Multiple sequence alignment - TraesCS5A01G363400

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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 TraesCS5A01G363400 chr5A 100.000 5357 0 0 561 5917 564074947 564080303 0.000000e+00 9893.0
1 TraesCS5A01G363400 chr5A 100.000 320 0 0 1 320 564074387 564074706 5.110000e-165 592.0
2 TraesCS5A01G363400 chr5D 94.338 5369 183 60 611 5917 446400690 446405999 0.000000e+00 8118.0
3 TraesCS5A01G363400 chr5D 89.908 109 8 3 629 735 522112037 522112144 2.880000e-28 137.0
4 TraesCS5A01G363400 chr5B 94.951 3763 140 21 2183 5917 544331268 544335008 0.000000e+00 5851.0
5 TraesCS5A01G363400 chr5B 86.796 1136 86 35 647 1757 544329637 544330733 0.000000e+00 1208.0
6 TraesCS5A01G363400 chr5B 85.618 445 50 7 1758 2190 544330802 544331244 6.990000e-124 455.0
7 TraesCS5A01G363400 chr5B 84.161 322 34 15 1 312 544329220 544329534 4.480000e-76 296.0
8 TraesCS5A01G363400 chr5B 98.824 85 0 1 658 741 658145702 658145786 3.690000e-32 150.0
9 TraesCS5A01G363400 chr3D 94.949 99 2 2 639 735 3302141 3302238 1.030000e-32 152.0
10 TraesCS5A01G363400 chr3D 100.000 30 0 0 4379 4408 605632510 605632539 8.280000e-04 56.5
11 TraesCS5A01G363400 chr3D 100.000 30 0 0 4379 4408 606003002 606003031 8.280000e-04 56.5
12 TraesCS5A01G363400 chr7A 97.701 87 0 1 649 735 618184365 618184449 1.330000e-31 148.0
13 TraesCS5A01G363400 chr7B 96.629 89 2 1 648 735 678837032 678836944 4.780000e-31 147.0
14 TraesCS5A01G363400 chr7B 92.157 102 5 3 636 736 678295771 678295870 2.220000e-29 141.0
15 TraesCS5A01G363400 chr7D 93.814 97 2 3 649 743 535550405 535550311 6.180000e-30 143.0
16 TraesCS5A01G363400 chrUn 100.000 30 0 0 4379 4408 42339704 42339675 8.280000e-04 56.5
17 TraesCS5A01G363400 chrUn 100.000 30 0 0 4379 4408 42529246 42529275 8.280000e-04 56.5
18 TraesCS5A01G363400 chrUn 100.000 30 0 0 4379 4408 391720320 391720291 8.280000e-04 56.5
19 TraesCS5A01G363400 chr3B 100.000 30 0 0 4379 4408 816039614 816039585 8.280000e-04 56.5
20 TraesCS5A01G363400 chr3A 90.476 42 4 0 4379 4420 738237063 738237022 8.280000e-04 56.5


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 TraesCS5A01G363400 chr5A 564074387 564080303 5916 False 5242.5 9893 100.0000 1 5917 2 chr5A.!!$F1 5916
1 TraesCS5A01G363400 chr5D 446400690 446405999 5309 False 8118.0 8118 94.3380 611 5917 1 chr5D.!!$F1 5306
2 TraesCS5A01G363400 chr5B 544329220 544335008 5788 False 1952.5 5851 87.8815 1 5917 4 chr5B.!!$F2 5916

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
748 765 0.861837 GACGGAGCTTGTTGACACTG 59.138 55.000 0.00 0.0 0.00 3.66 F
1362 1433 0.471022 AACCGCCAAACAAAGGGGAT 60.471 50.000 0.00 0.0 41.25 3.85 F
1365 1436 0.527565 CGCCAAACAAAGGGGATCAG 59.472 55.000 0.00 0.0 41.25 2.90 F
1366 1437 0.897621 GCCAAACAAAGGGGATCAGG 59.102 55.000 0.00 0.0 0.00 3.86 F
2506 2706 1.208776 ACCCCGAGTAAATACTGCCAC 59.791 52.381 0.00 0.0 36.50 5.01 F
4250 4459 0.171903 GCTTGTTTGCGCCATGAGAT 59.828 50.000 4.18 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2121 0.321653 AGGCAGTTTGGTGACCGATC 60.322 55.000 0.00 0.0 0.00 3.69 R
2916 3116 0.466124 CCGAAGACCCCTTCTCCATC 59.534 60.000 0.00 0.0 45.06 3.51 R
