Multiple sequence alignment - TraesCS6D01G207300

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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 TraesCS6D01G207300 chr6D 100.000 3087 0 0 1 3087 292739273 292736187 0.000000e+00 5701.0
1 TraesCS6D01G207300 chr6D 86.364 88 9 3 1519 1604 309719543 309719629 3.280000e-15 93.5
2 TraesCS6D01G207300 chr6B 92.077 2133 103 35 74 2171 457218233 457216132 0.000000e+00 2942.0
3 TraesCS6D01G207300 chr6B 82.166 471 55 16 2160 2611 457214987 457214527 8.080000e-101 377.0
4 TraesCS6D01G207300 chr6B 95.890 73 2 1 1 73 457218362 457218291 1.940000e-22 117.0
5 TraesCS6D01G207300 chr6A 91.838 1164 41 22 74 1220 428425092 428426218 0.000000e+00 1574.0
6 TraesCS6D01G207300 chr6A 92.567 1009 45 7 1266 2263 428426230 428427219 0.000000e+00 1421.0
7 TraesCS6D01G207300 chr6A 83.705 583 71 14 2267 2834 428427318 428427891 2.110000e-146 529.0
8 TraesCS6D01G207300 chr6A 94.444 72 4 0 3 74 428388408 428388479 9.050000e-21 111.0
9 TraesCS6D01G207300 chr2D 88.961 154 12 3 1523 1675 466723987 466723838 5.260000e-43 185.0
10 TraesCS6D01G207300 chr2B 88.961 154 12 4 1523 1675 545366056 545365907 5.260000e-43 185.0
11 TraesCS6D01G207300 chr2A 88.312 154 13 3 1523 1675 607841870 607841721 2.450000e-41 180.0
12 TraesCS6D01G207300 chr5A 86.170 94 11 2 1523 1615 676887309 676887401 1.960000e-17 100.0
13 TraesCS6D01G207300 chr4D 86.170 94 11 2 1523 1615 497126484 497126576 1.960000e-17 100.0
14 TraesCS6D01G207300 chr4B 86.170 94 11 2 1523 1615 637622199 637622291 1.960000e-17 100.0


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 TraesCS6D01G207300 chr6D 292736187 292739273 3086 True 5701.000000 5701 100.000000 1 3087 1 chr6D.!!$R1 3086
1 TraesCS6D01G207300 chr6B 457214527 457218362 3835 True 1145.333333 2942 90.044333 1 2611 3 chr6B.!!$R1 2610
2 TraesCS6D01G207300 chr6A 428425092 428427891 2799 False 1174.666667 1574 89.370000 74 2834 3 chr6A.!!$F2 2760

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
932 1012 1.063327 CGCCTCACTCGCTCACTAG 59.937 63.158 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2815 4201 0.178301 GTAGGGAGCTACTTGTGCCC 59.822 60.0 0.0 0.0 39.12 5.36 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
65 66 2.105821 CTGGTCCCACCTTTGTACTTCA 59.894 50.000 0.00 0.00 39.58 3.02
185 243 2.275253 GCAATGCACATAAAACGTACGC 59.725 45.455 16.72 0.00 0.00 4.42
303 361 5.408299 CACTAGCACTATTGTTAACAGCACA 59.592 40.000 16.32 0.39 0.00 4.57
308 366 7.881142 AGCACTATTGTTAACAGCACAAAATA 58.119 30.769 16.32 6.63 37.67 1.40
324 382 6.252869 GCACAAAATATATGCTAGCATCATGC 59.747 38.462 32.76 23.64 38.87 4.06
380 444 5.618561 GGTAACTAAAAATGAGACAGTGCG 58.381 41.667 0.00 0.00 0.00 5.34
386 450 2.693797 AATGAGACAGTGCGCAAAAG 57.306 45.000 14.00 7.67 0.00 2.27
431 495 5.460571 ACATGCGATATTATTGCTGATCG 57.539 39.130 15.34 0.00 43.11 3.69
472 536 2.439880 AGGATAGGAGGGCTAGCAAAAC 59.560 50.000 18.24 3.78 0.00 2.43
705 776 4.319839 CGAGAAAAAGAGGAGCAAAAGGTC 60.320 45.833 0.00 0.00 0.00 3.85
709 780 2.393271 AGAGGAGCAAAAGGTCGATG 57.607 50.000 0.00 0.00 0.00 3.84
710 781 1.065854 AGAGGAGCAAAAGGTCGATGG 60.066 52.381 0.00 0.00 0.00 3.51
732 803 1.735376 ATTAGCCGCGACACCGATCT 61.735 55.000 8.23 0.00 38.22 2.75
925 1005 4.803426 CCACCTCGCCTCACTCGC 62.803 72.222 0.00 0.00 0.00 5.03
926 1006 3.753434 CACCTCGCCTCACTCGCT 61.753 66.667 0.00 0.00 0.00 4.93
927 1007 3.444805 ACCTCGCCTCACTCGCTC 61.445 66.667 0.00 0.00 0.00 5.03
