Multiple sequence alignment - TraesCS5B01G356700

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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 TraesCS5B01G356700 chr5B 100.000 4121 0 0 1 4121 536325938 536321818 0.000000e+00 7611.0
1 TraesCS5B01G356700 chr5B 80.206 389 72 3 3732 4116 536919218 536919605 1.870000e-73 287.0
2 TraesCS5B01G356700 chr5B 82.667 300 49 1 3820 4116 536912216 536912515 3.160000e-66 263.0
3 TraesCS5B01G356700 chr5A 87.886 2782 209 50 954 3685 556891541 556888838 0.000000e+00 3153.0
4 TraesCS5B01G356700 chr5A 96.281 484 16 2 3639 4121 556879885 556879403 0.000000e+00 793.0
5 TraesCS5B01G356700 chr5A 88.391 379 43 1 3743 4120 556888839 556888461 4.860000e-124 455.0
6 TraesCS5B01G356700 chr5A 82.250 400 31 24 1 378 556892396 556892015 4.000000e-80 309.0
7 TraesCS5B01G356700 chr5A 91.071 112 9 1 3249 3359 556886046 556885935 2.570000e-32 150.0
8 TraesCS5B01G356700 chr5D 89.312 2573 185 40 997 3494 440920606 440918049 0.000000e+00 3145.0
9 TraesCS5B01G356700 chr5D 86.329 1302 124 26 2194 3480 440903830 440902568 0.000000e+00 1369.0
10 TraesCS5B01G356700 chr5D 94.026 703 26 8 3421 4121 440894766 440894078 0.000000e+00 1051.0
11 TraesCS5B01G356700 chr5D 88.670 609 56 4 3522 4121 440902569 440901965 0.000000e+00 730.0
12 TraesCS5B01G356700 chr5D 92.640 394 29 0 3728 4121 440917741 440917348 5.980000e-158 568.0
13 TraesCS5B01G356700 chr5D 84.211 380 43 12 1716 2082 440904262 440903887 1.820000e-93 353.0
14 TraesCS5B01G356700 chr5D 80.542 406 31 24 1 381 440921628 440921246 6.790000e-68 268.0
15 TraesCS5B01G356700 chr5D 84.277 159 24 1 1512 1669 440904534 440904376 1.980000e-33 154.0
16 TraesCS5B01G356700 chr5D 91.262 103 5 1 3021 3119 440890736 440890634 2.000000e-28 137.0
17 TraesCS5B01G356700 chr5D 77.974 227 21 16 696 913 440921000 440920794 9.360000e-22 115.0
18 TraesCS5B01G356700 chrUn 96.281 484 16 2 3639 4121 326872000 326871518 0.000000e+00 793.0
19 TraesCS5B01G356700 chrUn 96.281 484 16 2 3639 4121 334634371 334634853 0.000000e+00 793.0
20 TraesCS5B01G356700 chr6A 85.000 200 30 0 2919 3118 617690368 617690169 1.940000e-48 204.0
21 TraesCS5B01G356700 chr6A 85.000 200 30 0 2919 3118 617692652 617692453 1.940000e-48 204.0
22 TraesCS5B01G356700 chr6B 79.856 278 54 2 2839 3115 716973044 716973320 6.990000e-48 202.0
23 TraesCS5B01G356700 chr6B 94.595 37 2 0 2299 2335 716972525 716972561 1.600000e-04 58.4
24 TraesCS5B01G356700 chr6D 79.061 277 56 2 2839 3114 472302788 472303063 5.440000e-44 189.0
25 TraesCS5B01G356700 chr4A 82.143 140 13 7 2298 2426 736761860 736761998 4.360000e-20 110.0
26 TraesCS5B01G356700 chr4A 75.135 185 37 9 2671 2848 736729632 736729814 1.230000e-10 78.7
27 TraesCS5B01G356700 chr4A 88.889 63 6 1 1948 2010 735481452 735481391 4.420000e-10 76.8
28 TraesCS5B01G356700 chr4A 97.727 44 1 0 1932 1975 736729199 736729242 4.420000e-10 76.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G356700 chr5B 536321818 536325938 4120 True 7611.00 7611 100.00000 1 4121 1 chr5B.!!$R1 4120
1 TraesCS5B01G356700 chr5A 556885935 556892396 6461 True 1016.75 3153 87.39950 1 4120 4 chr5A.!!$R2 4119
2 TraesCS5B01G356700 chr5D 440917348 440921628 4280 True 1024.00 3145 85.11700 1 4121 4 chr5D.!!$R3 4120
3 TraesCS5B01G356700 chr5D 440901965 440904534 2569 True 651.50 1369 85.87175 1512 4121 4 chr5D.!!$R2 2609
4 TraesCS5B01G356700 chr5D 440890634 440894766 4132 True 594.00 1051 92.64400 3021 4121 2 chr5D.!!$R1 1100
