Multiple sequence alignment - TraesCS5B01G290800

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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 TraesCS5B01G290800 chr5B 100.000 4029 0 0 1 4029 476790311 476794339 0.000000e+00 7441.0
1 TraesCS5B01G290800 chr5D 87.492 1479 106 40 2162 3597 396796824 396798266 0.000000e+00 1633.0
2 TraesCS5B01G290800 chr5D 87.535 722 41 21 988 1668 396795628 396796341 0.000000e+00 789.0
3 TraesCS5B01G290800 chr5D 90.571 350 23 5 3659 3999 396798866 396799214 4.750000e-124 455.0
4 TraesCS5B01G290800 chr5D 87.500 80 3 3 3583 3659 396798554 396798629 7.170000e-13 86.1
5 TraesCS5B01G290800 chr4A 96.103 975 26 2 1 963 734085636 734084662 0.000000e+00 1580.0
6 TraesCS5B01G290800 chr4A 89.889 722 73 0 1 722 67165312 67166033 0.000000e+00 929.0
7 TraesCS5B01G290800 chr4A 82.054 964 164 5 6 962 563033756 563032795 0.000000e+00 813.0
8 TraesCS5B01G290800 chr5A 84.814 1587 115 52 2064 3563 502368265 502369812 0.000000e+00 1480.0
9 TraesCS5B01G290800 chr5A 88.157 1123 68 18 977 2065 502367144 502368235 0.000000e+00 1277.0
10 TraesCS5B01G290800 chr5A 97.183 639 18 0 1 639 548690790 548691428 0.000000e+00 1081.0
11 TraesCS5B01G290800 chr5A 81.036 965 168 9 6 962 317513045 317512088 0.000000e+00 754.0
12 TraesCS5B01G290800 chr1D 92.149 968 71 1 1 963 483238148 483239115 0.000000e+00 1362.0
13 TraesCS5B01G290800 chr2A 96.888 739 23 0 1 739 759029294 759028556 0.000000e+00 1238.0
14 TraesCS5B01G290800 chr1B 94.304 632 30 3 337 963 491755662 491755032 0.000000e+00 963.0
15 TraesCS5B01G290800 chr3B 82.555 963 161 3 6 962 542653396 542652435 0.000000e+00 841.0
16 TraesCS5B01G290800 chr6A 81.837 969 167 4 1 962 67116964 67117930 0.000000e+00 806.0
17 TraesCS5B01G290800 chr2D 92.791 541 39 0 1 541 470554699 470555239 0.000000e+00 784.0
18 TraesCS5B01G290800 chr2D 91.917 433 29 3 537 963 470556907 470557339 5.760000e-168 601.0


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 TraesCS5B01G290800 chr5B 476790311 476794339 4028 False 7441.000 7441 100.0000 1 4029 1 chr5B.!!$F1 4028
1 TraesCS5B01G290800 chr5D 396795628 396799214 3586 False 740.775 1633 88.2745 988 3999 4 chr5D.!!$F1 3011
2 TraesCS5B01G290800 chr4A 734084662 734085636 974 True 1580.000 1580 96.1030 1 963 1 chr4A.!!$R2 962
3 TraesCS5B01G290800 chr4A 67165312 67166033 721 False 929.000 929 89.8890 1 722 1 chr4A.!!$F1 721
4 TraesCS5B01G290800 chr4A 563032795 563033756 961 True 813.000 813 82.0540 6 962 1 chr4A.!!$R1 956
5 TraesCS5B01G290800 chr5A 502367144 502369812 2668 False 1378.500 1480 86.4855 977 3563 2 chr5A.!!$F2 2586
6 TraesCS5B01G290800 chr5A 548690790 548691428 638 False 1081.000 1081 97.1830 1 639 1 chr5A.!!$F1 638
7 TraesCS5B01G290800 chr5A 317512088 317513045 957 True 754.000 754 81.0360 6 962 1 chr5A.!!$R1 956
8 TraesCS5B01G290800 chr1D 483238148 483239115 967 False 1362.000 1362 92.1490 1 963 1 chr1D.!!$F1 962
9 TraesCS5B01G290800 chr2A 759028556 759029294 738 True 1238.000 1238 96.8880 1 739 1 chr2A.!!$R1 738
10 TraesCS5B01G290800 chr1B 491755032 491755662 630 True 963.000 963 94.3040 337 963 1 chr1B.!!$R1 626
11 TraesCS5B01G290800 chr3B 542652435 542653396 961 True 841.000 841 82.5550 6 962 1 chr3B.!!$R1 956
12 TraesCS5B01G290800 chr6A 67116964 67117930 966 False 806.000 806 81.8370 1 962 1 chr6A.!!$F1 961