2998 3198 1.964552 GCAAGGAGCACAGCTATGAT 58.035 50.000 0.00 0.0 44.79 2.45 R
3064 3264 5.049336 CGTCCATGTAGTAATGAGACGAGAT 60.049 44.000 16.34 0.0 44.74 2.75 R
4396 4607 0.950836 CGAGCATGACCACACCAAAA 59.049 50.000 0.00 0.0 0.00 2.44 R
5372 5587 1.949525 CAGAAGAGGTGGTGGTTGTTG 59.050 52.381 0.00 0.0 0.00 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
26 27 3.939592 GGAAGGAGTAAAGGTGATTTCGG 59.060 47.826 0.00 0.00 32.01 4.30
28 29 2.910977 AGGAGTAAAGGTGATTTCGGGT 59.089 45.455 0.00 0.00 32.01 5.28
40 41 4.698304 GTGATTTCGGGTTTCTGGATGTTA 59.302 41.667 0.00 0.00 0.00 2.41
45 46 4.658063 TCGGGTTTCTGGATGTTATTGTT 58.342 39.130 0.00 0.00 0.00 2.83
53 54 9.353999 GTTTCTGGATGTTATTGTTGAATTACC 57.646 33.333 0.00 0.00 0.00 2.85
61 62 8.024145 TGTTATTGTTGAATTACCCTGGTTTT 57.976 30.769 0.00 0.00 0.00 2.43
72 73 6.636454 TTACCCTGGTTTTCAGTAGATGAT 57.364 37.500 0.00 0.00 41.83 2.45
73 74 7.743116 TTACCCTGGTTTTCAGTAGATGATA 57.257 36.000 0.00 0.00 41.83 2.15
74 75 6.636454 ACCCTGGTTTTCAGTAGATGATAA 57.364 37.500 0.00 0.00 41.83 1.75
75 76 6.415573 ACCCTGGTTTTCAGTAGATGATAAC 58.584 40.000 0.00 3.51 44.51 1.89
109 110 5.246203 TGATATTATGACTTCTTCGAGGGGG 59.754 44.000 0.00 0.00 0.00 5.40
111 112 1.490574 ATGACTTCTTCGAGGGGGAG 58.509 55.000 0.00 0.00 0.00 4.30
118 119 3.330126 TCTTCGAGGGGGAGATACAAT 57.670 47.619 0.00 0.00 0.00 2.71
125 126 2.374504 AGGGGGAGATACAATGCTGATG 59.625 50.000 0.00 0.00 0.00 3.07
128 129 4.225942 GGGGGAGATACAATGCTGATGATA 59.774 45.833 0.00 0.00 0.00 2.15
131 132 6.413052 GGGAGATACAATGCTGATGATATGT 58.587 40.000 0.00 0.00 0.00 2.29
144 145 7.914871 TGCTGATGATATGTAATTTCCGTTTTG 59.085 33.333 0.00 0.00 0.00 2.44
145 146 7.096477 GCTGATGATATGTAATTTCCGTTTTGC 60.096 37.037 0.00 0.00 0.00 3.68
147 148 6.767524 TGATATGTAATTTCCGTTTTGCCT 57.232 33.333 0.00 0.00 0.00 4.75
148 149 6.559810 TGATATGTAATTTCCGTTTTGCCTG 58.440 36.000 0.00 0.00 0.00 4.85
149 150 3.019933 TGTAATTTCCGTTTTGCCTGC 57.980 42.857 0.00 0.00 0.00 4.85
150 151 1.982913 GTAATTTCCGTTTTGCCTGCG 59.017 47.619 0.00 0.00 0.00 5.18
151 152 0.943835 AATTTCCGTTTTGCCTGCGC 60.944 50.000 0.00 0.00 0.00 6.09
170 173 3.737663 GCGCCTGCATTTGATTTTATCCA 60.738 43.478 0.00 0.00 42.15 3.41
173 176 5.220453 CGCCTGCATTTGATTTTATCCAAAC 60.220 40.000 0.00 0.00 35.42 2.93
204 211 7.334090 TGCTTCATCTAGCAGAGAAATTAGTT 58.666 34.615 0.00 0.00 45.72 2.24
227 234 4.087907 TCTGCATTTTGGTCCATCAATCA 58.912 39.130 0.00 0.00 0.00 2.57
228 235 4.712829 TCTGCATTTTGGTCCATCAATCAT 59.287 37.500 0.00 0.00 0.00 2.45
231 238 5.180271 GCATTTTGGTCCATCAATCATTGT 58.820 37.500 0.00 0.00 0.00 2.71
295 306 5.068329 CACACAATATGCTCTCTGACTCCTA 59.932 44.000 0.00 0.00 0.00 2.94
300 311 3.107402 TGCTCTCTGACTCCTACCATT 57.893 47.619 0.00 0.00 0.00 3.16
304 315 4.679372 GCTCTCTGACTCCTACCATTTGAC 60.679 50.000 0.00 0.00 0.00 3.18
312 323 4.341520 ACTCCTACCATTTGACGTATCTCC 59.658 45.833 0.00 0.00 0.00 3.71
314 325 3.641906 CCTACCATTTGACGTATCTCCCT 59.358 47.826 0.00 0.00 0.00 4.20
315 326 3.543680 ACCATTTGACGTATCTCCCTG 57.456 47.619 0.00 0.00 0.00 4.45
316 327 2.213499 CCATTTGACGTATCTCCCTGC 58.787 52.381 0.00 0.00 0.00 4.85
317 328 2.158900 CCATTTGACGTATCTCCCTGCT 60.159 50.000 0.00 0.00 0.00 4.24
