Multiple sequence alignment - TraesCS3B01G168700

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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 TraesCS3B01G168700 chr3B 100.000 3748 0 0 1 3748 169423731 169427478 0.000000e+00 6922.0
1 TraesCS3B01G168700 chr3B 85.152 788 93 16 1047 1825 169432381 169433153 0.000000e+00 785.0
2 TraesCS3B01G168700 chr3B 82.456 855 140 7 1826 2678 169433227 169434073 0.000000e+00 739.0
3 TraesCS3B01G168700 chr3B 91.729 532 40 2 125 655 737336479 737337007 0.000000e+00 736.0
4 TraesCS3B01G168700 chr3D 97.662 1155 26 1 1826 2979 116011980 116013134 0.000000e+00 1982.0
5 TraesCS3B01G168700 chr3D 94.007 1168 56 5 664 1825 116010747 116011906 0.000000e+00 1757.0
6 TraesCS3B01G168700 chr3D 86.896 786 92 10 1047 1825 116022358 116023139 0.000000e+00 870.0
7 TraesCS3B01G168700 chr3D 83.041 855 135 7 1826 2678 116023213 116024059 0.000000e+00 767.0
8 TraesCS3B01G168700 chr3D 86.762 491 36 14 3260 3748 116013209 116013672 1.540000e-143 520.0
9 TraesCS3B01G168700 chr3D 82.707 133 16 7 3604 3735 33158826 33158952 1.100000e-20 111.0
10 TraesCS3B01G168700 chr3A 93.449 1267 67 7 1826 3087 112918861 112920116 0.000000e+00 1866.0
11 TraesCS3B01G168700 chr3A 93.124 1149 68 7 687 1825 112917640 112918787 0.000000e+00 1674.0
12 TraesCS3B01G168700 chr3A 86.364 792 95 12 1042 1825 112936700 112937486 0.000000e+00 852.0
13 TraesCS3B01G168700 chr3A 91.319 576 41 8 3174 3743 112920142 112920714 0.000000e+00 778.0
14 TraesCS3B01G168700 chr3A 82.264 857 141 8 1826 2678 112937560 112938409 0.000000e+00 730.0
15 TraesCS3B01G168700 chr3A 91.603 262 17 2 3482 3743 112921080 112921336 1.280000e-94 357.0
16 TraesCS3B01G168700 chr3A 93.333 150 8 2 1 149 701831069 701831217 1.750000e-53 220.0
17 TraesCS3B01G168700 chr3A 93.243 148 6 3 1 148 446583285 446583428 8.150000e-52 215.0
18 TraesCS3B01G168700 chr3A 97.600 125 3 0 1 125 521160881 521161005 8.150000e-52 215.0
19 TraesCS3B01G168700 chr3A 92.857 112 6 2 2978 3087 600923240 600923129 1.080000e-35 161.0
20 TraesCS3B01G168700 chr3A 90.517 116 10 1 2973 3087 17030884 17030769 6.480000e-33 152.0
21 TraesCS3B01G168700 chr3A 83.740 123 15 5 3615 3736 353636600 353636718 1.100000e-20 111.0
22 TraesCS3B01G168700 chr3A 95.000 60 3 0 3103 3162 112920102 112920161 1.110000e-15 95.3
23 TraesCS3B01G168700 chr5D 92.120 533 39 3 125 655 434722503 434721972 0.000000e+00 749.0
24 TraesCS3B01G168700 chr5D 90.824 534 41 6 125 655 456742352 456742880 0.000000e+00 708.0
25 TraesCS3B01G168700 chr5D 83.871 124 11 8 3616 3736 337206928 337206811 3.960000e-20 110.0
26 TraesCS3B01G168700 chr1B 91.296 540 42 5 125 662 553453476 553452940 0.000000e+00 732.0
27 TraesCS3B01G168700 chr1B 88.281 128 11 4 2961 3087 647530699 647530575 2.330000e-32 150.0
28 TraesCS3B01G168700 chr6B 91.557 533 40 5 125 655 652759059 652759588 0.000000e+00 730.0
29 TraesCS3B01G168700 chr1D 91.231 536 39 6 125 655 452753948 452753416 0.000000e+00 723.0
30 TraesCS3B01G168700 chr1D 90.994 533 43 4 125 655 110986595 110987124 0.000000e+00 713.0
31 TraesCS3B01G168700 chr1D 90.807 533 45 4 125 655 8743540 8744070 0.000000e+00 710.0
32 TraesCS3B01G168700 chr4A 90.619 533 46 4 125 655 690239731 690240261 0.000000e+00 704.0
