Multiple sequence alignment - TraesCS2B01G533400

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 TraesCS2B01G533400 chr2B 100.000 4776 0 0 1 4776 729765349 729770124 0.000000e+00 8820.0
1 TraesCS2B01G533400 chr2B 83.112 2635 346 66 1207 3782 548623949 548626543 0.000000e+00 2309.0
2 TraesCS2B01G533400 chr2B 86.856 2077 228 29 1045 3096 548609306 548611362 0.000000e+00 2281.0
3 TraesCS2B01G533400 chr2D 96.409 3732 119 8 785 4511 599925964 599929685 0.000000e+00 6135.0
4 TraesCS2B01G533400 chr2D 88.186 2844 291 27 1045 3865 469983835 469986656 0.000000e+00 3349.0
5 TraesCS2B01G533400 chr2D 83.037 2641 346 62 1207 3782 469990546 469993149 0.000000e+00 2302.0
6 TraesCS2B01G533400 chr2D 91.299 747 46 8 1 736 599925226 599925964 0.000000e+00 1002.0
7 TraesCS2B01G533400 chr2D 93.798 258 13 2 4515 4772 599930233 599930487 7.500000e-103 385.0
8 TraesCS2B01G533400 chr2D 80.000 80 14 2 1458 1536 76753781 76753703 1.860000e-04 58.4
9 TraesCS2B01G533400 chr2A 95.471 3533 131 14 998 4511 733628652 733632174 0.000000e+00 5611.0
10 TraesCS2B01G533400 chr2A 82.948 2639 351 61 1207 3782 611302787 611305389 0.000000e+00 2289.0
11 TraesCS2B01G533400 chr2A 87.650 1579 167 14 1158 2717 611296060 611297629 0.000000e+00 1810.0
12 TraesCS2B01G533400 chr2A 93.069 101 7 0 4515 4615 733632683 733632783 1.070000e-31 148.0
13 TraesCS2B01G533400 chr1D 84.037 2675 331 56 1240 3865 407672550 407669923 0.000000e+00 2486.0
14 TraesCS2B01G533400 chr5B 83.852 2669 328 58 1247 3865 13776132 13773517 0.000000e+00 2446.0
15 TraesCS2B01G533400 chr5A 83.632 2682 331 58 1238 3865 12194227 12191600 0.000000e+00 2422.0
16 TraesCS2B01G533400 chr1A 82.379 2724 388 48 1190 3859 8144563 8141878 0.000000e+00 2287.0
17 TraesCS2B01G533400 chr4B 81.610 2708 398 50 1182 3835 36635920 36633259 0.000000e+00 2150.0
18 TraesCS2B01G533400 chr1B 81.504 2687 388 69 1240 3867 10007492 10004856 0.000000e+00 2108.0
19 TraesCS2B01G533400 chr1B 81.640 2647 386 56 1189 3782 8867294 8864695 0.000000e+00 2104.0
20 TraesCS2B01G533400 chr1B 77.166 854 127 33 1178 1991 9281196 9282021 7.340000e-118 435.0
21 TraesCS2B01G533400 chr3B 78.404 2005 369 43 1755 3742 805337982 805339939 0.000000e+00 1245.0


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 TraesCS2B01G533400 chr2B 729765349 729770124 4775 False 8820.000000 8820 100.000000 1 4776 1 chr2B.!!$F3 4775
1 TraesCS2B01G533400 chr2B 548623949 548626543 2594 False 2309.000000 2309 83.112000 1207 3782 1 chr2B.!!$F2 2575
2 TraesCS2B01G533400 chr2B 548609306 548611362 2056 False 2281.000000 2281 86.856000 1045 3096 1 chr2B.!!$F1 2051
3 TraesCS2B01G533400 chr2D 469983835 469993149 9314 False 2825.500000 3349 85.611500 1045 3865 2 chr2D.!!$F1 2820
4 TraesCS2B01G533400 chr2D 599925226 599930487 5261 False 2507.333333 6135 93.835333 1 4772 3 chr2D.!!$F2 4771
5 TraesCS2B01G533400 chr2A 733628652 733632783 4131 False 2879.500000 5611 94.270000 998 4615 2 chr2A.!!$F3 3617
6 TraesCS2B01G533400 chr2A 611302787 611305389 2602 False 2289.000000 2289 82.948000 1207 3782 1 chr2A.!!$F2 2575
7 TraesCS2B01G533400 chr2A 611296060 611297629 1569 False 1810.000000 1810 87.650000 1158 2717 1 chr2A.!!$F1 1559
8 TraesCS2B01G533400 chr1D 407669923 407672550 2627 True 2486.000000 2486 84.037000 1240 3865 1 chr1D.!!$R1 2625
9 TraesCS2B01G533400 chr5B 13773517 13776132 2615 True 2446.000000 2446 83.852000 1247 3865 1 chr5B.!!$R1 2618
