Multiple sequence alignment - TraesCS2D01G207400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G207400 chr2D 100.000 5086 0 0 1 5086 161377896 161372811 0.000000e+00 9393
1 TraesCS2D01G207400 chr2A 95.133 3041 80 14 256 3272 172218559 172215563 0.000000e+00 4734
2 TraesCS2D01G207400 chr2A 98.213 1063 17 2 3430 4490 172215530 172214468 0.000000e+00 1857
3 TraesCS2D01G207400 chr2A 96.607 560 16 1 4524 5083 278454684 278455240 0.000000e+00 926
4 TraesCS2D01G207400 chr2A 85.981 321 28 7 1687 1995 396664017 396664332 1.370000e-85 327
5 TraesCS2D01G207400 chr2A 85.266 319 26 10 1690 1995 400562561 400562251 4.950000e-80 309
6 TraesCS2D01G207400 chr2B 96.796 2528 54 12 2010 4512 217792316 217789791 0.000000e+00 4194
7 TraesCS2D01G207400 chr2B 94.895 1900 49 23 129 2005 217794225 217792351 0.000000e+00 2928
8 TraesCS2D01G207400 chr2B 88.525 610 56 4 2234 2839 37606301 37606900 0.000000e+00 726
9 TraesCS2D01G207400 chr2B 85.890 326 28 8 1683 1995 37605655 37605975 1.060000e-86 331
10 TraesCS2D01G207400 chr2B 85.890 326 28 10 1683 1995 130060544 130060864 1.060000e-86 331
11 TraesCS2D01G207400 chr2B 85.556 270 20 3 2006 2269 37606038 37606294 1.090000e-66 265
12 TraesCS2D01G207400 chr4B 86.350 1033 73 29 883 1907 314324190 314325162 0.000000e+00 1064
13 TraesCS2D01G207400 chr4B 94.867 565 24 4 4524 5083 249067147 249067711 0.000000e+00 878
14 TraesCS2D01G207400 chr4B 92.111 431 30 2 1479 1907 605510408 605510836 5.630000e-169 604
15 TraesCS2D01G207400 chr4B 85.327 443 50 5 2514 2953 97356152 97355722 1.300000e-120 444
16 TraesCS2D01G207400 chr4B 89.630 270 20 4 2006 2269 97356817 97356550 2.270000e-88 337
17 TraesCS2D01G207400 chr4B 85.866 283 24 2 2234 2515 97356543 97356276 2.320000e-73 287
18 TraesCS2D01G207400 chr4B 83.986 281 28 8 1727 1995 97357150 97356875 2.350000e-63 254
19 TraesCS2D01G207400 chr6A 96.964 560 17 0 4524 5083 297658210 297658769 0.000000e+00 941
20 TraesCS2D01G207400 chr5D 89.665 716 58 5 2234 2945 353960862 353960159 0.000000e+00 898
21 TraesCS2D01G207400 chr5D 93.043 575 28 8 4524 5086 135068587 135068013 0.000000e+00 830
22 TraesCS2D01G207400 chr5D 81.002 579 56 20 1441 2003 353961720 353961180 1.320000e-110 411
23 TraesCS2D01G207400 chr5D 83.803 426 54 11 1124 1545 515118561 515118147 1.720000e-104 390
24 TraesCS2D01G207400 chr5A 96.007 551 22 0 4533 5083 608308041 608308591 0.000000e+00 896
25 TraesCS2D01G207400 chr5A 85.213 399 49 7 1149 1545 643332891 643332501 7.930000e-108 401
26 TraesCS2D01G207400 chr7A 95.044 565 23 2 4526 5086 263726242 263725679 0.000000e+00 883
27 TraesCS2D01G207400 chr3D 93.194 573 27 6 4523 5083 127336457 127337029 0.000000e+00 832
28 TraesCS2D01G207400 chr3D 92.894 577 29 6 4522 5086 526480152 526479576 0.000000e+00 828
29 TraesCS2D01G207400 chr3D 84.498 329 51 0 1215 1543 457018927 457019255 4.910000e-85 326
30 TraesCS2D01G207400 chr5B 87.534 730 74 6 2234 2958 111271923 111272640 0.000000e+00 828
31 TraesCS2D01G207400 chr5B 85.000 400 48 9 1149 1545 647944227 647943837 3.690000e-106 396
32 TraesCS2D01G207400 chr5B 90.647 278 20 2 1998 2269 111271639 111271916 1.040000e-96 364
33 TraesCS2D01G207400 chr5B 85.799 338 29 11 1670 1995 111271255 111271585 1.750000e-89 340
34 TraesCS2D01G207400 chr4D 92.882 576 29 6 4523 5086 395957387 395956812 0.000000e+00 826
35 TraesCS2D01G207400 chr1B 88.691 619 56 5 2234 2848 233942051 233941443 0.000000e+00 743
36 TraesCS2D01G207400 chr1B 84.969 326 31 8 1683 1995 233942696 233942376 1.060000e-81 315
37 TraesCS2D01G207400 chr1B 85.130 269 22 2 2006 2269 233942313 233942058 5.050000e-65 259
38 TraesCS2D01G207400 chr6B 88.548 620 55 6 2234 2848 627911535 627910927 0.000000e+00 737
39 TraesCS2D01G207400 chr6B 88.226 620 57 7 2234 2848 627681086 627680478 0.000000e+00 726
40 TraesCS2D01G207400 chr6B 84.871 271 21 3 2006 2269 627911799 627911542 6.530000e-64 255
41 TraesCS2D01G207400 chr6B 84.502 271 22 3 2006 2269 627681350 627681093 3.040000e-62 250
42 TraesCS2D01G207400 chr6B 94.286 140 8 0 2786 2925 475722572 475722433 1.110000e-51 215
43 TraesCS2D01G207400 chr3B 92.542 295 15 5 2048 2338 748431653 748431944 2.830000e-112 416
