Multiple sequence alignment - TraesCS2D01G588300

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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 TraesCS2D01G588300 chr2D 100.000 3988 0 0 1 3988 645721695 645725682 0.000000e+00 7365
1 TraesCS2D01G588300 chr2D 86.276 2543 237 42 972 3439 645817133 645814628 0.000000e+00 2660
2 TraesCS2D01G588300 chr2D 87.311 1584 123 25 1109 2621 645561029 645559453 0.000000e+00 1740
3 TraesCS2D01G588300 chr2D 86.801 1341 118 14 1874 3168 645791852 645793179 0.000000e+00 1441
4 TraesCS2D01G588300 chr2D 97.516 483 12 0 1 483 644993927 644994409 0.000000e+00 826
5 TraesCS2D01G588300 chr2D 97.474 475 12 0 1 475 441041955 441042429 0.000000e+00 811
6 TraesCS2D01G588300 chr2D 80.318 1133 162 31 1867 2964 645612968 645611862 0.000000e+00 800
7 TraesCS2D01G588300 chr2D 84.703 706 62 14 1202 1877 645788689 645789378 0.000000e+00 664
8 TraesCS2D01G588300 chr2D 85.818 550 53 11 3159 3685 645793547 645794094 9.680000e-156 560
9 TraesCS2D01G588300 chr2D 81.077 613 87 19 3086 3683 645611807 645611209 2.810000e-126 462
10 TraesCS2D01G588300 chr2D 93.421 304 15 4 465 767 644994443 644994742 2.830000e-121 446
11 TraesCS2D01G588300 chr2D 91.803 305 9 2 465 767 441042492 441042782 1.030000e-110 411
12 TraesCS2D01G588300 chr2D 80.153 524 68 12 2650 3154 645559391 645558885 3.790000e-95 359
13 TraesCS2D01G588300 chr2D 91.667 204 11 3 988 1186 645788434 645788636 1.090000e-70 278
14 TraesCS2D01G588300 chr2D 82.667 300 36 8 1337 1634 645613781 645613496 6.620000e-63 252
15 TraesCS2D01G588300 chr2D 93.694 111 5 2 659 767 553263670 553263560 8.870000e-37 165
16 TraesCS2D01G588300 chr2D 92.233 103 8 0 3808 3910 645794459 645794561 3.210000e-31 147
17 TraesCS2D01G588300 chr2D 93.407 91 6 0 1 91 612523554 612523464 6.950000e-28 135
18 TraesCS2D01G588300 chr2B 96.670 1862 50 3 1208 3057 790229719 790227858 0.000000e+00 3085
19 TraesCS2D01G588300 chr2B 87.687 1405 119 24 1868 3230 789790958 789792350 0.000000e+00 1587
20 TraesCS2D01G588300 chr2B 80.697 1119 163 32 1863 2961 790105003 790106088 0.000000e+00 821
21 TraesCS2D01G588300 chr2B 81.473 842 82 22 1016 1805 789790133 789790952 1.220000e-174 623
22 TraesCS2D01G588300 chr2B 92.818 362 8 2 835 1181 790230143 790229785 3.560000e-140 508
23 TraesCS2D01G588300 chr2B 85.714 462 48 11 3231 3683 693819207 693818755 4.670000e-129 472
24 TraesCS2D01G588300 chr2B 85.249 461 48 11 3231 3683 76368382 76367934 1.310000e-124 457
25 TraesCS2D01G588300 chr2B 87.391 230 26 2 3760 3988 789792400 789792627 1.100000e-65 261
26 TraesCS2D01G588300 chr2A 87.198 1695 161 15 1975 3625 771501458 771499776 0.000000e+00 1877
27 TraesCS2D01G588300 chr2A 80.035 1132 160 32 1873 2964 771126597 771125492 0.000000e+00 778
28 TraesCS2D01G588300 chr2A 82.825 885 86 35 970 1818 771502308 771501454 0.000000e+00 732
29 TraesCS2D01G588300 chr2A 79.178 1143 166 40 1867 2964 771073978 771072863 0.000000e+00 726
30 TraesCS2D01G588300 chr2A 79.093 1124 151 38 1945 3013 771345734 771346828 0.000000e+00 697
31 TraesCS2D01G588300 chr2A 85.900 461 49 9 3231 3683 763121948 763121496 1.000000e-130 477
32 TraesCS2D01G588300 chr2A 78.140 430 64 21 1211 1634 771127181 771126776 3.080000e-61 246
33 TraesCS2D01G588300 chr2A 85.165 182 24 1 981 1162 771074948 771074770 2.450000e-42 183
