Multiple sequence alignment - TraesCS5B01G178300

Loading Multiple Alignment...

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 TraesCS5B01G178300 chr5B 100.000 4737 0 0 1 4737 326087873 326083137 0.000000e+00 8748.0
1 TraesCS5B01G178300 chr5B 100.000 111 0 0 4901 5011 326082973 326082863 6.580000e-49 206.0
2 TraesCS5B01G178300 chr5A 94.643 4592 166 41 23 4568 379135778 379131221 0.000000e+00 7044.0
3 TraesCS5B01G178300 chr5A 86.207 116 11 1 4596 4711 379131100 379130990 2.450000e-23 121.0
4 TraesCS5B01G178300 chr5D 96.306 3655 99 18 918 4568 287307929 287304307 0.000000e+00 5969.0
5 TraesCS5B01G178300 chr5D 87.234 141 10 6 496 630 287401228 287401090 2.420000e-33 154.0
6 TraesCS5B01G178300 chr5D 90.426 94 9 0 4618 4711 287304168 287304075 1.890000e-24 124.0
7 TraesCS5B01G178300 chr3D 78.621 145 19 10 74 213 609135762 609135899 8.940000e-13 86.1


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 TraesCS5B01G178300 chr5B 326082863 326087873 5010 True 4477.0 8748 100.000 1 5011 2 chr5B.!!$R1 5010
1 TraesCS5B01G178300 chr5A 379130990 379135778 4788 True 3582.5 7044 90.425 23 4711 2 chr5A.!!$R1 4688
2 TraesCS5B01G178300 chr5D 287304075 287307929 3854 True 3046.5 5969 93.366 918 4711 2 chr5D.!!$R2 3793

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
908 930 0.033109 GGCTGGCCCAATTAGGTCTT 60.033 55.0 0.0 0.0 34.66 3.01 F
1343 1387 0.107116 AGGTCAGGAGCGACGACTAT 60.107 55.0 0.0 0.0 36.73 2.12 F
2143 2187 0.534203 TCCGCTTTGGTCACCAGAAC 60.534 55.0 0.0 0.0 39.52 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2575 2621 2.279741 GGCAATGAACTACATCGCAGA 58.720 47.619 0.00 0.00 40.32 4.26 R
2795 2841 6.099341 GTCAACAAAGTCCTGAAACAATTGT 58.901 36.000 4.92 4.92 34.76 2.71 R
4135 4181 0.105760 ACAATGGCCTCAACCCACAA 60.106 50.000 3.32 0.00 34.68 3.33 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
86 87 4.470462 CAATGAAGTTGTTGCTACAGAGC 58.530 43.478 0.37 0.00 39.91 4.09
87 88 7.494703 GCAATGAAGTTGTTGCTACAGAGCA 62.495 44.000 12.88 0.00 46.88 4.26
99 100 0.593128 ACAGAGCAAACATCGCAACC 59.407 50.000 0.00 0.00 0.00 3.77
105 106 0.110238 CAAACATCGCAACCACGAGG 60.110 55.000 0.00 0.00 46.69 4.63
119 120 0.814010 ACGAGGTTGTTGCAGTCCAC 60.814 55.000 0.00 0.00 0.00 4.02
123 124 1.092921 GGTTGTTGCAGTCCACGACA 61.093 55.000 8.53 0.00 34.60 4.35
124 125 0.944386 GTTGTTGCAGTCCACGACAT 59.056 50.000 2.35 0.00 34.60 3.06
128 129 1.459592 GTTGCAGTCCACGACATACAC 59.540 52.381 0.00 0.00 34.60 2.90
129 130 0.676736 TGCAGTCCACGACATACACA 59.323 50.000 0.00 0.00 34.60 3.72
141 142 3.809832 CGACATACACATTTGGGGAGATC 59.190 47.826 0.00 0.00 0.00 2.75
142 143 4.443457 CGACATACACATTTGGGGAGATCT 60.443 45.833 0.00 0.00 0.00 2.75
151 156 5.960202 ACATTTGGGGAGATCTGCTATTTTT 59.040 36.000 14.40 0.00 0.00 1.94
153 158 3.290710 TGGGGAGATCTGCTATTTTTGC 58.709 45.455 14.40 0.00 0.00 3.68
169 174 3.279875 GCGTCAATCGGATGGCCC 61.280 66.667 0.00 0.00 40.26 5.80
209 214 1.471287 TGTTCTATCCACCGACAGACG 59.529 52.381 0.00 0.00 42.18 4.18
210 215 1.471684 GTTCTATCCACCGACAGACGT 59.528 52.381 0.00 0.00 40.78 4.34
218 223 0.170561 ACCGACAGACGTGTAGCATC 59.829 55.000 0.00 0.00 36.88 3.91
225 230 1.681793 AGACGTGTAGCATCGCCTATT 59.318 47.619 0.00 0.00 0.00 1.73
226 231 2.882761 AGACGTGTAGCATCGCCTATTA 59.117 45.455 0.00 0.00 0.00 0.98
227 232 3.506455 AGACGTGTAGCATCGCCTATTAT 59.494 43.478 0.00 0.00 0.00 1.28
228 233 4.022242 AGACGTGTAGCATCGCCTATTATT 60.022 41.667 0.00 0.00 0.00 1.40
