Multiple sequence alignment - TraesCS6D01G395900

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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 TraesCS6D01G395900 chr6D 100.000 6367 0 0 1 6367 468186230 468179864 0.000000e+00 11758.0
1 TraesCS6D01G395900 chr6D 86.364 1254 157 11 107 1352 468100977 468099730 0.000000e+00 1356.0
2 TraesCS6D01G395900 chr6D 86.802 1038 136 1 4233 5269 468096641 468095604 0.000000e+00 1157.0
3 TraesCS6D01G395900 chr6D 85.095 1107 155 7 4193 5293 468168798 468167696 0.000000e+00 1122.0
4 TraesCS6D01G395900 chr6D 85.479 1033 149 1 4193 5224 468057329 468056297 0.000000e+00 1075.0
5 TraesCS6D01G395900 chr6D 84.040 990 104 28 1 969 468172544 468171588 0.000000e+00 904.0
6 TraesCS6D01G395900 chr6D 86.010 386 52 2 968 1353 468171427 468171044 4.590000e-111 412.0
7 TraesCS6D01G395900 chr6D 76.766 736 139 11 2013 2717 468152767 468152033 3.600000e-102 383.0
8 TraesCS6D01G395900 chr6D 81.450 469 61 12 940 1396 468060915 468060461 1.690000e-95 361.0
9 TraesCS6D01G395900 chr6D 93.074 231 16 0 3246 3476 26007083 26006853 7.910000e-89 339.0
10 TraesCS6D01G395900 chr6D 82.840 338 40 14 6039 6365 452702800 452703130 2.900000e-73 287.0
11 TraesCS6D01G395900 chr6D 82.687 335 43 12 6039 6365 332618602 332618929 3.760000e-72 283.0
12 TraesCS6D01G395900 chrUn 96.260 4305 108 23 1042 5329 211919524 211923792 0.000000e+00 7009.0
13 TraesCS6D01G395900 chrUn 96.553 3191 82 9 1874 5048 210239719 210236541 0.000000e+00 5258.0
14 TraesCS6D01G395900 chrUn 96.326 1116 26 4 764 1879 75283431 75284531 0.000000e+00 1820.0
15 TraesCS6D01G395900 chrUn 96.237 1116 27 4 764 1879 327314417 327313317 0.000000e+00 1814.0
16 TraesCS6D01G395900 chrUn 84.482 1379 154 30 1 1353 210220617 210219273 0.000000e+00 1306.0
17 TraesCS6D01G395900 chrUn 85.866 1033 142 3 4193 5224 346081747 346080718 0.000000e+00 1096.0
18 TraesCS6D01G395900 chrUn 96.928 586 14 3 5370 5951 210225648 210225063 0.000000e+00 979.0
19 TraesCS6D01G395900 chrUn 93.972 647 36 2 1 645 75282751 75283396 0.000000e+00 976.0
20 TraesCS6D01G395900 chrUn 93.972 647 36 2 1 645 327315097 327314452 0.000000e+00 976.0
21 TraesCS6D01G395900 chrUn 96.569 583 19 1 5370 5951 211923777 211924359 0.000000e+00 965.0
22 TraesCS6D01G395900 chrUn 98.091 419 8 0 5949 6367 211924482 211924900 0.000000e+00 730.0
23 TraesCS6D01G395900 chrUn 97.375 419 11 0 5949 6367 210224940 210224522 0.000000e+00 713.0
24 TraesCS6D01G395900 chrUn 95.985 274 9 1 574 845 211919251 211919524 1.630000e-120 444.0
25 TraesCS6D01G395900 chrUn 76.902 736 138 11 2013 2717 216381443 216382177 7.740000e-104 388.0
26 TraesCS6D01G395900 chrUn 97.906 191 4 0 655 845 479932506 479932316 1.320000e-86 331.0
27 TraesCS6D01G395900 chrUn 89.496 238 18 3 5642 5872 79237857 79237620 1.740000e-75 294.0
28 TraesCS6D01G395900 chrUn 93.333 75 5 0 5877 5951 45780349 45780423 1.880000e-20 111.0
29 TraesCS6D01G395900 chrUn 97.297 37 1 0 668 704 75283397 75283433 5.330000e-06 63.9
30 TraesCS6D01G395900 chr6B 96.240 4308 108 24 1042 5332 714410552 714406282 0.000000e+00 7009.0
31 TraesCS6D01G395900 chr6B 85.069 1085 155 7 4214 5293 714340738 714339656 0.000000e+00 1099.0
32 TraesCS6D01G395900 chr6B 84.003 1169 128 33 1 1146 714344027 714342895 0.000000e+00 1068.0
