Multiple sequence alignment - TraesCS4A01G398800

Loading Multiple Alignment...

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 TraesCS4A01G398800 chr4A 100.000 3016 0 0 1 3016 673775494 673772479 0.000000e+00 5570.0
1 TraesCS4A01G398800 chr4A 90.780 1692 126 13 966 2632 673802742 673804428 0.000000e+00 2233.0
2 TraesCS4A01G398800 chr4A 90.541 444 36 3 2174 2613 673750481 673750040 1.820000e-162 582.0
3 TraesCS4A01G398800 chr4A 100.000 236 0 0 3277 3512 673772218 673771983 1.500000e-118 436.0
4 TraesCS4A01G398800 chr4A 84.038 213 22 6 654 859 673802465 673802672 9.950000e-46 195.0
5 TraesCS4A01G398800 chr7D 93.025 1663 92 10 966 2613 58152797 58154450 0.000000e+00 2407.0
6 TraesCS4A01G398800 chr7D 90.623 1685 137 7 966 2633 58133971 58132291 0.000000e+00 2217.0
7 TraesCS4A01G398800 chr7D 87.668 373 36 7 5 375 57538942 57538578 3.240000e-115 425.0
8 TraesCS4A01G398800 chr7D 93.644 236 10 2 3277 3512 537239593 537239823 7.220000e-92 348.0
9 TraesCS4A01G398800 chr7D 93.182 220 14 1 2797 3016 537239302 537239520 4.370000e-84 322.0
10 TraesCS4A01G398800 chr7D 86.339 183 10 8 676 856 58152553 58152722 5.990000e-43 185.0
11 TraesCS4A01G398800 chr7D 82.609 92 9 2 2637 2727 58132218 58132133 1.350000e-09 75.0
12 TraesCS4A01G398800 chr7A 89.346 1971 132 24 689 2613 62475372 62477310 0.000000e+00 2405.0
13 TraesCS4A01G398800 chr7A 91.081 583 52 0 985 1567 62473491 62474073 0.000000e+00 789.0
14 TraesCS4A01G398800 chr7A 89.455 550 46 8 5 553 61889400 61888862 0.000000e+00 684.0
15 TraesCS4A01G398800 chr7A 93.439 442 17 5 2 438 62469547 62469981 0.000000e+00 645.0
16 TraesCS4A01G398800 chr7A 81.443 388 23 21 472 825 62471771 62472143 4.470000e-69 272.0
17 TraesCS4A01G398800 chr7A 92.647 136 10 0 2 137 62266546 62266681 2.770000e-46 196.0
18 TraesCS4A01G398800 chr2A 86.749 1547 182 11 970 2512 3523001 3524528 0.000000e+00 1700.0
19 TraesCS4A01G398800 chr2A 86.999 1523 162 13 1000 2508 3534369 3532869 0.000000e+00 1683.0
20 TraesCS4A01G398800 chr2A 84.397 987 120 19 1527 2509 505237988 505238944 0.000000e+00 939.0
21 TraesCS4A01G398800 chr6B 81.404 1538 238 28 996 2511 50483033 50484544 0.000000e+00 1212.0
22 TraesCS4A01G398800 chr6B 78.355 1520 288 24 1014 2517 23224898 23226392 0.000000e+00 946.0
23 TraesCS4A01G398800 chr6D 81.218 1544 239 36 996 2511 27452139 27453659 0.000000e+00 1197.0
24 TraesCS4A01G398800 chr6A 81.011 1543 247 30 996 2511 30869053 30867530 0.000000e+00 1184.0
25 TraesCS4A01G398800 chr3B 96.186 236 5 1 3277 3512 15908906 15908675 1.980000e-102 383.0
26 TraesCS4A01G398800 chr3B 92.275 233 16 2 2785 3016 15909212 15908981 2.610000e-86 329.0
27 TraesCS4A01G398800 chr7B 78.512 121 17 5 3340 3458 652947396 652947509 1.750000e-08 71.3


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 TraesCS4A01G398800 chr4A 673771983 673775494 3511 True 3003.00 5570 100.00000 1 3512 2 chr4A.!!$R2 3511
1 TraesCS4A01G398800 chr4A 673802465 673804428 1963 False 1214.00 2233 87.40900 654 2632 2 chr4A.!!$F1 1978
2 TraesCS4A01G398800 chr7D 58152553 58154450 1897 False 1296.00 2407 89.68200 676 2613 2 chr7D.!!$F1 1937
