Multiple sequence alignment - TraesCS7B01G167000

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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 TraesCS7B01G167000 chr7B 100.000 2348 0 0 1 2348 231385147 231387494 0.000000e+00 4337
1 TraesCS7B01G167000 chr7B 88.235 952 75 26 1426 2346 600271116 600272061 0.000000e+00 1103
2 TraesCS7B01G167000 chr7D 95.016 1264 63 0 2 1265 254167385 254168648 0.000000e+00 1986
3 TraesCS7B01G167000 chr7D 78.892 1246 255 7 5 1246 431016192 431014951 0.000000e+00 837
4 TraesCS7B01G167000 chr7D 89.820 167 16 1 1265 1431 248539287 248539122 1.830000e-51 213
5 TraesCS7B01G167000 chr6A 92.016 1265 96 4 1 1265 596616534 596615275 0.000000e+00 1772
6 TraesCS7B01G167000 chr6A 78.797 1264 258 9 5 1263 617698178 617696920 0.000000e+00 841
7 TraesCS7B01G167000 chr6A 87.500 168 19 2 1265 1431 184993355 184993189 2.380000e-45 193
8 TraesCS7B01G167000 chr6A 87.500 168 19 2 1265 1431 254900721 254900555 2.380000e-45 193
9 TraesCS7B01G167000 chr6A 87.500 168 19 2 1265 1431 254908858 254908692 2.380000e-45 193
10 TraesCS7B01G167000 chr5D 89.915 942 68 12 1426 2345 401270476 401269540 0.000000e+00 1188
11 TraesCS7B01G167000 chr4B 88.971 952 69 23 1426 2346 299293715 299292769 0.000000e+00 1144
12 TraesCS7B01G167000 chr4B 88.433 951 75 21 1426 2346 255637419 255636474 0.000000e+00 1114
13 TraesCS7B01G167000 chr1D 89.389 933 64 16 1426 2330 80853032 80853957 0.000000e+00 1142
14 TraesCS7B01G167000 chr1D 87.579 950 78 15 1426 2348 118742802 118741866 0.000000e+00 1064
15 TraesCS7B01G167000 chr1D 90.828 676 41 5 1426 2080 80861644 80862319 0.000000e+00 885
16 TraesCS7B01G167000 chr1D 91.617 167 13 1 1265 1431 234393446 234393281 1.810000e-56 230
17 TraesCS7B01G167000 chr2B 88.830 949 72 17 1426 2348 601863655 601862715 0.000000e+00 1134
18 TraesCS7B01G167000 chr2B 88.397 948 83 16 1426 2348 386202255 386203200 0.000000e+00 1116
19 TraesCS7B01G167000 chr3D 88.550 952 72 16 1424 2346 229018061 229019004 0.000000e+00 1120
20 TraesCS7B01G167000 chr3D 87.554 699 57 13 1426 2099 570404486 570403793 0.000000e+00 782
21 TraesCS7B01G167000 chr4A 88.303 949 77 17 1426 2348 722774315 722773375 0.000000e+00 1107
22 TraesCS7B01G167000 chr5B 88.143 953 79 21 1426 2348 569196559 569195611 0.000000e+00 1103
23 TraesCS7B01G167000 chr6D 87.907 951 80 15 1426 2348 285751768 285752711 0.000000e+00 1086
24 TraesCS7B01G167000 chr6D 88.922 677 43 13 1426 2079 301913542 301912875 0.000000e+00 806
25 TraesCS7B01G167000 chr6D 87.906 678 58 8 1426 2079 324890898 324890221 0.000000e+00 776
26 TraesCS7B01G167000 chr1A 88.260 937 73 23 1443 2348 65365063 65365993 0.000000e+00 1086
27 TraesCS7B01G167000 chr3A 87.421 954 85 17 1423 2348 670095638 670094692 0.000000e+00 1064
28 TraesCS7B01G167000 chr3A 87.574 169 19 2 1264 1431 510506318 510506485 6.620000e-46 195
29 TraesCS7B01G167000 chr3A 87.500 168 19 2 1265 1431 510513036 510513202 2.380000e-45 193
30 TraesCS7B01G167000 chr3A 86.982 169 20 2 1264 1431 108501484 108501317 3.080000e-44 189