34 TraesCS2D01G588300 chr2A 81.308 214 30 8 3086 3293 771072808 771072599 8.870000e-37 165
35 TraesCS2D01G588300 chr2A 88.550 131 15 0 1202 1332 771345379 771345509 4.130000e-35 159
36 TraesCS2D01G588300 chr2A 93.204 103 7 0 3808 3910 771497826 771497724 6.900000e-33 152
37 TraesCS2D01G588300 chr2A 92.647 68 5 0 1111 1178 771127317 771127250 9.120000e-17 99
38 TraesCS2D01G588300 chr3D 99.158 475 4 0 1 475 24087573 24088047 0.000000e+00 856
39 TraesCS2D01G588300 chr3D 97.895 475 10 0 1 475 20725008 20725482 0.000000e+00 822
40 TraesCS2D01G588300 chr3D 98.775 408 5 0 1 408 454227259 454227666 0.000000e+00 726
41 TraesCS2D01G588300 chr3D 95.410 305 12 2 465 767 454227770 454228074 5.990000e-133 484
42 TraesCS2D01G588300 chr3D 95.050 303 13 2 465 766 20725545 20725846 3.610000e-130 475
43 TraesCS2D01G588300 chr7D 98.945 474 5 0 1 474 561335614 561336087 0.000000e+00 848
44 TraesCS2D01G588300 chr7D 95.066 304 14 1 465 767 561336151 561336454 1.000000e-130 477
45 TraesCS2D01G588300 chr5D 98.945 474 5 0 1 474 335936841 335936368 0.000000e+00 848
46 TraesCS2D01G588300 chr5D 97.314 484 3 2 1 483 416801229 416800755 0.000000e+00 813
47 TraesCS2D01G588300 chr5D 99.223 386 3 0 90 475 169528150 169527765 0.000000e+00 697
48 TraesCS2D01G588300 chr5D 94.754 305 13 3 465 768 335936304 335936002 4.670000e-129 472
49 TraesCS2D01G588300 chr5D 94.426 305 12 4 465 769 416800731 416800432 7.810000e-127 464
50 TraesCS2D01G588300 chr5D 91.639 299 9 3 469 767 169527698 169527416 2.230000e-107 399
51 TraesCS2D01G588300 chr7B 85.683 461 50 9 3231 3683 490857674 490857222 4.670000e-129 472
52 TraesCS2D01G588300 chr6D 93.770 305 13 5 465 767 2396281 2396581 1.690000e-123 453
53 TraesCS2D01G588300 chr4B 85.799 338 39 7 3280 3615 55179884 55180214 2.280000e-92 350
54 TraesCS2D01G588300 chr4B 85.503 338 40 7 3280 3615 393835798 393836128 1.060000e-90 344
55 TraesCS2D01G588300 chr6B 84.911 338 42 7 3280 3615 124585394 124585064 2.300000e-87 333
56 TraesCS2D01G588300 chr1D 92.857 112 7 1 659 769 462983712 462983823 1.150000e-35 161
57 TraesCS2D01G588300 chr5B 94.505 91 5 0 1 91 688474329 688474419 1.490000e-29 141


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 TraesCS2D01G588300 chr2D 645721695 645725682 3987 False 7365.000000 7365 100.000000 1 3988 1 chr2D.!!$F1 3987
1 TraesCS2D01G588300 chr2D 645814628 645817133 2505 True 2660.000000 2660 86.276000 972 3439 1 chr2D.!!$R3 2467
2 TraesCS2D01G588300 chr2D 645558885 645561029 2144 True 1049.500000 1740 83.732000 1109 3154 2 chr2D.!!$R4 2045
3 TraesCS2D01G588300 chr2D 644993927 644994742 815 False 636.000000 826 95.468500 1 767 2 chr2D.!!$F3 766
4 TraesCS2D01G588300 chr2D 645788434 645794561 6127 False 618.000000 1441 88.244400 988 3910 5 chr2D.!!$F4 2922
5 TraesCS2D01G588300 chr2D 441041955 441042782 827 False 611.000000 811 94.638500 1 767 2 chr2D.!!$F2 766
6 TraesCS2D01G588300 chr2D 645611209 645613781 2572 True 504.666667 800 81.354000 1337 3683 3 chr2D.!!$R5 2346
7 TraesCS2D01G588300 chr2B 790227858 790230143 2285 True 1796.500000 3085 94.744000 835 3057 2 chr2B.!!$R3 2222
8 TraesCS2D01G588300 chr2B 789790133 789792627 2494 False 823.666667 1587 85.517000 1016 3988 3 chr2B.!!$F2 2972
9 TraesCS2D01G588300 chr2B 790105003 790106088 1085 False 821.000000 821 80.697000 1863 2961 1 chr2B.!!$F1 1098