318 329 3.535561 CATTTGACGTATCTCCCTGCTT 58.464 45.455 0.00 0.00 0.00 3.91
633 650 7.873739 AAAAATGTTGCATTTCTACAGTAGC 57.126 32.000 2.26 0.00 34.15 3.58
634 651 6.824305 AAATGTTGCATTTCTACAGTAGCT 57.176 33.333 2.26 0.00 34.15 3.32
640 657 8.236586 TGTTGCATTTCTACAGTAGCTAAAATG 58.763 33.333 19.73 19.73 37.23 2.32
642 659 8.201554 TGCATTTCTACAGTAGCTAAAATGAG 57.798 34.615 24.43 9.80 36.62 2.90
649 666 8.812972 TCTACAGTAGCTAAAATGAGAAGGAAA 58.187 33.333 2.26 0.00 0.00 3.13
650 667 9.436957 CTACAGTAGCTAAAATGAGAAGGAAAA 57.563 33.333 0.00 0.00 0.00 2.29
651 668 8.691661 ACAGTAGCTAAAATGAGAAGGAAAAA 57.308 30.769 0.00 0.00 0.00 1.94
744 761 1.335689 ACTACGACGGAGCTTGTTGAC 60.336 52.381 7.09 0.00 0.00 3.18
748 765 0.861837 GACGGAGCTTGTTGACACTG 59.138 55.000 0.00 0.00 0.00 3.66
759 776 4.002906 TGTTGACACTGATCTGGGTTAC 57.997 45.455 9.06 10.68 0.00 2.50
765 782 4.398319 ACACTGATCTGGGTTACCTTTTG 58.602 43.478 0.93 0.00 37.76 2.44
770 787 6.012858 ACTGATCTGGGTTACCTTTTGTATCA 60.013 38.462 0.00 2.49 37.76 2.15
780 797 7.093509 GGTTACCTTTTGTATCAATTGGACCAT 60.094 37.037 5.42 0.00 0.00 3.55
781 798 8.962679 GTTACCTTTTGTATCAATTGGACCATA 58.037 33.333 5.42 0.00 0.00 2.74
782 799 7.404671 ACCTTTTGTATCAATTGGACCATAC 57.595 36.000 5.42 6.81 0.00 2.39
783 800 6.951198 ACCTTTTGTATCAATTGGACCATACA 59.049 34.615 11.64 11.64 31.34 2.29
784 801 7.122650 ACCTTTTGTATCAATTGGACCATACAG 59.877 37.037 14.04 8.21 34.13 2.74
785 802 7.403312 TTTTGTATCAATTGGACCATACAGG 57.597 36.000 14.04 0.00 45.67 4.00
964 1000 1.614525 TGACCTCCTCCTGCATGCT 60.615 57.895 20.33 0.00 0.00 3.79
968 1004 3.092511 TCCTCCTGCATGCTCCCC 61.093 66.667 20.33 0.00 0.00 4.81
969 1005 4.201122 CCTCCTGCATGCTCCCCC 62.201 72.222 20.33 0.00 0.00 5.40
1144 1196 0.836400 TCTCCCGTTTCCTGCCTTCT 60.836 55.000 0.00 0.00 0.00 2.85
1155 1207 4.365514 TCCTGCCTTCTGAACATTACAA 57.634 40.909 0.00 0.00 0.00 2.41
1175 1245 4.508861 ACAATGCTGAAGAACATTTTGTGC 59.491 37.500 0.00 0.00 34.32 4.57
1176 1246 2.730069 TGCTGAAGAACATTTTGTGCG 58.270 42.857 0.00 0.00 28.94 5.34
1177 1247 2.098934 TGCTGAAGAACATTTTGTGCGT 59.901 40.909 0.00 0.00 28.94 5.24
1181 1252 5.231147 GCTGAAGAACATTTTGTGCGTTTTA 59.769 36.000 0.00 0.00 28.94 1.52
1194 1265 2.690173 CGTTTTACCGCCATGTTTCA 57.310 45.000 0.00 0.00 0.00 2.69
1195 1266 2.312348 CGTTTTACCGCCATGTTTCAC 58.688 47.619 0.00 0.00 0.00 3.18
1263 1334 1.973812 GCTGGACAACTGGAAGGCC 60.974 63.158 0.00 0.00 39.30 5.19
1356 1427 6.202954 CCAAAATGTAATAACCGCCAAACAAA 59.797 34.615 0.00 0.00 0.00 2.83
1362 1433 0.471022 AACCGCCAAACAAAGGGGAT 60.471 50.000 0.00 0.00 41.25 3.85
1364 1435 0.897863 CCGCCAAACAAAGGGGATCA 60.898 55.000 0.00 0.00 41.25 2.92
1365 1436 0.527565 CGCCAAACAAAGGGGATCAG 59.472 55.000 0.00 0.00 41.25 2.90
1366 1437 0.897621 GCCAAACAAAGGGGATCAGG 59.102 55.000 0.00 0.00 0.00 3.86
1370 1451 3.840078 CCAAACAAAGGGGATCAGGAAAT 59.160 43.478 0.00 0.00 0.00 2.17
1388 1469 4.142293 GGAAATTTCCTGCTCAAGACCATC 60.142 45.833 26.94 0.00 44.11 3.51
1397 1478 3.265791 GCTCAAGACCATCGTGAAATCT 58.734 45.455 0.00 0.00 34.66 2.40
1403 1484 3.055530 AGACCATCGTGAAATCTCAAGCT 60.056 43.478 0.00 0.00 31.88 3.74
1404 1485 3.679389 ACCATCGTGAAATCTCAAGCTT 58.321 40.909 0.00 0.00 31.88 3.74
