Multiple sequence alignment - TraesCS3B01G315600

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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 TraesCS3B01G315600 chr3B 100.000 3079 0 0 1 3079 507285480 507288558 0.000000e+00 5686.0
1 TraesCS3B01G315600 chr3B 86.432 199 19 4 2882 3079 254193186 254192995 8.650000e-51 211.0
2 TraesCS3B01G315600 chr3B 86.070 201 20 4 2880 3079 755478482 755478675 3.110000e-50 209.0
3 TraesCS3B01G315600 chr3B 86.325 117 12 4 1464 1578 525242494 525242380 1.160000e-24 124.0
4 TraesCS3B01G315600 chr3D 92.252 2749 110 39 1 2705 390040705 390043394 0.000000e+00 3801.0
5 TraesCS3B01G315600 chr3D 91.667 264 12 6 2822 3079 390043396 390043655 1.050000e-94 357.0
6 TraesCS3B01G315600 chr3D 86.082 194 19 5 2885 3077 565051682 565051496 5.210000e-48 202.0
7 TraesCS3B01G315600 chr3D 95.161 124 6 0 2705 2828 7308173 7308050 2.420000e-46 196.0
8 TraesCS3B01G315600 chr3D 86.325 117 12 4 1464 1578 399380487 399380373 1.160000e-24 124.0
9 TraesCS3B01G315600 chr3A 93.149 2058 86 26 202 2227 510662966 510665000 0.000000e+00 2968.0
10 TraesCS3B01G315600 chr3A 91.165 498 31 5 2218 2706 510665194 510665687 0.000000e+00 664.0
11 TraesCS3B01G315600 chr3A 91.923 260 15 6 2820 3076 510665686 510665942 2.920000e-95 359.0
12 TraesCS3B01G315600 chr3A 93.636 220 10 1 1 216 510662731 510662950 2.960000e-85 326.0
13 TraesCS3B01G315600 chr3A 94.262 122 7 0 2702 2823 702912137 702912258 1.460000e-43 187.0
14 TraesCS3B01G315600 chr3A 85.470 117 13 4 1464 1578 518642731 518642617 5.390000e-23 119.0
15 TraesCS3B01G315600 chr6D 88.623 167 19 0 2880 3046 472495712 472495878 1.450000e-48 204.0
16 TraesCS3B01G315600 chr6D 94.309 123 7 0 2699 2821 430998458 430998580 4.050000e-44 189.0
17 TraesCS3B01G315600 chr6B 85.572 201 20 4 2880 3079 628238925 628238733 5.210000e-48 202.0
18 TraesCS3B01G315600 chr4B 88.166 169 19 1 2880 3047 648268334 648268166 1.870000e-47 200.0
19 TraesCS3B01G315600 chr4B 90.580 138 11 2 2700 2836 572163159 572163023 6.780000e-42 182.0
20 TraesCS3B01G315600 chr7B 88.095 168 19 1 2880 3046 715716847 715717014 6.730000e-47 198.0
21 TraesCS3B01G315600 chr7B 92.188 128 10 0 2694 2821 263793420 263793547 6.780000e-42 182.0
22 TraesCS3B01G315600 chr7B 92.248 129 9 1 2695 2822 534546472 534546600 6.780000e-42 182.0
23 TraesCS3B01G315600 chr7B 91.473 129 11 0 2694 2822 271297960 271298088 8.770000e-41 178.0
24 TraesCS3B01G315600 chr7B 86.928 153 16 4 2670 2821 743210334 743210185 5.280000e-38 169.0
25 TraesCS3B01G315600 chr2D 95.902 122 5 0 2701 2822 263476601 263476480 6.730000e-47 198.0
26 TraesCS3B01G315600 chr7A 93.284 134 8 1 2690 2822 736543749 736543616 2.420000e-46 196.0
27 TraesCS3B01G315600 chr1B 93.284 134 8 1 2690 2822 623107046 623107179 2.420000e-46 196.0
28 TraesCS3B01G315600 chr1B 84.071 113 17 1 1466 1578 385296796 385296907 1.170000e-19 108.0
29 TraesCS3B01G315600 chr1B 90.323 62 5 1 1217 1278 670202734 670202794 2.550000e-11 80.5
30 TraesCS3B01G315600 chr1A 93.284 134 8 1 2690 2822 320509467 320509600 2.420000e-46 196.0