44 TraesCS2D01G207400 chr3B 85.890 326 28 8 1683 1995 162678256 162678576 1.060000e-86 331
45 TraesCS2D01G207400 chr3B 85.276 326 30 8 1683 1995 124056235 124055915 2.280000e-83 320
46 TraesCS2D01G207400 chr1A 83.721 344 54 2 1201 1543 487741422 487741080 1.770000e-84 324
47 TraesCS2D01G207400 chr1D 83.430 344 55 2 1201 1543 388651047 388650705 8.220000e-83 318


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G207400 chr2D 161372811 161377896 5085 True 9393.000000 9393 100.000000 1 5086 1 chr2D.!!$R1 5085
1 TraesCS2D01G207400 chr2A 172214468 172218559 4091 True 3295.500000 4734 96.673000 256 4490 2 chr2A.!!$R2 4234
2 TraesCS2D01G207400 chr2A 278454684 278455240 556 False 926.000000 926 96.607000 4524 5083 1 chr2A.!!$F1 559
3 TraesCS2D01G207400 chr2B 217789791 217794225 4434 True 3561.000000 4194 95.845500 129 4512 2 chr2B.!!$R1 4383
4 TraesCS2D01G207400 chr2B 37605655 37606900 1245 False 440.666667 726 86.657000 1683 2839 3 chr2B.!!$F2 1156
5 TraesCS2D01G207400 chr4B 314324190 314325162 972 False 1064.000000 1064 86.350000 883 1907 1 chr4B.!!$F2 1024
6 TraesCS2D01G207400 chr4B 249067147 249067711 564 False 878.000000 878 94.867000 4524 5083 1 chr4B.!!$F1 559
7 TraesCS2D01G207400 chr4B 97355722 97357150 1428 True 330.500000 444 86.202250 1727 2953 4 chr4B.!!$R1 1226
8 TraesCS2D01G207400 chr6A 297658210 297658769 559 False 941.000000 941 96.964000 4524 5083 1 chr6A.!!$F1 559
9 TraesCS2D01G207400 chr5D 135068013 135068587 574 True 830.000000 830 93.043000 4524 5086 1 chr5D.!!$R1 562
10 TraesCS2D01G207400 chr5D 353960159 353961720 1561 True 654.500000 898 85.333500 1441 2945 2 chr5D.!!$R3 1504
11 TraesCS2D01G207400 chr5A 608308041 608308591 550 False 896.000000 896 96.007000 4533 5083 1 chr5A.!!$F1 550
12 TraesCS2D01G207400 chr7A 263725679 263726242 563 True 883.000000 883 95.044000 4526 5086 1 chr7A.!!$R1 560
13 TraesCS2D01G207400 chr3D 127336457 127337029 572 False 832.000000 832 93.194000 4523 5083 1 chr3D.!!$F1 560
14 TraesCS2D01G207400 chr3D 526479576 526480152 576 True 828.000000 828 92.894000 4522 5086 1 chr3D.!!$R1 564
15 TraesCS2D01G207400 chr5B 111271255 111272640 1385 False 510.666667 828 87.993333 1670 2958 3 chr5B.!!$F1 1288
16 TraesCS2D01G207400 chr4D 395956812 395957387 575 True 826.000000 826 92.882000 4523 5086 1 chr4D.!!$R1 563
17 TraesCS2D01G207400 chr1B 233941443 233942696 1253 True 439.000000 743 86.263333 1683 2848 3 chr1B.!!$R1 1165
18 TraesCS2D01G207400 chr6B 627910927 627911799 872 True 496.000000 737 86.709500 2006 2848 2 chr6B.!!$R3 842
19 TraesCS2D01G207400 chr6B 627680478 627681350 872 True 488.000000 726 86.364000 2006 2848 2 chr6B.!!$R2 842

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
35 36 0.108186 TGCGTCATGGTTAGGCTCTG 60.108 55.0 0.00 0.0 0.00 3.35 F
600 612 0.110644 GAGAAGAAGGCAACGCAACG 60.111 55.0 0.00 0.0 46.39 4.10 F
1391 1422 0.038166 AAGCACCCCAACATCGTCAT 59.962 50.0 0.00 0.0 0.00 3.06 F
1724 1760 2.474359 CGATCGATCCTGTGAAGCAATC 59.526 50.0 19.51 0.0 0.00 2.67 F
2784 3083 1.762708 TTTCAGATGATTTCCGCCCC 58.237 50.0 0.00 0.0 0.00 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1422 0.675837 CTCGTACGTGTCCCTGAGGA 60.676 60.000 16.05 0.00 41.08 3.71 R
1703 1739 1.926561 TTGCTTCACAGGATCGATCG 58.073 50.000 18.81 9.36 0.00 3.69 R
2426 2596 2.033141 CCACAGTCCACAGGCCAG 59.967 66.667 5.01 0.00 0.00 4.85 R
3534 3843 2.162338 TACCCCTCGCCTTCAACACG 62.162 60.000 0.00 0.00 0.00 4.49 R
4513 4840 1.070309 GTGCTGCTTCAAGAAGTGTCG 60.070 52.381 11.14 0.16 40.45 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.713830 GGTCGCAGTACCGAATTGC 59.286 57.895 0.00 0.00 39.17 3.56
22 23 2.451693 GCAGTACCGAATTGCGTCA 58.548 52.632 0.00 0.00 38.67 4.35
23 24 1.006832 GCAGTACCGAATTGCGTCAT 58.993 50.000 0.00 0.00 38.67 3.06
24 25 1.267532 GCAGTACCGAATTGCGTCATG 60.268 52.381 0.00 0.00 38.67 3.07
25 26 1.327460 CAGTACCGAATTGCGTCATGG 59.673 52.381 0.00 0.00 38.67 3.66
26 27 1.066430 AGTACCGAATTGCGTCATGGT 60.066 47.619 0.00 0.00 38.67 3.55
27 28 1.735571 GTACCGAATTGCGTCATGGTT 59.264 47.619 0.00 0.00 38.67 3.67
