Multiple sequence alignment - TraesCS5A01G076900

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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 TraesCS5A01G076900 chr5A 100.000 5503 0 0 1 5503 92442140 92447642 0.000000e+00 10163.0
1 TraesCS5A01G076900 chr5A 88.218 348 39 2 3648 3994 106748637 106748291 1.100000e-111 414.0
2 TraesCS5A01G076900 chr5A 82.679 433 69 4 3140 3570 106749163 106748735 4.020000e-101 379.0
3 TraesCS5A01G076900 chr5A 76.103 544 94 27 1744 2276 106750522 106750004 9.150000e-63 252.0
4 TraesCS5A01G076900 chr5A 84.756 164 22 3 2412 2574 106749855 106749694 1.590000e-35 161.0
5 TraesCS5A01G076900 chr5B 93.704 5130 229 35 131 5217 103469980 103475058 0.000000e+00 7598.0
6 TraesCS5A01G076900 chr5B 94.505 4440 180 24 797 5217 105709920 105714314 0.000000e+00 6789.0
7 TraesCS5A01G076900 chr5B 82.110 872 130 21 3140 3994 105769860 105770722 0.000000e+00 723.0
8 TraesCS5A01G076900 chr5B 88.268 537 27 13 288 812 105701718 105702230 1.310000e-170 610.0
9 TraesCS5A01G076900 chr5B 86.413 368 45 5 3630 3994 103572170 103572535 1.110000e-106 398.0
10 TraesCS5A01G076900 chr5B 83.102 432 65 5 3140 3570 103571596 103572020 2.400000e-103 387.0
11 TraesCS5A01G076900 chr5B 89.716 282 10 8 1 282 105701102 105701364 5.280000e-90 342.0
12 TraesCS5A01G076900 chr5B 82.789 337 48 9 2707 3039 103571196 103571526 5.390000e-75 292.0
13 TraesCS5A01G076900 chr5B 75.671 559 105 27 1738 2281 103570220 103570762 3.290000e-62 250.0
14 TraesCS5A01G076900 chr5B 75.045 553 102 28 1738 2279 105768497 105769024 1.990000e-54 224.0
15 TraesCS5A01G076900 chr5B 85.629 167 21 3 2409 2574 103570906 103571070 7.330000e-39 172.0
16 TraesCS5A01G076900 chr5B 85.276 163 22 2 2406 2567 105769163 105769324 3.410000e-37 167.0
17 TraesCS5A01G076900 chr5B 82.000 100 10 5 1920 2018 103322539 103322631 1.640000e-10 78.7
18 TraesCS5A01G076900 chr5D 93.980 3555 174 20 1227 4761 97275311 97278845 0.000000e+00 5343.0
19 TraesCS5A01G076900 chr5D 92.597 878 48 11 1 867 97274101 97274972 0.000000e+00 1245.0
20 TraesCS5A01G076900 chr5D 84.453 759 83 17 4750 5503 97279640 97280368 0.000000e+00 715.0
21 TraesCS5A01G076900 chr5D 82.168 858 126 22 3140 3981 97325152 97325998 0.000000e+00 712.0
22 TraesCS5A01G076900 chr5D 75.269 558 110 24 1738 2280 97323771 97324315 1.980000e-59 241.0
23 TraesCS5A01G076900 chr5D 85.507 207 23 3 903 1109 97275047 97275246 5.590000e-50 209.0
24 TraesCS5A01G076900 chr5D 83.511 188 26 3 2384 2567 97324429 97324615 2.640000e-38 171.0
25 TraesCS5A01G076900 chr3D 81.342 477 79 9 5031 5501 524879146 524878674 4.020000e-101 379.0
26 TraesCS5A01G076900 chr3D 94.595 37 2 0 4948 4984 242073508 242073544 2.140000e-04 58.4
27 TraesCS5A01G076900 chr3D 94.595 37 2 0 4948 4984 242438015 242438051 2.140000e-04 58.4
28 TraesCS5A01G076900 chr2D 81.098 492 73 17 5023 5503 332513342 332513824 5.200000e-100 375.0
29 TraesCS5A01G076900 chr2D 79.704 473 80 14 5040 5503 586943991 586943526 1.480000e-85 327.0
