Multiple sequence alignment - TraesCS5D01G485500

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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 TraesCS5D01G485500 chr5D 100.000 4116 0 0 1 4116 520908715 520912830 0.000000e+00 7601.0
1 TraesCS5D01G485500 chr5B 89.976 3292 182 60 1 3202 656924467 656927700 0.000000e+00 4115.0
2 TraesCS5D01G485500 chr5B 86.025 644 56 15 3192 3805 656927719 656928358 0.000000e+00 660.0
3 TraesCS5D01G485500 chr5B 75.225 666 95 45 1310 1961 512212697 512213306 6.830000e-63 252.0
4 TraesCS5D01G485500 chr5B 85.561 187 10 7 3944 4116 656928654 656928837 3.270000e-41 180.0
5 TraesCS5D01G485500 chr5A 89.217 2068 147 36 1 2008 649440146 649442197 0.000000e+00 2514.0
6 TraesCS5D01G485500 chr5A 89.326 965 58 18 2094 3039 649449965 649450903 0.000000e+00 1170.0
7 TraesCS5D01G485500 chr5A 88.962 453 24 14 2934 3371 649450908 649451349 1.680000e-148 536.0
8 TraesCS5D01G485500 chr5A 89.308 318 19 5 3552 3857 649452443 649452757 6.450000e-103 385.0
9 TraesCS5D01G485500 chr5A 75.980 612 81 44 1362 1961 537626216 537626773 5.280000e-64 255.0
10 TraesCS5D01G485500 chr5A 90.476 63 4 2 2037 2098 649442204 649442265 9.480000e-12 82.4
11 TraesCS5D01G485500 chr4A 78.630 730 111 35 1282 1975 68126066 68125346 3.780000e-120 442.0
12 TraesCS5D01G485500 chr4A 76.364 660 117 25 1311 1961 68141484 68142113 6.640000e-83 318.0
13 TraesCS5D01G485500 chr2D 77.569 691 108 30 1302 1970 131777735 131777070 1.400000e-99 374.0
14 TraesCS5D01G485500 chr2A 77.047 684 110 32 1309 1970 138827284 138826626 2.350000e-92 350.0
15 TraesCS5D01G485500 chr2B 76.879 692 111 32 1302 1970 186311897 186312562 3.050000e-91 346.0
16 TraesCS5D01G485500 chr2B 86.522 230 25 5 1742 1970 185776765 185776541 8.840000e-62 248.0
17 TraesCS5D01G485500 chr4D 76.061 660 119 25 1311 1961 386831198 386831827 1.440000e-79 307.0
18 TraesCS5D01G485500 chr4D 72.781 338 55 29 1578 1904 121971124 121971435 3.410000e-11 80.5
19 TraesCS5D01G485500 chr4B 72.870 575 117 32 1406 1960 494692232 494691677 1.180000e-35 161.0
20 TraesCS5D01G485500 chr7A 72.944 462 90 26 1510 1961 631365348 631365784 1.200000e-25 128.0
21 TraesCS5D01G485500 chr7A 78.049 164 19 7 3328 3485 724171000 724171152 2.040000e-13 87.9
22 TraesCS5D01G485500 chr7B 72.511 462 92 30 1510 1961 590500845 590500409 2.600000e-22 117.0
23 TraesCS5D01G485500 chr7B 82.474 97 17 0 593 689 222312153 222312057 7.330000e-13 86.1
24 TraesCS5D01G485500 chr7D 72.234 461 95 26 1510 1961 547457920 547457484 1.210000e-20 111.0
25 TraesCS5D01G485500 chr6A 85.981 107 12 3 3186 3291 613608326 613608222 1.210000e-20 111.0
26 TraesCS5D01G485500 chr3D 82.883 111 15 4 3430 3537 594004249 594004140 3.390000e-16 97.1
27 TraesCS5D01G485500 chr1D 76.503 183 29 11 3298 3475 472184940 472184767 2.040000e-13 87.9
28 TraesCS5D01G485500 chr1A 80.000 110 19 2 3363 3472 497272796 497272690 1.230000e-10 78.7


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 TraesCS5D01G485500 chr5D 520908715 520912830 4115 False 7601.000000 7601 100.000000 1 4116 1 chr5D.!!$F1 4115
1 TraesCS5D01G485500 chr5B 656924467 656928837 4370 False 1651.666667 4115 87.187333 1 4116 3 chr5B.!!$F2 4115
2 TraesCS5D01G485500 chr5B 512212697 512213306 609 False 252.000000 252 75.225000 1310 1961 1 chr5B.!!$F1 651
3 TraesCS5D01G485500 chr5A 649440146 649442265 2119 False 1298.200000 2514 89.846500 1 2098 2 chr5A.!!$F2 2097
