Multiple sequence alignment - TraesCS3D01G016100

Loading Multiple Alignment...

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 TraesCS3D01G016100 chr3D 100.000 3119 0 0 1 3119 5682386 5679268 0.000000e+00 5760.0
1 TraesCS3D01G016100 chr3D 82.231 1587 154 67 970 2513 9948485 9946984 0.000000e+00 1251.0
2 TraesCS3D01G016100 chr3D 80.242 1159 152 41 998 2128 5609120 5610229 0.000000e+00 800.0
3 TraesCS3D01G016100 chr3D 88.671 459 42 5 3 456 9949061 9948608 4.550000e-153 551.0
4 TraesCS3D01G016100 chr3D 85.044 341 33 8 6 330 9882486 9882148 6.450000e-87 331.0
5 TraesCS3D01G016100 chr3D 88.686 274 23 4 2245 2513 9880761 9880491 8.340000e-86 327.0
6 TraesCS3D01G016100 chr3D 82.769 325 24 14 970 1285 9881951 9881650 8.580000e-66 261.0
7 TraesCS3D01G016100 chr3D 96.629 89 3 0 3031 3119 603689101 603689189 6.970000e-32 148.0
8 TraesCS3D01G016100 chr3D 83.333 138 23 0 1124 1261 29281841 29281978 9.080000e-26 128.0
9 TraesCS3D01G016100 chr3D 84.375 128 20 0 1124 1251 29309007 29308880 3.270000e-25 126.0
10 TraesCS3D01G016100 chr3D 98.113 53 0 1 2573 2625 9880451 9880400 1.190000e-14 91.6
11 TraesCS3D01G016100 chr3B 88.294 2298 114 59 815 3038 12181941 12179725 0.000000e+00 2610.0
12 TraesCS3D01G016100 chr3B 90.044 1577 72 32 888 2405 27993914 27995464 0.000000e+00 1964.0
13 TraesCS3D01G016100 chr3B 82.400 1625 178 61 970 2555 14223578 14222023 0.000000e+00 1317.0
14 TraesCS3D01G016100 chr3B 80.435 1196 150 47 970 2127 12401300 12400151 0.000000e+00 835.0
15 TraesCS3D01G016100 chr3B 83.014 783 117 12 1337 2116 28082169 28081400 0.000000e+00 695.0
16 TraesCS3D01G016100 chr3B 87.179 468 45 12 1 458 28519384 28518922 4.610000e-143 518.0
17 TraesCS3D01G016100 chr3B 86.809 470 46 9 1 456 14106481 14106014 7.720000e-141 510.0
18 TraesCS3D01G016100 chr3B 86.882 465 49 8 1 456 14133922 14133461 7.720000e-141 510.0
19 TraesCS3D01G016100 chr3B 86.724 467 49 10 1 458 28456723 28456261 9.980000e-140 507.0
20 TraesCS3D01G016100 chr3B 86.752 468 47 12 1 458 28530793 28530331 9.980000e-140 507.0
21 TraesCS3D01G016100 chr3B 86.207 464 52 8 1 456 14066481 14066022 2.790000e-135 492.0
22 TraesCS3D01G016100 chr3B 86.081 467 52 10 1 458 28410211 28409749 1.010000e-134 490.0
23 TraesCS3D01G016100 chr3B 86.081 467 52 10 1 458 28423375 28422913 1.010000e-134 490.0
24 TraesCS3D01G016100 chr3B 82.638 599 55 26 197 760 12184113 12183529 4.680000e-133 484.0
25 TraesCS3D01G016100 chr3B 87.798 336 17 6 2702 3035 27995637 27995950 3.800000e-99 372.0
26 TraesCS3D01G016100 chr3B 87.361 269 26 4 2245 2508 14111330 14111065 5.060000e-78 302.0
27 TraesCS3D01G016100 chr3B 81.143 350 33 19 970 1293 28082524 28082182 1.860000e-62 250.0
28 TraesCS3D01G016100 chr3B 90.323 93 7 1 2490 2580 27995465 27995557 1.520000e-23 121.0
29 TraesCS3D01G016100 chr3B 97.778 45 0 1 2634 2677 27995595 27995639 3.340000e-10 76.8
30 TraesCS3D01G016100 chr3B 100.000 31 0 0 866 896 27993882 27993912 1.210000e-04 58.4
31 TraesCS3D01G016100 chrUn 87.465 2122 122 59 972 3035 35795027 35797062 0.000000e+00 2313.0
32 TraesCS3D01G016100 chrUn 88.962 1513 75 37 895 2362 35203121 35204586 0.000000e+00 1784.0
33 TraesCS3D01G016100 chrUn 84.810 869 67 26 1716 2576 305025109 305025920 0.000000e+00 813.0
34 TraesCS3D01G016100 chrUn 84.573 726 66 21 102 795 35202287 35202998 0.000000e+00 678.0
35 TraesCS3D01G016100 chrUn 84.573 726 66 21 102 795 236915035 236914324 0.000000e+00 678.0
