Multiple sequence alignment - TraesCS7D01G007200

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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 TraesCS7D01G007200 chr7D 100.000 2357 0 0 1 2357 3598698 3596342 0.000000e+00 4353.0
1 TraesCS7D01G007200 chr7D 74.158 1099 203 44 514 1588 2354355 2355396 4.750000e-102 381.0
2 TraesCS7D01G007200 chr7D 73.985 788 157 27 516 1282 2500047 2500807 2.310000e-70 276.0
3 TraesCS7D01G007200 chr7A 86.106 2044 161 26 1 1995 2752921 2750952 0.000000e+00 2087.0
4 TraesCS7D01G007200 chr7A 87.003 1785 146 24 414 2151 2603584 2605329 0.000000e+00 1932.0
5 TraesCS7D01G007200 chr7A 80.841 856 100 39 1404 2228 2103325 2102503 4.310000e-172 614.0
6 TraesCS7D01G007200 chr7A 80.992 242 15 15 2017 2228 2748551 2748311 1.870000e-36 163.0
7 TraesCS7D01G007200 chr7A 98.333 60 1 0 2298 2357 2605323 2605382 3.200000e-19 106.0
8 TraesCS7D01G007200 chr7A 97.727 44 1 0 2117 2160 2102651 2102608 2.510000e-10 76.8
9 TraesCS7D01G007200 chr4A 87.231 1347 124 16 1 1338 742137647 742138954 0.000000e+00 1491.0
10 TraesCS7D01G007200 chr4A 81.852 1080 166 9 477 1553 10637235 10638287 0.000000e+00 881.0
11 TraesCS7D01G007200 chr4A 87.828 419 42 6 1398 1815 742138958 742139368 1.270000e-132 483.0
12 TraesCS7D01G007200 chr4A 87.805 164 19 1 862 1024 723082397 723082234 8.600000e-45 191.0
13 TraesCS7D01G007200 chr4A 87.195 164 20 1 862 1024 723054907 723054744 4.000000e-43 185.0
14 TraesCS7D01G007200 chr4A 76.020 196 39 5 515 706 741785697 741785888 6.930000e-16 95.3
15 TraesCS7D01G007200 chr4B 82.103 1084 163 15 477 1556 572554543 572553487 0.000000e+00 898.0
16 TraesCS7D01G007200 chr7B 82.716 81 13 1 631 710 708472624 708472704 1.170000e-08 71.3


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 TraesCS7D01G007200 chr7D 3596342 3598698 2356 True 4353.0 4353 100.0000 1 2357 1 chr7D.!!$R1 2356
1 TraesCS7D01G007200 chr7D 2354355 2355396 1041 False 381.0 381 74.1580 514 1588 1 chr7D.!!$F1 1074
2 TraesCS7D01G007200 chr7D 2500047 2500807 760 False 276.0 276 73.9850 516 1282 1 chr7D.!!$F2 766
3 TraesCS7D01G007200 chr7A 2748311 2752921 4610 True 1125.0 2087 83.5490 1 2228 2 chr7A.!!$R2 2227
4 TraesCS7D01G007200 chr7A 2603584 2605382 1798 False 1019.0 1932 92.6680 414 2357 2 chr7A.!!$F1 1943
5 TraesCS7D01G007200 chr7A 2102503 2103325 822 True 345.4 614 89.2840 1404 2228 2 chr7A.!!$R1 824
6 TraesCS7D01G007200 chr4A 742137647 742139368 1721 False 987.0 1491 87.5295 1 1815 2 chr4A.!!$F3 1814
7 TraesCS7D01G007200 chr4A 10637235 10638287 1052 False 881.0 881 81.8520 477 1553 1 chr4A.!!$F1 1076
8 TraesCS7D01G007200 chr4B 572553487 572554543 1056 True 898.0 898 82.1030 477 1556 1 chr4B.!!$R1 1079

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
530 549 0.107508 CGGACTCAGCAACCCATCAT 60.108 55.0 0.0 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2279 4787 0.03254 CAAAACAGCCTTCCCACAGC 59.967 55.0 0.0 0.0 0.0 4.4 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
72 75 0.944386 GACCTCTTTGCAGCGTCAAA 59.056 50.000 6.32 6.32 35.01 2.69
101 105 2.806244 ACTTGCTTTTTATGCGTCGAGT 59.194 40.909 0.00 0.00 0.00 4.18
143 147 0.248134 GACAAGACGTAGCGCTCGAT 60.248 55.000 27.66 16.52 0.00 3.59
148 152 0.585357 GACGTAGCGCTCGATTAGGA 59.415 55.000 27.66 2.28 0.00 2.94
149 153 1.197264 GACGTAGCGCTCGATTAGGAT 59.803 52.381 27.66 10.03 0.00 3.24
220 229 6.857777 ATTGTTCACTCTGACAGAAAAGAG 57.142 37.500 6.61 0.00 44.57 2.85
