Multiple sequence alignment - TraesCS7D01G089500

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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 TraesCS7D01G089500 chr7D 100.000 4962 0 0 1 4962 53991931 53996892 0.000000e+00 9164.0
1 TraesCS7D01G089500 chr7D 92.654 667 26 8 4312 4962 571252896 571252237 0.000000e+00 939.0
2 TraesCS7D01G089500 chr7D 100.000 28 0 0 387 414 365978146 365978173 9.000000e-03 52.8
3 TraesCS7D01G089500 chr4A 91.891 4390 232 53 1 4311 669676383 669680727 0.000000e+00 6021.0
4 TraesCS7D01G089500 chr4A 89.892 465 36 9 4335 4797 49214050 49213595 5.530000e-164 588.0
5 TraesCS7D01G089500 chr7A 92.849 3398 152 42 947 4311 57624100 57627439 0.000000e+00 4844.0
6 TraesCS7D01G089500 chr7A 90.108 465 36 7 4335 4797 625768562 625768106 3.310000e-166 595.0
7 TraesCS7D01G089500 chr5D 96.078 663 13 4 4312 4962 466568266 466567605 0.000000e+00 1068.0
8 TraesCS7D01G089500 chr5D 96.979 629 16 3 4335 4962 561916828 561916202 0.000000e+00 1053.0
9 TraesCS7D01G089500 chr5D 95.188 665 18 6 4311 4962 530374332 530374995 0.000000e+00 1038.0
10 TraesCS7D01G089500 chr3D 96.661 629 20 1 4335 4962 57324733 57324105 0.000000e+00 1044.0
11 TraesCS7D01G089500 chr3D 100.000 30 0 0 4311 4340 57324767 57324738 6.940000e-04 56.5
12 TraesCS7D01G089500 chr3B 88.380 611 46 7 4335 4930 795286539 795287139 0.000000e+00 712.0
13 TraesCS7D01G089500 chr6D 91.314 472 34 6 4335 4800 160218419 160218889 5.420000e-179 638.0
14 TraesCS7D01G089500 chr6D 94.444 36 0 1 4307 4340 160218379 160218414 2.000000e-03 54.7
15 TraesCS7D01G089500 chr1A 89.384 471 43 6 4335 4800 475198234 475198702 1.990000e-163 586.0
16 TraesCS7D01G089500 chr6B 88.377 499 37 8 4311 4797 658280845 658280356 9.260000e-162 580.0
17 TraesCS7D01G089500 chr2A 88.353 498 37 8 4312 4797 39314854 39315342 3.330000e-161 579.0
18 TraesCS7D01G089500 chr2A 91.294 425 34 3 4343 4765 351168874 351169297 1.200000e-160 577.0
19 TraesCS7D01G089500 chr2A 100.000 33 0 0 389 421 156035452 156035484 1.490000e-05 62.1
20 TraesCS7D01G089500 chr5A 88.559 472 40 5 4312 4771 69067372 69066903 1.210000e-155 560.0
21 TraesCS7D01G089500 chr5A 75.676 222 36 8 387 601 458314591 458314381 1.470000e-15 95.3
22 TraesCS7D01G089500 chr3A 95.556 225 7 2 4741 4962 41428982 41429206 1.700000e-94 357.0


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 TraesCS7D01G089500 chr7D 53991931 53996892 4961 False 9164.00 9164 100.0000 1 4962 1 chr7D.!!$F1 4961
1 TraesCS7D01G089500 chr7D 571252237 571252896 659 True 939.00 939 92.6540 4312 4962 1 chr7D.!!$R1 650
2 TraesCS7D01G089500 chr4A 669676383 669680727 4344 False 6021.00 6021 91.8910 1 4311 1 chr4A.!!$F1 4310
3 TraesCS7D01G089500 chr7A 57624100 57627439 3339 False 4844.00 4844 92.8490 947 4311 1 chr7A.!!$F1 3364
4 TraesCS7D01G089500 chr5D 466567605 466568266 661 True 1068.00 1068 96.0780 4312 4962 1 chr5D.!!$R1 650
5 TraesCS7D01G089500 chr5D 561916202 561916828 626 True 1053.00 1053 96.9790 4335 4962 1 chr5D.!!$R2 627
6 TraesCS7D01G089500 chr5D 530374332 530374995 663 False 1038.00 1038 95.1880 4311 4962 1 chr5D.!!$F1 651
7 TraesCS7D01G089500 chr3D 57324105 57324767 662 True 550.25 1044 98.3305 4311 4962 2 chr3D.!!$R1 651
8 TraesCS7D01G089500 chr3B 795286539 795287139 600 False 712.00 712 88.3800 4335 4930 1 chr3B.!!$F1 595
9 TraesCS7D01G089500 chr6D 160218379 160218889 510 False 346.35 638 92.8790 4307 4800 2 chr6D.!!$F1 493