3 TraesCS4A01G398800 chr7D 58132133 58133971 1838 True 1146.00 2217 86.61600 966 2727 2 chr7D.!!$R2 1761
4 TraesCS4A01G398800 chr7D 537239302 537239823 521 False 335.00 348 93.41300 2797 3512 2 chr7D.!!$F2 715
5 TraesCS4A01G398800 chr7A 62469547 62477310 7763 False 1027.75 2405 88.82725 2 2613 4 chr7A.!!$F2 2611
6 TraesCS4A01G398800 chr7A 61888862 61889400 538 True 684.00 684 89.45500 5 553 1 chr7A.!!$R1 548
7 TraesCS4A01G398800 chr2A 3523001 3524528 1527 False 1700.00 1700 86.74900 970 2512 1 chr2A.!!$F1 1542
8 TraesCS4A01G398800 chr2A 3532869 3534369 1500 True 1683.00 1683 86.99900 1000 2508 1 chr2A.!!$R1 1508
9 TraesCS4A01G398800 chr2A 505237988 505238944 956 False 939.00 939 84.39700 1527 2509 1 chr2A.!!$F2 982
10 TraesCS4A01G398800 chr6B 50483033 50484544 1511 False 1212.00 1212 81.40400 996 2511 1 chr6B.!!$F2 1515
11 TraesCS4A01G398800 chr6B 23224898 23226392 1494 False 946.00 946 78.35500 1014 2517 1 chr6B.!!$F1 1503
12 TraesCS4A01G398800 chr6D 27452139 27453659 1520 False 1197.00 1197 81.21800 996 2511 1 chr6D.!!$F1 1515
13 TraesCS4A01G398800 chr6A 30867530 30869053 1523 True 1184.00 1184 81.01100 996 2511 1 chr6A.!!$R1 1515
14 TraesCS4A01G398800 chr3B 15908675 15909212 537 True 356.00 383 94.23050 2785 3512 2 chr3B.!!$R1 727

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
955 6127 0.029834 CGGCATTAGCTGTGCAATCC 59.97 55.0 22.3 8.4 44.25 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2727 8078 0.179127 AGATGCCTCATCGTGTCACG 60.179 55.0 19.38 19.38 44.67 4.35 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
42 43 9.698309 CATCAAAGTCTTAGTCGGTCATATAAT 57.302 33.333 0.00 0.00 0.00 1.28
117 120 7.994425 TCAGCAATAAATTACCTGAAACTGA 57.006 32.000 0.00 0.00 29.85 3.41
206 209 8.107399 TGTAGGGTCTGATATAATGTACGAAG 57.893 38.462 0.00 0.00 0.00 3.79
243 247 5.890424 TTTTGACTTTTGTTCTTCTCCGT 57.110 34.783 0.00 0.00 0.00 4.69
278 282 8.999220 TTTGCAAAACAAAGCATATGATATGA 57.001 26.923 16.22 0.00 43.35 2.15
279 283 9.602568 TTTGCAAAACAAAGCATATGATATGAT 57.397 25.926 16.22 7.02 43.35 2.45
311 315 5.256474 AGCTTACACATTGCTTTGTAGGAT 58.744 37.500 0.00 0.00 32.61 3.24
313 317 6.540189 AGCTTACACATTGCTTTGTAGGATAG 59.460 38.462 0.00 0.00 32.61 2.08
318 323 8.630054 ACACATTGCTTTGTAGGATAGTAAAA 57.370 30.769 0.00 0.00 0.00 1.52
346 351 6.237313 ACAGGTGCGAAGATAAAGTAAAAC 57.763 37.500 0.00 0.00 0.00 2.43
450 455 0.402504 TGTTAAGCACCGGGAATGGT 59.597 50.000 6.32 0.00 45.21 3.55
473 2234 5.667539 ACAGTGAAGTAGATAGTGCACAT 57.332 39.130 21.04 10.51 37.59 3.21
497 2258 2.756400 TGGCTGGCCCAGTAACAG 59.244 61.111 13.35 0.00 39.18 3.16
521 2282 2.497107 GCAGCAGCAAAAGAAACAGA 57.503 45.000 0.00 0.00 41.58 3.41
558 2319 1.081892 GTGCTCGTCACGTAGGAGTA 58.918 55.000 0.00 4.52 41.30 2.59
583 2344 2.431954 AGATGCAGGCAGCTAAACAT 57.568 45.000 10.72 0.00 41.23 2.71
584 2345 2.731572 AGATGCAGGCAGCTAAACATT 58.268 42.857 10.72 0.00 41.23 2.71
585 2346 3.094572 AGATGCAGGCAGCTAAACATTT 58.905 40.909 10.72 0.00 41.23 2.32
586 2347 3.512724 AGATGCAGGCAGCTAAACATTTT 59.487 39.130 10.72 0.00 41.23 1.82