36 TraesCS3D01G016100 chrUn 90.026 381 21 10 2030 2396 35209512 35209889 7.830000e-131 477.0
37 TraesCS3D01G016100 chrUn 84.529 446 55 9 1 435 35793990 35794432 2.220000e-116 429.0
38 TraesCS3D01G016100 chrUn 91.810 232 19 0 2804 3035 35204591 35204822 1.080000e-84 324.0
39 TraesCS3D01G016100 chrUn 89.627 241 20 5 221 458 307487399 307487637 5.060000e-78 302.0
40 TraesCS3D01G016100 chrUn 89.627 241 20 5 221 458 328827719 328827957 5.060000e-78 302.0
41 TraesCS3D01G016100 chrUn 89.076 238 9 5 895 1121 236914201 236913970 2.370000e-71 279.0
42 TraesCS3D01G016100 chrUn 80.967 331 27 16 970 1274 35452400 35452080 2.420000e-56 230.0
43 TraesCS3D01G016100 chrUn 96.512 86 3 0 3034 3119 77927553 77927468 3.240000e-30 143.0
44 TraesCS3D01G016100 chrUn 96.250 80 3 0 3033 3112 48771124 48771203 7.020000e-27 132.0
45 TraesCS3D01G016100 chr3A 89.555 1551 74 40 921 2434 15603592 15605091 0.000000e+00 1886.0
46 TraesCS3D01G016100 chr3A 85.823 656 90 1 1376 2028 15694946 15694291 0.000000e+00 693.0
47 TraesCS3D01G016100 chr3A 87.192 406 30 10 2633 3036 15605211 15605596 2.850000e-120 442.0
48 TraesCS3D01G016100 chr3A 81.585 467 43 11 2 456 15603005 15603440 2.300000e-91 346.0
49 TraesCS3D01G016100 chr3A 81.132 318 33 16 998 1293 17258528 17258216 2.420000e-56 230.0
50 TraesCS3D01G016100 chr3A 79.701 335 34 21 970 1276 15780861 15780533 8.760000e-51 211.0
51 TraesCS3D01G016100 chr3A 78.730 315 34 20 998 1282 15695303 15694992 2.470000e-41 180.0
52 TraesCS3D01G016100 chr3A 77.483 302 43 15 994 1274 11629200 11628903 1.160000e-34 158.0
53 TraesCS3D01G016100 chr3A 78.723 141 11 9 2474 2610 15605089 15605214 3.340000e-10 76.8
54 TraesCS3D01G016100 chr2A 87.085 271 27 3 2245 2510 19662093 19661826 1.820000e-77 300.0
55 TraesCS3D01G016100 chr2A 95.506 89 4 0 3030 3118 383609660 383609572 3.240000e-30 143.0
56 TraesCS3D01G016100 chr2A 94.340 53 2 1 2573 2625 19661783 19661732 2.580000e-11 80.5
57 TraesCS3D01G016100 chr1B 94.737 95 5 0 3025 3119 345307969 345308063 6.970000e-32 148.0
58 TraesCS3D01G016100 chr7B 95.556 90 4 0 3030 3119 553438212 553438123 9.020000e-31 145.0
59 TraesCS3D01G016100 chr7D 96.512 86 3 0 3031 3116 50715802 50715887 3.240000e-30 143.0
60 TraesCS3D01G016100 chr2B 93.548 93 5 1 3028 3119 50222735 50222643 1.510000e-28 137.0
61 TraesCS3D01G016100 chr5A 94.253 87 5 0 3033 3119 6488376 6488290 1.950000e-27 134.0


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 TraesCS3D01G016100 chr3D 5679268 5682386 3118 True 5760.000000 5760 100.000000 1 3119 1 chr3D.!!$R1 3118
1 TraesCS3D01G016100 chr3D 9946984 9949061 2077 True 901.000000 1251 85.451000 3 2513 2 chr3D.!!$R4 2510
2 TraesCS3D01G016100 chr3D 5609120 5610229 1109 False 800.000000 800 80.242000 998 2128 1 chr3D.!!$F1 1130
3 TraesCS3D01G016100 chr3D 9880400 9882486 2086 True 252.650000 331 88.653000 6 2625 4 chr3D.!!$R3 2619
4 TraesCS3D01G016100 chr3B 12179725 12184113 4388 True 1547.000000 2610 85.466000 197 3038 2 chr3B.!!$R12 2841
5 TraesCS3D01G016100 chr3B 14222023 14223578 1555 True 1317.000000 1317 82.400000 970 2555 1 chr3B.!!$R6 1585
6 TraesCS3D01G016100 chr3B 12400151 12401300 1149 True 835.000000 835 80.435000 970 2127 1 chr3B.!!$R1 1157
7 TraesCS3D01G016100 chr3B 27993882 27995950 2068 False 518.440000 1964 93.188600 866 3035 5 chr3B.!!$F1 2169
8 TraesCS3D01G016100 chr3B 28081400 28082524 1124 True 472.500000 695 82.078500 970 2116 2 chr3B.!!$R13 1146
