Multiple sequence alignment - TraesCS4D01G190300

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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 TraesCS4D01G190300 chr4D 100.000 7607 0 0 1 7607 333067355 333074961 0.000000e+00 14048.0
1 TraesCS4D01G190300 chr4A 95.414 5648 180 18 2015 7607 140283970 140278347 0.000000e+00 8922.0
2 TraesCS4D01G190300 chr4A 88.932 1301 76 24 759 2015 140285303 140284027 0.000000e+00 1543.0
3 TraesCS4D01G190300 chr4A 90.795 717 34 14 3 701 140285998 140285296 0.000000e+00 929.0
4 TraesCS4D01G190300 chr4B 94.553 4112 147 16 2015 6102 411531342 411535400 0.000000e+00 6281.0
5 TraesCS4D01G190300 chr4B 87.113 2033 101 61 3 1971 411526698 411528633 0.000000e+00 2154.0
6 TraesCS4D01G190300 chr4B 95.248 968 21 2 6099 7041 411535502 411536469 0.000000e+00 1509.0
7 TraesCS4D01G190300 chr4B 94.231 572 33 0 7036 7607 411541501 411542072 0.000000e+00 874.0
8 TraesCS4D01G190300 chr4B 81.858 689 112 9 6929 7605 613351844 613351157 1.110000e-157 568.0
9 TraesCS4D01G190300 chr4B 98.077 52 1 0 1964 2015 411531234 411531285 2.920000e-14 91.6
10 TraesCS4D01G190300 chr7B 82.353 680 111 8 6929 7605 616404153 616403480 3.960000e-162 582.0
11 TraesCS4D01G190300 chr7B 84.651 215 26 4 5993 6206 149352757 149352549 2.780000e-49 207.0
12 TraesCS4D01G190300 chr7D 78.947 665 130 8 6947 7607 448689916 448689258 1.950000e-120 444.0
13 TraesCS4D01G190300 chr3D 82.514 183 22 3 6032 6206 309674506 309674686 1.320000e-32 152.0
14 TraesCS4D01G190300 chr5D 79.381 194 26 7 6027 6206 269731792 269731599 2.880000e-24 124.0


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 TraesCS4D01G190300 chr4D 333067355 333074961 7606 False 14048.0 14048 100.000000 1 7607 1 chr4D.!!$F1 7606
1 TraesCS4D01G190300 chr4A 140278347 140285998 7651 True 3798.0 8922 91.713667 3 7607 3 chr4A.!!$R1 7604
2 TraesCS4D01G190300 chr4B 411526698 411536469 9771 False 2508.9 6281 93.747750 3 7041 4 chr4B.!!$F2 7038
3 TraesCS4D01G190300 chr4B 411541501 411542072 571 False 874.0 874 94.231000 7036 7607 1 chr4B.!!$F1 571
4 TraesCS4D01G190300 chr4B 613351157 613351844 687 True 568.0 568 81.858000 6929 7605 1 chr4B.!!$R1 676
5 TraesCS4D01G190300 chr7B 616403480 616404153 673 True 582.0 582 82.353000 6929 7605 1 chr7B.!!$R2 676
6 TraesCS4D01G190300 chr7D 448689258 448689916 658 True 444.0 444 78.947000 6947 7607 1 chr7D.!!$R1 660

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
662 682 0.036765 AACACCGCAATTAGCTCGGA 60.037 50.0 16.85 0.00 45.53 4.55 F
664 684 0.179111 CACCGCAATTAGCTCGGAGA 60.179 55.0 16.85 0.00 45.53 3.71 F
665 685 0.535335 ACCGCAATTAGCTCGGAGAA 59.465 50.0 16.85 0.00 45.53 2.87 F
705 726 0.689412 CTCCCTCCCCTGAGACTTCC 60.689 65.0 0.00 0.00 41.42 3.46 F
995 1072 0.749454 CGGGAGGGGCAATCAAGAAG 60.749 60.0 0.00 0.00 0.00 2.85 F
2112 4938 0.753262 ACGGGCTGTATGATGAGGTC 59.247 55.0 0.00 0.00 0.00 3.85 F
3616 6443 0.601311 GCAAACAGAGACGAGGCTGT 60.601 55.0 0.00 0.00 46.59 4.40 F
3941 6768 0.882042 CAGCGAGCAAGAGGTGTGTT 60.882 55.0 0.00 0.00 0.00 3.32 F
4579 7424 0.040157 TGCATTTGTGAAGAGCGTGC 60.040 50.0 0.00 0.00 0.00 5.34 F
6383 9372 0.041312 CGGTTGTTGCAAAGAGACCG 60.041 55.0 21.63 21.63 37.40 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2614 5440 0.379669 GCATTCTGGAACATGCGGAG 59.620 55.000 0.00 0.00 38.20 4.63 R