13 TraesCS5B01G290800 chr2D 470554699 470557339 2640 False 692.500 784 92.3540 1 963 2 chr2D.!!$F1 962

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
964 2651 0.240945 CTTCCATCCAACACCGCAAC 59.759 55.0 0.0 0.0 0.0 4.17 F
1237 2952 0.108804 GCGGTTCATCGAGGTGAGAA 60.109 55.0 0.0 0.0 0.0 2.87 F
1659 3402 0.455633 GCGCCTCATGTCTGCTTTTG 60.456 55.0 0.0 0.0 0.0 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1853 3606 0.179032 ATCACAACCACAACCGCTCA 60.179 50.0 0.0 0.0 0.00 4.26 R
2840 4756 0.391130 TGACAGGCATACTTCGGTGC 60.391 55.0 0.0 0.0 40.55 5.01 R
3372 5353 0.249197 CTTCCGCTGCTCATGATCGA 60.249 55.0 0.0 0.0 0.00 3.59 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
239 240 0.546122 ACTCCAAATCGCCCATGCTA 59.454 50.000 0.00 0.00 34.43 3.49
441 450 3.565482 CCGCATAAGTGGCATGTATCTTT 59.435 43.478 0.00 0.00 38.83 2.52
654 2335 7.912773 CAGTATCATATGATAGGCAGAACGTAG 59.087 40.741 22.97 6.88 37.67 3.51
770 2452 7.932120 AAAGGACTGAAAATAGATCGTATCG 57.068 36.000 0.00 0.00 0.00 2.92
771 2453 5.462405 AGGACTGAAAATAGATCGTATCGC 58.538 41.667 0.00 0.00 0.00 4.58
831 2518 1.878102 CGATTTCTGGCGGATTAGGGG 60.878 57.143 0.00 0.00 0.00 4.79
872 2559 6.094186 GCCTTTTGAAGTTATCTCGAGGAATT 59.906 38.462 13.56 4.74 0.00 2.17
881 2568 9.838339 AAGTTATCTCGAGGAATTCAATTATGT 57.162 29.630 13.56 0.00 0.00 2.29
963 2650 0.893270 CCTTCCATCCAACACCGCAA 60.893 55.000 0.00 0.00 0.00 4.85
964 2651 0.240945 CTTCCATCCAACACCGCAAC 59.759 55.000 0.00 0.00 0.00 4.17
965 2652 0.466372 TTCCATCCAACACCGCAACA 60.466 50.000 0.00 0.00 0.00 3.33
966 2653 0.251121 TCCATCCAACACCGCAACAT 60.251 50.000 0.00 0.00 0.00 2.71
967 2654 0.602562 CCATCCAACACCGCAACATT 59.397 50.000 0.00 0.00 0.00 2.71
968 2655 1.669502 CCATCCAACACCGCAACATTG 60.670 52.381 0.00 0.00 0.00 2.82
969 2656 1.269174 CATCCAACACCGCAACATTGA 59.731 47.619 0.00 0.00 0.00 2.57
970 2657 1.614996 TCCAACACCGCAACATTGAT 58.385 45.000 0.00 0.00 0.00 2.57
971 2658 1.959985 TCCAACACCGCAACATTGATT 59.040 42.857 0.00 0.00 0.00 2.57
972 2659 2.363680 TCCAACACCGCAACATTGATTT 59.636 40.909 0.00 0.00 0.00 2.17
973 2660 3.129871 CCAACACCGCAACATTGATTTT 58.870 40.909 0.00 0.00 0.00 1.82
974 2661 3.059733 CCAACACCGCAACATTGATTTTG 60.060 43.478 0.00 0.00 0.00 2.44
975 2662 3.724508 ACACCGCAACATTGATTTTGA 57.275 38.095 0.00 0.00 0.00 2.69
985 2672 2.367030 TTGATTTTGAAGCATGGCCG 57.633 45.000 0.00 0.00 0.00 6.13
1007 2694 0.474854 TTGGGCCTGGTAGAACTGGA 60.475 55.000 4.53 0.00 0.00 3.86
1041 2728 2.383855 CAAACCCAAACCCAAGTCTCA 58.616 47.619 0.00 0.00 0.00 3.27
1125 2824 1.181786 CGCTCTCCTCTTCCTCTTGT 58.818 55.000 0.00 0.00 0.00 3.16
1237 2952 0.108804 GCGGTTCATCGAGGTGAGAA 60.109 55.000 0.00 0.00 0.00 2.87
1271 2986 1.982223 GCATCCTCTCGATCGATTTCG 59.018 52.381 19.78 7.03 40.46 3.46
1489 3217 1.192428 GGATCCGTCTGTTGGTAGGT 58.808 55.000 0.00 0.00 0.00 3.08
1490 3218 2.381911 GGATCCGTCTGTTGGTAGGTA 58.618 52.381 0.00 0.00 0.00 3.08
1491 3219 2.100418 GGATCCGTCTGTTGGTAGGTAC 59.900 54.545 0.00 0.00 0.00 3.34
1492 3220 2.592102 TCCGTCTGTTGGTAGGTACT 57.408 50.000 0.00 0.00 46.37 2.73
1534 3262 1.993948 GGTGGTAGAGGTGGGGGAC 60.994 68.421 0.00 0.00 0.00 4.46
1549 3288 1.678970 GGACTTGGGGCGCTGATTT 60.679 57.895 7.64 0.00 0.00 2.17
1641 3384 4.793028 GCCTGTTAACTTTGGTTTCAGAGC 60.793 45.833 7.22 10.29 37.84 4.09
1644 3387 0.668535 AACTTTGGTTTCAGAGCGCC 59.331 50.000 2.29 0.00 30.55 6.53