5 TraesCS5B01G356700 chr6A 617690169 617692652 2483 True 204.00 204 85.00000 2919 3118 2 chr6A.!!$R1 199

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
948 1093 0.042448 GAGACGTGTGCGAAAACCAC 60.042 55.0 0.00 0.00 42.00 4.16 F
1323 1526 0.099613 CGTCATCTCCTGGTGAGTCG 59.900 60.0 4.63 5.41 42.12 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2554 0.463474 GAGTGGAGCCTCCTGCATTC 60.463 60.0 12.94 1.78 41.64 2.67 R
3128 3526 0.178981 ACTGTTCATGGTTGCCTGCT 60.179 50.0 0.00 0.00 0.00 4.24 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
59 60 5.278858 CCGTCGCTATCCTATTTAAACCTCT 60.279 44.000 0.00 0.00 0.00 3.69
201 207 3.237741 CCCATCCTCCTCGCTCCC 61.238 72.222 0.00 0.00 0.00 4.30
203 209 2.123077 CATCCTCCTCGCTCCCCT 60.123 66.667 0.00 0.00 0.00 4.79
237 246 4.728882 GCATTCTTCAGGTAATCACGCTTG 60.729 45.833 0.00 0.00 0.00 4.01
243 252 3.500680 TCAGGTAATCACGCTTGAAAACC 59.499 43.478 15.56 15.56 39.39 3.27
245 254 3.502211 AGGTAATCACGCTTGAAAACCTG 59.498 43.478 21.77 0.00 43.98 4.00
290 300 2.436646 CTGGCAGCTTGGTACCGG 60.437 66.667 7.57 0.00 0.00 5.28
291 301 4.715523 TGGCAGCTTGGTACCGGC 62.716 66.667 18.36 18.36 0.00 6.13
317 343 3.081804 CCACCGTCTTTATTTGCTTCCT 58.918 45.455 0.00 0.00 0.00 3.36
324 350 6.594159 CCGTCTTTATTTGCTTCCTCTTCTTA 59.406 38.462 0.00 0.00 0.00 2.10
325 351 7.201565 CCGTCTTTATTTGCTTCCTCTTCTTAG 60.202 40.741 0.00 0.00 0.00 2.18
326 352 7.468441 GTCTTTATTTGCTTCCTCTTCTTAGC 58.532 38.462 0.00 0.00 0.00 3.09
328 354 7.885399 TCTTTATTTGCTTCCTCTTCTTAGCTT 59.115 33.333 0.00 0.00 34.77 3.74
329 355 5.893897 ATTTGCTTCCTCTTCTTAGCTTG 57.106 39.130 0.00 0.00 34.77 4.01
330 356 4.357918 TTGCTTCCTCTTCTTAGCTTGT 57.642 40.909 0.00 0.00 34.77 3.16
331 357 3.668447 TGCTTCCTCTTCTTAGCTTGTG 58.332 45.455 0.00 0.00 34.77 3.33
332 358 3.006247 GCTTCCTCTTCTTAGCTTGTGG 58.994 50.000 0.00 0.00 0.00 4.17
333 359 3.307059 GCTTCCTCTTCTTAGCTTGTGGA 60.307 47.826 0.00 0.00 0.00 4.02
334 360 4.502962 CTTCCTCTTCTTAGCTTGTGGAG 58.497 47.826 0.00 0.00 0.00 3.86
367 397 2.249557 CTGCTGCTGCGTTCCATGTC 62.250 60.000 11.21 0.00 43.34 3.06
378 443 5.060506 TGCGTTCCATGTCTTTTCTTCTTA 58.939 37.500 0.00 0.00 0.00 2.10
381 446 7.389330 TGCGTTCCATGTCTTTTCTTCTTATTA 59.611 33.333 0.00 0.00 0.00 0.98
390 455 9.807921 TGTCTTTTCTTCTTATTAATCCTTGGT 57.192 29.630 0.00 0.00 0.00 3.67
404 469 9.780186 ATTAATCCTTGGTGAATAGTAAGTAGC 57.220 33.333 0.00 0.00 0.00 3.58
408 473 5.294552 CCTTGGTGAATAGTAAGTAGCAAGC 59.705 44.000 0.00 0.00 42.39 4.01
435 500 3.250762 TGAGTCTTGGAGAAATTTGCGTG 59.749 43.478 0.00 0.00 0.00 5.34
437 502 3.251004 AGTCTTGGAGAAATTTGCGTGTC 59.749 43.478 0.00 0.00 0.00 3.67
438 503 2.552315 TCTTGGAGAAATTTGCGTGTCC 59.448 45.455 0.00 0.00 0.00 4.02
439 504 1.243902 TGGAGAAATTTGCGTGTCCC 58.756 50.000 0.00 0.00 0.00 4.46
440 505 0.526211 GGAGAAATTTGCGTGTCCCC 59.474 55.000 0.00 0.00 0.00 4.81
441 506 0.168128 GAGAAATTTGCGTGTCCCCG 59.832 55.000 0.00 0.00 0.00 5.73
461 526 4.418401 CGCCCGTCCGTCCGTTAA 62.418 66.667 0.00 0.00 0.00 2.01
478 543 1.960417 TAATTTGCATCATCGCCGGA 58.040 45.000 5.05 0.00 0.00 5.14
479 544 0.381801 AATTTGCATCATCGCCGGAC 59.618 50.000 5.05 0.00 0.00 4.79
511 576 2.289547 TCGCGTTTTCCTTTCCTCAAAG 59.710 45.455 5.77 0.00 39.11 2.77
513 578 2.223711 GCGTTTTCCTTTCCTCAAAGCA 60.224 45.455 0.00 0.00 38.19 3.91
554 620 2.225491 GCACAAGTGATTTACGCCTTCA 59.775 45.455 4.04 0.00 0.00 3.02
561 630 0.988832 ATTTACGCCTTCACCTCCCA 59.011 50.000 0.00 0.00 0.00 4.37
597 666 5.468540 AGGCATACCTCTTTTTGTTTTCC 57.531 39.130 0.00 0.00 46.34 3.13