10 TraesCS2B01G533400 chr5A 12191600 12194227 2627 True 2422.000000 2422 83.632000 1238 3865 1 chr5A.!!$R1 2627
11 TraesCS2B01G533400 chr1A 8141878 8144563 2685 True 2287.000000 2287 82.379000 1190 3859 1 chr1A.!!$R1 2669
12 TraesCS2B01G533400 chr4B 36633259 36635920 2661 True 2150.000000 2150 81.610000 1182 3835 1 chr4B.!!$R1 2653
13 TraesCS2B01G533400 chr1B 10004856 10007492 2636 True 2108.000000 2108 81.504000 1240 3867 1 chr1B.!!$R2 2627
14 TraesCS2B01G533400 chr1B 8864695 8867294 2599 True 2104.000000 2104 81.640000 1189 3782 1 chr1B.!!$R1 2593
15 TraesCS2B01G533400 chr1B 9281196 9282021 825 False 435.000000 435 77.166000 1178 1991 1 chr1B.!!$F1 813
16 TraesCS2B01G533400 chr3B 805337982 805339939 1957 False 1245.000000 1245 78.404000 1755 3742 1 chr3B.!!$F1 1987

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
763 774 0.037877 AAGCAGCTTGCCATGAGAGT 59.962 50.000 6.93 0.00 46.52 3.24 F
764 775 0.037877 AGCAGCTTGCCATGAGAGTT 59.962 50.000 0.00 0.00 46.52 3.01 F
1141 1162 0.105194 TGACTTCCCTGGTCAGTCCA 60.105 55.000 16.07 5.71 45.01 4.02 F
1669 1785 1.246649 CCAGCAGCATAAACACCACA 58.753 50.000 0.00 0.00 0.00 4.17 F
2929 3079 1.805345 AGTGACTCGAAGACTACCGTG 59.195 52.381 0.00 0.00 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1757 0.453390 GGTGTTTATGCTGCTGGCTC 59.547 55.000 0.00 0.00 42.39 4.70 R
2290 2421 1.827399 AATCCCGCGGTGACTTCTGT 61.827 55.000 26.12 1.89 0.00 3.41 R
2929 3079 1.067354 CCATCAAGCCTTTTCACTGCC 60.067 52.381 0.00 0.00 0.00 4.85 R
3079 3229 6.566079 TGACTATCAAGAGACCCATTGAAT 57.434 37.500 0.00 0.00 38.80 2.57 R
4088 10824 0.109597 GAAGCCTGCCACACATTTCG 60.110 55.000 0.00 0.00 0.00 3.46 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
58 59 4.058124 GTGTTGTTCTACATCAGACTGCA 58.942 43.478 0.00 0.00 29.40 4.41
118 121 2.711009 TGGTGCCAATATAGAAGGGGAG 59.289 50.000 0.00 0.00 0.00 4.30
151 154 7.040271 TGTTCTTTCAGATTCAGATGCATTGAA 60.040 33.333 19.58 19.58 38.76 2.69
153 156 6.657966 TCTTTCAGATTCAGATGCATTGAAGT 59.342 34.615 20.93 12.83 37.91 3.01
173 176 7.657336 TGAAGTGTGATTTATTTCCTTTGTCC 58.343 34.615 0.00 0.00 0.00 4.02
179 182 7.505585 TGTGATTTATTTCCTTTGTCCTGAACT 59.494 33.333 0.00 0.00 0.00 3.01
262 265 5.184892 ACCTTCTGCAGATTAACCATTCT 57.815 39.130 19.04 0.00 0.00 2.40
269 272 9.905713 TTCTGCAGATTAACCATTCTAACTTAT 57.094 29.630 19.04 0.00 0.00 1.73
326 329 3.728864 GCGTGTGATTGGTTGAGCTTATG 60.729 47.826 0.00 0.00 0.00 1.90
327 330 3.684305 CGTGTGATTGGTTGAGCTTATGA 59.316 43.478 0.00 0.00 0.00 2.15
353 356 2.584835 TTGGGGAATCAGTTCACTGG 57.415 50.000 7.11 0.00 43.91 4.00
395 398 1.609210 TGGTCCGATGAGCACTCCA 60.609 57.895 0.00 0.00 43.72 3.86
450 453 2.763448 GAGGTGAGCTTGGTACTCTGAT 59.237 50.000 0.00 0.00 35.12 2.90
453 456 4.965532 AGGTGAGCTTGGTACTCTGATATT 59.034 41.667 0.00 0.00 35.12 1.28
454 457 5.053145 GGTGAGCTTGGTACTCTGATATTG 58.947 45.833 0.00 0.00 35.12 1.90
456 459 4.061596 GAGCTTGGTACTCTGATATTGGC 58.938 47.826 0.00 0.00 0.00 4.52
474 477 2.556287 GCTTCTGCCACCGTTTCG 59.444 61.111 0.00 0.00 0.00 3.46
477 480 0.661020 CTTCTGCCACCGTTTCGTTT 59.339 50.000 0.00 0.00 0.00 3.60
483 486 1.065251 GCCACCGTTTCGTTTGGTTAA 59.935 47.619 8.20 0.00 32.48 2.01
505 509 1.985473 TGTGTTCATTGCTGGCTCTT 58.015 45.000 0.00 0.00 0.00 2.85
509 513 2.555325 TGTTCATTGCTGGCTCTTTCTG 59.445 45.455 0.00 0.00 0.00 3.02