1655 3398 2.186384 GAGCGCCTCATGTCTGCT 59.814 61.111 2.29 4.62 38.89 4.24
1659 3402 0.455633 GCGCCTCATGTCTGCTTTTG 60.456 55.000 0.00 0.00 0.00 2.44
1697 3450 1.273759 AGCAGCTCTGAGTGATTCCA 58.726 50.000 6.53 0.00 0.00 3.53
1730 3483 0.898320 GCTGCCACCTTCTGTCTCTA 59.102 55.000 0.00 0.00 0.00 2.43
1739 3492 3.201290 CCTTCTGTCTCTATTGCGCAAT 58.799 45.455 35.42 35.42 34.93 3.56
1740 3493 3.002042 CCTTCTGTCTCTATTGCGCAATG 59.998 47.826 38.81 28.44 32.50 2.82
1763 3516 2.433239 GCGTAACCTTGAGGATTCCCTA 59.567 50.000 3.59 0.00 44.53 3.53
1768 3521 3.736094 ACCTTGAGGATTCCCTACATCA 58.264 45.455 3.59 0.00 44.53 3.07
1779 3532 7.293535 AGGATTCCCTACATCAACTTAAGCTAT 59.706 37.037 1.29 0.00 42.15 2.97
1785 3538 4.455606 ACATCAACTTAAGCTATCAGGCC 58.544 43.478 1.29 0.00 0.00 5.19
1802 3555 1.339342 GGCCATTTTCCTTGCAAGCAT 60.339 47.619 21.43 6.86 0.00 3.79
1820 3573 2.416431 GCATTTGCCTTGTGATCCAGTC 60.416 50.000 0.00 0.00 34.31 3.51
1821 3574 2.655090 TTTGCCTTGTGATCCAGTCA 57.345 45.000 0.00 0.00 0.00 3.41
1847 3600 4.875536 GGCATTTCTTGTTTCAAACCTGTT 59.124 37.500 0.00 0.00 0.00 3.16
1848 3601 5.220643 GGCATTTCTTGTTTCAAACCTGTTG 60.221 40.000 0.00 0.00 0.00 3.33
1849 3602 5.727515 GCATTTCTTGTTTCAAACCTGTTGC 60.728 40.000 0.00 0.00 0.00 4.17
1850 3603 3.518634 TCTTGTTTCAAACCTGTTGCC 57.481 42.857 0.00 0.00 0.00 4.52
1851 3604 3.096092 TCTTGTTTCAAACCTGTTGCCT 58.904 40.909 0.00 0.00 0.00 4.75
1852 3605 2.957491 TGTTTCAAACCTGTTGCCTG 57.043 45.000 0.00 0.00 0.00 4.85
1853 3606 2.175202 TGTTTCAAACCTGTTGCCTGT 58.825 42.857 0.00 0.00 0.00 4.00
1860 3613 2.281070 CTGTTGCCTGTGAGCGGT 60.281 61.111 0.00 0.00 34.65 5.68
1892 3645 7.484140 TGTGATGTGTAGCAGTTTCTAGATAG 58.516 38.462 0.00 0.00 0.00 2.08
1895 3648 8.355913 TGATGTGTAGCAGTTTCTAGATAGATG 58.644 37.037 0.00 0.00 31.40 2.90
1896 3649 6.507900 TGTGTAGCAGTTTCTAGATAGATGC 58.492 40.000 10.55 10.55 36.56 3.91
1897 3650 6.096846 TGTGTAGCAGTTTCTAGATAGATGCA 59.903 38.462 17.16 0.00 37.97 3.96
1898 3651 6.640499 GTGTAGCAGTTTCTAGATAGATGCAG 59.360 42.308 17.16 0.40 37.97 4.41
1942 3763 5.424757 CCGATGTTGTAGGTTCTCCAATTA 58.575 41.667 0.00 0.00 35.89 1.40
2006 3829 0.837272 GCAGGTAGTATTGGCCCTGA 59.163 55.000 0.00 0.00 45.97 3.86
2007 3830 1.202698 GCAGGTAGTATTGGCCCTGAG 60.203 57.143 0.00 0.00 45.97 3.35
2008 3831 1.417890 CAGGTAGTATTGGCCCTGAGG 59.582 57.143 0.00 0.00 45.97 3.86
2009 3832 1.009675 AGGTAGTATTGGCCCTGAGGT 59.990 52.381 0.00 0.00 34.57 3.85
2078 3937 3.244105 CGTTCACGGTTCAGCAGG 58.756 61.111 0.00 0.00 35.37 4.85
2087 3947 0.804989 GGTTCAGCAGGTGCACATAC 59.195 55.000 20.43 6.36 45.16 2.39
2158 4047 1.996191 GTGAGCGTCATCCTTCAGAAC 59.004 52.381 0.00 0.00 0.00 3.01
2167 4056 4.024556 GTCATCCTTCAGAACGCCATAATG 60.025 45.833 0.00 0.00 0.00 1.90
2189 4078 2.637947 TGTGCTCTGTTTGCAAGTGTA 58.362 42.857 0.00 0.00 42.41 2.90
2200 4089 5.064834 TGTTTGCAAGTGTATGTCGTGTTAA 59.935 36.000 0.00 0.00 0.00 2.01
2205 4094 6.140110 GCAAGTGTATGTCGTGTTAATTTGT 58.860 36.000 0.00 0.00 0.00 2.83
2212 4101 5.752892 TGTCGTGTTAATTTGTGCCTTTA 57.247 34.783 0.00 0.00 0.00 1.85
2344 4246 9.696917 CTTTCTTGAAAATTGTAAGGCATAACT 57.303 29.630 0.00 0.00 0.00 2.24
2376 4285 6.311723 CGTTTACCTTGTGCTACTTATTTGG 58.688 40.000 0.00 0.00 0.00 3.28
2378 4287 7.520937 CGTTTACCTTGTGCTACTTATTTGGTT 60.521 37.037 0.00 0.00 0.00 3.67