599 668 5.602561 AGGCATACCTCTTTTTGTTTTCCTT 59.397 36.000 0.00 0.00 46.34 3.36
600 669 6.099701 AGGCATACCTCTTTTTGTTTTCCTTT 59.900 34.615 0.00 0.00 46.34 3.11
601 670 6.765989 GGCATACCTCTTTTTGTTTTCCTTTT 59.234 34.615 0.00 0.00 0.00 2.27
602 671 7.042051 GGCATACCTCTTTTTGTTTTCCTTTTC 60.042 37.037 0.00 0.00 0.00 2.29
604 673 9.599866 CATACCTCTTTTTGTTTTCCTTTTCTT 57.400 29.630 0.00 0.00 0.00 2.52
606 675 8.918202 ACCTCTTTTTGTTTTCCTTTTCTTTT 57.082 26.923 0.00 0.00 0.00 2.27
636 705 6.937436 TCTTTTTAAAAAGAGAGCCGTCTT 57.063 33.333 30.56 0.00 46.80 3.01
637 706 7.329588 TCTTTTTAAAAAGAGAGCCGTCTTT 57.670 32.000 30.56 5.29 46.80 2.52
638 707 8.441312 TCTTTTTAAAAAGAGAGCCGTCTTTA 57.559 30.769 30.56 11.16 46.80 1.85
639 708 8.340443 TCTTTTTAAAAAGAGAGCCGTCTTTAC 58.660 33.333 30.56 0.00 46.80 2.01
640 709 5.834239 TTAAAAAGAGAGCCGTCTTTACG 57.166 39.130 10.49 0.00 44.38 3.18
657 726 8.874745 GTCTTTACGATTTCATTTCATCGAAA 57.125 30.769 8.46 0.00 44.18 3.46
658 727 8.776802 GTCTTTACGATTTCATTTCATCGAAAC 58.223 33.333 8.46 0.00 44.18 2.78
659 728 7.960738 TCTTTACGATTTCATTTCATCGAAACC 59.039 33.333 8.46 0.00 44.18 3.27
660 729 5.621197 ACGATTTCATTTCATCGAAACCA 57.379 34.783 8.46 0.00 44.18 3.67
661 730 5.390613 ACGATTTCATTTCATCGAAACCAC 58.609 37.500 8.46 0.00 44.18 4.16
663 732 6.029607 CGATTTCATTTCATCGAAACCACAT 58.970 36.000 0.00 0.00 44.18 3.21
665 734 7.062138 CGATTTCATTTCATCGAAACCACATTT 59.938 33.333 0.00 0.00 44.18 2.32
666 735 8.606040 ATTTCATTTCATCGAAACCACATTTT 57.394 26.923 0.00 0.00 34.23 1.82
685 754 3.717842 TTTTTGTGGTAGCTCGCCT 57.282 47.368 8.47 0.00 0.00 5.52
686 755 1.519408 TTTTTGTGGTAGCTCGCCTC 58.481 50.000 8.47 5.77 0.00 4.70
688 757 0.246635 TTTGTGGTAGCTCGCCTCTC 59.753 55.000 8.47 1.47 0.00 3.20
689 758 1.934220 TTGTGGTAGCTCGCCTCTCG 61.934 60.000 8.47 0.00 40.15 4.04
691 760 3.518998 GGTAGCTCGCCTCTCGCA 61.519 66.667 0.00 0.00 37.30 5.10
692 761 2.490217 GTAGCTCGCCTCTCGCAA 59.510 61.111 0.00 0.00 37.30 4.85
735 804 1.475441 CGTCTCTTTCGGATCGCAGC 61.475 60.000 0.00 0.00 0.00 5.25
751 823 3.068165 TCGCAGCACAACTAGCATATACT 59.932 43.478 0.00 0.00 0.00 2.12
757 829 6.865726 CAGCACAACTAGCATATACTAGAAGG 59.134 42.308 15.63 7.56 41.92 3.46
770 850 2.303022 ACTAGAAGGTAGCAGCAGCAAA 59.697 45.455 3.17 0.00 45.49 3.68
771 851 1.528129 AGAAGGTAGCAGCAGCAAAC 58.472 50.000 3.17 0.67 45.49 2.93
781 861 1.717645 CAGCAGCAAACAAGATTTCGC 59.282 47.619 0.00 0.00 0.00 4.70
789 869 7.512297 CAGCAAACAAGATTTCGCAAATAAAT 58.488 30.769 0.00 0.00 0.00 1.40
791 871 7.171337 AGCAAACAAGATTTCGCAAATAAATGT 59.829 29.630 0.00 0.00 0.00 2.71
794 874 9.691362 AAACAAGATTTCGCAAATAAATGTAGT 57.309 25.926 0.00 0.00 0.00 2.73
826 906 2.686470 CTCCCTGGAGCTGGAGCA 60.686 66.667 4.98 0.00 41.59 4.26
827 907 2.203983 TCCCTGGAGCTGGAGCAA 60.204 61.111 0.00 0.00 45.16 3.91
828 908 1.617536 TCCCTGGAGCTGGAGCAAT 60.618 57.895 0.00 0.00 45.16 3.56
829 909 1.453379 CCCTGGAGCTGGAGCAATG 60.453 63.158 0.00 0.00 45.16 2.82
830 910 2.119655 CCTGGAGCTGGAGCAATGC 61.120 63.158 0.00 0.00 45.16 3.56
832 912 0.752009 CTGGAGCTGGAGCAATGCAT 60.752 55.000 8.35 0.00 45.16 3.96
847 927 4.048504 CAATGCATTGCCATCTACACATG 58.951 43.478 25.50 0.00 0.00 3.21
848 928 1.406180 TGCATTGCCATCTACACATGC 59.594 47.619 6.12 0.00 0.00 4.06
856 936 0.812811 ATCTACACATGCTGCGGCTG 60.813 55.000 20.27 16.21 39.59 4.85
883 963 2.081462 GTTCCGTTCCGTGGATCATTT 58.919 47.619 0.00 0.00 34.91 2.32
887 967 2.029970 CCGTTCCGTGGATCATTTAACG 59.970 50.000 10.68 10.68 38.28 3.18
910 1055 5.005203 CGATTTTGATCTCTGTTTCCTCTCG 59.995 44.000 0.00 0.00 0.00 4.04