243 252 4.672587 AGCACTCAAACTGTCTAACTCA 57.327 40.909 0.00 0.00 0.00 3.41
305 315 2.611751 CGAACACACAAGTTGACCATCA 59.388 45.455 10.54 0.00 0.00 3.07
364 381 6.957631 AGGACCATCTTGTATCACATTACAA 58.042 36.000 0.00 0.00 39.21 2.41
366 383 7.336931 AGGACCATCTTGTATCACATTACAAAC 59.663 37.037 0.00 0.00 40.53 2.93
372 389 7.935520 TCTTGTATCACATTACAAACAAGCAA 58.064 30.769 7.88 0.00 42.10 3.91
400 417 1.618343 GGCCACAACCAGCAAAGTAAT 59.382 47.619 0.00 0.00 0.00 1.89
530 549 0.107508 CGGACTCAGCAACCCATCAT 60.108 55.000 0.00 0.00 0.00 2.45
594 613 0.467290 AATTCCACACAGGCGGTTGT 60.467 50.000 0.00 0.00 37.29 3.32
595 614 0.467290 ATTCCACACAGGCGGTTGTT 60.467 50.000 0.00 0.00 37.29 2.83
596 615 1.380403 TTCCACACAGGCGGTTGTTG 61.380 55.000 0.00 0.00 37.29 3.33
597 616 1.821759 CCACACAGGCGGTTGTTGA 60.822 57.895 0.00 0.00 0.00 3.18
720 742 1.336440 CAACCATCCTTTGACACGCAA 59.664 47.619 0.00 0.00 33.88 4.85
789 814 2.751166 ACCTCTTCACATCCTTGTCG 57.249 50.000 0.00 0.00 32.34 4.35
790 815 1.971357 ACCTCTTCACATCCTTGTCGT 59.029 47.619 0.00 0.00 32.34 4.34
797 822 5.995282 TCTTCACATCCTTGTCGTTGTAATT 59.005 36.000 0.00 0.00 32.34 1.40
826 851 5.688823 CATAAAGCTGATTGTTGACAACGA 58.311 37.500 10.70 10.70 38.86 3.85
835 860 3.942539 TGTTGACAACGACAATGAGTG 57.057 42.857 13.46 0.00 37.46 3.51
836 861 2.611751 TGTTGACAACGACAATGAGTGG 59.388 45.455 13.46 0.00 37.46 4.00
837 862 2.869801 GTTGACAACGACAATGAGTGGA 59.130 45.455 1.86 0.00 0.00 4.02
838 863 2.754472 TGACAACGACAATGAGTGGAG 58.246 47.619 0.00 0.00 0.00 3.86
839 864 2.102420 TGACAACGACAATGAGTGGAGT 59.898 45.455 0.00 0.00 0.00 3.85
840 865 3.319689 TGACAACGACAATGAGTGGAGTA 59.680 43.478 0.00 0.00 0.00 2.59
841 866 3.914312 ACAACGACAATGAGTGGAGTAG 58.086 45.455 0.00 0.00 0.00 2.57
842 867 2.656560 ACGACAATGAGTGGAGTAGC 57.343 50.000 0.00 0.00 0.00 3.58
843 868 1.893137 ACGACAATGAGTGGAGTAGCA 59.107 47.619 0.00 0.00 0.00 3.49
844 869 2.263077 CGACAATGAGTGGAGTAGCAC 58.737 52.381 0.00 0.00 0.00 4.40
845 870 2.622436 GACAATGAGTGGAGTAGCACC 58.378 52.381 0.00 0.00 0.00 5.01
846 871 1.066858 ACAATGAGTGGAGTAGCACCG 60.067 52.381 0.00 0.00 0.00 4.94
847 872 0.537188 AATGAGTGGAGTAGCACCGG 59.463 55.000 0.00 0.00 0.00 5.28
848 873 1.961180 ATGAGTGGAGTAGCACCGGC 61.961 60.000 0.00 0.00 41.61 6.13
889 917 3.310860 ATTCCGTGGACGCCCTCAC 62.311 63.158 0.00 0.00 38.18 3.51
946 974 5.044919 TCCAAGTCATATTCCTCACCACATT 60.045 40.000 0.00 0.00 0.00 2.71
987 1015 3.261137 TGGTAACACCACCGATCACATAA 59.739 43.478 0.00 0.00 44.79 1.90
1021 1053 1.565156 GAACGCGCCAGAACACATCA 61.565 55.000 5.73 0.00 0.00 3.07
1031 1063 3.494048 CCAGAACACATCATCCTAGCCTC 60.494 52.174 0.00 0.00 0.00 4.70
1056 1088 1.384191 GCAAGGAAGGGGTGTCCAT 59.616 57.895 0.00 0.00 37.65 3.41
1058 1090 0.967380 CAAGGAAGGGGTGTCCATGC 60.967 60.000 0.00 0.00 37.65 4.06
1073 1105 2.303890 TCCATGCATGTGTCTCAGAGTT 59.696 45.455 24.58 0.00 0.00 3.01
1074 1106 2.418976 CCATGCATGTGTCTCAGAGTTG 59.581 50.000 24.58 1.31 0.00 3.16
1088 1120 1.146358 GAGTTGTACATCTCCGCGGC 61.146 60.000 23.51 4.74 0.00 6.53
1089 1121 1.447140 GTTGTACATCTCCGCGGCA 60.447 57.895 23.51 10.15 0.00 5.69
1096 1128 2.650116 ATCTCCGCGGCACTCAGTT 61.650 57.895 23.51 4.21 0.00 3.16
1105 1137 1.813862 CGGCACTCAGTTTCCTTCCAA 60.814 52.381 0.00 0.00 0.00 3.53
1106 1138 1.882623 GGCACTCAGTTTCCTTCCAAG 59.117 52.381 0.00 0.00 0.00 3.61
1107 1139 1.268079 GCACTCAGTTTCCTTCCAAGC 59.732 52.381 0.00 0.00 0.00 4.01