28 29 2.102070 ACCGAATTGCGTCATGGTTA 57.898 45.000 0.00 0.00 38.67 2.85
29 30 2.006888 ACCGAATTGCGTCATGGTTAG 58.993 47.619 0.00 0.00 38.67 2.34
30 31 1.330521 CCGAATTGCGTCATGGTTAGG 59.669 52.381 0.00 0.00 38.67 2.69
31 32 1.268032 CGAATTGCGTCATGGTTAGGC 60.268 52.381 0.00 0.00 34.64 3.93
32 33 2.017049 GAATTGCGTCATGGTTAGGCT 58.983 47.619 0.00 0.00 0.00 4.58
33 34 1.668419 ATTGCGTCATGGTTAGGCTC 58.332 50.000 0.00 0.00 0.00 4.70
34 35 0.613260 TTGCGTCATGGTTAGGCTCT 59.387 50.000 0.00 0.00 0.00 4.09
35 36 0.108186 TGCGTCATGGTTAGGCTCTG 60.108 55.000 0.00 0.00 0.00 3.35
36 37 0.811616 GCGTCATGGTTAGGCTCTGG 60.812 60.000 0.00 0.00 0.00 3.86
37 38 0.811616 CGTCATGGTTAGGCTCTGGC 60.812 60.000 0.00 0.00 37.82 4.85
38 39 0.811616 GTCATGGTTAGGCTCTGGCG 60.812 60.000 0.00 0.00 39.81 5.69
39 40 1.524621 CATGGTTAGGCTCTGGCGG 60.525 63.158 0.00 0.00 39.81 6.13
40 41 2.746375 ATGGTTAGGCTCTGGCGGG 61.746 63.158 0.00 0.00 39.81 6.13
41 42 3.081409 GGTTAGGCTCTGGCGGGA 61.081 66.667 0.00 0.00 39.81 5.14
42 43 2.666098 GGTTAGGCTCTGGCGGGAA 61.666 63.158 0.00 0.00 39.81 3.97
43 44 1.153349 GTTAGGCTCTGGCGGGAAG 60.153 63.158 0.00 0.00 39.81 3.46
44 45 1.305802 TTAGGCTCTGGCGGGAAGA 60.306 57.895 0.00 0.00 39.81 2.87
45 46 1.330655 TTAGGCTCTGGCGGGAAGAG 61.331 60.000 0.00 0.00 43.42 2.85
46 47 4.168291 GGCTCTGGCGGGAAGAGG 62.168 72.222 2.87 0.00 41.31 3.69
47 48 3.394836 GCTCTGGCGGGAAGAGGT 61.395 66.667 2.87 0.00 41.31 3.85
48 49 2.058595 GCTCTGGCGGGAAGAGGTA 61.059 63.158 2.87 0.00 41.31 3.08
49 50 1.817209 CTCTGGCGGGAAGAGGTAC 59.183 63.158 0.00 0.00 38.00 3.34
50 51 1.677637 CTCTGGCGGGAAGAGGTACC 61.678 65.000 2.73 2.73 38.00 3.34
54 55 3.522808 CGGGAAGAGGTACCGGAG 58.477 66.667 9.46 0.00 43.69 4.63
55 56 1.077212 CGGGAAGAGGTACCGGAGA 60.077 63.158 9.46 0.00 43.69 3.71
56 57 0.467659 CGGGAAGAGGTACCGGAGAT 60.468 60.000 9.46 0.00 43.69 2.75
57 58 1.790818 GGGAAGAGGTACCGGAGATT 58.209 55.000 9.46 0.00 0.00 2.40
58 59 1.413077 GGGAAGAGGTACCGGAGATTG 59.587 57.143 9.46 0.00 0.00 2.67
59 60 2.108970 GGAAGAGGTACCGGAGATTGT 58.891 52.381 9.46 0.00 0.00 2.71
60 61 2.101082 GGAAGAGGTACCGGAGATTGTC 59.899 54.545 9.46 0.00 0.00 3.18
61 62 1.390565 AGAGGTACCGGAGATTGTCG 58.609 55.000 9.46 0.00 0.00 4.35
62 63 1.064906 AGAGGTACCGGAGATTGTCGA 60.065 52.381 9.46 0.00 0.00 4.20
63 64 1.747355 GAGGTACCGGAGATTGTCGAA 59.253 52.381 9.46 0.00 0.00 3.71
64 65 1.475682 AGGTACCGGAGATTGTCGAAC 59.524 52.381 9.46 0.00 0.00 3.95
65 66 1.203052 GGTACCGGAGATTGTCGAACA 59.797 52.381 9.46 0.00 0.00 3.18
66 67 2.353011 GGTACCGGAGATTGTCGAACAA 60.353 50.000 9.46 0.00 42.95 2.83
67 68 2.080286 ACCGGAGATTGTCGAACAAG 57.920 50.000 9.46 0.00 41.94 3.16
68 69 1.616865 ACCGGAGATTGTCGAACAAGA 59.383 47.619 9.46 0.00 41.94 3.02
69 70 2.233922 ACCGGAGATTGTCGAACAAGAT 59.766 45.455 9.46 0.00 41.94 2.40
70 71 2.604914 CCGGAGATTGTCGAACAAGATG 59.395 50.000 0.00 0.00 41.94 2.90
71 72 3.254060 CGGAGATTGTCGAACAAGATGT 58.746 45.455 0.00 0.00 41.94 3.06
72 73 4.421058 CGGAGATTGTCGAACAAGATGTA 58.579 43.478 0.00 0.00 41.94 2.29
73 74 4.862574 CGGAGATTGTCGAACAAGATGTAA 59.137 41.667 0.00 0.00 41.94 2.41
74 75 5.347635 CGGAGATTGTCGAACAAGATGTAAA 59.652 40.000 0.00 0.00 41.94 2.01
75 76 6.036083 CGGAGATTGTCGAACAAGATGTAAAT 59.964 38.462 0.00 0.00 41.94 1.40
76 77 7.413000 CGGAGATTGTCGAACAAGATGTAAATT 60.413 37.037 0.00 0.00 41.94 1.82
77 78 7.693951 GGAGATTGTCGAACAAGATGTAAATTG 59.306 37.037 0.00 0.00 41.94 2.32
78 79 8.322906 AGATTGTCGAACAAGATGTAAATTGA 57.677 30.769 0.00 0.00 41.94 2.57
79 80 8.783093 AGATTGTCGAACAAGATGTAAATTGAA 58.217 29.630 0.00 0.00 41.94 2.69
80 81 8.728088 ATTGTCGAACAAGATGTAAATTGAAC 57.272 30.769 0.00 0.00 41.94 3.18
81 82 7.490962 TGTCGAACAAGATGTAAATTGAACT 57.509 32.000 0.00 0.00 0.00 3.01
82 83 7.925993 TGTCGAACAAGATGTAAATTGAACTT 58.074 30.769 0.00 0.00 0.00 2.66
83 84 8.067784 TGTCGAACAAGATGTAAATTGAACTTC 58.932 33.333 0.00 0.00 0.00 3.01
84 85 7.266335 GTCGAACAAGATGTAAATTGAACTTCG 59.734 37.037 0.00 0.00 35.49 3.79
85 86 7.170151 TCGAACAAGATGTAAATTGAACTTCGA 59.830 33.333 7.38 7.38 38.24 3.71
86 87 7.475565 CGAACAAGATGTAAATTGAACTTCGAG 59.524 37.037 0.00 4.26 35.86 4.04
