Multiple sequence alignment - TraesCS5A01G203500

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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 TraesCS5A01G203500 chr5A 100.000 5046 0 0 1 5046 413040252 413045297 0.000000e+00 9319.0
1 TraesCS5A01G203500 chr5A 74.372 597 137 14 1350 1938 238694896 238695484 1.820000e-59 241.0
2 TraesCS5A01G203500 chr5D 91.779 5109 171 95 21 5046 318440880 318445822 0.000000e+00 6878.0
3 TraesCS5A01G203500 chr5D 75.209 597 132 13 1350 1938 204075212 204075800 8.330000e-68 268.0
4 TraesCS5A01G203500 chr5D 85.882 85 6 1 4324 4402 125171177 125171261 9.000000e-13 86.1
5 TraesCS5A01G203500 chr5B 92.674 3126 138 40 46 3135 368485180 368488250 0.000000e+00 4420.0
6 TraesCS5A01G203500 chr5B 91.088 1066 61 17 3154 4192 368488208 368489266 0.000000e+00 1411.0
7 TraesCS5A01G203500 chr5B 85.973 442 31 8 4467 4898 368489795 368490215 1.290000e-120 444.0
8 TraesCS5A01G203500 chr5B 74.874 597 134 13 1350 1938 208258255 208258843 1.800000e-64 257.0
9 TraesCS5A01G203500 chr5B 88.679 106 7 3 4944 5046 368490534 368490637 1.910000e-24 124.0
10 TraesCS5A01G203500 chr5B 83.582 134 14 3 4290 4416 589034290 589034158 8.870000e-23 119.0
11 TraesCS5A01G203500 chr5B 84.034 119 13 1 4290 4402 92034998 92034880 5.340000e-20 110.0
12 TraesCS5A01G203500 chr5B 96.875 32 1 0 4915 4946 368490217 368490248 3.000000e-03 54.7
13 TraesCS5A01G203500 chr4D 80.180 222 36 8 3635 3852 402210766 402210983 5.230000e-35 159.0
14 TraesCS5A01G203500 chr4A 79.279 222 38 5 3635 3852 59484182 59484399 1.130000e-31 148.0
15 TraesCS5A01G203500 chr4B 78.667 225 40 5 3635 3855 497554113 497554333 5.270000e-30 143.0
16 TraesCS5A01G203500 chr2B 87.288 118 10 1 4290 4402 173057130 173057247 4.100000e-26 130.0
17 TraesCS5A01G203500 chr2B 83.929 112 12 2 4290 4395 429948251 429948362 8.940000e-18 102.0
18 TraesCS5A01G203500 chr7D 86.555 119 10 1 4290 4402 78414164 78414046 5.300000e-25 126.0
19 TraesCS5A01G203500 chr1D 84.874 119 12 1 4290 4402 406518693 406518811 1.150000e-21 115.0
20 TraesCS5A01G203500 chr7B 84.167 120 11 3 4290 4402 290305831 290305713 5.340000e-20 110.0
21 TraesCS5A01G203500 chr3B 83.036 112 13 2 4290 4395 315294631 315294742 4.160000e-16 97.1


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 TraesCS5A01G203500 chr5A 413040252 413045297 5045 False 9319.00 9319 100.0000 1 5046 1 chr5A.!!$F2 5045
1 TraesCS5A01G203500 chr5A 238694896 238695484 588 False 241.00 241 74.3720 1350 1938 1 chr5A.!!$F1 588
2 TraesCS5A01G203500 chr5D 318440880 318445822 4942 False 6878.00 6878 91.7790 21 5046 1 chr5D.!!$F3 5025
3 TraesCS5A01G203500 chr5D 204075212 204075800 588 False 268.00 268 75.2090 1350 1938 1 chr5D.!!$F2 588
4 TraesCS5A01G203500 chr5B 368485180 368490637 5457 False 1290.74 4420 91.0578 46 5046 5 chr5B.!!$F2 5000
5 TraesCS5A01G203500 chr5B 208258255 208258843 588 False 257.00 257 74.8740 1350 1938 1 chr5B.!!$F1 588

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
569 605 0.034337 CGAGTTTCCCCGGAGTTTCA 59.966 55.0 0.73 0.0 0.00 2.69 F
845 881 0.175760 TTGCCTCGCTAAATCTCGCT 59.824 50.0 0.00 0.0 0.00 4.93 F
2211 2247 0.259065 GGGGGAAGGGAAAGGATGTC 59.741 60.0 0.00 0.0 0.00 3.06 F
2866 2902 0.104855 TGATGGTACGCTGATGCCTC 59.895 55.0 0.00 0.0 35.36 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1689 0.739813 GATGGTAGTCGTGCACCCAC 60.740 60.0 12.15 8.41 38.62 4.61 R
2796 2832 0.039180 TCCGGTAGGCTGAGACAAGA 59.961 55.0 0.00 0.00 37.47 3.02 R
3621 3665 0.031178 CACCCTGCAGTGCAAAGAAC 59.969 55.0 20.22 0.00 38.41 3.01 R