33 TraesCS6D01G395900 chr6B 96.741 583 18 1 5370 5951 714406300 714405718 0.000000e+00 970.0
34 TraesCS6D01G395900 chr6B 98.329 419 7 0 5949 6367 714405595 714405177 0.000000e+00 736.0
35 TraesCS6D01G395900 chr6B 95.620 274 10 1 574 845 714410825 714410552 7.580000e-119 438.0
36 TraesCS6D01G395900 chr6B 76.255 737 141 13 2013 2717 714336222 714335488 1.690000e-95 361.0
37 TraesCS6D01G395900 chr6B 92.083 240 18 1 3238 3476 279333154 279332915 2.840000e-88 337.0
38 TraesCS6D01G395900 chr6B 81.319 91 8 5 3171 3254 638497976 638497888 1.480000e-06 65.8
39 TraesCS6D01G395900 chr6A 90.983 1109 87 10 252 1352 614166575 614165472 0.000000e+00 1482.0
40 TraesCS6D01G395900 chr6A 86.239 1061 138 7 4213 5269 614162850 614161794 0.000000e+00 1144.0
41 TraesCS6D01G395900 chr6A 95.885 243 7 3 4 246 614167480 614167241 2.150000e-104 390.0
42 TraesCS6D01G395900 chr6A 88.519 270 28 3 3247 3516 572214939 572214673 2.210000e-84 324.0
43 TraesCS6D01G395900 chr6A 86.747 83 7 2 3171 3249 610122252 610122334 8.790000e-14 89.8
44 TraesCS6D01G395900 chr6A 83.146 89 10 3 3171 3254 59961231 59961319 6.850000e-10 76.8
45 TraesCS6D01G395900 chr6A 84.000 75 8 2 3171 3241 202356906 202356980 1.150000e-07 69.4
46 TraesCS6D01G395900 chr3B 89.329 328 33 2 6035 6360 2047097 2047424 1.650000e-110 411.0
47 TraesCS6D01G395900 chr3B 90.948 232 15 2 5647 5872 803061108 803061339 2.230000e-79 307.0
48 TraesCS6D01G395900 chr3B 89.030 237 20 6 5642 5872 345709825 345710061 8.080000e-74 289.0
49 TraesCS6D01G395900 chr3B 76.074 326 51 21 5996 6311 250404072 250404380 1.850000e-30 145.0
50 TraesCS6D01G395900 chr3B 84.416 77 4 4 3171 3241 799710342 799710416 1.150000e-07 69.4
51 TraesCS6D01G395900 chr4A 88.720 328 31 5 6039 6365 604355900 604356222 4.630000e-106 396.0
52 TraesCS6D01G395900 chr4A 88.720 328 31 5 6039 6365 604559859 604560181 4.630000e-106 396.0
53 TraesCS6D01G395900 chr4A 87.111 225 21 5 1596 1819 642598356 642598573 1.370000e-61 248.0
54 TraesCS6D01G395900 chr4A 93.333 75 5 0 5877 5951 537419651 537419577 1.880000e-20 111.0
55 TraesCS6D01G395900 chr4A 86.885 61 2 5 6004 6064 672315049 672315103 5.330000e-06 63.9
56 TraesCS6D01G395900 chr5D 93.506 231 15 0 3246 3476 383710555 383710785 1.700000e-90 344.0
57 TraesCS6D01G395900 chr5D 74.510 357 38 41 6004 6339 91996333 91996657 8.730000e-19 106.0
58 TraesCS6D01G395900 chr5D 85.366 82 11 1 3628 3709 453016396 453016476 4.090000e-12 84.2
59 TraesCS6D01G395900 chr2D 93.074 231 16 0 3246 3476 83172475 83172245 7.910000e-89 339.0
60 TraesCS6D01G395900 chr2D 93.074 231 16 0 3246 3476 389895463 389895233 7.910000e-89 339.0
61 TraesCS6D01G395900 chr2D 90.278 72 7 0 1735 1806 534412682 534412753 1.890000e-15 95.3
62 TraesCS6D01G395900 chr1D 89.744 234 18 2 5645 5872 233088288 233088055 1.740000e-75 294.0
63 TraesCS6D01G395900 chr4D 83.234 334 39 13 6041 6365 433946951 433946626 2.250000e-74 291.0
64 TraesCS6D01G395900 chr5B 89.316 234 17 3 5645 5872 594138699 594138930 2.900000e-73 287.0
65 TraesCS6D01G395900 chr5B 88.136 59 1 5 3489 3542 81210700 81210643 1.480000e-06 65.8
66 TraesCS6D01G395900 chr1A 88.608 237 21 2 5642 5872 425262641 425262405 3.760000e-72 283.0
67 TraesCS6D01G395900 chr4B 76.645 304 38 28 5988 6275 550625096 550625382 3.100000e-28 137.0
68 TraesCS6D01G395900 chr4B 74.923 323 61 17 6002 6315 507670501 507670190 5.180000e-26 130.0
