Multiple sequence alignment - TraesCS2A01G468400

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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 TraesCS2A01G468400 chr2A 100.000 3560 0 0 1 3560 712316256 712319815 0.000000e+00 6575.0
1 TraesCS2A01G468400 chr2A 86.528 772 104 0 1789 2560 712707276 712706505 0.000000e+00 850.0
2 TraesCS2A01G468400 chr2A 84.638 690 98 6 1878 2560 712702485 712701797 0.000000e+00 680.0
3 TraesCS2A01G468400 chr2D 95.339 2639 102 15 1 2621 573850898 573853533 0.000000e+00 4172.0
4 TraesCS2A01G468400 chr2D 86.581 775 104 0 1789 2563 574346325 574345551 0.000000e+00 856.0
5 TraesCS2A01G468400 chr2D 86.905 336 19 10 2621 2955 573853583 573853894 1.570000e-93 353.0
6 TraesCS2A01G468400 chr2D 88.889 90 6 4 122 210 243656266 243656352 1.350000e-19 108.0
7 TraesCS2A01G468400 chr2B 93.814 1940 96 16 695 2624 689713926 689715851 0.000000e+00 2896.0
8 TraesCS2A01G468400 chr2B 90.390 718 50 12 1 707 689713198 689713907 0.000000e+00 926.0
9 TraesCS2A01G468400 chr2B 86.968 775 100 1 1789 2563 690211373 690210600 0.000000e+00 870.0
10 TraesCS2A01G468400 chr2B 88.701 177 14 3 2621 2797 689715890 689716060 1.000000e-50 211.0
11 TraesCS2A01G468400 chr2B 100.000 50 0 0 122 171 1863809 1863858 3.780000e-15 93.5
12 TraesCS2A01G468400 chr2B 100.000 50 0 0 122 171 79720442 79720491 3.780000e-15 93.5
13 TraesCS2A01G468400 chr3A 87.650 583 65 5 2981 3560 9525284 9525862 0.000000e+00 671.0
14 TraesCS2A01G468400 chr3A 84.948 485 65 7 2984 3464 660426024 660426504 5.340000e-133 484.0
15 TraesCS2A01G468400 chr3A 92.857 70 3 2 122 190 91016959 91017027 2.260000e-17 100.0
16 TraesCS2A01G468400 chr4D 84.948 578 79 6 2984 3558 467584661 467585233 2.380000e-161 579.0
17 TraesCS2A01G468400 chr4B 84.854 581 78 8 2984 3560 585667352 585667926 8.570000e-161 577.0
18 TraesCS2A01G468400 chr4B 93.939 66 3 1 122 186 90723774 90723709 8.130000e-17 99.0
19 TraesCS2A01G468400 chrUn 84.035 451 67 5 3112 3560 275419114 275418667 2.540000e-116 429.0
20 TraesCS2A01G468400 chrUn 84.035 451 67 5 3112 3560 324462107 324462554 2.540000e-116 429.0
21 TraesCS2A01G468400 chr6B 84.035 451 67 5 3112 3560 7128622 7129069 2.540000e-116 429.0
22 TraesCS2A01G468400 chr6D 84.450 373 53 3 3101 3468 4696759 4696387 2.610000e-96 363.0
23 TraesCS2A01G468400 chr6D 95.745 47 2 0 2955 3001 292846079 292846125 3.810000e-10 76.8
24 TraesCS2A01G468400 chr5D 86.544 327 39 5 3000 3321 38733369 38733695 4.370000e-94 355.0
25 TraesCS2A01G468400 chr5D 86.224 196 27 0 1526 1721 519545548 519545743 2.780000e-51 213.0
26 TraesCS2A01G468400 chr5D 93.182 44 3 0 2958 3001 559437858 559437815 8.250000e-07 65.8
27 TraesCS2A01G468400 chr5A 85.845 219 28 2 1503 1721 646058389 646058604 2.760000e-56 230.0
28 TraesCS2A01G468400 chr5A 91.837 49 4 0 2953 3001 556152754 556152802 6.380000e-08 69.4
29 TraesCS2A01G468400 chr5A 89.796 49 5 0 2953 3001 347451550 347451502 2.970000e-06 63.9
30 TraesCS2A01G468400 chr5B 86.802 197 26 0 1525 1721 654366169 654366365 1.660000e-53 220.0
31 TraesCS2A01G468400 chr3B 98.276 58 1 0 122 179 659583308 659583251 6.290000e-18 102.0
32 TraesCS2A01G468400 chr3B 93.617 47 3 0 2955 3001 697975739 697975693 1.770000e-08 71.3
33 TraesCS2A01G468400 chr1B 98.246 57 1 0 122 178 438171004 438171060 2.260000e-17 100.0
