Multiple sequence alignment - TraesCS4D01G130600

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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 TraesCS4D01G130600 chr4D 100.000 7239 0 0 1 7239 116812521 116819759 0.000000e+00 13369.0
1 TraesCS4D01G130600 chr4D 100.000 290 0 0 7579 7868 116820099 116820388 3.230000e-148 536.0
2 TraesCS4D01G130600 chr4A 95.367 3799 117 14 2804 6572 459635230 459631461 0.000000e+00 5986.0
3 TraesCS4D01G130600 chr4A 92.898 2253 67 31 461 2671 459637803 459635602 0.000000e+00 3188.0
4 TraesCS4D01G130600 chr4A 97.615 671 16 0 6569 7239 459631433 459630763 0.000000e+00 1151.0
5 TraesCS4D01G130600 chr4A 90.323 372 17 6 1 372 459638241 459637889 3.320000e-128 470.0
6 TraesCS4D01G130600 chr4A 96.000 175 5 1 2640 2812 459635549 459635375 4.650000e-72 283.0
7 TraesCS4D01G130600 chr4A 84.536 291 17 11 7579 7866 459630660 459630395 6.050000e-66 263.0
8 TraesCS4D01G130600 chr4A 97.059 68 2 0 410 477 459637887 459637820 1.790000e-21 115.0
9 TraesCS4D01G130600 chr4B 96.092 3352 97 12 2822 6163 178846647 178849974 0.000000e+00 5433.0
10 TraesCS4D01G130600 chr4B 93.617 2162 63 26 714 2812 178844337 178846486 0.000000e+00 3158.0
11 TraesCS4D01G130600 chr4B 91.398 930 31 22 6291 7173 178850293 178851220 0.000000e+00 1229.0
12 TraesCS4D01G130600 chr4B 90.909 517 25 12 1 512 178843299 178843798 0.000000e+00 675.0
13 TraesCS4D01G130600 chr4B 94.000 150 4 1 563 712 178843869 178844013 1.030000e-53 222.0
14 TraesCS4D01G130600 chr4B 97.638 127 3 0 7742 7868 178851263 178851389 1.330000e-52 219.0
15 TraesCS4D01G130600 chr4B 94.444 36 0 2 518 551 178843837 178843872 4.000000e-03 54.7
16 TraesCS4D01G130600 chr5D 78.087 2332 420 59 3555 5830 249791397 249789101 0.000000e+00 1391.0
17 TraesCS4D01G130600 chr5D 87.865 1129 118 11 1011 2132 249793923 249792807 0.000000e+00 1308.0
18 TraesCS4D01G130600 chr5D 82.812 512 67 16 6717 7221 249527173 249526676 9.370000e-119 438.0
19 TraesCS4D01G130600 chr5D 97.059 68 2 0 7799 7866 249526476 249526409 1.790000e-21 115.0
20 TraesCS4D01G130600 chr5B 88.781 1132 114 10 1011 2132 282393321 282392193 0.000000e+00 1375.0
21 TraesCS4D01G130600 chr5B 77.811 2357 421 68 3532 5827 282390515 282388200 0.000000e+00 1362.0
22 TraesCS4D01G130600 chr5B 83.430 519 69 15 6708 7221 282268468 282267962 4.300000e-127 466.0
23 TraesCS4D01G130600 chr5B 95.588 68 3 0 7799 7866 282267755 282267688 8.350000e-20 110.0
24 TraesCS4D01G130600 chr5A 77.669 2360 438 60 3532 5830 332300052 332297721 0.000000e+00 1356.0
25 TraesCS4D01G130600 chr5A 88.043 1129 119 11 1011 2132 332302925 332301806 0.000000e+00 1323.0
26 TraesCS4D01G130600 chr5A 82.129 526 71 20 6708 7221 332219136 332218622 5.640000e-116 429.0
27 TraesCS4D01G130600 chr5A 95.588 68 3 0 7799 7866 332218421 332218354 8.350000e-20 110.0
28 TraesCS4D01G130600 chr7B 83.022 1072 156 13 1027 2091 665725139 665726191 0.000000e+00 948.0
29 TraesCS4D01G130600 chr6B 82.636 1100 146 19 1027 2091 18590894 18591983 0.000000e+00 931.0
30 TraesCS4D01G130600 chr7A 86.607 112 15 0 1171 1282 115311199 115311310 2.980000e-24 124.0


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 TraesCS4D01G130600 chr4D 116812521 116820388 7867 False 6952.500000 13369 100.000000 1 7868 2 chr4D.!!$F1 7867
1 TraesCS4D01G130600 chr4A 459630395 459638241 7846 True 1636.571429 5986 93.399714 1 7866 7 chr4A.!!$R1 7865
