Multiple sequence alignment - TraesCS7A01G051700

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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 TraesCS7A01G051700 chr7A 100.000 3646 0 0 1 3646 24992017 24995662 0.000000e+00 6734.0
1 TraesCS7A01G051700 chr7A 90.944 1800 124 23 929 2711 24860781 24859004 0.000000e+00 2385.0
2 TraesCS7A01G051700 chr7A 84.044 1266 124 35 918 2154 43445001 43446217 0.000000e+00 1147.0
3 TraesCS7A01G051700 chr7A 83.351 967 96 31 1082 2032 43467713 43468630 0.000000e+00 833.0
4 TraesCS7A01G051700 chr7A 82.313 882 132 17 1692 2561 128149630 128148761 0.000000e+00 743.0
5 TraesCS7A01G051700 chr7A 79.717 424 63 17 1281 1694 128150122 128149712 5.960000e-73 285.0
6 TraesCS7A01G051700 chr7A 87.037 162 19 1 2573 2732 43446246 43446407 8.040000e-42 182.0
7 TraesCS7A01G051700 chr7A 71.681 339 80 15 2205 2533 25709955 25710287 3.020000e-11 80.5
8 TraesCS7A01G051700 chrUn 94.217 1833 93 6 901 2732 90141273 90139453 0.000000e+00 2785.0
9 TraesCS7A01G051700 chrUn 83.055 779 73 31 2896 3646 90139167 90138420 0.000000e+00 652.0
10 TraesCS7A01G051700 chr7D 92.028 1267 72 13 1457 2711 24371320 24370071 0.000000e+00 1753.0
11 TraesCS7A01G051700 chr7D 84.271 1297 117 37 918 2177 43481896 43483142 0.000000e+00 1184.0
12 TraesCS7A01G051700 chr7D 81.465 901 140 17 1692 2571 127342369 127341475 0.000000e+00 713.0
13 TraesCS7A01G051700 chr7D 84.168 499 43 22 918 1399 24371797 24371318 5.550000e-123 451.0
14 TraesCS7A01G051700 chr7D 80.562 427 64 13 1281 1699 127342851 127342436 9.830000e-81 311.0
15 TraesCS7A01G051700 chr7D 91.429 105 9 0 2628 2732 43483472 43483576 1.060000e-30 145.0
16 TraesCS7A01G051700 chr3A 98.224 901 15 1 1 901 30446616 30445717 0.000000e+00 1574.0
17 TraesCS7A01G051700 chr4A 98.109 899 16 1 1 899 582813441 582812544 0.000000e+00 1565.0
18 TraesCS7A01G051700 chr4A 97.121 903 21 5 1 901 577856936 577857835 0.000000e+00 1519.0
19 TraesCS7A01G051700 chr4A 89.103 312 34 0 1333 1644 707236409 707236098 4.410000e-104 388.0
20 TraesCS7A01G051700 chr4A 80.562 427 43 23 918 1332 707238160 707237762 3.560000e-75 292.0
21 TraesCS7A01G051700 chr2A 97.894 902 18 1 1 901 757881531 757880630 0.000000e+00 1559.0
22 TraesCS7A01G051700 chr1A 97.792 906 16 4 1 906 551574165 551575066 0.000000e+00 1559.0
23 TraesCS7A01G051700 chr1A 97.225 901 23 2 1 901 42529468 42528570 0.000000e+00 1524.0
24 TraesCS7A01G051700 chr1A 96.556 900 25 3 1 900 577713659 577712766 0.000000e+00 1485.0
25 TraesCS7A01G051700 chr6A 97.444 900 22 1 1 900 73546699 73545801 0.000000e+00 1533.0
26 TraesCS7A01G051700 chr6A 96.781 901 26 3 1 901 614285762 614286659 0.000000e+00 1500.0
27 TraesCS7A01G051700 chr7B 81.588 907 134 21 1689 2571 89001762 89002659 0.000000e+00 719.0


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 TraesCS7A01G051700 chr7A 24992017 24995662 3645 False 6734.0 6734 100.0000 1 3646 1 chr7A.!!$F1 3645