587 2348 3.749665 TGCAGGCAGCTAAACATTTTT 57.250 38.095 2.86 0.00 45.94 1.94
597 2387 7.029563 GCAGCTAAACATTTTTGTGCTATAGT 58.970 34.615 0.84 0.00 35.46 2.12
611 2401 5.038033 GTGCTATAGTCAGTCAACAGTAGC 58.962 45.833 0.84 0.00 36.10 3.58
623 2413 1.037493 ACAGTAGCACACGAGGTTGA 58.963 50.000 0.00 0.00 0.00 3.18
627 2417 2.486636 TAGCACACGAGGTTGAGCCG 62.487 60.000 0.00 0.00 43.70 5.52
632 2422 1.006102 ACGAGGTTGAGCCGAAGTG 60.006 57.895 0.00 0.00 43.70 3.16
674 2467 4.757149 AGTGTTCAAGTGCTAGATTCCAAC 59.243 41.667 0.00 0.00 0.00 3.77
691 2484 1.768684 AACGGAGCCTCCTTTCTGCA 61.769 55.000 9.52 0.00 33.30 4.41
728 5873 1.227380 CAGCGATAGGGGTGACAGC 60.227 63.158 0.00 0.00 37.61 4.40
741 5886 1.320555 GTGACAGCACGCTACAATACG 59.679 52.381 0.00 0.00 34.94 3.06
744 5889 0.179121 CAGCACGCTACAATACGGGA 60.179 55.000 0.00 0.00 33.57 5.14
766 5913 1.118838 AGCTCAGATCCCTAGTGCAC 58.881 55.000 9.40 9.40 0.00 4.57
774 5921 0.973632 TCCCTAGTGCACGTGAATGT 59.026 50.000 22.23 2.76 0.00 2.71
783 5930 1.852942 CACGTGAATGTCCGGGATAG 58.147 55.000 10.90 0.00 0.00 2.08
869 6035 1.663739 TCGTAGCAGCCACGAGTTT 59.336 52.632 12.33 0.00 43.05 2.66
882 6048 0.163788 CGAGTTTGATCCACACACGC 59.836 55.000 0.00 0.00 34.75 5.34
884 6050 0.889186 AGTTTGATCCACACACGCCC 60.889 55.000 0.00 0.00 34.75 6.13
885 6051 1.963855 TTTGATCCACACACGCCCG 60.964 57.895 0.00 0.00 0.00 6.13
900 6066 1.153086 CCCGGGAAGATCCAAGCTG 60.153 63.158 18.48 0.00 38.64 4.24
904 6070 1.808133 CGGGAAGATCCAAGCTGCTAC 60.808 57.143 0.90 0.00 38.64 3.58
907 6073 3.326297 GGGAAGATCCAAGCTGCTACTAT 59.674 47.826 0.90 0.00 38.64 2.12
908 6074 4.528596 GGGAAGATCCAAGCTGCTACTATA 59.471 45.833 0.90 0.00 38.64 1.31
909 6075 5.337169 GGGAAGATCCAAGCTGCTACTATAG 60.337 48.000 0.90 0.00 38.64 1.31
910 6076 5.245075 GGAAGATCCAAGCTGCTACTATAGT 59.755 44.000 10.87 10.87 36.28 2.12
911 6077 6.434652 GGAAGATCCAAGCTGCTACTATAGTA 59.565 42.308 12.05 12.05 36.28 1.82
922 6088 5.388654 TGCTACTATAGTACCCTACCAACC 58.611 45.833 8.59 0.00 0.00 3.77
955 6127 0.029834 CGGCATTAGCTGTGCAATCC 59.970 55.000 22.30 8.40 44.25 3.01
992 6190 3.345808 CAACCCGCACCACACGAG 61.346 66.667 0.00 0.00 0.00 4.18
993 6191 4.619227 AACCCGCACCACACGAGG 62.619 66.667 0.00 0.00 0.00 4.63
1281 6500 2.811317 GAGGCGTTCACGAGGCAG 60.811 66.667 2.87 0.00 43.02 4.85
1767 6986 3.623060 GCATATTGGACGGCATAATCGAT 59.377 43.478 0.00 0.00 0.00 3.59
1768 6987 4.808895 GCATATTGGACGGCATAATCGATA 59.191 41.667 0.00 0.00 0.00 2.92
1780 7023 5.043903 GCATAATCGATAGTCGTATGGCAT 58.956 41.667 4.88 4.88 41.35 4.40
1781 7024 5.520288 GCATAATCGATAGTCGTATGGCATT 59.480 40.000 4.78 0.00 41.35 3.56
1794 7037 0.888736 TGGCATTCAACACCTCCACG 60.889 55.000 0.00 0.00 0.00 4.94
1795 7038 1.586154 GGCATTCAACACCTCCACGG 61.586 60.000 0.00 0.00 39.35 4.94
1796 7039 0.605319 GCATTCAACACCTCCACGGA 60.605 55.000 0.00 0.00 36.31 4.69
2021 7294 2.579201 CGGCAAGGAGACCATCGT 59.421 61.111 0.00 0.00 0.00 3.73
2238 7511 2.280524 CCCGACGAGTTTGTGCCA 60.281 61.111 0.00 0.00 0.00 4.92
2255 7528 1.601171 CAGAGAGGTTCCTGGGCAG 59.399 63.158 0.00 0.00 0.00 4.85