2388 4297 2.719705 ACTTATTTGGTTCCAGGGTGGA 59.280 45.455 0.00 0.00 46.61 4.02
2403 4312 5.195940 CAGGGTGGATCATATTTGAGTGTT 58.804 41.667 0.00 0.00 34.73 3.32
2451 4360 3.054434 CCAGGGTGATCCATTAGTTGACA 60.054 47.826 0.00 0.00 38.24 3.58
2472 4381 2.952714 GACAGCTTGTCCATTGCCT 58.047 52.632 5.33 0.00 41.37 4.75
2476 4385 2.025981 ACAGCTTGTCCATTGCCTGATA 60.026 45.455 0.00 0.00 0.00 2.15
2477 4386 2.357009 CAGCTTGTCCATTGCCTGATAC 59.643 50.000 0.00 0.00 0.00 2.24
2483 4392 1.561076 TCCATTGCCTGATACTGTGCT 59.439 47.619 0.00 0.00 0.00 4.40
2686 4595 2.695613 TCATCGACATGAGCGAGATC 57.304 50.000 17.32 0.00 41.49 2.75
2718 4627 2.605837 TTCGGTGTGCACTAGAACAA 57.394 45.000 19.41 0.54 34.28 2.83
2723 4632 0.602638 TGTGCACTAGAACAAGGCCG 60.603 55.000 19.41 0.00 27.50 6.13
2771 4682 1.745653 GGCCTTTTGAGCTATGTGTCC 59.254 52.381 0.00 0.00 0.00 4.02
2818 4734 3.815401 GGCGTTGAAAGATGCATAGGTAT 59.185 43.478 0.00 0.00 33.18 2.73
2859 4782 0.391130 GCACCGAAGTATGCCTGTCA 60.391 55.000 0.00 0.00 35.73 3.58
2911 4835 0.741915 TGGGTTGAACTTTTGACCGC 59.258 50.000 0.00 0.00 32.91 5.68
2934 4858 0.607489 TCCAGGAGCAAGCAAGAAGC 60.607 55.000 0.00 0.00 46.19 3.86
2961 4885 3.980775 CCTGTTTTAACACGCCAAGATTG 59.019 43.478 0.00 0.00 34.70 2.67
3013 4942 2.358737 GTCCGTCTGCCCAACCTG 60.359 66.667 0.00 0.00 0.00 4.00
3023 4952 5.448632 CGTCTGCCCAACCTGTTTATTTATC 60.449 44.000 0.00 0.00 0.00 1.75
3108 5044 2.013400 ACAACCGCGCAATCATTCATA 58.987 42.857 8.75 0.00 0.00 2.15
3109 5045 2.421775 ACAACCGCGCAATCATTCATAA 59.578 40.909 8.75 0.00 0.00 1.90
3141 5077 4.323028 GGGATCCATTGCATCTCTCGATTA 60.323 45.833 15.23 0.00 0.00 1.75
3145 5081 7.550551 GGATCCATTGCATCTCTCGATTAATTA 59.449 37.037 6.95 0.00 0.00 1.40
3159 5095 8.860088 TCTCGATTAATTAATCTCTCATGGTGA 58.140 33.333 27.45 16.62 39.85 4.02
3165 5101 5.871396 TTAATCTCTCATGGTGAGTACCC 57.129 43.478 13.58 0.00 46.96 3.69
3176 5112 1.134670 GTGAGTACCCATGACTGGCTC 60.135 57.143 0.00 0.00 41.64 4.70
3241 5189 1.825090 TTTCAGAGGGTAGTACGCGA 58.175 50.000 15.93 0.00 36.04 5.87
3292 5246 5.106038 TGTGAGTTAAGGGTACATGTACGAG 60.106 44.000 25.69 0.00 36.94 4.18
3293 5247 4.400251 TGAGTTAAGGGTACATGTACGAGG 59.600 45.833 25.69 0.00 36.94 4.63
3297 5251 1.287146 AGGGTACATGTACGAGGGAGT 59.713 52.381 25.69 5.89 36.94 3.85
3298 5252 2.511218 AGGGTACATGTACGAGGGAGTA 59.489 50.000 25.69 0.00 36.94 2.59
3299 5253 2.620585 GGGTACATGTACGAGGGAGTAC 59.379 54.545 25.69 11.17 45.22 2.73
3372 5353 0.249363 TCGACCGACGATCTCGATCT 60.249 55.000 6.60 0.00 46.14 2.75
3465 5458 1.227147 CGCCCACGACGGAATGTAT 60.227 57.895 0.00 0.00 43.93 2.29
3468 5461 1.202440 GCCCACGACGGAATGTATGTA 60.202 52.381 0.00 0.00 36.56 2.29
3469 5462 2.547218 GCCCACGACGGAATGTATGTAT 60.547 50.000 0.00 0.00 36.56 2.29
3470 5463 3.057019 CCCACGACGGAATGTATGTATG 58.943 50.000 0.00 0.00 36.56 2.39
3471 5464 2.475111 CCACGACGGAATGTATGTATGC 59.525 50.000 0.00 0.00 36.56 3.14
3472 5465 3.120041 CACGACGGAATGTATGTATGCA 58.880 45.455 0.00 0.00 0.00 3.96
3473 5466 3.060540 CACGACGGAATGTATGTATGCAC 60.061 47.826 0.00 0.00 0.00 4.57
3479 5472 4.450976 GGAATGTATGTATGCACAGGTCA 58.549 43.478 0.00 0.00 38.30 4.02
3573 5570 0.514691 GCCTCGACAGCTTCTTGTTG 59.485 55.000 0.00 0.00 34.39 3.33
3581 5578 2.695147 ACAGCTTCTTGTTGAAAAGGGG 59.305 45.455 0.00 0.00 33.79 4.79
3587 5886 4.953940 TCTTGTTGAAAAGGGGAAATGG 57.046 40.909 0.00 0.00 0.00 3.16
