Multiple sequence alignment - TraesCS7A01G340800

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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 TraesCS7A01G340800 chr7A 100.000 3179 0 0 1 3179 500179605 500182783 0.000000e+00 5871.0
1 TraesCS7A01G340800 chr7A 89.113 744 34 15 1 723 500149124 500149841 0.000000e+00 881.0
2 TraesCS7A01G340800 chr7A 93.989 183 11 0 824 1006 500149979 500150161 8.680000e-71 278.0
3 TraesCS7A01G340800 chr7A 100.000 32 0 0 784 815 500149908 500149939 3.420000e-05 60.2
4 TraesCS7A01G340800 chr6A 93.837 1298 69 3 1892 3179 49100968 49099672 0.000000e+00 1943.0
5 TraesCS7A01G340800 chr3A 80.452 2210 363 37 1030 3179 601342346 601340146 0.000000e+00 1624.0
6 TraesCS7A01G340800 chr3A 87.553 948 90 8 1855 2802 235405061 235405980 0.000000e+00 1072.0
7 TraesCS7A01G340800 chr2A 80.308 2209 350 51 1030 3179 718926329 718924147 0.000000e+00 1591.0
8 TraesCS7A01G340800 chr2A 81.947 1346 216 17 1853 3177 207350184 207348845 0.000000e+00 1114.0
9 TraesCS7A01G340800 chr2A 82.020 1218 189 20 1943 3136 678124782 678125993 0.000000e+00 1009.0
10 TraesCS7A01G340800 chr5B 79.964 2216 366 49 1028 3179 392100222 392102423 0.000000e+00 1561.0
11 TraesCS7A01G340800 chr5B 80.095 2095 344 43 1028 3060 392041361 392043444 0.000000e+00 1491.0
12 TraesCS7A01G340800 chr5B 79.613 2168 361 51 1028 3129 392056382 392058534 0.000000e+00 1480.0
13 TraesCS7A01G340800 chrUn 84.487 1141 166 9 1431 2566 426443646 426444780 0.000000e+00 1116.0
14 TraesCS7A01G340800 chrUn 84.386 1140 169 7 1431 2566 426444947 426446081 0.000000e+00 1110.0
15 TraesCS7A01G340800 chrUn 78.317 927 151 28 1028 1911 429314776 429313857 1.290000e-153 553.0
16 TraesCS7A01G340800 chr4A 79.968 1258 232 14 1431 2677 722139279 722140527 0.000000e+00 909.0
17 TraesCS7A01G340800 chr1B 78.929 859 151 22 2343 3179 42065699 42064849 9.960000e-155 556.0
18 TraesCS7A01G340800 chr7B 90.047 211 10 7 1 206 449817270 449817474 2.430000e-66 263.0
19 TraesCS7A01G340800 chr7B 90.625 64 5 1 211 273 449817500 449817563 2.030000e-12 84.2
20 TraesCS7A01G340800 chr7D 88.785 214 13 6 1 206 432783723 432783513 5.260000e-63 252.0
21 TraesCS7A01G340800 chr7D 92.424 66 4 1 211 275 432783484 432783419 3.380000e-15 93.5
22 TraesCS7A01G340800 chr1A 80.128 156 27 4 2875 3027 58420570 58420724 2.590000e-21 113.0


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 TraesCS7A01G340800 chr7A 500179605 500182783 3178 False 5871.0 5871 100.000000 1 3179 1 chr7A.!!$F1 3178
1 TraesCS7A01G340800 chr7A 500149124 500150161 1037 False 406.4 881 94.367333 1 1006 3 chr7A.!!$F2 1005
2 TraesCS7A01G340800 chr6A 49099672 49100968 1296 True 1943.0 1943 93.837000 1892 3179 1 chr6A.!!$R1 1287
3 TraesCS7A01G340800 chr3A 601340146 601342346 2200 True 1624.0 1624 80.452000 1030 3179 1 chr3A.!!$R1 2149
4 TraesCS7A01G340800 chr3A 235405061 235405980 919 False 1072.0 1072 87.553000 1855 2802 1 chr3A.!!$F1 947
5 TraesCS7A01G340800 chr2A 718924147 718926329 2182 True 1591.0 1591 80.308000 1030 3179 1 chr2A.!!$R2 2149
6 TraesCS7A01G340800 chr2A 207348845 207350184 1339 True 1114.0 1114 81.947000 1853 3177 1 chr2A.!!$R1 1324
7 TraesCS7A01G340800 chr2A 678124782 678125993 1211 False 1009.0 1009 82.020000 1943 3136 1 chr2A.!!$F1 1193
8 TraesCS7A01G340800 chr5B 392100222 392102423 2201 False 1561.0 1561 79.964000 1028 3179 1 chr5B.!!$F3 2151
9 TraesCS7A01G340800 chr5B 392041361 392043444 2083 False 1491.0 1491 80.095000 1028 3060 1 chr5B.!!$F1 2032