2930 5756 1.134438 GGGGGATGGGGATGTACCTC 61.134 65.000 0.00 0.00 40.19 3.85 R
2938 5764 1.275297 TGTTCTTATGGGGGATGGGGA 60.275 52.381 0.00 0.00 0.00 4.81 R
3059 5886 1.361668 CCTCATCCAACGCTTCACCG 61.362 60.000 0.00 0.00 0.00 4.94 R
3125 5952 1.540363 GGTCTGAAGCTTCGGAACACA 60.540 52.381 37.41 17.08 46.98 3.72 R
3635 6462 0.317160 CCTCCGTTACACAGACAGCA 59.683 55.000 0.00 0.00 0.00 4.41 R
4579 7424 0.602106 ATCAGCATCTTCCGCATCCG 60.602 55.000 0.00 0.00 0.00 4.18 R
4810 7658 0.878523 TTCCACGACTGTTTCCAGCG 60.879 55.000 0.00 0.00 42.81 5.18 R
6422 9411 1.210204 TGGCCCTCTCAAGAATGGCT 61.210 55.000 15.82 0.00 40.16 4.75 R
7195 10211 0.108424 GCTGCGAGAACAGGACAGAT 60.108 55.000 0.00 0.00 38.16 2.90 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
119 120 0.684535 GTGGGGTTGGGGAATTTGTG 59.315 55.000 0.00 0.00 0.00 3.33
194 195 1.630244 GCCTACTGCGCTTGTGAGTG 61.630 60.000 9.73 0.00 36.46 3.51
282 286 1.156736 GACCGTTGTCTGGTTGGATG 58.843 55.000 0.00 0.00 40.63 3.51
283 287 0.889186 ACCGTTGTCTGGTTGGATGC 60.889 55.000 0.00 0.00 35.82 3.91
305 309 4.503991 GCGGATGTCCTTCCTGATTCTTAT 60.504 45.833 0.00 0.00 33.30 1.73
317 321 9.359653 CTTCCTGATTCTTATGGGATTAAACAT 57.640 33.333 0.00 0.00 0.00 2.71
365 371 1.153745 CACGGAGTAGGAGCTGTGC 60.154 63.158 0.00 0.00 41.61 4.57
426 442 0.110373 GTTGCACTCGGCCGTTAAAG 60.110 55.000 27.15 17.79 43.89 1.85
482 500 3.323243 CCACCTTCGAATTCAGTTACGT 58.677 45.455 6.22 0.00 0.00 3.57
601 619 1.317431 TGCACTACGCCGGAGTATGT 61.317 55.000 18.85 14.98 41.33 2.29
659 679 3.003480 AGAGAAACACCGCAATTAGCTC 58.997 45.455 0.00 0.00 42.61 4.09
660 680 1.732259 AGAAACACCGCAATTAGCTCG 59.268 47.619 0.00 0.00 42.61 5.03
662 682 0.036765 AACACCGCAATTAGCTCGGA 60.037 50.000 16.85 0.00 45.53 4.55
663 683 0.460284 ACACCGCAATTAGCTCGGAG 60.460 55.000 16.85 11.56 45.53 4.63
664 684 0.179111 CACCGCAATTAGCTCGGAGA 60.179 55.000 16.85 0.00 45.53 3.71
665 685 0.535335 ACCGCAATTAGCTCGGAGAA 59.465 50.000 16.85 0.00 45.53 2.87
701 722 3.151022 CGCTCCCTCCCCTGAGAC 61.151 72.222 0.00 0.00 41.42 3.36
705 726 0.689412 CTCCCTCCCCTGAGACTTCC 60.689 65.000 0.00 0.00 41.42 3.46
706 727 1.156322 TCCCTCCCCTGAGACTTCCT 61.156 60.000 0.00 0.00 41.42 3.36
707 728 0.689412 CCCTCCCCTGAGACTTCCTC 60.689 65.000 0.00 0.00 41.42 3.71
710 731 2.107366 CTCCCCTGAGACTTCCTCTTC 58.893 57.143 0.00 0.00 41.42 2.87
711 732 1.719378 TCCCCTGAGACTTCCTCTTCT 59.281 52.381 0.00 0.00 42.44 2.85
712 733 2.107366 CCCCTGAGACTTCCTCTTCTC 58.893 57.143 0.00 0.00 42.44 2.87
713 734 2.292192 CCCCTGAGACTTCCTCTTCTCT 60.292 54.545 0.00 0.00 42.44 3.10
714 735 3.023832 CCCTGAGACTTCCTCTTCTCTC 58.976 54.545 0.00 0.00 42.44 3.20
715 736 3.309121 CCCTGAGACTTCCTCTTCTCTCT 60.309 52.174 0.00 0.00 42.44 3.10
716 737 3.947834 CCTGAGACTTCCTCTTCTCTCTC 59.052 52.174 0.00 0.00 42.44 3.20
717 738 4.324563 CCTGAGACTTCCTCTTCTCTCTCT 60.325 50.000 0.00 0.00 42.44 3.10
718 739 4.843728 TGAGACTTCCTCTTCTCTCTCTC 58.156 47.826 0.00 0.00 42.44 3.20
719 740 4.536090 TGAGACTTCCTCTTCTCTCTCTCT 59.464 45.833 0.00 0.00 42.44 3.10
720 741 5.104259 AGACTTCCTCTTCTCTCTCTCTC 57.896 47.826 0.00 0.00 0.00 3.20
721 742 4.785376 AGACTTCCTCTTCTCTCTCTCTCT 59.215 45.833 0.00 0.00 0.00 3.10
722 743 5.104259 ACTTCCTCTTCTCTCTCTCTCTC 57.896 47.826 0.00 0.00 0.00 3.20
