Multiple sequence alignment - TraesCS3D01G470200

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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 TraesCS3D01G470200 chr3D 100.000 4444 0 0 2036 6479 572048347 572043904 0.000000e+00 8207.0
1 TraesCS3D01G470200 chr3D 100.000 1760 0 0 1 1760 572050382 572048623 0.000000e+00 3251.0
2 TraesCS3D01G470200 chr3D 89.250 1107 119 0 4334 5440 572085520 572084414 0.000000e+00 1386.0
3 TraesCS3D01G470200 chr3D 88.376 1084 125 1 4351 5433 572101793 572100710 0.000000e+00 1303.0
4 TraesCS3D01G470200 chr3D 90.602 830 66 4 891 1711 572088783 572087957 0.000000e+00 1090.0
5 TraesCS3D01G470200 chr3D 88.726 887 63 13 3187 4036 543807375 543806489 0.000000e+00 1050.0
6 TraesCS3D01G470200 chr3D 81.735 761 115 17 966 1711 572103041 572102290 1.190000e-171 614.0
7 TraesCS3D01G470200 chr3D 89.200 500 41 9 36 525 572096245 572095749 4.290000e-171 612.0
8 TraesCS3D01G470200 chr3D 90.840 131 9 2 652 781 572090878 572090750 8.640000e-39 172.0
9 TraesCS3D01G470200 chr3A 93.582 2306 119 14 4188 6479 706922700 706924990 0.000000e+00 3411.0
10 TraesCS3D01G470200 chr3A 95.926 1129 38 5 638 1760 706911006 706912132 0.000000e+00 1823.0
11 TraesCS3D01G470200 chr3A 88.100 1084 129 0 4357 5440 706851423 706852506 0.000000e+00 1288.0
12 TraesCS3D01G470200 chr3A 89.492 885 73 9 842 1711 706899495 706900374 0.000000e+00 1101.0
13 TraesCS3D01G470200 chr3A 94.700 566 25 3 2 563 706910449 706911013 0.000000e+00 874.0
14 TraesCS3D01G470200 chr3A 88.958 643 62 3 3187 3820 671003944 671004586 0.000000e+00 785.0
15 TraesCS3D01G470200 chr3A 92.338 509 29 7 2273 2779 706919302 706919802 0.000000e+00 715.0
16 TraesCS3D01G470200 chr3A 82.815 739 104 16 975 1703 706850167 706850892 1.970000e-179 640.0
17 TraesCS3D01G470200 chr3A 92.718 206 6 3 2764 2960 706922390 706922595 8.220000e-74 289.0
18 TraesCS3D01G470200 chr3A 91.813 171 14 0 2058 2228 706912208 706912378 8.400000e-59 239.0
19 TraesCS3D01G470200 chr3A 82.890 263 25 15 521 781 706899103 706899347 1.090000e-52 219.0
20 TraesCS3D01G470200 chr3A 84.615 143 22 0 2967 3109 743986715 743986857 6.770000e-30 143.0
21 TraesCS3D01G470200 chr3A 76.610 295 45 19 6068 6359 612766467 612766740 2.440000e-29 141.0
22 TraesCS3D01G470200 chr3A 92.063 63 5 0 283 345 706857195 706857257 8.950000e-14 89.8
23 TraesCS3D01G470200 chr3B 94.200 2224 113 12 4263 6479 761936832 761939046 0.000000e+00 3378.0
24 TraesCS3D01G470200 chr3B 90.209 2053 114 26 2036 4041 761934156 761936168 0.000000e+00 2597.0
25 TraesCS3D01G470200 chr3B 93.819 1731 74 16 36 1740 761932276 761933999 0.000000e+00 2573.0
26 TraesCS3D01G470200 chr3B 88.007 1084 130 0 4357 5440 761902264 761903347 0.000000e+00 1282.0
27 TraesCS3D01G470200 chr3B 82.086 748 108 18 975 1711 761901003 761901735 3.320000e-172 616.0
28 TraesCS3D01G470200 chr3B 92.414 145 11 0 4091 4235 761936157 761936301 2.370000e-49 207.0
29 TraesCS3D01G470200 chr3B 91.837 147 12 0 2967 3113 762488104 762488250 8.520000e-49 206.0
30 TraesCS3D01G470200 chr2B 85.244 1064 154 1 4381 5441 390925520 390926583 0.000000e+00 1092.0
31 TraesCS3D01G470200 chr2B 83.871 93 7 3 5583 5673 402372791 402372877 1.500000e-11 82.4
32 TraesCS3D01G470200 chr2B 100.000 29 0 0 5583 5611 168836931 168836959 3.000000e-03 54.7
33 TraesCS3D01G470200 chr2D 84.854 1063 158 1 4382 5441 323076868 323077930 0.000000e+00 1068.0
34 TraesCS3D01G470200 chr2D 88.376 628 45 9 3444 4043 322854566 322855193 0.000000e+00 730.0
35 TraesCS3D01G470200 chr2D 82.609 92 9 3 5583 5673 334095216 334095301 2.510000e-09 75.0