31 TraesCS3B01G315600 chr1A 84.071 113 17 1 1466 1578 355343728 355343839 1.170000e-19 108.0
32 TraesCS3B01G315600 chr5D 94.915 118 6 0 2705 2822 439217745 439217628 5.240000e-43 185.0
33 TraesCS3B01G315600 chr1D 84.071 113 17 1 1466 1578 283617844 283617955 1.170000e-19 108.0
34 TraesCS3B01G315600 chr1D 92.857 56 4 0 1229 1284 481603266 481603321 7.080000e-12 82.4
35 TraesCS3B01G315600 chr2B 90.566 53 3 2 1233 1284 648653128 648653077 5.510000e-08 69.4
36 TraesCS3B01G315600 chr2A 90.566 53 3 2 1233 1284 686214670 686214619 5.510000e-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 TraesCS3B01G315600 chr3B 507285480 507288558 3078 False 5686.00 5686 100.00000 1 3079 1 chr3B.!!$F1 3078
1 TraesCS3B01G315600 chr3D 390040705 390043655 2950 False 2079.00 3801 91.95950 1 3079 2 chr3D.!!$F1 3078
2 TraesCS3B01G315600 chr3A 510662731 510665942 3211 False 1079.25 2968 92.46825 1 3076 4 chr3A.!!$F2 3075

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
890 949 0.179 GTGGCATCGATCCAAGGAGT 59.821 55.0 15.34 0.0 35.01 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2709 3005 0.030369 CGAGTATTTCCGGACGGAGG 59.97 60.0 13.64 0.0 46.06 4.3 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
104 109 2.750888 GCGATGGCTGAACGGGTTC 61.751 63.158 4.63 4.63 39.91 3.62
120 125 6.613755 ACGGGTTCGAATAATCCATTAAAG 57.386 37.500 0.00 0.00 40.11 1.85
302 341 5.305128 TCATTGTTTCTCCTCCAAGCAAAAT 59.695 36.000 0.00 0.00 29.22 1.82
345 386 5.192927 CAGAATTACCATGCCCTTTACTGA 58.807 41.667 0.00 0.00 0.00 3.41
347 388 5.829924 AGAATTACCATGCCCTTTACTGATG 59.170 40.000 0.00 0.00 0.00 3.07
348 389 2.442236 ACCATGCCCTTTACTGATGG 57.558 50.000 0.00 0.00 39.66 3.51
349 390 1.035139 CCATGCCCTTTACTGATGGC 58.965 55.000 0.00 0.00 44.27 4.40
370 412 4.884164 GGCCATGTAGCTGAAAATTCTACT 59.116 41.667 0.00 0.00 35.10 2.57
372 414 6.017852 GGCCATGTAGCTGAAAATTCTACTAC 60.018 42.308 0.00 14.15 37.09 2.73
440 482 1.152567 CCTTTCAACCACCCCTGCA 60.153 57.895 0.00 0.00 0.00 4.41
489 532 2.402787 GTCTACTCGCCGGTCGAC 59.597 66.667 15.44 7.13 43.16 4.20
543 586 7.171630 TGACTGATAGATGAGATGATGATGG 57.828 40.000 0.00 0.00 0.00 3.51
614 659 2.261361 CCGTCACACGCTGGATCA 59.739 61.111 0.00 0.00 40.91 2.92
771 823 1.200483 GTCACGACGGCACATGATAG 58.800 55.000 0.00 0.00 0.00 2.08
889 948 0.533755 GGTGGCATCGATCCAAGGAG 60.534 60.000 15.34 0.00 35.01 3.69
890 949 0.179000 GTGGCATCGATCCAAGGAGT 59.821 55.000 15.34 0.00 35.01 3.85
891 950 1.412710 GTGGCATCGATCCAAGGAGTA 59.587 52.381 15.34 0.00 35.01 2.59
1359 1423 1.076777 CCTGGATTGGGACGGCATT 60.077 57.895 0.00 0.00 0.00 3.56
1363 1427 1.341877 TGGATTGGGACGGCATTCAAT 60.342 47.619 3.83 3.83 33.17 2.57
1369 1433 2.092158 TGGGACGGCATTCAATGGATTA 60.092 45.455 0.00 0.00 0.00 1.75
1370 1434 2.293399 GGGACGGCATTCAATGGATTAC 59.707 50.000 0.00 0.00 0.00 1.89
1383 1447 5.183713 TCAATGGATTACAGTTTGCTTCCTG 59.816 40.000 0.00 0.00 34.82 3.86
1387 1451 4.702131 GGATTACAGTTTGCTTCCTGTGAT 59.298 41.667 11.38 9.16 41.77 3.06
1391 1455 4.012374 ACAGTTTGCTTCCTGTGATATGG 58.988 43.478 2.60 0.00 40.30 2.74
