Multiple sequence alignment - TraesCS4B01G322500

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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 TraesCS4B01G322500 chr4B 100.000 6409 0 0 1 6409 613155892 613149484 0.000000e+00 11836.0
1 TraesCS4B01G322500 chr4B 90.594 202 19 0 4598 4799 577219510 577219309 1.060000e-67 268.0
2 TraesCS4B01G322500 chr4B 94.068 118 7 0 4040 4157 403837765 403837648 5.110000e-41 180.0
3 TraesCS4B01G322500 chr4D 95.361 3945 157 20 1752 5680 483061931 483057997 0.000000e+00 6248.0
4 TraesCS4B01G322500 chr4D 87.444 1330 103 36 25 1324 483063624 483062329 0.000000e+00 1472.0
5 TraesCS4B01G322500 chr4D 92.593 54 4 0 4148 4201 335044918 335044865 1.920000e-10 78.7
6 TraesCS4B01G322500 chr4D 95.833 48 1 1 4000 4047 335044971 335044925 6.890000e-10 76.8
7 TraesCS4B01G322500 chr5A 93.863 2314 91 12 1731 4009 663212148 663209851 0.000000e+00 3439.0
8 TraesCS4B01G322500 chr5A 89.872 1718 99 40 1 1690 663213812 663212142 0.000000e+00 2139.0
9 TraesCS4B01G322500 chr5A 91.354 1226 81 16 4479 5680 663209839 663208615 0.000000e+00 1653.0
10 TraesCS4B01G322500 chr5A 85.915 71 5 5 4000 4068 3702032 3702099 3.210000e-08 71.3
11 TraesCS4B01G322500 chr1A 97.119 729 21 0 5681 6409 213937034 213936306 0.000000e+00 1230.0
12 TraesCS4B01G322500 chr1A 84.466 103 6 4 1332 1433 526751908 526752001 6.840000e-15 93.5
13 TraesCS4B01G322500 chr7B 96.717 731 24 0 5679 6409 73479799 73479069 0.000000e+00 1218.0
14 TraesCS4B01G322500 chr7B 94.017 117 7 0 4035 4151 377994643 377994527 1.840000e-40 178.0
15 TraesCS4B01G322500 chr7B 90.741 54 4 1 3994 4046 245991950 245991897 3.210000e-08 71.3
16 TraesCS4B01G322500 chr2B 96.717 731 24 0 5679 6409 793364328 793363598 0.000000e+00 1218.0
17 TraesCS4B01G322500 chr2B 96.571 729 23 2 5679 6407 390802166 390802892 0.000000e+00 1206.0
18 TraesCS4B01G322500 chr2B 92.453 53 3 1 4001 4053 752488174 752488123 2.480000e-09 75.0
19 TraesCS4B01G322500 chr2A 96.580 731 25 0 5679 6409 192003382 192002652 0.000000e+00 1212.0
20 TraesCS4B01G322500 chr2A 96.443 731 26 0 5679 6409 89175425 89174695 0.000000e+00 1206.0
21 TraesCS4B01G322500 chr2A 87.061 541 45 11 228 748 23478884 23479419 7.160000e-164 588.0
22 TraesCS4B01G322500 chr2A 96.970 33 1 0 1352 1384 761126389 761126421 8.980000e-04 56.5
23 TraesCS4B01G322500 chr2D 96.453 733 26 0 5677 6409 308681370 308682102 0.000000e+00 1210.0
24 TraesCS4B01G322500 chr2D 96.429 112 4 0 4040 4151 10118409 10118298 1.100000e-42 185.0
25 TraesCS4B01G322500 chr2D 87.629 97 9 1 1335 1431 370630363 370630270 6.790000e-20 110.0
26 TraesCS4B01G322500 chr5B 96.438 730 26 0 5680 6409 677678771 677678042 0.000000e+00 1205.0
27 TraesCS4B01G322500 chr5B 96.306 731 27 0 5679 6409 59779596 59780326 0.000000e+00 1201.0
28 TraesCS4B01G322500 chr5B 93.490 722 45 2 4598 5318 35494609 35495329 0.000000e+00 1072.0
29 TraesCS4B01G322500 chr5B 92.510 721 54 0 4598 5318 302832892 302833612 0.000000e+00 1033.0
30 TraesCS4B01G322500 chr5B 92.453 53 4 0 4148 4200 702567692 702567744 6.890000e-10 76.8
31 TraesCS4B01G322500 chr5B 92.308 52 2 2 4003 4053 591529187 591529237 8.910000e-09 73.1
32 TraesCS4B01G322500 chr3B 93.343 721 45 3 4598 5316 512425282 512426001 0.000000e+00 1062.0
33 TraesCS4B01G322500 chr3B 95.745 47 0 2 4002 4047 73785940 73785985 2.480000e-09 75.0
34 TraesCS4B01G322500 chr1B 93.051 331 21 2 4989 5318 30437236 30436907 3.470000e-132 483.0
