Multiple sequence alignment - TraesCS2A01G189800

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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 TraesCS2A01G189800 chr2A 100.000 3545 0 0 1 3545 156480209 156483753 0.000000e+00 6547.0
1 TraesCS2A01G189800 chr2A 86.681 458 36 7 38 474 150449395 150448942 5.320000e-133 484.0
2 TraesCS2A01G189800 chr2A 91.803 61 4 1 712 772 464937712 464937771 2.270000e-12 84.2
3 TraesCS2A01G189800 chr2A 91.803 61 4 1 712 772 464954086 464954145 2.270000e-12 84.2
4 TraesCS2A01G189800 chr2A 91.803 61 4 1 712 772 465345514 465345573 2.270000e-12 84.2
5 TraesCS2A01G189800 chr2A 95.122 41 2 0 1 41 150449684 150449644 8.210000e-07 65.8
6 TraesCS2A01G189800 chr2D 92.032 2397 106 47 254 2624 145733933 145731596 0.000000e+00 3290.0
7 TraesCS2A01G189800 chr2D 89.451 910 77 7 2614 3511 145724981 145724079 0.000000e+00 1131.0
8 TraesCS2A01G189800 chr2D 82.615 650 79 11 53 681 150924071 150924707 8.660000e-151 544.0
9 TraesCS2A01G189800 chr2D 95.238 42 2 0 1 42 150923779 150923820 2.280000e-07 67.6
10 TraesCS2A01G189800 chr1D 82.163 1452 214 28 1119 2546 214266796 214268226 0.000000e+00 1205.0
11 TraesCS2A01G189800 chr1B 81.768 1459 215 25 1119 2546 307170942 307172380 0.000000e+00 1173.0
12 TraesCS2A01G189800 chr1B 73.106 528 117 20 2034 2550 26856170 26855657 7.870000e-37 165.0
13 TraesCS2A01G189800 chr1B 88.618 123 13 1 3390 3511 505097243 505097365 7.930000e-32 148.0
14 TraesCS2A01G189800 chr1B 87.903 124 13 2 3390 3511 312046763 312046640 1.030000e-30 145.0
15 TraesCS2A01G189800 chr1B 79.082 196 37 4 2034 2227 26592191 26592384 7.990000e-27 132.0
16 TraesCS2A01G189800 chr1B 85.484 62 9 0 2092 2153 26617633 26617694 8.210000e-07 65.8
17 TraesCS2A01G189800 chr2B 85.064 549 51 9 38 565 209836010 209836548 6.740000e-147 531.0
18 TraesCS2A01G189800 chr2B 96.875 32 1 0 1 32 209833168 209833199 2.000000e-03 54.7
19 TraesCS2A01G189800 chr3B 73.764 526 120 15 2035 2554 556368920 556369433 1.300000e-44 191.0
20 TraesCS2A01G189800 chr3B 88.618 123 13 1 3390 3511 253890353 253890475 7.930000e-32 148.0
21 TraesCS2A01G189800 chr3B 86.822 129 15 2 3389 3516 148436901 148436774 3.690000e-30 143.0
22 TraesCS2A01G189800 chr4D 85.616 146 17 2 3369 3511 358085752 358085896 2.200000e-32 150.0
23 TraesCS2A01G189800 chr7D 90.566 106 7 2 3406 3511 424718595 424718697 1.720000e-28 137.0
24 TraesCS2A01G189800 chr7B 85.938 128 15 1 3387 3511 35865116 35865243 2.220000e-27 134.0
25 TraesCS2A01G189800 chr1A 86.066 122 16 1 3390 3510 280462566 280462445 2.870000e-26 130.0
26 TraesCS2A01G189800 chr4A 85.484 124 15 2 3388 3509 107229141 107229019 3.720000e-25 126.0


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 TraesCS2A01G189800 chr2A 156480209 156483753 3544 False 6547.00 6547 100.0000 1 3545 1 chr2A.!!$F1 3544
1 TraesCS2A01G189800 chr2A 150448942 150449684 742 True 274.90 484 90.9015 1 474 2 chr2A.!!$R1 473
2 TraesCS2A01G189800 chr2D 145731596 145733933 2337 True 3290.00 3290 92.0320 254 2624 1 chr2D.!!$R2 2370
3 TraesCS2A01G189800 chr2D 145724079 145724981 902 True 1131.00 1131 89.4510 2614 3511 1 chr2D.!!$R1 897
4 TraesCS2A01G189800 chr2D 150923779 150924707 928 False 305.80 544 88.9265 1 681 2 chr2D.!!$F1 680
5 TraesCS2A01G189800 chr1D 214266796 214268226 1430 False 1205.00 1205 82.1630 1119 2546 1 chr1D.!!$F1 1427
6 TraesCS2A01G189800 chr1B 307170942 307172380 1438 False 1173.00 1173 81.7680 1119 2546 1 chr1B.!!$F3 1427
7 TraesCS2A01G189800 chr2B 209833168 209836548 3380 False 292.85 531 90.9695 1 565 2 chr2B.!!$F1 564

