Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002306.1 Hibiscus syriacus cultivar Beakdansim tig00004698_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: 82160
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5377 original size:20 final size:21
Alignment explanation
Indices: 5339--5378 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5329 ATTGCAGGAA
* *
5339 TTTATGGCTTCGACGAAAGAT
1 TTTATGGCCTCCACGAAAGAT
5360 TTTATGGCCTCCAC-AAAGA
1 TTTATGGCCTCCACGAAAGA
5379 CCTTGATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (21 bp):
TTTATGGCCTCCACGAAAGAT
Found at i:16935 original size:24 final size:24
Alignment explanation
Indices: 16908--16986 Score: 113
Period size: 24 Copynumber: 3.3 Consensus size: 24
16898 TACCTAACTA
*
16908 GGATTCTGATCGGATACTTGACCT
1 GGATTATGATCGGATACTTGACCT
* *
16932 GGATTATGATCGAATACTTGACAT
1 GGATTATGATCGGATACTTGACCT
* *
16956 GGATTTTGATCTGATACTTGACCT
1 GGATTATGATCGGATACTTGACCT
16980 GGATTAT
1 GGATTAT
16987 ATTTTGATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (24 bp):
GGATTATGATCGGATACTTGACCT
Found at i:26823 original size:40 final size:39
Alignment explanation
Indices: 26758--26864 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 39
26748 TAAAATGTGA
* *
26758 CATAACATATTCA-GTTGCACCCTAAAATGTGACATTCTT
1 CATAACAT-TTTAGGTTGCAACCTAAAATGTGACATTCTT
* * * *
26797 CATAACTTTTTTGGTTGACAACCTAAAATGTTACCTTCTT
1 CATAACATTTTAGGTTG-CAACCTAAAATGTGACATTCTT
** *
26837 TGTAACATTTTAGGTTGCAACCAAAAAT
1 CATAACATTTTAGGTTGCAACCTAAAAT
26865 ATTATAAAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
38 2 0.04
39 21 0.38
40 32 0.58
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.36
Consensus pattern (39 bp):
CATAACATTTTAGGTTGCAACCTAAAATGTGACATTCTT
Found at i:27118 original size:32 final size:32
Alignment explanation
Indices: 27081--27141 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
27071 TGTTCGAATC
27081 AATATCG-GATTGGTT-GACTTTTGGGTCGGTTT
1 AATATCGTG-TTGGTTAGA-TTTTGGGTCGGTTT
27113 AATATCGTGTTGGTTAGATTTTGGGTCGG
1 AATATCGTGTTGGTTAGATTTTGGGTCGG
27142 GACAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
32 24 0.89
33 3 0.11
ACGTcount: A:0.16, C:0.08, G:0.33, T:0.43
Consensus pattern (32 bp):
AATATCGTGTTGGTTAGATTTTGGGTCGGTTT
Found at i:29726 original size:16 final size:16
Alignment explanation
Indices: 29705--29737 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29695 ACATCAAAAT
29705 TCAATTTTGAGTATAG
1 TCAATTTTGAGTATAG
*
29721 TCAATTTTGATTATAG
1 TCAATTTTGAGTATAG
29737 T
1 T
29738 TTAGTCACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.48
Consensus pattern (16 bp):
TCAATTTTGAGTATAG
Found at i:30022 original size:39 final size:39
Alignment explanation
Indices: 29979--30085 Score: 137
Period size: 39 Copynumber: 2.7 Consensus size: 39
29969 ATTTTAATTC
29979 TAAATTTTTTCACTCTAACATTCTAAATTCATAATTTCT
1 TAAATTTTTTCACTCTAACATTCTAAATTCATAATTTCT
* * **
30018 TAAATTTTGTCACTAC-AACATTCTAATTTGTTAATTTCT
1 TAAATTTTTTCACT-CTAACATTCTAAATTCATAATTTCT
*
30057 TAAATTATTTCACAT-TAACATTCTAAATT
1 TAAATTTTTTCAC-TCTAACATTCTAAATT
30086 ATTTTTAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 56 0.97
40 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.48
Consensus pattern (39 bp):
