Multiple sequence alignment - TraesCS5A01G244600

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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 TraesCS5A01G244600 chr5A 100.000 2810 0 0 1 2810 458317790 458314981 0.000000e+00 5190.0
1 TraesCS5A01G244600 chr5A 82.427 239 42 0 1161 1399 458273294 458273056 2.840000e-50 209.0
2 TraesCS5A01G244600 chr5A 78.855 227 39 7 1159 1385 458524766 458524549 8.110000e-31 145.0
3 TraesCS5A01G244600 chr5B 90.821 2778 158 50 78 2802 421835221 421832488 0.000000e+00 3627.0
4 TraesCS5A01G244600 chr5B 81.224 245 45 1 1156 1399 421697170 421696926 2.210000e-46 196.0
5 TraesCS5A01G244600 chr5D 90.160 2683 167 50 78 2726 357062839 357060220 0.000000e+00 3402.0
6 TraesCS5A01G244600 chr5D 80.176 227 36 7 1159 1385 357159361 357159144 8.060000e-36 161.0
7 TraesCS5A01G244600 chr5D 97.368 76 2 0 3 78 511954780 511954705 2.270000e-26 130.0
8 TraesCS5A01G244600 chr2A 79.630 216 42 2 1158 1372 80476236 80476450 1.350000e-33 154.0
9 TraesCS5A01G244600 chr2A 98.718 78 1 0 1 78 112599172 112599249 3.770000e-29 139.0
10 TraesCS5A01G244600 chr2D 79.535 215 42 2 1159 1372 79874356 79874569 4.850000e-33 152.0
11 TraesCS5A01G244600 chr2D 97.403 77 2 0 3 79 139746299 139746223 6.320000e-27 132.0
12 TraesCS5A01G244600 chr2B 79.070 215 43 2 1159 1372 131286734 131286947 2.260000e-31 147.0
13 TraesCS5A01G244600 chr3A 96.429 84 3 0 1 84 598347039 598346956 3.770000e-29 139.0
14 TraesCS5A01G244600 chr7A 97.436 78 2 0 1 78 638839928 638839851 1.760000e-27 134.0
15 TraesCS5A01G244600 chr6B 97.403 77 2 0 3 79 290230489 290230565 6.320000e-27 132.0
16 TraesCS5A01G244600 chr3D 96.250 80 3 0 3 82 77158612 77158691 6.320000e-27 132.0
17 TraesCS5A01G244600 chr6A 97.368 76 2 0 3 78 616823973 616823898 2.270000e-26 130.0
18 TraesCS5A01G244600 chr1D 97.368 76 2 0 3 78 10337481 10337406 2.270000e-26 130.0
19 TraesCS5A01G244600 chr4D 100.000 28 0 0 915 942 12297267 12297240 5.000000e-03 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 TraesCS5A01G244600 chr5A 458314981 458317790 2809 True 5190 5190 100.000 1 2810 1 chr5A.!!$R2 2809
1 TraesCS5A01G244600 chr5B 421832488 421835221 2733 True 3627 3627 90.821 78 2802 1 chr5B.!!$R2 2724
2 TraesCS5A01G244600 chr5D 357060220 357062839 2619 True 3402 3402 90.160 78 2726 1 chr5D.!!$R1 2648

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
69 70 0.254747 TGGTGTATTGGGCTGGCTAC 59.745 55.0 0.0 0.0 0.00 3.58 F
418 451 0.396435 TGGAACGCCACTCAGATGTT 59.604 50.0 0.0 0.0 39.92 2.71 F
1235 1293 0.594602 CAACACGACCTCCGACTACA 59.405 55.0 0.0 0.0 41.76 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1588 1646 0.035317 TCTGATATCACCGCATGGCC 59.965 55.000 0.00 0.00 39.7 5.36 R
1608 1666 0.682292 TGATGTTGGCGTACACCTCA 59.318 50.000 0.85 1.57 0.0 3.86 R
2053 2115 1.004918 ACAGCAGCGGTAAGTGGAC 60.005 57.895 0.00 0.00 0.0 4.02 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
52 53 6.806668 ATTTTTATTAATGGACCACCCTGG 57.193 37.500 0.00 0.00 45.02 4.45
62 63 1.379843 CCACCCTGGTGTATTGGGC 60.380 63.158 14.89 0.00 44.56 5.36
63 64 1.691219 CACCCTGGTGTATTGGGCT 59.309 57.895 8.20 0.00 44.56 5.19