10 TraesCS2D01G588300 chr2A 771497724 771502308 4584 True 920.333333 1877 87.742333 970 3910 3 chr2A.!!$R4 2940
11 TraesCS2D01G588300 chr2A 771345379 771346828 1449 False 428.000000 697 83.821500 1202 3013 2 chr2A.!!$F1 1811
12 TraesCS2D01G588300 chr2A 771125492 771127317 1825 True 374.333333 778 83.607333 1111 2964 3 chr2A.!!$R3 1853
13 TraesCS2D01G588300 chr2A 771072599 771074948 2349 True 358.000000 726 81.883667 981 3293 3 chr2A.!!$R2 2312
14 TraesCS2D01G588300 chr3D 20725008 20725846 838 False 648.500000 822 96.472500 1 766 2 chr3D.!!$F2 765
15 TraesCS2D01G588300 chr3D 454227259 454228074 815 False 605.000000 726 97.092500 1 767 2 chr3D.!!$F3 766
16 TraesCS2D01G588300 chr7D 561335614 561336454 840 False 662.500000 848 97.005500 1 767 2 chr7D.!!$F1 766
17 TraesCS2D01G588300 chr5D 335936002 335936841 839 True 660.000000 848 96.849500 1 768 2 chr5D.!!$R2 767
18 TraesCS2D01G588300 chr5D 416800432 416801229 797 True 638.500000 813 95.870000 1 769 2 chr5D.!!$R3 768
19 TraesCS2D01G588300 chr5D 169527416 169528150 734 True 548.000000 697 95.431000 90 767 2 chr5D.!!$R1 677

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
563 689 1.145377 GGGCGGCGGAGATTTAGAA 59.855 57.895 9.78 0.00 0.00 2.10 F
1074 1249 0.107017 CCCCCACAAGATCTGCGAAT 60.107 55.000 0.00 0.00 0.00 3.34 F
1278 1522 0.955428 GTGGCGAGGTTGCAGATGAA 60.955 55.000 0.00 0.00 36.28 2.57 F
2070 5329 1.401905 GCCAACATCGATTTGGACCTC 59.598 52.381 28.48 15.43 45.69 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1750 1.070758 TCTTTCGTCTCCTTGCTGCTT 59.929 47.619 0.00 0.00 0.00 3.91 R
2070 5329 1.479323 CATTCCAGGAGTGGCCATTTG 59.521 52.381 9.72 0.00 44.60 2.32 R
2528 5820 1.600413 CGCAAGAAAGTTGCTTGGACC 60.600 52.381 22.61 7.51 42.23 4.46 R
3376 7136 0.324285 CTCAAGTTCCCAGCAGAGCT 59.676 55.000 0.00 0.00 40.77 4.09 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
505 631 4.758251 CTCGTCCGCATGGTGGCA 62.758 66.667 0.00 0.00 36.30 4.92
563 689 1.145377 GGGCGGCGGAGATTTAGAA 59.855 57.895 9.78 0.00 0.00 2.10
582 710 3.200825 AGAAGAGAGAGAGAGAGTGGAGG 59.799 52.174 0.00 0.00 0.00 4.30
657 787 2.165437 GTGAAACAGGTGGTGAAAGCAA 59.835 45.455 0.00 0.00 42.02 3.91
769 915 8.918202 ACTGAGACATTAGGAGTAGAGATAAG 57.082 38.462 0.00 0.00 0.00 1.73
770 916 7.447238 ACTGAGACATTAGGAGTAGAGATAAGC 59.553 40.741 0.00 0.00 0.00 3.09
771 917 6.428465 TGAGACATTAGGAGTAGAGATAAGCG 59.572 42.308 0.00 0.00 0.00 4.68
772 918 6.535540 AGACATTAGGAGTAGAGATAAGCGA 58.464 40.000 0.00 0.00 0.00 4.93
773 919 6.999272 AGACATTAGGAGTAGAGATAAGCGAA 59.001 38.462 0.00 0.00 0.00 4.70
774 920 7.174253 AGACATTAGGAGTAGAGATAAGCGAAG 59.826 40.741 0.00 0.00 0.00 3.79
792 938 3.361977 CGGTCGGGCCCAAACTTG 61.362 66.667 24.92 11.98 0.00 3.16
809 955 2.359975 GGCCTAACAGCCGTGCTT 60.360 61.111 0.00 0.00 44.57 3.91
810 956 2.399356 GGCCTAACAGCCGTGCTTC 61.399 63.158 0.00 0.00 44.57 3.86
811 957 2.740714 GCCTAACAGCCGTGCTTCG 61.741 63.158 0.00 0.00 36.40 3.79
812 958 1.374252 CCTAACAGCCGTGCTTCGT 60.374 57.895 0.00 0.00 36.40 3.85
813 959 1.626654 CCTAACAGCCGTGCTTCGTG 61.627 60.000 0.00 0.00 36.40 4.35
814 960 1.626654 CTAACAGCCGTGCTTCGTGG 61.627 60.000 0.00 0.00 36.40 4.94
815 961 4.988598 ACAGCCGTGCTTCGTGGG 62.989 66.667 0.00 0.00 36.40 4.61
956 1117 1.666553 CGGCGGTGAGTGTAGCAAA 60.667 57.895 0.00 0.00 0.00 3.68
1073 1248 1.198094 TCCCCCACAAGATCTGCGAA 61.198 55.000 0.00 0.00 0.00 4.70
