Multiple sequence alignment - TraesCS3D01G113600

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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 TraesCS3D01G113600 chr3D 100.000 5222 0 0 1 5222 67545653 67540432 0.000000e+00 9644
1 TraesCS3D01G113600 chr3D 96.829 883 23 2 1 879 306013760 306014641 0.000000e+00 1471
2 TraesCS3D01G113600 chr3D 96.036 883 29 3 1 879 552472888 552472008 0.000000e+00 1432
3 TraesCS3D01G113600 chr3B 89.720 3969 205 79 880 4722 114877544 114881435 0.000000e+00 4881
4 TraesCS3D01G113600 chr3B 95.070 142 7 0 4766 4907 806968745 806968604 1.890000e-54 224
5 TraesCS3D01G113600 chr3B 93.706 143 8 1 4765 4907 688578000 688577859 4.100000e-51 213
6 TraesCS3D01G113600 chr3B 92.958 142 10 0 4766 4907 56905512 56905653 1.910000e-49 207
7 TraesCS3D01G113600 chr3A 93.560 1910 89 22 2883 4765 78901059 78899157 0.000000e+00 2815
8 TraesCS3D01G113600 chr3A 92.372 1193 46 18 880 2039 78903317 78902137 0.000000e+00 1657
9 TraesCS3D01G113600 chr3A 85.674 356 30 11 2169 2513 78902008 78901663 6.430000e-94 355
10 TraesCS3D01G113600 chr3A 96.629 178 6 0 4902 5079 579042933 579042756 3.950000e-76 296
11 TraesCS3D01G113600 chr3A 86.175 217 11 11 2587 2794 78901318 78901112 3.170000e-52 217
12 TraesCS3D01G113600 chr7D 97.065 886 21 2 1 882 610710793 610709909 0.000000e+00 1487
13 TraesCS3D01G113600 chr7D 96.388 886 28 2 1 882 568380389 568379504 0.000000e+00 1456
14 TraesCS3D01G113600 chr7D 96.384 885 26 3 1 881 534622424 534621542 0.000000e+00 1452
15 TraesCS3D01G113600 chr2D 96.610 885 25 2 1 881 638775609 638774726 0.000000e+00 1463
16 TraesCS3D01G113600 chr2D 97.508 321 8 0 4902 5222 312054009 312053689 2.750000e-152 549
17 TraesCS3D01G113600 chr2D 96.629 178 5 1 4902 5079 604060656 604060832 1.420000e-75 294
18 TraesCS3D01G113600 chr2D 98.592 142 2 0 4766 4907 312054398 312054257 8.680000e-63 252
19 TraesCS3D01G113600 chr2D 92.466 146 9 2 4763 4907 604060264 604060408 1.910000e-49 207
20 TraesCS3D01G113600 chr5D 96.376 883 28 1 1 879 501156856 501157738 0.000000e+00 1450
21 TraesCS3D01G113600 chr7A 96.259 882 27 3 1 878 183661844 183660965 0.000000e+00 1441
22 TraesCS3D01G113600 chr7A 96.629 178 6 0 4902 5079 329162987 329163164 3.950000e-76 296
23 TraesCS3D01G113600 chr7A 94.595 148 8 0 5074 5221 509806978 509806831 4.070000e-56 230
24 TraesCS3D01G113600 chr1D 96.263 883 26 3 1 879 2468145 2467266 0.000000e+00 1441
25 TraesCS3D01G113600 chr6D 98.361 305 5 0 4902 5206 454296433 454296737 2.140000e-148 536
26 TraesCS3D01G113600 chr6D 96.129 155 4 2 4753 4906 454296031 454296184 8.680000e-63 252
27 TraesCS3D01G113600 chrUn 97.191 178 5 0 4902 5079 3260230 3260053 8.500000e-78 302
28 TraesCS3D01G113600 chr5A 97.191 178 5 0 4902 5079 431668468 431668645 8.500000e-78 302
29 TraesCS3D01G113600 chr4B 96.629 178 6 0 4902 5079 546124473 546124296 3.950000e-76 296