2382 7658 2.190578 CCGTTCATCCTGGCCTCC 59.809 66.667 3.32 0.00 0.00 4.30
2527 7803 3.618594 CACCTAATCAATGGACGTGACAG 59.381 47.826 0.00 0.00 0.00 3.51
2529 7805 2.479566 AATCAATGGACGTGACAGCT 57.520 45.000 0.00 0.00 0.00 4.24
2545 7821 3.728845 ACAGCTTGAAAGTACACGTCAT 58.271 40.909 0.00 0.00 0.00 3.06
2554 7830 6.978338 TGAAAGTACACGTCATAGTCTTTCT 58.022 36.000 18.23 0.00 39.56 2.52
2576 7852 3.829886 TCACCAAGATTTCGTGATTGC 57.170 42.857 0.00 0.00 31.74 3.56
2585 7861 6.355397 AGATTTCGTGATTGCATTACTCAG 57.645 37.500 0.00 0.00 0.00 3.35
2598 7879 6.042777 TGCATTACTCAGCTGTCTTATGTAC 58.957 40.000 14.67 3.69 0.00 2.90
2604 7885 5.011090 TCAGCTGTCTTATGTACATGTCC 57.989 43.478 18.81 4.41 0.00 4.02
2667 8017 9.391227 AGATTATCATTAGAACTTCCTCCATCT 57.609 33.333 0.00 0.00 0.00 2.90
2678 8028 5.256474 ACTTCCTCCATCTTAACATGTTGG 58.744 41.667 21.42 13.90 0.00 3.77
2684 8034 5.172934 TCCATCTTAACATGTTGGTCGTAC 58.827 41.667 21.42 0.00 0.00 3.67
2685 8035 4.932799 CCATCTTAACATGTTGGTCGTACA 59.067 41.667 21.42 0.00 0.00 2.90
2686 8036 5.063438 CCATCTTAACATGTTGGTCGTACAG 59.937 44.000 21.42 4.40 0.00 2.74
2692 8043 2.831685 TGTTGGTCGTACAGCATCTT 57.168 45.000 0.00 0.00 30.77 2.40
2698 8049 7.718525 TGTTGGTCGTACAGCATCTTATATTA 58.281 34.615 0.00 0.00 30.77 0.98
2699 8050 7.650504 TGTTGGTCGTACAGCATCTTATATTAC 59.349 37.037 0.00 0.00 30.77 1.89
2708 8059 6.040504 ACAGCATCTTATATTACAGGACACGA 59.959 38.462 0.00 0.00 0.00 4.35
2718 8069 5.670792 TTACAGGACACGAATGGAGTAAT 57.329 39.130 0.00 0.00 0.00 1.89
2720 8071 4.253685 ACAGGACACGAATGGAGTAATTG 58.746 43.478 0.00 0.00 0.00 2.32
2727 8078 3.190535 ACGAATGGAGTAATTGTTGTGGC 59.809 43.478 0.00 0.00 0.00 5.01
2728 8079 3.727673 CGAATGGAGTAATTGTTGTGGCG 60.728 47.826 0.00 0.00 0.00 5.69
2729 8080 2.264005 TGGAGTAATTGTTGTGGCGT 57.736 45.000 0.00 0.00 0.00 5.68
2730 8081 1.876799 TGGAGTAATTGTTGTGGCGTG 59.123 47.619 0.00 0.00 0.00 5.34
2731 8082 2.147958 GGAGTAATTGTTGTGGCGTGA 58.852 47.619 0.00 0.00 0.00 4.35
2732 8083 2.095919 GGAGTAATTGTTGTGGCGTGAC 60.096 50.000 0.00 0.00 0.00 3.67
2733 8084 2.546368 GAGTAATTGTTGTGGCGTGACA 59.454 45.455 0.00 0.00 0.00 3.58
2734 8085 2.289547 AGTAATTGTTGTGGCGTGACAC 59.710 45.455 0.00 0.00 41.68 3.67
2735 8086 0.028770 AATTGTTGTGGCGTGACACG 59.971 50.000 23.43 23.43 44.21 4.49
2736 8087 0.812014 ATTGTTGTGGCGTGACACGA 60.812 50.000 31.08 8.83 46.05 4.35
2737 8088 0.812014 TTGTTGTGGCGTGACACGAT 60.812 50.000 31.08 0.00 46.05 3.73
2738 8089 1.204062 GTTGTGGCGTGACACGATG 59.796 57.895 31.08 3.23 46.05 3.84
2739 8090 1.068250 TTGTGGCGTGACACGATGA 59.932 52.632 31.08 10.80 46.05 2.92
2740 8091 0.943835 TTGTGGCGTGACACGATGAG 60.944 55.000 31.08 2.44 46.05 2.90
2741 8092 2.094659 GTGGCGTGACACGATGAGG 61.095 63.158 31.08 1.66 46.05 3.86
2742 8093 3.188786 GGCGTGACACGATGAGGC 61.189 66.667 31.08 11.97 46.05 4.70
2743 8094 2.432456 GCGTGACACGATGAGGCA 60.432 61.111 31.08 0.00 46.05 4.75
2744 8095 1.811266 GCGTGACACGATGAGGCAT 60.811 57.895 31.08 0.00 46.05 4.40
2745 8096 1.756375 GCGTGACACGATGAGGCATC 61.756 60.000 31.08 6.44 46.05 3.91
2746 8097 0.179127 CGTGACACGATGAGGCATCT 60.179 55.000 23.39 0.00 46.05 2.90