4668 5170 0.036875 AGCACCTGACCTACTTTGCC 59.963 55.0 0.00 0.00 0.00 4.52 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
24 25 4.471908 ATGCACGCAGGCGGATCA 62.472 61.111 18.63 12.11 44.69 2.92
30 31 2.743752 CGCAGGCGGATCACTTGTG 61.744 63.158 5.63 0.00 35.56 3.33
42 43 4.378874 GGATCACTTGTGCTGTAAGAAAGC 60.379 45.833 0.00 0.00 41.22 3.51
43 44 2.878406 TCACTTGTGCTGTAAGAAAGCC 59.122 45.455 0.00 0.00 40.06 4.35
44 45 2.618241 CACTTGTGCTGTAAGAAAGCCA 59.382 45.455 0.00 0.00 40.06 4.75
57 58 1.332997 GAAAGCCAGAGCATTGATCGG 59.667 52.381 7.97 7.97 43.56 4.18
59 60 3.741860 CCAGAGCATTGATCGGGC 58.258 61.111 8.14 0.00 0.00 6.13
85 86 2.108952 GGATAATGCTGATCCCTTGGGT 59.891 50.000 5.51 0.00 37.49 4.51
86 87 3.416156 GATAATGCTGATCCCTTGGGTC 58.584 50.000 5.51 3.82 32.52 4.46
87 88 0.107017 AATGCTGATCCCTTGGGTCG 60.107 55.000 5.51 2.06 35.15 4.79
88 89 1.987807 ATGCTGATCCCTTGGGTCGG 61.988 60.000 5.51 8.71 41.88 4.79
99 100 1.480212 TTGGGTCGGTCAGTCAGCAT 61.480 55.000 0.00 0.00 0.00 3.79
100 101 0.613572 TGGGTCGGTCAGTCAGCATA 60.614 55.000 0.00 0.00 0.00 3.14
102 103 0.103208 GGTCGGTCAGTCAGCATAGG 59.897 60.000 0.00 0.00 0.00 2.57
119 120 0.243907 AGGCGACGATTATCCATCCG 59.756 55.000 0.00 0.00 0.00 4.18
141 142 0.098728 CCGGAAACAAATAGCGCCAG 59.901 55.000 2.29 0.00 0.00 4.85
145 146 0.243636 AAACAAATAGCGCCAGTGGC 59.756 50.000 25.07 25.07 46.75 5.01
160 161 3.128242 CCAGTGGCTTGTCATGAATTCTC 59.872 47.826 7.05 0.00 0.00 2.87
168 169 1.329906 GTCATGAATTCTCTGGCTGCG 59.670 52.381 7.05 0.00 0.00 5.18
184 185 2.433664 CGGTTAGGTGGACGGCAC 60.434 66.667 0.00 0.00 0.00 5.01
211 234 0.457166 CGAGACGCCCGTGTTTATCA 60.457 55.000 0.00 0.00 0.00 2.15
290 313 0.654683 GGCATCGCAGAGTTCATCAC 59.345 55.000 0.00 0.00 43.63 3.06
327 350 2.671963 AGCGGGGGCGAGAAAAAC 60.672 61.111 0.00 0.00 0.00 2.43
342 365 5.294552 CGAGAAAAACACTCTATCCATTCCC 59.705 44.000 0.00 0.00 32.87 3.97
356 379 2.418746 CCATTCCCGTTCCAGTCTAGTG 60.419 54.545 0.00 0.00 0.00 2.74
359 382 2.719739 TCCCGTTCCAGTCTAGTGTAG 58.280 52.381 0.00 0.00 0.00 2.74
361 384 3.264193 TCCCGTTCCAGTCTAGTGTAGTA 59.736 47.826 0.00 0.00 0.00 1.82
362 385 3.626670 CCCGTTCCAGTCTAGTGTAGTAG 59.373 52.174 0.00 0.00 0.00 2.57
364 387 4.332268 CCGTTCCAGTCTAGTGTAGTAGAC 59.668 50.000 15.77 15.77 46.47 2.59
400 423 0.458669 TCGCCTCCATTCCGTTACTC 59.541 55.000 0.00 0.00 0.00 2.59
401 424 0.529992 CGCCTCCATTCCGTTACTCC 60.530 60.000 0.00 0.00 0.00 3.85
409 432 3.488721 CCATTCCGTTACTCCTAGTCGTG 60.489 52.174 0.00 0.00 0.00 4.35
410 433 2.768253 TCCGTTACTCCTAGTCGTGA 57.232 50.000 0.00 0.00 0.00 4.35
411 434 3.272574 TCCGTTACTCCTAGTCGTGAT 57.727 47.619 0.00 0.00 0.00 3.06
412 435 4.406648 TCCGTTACTCCTAGTCGTGATA 57.593 45.455 0.00 0.00 0.00 2.15
427 454 6.285224 AGTCGTGATAGATAGATAGATCCCG 58.715 44.000 0.00 0.00 0.00 5.14
506 533 3.866582 CGCCTCCATCCACCTCCC 61.867 72.222 0.00 0.00 0.00 4.30
569 605 0.034337 CGAGTTTCCCCGGAGTTTCA 59.966 55.000 0.73 0.00 0.00 2.69
572 608 0.536460 GTTTCCCCGGAGTTTCAGCA 60.536 55.000 0.73 0.00 0.00 4.41
579 615 1.291877 CGGAGTTTCAGCAACCCTCG 61.292 60.000 0.00 0.00 35.77 4.63
586 622 2.048127 AGCAACCCTCGTTCGAGC 60.048 61.111 15.54 6.07 0.00 5.03
592 628 1.509703 ACCCTCGTTCGAGCTTTTTC 58.490 50.000 15.54 0.00 0.00 2.29
597 633 1.263217 TCGTTCGAGCTTTTTCTTGCC 59.737 47.619 0.00 0.00 0.00 4.52
708 744 2.974623 AGGAGCACCTGAGACTCTG 58.025 57.895 0.22 3.03 45.92 3.35
709 745 1.217779 GGAGCACCTGAGACTCTGC 59.782 63.158 3.68 5.57 0.00 4.26
710 746 1.217779 GAGCACCTGAGACTCTGCC 59.782 63.158 10.63 1.31 0.00 4.85