36 TraesCS3D01G470200 chr5A 88.990 881 66 11 3187 4036 703350478 703351358 0.000000e+00 1061.0
37 TraesCS3D01G470200 chr5A 82.581 155 17 8 6217 6369 606884246 606884100 1.900000e-25 128.0
38 TraesCS3D01G470200 chr5A 82.353 153 18 9 6220 6369 606889839 606889693 2.450000e-24 124.0
39 TraesCS3D01G470200 chr1D 88.876 872 65 11 3184 4024 494348012 494347142 0.000000e+00 1044.0
40 TraesCS3D01G470200 chr2A 84.398 1064 163 1 4381 5441 407740548 407739485 0.000000e+00 1042.0
41 TraesCS3D01G470200 chr2A 88.523 880 71 10 3187 4036 498109420 498110299 0.000000e+00 1038.0
42 TraesCS3D01G470200 chr2A 87.841 880 77 9 3187 4036 544284173 544283294 0.000000e+00 1005.0
43 TraesCS3D01G470200 chr2A 75.873 315 53 19 6141 6443 564615798 564615495 8.760000e-29 139.0
44 TraesCS3D01G470200 chr2A 78.919 185 33 5 6142 6324 101871293 101871473 3.170000e-23 121.0
45 TraesCS3D01G470200 chr2A 83.871 93 7 3 5583 5673 444792359 444792445 1.500000e-11 82.4
46 TraesCS3D01G470200 chr6A 88.189 889 73 11 3186 4043 85028389 85027502 0.000000e+00 1031.0
47 TraesCS3D01G470200 chr1A 89.843 699 63 5 3187 3877 32294930 32295628 0.000000e+00 891.0
48 TraesCS3D01G470200 chr1A 94.702 151 8 0 2967 3117 460081397 460081247 1.090000e-57 235.0
49 TraesCS3D01G470200 chr1A 78.723 141 23 6 6111 6248 146417359 146417495 3.220000e-13 87.9
50 TraesCS3D01G470200 chr5D 91.266 561 45 1 3190 3746 539147409 539146849 0.000000e+00 761.0
51 TraesCS3D01G470200 chr5D 89.286 364 18 7 3694 4036 539146849 539146486 2.770000e-118 436.0
52 TraesCS3D01G470200 chr7B 87.244 439 27 11 3626 4036 43945217 43944780 2.110000e-129 473.0
53 TraesCS3D01G470200 chrUn 95.270 148 7 0 2967 3114 259872077 259871930 1.090000e-57 235.0
54 TraesCS3D01G470200 chr7D 95.270 148 7 0 2967 3114 115023067 115023214 1.090000e-57 235.0
55 TraesCS3D01G470200 chr7D 81.013 237 35 8 6058 6291 535951040 535950811 5.160000e-41 180.0
56 TraesCS3D01G470200 chr7D 85.816 141 19 1 6222 6362 197675602 197675463 1.460000e-31 148.0
57 TraesCS3D01G470200 chr5B 94.595 148 8 0 2967 3114 458154887 458154740 5.050000e-56 230.0
58 TraesCS3D01G470200 chr5B 75.128 390 75 14 6059 6446 343825681 343825312 5.200000e-36 163.0
59 TraesCS3D01G470200 chr1B 91.333 150 13 0 2967 3116 107593980 107593831 8.520000e-49 206.0
60 TraesCS3D01G470200 chr1B 91.275 149 13 0 2968 3116 10546854 10546706 3.060000e-48 204.0
61 TraesCS3D01G470200 chr6D 83.000 100 10 5 5575 5673 126868450 126868543 4.160000e-12 84.2
62 TraesCS3D01G470200 chr4B 76.301 173 29 8 6283 6446 67849540 67849709 1.500000e-11 82.4
63 TraesCS3D01G470200 chr4A 92.500 40 3 0 5583 5622 342432268 342432229 2.520000e-04 58.4
64 TraesCS3D01G470200 chr7A 100.000 29 0 0 6428 6456 549377736 549377708 3.000000e-03 54.7


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 TraesCS3D01G470200 chr3D 572043904 572050382 6478 True 5729.000000 8207 100.000000 1 6479 2 chr3D.!!$R3 6478
1 TraesCS3D01G470200 chr3D 543806489 543807375 886 True 1050.000000 1050 88.726000 3187 4036 1 chr3D.!!$R1 849
2 TraesCS3D01G470200 chr3D 572100710 572103041 2331 True 958.500000 1303 85.055500 966 5433 2 chr3D.!!$R5 4467
3 TraesCS3D01G470200 chr3D 572084414 572090878 6464 True 882.666667 1386 90.230667 652 5440 3 chr3D.!!$R4 4788
4 TraesCS3D01G470200 chr3A 706919302 706924990 5688 False 1471.666667 3411 92.879333 2273 6479 3 chr3A.!!$F8 4206
5 TraesCS3D01G470200 chr3A 706910449 706912378 1929 False 978.666667 1823 94.146333 2 2228 3 chr3A.!!$F7 2226
6 TraesCS3D01G470200 chr3A 706850167 706852506 2339 False 964.000000 1288 85.457500 975 5440 2 chr3A.!!$F5 4465