33 TraesCS3B01G168700 chr5B 96.403 139 5 0 1 139 105545660 105545522 2.910000e-56 230.0
34 TraesCS3B01G168700 chr5B 94.444 144 5 2 1 144 187132130 187132270 6.300000e-53 219.0
35 TraesCS3B01G168700 chr5B 84.000 125 10 9 3616 3736 395706061 395705943 1.100000e-20 111.0
36 TraesCS3B01G168700 chr7A 92.810 153 8 3 1 151 712804643 712804794 6.300000e-53 219.0
37 TraesCS3B01G168700 chr2B 92.105 152 8 4 1 150 801070117 801070266 1.050000e-50 211.0
38 TraesCS3B01G168700 chr5A 91.195 159 7 6 1 158 82264658 82264506 3.790000e-50 209.0
39 TraesCS3B01G168700 chr5A 85.246 122 9 8 3617 3735 438406788 438406673 2.370000e-22 117.0
40 TraesCS3B01G168700 chr6D 88.889 171 15 4 1 169 467108790 467108958 1.360000e-49 207.0
41 TraesCS3B01G168700 chr6A 93.519 108 6 1 2980 3087 55716269 55716163 3.870000e-35 159.0
42 TraesCS3B01G168700 chr4D 92.793 111 7 1 2978 3087 64390632 64390522 3.870000e-35 159.0
43 TraesCS3B01G168700 chr4D 90.598 117 9 2 2977 3091 500456577 500456461 1.800000e-33 154.0
44 TraesCS3B01G168700 chr2D 92.793 111 7 1 2978 3087 157450256 157450366 3.870000e-35 159.0
45 TraesCS3B01G168700 chr2D 83.465 127 14 7 3612 3736 518616284 518616405 1.100000e-20 111.0
46 TraesCS3B01G168700 chr2A 90.833 120 9 2 2969 3087 419206985 419206867 3.870000e-35 159.0


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 TraesCS3B01G168700 chr3B 169423731 169427478 3747 False 6922.000000 6922 100.000000 1 3748 1 chr3B.!!$F1 3747
1 TraesCS3B01G168700 chr3B 169432381 169434073 1692 False 762.000000 785 83.804000 1047 2678 2 chr3B.!!$F3 1631
2 TraesCS3B01G168700 chr3B 737336479 737337007 528 False 736.000000 736 91.729000 125 655 1 chr3B.!!$F2 530
3 TraesCS3B01G168700 chr3D 116010747 116013672 2925 False 1419.666667 1982 92.810333 664 3748 3 chr3D.!!$F2 3084
4 TraesCS3B01G168700 chr3D 116022358 116024059 1701 False 818.500000 870 84.968500 1047 2678 2 chr3D.!!$F3 1631
5 TraesCS3B01G168700 chr3A 112917640 112921336 3696 False 954.060000 1866 92.899000 687 3743 5 chr3A.!!$F5 3056
6 TraesCS3B01G168700 chr3A 112936700 112938409 1709 False 791.000000 852 84.314000 1042 2678 2 chr3A.!!$F6 1636
7 TraesCS3B01G168700 chr5D 434721972 434722503 531 True 749.000000 749 92.120000 125 655 1 chr5D.!!$R2 530
8 TraesCS3B01G168700 chr5D 456742352 456742880 528 False 708.000000 708 90.824000 125 655 1 chr5D.!!$F1 530
9 TraesCS3B01G168700 chr1B 553452940 553453476 536 True 732.000000 732 91.296000 125 662 1 chr1B.!!$R1 537
10 TraesCS3B01G168700 chr6B 652759059 652759588 529 False 730.000000 730 91.557000 125 655 1 chr6B.!!$F1 530
11 TraesCS3B01G168700 chr1D 452753416 452753948 532 True 723.000000 723 91.231000 125 655 1 chr1D.!!$R1 530
12 TraesCS3B01G168700 chr1D 110986595 110987124 529 False 713.000000 713 90.994000 125 655 1 chr1D.!!$F2 530
13 TraesCS3B01G168700 chr1D 8743540 8744070 530 False 710.000000 710 90.807000 125 655 1 chr1D.!!$F1 530
14 TraesCS3B01G168700 chr4A 690239731 690240261 530 False 704.000000 704 90.619000 125 655 1 chr4A.!!$F1 530

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
667 674 0.742990 TTGCGGGTGCTCTAAATCCG 60.743 55.0 0.0 0.0 43.34 4.18 F
1077 1100 0.173708 CGCTTCTCTTACTCCCGCTT 59.826 55.0 0.0 0.0 0.00 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1670 0.107945 GCAAGCTTCTCGAGATGGGT 60.108 55.0 24.80 18.68 0.00 4.51 R