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
35 2598 0.108567 GCCTCTTCTTCCTGACGACC 60.109 60.0 0.00 0.0 0.0 4.79 F
928 3780 0.179000 CAGACCTGAATTCCCCTCCG 59.821 60.0 2.27 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1986 4891 0.036858 AGTTCGAGGGCTTCTTGCTC 60.037 55.0 0.0 0.0 44.1 4.26 R
2812 5721 0.105913 GGGGGTGGGAAGAACAAACA 60.106 55.0 0.0 0.0 0.0 2.83 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
28 29 1.831652 CGGGTGTGCCTCTTCTTCCT 61.832 60.000 0.00 0.00 34.45 3.36
35 2598 0.108567 GCCTCTTCTTCCTGACGACC 60.109 60.000 0.00 0.00 0.00 4.79
79 2894 2.603135 GATGGCGCTGGCAATGACAC 62.603 60.000 7.64 0.00 42.43 3.67
101 2916 3.255397 AGCCTGTCCAGCCTTGCT 61.255 61.111 0.00 0.00 40.77 3.91
120 2935 1.217779 GACAGGCTCACTCTCTGGC 59.782 63.158 0.00 0.00 33.19 4.85
121 2936 1.534959 ACAGGCTCACTCTCTGGCA 60.535 57.895 0.00 0.00 33.19 4.92
122 2937 1.123861 ACAGGCTCACTCTCTGGCAA 61.124 55.000 0.00 0.00 33.19 4.52
123 2938 0.252479 CAGGCTCACTCTCTGGCAAT 59.748 55.000 0.00 0.00 0.00 3.56
142 2978 0.627451 TGGCAGGAATGGATTGAGCT 59.373 50.000 0.00 0.00 0.00 4.09
145 2981 2.652590 GCAGGAATGGATTGAGCTTCT 58.347 47.619 0.00 0.00 0.00 2.85
180 3016 1.140804 GTCTTCTCCCTCGAGCAGC 59.859 63.158 6.99 0.00 35.94 5.25
194 3030 1.946650 GCAGCTCATCGACCGCTAC 60.947 63.158 4.83 0.00 31.80 3.58
221 3057 2.528743 GCGACACGGAGATGGCATG 61.529 63.158 3.81 0.00 0.00 4.06
255 3091 4.162690 GAACGGAGGGGCGCATCT 62.163 66.667 15.29 5.41 0.00 2.90
286 3122 1.153449 CGGCCGAGCTCACCATTTA 60.153 57.895 24.07 0.00 0.00 1.40
298 3134 6.582636 AGCTCACCATTTATGAGAATCGTTA 58.417 36.000 6.19 0.00 45.46 3.18
336 3172 0.889306 GTCTCTGGAAGGCGTGTACT 59.111 55.000 0.00 0.00 0.00 2.73
337 3173 2.089980 GTCTCTGGAAGGCGTGTACTA 58.910 52.381 0.00 0.00 0.00 1.82
338 3174 2.490903 GTCTCTGGAAGGCGTGTACTAA 59.509 50.000 0.00 0.00 0.00 2.24
409 3248 1.797933 CACCGCAGAACTCGTCGAG 60.798 63.158 20.57 20.57 35.52 4.04
423 3262 1.077357 TCGAGGAGCAGAGACCTCC 60.077 63.158 0.00 0.00 46.87 4.30
429 3268 0.393808 GAGCAGAGACCTCCGACTCT 60.394 60.000 0.00 0.00 43.13 3.24
487 3326 1.614903 AGTACCCAACAACGACGATGA 59.385 47.619 12.41 0.00 0.00 2.92
491 3330 1.194547 CCCAACAACGACGATGAACTG 59.805 52.381 12.41 5.99 0.00 3.16
714 3560 7.342769 TGACAGTTGACAACTAGAAGTAAGA 57.657 36.000 20.17 0.64 40.46 2.10
721 3567 8.880750 GTTGACAACTAGAAGTAAGAAAACACT 58.119 33.333 11.18 0.00 0.00 3.55
722 3568 8.644318 TGACAACTAGAAGTAAGAAAACACTC 57.356 34.615 0.00 0.00 0.00 3.51
734 3580 8.709308 AGTAAGAAAACACTCTGCATATATCCT 58.291 33.333 0.00 0.00 0.00 3.24
837 3683 1.547372 GGGAATGATATGGTGCCATGC 59.453 52.381 13.57 6.49 37.82 4.06
928 3780 0.179000 CAGACCTGAATTCCCCTCCG 59.821 60.000 2.27 0.00 0.00 4.63
962 3814 2.513897 CGGACCTGAATTCCCCGC 60.514 66.667 2.27 0.00 33.47 6.13
983 3835 3.055530 GCCAGATCCAACTTCTCTCTCAA 60.056 47.826 0.00 0.00 0.00 3.02
1006 3858 4.080919 AGCAGACCTGACTATTTATGCACA 60.081 41.667 0.47 0.00 34.93 4.57
1031 3883 2.043772 CCCCCACCCCATCCTGTA 59.956 66.667 0.00 0.00 0.00 2.74
1032 3884 2.383601 CCCCCACCCCATCCTGTAC 61.384 68.421 0.00 0.00 0.00 2.90
1033 3885 2.383601 CCCCACCCCATCCTGTACC 61.384 68.421 0.00 0.00 0.00 3.34
1034 3886 2.742116 CCCACCCCATCCTGTACCG 61.742 68.421 0.00 0.00 0.00 4.02
1035 3887 1.993391 CCACCCCATCCTGTACCGT 60.993 63.158 0.00 0.00 0.00 4.83
1036 3888 0.688418 CCACCCCATCCTGTACCGTA 60.688 60.000 0.00 0.00 0.00 4.02
1037 3889 0.462789 CACCCCATCCTGTACCGTAC 59.537 60.000 1.40 1.40 0.00 3.67