1405 1486 3.686726 ACCATCGTGAAATCTCAAGCTTC 59.313 43.478 0.00 0.00 31.88 3.86
1406 1487 3.064545 CCATCGTGAAATCTCAAGCTTCC 59.935 47.826 0.00 0.00 31.88 3.46
1407 1488 3.685139 TCGTGAAATCTCAAGCTTCCT 57.315 42.857 0.00 0.00 31.88 3.36
1408 1489 4.008074 TCGTGAAATCTCAAGCTTCCTT 57.992 40.909 0.00 0.00 31.88 3.36
1409 1490 4.389374 TCGTGAAATCTCAAGCTTCCTTT 58.611 39.130 0.00 0.00 31.88 3.11
1410 1491 4.214119 TCGTGAAATCTCAAGCTTCCTTTG 59.786 41.667 0.00 0.00 31.88 2.77
1411 1492 4.023707 CGTGAAATCTCAAGCTTCCTTTGT 60.024 41.667 0.00 0.00 31.88 2.83
1412 1493 5.456265 GTGAAATCTCAAGCTTCCTTTGTC 58.544 41.667 0.00 0.00 31.88 3.18
1413 1494 5.009010 GTGAAATCTCAAGCTTCCTTTGTCA 59.991 40.000 0.00 0.00 31.88 3.58
1414 1495 5.771666 TGAAATCTCAAGCTTCCTTTGTCAT 59.228 36.000 0.00 0.00 0.00 3.06
1415 1496 5.893897 AATCTCAAGCTTCCTTTGTCATC 57.106 39.130 0.00 0.00 0.00 2.92
1416 1497 3.679389 TCTCAAGCTTCCTTTGTCATCC 58.321 45.455 0.00 0.00 0.00 3.51
1417 1498 3.072915 TCTCAAGCTTCCTTTGTCATCCA 59.927 43.478 0.00 0.00 0.00 3.41
1418 1499 4.015084 CTCAAGCTTCCTTTGTCATCCAT 58.985 43.478 0.00 0.00 0.00 3.41
1750 1835 3.367395 GCTGTAAGTTCATTTTCCTGGGC 60.367 47.826 0.00 0.00 35.30 5.36
1910 2063 7.119992 TGTCTGATCTAGAGACACTGTAAGAAC 59.880 40.741 9.65 0.00 43.89 3.01
1925 2078 4.640201 TGTAAGAACCTATTTCATGCTGCC 59.360 41.667 0.00 0.00 36.57 4.85
1955 2114 7.650834 TTTTTCCGATGATGATTGTTTTTCC 57.349 32.000 0.00 0.00 0.00 3.13
1962 2121 6.474427 CGATGATGATTGTTTTTCCTGAATGG 59.526 38.462 0.00 0.00 37.10 3.16
1988 2147 3.181466 GGTCACCAAACTGCCTTTTCAAT 60.181 43.478 0.00 0.00 0.00 2.57
2021 2180 2.993899 ACGTCGGAAGCAATCACTTAAG 59.006 45.455 0.00 0.00 0.00 1.85
2084 2243 7.567771 GCTCTCGACAATGTAAGTTATGCATAC 60.568 40.741 5.74 0.00 32.69 2.39
2114 2274 8.556213 TTCAGTGTTCATTGTAGTATTAACCC 57.444 34.615 0.00 0.00 0.00 4.11
2134 2294 6.599356 ACCCCTTGATAAATTTACCACAAC 57.401 37.500 0.00 0.00 0.00 3.32
2149 2313 8.428186 TTTACCACAACTCTACTAGTTTGTTG 57.572 34.615 22.38 22.38 46.61 3.33
2349 2543 6.295292 GGCAACTGGATTTTTAGGAACTTCAT 60.295 38.462 0.00 0.00 41.75 2.57
2498 2698 7.178097 GGATCTGTAAGTATACCCCGAGTAAAT 59.822 40.741 0.00 0.00 31.88 1.40
2506 2706 1.208776 ACCCCGAGTAAATACTGCCAC 59.791 52.381 0.00 0.00 36.50 5.01
2843 3043 5.574443 GCTCCTTTTGCACTACAATTTCATC 59.426 40.000 0.00 0.00 38.31 2.92
2998 3198 3.621268 CGGTTTCTTTATCGGAGCAATGA 59.379 43.478 0.00 0.00 0.00 2.57
3064 3264 1.043816 GATGAAGCGATCCTCTCCCA 58.956 55.000 0.00 0.00 0.00 4.37
3148 3348 3.138304 AGAGCACGTTTACTGATGCAAA 58.862 40.909 0.00 0.00 40.63 3.68
3187 3393 4.112634 ACTTCTACATTTTGGCTTGGGA 57.887 40.909 0.00 0.00 0.00 4.37
3315 3521 4.625742 CCTTACAAGACGATGAACGACAAT 59.374 41.667 0.00 0.00 45.77 2.71
3370 3576 1.372087 CTTGGAACCGATCAGCCTGC 61.372 60.000 0.00 0.00 0.00 4.85
3443 3649 2.553247 GCAGGATAATAGGCCAGGGAAC 60.553 54.545 5.01 0.00 0.00 3.62
3749 3958 6.118195 CGTAATCGAAGCTTATTGTTTACCG 58.882 40.000 0.00 0.00 39.71 4.02
3802 4011 0.897621 TTGATCCGCTGAGCTTCTCA 59.102 50.000 1.78 0.00 38.25 3.27
4250 4459 0.171903 GCTTGTTTGCGCCATGAGAT 59.828 50.000 4.18 0.00 0.00 2.75
4289 4500 3.706594 TCGTAGAATGAGGGCAATCTTCT 59.293 43.478 0.00 0.00 35.86 2.85
4396 4607 0.949397 TGAAGAGCGACGTGTACAGT 59.051 50.000 0.00 0.00 0.00 3.55
