Multiple sequence alignment - TraesCS5B01G154000

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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 TraesCS5B01G154000 chr5B 100.000 7996 0 0 1 7996 283394444 283402439 0.000000e+00 14766.0
1 TraesCS5B01G154000 chr5B 98.460 779 10 1 7220 7996 593225033 593225811 0.000000e+00 1371.0
2 TraesCS5B01G154000 chr5B 98.207 781 10 2 7220 7996 143728179 143727399 0.000000e+00 1362.0
3 TraesCS5B01G154000 chr5B 97.832 784 12 4 7217 7996 670933272 670934054 0.000000e+00 1349.0
4 TraesCS5B01G154000 chr5D 95.721 3926 113 15 3322 7220 250596131 250600028 0.000000e+00 6268.0
5 TraesCS5B01G154000 chr5D 93.477 1855 59 23 446 2263 250587806 250589635 0.000000e+00 2699.0
6 TraesCS5B01G154000 chr5D 97.007 1069 15 3 2257 3324 250594778 250595830 0.000000e+00 1781.0
7 TraesCS5B01G154000 chr5D 86.184 456 31 7 1 424 250585121 250585576 1.570000e-126 464.0
8 TraesCS5B01G154000 chr5D 90.769 65 5 1 4607 4670 250597283 250597347 1.430000e-12 86.1
9 TraesCS5B01G154000 chr5A 89.106 2809 205 36 1 2759 334001782 334004539 0.000000e+00 3398.0
10 TraesCS5B01G154000 chr5A 93.114 2338 128 14 4158 6483 334007354 334009670 0.000000e+00 3395.0
11 TraesCS5B01G154000 chr5A 95.833 744 26 1 6482 7220 334009751 334010494 0.000000e+00 1197.0
12 TraesCS5B01G154000 chr5A 89.498 438 41 5 2876 3311 334004678 334005112 4.220000e-152 549.0
13 TraesCS5B01G154000 chr5A 93.137 102 5 2 1 100 333967653 333967754 1.800000e-31 148.0
14 TraesCS5B01G154000 chr5A 89.231 65 6 1 4607 4670 334007684 334007748 6.650000e-11 80.5
15 TraesCS5B01G154000 chr1B 98.588 779 8 2 7220 7996 323682364 323681587 0.000000e+00 1375.0
16 TraesCS5B01G154000 chr4A 98.203 779 12 1 7220 7996 696047419 696046641 0.000000e+00 1360.0
17 TraesCS5B01G154000 chr4A 93.258 89 6 0 5534 5622 186484180 186484092 1.810000e-26 132.0
18 TraesCS5B01G154000 chr7B 97.946 779 14 1 7220 7996 612985023 612984245 0.000000e+00 1349.0
19 TraesCS5B01G154000 chr7B 98.172 766 12 1 7233 7996 74654746 74655511 0.000000e+00 1336.0
20 TraesCS5B01G154000 chr7B 91.011 89 8 0 5534 5622 190056955 190056867 3.920000e-23 121.0
21 TraesCS5B01G154000 chr7B 91.011 89 8 0 5534 5622 558916912 558916824 3.920000e-23 121.0
22 TraesCS5B01G154000 chr7B 91.011 89 8 0 5534 5622 632806426 632806514 3.920000e-23 121.0
23 TraesCS5B01G154000 chr6B 97.946 779 14 1 7220 7996 30957933 30958711 0.000000e+00 1349.0
24 TraesCS5B01G154000 chr1A 97.078 787 17 4 7213 7996 25549925 25550708 0.000000e+00 1321.0
25 TraesCS5B01G154000 chr3B 91.011 89 8 0 5534 5622 814188151 814188239 3.920000e-23 121.0
26 TraesCS5B01G154000 chrUn 89.888 89 9 0 5534 5622 155140040 155139952 1.820000e-21 115.0
27 TraesCS5B01G154000 chrUn 89.888 89 9 0 5534 5622 155259860 155259772 1.820000e-21 115.0
28 TraesCS5B01G154000 chr2D 96.610 59 1 1 3372 3430 204143022 204143079 6.600000e-16 97.1
29 TraesCS5B01G154000 chr2B 94.915 59 2 1 3372 3430 258158518 258158575 3.070000e-14 91.6


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 TraesCS5B01G154000 chr5B 283394444 283402439 7995 False 14766.0 14766 100.0000 1 7996 1 chr5B.!!$F1 7995
