Multiple sequence alignment - TraesCS7D01G305700

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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 TraesCS7D01G305700 chr7D 100.000 7716 0 0 1 7716 386913492 386921207 0.000000e+00 14249.0
1 TraesCS7D01G305700 chr7D 92.537 67 2 2 243 306 116592490 116592556 8.240000e-15 93.5
2 TraesCS7D01G305700 chr7A 96.605 5567 149 11 834 6392 437052471 437058005 0.000000e+00 9197.0
3 TraesCS7D01G305700 chr7A 95.263 1330 53 7 6390 7716 437058145 437059467 0.000000e+00 2098.0
4 TraesCS7D01G305700 chr7A 83.221 447 27 23 346 757 437051645 437052078 4.400000e-97 366.0
5 TraesCS7D01G305700 chr7A 93.117 247 16 1 3 249 437051389 437051634 2.050000e-95 361.0
6 TraesCS7D01G305700 chr7A 88.462 78 6 2 232 306 721264923 721265000 2.970000e-14 91.6
7 TraesCS7D01G305700 chr7B 95.619 5478 143 27 1653 7121 382222687 382228076 0.000000e+00 8696.0
8 TraesCS7D01G305700 chr7B 87.081 1401 82 30 333 1668 382221272 382222638 0.000000e+00 1493.0
9 TraesCS7D01G305700 chr7B 81.898 569 70 14 7128 7695 382240030 382240566 4.250000e-122 449.0
10 TraesCS7D01G305700 chr7B 93.421 228 14 1 14 241 382221002 382221228 3.450000e-88 337.0
11 TraesCS7D01G305700 chr2D 93.750 64 2 1 245 306 480173317 480173380 2.290000e-15 95.3
12 TraesCS7D01G305700 chr4B 96.429 56 2 0 251 306 612271405 612271460 8.240000e-15 93.5
13 TraesCS7D01G305700 chr4A 92.188 64 3 1 248 309 440964911 440964848 1.070000e-13 89.8
14 TraesCS7D01G305700 chr2A 88.312 77 6 2 232 305 367831938 367832014 1.070000e-13 89.8
15 TraesCS7D01G305700 chr1B 93.443 61 2 1 248 306 529474290 529474350 1.070000e-13 89.8
16 TraesCS7D01G305700 chr1A 89.855 69 4 2 241 306 558377644 558377576 1.380000e-12 86.1
17 TraesCS7D01G305700 chr5B 88.889 72 3 4 239 306 105695931 105696001 4.960000e-12 84.2
18 TraesCS7D01G305700 chr1D 97.059 34 1 0 4369 4402 314437556 314437523 3.010000e-04 58.4
19 TraesCS7D01G305700 chr2B 100.000 28 0 0 7662 7689 447352084 447352057 1.400000e-02 52.8


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 TraesCS7D01G305700 chr7D 386913492 386921207 7715 False 14249.000000 14249 100.000000 1 7716 1 chr7D.!!$F2 7715
1 TraesCS7D01G305700 chr7A 437051389 437059467 8078 False 3005.500000 9197 92.051500 3 7716 4 chr7A.!!$F2 7713
2 TraesCS7D01G305700 chr7B 382221002 382228076 7074 False 3508.666667 8696 92.040333 14 7121 3 chr7B.!!$F2 7107
3 TraesCS7D01G305700 chr7B 382240030 382240566 536 False 449.000000 449 81.898000 7128 7695 1 chr7B.!!$F1 567

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
917 1280 0.803117 CCGAGCACGAGTAGTCTTGA 59.197 55.000 4.70 0.00 42.66 3.02 F
2664 3127 1.195900 CAATGCAATGCCAAGCACAAC 59.804 47.619 1.53 0.00 43.04 3.32 F
3362 3826 1.544724 ACGGTGATGGGGTGATTTTG 58.455 50.000 0.00 0.00 0.00 2.44 F
4605 5083 1.537202 GTCAACTGTGGCTGGCTTTAG 59.463 52.381 2.00 0.88 0.00 1.85 F
5991 6473 0.181350 GTAAGGGGATCTGGTGCTGG 59.819 60.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2761 3224 0.804989 AAGTAGCAAGCACCATTCGC 59.195 50.000 0.00 0.0 0.00 4.70 R