1074 1249 0.107017 CCCCCACAAGATCTGCGAAT 60.107 55.000 0.00 0.00 0.00 3.34
1175 1353 2.869192 GTTCAATTCTCGCTGAGGATCC 59.131 50.000 2.48 2.48 25.98 3.36
1278 1522 0.955428 GTGGCGAGGTTGCAGATGAA 60.955 55.000 0.00 0.00 36.28 2.57
1281 1525 1.661341 GCGAGGTTGCAGATGAAGAT 58.339 50.000 0.00 0.00 34.15 2.40
1316 1560 3.012518 AGATGAACGGAGGCAAATCAAG 58.987 45.455 0.00 0.00 0.00 3.02
1332 1576 6.625300 GCAAATCAAGTCAGCAGATCAAGAAT 60.625 38.462 0.00 0.00 0.00 2.40
1363 1622 1.480954 TCGAGATGGACCTAGGCAAAC 59.519 52.381 9.30 0.00 0.00 2.93
1592 1863 3.058016 CGTGACATGTCCAAGCTCAAATT 60.058 43.478 22.85 0.00 0.00 1.82
2070 5329 1.401905 GCCAACATCGATTTGGACCTC 59.598 52.381 28.48 15.43 45.69 3.85
2230 5489 9.099454 CCTGCCGTATTCTATTAAATATCCTTC 57.901 37.037 0.00 0.00 0.00 3.46
2453 5745 5.135508 ACAGTGGCTATCATACCGATAAC 57.864 43.478 0.00 0.00 36.14 1.89
2528 5820 2.159787 GCAGCAACTGTACTGTCAATCG 60.160 50.000 5.81 0.00 36.26 3.34
3074 6446 7.903145 TCTATTTCTCTGGTTTGCAAGTAGTA 58.097 34.615 0.00 0.00 0.00 1.82
3075 6447 8.540388 TCTATTTCTCTGGTTTGCAAGTAGTAT 58.460 33.333 0.00 0.00 0.00 2.12
3178 6927 3.916172 TGTGCGTATCGACTCTGTTTTAC 59.084 43.478 0.00 0.00 0.00 2.01
3217 6972 7.801716 TGTGTTTCTACTTTCATTACTGCTT 57.198 32.000 0.00 0.00 0.00 3.91
3225 6980 6.613755 ACTTTCATTACTGCTTTAACGTGT 57.386 33.333 0.00 0.00 0.00 4.49
3252 7007 4.019411 TCATGCTGTGGGAAGTATTTCTGA 60.019 41.667 0.00 0.00 33.68 3.27
3321 7081 7.801716 TTGTTAATATGCCATGTTACTCTCC 57.198 36.000 0.00 0.00 0.00 3.71
3364 7124 6.631016 TGCTTTCATTCTGTTACGACTAGAT 58.369 36.000 0.00 0.00 0.00 1.98
3376 7136 8.459911 TGTTACGACTAGATTCAGATGGATAA 57.540 34.615 0.00 0.00 0.00 1.75
3396 7156 0.036022 GCTCTGCTGGGAACTTGAGT 59.964 55.000 0.00 0.00 0.00 3.41
3400 7160 0.183492 TGCTGGGAACTTGAGTTGCT 59.817 50.000 13.81 0.00 44.36 3.91
3408 7168 3.510719 GAACTTGAGTTGCTGCAAAACA 58.489 40.909 17.80 16.27 38.56 2.83
3447 7207 1.200020 CTTGCTTAAAACCTCTGCCCG 59.800 52.381 0.00 0.00 0.00 6.13
3451 7211 0.766131 TTAAAACCTCTGCCCGGTCA 59.234 50.000 0.00 0.00 32.46 4.02
3454 7214 0.609131 AAACCTCTGCCCGGTCAATG 60.609 55.000 0.00 0.00 32.46 2.82
3470 7230 4.895297 GGTCAATGGGAATATGGAATGTGT 59.105 41.667 0.00 0.00 0.00 3.72
3507 7274 4.039852 TGGCTTCAGTTGTACACAGTATGA 59.960 41.667 0.00 0.00 39.69 2.15
3510 7277 5.389935 GCTTCAGTTGTACACAGTATGAAGC 60.390 44.000 26.62 26.62 46.80 3.86
3536 7303 7.094634 CCATGTTAAGTTGCTCATGAACTACTT 60.095 37.037 23.06 23.06 39.68 2.24
3544 7311 5.907207 TGCTCATGAACTACTTATCAGTCC 58.093 41.667 0.00 0.00 34.06 3.85
3579 7346 2.862541 TCAACTTGGTGCACAGCTATT 58.137 42.857 20.43 2.94 0.00 1.73
3580 7347 3.221771 TCAACTTGGTGCACAGCTATTT 58.778 40.909 20.43 0.42 0.00 1.40
3638 7405 2.230660 GTATGATACCCTTTGCCCAGC 58.769 52.381 0.00 0.00 0.00 4.85
3645 7418 1.425448 ACCCTTTGCCCAGCTATATCC 59.575 52.381 0.00 0.00 0.00 2.59
3662 7438 8.709308 AGCTATATCCATCTACTTCTGTTTTGT 58.291 33.333 0.00 0.00 0.00 2.83
3669 7445 7.232737 TCCATCTACTTCTGTTTTGTCAGTAGA 59.767 37.037 9.23 9.23 36.69 2.59
3675 7451 6.828785 ACTTCTGTTTTGTCAGTAGATGGTTT 59.171 34.615 7.19 0.00 36.69 3.27
3676 7452 6.618287 TCTGTTTTGTCAGTAGATGGTTTG 57.382 37.500 0.00 0.00 36.85 2.93
3683 7459 6.371809 TGTCAGTAGATGGTTTGTTTGTTC 57.628 37.500 0.00 0.00 0.00 3.18
3684 7460 5.883115 TGTCAGTAGATGGTTTGTTTGTTCA 59.117 36.000 0.00 0.00 0.00 3.18
