Multiple sequence alignment - TraesCS5D01G299100

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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 TraesCS5D01G299100 chr5D 100.000 7635 0 0 1 7635 396689122 396696756 0.000000e+00 14100
1 TraesCS5D01G299100 chr5D 96.341 82 0 1 6763 6841 396695807 396695888 1.730000e-26 132
2 TraesCS5D01G299100 chr5D 96.341 82 0 1 6686 6767 396695884 396695962 1.730000e-26 132
3 TraesCS5D01G299100 chr5A 96.005 6182 137 34 658 6764 502297887 502304033 0.000000e+00 9947
4 TraesCS5D01G299100 chr5A 90.640 609 11 14 23 607 502297286 502297872 0.000000e+00 767
5 TraesCS5D01G299100 chr5A 95.810 358 14 1 7152 7509 502304667 502305023 1.850000e-160 577
6 TraesCS5D01G299100 chr5A 84.878 410 22 18 6763 7140 502303955 502304356 2.010000e-100 377
7 TraesCS5D01G299100 chr5A 94.215 121 7 0 7515 7635 502305060 502305180 1.310000e-42 185
8 TraesCS5D01G299100 chr5B 88.050 2703 166 78 2 2634 476631334 476633949 0.000000e+00 3057
9 TraesCS5D01G299100 chr5B 96.475 1475 46 1 5293 6767 476636338 476637806 0.000000e+00 2431
10 TraesCS5D01G299100 chr5B 94.202 1259 52 13 4007 5255 476635092 476636339 0.000000e+00 1901
11 TraesCS5D01G299100 chr5B 93.292 1118 46 12 2791 3887 476633948 476635057 0.000000e+00 1622
12 TraesCS5D01G299100 chr5B 96.502 486 15 2 7152 7635 476638331 476638816 0.000000e+00 802
13 TraesCS5D01G299100 chr5B 90.952 210 14 3 6949 7157 476638064 476638269 2.100000e-70 278
14 TraesCS5D01G299100 chr5B 92.414 145 6 3 6763 6905 476637731 476637872 1.300000e-47 202
15 TraesCS5D01G299100 chr5B 82.609 207 23 4 4156 4349 355055037 355054831 3.660000e-38 171
16 TraesCS5D01G299100 chr4D 94.545 165 7 2 2633 2795 479687421 479687257 3.540000e-63 254
17 TraesCS5D01G299100 chr6B 94.479 163 7 2 2632 2792 36133503 36133665 4.570000e-62 250
18 TraesCS5D01G299100 chr4B 93.939 165 8 2 2633 2795 606916924 606916760 1.650000e-61 248
19 TraesCS5D01G299100 chr4B 84.293 191 18 6 4164 4342 272458883 272459073 7.870000e-40 176
20 TraesCS5D01G299100 chr3D 93.333 165 9 2 2633 2795 87926161 87925997 7.650000e-60 243
21 TraesCS5D01G299100 chr2D 93.373 166 8 3 2630 2793 296364046 296364210 7.650000e-60 243
22 TraesCS5D01G299100 chr2B 92.899 169 9 3 2630 2796 366017682 366017515 7.650000e-60 243
23 TraesCS5D01G299100 chr7B 92.814 167 10 2 2633 2797 490207990 490208156 2.750000e-59 241
24 TraesCS5D01G299100 chr2A 88.889 189 18 3 2631 2816 416924122 416923934 5.960000e-56 230


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 TraesCS5D01G299100 chr5D 396689122 396696756 7634 False 4788.000000 14100 97.560667 1 7635 3 chr5D.!!$F1 7634
1 TraesCS5D01G299100 chr5A 502297286 502305180 7894 False 2370.600000 9947 92.309600 23 7635 5 chr5A.!!$F1 7612
2 TraesCS5D01G299100 chr5B 476631334 476638816 7482 False 1470.428571 3057 93.126714 2 7635 7 chr5B.!!$F1 7633

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
303 318 0.035881 TCTCTCAGCCTGCCTTGTTG 59.964 55.0 0.00 0.0 0.00 3.33 F
828 913 0.103937 CATTCCTCTCCACTCTCCGC 59.896 60.0 0.00 0.0 0.00 5.54 F
1165 1273 0.395312 TCCCCTTTCGTTTCGCTTCT 59.605 50.0 0.00 0.0 0.00 2.85 F
1410 1533 0.455815 AATTGCCTCGGGATTTTCGC 59.544 50.0 0.00 0.0 0.00 4.70 F
1497 1620 1.009389 GGAGACTGTCGAAGCGTTGG 61.009 60.0 1.52 0.0 0.00 3.77 F
2018 2146 1.165270 CCCATTCCCAAGTGTCGTTC 58.835 55.0 0.00 0.0 0.00 3.95 F
3223 3381 1.172175 GCCCTCTCTCTTTTGCAAGG 58.828 55.0 0.00 0.0 0.00 3.61 F
5369 5566 2.413112 CACTCCATGTGTCGAATGTGTC 59.587 50.0 0.00 0.0 41.53 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 1636 0.176219 AAACAACACCGGACTCGTCA 59.824 50.000 9.46 0.00 33.95 4.35 R