948 1093 0.042448 GAGACGTGTGCGAAAACCAC 60.042 55.000 0.00 0.00 42.00 4.16
971 1159 1.261480 TGACTGAGGAGGAGACTTGC 58.739 55.000 0.00 0.00 44.43 4.01
1005 1199 2.517166 GCCGGGAAGAAGATGGGC 60.517 66.667 2.18 0.00 0.00 5.36
1137 1331 0.883833 GCAGGGACATGAACAAGGTG 59.116 55.000 0.00 0.00 0.00 4.00
1181 1381 8.088365 ACATTAAATTCTGTTTCAACCTTAGCC 58.912 33.333 0.00 0.00 0.00 3.93
1189 1392 7.103641 TCTGTTTCAACCTTAGCCTAATACTG 58.896 38.462 0.00 0.00 0.00 2.74
1200 1403 7.502561 CCTTAGCCTAATACTGCCTTTGTAATT 59.497 37.037 0.00 0.00 0.00 1.40
1202 1405 5.067805 AGCCTAATACTGCCTTTGTAATTGC 59.932 40.000 0.00 0.00 0.00 3.56
1217 1420 9.349713 CTTTGTAATTGCCTAATCCCATTACTA 57.650 33.333 0.00 0.00 0.00 1.82
1219 1422 8.041143 TGTAATTGCCTAATCCCATTACTACT 57.959 34.615 0.00 0.00 0.00 2.57
1296 1499 1.300620 CTCGCCAAGACGGTCACAA 60.301 57.895 11.27 0.00 36.97 3.33
1301 1504 1.877637 CCAAGACGGTCACAATGTCA 58.122 50.000 11.27 0.00 35.09 3.58
1323 1526 0.099613 CGTCATCTCCTGGTGAGTCG 59.900 60.000 4.63 5.41 42.12 4.18
1324 1527 1.464734 GTCATCTCCTGGTGAGTCGA 58.535 55.000 4.63 0.00 42.12 4.20
1353 1556 7.452880 TTCATCAGGTTTCATAGTTTCCAAG 57.547 36.000 0.00 0.00 0.00 3.61
1356 1559 6.877611 TCAGGTTTCATAGTTTCCAAGAAC 57.122 37.500 0.00 0.00 0.00 3.01
1388 1595 1.403249 GCTGCTGCAATTCGGTGAATT 60.403 47.619 11.11 0.00 42.14 2.17
1459 1694 5.393962 GGACAGAACATTCAGTAAACATGC 58.606 41.667 0.00 0.00 0.00 4.06
1589 1825 0.878086 GGCTAGCGTGCAAGATCCTC 60.878 60.000 9.00 0.00 34.04 3.71
1688 2005 4.082408 GCCATGATGATGTTGGTATCCATG 60.082 45.833 0.00 0.00 31.53 3.66
1710 2027 2.495669 TCATGATGCTAACAGTGTCCGA 59.504 45.455 0.00 0.00 0.00 4.55
1739 2061 3.119849 CGAAAAATGCAGGAAATCTCGGT 60.120 43.478 0.00 0.00 0.00 4.69
1930 2266 5.734720 TGTTAATTCACTCTGAGGATGTCC 58.265 41.667 9.85 0.00 0.00 4.02
2132 2468 1.111116 ACGAACACAACGAGGGGAGA 61.111 55.000 0.00 0.00 34.70 3.71
2146 2482 4.401519 CGAGGGGAGACAGATTGTAAGTTA 59.598 45.833 0.00 0.00 0.00 2.24
2185 2523 1.707989 TGGTTGGTTCTTGGGAGCATA 59.292 47.619 0.00 0.00 0.00 3.14
2216 2554 1.889829 AGAGAAACTGACTCGGACAGG 59.110 52.381 0.00 0.00 39.38 4.00
2348 2686 1.655885 CGACCATATCCGCGGTACA 59.344 57.895 27.15 11.93 34.99 2.90
2358 2700 1.402968 TCCGCGGTACATCTCTAACAC 59.597 52.381 27.15 0.00 0.00 3.32
2381 2723 8.575589 ACACACTGCAACATTTATCATTTCTAA 58.424 29.630 0.00 0.00 0.00 2.10
2385 2727 7.111247 TGCAACATTTATCATTTCTAAGGGG 57.889 36.000 0.00 0.00 0.00 4.79
2407 2756 4.102524 GGAAGGGGGTTTTGACTGAATTTT 59.897 41.667 0.00 0.00 0.00 1.82
2422 2771 6.804677 ACTGAATTTTGTGTTAACTGCATCA 58.195 32.000 7.22 6.04 0.00 3.07
2426 2775 5.528043 TTTTGTGTTAACTGCATCATGGT 57.472 34.783 7.22 0.00 0.00 3.55
2543 2892 4.468510 AGTTGATGGGGTACGAATCTACAA 59.531 41.667 13.71 0.00 31.26 2.41
2544 2893 4.395959 TGATGGGGTACGAATCTACAAC 57.604 45.455 0.00 0.00 0.00 3.32
2545 2894 3.133362 TGATGGGGTACGAATCTACAACC 59.867 47.826 0.00 0.00 0.00 3.77
2548 2897 3.175109 GGGTACGAATCTACAACCCTG 57.825 52.381 1.53 0.00 45.34 4.45
2549 2898 2.498885 GGGTACGAATCTACAACCCTGT 59.501 50.000 1.53 0.00 45.34 4.00
2550 2899 3.429960 GGGTACGAATCTACAACCCTGTC 60.430 52.174 1.53 0.00 45.34 3.51
2551 2900 3.446516 GGTACGAATCTACAACCCTGTCT 59.553 47.826 0.00 0.00 36.96 3.41
2552 2901 3.594603 ACGAATCTACAACCCTGTCTG 57.405 47.619 0.00 0.00 36.96 3.51
2553 2902 2.897969 ACGAATCTACAACCCTGTCTGT 59.102 45.455 0.00 0.00 36.96 3.41
2554 2903 3.056749 ACGAATCTACAACCCTGTCTGTC 60.057 47.826 0.00 0.00 36.96 3.51
2562 2923 0.905337 ACCCTGTCTGTCTACCTGCC 60.905 60.000 0.00 0.00 0.00 4.85