1038 3890 0.337428 ACCCCATCCTGTACCGTACT 59.663 55.000 10.03 0.00 0.00 2.73
1039 3891 1.038280 CCCCATCCTGTACCGTACTC 58.962 60.000 10.03 0.00 0.00 2.59
1040 3892 1.038280 CCCATCCTGTACCGTACTCC 58.962 60.000 10.03 0.00 0.00 3.85
1041 3893 1.038280 CCATCCTGTACCGTACTCCC 58.962 60.000 10.03 0.00 0.00 4.30
1042 3894 1.687054 CCATCCTGTACCGTACTCCCA 60.687 57.143 10.03 0.00 0.00 4.37
1043 3895 2.104967 CATCCTGTACCGTACTCCCAA 58.895 52.381 10.03 0.00 0.00 4.12
1044 3896 2.537633 TCCTGTACCGTACTCCCAAT 57.462 50.000 10.03 0.00 0.00 3.16
1045 3897 2.823959 TCCTGTACCGTACTCCCAATT 58.176 47.619 10.03 0.00 0.00 2.32
1046 3898 2.762327 TCCTGTACCGTACTCCCAATTC 59.238 50.000 10.03 0.00 0.00 2.17
1047 3899 2.480759 CCTGTACCGTACTCCCAATTCG 60.481 54.545 10.03 0.00 0.00 3.34
1048 3900 1.135024 TGTACCGTACTCCCAATTCGC 60.135 52.381 10.03 0.00 0.00 4.70
1049 3901 0.461135 TACCGTACTCCCAATTCGCC 59.539 55.000 0.00 0.00 0.00 5.54
1050 3902 1.881252 CCGTACTCCCAATTCGCCG 60.881 63.158 0.00 0.00 0.00 6.46
1051 3903 1.881252 CGTACTCCCAATTCGCCGG 60.881 63.158 0.00 0.00 0.00 6.13
1052 3904 2.178235 GTACTCCCAATTCGCCGGC 61.178 63.158 19.07 19.07 0.00 6.13
1055 3907 4.352607 TCCCAATTCGCCGGCCAA 62.353 61.111 23.46 16.63 0.00 4.52
1058 3910 2.179018 CAATTCGCCGGCCAACAG 59.821 61.111 23.46 6.36 0.00 3.16
1066 3918 2.110967 CCGGCCAACAGATCTGCAG 61.111 63.158 22.83 14.57 0.00 4.41
1336 4218 1.814169 GGGATGCTCGACGGTTTCC 60.814 63.158 0.00 0.00 0.00 3.13
1452 4340 3.066233 GACCCTCCGGCTCGAGTTC 62.066 68.421 15.13 6.08 0.00 3.01
1809 4714 2.105128 GCGGACCTCGACCATCTG 59.895 66.667 0.00 0.00 42.43 2.90
1821 4726 2.261361 CATCTGGTGGTCGACGCA 59.739 61.111 9.92 6.05 0.00 5.24
1986 4891 0.698238 TGAACCTCACATTCTGGGGG 59.302 55.000 0.00 0.00 46.61 5.40
1995 4901 1.005215 ACATTCTGGGGGAGCAAGAAG 59.995 52.381 0.00 0.00 33.67 2.85
2056 4962 2.203523 TCGTCCTCCGGTTCACCA 60.204 61.111 0.00 0.00 37.11 4.17
2142 5048 3.056328 GCCGACCTGCCTTCCAAC 61.056 66.667 0.00 0.00 0.00 3.77
2204 5110 2.125753 GCTCGAGGTCCTGCACAG 60.126 66.667 15.58 0.00 0.00 3.66
2341 5247 1.802508 CGCAGACATCACGCCAGATAA 60.803 52.381 0.00 0.00 0.00 1.75
2347 5253 3.270877 ACATCACGCCAGATAAAGTTCC 58.729 45.455 0.00 0.00 0.00 3.62
2414 5320 2.036098 CAGGGATGGCCAAGTGCA 59.964 61.111 10.96 0.00 43.89 4.57
2487 5393 3.887716 GGAGCACTCATGATAAAATGGCT 59.112 43.478 0.00 0.00 0.00 4.75
2490 5396 5.439721 AGCACTCATGATAAAATGGCTGTA 58.560 37.500 0.00 0.00 0.00 2.74
2549 5455 6.652481 GTCGATGTAATCTTGGGATGATCAAT 59.348 38.462 0.00 0.00 42.58 2.57
2610 5516 5.278061 AGCCTAGGGTTCTGTTGACTTATA 58.722 41.667 7.93 0.00 0.00 0.98
2612 5518 6.049790 GCCTAGGGTTCTGTTGACTTATAAG 58.950 44.000 11.72 11.05 0.00 1.73
2619 5525 7.298854 GGTTCTGTTGACTTATAAGAAAGTGC 58.701 38.462 19.38 4.91 39.78 4.40
2636 5543 7.497595 AGAAAGTGCGATATATGTACTCCAAA 58.502 34.615 0.00 0.00 30.68 3.28
2651 5558 9.927668 ATGTACTCCAAATTTTAACCTCAAATG 57.072 29.630 0.00 0.00 0.00 2.32
2661 5568 7.841282 TTTTAACCTCAAATGGTCACCAATA 57.159 32.000 0.00 0.00 39.83 1.90
2662 5569 7.841282 TTTAACCTCAAATGGTCACCAATAA 57.159 32.000 0.00 0.00 39.83 1.40
2666 5573 6.180472 ACCTCAAATGGTCACCAATAACTAG 58.820 40.000 0.00 0.00 36.95 2.57
2669 5576 7.066284 CCTCAAATGGTCACCAATAACTAGAAG 59.934 40.741 0.00 0.00 36.95 2.85
2670 5577 6.374333 TCAAATGGTCACCAATAACTAGAAGC 59.626 38.462 0.00 0.00 36.95 3.86
2671 5578 5.700402 ATGGTCACCAATAACTAGAAGCT 57.300 39.130 0.00 0.00 36.95 3.74
2672 5579 5.086104 TGGTCACCAATAACTAGAAGCTC 57.914 43.478 0.00 0.00 0.00 4.09
2673 5580 4.777896 TGGTCACCAATAACTAGAAGCTCT 59.222 41.667 0.00 0.00 0.00 4.09