928 1008 3.443925 CCTCGCCTCACTCGCTCA 61.444 66.667 0.00 0.00 0.00 4.26
929 1009 2.202544 CTCGCCTCACTCGCTCAC 60.203 66.667 0.00 0.00 0.00 3.51
930 1010 2.673341 TCGCCTCACTCGCTCACT 60.673 61.111 0.00 0.00 0.00 3.41
931 1011 1.369839 CTCGCCTCACTCGCTCACTA 61.370 60.000 0.00 0.00 0.00 2.74
932 1012 1.063327 CGCCTCACTCGCTCACTAG 59.937 63.158 0.00 0.00 0.00 2.57
933 1013 1.226831 GCCTCACTCGCTCACTAGC 60.227 63.158 0.00 0.00 45.86 3.42
1140 1230 3.368571 GCCAAGCTCACAGGTGCC 61.369 66.667 0.00 0.00 34.10 5.01
1141 1231 2.674380 CCAAGCTCACAGGTGCCC 60.674 66.667 0.00 0.00 34.10 5.36
1142 1232 2.113774 CAAGCTCACAGGTGCCCA 59.886 61.111 0.00 0.00 34.10 5.36
1143 1233 1.529010 CAAGCTCACAGGTGCCCAA 60.529 57.895 0.00 0.00 34.10 4.12
1144 1234 1.529244 AAGCTCACAGGTGCCCAAC 60.529 57.895 0.00 0.00 34.10 3.77
1194 1285 3.597675 TTGGGCTGCATGCGTACGA 62.598 57.895 21.65 4.52 44.05 3.43
1220 1311 1.225475 CGCATGCAAGTTCGTCGAC 60.225 57.895 19.57 5.18 0.00 4.20
1223 1314 0.439985 CATGCAAGTTCGTCGACCTG 59.560 55.000 10.58 0.00 0.00 4.00
1224 1315 0.033504 ATGCAAGTTCGTCGACCTGT 59.966 50.000 10.58 0.00 0.00 4.00
1227 1318 2.129607 GCAAGTTCGTCGACCTGTAAA 58.870 47.619 10.58 0.00 0.00 2.01
1228 1319 2.097056 GCAAGTTCGTCGACCTGTAAAC 60.097 50.000 10.58 7.08 0.00 2.01
1229 1320 2.428888 AGTTCGTCGACCTGTAAACC 57.571 50.000 10.58 0.00 0.00 3.27
1231 1322 1.039068 TTCGTCGACCTGTAAACCCA 58.961 50.000 10.58 0.00 0.00 4.51
1232 1323 1.039068 TCGTCGACCTGTAAACCCAA 58.961 50.000 10.58 0.00 0.00 4.12
1233 1324 1.000060 TCGTCGACCTGTAAACCCAAG 60.000 52.381 10.58 0.00 0.00 3.61
1234 1325 1.154197 GTCGACCTGTAAACCCAAGC 58.846 55.000 3.51 0.00 0.00 4.01
1235 1326 1.053424 TCGACCTGTAAACCCAAGCT 58.947 50.000 0.00 0.00 0.00 3.74
1236 1327 1.001633 TCGACCTGTAAACCCAAGCTC 59.998 52.381 0.00 0.00 0.00 4.09
1237 1328 1.270625 CGACCTGTAAACCCAAGCTCA 60.271 52.381 0.00 0.00 0.00 4.26
1240 1331 0.517316 CTGTAAACCCAAGCTCACGC 59.483 55.000 0.00 0.00 0.00 5.34
1241 1332 1.225376 TGTAAACCCAAGCTCACGCG 61.225 55.000 3.53 3.53 42.32 6.01
1246 1337 2.126618 CCAAGCTCACGCGTACGA 60.127 61.111 21.65 5.03 43.93 3.43
1251 1342 2.127003 CTCACGCGTACGAGCACA 60.127 61.111 21.65 2.04 43.93 4.57
1252 1343 1.514228 CTCACGCGTACGAGCACAT 60.514 57.895 21.65 0.00 43.93 3.21
1253 1344 0.247934 CTCACGCGTACGAGCACATA 60.248 55.000 21.65 0.00 43.93 2.29
1254 1345 0.521867 TCACGCGTACGAGCACATAC 60.522 55.000 21.65 0.00 43.93 2.39
1256 1347 1.297085 CGCGTACGAGCACATACGA 60.297 57.895 21.65 0.00 45.51 3.43
1257 1348 1.253690 CGCGTACGAGCACATACGAG 61.254 60.000 21.65 6.54 45.51 4.18
1258 1349 0.247974 GCGTACGAGCACATACGAGT 60.248 55.000 21.65 0.00 45.51 4.18
1259 1350 1.004610 GCGTACGAGCACATACGAGTA 60.005 52.381 21.65 0.00 45.51 2.59
1260 1351 2.622645 CGTACGAGCACATACGAGTAC 58.377 52.381 10.44 0.00 45.51 2.73
1261 1352 2.283617 CGTACGAGCACATACGAGTACT 59.716 50.000 10.44 0.00 45.51 2.73
1262 1353 3.487207 CGTACGAGCACATACGAGTACTA 59.513 47.826 10.44 0.00 45.51 1.82
1263 1354 4.149571 CGTACGAGCACATACGAGTACTAT 59.850 45.833 10.44 0.00 45.51 2.12
1420 1517 1.519408 CTTGTGGGGAAACAGGTACG 58.481 55.000 0.00 0.00 0.00 3.67
1421 1518 0.838608 TTGTGGGGAAACAGGTACGT 59.161 50.000 0.00 0.00 0.00 3.57
1422 1519 1.714541 TGTGGGGAAACAGGTACGTA 58.285 50.000 0.00 0.00 0.00 3.57
1425 1522 1.619827 TGGGGAAACAGGTACGTACTG 59.380 52.381 24.07 20.49 41.64 2.74
1426 1523 1.066645 GGGGAAACAGGTACGTACTGG 60.067 57.143 24.07 18.05 40.23 4.00
1428 1525 2.299867 GGGAAACAGGTACGTACTGGAA 59.700 50.000 24.07 0.00 40.23 3.53