7 TraesCS3D01G470200 chr3A 671003944 671004586 642 False 785.000000 785 88.958000 3187 3820 1 chr3A.!!$F2 633
8 TraesCS3D01G470200 chr3A 706899103 706900374 1271 False 660.000000 1101 86.191000 521 1711 2 chr3A.!!$F6 1190
9 TraesCS3D01G470200 chr3B 761932276 761939046 6770 False 2188.750000 3378 92.660500 36 6479 4 chr3B.!!$F3 6443
10 TraesCS3D01G470200 chr3B 761901003 761903347 2344 False 949.000000 1282 85.046500 975 5440 2 chr3B.!!$F2 4465
11 TraesCS3D01G470200 chr2B 390925520 390926583 1063 False 1092.000000 1092 85.244000 4381 5441 1 chr2B.!!$F2 1060
12 TraesCS3D01G470200 chr2D 323076868 323077930 1062 False 1068.000000 1068 84.854000 4382 5441 1 chr2D.!!$F2 1059
13 TraesCS3D01G470200 chr2D 322854566 322855193 627 False 730.000000 730 88.376000 3444 4043 1 chr2D.!!$F1 599
14 TraesCS3D01G470200 chr5A 703350478 703351358 880 False 1061.000000 1061 88.990000 3187 4036 1 chr5A.!!$F1 849
15 TraesCS3D01G470200 chr1D 494347142 494348012 870 True 1044.000000 1044 88.876000 3184 4024 1 chr1D.!!$R1 840
16 TraesCS3D01G470200 chr2A 407739485 407740548 1063 True 1042.000000 1042 84.398000 4381 5441 1 chr2A.!!$R1 1060
17 TraesCS3D01G470200 chr2A 498109420 498110299 879 False 1038.000000 1038 88.523000 3187 4036 1 chr2A.!!$F3 849
18 TraesCS3D01G470200 chr2A 544283294 544284173 879 True 1005.000000 1005 87.841000 3187 4036 1 chr2A.!!$R2 849
19 TraesCS3D01G470200 chr6A 85027502 85028389 887 True 1031.000000 1031 88.189000 3186 4043 1 chr6A.!!$R1 857
20 TraesCS3D01G470200 chr1A 32294930 32295628 698 False 891.000000 891 89.843000 3187 3877 1 chr1A.!!$F1 690
21 TraesCS3D01G470200 chr5D 539146486 539147409 923 True 598.500000 761 90.276000 3190 4036 2 chr5D.!!$R1 846

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
482 499 0.535553 TCACCCAAACGCTGGTTACC 60.536 55.000 0.00 0.00 44.76 2.85 F
514 534 0.738412 GTACCCATCACCGAACCGTG 60.738 60.000 0.00 0.00 34.93 4.94 F
1368 3370 1.296715 CTTCACCTTCCTCGTGGGG 59.703 63.158 3.23 0.32 35.33 4.96 F
2620 6575 1.445871 ACTTCGGGTATTCGCCAAAC 58.554 50.000 0.00 0.00 0.00 2.93 F
3552 10162 0.695924 TGAATTTCCGCTTCCAGGGA 59.304 50.000 0.00 0.00 0.00 4.20 F
5037 12303 0.395311 AGATCGCGGTGGGAACTCTA 60.395 55.000 6.13 0.00 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2415 6370 1.369209 CGCACCGAACAAGCACAAG 60.369 57.895 0.00 0.00 0.00 3.16 R
2416 6371 2.712539 CGCACCGAACAAGCACAA 59.287 55.556 0.00 0.00 0.00 3.33 R
3275 9870 1.001746 TGTACCGCGGTATGGTTGAAA 59.998 47.619 38.22 14.68 40.96 2.69 R
4159 10849 0.614979 GCTAGGCGGGGATCTGGATA 60.615 60.000 0.00 0.00 0.00 2.59 R
5445 12711 0.756294 AGACATTGACACCGGTGTGA 59.244 50.000 43.34 34.03 45.76 3.58 R
5925 13193 1.076533 ACCGTGTTTATCTGCTCGCG 61.077 55.000 0.00 0.00 0.00 5.87 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
20 21 3.499737 CTCCCGTTGCATCGCACC 61.500 66.667 11.68 0.00 38.71 5.01
51 52 7.187824 TGTGCTAGTCCTCTCTTAATGAAAT 57.812 36.000 0.00 0.00 0.00 2.17
89 92 4.154942 AGAAAAGATCATGCCACCTTTGT 58.845 39.130 0.00 0.00 0.00 2.83
193 197 8.315391 TCTTTCTGAGAATATGTTGACAAGTG 57.685 34.615 0.00 0.00 0.00 3.16
251 255 1.209019 CATGTGGAGGAGAGGGAGTTG 59.791 57.143 0.00 0.00 0.00 3.16
255 259 1.435563 TGGAGGAGAGGGAGTTGGTTA 59.564 52.381 0.00 0.00 0.00 2.85
354 360 4.284490 TGTATTGATGCATAGAGGTCCTCC 59.716 45.833 15.72 0.48 0.00 4.30
361 367 2.029828 GCATAGAGGTCCTCCGTGTATG 60.030 54.545 15.72 16.15 39.05 2.39
374 380 3.070446 TCCGTGTATGGAGAAACTTGTGT 59.930 43.478 0.00 0.00 33.05 3.72
420 437 7.465900 TGGAATATAAACTCCCATCTTTCCT 57.534 36.000 0.00 0.00 33.05 3.36