10 TraesCS7A01G340800 chr5B 392056382 392058534 2152 False 1480.0 1480 79.613000 1028 3129 1 chr5B.!!$F2 2101
11 TraesCS7A01G340800 chrUn 426443646 426446081 2435 False 1113.0 1116 84.436500 1431 2566 2 chrUn.!!$F1 1135
12 TraesCS7A01G340800 chrUn 429313857 429314776 919 True 553.0 553 78.317000 1028 1911 1 chrUn.!!$R1 883
13 TraesCS7A01G340800 chr4A 722139279 722140527 1248 False 909.0 909 79.968000 1431 2677 1 chr4A.!!$F1 1246
14 TraesCS7A01G340800 chr1B 42064849 42065699 850 True 556.0 556 78.929000 2343 3179 1 chr1B.!!$R1 836

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
209 210 0.031449 CAAATGGACGCGGTTTGGTT 59.969 50.0 12.47 0.0 31.08 3.67 F
656 678 0.179045 AGCTTCTCGTGCTTGTTGGT 60.179 50.0 0.00 0.0 37.52 3.67 F
1648 1766 0.109532 TCAAAATGGTCACCGAGCCA 59.890 50.0 0.00 0.0 39.33 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1747 0.109532 TGGCTCGGTGACCATTTTGA 59.890 50.000 1.11 0.0 0.00 2.69 R
1994 2112 0.539438 AAAGGTGGAGGCGAATGCAA 60.539 50.000 0.00 0.0 45.35 4.08 R
3070 3231 2.034879 GCGAGCACAGCCTAAGCAA 61.035 57.895 0.00 0.0 43.56 3.91 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
33 34 1.440188 CGCGCACGCAAAAGAATGA 60.440 52.632 16.04 0.00 42.06 2.57
79 80 0.179105 AAGCGAGATGAGCTGAGCTG 60.179 55.000 13.71 0.00 45.31 4.24
80 81 2.239124 GCGAGATGAGCTGAGCTGC 61.239 63.158 13.71 3.61 39.88 5.25
160 161 3.397482 CGGCCTAGTACTGTACTACGAT 58.603 50.000 20.74 3.16 40.14 3.73
175 176 1.355971 ACGATCACACACGTAATGGC 58.644 50.000 4.21 0.00 40.92 4.40
181 182 3.115892 ACACGTAATGGCACGCGG 61.116 61.111 12.47 0.00 45.77 6.46
182 183 2.811747 CACGTAATGGCACGCGGA 60.812 61.111 12.47 0.00 45.77 5.54
209 210 0.031449 CAAATGGACGCGGTTTGGTT 59.969 50.000 12.47 0.00 31.08 3.67
289 310 3.384789 TGAAGCCACTGTATGCTAGTAGG 59.615 47.826 4.66 0.00 36.66 3.18
290 311 3.314307 AGCCACTGTATGCTAGTAGGA 57.686 47.619 0.00 0.00 35.69 2.94
295 316 4.216687 CCACTGTATGCTAGTAGGAGTAGC 59.783 50.000 6.40 6.40 45.14 3.58
351 372 1.622607 CGGATGGTTGGCAGGGAGTA 61.623 60.000 0.00 0.00 0.00 2.59
354 375 2.441750 GGATGGTTGGCAGGGAGTAATA 59.558 50.000 0.00 0.00 0.00 0.98
358 379 4.105577 TGGTTGGCAGGGAGTAATAACTA 58.894 43.478 0.00 0.00 35.56 2.24
360 381 5.192923 TGGTTGGCAGGGAGTAATAACTAAT 59.807 40.000 0.00 0.00 35.56 1.73
361 382 5.531287 GGTTGGCAGGGAGTAATAACTAATG 59.469 44.000 0.00 0.00 35.56 1.90
363 384 4.072839 GGCAGGGAGTAATAACTAATGGC 58.927 47.826 0.00 0.00 35.56 4.40
364 385 4.202472 GGCAGGGAGTAATAACTAATGGCT 60.202 45.833 0.00 0.00 35.56 4.75
366 387 5.828328 GCAGGGAGTAATAACTAATGGCTTT 59.172 40.000 0.00 0.00 35.56 3.51
369 390 7.339466 CAGGGAGTAATAACTAATGGCTTTGTT 59.661 37.037 0.00 2.01 35.56 2.83
370 391 7.893833 AGGGAGTAATAACTAATGGCTTTGTTT 59.106 33.333 0.00 0.00 35.56 2.83
375 396 4.600692 AACTAATGGCTTTGTTTCACCC 57.399 40.909 0.00 0.00 27.85 4.61
376 397 2.556622 ACTAATGGCTTTGTTTCACCCG 59.443 45.455 0.00 0.00 0.00 5.28
378 399 1.112315 ATGGCTTTGTTTCACCCGCA 61.112 50.000 0.00 0.00 0.00 5.69
379 400 1.323271 TGGCTTTGTTTCACCCGCAA 61.323 50.000 0.00 0.00 0.00 4.85
380 401 0.179097 GGCTTTGTTTCACCCGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
381 402 1.646189 GCTTTGTTTCACCCGCAAAA 58.354 45.000 0.00 0.00 32.64 2.44
382 403 2.003301 GCTTTGTTTCACCCGCAAAAA 58.997 42.857 0.00 0.00 32.64 1.94
480 501 1.094650 GCTCAAGGCCTCAAGCTAGC 61.095 60.000 24.97 6.62 43.05 3.42
550 571 6.436027 ACTACTCCAGATTGAAGGTCTGATA 58.564 40.000 4.79 0.00 44.57 2.15
557 578 5.821470 CAGATTGAAGGTCTGATATGCAACT 59.179 40.000 0.00 0.00 44.57 3.16