35 TraesCS4B01G322500 chr3A 89.697 165 15 2 4035 4198 621664607 621664444 6.510000e-50 209.0
36 TraesCS4B01G322500 chr3A 80.272 147 23 6 1192 1334 269231221 269231365 8.790000e-19 106.0
37 TraesCS4B01G322500 chr3A 79.730 148 23 7 1192 1334 53299325 53299180 4.090000e-17 100.0
38 TraesCS4B01G322500 chr3D 97.391 115 3 0 4044 4158 508071978 508071864 5.070000e-46 196.0
39 TraesCS4B01G322500 chr6B 97.345 113 2 1 4044 4155 623368097 623367985 2.360000e-44 191.0
40 TraesCS4B01G322500 chr5D 98.148 108 2 0 4044 4151 81783105 81782998 8.480000e-44 189.0
41 TraesCS4B01G322500 chr5D 87.719 57 7 0 4148 4204 544493082 544493138 4.150000e-07 67.6
42 TraesCS4B01G322500 chr5D 87.755 49 3 1 1334 1382 440652021 440652066 3.000000e-03 54.7
43 TraesCS4B01G322500 chrUn 97.248 109 3 0 4043 4151 50628941 50628833 1.100000e-42 185.0
44 TraesCS4B01G322500 chr6A 94.000 50 1 2 3999 4047 499458743 499458791 2.480000e-09 75.0
45 TraesCS4B01G322500 chr6D 92.157 51 4 0 4148 4198 470575058 470575008 8.910000e-09 73.1
46 TraesCS4B01G322500 chr6D 90.566 53 5 0 4148 4200 91072562 91072614 3.210000e-08 71.3
47 TraesCS4B01G322500 chr1D 92.308 52 3 1 4002 4053 315817008 315816958 8.910000e-09 73.1
48 TraesCS4B01G322500 chr1D 95.556 45 2 0 4157 4201 333004637 333004593 8.910000e-09 73.1
49 TraesCS4B01G322500 chr7D 88.333 60 6 1 4140 4198 75944425 75944366 3.210000e-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 TraesCS4B01G322500 chr4B 613149484 613155892 6408 True 11836.000000 11836 100.000000 1 6409 1 chr4B.!!$R3 6408
1 TraesCS4B01G322500 chr4D 483057997 483063624 5627 True 3860.000000 6248 91.402500 25 5680 2 chr4D.!!$R2 5655
2 TraesCS4B01G322500 chr5A 663208615 663213812 5197 True 2410.333333 3439 91.696333 1 5680 3 chr5A.!!$R1 5679
3 TraesCS4B01G322500 chr1A 213936306 213937034 728 True 1230.000000 1230 97.119000 5681 6409 1 chr1A.!!$R1 728
4 TraesCS4B01G322500 chr7B 73479069 73479799 730 True 1218.000000 1218 96.717000 5679 6409 1 chr7B.!!$R1 730
5 TraesCS4B01G322500 chr2B 793363598 793364328 730 True 1218.000000 1218 96.717000 5679 6409 1 chr2B.!!$R2 730
6 TraesCS4B01G322500 chr2B 390802166 390802892 726 False 1206.000000 1206 96.571000 5679 6407 1 chr2B.!!$F1 728
7 TraesCS4B01G322500 chr2A 192002652 192003382 730 True 1212.000000 1212 96.580000 5679 6409 1 chr2A.!!$R2 730
8 TraesCS4B01G322500 chr2A 89174695 89175425 730 True 1206.000000 1206 96.443000 5679 6409 1 chr2A.!!$R1 730
9 TraesCS4B01G322500 chr2A 23478884 23479419 535 False 588.000000 588 87.061000 228 748 1 chr2A.!!$F1 520
10 TraesCS4B01G322500 chr2D 308681370 308682102 732 False 1210.000000 1210 96.453000 5677 6409 1 chr2D.!!$F1 732
11 TraesCS4B01G322500 chr5B 677678042 677678771 729 True 1205.000000 1205 96.438000 5680 6409 1 chr5B.!!$R1 729
12 TraesCS4B01G322500 chr5B 59779596 59780326 730 False 1201.000000 1201 96.306000 5679 6409 1 chr5B.!!$F2 730
13 TraesCS4B01G322500 chr5B 35494609 35495329 720 False 1072.000000 1072 93.490000 4598 5318 1 chr5B.!!$F1 720
14 TraesCS4B01G322500 chr5B 302832892 302833612 720 False 1033.000000 1033 92.510000 4598 5318 1 chr5B.!!$F3 720
15 TraesCS4B01G322500 chr3B 512425282 512426001 719 False 1062.000000 1062 93.343000 4598 5316 1 chr3B.!!$F2 718

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
866 917 0.109272 CTCGGCTACACACACGTCAT 60.109 55.0 0.00 0.00 0.00 3.06 F