517 521 2.555757 GCTGGCTCTTTCTGATGTGTTT 59.444 45.455 0.00 0.00 0.00 2.83
518 522 3.753272 GCTGGCTCTTTCTGATGTGTTTA 59.247 43.478 0.00 0.00 0.00 2.01
519 523 4.142730 GCTGGCTCTTTCTGATGTGTTTAG 60.143 45.833 0.00 0.00 0.00 1.85
520 524 5.227569 TGGCTCTTTCTGATGTGTTTAGA 57.772 39.130 0.00 0.00 0.00 2.10
522 526 6.240894 TGGCTCTTTCTGATGTGTTTAGATT 58.759 36.000 0.00 0.00 0.00 2.40
523 527 7.394016 TGGCTCTTTCTGATGTGTTTAGATTA 58.606 34.615 0.00 0.00 0.00 1.75
524 528 7.334421 TGGCTCTTTCTGATGTGTTTAGATTAC 59.666 37.037 0.00 0.00 0.00 1.89
525 529 7.334421 GGCTCTTTCTGATGTGTTTAGATTACA 59.666 37.037 0.00 0.00 0.00 2.41
526 530 8.887717 GCTCTTTCTGATGTGTTTAGATTACAT 58.112 33.333 0.00 0.00 37.72 2.29
528 532 9.383519 TCTTTCTGATGTGTTTAGATTACATCC 57.616 33.333 12.42 0.00 46.23 3.51
549 560 2.223249 CGTGTGAGGTTGGTCTTTTGTG 60.223 50.000 0.00 0.00 0.00 3.33
559 570 5.476945 GGTTGGTCTTTTGTGTTGATATCCT 59.523 40.000 0.00 0.00 0.00 3.24
572 583 8.747471 TGTGTTGATATCCTTTGAATTTGCATA 58.253 29.630 0.00 0.00 0.00 3.14
596 607 9.712305 ATATGTAATAGGCTCATTTACACAGAC 57.288 33.333 15.53 0.87 38.31 3.51
614 625 5.060816 CACAGACATTTGTGTTTGTGTGTTC 59.939 40.000 18.53 0.00 44.94 3.18
736 747 3.502237 CCATTGCTTGTTGGCTGAC 57.498 52.632 0.00 0.00 0.00 3.51
738 749 0.963962 CATTGCTTGTTGGCTGACCT 59.036 50.000 0.00 0.00 36.63 3.85
740 751 1.484038 TTGCTTGTTGGCTGACCTTT 58.516 45.000 0.00 0.00 36.63 3.11
741 752 2.356665 TGCTTGTTGGCTGACCTTTA 57.643 45.000 0.00 0.00 36.63 1.85
742 753 2.229792 TGCTTGTTGGCTGACCTTTAG 58.770 47.619 0.00 0.00 36.63 1.85
743 754 1.068264 GCTTGTTGGCTGACCTTTAGC 60.068 52.381 0.00 0.00 40.41 3.09
744 755 2.229792 CTTGTTGGCTGACCTTTAGCA 58.770 47.619 0.00 0.00 42.88 3.49
745 756 2.356665 TGTTGGCTGACCTTTAGCAA 57.643 45.000 0.00 0.00 42.88 3.91
746 757 2.229792 TGTTGGCTGACCTTTAGCAAG 58.770 47.619 0.00 0.00 42.88 4.01
747 758 1.068264 GTTGGCTGACCTTTAGCAAGC 60.068 52.381 0.00 0.00 42.88 4.01
748 759 0.110295 TGGCTGACCTTTAGCAAGCA 59.890 50.000 0.00 0.00 42.88 3.91
749 760 0.807496 GGCTGACCTTTAGCAAGCAG 59.193 55.000 0.00 0.00 42.88 4.24
750 761 0.169894 GCTGACCTTTAGCAAGCAGC 59.830 55.000 0.00 0.00 46.19 5.25
761 772 2.563297 CAAGCAGCTTGCCATGAGA 58.437 52.632 22.14 0.00 46.52 3.27
762 773 0.452184 CAAGCAGCTTGCCATGAGAG 59.548 55.000 22.14 0.00 46.52 3.20
763 774 0.037877 AAGCAGCTTGCCATGAGAGT 59.962 50.000 6.93 0.00 46.52 3.24
764 775 0.037877 AGCAGCTTGCCATGAGAGTT 59.962 50.000 0.00 0.00 46.52 3.01
765 776 0.170561 GCAGCTTGCCATGAGAGTTG 59.829 55.000 0.00 0.00 37.42 3.16
766 777 1.531423 CAGCTTGCCATGAGAGTTGT 58.469 50.000 0.00 0.00 0.00 3.32
767 778 1.467734 CAGCTTGCCATGAGAGTTGTC 59.532 52.381 0.00 0.00 0.00 3.18
768 779 1.350351 AGCTTGCCATGAGAGTTGTCT 59.650 47.619 0.00 0.00 34.86 3.41
769 780 2.157738 GCTTGCCATGAGAGTTGTCTT 58.842 47.619 0.00 0.00 30.97 3.01
770 781 2.161211 GCTTGCCATGAGAGTTGTCTTC 59.839 50.000 0.00 0.00 30.97 2.87
771 782 2.084610 TGCCATGAGAGTTGTCTTCG 57.915 50.000 0.00 0.00 30.97 3.79
772 783 1.618343 TGCCATGAGAGTTGTCTTCGA 59.382 47.619 0.00 0.00 30.97 3.71
773 784 2.037121 TGCCATGAGAGTTGTCTTCGAA 59.963 45.455 0.00 0.00 30.97 3.71
774 785 3.265791 GCCATGAGAGTTGTCTTCGAAT 58.734 45.455 0.00 0.00 30.97 3.34
775 786 3.063180 GCCATGAGAGTTGTCTTCGAATG 59.937 47.826 0.00 0.00 30.97 2.67
776 787 3.620374 CCATGAGAGTTGTCTTCGAATGG 59.380 47.826 0.00 0.00 30.97 3.16