1 TraesCS7A01G051700 chr7A 24859004 24860781 1777 True 2385.0 2385 90.9440 929 2711 1 chr7A.!!$R1 1782
2 TraesCS7A01G051700 chr7A 43467713 43468630 917 False 833.0 833 83.3510 1082 2032 1 chr7A.!!$F3 950
3 TraesCS7A01G051700 chr7A 43445001 43446407 1406 False 664.5 1147 85.5405 918 2732 2 chr7A.!!$F4 1814
4 TraesCS7A01G051700 chr7A 128148761 128150122 1361 True 514.0 743 81.0150 1281 2561 2 chr7A.!!$R2 1280
5 TraesCS7A01G051700 chrUn 90138420 90141273 2853 True 1718.5 2785 88.6360 901 3646 2 chrUn.!!$R1 2745
6 TraesCS7A01G051700 chr7D 24370071 24371797 1726 True 1102.0 1753 88.0980 918 2711 2 chr7D.!!$R1 1793
7 TraesCS7A01G051700 chr7D 43481896 43483576 1680 False 664.5 1184 87.8500 918 2732 2 chr7D.!!$F1 1814
8 TraesCS7A01G051700 chr7D 127341475 127342851 1376 True 512.0 713 81.0135 1281 2571 2 chr7D.!!$R2 1290
9 TraesCS7A01G051700 chr3A 30445717 30446616 899 True 1574.0 1574 98.2240 1 901 1 chr3A.!!$R1 900
10 TraesCS7A01G051700 chr4A 582812544 582813441 897 True 1565.0 1565 98.1090 1 899 1 chr4A.!!$R1 898
11 TraesCS7A01G051700 chr4A 577856936 577857835 899 False 1519.0 1519 97.1210 1 901 1 chr4A.!!$F1 900
12 TraesCS7A01G051700 chr4A 707236098 707238160 2062 True 340.0 388 84.8325 918 1644 2 chr4A.!!$R2 726
13 TraesCS7A01G051700 chr2A 757880630 757881531 901 True 1559.0 1559 97.8940 1 901 1 chr2A.!!$R1 900
14 TraesCS7A01G051700 chr1A 551574165 551575066 901 False 1559.0 1559 97.7920 1 906 1 chr1A.!!$F1 905
15 TraesCS7A01G051700 chr1A 42528570 42529468 898 True 1524.0 1524 97.2250 1 901 1 chr1A.!!$R1 900
16 TraesCS7A01G051700 chr1A 577712766 577713659 893 True 1485.0 1485 96.5560 1 900 1 chr1A.!!$R2 899
17 TraesCS7A01G051700 chr6A 73545801 73546699 898 True 1533.0 1533 97.4440 1 900 1 chr6A.!!$R1 899
18 TraesCS7A01G051700 chr6A 614285762 614286659 897 False 1500.0 1500 96.7810 1 901 1 chr6A.!!$F1 900
19 TraesCS7A01G051700 chr7B 89001762 89002659 897 False 719.0 719 81.5880 1689 2571 1 chr7B.!!$F1 882

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
893 896 1.949525 CCATGTGGCCCTTTTATCGAG 59.05 52.381 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2824 4735 0.181114 AAGCTGCACCAGAGTTCACA 59.819 50.0 1.02 0.0 32.44 3.58 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
34 35 5.752650 TCTAGATCCTTCTCGGTTAAGTCA 58.247 41.667 0.00 0.00 33.17 3.41
77 79 5.687730 GCTAGAGTTGTTGCTTTTCCTTTTC 59.312 40.000 0.00 0.00 0.00 2.29
178 180 6.715718 CCAAGGATAACTTATCTAGACGAGGA 59.284 42.308 8.41 0.00 37.29 3.71
306 308 4.747810 ACACTAGGTAACCCGAAATTACG 58.252 43.478 0.00 0.00 34.02 3.18
450 452 6.072064 TCCTGTTTTCAACGTGTTTTCCTTTA 60.072 34.615 0.00 0.00 0.00 1.85
567 569 2.489255 CCAAGAGGCTATCTCGGGTAGA 60.489 54.545 0.00 0.00 46.82 2.59
597 599 7.618117 TGAAGTCTACAGAAGAACATATGGGTA 59.382 37.037 7.80 0.00 35.47 3.69
662 664 9.391006 GAAATTGGGTGATTCTGTAGTATGTTA 57.609 33.333 0.00 0.00 0.00 2.41