3642 5941 3.074412 ACGTATGCCAACTTCTTCCTTG 58.926 45.455 0.00 0.00 0.00 3.61
3643 5942 3.244422 ACGTATGCCAACTTCTTCCTTGA 60.244 43.478 0.00 0.00 0.00 3.02
3647 5949 3.631250 TGCCAACTTCTTCCTTGAAACT 58.369 40.909 0.00 0.00 0.00 2.66
3727 6266 0.668535 GCAAGGTTGGCGTCTTCTTT 59.331 50.000 0.00 0.00 0.00 2.52
3737 6280 1.944430 GCGTCTTCTTTCCCGTGGAAT 60.944 52.381 6.25 0.00 41.71 3.01
3738 6281 2.423577 CGTCTTCTTTCCCGTGGAATT 58.576 47.619 6.25 0.00 41.71 2.17
3741 6284 2.107552 TCTTCTTTCCCGTGGAATTGGT 59.892 45.455 6.25 0.00 41.71 3.67
3747 6290 1.076350 TCCCGTGGAATTGGTTTGGAT 59.924 47.619 0.00 0.00 0.00 3.41
3848 6392 0.250553 ACGCTTTTGATTCCGTGGGA 60.251 50.000 0.00 0.00 32.07 4.37
3851 6395 2.706890 GCTTTTGATTCCGTGGGAGTA 58.293 47.619 0.00 0.00 31.21 2.59
3852 6396 2.418976 GCTTTTGATTCCGTGGGAGTAC 59.581 50.000 0.00 0.00 31.21 2.73
3873 6417 3.028850 CCACCTTTCATGAGCATGGAAT 58.971 45.455 10.31 0.00 35.85 3.01
3874 6418 3.449737 CCACCTTTCATGAGCATGGAATT 59.550 43.478 10.31 0.00 35.85 2.17
3876 6420 5.484715 CACCTTTCATGAGCATGGAATTTT 58.515 37.500 10.31 0.00 35.85 1.82
3877 6421 6.351202 CCACCTTTCATGAGCATGGAATTTTA 60.351 38.462 10.31 0.00 35.85 1.52
3881 6425 7.067859 CCTTTCATGAGCATGGAATTTTAGAGA 59.932 37.037 10.31 0.00 35.85 3.10
3916 6464 2.614734 CCCCAAGTACTCCCTTCGTTTC 60.615 54.545 0.00 0.00 0.00 2.78
3923 6471 6.029346 AGTACTCCCTTCGTTTCGAATTAA 57.971 37.500 0.00 0.00 44.85 1.40
3924 6472 6.458210 AGTACTCCCTTCGTTTCGAATTAAA 58.542 36.000 0.00 0.00 44.85 1.52
3927 6475 7.910441 ACTCCCTTCGTTTCGAATTAAATTA 57.090 32.000 0.00 0.00 44.85 1.40
3972 6520 7.667635 TCATCAGGTCTAGAGAAATACATCGAT 59.332 37.037 0.00 0.00 0.00 3.59
3978 6526 8.662141 GGTCTAGAGAAATACATCGATCTCTAC 58.338 40.741 14.34 10.03 45.05 2.59
4022 6570 8.567285 AAACTTCTATGGTTTAAGAGTCATGG 57.433 34.615 0.00 0.00 35.48 3.66
4023 6571 7.259088 ACTTCTATGGTTTAAGAGTCATGGT 57.741 36.000 0.00 0.00 0.00 3.55
4024 6572 7.331791 ACTTCTATGGTTTAAGAGTCATGGTC 58.668 38.462 0.00 0.00 0.00 4.02
4025 6573 6.867519 TCTATGGTTTAAGAGTCATGGTCA 57.132 37.500 0.00 0.00 0.00 4.02
4026 6574 7.252612 TCTATGGTTTAAGAGTCATGGTCAA 57.747 36.000 0.00 0.00 0.00 3.18
4027 6575 7.861629 TCTATGGTTTAAGAGTCATGGTCAAT 58.138 34.615 0.00 0.00 0.00 2.57
4028 6576 8.328758 TCTATGGTTTAAGAGTCATGGTCAATT 58.671 33.333 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
654 2335 2.289820 GAGAAACGGGGTCTTTTCACAC 59.710 50.000 0.00 0.00 34.70 3.82
770 2452 0.729690 GCTCAATGGAAGGAAGACGC 59.270 55.000 0.00 0.00 0.00 5.19
771 2453 1.373570 GGCTCAATGGAAGGAAGACG 58.626 55.000 0.00 0.00 0.00 4.18
831 2518 5.353123 TCAAAAGGCCGATTACATCACTTAC 59.647 40.000 0.00 0.00 0.00 2.34
881 2568 3.202906 GGCTTCGACAAGTATATGGCAA 58.797 45.455 0.00 0.00 31.45 4.52
963 2650 3.602483 GGCCATGCTTCAAAATCAATGT 58.398 40.909 0.00 0.00 0.00 2.71
964 2651 2.605818 CGGCCATGCTTCAAAATCAATG 59.394 45.455 2.24 0.00 0.00 2.82
965 2652 2.234414 ACGGCCATGCTTCAAAATCAAT 59.766 40.909 2.24 0.00 0.00 2.57
966 2653 1.617850 ACGGCCATGCTTCAAAATCAA 59.382 42.857 2.24 0.00 0.00 2.57
967 2654 1.067706 CACGGCCATGCTTCAAAATCA 60.068 47.619 2.24 0.00 0.00 2.57
968 2655 1.067635 ACACGGCCATGCTTCAAAATC 60.068 47.619 0.00 0.00 0.00 2.17
969 2656 0.968405 ACACGGCCATGCTTCAAAAT 59.032 45.000 0.00 0.00 0.00 1.82
970 2657 0.749649 AACACGGCCATGCTTCAAAA 59.250 45.000 0.00 0.00 0.00 2.44