64 65 0.680921 CACCCTGGTGTATTGGGCTG 60.681 60.000 8.20 0.00 44.56 4.85
65 66 1.076777 CCCTGGTGTATTGGGCTGG 60.077 63.158 0.00 0.00 33.88 4.85
66 67 1.754234 CCTGGTGTATTGGGCTGGC 60.754 63.158 0.00 0.00 0.00 4.85
67 68 1.304282 CTGGTGTATTGGGCTGGCT 59.696 57.895 0.00 0.00 0.00 4.75
68 69 0.546122 CTGGTGTATTGGGCTGGCTA 59.454 55.000 0.00 0.00 0.00 3.93
69 70 0.254747 TGGTGTATTGGGCTGGCTAC 59.745 55.000 0.00 0.00 0.00 3.58
70 71 0.814010 GGTGTATTGGGCTGGCTACG 60.814 60.000 0.00 0.00 0.00 3.51
71 72 1.153249 TGTATTGGGCTGGCTACGC 60.153 57.895 0.00 0.00 0.00 4.42
91 92 1.665679 CCACTGCTGGCAACGTATAAG 59.334 52.381 0.00 0.00 42.51 1.73
96 97 2.289756 TGCTGGCAACGTATAAGGACAA 60.290 45.455 0.00 0.00 42.51 3.18
98 99 2.676342 CTGGCAACGTATAAGGACAACC 59.324 50.000 0.00 0.00 42.51 3.77
111 112 1.674817 GGACAACCGAGTGTACCCATG 60.675 57.143 0.00 0.00 0.00 3.66
112 113 1.274167 GACAACCGAGTGTACCCATGA 59.726 52.381 0.00 0.00 0.00 3.07
118 119 2.170607 CCGAGTGTACCCATGAGGAAAT 59.829 50.000 7.17 0.00 39.89 2.17
122 123 5.253330 GAGTGTACCCATGAGGAAATTCAA 58.747 41.667 7.17 0.00 39.89 2.69
188 189 8.191534 TCTCCTAACTGTAAGCTTTTCTAAGT 57.808 34.615 3.20 0.00 37.60 2.24
194 195 5.103290 TGTAAGCTTTTCTAAGTTTGCGG 57.897 39.130 3.20 0.00 39.08 5.69
212 213 2.601763 GCGGACAAACTATAACTGGACG 59.398 50.000 0.00 0.00 0.00 4.79
215 216 3.855950 GGACAAACTATAACTGGACGACG 59.144 47.826 0.00 0.00 0.00 5.12
228 229 2.327002 GACGACGTACAGCCGGCATA 62.327 60.000 31.54 18.12 34.85 3.14
229 230 1.657487 CGACGTACAGCCGGCATAG 60.657 63.158 31.54 20.37 34.85 2.23
243 244 5.339008 CCGGCATAGGCAGTATTAATAGA 57.661 43.478 0.15 0.00 43.71 1.98
245 246 5.581085 CCGGCATAGGCAGTATTAATAGAAC 59.419 44.000 0.15 0.00 43.71 3.01
246 247 6.163476 CGGCATAGGCAGTATTAATAGAACA 58.837 40.000 0.15 0.00 43.71 3.18
249 250 8.846211 GGCATAGGCAGTATTAATAGAACAAAA 58.154 33.333 0.15 0.00 43.71 2.44
264 276 8.902540 ATAGAACAAAAGACACAGACATGTTA 57.097 30.769 0.00 0.00 37.65 2.41
275 287 8.902806 AGACACAGACATGTTATTTTTCTTTCA 58.097 29.630 0.00 0.00 37.65 2.69
292 304 5.473931 TCTTTCATTTTCCTCTCTGTCTCG 58.526 41.667 0.00 0.00 0.00 4.04
293 305 4.873746 TTCATTTTCCTCTCTGTCTCGT 57.126 40.909 0.00 0.00 0.00 4.18
294 306 4.873746 TCATTTTCCTCTCTGTCTCGTT 57.126 40.909 0.00 0.00 0.00 3.85
295 307 5.977489 TCATTTTCCTCTCTGTCTCGTTA 57.023 39.130 0.00 0.00 0.00 3.18
296 308 6.531503 TCATTTTCCTCTCTGTCTCGTTAT 57.468 37.500 0.00 0.00 0.00 1.89
297 309 7.640597 TCATTTTCCTCTCTGTCTCGTTATA 57.359 36.000 0.00 0.00 0.00 0.98
298 310 8.239038 TCATTTTCCTCTCTGTCTCGTTATAT 57.761 34.615 0.00 0.00 0.00 0.86
299 311 8.138074 TCATTTTCCTCTCTGTCTCGTTATATG 58.862 37.037 0.00 0.00 0.00 1.78
300 312 6.392625 TTTCCTCTCTGTCTCGTTATATGG 57.607 41.667 0.00 0.00 0.00 2.74
301 313 5.050126 TCCTCTCTGTCTCGTTATATGGT 57.950 43.478 0.00 0.00 0.00 3.55
302 314 5.064558 TCCTCTCTGTCTCGTTATATGGTC 58.935 45.833 0.00 0.00 0.00 4.02
303 315 5.067273 CCTCTCTGTCTCGTTATATGGTCT 58.933 45.833 0.00 0.00 0.00 3.85
304 316 5.533154 CCTCTCTGTCTCGTTATATGGTCTT 59.467 44.000 0.00 0.00 0.00 3.01
305 317 6.293735 CCTCTCTGTCTCGTTATATGGTCTTC 60.294 46.154 0.00 0.00 0.00 2.87