2 TraesCS4D01G130600 chr4B 178843299 178851389 8090 False 1570.100000 5433 94.014000 1 7868 7 chr4B.!!$F1 7867
3 TraesCS4D01G130600 chr5D 249789101 249793923 4822 True 1349.500000 1391 82.976000 1011 5830 2 chr5D.!!$R2 4819
4 TraesCS4D01G130600 chr5D 249526409 249527173 764 True 276.500000 438 89.935500 6717 7866 2 chr5D.!!$R1 1149
5 TraesCS4D01G130600 chr5B 282388200 282393321 5121 True 1368.500000 1375 83.296000 1011 5827 2 chr5B.!!$R2 4816
6 TraesCS4D01G130600 chr5B 282267688 282268468 780 True 288.000000 466 89.509000 6708 7866 2 chr5B.!!$R1 1158
7 TraesCS4D01G130600 chr5A 332297721 332302925 5204 True 1339.500000 1356 82.856000 1011 5830 2 chr5A.!!$R2 4819
8 TraesCS4D01G130600 chr5A 332218354 332219136 782 True 269.500000 429 88.858500 6708 7866 2 chr5A.!!$R1 1158
9 TraesCS4D01G130600 chr7B 665725139 665726191 1052 False 948.000000 948 83.022000 1027 2091 1 chr7B.!!$F1 1064
10 TraesCS4D01G130600 chr6B 18590894 18591983 1089 False 931.000000 931 82.636000 1027 2091 1 chr6B.!!$F1 1064

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
712 784 0.109551 AGCACTCACTGTCACGATCG 60.110 55.000 14.88 14.88 0.00 3.69 F
995 1420 1.012049 TCCCCTAATCCCAATCCCAGT 59.988 52.381 0.00 0.00 0.00 4.00 F
1628 2080 2.355193 GCCGCCTCTCTTCCTCTGT 61.355 63.158 0.00 0.00 0.00 3.41 F
3416 4856 1.134128 CCCAAAAGTGCCAGCCTTTTT 60.134 47.619 12.97 5.98 39.47 1.94 F
5185 6754 1.053264 AGATCCTGGCAGCTAGTGGG 61.053 60.000 9.56 0.00 0.00 4.61 F
5361 6942 0.600057 GACCAAGAAAAGCTGCAGGG 59.400 55.000 17.12 7.86 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2286 0.247736 GTCTGGTCGATGGAGCTTGT 59.752 55.000 8.42 0.0 41.26 3.16 R
2374 2981 2.807108 GCCGATCATGGGAGTAAGAACC 60.807 54.545 0.00 0.0 0.00 3.62 R
3554 5075 2.754552 AGCGAATCCATAAAGCTGCAAA 59.245 40.909 1.02 0.0 36.73 3.68 R
5227 6796 0.535335 TATCACCGTGGCCTTCACTC 59.465 55.000 3.32 0.0 43.94 3.51 R
6074 7661 0.888619 TGGACTTCAGCACTCTACCG 59.111 55.000 0.00 0.0 0.00 4.02 R
7212 9136 1.317613 TTCACCAGCGCTCAATGTTT 58.682 45.000 7.13 0.0 0.00 2.83 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
32 33 5.672051 ACAACACGACATGTAAAATACACG 58.328 37.500 0.00 0.00 42.31 4.49
55 56 4.712476 AGCTTGCAGGGTAGAGATATTTG 58.288 43.478 0.00 0.00 0.00 2.32
101 102 6.258230 TGTGAGCTGAGAATAAACCAAATG 57.742 37.500 0.00 0.00 0.00 2.32
166 167 2.881111 AACTAAAGTTGAGGGCCTCC 57.119 50.000 30.03 16.01 36.80 4.30
172 173 3.653835 AAGTTGAGGGCCTCCTATTTC 57.346 47.619 30.03 13.44 45.05 2.17
222 223 4.884247 TGCTTGCATGAATGATTTCACAA 58.116 34.783 3.33 0.00 44.36 3.33
230 231 5.874895 TGAATGATTTCACAAGCAGAGAG 57.125 39.130 0.00 0.00 36.94 3.20
234 235 0.250901 TTTCACAAGCAGAGAGGGGC 60.251 55.000 0.00 0.00 0.00 5.80
285 286 3.680937 TGTAAACGTTATCTTTCCGCCAG 59.319 43.478 0.00 0.00 0.00 4.85
291 292 0.901827 TATCTTTCCGCCAGCACAGA 59.098 50.000 0.00 0.00 0.00 3.41
296 297 0.881118 TTCCGCCAGCACAGAAATTC 59.119 50.000 0.00 0.00 0.00 2.17
311 312 6.939551 CAGAAATTCTGCATCATTTCGTTT 57.060 33.333 10.30 5.60 42.10 3.60
312 313 6.975126 CAGAAATTCTGCATCATTTCGTTTC 58.025 36.000 10.30 8.32 42.10 2.78
313 314 6.583427 CAGAAATTCTGCATCATTTCGTTTCA 59.417 34.615 10.30 0.00 42.10 2.69
314 315 7.115236 CAGAAATTCTGCATCATTTCGTTTCAA 59.885 33.333 10.30 0.00 42.10 2.69
341 342 8.291740 TCAATTAATATGACATCTTTGCCGATG 58.708 33.333 0.00 6.29 44.88 3.84
367 368 4.100529 CAATGAGCCAAATTTCGCAGTAG 58.899 43.478 10.48 0.00 0.00 2.57