893 896 1.949525 CCATGTGGCCCTTTTATCGAG 59.050 52.381 0.00 0.00 0.00 4.04
968 977 4.012374 CCTTACATGTTGAGAGCACCAAT 58.988 43.478 2.30 0.00 0.00 3.16
970 979 3.144657 ACATGTTGAGAGCACCAATCA 57.855 42.857 0.00 0.00 0.00 2.57
1018 1037 6.255215 ACAACATTTTCAACGTAGTGTTCTG 58.745 36.000 0.00 0.00 45.00 3.02
1021 1040 5.236478 ACATTTTCAACGTAGTGTTCTGGAG 59.764 40.000 0.00 0.00 45.00 3.86
1041 1066 3.309296 AGCTAGCTACCAAGAAGCCATA 58.691 45.455 17.69 0.00 41.02 2.74
1167 1198 0.033699 AGCCCAAATCCTTCTGCTCC 60.034 55.000 0.00 0.00 0.00 4.70
1192 1230 2.982470 CTCAAGGGTTCGTAACGTACAC 59.018 50.000 0.00 0.00 30.96 2.90
1218 1256 4.577834 TCATGCATGCAAATCGATCAAT 57.422 36.364 26.68 0.00 0.00 2.57
1230 1268 2.282407 TCGATCAATGTCCATGCAGTG 58.718 47.619 0.00 0.00 35.99 3.66
1403 2800 2.928396 CTCCGGTGGGACCAGGTT 60.928 66.667 0.00 0.00 38.47 3.50
1409 2806 3.164977 TGGGACCAGGTTCGCACA 61.165 61.111 0.00 0.00 33.78 4.57
1931 3471 2.383527 CGGCAAGTTCAGCGACCTC 61.384 63.158 0.00 0.00 0.00 3.85
2081 3632 0.939577 CAGTGACGACCAACTCCACG 60.940 60.000 0.00 0.00 33.37 4.94
2105 3665 4.555709 TTCGCCACCACGCCACTT 62.556 61.111 0.00 0.00 0.00 3.16
2138 3704 0.834687 TCAACCCGAGCCTGTACCTT 60.835 55.000 0.00 0.00 0.00 3.50
2354 3928 1.517832 CTACGACTTCCTGGGGCTG 59.482 63.158 0.00 0.00 0.00 4.85
2477 4051 3.999285 ACCTCCTCGGACCTGGCT 61.999 66.667 0.00 0.00 36.31 4.75
2537 4111 3.862402 CTCTACGACGTCGCCGCT 61.862 66.667 35.92 20.06 44.43 5.52
2691 4544 2.036475 TCGTAGCGTAGTAGAGGTAGGG 59.964 54.545 0.00 0.00 0.00 3.53
2732 4585 2.202987 GATGGCACGAGCTCCAGG 60.203 66.667 8.47 0.00 41.70 4.45
2754 4636 4.625311 GGCTTTTATGCATGTGTTGTAACC 59.375 41.667 10.16 0.00 34.04 2.85
2758 4640 5.621197 TTATGCATGTGTTGTAACCTGTC 57.379 39.130 10.16 0.00 0.00 3.51
2778 4684 6.078456 TGTCATTGAAGGAGACCCATAAAT 57.922 37.500 0.00 0.00 33.88 1.40
2779 4685 6.122277 TGTCATTGAAGGAGACCCATAAATC 58.878 40.000 0.00 0.00 33.88 2.17
2780 4686 6.122277 GTCATTGAAGGAGACCCATAAATCA 58.878 40.000 0.00 0.00 33.88 2.57
2781 4687 6.261826 GTCATTGAAGGAGACCCATAAATCAG 59.738 42.308 0.00 0.00 33.88 2.90
2782 4688 6.158520 TCATTGAAGGAGACCCATAAATCAGA 59.841 38.462 0.00 0.00 33.88 3.27
2783 4689 5.620738 TGAAGGAGACCCATAAATCAGAG 57.379 43.478 0.00 0.00 33.88 3.35
2784 4690 5.280499 TGAAGGAGACCCATAAATCAGAGA 58.720 41.667 0.00 0.00 33.88 3.10
2790 4701 6.238869 GGAGACCCATAAATCAGAGAAAATGC 60.239 42.308 0.00 0.00 0.00 3.56
2793 4704 5.954150 ACCCATAAATCAGAGAAAATGCTGT 59.046 36.000 0.00 0.00 33.90 4.40
2813 4724 1.028905 AAGCTTTACACAGCGCCAAA 58.971 45.000 2.29 0.00 45.24 3.28
2819 4730 0.536233 TACACAGCGCCAAACCATGT 60.536 50.000 2.29 0.00 0.00 3.21
2820 4731 1.081242 CACAGCGCCAAACCATGTC 60.081 57.895 2.29 0.00 0.00 3.06
2822 4733 1.237285 ACAGCGCCAAACCATGTCTC 61.237 55.000 2.29 0.00 0.00 3.36
2824 4735 0.250901 AGCGCCAAACCATGTCTCTT 60.251 50.000 2.29 0.00 0.00 2.85
2825 4736 0.109597 GCGCCAAACCATGTCTCTTG 60.110 55.000 0.00 0.00 0.00 3.02
