Multiple sequence alignment - TraesCS5D01G275500

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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 TraesCS5D01G275500 chr5D 100.000 2417 0 0 1 2417 378124579 378126995 0.000000e+00 4464
1 TraesCS5D01G275500 chr5D 92.157 153 12 0 2264 2416 129975579 129975427 1.460000e-52 217
2 TraesCS5D01G275500 chr5D 92.208 154 11 1 2261 2413 546004901 546005054 1.460000e-52 217
3 TraesCS5D01G275500 chrUn 90.941 2296 155 26 1 2262 171286122 171288398 0.000000e+00 3038
4 TraesCS5D01G275500 chrUn 92.791 1609 106 8 661 2264 67015294 67013691 0.000000e+00 2320
5 TraesCS5D01G275500 chrUn 92.728 1609 107 8 661 2264 171261971 171263574 0.000000e+00 2314
6 TraesCS5D01G275500 chrUn 92.728 1609 107 8 661 2264 171300987 171302590 0.000000e+00 2314
7 TraesCS5D01G275500 chrUn 90.752 1622 114 16 661 2262 171254207 171255812 0.000000e+00 2132
8 TraesCS5D01G275500 chrUn 92.672 1392 94 6 661 2047 347092867 347094255 0.000000e+00 1999
9 TraesCS5D01G275500 chrUn 93.245 1288 77 9 981 2264 171271472 171272753 0.000000e+00 1888
10 TraesCS5D01G275500 chrUn 92.935 1288 81 9 981 2264 171282145 171283426 0.000000e+00 1866
11 TraesCS5D01G275500 chrUn 91.204 1262 76 15 1 1231 171275449 171276706 0.000000e+00 1683
12 TraesCS5D01G275500 chrUn 93.544 666 38 4 1 664 171253294 171253956 0.000000e+00 987
13 TraesCS5D01G275500 chrUn 93.544 666 38 4 1 664 359324914 359324252 0.000000e+00 987
14 TraesCS5D01G275500 chrUn 93.393 666 39 4 1 664 67023682 67023020 0.000000e+00 981
15 TraesCS5D01G275500 chrUn 92.216 167 12 1 1 167 438178784 438178949 4.020000e-58 235
16 TraesCS5D01G275500 chr5A 92.603 1744 105 9 528 2264 478861107 478862833 0.000000e+00 2484
17 TraesCS5D01G275500 chr5A 91.416 1165 77 13 633 1781 478864353 478865510 0.000000e+00 1576
18 TraesCS5D01G275500 chr5A 92.473 279 18 1 1 276 478860827 478861105 1.740000e-106 396
19 TraesCS5D01G275500 chr5B 90.631 1633 112 25 665 2264 453726899 453725275 0.000000e+00 2130
20 TraesCS5D01G275500 chr5B 91.418 1107 76 4 678 1781 453723715 453722625 0.000000e+00 1500
21 TraesCS5D01G275500 chr5B 82.026 306 39 13 663 964 453688123 453687830 1.860000e-61 246
22 TraesCS5D01G275500 chr5B 86.726 113 14 1 1 113 453686193 453686082 9.070000e-25 124
23 TraesCS5D01G275500 chr7D 92.810 153 11 0 2261 2413 50709560 50709712 3.130000e-54 222
24 TraesCS5D01G275500 chr7D 92.157 153 12 0 2261 2413 512276320 512276472 1.460000e-52 217
25 TraesCS5D01G275500 chr2D 92.810 153 11 0 2261 2413 35551370 35551522 3.130000e-54 222
26 TraesCS5D01G275500 chr2D 92.157 153 12 0 2264 2416 450876107 450875955 1.460000e-52 217
27 TraesCS5D01G275500 chr4D 92.157 153 12 0 2265 2417 484619005 484619157 1.460000e-52 217
28 TraesCS5D01G275500 chr4B 91.667 156 11 2 2259 2413 291859866 291860020 5.230000e-52 215
29 TraesCS5D01G275500 chr1B 92.568 148 11 0 2266 2413 253045789 253045936 1.880000e-51 213


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 TraesCS5D01G275500 chr5D 378124579 378126995 2416 False 4464.000000 4464 100.0000 1 2417 1 chr5D.!!$F1 2416
1 TraesCS5D01G275500 chrUn 171282145 171288398 6253 False 2452.000000 3038 91.9380 1 2264 2 chrUn.!!$F7 2263
2 TraesCS5D01G275500 chrUn 67013691 67015294 1603 True 2320.000000 2320 92.7910 661 2264 1 chrUn.!!$R1 1603
