Multiple sequence alignment - TraesCS2A01G166000

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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 TraesCS2A01G166000 chr2A 100.000 3100 0 0 1 3100 118467065 118463966 0.000000e+00 5725.0
1 TraesCS2A01G166000 chr2A 90.840 131 9 2 2955 3084 9107169 9107041 4.110000e-39 172.0
2 TraesCS2A01G166000 chr2D 92.659 1798 88 22 530 2292 117126071 117124283 0.000000e+00 2549.0
3 TraesCS2A01G166000 chr2D 91.254 343 11 10 2568 2901 117123979 117123647 1.700000e-122 449.0
4 TraesCS2A01G166000 chr2D 91.342 231 15 4 2319 2548 117124285 117124059 8.350000e-81 311.0
5 TraesCS2A01G166000 chr2B 90.985 1808 74 39 789 2548 167477139 167475373 0.000000e+00 2353.0
6 TraesCS2A01G166000 chr2B 88.462 442 48 3 44 484 167478500 167478061 5.890000e-147 531.0
7 TraesCS2A01G166000 chr2B 96.032 252 10 0 2568 2819 167475296 167475045 8.000000e-111 411.0
8 TraesCS2A01G166000 chr2B 88.679 265 16 10 545 798 167477578 167477317 8.350000e-81 311.0
9 TraesCS2A01G166000 chr2B 94.167 120 6 1 2831 2950 167474911 167474793 6.830000e-42 182.0
10 TraesCS2A01G166000 chr6D 92.366 131 9 1 2955 3084 472360039 472360169 5.280000e-43 185.0
11 TraesCS2A01G166000 chr6D 100.000 37 0 0 1 37 468926722 468926686 5.550000e-08 69.4
12 TraesCS2A01G166000 chr7B 92.308 130 8 2 2956 3084 715574628 715574756 1.900000e-42 183.0
13 TraesCS2A01G166000 chrUn 90.909 132 10 2 2955 3084 17255013 17255144 3.180000e-40 176.0
14 TraesCS2A01G166000 chrUn 93.478 46 2 1 5 49 76192849 76192894 2.000000e-07 67.6
15 TraesCS2A01G166000 chr7A 91.538 130 7 4 2958 3084 383096213 383096085 3.180000e-40 176.0
16 TraesCS2A01G166000 chr7A 90.909 132 9 3 2955 3084 130089740 130089870 1.140000e-39 174.0
17 TraesCS2A01G166000 chr4B 90.909 132 10 2 2955 3084 518634881 518634750 3.180000e-40 176.0
18 TraesCS2A01G166000 chr7D 90.698 129 10 2 2955 3081 149980028 149980156 1.480000e-38 171.0
19 TraesCS2A01G166000 chr1D 90.152 132 11 2 2955 3084 488546695 488546826 1.480000e-38 171.0
20 TraesCS2A01G166000 chr1D 100.000 37 0 0 1 37 80875387 80875423 5.550000e-08 69.4
21 TraesCS2A01G166000 chr5A 100.000 39 0 0 1 39 514159803 514159841 4.290000e-09 73.1
22 TraesCS2A01G166000 chr6B 97.500 40 1 0 1 40 4661840 4661879 5.550000e-08 69.4
23 TraesCS2A01G166000 chr4A 100.000 37 0 0 1 37 165065320 165065356 5.550000e-08 69.4
24 TraesCS2A01G166000 chr3D 100.000 37 0 0 1 37 592963417 592963453 5.550000e-08 69.4
25 TraesCS2A01G166000 chr3A 97.500 40 1 0 1 40 736945049 736945088 5.550000e-08 69.4
26 TraesCS2A01G166000 chr1A 100.000 37 0 0 1 37 465433134 465433098 5.550000e-08 69.4


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 TraesCS2A01G166000 chr2A 118463966 118467065 3099 True 5725.0 5725 100.000000 1 3100 1 chr2A.!!$R2 3099
1 TraesCS2A01G166000 chr2D 117123647 117126071 2424 True 1103.0 2549 91.751667 530 2901 3 chr2D.!!$R1 2371
2 TraesCS2A01G166000 chr2B 167474793 167478500 3707 True 757.6 2353 91.665000 44 2950 5 chr2B.!!$R1 2906

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
439 440 0.034089 ACTTGCATCCCTAAGTGGCC 60.034 55.0 0.0 0.0 35.91 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2292 2960 0.239347 CAGCCCTTGCAAAACGAGAG 59.761 55.0 0.0 0.0 41.13 3.2 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
23 24 3.073735 CTCACTGGAGCTCGGCCT 61.074 66.667 7.83 0.00 33.67 5.19
24 25 3.071206 TCACTGGAGCTCGGCCTC 61.071 66.667 7.83 0.00 0.00 4.70
40 41 2.064573 CCTCCGTTGGCATTTTTCAC 57.935 50.000 0.00 0.00 0.00 3.18