1 TraesCS5B01G154000 chr5B 593225033 593225811 778 False 1371.0 1371 98.4600 7220 7996 1 chr5B.!!$F2 776
2 TraesCS5B01G154000 chr5B 143727399 143728179 780 True 1362.0 1362 98.2070 7220 7996 1 chr5B.!!$R1 776
3 TraesCS5B01G154000 chr5B 670933272 670934054 782 False 1349.0 1349 97.8320 7217 7996 1 chr5B.!!$F3 779
4 TraesCS5B01G154000 chr5D 250594778 250600028 5250 False 2711.7 6268 94.4990 2257 7220 3 chr5D.!!$F2 4963
5 TraesCS5B01G154000 chr5D 250585121 250589635 4514 False 1581.5 2699 89.8305 1 2263 2 chr5D.!!$F1 2262
6 TraesCS5B01G154000 chr5A 334001782 334010494 8712 False 1723.9 3398 91.3564 1 7220 5 chr5A.!!$F2 7219
7 TraesCS5B01G154000 chr1B 323681587 323682364 777 True 1375.0 1375 98.5880 7220 7996 1 chr1B.!!$R1 776
8 TraesCS5B01G154000 chr4A 696046641 696047419 778 True 1360.0 1360 98.2030 7220 7996 1 chr4A.!!$R2 776
9 TraesCS5B01G154000 chr7B 612984245 612985023 778 True 1349.0 1349 97.9460 7220 7996 1 chr7B.!!$R3 776
10 TraesCS5B01G154000 chr7B 74654746 74655511 765 False 1336.0 1336 98.1720 7233 7996 1 chr7B.!!$F1 763
11 TraesCS5B01G154000 chr6B 30957933 30958711 778 False 1349.0 1349 97.9460 7220 7996 1 chr6B.!!$F1 776
12 TraesCS5B01G154000 chr1A 25549925 25550708 783 False 1321.0 1321 97.0780 7213 7996 1 chr1A.!!$F1 783

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
489 2733 1.056660 ACCGTTTGATGGAGTGGTCT 58.943 50.000 0.00 0.00 0.00 3.85 F
1218 3500 0.179163 GTCCAAGCCGCTGTTATTGC 60.179 55.000 0.00 0.00 0.00 3.56 F
1307 3589 0.460987 GGCACAGATTCTCCTCCACG 60.461 60.000 0.00 0.00 0.00 4.94 F
1907 4190 2.936202 TGCAGGGAAATCAGGATAAGC 58.064 47.619 0.00 0.00 0.00 3.09 F
3484 7296 1.741028 TGGAAGTTGATCCCTGGTGA 58.259 50.000 0.00 0.00 38.82 4.02 F
4030 7850 0.315140 GCGCGGACTTTTATCGCTTC 60.315 55.000 8.83 0.00 46.23 3.86 F
4340 8164 0.746063 TGTTGCCTTGCCTTTGTCAG 59.254 50.000 0.00 0.00 0.00 3.51 F
5959 9790 0.250338 GGCAGTGGAAAGACGGTCTT 60.250 55.000 17.38 17.38 38.59 3.01 F
6394 10235 0.817634 CCCTGAGCAACAACCGTCAA 60.818 55.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 3587 0.107410 TGTCACAAGTTTCAGGGCGT 60.107 50.000 0.00 0.0 0.00 5.68 R
3074 5401 1.278127 GGGTAGCTGTAACAAGAGGCA 59.722 52.381 0.00 0.0 0.00 4.75 R
3249 5576 8.086522 GTGACTAGGTATGAAAGAGTGTAACAA 58.913 37.037 0.00 0.0 41.43 2.83 R
3900 7720 0.747644 TGATGGGCATAACAGCGTGG 60.748 55.000 0.00 0.0 34.64 4.94 R
4502 8330 2.169561 GGCTGCTTATATCTAGGAGGCC 59.830 54.545 16.65 0.0 46.37 5.19 R
4899 8727 2.361438 CGGTGTAGTATCTCCACTTCCC 59.639 54.545 0.00 0.0 0.00 3.97 R
6147 9978 2.974698 GTGCCTGACTTGTGCGCT 60.975 61.111 9.73 0.0 32.93 5.92 R
6986 10925 1.345089 TGAAGTGCAGGTTAAGGCGTA 59.655 47.619 0.00 0.0 0.00 4.42 R
7805 11750 2.046023 CCGATGCAGACTGGGCAA 60.046 61.111 4.26 0.0 45.60 4.52 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
69 72 9.403583 ACTCCAAAGAAAAATCTAAAGTACACA 57.596 29.630 0.00 0.00 0.00 3.72
70 73 9.665264 CTCCAAAGAAAAATCTAAAGTACACAC 57.335 33.333 0.00 0.00 0.00 3.82
178 212 1.745087 ACATCACCTAAATGCAAGCCG 59.255 47.619 0.00 0.00 0.00 5.52
199 233 6.017109 AGCCGTATGAATCAAACCACATTATC 60.017 38.462 0.00 0.00 0.00 1.75