1745 1872 1.744320 AAGAGGCGCCAAAACCCAAC 61.744 55.000 31.54 7.76 0.00 3.77 R
1976 2104 4.081420 GGAAGTCTCTTCTCATAGCCAACA 60.081 45.833 8.96 0.00 0.00 3.33 R
3171 3322 5.890424 ACTACTGACTAGCAAGAGAAGAC 57.110 43.478 0.00 0.00 0.00 3.01 R
3890 4078 3.498774 ATGATATGCAGTCACCCCTTC 57.501 47.619 6.72 0.00 0.00 3.46 R
4299 4493 1.047002 TCCCACCAAAACATTGGCTG 58.953 50.000 7.49 5.61 45.88 4.85 R
5443 5641 1.000506 GAGTTAAGAGCACCGACCACA 59.999 52.381 0.00 0.00 0.00 4.17 R
7300 7951 0.877071 CACCACCAGCTACTTTGCAG 59.123 55.000 0.00 0.00 34.99 4.41 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
154 160 4.759205 AAGGGGCCATTGCGTCCC 62.759 66.667 0.92 6.69 38.79 4.46
163 169 2.582436 TTGCGTCCCCGGAATCTC 59.418 61.111 0.73 0.00 39.61 2.75
164 170 1.987855 TTGCGTCCCCGGAATCTCT 60.988 57.895 0.73 0.00 39.61 3.10
165 171 1.956629 TTGCGTCCCCGGAATCTCTC 61.957 60.000 0.73 0.00 39.61 3.20
258 273 2.584418 CAGCTCACGCAGATCCCG 60.584 66.667 2.20 2.20 39.10 5.14
267 282 2.827423 CAGATCCCGCCTGCATCT 59.173 61.111 0.00 0.00 0.00 2.90
299 314 0.835543 AGTGTCTCTCAGCCTGCCTT 60.836 55.000 0.00 0.00 0.00 4.35
300 315 0.673022 GTGTCTCTCAGCCTGCCTTG 60.673 60.000 0.00 0.00 0.00 3.61
301 316 1.123861 TGTCTCTCAGCCTGCCTTGT 61.124 55.000 0.00 0.00 0.00 3.16
302 317 0.036022 GTCTCTCAGCCTGCCTTGTT 59.964 55.000 0.00 0.00 0.00 2.83
303 318 0.035881 TCTCTCAGCCTGCCTTGTTG 59.964 55.000 0.00 0.00 0.00 3.33
304 319 1.584380 CTCTCAGCCTGCCTTGTTGC 61.584 60.000 0.00 0.00 0.00 4.17
305 320 1.900016 CTCAGCCTGCCTTGTTGCA 60.900 57.895 0.00 0.00 39.37 4.08
306 321 1.455402 TCAGCCTGCCTTGTTGCAA 60.455 52.632 0.00 0.00 41.51 4.08
307 322 0.828762 TCAGCCTGCCTTGTTGCAAT 60.829 50.000 0.59 0.00 41.51 3.56
362 383 2.995258 CGAGGACCGAGCTATAGTACTC 59.005 54.545 0.00 10.99 41.76 2.59
394 415 3.932289 GCAGCAAGCAAGCAACAG 58.068 55.556 3.19 0.00 44.79 3.16
395 416 1.663702 GCAGCAAGCAAGCAACAGG 60.664 57.895 3.19 0.00 44.79 4.00
396 417 1.737816 CAGCAAGCAAGCAACAGGT 59.262 52.632 3.19 0.00 36.85 4.00
397 418 0.953727 CAGCAAGCAAGCAACAGGTA 59.046 50.000 3.19 0.00 36.85 3.08
398 419 1.337703 CAGCAAGCAAGCAACAGGTAA 59.662 47.619 3.19 0.00 36.85 2.85
399 420 2.031120 AGCAAGCAAGCAACAGGTAAA 58.969 42.857 3.19 0.00 36.85 2.01
400 421 2.127251 GCAAGCAAGCAACAGGTAAAC 58.873 47.619 0.00 0.00 0.00 2.01
401 422 2.481104 GCAAGCAAGCAACAGGTAAACA 60.481 45.455 0.00 0.00 0.00 2.83
402 423 3.779759 CAAGCAAGCAACAGGTAAACAA 58.220 40.909 0.00 0.00 0.00 2.83
403 424 4.180057 CAAGCAAGCAACAGGTAAACAAA 58.820 39.130 0.00 0.00 0.00 2.83
404 425 4.045636 AGCAAGCAACAGGTAAACAAAG 57.954 40.909 0.00 0.00 0.00 2.77
405 426 2.539688 GCAAGCAACAGGTAAACAAAGC 59.460 45.455 0.00 0.00 0.00 3.51
406 427 3.779759 CAAGCAACAGGTAAACAAAGCA 58.220 40.909 0.00 0.00 0.00 3.91
407 428 4.180057 CAAGCAACAGGTAAACAAAGCAA 58.820 39.130 0.00 0.00 0.00 3.91
408 429 4.045636 AGCAACAGGTAAACAAAGCAAG 57.954 40.909 0.00 0.00 0.00 4.01
409 430 2.539688 GCAACAGGTAAACAAAGCAAGC 59.460 45.455 0.00 0.00 0.00 4.01
410 431 3.779759 CAACAGGTAAACAAAGCAAGCA 58.220 40.909 0.00 0.00 0.00 3.91
411 432 4.180057 CAACAGGTAAACAAAGCAAGCAA 58.820 39.130 0.00 0.00 0.00 3.91
412 433 4.045636 ACAGGTAAACAAAGCAAGCAAG 57.954 40.909 0.00 0.00 0.00 4.01
413 434 2.796593 CAGGTAAACAAAGCAAGCAAGC 59.203 45.455 0.00 0.00 0.00 4.01
414 435 2.430332 AGGTAAACAAAGCAAGCAAGCA 59.570 40.909 3.19 0.00 36.85 3.91
415 436 2.796593 GGTAAACAAAGCAAGCAAGCAG 59.203 45.455 3.19 0.00 36.85 4.24