558 579 5.821470 AGATTGAAGGTCTGATATGCAACTG 59.179 40.000 0.00 0.00 0.00 3.16
577 598 3.319405 ACTGCGAAACTGATCCGATAGAT 59.681 43.478 0.00 0.00 38.17 1.98
580 601 4.051922 GCGAAACTGATCCGATAGATTGT 58.948 43.478 0.00 0.00 34.42 2.71
581 602 5.220381 GCGAAACTGATCCGATAGATTGTA 58.780 41.667 0.00 0.00 34.42 2.41
587 609 4.087182 TGATCCGATAGATTGTACCCTCC 58.913 47.826 0.00 0.00 34.42 4.30
589 611 3.918566 TCCGATAGATTGTACCCTCCAA 58.081 45.455 0.00 0.00 39.76 3.53
616 638 0.805614 ACGATCTCGCCGAGGATATG 59.194 55.000 15.08 2.98 44.43 1.78
637 659 0.527600 CTCGTGCTTGGCGCTACATA 60.528 55.000 7.64 0.00 40.11 2.29
638 660 0.527600 TCGTGCTTGGCGCTACATAG 60.528 55.000 7.64 0.00 40.11 2.23
651 673 2.537625 GCTACATAGCTTCTCGTGCTTG 59.462 50.000 3.56 0.00 45.62 4.01
653 675 3.045601 ACATAGCTTCTCGTGCTTGTT 57.954 42.857 0.00 0.00 41.46 2.83
656 678 0.179045 AGCTTCTCGTGCTTGTTGGT 60.179 50.000 0.00 0.00 37.52 3.67
767 818 3.767230 CGAACTGTGCCGCACTCG 61.767 66.667 23.52 19.57 35.11 4.18
768 819 4.077188 GAACTGTGCCGCACTCGC 62.077 66.667 23.52 7.61 35.11 5.03
815 866 1.068333 GGGCGAAACGACACTGTACTA 60.068 52.381 0.00 0.00 36.10 1.82
818 869 2.907392 GCGAAACGACACTGTACTACTC 59.093 50.000 0.00 0.00 0.00 2.59
820 871 3.188048 CGAAACGACACTGTACTACTCCT 59.812 47.826 0.00 0.00 0.00 3.69
822 873 5.619625 AAACGACACTGTACTACTCCTAC 57.380 43.478 0.00 0.00 0.00 3.18
879 961 2.192624 CACAAAAGGTTGGCAAACTCG 58.807 47.619 19.71 12.56 39.22 4.18
946 1028 1.462432 TAAGTGTGGCCCCACCTGA 60.462 57.895 15.36 0.00 45.63 3.86
967 1049 3.419759 GCCGTCGCGTCACCATTT 61.420 61.111 5.77 0.00 0.00 2.32
969 1051 2.474266 CGTCGCGTCACCATTTGG 59.526 61.111 5.77 0.00 42.17 3.28
970 1052 2.175811 GTCGCGTCACCATTTGGC 59.824 61.111 5.77 0.00 39.32 4.52
973 1055 4.776647 GCGTCACCATTTGGCCGC 62.777 66.667 11.44 11.44 40.82 6.53
975 1057 4.776647 GTCACCATTTGGCCGCGC 62.777 66.667 0.00 0.00 39.32 6.86
990 1072 3.710722 CGCCTGTGCTTCCTCCCT 61.711 66.667 0.00 0.00 34.43 4.20
991 1073 2.045536 GCCTGTGCTTCCTCCCTG 60.046 66.667 0.00 0.00 33.53 4.45
992 1074 2.596851 GCCTGTGCTTCCTCCCTGA 61.597 63.158 0.00 0.00 33.53 3.86
993 1075 1.601171 CCTGTGCTTCCTCCCTGAG 59.399 63.158 0.00 0.00 0.00 3.35
994 1076 1.078567 CTGTGCTTCCTCCCTGAGC 60.079 63.158 0.00 0.00 36.95 4.26
995 1077 1.537397 TGTGCTTCCTCCCTGAGCT 60.537 57.895 0.00 0.00 37.32 4.09
997 1079 1.229304 TGCTTCCTCCCTGAGCTCA 60.229 57.895 17.19 17.19 37.32 4.26
998 1080 0.837691 TGCTTCCTCCCTGAGCTCAA 60.838 55.000 18.85 1.66 37.32 3.02
999 1081 0.326264 GCTTCCTCCCTGAGCTCAAA 59.674 55.000 18.85 6.98 33.72 2.69
1000 1082 1.271597 GCTTCCTCCCTGAGCTCAAAA 60.272 52.381 18.85 5.06 33.72 2.44
1001 1083 2.620108 GCTTCCTCCCTGAGCTCAAAAT 60.620 50.000 18.85 0.00 33.72 1.82
1002 1084 2.795231 TCCTCCCTGAGCTCAAAATG 57.205 50.000 18.85 5.76 0.00 2.32
1004 1086 1.615116 CCTCCCTGAGCTCAAAATGCA 60.615 52.381 18.85 0.00 0.00 3.96
1005 1087 2.165167 CTCCCTGAGCTCAAAATGCAA 58.835 47.619 18.85 0.00 0.00 4.08
1006 1088 2.758979 CTCCCTGAGCTCAAAATGCAAT 59.241 45.455 18.85 0.00 0.00 3.56
1007 1089 3.949754 CTCCCTGAGCTCAAAATGCAATA 59.050 43.478 18.85 0.00 0.00 1.90
1008 1090 3.696051 TCCCTGAGCTCAAAATGCAATAC 59.304 43.478 18.85 0.00 0.00 1.89
1009 1091 3.698040 CCCTGAGCTCAAAATGCAATACT 59.302 43.478 18.85 0.00 0.00 2.12
1010 1092 4.883585 CCCTGAGCTCAAAATGCAATACTA 59.116 41.667 18.85 0.00 0.00 1.82
1011 1093 5.533903 CCCTGAGCTCAAAATGCAATACTAT 59.466 40.000 18.85 0.00 0.00 2.12
1012 1094 6.712095 CCCTGAGCTCAAAATGCAATACTATA 59.288 38.462 18.85 0.00 0.00 1.31