3 TraesCS5D01G275500 chrUn 171261971 171263574 1603 False 2314.000000 2314 92.7280 661 2264 1 chrUn.!!$F1 1603
4 TraesCS5D01G275500 chrUn 171300987 171302590 1603 False 2314.000000 2314 92.7280 661 2264 1 chrUn.!!$F2 1603
5 TraesCS5D01G275500 chrUn 347092867 347094255 1388 False 1999.000000 1999 92.6720 661 2047 1 chrUn.!!$F3 1386
6 TraesCS5D01G275500 chrUn 171271472 171276706 5234 False 1785.500000 1888 92.2245 1 2264 2 chrUn.!!$F6 2263
7 TraesCS5D01G275500 chrUn 171253294 171255812 2518 False 1559.500000 2132 92.1480 1 2262 2 chrUn.!!$F5 2261
8 TraesCS5D01G275500 chrUn 359324252 359324914 662 True 987.000000 987 93.5440 1 664 1 chrUn.!!$R3 663
9 TraesCS5D01G275500 chrUn 67023020 67023682 662 True 981.000000 981 93.3930 1 664 1 chrUn.!!$R2 663
10 TraesCS5D01G275500 chr5A 478860827 478865510 4683 False 1485.333333 2484 92.1640 1 2264 3 chr5A.!!$F1 2263
11 TraesCS5D01G275500 chr5B 453722625 453726899 4274 True 1815.000000 2130 91.0245 665 2264 2 chr5B.!!$R2 1599

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
812 5060 0.249911 AAGACAACTGCCGGTCTCAC 60.25 55.0 1.9 0.0 43.26 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2335 9145 0.041576 CGGACATGCGCATGAATGAG 60.042 55.0 46.9 29.99 41.2 2.9 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
79 4060 6.591935 AGTGTTCTCTGAATGTTCCTTTGTA 58.408 36.000 0.00 0.00 0.00 2.41
113 4094 4.418392 CATTGCTTTGCTCACATACCTTC 58.582 43.478 0.00 0.00 0.00 3.46
126 4107 3.632145 ACATACCTTCGGGATTGCATTTC 59.368 43.478 0.00 0.00 38.77 2.17
138 4119 4.024556 GGATTGCATTTCTGTATCACTCGG 60.025 45.833 0.00 0.00 0.00 4.63
158 4139 3.627123 CGGCATCAACTTATGTTCCATCA 59.373 43.478 0.00 0.00 33.52 3.07
161 4142 5.533903 GGCATCAACTTATGTTCCATCAGAT 59.466 40.000 0.00 0.00 33.52 2.90
181 4162 4.952335 AGATTTCCTGCCAGTTAAATGGAG 59.048 41.667 25.51 17.51 43.57 3.86
196 4177 0.610174 TGGAGCAGAGGTTAGCACTG 59.390 55.000 4.57 4.57 35.14 3.66
204 4185 2.043227 GAGGTTAGCACTGGAGGCTAT 58.957 52.381 0.00 0.00 42.91 2.97
258 4239 9.868277 GTGCATATAGACATCTAATCTAGCTTT 57.132 33.333 0.00 0.00 32.27 3.51
281 4262 1.818060 AGCTTGCGGCATTGTTGAATA 59.182 42.857 2.28 0.00 44.79 1.75
285 4266 4.674101 GCTTGCGGCATTGTTGAATAGTTA 60.674 41.667 2.28 0.00 41.35 2.24
337 4318 2.099756 GGCCATCAGAGAAAATTTCCCG 59.900 50.000 0.00 0.00 0.00 5.14
370 4351 5.305585 TCAGGTAGATGTGGAAAACAAGTC 58.694 41.667 0.00 0.00 43.61 3.01
376 4357 7.013369 GGTAGATGTGGAAAACAAGTCTTTCTT 59.987 37.037 0.00 0.00 43.61 2.52
386 4367 2.086054 AGTCTTTCTTAGGCACGCAG 57.914 50.000 0.00 0.00 0.00 5.18
405 4386 6.395629 ACGCAGTGTTATGTGAATACTAGTT 58.604 36.000 0.00 0.00 42.51 2.24
408 4389 7.253783 CGCAGTGTTATGTGAATACTAGTTCAG 60.254 40.741 0.00 0.00 38.68 3.02
418 4399 6.477033 GTGAATACTAGTTCAGCATTCATCGT 59.523 38.462 16.99 0.00 44.91 3.73
428 4409 4.039703 CAGCATTCATCGTATTGCTTTGG 58.960 43.478 0.00 0.00 42.52 3.28
463 4444 2.002586 CGAGTGTAAGTGCAATGGGAG 58.997 52.381 0.00 0.00 0.00 4.30
549 4531 2.185608 GGACGGAGCTCAGCTTCC 59.814 66.667 17.19 11.69 39.88 3.46
563 4548 4.836825 TCAGCTTCCTAATTGGACAAGAG 58.163 43.478 5.12 0.00 46.14 2.85
737 4977 4.329256 GGACGTAATGAGCTAACTCCAAAC 59.671 45.833 0.00 0.00 42.74 2.93