371 372 1.132453 GCCAAATTTCGCAGTAGACCC 59.868 52.381 2.65 0.00 0.00 4.46
490 524 5.243283 AGAAGGATTTTGCATATCTCATGGC 59.757 40.000 8.66 0.00 0.00 4.40
494 528 1.612676 TTGCATATCTCATGGCTGGC 58.387 50.000 0.00 0.00 0.00 4.85
512 549 0.672711 GCGGTACTGTCTTTCACCCC 60.673 60.000 3.10 0.00 0.00 4.95
519 556 2.024369 ACTGTCTTTCACCCCCTTTTGT 60.024 45.455 0.00 0.00 0.00 2.83
548 620 1.271656 AGAACAATCAAGCTTGGCTGC 59.728 47.619 25.73 10.92 39.62 5.25
549 621 1.000060 GAACAATCAAGCTTGGCTGCA 60.000 47.619 25.73 6.94 39.62 4.41
550 622 0.601558 ACAATCAAGCTTGGCTGCAG 59.398 50.000 25.73 10.11 39.62 4.41
551 623 0.601558 CAATCAAGCTTGGCTGCAGT 59.398 50.000 25.73 2.78 39.62 4.40
552 624 0.601558 AATCAAGCTTGGCTGCAGTG 59.398 50.000 25.73 3.58 39.62 3.66
553 625 0.538977 ATCAAGCTTGGCTGCAGTGT 60.539 50.000 25.73 0.00 39.62 3.55
554 626 1.007734 CAAGCTTGGCTGCAGTGTG 60.008 57.895 19.14 4.77 39.62 3.82
555 627 2.853290 AAGCTTGGCTGCAGTGTGC 61.853 57.895 16.64 14.25 45.29 4.57
556 628 4.353437 GCTTGGCTGCAGTGTGCC 62.353 66.667 16.64 18.33 44.23 5.01
653 725 0.890683 GTGCTCCCTCCACCAAATTG 59.109 55.000 0.00 0.00 0.00 2.32
664 736 7.402650 TCCCTCCACCAAATTGATAATTTTCAT 59.597 33.333 0.00 0.00 38.97 2.57
665 737 8.048514 CCCTCCACCAAATTGATAATTTTCATT 58.951 33.333 0.00 0.00 38.97 2.57
666 738 9.452287 CCTCCACCAAATTGATAATTTTCATTT 57.548 29.630 0.00 0.55 38.97 2.32
708 780 1.300465 AGCAGCACTCACTGTCACG 60.300 57.895 0.00 0.00 39.96 4.35
712 784 0.109551 AGCACTCACTGTCACGATCG 60.110 55.000 14.88 14.88 0.00 3.69
730 1124 4.742201 CCGTCGCTGTCAGGTGGG 62.742 72.222 1.14 0.00 0.00 4.61
774 1168 5.125900 AGAGGAAGAGCAGATATCATCATCG 59.874 44.000 5.32 0.00 32.29 3.84
789 1190 6.560003 TCATCATCGCCCATATATAAACCT 57.440 37.500 0.00 0.00 0.00 3.50
792 1193 6.222038 TCATCGCCCATATATAAACCTCTC 57.778 41.667 0.00 0.00 0.00 3.20
807 1208 1.908340 CTCTCCACCTGCCTTCCTGG 61.908 65.000 0.00 0.00 38.43 4.45
825 1226 4.711355 TCCTGGCCAATTATTTTCTTCCAG 59.289 41.667 7.01 0.00 39.49 3.86
826 1227 5.014808 CTGGCCAATTATTTTCTTCCAGG 57.985 43.478 7.01 0.00 36.96 4.45
827 1228 3.197549 TGGCCAATTATTTTCTTCCAGGC 59.802 43.478 0.61 0.00 38.84 4.85
828 1229 3.452264 GGCCAATTATTTTCTTCCAGGCT 59.548 43.478 0.00 0.00 39.48 4.58
829 1230 4.442052 GGCCAATTATTTTCTTCCAGGCTC 60.442 45.833 0.00 0.00 39.48 4.70
878 1279 4.519213 TGTTTCCACTATTACCAATCCGG 58.481 43.478 0.00 0.00 42.50 5.14
880 1281 2.404559 TCCACTATTACCAATCCGGCT 58.595 47.619 0.00 0.00 39.03 5.52
890 1291 1.472376 CCAATCCGGCTCTCAGAAGTC 60.472 57.143 0.00 0.00 0.00 3.01
892 1293 2.690497 CAATCCGGCTCTCAGAAGTCTA 59.310 50.000 0.00 0.00 0.00 2.59
893 1294 1.752683 TCCGGCTCTCAGAAGTCTAC 58.247 55.000 0.00 0.00 0.00 2.59
894 1295 1.282447 TCCGGCTCTCAGAAGTCTACT 59.718 52.381 0.00 0.00 0.00 2.57
896 1297 2.639065 CGGCTCTCAGAAGTCTACTCT 58.361 52.381 0.00 0.00 0.00 3.24
902 1303 4.255301 TCTCAGAAGTCTACTCTTCGTCC 58.745 47.826 0.00 0.00 45.69 4.79
903 1304 4.004314 CTCAGAAGTCTACTCTTCGTCCA 58.996 47.826 0.00 0.00 45.69 4.02
904 1305 4.004314 TCAGAAGTCTACTCTTCGTCCAG 58.996 47.826 0.00 0.00 45.69 3.86
905 1306 3.754323 CAGAAGTCTACTCTTCGTCCAGT 59.246 47.826 0.00 0.00 45.69 4.00
924 1343 1.077123 TGCGCGCGGAAAAGTAATAA 58.923 45.000 33.06 0.00 0.00 1.40
960 1379 2.834549 CTCCAGTGATTACCACCTGTCT 59.165 50.000 0.00 0.00 46.87 3.41
973 1392 3.057547 CTGTCTCTGACCCGCTCGG 62.058 68.421 0.48 0.48 37.81 4.63
995 1420 1.012049 TCCCCTAATCCCAATCCCAGT 59.988 52.381 0.00 0.00 0.00 4.00