207 241 9.993454 TGAATCAAACCACATTATCAAATTTCA 57.007 25.926 0.00 0.00 0.00 2.69
216 250 7.253850 CCACATTATCAAATTTCATCAACTGCG 60.254 37.037 0.00 0.00 0.00 5.18
257 292 6.763715 ATCACATAACCTAGCCCTAAATCA 57.236 37.500 0.00 0.00 0.00 2.57
264 299 5.320488 ACCTAGCCCTAAATCATTAACCC 57.680 43.478 0.00 0.00 0.00 4.11
283 318 2.424601 CCCCTGCACAAATGACATACAG 59.575 50.000 0.00 0.00 0.00 2.74
286 322 4.005650 CCTGCACAAATGACATACAGAGT 58.994 43.478 0.00 0.00 0.00 3.24
326 362 6.567602 ACTGGCTCTAATTCCTAAATCACT 57.432 37.500 0.00 0.00 0.00 3.41
383 419 2.122504 CCTTGGCCAAACCCCCAT 59.877 61.111 20.91 0.00 37.83 4.00
387 423 1.734420 TTGGCCAAACCCCCATCTCA 61.734 55.000 17.98 0.00 37.83 3.27
429 465 5.834204 AGAGGAGCAGATTTACTAACCGTAT 59.166 40.000 0.00 0.00 0.00 3.06
433 469 6.229936 AGCAGATTTACTAACCGTATCCAA 57.770 37.500 0.00 0.00 0.00 3.53
437 473 6.018994 CAGATTTACTAACCGTATCCAAGTGC 60.019 42.308 0.00 0.00 0.00 4.40
444 480 1.482593 CCGTATCCAAGTGCTTCCTCT 59.517 52.381 0.00 0.00 0.00 3.69
489 2733 1.056660 ACCGTTTGATGGAGTGGTCT 58.943 50.000 0.00 0.00 0.00 3.85
603 2847 9.506018 TCAATTGAAGACTAAATCAATGTGAGA 57.494 29.630 5.45 0.00 43.54 3.27
611 2855 8.954350 AGACTAAATCAATGTGAGATCCTTTTG 58.046 33.333 0.00 0.00 0.00 2.44
612 2856 7.542025 ACTAAATCAATGTGAGATCCTTTTGC 58.458 34.615 0.00 0.00 0.00 3.68
613 2857 5.988310 AATCAATGTGAGATCCTTTTGCA 57.012 34.783 0.00 0.00 0.00 4.08
614 2858 5.578005 ATCAATGTGAGATCCTTTTGCAG 57.422 39.130 0.00 0.00 0.00 4.41
617 2861 5.182570 TCAATGTGAGATCCTTTTGCAGAAG 59.817 40.000 9.98 9.98 0.00 2.85
618 2862 2.816087 TGTGAGATCCTTTTGCAGAAGC 59.184 45.455 11.42 0.00 42.57 3.86
620 2864 2.040813 TGAGATCCTTTTGCAGAAGCCT 59.959 45.455 11.42 7.76 41.13 4.58
621 2865 3.264193 TGAGATCCTTTTGCAGAAGCCTA 59.736 43.478 11.42 0.02 41.13 3.93
622 2866 4.080129 TGAGATCCTTTTGCAGAAGCCTAT 60.080 41.667 11.42 4.73 41.13 2.57
623 2867 4.205587 AGATCCTTTTGCAGAAGCCTATG 58.794 43.478 11.42 0.00 41.13 2.23
624 2868 3.439857 TCCTTTTGCAGAAGCCTATGT 57.560 42.857 11.42 0.00 41.13 2.29
625 2869 4.568072 TCCTTTTGCAGAAGCCTATGTA 57.432 40.909 11.42 0.00 41.13 2.29
626 2870 4.917385 TCCTTTTGCAGAAGCCTATGTAA 58.083 39.130 11.42 0.00 41.13 2.41
627 2871 5.321102 TCCTTTTGCAGAAGCCTATGTAAA 58.679 37.500 11.42 0.00 41.13 2.01
628 2872 5.951747 TCCTTTTGCAGAAGCCTATGTAAAT 59.048 36.000 11.42 0.00 41.13 1.40
629 2873 6.038356 CCTTTTGCAGAAGCCTATGTAAATG 58.962 40.000 11.42 0.00 41.13 2.32
630 2874 4.637483 TTGCAGAAGCCTATGTAAATGC 57.363 40.909 0.00 0.00 41.13 3.56
631 2875 2.951642 TGCAGAAGCCTATGTAAATGCC 59.048 45.455 0.00 0.00 41.13 4.40
632 2876 2.294512 GCAGAAGCCTATGTAAATGCCC 59.705 50.000 0.00 0.00 33.58 5.36
633 2877 3.825328 CAGAAGCCTATGTAAATGCCCT 58.175 45.455 0.00 0.00 0.00 5.19
634 2878 4.210331 CAGAAGCCTATGTAAATGCCCTT 58.790 43.478 0.00 0.00 0.00 3.95
635 2879 4.646492 CAGAAGCCTATGTAAATGCCCTTT 59.354 41.667 0.00 0.00 0.00 3.11
636 2880 5.127682 CAGAAGCCTATGTAAATGCCCTTTT 59.872 40.000 0.00 0.00 0.00 2.27
637 2881 5.721480 AGAAGCCTATGTAAATGCCCTTTTT 59.279 36.000 0.00 0.00 0.00 1.94
683 2927 4.228567 TCCACGTCAGCGCCAACA 62.229 61.111 2.29 0.00 42.83 3.33
1090 3372 4.595629 GCGCGCGATTTGATTCAT 57.404 50.000 37.18 0.00 0.00 2.57