812 5060 0.249911 AAGACAACTGCCGGTCTCAC 60.250 55.000 1.90 0.00 43.26 3.51
848 5098 2.552768 CGCGCATGAATCCATCCG 59.447 61.111 8.75 0.00 37.04 4.18
911 5161 0.818445 GCAGCACCATCAGATCCTGG 60.818 60.000 5.29 5.29 38.55 4.45
978 5236 1.136891 ACCACTCCAAAGCAAACAAGC 59.863 47.619 0.00 0.00 0.00 4.01
1335 5624 2.031595 CGAGGTCTATGTGGATGAGTCG 60.032 54.545 0.00 0.00 0.00 4.18
1339 5628 3.003897 GGTCTATGTGGATGAGTCGTCTC 59.996 52.174 12.07 2.47 40.79 3.36
1452 5741 8.924303 AGTTAAAAAGGCCAGAAGAATAAAGTT 58.076 29.630 5.01 0.00 0.00 2.66
1470 5759 2.147958 GTTAGTGAATGGTTCGGCACA 58.852 47.619 0.00 0.00 33.85 4.57
1500 5789 7.425577 TCACATGTTATGCAGAAGTATATGC 57.574 36.000 0.00 0.00 42.86 3.14
1503 5792 8.347771 CACATGTTATGCAGAAGTATATGCTTT 58.652 33.333 7.53 0.00 42.98 3.51
1513 5802 7.217070 GCAGAAGTATATGCTTTCGTTTTCTTG 59.783 37.037 7.53 0.00 39.38 3.02
1514 5803 8.230486 CAGAAGTATATGCTTTCGTTTTCTTGT 58.770 33.333 7.53 0.00 0.00 3.16
1516 5805 8.728088 AAGTATATGCTTTCGTTTTCTTGTTG 57.272 30.769 0.00 0.00 0.00 3.33
1548 5837 2.733026 GGTTGTTGCATGAATGTTGCTC 59.267 45.455 0.00 0.00 40.77 4.26
1575 5864 4.790937 TCAGCCCATGTTATGCAGAAATA 58.209 39.130 0.00 0.00 0.00 1.40
1578 5867 6.656270 TCAGCCCATGTTATGCAGAAATATAG 59.344 38.462 0.00 0.00 0.00 1.31
1693 5983 5.016031 ACTTATACCGTCTCCTATACCCCAT 59.984 44.000 0.00 0.00 0.00 4.00
1708 5998 1.615883 CCCCATATCGACCACTCTCAG 59.384 57.143 0.00 0.00 0.00 3.35
1738 6028 3.146066 TGTTGTCCCTATCTTTGTGTGC 58.854 45.455 0.00 0.00 0.00 4.57
1749 6039 5.886960 ATCTTTGTGTGCCAGAGAATAAC 57.113 39.130 0.00 0.00 37.78 1.89
1935 6226 0.815095 TCGACAGCAAGGCTCGAATA 59.185 50.000 0.87 0.00 36.40 1.75
2108 6402 7.524294 TCTTGTCTTGATTTTGTTTTCTTGC 57.476 32.000 0.00 0.00 0.00 4.01
2111 6405 5.288232 TGTCTTGATTTTGTTTTCTTGCGTG 59.712 36.000 0.00 0.00 0.00 5.34
2140 6434 4.669206 TGCTGAGAAAATGCAAAGGAAA 57.331 36.364 0.00 0.00 33.48 3.13
2193 6488 6.419484 AGCCAAAACTAGCCAAATTTAAGT 57.581 33.333 0.00 0.00 0.00 2.24
2230 6525 2.423185 TGACAAAACCAACACAGAGCAG 59.577 45.455 0.00 0.00 0.00 4.24
2264 6559 8.317679 ACTGCTATGGTTGAGGATTAGATTATC 58.682 37.037 0.00 0.00 0.00 1.75
2265 6560 7.323420 TGCTATGGTTGAGGATTAGATTATCG 58.677 38.462 0.00 0.00 0.00 2.92
2266 6561 7.178451 TGCTATGGTTGAGGATTAGATTATCGA 59.822 37.037 0.00 0.00 0.00 3.59
2267 6562 8.035394 GCTATGGTTGAGGATTAGATTATCGAA 58.965 37.037 0.00 0.00 0.00 3.71
2268 6563 9.929180 CTATGGTTGAGGATTAGATTATCGAAA 57.071 33.333 0.00 0.00 0.00 3.46
2269 6564 8.608844 ATGGTTGAGGATTAGATTATCGAAAC 57.391 34.615 0.00 0.00 0.00 2.78
2270 6565 7.792032 TGGTTGAGGATTAGATTATCGAAACT 58.208 34.615 0.00 0.00 0.00 2.66
2271 6566 7.710907 TGGTTGAGGATTAGATTATCGAAACTG 59.289 37.037 0.00 0.00 0.00 3.16
2272 6567 7.307455 GGTTGAGGATTAGATTATCGAAACTGC 60.307 40.741 0.00 0.00 0.00 4.40
2273 6568 7.055667 TGAGGATTAGATTATCGAAACTGCT 57.944 36.000 0.00 0.00 0.00 4.24
2274 6569 7.148641 TGAGGATTAGATTATCGAAACTGCTC 58.851 38.462 0.00 4.27 0.00 4.26
2275 6570 6.459923 AGGATTAGATTATCGAAACTGCTCC 58.540 40.000 0.00 0.00 0.00 4.70
2278 6573 4.471904 AGATTATCGAAACTGCTCCACA 57.528 40.909 0.00 0.00 0.00 4.17
2279 6574 4.184629 AGATTATCGAAACTGCTCCACAC 58.815 43.478 0.00 0.00 0.00 3.82
2280 6575 3.394674 TTATCGAAACTGCTCCACACA 57.605 42.857 0.00 0.00 0.00 3.72
