Multiple sequence alignment - TraesCS1D01G087000

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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 TraesCS1D01G087000 chr1D 100.000 3044 0 0 1 3044 72436751 72433708 0.000000e+00 5622.0
1 TraesCS1D01G087000 chr1D 81.806 1484 210 36 1575 3044 72443223 72441786 0.000000e+00 1190.0
2 TraesCS1D01G087000 chr1D 81.781 1482 213 34 1575 3044 72459630 72458194 0.000000e+00 1188.0
3 TraesCS1D01G087000 chr1D 74.667 1425 267 59 1224 2612 71639738 71638372 2.060000e-151 545.0
4 TraesCS1D01G087000 chr1D 76.984 882 187 13 3 879 441653559 441654429 9.810000e-135 490.0
5 TraesCS1D01G087000 chr1D 77.250 589 119 13 2207 2785 25140039 25140622 6.290000e-87 331.0
6 TraesCS1D01G087000 chr1B 93.642 2029 92 14 1023 3044 113499199 113497201 0.000000e+00 2998.0
7 TraesCS1D01G087000 chr1B 93.494 2029 98 13 1023 3044 113316411 113314410 0.000000e+00 2985.0
8 TraesCS1D01G087000 chr1B 93.988 1863 85 11 1182 3044 113213884 113212049 0.000000e+00 2795.0
9 TraesCS1D01G087000 chr1B 86.176 1794 203 23 1229 3006 113516577 113514813 0.000000e+00 1897.0
10 TraesCS1D01G087000 chr1B 93.519 324 20 1 2721 3044 113407767 113407445 5.900000e-132 481.0
11 TraesCS1D01G087000 chr1B 91.391 151 12 1 1023 1172 113214294 113214144 3.980000e-49 206.0
12 TraesCS1D01G087000 chr1B 94.643 56 2 1 1023 1077 113409188 113409133 5.410000e-13 86.1
13 TraesCS1D01G087000 chr1B 94.118 51 2 1 1023 1072 113211252 113211302 3.250000e-10 76.8
14 TraesCS1D01G087000 chr1B 92.593 54 3 1 1020 1072 113406649 113406702 3.250000e-10 76.8
15 TraesCS1D01G087000 chr1B 92.593 54 3 1 1020 1072 113496401 113496454 3.250000e-10 76.8
16 TraesCS1D01G087000 chrUn 93.958 1804 76 12 1079 2876 372932431 372934207 0.000000e+00 2697.0
17 TraesCS1D01G087000 chrUn 82.837 705 117 3 3 706 257143896 257144597 1.990000e-176 628.0
18 TraesCS1D01G087000 chrUn 82.837 705 117 3 3 706 318231798 318231097 1.990000e-176 628.0
19 TraesCS1D01G087000 chr7D 82.854 869 146 3 3 870 619117981 619118847 0.000000e+00 776.0
20 TraesCS1D01G087000 chr5B 77.496 1222 221 35 1629 2838 411744253 411743074 0.000000e+00 684.0
21 TraesCS1D01G087000 chr1A 74.917 1503 290 55 1224 2687 71724976 71723522 9.330000e-170 606.0
22 TraesCS1D01G087000 chr1A 76.508 796 176 11 84 873 12226177 12226967 1.010000e-114 424.0
23 TraesCS1D01G087000 chr1A 75.463 216 44 6 1247 1456 570787915 570787703 2.500000e-16 97.1
24 TraesCS1D01G087000 chr3D 79.603 755 128 23 138 879 32136137 32136878 4.500000e-143 518.0
25 TraesCS1D01G087000 chr3B 79.470 755 129 23 138 879 54703157 54703898 2.090000e-141 512.0
26 TraesCS1D01G087000 chr6B 76.362 863 187 15 6 861 254080367 254079515 5.990000e-122 448.0
27 TraesCS1D01G087000 chr6B 82.222 135 24 0 1231 1365 82958228 82958094 1.920000e-22 117.0
28 TraesCS1D01G087000 chr6B 80.734 109 16 5 773 879 674968095 674968200 2.520000e-11 80.5
29 TraesCS1D01G087000 chr2B 76.382 796 177 11 84 873 691408996 691409786 4.690000e-113 418.0


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 TraesCS1D01G087000 chr1D 72433708 72436751 3043 True 5622.00 5622 100.0000 1 3044 1 chr1D.!!$R2 3043