31 TraesCS7B01G167000 chr7A 87.500 168 19 2 1265 1431 298955311 298955145 2.380000e-45 193


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 TraesCS7B01G167000 chr7B 231385147 231387494 2347 False 4337 4337 100.000 1 2348 1 chr7B.!!$F1 2347
1 TraesCS7B01G167000 chr7B 600271116 600272061 945 False 1103 1103 88.235 1426 2346 1 chr7B.!!$F2 920
2 TraesCS7B01G167000 chr7D 254167385 254168648 1263 False 1986 1986 95.016 2 1265 1 chr7D.!!$F1 1263
3 TraesCS7B01G167000 chr7D 431014951 431016192 1241 True 837 837 78.892 5 1246 1 chr7D.!!$R2 1241
4 TraesCS7B01G167000 chr6A 596615275 596616534 1259 True 1772 1772 92.016 1 1265 1 chr6A.!!$R4 1264
5 TraesCS7B01G167000 chr6A 617696920 617698178 1258 True 841 841 78.797 5 1263 1 chr6A.!!$R5 1258
6 TraesCS7B01G167000 chr5D 401269540 401270476 936 True 1188 1188 89.915 1426 2345 1 chr5D.!!$R1 919
7 TraesCS7B01G167000 chr4B 299292769 299293715 946 True 1144 1144 88.971 1426 2346 1 chr4B.!!$R2 920
8 TraesCS7B01G167000 chr4B 255636474 255637419 945 True 1114 1114 88.433 1426 2346 1 chr4B.!!$R1 920
9 TraesCS7B01G167000 chr1D 80853032 80853957 925 False 1142 1142 89.389 1426 2330 1 chr1D.!!$F1 904
10 TraesCS7B01G167000 chr1D 118741866 118742802 936 True 1064 1064 87.579 1426 2348 1 chr1D.!!$R1 922
11 TraesCS7B01G167000 chr1D 80861644 80862319 675 False 885 885 90.828 1426 2080 1 chr1D.!!$F2 654
12 TraesCS7B01G167000 chr2B 601862715 601863655 940 True 1134 1134 88.830 1426 2348 1 chr2B.!!$R1 922
13 TraesCS7B01G167000 chr2B 386202255 386203200 945 False 1116 1116 88.397 1426 2348 1 chr2B.!!$F1 922
14 TraesCS7B01G167000 chr3D 229018061 229019004 943 False 1120 1120 88.550 1424 2346 1 chr3D.!!$F1 922
15 TraesCS7B01G167000 chr3D 570403793 570404486 693 True 782 782 87.554 1426 2099 1 chr3D.!!$R1 673
16 TraesCS7B01G167000 chr4A 722773375 722774315 940 True 1107 1107 88.303 1426 2348 1 chr4A.!!$R1 922
17 TraesCS7B01G167000 chr5B 569195611 569196559 948 True 1103 1103 88.143 1426 2348 1 chr5B.!!$R1 922
18 TraesCS7B01G167000 chr6D 285751768 285752711 943 False 1086 1086 87.907 1426 2348 1 chr6D.!!$F1 922
19 TraesCS7B01G167000 chr6D 301912875 301913542 667 True 806 806 88.922 1426 2079 1 chr6D.!!$R1 653
20 TraesCS7B01G167000 chr6D 324890221 324890898 677 True 776 776 87.906 1426 2079 1 chr6D.!!$R2 653
21 TraesCS7B01G167000 chr1A 65365063 65365993 930 False 1086 1086 88.260 1443 2348 1 chr1A.!!$F1 905
22 TraesCS7B01G167000 chr3A 670094692 670095638 946 True 1064 1064 87.421 1423 2348 1 chr3A.!!$R2 925

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
438 439 0.034186 CTGCAGGCCCTCCAACATTA 60.034 55.0 5.57 0.0 33.74 1.90 F
742 743 0.106708 AGAAGTGCGCAGTTTCCTCA 59.893 50.0 29.82 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1268 0.180406 AGCTTGATTATCCGGGCGTT 59.820 50.0 0.0 0.0 0.00 4.84 R
1543 1553 0.396435 ATCGGTGGACTGAACTGCAA 59.604 50.0 0.0 0.0 34.49 4.08 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