4359 4836 1.813862 GCTCCCGCATGCAATTAGGTA 60.814 52.381 19.57 0.0 35.78 3.08 R
4920 5398 1.661463 TGCAAGGGATCTTCTCCAGT 58.339 50.000 0.00 0.0 46.98 4.00 R
6318 6803 0.108186 AAGAATCGCACCTCGCATGA 60.108 50.000 0.00 0.0 42.60 3.07 R
7326 7953 0.106116 GGGACGAGTATGGGAGGTCT 60.106 60.000 0.00 0.0 0.00 3.85 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
73 74 2.909006 ACACAGAGAGGTCCAATCATGT 59.091 45.455 0.00 0.00 0.00 3.21
147 148 1.198178 CCAACCAACCCAATTCGTACG 59.802 52.381 9.53 9.53 0.00 3.67
262 263 8.310122 TGTACCTAAAAATATACTCCCTTCGT 57.690 34.615 0.00 0.00 0.00 3.85
263 264 8.416329 TGTACCTAAAAATATACTCCCTTCGTC 58.584 37.037 0.00 0.00 0.00 4.20
264 265 6.824553 ACCTAAAAATATACTCCCTTCGTCC 58.175 40.000 0.00 0.00 0.00 4.79
265 266 6.183361 ACCTAAAAATATACTCCCTTCGTCCC 60.183 42.308 0.00 0.00 0.00 4.46
266 267 5.703730 AAAAATATACTCCCTTCGTCCCA 57.296 39.130 0.00 0.00 0.00 4.37
267 268 5.906772 AAAATATACTCCCTTCGTCCCAT 57.093 39.130 0.00 0.00 0.00 4.00
268 269 7.383156 AAAAATATACTCCCTTCGTCCCATA 57.617 36.000 0.00 0.00 0.00 2.74
269 270 7.383156 AAAATATACTCCCTTCGTCCCATAA 57.617 36.000 0.00 0.00 0.00 1.90
270 271 7.569599 AAATATACTCCCTTCGTCCCATAAT 57.430 36.000 0.00 0.00 0.00 1.28
271 272 8.674925 AAATATACTCCCTTCGTCCCATAATA 57.325 34.615 0.00 0.00 0.00 0.98
272 273 8.855804 AATATACTCCCTTCGTCCCATAATAT 57.144 34.615 0.00 0.00 0.00 1.28
273 274 9.947189 AATATACTCCCTTCGTCCCATAATATA 57.053 33.333 0.00 0.00 0.00 0.86
274 275 9.947189 ATATACTCCCTTCGTCCCATAATATAA 57.053 33.333 0.00 0.00 0.00 0.98
275 276 6.607004 ACTCCCTTCGTCCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
276 277 6.320518 ACTCCCTTCGTCCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
277 278 6.437793 ACTCCCTTCGTCCCATAATATAAGAG 59.562 42.308 0.00 0.00 0.00 2.85
278 279 5.187186 TCCCTTCGTCCCATAATATAAGAGC 59.813 44.000 0.00 0.00 0.00 4.09
279 280 5.046591 CCCTTCGTCCCATAATATAAGAGCA 60.047 44.000 0.00 0.00 0.00 4.26
280 281 6.352222 CCCTTCGTCCCATAATATAAGAGCAT 60.352 42.308 0.00 0.00 0.00 3.79
281 282 7.106239 CCTTCGTCCCATAATATAAGAGCATT 58.894 38.462 0.00 0.00 0.00 3.56
282 283 7.607991 CCTTCGTCCCATAATATAAGAGCATTT 59.392 37.037 0.00 0.00 0.00 2.32
283 284 8.918202 TTCGTCCCATAATATAAGAGCATTTT 57.082 30.769 0.00 0.00 0.00 1.82
284 285 8.918202 TCGTCCCATAATATAAGAGCATTTTT 57.082 30.769 0.00 0.00 0.00 1.94
285 286 8.783093 TCGTCCCATAATATAAGAGCATTTTTG 58.217 33.333 0.00 0.00 0.00 2.44
286 287 8.783093 CGTCCCATAATATAAGAGCATTTTTGA 58.217 33.333 0.00 0.00 0.00 2.69
287 288 9.899226 GTCCCATAATATAAGAGCATTTTTGAC 57.101 33.333 0.00 0.00 0.00 3.18
288 289 9.639563 TCCCATAATATAAGAGCATTTTTGACA 57.360 29.630 0.00 0.00 0.00 3.58
289 290 9.683069 CCCATAATATAAGAGCATTTTTGACAC 57.317 33.333 0.00 0.00 0.00 3.67
320 321 8.021396 AGTGTCAAAAACTCTAGTGTCAAAAAC 58.979 33.333 0.00 0.00 30.04 2.43
321 322 8.021396 GTGTCAAAAACTCTAGTGTCAAAAACT 58.979 33.333 0.00 0.00 0.00 2.66
376 384 9.044150 CGGGGTCTAAAAATAAACGTTCATATA 57.956 33.333 0.00 0.00 0.00 0.86
422 432 9.295825 TCATATTTAAAACTGTTCACCAGATGT 57.704 29.630 0.00 0.00 44.49 3.06
474 492 7.530010 AGTTGTTCATGTGTGCTACAATATTC 58.470 34.615 0.00 0.00 43.77 1.75