4 TraesCS5D01G485500 chr5A 649449965 649452757 2792 False 697.000000 1170 89.198667 2094 3857 3 chr5A.!!$F3 1763
5 TraesCS5D01G485500 chr5A 537626216 537626773 557 False 255.000000 255 75.980000 1362 1961 1 chr5A.!!$F1 599
6 TraesCS5D01G485500 chr4A 68125346 68126066 720 True 442.000000 442 78.630000 1282 1975 1 chr4A.!!$R1 693
7 TraesCS5D01G485500 chr4A 68141484 68142113 629 False 318.000000 318 76.364000 1311 1961 1 chr4A.!!$F1 650
8 TraesCS5D01G485500 chr2D 131777070 131777735 665 True 374.000000 374 77.569000 1302 1970 1 chr2D.!!$R1 668
9 TraesCS5D01G485500 chr2A 138826626 138827284 658 True 350.000000 350 77.047000 1309 1970 1 chr2A.!!$R1 661
10 TraesCS5D01G485500 chr2B 186311897 186312562 665 False 346.000000 346 76.879000 1302 1970 1 chr2B.!!$F1 668
11 TraesCS5D01G485500 chr4D 386831198 386831827 629 False 307.000000 307 76.061000 1311 1961 1 chr4D.!!$F2 650

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
326 329 0.028770 CCGAACGCAACAAAGAGCAA 59.971 50.0 0.0 0.0 0.0 3.91 F
424 428 0.326264 ATGTGAAGGGGTGTCTCTGC 59.674 55.0 0.0 0.0 0.0 4.26 F
2024 2204 0.179171 AGACATCTACCGTTCGTGCG 60.179 55.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2204 0.306533 TTTGACAAAACTCTCGGCGC 59.693 50.0 0.0 0.0 0.0 6.53 R
2331 2516 0.827925 AACGGAGAGGAGAGTGTGCA 60.828 55.0 0.0 0.0 0.0 4.57 R
3423 3767 0.271927 AGCCATCCCTCTAATCCCCA 59.728 55.0 0.0 0.0 0.0 4.96 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
54 56 2.822006 GCGGGGTAGAGGAGAATATGGA 60.822 54.545 0.00 0.00 0.00 3.41
84 86 2.750637 GCTCTCCGTCAGTCCCGA 60.751 66.667 0.00 0.00 0.00 5.14
145 148 0.171903 ATCCATTGCGCTGCTCAAAC 59.828 50.000 9.73 0.00 0.00 2.93
147 150 1.207339 CATTGCGCTGCTCAAACGA 59.793 52.632 9.73 0.00 0.00 3.85
153 156 1.736645 GCTGCTCAAACGACGCCTA 60.737 57.895 0.00 0.00 0.00 3.93
160 163 1.134367 TCAAACGACGCCTAGATCCAG 59.866 52.381 0.00 0.00 0.00 3.86
164 167 1.448119 CGACGCCTAGATCCAGCAGA 61.448 60.000 0.00 0.00 0.00 4.26
165 168 0.747255 GACGCCTAGATCCAGCAGAA 59.253 55.000 0.00 0.00 0.00 3.02
223 226 4.028490 GGCGACCACCCCATGACA 62.028 66.667 0.00 0.00 0.00 3.58
313 316 5.712217 TCAATAAATAAGAGTGCCGAACG 57.288 39.130 0.00 0.00 0.00 3.95
326 329 0.028770 CCGAACGCAACAAAGAGCAA 59.971 50.000 0.00 0.00 0.00 3.91
328 331 1.512771 CGAACGCAACAAAGAGCAAAC 59.487 47.619 0.00 0.00 0.00 2.93
330 333 2.869233 ACGCAACAAAGAGCAAACAT 57.131 40.000 0.00 0.00 0.00 2.71
337 340 6.089820 CGCAACAAAGAGCAAACATAATTGAT 59.910 34.615 0.00 0.00 31.84 2.57
387 390 9.383519 CTATAAATGATGTACAGAAGGTGTGTT 57.616 33.333 0.33 0.00 40.69 3.32
395 398 6.350103 TGTACAGAAGGTGTGTTTAACATCA 58.650 36.000 0.00 0.00 42.92 3.07
398 401 6.061441 ACAGAAGGTGTGTTTAACATCATGA 58.939 36.000 0.00 0.00 42.92 3.07
424 428 0.326264 ATGTGAAGGGGTGTCTCTGC 59.674 55.000 0.00 0.00 0.00 4.26
434 438 3.148279 GTCTCTGCCGGATCCCGT 61.148 66.667 5.05 0.00 46.80 5.28
448 452 1.223487 CCCGTGGGATTTGATCGGT 59.777 57.895 0.00 0.00 39.62 4.69
460 464 2.455674 TGATCGGTGTTGGTCTTCAG 57.544 50.000 0.00 0.00 0.00 3.02
461 465 1.079503 GATCGGTGTTGGTCTTCAGC 58.920 55.000 0.00 0.00 0.00 4.26
499 503 4.333615 CAGTTACCGTTCGTTTTTCGTTT 58.666 39.130 0.00 0.00 40.80 3.60
503 507 0.841356 CGTTCGTTTTTCGTTTGGGC 59.159 50.000 0.00 0.00 40.80 5.36
510 514 2.196295 TTTTCGTTTGGGCGTTTCTG 57.804 45.000 0.00 0.00 0.00 3.02