777 788 4.248859 CATGAGAGTTGTCTTCGAATGGT 58.751 43.478 0.00 0.00 30.97 3.55
778 789 5.410924 CATGAGAGTTGTCTTCGAATGGTA 58.589 41.667 0.00 0.00 30.97 3.25
779 790 5.661056 TGAGAGTTGTCTTCGAATGGTAT 57.339 39.130 0.00 0.00 30.97 2.73
780 791 5.410924 TGAGAGTTGTCTTCGAATGGTATG 58.589 41.667 0.00 0.00 30.97 2.39
781 792 4.759782 AGAGTTGTCTTCGAATGGTATGG 58.240 43.478 0.00 0.00 0.00 2.74
782 793 4.223032 AGAGTTGTCTTCGAATGGTATGGT 59.777 41.667 0.00 0.00 0.00 3.55
783 794 4.906618 AGTTGTCTTCGAATGGTATGGTT 58.093 39.130 0.00 0.00 0.00 3.67
784 795 6.045072 AGTTGTCTTCGAATGGTATGGTTA 57.955 37.500 0.00 0.00 0.00 2.85
785 796 6.106673 AGTTGTCTTCGAATGGTATGGTTAG 58.893 40.000 0.00 0.00 0.00 2.34
786 797 4.439057 TGTCTTCGAATGGTATGGTTAGC 58.561 43.478 0.00 0.00 0.00 3.09
787 798 4.081365 TGTCTTCGAATGGTATGGTTAGCA 60.081 41.667 0.00 0.00 39.94 3.49
788 799 4.270325 GTCTTCGAATGGTATGGTTAGCAC 59.730 45.833 0.00 0.00 38.56 4.40
793 804 2.684001 TGGTATGGTTAGCACTTCCG 57.316 50.000 0.00 0.00 31.07 4.30
801 812 2.558554 TTAGCACTTCCGAGAGCGCC 62.559 60.000 2.29 0.00 43.25 6.53
802 813 4.443266 GCACTTCCGAGAGCGCCT 62.443 66.667 2.29 0.00 35.83 5.52
817 828 5.891451 AGAGCGCCTTAAAATACAATTTCC 58.109 37.500 2.29 0.00 0.00 3.13
831 842 2.809696 CAATTTCCCTGCAGGCAAAAAG 59.190 45.455 25.31 16.35 34.51 2.27
851 862 2.243221 AGCTTGGTGGAAGGCTCATAAT 59.757 45.455 0.00 0.00 31.56 1.28
869 880 5.705441 TCATAATTGACTTGACCTTGACCAC 59.295 40.000 0.00 0.00 0.00 4.16
871 882 1.116308 TGACTTGACCTTGACCACGA 58.884 50.000 0.00 0.00 0.00 4.35
875 886 1.341531 CTTGACCTTGACCACGAGTCT 59.658 52.381 10.78 0.00 46.46 3.24
876 887 2.281539 TGACCTTGACCACGAGTCTA 57.718 50.000 10.78 3.82 46.46 2.59
910 921 0.465097 ATCCTCCATTCAGCCGCTTG 60.465 55.000 0.00 0.00 0.00 4.01
984 995 3.686016 TCCTTGGTGGAAGCTCATAAAC 58.314 45.455 0.00 0.00 42.94 2.01
1103 1117 2.165641 CCAAGTGGATGCGTAGTACTGA 59.834 50.000 5.39 0.00 37.39 3.41
1132 1153 3.077359 GTCACCAATCTTGACTTCCCTG 58.923 50.000 0.00 0.00 40.30 4.45
1140 1161 1.002544 CTTGACTTCCCTGGTCAGTCC 59.997 57.143 16.07 3.78 43.29 3.85
1141 1162 0.105194 TGACTTCCCTGGTCAGTCCA 60.105 55.000 16.07 5.71 45.01 4.02
1176 1202 2.813754 TCTGCTTGTTCACACTATTGGC 59.186 45.455 0.00 0.00 0.00 4.52
1192 1222 3.582998 TTGGCCCTCTTCCATTCTATG 57.417 47.619 0.00 0.00 32.92 2.23
1201 1232 7.261325 CCCTCTTCCATTCTATGTATACATCG 58.739 42.308 21.49 15.54 37.76 3.84
1202 1233 7.261325 CCTCTTCCATTCTATGTATACATCGG 58.739 42.308 21.49 15.15 37.76 4.18
1268 1309 4.767928 CCATGTCTCCCCTCTACATACTAC 59.232 50.000 0.00 0.00 32.70 2.73
1271 1312 3.072184 GTCTCCCCTCTACATACTACCGA 59.928 52.174 0.00 0.00 0.00 4.69
1384 1440 1.517832 CAAGCTCGTCTCGGGGAAT 59.482 57.895 0.00 0.00 0.00 3.01
1468 1560 1.756950 CGGCTCCAGCTGGTACCTA 60.757 63.158 31.58 11.86 43.47 3.08
1647 1757 6.535150 ACTCACATTGTCAATAATAGGACACG 59.465 38.462 0.00 0.00 43.22 4.49
1669 1785 1.246649 CCAGCAGCATAAACACCACA 58.753 50.000 0.00 0.00 0.00 4.17
1705 1821 5.559035 CGTTGTCTTGAACAGTGGAAATCTC 60.559 44.000 0.00 0.00 39.58 2.75
1717 1833 2.304761 TGGAAATCTCGCCCTTACAGTT 59.695 45.455 0.00 0.00 0.00 3.16
2290 2421 2.111384 GACTGTATGGGGAGCTTCTCA 58.889 52.381 0.00 0.00 31.08 3.27
2426 2557 7.830697 CAGATATATTCAACCCCATTGCTCATA 59.169 37.037 0.00 0.00 38.29 2.15
2809 2956 2.409948 ATGAAGGTAGTTCTGCTGGC 57.590 50.000 0.00 0.00 35.99 4.85