41 42 1.339610 CCTCCGTTGGCATTTTTCACA 59.660 47.619 0.00 0.00 0.00 3.58
42 43 2.393764 CTCCGTTGGCATTTTTCACAC 58.606 47.619 0.00 0.00 0.00 3.82
69 70 5.458891 CATGCCTCTATTTGAAAGCTATGC 58.541 41.667 0.00 0.00 0.00 3.14
89 90 7.009540 GCTATGCATAAGATTGTTGTTTTGGTC 59.990 37.037 8.00 0.00 0.00 4.02
91 92 7.517614 TGCATAAGATTGTTGTTTTGGTCTA 57.482 32.000 0.00 0.00 0.00 2.59
108 109 5.180271 TGGTCTAACGTTCTTTGTGTTCTT 58.820 37.500 2.82 0.00 0.00 2.52
129 130 1.739466 TGCCTTGCTCATCTTAAAGCG 59.261 47.619 0.00 0.00 41.51 4.68
164 165 8.677300 TGATTTCTACTGTATTTCATTGCTTCC 58.323 33.333 0.00 0.00 0.00 3.46
195 196 7.945033 TGCAGAAATTTGGTATTTTCTTCAC 57.055 32.000 0.00 0.00 39.53 3.18
227 228 1.897560 ATCTTATAGCGGCCCTTTGC 58.102 50.000 0.00 0.00 40.16 3.68
239 240 1.135402 GCCCTTTGCTTTCGGTATGTG 60.135 52.381 0.00 0.00 36.87 3.21
241 242 2.556622 CCCTTTGCTTTCGGTATGTGTT 59.443 45.455 0.00 0.00 0.00 3.32
244 245 4.693566 CCTTTGCTTTCGGTATGTGTTCTA 59.306 41.667 0.00 0.00 0.00 2.10
250 251 4.644103 TTCGGTATGTGTTCTACTAGGC 57.356 45.455 0.00 0.00 0.00 3.93
251 252 3.894759 TCGGTATGTGTTCTACTAGGCT 58.105 45.455 0.00 0.00 0.00 4.58
253 254 5.061853 TCGGTATGTGTTCTACTAGGCTAG 58.938 45.833 19.83 19.83 0.00 3.42
257 258 4.985538 TGTGTTCTACTAGGCTAGAAGC 57.014 45.455 27.59 14.03 41.46 3.86
319 320 5.666969 TCAACATTAGACAGTGGTTTTCG 57.333 39.130 0.00 0.00 0.00 3.46
320 321 5.361427 TCAACATTAGACAGTGGTTTTCGA 58.639 37.500 0.00 0.00 0.00 3.71
331 332 0.729140 GGTTTTCGACATGCAAGCGG 60.729 55.000 0.00 0.00 0.00 5.52
332 333 0.237235 GTTTTCGACATGCAAGCGGA 59.763 50.000 0.00 0.00 0.00 5.54
333 334 1.135689 GTTTTCGACATGCAAGCGGAT 60.136 47.619 0.00 0.00 0.00 4.18
335 336 1.368345 TTCGACATGCAAGCGGATGG 61.368 55.000 0.00 0.00 44.75 3.51
336 337 2.410469 GACATGCAAGCGGATGGC 59.590 61.111 0.00 0.00 44.75 4.40
352 353 0.793861 TGGCGTCACGTGAATTAAGC 59.206 50.000 21.95 18.93 0.00 3.09
355 356 1.201921 GCGTCACGTGAATTAAGCCTG 60.202 52.381 21.95 4.02 0.00 4.85
366 367 5.876460 GTGAATTAAGCCTGGCATGAAAAAT 59.124 36.000 22.65 2.52 0.00 1.82
401 402 1.396653 TAGTGTACTTAGGGCCTCGC 58.603 55.000 10.74 1.02 0.00 5.03
438 439 1.098050 CACTTGCATCCCTAAGTGGC 58.902 55.000 6.13 0.00 46.16 5.01
439 440 0.034089 ACTTGCATCCCTAAGTGGCC 60.034 55.000 0.00 0.00 35.91 5.36
442 443 1.152881 GCATCCCTAAGTGGCCTGG 60.153 63.158 3.32 0.00 0.00 4.45
452 454 3.089874 TGGCCTGGATTCTCCCGG 61.090 66.667 3.32 0.00 43.06 5.73
458 460 1.229368 TGGATTCTCCCGGGTGTCA 60.229 57.895 22.86 10.02 35.03 3.58
487 908 4.948847 AGAACAACAAATTTTGAGGAGGC 58.051 39.130 15.81 1.41 0.00 4.70
491 912 5.683681 ACAACAAATTTTGAGGAGGCAAAT 58.316 33.333 15.81 0.00 37.57 2.32
498 919 6.866010 ATTTTGAGGAGGCAAATTTTGAAC 57.134 33.333 13.26 4.94 37.57 3.18
511 932 7.310052 GGCAAATTTTGAACCCTTAATCTCTCT 60.310 37.037 13.26 0.00 0.00 3.10
598 1026 4.320348 CCGCTTATTCCAAACGGTTTTGTA 60.320 41.667 2.79 0.00 40.61 2.41
605 1033 5.365403 TCCAAACGGTTTTGTATGATCAC 57.635 39.130 2.79 0.00 40.61 3.06
611 1047 8.687301 CAAACGGTTTTGTATGATCACTAAAAC 58.313 33.333 22.91 22.91 37.85 2.43
632 1068 4.694339 ACAAATACCATTCCTCTCGCTAC 58.306 43.478 0.00 0.00 0.00 3.58
665 1103 2.086869 CAACCAATTCATGCGGTCTCT 58.913 47.619 0.00 0.00 30.91 3.10
763 1201 3.649073 ACGAACTGTTGATGTCAATCGA 58.351 40.909 18.02 0.00 37.01 3.59
767 1205 5.505792 CGAACTGTTGATGTCAATCGAATTG 59.494 40.000 9.63 0.00 37.01 2.32
799 1425 1.737236 GTTGCGCATAAGACCACATGA 59.263 47.619 12.75 0.00 0.00 3.07
907 1543 1.856920 CCTACCTTCCTCTCTCCCTCT 59.143 57.143 0.00 0.00 0.00 3.69