416 437 2.678471 AAACAAAGCAAGCAAGCAGT 57.322 40.000 3.19 0.00 36.85 4.40
438 490 2.233922 ACTAGTCCAGTCGGTCCAATTG 59.766 50.000 0.00 0.00 28.33 2.32
611 682 3.766591 TCAAAGCAACCCACAAAGAAAGA 59.233 39.130 0.00 0.00 0.00 2.52
704 789 1.337387 CGGAGAAGAATACGGAGGACC 59.663 57.143 0.00 0.00 0.00 4.46
710 795 4.828387 AGAAGAATACGGAGGACCAGTATC 59.172 45.833 0.00 0.00 36.06 2.24
712 797 2.653234 ATACGGAGGACCAGTATCGT 57.347 50.000 0.00 0.00 33.88 3.73
717 802 2.805099 CGGAGGACCAGTATCGTAGTAC 59.195 54.545 0.00 0.00 35.59 2.73
828 913 0.103937 CATTCCTCTCCACTCTCCGC 59.896 60.000 0.00 0.00 0.00 5.54
1162 1270 1.666872 CGTCCCCTTTCGTTTCGCT 60.667 57.895 0.00 0.00 0.00 4.93
1163 1271 1.226030 CGTCCCCTTTCGTTTCGCTT 61.226 55.000 0.00 0.00 0.00 4.68
1165 1273 0.395312 TCCCCTTTCGTTTCGCTTCT 59.605 50.000 0.00 0.00 0.00 2.85
1230 1339 2.417936 GGGGGAAGATCTCGCGAC 59.582 66.667 3.71 0.00 37.88 5.19
1347 1457 2.282674 TGCGTCTGTCGGGGTAGT 60.283 61.111 0.00 0.00 40.26 2.73
1348 1458 1.002257 TGCGTCTGTCGGGGTAGTA 60.002 57.895 0.00 0.00 40.26 1.82
1350 1460 1.722636 GCGTCTGTCGGGGTAGTAGG 61.723 65.000 0.00 0.00 40.26 3.18
1351 1461 1.722636 CGTCTGTCGGGGTAGTAGGC 61.723 65.000 0.00 0.00 35.71 3.93
1352 1462 1.452651 TCTGTCGGGGTAGTAGGCG 60.453 63.158 0.00 0.00 0.00 5.52
1353 1463 1.751927 CTGTCGGGGTAGTAGGCGT 60.752 63.158 0.00 0.00 0.00 5.68
1408 1531 2.491693 TGTGAATTGCCTCGGGATTTTC 59.508 45.455 0.00 0.00 0.00 2.29
1410 1533 0.455815 AATTGCCTCGGGATTTTCGC 59.544 50.000 0.00 0.00 0.00 4.70
1420 1543 1.613255 GGGATTTTCGCTTCCTGGTGA 60.613 52.381 0.00 0.00 32.34 4.02
1422 1545 2.095212 GGATTTTCGCTTCCTGGTGAAC 60.095 50.000 0.00 0.00 35.78 3.18
1455 1578 2.411701 CCGTTCGGATCTGCGCTA 59.588 61.111 9.73 0.00 0.00 4.26
1497 1620 1.009389 GGAGACTGTCGAAGCGTTGG 61.009 60.000 1.52 0.00 0.00 3.77
1513 1636 3.213249 GTTGGTCGAACGATACTGACT 57.787 47.619 0.00 0.00 0.00 3.41
1520 1643 2.093941 CGAACGATACTGACTGACGAGT 59.906 50.000 0.00 0.00 33.98 4.18
1745 1872 4.838152 CGGAGGGGTGATGTGCGG 62.838 72.222 0.00 0.00 0.00 5.69
2018 2146 1.165270 CCCATTCCCAAGTGTCGTTC 58.835 55.000 0.00 0.00 0.00 3.95
2076 2215 5.537188 TGAAAACAGTGGATTGTATTTGGC 58.463 37.500 0.00 0.00 0.00 4.52
2260 2406 4.521146 ACTGCTATGATAACTTGCTTGCT 58.479 39.130 0.00 0.00 0.00 3.91
2761 2909 9.494271 GTATGCAGTCCATATTGAAATCTCTAA 57.506 33.333 0.00 0.00 38.60 2.10
3171 3322 6.422776 AATGCAGATTCTTTACACTAACCG 57.577 37.500 0.00 0.00 0.00 4.44
3223 3381 1.172175 GCCCTCTCTCTTTTGCAAGG 58.828 55.000 0.00 0.00 0.00 3.61
3631 3790 4.870021 AGATCTTCTTTGGCCCATAAGT 57.130 40.909 0.00 0.00 0.00 2.24
3890 4078 5.417754 AGGATGACTGCATATCATACCTG 57.582 43.478 16.24 0.00 38.05 4.00
4149 4343 4.563786 GGGTATGTCTATCCTGGCTAAAGC 60.564 50.000 0.00 0.00 41.14 3.51
4355 4549 9.698309 CATAAACCAAACACACCATTAATGTAA 57.302 29.630 14.25 0.00 0.00 2.41
5232 5429 2.423538 ACTGAACTTGTGAAACTGTGCC 59.576 45.455 0.00 0.00 38.04 5.01
5260 5457 6.500336 TCAAGTATCTTGGTAGTTACTCCCT 58.500 40.000 9.18 0.00 36.39 4.20
5369 5566 2.413112 CACTCCATGTGTCGAATGTGTC 59.587 50.000 0.00 0.00 41.53 3.67
5575 5773 2.979649 GTCGACTGTTCCTCCCCC 59.020 66.667 8.70 0.00 0.00 5.40
6028 6226 1.203441 TGCTCCCAGCTGTTGATCCT 61.203 55.000 13.81 0.00 42.97 3.24
6521 6719 6.475504 TCAGATGGCAAAGAAACAGAAGATA 58.524 36.000 0.00 0.00 0.00 1.98
6657 6855 5.721960 AGGGTGAGTATTCATTCTGTGTAGT 59.278 40.000 0.00 0.00 35.39 2.73
6748 6946 5.741011 ACTAGAAACAGAGAAACACAACCA 58.259 37.500 0.00 0.00 0.00 3.67
6749 6947 6.177610 ACTAGAAACAGAGAAACACAACCAA 58.822 36.000 0.00 0.00 0.00 3.67