475 493 7.391554 AGTTGTTCATGTGTGCTACAATATTCT 59.608 33.333 0.00 0.00 43.77 2.40
477 495 8.109705 TGTTCATGTGTGCTACAATATTCTTT 57.890 30.769 0.00 0.00 43.77 2.52
565 610 9.495572 AGGAAAACACAACAAACATAAAAGAAA 57.504 25.926 0.00 0.00 0.00 2.52
570 615 8.262715 ACACAACAAACATAAAAGAAAAAGGG 57.737 30.769 0.00 0.00 0.00 3.95
571 616 7.335673 ACACAACAAACATAAAAGAAAAAGGGG 59.664 33.333 0.00 0.00 0.00 4.79
576 621 8.325787 ACAAACATAAAAGAAAAAGGGGAAACT 58.674 29.630 0.00 0.00 0.00 2.66
587 632 3.147553 AGGGGAAACTGAAAAGAGAGC 57.852 47.619 0.00 0.00 0.00 4.09
664 709 2.656069 ATCGGTCCCGGTCCTGTTG 61.656 63.158 5.80 0.00 40.25 3.33
670 715 3.047877 CCGGTCCTGTTGCCGTTC 61.048 66.667 0.00 0.00 45.91 3.95
767 828 4.760047 CGCCTCCACAACTCCCCG 62.760 72.222 0.00 0.00 0.00 5.73
815 876 1.535444 TCGTCCTCCCCTTGCTTCA 60.535 57.895 0.00 0.00 0.00 3.02
822 883 2.115910 CCCTTGCTTCACAGCCCA 59.884 61.111 0.00 0.00 46.74 5.36
823 884 2.270986 CCCTTGCTTCACAGCCCAC 61.271 63.158 0.00 0.00 46.74 4.61
825 886 0.896940 CCTTGCTTCACAGCCCACAT 60.897 55.000 0.00 0.00 46.74 3.21
827 888 0.895100 TTGCTTCACAGCCCACATCC 60.895 55.000 0.00 0.00 46.74 3.51
844 1207 4.452733 CCCCGTTCAGCCGTCCTC 62.453 72.222 0.00 0.00 0.00 3.71
845 1208 4.796231 CCCGTTCAGCCGTCCTCG 62.796 72.222 0.00 0.00 0.00 4.63
850 1213 2.994671 TTCAGCCGTCCTCGCTCTG 61.995 63.158 0.00 0.00 37.42 3.35
890 1253 2.383527 GCGCCTGAGTCCGAACTTG 61.384 63.158 0.00 0.00 35.28 3.16
917 1280 0.803117 CCGAGCACGAGTAGTCTTGA 59.197 55.000 4.70 0.00 42.66 3.02
926 1289 3.314635 ACGAGTAGTCTTGACGTCTTGTT 59.685 43.478 17.92 1.48 31.69 2.83
934 1297 5.235186 AGTCTTGACGTCTTGTTCATTTCTG 59.765 40.000 17.92 0.00 0.00 3.02
941 1304 1.861542 TTGTTCATTTCTGCCGGCGG 61.862 55.000 30.18 30.18 0.00 6.13
1346 1730 2.106683 CCTAACAAAGCCGCCCTCG 61.107 63.158 0.00 0.00 0.00 4.63
1451 1850 4.712829 TGGGACACTCGAAGGTAATATCAA 59.287 41.667 0.00 0.00 0.00 2.57
1452 1851 5.048507 GGGACACTCGAAGGTAATATCAAC 58.951 45.833 0.00 0.00 0.00 3.18
1554 1953 5.361571 TGATAGTTTGGGTGCTCTCGTTATA 59.638 40.000 0.00 0.00 0.00 0.98
1614 2013 6.434018 AAGCATGCTCTTCTTAATTCTCAC 57.566 37.500 22.93 0.00 0.00 3.51
1748 2211 8.984891 TTGTGGTATTTCATCATTTGTTCATC 57.015 30.769 0.00 0.00 0.00 2.92
1823 2286 8.514330 ACACAGTTACAAATAGTTTTCCAAGA 57.486 30.769 0.00 0.00 0.00 3.02
2015 2478 3.475575 TGCTTAACTGTTGTGATGCAGA 58.524 40.909 2.69 0.00 34.11 4.26
2476 2939 6.600427 TCATTGGCCATGCAGTTCATATATAG 59.400 38.462 6.09 0.00 33.19 1.31
2664 3127 1.195900 CAATGCAATGCCAAGCACAAC 59.804 47.619 1.53 0.00 43.04 3.32
2675 3138 2.159393 CCAAGCACAACGGAATATGTGG 60.159 50.000 7.87 0.00 45.46 4.17
2725 3188 9.047371 TGGATTTAATTAATGCATGCTTGATTG 57.953 29.630 20.33 0.00 39.34 2.67
2750 3213 5.186996 ACATGGTTTGTCTGTTTGATGAC 57.813 39.130 0.00 0.00 30.89 3.06
2761 3224 6.016860 TGTCTGTTTGATGACTTTTCAGATGG 60.017 38.462 0.00 0.00 34.35 3.51
2763 3226 4.161333 GTTTGATGACTTTTCAGATGGCG 58.839 43.478 0.00 0.00 34.35 5.69
2859 3322 2.158696 GCTCATGATCAGGGGTAAGCTT 60.159 50.000 9.33 3.48 0.00 3.74