69 TraesCS6D01G395900 chr3A 93.333 75 5 0 5877 5951 725052091 725052165 1.880000e-20 111.0
70 TraesCS6D01G395900 chr3A 92.000 75 6 0 5877 5951 351788075 351788149 8.730000e-19 106.0
71 TraesCS6D01G395900 chr3A 87.931 58 2 4 3489 3543 697758539 697758594 5.330000e-06 63.9
72 TraesCS6D01G395900 chr1B 93.243 74 5 0 5877 5950 603335074 603335001 6.750000e-20 110.0
73 TraesCS6D01G395900 chr1B 73.333 300 71 8 2422 2717 2356976 2356682 1.130000e-17 102.0
74 TraesCS6D01G395900 chr1B 73.038 293 66 10 2429 2717 22824279 22823996 2.440000e-14 91.6
75 TraesCS6D01G395900 chr7D 94.203 69 4 0 5877 5945 275969708 275969776 8.730000e-19 106.0
76 TraesCS6D01G395900 chr7D 88.571 70 7 1 3186 3254 210558409 210558340 4.090000e-12 84.2
77 TraesCS6D01G395900 chr7D 88.571 70 7 1 3186 3254 489164201 489164132 4.090000e-12 84.2
78 TraesCS6D01G395900 chr7B 88.571 70 7 1 3186 3254 226198924 226198855 4.090000e-12 84.2
79 TraesCS6D01G395900 chr7A 85.542 83 8 2 3171 3249 80986613 80986695 4.090000e-12 84.2
80 TraesCS6D01G395900 chr5A 77.953 127 20 5 2860 2982 625737573 625737451 8.850000e-09 73.1


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 TraesCS6D01G395900 chr6D 468179864 468186230 6366 True 11758.000000 11758 100.000000 1 6367 1 chr6D.!!$R3 6366
1 TraesCS6D01G395900 chr6D 468095604 468100977 5373 True 1256.500000 1356 86.583000 107 5269 2 chr6D.!!$R5 5162
2 TraesCS6D01G395900 chr6D 468167696 468172544 4848 True 812.666667 1122 85.048333 1 5293 3 chr6D.!!$R6 5292
3 TraesCS6D01G395900 chr6D 468056297 468060915 4618 True 718.000000 1075 83.464500 940 5224 2 chr6D.!!$R4 4284
4 TraesCS6D01G395900 chr6D 468152033 468152767 734 True 383.000000 383 76.766000 2013 2717 1 chr6D.!!$R2 704
5 TraesCS6D01G395900 chrUn 210236541 210239719 3178 True 5258.000000 5258 96.553000 1874 5048 1 chrUn.!!$R2 3174
6 TraesCS6D01G395900 chrUn 211919251 211924900 5649 False 2287.000000 7009 96.726250 574 6367 4 chrUn.!!$F4 5793
7 TraesCS6D01G395900 chrUn 327313317 327315097 1780 True 1395.000000 1814 95.104500 1 1879 2 chrUn.!!$R6 1878
8 TraesCS6D01G395900 chrUn 346080718 346081747 1029 True 1096.000000 1096 85.866000 4193 5224 1 chrUn.!!$R3 1031
9 TraesCS6D01G395900 chrUn 210219273 210225648 6375 True 999.333333 1306 92.928333 1 6367 3 chrUn.!!$R5 6366
10 TraesCS6D01G395900 chrUn 75282751 75284531 1780 False 953.300000 1820 95.865000 1 1879 3 chrUn.!!$F3 1878
11 TraesCS6D01G395900 chrUn 216381443 216382177 734 False 388.000000 388 76.902000 2013 2717 1 chrUn.!!$F2 704
12 TraesCS6D01G395900 chr6B 714405177 714410825 5648 True 2288.250000 7009 96.732500 574 6367 4 chr6B.!!$R4 5793
13 TraesCS6D01G395900 chr6B 714335488 714344027 8539 True 842.666667 1099 81.775667 1 5293 3 chr6B.!!$R3 5292
14 TraesCS6D01G395900 chr6A 614161794 614167480 5686 True 1005.333333 1482 91.035667 4 5269 3 chr6A.!!$R2 5265

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
508 6225 0.250858 TTATGATCATGGCCCGCCTG 60.251 55.000 18.72 3.3 36.94 4.85 F
1307 7538 0.036732 GGTCACCTGCAATGACTCCA 59.963 55.000 23.18 0.0 44.88 3.86 F
1743 8340 0.174389 CTGGCACGTCTCATGCTACT 59.826 55.000 0.00 0.0 42.93 2.57 F
2719 9453 0.256752 CTGATGGATGCCAAGGTGGA 59.743 55.000 0.00 0.0 40.96 4.02 F
2720 9454 0.256752 TGATGGATGCCAAGGTGGAG 59.743 55.000 0.00 0.0 40.96 3.86 F