1116 1148 2.225068 TCCTTCCAAGCGAATCGATC 57.775 50.000 6.91 0.00 0.00 3.69
1144 1176 2.223340 GCGACATATGCCTTTTCACCAG 60.223 50.000 1.58 0.00 0.00 4.00
1161 1199 1.238439 CAGCACTTGTCGACCCAAAT 58.762 50.000 14.12 0.00 0.00 2.32
1167 1205 2.224670 ACTTGTCGACCCAAATAGGCAA 60.225 45.455 14.12 0.00 35.39 4.52
1168 1206 2.570415 TGTCGACCCAAATAGGCAAA 57.430 45.000 14.12 0.00 35.39 3.68
1206 1253 1.176527 CAGCCCGTGTCCATGAATTT 58.823 50.000 0.00 0.00 0.00 1.82
1222 1269 9.812347 TCCATGAATTTGTTAGGATGCTATATT 57.188 29.630 0.00 0.00 0.00 1.28
1254 1304 0.827507 GTGCCATCCCAAACACCAGT 60.828 55.000 0.00 0.00 0.00 4.00
1318 1368 0.099436 GCATTCGTCTTGTGGCATCC 59.901 55.000 0.00 0.00 0.00 3.51
1328 1378 2.356278 TGGCATCCTGGGCACTTC 59.644 61.111 0.00 0.00 38.55 3.01
1338 1388 2.125512 GGCACTTCGATCCAGCGT 60.126 61.111 0.00 0.00 0.00 5.07
1341 1391 1.874019 CACTTCGATCCAGCGTCCG 60.874 63.158 0.00 0.00 0.00 4.79
1343 1393 3.699955 CTTCGATCCAGCGTCCGCA 62.700 63.158 14.70 0.00 44.88 5.69
1402 1458 3.372241 GGAGAAGTAGAGCCAGTACTCCT 60.372 52.174 0.00 0.00 39.36 3.69
1420 1476 1.202533 CCTCTACGCCATTGTTCCGAT 60.203 52.381 0.00 0.00 0.00 4.18
1464 1520 1.673033 CGGACCAGCGAATTGAAGTCT 60.673 52.381 0.00 0.00 0.00 3.24
1465 1521 2.427506 GGACCAGCGAATTGAAGTCTT 58.572 47.619 0.00 0.00 0.00 3.01
1476 1532 5.559035 CGAATTGAAGTCTTGGTTCAGACAC 60.559 44.000 3.78 0.00 45.08 3.67
1509 1565 3.695606 TCTGACCTGGACAGCCGC 61.696 66.667 19.32 0.00 36.79 6.53
1589 1645 2.172372 CGTGCTGCTGCTCTCCATC 61.172 63.158 17.00 0.00 40.48 3.51
1595 1651 1.203441 TGCTGCTCTCCATCAACCCT 61.203 55.000 0.00 0.00 0.00 4.34
1719 1775 8.349983 AGTCAACAGTTAATAGTTTTGCGAATT 58.650 29.630 0.00 0.00 0.00 2.17
1724 1780 8.736244 ACAGTTAATAGTTTTGCGAATTGGTAT 58.264 29.630 0.00 0.00 0.00 2.73
1854 1937 9.971922 AATGAAGAGTTGAAAATCAGGTTAAAG 57.028 29.630 0.00 0.00 0.00 1.85
1855 1938 7.425606 TGAAGAGTTGAAAATCAGGTTAAAGC 58.574 34.615 0.00 0.00 0.00 3.51
1929 2012 3.735746 GCTTGGTTTAACAGTGAACATGC 59.264 43.478 0.00 0.00 0.00 4.06
1930 2013 4.736168 GCTTGGTTTAACAGTGAACATGCA 60.736 41.667 0.00 0.00 0.00 3.96
1931 2014 5.528043 TTGGTTTAACAGTGAACATGCAT 57.472 34.783 0.00 0.00 0.00 3.96
1932 2015 4.869215 TGGTTTAACAGTGAACATGCATG 58.131 39.130 25.09 25.09 0.00 4.06
1933 2016 4.236935 GGTTTAACAGTGAACATGCATGG 58.763 43.478 29.41 13.53 0.00 3.66
1934 2017 4.261994 GGTTTAACAGTGAACATGCATGGT 60.262 41.667 29.41 25.14 0.00 3.55
1935 2018 5.048364 GGTTTAACAGTGAACATGCATGGTA 60.048 40.000 29.41 13.01 0.00 3.25
1936 2019 5.878332 TTAACAGTGAACATGCATGGTAG 57.122 39.130 29.41 16.25 0.00 3.18
1937 2020 2.086869 ACAGTGAACATGCATGGTAGC 58.913 47.619 29.41 18.83 0.00 3.58
2084 4546 5.211973 ACCTAGAAGGAGATGCAAGACATA 58.788 41.667 0.00 0.00 36.90 2.29
2085 4547 5.843421 ACCTAGAAGGAGATGCAAGACATAT 59.157 40.000 0.00 0.00 36.90 1.78
2176 4684 4.511443 GCGCGCACTGCTAGCTTG 62.511 66.667 29.10 13.86 43.27 4.01
2204 4712 7.039313 TGCTTTACTTTCTTTTTCCTTCTCC 57.961 36.000 0.00 0.00 0.00 3.71
2228 4736 5.337578 TTTGCTTCCACTTTTGCTTTACT 57.662 34.783 0.00 0.00 0.00 2.24
2229 4737 6.458232 TTTGCTTCCACTTTTGCTTTACTA 57.542 33.333 0.00 0.00 0.00 1.82
2230 4738 5.689383 TGCTTCCACTTTTGCTTTACTAG 57.311 39.130 0.00 0.00 0.00 2.57
2231 4739 5.130350 TGCTTCCACTTTTGCTTTACTAGT 58.870 37.500 0.00 0.00 0.00 2.57
2232 4740 6.292923 TGCTTCCACTTTTGCTTTACTAGTA 58.707 36.000 0.00 0.00 0.00 1.82