1397 1461 2.615912 GCTTCCTGTGATATGGTCTTGC 59.384 50.000 0.00 0.00 0.00 4.01
1415 1479 0.458543 GCGCTCTTCGATTGAGTCCA 60.459 55.000 0.00 0.00 41.67 4.02
1416 1480 1.804372 GCGCTCTTCGATTGAGTCCAT 60.804 52.381 0.00 0.00 41.67 3.41
1441 1505 0.036732 TGGCGAGGTTTGCTGATCTT 59.963 50.000 0.00 0.00 0.00 2.40
1442 1506 0.729690 GGCGAGGTTTGCTGATCTTC 59.270 55.000 0.00 0.00 0.00 2.87
1458 1522 5.518812 TGATCTTCGTTTGGTGTTCAATTG 58.481 37.500 0.00 0.00 34.98 2.32
1670 1737 2.187946 CCCGAGCCAGCGAAATCT 59.812 61.111 0.00 0.00 0.00 2.40
1860 1927 0.388520 GCCCATGTTCTTCGGCAAAC 60.389 55.000 3.79 0.00 41.25 2.93
2125 2199 3.068732 CAGGTCTCCAATAAGATCGAGCA 59.931 47.826 2.38 0.00 31.36 4.26
2175 2253 3.378742 TCTCTTGCGCTTTTGTTGGTTAA 59.621 39.130 9.73 0.00 0.00 2.01
2176 2254 4.037446 TCTCTTGCGCTTTTGTTGGTTAAT 59.963 37.500 9.73 0.00 0.00 1.40
2177 2255 4.688021 TCTTGCGCTTTTGTTGGTTAATT 58.312 34.783 9.73 0.00 0.00 1.40
2178 2256 5.833082 TCTTGCGCTTTTGTTGGTTAATTA 58.167 33.333 9.73 0.00 0.00 1.40
2194 2272 8.617290 TGGTTAATTAGTTTTCTCACCTTCTC 57.383 34.615 1.55 0.00 0.00 2.87
2229 2510 8.607459 CCTTCTTTTACTCATACATTAGCACAG 58.393 37.037 0.00 0.00 0.00 3.66
2255 2537 7.855375 AGAAGAATCTGAGACATTACCATTGA 58.145 34.615 0.00 0.00 33.59 2.57
2278 2560 7.919690 TGAACATATTGATTGGACGAGAAATC 58.080 34.615 0.00 0.00 34.11 2.17
2286 2568 0.249114 GGACGAGAAATCGAGAGGGC 60.249 60.000 4.44 0.00 36.85 5.19
2292 2574 3.712187 GAGAAATCGAGAGGGCTACAAG 58.288 50.000 0.00 0.00 0.00 3.16
2367 2657 1.954528 CGGTCGCCGGTAGATACAT 59.045 57.895 1.90 0.00 44.15 2.29
2378 2674 7.710044 TCGCCGGTAGATACATACAAATAAAAA 59.290 33.333 1.90 0.00 0.00 1.94
2419 2715 4.818534 TCTTCAACTTTTGCACTGCTAG 57.181 40.909 1.98 0.24 0.00 3.42
2420 2716 4.199310 TCTTCAACTTTTGCACTGCTAGT 58.801 39.130 1.98 0.85 0.00 2.57
2421 2717 5.364778 TCTTCAACTTTTGCACTGCTAGTA 58.635 37.500 1.98 0.00 0.00 1.82
2422 2718 5.236478 TCTTCAACTTTTGCACTGCTAGTAC 59.764 40.000 1.98 0.00 0.00 2.73
2423 2719 4.447290 TCAACTTTTGCACTGCTAGTACA 58.553 39.130 1.98 0.00 0.00 2.90
2424 2720 5.063204 TCAACTTTTGCACTGCTAGTACAT 58.937 37.500 1.98 0.00 0.00 2.29
2425 2721 5.530915 TCAACTTTTGCACTGCTAGTACATT 59.469 36.000 1.98 0.00 0.00 2.71
2426 2722 6.708502 TCAACTTTTGCACTGCTAGTACATTA 59.291 34.615 1.98 0.00 0.00 1.90
2473 2769 4.248691 TCATGACGCATGAAGAGGATAG 57.751 45.455 16.67 0.00 46.17 2.08
2506 2802 2.094675 CATGGCGGTGGAAATCTTTCT 58.905 47.619 2.93 0.00 37.35 2.52
2545 2841 4.180057 GTCAAGCACTCTGAATCCTACTG 58.820 47.826 0.00 0.00 0.00 2.74
2689 2985 9.743581 TGCAAATGTACTATATGATCAATCCAT 57.256 29.630 0.00 0.00 0.00 3.41
2710 3006 8.990163 TCCATTGGAACTAATTTAATACTCCC 57.010 34.615 1.94 0.00 0.00 4.30
2711 3007 8.787818 TCCATTGGAACTAATTTAATACTCCCT 58.212 33.333 1.94 0.00 0.00 4.20
2712 3008 9.067986 CCATTGGAACTAATTTAATACTCCCTC 57.932 37.037 0.00 0.00 0.00 4.30
2713 3009 9.067986 CATTGGAACTAATTTAATACTCCCTCC 57.932 37.037 0.00 0.00 0.00 4.30
2714 3010 6.823497 TGGAACTAATTTAATACTCCCTCCG 58.177 40.000 0.00 0.00 0.00 4.63