511 515 1.380524 TTTCGTTTGGGCGTTTCTGA 58.619 45.000 0.00 0.00 0.00 3.27
516 520 1.673920 GTTTGGGCGTTTCTGAGTTGA 59.326 47.619 0.00 0.00 0.00 3.18
517 521 2.270352 TTGGGCGTTTCTGAGTTGAT 57.730 45.000 0.00 0.00 0.00 2.57
561 567 7.096065 CGTCTTCATCAGCGATGATTATTGTTA 60.096 37.037 14.62 0.00 46.52 2.41
577 583 1.338674 TGTTATGTTCCGCTGGTCCTG 60.339 52.381 0.00 0.00 0.00 3.86
625 652 1.546476 CAGCTCGGGTAAGTGAAGAGT 59.454 52.381 0.00 0.00 0.00 3.24
633 660 4.142160 CGGGTAAGTGAAGAGTGATGATGA 60.142 45.833 0.00 0.00 0.00 2.92
634 661 5.112686 GGGTAAGTGAAGAGTGATGATGAC 58.887 45.833 0.00 0.00 0.00 3.06
637 664 1.929836 GTGAAGAGTGATGATGACGGC 59.070 52.381 0.00 0.00 0.00 5.68
685 712 2.938869 AGTCGTCGCTAAGTGGTTTAC 58.061 47.619 0.00 0.00 0.00 2.01
690 717 3.924686 CGTCGCTAAGTGGTTTACAGATT 59.075 43.478 0.00 0.00 0.00 2.40
720 747 7.439381 TGTAGTTTTAGTTACTTCCAGTCAGG 58.561 38.462 0.00 0.00 39.47 3.86
792 844 2.683968 ACGACAGATGTACATTGCGTT 58.316 42.857 10.30 6.85 0.00 4.84
899 960 1.023502 TTACACGTCATATCCGCCGA 58.976 50.000 0.00 0.00 0.00 5.54
1043 1109 3.549221 CGCAAATAAAACCCACGTGTCTT 60.549 43.478 15.65 1.73 0.00 3.01
1142 1208 1.805428 GCTCTCATCTCCCTCCTCGC 61.805 65.000 0.00 0.00 0.00 5.03
1233 1305 6.737254 TCAAATCTTCCGGTCAATTTACTC 57.263 37.500 0.00 0.00 0.00 2.59
1245 1320 6.617879 GGTCAATTTACTCGGTTTGCTAATT 58.382 36.000 0.00 0.00 0.00 1.40
1253 1328 2.224549 TCGGTTTGCTAATTGTTGGTCG 59.775 45.455 0.00 0.00 0.00 4.79
2020 2200 0.591741 GCCGAGACATCTACCGTTCG 60.592 60.000 0.00 0.00 0.00 3.95
2023 2203 1.546834 GAGACATCTACCGTTCGTGC 58.453 55.000 0.00 0.00 0.00 5.34
2024 2204 0.179171 AGACATCTACCGTTCGTGCG 60.179 55.000 0.00 0.00 0.00 5.34
2026 2206 2.578713 ATCTACCGTTCGTGCGCG 60.579 61.111 14.79 14.79 39.92 6.86
2081 2261 0.612732 TCCATGGCTCCCAAAAGCAG 60.613 55.000 6.96 0.00 44.35 4.24
2085 2265 1.181098 TGGCTCCCAAAAGCAGAAGC 61.181 55.000 0.00 0.00 44.35 3.86
2090 2270 3.387397 CTCCCAAAAGCAGAAGCAAAAG 58.613 45.455 0.00 0.00 45.49 2.27
2192 2372 2.280524 CGGCCAACAACGACCTCA 60.281 61.111 2.24 0.00 0.00 3.86
2210 2390 3.274586 CCGCGTCCGTCCGAGATA 61.275 66.667 4.92 0.00 0.00 1.98
2212 2392 2.532256 CGCGTCCGTCCGAGATAGT 61.532 63.158 0.00 0.00 0.00 2.12
2350 2535 0.827925 TGCACACTCTCCTCTCCGTT 60.828 55.000 0.00 0.00 0.00 4.44
2402 2588 2.086426 ACTGACGTGTACGCATGCG 61.086 57.895 36.79 36.79 44.43 4.73
2416 2602 3.575630 CGCATGCGTACTCCATATTAGT 58.424 45.455 31.33 0.00 34.35 2.24
2417 2603 4.729595 CGCATGCGTACTCCATATTAGTA 58.270 43.478 31.33 0.00 34.35 1.82
2418 2604 5.340803 CGCATGCGTACTCCATATTAGTAT 58.659 41.667 31.33 0.00 32.34 2.12
2419 2605 6.492254 CGCATGCGTACTCCATATTAGTATA 58.508 40.000 31.33 0.00 32.34 1.47
2420 2606 7.139392 CGCATGCGTACTCCATATTAGTATAT 58.861 38.462 31.33 0.00 32.34 0.86
2421 2607 8.287503 CGCATGCGTACTCCATATTAGTATATA 58.712 37.037 31.33 0.00 32.34 0.86
2422 2608 9.395707 GCATGCGTACTCCATATTAGTATATAC 57.604 37.037 0.00 4.60 32.34 1.47
2450 2636 3.416277 CATTAACATTTCGTGCTGACGG 58.584 45.455 0.00 0.00 46.11 4.79
3127 3428 6.944557 TGTGTACGAATCTTGAAGTGTATG 57.055 37.500 0.00 0.00 0.00 2.39
3197 3527 3.482110 CGTCTTTTTCTTCGGTTTTGCTG 59.518 43.478 0.00 0.00 0.00 4.41
3249 3580 4.127907 GTCGGTCACTTTTTCCTTCTTCT 58.872 43.478 0.00 0.00 0.00 2.85
3250 3581 4.211584 GTCGGTCACTTTTTCCTTCTTCTC 59.788 45.833 0.00 0.00 0.00 2.87