723 744 4.785376 ACTTCCTCTTCTCTCTCTCTCTCT 59.215 45.833 0.00 0.00 0.00 3.10
724 745 5.104735 ACTTCCTCTTCTCTCTCTCTCTCTC 60.105 48.000 0.00 0.00 0.00 3.20
725 746 4.624913 TCCTCTTCTCTCTCTCTCTCTCT 58.375 47.826 0.00 0.00 0.00 3.10
726 747 4.651503 TCCTCTTCTCTCTCTCTCTCTCTC 59.348 50.000 0.00 0.00 0.00 3.20
727 748 4.653341 CCTCTTCTCTCTCTCTCTCTCTCT 59.347 50.000 0.00 0.00 0.00 3.10
728 749 5.221422 CCTCTTCTCTCTCTCTCTCTCTCTC 60.221 52.000 0.00 0.00 0.00 3.20
729 750 5.523588 TCTTCTCTCTCTCTCTCTCTCTCT 58.476 45.833 0.00 0.00 0.00 3.10
730 751 5.596361 TCTTCTCTCTCTCTCTCTCTCTCTC 59.404 48.000 0.00 0.00 0.00 3.20
779 800 3.090037 CCCTGGAAGTACGAGAAAGAGA 58.910 50.000 0.00 0.00 0.00 3.10
846 877 2.208132 TTGGGCCTTCATTTAGCGAA 57.792 45.000 4.53 0.00 0.00 4.70
868 921 4.362677 AGCCAATCCTAAAGTGTAGGAGA 58.637 43.478 14.60 0.00 45.89 3.71
927 980 4.217035 CGGGATCGGCAATCAACA 57.783 55.556 1.34 0.00 35.96 3.33
995 1072 0.749454 CGGGAGGGGCAATCAAGAAG 60.749 60.000 0.00 0.00 0.00 2.85
1180 1257 1.348008 CCATGCTGCTCCCTCCCTTA 61.348 60.000 0.00 0.00 0.00 2.69
1184 1261 1.044611 GCTGCTCCCTCCCTTACTAG 58.955 60.000 0.00 0.00 0.00 2.57
1185 1262 1.710816 CTGCTCCCTCCCTTACTAGG 58.289 60.000 0.00 0.00 41.60 3.02
1186 1263 1.218196 CTGCTCCCTCCCTTACTAGGA 59.782 57.143 0.00 0.00 45.05 2.94
1210 1287 6.947464 AGTATCTCGGATTTCTTTCTTTCCA 58.053 36.000 0.00 0.00 0.00 3.53
1225 1302 7.995488 TCTTTCTTTCCATTGAGTTTCTCTCTT 59.005 33.333 0.00 0.00 43.13 2.85
1226 1303 7.736447 TTCTTTCCATTGAGTTTCTCTCTTC 57.264 36.000 0.00 0.00 43.13 2.87
1227 1304 7.072263 TCTTTCCATTGAGTTTCTCTCTTCT 57.928 36.000 0.00 0.00 43.13 2.85
1228 1305 7.512992 TCTTTCCATTGAGTTTCTCTCTTCTT 58.487 34.615 0.00 0.00 43.13 2.52
1229 1306 7.995488 TCTTTCCATTGAGTTTCTCTCTTCTTT 59.005 33.333 0.00 0.00 43.13 2.52
1262 1339 5.951148 TCTATCCCATGAATTCTTGCAAACA 59.049 36.000 14.34 0.00 0.00 2.83
1270 1354 6.601741 TGAATTCTTGCAAACATTTTGGAC 57.398 33.333 7.05 0.00 0.00 4.02
1290 1377 7.015226 TGGACTATTATTTTTGCGTCATGAG 57.985 36.000 0.00 0.00 0.00 2.90
1296 1383 3.454042 TTTTTGCGTCATGAGTCATCG 57.546 42.857 1.56 6.25 0.00 3.84
1301 1388 2.287608 TGCGTCATGAGTCATCGGTATC 60.288 50.000 14.06 1.15 0.00 2.24
1302 1389 2.287608 GCGTCATGAGTCATCGGTATCA 60.288 50.000 14.06 0.00 0.00 2.15
1303 1390 3.612717 GCGTCATGAGTCATCGGTATCAT 60.613 47.826 14.06 0.00 32.70 2.45
1315 1402 1.680338 GGTATCATTGGGTCAGTGGC 58.320 55.000 0.00 0.00 0.00 5.01
1357 1444 8.121305 TCACCTAATGCTTTTGTTATGAACAT 57.879 30.769 0.00 0.00 41.79 2.71
1543 1630 8.311395 TCTCTTGTCATCATATAACTTCCACT 57.689 34.615 0.00 0.00 0.00 4.00
1582 1669 5.428457 TGTTCCCATTCATGTACTGGTAGAT 59.572 40.000 0.00 0.00 0.00 1.98
1583 1670 6.069673 TGTTCCCATTCATGTACTGGTAGATT 60.070 38.462 0.00 0.00 0.00 2.40
1584 1671 6.575244 TCCCATTCATGTACTGGTAGATTT 57.425 37.500 0.00 0.00 0.00 2.17
1585 1672 6.969043 TCCCATTCATGTACTGGTAGATTTT 58.031 36.000 0.00 0.00 0.00 1.82
1586 1673 7.410174 TCCCATTCATGTACTGGTAGATTTTT 58.590 34.615 0.00 0.00 0.00 1.94
1679 1771 4.301072 TTGACCCCTAGAAATCACAAGG 57.699 45.455 0.00 0.00 0.00 3.61
1697 1789 2.250031 AGGTGCTGCATTCCAATTGAA 58.750 42.857 5.27 0.00 37.38 2.69
1702 1794 4.933400 GTGCTGCATTCCAATTGAATTTCT 59.067 37.500 5.27 0.00 41.85 2.52
1704 1796 5.172934 GCTGCATTCCAATTGAATTTCTCA 58.827 37.500 7.12 0.00 41.85 3.27