2826 4737 1.238439 CGCCAAACCATGTCTCTTGT 58.762 50.000 0.00 0.00 0.00 3.16
2829 4752 2.622942 GCCAAACCATGTCTCTTGTGAA 59.377 45.455 0.00 0.00 0.00 3.18
2867 4790 4.150980 GTGGTGCATGAATTTGTGAACATG 59.849 41.667 0.00 0.00 41.72 3.21
2871 4827 5.118050 GTGCATGAATTTGTGAACATGTGAG 59.882 40.000 0.00 0.00 41.14 3.51
2876 4832 2.936919 TTGTGAACATGTGAGCCTCT 57.063 45.000 0.00 0.00 0.00 3.69
2878 4834 1.271001 TGTGAACATGTGAGCCTCTGG 60.271 52.381 0.00 0.00 0.00 3.86
2897 4853 5.198965 TCTGGCTTAGACTTACCGTATTCT 58.801 41.667 0.00 0.00 0.00 2.40
2899 4855 6.830324 TCTGGCTTAGACTTACCGTATTCTTA 59.170 38.462 0.00 0.00 0.00 2.10
2911 4885 5.677567 ACCGTATTCTTACCAGGTTTATGG 58.322 41.667 0.00 0.64 46.47 2.74
2924 4898 5.496556 CAGGTTTATGGTATGTGAGGAACA 58.503 41.667 0.00 0.00 44.79 3.18
2931 4905 5.621197 TGGTATGTGAGGAACAAATTTCG 57.379 39.130 0.00 0.00 43.61 3.46
2936 4910 3.049912 GTGAGGAACAAATTTCGTTGGC 58.950 45.455 9.70 0.00 32.50 4.52
2938 4912 1.000717 AGGAACAAATTTCGTTGGCCG 60.001 47.619 0.00 0.00 34.24 6.13
2939 4913 1.001158 GGAACAAATTTCGTTGGCCGA 60.001 47.619 0.00 0.00 45.66 5.54
2952 4926 0.881118 TGGCCGAGACAAATTTCAGC 59.119 50.000 0.00 0.00 0.00 4.26
2954 4928 1.541588 GGCCGAGACAAATTTCAGCTT 59.458 47.619 0.00 0.00 0.00 3.74
2958 4932 4.616835 GCCGAGACAAATTTCAGCTTGATT 60.617 41.667 0.00 0.00 0.00 2.57
2965 4939 8.411683 AGACAAATTTCAGCTTGATTATGGATC 58.588 33.333 0.00 0.00 35.21 3.36
2970 4944 5.233083 TCAGCTTGATTATGGATCGGATT 57.767 39.130 0.00 0.00 37.60 3.01
2977 4951 8.116753 GCTTGATTATGGATCGGATTTATTACG 58.883 37.037 0.00 0.00 37.60 3.18
3026 5000 6.909550 TTCAGGGCAATGTATTTTAGTTGT 57.090 33.333 0.00 0.00 0.00 3.32
3027 5001 6.909550 TCAGGGCAATGTATTTTAGTTGTT 57.090 33.333 0.00 0.00 0.00 2.83
3030 5004 6.365789 CAGGGCAATGTATTTTAGTTGTTGTG 59.634 38.462 0.00 0.00 0.00 3.33
3032 5006 7.231722 AGGGCAATGTATTTTAGTTGTTGTGTA 59.768 33.333 0.00 0.00 0.00 2.90
3061 5035 3.508744 ACGGCCTTCATAATTTGCAAG 57.491 42.857 0.00 0.00 0.00 4.01
3063 5037 3.258123 ACGGCCTTCATAATTTGCAAGTT 59.742 39.130 12.16 12.16 0.00 2.66
3065 5039 4.380867 CGGCCTTCATAATTTGCAAGTTCT 60.381 41.667 10.79 0.00 0.00 3.01
3083 5062 9.099454 GCAAGTTCTATATATATTGCCCACTAC 57.901 37.037 14.08 0.00 37.62 2.73
3091 5070 0.892755 ATTGCCCACTACGAGTTCGA 59.107 50.000 8.72 0.00 43.02 3.71
3092 5071 0.675083 TTGCCCACTACGAGTTCGAA 59.325 50.000 8.72 0.00 43.02 3.71
3111 5090 0.886563 ACTCTTGCTTGCCTTGATGC 59.113 50.000 0.00 0.00 0.00 3.91
3113 5092 0.890542 TCTTGCTTGCCTTGATGCGT 60.891 50.000 0.00 0.00 0.00 5.24
3115 5094 0.388659 TTGCTTGCCTTGATGCGTTT 59.611 45.000 0.00 0.00 0.00 3.60
3116 5095 0.388659 TGCTTGCCTTGATGCGTTTT 59.611 45.000 0.00 0.00 0.00 2.43
3120 5099 3.492313 CTTGCCTTGATGCGTTTTCTAC 58.508 45.455 0.00 0.00 0.00 2.59
3122 5101 2.742053 TGCCTTGATGCGTTTTCTACTC 59.258 45.455 0.00 0.00 0.00 2.59
3127 5106 0.249398 ATGCGTTTTCTACTCGGCCT 59.751 50.000 0.00 0.00 0.00 5.19