2948 3054 0.755686 TTTTGAAACCCAAGCGCCAT 59.244 45.0 2.29 0.00 35.94 4.40 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
30 31 6.429791 TTCACACATGTATTATGTTTCCGG 57.570 37.500 0.00 0.00 0.00 5.14
31 32 5.492895 TCACACATGTATTATGTTTCCGGT 58.507 37.500 0.00 0.00 0.00 5.28
32 33 5.941058 TCACACATGTATTATGTTTCCGGTT 59.059 36.000 0.00 0.00 0.00 4.44
33 34 7.104290 TCACACATGTATTATGTTTCCGGTTA 58.896 34.615 0.00 0.00 0.00 2.85
34 35 7.606839 TCACACATGTATTATGTTTCCGGTTAA 59.393 33.333 0.00 0.00 0.00 2.01
35 36 8.402472 CACACATGTATTATGTTTCCGGTTAAT 58.598 33.333 0.00 1.95 0.00 1.40
36 37 9.616156 ACACATGTATTATGTTTCCGGTTAATA 57.384 29.630 0.00 0.00 0.00 0.98
47 48 9.787435 ATGTTTCCGGTTAATATATTTCTAGCA 57.213 29.630 2.68 0.00 0.00 3.49
48 49 9.787435 TGTTTCCGGTTAATATATTTCTAGCAT 57.213 29.630 2.68 0.00 0.00 3.79
111 112 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
123 124 4.982241 CCTCTAGGGCATATTTCCTTCA 57.018 45.455 0.00 0.00 34.75 3.02
130 131 4.952335 AGGGCATATTTCCTTCAAAGACTG 59.048 41.667 0.00 0.00 0.00 3.51
283 284 3.442977 GCCAAAGAGAAGTACGAGGAGTA 59.557 47.826 0.00 0.00 0.00 2.59
337 338 3.443925 CGACCTCTGCAGCTCCGA 61.444 66.667 9.47 0.00 0.00 4.55
391 392 1.740296 CGTCCATTTTCCCGCGACT 60.740 57.895 8.23 0.00 0.00 4.18
422 424 4.723309 GTTAGATCCGACCCCTCTAGTAA 58.277 47.826 0.00 0.00 0.00 2.24
475 480 6.058827 TGTTTGTAGTGTGTTGATCATGTG 57.941 37.500 0.00 0.00 0.00 3.21
600 607 1.735559 GCGCTAGTTTTCGACCCGT 60.736 57.895 0.00 0.00 0.00 5.28
656 663 1.600912 CGGGTTAAGTTTTTGCGGGTG 60.601 52.381 0.00 0.00 0.00 4.61
657 664 1.493772 GGTTAAGTTTTTGCGGGTGC 58.506 50.000 0.00 0.00 43.20 5.01
658 665 1.067974 GGTTAAGTTTTTGCGGGTGCT 59.932 47.619 0.00 0.00 43.34 4.40
662 669 1.975660 AGTTTTTGCGGGTGCTCTAA 58.024 45.000 0.00 0.00 43.34 2.10
663 670 2.303175 AGTTTTTGCGGGTGCTCTAAA 58.697 42.857 0.00 0.00 43.34 1.85
664 671 2.890945 AGTTTTTGCGGGTGCTCTAAAT 59.109 40.909 0.00 0.00 43.34 1.40
665 672 3.057526 AGTTTTTGCGGGTGCTCTAAATC 60.058 43.478 0.00 0.00 43.34 2.17
666 673 1.459450 TTTGCGGGTGCTCTAAATCC 58.541 50.000 0.00 0.00 43.34 3.01
667 674 0.742990 TTGCGGGTGCTCTAAATCCG 60.743 55.000 0.00 0.00 43.34 4.18
668 675 1.143183 GCGGGTGCTCTAAATCCGA 59.857 57.895 0.00 0.00 42.94 4.55
739 748 3.662078 TCCAGAATCCAGATCCAGATGT 58.338 45.455 0.00 0.00 0.00 3.06
740 749 3.645212 TCCAGAATCCAGATCCAGATGTC 59.355 47.826 0.00 0.00 0.00 3.06
753 765 2.516923 CAGATGTCGTAGGTTCACGTC 58.483 52.381 0.00 0.00 42.51 4.34
860 873 4.011517 TCCGCCTCCGACCCAAAC 62.012 66.667 0.00 0.00 36.29 2.93
865 878 2.221299 CCTCCGACCCAAACCTCCA 61.221 63.158 0.00 0.00 0.00 3.86
881 897 2.417651 CCTCCAAGATTACGGCGTAACA 60.418 50.000 32.11 14.25 30.49 2.41
909 925 6.875076 ACAACAACCTCTCTTATTATACGCT 58.125 36.000 0.00 0.00 0.00 5.07
923 939 3.644884 ATACGCTATCTTTCACCTCGG 57.355 47.619 0.00 0.00 0.00 4.63
1068 1091 1.335182 CTCCTCATCGCGCTTCTCTTA 59.665 52.381 5.56 0.00 0.00 2.10
1075 1098 1.878975 GCGCTTCTCTTACTCCCGC 60.879 63.158 0.00 0.00 0.00 6.13
1077 1100 0.173708 CGCTTCTCTTACTCCCGCTT 59.826 55.000 0.00 0.00 0.00 4.68
1241 1264 2.232298 CTCCTGTCCCACTCCTTCGC 62.232 65.000 0.00 0.00 0.00 4.70
1488 1511 2.646719 GACGTCACCAGGTACGCA 59.353 61.111 11.55 0.00 42.74 5.24