2747 8098 1.737029 CGTGACACGATGAGGCATCTT 60.737 52.381 23.39 0.00 46.05 2.40
2748 8099 2.350522 GTGACACGATGAGGCATCTTT 58.649 47.619 0.00 0.00 38.59 2.52
2749 8100 2.744202 GTGACACGATGAGGCATCTTTT 59.256 45.455 0.00 0.00 38.59 2.27
2750 8101 3.002791 TGACACGATGAGGCATCTTTTC 58.997 45.455 0.00 0.67 38.59 2.29
2751 8102 2.002586 ACACGATGAGGCATCTTTTCG 58.997 47.619 14.23 14.23 38.59 3.46
2752 8103 2.002586 CACGATGAGGCATCTTTTCGT 58.997 47.619 15.24 15.24 38.59 3.85
2753 8104 3.186909 CACGATGAGGCATCTTTTCGTA 58.813 45.455 18.72 0.00 38.59 3.43
2754 8105 3.000322 CACGATGAGGCATCTTTTCGTAC 60.000 47.826 18.72 0.00 38.59 3.67
2755 8106 2.540101 CGATGAGGCATCTTTTCGTACC 59.460 50.000 0.00 0.00 38.59 3.34
2756 8107 3.738281 CGATGAGGCATCTTTTCGTACCT 60.738 47.826 0.00 0.00 38.59 3.08
2757 8108 3.695830 TGAGGCATCTTTTCGTACCTT 57.304 42.857 0.00 0.00 0.00 3.50
2758 8109 4.811969 TGAGGCATCTTTTCGTACCTTA 57.188 40.909 0.00 0.00 0.00 2.69
2759 8110 5.155278 TGAGGCATCTTTTCGTACCTTAA 57.845 39.130 0.00 0.00 0.00 1.85
2760 8111 5.175859 TGAGGCATCTTTTCGTACCTTAAG 58.824 41.667 0.00 0.00 0.00 1.85
2761 8112 4.514401 AGGCATCTTTTCGTACCTTAAGG 58.486 43.478 20.42 20.42 42.17 2.69
2762 8113 3.064958 GGCATCTTTTCGTACCTTAAGGC 59.935 47.826 21.92 5.23 39.32 4.35
2763 8114 3.687698 GCATCTTTTCGTACCTTAAGGCA 59.312 43.478 21.92 5.75 39.32 4.75
2764 8115 4.335594 GCATCTTTTCGTACCTTAAGGCAT 59.664 41.667 21.92 5.61 39.32 4.40
2765 8116 5.504173 GCATCTTTTCGTACCTTAAGGCATC 60.504 44.000 21.92 10.74 39.32 3.91
2766 8117 5.416271 TCTTTTCGTACCTTAAGGCATCT 57.584 39.130 21.92 4.44 39.32 2.90
2767 8118 5.801380 TCTTTTCGTACCTTAAGGCATCTT 58.199 37.500 21.92 4.04 39.32 2.40
2768 8119 6.235664 TCTTTTCGTACCTTAAGGCATCTTT 58.764 36.000 21.92 3.26 39.32 2.52
2769 8120 6.713450 TCTTTTCGTACCTTAAGGCATCTTTT 59.287 34.615 21.92 2.49 39.32 2.27
2770 8121 5.873179 TTCGTACCTTAAGGCATCTTTTG 57.127 39.130 21.92 3.41 39.32 2.44
2771 8122 5.155278 TCGTACCTTAAGGCATCTTTTGA 57.845 39.130 21.92 5.67 39.32 2.69
2772 8123 5.741011 TCGTACCTTAAGGCATCTTTTGAT 58.259 37.500 21.92 0.19 39.32 2.57
2773 8124 5.815740 TCGTACCTTAAGGCATCTTTTGATC 59.184 40.000 21.92 0.00 39.32 2.92
2774 8125 5.584649 CGTACCTTAAGGCATCTTTTGATCA 59.415 40.000 21.92 0.00 39.32 2.92
2775 8126 6.260936 CGTACCTTAAGGCATCTTTTGATCAT 59.739 38.462 21.92 0.00 39.32 2.45
2776 8127 7.441157 CGTACCTTAAGGCATCTTTTGATCATA 59.559 37.037 21.92 0.00 39.32 2.15
2777 8128 9.289782 GTACCTTAAGGCATCTTTTGATCATAT 57.710 33.333 21.92 0.00 39.32 1.78
2778 8129 8.773033 ACCTTAAGGCATCTTTTGATCATATT 57.227 30.769 21.92 0.00 39.32 1.28
2779 8130 9.866655 ACCTTAAGGCATCTTTTGATCATATTA 57.133 29.630 21.92 0.00 39.32 0.98
2914 8265 0.472471 TTCACCTGGAAGCGTCCTTT 59.528 50.000 19.81 0.96 45.22 3.11
2915 8266 1.344065 TCACCTGGAAGCGTCCTTTA 58.656 50.000 19.81 0.00 45.22 1.85
2965 8316 2.704190 TCTTCTTCCCTGTGACCTCT 57.296 50.000 0.00 0.00 0.00 3.69
2966 8317 2.251818 TCTTCTTCCCTGTGACCTCTG 58.748 52.381 0.00 0.00 0.00 3.35
3489 8841 6.149308 GTCAATTTTGCTTCAAATTTAGGGGG 59.851 38.462 0.00 0.00 33.19 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 120 0.034574 TTTGTGCCCTCGCCATACAT 60.035 50.000 0.00 0.00 0.00 2.29