1181 1244 0.040870 CGTCTCGGATCTGATGGTCG 60.041 60.0 4.28 0.55 0.00 4.79 F
1732 1834 0.032403 TGCACATGTTTCTTGCCAGC 59.968 50.0 0.00 0.00 35.26 4.85 F
1779 1914 0.032815 TTGTCACGTCGGAATGCTGA 59.967 50.0 0.00 0.00 0.00 4.26 F
2739 2876 0.820871 TTCCCAACAAAAGCGCAACT 59.179 45.0 11.47 0.00 0.00 3.16 F
3365 3504 0.259938 AATGGCAAGAGGTGATCCCC 59.740 55.0 0.00 0.00 0.00 4.81 F
5143 5322 0.522626 TTGCCATGTCGTGCAATCTG 59.477 50.0 3.34 0.00 42.19 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 1818 1.032014 AACGCTGGCAAGAAACATGT 58.968 45.000 0.00 0.00 0.00 3.21 R
2966 3103 0.950836 TGGTTTGATGCAACTGACCG 59.049 50.000 12.25 0.00 0.00 4.79 R
3155 3294 4.161942 CAGGGAAACATGGCCAAATTGATA 59.838 41.667 10.96 0.00 38.79 2.15 R
3241 3380 7.792763 ATACAAGTGTAAGACGGAAGTAATGCA 60.793 37.037 0.00 0.00 38.18 3.96 R
4009 4182 2.271777 ACTTATTTTGGGACGGAGGGA 58.728 47.619 0.00 0.00 0.00 4.20 R
5336 5516 0.530211 CGATCTTCTGCTGCTGGGAG 60.530 60.000 6.69 5.76 34.52 4.30 R
6118 6319 0.030908 CTTCTCAGGGGTACGATCGC 59.969 60.000 16.60 0.00 0.00 4.58 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
22 23 1.666311 GCGTGATATCCTACGAGCACC 60.666 57.143 17.12 0.00 42.54 5.01
23 24 1.607148 CGTGATATCCTACGAGCACCA 59.393 52.381 9.38 0.00 42.54 4.17
50 52 3.367646 TCACACCGGATAGAAGTCTCT 57.632 47.619 9.46 0.00 35.52 3.10
83 86 2.409378 CGCAATGGATCAAAGTGCAAAC 59.591 45.455 16.89 0.00 34.87 2.93
99 102 0.947244 AAACGCAGCAAGGAGAACTG 59.053 50.000 0.00 0.00 34.48 3.16
162 165 3.882888 AGGAACTGCAATCGAAGAAACAA 59.117 39.130 0.00 0.00 37.45 2.83
172 175 6.861055 GCAATCGAAGAAACAAAATCACCTTA 59.139 34.615 0.00 0.00 43.58 2.69
173 176 7.542130 GCAATCGAAGAAACAAAATCACCTTAT 59.458 33.333 0.00 0.00 43.58 1.73
319 336 4.202461 ACAGACCTACAGAAAAAGCATCCA 60.202 41.667 0.00 0.00 0.00 3.41
324 341 2.795329 ACAGAAAAAGCATCCATCCGT 58.205 42.857 0.00 0.00 0.00 4.69
376 398 1.151810 AGAAGTGGGGAAGGGAGCA 60.152 57.895 0.00 0.00 0.00 4.26
757 796 1.141019 GGTGGTAGCGATGCGAGAA 59.859 57.895 0.00 0.00 0.00 2.87
798 849 3.083997 GGTGGAGCCAGACCGGAT 61.084 66.667 9.46 0.00 36.56 4.18
800 851 1.742768 GTGGAGCCAGACCGGATAG 59.257 63.158 9.46 0.00 36.56 2.08
845 896 2.902846 CGGTCGCACCACCCAAAA 60.903 61.111 6.21 0.00 38.47 2.44
853 904 0.609131 CACCACCCAAAATCTCGGCT 60.609 55.000 0.00 0.00 0.00 5.52
854 905 0.988832 ACCACCCAAAATCTCGGCTA 59.011 50.000 0.00 0.00 0.00 3.93
855 906 1.339727 ACCACCCAAAATCTCGGCTAC 60.340 52.381 0.00 0.00 0.00 3.58
856 907 1.339631 CCACCCAAAATCTCGGCTACA 60.340 52.381 0.00 0.00 0.00 2.74
866 917 0.109272 CTCGGCTACACACACGTCAT 60.109 55.000 0.00 0.00 0.00 3.06
1041 1097 4.755614 GCGCTCCTCGTCGTCGTT 62.756 66.667 0.00 0.00 41.07 3.85
1047 1103 3.164011 CTCGTCGTCGTTGTCGCC 61.164 66.667 1.33 0.00 38.33 5.54
1109 1165 1.519455 CGGATCGGAAGGTCAGTGC 60.519 63.158 0.00 0.00 45.13 4.40
1146 1209 1.363443 CCGCTCCTCAGATCTCAGC 59.637 63.158 0.00 0.00 0.00 4.26
1181 1244 0.040870 CGTCTCGGATCTGATGGTCG 60.041 60.000 4.28 0.55 0.00 4.79
1183 1246 1.405821 GTCTCGGATCTGATGGTCGTT 59.594 52.381 4.28 0.00 0.00 3.85
1186 1249 1.548719 TCGGATCTGATGGTCGTTTGT 59.451 47.619 0.00 0.00 0.00 2.83
1343 1409 2.817665 ACCTACACAAGTACTCCCTCC 58.182 52.381 0.00 0.00 0.00 4.30
1350 1416 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
1351 1417 0.614134 AGTACTCCCTCCGTCCCAAC 60.614 60.000 0.00 0.00 0.00 3.77
1352 1418 0.901580 GTACTCCCTCCGTCCCAACA 60.902 60.000 0.00 0.00 0.00 3.33