908 1544 2.158519 CCTACCTTCCTCTCTCCCTCTC 60.159 59.091 0.00 0.00 0.00 3.20
909 1545 0.634465 ACCTTCCTCTCTCCCTCTCC 59.366 60.000 0.00 0.00 0.00 3.71
910 1546 0.105709 CCTTCCTCTCTCCCTCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
931 1567 1.217942 TCTCCAATCTCCATCTCCGGA 59.782 52.381 2.93 2.93 0.00 5.14
976 1623 6.201806 CGGAGGCATCTATCTTTAAAGAAGTG 59.798 42.308 21.26 16.61 38.77 3.16
977 1624 7.051000 GGAGGCATCTATCTTTAAAGAAGTGT 58.949 38.462 21.26 8.02 38.77 3.55
978 1625 8.204836 GGAGGCATCTATCTTTAAAGAAGTGTA 58.795 37.037 21.26 8.73 38.77 2.90
979 1626 9.255304 GAGGCATCTATCTTTAAAGAAGTGTAG 57.745 37.037 21.26 16.92 38.77 2.74
980 1627 7.713073 AGGCATCTATCTTTAAAGAAGTGTAGC 59.287 37.037 21.26 18.52 38.77 3.58
981 1628 7.495934 GGCATCTATCTTTAAAGAAGTGTAGCA 59.504 37.037 21.26 9.15 38.77 3.49
982 1629 8.547069 GCATCTATCTTTAAAGAAGTGTAGCAG 58.453 37.037 21.26 13.43 38.77 4.24
983 1630 9.809096 CATCTATCTTTAAAGAAGTGTAGCAGA 57.191 33.333 21.26 12.86 38.77 4.26
986 1633 9.862371 CTATCTTTAAAGAAGTGTAGCAGAAGA 57.138 33.333 21.26 0.00 38.77 2.87
990 1645 8.594881 TTTAAAGAAGTGTAGCAGAAGAAGAG 57.405 34.615 0.00 0.00 0.00 2.85
995 1650 4.016444 AGTGTAGCAGAAGAAGAGGAGAG 58.984 47.826 0.00 0.00 0.00 3.20
1002 1657 1.756538 GAAGAAGAGGAGAGGAGCAGG 59.243 57.143 0.00 0.00 0.00 4.85
1027 1684 1.181786 GGAGTGAGGAGAGAGGTGTG 58.818 60.000 0.00 0.00 0.00 3.82
1056 1713 3.053831 GCCGTAGCTAGAGAGAGAGAT 57.946 52.381 0.00 0.00 35.50 2.75
1071 1728 0.759346 GAGATATGGAGGTGGCGGTT 59.241 55.000 0.00 0.00 0.00 4.44
2048 2715 4.468615 GACGACGCAGCTCGCTCT 62.469 66.667 12.44 0.00 43.23 4.09
2133 2801 2.293399 ACAGTTTCATTCGTTTGCTCCC 59.707 45.455 0.00 0.00 0.00 4.30
2292 2960 6.376978 CAAGAACTCAATCACACCTTGAATC 58.623 40.000 0.00 0.00 37.92 2.52
2304 2990 3.250762 CACCTTGAATCTCTCGTTTTGCA 59.749 43.478 0.00 0.00 0.00 4.08
2307 2993 4.470462 CTTGAATCTCTCGTTTTGCAAGG 58.530 43.478 0.00 0.00 0.00 3.61
2324 3011 1.289160 AGGGCTGTCTGCTAATTCCA 58.711 50.000 1.44 0.00 42.39 3.53
2325 3012 1.849039 AGGGCTGTCTGCTAATTCCAT 59.151 47.619 1.44 0.00 42.39 3.41
2326 3013 1.952296 GGGCTGTCTGCTAATTCCATG 59.048 52.381 1.44 0.00 42.39 3.66
2327 3014 1.336125 GGCTGTCTGCTAATTCCATGC 59.664 52.381 1.44 0.00 42.39 4.06
2368 3056 2.577300 GCATCGGCACACGTATATTG 57.423 50.000 0.00 0.00 44.69 1.90
2369 3057 1.864711 GCATCGGCACACGTATATTGT 59.135 47.619 0.00 0.00 44.69 2.71
2370 3058 2.096909 GCATCGGCACACGTATATTGTC 60.097 50.000 0.00 0.00 44.69 3.18
2371 3059 1.830086 TCGGCACACGTATATTGTCG 58.170 50.000 6.36 6.36 44.69 4.35
2475 3168 4.899687 GCTGCGTGCATGCGATGG 62.900 66.667 25.05 15.57 42.31 3.51
2490 3183 0.538977 GATGGGATGCTGGGTGGATG 60.539 60.000 0.00 0.00 0.00 3.51
2501 3194 1.293498 GGTGGATGGATCGATCGGG 59.707 63.158 18.81 0.00 0.00 5.14
2508 3201 3.978491 GATCGATCGGGCTCGGCA 61.978 66.667 16.41 0.00 39.13 5.69
2547 3240 4.430765 CTGTTCCGCGGGCGTAGT 62.431 66.667 27.83 0.00 37.81 2.73
2548 3241 4.424566 TGTTCCGCGGGCGTAGTC 62.425 66.667 27.83 8.54 37.81 2.59
2622 3374 6.877611 TCTGACATTCCCAGAGTTTAAAAC 57.122 37.500 0.00 0.00 35.89 2.43
2631 3383 3.763897 CCAGAGTTTAAAACTGATGGGGG 59.236 47.826 18.95 4.22 43.03 5.40
2673 3427 5.410067 CATGATTAGAGCCTTAGAGCTAGC 58.590 45.833 6.62 6.62 45.15 3.42
2708 3462 5.065859 TGAGGTGTTGATGTGTTTGTTACTG 59.934 40.000 0.00 0.00 0.00 2.74
2772 3532 1.059006 ATCACCCATCTGCCTCTCCC 61.059 60.000 0.00 0.00 0.00 4.30
2819 3579 7.756395 TTGCAAAGATTCTCTTTCTTCTCAT 57.244 32.000 0.00 0.00 42.60 2.90