2864 3327 5.608437 TCATGATCAGGGGTAAGCTTTAGAT 59.392 40.000 3.20 0.00 0.00 1.98
3239 3703 9.968743 GAAAATCTAACACTGGAACTAAATACG 57.031 33.333 0.00 0.00 0.00 3.06
3279 3743 3.178046 TGTTCTACAGGTGGCCTATCAA 58.822 45.455 3.32 0.00 29.64 2.57
3362 3826 1.544724 ACGGTGATGGGGTGATTTTG 58.455 50.000 0.00 0.00 0.00 2.44
3651 4115 4.081420 TCCTTTTCACTGGCTACTGAGATC 60.081 45.833 0.00 0.00 0.00 2.75
3792 4256 6.182039 ACTAACCACAACAATCATGAATCG 57.818 37.500 0.00 0.00 0.00 3.34
3793 4257 5.705441 ACTAACCACAACAATCATGAATCGT 59.295 36.000 0.00 0.00 0.00 3.73
3794 4258 4.685169 ACCACAACAATCATGAATCGTC 57.315 40.909 0.00 0.00 0.00 4.20
3795 4259 4.071423 ACCACAACAATCATGAATCGTCA 58.929 39.130 0.00 0.00 38.41 4.35
3796 4260 4.518590 ACCACAACAATCATGAATCGTCAA 59.481 37.500 0.00 0.00 37.30 3.18
3797 4261 5.183713 ACCACAACAATCATGAATCGTCAAT 59.816 36.000 0.00 0.00 37.30 2.57
3798 4262 5.740569 CCACAACAATCATGAATCGTCAATC 59.259 40.000 0.00 0.00 37.30 2.67
3799 4263 6.316319 CACAACAATCATGAATCGTCAATCA 58.684 36.000 0.00 0.00 37.30 2.57
3800 4264 6.970613 CACAACAATCATGAATCGTCAATCAT 59.029 34.615 0.00 0.00 37.30 2.45
4131 4608 5.938322 TCTTGTCCTTTCGCAATATCAAAC 58.062 37.500 0.00 0.00 0.00 2.93
4144 4621 7.766738 TCGCAATATCAAACTGATTTAGTGGTA 59.233 33.333 0.00 0.00 40.26 3.25
4305 4782 5.890334 TCAGGTTCAGTTTGATTTTGACAC 58.110 37.500 0.00 0.00 0.00 3.67
4473 4951 4.797471 TGCATGTGTGAGAAAACATAAGC 58.203 39.130 0.00 0.00 36.70 3.09
4482 4960 9.722056 GTGTGAGAAAACATAAGCTATTAATGG 57.278 33.333 0.00 0.00 31.49 3.16
4565 5043 6.469410 TCCTATGTTCTGTTATTGTTTCGGT 58.531 36.000 0.00 0.00 0.00 4.69
4605 5083 1.537202 GTCAACTGTGGCTGGCTTTAG 59.463 52.381 2.00 0.88 0.00 1.85
4635 5113 6.092259 GGACATTACAAACCTAACTAGCTGTG 59.908 42.308 0.00 0.00 0.00 3.66
4772 5250 8.458573 TCTTTTGTTACACATGTTGGAGTTAT 57.541 30.769 0.00 0.00 0.00 1.89
4773 5251 8.908903 TCTTTTGTTACACATGTTGGAGTTATT 58.091 29.630 0.00 0.00 0.00 1.40
4920 5398 9.434275 TCAGGTGATAAAGGACATTCTAATCTA 57.566 33.333 0.00 0.00 0.00 1.98
4953 5431 4.661222 TCCCTTGCAATGAACTTGTATCA 58.339 39.130 0.00 0.00 37.18 2.15
5155 5633 7.841282 TCATTTTACAAATGTTGGGGTTCTA 57.159 32.000 8.65 0.00 34.12 2.10
5232 5710 7.233348 AGCTTTTGGTTCTCCATTTATCTTCAA 59.767 33.333 0.00 0.00 43.91 2.69
5236 5714 7.395190 TGGTTCTCCATTTATCTTCAACATG 57.605 36.000 0.00 0.00 39.03 3.21
5320 5798 8.690203 TCATTATTCCTTTCTCACTGTTTTGA 57.310 30.769 0.00 0.00 0.00 2.69
5466 5945 1.208165 ACCATGGGTGACTTCCCCTC 61.208 60.000 18.09 0.00 46.48 4.30
5656 6137 4.892934 TGCTTTCCACATTCCTTGTAACTT 59.107 37.500 0.00 0.00 36.57 2.66
5808 6290 3.901222 TGTGGATTACTGAAGTGACTCCA 59.099 43.478 6.45 6.45 32.52 3.86
5991 6473 0.181350 GTAAGGGGATCTGGTGCTGG 59.819 60.000 0.00 0.00 0.00 4.85
6016 6498 3.599730 TCTGAATCTGACGCACAAGAT 57.400 42.857 0.00 0.00 0.00 2.40
6095 6580 9.917129 TGTGAATTTTGAGTATCGAAGTTACTA 57.083 29.630 0.00 0.00 38.39 1.82
6105 6590 7.479150 AGTATCGAAGTTACTACAAACCTAGC 58.521 38.462 0.00 0.00 0.00 3.42
6200 6685 7.147567 TGGTATGATGAAATAGACAACCTAGCA 60.148 37.037 0.00 0.00 0.00 3.49
6215 6700 2.751259 CCTAGCATTTTCTGAAGCTGCA 59.249 45.455 20.92 0.00 37.94 4.41