229 234 4.628074 ACGTGTAGCATCGCCTATTATTT 58.372 39.130 0.00 0.00 0.00 1.40
230 235 5.775686 ACGTGTAGCATCGCCTATTATTTA 58.224 37.500 0.00 0.00 0.00 1.40
310 315 7.178451 GGAACCAATCCTTTCTATTTTGAAGGA 59.822 37.037 6.53 6.53 45.56 3.36
333 338 3.393278 ACAAAAACACTAGCCTAGACCCA 59.607 43.478 5.58 0.00 0.00 4.51
334 339 4.141344 ACAAAAACACTAGCCTAGACCCAA 60.141 41.667 5.58 0.00 0.00 4.12
406 414 9.941325 GATTTCAGATACATATCATCTCACCTT 57.059 33.333 1.88 0.00 35.17 3.50
419 427 7.443302 TCATCTCACCTTTTATGATCTTCCT 57.557 36.000 0.00 0.00 0.00 3.36
440 448 6.009589 TCCTATTTCTGTGAGGCATCAAAAA 58.990 36.000 0.92 4.98 37.14 1.94
441 449 6.664816 TCCTATTTCTGTGAGGCATCAAAAAT 59.335 34.615 0.92 11.92 37.14 1.82
442 450 7.833682 TCCTATTTCTGTGAGGCATCAAAAATA 59.166 33.333 0.92 12.38 37.14 1.40
518 526 3.257469 TGTTTCACTTGGCATGCAAAA 57.743 38.095 21.36 12.27 0.00 2.44
576 584 9.520515 AATCATAAAGTTTGTTCATGTAGACCT 57.479 29.630 0.00 0.00 0.00 3.85
589 597 4.764050 TGTAGACCTGAAACTGTTTCCA 57.236 40.909 25.66 14.14 38.90 3.53
592 600 1.609072 GACCTGAAACTGTTTCCAGCC 59.391 52.381 25.66 9.72 42.81 4.85
614 622 5.687828 CCGCACGTAAAGTTTTTATACCAA 58.312 37.500 0.00 0.00 0.00 3.67
693 703 3.417069 AACTCCGACAATCATGGTTCA 57.583 42.857 0.00 0.00 0.00 3.18
694 704 3.634397 ACTCCGACAATCATGGTTCAT 57.366 42.857 0.00 0.00 0.00 2.57
695 705 3.955471 ACTCCGACAATCATGGTTCATT 58.045 40.909 0.00 0.00 0.00 2.57
696 706 4.335416 ACTCCGACAATCATGGTTCATTT 58.665 39.130 0.00 0.00 0.00 2.32
841 854 8.633075 TTGTTTTGAGACAAAAACTGATGATC 57.367 30.769 10.49 0.00 45.90 2.92
842 855 7.770201 TGTTTTGAGACAAAAACTGATGATCA 58.230 30.769 10.49 0.00 45.90 2.92
847 860 8.168790 TGAGACAAAAACTGATGATCAATGAA 57.831 30.769 0.00 0.00 0.00 2.57
888 910 4.191033 ACGAAAACACCGGTATCACATA 57.809 40.909 6.87 0.00 0.00 2.29
907 929 0.921256 AGGCTGGCCCAATTAGGTCT 60.921 55.000 8.11 0.00 36.58 3.85
908 930 0.033109 GGCTGGCCCAATTAGGTCTT 60.033 55.000 0.00 0.00 34.66 3.01
910 932 1.106285 CTGGCCCAATTAGGTCTTGC 58.894 55.000 0.00 0.00 34.66 4.01
916 938 3.635591 CCCAATTAGGTCTTGCTGGATT 58.364 45.455 0.00 0.00 34.66 3.01
952 994 2.304751 TAGGATTTTCGTTCCGCTCC 57.695 50.000 0.00 0.00 38.36 4.70
982 1024 1.308746 TCCCCATTCCTTCTCCCCC 60.309 63.158 0.00 0.00 0.00 5.40
1088 1132 1.500474 GGGAGGTGATGGAGATGACA 58.500 55.000 0.00 0.00 0.00 3.58
1205 1249 2.657296 CACCACTGCGACGACGTT 60.657 61.111 9.33 0.00 41.98 3.99
1343 1387 0.107116 AGGTCAGGAGCGACGACTAT 60.107 55.000 0.00 0.00 36.73 2.12
1464 1508 5.516339 CCAATTATTCGGTCATTGCAAGTTC 59.484 40.000 4.94 0.00 0.00 3.01
1630 1674 0.792640 CAAGAAATCGTGCAGCTCGT 59.207 50.000 16.02 1.91 0.00 4.18
1870 1914 1.898154 CGTCCCCGAGGAGAACATT 59.102 57.895 0.00 0.00 45.21 2.71
1912 1956 0.963225 TACAACGCTACTGTGGCTCA 59.037 50.000 14.29 0.00 0.00 4.26
2143 2187 0.534203 TCCGCTTTGGTCACCAGAAC 60.534 55.000 0.00 0.00 39.52 3.01
2152 2196 1.000843 GGTCACCAGAACATTTTGGCC 59.999 52.381 0.00 0.00 38.03 5.36
2342 2386 5.511202 CCCCTTGCACACAATTCTTGTATTT 60.511 40.000 0.00 0.00 43.23 1.40
2575 2621 7.754851 ACTGTAAAATTTTCCCGTGTAGATT 57.245 32.000 6.72 0.00 0.00 2.40
2795 2841 5.684853 AAAATCCCATGGATATCCTGGAA 57.315 39.130 28.32 17.31 42.27 3.53
2993 3039 9.645128 ATGTGGATTGATACCATCAGAAATTTA 57.355 29.630 0.00 0.00 40.94 1.40
3590 3636 1.863454 CTTGCTGCGTCTGATGGTATC 59.137 52.381 0.00 0.00 0.00 2.24
3872 3918 4.072131 TCTTCTCCAGTTACATTTGGTGC 58.928 43.478 0.00 0.00 35.89 5.01
4135 4181 2.892852 ACCATTAATGTGCTGCAGTTGT 59.107 40.909 16.64 0.00 0.00 3.32