3130 5109 1.630148 CGTTTTCTACTCGGCCTCAG 58.370 55.000 0.00 0.00 0.00 3.35
3147 5126 0.750249 CAGCCCAAAACGGTTTTCCT 59.250 50.000 15.53 9.66 37.95 3.36
3167 5153 6.421892 TCCTTTCCTAGGTACCCTAAAGTA 57.578 41.667 8.74 0.00 45.03 2.24
3170 5156 7.180946 TCCTTTCCTAGGTACCCTAAAGTAAAC 59.819 40.741 8.74 0.00 45.03 2.01
3171 5157 6.530019 TTCCTAGGTACCCTAAAGTAAACG 57.470 41.667 8.74 0.00 35.49 3.60
3173 5159 4.711846 CCTAGGTACCCTAAAGTAAACGGT 59.288 45.833 8.74 0.00 35.49 4.83
3174 5160 5.187772 CCTAGGTACCCTAAAGTAAACGGTT 59.812 44.000 8.74 0.00 35.49 4.44
3175 5161 5.567037 AGGTACCCTAAAGTAAACGGTTT 57.433 39.130 8.74 11.33 28.47 3.27
3176 5162 5.940617 AGGTACCCTAAAGTAAACGGTTTT 58.059 37.500 11.87 0.00 28.47 2.43
3252 5239 4.211125 TGCATGACTCCCTTCTACTAGAG 58.789 47.826 0.00 0.00 0.00 2.43
3254 5241 4.037446 GCATGACTCCCTTCTACTAGAGTG 59.963 50.000 0.00 0.00 39.62 3.51
3255 5242 3.622630 TGACTCCCTTCTACTAGAGTGC 58.377 50.000 0.00 0.00 39.62 4.40
3257 5244 4.473922 TGACTCCCTTCTACTAGAGTGCTA 59.526 45.833 0.00 0.00 39.62 3.49
3259 5246 4.722781 ACTCCCTTCTACTAGAGTGCTAGA 59.277 45.833 6.92 0.00 45.71 2.43
3260 5247 5.038651 TCCCTTCTACTAGAGTGCTAGAC 57.961 47.826 6.92 0.00 45.71 2.59
3261 5248 4.722781 TCCCTTCTACTAGAGTGCTAGACT 59.277 45.833 6.92 0.00 45.71 3.24
3262 5249 5.192121 TCCCTTCTACTAGAGTGCTAGACTT 59.808 44.000 6.92 0.00 45.71 3.01
3264 5251 5.529800 CCTTCTACTAGAGTGCTAGACTTCC 59.470 48.000 6.92 0.00 45.71 3.46
3266 5253 6.316280 TCTACTAGAGTGCTAGACTTCCTT 57.684 41.667 6.92 0.00 45.71 3.36
3267 5254 6.350906 TCTACTAGAGTGCTAGACTTCCTTC 58.649 44.000 6.92 0.00 45.71 3.46
3269 5256 6.316280 ACTAGAGTGCTAGACTTCCTTCTA 57.684 41.667 6.92 0.00 45.71 2.10
3270 5257 6.117488 ACTAGAGTGCTAGACTTCCTTCTAC 58.883 44.000 6.92 0.00 45.71 2.59
3271 5258 5.187621 AGAGTGCTAGACTTCCTTCTACT 57.812 43.478 0.00 0.00 33.83 2.57
3272 5259 6.316280 AGAGTGCTAGACTTCCTTCTACTA 57.684 41.667 0.00 0.00 33.83 1.82
3273 5260 6.354130 AGAGTGCTAGACTTCCTTCTACTAG 58.646 44.000 0.00 0.00 33.83 2.57
3274 5261 6.157297 AGAGTGCTAGACTTCCTTCTACTAGA 59.843 42.308 0.00 0.00 33.83 2.43
3275 5262 6.354130 AGTGCTAGACTTCCTTCTACTAGAG 58.646 44.000 0.00 0.00 34.36 2.43
3276 5263 6.069847 AGTGCTAGACTTCCTTCTACTAGAGT 60.070 42.308 0.00 0.00 34.36 3.24
3277 5264 6.037830 GTGCTAGACTTCCTTCTACTAGAGTG 59.962 46.154 0.00 0.00 34.36 3.51
3278 5265 5.008316 GCTAGACTTCCTTCTACTAGAGTGC 59.992 48.000 0.00 0.00 34.36 4.40
3279 5266 5.187621 AGACTTCCTTCTACTAGAGTGCT 57.812 43.478 0.00 0.00 0.00 4.40
3280 5267 6.316280 AGACTTCCTTCTACTAGAGTGCTA 57.684 41.667 0.00 0.00 0.00 3.49
3292 5279 3.390175 AGAGTGCTAGTGGTATCAGGT 57.610 47.619 0.00 0.00 0.00 4.00
3293 5280 4.521536 AGAGTGCTAGTGGTATCAGGTA 57.478 45.455 0.00 0.00 0.00 3.08
3294 5281 4.868268 AGAGTGCTAGTGGTATCAGGTAA 58.132 43.478 0.00 0.00 0.00 2.85
3299 5286 7.048512 AGTGCTAGTGGTATCAGGTAATTTTC 58.951 38.462 0.00 0.00 0.00 2.29
3344 5334 8.237811 TCTTTTCTCTTTTTGTTGCTATTCCT 57.762 30.769 0.00 0.00 0.00 3.36