2233 4741 6.768861 TGCTTCCACTTTTGCTTTACTAGTAA 59.231 34.615 11.38 11.38 0.00 2.24
2234 4742 7.041372 TGCTTCCACTTTTGCTTTACTAGTAAG 60.041 37.037 14.73 10.54 29.82 2.34
2235 4743 7.172703 GCTTCCACTTTTGCTTTACTAGTAAGA 59.827 37.037 14.73 6.43 29.82 2.10
2236 4744 7.958053 TCCACTTTTGCTTTACTAGTAAGAC 57.042 36.000 14.73 11.57 29.82 3.01
2237 4745 7.502696 TCCACTTTTGCTTTACTAGTAAGACA 58.497 34.615 14.73 13.74 29.82 3.41
2238 4746 7.988599 TCCACTTTTGCTTTACTAGTAAGACAA 59.011 33.333 20.17 20.17 29.82 3.18
2239 4747 8.068380 CCACTTTTGCTTTACTAGTAAGACAAC 58.932 37.037 22.27 11.26 29.82 3.32
2240 4748 8.068380 CACTTTTGCTTTACTAGTAAGACAACC 58.932 37.037 22.27 9.20 29.82 3.77
2241 4749 7.991460 ACTTTTGCTTTACTAGTAAGACAACCT 59.009 33.333 22.27 11.32 29.82 3.50
2242 4750 8.741603 TTTTGCTTTACTAGTAAGACAACCTT 57.258 30.769 22.27 0.00 38.87 3.50
2243 4751 8.741603 TTTGCTTTACTAGTAAGACAACCTTT 57.258 30.769 22.27 0.00 36.34 3.11
2244 4752 9.835389 TTTGCTTTACTAGTAAGACAACCTTTA 57.165 29.630 22.27 11.50 36.34 1.85
2245 4753 9.485206 TTGCTTTACTAGTAAGACAACCTTTAG 57.515 33.333 20.17 11.50 36.34 1.85
2246 4754 7.601508 TGCTTTACTAGTAAGACAACCTTTAGC 59.398 37.037 14.73 15.68 36.34 3.09
2247 4755 7.601508 GCTTTACTAGTAAGACAACCTTTAGCA 59.398 37.037 14.73 0.00 36.34 3.49
2248 4756 9.141400 CTTTACTAGTAAGACAACCTTTAGCAG 57.859 37.037 14.73 1.87 36.34 4.24
2249 4757 6.912951 ACTAGTAAGACAACCTTTAGCAGA 57.087 37.500 0.00 0.00 36.34 4.26
2250 4758 6.926313 ACTAGTAAGACAACCTTTAGCAGAG 58.074 40.000 0.00 0.00 36.34 3.35
2251 4759 5.153950 AGTAAGACAACCTTTAGCAGAGG 57.846 43.478 0.00 0.00 40.24 3.69
2252 4760 3.425162 AAGACAACCTTTAGCAGAGGG 57.575 47.619 5.23 0.00 38.65 4.30
2253 4761 1.630878 AGACAACCTTTAGCAGAGGGG 59.369 52.381 5.23 0.00 38.65 4.79
2254 4762 1.351350 GACAACCTTTAGCAGAGGGGT 59.649 52.381 5.23 3.11 38.65 4.95
2255 4763 2.570302 GACAACCTTTAGCAGAGGGGTA 59.430 50.000 5.23 0.00 38.65 3.69
2256 4764 2.305052 ACAACCTTTAGCAGAGGGGTAC 59.695 50.000 5.23 0.00 38.65 3.34
2257 4765 1.192428 ACCTTTAGCAGAGGGGTACG 58.808 55.000 5.23 0.00 38.65 3.67
2258 4766 0.464452 CCTTTAGCAGAGGGGTACGG 59.536 60.000 0.00 0.00 0.00 4.02
2259 4767 1.192428 CTTTAGCAGAGGGGTACGGT 58.808 55.000 0.00 0.00 0.00 4.83
2260 4768 0.899720 TTTAGCAGAGGGGTACGGTG 59.100 55.000 0.00 0.00 0.00 4.94
2261 4769 1.610554 TTAGCAGAGGGGTACGGTGC 61.611 60.000 0.00 0.00 34.13 5.01
2262 4770 2.791613 TAGCAGAGGGGTACGGTGCA 62.792 60.000 0.00 0.00 35.76 4.57
2263 4771 3.065306 CAGAGGGGTACGGTGCAA 58.935 61.111 0.00 0.00 0.00 4.08
2264 4772 1.375523 CAGAGGGGTACGGTGCAAC 60.376 63.158 0.00 0.00 0.00 4.17
2278 4786 3.951979 GTGCAACCTCCATATTTCGAG 57.048 47.619 0.00 0.00 0.00 4.04
2283 4791 2.918712 CCTCCATATTTCGAGGCTGT 57.081 50.000 0.00 0.00 39.36 4.40
2284 4792 2.487934 CCTCCATATTTCGAGGCTGTG 58.512 52.381 0.00 0.00 39.36 3.66
2285 4793 2.487934 CTCCATATTTCGAGGCTGTGG 58.512 52.381 0.00 0.00 0.00 4.17
2286 4794 1.140852 TCCATATTTCGAGGCTGTGGG 59.859 52.381 0.00 0.00 0.00 4.61
2287 4795 1.140852 CCATATTTCGAGGCTGTGGGA 59.859 52.381 0.00 0.00 0.00 4.37
2288 4796 2.421388 CCATATTTCGAGGCTGTGGGAA 60.421 50.000 0.00 0.00 0.00 3.97
2289 4797 2.691409 TATTTCGAGGCTGTGGGAAG 57.309 50.000 0.00 0.00 0.00 3.46
2290 4798 0.035056 ATTTCGAGGCTGTGGGAAGG 60.035 55.000 0.00 0.00 0.00 3.46
2291 4799 2.748058 TTTCGAGGCTGTGGGAAGGC 62.748 60.000 0.00 0.00 42.87 4.35
2295 4803 2.116125 GGCTGTGGGAAGGCTGTT 59.884 61.111 0.00 0.00 39.56 3.16