30 TraesCS5A01G076900 chr2B 80.808 495 69 23 5023 5503 136816188 136815706 1.130000e-96 364.0
31 TraesCS5A01G076900 chr2B 80.612 490 75 17 5022 5503 137132030 137131553 1.460000e-95 361.0
32 TraesCS5A01G076900 chr2B 80.204 490 78 18 5022 5503 137703318 137702840 3.150000e-92 350.0
33 TraesCS5A01G076900 chr1A 79.796 490 79 17 5023 5503 321394211 321394689 6.830000e-89 339.0
34 TraesCS5A01G076900 chr1A 100.000 34 0 0 3302 3335 377013540 377013573 4.600000e-06 63.9
35 TraesCS5A01G076900 chr3A 81.019 432 67 13 5041 5462 55025875 55025449 4.110000e-86 329.0
36 TraesCS5A01G076900 chr2A 100.000 28 0 0 4957 4984 253969206 253969179 1.000000e-02 52.8


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 TraesCS5A01G076900 chr5A 92442140 92447642 5502 False 10163.000000 10163 100.000000 1 5503 1 chr5A.!!$F1 5502
1 TraesCS5A01G076900 chr5A 106748291 106750522 2231 True 301.500000 414 82.939000 1744 3994 4 chr5A.!!$R1 2250
2 TraesCS5A01G076900 chr5B 103469980 103475058 5078 False 7598.000000 7598 93.704000 131 5217 1 chr5B.!!$F2 5086
3 TraesCS5A01G076900 chr5B 105709920 105714314 4394 False 6789.000000 6789 94.505000 797 5217 1 chr5B.!!$F3 4420
4 TraesCS5A01G076900 chr5B 105701102 105702230 1128 False 476.000000 610 88.992000 1 812 2 chr5B.!!$F5 811
5 TraesCS5A01G076900 chr5B 105768497 105770722 2225 False 371.333333 723 80.810333 1738 3994 3 chr5B.!!$F6 2256
6 TraesCS5A01G076900 chr5B 103570220 103572535 2315 False 299.800000 398 82.720800 1738 3994 5 chr5B.!!$F4 2256
7 TraesCS5A01G076900 chr5D 97274101 97280368 6267 False 1878.000000 5343 89.134250 1 5503 4 chr5D.!!$F1 5502
8 TraesCS5A01G076900 chr5D 97323771 97325998 2227 False 374.666667 712 80.316000 1738 3981 3 chr5D.!!$F2 2243

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
894 1312 0.036732 ATTGACAGCCCTCGCAAAGA 59.963 50.000 0.00 0.0 37.52 2.52 F
989 1409 0.250295 TGTCTTCTTGGGAGCAACGG 60.250 55.000 0.00 0.0 0.00 4.44 F
1175 1601 1.068434 CTTCTCCTTCTCCTGGCGATC 59.932 57.143 0.00 0.0 0.00 3.69 F
1769 2209 1.276138 TGCGAGCCTGAAAATGAGAGA 59.724 47.619 0.00 0.0 0.00 3.10 F
3595 4097 0.824109 TGACTCGGTGAGGCCATAAG 59.176 55.000 5.01 0.0 36.76 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2601 0.984230 GGTGAGGACAGGATTGGACA 59.016 55.000 0.00 0.0 0.00 4.02 R
2148 2602 1.065854 CAGGTGAGGACAGGATTGGAC 60.066 57.143 0.00 0.0 0.00 4.02 R
2149 2603 1.279496 CAGGTGAGGACAGGATTGGA 58.721 55.000 0.00 0.0 0.00 3.53 R
3765 4370 1.739562 CTGCTTCTGCCTGTCGACC 60.740 63.158 14.12 0.0 38.71 4.79 R
4641 5249 0.541392 CACATCGACTGATTCCCCCA 59.459 55.000 0.00 0.0 30.49 4.96 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
58 59 1.811266 CGTCTGCCTCATTCACGGG 60.811 63.158 0.00 0.00 0.00 5.28
272 284 4.093703 CGCCGTACCATAGAGATAGAGAAG 59.906 50.000 0.00 0.00 0.00 2.85
273 285 4.396790 GCCGTACCATAGAGATAGAGAAGG 59.603 50.000 0.00 0.00 0.00 3.46
305 663 1.222567 GGAGAGAGAGAGGGGAGAGT 58.777 60.000 0.00 0.00 0.00 3.24
366 730 0.470341 GGGTGAGGATTGGGTAGCTC 59.530 60.000 0.00 0.00 0.00 4.09
383 747 0.610687 CTCTCTGTTCCTGTGGGGAC 59.389 60.000 0.00 0.00 45.03 4.46