1509 1618 6.036953 ACAAAACACATGCACTTAATTTGTGG 59.963 34.615 16.35 3.87 41.45 4.17
1512 1621 4.099266 ACACATGCACTTAATTTGTGGTGT 59.901 37.500 16.35 11.45 41.45 4.16
1678 1790 2.630317 CGCGAGATCATGCAAGGC 59.370 61.111 0.00 0.00 0.00 4.35
1717 1829 2.641559 GTCCAAGACGACGACGGT 59.358 61.111 12.58 0.00 44.46 4.83
1768 1880 1.884926 GGCTAGCCATCACGCAGAC 60.885 63.158 29.33 0.00 35.81 3.51
1852 1964 2.501128 ATGGCGGACATGGACGAG 59.499 61.111 14.33 0.11 38.70 4.18
1955 2067 1.002403 TCCAGCGGGGAGATTACCA 59.998 57.895 2.05 0.00 42.15 3.25
2093 2205 1.955080 TCGCTTTCTACTAGCCTAGCC 59.045 52.381 0.00 0.00 35.18 3.93
2096 2208 3.189702 CGCTTTCTACTAGCCTAGCCTAG 59.810 52.174 6.21 6.21 40.47 3.02
2139 2253 3.421687 GAGGGTACACGTAGCGGCC 62.422 68.421 0.00 0.00 34.59 6.13
2183 3453 2.526120 GGATGCGTCGCCAACTAGC 61.526 63.158 15.88 0.00 0.00 3.42
2238 3509 3.258123 GGCATGTTTGGCTCCTTTTAGAA 59.742 43.478 0.00 0.00 44.68 2.10
2252 3524 7.591421 TCCTTTTAGAACAACTTTTTAGGGG 57.409 36.000 0.00 0.00 0.00 4.79
2331 3698 3.429372 AAAGGTGCACCCGAGCCAA 62.429 57.895 32.29 0.00 38.74 4.52
2358 3727 1.135575 CACGTACTCTCCCCGTTACAC 60.136 57.143 0.00 0.00 31.46 2.90
2361 3730 2.229784 CGTACTCTCCCCGTTACACTTT 59.770 50.000 0.00 0.00 0.00 2.66
2362 3731 3.440173 CGTACTCTCCCCGTTACACTTTA 59.560 47.826 0.00 0.00 0.00 1.85
2363 3732 3.949842 ACTCTCCCCGTTACACTTTAC 57.050 47.619 0.00 0.00 0.00 2.01
2364 3733 3.504375 ACTCTCCCCGTTACACTTTACT 58.496 45.455 0.00 0.00 0.00 2.24
2366 3735 3.762823 CTCTCCCCGTTACACTTTACTCT 59.237 47.826 0.00 0.00 0.00 3.24
2367 3736 4.922206 TCTCCCCGTTACACTTTACTCTA 58.078 43.478 0.00 0.00 0.00 2.43
2368 3737 5.513233 TCTCCCCGTTACACTTTACTCTAT 58.487 41.667 0.00 0.00 0.00 1.98
2370 3739 4.403432 TCCCCGTTACACTTTACTCTATGG 59.597 45.833 0.00 0.00 0.00 2.74
2379 3748 7.407393 ACACTTTACTCTATGGGTCTAACTC 57.593 40.000 0.00 0.00 0.00 3.01
2387 3756 5.862845 TCTATGGGTCTAACTCCTACTACG 58.137 45.833 0.00 0.00 0.00 3.51
2394 3763 4.033472 GTCTAACTCCTACTACGTCCGTTC 59.967 50.000 0.00 0.00 0.00 3.95
2395 3764 2.777832 ACTCCTACTACGTCCGTTCT 57.222 50.000 0.00 0.00 0.00 3.01
2477 3849 7.601073 AACAGATGGTGTATTATGCATATCG 57.399 36.000 7.36 0.74 39.03 2.92
2525 3900 7.659799 TGGTCATGTACTTATGCCATTATGTAC 59.340 37.037 0.00 0.00 35.15 2.90
2603 3979 9.552114 GACTTTGTTCTATTCTCACAAATCATG 57.448 33.333 0.00 0.00 39.17 3.07
2625 4001 2.319136 TTACACTGCCTTGTTCGTGT 57.681 45.000 0.00 0.00 42.61 4.49
2626 4002 1.577468 TACACTGCCTTGTTCGTGTG 58.423 50.000 0.00 0.00 40.47 3.82
2627 4003 0.392461 ACACTGCCTTGTTCGTGTGT 60.392 50.000 0.00 0.00 38.99 3.72
2679 4055 1.720694 CCTTGTTGGGCGTTCGTGTT 61.721 55.000 0.00 0.00 0.00 3.32
2685 4061 2.547798 GGCGTTCGTGTTCGTTCC 59.452 61.111 0.00 0.00 38.33 3.62
2694 4070 1.328374 CGTGTTCGTTCCGTCCTTTTT 59.672 47.619 0.00 0.00 0.00 1.94
2750 4126 5.161943 TCTGTTACCCTAAAGAAAGGAGC 57.838 43.478 0.00 0.00 39.15 4.70
2751 4127 3.933332 CTGTTACCCTAAAGAAAGGAGCG 59.067 47.826 0.00 0.00 39.15 5.03
2753 4129 0.035343 ACCCTAAAGAAAGGAGCGGC 60.035 55.000 0.00 0.00 39.15 6.53
2759 4145 3.906720 AAAGAAAGGAGCGGCTATGTA 57.093 42.857 0.60 0.00 0.00 2.29
2760 4146 4.423625 AAAGAAAGGAGCGGCTATGTAT 57.576 40.909 0.60 0.00 0.00 2.29
2762 4148 3.733337 AGAAAGGAGCGGCTATGTATTG 58.267 45.455 0.60 0.00 0.00 1.90
2768 4154 3.516615 GAGCGGCTATGTATTGAGATCC 58.483 50.000 0.60 0.00 0.00 3.36
2774 4160 5.486526 GGCTATGTATTGAGATCCAAGGAG 58.513 45.833 0.00 0.00 38.31 3.69