2929 3079 1.805345 AGTGACTCGAAGACTACCGTG 59.195 52.381 0.00 0.00 0.00 4.94
3892 10628 6.176896 TGTAGCAAAATATGGCAGAACTACA 58.823 36.000 0.00 1.19 36.16 2.74
3925 10661 8.519526 TGTATGTTTTGTTGATTGGATAGTTCC 58.480 33.333 0.00 0.00 42.94 3.62
3946 10682 7.557719 AGTTCCACACATATCCTTAAATCCTTG 59.442 37.037 0.00 0.00 0.00 3.61
3947 10683 6.969043 TCCACACATATCCTTAAATCCTTGT 58.031 36.000 0.00 0.00 0.00 3.16
4017 10753 0.911525 AGAGCACACATAGCCTGGGT 60.912 55.000 2.98 2.98 44.42 4.51
4037 10773 0.107312 GTGCCTCATGCTCACTCCAT 60.107 55.000 0.00 0.00 42.00 3.41
4088 10824 2.700773 GGCCCCACATTTGCTCGAC 61.701 63.158 0.00 0.00 0.00 4.20
4097 10833 2.548057 ACATTTGCTCGACGAAATGTGT 59.452 40.909 20.13 9.99 46.25 3.72
4195 10931 3.495001 GCCAAAGCTGATAAGACCGTATC 59.505 47.826 0.00 0.00 35.50 2.24
4206 10942 9.574458 CTGATAAGACCGTATCTAATATGTTGG 57.426 37.037 4.98 0.00 36.27 3.77
4278 11014 5.044919 TGGCCTTCTTCTTTTGAGGATATGA 60.045 40.000 3.32 0.00 34.44 2.15
4345 11081 9.388506 CTCTTATTTCAGATTCACCATGTTACT 57.611 33.333 0.00 0.00 0.00 2.24
4353 11090 5.355350 AGATTCACCATGTTACTAAGCAAGC 59.645 40.000 0.00 0.00 0.00 4.01
4392 11134 9.746711 CTGTTATTTCGTTCTAGAGATTGTTTG 57.253 33.333 0.00 0.00 0.00 2.93
4455 11197 4.271776 AGAAACCCGTAGAAGAAAACAACG 59.728 41.667 0.00 0.00 0.00 4.10
4467 11210 2.503920 AAACAACGCAGTAGACGAGT 57.496 45.000 0.00 0.00 45.00 4.18
4469 11212 3.844577 AACAACGCAGTAGACGAGTAT 57.155 42.857 0.00 0.00 45.00 2.12
4484 11227 3.671928 ACGAGTATGTGTTGCGTAAAGAC 59.328 43.478 0.00 0.00 32.94 3.01
4511 11262 4.471386 AGTGACATTCATAACCCTGCTAGT 59.529 41.667 0.00 0.00 0.00 2.57
4513 11264 6.327626 AGTGACATTCATAACCCTGCTAGTAT 59.672 38.462 0.00 0.00 0.00 2.12
4583 11878 7.232534 AGCATAAGAGAGGATGAAGGTTACTAG 59.767 40.741 0.00 0.00 0.00 2.57
4675 11970 6.319152 AGAGACTGTGTAAGCTGTATAATCGT 59.681 38.462 0.00 0.00 0.00 3.73
4683 11978 7.537991 GTGTAAGCTGTATAATCGTCTGGTATC 59.462 40.741 0.00 0.00 0.00 2.24
4697 11992 8.786826 TCGTCTGGTATCTTCAAATTTATGTT 57.213 30.769 0.00 0.00 0.00 2.71
4699 11994 9.840427 CGTCTGGTATCTTCAAATTTATGTTTT 57.160 29.630 0.00 0.00 0.00 2.43
4733 12028 8.708742 CATTTTTCGTATTCTGTCAGTGTAGAA 58.291 33.333 12.62 12.62 37.34 2.10
4742 12037 4.118410 CTGTCAGTGTAGAAGATGCATCC 58.882 47.826 23.06 8.93 0.00 3.51
4772 12067 5.090139 ACTCTCTGGGTGCTATGCTATATT 58.910 41.667 0.00 0.00 0.00 1.28
4773 12068 5.545723 ACTCTCTGGGTGCTATGCTATATTT 59.454 40.000 0.00 0.00 0.00 1.40
4774 12069 6.042638 TCTCTGGGTGCTATGCTATATTTC 57.957 41.667 0.00 0.00 0.00 2.17
4775 12070 5.046304 TCTCTGGGTGCTATGCTATATTTCC 60.046 44.000 0.00 0.00 0.00 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 8.184304 TGGCACCAATTTTACTAAACAGTATT 57.816 30.769 0.00 0.00 0.00 1.89
81 82 7.584122 TTGGCACCAATTTTACTAAACAGTA 57.416 32.000 0.00 0.00 0.00 2.74
93 96 4.901250 CCCCTTCTATATTGGCACCAATTT 59.099 41.667 19.49 14.22 43.32 1.82
151 154 7.004086 TCAGGACAAAGGAAATAAATCACACT 58.996 34.615 0.00 0.00 0.00 3.55
153 156 7.505585 AGTTCAGGACAAAGGAAATAAATCACA 59.494 33.333 0.00 0.00 0.00 3.58
173 176 4.527564 CTTTGTAGCGTTTCCAAGTTCAG 58.472 43.478 0.00 0.00 0.00 3.02
179 182 4.735283 GCTTTTCCTTTGTAGCGTTTCCAA 60.735 41.667 0.00 0.00 0.00 3.53
206 209 4.499183 CAACTCAGGAACCTAACAGCTAG 58.501 47.826 0.00 0.00 0.00 3.42
215 218 1.771255 AGACAAGCAACTCAGGAACCT 59.229 47.619 0.00 0.00 0.00 3.50
262 265 8.879759 CAGTTCTCCGCAAAATCTTATAAGTTA 58.120 33.333 12.19 0.00 0.00 2.24