306 318 6.358178 TCTCTGTCTCGTTATATGGTCTTCT 58.642 40.000 0.00 0.00 0.00 2.85
307 319 6.261158 TCTCTGTCTCGTTATATGGTCTTCTG 59.739 42.308 0.00 0.00 0.00 3.02
308 320 5.886474 TCTGTCTCGTTATATGGTCTTCTGT 59.114 40.000 0.00 0.00 0.00 3.41
309 321 6.038382 TCTGTCTCGTTATATGGTCTTCTGTC 59.962 42.308 0.00 0.00 0.00 3.51
310 322 5.886474 TGTCTCGTTATATGGTCTTCTGTCT 59.114 40.000 0.00 0.00 0.00 3.41
311 323 6.038382 TGTCTCGTTATATGGTCTTCTGTCTC 59.962 42.308 0.00 0.00 0.00 3.36
312 324 5.236695 TCTCGTTATATGGTCTTCTGTCTCG 59.763 44.000 0.00 0.00 0.00 4.04
313 325 4.880120 TCGTTATATGGTCTTCTGTCTCGT 59.120 41.667 0.00 0.00 0.00 4.18
314 326 5.356190 TCGTTATATGGTCTTCTGTCTCGTT 59.644 40.000 0.00 0.00 0.00 3.85
315 327 6.539826 TCGTTATATGGTCTTCTGTCTCGTTA 59.460 38.462 0.00 0.00 0.00 3.18
323 335 5.299782 GGTCTTCTGTCTCGTTATATGGTCT 59.700 44.000 0.00 0.00 0.00 3.85
362 382 1.136252 CCAACACTGATCGCGTCAAAG 60.136 52.381 5.77 7.16 36.14 2.77
376 396 3.012518 CGTCAAAGCATTCTCCTTCCAT 58.987 45.455 0.00 0.00 0.00 3.41
378 398 4.673580 CGTCAAAGCATTCTCCTTCCATTG 60.674 45.833 0.00 0.00 0.00 2.82
379 399 4.219288 GTCAAAGCATTCTCCTTCCATTGT 59.781 41.667 0.00 0.00 0.00 2.71
380 400 4.460382 TCAAAGCATTCTCCTTCCATTGTC 59.540 41.667 0.00 0.00 0.00 3.18
381 401 3.010200 AGCATTCTCCTTCCATTGTCC 57.990 47.619 0.00 0.00 0.00 4.02
382 402 2.579860 AGCATTCTCCTTCCATTGTCCT 59.420 45.455 0.00 0.00 0.00 3.85
401 434 5.542635 TGTCCTTACCTATATAAGCACCTGG 59.457 44.000 0.00 0.00 31.80 4.45
405 438 4.602340 ACCTATATAAGCACCTGGAACG 57.398 45.455 0.00 0.00 0.00 3.95
413 446 1.669115 CACCTGGAACGCCACTCAG 60.669 63.158 0.00 0.00 39.92 3.35
416 449 0.742281 CCTGGAACGCCACTCAGATG 60.742 60.000 0.00 0.00 39.92 2.90
418 451 0.396435 TGGAACGCCACTCAGATGTT 59.604 50.000 0.00 0.00 39.92 2.71
434 470 2.427905 TTCGTGGAAGCGACGACG 60.428 61.111 2.12 2.12 43.41 5.12
456 492 5.091431 CGGCAGCTAATTTTCTTCAGAAAG 58.909 41.667 2.35 0.00 43.90 2.62
488 524 0.764890 CACTTCCTTGTGTCCCCTCA 59.235 55.000 0.00 0.00 33.61 3.86
508 544 2.563050 TTCTCCTCATCTGCGTGGCG 62.563 60.000 0.00 0.00 0.00 5.69
542 578 3.532155 GGTCGCAGGAGGCTCGAT 61.532 66.667 8.69 0.00 41.67 3.59
543 579 2.026879 GTCGCAGGAGGCTCGATC 59.973 66.667 8.69 0.00 41.67 3.69
544 580 3.586961 TCGCAGGAGGCTCGATCG 61.587 66.667 9.36 9.36 41.67 3.69
608 644 4.223743 GCAGTAGCAACAGCGTAGATGAA 61.224 47.826 0.00 0.00 44.50 2.57
683 719 0.820871 ACCAGAGCGATCAGAAGGAC 59.179 55.000 2.38 0.00 0.00 3.85
764 800 1.748122 AGGCTACGTGACCGTCGAT 60.748 57.895 0.00 0.00 46.28 3.59
769 805 1.598132 CTACGTGACCGTCGATGAGAT 59.402 52.381 6.11 0.00 46.28 2.75
779 815 1.951130 CGATGAGATGAACGGCCGG 60.951 63.158 31.76 11.88 0.00 6.13
885 921 5.588568 GCATACATAGAGATGCACTTGTC 57.411 43.478 0.00 0.00 46.29 3.18
887 923 5.177142 GCATACATAGAGATGCACTTGTCTG 59.823 44.000 0.00 0.00 46.29 3.51
888 924 6.510536 CATACATAGAGATGCACTTGTCTGA 58.489 40.000 0.00 0.00 36.43 3.27
889 925 5.411831 ACATAGAGATGCACTTGTCTGAA 57.588 39.130 0.00 0.00 36.43 3.02
890 926 5.987098 ACATAGAGATGCACTTGTCTGAAT 58.013 37.500 0.00 0.00 36.43 2.57
891 927 5.816258 ACATAGAGATGCACTTGTCTGAATG 59.184 40.000 0.00 0.00 36.43 2.67