2778 4164 4.361783 TGTATTGAGATCCAAGGAGGTCA 58.638 43.478 0.00 0.00 38.31 4.02
2781 4167 0.461961 GAGATCCAAGGAGGTCACGG 59.538 60.000 0.00 0.00 39.02 4.94
2787 4173 0.671781 CAAGGAGGTCACGGCTCAAG 60.672 60.000 0.00 0.00 0.00 3.02
2815 4201 2.528743 CCAGCGCTGCTATTGGACG 61.529 63.158 31.96 11.00 36.40 4.79
2817 4203 3.272334 GCGCTGCTATTGGACGGG 61.272 66.667 0.00 0.00 0.00 5.28
2834 4220 0.178301 GGGCACAAGTAGCTCCCTAC 59.822 60.000 0.00 0.00 43.46 3.18
2835 4221 0.179108 GGCACAAGTAGCTCCCTACG 60.179 60.000 0.00 0.00 46.81 3.51
2836 4222 0.179108 GCACAAGTAGCTCCCTACGG 60.179 60.000 0.00 0.00 46.81 4.02
2837 4223 0.460311 CACAAGTAGCTCCCTACGGG 59.540 60.000 0.00 0.00 46.81 5.28
2838 4224 0.040794 ACAAGTAGCTCCCTACGGGT 59.959 55.000 0.00 0.00 46.81 5.28
2839 4225 1.192428 CAAGTAGCTCCCTACGGGTT 58.808 55.000 0.00 0.00 46.81 4.11
2840 4226 2.291800 ACAAGTAGCTCCCTACGGGTTA 60.292 50.000 0.00 0.00 46.81 2.85
2841 4227 2.361438 CAAGTAGCTCCCTACGGGTTAG 59.639 54.545 0.00 0.00 46.81 2.34
2842 4228 1.568123 AGTAGCTCCCTACGGGTTAGT 59.432 52.381 0.00 0.00 46.81 2.24
2843 4229 2.024560 AGTAGCTCCCTACGGGTTAGTT 60.025 50.000 0.00 0.00 46.81 2.24
2844 4230 1.948391 AGCTCCCTACGGGTTAGTTT 58.052 50.000 0.00 0.00 44.74 2.66
2845 4231 1.553704 AGCTCCCTACGGGTTAGTTTG 59.446 52.381 0.00 0.00 44.74 2.93
2846 4232 1.277273 GCTCCCTACGGGTTAGTTTGT 59.723 52.381 0.00 0.00 44.74 2.83
2847 4233 2.289882 GCTCCCTACGGGTTAGTTTGTT 60.290 50.000 0.00 0.00 44.74 2.83
2848 4234 3.808265 GCTCCCTACGGGTTAGTTTGTTT 60.808 47.826 0.00 0.00 44.74 2.83
2849 4235 4.563374 GCTCCCTACGGGTTAGTTTGTTTA 60.563 45.833 0.00 0.00 44.74 2.01
2850 4236 5.737860 CTCCCTACGGGTTAGTTTGTTTAT 58.262 41.667 0.00 0.00 44.74 1.40
2851 4237 6.630188 GCTCCCTACGGGTTAGTTTGTTTATA 60.630 42.308 0.00 0.00 44.74 0.98
2852 4238 7.436320 TCCCTACGGGTTAGTTTGTTTATAT 57.564 36.000 0.00 0.00 44.74 0.86
2853 4239 7.860584 TCCCTACGGGTTAGTTTGTTTATATT 58.139 34.615 0.00 0.00 44.74 1.28
2854 4240 8.328014 TCCCTACGGGTTAGTTTGTTTATATTT 58.672 33.333 0.00 0.00 44.74 1.40
2855 4241 8.959548 CCCTACGGGTTAGTTTGTTTATATTTT 58.040 33.333 0.00 0.00 38.25 1.82
2893 4279 8.728088 ACTAATTACAGAGTTTTGAAAATGCG 57.272 30.769 0.00 0.00 0.00 4.73
2894 4280 8.564574 ACTAATTACAGAGTTTTGAAAATGCGA 58.435 29.630 0.00 0.00 0.00 5.10
2895 4281 9.393249 CTAATTACAGAGTTTTGAAAATGCGAA 57.607 29.630 0.00 0.00 0.00 4.70
2896 4282 7.623268 ATTACAGAGTTTTGAAAATGCGAAC 57.377 32.000 0.00 0.00 0.00 3.95
2897 4283 4.992688 ACAGAGTTTTGAAAATGCGAACA 58.007 34.783 0.00 0.00 0.00 3.18
2898 4284 4.798387 ACAGAGTTTTGAAAATGCGAACAC 59.202 37.500 0.00 0.00 0.00 3.32
2899 4285 5.036737 CAGAGTTTTGAAAATGCGAACACT 58.963 37.500 0.00 0.00 0.00 3.55
2900 4286 5.516339 CAGAGTTTTGAAAATGCGAACACTT 59.484 36.000 0.00 0.00 0.00 3.16
2901 4287 6.034898 CAGAGTTTTGAAAATGCGAACACTTT 59.965 34.615 0.00 0.00 0.00 2.66
2902 4288 6.589907 AGAGTTTTGAAAATGCGAACACTTTT 59.410 30.769 0.00 0.00 0.00 2.27
2903 4289 7.117667 AGAGTTTTGAAAATGCGAACACTTTTT 59.882 29.630 0.00 0.00 31.71 1.94
2904 4290 7.233689 AGTTTTGAAAATGCGAACACTTTTTC 58.766 30.769 0.00 8.05 40.97 2.29
2905 4291 5.710613 TTGAAAATGCGAACACTTTTTCC 57.289 34.783 10.99 0.00 40.38 3.13
2906 4292 4.748892 TGAAAATGCGAACACTTTTTCCA 58.251 34.783 10.99 0.00 40.38 3.53
2907 4293 4.803088 TGAAAATGCGAACACTTTTTCCAG 59.197 37.500 10.99 0.00 40.38 3.86
2908 4294 4.647424 AAATGCGAACACTTTTTCCAGA 57.353 36.364 0.00 0.00 0.00 3.86
2909 4295 4.853924 AATGCGAACACTTTTTCCAGAT 57.146 36.364 0.00 0.00 0.00 2.90