9 TraesCS3D01G016100 chrUn 35793990 35797062 3072 False 1371.000000 2313 85.997000 1 3035 2 chrUn.!!$F7 3034
10 TraesCS3D01G016100 chrUn 35202287 35204822 2535 False 928.666667 1784 88.448333 102 3035 3 chrUn.!!$F6 2933
11 TraesCS3D01G016100 chrUn 305025109 305025920 811 False 813.000000 813 84.810000 1716 2576 1 chrUn.!!$F3 860
12 TraesCS3D01G016100 chrUn 236913970 236915035 1065 True 478.500000 678 86.824500 102 1121 2 chrUn.!!$R3 1019
13 TraesCS3D01G016100 chr3A 15603005 15605596 2591 False 687.700000 1886 84.263750 2 3036 4 chr3A.!!$F1 3034
14 TraesCS3D01G016100 chr3A 15694291 15695303 1012 True 436.500000 693 82.276500 998 2028 2 chr3A.!!$R4 1030

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
801 2447 0.111061 TGCAGCTGGTTGGAACATCT 59.889 50.0 17.12 0.0 39.3 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2543 4534 1.276138 CATAGGCGGTATCCTGCATGA 59.724 52.381 0.0 0.0 37.01 3.07 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
26 27 4.502645 GGCTTGTGTTCATGTTGTTGTTAC 59.497 41.667 0.00 0.00 0.00 2.50
86 99 2.501223 GATGACAGTGGGAACGGCGA 62.501 60.000 16.62 0.00 0.00 5.54
89 102 2.342279 CAGTGGGAACGGCGAGAA 59.658 61.111 16.62 0.00 0.00 2.87
135 148 3.414700 CGCGTCTGTGTTGCTCCC 61.415 66.667 0.00 0.00 0.00 4.30
152 165 6.321821 TGCTCCCTTGTACTATTTGGTTAT 57.678 37.500 0.00 0.00 0.00 1.89
165 178 1.473258 TGGTTATGCATGTCCCTTGC 58.527 50.000 10.16 0.00 40.55 4.01
176 189 0.391130 GTCCCTTGCGCTGACACATA 60.391 55.000 9.73 0.00 0.00 2.29
274 289 5.448632 CCGTGTATCAATTAAGCAGGAAACC 60.449 44.000 0.00 0.00 0.00 3.27
420 458 8.297470 ACATGGACAAAGTAGCAATAATGAAT 57.703 30.769 0.00 0.00 0.00 2.57
457 497 8.794553 GCACGGCTTATATCTATACCATATAGT 58.205 37.037 3.43 0.00 0.00 2.12
489 554 7.371159 TCTAATCGAGCATATACAAGGAAGTG 58.629 38.462 0.00 0.00 0.00 3.16
504 573 5.683876 AGGAAGTGCTCACAACATATACT 57.316 39.130 2.63 0.00 0.00 2.12
563 719 0.948678 GCAGCCGGTTAAGAACACAA 59.051 50.000 1.90 0.00 0.00 3.33
564 720 1.539827 GCAGCCGGTTAAGAACACAAT 59.460 47.619 1.90 0.00 0.00 2.71
565 721 2.745281 GCAGCCGGTTAAGAACACAATA 59.255 45.455 1.90 0.00 0.00 1.90
566 722 3.181510 GCAGCCGGTTAAGAACACAATAG 60.182 47.826 1.90 0.00 0.00 1.73
648 804 2.965572 TACGCTAATTACGGCAACCT 57.034 45.000 10.67 0.00 34.00 3.50
679 844 5.090139 TGGAGAGGATGGAGAGGAATAATC 58.910 45.833 0.00 0.00 0.00 1.75
684 849 5.893500 AGGATGGAGAGGAATAATCGAGTA 58.106 41.667 0.00 0.00 0.00 2.59
688 853 5.784177 TGGAGAGGAATAATCGAGTATTGC 58.216 41.667 24.03 24.03 33.34 3.56
703 868 6.316140 TCGAGTATTGCAGATATTTGCTTTGT 59.684 34.615 18.11 5.44 44.38 2.83
708 873 9.443283 GTATTGCAGATATTTGCTTTGTCTAAG 57.557 33.333 18.11 0.00 44.38 2.18
750 915 9.976511 CTACCTCCGTATAAAAATATCAGACAA 57.023 33.333 0.00 0.00 0.00 3.18
795 2441 1.004628 ACATACATGCAGCTGGTTGGA 59.995 47.619 17.12 0.00 0.00 3.53
796 2442 2.093890 CATACATGCAGCTGGTTGGAA 58.906 47.619 17.12 0.00 0.00 3.53
800 2446 1.135199 CATGCAGCTGGTTGGAACATC 60.135 52.381 17.12 0.00 39.30 3.06
801 2447 0.111061 TGCAGCTGGTTGGAACATCT 59.889 50.000 17.12 0.00 39.30 2.90
802 2448 1.350684 TGCAGCTGGTTGGAACATCTA 59.649 47.619 17.12 0.00 39.30 1.98
803 2449 1.740025 GCAGCTGGTTGGAACATCTAC 59.260 52.381 17.12 0.00 39.30 2.59
804 2450 2.616510 GCAGCTGGTTGGAACATCTACT 60.617 50.000 17.12 0.00 39.30 2.57
805 2451 3.679389 CAGCTGGTTGGAACATCTACTT 58.321 45.455 5.57 0.00 39.30 2.24
806 2452 4.074970 CAGCTGGTTGGAACATCTACTTT 58.925 43.478 5.57 0.00 39.30 2.66
807 2453 5.245531 CAGCTGGTTGGAACATCTACTTTA 58.754 41.667 5.57 0.00 39.30 1.85