1489 1512 1.214589 GACGTCACCAGGTACGCAT 59.785 57.895 11.55 3.96 42.74 4.73
1491 1514 1.214325 CGTCACCAGGTACGCATCA 59.786 57.895 0.00 0.00 31.66 3.07
1638 1670 0.459899 AGCACGCCGATCTGATTGTA 59.540 50.000 4.27 0.00 0.00 2.41
1785 1817 0.389817 CGTTCCACTCCAGCGATGAA 60.390 55.000 0.06 0.00 0.00 2.57
1803 1835 2.443632 TGAATTCTGGTACACCAACCCA 59.556 45.455 7.05 0.00 46.97 4.51
1830 1935 0.324943 AGTACATTGAGGCCGTGCTT 59.675 50.000 0.00 0.00 0.00 3.91
1881 1986 1.118965 TGTCAACCCGCTTCTCTGGA 61.119 55.000 0.00 0.00 0.00 3.86
1904 2009 2.114670 AATCACCGGCATTGGCTCG 61.115 57.895 0.00 0.90 40.87 5.03
1922 2027 4.261530 GGCTCGTTCAATCTACCTACCTAC 60.262 50.000 0.00 0.00 0.00 3.18
1970 2075 3.036429 GCTCCTGGACGGCAAGGAT 62.036 63.158 17.02 0.00 41.74 3.24
2145 2250 0.623723 TGGGCTGGATGGTAAGTTCC 59.376 55.000 0.00 0.00 0.00 3.62
2446 2551 3.256383 TCACTTGTCAAATTGGGCATCAG 59.744 43.478 0.00 0.00 0.00 2.90
2516 2621 0.950555 GGAATGCACAGTCAGCACGA 60.951 55.000 0.15 0.00 45.95 4.35
2531 2636 1.927895 CACGAGGCACTATGAAGGTC 58.072 55.000 0.00 0.00 41.55 3.85
2561 2666 0.104882 TGGTGGTTAGTGGACTGGGA 60.105 55.000 0.00 0.00 0.00 4.37
2659 2764 7.065085 CACTATAATTTCTGACAACTCTGGTGG 59.935 40.741 0.00 0.00 0.00 4.61
2765 2870 5.163023 ACTGTAACTTGGAATTAAGGTGGGT 60.163 40.000 0.00 0.00 31.94 4.51
2859 2964 9.961265 TCGTTCATGTACTAGGTAAGAAATATG 57.039 33.333 0.77 0.00 0.00 1.78
2860 2965 8.700644 CGTTCATGTACTAGGTAAGAAATATGC 58.299 37.037 0.77 0.00 0.00 3.14
2888 2994 5.830799 ATTATCTCTACATGCATCCCACA 57.169 39.130 0.00 0.00 0.00 4.17
2985 3091 7.938140 TTCAAAATATTCCAAGTACTCCCTG 57.062 36.000 0.00 0.00 0.00 4.45
2992 3098 1.978580 CCAAGTACTCCCTGTGTTCCT 59.021 52.381 0.00 0.00 0.00 3.36
2998 3108 7.365652 CCAAGTACTCCCTGTGTTCCTAAATAT 60.366 40.741 0.00 0.00 0.00 1.28
3003 3113 8.849543 ACTCCCTGTGTTCCTAAATATAAGTA 57.150 34.615 0.00 0.00 0.00 2.24
3035 3145 8.645814 AGATTCCAATATACACTACATACGGA 57.354 34.615 0.00 0.00 0.00 4.69
3060 3171 9.102757 GAGCAAAATGAATGAATCTACACTCTA 57.897 33.333 0.00 0.00 0.00 2.43
3166 3277 9.230122 TCAAATATTTCTGAACTTATCACTGCA 57.770 29.630 0.00 0.00 33.47 4.41
3167 3278 9.844790 CAAATATTTCTGAACTTATCACTGCAA 57.155 29.630 0.00 0.00 33.47 4.08
3201 3312 9.765795 ATATTTCTGAACTTATTAACCGGAGAG 57.234 33.333 9.46 0.00 0.00 3.20
3228 3339 9.286170 GTATAAAGAGACTGGTTTCCTTTTTCT 57.714 33.333 0.00 0.00 0.00 2.52
3232 3343 5.131142 AGAGACTGGTTTCCTTTTTCTCTGA 59.869 40.000 0.00 0.00 37.54 3.27
3233 3344 5.946486 AGACTGGTTTCCTTTTTCTCTGAT 58.054 37.500 0.00 0.00 0.00 2.90
3234 3345 6.000840 AGACTGGTTTCCTTTTTCTCTGATC 58.999 40.000 0.00 0.00 0.00 2.92
3235 3346 5.694995 ACTGGTTTCCTTTTTCTCTGATCA 58.305 37.500 0.00 0.00 0.00 2.92
3236 3347 6.310149 ACTGGTTTCCTTTTTCTCTGATCAT 58.690 36.000 0.00 0.00 0.00 2.45
3237 3348 7.461749 ACTGGTTTCCTTTTTCTCTGATCATA 58.538 34.615 0.00 0.00 0.00 2.15
3238 3349 7.391833 ACTGGTTTCCTTTTTCTCTGATCATAC 59.608 37.037 0.00 0.00 0.00 2.39
3239 3350 6.659242 TGGTTTCCTTTTTCTCTGATCATACC 59.341 38.462 0.00 0.00 0.00 2.73
3240 3351 6.659242 GGTTTCCTTTTTCTCTGATCATACCA 59.341 38.462 0.00 0.00 0.00 3.25
3241 3352 7.340487 GGTTTCCTTTTTCTCTGATCATACCAT 59.660 37.037 0.00 0.00 0.00 3.55
3242 3353 7.870509 TTCCTTTTTCTCTGATCATACCATG 57.129 36.000 0.00 0.00 0.00 3.66