1 TraesCS1D01G087000 chr1D 72441786 72443223 1437 True 1190.00 1190 81.8060 1575 3044 1 chr1D.!!$R3 1469
2 TraesCS1D01G087000 chr1D 72458194 72459630 1436 True 1188.00 1188 81.7810 1575 3044 1 chr1D.!!$R4 1469
3 TraesCS1D01G087000 chr1D 71638372 71639738 1366 True 545.00 545 74.6670 1224 2612 1 chr1D.!!$R1 1388
4 TraesCS1D01G087000 chr1D 441653559 441654429 870 False 490.00 490 76.9840 3 879 1 chr1D.!!$F2 876
5 TraesCS1D01G087000 chr1D 25140039 25140622 583 False 331.00 331 77.2500 2207 2785 1 chr1D.!!$F1 578
6 TraesCS1D01G087000 chr1B 113497201 113499199 1998 True 2998.00 2998 93.6420 1023 3044 1 chr1B.!!$R2 2021
7 TraesCS1D01G087000 chr1B 113314410 113316411 2001 True 2985.00 2985 93.4940 1023 3044 1 chr1B.!!$R1 2021
8 TraesCS1D01G087000 chr1B 113514813 113516577 1764 True 1897.00 1897 86.1760 1229 3006 1 chr1B.!!$R3 1777
9 TraesCS1D01G087000 chr1B 113212049 113214294 2245 True 1500.50 2795 92.6895 1023 3044 2 chr1B.!!$R4 2021
10 TraesCS1D01G087000 chr1B 113407445 113409188 1743 True 283.55 481 94.0810 1023 3044 2 chr1B.!!$R5 2021
11 TraesCS1D01G087000 chrUn 372932431 372934207 1776 False 2697.00 2697 93.9580 1079 2876 1 chrUn.!!$F2 1797
12 TraesCS1D01G087000 chrUn 257143896 257144597 701 False 628.00 628 82.8370 3 706 1 chrUn.!!$F1 703
13 TraesCS1D01G087000 chrUn 318231097 318231798 701 True 628.00 628 82.8370 3 706 1 chrUn.!!$R1 703
14 TraesCS1D01G087000 chr7D 619117981 619118847 866 False 776.00 776 82.8540 3 870 1 chr7D.!!$F1 867
15 TraesCS1D01G087000 chr5B 411743074 411744253 1179 True 684.00 684 77.4960 1629 2838 1 chr5B.!!$R1 1209
16 TraesCS1D01G087000 chr1A 71723522 71724976 1454 True 606.00 606 74.9170 1224 2687 1 chr1A.!!$R1 1463
17 TraesCS1D01G087000 chr1A 12226177 12226967 790 False 424.00 424 76.5080 84 873 1 chr1A.!!$F1 789
18 TraesCS1D01G087000 chr3D 32136137 32136878 741 False 518.00 518 79.6030 138 879 1 chr3D.!!$F1 741
19 TraesCS1D01G087000 chr3B 54703157 54703898 741 False 512.00 512 79.4700 138 879 1 chr3B.!!$F1 741
20 TraesCS1D01G087000 chr6B 254079515 254080367 852 True 448.00 448 76.3620 6 861 1 chr6B.!!$R2 855
21 TraesCS1D01G087000 chr2B 691408996 691409786 790 False 418.00 418 76.3820 84 873 1 chr2B.!!$F1 789

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
942 946 0.323725 AGACCCGCAAGATGCCAATT 60.324 50.0 0.00 0.00 41.12 2.32 F
1002 1006 0.169672 CAACAAGCCGAGCAGGAATG 59.830 55.0 2.12 2.89 45.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2260 1.538687 AAAGGCCCAACATCTGCAGC 61.539 55.0 9.47 0.0 0.00 5.25 R
2649 2955 2.284263 TCTAGCAGCGTGAGTTGATG 57.716 50.0 0.00 0.0 46.01 3.07 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
49 50 4.263331 CCTCTCTTGCTACCCTACCAAAAA 60.263 45.833 0.00 0.00 0.00 1.94
74 75 6.768381 AGCTTTAATCATAGAAGTTAGGTGCC 59.232 38.462 0.00 0.00 0.00 5.01
76 77 4.755266 AATCATAGAAGTTAGGTGCCGT 57.245 40.909 0.00 0.00 0.00 5.68
77 78 5.864418 AATCATAGAAGTTAGGTGCCGTA 57.136 39.130 0.00 0.00 0.00 4.02
79 80 5.864418 TCATAGAAGTTAGGTGCCGTAAT 57.136 39.130 0.00 0.00 0.00 1.89