6750 6948 6.828785 ACTAGAAACAGAGAAACACAACCAAT 59.171 34.615 0.00 0.00 0.00 3.16
6751 6949 7.990886 ACTAGAAACAGAGAAACACAACCAATA 59.009 33.333 0.00 0.00 0.00 1.90
6752 6950 7.823745 AGAAACAGAGAAACACAACCAATAT 57.176 32.000 0.00 0.00 0.00 1.28
6753 6951 8.237811 AGAAACAGAGAAACACAACCAATATT 57.762 30.769 0.00 0.00 0.00 1.28
6754 6952 8.137437 AGAAACAGAGAAACACAACCAATATTG 58.863 33.333 8.58 8.58 35.59 1.90
6755 6953 7.581213 AACAGAGAAACACAACCAATATTGA 57.419 32.000 17.23 0.00 33.57 2.57
6756 6954 7.581213 ACAGAGAAACACAACCAATATTGAA 57.419 32.000 17.23 0.00 33.57 2.69
6757 6955 8.181904 ACAGAGAAACACAACCAATATTGAAT 57.818 30.769 17.23 1.72 33.57 2.57
6758 6956 8.641541 ACAGAGAAACACAACCAATATTGAATT 58.358 29.630 17.23 7.92 33.57 2.17
6761 6959 8.986477 AGAAACACAACCAATATTGAATTAGC 57.014 30.769 17.23 0.00 33.57 3.09
6762 6960 8.034804 AGAAACACAACCAATATTGAATTAGCC 58.965 33.333 17.23 0.00 33.57 3.93
6763 6961 6.220726 ACACAACCAATATTGAATTAGCCC 57.779 37.500 17.23 0.00 33.57 5.19
6764 6962 5.957774 ACACAACCAATATTGAATTAGCCCT 59.042 36.000 17.23 0.00 33.57 5.19
6765 6963 6.440328 ACACAACCAATATTGAATTAGCCCTT 59.560 34.615 17.23 0.00 33.57 3.95
6766 6964 6.757947 CACAACCAATATTGAATTAGCCCTTG 59.242 38.462 17.23 3.69 33.57 3.61
6767 6965 5.535753 ACCAATATTGAATTAGCCCTTGC 57.464 39.130 17.23 0.00 37.95 4.01
6768 6966 4.961730 ACCAATATTGAATTAGCCCTTGCA 59.038 37.500 17.23 0.00 41.13 4.08
6769 6967 5.069516 ACCAATATTGAATTAGCCCTTGCAG 59.930 40.000 17.23 0.00 41.13 4.41
6770 6968 5.510179 CCAATATTGAATTAGCCCTTGCAGG 60.510 44.000 17.23 0.00 41.13 4.85
6771 6969 2.897271 TTGAATTAGCCCTTGCAGGA 57.103 45.000 0.00 0.00 37.67 3.86
6772 6970 3.386932 TTGAATTAGCCCTTGCAGGAT 57.613 42.857 0.00 0.00 37.67 3.24
6773 6971 2.936202 TGAATTAGCCCTTGCAGGATC 58.064 47.619 0.00 0.00 37.67 3.36
6774 6972 2.241941 TGAATTAGCCCTTGCAGGATCA 59.758 45.455 0.00 0.00 37.67 2.92
6775 6973 3.290710 GAATTAGCCCTTGCAGGATCAA 58.709 45.455 0.00 0.00 37.67 2.57
6776 6974 2.897271 TTAGCCCTTGCAGGATCAAA 57.103 45.000 0.00 0.00 37.67 2.69
6777 6975 3.386932 TTAGCCCTTGCAGGATCAAAT 57.613 42.857 0.00 0.00 37.67 2.32
6778 6976 2.242882 AGCCCTTGCAGGATCAAATT 57.757 45.000 0.00 0.00 37.67 1.82
6779 6977 3.386932 AGCCCTTGCAGGATCAAATTA 57.613 42.857 0.00 0.00 37.67 1.40
6780 6978 3.919834 AGCCCTTGCAGGATCAAATTAT 58.080 40.909 0.00 0.00 37.67 1.28
6781 6979 4.292643 AGCCCTTGCAGGATCAAATTATT 58.707 39.130 0.00 0.00 37.67 1.40
6782 6980 4.343239 AGCCCTTGCAGGATCAAATTATTC 59.657 41.667 0.00 0.00 37.67 1.75
6783 6981 4.343239 GCCCTTGCAGGATCAAATTATTCT 59.657 41.667 0.00 0.00 37.67 2.40
6784 6982 5.163374 GCCCTTGCAGGATCAAATTATTCTT 60.163 40.000 0.00 0.00 37.67 2.52
6785 6983 6.278363 CCCTTGCAGGATCAAATTATTCTTG 58.722 40.000 0.00 0.00 37.67 3.02
6786 6984 6.127253 CCCTTGCAGGATCAAATTATTCTTGT 60.127 38.462 0.00 0.00 37.67 3.16
6787 6985 7.325694 CCTTGCAGGATCAAATTATTCTTGTT 58.674 34.615 0.00 0.00 37.67 2.83
6788 6986 7.490402 CCTTGCAGGATCAAATTATTCTTGTTC 59.510 37.037 0.00 0.00 37.67 3.18
6789 6987 7.465353 TGCAGGATCAAATTATTCTTGTTCA 57.535 32.000 0.00 0.00 0.00 3.18
6790 6988 8.070034 TGCAGGATCAAATTATTCTTGTTCAT 57.930 30.769 0.00 0.00 0.00 2.57
6791 6989 8.533657 TGCAGGATCAAATTATTCTTGTTCATT 58.466 29.630 0.00 0.00 0.00 2.57
6817 7015 8.874744 ACTCTTAACTAGAAACAGAGAAACAC 57.125 34.615 15.34 0.00 35.51 3.32
6818 7016 8.475639 ACTCTTAACTAGAAACAGAGAAACACA 58.524 33.333 15.34 0.00 35.51 3.72
6819 7017 9.314321 CTCTTAACTAGAAACAGAGAAACACAA 57.686 33.333 0.00 0.00 34.06 3.33