971 2658 0.031857 CAACACGGCCATGCTTCAAA 59.968 50.000 0.00 0.00 0.00 2.69
972 2659 1.659233 CAACACGGCCATGCTTCAA 59.341 52.632 0.00 0.00 0.00 2.69
973 2660 2.267351 CCAACACGGCCATGCTTCA 61.267 57.895 0.00 0.00 0.00 3.02
974 2661 2.568090 CCAACACGGCCATGCTTC 59.432 61.111 0.00 0.00 0.00 3.86
975 2662 2.990967 CCCAACACGGCCATGCTT 60.991 61.111 0.00 0.00 0.00 3.91
985 2672 0.400594 AGTTCTACCAGGCCCAACAC 59.599 55.000 0.00 0.00 0.00 3.32
1007 2694 1.395635 GGTTTGGGTTCGAAACTGGT 58.604 50.000 13.88 0.00 34.36 4.00
1041 2728 4.778143 GCCGTTGACCCGCTCCAT 62.778 66.667 0.00 0.00 0.00 3.41
1210 2925 2.789917 GATGAACCGCTGCAGCTG 59.210 61.111 34.22 30.22 39.32 4.24
1237 2952 3.382803 GATGCTGCGCAGAGGGAGT 62.383 63.158 40.21 17.70 43.65 3.85
1271 2986 1.592939 GCGGGGCTCGAGAAATCTC 60.593 63.158 18.75 0.00 42.43 2.75
1273 2988 2.589159 GGCGGGGCTCGAGAAATC 60.589 66.667 18.75 0.00 42.43 2.17
1468 3196 0.102481 CTACCAACAGACGGATCCGG 59.898 60.000 35.87 21.60 44.69 5.14
1489 3217 1.964223 GCATAGCCTGAGCCTGTAGTA 59.036 52.381 0.00 0.00 41.25 1.82
1490 3218 0.755686 GCATAGCCTGAGCCTGTAGT 59.244 55.000 0.00 0.00 41.25 2.73
1491 3219 1.000731 GAGCATAGCCTGAGCCTGTAG 59.999 57.143 0.00 0.00 41.25 2.74
1492 3220 1.043816 GAGCATAGCCTGAGCCTGTA 58.956 55.000 0.00 0.00 41.25 2.74
1534 3262 0.388907 CACAAAATCAGCGCCCCAAG 60.389 55.000 2.29 0.00 0.00 3.61
1549 3288 2.425592 CGCTCCAGTCACCCACAA 59.574 61.111 0.00 0.00 0.00 3.33
1582 3321 1.404479 AACAGGCAGTGTGGACCGTA 61.404 55.000 0.00 0.00 40.26 4.02
1641 3384 0.455633 GCAAAAGCAGACATGAGGCG 60.456 55.000 0.00 0.00 0.00 5.52
1644 3387 1.463034 CGACGCAAAAGCAGACATGAG 60.463 52.381 0.00 0.00 0.00 2.90
1739 3492 0.988832 AATCCTCAAGGTTACGCCCA 59.011 50.000 0.00 0.00 38.26 5.36
1740 3493 1.664873 GAATCCTCAAGGTTACGCCC 58.335 55.000 0.00 0.00 38.26 6.13
1747 3500 3.736094 TGATGTAGGGAATCCTCAAGGT 58.264 45.455 0.00 0.00 43.66 3.50
1763 3516 4.080356 TGGCCTGATAGCTTAAGTTGATGT 60.080 41.667 3.32 0.00 0.00 3.06
1768 3521 5.360999 GGAAAATGGCCTGATAGCTTAAGTT 59.639 40.000 3.32 0.00 0.00 2.66
1779 3532 1.619827 CTTGCAAGGAAAATGGCCTGA 59.380 47.619 19.14 0.00 35.50 3.86
1802 3555 2.655090 TGACTGGATCACAAGGCAAA 57.345 45.000 0.00 0.00 29.99 3.68
1820 3573 4.270808 GGTTTGAAACAAGAAATGCCAGTG 59.729 41.667 10.53 0.00 0.00 3.66
1821 3574 4.162131 AGGTTTGAAACAAGAAATGCCAGT 59.838 37.500 10.53 0.00 0.00 4.00
1847 3600 2.591429 CACAACCGCTCACAGGCA 60.591 61.111 0.00 0.00 0.00 4.75
1848 3601 3.357079 CCACAACCGCTCACAGGC 61.357 66.667 0.00 0.00 0.00 4.85
1849 3602 1.525995 AACCACAACCGCTCACAGG 60.526 57.895 0.00 0.00 0.00 4.00
1850 3603 1.095228 ACAACCACAACCGCTCACAG 61.095 55.000 0.00 0.00 0.00 3.66
1851 3604 1.078072 ACAACCACAACCGCTCACA 60.078 52.632 0.00 0.00 0.00 3.58
1852 3605 1.092921 TCACAACCACAACCGCTCAC 61.093 55.000 0.00 0.00 0.00 3.51
1853 3606 0.179032 ATCACAACCACAACCGCTCA 60.179 50.000 0.00 0.00 0.00 4.26
1860 3613 2.877786 CTGCTACACATCACAACCACAA 59.122 45.455 0.00 0.00 0.00 3.33
1892 3645 2.360165 CCAAAACTCATAGGCCTGCATC 59.640 50.000 17.99 0.00 0.00 3.91
1895 3648 0.457443 GCCAAAACTCATAGGCCTGC 59.543 55.000 17.99 1.28 41.25 4.85
1962 3785 7.965655 GCAAGCTAAAACTAAAGAAGGAGATTC 59.034 37.037 0.00 0.00 38.28 2.52
1969 3792 6.319141 ACCTGCAAGCTAAAACTAAAGAAG 57.681 37.500 0.00 0.00 0.00 2.85
1974 3797 7.335924 CCAATACTACCTGCAAGCTAAAACTAA 59.664 37.037 0.00 0.00 0.00 2.24