1764 1860 3.274288 GGAGACGATCATTGGCTTTTCT 58.726 45.455 0.00 0.00 0.00 2.52
1783 1879 6.624352 TTTCTGTTCTTCATCAACTTCAGG 57.376 37.500 0.00 0.00 0.00 3.86
1859 1955 7.712639 ACAACTCTGCTATAATATCCTTGTGTG 59.287 37.037 0.00 0.00 0.00 3.82
1936 2039 9.724839 GACATAGTACTAGTTCAATCTTCAGTC 57.275 37.037 8.85 0.00 0.00 3.51
1979 4690 3.694072 TGGTGTAGCAGTGGCATTTAATC 59.306 43.478 0.00 0.00 44.61 1.75
2024 4792 7.467623 AGACGAAATTTCTGCATTCATAACTC 58.532 34.615 15.92 0.96 0.00 3.01
2053 4879 2.368221 TGACCATGATGCCATCGTATGA 59.632 45.455 0.00 0.00 0.00 2.15
2112 4938 0.753262 ACGGGCTGTATGATGAGGTC 59.247 55.000 0.00 0.00 0.00 3.85
2263 5089 1.678101 GCACAGAGCACAAACTTCCTT 59.322 47.619 0.00 0.00 44.79 3.36
2502 5328 4.580167 TCTGTCTTTTGTGAATTGGAGGTG 59.420 41.667 0.00 0.00 0.00 4.00
2560 5386 6.281405 GTCAACTTTCAGGTATGATATCGGT 58.719 40.000 0.00 0.00 34.73 4.69
2596 5422 3.244044 GCATGAAGAGATACTCAGACCCC 60.244 52.174 0.00 0.00 32.06 4.95
2614 5440 1.433534 CCGCCTTCTTCAAGACAGAC 58.566 55.000 0.00 0.00 0.00 3.51
2825 5651 9.555727 AAGTTTCTTGTGCTAACTGTTTATCTA 57.444 29.630 0.00 0.00 32.76 1.98
2890 5716 1.377202 GGCCGAACCTGCAGAATGA 60.377 57.895 17.39 0.00 34.03 2.57
2930 5756 1.667724 GATGGAGCCAACAATGACTCG 59.332 52.381 0.00 0.00 36.96 4.18
2938 5764 3.861840 CCAACAATGACTCGAGGTACAT 58.138 45.455 18.41 15.42 0.00 2.29
3059 5886 6.767902 TGCATAGGTTCAAGACTGATTTATCC 59.232 38.462 0.00 0.00 0.00 2.59
3125 5952 3.900446 CCGACAACTAAACGGGACT 57.100 52.632 0.00 0.00 42.48 3.85
3245 6072 3.667282 ACCGACTCACCCGACACG 61.667 66.667 0.00 0.00 0.00 4.49
3251 6078 3.553437 CTCACCCGACACGAACGCT 62.553 63.158 0.00 0.00 0.00 5.07
3534 6361 1.690633 TCTGATCCTCAGGGTGCCC 60.691 63.158 0.00 0.00 44.39 5.36
3616 6443 0.601311 GCAAACAGAGACGAGGCTGT 60.601 55.000 0.00 0.00 46.59 4.40
3689 6516 3.511934 GTGGTGAACATGAGAGGACTAGT 59.488 47.826 0.00 0.00 0.00 2.57
3769 6596 1.988107 TTCCTTGGAGGAACTGCTCAT 59.012 47.619 5.33 0.00 46.88 2.90
3836 6663 2.216898 GAGTCCAGTGGCAATGCTATC 58.783 52.381 9.87 2.73 0.00 2.08
3893 6720 1.722271 ACTAAAAGGGCCAAGGGGAAT 59.278 47.619 6.18 0.00 35.59 3.01
3941 6768 0.882042 CAGCGAGCAAGAGGTGTGTT 60.882 55.000 0.00 0.00 0.00 3.32
4007 6834 4.268359 GGAAACTCTCCAAGAAGCATGAT 58.732 43.478 0.00 0.00 44.67 2.45
4376 7209 5.012561 TCCCAAAGAAGAAGAAGAGGAAGAG 59.987 44.000 0.00 0.00 0.00 2.85
4385 7230 5.716703 AGAAGAAGAGGAAGAGGAAGAAGAG 59.283 44.000 0.00 0.00 0.00 2.85
4503 7348 5.781210 TCAAGAGCACACTGAGGATATAG 57.219 43.478 0.00 0.00 0.00 1.31
4568 7413 6.576185 AGATTTGAAAGAAGTGTGCATTTGT 58.424 32.000 0.00 0.00 0.00 2.83
4579 7424 0.040157 TGCATTTGTGAAGAGCGTGC 60.040 50.000 0.00 0.00 0.00 5.34
4581 7426 0.453282 CATTTGTGAAGAGCGTGCGG 60.453 55.000 0.00 0.00 0.00 5.69
4612 7457 2.730382 TGCTGATGGATGCAGTGAATT 58.270 42.857 0.00 0.00 35.81 2.17
4627 7472 6.428465 TGCAGTGAATTTGATGAAAATGCATT 59.572 30.769 5.99 5.99 44.16 3.56
4631 7476 7.118680 AGTGAATTTGATGAAAATGCATTGGAC 59.881 33.333 13.82 8.12 44.16 4.02
4644 7489 3.567585 TGCATTGGACGAAGAAATCACAA 59.432 39.130 0.00 0.00 0.00 3.33
4647 7492 3.896648 TGGACGAAGAAATCACAAAGC 57.103 42.857 0.00 0.00 0.00 3.51
4677 7522 3.713248 AGAACATGTGGCTCCAGATGATA 59.287 43.478 26.55 0.00 46.58 2.15
4741 7589 4.932200 CCAAGTAACTCCATTCACTCTCAC 59.068 45.833 0.00 0.00 0.00 3.51