788 824 2.702270 AGGGGGAATTTGTTTCTGCT 57.298 45.000 0.00 0.00 34.56 4.24
845 881 0.175760 TTGCCTCGCTAAATCTCGCT 59.824 50.000 0.00 0.00 0.00 4.93
856 892 4.084797 GCTAAATCTCGCTCGGATTTCTTC 60.085 45.833 16.18 8.12 41.66 2.87
857 893 3.810310 AATCTCGCTCGGATTTCTTCT 57.190 42.857 0.00 0.00 30.26 2.85
858 894 2.853731 TCTCGCTCGGATTTCTTCTC 57.146 50.000 0.00 0.00 0.00 2.87
875 911 1.229853 TCCTTCCCCTTGGACTCCC 60.230 63.158 0.00 0.00 41.57 4.30
882 918 3.787001 CTTGGACTCCCTCCCGGC 61.787 72.222 0.00 0.00 38.49 6.13
895 931 3.204827 CCGGCCGCAGATCCTTTG 61.205 66.667 22.85 0.00 0.00 2.77
925 961 1.310933 CGCCCATTCTTGCTCTGCTT 61.311 55.000 0.00 0.00 0.00 3.91
927 963 1.954258 GCCCATTCTTGCTCTGCTTCT 60.954 52.381 0.00 0.00 0.00 2.85
931 967 3.127203 CCATTCTTGCTCTGCTTCTTCAG 59.873 47.826 0.00 0.00 35.46 3.02
1653 1689 2.711922 CCCCGAGGAGGACTTCGTG 61.712 68.421 0.00 0.00 45.00 4.35
1839 1875 3.005684 TGATTGGCTTCCACACATTTGAC 59.994 43.478 0.00 0.00 30.78 3.18
1920 1956 2.777692 GAGGGGATACATTGGACTGGAA 59.222 50.000 0.00 0.00 39.74 3.53
1973 2009 1.675552 CCGGTGGGGATACATTTGAC 58.324 55.000 0.00 0.00 38.47 3.18
2211 2247 0.259065 GGGGGAAGGGAAAGGATGTC 59.741 60.000 0.00 0.00 0.00 3.06
2307 2343 2.061773 GTCATATTGATCGACAGGCCG 58.938 52.381 0.00 0.00 0.00 6.13
2349 2385 3.689161 TGGCATACTATGTTGTTGCTGAC 59.311 43.478 0.00 0.00 33.86 3.51
2418 2454 4.063998 TGAGTACATCATTGCTAGGCAG 57.936 45.455 0.00 0.00 34.35 4.85
2866 2902 0.104855 TGATGGTACGCTGATGCCTC 59.895 55.000 0.00 0.00 35.36 4.70
2893 2929 0.733150 GTTTGGTAAGATGCCGAGCC 59.267 55.000 0.00 0.00 0.00 4.70
2896 2932 2.280186 GTAAGATGCCGAGCCCCG 60.280 66.667 0.00 0.00 38.18 5.73
2905 2941 1.436983 GCCGAGCCCCGAAACAATAG 61.437 60.000 0.00 0.00 41.76 1.73
2922 2958 5.072741 ACAATAGACATGTTGAACAGCCTT 58.927 37.500 3.74 0.00 32.31 4.35
2941 2977 2.432206 TTGTCGCGATGAGAAGAACA 57.568 45.000 14.06 0.00 0.00 3.18
2972 3008 1.228124 CAAGCACAAAGACCCGGGA 60.228 57.895 32.02 0.00 0.00 5.14
3068 3104 6.499106 AATTCCAACTGTTCCCTGAAAATT 57.501 33.333 0.00 0.00 0.00 1.82
3069 3105 5.529581 TTCCAACTGTTCCCTGAAAATTC 57.470 39.130 0.00 0.00 0.00 2.17
3102 3138 9.394477 GTACCTTCATTGTTGAAATGAAACTAC 57.606 33.333 12.96 10.98 43.55 2.73
3104 3140 9.349713 ACCTTCATTGTTGAAATGAAACTACTA 57.650 29.630 12.96 0.00 43.55 1.82
3105 3141 9.612620 CCTTCATTGTTGAAATGAAACTACTAC 57.387 33.333 12.96 0.00 43.55 2.73
3179 3215 6.774354 TGTTGAAACGAAACTACTATCACC 57.226 37.500 0.00 0.00 0.00 4.02
3211 3249 6.735678 TGTACTGCACATTTAACCTGTATG 57.264 37.500 0.00 0.00 30.04 2.39
3251 3289 2.094545 CCATTTTGCTGTAGGCTGGAAC 60.095 50.000 0.00 0.00 42.39 3.62
3281 3319 4.101448 GGGAGACATGCGGCCTGT 62.101 66.667 10.75 10.75 0.00 4.00
3379 3417 2.166459 CGAGGACAAGGAGACAGCAATA 59.834 50.000 0.00 0.00 0.00 1.90
3392 3430 1.660607 CAGCAATAGTGTGGTGCTACG 59.339 52.381 0.00 0.00 46.66 3.51
3400 3438 4.111016 TGGTGCTACGAGGACGCG 62.111 66.667 3.53 3.53 43.96 6.01
3405 3443 3.129502 CTACGAGGACGCGGACCA 61.130 66.667 22.50 5.13 43.96 4.02
3533 3571 2.293399 CCACAGGTAAAGTTTGGCTGAC 59.707 50.000 0.00 0.00 0.00 3.51
3595 3637 2.941333 CGCCACTGCACTTCTGTG 59.059 61.111 0.00 0.00 46.37 3.66
3621 3665 1.878953 ACAACACTAAGCCAGGAACG 58.121 50.000 0.00 0.00 0.00 3.95
3855 3909 2.505819 CAAGGCCAAGTACTACCTGGAT 59.494 50.000 15.03 1.22 31.32 3.41
3858 3912 2.103263 GGCCAAGTACTACCTGGATGAG 59.897 54.545 15.03 0.00 0.00 2.90
4016 4088 4.475135 GGGGAAGCCGGCAGAGAC 62.475 72.222 31.54 14.35 0.00 3.36
4144 4229 6.195983 CGTTGTGTATATAGACTCCGTTGAAC 59.804 42.308 11.01 4.82 0.00 3.18