2603 2964 9.346725 CTGTATTCATTTTAAAAGCTCTGAACC 57.653 33.333 13.99 9.88 0.00 3.62
2622 2983 6.834168 GAACCTAATTCAGGGTTCATTCAA 57.166 37.500 22.25 0.00 44.53 2.69
2648 3009 4.593206 TCACTCCAATGACCAAGTACTTCT 59.407 41.667 4.77 0.00 0.00 2.85
2660 3021 4.531332 CAAGTACTTCTCTTTGCAGCAAC 58.469 43.478 7.54 0.00 0.00 4.17
2738 3099 1.205655 CTGACACATCACTGTCCCGAT 59.794 52.381 0.00 0.00 40.02 4.18
2779 3177 2.807392 GTGTCGTCCCCGAAAACAATTA 59.193 45.455 0.00 0.00 46.26 1.40
2787 3185 4.703093 TCCCCGAAAACAATTATCTGAACC 59.297 41.667 0.00 0.00 0.00 3.62
2802 3200 4.065088 TCTGAACCCACTCTGAAAATTCG 58.935 43.478 0.00 0.00 0.00 3.34
3000 3398 1.449423 CGCCATGAACATCGGGACA 60.449 57.895 0.00 0.00 0.00 4.02
3125 3523 1.767681 GTCCATCCTCTCCTGAAGCAT 59.232 52.381 0.00 0.00 0.00 3.79
3126 3524 1.767088 TCCATCCTCTCCTGAAGCATG 59.233 52.381 0.00 0.00 0.00 4.06
3127 3525 1.767088 CCATCCTCTCCTGAAGCATGA 59.233 52.381 0.00 0.00 0.00 3.07
3128 3526 2.172082 CCATCCTCTCCTGAAGCATGAA 59.828 50.000 0.00 0.00 0.00 2.57
3129 3527 3.468770 CATCCTCTCCTGAAGCATGAAG 58.531 50.000 0.00 0.00 0.00 3.02
3130 3528 1.209019 TCCTCTCCTGAAGCATGAAGC 59.791 52.381 0.00 0.00 46.19 3.86
3178 3576 0.839946 ATGGGTCAGGGAGAATTCCG 59.160 55.000 0.65 0.00 40.64 4.30
3243 3647 3.935203 AGACACGCCATTCTTTCTGTATG 59.065 43.478 0.00 0.00 0.00 2.39
3342 3750 5.772169 CACTAGTGGATGGATCTCTGTGATA 59.228 44.000 15.49 0.00 35.14 2.15
3419 3827 8.576442 ACTAACACTTAATTTGACCCAGATTTG 58.424 33.333 0.00 0.00 0.00 2.32
3432 3840 3.305608 CCCAGATTTGGCAAGACAGTTTC 60.306 47.826 0.00 0.00 43.58 2.78
3557 3967 1.120530 TAATCCCCTGCCGACTTCTC 58.879 55.000 0.00 0.00 0.00 2.87
3593 4012 5.105106 TGCGGACTTCTGAATTCCAGTATAA 60.105 40.000 21.97 3.03 43.38 0.98
3632 4056 9.860898 AACAATTTATTTCAGTATGGAAAGAGC 57.139 29.630 0.00 0.00 36.98 4.09
3633 4057 9.023962 ACAATTTATTTCAGTATGGAAAGAGCA 57.976 29.630 0.00 0.00 36.98 4.26
3661 4085 3.584848 GACACATATATCCCCTGGCTCTT 59.415 47.826 0.00 0.00 0.00 2.85
3924 4449 4.644234 CCATTTATCATTGCAGGTACCACA 59.356 41.667 15.94 9.25 0.00 4.17
4018 4543 4.724399 TCTTGCCTTCATAGGTGTTCAAA 58.276 39.130 0.00 0.00 44.00 2.69
4103 4628 7.006509 CACATTTTCCATATCCTTCCTATGGT 58.993 38.462 8.72 0.00 44.03 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.790207 GAGACACGTACGTACACGGA 59.210 55.000 22.34 0.00 46.12 4.69
17 18 0.179215 GGAGACACGTACGTACACGG 60.179 60.000 22.34 10.93 46.12 4.94
18 19 3.099264 ACGGAGACACGTACGTACACG 62.099 57.143 22.34 23.66 46.58 4.49
59 60 0.633921 CCAGAGAGGAGGAGGAGGAA 59.366 60.000 0.00 0.00 41.22 3.36
179 185 2.503382 GCGAGGAGGATGGGGAGAC 61.503 68.421 0.00 0.00 0.00 3.36
237 246 1.203287 GGATGCAGAAGCCAGGTTTTC 59.797 52.381 0.00 0.00 41.13 2.29
243 252 3.570638 CGCGGATGCAGAAGCCAG 61.571 66.667 0.00 0.00 42.97 4.85
245 254 2.590007 ATCGCGGATGCAGAAGCC 60.590 61.111 6.13 0.00 42.97 4.35
274 284 4.715523 GCCGGTACCAAGCTGCCA 62.716 66.667 13.54 0.00 0.00 4.92
283 293 4.710167 GGTGGTGGTGCCGGTACC 62.710 72.222 32.67 32.67 41.21 3.34
290 300 1.530323 AATAAAGACGGTGGTGGTGC 58.470 50.000 0.00 0.00 0.00 5.01
291 301 2.351350 GCAAATAAAGACGGTGGTGGTG 60.351 50.000 0.00 0.00 0.00 4.17
332 358 0.678950 GCAGGTAGGAGATGGAGCTC 59.321 60.000 4.71 4.71 0.00 4.09
333 359 0.264359 AGCAGGTAGGAGATGGAGCT 59.736 55.000 0.00 0.00 0.00 4.09
334 360 0.392336 CAGCAGGTAGGAGATGGAGC 59.608 60.000 0.00 0.00 0.00 4.70
378 443 9.780186 GCTACTTACTATTCACCAAGGATTAAT 57.220 33.333 0.00 0.00 0.00 1.40
381 446 7.195374 TGCTACTTACTATTCACCAAGGATT 57.805 36.000 0.00 0.00 0.00 3.01