1013 1095 7.094890 CCCTGAGCTCAAAATGCAATACTATAG 60.095 40.741 18.85 0.00 0.00 1.31
1015 1097 8.962884 TGAGCTCAAAATGCAATACTATAGAA 57.037 30.769 15.67 0.00 0.00 2.10
1023 1105 9.546428 AAAATGCAATACTATAGAAAAATGCCC 57.454 29.630 6.78 0.00 0.00 5.36
1024 1106 7.838079 ATGCAATACTATAGAAAAATGCCCA 57.162 32.000 6.78 0.00 0.00 5.36
1026 1108 6.040391 TGCAATACTATAGAAAAATGCCCACC 59.960 38.462 6.78 0.00 0.00 4.61
1168 1250 4.724697 CAGCTGTTTCGGCGCGTG 62.725 66.667 8.43 0.00 41.21 5.34
1170 1252 4.307908 GCTGTTTCGGCGCGTGTT 62.308 61.111 8.43 0.00 0.00 3.32
1174 1256 4.007940 TTTCGGCGCGTGTTGCTC 62.008 61.111 8.43 0.00 43.27 4.26
1240 1322 4.758251 CGTCCCATGGTCGCTGCA 62.758 66.667 11.73 0.00 0.00 4.41
1241 1323 2.124570 GTCCCATGGTCGCTGCAT 60.125 61.111 11.73 0.00 0.00 3.96
1244 1326 2.048023 CCCATGGTCGCTGCATTGT 61.048 57.895 11.73 0.00 0.00 2.71
1245 1327 1.597797 CCCATGGTCGCTGCATTGTT 61.598 55.000 11.73 0.00 0.00 2.83
1252 1334 4.705519 GCTGCATTGTTGCCGCGT 62.706 61.111 4.92 0.00 46.72 6.01
1257 1339 2.031919 ATTGTTGCCGCGTCTGGA 59.968 55.556 4.92 0.00 0.00 3.86
1260 1342 3.195698 GTTGCCGCGTCTGGATCC 61.196 66.667 4.20 4.20 0.00 3.36
1272 1354 2.017559 CTGGATCCGAGTTCGTCCCC 62.018 65.000 7.39 3.53 34.70 4.81
1290 1372 4.070552 GAGTCGCCGCTGGGTTCT 62.071 66.667 0.00 0.00 34.97 3.01
1303 1385 4.329545 GTTCTGGCCCGCTGGTGA 62.330 66.667 0.00 0.00 0.00 4.02
1321 1403 4.200283 CCGGCTCAGTCGCTCCTC 62.200 72.222 0.00 0.00 0.00 3.71
1323 1405 3.844090 GGCTCAGTCGCTCCTCCC 61.844 72.222 0.00 0.00 0.00 4.30
1324 1406 3.844090 GCTCAGTCGCTCCTCCCC 61.844 72.222 0.00 0.00 0.00 4.81
1343 1437 4.207281 CGAATCGGCTCGCCCTGA 62.207 66.667 1.72 0.00 31.04 3.86
1353 1447 4.247380 CGCCCTGAGCCTGGATCC 62.247 72.222 9.83 4.20 38.78 3.36
1376 1470 3.825160 TTCACTGCGAGGTGGGTGC 62.825 63.158 8.03 0.00 37.75 5.01
1384 1478 4.740822 AGGTGGGTGCGGGCATTC 62.741 66.667 0.00 0.00 0.00 2.67
1420 1517 2.042404 GCTCTCCAGCCCATCTCCAG 62.042 65.000 0.00 0.00 40.14 3.86
1423 1520 2.192443 CCAGCCCATCTCCAGCAG 59.808 66.667 0.00 0.00 0.00 4.24
1425 1522 3.013327 AGCCCATCTCCAGCAGCA 61.013 61.111 0.00 0.00 0.00 4.41
1426 1523 2.044650 GCCCATCTCCAGCAGCAA 60.045 61.111 0.00 0.00 0.00 3.91
1428 1525 2.110967 CCCATCTCCAGCAGCAACG 61.111 63.158 0.00 0.00 0.00 4.10
1467 1585 3.357079 GTGACCGGTGCTTGGCAG 61.357 66.667 14.63 0.00 40.08 4.85
1476 1594 3.782244 GCTTGGCAGCTCGTCACG 61.782 66.667 0.00 0.00 43.51 4.35
1523 1641 0.905809 TTGCCTGGCCAAGCATTCAT 60.906 50.000 29.08 0.00 39.11 2.57
1534 1652 3.513225 CATTCATGCCGTCCACCC 58.487 61.111 0.00 0.00 0.00 4.61
1557 1675 2.052104 ATGGTGGCTTAAAGGGCGC 61.052 57.895 0.00 0.00 40.76 6.53
1584 1702 0.610232 GTTGCCTTGCTCCTGGACAT 60.610 55.000 0.00 0.00 0.00 3.06
1599 1717 2.816958 CATCGCGCCTCAGCTTGT 60.817 61.111 0.00 0.00 36.60 3.16
1605 1723 2.375766 CGCCTCAGCTTGTCGTGAC 61.376 63.158 0.00 0.00 36.60 3.67
1611 1729 0.798776 CAGCTTGTCGTGACCCATTC 59.201 55.000 0.00 0.00 0.00 2.67
1614 1732 1.635663 CTTGTCGTGACCCATTCCGC 61.636 60.000 0.00 0.00 0.00 5.54
1638 1756 0.883833 CTCGCTGCCTTCAAAATGGT 59.116 50.000 0.00 0.00 0.00 3.55
1647 1765 1.200020 CTTCAAAATGGTCACCGAGCC 59.800 52.381 0.00 0.00 0.00 4.70
1648 1766 0.109532 TCAAAATGGTCACCGAGCCA 59.890 50.000 0.00 0.00 39.33 4.75
1650 1768 0.609131 AAAATGGTCACCGAGCCAGG 60.609 55.000 0.00 0.00 38.27 4.45
1662 1780 4.032653 GCCAGGGGCTGCAATAAA 57.967 55.556 0.50 0.00 46.69 1.40
1674 1792 1.075979 GCAATAAAAAGTGGCGCCCG 61.076 55.000 26.77 1.06 0.00 6.13
1680 1798 0.820482 AAAAGTGGCGCCCGTTAAGT 60.820 50.000 26.77 4.24 0.00 2.24