2674 5581 5.112686 GGTCACCAATAACTAGAAGCTCTG 58.887 45.833 0.00 0.00 0.00 3.35
2675 5582 5.105310 GGTCACCAATAACTAGAAGCTCTGA 60.105 44.000 0.00 0.00 0.00 3.27
2676 5583 5.808030 GTCACCAATAACTAGAAGCTCTGAC 59.192 44.000 0.00 0.00 0.00 3.51
2677 5584 5.717178 TCACCAATAACTAGAAGCTCTGACT 59.283 40.000 0.00 0.00 0.00 3.41
2695 5602 7.572168 GCTCTGACTAACCTTGAACTTCAAATC 60.572 40.741 5.72 0.00 35.73 2.17
2711 5618 3.320541 TCAAATCCGTCCAATTTGCAACT 59.679 39.130 0.00 0.00 41.66 3.16
2717 5624 4.764823 TCCGTCCAATTTGCAACTCTAAAT 59.235 37.500 0.00 0.00 0.00 1.40
2731 5638 7.174253 TGCAACTCTAAATTCTCAAAACCGTAT 59.826 33.333 0.00 0.00 0.00 3.06
2744 5651 8.362639 TCTCAAAACCGTATAACTTACAACTCT 58.637 33.333 0.00 0.00 0.00 3.24
2769 5676 2.701423 TCCCCTTAAACCTGTTTTTGGC 59.299 45.455 0.00 0.00 34.23 4.52
2812 5721 0.690411 CATGTCAGCCCCCTCTCTCT 60.690 60.000 0.00 0.00 0.00 3.10
2813 5722 0.690411 ATGTCAGCCCCCTCTCTCTG 60.690 60.000 0.00 0.00 0.00 3.35
2831 5740 0.105913 TGTTTGTTCTTCCCACCCCC 60.106 55.000 0.00 0.00 0.00 5.40
2842 5751 3.461773 CACCCCCGACTCGCATCT 61.462 66.667 0.00 0.00 0.00 2.90
2843 5752 3.148279 ACCCCCGACTCGCATCTC 61.148 66.667 0.00 0.00 0.00 2.75
2856 5765 2.366972 ATCTCTCCCAACCCCCGG 60.367 66.667 0.00 0.00 0.00 5.73
2892 5801 4.489771 CCACCAGATGCCCCCGAC 62.490 72.222 0.00 0.00 0.00 4.79
2932 5841 1.202639 TGAGGAGCACAACATTGTCGT 60.203 47.619 0.00 0.00 39.91 4.34
2936 5845 1.371635 GCACAACATTGTCGTGGGC 60.372 57.895 9.77 5.07 39.91 5.36
2937 5846 1.082169 CACAACATTGTCGTGGGCG 60.082 57.895 0.00 0.00 39.91 6.13
2979 5888 2.266055 AGGTAGCTTGCCTCACGC 59.734 61.111 0.00 0.00 38.31 5.34
3003 5912 0.675837 CCATGAGGTGACACCAGCAG 60.676 60.000 26.30 12.82 41.95 4.24
3007 5916 0.322975 GAGGTGACACCAGCAGACAT 59.677 55.000 26.30 2.72 41.95 3.06
3024 5933 1.156736 CATGGTCGAGTTGTGGGAAC 58.843 55.000 0.00 0.00 0.00 3.62
3037 5946 4.424711 GGAACTGCCCGGCATCCA 62.425 66.667 22.41 0.00 37.57 3.41
3068 5977 1.831389 CGTGACAGTGGCCGAAGTTG 61.831 60.000 0.00 0.00 0.00 3.16
3091 6000 1.201181 CTCCCTCACGAGTCACTTCAG 59.799 57.143 0.00 0.00 0.00 3.02
3122 6031 1.536943 CCTCCGCTATCCACCTAGGC 61.537 65.000 9.30 0.00 37.29 3.93
3124 6033 2.651361 CGCTATCCACCTAGGCCG 59.349 66.667 9.30 0.00 37.29 6.13
3148 6057 0.320374 CTTAGGAGCACGGTGGACAA 59.680 55.000 10.60 0.00 0.00 3.18
3149 6058 0.981183 TTAGGAGCACGGTGGACAAT 59.019 50.000 10.60 0.00 0.00 2.71
3154 6063 3.027170 GCACGGTGGACAATGCTCG 62.027 63.158 10.60 0.00 35.16 5.03
3161 6070 1.134699 GTGGACAATGCTCGATCTCCA 60.135 52.381 0.00 0.00 0.00 3.86
3165 6074 1.227380 AATGCTCGATCTCCACGGC 60.227 57.895 0.00 0.00 0.00 5.68
3171 6080 1.140161 CGATCTCCACGGCGGTAAA 59.860 57.895 13.24 0.00 35.57 2.01
3174 6083 0.175073 ATCTCCACGGCGGTAAAGAC 59.825 55.000 13.24 0.00 35.57 3.01
3194 6103 4.002506 ATGTGTGTGCGCCTCCGA 62.003 61.111 4.18 0.00 36.29 4.55
3195 6104 3.939837 ATGTGTGTGCGCCTCCGAG 62.940 63.158 4.18 0.00 36.29 4.63
3233 6142 2.102420 TGAGTCGTTGAAGCCTTTCTCA 59.898 45.455 0.00 0.00 34.31 3.27
3243 6152 1.743252 CCTTTCTCACTGGCGAGCC 60.743 63.158 7.26 7.26 32.75 4.70
3262 6171 1.442769 CACTCAAGGTGCGCATACTT 58.557 50.000 15.91 18.75 39.22 2.24
3266 6175 0.447801 CAAGGTGCGCATACTTGGTC 59.552 55.000 32.79 14.00 38.29 4.02
3316 6225 3.328505 CAACAGGAATTTGAATGGCCAC 58.671 45.455 8.16 0.00 0.00 5.01
3340 6249 4.507879 GCATGGTGCCAGATTTGC 57.492 55.556 0.00 0.00 37.42 3.68
3355 6264 2.452600 TTTGCAGAAGAAGGGGTTGT 57.547 45.000 0.00 0.00 0.00 3.32
3368 6277 2.100631 GGTTGTGGGAGATCGTGCG 61.101 63.158 0.00 0.00 0.00 5.34