2715 3011 6.384886 TGGAACTAATTTAATACTCCCTCCGT 59.615 38.462 0.00 0.00 0.00 4.69
2716 3012 6.927936 GGAACTAATTTAATACTCCCTCCGTC 59.072 42.308 0.00 0.00 0.00 4.79
2717 3013 6.416631 ACTAATTTAATACTCCCTCCGTCC 57.583 41.667 0.00 0.00 0.00 4.79
2718 3014 4.332428 AATTTAATACTCCCTCCGTCCG 57.668 45.455 0.00 0.00 0.00 4.79
2719 3015 1.696063 TTAATACTCCCTCCGTCCGG 58.304 55.000 0.00 0.00 0.00 5.14
2720 3016 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
2721 3017 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2722 3018 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2723 3019 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2724 3020 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2725 3021 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2726 3022 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2727 3023 0.388294 CCCTCCGTCCGGAAATACTC 59.612 60.000 5.23 0.00 44.66 2.59
2728 3024 0.030369 CCTCCGTCCGGAAATACTCG 59.970 60.000 5.23 3.90 44.66 4.18
2729 3025 0.737219 CTCCGTCCGGAAATACTCGT 59.263 55.000 5.23 0.00 44.66 4.18
2730 3026 0.734889 TCCGTCCGGAAATACTCGTC 59.265 55.000 5.23 0.00 42.05 4.20
2731 3027 0.590732 CCGTCCGGAAATACTCGTCG 60.591 60.000 5.23 1.25 37.50 5.12
2732 3028 0.590732 CGTCCGGAAATACTCGTCGG 60.591 60.000 5.23 0.00 41.80 4.79
2733 3029 0.734889 GTCCGGAAATACTCGTCGGA 59.265 55.000 5.23 0.00 46.06 4.55
2734 3030 1.019673 TCCGGAAATACTCGTCGGAG 58.980 55.000 0.00 0.00 43.84 4.63
2735 3031 0.030369 CCGGAAATACTCGTCGGAGG 59.970 60.000 0.00 0.00 44.93 4.30
2736 3032 1.019673 CGGAAATACTCGTCGGAGGA 58.980 55.000 0.00 0.00 44.93 3.71
2737 3033 1.402968 CGGAAATACTCGTCGGAGGAA 59.597 52.381 1.73 0.00 44.93 3.36
2738 3034 2.034305 CGGAAATACTCGTCGGAGGAAT 59.966 50.000 1.73 0.00 44.93 3.01
2739 3035 3.490419 CGGAAATACTCGTCGGAGGAATT 60.490 47.826 1.73 0.00 44.93 2.17
2740 3036 3.802685 GGAAATACTCGTCGGAGGAATTG 59.197 47.826 1.73 0.00 44.93 2.32
2741 3037 4.441079 GGAAATACTCGTCGGAGGAATTGA 60.441 45.833 1.73 0.00 44.93 2.57
2742 3038 4.939052 AATACTCGTCGGAGGAATTGAT 57.061 40.909 1.73 0.00 44.93 2.57
2743 3039 2.586258 ACTCGTCGGAGGAATTGATG 57.414 50.000 1.73 0.00 44.93 3.07
2744 3040 1.825474 ACTCGTCGGAGGAATTGATGT 59.175 47.619 1.73 0.00 44.93 3.06
2745 3041 3.021695 ACTCGTCGGAGGAATTGATGTA 58.978 45.455 1.73 0.00 44.93 2.29
2746 3042 3.637229 ACTCGTCGGAGGAATTGATGTAT 59.363 43.478 1.73 0.00 44.93 2.29
2747 3043 4.230657 CTCGTCGGAGGAATTGATGTATC 58.769 47.826 1.73 0.00 36.61 2.24
2748 3044 3.889538 TCGTCGGAGGAATTGATGTATCT 59.110 43.478 0.00 0.00 0.00 1.98
2749 3045 5.067954 TCGTCGGAGGAATTGATGTATCTA 58.932 41.667 0.00 0.00 0.00 1.98
2750 3046 5.181433 TCGTCGGAGGAATTGATGTATCTAG 59.819 44.000 0.00 0.00 0.00 2.43
2751 3047 5.181433 CGTCGGAGGAATTGATGTATCTAGA 59.819 44.000 0.00 0.00 0.00 2.43
2752 3048 6.127869 CGTCGGAGGAATTGATGTATCTAGAT 60.128 42.308 10.73 10.73 0.00 1.98
2753 3049 7.032580 GTCGGAGGAATTGATGTATCTAGATG 58.967 42.308 15.79 0.00 0.00 2.90
2754 3050 6.721668 TCGGAGGAATTGATGTATCTAGATGT 59.278 38.462 15.79 1.25 0.00 3.06