893 929 4.252073 AGAGATGCACTTGTCTGAATGTC 58.748 43.478 0.00 0.00 0.00 3.06
894 930 4.020396 AGAGATGCACTTGTCTGAATGTCT 60.020 41.667 0.00 0.00 0.00 3.41
895 931 4.252073 AGATGCACTTGTCTGAATGTCTC 58.748 43.478 0.00 0.00 0.00 3.36
897 933 2.224042 TGCACTTGTCTGAATGTCTCGT 60.224 45.455 0.00 0.00 0.00 4.18
898 934 2.410053 GCACTTGTCTGAATGTCTCGTC 59.590 50.000 0.00 0.00 0.00 4.20
900 936 3.917380 CACTTGTCTGAATGTCTCGTCTC 59.083 47.826 0.00 0.00 0.00 3.36
901 937 3.823873 ACTTGTCTGAATGTCTCGTCTCT 59.176 43.478 0.00 0.00 0.00 3.10
902 938 4.083003 ACTTGTCTGAATGTCTCGTCTCTC 60.083 45.833 0.00 0.00 0.00 3.20
903 939 3.412386 TGTCTGAATGTCTCGTCTCTCA 58.588 45.455 0.00 0.00 0.00 3.27
904 940 4.013050 TGTCTGAATGTCTCGTCTCTCAT 58.987 43.478 0.00 0.00 0.00 2.90
905 941 5.186198 TGTCTGAATGTCTCGTCTCTCATA 58.814 41.667 0.00 0.00 0.00 2.15
906 942 5.065346 TGTCTGAATGTCTCGTCTCTCATAC 59.935 44.000 0.00 0.00 0.00 2.39
908 944 3.939592 TGAATGTCTCGTCTCTCATACGT 59.060 43.478 0.00 0.00 41.08 3.57
910 946 5.583457 TGAATGTCTCGTCTCTCATACGTTA 59.417 40.000 0.00 0.00 41.08 3.18
911 947 6.260271 TGAATGTCTCGTCTCTCATACGTTAT 59.740 38.462 0.00 0.00 41.08 1.89
913 949 4.874396 TGTCTCGTCTCTCATACGTTATGT 59.126 41.667 0.00 0.00 41.08 2.29
938 992 5.835113 AATGATCTTACATTTTGGGACGG 57.165 39.130 0.00 0.00 37.20 4.79
960 1014 6.874134 ACGGAGTACTTGATATATTTCCATGC 59.126 38.462 0.00 0.00 41.94 4.06
961 1015 6.035005 CGGAGTACTTGATATATTTCCATGCG 59.965 42.308 0.00 0.00 0.00 4.73
1012 1066 2.832201 GAGCAATGGGGGAGCTGC 60.832 66.667 0.00 0.00 39.02 5.25
1070 1124 2.665185 AAACGAGCACGCCTGGAC 60.665 61.111 2.62 0.00 43.96 4.02
1085 1139 1.078637 GGACCAACGGTTAGGGAGC 60.079 63.158 4.42 0.00 35.25 4.70
1103 1157 3.317993 GGAGCCACAACATTACAACAACT 59.682 43.478 0.00 0.00 0.00 3.16
1105 1159 3.068024 AGCCACAACATTACAACAACTGG 59.932 43.478 0.00 0.00 0.00 4.00
1235 1293 0.594602 CAACACGACCTCCGACTACA 59.405 55.000 0.00 0.00 41.76 2.74
1308 1366 2.577593 GTTCGAGAGGTTCCCGGG 59.422 66.667 16.85 16.85 0.00 5.73
1431 1489 1.002315 ACAGGGTATTTTGGTACGCGT 59.998 47.619 19.17 19.17 41.02 6.01
1509 1567 8.918961 AGTGAAGATCGTATAATATAGCTTGC 57.081 34.615 0.00 0.00 0.00 4.01
1519 1577 8.343366 CGTATAATATAGCTTGCGGATCTCTAA 58.657 37.037 0.00 0.00 0.00 2.10
1563 1621 9.059260 CCATATCTTGATGATAACATGAACACA 57.941 33.333 0.00 0.00 40.62 3.72
1574 1632 2.693074 ACATGAACACAAAAGGGGTGAC 59.307 45.455 0.00 0.00 39.53 3.67
1593 1651 2.971598 CGACTTCCTGTGGGGCCAT 61.972 63.158 4.39 0.00 34.39 4.40
1596 1654 4.738998 TTCCTGTGGGGCCATGCG 62.739 66.667 4.39 0.00 34.39 4.73
1608 1666 1.339438 GGCCATGCGGTGATATCAGAT 60.339 52.381 5.42 0.00 33.28 2.90
1641 1699 1.242076 ACATCACCAAGAGCTGCAAC 58.758 50.000 1.02 0.00 0.00 4.17
1782 1840 2.501723 CCCCAGCCGCTATGTAAGATAT 59.498 50.000 0.00 0.00 0.00 1.63
1783 1841 3.704566 CCCCAGCCGCTATGTAAGATATA 59.295 47.826 0.00 0.00 0.00 0.86
1784 1842 4.441634 CCCCAGCCGCTATGTAAGATATAC 60.442 50.000 0.00 0.00 0.00 1.47
1785 1843 4.352039 CCAGCCGCTATGTAAGATATACG 58.648 47.826 0.00 0.00 0.00 3.06
1841 1903 7.272515 GCAAATTATATGCACGTAACACACTTT 59.727 33.333 0.00 0.00 43.29 2.66