4244 4710 5.947503 TTTGAAACAATGCACTTTCTTCG 57.052 34.783 12.27 0.00 0.00 3.79
4245 4711 3.371168 TGAAACAATGCACTTTCTTCGC 58.629 40.909 12.27 0.00 0.00 4.70
4246 4712 3.066621 TGAAACAATGCACTTTCTTCGCT 59.933 39.130 12.27 0.00 0.00 4.93
4247 4713 3.715628 AACAATGCACTTTCTTCGCTT 57.284 38.095 0.00 0.00 0.00 4.68
4248 4714 3.715628 ACAATGCACTTTCTTCGCTTT 57.284 38.095 0.00 0.00 0.00 3.51
4249 4715 4.045636 ACAATGCACTTTCTTCGCTTTT 57.954 36.364 0.00 0.00 0.00 2.27
4250 4716 4.432712 ACAATGCACTTTCTTCGCTTTTT 58.567 34.783 0.00 0.00 0.00 1.94
4295 4775 2.297701 GTTGGTCTGAGAACTTGGCAA 58.702 47.619 0.00 0.00 0.00 4.52
4323 4803 2.925706 TTCGCACCCAGCCCACTA 60.926 61.111 0.00 0.00 41.38 2.74
4337 4817 1.130749 CCCACTAGTGTTCGAGTCTCG 59.869 57.143 21.18 16.33 42.10 4.04
4356 4836 4.504916 CTCGAGCGCCTGGTGGAG 62.505 72.222 2.29 3.61 41.07 3.86
4395 4881 0.103208 CCAACAGCCTAGTCTAGCCG 59.897 60.000 0.86 0.00 0.00 5.52
4396 4882 0.103208 CAACAGCCTAGTCTAGCCGG 59.897 60.000 0.00 0.00 0.00 6.13
4432 4925 1.730772 CGTTGGTCTTGCTCTCTCTCG 60.731 57.143 0.00 0.00 0.00 4.04
4470 4963 2.997315 CCTGGCCGAGTGGAGTGA 60.997 66.667 0.00 0.00 37.49 3.41
4487 4980 1.202114 GTGAAGGCGCCAATGATTTCA 59.798 47.619 31.54 24.42 0.00 2.69
4488 4981 1.473677 TGAAGGCGCCAATGATTTCAG 59.526 47.619 31.54 0.00 0.00 3.02
4600 5101 8.488651 TTTCGGATAAGAAACAGGATTAGAAC 57.511 34.615 0.00 0.00 35.44 3.01
4611 5112 4.192317 CAGGATTAGAACTAGGTGTTGCC 58.808 47.826 0.00 0.00 39.30 4.52
4619 5121 0.593128 CTAGGTGTTGCCACTGTTGC 59.407 55.000 0.00 0.00 41.53 4.17
4665 5167 1.282653 TTTGTCACTGGTGGGGGTGA 61.283 55.000 0.70 0.00 39.71 4.02
4668 5170 1.536418 TCACTGGTGGGGGTGAGAG 60.536 63.158 0.70 0.00 37.52 3.20
4670 5172 3.721706 CTGGTGGGGGTGAGAGGC 61.722 72.222 0.00 0.00 0.00 4.70
4672 5174 3.256960 GGTGGGGGTGAGAGGCAA 61.257 66.667 0.00 0.00 0.00 4.52
4744 5248 4.619227 CGCAGTCGGGTTGGTGGT 62.619 66.667 0.00 0.00 0.00 4.16
4745 5249 2.203294 GCAGTCGGGTTGGTGGTT 60.203 61.111 0.00 0.00 0.00 3.67
4746 5250 1.071814 GCAGTCGGGTTGGTGGTTA 59.928 57.895 0.00 0.00 0.00 2.85
4747 5251 1.232621 GCAGTCGGGTTGGTGGTTAC 61.233 60.000 0.00 0.00 0.00 2.50
4750 5254 0.668401 GTCGGGTTGGTGGTTACTCG 60.668 60.000 0.00 0.00 39.54 4.18
4812 5316 4.321601 GCCATGCCATGTCTAGTCTACTAG 60.322 50.000 10.35 10.35 45.57 2.57
4813 5317 4.830046 CCATGCCATGTCTAGTCTACTAGT 59.170 45.833 15.06 0.00 44.74 2.57
4814 5318 6.004574 CCATGCCATGTCTAGTCTACTAGTA 58.995 44.000 15.06 1.89 44.74 1.82
4815 5319 6.661377 CCATGCCATGTCTAGTCTACTAGTAT 59.339 42.308 15.06 9.39 44.74 2.12
4816 5320 7.829706 CCATGCCATGTCTAGTCTACTAGTATA 59.170 40.741 15.06 0.00 44.74 1.47
4817 5321 8.888716 CATGCCATGTCTAGTCTACTAGTATAG 58.111 40.741 15.06 3.05 44.74 1.31
4865 5370 2.305009 CAAATGGCCAAGAGAGATCCC 58.695 52.381 10.96 0.00 0.00 3.85
4883 5388 1.699054 CCCTGCCAGATCGGATTGGA 61.699 60.000 17.73 1.77 36.55 3.53
4898 5403 1.949799 TTGGATTGGATTGGGTTGGG 58.050 50.000 0.00 0.00 0.00 4.12
4899 5404 0.789687 TGGATTGGATTGGGTTGGGT 59.210 50.000 0.00 0.00 0.00 4.51
4900 5405 1.150986 TGGATTGGATTGGGTTGGGTT 59.849 47.619 0.00 0.00 0.00 4.11
4901 5406 1.554617 GGATTGGATTGGGTTGGGTTG 59.445 52.381 0.00 0.00 0.00 3.77
4902 5407 1.554617 GATTGGATTGGGTTGGGTTGG 59.445 52.381 0.00 0.00 0.00 3.77
4903 5408 0.472734 TTGGATTGGGTTGGGTTGGG 60.473 55.000 0.00 0.00 0.00 4.12
4904 5409 1.157513 GGATTGGGTTGGGTTGGGT 59.842 57.895 0.00 0.00 0.00 4.51
4905 5410 0.472925 GGATTGGGTTGGGTTGGGTT 60.473 55.000 0.00 0.00 0.00 4.11
4906 5411 0.684535 GATTGGGTTGGGTTGGGTTG 59.315 55.000 0.00 0.00 0.00 3.77