2755 3051 7.888546 TCGGAGGAATTGATGTATCTAGATGTA 59.111 37.037 15.79 4.44 0.00 2.29
2756 3052 8.690884 CGGAGGAATTGATGTATCTAGATGTAT 58.309 37.037 15.79 9.11 0.00 2.29
2786 3082 9.453572 AGTTCTAGATACATTCATTTTTCTGCA 57.546 29.630 0.00 0.00 0.00 4.41
2792 3088 9.374838 AGATACATTCATTTTTCTGCATTTTCC 57.625 29.630 0.00 0.00 0.00 3.13
2793 3089 6.806388 ACATTCATTTTTCTGCATTTTCCC 57.194 33.333 0.00 0.00 0.00 3.97
2794 3090 5.409214 ACATTCATTTTTCTGCATTTTCCCG 59.591 36.000 0.00 0.00 0.00 5.14
2795 3091 4.862902 TCATTTTTCTGCATTTTCCCGA 57.137 36.364 0.00 0.00 0.00 5.14
2796 3092 4.555262 TCATTTTTCTGCATTTTCCCGAC 58.445 39.130 0.00 0.00 0.00 4.79
2797 3093 4.038522 TCATTTTTCTGCATTTTCCCGACA 59.961 37.500 0.00 0.00 0.00 4.35
2798 3094 4.392921 TTTTTCTGCATTTTCCCGACAA 57.607 36.364 0.00 0.00 0.00 3.18
2799 3095 3.641437 TTTCTGCATTTTCCCGACAAG 57.359 42.857 0.00 0.00 0.00 3.16
2800 3096 2.270352 TCTGCATTTTCCCGACAAGT 57.730 45.000 0.00 0.00 0.00 3.16
2801 3097 3.410631 TCTGCATTTTCCCGACAAGTA 57.589 42.857 0.00 0.00 0.00 2.24
2802 3098 3.950397 TCTGCATTTTCCCGACAAGTAT 58.050 40.909 0.00 0.00 0.00 2.12
2803 3099 4.331968 TCTGCATTTTCCCGACAAGTATT 58.668 39.130 0.00 0.00 0.00 1.89
2804 3100 4.764823 TCTGCATTTTCCCGACAAGTATTT 59.235 37.500 0.00 0.00 0.00 1.40
2805 3101 5.242838 TCTGCATTTTCCCGACAAGTATTTT 59.757 36.000 0.00 0.00 0.00 1.82
2806 3102 5.465935 TGCATTTTCCCGACAAGTATTTTC 58.534 37.500 0.00 0.00 0.00 2.29
2807 3103 4.557301 GCATTTTCCCGACAAGTATTTTCG 59.443 41.667 0.00 0.00 0.00 3.46
2813 3109 2.598589 CGACAAGTATTTTCGGACGGA 58.401 47.619 0.00 0.00 0.00 4.69
2814 3110 2.597305 CGACAAGTATTTTCGGACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2815 3111 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2816 3112 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2817 3113 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2818 3114 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2831 3127 6.427547 CGGACGGAGGGAGTATCTTATATATC 59.572 46.154 0.00 0.00 33.73 1.63
2903 3199 2.424956 GGGCCTCTTTGATTCACATGAC 59.575 50.000 0.84 0.00 0.00 3.06
2938 3236 8.278639 TGCTGGAATAGGAAAAACATAGGATTA 58.721 33.333 0.00 0.00 0.00 1.75
2972 3270 7.348815 TGGTCATCTCAATCCTACATGATTTT 58.651 34.615 0.00 0.00 32.71 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.715046 GGATGCATGTCCTCAACTTCA 58.285 47.619 2.46 0.00 35.32 3.02
104 109 8.854979 TGATGCAAACTTTAATGGATTATTCG 57.145 30.769 0.00 0.00 0.00 3.34
302 341 1.968493 GGTACAGACCTGGTGTTCTCA 59.032 52.381 2.82 0.00 43.16 3.27
345 386 4.284178 AGAATTTTCAGCTACATGGCCAT 58.716 39.130 14.09 14.09 0.00 4.40
347 388 4.884164 AGTAGAATTTTCAGCTACATGGCC 59.116 41.667 0.00 0.00 37.54 5.36
348 389 6.292381 CGTAGTAGAATTTTCAGCTACATGGC 60.292 42.308 16.84 0.00 37.54 4.40
349 390 6.978659 TCGTAGTAGAATTTTCAGCTACATGG 59.021 38.462 16.84 7.52 37.54 3.66
489 532 2.661594 TCGATCTCAATTACGCATCCG 58.338 47.619 0.00 0.00 41.14 4.18
492 535 3.069586 TCCCTTCGATCTCAATTACGCAT 59.930 43.478 0.00 0.00 0.00 4.73
498 541 2.503356 AGCTGTCCCTTCGATCTCAATT 59.497 45.455 0.00 0.00 0.00 2.32
