Multiple sequence alignment - TraesCS6B01G443500

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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 TraesCS6B01G443500 chr6B 100.000 2432 0 0 1 2432 706529361 706531792 0.000000e+00 4492.0
1 TraesCS6B01G443500 chr6B 94.225 2199 80 25 1 2175 706444283 706446458 0.000000e+00 3314.0
2 TraesCS6B01G443500 chr6B 81.320 1424 192 43 827 2192 705643062 705644469 0.000000e+00 1088.0
3 TraesCS6B01G443500 chr6B 80.292 1370 176 48 906 2192 705939582 705940940 0.000000e+00 948.0
4 TraesCS6B01G443500 chr6B 83.218 864 113 14 920 1753 705826561 705827422 0.000000e+00 763.0
5 TraesCS6B01G443500 chr6B 80.410 975 146 20 1259 2192 705841317 705842287 0.000000e+00 701.0
6 TraesCS6B01G443500 chr6B 80.215 743 121 7 1473 2192 705503599 705504338 3.560000e-148 534.0
7 TraesCS6B01G443500 chr6B 88.378 370 36 3 920 1283 705502685 705503053 2.870000e-119 438.0
8 TraesCS6B01G443500 chr6B 81.909 503 69 12 1269 1750 705503081 705503582 2.910000e-109 405.0
9 TraesCS6B01G443500 chr6B 96.721 244 5 3 2175 2416 706462950 706463192 1.050000e-108 403.0
10 TraesCS6B01G443500 chr6B 90.083 242 16 5 200 436 706112190 706112428 8.450000e-80 307.0
11 TraesCS6B01G443500 chr6B 89.069 247 22 3 194 436 705758467 705758712 3.930000e-78 302.0
12 TraesCS6B01G443500 chr6B 88.688 221 18 3 222 436 706352616 706352835 1.850000e-66 263.0
13 TraesCS6B01G443500 chr6B 88.688 221 18 3 222 436 706409602 706409821 1.850000e-66 263.0
14 TraesCS6B01G443500 chr6B 79.832 357 66 6 1839 2192 705708613 705708966 3.100000e-64 255.0
15 TraesCS6B01G443500 chr6B 95.238 42 1 1 598 639 705760001 705760041 5.610000e-07 65.8
16 TraesCS6B01G443500 chr6A 88.466 1682 101 36 178 1826 609821567 609823188 0.000000e+00 1945.0
17 TraesCS6B01G443500 chr6A 81.544 894 100 24 920 1753 609573230 609574118 0.000000e+00 676.0
18 TraesCS6B01G443500 chr6A 79.101 957 150 25 1281 2192 609669089 609670040 4.440000e-172 614.0
19 TraesCS6B01G443500 chr6A 88.889 360 36 2 920 1276 609668678 609669036 7.980000e-120 440.0
20 TraesCS6B01G443500 chr6A 91.064 235 19 2 200 434 609816015 609816247 1.400000e-82 316.0
21 TraesCS6B01G443500 chr6D 91.340 970 68 5 858 1826 463123845 463124799 0.000000e+00 1312.0
22 TraesCS6B01G443500 chr6D 94.017 351 15 2 197 547 463091537 463091881 5.960000e-146 527.0
23 TraesCS6B01G443500 chr6D 80.191 732 114 18 1485 2192 462857298 462858022 9.970000e-144 520.0
24 TraesCS6B01G443500 chr6D 95.486 288 13 0 575 862 463091877 463092164 6.130000e-126 460.0
25 TraesCS6B01G443500 chr6D 89.091 220 18 2 222 436 463073952 463074170 3.990000e-68 268.0
26 TraesCS6B01G443500 chr6D 92.045 176 11 3 1 175 463091023 463091196 6.720000e-61 244.0
27 TraesCS6B01G443500 chr6D 84.559 136 14 6 61 193 224772895 224773026 7.060000e-26 128.0
28 TraesCS6B01G443500 chr7B 77.304 868 170 19 981 1828 744217365 744216505 1.010000e-133 486.0
29 TraesCS6B01G443500 chr2D 91.304 115 10 0 61 175 15520512 15520398 9.000000e-35 158.0
30 TraesCS6B01G443500 chr2D 100.000 28 0 0 522 549 458736120 458736093 4.000000e-03 52.8
31 TraesCS6B01G443500 chr1B 88.148 135 12 4 61 193 458013924 458013792 9.000000e-35 158.0
32 TraesCS6B01G443500 chr5A 91.743 109 9 0 62 170 616354833 616354941 4.190000e-33 152.0
33 TraesCS6B01G443500 chr7D 89.565 115 12 0 61 175 115138490 115138376 1.950000e-31 147.0
34 TraesCS6B01G443500 chr3D 86.885 122 12 4 53 174 514684047 514684164 1.520000e-27 134.0
35 TraesCS6B01G443500 chr4B 86.179 123 15 2 61 182 10396633 10396512 5.460000e-27 132.0