808 2454 5.705441 CAGCTGGTTGGAACATCTACTTTAA 59.295 40.000 5.57 0.00 39.30 1.52
809 2455 6.375455 CAGCTGGTTGGAACATCTACTTTAAT 59.625 38.462 5.57 0.00 39.30 1.40
810 2456 6.375455 AGCTGGTTGGAACATCTACTTTAATG 59.625 38.462 0.00 0.00 39.30 1.90
811 2457 6.509418 TGGTTGGAACATCTACTTTAATGC 57.491 37.500 0.00 0.00 39.30 3.56
812 2458 6.007076 TGGTTGGAACATCTACTTTAATGCA 58.993 36.000 0.00 0.00 39.30 3.96
813 2459 6.150976 TGGTTGGAACATCTACTTTAATGCAG 59.849 38.462 0.00 0.00 39.30 4.41
844 2566 4.577152 TGTGGAACAGTGGCAAGG 57.423 55.556 0.00 0.00 45.67 3.61
845 2567 1.612513 TGTGGAACAGTGGCAAGGT 59.387 52.632 0.00 0.00 45.67 3.50
846 2568 0.751277 TGTGGAACAGTGGCAAGGTG 60.751 55.000 0.00 0.00 45.67 4.00
847 2569 1.827789 TGGAACAGTGGCAAGGTGC 60.828 57.895 0.00 0.00 44.08 5.01
909 2650 4.880537 CAGTAGCTGCCTCGGCCG 62.881 72.222 22.12 22.12 41.09 6.13
1051 2854 4.452733 CTTCGCCGGACCAGGGTC 62.453 72.222 5.05 10.03 43.87 4.46
1252 3082 3.630289 CCCCCGTCTTCCAGGTAG 58.370 66.667 0.00 0.00 0.00 3.18
1253 3083 2.064581 CCCCCGTCTTCCAGGTAGG 61.065 68.421 0.00 0.00 39.47 3.18
1254 3084 1.305887 CCCCGTCTTCCAGGTAGGT 60.306 63.158 0.00 0.00 39.02 3.08
1255 3085 0.908180 CCCCGTCTTCCAGGTAGGTT 60.908 60.000 0.00 0.00 39.02 3.50
1256 3086 0.535797 CCCGTCTTCCAGGTAGGTTC 59.464 60.000 0.00 0.00 39.02 3.62
1257 3087 0.535797 CCGTCTTCCAGGTAGGTTCC 59.464 60.000 0.00 0.00 39.02 3.62
1258 3088 1.558233 CGTCTTCCAGGTAGGTTCCT 58.442 55.000 0.00 0.00 39.02 3.36
1259 3089 1.477295 CGTCTTCCAGGTAGGTTCCTC 59.523 57.143 0.00 0.00 39.02 3.71
1260 3090 2.822697 GTCTTCCAGGTAGGTTCCTCT 58.177 52.381 0.00 0.00 39.02 3.69
1261 3091 3.624205 CGTCTTCCAGGTAGGTTCCTCTA 60.624 52.174 0.00 0.00 39.02 2.43
1262 3092 4.548669 GTCTTCCAGGTAGGTTCCTCTAT 58.451 47.826 0.00 0.00 39.02 1.98
1263 3093 4.963628 GTCTTCCAGGTAGGTTCCTCTATT 59.036 45.833 0.00 0.00 39.02 1.73
1293 3140 2.363788 TTTCTTCCACACTCGATCGG 57.636 50.000 16.41 8.65 0.00 4.18
1294 3141 0.108804 TTCTTCCACACTCGATCGGC 60.109 55.000 16.41 0.00 0.00 5.54
1329 3191 5.786121 AAGATCCATTCTTTCCTTCCTCA 57.214 39.130 0.00 0.00 42.15 3.86
1330 3192 5.786121 AGATCCATTCTTTCCTTCCTCAA 57.214 39.130 0.00 0.00 0.00 3.02
1331 3193 6.338591 AGATCCATTCTTTCCTTCCTCAAT 57.661 37.500 0.00 0.00 0.00 2.57
1786 3673 2.803817 AACCGCGTGTTCCTCCTGT 61.804 57.895 4.92 0.00 28.45 4.00
2036 3938 4.194720 GCCAGCAGCAGCAGCATC 62.195 66.667 12.92 0.00 45.49 3.91
2037 3939 2.750237 CCAGCAGCAGCAGCATCA 60.750 61.111 12.92 0.00 45.49 3.07
2156 4100 1.130561 GGCAGTTCGTGGTTGCTTATC 59.869 52.381 0.00 0.00 37.93 1.75
2316 4294 2.583024 TCCTGTGGTGAAATGCATCA 57.417 45.000 0.00 0.00 34.56 3.07
2461 4444 0.648958 CGACGCTTAATCCGGGTTTC 59.351 55.000 4.62 0.00 0.00 2.78
2471 4454 4.963878 CGGGTTTCCTGGAGGATG 57.036 61.111 0.00 0.00 44.98 3.51
2477 4460 1.630878 GTTTCCTGGAGGATGGTGAGT 59.369 52.381 0.00 0.00 44.98 3.41
2480 4463 2.467880 TCCTGGAGGATGGTGAGTAAC 58.532 52.381 0.00 0.00 39.78 2.50
2500 4483 2.108952 ACAAAGGAGGCCTTCTGTCAAT 59.891 45.455 16.53 0.00 43.92 2.57
2648 4653 6.400568 AGCAACCATTCCATATTTGTTCAAG 58.599 36.000 0.00 0.00 0.00 3.02
2687 4692 0.670162 TCAGTTTTGCAGGCAGAAGC 59.330 50.000 0.00 0.00 41.10 3.86
2688 4693 0.386476 CAGTTTTGCAGGCAGAAGCA 59.614 50.000 0.00 0.00 44.61 3.91
2843 4853 3.117046 GAGCATACGACCTACTTTGCTC 58.883 50.000 6.93 6.93 46.21 4.26
2852 4862 4.093556 CGACCTACTTTGCTCATTTCTTCC 59.906 45.833 0.00 0.00 0.00 3.46