4136 4182 3.321682 ACCATTAATGTGCTGCAGTTGTT 59.678 39.130 16.64 8.13 0.00 2.83
4137 4183 3.676172 CCATTAATGTGCTGCAGTTGTTG 59.324 43.478 16.64 4.12 0.00 3.33
4142 4188 1.379710 TGCTGCAGTTGTTGTGGGT 60.380 52.632 16.64 0.00 0.00 4.51
4153 4199 0.318120 GTTGTGGGTTGAGGCCATTG 59.682 55.000 5.01 0.00 0.00 2.82
4171 4217 2.969821 TGTACTGGGCAAGTGGAATT 57.030 45.000 4.33 0.00 40.26 2.17
4225 4271 7.849804 TTCTAGTCTGCAGATTATTTTGGTC 57.150 36.000 21.47 2.37 0.00 4.02
4227 4273 7.624549 TCTAGTCTGCAGATTATTTTGGTCTT 58.375 34.615 21.47 0.00 0.00 3.01
4250 4296 7.946219 TCTTGTTATTCTCATTATGGATGCCAT 59.054 33.333 4.18 4.18 46.99 4.40
4253 4299 8.162746 TGTTATTCTCATTATGGATGCCATGTA 58.837 33.333 9.14 0.00 44.84 2.29
4256 4302 5.554070 TCTCATTATGGATGCCATGTAGTG 58.446 41.667 9.14 3.37 44.84 2.74
4270 4316 5.898174 CCATGTAGTGGTATCGTTTCTGTA 58.102 41.667 0.00 0.00 43.44 2.74
4290 4336 8.958119 TCTGTAACTTTTCAACATTCTGTAGT 57.042 30.769 0.00 0.00 0.00 2.73
4309 4355 8.375506 TCTGTAGTTTCAGATAGGACATTTTGT 58.624 33.333 0.00 0.00 39.20 2.83
4310 4356 8.322906 TGTAGTTTCAGATAGGACATTTTGTG 57.677 34.615 0.00 0.00 0.00 3.33
4376 4422 4.398319 ACCTGATGTTAGTTTGTGAAGGG 58.602 43.478 0.00 0.00 0.00 3.95
4382 4428 0.771127 TAGTTTGTGAAGGGCCTGCT 59.229 50.000 14.07 0.00 0.00 4.24
4468 4515 4.818546 CCATAGGACCTGTGAATTGTGATC 59.181 45.833 19.19 0.00 0.00 2.92
4473 4520 3.149196 ACCTGTGAATTGTGATCGCTTT 58.851 40.909 7.94 1.36 0.00 3.51
4474 4521 4.323417 ACCTGTGAATTGTGATCGCTTTA 58.677 39.130 7.94 0.00 0.00 1.85
4494 4541 6.753279 GCTTTAGAGAGATGATGCATAGCTAG 59.247 42.308 0.00 0.00 0.00 3.42
4498 4548 2.931325 GAGATGATGCATAGCTAGCTGC 59.069 50.000 27.68 23.02 43.29 5.25
4499 4549 2.008329 GATGATGCATAGCTAGCTGCC 58.992 52.381 27.68 14.77 44.23 4.85
4500 4550 1.054231 TGATGCATAGCTAGCTGCCT 58.946 50.000 27.68 16.27 44.23 4.75
4501 4551 2.250924 TGATGCATAGCTAGCTGCCTA 58.749 47.619 27.68 7.52 44.23 3.93
4502 4552 2.233186 TGATGCATAGCTAGCTGCCTAG 59.767 50.000 27.68 12.54 44.23 3.02
4546 4596 9.084164 GGAACTTTCATGATTCATTGATTCTTG 57.916 33.333 13.94 13.94 0.00 3.02
4552 4602 5.571784 TGATTCATTGATTCTTGTCCTGC 57.428 39.130 9.32 0.00 0.00 4.85
4568 4618 3.285215 GCATCCTGCATCTGGGCG 61.285 66.667 0.00 0.00 44.26 6.13
4569 4619 2.507452 CATCCTGCATCTGGGCGA 59.493 61.111 0.00 0.00 36.28 5.54
4570 4620 1.072678 CATCCTGCATCTGGGCGAT 59.927 57.895 0.00 0.00 36.28 4.58
4571 4621 0.954449 CATCCTGCATCTGGGCGATC 60.954 60.000 0.00 0.00 36.28 3.69
4572 4622 1.413256 ATCCTGCATCTGGGCGATCA 61.413 55.000 0.00 0.00 36.28 2.92
4573 4623 1.072678 CCTGCATCTGGGCGATCAT 59.927 57.895 0.00 0.00 36.28 2.45
4576 4683 2.497138 CTGCATCTGGGCGATCATAAA 58.503 47.619 0.00 0.00 36.28 1.40
4580 4687 3.503363 GCATCTGGGCGATCATAAATTCA 59.497 43.478 0.00 0.00 0.00 2.57
4603 4751 5.499139 TGGATGAACACACTTTTCTTGTC 57.501 39.130 0.00 0.00 0.00 3.18
4616 4764 7.123547 ACACTTTTCTTGTCACCCTTATTTTCA 59.876 33.333 0.00 0.00 0.00 2.69
4623 4771 5.825532 TGTCACCCTTATTTTCATGATCCA 58.174 37.500 0.00 0.00 0.00 3.41
4624 4772 5.887598 TGTCACCCTTATTTTCATGATCCAG 59.112 40.000 0.00 0.00 0.00 3.86
4657 4805 8.798859 ATTGCCTTAATCTATATTGTAGCCTG 57.201 34.615 0.00 0.00 0.00 4.85
4689 4837 3.525800 ACCACAGGGCTTATCTGTTTT 57.474 42.857 0.00 0.00 42.87 2.43
4698 4846 9.923143 ACAGGGCTTATCTGTTTTTATTTTTAC 57.077 29.630 0.00 0.00 42.17 2.01
4931 5079 4.373348 CTAGTGTTACTAGTCTGGTGCC 57.627 50.000 0.00 0.00 42.41 5.01
4932 5080 2.605257 AGTGTTACTAGTCTGGTGCCA 58.395 47.619 0.00 0.00 0.00 4.92