1734 1852 3.710722 CTTCCCCGACCAGCTGCT 61.711 66.667 8.66 0.00 0.00 4.24
1735 1853 2.284331 TTCCCCGACCAGCTGCTA 60.284 61.111 8.66 0.00 0.00 3.49
1740 1858 1.320344 CCCGACCAGCTGCTACTGTA 61.320 60.000 8.66 0.00 35.83 2.74
1742 1860 1.095600 CGACCAGCTGCTACTGTAGA 58.904 55.000 18.64 3.34 35.83 2.59
1743 1861 1.202200 CGACCAGCTGCTACTGTAGAC 60.202 57.143 18.64 10.06 35.83 2.59
1744 1862 2.096248 GACCAGCTGCTACTGTAGACT 58.904 52.381 18.64 8.96 35.83 3.24
1745 1863 1.821753 ACCAGCTGCTACTGTAGACTG 59.178 52.381 18.64 18.49 35.83 3.51
1746 1864 1.470632 CCAGCTGCTACTGTAGACTGC 60.471 57.143 18.64 20.46 35.83 4.40
1747 1865 1.203287 CAGCTGCTACTGTAGACTGCA 59.797 52.381 26.12 16.27 33.09 4.41
1748 1866 2.106566 AGCTGCTACTGTAGACTGCAT 58.893 47.619 26.12 16.51 33.09 3.96
1752 1870 1.269309 GCTACTGTAGACTGCATCCCG 60.269 57.143 18.64 0.00 0.00 5.14
1753 1871 2.298610 CTACTGTAGACTGCATCCCGA 58.701 52.381 9.22 0.00 0.00 5.14
1754 1872 0.818296 ACTGTAGACTGCATCCCGAC 59.182 55.000 0.00 0.00 0.00 4.79
1764 1882 1.898154 CATCCCGACTCCCGTCTTT 59.102 57.895 0.00 0.00 38.03 2.52
1802 1920 3.965026 CTCTCCCTCAGCCCCGTCA 62.965 68.421 0.00 0.00 0.00 4.35
1804 1922 3.965026 CTCCCTCAGCCCCGTCAGA 62.965 68.421 0.00 0.00 0.00 3.27
1815 1933 1.739562 CCGTCAGAAGCTGCTGTCC 60.740 63.158 21.55 12.14 37.20 4.02
1817 1935 1.290324 GTCAGAAGCTGCTGTCCGA 59.710 57.895 21.55 0.00 37.20 4.55
1822 1940 2.778309 GAAGCTGCTGTCCGACTGCT 62.778 60.000 25.24 14.53 42.56 4.24
1829 1947 2.099652 CTGTCCGACTGCTCCAACCA 62.100 60.000 0.00 0.00 0.00 3.67
1830 1948 1.296715 GTCCGACTGCTCCAACCAT 59.703 57.895 0.00 0.00 0.00 3.55
1833 1951 1.672030 CGACTGCTCCAACCATGCA 60.672 57.895 0.00 0.00 35.30 3.96
1851 1969 1.410004 CAATGCCAAGGCTGGATGAT 58.590 50.000 12.96 0.00 46.92 2.45
1888 2006 1.297456 GGAGGACTTCGTCGTCGTCT 61.297 60.000 20.18 7.15 44.99 4.18
1935 2053 2.437359 GCGCTGCTCTCCACCAAT 60.437 61.111 0.00 0.00 0.00 3.16
2085 2203 5.670792 ATCTCGTCAGGTTTATGTACCAA 57.329 39.130 0.00 0.00 40.82 3.67
2086 2204 5.471556 TCTCGTCAGGTTTATGTACCAAA 57.528 39.130 0.00 0.00 40.82 3.28
2270 2388 4.111016 TCGCGTTCGTCATCGGCT 62.111 61.111 5.77 0.00 37.69 5.52
2370 2488 2.566010 CAACCCCAACGCCATTCG 59.434 61.111 0.00 0.00 45.38 3.34
2521 2655 0.807667 CGCCGCTAGCTGACATCTTT 60.808 55.000 13.93 0.00 40.39 2.52
2808 2962 1.416401 AGGTGTTGGACTTGATGTCGT 59.584 47.619 0.00 0.00 46.24 4.34
2831 2991 4.147449 CGCCTCCGCACCAGATCA 62.147 66.667 0.00 0.00 34.03 2.92
2856 3016 2.716017 GCTCAGGCTCCGCTAGTGT 61.716 63.158 1.99 0.00 35.22 3.55
2857 3017 1.893786 CTCAGGCTCCGCTAGTGTT 59.106 57.895 1.99 0.00 0.00 3.32
2983 3143 2.766400 GGTCTCGCCTCCACTCTCG 61.766 68.421 0.00 0.00 0.00 4.04
3049 3210 3.085296 GGGCTACGGCAACCCCTA 61.085 66.667 0.00 0.00 40.87 3.53
3116 3277 0.755686 CTGCTCCCGCCTTTATCTCT 59.244 55.000 0.00 0.00 34.43 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.364970 TGGCAGCAAAAATACAGCAACT 59.635 40.909 0.00 0.00 0.00 3.16
160 161 1.561717 GCGTGCCATTACGTGTGTGA 61.562 55.000 0.00 0.00 45.36 3.58
175 176 1.390123 CATTTGTACTCTGTCCGCGTG 59.610 52.381 4.92 0.00 0.00 5.34
181 182 1.654105 CGCGTCCATTTGTACTCTGTC 59.346 52.381 0.00 0.00 0.00 3.51
182 183 1.671850 CCGCGTCCATTTGTACTCTGT 60.672 52.381 4.92 0.00 0.00 3.41
209 210 1.929230 TTTGCTCAAGACGACACGAA 58.071 45.000 0.00 0.00 0.00 3.85
240 261 2.879103 TTGCTCCCGGAGAGAAAAAT 57.121 45.000 19.33 0.00 46.50 1.82
289 310 1.546476 AGTGCCACTACAGTGCTACTC 59.454 52.381 0.00 0.00 44.34 2.59
290 311 1.546476 GAGTGCCACTACAGTGCTACT 59.454 52.381 0.00 13.29 44.34 2.57