3396 5386 7.334858 ACATTTGTGATTTTGTTTACCTGGTT 58.665 30.769 3.84 0.00 0.00 3.67
3409 5399 3.806949 ACCTGGTTTGTGGTATGTGAT 57.193 42.857 0.00 0.00 34.36 3.06
3417 5407 6.709397 TGGTTTGTGGTATGTGATAAACGTAA 59.291 34.615 0.00 0.00 31.98 3.18
3431 5421 0.321830 ACGTAATTGGTTGGTCGGGG 60.322 55.000 0.00 0.00 0.00 5.73
3440 5430 1.683629 GGTTGGTCGGGGCATATTTCA 60.684 52.381 0.00 0.00 0.00 2.69
3443 5433 0.465460 GGTCGGGGCATATTTCAGCA 60.465 55.000 0.00 0.00 0.00 4.41
3444 5434 0.947244 GTCGGGGCATATTTCAGCAG 59.053 55.000 0.00 0.00 0.00 4.24
3445 5435 0.546122 TCGGGGCATATTTCAGCAGT 59.454 50.000 0.00 0.00 0.00 4.40
3455 5445 7.308435 GGCATATTTCAGCAGTATTATGGAAC 58.692 38.462 0.00 0.00 0.00 3.62
3459 5449 7.902920 ATTTCAGCAGTATTATGGAACCAAT 57.097 32.000 0.00 0.00 0.00 3.16
3506 5504 0.966179 AAACGTGAAAATGGCCTCCC 59.034 50.000 3.32 0.00 0.00 4.30
3519 5517 2.500910 TGGCCTCCCTAATTTGCAAATG 59.499 45.455 24.74 13.25 0.00 2.32
3525 5523 4.947645 TCCCTAATTTGCAAATGCTATGC 58.052 39.130 24.74 2.57 44.08 3.14
3541 5539 3.556817 TGCATCACCTACTGCAAGG 57.443 52.632 2.71 2.71 44.87 3.61
3576 5574 3.270027 TGCTTTATGCGCTCATTAGTGT 58.730 40.909 9.73 0.00 46.63 3.55
3602 5600 4.098416 GGAGCGCACATCAGTTTTATTTC 58.902 43.478 11.47 0.00 0.00 2.17
3604 5602 3.758554 AGCGCACATCAGTTTTATTTCCT 59.241 39.130 11.47 0.00 0.00 3.36
3606 5604 5.414454 AGCGCACATCAGTTTTATTTCCTTA 59.586 36.000 11.47 0.00 0.00 2.69
3624 5622 3.129988 CCTTAGTTACCCTAGTGTCACGG 59.870 52.174 0.00 0.00 0.00 4.94
3625 5623 2.299326 AGTTACCCTAGTGTCACGGT 57.701 50.000 6.33 6.33 0.00 4.83
3626 5624 2.601905 AGTTACCCTAGTGTCACGGTT 58.398 47.619 6.38 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.345854 AGTGACTTAACCGAGAAGGATCT 58.654 43.478 0.00 0.00 45.00 2.75
77 79 6.072452 GGTATTCTCAACCTCCAAAGAAGTTG 60.072 42.308 0.00 0.00 43.16 3.16
178 180 3.056607 CGCAGAAATTTGGTCCTTTCCAT 60.057 43.478 0.00 0.00 37.33 3.41
932 935 1.071699 TGTAAGGGGAGAGTGTGTTGC 59.928 52.381 0.00 0.00 0.00 4.17
933 936 3.244561 ACATGTAAGGGGAGAGTGTGTTG 60.245 47.826 0.00 0.00 0.00 3.33
939 944 3.772025 CTCTCAACATGTAAGGGGAGAGT 59.228 47.826 21.25 0.00 41.98 3.24
968 977 8.996651 TCCGATTTGGCTCTATATATAGATGA 57.003 34.615 20.31 7.04 36.22 2.92
970 979 9.201989 TGTTCCGATTTGGCTCTATATATAGAT 57.798 33.333 20.31 6.91 36.22 1.98
1018 1037 1.202592 GGCTTCTTGGTAGCTAGCTCC 60.203 57.143 23.26 21.34 38.67 4.70
1021 1040 2.629336 ATGGCTTCTTGGTAGCTAGC 57.371 50.000 16.08 16.08 38.67 3.42
1041 1066 1.215647 GACGACGAGGGAGCACATT 59.784 57.895 0.00 0.00 0.00 2.71
1133 1164 3.123620 GCTCCAAGTGGCTGCTCG 61.124 66.667 0.00 0.00 33.71 5.03
1136 1167 4.666253 TGGGCTCCAAGTGGCTGC 62.666 66.667 0.00 0.00 35.00 5.25
1167 1198 1.017701 GTTACGAACCCTTGAGGCCG 61.018 60.000 0.00 0.00 40.58 6.13
1230 1268 1.133668 AGCCATGAAACCTATGGAGCC 60.134 52.381 8.13 0.00 46.42 4.70
1238 1276 2.738743 CATGGGTTAGCCATGAAACCT 58.261 47.619 32.54 0.86 45.40 3.50