87 88 7.730364 ACAAGATGTAAATTGAACTTCGAGT 57.270 32.000 0.00 0.00 0.00 4.18
88 89 8.827177 ACAAGATGTAAATTGAACTTCGAGTA 57.173 30.769 0.00 0.00 0.00 2.59
89 90 9.268268 ACAAGATGTAAATTGAACTTCGAGTAA 57.732 29.630 0.00 0.00 0.00 2.24
92 93 8.391106 AGATGTAAATTGAACTTCGAGTAATGC 58.609 33.333 0.00 0.00 0.00 3.56
93 94 7.428282 TGTAAATTGAACTTCGAGTAATGCA 57.572 32.000 0.00 0.00 0.00 3.96
94 95 7.866729 TGTAAATTGAACTTCGAGTAATGCAA 58.133 30.769 0.00 0.00 0.00 4.08
95 96 8.015087 TGTAAATTGAACTTCGAGTAATGCAAG 58.985 33.333 0.00 0.00 0.00 4.01
96 97 6.801539 AATTGAACTTCGAGTAATGCAAGA 57.198 33.333 0.00 0.00 0.00 3.02
97 98 6.801539 ATTGAACTTCGAGTAATGCAAGAA 57.198 33.333 0.00 0.00 0.00 2.52
98 99 6.801539 TTGAACTTCGAGTAATGCAAGAAT 57.198 33.333 0.00 0.00 0.00 2.40
99 100 6.801539 TGAACTTCGAGTAATGCAAGAATT 57.198 33.333 0.00 0.00 0.00 2.17
100 101 7.202016 TGAACTTCGAGTAATGCAAGAATTT 57.798 32.000 0.00 0.00 0.00 1.82
101 102 7.648142 TGAACTTCGAGTAATGCAAGAATTTT 58.352 30.769 0.00 0.00 0.00 1.82
102 103 8.134895 TGAACTTCGAGTAATGCAAGAATTTTT 58.865 29.630 0.00 0.00 0.00 1.94
126 127 9.878599 TTTTTCGCAAAAATAAAAACAAGAACA 57.121 22.222 0.00 0.00 35.57 3.18
127 128 9.535270 TTTTCGCAAAAATAAAAACAAGAACAG 57.465 25.926 0.00 0.00 29.44 3.16
128 129 8.467402 TTCGCAAAAATAAAAACAAGAACAGA 57.533 26.923 0.00 0.00 0.00 3.41
129 130 7.890763 TCGCAAAAATAAAAACAAGAACAGAC 58.109 30.769 0.00 0.00 0.00 3.51
130 131 7.757624 TCGCAAAAATAAAAACAAGAACAGACT 59.242 29.630 0.00 0.00 0.00 3.24
131 132 9.015577 CGCAAAAATAAAAACAAGAACAGACTA 57.984 29.630 0.00 0.00 0.00 2.59
145 146 5.422650 AGAACAGACTAAGGTATGGGAGAAC 59.577 44.000 0.00 0.00 38.81 3.01
151 152 4.717280 ACTAAGGTATGGGAGAACAGAAGG 59.283 45.833 0.00 0.00 0.00 3.46
159 160 2.537143 GGAGAACAGAAGGTACCCTCA 58.463 52.381 13.09 0.00 30.89 3.86
175 176 2.240667 CCCTCATCATCTCACCCACTTT 59.759 50.000 0.00 0.00 0.00 2.66
217 218 6.630071 TCTTTATATCTTGCAAGGCCAAAAC 58.370 36.000 25.73 0.00 0.00 2.43
218 219 3.893326 ATATCTTGCAAGGCCAAAACC 57.107 42.857 25.73 0.00 0.00 3.27
219 220 0.686789 ATCTTGCAAGGCCAAAACCC 59.313 50.000 25.73 0.00 0.00 4.11
221 222 0.249996 CTTGCAAGGCCAAAACCCAG 60.250 55.000 19.14 0.00 0.00 4.45
222 223 0.689080 TTGCAAGGCCAAAACCCAGA 60.689 50.000 5.01 0.00 0.00 3.86
223 224 0.689080 TGCAAGGCCAAAACCCAGAA 60.689 50.000 5.01 0.00 0.00 3.02
224 225 0.467804 GCAAGGCCAAAACCCAGAAA 59.532 50.000 5.01 0.00 0.00 2.52
226 227 2.682269 GCAAGGCCAAAACCCAGAAAAA 60.682 45.455 5.01 0.00 0.00 1.94
227 228 2.942376 CAAGGCCAAAACCCAGAAAAAC 59.058 45.455 5.01 0.00 0.00 2.43
229 230 0.934496 GCCAAAACCCAGAAAAACGC 59.066 50.000 0.00 0.00 0.00 4.84
230 231 1.740718 GCCAAAACCCAGAAAAACGCA 60.741 47.619 0.00 0.00 0.00 5.24
231 232 1.930503 CCAAAACCCAGAAAAACGCAC 59.069 47.619 0.00 0.00 0.00 5.34
232 233 2.611518 CAAAACCCAGAAAAACGCACA 58.388 42.857 0.00 0.00 0.00 4.57
233 234 2.287393 AAACCCAGAAAAACGCACAC 57.713 45.000 0.00 0.00 0.00 3.82
312 313 5.399013 CACGGTGGGATTAAATGTTTCTTC 58.601 41.667 0.00 0.00 0.00 2.87
330 334 4.312443 TCTTCTGTACCCATGAAAACGTC 58.688 43.478 0.00 0.00 0.00 4.34
411 417 1.715785 AAATCCACCCACCAAACCTG 58.284 50.000 0.00 0.00 0.00 4.00
483 493 0.189822 CCCCCAAAAAGTTCTCCCCA 59.810 55.000 0.00 0.00 0.00 4.96
484 494 1.413808 CCCCCAAAAAGTTCTCCCCAA 60.414 52.381 0.00 0.00 0.00 4.12
485 495 1.691976 CCCCAAAAAGTTCTCCCCAAC 59.308 52.381 0.00 0.00 0.00 3.77
492 502 2.658807 AGTTCTCCCCAACAAAGTCC 57.341 50.000 0.00 0.00 0.00 3.85
536 547 5.292589 CCGCGTAGTACATAAAAATGGAACT 59.707 40.000 4.92 0.00 0.00 3.01
600 612 0.110644 GAGAAGAAGGCAACGCAACG 60.111 55.000 0.00 0.00 46.39 4.10
605 617 0.163146 GAAGGCAACGCAACGTACTC 59.837 55.000 0.00 0.00 39.99 2.59
611 631 0.956633 AACGCAACGTACTCCAGAGA 59.043 50.000 0.70 0.00 39.99 3.10
612 632 0.522180 ACGCAACGTACTCCAGAGAG 59.478 55.000 0.70 0.00 38.73 3.20
615 635 2.085320 GCAACGTACTCCAGAGAGAGA 58.915 52.381 0.70 0.00 43.39 3.10
616 636 2.096819 GCAACGTACTCCAGAGAGAGAG 59.903 54.545 0.70 0.00 43.39 3.20
848 874 2.121918 CCACCCCTATCCCCCTCC 60.122 72.222 0.00 0.00 0.00 4.30
849 875 2.121918 CACCCCTATCCCCCTCCC 60.122 72.222 0.00 0.00 0.00 4.30