4933 5081 3.173965 AGTGTTACTAGTCTGGTGCCAT 58.826 45.455 0.00 0.00 0.00 4.40
4934 5082 3.055819 AGTGTTACTAGTCTGGTGCCATG 60.056 47.826 0.00 0.00 0.00 3.66
4935 5083 3.056107 GTGTTACTAGTCTGGTGCCATGA 60.056 47.826 0.00 0.00 0.00 3.07
4936 5084 3.580895 TGTTACTAGTCTGGTGCCATGAA 59.419 43.478 0.00 0.00 0.00 2.57
4937 5085 4.041075 TGTTACTAGTCTGGTGCCATGAAA 59.959 41.667 0.00 0.00 0.00 2.69
4938 5086 3.059352 ACTAGTCTGGTGCCATGAAAC 57.941 47.619 0.00 0.00 0.00 2.78
4939 5087 2.639839 ACTAGTCTGGTGCCATGAAACT 59.360 45.455 0.00 0.00 0.00 2.66
4940 5088 3.838317 ACTAGTCTGGTGCCATGAAACTA 59.162 43.478 0.00 0.00 0.00 2.24
4941 5089 4.471386 ACTAGTCTGGTGCCATGAAACTAT 59.529 41.667 0.00 0.00 0.00 2.12
4942 5090 5.661312 ACTAGTCTGGTGCCATGAAACTATA 59.339 40.000 0.00 0.00 0.00 1.31
4943 5091 5.028549 AGTCTGGTGCCATGAAACTATAG 57.971 43.478 0.00 0.00 0.00 1.31
4944 5092 4.716784 AGTCTGGTGCCATGAAACTATAGA 59.283 41.667 6.78 0.00 0.00 1.98
4945 5093 5.367937 AGTCTGGTGCCATGAAACTATAGAT 59.632 40.000 6.78 0.00 0.00 1.98
4946 5094 5.698545 GTCTGGTGCCATGAAACTATAGATC 59.301 44.000 6.78 5.14 0.00 2.75
4947 5095 4.631131 TGGTGCCATGAAACTATAGATCG 58.369 43.478 6.78 0.00 0.00 3.69
4948 5096 4.100963 TGGTGCCATGAAACTATAGATCGT 59.899 41.667 6.78 3.18 0.00 3.73
4949 5097 4.449068 GGTGCCATGAAACTATAGATCGTG 59.551 45.833 6.78 14.29 0.00 4.35
4950 5098 5.289595 GTGCCATGAAACTATAGATCGTGA 58.710 41.667 22.76 9.91 32.98 4.35
4951 5099 5.403766 GTGCCATGAAACTATAGATCGTGAG 59.596 44.000 22.76 16.84 32.98 3.51
4953 5101 5.631512 GCCATGAAACTATAGATCGTGAGAC 59.368 44.000 22.76 13.71 46.97 3.36
4954 5102 6.515862 GCCATGAAACTATAGATCGTGAGACT 60.516 42.308 22.76 0.00 46.97 3.24
4955 5103 7.081349 CCATGAAACTATAGATCGTGAGACTC 58.919 42.308 22.76 0.00 46.97 3.36
4956 5104 7.040755 CCATGAAACTATAGATCGTGAGACTCT 60.041 40.741 22.76 0.00 46.97 3.24
4957 5105 7.252965 TGAAACTATAGATCGTGAGACTCTG 57.747 40.000 6.78 0.00 46.97 3.35
4958 5106 6.261158 TGAAACTATAGATCGTGAGACTCTGG 59.739 42.308 6.78 0.00 46.97 3.86
4959 5107 4.647611 ACTATAGATCGTGAGACTCTGGG 58.352 47.826 6.78 0.00 46.97 4.45
4960 5108 3.586470 ATAGATCGTGAGACTCTGGGT 57.414 47.619 3.68 0.00 46.97 4.51
4961 5109 4.708576 ATAGATCGTGAGACTCTGGGTA 57.291 45.455 3.68 0.00 46.97 3.69
4962 5110 2.925724 AGATCGTGAGACTCTGGGTAG 58.074 52.381 3.68 0.00 46.97 3.18
4963 5111 1.950909 GATCGTGAGACTCTGGGTAGG 59.049 57.143 3.68 0.00 46.97 3.18
4964 5112 0.989602 TCGTGAGACTCTGGGTAGGA 59.010 55.000 3.68 0.00 33.31 2.94
4965 5113 1.353358 TCGTGAGACTCTGGGTAGGAA 59.647 52.381 3.68 0.00 33.31 3.36
4966 5114 1.746220 CGTGAGACTCTGGGTAGGAAG 59.254 57.143 3.68 0.00 0.00 3.46
4967 5115 2.618302 CGTGAGACTCTGGGTAGGAAGA 60.618 54.545 3.68 0.00 0.00 2.87
4968 5116 3.432378 GTGAGACTCTGGGTAGGAAGAA 58.568 50.000 3.68 0.00 0.00 2.52
4969 5117 3.445805 GTGAGACTCTGGGTAGGAAGAAG 59.554 52.174 3.68 0.00 0.00 2.85
4970 5118 3.076182 TGAGACTCTGGGTAGGAAGAAGT 59.924 47.826 3.68 0.00 0.00 3.01
4971 5119 4.090819 GAGACTCTGGGTAGGAAGAAGTT 58.909 47.826 0.00 0.00 0.00 2.66
4972 5120 4.090819 AGACTCTGGGTAGGAAGAAGTTC 58.909 47.826 0.00 0.00 0.00 3.01
4984 5132 3.641017 GAAGTTCCTTCTGGCTGCT 57.359 52.632 0.00 0.00 37.49 4.24
4985 5133 1.447945 GAAGTTCCTTCTGGCTGCTC 58.552 55.000 0.00 0.00 37.49 4.26
4986 5134 1.003003 GAAGTTCCTTCTGGCTGCTCT 59.997 52.381 0.00 0.00 37.49 4.09
4987 5135 0.324285 AGTTCCTTCTGGCTGCTCTG 59.676 55.000 0.00 0.00 0.00 3.35
4988 5136 0.676151 GTTCCTTCTGGCTGCTCTGG 60.676 60.000 0.00 0.00 0.00 3.86