6820 7018 9.095065 TCTTAACTAGAAACAGAGAAACACAAC 57.905 33.333 0.00 0.00 0.00 3.32
6821 7019 6.679327 AACTAGAAACAGAGAAACACAACC 57.321 37.500 0.00 0.00 0.00 3.77
6879 7078 6.959606 ATATACTAATGAAGACTGCCCCAT 57.040 37.500 0.00 0.00 0.00 4.00
6899 7099 4.164988 CCATGTGAAAGGGGACTAGAGATT 59.835 45.833 0.00 0.00 42.68 2.40
6905 7105 5.726308 TGAAAGGGGACTAGAGATTTCATGA 59.274 40.000 0.00 0.00 42.68 3.07
6906 7106 5.622346 AAGGGGACTAGAGATTTCATGAC 57.378 43.478 0.00 0.00 42.68 3.06
6907 7107 4.889780 AGGGGACTAGAGATTTCATGACT 58.110 43.478 0.00 0.00 40.61 3.41
6908 7108 6.031964 AGGGGACTAGAGATTTCATGACTA 57.968 41.667 0.00 0.00 40.61 2.59
6931 7157 3.565307 TCTTCTCCATTGGCTTTGTTGT 58.435 40.909 0.00 0.00 0.00 3.32
6934 7160 4.057406 TCTCCATTGGCTTTGTTGTTTG 57.943 40.909 0.00 0.00 0.00 2.93
6935 7161 3.450457 TCTCCATTGGCTTTGTTGTTTGT 59.550 39.130 0.00 0.00 0.00 2.83
6936 7162 4.646945 TCTCCATTGGCTTTGTTGTTTGTA 59.353 37.500 0.00 0.00 0.00 2.41
6939 7165 4.690280 CCATTGGCTTTGTTGTTTGTATCC 59.310 41.667 0.00 0.00 0.00 2.59
6940 7166 5.295950 CATTGGCTTTGTTGTTTGTATCCA 58.704 37.500 0.00 0.00 0.00 3.41
6943 7169 4.343526 TGGCTTTGTTGTTTGTATCCACAT 59.656 37.500 0.00 0.00 33.76 3.21
6945 7171 6.040955 TGGCTTTGTTGTTTGTATCCACATAA 59.959 34.615 0.00 0.00 33.76 1.90
7017 7367 5.634859 GCATGTACATAAAGCTTGCAAGTTT 59.365 36.000 26.55 23.92 34.68 2.66
7022 7372 8.410141 TGTACATAAAGCTTGCAAGTTTTAGTT 58.590 29.630 35.69 29.29 42.32 2.24
7040 7390 3.740115 AGTTCCACAGTTGCTTTCGTAT 58.260 40.909 0.00 0.00 0.00 3.06
7043 7393 5.067283 AGTTCCACAGTTGCTTTCGTATTTT 59.933 36.000 0.00 0.00 0.00 1.82
7090 7440 5.841810 AGTTAAAAGTGCAGCTTTGCATTA 58.158 33.333 12.87 0.00 45.91 1.90
7117 7467 9.629878 TTCCATGTGGTTTCTTAACTACTTTTA 57.370 29.630 0.00 0.00 43.74 1.52
7195 7844 4.361451 CTGTGCAGGATATTTGGTGTTC 57.639 45.455 0.00 0.00 0.00 3.18
7321 7972 1.866853 GCAAAGTAGCTGGTGGTGGC 61.867 60.000 0.00 0.00 0.00 5.01
7331 7982 3.570212 GTGGTGGCTGGTGTCCCT 61.570 66.667 0.00 0.00 0.00 4.20
7546 8228 7.706607 AGGATTGCTGTAAAGAAACTTGTTTTC 59.293 33.333 0.06 0.00 43.67 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.256174 TGACGCTACGCTACATTTGAC 58.744 47.619 0.00 0.00 0.00 3.18
2 3 2.640346 TGACGCTACGCTACATTTGA 57.360 45.000 0.00 0.00 0.00 2.69
3 4 5.576337 ATTATGACGCTACGCTACATTTG 57.424 39.130 0.00 0.00 0.00 2.32
6 7 4.866921 TCAATTATGACGCTACGCTACAT 58.133 39.130 0.00 0.00 0.00 2.29
7 8 4.287720 CTCAATTATGACGCTACGCTACA 58.712 43.478 0.00 0.00 0.00 2.74
8 9 3.119792 GCTCAATTATGACGCTACGCTAC 59.880 47.826 0.00 0.00 31.28 3.58
10 11 2.128035 GCTCAATTATGACGCTACGCT 58.872 47.619 0.00 0.00 31.28 5.07
114 119 9.342308 CCTTTTAGCATATGTATCTTTCAAGGA 57.658 33.333 4.29 0.00 0.00 3.36
154 160 3.071602 AGAGAGAGAGAGAGAGATTCCGG 59.928 52.174 0.00 0.00 0.00 5.14
160 166 2.481441 AGCCAGAGAGAGAGAGAGAGA 58.519 52.381 0.00 0.00 0.00 3.10
161 167 2.947652 CAAGCCAGAGAGAGAGAGAGAG 59.052 54.545 0.00 0.00 0.00 3.20
162 168 2.357050 CCAAGCCAGAGAGAGAGAGAGA 60.357 54.545 0.00 0.00 0.00 3.10
163 169 2.026641 CCAAGCCAGAGAGAGAGAGAG 58.973 57.143 0.00 0.00 0.00 3.20
164 170 1.638070 TCCAAGCCAGAGAGAGAGAGA 59.362 52.381 0.00 0.00 0.00 3.10
165 171 1.750778 GTCCAAGCCAGAGAGAGAGAG 59.249 57.143 0.00 0.00 0.00 3.20
267 282 2.697229 AGAGACACTGCTATGCTATGCA 59.303 45.455 0.00 0.00 44.86 3.96
303 318 2.405025 CGTTTTCCGAAAGCAAGATTGC 59.595 45.455 9.54 9.54 46.90 3.56
304 319 2.405025 GCGTTTTCCGAAAGCAAGATTG 59.595 45.455 8.25 0.00 39.56 2.67
305 320 2.607038 GGCGTTTTCCGAAAGCAAGATT 60.607 45.455 8.25 0.00 39.56 2.40