1966 2028 0.879765 CTGAGGTGCAAAAGGCTCTG 59.120 55.000 0.00 0.00 45.15 3.35
2014 2076 3.548268 GCTGCACGTAAGAGTTAGCTTAG 59.452 47.826 0.00 0.00 43.62 2.18
2053 2115 2.028294 ACTCTTGTGAGCATCCACTCAG 60.028 50.000 0.00 0.00 47.00 3.35
2064 2126 1.254026 TCCACTCAGTCCACTTACCG 58.746 55.000 0.00 0.00 0.00 4.02
2067 2129 0.603569 ACTCAGTCCACTTACCGCTG 59.396 55.000 0.00 0.00 0.00 5.18
2073 2135 2.680913 CCACTTACCGCTGCTGTGC 61.681 63.158 6.98 0.00 0.00 4.57
2307 2369 0.244721 GTTTACCGCCACGAGGTACT 59.755 55.000 0.00 0.00 43.27 2.73
2328 2390 1.216175 CCATCCATCCATGACCTTGGT 59.784 52.381 0.00 0.00 38.01 3.67
2335 2397 2.047274 ATGACCTTGGTGTCGCCG 60.047 61.111 0.00 0.00 41.21 6.46
2534 2598 1.203313 TCAGGTCCCTTACTTCCAGCT 60.203 52.381 0.00 0.00 0.00 4.24
2635 2699 5.411669 GGACCTAAGTAAGAATTGTGGTGTG 59.588 44.000 0.00 0.00 0.00 3.82
2636 2700 5.937111 ACCTAAGTAAGAATTGTGGTGTGT 58.063 37.500 0.00 0.00 0.00 3.72
2637 2701 5.995897 ACCTAAGTAAGAATTGTGGTGTGTC 59.004 40.000 0.00 0.00 0.00 3.67
2638 2702 5.995282 CCTAAGTAAGAATTGTGGTGTGTCA 59.005 40.000 0.00 0.00 0.00 3.58
2639 2703 6.655003 CCTAAGTAAGAATTGTGGTGTGTCAT 59.345 38.462 0.00 0.00 0.00 3.06
2640 2704 6.560253 AAGTAAGAATTGTGGTGTGTCATC 57.440 37.500 0.00 0.00 0.00 2.92
2655 2719 5.012046 GTGTGTCATCCATCCAGATATGGTA 59.988 44.000 6.21 0.00 45.67 3.25
2748 2812 8.766994 ATACAACAAATTTATGGCACCTCTAT 57.233 30.769 0.00 0.00 0.00 1.98
2802 2866 3.244284 ACCTAACGTGTGGCACTTATCAA 60.244 43.478 19.83 0.00 31.34 2.57
2803 2867 3.124636 CCTAACGTGTGGCACTTATCAAC 59.875 47.826 19.83 6.32 31.34 3.18
2804 2868 2.248280 ACGTGTGGCACTTATCAACA 57.752 45.000 19.83 0.00 31.34 3.33
2805 2869 2.566913 ACGTGTGGCACTTATCAACAA 58.433 42.857 19.83 0.00 31.34 2.83
2806 2870 3.146066 ACGTGTGGCACTTATCAACAAT 58.854 40.909 19.83 0.00 31.34 2.71
2807 2871 3.568007 ACGTGTGGCACTTATCAACAATT 59.432 39.130 19.83 0.00 31.34 2.32
2808 2872 4.757657 ACGTGTGGCACTTATCAACAATTA 59.242 37.500 19.83 0.00 31.34 1.40
2809 2873 5.106712 ACGTGTGGCACTTATCAACAATTAG 60.107 40.000 19.83 0.00 31.34 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 8.933653 CCAGGGTGGTCCATTAATAAAAATATT 58.066 33.333 0.00 0.00 38.24 1.28
27 28 8.491045 CCAGGGTGGTCCATTAATAAAAATAT 57.509 34.615 0.00 0.00 38.24 1.28
28 29 7.906199 CCAGGGTGGTCCATTAATAAAAATA 57.094 36.000 0.00 0.00 38.24 1.40
29 30 6.806668 CCAGGGTGGTCCATTAATAAAAAT 57.193 37.500 0.00 0.00 38.24 1.82
46 47 1.691219 CAGCCCAATACACCAGGGT 59.309 57.895 0.00 0.00 44.69 4.34
47 48 1.076777 CCAGCCCAATACACCAGGG 60.077 63.158 0.00 0.00 45.68 4.45
48 49 1.754234 GCCAGCCCAATACACCAGG 60.754 63.158 0.00 0.00 0.00 4.45
49 50 0.546122 TAGCCAGCCCAATACACCAG 59.454 55.000 0.00 0.00 0.00 4.00
50 51 0.254747 GTAGCCAGCCCAATACACCA 59.745 55.000 0.00 0.00 0.00 4.17
51 52 0.814010 CGTAGCCAGCCCAATACACC 60.814 60.000 0.00 0.00 0.00 4.16
52 53 2.690326 CGTAGCCAGCCCAATACAC 58.310 57.895 0.00 0.00 0.00 2.90
72 73 1.665679 CCTTATACGTTGCCAGCAGTG 59.334 52.381 0.00 0.00 0.00 3.66
73 74 1.553248 TCCTTATACGTTGCCAGCAGT 59.447 47.619 0.00 0.00 0.00 4.40
74 75 1.933853 GTCCTTATACGTTGCCAGCAG 59.066 52.381 0.00 0.00 0.00 4.24