2910 4296 4.853924 ATGCGAACACTTTTTCCAGATT 57.146 36.364 0.00 0.00 0.00 2.40
2911 4297 5.957842 ATGCGAACACTTTTTCCAGATTA 57.042 34.783 0.00 0.00 0.00 1.75
2912 4298 5.957842 TGCGAACACTTTTTCCAGATTAT 57.042 34.783 0.00 0.00 0.00 1.28
2913 4299 5.698832 TGCGAACACTTTTTCCAGATTATG 58.301 37.500 0.00 0.00 0.00 1.90
2914 4300 5.471797 TGCGAACACTTTTTCCAGATTATGA 59.528 36.000 0.00 0.00 0.00 2.15
2915 4301 6.016693 TGCGAACACTTTTTCCAGATTATGAA 60.017 34.615 0.00 0.00 0.00 2.57
2916 4302 6.524586 GCGAACACTTTTTCCAGATTATGAAG 59.475 38.462 0.00 0.00 0.00 3.02
2917 4303 7.573096 GCGAACACTTTTTCCAGATTATGAAGA 60.573 37.037 0.00 0.00 0.00 2.87
2918 4304 8.454106 CGAACACTTTTTCCAGATTATGAAGAT 58.546 33.333 0.00 0.00 0.00 2.40
2926 4312 9.784531 TTTTCCAGATTATGAAGATAGATCCAC 57.215 33.333 0.00 0.00 0.00 4.02
2927 4313 7.163001 TCCAGATTATGAAGATAGATCCACG 57.837 40.000 0.00 0.00 0.00 4.94
2928 4314 6.153510 TCCAGATTATGAAGATAGATCCACGG 59.846 42.308 0.00 0.00 0.00 4.94
2929 4315 6.153510 CCAGATTATGAAGATAGATCCACGGA 59.846 42.308 0.00 0.00 0.00 4.69
2930 4316 7.310052 CCAGATTATGAAGATAGATCCACGGAA 60.310 40.741 0.00 0.00 0.00 4.30
2931 4317 8.090831 CAGATTATGAAGATAGATCCACGGAAA 58.909 37.037 0.00 0.00 0.00 3.13
2932 4318 8.651389 AGATTATGAAGATAGATCCACGGAAAA 58.349 33.333 0.00 0.00 0.00 2.29
2933 4319 9.273016 GATTATGAAGATAGATCCACGGAAAAA 57.727 33.333 0.00 0.00 0.00 1.94
3015 4401 4.661125 TCATAAGCAACTTTAAGCATGCG 58.339 39.130 13.01 0.00 43.39 4.73
3016 4402 4.394610 TCATAAGCAACTTTAAGCATGCGA 59.605 37.500 13.01 0.90 43.39 5.10
3017 4403 3.855689 AAGCAACTTTAAGCATGCGAT 57.144 38.095 13.01 8.21 43.39 4.58
3018 4404 3.855689 AGCAACTTTAAGCATGCGATT 57.144 38.095 13.01 4.59 43.39 3.34
3019 4405 4.963276 AGCAACTTTAAGCATGCGATTA 57.037 36.364 13.01 3.48 43.39 1.75
3020 4406 5.505173 AGCAACTTTAAGCATGCGATTAT 57.495 34.783 13.01 0.11 43.39 1.28
3021 4407 5.894807 AGCAACTTTAAGCATGCGATTATT 58.105 33.333 13.01 2.96 43.39 1.40
3022 4408 6.332630 AGCAACTTTAAGCATGCGATTATTT 58.667 32.000 13.01 2.16 43.39 1.40
3023 4409 6.813152 AGCAACTTTAAGCATGCGATTATTTT 59.187 30.769 13.01 1.37 43.39 1.82
3024 4410 7.331687 AGCAACTTTAAGCATGCGATTATTTTT 59.668 29.630 13.01 0.57 43.39 1.94
3046 4432 8.635877 TTTTTGCAATACGTGAATACTTGTTT 57.364 26.923 0.00 0.00 0.00 2.83
3047 4433 8.635877 TTTTGCAATACGTGAATACTTGTTTT 57.364 26.923 0.00 0.00 0.00 2.43
3048 4434 7.845617 TTGCAATACGTGAATACTTGTTTTC 57.154 32.000 0.00 0.00 0.00 2.29
3049 4435 6.960468 TGCAATACGTGAATACTTGTTTTCA 58.040 32.000 0.00 3.24 0.00 2.69
3050 4436 7.589395 TGCAATACGTGAATACTTGTTTTCAT 58.411 30.769 0.00 0.00 34.60 2.57
3051 4437 7.536964 TGCAATACGTGAATACTTGTTTTCATG 59.463 33.333 17.98 17.98 42.12 3.07
3057 4443 9.431887 ACGTGAATACTTGTTTTCATGTATACT 57.568 29.630 21.40 5.67 45.53 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 9.325198 CAGCTTGTCCTATTTATACATACAACA 57.675 33.333 0.00 0.00 0.00 3.33
65 66 8.853126 ACGTTAGCCTTTTCCTTTTTATAAACT 58.147 29.630 0.00 0.00 0.00 2.66
185 243 4.974721 AAGGGCTGGGGCGTGTTG 62.975 66.667 0.00 0.00 39.81 3.33
261 319 6.488006 TGCTAGTGCATCTTCTTTTCTTTTCT 59.512 34.615 0.00 0.00 45.31 2.52
324 382 2.376956 GCGCATCTAGTAGACGAACAG 58.623 52.381 12.87 0.10 0.00 3.16
333 391 0.380733 CTCGTGTGGCGCATCTAGTA 59.619 55.000 10.83 0.00 41.07 1.82
380 444 6.147164 GGAAGTTTGGGCTTAATAACTTTTGC 59.853 38.462 0.00 0.00 40.00 3.68
386 450 5.995565 AAGGGAAGTTTGGGCTTAATAAC 57.004 39.130 0.00 0.00 0.00 1.89
448 512 1.271856 GCTAGCCCTCCTATCCTTCC 58.728 60.000 2.29 0.00 0.00 3.46