34 TraesCS2A01G468400 chr4A 93.846 65 3 1 122 186 739032318 739032381 2.930000e-16 97.1
35 TraesCS2A01G468400 chr7A 92.537 67 3 2 122 188 641235380 641235316 1.050000e-15 95.3
36 TraesCS2A01G468400 chr6A 94.340 53 2 1 2955 3006 3666837 3666889 2.950000e-11 80.5
37 TraesCS2A01G468400 chr3D 95.745 47 2 0 2955 3001 8196891 8196845 3.810000e-10 76.8
38 TraesCS2A01G468400 chr3D 93.878 49 3 0 2955 3003 4184537 4184585 1.370000e-09 75.0
39 TraesCS2A01G468400 chr7B 90.909 55 2 2 2953 3006 336835386 336835438 1.770000e-08 71.3
40 TraesCS2A01G468400 chr7D 74.375 160 36 3 2260 2415 514093511 514093669 2.970000e-06 63.9
41 TraesCS2A01G468400 chr7D 74.375 160 36 3 2260 2415 515236535 515236377 2.970000e-06 63.9
42 TraesCS2A01G468400 chr7D 85.000 60 9 0 2260 2319 515220329 515220270 1.070000e-05 62.1


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 TraesCS2A01G468400 chr2A 712316256 712319815 3559 False 6575.000000 6575 100.000000 1 3560 1 chr2A.!!$F1 3559
1 TraesCS2A01G468400 chr2A 712706505 712707276 771 True 850.000000 850 86.528000 1789 2560 1 chr2A.!!$R2 771
2 TraesCS2A01G468400 chr2A 712701797 712702485 688 True 680.000000 680 84.638000 1878 2560 1 chr2A.!!$R1 682
3 TraesCS2A01G468400 chr2D 573850898 573853894 2996 False 2262.500000 4172 91.122000 1 2955 2 chr2D.!!$F2 2954
4 TraesCS2A01G468400 chr2D 574345551 574346325 774 True 856.000000 856 86.581000 1789 2563 1 chr2D.!!$R1 774
5 TraesCS2A01G468400 chr2B 689713198 689716060 2862 False 1344.333333 2896 90.968333 1 2797 3 chr2B.!!$F3 2796
6 TraesCS2A01G468400 chr2B 690210600 690211373 773 True 870.000000 870 86.968000 1789 2563 1 chr2B.!!$R1 774
7 TraesCS2A01G468400 chr3A 9525284 9525862 578 False 671.000000 671 87.650000 2981 3560 1 chr3A.!!$F1 579
8 TraesCS2A01G468400 chr4D 467584661 467585233 572 False 579.000000 579 84.948000 2984 3558 1 chr4D.!!$F1 574
9 TraesCS2A01G468400 chr4B 585667352 585667926 574 False 577.000000 577 84.854000 2984 3560 1 chr4B.!!$F1 576

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
126 127 0.044092 TTCCCTGGTCATGGAGCCTA 59.956 55.0 0.0 0.0 30.91 3.93 F
133 134 0.107165 GTCATGGAGCCTACCCCAAC 60.107 60.0 0.0 0.0 35.85 3.77 F
1677 1730 0.178990 GCCCTTCAACAAGTGTCCCT 60.179 55.0 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1043 1096 0.035630 GCAGCAGGGAGAGACAACAT 60.036 55.0 0.0 0.0 0.00 2.71 R
1758 1811 0.037326 GACTGCCGGTGAAGTGATCA 60.037 55.0 1.9 0.0 35.05 2.92 R
2686 2796 0.102663 GGCAAGTACTCCGTAGAGGC 59.897 60.0 0.0 0.0 45.11 4.70 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
123 124 0.548031 TGATTCCCTGGTCATGGAGC 59.452 55.000 0.00 0.00 30.91 4.70
124 125 0.179006 GATTCCCTGGTCATGGAGCC 60.179 60.000 0.00 0.00 30.91 4.70
125 126 0.625683 ATTCCCTGGTCATGGAGCCT 60.626 55.000 0.00 0.00 30.91 4.58
126 127 0.044092 TTCCCTGGTCATGGAGCCTA 59.956 55.000 0.00 0.00 30.91 3.93
127 128 0.691078 TCCCTGGTCATGGAGCCTAC 60.691 60.000 0.00 0.00 0.00 3.18
129 130 1.700042 CCTGGTCATGGAGCCTACCC 61.700 65.000 0.00 0.00 0.00 3.69
130 131 1.692749 TGGTCATGGAGCCTACCCC 60.693 63.158 0.00 0.00 0.00 4.95
132 133 1.279025 GGTCATGGAGCCTACCCCAA 61.279 60.000 0.00 0.00 35.85 4.12
133 134 0.107165 GTCATGGAGCCTACCCCAAC 60.107 60.000 0.00 0.00 35.85 3.77
135 136 0.625849 CATGGAGCCTACCCCAACTT 59.374 55.000 0.00 0.00 35.85 2.66