1628 2080 2.355193 GCCGCCTCTCTTCCTCTGT 61.355 63.158 0.00 0.00 0.00 3.41
1827 2286 2.361610 GTGTCCTCCCCGTCGGTA 60.362 66.667 11.06 0.00 0.00 4.02
2222 2703 8.903059 TCCTATTCTCTTCTCTTTCTACCTTT 57.097 34.615 0.00 0.00 0.00 3.11
2349 2954 7.166691 TGTTCCTTAGATGTCTGGTTACTAC 57.833 40.000 0.00 0.00 0.00 2.73
2354 2959 7.774157 TCCTTAGATGTCTGGTTACTACTACTG 59.226 40.741 0.00 0.00 0.00 2.74
2374 2981 5.978814 ACTGCCTACTAACAAGGATTACTG 58.021 41.667 0.00 0.00 36.08 2.74
2442 3063 3.937706 GAGTGCAGATTTGTCTGTATGCT 59.062 43.478 7.22 0.00 39.76 3.79
2689 3403 3.408634 CCTTTGGAGGTTACGTTGATGT 58.591 45.455 0.00 0.00 38.32 3.06
3166 4604 2.233922 CGAAGGGTGATGGAGTACTGTT 59.766 50.000 0.00 0.00 0.00 3.16
3170 4608 4.362677 AGGGTGATGGAGTACTGTTGTAT 58.637 43.478 0.00 0.00 0.00 2.29
3171 4609 4.162320 AGGGTGATGGAGTACTGTTGTATG 59.838 45.833 0.00 0.00 0.00 2.39
3226 4664 1.142060 TCCTGTTGTTCCACCGTCATT 59.858 47.619 0.00 0.00 0.00 2.57
3292 4732 9.746457 AGGCACTAAAGATAAAAAGAGAGAAAT 57.254 29.630 0.00 0.00 36.02 2.17
3416 4856 1.134128 CCCAAAAGTGCCAGCCTTTTT 60.134 47.619 12.97 5.98 39.47 1.94
3440 4880 7.553881 TTTTCTGAAAAGAGAAGTGTACCAG 57.446 36.000 11.33 0.00 33.50 4.00
3521 5012 5.241662 GTTCTCTGTACTCCATTTTGCTCT 58.758 41.667 0.00 0.00 0.00 4.09
3525 5016 4.756642 TCTGTACTCCATTTTGCTCTTGTG 59.243 41.667 0.00 0.00 0.00 3.33
3529 5020 4.660168 ACTCCATTTTGCTCTTGTGATCT 58.340 39.130 0.00 0.00 0.00 2.75
3550 5071 2.552599 TGGCCTAACGATGTCAAACA 57.447 45.000 3.32 0.00 0.00 2.83
3554 5075 3.190535 GGCCTAACGATGTCAAACATGTT 59.809 43.478 4.92 4.92 39.27 2.71
3738 5261 1.421268 ACAGCTGAAGACCATCACCAA 59.579 47.619 23.35 0.00 0.00 3.67
3862 5390 9.539825 TTTTAAATAATTGATGCATATGCCGTT 57.460 25.926 24.54 13.54 41.18 4.44
3881 5414 5.682862 GCCGTTGTTTTGATAGATGCATAAG 59.317 40.000 0.00 0.00 0.00 1.73
4211 5750 4.834406 TCACCCCCATCTATCTCTAACT 57.166 45.455 0.00 0.00 0.00 2.24
4212 5751 5.157770 TCACCCCCATCTATCTCTAACTT 57.842 43.478 0.00 0.00 0.00 2.66
4477 6046 6.487828 TGATGATTTGAATCTGAAACCTCCT 58.512 36.000 5.42 0.00 36.39 3.69
4547 6116 1.470098 GGCAAACATCACCTAGTGCTG 59.530 52.381 0.00 0.00 36.01 4.41
4611 6180 1.512926 CAGAAACCTTCACACCTCGG 58.487 55.000 0.00 0.00 0.00 4.63
4743 6312 1.841302 AAGTCAATGGAGAGGCGCCA 61.841 55.000 31.54 7.75 37.78 5.69
4748 6317 2.615227 AATGGAGAGGCGCCATGGTC 62.615 60.000 31.54 17.81 42.92 4.02
4752 6321 2.361104 GAGGCGCCATGGTCCAAA 60.361 61.111 31.54 0.00 0.00 3.28
4755 6324 2.569354 GGCGCCATGGTCCAAACAA 61.569 57.895 24.80 0.00 0.00 2.83
4900 6469 2.115291 GGATTGGGCCGACTCAAGC 61.115 63.158 7.41 3.48 0.00 4.01
5185 6754 1.053264 AGATCCTGGCAGCTAGTGGG 61.053 60.000 9.56 0.00 0.00 4.61
5218 6787 6.042093 TGAAGATCCTGGTAGAATCATGTACC 59.958 42.308 3.78 3.78 43.97 3.34
5226 6795 3.667497 AGAATCATGTACCGCGATCAT 57.333 42.857 8.23 6.23 0.00 2.45
5227 6796 3.320626 AGAATCATGTACCGCGATCATG 58.679 45.455 22.29 22.29 39.87 3.07
5255 6827 2.038557 GGCCACGGTGATAAGGTGATAT 59.961 50.000 10.28 0.00 33.58 1.63
5269 6841 0.856982 TGATATTTTCCCCCGGGCAT 59.143 50.000 17.73 3.69 34.68 4.40
5361 6942 0.600057 GACCAAGAAAAGCTGCAGGG 59.400 55.000 17.12 7.86 0.00 4.45
5669 7253 1.202568 TCGGTGCAATGGAGCAGATAG 60.203 52.381 4.63 0.00 46.69 2.08
5830 7417 1.451567 CATGGCAGCAGTCAGGGAG 60.452 63.158 0.00 0.00 29.55 4.30
5999 7586 3.726291 TGATGATGCATTGCCTTCATG 57.274 42.857 21.86 0.00 32.98 3.07