2821 3581 6.938596 TGCAAAGATTCTCTTTCTTCTCATCA 59.061 34.615 0.00 0.00 42.60 3.07
2823 3583 7.750014 GCAAAGATTCTCTTTCTTCTCATCAAC 59.250 37.037 0.00 0.00 42.60 3.18
2824 3584 9.001542 CAAAGATTCTCTTTCTTCTCATCAACT 57.998 33.333 0.00 0.00 42.60 3.16
2825 3585 8.550710 AAGATTCTCTTTCTTCTCATCAACTG 57.449 34.615 0.00 0.00 31.57 3.16
2826 3586 7.104939 AGATTCTCTTTCTTCTCATCAACTGG 58.895 38.462 0.00 0.00 0.00 4.00
2828 3588 5.788450 TCTCTTTCTTCTCATCAACTGGAC 58.212 41.667 0.00 0.00 0.00 4.02
2829 3589 5.305386 TCTCTTTCTTCTCATCAACTGGACA 59.695 40.000 0.00 0.00 0.00 4.02
2835 3717 4.193826 TCTCATCAACTGGACAAGTAGC 57.806 45.455 0.00 0.00 38.56 3.58
2868 3750 3.287867 TCTCTGGCCTGGATTTCAATC 57.712 47.619 10.07 0.00 34.66 2.67
2871 3753 1.402968 CTGGCCTGGATTTCAATCGTG 59.597 52.381 3.32 0.00 36.27 4.35
2901 3783 1.613437 GTTGATTGGTTGGGACTGTGG 59.387 52.381 0.00 0.00 0.00 4.17
2934 3816 5.467399 TGTTTATTAACTGAACACCACTCGG 59.533 40.000 0.00 0.00 35.24 4.63
2949 3831 3.179830 CACTCGGTGGAAGAAAGATACG 58.820 50.000 0.00 0.00 0.00 3.06
2950 3832 2.194271 CTCGGTGGAAGAAAGATACGC 58.806 52.381 0.00 0.00 0.00 4.42
2951 3833 1.822990 TCGGTGGAAGAAAGATACGCT 59.177 47.619 0.00 0.00 0.00 5.07
2952 3834 1.927174 CGGTGGAAGAAAGATACGCTG 59.073 52.381 0.00 0.00 0.00 5.18
2953 3835 1.666189 GGTGGAAGAAAGATACGCTGC 59.334 52.381 0.00 0.00 0.00 5.25
2954 3836 2.622436 GTGGAAGAAAGATACGCTGCT 58.378 47.619 0.00 0.00 0.00 4.24
2955 3837 3.003480 GTGGAAGAAAGATACGCTGCTT 58.997 45.455 0.00 0.00 0.00 3.91
2956 3838 4.181578 GTGGAAGAAAGATACGCTGCTTA 58.818 43.478 0.00 0.00 0.00 3.09
2957 3839 4.811557 GTGGAAGAAAGATACGCTGCTTAT 59.188 41.667 0.00 0.00 0.00 1.73
2958 3840 5.294552 GTGGAAGAAAGATACGCTGCTTATT 59.705 40.000 0.00 0.00 0.00 1.40
2959 3841 5.294306 TGGAAGAAAGATACGCTGCTTATTG 59.706 40.000 0.00 0.00 0.00 1.90
2960 3842 5.277538 GGAAGAAAGATACGCTGCTTATTGG 60.278 44.000 0.00 0.00 0.00 3.16
2961 3843 4.770795 AGAAAGATACGCTGCTTATTGGT 58.229 39.130 0.00 0.00 0.00 3.67
2962 3844 4.811557 AGAAAGATACGCTGCTTATTGGTC 59.188 41.667 0.00 0.00 0.00 4.02
2963 3845 4.408182 AAGATACGCTGCTTATTGGTCT 57.592 40.909 0.00 0.00 0.00 3.85
2964 3846 4.408182 AGATACGCTGCTTATTGGTCTT 57.592 40.909 0.00 0.00 0.00 3.01
2965 3847 4.372656 AGATACGCTGCTTATTGGTCTTC 58.627 43.478 0.00 0.00 0.00 2.87
2966 3848 2.472695 ACGCTGCTTATTGGTCTTCA 57.527 45.000 0.00 0.00 0.00 3.02
2967 3849 2.991250 ACGCTGCTTATTGGTCTTCAT 58.009 42.857 0.00 0.00 0.00 2.57
2968 3850 3.347216 ACGCTGCTTATTGGTCTTCATT 58.653 40.909 0.00 0.00 0.00 2.57
2969 3851 3.127548 ACGCTGCTTATTGGTCTTCATTG 59.872 43.478 0.00 0.00 0.00 2.82
2970 3852 3.127548 CGCTGCTTATTGGTCTTCATTGT 59.872 43.478 0.00 0.00 0.00 2.71
2971 3853 4.332543 CGCTGCTTATTGGTCTTCATTGTA 59.667 41.667 0.00 0.00 0.00 2.41
2972 3854 5.163764 CGCTGCTTATTGGTCTTCATTGTAA 60.164 40.000 0.00 0.00 0.00 2.41
2973 3855 6.458751 CGCTGCTTATTGGTCTTCATTGTAAT 60.459 38.462 0.00 0.00 0.00 1.89
2974 3856 6.914757 GCTGCTTATTGGTCTTCATTGTAATC 59.085 38.462 0.00 0.00 0.00 1.75
2975 3857 7.201767 GCTGCTTATTGGTCTTCATTGTAATCT 60.202 37.037 0.00 0.00 0.00 2.40
2976 3858 9.330063 CTGCTTATTGGTCTTCATTGTAATCTA 57.670 33.333 0.00 0.00 0.00 1.98
2977 3859 9.851686 TGCTTATTGGTCTTCATTGTAATCTAT 57.148 29.630 0.00 0.00 0.00 1.98
2980 3862 6.942532 TTGGTCTTCATTGTAATCTATGCC 57.057 37.500 0.00 0.00 0.00 4.40
2981 3863 6.000246 TGGTCTTCATTGTAATCTATGCCA 58.000 37.500 0.00 0.00 0.00 4.92
2982 3864 6.422333 TGGTCTTCATTGTAATCTATGCCAA 58.578 36.000 0.00 0.00 0.00 4.52