306 321 1.068541 GGCGTTTTCCGAAAGCAAGAT 60.069 47.619 8.25 0.00 39.56 2.40
307 322 0.309612 GGCGTTTTCCGAAAGCAAGA 59.690 50.000 8.25 0.00 39.56 3.02
362 383 2.049526 TGCCTGCAGTGTCGTACG 60.050 61.111 13.81 9.53 0.00 3.67
390 411 4.432712 CTTGCTTGCTTTGTTTACCTGTT 58.567 39.130 0.00 0.00 0.00 3.16
391 412 3.737972 GCTTGCTTGCTTTGTTTACCTGT 60.738 43.478 0.00 0.00 0.00 4.00
392 413 2.796593 GCTTGCTTGCTTTGTTTACCTG 59.203 45.455 0.00 0.00 0.00 4.00
393 414 2.430332 TGCTTGCTTGCTTTGTTTACCT 59.570 40.909 3.47 0.00 0.00 3.08
394 415 2.796593 CTGCTTGCTTGCTTTGTTTACC 59.203 45.455 3.47 0.00 0.00 2.85
395 416 3.447742 ACTGCTTGCTTGCTTTGTTTAC 58.552 40.909 3.47 0.00 0.00 2.01
396 417 3.799281 ACTGCTTGCTTGCTTTGTTTA 57.201 38.095 3.47 0.00 0.00 2.01
397 418 2.678471 ACTGCTTGCTTGCTTTGTTT 57.322 40.000 3.47 0.00 0.00 2.83
398 419 2.689983 AGTACTGCTTGCTTGCTTTGTT 59.310 40.909 0.00 0.00 0.00 2.83
399 420 2.301346 AGTACTGCTTGCTTGCTTTGT 58.699 42.857 0.00 3.11 0.00 2.83
400 421 3.499918 ACTAGTACTGCTTGCTTGCTTTG 59.500 43.478 5.39 0.00 0.00 2.77
401 422 3.744660 ACTAGTACTGCTTGCTTGCTTT 58.255 40.909 5.39 0.00 0.00 3.51
402 423 3.330267 GACTAGTACTGCTTGCTTGCTT 58.670 45.455 5.39 0.00 0.00 3.91
403 424 2.354203 GGACTAGTACTGCTTGCTTGCT 60.354 50.000 5.39 0.00 0.00 3.91
404 425 2.003301 GGACTAGTACTGCTTGCTTGC 58.997 52.381 5.39 0.00 0.00 4.01
405 426 3.257393 CTGGACTAGTACTGCTTGCTTG 58.743 50.000 6.66 0.00 0.00 4.01
406 427 2.900546 ACTGGACTAGTACTGCTTGCTT 59.099 45.455 11.69 0.00 38.04 3.91
407 428 2.494073 GACTGGACTAGTACTGCTTGCT 59.506 50.000 11.69 0.00 40.53 3.91
408 429 2.732597 CGACTGGACTAGTACTGCTTGC 60.733 54.545 11.69 0.00 40.53 4.01
409 430 2.159366 CCGACTGGACTAGTACTGCTTG 60.159 54.545 11.69 2.44 40.53 4.01
410 431 2.093106 CCGACTGGACTAGTACTGCTT 58.907 52.381 11.69 0.00 40.53 3.91
411 432 1.004511 ACCGACTGGACTAGTACTGCT 59.995 52.381 11.69 0.00 40.53 4.24
412 433 1.401199 GACCGACTGGACTAGTACTGC 59.599 57.143 11.69 4.50 40.53 4.40
413 434 2.015587 GGACCGACTGGACTAGTACTG 58.984 57.143 10.29 10.29 40.53 2.74
414 435 1.632409 TGGACCGACTGGACTAGTACT 59.368 52.381 6.66 0.00 40.53 2.73
415 436 2.119801 TGGACCGACTGGACTAGTAC 57.880 55.000 0.00 0.00 40.53 2.73
416 437 2.885135 TTGGACCGACTGGACTAGTA 57.115 50.000 0.00 0.00 40.53 1.82
438 490 1.743252 CGCTTTCCTCTGCCTGTCC 60.743 63.158 0.00 0.00 0.00 4.02
520 591 0.627451 AAGGGAGCCATCAATCAGCA 59.373 50.000 0.00 0.00 0.00 4.41
704 789 5.046529 ACGACTAGTGGTACTACGATACTG 58.953 45.833 8.99 0.00 28.72 2.74
741 826 8.985805 CGAGCGGTTCCTTTATTATTAGTATTT 58.014 33.333 0.00 0.00 0.00 1.40
782 867 4.752879 TTTTCCGCCGAGCCGAGG 62.753 66.667 0.00 0.54 0.00 4.63
783 868 2.740826 TTTTTCCGCCGAGCCGAG 60.741 61.111 0.00 0.00 0.00 4.63
784 869 3.045492 GTTTTTCCGCCGAGCCGA 61.045 61.111 0.00 0.00 0.00 5.54
785 870 2.195123 ATTGTTTTTCCGCCGAGCCG 62.195 55.000 0.00 0.00 0.00 5.52
786 871 0.038618 AATTGTTTTTCCGCCGAGCC 60.039 50.000 0.00 0.00 0.00 4.70
787 872 1.336877 GAATTGTTTTTCCGCCGAGC 58.663 50.000 0.00 0.00 0.00 5.03
845 930 2.125753 GCGTCTGCCACTGAGAGG 60.126 66.667 0.00 0.00 33.98 3.69
847 932 1.590610 GAGAGCGTCTGCCACTGAGA 61.591 60.000 0.00 0.00 44.31 3.27
998 1095 2.508891 CGCAGCGACGACTTCATCC 61.509 63.158 9.98 0.00 34.06 3.51
1143 1240 2.674084 GCGAAACGAAAGGGGACGG 61.674 63.158 0.00 0.00 0.00 4.79
1144 1241 1.226030 AAGCGAAACGAAAGGGGACG 61.226 55.000 0.00 0.00 0.00 4.79
1145 1242 0.516001 GAAGCGAAACGAAAGGGGAC 59.484 55.000 0.00 0.00 0.00 4.46
1146 1243 0.395312 AGAAGCGAAACGAAAGGGGA 59.605 50.000 0.00 0.00 0.00 4.81