6074 7661 5.934043 TCACTGTTATATATGGTGATGCAGC 59.066 40.000 0.00 0.00 32.91 5.25
6083 7670 0.807667 GGTGATGCAGCGGTAGAGTG 60.808 60.000 0.00 0.00 0.00 3.51
6099 7686 4.052159 AGAGTGCTGAAGTCCATAATCG 57.948 45.455 0.00 0.00 0.00 3.34
6124 7711 2.837591 GGTAATTCCAGGTTTGGCCAAT 59.162 45.455 21.26 0.42 44.63 3.16
6176 8047 7.880160 TGAAATATGTAAATGCTAGTGGCTT 57.120 32.000 0.00 0.00 42.39 4.35
6185 8056 8.044309 TGTAAATGCTAGTGGCTTACATTCTAA 58.956 33.333 8.62 0.00 36.96 2.10
6190 8061 7.792032 TGCTAGTGGCTTACATTCTAATTAGT 58.208 34.615 12.19 0.00 42.39 2.24
6219 8090 1.061857 GTTTGGCCAACTTGTTTTGCG 59.938 47.619 20.35 0.00 31.92 4.85
6239 8110 4.226761 GCGACGAAGGTTCAAATTGAAAT 58.773 39.130 10.27 0.00 38.22 2.17
6255 8126 8.495148 CAAATTGAAATTTGTAAGGTTAGTGGC 58.505 33.333 16.80 0.00 46.27 5.01
6265 8136 2.970987 AGGTTAGTGGCCCAACATTTT 58.029 42.857 0.00 0.00 0.00 1.82
6276 8147 6.037062 GTGGCCCAACATTTTATATTTTCAGC 59.963 38.462 0.00 0.00 0.00 4.26
6288 8159 8.472683 TTTATATTTTCAGCGTTGGGAATTTG 57.527 30.769 0.00 0.00 0.00 2.32
6329 8200 3.074412 GGTGGTGTAGGTTCATGTTGAG 58.926 50.000 0.00 0.00 0.00 3.02
6678 8592 2.747855 GCAGGAAGCCCGTTCTGG 60.748 66.667 0.00 0.00 37.23 3.86
6709 8623 3.132646 CCAGCAGGCTATGATATCTCTCC 59.867 52.174 3.98 0.58 0.00 3.71
6802 8716 2.349886 GACAACATCTCCAACATCGCTC 59.650 50.000 0.00 0.00 0.00 5.03
6968 8888 1.725164 GCCGTAGTTTCAGTACACAGC 59.275 52.381 0.00 0.00 0.00 4.40
7173 9097 1.211457 AGGTAGCTCCATTCCTGCAAG 59.789 52.381 0.00 0.00 39.02 4.01
7632 9565 7.673641 AGATGTTCAGAAGATGAGGTAATCT 57.326 36.000 0.00 0.00 39.68 2.40
7668 9603 2.557924 TGTTTGTTCCATCTGCCATGAC 59.442 45.455 0.00 0.00 0.00 3.06
7679 9614 3.953201 GCCATGACAAATAGGCTGC 57.047 52.632 0.00 0.00 43.70 5.25
7680 9615 1.396653 GCCATGACAAATAGGCTGCT 58.603 50.000 0.00 0.00 43.70 4.24
7681 9616 2.575532 GCCATGACAAATAGGCTGCTA 58.424 47.619 0.00 0.00 43.70 3.49
7682 9617 2.951642 GCCATGACAAATAGGCTGCTAA 59.048 45.455 0.00 0.00 43.70 3.09
7683 9618 3.243201 GCCATGACAAATAGGCTGCTAAC 60.243 47.826 0.00 0.00 43.70 2.34
7684 9619 3.947196 CCATGACAAATAGGCTGCTAACA 59.053 43.478 0.00 0.00 0.00 2.41
7685 9620 4.581824 CCATGACAAATAGGCTGCTAACAT 59.418 41.667 0.00 0.00 0.00 2.71
7686 9621 5.068198 CCATGACAAATAGGCTGCTAACATT 59.932 40.000 0.00 0.00 0.00 2.71
7687 9622 6.406177 CCATGACAAATAGGCTGCTAACATTT 60.406 38.462 0.00 0.00 0.00 2.32
7688 9623 6.588719 TGACAAATAGGCTGCTAACATTTT 57.411 33.333 0.00 0.00 0.00 1.82
7689 9624 6.991938 TGACAAATAGGCTGCTAACATTTTT 58.008 32.000 0.00 0.00 0.00 1.94
7722 9657 9.539825 CAATAGTCTGCTAACTCATGAACTATT 57.460 33.333 14.92 14.92 0.00 1.73
7729 9664 7.941919 TGCTAACTCATGAACTATTCGTAGAT 58.058 34.615 0.00 0.00 35.04 1.98
7731 9666 7.327275 GCTAACTCATGAACTATTCGTAGATGG 59.673 40.741 0.00 0.00 35.04 3.51
7732 9667 6.961360 ACTCATGAACTATTCGTAGATGGA 57.039 37.500 0.00 0.00 35.04 3.41
7733 9668 7.531857 ACTCATGAACTATTCGTAGATGGAT 57.468 36.000 0.00 0.00 35.04 3.41
7734 9669 7.598278 ACTCATGAACTATTCGTAGATGGATC 58.402 38.462 0.00 0.00 35.04 3.36
7737 9675 8.300286 TCATGAACTATTCGTAGATGGATCTTC 58.700 37.037 0.00 0.00 38.32 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.615588 AATATCTCTACCCTGCAAGCTC 57.384 45.455 0.00 0.00 0.00 4.09
55 56 6.016276 ACATCTCATCCAAAAAGGTGTACAAC 60.016 38.462 1.50 1.50 32.71 3.32
101 102 1.678970 GATTCCACTGGTGCACCCC 60.679 63.158 32.62 10.22 34.29 4.95
222 223 1.194781 TCTTTTCGCCCCTCTCTGCT 61.195 55.000 0.00 0.00 0.00 4.24