603 977 3.988385 CGCGCGAATGATGACCGG 61.988 66.667 28.94 0.00 0.00 5.28
604 978 4.299316 GCGCGAATGATGACCGGC 62.299 66.667 12.10 0.00 0.00 6.13
644 1018 2.358737 GCCCACCACCTGTTCGAG 60.359 66.667 0.00 0.00 0.00 4.04
649 1023 0.532862 CACCACCTGTTCGAGCAAGT 60.533 55.000 2.85 0.00 0.00 3.16
712 1093 1.973281 CCATGGCTGCGAACAACCT 60.973 57.895 0.00 0.00 32.88 3.50
741 1122 2.202362 CGTCAGAGAGCCACGTCG 60.202 66.667 0.00 0.00 0.00 5.12
763 1144 1.294659 GCCACGGTTCTTGCTCTCAG 61.295 60.000 0.00 0.00 0.00 3.35
838 1219 7.717568 TCCTTACCGAATGATCTTTTCTCTAG 58.282 38.462 0.00 0.00 0.00 2.43
849 1230 7.155328 TGATCTTTTCTCTAGGTCTGTCAAAC 58.845 38.462 0.00 0.00 0.00 2.93
894 1312 0.036732 ATTGACAGCCCTCGCAAAGA 59.963 50.000 0.00 0.00 37.52 2.52
967 1387 4.424061 TGACGCCATTTTTCAATCTCAG 57.576 40.909 0.00 0.00 0.00 3.35
989 1409 0.250295 TGTCTTCTTGGGAGCAACGG 60.250 55.000 0.00 0.00 0.00 4.44
1022 1442 1.538419 GCCTACACGCCTACCTCAATC 60.538 57.143 0.00 0.00 0.00 2.67
1030 1450 1.952296 GCCTACCTCAATCATTGGCTG 59.048 52.381 0.00 0.00 36.32 4.85
1149 1569 4.621747 GCTGCTGTCTCTTGTTGGTATACT 60.622 45.833 2.25 0.00 0.00 2.12
1168 1594 4.140575 ACTTTCTCCTTCTCCTTCTCCT 57.859 45.455 0.00 0.00 0.00 3.69
1175 1601 1.068434 CTTCTCCTTCTCCTGGCGATC 59.932 57.143 0.00 0.00 0.00 3.69
1230 1656 4.774124 TGCAGTCTATATGCTTGCTCTTT 58.226 39.130 0.00 0.00 44.17 2.52
1231 1657 5.188434 TGCAGTCTATATGCTTGCTCTTTT 58.812 37.500 0.00 0.00 44.17 2.27
1250 1676 7.855409 GCTCTTTTCTTCTTCTTGTTCTTCTTC 59.145 37.037 0.00 0.00 0.00 2.87
1333 1759 2.810439 TATGGCTGTTTGTTTGTGCC 57.190 45.000 0.00 0.00 43.49 5.01
1488 1923 4.331968 TCACCACTCTTGTTCAACAGTTT 58.668 39.130 0.00 0.00 0.00 2.66
1522 1959 2.108566 CATCCTGCAGGGCGAGAG 59.891 66.667 32.23 12.05 35.41 3.20
1643 2080 3.104602 CTGCGCGGAGGCAAATCTG 62.105 63.158 21.08 0.00 43.39 2.90
1769 2209 1.276138 TGCGAGCCTGAAAATGAGAGA 59.724 47.619 0.00 0.00 0.00 3.10
2033 2480 3.500299 GGGAAGACTTCTCTTTTGCACTC 59.500 47.826 14.72 0.00 36.82 3.51
2087 2538 9.175312 CTATACTGTGTTACCTCAACTTCTCTA 57.825 37.037 0.00 0.00 38.05 2.43
2147 2601 7.331026 TCGTCATATTCCTGAGACTGAAAAAT 58.669 34.615 0.00 0.00 0.00 1.82
2148 2602 7.278646 TCGTCATATTCCTGAGACTGAAAAATG 59.721 37.037 0.00 0.00 0.00 2.32
2149 2603 7.065085 CGTCATATTCCTGAGACTGAAAAATGT 59.935 37.037 0.00 0.00 0.00 2.71
2151 2605 7.554118 TCATATTCCTGAGACTGAAAAATGTCC 59.446 37.037 0.00 0.00 34.02 4.02
2152 2606 4.705110 TCCTGAGACTGAAAAATGTCCA 57.295 40.909 0.00 0.00 34.02 4.02
2153 2607 5.047566 TCCTGAGACTGAAAAATGTCCAA 57.952 39.130 0.00 0.00 34.02 3.53
2155 2609 5.707298 TCCTGAGACTGAAAAATGTCCAATC 59.293 40.000 0.00 0.00 34.02 2.67
2156 2610 5.105997 CCTGAGACTGAAAAATGTCCAATCC 60.106 44.000 0.00 0.00 34.02 3.01
2164 2618 4.387026 AAAATGTCCAATCCTGTCCTCA 57.613 40.909 0.00 0.00 0.00 3.86
2293 2752 6.396829 AAGCTTGCCTATAAATTCACCATC 57.603 37.500 0.00 0.00 0.00 3.51
2296 2755 5.008613 GCTTGCCTATAAATTCACCATCGAA 59.991 40.000 0.00 0.00 0.00 3.71
2298 2757 7.581213 TTGCCTATAAATTCACCATCGAAAT 57.419 32.000 0.00 0.00 0.00 2.17