850 876 3.468321 ACCCCTATCCCCCTCCCC 61.468 72.222 0.00 0.00 0.00 4.81
851 877 3.467347 CCCCTATCCCCCTCCCCA 61.467 72.222 0.00 0.00 0.00 4.96
852 878 2.121918 CCCTATCCCCCTCCCCAC 60.122 72.222 0.00 0.00 0.00 4.61
853 879 2.709396 CCTATCCCCCTCCCCACA 59.291 66.667 0.00 0.00 0.00 4.17
854 880 1.770518 CCTATCCCCCTCCCCACAC 60.771 68.421 0.00 0.00 0.00 3.82
855 881 1.004230 CTATCCCCCTCCCCACACA 59.996 63.158 0.00 0.00 0.00 3.72
899 925 3.244526 GCCCACCATTTTCTTGATTTGGT 60.245 43.478 0.00 0.00 41.27 3.67
1311 1342 3.055240 AGTCCATCTCCAAGAAGAAGCTG 60.055 47.826 0.00 0.00 0.00 4.24
1391 1422 0.038166 AAGCACCCCAACATCGTCAT 59.962 50.000 0.00 0.00 0.00 3.06
1708 1744 7.229228 TGTTTCATTGAATAGGTTACGATCG 57.771 36.000 14.88 14.88 0.00 3.69
1724 1760 2.474359 CGATCGATCCTGTGAAGCAATC 59.526 50.000 19.51 0.00 0.00 2.67
2096 2213 6.616947 TGTATTGTTTGCCTAATGTGCTAAC 58.383 36.000 0.00 0.00 42.29 2.34
2426 2596 2.507407 TATTTTGCCTCTGGGGTGAC 57.493 50.000 0.00 0.00 37.43 3.67
2530 2826 9.512435 CTTCCATTTTATAATGCAGAAACTGAG 57.488 33.333 2.81 0.00 39.87 3.35
2784 3083 1.762708 TTTCAGATGATTTCCGCCCC 58.237 50.000 0.00 0.00 0.00 5.80
2816 3115 2.780065 TTGCATTGCTTGTGTCTCAC 57.220 45.000 10.49 0.00 34.56 3.51
3019 3320 7.095187 ACGTTAGACTTGCTTTCTAGGAATTTG 60.095 37.037 0.00 0.00 30.84 2.32
3112 3413 6.604795 AGGATATGTTTGAAAAGATGGACCTG 59.395 38.462 0.00 0.00 0.00 4.00
3121 3422 5.299279 TGAAAAGATGGACCTGAACAAAGAC 59.701 40.000 0.00 0.00 0.00 3.01
3276 3577 7.230510 TGCAACTCTTTGTTATTACACTGGAAT 59.769 33.333 0.00 0.00 37.07 3.01
3304 3605 7.770801 TTGTTTCTATGTAGAATCACCATCG 57.229 36.000 11.24 0.00 41.52 3.84
3373 3674 4.423625 AGATCATACCTGGTAAACTGGC 57.576 45.455 11.17 1.93 41.59 4.85
3393 3694 4.467082 TGGCTGAAATGGAATTGTTAGCAT 59.533 37.500 0.00 0.00 38.37 3.79
3534 3843 7.270047 TGGGTGCACTTTCTACATATTACTAC 58.730 38.462 17.98 0.00 0.00 2.73
3553 3862 1.675219 GTGTTGAAGGCGAGGGGTA 59.325 57.895 0.00 0.00 0.00 3.69
3561 3870 4.457466 TGAAGGCGAGGGGTATTTTTATC 58.543 43.478 0.00 0.00 0.00 1.75
4135 4453 4.283212 TGAATTCCAGATGAAAACCAACCC 59.717 41.667 2.27 0.00 36.33 4.11
4483 4802 3.056107 TCACATACTCCCTCGTTCCAAAG 60.056 47.826 0.00 0.00 0.00 2.77
4487 4806 5.189145 ACATACTCCCTCGTTCCAAAGTAAT 59.811 40.000 0.00 0.00 0.00 1.89
4492 4811 4.069304 CCCTCGTTCCAAAGTAATTGTCA 58.931 43.478 0.00 0.00 37.32 3.58
4496 4823 7.094549 CCCTCGTTCCAAAGTAATTGTCATAAA 60.095 37.037 0.00 0.00 37.32 1.40
4514 4841 9.239002 TGTCATAAATTTGAACTAAAACCAACG 57.761 29.630 0.00 0.00 0.00 4.10
4515 4842 9.453325 GTCATAAATTTGAACTAAAACCAACGA 57.547 29.630 0.00 0.00 0.00 3.85
4516 4843 9.453325 TCATAAATTTGAACTAAAACCAACGAC 57.547 29.630 0.00 0.00 0.00 4.34
4517 4844 9.239002 CATAAATTTGAACTAAAACCAACGACA 57.761 29.630 0.00 0.00 0.00 4.35
4518 4845 7.514573 AAATTTGAACTAAAACCAACGACAC 57.485 32.000 0.00 0.00 0.00 3.67
4519 4846 5.883503 TTTGAACTAAAACCAACGACACT 57.116 34.783 0.00 0.00 0.00 3.55
4520 4847 5.883503 TTGAACTAAAACCAACGACACTT 57.116 34.783 0.00 0.00 0.00 3.16
4555 4882 0.846693 AGGTTGTGGAGGAGCAACTT 59.153 50.000 7.25 0.00 43.07 2.66
4666 4993 2.170187 CTGATAGGGCAGCAAGAGTTCT 59.830 50.000 0.00 0.00 0.00 3.01
4771 5098 3.764434 CTGCCTACAAAGTAGAGGTGAGA 59.236 47.826 5.78 0.00 32.53 3.27
4869 5197 5.878406 AGGTTCACCATTCTACTCATAGG 57.122 43.478 0.00 0.00 38.89 2.57
5083 5427 0.456628 GGTAGAGAGTCAAGTCCGCC 59.543 60.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.713830 GCAATTCGGTACTGCGACC 59.286 57.895 0.00 0.00 36.00 4.79
5 6 1.327460 CCATGACGCAATTCGGTACTG 59.673 52.381 0.00 0.00 43.86 2.74
6 7 1.066430 ACCATGACGCAATTCGGTACT 60.066 47.619 0.00 0.00 43.86 2.73
7 8 1.365699 ACCATGACGCAATTCGGTAC 58.634 50.000 0.00 0.00 43.86 3.34
8 9 2.102070 AACCATGACGCAATTCGGTA 57.898 45.000 0.00 0.00 43.86 4.02
9 10 2.006888 CTAACCATGACGCAATTCGGT 58.993 47.619 0.00 0.00 43.86 4.69
10 11 1.330521 CCTAACCATGACGCAATTCGG 59.669 52.381 0.00 0.00 43.86 4.30
11 12 1.268032 GCCTAACCATGACGCAATTCG 60.268 52.381 0.00 0.00 45.38 3.34
12 13 2.017049 AGCCTAACCATGACGCAATTC 58.983 47.619 0.00 0.00 0.00 2.17
13 14 2.017049 GAGCCTAACCATGACGCAATT 58.983 47.619 0.00 0.00 0.00 2.32