230 231 0.037734 TTTCCCTCTCTTTTCGCCCC 59.962 55.000 0.00 0.00 0.00 5.80
234 235 5.539048 TCAGTTAGTTTCCCTCTCTTTTCG 58.461 41.667 0.00 0.00 0.00 3.46
285 286 4.264614 CGAAATGATGCAGAATTTCTGTGC 59.735 41.667 23.66 14.15 45.94 4.57
291 292 7.599621 TGATTGAAACGAAATGATGCAGAATTT 59.400 29.630 8.66 8.66 0.00 1.82
296 297 6.880822 ATTGATTGAAACGAAATGATGCAG 57.119 33.333 0.00 0.00 0.00 4.41
311 312 9.970395 GGCAAAGATGTCATATTAATTGATTGA 57.030 29.630 0.00 0.00 0.00 2.57
312 313 8.908678 CGGCAAAGATGTCATATTAATTGATTG 58.091 33.333 0.00 1.23 0.00 2.67
313 314 8.849168 TCGGCAAAGATGTCATATTAATTGATT 58.151 29.630 0.00 0.00 0.00 2.57
314 315 8.394971 TCGGCAAAGATGTCATATTAATTGAT 57.605 30.769 0.00 0.00 0.00 2.57
360 361 4.208686 GCCTCCGGGTCTACTGCG 62.209 72.222 0.00 0.00 34.45 5.18
395 396 3.839432 GGCTCCGGTTCTCTCCCG 61.839 72.222 0.00 0.00 45.07 5.14
434 435 1.202348 CGGGATCTAGCGCTATGGATG 60.202 57.143 19.19 5.90 0.00 3.51
490 524 1.429463 GTGAAAGACAGTACCGCCAG 58.571 55.000 0.00 0.00 0.00 4.85
494 528 0.036671 GGGGGTGAAAGACAGTACCG 60.037 60.000 0.00 0.00 34.01 4.02
519 556 6.169094 CAAGCTTGATTGTTCTCTTCTCCTA 58.831 40.000 22.31 0.00 0.00 2.94
564 636 3.478780 TGGGTAGACCACTGTGCC 58.521 61.111 1.29 0.00 46.80 5.01
630 702 2.081787 TGGTGGAGGGAGCACCAAA 61.082 57.895 0.00 0.00 44.94 3.28
653 725 8.946085 GTGGGGGAAAAGAAAATGAAAATTATC 58.054 33.333 0.00 0.00 0.00 1.75
664 736 2.516277 TCTGGAGTGGGGGAAAAGAAAA 59.484 45.455 0.00 0.00 0.00 2.29
665 737 2.140224 TCTGGAGTGGGGGAAAAGAAA 58.860 47.619 0.00 0.00 0.00 2.52
666 738 1.827792 TCTGGAGTGGGGGAAAAGAA 58.172 50.000 0.00 0.00 0.00 2.52
667 739 1.827792 TTCTGGAGTGGGGGAAAAGA 58.172 50.000 0.00 0.00 0.00 2.52
668 740 2.519013 CTTTCTGGAGTGGGGGAAAAG 58.481 52.381 0.00 0.00 0.00 2.27
708 780 2.951745 CTGACAGCGACGGCGATC 60.952 66.667 18.90 9.30 46.35 3.69
774 1168 4.536489 AGGTGGAGAGGTTTATATATGGGC 59.464 45.833 0.00 0.00 0.00 5.36
789 1190 1.920325 CCAGGAAGGCAGGTGGAGA 60.920 63.158 0.00 0.00 31.04 3.71
807 1208 4.686972 GAGCCTGGAAGAAAATAATTGGC 58.313 43.478 0.00 0.00 34.07 4.52
863 1264 3.305720 TGAGAGCCGGATTGGTAATAGT 58.694 45.455 5.05 0.00 41.21 2.12
870 1271 0.539051 ACTTCTGAGAGCCGGATTGG 59.461 55.000 5.05 0.00 42.50 3.16
878 1279 3.687698 ACGAAGAGTAGACTTCTGAGAGC 59.312 47.826 0.00 0.00 42.58 4.09
880 1281 4.255301 GGACGAAGAGTAGACTTCTGAGA 58.745 47.826 0.00 0.00 42.58 3.27
890 1291 0.798771 GCGCACTGGACGAAGAGTAG 60.799 60.000 0.30 0.00 0.00 2.57
892 1293 2.049063 GCGCACTGGACGAAGAGT 60.049 61.111 0.30 0.00 0.00 3.24
893 1294 3.175240 CGCGCACTGGACGAAGAG 61.175 66.667 8.75 0.00 0.00 2.85
902 1303 2.165362 TTACTTTTCCGCGCGCACTG 62.165 55.000 32.61 18.70 0.00 3.66
903 1304 1.296056 ATTACTTTTCCGCGCGCACT 61.296 50.000 32.61 6.62 0.00 4.40
904 1305 0.370958 TATTACTTTTCCGCGCGCAC 59.629 50.000 32.61 2.05 0.00 5.34
905 1306 1.077123 TTATTACTTTTCCGCGCGCA 58.923 45.000 32.61 6.90 0.00 6.09
924 1343 0.253160 TGGAGGGACCTGGTTGCTAT 60.253 55.000 0.00 0.00 39.86 2.97
973 1392 0.405973 GGGATTGGGATTAGGGGAGC 59.594 60.000 0.00 0.00 0.00 4.70
980 1405 2.135189 CTGGGACTGGGATTGGGATTA 58.865 52.381 0.00 0.00 0.00 1.75
1827 2286 0.247736 GTCTGGTCGATGGAGCTTGT 59.752 55.000 8.42 0.00 41.26 3.16
2222 2703 3.380004 CCCTAAGCATAAACAATTGGCGA 59.620 43.478 10.83 0.00 0.00 5.54
2349 2954 7.203910 CAGTAATCCTTGTTAGTAGGCAGTAG 58.796 42.308 0.00 0.00 32.59 2.57