4989 5137 1.130054 TTCCTTCTGGCTGCTCTGGT 61.130 55.000 0.00 0.00 0.00 4.00
4990 5138 1.078567 CCTTCTGGCTGCTCTGGTC 60.079 63.158 0.00 0.00 0.00 4.02
4991 5139 1.551908 CCTTCTGGCTGCTCTGGTCT 61.552 60.000 0.00 0.00 0.00 3.85
4992 5140 0.391395 CTTCTGGCTGCTCTGGTCTG 60.391 60.000 0.00 0.00 0.00 3.51
4993 5141 1.123861 TTCTGGCTGCTCTGGTCTGT 61.124 55.000 0.00 0.00 0.00 3.41
4994 5142 1.375652 CTGGCTGCTCTGGTCTGTG 60.376 63.158 0.00 0.00 0.00 3.66
4995 5143 2.745492 GGCTGCTCTGGTCTGTGC 60.745 66.667 0.00 0.00 0.00 4.57
4996 5144 2.346739 GCTGCTCTGGTCTGTGCT 59.653 61.111 0.00 0.00 0.00 4.40
4997 5145 1.302351 GCTGCTCTGGTCTGTGCTT 60.302 57.895 0.00 0.00 0.00 3.91
4998 5146 0.036952 GCTGCTCTGGTCTGTGCTTA 60.037 55.000 0.00 0.00 0.00 3.09
4999 5147 1.609061 GCTGCTCTGGTCTGTGCTTAA 60.609 52.381 0.00 0.00 0.00 1.85
5000 5148 2.938756 GCTGCTCTGGTCTGTGCTTAAT 60.939 50.000 0.00 0.00 0.00 1.40
5001 5149 3.341823 CTGCTCTGGTCTGTGCTTAATT 58.658 45.455 0.00 0.00 0.00 1.40
5002 5150 3.338249 TGCTCTGGTCTGTGCTTAATTC 58.662 45.455 0.00 0.00 0.00 2.17
5003 5151 2.349886 GCTCTGGTCTGTGCTTAATTCG 59.650 50.000 0.00 0.00 0.00 3.34
5004 5152 3.849911 CTCTGGTCTGTGCTTAATTCGA 58.150 45.455 0.00 0.00 0.00 3.71
5005 5153 4.245660 CTCTGGTCTGTGCTTAATTCGAA 58.754 43.478 0.00 0.00 0.00 3.71
5006 5154 4.832248 TCTGGTCTGTGCTTAATTCGAAT 58.168 39.130 4.39 4.39 0.00 3.34
5007 5155 5.972935 TCTGGTCTGTGCTTAATTCGAATA 58.027 37.500 11.83 0.00 0.00 1.75
5008 5156 6.582636 TCTGGTCTGTGCTTAATTCGAATAT 58.417 36.000 11.83 4.70 0.00 1.28
5009 5157 7.722363 TCTGGTCTGTGCTTAATTCGAATATA 58.278 34.615 11.83 3.73 0.00 0.86
5010 5158 8.201464 TCTGGTCTGTGCTTAATTCGAATATAA 58.799 33.333 11.83 10.88 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.396060 TTGCAAATCCACCCAAAGCC 59.604 50.000 0.00 0.00 0.00 4.35
51 52 2.971330 ACTTCATTGCAAATCCACCCAA 59.029 40.909 1.71 0.00 0.00 4.12
80 81 0.593128 GGTTGCGATGTTTGCTCTGT 59.407 50.000 0.00 0.00 0.00 3.41
86 87 0.110238 CCTCGTGGTTGCGATGTTTG 60.110 55.000 0.00 0.00 40.29 2.93
87 88 0.534203 ACCTCGTGGTTGCGATGTTT 60.534 50.000 2.61 0.00 46.05 2.83
99 100 0.813610 TGGACTGCAACAACCTCGTG 60.814 55.000 0.00 0.00 0.00 4.35
105 106 0.944386 ATGTCGTGGACTGCAACAAC 59.056 50.000 0.00 0.00 33.15 3.32
113 114 3.334691 CCAAATGTGTATGTCGTGGACT 58.665 45.455 0.00 0.00 33.15 3.85
114 115 2.418628 CCCAAATGTGTATGTCGTGGAC 59.581 50.000 0.00 0.00 0.00 4.02
119 120 3.260475 TCTCCCCAAATGTGTATGTCG 57.740 47.619 0.00 0.00 0.00 4.35
123 124 3.461085 AGCAGATCTCCCCAAATGTGTAT 59.539 43.478 0.00 0.00 0.00 2.29
124 125 2.846206 AGCAGATCTCCCCAAATGTGTA 59.154 45.455 0.00 0.00 0.00 2.90
128 129 6.278363 CAAAAATAGCAGATCTCCCCAAATG 58.722 40.000 0.00 0.00 0.00 2.32
129 130 5.163374 GCAAAAATAGCAGATCTCCCCAAAT 60.163 40.000 0.00 0.00 0.00 2.32
141 142 3.100817 CCGATTGACGCAAAAATAGCAG 58.899 45.455 0.00 0.00 41.07 4.24
142 143 2.744741 TCCGATTGACGCAAAAATAGCA 59.255 40.909 0.00 0.00 41.07 3.49
151 156 2.513666 GGCCATCCGATTGACGCA 60.514 61.111 0.00 0.00 41.07 5.24
153 158 2.591715 GGGGCCATCCGATTGACG 60.592 66.667 4.39 0.00 42.18 4.35
185 190 4.753107 GTCTGTCGGTGGATAGAACAAAAA 59.247 41.667 0.00 0.00 41.35 1.94
190 195 1.471684 ACGTCTGTCGGTGGATAGAAC 59.528 52.381 0.00 0.00 41.35 3.01
192 197 1.092348 CACGTCTGTCGGTGGATAGA 58.908 55.000 0.00 0.00 44.69 1.98
202 207 1.140407 GGCGATGCTACACGTCTGTC 61.140 60.000 0.00 0.00 31.56 3.51
204 209 0.380733 TAGGCGATGCTACACGTCTG 59.619 55.000 0.00 0.00 44.04 3.51