4907 5412 0.266152 ATTGGGTTGGGTTGGGTTGA 59.734 50.000 0.00 0.00 0.00 3.18
4909 5414 0.470833 TGGGTTGGGTTGGGTTGATG 60.471 55.000 0.00 0.00 0.00 3.07
4910 5415 1.671166 GGTTGGGTTGGGTTGATGC 59.329 57.895 0.00 0.00 0.00 3.91
4911 5416 1.118356 GGTTGGGTTGGGTTGATGCA 61.118 55.000 0.00 0.00 0.00 3.96
4912 5417 0.755686 GTTGGGTTGGGTTGATGCAA 59.244 50.000 0.00 0.00 0.00 4.08
4913 5418 1.047002 TTGGGTTGGGTTGATGCAAG 58.953 50.000 0.00 0.00 0.00 4.01
4914 5419 0.831288 TGGGTTGGGTTGATGCAAGG 60.831 55.000 0.00 0.00 0.00 3.61
4915 5420 1.293179 GGTTGGGTTGATGCAAGGC 59.707 57.895 0.00 0.00 0.00 4.35
4916 5421 1.470996 GGTTGGGTTGATGCAAGGCA 61.471 55.000 0.00 0.00 44.86 4.75
4917 5422 0.392336 GTTGGGTTGATGCAAGGCAA 59.608 50.000 0.00 0.00 43.62 4.52
4918 5423 1.126488 TTGGGTTGATGCAAGGCAAA 58.874 45.000 0.00 0.00 43.62 3.68
4919 5424 0.680618 TGGGTTGATGCAAGGCAAAG 59.319 50.000 0.00 0.00 43.62 2.77
4920 5425 0.671472 GGGTTGATGCAAGGCAAAGC 60.671 55.000 0.00 0.00 43.62 3.51
4930 5435 2.962569 GGCAAAGCCTTCCGGTTC 59.037 61.111 0.00 0.00 46.69 3.62
4931 5436 2.561373 GCAAAGCCTTCCGGTTCG 59.439 61.111 0.00 0.00 0.00 3.95
4932 5437 2.258726 GCAAAGCCTTCCGGTTCGT 61.259 57.895 0.00 0.00 0.00 3.85
4933 5438 1.574428 CAAAGCCTTCCGGTTCGTG 59.426 57.895 0.00 0.00 0.00 4.35
4960 5763 7.792032 TGGTTAGGTTAATGAATCTACTCCAG 58.208 38.462 3.31 0.00 32.24 3.86
4973 5776 1.302832 CTCCAGGGTGGTGTTGCTC 60.303 63.158 0.00 0.00 39.03 4.26
4974 5777 1.770110 TCCAGGGTGGTGTTGCTCT 60.770 57.895 0.00 0.00 39.03 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.945434 GATCCGCCTGCGTGCATG 61.945 66.667 10.94 0.09 37.81 4.06
7 8 4.471908 TGATCCGCCTGCGTGCAT 62.472 61.111 10.94 0.00 37.81 3.96
10 11 2.434884 AAGTGATCCGCCTGCGTG 60.435 61.111 10.94 2.41 37.81 5.34
11 12 2.434884 CAAGTGATCCGCCTGCGT 60.435 61.111 10.94 0.00 37.81 5.24
12 13 2.434884 ACAAGTGATCCGCCTGCG 60.435 61.111 4.20 4.20 39.44 5.18
13 14 3.044059 GCACAAGTGATCCGCCTGC 62.044 63.158 4.04 0.00 0.00 4.85
14 15 1.376424 AGCACAAGTGATCCGCCTG 60.376 57.895 4.04 0.00 0.00 4.85
15 16 1.376424 CAGCACAAGTGATCCGCCT 60.376 57.895 4.04 0.00 0.00 5.52
16 17 0.391130 TACAGCACAAGTGATCCGCC 60.391 55.000 4.04 0.00 0.00 6.13
17 18 1.394917 CTTACAGCACAAGTGATCCGC 59.605 52.381 4.04 0.00 0.00 5.54
18 19 2.959516 TCTTACAGCACAAGTGATCCG 58.040 47.619 4.04 0.00 0.00 4.18
19 20 4.378874 GCTTTCTTACAGCACAAGTGATCC 60.379 45.833 4.04 0.00 37.22 3.36
24 25 2.880890 CTGGCTTTCTTACAGCACAAGT 59.119 45.455 0.00 0.00 39.21 3.16
30 31 1.813513 TGCTCTGGCTTTCTTACAGC 58.186 50.000 0.00 0.00 39.59 4.40
42 43 2.249535 CGCCCGATCAATGCTCTGG 61.250 63.158 0.00 0.00 0.00 3.86
43 44 2.249535 CCGCCCGATCAATGCTCTG 61.250 63.158 0.00 0.00 0.00 3.35
44 45 1.762522 ATCCGCCCGATCAATGCTCT 61.763 55.000 0.00 0.00 0.00 4.09
57 58 2.012673 GATCAGCATTATCCATCCGCC 58.987 52.381 0.00 0.00 0.00 6.13
59 60 2.238144 AGGGATCAGCATTATCCATCCG 59.762 50.000 12.41 0.00 44.08 4.18
85 86 1.816537 GCCTATGCTGACTGACCGA 59.183 57.895 0.00 0.00 33.53 4.69
86 87 1.589993 CGCCTATGCTGACTGACCG 60.590 63.158 0.00 0.00 34.43 4.79
87 88 0.528684 GTCGCCTATGCTGACTGACC 60.529 60.000 7.39 0.00 37.74 4.02
88 89 0.867753 CGTCGCCTATGCTGACTGAC 60.868 60.000 11.02 1.10 38.22 3.51
99 100 1.471287 CGGATGGATAATCGTCGCCTA 59.529 52.381 0.00 0.00 35.99 3.93
100 101 0.243907 CGGATGGATAATCGTCGCCT 59.756 55.000 0.00 0.00 35.99 5.52
102 103 1.337821 GACGGATGGATAATCGTCGC 58.662 55.000 0.00 0.00 35.99 5.19
119 120 0.098200 GCGCTATTTGTTTCCGGGAC 59.902 55.000 0.00 1.11 0.00 4.46
141 142 3.128242 CCAGAGAATTCATGACAAGCCAC 59.872 47.826 8.44 0.00 0.00 5.01