TAAATTTTTTCACTCTAACATTCTAAATTCATAATTTCT
Found at i:30722 original size:21 final size:21
Alignment explanation
Indices: 30696--30738 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
30686 TGATTAAATA
30696 TTTAA-TAAATATTTATATTTT
1 TTTAATTAAATATTTAT-TTTT
30717 TTTAATTTAAATATTTATTTTT
1 TTTAA-TTAAATATTTATTTTT
30739 ACATGAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTAATTAAATATTTATTTTT
Found at i:32620 original size:3 final size:3
Alignment explanation
Indices: 32614--32682 Score: 63
Period size: 3 Copynumber: 22.3 Consensus size: 3
32604 TGTTGTCCGG
*
32614 ATT ATT ATT AACTT -TT AAT ATT ATT ATT ATT -TAT ATT ATT ATT ATTT
1 ATT ATT ATT -A-TT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT A-TT
32661 ATT ATT -TAT ATT ATT ATT ATT A
1 ATT ATT AT-T ATT ATT ATT ATT A
32683 CTAATTTTCA
Statistics
Matches: 56, Mismatches: 2, Indels: 16
0.76 0.03 0.22
Matches are distributed among these distances:
2 4 0.07
3 44 0.79
4 6 0.11
5 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:32696 original size:22 final size:21
Alignment explanation
Indices: 32614--32682 Score: 93
Period size: 22 Copynumber: 3.2 Consensus size: 21
32604 TGTTGTCCGG
* * *
32614 ATTATTATTAACTTTTAATATT
1 ATTATTATTTA-TATTATTATT
32636 ATTATTATTTATATTATTATT
1 ATTATTATTTATATTATTATT
32657 ATTTATTATTTATATTATTATT
1 A-TTATTATTTATATTATTATT
32679 ATTA
1 ATTA
32683 CTAATTTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
21 12 0.28
22 31 0.72
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTATTATTTATATTATTATT
Found at i:38902 original size:90 final size:88
Alignment explanation
Indices: 38750--38922 Score: 274
Period size: 90 Copynumber: 1.9 Consensus size: 88
38740 CTAACACACC
* *
38750 CTTTTAAAGCCAAATTACCCTAATCATCTTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
1 CTTTTAAAGCCAAATTACCCTAATCATATTAGGGTTTTATTATTTCAAACTAATTAAATCTATAT
*
38815 TTAATTAATTAGAATTTAATAATT
66 TTAATTAATT-GAAATTAATAATT
* * *
38839 CTTTTATATCCAAGTTACCCTAATCATATTAGGAGTTTTATTATTTCAAACTAATTAAATCTATA
1 CTTTTAAAGCCAAATTACCCTAATCATATTAGG-GTTTTATTATTTCAAACTAATTAAATCTATA
38904 TTTAATTAATTGAAATTAA
65 TTTAATTAATTGAAATTAA
38923 ATATTTGGGA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 36 0.47
90 41 0.53
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.45
Consensus pattern (88 bp):
CTTTTAAAGCCAAATTACCCTAATCATATTAGGGTTTTATTATTTCAAACTAATTAAATCTATAT
TTAATTAATTGAAATTAATAATT
Found at i:43422 original size:255 final size:256
Alignment explanation
Indices: 42625--43715 Score: 1237
Period size: 255 Copynumber: 4.2 Consensus size: 256
42615 TTCTTACTTA
* * ** * *
42625 GTAAGTCCTTCGAGCCATGAGTAAGTCTTTTAAGCATGATGATTAAATCCTTCGCGTCATCTGTA
1 GTAAGTCATTCG-GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTC
* * *
42690 AGTCTTTCGAGCAAGTTGATAAGTCCTTCGGGCCATCTATAAGACTTTTGGGCAGGATG-TTTCT
65 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGG-AGGATGTTTTC-
* * * * *
42754 ACATGATTTTGGAAAAATAAGAAAGCGATTT-CAGAAGTTTCTCATTTAAATCTTTT-TTGAAAA
128 ACATGAATTT-GAAAAATGAGAAAGCGATTTCCA-AAGTTTCTCATTT-AATGTTTTCATAAAAA
* *
42817 TGAAATTTTTGAAAAGTAAGAAAGCGA--TCCAAAGTTTCTTACCTAGTAAATTATTTCCAAAAT
190 TGAAATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAAT
**
42880 CA