36 TraesCS6B01G443500 chr2B 100.000 28 0 0 522 549 539706610 539706583 4.000000e-03 52.8


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 TraesCS6B01G443500 chr6B 706529361 706531792 2431 False 4492.000000 4492 100.000000 1 2432 1 chr6B.!!$F11 2431
1 TraesCS6B01G443500 chr6B 706444283 706446458 2175 False 3314.000000 3314 94.225000 1 2175 1 chr6B.!!$F9 2174
2 TraesCS6B01G443500 chr6B 705643062 705644469 1407 False 1088.000000 1088 81.320000 827 2192 1 chr6B.!!$F1 1365
3 TraesCS6B01G443500 chr6B 705939582 705940940 1358 False 948.000000 948 80.292000 906 2192 1 chr6B.!!$F5 1286
4 TraesCS6B01G443500 chr6B 705826561 705827422 861 False 763.000000 763 83.218000 920 1753 1 chr6B.!!$F3 833
5 TraesCS6B01G443500 chr6B 705841317 705842287 970 False 701.000000 701 80.410000 1259 2192 1 chr6B.!!$F4 933
6 TraesCS6B01G443500 chr6B 705502685 705504338 1653 False 459.000000 534 83.500667 920 2192 3 chr6B.!!$F12 1272
7 TraesCS6B01G443500 chr6A 609821567 609823188 1621 False 1945.000000 1945 88.466000 178 1826 1 chr6A.!!$F3 1648
8 TraesCS6B01G443500 chr6A 609573230 609574118 888 False 676.000000 676 81.544000 920 1753 1 chr6A.!!$F1 833
9 TraesCS6B01G443500 chr6A 609668678 609670040 1362 False 527.000000 614 83.995000 920 2192 2 chr6A.!!$F4 1272
10 TraesCS6B01G443500 chr6D 463123845 463124799 954 False 1312.000000 1312 91.340000 858 1826 1 chr6D.!!$F4 968
11 TraesCS6B01G443500 chr6D 462857298 462858022 724 False 520.000000 520 80.191000 1485 2192 1 chr6D.!!$F2 707
12 TraesCS6B01G443500 chr6D 463091023 463092164 1141 False 410.333333 527 93.849333 1 862 3 chr6D.!!$F5 861
13 TraesCS6B01G443500 chr7B 744216505 744217365 860 True 486.000000 486 77.304000 981 1828 1 chr7B.!!$R1 847

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
350 671 0.317479 GGTTACGAGGTGTGTCAGCT 59.683 55.0 1.03 1.03 45.28 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2814 0.168788 ATGCACCGTGAATTCTTGCG 59.831 50.0 7.05 8.55 35.9 4.85 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
144 146 4.082523 GCACACAGCCGGCCTCTA 62.083 66.667 26.15 0.00 37.23 2.43
175 177 2.631428 CACACAGCCAACCGAACG 59.369 61.111 0.00 0.00 0.00 3.95
252 573 2.732289 GCACCTTTGCCCAAGAGAA 58.268 52.632 0.00 0.00 43.66 2.87
350 671 0.317479 GGTTACGAGGTGTGTCAGCT 59.683 55.000 1.03 1.03 45.28 4.24
449 770 3.278668 AGAAAGAGTGCTGCTATGCAT 57.721 42.857 3.79 3.79 45.23 3.96
499 820 1.154338 GCGTATATCCGTCCGTCCG 60.154 63.158 0.00 0.00 0.00 4.79
716 1038 7.166473 CGGCAGCATGTAGAAAAAGAATTTATC 59.834 37.037 0.00 0.00 35.90 1.75
783 1105 2.105006 AATGCGAGCATGACTTGTCT 57.895 45.000 11.64 0.00 36.68 3.41
1059 1428 4.603131 TGCTCCTTTGCCTATTGATCTTT 58.397 39.130 0.00 0.00 0.00 2.52
1316 1763 3.682696 TGAGCAGATCATTGAGCTTGTT 58.317 40.909 0.71 0.00 37.48 2.83
1322 1769 0.599558 TCATTGAGCTTGTTGGCAGC 59.400 50.000 0.00 0.00 34.17 5.25
1326 1773 2.970974 GAGCTTGTTGGCAGCGGAC 61.971 63.158 0.00 0.00 34.17 4.79
1328 1775 2.639286 CTTGTTGGCAGCGGACAC 59.361 61.111 0.00 0.00 0.00 3.67
1329 1776 2.124529 TTGTTGGCAGCGGACACA 60.125 55.556 0.00 0.00 0.00 3.72
1330 1777 2.121564 CTTGTTGGCAGCGGACACAG 62.122 60.000 0.00 0.00 0.00 3.66
1338 1785 2.210013 AGCGGACACAGGCTCTTCA 61.210 57.895 0.00 0.00 33.32 3.02
1360 1807 5.242838 TCATTGGCTACTTTACAAAACCTGG 59.757 40.000 0.00 0.00 0.00 4.45
1375 1827 3.421394 ACCTGGGGTATCTTGATCTGA 57.579 47.619 0.00 0.00 32.11 3.27
1376 1828 3.312890 ACCTGGGGTATCTTGATCTGAG 58.687 50.000 0.00 0.00 32.11 3.35
1377 1829 2.038295 CCTGGGGTATCTTGATCTGAGC 59.962 54.545 0.00 0.00 0.00 4.26
1378 1830 1.688735 TGGGGTATCTTGATCTGAGCG 59.311 52.381 0.00 0.00 0.00 5.03