2281 6576 1.512926 ATCGAAACTGCTCCACACAC 58.487 50.000 0.00 0.00 0.00 3.82
2282 6577 0.176910 TCGAAACTGCTCCACACACA 59.823 50.000 0.00 0.00 0.00 3.72
2285 6580 2.602933 CGAAACTGCTCCACACACAATG 60.603 50.000 0.00 0.00 0.00 2.82
2286 6581 2.057137 AACTGCTCCACACACAATGT 57.943 45.000 0.00 0.00 44.81 2.71
2287 6582 2.057137 ACTGCTCCACACACAATGTT 57.943 45.000 0.00 0.00 40.64 2.71
2289 6584 2.358898 ACTGCTCCACACACAATGTTTC 59.641 45.455 0.00 0.00 40.64 2.78
2292 6587 2.859806 GCTCCACACACAATGTTTCTGC 60.860 50.000 0.00 0.00 40.64 4.26
2293 6588 1.680735 TCCACACACAATGTTTCTGCC 59.319 47.619 0.00 0.00 40.64 4.85
2294 6589 1.269726 CCACACACAATGTTTCTGCCC 60.270 52.381 0.00 0.00 40.64 5.36
2295 6590 0.667993 ACACACAATGTTTCTGCCCG 59.332 50.000 0.00 0.00 38.98 6.13
2296 6591 0.950836 CACACAATGTTTCTGCCCGA 59.049 50.000 0.00 0.00 0.00 5.14
2297 6592 1.541147 CACACAATGTTTCTGCCCGAT 59.459 47.619 0.00 0.00 0.00 4.18
2298 6593 1.812571 ACACAATGTTTCTGCCCGATC 59.187 47.619 0.00 0.00 0.00 3.69
2299 6594 2.086869 CACAATGTTTCTGCCCGATCT 58.913 47.619 0.00 0.00 0.00 2.75
2300 6595 3.270027 CACAATGTTTCTGCCCGATCTA 58.730 45.455 0.00 0.00 0.00 1.98
2304 6599 1.209261 TGTTTCTGCCCGATCTATGCA 59.791 47.619 0.00 0.00 0.00 3.96
2305 6600 2.158769 TGTTTCTGCCCGATCTATGCAT 60.159 45.455 3.79 3.79 33.97 3.96
2306 6601 2.174363 TTCTGCCCGATCTATGCATG 57.826 50.000 10.16 0.00 33.97 4.06
2308 6603 1.001293 TCTGCCCGATCTATGCATGAC 59.999 52.381 10.16 0.00 33.97 3.06
2314 9124 3.494924 CCCGATCTATGCATGACCTGAAA 60.495 47.826 10.16 0.00 0.00 2.69
2318 9128 5.106791 CGATCTATGCATGACCTGAAAATCC 60.107 44.000 10.16 0.00 0.00 3.01
2324 9134 1.538047 TGACCTGAAAATCCAGCAGC 58.462 50.000 0.00 0.00 32.97 5.25
2325 9135 0.813821 GACCTGAAAATCCAGCAGCC 59.186 55.000 0.00 0.00 32.97 4.85
2327 9137 1.660560 CCTGAAAATCCAGCAGCCGG 61.661 60.000 0.00 0.00 32.97 6.13
2328 9138 0.962356 CTGAAAATCCAGCAGCCGGT 60.962 55.000 1.90 0.00 0.00 5.28
2329 9139 0.326595 TGAAAATCCAGCAGCCGGTA 59.673 50.000 1.90 0.00 0.00 4.02
2331 9141 0.679960 AAAATCCAGCAGCCGGTACC 60.680 55.000 1.90 0.16 0.00 3.34
2332 9142 2.552231 AAATCCAGCAGCCGGTACCC 62.552 60.000 6.25 0.00 0.00 3.69
2333 9143 4.715130 TCCAGCAGCCGGTACCCT 62.715 66.667 6.25 0.00 0.00 4.34
2334 9144 4.473520 CCAGCAGCCGGTACCCTG 62.474 72.222 6.25 10.01 0.00 4.45
2338 9148 3.390521 CAGCCGGTACCCTGCTCA 61.391 66.667 18.27 0.00 42.01 4.26
2339 9149 2.365635 AGCCGGTACCCTGCTCAT 60.366 61.111 15.98 0.00 39.89 2.90
2340 9150 1.995626 AGCCGGTACCCTGCTCATT 60.996 57.895 15.98 0.00 39.89 2.57
2341 9151 1.523938 GCCGGTACCCTGCTCATTC 60.524 63.158 6.25 0.00 31.02 2.67
2343 9153 0.469917 CCGGTACCCTGCTCATTCAT 59.530 55.000 6.25 0.00 0.00 2.57
2345 9155 1.312815 GGTACCCTGCTCATTCATGC 58.687 55.000 0.00 0.00 0.00 4.06
2346 9156 0.940126 GTACCCTGCTCATTCATGCG 59.060 55.000 0.00 0.00 0.00 4.73
2347 9157 0.815213 TACCCTGCTCATTCATGCGC 60.815 55.000 0.00 0.00 38.88 6.09
2348 9158 2.116533 CCCTGCTCATTCATGCGCA 61.117 57.895 14.96 14.96 45.16 6.09
2349 9159 1.452953 CCCTGCTCATTCATGCGCAT 61.453 55.000 19.28 19.28 46.01 4.73
2351 9161 0.380733 CTGCTCATTCATGCGCATGT 59.619 50.000 40.57 25.76 46.01 3.21
2353 9163 0.317603 GCTCATTCATGCGCATGTCC 60.318 55.000 40.57 22.99 38.33 4.02
2354 9164 0.041576 CTCATTCATGCGCATGTCCG 60.042 55.000 40.57 30.19 39.72 4.79