3269 3612 1.139734 GGCGCACGAGATGAAGAGA 59.860 57.895 10.83 0.00 0.00 3.10
3280 3623 0.034380 ATGAAGAGACCGGACCTCGA 60.034 55.000 9.46 4.66 42.43 4.04
3282 3625 1.979831 GAAGAGACCGGACCTCGACG 61.980 65.000 9.46 0.00 42.43 5.12
3318 3661 6.619852 AGCCCCACTATCTATCTTAAGGAAAA 59.380 38.462 1.85 0.00 0.00 2.29
3350 3694 5.483231 TCCATCATCTATCTTAGGGAAGCAG 59.517 44.000 0.00 0.00 32.21 4.24
3353 3697 4.655649 TCATCTATCTTAGGGAAGCAGCAA 59.344 41.667 0.00 0.00 32.21 3.91
3373 3717 6.013379 CAGCAACCCCATTATCTATCTTAGGA 60.013 42.308 0.00 0.00 0.00 2.94
3378 3722 5.426833 CCCCATTATCTATCTTAGGAGTGGG 59.573 48.000 0.00 0.00 38.08 4.61
3383 3727 3.414057 TCTATCTTAGGAGTGGGGGAGA 58.586 50.000 0.00 0.00 0.00 3.71
3400 3744 2.769621 AGGGGATGCAGCGGATCA 60.770 61.111 10.91 0.00 0.00 2.92
3401 3745 2.121992 GAGGGGATGCAGCGGATCAT 62.122 60.000 10.91 0.00 0.00 2.45
3402 3746 0.837691 AGGGGATGCAGCGGATCATA 60.838 55.000 10.91 0.00 0.00 2.15
3416 3760 4.513442 CGGATCATAGGAGGTTTTCAACA 58.487 43.478 0.00 0.00 0.00 3.33
3420 3764 5.560722 TCATAGGAGGTTTTCAACAGTGA 57.439 39.130 0.00 0.00 0.00 3.41
3423 3767 7.861629 TCATAGGAGGTTTTCAACAGTGATAT 58.138 34.615 0.00 0.00 32.48 1.63
3442 3786 0.271927 TGGGGATTAGAGGGATGGCT 59.728 55.000 0.00 0.00 0.00 4.75
3484 4314 2.692741 GGGGGAGGTTGAGGGGAG 60.693 72.222 0.00 0.00 0.00 4.30
3485 4315 2.454941 GGGGAGGTTGAGGGGAGA 59.545 66.667 0.00 0.00 0.00 3.71
3486 4316 1.690985 GGGGAGGTTGAGGGGAGAG 60.691 68.421 0.00 0.00 0.00 3.20
3499 4329 4.154347 GAGAGCGGGGCAGTGAGG 62.154 72.222 0.00 0.00 0.00 3.86
3568 4826 3.390521 TCGGCGGTTGCAGAGGAT 61.391 61.111 7.21 0.00 45.35 3.24
3576 4834 2.679059 CGGTTGCAGAGGATGATGAACT 60.679 50.000 0.00 0.00 0.00 3.01
3813 5223 7.389053 GGTTCTCCATATAACAATAGAGGCTTG 59.611 40.741 0.00 0.00 0.00 4.01
3820 5230 9.376075 CATATAACAATAGAGGCTTGAGTATGG 57.624 37.037 0.00 0.00 0.00 2.74
3863 5273 6.390987 CTGTTTTCAGTAGTTGATCCGTAC 57.609 41.667 0.00 0.00 42.48 3.67
3865 5275 7.218228 TGTTTTCAGTAGTTGATCCGTACTA 57.782 36.000 0.00 0.00 35.27 1.82
3866 5276 7.310664 TGTTTTCAGTAGTTGATCCGTACTAG 58.689 38.462 0.00 0.00 35.27 2.57
3867 5277 7.175467 TGTTTTCAGTAGTTGATCCGTACTAGA 59.825 37.037 0.00 0.00 35.27 2.43
3868 5278 6.922247 TTCAGTAGTTGATCCGTACTAGAG 57.078 41.667 0.00 0.00 35.27 2.43
3869 5279 5.987098 TCAGTAGTTGATCCGTACTAGAGT 58.013 41.667 0.00 0.00 0.00 3.24
3870 5280 7.117285 TCAGTAGTTGATCCGTACTAGAGTA 57.883 40.000 0.00 0.00 0.00 2.59
3871 5281 7.559486 TCAGTAGTTGATCCGTACTAGAGTAA 58.441 38.462 0.00 0.00 31.52 2.24
3872 5282 7.710044 TCAGTAGTTGATCCGTACTAGAGTAAG 59.290 40.741 0.00 0.00 31.52 2.34
3873 5283 6.991531 AGTAGTTGATCCGTACTAGAGTAAGG 59.008 42.308 13.66 13.66 46.84 2.69
3886 5296 7.540474 ACTAGAGTAAGGAGTGTTTCAATGA 57.460 36.000 0.00 0.00 0.00 2.57
3912 5322 2.434185 GTTGACAGCGATCGGGCA 60.434 61.111 18.30 6.52 34.64 5.36
3913 5323 2.125552 TTGACAGCGATCGGGCAG 60.126 61.111 18.30 0.00 34.64 4.85
3914 5324 2.645192 TTGACAGCGATCGGGCAGA 61.645 57.895 18.30 0.00 34.64 4.26
3916 5326 1.227380 GACAGCGATCGGGCAGATT 60.227 57.895 18.30 0.00 40.26 2.40
3919 5329 0.811219 CAGCGATCGGGCAGATTTCA 60.811 55.000 18.30 0.00 40.26 2.69
3920 5330 0.107703 AGCGATCGGGCAGATTTCAA 60.108 50.000 18.30 0.00 40.26 2.69
3921 5331 0.028110 GCGATCGGGCAGATTTCAAC 59.972 55.000 18.30 0.00 40.26 3.18
3923 5333 1.651987 GATCGGGCAGATTTCAACGA 58.348 50.000 0.68 0.00 40.26 3.85