295 316 1.344438 TCCTTGAGTGCCACTACAGTG 59.656 52.381 0.00 2.23 45.23 3.66
327 348 3.958147 CTGCCAACCATCCGTCGCT 62.958 63.158 0.00 0.00 0.00 4.93
351 372 6.571537 CGGGTGAAACAAAGCCATTAGTTATT 60.572 38.462 0.00 0.00 39.98 1.40
354 375 3.005367 CGGGTGAAACAAAGCCATTAGTT 59.995 43.478 0.00 0.00 39.98 2.24
358 379 0.033366 GCGGGTGAAACAAAGCCATT 59.967 50.000 0.00 0.00 39.98 3.16
360 381 1.323271 TTGCGGGTGAAACAAAGCCA 61.323 50.000 0.00 0.00 39.98 4.75
361 382 0.179097 TTTGCGGGTGAAACAAAGCC 60.179 50.000 0.00 0.00 39.98 4.35
385 406 7.361628 CCAACACAAACAAAGCCATTAGTTTTT 60.362 33.333 0.00 0.00 32.34 1.94
386 407 6.093357 CCAACACAAACAAAGCCATTAGTTTT 59.907 34.615 0.00 0.00 32.34 2.43
387 408 5.584251 CCAACACAAACAAAGCCATTAGTTT 59.416 36.000 0.00 0.00 34.78 2.66
550 571 1.470098 GGATCAGTTTCGCAGTTGCAT 59.530 47.619 4.84 0.00 42.21 3.96
557 578 4.051237 CAATCTATCGGATCAGTTTCGCA 58.949 43.478 0.00 0.00 32.76 5.10
558 579 4.051922 ACAATCTATCGGATCAGTTTCGC 58.948 43.478 0.00 0.00 32.76 4.70
577 598 3.681593 GTGCAACTATTGGAGGGTACAA 58.318 45.455 0.00 0.00 0.00 2.41
580 601 2.181125 TCGTGCAACTATTGGAGGGTA 58.819 47.619 0.00 0.00 37.45 3.69
581 602 0.981183 TCGTGCAACTATTGGAGGGT 59.019 50.000 0.00 0.00 37.45 4.34
587 609 1.258982 GGCGAGATCGTGCAACTATTG 59.741 52.381 13.14 0.00 42.22 1.90
589 611 0.595053 CGGCGAGATCGTGCAACTAT 60.595 55.000 0.00 0.00 42.22 2.12
637 659 0.179045 ACCAACAAGCACGAGAAGCT 60.179 50.000 0.00 0.00 45.97 3.74
638 660 1.508632 TACCAACAAGCACGAGAAGC 58.491 50.000 0.00 0.00 0.00 3.86
651 673 3.011818 CCCCTGAACGGTTTATACCAAC 58.988 50.000 3.13 0.00 45.31 3.77
653 675 2.236893 GTCCCCTGAACGGTTTATACCA 59.763 50.000 3.13 0.00 45.31 3.25
656 678 2.236893 GGTGTCCCCTGAACGGTTTATA 59.763 50.000 0.00 0.00 0.00 0.98
673 695 2.446994 TTCACGGGACAGGGGTGT 60.447 61.111 0.00 0.00 33.51 4.16
681 703 2.943449 TTTGTTTTGGTTCACGGGAC 57.057 45.000 0.00 0.00 0.00 4.46
767 818 4.114997 CAATGGTTGTCCCGCGGC 62.115 66.667 22.85 7.92 35.15 6.53
768 819 4.114997 GCAATGGTTGTCCCGCGG 62.115 66.667 21.04 21.04 35.15 6.46
769 820 4.459331 CGCAATGGTTGTCCCGCG 62.459 66.667 0.00 0.00 38.67 6.46
770 821 3.053291 TCGCAATGGTTGTCCCGC 61.053 61.111 0.00 0.00 35.15 6.13
771 822 2.867472 GTCGCAATGGTTGTCCCG 59.133 61.111 0.00 0.00 35.15 5.14
772 823 2.867472 CGTCGCAATGGTTGTCCC 59.133 61.111 0.00 0.00 0.00 4.46
773 824 2.175811 GCGTCGCAATGGTTGTCC 59.824 61.111 13.44 0.00 0.00 4.02
774 825 2.165362 TTCGCGTCGCAATGGTTGTC 62.165 55.000 18.75 0.00 0.00 3.18
775 826 1.777030 TTTCGCGTCGCAATGGTTGT 61.777 50.000 18.75 0.00 0.00 3.32
776 827 1.059657 CTTTCGCGTCGCAATGGTTG 61.060 55.000 18.75 0.00 0.00 3.77
777 828 1.206578 CTTTCGCGTCGCAATGGTT 59.793 52.632 18.75 0.00 0.00 3.67
778 829 2.677003 CCTTTCGCGTCGCAATGGT 61.677 57.895 18.75 0.00 0.00 3.55
780 831 2.098298 CCCTTTCGCGTCGCAATG 59.902 61.111 18.75 11.90 0.00 2.82
781 832 3.799755 GCCCTTTCGCGTCGCAAT 61.800 61.111 18.75 0.00 0.00 3.56
815 866 0.889306 GGCAGAGTGAACGTAGGAGT 59.111 55.000 0.00 0.00 0.00 3.85
818 869 1.153823 CGGGCAGAGTGAACGTAGG 60.154 63.158 0.00 0.00 0.00 3.18
820 871 1.582968 GTCGGGCAGAGTGAACGTA 59.417 57.895 0.00 0.00 0.00 3.57
822 873 2.432628 GGTCGGGCAGAGTGAACG 60.433 66.667 0.00 0.00 0.00 3.95
950 1032 3.419759 AAATGGTGACGCGACGGC 61.420 61.111 15.93 3.44 34.27 5.68
951 1033 2.474266 CAAATGGTGACGCGACGG 59.526 61.111 15.93 0.00 0.00 4.79
954 1036 3.053291 GGCCAAATGGTGACGCGA 61.053 61.111 15.93 0.00 37.57 5.87
955 1037 4.459331 CGGCCAAATGGTGACGCG 62.459 66.667 3.53 3.53 37.57 6.01