86 87 6.638468 CACAAACCAGAGCTAAAGAATGAAAC 59.362 38.462 0.00 0.00 0.00 2.78
202 203 2.260869 ACATGGAGGTTGTGCGTGC 61.261 57.895 0.00 0.00 37.00 5.34
251 252 7.341805 ACAATTGTCAGCAAGTATCCTATTCT 58.658 34.615 4.92 0.00 38.10 2.40
344 345 5.010012 GGTATCACCAGATAAAATTGGCAGG 59.990 44.000 0.00 0.00 38.41 4.85
349 350 2.363359 CAGATAAAATTGGCAGGAGGGC 59.637 50.000 0.00 0.00 43.73 5.19
362 363 3.371595 GCAGGAGGGCAGGAGTATAAAAA 60.372 47.826 0.00 0.00 0.00 1.94
384 385 6.713762 AAAACATTCACAACTCATTCAGGA 57.286 33.333 0.00 0.00 0.00 3.86
438 439 0.034186 CTGCAGGCCCTCCAACATTA 60.034 55.000 5.57 0.00 33.74 1.90
442 443 2.949963 GCAGGCCCTCCAACATTAATCA 60.950 50.000 0.00 0.00 33.74 2.57
476 477 3.315142 CTCTACGCCCCTTGCTGCA 62.315 63.158 0.00 0.00 38.05 4.41
622 623 0.383949 GTGTGCTTTCGGGCAAAAGA 59.616 50.000 13.79 0.00 44.18 2.52
626 627 2.284150 GTGCTTTCGGGCAAAAGAAAAC 59.716 45.455 13.79 6.38 44.18 2.43
627 628 1.521006 GCTTTCGGGCAAAAGAAAACG 59.479 47.619 13.79 0.00 38.30 3.60
644 645 1.598130 CGGCTTACCTAGGGCATGC 60.598 63.158 14.81 9.90 0.00 4.06
676 677 3.072915 ACATGGTGTCTCAACAGATCCAA 59.927 43.478 0.00 0.00 38.30 3.53
717 718 1.586028 GTGGCATGTTCCACGCAAT 59.414 52.632 6.73 0.00 45.95 3.56
742 743 0.106708 AGAAGTGCGCAGTTTCCTCA 59.893 50.000 29.82 0.00 0.00 3.86
744 745 0.886490 AAGTGCGCAGTTTCCTCAGG 60.886 55.000 24.51 0.00 0.00 3.86
761 762 1.064758 CAGGTTGGCTGGCTATTACCA 60.065 52.381 2.00 0.00 38.29 3.25
848 849 3.119173 CCTTTTGTGTGGACAGCTGAAAA 60.119 43.478 23.35 13.26 32.26 2.29
880 881 2.135139 TCGAGTTACTGCAGCAAAGTG 58.865 47.619 15.27 6.91 0.00 3.16
965 966 3.181451 GCATGTGATTATGGAGTGGGAGA 60.181 47.826 0.00 0.00 0.00 3.71
1024 1025 0.318120 CAAAACGCTGGCTCCCAAAT 59.682 50.000 0.00 0.00 30.80 2.32
1070 1071 4.489306 AGGAGTGTTTGGCTATCCTTAC 57.511 45.455 0.00 0.00 37.05 2.34
1072 1073 3.118884 GGAGTGTTTGGCTATCCTTACGA 60.119 47.826 0.00 0.00 0.00 3.43
1081 1082 2.950309 GCTATCCTTACGACAGTGGAGA 59.050 50.000 0.00 0.00 31.59 3.71
1143 1144 4.219944 AGAACGGATCAGCACAGTTTAGTA 59.780 41.667 0.00 0.00 0.00 1.82
1146 1147 4.242475 CGGATCAGCACAGTTTAGTACAA 58.758 43.478 0.00 0.00 0.00 2.41
1169 1170 7.500227 ACAATTGGATGATCAACGACTATCAAT 59.500 33.333 10.83 0.00 35.82 2.57
1221 1222 0.606944 TGGTCCCGCGCTACAAAATT 60.607 50.000 5.56 0.00 0.00 1.82
1247 1248 2.112297 GCAAGGGACCACCAACGA 59.888 61.111 0.00 0.00 43.89 3.85
1253 1254 1.302511 GGACCACCAACGATGCAGT 60.303 57.895 0.00 0.00 35.97 4.40
1271 1272 2.348666 CAGTAGATGCCTTGTGTAACGC 59.651 50.000 0.00 0.00 42.39 4.84
1272 1273 1.664151 GTAGATGCCTTGTGTAACGCC 59.336 52.381 0.00 0.00 42.39 5.68
1273 1274 0.676782 AGATGCCTTGTGTAACGCCC 60.677 55.000 0.00 0.00 42.39 6.13
1274 1275 1.977594 GATGCCTTGTGTAACGCCCG 61.978 60.000 0.00 0.00 42.39 6.13
1275 1276 3.428282 GCCTTGTGTAACGCCCGG 61.428 66.667 0.00 0.00 42.39 5.73
1276 1277 2.344500 CCTTGTGTAACGCCCGGA 59.656 61.111 0.73 0.00 42.39 5.14
1277 1278 1.078708 CCTTGTGTAACGCCCGGAT 60.079 57.895 0.73 0.00 42.39 4.18