30 TraesCS3D01G113600 chr4B 95.862 145 6 0 4763 4907 636704270 636704414 8.740000e-58 235
31 TraesCS3D01G113600 chr4B 81.557 244 35 8 4417 4655 33621816 33621578 5.340000e-45 193
32 TraesCS3D01G113600 chr1A 96.067 178 7 0 4902 5079 6645851 6646028 1.840000e-74 291
33 TraesCS3D01G113600 chr4D 93.151 146 10 0 5076 5221 19506366 19506221 1.140000e-51 215
34 TraesCS3D01G113600 chr4D 83.626 171 23 5 4421 4588 21152620 21152788 7.000000e-34 156
35 TraesCS3D01G113600 chr6B 93.662 142 9 0 4766 4907 65854866 65854725 4.100000e-51 213
36 TraesCS3D01G113600 chr6B 93.662 142 9 0 4766 4907 65875360 65875219 4.100000e-51 213
37 TraesCS3D01G113600 chr4A 81.557 244 35 10 4421 4658 580304476 580304715 5.340000e-45 193


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 TraesCS3D01G113600 chr3D 67540432 67545653 5221 True 9644.0 9644 100.00000 1 5222 1 chr3D.!!$R1 5221
1 TraesCS3D01G113600 chr3D 306013760 306014641 881 False 1471.0 1471 96.82900 1 879 1 chr3D.!!$F1 878
2 TraesCS3D01G113600 chr3D 552472008 552472888 880 True 1432.0 1432 96.03600 1 879 1 chr3D.!!$R2 878
3 TraesCS3D01G113600 chr3B 114877544 114881435 3891 False 4881.0 4881 89.72000 880 4722 1 chr3B.!!$F2 3842
4 TraesCS3D01G113600 chr3A 78899157 78903317 4160 True 1261.0 2815 89.44525 880 4765 4 chr3A.!!$R2 3885
5 TraesCS3D01G113600 chr7D 610709909 610710793 884 True 1487.0 1487 97.06500 1 882 1 chr7D.!!$R3 881
6 TraesCS3D01G113600 chr7D 568379504 568380389 885 True 1456.0 1456 96.38800 1 882 1 chr7D.!!$R2 881
7 TraesCS3D01G113600 chr7D 534621542 534622424 882 True 1452.0 1452 96.38400 1 881 1 chr7D.!!$R1 880
8 TraesCS3D01G113600 chr2D 638774726 638775609 883 True 1463.0 1463 96.61000 1 881 1 chr2D.!!$R1 880
9 TraesCS3D01G113600 chr2D 312053689 312054398 709 True 400.5 549 98.05000 4766 5222 2 chr2D.!!$R2 456
10 TraesCS3D01G113600 chr2D 604060264 604060832 568 False 250.5 294 94.54750 4763 5079 2 chr2D.!!$F1 316
11 TraesCS3D01G113600 chr5D 501156856 501157738 882 False 1450.0 1450 96.37600 1 879 1 chr5D.!!$F1 878
12 TraesCS3D01G113600 chr7A 183660965 183661844 879 True 1441.0 1441 96.25900 1 878 1 chr7A.!!$R1 877
13 TraesCS3D01G113600 chr1D 2467266 2468145 879 True 1441.0 1441 96.26300 1 879 1 chr1D.!!$R1 878
14 TraesCS3D01G113600 chr6D 454296031 454296737 706 False 394.0 536 97.24500 4753 5206 2 chr6D.!!$F1 453

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
582 587 0.949105 ACAACGATCGGAGCACCAAC 60.949 55.0 20.98 0.0 35.59 3.77 F
1085 1102 0.450184 AAAACTCCACACACACACGC 59.550 50.0 0.00 0.0 0.00 5.34 F
2258 2375 0.102300 ACTTTTGTTCTGTTGCGGGC 59.898 50.0 0.00 0.0 0.00 6.13 F
2861 3347 0.180406 AGCGTGTGGGAGTTTTGAGT 59.820 50.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2070 2155 0.108756 GACCACTCAACCTAGCCGAC 60.109 60.0 0.00 0.0 0.00 4.79 R
2967 3453 0.317854 GCACTTTTCTGCCGAACCAC 60.318 55.0 0.00 0.0 0.00 4.16 R