3991 11646 1.608590 AGGCAACCATTGTTCAAGTCG 59.391 47.619 0.00 0.0 30.42 4.18 F
4713 12676 2.621070 AGGAACCTCTCAACTTAGGCA 58.379 47.619 0.00 0.0 36.24 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 8047 0.792640 CATGAGACGTGCCAGTTCAC 59.207 55.000 0.00 0.0 0.00 3.18 R
2609 9343 0.742281 CAGTAGCTGTTGCCGCTGAT 60.742 55.000 0.00 0.0 41.04 2.90 R
2782 9631 1.135774 TGCACTCGTCGATGTCTGTAC 60.136 52.381 4.21 0.0 0.00 2.90 R
3977 11632 2.009774 CTAGGCCGACTTGAACAATGG 58.990 52.381 0.00 0.0 0.00 3.16 R
4713 12676 2.016318 TGCAGCAATACTTAAGCGCAT 58.984 42.857 11.47 0.0 34.65 4.73 R
5334 13298 0.034670 GAGATGGTGGCTTCAGGCTT 60.035 55.000 1.64 0.0 41.69 4.35 R
5534 13498 2.230508 TGGAACCTCGTATCAGTGACAC 59.769 50.000 0.00 0.0 0.00 3.67 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
29 5061 2.904011 TTCGTTGTCAGCACGTTTTT 57.096 40.000 0.00 0.00 0.00 1.94
303 6014 6.662663 TCCATTGTATGAACACCAAATCATGA 59.337 34.615 0.00 0.00 36.93 3.07
314 6025 3.164268 CCAAATCATGAGGGACAAACCA 58.836 45.455 0.09 0.00 41.20 3.67
508 6225 0.250858 TTATGATCATGGCCCGCCTG 60.251 55.000 18.72 3.30 36.94 4.85
724 6509 6.827251 AGATGCATTTCTAAAGCAGAGAATCA 59.173 34.615 0.00 0.00 42.14 2.57
735 6520 3.521126 AGCAGAGAATCAGAGCCCTTTTA 59.479 43.478 0.00 0.00 37.82 1.52
736 6521 3.876320 GCAGAGAATCAGAGCCCTTTTAG 59.124 47.826 0.00 0.00 37.82 1.85
737 6522 4.383552 GCAGAGAATCAGAGCCCTTTTAGA 60.384 45.833 0.00 0.00 37.82 2.10
738 6523 5.738909 CAGAGAATCAGAGCCCTTTTAGAA 58.261 41.667 0.00 0.00 37.82 2.10
742 6527 6.413892 AGAATCAGAGCCCTTTTAGAAAGAG 58.586 40.000 2.15 0.00 0.00 2.85
746 6531 4.940654 CAGAGCCCTTTTAGAAAGAGAAGG 59.059 45.833 2.15 0.00 38.67 3.46
748 6533 2.420372 GCCCTTTTAGAAAGAGAAGGCG 59.580 50.000 2.15 0.00 37.83 5.52
749 6534 3.010420 CCCTTTTAGAAAGAGAAGGCGG 58.990 50.000 2.15 0.00 37.83 6.13
757 6542 1.909700 AAGAGAAGGCGGCAATTTCA 58.090 45.000 13.08 0.00 0.00 2.69
783 6627 1.873698 TGGTACGTGTTCCAGCTTTC 58.126 50.000 0.00 0.00 0.00 2.62
881 6923 9.478019 CTTCAAATAAACAAGCGTCTTATAGTG 57.522 33.333 0.00 0.00 0.00 2.74
956 6998 1.882623 GGGTATAGTAGAACCGTCGGG 59.117 57.143 17.28 0.00 36.57 5.14
1054 7258 4.238514 CAAGTTAGCTTACAAGAGAGCGT 58.761 43.478 5.55 0.00 43.53 5.07
1055 7259 3.839293 AGTTAGCTTACAAGAGAGCGTG 58.161 45.455 5.55 0.00 43.53 5.34
1120 7339 2.040178 CCGCTCCCAGTAATCCTACTT 58.960 52.381 0.00 0.00 36.14 2.24
1122 7341 2.959707 CGCTCCCAGTAATCCTACTTCT 59.040 50.000 0.00 0.00 36.14 2.85
1123 7342 3.004944 CGCTCCCAGTAATCCTACTTCTC 59.995 52.174 0.00 0.00 36.14 2.87
1124 7343 4.219919 GCTCCCAGTAATCCTACTTCTCT 58.780 47.826 0.00 0.00 36.14 3.10
1125 7344 4.651962 GCTCCCAGTAATCCTACTTCTCTT 59.348 45.833 0.00 0.00 36.14 2.85
1126 7345 5.129650 GCTCCCAGTAATCCTACTTCTCTTT 59.870 44.000 0.00 0.00 36.14 2.52
1127 7346 6.684362 GCTCCCAGTAATCCTACTTCTCTTTC 60.684 46.154 0.00 0.00 36.14 2.62
1128 7347 6.503944 TCCCAGTAATCCTACTTCTCTTTCT 58.496 40.000 0.00 0.00 36.14 2.52
1129 7348 6.608002 TCCCAGTAATCCTACTTCTCTTTCTC 59.392 42.308 0.00 0.00 36.14 2.87
1130 7349 6.609616 CCCAGTAATCCTACTTCTCTTTCTCT 59.390 42.308 0.00 0.00 36.14 3.10
1154 7385 3.782244 CAGCGGCGACTCACTTGC 61.782 66.667 12.98 0.00 0.00 4.01
1184 7415 1.130749 CTGCTGCTGCTGAACAAGATC 59.869 52.381 17.00 0.00 40.01 2.75
1307 7538 0.036732 GGTCACCTGCAATGACTCCA 59.963 55.000 23.18 0.00 44.88 3.86