1379 1831 1.001406 GGGGTATCTTGATCTGAGCGG 59.999 57.143 0.00 0.00 0.00 5.52
1428 1880 2.306847 GTGTTCTTGGCTTCCCTCAAA 58.693 47.619 0.00 0.00 0.00 2.69
1494 1946 5.184892 AGAATACCTTCTCAACTTGGCAT 57.815 39.130 0.00 0.00 37.09 4.40
1512 1964 5.553123 TGGCATTCTCTCAAAATTGCATTT 58.447 33.333 0.00 0.00 0.00 2.32
1575 2049 2.408565 TGGTCACCAGGTCTCTCTTTT 58.591 47.619 0.00 0.00 0.00 2.27
1593 2067 2.275134 TTGCTGAGCCATCTTGACAA 57.725 45.000 0.23 0.00 0.00 3.18
1655 2129 4.043435 AGAGGGTTAACATGCTTCCTTCTT 59.957 41.667 8.10 0.00 32.11 2.52
1766 2534 8.981659 TCCTTGATATGTCTGAGAATAACTTCA 58.018 33.333 0.00 0.00 33.56 3.02
1785 2553 3.544684 TCAACACTTCACTCAAGCATGT 58.455 40.909 0.00 0.00 35.17 3.21
1794 2562 4.671377 TCACTCAAGCATGTGTTGTTTTC 58.329 39.130 9.06 0.00 35.82 2.29
1845 2633 4.442052 CCTCTCCTATTGCGAGTGATTTGA 60.442 45.833 0.00 0.00 0.00 2.69
1871 2659 2.455674 TGACGTCCCTTCAAGTCATG 57.544 50.000 14.12 0.00 38.52 3.07
2020 2814 2.689983 CAAAGGGCTCATGGAATACACC 59.310 50.000 0.00 0.00 0.00 4.16
2183 2977 2.684001 TGAAAACACGTGACCTCAGT 57.316 45.000 25.01 0.00 0.00 3.41
2192 2986 5.227908 ACACGTGACCTCAGTTACAATAAG 58.772 41.667 25.01 0.00 32.14 1.73
2193 2987 5.221382 ACACGTGACCTCAGTTACAATAAGT 60.221 40.000 25.01 0.00 32.14 2.24
2194 2988 5.694910 CACGTGACCTCAGTTACAATAAGTT 59.305 40.000 10.90 0.00 32.14 2.66
2195 2989 6.202188 CACGTGACCTCAGTTACAATAAGTTT 59.798 38.462 10.90 0.00 32.14 2.66
2196 2990 6.764560 ACGTGACCTCAGTTACAATAAGTTTT 59.235 34.615 0.00 0.00 32.14 2.43
2197 2991 7.042254 ACGTGACCTCAGTTACAATAAGTTTTC 60.042 37.037 0.00 0.00 32.14 2.29
2198 2992 7.170998 CGTGACCTCAGTTACAATAAGTTTTCT 59.829 37.037 0.00 0.00 32.14 2.52
2199 2993 8.837389 GTGACCTCAGTTACAATAAGTTTTCTT 58.163 33.333 0.00 0.00 36.94 2.52
2200 2994 9.052759 TGACCTCAGTTACAATAAGTTTTCTTC 57.947 33.333 0.00 0.00 40.91 2.87
2201 2995 9.274206 GACCTCAGTTACAATAAGTTTTCTTCT 57.726 33.333 0.00 0.00 40.91 2.85
2202 2996 9.628500 ACCTCAGTTACAATAAGTTTTCTTCTT 57.372 29.630 0.00 0.00 40.91 2.52
2230 3024 7.654022 TTTTTAGATGGAGGTGAGTGTTTTT 57.346 32.000 0.00 0.00 0.00 1.94
2255 3049 6.446781 TTTCTTTGAGATTGAGATGATGCC 57.553 37.500 0.00 0.00 0.00 4.40
2256 3050 4.458397 TCTTTGAGATTGAGATGATGCCC 58.542 43.478 0.00 0.00 0.00 5.36
2257 3051 2.945080 TGAGATTGAGATGATGCCCC 57.055 50.000 0.00 0.00 0.00 5.80
2258 3052 2.129363 TGAGATTGAGATGATGCCCCA 58.871 47.619 0.00 0.00 0.00 4.96
2259 3053 2.714793 TGAGATTGAGATGATGCCCCAT 59.285 45.455 0.00 0.00 0.00 4.00
2260 3054 3.082548 GAGATTGAGATGATGCCCCATG 58.917 50.000 0.00 0.00 0.00 3.66
2261 3055 2.445905 AGATTGAGATGATGCCCCATGT 59.554 45.455 0.00 0.00 0.00 3.21
2262 3056 3.654321 AGATTGAGATGATGCCCCATGTA 59.346 43.478 0.00 0.00 0.00 2.29
2263 3057 4.291513 AGATTGAGATGATGCCCCATGTAT 59.708 41.667 0.00 0.00 0.00 2.29
2264 3058 4.458256 TTGAGATGATGCCCCATGTATT 57.542 40.909 0.00 0.00 0.00 1.89
2265 3059 4.458256 TGAGATGATGCCCCATGTATTT 57.542 40.909 0.00 0.00 0.00 1.40
2266 3060 4.806892 TGAGATGATGCCCCATGTATTTT 58.193 39.130 0.00 0.00 0.00 1.82
2267 3061 5.210430 TGAGATGATGCCCCATGTATTTTT 58.790 37.500 0.00 0.00 0.00 1.94
2286 3080 5.837586 TTTTTAAATGGAAATGAGCACGC 57.162 34.783 0.00 0.00 0.00 5.34
2287 3081 4.511617 TTTAAATGGAAATGAGCACGCA 57.488 36.364 0.00 0.00 0.00 5.24
2288 3082 4.511617 TTAAATGGAAATGAGCACGCAA 57.488 36.364 0.00 0.00 0.00 4.85
2289 3083 2.352503 AATGGAAATGAGCACGCAAC 57.647 45.000 0.00 0.00 0.00 4.17
2290 3084 1.246649 ATGGAAATGAGCACGCAACA 58.753 45.000 0.00 0.00 0.00 3.33
