCGGCCAACGATCTCGAGCACAGATCAC
66 AACTTCTAAAAAGCTCCTTACATGACTCCAGTTGGTTTCGGCCAACGATCTCGAGCACAGATCAC
41806 AGAGTTAAATATAGACTAACGCAAGAG
131 AGAGTTAAATATAGACTAACGCAAGAG
41833 AAA
1 AAA
41836 TTGTGTCATC
Statistics
Matches: 159, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 159 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (157 bp):
AAAAATGCCAAACTAATGAAACATGAGACATAAAAAAAACCCTTAAAATGATAAACAGGTGAATG
AACTTCTAAAAAGCTCCTTACATGACTCCAGTTGGTTTCGGCCAACGATCTCGAGCACAGATCAC
AGAGTTAAATATAGACTAACGCAAGAG
Found at i:43332 original size:26 final size:26
Alignment explanation
Indices: 43283--43331 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
43273 TTTTATAATA
**
43283 ATAAATTTTTTATAATTTTAAAAATT
1 ATAAATTTCATATAATTTTAAAAATT
43309 ATAAATTTCATAT-ATTTTAAAAA
1 ATAAATTTCATATAATTTTAAAAA
43332 AAATATTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAAATTTCATATAATTTTAAAAATT
Found at i:44079 original size:339 final size:334
Alignment explanation
Indices: 43329--44156 Score: 1297
Period size: 336 Copynumber: 2.5 Consensus size: 334
43319 TATATTTTAA
* *
43329 AAAAAATATTGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTTTAATA-TTT
* *
43394 TTATATTTTTAAACAATTAATTTTGAAAGGCAATAATTTTTTCAAAAATTTATGAAATTTATAAT
65 TTATATTTTTAAACAATTAATTTTAAAAGG-AATAATTTTTTCAAAAATATATGAAATTTATAAT
* * *
43459 TTTTTAAATTATAAAATA-T-TTATCATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAA
129 TTTTAAAATTATAAAATATTATTATTATCATCATCATCATTTTGTAAAAGAAATACTAATTATAA
* *
43522 AACTTTTATAAAATTATTCATATTTTAAAATACTTATCCTCAAAGTTTTTATACTAGATTATATG
194 AACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATACTAGATTATACG
* ** *
43587 TATTATGTAATTTAATGCAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAACTGT
259 TATTATATAATTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACCGT
*
43652 TGTTAAAAATT
324 TGTTAAAAAAT
* * *
43663 AAAAATTAATAAATAATAATTCATTTGATCACTCAATTGTAATTAAAATTTTATTTTTATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTTTAATATTTT
43728 TATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAATT
66 TATATTTTTAAACAATTAATTTTAAAAGG-AATAATTTTTTCAAAAATATATGAAATTTATAATT
*
43793 TTTAAAATTATAAAATATTTATTATTATCATCATCATCATTTTGTAAAATAAATACTAATTATAA
130 TTTAAAATTATAAAATA-TTATTATTATCATCATCATCATTTTGTAAAAGAAATACTAATTATAA
*
43858 AACTTTTATAAAATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCCTATACTAGATTATA
194 AACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTT--TATACTAGATTATA
*
43923 CGTATTGTATAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAAC
257 CGTATTATATAA-TTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAAC
43988 CGTTGTTAAAAAAAT
321 CGTTGTT-AAAAAAT
* * *
44003 AAAAATTAATGAATAATAATTCATTTGATCTCTTAATTGTAATTAAAAGTGTATTTTAATA-TTT
1 AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTTTAATATTTT
** *
44067 TATATTTTTAAACAATTAATTTTAAAA-GAATTTTTTTTTC-AAAATATATGAAATTCATAATTT
66 TATATTTTTAAACAATTAATTTTAAAAGGAATAATTTTTTCAAAAATATATGAAATTTATAATTT
*
44130 TTAAAATTATAAAAAAATTATTATTAT
131 TTAAAATTAT-AAAATATTATTATTAT
44157 AAAAATAAAC
Statistics
Matches: 455, Mismatches: 31, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
333 82 0.18
334 56 0.12
335 1 0.00
336 130 0.29
337 15 0.03
338 24 0.05
339 86 0.19
340 61 0.13
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (334 bp):
AAAAATTAATGAATAATAATTCATTTGATCACTCAATTGTAATTAAAAGTTTATTTTAATATTTT
TATATTTTTAAACAATTAATTTTAAAAGGAATAATTTTTTCAAAAATATATGAAATTTATAATTT
TTAAAATTATAAAATATTATTATTATCATCATCATCATTTTGTAAAAGAAATACTAATTATAAAA
CTTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATACTAGATTATACGTA
TTATATAATTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAACCGTTG
TTAAAAAAT
Found at i:47358 original size:13 final size:14
Alignment explanation
Indices: 47326--47363 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
47316 AGATATGCAG
47326 TAAATATTATTATTTT
1 TAAATA-TATTA-TTT
47342 TAAATATATTA-TT
1 TAAATATATTATTT
47355 TAAATATAT
1 TAAATATAT
47364 AAATTGATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.50
15 5 0.23
16 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAAATATATTATTT
Found at i:48798 original size:19 final size:18
Alignment explanation
Indices: 48774--48809 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
48764 GTTTTAATAA
*
48774 TAATTATTTTAATTTTTAT
1 TAATTAATTT-ATTTTTAT
48793 TAATTAATTTATTTTTA
1 TAATTAATTTATTTTTA
48810 AGTTGTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATTAATTTATTTTTAT
Found at i:58472 original size:82 final size:82
Alignment explanation
Indices: 58331--58587 Score: 363
Period size: 82 Copynumber: 3.1 Consensus size: 82
58321 GGTAGTATAA
* *
58331 TGTAGATTCTCTGATTCTCTAAAATTTTTAAGTTTATCTGAGTTGACGTGAAATATCAATGAAAA
1 TGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTGATGTGAAATATCAATGAAAA
* *
58396 GTATAGGACGTGAATAG
66 GAAAAGGACGTGAATAG
* *
58413 TGTAGATTCTCTGACTCTTTAAAATTTTTAAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAA
1 TGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTGATGTGAAATATCAATGAAAA
* *
58478 GAAAAGGATGCGAATAG
66 GAAAAGGACGTGAATAG
* * * * * * *
58495 TATAAATTCTCTGACTCTCTAAATTTTTTCATTTTATCTGAGTCGATGTGAAATTTCAATGAAAA
1 TGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTGATGTGAAATATCAATGAAAA
*
58560 -CAAAGGACGTGAATAG
66 GAAAAGGACGTGAATAG
58576 TGTAGATTCTCT
1 TGTAGATTCTCT
58588 ACAAGGCATG
Statistics
Matches: 154, Mismatches: 21, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
81 23 0.15
82 131 0.85
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (82 bp):
TGTAGATTCTCTGACTCTCTAAAATTTTTAAGTTTATCTGAGTTGATGTGAAATATCAATGAAAA
GAAAAGGACGTGAATAG
Done.