82 83 4.667519 AGAAGTTAGGTGCCGTAATAGG 57.332 45.455 0.00 0.00 0.00 2.57
109 110 5.238650 ACGAGGGAGTTTAAAACAAGACATG 59.761 40.000 0.00 0.00 0.00 3.21
115 116 7.229907 GGGAGTTTAAAACAAGACATGGAGTAA 59.770 37.037 0.00 0.00 0.00 2.24
118 119 9.185680 AGTTTAAAACAAGACATGGAGTAAACT 57.814 29.630 0.00 0.00 37.60 2.66
133 134 3.388350 AGTAAACTGGTATAGCCTGAGCC 59.612 47.826 0.00 0.00 41.25 4.70
159 160 9.007901 CACTGATTTTATCAAGACTTCCTTTCT 57.992 33.333 0.00 0.00 39.11 2.52
256 257 1.002069 TCTTTGATGCCCCCACATCT 58.998 50.000 6.13 0.00 45.51 2.90
397 400 8.321353 TCTTTATTTATTCTCTGACCAGAAGCA 58.679 33.333 1.08 0.00 35.83 3.91
452 455 2.169352 TCAGCTCCCTCTGTATTTGCTC 59.831 50.000 0.00 0.00 35.63 4.26
541 544 6.718454 CCTTAATGCCACCAAGATTAGATGAT 59.282 38.462 0.00 0.00 0.00 2.45
546 549 5.951148 TGCCACCAAGATTAGATGATTGAAA 59.049 36.000 0.00 0.00 0.00 2.69
548 551 7.779326 TGCCACCAAGATTAGATGATTGAAATA 59.221 33.333 0.00 0.00 0.00 1.40
614 617 7.698163 AAGAGGTATGGTGAAATAGGATCTT 57.302 36.000 0.00 0.00 0.00 2.40
628 631 1.619332 GGATCTTCCTGACGGATACCC 59.381 57.143 0.00 0.00 39.58 3.69
629 632 2.317040 GATCTTCCTGACGGATACCCA 58.683 52.381 0.00 0.00 39.58 4.51
654 658 7.552687 CAGTGTAGGGTTAAATTCATCAGCTTA 59.447 37.037 0.00 0.00 0.00 3.09
717 721 6.262273 CCATGTCCATAACTATGTTAACCCAC 59.738 42.308 2.48 0.00 31.82 4.61
738 742 2.768527 CCTCTCAGTGAATCCCAGCTTA 59.231 50.000 0.00 0.00 0.00 3.09
747 751 5.767168 AGTGAATCCCAGCTTAAGCATAATC 59.233 40.000 28.39 17.53 45.16 1.75
803 807 5.382616 TGCCTTCATCATATCAAGCTTCAT 58.617 37.500 0.00 0.00 0.00 2.57
804 808 5.240844 TGCCTTCATCATATCAAGCTTCATG 59.759 40.000 0.00 0.71 0.00 3.07
824 828 2.626088 GCACAATGCCTGTTTCTCTC 57.374 50.000 0.00 0.00 37.42 3.20
826 830 2.294233 GCACAATGCCTGTTTCTCTCAA 59.706 45.455 0.00 0.00 37.42 3.02
838 842 6.372937 CCTGTTTCTCTCAACCTTATTTCTCC 59.627 42.308 0.00 0.00 0.00 3.71
875 879 7.674120 AGACACTCATAAGCAGCAATGATATA 58.326 34.615 10.08 0.00 31.95 0.86
876 880 8.319881 AGACACTCATAAGCAGCAATGATATAT 58.680 33.333 10.08 0.00 31.95 0.86
877 881 9.591792 GACACTCATAAGCAGCAATGATATATA 57.408 33.333 10.08 0.00 31.95 0.86
934 938 8.918202 ATATATTTTAAATGAGACCCGCAAGA 57.082 30.769 0.00 0.00 43.02 3.02
935 939 7.823745 ATATTTTAAATGAGACCCGCAAGAT 57.176 32.000 0.00 0.00 43.02 2.40
936 940 4.963276 TTTAAATGAGACCCGCAAGATG 57.037 40.909 0.00 0.00 43.02 2.90
937 941 1.098050 AAATGAGACCCGCAAGATGC 58.902 50.000 0.00 0.00 40.69 3.91
938 942 0.749454 AATGAGACCCGCAAGATGCC 60.749 55.000 0.00 0.00 41.12 4.40
939 943 1.913951 ATGAGACCCGCAAGATGCCA 61.914 55.000 0.00 0.00 41.12 4.92
940 944 1.377202 GAGACCCGCAAGATGCCAA 60.377 57.895 0.00 0.00 41.12 4.52
941 945 0.749454 GAGACCCGCAAGATGCCAAT 60.749 55.000 0.00 0.00 41.12 3.16
942 946 0.323725 AGACCCGCAAGATGCCAATT 60.324 50.000 0.00 0.00 41.12 2.32
943 947 0.532115 GACCCGCAAGATGCCAATTT 59.468 50.000 0.00 0.00 41.12 1.82
944 948 0.975887 ACCCGCAAGATGCCAATTTT 59.024 45.000 0.00 0.00 41.12 1.82
945 949 1.347378 ACCCGCAAGATGCCAATTTTT 59.653 42.857 0.00 0.00 41.12 1.94