543 586 2.887568 CTCTGCGTCCATCGGTGC 60.888 66.667 0.00 0.00 40.26 5.01
609 652 3.505293 GGCTTGGCTTGAGAATATGATCC 59.495 47.826 0.00 0.00 0.00 3.36
614 659 3.549794 GACAGGCTTGGCTTGAGAATAT 58.450 45.455 8.54 0.00 37.87 1.28
713 765 2.766651 GTGCGATAGGGTGGGGGA 60.767 66.667 0.00 0.00 0.00 4.81
985 1044 2.094894 CGTCCATGCAACAAGATCTGAC 59.905 50.000 0.00 0.00 0.00 3.51
988 1047 1.742761 CCGTCCATGCAACAAGATCT 58.257 50.000 0.00 0.00 0.00 2.75
1286 1345 7.546667 GGTGACTTAAATTAGGTCGTACATGAA 59.453 37.037 10.07 0.00 37.58 2.57
1359 1423 5.183713 CAGGAAGCAAACTGTAATCCATTGA 59.816 40.000 0.00 0.00 0.00 2.57
1363 1427 3.820467 CACAGGAAGCAAACTGTAATCCA 59.180 43.478 6.84 0.00 45.52 3.41
1370 1434 4.012374 ACCATATCACAGGAAGCAAACTG 58.988 43.478 0.00 0.00 40.48 3.16
1383 1447 2.231215 AGAGCGCAAGACCATATCAC 57.769 50.000 11.47 0.00 43.02 3.06
1387 1451 0.815095 TCGAAGAGCGCAAGACCATA 59.185 50.000 11.47 0.00 40.61 2.74
1391 1455 1.322936 CTCAATCGAAGAGCGCAAGAC 59.677 52.381 11.47 0.00 43.63 3.01
1397 1461 2.215907 ATGGACTCAATCGAAGAGCG 57.784 50.000 15.70 0.00 43.63 5.03
1415 1479 0.670162 GCAAACCTCGCCATGCATAT 59.330 50.000 0.00 0.00 38.63 1.78
1416 1480 0.394216 AGCAAACCTCGCCATGCATA 60.394 50.000 0.00 0.00 41.18 3.14
1441 1505 1.671328 TCGCAATTGAACACCAAACGA 59.329 42.857 10.34 2.18 38.43 3.85
1442 1506 2.043411 CTCGCAATTGAACACCAAACG 58.957 47.619 10.34 0.00 38.43 3.60
1458 1522 0.528684 CTGTAGTAAGCCCTGCTCGC 60.529 60.000 0.00 0.00 38.25 5.03
1931 1998 3.179939 GCGTCGTCTTCTTCGCCC 61.180 66.667 0.00 0.00 42.33 6.13
2066 2136 0.742281 GACATGCTCACGTCATGGCT 60.742 55.000 17.12 0.81 44.48 4.75
2086 2156 0.318441 CTGTCCCACACGTCAGACAT 59.682 55.000 0.41 0.00 38.49 3.06
2125 2199 8.819974 CATGAAACTAAAACTGCAATTTTGTCT 58.180 29.630 15.70 1.04 33.80 3.41
2175 2253 6.842676 ACCAAGAGAAGGTGAGAAAACTAAT 58.157 36.000 0.00 0.00 38.13 1.73
2176 2254 6.248569 ACCAAGAGAAGGTGAGAAAACTAA 57.751 37.500 0.00 0.00 38.13 2.24
2177 2255 5.888982 ACCAAGAGAAGGTGAGAAAACTA 57.111 39.130 0.00 0.00 38.13 2.24
2178 2256 4.779993 ACCAAGAGAAGGTGAGAAAACT 57.220 40.909 0.00 0.00 38.13 2.66
2194 2272 7.876068 TGTATGAGTAAAAGAAGGTACACCAAG 59.124 37.037 0.38 0.00 38.89 3.61
2229 2510 7.984050 TCAATGGTAATGTCTCAGATTCTTCTC 59.016 37.037 0.00 0.00 0.00 2.87
2255 2537 6.761242 TCGATTTCTCGTCCAATCAATATGTT 59.239 34.615 0.00 0.00 45.25 2.71
2286 2568 3.056607 CCATTGACAAAAGGGGCTTGTAG 60.057 47.826 0.00 0.00 37.14 2.74
2292 2574 2.493035 CAAACCATTGACAAAAGGGGC 58.507 47.619 12.92 0.00 38.94 5.80
2378 2674 8.072321 TGAAGATCTTCTAATGCTCACTACTT 57.928 34.615 30.45 0.00 40.14 2.24
2382 2678 6.945218 AGTTGAAGATCTTCTAATGCTCACT 58.055 36.000 30.45 14.94 40.14 3.41
2419 2715 7.387948 CCTTGACCTAGGCAATGTATAATGTAC 59.612 40.741 9.30 0.00 0.00 2.90
2420 2716 7.071950 ACCTTGACCTAGGCAATGTATAATGTA 59.928 37.037 18.28 0.00 38.99 2.29
2421 2717 6.126478 ACCTTGACCTAGGCAATGTATAATGT 60.126 38.462 18.28 6.77 38.99 2.71
2422 2718 6.299141 ACCTTGACCTAGGCAATGTATAATG 58.701 40.000 18.28 7.40 38.99 1.90