1278 1279 0.176219 CCTTGTGTAACGCCCGGATA 59.824 55.000 0.73 0.00 42.39 2.59
1279 1280 1.405797 CCTTGTGTAACGCCCGGATAA 60.406 52.381 0.73 0.00 42.39 1.75
1280 1281 2.557317 CTTGTGTAACGCCCGGATAAT 58.443 47.619 0.73 0.00 42.39 1.28
1281 1282 2.228138 TGTGTAACGCCCGGATAATC 57.772 50.000 0.73 0.00 42.39 1.75
1282 1283 1.481363 TGTGTAACGCCCGGATAATCA 59.519 47.619 0.73 0.00 42.39 2.57
1283 1284 2.093606 TGTGTAACGCCCGGATAATCAA 60.094 45.455 0.73 0.00 42.39 2.57
1284 1285 2.542595 GTGTAACGCCCGGATAATCAAG 59.457 50.000 0.73 0.00 0.00 3.02
1285 1286 1.529865 GTAACGCCCGGATAATCAAGC 59.470 52.381 0.73 0.00 0.00 4.01
1286 1287 0.180406 AACGCCCGGATAATCAAGCT 59.820 50.000 0.73 0.00 0.00 3.74
1287 1288 1.045407 ACGCCCGGATAATCAAGCTA 58.955 50.000 0.73 0.00 0.00 3.32
1288 1289 1.270147 ACGCCCGGATAATCAAGCTAC 60.270 52.381 0.73 0.00 0.00 3.58
1289 1290 1.270094 CGCCCGGATAATCAAGCTACA 60.270 52.381 0.73 0.00 0.00 2.74
1290 1291 2.417719 GCCCGGATAATCAAGCTACAG 58.582 52.381 0.73 0.00 0.00 2.74
1291 1292 2.224305 GCCCGGATAATCAAGCTACAGT 60.224 50.000 0.73 0.00 0.00 3.55
1292 1293 3.006537 GCCCGGATAATCAAGCTACAGTA 59.993 47.826 0.73 0.00 0.00 2.74
1293 1294 4.502604 GCCCGGATAATCAAGCTACAGTAA 60.503 45.833 0.73 0.00 0.00 2.24
1294 1295 5.794894 CCCGGATAATCAAGCTACAGTAAT 58.205 41.667 0.73 0.00 0.00 1.89
1295 1296 5.869888 CCCGGATAATCAAGCTACAGTAATC 59.130 44.000 0.73 0.00 0.00 1.75
1296 1297 5.869888 CCGGATAATCAAGCTACAGTAATCC 59.130 44.000 0.00 0.00 0.00 3.01
1297 1298 5.869888 CGGATAATCAAGCTACAGTAATCCC 59.130 44.000 0.00 0.00 0.00 3.85
1298 1299 6.174049 GGATAATCAAGCTACAGTAATCCCC 58.826 44.000 0.00 0.00 0.00 4.81
1299 1300 6.013293 GGATAATCAAGCTACAGTAATCCCCT 60.013 42.308 0.00 0.00 0.00 4.79
1300 1301 4.696479 ATCAAGCTACAGTAATCCCCTG 57.304 45.455 0.00 0.00 36.01 4.45
1301 1302 2.170607 TCAAGCTACAGTAATCCCCTGC 59.829 50.000 0.00 0.00 33.09 4.85
1302 1303 2.171448 CAAGCTACAGTAATCCCCTGCT 59.829 50.000 0.00 0.00 33.09 4.24
1303 1304 3.330126 AGCTACAGTAATCCCCTGCTA 57.670 47.619 0.00 0.00 33.09 3.49
1304 1305 3.654273 AGCTACAGTAATCCCCTGCTAA 58.346 45.455 0.00 0.00 33.09 3.09
1305 1306 4.235372 AGCTACAGTAATCCCCTGCTAAT 58.765 43.478 0.00 0.00 33.09 1.73
1306 1307 4.040952 AGCTACAGTAATCCCCTGCTAATG 59.959 45.833 0.00 0.00 33.09 1.90
1307 1308 4.040461 GCTACAGTAATCCCCTGCTAATGA 59.960 45.833 0.00 0.00 33.09 2.57
1308 1309 5.280215 GCTACAGTAATCCCCTGCTAATGAT 60.280 44.000 0.00 0.00 33.09 2.45
1309 1310 4.978099 ACAGTAATCCCCTGCTAATGATG 58.022 43.478 0.00 0.00 33.09 3.07
1310 1311 3.755378 CAGTAATCCCCTGCTAATGATGC 59.245 47.826 0.00 0.00 0.00 3.91
1311 1312 2.299326 AATCCCCTGCTAATGATGCC 57.701 50.000 0.00 0.00 0.00 4.40
1312 1313 1.151760 ATCCCCTGCTAATGATGCCA 58.848 50.000 0.00 0.00 0.00 4.92
1313 1314 1.151760 TCCCCTGCTAATGATGCCAT 58.848 50.000 0.00 0.00 33.66 4.40
1314 1315 1.202964 TCCCCTGCTAATGATGCCATG 60.203 52.381 0.00 0.00 32.36 3.66
1315 1316 1.479942 CCCCTGCTAATGATGCCATGT 60.480 52.381 0.00 0.00 32.36 3.21
1316 1317 1.884579 CCCTGCTAATGATGCCATGTC 59.115 52.381 0.00 0.00 32.36 3.06