2291 3085 1.246649 TGGAAATGAGCACGCAACAT 58.753 45.000 0.00 0.00 0.00 2.71
2292 3086 1.068402 TGGAAATGAGCACGCAACATG 60.068 47.619 0.00 0.00 0.00 3.21
2293 3087 0.986992 GAAATGAGCACGCAACATGC 59.013 50.000 0.00 0.00 43.74 4.06
2294 3088 0.388907 AAATGAGCACGCAACATGCC 60.389 50.000 0.00 0.00 44.53 4.40
2295 3089 1.525718 AATGAGCACGCAACATGCCA 61.526 50.000 0.00 0.00 44.53 4.92
2296 3090 2.126734 GAGCACGCAACATGCCAC 60.127 61.111 0.00 0.00 44.53 5.01
2297 3091 3.933900 GAGCACGCAACATGCCACG 62.934 63.158 0.00 0.00 44.53 4.94
2298 3092 4.326766 GCACGCAACATGCCACGT 62.327 61.111 0.00 0.00 41.12 4.49
2300 3094 2.590291 ACGCAACATGCCACGTGA 60.590 55.556 19.30 0.00 41.12 4.35
2301 3095 2.127270 CGCAACATGCCACGTGAC 60.127 61.111 19.30 5.85 41.12 3.67
2302 3096 2.891221 CGCAACATGCCACGTGACA 61.891 57.895 19.30 13.27 41.12 3.58
2303 3097 1.370414 GCAACATGCCACGTGACAC 60.370 57.895 19.30 6.69 37.42 3.67
2304 3098 1.785041 GCAACATGCCACGTGACACT 61.785 55.000 19.30 0.00 37.42 3.55
2305 3099 0.662619 CAACATGCCACGTGACACTT 59.337 50.000 19.30 3.82 0.00 3.16
2306 3100 0.662619 AACATGCCACGTGACACTTG 59.337 50.000 19.30 10.63 0.00 3.16
2307 3101 1.081906 CATGCCACGTGACACTTGC 60.082 57.895 19.30 11.32 0.00 4.01
2308 3102 1.227943 ATGCCACGTGACACTTGCT 60.228 52.632 19.30 0.00 0.00 3.91
2309 3103 1.509644 ATGCCACGTGACACTTGCTG 61.510 55.000 19.30 0.00 0.00 4.41
2310 3104 2.896801 GCCACGTGACACTTGCTGG 61.897 63.158 19.30 5.54 0.00 4.85
2311 3105 1.523711 CCACGTGACACTTGCTGGT 60.524 57.895 19.30 0.00 0.00 4.00
2312 3106 1.095228 CCACGTGACACTTGCTGGTT 61.095 55.000 19.30 0.00 0.00 3.67
2313 3107 1.577468 CACGTGACACTTGCTGGTTA 58.423 50.000 10.90 0.00 0.00 2.85
2314 3108 2.143122 CACGTGACACTTGCTGGTTAT 58.857 47.619 10.90 0.00 0.00 1.89
2315 3109 2.157668 CACGTGACACTTGCTGGTTATC 59.842 50.000 10.90 0.00 0.00 1.75
2316 3110 2.037251 ACGTGACACTTGCTGGTTATCT 59.963 45.455 3.68 0.00 0.00 1.98
2317 3111 2.413112 CGTGACACTTGCTGGTTATCTG 59.587 50.000 3.68 0.00 0.00 2.90
2318 3112 3.403038 GTGACACTTGCTGGTTATCTGT 58.597 45.455 0.00 0.00 0.00 3.41
2319 3113 3.187227 GTGACACTTGCTGGTTATCTGTG 59.813 47.826 0.00 0.00 0.00 3.66
2320 3114 3.181455 TGACACTTGCTGGTTATCTGTGT 60.181 43.478 0.00 0.00 39.44 3.72
2321 3115 3.141398 ACACTTGCTGGTTATCTGTGTG 58.859 45.455 0.00 0.00 36.10 3.82
2322 3116 3.181455 ACACTTGCTGGTTATCTGTGTGA 60.181 43.478 0.00 0.00 36.10 3.58
2323 3117 3.434641 CACTTGCTGGTTATCTGTGTGAG 59.565 47.826 0.00 0.00 0.00 3.51
2324 3118 2.099141 TGCTGGTTATCTGTGTGAGC 57.901 50.000 0.00 0.00 0.00 4.26
2325 3119 1.347378 TGCTGGTTATCTGTGTGAGCA 59.653 47.619 0.00 0.00 0.00 4.26
2326 3120 2.224499 TGCTGGTTATCTGTGTGAGCAA 60.224 45.455 0.00 0.00 0.00 3.91
2327 3121 2.417933 GCTGGTTATCTGTGTGAGCAAG 59.582 50.000 0.00 0.00 0.00 4.01
2328 3122 3.866066 GCTGGTTATCTGTGTGAGCAAGA 60.866 47.826 0.00 0.00 0.00 3.02
2329 3123 4.511527 CTGGTTATCTGTGTGAGCAAGAT 58.488 43.478 0.00 0.00 0.00 2.40
2330 3124 4.910195 TGGTTATCTGTGTGAGCAAGATT 58.090 39.130 0.00 0.00 0.00 2.40
2331 3125 4.937620 TGGTTATCTGTGTGAGCAAGATTC 59.062 41.667 0.00 0.00 0.00 2.52
2332 3126 4.333926 GGTTATCTGTGTGAGCAAGATTCC 59.666 45.833 0.00 0.00 0.00 3.01
2333 3127 3.996921 ATCTGTGTGAGCAAGATTCCT 57.003 42.857 0.00 0.00 0.00 3.36
2334 3128 3.777106 TCTGTGTGAGCAAGATTCCTT 57.223 42.857 0.00 0.00 0.00 3.36
2335 3129 4.090761 TCTGTGTGAGCAAGATTCCTTT 57.909 40.909 0.00 0.00 0.00 3.11
2336 3130 4.464008 TCTGTGTGAGCAAGATTCCTTTT 58.536 39.130 0.00 0.00 0.00 2.27
2337 3131 4.889409 TCTGTGTGAGCAAGATTCCTTTTT 59.111 37.500 0.00 0.00 0.00 1.94
2355 3149 3.992943 TTTTAAGATGAAGGCGAGGGA 57.007 42.857 0.00 0.00 0.00 4.20