2356 9166 2.837883 ATTCATGCGCATGTCCGGC 61.838 57.895 40.57 0.00 39.72 6.13
2357 9167 3.974835 TTCATGCGCATGTCCGGCT 62.975 57.895 40.57 10.29 39.72 5.52
2358 9168 4.246206 CATGCGCATGTCCGGCTG 62.246 66.667 36.45 15.20 34.23 4.85
2370 9180 2.325583 TCCGGCTGGATTTATGTGTC 57.674 50.000 11.27 0.00 40.17 3.67
2371 9181 0.937304 CCGGCTGGATTTATGTGTCG 59.063 55.000 5.28 0.00 37.49 4.35
2374 9184 2.356135 GGCTGGATTTATGTGTCGTGT 58.644 47.619 0.00 0.00 0.00 4.49
2375 9185 2.095853 GGCTGGATTTATGTGTCGTGTG 59.904 50.000 0.00 0.00 0.00 3.82
2376 9186 2.742053 GCTGGATTTATGTGTCGTGTGT 59.258 45.455 0.00 0.00 0.00 3.72
2378 9188 3.993736 CTGGATTTATGTGTCGTGTGTGA 59.006 43.478 0.00 0.00 0.00 3.58
2379 9189 4.381411 TGGATTTATGTGTCGTGTGTGAA 58.619 39.130 0.00 0.00 0.00 3.18
2380 9190 5.000591 TGGATTTATGTGTCGTGTGTGAAT 58.999 37.500 0.00 0.00 0.00 2.57
2381 9191 5.471797 TGGATTTATGTGTCGTGTGTGAATT 59.528 36.000 0.00 0.00 0.00 2.17
2382 9192 5.794945 GGATTTATGTGTCGTGTGTGAATTG 59.205 40.000 0.00 0.00 0.00 2.32
2384 9194 3.878086 ATGTGTCGTGTGTGAATTGTC 57.122 42.857 0.00 0.00 0.00 3.18
2385 9195 2.899976 TGTGTCGTGTGTGAATTGTCT 58.100 42.857 0.00 0.00 0.00 3.41
2386 9196 2.607180 TGTGTCGTGTGTGAATTGTCTG 59.393 45.455 0.00 0.00 0.00 3.51
2387 9197 2.863740 GTGTCGTGTGTGAATTGTCTGA 59.136 45.455 0.00 0.00 0.00 3.27
2388 9198 3.308595 GTGTCGTGTGTGAATTGTCTGAA 59.691 43.478 0.00 0.00 0.00 3.02
2389 9199 4.024893 GTGTCGTGTGTGAATTGTCTGAAT 60.025 41.667 0.00 0.00 0.00 2.57
2390 9200 4.574421 TGTCGTGTGTGAATTGTCTGAATT 59.426 37.500 0.00 0.00 0.00 2.17
2392 9202 5.050091 GTCGTGTGTGAATTGTCTGAATTCT 60.050 40.000 7.05 0.00 37.50 2.40
2394 9204 5.277490 CGTGTGTGAATTGTCTGAATTCTGT 60.277 40.000 7.05 0.00 37.50 3.41
2395 9205 6.138761 GTGTGTGAATTGTCTGAATTCTGTC 58.861 40.000 7.05 4.90 37.50 3.51
2398 9208 5.177511 TGTGAATTGTCTGAATTCTGTCGTC 59.822 40.000 7.05 4.45 37.50 4.20
2400 9210 2.347697 TGTCTGAATTCTGTCGTCCG 57.652 50.000 7.05 0.00 0.00 4.79
2401 9211 1.611977 TGTCTGAATTCTGTCGTCCGT 59.388 47.619 7.05 0.00 0.00 4.69
2402 9212 2.815503 TGTCTGAATTCTGTCGTCCGTA 59.184 45.455 7.05 0.00 0.00 4.02
2404 9214 4.637091 TGTCTGAATTCTGTCGTCCGTATA 59.363 41.667 7.05 0.00 0.00 1.47
2407 9217 3.379057 TGAATTCTGTCGTCCGTATAGCA 59.621 43.478 7.05 0.00 0.00 3.49
2408 9218 2.838386 TTCTGTCGTCCGTATAGCAC 57.162 50.000 0.00 0.00 0.00 4.40
2409 9219 2.034104 TCTGTCGTCCGTATAGCACT 57.966 50.000 0.00 0.00 0.00 4.40
2410 9220 1.669265 TCTGTCGTCCGTATAGCACTG 59.331 52.381 0.00 0.00 0.00 3.66
2413 9223 1.600957 GTCGTCCGTATAGCACTGCTA 59.399 52.381 13.19 13.19 45.55 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 4032 8.877779 CAAAGGAACATTCAGAGAACACTATAG 58.122 37.037 0.00 0.00 0.00 1.31
113 4094 3.879295 AGTGATACAGAAATGCAATCCCG 59.121 43.478 0.00 0.00 0.00 5.14
126 4107 3.170791 AGTTGATGCCGAGTGATACAG 57.829 47.619 0.00 0.00 0.00 2.74
158 4139 4.934356 TCCATTTAACTGGCAGGAAATCT 58.066 39.130 20.34 2.30 36.16 2.40
161 4142 2.825532 GCTCCATTTAACTGGCAGGAAA 59.174 45.455 20.34 17.90 36.16 3.13
181 4162 0.107945 CCTCCAGTGCTAACCTCTGC 60.108 60.000 0.00 0.00 34.51 4.26
196 4177 1.602311 CCATCTGCAACATAGCCTCC 58.398 55.000 0.00 0.00 0.00 4.30
204 4185 2.364970 CCAAAGTTTCCCATCTGCAACA 59.635 45.455 0.00 0.00 0.00 3.33