255 TT
* * * * * *
42882 GTAAGTTATTTGGGCCATCAGTAAGTCTTTCGCGAATGGTGATTAAATCCTTC-AGGTTATCTGT
1 GTAAGTCA-TTCGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGA-GTCATCTGT
* * * * *
42946 AAGTCTTTCAAGCAAGATGATAAGTCCTTCGGTCCATCCTA-AA-ACCTTCGAGTAGGATATTTT
64 CAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT-CTATAAGACCTTCG-GGAGGATGTTTT
* * * * * *
43009 TACATGAATTTGAAAAATGAGAAAGCTATTTTCAAAGTTTCTCATTTAGTATTTTCA-GAAAAT-
127 CACATGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCATAAAAATG
* * ** * * *
43072 AAATTTTTTGAAAACTAAGTAAGTGATTTCCAAATTTTCTCA-CTCAATAAACTATTTCCAAAAT
192 AAA-TTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCT-AGTAAACTATTTCCAAAAT
43136 TT
255 TT
* * *
43138 GTAAGTCTTTCAGGCCATCAGTCAGTCTTTCGAGCATGATGATAAAATCCTTCGAGTCATCTGTC
1 GTAAGTCATTC-GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTC
* * * * *
43203 AGTCTTTCGAGCGAGATGATAAGTCCTTTGGGCCATAC-GTAAGACCTTCAGG-TGATGTTTTCA
65 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT-CTATAAGACCTTCGGGAGGATGTTTTCA
* *
43266 AATGAATCTGAAAGAA-GAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCAT-AAAATGA
129 CATGAATTTGAAA-AATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCATAAAAATGA
* * * * *
43329 AATTTTTAAAAAGTAAGAAAGCAATTTCCATAGTTTCTTACATGGTAAACTATTTCCCAAA-TT
193 AATTTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTT
*
43392 GATAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGT
1 G-TAAGTCATTC-GGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGT
* * *
43457 CAGTCTTTCTAGCAAGATGATAAGTCCTTTGGGCCATCTATAAGACCTTCGGGAAGGATGTTTCC
64 CAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGG-AGGATGTTTTC
* * *
43522 ACATGATTTTTGAAAAACGAGAAAGTGATTTCCAAAGTTTCTCATTTAATGTTTTC-TAAAAATG
128 ACATGA-ATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCATAAAAATG
* * *
43586 AAATTTTTGAAAAGTAAGAAAG-AGATTTCCAATGTTTCTTACCTTGTAGACTATTTCCAAAATT
192 AAATTTTTGAAAAGTAAGAAAGCA-ATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATT
43650 T
256 T
* * *
43651 GTAAGTCATTCGAGCCATCAGTAAATCTTTCGAGCATGATGATTAAATCCTTCGGGTTATCTGTC
1 GTAAGTCATTCG-GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTC
43716 GGCTTCACTT
Statistics
Matches: 708, Mismatches: 97, Indels: 57
0.82 0.11 0.07
Matches are distributed among these distances:
253 3 0.00
254 35 0.05
255 246 0.35
256 142 0.20
257 113 0.16
258 166 0.23
259 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (256 bp):
GTAAGTCATTCGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTCA
GTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCGGGAGGATGTTTTCACA
TGAATTTGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTTTCATAAAAATGAAAT
TTTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACCTAGTAAACTATTTCCAAAATTT
Found at i:43595 original size:513 final size:512
Alignment explanation
Indices: 42625--43715 Score: 1325
Period size: 513 Copynumber: 2.1 Consensus size: 512
42615 TTCTTACTTA
* * ** * *
42625 GTAAGTCCTTCGAGCCATGAGTAAGTCTTTTAAGCATGATGATTAAATCCTTCGCGTCATCTGTA
1 GTAAGTCATTCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTC
* * **
42690 AGTCTTTCGAGCAAGTTGATAAGTCCTTCGGGCCATCTATAAGACTTTTGGGCAGGATGTTTCTA
66 AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGG-AGGATGTTTCTA