145 146 3.181499 GCAGCCAGAGAATTCATGACAAG 60.181 47.826 8.44 0.00 0.00 3.16
160 161 2.436646 CCACCTAACCGCAGCCAG 60.437 66.667 0.00 0.00 0.00 4.85
168 169 2.433664 CGTGCCGTCCACCTAACC 60.434 66.667 0.00 0.00 41.53 2.85
195 218 0.725117 CCTTGATAAACACGGGCGTC 59.275 55.000 0.00 0.00 34.75 5.19
314 337 2.467566 TAGAGTGTTTTTCTCGCCCC 57.532 50.000 0.00 0.00 37.07 5.80
327 350 2.434336 TGGAACGGGAATGGATAGAGTG 59.566 50.000 0.00 0.00 0.00 3.51
342 365 5.467902 GTCTACTACACTAGACTGGAACG 57.532 47.826 0.00 0.00 39.69 3.95
356 379 7.604549 AGGCTTTTGTTTCTCTAGTCTACTAC 58.395 38.462 0.00 0.00 0.00 2.73
359 382 5.573669 CGAGGCTTTTGTTTCTCTAGTCTAC 59.426 44.000 0.00 0.00 0.00 2.59
361 384 4.561105 CGAGGCTTTTGTTTCTCTAGTCT 58.439 43.478 0.00 0.00 0.00 3.24
362 385 3.123790 GCGAGGCTTTTGTTTCTCTAGTC 59.876 47.826 0.00 0.00 0.00 2.59
364 387 2.416893 GGCGAGGCTTTTGTTTCTCTAG 59.583 50.000 0.00 0.00 0.00 2.43
400 423 7.876068 GGGATCTATCTATCTATCACGACTAGG 59.124 44.444 0.00 0.00 0.00 3.02
401 424 7.597369 CGGGATCTATCTATCTATCACGACTAG 59.403 44.444 0.00 0.00 45.71 2.57
409 432 4.083565 GGGGCGGGATCTATCTATCTATC 58.916 52.174 0.00 0.00 0.00 2.08
410 433 3.498841 CGGGGCGGGATCTATCTATCTAT 60.499 52.174 0.00 0.00 0.00 1.98
411 434 2.158652 CGGGGCGGGATCTATCTATCTA 60.159 54.545 0.00 0.00 0.00 1.98
412 435 1.410365 CGGGGCGGGATCTATCTATCT 60.410 57.143 0.00 0.00 0.00 1.98
487 514 4.554036 GAGGTGGATGGAGGCGGC 62.554 72.222 0.00 0.00 0.00 6.53
492 519 3.866582 GGCGGGAGGTGGATGGAG 61.867 72.222 0.00 0.00 0.00 3.86
521 548 1.306226 AAAGACGGAGGAGGGAGGG 60.306 63.158 0.00 0.00 0.00 4.30
569 605 2.048127 GCTCGAACGAGGGTTGCT 60.048 61.111 22.44 0.00 42.19 3.91
572 608 1.871676 GAAAAAGCTCGAACGAGGGTT 59.128 47.619 22.44 13.32 42.19 4.11
579 615 1.663161 CCGGCAAGAAAAAGCTCGAAC 60.663 52.381 0.00 0.00 0.00 3.95
586 622 3.674753 CAGCATTAACCGGCAAGAAAAAG 59.325 43.478 0.00 0.00 0.00 2.27
592 628 0.451783 GACCAGCATTAACCGGCAAG 59.548 55.000 0.00 0.00 0.00 4.01
597 633 0.748005 CCCAGGACCAGCATTAACCG 60.748 60.000 0.00 0.00 0.00 4.44
730 766 0.881796 CTTTCGGTCAAAGGGAAGGC 59.118 55.000 0.00 0.00 38.32 4.35
788 824 1.878102 GCAAAGGAAGTCGCCAGAAGA 60.878 52.381 0.00 0.00 0.00 2.87
845 881 1.838077 GGGGAAGGAGAAGAAATCCGA 59.162 52.381 0.00 0.00 42.02 4.55
882 918 1.821332 GGAGGCAAAGGATCTGCGG 60.821 63.158 0.00 0.00 40.88 5.69
952 988 3.378112 CCAACAAACTCAGCAAGAACTCA 59.622 43.478 0.00 0.00 0.00 3.41
1653 1689 0.739813 GATGGTAGTCGTGCACCCAC 60.740 60.000 12.15 8.41 38.62 4.61
1920 1956 4.649674 ACAGTGACAGTCCGTCCATAATAT 59.350 41.667 0.00 0.00 44.71 1.28
2190 2226 1.083912 ACATCCTTTCCCTTCCCCCTA 59.916 52.381 0.00 0.00 0.00 3.53
2211 2247 2.102252 GCTCTCATCCTGTACCTCCTTG 59.898 54.545 0.00 0.00 0.00 3.61
2307 2343 3.391965 CATCCTCTCATAGAAGTGCAGC 58.608 50.000 0.00 0.00 0.00 5.25
2349 2385 3.730761 GCGGTCACCAAGCAGCAG 61.731 66.667 0.00 0.00 0.00 4.24
2418 2454 3.200825 TCCTGTCAATCTTCTCATTCCCC 59.799 47.826 0.00 0.00 0.00 4.81
2726 2762 3.884037 ACCTTAGCCCAAATCCTATGG 57.116 47.619 0.00 0.00 35.86 2.74
2796 2832 0.039180 TCCGGTAGGCTGAGACAAGA 59.961 55.000 0.00 0.00 37.47 3.02
2866 2902 4.672542 CGGCATCTTACCAAACAATGACTG 60.673 45.833 0.00 0.00 0.00 3.51
2873 2909 1.448985 GCTCGGCATCTTACCAAACA 58.551 50.000 0.00 0.00 0.00 2.83
2893 2929 5.049060 TGTTCAACATGTCTATTGTTTCGGG 60.049 40.000 0.00 0.00 35.18 5.14
2896 2932 5.858581 GGCTGTTCAACATGTCTATTGTTTC 59.141 40.000 0.00 0.00 35.18 2.78
2905 2941 3.632189 GACAAAGGCTGTTCAACATGTC 58.368 45.455 0.00 5.65 38.84 3.06
2922 2958 2.432206 TGTTCTTCTCATCGCGACAA 57.568 45.000 12.93 0.43 0.00 3.18