975 979 3.544772 AAAAACAACCAGGCCCGG 58.455 55.556 2.45 2.45 0.00 5.73
976 980 1.382009 AAAAACAACCAGGCCCGGT 60.382 52.632 4.23 4.23 42.71 5.28
977 981 1.396607 AAAAACAACCAGGCCCGGTC 61.397 55.000 12.19 0.00 38.76 4.79
978 982 3.802852 AAACAACCAGGCCCGGTCC 62.803 63.158 12.19 0.00 38.76 4.46
980 984 4.722700 CAACCAGGCCCGGTCCAG 62.723 72.222 12.19 0.00 38.76 3.86
988 992 4.278513 CCCGGTCCAGCCCAACAA 62.279 66.667 0.00 0.00 0.00 2.83
989 993 2.672996 CCGGTCCAGCCCAACAAG 60.673 66.667 0.00 0.00 0.00 3.16
990 994 3.365265 CGGTCCAGCCCAACAAGC 61.365 66.667 0.00 0.00 0.00 4.01
991 995 2.991540 GGTCCAGCCCAACAAGCC 60.992 66.667 0.00 0.00 0.00 4.35
992 996 3.365265 GTCCAGCCCAACAAGCCG 61.365 66.667 0.00 0.00 0.00 5.52
993 997 3.565214 TCCAGCCCAACAAGCCGA 61.565 61.111 0.00 0.00 0.00 5.54
994 998 3.058160 CCAGCCCAACAAGCCGAG 61.058 66.667 0.00 0.00 0.00 4.63
995 999 3.741476 CAGCCCAACAAGCCGAGC 61.741 66.667 0.00 0.00 0.00 5.03
996 1000 4.269523 AGCCCAACAAGCCGAGCA 62.270 61.111 0.00 0.00 0.00 4.26
997 1001 3.741476 GCCCAACAAGCCGAGCAG 61.741 66.667 0.00 0.00 0.00 4.24
998 1002 3.058160 CCCAACAAGCCGAGCAGG 61.058 66.667 0.00 0.00 44.97 4.85
999 1003 2.032528 CCAACAAGCCGAGCAGGA 59.967 61.111 2.12 0.00 45.00 3.86
1000 1004 1.600636 CCAACAAGCCGAGCAGGAA 60.601 57.895 2.12 0.00 45.00 3.36
1001 1005 0.962356 CCAACAAGCCGAGCAGGAAT 60.962 55.000 2.12 0.00 45.00 3.01
1002 1006 0.169672 CAACAAGCCGAGCAGGAATG 59.830 55.000 2.12 2.89 45.00 2.67
1003 1007 0.250901 AACAAGCCGAGCAGGAATGT 60.251 50.000 2.12 3.47 45.00 2.71
1004 1008 0.957395 ACAAGCCGAGCAGGAATGTG 60.957 55.000 2.12 0.00 45.00 3.21
1005 1009 2.042831 AAGCCGAGCAGGAATGTGC 61.043 57.895 2.12 0.00 45.00 4.57
1006 1010 3.512516 GCCGAGCAGGAATGTGCC 61.513 66.667 2.12 0.00 45.20 5.01
1007 1011 2.046023 CCGAGCAGGAATGTGCCA 60.046 61.111 0.00 0.00 45.20 4.92
1008 1012 1.452651 CCGAGCAGGAATGTGCCAT 60.453 57.895 0.00 0.00 45.20 4.40
1009 1013 1.442526 CCGAGCAGGAATGTGCCATC 61.443 60.000 0.00 0.00 45.20 3.51
1010 1014 1.769098 CGAGCAGGAATGTGCCATCG 61.769 60.000 0.00 0.00 45.20 3.84
1011 1015 0.745845 GAGCAGGAATGTGCCATCGT 60.746 55.000 0.00 0.00 45.20 3.73
1012 1016 0.322816 AGCAGGAATGTGCCATCGTT 60.323 50.000 0.00 0.00 45.20 3.85
1013 1017 0.179156 GCAGGAATGTGCCATCGTTG 60.179 55.000 0.00 0.00 37.49 4.10
1014 1018 0.452987 CAGGAATGTGCCATCGTTGG 59.547 55.000 8.23 8.23 46.66 3.77
1015 1019 0.327924 AGGAATGTGCCATCGTTGGA 59.672 50.000 16.83 0.00 46.92 3.53
1016 1020 1.173043 GGAATGTGCCATCGTTGGAA 58.827 50.000 16.83 2.29 46.92 3.53
1017 1021 1.133025 GGAATGTGCCATCGTTGGAAG 59.867 52.381 16.83 0.00 46.92 3.46
1018 1022 0.527565 AATGTGCCATCGTTGGAAGC 59.472 50.000 16.83 5.71 46.92 3.86
1019 1023 0.322816 ATGTGCCATCGTTGGAAGCT 60.323 50.000 16.83 0.00 46.92 3.74
1020 1024 1.236616 TGTGCCATCGTTGGAAGCTG 61.237 55.000 16.83 0.00 46.92 4.24
1021 1025 1.675310 TGCCATCGTTGGAAGCTGG 60.675 57.895 16.83 0.00 46.92 4.85
1028 1032 1.202879 TCGTTGGAAGCTGGAACCAAT 60.203 47.619 14.70 0.00 43.89 3.16
1033 1037 1.285078 GGAAGCTGGAACCAATACCCT 59.715 52.381 0.00 0.00 0.00 4.34