205 210 1.319541 ATAGGCGATGCTACACGTCT 58.680 50.000 0.00 0.00 46.01 4.18
206 211 2.135664 AATAGGCGATGCTACACGTC 57.864 50.000 0.00 0.00 0.00 4.34
209 214 8.770828 TCTTTTAAATAATAGGCGATGCTACAC 58.229 33.333 0.00 0.00 0.00 2.90
210 215 8.896320 TCTTTTAAATAATAGGCGATGCTACA 57.104 30.769 0.00 0.00 0.00 2.74
248 253 7.559335 AGGGCTCCAAAAGAAAAATAAATCT 57.441 32.000 0.00 0.00 0.00 2.40
249 254 7.334421 GGAAGGGCTCCAAAAGAAAAATAAATC 59.666 37.037 0.00 0.00 44.67 2.17
250 255 7.168219 GGAAGGGCTCCAAAAGAAAAATAAAT 58.832 34.615 0.00 0.00 44.67 1.40
252 257 6.109156 GGAAGGGCTCCAAAAGAAAAATAA 57.891 37.500 0.00 0.00 44.67 1.40
253 258 5.738619 GGAAGGGCTCCAAAAGAAAAATA 57.261 39.130 0.00 0.00 44.67 1.40
254 259 4.623932 GGAAGGGCTCCAAAAGAAAAAT 57.376 40.909 0.00 0.00 44.67 1.82
289 294 9.762933 TTTGTTCCTTCAAAATAGAAAGGATTG 57.237 29.630 4.06 0.00 34.90 2.67
303 308 4.953579 AGGCTAGTGTTTTTGTTCCTTCAA 59.046 37.500 0.00 0.00 0.00 2.69
304 309 4.532834 AGGCTAGTGTTTTTGTTCCTTCA 58.467 39.130 0.00 0.00 0.00 3.02
310 315 4.141344 TGGGTCTAGGCTAGTGTTTTTGTT 60.141 41.667 20.45 0.00 0.00 2.83
406 414 7.716998 GCCTCACAGAAATAGGAAGATCATAAA 59.283 37.037 0.00 0.00 31.64 1.40
407 415 7.147497 TGCCTCACAGAAATAGGAAGATCATAA 60.147 37.037 0.00 0.00 31.64 1.90
494 502 3.391965 TGCATGCCAAGTGAAACAAATC 58.608 40.909 16.68 0.00 41.43 2.17
559 567 6.038271 ACAGTTTCAGGTCTACATGAACAAAC 59.962 38.462 9.51 6.27 44.84 2.93
589 597 4.142838 GGTATAAAAACTTTACGTGCGGCT 60.143 41.667 0.00 0.00 0.00 5.52
592 600 6.797995 ACATTGGTATAAAAACTTTACGTGCG 59.202 34.615 0.00 0.00 0.00 5.34
643 653 8.807667 AAACATTCTCTTGAACACATGATTTC 57.192 30.769 0.00 1.72 34.71 2.17
810 823 8.707839 TCAGTTTTTGTCTCAAAACAAATCAAC 58.292 29.630 10.73 6.14 45.70 3.18
860 873 1.545136 ACCGGTGTTTTCGTTGGTTTT 59.455 42.857 6.12 0.00 0.00 2.43
864 877 2.096119 GTGATACCGGTGTTTTCGTTGG 60.096 50.000 19.93 0.00 0.00 3.77
888 910 1.615262 GACCTAATTGGGCCAGCCT 59.385 57.895 6.23 0.00 38.13 4.58
908 930 2.334946 GCCAGTTGCGAATCCAGCA 61.335 57.895 0.00 0.00 43.59 4.41
982 1024 3.764972 ACCCTAGAGAGAGAAAACGAAGG 59.235 47.826 0.00 0.00 0.00 3.46
1088 1132 2.919856 ACCGACTGCAGCACCTCT 60.920 61.111 15.27 0.00 0.00 3.69
1205 1249 2.441348 TCGTAGGGGATGAGCGCA 60.441 61.111 11.47 0.00 0.00 6.09
1343 1387 4.586884 ACACGTACATTCTGTAGAGGAGA 58.413 43.478 0.00 0.00 32.84 3.71
1367 1411 3.650950 GGGAGGTGGCAGCAGGAA 61.651 66.667 20.04 0.00 0.00 3.36
1870 1914 4.546674 TCCCTTCTATATGTGTCTGCAGA 58.453 43.478 13.74 13.74 0.00 4.26
2143 2187 3.359033 TGAGGAATGAGAGGCCAAAATG 58.641 45.455 5.01 0.00 0.00 2.32
2152 2196 5.065731 GCTTACACCAAATGAGGAATGAGAG 59.934 44.000 0.00 0.00 0.00 3.20
2342 2386 3.405831 CAGAGCCTGTTGTCTTGAATCA 58.594 45.455 0.00 0.00 0.00 2.57
2566 2612 3.953766 ACTACATCGCAGAATCTACACG 58.046 45.455 0.00 0.00 43.58 4.49
2575 2621 2.279741 GGCAATGAACTACATCGCAGA 58.720 47.619 0.00 0.00 40.32 4.26
2748 2794 8.768501 TTCTCACTCCAGATACTGTACATAAT 57.231 34.615 0.00 0.00 0.00 1.28
2795 2841 6.099341 GTCAACAAAGTCCTGAAACAATTGT 58.901 36.000 4.92 4.92 34.76 2.71
3390 3436 9.353431 TGCATACATCATGTTAACCTTTATGAT 57.647 29.630 11.46 11.46 40.00 2.45
3872 3918 7.633361 TTACAACTAGCTAAGTGAGTTTTCG 57.367 36.000 9.70 0.00 38.88 3.46
4114 4160 2.892852 ACAACTGCAGCACATTAATGGT 59.107 40.909 19.37 3.20 0.00 3.55
4135 4181 0.105760 ACAATGGCCTCAACCCACAA 60.106 50.000 3.32 0.00 34.68 3.33
4136 4182 0.774276 TACAATGGCCTCAACCCACA 59.226 50.000 3.32 0.00 34.68 4.17