1370 1436 5.393027 CCCAACACAATATAAGAGCGCTTTT 60.393 40.000 17.98 17.98 35.56 2.27
1413 1479 7.478667 CAGTGTCAAAAACGCTCTTATATTGTC 59.521 37.037 0.00 0.00 45.69 3.18
1414 1480 7.172532 AGTGTCAAAAACGCTCTTATATTGTCA 59.827 33.333 0.00 0.00 45.69 3.58
1417 1483 7.688578 GTCAAAAACGCTCTTATATTGTCAGAC 59.311 37.037 0.00 0.00 0.00 3.51
1427 1493 0.898320 ATTGTCAGACGGAGGGAGTG 59.102 55.000 0.00 0.00 0.00 3.51
1433 1499 1.137086 CAGACGGAGGGAGTGGTAATG 59.863 57.143 0.00 0.00 0.00 1.90
1434 1500 0.179081 GACGGAGGGAGTGGTAATGC 60.179 60.000 0.00 0.00 0.00 3.56
1478 1544 0.736636 ATTGACATGCTGCGATGTGG 59.263 50.000 17.99 0.00 36.67 4.17
1489 1555 2.345876 TGCGATGTGGTTCATGTAGTG 58.654 47.619 0.00 0.00 36.83 2.74
1566 1632 2.439880 TGGTCACCAGTATCCACAAACA 59.560 45.455 0.00 0.00 0.00 2.83
1622 1701 5.458779 GCCGTGAATATTTTTACCAGAATGC 59.541 40.000 0.00 0.00 31.97 3.56
1644 1723 9.461312 AATGCAAAATAGGTCACTGTATTAGAA 57.539 29.630 0.00 0.00 0.00 2.10
1708 1810 8.732746 AGCATTAACTAGAATTATTCCGTTGT 57.267 30.769 15.67 3.42 0.00 3.32
1709 1811 8.612619 AGCATTAACTAGAATTATTCCGTTGTG 58.387 33.333 15.67 14.55 0.00 3.33
1716 1818 4.759693 AGAATTATTCCGTTGTGAAGTGCA 59.240 37.500 0.78 0.00 0.00 4.57
1729 1831 2.223782 TGAAGTGCACATGTTTCTTGCC 60.224 45.455 21.04 0.00 35.26 4.52
1732 1834 0.032403 TGCACATGTTTCTTGCCAGC 59.968 50.000 0.00 0.00 35.26 4.85
1745 1847 7.119992 TGTTTCTTGCCAGCGTTATTCTAATAA 59.880 33.333 0.00 0.00 0.00 1.40
1766 1901 8.970691 AATAATCTGTTTGTGCTATTTGTCAC 57.029 30.769 0.00 0.00 0.00 3.67
1779 1914 0.032815 TTGTCACGTCGGAATGCTGA 59.967 50.000 0.00 0.00 0.00 4.26
1845 1982 3.963428 GAGCCTGTCTCCAAAGTCTTA 57.037 47.619 0.00 0.00 35.77 2.10
1902 2039 1.772182 CGATCAGAGCATTCGGTACC 58.228 55.000 0.16 0.16 0.00 3.34
1945 2082 7.974501 GTCTCAGTAGTATTCTTCCGATTGAAA 59.025 37.037 0.00 0.00 31.06 2.69
2046 2183 8.133024 AGATTCTTCACTTAGATGTCTTGACT 57.867 34.615 2.35 0.00 0.00 3.41
2124 2261 4.999950 CAGCTTGTTGTCTTTCAGGATAGT 59.000 41.667 0.00 0.00 0.00 2.12
2154 2291 3.600433 TCTGTCCCCTTACCCTGTTAAA 58.400 45.455 0.00 0.00 0.00 1.52
2440 2577 4.352595 TGAAGGGTGAATTCTCCAGGTTTA 59.647 41.667 24.13 10.85 0.00 2.01
2450 2587 6.627087 ATTCTCCAGGTTTATCTCTGTTCA 57.373 37.500 0.00 0.00 0.00 3.18
2452 2589 6.627087 TCTCCAGGTTTATCTCTGTTCAAT 57.373 37.500 0.00 0.00 0.00 2.57
2453 2590 7.020827 TCTCCAGGTTTATCTCTGTTCAATT 57.979 36.000 0.00 0.00 0.00 2.32
2456 2593 8.477419 TCCAGGTTTATCTCTGTTCAATTTTT 57.523 30.769 0.00 0.00 0.00 1.94
2485 2622 6.695292 TTAAGTAGCTTAACTTGTACGTGC 57.305 37.500 11.42 0.00 39.95 5.34
2500 2637 1.269569 ACGTGCGTTGAGAAGTCATGA 60.270 47.619 0.00 0.00 30.85 3.07
2510 2647 6.536582 CGTTGAGAAGTCATGACCAGAAATAT 59.463 38.462 22.21 0.00 30.85 1.28
2739 2876 0.820871 TTCCCAACAAAAGCGCAACT 59.179 45.000 11.47 0.00 0.00 3.16
2773 2910 5.982516 TGAATGCTTTTACATGTCCAACAAC 59.017 36.000 0.00 0.00 0.00 3.32
2966 3103 5.294552 AGAAAAGCTCATCGTAAAGGTATGC 59.705 40.000 0.00 0.00 0.00 3.14
3048 3185 8.134202 TCTTTGATCTATTGAGTTCCACTGTA 57.866 34.615 0.00 0.00 0.00 2.74
3062 3199 5.836024 TCCACTGTACCAGACCTAATTTT 57.164 39.130 0.00 0.00 35.18 1.82
3149 3288 6.951971 AGCTTTAGATCCTCTTAACACACAT 58.048 36.000 0.00 0.00 0.00 3.21
3155 3294 9.739276 TTAGATCCTCTTAACACACATGAAAAT 57.261 29.630 0.00 0.00 0.00 1.82
3241 3380 6.751888 GCGCTTCCAGTAATGTGAATAATTTT 59.248 34.615 0.00 0.00 0.00 1.82