2983 3865 6.889177 TGGTCTTCATTGTAATCTATGCCAAA 59.111 34.615 0.00 0.00 0.00 3.28
2984 3866 7.560991 TGGTCTTCATTGTAATCTATGCCAAAT 59.439 33.333 0.00 0.00 0.00 2.32
2985 3867 8.416329 GGTCTTCATTGTAATCTATGCCAAATT 58.584 33.333 0.00 0.00 0.00 1.82
2986 3868 9.807649 GTCTTCATTGTAATCTATGCCAAATTT 57.192 29.630 0.00 0.00 0.00 1.82
3025 3907 8.970691 ACTAACAAAAAGTTCATGCATATCAC 57.029 30.769 0.00 0.00 41.64 3.06
3026 3908 8.575589 ACTAACAAAAAGTTCATGCATATCACA 58.424 29.630 0.00 0.00 41.64 3.58
3027 3909 9.409312 CTAACAAAAAGTTCATGCATATCACAA 57.591 29.630 0.00 0.00 41.64 3.33
3028 3910 8.659925 AACAAAAAGTTCATGCATATCACAAA 57.340 26.923 0.00 0.00 34.74 2.83
3029 3911 8.659925 ACAAAAAGTTCATGCATATCACAAAA 57.340 26.923 0.00 0.00 0.00 2.44
3030 3912 9.107177 ACAAAAAGTTCATGCATATCACAAAAA 57.893 25.926 0.00 0.00 0.00 1.94
3065 3947 8.667987 TGAAAACTATGTTCAAATACGAATGC 57.332 30.769 0.00 0.00 32.13 3.56
3066 3948 8.293157 TGAAAACTATGTTCAAATACGAATGCA 58.707 29.630 0.00 0.00 32.13 3.96
3067 3949 9.123709 GAAAACTATGTTCAAATACGAATGCAA 57.876 29.630 0.00 0.00 0.00 4.08
3068 3950 9.638239 AAAACTATGTTCAAATACGAATGCAAT 57.362 25.926 0.00 0.00 0.00 3.56
3069 3951 8.619146 AACTATGTTCAAATACGAATGCAATG 57.381 30.769 0.00 0.00 0.00 2.82
3070 3952 7.984391 ACTATGTTCAAATACGAATGCAATGA 58.016 30.769 0.00 0.00 0.00 2.57
3071 3953 8.623903 ACTATGTTCAAATACGAATGCAATGAT 58.376 29.630 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.073735 AGGCCGAGCTCCAGTGAG 61.074 66.667 8.47 0.00 41.84 3.51
7 8 3.071206 GAGGCCGAGCTCCAGTGA 61.071 66.667 8.47 0.00 0.00 3.41
8 9 4.154347 GGAGGCCGAGCTCCAGTG 62.154 72.222 8.47 0.00 39.45 3.66
21 22 1.339610 TGTGAAAAATGCCAACGGAGG 59.660 47.619 0.00 0.00 0.00 4.30
22 23 2.034558 AGTGTGAAAAATGCCAACGGAG 59.965 45.455 0.00 0.00 0.00 4.63
23 24 2.028130 AGTGTGAAAAATGCCAACGGA 58.972 42.857 0.00 0.00 0.00 4.69
24 25 2.507339 AGTGTGAAAAATGCCAACGG 57.493 45.000 0.00 0.00 0.00 4.44
25 26 3.243234 TGGTAGTGTGAAAAATGCCAACG 60.243 43.478 0.00 0.00 0.00 4.10
26 27 4.314740 TGGTAGTGTGAAAAATGCCAAC 57.685 40.909 0.00 0.00 0.00 3.77
27 28 4.798924 GCATGGTAGTGTGAAAAATGCCAA 60.799 41.667 0.00 0.00 30.99 4.52
28 29 3.305950 GCATGGTAGTGTGAAAAATGCCA 60.306 43.478 0.00 0.00 0.00 4.92
29 30 3.253230 GCATGGTAGTGTGAAAAATGCC 58.747 45.455 0.00 0.00 0.00 4.40
30 31 3.056607 AGGCATGGTAGTGTGAAAAATGC 60.057 43.478 0.00 0.00 0.00 3.56
31 32 4.460382 AGAGGCATGGTAGTGTGAAAAATG 59.540 41.667 0.00 0.00 0.00 2.32
32 33 4.666512 AGAGGCATGGTAGTGTGAAAAAT 58.333 39.130 0.00 0.00 0.00 1.82
33 34 4.098914 AGAGGCATGGTAGTGTGAAAAA 57.901 40.909 0.00 0.00 0.00 1.94
34 35 3.788227 AGAGGCATGGTAGTGTGAAAA 57.212 42.857 0.00 0.00 0.00 2.29
35 36 5.435686 AATAGAGGCATGGTAGTGTGAAA 57.564 39.130 0.00 0.00 0.00 2.69
36 37 5.045942 TCAAATAGAGGCATGGTAGTGTGAA 60.046 40.000 0.00 0.00 0.00 3.18
37 38 4.469586 TCAAATAGAGGCATGGTAGTGTGA 59.530 41.667 0.00 0.00 0.00 3.58
38 39 4.769688 TCAAATAGAGGCATGGTAGTGTG 58.230 43.478 0.00 0.00 0.00 3.82
39 40 5.435686 TTCAAATAGAGGCATGGTAGTGT 57.564 39.130 0.00 0.00 0.00 3.55
40 41 5.220931 GCTTTCAAATAGAGGCATGGTAGTG 60.221 44.000 0.00 0.00 0.00 2.74
41 42 4.884164 GCTTTCAAATAGAGGCATGGTAGT 59.116 41.667 0.00 0.00 0.00 2.73
42 43 5.128919 AGCTTTCAAATAGAGGCATGGTAG 58.871 41.667 0.00 0.00 31.93 3.18
69 70 8.073768 ACGTTAGACCAAAACAACAATCTTATG 58.926 33.333 0.00 0.00 0.00 1.90
89 90 4.733405 GGCAAAGAACACAAAGAACGTTAG 59.267 41.667 0.00 0.00 0.00 2.34
91 92 3.192633 AGGCAAAGAACACAAAGAACGTT 59.807 39.130 0.00 0.00 0.00 3.99
108 109 2.162208 CGCTTTAAGATGAGCAAGGCAA 59.838 45.455 0.00 0.00 38.81 4.52