1360 2756 4.382320 GCAAGGACGGCACCGGTA 62.382 66.667 6.87 0.00 44.69 4.02
1409 2806 2.030045 GCCTTCCTCCGGACATACTCT 61.030 57.143 0.00 0.00 0.00 3.24
2063 3614 1.105167 TCGTGGAGTTGGTCGTCACT 61.105 55.000 0.00 0.00 0.00 3.41
2105 3665 1.375908 GTTGATGGCGCTCCTGACA 60.376 57.895 7.64 0.00 0.00 3.58
2185 3759 3.382832 CGGAGAAGACCACCGGCT 61.383 66.667 0.00 0.00 42.48 5.52
2354 3928 2.668550 GGCACCCTCACGTTGGTC 60.669 66.667 0.00 0.00 30.70 4.02
2477 4051 1.447838 GTTGCCGATGAAGCCGAGA 60.448 57.895 0.00 0.00 0.00 4.04
2563 4137 0.942410 TGCCGTCGAACACTAACAGC 60.942 55.000 0.00 0.00 0.00 4.40
2691 4544 2.688958 ACGAACTCATCCTGGTAGCTAC 59.311 50.000 15.88 15.88 0.00 3.58
2732 4585 5.345741 CAGGTTACAACACATGCATAAAAGC 59.654 40.000 0.00 0.00 0.00 3.51
2754 4636 3.641434 ATGGGTCTCCTTCAATGACAG 57.359 47.619 0.00 0.00 32.84 3.51
2758 4640 6.359804 TCTGATTTATGGGTCTCCTTCAATG 58.640 40.000 0.00 0.00 0.00 2.82
2778 4684 6.710295 TGTAAAGCTTACAGCATTTTCTCTGA 59.290 34.615 0.00 0.00 45.56 3.27
2779 4685 6.798959 GTGTAAAGCTTACAGCATTTTCTCTG 59.201 38.462 0.00 0.00 45.56 3.35
2780 4686 6.486657 TGTGTAAAGCTTACAGCATTTTCTCT 59.513 34.615 0.00 0.00 45.56 3.10
2781 4687 6.668323 TGTGTAAAGCTTACAGCATTTTCTC 58.332 36.000 0.00 0.00 45.56 2.87
2782 4688 6.633500 TGTGTAAAGCTTACAGCATTTTCT 57.367 33.333 0.00 0.00 45.56 2.52
2783 4689 6.918043 CTGTGTAAAGCTTACAGCATTTTC 57.082 37.500 13.47 1.23 45.56 2.29
2790 4701 1.128692 GGCGCTGTGTAAAGCTTACAG 59.871 52.381 19.30 19.30 43.49 2.74
2793 4704 1.885560 TTGGCGCTGTGTAAAGCTTA 58.114 45.000 7.64 0.00 41.24 3.09
2813 4724 3.244353 CCAGAGTTCACAAGAGACATGGT 60.244 47.826 0.00 0.00 0.00 3.55
2819 4730 1.762370 TGCACCAGAGTTCACAAGAGA 59.238 47.619 0.00 0.00 0.00 3.10
2820 4731 2.141517 CTGCACCAGAGTTCACAAGAG 58.858 52.381 0.00 0.00 32.44 2.85
2822 4733 0.590195 GCTGCACCAGAGTTCACAAG 59.410 55.000 0.00 0.00 32.44 3.16
2824 4735 0.181114 AAGCTGCACCAGAGTTCACA 59.819 50.000 1.02 0.00 32.44 3.58
2825 4736 0.590195 CAAGCTGCACCAGAGTTCAC 59.410 55.000 1.02 0.00 32.44 3.18
2826 4737 0.181114 ACAAGCTGCACCAGAGTTCA 59.819 50.000 1.02 0.00 32.44 3.18
2829 4752 1.228063 CCACAAGCTGCACCAGAGT 60.228 57.895 1.02 0.00 32.44 3.24
2855 4778 3.504906 CAGAGGCTCACATGTTCACAAAT 59.495 43.478 18.26 0.00 0.00 2.32
2876 4832 5.927281 AAGAATACGGTAAGTCTAAGCCA 57.073 39.130 5.46 0.00 0.00 4.75
2878 4834 6.799512 TGGTAAGAATACGGTAAGTCTAAGC 58.200 40.000 5.46 0.00 32.51 3.09
2911 4885 5.856455 CCAACGAAATTTGTTCCTCACATAC 59.144 40.000 0.00 0.00 34.43 2.39
2916 4890 2.035321 GGCCAACGAAATTTGTTCCTCA 59.965 45.455 0.00 0.00 0.00 3.86
2931 4905 2.922335 GCTGAAATTTGTCTCGGCCAAC 60.922 50.000 2.24 0.00 37.89 3.77
2936 4910 4.691860 ATCAAGCTGAAATTTGTCTCGG 57.308 40.909 0.00 0.00 0.00 4.63
2938 4912 7.765307 TCCATAATCAAGCTGAAATTTGTCTC 58.235 34.615 0.00 0.00 0.00 3.36
2939 4913 7.707624 TCCATAATCAAGCTGAAATTTGTCT 57.292 32.000 0.00 0.00 0.00 3.41