1207 3489 2.296190 CAGGTTTTACTTGGTCCAAGCC 59.704 50.000 28.34 20.76 44.43 4.35
1218 3500 0.179163 GTCCAAGCCGCTGTTATTGC 60.179 55.000 0.00 0.00 0.00 3.56
1231 3513 1.006086 TTATTGCGCGTCCATCTGTG 58.994 50.000 8.43 0.00 0.00 3.66
1284 3566 9.547753 TCATTGGTAGTAATTCTAGATTTCTGC 57.452 33.333 3.20 5.26 0.00 4.26
1305 3587 1.361204 TTGGCACAGATTCTCCTCCA 58.639 50.000 0.00 0.00 42.39 3.86
1307 3589 0.460987 GGCACAGATTCTCCTCCACG 60.461 60.000 0.00 0.00 0.00 4.94
1349 3631 5.004448 AGAGAATATCTATCAAGACCGCGA 58.996 41.667 8.23 0.00 36.10 5.87
1502 3785 5.389935 CGGTAGTTCTTTTGCAGATCTTCAC 60.390 44.000 0.00 0.00 34.05 3.18
1647 3930 2.957402 ATCGCATCCCCATTGTGTAT 57.043 45.000 0.00 0.00 0.00 2.29
1708 3991 5.415077 AGTTGCAGAGAATTCTCATGGAAAG 59.585 40.000 31.79 15.58 45.21 2.62
1774 4057 4.754322 TGTTTTCTCCTGCAAAAACTTCC 58.246 39.130 19.74 1.18 42.87 3.46
1907 4190 2.936202 TGCAGGGAAATCAGGATAAGC 58.064 47.619 0.00 0.00 0.00 3.09
2270 4559 5.049398 TGCCGTGTATATGGTTTTTGAAC 57.951 39.130 0.00 0.00 35.28 3.18
3058 5385 6.430925 TCTTGTTTGCAGTAATGAAGCATACT 59.569 34.615 0.00 0.00 39.74 2.12
3074 5401 6.840780 AGCATACTTATTTCTTTTGCAGGT 57.159 33.333 0.00 0.00 0.00 4.00
3347 7157 2.497675 ACAAGAGACGGTCATGCTACAT 59.502 45.455 11.27 0.00 0.00 2.29
3354 7164 4.464244 AGACGGTCATGCTACATATGCTAT 59.536 41.667 11.27 0.00 0.00 2.97
3484 7296 1.741028 TGGAAGTTGATCCCTGGTGA 58.259 50.000 0.00 0.00 38.82 4.02
3608 7420 2.163412 TGATTCTAATGGTGCCGTTTGC 59.837 45.455 0.58 0.00 41.77 3.68
3715 7535 1.843421 TTGGGTCCCACCAACTGAG 59.157 57.895 11.24 0.00 45.19 3.35
3719 7539 3.256960 TCCCACCAACTGAGGGCC 61.257 66.667 0.00 0.00 42.52 5.80
3900 7720 4.090057 GCTCGCCTTGGCGTGAAC 62.090 66.667 31.42 17.46 34.52 3.18
3958 7778 1.668294 CGGGTTGTCTCAGCTCTGT 59.332 57.895 0.00 0.00 0.00 3.41
4030 7850 0.315140 GCGCGGACTTTTATCGCTTC 60.315 55.000 8.83 0.00 46.23 3.86
4040 7860 6.315393 GGACTTTTATCGCTTCCTGATTGTAA 59.685 38.462 0.00 0.00 0.00 2.41
4094 7914 2.290464 AGCTCATGAGATTGCTTCTGC 58.710 47.619 27.04 7.52 33.74 4.26
4095 7915 1.334243 GCTCATGAGATTGCTTCTGCC 59.666 52.381 27.04 0.00 38.71 4.85
4160 7980 2.233271 CCAGATTGCTCCTGTTGTTGT 58.767 47.619 0.00 0.00 0.00 3.32
4340 8164 0.746063 TGTTGCCTTGCCTTTGTCAG 59.254 50.000 0.00 0.00 0.00 3.51
4502 8330 9.166173 TCAAGGAAATACATCATCACTTGTAAG 57.834 33.333 0.00 0.00 36.42 2.34
4556 8384 4.566426 AAAGCAGACTCTATCAGGCTTT 57.434 40.909 0.00 0.00 36.97 3.51
4660 8488 6.706295 AGATATAAGCAGCCTGAGGATTTAC 58.294 40.000 0.65 0.00 0.00 2.01
4793 8621 3.810310 ACCTGTTCTAGAGCATGCTAC 57.190 47.619 22.74 15.43 0.00 3.58
4899 8727 1.016130 AGGTTGATTGCTCGTCTGCG 61.016 55.000 0.00 0.00 39.92 5.18
5000 8828 5.674569 GCGTTGCATCACATGTAGAAGAAAT 60.675 40.000 0.00 0.00 0.00 2.17
5198 9026 7.756722 CACCCTTAATGATCTCAATTGTCAAAC 59.243 37.037 5.13 0.00 0.00 2.93
5560 9388 2.092429 TCAGATAGTCCACCAATTGGCC 60.092 50.000 24.79 9.90 46.47 5.36
5737 9565 2.192861 CGGCCTGCTTTGTTGGACA 61.193 57.895 0.00 0.00 0.00 4.02
5748 9576 4.627058 CTTTGTTGGACAAACCCAATACC 58.373 43.478 2.34 0.00 46.69 2.73
5959 9790 0.250338 GGCAGTGGAAAGACGGTCTT 60.250 55.000 17.38 17.38 38.59 3.01