3686 7462 6.857964 GTCAGTAGATGGTTTGTTTGTTCATG 59.142 38.462 0.00 0.00 0.00 3.07
3687 7463 6.016360 TCAGTAGATGGTTTGTTTGTTCATGG 60.016 38.462 0.00 0.00 0.00 3.66
3688 7464 3.993920 AGATGGTTTGTTTGTTCATGGC 58.006 40.909 0.00 0.00 0.00 4.40
3690 7466 2.898705 TGGTTTGTTTGTTCATGGCAC 58.101 42.857 0.00 0.00 0.00 5.01
3691 7467 1.857837 GGTTTGTTTGTTCATGGCACG 59.142 47.619 0.00 0.00 0.00 5.34
3692 7468 1.857837 GTTTGTTTGTTCATGGCACGG 59.142 47.619 0.00 0.00 0.00 4.94
3693 7469 1.107114 TTGTTTGTTCATGGCACGGT 58.893 45.000 0.00 0.00 0.00 4.83
3694 7470 1.107114 TGTTTGTTCATGGCACGGTT 58.893 45.000 0.00 0.00 0.00 4.44
3695 7471 1.478510 TGTTTGTTCATGGCACGGTTT 59.521 42.857 0.00 0.00 0.00 3.27
3696 7472 1.857837 GTTTGTTCATGGCACGGTTTG 59.142 47.619 0.00 0.00 0.00 2.93
3697 7473 1.393603 TTGTTCATGGCACGGTTTGA 58.606 45.000 0.00 0.00 0.00 2.69
3698 7474 1.614996 TGTTCATGGCACGGTTTGAT 58.385 45.000 0.00 0.00 0.00 2.57
3699 7475 1.269174 TGTTCATGGCACGGTTTGATG 59.731 47.619 0.00 0.00 0.00 3.07
3700 7476 1.539388 GTTCATGGCACGGTTTGATGA 59.461 47.619 0.00 0.00 0.00 2.92
3701 7477 2.127271 TCATGGCACGGTTTGATGAT 57.873 45.000 0.00 0.00 0.00 2.45
3703 7479 0.457035 ATGGCACGGTTTGATGATGC 59.543 50.000 0.00 0.00 35.51 3.91
3706 7482 1.064060 GGCACGGTTTGATGATGCTAC 59.936 52.381 0.00 0.00 36.52 3.58
3707 7483 1.064060 GCACGGTTTGATGATGCTACC 59.936 52.381 0.00 0.00 33.44 3.18
3708 7484 2.632377 CACGGTTTGATGATGCTACCT 58.368 47.619 0.00 0.00 0.00 3.08
3709 7485 3.009723 CACGGTTTGATGATGCTACCTT 58.990 45.455 0.00 0.00 0.00 3.50
3710 7486 3.440173 CACGGTTTGATGATGCTACCTTT 59.560 43.478 0.00 0.00 0.00 3.11
3711 7487 3.689649 ACGGTTTGATGATGCTACCTTTC 59.310 43.478 0.00 0.00 0.00 2.62
3712 7488 3.689161 CGGTTTGATGATGCTACCTTTCA 59.311 43.478 0.00 0.00 0.00 2.69
3716 7492 6.459298 GGTTTGATGATGCTACCTTTCATGAG 60.459 42.308 0.00 0.00 30.48 2.90
3717 7493 4.711399 TGATGATGCTACCTTTCATGAGG 58.289 43.478 0.00 0.00 42.75 3.86
3725 7501 2.472695 CCTTTCATGAGGTCGGTTGA 57.527 50.000 0.00 0.00 31.89 3.18
3726 7502 2.350522 CCTTTCATGAGGTCGGTTGAG 58.649 52.381 0.00 0.00 31.89 3.02
3727 7503 2.028112 CCTTTCATGAGGTCGGTTGAGA 60.028 50.000 0.00 0.00 31.89 3.27
3728 7504 3.369892 CCTTTCATGAGGTCGGTTGAGAT 60.370 47.826 0.00 0.00 31.89 2.75
3730 7506 3.981071 TCATGAGGTCGGTTGAGATTT 57.019 42.857 0.00 0.00 0.00 2.17
3731 7507 4.286297 TCATGAGGTCGGTTGAGATTTT 57.714 40.909 0.00 0.00 0.00 1.82
3732 7508 4.253685 TCATGAGGTCGGTTGAGATTTTC 58.746 43.478 0.00 0.00 0.00 2.29
3733 7509 4.020218 TCATGAGGTCGGTTGAGATTTTCT 60.020 41.667 0.00 0.00 0.00 2.52
3734 7510 3.926616 TGAGGTCGGTTGAGATTTTCTC 58.073 45.455 0.00 0.00 43.65 2.87
3735 7511 3.263261 GAGGTCGGTTGAGATTTTCTCC 58.737 50.000 2.26 0.00 42.73 3.71
3736 7512 2.637872 AGGTCGGTTGAGATTTTCTCCA 59.362 45.455 2.26 0.00 42.73 3.86
3737 7513 3.072476 AGGTCGGTTGAGATTTTCTCCAA 59.928 43.478 2.26 0.00 42.73 3.53
3741 7517 6.150474 GGTCGGTTGAGATTTTCTCCAAAATA 59.850 38.462 2.26 0.00 42.73 1.40
3742 7518 7.148069 GGTCGGTTGAGATTTTCTCCAAAATAT 60.148 37.037 2.26 0.00 42.73 1.28
3743 7519 7.910683 GTCGGTTGAGATTTTCTCCAAAATATC 59.089 37.037 7.54 7.54 44.98 1.63
3744 7520 6.907212 CGGTTGAGATTTTCTCCAAAATATCG 59.093 38.462 9.20 0.00 46.56 2.92
3746 7522 8.624776 GGTTGAGATTTTCTCCAAAATATCGAT 58.375 33.333 2.16 2.16 46.56 3.59
3749 7525 9.394767 TGAGATTTTCTCCAAAATATCGATTGA 57.605 29.630 1.71 0.00 46.56 2.57