2423 2719 6.101150 TGACCTTGACCTAGGCAATGTATAAT 59.899 38.462 19.14 4.84 38.99 1.28
2424 2720 5.427157 TGACCTTGACCTAGGCAATGTATAA 59.573 40.000 19.14 10.55 38.99 0.98
2425 2721 4.966168 TGACCTTGACCTAGGCAATGTATA 59.034 41.667 19.14 12.55 38.99 1.47
2426 2722 3.780294 TGACCTTGACCTAGGCAATGTAT 59.220 43.478 19.14 8.11 38.99 2.29
2506 2802 6.092670 GTGCTTGACAAGTAATTGCTGAGATA 59.907 38.462 16.39 0.00 0.00 1.98
2591 2887 7.658261 ACTTGATTAAACCTAAGGAAGTTTGC 58.342 34.615 0.00 0.00 36.85 3.68
2639 2935 7.536622 GCATGCTCTATACATTAGATTTTGTGC 59.463 37.037 11.37 0.00 0.00 4.57
2645 2941 9.293404 ACATTTGCATGCTCTATACATTAGATT 57.707 29.630 20.33 0.00 33.05 2.40
2689 2985 7.092757 ACGGAGGGAGTATTAAATTAGTTCCAA 60.093 37.037 0.00 0.00 0.00 3.53
2692 2988 6.927936 GGACGGAGGGAGTATTAAATTAGTTC 59.072 42.308 0.00 0.00 0.00 3.01
2704 3000 0.032813 ATTTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
2705 3001 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
2706 3002 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2707 3003 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2708 3004 0.388294 GAGTATTTCCGGACGGAGGG 59.612 60.000 13.64 0.00 46.06 4.30
2709 3005 0.030369 CGAGTATTTCCGGACGGAGG 59.970 60.000 13.64 0.00 46.06 4.30
2710 3006 0.737219 ACGAGTATTTCCGGACGGAG 59.263 55.000 13.64 3.15 46.06 4.63
2711 3007 0.734889 GACGAGTATTTCCGGACGGA 59.265 55.000 1.83 9.76 43.52 4.69
2712 3008 0.590732 CGACGAGTATTTCCGGACGG 60.591 60.000 1.83 3.96 0.00 4.79
2713 3009 0.590732 CCGACGAGTATTTCCGGACG 60.591 60.000 1.83 5.89 42.49 4.79
2714 3010 0.734889 TCCGACGAGTATTTCCGGAC 59.265 55.000 1.83 0.00 43.47 4.79
2715 3011 1.019673 CTCCGACGAGTATTTCCGGA 58.980 55.000 0.00 0.00 45.74 5.14
2716 3012 0.030369 CCTCCGACGAGTATTTCCGG 59.970 60.000 0.00 0.00 41.36 5.14
2717 3013 1.019673 TCCTCCGACGAGTATTTCCG 58.980 55.000 0.00 0.00 33.93 4.30
2718 3014 3.729862 ATTCCTCCGACGAGTATTTCC 57.270 47.619 0.00 0.00 33.93 3.13
2719 3015 4.679662 TCAATTCCTCCGACGAGTATTTC 58.320 43.478 0.00 0.00 33.93 2.17
2720 3016 4.730949 TCAATTCCTCCGACGAGTATTT 57.269 40.909 0.00 0.00 33.93 1.40
2721 3017 4.099573 ACATCAATTCCTCCGACGAGTATT 59.900 41.667 0.00 0.00 33.93 1.89
2722 3018 3.637229 ACATCAATTCCTCCGACGAGTAT 59.363 43.478 0.00 0.00 33.93 2.12
2723 3019 3.021695 ACATCAATTCCTCCGACGAGTA 58.978 45.455 0.00 0.00 33.93 2.59
2724 3020 1.825474 ACATCAATTCCTCCGACGAGT 59.175 47.619 0.00 0.00 33.93 4.18
2725 3021 2.586258 ACATCAATTCCTCCGACGAG 57.414 50.000 0.00 0.00 35.72 4.18
2726 3022 3.889538 AGATACATCAATTCCTCCGACGA 59.110 43.478 0.00 0.00 0.00 4.20
2727 3023 4.244425 AGATACATCAATTCCTCCGACG 57.756 45.455 0.00 0.00 0.00 5.12
2728 3024 6.576662 TCTAGATACATCAATTCCTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
2729 3025 6.721668 ACATCTAGATACATCAATTCCTCCGA 59.278 38.462 4.54 0.00 0.00 4.55
2730 3026 6.929625 ACATCTAGATACATCAATTCCTCCG 58.070 40.000 4.54 0.00 0.00 4.63
2760 3056 9.453572 TGCAGAAAAATGAATGTATCTAGAACT 57.546 29.630 0.00 0.00 0.00 3.01
2766 3062 9.374838 GGAAAATGCAGAAAAATGAATGTATCT 57.625 29.630 0.00 0.00 0.00 1.98