383 448 6.614694 TTGCTACTTACTATTCACCAAGGA 57.385 37.500 0.00 0.00 0.00 3.36
390 455 4.401519 ACGGAGCTTGCTACTTACTATTCA 59.598 41.667 3.17 0.00 0.00 2.57
397 462 2.163815 GACTCACGGAGCTTGCTACTTA 59.836 50.000 3.17 0.00 32.04 2.24
400 465 0.528470 AGACTCACGGAGCTTGCTAC 59.472 55.000 0.00 0.00 32.04 3.58
404 469 0.318441 TCCAAGACTCACGGAGCTTG 59.682 55.000 19.11 19.11 40.22 4.01
408 473 3.601443 ATTTCTCCAAGACTCACGGAG 57.399 47.619 8.57 8.57 46.49 4.63
446 511 0.722848 CAAATTAACGGACGGACGGG 59.277 55.000 6.00 0.00 38.39 5.28
459 524 1.601903 GTCCGGCGATGATGCAAATTA 59.398 47.619 9.30 0.00 36.28 1.40
460 525 0.381801 GTCCGGCGATGATGCAAATT 59.618 50.000 9.30 0.00 36.28 1.82
461 526 1.775039 CGTCCGGCGATGATGCAAAT 61.775 55.000 9.30 0.00 44.77 2.32
493 558 3.708563 TGCTTTGAGGAAAGGAAAACG 57.291 42.857 0.00 0.00 36.66 3.60
511 576 0.107508 TTAGAGAGGCAGCACCATGC 60.108 55.000 0.00 0.00 45.46 4.06
513 578 0.179936 GCTTAGAGAGGCAGCACCAT 59.820 55.000 0.00 0.00 43.14 3.55
525 591 4.490959 CGTAAATCACTTGTGCGCTTAGAG 60.491 45.833 9.73 3.97 0.00 2.43
554 620 1.305802 TCAGCATACGGTGGGAGGT 60.306 57.895 0.00 0.00 41.13 3.85
561 630 1.676968 TGCCTTGTCAGCATACGGT 59.323 52.632 0.00 0.00 34.69 4.83
614 683 7.320560 CGTAAAGACGGCTCTCTTTTTAAAAAG 59.679 37.037 27.60 27.60 45.63 2.27
615 684 7.127686 CGTAAAGACGGCTCTCTTTTTAAAAA 58.872 34.615 12.62 12.62 45.63 1.94
616 685 6.652245 CGTAAAGACGGCTCTCTTTTTAAAA 58.348 36.000 12.49 0.00 45.63 1.52
617 686 6.219302 CGTAAAGACGGCTCTCTTTTTAAA 57.781 37.500 12.49 0.00 45.63 1.52
618 687 5.834239 CGTAAAGACGGCTCTCTTTTTAA 57.166 39.130 12.49 0.00 45.63 1.52
632 701 8.776802 GTTTCGATGAAATGAAATCGTAAAGAC 58.223 33.333 5.12 0.00 44.63 3.01
634 703 7.748683 TGGTTTCGATGAAATGAAATCGTAAAG 59.251 33.333 5.12 0.00 44.63 1.85
635 704 7.535940 GTGGTTTCGATGAAATGAAATCGTAAA 59.464 33.333 5.12 2.97 44.63 2.01
636 705 7.018826 GTGGTTTCGATGAAATGAAATCGTAA 58.981 34.615 5.12 0.00 44.63 3.18
637 706 6.147985 TGTGGTTTCGATGAAATGAAATCGTA 59.852 34.615 5.12 0.00 44.63 3.43
638 707 5.049060 TGTGGTTTCGATGAAATGAAATCGT 60.049 36.000 5.12 0.00 44.63 3.73
639 708 5.389778 TGTGGTTTCGATGAAATGAAATCG 58.610 37.500 0.00 0.00 45.46 3.34
640 709 7.816945 AATGTGGTTTCGATGAAATGAAATC 57.183 32.000 0.00 0.00 36.57 2.17
641 710 8.606040 AAAATGTGGTTTCGATGAAATGAAAT 57.394 26.923 0.00 0.00 36.57 2.17
668 737 0.685097 AGAGGCGAGCTACCACAAAA 59.315 50.000 7.94 0.00 0.00 2.44
670 739 1.890894 GAGAGGCGAGCTACCACAA 59.109 57.895 7.94 0.00 0.00 3.33
671 740 2.407428 CGAGAGGCGAGCTACCACA 61.407 63.158 7.94 0.00 44.57 4.17
672 741 2.409651 CGAGAGGCGAGCTACCAC 59.590 66.667 7.94 1.60 44.57 4.16
689 758 1.214589 CCTCATGGCAGCAAGTTGC 59.785 57.895 20.44 20.44 45.46 4.17
691 760 0.694771 TCTCCTCATGGCAGCAAGTT 59.305 50.000 0.00 0.00 0.00 2.66
692 761 0.252479 CTCTCCTCATGGCAGCAAGT 59.748 55.000 0.00 0.00 0.00 3.16
731 800 5.773575 TCTAGTATATGCTAGTTGTGCTGC 58.226 41.667 22.50 0.00 39.44 5.25
735 804 8.024285 GCTACCTTCTAGTATATGCTAGTTGTG 58.976 40.741 22.50 14.11 39.44 3.33
751 823 2.038426 TGTTTGCTGCTGCTACCTTCTA 59.962 45.455 17.00 0.00 40.48 2.10
757 829 3.565905 AATCTTGTTTGCTGCTGCTAC 57.434 42.857 17.00 14.22 40.48 3.58
770 850 9.988350 CTACTACATTTATTTGCGAAATCTTGT 57.012 29.630 0.00 0.00 32.38 3.16
771 851 9.988350 ACTACTACATTTATTTGCGAAATCTTG 57.012 29.630 0.00 0.00 32.38 3.02
825 905 3.786516 TGTGTAGATGGCAATGCATTG 57.213 42.857 30.92 30.92 40.66 2.82
826 906 3.491964 GCATGTGTAGATGGCAATGCATT 60.492 43.478 5.99 5.99 34.31 3.56