* * * *
42755 CATGATTTTGGAAAAATAAGAAAGCGATTTCAGAAGTTTCTCATTTAAATCTTTTTTGAAAATGA
130 AATGAATCTGGAAAAATAAGAAAGCGATTTCAGAAGTTTCTCATTTAAATCTTTTATGAAAATGA
* * * *
42820 AATTTTTGAAAAGTAAGAAAGCGATCCAAAGTTTCTTACCTAGTAAATTATTTCCAAAATCAGTA
195 AATTTTTAAAAAGTAAGAAAGCAATCCAAAGTTTCTTACATAGTAAACTATTTCCAAAATCAGTA
* ** * * *
42885 AGTTATTTGGGCCATCAGTAAGTCTTTCGCGAATGGTGATTAAATCCTTCAGGTTATCTGTAAGT
260 AGTCATTCAGGCCATCAGTAAGTCTTTCGAGAATGATGATTAAATCCTTCAGGTCATCTGTAAGT
* * **
42950 CTTTCAAGCAAGATGATAAGTCCTTCGGTCCATCCTAAAACCTTCGAGTAGGATATTTTTACATG
325 CTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCCTAAAACCTTCGAGAAGGATATTTCCACATG
* * *
43015 AATTTGAAAAATGAGAAAGCTATTTTCAAAGTTTCTCATTTAGTATTTTCAGAAAATAAATTTTT
390 AATTTGAAAAACGAGAAAGCTATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAATAAATTTTT
* *
43080 TGAAAACTAAGTAAGTGATTTCCAAAT-TTTCTCA-CTCAATAAACTATTTCCAAAATTT
455 TGAAAACTAAGAAAGAGATTTCC-AATGTTTCTCACCT-AATAAACTATTTCCAAAATTT
* * *
43138 GTAAGTCTTTC-AGGCCATCAGTCAGTCTTTCGAGCATGATGATAAAATCCTTCGAGTCATCTGT
1 GTAAGTCATTCGA-GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGT
* * * *
43202 CAGTCTTTCGAGCGAGATGATAAGTCCTTTGGGCCATAC-GTAAGACCTTCAGG-TGATGTTT-T
65 CAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCAT-CTATAAGACCTTCAGGAGGATGTTTCT
* *
43264 CAAATGAATCT-GAAAGAA-GAGAAAGCGATTTCCA-AAGTTTCTCATTT-AATGTTTTCAT-AA
129 -AAATGAATCTGGAAA-AATAAGAAAGCGATTT-CAGAAGTTTCTCATTTAAATCTTTT-ATGAA
* * *
43324 AATGAAATTTTTAAAAAGTAAGAAAGCAATTTCCATAGTTTCTTACATGGTAAACTATTTCCCAA
190 AATGAAATTTTTAAAAAGTAAGAAAGCAA--TCCAAAGTTTCTTACATAGTAAACTATTTCCAAA
* * *
43389 AT-TGATAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTC-GAGTCA
253 ATCAG-TAAGTCATTCAGGCCATCAGTAAGTCTTTCGAGAATGATGATTAAATCCTTCAG-GTCA
* * * *
43452 TCTGTCAGTCTTTCTAGCAAGATGATAAGTCCTTTGGGCCAT-CTATAAGACCTTCGGGAAGGAT
316 TCTGTAAGTCTTTCAAGCAAGATGATAAGTCCTTCGGGCCATCCTA-AA-ACCTTCGAGAAGGAT
* * *
43516 GTTTCCACATGATTTTTGAAAAACGAGAAAG-TGATTTCCAAAGTTTCTCATTTAATGTTTTCTA
379 ATTTCCACATGA-ATTTGAAAAACGAGAAAGCT-ATTTCCAAAGTTTCTCATTTAATATTTTC-A
* * ** *
43580 -AAAATGAAA-TTTTTGAAAAGTAAGAAAGAGATTTCCAATGTTTCTTACCTTGTAGACTATTTC
441 GAAAAT-AAATTTTTTGAAAACTAAGAAAGAGATTTCCAATGTTTCTCACCTAATAAACTATTTC
43643 CAAAATTT
505 CAAAATTT
* * *
43651 GTAAGTCATTCGAGCCATCAGTAAATCTTTCGAGCATGATGATTAAATCCTTCGGGTTATCTGTC
1 GTAAGTCATTCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTC
43716 GGCTTCACTT
Statistics
Matches: 494, Mismatches: 65, Indels: 38
0.83 0.11 0.06
Matches are distributed among these distances:
509 36 0.07
510 36 0.07
511 137 0.28
512 27 0.05
513 250 0.51
514 8 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (512 bp):
GTAAGTCATTCGAGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTCATCTGTC
AGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTCAGGAGGATGTTTCTAA
ATGAATCTGGAAAAATAAGAAAGCGATTTCAGAAGTTTCTCATTTAAATCTTTTATGAAAATGAA
ATTTTTAAAAAGTAAGAAAGCAATCCAAAGTTTCTTACATAGTAAACTATTTCCAAAATCAGTAA
GTCATTCAGGCCATCAGTAAGTCTTTCGAGAATGATGATTAAATCCTTCAGGTCATCTGTAAGTC
TTTCAAGCAAGATGATAAGTCCTTCGGGCCATCCTAAAACCTTCGAGAAGGATATTTCCACATGA
ATTTGAAAAACGAGAAAGCTATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAATAAATTTTTT
GAAAACTAAGAAAGAGATTTCCAATGTTTCTCACCTAATAAACTATTTCCAAAATTT