3253 3392 8.633075 ATGTGAATAATTTTGCATTACTTCCG 57.367 30.769 0.00 0.00 0.00 4.30
3360 3499 3.499338 ACAAATCAATGGCAAGAGGTGA 58.501 40.909 0.00 0.00 0.00 4.02
3365 3504 0.259938 AATGGCAAGAGGTGATCCCC 59.740 55.000 0.00 0.00 0.00 4.81
3367 3506 2.190578 GCAAGAGGTGATCCCCCG 59.809 66.667 0.00 0.00 0.00 5.73
3378 3517 2.305927 GTGATCCCCCGTTGGATGATAT 59.694 50.000 7.62 0.00 45.25 1.63
3765 3933 5.522460 GTGAAGTTGTGAACTGTAGCTAACA 59.478 40.000 0.00 0.00 41.91 2.41
3966 4139 8.107095 TGAGGTACAATTACTTTAAGCCTCAAT 58.893 33.333 9.95 0.00 44.51 2.57
4009 4182 8.214364 GGATCAAGGACTCAGGAAAAATATACT 58.786 37.037 0.00 0.00 0.00 2.12
4123 4296 4.338400 AGTTCAAAACCAGCTGTCTAAACC 59.662 41.667 13.81 0.00 0.00 3.27
4136 4309 6.025896 GCTGTCTAAACCGCCTTATAAAAAC 58.974 40.000 0.00 0.00 30.10 2.43
4154 4327 5.349061 AAAACGAACGGAGGGAGTATAAT 57.651 39.130 0.00 0.00 0.00 1.28
4185 4358 8.882415 ACTAAAGTTGAGACACTTATTTTCGA 57.118 30.769 0.00 0.00 35.87 3.71
4193 4366 5.238583 AGACACTTATTTTCGAACAGAGGG 58.761 41.667 0.00 0.00 0.00 4.30
4211 4384 7.440198 ACAGAGGGAGTACAAAGTTAACTTAC 58.560 38.462 20.83 15.09 34.61 2.34
4260 4433 9.899661 TGTGGAGCAATGTAATAACTTATAACT 57.100 29.630 0.00 0.00 0.00 2.24
4277 4450 8.548877 ACTTATAACTAGGAAAGCATTGAAGGA 58.451 33.333 0.00 0.00 0.00 3.36
4314 4487 6.771267 CCCAAAAGGTTGTTTAGTCTAGTTCT 59.229 38.462 0.00 0.00 32.40 3.01
4545 4719 5.757850 ACTGGAACTGAACATCAAGTTTC 57.242 39.130 0.00 0.00 41.51 2.78
4623 4797 4.630111 TGCAGATCAAATTTGAACCCAAC 58.370 39.130 23.91 12.23 41.13 3.77
4629 4803 7.485913 CAGATCAAATTTGAACCCAACGATTAG 59.514 37.037 23.91 0.00 41.13 1.73
4810 4986 3.693085 TGCTGATTTCTGATGGCTCTTTC 59.307 43.478 0.00 0.00 0.00 2.62
4855 5031 0.529378 CTGTTCAGCAAATCCAGGGC 59.471 55.000 0.00 0.00 0.00 5.19
4919 5095 3.937814 TCATTGCACGATTTGTCTAGGT 58.062 40.909 0.00 0.00 0.00 3.08
5075 5251 1.599542 GCTCAACAAACTTCTGCGACT 59.400 47.619 0.00 0.00 0.00 4.18
5143 5322 0.522626 TTGCCATGTCGTGCAATCTG 59.477 50.000 3.34 0.00 42.19 2.90
5336 5516 5.676331 GCAAGACATAGAAAACCGGATTTCC 60.676 44.000 27.80 15.39 39.59 3.13
5429 5610 4.240175 AGCGAATCCGGTCTTATCTTAC 57.760 45.455 0.00 0.00 43.77 2.34
5432 5613 4.386049 GCGAATCCGGTCTTATCTTACATG 59.614 45.833 0.00 0.00 36.06 3.21
5520 5702 3.133183 CCTAGTTCCTGAGGCTAGGTTTC 59.867 52.174 18.78 0.00 44.07 2.78
5521 5703 1.909986 AGTTCCTGAGGCTAGGTTTCC 59.090 52.381 0.00 0.00 38.99 3.13
5546 5732 7.965655 CCTAGACTCTGTAATGTGATATAAGCG 59.034 40.741 0.00 0.00 0.00 4.68
5549 5735 5.011125 ACTCTGTAATGTGATATAAGCGCCT 59.989 40.000 2.29 0.00 0.00 5.52
5640 5835 3.889538 GGACTCCTTTTGCTTAAGTGGTT 59.110 43.478 4.02 0.00 0.00 3.67
5663 5863 3.500448 TGTTCCAGATTAGTGGTGCAA 57.500 42.857 0.00 0.00 38.88 4.08
5666 5866 4.832266 TGTTCCAGATTAGTGGTGCAATTT 59.168 37.500 0.00 0.00 38.88 1.82
5674 5874 6.435277 AGATTAGTGGTGCAATTTCATCTGTT 59.565 34.615 0.00 0.00 0.00 3.16
5820 6020 0.877071 ACTTGGCAAGTTCATGAGCG 59.123 50.000 26.54 0.47 39.04 5.03
5836 6036 6.106003 TCATGAGCGACTTTATTTGCTTCTA 58.894 36.000 0.00 0.00 37.91 2.10
5933 6134 0.824759 CCCGAAGATCGTCCTCCTTT 59.175 55.000 2.90 0.00 38.40 3.11
6012 6213 2.346803 GTCCTTTGTGCAAGCGATAGA 58.653 47.619 0.00 0.00 39.76 1.98
6139 6340 0.389757 GATCGTACCCCTGAGAAGGC 59.610 60.000 0.00 0.00 0.00 4.35
6245 6446 3.489229 GGCGAGGAGGCATTAACAAAATC 60.489 47.826 0.00 0.00 45.92 2.17