1092 1097 1.218047 CTCGCCGGACATGAAGGAA 59.782 57.895 5.05 0.00 0.00 3.36
1216 1471 1.870402 CACACAAACTGGCACGTGATA 59.130 47.619 22.23 5.82 33.56 2.15
1256 1511 2.945008 TCATCAACAATCTTCCGGATGC 59.055 45.455 4.15 0.00 34.45 3.91
1303 1558 2.654877 CCACCAAGTACGGCGTCT 59.345 61.111 19.21 11.21 0.00 4.18
1305 1560 1.736645 CACCAAGTACGGCGTCTGG 60.737 63.158 25.36 25.36 0.00 3.86
1372 1627 3.358076 CTCAACCTCGACGCCTCCC 62.358 68.421 0.00 0.00 0.00 4.30
1522 1777 4.810661 AAGCCGCTGAGCTCGAGC 62.811 66.667 30.01 30.01 44.11 5.03
1564 1819 1.056660 GGACAACCTCCAGGAACTCA 58.943 55.000 0.00 0.00 39.21 3.41
1584 1839 5.527951 ACTCAATATCGTCTTCTCGCTCTTA 59.472 40.000 0.00 0.00 0.00 2.10
1595 1850 6.575942 GTCTTCTCGCTCTTAGAATATTCGTC 59.424 42.308 9.78 0.00 32.72 4.20
1767 2023 1.883084 GCGCGTTTCCATCTCCGAT 60.883 57.895 8.43 0.00 0.00 4.18
1878 2134 1.833630 TCGCCAACTCTCAGGATCATT 59.166 47.619 0.00 0.00 0.00 2.57
1903 2159 3.691049 TCTCTTGTTTGTTTGAAGGCG 57.309 42.857 0.00 0.00 0.00 5.52
1905 2161 3.312421 TCTCTTGTTTGTTTGAAGGCGAG 59.688 43.478 0.00 0.00 0.00 5.03
2004 2260 1.084289 GGGTTGTTAGCGCACCTAAG 58.916 55.000 11.47 0.00 36.72 2.18
2041 2297 0.911769 TTTGTCTCCCCGCATCTCAT 59.088 50.000 0.00 0.00 0.00 2.90
2084 2340 4.223923 AGTCTTCTAGGTAACAGCTGCATT 59.776 41.667 15.27 3.96 41.41 3.56
2094 2350 5.163499 GGTAACAGCTGCATTAGTCTCTAGT 60.163 44.000 15.27 0.00 0.00 2.57
2095 2351 6.039493 GGTAACAGCTGCATTAGTCTCTAGTA 59.961 42.308 15.27 0.00 0.00 1.82
2096 2352 5.766150 ACAGCTGCATTAGTCTCTAGTAG 57.234 43.478 15.27 0.00 0.00 2.57
2097 2353 4.582656 ACAGCTGCATTAGTCTCTAGTAGG 59.417 45.833 15.27 0.00 0.00 3.18
2098 2354 3.572255 AGCTGCATTAGTCTCTAGTAGGC 59.428 47.826 1.02 0.00 0.00 3.93
2100 2356 4.320935 GCTGCATTAGTCTCTAGTAGGCTC 60.321 50.000 0.00 0.00 40.17 4.70
2101 2357 5.055265 TGCATTAGTCTCTAGTAGGCTCT 57.945 43.478 0.00 0.00 40.17 4.09
2102 2358 5.450453 TGCATTAGTCTCTAGTAGGCTCTT 58.550 41.667 0.00 0.00 40.17 2.85
2104 2360 7.061054 TGCATTAGTCTCTAGTAGGCTCTTAA 58.939 38.462 0.00 0.00 40.17 1.85
2246 2520 4.097892 GGTTTTGGCTCTCAAGTTTTCTGA 59.902 41.667 0.00 0.00 36.62 3.27
2575 2881 4.520743 GCTTTGCCAAGTTCTTTGTTTC 57.479 40.909 0.00 0.00 34.87 2.78
2649 2955 4.872691 ACATCGACAAGAAATGGATGACTC 59.127 41.667 6.35 0.00 38.24 3.36
2687 2993 3.467803 AGAAGTGGAAACAAGACCTTCG 58.532 45.455 0.00 0.00 46.06 3.79
2771 3082 1.881252 CTTATCCGTTGCCGACCCG 60.881 63.158 0.00 0.00 35.63 5.28
2785 3096 0.307760 GACCCGTTCAGCTGTTGTTG 59.692 55.000 14.67 3.78 0.00 3.33
2845 3161 3.638627 TGATCTGTCAATGGCGTATCTCT 59.361 43.478 0.00 0.00 0.00 3.10
2861 3177 2.912771 TCTCTTTGGTTGCTTCGTTCA 58.087 42.857 0.00 0.00 0.00 3.18
2862 3178 3.476552 TCTCTTTGGTTGCTTCGTTCAT 58.523 40.909 0.00 0.00 0.00 2.57
2863 3179 3.250762 TCTCTTTGGTTGCTTCGTTCATG 59.749 43.478 0.00 0.00 0.00 3.07
2880 3200 7.496747 TCGTTCATGAATTATGTACCTGATGA 58.503 34.615 12.12 0.00 38.01 2.92
2989 3310 1.803334 TTGCTAGTTTCAATCGGCGT 58.197 45.000 6.85 0.00 0.00 5.68
2992 3313 2.550606 TGCTAGTTTCAATCGGCGTTTT 59.449 40.909 6.85 0.00 0.00 2.43
3006 3327 3.672867 CGGCGTTTTATGCTTGTTTTGAT 59.327 39.130 0.00 0.00 0.00 2.57