1147 1244 0.517316 CAGAAGCGAAACGAAAGGGG 59.483 55.000 0.00 0.00 0.00 4.79
1162 1270 2.661537 CGCACACTCCACGCAGAA 60.662 61.111 0.00 0.00 0.00 3.02
1163 1271 3.911698 ACGCACACTCCACGCAGA 61.912 61.111 0.00 0.00 0.00 4.26
1334 1444 1.452651 CGCCTACTACCCCGACAGA 60.453 63.158 0.00 0.00 0.00 3.41
1344 1454 2.975536 GCCACACCACGCCTACTA 59.024 61.111 0.00 0.00 0.00 1.82
1369 1479 1.307343 ATGGCACTAGAGGGGCAGT 60.307 57.895 13.90 0.00 43.15 4.40
1377 1487 2.025981 AGGCAATTCACATGGCACTAGA 60.026 45.455 0.00 0.00 45.08 2.43
1408 1531 2.328099 GGCAGTTCACCAGGAAGCG 61.328 63.158 0.00 0.00 35.82 4.68
1410 1533 1.171308 CATGGCAGTTCACCAGGAAG 58.829 55.000 0.00 0.00 41.48 3.46
1497 1620 2.093310 TCGTCAGTCAGTATCGTTCGAC 59.907 50.000 0.00 0.00 0.00 4.20
1513 1636 0.176219 AAACAACACCGGACTCGTCA 59.824 50.000 9.46 0.00 33.95 4.35
1520 1643 2.435069 TGGACTAGAAAACAACACCGGA 59.565 45.455 9.46 0.00 0.00 5.14
1745 1872 1.744320 AAGAGGCGCCAAAACCCAAC 61.744 55.000 31.54 7.76 0.00 3.77
1975 2103 4.734398 AGTCTCTTCTCATAGCCAACAG 57.266 45.455 0.00 0.00 0.00 3.16
1976 2104 4.081420 GGAAGTCTCTTCTCATAGCCAACA 60.081 45.833 8.96 0.00 0.00 3.33
2018 2146 5.043248 AGTCGGCAGTTTCATTTTGAAAAG 58.957 37.500 4.37 2.71 46.53 2.27
2076 2215 6.096673 AGGTTTTACTGCTGGTAAATTTGG 57.903 37.500 13.37 0.00 45.97 3.28
2761 2909 7.419865 CCCTCCGTTCCTAAATATAAGTCCTTT 60.420 40.741 0.00 0.00 0.00 3.11
2847 2998 8.970020 AGTCATCAACTAATTATTGGCATTCAA 58.030 29.630 0.00 0.00 36.07 2.69
3171 3322 5.890424 ACTACTGACTAGCAAGAGAAGAC 57.110 43.478 0.00 0.00 0.00 3.01
3890 4078 3.498774 ATGATATGCAGTCACCCCTTC 57.501 47.619 6.72 0.00 0.00 3.46
4149 4343 3.747529 ACAAAATTTGGTAGGGTACGACG 59.252 43.478 10.71 0.00 34.12 5.12
4299 4493 1.047002 TCCCACCAAAACATTGGCTG 58.953 50.000 7.49 5.61 45.88 4.85
5232 5429 6.331061 AGTAACTACCAAGATACTTGAAGCG 58.669 40.000 12.25 0.00 37.91 4.68
5369 5566 8.836413 TGGCATTTACCTATTTAGATCTTTTCG 58.164 33.333 0.00 0.00 0.00 3.46
5443 5641 1.000506 GAGTTAAGAGCACCGACCACA 59.999 52.381 0.00 0.00 0.00 4.17
5575 5773 4.416620 GGACTCTCAAGATAGTGAACACG 58.583 47.826 0.00 0.00 36.20 4.49
6028 6226 6.661377 TCAAATTGTTATAGCCTGGTAAAGCA 59.339 34.615 0.00 0.00 0.00 3.91
6521 6719 1.215423 AGCGGCCCCTTTATCTTGATT 59.785 47.619 0.00 0.00 0.00 2.57
6657 6855 2.754552 AGTTCAAAAACAGACTGCAGCA 59.245 40.909 15.27 0.00 37.88 4.41
6763 6961 8.030692 TGAACAAGAATAATTTGATCCTGCAAG 58.969 33.333 0.00 0.00 0.00 4.01
6764 6962 7.894708 TGAACAAGAATAATTTGATCCTGCAA 58.105 30.769 0.00 0.00 0.00 4.08
6765 6963 7.465353 TGAACAAGAATAATTTGATCCTGCA 57.535 32.000 0.00 0.00 0.00 4.41
6766 6964 8.937634 AATGAACAAGAATAATTTGATCCTGC 57.062 30.769 0.00 0.00 0.00 4.85
6791 6989 9.962783 GTGTTTCTCTGTTTCTAGTTAAGAGTA 57.037 33.333 11.51 3.57 36.56 2.59
6792 6990 8.475639 TGTGTTTCTCTGTTTCTAGTTAAGAGT 58.524 33.333 11.51 0.00 36.56 3.24
6793 6991 8.873215 TGTGTTTCTCTGTTTCTAGTTAAGAG 57.127 34.615 7.66 7.66 35.05 2.85
6794 6992 9.095065 GTTGTGTTTCTCTGTTTCTAGTTAAGA 57.905 33.333 0.00 0.00 0.00 2.10
6795 6993 8.336080 GGTTGTGTTTCTCTGTTTCTAGTTAAG 58.664 37.037 0.00 0.00 0.00 1.85
6796 6994 7.825270 TGGTTGTGTTTCTCTGTTTCTAGTTAA 59.175 33.333 0.00 0.00 0.00 2.01
6797 6995 7.332557 TGGTTGTGTTTCTCTGTTTCTAGTTA 58.667 34.615 0.00 0.00 0.00 2.24
6798 6996 6.177610 TGGTTGTGTTTCTCTGTTTCTAGTT 58.822 36.000 0.00 0.00 0.00 2.24
6799 6997 5.741011 TGGTTGTGTTTCTCTGTTTCTAGT 58.259 37.500 0.00 0.00 0.00 2.57
6800 6998 6.677781 TTGGTTGTGTTTCTCTGTTTCTAG 57.322 37.500 0.00 0.00 0.00 2.43
6801 6999 8.918202 ATATTGGTTGTGTTTCTCTGTTTCTA 57.082 30.769 0.00 0.00 0.00 2.10