6260 6461 4.521062 ATCGGCAGTGAGAGCGCC 62.521 66.667 2.29 0.00 42.64 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.632377 CGGTGTGAAGAATATGGTGCT 58.368 47.619 0.00 0.00 0.00 4.40
22 23 6.516718 ACTTCTATCCGGTGTGAAGAATATG 58.483 40.000 26.69 11.82 39.17 1.78
23 24 6.551601 AGACTTCTATCCGGTGTGAAGAATAT 59.448 38.462 26.69 13.13 39.17 1.28
67 70 3.863681 GCGTTTGCACTTTGATCCA 57.136 47.368 0.00 0.00 42.15 3.41
83 86 1.294659 GGTCAGTTCTCCTTGCTGCG 61.295 60.000 0.00 0.00 0.00 5.18
99 102 1.387295 GCTTGGCTTGCCCATAGGTC 61.387 60.000 9.35 0.00 44.89 3.85
188 196 8.570038 TCCTGTTCCCATACCAACTAAATATA 57.430 34.615 0.00 0.00 0.00 0.86
190 198 6.894735 TCCTGTTCCCATACCAACTAAATA 57.105 37.500 0.00 0.00 0.00 1.40
192 200 5.311121 TCTTCCTGTTCCCATACCAACTAAA 59.689 40.000 0.00 0.00 0.00 1.85
193 201 4.847512 TCTTCCTGTTCCCATACCAACTAA 59.152 41.667 0.00 0.00 0.00 2.24
195 203 3.256704 TCTTCCTGTTCCCATACCAACT 58.743 45.455 0.00 0.00 0.00 3.16
203 219 3.053991 TCAACTGTTTCTTCCTGTTCCCA 60.054 43.478 0.00 0.00 0.00 4.37
206 222 4.036734 TGCATCAACTGTTTCTTCCTGTTC 59.963 41.667 0.00 0.00 0.00 3.18
207 223 3.953612 TGCATCAACTGTTTCTTCCTGTT 59.046 39.130 0.00 0.00 0.00 3.16
210 226 3.953612 TGTTGCATCAACTGTTTCTTCCT 59.046 39.130 10.52 0.00 43.85 3.36
376 398 1.828660 CTCCGCCTCCTCGTGGTAT 60.829 63.158 2.99 0.00 34.83 2.73
636 661 2.801579 GATAGAGTAGGCGCGCGC 60.802 66.667 44.40 44.40 41.06 6.86
637 662 1.154376 GAGATAGAGTAGGCGCGCG 60.154 63.158 28.44 28.44 0.00 6.86
639 664 0.889638 TGGGAGATAGAGTAGGCGCG 60.890 60.000 0.00 0.00 0.00 6.86
641 666 0.875728 CGTGGGAGATAGAGTAGGCG 59.124 60.000 0.00 0.00 0.00 5.52
643 668 1.249407 GCCGTGGGAGATAGAGTAGG 58.751 60.000 0.00 0.00 0.00 3.18
645 670 0.471191 TCGCCGTGGGAGATAGAGTA 59.529 55.000 0.00 0.00 0.00 2.59
741 780 0.179111 CCTTTCTCGCATCGCTACCA 60.179 55.000 0.00 0.00 0.00 3.25
797 848 1.320344 TGCGACTTCCGACTGGCTAT 61.320 55.000 0.00 0.00 41.76 2.97
798 849 1.934220 CTGCGACTTCCGACTGGCTA 61.934 60.000 0.00 0.00 41.76 3.93
800 851 2.811317 CTGCGACTTCCGACTGGC 60.811 66.667 0.00 0.00 41.76 4.85
845 896 0.170561 GACGTGTGTGTAGCCGAGAT 59.829 55.000 0.00 0.00 0.00 2.75
853 904 4.517832 AGACAAGAGTATGACGTGTGTGTA 59.482 41.667 0.00 0.00 31.12 2.90
854 905 3.318275 AGACAAGAGTATGACGTGTGTGT 59.682 43.478 0.00 0.00 31.12 3.72
855 906 3.902150 AGACAAGAGTATGACGTGTGTG 58.098 45.455 0.00 0.00 31.12 3.82
856 907 4.278669 AGAAGACAAGAGTATGACGTGTGT 59.721 41.667 0.00 0.00 31.12 3.72
866 917 2.168496 CCGTGGGAGAAGACAAGAGTA 58.832 52.381 0.00 0.00 0.00 2.59
1124 1187 3.532155 GATCTGAGGAGCGGGCGT 61.532 66.667 0.00 0.00 0.00 5.68
1156 1219 1.530323 TCAGATCCGAGACGTCAACA 58.470 50.000 19.50 0.00 0.00 3.33
1181 1244 2.329379 ACGCGAGAGAAGATCACAAAC 58.671 47.619 15.93 0.00 0.00 2.93
1183 1246 2.328473 CAACGCGAGAGAAGATCACAA 58.672 47.619 15.93 0.00 0.00 3.33
1186 1249 0.243636 TGCAACGCGAGAGAAGATCA 59.756 50.000 15.93 0.00 0.00 2.92
1343 1409 3.245284 CGCTCTTATATTGTGTTGGGACG 59.755 47.826 0.00 0.00 0.00 4.79
1350 1416 5.411361 TGTCAAAAGCGCTCTTATATTGTGT 59.589 36.000 12.06 0.00 31.02 3.72
1351 1417 5.734498 GTGTCAAAAGCGCTCTTATATTGTG 59.266 40.000 12.06 0.00 31.02 3.33
1352 1418 5.643777 AGTGTCAAAAGCGCTCTTATATTGT 59.356 36.000 12.06 0.00 31.02 2.71
1389 1455 7.295201 TGACAATATAAGAGCGTTTTTGACAC 58.705 34.615 0.00 0.00 0.00 3.67
1413 1479 1.137086 CATTACCACTCCCTCCGTCTG 59.863 57.143 0.00 0.00 0.00 3.51
1414 1480 1.486211 CATTACCACTCCCTCCGTCT 58.514 55.000 0.00 0.00 0.00 4.18