957 1039 4.459331 CGCGGCCAAATGGTGACG 62.459 66.667 2.24 5.32 37.57 4.35
958 1040 4.776647 GCGCGGCCAAATGGTGAC 62.777 66.667 8.83 0.00 37.57 3.67
975 1057 1.601171 CTCAGGGAGGAAGCACAGG 59.399 63.158 0.00 0.00 0.00 4.00
977 1059 1.537397 AGCTCAGGGAGGAAGCACA 60.537 57.895 0.00 0.00 0.00 4.57
978 1060 1.220477 GAGCTCAGGGAGGAAGCAC 59.780 63.158 9.40 0.00 0.00 4.40
981 1063 2.867109 TTTTGAGCTCAGGGAGGAAG 57.133 50.000 17.43 0.00 0.00 3.46
982 1064 2.881403 GCATTTTGAGCTCAGGGAGGAA 60.881 50.000 17.43 4.21 0.00 3.36
983 1065 1.340405 GCATTTTGAGCTCAGGGAGGA 60.340 52.381 17.43 0.00 0.00 3.71
984 1066 1.101331 GCATTTTGAGCTCAGGGAGG 58.899 55.000 17.43 9.61 0.00 4.30
986 1068 2.291209 TTGCATTTTGAGCTCAGGGA 57.709 45.000 17.43 7.34 0.00 4.20
987 1069 3.698040 AGTATTGCATTTTGAGCTCAGGG 59.302 43.478 17.43 8.86 0.00 4.45
990 1072 8.962884 TTCTATAGTATTGCATTTTGAGCTCA 57.037 30.769 13.74 13.74 0.00 4.26
997 1079 9.546428 GGGCATTTTTCTATAGTATTGCATTTT 57.454 29.630 0.00 0.00 0.00 1.82
998 1080 8.703743 TGGGCATTTTTCTATAGTATTGCATTT 58.296 29.630 0.00 0.00 0.00 2.32
999 1081 8.143835 GTGGGCATTTTTCTATAGTATTGCATT 58.856 33.333 0.00 0.00 0.00 3.56
1000 1082 7.255942 GGTGGGCATTTTTCTATAGTATTGCAT 60.256 37.037 0.00 0.00 0.00 3.96
1001 1083 6.040391 GGTGGGCATTTTTCTATAGTATTGCA 59.960 38.462 0.00 0.00 0.00 4.08
1002 1084 6.447162 GGTGGGCATTTTTCTATAGTATTGC 58.553 40.000 0.00 3.98 0.00 3.56
1004 1086 6.549736 GTGGGTGGGCATTTTTCTATAGTATT 59.450 38.462 0.00 0.00 0.00 1.89
1005 1087 6.068670 GTGGGTGGGCATTTTTCTATAGTAT 58.931 40.000 0.00 0.00 0.00 2.12
1006 1088 5.442391 GTGGGTGGGCATTTTTCTATAGTA 58.558 41.667 0.00 0.00 0.00 1.82
1007 1089 4.278310 GTGGGTGGGCATTTTTCTATAGT 58.722 43.478 0.00 0.00 0.00 2.12
1008 1090 3.636764 GGTGGGTGGGCATTTTTCTATAG 59.363 47.826 0.00 0.00 0.00 1.31
1009 1091 3.628769 GGGTGGGTGGGCATTTTTCTATA 60.629 47.826 0.00 0.00 0.00 1.31
1010 1092 2.466846 GGTGGGTGGGCATTTTTCTAT 58.533 47.619 0.00 0.00 0.00 1.98
1011 1093 1.551329 GGGTGGGTGGGCATTTTTCTA 60.551 52.381 0.00 0.00 0.00 2.10
1012 1094 0.835971 GGGTGGGTGGGCATTTTTCT 60.836 55.000 0.00 0.00 0.00 2.52
1013 1095 0.835971 AGGGTGGGTGGGCATTTTTC 60.836 55.000 0.00 0.00 0.00 2.29
1015 1097 1.229177 GAGGGTGGGTGGGCATTTT 60.229 57.895 0.00 0.00 0.00 1.82
1017 1099 3.672503 GGAGGGTGGGTGGGCATT 61.673 66.667 0.00 0.00 0.00 3.56
1200 1282 2.187946 GACACCAGATCCGCCCAG 59.812 66.667 0.00 0.00 0.00 4.45
1239 1321 1.647545 ATCCAGACGCGGCAACAATG 61.648 55.000 17.71 1.97 0.00 2.82
1240 1322 1.369091 GATCCAGACGCGGCAACAAT 61.369 55.000 17.71 0.80 0.00 2.71
1241 1323 2.031919 ATCCAGACGCGGCAACAA 59.968 55.556 17.71 0.00 0.00 2.83
1244 1326 4.812476 CGGATCCAGACGCGGCAA 62.812 66.667 17.71 0.00 0.00 4.52
1252 1334 1.035932 GGGACGAACTCGGATCCAGA 61.036 60.000 13.41 9.21 44.95 3.86
1254 1336 2.056223 GGGGACGAACTCGGATCCA 61.056 63.158 13.41 0.00 44.95 3.41
1298 1380 3.680786 CGACTGAGCCGGTCACCA 61.681 66.667 1.90 0.00 39.51 4.17
1305 1387 4.200283 GGAGGAGCGACTGAGCCG 62.200 72.222 0.00 0.00 38.01 5.52
1308 1390 3.151022 GGGGGAGGAGCGACTGAG 61.151 72.222 0.00 0.00 0.00 3.35
1326 1408 4.207281 TCAGGGCGAGCCGATTCG 62.207 66.667 8.14 0.00 43.23 3.34
1327 1409 2.279784 CTCAGGGCGAGCCGATTC 60.280 66.667 8.14 0.00 34.18 2.52
1335 1417 3.157252 GATCCAGGCTCAGGGCGA 61.157 66.667 0.00 0.00 42.94 5.54
1336 1418 4.247380 GGATCCAGGCTCAGGGCG 62.247 72.222 6.95 0.00 42.94 6.13
1337 1419 4.247380 CGGATCCAGGCTCAGGGC 62.247 72.222 13.41 0.00 40.90 5.19
1338 1420 3.554342 CCGGATCCAGGCTCAGGG 61.554 72.222 13.41 0.00 0.00 4.45