2008 3831 5.349543 CCTTACAAGTTACGTTGGTATGGAC 59.650 44.000 0.00 0.00 0.00 4.02
2009 3832 5.245751 TCCTTACAAGTTACGTTGGTATGGA 59.754 40.000 0.00 0.00 0.00 3.41
2020 3843 9.169592 TGCCACTAAATAATCCTTACAAGTTAC 57.830 33.333 0.00 0.00 0.00 2.50
2061 3884 1.594293 ACCTGCTGAACCGTGAACG 60.594 57.895 0.00 0.00 39.44 3.95
2087 3947 1.648720 CTGCAGGTGGTTCAACACG 59.351 57.895 5.57 0.00 42.23 4.49
2158 4047 1.739466 ACAGAGCACAACATTATGGCG 59.261 47.619 0.00 0.00 0.00 5.69
2167 4056 2.187707 CACTTGCAAACAGAGCACAAC 58.812 47.619 0.00 0.00 42.54 3.32
2189 4078 4.846779 AAGGCACAAATTAACACGACAT 57.153 36.364 0.00 0.00 0.00 3.06
2212 4101 1.078823 TGACTATCCATATCCGCCCCT 59.921 52.381 0.00 0.00 0.00 4.79
2221 4114 6.398095 CAAACTGTGTCACTGACTATCCATA 58.602 40.000 15.96 0.00 33.15 2.74
2273 4170 9.208022 CAGAACATAACATACCGATGATAACAT 57.792 33.333 0.00 0.00 39.67 2.71
2274 4171 7.655732 CCAGAACATAACATACCGATGATAACA 59.344 37.037 0.00 0.00 36.48 2.41
2313 4215 8.522830 TGCCTTACAATTTTCAAGAAAGATAGG 58.477 33.333 0.00 0.00 0.00 2.57
2330 4232 5.933790 CGCAAGTTAAGTTATGCCTTACAA 58.066 37.500 0.00 0.00 35.41 2.41
2403 4312 0.923729 ATGGGTAATGGTCAGGGGCA 60.924 55.000 0.00 0.00 0.00 5.36
2469 4378 1.065854 AGTTGGAGCACAGTATCAGGC 60.066 52.381 0.00 0.00 0.00 4.85
2472 4381 2.224499 TGCAAGTTGGAGCACAGTATCA 60.224 45.455 4.75 0.00 35.51 2.15
2476 4385 1.027357 CTTGCAAGTTGGAGCACAGT 58.973 50.000 18.65 0.00 41.05 3.55
2477 4386 1.002033 GACTTGCAAGTTGGAGCACAG 60.002 52.381 31.58 2.61 41.05 3.66
2483 4392 3.219281 GGGTTAAGACTTGCAAGTTGGA 58.781 45.455 31.58 17.15 39.88 3.53
2660 4569 2.736719 CGCTCATGTCGATGAACCTCTT 60.737 50.000 4.55 0.00 38.17 2.85
2704 4613 0.602638 CGGCCTTGTTCTAGTGCACA 60.603 55.000 21.04 4.13 0.00 4.57
2706 4615 1.671054 GCGGCCTTGTTCTAGTGCA 60.671 57.895 0.00 0.00 0.00 4.57
2735 4646 2.195567 GCCAGGAAGCAACTGCACA 61.196 57.895 4.22 0.00 45.16 4.57
2771 4682 1.135972 CAAAATCCGCTCACACCGAAG 60.136 52.381 0.00 0.00 0.00 3.79
2818 4734 2.510382 TCAGTTAAACCCCCACTGAACA 59.490 45.455 0.00 0.00 43.12 3.18
2840 4756 0.391130 TGACAGGCATACTTCGGTGC 60.391 55.000 0.00 0.00 40.55 5.01
2859 4782 7.556844 AGAATTACTACAAGGATGACGACAAT 58.443 34.615 0.00 0.00 0.00 2.71
2961 4885 2.686405 AGGACCAAACGAAAAGGAACAC 59.314 45.455 0.00 0.00 0.00 3.32
3013 4942 9.727627 CAGCAAATCTTCTCTGGATAAATAAAC 57.272 33.333 0.00 0.00 0.00 2.01
3023 4952 3.269178 GTCTCCAGCAAATCTTCTCTGG 58.731 50.000 0.92 0.92 45.59 3.86
3108 5044 2.689983 GCAATGGATCCCAGAATTCGTT 59.310 45.455 9.90 0.00 36.75 3.85
3109 5045 2.301346 GCAATGGATCCCAGAATTCGT 58.699 47.619 9.90 0.00 36.75 3.85
3165 5101 1.462283 CAACTTCACGAGCCAGTCATG 59.538 52.381 0.00 0.00 0.00 3.07
3176 5112 3.818961 TCGTACTACTCCAACTTCACG 57.181 47.619 0.00 0.00 0.00 4.35
3241 5189 4.210331 AGAAGACTTGGTGATTGCTTGTT 58.790 39.130 0.00 0.00 0.00 2.83
3292 5246 4.638865 GGTTGGTTGTTGATATGTACTCCC 59.361 45.833 0.00 0.00 0.00 4.30
3293 5247 5.250200 TGGTTGGTTGTTGATATGTACTCC 58.750 41.667 0.00 0.00 0.00 3.85
3297 5251 7.093988 CCAAATCTGGTTGGTTGTTGATATGTA 60.094 37.037 0.00 0.00 42.74 2.29
3298 5252 6.295236 CCAAATCTGGTTGGTTGTTGATATGT 60.295 38.462 0.00 0.00 42.74 2.29
3299 5253 6.101332 CCAAATCTGGTTGGTTGTTGATATG 58.899 40.000 0.00 0.00 42.74 1.78
3300 5254 6.284891 CCAAATCTGGTTGGTTGTTGATAT 57.715 37.500 0.00 0.00 42.74 1.63