2356 3150 4.503714 TTTTAAGATGAAGGCGAGGGAT 57.496 40.909 0.00 0.00 0.00 3.85
2357 3151 4.503714 TTTAAGATGAAGGCGAGGGATT 57.496 40.909 0.00 0.00 0.00 3.01
2358 3152 4.503714 TTAAGATGAAGGCGAGGGATTT 57.496 40.909 0.00 0.00 0.00 2.17
2359 3153 3.372440 AAGATGAAGGCGAGGGATTTT 57.628 42.857 0.00 0.00 0.00 1.82
2360 3154 3.372440 AGATGAAGGCGAGGGATTTTT 57.628 42.857 0.00 0.00 0.00 1.94
2383 3177 9.816787 TTTTTGTAGGTAAAGATAAGAACCCAT 57.183 29.630 0.00 0.00 32.10 4.00
2384 3178 8.801882 TTTGTAGGTAAAGATAAGAACCCATG 57.198 34.615 0.00 0.00 32.10 3.66
2385 3179 7.504926 TGTAGGTAAAGATAAGAACCCATGT 57.495 36.000 0.00 0.00 32.10 3.21
2386 3180 8.612486 TGTAGGTAAAGATAAGAACCCATGTA 57.388 34.615 0.00 0.00 32.10 2.29
2387 3181 9.220906 TGTAGGTAAAGATAAGAACCCATGTAT 57.779 33.333 0.00 0.00 32.10 2.29
2390 3184 9.628500 AGGTAAAGATAAGAACCCATGTATTTC 57.372 33.333 0.00 0.00 32.10 2.17
2391 3185 9.628500 GGTAAAGATAAGAACCCATGTATTTCT 57.372 33.333 0.00 0.00 0.00 2.52
2401 3195 9.753674 AGAACCCATGTATTTCTTTTTAGATGA 57.246 29.630 0.00 0.00 0.00 2.92
2412 3206 8.864069 TTTCTTTTTAGATGAAAACGAATGCA 57.136 26.923 0.00 0.00 41.94 3.96
2413 3207 7.851822 TCTTTTTAGATGAAAACGAATGCAC 57.148 32.000 0.00 0.00 36.74 4.57
2414 3208 7.421599 TCTTTTTAGATGAAAACGAATGCACA 58.578 30.769 0.00 0.00 36.74 4.57
2415 3209 7.591057 TCTTTTTAGATGAAAACGAATGCACAG 59.409 33.333 0.00 0.00 36.74 3.66
2416 3210 3.207474 AGATGAAAACGAATGCACAGC 57.793 42.857 0.00 0.00 0.00 4.40
2417 3211 2.816087 AGATGAAAACGAATGCACAGCT 59.184 40.909 0.00 0.00 0.00 4.24
2418 3212 3.254166 AGATGAAAACGAATGCACAGCTT 59.746 39.130 0.00 0.00 0.00 3.74
2419 3213 2.998772 TGAAAACGAATGCACAGCTTC 58.001 42.857 0.00 0.00 0.00 3.86
2420 3214 2.618241 TGAAAACGAATGCACAGCTTCT 59.382 40.909 0.00 0.00 0.00 2.85
2421 3215 3.066621 TGAAAACGAATGCACAGCTTCTT 59.933 39.130 0.00 0.00 0.00 2.52
2422 3216 2.977405 AACGAATGCACAGCTTCTTC 57.023 45.000 0.00 0.00 0.00 2.87
2423 3217 2.175878 ACGAATGCACAGCTTCTTCT 57.824 45.000 0.00 0.00 0.00 2.85
2424 3218 2.072298 ACGAATGCACAGCTTCTTCTC 58.928 47.619 0.00 0.00 0.00 2.87
2425 3219 2.071540 CGAATGCACAGCTTCTTCTCA 58.928 47.619 0.00 0.00 0.00 3.27
2426 3220 2.481568 CGAATGCACAGCTTCTTCTCAA 59.518 45.455 0.00 0.00 0.00 3.02
2427 3221 3.424565 CGAATGCACAGCTTCTTCTCAAG 60.425 47.826 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 146 2.993899 GCTGTGTGCATCTTAGTTACGT 59.006 45.455 0.00 0.00 42.31 3.57
175 177 3.880490 TCCATGTGTGTTTTCCTGTGTAC 59.120 43.478 0.00 0.00 0.00 2.90
252 573 3.419154 AAGGTGCCCTAGCTACCTT 57.581 52.632 11.40 11.40 46.58 3.50
333 654 1.037493 ACAGCTGACACACCTCGTAA 58.963 50.000 23.35 0.00 0.00 3.18
350 671 1.486310 ACTCAACTCACAGGCTTCACA 59.514 47.619 0.00 0.00 0.00 3.58
449 770 2.125202 ATCGTCCGCGCATCATCGTA 62.125 55.000 8.75 0.00 38.14 3.43
490 811 0.934901 CTGATATGCACGGACGGACG 60.935 60.000 0.00 0.00 40.31 4.79
499 820 5.812642 ACAGCTACACTTTACTGATATGCAC 59.187 40.000 0.00 0.00 34.25 4.57
729 1051 6.402550 CCATTCCTCAAGTTTGTTGATCGTAG 60.403 42.308 0.00 0.00 0.00 3.51
783 1105 7.339466 AGTGCCTTCTTAAAAGTCTTCTTTGAA 59.661 33.333 0.00 0.00 42.26 2.69
1059 1428 1.761174 GGAAGTGGACCCTGCTTGA 59.239 57.895 0.00 0.00 0.00 3.02
1322 1769 1.081892 CAATGAAGAGCCTGTGTCCG 58.918 55.000 0.00 0.00 0.00 4.79
1326 1773 2.012673 GTAGCCAATGAAGAGCCTGTG 58.987 52.381 0.00 0.00 0.00 3.66
1328 1775 2.706339 AGTAGCCAATGAAGAGCCTG 57.294 50.000 0.00 0.00 0.00 4.85
1329 1776 3.728385 AAAGTAGCCAATGAAGAGCCT 57.272 42.857 0.00 0.00 0.00 4.58
1330 1777 4.261801 TGTAAAGTAGCCAATGAAGAGCC 58.738 43.478 0.00 0.00 0.00 4.70