2941 2977 2.710377 TGTGCTTGCGATTAAGACCAT 58.290 42.857 0.00 0.00 0.00 3.55
2972 3008 5.799213 CTGAGAACCATTCACTTAAGGTCT 58.201 41.667 7.53 0.00 32.05 3.85
3110 3146 9.956640 ACAGTACAAAGTCATAGTAGTAGTAGT 57.043 33.333 0.00 0.00 0.00 2.73
3113 3149 9.730705 TGTACAGTACAAAGTCATAGTAGTAGT 57.269 33.333 11.21 0.00 35.38 2.73
3143 3179 9.021863 GTTTCGTTTCAACAATGGTGTTAATTA 57.978 29.630 0.00 0.00 46.47 1.40
3179 3215 4.818534 AATGTGCAGTACAAAGTCAGTG 57.181 40.909 0.00 0.00 43.77 3.66
3211 3249 8.707839 CAAAATGGTGTTAATTGGAATGTACAC 58.292 33.333 0.00 0.00 34.96 2.90
3251 3289 1.137675 TGTCTCCCATTCTGCATCTCG 59.862 52.381 0.00 0.00 0.00 4.04
3281 3319 3.117491 CTTCCAGCTGAAGTCTGTTGA 57.883 47.619 17.39 0.00 44.59 3.18
3309 3347 1.596934 GTCTTCATCACCGGCTCCA 59.403 57.895 0.00 0.00 0.00 3.86
3379 3417 1.863662 CGTCCTCGTAGCACCACACT 61.864 60.000 0.00 0.00 0.00 3.55
3392 3430 0.462047 AAATCATGGTCCGCGTCCTC 60.462 55.000 16.35 0.00 0.00 3.71
3400 3438 3.181472 GGCAAGATCCAAAATCATGGTCC 60.181 47.826 0.00 0.00 41.46 4.46
3405 3443 2.433239 GCCTGGCAAGATCCAAAATCAT 59.567 45.455 15.17 0.00 35.36 2.45
3463 3501 1.753930 TGACTGATACCGGCTCGTTA 58.246 50.000 0.00 0.00 0.00 3.18
3494 3532 2.744202 GTGGCTTCACCTCAACATAGTG 59.256 50.000 0.00 0.00 40.22 2.74
3595 3637 3.191371 CCTGGCTTAGTGTTGTTTCCATC 59.809 47.826 0.00 0.00 0.00 3.51
3621 3665 0.031178 CACCCTGCAGTGCAAAGAAC 59.969 55.000 20.22 0.00 38.41 3.01
3855 3909 3.664025 CTTGATGTCGGCGGGCTCA 62.664 63.158 7.21 4.51 0.00 4.26
4144 4229 9.917129 AATTTTTAGTCGGTAATTTAACCAAGG 57.083 29.630 0.00 0.00 39.71 3.61
4227 4693 3.715628 AAGCGAAGAAAGTGCATTGTT 57.284 38.095 0.00 0.00 0.00 2.83
4250 4716 9.174166 ACAGCAAAGAAAGAGTAGTTCTAAAAA 57.826 29.630 0.00 0.00 34.19 1.94
4251 4717 8.732746 ACAGCAAAGAAAGAGTAGTTCTAAAA 57.267 30.769 0.00 0.00 34.19 1.52
4252 4718 8.612619 CAACAGCAAAGAAAGAGTAGTTCTAAA 58.387 33.333 0.00 0.00 34.19 1.85
4253 4719 7.226720 CCAACAGCAAAGAAAGAGTAGTTCTAA 59.773 37.037 0.00 0.00 34.19 2.10
4254 4720 6.706270 CCAACAGCAAAGAAAGAGTAGTTCTA 59.294 38.462 0.00 0.00 34.19 2.10
4255 4721 5.529060 CCAACAGCAAAGAAAGAGTAGTTCT 59.471 40.000 0.00 0.00 36.90 3.01
4256 4722 5.297029 ACCAACAGCAAAGAAAGAGTAGTTC 59.703 40.000 0.00 0.00 0.00 3.01
4257 4723 5.193679 ACCAACAGCAAAGAAAGAGTAGTT 58.806 37.500 0.00 0.00 0.00 2.24
4258 4724 4.781934 ACCAACAGCAAAGAAAGAGTAGT 58.218 39.130 0.00 0.00 0.00 2.73
4259 4725 5.049818 CAGACCAACAGCAAAGAAAGAGTAG 60.050 44.000 0.00 0.00 0.00 2.57
4260 4726 4.816385 CAGACCAACAGCAAAGAAAGAGTA 59.184 41.667 0.00 0.00 0.00 2.59
4261 4727 3.629398 CAGACCAACAGCAAAGAAAGAGT 59.371 43.478 0.00 0.00 0.00 3.24
4262 4728 3.879295 TCAGACCAACAGCAAAGAAAGAG 59.121 43.478 0.00 0.00 0.00 2.85
4263 4729 3.879295 CTCAGACCAACAGCAAAGAAAGA 59.121 43.478 0.00 0.00 0.00 2.52
4323 4803 1.877367 GAGCCGAGACTCGAACACT 59.123 57.895 26.11 16.23 43.74 3.55
4383 4869 1.765230 ACAACTCCGGCTAGACTAGG 58.235 55.000 11.48 0.00 0.00 3.02
4460 4953 2.435059 GGCGCCTTCACTCCACTC 60.435 66.667 22.15 0.00 0.00 3.51
4462 4955 1.675641 ATTGGCGCCTTCACTCCAC 60.676 57.895 29.70 0.00 0.00 4.02
4463 4956 1.675310 CATTGGCGCCTTCACTCCA 60.675 57.895 29.70 0.07 0.00 3.86
4464 4957 0.749454 ATCATTGGCGCCTTCACTCC 60.749 55.000 29.70 0.00 0.00 3.85
4465 4958 1.098050 AATCATTGGCGCCTTCACTC 58.902 50.000 29.70 0.00 0.00 3.51
4470 4963 0.174162 GCTGAAATCATTGGCGCCTT 59.826 50.000 29.70 12.63 0.00 4.35
4503 4996 1.522806 AGCACGAGCCGAAACACAA 60.523 52.632 0.00 0.00 43.56 3.33
4505 4998 2.551270 CAGCACGAGCCGAAACAC 59.449 61.111 0.00 0.00 43.56 3.32