6233 6718 2.486472 CAGAGGAACCTGCTGTGATT 57.514 50.000 0.00 0.00 30.66 2.57
6318 6803 1.125711 AGTTAACGTCAGCCCTGGGT 61.126 55.000 15.56 0.00 0.00 4.51
6462 7089 3.201290 CCTCTGCTGCATTGTACCTAAG 58.799 50.000 1.31 0.00 0.00 2.18
6929 7556 5.967674 CGAGGATTAATGAAACATTGCAGAC 59.032 40.000 7.16 0.00 0.00 3.51
7136 7763 7.441836 TGACTAGATAATTGTCTGTGTGTTGT 58.558 34.615 14.43 2.89 35.06 3.32
7267 7894 8.564509 AATATGTGTTTGCTGGCAAATTTATT 57.435 26.923 21.04 16.93 45.90 1.40
7313 7940 0.457443 GCCATGGCAAGTCCTTAAGC 59.543 55.000 32.08 0.00 41.49 3.09
7318 7945 0.811281 GGCAAGTCCTTAAGCGCATT 59.189 50.000 11.47 3.50 0.00 3.56
7326 7953 3.189702 GTCCTTAAGCGCATTTACAACCA 59.810 43.478 11.47 0.00 0.00 3.67
7340 7967 2.188817 ACAACCAGACCTCCCATACTC 58.811 52.381 0.00 0.00 0.00 2.59
7344 7971 1.033574 CAGACCTCCCATACTCGTCC 58.966 60.000 0.00 0.00 0.00 4.79
7347 7974 0.397254 ACCTCCCATACTCGTCCCAG 60.397 60.000 0.00 0.00 0.00 4.45
7349 7976 1.481428 CCTCCCATACTCGTCCCAGAT 60.481 57.143 0.00 0.00 0.00 2.90
7351 7978 0.034059 CCCATACTCGTCCCAGATGC 59.966 60.000 0.00 0.00 0.00 3.91
7352 7979 0.034059 CCATACTCGTCCCAGATGCC 59.966 60.000 0.00 0.00 0.00 4.40
7377 8004 2.413142 GGCTGCCTGGTCATTGCTC 61.413 63.158 12.43 0.00 0.00 4.26
7378 8005 2.758089 GCTGCCTGGTCATTGCTCG 61.758 63.158 0.00 0.00 0.00 5.03
7401 8028 0.898326 GATTTTCGGCCACCCAACCT 60.898 55.000 2.24 0.00 0.00 3.50
7419 8046 2.285442 GGCTCCCCACACCTACCT 60.285 66.667 0.00 0.00 0.00 3.08
7452 8079 2.435693 GGCCGGCACTCTCCATACT 61.436 63.158 30.85 0.00 0.00 2.12
7457 8084 1.395826 GGCACTCTCCATACTCGGCT 61.396 60.000 0.00 0.00 0.00 5.52
7501 8128 4.838152 CCGGACGTGGGCTCCATG 62.838 72.222 0.00 10.80 45.34 3.66
7524 8151 3.443045 CTGACCGCAATGGCCCAC 61.443 66.667 0.00 0.00 43.94 4.61
7525 8152 4.277009 TGACCGCAATGGCCCACA 62.277 61.111 0.00 0.00 43.94 4.17
7545 8172 2.029244 CACGGTCACACAAATAGATCGC 59.971 50.000 0.00 0.00 39.36 4.58
7550 8177 3.684788 GTCACACAAATAGATCGCTGGTT 59.315 43.478 0.00 0.00 0.00 3.67
7565 8192 4.415332 GTTCGACGAGCGCCTCCA 62.415 66.667 2.29 0.00 40.61 3.86
7698 8326 3.255379 CTTCGCCGCCGCTACTTC 61.255 66.667 0.00 0.00 0.00 3.01
7707 8335 1.139095 CCGCTACTTCCGACCTGTC 59.861 63.158 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.186198 GGCTTGTTCTAATCATGTGGTACT 58.814 41.667 0.00 0.00 0.00 2.73
1 2 4.335594 GGGCTTGTTCTAATCATGTGGTAC 59.664 45.833 0.00 0.00 0.00 3.34
6 7 4.263905 TGGAAGGGCTTGTTCTAATCATGT 60.264 41.667 0.00 0.00 0.00 3.21
9 10 3.330701 AGTGGAAGGGCTTGTTCTAATCA 59.669 43.478 0.00 0.00 0.00 2.57
54 55 4.383552 GCTTACATGATTGGACCTCTCTGT 60.384 45.833 0.00 0.00 0.00 3.41
73 74 4.441634 GGACCTCGCTTAGAAATGAGCTTA 60.442 45.833 0.00 0.00 36.76 3.09
252 253 6.320518 TCTTATATTATGGGACGAAGGGAGT 58.679 40.000 0.00 0.00 0.00 3.85
253 254 6.628398 GCTCTTATATTATGGGACGAAGGGAG 60.628 46.154 0.00 0.00 0.00 4.30
254 255 5.187186 GCTCTTATATTATGGGACGAAGGGA 59.813 44.000 0.00 0.00 0.00 4.20
255 256 5.046591 TGCTCTTATATTATGGGACGAAGGG 60.047 44.000 0.00 0.00 0.00 3.95
256 257 6.037786 TGCTCTTATATTATGGGACGAAGG 57.962 41.667 0.00 0.00 0.00 3.46