1338 1785 4.526650 CCCAGGTTTTGTAAAGTAGCCAAT 59.473 41.667 0.00 0.00 0.00 3.16
1360 1807 1.001406 CCCGCTCAGATCAAGATACCC 59.999 57.143 0.00 0.00 0.00 3.69
1375 1827 2.289195 TGTCGTTGAAGTAATTCCCGCT 60.289 45.455 0.00 0.00 0.00 5.52
1376 1828 2.070783 TGTCGTTGAAGTAATTCCCGC 58.929 47.619 0.00 1.32 0.00 6.13
1377 1829 3.061322 TGTGTCGTTGAAGTAATTCCCG 58.939 45.455 0.00 3.35 0.00 5.14
1378 1830 4.612939 GCTTGTGTCGTTGAAGTAATTCCC 60.613 45.833 0.00 0.00 0.00 3.97
1379 1831 4.024387 TGCTTGTGTCGTTGAAGTAATTCC 60.024 41.667 0.00 0.00 0.00 3.01
1512 1964 7.528996 AAATCATTCCAACTGACATCAAGAA 57.471 32.000 0.00 0.00 0.00 2.52
1543 2016 2.100252 CTGGTGACCATGCAATTCCATC 59.900 50.000 4.03 0.00 30.82 3.51
1549 2022 0.700564 AGACCTGGTGACCATGCAAT 59.299 50.000 4.03 0.00 30.82 3.56
1575 2049 1.348696 TCTTGTCAAGATGGCTCAGCA 59.651 47.619 11.36 0.00 31.20 4.41
1593 2067 1.853963 ACTAAGATCCGCACCACTCT 58.146 50.000 0.00 0.00 0.00 3.24
1655 2129 3.295973 AGGGCAACAGAAGCACTTTAAA 58.704 40.909 0.00 0.00 44.98 1.52
1716 2484 7.337942 GGACTTTTAGATGTGTGAGATTGGAAT 59.662 37.037 0.00 0.00 0.00 3.01
1766 2534 3.282021 ACACATGCTTGAGTGAAGTGTT 58.718 40.909 6.60 0.00 39.03 3.32
1785 2553 2.680841 CCTGTGAGGTTCGAAAACAACA 59.319 45.455 0.00 2.15 37.10 3.33
1833 2601 3.908382 GTCATGTTTGTCAAATCACTCGC 59.092 43.478 0.40 0.00 0.00 5.03
1845 2633 2.631160 TGAAGGGACGTCATGTTTGT 57.369 45.000 18.91 0.00 42.83 2.83
1871 2659 6.293626 CCACGATATGATTTCATTGGAAGTCC 60.294 42.308 0.00 0.00 38.57 3.85
1878 2666 9.184062 CATTAAACCCACGATATGATTTCATTG 57.816 33.333 0.00 0.00 37.76 2.82
1879 2667 7.867403 GCATTAAACCCACGATATGATTTCATT 59.133 33.333 0.00 0.00 37.76 2.57
1880 2668 7.370383 GCATTAAACCCACGATATGATTTCAT 58.630 34.615 0.00 0.00 40.22 2.57
1883 2677 5.596361 TGGCATTAAACCCACGATATGATTT 59.404 36.000 0.00 0.00 0.00 2.17
2020 2814 0.168788 ATGCACCGTGAATTCTTGCG 59.831 50.000 7.05 8.55 35.90 4.85
2081 2875 5.240891 TGAAGAACACTGAGATTGGTCATC 58.759 41.667 0.00 0.00 32.67 2.92
2206 3000 7.654022 AAAAACACTCACCTCCATCTAAAAA 57.346 32.000 0.00 0.00 0.00 1.94
2230 3024 7.318141 GGCATCATCTCAATCTCAAAGAAAAA 58.682 34.615 0.00 0.00 0.00 1.94
2231 3025 6.127535 GGGCATCATCTCAATCTCAAAGAAAA 60.128 38.462 0.00 0.00 0.00 2.29
2232 3026 5.359009 GGGCATCATCTCAATCTCAAAGAAA 59.641 40.000 0.00 0.00 0.00 2.52
2233 3027 4.885907 GGGCATCATCTCAATCTCAAAGAA 59.114 41.667 0.00 0.00 0.00 2.52
2234 3028 4.458397 GGGCATCATCTCAATCTCAAAGA 58.542 43.478 0.00 0.00 0.00 2.52
2235 3029 3.568853 GGGGCATCATCTCAATCTCAAAG 59.431 47.826 0.00 0.00 0.00 2.77
2236 3030 3.053470 TGGGGCATCATCTCAATCTCAAA 60.053 43.478 0.00 0.00 0.00 2.69
2237 3031 2.510800 TGGGGCATCATCTCAATCTCAA 59.489 45.455 0.00 0.00 0.00 3.02
2238 3032 2.129363 TGGGGCATCATCTCAATCTCA 58.871 47.619 0.00 0.00 0.00 3.27
2239 3033 2.945080 TGGGGCATCATCTCAATCTC 57.055 50.000 0.00 0.00 0.00 2.75
2240 3034 2.445905 ACATGGGGCATCATCTCAATCT 59.554 45.455 0.00 0.00 0.00 2.40
2241 3035 2.872732 ACATGGGGCATCATCTCAATC 58.127 47.619 0.00 0.00 0.00 2.67
2242 3036 4.669866 ATACATGGGGCATCATCTCAAT 57.330 40.909 0.00 0.00 0.00 2.57
2243 3037 4.458256 AATACATGGGGCATCATCTCAA 57.542 40.909 0.00 0.00 0.00 3.02
2244 3038 4.458256 AAATACATGGGGCATCATCTCA 57.542 40.909 0.00 0.00 0.00 3.27
2245 3039 5.796424 AAAAATACATGGGGCATCATCTC 57.204 39.130 0.00 0.00 0.00 2.75
2264 3058 5.292765 TGCGTGCTCATTTCCATTTAAAAA 58.707 33.333 0.00 0.00 0.00 1.94
2265 3059 4.876125 TGCGTGCTCATTTCCATTTAAAA 58.124 34.783 0.00 0.00 0.00 1.52
2266 3060 4.511617 TGCGTGCTCATTTCCATTTAAA 57.488 36.364 0.00 0.00 0.00 1.52