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
823 863 0.030773 CATCGGTCGGTCGATCATGT 59.969 55.000 10.05 0.0 46.59 3.21 F
1350 1411 0.028242 CTCCTTCGTCGTCATCCTCG 59.972 60.000 0.00 0.0 0.00 4.63 F
1351 1412 1.586564 CCTTCGTCGTCATCCTCGC 60.587 63.158 0.00 0.0 0.00 5.03 F
2223 2298 1.345415 AGCTGCTTTTGGGTTGAATGG 59.655 47.619 0.00 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1762 0.182537 TGTTTCAGTGTCAGTGGGGG 59.817 55.000 7.82 0.0 0.00 5.40 R
2223 2298 1.356494 ATTCTTAGCCTGCCCCTCCC 61.356 60.000 0.00 0.0 0.00 4.30 R
3152 3244 1.712350 GCAACTACACGTCTACACACG 59.288 52.381 0.00 0.0 45.65 4.49 R
4133 4235 0.028110 GACGCCGATCTTGCAAATCC 59.972 55.000 0.00 0.0 0.00 3.01 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
71 72 1.886585 CACAGGAGGACGAGGAGTG 59.113 63.158 0.00 0.00 0.00 3.51
136 137 3.262686 GAATCGACGGCGGCCTTC 61.263 66.667 12.58 16.59 38.28 3.46
141 142 4.208686 GACGGCGGCCTTCGATCT 62.209 66.667 18.34 0.00 42.43 2.75
156 157 2.056481 GATCTGGCCATGTCGCTTGC 62.056 60.000 5.51 0.00 0.00 4.01
158 159 4.695993 TGGCCATGTCGCTTGCGA 62.696 61.111 13.93 13.93 0.00 5.10
161 162 2.125552 CCATGTCGCTTGCGAGGA 60.126 61.111 18.25 8.41 0.00 3.71
163 164 1.446792 CATGTCGCTTGCGAGGACT 60.447 57.895 18.25 0.76 0.00 3.85
188 189 3.673484 GTGGCAGTGGCGTGCATT 61.673 61.111 12.58 0.00 45.93 3.56
226 227 3.535629 TTGAGCAGCGTGTGGGAGG 62.536 63.158 0.00 0.00 0.00 4.30
231 232 3.322466 AGCGTGTGGGAGGGGAAG 61.322 66.667 0.00 0.00 0.00 3.46
233 234 2.890766 GCGTGTGGGAGGGGAAGAA 61.891 63.158 0.00 0.00 0.00 2.52
251 256 6.071334 GGGAAGAAAGGGGAAGATTTTTACTG 60.071 42.308 0.00 0.00 0.00 2.74
254 259 5.712446 AGAAAGGGGAAGATTTTTACTGCTC 59.288 40.000 0.00 0.00 0.00 4.26
256 261 3.263425 AGGGGAAGATTTTTACTGCTCGA 59.737 43.478 0.00 0.00 0.00 4.04
343 371 6.069705 TGTTTTAGAGGAATAAACCGGGAT 57.930 37.500 6.32 0.00 32.25 3.85
346 374 7.452189 TGTTTTAGAGGAATAAACCGGGATTTT 59.548 33.333 6.32 0.00 32.25 1.82
359 387 4.533311 ACCGGGATTTTTACTCCTCTAACA 59.467 41.667 6.32 0.00 33.05 2.41
376 404 6.248569 TCTAACAGGATTTAGGGGATCAAC 57.751 41.667 0.00 0.00 31.01 3.18
387 415 1.576356 GGGATCAACGAGAGATGCAC 58.424 55.000 0.00 0.00 35.77 4.57
482 513 9.680315 CATTTACTTATCTTACTTAGGAGGACG 57.320 37.037 0.00 0.00 0.00 4.79
486 517 7.341805 ACTTATCTTACTTAGGAGGACGTGTA 58.658 38.462 0.00 0.00 0.00 2.90
509 540 1.523258 CCGGCTCTTGCATCAGAGG 60.523 63.158 15.55 5.55 40.79 3.69
584 623 5.927281 TGTAAGTAGTCTTATGACCCACC 57.073 43.478 5.19 0.00 43.91 4.61
596 635 4.796110 ATGACCCACCATTATACTTGCT 57.204 40.909 0.00 0.00 0.00 3.91
604 643 4.982916 CACCATTATACTTGCTCGTAGGAC 59.017 45.833 0.00 0.00 0.00 3.85
610 649 7.578310 TTATACTTGCTCGTAGGACTAACAT 57.422 36.000 0.00 0.00 0.00 2.71
624 663 6.922136 AGGACTAACATGATGAGTTAGCCCC 61.922 48.000 12.72 12.85 46.83 5.80
632 671 0.714180 TGAGTTAGCCCCAGGGAGTA 59.286 55.000 7.25 0.00 37.50 2.59
657 697 4.079901 CCGCTCTACCCTCCTATAATCCTA 60.080 50.000 0.00 0.00 0.00 2.94
659 699 6.130569 CGCTCTACCCTCCTATAATCCTATT 58.869 44.000 0.00 0.00 0.00 1.73
660 700 6.039941 CGCTCTACCCTCCTATAATCCTATTG 59.960 46.154 0.00 0.00 0.00 1.90
661 701 6.898521 GCTCTACCCTCCTATAATCCTATTGT 59.101 42.308 0.00 0.00 0.00 2.71
662 702 7.068962 GCTCTACCCTCCTATAATCCTATTGTC 59.931 44.444 0.00 0.00 0.00 3.18
663 703 7.420029 TCTACCCTCCTATAATCCTATTGTCC 58.580 42.308 0.00 0.00 0.00 4.02