14 15 1.210478 AGAGCCTAACCATGACGCAAT 59.790 47.619 0.00 0.00 0.00 3.56
15 16 0.613260 AGAGCCTAACCATGACGCAA 59.387 50.000 0.00 0.00 0.00 4.85
16 17 0.108186 CAGAGCCTAACCATGACGCA 60.108 55.000 0.00 0.00 0.00 5.24
17 18 0.811616 CCAGAGCCTAACCATGACGC 60.812 60.000 0.00 0.00 0.00 5.19
18 19 0.811616 GCCAGAGCCTAACCATGACG 60.812 60.000 0.00 0.00 0.00 4.35
19 20 0.811616 CGCCAGAGCCTAACCATGAC 60.812 60.000 0.00 0.00 34.57 3.06
20 21 1.522092 CGCCAGAGCCTAACCATGA 59.478 57.895 0.00 0.00 34.57 3.07
21 22 1.524621 CCGCCAGAGCCTAACCATG 60.525 63.158 0.00 0.00 34.57 3.66
22 23 2.746375 CCCGCCAGAGCCTAACCAT 61.746 63.158 0.00 0.00 34.57 3.55
23 24 3.399181 CCCGCCAGAGCCTAACCA 61.399 66.667 0.00 0.00 34.57 3.67
24 25 2.595009 CTTCCCGCCAGAGCCTAACC 62.595 65.000 0.00 0.00 34.57 2.85
25 26 1.153349 CTTCCCGCCAGAGCCTAAC 60.153 63.158 0.00 0.00 34.57 2.34
26 27 1.305802 TCTTCCCGCCAGAGCCTAA 60.306 57.895 0.00 0.00 34.57 2.69
27 28 1.758514 CTCTTCCCGCCAGAGCCTA 60.759 63.158 0.00 0.00 31.65 3.93
28 29 3.080121 CTCTTCCCGCCAGAGCCT 61.080 66.667 0.00 0.00 31.65 4.58
29 30 4.168291 CCTCTTCCCGCCAGAGCC 62.168 72.222 0.00 0.00 37.11 4.70
30 31 2.058595 TACCTCTTCCCGCCAGAGC 61.059 63.158 0.00 0.00 37.11 4.09
31 32 1.677637 GGTACCTCTTCCCGCCAGAG 61.678 65.000 4.06 0.00 38.03 3.35
32 33 1.684734 GGTACCTCTTCCCGCCAGA 60.685 63.158 4.06 0.00 0.00 3.86
33 34 2.901042 GGTACCTCTTCCCGCCAG 59.099 66.667 4.06 0.00 0.00 4.85
34 35 3.072468 CGGTACCTCTTCCCGCCA 61.072 66.667 10.90 0.00 34.62 5.69
35 36 3.846430 CCGGTACCTCTTCCCGCC 61.846 72.222 10.90 0.00 40.38 6.13
36 37 2.757099 TCCGGTACCTCTTCCCGC 60.757 66.667 10.90 0.00 40.38 6.13
37 38 0.467659 ATCTCCGGTACCTCTTCCCG 60.468 60.000 10.90 0.00 41.37 5.14
38 39 1.413077 CAATCTCCGGTACCTCTTCCC 59.587 57.143 10.90 0.00 0.00 3.97
39 40 2.101082 GACAATCTCCGGTACCTCTTCC 59.899 54.545 10.90 0.00 0.00 3.46
40 41 2.223525 CGACAATCTCCGGTACCTCTTC 60.224 54.545 10.90 0.00 0.00 2.87
41 42 1.749634 CGACAATCTCCGGTACCTCTT 59.250 52.381 10.90 0.00 0.00 2.85
42 43 1.064906 TCGACAATCTCCGGTACCTCT 60.065 52.381 10.90 0.00 0.00 3.69
43 44 1.386533 TCGACAATCTCCGGTACCTC 58.613 55.000 10.90 0.00 0.00 3.85
44 45 1.475682 GTTCGACAATCTCCGGTACCT 59.524 52.381 10.90 0.00 0.00 3.08
45 46 1.203052 TGTTCGACAATCTCCGGTACC 59.797 52.381 0.16 0.16 0.00 3.34
46 47 2.642139 TGTTCGACAATCTCCGGTAC 57.358 50.000 0.00 0.00 0.00 3.34
47 48 2.821378 TCTTGTTCGACAATCTCCGGTA 59.179 45.455 0.00 0.00 37.48 4.02
48 49 1.616865 TCTTGTTCGACAATCTCCGGT 59.383 47.619 0.00 0.00 37.48 5.28
49 50 2.363788 TCTTGTTCGACAATCTCCGG 57.636 50.000 0.00 0.00 37.48 5.14
50 51 3.254060 ACATCTTGTTCGACAATCTCCG 58.746 45.455 0.00 0.00 37.48 4.63
51 52 6.721571 TTTACATCTTGTTCGACAATCTCC 57.278 37.500 0.00 0.00 37.48 3.71
52 53 8.443160 TCAATTTACATCTTGTTCGACAATCTC 58.557 33.333 0.00 0.00 37.48 2.75
53 54 8.322906 TCAATTTACATCTTGTTCGACAATCT 57.677 30.769 0.00 0.00 37.48 2.40
54 55 8.840867 GTTCAATTTACATCTTGTTCGACAATC 58.159 33.333 0.00 0.00 37.48 2.67
55 56 8.567948 AGTTCAATTTACATCTTGTTCGACAAT 58.432 29.630 0.00 0.00 37.48 2.71
56 57 7.925993 AGTTCAATTTACATCTTGTTCGACAA 58.074 30.769 0.00 0.00 36.54 3.18
57 58 7.490962 AGTTCAATTTACATCTTGTTCGACA 57.509 32.000 0.00 0.00 0.00 4.35
58 59 7.266335 CGAAGTTCAATTTACATCTTGTTCGAC 59.734 37.037 3.32 0.00 33.67 4.20
59 60 7.170151 TCGAAGTTCAATTTACATCTTGTTCGA 59.830 33.333 3.32 0.00 36.20 3.71
60 61 7.287950 TCGAAGTTCAATTTACATCTTGTTCG 58.712 34.615 3.32 0.00 33.39 3.95
61 62 8.283291 ACTCGAAGTTCAATTTACATCTTGTTC 58.717 33.333 3.32 0.00 0.00 3.18
62 63 8.154649 ACTCGAAGTTCAATTTACATCTTGTT 57.845 30.769 3.32 0.00 0.00 2.83
63 64 7.730364 ACTCGAAGTTCAATTTACATCTTGT 57.270 32.000 3.32 0.00 0.00 3.16
66 67 8.391106 GCATTACTCGAAGTTCAATTTACATCT 58.609 33.333 3.32 0.00 0.00 2.90
67 68 8.175069 TGCATTACTCGAAGTTCAATTTACATC 58.825 33.333 3.32 0.00 0.00 3.06
68 69 8.039603 TGCATTACTCGAAGTTCAATTTACAT 57.960 30.769 3.32 0.00 0.00 2.29
69 70 7.428282 TGCATTACTCGAAGTTCAATTTACA 57.572 32.000 3.32 0.00 0.00 2.41
70 71 8.227791 TCTTGCATTACTCGAAGTTCAATTTAC 58.772 33.333 3.32 0.00 0.00 2.01
71 72 8.317891 TCTTGCATTACTCGAAGTTCAATTTA 57.682 30.769 3.32 0.00 0.00 1.40