269 272 4.690748 CACTCAGTTCTCCGCAAAATCTTA 59.309 41.667 0.00 0.00 0.00 2.10
274 277 0.944386 GCACTCAGTTCTCCGCAAAA 59.056 50.000 0.00 0.00 0.00 2.44
307 310 5.164620 TCTCATAAGCTCAACCAATCACA 57.835 39.130 0.00 0.00 0.00 3.58
326 329 2.131023 ACTGATTCCCCAATCCCTCTC 58.869 52.381 0.00 0.00 38.14 3.20
327 330 2.293598 ACTGATTCCCCAATCCCTCT 57.706 50.000 0.00 0.00 38.14 3.69
353 356 3.548214 GGTCTTCTTGTTCGACAAAAGGC 60.548 47.826 0.00 2.53 37.69 4.35
395 398 2.644798 ACAAGCTATGGAACTGTCCCTT 59.355 45.455 0.00 0.00 44.23 3.95
456 459 2.556287 GAAACGGTGGCAGAAGCG 59.444 61.111 0.00 3.73 46.11 4.68
474 477 7.125113 CAGCAATGAACACAAATTAACCAAAC 58.875 34.615 0.00 0.00 0.00 2.93
477 480 5.295950 CCAGCAATGAACACAAATTAACCA 58.704 37.500 0.00 0.00 0.00 3.67
483 486 2.895404 AGAGCCAGCAATGAACACAAAT 59.105 40.909 0.00 0.00 0.00 2.32
505 509 7.277760 CACGGATGTAATCTAAACACATCAGAA 59.722 37.037 17.02 0.00 46.72 3.02
509 513 6.533723 TCACACGGATGTAATCTAAACACATC 59.466 38.462 5.56 5.56 44.71 3.06
517 521 4.142026 CCAACCTCACACGGATGTAATCTA 60.142 45.833 0.00 0.00 44.71 1.98
518 522 3.369471 CCAACCTCACACGGATGTAATCT 60.369 47.826 0.00 0.00 44.71 2.40
519 523 2.936498 CCAACCTCACACGGATGTAATC 59.064 50.000 0.00 0.00 44.55 1.75
520 524 2.304761 ACCAACCTCACACGGATGTAAT 59.695 45.455 0.00 0.00 36.72 1.89
522 526 1.274167 GACCAACCTCACACGGATGTA 59.726 52.381 0.00 0.00 36.72 2.29
523 527 0.034896 GACCAACCTCACACGGATGT 59.965 55.000 0.00 0.00 40.80 3.06
524 528 0.321671 AGACCAACCTCACACGGATG 59.678 55.000 0.00 0.00 0.00 3.51
525 529 1.056660 AAGACCAACCTCACACGGAT 58.943 50.000 0.00 0.00 0.00 4.18
526 530 0.834612 AAAGACCAACCTCACACGGA 59.165 50.000 0.00 0.00 0.00 4.69
528 532 2.014128 ACAAAAGACCAACCTCACACG 58.986 47.619 0.00 0.00 0.00 4.49
549 560 9.754382 ACATATGCAAATTCAAAGGATATCAAC 57.246 29.630 1.58 0.00 0.00 3.18
559 570 8.911965 TGAGCCTATTACATATGCAAATTCAAA 58.088 29.630 1.58 0.00 0.00 2.69
572 583 7.564793 TGTCTGTGTAAATGAGCCTATTACAT 58.435 34.615 0.00 0.00 40.47 2.29
594 605 4.162812 ACGAACACACAAACACAAATGTC 58.837 39.130 0.00 0.00 38.45 3.06
596 607 5.797934 ACTAACGAACACACAAACACAAATG 59.202 36.000 0.00 0.00 0.00 2.32
698 709 5.628797 TGGCCTGAATGATCACTGTATTA 57.371 39.130 3.32 0.00 0.00 0.98
743 754 0.452184 CTCTCATGGCAAGCTGCTTG 59.548 55.000 32.35 32.35 44.28 4.01
744 755 0.037877 ACTCTCATGGCAAGCTGCTT 59.962 50.000 9.53 9.53 44.28 3.91
745 756 0.037877 AACTCTCATGGCAAGCTGCT 59.962 50.000 0.00 0.00 44.28 4.24
746 757 0.170561 CAACTCTCATGGCAAGCTGC 59.829 55.000 0.00 0.00 44.08 5.25
747 758 1.467734 GACAACTCTCATGGCAAGCTG 59.532 52.381 0.00 0.00 0.00 4.24
748 759 1.350351 AGACAACTCTCATGGCAAGCT 59.650 47.619 0.00 0.00 0.00 3.74
749 760 1.818642 AGACAACTCTCATGGCAAGC 58.181 50.000 0.00 0.00 0.00 4.01
750 761 2.414481 CGAAGACAACTCTCATGGCAAG 59.586 50.000 0.00 0.00 0.00 4.01
751 762 2.037121 TCGAAGACAACTCTCATGGCAA 59.963 45.455 0.00 0.00 0.00 4.52
752 763 1.618343 TCGAAGACAACTCTCATGGCA 59.382 47.619 0.00 0.00 0.00 4.92
753 764 2.370281 TCGAAGACAACTCTCATGGC 57.630 50.000 0.00 0.00 0.00 4.40
754 765 3.620374 CCATTCGAAGACAACTCTCATGG 59.380 47.826 3.35 0.00 34.32 3.66
755 766 4.248859 ACCATTCGAAGACAACTCTCATG 58.751 43.478 3.35 0.00 34.32 3.07
756 767 4.543590 ACCATTCGAAGACAACTCTCAT 57.456 40.909 3.35 0.00 34.32 2.90
757 768 5.410924 CATACCATTCGAAGACAACTCTCA 58.589 41.667 3.35 0.00 34.32 3.27