136 137 0.625849 ATGGAGCCTACCCCAACTTG 59.374 55.000 0.00 0.00 35.85 3.16
138 139 0.404426 GGAGCCTACCCCAACTTGTT 59.596 55.000 0.00 0.00 0.00 2.83
139 140 1.203013 GGAGCCTACCCCAACTTGTTT 60.203 52.381 0.00 0.00 0.00 2.83
140 141 1.886542 GAGCCTACCCCAACTTGTTTG 59.113 52.381 0.00 0.00 34.63 2.93
151 152 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
152 153 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
154 155 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
155 156 4.099419 ACTTGTTTGGGACTAAAGGCTTTG 59.901 41.667 22.32 13.97 0.00 2.77
156 157 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
158 159 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
159 160 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
160 161 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
161 162 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
165 166 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
167 168 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
281 293 5.300034 ACTTTCTGCACAAGTGATGATGAAA 59.700 36.000 4.04 5.65 33.04 2.69
313 325 5.185635 TGAAAAGCTAGCATACAAGGCAATT 59.814 36.000 18.83 0.00 0.00 2.32
381 393 5.316167 AGAATTGACCTGACATTGTTGCTA 58.684 37.500 0.00 0.00 0.00 3.49
412 424 1.912043 AGGAACTAGGAAGCATGCAGT 59.088 47.619 21.98 11.28 36.02 4.40
577 590 0.333312 TTGGTTGGTTGTCAGGGTGT 59.667 50.000 0.00 0.00 0.00 4.16
578 591 1.214217 TGGTTGGTTGTCAGGGTGTA 58.786 50.000 0.00 0.00 0.00 2.90
754 798 9.788889 TCATGCAATTGAGAATAGAGTATGATT 57.211 29.630 10.34 0.00 0.00 2.57
922 967 6.716628 TGCATTAGAGAAAACAATTGACTCCT 59.283 34.615 13.59 3.78 0.00 3.69
946 994 0.914644 CCCATGTCAGACATCCTGGT 59.085 55.000 13.53 0.00 43.12 4.00
953 1006 0.742281 CAGACATCCTGGTTCCTGCG 60.742 60.000 0.00 0.00 39.23 5.18
1033 1086 1.026718 GCCGCTGCTGGTTGTTATCT 61.027 55.000 11.14 0.00 33.53 1.98
1043 1096 4.744570 CTGGTTGTTATCTTCACGCTCTA 58.255 43.478 0.00 0.00 0.00 2.43
1107 1160 1.867233 GTGACTGTGGCACAACTACTG 59.133 52.381 22.31 11.13 44.16 2.74
1113 1166 2.854522 GGCACAACTACTGCCGATT 58.145 52.632 0.00 0.00 44.78 3.34
1341 1394 3.196207 ATGGAAGGCAGCGTGTGGT 62.196 57.895 0.00 0.00 0.00 4.16
1607 1660 0.765510 GGTGGGTGAAAGACCTCACT 59.234 55.000 0.00 0.00 45.33 3.41
1611 1664 1.416401 GGGTGAAAGACCTCACTGTGA 59.584 52.381 10.50 10.50 45.33 3.58
1677 1730 0.178990 GCCCTTCAACAAGTGTCCCT 60.179 55.000 0.00 0.00 0.00 4.20
1681 1734 2.422803 CCTTCAACAAGTGTCCCTTCCA 60.423 50.000 0.00 0.00 0.00 3.53
1738 1791 5.521010 TCCATCCGATTTCGTTACACATAAC 59.479 40.000 0.00 0.00 37.85 1.89
1739 1792 5.522460 CCATCCGATTTCGTTACACATAACT 59.478 40.000 0.00 0.00 38.89 2.24
1758 1811 7.776969 ACATAACTGGAATATCATCTTGCACTT 59.223 33.333 0.00 0.00 0.00 3.16
2402 2462 1.930908 ATCAAGGGGACGTCGTCGAC 61.931 60.000 18.61 15.51 40.62 4.20
2597 2657 2.512515 GGATGCTGGTGCGACCTC 60.513 66.667 6.83 0.88 43.34 3.85
2614 2674 5.873164 GCGACCTCAATTTAGTTCTCCTTTA 59.127 40.000 0.00 0.00 0.00 1.85
2633 2743 6.039382 TCCTTTACTTCTTTTCCTGTTGCTTC 59.961 38.462 0.00 0.00 0.00 3.86
2686 2796 1.715585 CCAATTGCTGGCGTCTACG 59.284 57.895 0.00 0.00 38.76 3.51
2709 2824 2.291190 CTCTACGGAGTACTTGCCTAGC 59.709 54.545 0.00 0.00 45.11 3.42
2721 2836 1.197812 TGCCTAGCTGCTCAATCAGA 58.802 50.000 4.91 0.00 36.19 3.27