664 704 5.351405 ACCCTCCTATAATCCTATTGTCCC 58.649 45.833 0.00 0.00 0.00 4.46
676 716 5.155905 TCCTATTGTCCCTCCTCCTAATTC 58.844 45.833 0.00 0.00 0.00 2.17
678 718 2.191981 TGTCCCTCCTCCTAATTCCC 57.808 55.000 0.00 0.00 0.00 3.97
681 721 1.367840 CCTCCTCCTAATTCCCGCG 59.632 63.158 0.00 0.00 0.00 6.46
705 745 4.498177 GCTCTTTCACACACCTTTTCTTCC 60.498 45.833 0.00 0.00 0.00 3.46
707 747 1.305201 TCACACACCTTTTCTTCCGC 58.695 50.000 0.00 0.00 0.00 5.54
711 751 1.535462 CACACCTTTTCTTCCGCGATT 59.465 47.619 8.23 0.00 0.00 3.34
722 762 1.137459 TCCGCGATTCGTCATTGTCG 61.137 55.000 8.23 0.71 36.19 4.35
740 780 2.244651 GCCTTGCTGTCGTCGTTGT 61.245 57.895 0.00 0.00 0.00 3.32
742 782 0.232303 CCTTGCTGTCGTCGTTGTTC 59.768 55.000 0.00 0.00 0.00 3.18
744 784 0.927537 TTGCTGTCGTCGTTGTTCTG 59.072 50.000 0.00 0.00 0.00 3.02
756 796 1.197721 GTTGTTCTGCTGATTGGTCGG 59.802 52.381 0.00 0.00 0.00 4.79
774 814 1.278127 CGGCTACCCTCTTCTTTTCCA 59.722 52.381 0.00 0.00 0.00 3.53
780 820 3.049344 ACCCTCTTCTTTTCCACTGTCT 58.951 45.455 0.00 0.00 0.00 3.41
792 832 1.066573 CCACTGTCTCGCCATTTCTCT 60.067 52.381 0.00 0.00 0.00 3.10
795 835 2.275318 CTGTCTCGCCATTTCTCTTCC 58.725 52.381 0.00 0.00 0.00 3.46
797 837 2.093973 TGTCTCGCCATTTCTCTTCCTC 60.094 50.000 0.00 0.00 0.00 3.71
801 841 4.405680 TCTCGCCATTTCTCTTCCTCATAA 59.594 41.667 0.00 0.00 0.00 1.90
811 851 5.661458 TCTCTTCCTCATAAAACATCGGTC 58.339 41.667 0.00 0.00 0.00 4.79
812 852 4.430007 TCTTCCTCATAAAACATCGGTCG 58.570 43.478 0.00 0.00 0.00 4.79
823 863 0.030773 CATCGGTCGGTCGATCATGT 59.969 55.000 10.05 0.00 46.59 3.21
824 864 0.311165 ATCGGTCGGTCGATCATGTC 59.689 55.000 4.49 0.00 45.43 3.06
831 872 2.492088 TCGGTCGATCATGTCTTTGACT 59.508 45.455 0.00 0.00 33.15 3.41
835 876 5.651530 GGTCGATCATGTCTTTGACTAAGA 58.348 41.667 0.00 0.00 40.57 2.10
841 882 6.861065 TCATGTCTTTGACTAAGAAACCAC 57.139 37.500 0.71 0.00 44.25 4.16
842 883 6.591935 TCATGTCTTTGACTAAGAAACCACT 58.408 36.000 0.71 0.00 44.25 4.00
847 888 9.403583 TGTCTTTGACTAAGAAACCACTATTTT 57.596 29.630 0.71 0.00 44.25 1.82
894 938 6.817140 ACTATTTCCTCCGTGAAATACTTGTC 59.183 38.462 7.52 0.00 41.83 3.18
909 956 3.083293 ACTTGTCCGGAGAAGAGAGTAC 58.917 50.000 39.37 11.69 0.00 2.73
913 960 2.359531 GTCCGGAGAAGAGAGTACATGG 59.640 54.545 3.06 0.00 0.00 3.66
961 1008 4.097286 ACGTGTAGGTGTGAAAATGCTTTT 59.903 37.500 0.00 0.00 35.12 2.27
1020 1067 2.418368 TGGACACATGTATTGCCTCC 57.582 50.000 0.00 0.00 0.00 4.30
1054 1102 1.618343 CCAATCCAACCCAACAACCTC 59.382 52.381 0.00 0.00 0.00 3.85
1341 1402 4.194720 CCTCCCGCTCCTTCGTCG 62.195 72.222 0.00 0.00 0.00 5.12
1344 1405 3.744719 CCCGCTCCTTCGTCGTCA 61.745 66.667 0.00 0.00 0.00 4.35
1345 1406 2.490217 CCGCTCCTTCGTCGTCAT 59.510 61.111 0.00 0.00 0.00 3.06
1346 1407 1.586564 CCGCTCCTTCGTCGTCATC 60.587 63.158 0.00 0.00 0.00 2.92
1347 1408 1.586564 CGCTCCTTCGTCGTCATCC 60.587 63.158 0.00 0.00 0.00 3.51
1348 1409 1.810532 GCTCCTTCGTCGTCATCCT 59.189 57.895 0.00 0.00 0.00 3.24
1349 1410 0.248702 GCTCCTTCGTCGTCATCCTC 60.249 60.000 0.00 0.00 0.00 3.71
1350 1411 0.028242 CTCCTTCGTCGTCATCCTCG 59.972 60.000 0.00 0.00 0.00 4.63
1351 1412 1.586564 CCTTCGTCGTCATCCTCGC 60.587 63.158 0.00 0.00 0.00 5.03
1352 1413 1.586564 CTTCGTCGTCATCCTCGCC 60.587 63.158 0.00 0.00 0.00 5.54
1353 1414 2.938539 CTTCGTCGTCATCCTCGCCC 62.939 65.000 0.00 0.00 0.00 6.13
1354 1415 4.570663 CGTCGTCATCCTCGCCCC 62.571 72.222 0.00 0.00 0.00 5.80