1480 7711 6.368779 TGTATAGTTTGTTGGCTCTAAGGT 57.631 37.500 0.00 0.00 0.00 3.50
1640 7968 3.492137 GCATAACTAACCCACCTACCGAG 60.492 52.174 0.00 0.00 0.00 4.63
1719 8047 1.394917 CAAGAAAAGATGGCTCGACCG 59.605 52.381 0.00 0.00 43.94 4.79
1743 8340 0.174389 CTGGCACGTCTCATGCTACT 59.826 55.000 0.00 0.00 42.93 2.57
1856 8453 7.336396 ACTAAACAAACCATGGACTATACCTC 58.664 38.462 21.47 0.00 0.00 3.85
1987 8677 1.210478 CAGGAAGGGTGGTACCATCAG 59.790 57.143 26.35 8.66 41.02 2.90
2277 9009 0.321564 CTCACCTGCATTTCCGACCA 60.322 55.000 0.00 0.00 0.00 4.02
2528 9260 1.272648 CCAAGAGATTTCCAAGGGGCA 60.273 52.381 0.00 0.00 0.00 5.36
2609 9343 2.351244 CCTCCAGACTACGCCTGCA 61.351 63.158 0.00 0.00 0.00 4.41
2719 9453 0.256752 CTGATGGATGCCAAGGTGGA 59.743 55.000 0.00 0.00 40.96 4.02
2720 9454 0.256752 TGATGGATGCCAAGGTGGAG 59.743 55.000 0.00 0.00 40.96 3.86
2782 9631 9.594478 ACAAACTGTCTTTTAATTTTACCCTTG 57.406 29.630 0.00 0.00 0.00 3.61
3305 10284 3.490761 CGAGCCCAACTCAACAAATTTGT 60.491 43.478 18.13 18.13 46.63 2.83
3482 10461 8.233349 AGTAACATAGTCTAGGGATGATCCTA 57.767 38.462 11.87 1.33 38.30 2.94
3563 10556 9.907229 AGACTTTATTTATTAGCTTGTAGGCTT 57.093 29.630 0.00 0.00 42.97 4.35
3581 10574 4.592778 AGGCTTATTTTCTTTTGGGAAGCA 59.407 37.500 6.11 0.00 39.61 3.91
3584 10577 5.406477 GCTTATTTTCTTTTGGGAAGCACAG 59.594 40.000 0.00 0.00 38.14 3.66
3778 10808 3.629282 GGGTAGGTACTGTCTGGTGGTAT 60.629 52.174 0.00 0.00 41.52 2.73
3779 10809 4.386761 GGGTAGGTACTGTCTGGTGGTATA 60.387 50.000 0.00 0.00 41.52 1.47
3923 11578 3.875134 CCCCATGTTACCAATCGTTACTC 59.125 47.826 0.00 0.00 0.00 2.59
3977 11632 2.033492 GTGTGTGTTACGTGTAGGCAAC 60.033 50.000 0.00 0.00 0.00 4.17
3991 11646 1.608590 AGGCAACCATTGTTCAAGTCG 59.391 47.619 0.00 0.00 30.42 4.18
4144 12099 5.759963 CGGGTGTTCTGTATAGATCACTAC 58.240 45.833 22.43 16.77 46.07 2.73
4298 12260 6.239317 GGGGTATTTCTTTAATGGCAATCCTC 60.239 42.308 0.00 0.00 0.00 3.71
4499 12462 7.406916 TGGGCCTTCTTAATAATGAACAAGTA 58.593 34.615 4.53 0.00 0.00 2.24
4553 12516 7.596494 TCCTAGAGAATGAACAATTTGCAAAG 58.404 34.615 18.19 7.44 0.00 2.77
4713 12676 2.621070 AGGAACCTCTCAACTTAGGCA 58.379 47.619 0.00 0.00 36.24 4.75
4772 12735 5.330455 TGGTTTATCTGCACACAAAAACA 57.670 34.783 0.00 0.00 30.36 2.83
5320 13284 9.923143 TCCGTCAAATAAGATATGTAACTATGG 57.077 33.333 0.00 0.00 0.00 2.74
5321 13285 9.923143 CCGTCAAATAAGATATGTAACTATGGA 57.077 33.333 0.00 0.00 0.00 3.41
5326 13290 9.686683 AAATAAGATATGTAACTATGGATGGGC 57.313 33.333 0.00 0.00 0.00 5.36
5327 13291 5.700402 AGATATGTAACTATGGATGGGCC 57.300 43.478 0.00 0.00 37.10 5.80
5337 13301 1.999648 TGGATGGGCCATCAATAAGC 58.000 50.000 39.34 24.87 43.33 3.09
5338 13302 1.260544 GGATGGGCCATCAATAAGCC 58.739 55.000 39.34 22.60 42.13 4.35
5339 13303 1.203100 GGATGGGCCATCAATAAGCCT 60.203 52.381 39.34 8.82 46.31 4.58
5340 13304 1.891150 GATGGGCCATCAATAAGCCTG 59.109 52.381 35.84 0.00 46.31 4.85
5341 13305 0.925558 TGGGCCATCAATAAGCCTGA 59.074 50.000 0.00 0.00 46.31 3.86
5342 13306 1.287442 TGGGCCATCAATAAGCCTGAA 59.713 47.619 0.00 0.00 46.31 3.02
5343 13307 1.959282 GGGCCATCAATAAGCCTGAAG 59.041 52.381 4.39 0.00 46.31 3.02
5344 13308 1.339291 GGCCATCAATAAGCCTGAAGC 59.661 52.381 0.00 0.00 43.62 3.86
5345 13309 1.339291 GCCATCAATAAGCCTGAAGCC 59.661 52.381 0.00 0.00 45.47 4.35