275 279 7.310664 CAATGTGTAAGCTCAAACTTCATCAT 58.689 34.615 0.00 0.00 0.00 2.45
276 280 6.671190 CAATGTGTAAGCTCAAACTTCATCA 58.329 36.000 0.00 0.00 0.00 3.07
277 281 5.570589 GCAATGTGTAAGCTCAAACTTCATC 59.429 40.000 0.00 0.00 0.00 2.92
278 282 5.242393 AGCAATGTGTAAGCTCAAACTTCAT 59.758 36.000 0.00 0.00 32.05 2.57
279 283 4.580167 AGCAATGTGTAAGCTCAAACTTCA 59.420 37.500 0.00 0.00 32.05 3.02
289 293 5.567138 ATCCTACAAAGCAATGTGTAAGC 57.433 39.130 4.80 0.00 34.75 3.09
450 455 6.377146 TGATGTGCACTATCTACTTCACTGTA 59.623 38.462 19.41 0.00 0.00 2.74
455 460 6.530019 TCTTGATGTGCACTATCTACTTCA 57.470 37.500 19.41 5.49 0.00 3.02
456 461 7.042187 CCATTCTTGATGTGCACTATCTACTTC 60.042 40.741 19.41 3.07 33.71 3.01
457 462 6.765036 CCATTCTTGATGTGCACTATCTACTT 59.235 38.462 19.41 3.36 33.71 2.24
458 463 6.286758 CCATTCTTGATGTGCACTATCTACT 58.713 40.000 19.41 2.39 33.71 2.57
459 464 5.049818 GCCATTCTTGATGTGCACTATCTAC 60.050 44.000 19.41 3.78 34.23 2.59
460 465 5.059161 GCCATTCTTGATGTGCACTATCTA 58.941 41.667 19.41 14.03 34.23 1.98
463 468 3.630769 CAGCCATTCTTGATGTGCACTAT 59.369 43.478 19.41 9.88 35.59 2.12
464 469 3.011818 CAGCCATTCTTGATGTGCACTA 58.988 45.455 19.41 4.84 35.59 2.74
465 470 1.816835 CAGCCATTCTTGATGTGCACT 59.183 47.619 19.41 3.19 35.59 4.40
467 472 1.179152 CCAGCCATTCTTGATGTGCA 58.821 50.000 0.00 0.00 35.59 4.57
473 2234 1.000521 CTGGGCCAGCCATTCTTGA 60.001 57.895 22.68 0.00 37.98 3.02
511 2272 6.072783 GCTACTCTGCATCTTTCTGTTTCTTT 60.073 38.462 0.00 0.00 0.00 2.52
564 2325 2.431954 ATGTTTAGCTGCCTGCATCT 57.568 45.000 0.00 0.81 45.94 2.90
575 2336 8.237267 ACTGACTATAGCACAAAAATGTTTAGC 58.763 33.333 0.00 0.00 0.00 3.09
580 2341 7.228507 TGTTGACTGACTATAGCACAAAAATGT 59.771 33.333 0.00 0.00 0.00 2.71
583 2344 6.765989 ACTGTTGACTGACTATAGCACAAAAA 59.234 34.615 0.00 0.00 0.00 1.94
584 2345 6.288294 ACTGTTGACTGACTATAGCACAAAA 58.712 36.000 0.00 0.00 0.00 2.44
585 2346 5.853936 ACTGTTGACTGACTATAGCACAAA 58.146 37.500 0.00 0.00 0.00 2.83
586 2347 5.468540 ACTGTTGACTGACTATAGCACAA 57.531 39.130 0.00 0.00 0.00 3.33
587 2348 5.393135 GCTACTGTTGACTGACTATAGCACA 60.393 44.000 0.00 0.00 35.54 4.57
597 2387 1.679153 TCGTGTGCTACTGTTGACTGA 59.321 47.619 0.00 0.00 0.00 3.41
611 2401 1.284982 CTTCGGCTCAACCTCGTGTG 61.285 60.000 0.00 0.00 35.61 3.82
623 2413 2.363038 TGTTACAGTGTACACTTCGGCT 59.637 45.455 25.89 8.63 40.20 5.52
627 2417 5.756347 TCCACAATGTTACAGTGTACACTTC 59.244 40.000 25.89 15.82 40.73 3.01
632 2422 5.054477 ACACTCCACAATGTTACAGTGTAC 58.946 41.667 17.94 0.00 40.73 2.90
674 2467 1.094073 CATGCAGAAAGGAGGCTCCG 61.094 60.000 27.11 14.02 42.75 4.63
728 5873 0.173935 TGGTCCCGTATTGTAGCGTG 59.826 55.000 0.00 0.00 0.00 5.34
741 5886 3.235369 GGGATCTGAGCTGGTCCC 58.765 66.667 6.63 6.63 43.20 4.46
744 5889 1.786937 CACTAGGGATCTGAGCTGGT 58.213 55.000 0.00 0.00 0.00 4.00
766 5913 1.681793 ACTCTATCCCGGACATTCACG 59.318 52.381 0.73 0.00 0.00 4.35
806 5958 3.258872 TCACAGAAAAATGCCAATGGAGG 59.741 43.478 2.05 0.00 0.00 4.30