1355 1416 4.222847 GTCGTCATCCTCGCCCCC 62.223 72.222 0.00 0.00 0.00 5.40
1648 1719 1.729131 CACGTGCGTGCCATTTTCC 60.729 57.895 11.81 0.00 39.39 3.13
1662 1733 5.994668 TGCCATTTTCCACTTTTGGTTATTC 59.005 36.000 0.00 0.00 44.35 1.75
1701 1772 3.263425 TCTCAAGTAAATCCCCCACTGAC 59.737 47.826 0.00 0.00 0.00 3.51
1759 1832 6.392354 TGATTTGCTTGATTTGATTCCTGAC 58.608 36.000 0.00 0.00 0.00 3.51
1812 1885 3.124921 ACGGCGAAATTCTGCGGG 61.125 61.111 16.62 8.86 35.93 6.13
1815 1888 3.439540 GCGAAATTCTGCGGGGCA 61.440 61.111 0.00 0.00 36.92 5.36
1935 2008 4.281941 TGATCTGTGCTCTGTTACTGACTT 59.718 41.667 0.00 0.00 0.00 3.01
1942 2015 3.193691 GCTCTGTTACTGACTTGCCTCTA 59.806 47.826 0.00 0.00 0.00 2.43
1943 2016 4.142049 GCTCTGTTACTGACTTGCCTCTAT 60.142 45.833 0.00 0.00 0.00 1.98
1975 2048 2.595463 GCCTGTGGCTTGTGCTGA 60.595 61.111 0.73 0.00 46.69 4.26
1990 2063 1.675483 TGCTGATTTGCGTTCACTGTT 59.325 42.857 0.00 0.00 35.36 3.16
1992 2065 2.468777 GCTGATTTGCGTTCACTGTTTG 59.531 45.455 0.00 0.00 0.00 2.93
2001 2074 2.604614 CGTTCACTGTTTGCTTAAGCCC 60.605 50.000 24.30 12.65 41.18 5.19
2153 2226 8.910666 CGAGTTACTTCTTCTCTTATGCATATG 58.089 37.037 7.36 10.23 0.00 1.78
2223 2298 1.345415 AGCTGCTTTTGGGTTGAATGG 59.655 47.619 0.00 0.00 0.00 3.16
2249 2324 3.181439 GGGGCAGGCTAAGAATATCTTGT 60.181 47.826 2.94 0.00 37.29 3.16
2257 2342 7.766278 CAGGCTAAGAATATCTTGTTGTGTACT 59.234 37.037 2.94 0.00 37.29 2.73
2350 2438 8.451908 AATAGCTTTCTTATACACCATGTTCC 57.548 34.615 0.00 0.00 0.00 3.62
2744 2833 7.888546 AGTAAGGTTGTAATAGCCTCATTGTTT 59.111 33.333 0.00 0.00 39.36 2.83
2778 2867 4.062991 CCACTAAAGTTCGGTGTAGCTTT 58.937 43.478 0.00 0.00 35.62 3.51
2793 2882 6.017852 GGTGTAGCTTTCATAAGTAGAATGGC 60.018 42.308 0.00 0.00 33.74 4.40
2809 2898 8.636213 AGTAGAATGGCTGAATGAATAAATTGG 58.364 33.333 0.00 0.00 0.00 3.16
2894 2983 4.634012 ATTTGCAGTGTGTAGGGTTAGA 57.366 40.909 0.00 0.00 0.00 2.10
2913 3002 3.926616 AGATAACAAGTTCACCGTCCTG 58.073 45.455 0.00 0.00 0.00 3.86
3143 3235 8.924511 ACATTAATACTGGGATATTTCAGGTG 57.075 34.615 9.91 0.00 35.47 4.00
3144 3236 8.502738 ACATTAATACTGGGATATTTCAGGTGT 58.497 33.333 9.91 0.00 35.47 4.16
3145 3237 8.786898 CATTAATACTGGGATATTTCAGGTGTG 58.213 37.037 9.91 0.00 35.47 3.82
3146 3238 5.975988 ATACTGGGATATTTCAGGTGTGT 57.024 39.130 9.91 0.00 35.47 3.72
3147 3239 4.657814 ACTGGGATATTTCAGGTGTGTT 57.342 40.909 9.91 0.00 35.47 3.32
3148 3240 4.998051 ACTGGGATATTTCAGGTGTGTTT 58.002 39.130 9.91 0.00 35.47 2.83
3149 3241 5.393866 ACTGGGATATTTCAGGTGTGTTTT 58.606 37.500 9.91 0.00 35.47 2.43
3150 3242 5.476945 ACTGGGATATTTCAGGTGTGTTTTC 59.523 40.000 9.91 0.00 35.47 2.29
3151 3243 5.389520 TGGGATATTTCAGGTGTGTTTTCA 58.610 37.500 0.00 0.00 0.00 2.69
3152 3244 8.871033 ACTGGGATATTTCAGGTGTGTTTTCAC 61.871 40.741 9.91 0.00 41.55 3.18
3163 3255 3.214699 GTGTTTTCACGTGTGTAGACG 57.785 47.619 16.51 0.00 45.09 4.18
3194 3286 5.144359 GCCGTGTCAAAACTTACATAAGTG 58.856 41.667 5.08 0.00 45.17 3.16
3247 3339 9.599322 GTCATCAGTTGAAACTAGTATGTTTTG 57.401 33.333 0.00 0.00 39.86 2.44
3250 3342 7.847487 TCAGTTGAAACTAGTATGTTTTGACG 58.153 34.615 0.00 0.00 39.86 4.35
3260 3352 6.747659 AGTATGTTTTGACGCAATGTTTTC 57.252 33.333 0.00 0.00 0.00 2.29
3261 3353 6.269315 AGTATGTTTTGACGCAATGTTTTCA 58.731 32.000 0.00 0.00 0.00 2.69
3325 3420 1.326213 TTGGGCCAAATACCATGCCG 61.326 55.000 18.51 0.00 44.96 5.69