2755 2870 0.536006 GACAAGTGGGCTCTGTGCTT 60.536 55.000 1.44 0.00 42.39 3.91
2756 2871 0.764890 ACAAGTGGGCTCTGTGCTTA 59.235 50.000 1.44 0.00 42.39 3.09
2757 2872 1.352352 ACAAGTGGGCTCTGTGCTTAT 59.648 47.619 1.44 0.00 42.39 1.73
2758 2873 1.741706 CAAGTGGGCTCTGTGCTTATG 59.258 52.381 1.44 0.00 42.39 1.90
2759 2874 0.987294 AGTGGGCTCTGTGCTTATGT 59.013 50.000 1.44 0.00 42.39 2.29
2760 2875 1.352352 AGTGGGCTCTGTGCTTATGTT 59.648 47.619 1.44 0.00 42.39 2.71
2761 2876 1.470098 GTGGGCTCTGTGCTTATGTTG 59.530 52.381 1.44 0.00 42.39 3.33
2762 2877 1.350684 TGGGCTCTGTGCTTATGTTGA 59.649 47.619 1.44 0.00 42.39 3.18
2763 2878 1.740025 GGGCTCTGTGCTTATGTTGAC 59.260 52.381 1.44 0.00 42.39 3.18
2764 2879 1.394917 GGCTCTGTGCTTATGTTGACG 59.605 52.381 1.44 0.00 42.39 4.35
2765 2880 2.337583 GCTCTGTGCTTATGTTGACGA 58.662 47.619 0.00 0.00 38.95 4.20
2766 2881 2.932614 GCTCTGTGCTTATGTTGACGAT 59.067 45.455 0.00 0.00 38.95 3.73
2767 2882 3.000724 GCTCTGTGCTTATGTTGACGATC 59.999 47.826 0.00 0.00 38.95 3.69
2768 2883 4.176271 CTCTGTGCTTATGTTGACGATCA 58.824 43.478 0.00 0.00 0.00 2.92
2769 2884 4.176271 TCTGTGCTTATGTTGACGATCAG 58.824 43.478 0.00 0.00 0.00 2.90
2770 2885 3.925379 TGTGCTTATGTTGACGATCAGT 58.075 40.909 0.00 0.00 0.00 3.41
2771 2886 3.679502 TGTGCTTATGTTGACGATCAGTG 59.320 43.478 0.00 0.00 0.00 3.66
2772 2887 3.679980 GTGCTTATGTTGACGATCAGTGT 59.320 43.478 0.00 0.00 0.00 3.55
2773 2888 4.152402 GTGCTTATGTTGACGATCAGTGTT 59.848 41.667 0.00 0.00 0.00 3.32
2774 2889 4.388773 TGCTTATGTTGACGATCAGTGTTC 59.611 41.667 0.00 0.00 0.00 3.18
2803 2918 3.307242 GGACGATCAGTGTGCTTATGTTC 59.693 47.826 0.00 0.00 0.00 3.18
2808 2923 3.138304 TCAGTGTGCTTATGTTCACCAC 58.862 45.455 0.00 0.00 32.51 4.16
2815 2930 2.554032 GCTTATGTTCACCACTGTGCTT 59.446 45.455 1.29 0.00 42.46 3.91
2828 2943 2.031682 ACTGTGCTTTGTGCTCGAAATC 60.032 45.455 0.00 0.00 43.37 2.17
2848 2963 5.552870 ATCGGGAATCTGTTATTGTAGCT 57.447 39.130 0.00 0.00 0.00 3.32
2923 3039 1.448922 GCTACCTCGAGCCGTCAGAT 61.449 60.000 6.99 0.00 36.38 2.90
2928 3044 4.899239 CGAGCCGTCAGATGCCCC 62.899 72.222 0.00 0.00 0.00 5.80
2955 3071 1.659794 GCGTGGCCAAGTCAACATT 59.340 52.632 20.23 0.00 0.00 2.71
2956 3072 0.031994 GCGTGGCCAAGTCAACATTT 59.968 50.000 20.23 0.00 0.00 2.32
2957 3073 1.537990 GCGTGGCCAAGTCAACATTTT 60.538 47.619 20.23 0.00 0.00 1.82
2958 3074 2.820330 CGTGGCCAAGTCAACATTTTT 58.180 42.857 7.24 0.00 0.00 1.94
2959 3075 2.794350 CGTGGCCAAGTCAACATTTTTC 59.206 45.455 7.24 0.00 0.00 2.29
2960 3076 2.794350 GTGGCCAAGTCAACATTTTTCG 59.206 45.455 7.24 0.00 0.00 3.46
2961 3077 2.690497 TGGCCAAGTCAACATTTTTCGA 59.310 40.909 0.61 0.00 0.00 3.71
2962 3078 3.049912 GGCCAAGTCAACATTTTTCGAC 58.950 45.455 0.00 0.00 0.00 4.20
2963 3079 3.490078 GGCCAAGTCAACATTTTTCGACA 60.490 43.478 0.00 0.00 0.00 4.35
2964 3080 4.109050 GCCAAGTCAACATTTTTCGACAA 58.891 39.130 0.00 0.00 0.00 3.18
2965 3081 4.564769 GCCAAGTCAACATTTTTCGACAAA 59.435 37.500 0.00 0.00 0.00 2.83
2966 3082 5.062809 GCCAAGTCAACATTTTTCGACAAAA 59.937 36.000 0.11 4.66 0.00 2.44
2967 3083 6.401581 GCCAAGTCAACATTTTTCGACAAAAA 60.402 34.615 0.11 0.00 43.92 1.94
3017 3135 2.795231 ACATCAGCAGCACTAACCAT 57.205 45.000 0.00 0.00 0.00 3.55
3020 3138 3.211865 CATCAGCAGCACTAACCATCAT 58.788 45.455 0.00 0.00 0.00 2.45
3022 3140 1.945394 CAGCAGCACTAACCATCATCC 59.055 52.381 0.00 0.00 0.00 3.51