3982 4482 0.036010 CATGCCAAGGTTCTCTCGGT 60.036 55.0 0.00 0.0 0.00 4.69 R
4764 5289 0.179134 GCACGGGCAGTCTACTAGTG 60.179 60.0 3.77 0.0 40.72 2.74 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
103 104 9.176460 GGTCTTTTACAGTAGACTCTATGTACT 57.824 37.037 0.00 0.00 40.45 2.73
109 110 4.333095 CAGTAGACTCTATGTACTGTGCGT 59.667 45.833 3.68 0.00 45.77 5.24
130 131 3.678056 TCACACATTCTGAGGTACCAC 57.322 47.619 15.94 8.81 0.00 4.16
282 287 5.007234 TGTTGTTTTTGTACTCATGACGAGG 59.993 40.000 0.00 0.00 46.98 4.63
363 368 7.442969 TCCAAATAGCGTCAAATTTATATCCGT 59.557 33.333 0.00 0.00 0.00 4.69
446 451 2.302157 GCTTATAAGGGTGGGAGCGTAT 59.698 50.000 14.28 0.00 0.00 3.06
551 556 2.882324 TGTACGCAATCGCTTCATACA 58.118 42.857 0.00 0.00 39.84 2.29
582 587 0.949105 ACAACGATCGGAGCACCAAC 60.949 55.000 20.98 0.00 35.59 3.77
594 599 1.444119 GCACCAACCGCTGTTCAAGA 61.444 55.000 0.00 0.00 30.42 3.02
802 807 3.472283 CATCTCAGTTATGCAGAGGCT 57.528 47.619 0.00 0.00 41.91 4.58
1042 1059 4.832823 CCAAACTCCATTTAAGGAACCAGT 59.167 41.667 0.00 0.00 37.20 4.00
1082 1099 1.821753 CCCAAAAACTCCACACACACA 59.178 47.619 0.00 0.00 0.00 3.72
1083 1100 2.416701 CCCAAAAACTCCACACACACAC 60.417 50.000 0.00 0.00 0.00 3.82
1084 1101 2.514902 CAAAAACTCCACACACACACG 58.485 47.619 0.00 0.00 0.00 4.49
1085 1102 0.450184 AAAACTCCACACACACACGC 59.550 50.000 0.00 0.00 0.00 5.34
1086 1103 1.701545 AAACTCCACACACACACGCG 61.702 55.000 3.53 3.53 0.00 6.01
1087 1104 4.000557 CTCCACACACACACGCGC 62.001 66.667 5.73 0.00 0.00 6.86
1581 1623 0.552363 TATGCACATGCTCCCACCAT 59.448 50.000 5.31 0.00 42.66 3.55
1659 1705 3.768185 ATCGTTGATCCGGTCGCGG 62.768 63.158 6.13 0.00 0.00 6.46
1668 1714 4.253257 CGGTCGCGGGAGTAGAGC 62.253 72.222 6.13 0.00 35.16 4.09
1686 1732 2.257067 GAGCTAGATCCGCTCGCC 59.743 66.667 16.09 0.00 43.69 5.54
1711 1757 1.412361 GGTAGATCTGGGGAGCAGAGT 60.412 57.143 5.18 0.00 31.61 3.24
1712 1758 2.393646 GTAGATCTGGGGAGCAGAGTT 58.606 52.381 5.18 0.00 31.61 3.01
1803 1872 1.355381 TCGTGGGTAGGTAGTGGAGAA 59.645 52.381 0.00 0.00 0.00 2.87
1812 1881 5.659971 GGTAGGTAGTGGAGAAGATTGGTTA 59.340 44.000 0.00 0.00 0.00 2.85
1839 1908 3.083997 GGTCGGGGAGGCTGTCAT 61.084 66.667 0.00 0.00 0.00 3.06
1845 1914 2.606587 GGGAGGCTGTCATGTGGGT 61.607 63.158 0.00 0.00 0.00 4.51
1960 2031 2.046892 CCGGAGTGGTGAAGCAGG 60.047 66.667 0.00 0.00 0.00 4.85
1989 2066 0.657840 GTGTGTGCCTGTGAAGTGTC 59.342 55.000 0.00 0.00 0.00 3.67
1998 2075 2.744202 CCTGTGAAGTGTCAAGCATACC 59.256 50.000 0.00 0.00 34.87 2.73
1999 2076 3.402110 CTGTGAAGTGTCAAGCATACCA 58.598 45.455 0.00 0.00 34.87 3.25
2008 2085 3.055747 TGTCAAGCATACCACCGTGATTA 60.056 43.478 0.00 0.00 0.00 1.75
2013 2090 2.878406 GCATACCACCGTGATTAGCAAT 59.122 45.455 0.00 0.00 0.00 3.56
2014 2091 3.315191 GCATACCACCGTGATTAGCAATT 59.685 43.478 0.00 0.00 0.00 2.32
2015 2092 4.554723 GCATACCACCGTGATTAGCAATTC 60.555 45.833 0.00 0.00 0.00 2.17