827 907 2.035449 GCATGTGTAGATGGCAATGCAT 59.965 45.455 7.79 0.00 34.31 3.96
828 908 1.406180 GCATGTGTAGATGGCAATGCA 59.594 47.619 7.79 0.00 34.31 3.96
829 909 1.679680 AGCATGTGTAGATGGCAATGC 59.320 47.619 9.45 9.45 0.00 3.56
830 910 2.543031 GCAGCATGTGTAGATGGCAATG 60.543 50.000 0.00 0.00 39.31 2.82
832 912 1.097232 GCAGCATGTGTAGATGGCAA 58.903 50.000 0.00 0.00 39.31 4.52
883 963 7.386851 AGAGGAAACAGAGATCAAAATCGTTA 58.613 34.615 0.00 0.00 36.97 3.18
887 967 5.220567 GCGAGAGGAAACAGAGATCAAAATC 60.221 44.000 0.00 0.00 0.00 2.17
938 1083 0.310854 CAGTCAAGGGTGGTTTTCGC 59.689 55.000 0.00 0.00 0.00 4.70
939 1084 1.873591 CTCAGTCAAGGGTGGTTTTCG 59.126 52.381 0.00 0.00 0.00 3.46
948 1093 1.190643 GTCTCCTCCTCAGTCAAGGG 58.809 60.000 0.00 0.00 37.02 3.95
1005 1199 1.803519 GACGAGCAGCGACAGGAAG 60.804 63.158 5.99 0.00 44.57 3.46
1137 1331 1.105759 GTGCCCATGGAAGCTGGATC 61.106 60.000 15.22 0.00 35.70 3.36
1181 1381 6.699575 AGGCAATTACAAAGGCAGTATTAG 57.300 37.500 0.00 0.00 0.00 1.73
1189 1392 3.704061 TGGGATTAGGCAATTACAAAGGC 59.296 43.478 0.00 0.00 0.00 4.35
1200 1403 6.321821 ACAAAGTAGTAATGGGATTAGGCA 57.678 37.500 0.00 0.00 0.00 4.75
1202 1405 9.462606 AGAAAACAAAGTAGTAATGGGATTAGG 57.537 33.333 0.00 0.00 0.00 2.69
1217 1420 2.466846 ACCTGCCCAAGAAAACAAAGT 58.533 42.857 0.00 0.00 0.00 2.66
1219 1422 2.569404 ACAACCTGCCCAAGAAAACAAA 59.431 40.909 0.00 0.00 0.00 2.83
1296 1499 1.753649 CCAGGAGATGACGTCTGACAT 59.246 52.381 17.92 1.61 37.29 3.06
1301 1504 3.672066 TCACCAGGAGATGACGTCT 57.328 52.632 17.92 0.00 40.81 4.18
1324 1527 7.363268 GGAAACTATGAAACCTGATGAAAGCAT 60.363 37.037 0.00 0.00 37.47 3.79
1369 1576 2.095110 TGAATTCACCGAATTGCAGCAG 60.095 45.455 3.38 0.00 41.56 4.24
1388 1595 8.731275 TGACAATCAGAGAACTTTTTAAGTGA 57.269 30.769 0.00 0.00 41.91 3.41
1589 1825 4.715892 AAATGCGGCGGCGGTTTG 62.716 61.111 33.02 4.80 44.10 2.93
1641 1877 6.324819 CAACTCAAAGTCTGACATTTTGTGT 58.675 36.000 17.31 17.31 45.83 3.72
1642 1878 5.230726 GCAACTCAAAGTCTGACATTTTGTG 59.769 40.000 17.02 16.72 34.35 3.33
1646 1882 3.953612 TGGCAACTCAAAGTCTGACATTT 59.046 39.130 10.88 5.17 37.61 2.32
1688 2005 2.604914 CGGACACTGTTAGCATCATGAC 59.395 50.000 0.00 0.00 0.00 3.06
1710 2027 2.513753 TCCTGCATTTTTCGTCCATGT 58.486 42.857 0.00 0.00 0.00 3.21
1718 2035 4.440839 ACCGAGATTTCCTGCATTTTTC 57.559 40.909 0.00 0.00 0.00 2.29
1739 2061 0.179137 CGACGATCAGCAGCAGGTTA 60.179 55.000 0.00 0.00 0.00 2.85
1892 2223 2.145397 TAACAGCCTGATCTCTCGGT 57.855 50.000 0.00 0.00 0.00 4.69
1930 2266 4.711949 AGAGGCCACCAAGCTGCG 62.712 66.667 5.01 0.00 0.00 5.18
2033 2369 2.945398 GATGCTCCTCGTCGCTGTCC 62.945 65.000 0.00 0.00 0.00 4.02
2132 2468 8.918202 TGGACAATTCTTAACTTACAATCTGT 57.082 30.769 0.00 0.00 0.00 3.41
2146 2482 3.966665 ACCAACCAACATGGACAATTCTT 59.033 39.130 2.85 0.00 40.96 2.52
2216 2554 0.463474 GAGTGGAGCCTCCTGCATTC 60.463 60.000 12.94 1.78 41.64 2.67
2284 2622 2.045926 GTGCACGGCCTCCTTCAT 60.046 61.111 0.00 0.00 0.00 2.57
2348 2686 7.607607 TGATAAATGTTGCAGTGTGTTAGAGAT 59.392 33.333 0.00 0.00 0.00 2.75
2358 2700 7.703621 CCCTTAGAAATGATAAATGTTGCAGTG 59.296 37.037 0.00 0.00 0.00 3.66
2381 2723 0.704813 AGTCAAAACCCCCTTCCCCT 60.705 55.000 0.00 0.00 0.00 4.79
2385 2727 4.955811 AAATTCAGTCAAAACCCCCTTC 57.044 40.909 0.00 0.00 0.00 3.46
2407 2756 5.159273 TCTACCATGATGCAGTTAACACA 57.841 39.130 8.61 6.09 0.00 3.72
2422 2771 7.013274 CCAACAACGAATCCAATTATCTACCAT 59.987 37.037 0.00 0.00 0.00 3.55
2426 2775 5.298276 GCCCAACAACGAATCCAATTATCTA 59.702 40.000 0.00 0.00 0.00 1.98