472 536 3.393089 ACTACTGACTCTTGCAACAGG 57.607 47.619 16.47 5.11 35.08 4.00
705 776 1.300620 TCGCGGCTAATTCCCATCG 60.301 57.895 6.13 0.00 0.00 3.84
709 780 2.178235 GGTGTCGCGGCTAATTCCC 61.178 63.158 13.81 0.00 0.00 3.97
710 781 2.522638 CGGTGTCGCGGCTAATTCC 61.523 63.158 13.81 5.86 0.00 3.01
860 931 0.498927 GCATATATACTAGCGCGCGC 59.501 55.000 45.10 45.10 42.33 6.86
861 932 1.775770 CTGCATATATACTAGCGCGCG 59.224 52.381 28.44 28.44 0.00 6.86
925 1005 2.439507 AGGGAGAGAGAGAGCTAGTGAG 59.560 54.545 0.00 0.00 0.00 3.51
926 1006 2.172505 CAGGGAGAGAGAGAGCTAGTGA 59.827 54.545 0.00 0.00 0.00 3.41
927 1007 2.575532 CAGGGAGAGAGAGAGCTAGTG 58.424 57.143 0.00 0.00 0.00 2.74
928 1008 1.494721 CCAGGGAGAGAGAGAGCTAGT 59.505 57.143 0.00 0.00 0.00 2.57
929 1009 1.202927 CCCAGGGAGAGAGAGAGCTAG 60.203 61.905 0.00 0.00 0.00 3.42
930 1010 0.850100 CCCAGGGAGAGAGAGAGCTA 59.150 60.000 0.00 0.00 0.00 3.32
931 1011 1.620259 CCCAGGGAGAGAGAGAGCT 59.380 63.158 0.00 0.00 0.00 4.09
932 1012 1.457455 CCCCAGGGAGAGAGAGAGC 60.457 68.421 7.25 0.00 37.50 4.09
974 1064 6.481644 TCCAACAATCACTTGCAAAAATTACC 59.518 34.615 0.00 0.00 35.69 2.85
981 1071 4.100653 TCCATTCCAACAATCACTTGCAAA 59.899 37.500 0.00 0.00 35.69 3.68
1140 1230 3.974871 TGATCATGATCATTGCGTTGG 57.025 42.857 30.27 0.00 42.42 3.77
1170 1260 1.481772 ACGCATGCAGCCCAAATTAAT 59.518 42.857 19.57 0.00 41.38 1.40
1220 1311 1.156736 CGTGAGCTTGGGTTTACAGG 58.843 55.000 0.00 0.00 0.00 4.00
1234 1325 0.247934 TATGTGCTCGTACGCGTGAG 60.248 55.000 24.59 21.42 39.49 3.51
1235 1326 0.521867 GTATGTGCTCGTACGCGTGA 60.522 55.000 24.59 10.89 39.49 4.35
1236 1327 1.908089 GTATGTGCTCGTACGCGTG 59.092 57.895 24.59 6.04 39.49 5.34
1237 1328 4.372235 GTATGTGCTCGTACGCGT 57.628 55.556 19.17 19.17 39.49 6.01
1241 1332 3.940657 AGTACTCGTATGTGCTCGTAC 57.059 47.619 7.88 7.88 33.95 3.67
1245 1336 5.866335 AGCTATAGTACTCGTATGTGCTC 57.134 43.478 0.00 0.00 34.81 4.26
1246 1337 6.128227 GCTTAGCTATAGTACTCGTATGTGCT 60.128 42.308 0.00 5.35 36.82 4.40
1248 1339 7.367159 AGCTTAGCTATAGTACTCGTATGTG 57.633 40.000 4.30 0.00 36.99 3.21
1249 1340 6.310956 CGAGCTTAGCTATAGTACTCGTATGT 59.689 42.308 6.75 0.00 39.88 2.29
1251 1342 6.890663 CGAGCTTAGCTATAGTACTCGTAT 57.109 41.667 6.75 0.00 39.88 3.06
1256 1347 5.978322 GCAAAACGAGCTTAGCTATAGTACT 59.022 40.000 6.75 0.00 39.88 2.73
1257 1348 5.978322 AGCAAAACGAGCTTAGCTATAGTAC 59.022 40.000 6.75 0.00 39.88 2.73
1258 1349 5.977725 CAGCAAAACGAGCTTAGCTATAGTA 59.022 40.000 6.75 0.00 41.14 1.82
1259 1350 4.806247 CAGCAAAACGAGCTTAGCTATAGT 59.194 41.667 6.75 5.15 41.14 2.12
1260 1351 4.318404 GCAGCAAAACGAGCTTAGCTATAG 60.318 45.833 6.75 4.46 41.14 1.31
1261 1352 3.555956 GCAGCAAAACGAGCTTAGCTATA 59.444 43.478 6.75 0.00 41.14 1.31
1262 1353 2.352960 GCAGCAAAACGAGCTTAGCTAT 59.647 45.455 6.75 0.00 41.14 2.97
1263 1354 1.732259 GCAGCAAAACGAGCTTAGCTA 59.268 47.619 6.75 0.00 41.14 3.32
1469 1578 2.749621 GTTTTGTGAGCTCGATCCCATT 59.250 45.455 9.64 0.00 0.00 3.16
1509 1618 1.293924 CCATCTGGCAGATCGAACAC 58.706 55.000 26.62 0.00 31.32 3.32
1512 1621 0.103026 CGACCATCTGGCAGATCGAA 59.897 55.000 26.63 4.30 39.32 3.71
1705 1817 4.702081 GCAGCACCGTCGTCGTCT 62.702 66.667 0.71 0.00 35.01 4.18
1852 1964 0.669625 GGTGGTCGTACTGCAGGAAC 60.670 60.000 19.93 14.57 0.00 3.62
2139 2253 1.262950 CACCAACACCACACGTACATG 59.737 52.381 0.00 0.00 0.00 3.21
2183 3453 2.494918 CTAGTCGAAGTGGGGGCG 59.505 66.667 0.00 0.00 0.00 6.13
2225 3495 7.145985 CCTAAAAAGTTGTTCTAAAAGGAGCC 58.854 38.462 0.00 0.00 0.00 4.70