1345 1439 0.816825 CAGTGAATGCCGGATCCAGG 60.817 60.000 13.41 14.81 0.00 4.45
1377 1471 3.195698 GACGCGGAGTGAATGCCC 61.196 66.667 12.47 0.00 43.07 5.36
1393 1490 3.760035 GCTGGAGAGCGTTCCCGA 61.760 66.667 7.02 0.00 36.35 5.14
1403 1500 2.068821 GCTGGAGATGGGCTGGAGA 61.069 63.158 0.00 0.00 0.00 3.71
1461 1579 2.355837 GACGTGACGAGCTGCCAA 60.356 61.111 13.70 0.00 0.00 4.52
1531 1649 0.849094 TTAAGCCACCATGGGAGGGT 60.849 55.000 20.67 20.67 45.45 4.34
1534 1652 1.686115 CCCTTTAAGCCACCATGGGAG 60.686 57.143 18.09 7.87 38.19 4.30
1557 1675 4.712425 GCAAGGCAACGGCAGCAG 62.712 66.667 0.00 0.00 43.71 4.24
1566 1684 0.322816 GATGTCCAGGAGCAAGGCAA 60.323 55.000 0.00 0.00 0.00 4.52
1599 1717 2.264480 CAGCGGAATGGGTCACGA 59.736 61.111 0.00 0.00 0.00 4.35
1605 1723 2.587194 CGAGAGCAGCGGAATGGG 60.587 66.667 0.00 0.00 0.00 4.00
1629 1747 0.109532 TGGCTCGGTGACCATTTTGA 59.890 50.000 1.11 0.00 0.00 2.69
1647 1765 2.354003 CCACTTTTTATTGCAGCCCCTG 60.354 50.000 0.00 0.00 34.12 4.45
1648 1766 1.901833 CCACTTTTTATTGCAGCCCCT 59.098 47.619 0.00 0.00 0.00 4.79
1650 1768 1.725641 GCCACTTTTTATTGCAGCCC 58.274 50.000 0.00 0.00 0.00 5.19
1653 1771 1.349234 GGCGCCACTTTTTATTGCAG 58.651 50.000 24.80 0.00 0.00 4.41
1659 1777 1.536331 CTTAACGGGCGCCACTTTTTA 59.464 47.619 30.85 13.94 0.00 1.52
1662 1780 0.820482 AACTTAACGGGCGCCACTTT 60.820 50.000 30.85 19.44 0.00 2.66
1674 1792 1.583495 GGCACGGCAGGGAACTTAAC 61.583 60.000 0.00 0.00 40.21 2.01
1734 1852 2.022195 GTCGGGATGCAGTCTACAGTA 58.978 52.381 0.00 0.00 0.00 2.74
1735 1853 0.818296 GTCGGGATGCAGTCTACAGT 59.182 55.000 0.00 0.00 0.00 3.55
1740 1858 2.060980 GGGAGTCGGGATGCAGTCT 61.061 63.158 0.00 0.00 0.00 3.24
1742 1860 3.461773 CGGGAGTCGGGATGCAGT 61.462 66.667 0.00 0.00 34.75 4.40
1743 1861 3.461773 ACGGGAGTCGGGATGCAG 61.462 66.667 0.00 0.00 40.62 4.41
1794 1912 4.400961 AGCAGCTTCTGACGGGGC 62.401 66.667 0.00 0.00 32.44 5.80
1799 1917 1.011451 GTCGGACAGCAGCTTCTGAC 61.011 60.000 20.65 21.10 40.14 3.51
1802 1920 1.291588 CAGTCGGACAGCAGCTTCT 59.708 57.895 11.27 0.00 0.00 2.85
1804 1922 2.358003 GCAGTCGGACAGCAGCTT 60.358 61.111 19.05 0.00 30.40 3.74
1815 1933 1.236616 TTGCATGGTTGGAGCAGTCG 61.237 55.000 0.00 0.00 39.72 4.18
1817 1935 0.892755 CATTGCATGGTTGGAGCAGT 59.107 50.000 0.00 0.00 39.72 4.40
1822 1940 0.609151 CTTGGCATTGCATGGTTGGA 59.391 50.000 11.39 0.00 0.00 3.53
1829 1947 0.689745 ATCCAGCCTTGGCATTGCAT 60.690 50.000 14.54 0.00 44.63 3.96
1830 1948 1.305465 ATCCAGCCTTGGCATTGCA 60.305 52.632 14.54 0.00 44.63 4.08
1833 1951 1.410004 CATCATCCAGCCTTGGCATT 58.590 50.000 14.54 0.00 44.63 3.56
1888 2006 4.147449 CATCTCCGGCGTGGCTGA 62.147 66.667 6.01 0.00 37.02 4.26
1947 2065 2.359975 CGGGCTCCCTCAAACCAC 60.360 66.667 3.11 0.00 0.00 4.16
1994 2112 0.539438 AAAGGTGGAGGCGAATGCAA 60.539 50.000 0.00 0.00 45.35 4.08
2370 2488 2.670401 CGTGAGCCACTTCACTTTTC 57.330 50.000 4.83 0.00 44.13 2.29
2439 2572 1.340405 GGTCAAGGTGGATCAGCACAT 60.340 52.381 4.76 0.00 33.95 3.21
2508 2641 4.284490 AGGTGAACTCAAAGATGTCAGCTA 59.716 41.667 2.09 0.00 33.53 3.32
2612 2746 2.723271 GTCGTCGTTGTCGCGTCA 60.723 61.111 5.77 3.17 37.64 4.35
2614 2756 4.297891 TCGTCGTCGTTGTCGCGT 62.298 61.111 5.77 0.00 37.64 6.01
2831 2991 3.806667 GGAGCCTGAGCCCAGCAT 61.807 66.667 0.00 0.00 41.25 3.79
2983 3143 2.899838 TGGCAACACTGACGTGGC 60.900 61.111 0.00 0.00 46.17 5.01
3070 3231 2.034879 GCGAGCACAGCCTAAGCAA 61.035 57.895 0.00 0.00 43.56 3.91


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

AutoCloner maintained by Alex Coulton.