3924 5334 1.327764 GATCGGGCAGATTTCAACGAC 59.672 52.381 0.68 0.00 40.26 4.34
3925 5335 0.034198 TCGGGCAGATTTCAACGACA 59.966 50.000 0.00 0.00 0.00 4.35
3926 5336 0.443869 CGGGCAGATTTCAACGACAG 59.556 55.000 0.00 0.00 0.00 3.51
3927 5337 1.808411 GGGCAGATTTCAACGACAGA 58.192 50.000 0.00 0.00 0.00 3.41
3928 5338 1.464997 GGGCAGATTTCAACGACAGAC 59.535 52.381 0.00 0.00 0.00 3.51
3985 5422 7.104290 TGTTCACGTATGTCACCCAAATTATA 58.896 34.615 0.00 0.00 0.00 0.98
3991 5428 8.092687 ACGTATGTCACCCAAATTATATCTACC 58.907 37.037 0.00 0.00 0.00 3.18
3993 5430 5.860611 TGTCACCCAAATTATATCTACCGG 58.139 41.667 0.00 0.00 0.00 5.28
3994 5431 5.603395 TGTCACCCAAATTATATCTACCGGA 59.397 40.000 9.46 0.00 0.00 5.14
4012 5460 1.418264 GGAGGCAGATAAAGGAGGTCC 59.582 57.143 0.00 0.00 0.00 4.46
4034 5482 2.622064 ACGAGGAAAACACTTGCTCT 57.378 45.000 4.78 0.00 35.15 4.09
4036 5484 1.457303 CGAGGAAAACACTTGCTCTCG 59.543 52.381 4.78 0.00 35.15 4.04
4037 5485 1.195674 GAGGAAAACACTTGCTCTCGC 59.804 52.381 0.00 0.00 34.58 5.03
4038 5486 1.202698 AGGAAAACACTTGCTCTCGCT 60.203 47.619 0.00 0.00 36.97 4.93
4040 5488 0.947244 AAAACACTTGCTCTCGCTGG 59.053 50.000 0.00 0.00 36.97 4.85
4041 5489 0.886490 AAACACTTGCTCTCGCTGGG 60.886 55.000 0.00 0.00 36.97 4.45
4042 5490 3.123620 CACTTGCTCTCGCTGGGC 61.124 66.667 0.00 0.00 36.97 5.36
4043 5491 3.630013 ACTTGCTCTCGCTGGGCA 61.630 61.111 0.00 0.00 36.97 5.36
4044 5492 3.123620 CTTGCTCTCGCTGGGCAC 61.124 66.667 2.33 0.00 35.62 5.01
4045 5493 3.602513 CTTGCTCTCGCTGGGCACT 62.603 63.158 2.33 0.00 35.62 4.40
4046 5494 2.230994 CTTGCTCTCGCTGGGCACTA 62.231 60.000 2.33 0.00 35.62 2.74
4047 5495 2.202810 GCTCTCGCTGGGCACTAC 60.203 66.667 0.00 0.00 0.00 2.73
4048 5496 2.716017 GCTCTCGCTGGGCACTACT 61.716 63.158 0.00 0.00 0.00 2.57
4049 5497 1.140589 CTCTCGCTGGGCACTACTG 59.859 63.158 0.00 0.00 0.00 2.74
4051 5499 1.153745 CTCGCTGGGCACTACTGTC 60.154 63.158 0.00 0.00 0.00 3.51
4053 5501 1.446792 CGCTGGGCACTACTGTCAG 60.447 63.158 0.00 0.00 0.00 3.51
4066 5514 0.319040 CTGTCAGTGTCAGGTGACCG 60.319 60.000 9.26 3.51 44.15 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.666122 GGATGAGGCCCAGTCCAT 58.334 61.111 11.86 3.05 0.00 3.41
54 56 3.208884 GAGAGCCGTGTGTGGACGT 62.209 63.158 0.00 0.00 37.66 4.34
77 79 2.752238 CGCACTCCTCTCGGGACT 60.752 66.667 0.00 0.00 39.58 3.85
78 80 4.500116 GCGCACTCCTCTCGGGAC 62.500 72.222 0.30 0.00 39.58 4.46
108 110 5.215252 TGGATTCCTACTGGATCGATTTC 57.785 43.478 0.00 0.00 42.81 2.17
121 123 0.181114 AGCAGCGCAATGGATTCCTA 59.819 50.000 11.47 0.00 0.00 2.94
134 136 4.430423 GGCGTCGTTTGAGCAGCG 62.430 66.667 0.00 0.00 0.00 5.18
145 148 1.007964 CTGCTGGATCTAGGCGTCG 60.008 63.158 8.31 0.00 0.00 5.12
147 150 1.418334 ATTCTGCTGGATCTAGGCGT 58.582 50.000 8.31 0.00 0.00 5.68
153 156 1.684248 GCCACCAATTCTGCTGGATCT 60.684 52.381 0.00 0.00 37.40 2.75
160 163 1.065126 ACCTAGAGCCACCAATTCTGC 60.065 52.381 0.00 0.00 0.00 4.26
164 167 0.392998 CGCACCTAGAGCCACCAATT 60.393 55.000 0.00 0.00 0.00 2.32
165 168 1.221840 CGCACCTAGAGCCACCAAT 59.778 57.895 0.00 0.00 0.00 3.16
208 211 2.436646 GCTGTCATGGGGTGGTCG 60.437 66.667 0.00 0.00 0.00 4.79
223 226 0.960364 CACCATACCAAGGTTGCGCT 60.960 55.000 9.73 0.00 37.23 5.92
285 288 8.050778 TCGGCACTCTTATTTATTGAAAATGT 57.949 30.769 0.00 0.00 0.00 2.71
307 310 0.028770 TTGCTCTTTGTTGCGTTCGG 59.971 50.000 0.00 0.00 0.00 4.30