6003 9834 5.011431 TGCTGAAGACGATATGGATCTTGAT 59.989 40.000 0.00 0.00 32.83 2.57
6006 9837 6.612306 TGAAGACGATATGGATCTTGATACG 58.388 40.000 0.00 0.00 32.83 3.06
6027 9858 4.400884 ACGAATGAGTTGTCAGCTCTAGAT 59.599 41.667 16.53 0.94 35.66 1.98
6028 9859 4.975502 CGAATGAGTTGTCAGCTCTAGATC 59.024 45.833 16.53 9.00 35.66 2.75
6104 9935 0.931662 GGCTTCAATTGCATAGCGCG 60.932 55.000 0.00 0.00 46.97 6.86
6115 9946 1.326245 GCATAGCGCGTTGATTGTGTA 59.674 47.619 15.49 0.00 0.00 2.90
6117 9948 3.787826 CATAGCGCGTTGATTGTGTATC 58.212 45.455 8.43 0.00 0.00 2.24
6147 9978 3.446873 TCTTTTGCAGAAAGAACAAGGCA 59.553 39.130 16.60 0.00 33.72 4.75
6163 9994 2.974148 CAGCGCACAAGTCAGGCA 60.974 61.111 11.47 0.00 0.00 4.75
6271 10102 3.627577 CAGTTTACTTGAACACCACTGCT 59.372 43.478 0.00 0.00 31.94 4.24
6340 10181 7.861872 TGAATTTTGTGTACATGTGATGTTCTG 59.138 33.333 9.11 0.00 41.63 3.02
6371 10212 1.588239 AATGTGCCAGATCTCTCCCA 58.412 50.000 0.00 0.00 0.00 4.37
6372 10213 1.129917 ATGTGCCAGATCTCTCCCAG 58.870 55.000 0.00 0.00 0.00 4.45
6376 10217 2.146061 CCAGATCTCTCCCAGCCCC 61.146 68.421 0.00 0.00 0.00 5.80
6385 10226 4.748144 CCCAGCCCCCTGAGCAAC 62.748 72.222 0.00 0.00 41.77 4.17
6386 10227 3.970410 CCAGCCCCCTGAGCAACA 61.970 66.667 0.00 0.00 41.77 3.33
6387 10228 2.115910 CAGCCCCCTGAGCAACAA 59.884 61.111 0.00 0.00 41.77 2.83
6388 10229 2.116125 AGCCCCCTGAGCAACAAC 59.884 61.111 0.00 0.00 0.00 3.32
6389 10230 2.991540 GCCCCCTGAGCAACAACC 60.992 66.667 0.00 0.00 0.00 3.77
6390 10231 2.672996 CCCCCTGAGCAACAACCG 60.673 66.667 0.00 0.00 0.00 4.44
6391 10232 2.113139 CCCCTGAGCAACAACCGT 59.887 61.111 0.00 0.00 0.00 4.83
6392 10233 1.966451 CCCCTGAGCAACAACCGTC 60.966 63.158 0.00 0.00 0.00 4.79
6393 10234 1.227823 CCCTGAGCAACAACCGTCA 60.228 57.895 0.00 0.00 0.00 4.35
6394 10235 0.817634 CCCTGAGCAACAACCGTCAA 60.818 55.000 0.00 0.00 0.00 3.18
6395 10236 1.238439 CCTGAGCAACAACCGTCAAT 58.762 50.000 0.00 0.00 0.00 2.57
6509 10432 5.088739 GGCAGTTACAAGTTTCATCGAATG 58.911 41.667 0.00 0.00 0.00 2.67
6513 10436 8.600625 GCAGTTACAAGTTTCATCGAATGTATA 58.399 33.333 0.00 0.00 0.00 1.47
6612 10538 3.950395 GGAGCTGTGCAAAATTCTCCTAT 59.050 43.478 10.66 0.00 37.65 2.57
6634 10560 2.576648 GGACAAATCTACCCCAGAACCT 59.423 50.000 0.00 0.00 36.67 3.50
6700 10634 3.355378 TCCCTAAACATGCATCAAGTGG 58.645 45.455 0.00 0.00 0.00 4.00
6716 10650 4.947388 TCAAGTGGCGCTTTAATATTTCCT 59.053 37.500 11.25 0.00 34.69 3.36
6746 10680 4.928661 AGCTTTAGAAAGTGTACATGCG 57.071 40.909 0.00 0.00 38.28 4.73
6789 10723 7.539712 TGCAGTGCTTTGTATAGTTCTTATC 57.460 36.000 17.60 0.00 0.00 1.75
6794 10728 9.593134 AGTGCTTTGTATAGTTCTTATCAGAAG 57.407 33.333 0.00 0.00 39.86 2.85
6825 10764 7.793927 TCTTTTCTTTTCTTTCTGAGGAGAC 57.206 36.000 0.00 0.00 0.00 3.36
6846 10785 1.549203 AGCAAATGCACTGGTTAGGG 58.451 50.000 8.28 0.00 45.16 3.53
6938 10877 3.715628 AAACGCAAAGCTCAAGATGTT 57.284 38.095 0.00 0.00 0.00 2.71
6986 10925 3.120199 CCAAAAGCGTTCGAACATCTGAT 60.120 43.478 26.71 7.45 0.00 2.90
7633 11578 1.263356 CCGTGGGACTCCAAGTTCTA 58.737 55.000 0.00 0.00 46.04 2.10