4586 4797 2.182791 CAGCTCCACGACAGCGAT 59.817 61.111 0.00 0.00 42.14 4.58
4665 4876 2.506217 GCTTCGCCGACGTGATCA 60.506 61.111 0.00 0.00 41.18 2.92
4687 4898 3.114616 CTGCGTCCAGGTTCAGCG 61.115 66.667 0.00 0.00 35.38 5.18
4790 5003 1.782201 AATGCCTGCAGTCTGACCCA 61.782 55.000 13.81 1.50 0.00 4.51
4792 5005 2.047844 CCTGCAGTCTGACCCACG 60.048 66.667 13.81 0.00 0.00 4.94
4794 5007 2.842462 TGCAGTCTGACCCACGGT 60.842 61.111 3.32 0.00 39.44 4.83
4796 5009 1.961277 GCAGTCTGACCCACGGTTG 60.961 63.158 3.32 0.00 35.25 3.77
4820 5033 1.679311 GCCCATGTCAGAGGTGTCA 59.321 57.895 0.00 0.00 0.00 3.58
4889 5102 4.129737 GGCCTCTACAGCGCGTCA 62.130 66.667 8.43 0.00 0.00 4.35
4933 5146 0.839277 TGATGCCCGTCCATCTGAAT 59.161 50.000 12.08 0.00 41.65 2.57
5085 5298 4.273480 GTGAACATGTAACTGCACTGAGTT 59.727 41.667 0.00 0.00 39.54 3.01
5162 5376 8.225603 TGATACTTCACTGAAAAGAAAGCTTT 57.774 30.769 12.53 12.53 45.95 3.51
5256 5471 0.171231 CTCGTTGATCACCTCTCGCA 59.829 55.000 0.00 0.00 0.00 5.10
5283 5498 2.798145 GCAAACACCACACAAGGCTAAC 60.798 50.000 0.00 0.00 0.00 2.34
5296 5511 3.654201 CTAACACAGCAAGCGCCA 58.346 55.556 2.29 0.00 39.83 5.69
5334 5549 4.816392 TCTAATACACAATGACACGCACT 58.184 39.130 0.00 0.00 0.00 4.40
5372 5587 6.140265 CGAGAAAAGAAAACGAAAAAGGCTAC 59.860 38.462 0.00 0.00 0.00 3.58
5523 5738 1.321474 CACCACTGCAAGGACATTGT 58.679 50.000 11.56 0.00 41.29 2.71
5534 5749 2.086869 AGGACATTGTTTGATGCCTCG 58.913 47.619 0.00 0.00 32.01 4.63
5542 5757 1.806542 GTTTGATGCCTCGACACACAT 59.193 47.619 0.00 0.00 0.00 3.21
5561 5783 3.587061 ACATTAGGGTCACATCACAAGGA 59.413 43.478 0.00 0.00 0.00 3.36
5849 6072 2.033141 TGCTTCCTCCAGTGCAGC 59.967 61.111 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.081804 ACATCCAGAAACCCGAAATCAC 58.918 45.455 0.00 0.00 0.00 3.06
26 27 9.353999 GTAATTCAACAATAACATCCAGAAACC 57.646 33.333 0.00 0.00 0.00 3.27
28 29 8.527810 GGGTAATTCAACAATAACATCCAGAAA 58.472 33.333 0.00 0.00 0.00 2.52
40 41 6.739331 TGAAAACCAGGGTAATTCAACAAT 57.261 33.333 13.94 0.00 33.87 2.71
83 84 7.390027 CCCCTCGAAGAAGTCATAATATCATT 58.610 38.462 0.00 0.00 34.09 2.57
92 93 1.007238 TCTCCCCCTCGAAGAAGTCAT 59.993 52.381 0.00 0.00 34.09 3.06
99 100 2.548920 GCATTGTATCTCCCCCTCGAAG 60.549 54.545 0.00 0.00 0.00 3.79
118 119 7.566760 AAACGGAAATTACATATCATCAGCA 57.433 32.000 0.00 0.00 0.00 4.41
125 126 5.458779 GCAGGCAAAACGGAAATTACATATC 59.541 40.000 0.00 0.00 0.00 1.63
128 129 3.584834 GCAGGCAAAACGGAAATTACAT 58.415 40.909 0.00 0.00 0.00 2.29
131 132 1.667467 GCGCAGGCAAAACGGAAATTA 60.667 47.619 0.30 0.00 39.62 1.40
148 149 2.796593 GGATAAAATCAAATGCAGGCGC 59.203 45.455 0.00 0.00 39.24 6.53
149 150 4.044336 TGGATAAAATCAAATGCAGGCG 57.956 40.909 0.00 0.00 0.00 5.52
150 151 5.065090 GGTTTGGATAAAATCAAATGCAGGC 59.935 40.000 0.00 0.00 35.66 4.85
151 152 5.585844 GGGTTTGGATAAAATCAAATGCAGG 59.414 40.000 0.00 0.00 35.66 4.85
161 164 3.790126 AGCAGGTGGGTTTGGATAAAAT 58.210 40.909 0.00 0.00 0.00 1.82
166 169 0.482446 TGAAGCAGGTGGGTTTGGAT 59.518 50.000 0.00 0.00 37.33 3.41
167 170 0.482446 ATGAAGCAGGTGGGTTTGGA 59.518 50.000 0.00 0.00 37.33 3.53
168 171 0.890683 GATGAAGCAGGTGGGTTTGG 59.109 55.000 0.00 0.00 37.33 3.28