4137 4183 1.173913 GTACAATGGCCTCAACCCAC 58.826 55.000 3.32 0.00 34.68 4.61
4142 4188 0.323360 GCCCAGTACAATGGCCTCAA 60.323 55.000 3.32 0.00 39.17 3.02
4153 4199 3.153919 TGAAATTCCACTTGCCCAGTAC 58.846 45.455 0.00 0.00 32.76 2.73
4225 4271 7.514784 TGGCATCCATAATGAGAATAACAAG 57.485 36.000 0.00 0.00 37.59 3.16
4227 4273 7.005902 ACATGGCATCCATAATGAGAATAACA 58.994 34.615 0.00 0.00 43.15 2.41
4250 4296 6.579666 AGTTACAGAAACGATACCACTACA 57.420 37.500 0.00 0.00 43.29 2.74
4253 4299 6.987992 TGAAAAGTTACAGAAACGATACCACT 59.012 34.615 0.00 0.00 43.29 4.00
4256 4302 7.632721 TGTTGAAAAGTTACAGAAACGATACC 58.367 34.615 0.00 0.00 43.29 2.73
4290 4336 5.048083 GCCACACAAAATGTCCTATCTGAAA 60.048 40.000 0.00 0.00 40.64 2.69
4340 4386 2.159327 TCAGGTCATCTATGCGCATG 57.841 50.000 32.48 21.08 0.00 4.06
4342 4388 1.413812 ACATCAGGTCATCTATGCGCA 59.586 47.619 14.96 14.96 0.00 6.09
4343 4389 2.160822 ACATCAGGTCATCTATGCGC 57.839 50.000 0.00 0.00 0.00 6.09
4344 4390 4.876125 ACTAACATCAGGTCATCTATGCG 58.124 43.478 0.00 0.00 0.00 4.73
4376 4422 0.960861 GGGTGGTTCAAGTAGCAGGC 60.961 60.000 0.00 0.00 0.00 4.85
4382 4428 1.489649 TGTTTCCGGGTGGTTCAAGTA 59.510 47.619 0.00 0.00 36.30 2.24
4468 4515 4.326817 GCTATGCATCATCTCTCTAAAGCG 59.673 45.833 0.19 0.00 0.00 4.68
4473 4520 5.357596 CAGCTAGCTATGCATCATCTCTCTA 59.642 44.000 18.86 0.00 0.00 2.43
4474 4521 4.158949 CAGCTAGCTATGCATCATCTCTCT 59.841 45.833 18.86 0.00 0.00 3.10
4552 4602 0.954449 GATCGCCCAGATGCAGGATG 60.954 60.000 0.00 0.00 40.26 3.51
4580 4687 5.593909 TGACAAGAAAAGTGTGTTCATCCAT 59.406 36.000 0.00 0.00 0.00 3.41
4593 4700 8.359642 TCATGAAAATAAGGGTGACAAGAAAAG 58.640 33.333 0.00 0.00 0.00 2.27
4594 4701 8.243961 TCATGAAAATAAGGGTGACAAGAAAA 57.756 30.769 0.00 0.00 0.00 2.29
4603 4751 6.828273 TGTACTGGATCATGAAAATAAGGGTG 59.172 38.462 0.00 0.00 0.00 4.61
4616 4764 8.995027 TTAAGGCAATTAATGTACTGGATCAT 57.005 30.769 0.00 0.00 0.00 2.45
4657 4805 2.316108 CCCTGTGGTTTTATATGCCCC 58.684 52.381 0.00 0.00 0.00 5.80
4669 4817 3.525800 AAAACAGATAAGCCCTGTGGT 57.474 42.857 0.00 0.00 43.42 4.16
4673 4821 9.366216 GGTAAAAATAAAAACAGATAAGCCCTG 57.634 33.333 0.00 0.00 37.64 4.45
4675 4823 9.582431 GAGGTAAAAATAAAAACAGATAAGCCC 57.418 33.333 0.00 0.00 0.00 5.19
4911 5059 3.770046 TGGCACCAGACTAGTAACACTA 58.230 45.455 0.00 0.00 0.00 2.74
4912 5060 2.605257 TGGCACCAGACTAGTAACACT 58.395 47.619 0.00 0.00 0.00 3.55
4913 5061 3.056107 TCATGGCACCAGACTAGTAACAC 60.056 47.826 0.00 0.00 0.00 3.32
4914 5062 3.169908 TCATGGCACCAGACTAGTAACA 58.830 45.455 0.00 0.00 0.00 2.41
4915 5063 3.887621 TCATGGCACCAGACTAGTAAC 57.112 47.619 0.00 0.00 0.00 2.50
4916 5064 4.286032 AGTTTCATGGCACCAGACTAGTAA 59.714 41.667 0.00 0.00 0.00 2.24
4917 5065 3.838317 AGTTTCATGGCACCAGACTAGTA 59.162 43.478 0.00 0.00 0.00 1.82
4918 5066 2.639839 AGTTTCATGGCACCAGACTAGT 59.360 45.455 0.00 0.00 0.00 2.57
4919 5067 3.340814 AGTTTCATGGCACCAGACTAG 57.659 47.619 0.00 0.00 0.00 2.57
4920 5068 5.897250 TCTATAGTTTCATGGCACCAGACTA 59.103 40.000 0.00 0.00 0.00 2.59
4921 5069 4.716784 TCTATAGTTTCATGGCACCAGACT 59.283 41.667 0.00 0.00 0.00 3.24
4922 5070 5.023533 TCTATAGTTTCATGGCACCAGAC 57.976 43.478 0.00 0.00 0.00 3.51
4923 5071 5.509670 CGATCTATAGTTTCATGGCACCAGA 60.510 44.000 0.00 0.00 0.00 3.86
4924 5072 4.687948 CGATCTATAGTTTCATGGCACCAG 59.312 45.833 0.00 0.00 0.00 4.00
4925 5073 4.100963 ACGATCTATAGTTTCATGGCACCA 59.899 41.667 0.00 0.00 0.00 4.17
4926 5074 4.449068 CACGATCTATAGTTTCATGGCACC 59.551 45.833 0.00 0.00 0.00 5.01