758 769 4.806247 CCATACCATTCGAAGACAACTCTC 59.194 45.833 3.35 0.00 34.32 3.20
759 770 4.223032 ACCATACCATTCGAAGACAACTCT 59.777 41.667 3.35 0.00 34.32 3.24
760 771 4.504858 ACCATACCATTCGAAGACAACTC 58.495 43.478 3.35 0.00 34.32 3.01
761 772 4.553330 ACCATACCATTCGAAGACAACT 57.447 40.909 3.35 0.00 34.32 3.16
762 773 5.220605 GCTAACCATACCATTCGAAGACAAC 60.221 44.000 3.35 0.00 34.32 3.32
763 774 4.873827 GCTAACCATACCATTCGAAGACAA 59.126 41.667 3.35 0.00 34.32 3.18
764 775 4.081365 TGCTAACCATACCATTCGAAGACA 60.081 41.667 3.35 0.00 34.32 3.41
765 776 4.270325 GTGCTAACCATACCATTCGAAGAC 59.730 45.833 3.35 0.00 34.32 3.01
766 777 4.161565 AGTGCTAACCATACCATTCGAAGA 59.838 41.667 3.35 0.00 0.00 2.87
767 778 4.442706 AGTGCTAACCATACCATTCGAAG 58.557 43.478 3.35 0.00 0.00 3.79
768 779 4.481368 AGTGCTAACCATACCATTCGAA 57.519 40.909 0.00 0.00 0.00 3.71
769 780 4.439057 GAAGTGCTAACCATACCATTCGA 58.561 43.478 0.00 0.00 0.00 3.71
770 781 3.560068 GGAAGTGCTAACCATACCATTCG 59.440 47.826 0.00 0.00 0.00 3.34
771 782 3.560068 CGGAAGTGCTAACCATACCATTC 59.440 47.826 0.00 0.00 0.00 2.67
772 783 3.199071 TCGGAAGTGCTAACCATACCATT 59.801 43.478 0.00 0.00 0.00 3.16
773 784 2.769663 TCGGAAGTGCTAACCATACCAT 59.230 45.455 0.00 0.00 0.00 3.55
774 785 2.167693 CTCGGAAGTGCTAACCATACCA 59.832 50.000 0.00 0.00 0.00 3.25
775 786 2.429610 TCTCGGAAGTGCTAACCATACC 59.570 50.000 0.00 0.00 0.00 2.73
776 787 3.707793 CTCTCGGAAGTGCTAACCATAC 58.292 50.000 0.00 0.00 0.00 2.39
777 788 2.100916 GCTCTCGGAAGTGCTAACCATA 59.899 50.000 0.00 0.00 38.64 2.74
778 789 1.134670 GCTCTCGGAAGTGCTAACCAT 60.135 52.381 0.00 0.00 38.64 3.55
779 790 0.246635 GCTCTCGGAAGTGCTAACCA 59.753 55.000 0.00 0.00 38.64 3.67
780 791 0.802607 CGCTCTCGGAAGTGCTAACC 60.803 60.000 0.00 0.00 39.36 2.85
781 792 1.414527 GCGCTCTCGGAAGTGCTAAC 61.415 60.000 13.89 0.00 46.74 2.34
782 793 1.153823 GCGCTCTCGGAAGTGCTAA 60.154 57.895 13.89 0.00 46.74 3.09
783 794 2.490217 GCGCTCTCGGAAGTGCTA 59.510 61.111 13.89 0.00 46.74 3.49
786 797 0.108804 TTAAGGCGCTCTCGGAAGTG 60.109 55.000 7.64 0.00 35.95 3.16
787 798 0.606604 TTTAAGGCGCTCTCGGAAGT 59.393 50.000 7.64 0.00 35.95 3.01
788 799 1.722011 TTTTAAGGCGCTCTCGGAAG 58.278 50.000 7.64 0.00 35.95 3.46
793 804 5.971792 GGAAATTGTATTTTAAGGCGCTCTC 59.028 40.000 7.64 0.00 0.00 3.20
801 812 5.812127 GCCTGCAGGGAAATTGTATTTTAAG 59.188 40.000 33.46 2.18 37.23 1.85
802 813 5.247110 TGCCTGCAGGGAAATTGTATTTTAA 59.753 36.000 33.46 0.00 37.23 1.52
817 828 0.601841 CCAAGCTTTTTGCCTGCAGG 60.602 55.000 29.34 29.34 44.23 4.85
831 842 2.128771 TTATGAGCCTTCCACCAAGC 57.871 50.000 0.00 0.00 0.00 4.01
838 849 4.336713 GGTCAAGTCAATTATGAGCCTTCC 59.663 45.833 0.00 0.00 35.88 3.46
851 862 1.483004 TCGTGGTCAAGGTCAAGTCAA 59.517 47.619 0.00 0.00 0.00 3.18
889 900 1.146930 GCGGCTGAATGGAGGATGA 59.853 57.895 0.00 0.00 0.00 2.92
890 901 0.465097 AAGCGGCTGAATGGAGGATG 60.465 55.000 1.81 0.00 0.00 3.51
891 902 0.465097 CAAGCGGCTGAATGGAGGAT 60.465 55.000 1.81 0.00 0.00 3.24
951 962 2.705658 CCACCAAGGAGTATAGCCATCA 59.294 50.000 0.00 0.00 41.22 3.07
1103 1117 5.091261 GTCAAGATTGGTGACTAGGACAT 57.909 43.478 0.00 0.00 41.80 3.06
1140 1161 2.298610 AGCAGATTGGCATGATCAGTG 58.701 47.619 0.09 1.26 35.83 3.66
1141 1162 2.688446 CAAGCAGATTGGCATGATCAGT 59.312 45.455 0.09 0.00 34.59 3.41
1146 1167 2.229543 GTGAACAAGCAGATTGGCATGA 59.770 45.455 2.92 0.00 43.68 3.07