1317 1318 2.578786 CCTGCTAATGATGCCATGTCA 58.421 47.619 0.00 0.00 32.36 3.58
1318 1319 2.292569 CCTGCTAATGATGCCATGTCAC 59.707 50.000 0.00 0.00 32.36 3.67
1319 1320 2.292569 CTGCTAATGATGCCATGTCACC 59.707 50.000 0.00 0.00 32.36 4.02
1320 1321 2.300433 GCTAATGATGCCATGTCACCA 58.700 47.619 0.00 0.00 32.36 4.17
1321 1322 2.889045 GCTAATGATGCCATGTCACCAT 59.111 45.455 0.00 0.00 32.36 3.55
1322 1323 3.305131 GCTAATGATGCCATGTCACCATG 60.305 47.826 0.00 0.00 46.65 3.66
1339 1340 9.685276 TGTCACCATGATTATTGTTTCTAATCT 57.315 29.630 0.00 0.00 36.80 2.40
1396 1397 9.961264 TTAAATTTAAAGGGAAACAACAAAGGT 57.039 25.926 8.20 0.00 0.00 3.50
1397 1398 8.871629 AAATTTAAAGGGAAACAACAAAGGTT 57.128 26.923 0.00 0.00 37.87 3.50
1398 1399 8.871629 AATTTAAAGGGAAACAACAAAGGTTT 57.128 26.923 0.00 0.00 40.91 3.27
1399 1400 8.871629 ATTTAAAGGGAAACAACAAAGGTTTT 57.128 26.923 0.00 0.00 38.50 2.43
1400 1401 7.908827 TTAAAGGGAAACAACAAAGGTTTTC 57.091 32.000 0.00 0.00 38.50 2.29
1401 1402 5.491323 AAGGGAAACAACAAAGGTTTTCA 57.509 34.783 0.00 0.00 38.50 2.69
1402 1403 5.491323 AGGGAAACAACAAAGGTTTTCAA 57.509 34.783 0.00 0.00 38.50 2.69
1403 1404 5.870706 AGGGAAACAACAAAGGTTTTCAAA 58.129 33.333 0.00 0.00 38.50 2.69
1404 1405 6.299922 AGGGAAACAACAAAGGTTTTCAAAA 58.700 32.000 0.00 0.00 38.50 2.44
1405 1406 6.429692 AGGGAAACAACAAAGGTTTTCAAAAG 59.570 34.615 0.00 0.00 38.50 2.27
1406 1407 6.205853 GGGAAACAACAAAGGTTTTCAAAAGT 59.794 34.615 0.00 0.00 38.50 2.66
1407 1408 7.255312 GGGAAACAACAAAGGTTTTCAAAAGTT 60.255 33.333 0.00 0.00 38.50 2.66
1408 1409 8.775527 GGAAACAACAAAGGTTTTCAAAAGTTA 58.224 29.630 0.00 0.00 38.50 2.24
1412 1413 9.938670 ACAACAAAGGTTTTCAAAAGTTAAAAC 57.061 25.926 4.54 4.54 42.28 2.43
1490 1500 3.260380 ACTCTCTTCTACATGCTGCACTT 59.740 43.478 3.57 0.00 0.00 3.16
1512 1522 2.993899 CCAAAAGCGTAGTCTTCGACAT 59.006 45.455 2.72 0.00 34.60 3.06
1534 1544 4.678256 TGACTAGCTATCCCCCTCTTATG 58.322 47.826 0.00 0.00 0.00 1.90
1543 1553 1.412074 CCCCCTCTTATGCTGGCATTT 60.412 52.381 13.39 0.00 37.82 2.32
1564 1574 1.621317 TGCAGTTCAGTCCACCGATAA 59.379 47.619 0.00 0.00 0.00 1.75
1577 1587 3.486383 CACCGATAATGCCCCTTTACAT 58.514 45.455 0.00 0.00 0.00 2.29
1612 1622 5.866633 GCATATGTAGTGTAGATCCTTGCTC 59.133 44.000 4.29 0.00 0.00 4.26
1614 1624 3.353557 TGTAGTGTAGATCCTTGCTCGT 58.646 45.455 0.00 0.00 0.00 4.18
1678 1693 1.628846 CCCCCTTTCCTTTCTTCTCGA 59.371 52.381 0.00 0.00 0.00 4.04
1735 1756 1.094073 CCACCGACGACGACTCCTAT 61.094 60.000 9.28 0.00 42.66 2.57
1876 1913 6.142817 GGCAACTTGTTTACTTATGTCTGTG 58.857 40.000 0.00 0.00 0.00 3.66
1902 1939 3.953612 AGATTTTGTTGCTTCCACTGACA 59.046 39.130 0.00 0.00 0.00 3.58
1914 1951 3.352648 TCCACTGACACGTCTATGATCA 58.647 45.455 0.00 0.00 0.00 2.92
1921 1958 4.398044 TGACACGTCTATGATCAAGCACTA 59.602 41.667 0.00 0.00 0.00 2.74
2028 2066 3.137913 CCCATGAGTCCCTGATCTTGATT 59.862 47.826 0.00 0.00 0.00 2.57
2036 2074 4.818546 GTCCCTGATCTTGATTGTACATGG 59.181 45.833 0.00 0.00 0.00 3.66