3453 3548 2.564721 GCCTTTCCTGCCGCAACTT 61.565 57.895 0.00 0.00 0.00 2.66
3485 3580 8.106462 TCTCATCATTTCCCATGTTACAGTTTA 58.894 33.333 0.00 0.00 0.00 2.01
3507 3602 5.819825 ATCTTCCGTTATTTTCCTCTTGC 57.180 39.130 0.00 0.00 0.00 4.01
3508 3603 4.647611 TCTTCCGTTATTTTCCTCTTGCA 58.352 39.130 0.00 0.00 0.00 4.08
3621 3718 7.141363 AGTGTTTTAGAAATCAACTGCATGAC 58.859 34.615 0.00 0.00 30.82 3.06
3668 3765 0.607489 AGTGCCAGATTGGTGCTCAC 60.607 55.000 0.00 0.00 40.46 3.51
3821 3920 3.898509 CCGAGAGAGGGCAGAGCG 61.899 72.222 0.00 0.00 0.00 5.03
3968 4067 2.763039 TCTCCAACCTATGATGAGCCA 58.237 47.619 0.00 0.00 0.00 4.75
3978 4077 1.131638 TGATGAGCCAGGACCATACC 58.868 55.000 0.00 0.00 0.00 2.73
3984 4083 0.618458 GCCAGGACCATACCACTTCA 59.382 55.000 0.00 0.00 0.00 3.02
3997 4096 6.936900 CCATACCACTTCATCTTCGGATTTAT 59.063 38.462 0.00 0.00 31.35 1.40
4059 4161 2.286184 GCACGCCATGTATTTCTTACGG 60.286 50.000 0.00 0.00 33.15 4.02
4084 4186 7.237871 GTGTCGATAGCTACAGTAGATATGTG 58.762 42.308 20.76 13.52 37.50 3.21
4128 4230 0.108424 CAGAAGGGCAGAAGAGGACG 60.108 60.000 0.00 0.00 0.00 4.79
4132 4234 2.683933 GGCAGAAGAGGACGGGGA 60.684 66.667 0.00 0.00 0.00 4.81
4133 4235 2.726351 GGCAGAAGAGGACGGGGAG 61.726 68.421 0.00 0.00 0.00 4.30
4169 4273 1.983605 CGTCGTGGATATATTGACGGC 59.016 52.381 16.45 13.71 46.19 5.68
4171 4275 2.987149 GTCGTGGATATATTGACGGCTG 59.013 50.000 12.38 0.00 33.73 4.85
4172 4276 1.726791 CGTGGATATATTGACGGCTGC 59.273 52.381 8.77 0.00 0.00 5.25
4222 4326 5.968254 TGTATAAGAACTTGCACGGATGTA 58.032 37.500 0.00 0.00 0.00 2.29
4230 4334 1.819928 TGCACGGATGTACTTGCATT 58.180 45.000 0.00 0.00 40.01 3.56
4233 4337 2.355756 GCACGGATGTACTTGCATTGAT 59.644 45.455 0.00 0.00 34.97 2.57
4238 4342 5.237127 ACGGATGTACTTGCATTGATACATG 59.763 40.000 14.02 0.00 38.16 3.21
4263 4367 7.661437 TGTACAAACTGAAGATGAAGTTGCTAT 59.339 33.333 0.00 0.00 36.75 2.97
4264 4368 6.906659 ACAAACTGAAGATGAAGTTGCTATG 58.093 36.000 0.00 0.00 36.75 2.23
4305 4409 9.997482 GAACTATACTAGATGAAGTAGCTATGC 57.003 37.037 0.00 0.00 35.50 3.14
4382 4497 7.465900 AGGAAAATTTATGTCCCATCTCCTA 57.534 36.000 4.13 0.00 31.25 2.94
4452 4568 2.159382 CCCAACGCACTTCCTTTATGT 58.841 47.619 0.00 0.00 0.00 2.29
4461 4577 3.323403 CACTTCCTTTATGTTGGCCCAAA 59.677 43.478 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.038329 CCTCCTCCCACGGTACCA 59.962 66.667 13.54 0.00 0.00 3.25
49 50 4.803426 CTCGTCCTCCTGTGCCGC 62.803 72.222 0.00 0.00 0.00 6.53
71 72 1.996187 GGTTCCACCTCCTCCTCCC 60.996 68.421 0.00 0.00 34.73 4.30
112 113 4.210304 GCCGTCGATTCACAGCGC 62.210 66.667 0.00 0.00 0.00 5.92
113 114 3.902063 CGCCGTCGATTCACAGCG 61.902 66.667 0.00 0.00 38.10 5.18
118 119 4.077184 AAGGCCGCCGTCGATTCA 62.077 61.111 3.05 0.00 38.10 2.57
124 125 4.208686 AGATCGAAGGCCGCCGTC 62.209 66.667 14.79 14.79 38.37 4.79
125 126 4.514577 CAGATCGAAGGCCGCCGT 62.515 66.667 17.10 0.00 38.37 5.68
136 137 1.522355 AAGCGACATGGCCAGATCG 60.522 57.895 28.51 28.51 37.63 3.69
141 142 4.695993 TCGCAAGCGACATGGCCA 62.696 61.111 8.56 8.56 44.01 5.36
197 198 0.376502 GCTGCTCAAATCTCCTTCGC 59.623 55.000 0.00 0.00 0.00 4.70
206 207 0.957395 CTCCCACACGCTGCTCAAAT 60.957 55.000 0.00 0.00 0.00 2.32
207 208 1.597854 CTCCCACACGCTGCTCAAA 60.598 57.895 0.00 0.00 0.00 2.69
226 227 6.017192 AGTAAAAATCTTCCCCTTTCTTCCC 58.983 40.000 0.00 0.00 0.00 3.97
229 230 6.077993 AGCAGTAAAAATCTTCCCCTTTCTT 58.922 36.000 0.00 0.00 0.00 2.52