3243 3354 7.199167 TCCTTTTTCTCTGATCATACCATGA 57.801 36.000 0.00 0.00 44.55 3.07
3244 3355 7.278135 TCCTTTTTCTCTGATCATACCATGAG 58.722 38.462 0.00 0.00 43.53 2.90
3245 3356 6.017275 CCTTTTTCTCTGATCATACCATGAGC 60.017 42.308 0.00 0.00 45.45 4.26
3252 3363 4.681835 GATCATACCATGAGCATTCAGC 57.318 45.455 0.00 0.00 44.65 4.26
3283 3421 6.438425 ACTCAAGATTTGCAATAGGGTTGATT 59.562 34.615 0.00 0.00 0.00 2.57
3297 3435 3.196254 GGGTTGATTGCACAGGATTGATT 59.804 43.478 0.00 0.00 0.00 2.57
3372 3515 8.709386 TCTCTACTTCTTTGTCTGAATAATGC 57.291 34.615 0.00 0.00 0.00 3.56
3385 3528 3.506844 TGAATAATGCAGCTTGCTGTTGA 59.493 39.130 21.55 8.59 45.31 3.18
3386 3529 4.022155 TGAATAATGCAGCTTGCTGTTGAA 60.022 37.500 21.55 8.05 45.31 2.69
3416 3559 0.922717 CGCAATTTAAATGGCCAGCG 59.077 50.000 19.69 14.75 37.91 5.18
3417 3560 1.289276 GCAATTTAAATGGCCAGCGG 58.711 50.000 15.63 0.00 28.70 5.52
3440 3584 6.477742 GGTTTGCTTTTGACAGAAAATTGTC 58.522 36.000 0.00 0.00 46.02 3.18
3455 3599 5.628797 AAATTGTCCCACAAAAACAGGAT 57.371 34.783 0.00 0.00 41.96 3.24
3510 3654 5.514274 ACCCATAAATTTGTATTGCCGAG 57.486 39.130 0.00 0.00 0.00 4.63
3534 3700 6.595716 AGGTGTCTAAATAATCACTTGCACTC 59.404 38.462 0.00 0.00 0.00 3.51
3535 3701 6.183360 GGTGTCTAAATAATCACTTGCACTCC 60.183 42.308 0.00 0.00 0.00 3.85
3537 3703 6.371548 TGTCTAAATAATCACTTGCACTCCAC 59.628 38.462 0.00 0.00 0.00 4.02
3539 3705 5.633830 AAATAATCACTTGCACTCCACAG 57.366 39.130 0.00 0.00 0.00 3.66
3540 3706 2.936919 AATCACTTGCACTCCACAGA 57.063 45.000 0.00 0.00 0.00 3.41
3541 3707 3.430042 AATCACTTGCACTCCACAGAT 57.570 42.857 0.00 0.00 0.00 2.90
3543 3709 4.767578 ATCACTTGCACTCCACAGATAT 57.232 40.909 0.00 0.00 0.00 1.63
3544 3710 3.865446 TCACTTGCACTCCACAGATATG 58.135 45.455 0.00 0.00 0.00 1.78
3545 3711 2.353889 CACTTGCACTCCACAGATATGC 59.646 50.000 0.00 0.00 35.53 3.14
3546 3712 2.026915 ACTTGCACTCCACAGATATGCA 60.027 45.455 0.00 0.00 40.43 3.96
3547 3713 2.028420 TGCACTCCACAGATATGCAC 57.972 50.000 0.00 0.00 38.45 4.57
3548 3714 1.556451 TGCACTCCACAGATATGCACT 59.444 47.619 0.00 0.00 38.45 4.40
3549 3715 2.208431 GCACTCCACAGATATGCACTC 58.792 52.381 0.00 0.00 35.22 3.51
3550 3716 2.467838 CACTCCACAGATATGCACTCG 58.532 52.381 0.00 0.00 0.00 4.18
3551 3717 2.103373 ACTCCACAGATATGCACTCGT 58.897 47.619 0.00 0.00 0.00 4.18
3552 3718 2.159184 ACTCCACAGATATGCACTCGTG 60.159 50.000 0.00 2.65 0.00 4.35
3574 3740 9.522804 TCGTGCTTAAAATCATTTTGTTTACTT 57.477 25.926 5.56 0.00 34.19 2.24
3652 3818 4.567971 TGATGCCAAAAATTGTCATGTCC 58.432 39.130 0.00 0.00 0.00 4.02
3680 3846 9.678260 AATTTGGCAAATGTTTAATATTGGCTA 57.322 25.926 24.96 5.00 45.42 3.93
3697 3863 4.730966 TGGCTAAGTGATTGGTTGGTTAA 58.269 39.130 0.00 0.00 0.00 2.01
3710 4498 7.793927 TTGGTTGGTTAACATTTTCCATTTC 57.206 32.000 8.10 0.00 38.58 2.17
3714 4502 3.610677 GGTTAACATTTTCCATTTCGGCG 59.389 43.478 8.10 0.00 33.14 6.46
3735 4523 3.721035 GAAGCTCACAAAAGTTGCCAAT 58.279 40.909 0.00 0.00 0.00 3.16
3743 4531 7.148755 GCTCACAAAAGTTGCCAATATAAGTTG 60.149 37.037 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.783093 CCGGAAACATAATACATGTGTGAATAT 58.217 33.333 9.11 0.00 31.80 1.28
5 6 7.771361 ACCGGAAACATAATACATGTGTGAATA 59.229 33.333 9.46 0.00 31.80 1.75
6 7 6.601613 ACCGGAAACATAATACATGTGTGAAT 59.398 34.615 9.46 0.00 31.80 2.57