5346 13310 2.658285 CCATCAATAAGCCTGAAGCCA 58.342 47.619 0.00 0.00 45.47 4.75
5347 13311 2.360165 CCATCAATAAGCCTGAAGCCAC 59.640 50.000 0.00 0.00 45.47 5.01
5348 13312 2.128771 TCAATAAGCCTGAAGCCACC 57.871 50.000 0.00 0.00 45.47 4.61
5349 13313 1.354031 TCAATAAGCCTGAAGCCACCA 59.646 47.619 0.00 0.00 45.47 4.17
5350 13314 2.025037 TCAATAAGCCTGAAGCCACCAT 60.025 45.455 0.00 0.00 45.47 3.55
5351 13315 2.355010 ATAAGCCTGAAGCCACCATC 57.645 50.000 0.00 0.00 45.47 3.51
5352 13316 1.289160 TAAGCCTGAAGCCACCATCT 58.711 50.000 0.00 0.00 45.47 2.90
5353 13317 0.034670 AAGCCTGAAGCCACCATCTC 60.035 55.000 0.00 0.00 45.47 2.75
5354 13318 1.452833 GCCTGAAGCCACCATCTCC 60.453 63.158 0.00 0.00 34.35 3.71
5355 13319 1.153289 CCTGAAGCCACCATCTCCG 60.153 63.158 0.00 0.00 0.00 4.63
5356 13320 1.599047 CTGAAGCCACCATCTCCGT 59.401 57.895 0.00 0.00 0.00 4.69
5357 13321 0.036010 CTGAAGCCACCATCTCCGTT 60.036 55.000 0.00 0.00 0.00 4.44
5358 13322 0.400213 TGAAGCCACCATCTCCGTTT 59.600 50.000 0.00 0.00 0.00 3.60
5359 13323 1.087501 GAAGCCACCATCTCCGTTTC 58.912 55.000 0.00 0.00 0.00 2.78
5360 13324 0.693049 AAGCCACCATCTCCGTTTCT 59.307 50.000 0.00 0.00 0.00 2.52
5433 13397 7.502226 TGTGAACAAAATCTTCCACATAGAAGT 59.498 33.333 0.00 0.00 43.17 3.01
5581 13545 7.038017 ACTCTTATTCCTGAATCCTGAAGAACA 60.038 37.037 0.00 0.00 32.50 3.18
5687 13652 7.534085 CTTTATAAGCAACGATCCAGTTACA 57.466 36.000 0.00 0.00 32.35 2.41
5769 13734 0.472471 CTACACCACCCCACACAACT 59.528 55.000 0.00 0.00 0.00 3.16
5894 13859 5.856455 ACTGTGAATAAAATTTCCTTTCGCG 59.144 36.000 0.00 0.00 31.24 5.87
5917 13882 5.345741 CGGCAAAATCCAAAAGTTGTCTATG 59.654 40.000 0.00 0.00 0.00 2.23
5920 13885 7.063780 GGCAAAATCCAAAAGTTGTCTATGATG 59.936 37.037 0.00 0.00 0.00 3.07
5926 13891 5.404946 CAAAAGTTGTCTATGATGCAAGGG 58.595 41.667 0.00 0.00 0.00 3.95
5997 14087 5.186996 TGTCAAGAAGGCAATGAGAAAAC 57.813 39.130 0.00 0.00 0.00 2.43
6057 15929 3.140144 TGTGAAGTGGGGGAGAGAAAAAT 59.860 43.478 0.00 0.00 0.00 1.82
6143 16015 1.806496 TGATGATGTCTCCCCGGAAT 58.194 50.000 0.73 0.00 0.00 3.01
6193 16065 7.333528 TGTAGACTGCATTGGATTTTTATCC 57.666 36.000 0.00 0.00 41.10 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
303 6014 1.842052 ACAACGTTTGGTTTGTCCCT 58.158 45.000 0.00 0.00 36.49 4.20
314 6025 6.401688 CGTGATATGGTGTTCATACAACGTTT 60.402 38.462 0.00 0.00 45.25 3.60
462 6179 1.745653 CCTCTTCGCCCTTTTGGATTC 59.254 52.381 0.00 0.00 44.07 2.52
508 6225 4.275196 ACGGCCTTCTTTCTGTTTTCTAAC 59.725 41.667 0.00 0.00 34.75 2.34
724 6509 4.566697 GCCTTCTCTTTCTAAAAGGGCTCT 60.567 45.833 9.03 0.00 38.96 4.09
735 6520 2.206576 AATTGCCGCCTTCTCTTTCT 57.793 45.000 0.00 0.00 0.00 2.52
736 6521 2.228822 TGAAATTGCCGCCTTCTCTTTC 59.771 45.455 0.00 0.00 0.00 2.62
737 6522 2.238521 TGAAATTGCCGCCTTCTCTTT 58.761 42.857 0.00 0.00 0.00 2.52
738 6523 1.909700 TGAAATTGCCGCCTTCTCTT 58.090 45.000 0.00 0.00 0.00 2.85
757 6542 2.487762 CTGGAACACGTACCATTGCAAT 59.512 45.455 5.99 5.99 35.54 3.56
881 6923 9.533253 CTAATCTTCATCTTCTCCTCTCTTTTC 57.467 37.037 0.00 0.00 0.00 2.29
956 6998 8.397148 GTCGTCTAGACTTATATATTGGTAGCC 58.603 40.741 20.34 0.00 46.13 3.93
1054 7258 3.081061 GGTCATGCTGGTGTATGTTTCA 58.919 45.455 0.00 0.00 37.52 2.69
1055 7259 3.081061 TGGTCATGCTGGTGTATGTTTC 58.919 45.455 0.00 0.00 37.52 2.78
1120 7339 3.306364 CCGCTGAAAGGAAGAGAAAGAGA 60.306 47.826 0.00 0.00 0.00 3.10