7805 11750 1.945387 CGCCTATCATCAACACAGCT 58.055 50.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.729281 TTATTTAGGTGATAAGGTCGACTTTTT 57.271 29.630 18.63 10.70 40.64 1.94
79 82 8.225107 CGTAAAGTTCGAAATTTAGGTGATTCA 58.775 33.333 28.74 10.23 32.77 2.57
126 146 7.195374 TGTAGTAATGTTCAGCCTTATTCCT 57.805 36.000 0.00 0.00 0.00 3.36
199 233 6.939551 AAAGATCGCAGTTGATGAAATTTG 57.060 33.333 0.00 0.00 0.00 2.32
207 241 6.528423 GTCGCTATATAAAGATCGCAGTTGAT 59.472 38.462 0.00 0.00 0.00 2.57
257 292 3.505386 TGTCATTTGTGCAGGGGTTAAT 58.495 40.909 0.00 0.00 0.00 1.40
264 299 4.005650 ACTCTGTATGTCATTTGTGCAGG 58.994 43.478 0.00 0.00 0.00 4.85
301 337 6.825721 AGTGATTTAGGAATTAGAGCCAGTTG 59.174 38.462 0.00 0.00 0.00 3.16
302 338 6.825721 CAGTGATTTAGGAATTAGAGCCAGTT 59.174 38.462 0.00 0.00 0.00 3.16
305 341 6.349300 GTCAGTGATTTAGGAATTAGAGCCA 58.651 40.000 0.00 0.00 0.00 4.75
326 362 3.145286 TGATCAGCAATTTTGGTCGTCA 58.855 40.909 0.00 0.00 36.65 4.35
359 395 1.479757 GGGTTTGGCCAAGGTCACTTA 60.480 52.381 19.48 0.00 39.65 2.24
383 419 6.054941 TCTTGTGTTTTAGATGCACTTGAGA 58.945 36.000 0.00 0.00 34.52 3.27
387 423 5.376625 TCCTCTTGTGTTTTAGATGCACTT 58.623 37.500 0.00 0.00 34.52 3.16
429 465 1.073923 GGGAAAGAGGAAGCACTTGGA 59.926 52.381 0.00 0.00 0.00 3.53
433 469 2.376518 TCAATGGGAAAGAGGAAGCACT 59.623 45.455 0.00 0.00 0.00 4.40
437 473 5.320549 CATTGTCAATGGGAAAGAGGAAG 57.679 43.478 16.53 0.00 35.23 3.46
485 2729 1.086634 GTGATCTTGGCGAGCAGACC 61.087 60.000 0.00 0.00 38.99 3.85
489 2733 1.375908 GTGGTGATCTTGGCGAGCA 60.376 57.895 0.00 0.00 35.28 4.26
528 2772 1.137675 CTCTCTCATCATGGCGGTGAA 59.862 52.381 0.00 0.00 0.00 3.18
603 2847 3.973425 ACATAGGCTTCTGCAAAAGGAT 58.027 40.909 1.19 0.00 41.91 3.24
611 2855 2.294512 GGGCATTTACATAGGCTTCTGC 59.705 50.000 0.00 0.00 38.76 4.26
612 2856 3.825328 AGGGCATTTACATAGGCTTCTG 58.175 45.455 0.00 0.00 0.00 3.02
613 2857 4.526438 AAGGGCATTTACATAGGCTTCT 57.474 40.909 0.00 0.00 0.00 2.85
614 2858 5.598416 AAAAGGGCATTTACATAGGCTTC 57.402 39.130 0.00 0.00 0.00 3.86
635 2879 4.299978 GGCGTTTACATGGTTGCTAAAAA 58.700 39.130 0.00 0.00 0.00 1.94
636 2880 3.305471 GGGCGTTTACATGGTTGCTAAAA 60.305 43.478 0.00 0.00 0.00 1.52
637 2881 2.229302 GGGCGTTTACATGGTTGCTAAA 59.771 45.455 0.00 0.00 0.00 1.85
638 2882 1.813786 GGGCGTTTACATGGTTGCTAA 59.186 47.619 0.00 0.00 0.00 3.09
639 2883 1.003812 AGGGCGTTTACATGGTTGCTA 59.996 47.619 0.00 0.00 0.00 3.49
640 2884 0.251165 AGGGCGTTTACATGGTTGCT 60.251 50.000 0.00 0.00 0.00 3.91
641 2885 0.170339 GAGGGCGTTTACATGGTTGC 59.830 55.000 0.00 0.00 0.00 4.17
642 2886 0.808755 GGAGGGCGTTTACATGGTTG 59.191 55.000 0.00 0.00 0.00 3.77
643 2887 0.696501 AGGAGGGCGTTTACATGGTT 59.303 50.000 0.00 0.00 0.00 3.67
644 2888 0.696501 AAGGAGGGCGTTTACATGGT 59.303 50.000 0.00 0.00 0.00 3.55
645 2889 1.472480 CAAAGGAGGGCGTTTACATGG 59.528 52.381 0.00 0.00 31.46 3.66
646 2890 2.159382 ACAAAGGAGGGCGTTTACATG 58.841 47.619 0.00 0.00 31.46 3.21
683 2927 3.997021 CGAGCGGGATAAAAATCTGCTAT 59.003 43.478 0.00 0.00 34.29 2.97
709 2953 4.470664 AGGAGGCCATAAAATTGCAAATGA 59.529 37.500 5.01 0.00 0.00 2.57
1284 3566 2.290514 TGGAGGAGAATCTGTGCCAAAG 60.291 50.000 0.00 0.00 33.73 2.77
1305 3587 0.107410 TGTCACAAGTTTCAGGGCGT 60.107 50.000 0.00 0.00 0.00 5.68