479 496 0.673437 CAATCACCCAAACGCTGGTT 59.327 50.000 3.63 0.00 44.76 3.67
482 499 0.535553 TCACCCAAACGCTGGTTACC 60.536 55.000 0.00 0.00 44.76 2.85
514 534 0.738412 GTACCCATCACCGAACCGTG 60.738 60.000 0.00 0.00 34.93 4.94
889 2882 1.930251 TAAGCAGACTGAGCTGAGGT 58.070 50.000 6.65 0.00 42.53 3.85
918 2911 3.692406 GTGACCCGACGGAAGCCT 61.692 66.667 17.49 0.00 0.00 4.58
988 2990 3.951775 ATTCGTCCATCCATAGCTCTC 57.048 47.619 0.00 0.00 0.00 3.20
1368 3370 1.296715 CTTCACCTTCCTCGTGGGG 59.703 63.158 3.23 0.32 35.33 4.96
1499 3509 3.568430 TGATTCTTCTGCATGATGCCATC 59.432 43.478 15.70 0.00 44.23 3.51
1703 3797 3.381272 TCCAAGAAGTTTGACTGCTTTGG 59.619 43.478 0.00 5.19 41.26 3.28
1713 3812 2.129607 GACTGCTTTGGTGTTTGCATG 58.870 47.619 0.00 0.00 34.79 4.06
2103 6050 5.444663 AAACAAATGCAAGAGAGTTCTCC 57.555 39.130 5.55 0.00 43.88 3.71
2104 6051 4.090761 ACAAATGCAAGAGAGTTCTCCA 57.909 40.909 5.55 0.00 43.88 3.86
2403 6358 1.667724 CGGTGATGACTTTGGAGATGC 59.332 52.381 0.00 0.00 0.00 3.91
2413 6368 5.121380 ACTTTGGAGATGCTGGACATATT 57.879 39.130 0.00 0.00 39.84 1.28
2414 6369 4.885907 ACTTTGGAGATGCTGGACATATTG 59.114 41.667 0.00 0.00 39.84 1.90
2415 6370 2.854963 TGGAGATGCTGGACATATTGC 58.145 47.619 0.00 0.00 39.84 3.56
2416 6371 2.440627 TGGAGATGCTGGACATATTGCT 59.559 45.455 0.00 0.00 39.84 3.91
2417 6372 3.117776 TGGAGATGCTGGACATATTGCTT 60.118 43.478 0.00 0.00 39.84 3.91
2418 6373 3.252701 GGAGATGCTGGACATATTGCTTG 59.747 47.826 0.00 0.00 39.84 4.01
2432 6387 1.658409 GCTTGTGCTTGTTCGGTGC 60.658 57.895 0.00 0.00 36.03 5.01
2549 6504 3.302555 CTTGCGTTAGTGTCACGTCTTA 58.697 45.455 0.00 0.00 39.92 2.10
2620 6575 1.445871 ACTTCGGGTATTCGCCAAAC 58.554 50.000 0.00 0.00 0.00 2.93
2624 6579 2.011222 TCGGGTATTCGCCAAACAATC 58.989 47.619 0.00 0.00 0.00 2.67
2710 6665 9.632807 GGTAAATCTAGTAATGAGTGATAGCTG 57.367 37.037 0.00 0.00 0.00 4.24
2960 9541 2.188161 GTGTTTTTCACGGGCCGGA 61.188 57.895 31.78 21.17 37.31 5.14
3025 9610 2.952310 GAGTGGGTTCAGTTCTTTGCTT 59.048 45.455 0.00 0.00 0.00 3.91
3093 9688 2.438868 GTTCACTTGAACCCAATGCC 57.561 50.000 10.50 0.00 46.42 4.40
3170 9765 5.750067 GGCATGATATTTTGTGGTCATGTTC 59.250 40.000 13.67 5.47 45.95 3.18
3171 9766 5.456497 GCATGATATTTTGTGGTCATGTTCG 59.544 40.000 13.67 0.00 45.95 3.95
3172 9767 6.554419 CATGATATTTTGTGGTCATGTTCGT 58.446 36.000 6.14 0.00 41.71 3.85
3173 9768 6.567687 TGATATTTTGTGGTCATGTTCGTT 57.432 33.333 0.00 0.00 0.00 3.85
3174 9769 6.976088 TGATATTTTGTGGTCATGTTCGTTT 58.024 32.000 0.00 0.00 0.00 3.60
3175 9770 7.429633 TGATATTTTGTGGTCATGTTCGTTTT 58.570 30.769 0.00 0.00 0.00 2.43
3176 9771 7.923344 TGATATTTTGTGGTCATGTTCGTTTTT 59.077 29.630 0.00 0.00 0.00 1.94
3232 9827 5.946377 AGTTTTATTCCACAATGAGAGGGTC 59.054 40.000 0.00 0.00 0.00 4.46
3275 9870 2.118679 TCACACCATGGAGGAATCGAT 58.881 47.619 21.47 0.00 41.22 3.59
3345 9945 6.949352 ATTGATGTGCTACCCTATTTTGAG 57.051 37.500 0.00 0.00 0.00 3.02
3391 9995 3.285484 ACTTCCTGCCATATGAGCTTTG 58.715 45.455 3.65 1.90 0.00 2.77
3393 9997 2.923121 TCCTGCCATATGAGCTTTGAC 58.077 47.619 3.65 0.00 0.00 3.18
3397 10001 2.507058 TGCCATATGAGCTTTGACCTCT 59.493 45.455 3.65 0.00 0.00 3.69
3453 10063 1.068753 CGCTCGAGAGAATGGCCAT 59.931 57.895 18.75 14.09 41.32 4.40
3502 10112 1.651240 CTTGGCAGTCCGAATGCTGG 61.651 60.000 19.38 7.18 43.35 4.85
3510 10120 2.484062 CCGAATGCTGGATGGCCAC 61.484 63.158 8.16 1.35 39.92 5.01
3552 10162 0.695924 TGAATTTCCGCTTCCAGGGA 59.304 50.000 0.00 0.00 0.00 4.20
3609 10219 2.938956 ATCATTGATCCGTTCTCCCC 57.061 50.000 0.00 0.00 0.00 4.81
3673 10283 4.906618 AGAATGAACCGTCTACCAACAAT 58.093 39.130 0.00 0.00 0.00 2.71