231 232 5.392057 CGAGCAGTAAAAATCTTCCCCTTTC 60.392 44.000 0.00 0.00 0.00 2.62
233 234 4.010349 CGAGCAGTAAAAATCTTCCCCTT 58.990 43.478 0.00 0.00 0.00 3.95
254 259 2.459421 AATACTCGCCCGCTCGATCG 62.459 60.000 9.36 9.36 37.87 3.69
256 261 0.104304 AAAATACTCGCCCGCTCGAT 59.896 50.000 0.00 0.00 37.87 3.59
315 320 7.012044 CCCGGTTTATTCCTCTAAAACATACAG 59.988 40.741 0.00 0.00 35.33 2.74
320 325 5.502089 TCCCGGTTTATTCCTCTAAAACA 57.498 39.130 0.00 0.00 35.33 2.83
359 387 3.643792 CTCTCGTTGATCCCCTAAATCCT 59.356 47.826 0.00 0.00 0.00 3.24
369 397 2.159184 TGAGTGCATCTCTCGTTGATCC 60.159 50.000 14.60 0.00 43.13 3.36
373 401 3.774066 TGTATGAGTGCATCTCTCGTTG 58.226 45.455 14.60 0.00 43.13 4.10
376 404 5.159925 CCTATTGTATGAGTGCATCTCTCG 58.840 45.833 14.60 0.00 43.13 4.04
387 415 8.871125 ACCTTATAGTCAACCCTATTGTATGAG 58.129 37.037 0.00 0.00 0.00 2.90
399 427 4.489306 AGAGCCAACCTTATAGTCAACC 57.511 45.455 0.00 0.00 0.00 3.77
435 463 8.511604 AAATGAGAAAGAGAGAAAGTGAAACA 57.488 30.769 0.00 0.00 41.43 2.83
482 513 1.362406 GCAAGAGCCGGCTTCTACAC 61.362 60.000 33.34 17.04 33.58 2.90
486 517 1.451028 GATGCAAGAGCCGGCTTCT 60.451 57.895 33.34 24.82 41.13 2.85
509 540 4.587262 ACAACCAAAATGAAAGGGAGTACC 59.413 41.667 0.00 0.00 40.67 3.34
559 598 6.127140 GGTGGGTCATAAGACTACTTACATGT 60.127 42.308 2.69 2.69 44.36 3.21
568 607 8.647796 CAAGTATAATGGTGGGTCATAAGACTA 58.352 37.037 0.00 0.00 44.36 2.59
578 617 2.504175 ACGAGCAAGTATAATGGTGGGT 59.496 45.455 0.00 0.00 0.00 4.51
584 623 7.423199 TGTTAGTCCTACGAGCAAGTATAATG 58.577 38.462 0.00 0.00 0.00 1.90
596 635 6.238676 GCTAACTCATCATGTTAGTCCTACGA 60.239 42.308 13.03 0.00 44.99 3.43
604 643 4.384056 CTGGGGCTAACTCATCATGTTAG 58.616 47.826 8.71 8.71 45.59 2.34
610 649 0.044092 TCCCTGGGGCTAACTCATCA 59.956 55.000 14.00 0.00 34.68 3.07
623 662 1.249407 GTAGAGCGGATACTCCCTGG 58.751 60.000 0.00 0.00 37.39 4.45
624 663 1.249407 GGTAGAGCGGATACTCCCTG 58.751 60.000 0.00 0.00 37.39 4.45
632 671 4.538738 GATTATAGGAGGGTAGAGCGGAT 58.461 47.826 0.00 0.00 0.00 4.18
657 697 3.056832 GGGAATTAGGAGGAGGGACAAT 58.943 50.000 0.00 0.00 0.00 2.71
659 699 1.691482 CGGGAATTAGGAGGAGGGACA 60.691 57.143 0.00 0.00 0.00 4.02
660 700 1.049402 CGGGAATTAGGAGGAGGGAC 58.951 60.000 0.00 0.00 0.00 4.46
661 701 0.763223 GCGGGAATTAGGAGGAGGGA 60.763 60.000 0.00 0.00 0.00 4.20
662 702 1.755384 GCGGGAATTAGGAGGAGGG 59.245 63.158 0.00 0.00 0.00 4.30
663 703 1.367840 CGCGGGAATTAGGAGGAGG 59.632 63.158 0.00 0.00 0.00 4.30
664 704 1.367840 CCGCGGGAATTAGGAGGAG 59.632 63.158 20.10 0.00 0.00 3.69
676 716 3.423154 GTGTGAAAGAGCCGCGGG 61.423 66.667 29.38 8.95 0.00 6.13
678 718 2.551270 GTGTGTGAAAGAGCCGCG 59.449 61.111 0.00 0.00 0.00 6.46
681 721 2.952310 AGAAAAGGTGTGTGAAAGAGCC 59.048 45.455 0.00 0.00 0.00 4.70
707 747 0.999406 AAGGCGACAATGACGAATCG 59.001 50.000 9.52 0.00 37.63 3.34
711 751 1.005037 AGCAAGGCGACAATGACGA 60.005 52.632 9.52 0.00 0.00 4.20
722 762 1.772063 AACAACGACGACAGCAAGGC 61.772 55.000 0.00 0.00 0.00 4.35
740 780 0.901827 TAGCCGACCAATCAGCAGAA 59.098 50.000 0.00 0.00 29.89 3.02
742 782 2.682893 GTAGCCGACCAATCAGCAG 58.317 57.895 0.00 0.00 29.89 4.24
756 796 3.244596 ACAGTGGAAAAGAAGAGGGTAGC 60.245 47.826 0.00 0.00 0.00 3.58
774 814 2.354203 GGAAGAGAAATGGCGAGACAGT 60.354 50.000 0.00 0.00 0.00 3.55
780 820 4.753516 TTATGAGGAAGAGAAATGGCGA 57.246 40.909 0.00 0.00 0.00 5.54
792 832 3.055675 ACCGACCGATGTTTTATGAGGAA 60.056 43.478 0.00 0.00 0.00 3.36