2864 4874 4.507710 TCATTTCTTCCATCTTGTCTCCG 58.492 43.478 0.00 0.00 0.00 4.63
2910 4920 7.122501 TGAGCACATTCCAATGATTAAAAGCTA 59.877 33.333 6.29 0.00 39.67 3.32
2997 5007 4.905429 TGCAGCAAAGGTTCTAGATGTAA 58.095 39.130 0.00 0.00 0.00 2.41
3008 5018 7.699878 AGGTTCTAGATGTAATTCCAAAAGGT 58.300 34.615 0.00 0.00 0.00 3.50
3042 5052 3.884226 CCTTCCTAAGGGCCTGTTC 57.116 57.895 6.92 0.00 45.27 3.18
3043 5053 0.107654 CCTTCCTAAGGGCCTGTTCG 60.108 60.000 6.92 0.00 45.27 3.95
3044 5054 0.107654 CTTCCTAAGGGCCTGTTCGG 60.108 60.000 6.92 5.51 0.00 4.30
3045 5055 0.838987 TTCCTAAGGGCCTGTTCGGT 60.839 55.000 6.92 0.00 34.25 4.69
3046 5056 0.838987 TCCTAAGGGCCTGTTCGGTT 60.839 55.000 6.92 0.00 34.25 4.44
3047 5057 0.676782 CCTAAGGGCCTGTTCGGTTG 60.677 60.000 6.92 0.00 34.25 3.77
3048 5058 0.323629 CTAAGGGCCTGTTCGGTTGA 59.676 55.000 6.92 0.00 34.25 3.18
3049 5059 0.035739 TAAGGGCCTGTTCGGTTGAC 59.964 55.000 6.92 0.00 34.25 3.18
3050 5060 1.990160 AAGGGCCTGTTCGGTTGACA 61.990 55.000 6.92 0.00 34.25 3.58
3051 5061 1.966451 GGGCCTGTTCGGTTGACAG 60.966 63.158 0.84 0.00 43.19 3.51
3055 5065 3.698250 CTGTTCGGTTGACAGGGAA 57.302 52.632 0.00 0.00 40.58 3.97
3056 5066 1.961793 CTGTTCGGTTGACAGGGAAA 58.038 50.000 0.00 0.00 40.58 3.13
3057 5067 2.294074 CTGTTCGGTTGACAGGGAAAA 58.706 47.619 0.00 0.00 40.58 2.29
3058 5068 2.884639 CTGTTCGGTTGACAGGGAAAAT 59.115 45.455 0.00 0.00 40.58 1.82
3059 5069 2.621055 TGTTCGGTTGACAGGGAAAATG 59.379 45.455 0.00 0.00 0.00 2.32
3060 5070 1.904287 TCGGTTGACAGGGAAAATGG 58.096 50.000 0.00 0.00 0.00 3.16
3061 5071 1.422024 TCGGTTGACAGGGAAAATGGA 59.578 47.619 0.00 0.00 0.00 3.41
3062 5072 1.812571 CGGTTGACAGGGAAAATGGAG 59.187 52.381 0.00 0.00 0.00 3.86
3063 5073 2.171003 GGTTGACAGGGAAAATGGAGG 58.829 52.381 0.00 0.00 0.00 4.30
3064 5074 2.171003 GTTGACAGGGAAAATGGAGGG 58.829 52.381 0.00 0.00 0.00 4.30
3065 5075 0.704076 TGACAGGGAAAATGGAGGGG 59.296 55.000 0.00 0.00 0.00 4.79
3066 5076 0.704664 GACAGGGAAAATGGAGGGGT 59.295 55.000 0.00 0.00 0.00 4.95
3067 5077 1.077169 GACAGGGAAAATGGAGGGGTT 59.923 52.381 0.00 0.00 0.00 4.11
3068 5078 1.507742 ACAGGGAAAATGGAGGGGTTT 59.492 47.619 0.00 0.00 0.00 3.27
3069 5079 1.901833 CAGGGAAAATGGAGGGGTTTG 59.098 52.381 0.00 0.00 0.00 2.93
3070 5080 1.203300 AGGGAAAATGGAGGGGTTTGG 60.203 52.381 0.00 0.00 0.00 3.28
3071 5081 0.613260 GGAAAATGGAGGGGTTTGGC 59.387 55.000 0.00 0.00 0.00 4.52
3072 5082 1.347062 GAAAATGGAGGGGTTTGGCA 58.653 50.000 0.00 0.00 0.00 4.92
3073 5083 1.276138 GAAAATGGAGGGGTTTGGCAG 59.724 52.381 0.00 0.00 0.00 4.85
3074 5084 0.545071 AAATGGAGGGGTTTGGCAGG 60.545 55.000 0.00 0.00 0.00 4.85
3075 5085 2.460476 AATGGAGGGGTTTGGCAGGG 62.460 60.000 0.00 0.00 0.00 4.45
3076 5086 3.264845 GGAGGGGTTTGGCAGGGA 61.265 66.667 0.00 0.00 0.00 4.20
3077 5087 2.626467 GGAGGGGTTTGGCAGGGAT 61.626 63.158 0.00 0.00 0.00 3.85
3078 5088 1.388133 GAGGGGTTTGGCAGGGATT 59.612 57.895 0.00 0.00 0.00 3.01
3079 5089 0.629058 GAGGGGTTTGGCAGGGATTA 59.371 55.000 0.00 0.00 0.00 1.75
3080 5090 0.335019 AGGGGTTTGGCAGGGATTAC 59.665 55.000 0.00 0.00 0.00 1.89
3081 5091 0.040499 GGGGTTTGGCAGGGATTACA 59.960 55.000 0.00 0.00 0.00 2.41
3082 5092 1.182667 GGGTTTGGCAGGGATTACAC 58.817 55.000 0.00 0.00 0.00 2.90
3083 5093 1.182667 GGTTTGGCAGGGATTACACC 58.817 55.000 0.00 0.00 0.00 4.16
3094 5104 4.403585 GGGATTACACCCTCTACAAGTC 57.596 50.000 0.00 0.00 45.90 3.01
3095 5105 3.773119 GGGATTACACCCTCTACAAGTCA 59.227 47.826 0.00 0.00 45.90 3.41