160 161 5.993441 ACCAAATTTCTGCAATCAAAGGAAG 59.007 36.000 0.00 0.00 0.00 3.46
162 163 5.549742 ACCAAATTTCTGCAATCAAAGGA 57.450 34.783 0.00 0.00 0.00 3.36
164 165 9.815936 GAAAATACCAAATTTCTGCAATCAAAG 57.184 29.630 0.00 0.00 33.72 2.77
195 196 8.021396 GGCCGCTATAAGATTTATTAAAGTTGG 58.979 37.037 0.00 0.00 0.00 3.77
199 200 7.923414 AGGGCCGCTATAAGATTTATTAAAG 57.077 36.000 0.00 0.00 0.00 1.85
217 218 1.029947 ATACCGAAAGCAAAGGGCCG 61.030 55.000 0.00 0.00 46.50 6.13
227 228 5.041940 GCCTAGTAGAACACATACCGAAAG 58.958 45.833 0.00 0.00 0.00 2.62
239 240 7.571080 TCTTAAGCTTCTAGCCTAGTAGAAC 57.429 40.000 0.00 0.00 43.77 3.01
241 242 7.575505 TCTTCTTAAGCTTCTAGCCTAGTAGA 58.424 38.462 0.00 0.00 43.77 2.59
244 245 8.950007 ATATCTTCTTAAGCTTCTAGCCTAGT 57.050 34.615 0.00 0.00 43.77 2.57
253 254 9.846248 TTGCAAAGAAATATCTTCTTAAGCTTC 57.154 29.630 0.00 0.00 45.19 3.86
288 289 7.448161 ACCACTGTCTAATGTTGAATGAAATGA 59.552 33.333 0.00 0.00 0.00 2.57
293 294 7.519809 CGAAAACCACTGTCTAATGTTGAATGA 60.520 37.037 0.00 0.00 0.00 2.57
319 320 2.410469 GCCATCCGCTTGCATGTC 59.590 61.111 1.14 0.00 0.00 3.06
320 321 3.511595 CGCCATCCGCTTGCATGT 61.512 61.111 1.14 0.00 34.21 3.21
331 332 2.536928 GCTTAATTCACGTGACGCCATC 60.537 50.000 19.90 2.99 0.00 3.51
332 333 1.396996 GCTTAATTCACGTGACGCCAT 59.603 47.619 19.90 6.15 0.00 4.40
333 334 0.793861 GCTTAATTCACGTGACGCCA 59.206 50.000 19.90 3.47 0.00 5.69
335 336 1.076332 AGGCTTAATTCACGTGACGC 58.924 50.000 19.90 14.89 0.00 5.19
336 337 1.393539 CCAGGCTTAATTCACGTGACG 59.606 52.381 19.90 2.24 0.00 4.35
337 338 1.130561 GCCAGGCTTAATTCACGTGAC 59.869 52.381 19.90 5.30 0.00 3.67
338 339 1.271108 TGCCAGGCTTAATTCACGTGA 60.271 47.619 15.76 15.76 0.00 4.35
339 340 1.164411 TGCCAGGCTTAATTCACGTG 58.836 50.000 14.15 9.94 0.00 4.49
352 353 6.222389 TGTTACTTTGATTTTTCATGCCAGG 58.778 36.000 0.00 0.00 0.00 4.45
355 356 8.364129 TCTTTGTTACTTTGATTTTTCATGCC 57.636 30.769 0.00 0.00 0.00 4.40
413 414 1.549243 TAGGGATGCAAGTGGACGCA 61.549 55.000 0.00 0.00 43.45 5.24
420 421 0.034089 GGCCACTTAGGGATGCAAGT 60.034 55.000 0.00 0.00 38.09 3.16
442 443 3.553828 TTTATGACACCCGGGAGAATC 57.446 47.619 32.02 18.46 0.00 2.52
466 468 4.692228 TGCCTCCTCAAAATTTGTTGTTC 58.308 39.130 5.56 0.00 0.00 3.18
467 469 4.751767 TGCCTCCTCAAAATTTGTTGTT 57.248 36.364 5.56 0.00 0.00 2.83
469 471 6.622833 AATTTGCCTCCTCAAAATTTGTTG 57.377 33.333 5.56 0.75 39.13 3.33
473 475 7.201812 GGTTCAAAATTTGCCTCCTCAAAATTT 60.202 33.333 0.00 0.00 38.72 1.82
481 902 2.976440 AGGGTTCAAAATTTGCCTCCT 58.024 42.857 0.00 4.59 0.00 3.69
563 991 6.982160 TGGAATAAGCGGGTAACTATCTTA 57.018 37.500 0.00 0.00 0.00 2.10
571 999 2.290197 ACCGTTTGGAATAAGCGGGTAA 60.290 45.455 16.96 0.00 45.85 2.85
598 1026 9.479549 AGGAATGGTATTTGTTTTAGTGATCAT 57.520 29.630 0.00 0.00 0.00 2.45
605 1033 6.316390 AGCGAGAGGAATGGTATTTGTTTTAG 59.684 38.462 0.00 0.00 0.00 1.85
611 1047 4.508124 GTGTAGCGAGAGGAATGGTATTTG 59.492 45.833 0.00 0.00 0.00 2.32
623 1059 2.663602 GTGAATGTGTGTGTAGCGAGAG 59.336 50.000 0.00 0.00 0.00 3.20
632 1068 3.731652 ATTGGTTGGTGAATGTGTGTG 57.268 42.857 0.00 0.00 0.00 3.82
763 1201 2.788786 CGCAACTTGCTCGTTTTCAATT 59.211 40.909 11.93 0.00 42.25 2.32
767 1205 0.591236 TGCGCAACTTGCTCGTTTTC 60.591 50.000 8.16 0.00 42.25 2.29
785 1223 5.536260 AGACATCGATCATGTGGTCTTATG 58.464 41.667 13.33 4.77 46.53 1.90
907 1543 2.427002 GGAGATGGAGATTGGAGAGGGA 60.427 54.545 0.00 0.00 0.00 4.20
908 1544 1.977129 GGAGATGGAGATTGGAGAGGG 59.023 57.143 0.00 0.00 0.00 4.30