257 258 8.553459 AAATGCTCTTATATTATGGGACGAAG 57.447 34.615 0.00 0.00 0.00 3.79
258 259 8.918202 AAAATGCTCTTATATTATGGGACGAA 57.082 30.769 0.00 0.00 0.00 3.85
259 260 8.783093 CAAAAATGCTCTTATATTATGGGACGA 58.217 33.333 0.00 0.00 0.00 4.20
260 261 8.783093 TCAAAAATGCTCTTATATTATGGGACG 58.217 33.333 0.00 0.00 0.00 4.79
261 262 9.899226 GTCAAAAATGCTCTTATATTATGGGAC 57.101 33.333 0.00 0.00 0.00 4.46
262 263 9.639563 TGTCAAAAATGCTCTTATATTATGGGA 57.360 29.630 0.00 0.00 0.00 4.37
263 264 9.683069 GTGTCAAAAATGCTCTTATATTATGGG 57.317 33.333 0.00 0.00 0.00 4.00
271 272 9.155975 CACTAGTAGTGTCAAAAATGCTCTTAT 57.844 33.333 20.29 0.00 41.19 1.73
272 273 8.534333 CACTAGTAGTGTCAAAAATGCTCTTA 57.466 34.615 20.29 0.00 41.19 2.10
273 274 7.426929 CACTAGTAGTGTCAAAAATGCTCTT 57.573 36.000 20.29 0.00 41.19 2.85
293 294 8.780846 TTTTGACACTAGAGTTTTTGACACTA 57.219 30.769 0.00 0.00 31.36 2.74
294 295 7.681939 TTTTGACACTAGAGTTTTTGACACT 57.318 32.000 0.00 0.00 33.55 3.55
295 296 8.021396 AGTTTTTGACACTAGAGTTTTTGACAC 58.979 33.333 0.00 0.00 0.00 3.67
296 297 8.106247 AGTTTTTGACACTAGAGTTTTTGACA 57.894 30.769 0.00 0.00 0.00 3.58
297 298 8.451748 AGAGTTTTTGACACTAGAGTTTTTGAC 58.548 33.333 0.00 0.00 0.00 3.18
298 299 8.561738 AGAGTTTTTGACACTAGAGTTTTTGA 57.438 30.769 0.00 0.00 0.00 2.69
299 300 8.669243 AGAGAGTTTTTGACACTAGAGTTTTTG 58.331 33.333 0.00 0.00 28.71 2.44
300 301 8.794335 AGAGAGTTTTTGACACTAGAGTTTTT 57.206 30.769 0.00 0.00 28.71 1.94
301 302 8.794335 AAGAGAGTTTTTGACACTAGAGTTTT 57.206 30.769 0.00 0.00 28.71 2.43
533 577 5.474825 TGTTTGTTGTGTTTTCCTTCTTCC 58.525 37.500 0.00 0.00 0.00 3.46
565 610 3.891977 GCTCTCTTTTCAGTTTCCCCTTT 59.108 43.478 0.00 0.00 0.00 3.11
568 613 2.863809 TGCTCTCTTTTCAGTTTCCCC 58.136 47.619 0.00 0.00 0.00 4.81
597 642 2.851195 TCTGGACACCTTTTTCTCTGC 58.149 47.619 0.00 0.00 0.00 4.26
793 854 2.982130 CAAGGGGAGGACGACTGG 59.018 66.667 0.00 0.00 0.00 4.00
822 883 4.096003 CGGCTGAACGGGGGATGT 62.096 66.667 0.00 0.00 0.00 3.06
823 884 4.096003 ACGGCTGAACGGGGGATG 62.096 66.667 0.00 0.00 38.39 3.51
827 888 4.452733 GAGGACGGCTGAACGGGG 62.453 72.222 0.00 0.00 38.39 5.73
909 1272 6.420903 CAGAAATGAACAAGACGTCAAGACTA 59.579 38.462 19.50 0.00 0.00 2.59
917 1280 1.531149 CGGCAGAAATGAACAAGACGT 59.469 47.619 0.00 0.00 0.00 4.34
941 1304 2.818274 GACGTCCCAATCGGTGCC 60.818 66.667 3.51 0.00 0.00 5.01
949 1312 1.553248 CAGGTATTCAGGACGTCCCAA 59.447 52.381 30.82 23.13 37.41 4.12
1233 1596 4.477975 GTCGTAGTCGCAGCCGCT 62.478 66.667 0.00 0.00 36.96 5.52
1451 1850 2.151202 ACGACTTGCGATTGAAATGGT 58.849 42.857 0.00 0.00 44.57 3.55
1452 1851 2.900122 ACGACTTGCGATTGAAATGG 57.100 45.000 0.00 0.00 44.57 3.16
1554 1953 1.987807 AAGCTGTGTGGGCAGACACT 61.988 55.000 16.94 0.00 45.52 3.55
1610 2009 2.231235 GGGTTTGTAAATGGCAGGTGAG 59.769 50.000 0.00 0.00 0.00 3.51
1614 2013 1.967066 TGTGGGTTTGTAAATGGCAGG 59.033 47.619 0.00 0.00 0.00 4.85
1680 2143 6.150140 ACAATAGTGAAAACTCAAGAGCATCC 59.850 38.462 0.00 0.00 33.66 3.51
1776 2239 4.150897 ACAGTACTTCTTGTGGCTTTCA 57.849 40.909 0.00 0.00 0.00 2.69