313 316 6.768029 TCAATTATGTTTGCTCTTTGTTGC 57.232 33.333 0.00 0.00 0.00 4.17
363 366 8.635765 AAACACACCTTCTGTACATCATTTAT 57.364 30.769 0.00 0.00 0.00 1.40
375 378 6.427853 TCTCATGATGTTAAACACACCTTCTG 59.572 38.462 0.00 0.00 38.61 3.02
387 390 4.080413 TCACATGCCCTCTCATGATGTTAA 60.080 41.667 10.31 0.00 44.94 2.01
395 398 0.549950 CCCTTCACATGCCCTCTCAT 59.450 55.000 0.00 0.00 0.00 2.90
398 401 1.542375 ACCCCTTCACATGCCCTCT 60.542 57.895 0.00 0.00 0.00 3.69
434 438 1.074727 ACCAACACCGATCAAATCCCA 59.925 47.619 0.00 0.00 0.00 4.37
443 447 0.670546 CGCTGAAGACCAACACCGAT 60.671 55.000 0.00 0.00 0.00 4.18
448 452 0.976641 AGATCCGCTGAAGACCAACA 59.023 50.000 0.00 0.00 0.00 3.33
499 503 2.151202 GAATCAACTCAGAAACGCCCA 58.849 47.619 0.00 0.00 0.00 5.36
503 507 6.060028 TCAAAAGGAATCAACTCAGAAACG 57.940 37.500 0.00 0.00 0.00 3.60
510 514 8.226448 CGCATATAGATCAAAAGGAATCAACTC 58.774 37.037 0.00 0.00 0.00 3.01
511 515 7.716998 ACGCATATAGATCAAAAGGAATCAACT 59.283 33.333 0.00 0.00 0.00 3.16
516 520 7.933577 TGAAGACGCATATAGATCAAAAGGAAT 59.066 33.333 0.00 0.00 0.00 3.01
517 521 7.272244 TGAAGACGCATATAGATCAAAAGGAA 58.728 34.615 0.00 0.00 0.00 3.36
561 567 1.003355 CACAGGACCAGCGGAACAT 60.003 57.895 0.00 0.00 0.00 2.71
577 583 7.417612 CAAACCATGTTATACTAAGGCATCAC 58.582 38.462 0.00 0.00 0.00 3.06
610 637 3.868757 TCATCACTCTTCACTTACCCG 57.131 47.619 0.00 0.00 0.00 5.28
611 638 5.112686 GTCATCATCACTCTTCACTTACCC 58.887 45.833 0.00 0.00 0.00 3.69
625 652 2.511373 GGCACGCCGTCATCATCA 60.511 61.111 0.00 0.00 0.00 3.07
633 660 2.125512 GATCTGAAGGCACGCCGT 60.126 61.111 1.61 0.00 41.95 5.68
634 661 3.257561 CGATCTGAAGGCACGCCG 61.258 66.667 1.61 0.00 41.95 6.46
637 664 1.880340 GGAGCGATCTGAAGGCACG 60.880 63.158 0.00 0.00 0.00 5.34
713 740 7.065120 AGAATTCCTGATCTATTCCTGACTG 57.935 40.000 0.65 0.00 0.00 3.51
717 744 8.743085 TGAAAAGAATTCCTGATCTATTCCTG 57.257 34.615 0.65 0.00 0.00 3.86
746 797 3.814945 CGCAGTCCATTGAGACTTTTTC 58.185 45.455 5.40 0.00 44.83 2.29
783 835 4.743558 CGAATCGCAACGCAATGT 57.256 50.000 0.00 0.00 0.00 2.71
963 1024 5.010719 CAGGCGTTGAGGGTATTTATAGAGA 59.989 44.000 0.00 0.00 0.00 3.10
1043 1109 0.542805 GTGGCCGGTATGGTTAGGAA 59.457 55.000 1.90 0.00 41.21 3.36
1142 1208 2.183811 CTGAGACGAGCAGCAGGG 59.816 66.667 0.00 0.00 0.00 4.45
1233 1305 2.580589 CGACCAACAATTAGCAAACCG 58.419 47.619 0.00 0.00 0.00 4.44
1245 1320 2.416747 CTGAAGAATCAGCGACCAACA 58.583 47.619 0.00 0.00 46.11 3.33
2008 2188 2.845739 CGCGCACGAACGGTAGATG 61.846 63.158 8.75 0.00 43.93 2.90
2020 2200 3.712881 AAAACTCTCGGCGCGCAC 61.713 61.111 34.42 20.89 0.00 5.34
2023 2203 1.827315 TTGACAAAACTCTCGGCGCG 61.827 55.000 0.00 0.00 0.00 6.86
2024 2204 0.306533 TTTGACAAAACTCTCGGCGC 59.693 50.000 0.00 0.00 0.00 6.53
2026 2206 1.673920 TGGTTTGACAAAACTCTCGGC 59.326 47.619 16.61 0.00 44.32 5.54
2027 2207 4.364415 TTTGGTTTGACAAAACTCTCGG 57.636 40.909 16.61 0.00 44.32 4.63
2028 2208 5.511729 GTCTTTTGGTTTGACAAAACTCTCG 59.488 40.000 16.61 4.05 43.26 4.04
2029 2209 6.386654 TGTCTTTTGGTTTGACAAAACTCTC 58.613 36.000 16.61 0.00 43.26 3.20
2030 2210 6.339587 TGTCTTTTGGTTTGACAAAACTCT 57.660 33.333 16.61 0.00 43.26 3.24
2090 2270 5.465935 CGGCTATCTAGAGGTCAAAAGATC 58.534 45.833 0.00 0.00 31.38 2.75
2128 2308 2.591715 AACCGGACAGCAGTGCAC 60.592 61.111 19.20 9.40 35.57 4.57
2209 2389 3.376078 GTGCCACCGACCGGACTA 61.376 66.667 16.07 0.00 38.96 2.59