2045 2130 4.160814 TGCCACTTTCGTCCTTATTAGCTA 59.839 41.667 0.00 0.00 0.00 3.32
2051 2136 3.216800 TCGTCCTTATTAGCTAAGCCGA 58.783 45.455 12.54 9.42 37.15 5.54
2052 2137 3.252701 TCGTCCTTATTAGCTAAGCCGAG 59.747 47.826 12.54 6.74 35.84 4.63
2053 2138 3.318886 GTCCTTATTAGCTAAGCCGAGC 58.681 50.000 12.54 0.00 43.19 5.03
2062 2147 3.642778 TAAGCCGAGCCTGTGACGC 62.643 63.158 0.00 0.00 0.00 5.19
2097 2182 3.998672 TTGAGTGGTCCCGTCGCC 61.999 66.667 0.00 0.00 0.00 5.54
2135 2220 2.238646 TGCCTGGAACCGATAAGAATGT 59.761 45.455 0.00 0.00 0.00 2.71
2258 2375 0.102300 ACTTTTGTTCTGTTGCGGGC 59.898 50.000 0.00 0.00 0.00 6.13
2359 2485 4.302509 TGTGGTACGGTGGTGGCG 62.303 66.667 0.00 0.00 0.00 5.69
2360 2486 4.303993 GTGGTACGGTGGTGGCGT 62.304 66.667 0.00 0.00 0.00 5.68
2361 2487 3.993584 TGGTACGGTGGTGGCGTC 61.994 66.667 0.00 0.00 0.00 5.19
2362 2488 4.747529 GGTACGGTGGTGGCGTCC 62.748 72.222 0.00 0.00 0.00 4.79
2363 2489 3.993584 GTACGGTGGTGGCGTCCA 61.994 66.667 0.00 0.00 34.85 4.02
2364 2490 3.687102 TACGGTGGTGGCGTCCAG 61.687 66.667 1.49 0.00 38.23 3.86
2372 2498 1.375523 GTGGCGTCCAGTGGGTTAG 60.376 63.158 9.92 0.00 32.34 2.34
2384 2510 1.209523 TGGGTTAGGGGTGGTTAGGC 61.210 60.000 0.00 0.00 0.00 3.93
2388 2514 1.209747 GTTAGGGGTGGTTAGGCAGAG 59.790 57.143 0.00 0.00 0.00 3.35
2500 2672 2.039818 TGACCTCTAGGCGTACTGAG 57.960 55.000 0.00 0.00 39.32 3.35
2509 2681 2.522185 AGGCGTACTGAGTTGGACTTA 58.478 47.619 0.00 0.00 0.00 2.24
2515 2687 5.710984 CGTACTGAGTTGGACTTATTGACT 58.289 41.667 0.00 0.00 0.00 3.41
2516 2688 5.800941 CGTACTGAGTTGGACTTATTGACTC 59.199 44.000 0.00 0.00 37.75 3.36
2518 2690 4.281182 ACTGAGTTGGACTTATTGACTCGT 59.719 41.667 0.00 0.00 39.57 4.18
2540 2718 1.728971 CCTAGCGATGATGGCGATTTC 59.271 52.381 0.00 0.00 35.00 2.17
2570 2754 4.098044 TCTGGCTAGGAGTTGTCTTAATCG 59.902 45.833 0.00 0.00 0.00 3.34
2581 2765 7.011202 GGAGTTGTCTTAATCGGGATTAGTTTC 59.989 40.741 1.79 0.00 35.02 2.78
2587 2771 2.981859 TCGGGATTAGTTTCAGGCTC 57.018 50.000 0.00 0.00 0.00 4.70
2652 3106 3.071023 GCCAGATTATGCCTGTAGGTGTA 59.929 47.826 0.00 0.00 37.57 2.90
2653 3107 4.800914 GCCAGATTATGCCTGTAGGTGTAG 60.801 50.000 0.00 0.00 37.57 2.74
2654 3108 4.262635 CCAGATTATGCCTGTAGGTGTAGG 60.263 50.000 0.00 0.00 37.57 3.18
2655 3109 4.345257 CAGATTATGCCTGTAGGTGTAGGT 59.655 45.833 0.00 0.00 36.44 3.08
2656 3110 4.345257 AGATTATGCCTGTAGGTGTAGGTG 59.655 45.833 0.00 0.00 36.44 4.00
2657 3111 1.952621 ATGCCTGTAGGTGTAGGTGT 58.047 50.000 0.00 0.00 36.44 4.16
2679 3133 4.342862 TGTCCTTGCCAGATAAGATAGC 57.657 45.455 0.00 0.00 0.00 2.97
2680 3134 3.969976 TGTCCTTGCCAGATAAGATAGCT 59.030 43.478 0.00 0.00 0.00 3.32
2688 3142 4.837896 CAGATAAGATAGCTGGTGTCGA 57.162 45.455 0.00 0.00 38.48 4.20
2697 3156 0.654683 GCTGGTGTCGATCTGAATGC 59.345 55.000 0.00 0.00 0.00 3.56
2745 3205 0.533755 GTCGGAGAGCCCATCCATTG 60.534 60.000 0.92 0.00 36.95 2.82
2767 3227 2.028925 GCTTTTGTTGCCCACCGG 59.971 61.111 0.00 0.00 0.00 5.28