2157 2198 7.118390 CCGAAGTTGAGTCTAGTCATTGAATTT 59.882 37.037 0.00 0.00 0.00 1.82
2187 2230 1.174712 ATGGATGTGCGGCTTATGGC 61.175 55.000 0.00 0.00 40.90 4.40
2337 2388 0.811616 CGGAGAGCCCCTTCATTTCG 60.812 60.000 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 2.028930 AGTTCCTTAACCTGACGCTCAG 60.029 50.000 7.72 7.72 43.91 3.35
202 203 4.642445 TGGCATTCAAGCATCTGTAATG 57.358 40.909 0.00 0.00 35.83 1.90
247 248 6.152492 TCGAGCAGCTCATCTATAATCAGAAT 59.848 38.462 22.49 0.00 0.00 2.40
251 252 5.416952 TCATCGAGCAGCTCATCTATAATCA 59.583 40.000 22.49 0.00 0.00 2.57
335 336 2.220786 CTCCTGCCCTCCTGCCAATT 62.221 60.000 0.00 0.00 0.00 2.32
362 363 5.593909 TGTCCTGAATGAGTTGTGAATGTTT 59.406 36.000 0.00 0.00 0.00 2.83
438 439 3.871594 GAGTACAAGTAATGGCGCTGATT 59.128 43.478 7.64 8.89 0.00 2.57
442 443 3.488721 CGTAGAGTACAAGTAATGGCGCT 60.489 47.826 7.64 0.00 0.00 5.92
622 623 0.694196 TGCCCTAGGTAAGCCGTTTT 59.306 50.000 8.29 0.00 40.50 2.43
626 627 1.598130 GCATGCCCTAGGTAAGCCG 60.598 63.158 6.36 0.00 40.50 5.52
627 628 1.056660 TAGCATGCCCTAGGTAAGCC 58.943 55.000 15.66 0.00 32.76 4.35
644 645 5.077134 TGAGACACCATGTTCAGTGATAG 57.923 43.478 6.80 0.00 37.43 2.08
676 677 7.141363 CACTTTTTGATGGTCTCGATCTTTTT 58.859 34.615 0.00 0.00 0.00 1.94
687 688 3.665745 ACATGCCACTTTTTGATGGTC 57.334 42.857 0.00 0.00 38.34 4.02
717 718 3.744426 GGAAACTGCGCACTTCTTTACTA 59.256 43.478 20.95 0.00 0.00 1.82
742 743 1.295020 TGGTAATAGCCAGCCAACCT 58.705 50.000 0.00 0.00 33.97 3.50
761 762 3.429410 GCCAAAGTGCTTGACAAACTTCT 60.429 43.478 5.87 0.00 37.17 2.85
822 823 1.336240 GCTGTCCACACAAAAGGATGC 60.336 52.381 0.00 0.00 36.11 3.91
848 849 4.495422 CAGTAACTCGAATGCCTTAGTGT 58.505 43.478 0.00 0.00 0.00 3.55
880 881 2.351157 GCAAAACAGGTGCAGAGATCAC 60.351 50.000 0.00 0.00 41.80 3.06
965 966 2.104792 TGACCTGCTTGCTGAAGTACTT 59.895 45.455 8.13 8.13 0.00 2.24
1024 1025 1.980036 GTAGGTGGACAAACCCCTGTA 59.020 52.381 0.00 0.00 41.54 2.74
1070 1071 0.389817 TCGCCATTTCTCCACTGTCG 60.390 55.000 0.00 0.00 0.00 4.35
1072 1073 0.321653 GGTCGCCATTTCTCCACTGT 60.322 55.000 0.00 0.00 0.00 3.55
1081 1082 2.355412 GGTGTAGGTAAGGTCGCCATTT 60.355 50.000 0.00 0.00 0.00 2.32
1143 1144 6.348498 TGATAGTCGTTGATCATCCAATTGT 58.652 36.000 4.43 0.00 0.00 2.71
1146 1147 8.370940 ACTATTGATAGTCGTTGATCATCCAAT 58.629 33.333 0.00 3.05 39.27 3.16
1169 1170 0.108396 TGCTTTCTGCTGCCACACTA 59.892 50.000 0.00 0.00 43.37 2.74
1205 1206 0.109504 GCAAATTTTGTAGCGCGGGA 60.110 50.000 8.83 0.00 0.00 5.14
1208 1209 2.173964 GGTAGCAAATTTTGTAGCGCG 58.826 47.619 0.00 0.00 0.00 6.86
1253 1254 1.406341 GGGCGTTACACAAGGCATCTA 60.406 52.381 4.68 0.00 45.29 1.98
1265 1266 1.529865 GCTTGATTATCCGGGCGTTAC 59.470 52.381 0.00 0.00 0.00 2.50
1266 1267 1.414919 AGCTTGATTATCCGGGCGTTA 59.585 47.619 0.00 0.00 0.00 3.18
1267 1268 0.180406 AGCTTGATTATCCGGGCGTT 59.820 50.000 0.00 0.00 0.00 4.84
1268 1269 1.045407 TAGCTTGATTATCCGGGCGT 58.955 50.000 0.00 0.00 0.00 5.68
1269 1270 1.270094 TGTAGCTTGATTATCCGGGCG 60.270 52.381 0.00 0.00 0.00 6.13