2318 2777 3.428746 TGACCGTTTTGAATTGTGTGG 57.571 42.857 0.00 0.00 0.00 4.17
2319 2778 2.124122 GACCGTTTTGAATTGTGTGGC 58.876 47.619 0.00 0.00 0.00 5.01
2321 2795 2.126467 CCGTTTTGAATTGTGTGGCTG 58.874 47.619 0.00 0.00 0.00 4.85
2497 2978 1.693606 CCTTTTGTTGAATGGGGTGCT 59.306 47.619 0.00 0.00 0.00 4.40
2659 3154 5.240183 TGAGAATCTGCTCAAAGGTTTTCTG 59.760 40.000 0.00 0.00 41.65 3.02
2813 3309 5.930135 ACTCCAAGTGTGTTGTCTATCTTT 58.070 37.500 0.00 0.00 0.00 2.52
2816 3312 6.353323 TCCAAGTGTGTTGTCTATCTTTTCA 58.647 36.000 0.00 0.00 0.00 2.69
3104 3606 4.092091 CAGTTACGGTGATTCTCTTTCTGC 59.908 45.833 0.00 0.00 0.00 4.26
3361 3863 4.516698 CCATACATGATTGGCAGGTTAGTC 59.483 45.833 0.00 0.00 38.59 2.59
3436 3938 8.980596 TCATAAATACAAGAATGGGCATTTCTT 58.019 29.630 7.78 7.78 0.00 2.52
3582 4084 2.959516 TCTGGTAAATGCTGTGACTCG 58.040 47.619 0.00 0.00 0.00 4.18
3595 4097 0.824109 TGACTCGGTGAGGCCATAAG 59.176 55.000 5.01 0.00 36.76 1.73
3765 4370 1.291184 TTGAGCAATGCCTGTCGTCG 61.291 55.000 0.00 0.00 0.00 5.12
3882 4487 0.693049 AACCAATGGGACGAGAAGCT 59.307 50.000 3.55 0.00 38.05 3.74
3928 4533 1.022735 GGTCGATCTCGCCTTCTACA 58.977 55.000 0.00 0.00 39.60 2.74
3984 4590 6.551601 CAGTCTATCAGGTATGTCCCTAGTTT 59.448 42.308 0.00 0.00 36.75 2.66
3985 4591 7.070074 CAGTCTATCAGGTATGTCCCTAGTTTT 59.930 40.741 0.00 0.00 36.75 2.43
4048 4654 3.181477 TGCACTTGGTTCAAATGACAAGG 60.181 43.478 14.53 7.66 43.36 3.61
4049 4655 3.181476 GCACTTGGTTCAAATGACAAGGT 60.181 43.478 14.53 2.87 43.36 3.50
4068 4674 5.599999 AGGTCCAGTAAGTACTATTGCTG 57.400 43.478 0.00 0.35 41.10 4.41
4077 4683 6.986817 AGTAAGTACTATTGCTGGTAATGCTG 59.013 38.462 0.00 0.00 34.13 4.41
4091 4697 8.946085 GCTGGTAATGCTGCTGTAAATATTATA 58.054 33.333 0.00 0.00 0.00 0.98
4125 4732 7.118390 GGCATAAAGCTTACATATCCTGTACAG 59.882 40.741 16.34 16.34 44.79 2.74
4340 4948 4.527038 AGTCACTTCAGGGATTTCGACTTA 59.473 41.667 0.00 0.00 0.00 2.24
4348 4956 1.931841 GGATTTCGACTTAGGGTTCGC 59.068 52.381 0.00 0.00 0.00 4.70
4433 5041 7.493320 GGCAATGTGTATGATCATTTCACAATT 59.507 33.333 30.99 24.78 37.67 2.32
4522 5130 1.859302 AGCCCCAACACTTTCAAACA 58.141 45.000 0.00 0.00 0.00 2.83
4533 5141 4.956075 ACACTTTCAAACAGGGAATCAGTT 59.044 37.500 0.00 0.00 0.00 3.16
4567 5175 0.969917 TTGCTGGTTTGTGTGTGGCT 60.970 50.000 0.00 0.00 0.00 4.75
4574 5182 2.884639 GGTTTGTGTGTGGCTCAATACT 59.115 45.455 0.00 0.00 31.66 2.12
4641 5249 2.846206 TGAAGCCCCAGTACATTCAGAT 59.154 45.455 0.00 0.00 0.00 2.90
4774 6188 5.050295 CGGTTCTTAAGTTTCAGTTCTGGAC 60.050 44.000 1.63 0.65 0.00 4.02
4777 6191 7.713942 GGTTCTTAAGTTTCAGTTCTGGACTTA 59.286 37.037 17.11 17.11 36.10 2.24
4782 6196 5.741011 AGTTTCAGTTCTGGACTTACAACA 58.259 37.500 0.00 0.00 36.10 3.33
4792 6206 9.313118 GTTCTGGACTTACAACATTCAAAATTT 57.687 29.630 0.00 0.00 0.00 1.82
4793 6207 8.870160 TCTGGACTTACAACATTCAAAATTTG 57.130 30.769 0.00 0.00 0.00 2.32
4854 6268 9.693157 CGGATGCTGAATTCAAAATTTTAAATC 57.307 29.630 9.88 3.01 0.00 2.17
4978 6399 2.993937 GGGACCAATAAACCATGACGA 58.006 47.619 0.00 0.00 0.00 4.20