909 1545 1.617850 CGGAGATGGAGATTGGAGAGG 59.382 57.143 0.00 0.00 0.00 3.69
910 1546 1.617850 CCGGAGATGGAGATTGGAGAG 59.382 57.143 0.00 0.00 0.00 3.20
931 1567 3.945285 CCGGATTTTGCTTATGTAGGTGT 59.055 43.478 0.00 0.00 0.00 4.16
976 1623 3.626930 TCCTCTCCTCTTCTTCTGCTAC 58.373 50.000 0.00 0.00 0.00 3.58
977 1624 3.897239 CTCCTCTCCTCTTCTTCTGCTA 58.103 50.000 0.00 0.00 0.00 3.49
978 1625 2.738743 CTCCTCTCCTCTTCTTCTGCT 58.261 52.381 0.00 0.00 0.00 4.24
979 1626 1.136891 GCTCCTCTCCTCTTCTTCTGC 59.863 57.143 0.00 0.00 0.00 4.26
980 1627 2.428171 CTGCTCCTCTCCTCTTCTTCTG 59.572 54.545 0.00 0.00 0.00 3.02
981 1628 2.624029 CCTGCTCCTCTCCTCTTCTTCT 60.624 54.545 0.00 0.00 0.00 2.85
982 1629 1.756538 CCTGCTCCTCTCCTCTTCTTC 59.243 57.143 0.00 0.00 0.00 2.87
983 1630 1.622173 CCCTGCTCCTCTCCTCTTCTT 60.622 57.143 0.00 0.00 0.00 2.52
986 1633 1.002792 CCCCTGCTCCTCTCCTCTT 59.997 63.158 0.00 0.00 0.00 2.85
1002 1657 4.779733 TCTCCTCACTCCCCGCCC 62.780 72.222 0.00 0.00 0.00 6.13
1043 1700 5.500234 CCACCTCCATATCTCTCTCTCTAG 58.500 50.000 0.00 0.00 0.00 2.43
1048 1705 1.543802 CGCCACCTCCATATCTCTCTC 59.456 57.143 0.00 0.00 0.00 3.20
1056 1713 1.306654 AGGAACCGCCACCTCCATA 60.307 57.895 0.00 0.00 40.02 2.74
1071 1728 4.147449 CTCGGCGCCATGACAGGA 62.147 66.667 28.98 12.64 0.00 3.86
1135 1792 2.104963 AGTAGCTAGGTAAATGGCTGCC 59.895 50.000 12.87 12.87 39.63 4.85
1138 1795 3.477210 GCAGTAGCTAGGTAAATGGCT 57.523 47.619 2.58 0.00 40.48 4.75
1232 1889 1.342796 GAAGGCGAAGTCGAACGTCC 61.343 60.000 4.59 9.70 43.02 4.79
1233 1890 1.662845 CGAAGGCGAAGTCGAACGTC 61.663 60.000 4.59 4.75 43.02 4.34
1263 1920 2.985456 GTGGACTCCCTGAGCTGG 59.015 66.667 0.00 0.00 32.04 4.85
1368 2028 1.748122 GGAGGCGTAGTCCTCGTCA 60.748 63.158 3.98 0.00 46.64 4.35
1485 2145 3.775654 GACCTGCCCCTCGTCTGG 61.776 72.222 0.00 0.00 0.00 3.86
1674 2337 2.035442 GTCCTTGAGCCGCCACTTC 61.035 63.158 0.00 0.00 0.00 3.01
2133 2801 4.394712 AGGAGGGCGAACCAAGCG 62.395 66.667 0.00 0.00 43.89 4.68
2271 2939 5.936956 AGAGATTCAAGGTGTGATTGAGTTC 59.063 40.000 0.00 0.00 37.91 3.01
2279 2947 4.336889 AAACGAGAGATTCAAGGTGTGA 57.663 40.909 0.00 0.00 0.00 3.58
2292 2960 0.239347 CAGCCCTTGCAAAACGAGAG 59.761 55.000 0.00 0.00 41.13 3.20
2367 3055 7.710907 CCTGGTTTCTCATTAGATTAATCGACA 59.289 37.037 9.78 0.00 0.00 4.35
2368 3056 7.171678 CCCTGGTTTCTCATTAGATTAATCGAC 59.828 40.741 9.78 0.35 0.00 4.20
2369 3057 7.070696 TCCCTGGTTTCTCATTAGATTAATCGA 59.929 37.037 9.78 1.74 0.00 3.59
2370 3058 7.217200 TCCCTGGTTTCTCATTAGATTAATCG 58.783 38.462 9.78 0.00 0.00 3.34
2371 3059 7.663493 CCTCCCTGGTTTCTCATTAGATTAATC 59.337 40.741 7.41 7.41 0.00 1.75
2475 3168 0.251077 GATCCATCCACCCAGCATCC 60.251 60.000 0.00 0.00 0.00 3.51
2482 3175 1.293498 CCGATCGATCCATCCACCC 59.707 63.158 18.66 0.00 0.00 4.61
2490 3183 4.726351 GCCGAGCCCGATCGATCC 62.726 72.222 18.66 5.96 45.56 3.36
2542 3235 2.353607 GATGCGGCGAGGACTACG 60.354 66.667 12.98 0.00 0.00 3.51
2543 3236 2.353607 CGATGCGGCGAGGACTAC 60.354 66.667 12.98 0.00 0.00 2.73
2544 3237 4.266070 GCGATGCGGCGAGGACTA 62.266 66.667 12.98 0.00 0.00 2.59
2622 3374 0.846015 TAGCATCCAACCCCCATCAG 59.154 55.000 0.00 0.00 0.00 2.90
2631 3383 1.296727 GCCGGTTACTAGCATCCAAC 58.703 55.000 1.90 0.00 0.00 3.77
2673 3427 2.233186 TCAACACCTCAGCTCATCTCAG 59.767 50.000 0.00 0.00 0.00 3.35
2708 3462 1.469423 GCAAGTCTCTACGCTACCACC 60.469 57.143 0.00 0.00 0.00 4.61
2734 3494 2.278596 CGCCTGCTTGCATCATGC 60.279 61.111 1.35 1.35 45.29 4.06
2735 3495 2.278596 GCGCCTGCTTGCATCATG 60.279 61.111 0.00 0.00 38.39 3.07