4508 5002 4.314440 AGCCAGCACGAGCCGAAA 62.314 61.111 0.00 0.00 43.56 3.46
4548 5049 3.665675 GACCAGCCAGCACTACGGG 62.666 68.421 0.00 0.00 36.56 5.28
4611 5112 1.669115 CCGGGAGACTGCAACAGTG 60.669 63.158 4.71 0.00 45.44 3.66
4619 5121 1.019673 CATCATTTGCCGGGAGACTG 58.980 55.000 2.18 0.00 0.00 3.51
4665 5167 1.625818 CACCTGACCTACTTTGCCTCT 59.374 52.381 0.00 0.00 0.00 3.69
4668 5170 0.036875 AGCACCTGACCTACTTTGCC 59.963 55.000 0.00 0.00 0.00 4.52
4670 5172 1.072331 ACCAGCACCTGACCTACTTTG 59.928 52.381 0.00 0.00 32.44 2.77
4672 5174 0.977395 GACCAGCACCTGACCTACTT 59.023 55.000 0.00 0.00 32.44 2.24
4815 5319 9.544579 TGCCAGAGTACTATAGACTATAGACTA 57.455 37.037 28.61 13.19 40.43 2.59
4816 5320 8.438618 TGCCAGAGTACTATAGACTATAGACT 57.561 38.462 28.61 24.74 40.43 3.24
4819 5323 9.550406 GGTATGCCAGAGTACTATAGACTATAG 57.450 40.741 22.71 22.71 38.40 1.31
4820 5324 9.054580 TGGTATGCCAGAGTACTATAGACTATA 57.945 37.037 6.78 2.24 40.46 1.31
4821 5325 7.929959 TGGTATGCCAGAGTACTATAGACTAT 58.070 38.462 6.78 0.00 40.46 2.12
4822 5326 7.325725 TGGTATGCCAGAGTACTATAGACTA 57.674 40.000 6.78 0.00 40.46 2.59
4823 5327 6.202202 TGGTATGCCAGAGTACTATAGACT 57.798 41.667 6.78 5.69 40.46 3.24
4824 5328 6.896021 TTGGTATGCCAGAGTACTATAGAC 57.104 41.667 6.78 0.59 46.91 2.59
4825 5329 7.039011 CCATTTGGTATGCCAGAGTACTATAGA 60.039 40.741 6.78 0.00 46.91 1.98
4826 5330 7.099764 CCATTTGGTATGCCAGAGTACTATAG 58.900 42.308 1.75 0.00 46.91 1.31
4827 5331 6.520061 GCCATTTGGTATGCCAGAGTACTATA 60.520 42.308 1.75 0.00 46.91 1.31
4828 5332 5.746065 GCCATTTGGTATGCCAGAGTACTAT 60.746 44.000 1.75 0.00 46.91 2.12
4865 5370 0.399454 ATCCAATCCGATCTGGCAGG 59.601 55.000 15.73 0.00 37.80 4.85
4883 5388 1.655372 CCAACCCAACCCAATCCAAT 58.345 50.000 0.00 0.00 0.00 3.16
4898 5403 0.392336 TTGCCTTGCATCAACCCAAC 59.608 50.000 0.00 0.00 38.76 3.77
4899 5404 1.070445 CTTTGCCTTGCATCAACCCAA 59.930 47.619 0.00 0.00 38.76 4.12
4900 5405 0.680618 CTTTGCCTTGCATCAACCCA 59.319 50.000 0.00 0.00 38.76 4.51
4901 5406 0.671472 GCTTTGCCTTGCATCAACCC 60.671 55.000 0.00 0.00 38.76 4.11
4902 5407 0.671472 GGCTTTGCCTTGCATCAACC 60.671 55.000 0.73 0.00 46.69 3.77
4903 5408 2.831597 GGCTTTGCCTTGCATCAAC 58.168 52.632 0.73 0.00 46.69 3.18
4921 5426 0.320073 TAACCAGCACGAACCGGAAG 60.320 55.000 9.46 0.32 0.00 3.46
4922 5427 0.320073 CTAACCAGCACGAACCGGAA 60.320 55.000 9.46 0.00 0.00 4.30
4923 5428 1.290955 CTAACCAGCACGAACCGGA 59.709 57.895 9.46 0.00 0.00 5.14
4924 5429 1.740296 CCTAACCAGCACGAACCGG 60.740 63.158 0.00 0.00 0.00 5.28
4925 5430 0.601841 AACCTAACCAGCACGAACCG 60.602 55.000 0.00 0.00 0.00 4.44
4926 5431 2.460757 TAACCTAACCAGCACGAACC 57.539 50.000 0.00 0.00 0.00 3.62
4927 5432 3.998341 TCATTAACCTAACCAGCACGAAC 59.002 43.478 0.00 0.00 0.00 3.95
4928 5433 4.274602 TCATTAACCTAACCAGCACGAA 57.725 40.909 0.00 0.00 0.00 3.85
4929 5434 3.965379 TCATTAACCTAACCAGCACGA 57.035 42.857 0.00 0.00 0.00 4.35
4930 5435 4.876107 AGATTCATTAACCTAACCAGCACG 59.124 41.667 0.00 0.00 0.00 5.34
4931 5436 7.048512 AGTAGATTCATTAACCTAACCAGCAC 58.951 38.462 0.00 0.00 0.00 4.40
4932 5437 7.195374 AGTAGATTCATTAACCTAACCAGCA 57.805 36.000 0.00 0.00 0.00 4.41
4933 5438 6.706716 GGAGTAGATTCATTAACCTAACCAGC 59.293 42.308 0.00 0.00 0.00 4.85
4960 5763 2.359900 CATCTAAGAGCAACACCACCC 58.640 52.381 0.00 0.00 0.00 4.61
4973 5776 1.324736 GCGTTGCGTCTTCCATCTAAG 59.675 52.381 0.00 0.00 0.00 2.18
4974 5777 1.355971 GCGTTGCGTCTTCCATCTAA 58.644 50.000 0.00 0.00 0.00 2.10


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

AutoCloner maintained by Alex Coulton.