3096 5106 4.224370 GGGATTACACCCTCTACAAGTCAA 59.776 45.833 0.00 0.00 45.90 3.18
3097 5107 5.280317 GGGATTACACCCTCTACAAGTCAAA 60.280 44.000 0.00 0.00 45.90 2.69
3098 5108 6.235664 GGATTACACCCTCTACAAGTCAAAA 58.764 40.000 0.00 0.00 0.00 2.44
3099 5109 6.148976 GGATTACACCCTCTACAAGTCAAAAC 59.851 42.308 0.00 0.00 0.00 2.43
3100 5110 3.816994 ACACCCTCTACAAGTCAAAACC 58.183 45.455 0.00 0.00 0.00 3.27
3101 5111 3.458487 ACACCCTCTACAAGTCAAAACCT 59.542 43.478 0.00 0.00 0.00 3.50
3102 5112 4.065789 CACCCTCTACAAGTCAAAACCTC 58.934 47.826 0.00 0.00 0.00 3.85
3103 5113 3.072622 ACCCTCTACAAGTCAAAACCTCC 59.927 47.826 0.00 0.00 0.00 4.30
3104 5114 3.328050 CCCTCTACAAGTCAAAACCTCCT 59.672 47.826 0.00 0.00 0.00 3.69
3105 5115 4.563786 CCCTCTACAAGTCAAAACCTCCTC 60.564 50.000 0.00 0.00 0.00 3.71
3106 5116 4.563786 CCTCTACAAGTCAAAACCTCCTCC 60.564 50.000 0.00 0.00 0.00 4.30
3107 5117 3.971305 TCTACAAGTCAAAACCTCCTCCA 59.029 43.478 0.00 0.00 0.00 3.86
3108 5118 3.662759 ACAAGTCAAAACCTCCTCCAA 57.337 42.857 0.00 0.00 0.00 3.53
3109 5119 4.184649 ACAAGTCAAAACCTCCTCCAAT 57.815 40.909 0.00 0.00 0.00 3.16
3110 5120 4.145052 ACAAGTCAAAACCTCCTCCAATC 58.855 43.478 0.00 0.00 0.00 2.67
3111 5121 3.441500 AGTCAAAACCTCCTCCAATCC 57.558 47.619 0.00 0.00 0.00 3.01
3112 5122 2.716424 AGTCAAAACCTCCTCCAATCCA 59.284 45.455 0.00 0.00 0.00 3.41
3113 5123 2.820197 GTCAAAACCTCCTCCAATCCAC 59.180 50.000 0.00 0.00 0.00 4.02
3114 5124 2.171003 CAAAACCTCCTCCAATCCACC 58.829 52.381 0.00 0.00 0.00 4.61
3115 5125 1.760405 AAACCTCCTCCAATCCACCT 58.240 50.000 0.00 0.00 0.00 4.00
3116 5126 1.290134 AACCTCCTCCAATCCACCTC 58.710 55.000 0.00 0.00 0.00 3.85
3117 5127 0.119155 ACCTCCTCCAATCCACCTCA 59.881 55.000 0.00 0.00 0.00 3.86
3118 5128 1.289160 CCTCCTCCAATCCACCTCAA 58.711 55.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.400884 ACCAGCAAGTAACAACAACATGAA 59.599 37.500 0.00 0.00 0.00 2.57
46 47 4.954442 TCGATCGACACATACGACATATC 58.046 43.478 15.15 0.00 42.37 1.63
52 65 2.610374 TGTCATCGATCGACACATACGA 59.390 45.455 22.06 5.69 38.45 3.43
86 99 0.694444 ACCCAGGTCACCACACTTCT 60.694 55.000 0.00 0.00 0.00 2.85
89 102 1.383943 TCACCCAGGTCACCACACT 60.384 57.895 0.00 0.00 0.00 3.55
135 148 7.417612 GGACATGCATAACCAAATAGTACAAG 58.582 38.462 14.08 0.00 0.00 3.16
165 178 6.851222 AAGAAAAGGATATATGTGTCAGCG 57.149 37.500 0.00 0.00 0.00 5.18
176 189 8.065007 TGGTAGCCCATAAAAAGAAAAGGATAT 58.935 33.333 0.00 0.00 35.17 1.63
199 212 1.757682 AACACCATCAAACACGTGGT 58.242 45.000 21.57 11.47 46.72 4.16
420 458 7.217200 AGATATAAGCCGTGCTCTTAATCAAA 58.783 34.615 0.00 0.00 38.25 2.69
458 498 9.862371 CCTTGTATATGCTCGATTAGAACTTAT 57.138 33.333 0.00 0.00 0.00 1.73
460 500 7.952671 TCCTTGTATATGCTCGATTAGAACTT 58.047 34.615 0.00 0.00 0.00 2.66
461 501 7.526142 TCCTTGTATATGCTCGATTAGAACT 57.474 36.000 0.00 0.00 0.00 3.01
463 503 7.867909 CACTTCCTTGTATATGCTCGATTAGAA 59.132 37.037 0.00 0.00 0.00 2.10
464 504 7.371159 CACTTCCTTGTATATGCTCGATTAGA 58.629 38.462 0.00 0.00 0.00 2.10
465 505 6.090088 GCACTTCCTTGTATATGCTCGATTAG 59.910 42.308 0.00 0.00 0.00 1.73
474 539 5.643348 TGTTGTGAGCACTTCCTTGTATATG 59.357 40.000 1.99 0.00 0.00 1.78
648 804 5.193527 CCTCTCCATCCTCTCCATATCTAGA 59.806 48.000 0.00 0.00 0.00 2.43
679 844 6.489675 ACAAAGCAAATATCTGCAATACTCG 58.510 36.000 3.41 0.00 45.18 4.18
758 2401 7.805071 GCATGTATGTTATCTCATTGTTTAGCC 59.195 37.037 0.00 0.00 0.00 3.93
771 2414 4.261322 CCAACCAGCTGCATGTATGTTATC 60.261 45.833 8.66 0.00 0.00 1.75