2861 3347 0.180406 AGCGTGTGGGAGTTTTGAGT 59.820 50.000 0.00 0.00 0.00 3.41
2865 3351 3.463944 CGTGTGGGAGTTTTGAGTAGTT 58.536 45.455 0.00 0.00 0.00 2.24
2868 3354 5.508489 CGTGTGGGAGTTTTGAGTAGTTAGA 60.508 44.000 0.00 0.00 0.00 2.10
2878 3364 9.145442 AGTTTTGAGTAGTTAGAGGAGTACTTT 57.855 33.333 0.00 0.00 36.24 2.66
2967 3453 1.282248 CGCCCGTACCTTGATATGCG 61.282 60.000 0.00 0.00 34.52 4.73
3045 3535 1.761198 AGGACAGCCTACGGGAATTAC 59.239 52.381 0.00 0.00 44.74 1.89
3063 3553 2.677542 ACGGGAGCATCTACAGGATA 57.322 50.000 0.00 0.00 32.64 2.59
3071 3561 6.064717 GGAGCATCTACAGGATATTGGTTTT 58.935 40.000 0.00 0.00 32.64 2.43
3091 3581 2.985896 TGGTACTACAGCAAATCCAGC 58.014 47.619 0.00 0.00 0.00 4.85
3110 3603 3.908382 CAGCGCTGACATTTCAAACTTAC 59.092 43.478 33.66 0.00 0.00 2.34
3447 3944 3.426568 GTGCTGACGGCCAAGCTC 61.427 66.667 19.53 13.83 40.92 4.09
3587 4084 1.153628 CCGTGAAGATGTCCGGGAC 60.154 63.158 20.36 20.36 36.79 4.46
3624 4121 1.590147 GTCGTCGGTGATGGAGGTT 59.410 57.895 0.00 0.00 0.00 3.50
3981 4481 0.790207 TCGCTTTGCTTTGCTAGACG 59.210 50.000 0.00 0.00 0.00 4.18
3982 4482 0.790207 CGCTTTGCTTTGCTAGACGA 59.210 50.000 0.00 0.00 0.00 4.20
3983 4483 1.462541 CGCTTTGCTTTGCTAGACGAC 60.463 52.381 0.00 0.00 0.00 4.34
4050 4558 2.186384 GAGCTCTGCTGATGCGGT 59.814 61.111 6.43 0.00 45.38 5.68
4053 4561 2.789917 CTCTGCTGATGCGGTTGC 59.210 61.111 0.00 0.00 45.38 4.17
4069 4577 4.792704 GCGGTTGCTTGGTTGATATATTGG 60.793 45.833 0.00 0.00 38.39 3.16
4158 4670 6.978659 TGAGCAATACGTTACCATTCTTAGAG 59.021 38.462 0.00 0.00 0.00 2.43
4240 4752 5.391312 ACCTGCATTTGGTTACTTGATTC 57.609 39.130 0.00 0.00 33.34 2.52
4256 4768 6.051074 ACTTGATTCATGATCGCTTGTATGA 58.949 36.000 0.00 0.00 37.60 2.15
4263 4775 4.277257 TGATCGCTTGTATGATTGCAAC 57.723 40.909 0.00 0.00 0.00 4.17
4299 4812 2.099756 GAGGCATGGCGCTTTTAGATTT 59.900 45.455 15.84 0.00 41.91 2.17
4324 4841 3.755112 TTTTGAGTCGTGTATGGTGGA 57.245 42.857 0.00 0.00 0.00 4.02
4351 4868 1.526917 CTGCGGGCCATAGGGAAAG 60.527 63.158 4.39 0.00 35.59 2.62
4352 4869 2.270874 CTGCGGGCCATAGGGAAAGT 62.271 60.000 4.39 0.00 35.59 2.66
4449 4972 3.181465 CGTTTAGTCCCACATGGCTAGAT 60.181 47.826 0.00 0.00 0.00 1.98
4450 4973 4.683400 CGTTTAGTCCCACATGGCTAGATT 60.683 45.833 0.00 0.00 0.00 2.40
4459 4982 5.396772 CCCACATGGCTAGATTAGAAGAACA 60.397 44.000 0.00 0.00 0.00 3.18
4461 4984 6.426328 CCACATGGCTAGATTAGAAGAACATC 59.574 42.308 0.00 0.00 0.00 3.06
4545 5068 3.379650 CGTAGATGAACGGGGCAAT 57.620 52.632 0.00 0.00 39.19 3.56
4607 5130 5.734220 GCAGCTCTCTGAAATCTCACTAGAG 60.734 48.000 0.00 0.00 42.95 2.43
4659 5184 1.596934 CTCCCGCAGCTTGTTAGGA 59.403 57.895 0.00 0.00 0.00 2.94
4660 5185 0.036388 CTCCCGCAGCTTGTTAGGAA 60.036 55.000 0.00 0.00 0.00 3.36
4663 5188 1.234821 CCGCAGCTTGTTAGGAAACA 58.765 50.000 0.00 0.00 43.85 2.83
4708 5233 0.106819 AGTATCCGTGTACCGCTCCT 60.107 55.000 0.00 0.00 34.38 3.69