3757 7533 8.939929 TCTCCAAAATATCGATTGATTGATAGC 58.060 33.333 1.71 0.00 36.78 2.97
3758 7534 8.620116 TCCAAAATATCGATTGATTGATAGCA 57.380 30.769 1.71 0.00 36.78 3.49
3768 7544 6.193410 CGATTGATTGATAGCAAAGTCAAACG 59.807 38.462 18.61 18.61 39.99 3.60
3775 7556 6.545508 TGATAGCAAAGTCAAACGATCAATG 58.454 36.000 0.00 0.00 0.00 2.82
3785 7566 5.796935 GTCAAACGATCAATGACCATGAAAG 59.203 40.000 10.05 0.00 37.97 2.62
3789 7570 6.422776 ACGATCAATGACCATGAAAGTTAC 57.577 37.500 0.00 0.00 0.00 2.50
3873 9430 6.750501 CAGAAATCAGAAAAATGTCGATGCAT 59.249 34.615 0.00 0.00 0.00 3.96
3914 9471 3.498082 GGTCGTTACCACAAATTGCATC 58.502 45.455 0.00 0.00 45.98 3.91
3916 9473 4.158384 GTCGTTACCACAAATTGCATCTG 58.842 43.478 0.00 0.00 0.00 2.90
3923 9480 3.119602 CCACAAATTGCATCTGTGAGAGG 60.120 47.826 19.45 4.67 42.48 3.69
3976 9534 6.703165 GCTTGGAAGCCATTGGATTTTTATAG 59.297 38.462 7.76 3.37 46.20 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
167 168 3.329889 AGCACCTTCCCCATCGCA 61.330 61.111 0.00 0.00 0.00 5.10
284 285 1.146982 CCTTTCCTTTTCCCACCCTCA 59.853 52.381 0.00 0.00 0.00 3.86
505 631 3.893763 CATCCGGCTCTCGCGTCT 61.894 66.667 5.77 0.00 37.59 4.18
563 689 1.212935 GCCTCCACTCTCTCTCTCTCT 59.787 57.143 0.00 0.00 0.00 3.10
582 710 4.244802 CCTCTCGTCGCTCCTCGC 62.245 72.222 0.00 0.00 38.27 5.03
699 845 0.178533 TTCGTCCCACCACTTTCGTT 59.821 50.000 0.00 0.00 0.00 3.85
775 921 3.361977 CAAGTTTGGGCCCGACCG 61.362 66.667 19.37 8.87 40.62 4.79
776 922 2.989253 CCAAGTTTGGGCCCGACC 60.989 66.667 19.37 8.20 44.70 4.79
793 939 2.740714 CGAAGCACGGCTGTTAGGC 61.741 63.158 0.00 0.00 39.62 3.93
794 940 3.474806 CGAAGCACGGCTGTTAGG 58.525 61.111 0.00 0.00 39.62 2.69
820 966 0.677731 ATTCATGTGCCGTGTCTGGG 60.678 55.000 0.00 0.00 0.00 4.45
821 967 0.448990 CATTCATGTGCCGTGTCTGG 59.551 55.000 0.00 0.00 0.00 3.86
822 968 1.129251 GACATTCATGTGCCGTGTCTG 59.871 52.381 0.00 0.00 41.95 3.51
823 969 1.002430 AGACATTCATGTGCCGTGTCT 59.998 47.619 0.00 12.12 43.26 3.41
824 970 1.129251 CAGACATTCATGTGCCGTGTC 59.871 52.381 0.00 2.09 41.95 3.67
825 971 1.159285 CAGACATTCATGTGCCGTGT 58.841 50.000 0.00 0.00 41.95 4.49
826 972 0.448990 CCAGACATTCATGTGCCGTG 59.551 55.000 0.00 0.00 41.95 4.94
827 973 0.324614 TCCAGACATTCATGTGCCGT 59.675 50.000 0.00 0.00 41.95 5.68
828 974 0.729116 GTCCAGACATTCATGTGCCG 59.271 55.000 0.00 0.00 41.95 5.69
829 975 0.729116 CGTCCAGACATTCATGTGCC 59.271 55.000 0.00 0.00 41.95 5.01
830 976 0.729116 CCGTCCAGACATTCATGTGC 59.271 55.000 0.00 0.00 41.95 4.57
831 977 1.372582 CCCGTCCAGACATTCATGTG 58.627 55.000 0.00 0.00 41.95 3.21
832 978 0.392998 GCCCGTCCAGACATTCATGT 60.393 55.000 0.00 0.00 45.16 3.21
833 979 1.097547 GGCCCGTCCAGACATTCATG 61.098 60.000 0.00 0.00 34.01 3.07
948 1109 2.872245 GTTGACTGCTGAGTTTGCTACA 59.128 45.455 0.00 0.00 30.16 2.74
956 1117 1.056700 AGGGGTGTTGACTGCTGAGT 61.057 55.000 0.00 0.00 33.98 3.41
1113 1288 2.483288 CGGATTTTGAACGGCGGG 59.517 61.111 13.24 0.00 0.00 6.13
1175 1353 1.874019 CCGATCTTGCCGTCACTCG 60.874 63.158 0.00 0.00 39.52 4.18
1199 1398 0.250640 GGCAGGCATCGAATCCATCT 60.251 55.000 8.72 0.00 0.00 2.90
1246 1490 0.034198 TCGCCACACTTGAATTCGGA 59.966 50.000 0.04 0.00 0.00 4.55
1278 1522 3.196469 TCATCTTGTCCTTGCGAAGATCT 59.804 43.478 0.00 0.00 34.82 2.75
1281 1525 3.067106 GTTCATCTTGTCCTTGCGAAGA 58.933 45.455 0.00 0.00 0.00 2.87