Found at i:44156 original size:36 final size:36
Alignment explanation
Indices: 44111--44189 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
44101 CACTGTGCCA
*
44111 AAATCATCATCTCGTATCAAATAGTAAAGGGGAACC
1 AAATCATCATCTCGCATCAAATAGTAAAGGGGAACC
44147 AAATCATCATCTCGCATCAAATAGTAAAGGGGAACC
1 AAATCATCATCTCGCATCAAATAGTAAAGGGGAACC
44183 AAATCAT
1 AAATCAT
44190 AAAAAATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (36 bp):
AAATCATCATCTCGCATCAAATAGTAAAGGGGAACC
Found at i:46017 original size:14 final size:14
Alignment explanation
Indices: 45998--46024 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45988 TTTTTATCTT
45998 TTAAAATTATTTTC
1 TTAAAATTATTTTC
46012 TTAAAATTATTTT
1 TTAAAATTATTTT
46025 AAAAGGTTTT
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:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTC
Found at i:46576 original size:14 final size:15
Alignment explanation
Indices: 46555--46595 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
46545 TATTATTCAA
46555 GATTTAAGATGTTAC
1 GATTTAAGATGTTAC
* *
46570 G-TTTAAGATTTTAT
1 GATTTAAGATGTTAC
46584 GATTTAAGATGT
1 GATTTAAGATGT
46596 ATTTCTTTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (15 bp):
GATTTAAGATGTTAC
Found at i:50023 original size:46 final size:47
Alignment explanation
Indices: 49930--50035 Score: 160
Period size: 46 Copynumber: 2.3 Consensus size: 47
49920 TTATTCATTA
* * *
49930 ATTTCATTTATGGCATCCTTTCATACCTTTAATGCACCCTTTCATGC
1 ATTTCATTTATGGCATCATTCCATACCTTTAATGCACCATTTCATGC
* *
49977 ATTTCATTTATGGCATCATTCCATGCC-TTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCATTCCATACCTTTAATGCACCATTTCATGC
50023 ATTTCATTTATGG
1 ATTTCATTTATGG
50036 ATTCGTTTCA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 30 0.56
47 24 0.44
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.43
Consensus pattern (47 bp):
ATTTCATTTATGGCATCATTCCATACCTTTAATGCACCATTTCATGC
Found at i:51572 original size:55 final size:55
Alignment explanation
Indices: 51486--51642 Score: 197
Period size: 55 Copynumber: 2.8 Consensus size: 55
51476 ATGACACTGA
* * * *
51486 GTGTGCAAAAAGTTGAGAAATTCATAGTAAGTGTACGAATATCCGTAAGGGCACTTT
1 GTGTGC-AAAA-TTGAGAAATTCATACTAAGTGTATGAATTTCCGTAAGAGCACTTT
* *
51543 GTGTGCAAAATTGAGAAATTCATACTAAGTGTATGAATTTACGTATGAGCACTTT
1 GTGTGCAAAATTGAGAAATTCATACTAAGTGTATGAATTTCCGTAAGAGCACTTT
* * * * *
51598 CTGTGTAAAACTGAGAAACTCATACTACGTGTATGAATTTCCGTA
1 GTGTGCAAAATTGAGAAATTCATACTAAGTGTATGAATTTCCGTA
51643 TGGACACTAC
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
55 78 0.89
56 4 0.05
57 6 0.07
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (55 bp):
GTGTGCAAAATTGAGAAATTCATACTAAGTGTATGAATTTCCGTAAGAGCACTTT
Found at i:52025 original size:67 final size:68
Alignment explanation
Indices: 51951--52099 Score: 230
Period size: 67 Copynumber: 2.2 Consensus size: 68
51941 AATTTATGTG
51951 AGTTAGATGAAAGGCTAAGTGCCTTTGA-GTCATAACTGTGCATATGACAGAAA-GTGTAAATTA
1 AGTTAGATGAAAGGCTAAGTGCCTTTGAGGTC-TAACTGTGCATATGACAGAAAGGTGTAAATTA
52014 TGCC
65 TGCC
* * * *
52018 AGTTAGATGAAACGCTAAGTGCCTTTGAGGTCTAACTGTGCATTTGACAGAAAGGTGTCATTTAT
1 AGTTAGATGAAAGGCTAAGTGCCTTTGAGGTCTAACTGTGCATATGACAGAAAGGTGTAAATTAT
*
52083 TCC
66 GCC
52086 AGTTAGATGAAAGG
1 AGTTAGATGAAAGG