3046 3164 6.920758 CCAAGACAACATCCGAAATACAAAAA 59.079 34.615 0.00 0.00 0.00 1.94
3070 3188 0.108585 TCTCCAAAAGCAACGCCTCT 59.891 50.000 0.00 0.00 0.00 3.69
3091 3209 6.239008 CCTCTAAGAAGGAAACAATGCACAAA 60.239 38.462 0.00 0.00 38.87 2.83
3130 3248 4.803452 TCAAAGATCTTGGGTTTTCACCT 58.197 39.130 9.17 0.00 43.65 4.00
3131 3249 4.584325 TCAAAGATCTTGGGTTTTCACCTG 59.416 41.667 9.17 0.00 43.65 4.00
3138 3257 3.611025 TGGGTTTTCACCTGGAGAAAT 57.389 42.857 17.97 0.00 43.65 2.17
3139 3258 4.733077 TGGGTTTTCACCTGGAGAAATA 57.267 40.909 17.97 8.25 43.65 1.40
3147 3266 8.360390 GTTTTCACCTGGAGAAATATTGAGTTT 58.640 33.333 17.97 0.00 35.17 2.66
3172 3291 4.344679 TCCAAGAACAATGCCTTCAACAAT 59.655 37.500 0.00 0.00 0.00 2.71
3174 3293 4.942761 AGAACAATGCCTTCAACAATGT 57.057 36.364 0.00 0.00 0.00 2.71
3181 3300 2.288948 TGCCTTCAACAATGTCATTGCC 60.289 45.455 22.79 6.01 43.98 4.52
3191 3310 2.949177 TGTCATTGCCAGGTACAACT 57.051 45.000 0.00 0.00 0.00 3.16
3251 3371 1.751924 GACTTGGTACTCGAGGAGCAT 59.248 52.381 29.03 16.29 32.04 3.79
3254 3374 2.073252 TGGTACTCGAGGAGCATCAT 57.927 50.000 25.35 0.00 36.25 2.45
3330 3450 1.949525 GTCACCAACACAATGAGCAGT 59.050 47.619 0.00 0.00 0.00 4.40
3348 3468 3.071312 GCAGTGGATCATCATCTTCTCCT 59.929 47.826 0.00 0.00 0.00 3.69
3353 3473 5.246656 GTGGATCATCATCTTCTCCTCATCT 59.753 44.000 0.00 0.00 0.00 2.90
3356 3476 8.342270 TGGATCATCATCTTCTCCTCATCTATA 58.658 37.037 0.00 0.00 0.00 1.31
3358 3478 9.412460 GATCATCATCTTCTCCTCATCTATAGT 57.588 37.037 0.00 0.00 0.00 2.12
3394 3514 4.023878 GGACATCCAGTGATAGTAGACGAC 60.024 50.000 0.00 0.00 35.64 4.34
3398 3518 2.544686 CCAGTGATAGTAGACGACCTCG 59.455 54.545 0.00 0.00 46.33 4.63
3438 3558 4.498345 CGAGATAACACCTTCAGAGCCTAC 60.498 50.000 0.00 0.00 0.00 3.18
3443 3563 2.499289 ACACCTTCAGAGCCTACTGATG 59.501 50.000 6.68 8.61 44.67 3.07
3484 3604 0.770166 TCCCCATGTCCACACCTTGA 60.770 55.000 0.00 0.00 0.00 3.02
3485 3605 0.112218 CCCCATGTCCACACCTTGAA 59.888 55.000 0.00 0.00 0.00 2.69
3486 3606 1.480312 CCCCATGTCCACACCTTGAAA 60.480 52.381 0.00 0.00 0.00 2.69
3497 3617 1.969923 CACCTTGAAAAATCAGGGCCA 59.030 47.619 6.18 0.00 40.11 5.36
3501 3621 2.323999 TGAAAAATCAGGGCCATGGT 57.676 45.000 18.94 7.72 0.00 3.55
3530 3650 1.883021 CCGATGTTTCCAAGGTGGC 59.117 57.895 0.00 0.00 37.47 5.01
3540 3660 0.606401 CCAAGGTGGCGACAATCTGT 60.606 55.000 0.00 0.00 46.06 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 131 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
132 133 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
133 134 4.099419 ACAAAGCCTTTAGTCCCAAACAAG 59.901 41.667 0.00 0.00 0.00 3.16
135 136 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
136 137 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
138 139 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
139 140 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
140 141 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
141 142 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
142 143 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
143 144 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
144 145 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
145 146 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
146 147 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