2767 3063 8.606602 GGGAAAATGCAGAAAAATGAATGTATC 58.393 33.333 0.00 0.00 0.00 2.24
2768 3064 7.278424 CGGGAAAATGCAGAAAAATGAATGTAT 59.722 33.333 0.00 0.00 0.00 2.29
2769 3065 6.589523 CGGGAAAATGCAGAAAAATGAATGTA 59.410 34.615 0.00 0.00 0.00 2.29
2770 3066 5.409214 CGGGAAAATGCAGAAAAATGAATGT 59.591 36.000 0.00 0.00 0.00 2.71
2771 3067 5.638657 TCGGGAAAATGCAGAAAAATGAATG 59.361 36.000 0.00 0.00 0.00 2.67
2772 3068 5.639082 GTCGGGAAAATGCAGAAAAATGAAT 59.361 36.000 0.00 0.00 0.00 2.57
2773 3069 4.987912 GTCGGGAAAATGCAGAAAAATGAA 59.012 37.500 0.00 0.00 0.00 2.57
2774 3070 4.038522 TGTCGGGAAAATGCAGAAAAATGA 59.961 37.500 0.00 0.00 0.00 2.57
2775 3071 4.305769 TGTCGGGAAAATGCAGAAAAATG 58.694 39.130 0.00 0.00 0.00 2.32
2776 3072 4.599047 TGTCGGGAAAATGCAGAAAAAT 57.401 36.364 0.00 0.00 0.00 1.82
2777 3073 4.142049 ACTTGTCGGGAAAATGCAGAAAAA 60.142 37.500 0.00 0.00 0.00 1.94
2778 3074 3.383185 ACTTGTCGGGAAAATGCAGAAAA 59.617 39.130 0.00 0.00 0.00 2.29
2779 3075 2.955660 ACTTGTCGGGAAAATGCAGAAA 59.044 40.909 0.00 0.00 0.00 2.52
2780 3076 2.582052 ACTTGTCGGGAAAATGCAGAA 58.418 42.857 0.00 0.00 0.00 3.02
2781 3077 2.270352 ACTTGTCGGGAAAATGCAGA 57.730 45.000 0.00 0.00 0.00 4.26
2782 3078 4.701956 AATACTTGTCGGGAAAATGCAG 57.298 40.909 0.00 0.00 0.00 4.41
2783 3079 5.461032 AAAATACTTGTCGGGAAAATGCA 57.539 34.783 0.00 0.00 0.00 3.96
2784 3080 4.557301 CGAAAATACTTGTCGGGAAAATGC 59.443 41.667 0.00 0.00 0.00 3.56
2793 3089 2.597305 CTCCGTCCGAAAATACTTGTCG 59.403 50.000 0.00 0.00 34.58 4.35
2794 3090 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2795 3091 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2796 3092 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2797 3093 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2798 3094 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2799 3095 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2800 3096 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2801 3097 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2802 3098 1.753073 GATACTCCCTCCGTCCGAAAA 59.247 52.381 0.00 0.00 0.00 2.29
2803 3099 1.064166 AGATACTCCCTCCGTCCGAAA 60.064 52.381 0.00 0.00 0.00 3.46
2804 3100 0.549950 AGATACTCCCTCCGTCCGAA 59.450 55.000 0.00 0.00 0.00 4.30
2805 3101 0.549950 AAGATACTCCCTCCGTCCGA 59.450 55.000 0.00 0.00 0.00 4.55
2806 3102 2.267174 TAAGATACTCCCTCCGTCCG 57.733 55.000 0.00 0.00 0.00 4.79
2807 3103 6.427547 CGATATATAAGATACTCCCTCCGTCC 59.572 46.154 0.00 0.00 0.00 4.79
2808 3104 6.427547 CCGATATATAAGATACTCCCTCCGTC 59.572 46.154 0.00 0.00 0.00 4.79
2809 3105 6.126536 ACCGATATATAAGATACTCCCTCCGT 60.127 42.308 0.00 0.00 0.00 4.69
2810 3106 6.297582 ACCGATATATAAGATACTCCCTCCG 58.702 44.000 0.00 0.00 0.00 4.63
2903 3199 9.358872 GTTTTTCCTATTCCAGCATTTTTAGAG 57.641 33.333 0.00 0.00 0.00 2.43
2912 3208 6.073447 TCCTATGTTTTTCCTATTCCAGCA 57.927 37.500 0.00 0.00 0.00 4.41
2938 3236 5.132312 AGGATTGAGATGACCATGACATTCT 59.868 40.000 0.00 0.33 0.00 2.40


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

AutoCloner maintained by Alex Coulton.