810 2456 2.036256 ACAACCCCCTGCATCTGC 59.964 61.111 0.00 0.00 42.50 4.26
811 2457 1.075482 ACACAACCCCCTGCATCTG 59.925 57.895 0.00 0.00 0.00 2.90
812 2458 1.075482 CACACAACCCCCTGCATCT 59.925 57.895 0.00 0.00 0.00 2.90
813 2459 1.978617 CCACACAACCCCCTGCATC 60.979 63.158 0.00 0.00 0.00 3.91
844 2566 0.605319 TTCCTCATTGACCGGTGCAC 60.605 55.000 14.63 8.80 0.00 4.57
845 2567 0.321564 CTTCCTCATTGACCGGTGCA 60.322 55.000 14.63 7.32 0.00 4.57
846 2568 1.026718 CCTTCCTCATTGACCGGTGC 61.027 60.000 14.63 4.13 0.00 5.01
847 2569 0.613260 TCCTTCCTCATTGACCGGTG 59.387 55.000 14.63 0.00 0.00 4.94
909 2650 2.866156 GCAAAGGTCCAAGAACAAAAGC 59.134 45.455 0.00 0.00 0.00 3.51
1251 3081 6.470456 AAAAGGAAGGAAATAGAGGAACCT 57.530 37.500 0.00 0.00 0.00 3.50
1329 3191 5.295292 CGGTGAATCAGCACATCTTCTTATT 59.705 40.000 13.13 0.00 40.52 1.40
1330 3192 4.813161 CGGTGAATCAGCACATCTTCTTAT 59.187 41.667 13.13 0.00 40.52 1.73
1331 3193 4.081697 TCGGTGAATCAGCACATCTTCTTA 60.082 41.667 13.13 0.00 40.52 2.10
1704 3585 4.729918 CGGAGCTGGCTGGCCTTT 62.730 66.667 13.05 0.00 36.94 3.11
1876 3763 1.843421 CCTCCAGGTTGACCCACAA 59.157 57.895 0.00 0.00 36.42 3.33
2156 4100 5.998363 ACTTAGTTTAAGCTGGAACTCCAAG 59.002 40.000 15.84 16.02 41.22 3.61
2316 4294 5.496556 TGGAATGACATAACAACGGAAGAT 58.503 37.500 0.00 0.00 0.00 2.40
2461 4444 2.187958 TGTTACTCACCATCCTCCAGG 58.812 52.381 0.00 0.00 0.00 4.45
2471 4454 1.351350 AGGCCTCCTTTGTTACTCACC 59.649 52.381 0.00 0.00 0.00 4.02
2477 4460 2.708861 TGACAGAAGGCCTCCTTTGTTA 59.291 45.455 5.23 2.41 44.82 2.41
2480 4463 2.276732 TTGACAGAAGGCCTCCTTTG 57.723 50.000 5.23 4.88 44.82 2.77
2543 4534 1.276138 CATAGGCGGTATCCTGCATGA 59.724 52.381 0.00 0.00 37.01 3.07
2648 4653 5.239525 ACTGAACAAACTTTCATAGCAGACC 59.760 40.000 0.00 0.00 34.96 3.85
2687 4692 5.220739 CGCTAGAAGAAGTCCCATTGATTTG 60.221 44.000 0.00 0.00 0.00 2.32
2688 4693 4.878397 CGCTAGAAGAAGTCCCATTGATTT 59.122 41.667 0.00 0.00 0.00 2.17
2689 4694 4.446371 CGCTAGAAGAAGTCCCATTGATT 58.554 43.478 0.00 0.00 0.00 2.57
2690 4695 3.181461 CCGCTAGAAGAAGTCCCATTGAT 60.181 47.826 0.00 0.00 0.00 2.57
2691 4696 2.168521 CCGCTAGAAGAAGTCCCATTGA 59.831 50.000 0.00 0.00 0.00 2.57
2768 4778 3.512724 CCTCCGGAACTTCTACCAAAGTA 59.487 47.826 5.23 0.00 38.52 2.24
2843 4853 3.624861 CCGGAGACAAGATGGAAGAAATG 59.375 47.826 0.00 0.00 0.00 2.32
2852 4862 3.533606 ATGAAGACCGGAGACAAGATG 57.466 47.619 9.46 0.00 0.00 2.90
2864 4874 5.295540 GCTCAATCCTGTAAGAATGAAGACC 59.704 44.000 0.00 0.00 34.07 3.85
2910 4920 5.933617 TCTTAGCAAGATTATGAGCCACAT 58.066 37.500 0.00 0.00 36.47 3.21
3008 5018 5.832539 AGGAAGGAGATGACTTCAAAAGA 57.167 39.130 7.39 0.00 44.69 2.52
3038 5048 2.421751 TTTTCCCTGTCAACCGAACA 57.578 45.000 0.00 0.00 0.00 3.18
3039 5049 2.030274 CCATTTTCCCTGTCAACCGAAC 60.030 50.000 0.00 0.00 0.00 3.95
3040 5050 2.158593 TCCATTTTCCCTGTCAACCGAA 60.159 45.455 0.00 0.00 0.00 4.30
3041 5051 1.422024 TCCATTTTCCCTGTCAACCGA 59.578 47.619 0.00 0.00 0.00 4.69
3042 5052 1.812571 CTCCATTTTCCCTGTCAACCG 59.187 52.381 0.00 0.00 0.00 4.44
3043 5053 2.171003 CCTCCATTTTCCCTGTCAACC 58.829 52.381 0.00 0.00 0.00 3.77
3044 5054 2.171003 CCCTCCATTTTCCCTGTCAAC 58.829 52.381 0.00 0.00 0.00 3.18
3045 5055 1.077005 CCCCTCCATTTTCCCTGTCAA 59.923 52.381 0.00 0.00 0.00 3.18
3046 5056 0.704076 CCCCTCCATTTTCCCTGTCA 59.296 55.000 0.00 0.00 0.00 3.58
3047 5057 0.704664 ACCCCTCCATTTTCCCTGTC 59.295 55.000 0.00 0.00 0.00 3.51
3048 5058 1.167033 AACCCCTCCATTTTCCCTGT 58.833 50.000 0.00 0.00 0.00 4.00