6802 7000 7.823745 ATATTGGTTGTGTTTCTCTGTTTCT 57.176 32.000 0.00 0.00 0.00 2.52
6803 7001 8.134895 TCAATATTGGTTGTGTTTCTCTGTTTC 58.865 33.333 15.36 0.00 0.00 2.78
6804 7002 8.006298 TCAATATTGGTTGTGTTTCTCTGTTT 57.994 30.769 15.36 0.00 0.00 2.83
6805 7003 7.581213 TCAATATTGGTTGTGTTTCTCTGTT 57.419 32.000 15.36 0.00 0.00 3.16
6806 7004 7.581213 TTCAATATTGGTTGTGTTTCTCTGT 57.419 32.000 15.36 0.00 0.00 3.41
6809 7007 9.076596 GCTAATTCAATATTGGTTGTGTTTCTC 57.923 33.333 15.36 0.00 0.00 2.87
6810 7008 8.034804 GGCTAATTCAATATTGGTTGTGTTTCT 58.965 33.333 15.36 0.00 0.00 2.52
6811 7009 7.277760 GGGCTAATTCAATATTGGTTGTGTTTC 59.722 37.037 15.36 0.00 0.00 2.78
6812 7010 7.038373 AGGGCTAATTCAATATTGGTTGTGTTT 60.038 33.333 15.36 2.69 0.00 2.83
6813 7011 6.440328 AGGGCTAATTCAATATTGGTTGTGTT 59.560 34.615 15.36 4.86 0.00 3.32
6814 7012 5.957774 AGGGCTAATTCAATATTGGTTGTGT 59.042 36.000 15.36 0.00 0.00 3.72
6815 7013 6.469782 AGGGCTAATTCAATATTGGTTGTG 57.530 37.500 15.36 9.21 0.00 3.33
6816 7014 6.667414 TCAAGGGCTAATTCAATATTGGTTGT 59.333 34.615 15.36 2.01 0.00 3.32
6817 7015 7.111247 TCAAGGGCTAATTCAATATTGGTTG 57.889 36.000 15.36 4.21 0.00 3.77
6818 7016 7.732222 TTCAAGGGCTAATTCAATATTGGTT 57.268 32.000 15.36 12.49 0.00 3.67
6819 7017 7.564660 TCATTCAAGGGCTAATTCAATATTGGT 59.435 33.333 15.36 2.30 0.00 3.67
6820 7018 7.869429 GTCATTCAAGGGCTAATTCAATATTGG 59.131 37.037 15.36 0.21 0.00 3.16
6821 7019 8.636213 AGTCATTCAAGGGCTAATTCAATATTG 58.364 33.333 9.29 9.29 0.00 1.90
6861 7059 2.947652 CACATGGGGCAGTCTTCATTAG 59.052 50.000 0.00 0.00 0.00 1.73
6879 7078 4.844085 TGAAATCTCTAGTCCCCTTTCACA 59.156 41.667 0.00 0.00 30.15 3.58
6899 7099 5.627735 GCCAATGGAGAAGAGTAGTCATGAA 60.628 44.000 2.05 0.00 0.00 2.57
6905 7105 4.042187 ACAAAGCCAATGGAGAAGAGTAGT 59.958 41.667 2.05 0.00 0.00 2.73
6906 7106 4.583871 ACAAAGCCAATGGAGAAGAGTAG 58.416 43.478 2.05 0.00 0.00 2.57
6907 7107 4.640771 ACAAAGCCAATGGAGAAGAGTA 57.359 40.909 2.05 0.00 0.00 2.59
6908 7108 3.515602 ACAAAGCCAATGGAGAAGAGT 57.484 42.857 2.05 0.00 0.00 3.24
6934 7160 7.280205 CCCTTCACAAGTAGTTTATGTGGATAC 59.720 40.741 5.41 0.00 43.53 2.24
6935 7161 7.335627 CCCTTCACAAGTAGTTTATGTGGATA 58.664 38.462 5.41 0.00 43.53 2.59
6936 7162 6.180472 CCCTTCACAAGTAGTTTATGTGGAT 58.820 40.000 5.41 0.00 43.53 3.41
6939 7165 4.700213 CCCCCTTCACAAGTAGTTTATGTG 59.300 45.833 0.00 0.00 44.45 3.21
6940 7166 4.600111 TCCCCCTTCACAAGTAGTTTATGT 59.400 41.667 0.00 0.00 0.00 2.29
6943 7169 4.661709 AGTTCCCCCTTCACAAGTAGTTTA 59.338 41.667 0.00 0.00 0.00 2.01
6945 7171 3.053826 AGTTCCCCCTTCACAAGTAGTT 58.946 45.455 0.00 0.00 0.00 2.24
7017 7367 3.537580 ACGAAAGCAACTGTGGAACTAA 58.462 40.909 0.00 0.00 38.04 2.24
7022 7372 4.576873 TGAAAATACGAAAGCAACTGTGGA 59.423 37.500 0.00 0.00 0.00 4.02
7063 7413 4.090498 GCAAAGCTGCACTTTTAACTATGC 59.910 41.667 1.02 7.37 46.73 3.14
7090 7440 8.706322 AAAGTAGTTAAGAAACCACATGGAAT 57.294 30.769 4.53 0.00 36.15 3.01
7117 7467 7.992754 ATAGAGCTTTCAACATTTCTGACTT 57.007 32.000 0.00 0.00 0.00 3.01
7123 7473 9.683069 TTTCTTGAATAGAGCTTTCAACATTTC 57.317 29.630 7.77 0.00 37.97 2.17
7300 7951 0.877071 CACCACCAGCTACTTTGCAG 59.123 55.000 0.00 0.00 34.99 4.41
7321 7972 2.305927 ACTCAACCATAAGGGACACCAG 59.694 50.000 0.00 0.00 41.15 4.00
7331 7982 4.709250 TGCACAACTACACTCAACCATAA 58.291 39.130 0.00 0.00 0.00 1.90
7546 8228 8.110271 TCCATTAGACATCTACCTATCCTACAG 58.890 40.741 0.00 0.00 0.00 2.74
7547 8229 7.996788 TCCATTAGACATCTACCTATCCTACA 58.003 38.462 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.