3009 3330 6.034470 CGGCGTTTTATGCTTGTTTTGATAAT 59.966 34.615 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.218417 GGTAGCAAGAGAGGCAAATGAAAA 59.782 41.667 0.00 0.00 0.00 2.29
21 22 1.918957 AGGGTAGCAAGAGAGGCAAAT 59.081 47.619 0.00 0.00 0.00 2.32
49 50 6.768381 GGCACCTAACTTCTATGATTAAAGCT 59.232 38.462 0.00 0.00 0.00 3.74
74 75 0.314302 CTCCCTCGTGGCCTATTACG 59.686 60.000 3.32 5.50 41.38 3.18
76 77 2.170012 AACTCCCTCGTGGCCTATTA 57.830 50.000 3.32 0.00 0.00 0.98
77 78 1.286248 AAACTCCCTCGTGGCCTATT 58.714 50.000 3.32 0.00 0.00 1.73
79 80 1.941377 TTAAACTCCCTCGTGGCCTA 58.059 50.000 3.32 0.00 0.00 3.93
82 83 2.223745 TGTTTTAAACTCCCTCGTGGC 58.776 47.619 9.33 0.00 0.00 5.01
85 86 4.773013 TGTCTTGTTTTAAACTCCCTCGT 58.227 39.130 9.33 0.00 0.00 4.18
109 110 4.501743 GCTCAGGCTATACCAGTTTACTCC 60.502 50.000 0.00 0.00 43.14 3.85
115 116 1.486726 GTGGCTCAGGCTATACCAGTT 59.513 52.381 0.00 0.00 43.14 3.16
118 119 1.123077 CAGTGGCTCAGGCTATACCA 58.877 55.000 0.00 0.00 43.14 3.25
133 134 9.007901 AGAAAGGAAGTCTTGATAAAATCAGTG 57.992 33.333 0.00 0.00 40.94 3.66
159 160 7.826252 GGATGGAGAAATTATTATCTGCAGCTA 59.174 37.037 9.47 0.00 45.82 3.32
256 257 4.298626 AGAAGTATCTTGGGATGCCTACA 58.701 43.478 4.35 0.00 35.59 2.74
397 400 4.460382 CACCTTCTGGAAACATATGCACTT 59.540 41.667 1.58 0.00 41.51 3.16
546 549 7.277396 CCTTTCATGCCTTTTGAAATCCATAT 58.723 34.615 0.00 0.00 41.03 1.78
548 551 5.493809 CCTTTCATGCCTTTTGAAATCCAT 58.506 37.500 0.00 0.00 41.03 3.41
565 568 0.840288 TGGTAGCAGAGGGCCTTTCA 60.840 55.000 7.89 0.00 46.50 2.69
628 631 5.882557 AGCTGATGAATTTAACCCTACACTG 59.117 40.000 0.00 0.00 0.00 3.66
629 632 6.067217 AGCTGATGAATTTAACCCTACACT 57.933 37.500 0.00 0.00 0.00 3.55
654 658 9.753674 TCATTCTTAGTCCTTTTTAATGGTCAT 57.246 29.630 0.00 0.00 0.00 3.06
717 721 1.202330 AGCTGGGATTCACTGAGAGG 58.798 55.000 0.00 0.00 0.00 3.69
747 751 5.973565 GGTTGAATGGAATTATTTGAGAGCG 59.026 40.000 0.00 0.00 36.07 5.03
818 822 6.935240 TGAGGAGAAATAAGGTTGAGAGAA 57.065 37.500 0.00 0.00 0.00 2.87
820 824 6.882656 TCATGAGGAGAAATAAGGTTGAGAG 58.117 40.000 0.00 0.00 0.00 3.20
824 828 8.059798 ACATTTCATGAGGAGAAATAAGGTTG 57.940 34.615 0.00 0.00 42.17 3.77
826 830 8.772250 TCTACATTTCATGAGGAGAAATAAGGT 58.228 33.333 0.00 0.00 42.17 3.50
838 842 7.493645 TGCTTATGAGTGTCTACATTTCATGAG 59.506 37.037 18.05 18.05 38.25 2.90
909 913 8.918202 TCTTGCGGGTCTCATTTAAAATATAT 57.082 30.769 0.00 0.00 0.00 0.86
910 914 8.783093 CATCTTGCGGGTCTCATTTAAAATATA 58.217 33.333 0.00 0.00 0.00 0.86
911 915 7.651808 CATCTTGCGGGTCTCATTTAAAATAT 58.348 34.615 0.00 0.00 0.00 1.28
912 916 6.459573 GCATCTTGCGGGTCTCATTTAAAATA 60.460 38.462 0.00 0.00 31.71 1.40
913 917 5.679638 GCATCTTGCGGGTCTCATTTAAAAT 60.680 40.000 0.00 0.00 31.71 1.82
914 918 4.380444 GCATCTTGCGGGTCTCATTTAAAA 60.380 41.667 0.00 0.00 31.71 1.52
915 919 3.128589 GCATCTTGCGGGTCTCATTTAAA 59.871 43.478 0.00 0.00 31.71 1.52
916 920 2.682856 GCATCTTGCGGGTCTCATTTAA 59.317 45.455 0.00 0.00 31.71 1.52
917 921 2.288666 GCATCTTGCGGGTCTCATTTA 58.711 47.619 0.00 0.00 31.71 1.40