75 76 1.276705 TGTCCTTATACGTTGCCAGCA 59.723 47.619 0.00 0.00 0.00 4.41
76 77 2.018542 TGTCCTTATACGTTGCCAGC 57.981 50.000 0.00 0.00 0.00 4.85
91 92 0.611714 ATGGGTACACTCGGTTGTCC 59.388 55.000 0.00 0.00 0.00 4.02
96 97 0.040646 TCCTCATGGGTACACTCGGT 59.959 55.000 0.00 0.00 36.25 4.69
98 99 3.543680 ATTTCCTCATGGGTACACTCG 57.456 47.619 0.00 0.00 36.25 4.18
111 112 9.294030 GTGATGTATGATTGTTTGAATTTCCTC 57.706 33.333 0.00 0.00 0.00 3.71
112 113 8.253113 GGTGATGTATGATTGTTTGAATTTCCT 58.747 33.333 0.00 0.00 0.00 3.36
118 119 4.397730 CCCGGTGATGTATGATTGTTTGAA 59.602 41.667 0.00 0.00 0.00 2.69
122 123 2.930950 CCCCGGTGATGTATGATTGTT 58.069 47.619 0.00 0.00 0.00 2.83
160 161 7.489239 AGAAAAGCTTACAGTTAGGAGAGAT 57.511 36.000 0.00 0.00 0.00 2.75
188 189 4.453136 GTCCAGTTATAGTTTGTCCGCAAA 59.547 41.667 0.00 0.00 41.77 3.68
194 195 4.479619 ACGTCGTCCAGTTATAGTTTGTC 58.520 43.478 0.00 0.00 0.00 3.18
212 213 1.299926 CCTATGCCGGCTGTACGTC 60.300 63.158 29.70 0.00 0.00 4.34
228 229 8.947115 GTGTCTTTTGTTCTATTAATACTGCCT 58.053 33.333 0.00 0.00 0.00 4.75
229 230 8.726988 TGTGTCTTTTGTTCTATTAATACTGCC 58.273 33.333 0.00 0.00 0.00 4.85
238 239 7.807977 ACATGTCTGTGTCTTTTGTTCTATT 57.192 32.000 0.00 0.00 33.22 1.73
240 241 8.902540 ATAACATGTCTGTGTCTTTTGTTCTA 57.097 30.769 0.00 0.00 35.22 2.10
241 242 7.807977 ATAACATGTCTGTGTCTTTTGTTCT 57.192 32.000 0.00 0.00 35.22 3.01
242 243 8.856490 AAATAACATGTCTGTGTCTTTTGTTC 57.144 30.769 0.00 0.00 35.22 3.18
243 244 9.651913 AAAAATAACATGTCTGTGTCTTTTGTT 57.348 25.926 0.00 0.00 35.22 2.83
245 246 9.520204 AGAAAAATAACATGTCTGTGTCTTTTG 57.480 29.630 0.00 0.00 35.22 2.44
249 250 8.902806 TGAAAGAAAAATAACATGTCTGTGTCT 58.097 29.630 0.00 0.00 35.22 3.41
264 276 9.140874 AGACAGAGAGGAAAATGAAAGAAAAAT 57.859 29.630 0.00 0.00 0.00 1.82
275 287 7.070074 ACCATATAACGAGACAGAGAGGAAAAT 59.930 37.037 0.00 0.00 0.00 1.82
283 295 6.038825 ACAGAAGACCATATAACGAGACAGAG 59.961 42.308 0.00 0.00 0.00 3.35
285 297 6.038825 AGACAGAAGACCATATAACGAGACAG 59.961 42.308 0.00 0.00 0.00 3.51
294 306 8.957466 CCATATAACGAGACAGAAGACCATATA 58.043 37.037 0.00 0.00 0.00 0.86
295 307 7.451877 ACCATATAACGAGACAGAAGACCATAT 59.548 37.037 0.00 0.00 0.00 1.78
296 308 6.776116 ACCATATAACGAGACAGAAGACCATA 59.224 38.462 0.00 0.00 0.00 2.74
297 309 5.598830 ACCATATAACGAGACAGAAGACCAT 59.401 40.000 0.00 0.00 0.00 3.55
298 310 4.954202 ACCATATAACGAGACAGAAGACCA 59.046 41.667 0.00 0.00 0.00 4.02
299 311 5.299782 AGACCATATAACGAGACAGAAGACC 59.700 44.000 0.00 0.00 0.00 3.85
300 312 6.038382 TCAGACCATATAACGAGACAGAAGAC 59.962 42.308 0.00 0.00 0.00 3.01
301 313 6.120220 TCAGACCATATAACGAGACAGAAGA 58.880 40.000 0.00 0.00 0.00 2.87
302 314 6.378710 TCAGACCATATAACGAGACAGAAG 57.621 41.667 0.00 0.00 0.00 2.85
303 315 6.602009 TCTTCAGACCATATAACGAGACAGAA 59.398 38.462 0.00 0.00 0.00 3.02
304 316 6.120220 TCTTCAGACCATATAACGAGACAGA 58.880 40.000 0.00 0.00 0.00 3.41
305 317 6.378710 TCTTCAGACCATATAACGAGACAG 57.621 41.667 0.00 0.00 0.00 3.51
306 318 6.377429 AGTTCTTCAGACCATATAACGAGACA 59.623 38.462 0.00 0.00 0.00 3.41
307 319 6.797454 AGTTCTTCAGACCATATAACGAGAC 58.203 40.000 0.00 0.00 0.00 3.36
308 320 7.406031 AAGTTCTTCAGACCATATAACGAGA 57.594 36.000 0.00 0.00 0.00 4.04