3381 6290 4.492160 GTGCGATCGCTCGGGACA 62.492 66.667 37.01 15.56 45.15 4.02
3433 6351 5.551305 ATCATCATACGATCAAACCAGGA 57.449 39.130 0.00 0.00 0.00 3.86
3454 6372 7.412853 CAGGAACACTATGAAGATGCATTAAC 58.587 38.462 0.00 0.00 0.00 2.01
3463 6381 7.807977 ATGAAGATGCATTAACGGTTTAGAT 57.192 32.000 0.00 0.00 0.00 1.98
3505 6423 0.179111 TGCAGCGGAATAAGAGTCGG 60.179 55.000 0.00 0.00 0.00 4.79
3511 6429 2.098770 GCGGAATAAGAGTCGGTGTAGT 59.901 50.000 0.00 0.00 0.00 2.73
3512 6430 3.791455 GCGGAATAAGAGTCGGTGTAGTC 60.791 52.174 0.00 0.00 0.00 2.59
3513 6431 3.243002 CGGAATAAGAGTCGGTGTAGTCC 60.243 52.174 3.87 3.87 0.00 3.85
3514 6432 3.698040 GGAATAAGAGTCGGTGTAGTCCA 59.302 47.826 7.40 0.00 32.32 4.02
3515 6433 4.341520 GGAATAAGAGTCGGTGTAGTCCAT 59.658 45.833 7.40 0.00 32.32 3.41
3516 6434 5.507650 GGAATAAGAGTCGGTGTAGTCCATC 60.508 48.000 7.40 0.00 32.32 3.51
3524 6442 2.889852 GGTGTAGTCCATCGAACCTTC 58.110 52.381 0.00 0.00 0.00 3.46
3525 6443 2.232941 GGTGTAGTCCATCGAACCTTCA 59.767 50.000 0.00 0.00 0.00 3.02
3526 6444 3.118738 GGTGTAGTCCATCGAACCTTCAT 60.119 47.826 0.00 0.00 0.00 2.57
3527 6445 3.865745 GTGTAGTCCATCGAACCTTCATG 59.134 47.826 0.00 0.00 0.00 3.07
3528 6446 3.767131 TGTAGTCCATCGAACCTTCATGA 59.233 43.478 0.00 0.00 0.00 3.07
3529 6447 3.981071 AGTCCATCGAACCTTCATGAA 57.019 42.857 8.12 8.12 0.00 2.57
3530 6448 3.600388 AGTCCATCGAACCTTCATGAAC 58.400 45.455 3.38 0.00 0.00 3.18
3531 6449 2.348666 GTCCATCGAACCTTCATGAACG 59.651 50.000 3.38 6.94 0.00 3.95
3532 6450 2.232696 TCCATCGAACCTTCATGAACGA 59.767 45.455 17.75 17.75 0.00 3.85
3533 6451 3.118775 TCCATCGAACCTTCATGAACGAT 60.119 43.478 20.01 20.01 40.26 3.73
3534 6452 4.098807 TCCATCGAACCTTCATGAACGATA 59.901 41.667 23.26 12.03 38.17 2.92
3535 6453 4.209288 CCATCGAACCTTCATGAACGATAC 59.791 45.833 23.26 7.68 38.17 2.24
3536 6454 3.777478 TCGAACCTTCATGAACGATACC 58.223 45.455 13.11 0.00 0.00 2.73
3537 6455 3.446161 TCGAACCTTCATGAACGATACCT 59.554 43.478 13.11 0.00 0.00 3.08
3538 6456 3.797256 CGAACCTTCATGAACGATACCTC 59.203 47.826 3.38 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.888436 GCTCAGGGACATGGTCGTCA 61.888 60.000 0.00 0.00 37.66 4.35
35 2598 0.982852 TGGGGTAGCTCAGGGACATG 60.983 60.000 0.00 0.00 0.00 3.21
98 2913 0.541530 AGAGAGTGAGCCTGTCAGCA 60.542 55.000 0.00 0.00 35.93 4.41
101 2916 1.539560 GCCAGAGAGTGAGCCTGTCA 61.540 60.000 0.00 0.00 35.93 3.58
120 2935 2.223971 GCTCAATCCATTCCTGCCATTG 60.224 50.000 0.00 0.00 0.00 2.82
121 2936 2.037144 GCTCAATCCATTCCTGCCATT 58.963 47.619 0.00 0.00 0.00 3.16
122 2937 1.217183 AGCTCAATCCATTCCTGCCAT 59.783 47.619 0.00 0.00 0.00 4.40
123 2938 0.627451 AGCTCAATCCATTCCTGCCA 59.373 50.000 0.00 0.00 0.00 4.92
142 2978 3.251484 ACCTCCAAGTGAAGGATCAGAA 58.749 45.455 0.00 0.00 35.88 3.02
145 2981 2.907892 AGACCTCCAAGTGAAGGATCA 58.092 47.619 0.00 0.00 33.99 2.92
180 3016 0.029567 GGTGAGTAGCGGTCGATGAG 59.970 60.000 0.00 0.00 0.00 2.90
205 3041 2.182842 GGCATGCCATCTCCGTGTC 61.183 63.158 32.08 0.00 35.81 3.67
221 3057 1.039856 TTCCAGGCTCTTTTGTTGGC 58.960 50.000 0.00 0.00 0.00 4.52
254 3090 0.999406 CGGCCGACACATTGAGTAAG 59.001 55.000 24.07 0.00 0.00 2.34
255 3091 0.604073 TCGGCCGACACATTGAGTAA 59.396 50.000 27.28 0.00 0.00 2.24
286 3122 4.386867 TTTCGAGGCTAACGATTCTCAT 57.613 40.909 0.00 0.00 39.45 2.90
298 3134 1.066143 ACATCACCGATTTTCGAGGCT 60.066 47.619 0.00 0.00 43.74 4.58
336 3172 0.458889 CGGCCGTCGTCTGGATTTTA 60.459 55.000 19.50 0.00 0.00 1.52
337 3173 1.740296 CGGCCGTCGTCTGGATTTT 60.740 57.895 19.50 0.00 0.00 1.82