4984 6405 5.562635 ACCAATAAACCATGACGAAGGTAA 58.437 37.500 0.00 0.00 37.07 2.85
5017 6438 9.280174 AGAAAATAAGTATTCTTGGTTCGTCAA 57.720 29.630 0.00 0.00 32.05 3.18
5026 6447 9.326339 GTATTCTTGGTTCGTCAAGTTATTTTC 57.674 33.333 12.71 0.00 43.25 2.29
5034 6455 7.378728 GGTTCGTCAAGTTATTTTCCAGAAAAG 59.621 37.037 10.96 0.00 42.72 2.27
5093 6514 9.190317 AGTTTTAAGTCAGATTTCCTCTTTTGT 57.810 29.630 0.00 0.00 29.16 2.83
5095 6516 8.746052 TTTAAGTCAGATTTCCTCTTTTGTCA 57.254 30.769 0.00 0.00 29.16 3.58
5180 6604 8.813643 TTCTATATCTTTTAAACGCTAGCTCC 57.186 34.615 13.93 0.00 0.00 4.70
5309 6735 1.341209 TCAATAGCGCATGATCCGTCT 59.659 47.619 11.47 0.00 0.00 4.18
5310 6736 1.723542 CAATAGCGCATGATCCGTCTC 59.276 52.381 11.47 0.00 0.00 3.36
5315 6741 2.036475 AGCGCATGATCCGTCTCTATTT 59.964 45.455 11.47 0.00 0.00 1.40
5317 6743 3.642705 CGCATGATCCGTCTCTATTTCA 58.357 45.455 0.00 0.00 0.00 2.69
5321 6747 3.995199 TGATCCGTCTCTATTTCATGCC 58.005 45.455 0.00 0.00 0.00 4.40
5322 6748 2.509052 TCCGTCTCTATTTCATGCCG 57.491 50.000 0.00 0.00 0.00 5.69
5326 6752 2.481276 CGTCTCTATTTCATGCCGGTGA 60.481 50.000 1.90 0.00 0.00 4.02
5345 6771 6.677781 GGTGACGATCCAGATTGAAAATAA 57.322 37.500 1.79 0.00 0.00 1.40
5346 6772 7.083875 GGTGACGATCCAGATTGAAAATAAA 57.916 36.000 1.79 0.00 0.00 1.40
5363 6789 7.708752 TGAAAATAAACACCTTAGCAAAACCAG 59.291 33.333 0.00 0.00 0.00 4.00
5368 6794 6.969993 AACACCTTAGCAAAACCAGAATTA 57.030 33.333 0.00 0.00 0.00 1.40
5373 6799 7.337942 CACCTTAGCAAAACCAGAATTAGAGAT 59.662 37.037 0.00 0.00 0.00 2.75
5394 6820 8.214364 AGAGATGAAAGAAACCATCTATAACCC 58.786 37.037 0.00 0.00 46.64 4.11
5397 6823 3.487120 AGAAACCATCTATAACCCCGC 57.513 47.619 0.00 0.00 36.32 6.13
5398 6824 2.775384 AGAAACCATCTATAACCCCGCA 59.225 45.455 0.00 0.00 36.32 5.69
5401 6827 1.271379 ACCATCTATAACCCCGCATGC 60.271 52.381 7.91 7.91 0.00 4.06
5402 6828 1.271325 CCATCTATAACCCCGCATGCA 60.271 52.381 19.57 0.00 0.00 3.96
5416 6842 1.936203 GCATGCACGCCTTGTCAAAAT 60.936 47.619 14.21 0.00 0.00 1.82
5422 6848 1.531149 ACGCCTTGTCAAAATCTCACG 59.469 47.619 0.00 0.00 0.00 4.35
5423 6849 1.135972 CGCCTTGTCAAAATCTCACGG 60.136 52.381 0.00 0.00 0.00 4.94
5456 6882 6.382608 TCGATTTCTTATCTTATGCCGAGAG 58.617 40.000 0.00 0.00 0.00 3.20
5460 6886 6.567687 TTCTTATCTTATGCCGAGAGAGAG 57.432 41.667 0.00 0.00 0.00 3.20
5461 6887 5.870706 TCTTATCTTATGCCGAGAGAGAGA 58.129 41.667 0.00 0.00 0.00 3.10
5462 6888 5.703592 TCTTATCTTATGCCGAGAGAGAGAC 59.296 44.000 0.00 0.00 0.00 3.36
5463 6889 2.214347 TCTTATGCCGAGAGAGAGACG 58.786 52.381 0.00 0.00 0.00 4.18
5464 6890 0.663688 TTATGCCGAGAGAGAGACGC 59.336 55.000 0.00 0.00 0.00 5.19
5469 6895 1.380524 CCGAGAGAGAGACGCCTTAA 58.619 55.000 0.00 0.00 0.00 1.85
5488 6914 6.516527 GCCTTAAGATTGACAACATCCAAACA 60.517 38.462 3.36 0.00 0.00 2.83
5490 6916 5.850557 AAGATTGACAACATCCAAACACA 57.149 34.783 0.00 0.00 0.00 3.72
5492 6918 7.523293 AAGATTGACAACATCCAAACACATA 57.477 32.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 194 4.570663 CGCGTCGAGGGGATGGTC 62.571 72.222 16.26 0.00 31.98 4.02