1846 2309 8.156820 TCCATGTCATCTTTCAGAAGAAGTTAA 58.843 33.333 0.00 0.00 44.61 2.01
1847 2310 7.604164 GTCCATGTCATCTTTCAGAAGAAGTTA 59.396 37.037 0.00 0.00 44.61 2.24
2091 2554 9.671279 TCTAATGTTTCATGTGACTGATACAAT 57.329 29.630 10.35 6.80 39.45 2.71
2541 3004 9.755804 CATCTCAATGTATATCCATAGCGTATT 57.244 33.333 0.00 0.00 0.00 1.89
2664 3127 6.073331 ACAAAATTTGTTTGCCACATATTCCG 60.073 34.615 5.41 1.81 42.22 4.30
2725 3188 6.198966 GTCATCAAACAGACAAACCATGTTTC 59.801 38.462 0.00 0.00 43.37 2.78
2750 3213 2.733227 GCACCATTCGCCATCTGAAAAG 60.733 50.000 0.00 0.00 0.00 2.27
2761 3224 0.804989 AAGTAGCAAGCACCATTCGC 59.195 50.000 0.00 0.00 0.00 4.70
2763 3226 2.268730 GCAAGTAGCAAGCACCATTC 57.731 50.000 0.00 0.00 44.79 2.67
2958 3421 6.830324 AGAAAATTAGCATATGTGAGGAGCAA 59.170 34.615 4.29 0.00 0.00 3.91
3205 3669 4.321230 CCAGTGTTAGATTTTCTGGTTGGC 60.321 45.833 0.00 0.00 40.25 4.52
3279 3743 1.539065 GCGATCACCGTCCTCATCAAT 60.539 52.381 0.00 0.00 41.15 2.57
3699 4163 4.868450 TTGACACCTAAAACTTGTGACG 57.132 40.909 0.00 0.00 34.18 4.35
4336 4813 9.220767 GGTAAGTATTCAAGAGAAAATGACAGT 57.779 33.333 0.00 0.00 37.29 3.55
4337 4814 9.442047 AGGTAAGTATTCAAGAGAAAATGACAG 57.558 33.333 0.00 0.00 37.29 3.51
4344 4821 9.733556 TGCAATTAGGTAAGTATTCAAGAGAAA 57.266 29.630 0.00 0.00 37.29 2.52
4345 4822 9.905713 ATGCAATTAGGTAAGTATTCAAGAGAA 57.094 29.630 0.00 0.00 38.31 2.87
4346 4823 9.330063 CATGCAATTAGGTAAGTATTCAAGAGA 57.670 33.333 0.00 0.00 0.00 3.10
4347 4824 8.072567 GCATGCAATTAGGTAAGTATTCAAGAG 58.927 37.037 14.21 0.00 0.00 2.85
4348 4825 7.254761 CGCATGCAATTAGGTAAGTATTCAAGA 60.255 37.037 19.57 0.00 0.00 3.02
4349 4826 6.852853 CGCATGCAATTAGGTAAGTATTCAAG 59.147 38.462 19.57 0.00 0.00 3.02
4350 4827 6.238621 CCGCATGCAATTAGGTAAGTATTCAA 60.239 38.462 19.57 0.00 0.00 2.69
4351 4828 5.238432 CCGCATGCAATTAGGTAAGTATTCA 59.762 40.000 19.57 0.00 0.00 2.57
4352 4829 5.334879 CCCGCATGCAATTAGGTAAGTATTC 60.335 44.000 19.57 0.00 0.00 1.75
4353 4830 4.518970 CCCGCATGCAATTAGGTAAGTATT 59.481 41.667 19.57 0.00 0.00 1.89
4354 4831 4.072131 CCCGCATGCAATTAGGTAAGTAT 58.928 43.478 19.57 0.00 0.00 2.12
4355 4832 3.134985 TCCCGCATGCAATTAGGTAAGTA 59.865 43.478 19.57 0.00 0.00 2.24
4356 4833 2.092646 TCCCGCATGCAATTAGGTAAGT 60.093 45.455 19.57 0.00 0.00 2.24
4357 4834 2.549754 CTCCCGCATGCAATTAGGTAAG 59.450 50.000 19.57 6.21 0.00 2.34
4358 4835 2.571212 CTCCCGCATGCAATTAGGTAA 58.429 47.619 19.57 0.08 0.00 2.85
4359 4836 1.813862 GCTCCCGCATGCAATTAGGTA 60.814 52.381 19.57 0.00 35.78 3.08
4502 4980 7.991084 ATACATCGAATGACATTGATGGAAT 57.009 32.000 26.57 20.80 41.89 3.01
4565 5043 3.221771 ACCCGCGGTACTTATGTGTATA 58.778 45.455 26.12 0.00 32.11 1.47
4582 5060 2.669569 CCAGCCACAGTTGACCCG 60.670 66.667 0.00 0.00 0.00 5.28
4605 5083 6.644248 AGTTAGGTTTGTAATGTCCCAAAC 57.356 37.500 6.69 6.69 46.06 2.93
4635 5113 8.821894 CAGTATAAGAACTAAGAAGATTGCCAC 58.178 37.037 0.00 0.00 0.00 5.01
4772 5250 9.733556 TTAACTCCTCAATGAGCTGTAAATAAA 57.266 29.630 4.40 0.00 35.72 1.40
4773 5251 9.733556 TTTAACTCCTCAATGAGCTGTAAATAA 57.266 29.630 4.40 0.00 35.72 1.40
4920 5398 1.661463 TGCAAGGGATCTTCTCCAGT 58.339 50.000 0.00 0.00 46.98 4.00