1316 1560 3.204526 CCTGGATTCTTGATCTGCTGAC 58.795 50.000 0.00 0.00 35.02 3.51
1332 1576 1.075970 CATCTCGACCTCCCCTGGA 60.076 63.158 0.00 0.00 0.00 3.86
1363 1622 4.204799 TGCTCAGAGATGATGGAATTTGG 58.795 43.478 0.00 0.00 0.00 3.28
1485 1750 1.070758 TCTTTCGTCTCCTTGCTGCTT 59.929 47.619 0.00 0.00 0.00 3.91
1592 1863 1.758592 CGGAAAGGGGTCAGTTCCA 59.241 57.895 2.85 0.00 40.80 3.53
2070 5329 1.479323 CATTCCAGGAGTGGCCATTTG 59.521 52.381 9.72 0.00 44.60 2.32
2528 5820 1.600413 CGCAAGAAAGTTGCTTGGACC 60.600 52.381 22.61 7.51 42.23 4.46
3061 6433 7.913297 TGAACAGACAAAATACTACTTGCAAAC 59.087 33.333 0.00 0.00 0.00 2.93
3114 6486 5.069119 AGCAGATCGATACAACAATAGGTCA 59.931 40.000 0.00 0.00 0.00 4.02
3206 6961 6.924612 TGACTTACACGTTAAAGCAGTAATGA 59.075 34.615 0.00 0.00 0.00 2.57
3217 6972 3.743911 CCACAGCATGACTTACACGTTAA 59.256 43.478 0.00 0.00 39.69 2.01
3225 6980 5.435686 AATACTTCCCACAGCATGACTTA 57.564 39.130 0.00 0.00 39.69 2.24
3252 7007 3.221771 TGTGCCTGCTTAACAGTCAAAT 58.778 40.909 0.00 0.00 45.68 2.32
3284 7039 9.420118 TGGCATATTAACAAAATATTCCAGACT 57.580 29.630 5.39 0.00 33.20 3.24
3357 7117 7.315142 CAGAGCTTATCCATCTGAATCTAGTC 58.685 42.308 0.00 0.00 42.48 2.59
3364 7124 3.181457 CCAGCAGAGCTTATCCATCTGAA 60.181 47.826 5.65 0.00 42.48 3.02
3376 7136 0.324285 CTCAAGTTCCCAGCAGAGCT 59.676 55.000 0.00 0.00 40.77 4.09
3396 7156 3.591196 AAACTGAGTGTTTTGCAGCAA 57.409 38.095 2.83 2.83 45.69 3.91
3447 7207 4.895297 ACACATTCCATATTCCCATTGACC 59.105 41.667 0.00 0.00 0.00 4.02
3451 7211 5.360714 GTGACACACATTCCATATTCCCATT 59.639 40.000 0.00 0.00 34.08 3.16
3454 7214 4.336433 CAGTGACACACATTCCATATTCCC 59.664 45.833 8.59 0.00 36.74 3.97
3456 7216 4.943705 ACCAGTGACACACATTCCATATTC 59.056 41.667 8.59 0.00 36.74 1.75
3482 7249 1.526887 CTGTGTACAACTGAAGCCACG 59.473 52.381 0.00 0.00 0.00 4.94
3488 7255 4.994852 GGCTTCATACTGTGTACAACTGAA 59.005 41.667 0.00 2.30 0.00 3.02
3507 7274 4.081406 TCATGAGCAACTTAACATGGCTT 58.919 39.130 0.00 0.00 40.00 4.35
3510 7277 5.633830 AGTTCATGAGCAACTTAACATGG 57.366 39.130 12.41 0.00 40.00 3.66
3536 7303 7.619965 TGATCACATGTTAAACAGGACTGATA 58.380 34.615 6.29 0.00 29.68 2.15
3544 7311 6.638063 CACCAAGTTGATCACATGTTAAACAG 59.362 38.462 3.87 0.00 0.00 3.16
3579 7346 4.639755 TCTTCTGTCACAACATTCTGCAAA 59.360 37.500 0.00 0.00 34.13 3.68
3580 7347 4.198530 TCTTCTGTCACAACATTCTGCAA 58.801 39.130 0.00 0.00 34.13 4.08
3662 7438 6.016360 CCATGAACAAACAAACCATCTACTGA 60.016 38.462 0.00 0.00 0.00 3.41
3669 7445 3.465871 GTGCCATGAACAAACAAACCAT 58.534 40.909 0.00 0.00 0.00 3.55
3675 7451 1.107114 AACCGTGCCATGAACAAACA 58.893 45.000 0.00 0.00 0.00 2.83
3676 7452 1.857837 CAAACCGTGCCATGAACAAAC 59.142 47.619 0.00 0.00 0.00 2.93
3683 7459 1.799917 GCATCATCAAACCGTGCCATG 60.800 52.381 0.00 0.00 0.00 3.66
3684 7460 0.457035 GCATCATCAAACCGTGCCAT 59.543 50.000 0.00 0.00 0.00 4.40
3686 7462 1.064060 GTAGCATCATCAAACCGTGCC 59.936 52.381 0.00 0.00 36.50 5.01
3687 7463 1.064060 GGTAGCATCATCAAACCGTGC 59.936 52.381 0.00 0.00 36.11 5.34
3688 7464 2.632377 AGGTAGCATCATCAAACCGTG 58.368 47.619 0.00 0.00 35.32 4.94
3690 7466 3.689161 TGAAAGGTAGCATCATCAAACCG 59.311 43.478 0.00 0.00 35.32 4.44
3691 7467 5.357878 TCATGAAAGGTAGCATCATCAAACC 59.642 40.000 9.48 0.00 31.65 3.27
3692 7468 6.441093 TCATGAAAGGTAGCATCATCAAAC 57.559 37.500 9.48 0.00 31.65 2.93
3693 7469 5.591472 CCTCATGAAAGGTAGCATCATCAAA 59.409 40.000 9.48 0.91 31.65 2.69