2354 2959 5.354842 ACCAGTAATCCTTGTTAGTAGGC 57.645 43.478 0.00 0.00 32.59 3.93
2374 2981 2.807108 GCCGATCATGGGAGTAAGAACC 60.807 54.545 0.00 0.00 0.00 3.62
2442 3063 6.894654 TGGTAGAAAAATAATCAGGCCAATGA 59.105 34.615 5.01 0.00 0.00 2.57
2689 3403 8.038944 ACAACTTCAGTCTGTACTTTACTCAAA 58.961 33.333 0.00 0.00 31.97 2.69
3166 4604 6.018098 ACAAATTTTCGTACGACAACCATACA 60.018 34.615 19.36 0.00 0.00 2.29
3170 4608 4.550447 CGACAAATTTTCGTACGACAACCA 60.550 41.667 19.36 0.00 0.00 3.67
3171 4609 3.896030 CGACAAATTTTCGTACGACAACC 59.104 43.478 19.36 5.12 0.00 3.77
3226 4664 5.091552 AGGTACTCTGAATTCTTACACCCA 58.908 41.667 7.05 0.00 0.00 4.51
3312 4752 8.552865 TGTCTTTTCATGAAAATGCATTTCTTG 58.447 29.630 28.86 21.36 46.27 3.02
3416 4856 6.038271 GCTGGTACACTTCTCTTTTCAGAAAA 59.962 38.462 8.09 8.09 31.86 2.29
3418 4858 5.057149 GCTGGTACACTTCTCTTTTCAGAA 58.943 41.667 0.00 0.00 0.00 3.02
3421 4861 4.689612 AGCTGGTACACTTCTCTTTTCA 57.310 40.909 0.00 0.00 0.00 2.69
3423 4863 7.483580 AGTATAGCTGGTACACTTCTCTTTT 57.516 36.000 12.02 0.00 0.00 2.27
3424 4864 7.483580 AAGTATAGCTGGTACACTTCTCTTT 57.516 36.000 4.81 0.00 0.00 2.52
3425 4865 8.591114 TTAAGTATAGCTGGTACACTTCTCTT 57.409 34.615 13.21 0.00 32.09 2.85
3426 4866 7.201839 GCTTAAGTATAGCTGGTACACTTCTCT 60.202 40.741 13.21 0.00 35.74 3.10
3427 4867 6.919115 GCTTAAGTATAGCTGGTACACTTCTC 59.081 42.308 13.21 2.17 35.74 2.87
3428 4868 6.380274 TGCTTAAGTATAGCTGGTACACTTCT 59.620 38.462 13.21 0.00 39.38 2.85
3431 4871 6.154706 AGTTGCTTAAGTATAGCTGGTACACT 59.845 38.462 4.02 0.00 39.38 3.55
3432 4872 6.255887 CAGTTGCTTAAGTATAGCTGGTACAC 59.744 42.308 4.02 0.00 39.38 2.90
3433 4873 6.338146 CAGTTGCTTAAGTATAGCTGGTACA 58.662 40.000 4.02 0.00 39.38 2.90
3435 4875 5.105106 TGCAGTTGCTTAAGTATAGCTGGTA 60.105 40.000 16.04 0.00 42.66 3.25
3436 4876 4.192317 GCAGTTGCTTAAGTATAGCTGGT 58.808 43.478 16.04 0.00 39.38 4.00
3437 4877 4.191544 TGCAGTTGCTTAAGTATAGCTGG 58.808 43.478 16.04 5.01 42.66 4.85
3438 4878 5.111989 TCTGCAGTTGCTTAAGTATAGCTG 58.888 41.667 14.67 9.48 42.66 4.24
3440 4880 5.112686 ACTCTGCAGTTGCTTAAGTATAGC 58.887 41.667 14.67 5.08 42.66 2.97
3521 5012 3.410631 TCGTTAGGCCAAAGATCACAA 57.589 42.857 5.01 0.00 0.00 3.33
3525 5016 3.531538 TGACATCGTTAGGCCAAAGATC 58.468 45.455 5.01 2.08 33.67 2.75
3529 5020 3.215151 TGTTTGACATCGTTAGGCCAAA 58.785 40.909 5.01 0.00 0.00 3.28
3550 5071 5.104374 CGAATCCATAAAGCTGCAAAACAT 58.896 37.500 1.02 0.00 0.00 2.71
3554 5075 2.754552 AGCGAATCCATAAAGCTGCAAA 59.245 40.909 1.02 0.00 36.73 3.68
4211 5750 7.235079 TCCAATGTAAGGTTGTCATTCCTTAA 58.765 34.615 14.60 8.73 44.52 1.85
4212 5751 6.785076 TCCAATGTAAGGTTGTCATTCCTTA 58.215 36.000 10.94 10.94 42.95 2.69
4471 6040 1.980765 TGTGCAAAGATCTGAGGAGGT 59.019 47.619 0.00 0.00 0.00 3.85
4477 6046 2.957402 AGGGTTGTGCAAAGATCTGA 57.043 45.000 0.00 0.00 0.00 3.27
4547 6116 1.664321 CCAGAAGCTGCTGAATGCCC 61.664 60.000 24.34 0.00 42.00 5.36
4611 6180 3.817647 ACTCAAATCAGAACCTTGTGCTC 59.182 43.478 0.00 0.00 0.00 4.26
4743 6312 5.139727 TGTCATTCTTCTTGTTTGGACCAT 58.860 37.500 0.00 0.00 0.00 3.55
4748 6317 5.221303 ACCACATGTCATTCTTCTTGTTTGG 60.221 40.000 0.00 0.00 0.00 3.28
4752 6321 6.294176 GCTAAACCACATGTCATTCTTCTTGT 60.294 38.462 0.00 0.00 0.00 3.16
4755 6324 5.564550 AGCTAAACCACATGTCATTCTTCT 58.435 37.500 0.00 0.00 0.00 2.85
4900 6469 2.564947 AGTGCCAGTCTTTCCTCTGTAG 59.435 50.000 0.00 0.00 0.00 2.74
5185 6754 2.996631 ACCAGGATCTTCAGTTGATGC 58.003 47.619 0.00 0.00 33.36 3.91