4722 5247 0.248843 GCTCCTGCAGCTTGTCTAGT 59.751 55.000 8.66 0.00 45.83 2.57
5116 5894 2.780924 AACCAGGGGTGGAGGCAA 60.781 61.111 0.00 0.00 35.34 4.52
5195 5973 3.275617 ACTACTGGAAACTTGTGTGCA 57.724 42.857 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 1.072331 AGGTTCCAGCGAAACACATCT 59.928 47.619 0.00 0.00 38.24 2.90
109 110 3.646162 AGTGGTACCTCAGAATGTGTGAA 59.354 43.478 14.36 0.00 37.40 3.18
282 287 4.692228 TGGAAAAAGAGGTGTTTGATTGC 58.308 39.130 0.00 0.00 0.00 3.56
446 451 2.083774 CAGAGCGACCAAATTAAGGCA 58.916 47.619 0.00 0.00 0.00 4.75
551 556 3.305403 CCGATCGTTGTAGCATAGACCAT 60.305 47.826 15.09 0.00 0.00 3.55
582 587 1.594293 ACACCGTCTTGAACAGCGG 60.594 57.895 0.00 0.00 43.74 5.52
594 599 2.625973 TTCAACCGCGTACACACCGT 62.626 55.000 4.92 0.00 0.00 4.83
802 807 8.871629 ATACAAAACATTATGAGTAACACCCA 57.128 30.769 0.00 0.00 0.00 4.51
1086 1103 4.704833 TGGGCTTCTGTGAGGCGC 62.705 66.667 0.00 0.00 45.06 6.53
1087 1104 2.435586 CTGGGCTTCTGTGAGGCG 60.436 66.667 0.00 0.00 42.68 5.52
1659 1705 2.081462 GGATCTAGCTCGCTCTACTCC 58.919 57.143 0.00 0.00 0.00 3.85
1682 1728 4.889112 AGATCTACCCGCGGGCGA 62.889 66.667 43.58 36.66 42.83 5.54
1686 1732 3.616721 CCCCAGATCTACCCGCGG 61.617 72.222 21.04 21.04 0.00 6.46
1711 1757 6.095860 CCATCCATCAGCTTTTGACTTATCAA 59.904 38.462 0.00 0.00 43.28 2.57
1712 1758 5.591472 CCATCCATCAGCTTTTGACTTATCA 59.409 40.000 0.00 0.00 38.99 2.15
1803 1872 1.203994 CCGACACCGTCTAACCAATCT 59.796 52.381 0.00 0.00 0.00 2.40
1893 1962 3.377172 AGCCGTTAATTACTCCATGCAAC 59.623 43.478 0.00 0.00 0.00 4.17
1895 1964 3.275617 AGCCGTTAATTACTCCATGCA 57.724 42.857 0.00 0.00 0.00 3.96
1960 2031 3.044305 GCACACACCACGAGCTCC 61.044 66.667 8.47 0.00 0.00 4.70
1989 2066 2.287915 GCTAATCACGGTGGTATGCTTG 59.712 50.000 8.50 0.00 0.00 4.01
1998 2075 2.355756 CCTGGAATTGCTAATCACGGTG 59.644 50.000 0.56 0.56 0.00 4.94
1999 2076 2.643551 CCTGGAATTGCTAATCACGGT 58.356 47.619 0.00 0.00 0.00 4.83
2013 2090 1.172180 CGAAAGTGGCAAGCCTGGAA 61.172 55.000 12.96 0.00 36.94 3.53
2014 2091 1.600636 CGAAAGTGGCAAGCCTGGA 60.601 57.895 12.96 0.00 36.94 3.86
2015 2092 1.898574 ACGAAAGTGGCAAGCCTGG 60.899 57.895 12.96 0.00 46.97 4.45
2070 2155 0.108756 GACCACTCAACCTAGCCGAC 60.109 60.000 0.00 0.00 0.00 4.79
2074 2159 1.218316 CGGGACCACTCAACCTAGC 59.782 63.158 0.00 0.00 0.00 3.42
2097 2182 0.591741 GCAGCTACTAGTACGTGCCG 60.592 60.000 16.26 6.12 0.00 5.69
2163 2268 0.958382 CCTGAAACGCCGGGATTTCA 60.958 55.000 19.65 19.65 41.38 2.69
2258 2375 1.201578 CCGCATTACGCATACGCAG 59.798 57.895 0.00 0.00 45.53 5.18
2359 2485 1.683441 CACCCCTAACCCACTGGAC 59.317 63.158 0.00 0.00 34.81 4.02
2360 2486 1.540367 CCACCCCTAACCCACTGGA 60.540 63.158 0.00 0.00 34.81 3.86
2361 2487 1.432023 AACCACCCCTAACCCACTGG 61.432 60.000 0.00 0.00 37.80 4.00
2362 2488 1.280998 CTAACCACCCCTAACCCACTG 59.719 57.143 0.00 0.00 0.00 3.66
2363 2489 1.665137 CTAACCACCCCTAACCCACT 58.335 55.000 0.00 0.00 0.00 4.00