338 3174 2.125673 CGGCCGTCGTCTGGATTT 60.126 61.111 19.50 0.00 0.00 2.17
409 3248 1.379309 AGTCGGAGGTCTCTGCTCC 60.379 63.158 2.06 0.00 35.96 4.70
423 3262 3.194542 AGTCCATTCCTTCTTCAGAGTCG 59.805 47.826 0.00 0.00 0.00 4.18
429 3268 2.026822 GGAGCAGTCCATTCCTTCTTCA 60.027 50.000 0.00 0.00 43.31 3.02
487 3326 4.265073 GACATATTGAGCCAGAACCAGTT 58.735 43.478 0.00 0.00 0.00 3.16
491 3330 2.213499 CCGACATATTGAGCCAGAACC 58.787 52.381 0.00 0.00 0.00 3.62
633 3479 0.620556 AGAGGATGCCATTGACGGTT 59.379 50.000 0.00 0.00 0.00 4.44
714 3560 7.112122 TCACAAGGATATATGCAGAGTGTTTT 58.888 34.615 16.97 0.00 0.00 2.43
721 3567 4.349048 AGGCTTCACAAGGATATATGCAGA 59.651 41.667 7.02 0.00 0.00 4.26
722 3568 4.649692 AGGCTTCACAAGGATATATGCAG 58.350 43.478 7.02 1.42 0.00 4.41
732 3578 1.741706 CTGCACATAGGCTTCACAAGG 59.258 52.381 0.00 0.00 34.04 3.61
734 3580 2.857186 TCTGCACATAGGCTTCACAA 57.143 45.000 0.00 0.00 34.04 3.33
793 3639 4.888917 TGGAGTATTTGTTCACATCGACA 58.111 39.130 0.00 0.00 0.00 4.35
928 3780 1.521681 CGCCCAGGGAGTTCGATTC 60.522 63.158 10.89 0.00 0.00 2.52
962 3814 4.757594 CTTGAGAGAGAAGTTGGATCTGG 58.242 47.826 0.00 0.00 0.00 3.86
983 3835 4.080919 TGTGCATAAATAGTCAGGTCTGCT 60.081 41.667 0.00 0.00 0.00 4.24
1022 3874 1.038280 GGGAGTACGGTACAGGATGG 58.962 60.000 19.62 0.00 43.62 3.51
1026 3878 2.480759 CGAATTGGGAGTACGGTACAGG 60.481 54.545 19.62 0.00 0.00 4.00
1027 3879 2.805845 CGAATTGGGAGTACGGTACAG 58.194 52.381 19.62 0.00 0.00 2.74
1028 3880 1.135024 GCGAATTGGGAGTACGGTACA 60.135 52.381 19.62 0.00 0.00 2.90
1029 3881 1.564207 GCGAATTGGGAGTACGGTAC 58.436 55.000 10.29 10.29 0.00 3.34
1030 3882 0.461135 GGCGAATTGGGAGTACGGTA 59.539 55.000 0.00 0.00 0.00 4.02
1031 3883 1.219935 GGCGAATTGGGAGTACGGT 59.780 57.895 0.00 0.00 0.00 4.83
1032 3884 1.881252 CGGCGAATTGGGAGTACGG 60.881 63.158 0.00 0.00 0.00 4.02
1033 3885 1.881252 CCGGCGAATTGGGAGTACG 60.881 63.158 9.30 0.00 0.00 3.67
1034 3886 2.178235 GCCGGCGAATTGGGAGTAC 61.178 63.158 12.58 0.00 0.00 2.73
1035 3887 2.188469 GCCGGCGAATTGGGAGTA 59.812 61.111 12.58 0.00 0.00 2.59
1036 3888 4.796495 GGCCGGCGAATTGGGAGT 62.796 66.667 22.54 0.00 0.00 3.85
1037 3889 4.794648 TGGCCGGCGAATTGGGAG 62.795 66.667 22.54 0.00 0.00 4.30
1038 3890 4.352607 TTGGCCGGCGAATTGGGA 62.353 61.111 20.90 0.00 0.00 4.37
1039 3891 4.128388 GTTGGCCGGCGAATTGGG 62.128 66.667 27.12 0.00 0.00 4.12
1040 3892 3.340953 CTGTTGGCCGGCGAATTGG 62.341 63.158 27.12 15.38 0.00 3.16
1041 3893 1.656818 ATCTGTTGGCCGGCGAATTG 61.657 55.000 27.12 20.76 0.00 2.32
1042 3894 1.376609 GATCTGTTGGCCGGCGAATT 61.377 55.000 27.12 12.28 0.00 2.17
1043 3895 1.819632 GATCTGTTGGCCGGCGAAT 60.820 57.895 27.12 11.14 0.00 3.34
1044 3896 2.435938 GATCTGTTGGCCGGCGAA 60.436 61.111 20.90 20.90 0.00 4.70
1045 3897 3.390521 AGATCTGTTGGCCGGCGA 61.391 61.111 22.54 15.52 0.00 5.54
1046 3898 3.197790 CAGATCTGTTGGCCGGCG 61.198 66.667 22.54 6.07 0.00 6.46
1047 3899 3.512516 GCAGATCTGTTGGCCGGC 61.513 66.667 21.18 21.18 0.00 6.13
1048 3900 2.046023 TGCAGATCTGTTGGCCGG 60.046 61.111 23.38 0.00 0.00 6.13
1049 3901 2.758089 GCTGCAGATCTGTTGGCCG 61.758 63.158 23.38 7.15 0.00 6.13
1050 3902 2.413142 GGCTGCAGATCTGTTGGCC 61.413 63.158 26.88 26.88 35.74 5.36
1051 3903 1.035932 ATGGCTGCAGATCTGTTGGC 61.036 55.000 23.38 24.50 0.00 4.52
1052 3904 0.738975 CATGGCTGCAGATCTGTTGG 59.261 55.000 23.38 14.25 0.00 3.77
1055 3907 0.180642 CTCCATGGCTGCAGATCTGT 59.819 55.000 23.38 0.00 0.00 3.41
1058 3910 1.595466 CTTCTCCATGGCTGCAGATC 58.405 55.000 20.43 9.32 0.00 2.75