247 259 1.132643 CTATCTCTATGGTACGGCGGC 59.867 57.143 13.24 0.00 0.00 6.53
272 284 1.220750 TCTCTCCCCCTCTGTAATCCC 59.779 57.143 0.00 0.00 0.00 3.85
273 285 2.178106 TCTCTCTCCCCCTCTGTAATCC 59.822 54.545 0.00 0.00 0.00 3.01
343 706 4.856801 CCCAATCCTCACCCGCGG 62.857 72.222 21.04 21.04 0.00 6.46
346 710 1.146263 GCTACCCAATCCTCACCCG 59.854 63.158 0.00 0.00 0.00 5.28
383 747 5.798434 ACGTTTTTCTTTTCTTTTCTCACCG 59.202 36.000 0.00 0.00 0.00 4.94
551 925 0.458543 CTCATGTTCCAGACCCGACG 60.459 60.000 0.00 0.00 0.00 5.12
594 968 2.094757 AACAGTCACGCCGGTCATCA 62.095 55.000 1.90 0.00 0.00 3.07
603 977 2.047179 GGAGGGGAACAGTCACGC 60.047 66.667 0.00 0.00 0.00 5.34
604 978 1.592223 GAGGAGGGGAACAGTCACG 59.408 63.158 0.00 0.00 0.00 4.35
644 1018 3.057736 CCATAGCATAGCATGGAACTTGC 60.058 47.826 12.19 0.00 38.51 4.01
649 1023 3.009805 AGCATCCATAGCATAGCATGGAA 59.990 43.478 19.42 9.34 43.53 3.53
727 1108 2.202362 CGTCGACGTGGCTCTCTG 60.202 66.667 29.08 0.00 34.11 3.35
741 1122 2.665185 AGCAAGAACCGTGGCGTC 60.665 61.111 0.00 0.00 0.00 5.19
763 1144 3.513515 TGATCAAATTACCAGGCAAACCC 59.486 43.478 0.00 0.00 36.11 4.11
815 1196 7.493367 ACCTAGAGAAAAGATCATTCGGTAAG 58.507 38.462 0.00 0.00 32.04 2.34
838 1219 5.305585 TGGTGAAGATTAGTTTGACAGACC 58.694 41.667 0.00 0.00 0.00 3.85
967 1387 2.287009 CGTTGCTCCCAAGAAGACAAAC 60.287 50.000 0.00 0.00 0.00 2.93
989 1409 3.676324 GCGTGTAGGCATAGGATACCATC 60.676 52.174 0.00 0.00 37.17 3.51
1022 1442 6.509656 AGAATGCACAAATATACAGCCAATG 58.490 36.000 0.00 0.00 0.00 2.82
1030 1450 5.527582 ACCGAGGAAGAATGCACAAATATAC 59.472 40.000 0.00 0.00 0.00 1.47
1149 1569 3.177228 CCAGGAGAAGGAGAAGGAGAAA 58.823 50.000 0.00 0.00 0.00 2.52
1230 1656 7.495934 ACAATCGAAGAAGAACAAGAAGAAGAA 59.504 33.333 0.00 0.00 43.58 2.52
1231 1657 6.986817 ACAATCGAAGAAGAACAAGAAGAAGA 59.013 34.615 0.00 0.00 43.58 2.87
1250 1676 4.152402 CACTCCCAACTAAGACAACAATCG 59.848 45.833 0.00 0.00 0.00 3.34
1522 1959 0.750850 TACCTCTACCCATTCGCTGC 59.249 55.000 0.00 0.00 0.00 5.25
1529 1966 4.016479 TGGAAGAACTCTACCTCTACCCAT 60.016 45.833 0.00 0.00 0.00 4.00
1617 2054 1.964448 CCTCCGCGCAGATATACCA 59.036 57.895 8.75 0.00 0.00 3.25
1643 2080 5.882557 AGGTGGATTGAGATCATGTTACAAC 59.117 40.000 0.00 0.00 33.77 3.32
1735 2175 1.865655 GCTCGCAGATCGCATCACTAA 60.866 52.381 9.58 0.00 42.60 2.24
1769 2209 2.783135 CATAGCACTGGAGGTTGTTGT 58.217 47.619 0.00 0.00 0.00 3.32
2033 2480 3.755378 CCTTCATCAGACCACCAGAAAAG 59.245 47.826 0.00 0.00 0.00 2.27
2123 2577 6.968131 TTTTTCAGTCTCAGGAATATGACG 57.032 37.500 0.00 0.00 34.92 4.35
2147 2601 0.984230 GGTGAGGACAGGATTGGACA 59.016 55.000 0.00 0.00 0.00 4.02
2148 2602 1.065854 CAGGTGAGGACAGGATTGGAC 60.066 57.143 0.00 0.00 0.00 4.02
2149 2603 1.279496 CAGGTGAGGACAGGATTGGA 58.721 55.000 0.00 0.00 0.00 3.53
2151 2605 3.007940 TGTTACAGGTGAGGACAGGATTG 59.992 47.826 0.00 0.00 0.00 2.67
2152 2606 3.248024 TGTTACAGGTGAGGACAGGATT 58.752 45.455 0.00 0.00 0.00 3.01
2153 2607 2.834549 CTGTTACAGGTGAGGACAGGAT 59.165 50.000 4.14 0.00 35.32 3.24