258 4239 0.318869 CAACAATGCCGCAAGCTGAA 60.319 50.000 0.00 0.00 44.23 3.02
281 4262 6.170506 TCAACAACACAGAAAGTCAGTAACT 58.829 36.000 0.00 0.00 41.10 2.24
285 4266 6.515272 AAATCAACAACACAGAAAGTCAGT 57.485 33.333 0.00 0.00 0.00 3.41
337 4318 4.941873 CCACATCTACCTGAACCTAAAACC 59.058 45.833 0.00 0.00 0.00 3.27
370 4351 1.512926 ACACTGCGTGCCTAAGAAAG 58.487 50.000 8.31 0.00 36.98 2.62
376 4357 1.273886 TCACATAACACTGCGTGCCTA 59.726 47.619 8.31 2.32 36.98 3.93
386 4367 7.827819 TGCTGAACTAGTATTCACATAACAC 57.172 36.000 0.00 0.00 34.84 3.32
398 4379 6.420903 GCAATACGATGAATGCTGAACTAGTA 59.579 38.462 0.00 0.00 35.93 1.82
408 4389 4.032703 ACCAAAGCAATACGATGAATGC 57.967 40.909 0.00 0.00 39.06 3.56
428 4409 2.676342 ACACTCGAACAACCTTTGTGAC 59.324 45.455 3.08 0.00 44.59 3.67
437 4418 3.936902 TTGCACTTACACTCGAACAAC 57.063 42.857 0.00 0.00 0.00 3.32
463 4444 4.486090 TCTCGAGTGATACAAAGTTCAGC 58.514 43.478 13.13 0.00 0.00 4.26
519 4500 3.143728 GCTCCGTCCCAAGTAAGAAAAA 58.856 45.455 0.00 0.00 0.00 1.94
533 4515 0.818296 TTAGGAAGCTGAGCTCCGTC 59.182 55.000 7.72 0.95 38.25 4.79
549 4531 3.012518 CCCAGTGCTCTTGTCCAATTAG 58.987 50.000 0.00 0.00 0.00 1.73
563 4548 1.896465 AGAGTGTAGAAGTCCCAGTGC 59.104 52.381 0.00 0.00 0.00 4.40
911 5161 5.073311 TGAGCTTGTGGTACTTGATAGAC 57.927 43.478 0.00 0.00 0.00 2.59
1335 5624 3.706594 TGATGGTGACCTTATCAGGAGAC 59.293 47.826 2.11 0.00 44.19 3.36
1339 5628 4.684485 GGTCTTGATGGTGACCTTATCAGG 60.684 50.000 2.11 5.47 46.65 3.86
1452 5741 1.943968 GCTGTGCCGAACCATTCACTA 60.944 52.381 0.00 0.00 0.00 2.74
1470 5759 3.678289 TCTGCATAACATGTGAACTGCT 58.322 40.909 17.60 0.00 0.00 4.24
1503 5792 9.280174 ACCTTTATTAGATCAACAAGAAAACGA 57.720 29.630 0.00 0.00 0.00 3.85
1513 5802 8.243426 TCATGCAACAACCTTTATTAGATCAAC 58.757 33.333 0.00 0.00 0.00 3.18
1514 5803 8.347004 TCATGCAACAACCTTTATTAGATCAA 57.653 30.769 0.00 0.00 0.00 2.57
1516 5805 9.241317 CATTCATGCAACAACCTTTATTAGATC 57.759 33.333 0.00 0.00 0.00 2.75
1548 5837 1.410153 GCATAACATGGGCTGAAAGGG 59.590 52.381 0.00 0.00 0.00 3.95
1575 5864 8.173542 ACATTACAAAGAAAACGGAAACCTAT 57.826 30.769 0.00 0.00 0.00 2.57
1578 5867 8.806177 ATTACATTACAAAGAAAACGGAAACC 57.194 30.769 0.00 0.00 0.00 3.27
1679 5969 3.594685 TGGTCGATATGGGGTATAGGAGA 59.405 47.826 0.00 0.00 0.00 3.71
1688 5978 1.615883 CTGAGAGTGGTCGATATGGGG 59.384 57.143 0.00 0.00 0.00 4.96
1693 5983 2.025155 GGAAGCTGAGAGTGGTCGATA 58.975 52.381 0.00 0.00 0.00 2.92
1708 5998 0.690762 TAGGGACAACAGTGGGAAGC 59.309 55.000 0.00 0.00 0.00 3.86
1738 6028 4.336889 TGATAAGGCCGTTATTCTCTGG 57.663 45.455 0.00 0.00 30.93 3.86
1749 6039 6.149633 GCTTAATTATTGGTTGATAAGGCCG 58.850 40.000 0.00 0.00 0.00 6.13
1833 6123 9.790344 AAAATCAACATGAAAATCCAAATACCA 57.210 25.926 0.00 0.00 0.00 3.25
2108 6402 4.488126 TTTTCTCAGCAATCTTTCCACG 57.512 40.909 0.00 0.00 0.00 4.94
2111 6405 4.813027 TGCATTTTCTCAGCAATCTTTCC 58.187 39.130 0.00 0.00 34.97 3.13
2140 6434 5.046663 TGGTTTCTGCTTTTGTCCTCTTTTT 60.047 36.000 0.00 0.00 0.00 1.94
2193 6488 7.776030 TGGTTTTGTCATTCTCTTTTACCAGTA 59.224 33.333 0.00 0.00 0.00 2.74
2230 6525 4.442192 CCTCAACCATAGCAGTAGGAGTTC 60.442 50.000 0.00 0.00 0.00 3.01
2264 6559 1.013596 TTGTGTGTGGAGCAGTTTCG 58.986 50.000 0.00 0.00 0.00 3.46
2265 6560 2.358898 ACATTGTGTGTGGAGCAGTTTC 59.641 45.455 0.00 0.00 40.28 2.78