3301 5255 5.720371 CCAAATCTGGTTGGTTGTTGATA 57.280 39.130 0.00 0.00 42.74 2.15
3302 5256 4.605640 CCAAATCTGGTTGGTTGTTGAT 57.394 40.909 0.00 0.00 42.74 2.57
3333 5298 5.750067 GTCGACGCCACCTTTATCTTTATAA 59.250 40.000 0.00 0.00 0.00 0.98
3336 5301 3.514645 GTCGACGCCACCTTTATCTTTA 58.485 45.455 0.00 0.00 0.00 1.85
3372 5353 0.249197 CTTCCGCTGCTCATGATCGA 60.249 55.000 0.00 0.00 0.00 3.59
3376 5357 1.219124 GTCCTTCCGCTGCTCATGA 59.781 57.895 0.00 0.00 0.00 3.07
3377 5358 2.169789 CGTCCTTCCGCTGCTCATG 61.170 63.158 0.00 0.00 0.00 3.07
3378 5359 2.185350 CGTCCTTCCGCTGCTCAT 59.815 61.111 0.00 0.00 0.00 2.90
3379 5360 2.989253 TCGTCCTTCCGCTGCTCA 60.989 61.111 0.00 0.00 0.00 4.26
3380 5361 2.507324 GTCGTCCTTCCGCTGCTC 60.507 66.667 0.00 0.00 0.00 4.26
3381 5362 4.421479 CGTCGTCCTTCCGCTGCT 62.421 66.667 0.00 0.00 0.00 4.24
3465 5458 2.168326 CACACTGACCTGTGCATACA 57.832 50.000 6.90 0.00 41.30 2.29
3479 5472 2.173519 CCATTTCATTCCCAGCACACT 58.826 47.619 0.00 0.00 0.00 3.55
3532 5525 0.878523 TGAGCTCGTTCGTTGGTTGG 60.879 55.000 9.64 0.00 0.00 3.77
3573 5570 2.319025 TGGTCCCATTTCCCCTTTTC 57.681 50.000 0.00 0.00 0.00 2.29
3618 5917 2.601763 GGAAGAAGTTGGCATACGTACG 59.398 50.000 15.01 15.01 0.00 3.67
3619 5918 3.858247 AGGAAGAAGTTGGCATACGTAC 58.142 45.455 0.00 0.00 0.00 3.67
3620 5919 4.020928 TCAAGGAAGAAGTTGGCATACGTA 60.021 41.667 0.00 0.00 0.00 3.57
3621 5920 3.074412 CAAGGAAGAAGTTGGCATACGT 58.926 45.455 0.00 0.00 0.00 3.57
3642 5941 7.379797 GGCAACATCTACTTTTCTTTCAGTTTC 59.620 37.037 0.00 0.00 0.00 2.78
3643 5942 7.068716 AGGCAACATCTACTTTTCTTTCAGTTT 59.931 33.333 0.00 0.00 41.41 2.66
3647 5949 7.362056 GCATAGGCAACATCTACTTTTCTTTCA 60.362 37.037 0.00 0.00 40.72 2.69
3727 6266 0.478942 TCCAAACCAATTCCACGGGA 59.521 50.000 0.00 0.00 0.00 5.14
3741 6284 2.030401 CGTCGCGGGTTCATCCAAA 61.030 57.895 6.13 0.00 38.11 3.28
3848 6392 3.614092 CATGCTCATGAAAGGTGGTACT 58.386 45.455 3.88 0.00 41.20 2.73
3851 6395 1.355381 TCCATGCTCATGAAAGGTGGT 59.645 47.619 11.17 0.00 41.20 4.16
3852 6396 2.133281 TCCATGCTCATGAAAGGTGG 57.867 50.000 11.17 3.45 41.20 4.61
3862 6406 4.191544 CCGTCTCTAAAATTCCATGCTCA 58.808 43.478 0.00 0.00 0.00 4.26
3873 6417 3.334691 CTGCATTCACCCGTCTCTAAAA 58.665 45.455 0.00 0.00 0.00 1.52
3874 6418 2.935238 GCTGCATTCACCCGTCTCTAAA 60.935 50.000 0.00 0.00 0.00 1.85
3876 6420 0.175760 GCTGCATTCACCCGTCTCTA 59.824 55.000 0.00 0.00 0.00 2.43
3877 6421 1.078848 GCTGCATTCACCCGTCTCT 60.079 57.895 0.00 0.00 0.00 3.10
3881 6425 4.740822 GGGGCTGCATTCACCCGT 62.741 66.667 0.50 0.00 45.27 5.28
3931 6479 3.374988 CCTGATGATCAAGCTTACGCAAA 59.625 43.478 0.00 0.00 39.10 3.68
3933 6481 2.093500 ACCTGATGATCAAGCTTACGCA 60.093 45.455 0.00 0.00 39.10 5.24
3934 6482 2.541762 GACCTGATGATCAAGCTTACGC 59.458 50.000 0.00 0.00 0.00 4.42
3935 6483 4.052159 AGACCTGATGATCAAGCTTACG 57.948 45.455 0.00 0.00 0.00 3.18
3945 6493 7.667635 TCGATGTATTTCTCTAGACCTGATGAT 59.332 37.037 0.00 0.00 0.00 2.45
3999 6547 7.038302 TGACCATGACTCTTAAACCATAGAAGT 60.038 37.037 0.00 0.00 0.00 3.01
4000 6548 7.331026 TGACCATGACTCTTAAACCATAGAAG 58.669 38.462 0.00 0.00 0.00 2.85
4001 6549 7.252612 TGACCATGACTCTTAAACCATAGAA 57.747 36.000 0.00 0.00 0.00 2.10
4002 6550 6.867519 TGACCATGACTCTTAAACCATAGA 57.132 37.500 0.00 0.00 0.00 1.98
4003 6551 8.511604 AATTGACCATGACTCTTAAACCATAG 57.488 34.615 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.