2277 3643 8.465201 CCTTTTCTTCCATTTCTATCTTTCCAG 58.535 37.037 0.00 0.00 0.00 3.86
2289 3655 3.308401 ACACCTGCCTTTTCTTCCATTT 58.692 40.909 0.00 0.00 0.00 2.32
2294 3660 4.363138 CTTTGAACACCTGCCTTTTCTTC 58.637 43.478 0.00 0.00 0.00 2.87
2331 3698 1.408544 GGGGAGAGTACGTGAGCTAGT 60.409 57.143 0.00 0.00 0.00 2.57
2358 3727 8.000127 AGTAGGAGTTAGACCCATAGAGTAAAG 59.000 40.741 0.00 0.00 0.00 1.85
2361 3730 7.256119 CGTAGTAGGAGTTAGACCCATAGAGTA 60.256 44.444 0.00 0.00 0.00 2.59
2362 3731 5.998128 AGTAGGAGTTAGACCCATAGAGT 57.002 43.478 0.00 0.00 0.00 3.24
2363 3732 5.933463 CGTAGTAGGAGTTAGACCCATAGAG 59.067 48.000 0.00 0.00 0.00 2.43
2364 3733 5.367937 ACGTAGTAGGAGTTAGACCCATAGA 59.632 44.000 0.00 0.00 41.94 1.98
2366 3735 5.636903 ACGTAGTAGGAGTTAGACCCATA 57.363 43.478 0.00 0.00 41.94 2.74
2367 3736 4.516652 ACGTAGTAGGAGTTAGACCCAT 57.483 45.455 0.00 0.00 41.94 4.00
2379 3748 9.604626 CTTATATTTAAGAACGGACGTAGTAGG 57.395 37.037 0.00 0.00 38.16 3.18
2496 3868 9.399797 CATAATGGCATAAGTACATGACCATAT 57.600 33.333 15.80 11.47 39.64 1.78
2499 3871 6.600388 ACATAATGGCATAAGTACATGACCA 58.400 36.000 0.00 4.05 36.89 4.02
2501 3873 8.833231 AGTACATAATGGCATAAGTACATGAC 57.167 34.615 25.48 11.40 34.19 3.06
2541 3916 9.439500 AGAGAGTATAACTATTATCGTCCAGAC 57.561 37.037 0.00 0.00 0.00 3.51
2603 3979 3.181504 ACACGAACAAGGCAGTGTAAAAC 60.182 43.478 0.00 0.00 44.79 2.43
2625 4001 8.731605 TGGCACGAATAACAAAAATAGATAACA 58.268 29.630 0.00 0.00 0.00 2.41
2626 4002 9.730420 ATGGCACGAATAACAAAAATAGATAAC 57.270 29.630 0.00 0.00 0.00 1.89
2627 4003 9.729023 CATGGCACGAATAACAAAAATAGATAA 57.271 29.630 0.00 0.00 0.00 1.75
2731 4107 3.268330 CCGCTCCTTTCTTTAGGGTAAC 58.732 50.000 0.00 0.00 35.90 2.50
2732 4108 2.355412 GCCGCTCCTTTCTTTAGGGTAA 60.355 50.000 0.00 0.00 35.90 2.85
2733 4109 1.208776 GCCGCTCCTTTCTTTAGGGTA 59.791 52.381 0.00 0.00 35.90 3.69
2749 4125 3.319137 TGGATCTCAATACATAGCCGC 57.681 47.619 0.00 0.00 0.00 6.53
2750 4126 4.021104 TCCTTGGATCTCAATACATAGCCG 60.021 45.833 0.00 0.00 34.45 5.52
2751 4127 5.486526 CTCCTTGGATCTCAATACATAGCC 58.513 45.833 0.00 0.00 34.45 3.93
2753 4129 6.268617 TGACCTCCTTGGATCTCAATACATAG 59.731 42.308 0.00 0.00 39.71 2.23
2759 4145 2.169352 CGTGACCTCCTTGGATCTCAAT 59.831 50.000 0.00 0.00 39.71 2.57
2760 4146 1.550524 CGTGACCTCCTTGGATCTCAA 59.449 52.381 0.00 0.00 39.71 3.02
2762 4148 0.461961 CCGTGACCTCCTTGGATCTC 59.538 60.000 0.00 0.00 39.71 2.75
2768 4154 0.671781 CTTGAGCCGTGACCTCCTTG 60.672 60.000 0.00 0.00 0.00 3.61
2774 4160 2.358737 CACCCTTGAGCCGTGACC 60.359 66.667 0.00 0.00 0.00 4.02
2796 4182 1.153369 GTCCAATAGCAGCGCTGGA 60.153 57.895 36.47 23.28 40.10 3.86
2815 4201 0.178301 GTAGGGAGCTACTTGTGCCC 59.822 60.000 0.00 0.00 39.12 5.36
2817 4203 3.347411 CGTAGGGAGCTACTTGTGC 57.653 57.895 0.00 0.00 0.00 4.57
2867 4253 9.820229 CGCATTTTCAAAACTCTGTAATTAGTA 57.180 29.630 0.00 0.00 0.00 1.82
2868 4254 8.564574 TCGCATTTTCAAAACTCTGTAATTAGT 58.435 29.630 0.00 0.00 0.00 2.24
2869 4255 8.948853 TCGCATTTTCAAAACTCTGTAATTAG 57.051 30.769 0.00 0.00 0.00 1.73
2870 4256 9.176181 GTTCGCATTTTCAAAACTCTGTAATTA 57.824 29.630 0.00 0.00 0.00 1.40
2871 4257 7.704472 TGTTCGCATTTTCAAAACTCTGTAATT 59.296 29.630 0.00 0.00 0.00 1.40
2872 4258 7.167468 GTGTTCGCATTTTCAAAACTCTGTAAT 59.833 33.333 0.00 0.00 0.00 1.89
2873 4259 6.470877 GTGTTCGCATTTTCAAAACTCTGTAA 59.529 34.615 0.00 0.00 0.00 2.41
2874 4260 5.968848 GTGTTCGCATTTTCAAAACTCTGTA 59.031 36.000 0.00 0.00 0.00 2.74