4810 7658 2.681848 CTGAAATGGAGCATGTCACCTC 59.318 50.000 0.00 0.00 33.67 3.85
4910 7758 3.653344 TGATGAACAGTGCTGTCTACAC 58.347 45.455 5.22 0.00 44.13 2.90
4927 7775 6.324512 TGTCTACACCCAGAAACTAGTTTACA 59.675 38.462 20.58 13.61 32.11 2.41
4931 7779 5.820947 ACACCCAGAAACTAGTTTACAACAG 59.179 40.000 20.58 12.00 32.11 3.16
4986 7834 3.491276 CCAAAATGAGCAACTGCAACTGA 60.491 43.478 4.22 0.00 45.16 3.41
5117 7965 1.477553 TTGCAGATCAATTGGCTCCC 58.522 50.000 5.42 0.00 0.00 4.30
5123 7971 1.139853 GATCAATTGGCTCCCGACTCT 59.860 52.381 5.42 0.00 0.00 3.24
5124 7972 0.250234 TCAATTGGCTCCCGACTCTG 59.750 55.000 5.42 0.00 0.00 3.35
5184 8032 5.652014 TGGATGCTTAGTGGTTTAATGAAGG 59.348 40.000 0.00 0.00 0.00 3.46
5408 8256 7.530426 AGAAAATGAAAATAACTCTGCACCT 57.470 32.000 0.00 0.00 0.00 4.00
5423 8271 1.666888 GCACCTGGCGAAACAAATCAG 60.667 52.381 0.00 0.00 0.00 2.90
5489 8337 3.140953 TTCGCAGAAGGAAATGGCACAT 61.141 45.455 0.00 0.00 44.65 3.21
5542 8390 6.892456 ACAGATCTGTTACCTGAGAGTGATTA 59.108 38.462 22.89 0.00 41.83 1.75
5646 8494 4.085210 GCAACACAGACGTTACTTCAGTAC 60.085 45.833 0.00 0.00 0.00 2.73
5715 8563 1.548357 GGAGGCTTGGTCTGAGCTCA 61.548 60.000 17.19 17.19 40.01 4.26
5909 8793 0.686789 AACCAAATGGGCTTCCTTGC 59.313 50.000 4.17 0.00 42.05 4.01
5960 8844 5.809001 TCAGTGCAACAGGAAGATAAATCT 58.191 37.500 0.00 0.00 41.43 2.40
6383 9372 0.041312 CGGTTGTTGCAAAGAGACCG 60.041 55.000 21.63 21.63 37.40 4.79
6431 9420 1.969862 GCAAGTGGCAGCCATTCTT 59.030 52.632 19.75 14.57 43.97 2.52
6467 9456 0.037160 TTCGCCAGGTTAAACCCTCC 59.963 55.000 0.00 0.00 39.75 4.30
6803 9793 0.314935 CGGGGCATGCCATATGTTTC 59.685 55.000 36.56 17.20 37.98 2.78
6813 9803 7.712205 GGCATGCCATATGTTTCTTATCTTTTT 59.288 33.333 32.08 0.00 35.81 1.94
6871 9861 4.276678 TGTATGTGTACGCCCATAGACTAC 59.723 45.833 3.51 0.00 33.36 2.73
7195 10211 2.224329 ACCACGTTTGTACCTATGCACA 60.224 45.455 0.00 0.00 0.00 4.57
7200 10216 3.932710 CGTTTGTACCTATGCACATCTGT 59.067 43.478 0.00 0.00 0.00 3.41
7327 10350 4.141390 ACGCTTTCCTCCCAATCATAGAAT 60.141 41.667 0.00 0.00 0.00 2.40
7377 10402 2.306219 GGCCAAACTTCTCTCTAAGGGT 59.694 50.000 0.00 0.00 0.00 4.34
7391 10416 4.287552 TCTAAGGGTGACAGACTTATCCC 58.712 47.826 0.00 0.00 35.56 3.85
7396 10421 2.622436 GTGACAGACTTATCCCACTGC 58.378 52.381 0.00 0.00 34.25 4.40
7414 10439 2.772691 CCGGCTGTACTCGACTCCC 61.773 68.421 0.00 0.00 0.00 4.30
7466 10492 7.982354 CCTTATTCCGAAGAGTGTTCTAGAAAT 59.018 37.037 6.78 0.00 31.96 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 120 3.230990 GCCCAACCACAACACCCC 61.231 66.667 0.00 0.00 0.00 4.95
194 195 1.654501 GCGTTACACGACGAAAACACC 60.655 52.381 0.00 0.00 46.05 4.16
240 241 0.603065 GGGCAAAACCAGCTAGTTGG 59.397 55.000 22.88 22.88 44.09 3.77
282 286 1.139853 AGAATCAGGAAGGACATCCGC 59.860 52.381 0.00 0.00 44.60 5.54
283 287 3.550437 AAGAATCAGGAAGGACATCCG 57.450 47.619 0.00 0.00 44.60 4.18
305 309 5.825679 ACTTATAAGCGCATGTTTAATCCCA 59.174 36.000 11.47 0.00 0.00 4.37
317 321 6.735678 TTCAGATTTTCACTTATAAGCGCA 57.264 33.333 11.47 0.00 0.00 6.09
365 371 4.685628 ACCTTCGCATTTGCAATTTACTTG 59.314 37.500 0.00 0.00 42.21 3.16
383 398 0.034670 AGCTTCCCATGAGCACCTTC 60.035 55.000 7.54 0.00 42.56 3.46
419 435 2.411547 CCGTCTGCAAAGAGCTTTAACG 60.412 50.000 0.00 4.40 45.94 3.18