2266 6561 2.378038 ACATTGTGTGTGGAGCAGTTT 58.622 42.857 0.00 0.00 40.28 2.66
2267 6562 2.057137 ACATTGTGTGTGGAGCAGTT 57.943 45.000 0.00 0.00 40.28 3.16
2268 6563 2.057137 AACATTGTGTGTGGAGCAGT 57.943 45.000 0.00 0.00 41.14 4.40
2269 6564 2.620115 AGAAACATTGTGTGTGGAGCAG 59.380 45.455 0.00 0.00 41.14 4.24
2270 6565 2.358582 CAGAAACATTGTGTGTGGAGCA 59.641 45.455 0.00 0.00 41.14 4.26
2271 6566 2.859806 GCAGAAACATTGTGTGTGGAGC 60.860 50.000 6.28 0.00 41.14 4.70
2272 6567 2.287788 GGCAGAAACATTGTGTGTGGAG 60.288 50.000 6.28 0.00 41.14 3.86
2273 6568 1.680735 GGCAGAAACATTGTGTGTGGA 59.319 47.619 6.28 0.00 41.14 4.02
2274 6569 1.269726 GGGCAGAAACATTGTGTGTGG 60.270 52.381 6.28 0.00 41.14 4.17
2275 6570 1.600164 CGGGCAGAAACATTGTGTGTG 60.600 52.381 0.00 0.00 41.14 3.82
2278 6573 1.812571 GATCGGGCAGAAACATTGTGT 59.187 47.619 0.00 0.00 0.00 3.72
2279 6574 2.086869 AGATCGGGCAGAAACATTGTG 58.913 47.619 0.00 0.00 0.00 3.33
2280 6575 2.496899 AGATCGGGCAGAAACATTGT 57.503 45.000 0.00 0.00 0.00 2.71
2281 6576 3.304257 GCATAGATCGGGCAGAAACATTG 60.304 47.826 0.00 0.00 0.00 2.82
2282 6577 2.880890 GCATAGATCGGGCAGAAACATT 59.119 45.455 0.00 0.00 0.00 2.71
2285 6580 1.953559 TGCATAGATCGGGCAGAAAC 58.046 50.000 5.11 0.00 32.95 2.78
2286 6581 2.104622 TCATGCATAGATCGGGCAGAAA 59.895 45.455 0.00 1.38 41.40 2.52
2287 6582 1.693606 TCATGCATAGATCGGGCAGAA 59.306 47.619 0.00 3.34 41.40 3.02
2289 6584 1.436600 GTCATGCATAGATCGGGCAG 58.563 55.000 0.00 7.06 41.40 4.85
2292 6587 1.620323 TCAGGTCATGCATAGATCGGG 59.380 52.381 0.00 0.00 0.00 5.14
2293 6588 3.391506 TTCAGGTCATGCATAGATCGG 57.608 47.619 0.00 1.12 0.00 4.18
2294 6589 5.106791 GGATTTTCAGGTCATGCATAGATCG 60.107 44.000 0.00 0.00 0.00 3.69
2295 6590 5.766670 TGGATTTTCAGGTCATGCATAGATC 59.233 40.000 0.00 0.00 0.00 2.75
2296 6591 5.698104 TGGATTTTCAGGTCATGCATAGAT 58.302 37.500 0.00 0.00 0.00 1.98
2297 6592 5.114764 TGGATTTTCAGGTCATGCATAGA 57.885 39.130 0.00 0.00 0.00 1.98
2298 6593 4.261489 GCTGGATTTTCAGGTCATGCATAG 60.261 45.833 0.00 0.00 35.43 2.23
2299 6594 3.633525 GCTGGATTTTCAGGTCATGCATA 59.366 43.478 0.00 0.00 35.43 3.14
2300 6595 2.429610 GCTGGATTTTCAGGTCATGCAT 59.570 45.455 0.00 0.00 35.43 3.96
2304 6599 2.097825 GCTGCTGGATTTTCAGGTCAT 58.902 47.619 0.00 0.00 35.43 3.06
2305 6600 1.538047 GCTGCTGGATTTTCAGGTCA 58.462 50.000 0.00 0.00 35.43 4.02
2306 6601 0.813821 GGCTGCTGGATTTTCAGGTC 59.186 55.000 0.00 0.00 35.43 3.85
2308 6603 1.660560 CCGGCTGCTGGATTTTCAGG 61.661 60.000 23.22 0.00 35.43 3.86
2314 9124 2.590092 GGTACCGGCTGCTGGATT 59.410 61.111 33.15 14.93 33.36 3.01
2327 9137 0.940126 CGCATGAATGAGCAGGGTAC 59.060 55.000 0.00 0.00 0.00 3.34
2328 9138 3.384816 CGCATGAATGAGCAGGGTA 57.615 52.632 0.00 0.00 0.00 3.69
2329 9139 4.230603 CGCATGAATGAGCAGGGT 57.769 55.556 0.00 0.00 0.00 4.34
2335 9145 0.041576 CGGACATGCGCATGAATGAG 60.042 55.000 46.90 29.99 41.20 2.90
2336 9146 1.438562 CCGGACATGCGCATGAATGA 61.439 55.000 46.90 10.98 41.20 2.57
2337 9147 1.009335 CCGGACATGCGCATGAATG 60.009 57.895 46.90 33.95 41.20 2.67
2338 9148 2.837883 GCCGGACATGCGCATGAAT 61.838 57.895 46.90 31.30 41.20 2.57
2339 9149 3.507924 GCCGGACATGCGCATGAA 61.508 61.111 46.90 13.12 41.20 2.57
2340 9150 4.471908 AGCCGGACATGCGCATGA 62.472 61.111 46.90 13.55 41.20 3.07