3049 5059 1.901833 CAAACCCCTCCATTTTCCCTG 59.098 52.381 0.00 0.00 0.00 4.45
3050 5060 1.203300 CCAAACCCCTCCATTTTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
3051 5061 1.275666 CCAAACCCCTCCATTTTCCC 58.724 55.000 0.00 0.00 0.00 3.97
3052 5062 0.613260 GCCAAACCCCTCCATTTTCC 59.387 55.000 0.00 0.00 0.00 3.13
3053 5063 1.276138 CTGCCAAACCCCTCCATTTTC 59.724 52.381 0.00 0.00 0.00 2.29
3054 5064 1.351076 CTGCCAAACCCCTCCATTTT 58.649 50.000 0.00 0.00 0.00 1.82
3055 5065 0.545071 CCTGCCAAACCCCTCCATTT 60.545 55.000 0.00 0.00 0.00 2.32
3056 5066 1.079073 CCTGCCAAACCCCTCCATT 59.921 57.895 0.00 0.00 0.00 3.16
3057 5067 2.772924 CCTGCCAAACCCCTCCAT 59.227 61.111 0.00 0.00 0.00 3.41
3058 5068 3.589542 CCCTGCCAAACCCCTCCA 61.590 66.667 0.00 0.00 0.00 3.86
3059 5069 2.168272 AATCCCTGCCAAACCCCTCC 62.168 60.000 0.00 0.00 0.00 4.30
3060 5070 0.629058 TAATCCCTGCCAAACCCCTC 59.371 55.000 0.00 0.00 0.00 4.30
3061 5071 0.335019 GTAATCCCTGCCAAACCCCT 59.665 55.000 0.00 0.00 0.00 4.79
3062 5072 0.040499 TGTAATCCCTGCCAAACCCC 59.960 55.000 0.00 0.00 0.00 4.95
3063 5073 1.182667 GTGTAATCCCTGCCAAACCC 58.817 55.000 0.00 0.00 0.00 4.11
3064 5074 1.182667 GGTGTAATCCCTGCCAAACC 58.817 55.000 0.00 0.00 0.00 3.27
3065 5075 1.182667 GGGTGTAATCCCTGCCAAAC 58.817 55.000 0.00 0.00 43.85 2.93
3066 5076 3.681909 GGGTGTAATCCCTGCCAAA 57.318 52.632 0.00 0.00 43.85 3.28
3074 5084 5.416271 TTGACTTGTAGAGGGTGTAATCC 57.584 43.478 0.00 0.00 0.00 3.01
3075 5085 6.148976 GGTTTTGACTTGTAGAGGGTGTAATC 59.851 42.308 0.00 0.00 0.00 1.75
3076 5086 6.002082 GGTTTTGACTTGTAGAGGGTGTAAT 58.998 40.000 0.00 0.00 0.00 1.89
3077 5087 5.131475 AGGTTTTGACTTGTAGAGGGTGTAA 59.869 40.000 0.00 0.00 0.00 2.41
3078 5088 4.657039 AGGTTTTGACTTGTAGAGGGTGTA 59.343 41.667 0.00 0.00 0.00 2.90
3079 5089 3.458487 AGGTTTTGACTTGTAGAGGGTGT 59.542 43.478 0.00 0.00 0.00 4.16
3080 5090 4.065789 GAGGTTTTGACTTGTAGAGGGTG 58.934 47.826 0.00 0.00 0.00 4.61
3081 5091 3.072622 GGAGGTTTTGACTTGTAGAGGGT 59.927 47.826 0.00 0.00 0.00 4.34
3082 5092 3.328050 AGGAGGTTTTGACTTGTAGAGGG 59.672 47.826 0.00 0.00 0.00 4.30
3083 5093 4.563786 GGAGGAGGTTTTGACTTGTAGAGG 60.564 50.000 0.00 0.00 0.00 3.69
3084 5094 4.040461 TGGAGGAGGTTTTGACTTGTAGAG 59.960 45.833 0.00 0.00 0.00 2.43
3085 5095 3.971305 TGGAGGAGGTTTTGACTTGTAGA 59.029 43.478 0.00 0.00 0.00 2.59
3086 5096 4.351874 TGGAGGAGGTTTTGACTTGTAG 57.648 45.455 0.00 0.00 0.00 2.74
3087 5097 4.781775 TTGGAGGAGGTTTTGACTTGTA 57.218 40.909 0.00 0.00 0.00 2.41
3088 5098 3.662759 TTGGAGGAGGTTTTGACTTGT 57.337 42.857 0.00 0.00 0.00 3.16
3089 5099 3.507622 GGATTGGAGGAGGTTTTGACTTG 59.492 47.826 0.00 0.00 0.00 3.16
3090 5100 3.140144 TGGATTGGAGGAGGTTTTGACTT 59.860 43.478 0.00 0.00 0.00 3.01
3091 5101 2.716424 TGGATTGGAGGAGGTTTTGACT 59.284 45.455 0.00 0.00 0.00 3.41
3092 5102 2.820197 GTGGATTGGAGGAGGTTTTGAC 59.180 50.000 0.00 0.00 0.00 3.18
3093 5103 2.225017 GGTGGATTGGAGGAGGTTTTGA 60.225 50.000 0.00 0.00 0.00 2.69
3094 5104 2.171003 GGTGGATTGGAGGAGGTTTTG 58.829 52.381 0.00 0.00 0.00 2.44
3095 5105 2.041755 GAGGTGGATTGGAGGAGGTTTT 59.958 50.000 0.00 0.00 0.00 2.43
3096 5106 1.636003 GAGGTGGATTGGAGGAGGTTT 59.364 52.381 0.00 0.00 0.00 3.27
3097 5107 1.290134 GAGGTGGATTGGAGGAGGTT 58.710 55.000 0.00 0.00 0.00 3.50
3098 5108 0.119155 TGAGGTGGATTGGAGGAGGT 59.881 55.000 0.00 0.00 0.00 3.85
3099 5109 1.289160 TTGAGGTGGATTGGAGGAGG 58.711 55.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.