426 442 3.044305 ACGCCGTCTGCAAAGAGC 61.044 61.111 0.00 0.00 45.96 4.09
482 500 3.583276 CTTCACTGCCGTGCCCGTA 62.583 63.158 2.98 0.00 40.99 4.02
551 569 5.034554 ACTTGTTAATGCACAATGAGTCG 57.965 39.130 0.00 0.00 36.08 4.18
659 679 4.813750 TTAAAGGGGTTACTCTTCTCCG 57.186 45.455 0.00 0.00 0.00 4.63
660 680 6.563037 AGATTAAAGGGGTTACTCTTCTCC 57.437 41.667 0.00 0.00 29.72 3.71
661 681 6.274579 CGAGATTAAAGGGGTTACTCTTCTC 58.725 44.000 0.00 0.00 33.18 2.87
662 682 5.395435 GCGAGATTAAAGGGGTTACTCTTCT 60.395 44.000 0.00 0.00 33.18 2.85
663 683 4.809958 GCGAGATTAAAGGGGTTACTCTTC 59.190 45.833 0.00 0.00 33.18 2.87
664 684 4.470304 AGCGAGATTAAAGGGGTTACTCTT 59.530 41.667 0.00 0.00 33.18 2.85
665 685 4.031611 AGCGAGATTAAAGGGGTTACTCT 58.968 43.478 0.00 0.00 35.12 3.24
701 722 5.130145 AGAGAGAGAGAGAGAGAAGAGGAAG 59.870 48.000 0.00 0.00 0.00 3.46
705 726 5.598005 AGAGAGAGAGAGAGAGAGAGAAGAG 59.402 48.000 0.00 0.00 0.00 2.85
706 727 5.523588 AGAGAGAGAGAGAGAGAGAGAAGA 58.476 45.833 0.00 0.00 0.00 2.87
707 728 5.598005 AGAGAGAGAGAGAGAGAGAGAGAAG 59.402 48.000 0.00 0.00 0.00 2.85
710 731 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
711 732 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
712 733 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
713 734 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
714 735 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
715 736 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
716 737 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
717 738 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
718 739 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
719 740 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
720 741 4.501229 GCAGAGAGAGAGAGAGAGAGAGAG 60.501 54.167 0.00 0.00 0.00 3.20
721 742 3.386078 GCAGAGAGAGAGAGAGAGAGAGA 59.614 52.174 0.00 0.00 0.00 3.10
722 743 3.387374 AGCAGAGAGAGAGAGAGAGAGAG 59.613 52.174 0.00 0.00 0.00 3.20
723 744 3.378512 AGCAGAGAGAGAGAGAGAGAGA 58.621 50.000 0.00 0.00 0.00 3.10
724 745 3.834489 AGCAGAGAGAGAGAGAGAGAG 57.166 52.381 0.00 0.00 0.00 3.20
725 746 5.614308 CATAAGCAGAGAGAGAGAGAGAGA 58.386 45.833 0.00 0.00 0.00 3.10
726 747 4.214971 GCATAAGCAGAGAGAGAGAGAGAG 59.785 50.000 0.00 0.00 41.58 3.20
727 748 4.136796 GCATAAGCAGAGAGAGAGAGAGA 58.863 47.826 0.00 0.00 41.58 3.10
728 749 3.058708 CGCATAAGCAGAGAGAGAGAGAG 60.059 52.174 0.00 0.00 42.27 3.20
729 750 2.877786 CGCATAAGCAGAGAGAGAGAGA 59.122 50.000 0.00 0.00 42.27 3.10
730 751 2.605338 GCGCATAAGCAGAGAGAGAGAG 60.605 54.545 0.30 0.00 42.27 3.20
779 800 2.113139 CGGTGGCCTTTCCTGTGT 59.887 61.111 3.32 0.00 35.26 3.72
846 877 4.362677 TCTCCTACACTTTAGGATTGGCT 58.637 43.478 0.46 0.00 42.34 4.75
868 921 1.698506 CGCAGAGGTCTAGGAGGATT 58.301 55.000 0.00 0.00 0.00 3.01
927 980 1.000506 CAGCAATGGCAGCTTTTCTGT 59.999 47.619 0.00 0.00 44.66 3.41
995 1072 0.967380 CCTTGACAGGGGCATTGTCC 60.967 60.000 15.23 0.00 43.32 4.02
1180 1257 7.064229 AGAAAGAAATCCGAGATACTCCTAGT 58.936 38.462 0.00 0.00 0.00 2.57
1184 1261 6.480651 GGAAAGAAAGAAATCCGAGATACTCC 59.519 42.308 0.00 0.00 0.00 3.85
1185 1262 7.042335 TGGAAAGAAAGAAATCCGAGATACTC 58.958 38.462 0.00 0.00 34.60 2.59
1186 1263 6.947464 TGGAAAGAAAGAAATCCGAGATACT 58.053 36.000 0.00 0.00 34.60 2.12
1187 1264 7.793927 ATGGAAAGAAAGAAATCCGAGATAC 57.206 36.000 0.00 0.00 34.60 2.24