52100 TTAAATACCA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
67 47 0.64
68 27 0.36
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (68 bp):
AGTTAGATGAAAGGCTAAGTGCCTTTGAGGTCTAACTGTGCATATGACAGAAAGGTGTAAATTAT
GCC
Found at i:52186 original size:81 final size:81
Alignment explanation
Indices: 52049--52347 Score: 409
Period size: 81 Copynumber: 3.7 Consensus size: 81
52039 CCTTTGAGGT
* * * * * * *
52049 CTAACTGTGCATTTGACAGAAAGGTGTCATTTATTCCAGTTAGATGAAAGGTTAAATACCATTGA
1 CTAACTGAGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCATTGA
52114 GTAAAAGAATAATGGC
66 GTAAAAGAATAATGGC
* * *
52130 CAAACTGAGCAATTGGCAGAAATATGTCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGA
1 CTAACTGAGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCATTGA
52195 GTAAAAGAATAATGGC
66 GTAAAAGAATAATGGC
* * * *
52211 CTAACTCAGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAAATGAACAGTTAAATACCTTTGA
1 CTAACTGAGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCATTGA
*
52276 GTAAAACAATAATGGC
66 GTAAAAGAATAATGGC
* * * * * *
52292 CTAACTGCGCAATTGGCAGAAAGGTGTCAATGATGCCAATTAGAAGAATGGTTAAA
1 CTAACTGAGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAA
52348 CATTGTTCAG
Statistics
Matches: 192, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 192 1.00
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.26
Consensus pattern (81 bp):
CTAACTGAGCAATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACCATTGA
GTAAAAGAATAATGGC
Found at i:57147 original size:55 final size:52
Alignment explanation
Indices: 57030--57170 Score: 162
Period size: 55 Copynumber: 2.7 Consensus size: 52
57020 TGTAAAAAGT
* * *
57030 TGAGAAATTCATAGTAAGTGTATGAATTTCCG--T-CACTTTGTGTGCAAAA
1 TGAGAAATTCATACTAAGTGTATGAATTTACGTATGCACTTTCTGTGCAAAA
*
57079 TCGAGAAATTCATACTAAGTGTATGAATTTACGTATGAGCACTTTCTGTGTAAAA
1 T-GAGAAATTCATACTAAGTGTATGAATTTACGTAT--GCACTTTCTGTGCAAAA
* * *
57134 CTGAGAAACTCATACTACGTGTATGAATTTTCGTATG
1 -TGAGAAATTCATACTAAGTGTATGAATTTACGTATG
57171 GACACTACGT
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
49 1 0.01
50 29 0.37
52 1 0.01
53 1 0.01
55 45 0.58
56 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (52 bp):
TGAGAAATTCATACTAAGTGTATGAATTTACGTATGCACTTTCTGTGCAAAA
Found at i:57515 original size:68 final size:68
Alignment explanation
Indices: 57436--57759 Score: 415
Period size: 68 Copynumber: 4.8 Consensus size: 68
57426 AAAGATTAAT
* * * * *
57436 AGGCCTAACTGTACATTTGATAGGAA-GATGTCATTTATGCCTA-TTAGATAAAAGGCTAAGTGC
1 AGGCCTAACTGTGCATTTGACAGAAATG-TGTCAATTATGCC-AGTTAGATGAAAGGCTAAGTGC
57499 CTTTG
64 CTTTG
* *
57504 AGGCCTAACTGTGCATTTGAAAGAAATGTGTCAATTATGCCAGTTATATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
57569 TTG
66 TTG
* * *
57572 AGGCCAAACTGTGCATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAAAGGCTCAA-TGCC
1 AGGCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCT-AAGTGCC
57636 TTTG
65 TTTG
* *
57640 AGGCCTAATTGTGCATTTGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
57705 TTG
66 TTG
* * * * *
57708 AGGCCTAACAATGT-AATTGGA-AAAAAGGTGTCAATTATGCCAGTTAAATGAA
1 AGGCCTAAC--TGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
57760 TGGTTAAATA
Statistics