170 173 2.619074 GCTAGATGAAGCAGGTGGGTTT 60.619 50.000 0.00 0.00 42.30 3.27
173 176 3.393472 GCTAGATGAAGCAGGTGGG 57.607 57.895 0.00 0.00 42.30 4.61
204 211 4.527427 TGATTGATGGACCAAAATGCAGAA 59.473 37.500 9.82 0.00 0.00 3.02
215 222 5.474876 GGAGGAATACAATGATTGATGGACC 59.525 44.000 12.80 8.28 0.00 4.46
249 259 8.874816 GTGTGCACAAATTAAACTAAGGAAAAA 58.125 29.630 23.59 0.00 0.00 1.94
252 262 7.101652 TGTGTGCACAAATTAAACTAAGGAA 57.898 32.000 23.59 0.00 38.56 3.36
253 263 6.701145 TGTGTGCACAAATTAAACTAAGGA 57.299 33.333 23.59 0.00 38.56 3.36
274 284 4.586841 GGTAGGAGTCAGAGAGCATATTGT 59.413 45.833 0.00 0.00 0.00 2.71
295 306 2.420129 GCAGGGAGATACGTCAAATGGT 60.420 50.000 0.00 0.00 0.00 3.55
593 604 8.807581 GCAACATTTTTAGCCATGTTAGTAATC 58.192 33.333 0.00 0.00 40.85 1.75
594 605 8.310382 TGCAACATTTTTAGCCATGTTAGTAAT 58.690 29.630 0.00 0.00 40.85 1.89
596 607 7.220741 TGCAACATTTTTAGCCATGTTAGTA 57.779 32.000 0.00 0.00 40.85 1.82
597 608 6.095432 TGCAACATTTTTAGCCATGTTAGT 57.905 33.333 0.00 0.00 40.85 2.24
598 609 7.599630 AATGCAACATTTTTAGCCATGTTAG 57.400 32.000 0.00 0.00 40.85 2.34
599 610 7.877097 AGAAATGCAACATTTTTAGCCATGTTA 59.123 29.630 6.97 0.00 40.85 2.41
600 611 6.711645 AGAAATGCAACATTTTTAGCCATGTT 59.288 30.769 6.97 0.00 43.06 2.71
602 613 6.730960 AGAAATGCAACATTTTTAGCCATG 57.269 33.333 6.97 0.00 0.00 3.66
604 615 6.753180 TGTAGAAATGCAACATTTTTAGCCA 58.247 32.000 6.97 0.17 0.00 4.75
605 616 6.868339 ACTGTAGAAATGCAACATTTTTAGCC 59.132 34.615 6.97 0.00 0.00 3.93
606 617 7.873739 ACTGTAGAAATGCAACATTTTTAGC 57.126 32.000 6.97 3.05 0.00 3.09
608 619 8.792633 AGCTACTGTAGAAATGCAACATTTTTA 58.207 29.630 18.64 3.59 0.00 1.52
609 620 7.661040 AGCTACTGTAGAAATGCAACATTTTT 58.339 30.769 18.64 4.49 0.00 1.94
744 761 4.398319 ACAAAAGGTAACCCAGATCAGTG 58.602 43.478 0.00 0.00 37.17 3.66
748 765 7.881775 ATTGATACAAAAGGTAACCCAGATC 57.118 36.000 0.00 0.00 35.14 2.75
759 776 7.403312 TGTATGGTCCAATTGATACAAAAGG 57.597 36.000 7.12 0.00 30.23 3.11
780 797 1.248785 GGCGTCTCACCTGACCTGTA 61.249 60.000 0.00 0.00 33.70 2.74
781 798 2.574955 GGCGTCTCACCTGACCTGT 61.575 63.158 0.00 0.00 33.70 4.00
782 799 2.262915 GGCGTCTCACCTGACCTG 59.737 66.667 0.00 0.00 33.70 4.00
783 800 2.997897 GGGCGTCTCACCTGACCT 60.998 66.667 0.00 0.00 33.70 3.85
784 801 4.083862 GGGGCGTCTCACCTGACC 62.084 72.222 0.00 0.00 33.70 4.02
785 802 2.660064 ATGGGGCGTCTCACCTGAC 61.660 63.158 0.00 0.00 0.00 3.51
786 803 2.284625 ATGGGGCGTCTCACCTGA 60.285 61.111 0.00 0.00 0.00 3.86
808 825 3.003480 CGTTTTGAAGGTCCCATCTCTC 58.997 50.000 0.00 0.00 0.00 3.20
809 826 2.637872 TCGTTTTGAAGGTCCCATCTCT 59.362 45.455 0.00 0.00 0.00 3.10
970 1006 3.775654 GAGGACCGGGCCTGTCAG 61.776 72.222 40.32 6.54 38.73 3.51
1028 1076 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
1030 1078 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1031 1079 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1036 1084 0.478507 GAGAGGAGGAGGAGGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
1037 1085 0.996762 GGAGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1039 1087 1.150536 CGGAGAGGAGGAGGAGGAG 59.849 68.421 0.00 0.00 0.00 3.69
1040 1088 3.063197 GCGGAGAGGAGGAGGAGGA 62.063 68.421 0.00 0.00 0.00 3.71