795 835 2.534349 CGACCGACCGATGTTTTATGAG 59.466 50.000 0.00 0.00 0.00 2.90
797 837 2.532235 TCGACCGACCGATGTTTTATG 58.468 47.619 0.00 0.00 33.14 1.90
811 851 2.881074 AGTCAAAGACATGATCGACCG 58.119 47.619 0.00 0.00 34.60 4.79
812 852 5.651530 TCTTAGTCAAAGACATGATCGACC 58.348 41.667 0.00 0.00 39.36 4.79
856 897 8.674607 ACGGAGGAAATAGTCATGAATAAAAAC 58.325 33.333 7.01 0.00 0.00 2.43
858 899 8.044309 TCACGGAGGAAATAGTCATGAATAAAA 58.956 33.333 7.01 0.00 0.00 1.52
861 902 6.724893 TCACGGAGGAAATAGTCATGAATA 57.275 37.500 5.19 5.19 0.00 1.75
865 906 6.986817 AGTATTTCACGGAGGAAATAGTCATG 59.013 38.462 15.16 0.00 44.31 3.07
868 909 6.817140 ACAAGTATTTCACGGAGGAAATAGTC 59.183 38.462 18.72 10.50 45.70 2.59
873 914 4.320870 GGACAAGTATTTCACGGAGGAAA 58.679 43.478 2.39 2.39 40.72 3.13
894 938 2.656002 TCCATGTACTCTCTTCTCCGG 58.344 52.381 0.00 0.00 0.00 5.14
909 956 5.291178 TGCACTTCAAATCTTTGTTCCATG 58.709 37.500 2.82 0.00 39.18 3.66
913 960 4.301628 CCCTGCACTTCAAATCTTTGTTC 58.698 43.478 2.82 0.00 39.18 3.18
920 967 2.657297 TGCCCCTGCACTTCAAATC 58.343 52.632 0.00 0.00 44.23 2.17
961 1008 1.682849 GCACACATACCTCCACCCA 59.317 57.895 0.00 0.00 0.00 4.51
1005 1052 2.301346 GGGAAGGAGGCAATACATGTG 58.699 52.381 9.11 0.00 0.00 3.21
1012 1059 0.548510 GTAGCTGGGAAGGAGGCAAT 59.451 55.000 0.00 0.00 0.00 3.56
1014 1061 1.995626 GGTAGCTGGGAAGGAGGCA 60.996 63.158 0.00 0.00 0.00 4.75
1020 1067 1.141858 GGATTGGAGGTAGCTGGGAAG 59.858 57.143 0.00 0.00 0.00 3.46
1261 1322 2.033141 CCTGGACAGGTGGCTGTG 59.967 66.667 10.22 0.00 43.61 3.66
1329 1390 1.586564 GGATGACGACGAAGGAGCG 60.587 63.158 0.00 0.00 37.29 5.03
1335 1396 2.488355 GGCGAGGATGACGACGAA 59.512 61.111 0.00 0.00 0.00 3.85
1662 1733 5.940470 ACTTGAGAAAATGCTACTAGTTGGG 59.060 40.000 0.00 0.00 0.00 4.12
1691 1762 0.182537 TGTTTCAGTGTCAGTGGGGG 59.817 55.000 7.82 0.00 0.00 5.40
1782 1855 2.258286 GCCGTGTTGTGCCATTCC 59.742 61.111 0.00 0.00 0.00 3.01
1815 1888 4.684134 ACTGCCTTTGCCCCGCAT 62.684 61.111 0.00 0.00 38.76 4.73
1935 2008 3.009723 GCTGCAAACACTAATAGAGGCA 58.990 45.455 0.00 0.00 0.00 4.75
1942 2015 1.542915 CAGGCAGCTGCAAACACTAAT 59.457 47.619 37.63 10.41 44.36 1.73
1943 2016 0.953727 CAGGCAGCTGCAAACACTAA 59.046 50.000 37.63 0.00 44.36 2.24
1975 2048 2.869233 AGCAAACAGTGAACGCAAAT 57.131 40.000 0.00 0.00 0.00 2.32
1990 2063 2.103941 CCACCAAAAAGGGCTTAAGCAA 59.896 45.455 27.83 0.00 43.89 3.91
1992 2065 1.967779 TCCACCAAAAAGGGCTTAAGC 59.032 47.619 19.53 19.53 43.89 3.09
2001 2074 3.132925 CAACCTGCAATCCACCAAAAAG 58.867 45.455 0.00 0.00 0.00 2.27
2173 2248 8.822652 AAAATTTAAGAGAACAAAGGATGCAG 57.177 30.769 0.00 0.00 0.00 4.41
2223 2298 1.356494 ATTCTTAGCCTGCCCCTCCC 61.356 60.000 0.00 0.00 0.00 4.30
2249 2324 5.220777 GCTGACAGCAACTTTTAGTACACAA 60.221 40.000 22.62 0.00 41.89 3.33
2257 2342 2.878406 GACAGGCTGACAGCAACTTTTA 59.122 45.455 27.87 0.00 44.75 1.52
2342 2427 2.332063 AAGCAGGATACGGAACATGG 57.668 50.000 0.00 0.00 46.39 3.66
2350 2438 7.534085 TTTTACAACATCTAAGCAGGATACG 57.466 36.000 0.00 0.00 46.39 3.06
2385 2473 4.733850 TCTGTAAGCATGACTAACGTGAG 58.266 43.478 0.00 0.00 37.69 3.51
2466 2554 8.603898 TCTTATCCCTGTAACTGAGATTTACA 57.396 34.615 0.00 0.00 37.15 2.41
2636 2725 9.793259 TGTGTATTAAAAGAAACTGGATCTCTT 57.207 29.630 0.00 0.00 0.00 2.85
2744 2833 5.697633 CGAACTTTAGTGGTTACAGGCTTAA 59.302 40.000 0.00 0.00 0.00 1.85