807 5959 4.524316 TCACAGAAAAATGCCAATGGAG 57.476 40.909 2.05 0.00 0.00 3.86
869 6035 4.386951 CCGGGCGTGTGTGGATCA 62.387 66.667 0.00 0.00 0.00 2.92
882 6048 1.153086 CAGCTTGGATCTTCCCGGG 60.153 63.158 16.85 16.85 35.03 5.73
884 6050 0.465705 TAGCAGCTTGGATCTTCCCG 59.534 55.000 0.00 0.00 35.03 5.14
885 6051 1.488393 AGTAGCAGCTTGGATCTTCCC 59.512 52.381 0.00 0.00 35.03 3.97
900 6066 5.388654 TGGTTGGTAGGGTACTATAGTAGC 58.611 45.833 26.86 26.86 45.42 3.58
904 6070 4.889409 TCGTTGGTTGGTAGGGTACTATAG 59.111 45.833 0.00 0.00 0.00 1.31
907 6073 3.168035 TCGTTGGTTGGTAGGGTACTA 57.832 47.619 0.00 0.00 0.00 1.82
908 6074 2.014010 TCGTTGGTTGGTAGGGTACT 57.986 50.000 0.00 0.00 0.00 2.73
909 6075 2.837532 TTCGTTGGTTGGTAGGGTAC 57.162 50.000 0.00 0.00 0.00 3.34
910 6076 3.559597 CCATTTCGTTGGTTGGTAGGGTA 60.560 47.826 0.00 0.00 31.74 3.69
911 6077 2.510613 CATTTCGTTGGTTGGTAGGGT 58.489 47.619 0.00 0.00 0.00 4.34
955 6127 0.032678 CTCAGGCGGGCTATGTAGTG 59.967 60.000 2.84 0.00 0.00 2.74
992 6190 0.034616 CTCGATCTCCATTGGCTCCC 59.965 60.000 0.00 0.00 0.00 4.30
993 6191 0.602372 GCTCGATCTCCATTGGCTCC 60.602 60.000 0.00 0.00 0.00 4.70
1629 6848 2.750637 ATCACCGCGACGAGGTCT 60.751 61.111 21.06 8.38 40.59 3.85
1767 6986 3.196901 AGGTGTTGAATGCCATACGACTA 59.803 43.478 0.00 0.00 0.00 2.59
1768 6987 2.027192 AGGTGTTGAATGCCATACGACT 60.027 45.455 0.00 0.00 0.00 4.18
1794 7037 1.079750 GTCACCGTGCTTCTCCTCC 60.080 63.158 0.00 0.00 0.00 4.30
1795 7038 0.318762 AAGTCACCGTGCTTCTCCTC 59.681 55.000 0.00 0.00 0.00 3.71
1796 7039 0.318762 GAAGTCACCGTGCTTCTCCT 59.681 55.000 19.81 0.00 38.36 3.69
2120 7393 1.002274 ATCTCCACGCCTTCCTCCT 59.998 57.895 0.00 0.00 0.00 3.69
2238 7511 4.143740 CTGCCCAGGAACCTCTCT 57.856 61.111 0.00 0.00 0.00 3.10
2275 7551 1.675641 CCTTGCCCCGAAAGTCCAG 60.676 63.158 0.00 0.00 0.00 3.86
2527 7803 5.162075 AGACTATGACGTGTACTTTCAAGC 58.838 41.667 0.00 0.00 0.00 4.01
2529 7805 7.431249 AGAAAGACTATGACGTGTACTTTCAA 58.569 34.615 18.95 0.00 41.93 2.69
2576 7852 7.708322 ACATGTACATAAGACAGCTGAGTAATG 59.292 37.037 23.35 18.99 0.00 1.90
2585 7861 4.503910 TGTGGACATGTACATAAGACAGC 58.496 43.478 15.33 0.00 0.00 4.40
2666 8016 3.743911 TGCTGTACGACCAACATGTTAAG 59.256 43.478 11.53 8.46 0.00 1.85
2667 8017 3.729966 TGCTGTACGACCAACATGTTAA 58.270 40.909 11.53 0.00 0.00 2.01
2668 8018 3.388345 TGCTGTACGACCAACATGTTA 57.612 42.857 11.53 0.00 0.00 2.41
2669 8019 2.248280 TGCTGTACGACCAACATGTT 57.752 45.000 4.92 4.92 0.00 2.71
2670 8020 2.028112 AGATGCTGTACGACCAACATGT 60.028 45.455 0.00 0.00 0.00 3.21
2671 8021 2.621338 AGATGCTGTACGACCAACATG 58.379 47.619 0.00 0.00 0.00 3.21
2678 8028 7.537991 GTCCTGTAATATAAGATGCTGTACGAC 59.462 40.741 0.00 0.00 0.00 4.34
2684 8034 6.447162 TCGTGTCCTGTAATATAAGATGCTG 58.553 40.000 0.00 0.00 0.00 4.41
2685 8035 6.650427 TCGTGTCCTGTAATATAAGATGCT 57.350 37.500 0.00 0.00 0.00 3.79
2686 8036 7.148573 CCATTCGTGTCCTGTAATATAAGATGC 60.149 40.741 0.00 0.00 0.00 3.91
2692 8043 6.971726 ACTCCATTCGTGTCCTGTAATATA 57.028 37.500 0.00 0.00 0.00 0.86
2698 8049 4.253685 CAATTACTCCATTCGTGTCCTGT 58.746 43.478 0.00 0.00 0.00 4.00