1188 1265 8.046708 TCAATGGAAAGAAAGAAATCCGAGATA 58.953 33.333 0.00 0.00 34.60 1.98
1189 1266 6.886459 TCAATGGAAAGAAAGAAATCCGAGAT 59.114 34.615 0.00 0.00 34.60 2.75
1225 1302 9.759473 ATTCATGGGATAGAAGAAAAGAAAAGA 57.241 29.630 0.00 0.00 0.00 2.52
1228 1305 9.759473 AGAATTCATGGGATAGAAGAAAAGAAA 57.241 29.630 8.44 0.00 0.00 2.52
1229 1306 9.759473 AAGAATTCATGGGATAGAAGAAAAGAA 57.241 29.630 8.44 0.00 0.00 2.52
1262 1339 9.086336 CATGACGCAAAAATAATAGTCCAAAAT 57.914 29.630 0.00 0.00 0.00 1.82
1270 1354 7.528516 CGATGACTCATGACGCAAAAATAATAG 59.471 37.037 0.00 0.00 0.00 1.73
1290 1377 3.181465 ACTGACCCAATGATACCGATGAC 60.181 47.826 0.00 0.00 0.00 3.06
1296 1383 1.680338 GCCACTGACCCAATGATACC 58.320 55.000 0.00 0.00 0.00 2.73
1301 1388 0.888736 TCAACGCCACTGACCCAATG 60.889 55.000 0.00 0.00 0.00 2.82
1302 1389 0.889186 GTCAACGCCACTGACCCAAT 60.889 55.000 0.00 0.00 37.77 3.16
1303 1390 1.525077 GTCAACGCCACTGACCCAA 60.525 57.895 0.00 0.00 37.77 4.12
1315 1402 2.263077 GTGATCTACCTGCTGTCAACG 58.737 52.381 0.00 0.00 0.00 4.10
1357 1444 2.640826 AGGGTCTGAAAACCACCGAATA 59.359 45.455 0.00 0.00 41.40 1.75
1587 1674 9.784531 CCTTGAGGCTCTATAGAATAATCAAAA 57.215 33.333 16.72 0.00 0.00 2.44
1679 1771 4.933400 AGAAATTCAATTGGAATGCAGCAC 59.067 37.500 5.42 0.00 45.46 4.40
1732 1828 1.252175 ATCGTCTCCATCGATCCCAG 58.748 55.000 0.00 0.00 43.12 4.45
1764 1860 6.603201 AGAAAACCTGAAGTTGATGAAGAACA 59.397 34.615 0.00 0.00 39.19 3.18
1840 1936 5.063204 GCCACACACAAGGATATTATAGCA 58.937 41.667 0.00 0.00 0.00 3.49
1859 1955 2.887152 ACCTCTGAAACATTGAAGCCAC 59.113 45.455 0.00 0.00 0.00 5.01
1953 2056 1.769026 TGCCACTGCTACACCAAAAA 58.231 45.000 0.00 0.00 38.71 1.94
1979 4690 5.107683 CGTCTCAGAAGAAAAGTGCTTACTG 60.108 44.000 0.00 0.00 31.93 2.74
2024 4792 0.647410 GCATCATGGTCAAGACGTCG 59.353 55.000 10.46 0.00 0.00 5.12
2178 5004 2.163509 CAGACGTCTTTCTCCAGGAGA 58.836 52.381 17.26 15.98 36.86 3.71
2263 5089 5.827797 AGTCCAAAGATGCAAGTTTACAGAA 59.172 36.000 0.00 0.00 0.00 3.02
2560 5386 4.015406 ATGCACGTTCCCTCGCCA 62.015 61.111 0.00 0.00 0.00 5.69
2596 5422 2.333014 GAGTCTGTCTTGAAGAAGGCG 58.667 52.381 0.00 0.00 36.51 5.52
2614 5440 0.379669 GCATTCTGGAACATGCGGAG 59.620 55.000 0.00 0.00 38.20 4.63
2930 5756 1.134438 GGGGGATGGGGATGTACCTC 61.134 65.000 0.00 0.00 40.19 3.85
2938 5764 1.275297 TGTTCTTATGGGGGATGGGGA 60.275 52.381 0.00 0.00 0.00 4.81
3059 5886 1.361668 CCTCATCCAACGCTTCACCG 61.362 60.000 0.00 0.00 0.00 4.94
3125 5952 1.540363 GGTCTGAAGCTTCGGAACACA 60.540 52.381 37.41 17.08 46.98 3.72
3245 6072 5.431420 TGATATCTCTCTCTTCAGCGTTC 57.569 43.478 3.98 0.00 0.00 3.95
3251 6078 5.538053 GTCCACCATGATATCTCTCTCTTCA 59.462 44.000 3.98 0.00 0.00 3.02
3635 6462 0.317160 CCTCCGTTACACAGACAGCA 59.683 55.000 0.00 0.00 0.00 4.41
3689 6516 3.549221 GCGAAAACAATTCCTCCAACGAA 60.549 43.478 0.00 0.00 0.00 3.85
3769 6596 4.565652 GCTCTGAAAGAAGTATGTCCCCAA 60.566 45.833 0.00 0.00 46.34 4.12
3836 6663 3.349488 TCGGATGTAGCATTACTGACG 57.651 47.619 0.00 0.00 0.00 4.35
3893 6720 4.082845 TGAAGGAAATGGCCGAAACATTA 58.917 39.130 0.00 0.00 37.55 1.90
4007 6834 2.017782 CGGAGAGAATCAGAGAACGGA 58.982 52.381 0.00 0.00 37.82 4.69
4118 6945 1.606668 GCCATTTTCCGACACTTGACA 59.393 47.619 0.00 0.00 0.00 3.58