2341 9151 4.246206 CAGCCGGACATGCGCATG 62.246 66.667 41.02 41.02 44.15 4.06
2345 9155 0.813610 TAAATCCAGCCGGACATGCG 60.814 55.000 5.05 0.00 46.79 4.73
2346 9156 1.267806 CATAAATCCAGCCGGACATGC 59.732 52.381 5.05 0.00 46.79 4.06
2347 9157 2.291465 CACATAAATCCAGCCGGACATG 59.709 50.000 5.05 0.00 46.79 3.21
2348 9158 2.092429 ACACATAAATCCAGCCGGACAT 60.092 45.455 5.05 0.00 46.79 3.06
2349 9159 1.280710 ACACATAAATCCAGCCGGACA 59.719 47.619 5.05 0.00 46.79 4.02
2353 9163 1.327460 CACGACACATAAATCCAGCCG 59.673 52.381 0.00 0.00 0.00 5.52
2354 9164 2.095853 CACACGACACATAAATCCAGCC 59.904 50.000 0.00 0.00 0.00 4.85
2356 9166 3.993736 TCACACACGACACATAAATCCAG 59.006 43.478 0.00 0.00 0.00 3.86
2357 9167 3.996480 TCACACACGACACATAAATCCA 58.004 40.909 0.00 0.00 0.00 3.41
2358 9168 5.545658 ATTCACACACGACACATAAATCC 57.454 39.130 0.00 0.00 0.00 3.01
2359 9169 6.370593 ACAATTCACACACGACACATAAATC 58.629 36.000 0.00 0.00 0.00 2.17
2360 9170 6.204688 AGACAATTCACACACGACACATAAAT 59.795 34.615 0.00 0.00 0.00 1.40
2362 9172 5.050431 CAGACAATTCACACACGACACATAA 60.050 40.000 0.00 0.00 0.00 1.90
2363 9173 4.447389 CAGACAATTCACACACGACACATA 59.553 41.667 0.00 0.00 0.00 2.29
2364 9174 3.248363 CAGACAATTCACACACGACACAT 59.752 43.478 0.00 0.00 0.00 3.21
2365 9175 2.607180 CAGACAATTCACACACGACACA 59.393 45.455 0.00 0.00 0.00 3.72
2366 9176 2.863740 TCAGACAATTCACACACGACAC 59.136 45.455 0.00 0.00 0.00 3.67
2367 9177 3.172229 TCAGACAATTCACACACGACA 57.828 42.857 0.00 0.00 0.00 4.35
2368 9178 4.732285 ATTCAGACAATTCACACACGAC 57.268 40.909 0.00 0.00 0.00 4.34
2369 9179 5.050159 CAGAATTCAGACAATTCACACACGA 60.050 40.000 8.44 0.00 38.70 4.35
2370 9180 5.142265 CAGAATTCAGACAATTCACACACG 58.858 41.667 8.44 0.00 38.70 4.49
2371 9181 6.064846 ACAGAATTCAGACAATTCACACAC 57.935 37.500 8.44 0.00 38.70 3.82
2374 9184 5.056480 ACGACAGAATTCAGACAATTCACA 58.944 37.500 8.44 0.00 38.70 3.58
2375 9185 5.389935 GGACGACAGAATTCAGACAATTCAC 60.390 44.000 8.44 1.35 38.70 3.18
2376 9186 4.690748 GGACGACAGAATTCAGACAATTCA 59.309 41.667 8.44 0.00 38.70 2.57
2378 9188 3.679980 CGGACGACAGAATTCAGACAATT 59.320 43.478 8.44 0.00 0.00 2.32
2379 9189 3.254060 CGGACGACAGAATTCAGACAAT 58.746 45.455 8.44 0.00 0.00 2.71
2380 9190 2.035449 ACGGACGACAGAATTCAGACAA 59.965 45.455 8.44 0.00 0.00 3.18
2381 9191 1.611977 ACGGACGACAGAATTCAGACA 59.388 47.619 8.44 0.00 0.00 3.41
2382 9192 2.349297 ACGGACGACAGAATTCAGAC 57.651 50.000 8.44 0.00 0.00 3.51
2384 9194 3.975670 GCTATACGGACGACAGAATTCAG 59.024 47.826 8.44 1.65 0.00 3.02
2385 9195 3.379057 TGCTATACGGACGACAGAATTCA 59.621 43.478 8.44 0.00 0.00 2.57
2386 9196 3.729716 GTGCTATACGGACGACAGAATTC 59.270 47.826 0.00 0.00 0.00 2.17
2387 9197 3.380637 AGTGCTATACGGACGACAGAATT 59.619 43.478 0.00 0.00 39.22 2.17
2388 9198 2.950309 AGTGCTATACGGACGACAGAAT 59.050 45.455 0.00 0.00 39.22 2.40
2389 9199 2.096980 CAGTGCTATACGGACGACAGAA 59.903 50.000 0.00 0.00 39.22 3.02
2390 9200 1.669265 CAGTGCTATACGGACGACAGA 59.331 52.381 0.00 0.00 39.22 3.41
2392 9202 0.099968 GCAGTGCTATACGGACGACA 59.900 55.000 8.18 0.00 39.22 4.35
2394 9204 1.957668 TAGCAGTGCTATACGGACGA 58.042 50.000 21.00 0.00 40.44 4.20


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

AutoCloner maintained by Alex Coulton.