309 321 8.480643 AAAAGTTCTTCAGACCATATAACGAG 57.519 34.615 0.00 0.00 0.00 4.18
310 322 8.092068 TGAAAAGTTCTTCAGACCATATAACGA 58.908 33.333 0.00 0.00 31.67 3.85
311 323 8.251750 TGAAAAGTTCTTCAGACCATATAACG 57.748 34.615 0.00 0.00 31.67 3.18
313 325 9.231297 CCTTGAAAAGTTCTTCAGACCATATAA 57.769 33.333 2.30 0.00 44.25 0.98
314 326 7.336931 GCCTTGAAAAGTTCTTCAGACCATATA 59.663 37.037 2.30 0.00 44.25 0.86
315 327 6.151817 GCCTTGAAAAGTTCTTCAGACCATAT 59.848 38.462 2.30 0.00 44.25 1.78
318 330 3.632145 GCCTTGAAAAGTTCTTCAGACCA 59.368 43.478 2.30 0.00 44.25 4.02
323 335 3.897239 TGGAGCCTTGAAAAGTTCTTCA 58.103 40.909 0.00 0.00 44.25 3.02
362 382 3.010200 AGGACAATGGAAGGAGAATGC 57.990 47.619 0.00 0.00 0.00 3.56
378 398 5.778750 TCCAGGTGCTTATATAGGTAAGGAC 59.221 44.000 8.49 8.49 46.22 3.85
379 399 5.972698 TCCAGGTGCTTATATAGGTAAGGA 58.027 41.667 0.00 0.00 33.31 3.36
380 400 6.465084 GTTCCAGGTGCTTATATAGGTAAGG 58.535 44.000 0.00 0.00 33.31 2.69
381 401 6.157211 CGTTCCAGGTGCTTATATAGGTAAG 58.843 44.000 0.00 0.00 35.31 2.34
382 402 5.510179 GCGTTCCAGGTGCTTATATAGGTAA 60.510 44.000 0.00 0.00 0.00 2.85
401 434 0.716108 CGAACATCTGAGTGGCGTTC 59.284 55.000 0.00 0.00 34.10 3.95
405 438 2.460330 CCACGAACATCTGAGTGGC 58.540 57.895 0.29 0.00 46.06 5.01
413 446 0.731514 TCGTCGCTTCCACGAACATC 60.732 55.000 0.00 0.00 44.93 3.06
418 451 4.394078 CCGTCGTCGCTTCCACGA 62.394 66.667 5.13 0.00 43.85 4.35
425 458 2.558554 AATTAGCTGCCGTCGTCGCT 62.559 55.000 0.00 5.66 36.56 4.93
434 470 4.861462 GCTTTCTGAAGAAAATTAGCTGCC 59.139 41.667 6.92 0.00 42.72 4.85
437 473 7.458409 TGATGCTTTCTGAAGAAAATTAGCT 57.542 32.000 13.03 0.00 42.72 3.32
481 517 2.687297 CAGATGAGGAGAATGAGGGGA 58.313 52.381 0.00 0.00 0.00 4.81
482 518 1.072015 GCAGATGAGGAGAATGAGGGG 59.928 57.143 0.00 0.00 0.00 4.79
483 519 1.270199 CGCAGATGAGGAGAATGAGGG 60.270 57.143 0.00 0.00 0.00 4.30
488 524 0.179062 GCCACGCAGATGAGGAGAAT 60.179 55.000 0.00 0.00 0.00 2.40
542 578 1.107114 GGATCAACTCTCTGAGCCGA 58.893 55.000 0.00 0.00 41.73 5.54
543 579 3.657956 GGATCAACTCTCTGAGCCG 57.342 57.895 0.00 0.00 41.73 5.52
608 644 2.043227 GCAGTAGCTCCTATCCTTGGT 58.957 52.381 0.00 0.00 37.91 3.67
613 649 0.682292 GGTGGCAGTAGCTCCTATCC 59.318 60.000 0.00 0.00 41.70 2.59
636 672 4.828925 GTGCTCTGCTCGGAGGCC 62.829 72.222 7.20 0.00 34.21 5.19
764 800 4.467084 GCCCGGCCGTTCATCTCA 62.467 66.667 26.12 0.00 0.00 3.27
779 815 1.477295 ACAAGGTAGTAGAAGAGCGCC 59.523 52.381 2.29 0.00 0.00 6.53
830 866 0.038526 CGTTAAGCCACAGGACGAGT 60.039 55.000 0.00 0.00 35.90 4.18
885 921 4.034626 ACGTATGAGAGACGAGACATTCAG 59.965 45.833 1.71 0.00 42.98 3.02
887 923 4.539509 ACGTATGAGAGACGAGACATTC 57.460 45.455 1.71 0.00 42.98 2.67
888 924 4.966965 AACGTATGAGAGACGAGACATT 57.033 40.909 1.71 0.00 42.98 2.71
889 925 5.527951 ACATAACGTATGAGAGACGAGACAT 59.472 40.000 10.64 0.00 42.98 3.06
890 926 4.874396 ACATAACGTATGAGAGACGAGACA 59.126 41.667 10.64 0.00 42.98 3.41
891 927 5.406767 ACATAACGTATGAGAGACGAGAC 57.593 43.478 10.64 0.00 42.98 3.36
893 929 8.682895 CATTTTACATAACGTATGAGAGACGAG 58.317 37.037 10.64 0.00 42.98 4.18