4254 7084 2.224843 TGTCAGCAGTTGGGACATCATT 60.225 45.455 0.00 0.00 39.30 2.57
4376 7209 3.031013 CTCCTCCTCTTCCTCTTCTTCC 58.969 54.545 0.00 0.00 0.00 3.46
4385 7230 1.289530 TCTTCCTCCTCCTCCTCTTCC 59.710 57.143 0.00 0.00 0.00 3.46
4503 7348 2.961526 TCAGAAGCACCTTCGGTATC 57.038 50.000 5.32 0.00 44.34 2.24
4568 7413 2.815211 GCATCCGCACGCTCTTCA 60.815 61.111 0.00 0.00 38.36 3.02
4579 7424 0.602106 ATCAGCATCTTCCGCATCCG 60.602 55.000 0.00 0.00 0.00 4.18
4581 7426 0.873054 CCATCAGCATCTTCCGCATC 59.127 55.000 0.00 0.00 0.00 3.91
4612 7457 4.780275 TCGTCCAATGCATTTTCATCAA 57.220 36.364 9.83 0.00 0.00 2.57
4627 7472 3.003275 GTGCTTTGTGATTTCTTCGTCCA 59.997 43.478 0.00 0.00 0.00 4.02
4631 7476 3.951306 TGTGTGCTTTGTGATTTCTTCG 58.049 40.909 0.00 0.00 0.00 3.79
4644 7489 2.224606 CACATGTTCTCCTGTGTGCTT 58.775 47.619 0.00 0.00 38.33 3.91
4647 7492 0.877071 GCCACATGTTCTCCTGTGTG 59.123 55.000 0.00 0.00 40.89 3.82
4677 7522 2.037641 TGGATGAAATCGGCGAGATCAT 59.962 45.455 28.97 28.97 46.86 2.45
4810 7658 0.878523 TTCCACGACTGTTTCCAGCG 60.879 55.000 0.00 0.00 42.81 5.18
4931 7779 4.081642 TCACAGCTACCAAGAACAGTATCC 60.082 45.833 0.00 0.00 0.00 2.59
4986 7834 3.542648 CAGACATCATGGATGAGCTGTT 58.457 45.455 12.79 0.00 42.09 3.16
5184 8032 2.158449 CAGGAAGCACGTTCAATGACTC 59.842 50.000 0.00 0.00 36.82 3.36
5408 8256 3.191162 CAGATTCCTGATTTGTTTCGCCA 59.809 43.478 0.00 0.00 43.02 5.69
5542 8390 8.884124 TCCTTCTTGGACATTATTTTCTTGAT 57.116 30.769 0.00 0.00 40.56 2.57
5646 8494 2.158058 AAAGTGTGCATGTCGTCGCG 62.158 55.000 0.00 0.00 0.00 5.87
5715 8563 7.896811 TGCTTCAGTATCGGTTTCATATCTAT 58.103 34.615 0.00 0.00 0.00 1.98
5872 8756 9.101655 CATTTGGTTTGTTTTCTTCTGAATCTT 57.898 29.630 0.00 0.00 31.56 2.40
5960 8844 5.964477 AGAGAACTCCCTAACCATGTCATTA 59.036 40.000 0.00 0.00 0.00 1.90
6097 8981 5.705609 AAAAACGCAGAACATGGAAGTAT 57.294 34.783 0.00 0.00 0.00 2.12
6283 9272 3.550561 ACAACGATGTTGTTTATGTGCG 58.449 40.909 9.39 0.00 35.91 5.34
6341 9330 5.351458 GGTTTCAAGTTGAAAGTCTGCAAT 58.649 37.500 27.29 0.00 45.83 3.56
6383 9372 2.094675 CTTGGACCACCCATCACATTC 58.905 52.381 0.00 0.00 46.10 2.67
6422 9411 1.210204 TGGCCCTCTCAAGAATGGCT 61.210 55.000 15.82 0.00 40.16 4.75
6431 9420 2.852495 GAATCGCGTTGGCCCTCTCA 62.852 60.000 5.77 0.00 35.02 3.27
6467 9456 5.004821 GCAAGATATATACACGATGAAGCGG 59.995 44.000 0.00 0.00 35.12 5.52
6709 9699 5.091431 CGAGATGAAGAAAAAGGTGCATTC 58.909 41.667 0.00 0.00 0.00 2.67
6803 9793 7.337942 ACTTCAGGAGGCACATAAAAAGATAAG 59.662 37.037 0.00 0.00 0.00 1.73
6813 9803 4.574674 ATCAAACTTCAGGAGGCACATA 57.425 40.909 0.00 0.00 0.00 2.29
6871 9861 6.363577 ACACTCAAGTTACAACAATCACAG 57.636 37.500 0.00 0.00 0.00 3.66
6907 9897 3.132646 TGGCTTCAGAATGTGCACTTTTT 59.867 39.130 19.41 10.53 38.09 1.94
7148 10164 5.235850 TGTGAAGTTTATAGTGAGGCCAA 57.764 39.130 5.01 0.00 0.00 4.52
7195 10211 0.108424 GCTGCGAGAACAGGACAGAT 60.108 55.000 0.00 0.00 38.16 2.90
7200 10216 2.989253 TCGGCTGCGAGAACAGGA 60.989 61.111 0.00 0.00 38.16 3.86
7377 10402 1.555075 GGCAGTGGGATAAGTCTGTCA 59.445 52.381 0.00 0.00 33.46 3.58
7391 10416 2.507102 CGAGTACAGCCGGCAGTG 60.507 66.667 32.28 23.22 0.00 3.66
7396 10421 2.772691 GGGAGTCGAGTACAGCCGG 61.773 68.421 4.52 0.00 0.00 6.13
7414 10439 5.654650 AGACAGACATAAAGTAGACCAGGAG 59.345 44.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.