3822 10490 7.042658 CCTCACCAAATTTAGCGACTTATACTC 60.043 40.741 0.00 0.00 0.00 2.59
3834 10502 8.397575 AGCGACTTATACTCTCAAGATAATCA 57.602 34.615 0.00 0.00 0.00 2.57
3919 10587 3.321111 ACGCCAGATCGTCATAATTACCT 59.679 43.478 0.00 0.00 38.44 3.08
3920 10588 3.921021 CGCCAGATCGTCATAATTACCTC 59.079 47.826 0.00 0.00 0.00 3.85
3921 10589 4.321304 CGCCAGATCGTCATAATTACCTCT 60.321 45.833 0.00 0.00 0.00 3.69
3922 10590 5.106277 CGCCAGATCGTCATAATTACCTCTA 60.106 44.000 0.00 0.00 0.00 2.43
3924 10592 6.071840 GCCAGATCGTCATAATTACCTCTACT 60.072 42.308 0.00 0.00 0.00 2.57
3925 10593 7.309177 CCAGATCGTCATAATTACCTCTACTG 58.691 42.308 0.00 0.00 0.00 2.74
3926 10594 7.309177 CAGATCGTCATAATTACCTCTACTGG 58.691 42.308 0.00 0.00 0.00 4.00
4043 10733 3.577667 GTGCATGCATGAAAACTGCTTA 58.422 40.909 30.64 0.00 40.34 3.09
4044 10734 4.178540 GTGCATGCATGAAAACTGCTTAT 58.821 39.130 30.64 0.00 40.34 1.73
4045 10735 5.342433 GTGCATGCATGAAAACTGCTTATA 58.658 37.500 30.64 0.00 40.34 0.98
4046 10736 5.457799 GTGCATGCATGAAAACTGCTTATAG 59.542 40.000 30.64 0.00 40.34 1.31
4047 10737 5.125900 TGCATGCATGAAAACTGCTTATAGT 59.874 36.000 30.64 0.00 40.34 2.12
4048 10738 5.684626 GCATGCATGAAAACTGCTTATAGTC 59.315 40.000 30.64 2.07 40.34 2.59
4049 10739 5.818136 TGCATGAAAACTGCTTATAGTCC 57.182 39.130 0.00 0.00 40.34 3.85
4050 10740 5.500234 TGCATGAAAACTGCTTATAGTCCT 58.500 37.500 0.00 0.00 40.34 3.85
4051 10741 5.945784 TGCATGAAAACTGCTTATAGTCCTT 59.054 36.000 0.00 0.00 40.34 3.36
4052 10742 6.434028 TGCATGAAAACTGCTTATAGTCCTTT 59.566 34.615 0.00 0.00 40.34 3.11
4053 10743 7.039784 TGCATGAAAACTGCTTATAGTCCTTTT 60.040 33.333 0.00 0.00 40.34 2.27
4054 10744 7.814587 GCATGAAAACTGCTTATAGTCCTTTTT 59.185 33.333 0.00 0.00 36.68 1.94
4055 10745 9.346725 CATGAAAACTGCTTATAGTCCTTTTTC 57.653 33.333 0.00 0.00 30.19 2.29
4056 10746 7.882179 TGAAAACTGCTTATAGTCCTTTTTCC 58.118 34.615 0.00 0.00 29.19 3.13
4057 10747 7.724061 TGAAAACTGCTTATAGTCCTTTTTCCT 59.276 33.333 0.00 0.00 29.19 3.36
4058 10748 9.227777 GAAAACTGCTTATAGTCCTTTTTCCTA 57.772 33.333 0.00 0.00 0.00 2.94
4059 10749 9.582648 AAAACTGCTTATAGTCCTTTTTCCTAA 57.417 29.630 0.00 0.00 0.00 2.69
4060 10750 9.582648 AAACTGCTTATAGTCCTTTTTCCTAAA 57.417 29.630 0.00 0.00 0.00 1.85
4061 10751 9.582648 AACTGCTTATAGTCCTTTTTCCTAAAA 57.417 29.630 0.00 0.00 0.00 1.52
4062 10752 9.582648 ACTGCTTATAGTCCTTTTTCCTAAAAA 57.417 29.630 0.00 0.00 37.99 1.94
4102 10792 8.511604 TTTCCAATCTATTCATCAGAACTTCC 57.488 34.615 0.00 0.00 36.39 3.46
4103 10793 6.283694 TCCAATCTATTCATCAGAACTTCCG 58.716 40.000 0.00 0.00 36.39 4.30
4104 10794 6.098266 TCCAATCTATTCATCAGAACTTCCGA 59.902 38.462 0.00 0.00 36.39 4.55
4105 10795 6.933521 CCAATCTATTCATCAGAACTTCCGAT 59.066 38.462 0.00 0.00 36.39 4.18
4106 10796 7.117523 CCAATCTATTCATCAGAACTTCCGATC 59.882 40.741 0.00 0.00 36.39 3.69
4107 10797 6.968263 TCTATTCATCAGAACTTCCGATCT 57.032 37.500 0.00 0.00 36.39 2.75
4108 10798 8.642935 ATCTATTCATCAGAACTTCCGATCTA 57.357 34.615 0.00 0.00 36.39 1.98
4109 10799 8.642935 TCTATTCATCAGAACTTCCGATCTAT 57.357 34.615 0.00 0.00 36.39 1.98
4110 10800 9.083422 TCTATTCATCAGAACTTCCGATCTATT 57.917 33.333 0.00 0.00 36.39 1.73
4111 10801 9.352784 CTATTCATCAGAACTTCCGATCTATTC 57.647 37.037 0.00 0.00 36.39 1.75
4112 10802 6.865726 ATTCATCAGAACTTCCGATCTATTCG 59.134 38.462 0.00 0.00 41.15 3.34
4113 10803 5.299531 TCATCAGAACTTCCGATCTATTCGT 59.700 40.000 0.00 0.00 46.65 3.85
4114 10804 4.921547 TCAGAACTTCCGATCTATTCGTG 58.078 43.478 0.00 0.00 46.65 4.35
4126 10816 4.280436 TCTATTCGTGTTCAACCATGGT 57.720 40.909 13.00 13.00 0.00 3.55