2296 4804 1.531602 GGCTGTGGGAAGGCTGTTT 60.532 57.895 0.00 0.00 39.56 2.83
2297 4805 1.115326 GGCTGTGGGAAGGCTGTTTT 61.115 55.000 0.00 0.00 39.56 2.43
2298 4806 0.032540 GCTGTGGGAAGGCTGTTTTG 59.967 55.000 0.00 0.00 0.00 2.44
2299 4807 0.675633 CTGTGGGAAGGCTGTTTTGG 59.324 55.000 0.00 0.00 0.00 3.28
2300 4808 0.260230 TGTGGGAAGGCTGTTTTGGA 59.740 50.000 0.00 0.00 0.00 3.53
2301 4809 1.342474 TGTGGGAAGGCTGTTTTGGAA 60.342 47.619 0.00 0.00 0.00 3.53
2302 4810 1.970640 GTGGGAAGGCTGTTTTGGAAT 59.029 47.619 0.00 0.00 0.00 3.01
2303 4811 1.969923 TGGGAAGGCTGTTTTGGAATG 59.030 47.619 0.00 0.00 0.00 2.67
2334 4842 4.189231 ACCCAATCACATTAACGCTACTC 58.811 43.478 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 75 1.873698 TAAAAAGCAAGTCGTCGCCT 58.126 45.000 0.00 0.00 0.00 5.52
80 83 2.806244 ACTCGACGCATAAAAAGCAAGT 59.194 40.909 0.00 0.00 0.00 3.16
101 105 2.818751 AGTTTGTTGTGGGTTCAGGA 57.181 45.000 0.00 0.00 0.00 3.86
194 202 8.908786 TCTTTTCTGTCAGAGTGAACAATTAT 57.091 30.769 2.12 0.00 0.00 1.28
195 203 8.204160 TCTCTTTTCTGTCAGAGTGAACAATTA 58.796 33.333 2.12 0.00 38.20 1.40
197 205 6.586344 TCTCTTTTCTGTCAGAGTGAACAAT 58.414 36.000 2.12 0.00 38.20 2.71
208 216 4.406648 TGAGTGCTTCTCTTTTCTGTCA 57.593 40.909 9.94 0.00 43.13 3.58
220 229 5.050490 TGAGTTAGACAGTTTGAGTGCTTC 58.950 41.667 0.00 0.00 0.00 3.86
233 242 8.410673 AGTCTATCTTTGAGTTGAGTTAGACA 57.589 34.615 17.21 0.00 42.35 3.41
243 252 7.671302 TGCTTCTGTTAGTCTATCTTTGAGTT 58.329 34.615 0.00 0.00 0.00 3.01
316 333 7.869429 CCTCTTGATCTTGCTTGTTATTGTTTT 59.131 33.333 0.00 0.00 0.00 2.43
380 397 1.036707 TTACTTTGCTGGTTGTGGCC 58.963 50.000 0.00 0.00 0.00 5.36
381 398 3.254657 TGTATTACTTTGCTGGTTGTGGC 59.745 43.478 0.00 0.00 0.00 5.01
382 399 5.446143 TTGTATTACTTTGCTGGTTGTGG 57.554 39.130 0.00 0.00 0.00 4.17
383 400 9.638239 AATATTTGTATTACTTTGCTGGTTGTG 57.362 29.630 0.00 0.00 0.00 3.33
441 459 7.461749 TCCTCTGACCTTCTTGAATATTTGTT 58.538 34.615 0.00 0.00 0.00 2.83
530 549 4.018415 AGAGCTTCCTTTATAACTTGGCCA 60.018 41.667 0.00 0.00 0.00 5.36
594 613 2.337849 TCATGGATCCCGGATGATCAA 58.662 47.619 18.75 10.73 42.41 2.57
595 614 2.028561 TCATGGATCCCGGATGATCA 57.971 50.000 18.75 0.00 42.41 2.92
596 615 3.054875 TCATTCATGGATCCCGGATGATC 60.055 47.826 15.30 7.69 40.37 2.92
597 616 2.914941 TCATTCATGGATCCCGGATGAT 59.085 45.455 15.30 0.00 0.00 2.45
720 742 4.562143 GCTCTTGGAAAATTGCCTGAACAT 60.562 41.667 0.00 0.00 0.00 2.71
826 851 1.066858 CGGTGCTACTCCACTCATTGT 60.067 52.381 0.00 0.00 36.03 2.71
831 856 2.184579 GCCGGTGCTACTCCACTC 59.815 66.667 1.90 0.00 36.03 3.51
832 857 3.760035 CGCCGGTGCTACTCCACT 61.760 66.667 0.00 0.00 36.03 4.00
833 858 3.077519 ATCGCCGGTGCTACTCCAC 62.078 63.158 11.05 0.00 34.43 4.02
834 859 2.758327 ATCGCCGGTGCTACTCCA 60.758 61.111 11.05 0.00 34.43 3.86
835 860 2.279517 CATCGCCGGTGCTACTCC 60.280 66.667 11.05 0.00 34.43 3.85
836 861 1.299468 CTCATCGCCGGTGCTACTC 60.299 63.158 11.05 0.00 34.43 2.59
837 862 2.052690 ACTCATCGCCGGTGCTACT 61.053 57.895 11.05 0.00 34.43 2.57
838 863 1.878522 CACTCATCGCCGGTGCTAC 60.879 63.158 11.05 0.00 34.43 3.58
839 864 2.494445 CACTCATCGCCGGTGCTA 59.506 61.111 11.05 0.00 34.43 3.49
840 865 4.457496 CCACTCATCGCCGGTGCT 62.457 66.667 11.05 0.00 34.43 4.40
841 866 4.451150 TCCACTCATCGCCGGTGC 62.451 66.667 11.05 0.00 0.00 5.01
842 867 2.202797 CTCCACTCATCGCCGGTG 60.203 66.667 9.28 9.28 0.00 4.94
843 868 3.461773 CCTCCACTCATCGCCGGT 61.462 66.667 1.90 0.00 0.00 5.28