1144 1196 6.631971 TGTTCTTCAGCATTGTAATGTTCA 57.368 33.333 6.48 0.00 38.65 3.18
1155 1207 3.243501 ACGCACAAAATGTTCTTCAGCAT 60.244 39.130 0.00 0.00 0.00 3.79
1175 1245 2.312348 GTGAAACATGGCGGTAAAACG 58.688 47.619 0.00 0.00 36.32 3.60
1176 1246 2.034812 TGGTGAAACATGGCGGTAAAAC 59.965 45.455 0.00 0.00 39.98 2.43
1177 1247 2.294791 CTGGTGAAACATGGCGGTAAAA 59.705 45.455 0.00 0.00 39.98 1.52
1181 1252 1.150536 ACTGGTGAAACATGGCGGT 59.849 52.632 0.00 0.00 39.98 5.68
1194 1265 3.241530 TTCAGCGCCTCCACTGGT 61.242 61.111 2.29 0.00 34.57 4.00
1195 1266 2.743928 GTTCAGCGCCTCCACTGG 60.744 66.667 2.29 0.00 34.57 4.00
1366 1437 4.437930 CGATGGTCTTGAGCAGGAAATTTC 60.438 45.833 9.83 9.83 0.00 2.17
1370 1451 1.347707 ACGATGGTCTTGAGCAGGAAA 59.652 47.619 8.47 0.00 0.00 3.13
1374 1455 2.084610 TTCACGATGGTCTTGAGCAG 57.915 50.000 8.47 0.00 0.00 4.24
1388 1469 4.023707 ACAAAGGAAGCTTGAGATTTCACG 60.024 41.667 2.10 0.00 31.71 4.35
1397 1478 3.507162 TGGATGACAAAGGAAGCTTGA 57.493 42.857 2.10 0.00 0.00 3.02
1403 1484 2.287584 AGGGGATGGATGACAAAGGAA 58.712 47.619 0.00 0.00 0.00 3.36
1404 1485 1.985622 AGGGGATGGATGACAAAGGA 58.014 50.000 0.00 0.00 0.00 3.36
1405 1486 2.243221 AGAAGGGGATGGATGACAAAGG 59.757 50.000 0.00 0.00 0.00 3.11
1406 1487 3.659183 AGAAGGGGATGGATGACAAAG 57.341 47.619 0.00 0.00 0.00 2.77
1407 1488 3.309121 GGAAGAAGGGGATGGATGACAAA 60.309 47.826 0.00 0.00 0.00 2.83
1408 1489 2.242196 GGAAGAAGGGGATGGATGACAA 59.758 50.000 0.00 0.00 0.00 3.18
1409 1490 1.846439 GGAAGAAGGGGATGGATGACA 59.154 52.381 0.00 0.00 0.00 3.58
1410 1491 2.105649 GAGGAAGAAGGGGATGGATGAC 59.894 54.545 0.00 0.00 0.00 3.06
1411 1492 2.293788 TGAGGAAGAAGGGGATGGATGA 60.294 50.000 0.00 0.00 0.00 2.92
1412 1493 2.130193 TGAGGAAGAAGGGGATGGATG 58.870 52.381 0.00 0.00 0.00 3.51
1413 1494 2.131023 GTGAGGAAGAAGGGGATGGAT 58.869 52.381 0.00 0.00 0.00 3.41
1414 1495 1.203428 TGTGAGGAAGAAGGGGATGGA 60.203 52.381 0.00 0.00 0.00 3.41
1415 1496 1.065126 GTGTGAGGAAGAAGGGGATGG 60.065 57.143 0.00 0.00 0.00 3.51
1416 1497 1.630369 TGTGTGAGGAAGAAGGGGATG 59.370 52.381 0.00 0.00 0.00 3.51
1417 1498 1.912043 CTGTGTGAGGAAGAAGGGGAT 59.088 52.381 0.00 0.00 0.00 3.85
1418 1499 1.132849 TCTGTGTGAGGAAGAAGGGGA 60.133 52.381 0.00 0.00 0.00 4.81
1459 1543 1.094073 ATGCAGAGCGATCAAGCCAC 61.094 55.000 14.17 0.00 38.01 5.01
1546 1630 4.218417 GGCATGACTCACAATTTGGTTACT 59.782 41.667 0.00 0.00 0.00 2.24
1910 2063 1.959042 AGACGGCAGCATGAAATAGG 58.041 50.000 0.00 0.00 39.69 2.57
1937 2090 6.474427 CCATTCAGGAAAAACAATCATCATCG 59.526 38.462 0.00 0.00 41.22 3.84
1938 2091 7.549839 TCCATTCAGGAAAAACAATCATCATC 58.450 34.615 0.00 0.00 45.65 2.92
1955 2114 2.401583 TTGGTGACCGATCCATTCAG 57.598 50.000 0.00 0.00 33.50 3.02
1962 2121 0.321653 AGGCAGTTTGGTGACCGATC 60.322 55.000 0.00 0.00 0.00 3.69
1988 2147 2.355363 CGACGTTTCTGCGGTCCA 60.355 61.111 0.00 0.00 35.98 4.02
2021 2180 4.980805 TGTCCGTCAACTGCCCGC 62.981 66.667 0.00 0.00 0.00 6.13
2114 2274 9.449719 AGTAGAGTTGTGGTAAATTTATCAAGG 57.550 33.333 12.70 0.00 0.00 3.61
2134 2294 6.034683 GCGACATTACCAACAAACTAGTAGAG 59.965 42.308 3.59 0.00 0.00 2.43
2149 2313 2.159338 TCTCTGTTACCGCGACATTACC 60.159 50.000 8.23 0.00 0.00 2.85