147 148 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
148 149 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
149 150 3.666638 GCAACAACAACAACAACAAAGCC 60.667 43.478 0.00 0.00 0.00 4.35
150 151 3.186205 AGCAACAACAACAACAACAAAGC 59.814 39.130 0.00 0.00 0.00 3.51
151 152 4.447054 TCAGCAACAACAACAACAACAAAG 59.553 37.500 0.00 0.00 0.00 2.77
152 153 4.210120 GTCAGCAACAACAACAACAACAAA 59.790 37.500 0.00 0.00 0.00 2.83
154 155 3.005261 AGTCAGCAACAACAACAACAACA 59.995 39.130 0.00 0.00 0.00 3.33
155 156 3.574614 AGTCAGCAACAACAACAACAAC 58.425 40.909 0.00 0.00 0.00 3.32
156 157 3.932545 AGTCAGCAACAACAACAACAA 57.067 38.095 0.00 0.00 0.00 2.83
158 159 3.730715 GCATAGTCAGCAACAACAACAAC 59.269 43.478 0.00 0.00 0.00 3.32
159 160 3.379688 TGCATAGTCAGCAACAACAACAA 59.620 39.130 0.00 0.00 39.39 2.83
160 161 2.948315 TGCATAGTCAGCAACAACAACA 59.052 40.909 0.00 0.00 39.39 3.33
161 162 3.003689 ACTGCATAGTCAGCAACAACAAC 59.996 43.478 0.00 0.00 42.17 3.32
165 166 4.641396 ACTTACTGCATAGTCAGCAACAA 58.359 39.130 0.00 0.00 42.17 2.83
167 168 5.411781 ACTACTTACTGCATAGTCAGCAAC 58.588 41.667 0.00 0.00 42.17 4.17
281 293 6.467677 TGTATGCTAGCTTTTCAAGAGAAGT 58.532 36.000 17.23 0.00 34.71 3.01
313 325 4.019411 TGTGAGTCTGAAGCCCAATATTCA 60.019 41.667 0.00 0.00 34.41 2.57
381 393 4.477536 TCCTAGTTCCTATCTCAGCCAT 57.522 45.455 0.00 0.00 0.00 4.40
412 424 2.287909 CGTTTTTCCGCTCCAATCCAAA 60.288 45.455 0.00 0.00 0.00 3.28
577 590 9.837681 TTCTACCCCTCTTATGATCAACATATA 57.162 33.333 0.00 0.00 40.56 0.86
578 591 8.742125 TTCTACCCCTCTTATGATCAACATAT 57.258 34.615 0.00 0.00 40.56 1.78
819 863 9.734984 ATTCATAGTGATATCATCTCAATTGCA 57.265 29.630 9.02 0.00 0.00 4.08
922 967 3.389002 CAGGATGTCTGACATGGGTATGA 59.611 47.826 26.71 0.00 46.18 2.15
946 994 1.301716 GACCTCAGCAACGCAGGAA 60.302 57.895 0.00 0.00 0.00 3.36
953 1006 1.961277 CACCCGTGACCTCAGCAAC 60.961 63.158 0.00 0.00 0.00 4.17
1029 1082 5.590663 AGAGACAACATAGAGCGTGAAGATA 59.409 40.000 0.00 0.00 0.00 1.98
1033 1086 3.119459 GGAGAGACAACATAGAGCGTGAA 60.119 47.826 0.00 0.00 0.00 3.18
1043 1096 0.035630 GCAGCAGGGAGAGACAACAT 60.036 55.000 0.00 0.00 0.00 2.71
1080 1133 1.137282 TGTGCCACAGTCACGTTCTTA 59.863 47.619 0.00 0.00 37.26 2.10
1113 1166 3.301070 CCCCCATGGTACGACGAA 58.699 61.111 11.73 0.00 0.00 3.85
1346 1399 3.825160 AACAGCGTCACCGTGCCAT 62.825 57.895 0.00 0.00 36.15 4.40
1607 1660 1.877637 CATTGTTCTGTCCGGTCACA 58.122 50.000 0.00 0.00 0.00 3.58
1611 1664 0.038166 ATGGCATTGTTCTGTCCGGT 59.962 50.000 0.00 0.00 0.00 5.28
1738 1791 6.485648 TGATCAAGTGCAAGATGATATTCCAG 59.514 38.462 9.39 0.00 34.10 3.86
1739 1792 6.261603 GTGATCAAGTGCAAGATGATATTCCA 59.738 38.462 0.00 2.75 34.10 3.53
1758 1811 0.037326 GACTGCCGGTGAAGTGATCA 60.037 55.000 1.90 0.00 35.05 2.92
2170 2223 0.889186 GTGCCCACGAAGGTCATGTT 60.889 55.000 0.00 0.00 34.66 2.71
2566 2626 3.067742 CCAGCATCCACCAGAATCAAATC 59.932 47.826 0.00 0.00 0.00 2.17
2614 2674 3.541632 TCGAAGCAACAGGAAAAGAAGT 58.458 40.909 0.00 0.00 0.00 3.01
2633 2743 1.512364 CGCACACACACAAAACATTCG 59.488 47.619 0.00 0.00 0.00 3.34
2680 2790 1.864082 GTACTCCGTAGAGGCGTAGAC 59.136 57.143 0.00 0.00 45.11 2.59
2681 2791 1.759445 AGTACTCCGTAGAGGCGTAGA 59.241 52.381 0.00 0.00 45.11 2.59
2682 2792 2.237393 AGTACTCCGTAGAGGCGTAG 57.763 55.000 0.00 0.00 45.11 3.51