1066 3918 2.105124 GCTTCTGCTTCTCCATGGC 58.895 57.895 6.96 0.00 36.03 4.40
1323 4205 3.119096 GCCAGGAAACCGTCGAGC 61.119 66.667 0.00 0.00 0.00 5.03
1474 4362 1.403914 GGCGATCAGATGCTCGATGAT 60.404 52.381 10.02 0.00 35.92 2.45
1475 4363 0.038801 GGCGATCAGATGCTCGATGA 60.039 55.000 10.02 0.00 35.92 2.92
1484 4372 4.957684 CAGCGGCGGCGATCAGAT 62.958 66.667 36.87 9.66 46.35 2.90
1821 4726 2.671070 CTCATGGCTGAACCCGGT 59.329 61.111 0.00 0.00 37.83 5.28
1833 4738 1.226802 CACGACGAGCTCCCTCATG 60.227 63.158 8.47 0.00 38.00 3.07
1986 4891 0.036858 AGTTCGAGGGCTTCTTGCTC 60.037 55.000 0.00 0.00 44.10 4.26
1995 4901 2.184579 CCGAGGAAGTTCGAGGGC 59.815 66.667 0.00 0.00 43.03 5.19
2056 4962 0.550147 ACCACCCATCTACTTGGCCT 60.550 55.000 3.32 0.00 35.29 5.19
2139 5045 1.372997 CCACGAGACGTCCCAGTTG 60.373 63.158 13.01 0.00 38.32 3.16
2142 5048 4.436998 GGCCACGAGACGTCCCAG 62.437 72.222 13.01 6.45 38.32 4.45
2286 5192 0.613260 CCACCTCCTTCATGTTCCGA 59.387 55.000 0.00 0.00 0.00 4.55
2347 5253 2.770802 ACATCCTCACAAGATCCCTCAG 59.229 50.000 0.00 0.00 0.00 3.35
2414 5320 3.200825 CCAATCCCAGAGTCCATTGTACT 59.799 47.826 0.00 0.00 0.00 2.73
2487 5393 3.616821 CAGGCTCGATCATTTTCGTTACA 59.383 43.478 0.00 0.00 40.03 2.41
2490 5396 1.398390 GCAGGCTCGATCATTTTCGTT 59.602 47.619 0.00 0.00 40.03 3.85
2563 5469 9.076596 GCTTTTCCAACAACTATCATCAATAAC 57.923 33.333 0.00 0.00 0.00 1.89
2610 5516 7.050970 TGGAGTACATATATCGCACTTTCTT 57.949 36.000 0.00 0.00 0.00 2.52
2612 5518 7.709269 TTTGGAGTACATATATCGCACTTTC 57.291 36.000 0.00 0.00 0.00 2.62
2636 5543 6.739331 TTGGTGACCATTTGAGGTTAAAAT 57.261 33.333 4.56 0.00 43.38 1.82
2651 5558 5.105310 TCAGAGCTTCTAGTTATTGGTGACC 60.105 44.000 0.00 0.00 0.00 4.02
2661 5568 5.775701 TCAAGGTTAGTCAGAGCTTCTAGTT 59.224 40.000 0.00 0.00 32.93 2.24
2662 5569 5.326069 TCAAGGTTAGTCAGAGCTTCTAGT 58.674 41.667 0.00 0.00 32.93 2.57
2666 5573 4.888917 AGTTCAAGGTTAGTCAGAGCTTC 58.111 43.478 0.00 0.00 32.93 3.86
2669 5576 4.632153 TGAAGTTCAAGGTTAGTCAGAGC 58.368 43.478 2.20 0.00 0.00 4.09
2670 5577 7.095017 GGATTTGAAGTTCAAGGTTAGTCAGAG 60.095 40.741 17.36 0.00 37.70 3.35
2671 5578 6.710744 GGATTTGAAGTTCAAGGTTAGTCAGA 59.289 38.462 17.36 0.53 37.70 3.27
2672 5579 6.347725 CGGATTTGAAGTTCAAGGTTAGTCAG 60.348 42.308 17.36 8.09 37.70 3.51
2673 5580 5.468746 CGGATTTGAAGTTCAAGGTTAGTCA 59.531 40.000 17.36 1.93 37.70 3.41
2674 5581 5.469084 ACGGATTTGAAGTTCAAGGTTAGTC 59.531 40.000 17.36 10.19 37.70 2.59
2675 5582 5.374071 ACGGATTTGAAGTTCAAGGTTAGT 58.626 37.500 17.36 12.39 37.70 2.24
2676 5583 5.106673 GGACGGATTTGAAGTTCAAGGTTAG 60.107 44.000 17.36 11.85 37.70 2.34
2677 5584 4.758165 GGACGGATTTGAAGTTCAAGGTTA 59.242 41.667 17.36 4.42 37.70 2.85
2695 5602 4.497473 TTTAGAGTTGCAAATTGGACGG 57.503 40.909 0.00 0.00 0.00 4.79
2717 5624 8.891671 AGTTGTAAGTTATACGGTTTTGAGAA 57.108 30.769 0.00 0.00 0.00 2.87
2731 5638 4.748701 AGGGGAGTCAGAGTTGTAAGTTA 58.251 43.478 0.00 0.00 0.00 2.24
2744 5651 4.529716 AAAACAGGTTTAAGGGGAGTCA 57.470 40.909 0.00 0.00 31.63 3.41
2780 5687 2.804647 CTGACATGTCGCGTACCAATA 58.195 47.619 20.54 0.00 0.00 1.90
2791 5698 0.980231 AGAGAGGGGGCTGACATGTC 60.980 60.000 19.27 19.27 0.00 3.06
2794 5703 0.690411 CAGAGAGAGGGGGCTGACAT 60.690 60.000 0.00 0.00 0.00 3.06
2805 5714 4.061596 GTGGGAAGAACAAACAGAGAGAG 58.938 47.826 0.00 0.00 0.00 3.20
2812 5721 0.105913 GGGGGTGGGAAGAACAAACA 60.106 55.000 0.00 0.00 0.00 2.83
2813 5722 1.176619 CGGGGGTGGGAAGAACAAAC 61.177 60.000 0.00 0.00 0.00 2.93
2831 5740 0.526524 GTTGGGAGAGATGCGAGTCG 60.527 60.000 8.54 8.54 0.00 4.18