918 922 1.098050 GCATCTTGCGGGTCTCATTT 58.902 50.000 0.00 0.00 31.71 2.32
919 923 0.749454 GGCATCTTGCGGGTCTCATT 60.749 55.000 0.00 0.00 46.21 2.57
920 924 1.153086 GGCATCTTGCGGGTCTCAT 60.153 57.895 0.00 0.00 46.21 2.90
921 925 2.123248 TTGGCATCTTGCGGGTCTCA 62.123 55.000 0.00 0.00 46.21 3.27
922 926 0.749454 ATTGGCATCTTGCGGGTCTC 60.749 55.000 0.00 0.00 46.21 3.36
923 927 0.323725 AATTGGCATCTTGCGGGTCT 60.324 50.000 0.00 0.00 46.21 3.85
924 928 0.532115 AAATTGGCATCTTGCGGGTC 59.468 50.000 0.00 0.00 46.21 4.46
925 929 0.975887 AAAATTGGCATCTTGCGGGT 59.024 45.000 0.00 0.00 46.21 5.28
926 930 2.097680 AAAAATTGGCATCTTGCGGG 57.902 45.000 0.00 0.00 46.21 6.13
958 962 1.382009 ACCGGGCCTGGTTGTTTTT 60.382 52.632 31.91 6.05 39.99 1.94
959 963 1.830847 GACCGGGCCTGGTTGTTTT 60.831 57.895 36.96 13.91 44.01 2.43
960 964 2.203437 GACCGGGCCTGGTTGTTT 60.203 61.111 36.96 14.77 44.01 2.83
961 965 4.280019 GGACCGGGCCTGGTTGTT 62.280 66.667 36.96 15.21 44.01 2.83
963 967 4.722700 CTGGACCGGGCCTGGTTG 62.723 72.222 36.96 24.51 44.01 3.77
971 975 4.278513 TTGTTGGGCTGGACCGGG 62.279 66.667 6.32 0.00 40.62 5.73
972 976 2.672996 CTTGTTGGGCTGGACCGG 60.673 66.667 0.00 0.00 40.62 5.28
973 977 3.365265 GCTTGTTGGGCTGGACCG 61.365 66.667 0.00 0.00 40.62 4.79
974 978 2.991540 GGCTTGTTGGGCTGGACC 60.992 66.667 0.00 0.00 37.93 4.46
975 979 3.365265 CGGCTTGTTGGGCTGGAC 61.365 66.667 0.00 0.00 32.91 4.02
976 980 3.551496 CTCGGCTTGTTGGGCTGGA 62.551 63.158 0.00 0.00 36.77 3.86
977 981 3.058160 CTCGGCTTGTTGGGCTGG 61.058 66.667 0.00 0.00 36.77 4.85
978 982 3.741476 GCTCGGCTTGTTGGGCTG 61.741 66.667 0.00 0.00 37.41 4.85
979 983 4.269523 TGCTCGGCTTGTTGGGCT 62.270 61.111 0.00 0.00 0.00 5.19
980 984 3.741476 CTGCTCGGCTTGTTGGGC 61.741 66.667 0.00 0.00 0.00 5.36
981 985 3.058160 CCTGCTCGGCTTGTTGGG 61.058 66.667 0.00 0.00 0.00 4.12
982 986 0.962356 ATTCCTGCTCGGCTTGTTGG 60.962 55.000 0.00 0.00 0.00 3.77
983 987 0.169672 CATTCCTGCTCGGCTTGTTG 59.830 55.000 0.00 0.00 0.00 3.33
984 988 0.250901 ACATTCCTGCTCGGCTTGTT 60.251 50.000 0.00 0.00 0.00 2.83
985 989 0.957395 CACATTCCTGCTCGGCTTGT 60.957 55.000 0.00 0.00 0.00 3.16
986 990 1.798735 CACATTCCTGCTCGGCTTG 59.201 57.895 0.00 0.00 0.00 4.01
987 991 2.042831 GCACATTCCTGCTCGGCTT 61.043 57.895 0.00 0.00 34.06 4.35
988 992 2.437359 GCACATTCCTGCTCGGCT 60.437 61.111 0.00 0.00 34.06 5.52
989 993 3.512516 GGCACATTCCTGCTCGGC 61.513 66.667 0.00 0.00 37.33 5.54
990 994 2.046023 TGGCACATTCCTGCTCGG 60.046 61.111 0.00 0.00 37.33 4.63
1006 1010 0.804989 GGTTCCAGCTTCCAACGATG 59.195 55.000 0.00 0.00 0.00 3.84
1007 1011 0.400213 TGGTTCCAGCTTCCAACGAT 59.600 50.000 0.00 0.00 0.00 3.73
1008 1012 0.181587 TTGGTTCCAGCTTCCAACGA 59.818 50.000 0.00 0.00 36.48 3.85
1009 1013 1.247567 ATTGGTTCCAGCTTCCAACG 58.752 50.000 10.33 0.00 42.75 4.10
1010 1014 2.492088 GGTATTGGTTCCAGCTTCCAAC 59.508 50.000 10.33 2.08 42.75 3.77
1011 1015 2.556559 GGGTATTGGTTCCAGCTTCCAA 60.557 50.000 10.47 10.47 43.83 3.53
1012 1016 1.005450 GGGTATTGGTTCCAGCTTCCA 59.995 52.381 0.00 0.00 0.00 3.53
1013 1017 1.285078 AGGGTATTGGTTCCAGCTTCC 59.715 52.381 0.00 0.00 0.00 3.46