1122 7341 2.872038 GCCGCTGAAAGGAAGAGAAAGA 60.872 50.000 0.00 0.00 0.00 2.52
1123 7342 1.466558 GCCGCTGAAAGGAAGAGAAAG 59.533 52.381 0.00 0.00 0.00 2.62
1124 7343 1.523758 GCCGCTGAAAGGAAGAGAAA 58.476 50.000 0.00 0.00 0.00 2.52
1125 7344 0.670546 CGCCGCTGAAAGGAAGAGAA 60.671 55.000 0.00 0.00 0.00 2.87
1126 7345 1.079819 CGCCGCTGAAAGGAAGAGA 60.080 57.895 0.00 0.00 0.00 3.10
1127 7346 1.079819 TCGCCGCTGAAAGGAAGAG 60.080 57.895 0.00 0.00 0.00 2.85
1128 7347 1.374252 GTCGCCGCTGAAAGGAAGA 60.374 57.895 0.00 0.00 0.00 2.87
1129 7348 1.355066 GAGTCGCCGCTGAAAGGAAG 61.355 60.000 0.00 0.00 0.00 3.46
1130 7349 1.374252 GAGTCGCCGCTGAAAGGAA 60.374 57.895 0.00 0.00 0.00 3.36
1154 7385 3.400928 AGCAGCAGCCTCCAGGAG 61.401 66.667 9.90 9.90 43.56 3.69
1184 7415 2.435410 TGTGATCCGCTGCTGCTG 60.435 61.111 14.03 7.35 36.97 4.41
1307 7538 4.910585 GGCGCGATGGGGATTCGT 62.911 66.667 12.10 0.00 38.81 3.85
1480 7711 0.934496 GCGTGTGTGTGTAGCTTCAA 59.066 50.000 0.00 0.00 0.00 2.69
1649 7977 2.961721 CGTGGGATGGCACGATCG 60.962 66.667 14.88 14.88 46.46 3.69
1719 8047 0.792640 CATGAGACGTGCCAGTTCAC 59.207 55.000 0.00 0.00 0.00 3.18
1743 8340 6.096141 TGTTTATCTTTGAGGTCTGTTTGCAA 59.904 34.615 0.00 0.00 0.00 4.08
1856 8453 9.877178 ATGTTAGAGTACTTCTAATCTTGTTGG 57.123 33.333 14.06 0.00 46.99 3.77
1987 8677 4.677673 ATTGCCTTCTTTATGCCAATCC 57.322 40.909 0.00 0.00 0.00 3.01
2277 9009 3.667217 AATTGCGGCAGGCCCATCT 62.667 57.895 1.67 0.00 42.61 2.90
2528 9260 4.510167 AGAAATCGAGGACAAATGGGAT 57.490 40.909 0.00 0.00 0.00 3.85
2609 9343 0.742281 CAGTAGCTGTTGCCGCTGAT 60.742 55.000 0.00 0.00 41.04 2.90
2782 9631 1.135774 TGCACTCGTCGATGTCTGTAC 60.136 52.381 4.21 0.00 0.00 2.90
3229 10208 7.122799 TGACTAGTCTATGACACTTTGCACTAT 59.877 37.037 23.01 0.00 34.60 2.12
3305 10284 9.734620 CTCTTCATTAATTCATCGCCATAAAAA 57.265 29.630 0.00 0.00 0.00 1.94
3308 10287 8.150296 TCTCTCTTCATTAATTCATCGCCATAA 58.850 33.333 0.00 0.00 0.00 1.90
3318 10297 9.877178 TCAAACTACCTCTCTCTTCATTAATTC 57.123 33.333 0.00 0.00 0.00 2.17
3563 10556 5.362430 ACACTGTGCTTCCCAAAAGAAAATA 59.638 36.000 7.90 0.00 0.00 1.40
3697 10690 8.272889 ACACTAGTCACATAGGAGTAACATAGA 58.727 37.037 0.00 0.00 0.00 1.98
3737 10731 7.842743 ACCTACCCAGATCTGTTTGTTATACTA 59.157 37.037 21.11 0.00 0.00 1.82
3778 10808 3.458857 TCAAACCCCAAACACCACTACTA 59.541 43.478 0.00 0.00 0.00 1.82
3779 10809 2.242708 TCAAACCCCAAACACCACTACT 59.757 45.455 0.00 0.00 0.00 2.57
3840 11487 7.978975 ACTGATAAAAGCAAAAGCAGTAAACAA 59.021 29.630 0.00 0.00 33.78 2.83
3923 11578 8.792830 TTTGACTGGAATATTCTCTACAAAGG 57.207 34.615 14.95 0.00 0.00 3.11
3977 11632 2.009774 CTAGGCCGACTTGAACAATGG 58.990 52.381 0.00 0.00 0.00 3.16
4298 12260 6.668541 TTGCGAAGAAGAATAAGGAATGAG 57.331 37.500 0.00 0.00 0.00 2.90
4499 12462 2.307098 ACTAATTGGCTCCTTCAGTGCT 59.693 45.455 0.00 0.00 35.28 4.40
4553 12516 5.486526 ACTTGAGACTGAATGATGACTTCC 58.513 41.667 0.00 0.00 0.00 3.46
4713 12676 2.016318 TGCAGCAATACTTAAGCGCAT 58.984 42.857 11.47 0.00 34.65 4.73
4772 12735 6.357367 GTCACCATGTAGGATCTTGGTATTT 58.643 40.000 4.42 0.00 41.70 1.40
5319 13283 1.203100 AGGCTTATTGATGGCCCATCC 60.203 52.381 20.85 4.25 46.31 3.51
5320 13284 1.891150 CAGGCTTATTGATGGCCCATC 59.109 52.381 17.13 17.13 46.31 3.51
5321 13285 1.500303 TCAGGCTTATTGATGGCCCAT 59.500 47.619 0.00 0.00 46.31 4.00