72 73 7.202016 TCTTGCATTACTCGAAGTTCAATTT 57.798 32.000 3.32 0.00 0.00 1.82
73 74 6.801539 TCTTGCATTACTCGAAGTTCAATT 57.198 33.333 3.32 0.00 0.00 2.32
74 75 6.801539 TTCTTGCATTACTCGAAGTTCAAT 57.198 33.333 3.32 0.00 0.00 2.57
75 76 6.801539 ATTCTTGCATTACTCGAAGTTCAA 57.198 33.333 3.32 0.00 0.00 2.69
76 77 6.801539 AATTCTTGCATTACTCGAAGTTCA 57.198 33.333 3.32 0.00 0.00 3.18
77 78 8.507470 AAAAATTCTTGCATTACTCGAAGTTC 57.493 30.769 0.00 0.00 0.00 3.01
100 101 9.878599 TGTTCTTGTTTTTATTTTTGCGAAAAA 57.121 22.222 15.68 11.60 43.76 1.94
101 102 9.535270 CTGTTCTTGTTTTTATTTTTGCGAAAA 57.465 25.926 14.16 14.16 38.96 2.29
102 103 8.926710 TCTGTTCTTGTTTTTATTTTTGCGAAA 58.073 25.926 0.00 0.00 0.00 3.46
103 104 8.376942 GTCTGTTCTTGTTTTTATTTTTGCGAA 58.623 29.630 0.00 0.00 0.00 4.70
104 105 7.757624 AGTCTGTTCTTGTTTTTATTTTTGCGA 59.242 29.630 0.00 0.00 0.00 5.10
105 106 7.894847 AGTCTGTTCTTGTTTTTATTTTTGCG 58.105 30.769 0.00 0.00 0.00 4.85
113 114 9.280174 CCATACCTTAGTCTGTTCTTGTTTTTA 57.720 33.333 0.00 0.00 0.00 1.52
114 115 7.230712 CCCATACCTTAGTCTGTTCTTGTTTTT 59.769 37.037 0.00 0.00 0.00 1.94
115 116 6.715264 CCCATACCTTAGTCTGTTCTTGTTTT 59.285 38.462 0.00 0.00 0.00 2.43
116 117 6.043938 TCCCATACCTTAGTCTGTTCTTGTTT 59.956 38.462 0.00 0.00 0.00 2.83
117 118 5.546499 TCCCATACCTTAGTCTGTTCTTGTT 59.454 40.000 0.00 0.00 0.00 2.83
118 119 5.091552 TCCCATACCTTAGTCTGTTCTTGT 58.908 41.667 0.00 0.00 0.00 3.16
119 120 5.422331 TCTCCCATACCTTAGTCTGTTCTTG 59.578 44.000 0.00 0.00 0.00 3.02
120 121 5.590818 TCTCCCATACCTTAGTCTGTTCTT 58.409 41.667 0.00 0.00 0.00 2.52
121 122 5.208294 TCTCCCATACCTTAGTCTGTTCT 57.792 43.478 0.00 0.00 0.00 3.01
122 123 5.187186 TGTTCTCCCATACCTTAGTCTGTTC 59.813 44.000 0.00 0.00 0.00 3.18
123 124 5.091552 TGTTCTCCCATACCTTAGTCTGTT 58.908 41.667 0.00 0.00 0.00 3.16
124 125 4.684724 TGTTCTCCCATACCTTAGTCTGT 58.315 43.478 0.00 0.00 0.00 3.41
125 126 4.956700 TCTGTTCTCCCATACCTTAGTCTG 59.043 45.833 0.00 0.00 0.00 3.51
126 127 5.208294 TCTGTTCTCCCATACCTTAGTCT 57.792 43.478 0.00 0.00 0.00 3.24
127 128 5.163395 CCTTCTGTTCTCCCATACCTTAGTC 60.163 48.000 0.00 0.00 0.00 2.59
128 129 4.717280 CCTTCTGTTCTCCCATACCTTAGT 59.283 45.833 0.00 0.00 0.00 2.24
129 130 4.717280 ACCTTCTGTTCTCCCATACCTTAG 59.283 45.833 0.00 0.00 0.00 2.18
130 131 4.695606 ACCTTCTGTTCTCCCATACCTTA 58.304 43.478 0.00 0.00 0.00 2.69
131 132 3.532102 ACCTTCTGTTCTCCCATACCTT 58.468 45.455 0.00 0.00 0.00 3.50
132 133 3.207044 ACCTTCTGTTCTCCCATACCT 57.793 47.619 0.00 0.00 0.00 3.08
151 152 2.103263 GTGGGTGAGATGATGAGGGTAC 59.897 54.545 0.00 0.00 0.00 3.34
159 160 3.600388 GACGAAAAGTGGGTGAGATGAT 58.400 45.455 0.00 0.00 0.00 2.45
175 176 4.903045 AAGAGGAGGTAAAATGGACGAA 57.097 40.909 0.00 0.00 0.00 3.85
217 218 0.594796 GCTGTGTGCGTTTTTCTGGG 60.595 55.000 0.00 0.00 0.00 4.45
218 219 0.100325 TGCTGTGTGCGTTTTTCTGG 59.900 50.000 0.00 0.00 46.63 3.86
219 220 1.469917 CTGCTGTGTGCGTTTTTCTG 58.530 50.000 0.00 0.00 46.63 3.02
221 222 0.525242 TGCTGCTGTGTGCGTTTTTC 60.525 50.000 0.00 0.00 46.63 2.29
222 223 0.801836 GTGCTGCTGTGTGCGTTTTT 60.802 50.000 0.00 0.00 46.63 1.94
223 224 1.226660 GTGCTGCTGTGTGCGTTTT 60.227 52.632 0.00 0.00 46.63 2.43
224 225 1.727511 ATGTGCTGCTGTGTGCGTTT 61.728 50.000 0.00 0.00 46.63 3.60
226 227 2.592574 ATGTGCTGCTGTGTGCGT 60.593 55.556 0.00 0.00 46.63 5.24
227 228 1.918868 ATCATGTGCTGCTGTGTGCG 61.919 55.000 0.00 0.00 46.63 5.34
229 230 0.879090 ACATCATGTGCTGCTGTGTG 59.121 50.000 0.00 0.00 33.08 3.82
230 231 1.268625 CAACATCATGTGCTGCTGTGT 59.731 47.619 0.00 0.00 34.53 3.72
231 232 1.538075 TCAACATCATGTGCTGCTGTG 59.462 47.619 0.00 0.00 34.53 3.66
232 233 1.900245 TCAACATCATGTGCTGCTGT 58.100 45.000 0.00 0.00 35.77 4.40
233 234 3.503827 AATCAACATCATGTGCTGCTG 57.496 42.857 0.00 0.00 0.00 4.41
312 313 1.127951 GCGACGTTTTCATGGGTACAG 59.872 52.381 0.00 0.00 0.00 2.74
411 417 5.953548 TGGGGTAGTAAATAAAGGAAAAGGC 59.046 40.000 0.00 0.00 0.00 4.35
483 493 0.693049 ATGGCGAGGAGGACTTTGTT 59.307 50.000 0.00 0.00 0.00 2.83
484 494 0.693049 AATGGCGAGGAGGACTTTGT 59.307 50.000 0.00 0.00 0.00 2.83
485 495 2.691409 TAATGGCGAGGAGGACTTTG 57.309 50.000 0.00 0.00 0.00 2.77