2155 2609 1.338200 GCTGTTACAGGTGAGGACAGG 60.338 57.143 14.63 0.00 38.46 4.00
2156 2610 1.338200 GGCTGTTACAGGTGAGGACAG 60.338 57.143 14.63 0.00 40.40 3.51
2164 2618 4.821935 GCTTGGGCTGTTACAGGT 57.178 55.556 14.63 0.00 35.22 4.00
2198 2652 1.612199 GGGTTCGCAAAGGTGACCATA 60.612 52.381 3.63 0.00 32.18 2.74
2293 2752 4.737765 ACACAATTCAAAACGGTCATTTCG 59.262 37.500 0.00 0.00 0.00 3.46
2296 2755 4.367450 CCACACAATTCAAAACGGTCATT 58.633 39.130 0.00 0.00 0.00 2.57
2298 2757 2.480416 GCCACACAATTCAAAACGGTCA 60.480 45.455 0.00 0.00 0.00 4.02
2318 2777 6.141844 CGATGCATATTCTCATGAAAAACAGC 59.858 38.462 0.00 0.00 35.63 4.40
2319 2778 7.191551 ACGATGCATATTCTCATGAAAAACAG 58.808 34.615 0.00 0.00 35.63 3.16
2321 2795 9.669353 AATACGATGCATATTCTCATGAAAAAC 57.331 29.630 0.00 0.00 35.63 2.43
2371 2846 8.353684 TGAAGACAGTTATCTTGTATAGCTAGC 58.646 37.037 6.62 6.62 39.08 3.42
2659 3154 8.663911 TGATTCAAAACAAAAACAAATGACCTC 58.336 29.630 0.00 0.00 0.00 3.85
2813 3309 8.930760 CACAATTTCAAAACAGGTTAAAGTGAA 58.069 29.630 11.15 5.43 31.61 3.18
2816 3312 9.097257 CATCACAATTTCAAAACAGGTTAAAGT 57.903 29.630 0.00 0.00 0.00 2.66
3024 3526 2.629017 AACCAAGATGGGCAGGAAAT 57.371 45.000 0.87 0.00 43.37 2.17
3436 3938 4.593206 AGTCTCTTTCATGGTTACCACTGA 59.407 41.667 6.10 9.18 35.80 3.41
3582 4084 1.840635 AGGAAGACTTATGGCCTCACC 59.159 52.381 3.32 0.78 39.84 4.02
3765 4370 1.739562 CTGCTTCTGCCTGTCGACC 60.740 63.158 14.12 0.00 38.71 4.79
3882 4487 2.605601 TGCCAGAGCTCCTGCAGA 60.606 61.111 20.42 0.00 41.57 4.26
3928 4533 7.092891 TGTCCTTTCATAGTTATGGACATGACT 60.093 37.037 13.25 13.25 45.86 3.41
3984 4590 3.554934 ACTTCAGTCTGGTGCAAATGAA 58.445 40.909 0.00 0.00 0.00 2.57
3985 4591 3.213206 ACTTCAGTCTGGTGCAAATGA 57.787 42.857 0.00 0.00 0.00 2.57
4034 4640 5.531287 ACTTACTGGACCTTGTCATTTGAAC 59.469 40.000 0.00 0.00 33.68 3.18
4039 4645 7.735326 ATAGTACTTACTGGACCTTGTCATT 57.265 36.000 0.00 0.00 37.10 2.57
4048 4654 5.340439 ACCAGCAATAGTACTTACTGGAC 57.660 43.478 26.82 5.03 46.10 4.02
4049 4655 7.497595 CATTACCAGCAATAGTACTTACTGGA 58.502 38.462 26.82 14.16 46.10 3.86
4091 4697 8.980481 ATATGTAAGCTTTATGCCTGTAAACT 57.020 30.769 3.20 0.00 44.23 2.66
4281 4889 3.421919 TGTGGTGAATGCTGAATCTGA 57.578 42.857 0.00 0.00 0.00 3.27
4340 4948 2.032681 GTGAGCTTGGCGAACCCT 59.967 61.111 0.00 0.00 33.59 4.34
4348 4956 1.600636 TTGAAGGCCGTGAGCTTGG 60.601 57.895 0.00 0.00 43.05 3.61
4522 5130 5.441718 TTAGCAGATCAAACTGATTCCCT 57.558 39.130 0.00 0.00 37.20 4.20
4533 5141 3.018856 CCAGCAACCATTAGCAGATCAA 58.981 45.455 0.00 0.00 0.00 2.57
4626 5234 1.143684 CCCCCATCTGAATGTACTGGG 59.856 57.143 7.04 7.04 45.15 4.45
4641 5249 0.541392 CACATCGACTGATTCCCCCA 59.459 55.000 0.00 0.00 30.49 4.96
4808 6222 6.022163 TCCGTGGTTTGAAACTTAAAAACA 57.978 33.333 8.09 0.00 35.88 2.83
4827 6241 8.600449 TTTAAAATTTTGAATTCAGCATCCGT 57.400 26.923 13.76 0.00 0.00 4.69
5008 6429 5.934935 TCTGGAAAATAACTTGACGAACC 57.065 39.130 0.00 0.00 0.00 3.62
5017 6438 5.833131 TCAGGTGCTTTTCTGGAAAATAACT 59.167 36.000 8.64 6.86 39.29 2.24