2875 4261 4.798387 GTGTTCGCATTTTCAAAACTCTGT 59.202 37.500 0.00 0.00 0.00 3.41
2876 4262 5.036737 AGTGTTCGCATTTTCAAAACTCTG 58.963 37.500 0.00 0.00 0.00 3.35
2877 4263 5.248870 AGTGTTCGCATTTTCAAAACTCT 57.751 34.783 0.00 0.00 0.00 3.24
2878 4264 5.949233 AAGTGTTCGCATTTTCAAAACTC 57.051 34.783 0.00 0.00 0.00 3.01
2879 4265 6.720012 AAAAGTGTTCGCATTTTCAAAACT 57.280 29.167 0.00 0.00 36.26 2.66
2880 4266 6.464519 GGAAAAAGTGTTCGCATTTTCAAAAC 59.535 34.615 20.25 6.91 41.34 2.43
2881 4267 6.147821 TGGAAAAAGTGTTCGCATTTTCAAAA 59.852 30.769 20.25 9.03 41.34 2.44
2882 4268 5.639506 TGGAAAAAGTGTTCGCATTTTCAAA 59.360 32.000 20.25 10.69 41.34 2.69
2883 4269 5.171476 TGGAAAAAGTGTTCGCATTTTCAA 58.829 33.333 20.25 11.89 41.34 2.69
2884 4270 4.748892 TGGAAAAAGTGTTCGCATTTTCA 58.251 34.783 20.25 9.08 41.34 2.69
2885 4271 5.040635 TCTGGAAAAAGTGTTCGCATTTTC 58.959 37.500 14.31 14.31 36.26 2.29
2886 4272 5.004922 TCTGGAAAAAGTGTTCGCATTTT 57.995 34.783 0.18 0.18 38.44 1.82
2887 4273 4.647424 TCTGGAAAAAGTGTTCGCATTT 57.353 36.364 0.00 0.00 0.00 2.32
2888 4274 4.853924 ATCTGGAAAAAGTGTTCGCATT 57.146 36.364 0.00 0.00 0.00 3.56
2889 4275 4.853924 AATCTGGAAAAAGTGTTCGCAT 57.146 36.364 0.00 0.00 0.00 4.73
2890 4276 5.471797 TCATAATCTGGAAAAAGTGTTCGCA 59.528 36.000 0.00 0.00 0.00 5.10
2891 4277 5.938322 TCATAATCTGGAAAAAGTGTTCGC 58.062 37.500 0.00 0.00 0.00 4.70
2892 4278 7.806690 TCTTCATAATCTGGAAAAAGTGTTCG 58.193 34.615 0.00 0.00 0.00 3.95
2900 4286 9.784531 GTGGATCTATCTTCATAATCTGGAAAA 57.215 33.333 0.00 0.00 0.00 2.29
2901 4287 8.090831 CGTGGATCTATCTTCATAATCTGGAAA 58.909 37.037 0.00 0.00 0.00 3.13
2902 4288 7.310052 CCGTGGATCTATCTTCATAATCTGGAA 60.310 40.741 0.00 0.00 0.00 3.53
2903 4289 6.153510 CCGTGGATCTATCTTCATAATCTGGA 59.846 42.308 0.00 0.00 0.00 3.86
2904 4290 6.153510 TCCGTGGATCTATCTTCATAATCTGG 59.846 42.308 0.00 0.00 0.00 3.86
2905 4291 7.163001 TCCGTGGATCTATCTTCATAATCTG 57.837 40.000 0.00 0.00 0.00 2.90
2906 4292 7.782897 TTCCGTGGATCTATCTTCATAATCT 57.217 36.000 0.00 0.00 0.00 2.40
2907 4293 8.833231 TTTTCCGTGGATCTATCTTCATAATC 57.167 34.615 0.00 0.00 0.00 1.75
2992 4378 4.731961 CGCATGCTTAAAGTTGCTTATGAG 59.268 41.667 17.13 0.00 32.97 2.90
2993 4379 4.394610 TCGCATGCTTAAAGTTGCTTATGA 59.605 37.500 17.13 0.00 32.97 2.15
2994 4380 4.661125 TCGCATGCTTAAAGTTGCTTATG 58.339 39.130 17.13 0.00 32.97 1.90
2995 4381 4.963276 TCGCATGCTTAAAGTTGCTTAT 57.037 36.364 17.13 0.00 32.97 1.73
2996 4382 4.963276 ATCGCATGCTTAAAGTTGCTTA 57.037 36.364 17.13 0.00 32.97 3.09
2997 4383 3.855689 ATCGCATGCTTAAAGTTGCTT 57.144 38.095 17.13 0.00 32.97 3.91
2998 4384 3.855689 AATCGCATGCTTAAAGTTGCT 57.144 38.095 17.13 0.00 32.97 3.91
2999 4385 6.573617 AAATAATCGCATGCTTAAAGTTGC 57.426 33.333 17.13 0.00 0.00 4.17
3021 4407 8.635877 AAACAAGTATTCACGTATTGCAAAAA 57.364 26.923 1.71 0.00 0.00 1.94
3022 4408 8.635877 AAAACAAGTATTCACGTATTGCAAAA 57.364 26.923 1.71 0.00 0.00 2.44
3023 4409 7.915923 TGAAAACAAGTATTCACGTATTGCAAA 59.084 29.630 1.71 0.00 30.94 3.68
3024 4410 7.418408 TGAAAACAAGTATTCACGTATTGCAA 58.582 30.769 0.00 0.00 30.94 4.08
3025 4411 6.960468 TGAAAACAAGTATTCACGTATTGCA 58.040 32.000 0.00 0.00 30.94 4.08
3026 4412 7.537306 ACATGAAAACAAGTATTCACGTATTGC 59.463 33.333 0.00 0.00 38.29 3.56
3027 4413 8.948853 ACATGAAAACAAGTATTCACGTATTG 57.051 30.769 0.00 0.00 38.29 1.90
3031 4417 9.431887 AGTATACATGAAAACAAGTATTCACGT 57.568 29.630 5.50 0.00 38.29 4.49


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

AutoCloner maintained by Alex Coulton.