1176 1202 7.261325 CGATGTATACATAGAATGGAAGAGGG 58.739 42.308 18.28 0.00 36.57 4.30
1192 1222 3.915536 GGAGGAAGAAGCCGATGTATAC 58.084 50.000 0.00 0.00 0.00 1.47
1201 1232 3.753294 TGATATTCGGAGGAAGAAGCC 57.247 47.619 0.00 0.00 35.19 4.35
1202 1233 4.024472 GCTTTGATATTCGGAGGAAGAAGC 60.024 45.833 0.00 0.00 35.19 3.86
1268 1309 0.543749 AAGAGGAGAAGCCCAATCGG 59.456 55.000 0.00 0.00 37.37 4.18
1271 1312 0.700564 TGCAAGAGGAGAAGCCCAAT 59.299 50.000 0.00 0.00 37.37 3.16
1384 1440 2.664851 CCGAGTGCGAACTTGCCA 60.665 61.111 5.09 0.00 40.82 4.92
1468 1560 5.133221 GGTATCTTGTTGAACCATATGCCT 58.867 41.667 0.00 0.00 32.04 4.75
1647 1757 0.453390 GGTGTTTATGCTGCTGGCTC 59.547 55.000 0.00 0.00 42.39 4.70
1685 1801 3.120511 GCGAGATTTCCACTGTTCAAGAC 60.121 47.826 0.00 0.00 0.00 3.01
1705 1821 2.735762 GCTCTCTGTAACTGTAAGGGCG 60.736 54.545 0.00 0.00 39.30 6.13
1717 1833 3.580039 TGATGATGATGGGCTCTCTGTA 58.420 45.455 0.00 0.00 0.00 2.74
2290 2421 1.827399 AATCCCGCGGTGACTTCTGT 61.827 55.000 26.12 1.89 0.00 3.41
2426 2557 3.582208 TGTGGGTTGTAGGGTAACGTAAT 59.418 43.478 0.00 0.00 38.93 1.89
2929 3079 1.067354 CCATCAAGCCTTTTCACTGCC 60.067 52.381 0.00 0.00 0.00 4.85
3079 3229 6.566079 TGACTATCAAGAGACCCATTGAAT 57.434 37.500 0.00 0.00 38.80 2.57
3925 10661 8.712363 CGATACAAGGATTTAAGGATATGTGTG 58.288 37.037 0.00 0.00 0.00 3.82
3927 10663 9.489084 TTCGATACAAGGATTTAAGGATATGTG 57.511 33.333 0.00 0.00 0.00 3.21
3929 10665 9.155975 CCTTCGATACAAGGATTTAAGGATATG 57.844 37.037 0.00 0.00 45.41 1.78
3946 10682 2.846039 TCGACAGCTTCCTTCGATAC 57.154 50.000 3.09 0.00 36.87 2.24
4037 10773 2.616256 GCCATGTCAGAAGGTCACATCA 60.616 50.000 0.00 0.00 0.00 3.07
4079 10815 1.262950 CCACACATTTCGTCGAGCAAA 59.737 47.619 0.00 0.00 0.00 3.68
4088 10824 0.109597 GAAGCCTGCCACACATTTCG 60.110 55.000 0.00 0.00 0.00 3.46
4097 10833 1.980232 CCAGCATTGAAGCCTGCCA 60.980 57.895 0.00 0.00 39.22 4.92
4186 10922 8.867097 ACATAACCAACATATTAGATACGGTCT 58.133 33.333 0.00 0.00 41.11 3.85
4190 10926 8.922676 GTGGACATAACCAACATATTAGATACG 58.077 37.037 0.00 0.00 41.87 3.06
4206 10942 9.256477 TCGAGTGAATTTATATGTGGACATAAC 57.744 33.333 3.65 0.00 41.60 1.89
4278 11014 8.579863 CAATCTCCAAGAAACTTACAAGGAAAT 58.420 33.333 0.00 0.00 0.00 2.17
4353 11090 4.031991 CGAAATAACAGTGGCAATGCATTG 59.968 41.667 30.92 30.92 40.66 2.82
4434 11176 3.242837 GCGTTGTTTTCTTCTACGGGTTT 60.243 43.478 0.00 0.00 35.43 3.27
4455 11197 2.599082 GCAACACATACTCGTCTACTGC 59.401 50.000 0.00 0.00 0.00 4.40
4484 11227 3.618594 CAGGGTTATGAATGTCACTGTCG 59.381 47.826 0.00 0.00 0.00 4.35
4533 11828 4.040339 CCTTATTTCCCTTGGTTGCTTGTT 59.960 41.667 0.00 0.00 0.00 2.83
4536 11831 4.089361 CTCCTTATTTCCCTTGGTTGCTT 58.911 43.478 0.00 0.00 0.00 3.91
4538 11833 2.166459 GCTCCTTATTTCCCTTGGTTGC 59.834 50.000 0.00 0.00 0.00 4.17
4658 11953 5.847111 ACCAGACGATTATACAGCTTACA 57.153 39.130 0.00 0.00 0.00 2.41
4699 11994 9.058174 TGACAGAATACGAAAAATGGTAAAGAA 57.942 29.630 0.00 0.00 0.00 2.52
4700 11995 8.610248 TGACAGAATACGAAAAATGGTAAAGA 57.390 30.769 0.00 0.00 0.00 2.52
4701 11996 8.504005 ACTGACAGAATACGAAAAATGGTAAAG 58.496 33.333 10.08 0.00 0.00 1.85
4705 12000 5.763204 ACACTGACAGAATACGAAAAATGGT 59.237 36.000 10.08 0.00 0.00 3.55
4733 12028 5.245751 CCAGAGAGTACAATAGGATGCATCT 59.754 44.000 25.28 14.04 0.00 2.90
4742 12037 5.777802 CATAGCACCCAGAGAGTACAATAG 58.222 45.833 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.