2699 8050 4.253685 ACAATTACTCCATTCGTGTCCTG 58.746 43.478 0.00 0.00 0.00 3.86
2708 8059 3.057596 CACGCCACAACAATTACTCCATT 60.058 43.478 0.00 0.00 0.00 3.16
2718 8069 0.812014 ATCGTGTCACGCCACAACAA 60.812 50.000 20.56 0.86 42.21 2.83
2720 8071 1.204062 CATCGTGTCACGCCACAAC 59.796 57.895 20.56 0.00 42.21 3.32
2727 8078 0.179127 AGATGCCTCATCGTGTCACG 60.179 55.000 19.38 19.38 44.67 4.35
2728 8079 2.015736 AAGATGCCTCATCGTGTCAC 57.984 50.000 0.00 0.00 44.67 3.67
2729 8080 2.768253 AAAGATGCCTCATCGTGTCA 57.232 45.000 1.65 0.00 44.67 3.58
2730 8081 2.029728 CGAAAAGATGCCTCATCGTGTC 59.970 50.000 3.76 3.76 44.67 3.67
2731 8082 2.002586 CGAAAAGATGCCTCATCGTGT 58.997 47.619 1.65 0.00 44.67 4.49
2732 8083 2.002586 ACGAAAAGATGCCTCATCGTG 58.997 47.619 13.58 0.00 44.67 4.35
2733 8084 2.386661 ACGAAAAGATGCCTCATCGT 57.613 45.000 10.19 10.19 44.67 3.73
2734 8085 2.540101 GGTACGAAAAGATGCCTCATCG 59.460 50.000 9.21 9.21 44.67 3.84
2735 8086 3.798202 AGGTACGAAAAGATGCCTCATC 58.202 45.455 0.00 0.00 40.80 2.92
2736 8087 3.914426 AGGTACGAAAAGATGCCTCAT 57.086 42.857 0.00 0.00 0.00 2.90
2737 8088 3.695830 AAGGTACGAAAAGATGCCTCA 57.304 42.857 0.00 0.00 0.00 3.86
2738 8089 4.571176 CCTTAAGGTACGAAAAGATGCCTC 59.429 45.833 13.83 0.00 0.00 4.70
2739 8090 4.514401 CCTTAAGGTACGAAAAGATGCCT 58.486 43.478 13.83 0.00 0.00 4.75
2740 8091 3.064958 GCCTTAAGGTACGAAAAGATGCC 59.935 47.826 22.55 0.00 37.57 4.40
2741 8092 3.687698 TGCCTTAAGGTACGAAAAGATGC 59.312 43.478 22.55 4.16 37.57 3.91
2742 8093 5.817816 AGATGCCTTAAGGTACGAAAAGATG 59.182 40.000 22.55 0.00 37.57 2.90
2743 8094 5.990668 AGATGCCTTAAGGTACGAAAAGAT 58.009 37.500 22.55 0.42 37.57 2.40
2744 8095 5.416271 AGATGCCTTAAGGTACGAAAAGA 57.584 39.130 22.55 0.00 37.57 2.52
2745 8096 6.496338 AAAGATGCCTTAAGGTACGAAAAG 57.504 37.500 22.55 0.00 37.57 2.27
2746 8097 6.487331 TCAAAAGATGCCTTAAGGTACGAAAA 59.513 34.615 22.55 0.00 37.57 2.29
2747 8098 5.998981 TCAAAAGATGCCTTAAGGTACGAAA 59.001 36.000 22.55 2.93 37.57 3.46
2748 8099 5.553123 TCAAAAGATGCCTTAAGGTACGAA 58.447 37.500 22.55 4.63 37.57 3.85
2749 8100 5.155278 TCAAAAGATGCCTTAAGGTACGA 57.845 39.130 22.55 5.36 37.57 3.43
2750 8101 5.584649 TGATCAAAAGATGCCTTAAGGTACG 59.415 40.000 22.55 4.39 37.57 3.67
2751 8102 7.573968 ATGATCAAAAGATGCCTTAAGGTAC 57.426 36.000 22.55 13.57 37.57 3.34
2752 8103 9.866655 AATATGATCAAAAGATGCCTTAAGGTA 57.133 29.630 22.55 19.04 37.57 3.08
2753 8104 8.773033 AATATGATCAAAAGATGCCTTAAGGT 57.227 30.769 22.55 3.64 37.57 3.50
2787 8138 6.750039 CGCTTTCAATTGTTTCCCGTATATTT 59.250 34.615 5.13 0.00 0.00 1.40
2794 8145 1.000717 ACCGCTTTCAATTGTTTCCCG 60.001 47.619 5.13 3.72 0.00 5.14
2914 8265 9.288576 GTGGTAGAATGAATGAATGAATGGATA 57.711 33.333 0.00 0.00 0.00 2.59
2915 8266 7.040892 CGTGGTAGAATGAATGAATGAATGGAT 60.041 37.037 0.00 0.00 0.00 3.41
3315 8667 1.979155 TCTCCAGCACCTCACCTCG 60.979 63.158 0.00 0.00 0.00 4.63
3433 8785 5.072741 TCCAGCAAAAATAGAAGTGCTTCT 58.927 37.500 17.23 17.23 44.79 2.85
3489 8841 2.742372 CAGCTACGGCACCACCAC 60.742 66.667 0.00 0.00 41.70 4.16


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

AutoCloner maintained by Alex Coulton.