4156 10846 6.591313 ACGAACGCCAAAAATAACAAAAAT 57.409 29.167 0.00 0.00 0.00 1.82
4159 10849 8.766151 ACGAACGCCAAAAATAACAAAAATTAT 58.234 25.926 0.00 0.00 0.00 1.28
4181 10871 4.964241 AGATCCCCGCCTAGCCCC 62.964 72.222 0.00 0.00 0.00 5.80
4251 10958 9.309516 TGTCGGTCTATTGAAAATTATAGTCAC 57.690 33.333 0.00 0.00 0.00 3.67
4355 11611 5.601583 AAATCAAGCATGCCACATGATTA 57.398 34.783 25.78 6.10 39.19 1.75
5037 12303 0.395311 AGATCGCGGTGGGAACTCTA 60.395 55.000 6.13 0.00 0.00 2.43
5151 12417 3.626924 GTGTGGTCGTGGGGAGCT 61.627 66.667 0.00 0.00 43.60 4.09
5163 12429 1.460305 GGGAGCTCTGGGATGGCTA 60.460 63.158 14.64 0.00 36.37 3.93
5367 12633 1.952621 TCCTTCCGGAGACCAAGAAT 58.047 50.000 3.34 0.00 33.30 2.40
5427 12693 3.726557 TGGTTCTGGAGCAGATTCATT 57.273 42.857 0.00 0.00 40.39 2.57
5443 12709 2.632544 ATTGGAGACGCCGACGACA 61.633 57.895 0.00 0.00 43.93 4.35
5445 12711 2.149803 TTGGAGACGCCGACGACATT 62.150 55.000 0.00 0.00 43.93 2.71
5463 12729 1.588674 TTCACACCGGTGTCAATGTC 58.411 50.000 36.92 0.00 45.45 3.06
5479 12745 6.109359 GTCAATGTCTTAGCATCAACCTAGT 58.891 40.000 0.00 0.00 0.00 2.57
5546 12813 7.456684 TTTGTTGATTAATTTGGTGTGAACG 57.543 32.000 0.00 0.00 0.00 3.95
5550 12817 6.862711 TGATTAATTTGGTGTGAACGTACA 57.137 33.333 0.00 0.00 0.00 2.90
5611 12878 3.431207 GGGGTGCGTGAAAGTTAGCTATA 60.431 47.826 0.00 0.00 0.00 1.31
5617 12884 5.030295 GCGTGAAAGTTAGCTATACACGTA 58.970 41.667 24.34 0.00 42.01 3.57
5644 12911 5.413833 AGTGCCAGAACTATGAGTTGATTTG 59.586 40.000 0.00 0.00 38.80 2.32
5730 12998 2.148916 GTGTGATCACAACACGAGGA 57.851 50.000 29.42 1.05 43.77 3.71
5772 13040 1.607467 GCTCATGGCCACTGGGTTT 60.607 57.895 8.16 0.00 36.17 3.27
5786 13054 3.199946 ACTGGGTTTTGACTTCTGACAGA 59.800 43.478 0.00 0.00 0.00 3.41
5792 13060 6.405842 GGGTTTTGACTTCTGACAGATGTTTT 60.406 38.462 21.21 3.15 33.42 2.43
5925 13193 2.356069 GGATCCGTGAATCCAAAGCTTC 59.644 50.000 0.00 0.00 44.04 3.86
6022 13290 6.601332 AGTTCAACAAAAGGTAGATCCAGAA 58.399 36.000 0.00 0.00 39.02 3.02
6047 13315 7.542534 AAATGAAAATAAGTACGATACGCCA 57.457 32.000 0.00 0.00 0.00 5.69
6050 13318 2.719426 ATAAGTACGATACGCCAGGC 57.281 50.000 0.00 0.00 0.00 4.85
6193 13462 6.927416 TGATAGCTTGCAAAATTTCATCACT 58.073 32.000 0.00 0.00 0.00 3.41
6215 13484 9.547753 TCACTAGATAACATTTTAGGAGAATGC 57.452 33.333 0.00 0.00 37.89 3.56
6253 13522 9.549509 CAAAATCAATGCTCCAAAATGTTATTG 57.450 29.630 0.00 0.00 0.00 1.90
6267 13536 9.855361 CAAAATGTTATTGTCAAACGCATTTTA 57.145 25.926 22.43 0.00 40.67 1.52
6279 13548 6.644181 TCAAACGCATTTTAAAGCATTGATCA 59.356 30.769 10.84 0.00 33.84 2.92
6296 13565 5.273674 TGATCATGTTTTTCTTTGCCACA 57.726 34.783 0.00 0.00 0.00 4.17
6302 13571 5.596836 TGTTTTTCTTTGCCACATCTTCT 57.403 34.783 0.00 0.00 0.00 2.85
6369 13639 9.824534 AAATTTGTCAATGTTTCACAAAAGAAC 57.175 25.926 2.80 0.00 41.93 3.01
6373 13643 6.099341 GTCAATGTTTCACAAAAGAACCAGT 58.901 36.000 0.00 0.00 0.00 4.00
6445 13718 3.742433 ATGAGCTCGGGATTAGAACAG 57.258 47.619 9.64 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 1.098869 TTCTTTGACGTGCAAGGCAA 58.901 45.000 17.48 17.48 41.47 4.52
89 92 1.410083 GGCCTGCCACCAATTGATAGA 60.410 52.381 7.12 0.00 35.81 1.98
193 197 1.066114 GCGAGATGTCTATACGCGGC 61.066 60.000 12.47 0.00 39.90 6.53
239 243 1.555533 CTGGTAACCAACTCCCTCTCC 59.444 57.143 0.00 0.00 30.80 3.71
272 278 4.638421 CCGATCTGCAACCCTATTTTGTTA 59.362 41.667 0.00 0.00 0.00 2.41
354 360 4.307432 AGACACAAGTTTCTCCATACACG 58.693 43.478 0.00 0.00 0.00 4.49
374 380 9.958180 TTCCATGATAAGTTAACAATTGAGAGA 57.042 29.630 13.59 0.00 0.00 3.10
420 437 7.358517 GCGCGTTAGGTGATTTTTATTTTTCAA 60.359 33.333 8.43 0.00 0.00 2.69