3694 7470 5.128205 CCTCATGAAAGGTAGCATCATCAA 58.872 41.667 9.48 2.77 31.65 2.57
3695 7471 4.711399 CCTCATGAAAGGTAGCATCATCA 58.289 43.478 9.48 1.92 31.65 3.07
3706 7482 2.028112 TCTCAACCGACCTCATGAAAGG 60.028 50.000 0.00 0.00 42.55 3.11
3707 7483 3.319137 TCTCAACCGACCTCATGAAAG 57.681 47.619 0.00 0.00 0.00 2.62
3708 7484 3.981071 ATCTCAACCGACCTCATGAAA 57.019 42.857 0.00 0.00 0.00 2.69
3709 7485 3.981071 AATCTCAACCGACCTCATGAA 57.019 42.857 0.00 0.00 0.00 2.57
3710 7486 3.981071 AAATCTCAACCGACCTCATGA 57.019 42.857 0.00 0.00 0.00 3.07
3711 7487 4.256920 AGAAAATCTCAACCGACCTCATG 58.743 43.478 0.00 0.00 0.00 3.07
3712 7488 4.508662 GAGAAAATCTCAACCGACCTCAT 58.491 43.478 2.57 0.00 42.90 2.90
3716 7492 3.053831 TGGAGAAAATCTCAACCGACC 57.946 47.619 9.40 0.00 45.12 4.79
3717 7493 5.432885 TTTTGGAGAAAATCTCAACCGAC 57.567 39.130 9.40 0.00 45.12 4.79
3718 7494 7.201609 CGATATTTTGGAGAAAATCTCAACCGA 60.202 37.037 9.40 0.00 45.12 4.69
3719 7495 6.907212 CGATATTTTGGAGAAAATCTCAACCG 59.093 38.462 9.40 0.00 45.12 4.44
3720 7496 7.985476 TCGATATTTTGGAGAAAATCTCAACC 58.015 34.615 9.40 0.00 45.12 3.77
3731 7507 8.939929 GCTATCAATCAATCGATATTTTGGAGA 58.060 33.333 0.00 0.00 0.00 3.71
3732 7508 8.724229 TGCTATCAATCAATCGATATTTTGGAG 58.276 33.333 0.00 5.71 0.00 3.86
3733 7509 8.620116 TGCTATCAATCAATCGATATTTTGGA 57.380 30.769 0.00 0.00 0.00 3.53
3734 7510 9.681692 TTTGCTATCAATCAATCGATATTTTGG 57.318 29.630 0.00 0.00 31.33 3.28
3741 7517 7.558161 TTGACTTTGCTATCAATCAATCGAT 57.442 32.000 0.00 0.00 29.89 3.59
3742 7518 6.983474 TTGACTTTGCTATCAATCAATCGA 57.017 33.333 0.00 0.00 29.89 3.59
3743 7519 6.193410 CGTTTGACTTTGCTATCAATCAATCG 59.807 38.462 9.74 9.74 34.87 3.34
3744 7520 7.243487 TCGTTTGACTTTGCTATCAATCAATC 58.757 34.615 0.00 0.00 34.87 2.67
3746 7522 6.552859 TCGTTTGACTTTGCTATCAATCAA 57.447 33.333 0.00 0.00 34.87 2.57
3747 7523 6.371271 TGATCGTTTGACTTTGCTATCAATCA 59.629 34.615 0.00 0.00 34.87 2.57
3748 7524 6.775088 TGATCGTTTGACTTTGCTATCAATC 58.225 36.000 0.00 0.00 34.87 2.67
3749 7525 6.741992 TGATCGTTTGACTTTGCTATCAAT 57.258 33.333 0.00 0.00 34.87 2.57
3750 7526 6.552859 TTGATCGTTTGACTTTGCTATCAA 57.447 33.333 0.00 0.00 33.03 2.57
3753 7529 6.403636 GGTCATTGATCGTTTGACTTTGCTAT 60.404 38.462 17.02 0.00 39.70 2.97
3755 7531 4.320494 GGTCATTGATCGTTTGACTTTGCT 60.320 41.667 17.02 0.00 39.70 3.91
3756 7532 3.914364 GGTCATTGATCGTTTGACTTTGC 59.086 43.478 17.02 3.16 39.70 3.68
3757 7533 5.107109 TGGTCATTGATCGTTTGACTTTG 57.893 39.130 17.02 0.00 39.70 2.77
3758 7534 5.473162 TCATGGTCATTGATCGTTTGACTTT 59.527 36.000 17.02 6.98 39.70 2.66
3768 7544 7.335422 ACAGAGTAACTTTCATGGTCATTGATC 59.665 37.037 0.00 0.00 0.00 2.92
3775 7556 5.305585 TGGAACAGAGTAACTTTCATGGTC 58.694 41.667 0.00 0.00 0.00 4.02
3789 7570 9.334947 ACATGAATAAGATGTAATGGAACAGAG 57.665 33.333 0.00 0.00 35.03 3.35
3819 9376 2.765699 TGGCAAGGAAAAGCAAGAAAGT 59.234 40.909 0.00 0.00 0.00 2.66
3820 9377 3.068590 TCTGGCAAGGAAAAGCAAGAAAG 59.931 43.478 0.00 0.00 37.85 2.62
3873 9430 5.404366 CGACCTTGTCTTGTTTTCTTCGATA 59.596 40.000 0.00 0.00 0.00 2.92
3877 9434 4.877323 ACGACCTTGTCTTGTTTTCTTC 57.123 40.909 0.00 0.00 0.00 2.87
3933 9490 9.643693 CTTCCAAGCATTCAAAACTAAATGTAT 57.356 29.630 0.00 0.00 35.70 2.29


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

AutoCloner maintained by Alex Coulton.