Matches: 227, Mismatches: 23, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
67 3 0.01
68 213 0.94
69 8 0.04
70 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:57847 original size:81 final size:81
Alignment explanation
Indices: 57722--58108 Score: 490
Period size: 81 Copynumber: 4.8 Consensus size: 81
57712 CTAACAATGT
* * * *
57722 AATTGGAAAAAAGGTGTCAATTATGCCAGTTAAATGAATGGTTAAATACCGTTGAGTAAAAGAAT
1 AATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCGTTGAGTAAAAGAAT
*
57787 AATGGACTAACTGAGC
66 AATGGCCTAACTGAGC
57803 AATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCGTTGAGTAAAAGAAT
1 AATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCGTTGAGTAAAAGAAT
* *
57868 AATGTCCTAGCTGAGC
66 AATGGCCTAACTGAGC
* * * * *
57884 AATTGGCAGAATGGTGTCAATTATGCCATTTAGATGAACGGTTAAATACTGATGAGTAAAAGAAT
1 AATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCGTTGAGTAAAAGAAT
*
57949 AATGTCCTAACTGAGC
66 AATGGCCTAACTGAGC
* * * * * * *
57965 AATTGGCAGAAACGTGTCAATTATGCCAATTAGATGAACGATTAAATACCATTAAGTAAAATAAT
1 AATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCGTTGAGTAAAAGAAT
* *
58030 AATTGTCTAACT-ATGC
66 AATGGCCTAACTGA-GC
* * * * **
58046 AATTGGCAGAAAGGTGTCAATGATGCCAGCTAGAAGAACA-GTTAAACACTATTGAGTAAAAGA
1 AATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA-AGGTTAAATACCGTTGAGTAAAAGA
58109 TGAAAGGTTA
Statistics
Matches: 268, Mismatches: 36, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
80 1 0.00
81 267 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (81 bp):
AATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACCGTTGAGTAAAAGAAT
AATGGCCTAACTGAGC
Found at i:65018 original size:46 final size:46
Alignment explanation
Indices: 64923--65061 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
64913 TTATTCGTTA
* * *
64923 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGTACCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTAATGCC-TTAATGCATCCTTTCATGC
* *
64970 ATTTCATTTATGACATCCTTTAATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGC
65016 ATTTCATTTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGC
65062 CTTAATGCAT
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
46 60 0.71
47 25 0.29
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTAATGCCTTAATGCATCCTTTCATGC
Found at i:65062 original size:66 final size:66
Alignment explanation
Indices: 64983--65127 Score: 254
Period size: 66 Copynumber: 2.2 Consensus size: 66
64973 TCATTTATGA
* *
64983 CATCCTTTAATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTAATGCCTTAAT
1 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTAACGCCTTAAT
65048 G
66 G
* *
65049 CATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCACGCCTTAAT
1 CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTAACGCCTTAAT
65114 G
66 G
65115 CATCCTTTCATGC
1 CATCCTTTCATGC
65128 ATTTCATTTA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 75 1.00
ACGTcount: A:0.21, C:0.27, G:0.10, T:0.41
Consensus pattern (66 bp):
CATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTAACGCCTTAAT
G
Found at i:65082 original size:112 final size:111
Alignment explanation
Indices: 64935--65252 Score: 412
Period size: 112 Copynumber: 2.8 Consensus size: 111
64925 TTCATTTATG
* * *