2267 3061 4.233789 GTTGCGTGCTCATTTCCATTTAA 58.766 39.130 0.00 0.00 0.00 1.52
2268 3062 3.254411 TGTTGCGTGCTCATTTCCATTTA 59.746 39.130 0.00 0.00 0.00 1.40
2269 3063 2.035704 TGTTGCGTGCTCATTTCCATTT 59.964 40.909 0.00 0.00 0.00 2.32
2270 3064 1.612950 TGTTGCGTGCTCATTTCCATT 59.387 42.857 0.00 0.00 0.00 3.16
2271 3065 1.246649 TGTTGCGTGCTCATTTCCAT 58.753 45.000 0.00 0.00 0.00 3.41
2272 3066 1.068402 CATGTTGCGTGCTCATTTCCA 60.068 47.619 0.00 0.00 0.00 3.53
2273 3067 1.621107 CATGTTGCGTGCTCATTTCC 58.379 50.000 0.00 0.00 0.00 3.13
2274 3068 0.986992 GCATGTTGCGTGCTCATTTC 59.013 50.000 6.12 0.00 42.44 2.17
2275 3069 0.388907 GGCATGTTGCGTGCTCATTT 60.389 50.000 12.26 0.00 46.21 2.32
2276 3070 1.213537 GGCATGTTGCGTGCTCATT 59.786 52.632 12.26 0.00 46.21 2.57
2277 3071 1.972752 TGGCATGTTGCGTGCTCAT 60.973 52.632 12.26 0.00 46.21 2.90
2278 3072 2.594013 TGGCATGTTGCGTGCTCA 60.594 55.556 12.26 6.79 46.21 4.26
2279 3073 2.126734 GTGGCATGTTGCGTGCTC 60.127 61.111 12.26 4.61 46.21 4.26
2280 3074 4.029186 CGTGGCATGTTGCGTGCT 62.029 61.111 12.26 0.00 46.21 4.40
2281 3075 4.326766 ACGTGGCATGTTGCGTGC 62.327 61.111 6.51 4.87 46.21 5.34
2282 3076 2.427245 CACGTGGCATGTTGCGTG 60.427 61.111 10.21 11.37 46.21 5.34
2283 3077 2.590291 TCACGTGGCATGTTGCGT 60.590 55.556 17.00 1.30 46.21 5.24
2284 3078 2.127270 GTCACGTGGCATGTTGCG 60.127 61.111 16.80 0.54 46.21 4.85
2285 3079 1.370414 GTGTCACGTGGCATGTTGC 60.370 57.895 27.60 9.20 44.08 4.17
2286 3080 0.662619 AAGTGTCACGTGGCATGTTG 59.337 50.000 27.60 6.30 29.66 3.33
2287 3081 0.662619 CAAGTGTCACGTGGCATGTT 59.337 50.000 27.60 19.41 29.66 2.71
2288 3082 1.785041 GCAAGTGTCACGTGGCATGT 61.785 55.000 27.60 14.22 29.66 3.21
2289 3083 1.081906 GCAAGTGTCACGTGGCATG 60.082 57.895 27.60 21.82 29.66 4.06
2290 3084 1.227943 AGCAAGTGTCACGTGGCAT 60.228 52.632 27.60 8.52 29.66 4.40
2291 3085 2.179547 CAGCAAGTGTCACGTGGCA 61.180 57.895 20.89 20.89 0.00 4.92
2292 3086 2.633657 CAGCAAGTGTCACGTGGC 59.366 61.111 14.58 14.58 0.00 5.01
2293 3087 1.095228 AACCAGCAAGTGTCACGTGG 61.095 55.000 17.00 15.30 0.00 4.94
2294 3088 1.577468 TAACCAGCAAGTGTCACGTG 58.423 50.000 9.94 9.94 0.00 4.49
2295 3089 2.037251 AGATAACCAGCAAGTGTCACGT 59.963 45.455 0.00 0.00 0.00 4.49
2296 3090 2.413112 CAGATAACCAGCAAGTGTCACG 59.587 50.000 0.00 0.00 0.00 4.35
2297 3091 3.187227 CACAGATAACCAGCAAGTGTCAC 59.813 47.826 0.00 0.00 0.00 3.67
2298 3092 3.181455 ACACAGATAACCAGCAAGTGTCA 60.181 43.478 0.00 0.00 33.94 3.58
2299 3093 3.187227 CACACAGATAACCAGCAAGTGTC 59.813 47.826 0.00 0.00 36.69 3.67
2300 3094 3.141398 CACACAGATAACCAGCAAGTGT 58.859 45.455 0.00 0.00 39.09 3.55
2301 3095 3.402110 TCACACAGATAACCAGCAAGTG 58.598 45.455 0.00 0.00 0.00 3.16
2302 3096 3.668447 CTCACACAGATAACCAGCAAGT 58.332 45.455 0.00 0.00 0.00 3.16
2303 3097 2.417933 GCTCACACAGATAACCAGCAAG 59.582 50.000 0.00 0.00 0.00 4.01
2304 3098 2.224499 TGCTCACACAGATAACCAGCAA 60.224 45.455 0.00 0.00 32.59 3.91
2305 3099 1.347378 TGCTCACACAGATAACCAGCA 59.653 47.619 0.00 0.00 33.08 4.41
2306 3100 2.099141 TGCTCACACAGATAACCAGC 57.901 50.000 0.00 0.00 0.00 4.85
2307 3101 3.930336 TCTTGCTCACACAGATAACCAG 58.070 45.455 0.00 0.00 0.00 4.00
2308 3102 4.558226 ATCTTGCTCACACAGATAACCA 57.442 40.909 0.00 0.00 0.00 3.67
2309 3103 4.333926 GGAATCTTGCTCACACAGATAACC 59.666 45.833 0.00 0.00 0.00 2.85
2310 3104 5.181748 AGGAATCTTGCTCACACAGATAAC 58.818 41.667 0.00 0.00 0.00 1.89
2311 3105 5.426689 AGGAATCTTGCTCACACAGATAA 57.573 39.130 0.00 0.00 0.00 1.75
2312 3106 5.426689 AAGGAATCTTGCTCACACAGATA 57.573 39.130 0.00 0.00 0.00 1.98