7 8 5.941058 ACCGGAAACATAATACATGTGTGAA 59.059 36.000 9.46 0.00 31.80 3.18
8 9 5.492895 ACCGGAAACATAATACATGTGTGA 58.507 37.500 9.46 0.00 31.80 3.58
9 10 5.811399 ACCGGAAACATAATACATGTGTG 57.189 39.130 9.46 4.81 31.80 3.82
10 11 7.925043 TTAACCGGAAACATAATACATGTGT 57.075 32.000 9.46 0.00 31.80 3.72
21 22 9.787435 TGCTAGAAATATATTAACCGGAAACAT 57.213 29.630 9.46 0.00 0.00 2.71
22 23 9.787435 ATGCTAGAAATATATTAACCGGAAACA 57.213 29.630 9.46 0.00 0.00 2.83
102 103 4.982241 TGAAGGAAATATGCCCTAGAGG 57.018 45.455 0.00 0.00 39.47 3.69
103 104 6.484977 GTCTTTGAAGGAAATATGCCCTAGAG 59.515 42.308 0.00 0.00 31.36 2.43
104 105 6.158695 AGTCTTTGAAGGAAATATGCCCTAGA 59.841 38.462 0.00 0.00 31.36 2.43
105 106 6.261826 CAGTCTTTGAAGGAAATATGCCCTAG 59.738 42.308 0.00 0.00 31.36 3.02
106 107 6.122277 CAGTCTTTGAAGGAAATATGCCCTA 58.878 40.000 0.00 0.00 31.36 3.53
107 108 4.952335 CAGTCTTTGAAGGAAATATGCCCT 59.048 41.667 0.00 0.00 0.00 5.19
108 109 4.440663 GCAGTCTTTGAAGGAAATATGCCC 60.441 45.833 0.00 0.00 0.00 5.36
109 110 4.676546 GCAGTCTTTGAAGGAAATATGCC 58.323 43.478 0.00 0.00 0.00 4.40
110 111 4.142600 ACGCAGTCTTTGAAGGAAATATGC 60.143 41.667 0.00 0.00 29.74 3.14
111 112 5.551760 ACGCAGTCTTTGAAGGAAATATG 57.448 39.130 0.00 0.00 29.74 1.78
203 204 3.513768 TTCGAGCTGCTTGGCGTGA 62.514 57.895 16.59 1.38 37.29 4.35
266 267 2.553086 CGCTACTCCTCGTACTTCTCT 58.447 52.381 0.00 0.00 0.00 3.10
307 308 2.161808 CAGAGGTCGATGTACTTCACGT 59.838 50.000 9.22 7.57 0.00 4.49
337 338 0.173708 GAACGCTCAATCCTCCTCGT 59.826 55.000 0.00 0.00 0.00 4.18
391 392 1.812093 CGGATCTAACGGCGGCAAA 60.812 57.895 13.24 0.00 0.00 3.68
641 648 1.975660 AGAGCACCCGCAAAAACTTA 58.024 45.000 0.00 0.00 42.27 2.24
667 674 4.883354 CCCAGCCCAGCCGGATTC 62.883 72.222 5.05 0.00 0.00 2.52
675 682 2.124403 GTGATGAGCCCAGCCCAG 60.124 66.667 0.00 0.00 0.00 4.45
676 683 3.731728 GGTGATGAGCCCAGCCCA 61.732 66.667 0.00 0.00 0.00 5.36
682 689 2.821366 CGTGCTGGTGATGAGCCC 60.821 66.667 0.00 0.00 35.43 5.19
739 748 0.877071 GTGGAGACGTGAACCTACGA 59.123 55.000 0.00 0.00 46.46 3.43
843 856 4.011517 GTTTGGGTCGGAGGCGGA 62.012 66.667 0.00 0.00 0.00 5.54
860 873 2.199236 GTTACGCCGTAATCTTGGAGG 58.801 52.381 13.40 0.00 30.49 4.30
881 897 7.487189 CGTATAATAAGAGAGGTTGTTGTCGTT 59.513 37.037 0.00 0.00 0.00 3.85
909 925 4.323715 GGGGTTTAACCGAGGTGAAAGATA 60.324 45.833 8.14 0.00 39.83 1.98
1033 1053 3.403558 GAGGAGGAGGTGGTGGCC 61.404 72.222 0.00 0.00 0.00 5.36
1037 1057 0.031616 GATGAGGAGGAGGAGGTGGT 60.032 60.000 0.00 0.00 0.00 4.16
1040 1060 1.456705 GCGATGAGGAGGAGGAGGT 60.457 63.158 0.00 0.00 0.00 3.85
1638 1670 0.107945 GCAAGCTTCTCGAGATGGGT 60.108 55.000 24.80 18.68 0.00 4.51
1830 1935 1.606668 GATGACAGTGAACGGCCAAAA 59.393 47.619 2.24 0.00 0.00 2.44
1904 2009 5.824904 TGTCGTAGGTAGGTAGATTGAAC 57.175 43.478 0.00 0.00 0.00 3.18
1922 2027 3.742882 AGAATGGCGTGATATCAATGTCG 59.257 43.478 7.07 8.00 0.00 4.35
1970 2075 3.196469 TGACAGCAAACCCAAAATTGTGA 59.804 39.130 0.00 0.00 0.00 3.58
2446 2551 2.416162 CCACCTAAGACACTCTTCTCGC 60.416 54.545 0.00 0.00 37.89 5.03
2516 2621 3.840666 TCTTCTTGACCTTCATAGTGCCT 59.159 43.478 0.00 0.00 0.00 4.75
2531 2636 5.534654 TCCACTAACCACCAAATTCTTCTTG 59.465 40.000 0.00 0.00 0.00 3.02
2659 2764 1.131315 GCGATCCCTTTGAGCAAGAAC 59.869 52.381 0.00 0.00 33.80 3.01