1270 1271 2.224305 ACTGTAGCTTGATTATCCGGGC 60.224 50.000 0.00 0.00 0.00 6.13
1271 1272 3.753294 ACTGTAGCTTGATTATCCGGG 57.247 47.619 0.00 0.00 0.00 5.73
1272 1273 5.869888 GGATTACTGTAGCTTGATTATCCGG 59.130 44.000 0.00 0.00 0.00 5.14
1273 1274 5.869888 GGGATTACTGTAGCTTGATTATCCG 59.130 44.000 0.00 0.00 31.87 4.18
1274 1275 6.013293 AGGGGATTACTGTAGCTTGATTATCC 60.013 42.308 0.00 0.00 0.00 2.59
1275 1276 6.876257 CAGGGGATTACTGTAGCTTGATTATC 59.124 42.308 0.00 0.00 0.00 1.75
1276 1277 6.745474 GCAGGGGATTACTGTAGCTTGATTAT 60.745 42.308 0.00 0.00 38.22 1.28
1277 1278 5.454755 GCAGGGGATTACTGTAGCTTGATTA 60.455 44.000 0.00 0.00 38.22 1.75
1278 1279 4.687219 GCAGGGGATTACTGTAGCTTGATT 60.687 45.833 0.00 0.00 38.22 2.57
1279 1280 3.181450 GCAGGGGATTACTGTAGCTTGAT 60.181 47.826 0.00 0.00 38.22 2.57
1280 1281 2.170607 GCAGGGGATTACTGTAGCTTGA 59.829 50.000 0.00 0.00 38.22 3.02
1281 1282 2.171448 AGCAGGGGATTACTGTAGCTTG 59.829 50.000 0.00 0.00 38.22 4.01
1282 1283 2.482494 AGCAGGGGATTACTGTAGCTT 58.518 47.619 0.00 0.00 38.22 3.74
1283 1284 2.182516 AGCAGGGGATTACTGTAGCT 57.817 50.000 0.00 0.00 38.22 3.32
1284 1285 4.040461 TCATTAGCAGGGGATTACTGTAGC 59.960 45.833 0.00 0.00 38.22 3.58
1285 1286 5.808366 TCATTAGCAGGGGATTACTGTAG 57.192 43.478 0.00 0.00 38.22 2.74
1286 1287 5.513094 GCATCATTAGCAGGGGATTACTGTA 60.513 44.000 0.00 0.00 38.22 2.74
1287 1288 4.747931 GCATCATTAGCAGGGGATTACTGT 60.748 45.833 0.00 0.00 38.22 3.55
1288 1289 3.755378 GCATCATTAGCAGGGGATTACTG 59.245 47.826 0.00 0.00 38.95 2.74
1289 1290 3.245052 GGCATCATTAGCAGGGGATTACT 60.245 47.826 0.00 0.00 0.00 2.24
1290 1291 3.084786 GGCATCATTAGCAGGGGATTAC 58.915 50.000 0.00 0.00 0.00 1.89
1291 1292 2.715880 TGGCATCATTAGCAGGGGATTA 59.284 45.455 0.00 0.00 0.00 1.75
1292 1293 1.500303 TGGCATCATTAGCAGGGGATT 59.500 47.619 0.00 0.00 0.00 3.01
1293 1294 1.151760 TGGCATCATTAGCAGGGGAT 58.848 50.000 0.00 0.00 0.00 3.85
1294 1295 1.151760 ATGGCATCATTAGCAGGGGA 58.848 50.000 0.00 0.00 0.00 4.81
1295 1296 1.254026 CATGGCATCATTAGCAGGGG 58.746 55.000 0.00 0.00 0.00 4.79
1296 1297 1.884579 GACATGGCATCATTAGCAGGG 59.115 52.381 0.00 0.00 0.00 4.45
1297 1298 2.292569 GTGACATGGCATCATTAGCAGG 59.707 50.000 3.50 0.00 0.00 4.85
1298 1299 2.292569 GGTGACATGGCATCATTAGCAG 59.707 50.000 7.03 0.00 0.00 4.24
1299 1300 2.300433 GGTGACATGGCATCATTAGCA 58.700 47.619 7.03 0.00 0.00 3.49
1300 1301 2.300433 TGGTGACATGGCATCATTAGC 58.700 47.619 11.50 0.00 33.40 3.09
1313 1314 9.685276 AGATTAGAAACAATAATCATGGTGACA 57.315 29.630 8.06 0.00 40.55 3.58
1370 1371 9.961264 ACCTTTGTTGTTTCCCTTTAAATTTAA 57.039 25.926 6.54 6.54 0.00 1.52
1371 1372 9.961264 AACCTTTGTTGTTTCCCTTTAAATTTA 57.039 25.926 0.00 0.00 32.13 1.40
1372 1373 8.871629 AACCTTTGTTGTTTCCCTTTAAATTT 57.128 26.923 0.00 0.00 32.13 1.82
1373 1374 8.871629 AAACCTTTGTTGTTTCCCTTTAAATT 57.128 26.923 0.00 0.00 34.13 1.82
1374 1375 8.871629 AAAACCTTTGTTGTTTCCCTTTAAAT 57.128 26.923 0.00 0.00 34.97 1.40
1375 1376 7.937394 TGAAAACCTTTGTTGTTTCCCTTTAAA 59.063 29.630 0.00 0.00 34.97 1.52