1307 3589 2.687935 TCTTTGTCACAAGTTTCAGGGC 59.312 45.455 0.00 0.00 0.00 5.19
1349 3631 0.744414 CGGGCAATCGGAGACAATGT 60.744 55.000 0.00 0.00 42.51 2.71
1540 3823 4.947388 TCCATGTTATCTAAAACACCTGCC 59.053 41.667 0.00 0.00 41.89 4.85
1647 3930 1.067295 ACTGCCAGATCTCCCAAACA 58.933 50.000 0.00 0.00 0.00 2.83
1708 3991 3.722082 CGCTTCGATACTTCACAAGCAAC 60.722 47.826 0.00 0.00 37.30 4.17
1774 4057 3.567576 ACTCTCTGTTCATGACACTCG 57.432 47.619 0.00 0.00 33.82 4.18
1907 4190 2.905959 TGAATGCTTCGTGCTGATTG 57.094 45.000 5.00 0.00 43.37 2.67
2251 4540 5.506832 GCTTCGTTCAAAAACCATATACACG 59.493 40.000 0.00 0.00 31.27 4.49
2270 4559 4.278678 AGTTCACAAAAACTCAGCTTCG 57.721 40.909 0.00 0.00 34.37 3.79
2815 5105 8.808529 CCTCAAATGAGTAAACTAATGTAGTCG 58.191 37.037 9.43 0.00 40.48 4.18
2883 5209 5.957798 TGCTATTTTTCTCTTGCAAGGATG 58.042 37.500 25.73 15.83 0.00 3.51
2884 5210 6.606395 AGATGCTATTTTTCTCTTGCAAGGAT 59.394 34.615 25.73 12.41 34.07 3.24
2885 5211 5.948162 AGATGCTATTTTTCTCTTGCAAGGA 59.052 36.000 25.73 18.20 34.07 3.36
2886 5212 6.205101 AGATGCTATTTTTCTCTTGCAAGG 57.795 37.500 25.73 16.25 34.07 3.61
2887 5213 8.121708 GTCTAGATGCTATTTTTCTCTTGCAAG 58.878 37.037 20.81 20.81 34.07 4.01
3058 5385 4.151883 AGAGGCACCTGCAAAAGAAATAA 58.848 39.130 0.00 0.00 44.36 1.40
3074 5401 1.278127 GGGTAGCTGTAACAAGAGGCA 59.722 52.381 0.00 0.00 0.00 4.75
3248 5575 8.304596 TGACTAGGTATGAAAGAGTGTAACAAG 58.695 37.037 0.00 0.00 41.43 3.16
3249 5576 8.086522 GTGACTAGGTATGAAAGAGTGTAACAA 58.913 37.037 0.00 0.00 41.43 2.83
3484 7296 4.643387 GAGCGCCACCAACCCACT 62.643 66.667 2.29 0.00 0.00 4.00
3608 7420 4.214971 CCTTTCACATTCTCACAGTTGGAG 59.785 45.833 0.00 0.00 0.00 3.86
3719 7539 1.377202 CCACATTGGTCCTCACCCG 60.377 63.158 0.00 0.00 42.99 5.28
3729 7549 1.234615 AAACGAGCCGTCCACATTGG 61.235 55.000 0.69 0.00 39.99 3.16
3823 7643 2.624316 TGTCATACCTCAACGACGTC 57.376 50.000 5.18 5.18 0.00 4.34
3900 7720 0.747644 TGATGGGCATAACAGCGTGG 60.748 55.000 0.00 0.00 34.64 4.94
3958 7778 3.706594 GACATGTCCTGACCTCCATTCTA 59.293 47.826 15.31 0.00 0.00 2.10
4030 7850 7.337689 TCTGATCAGGACAAAATTACAATCAGG 59.662 37.037 22.42 0.00 38.59 3.86
4040 7860 6.955364 TGATCTCTTCTGATCAGGACAAAAT 58.045 36.000 22.42 9.49 45.29 1.82
4094 7914 0.611062 TCCAGTACCGGACAGACAGG 60.611 60.000 9.46 7.05 39.69 4.00
4095 7915 0.811915 CTCCAGTACCGGACAGACAG 59.188 60.000 9.46 0.00 0.00 3.51
4160 7980 5.818678 AACAGGGTGAATACAGTCTGTAA 57.181 39.130 16.50 0.00 38.52 2.41
4358 8182 3.904136 AAACACAAAAGAGCCATCTCG 57.096 42.857 0.00 0.00 44.02 4.04
4502 8330 2.169561 GGCTGCTTATATCTAGGAGGCC 59.830 54.545 16.65 0.00 46.37 5.19
4556 8384 2.749076 GCAGTATCACCATTCAGCACAA 59.251 45.455 0.00 0.00 0.00 3.33
4660 8488 3.248602 GGTGTTAGACTGTGTCTGCTTTG 59.751 47.826 10.14 0.00 43.30 2.77
4793 8621 3.503748 GGATTCTTTCCCAGAACACACAG 59.496 47.826 0.00 0.00 44.70 3.66
4899 8727 2.361438 CGGTGTAGTATCTCCACTTCCC 59.639 54.545 0.00 0.00 0.00 3.97
5000 8828 3.010027 TCCAGTTCTGTTGATAATGCCCA 59.990 43.478 0.00 0.00 0.00 5.36
5198 9026 3.062763 CAAGCACTACTGTCTGACTTGG 58.937 50.000 9.51 0.98 31.63 3.61