1417 1483 0.541863 AAGCATTACCACTCCCTCCG 59.458 55.000 0.00 0.00 0.00 4.63
1427 1493 2.287308 TGACACGCACAAAAGCATTACC 60.287 45.455 0.00 0.00 0.00 2.85
1455 1521 1.002792 CATCGCAGCATGTCAATCAGG 60.003 52.381 0.00 0.00 39.31 3.86
1478 1544 6.426980 TCATGAAATGCTCACTACATGAAC 57.573 37.500 0.00 0.00 46.21 3.18
1489 1555 3.004524 GGCCTCAGATTCATGAAATGCTC 59.995 47.826 13.09 5.43 46.21 4.26
1591 1657 4.965119 AAAAATATTCACGGCTGAGACC 57.035 40.909 0.00 0.00 0.00 3.85
1607 1673 8.592809 TGACCTATTTTGCATTCTGGTAAAAAT 58.407 29.630 0.00 0.00 36.27 1.82
1689 1791 7.360946 GCACTTCACAACGGAATAATTCTAGTT 60.361 37.037 0.00 0.00 33.37 2.24
1694 1796 4.851558 GTGCACTTCACAACGGAATAATTC 59.148 41.667 10.32 0.00 44.98 2.17
1697 1799 3.889196 GTGCACTTCACAACGGAATAA 57.111 42.857 10.32 0.00 44.98 1.40
1708 1810 2.223782 GGCAAGAAACATGTGCACTTCA 60.224 45.455 19.41 0.00 40.12 3.02
1709 1811 2.223782 TGGCAAGAAACATGTGCACTTC 60.224 45.455 19.41 13.08 40.12 3.01
1716 1818 1.032014 AACGCTGGCAAGAAACATGT 58.968 45.000 0.00 0.00 0.00 3.21
1729 1831 9.425893 CACAAACAGATTATTAGAATAACGCTG 57.574 33.333 17.06 17.06 39.72 5.18
1745 1847 4.515191 ACGTGACAAATAGCACAAACAGAT 59.485 37.500 0.00 0.00 34.78 2.90
1766 1901 2.540515 AGTAACATCAGCATTCCGACG 58.459 47.619 0.00 0.00 0.00 5.12
1836 1973 3.888930 TGGGAAAAGCCAGTAAGACTTTG 59.111 43.478 0.00 0.00 38.95 2.77
1845 1982 1.133199 TGGATGTTGGGAAAAGCCAGT 60.133 47.619 0.00 0.00 38.95 4.00
1902 2039 1.348036 AGACCCTTCACTTTTCCCTCG 59.652 52.381 0.00 0.00 0.00 4.63
1945 2082 2.664402 ACACCAGAAGGCTCAACAAT 57.336 45.000 0.00 0.00 39.06 2.71
2046 2183 5.001232 GGCTGGAGAAAGTGTGTAAATACA 58.999 41.667 0.00 0.00 0.00 2.29
2124 2261 4.287552 GGTAAGGGGACAGATAGTGAGAA 58.712 47.826 0.00 0.00 0.00 2.87
2133 2270 3.278987 TTAACAGGGTAAGGGGACAGA 57.721 47.619 0.00 0.00 0.00 3.41
2139 2276 3.585732 TCTGGACTTTAACAGGGTAAGGG 59.414 47.826 0.00 0.00 35.47 3.95
2154 2291 3.887352 TCTGATACTAAGCGTCTGGACT 58.113 45.455 0.00 0.00 0.00 3.85
2456 2593 9.919348 CGTACAAGTTAAGCTACTTAAAACAAA 57.081 29.630 1.56 0.00 37.62 2.83
2457 2594 9.097257 ACGTACAAGTTAAGCTACTTAAAACAA 57.903 29.630 1.56 0.00 37.62 2.83
2472 2609 3.352554 TCTCAACGCACGTACAAGTTA 57.647 42.857 0.00 0.00 0.00 2.24
2485 2622 3.303881 TCTGGTCATGACTTCTCAACG 57.696 47.619 24.50 4.61 0.00 4.10
2510 2647 8.349983 GCCTACAAACAGAAAAACAGAATTAGA 58.650 33.333 0.00 0.00 0.00 2.10
2521 2658 5.529800 GGTAGTCAAGCCTACAAACAGAAAA 59.470 40.000 0.00 0.00 39.26 2.29
2527 2664 3.995048 GACTGGTAGTCAAGCCTACAAAC 59.005 47.826 4.20 0.00 44.45 2.93
2676 2813 7.793927 AATAAATAGCAGCAGTACCTTCTTC 57.206 36.000 0.00 0.00 0.00 2.87
2739 2876 8.522003 ACATGTAAAAGCATTCAACATACATGA 58.478 29.630 21.35 0.00 45.93 3.07
2773 2910 2.094675 CCAGTTGGGTCTGCAATAAGG 58.905 52.381 0.00 0.00 34.47 2.69
2843 2980 8.607713 TCTTGAAGAGGTAAACCATAACCAATA 58.392 33.333 1.26 0.00 38.30 1.90
2966 3103 0.950836 TGGTTTGATGCAACTGACCG 59.049 50.000 12.25 0.00 0.00 4.79
3048 3185 9.699410 TCAAATGATATGAAAATTAGGTCTGGT 57.301 29.630 0.00 0.00 0.00 4.00
3102 3241 6.397217 TTGGGGCTTTCCTAAATAAGTACT 57.603 37.500 0.00 0.00 32.74 2.73
3149 3288 7.336427 GGAAACATGGCCAAATTGATATTTTCA 59.664 33.333 10.96 0.00 31.63 2.69
3155 3294 4.161942 CAGGGAAACATGGCCAAATTGATA 59.838 41.667 10.96 0.00 38.79 2.15
3241 3380 7.792763 ATACAAGTGTAAGACGGAAGTAATGCA 60.793 37.037 0.00 0.00 38.18 3.96
3395 3534 8.554835 TTTGTTACAACGATGAATAGGATGAA 57.445 30.769 0.00 0.00 0.00 2.57