5322 13286 0.925558 TCAGGCTTATTGATGGCCCA 59.074 50.000 0.00 0.00 46.31 5.36
5323 13287 1.959282 CTTCAGGCTTATTGATGGCCC 59.041 52.381 0.00 0.00 46.31 5.80
5324 13288 1.339291 GCTTCAGGCTTATTGATGGCC 59.661 52.381 0.00 0.00 45.57 5.36
5325 13289 1.339291 GGCTTCAGGCTTATTGATGGC 59.661 52.381 0.00 0.00 41.46 4.40
5326 13290 2.360165 GTGGCTTCAGGCTTATTGATGG 59.640 50.000 1.64 0.00 41.69 3.51
5327 13291 2.360165 GGTGGCTTCAGGCTTATTGATG 59.640 50.000 1.64 0.00 41.69 3.07
5328 13292 2.025037 TGGTGGCTTCAGGCTTATTGAT 60.025 45.455 1.64 0.00 41.69 2.57
5329 13293 1.354031 TGGTGGCTTCAGGCTTATTGA 59.646 47.619 1.64 0.00 41.69 2.57
5330 13294 1.838112 TGGTGGCTTCAGGCTTATTG 58.162 50.000 1.64 0.00 41.69 1.90
5331 13295 2.243221 AGATGGTGGCTTCAGGCTTATT 59.757 45.455 1.64 0.00 41.69 1.40
5332 13296 1.849039 AGATGGTGGCTTCAGGCTTAT 59.151 47.619 1.64 0.00 41.69 1.73
5333 13297 1.210478 GAGATGGTGGCTTCAGGCTTA 59.790 52.381 1.64 0.00 41.69 3.09
5334 13298 0.034670 GAGATGGTGGCTTCAGGCTT 60.035 55.000 1.64 0.00 41.69 4.35
5335 13299 1.606531 GAGATGGTGGCTTCAGGCT 59.393 57.895 1.64 0.00 41.69 4.58
5336 13300 1.452833 GGAGATGGTGGCTTCAGGC 60.453 63.158 0.00 0.00 41.50 4.85
5337 13301 1.153289 CGGAGATGGTGGCTTCAGG 60.153 63.158 0.00 0.00 0.00 3.86
5338 13302 0.036010 AACGGAGATGGTGGCTTCAG 60.036 55.000 0.00 0.00 0.00 3.02
5339 13303 0.400213 AAACGGAGATGGTGGCTTCA 59.600 50.000 0.00 0.00 0.00 3.02
5340 13304 1.087501 GAAACGGAGATGGTGGCTTC 58.912 55.000 0.00 0.00 0.00 3.86
5341 13305 0.693049 AGAAACGGAGATGGTGGCTT 59.307 50.000 0.00 0.00 0.00 4.35
5342 13306 1.568504 TAGAAACGGAGATGGTGGCT 58.431 50.000 0.00 0.00 0.00 4.75
5343 13307 2.396590 TTAGAAACGGAGATGGTGGC 57.603 50.000 0.00 0.00 0.00 5.01
5366 13330 3.260632 GTGTTGGCCCATCCATAGTTTTT 59.739 43.478 0.00 0.00 46.04 1.94
5367 13331 2.831526 GTGTTGGCCCATCCATAGTTTT 59.168 45.455 0.00 0.00 46.04 2.43
5368 13332 2.042979 AGTGTTGGCCCATCCATAGTTT 59.957 45.455 0.00 0.00 46.04 2.66
5369 13333 1.640670 AGTGTTGGCCCATCCATAGTT 59.359 47.619 0.00 0.00 46.04 2.24
5389 13353 7.817641 TGTTCACAACGGCAATATAAACATAA 58.182 30.769 0.00 0.00 0.00 1.90
5534 13498 2.230508 TGGAACCTCGTATCAGTGACAC 59.769 50.000 0.00 0.00 0.00 3.67
5675 13640 4.062293 TGAGGTTTGTTGTAACTGGATCG 58.938 43.478 0.00 0.00 0.00 3.69
5686 13651 4.578516 TGTGGAGTTGTATGAGGTTTGTTG 59.421 41.667 0.00 0.00 0.00 3.33
5687 13652 4.578928 GTGTGGAGTTGTATGAGGTTTGTT 59.421 41.667 0.00 0.00 0.00 2.83
5769 13734 7.730332 TCTCTTCCATATTGTAGATAGCTTGGA 59.270 37.037 0.00 0.00 0.00 3.53
5894 13859 6.454795 TCATAGACAACTTTTGGATTTTGCC 58.545 36.000 0.00 0.00 34.12 4.52
5917 13882 5.652994 TTATGTTGGTTTACCCTTGCATC 57.347 39.130 0.00 0.00 34.29 3.91
5920 13885 7.580600 CAATTTTTATGTTGGTTTACCCTTGC 58.419 34.615 0.00 0.00 34.29 4.01
5926 13891 7.359681 CCCTTCGCAATTTTTATGTTGGTTTAC 60.360 37.037 0.00 0.00 0.00 2.01
5997 14087 9.480053 TTTTTATTTGCCTCTCTCTTTTCATTG 57.520 29.630 0.00 0.00 0.00 2.82
6057 15929 4.527816 ACTTTATTTGCCATTTGCCTCTCA 59.472 37.500 0.00 0.00 40.16 3.27
6143 16015 2.528564 CAGGAAGAATTTCTTGCCCCA 58.471 47.619 22.41 0.00 44.58 4.96
6149 16021 7.604545 GTCTACAAGTAGCAGGAAGAATTTCTT 59.395 37.037 11.40 11.40 34.82 2.52
6193 16065 2.612471 GCATCATCCTCTCATCTTCGGG 60.612 54.545 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.