4927 5075 5.289595 TCACGATCTATAGTTTCATGGCAC 58.710 41.667 0.00 0.00 0.00 5.01
4928 5076 5.301805 TCTCACGATCTATAGTTTCATGGCA 59.698 40.000 0.00 0.00 0.00 4.92
4929 5077 5.631512 GTCTCACGATCTATAGTTTCATGGC 59.368 44.000 0.00 0.00 0.00 4.40
4930 5078 6.976088 AGTCTCACGATCTATAGTTTCATGG 58.024 40.000 0.00 0.00 0.00 3.66
4931 5079 7.802720 CAGAGTCTCACGATCTATAGTTTCATG 59.197 40.741 1.94 0.00 0.00 3.07
4932 5080 7.040755 CCAGAGTCTCACGATCTATAGTTTCAT 60.041 40.741 1.94 0.00 0.00 2.57
4933 5081 6.261158 CCAGAGTCTCACGATCTATAGTTTCA 59.739 42.308 1.94 0.00 0.00 2.69
4934 5082 6.293735 CCCAGAGTCTCACGATCTATAGTTTC 60.294 46.154 1.94 0.00 0.00 2.78
4935 5083 5.533154 CCCAGAGTCTCACGATCTATAGTTT 59.467 44.000 1.94 0.00 0.00 2.66
4936 5084 5.067273 CCCAGAGTCTCACGATCTATAGTT 58.933 45.833 1.94 0.00 0.00 2.24
4937 5085 4.103469 ACCCAGAGTCTCACGATCTATAGT 59.897 45.833 1.94 0.00 0.00 2.12
4938 5086 4.647611 ACCCAGAGTCTCACGATCTATAG 58.352 47.826 1.94 0.00 0.00 1.31
4939 5087 4.708576 ACCCAGAGTCTCACGATCTATA 57.291 45.455 1.94 0.00 0.00 1.31
4940 5088 3.586470 ACCCAGAGTCTCACGATCTAT 57.414 47.619 1.94 0.00 0.00 1.98
4941 5089 3.181453 CCTACCCAGAGTCTCACGATCTA 60.181 52.174 1.94 0.00 0.00 1.98
4942 5090 2.422235 CCTACCCAGAGTCTCACGATCT 60.422 54.545 1.94 0.00 0.00 2.75
4943 5091 1.950909 CCTACCCAGAGTCTCACGATC 59.049 57.143 1.94 0.00 0.00 3.69
4944 5092 1.564818 TCCTACCCAGAGTCTCACGAT 59.435 52.381 1.94 0.00 0.00 3.73
4945 5093 0.989602 TCCTACCCAGAGTCTCACGA 59.010 55.000 1.94 0.00 0.00 4.35
4946 5094 1.746220 CTTCCTACCCAGAGTCTCACG 59.254 57.143 1.94 0.00 0.00 4.35
4947 5095 3.088789 TCTTCCTACCCAGAGTCTCAC 57.911 52.381 1.94 0.00 0.00 3.51
4948 5096 3.076182 ACTTCTTCCTACCCAGAGTCTCA 59.924 47.826 1.94 0.00 0.00 3.27
4949 5097 3.703921 ACTTCTTCCTACCCAGAGTCTC 58.296 50.000 0.00 0.00 0.00 3.36
4950 5098 3.837399 ACTTCTTCCTACCCAGAGTCT 57.163 47.619 0.00 0.00 0.00 3.24
4951 5099 3.196039 GGAACTTCTTCCTACCCAGAGTC 59.804 52.174 0.00 0.00 42.72 3.36
4952 5100 3.174779 GGAACTTCTTCCTACCCAGAGT 58.825 50.000 0.00 0.00 42.72 3.24
4953 5101 3.897141 GGAACTTCTTCCTACCCAGAG 57.103 52.381 0.00 0.00 42.72 3.35
4969 5117 0.676151 CCAGAGCAGCCAGAAGGAAC 60.676 60.000 0.00 0.00 36.89 3.62
4970 5118 1.130054 ACCAGAGCAGCCAGAAGGAA 61.130 55.000 0.00 0.00 36.89 3.36
4971 5119 1.537397 ACCAGAGCAGCCAGAAGGA 60.537 57.895 0.00 0.00 36.89 3.36
4972 5120 1.078567 GACCAGAGCAGCCAGAAGG 60.079 63.158 0.00 0.00 38.23 3.46
4973 5121 0.391395 CAGACCAGAGCAGCCAGAAG 60.391 60.000 0.00 0.00 0.00 2.85
4974 5122 1.123861 ACAGACCAGAGCAGCCAGAA 61.124 55.000 0.00 0.00 0.00 3.02
4975 5123 1.534959 ACAGACCAGAGCAGCCAGA 60.535 57.895 0.00 0.00 0.00 3.86
4976 5124 1.375652 CACAGACCAGAGCAGCCAG 60.376 63.158 0.00 0.00 0.00 4.85
4977 5125 2.745698 CACAGACCAGAGCAGCCA 59.254 61.111 0.00 0.00 0.00 4.75
4978 5126 2.744768 AAGCACAGACCAGAGCAGCC 62.745 60.000 0.00 0.00 0.00 4.85
4979 5127 0.036952 TAAGCACAGACCAGAGCAGC 60.037 55.000 0.00 0.00 0.00 5.25
4980 5128 2.462456 TTAAGCACAGACCAGAGCAG 57.538 50.000 0.00 0.00 0.00 4.24
4981 5129 3.338249 GAATTAAGCACAGACCAGAGCA 58.662 45.455 0.00 0.00 0.00 4.26
4982 5130 2.349886 CGAATTAAGCACAGACCAGAGC 59.650 50.000 0.00 0.00 0.00 4.09
4983 5131 3.849911 TCGAATTAAGCACAGACCAGAG 58.150 45.455 0.00 0.00 0.00 3.35
4984 5132 3.953712 TCGAATTAAGCACAGACCAGA 57.046 42.857 0.00 0.00 0.00 3.86
4985 5133 6.851222 ATATTCGAATTAAGCACAGACCAG 57.149 37.500 17.19 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.