2331 2516 0.827925 AACGGAGAGGAGAGTGTGCA 60.828 55.000 0.00 0.00 0.00 4.57
2419 2605 9.555727 AGCACGAAATGTTAATGGTATAAGTAT 57.444 29.630 0.00 0.00 0.00 2.12
2420 2606 8.822855 CAGCACGAAATGTTAATGGTATAAGTA 58.177 33.333 0.00 0.00 0.00 2.24
2421 2607 7.551262 TCAGCACGAAATGTTAATGGTATAAGT 59.449 33.333 0.00 0.00 0.00 2.24
2422 2608 7.850982 GTCAGCACGAAATGTTAATGGTATAAG 59.149 37.037 0.00 0.00 0.00 1.73
2423 2609 7.690228 GTCAGCACGAAATGTTAATGGTATAA 58.310 34.615 0.00 0.00 0.00 0.98
2450 2636 4.463209 CACAACACATGATGGAAACGTAC 58.537 43.478 0.00 0.00 0.00 3.67
2459 2645 0.239082 ACGCTGCACAACACATGATG 59.761 50.000 0.00 0.00 0.00 3.07
2462 2648 0.029167 TTCACGCTGCACAACACATG 59.971 50.000 0.00 0.00 0.00 3.21
2649 2837 4.794439 TGGTCGATCACTGCGGCG 62.794 66.667 0.51 0.51 33.49 6.46
2652 2840 0.388520 TTGAGTGGTCGATCACTGCG 60.389 55.000 34.94 0.00 46.76 5.18
3043 3344 9.210329 CCCAAACTAATTTACAAACCCAAATAC 57.790 33.333 0.00 0.00 0.00 1.89
3045 3346 6.712998 GCCCAAACTAATTTACAAACCCAAAT 59.287 34.615 0.00 0.00 0.00 2.32
3127 3428 3.418047 ACATACACCCTAAACTGCAACC 58.582 45.455 0.00 0.00 0.00 3.77
3174 3475 3.128068 AGCAAAACCGAAGAAAAAGACGT 59.872 39.130 0.00 0.00 0.00 4.34
3197 3527 8.655970 ACAAAAAGTTTCATGTAGCTGAAAAAC 58.344 29.630 0.00 0.34 44.38 2.43
3249 3580 2.202610 CTTCATCTCGTGCGCCGA 60.203 61.111 17.76 17.76 45.00 5.54
3250 3581 2.202610 TCTTCATCTCGTGCGCCG 60.203 61.111 4.18 8.64 38.13 6.46
3280 3623 2.434774 GGGCTGGTTTTCTCCCGT 59.565 61.111 0.00 0.00 0.00 5.28
3282 3625 1.606601 GTGGGGCTGGTTTTCTCCC 60.607 63.158 0.00 0.00 38.03 4.30
3318 3661 7.038445 CCCTAAGATAGATGATGGAGATGTTGT 60.038 40.741 0.00 0.00 0.00 3.32
3350 3694 6.013293 ACTCCTAAGATAGATAATGGGGTTGC 60.013 42.308 0.00 0.00 0.00 4.17
3353 3697 6.026186 CCACTCCTAAGATAGATAATGGGGT 58.974 44.000 0.00 0.00 0.00 4.95
3373 3717 2.374342 CATCCCCTCTCCCCCACT 59.626 66.667 0.00 0.00 0.00 4.00
3378 3722 4.247380 CGCTGCATCCCCTCTCCC 62.247 72.222 0.00 0.00 0.00 4.30
3383 3727 0.837691 TATGATCCGCTGCATCCCCT 60.838 55.000 0.00 0.00 0.00 4.79
3416 3760 4.785173 TCCCTCTAATCCCCATATCACT 57.215 45.455 0.00 0.00 0.00 3.41
3420 3764 3.126453 GCCATCCCTCTAATCCCCATAT 58.874 50.000 0.00 0.00 0.00 1.78
3423 3767 0.271927 AGCCATCCCTCTAATCCCCA 59.728 55.000 0.00 0.00 0.00 4.96
3462 4292 2.190578 CTCAACCTCCCCCATCGC 59.809 66.667 0.00 0.00 0.00 4.58
3463 4293 2.746375 CCCTCAACCTCCCCCATCG 61.746 68.421 0.00 0.00 0.00 3.84
3566 4824 4.250116 AGCCACGATCTAGTTCATCATC 57.750 45.455 0.00 0.00 0.00 2.92
3568 4826 3.447229 TCAAGCCACGATCTAGTTCATCA 59.553 43.478 0.00 0.00 0.00 3.07
3576 4834 2.437085 TCTCCTCAAGCCACGATCTA 57.563 50.000 0.00 0.00 0.00 1.98
3705 4976 1.609072 GAGTGAAAGAAACAGGGGTGC 59.391 52.381 0.00 0.00 0.00 5.01
3787 5058 7.010339 AGCCTCTATTGTTATATGGAGAACC 57.990 40.000 0.00 0.00 35.75 3.62
3813 5223 3.570926 TCGGATACAATCGCCATACTC 57.429 47.619 0.00 0.00 0.00 2.59
3820 5230 2.738846 AGCAATGATCGGATACAATCGC 59.261 45.455 0.00 0.00 0.00 4.58
3863 5273 7.378966 TGTCATTGAAACACTCCTTACTCTAG 58.621 38.462 0.00 0.00 0.00 2.43
3865 5275 6.174720 TGTCATTGAAACACTCCTTACTCT 57.825 37.500 0.00 0.00 0.00 3.24
3866 5276 6.706270 TCTTGTCATTGAAACACTCCTTACTC 59.294 38.462 0.00 0.00 0.00 2.59
3867 5277 6.483640 GTCTTGTCATTGAAACACTCCTTACT 59.516 38.462 0.00 0.00 0.00 2.24
3868 5278 6.564125 CGTCTTGTCATTGAAACACTCCTTAC 60.564 42.308 0.00 0.00 0.00 2.34