479 496 7.771826 GTGATGGGTACTTTAATTAAGCTGGTA 59.228 37.037 0.00 0.00 37.37 3.25
482 499 6.238374 CGGTGATGGGTACTTTAATTAAGCTG 60.238 42.308 0.00 0.00 37.37 4.24
541 561 6.892691 CGCAAGTCAAGAAAAAGTCTAGATT 58.107 36.000 0.00 0.00 34.56 2.40
632 661 4.214332 CGGAATAAGCTAAATGAAGCCCTC 59.786 45.833 0.00 0.00 43.86 4.30
860 1024 4.682859 GCTCAGTCTGCTTATTCCACAGAT 60.683 45.833 0.00 0.00 42.08 2.90
918 2911 8.718158 TTCCCAATGTTGAATATATAATGCCA 57.282 30.769 0.00 0.00 0.00 4.92
1703 3797 1.960689 ACAACCTACCCATGCAAACAC 59.039 47.619 0.00 0.00 0.00 3.32
2403 6358 3.192001 ACAAGCACAAGCAATATGTCCAG 59.808 43.478 0.00 0.00 45.49 3.86
2413 6368 1.726865 CACCGAACAAGCACAAGCA 59.273 52.632 0.00 0.00 45.49 3.91
2414 6369 1.658409 GCACCGAACAAGCACAAGC 60.658 57.895 0.00 0.00 42.56 4.01
2415 6370 1.369209 CGCACCGAACAAGCACAAG 60.369 57.895 0.00 0.00 0.00 3.16
2416 6371 2.712539 CGCACCGAACAAGCACAA 59.287 55.556 0.00 0.00 0.00 3.33
2417 6372 3.947841 GCGCACCGAACAAGCACA 61.948 61.111 0.30 0.00 0.00 4.57
2418 6373 4.683334 GGCGCACCGAACAAGCAC 62.683 66.667 10.83 0.00 0.00 4.40
2432 6387 2.742372 CCCCGAACAAGTGAGGCG 60.742 66.667 0.00 0.00 0.00 5.52
2729 6684 7.064253 GCCTACATATACCAATTGATACCGTTC 59.936 40.741 7.12 0.00 0.00 3.95
2883 9464 2.582052 CCAGGAGTGGCAGTTTTGTAA 58.418 47.619 0.00 0.00 36.89 2.41
2960 9541 1.151760 TGATAATCCTGGCTGGGCAT 58.848 50.000 10.79 1.68 36.20 4.40
2965 9546 4.219944 CCCAATGATTGATAATCCTGGCTG 59.780 45.833 6.76 0.00 38.02 4.85
3038 9623 8.958119 TTGACATGTCCCTTATAGATTTACAC 57.042 34.615 22.85 0.00 0.00 2.90
3049 9634 6.070881 CCCAATGAAATTTGACATGTCCCTTA 60.071 38.462 22.85 1.07 31.22 2.69
3254 9849 1.905894 TCGATTCCTCCATGGTGTGAA 59.094 47.619 12.58 14.46 37.07 3.18
3275 9870 1.001746 TGTACCGCGGTATGGTTGAAA 59.998 47.619 38.22 14.68 40.96 2.69
3345 9945 7.907214 TTGTTCCTCTAAAAGTTAGCAGATC 57.093 36.000 0.00 0.00 0.00 2.75
3391 9995 1.068434 GGTCATCTAGCTGCAGAGGTC 59.932 57.143 20.43 0.00 0.00 3.85
3393 9997 1.117994 TGGTCATCTAGCTGCAGAGG 58.882 55.000 20.43 6.28 0.00 3.69
3397 10001 1.345741 GCCTATGGTCATCTAGCTGCA 59.654 52.381 1.02 0.00 0.00 4.41
3453 10063 8.339344 TGTTCAATCAGATTCTTCAAATGCTA 57.661 30.769 0.00 0.00 0.00 3.49
3485 10095 1.913951 ATCCAGCATTCGGACTGCCA 61.914 55.000 15.65 2.30 40.56 4.92
3510 10120 3.012518 GCTATTATGCAGGGTATGGCAG 58.987 50.000 0.00 0.00 44.24 4.85
3552 10162 9.920946 ATAGGTACATTTTCCACTGTAATGATT 57.079 29.630 7.75 0.00 34.28 2.57
3582 10192 5.782047 AGAACGGATCAATGATTTTTGCAA 58.218 33.333 0.00 0.00 0.00 4.08
3609 10219 2.924922 GATTGGCATGGTGCTTCGCG 62.925 60.000 0.00 0.00 44.28 5.87
3673 10283 1.302949 GCCTATGGACTGGGTTGCA 59.697 57.895 0.00 0.00 0.00 4.08
3738 10348 1.471287 CGTTGTATGAGGACAGTCGGA 59.529 52.381 0.00 0.00 0.00 4.55
3921 10589 1.481871 GTAGTGCAGCTACCCCAGTA 58.518 55.000 12.68 0.00 43.20 2.74
3922 10590 2.287829 GTAGTGCAGCTACCCCAGT 58.712 57.895 12.68 0.00 43.20 4.00
4076 10766 9.129532 GGAAGTTCTGATGAATAGATTGGAAAT 57.870 33.333 2.25 0.00 34.40 2.17
4077 10767 7.280876 CGGAAGTTCTGATGAATAGATTGGAAA 59.719 37.037 5.73 0.00 34.40 3.13
4078 10768 6.763135 CGGAAGTTCTGATGAATAGATTGGAA 59.237 38.462 5.73 0.00 34.40 3.53
4079 10769 6.098266 TCGGAAGTTCTGATGAATAGATTGGA 59.902 38.462 10.47 0.00 34.40 3.53
4082 10772 7.961351 AGATCGGAAGTTCTGATGAATAGATT 58.039 34.615 28.09 5.25 42.24 2.40
4103 10793 4.876107 ACCATGGTTGAACACGAATAGATC 59.124 41.667 13.00 0.00 0.00 2.75
4104 10794 4.843728 ACCATGGTTGAACACGAATAGAT 58.156 39.130 13.00 0.00 0.00 1.98
4105 10795 4.280436 ACCATGGTTGAACACGAATAGA 57.720 40.909 13.00 0.00 0.00 1.98