2793 2882 9.709495 TCAAACTTTCCCAATTTATTCATTCAG 57.291 29.630 0.00 0.00 0.00 3.02
2809 2898 9.371136 AGAACAAGAATTTCTTTCAAACTTTCC 57.629 29.630 8.95 0.00 33.78 3.13
2894 2983 3.764237 ACAGGACGGTGAACTTGTTAT 57.236 42.857 0.00 0.00 0.00 1.89
2952 3041 1.992557 TCCCCTGGCTACAAACAGAAT 59.007 47.619 0.00 0.00 36.86 2.40
3140 3232 2.931325 TCTACACACGTGAAAACACACC 59.069 45.455 25.01 0.00 37.48 4.16
3141 3233 3.540744 CGTCTACACACGTGAAAACACAC 60.541 47.826 25.01 8.45 34.95 3.82
3142 3234 2.599527 CGTCTACACACGTGAAAACACA 59.400 45.455 25.01 0.00 34.95 3.72
3143 3235 3.214699 CGTCTACACACGTGAAAACAC 57.785 47.619 25.01 11.61 34.95 3.32
3152 3244 1.712350 GCAACTACACGTCTACACACG 59.288 52.381 0.00 0.00 45.65 4.49
3163 3255 2.353579 AGTTTTGACACGGCAACTACAC 59.646 45.455 0.00 0.00 0.00 2.90
3171 3263 5.144359 CACTTATGTAAGTTTTGACACGGC 58.856 41.667 2.77 0.00 43.57 5.68
3247 3339 1.720852 GGCACATGAAAACATTGCGTC 59.279 47.619 0.00 0.00 33.84 5.19
3250 3342 3.132925 ACTTGGCACATGAAAACATTGC 58.867 40.909 0.00 0.00 39.30 3.56
3260 3352 1.888215 ACTGTCAGACTTGGCACATG 58.112 50.000 6.91 0.00 39.30 3.21
3261 3353 2.105477 AGAACTGTCAGACTTGGCACAT 59.895 45.455 6.91 0.00 39.30 3.21
3477 3572 9.374838 GAGGAAAATAACGGAAGATAAACTGTA 57.625 33.333 0.00 0.00 0.00 2.74
3485 3580 5.253330 TGCAAGAGGAAAATAACGGAAGAT 58.747 37.500 0.00 0.00 0.00 2.40
3668 3765 5.332808 CGTGTACGACAAAAGTAGAAAAGGG 60.333 44.000 0.00 0.00 43.02 3.95
3677 3774 2.212869 TCTGCGTGTACGACAAAAGT 57.787 45.000 8.82 0.00 43.02 2.66
3713 3812 1.858458 CGCTTTCTTGACGTCTTCACA 59.142 47.619 17.92 0.00 32.26 3.58
3838 3937 2.182030 GGTTCCTCGCTCTCCACG 59.818 66.667 0.00 0.00 0.00 4.94
3880 3979 2.165301 GTGGTGAGCGATGGCGTAC 61.165 63.158 0.00 0.00 46.35 3.67
3968 4067 3.133003 CGAAGATGAAGTGGTATGGTCCT 59.867 47.826 0.00 0.00 0.00 3.85
3978 4077 4.576053 TGCCATAAATCCGAAGATGAAGTG 59.424 41.667 0.00 0.00 31.29 3.16
3984 4083 2.224867 CCCCTGCCATAAATCCGAAGAT 60.225 50.000 0.00 0.00 0.00 2.40
3997 4096 2.422803 GCTATACAAACATCCCCTGCCA 60.423 50.000 0.00 0.00 0.00 4.92
4059 4161 7.237871 CACATATCTACTGTAGCTATCGACAC 58.762 42.308 9.98 0.00 0.00 3.67
4084 4186 2.200373 ACCACCAGCAATGAGTAACC 57.800 50.000 0.00 0.00 0.00 2.85
4128 4230 1.312815 CGATCTTGCAAATCCTCCCC 58.687 55.000 0.00 0.00 0.00 4.81
4132 4234 0.392998 ACGCCGATCTTGCAAATCCT 60.393 50.000 0.00 0.00 0.00 3.24
4133 4235 0.028110 GACGCCGATCTTGCAAATCC 59.972 55.000 0.00 0.00 0.00 3.01
4169 4273 4.458295 ACTCTGAAATCAAATCACCAGCAG 59.542 41.667 0.00 0.00 0.00 4.24
4171 4275 4.217118 ACACTCTGAAATCAAATCACCAGC 59.783 41.667 0.00 0.00 0.00 4.85
4172 4276 5.954296 ACACTCTGAAATCAAATCACCAG 57.046 39.130 0.00 0.00 0.00 4.00
4222 4326 7.174772 TCAGTTTGTACATGTATCAATGCAAGT 59.825 33.333 9.18 1.69 0.00 3.16
4230 4334 9.154847 CTTCATCTTCAGTTTGTACATGTATCA 57.845 33.333 9.18 6.46 0.00 2.15
4233 4337 8.773645 CAACTTCATCTTCAGTTTGTACATGTA 58.226 33.333 0.08 0.08 30.48 2.29
4238 4342 6.305693 AGCAACTTCATCTTCAGTTTGTAC 57.694 37.500 0.00 0.00 30.48 2.90
4305 4409 3.949313 GCTAGACGCGTCCAAAAAG 57.051 52.632 34.08 22.90 0.00 2.27
4382 4497 3.983044 ATCAAGCGGACTTTCCTAACT 57.017 42.857 0.00 0.00 33.30 2.24
4426 4541 0.321653 GGAAGTGCGTTGGGAGATGT 60.322 55.000 0.00 0.00 0.00 3.06
4452 4568 4.820716 CACATGAAAAAGAATTTGGGCCAA 59.179 37.500 16.66 16.66 39.02 4.52
4461 4577 3.575256 TGGCAGAGCACATGAAAAAGAAT 59.425 39.130 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.