2364 2490 0.622136 CCTAACCACCCCTAACCCAC 59.378 60.000 0.00 0.00 0.00 4.61
2365 2491 1.209523 GCCTAACCACCCCTAACCCA 61.210 60.000 0.00 0.00 0.00 4.51
2366 2492 1.209523 TGCCTAACCACCCCTAACCC 61.210 60.000 0.00 0.00 0.00 4.11
2372 2498 1.602771 GACTCTGCCTAACCACCCC 59.397 63.158 0.00 0.00 0.00 4.95
2509 2681 1.338337 CATCGCTAGGGACGAGTCAAT 59.662 52.381 12.26 0.00 43.74 2.57
2515 2687 1.806461 GCCATCATCGCTAGGGACGA 61.806 60.000 12.26 10.08 44.75 4.20
2516 2688 1.373497 GCCATCATCGCTAGGGACG 60.373 63.158 12.26 3.73 0.00 4.79
2518 2690 0.900182 ATCGCCATCATCGCTAGGGA 60.900 55.000 12.40 12.40 0.00 4.20
2542 2720 2.102252 GACAACTCCTAGCCAGATGAGG 59.898 54.545 4.74 0.00 0.00 3.86
2544 2722 3.107402 AGACAACTCCTAGCCAGATGA 57.893 47.619 4.74 0.00 0.00 2.92
2545 2723 3.902881 AAGACAACTCCTAGCCAGATG 57.097 47.619 0.00 0.00 0.00 2.90
2546 2724 5.221342 CGATTAAGACAACTCCTAGCCAGAT 60.221 44.000 0.00 0.00 0.00 2.90
2550 2734 3.492829 CCCGATTAAGACAACTCCTAGCC 60.493 52.174 0.00 0.00 0.00 3.93
2556 2740 7.548075 TGAAACTAATCCCGATTAAGACAACTC 59.452 37.037 0.00 0.00 33.34 3.01
2557 2741 7.391620 TGAAACTAATCCCGATTAAGACAACT 58.608 34.615 0.00 0.00 33.34 3.16
2570 2754 1.300481 GCGAGCCTGAAACTAATCCC 58.700 55.000 0.00 0.00 0.00 3.85
2581 2765 1.590932 ATAATCAAGCTGCGAGCCTG 58.409 50.000 4.77 3.13 43.77 4.85
2587 2771 5.023920 CCGCATAATAATAATCAAGCTGCG 58.976 41.667 6.16 6.16 46.70 5.18
2652 3106 0.773644 ATCTGGCAAGGACAACACCT 59.226 50.000 0.00 0.00 42.69 4.00
2653 3107 2.489938 TATCTGGCAAGGACAACACC 57.510 50.000 0.00 0.00 0.00 4.16
2654 3108 3.674997 TCTTATCTGGCAAGGACAACAC 58.325 45.455 0.00 0.00 0.00 3.32
2655 3109 4.574674 ATCTTATCTGGCAAGGACAACA 57.425 40.909 0.00 0.00 0.00 3.33
2656 3110 4.513318 GCTATCTTATCTGGCAAGGACAAC 59.487 45.833 0.00 0.00 0.00 3.32
2657 3111 4.410228 AGCTATCTTATCTGGCAAGGACAA 59.590 41.667 0.00 0.00 0.00 3.18
2679 3133 2.014335 TGCATTCAGATCGACACCAG 57.986 50.000 0.00 0.00 0.00 4.00
2680 3134 2.282407 CATGCATTCAGATCGACACCA 58.718 47.619 0.00 0.00 0.00 4.17
2745 3205 0.598419 GTGGGCAACAAAAGCAGAGC 60.598 55.000 0.00 0.00 39.74 4.09
2767 3227 2.111878 ACTGACCAGCACACCAGC 59.888 61.111 0.00 0.00 0.00 4.85
2841 3327 1.414919 ACTCAAAACTCCCACACGCTA 59.585 47.619 0.00 0.00 0.00 4.26
2847 3333 5.245526 TCCTCTAACTACTCAAAACTCCCAC 59.754 44.000 0.00 0.00 0.00 4.61
2878 3364 5.064325 GCGCTGCAATCTAATCATCATCATA 59.936 40.000 0.00 0.00 0.00 2.15
2915 3401 4.094294 CACGAACAAAACACCAAGAGAGAA 59.906 41.667 0.00 0.00 0.00 2.87
2967 3453 0.317854 GCACTTTTCTGCCGAACCAC 60.318 55.000 0.00 0.00 0.00 4.16
3045 3535 3.368843 CCAATATCCTGTAGATGCTCCCG 60.369 52.174 0.00 0.00 36.33 5.14
3063 3553 6.295067 GGATTTGCTGTAGTACCAAAACCAAT 60.295 38.462 18.27 2.54 39.64 3.16
3071 3561 2.676750 CGCTGGATTTGCTGTAGTACCA 60.677 50.000 0.00 0.00 0.00 3.25
3091 3581 5.747565 TGAAGTAAGTTTGAAATGTCAGCG 58.252 37.500 0.00 0.00 34.49 5.18