2683 2793 2.283298 CAAGTACTCCGTAGAGGCGTA 58.717 52.381 0.00 0.00 45.11 4.42
2684 2794 1.093159 CAAGTACTCCGTAGAGGCGT 58.907 55.000 0.00 0.00 45.11 5.68
2685 2795 0.248539 GCAAGTACTCCGTAGAGGCG 60.249 60.000 0.00 0.00 45.11 5.52
2686 2796 0.102663 GGCAAGTACTCCGTAGAGGC 59.897 60.000 0.00 0.00 45.11 4.70
2687 2797 1.765230 AGGCAAGTACTCCGTAGAGG 58.235 55.000 0.00 0.00 45.11 3.69
2688 2798 2.291190 GCTAGGCAAGTACTCCGTAGAG 59.709 54.545 19.32 6.78 46.36 2.43
2709 2824 3.500558 TCGAGTTCTCTGATTGAGCAG 57.499 47.619 0.00 0.00 42.38 4.24
2721 2836 2.814919 ACTTGTCAGACGATCGAGTTCT 59.185 45.455 24.34 11.71 0.00 3.01
2726 2841 0.526211 CCCACTTGTCAGACGATCGA 59.474 55.000 24.34 0.00 0.00 3.59
2755 2870 7.275560 CACATAAGAACACTGATCGTCAACATA 59.724 37.037 0.00 0.00 0.00 2.29
2756 2871 6.091305 CACATAAGAACACTGATCGTCAACAT 59.909 38.462 0.00 0.00 0.00 2.71
2757 2872 5.405269 CACATAAGAACACTGATCGTCAACA 59.595 40.000 0.00 0.00 0.00 3.33
2758 2873 5.163953 CCACATAAGAACACTGATCGTCAAC 60.164 44.000 0.00 0.00 0.00 3.18
2759 2874 4.929211 CCACATAAGAACACTGATCGTCAA 59.071 41.667 0.00 0.00 0.00 3.18
2760 2875 4.219725 TCCACATAAGAACACTGATCGTCA 59.780 41.667 0.00 0.00 0.00 4.35
2761 2876 4.563184 GTCCACATAAGAACACTGATCGTC 59.437 45.833 0.00 0.00 0.00 4.20
2762 2877 4.495422 GTCCACATAAGAACACTGATCGT 58.505 43.478 0.00 0.00 0.00 3.73
2763 2878 3.547868 CGTCCACATAAGAACACTGATCG 59.452 47.826 0.00 0.00 0.00 3.69
2764 2879 4.744570 TCGTCCACATAAGAACACTGATC 58.255 43.478 0.00 0.00 0.00 2.92
2765 2880 4.801330 TCGTCCACATAAGAACACTGAT 57.199 40.909 0.00 0.00 0.00 2.90
2766 2881 4.219725 TGATCGTCCACATAAGAACACTGA 59.780 41.667 0.00 0.00 0.00 3.41
2767 2882 4.494484 TGATCGTCCACATAAGAACACTG 58.506 43.478 0.00 0.00 0.00 3.66
2768 2883 4.220821 ACTGATCGTCCACATAAGAACACT 59.779 41.667 0.00 0.00 0.00 3.55
2769 2884 4.327357 CACTGATCGTCCACATAAGAACAC 59.673 45.833 0.00 0.00 0.00 3.32
2770 2885 4.021456 ACACTGATCGTCCACATAAGAACA 60.021 41.667 0.00 0.00 0.00 3.18
2771 2886 4.327357 CACACTGATCGTCCACATAAGAAC 59.673 45.833 0.00 0.00 0.00 3.01
2772 2887 4.494484 CACACTGATCGTCCACATAAGAA 58.506 43.478 0.00 0.00 0.00 2.52
2773 2888 3.676049 GCACACTGATCGTCCACATAAGA 60.676 47.826 0.00 0.00 0.00 2.10
2774 2889 2.604914 GCACACTGATCGTCCACATAAG 59.395 50.000 0.00 0.00 0.00 1.73
2815 2930 2.006888 GATTCCCGATTTCGAGCACAA 58.993 47.619 0.67 0.00 43.02 3.33
2828 2943 4.747108 CAGAGCTACAATAACAGATTCCCG 59.253 45.833 0.00 0.00 0.00 5.14
2848 2963 0.603065 ATGCGTCACTACAGTGCAGA 59.397 50.000 4.43 0.00 45.25 4.26
2939 3055 2.794350 CGAAAAATGTTGACTTGGCCAC 59.206 45.455 3.88 0.00 0.00 5.01
2940 3056 2.690497 TCGAAAAATGTTGACTTGGCCA 59.310 40.909 0.00 0.00 0.00 5.36
2941 3057 3.049912 GTCGAAAAATGTTGACTTGGCC 58.950 45.455 0.00 0.00 0.00 5.36
2979 3095 9.358872 GCTGATGTAATTGATATCTTCACGATA 57.641 33.333 3.98 0.00 38.88 2.92
2980 3096 7.874528 TGCTGATGTAATTGATATCTTCACGAT 59.125 33.333 3.98 0.00 32.84 3.73
2981 3097 7.209475 TGCTGATGTAATTGATATCTTCACGA 58.791 34.615 3.98 0.00 32.84 4.35
2982 3098 7.412137 TGCTGATGTAATTGATATCTTCACG 57.588 36.000 3.98 0.00 32.84 4.35
2983 3099 7.041576 TGCTGCTGATGTAATTGATATCTTCAC 60.042 37.037 3.98 0.00 32.84 3.18
2984 3100 6.993902 TGCTGCTGATGTAATTGATATCTTCA 59.006 34.615 3.98 0.00 0.00 3.02
2985 3101 7.172875 AGTGCTGCTGATGTAATTGATATCTTC 59.827 37.037 3.98 0.00 0.00 2.87