1376 1377 7.450903 TGAAAACCTTTGTTGTTTCCCTTTAA 58.549 30.769 0.00 0.00 34.97 1.52
1377 1378 7.005709 TGAAAACCTTTGTTGTTTCCCTTTA 57.994 32.000 0.00 0.00 34.97 1.85
1378 1379 5.870706 TGAAAACCTTTGTTGTTTCCCTTT 58.129 33.333 0.00 0.00 34.97 3.11
1379 1380 5.491323 TGAAAACCTTTGTTGTTTCCCTT 57.509 34.783 0.00 0.00 34.97 3.95
1380 1381 5.491323 TTGAAAACCTTTGTTGTTTCCCT 57.509 34.783 0.00 0.00 34.97 4.20
1381 1382 6.205853 ACTTTTGAAAACCTTTGTTGTTTCCC 59.794 34.615 0.00 0.00 34.97 3.97
1382 1383 7.197071 ACTTTTGAAAACCTTTGTTGTTTCC 57.803 32.000 0.00 0.00 34.97 3.13
1386 1387 9.938670 GTTTTAACTTTTGAAAACCTTTGTTGT 57.061 25.926 3.44 0.00 38.86 3.32
1410 1411 9.908152 GCATAAACCTACTCAAACATTTTAGTT 57.092 29.630 0.00 0.00 0.00 2.24
1411 1412 9.297037 AGCATAAACCTACTCAAACATTTTAGT 57.703 29.630 0.00 0.00 0.00 2.24
1415 1416 8.190784 GCATAGCATAAACCTACTCAAACATTT 58.809 33.333 0.00 0.00 0.00 2.32
1416 1417 7.467267 CGCATAGCATAAACCTACTCAAACATT 60.467 37.037 0.00 0.00 0.00 2.71
1417 1418 6.017934 CGCATAGCATAAACCTACTCAAACAT 60.018 38.462 0.00 0.00 0.00 2.71
1418 1419 5.293324 CGCATAGCATAAACCTACTCAAACA 59.707 40.000 0.00 0.00 0.00 2.83
1419 1420 5.522460 TCGCATAGCATAAACCTACTCAAAC 59.478 40.000 0.00 0.00 0.00 2.93
1420 1421 5.666462 TCGCATAGCATAAACCTACTCAAA 58.334 37.500 0.00 0.00 0.00 2.69
1421 1422 5.270893 TCGCATAGCATAAACCTACTCAA 57.729 39.130 0.00 0.00 0.00 3.02
1512 1522 4.678256 CATAAGAGGGGGATAGCTAGTCA 58.322 47.826 0.00 0.00 0.00 3.41
1534 1544 1.269936 ACTGAACTGCAAAATGCCAGC 60.270 47.619 0.00 0.00 44.23 4.85
1543 1553 0.396435 ATCGGTGGACTGAACTGCAA 59.604 50.000 0.00 0.00 34.49 4.08
1564 1574 4.247814 TGGGTATCTATGTAAAGGGGCAT 58.752 43.478 0.00 0.00 0.00 4.40
1577 1587 8.113462 TCTACACTACATATGCATGGGTATCTA 58.887 37.037 10.16 1.51 36.39 1.98
1678 1693 2.552338 CCAGCATCTGGTTGCGACAAT 61.552 52.381 6.39 0.00 45.82 2.71
1735 1756 3.317149 CCTGCACGTAGTAGTAGGCATAA 59.683 47.826 0.00 0.00 41.61 1.90
1876 1913 4.919754 CAGTGGAAGCAACAAAATCTAAGC 59.080 41.667 0.00 0.00 0.00 3.09
1902 1939 6.885952 ATACTAGTGCTTGATCATAGACGT 57.114 37.500 5.39 0.00 0.00 4.34
1914 1951 2.362717 GAGGGCTCGAATACTAGTGCTT 59.637 50.000 5.39 0.00 0.00 3.91
1983 2020 7.721842 TGGGAAAATATCACAACACAACTCTAA 59.278 33.333 0.00 0.00 38.94 2.10
2003 2041 2.850833 AGATCAGGGACTCATGGGAAA 58.149 47.619 0.00 0.00 34.60 3.13
2028 2066 0.520847 CATGCACGCAACCATGTACA 59.479 50.000 0.00 0.00 35.33 2.90
2036 2074 2.900122 ACACTAATCATGCACGCAAC 57.100 45.000 0.00 0.00 0.00 4.17
2157 2198 4.380023 GCCGCACATCCATGTTAGTAAAAA 60.380 41.667 0.00 0.00 39.39 1.94
2187 2230 3.430862 CCCAATGGCGACGTGTGG 61.431 66.667 0.00 5.08 0.00 4.17
2189 2233 2.668212 CACCCAATGGCGACGTGT 60.668 61.111 0.00 0.00 33.59 4.49
2311 2359 3.009714 GGGGCTCTCCGGGAAAGT 61.010 66.667 0.00 0.00 36.01 2.66
2312 2360 2.258748 GAAGGGGCTCTCCGGGAAAG 62.259 65.000 0.00 0.00 36.01 2.62


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

AutoCloner maintained by Alex Coulton.