4009 4182 2.271777 ACTTATTTTGGGACGGAGGGA 58.728 47.619 0.00 0.00 0.00 4.20
4123 4296 3.242188 CCTCCGTTCGTTTTTATAAGGCG 60.242 47.826 0.00 0.00 0.00 5.52
4136 4309 5.114081 ACAAAATTATACTCCCTCCGTTCG 58.886 41.667 0.00 0.00 0.00 3.95
4185 4358 6.496144 AGTTAACTTTGTACTCCCTCTGTT 57.504 37.500 1.12 0.00 0.00 3.16
4193 4366 9.525409 TCTGAGTTGTAAGTTAACTTTGTACTC 57.475 33.333 28.01 28.01 38.42 2.59
4255 4428 6.825721 CAGTCCTTCAATGCTTTCCTAGTTAT 59.174 38.462 0.00 0.00 0.00 1.89
4260 4433 3.587061 TCCAGTCCTTCAATGCTTTCCTA 59.413 43.478 0.00 0.00 0.00 2.94
4262 4435 2.795329 TCCAGTCCTTCAATGCTTTCC 58.205 47.619 0.00 0.00 0.00 3.13
4263 4436 4.012374 TCATCCAGTCCTTCAATGCTTTC 58.988 43.478 0.00 0.00 0.00 2.62
4314 4487 6.542005 CCACCATAACAAATATCACAGCAGTA 59.458 38.462 0.00 0.00 0.00 2.74
4394 4567 2.287977 AAGTAGTTTGGCACTTCCCC 57.712 50.000 0.00 0.00 36.88 4.81
4473 4646 2.706190 AGCACCCTGAACTTTCACTAGT 59.294 45.455 0.00 0.00 32.90 2.57
4475 4648 4.157246 TCTAGCACCCTGAACTTTCACTA 58.843 43.478 0.00 0.00 32.90 2.74
4477 4650 3.402628 TCTAGCACCCTGAACTTTCAC 57.597 47.619 0.00 0.00 32.90 3.18
4623 4797 5.181622 GGTCATGTCTCCTACCTACTAATCG 59.818 48.000 0.00 0.00 0.00 3.34
4629 4803 3.633418 AGTGGTCATGTCTCCTACCTAC 58.367 50.000 0.00 0.00 32.99 3.18
4855 5031 3.126514 CAGCTAAGCACTGGTGAAAGATG 59.873 47.826 4.79 3.68 34.02 2.90
4919 5095 2.233676 TGCAAGATTTAGCGTCTCCAGA 59.766 45.455 0.00 0.00 0.00 3.86
5118 5296 1.915614 GCACGACATGGCAAGGTCAG 61.916 60.000 18.74 14.27 36.92 3.51
5143 5322 0.727398 CGGAAAGGCGGTCAAGATTC 59.273 55.000 0.00 0.00 0.00 2.52
5336 5516 0.530211 CGATCTTCTGCTGCTGGGAG 60.530 60.000 6.69 5.76 34.52 4.30
5429 5610 8.200120 TGACCTTCAGTCTAATCACTAATCATG 58.800 37.037 0.00 0.00 46.46 3.07
5432 5613 8.637986 AGATGACCTTCAGTCTAATCACTAATC 58.362 37.037 0.00 0.00 46.46 1.75
5520 5702 7.965655 CGCTTATATCACATTACAGAGTCTAGG 59.034 40.741 0.00 0.00 0.00 3.02
5521 5703 7.483375 GCGCTTATATCACATTACAGAGTCTAG 59.517 40.741 0.00 0.00 0.00 2.43
5527 5711 5.468540 AGGCGCTTATATCACATTACAGA 57.531 39.130 7.64 0.00 0.00 3.41
5528 5712 7.652300 TTAAGGCGCTTATATCACATTACAG 57.348 36.000 7.64 0.00 0.00 2.74
5534 5720 7.744087 AAATGATTAAGGCGCTTATATCACA 57.256 32.000 15.51 5.28 32.37 3.58
5535 5721 7.538678 CCAAAATGATTAAGGCGCTTATATCAC 59.461 37.037 15.51 0.00 32.37 3.06
5579 5765 6.927381 CCCCATGATTTCTTTTTAGATGATGC 59.073 38.462 0.00 0.00 0.00 3.91
5580 5766 8.241497 TCCCCATGATTTCTTTTTAGATGATG 57.759 34.615 0.00 0.00 0.00 3.07
5581 5767 8.699130 GTTCCCCATGATTTCTTTTTAGATGAT 58.301 33.333 0.00 0.00 0.00 2.45
5583 5769 7.093377 TGGTTCCCCATGATTTCTTTTTAGATG 60.093 37.037 0.00 0.00 35.17 2.90
5584 5770 6.959366 TGGTTCCCCATGATTTCTTTTTAGAT 59.041 34.615 0.00 0.00 35.17 1.98
5585 5771 6.210584 GTGGTTCCCCATGATTTCTTTTTAGA 59.789 38.462 0.00 0.00 44.35 2.10
5640 5835 5.172687 TGCACCACTAATCTGGAACAATA 57.827 39.130 0.00 0.00 38.70 1.90
5777 5977 9.466497 AGTTGGCTAGATTTTCATTCATTTCTA 57.534 29.630 0.00 0.00 0.00 2.10
5919 6120 3.369892 CCATGAACAAAGGAGGACGATCT 60.370 47.826 0.00 0.00 0.00 2.75
5933 6134 2.166459 GAGGTGATCGAGACCATGAACA 59.834 50.000 16.60 0.00 35.76 3.18
6012 6213 4.066646 AGCTTTGGCGTTAAAATTTGGT 57.933 36.364 0.00 0.00 44.37 3.67
6118 6319 0.030908 CTTCTCAGGGGTACGATCGC 59.969 60.000 16.60 0.00 0.00 4.58
6139 6340 1.879380 TGATGCTTCTTTTGACCACGG 59.121 47.619 0.88 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.