2336 2530 7.339466 GGAGAAATAGCCAATGAAGTTCCTAAA 59.661 37.037 0.00 0.00 0.00 1.85
2349 2543 5.191727 TGATCCAAAGGAGAAATAGCCAA 57.808 39.130 0.00 0.00 34.05 4.52
2437 2637 0.948623 TTGGCCAGAACGTCGACATG 60.949 55.000 17.16 8.11 0.00 3.21
2498 2698 2.969821 ATTGGTTTGAGGTGGCAGTA 57.030 45.000 0.00 0.00 0.00 2.74
2506 2706 4.448537 TGGCGATAAAATTGGTTTGAGG 57.551 40.909 0.00 0.00 0.00 3.86
2843 3043 4.871513 TGTAGTTAGCACTGTCAGAACTG 58.128 43.478 6.91 0.00 34.06 3.16
2916 3116 0.466124 CCGAAGACCCCTTCTCCATC 59.534 60.000 0.00 0.00 45.06 3.51
2998 3198 1.964552 GCAAGGAGCACAGCTATGAT 58.035 50.000 0.00 0.00 44.79 2.45
3064 3264 5.049336 CGTCCATGTAGTAATGAGACGAGAT 60.049 44.000 16.34 0.00 44.74 2.75
3450 3656 4.429108 CATATTTTGCCTTGTAAACCCGG 58.571 43.478 0.00 0.00 0.00 5.73
3465 3671 2.802719 ACCTGTCCGTTGGCATATTTT 58.197 42.857 0.00 0.00 0.00 1.82
3726 3935 6.898189 CACGGTAAACAATAAGCTTCGATTAC 59.102 38.462 0.00 8.41 0.00 1.89
3749 3958 3.841643 CCAGCACCTGAAAAATCATCAC 58.158 45.455 0.00 0.00 32.44 3.06
3802 4011 1.964223 TCCACAAAGTCGCTTCTCTCT 59.036 47.619 0.00 0.00 0.00 3.10
4078 4287 5.842907 ACAGAAACAAAACCTTTAGCATCC 58.157 37.500 0.00 0.00 0.00 3.51
4250 4459 5.463286 TCTACGAGCAAGTGAAAATCGTTA 58.537 37.500 3.74 0.00 43.51 3.18
4289 4500 3.009363 TCCTGCAGAGAATTTCCATGTCA 59.991 43.478 17.39 0.00 0.00 3.58
4368 4579 1.840741 CGTCGCTCTTCATCGTGTAAG 59.159 52.381 0.00 0.00 0.00 2.34
4396 4607 0.950836 CGAGCATGACCACACCAAAA 59.049 50.000 0.00 0.00 0.00 2.44
4725 4936 9.745323 GCAGTTTTCAGATTTAATTTTACATGC 57.255 29.630 0.00 0.00 0.00 4.06
4804 5017 1.338484 CCTGTGACACCTCTGACATGG 60.338 57.143 2.45 0.00 0.00 3.66
4811 5024 0.178950 TGAGCTCCTGTGACACCTCT 60.179 55.000 12.15 0.00 0.00 3.69
4820 5033 3.699894 CAGCCGGTGAGCTCCTGT 61.700 66.667 12.15 0.00 42.61 4.00
4872 5085 2.907897 ATTGACGCGCTGTAGAGGCC 62.908 60.000 5.73 0.00 0.00 5.19
4873 5086 1.519455 ATTGACGCGCTGTAGAGGC 60.519 57.895 5.73 0.00 0.00 4.70
4889 5102 2.520039 CGAGATGTCGCTGCGCATT 61.520 57.895 24.66 17.23 39.88 3.56
4902 5115 0.109342 GGGCATCACCAATCCGAGAT 59.891 55.000 0.00 0.00 42.05 2.75
4933 5146 9.244292 CCCTCATATGCTGTTCTAGTAAGTATA 57.756 37.037 0.00 0.00 0.00 1.47
4951 5164 3.523564 ACCAGTGTTGCTTACCCTCATAT 59.476 43.478 0.00 0.00 0.00 1.78
5085 5298 2.721425 AAACACACGGGGAAAGAAGA 57.279 45.000 0.00 0.00 0.00 2.87
5162 5376 3.521937 ACTACCTACTTATGCTTGCCCAA 59.478 43.478 0.00 0.00 0.00 4.12
5256 5471 2.418368 TGTGTGGTGTTTGCTCTCTT 57.582 45.000 0.00 0.00 0.00 2.85
5283 5498 2.789917 GAGATGGCGCTTGCTGTG 59.210 61.111 7.64 0.00 39.13 3.66
5296 5511 6.926272 GTGTATTAGAAGAAGAATGCCGAGAT 59.074 38.462 0.00 0.00 0.00 2.75
5334 5549 3.248363 TCTTTTCTCGAACACTCGTCGTA 59.752 43.478 0.00 0.00 45.62 3.43
5372 5587 1.949525 CAGAAGAGGTGGTGGTTGTTG 59.050 52.381 0.00 0.00 0.00 3.33
5523 5738 2.183478 ATGTGTGTCGAGGCATCAAA 57.817 45.000 0.00 0.00 0.00 2.69
5534 5749 3.684788 GTGATGTGACCCTAATGTGTGTC 59.315 47.826 0.00 0.00 0.00 3.67
5542 5757 3.907474 TCTTCCTTGTGATGTGACCCTAA 59.093 43.478 0.00 0.00 0.00 2.69
5561 5783 4.307432 CACCGTGATGTGAAGTACTTCTT 58.693 43.478 30.47 18.17 40.14 2.52


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

AutoCloner maintained by Alex Coulton.