2313 3107 3.996921 AGGAATCTTGCTCACACAGAT 57.003 42.857 0.00 0.00 0.00 2.90
2314 3108 3.777106 AAGGAATCTTGCTCACACAGA 57.223 42.857 0.00 0.00 0.00 3.41
2315 3109 4.843220 AAAAGGAATCTTGCTCACACAG 57.157 40.909 0.00 0.00 32.75 3.66
2334 3128 4.295141 TCCCTCGCCTTCATCTTAAAAA 57.705 40.909 0.00 0.00 0.00 1.94
2335 3129 3.992943 TCCCTCGCCTTCATCTTAAAA 57.007 42.857 0.00 0.00 0.00 1.52
2336 3130 4.503714 AATCCCTCGCCTTCATCTTAAA 57.496 40.909 0.00 0.00 0.00 1.52
2337 3131 4.503714 AAATCCCTCGCCTTCATCTTAA 57.496 40.909 0.00 0.00 0.00 1.85
2338 3132 4.503714 AAAATCCCTCGCCTTCATCTTA 57.496 40.909 0.00 0.00 0.00 2.10
2339 3133 3.372440 AAAATCCCTCGCCTTCATCTT 57.628 42.857 0.00 0.00 0.00 2.40
2340 3134 3.372440 AAAAATCCCTCGCCTTCATCT 57.628 42.857 0.00 0.00 0.00 2.90
2357 3151 9.816787 ATGGGTTCTTATCTTTACCTACAAAAA 57.183 29.630 0.00 0.00 0.00 1.94
2358 3152 9.238368 CATGGGTTCTTATCTTTACCTACAAAA 57.762 33.333 0.00 0.00 0.00 2.44
2359 3153 8.387813 ACATGGGTTCTTATCTTTACCTACAAA 58.612 33.333 0.00 0.00 0.00 2.83
2360 3154 7.924541 ACATGGGTTCTTATCTTTACCTACAA 58.075 34.615 0.00 0.00 0.00 2.41
2361 3155 7.504926 ACATGGGTTCTTATCTTTACCTACA 57.495 36.000 0.00 0.00 0.00 2.74
2364 3158 9.628500 GAAATACATGGGTTCTTATCTTTACCT 57.372 33.333 0.00 0.00 0.00 3.08
2365 3159 9.628500 AGAAATACATGGGTTCTTATCTTTACC 57.372 33.333 0.00 0.00 0.00 2.85
2375 3169 9.753674 TCATCTAAAAAGAAATACATGGGTTCT 57.246 29.630 0.00 0.00 33.01 3.01
2389 3183 7.421599 TGTGCATTCGTTTTCATCTAAAAAGA 58.578 30.769 0.00 0.00 41.74 2.52
2390 3184 7.617935 GCTGTGCATTCGTTTTCATCTAAAAAG 60.618 37.037 0.00 0.00 38.76 2.27
2391 3185 6.143758 GCTGTGCATTCGTTTTCATCTAAAAA 59.856 34.615 0.00 0.00 38.76 1.94
2392 3186 5.629020 GCTGTGCATTCGTTTTCATCTAAAA 59.371 36.000 0.00 0.00 34.66 1.52
2393 3187 5.048782 AGCTGTGCATTCGTTTTCATCTAAA 60.049 36.000 0.00 0.00 0.00 1.85
2394 3188 4.455533 AGCTGTGCATTCGTTTTCATCTAA 59.544 37.500 0.00 0.00 0.00 2.10
2395 3189 4.002982 AGCTGTGCATTCGTTTTCATCTA 58.997 39.130 0.00 0.00 0.00 1.98
2396 3190 2.816087 AGCTGTGCATTCGTTTTCATCT 59.184 40.909 0.00 0.00 0.00 2.90
2397 3191 3.207474 AGCTGTGCATTCGTTTTCATC 57.793 42.857 0.00 0.00 0.00 2.92
2398 3192 3.254166 AGAAGCTGTGCATTCGTTTTCAT 59.746 39.130 0.00 0.00 0.00 2.57
2399 3193 2.618241 AGAAGCTGTGCATTCGTTTTCA 59.382 40.909 0.00 0.00 0.00 2.69
2400 3194 3.273919 AGAAGCTGTGCATTCGTTTTC 57.726 42.857 0.00 0.00 0.00 2.29
2401 3195 3.316308 AGAAGAAGCTGTGCATTCGTTTT 59.684 39.130 0.00 0.00 0.00 2.43
2402 3196 2.880890 AGAAGAAGCTGTGCATTCGTTT 59.119 40.909 0.00 0.00 0.00 3.60
2403 3197 2.481952 GAGAAGAAGCTGTGCATTCGTT 59.518 45.455 0.00 0.00 0.00 3.85
2404 3198 2.072298 GAGAAGAAGCTGTGCATTCGT 58.928 47.619 0.00 0.00 0.00 3.85
2405 3199 2.071540 TGAGAAGAAGCTGTGCATTCG 58.928 47.619 0.00 0.00 0.00 3.34
2406 3200 3.670091 GCTTGAGAAGAAGCTGTGCATTC 60.670 47.826 0.00 0.00 44.26 2.67
2407 3201 2.228343 GCTTGAGAAGAAGCTGTGCATT 59.772 45.455 0.00 0.00 44.26 3.56
2408 3202 1.811359 GCTTGAGAAGAAGCTGTGCAT 59.189 47.619 0.00 0.00 44.26 3.96
2409 3203 1.233019 GCTTGAGAAGAAGCTGTGCA 58.767 50.000 0.00 0.00 44.26 4.57
2410 3204 0.165511 CGCTTGAGAAGAAGCTGTGC 59.834 55.000 0.00 0.00 45.26 4.57
2411 3205 0.795085 CCGCTTGAGAAGAAGCTGTG 59.205 55.000 0.00 0.00 45.26 3.66
2412 3206 0.952984 GCCGCTTGAGAAGAAGCTGT 60.953 55.000 0.00 0.00 45.26 4.40
2413 3207 1.792941 GCCGCTTGAGAAGAAGCTG 59.207 57.895 0.00 0.00 45.26 4.24
2414 3208 4.292784 GCCGCTTGAGAAGAAGCT 57.707 55.556 0.00 0.00 45.26 3.74


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

AutoCloner maintained by Alex Coulton.