2986 3102 6.996879 AGTGCTGCTGATGTAATTGATATCTT 59.003 34.615 3.98 0.00 0.00 2.40
2987 3103 6.531923 AGTGCTGCTGATGTAATTGATATCT 58.468 36.000 3.98 0.00 0.00 1.98
2988 3104 6.798315 AGTGCTGCTGATGTAATTGATATC 57.202 37.500 0.00 0.00 0.00 1.63
2989 3105 7.173907 GGTTAGTGCTGCTGATGTAATTGATAT 59.826 37.037 0.00 0.00 0.00 1.63
2990 3106 6.483307 GGTTAGTGCTGCTGATGTAATTGATA 59.517 38.462 0.00 0.00 0.00 2.15
2995 3111 4.220693 TGGTTAGTGCTGCTGATGTAAT 57.779 40.909 0.00 0.00 0.00 1.89
2997 3113 3.197549 TGATGGTTAGTGCTGCTGATGTA 59.802 43.478 0.00 0.00 0.00 2.29
3017 3135 3.694043 TTCGGATGTTGTCTTGGATGA 57.306 42.857 0.00 0.00 0.00 2.92
3020 3138 4.900684 TGTATTTCGGATGTTGTCTTGGA 58.099 39.130 0.00 0.00 0.00 3.53
3022 3140 7.922505 TTTTTGTATTTCGGATGTTGTCTTG 57.077 32.000 0.00 0.00 0.00 3.02
3046 3164 1.067060 GCGTTGCTTTTGGAGAACCTT 59.933 47.619 0.00 0.00 37.04 3.50
3070 3188 5.163602 ACGTTTGTGCATTGTTTCCTTCTTA 60.164 36.000 0.00 0.00 0.00 2.10
3110 3228 3.897505 CCAGGTGAAAACCCAAGATCTTT 59.102 43.478 4.86 0.00 0.00 2.52
3130 3248 9.973661 TTCTTGGATAAACTCAATATTTCTCCA 57.026 29.630 1.65 1.65 39.33 3.86
3138 3257 7.615365 AGGCATTGTTCTTGGATAAACTCAATA 59.385 33.333 0.00 0.00 0.00 1.90
3139 3258 6.438425 AGGCATTGTTCTTGGATAAACTCAAT 59.562 34.615 0.00 0.00 0.00 2.57
3147 3266 5.076182 TGTTGAAGGCATTGTTCTTGGATA 58.924 37.500 0.00 0.00 0.00 2.59
3154 3273 4.619973 TGACATTGTTGAAGGCATTGTTC 58.380 39.130 0.00 0.00 32.69 3.18
3172 3291 2.949177 AGTTGTACCTGGCAATGACA 57.051 45.000 0.00 0.00 0.00 3.58
3174 3293 6.601613 CCTTTATTAGTTGTACCTGGCAATGA 59.398 38.462 0.00 0.00 0.00 2.57
3181 3300 5.585047 GTCTGGCCTTTATTAGTTGTACCTG 59.415 44.000 3.32 0.00 0.00 4.00
3235 3355 1.957177 GATGATGCTCCTCGAGTACCA 59.043 52.381 12.31 5.18 31.39 3.25
3251 3371 3.760151 CTGGAGGACTGCATTTTTGATGA 59.240 43.478 0.00 0.00 0.00 2.92
3254 3374 2.886523 CACTGGAGGACTGCATTTTTGA 59.113 45.455 0.00 0.00 0.00 2.69
3302 3422 0.814457 TGTGTTGGTGACTTGCAACC 59.186 50.000 0.00 0.00 31.36 3.77
3330 3450 5.404395 AGATGAGGAGAAGATGATGATCCA 58.596 41.667 0.00 0.00 32.21 3.41
3348 3468 5.222151 CCCAGGGAGTACTCACTATAGATGA 60.222 48.000 26.99 5.87 42.42 2.92
3353 3473 3.789840 TGTCCCAGGGAGTACTCACTATA 59.210 47.826 26.99 12.61 42.42 1.31
3356 3476 0.784495 TGTCCCAGGGAGTACTCACT 59.216 55.000 22.35 22.35 45.87 3.41
3358 3478 1.343075 GGATGTCCCAGGGAGTACTCA 60.343 57.143 23.91 2.77 29.39 3.41
3380 3500 3.456280 AGTCGAGGTCGTCTACTATCAC 58.544 50.000 0.00 0.00 40.80 3.06
3381 3501 3.131755 TGAGTCGAGGTCGTCTACTATCA 59.868 47.826 0.00 0.00 37.82 2.15
3438 3558 0.790207 CGGTCGTGGTTGAACATCAG 59.210 55.000 0.00 0.00 0.00 2.90
3443 3563 1.890510 AAGGCGGTCGTGGTTGAAC 60.891 57.895 0.00 0.00 0.00 3.18
3484 3604 1.278537 CCACCATGGCCCTGATTTTT 58.721 50.000 13.04 0.00 0.00 1.94
3485 3605 0.116940 ACCACCATGGCCCTGATTTT 59.883 50.000 13.04 0.00 42.67 1.82
3486 3606 0.615544 CACCACCATGGCCCTGATTT 60.616 55.000 13.04 0.00 42.67 2.17
3501 3621 1.184322 AAACATCGGCATTGGCACCA 61.184 50.000 11.10 0.00 43.71 4.17
3508 3628 1.545582 CACCTTGGAAACATCGGCATT 59.454 47.619 0.00 0.00 42.32 3.56
3530 3650 9.734063 TTGGTGATTGTCAACAACAGATTGTCG 62.734 40.741 6.34 0.00 46.02 4.35


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

AutoCloner maintained by Alex Coulton.