2543 2892 0.905337 GGCAGGTAGACAGACAGGGT 60.905 60.000 0.00 0.00 0.00 4.34
2544 2893 1.901085 GGCAGGTAGACAGACAGGG 59.099 63.158 0.00 0.00 0.00 4.45
2545 2894 0.965866 TCGGCAGGTAGACAGACAGG 60.966 60.000 0.00 0.00 0.00 4.00
2546 2895 1.107114 ATCGGCAGGTAGACAGACAG 58.893 55.000 0.00 0.00 0.00 3.51
2547 2896 0.817654 CATCGGCAGGTAGACAGACA 59.182 55.000 0.00 0.00 0.00 3.41
2548 2897 1.103803 TCATCGGCAGGTAGACAGAC 58.896 55.000 0.00 0.00 0.00 3.51
2549 2898 2.073252 ATCATCGGCAGGTAGACAGA 57.927 50.000 0.00 0.00 0.00 3.41
2550 2899 4.527509 ATTATCATCGGCAGGTAGACAG 57.472 45.455 0.00 0.00 0.00 3.51
2551 2900 4.955811 AATTATCATCGGCAGGTAGACA 57.044 40.909 0.00 0.00 0.00 3.41
2552 2901 6.293462 GGAAAAATTATCATCGGCAGGTAGAC 60.293 42.308 0.00 0.00 0.00 2.59
2553 2902 5.763204 GGAAAAATTATCATCGGCAGGTAGA 59.237 40.000 0.00 0.00 0.00 2.59
2554 2903 5.765182 AGGAAAAATTATCATCGGCAGGTAG 59.235 40.000 0.00 0.00 0.00 3.18
2603 2964 7.555554 AGTGAGATTGAATGAACCCTGAATTAG 59.444 37.037 0.00 0.00 0.00 1.73
2612 2973 5.649395 TCATTGGAGTGAGATTGAATGAACC 59.351 40.000 0.00 0.00 29.23 3.62
2622 2983 4.780021 AGTACTTGGTCATTGGAGTGAGAT 59.220 41.667 0.00 0.00 0.00 2.75
2648 3009 2.721231 GTGCCGTTGCTGCAAAGA 59.279 55.556 26.08 7.63 41.06 2.52
2660 3021 1.893808 GATGCAGGGTATGGTGCCG 60.894 63.158 0.00 0.00 39.04 5.69
2738 3099 2.169144 ACTGTGCGGATGATCTTGATGA 59.831 45.455 0.00 0.00 0.00 2.92
2779 3177 4.697352 CGAATTTTCAGAGTGGGTTCAGAT 59.303 41.667 0.00 0.00 0.00 2.90
2787 3185 2.807967 TGCAGACGAATTTTCAGAGTGG 59.192 45.455 0.00 0.00 0.00 4.00
3000 3398 2.358615 TCGAACAGCTGCGCCATT 60.359 55.556 15.27 0.00 0.00 3.16
3125 3523 0.961019 GTTCATGGTTGCCTGCTTCA 59.039 50.000 0.00 0.00 0.00 3.02
3126 3524 0.961019 TGTTCATGGTTGCCTGCTTC 59.039 50.000 0.00 0.00 0.00 3.86
3127 3525 0.963962 CTGTTCATGGTTGCCTGCTT 59.036 50.000 0.00 0.00 0.00 3.91
3128 3526 0.178981 ACTGTTCATGGTTGCCTGCT 60.179 50.000 0.00 0.00 0.00 4.24
3129 3527 0.675633 AACTGTTCATGGTTGCCTGC 59.324 50.000 0.00 0.00 0.00 4.85
3130 3528 1.955778 TGAACTGTTCATGGTTGCCTG 59.044 47.619 18.69 0.00 34.08 4.85
3131 3529 2.363306 TGAACTGTTCATGGTTGCCT 57.637 45.000 18.69 0.00 34.08 4.75
3178 3576 8.106247 TGAACACTTTACAAATGGAATCTACC 57.894 34.615 0.00 0.00 0.00 3.18
3206 3604 3.673809 GCGTGTCTACTTACAAACTCTGG 59.326 47.826 0.00 0.00 0.00 3.86
3243 3647 9.909644 TCGATAAAGAATGGACTAGTATTTAGC 57.090 33.333 0.00 0.00 0.00 3.09
3271 3677 7.928706 ACAGGCTGAATATGAACTACTATGTTC 59.071 37.037 23.66 0.00 44.60 3.18
3278 3686 5.053145 CAGGACAGGCTGAATATGAACTAC 58.947 45.833 23.66 0.00 0.00 2.73
3283 3691 2.121948 AGCAGGACAGGCTGAATATGA 58.878 47.619 23.66 0.00 40.80 2.15
3287 3695 1.891150 CAAAAGCAGGACAGGCTGAAT 59.109 47.619 23.66 0.00 41.66 2.57
3419 3827 1.202245 TGTTTGCGAAACTGTCTTGCC 60.202 47.619 11.34 0.00 41.90 4.52
3557 3967 0.034059 AGTCCGCAGAACCAGAGTTG 59.966 55.000 0.00 0.00 35.94 3.16
3632 4056 6.687393 GCCAGGGGATATATGTGTCTATGATG 60.687 46.154 0.00 0.00 0.00 3.07
3633 4057 5.367937 GCCAGGGGATATATGTGTCTATGAT 59.632 44.000 0.00 0.00 0.00 2.45
3634 4058 4.716784 GCCAGGGGATATATGTGTCTATGA 59.283 45.833 0.00 0.00 0.00 2.15
3851 4376 3.314635 CTGGATATCAGTGCTTCCAAAGC 59.685 47.826 4.83 4.74 43.66 3.51
3924 4449 2.456577 AGGTAATGAAATTTGGCGCCT 58.543 42.857 29.70 6.37 37.87 5.52
4018 4543 5.669477 GAACTCCATCTCAGAGCAATAGTT 58.331 41.667 7.42 7.42 34.56 2.24
4057 4582 2.821546 TGCCAATATAGCACACTCGAC 58.178 47.619 0.00 0.00 34.69 4.20


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

AutoCloner maintained by Alex Coulton.