894 930 8.400186 TCATTTTACATAACGTATGAGAGACGA 58.600 33.333 10.64 1.19 42.98 4.20
895 931 8.556517 TCATTTTACATAACGTATGAGAGACG 57.443 34.615 10.64 0.00 45.75 4.18
938 992 6.874134 ACCGCATGGAAATATATCAAGTACTC 59.126 38.462 0.00 0.00 39.21 2.59
944 998 4.140536 TGCACCGCATGGAAATATATCAA 58.859 39.130 0.00 0.00 39.21 2.57
960 1014 2.124983 CATCCTGGACCTGCACCG 60.125 66.667 0.00 0.00 0.00 4.94
961 1015 2.439156 GCATCCTGGACCTGCACC 60.439 66.667 15.61 0.00 35.96 5.01
1070 1124 1.376812 GTGGCTCCCTAACCGTTGG 60.377 63.158 0.00 0.00 0.00 3.77
1085 1139 4.647424 ACCAGTTGTTGTAATGTTGTGG 57.353 40.909 0.00 0.00 0.00 4.17
1122 1176 0.531974 ACATGTCACGTGTGGGTCAC 60.532 55.000 16.51 5.62 43.03 3.67
1168 1226 2.477357 CGATTCGAGGAAGAGCACGTTA 60.477 50.000 0.00 0.00 0.00 3.18
1204 1262 3.326880 AGGTCGTGTTGGAGTAGGAAAAT 59.673 43.478 0.00 0.00 0.00 1.82
1235 1293 0.605589 CTCTGGTCTCCGCTCTTGTT 59.394 55.000 0.00 0.00 0.00 2.83
1308 1366 2.871216 GAAGGAGCGGCCCTTGTACC 62.871 65.000 22.15 8.50 45.97 3.34
1509 1567 4.503296 CCCACCTAACCAATTAGAGATCCG 60.503 50.000 0.00 0.00 40.38 4.18
1519 1577 0.252057 GGGTTGCCCACCTAACCAAT 60.252 55.000 8.25 0.00 46.39 3.16
1563 1621 0.109913 GGAAGTCGGTCACCCCTTTT 59.890 55.000 0.00 0.00 0.00 2.27
1574 1632 4.410400 GGCCCCACAGGAAGTCGG 62.410 72.222 0.00 0.00 38.24 4.79
1588 1646 0.035317 TCTGATATCACCGCATGGCC 59.965 55.000 0.00 0.00 39.70 5.36
1593 1651 2.036346 CACCTCATCTGATATCACCGCA 59.964 50.000 0.00 0.00 0.00 5.69
1596 1654 4.799678 CGTACACCTCATCTGATATCACC 58.200 47.826 0.00 0.00 0.00 4.02
1608 1666 0.682292 TGATGTTGGCGTACACCTCA 59.318 50.000 0.85 1.57 0.00 3.86
1782 1840 9.146984 CAGAAAAGATGTACTCCAAAATACGTA 57.853 33.333 0.00 0.00 0.00 3.57
1783 1841 7.876068 TCAGAAAAGATGTACTCCAAAATACGT 59.124 33.333 0.00 0.00 0.00 3.57
1784 1842 8.251750 TCAGAAAAGATGTACTCCAAAATACG 57.748 34.615 0.00 0.00 0.00 3.06
1870 1932 4.067896 CCTGCACAATTTAGAGCGGATAT 58.932 43.478 0.00 0.00 33.97 1.63
1966 2028 2.159627 CCACTTGGTCGTTCTAACATGC 59.840 50.000 0.00 0.00 0.00 4.06
1990 2052 1.641577 CTAACTCTTACGTGCAGCCC 58.358 55.000 0.00 0.00 0.00 5.19
2014 2076 4.793201 AGAGTATTTATCTTGGCCCCAAC 58.207 43.478 0.00 0.00 0.00 3.77
2053 2115 1.004918 ACAGCAGCGGTAAGTGGAC 60.005 57.895 0.00 0.00 0.00 4.02
2265 2327 1.800315 ACACGGAGTCGAAATCGCG 60.800 57.895 0.00 0.00 41.61 5.87
2307 2369 1.496001 CCAAGGTCATGGATGGATGGA 59.504 52.381 0.00 0.00 43.54 3.41
2308 2370 1.216175 ACCAAGGTCATGGATGGATGG 59.784 52.381 12.05 7.50 43.54 3.51
2309 2371 2.304092 CACCAAGGTCATGGATGGATG 58.696 52.381 12.05 5.28 43.54 3.51
2310 2372 1.925255 ACACCAAGGTCATGGATGGAT 59.075 47.619 12.05 0.71 43.54 3.41
2405 2467 4.793216 CAGTCAGTACAAACAAACAAGTGC 59.207 41.667 0.00 0.00 0.00 4.40
2639 2703 9.430533 GCTAAGGCAATACCATATCTGGATGGA 62.431 44.444 9.38 0.00 42.54 3.41
2640 2704 7.355301 GCTAAGGCAATACCATATCTGGATGG 61.355 46.154 3.76 0.81 43.96 3.51
2682 2746 6.710744 TCCATTTGAAGAGGTAAAAGACAGAC 59.289 38.462 0.00 0.00 0.00 3.51
2693 2757 1.271379 CCCGTGTCCATTTGAAGAGGT 60.271 52.381 0.00 0.00 0.00 3.85
2748 2812 3.701532 CGGAAGGCAGTTGTAACAAAA 57.298 42.857 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.