5218 6787 1.493950 GGCCTTCACTCATGATCGCG 61.494 60.000 0.00 0.00 33.85 5.87
5226 6795 1.480212 ATCACCGTGGCCTTCACTCA 61.480 55.000 3.32 0.00 43.94 3.41
5227 6796 0.535335 TATCACCGTGGCCTTCACTC 59.465 55.000 3.32 0.00 43.94 3.51
5255 6827 2.944390 AGGATGCCCGGGGGAAAA 60.944 61.111 25.28 0.00 37.50 2.29
5269 6841 1.438651 CACGAATTTTGGCGAGAGGA 58.561 50.000 0.00 0.00 0.00 3.71
5361 6942 1.025041 GGAAATGCTCGGTGATTCCC 58.975 55.000 0.00 0.00 34.74 3.97
5743 7330 1.421646 CACTTGACCTTCAGTTCCCCT 59.578 52.381 0.00 0.00 0.00 4.79
5830 7417 3.727726 CAAACCTCCAAAACCATTGTCC 58.272 45.455 0.00 0.00 0.00 4.02
5999 7586 9.894783 ACAATCGATATATACTTGCCGATATAC 57.105 33.333 0.00 0.00 35.98 1.47
6074 7661 0.888619 TGGACTTCAGCACTCTACCG 59.111 55.000 0.00 0.00 0.00 4.02
6083 7670 2.213499 CCACCGATTATGGACTTCAGC 58.787 52.381 0.00 0.00 39.87 4.26
6099 7686 2.176045 CCAAACCTGGAATTACCCACC 58.824 52.381 0.00 0.00 46.92 4.61
6124 7711 6.539173 TGAACCTACAAATTAGCAGGAGAAA 58.461 36.000 6.23 0.00 32.25 2.52
6185 8056 7.862675 AGTTGGCCAAACTCTTAGATACTAAT 58.137 34.615 22.47 0.00 46.60 1.73
6239 8110 3.224269 GTTGGGCCACTAACCTTACAAA 58.776 45.455 5.23 0.00 32.49 2.83
6242 8113 2.572209 TGTTGGGCCACTAACCTTAC 57.428 50.000 5.23 0.00 37.28 2.34
6255 8126 7.201513 CCAACGCTGAAAATATAAAATGTTGGG 60.202 37.037 0.00 0.00 45.39 4.12
6265 8136 6.568869 CCAAATTCCCAACGCTGAAAATATA 58.431 36.000 0.00 0.00 0.00 0.86
6288 8159 3.447229 ACCATAAGCATAACAAGTTGGCC 59.553 43.478 7.96 0.00 0.00 5.36
6554 8437 6.071952 GCATTCTCCAATCTTACCAGTTTTGA 60.072 38.462 0.00 0.00 0.00 2.69
6644 8558 5.314923 TCCTGCTAAAATCAAAGCATGTC 57.685 39.130 0.00 0.00 46.96 3.06
6678 8592 4.708177 TCATAGCCTGCTGGAGAAATTAC 58.292 43.478 14.77 0.00 34.57 1.89
6709 8623 4.409570 GCAAGCACAAGTGATGTAAGATG 58.590 43.478 4.04 0.00 41.46 2.90
6968 8888 7.096884 TGTACTTACCTACTAATGCTGAGTG 57.903 40.000 0.00 0.00 0.00 3.51
7212 9136 1.317613 TTCACCAGCGCTCAATGTTT 58.682 45.000 7.13 0.00 0.00 2.83
7686 9621 8.232913 AGTTAGCAGACTATTGTTTCCAAAAA 57.767 30.769 0.00 0.00 33.44 1.94
7687 9622 7.500892 TGAGTTAGCAGACTATTGTTTCCAAAA 59.499 33.333 0.00 0.00 33.44 2.44
7688 9623 6.995686 TGAGTTAGCAGACTATTGTTTCCAAA 59.004 34.615 0.00 0.00 33.44 3.28
7689 9624 6.530120 TGAGTTAGCAGACTATTGTTTCCAA 58.470 36.000 0.00 0.00 34.45 3.53
7690 9625 6.109156 TGAGTTAGCAGACTATTGTTTCCA 57.891 37.500 0.00 0.00 0.00 3.53
7691 9626 6.818644 TCATGAGTTAGCAGACTATTGTTTCC 59.181 38.462 0.00 0.00 0.00 3.13
7692 9627 7.834068 TCATGAGTTAGCAGACTATTGTTTC 57.166 36.000 0.00 0.00 0.00 2.78
7693 9628 7.880195 AGTTCATGAGTTAGCAGACTATTGTTT 59.120 33.333 0.00 0.00 0.00 2.83
7694 9629 7.390027 AGTTCATGAGTTAGCAGACTATTGTT 58.610 34.615 0.00 0.00 0.00 2.83
7695 9630 6.940739 AGTTCATGAGTTAGCAGACTATTGT 58.059 36.000 0.00 0.00 0.00 2.71
7696 9631 9.539825 AATAGTTCATGAGTTAGCAGACTATTG 57.460 33.333 17.97 0.00 0.00 1.90
7697 9632 9.757227 GAATAGTTCATGAGTTAGCAGACTATT 57.243 33.333 18.42 18.42 31.79 1.73
7698 9633 8.079203 CGAATAGTTCATGAGTTAGCAGACTAT 58.921 37.037 6.61 6.61 0.00 2.12
7699 9634 7.067129 ACGAATAGTTCATGAGTTAGCAGACTA 59.933 37.037 0.00 0.00 0.00 2.59
7700 9635 6.127591 ACGAATAGTTCATGAGTTAGCAGACT 60.128 38.462 0.00 0.00 0.00 3.24
7701 9636 6.037098 ACGAATAGTTCATGAGTTAGCAGAC 58.963 40.000 0.00 0.00 0.00 3.51
7702 9637 6.208988 ACGAATAGTTCATGAGTTAGCAGA 57.791 37.500 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.