3869 5279 5.465390 CGTCTTGTCATTGAAACACTCCTTA 59.535 40.000 0.00 0.00 0.00 2.69
3870 5280 4.273480 CGTCTTGTCATTGAAACACTCCTT 59.727 41.667 0.00 0.00 0.00 3.36
3871 5281 3.809832 CGTCTTGTCATTGAAACACTCCT 59.190 43.478 0.00 0.00 0.00 3.69
3872 5282 3.058914 CCGTCTTGTCATTGAAACACTCC 60.059 47.826 0.00 0.00 0.00 3.85
3873 5283 3.058914 CCCGTCTTGTCATTGAAACACTC 60.059 47.826 0.00 0.00 0.00 3.51
3874 5284 2.878406 CCCGTCTTGTCATTGAAACACT 59.122 45.455 0.00 0.00 0.00 3.55
3886 5296 1.594293 CGCTGTCAACCCGTCTTGT 60.594 57.895 0.00 0.00 0.00 3.16
3912 5322 1.429463 GCCGTCTGTCGTTGAAATCT 58.571 50.000 0.00 0.00 37.94 2.40
3913 5323 0.442699 GGCCGTCTGTCGTTGAAATC 59.557 55.000 0.00 0.00 37.94 2.17
3914 5324 0.953960 GGGCCGTCTGTCGTTGAAAT 60.954 55.000 0.00 0.00 37.94 2.17
3916 5326 2.029964 GGGCCGTCTGTCGTTGAA 59.970 61.111 0.00 0.00 37.94 2.69
3932 5342 4.074970 AGCATAAATTTATCTGCCTCCGG 58.925 43.478 16.54 0.00 0.00 5.14
3934 5344 6.211515 CAACAGCATAAATTTATCTGCCTCC 58.788 40.000 23.35 3.44 0.00 4.30
3935 5345 5.689068 GCAACAGCATAAATTTATCTGCCTC 59.311 40.000 23.35 14.97 0.00 4.70
3937 5347 5.461078 CAGCAACAGCATAAATTTATCTGCC 59.539 40.000 23.35 16.79 0.00 4.85
3938 5348 6.038356 ACAGCAACAGCATAAATTTATCTGC 58.962 36.000 23.35 19.31 0.00 4.26
3939 5349 7.756272 TGAACAGCAACAGCATAAATTTATCTG 59.244 33.333 22.57 22.57 0.00 2.90
3940 5350 7.756722 GTGAACAGCAACAGCATAAATTTATCT 59.243 33.333 7.76 6.13 0.00 1.98
3941 5351 7.253420 CGTGAACAGCAACAGCATAAATTTATC 60.253 37.037 7.76 4.10 0.00 1.75
3942 5352 6.527722 CGTGAACAGCAACAGCATAAATTTAT 59.472 34.615 4.81 4.81 0.00 1.40
3991 5428 1.069358 GACCTCCTTTATCTGCCTCCG 59.931 57.143 0.00 0.00 0.00 4.63
3993 5430 1.418264 GGGACCTCCTTTATCTGCCTC 59.582 57.143 0.00 0.00 35.95 4.70
3994 5431 1.010170 AGGGACCTCCTTTATCTGCCT 59.990 52.381 0.00 0.00 45.47 4.75
3996 5433 2.036089 CGTAGGGACCTCCTTTATCTGC 59.964 54.545 0.00 0.00 45.47 4.26
3997 5434 3.563223 TCGTAGGGACCTCCTTTATCTG 58.437 50.000 0.00 0.00 45.47 2.90
3998 5435 3.436761 CCTCGTAGGGACCTCCTTTATCT 60.437 52.174 0.00 0.00 45.47 1.98
3999 5436 2.892215 CCTCGTAGGGACCTCCTTTATC 59.108 54.545 0.00 0.00 45.47 1.75
4005 5453 1.206610 GTTTTCCTCGTAGGGACCTCC 59.793 57.143 0.00 0.00 35.59 4.30
4012 5460 2.737252 GAGCAAGTGTTTTCCTCGTAGG 59.263 50.000 0.00 0.00 36.46 3.18
4034 5482 1.877576 CTGACAGTAGTGCCCAGCGA 61.878 60.000 0.00 0.00 0.00 4.93
4036 5484 0.671781 CACTGACAGTAGTGCCCAGC 60.672 60.000 8.02 0.00 41.31 4.85
4037 5485 3.521995 CACTGACAGTAGTGCCCAG 57.478 57.895 8.02 15.22 41.31 4.45
4043 5491 2.623889 GTCACCTGACACTGACAGTAGT 59.376 50.000 8.02 8.93 44.18 2.73
4044 5492 2.029828 GGTCACCTGACACTGACAGTAG 60.030 54.545 8.02 2.19 46.47 2.57
4045 5493 1.961394 GGTCACCTGACACTGACAGTA 59.039 52.381 8.02 0.00 46.47 2.74
4046 5494 0.753262 GGTCACCTGACACTGACAGT 59.247 55.000 1.07 1.07 46.47 3.55
4047 5495 0.319040 CGGTCACCTGACACTGACAG 60.319 60.000 7.71 0.00 46.47 3.51
4048 5496 0.753848 TCGGTCACCTGACACTGACA 60.754 55.000 7.71 0.00 46.47 3.58
4049 5497 0.039074 CTCGGTCACCTGACACTGAC 60.039 60.000 7.71 1.30 46.47 3.51
4051 5499 1.244816 TACTCGGTCACCTGACACTG 58.755 55.000 7.71 0.00 46.47 3.66
4053 5501 1.336609 GGTTACTCGGTCACCTGACAC 60.337 57.143 7.71 0.00 46.47 3.67
4090 5538 2.955614 TGCTAAAACTAGACGGTCTGC 58.044 47.619 20.58 13.23 0.00 4.26


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

AutoCloner maintained by Alex Coulton.