2914 5823 1.229428 CACGACAATGTTGTGCTCCT 58.771 50.000 19.49 0.00 40.42 3.69
2921 5830 2.258013 ACCGCCCACGACAATGTTG 61.258 57.895 0.00 0.00 43.93 3.33
2943 5852 3.842126 CACACATCTGTCGCCGCG 61.842 66.667 6.39 6.39 0.00 6.46
2979 5888 4.758251 TGTCACCTCATGGCGCCG 62.758 66.667 23.90 8.74 34.72 6.46
2982 5891 1.742880 CTGGTGTCACCTCATGGCG 60.743 63.158 22.56 0.00 39.58 5.69
3003 5912 0.320374 TCCCACAACTCGACCATGTC 59.680 55.000 0.00 0.00 0.00 3.06
3007 5916 0.105964 CAGTTCCCACAACTCGACCA 59.894 55.000 0.00 0.00 0.00 4.02
3011 5920 3.655481 GGCAGTTCCCACAACTCG 58.345 61.111 0.00 0.00 0.00 4.18
3049 5958 1.594293 AACTTCGGCCACTGTCACG 60.594 57.895 2.24 0.00 0.00 4.35
3068 5977 1.249407 AGTGACTCGTGAGGGAGAAC 58.751 55.000 1.43 0.00 37.49 3.01
3122 6031 2.125106 GTGCTCCTAAGGCCACGG 60.125 66.667 5.01 1.31 0.00 4.94
3124 6033 2.125106 CCGTGCTCCTAAGGCCAC 60.125 66.667 5.01 0.00 0.00 5.01
3148 6057 2.419198 GCCGTGGAGATCGAGCAT 59.581 61.111 2.38 0.00 0.00 3.79
3149 6058 4.193334 CGCCGTGGAGATCGAGCA 62.193 66.667 2.38 0.00 0.00 4.26
3154 6063 0.458669 TCTTTACCGCCGTGGAGATC 59.541 55.000 4.58 0.00 42.00 2.75
3161 6070 0.034337 ACATGTGTCTTTACCGCCGT 59.966 50.000 0.00 0.00 0.00 5.68
3194 6103 1.833630 TCATCAATGTCCGCTTCCTCT 59.166 47.619 0.00 0.00 0.00 3.69
3195 6104 2.208431 CTCATCAATGTCCGCTTCCTC 58.792 52.381 0.00 0.00 0.00 3.71
3209 6118 2.839486 AAGGCTTCAACGACTCATCA 57.161 45.000 0.00 0.00 0.00 3.07
3262 6171 3.307906 ACTAGTTGGCGGCGACCA 61.308 61.111 24.63 15.03 38.16 4.02
3329 6238 2.165167 CCTTCTTCTGCAAATCTGGCA 58.835 47.619 0.00 0.00 39.32 4.92
3332 6241 2.800250 ACCCCTTCTTCTGCAAATCTG 58.200 47.619 0.00 0.00 0.00 2.90
3333 6242 3.160269 CAACCCCTTCTTCTGCAAATCT 58.840 45.455 0.00 0.00 0.00 2.40
3334 6243 2.893489 ACAACCCCTTCTTCTGCAAATC 59.107 45.455 0.00 0.00 0.00 2.17
3340 6249 0.771127 TCCCACAACCCCTTCTTCTG 59.229 55.000 0.00 0.00 0.00 3.02
3355 6264 2.721859 CGATCGCACGATCTCCCA 59.278 61.111 25.45 0.00 46.36 4.37
3368 6277 1.143305 CAATCATGTCCCGAGCGATC 58.857 55.000 0.00 0.00 0.00 3.69
3380 6289 2.295909 ACGTTTCCCAACACCAATCATG 59.704 45.455 0.00 0.00 32.54 3.07
3381 6290 2.593026 ACGTTTCCCAACACCAATCAT 58.407 42.857 0.00 0.00 32.54 2.45
3417 6335 4.553330 AGTGTTCCTGGTTTGATCGTAT 57.447 40.909 0.00 0.00 0.00 3.06
3429 6347 7.412853 GTTAATGCATCTTCATAGTGTTCCTG 58.587 38.462 0.00 0.00 0.00 3.86
3433 6351 5.880332 ACCGTTAATGCATCTTCATAGTGTT 59.120 36.000 0.00 0.00 0.00 3.32
3454 6372 2.454055 GTAACGACCCGATCTAAACCG 58.546 52.381 0.00 0.00 0.00 4.44
3482 6400 3.003480 GACTCTTATTCCGCTGCAACTT 58.997 45.455 0.00 0.00 0.00 2.66
3492 6410 3.698040 TGGACTACACCGACTCTTATTCC 59.302 47.826 0.00 0.00 0.00 3.01
3505 6423 3.587797 TGAAGGTTCGATGGACTACAC 57.412 47.619 0.00 0.00 0.00 2.90
3511 6429 2.232696 TCGTTCATGAAGGTTCGATGGA 59.767 45.455 23.46 3.45 0.00 3.41
3512 6430 2.616960 TCGTTCATGAAGGTTCGATGG 58.383 47.619 23.46 1.00 0.00 3.51
3513 6431 4.209288 GGTATCGTTCATGAAGGTTCGATG 59.791 45.833 28.20 7.75 38.25 3.84
3514 6432 4.099573 AGGTATCGTTCATGAAGGTTCGAT 59.900 41.667 25.48 25.48 40.30 3.59
3515 6433 3.446161 AGGTATCGTTCATGAAGGTTCGA 59.554 43.478 23.46 20.55 0.00 3.71
3516 6434 3.782046 AGGTATCGTTCATGAAGGTTCG 58.218 45.455 23.46 16.53 0.00 3.95
3517 6435 3.797256 CGAGGTATCGTTCATGAAGGTTC 59.203 47.826 23.46 15.62 44.09 3.62
3518 6436 3.782046 CGAGGTATCGTTCATGAAGGTT 58.218 45.455 23.46 18.74 44.09 3.50
3519 6437 3.438297 CGAGGTATCGTTCATGAAGGT 57.562 47.619 23.46 15.06 44.09 3.50


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

AutoCloner maintained by Alex Coulton.