844 869 3.144120 CTCCTCCACTCATCGCCGG 62.144 68.421 0.00 0.00 0.00 6.13
845 870 2.415010 CTCCTCCACTCATCGCCG 59.585 66.667 0.00 0.00 0.00 6.46
846 871 2.107953 GCTCCTCCACTCATCGCC 59.892 66.667 0.00 0.00 0.00 5.54
847 872 1.520342 GTGCTCCTCCACTCATCGC 60.520 63.158 0.00 0.00 33.02 4.58
848 873 1.142748 GGTGCTCCTCCACTCATCG 59.857 63.158 0.00 0.00 36.03 3.84
849 874 1.142748 CGGTGCTCCTCCACTCATC 59.857 63.158 2.85 0.00 36.03 2.92
850 875 2.362369 CCGGTGCTCCTCCACTCAT 61.362 63.158 2.85 0.00 36.03 2.90
851 876 2.997315 CCGGTGCTCCTCCACTCA 60.997 66.667 2.85 0.00 36.03 3.41
876 901 2.034879 CATGTGTGAGGGCGTCCAC 61.035 63.158 9.71 1.19 34.83 4.02
878 906 1.298859 GAACATGTGTGAGGGCGTCC 61.299 60.000 0.00 0.00 0.00 4.79
881 909 1.354337 CGAGAACATGTGTGAGGGCG 61.354 60.000 0.00 0.00 0.00 6.13
889 917 2.544685 GAGGGTCATCGAGAACATGTG 58.455 52.381 0.00 0.00 34.85 3.21
946 974 4.337145 ACCAACAACAACAAGGTACTGAA 58.663 39.130 0.00 0.00 40.86 3.02
987 1015 1.067635 GCGTTCATGGATGGCAAGTTT 60.068 47.619 0.00 0.00 0.00 2.66
1021 1053 3.752665 CTTGCATGAATGAGGCTAGGAT 58.247 45.455 0.00 0.00 31.60 3.24
1031 1063 1.479323 CACCCCTTCCTTGCATGAATG 59.521 52.381 0.00 0.00 0.00 2.67
1056 1088 2.916702 ACAACTCTGAGACACATGCA 57.083 45.000 12.44 0.00 0.00 3.96
1058 1090 5.718146 AGATGTACAACTCTGAGACACATG 58.282 41.667 12.44 4.92 0.00 3.21
1073 1105 2.183300 GTGCCGCGGAGATGTACA 59.817 61.111 33.48 12.98 0.00 2.90
1074 1106 1.589196 GAGTGCCGCGGAGATGTAC 60.589 63.158 33.48 16.31 0.00 2.90
1088 1120 1.532868 CGCTTGGAAGGAAACTGAGTG 59.467 52.381 0.00 0.00 42.68 3.51
1089 1121 1.416401 TCGCTTGGAAGGAAACTGAGT 59.584 47.619 0.00 0.00 42.68 3.41
1096 1128 2.550978 GATCGATTCGCTTGGAAGGAA 58.449 47.619 0.00 0.00 38.24 3.36
1144 1176 1.737793 CCTATTTGGGTCGACAAGTGC 59.262 52.381 18.91 0.00 0.00 4.40
1161 1199 0.394938 TGAACTCACCGCTTTGCCTA 59.605 50.000 0.00 0.00 0.00 3.93
1167 1205 0.389948 GTCCGATGAACTCACCGCTT 60.390 55.000 0.00 0.00 29.75 4.68
1168 1206 1.215647 GTCCGATGAACTCACCGCT 59.784 57.895 0.00 0.00 29.75 5.52
1186 1224 0.680921 AATTCATGGACACGGGCTGG 60.681 55.000 0.00 0.00 0.00 4.85
1193 1240 5.126061 AGCATCCTAACAAATTCATGGACAC 59.874 40.000 0.00 0.00 0.00 3.67
1309 1359 2.769652 GAAGTGCCCAGGATGCCACA 62.770 60.000 0.00 0.00 38.66 4.17
1318 1368 1.817099 GCTGGATCGAAGTGCCCAG 60.817 63.158 13.38 13.38 46.67 4.45
1328 1378 4.498520 ACTGCGGACGCTGGATCG 62.499 66.667 23.64 6.78 43.03 3.69
1338 1388 2.149803 CTTACGACCCACACTGCGGA 62.150 60.000 0.00 0.00 0.00 5.54
1341 1391 0.673644 ATGCTTACGACCCACACTGC 60.674 55.000 0.00 0.00 0.00 4.40
1343 1393 0.249398 GGATGCTTACGACCCACACT 59.751 55.000 0.00 0.00 0.00 3.55
1379 1435 2.953648 GAGTACTGGCTCTACTTCTCCC 59.046 54.545 0.00 0.00 32.99 4.30
1402 1458 1.934589 CATCGGAACAATGGCGTAGA 58.065 50.000 0.00 0.00 0.00 2.59
1420 1476 2.134287 GGGAGATCTACCGCCTGCA 61.134 63.158 8.66 0.00 0.00 4.41
1464 1520 1.885388 CGTGGCGTGTCTGAACCAA 60.885 57.895 0.00 0.00 33.03 3.67
1465 1521 2.279851 CGTGGCGTGTCTGAACCA 60.280 61.111 0.00 0.00 0.00 3.67
1476 1532 2.279517 GACTATGGCTCCGTGGCG 60.280 66.667 0.00 0.00 45.14 5.69
1509 1565 2.429610 CCTTTCCATCAAATGCCTCCTG 59.570 50.000 0.00 0.00 0.00 3.86
1589 1645 2.432628 GTCTCGGCGACAGGGTTG 60.433 66.667 4.99 0.00 42.37 3.77
1595 1651 2.483745 GTCATCGTCTCGGCGACA 59.516 61.111 4.99 0.00 43.99 4.35
1662 1718 2.125350 GAGGGCAGAACAGGAGCG 60.125 66.667 0.00 0.00 0.00 5.03