4106 10796 6.677781 AATACCATGGTTGAACACGAATAG 57.322 37.500 25.38 0.00 0.00 1.73
4107 10797 7.104290 TGTAATACCATGGTTGAACACGAATA 58.896 34.615 25.38 0.00 0.00 1.75
4108 10798 5.941058 TGTAATACCATGGTTGAACACGAAT 59.059 36.000 25.38 3.66 0.00 3.34
4109 10799 5.306394 TGTAATACCATGGTTGAACACGAA 58.694 37.500 25.38 0.81 0.00 3.85
4110 10800 4.895961 TGTAATACCATGGTTGAACACGA 58.104 39.130 25.38 1.68 0.00 4.35
4111 10801 5.387279 GTTGTAATACCATGGTTGAACACG 58.613 41.667 25.38 0.00 0.00 4.49
4112 10802 5.179742 TCGTTGTAATACCATGGTTGAACAC 59.820 40.000 25.38 14.20 0.00 3.32
4113 10803 5.306394 TCGTTGTAATACCATGGTTGAACA 58.694 37.500 25.38 20.31 0.00 3.18
4114 10804 5.866335 TCGTTGTAATACCATGGTTGAAC 57.134 39.130 25.38 18.00 0.00 3.18
4126 10816 7.358066 TGTTATTTTTGGCGTTCGTTGTAATA 58.642 30.769 0.00 0.00 0.00 0.98
4156 10846 2.642171 AGGCGGGGATCTGGATATAA 57.358 50.000 0.00 0.00 0.00 0.98
4159 10849 0.614979 GCTAGGCGGGGATCTGGATA 60.615 60.000 0.00 0.00 0.00 2.59
4181 10871 5.699915 CCAATAACATGATCTACAGCTCCAG 59.300 44.000 0.00 0.00 0.00 3.86
4251 10958 9.605955 TCACTCAATGTTTTTACAATAATGTCG 57.394 29.630 0.00 0.00 41.05 4.35
4323 11533 9.531942 TGTGGCATGCTTGATTTATTTTATAAG 57.468 29.630 18.92 0.00 0.00 1.73
4355 11611 8.994429 TGCGTACCAAAATAATCATTCAATTT 57.006 26.923 0.00 0.00 0.00 1.82
5037 12303 2.125673 CCGAACCTCACCGCGATT 60.126 61.111 8.23 0.00 0.00 3.34
5163 12429 0.820871 GGAAGATCTCACTCGGCACT 59.179 55.000 0.00 0.00 0.00 4.40
5211 12477 3.584834 CATGTTCACCGACACAGTGATA 58.415 45.455 7.81 0.00 43.46 2.15
5367 12633 1.638679 CCATCTCCTCCATGGGCACA 61.639 60.000 13.02 0.00 37.71 4.57
5421 12687 0.806102 CGTCGGCGTCTCCAATGAAT 60.806 55.000 6.85 0.00 34.01 2.57
5427 12693 2.537792 GAATGTCGTCGGCGTCTCCA 62.538 60.000 10.18 2.60 39.49 3.86
5443 12709 2.151202 GACATTGACACCGGTGTGAAT 58.849 47.619 43.34 39.79 45.76 2.57
5445 12711 0.756294 AGACATTGACACCGGTGTGA 59.244 50.000 43.34 34.03 45.76 3.58
5546 12813 4.094739 TGCAGTGATGCATATTGTGTGTAC 59.905 41.667 0.00 0.00 40.23 2.90
5550 12817 2.686405 CCTGCAGTGATGCATATTGTGT 59.314 45.455 13.81 0.00 44.47 3.72
5611 12878 0.249741 GTTCTGGCACTGGTACGTGT 60.250 55.000 0.00 0.00 35.84 4.49
5617 12884 2.260822 ACTCATAGTTCTGGCACTGGT 58.739 47.619 0.00 0.00 0.00 4.00
5644 12911 7.100409 ACTAGAGCTGAAACCTTTAAGATCAC 58.900 38.462 0.00 0.00 36.68 3.06
5653 12921 8.776061 ATAAGATAGACTAGAGCTGAAACCTT 57.224 34.615 0.00 0.00 0.00 3.50
5654 12922 8.776061 AATAAGATAGACTAGAGCTGAAACCT 57.224 34.615 0.00 0.00 0.00 3.50
5730 12998 5.356190 CACATGACTTATGAAGCATTGTCCT 59.644 40.000 0.00 0.00 39.21 3.85
5772 13040 5.116180 ACGAAAACATCTGTCAGAAGTCAA 58.884 37.500 10.97 0.00 0.00 3.18
5786 13054 4.142556 ACGAACTTCAACCAACGAAAACAT 60.143 37.500 0.00 0.00 0.00 2.71
5792 13060 3.979948 TGATACGAACTTCAACCAACGA 58.020 40.909 0.00 0.00 0.00 3.85
5925 13193 1.076533 ACCGTGTTTATCTGCTCGCG 61.077 55.000 0.00 0.00 0.00 5.87
6022 13290 7.976826 TGGCGTATCGTACTTATTTTCATTTT 58.023 30.769 0.00 0.00 0.00 1.82
6050 13318 2.456119 GGATCAGAACAGCCGCGTG 61.456 63.158 4.92 0.00 0.00 5.34
6193 13462 6.426937 GCCGCATTCTCCTAAAATGTTATCTA 59.573 38.462 0.00 0.00 36.65 1.98
6234 13503 7.095691 CGTTTGACAATAACATTTTGGAGCATT 60.096 33.333 0.00 0.00 0.00 3.56
6253 13522 6.209129 TCAATGCTTTAAAATGCGTTTGAC 57.791 33.333 4.29 0.00 36.51 3.18
6267 13536 7.357303 GCAAAGAAAAACATGATCAATGCTTT 58.643 30.769 0.00 0.54 40.22 3.51
6279 13548 6.165700 AGAAGATGTGGCAAAGAAAAACAT 57.834 33.333 0.00 0.00 34.28 2.71


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

AutoCloner maintained by Alex Coulton.