2857 2962 6.301486 TGCATGTAGAGATAATTCCAAGCAT 58.699 36.000 0.00 0.00 0.00 3.79
2858 2963 5.683681 TGCATGTAGAGATAATTCCAAGCA 58.316 37.500 0.00 0.00 0.00 3.91
2859 2964 6.128063 GGATGCATGTAGAGATAATTCCAAGC 60.128 42.308 2.46 0.00 0.00 4.01
2860 2965 6.373774 GGGATGCATGTAGAGATAATTCCAAG 59.626 42.308 2.46 0.00 0.00 3.61
2878 2984 3.719268 AGACTTACAATGTGGGATGCA 57.281 42.857 0.00 0.00 0.00 3.96
2948 3054 0.755686 TTTTGAAACCCAAGCGCCAT 59.244 45.000 2.29 0.00 35.94 4.40
3023 3133 5.794687 TTCATTTTGCTCCGTATGTAGTG 57.205 39.130 0.00 0.00 0.00 2.74
3035 3145 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
3100 3211 9.830975 AATGCAAACTACATACAGATGTATACA 57.169 29.630 8.27 8.27 45.42 2.29
3103 3214 8.962884 TCAATGCAAACTACATACAGATGTAT 57.037 30.769 0.00 0.00 45.42 2.29
3104 3215 8.785329 TTCAATGCAAACTACATACAGATGTA 57.215 30.769 0.00 0.00 44.77 2.29
3111 3222 9.173939 GCATCTATTTCAATGCAAACTACATAC 57.826 33.333 0.00 0.00 45.97 2.39
3175 3286 9.765795 CTCTCCGGTTAATAAGTTCAGAAATAT 57.234 33.333 0.00 0.00 0.00 1.28
3176 3287 8.202137 CCTCTCCGGTTAATAAGTTCAGAAATA 58.798 37.037 0.00 0.00 0.00 1.40
3177 3288 7.048512 CCTCTCCGGTTAATAAGTTCAGAAAT 58.951 38.462 0.00 0.00 0.00 2.17
3178 3289 6.013984 ACCTCTCCGGTTAATAAGTTCAGAAA 60.014 38.462 0.00 0.00 46.37 2.52
3179 3290 5.482878 ACCTCTCCGGTTAATAAGTTCAGAA 59.517 40.000 0.00 0.00 46.37 3.02
3180 3291 5.021458 ACCTCTCCGGTTAATAAGTTCAGA 58.979 41.667 0.00 0.00 46.37 3.27
3181 3292 5.340439 ACCTCTCCGGTTAATAAGTTCAG 57.660 43.478 0.00 0.00 46.37 3.02
3182 3293 8.537728 TTATACCTCTCCGGTTAATAAGTTCA 57.462 34.615 0.00 0.00 46.37 3.18
3183 3294 9.473640 CTTTATACCTCTCCGGTTAATAAGTTC 57.526 37.037 0.00 0.00 46.37 3.01
3184 3295 9.205513 TCTTTATACCTCTCCGGTTAATAAGTT 57.794 33.333 0.00 0.00 46.37 2.66
3185 3296 8.773033 TCTTTATACCTCTCCGGTTAATAAGT 57.227 34.615 0.00 0.00 46.37 2.24
3186 3297 9.075678 TCTCTTTATACCTCTCCGGTTAATAAG 57.924 37.037 0.00 0.00 46.37 1.73
3187 3298 8.854117 GTCTCTTTATACCTCTCCGGTTAATAA 58.146 37.037 0.00 0.00 46.37 1.40
3188 3299 8.223330 AGTCTCTTTATACCTCTCCGGTTAATA 58.777 37.037 0.00 0.00 46.37 0.98
3189 3300 7.014422 CAGTCTCTTTATACCTCTCCGGTTAAT 59.986 40.741 0.00 0.00 46.37 1.40
3190 3301 6.320672 CAGTCTCTTTATACCTCTCCGGTTAA 59.679 42.308 0.00 0.00 46.37 2.01
3191 3302 5.826737 CAGTCTCTTTATACCTCTCCGGTTA 59.173 44.000 0.00 0.00 46.37 2.85
3192 3303 4.645588 CAGTCTCTTTATACCTCTCCGGTT 59.354 45.833 0.00 0.00 46.37 4.44
3201 3312 7.997773 AAAAGGAAACCAGTCTCTTTATACC 57.002 36.000 0.00 0.00 0.00 2.73
3228 3339 5.548406 CTGAATGCTCATGGTATGATCAGA 58.452 41.667 0.09 0.00 41.67 3.27
3232 3343 4.094830 TGCTGAATGCTCATGGTATGAT 57.905 40.909 0.00 0.00 43.37 2.45
3233 3344 3.564053 TGCTGAATGCTCATGGTATGA 57.436 42.857 0.00 0.00 43.37 2.15
3234 3345 3.190744 GGATGCTGAATGCTCATGGTATG 59.809 47.826 0.00 0.00 43.37 2.39
3235 3346 3.181437 TGGATGCTGAATGCTCATGGTAT 60.181 43.478 0.00 0.00 43.37 2.73
3236 3347 2.173143 TGGATGCTGAATGCTCATGGTA 59.827 45.455 0.00 0.00 43.37 3.25
3237 3348 1.064240 TGGATGCTGAATGCTCATGGT 60.064 47.619 0.00 0.00 43.37 3.55
3238 3349 1.687563 TGGATGCTGAATGCTCATGG 58.312 50.000 0.00 0.00 43.37 3.66
3239 3350 2.688446 AGTTGGATGCTGAATGCTCATG 59.312 45.455 0.00 0.00 43.37 3.07