1670 1726 2.820178 TGTCAGATAGTGAGGGCAGAA 58.180 47.619 0.00 0.00 35.13 3.02
1775 1832 1.987770 GTGTCGCATGCCAAAATTCTG 59.012 47.619 13.15 0.00 0.00 3.02
1854 1937 5.560966 TTAATTGGACTTGGATTCTTCGC 57.439 39.130 0.00 0.00 0.00 4.70
1929 2012 8.149647 AGTACTACACTACTACTAGCTACCATG 58.850 40.741 0.00 0.00 34.98 3.66
1930 2013 8.261349 AGTACTACACTACTACTAGCTACCAT 57.739 38.462 0.00 0.00 34.98 3.55
1931 2014 7.667575 AGTACTACACTACTACTAGCTACCA 57.332 40.000 0.00 0.00 34.98 3.25
1932 2015 9.471084 GTTAGTACTACACTACTACTAGCTACC 57.529 40.741 0.91 0.00 39.52 3.18
1933 2016 9.471084 GGTTAGTACTACACTACTACTAGCTAC 57.529 40.741 0.91 0.00 39.52 3.58
1934 2017 8.353684 CGGTTAGTACTACACTACTACTAGCTA 58.646 40.741 0.91 0.00 39.52 3.32
1935 2018 7.206687 CGGTTAGTACTACACTACTACTAGCT 58.793 42.308 0.91 0.00 39.52 3.32
1936 2019 6.422400 CCGGTTAGTACTACACTACTACTAGC 59.578 46.154 0.91 0.00 39.52 3.42
1937 2020 7.717568 TCCGGTTAGTACTACACTACTACTAG 58.282 42.308 0.91 0.00 39.52 2.57
2084 4546 0.545171 ACTGCATGCTCCACTGCTAT 59.455 50.000 20.33 0.00 39.16 2.97
2085 4547 0.107993 GACTGCATGCTCCACTGCTA 60.108 55.000 20.33 0.00 39.16 3.49
2176 4684 7.492669 AGAAGGAAAAAGAAAGTAAAGCAAAGC 59.507 33.333 0.00 0.00 0.00 3.51
2204 4712 5.812127 AGTAAAGCAAAAGTGGAAGCAAAAG 59.188 36.000 0.00 0.00 0.00 2.27
2228 4736 5.187186 CCCTCTGCTAAAGGTTGTCTTACTA 59.813 44.000 0.00 0.00 34.78 1.82
2229 4737 4.020128 CCCTCTGCTAAAGGTTGTCTTACT 60.020 45.833 0.00 0.00 34.78 2.24
2230 4738 4.254492 CCCTCTGCTAAAGGTTGTCTTAC 58.746 47.826 0.00 0.00 34.78 2.34
2231 4739 3.263425 CCCCTCTGCTAAAGGTTGTCTTA 59.737 47.826 0.00 0.00 34.78 2.10
2232 4740 2.040412 CCCCTCTGCTAAAGGTTGTCTT 59.960 50.000 0.00 0.00 37.28 3.01
2233 4741 1.630878 CCCCTCTGCTAAAGGTTGTCT 59.369 52.381 0.00 0.00 31.51 3.41
2234 4742 1.351350 ACCCCTCTGCTAAAGGTTGTC 59.649 52.381 0.00 0.00 31.51 3.18
2235 4743 1.446016 ACCCCTCTGCTAAAGGTTGT 58.554 50.000 0.00 0.00 31.51 3.32
2236 4744 2.677037 CGTACCCCTCTGCTAAAGGTTG 60.677 54.545 0.00 0.00 31.51 3.77
2237 4745 1.553704 CGTACCCCTCTGCTAAAGGTT 59.446 52.381 0.00 0.00 31.51 3.50
2238 4746 1.192428 CGTACCCCTCTGCTAAAGGT 58.808 55.000 0.00 0.00 31.51 3.50
2239 4747 0.464452 CCGTACCCCTCTGCTAAAGG 59.536 60.000 0.00 0.00 0.00 3.11
2240 4748 1.134788 CACCGTACCCCTCTGCTAAAG 60.135 57.143 0.00 0.00 0.00 1.85
2241 4749 0.899720 CACCGTACCCCTCTGCTAAA 59.100 55.000 0.00 0.00 0.00 1.85
2242 4750 1.610554 GCACCGTACCCCTCTGCTAA 61.611 60.000 0.00 0.00 0.00 3.09
2243 4751 2.056223 GCACCGTACCCCTCTGCTA 61.056 63.158 0.00 0.00 0.00 3.49
2244 4752 3.391382 GCACCGTACCCCTCTGCT 61.391 66.667 0.00 0.00 0.00 4.24
2245 4753 3.248446 TTGCACCGTACCCCTCTGC 62.248 63.158 0.00 0.00 0.00 4.26
2246 4754 1.375523 GTTGCACCGTACCCCTCTG 60.376 63.158 0.00 0.00 0.00 3.35
2247 4755 2.590114 GGTTGCACCGTACCCCTCT 61.590 63.158 0.00 0.00 0.00 3.69
2248 4756 2.046604 GGTTGCACCGTACCCCTC 60.047 66.667 0.00 0.00 0.00 4.30
2249 4757 2.528378 AGGTTGCACCGTACCCCT 60.528 61.111 1.55 0.00 44.90 4.79
2250 4758 2.046604 GAGGTTGCACCGTACCCC 60.047 66.667 1.55 0.00 44.90 4.95
2251 4759 2.046604 GGAGGTTGCACCGTACCC 60.047 66.667 1.55 0.00 44.90 3.69
2252 4760 0.538118 TATGGAGGTTGCACCGTACC 59.462 55.000 0.00 0.00 44.90 3.34
2253 4761 2.614829 ATATGGAGGTTGCACCGTAC 57.385 50.000 0.00 0.00 44.90 3.67
2254 4762 3.537580 GAAATATGGAGGTTGCACCGTA 58.462 45.455 0.00 0.00 44.90 4.02
2255 4763 2.365582 GAAATATGGAGGTTGCACCGT 58.634 47.619 0.00 0.00 44.90 4.83