64935 GCATCCTTTCATGCCTTTAATGTACCCTTTCATGCATTTCATTTATGACATCCTTTAATGCCTTA
1 GCATCCTTTCATGCC-TTAATGCATCCTTTCATGCATTTCATTTATG-CATCCTTTCATGCCTTA
*
65000 ATGCATCATTTCATGCATTTCATTTATGGCATCCTTTAATGCCTTAAT
64 ATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTAATGCCTTAAT
*
65048 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCACGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTAT-GCATCCTTTCATGCCTTAA
* *
65113 TGCATCCTTTCATGCATTTCATTTATGGGATCCTTTCATGCCTTAAT
65 TGCATCCTTTCATGCATTTCATTTATGGCATCCTTTAATGCCTTAAT
* * * *
65160 GCATCCTTTCTTGCATTTTATTTATGGCATCC-TT--T-CA-TTCCTTAATGCATCCTTTCATGC
1 GCATCCTTTCATGC--CTTA---AT-GCATCCTTTCATGCATTTCATTTATGCATCCTTTCATGC
*
65220 CTTAATGCATCCTTTCATGCATTTTATTTATGG
60 CTTAATGCATCCTTTCATGCATTTCATTTATGG
65253 ATTCATTTTA
Statistics
Matches: 185, Mismatches: 13, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
112 146 0.79
113 23 0.12
114 5 0.03
115 1 0.01
117 4 0.02
118 6 0.03
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.44
Consensus pattern (111 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGCATCCTTTCATGCCTTAAT
GCATCCTTTCATGCATTTCATTTATGGCATCCTTTAATGCCTTAAT
Found at i:65098 original size:46 final size:46
Alignment explanation
Indices: 65048--65219 Score: 299
Period size: 46 Copynumber: 3.7 Consensus size: 46
65038 ATGCCTTAAT
65048 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATG
*
65094 GCATCCTTTCACGCCTTAATGCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATG
* * *
65140 GGATCCTTTCATGCCTTAATGCATCCTTTCTTGCATTTTATTTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATG
*
65186 GCATCCTTTCATTCCTTAATGCATCCTTTCATGC
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGC
65220 CTTAATGCAT
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 118 1.00
ACGTcount: A:0.19, C:0.27, G:0.11, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATG
Found at i:65192 original size:158 final size:159
Alignment explanation
Indices: 64923--65252 Score: 545
Period size: 158 Copynumber: 2.1 Consensus size: 159
64913 TTATTCGTTA
* *
64923 ATTTCATTTATGGCATCCTTTCATGCCTTTAATGTACCCTTTCATGCATTTCATTTATGACATCC
1 ATTTCATTTATGGCATCCTTTCACGCCTTTAATGCACCCTTTCATGCATTTCATTTATGACATCC
64988 TTTAATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTAATGCCTTAATGCATC
66 TTTAATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTAATGCCTTAATGCATC
65053 CTTTCATGCCTTAATGCATCCTTTCATGC
131 CTTTCATGCCTTAATGCATCCTTTCATGC
* **
65082 ATTTCATTTATGGCATCCTTTCACGCC-TTAATGCATCCTTTCATGCATTTCATTTATGGGATCC
1 ATTTCATTTATGGCATCCTTTCACGCCTTTAATGCACCCTTTCATGCATTTCATTTATGACATCC
* * * * * *
65146 TTTCATGCCTTAATGCATCCTTTCTTGCATTTTATTTATGGCATCCTTTCATTCCTTAATGCATC
66 TTTAATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTAATGCCTTAATGCATC
65211 CTTTCATGCCTTAATGCATCCTTTCATGC
131 CTTTCATGCCTTAATGCATCCTTTCATGC
*
65240 ATTTTATTTATGG
1 ATTTCATTTATGG
65253 ATTCATTTTA
Statistics
Matches: 159, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
158 133 0.84
159 26 0.16
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (159 bp):
ATTTCATTTATGGCATCCTTTCACGCCTTTAATGCACCCTTTCATGCATTTCATTTATGACATCC
TTTAATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCTTTAATGCCTTAATGCATC
CTTTCATGCCTTAATGCATCCTTTCATGC
Done.