2736 3496 2.752640 TGCGCCTGCTTGCATCAT 60.753 55.556 4.18 0.00 43.34 2.45
2772 3532 6.988622 AGAAAAGCTCAGATGAGAATCTTG 57.011 37.500 13.98 0.00 44.74 3.02
2819 3579 1.961394 ACTCGCTACTTGTCCAGTTGA 59.039 47.619 0.00 0.00 36.88 3.18
2821 3581 3.155501 ACTACTCGCTACTTGTCCAGTT 58.844 45.455 0.00 0.00 36.88 3.16
2823 3583 4.959596 TTACTACTCGCTACTTGTCCAG 57.040 45.455 0.00 0.00 0.00 3.86
2824 3584 5.909621 AATTACTACTCGCTACTTGTCCA 57.090 39.130 0.00 0.00 0.00 4.02
2825 3585 7.034397 AGAAAATTACTACTCGCTACTTGTCC 58.966 38.462 0.00 0.00 0.00 4.02
2826 3586 7.969508 AGAGAAAATTACTACTCGCTACTTGTC 59.030 37.037 0.00 0.00 34.98 3.18
2828 3588 7.221067 CCAGAGAAAATTACTACTCGCTACTTG 59.779 40.741 0.00 0.00 34.98 3.16
2829 3589 7.259161 CCAGAGAAAATTACTACTCGCTACTT 58.741 38.462 0.00 0.00 34.98 2.24
2835 3717 4.806247 CAGGCCAGAGAAAATTACTACTCG 59.194 45.833 5.01 0.00 34.98 4.18
2868 3750 2.414029 CCAATCAACCGACAATTCCACG 60.414 50.000 0.00 0.00 0.00 4.94
2871 3753 3.574614 CAACCAATCAACCGACAATTCC 58.425 45.455 0.00 0.00 0.00 3.01
2934 3816 2.622436 AGCAGCGTATCTTTCTTCCAC 58.378 47.619 0.00 0.00 0.00 4.02
2943 3825 4.141937 TGAAGACCAATAAGCAGCGTATCT 60.142 41.667 0.92 0.00 0.00 1.98
2944 3826 4.119862 TGAAGACCAATAAGCAGCGTATC 58.880 43.478 0.92 0.00 0.00 2.24
2945 3827 4.137116 TGAAGACCAATAAGCAGCGTAT 57.863 40.909 0.00 0.00 0.00 3.06
2946 3828 3.603158 TGAAGACCAATAAGCAGCGTA 57.397 42.857 0.00 0.00 0.00 4.42
2947 3829 2.472695 TGAAGACCAATAAGCAGCGT 57.527 45.000 0.00 0.00 0.00 5.07
2948 3830 3.127548 ACAATGAAGACCAATAAGCAGCG 59.872 43.478 0.00 0.00 0.00 5.18
2949 3831 4.708726 ACAATGAAGACCAATAAGCAGC 57.291 40.909 0.00 0.00 0.00 5.25
2950 3832 8.218338 AGATTACAATGAAGACCAATAAGCAG 57.782 34.615 0.00 0.00 0.00 4.24
2951 3833 9.851686 ATAGATTACAATGAAGACCAATAAGCA 57.148 29.630 0.00 0.00 0.00 3.91
2954 3836 9.066892 GGCATAGATTACAATGAAGACCAATAA 57.933 33.333 0.00 0.00 0.00 1.40
2955 3837 8.217111 TGGCATAGATTACAATGAAGACCAATA 58.783 33.333 0.00 0.00 0.00 1.90
2956 3838 7.062322 TGGCATAGATTACAATGAAGACCAAT 58.938 34.615 0.00 0.00 0.00 3.16
2957 3839 6.422333 TGGCATAGATTACAATGAAGACCAA 58.578 36.000 0.00 0.00 0.00 3.67
2958 3840 6.000246 TGGCATAGATTACAATGAAGACCA 58.000 37.500 0.00 0.00 0.00 4.02
2959 3841 6.942532 TTGGCATAGATTACAATGAAGACC 57.057 37.500 0.00 0.00 0.00 3.85
2960 3842 9.807649 AAATTTGGCATAGATTACAATGAAGAC 57.192 29.630 0.00 0.00 0.00 3.01
2999 3881 9.410556 GTGATATGCATGAACTTTTTGTTAGTT 57.589 29.630 10.16 0.00 39.30 2.24
3000 3882 8.575589 TGTGATATGCATGAACTTTTTGTTAGT 58.424 29.630 10.16 0.00 39.30 2.24
3001 3883 8.969121 TGTGATATGCATGAACTTTTTGTTAG 57.031 30.769 10.16 0.00 39.30 2.34
3002 3884 9.755804 TTTGTGATATGCATGAACTTTTTGTTA 57.244 25.926 10.16 0.00 39.30 2.41
3003 3885 8.659925 TTTGTGATATGCATGAACTTTTTGTT 57.340 26.923 10.16 0.00 42.38 2.83
3004 3886 8.659925 TTTTGTGATATGCATGAACTTTTTGT 57.340 26.923 10.16 0.00 0.00 2.83
3039 3921 9.123709 GCATTCGTATTTGAACATAGTTTTCAA 57.876 29.630 0.00 0.00 40.42 2.69
3040 3922 8.293157 TGCATTCGTATTTGAACATAGTTTTCA 58.707 29.630 0.00 0.00 0.00 2.69
3041 3923 8.667987 TGCATTCGTATTTGAACATAGTTTTC 57.332 30.769 0.00 0.00 0.00 2.29
3042 3924 9.638239 ATTGCATTCGTATTTGAACATAGTTTT 57.362 25.926 0.00 0.00 0.00 2.43
3043 3925 9.075519 CATTGCATTCGTATTTGAACATAGTTT 57.924 29.630 0.00 0.00 0.00 2.66
3044 3926 8.458052 TCATTGCATTCGTATTTGAACATAGTT 58.542 29.630 0.00 0.00 0.00 2.24
3045 3927 7.984391 TCATTGCATTCGTATTTGAACATAGT 58.016 30.769 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.