1014 1018 2.808906 AGGGTATTGGTTCCAGCTTC 57.191 50.000 0.00 0.00 0.00 3.86
1015 1019 2.241430 GGTAGGGTATTGGTTCCAGCTT 59.759 50.000 0.00 0.00 0.00 3.74
1016 1020 1.844497 GGTAGGGTATTGGTTCCAGCT 59.156 52.381 0.00 0.00 0.00 4.24
1017 1021 1.133884 GGGTAGGGTATTGGTTCCAGC 60.134 57.143 0.00 0.00 0.00 4.85
1018 1022 2.201830 TGGGTAGGGTATTGGTTCCAG 58.798 52.381 0.00 0.00 0.00 3.86
1019 1023 2.362797 TGGGTAGGGTATTGGTTCCA 57.637 50.000 0.00 0.00 0.00 3.53
1020 1024 3.743092 TTTGGGTAGGGTATTGGTTCC 57.257 47.619 0.00 0.00 0.00 3.62
1021 1025 4.647853 GGAATTTGGGTAGGGTATTGGTTC 59.352 45.833 0.00 0.00 0.00 3.62
1028 1032 1.215140 CGGGGAATTTGGGTAGGGTA 58.785 55.000 0.00 0.00 0.00 3.69
1033 1037 0.917333 AGGAGCGGGGAATTTGGGTA 60.917 55.000 0.00 0.00 0.00 3.69
1110 1115 1.150567 CCTCATTCTTCTCGGCAGCG 61.151 60.000 0.00 0.00 0.00 5.18
1113 1118 1.153568 CGCCTCATTCTTCTCGGCA 60.154 57.895 0.00 0.00 40.72 5.69
1115 1120 0.108138 AACCGCCTCATTCTTCTCGG 60.108 55.000 0.00 0.00 42.24 4.63
1167 1416 4.373116 GACCCAGCCGCTTCGTCA 62.373 66.667 10.47 0.00 0.00 4.35
1177 1426 3.721706 CCTGGACCTGGACCCAGC 61.722 72.222 24.40 0.00 46.52 4.85
1256 1511 2.280389 CGATGGTGGCGAGGATGG 60.280 66.667 0.00 0.00 0.00 3.51
1372 1627 1.734477 CGTTGGAGCAGAGGTCGTG 60.734 63.158 0.00 0.00 0.00 4.35
1522 1777 2.742372 CGGGGAGTTGAACCAGCG 60.742 66.667 0.00 0.00 0.00 5.18
1564 1819 6.621316 TTCTAAGAGCGAGAAGACGATATT 57.379 37.500 0.00 0.00 37.00 1.28
1584 1839 4.950475 TCAGACTGTCCAGACGAATATTCT 59.050 41.667 13.45 0.93 0.00 2.40
1595 1850 2.801483 TCTCCTTCTCAGACTGTCCAG 58.199 52.381 3.76 1.09 0.00 3.86
1767 2023 1.899437 GCACCCCGGAGAAGACATCA 61.899 60.000 0.73 0.00 0.00 3.07
1878 2134 5.450412 GCCTTCAAACAAACAAGAGATGACA 60.450 40.000 0.00 0.00 0.00 3.58
1903 2159 5.310409 TCCATAATGACCAATTCTCCCTC 57.690 43.478 0.00 0.00 0.00 4.30
1905 2161 4.401925 CCTCCATAATGACCAATTCTCCC 58.598 47.826 0.00 0.00 0.00 4.30
2004 2260 1.538687 AAAGGCCCAACATCTGCAGC 61.539 55.000 9.47 0.00 0.00 5.25
2068 2324 4.956700 AGAGACTAATGCAGCTGTTACCTA 59.043 41.667 16.64 0.00 0.00 3.08
2095 2351 8.907885 GTGAGAATTCCATTTAATTAAGAGCCT 58.092 33.333 0.65 0.00 0.00 4.58
2096 2352 8.907885 AGTGAGAATTCCATTTAATTAAGAGCC 58.092 33.333 0.65 0.00 0.00 4.70
2471 2776 4.166725 AGGCATTTGATTGGATCTAGTGGA 59.833 41.667 0.00 0.00 0.00 4.02
2575 2881 4.497473 TCCTTTACCACTTTTGCATTCG 57.503 40.909 0.00 0.00 0.00 3.34
2649 2955 2.284263 TCTAGCAGCGTGAGTTGATG 57.716 50.000 0.00 0.00 46.01 3.07
2687 2993 5.412594 TCTGAATTTGAATACAGTGTCTGGC 59.587 40.000 0.00 0.00 35.51 4.85
2771 3082 4.728608 CGTCTAAAACAACAACAGCTGAAC 59.271 41.667 23.35 0.00 0.00 3.18
2845 3161 4.582701 ATTCATGAACGAAGCAACCAAA 57.417 36.364 11.07 0.00 0.00 3.28
2861 3177 8.985315 ACACAATCATCAGGTACATAATTCAT 57.015 30.769 0.00 0.00 0.00 2.57
2862 3178 8.676401 CAACACAATCATCAGGTACATAATTCA 58.324 33.333 0.00 0.00 0.00 2.57
2863 3179 8.677300 ACAACACAATCATCAGGTACATAATTC 58.323 33.333 0.00 0.00 0.00 2.17
2880 3200 3.469008 TCAGACGGAAGACAACACAAT 57.531 42.857 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.