4953 5431 6.044682 GCATTTCCGGAATCTTGAAATTGAT 58.955 36.000 19.62 0.24 36.77 2.57
5320 5798 2.555732 ATGTCCCCTGCCATTCATTT 57.444 45.000 0.00 0.00 0.00 2.32
5656 6137 1.761449 TTGAAACTGAAGGCACAGCA 58.239 45.000 10.71 0.61 41.06 4.41
5808 6290 5.163416 GCAGTGCCCCTTCAATTTATGTAAT 60.163 40.000 2.85 0.00 0.00 1.89
5991 6473 3.002791 TGTGCGTCAGATTCAGAAATCC 58.997 45.455 0.00 0.00 41.97 3.01
6016 6498 5.932303 GTGCTTTACCTTCTCAGATGTTGTA 59.068 40.000 0.00 0.00 0.00 2.41
6095 6580 2.838736 CATATCGCCAGCTAGGTTTGT 58.161 47.619 0.00 0.00 40.61 2.83
6105 6590 1.707632 GAGCACTAGCATATCGCCAG 58.292 55.000 0.00 0.00 45.49 4.85
6120 6605 3.592898 TTAGCAATTCAGACTCGAGCA 57.407 42.857 13.61 0.00 0.00 4.26
6200 6685 3.430042 TCCTCTGCAGCTTCAGAAAAT 57.570 42.857 16.93 0.00 41.99 1.82
6215 6700 4.566488 CCTTTAATCACAGCAGGTTCCTCT 60.566 45.833 0.00 0.00 0.00 3.69
6231 6716 5.197451 TGCGGGTTTATCATCACCTTTAAT 58.803 37.500 0.00 0.00 33.09 1.40
6232 6717 4.590918 TGCGGGTTTATCATCACCTTTAA 58.409 39.130 0.00 0.00 33.09 1.52
6233 6718 4.080807 TCTGCGGGTTTATCATCACCTTTA 60.081 41.667 0.00 0.00 33.09 1.85
6318 6803 0.108186 AAGAATCGCACCTCGCATGA 60.108 50.000 0.00 0.00 42.60 3.07
6338 6823 9.232473 GGAAGATTGTCTTGTTTTAATAGAGGT 57.768 33.333 0.00 0.00 36.73 3.85
6344 6829 8.237811 ACACAGGAAGATTGTCTTGTTTTAAT 57.762 30.769 0.00 0.00 36.73 1.40
6462 7089 2.378084 GCTTTCGTTCGGTCGACCC 61.378 63.158 28.52 13.88 39.58 4.46
6742 7369 2.672961 ACGCATGTAGTGTGCACTAT 57.327 45.000 19.41 9.00 44.73 2.12
6929 7556 3.428725 CCTCCTCGATTCTCAGACAAGTG 60.429 52.174 0.00 0.00 0.00 3.16
7244 7871 7.804712 CAAATAAATTTGCCAGCAAACACATA 58.195 30.769 19.29 10.58 46.80 2.29
7267 7894 2.097791 GGAAAACTTGCCGTGTGTACAA 59.902 45.455 0.00 0.00 0.00 2.41
7313 7940 1.737793 GGAGGTCTGGTTGTAAATGCG 59.262 52.381 0.00 0.00 0.00 4.73
7318 7945 3.773119 GAGTATGGGAGGTCTGGTTGTAA 59.227 47.826 0.00 0.00 0.00 2.41
7326 7953 0.106116 GGGACGAGTATGGGAGGTCT 60.106 60.000 0.00 0.00 0.00 3.85
7366 7993 2.715749 AATCATCCGAGCAATGACCA 57.284 45.000 0.00 0.00 36.04 4.02
7369 7996 2.613595 CCGAAAATCATCCGAGCAATGA 59.386 45.455 0.00 0.00 37.53 2.57
7377 8004 1.724582 GGGTGGCCGAAAATCATCCG 61.725 60.000 0.00 0.00 0.00 4.18
7378 8005 0.682855 TGGGTGGCCGAAAATCATCC 60.683 55.000 0.00 0.00 32.55 3.51
7401 8028 2.609610 GGTAGGTGTGGGGAGCCA 60.610 66.667 0.00 0.00 0.00 4.75
7419 8046 2.281484 GCCAGCCCAGACGTTTGA 60.281 61.111 7.81 0.00 0.00 2.69
7452 8079 0.965866 CCGCCCTAGATATGAGCCGA 60.966 60.000 0.00 0.00 0.00 5.54
7501 8128 1.639298 GCCATTGCGGTCAGTCTGAC 61.639 60.000 22.61 22.61 46.23 3.51
7524 8151 2.029244 GCGATCTATTTGTGTGACCGTG 59.971 50.000 0.00 0.00 0.00 4.94
7525 8152 2.094182 AGCGATCTATTTGTGTGACCGT 60.094 45.455 0.00 0.00 0.00 4.83
7545 8172 4.421479 AGGCGCTCGTCGAACCAG 62.421 66.667 7.64 0.00 41.67 4.00
7550 8177 3.889044 GATGGAGGCGCTCGTCGA 61.889 66.667 7.64 0.00 41.67 4.20
7698 8326 3.449227 TAGCGGCAGACAGGTCGG 61.449 66.667 1.45 0.00 36.17 4.79


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

AutoCloner maintained by Alex Coulton.