2256 4764 1.330521 CGAAATATGGAGGTTGCACCG 59.669 52.381 0.00 0.00 44.90 4.94
2257 4765 2.614057 CTCGAAATATGGAGGTTGCACC 59.386 50.000 0.00 0.00 38.99 5.01
2258 4766 2.614057 CCTCGAAATATGGAGGTTGCAC 59.386 50.000 8.78 0.00 44.24 4.57
2259 4767 2.917933 CCTCGAAATATGGAGGTTGCA 58.082 47.619 8.78 0.00 44.24 4.08
2265 4773 2.487934 CCACAGCCTCGAAATATGGAG 58.512 52.381 0.00 0.00 0.00 3.86
2266 4774 1.140852 CCCACAGCCTCGAAATATGGA 59.859 52.381 4.43 0.00 0.00 3.41
2267 4775 1.140852 TCCCACAGCCTCGAAATATGG 59.859 52.381 0.00 0.00 0.00 2.74
2268 4776 2.620251 TCCCACAGCCTCGAAATATG 57.380 50.000 0.00 0.00 0.00 1.78
2269 4777 2.158755 CCTTCCCACAGCCTCGAAATAT 60.159 50.000 0.00 0.00 0.00 1.28
2270 4778 1.209504 CCTTCCCACAGCCTCGAAATA 59.790 52.381 0.00 0.00 0.00 1.40
2271 4779 0.035056 CCTTCCCACAGCCTCGAAAT 60.035 55.000 0.00 0.00 0.00 2.17
2272 4780 1.374947 CCTTCCCACAGCCTCGAAA 59.625 57.895 0.00 0.00 0.00 3.46
2273 4781 3.068881 CCTTCCCACAGCCTCGAA 58.931 61.111 0.00 0.00 0.00 3.71
2274 4782 3.706373 GCCTTCCCACAGCCTCGA 61.706 66.667 0.00 0.00 0.00 4.04
2275 4783 3.710722 AGCCTTCCCACAGCCTCG 61.711 66.667 0.00 0.00 0.00 4.63
2276 4784 2.045536 CAGCCTTCCCACAGCCTC 60.046 66.667 0.00 0.00 0.00 4.70
2277 4785 2.011617 AAACAGCCTTCCCACAGCCT 62.012 55.000 0.00 0.00 0.00 4.58
2278 4786 1.115326 AAAACAGCCTTCCCACAGCC 61.115 55.000 0.00 0.00 0.00 4.85
2279 4787 0.032540 CAAAACAGCCTTCCCACAGC 59.967 55.000 0.00 0.00 0.00 4.40
2280 4788 0.675633 CCAAAACAGCCTTCCCACAG 59.324 55.000 0.00 0.00 0.00 3.66
2281 4789 0.260230 TCCAAAACAGCCTTCCCACA 59.740 50.000 0.00 0.00 0.00 4.17
2282 4790 1.408969 TTCCAAAACAGCCTTCCCAC 58.591 50.000 0.00 0.00 0.00 4.61
2283 4791 1.969923 CATTCCAAAACAGCCTTCCCA 59.030 47.619 0.00 0.00 0.00 4.37
2284 4792 1.338105 GCATTCCAAAACAGCCTTCCC 60.338 52.381 0.00 0.00 0.00 3.97
2285 4793 1.344114 TGCATTCCAAAACAGCCTTCC 59.656 47.619 0.00 0.00 0.00 3.46
2286 4794 2.818130 TGCATTCCAAAACAGCCTTC 57.182 45.000 0.00 0.00 0.00 3.46
2287 4795 3.325716 AGAATGCATTCCAAAACAGCCTT 59.674 39.130 31.05 9.35 37.51 4.35
2288 4796 2.901839 AGAATGCATTCCAAAACAGCCT 59.098 40.909 31.05 9.84 37.51 4.58
2289 4797 2.997986 CAGAATGCATTCCAAAACAGCC 59.002 45.455 31.05 7.48 37.51 4.85
2290 4798 3.916761 TCAGAATGCATTCCAAAACAGC 58.083 40.909 31.05 8.19 37.51 4.40
2291 4799 4.687483 GGTTCAGAATGCATTCCAAAACAG 59.313 41.667 31.05 14.89 37.51 3.16
2292 4800 4.502950 GGGTTCAGAATGCATTCCAAAACA 60.503 41.667 31.05 10.69 37.51 2.83
2293 4801 3.996363 GGGTTCAGAATGCATTCCAAAAC 59.004 43.478 31.05 27.99 37.51 2.43
2294 4802 3.645212 TGGGTTCAGAATGCATTCCAAAA 59.355 39.130 31.05 20.87 37.51 2.44
2295 4803 3.237746 TGGGTTCAGAATGCATTCCAAA 58.762 40.909 31.05 23.04 37.51 3.28
2296 4804 2.886913 TGGGTTCAGAATGCATTCCAA 58.113 42.857 31.05 22.32 37.51 3.53
2297 4805 2.601240 TGGGTTCAGAATGCATTCCA 57.399 45.000 31.05 20.65 37.51 3.53
2298 4806 3.448301 TGATTGGGTTCAGAATGCATTCC 59.552 43.478 31.05 18.58 37.51 3.01
2299 4807 4.082081 TGTGATTGGGTTCAGAATGCATTC 60.082 41.667 28.44 28.44 34.76 2.67
2300 4808 3.833650 TGTGATTGGGTTCAGAATGCATT 59.166 39.130 12.83 12.83 34.76 3.56
2301 4809 3.433343 TGTGATTGGGTTCAGAATGCAT 58.567 40.909 0.00 0.00 34.76 3.96
2302 4810 2.874014 TGTGATTGGGTTCAGAATGCA 58.126 42.857 0.00 0.00 34.76 3.96
2303 4811 4.460948 AATGTGATTGGGTTCAGAATGC 57.539 40.909 0.00 0.00 34.76 3.56
2334 4842 3.149981 GGGAGGAAGGAGTTGAAAGTTG 58.850 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.