5026 6447 3.571401 AGAAACATCAGGTGCTTTTCTGG 59.429 43.478 0.00 0.00 34.00 3.86
5034 6455 4.009675 TGATTACCAGAAACATCAGGTGC 58.990 43.478 3.46 0.00 35.62 5.01
5062 6483 7.875554 AGAGGAAATCTGACTTAAAACTGACTC 59.124 37.037 0.00 0.00 36.69 3.36
5093 6514 4.249638 CCCAATTATCAGGGGTTTCTGA 57.750 45.455 0.00 0.00 46.32 3.27
5264 6690 8.838649 ATTAAGGTTGCACCCTAAATAGAATT 57.161 30.769 1.94 0.00 39.75 2.17
5268 6694 7.639113 TTGATTAAGGTTGCACCCTAAATAG 57.361 36.000 1.94 0.00 39.75 1.73
5272 6698 5.592688 GCTATTGATTAAGGTTGCACCCTAA 59.407 40.000 1.94 1.15 39.75 2.69
5283 6709 4.201753 CGGATCATGCGCTATTGATTAAGG 60.202 45.833 17.80 7.89 0.00 2.69
5295 6721 2.071688 AATAGAGACGGATCATGCGC 57.928 50.000 0.00 0.00 33.30 6.09
5309 6735 1.478916 TCGTCACCGGCATGAAATAGA 59.521 47.619 0.00 0.00 33.95 1.98
5310 6736 1.934589 TCGTCACCGGCATGAAATAG 58.065 50.000 0.00 0.00 33.95 1.73
5315 6741 2.296814 CTGGATCGTCACCGGCATGA 62.297 60.000 0.00 0.00 33.95 3.07
5317 6743 1.402896 ATCTGGATCGTCACCGGCAT 61.403 55.000 0.00 0.00 34.13 4.40
5321 6747 2.293677 TTCAATCTGGATCGTCACCG 57.706 50.000 0.00 0.00 0.00 4.94
5322 6748 6.677781 TTATTTTCAATCTGGATCGTCACC 57.322 37.500 0.00 0.00 0.00 4.02
5326 6752 6.659242 AGGTGTTTATTTTCAATCTGGATCGT 59.341 34.615 0.00 0.00 0.00 3.73
5329 6755 8.470002 GCTAAGGTGTTTATTTTCAATCTGGAT 58.530 33.333 0.00 0.00 0.00 3.41
5344 6770 5.869649 ATTCTGGTTTTGCTAAGGTGTTT 57.130 34.783 0.00 0.00 0.00 2.83
5345 6771 5.869649 AATTCTGGTTTTGCTAAGGTGTT 57.130 34.783 0.00 0.00 0.00 3.32
5346 6772 6.303839 TCTAATTCTGGTTTTGCTAAGGTGT 58.696 36.000 0.00 0.00 0.00 4.16
5360 6786 7.928307 TGGTTTCTTTCATCTCTAATTCTGG 57.072 36.000 0.00 0.00 0.00 3.86
5368 6794 8.214364 GGGTTATAGATGGTTTCTTTCATCTCT 58.786 37.037 8.81 3.46 44.63 3.10
5373 6799 5.433526 CGGGGTTATAGATGGTTTCTTTCA 58.566 41.667 0.00 0.00 35.79 2.69
5394 6820 4.465512 GACAAGGCGTGCATGCGG 62.466 66.667 23.96 17.65 35.06 5.69
5397 6823 1.987770 GATTTTGACAAGGCGTGCATG 59.012 47.619 0.09 0.09 0.00 4.06
5398 6824 1.888512 AGATTTTGACAAGGCGTGCAT 59.111 42.857 0.00 0.00 0.00 3.96
5401 6827 2.662791 CGTGAGATTTTGACAAGGCGTG 60.663 50.000 0.00 0.00 0.00 5.34
5402 6828 1.531149 CGTGAGATTTTGACAAGGCGT 59.469 47.619 0.00 0.00 0.00 5.68
5431 6857 6.925211 TCTCGGCATAAGATAAGAAATCGAT 58.075 36.000 0.00 0.00 0.00 3.59
5433 6859 6.382608 TCTCTCGGCATAAGATAAGAAATCG 58.617 40.000 0.00 0.00 0.00 3.34
5445 6871 0.663688 GCGTCTCTCTCTCGGCATAA 59.336 55.000 0.00 0.00 0.00 1.90
5456 6882 4.111375 TGTCAATCTTAAGGCGTCTCTC 57.889 45.455 1.85 0.00 0.00 3.20
5460 6886 4.201822 GGATGTTGTCAATCTTAAGGCGTC 60.202 45.833 1.85 0.00 0.00 5.19
5461 6887 3.689649 GGATGTTGTCAATCTTAAGGCGT 59.310 43.478 1.85 0.00 0.00 5.68
5462 6888 3.689161 TGGATGTTGTCAATCTTAAGGCG 59.311 43.478 1.85 0.00 0.00 5.52
5463 6889 5.643379 TTGGATGTTGTCAATCTTAAGGC 57.357 39.130 1.85 0.00 0.00 4.35
5464 6890 6.863126 GTGTTTGGATGTTGTCAATCTTAAGG 59.137 38.462 1.85 0.00 0.00 2.69
5469 6895 6.716628 ACTATGTGTTTGGATGTTGTCAATCT 59.283 34.615 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.