5560 9388 7.332926 ACACTCTATTAACAGCTGAAGTTCATG 59.667 37.037 23.35 5.47 0.00 3.07
5737 9565 6.003950 CCATATCATCTTCGGTATTGGGTTT 58.996 40.000 0.00 0.00 0.00 3.27
5748 9576 6.685657 TGAGTCAAGATCCATATCATCTTCG 58.314 40.000 0.00 2.36 38.33 3.79
6003 9834 4.941873 TCTAGAGCTGACAACTCATTCGTA 59.058 41.667 8.51 0.00 36.58 3.43
6006 9837 5.900425 TGATCTAGAGCTGACAACTCATTC 58.100 41.667 9.79 0.94 36.58 2.67
6054 9885 8.311650 ACTTTATGCATTCGATATACTTGGTC 57.688 34.615 3.54 0.00 0.00 4.02
6115 9946 7.672983 TCTTTCTGCAAAAGATAAGAACGAT 57.327 32.000 15.57 0.00 33.18 3.73
6117 9948 7.540362 GTTCTTTCTGCAAAAGATAAGAACG 57.460 36.000 18.44 2.75 43.43 3.95
6147 9978 2.974698 GTGCCTGACTTGTGCGCT 60.975 61.111 9.73 0.00 32.93 5.92
6324 10165 6.980978 AGCTGTATACAGAACATCACATGTAC 59.019 38.462 32.39 12.01 46.59 2.90
6325 10166 7.112452 AGCTGTATACAGAACATCACATGTA 57.888 36.000 32.39 0.00 46.59 2.29
6340 10181 7.551585 AGATCTGGCACATTATAGCTGTATAC 58.448 38.462 0.00 0.00 38.20 1.47
6371 10212 2.116125 GTTGTTGCTCAGGGGGCT 59.884 61.111 0.00 0.00 0.00 5.19
6372 10213 2.991540 GGTTGTTGCTCAGGGGGC 60.992 66.667 0.00 0.00 0.00 5.80
6376 10217 1.238439 ATTGACGGTTGTTGCTCAGG 58.762 50.000 0.00 0.00 0.00 3.86
6383 10224 6.827586 ATTATGTTGGTATTGACGGTTGTT 57.172 33.333 0.00 0.00 0.00 2.83
6384 10225 6.657541 AGAATTATGTTGGTATTGACGGTTGT 59.342 34.615 0.00 0.00 0.00 3.32
6385 10226 7.083875 AGAATTATGTTGGTATTGACGGTTG 57.916 36.000 0.00 0.00 0.00 3.77
6386 10227 7.696992 AAGAATTATGTTGGTATTGACGGTT 57.303 32.000 0.00 0.00 0.00 4.44
6387 10228 7.696992 AAAGAATTATGTTGGTATTGACGGT 57.303 32.000 0.00 0.00 0.00 4.83
6388 10229 8.889717 ACTAAAGAATTATGTTGGTATTGACGG 58.110 33.333 0.00 0.00 0.00 4.79
6445 10286 8.951243 CAGATGCTTGATCAGATTCATCATAAT 58.049 33.333 20.48 6.71 34.42 1.28
6513 10436 9.705290 GGTTAAAACATCATGGTGAAAATAGTT 57.295 29.630 14.29 0.00 0.00 2.24
6524 10447 3.128589 CCCGTCAGGTTAAAACATCATGG 59.871 47.826 0.00 0.00 35.12 3.66
6536 10459 6.184789 ATGTATTTCATTTACCCGTCAGGTT 58.815 36.000 0.00 0.00 41.12 3.50
6612 10538 2.307686 GGTTCTGGGGTAGATTTGTCCA 59.692 50.000 0.00 0.00 34.80 4.02
6700 10634 6.862711 AGGAGTAAGGAAATATTAAAGCGC 57.137 37.500 0.00 0.00 0.00 5.92
6716 10650 8.863086 TGTACACTTTCTAAAGCTAAGGAGTAA 58.137 33.333 2.37 0.00 39.63 2.24
6734 10668 6.593770 TGTAAAGATTCATCGCATGTACACTT 59.406 34.615 0.00 0.00 0.00 3.16
6789 10723 9.591792 AAAGAAAAGAAAAGAATGGAACTTCTG 57.408 29.630 0.00 0.00 35.67 3.02
6794 10728 9.242477 CTCAGAAAGAAAAGAAAAGAATGGAAC 57.758 33.333 0.00 0.00 0.00 3.62
6825 10764 2.353011 CCCTAACCAGTGCATTTGCTTG 60.353 50.000 3.94 2.86 42.66 4.01
6893 10832 6.160576 ACCTACAAAGACACATGCAAAATT 57.839 33.333 0.00 0.00 0.00 1.82
6986 10925 1.345089 TGAAGTGCAGGTTAAGGCGTA 59.655 47.619 0.00 0.00 0.00 4.42
7200 11140 2.126734 GCTTGTGGCGTGTGATGC 60.127 61.111 0.00 0.00 0.00 3.91
7633 11578 5.453903 CCATTTGGATAGACTCGGTTCTCAT 60.454 44.000 0.00 0.00 37.39 2.90
7688 11633 2.866085 ATCAAGCACCGAGGCAGAGC 62.866 60.000 1.23 0.00 35.83 4.09
7805 11750 2.046023 CCGATGCAGACTGGGCAA 60.046 61.111 4.26 0.00 45.60 4.52


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

AutoCloner maintained by Alex Coulton.