3110 3603 3.251479 TCGTGATCTGGAACCATGAAG 57.749 47.619 0.00 0.00 0.00 3.02
3587 4084 3.368190 CTCAGCACCTCCCTGCTCG 62.368 68.421 0.00 0.00 44.58 5.03
3588 4085 2.583520 CTCAGCACCTCCCTGCTC 59.416 66.667 0.00 0.00 44.58 4.26
3593 4090 2.997897 ACGACCTCAGCACCTCCC 60.998 66.667 0.00 0.00 0.00 4.30
3595 4092 2.179517 CGACGACCTCAGCACCTC 59.820 66.667 0.00 0.00 0.00 3.85
3604 4101 2.052690 CCTCCATCACCGACGACCT 61.053 63.158 0.00 0.00 0.00 3.85
3605 4102 1.885163 AACCTCCATCACCGACGACC 61.885 60.000 0.00 0.00 0.00 4.79
3624 4121 1.545841 CCTCCCGGATCATGTCGATA 58.454 55.000 0.73 0.00 33.17 2.92
3981 4481 0.250513 ATGCCAAGGTTCTCTCGGTC 59.749 55.000 0.00 0.00 0.00 4.79
3982 4482 0.036010 CATGCCAAGGTTCTCTCGGT 60.036 55.000 0.00 0.00 0.00 4.69
3983 4483 1.372087 GCATGCCAAGGTTCTCTCGG 61.372 60.000 6.36 0.00 0.00 4.63
4050 4558 4.955450 AGCACCAATATATCAACCAAGCAA 59.045 37.500 0.00 0.00 0.00 3.91
4053 4561 8.169977 ACATTAGCACCAATATATCAACCAAG 57.830 34.615 0.00 0.00 0.00 3.61
4069 4577 7.537306 CAGGTACAAATACAACAACATTAGCAC 59.463 37.037 0.00 0.00 32.40 4.40
4132 4644 7.324935 TCTAAGAATGGTAACGTATTGCTCAA 58.675 34.615 0.00 0.00 42.51 3.02
4133 4645 6.869695 TCTAAGAATGGTAACGTATTGCTCA 58.130 36.000 0.00 0.00 42.51 4.26
4240 4752 4.477302 TGCAATCATACAAGCGATCATG 57.523 40.909 0.00 0.00 0.00 3.07
4256 4768 1.271597 GGTCCCTCTGAGTGTTGCAAT 60.272 52.381 0.59 0.00 0.00 3.56
4263 4775 1.612395 GCCTCTGGTCCCTCTGAGTG 61.612 65.000 3.66 0.00 32.88 3.51
4324 4841 2.032681 GGCCCGCAGAGACAAAGT 59.967 61.111 0.00 0.00 0.00 2.66
4351 4868 2.185004 TCTTGTGCTGGGCTTTAGAC 57.815 50.000 0.00 0.00 0.00 2.59
4352 4869 2.783135 CTTCTTGTGCTGGGCTTTAGA 58.217 47.619 0.00 0.00 0.00 2.10
4413 4936 1.802365 CTAAACGAAACCCAACCTCGG 59.198 52.381 0.00 0.00 36.90 4.63
4449 4972 8.842358 ATTTAAAGTGGTCGATGTTCTTCTAA 57.158 30.769 0.00 0.00 0.00 2.10
4450 4973 9.582431 CTATTTAAAGTGGTCGATGTTCTTCTA 57.418 33.333 0.00 0.00 0.00 2.10
4459 4982 3.793559 AGCGCTATTTAAAGTGGTCGAT 58.206 40.909 8.99 0.00 32.50 3.59
4461 4984 3.369756 TGAAGCGCTATTTAAAGTGGTCG 59.630 43.478 12.05 0.00 36.74 4.79
4545 5068 2.585330 TGTGAGGCTTGCAAATTCTGA 58.415 42.857 0.00 0.00 0.00 3.27
4607 5130 2.088950 TACCAGTCCGCTTGCTTAAC 57.911 50.000 0.00 0.00 0.00 2.01
4656 5181 7.775053 TGCTTAATTAAATCCAGTGTTTCCT 57.225 32.000 0.00 0.00 0.00 3.36
4659 5184 6.586082 CGCTTGCTTAATTAAATCCAGTGTTT 59.414 34.615 0.00 0.00 0.00 2.83
4660 5185 6.092748 CGCTTGCTTAATTAAATCCAGTGTT 58.907 36.000 0.00 0.00 0.00 3.32
4663 5188 4.947388 TCCGCTTGCTTAATTAAATCCAGT 59.053 37.500 0.00 0.00 0.00 4.00
4708 5233 7.510549 AAAAGAATTTACTAGACAAGCTGCA 57.489 32.000 1.02 0.00 37.28 4.41
4764 5289 0.179134 GCACGGGCAGTCTACTAGTG 60.179 60.000 3.77 0.00 40.72 2.74
5116 5894 0.038744 CTTGGGGAGTGGCAGAATGT 59.961 55.000 0.00 0.00 39.31 2.71


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

AutoCloner maintained by Alex Coulton.