3240 3351 2.950309 GAGTTGGATGCTGAATGCTCAT 59.050 45.455 0.00 0.00 43.37 2.90
3241 3352 2.290450 TGAGTTGGATGCTGAATGCTCA 60.290 45.455 0.00 0.00 43.37 4.26
3242 3353 2.362736 TGAGTTGGATGCTGAATGCTC 58.637 47.619 0.00 0.00 43.37 4.26
3243 3354 2.502142 TGAGTTGGATGCTGAATGCT 57.498 45.000 0.00 0.00 43.37 3.79
3244 3355 2.751259 TCTTGAGTTGGATGCTGAATGC 59.249 45.455 0.00 0.00 43.25 3.56
3245 3356 5.578005 AATCTTGAGTTGGATGCTGAATG 57.422 39.130 0.00 0.00 0.00 2.67
3246 3357 5.623824 GCAAATCTTGAGTTGGATGCTGAAT 60.624 40.000 11.81 0.00 0.00 2.57
3247 3358 4.321452 GCAAATCTTGAGTTGGATGCTGAA 60.321 41.667 11.81 0.00 0.00 3.02
3248 3359 3.192001 GCAAATCTTGAGTTGGATGCTGA 59.808 43.478 11.81 0.00 0.00 4.26
3249 3360 3.057104 TGCAAATCTTGAGTTGGATGCTG 60.057 43.478 11.81 0.00 0.00 4.41
3250 3361 3.159472 TGCAAATCTTGAGTTGGATGCT 58.841 40.909 11.81 0.00 0.00 3.79
3251 3362 3.581024 TGCAAATCTTGAGTTGGATGC 57.419 42.857 11.81 0.28 0.00 3.91
3252 3363 6.270815 CCTATTGCAAATCTTGAGTTGGATG 58.729 40.000 1.71 4.15 0.00 3.51
3253 3364 5.361857 CCCTATTGCAAATCTTGAGTTGGAT 59.638 40.000 1.71 3.75 0.00 3.41
3254 3365 4.706476 CCCTATTGCAAATCTTGAGTTGGA 59.294 41.667 1.71 6.89 0.00 3.53
3255 3366 4.463891 ACCCTATTGCAAATCTTGAGTTGG 59.536 41.667 1.71 0.00 0.00 3.77
3256 3367 5.649782 ACCCTATTGCAAATCTTGAGTTG 57.350 39.130 1.71 6.46 0.00 3.16
3257 3368 5.774690 TCAACCCTATTGCAAATCTTGAGTT 59.225 36.000 1.71 0.00 0.00 3.01
3258 3369 5.324409 TCAACCCTATTGCAAATCTTGAGT 58.676 37.500 1.71 0.00 0.00 3.41
3306 3447 4.153117 GCATATTGTCTTTAGCTCATCCGG 59.847 45.833 0.00 0.00 0.00 5.14
3416 3559 6.421377 ACAATTTTCTGTCAAAAGCAAACC 57.579 33.333 0.00 0.00 0.00 3.27
3417 3560 6.456853 GGGACAATTTTCTGTCAAAAGCAAAC 60.457 38.462 6.12 0.00 46.31 2.93
3440 3584 5.582689 GGATTCTATCCTGTTTTTGTGGG 57.417 43.478 0.00 0.00 46.19 4.61
3506 3650 5.006746 GCAAGTGATTATTTAGACACCTCGG 59.993 44.000 0.00 0.00 34.33 4.63
3510 3654 6.183360 GGAGTGCAAGTGATTATTTAGACACC 60.183 42.308 0.00 0.00 34.33 4.16
3545 3711 6.991485 ACAAAATGATTTTAAGCACGAGTG 57.009 33.333 2.42 0.00 0.00 3.51
3546 3712 8.964150 GTAAACAAAATGATTTTAAGCACGAGT 58.036 29.630 2.42 0.00 0.00 4.18
3547 3713 9.180678 AGTAAACAAAATGATTTTAAGCACGAG 57.819 29.630 2.42 0.00 0.00 4.18
3548 3714 9.522804 AAGTAAACAAAATGATTTTAAGCACGA 57.477 25.926 2.42 0.00 0.00 4.35
3558 3724 9.899226 GAGAAGTGCTAAGTAAACAAAATGATT 57.101 29.630 0.00 0.00 0.00 2.57
3559 3725 9.289782 AGAGAAGTGCTAAGTAAACAAAATGAT 57.710 29.630 0.00 0.00 0.00 2.45
3560 3726 8.677148 AGAGAAGTGCTAAGTAAACAAAATGA 57.323 30.769 0.00 0.00 0.00 2.57
3563 3729 8.833493 GGTTAGAGAAGTGCTAAGTAAACAAAA 58.167 33.333 0.00 0.00 0.00 2.44
3574 3740 3.700038 GCTAGGTGGTTAGAGAAGTGCTA 59.300 47.826 0.00 0.00 0.00 3.49
3652 3818 9.074443 GCCAATATTAAACATTTGCCAAATTTG 57.926 29.630 11.40 11.40 0.00 2.32
3669 3835 7.122715 ACCAACCAATCACTTAGCCAATATTA 58.877 34.615 0.00 0.00 0.00 0.98
3680 3846 6.989759 GGAAAATGTTAACCAACCAATCACTT 59.010 34.615 2.48 0.00 33.41 3.16
3697 3863 2.671070 GCTTCGCCGAAATGGAAAATGT 60.671 45.455 0.00 0.00 42.00 2.71
3710 4498 0.307760 AACTTTTGTGAGCTTCGCCG 59.692 50.000 0.00 0.00 0.00 6.46
3714 4502 2.869233 TGGCAACTTTTGTGAGCTTC 57.131 45.000 0.00 0.00 35.47 3.86


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

AutoCloner maintained by Alex Coulton.