492 502 2.159379 GGCTTTGTTTAATGGCGAGGAG 60.159 50.000 0.00 0.00 0.00 3.69
536 547 7.117241 TGTTGCGTTTTTGTTGTTTATTTCA 57.883 28.000 0.00 0.00 0.00 2.69
600 612 3.275617 TGCTCTCTCTCTCTGGAGTAC 57.724 52.381 0.00 0.00 40.29 2.73
605 617 1.184431 TGCTTGCTCTCTCTCTCTGG 58.816 55.000 0.00 0.00 0.00 3.86
611 631 0.399454 TTGCCTTGCTTGCTCTCTCT 59.601 50.000 0.00 0.00 0.00 3.10
612 632 0.803740 CTTGCCTTGCTTGCTCTCTC 59.196 55.000 0.00 0.00 0.00 3.20
615 635 2.273912 GCCTTGCCTTGCTTGCTCT 61.274 57.895 0.00 0.00 0.00 4.09
616 636 2.210341 GAGCCTTGCCTTGCTTGCTC 62.210 60.000 0.00 0.00 38.11 4.26
848 874 2.203337 CTGGTGTGGGTGTGTGGG 60.203 66.667 0.00 0.00 0.00 4.61
849 875 1.525995 GTCTGGTGTGGGTGTGTGG 60.526 63.158 0.00 0.00 0.00 4.17
850 876 1.887242 CGTCTGGTGTGGGTGTGTG 60.887 63.158 0.00 0.00 0.00 3.82
851 877 2.504032 CGTCTGGTGTGGGTGTGT 59.496 61.111 0.00 0.00 0.00 3.72
852 878 2.972505 GCGTCTGGTGTGGGTGTG 60.973 66.667 0.00 0.00 0.00 3.82
853 879 4.602259 CGCGTCTGGTGTGGGTGT 62.602 66.667 0.00 0.00 0.00 4.16
899 925 1.002274 GAGCAGAGAGGGGAAGGGA 59.998 63.158 0.00 0.00 0.00 4.20
1391 1422 0.675837 CTCGTACGTGTCCCTGAGGA 60.676 60.000 16.05 0.00 41.08 3.71
1703 1739 1.926561 TTGCTTCACAGGATCGATCG 58.073 50.000 18.81 9.36 0.00 3.69
1708 1744 6.034591 CAGAAATTGATTGCTTCACAGGATC 58.965 40.000 0.00 0.00 32.84 3.36
1724 1760 4.508492 TGACAACAGCAAATGCAGAAATTG 59.492 37.500 8.28 6.82 45.16 2.32
2096 2213 3.297830 TCACCTACACATCACGAACAG 57.702 47.619 0.00 0.00 0.00 3.16
2338 2499 3.433615 GCAGACAGGACATAAGAACACAC 59.566 47.826 0.00 0.00 0.00 3.82
2426 2596 2.033141 CCACAGTCCACAGGCCAG 59.967 66.667 5.01 0.00 0.00 4.85
2512 2683 5.945784 ACCTTGCTCAGTTTCTGCATTATAA 59.054 36.000 0.00 0.00 36.55 0.98
2686 2982 7.492352 ACAGTACAGTTAACTTGTGGAAATC 57.508 36.000 5.07 0.00 0.00 2.17
2784 3083 9.697250 CACAAGCAATGCAATTAAATTATCTTG 57.303 29.630 8.35 15.66 32.46 3.02
2816 3115 8.673711 TCTGGAAGAAAATACAAATTATGGACG 58.326 33.333 0.00 0.00 42.31 4.79
3268 3569 8.783093 TCTACATAGAAACAAAACATTCCAGTG 58.217 33.333 0.00 0.00 0.00 3.66
3276 3577 8.684386 TGGTGATTCTACATAGAAACAAAACA 57.316 30.769 11.79 9.34 43.56 2.83
3304 3605 5.438761 AACTCAGTTGATAAAAGTGTGGC 57.561 39.130 0.00 0.00 0.00 5.01
3373 3674 9.113838 ACTAGTATGCTAACAATTCCATTTCAG 57.886 33.333 0.00 0.00 0.00 3.02
3435 3744 5.066505 ACATTTGCTATACTGCCTTACAAGC 59.933 40.000 0.00 0.00 0.00 4.01
3501 3810 4.307032 AGAAAGTGCACCCATCTAATGT 57.693 40.909 14.63 0.00 0.00 2.71
3514 3823 7.982371 ACACGTAGTAATATGTAGAAAGTGC 57.018 36.000 0.00 0.00 41.61 4.40
3534 3843 2.162338 TACCCCTCGCCTTCAACACG 62.162 60.000 0.00 0.00 0.00 4.49
3852 4169 8.519799 TCAAAAGGATGAGAAACAAAACTAGT 57.480 30.769 0.00 0.00 0.00 2.57
4135 4453 3.214328 ACAAAACCAGGAAGCTACACAG 58.786 45.455 0.00 0.00 0.00 3.66
4492 4811 9.240159 GTGTCGTTGGTTTTAGTTCAAATTTAT 57.760 29.630 0.00 0.00 0.00 1.40
4496 4823 6.445357 AGTGTCGTTGGTTTTAGTTCAAAT 57.555 33.333 0.00 0.00 0.00 2.32
4512 4839 1.221414 GCTGCTTCAAGAAGTGTCGT 58.779 50.000 11.14 0.00 40.45 4.34
4513 4840 1.070309 GTGCTGCTTCAAGAAGTGTCG 60.070 52.381 11.14 0.16 40.45 4.35
4514 4841 1.942657 TGTGCTGCTTCAAGAAGTGTC 59.057 47.619 11.14 2.16 40.45 3.67
4515 4842 2.042686 TGTGCTGCTTCAAGAAGTGT 57.957 45.000 11.14 0.00 40.45 3.55
4516 4843 3.369385 CTTTGTGCTGCTTCAAGAAGTG 58.631 45.455 11.14 6.24 40.45 3.16
4517 4844 2.360165 CCTTTGTGCTGCTTCAAGAAGT 59.640 45.455 11.14 0.00 40.45 3.01
4518 4845 2.360165 ACCTTTGTGCTGCTTCAAGAAG 59.640 45.455 5.46 5.46 41.24 2.85
4519 4846 2.378038 ACCTTTGTGCTGCTTCAAGAA 58.622 42.857 0.00 0.00 0.00 2.52
4520 4847 2.057137 ACCTTTGTGCTGCTTCAAGA 57.943 45.000 0.00 0.00 0.00 3.02
4555 4882 2.566833 ACATTGTAGCAGCAAGGTGA 57.433 45.000 9.20 0.00 41.06 4.02
4666 4993 2.023404 TGTGCCCTAGGAGTTCTGGATA 60.023 50.000 11.48 0.00 0.00 2.59
4771 5098 5.674958 TCCCAAAGCCCTATAAATAGAGGTT 59.325 40.000 0.81 0.00 32.85 3.50
4923 5255 9.088512 GATACTTCTGTTGTGGTCTAGTATTTG 57.911 37.037 0.00 0.00 30.01 2.32
5007 5351 1.476110 CGAGTTCCAAACAACCAGGGA 60.476 52.381 0.00 0.00 0.00 4.20


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.