2942 4916 6.639686 CCGATCCATAATCAAGCTGAAATTTG 59.360 38.462 0.00 0.00 33.65 2.32
2952 4926 9.366216 TCGTAATAAATCCGATCCATAATCAAG 57.634 33.333 0.00 0.00 33.65 3.02
2954 4928 9.713713 TTTCGTAATAAATCCGATCCATAATCA 57.286 29.630 0.00 0.00 33.65 2.57
3026 5000 1.063764 GGCCGTTTTCACGTTACACAA 59.936 47.619 0.00 0.00 45.62 3.33
3027 5001 0.656785 GGCCGTTTTCACGTTACACA 59.343 50.000 0.00 0.00 45.62 3.72
3030 5004 1.598601 TGAAGGCCGTTTTCACGTTAC 59.401 47.619 0.00 0.00 45.62 2.50
3032 5006 1.314730 ATGAAGGCCGTTTTCACGTT 58.685 45.000 7.99 0.00 45.62 3.99
3061 5035 8.684520 ACTCGTAGTGGGCAATATATATAGAAC 58.315 37.037 0.00 0.00 0.00 3.01
3063 5037 8.818622 AACTCGTAGTGGGCAATATATATAGA 57.181 34.615 0.00 0.00 0.00 1.98
3065 5039 7.553760 TCGAACTCGTAGTGGGCAATATATATA 59.446 37.037 0.00 0.00 40.80 0.86
3074 5053 0.038892 GTTCGAACTCGTAGTGGGCA 60.039 55.000 20.97 0.00 40.80 5.36
3091 5070 1.271656 GCATCAAGGCAAGCAAGAGTT 59.728 47.619 0.00 0.00 0.00 3.01
3092 5071 0.886563 GCATCAAGGCAAGCAAGAGT 59.113 50.000 0.00 0.00 0.00 3.24
3096 5075 0.388659 AAACGCATCAAGGCAAGCAA 59.611 45.000 0.00 0.00 0.00 3.91
3111 5090 1.630148 CTGAGGCCGAGTAGAAAACG 58.370 55.000 0.00 0.00 0.00 3.60
3113 5092 3.834732 GCTGAGGCCGAGTAGAAAA 57.165 52.632 0.00 0.00 0.00 2.29
3127 5106 0.747852 GGAAAACCGTTTTGGGCTGA 59.252 50.000 13.95 0.00 44.64 4.26
3130 5109 2.206750 GAAAGGAAAACCGTTTTGGGC 58.793 47.619 13.95 0.14 44.64 5.36
3225 5212 1.558756 AGAAGGGAGTCATGCAAGAGG 59.441 52.381 0.00 0.00 0.00 3.69
3239 5226 5.043737 AGTCTAGCACTCTAGTAGAAGGG 57.956 47.826 0.64 0.00 42.28 3.95
3252 5239 6.037830 CACTCTAGTAGAAGGAAGTCTAGCAC 59.962 46.154 0.64 0.00 30.70 4.40
3254 5241 5.008316 GCACTCTAGTAGAAGGAAGTCTAGC 59.992 48.000 0.64 0.00 30.70 3.42
3255 5242 6.354130 AGCACTCTAGTAGAAGGAAGTCTAG 58.646 44.000 0.64 0.00 30.70 2.43
3257 5244 5.187621 AGCACTCTAGTAGAAGGAAGTCT 57.812 43.478 0.64 0.00 0.00 3.24
3258 5245 6.613755 CTAGCACTCTAGTAGAAGGAAGTC 57.386 45.833 0.64 0.00 37.97 3.01
3270 5257 4.465886 ACCTGATACCACTAGCACTCTAG 58.534 47.826 0.00 0.00 46.06 2.43
3271 5258 4.521536 ACCTGATACCACTAGCACTCTA 57.478 45.455 0.00 0.00 0.00 2.43
3272 5259 3.390175 ACCTGATACCACTAGCACTCT 57.610 47.619 0.00 0.00 0.00 3.24
3273 5260 5.793030 ATTACCTGATACCACTAGCACTC 57.207 43.478 0.00 0.00 0.00 3.51
3274 5261 6.561519 AAATTACCTGATACCACTAGCACT 57.438 37.500 0.00 0.00 0.00 4.40
3275 5262 7.048512 AGAAAATTACCTGATACCACTAGCAC 58.951 38.462 0.00 0.00 0.00 4.40
3276 5263 7.125811 AGAGAAAATTACCTGATACCACTAGCA 59.874 37.037 0.00 0.00 0.00 3.49
3277 5264 7.501844 AGAGAAAATTACCTGATACCACTAGC 58.498 38.462 0.00 0.00 0.00 3.42
3278 5265 9.892130 AAAGAGAAAATTACCTGATACCACTAG 57.108 33.333 0.00 0.00 0.00 2.57
3280 5267 9.588096 AAAAAGAGAAAATTACCTGATACCACT 57.412 29.630 0.00 0.00 0.00 4.00
3281 5268 9.841880 GAAAAAGAGAAAATTACCTGATACCAC 57.158 33.333 0.00 0.00 0.00 4.16
3282 5269 9.020731 GGAAAAAGAGAAAATTACCTGATACCA 57.979 33.333 0.00 0.00 0.00 3.25
3283 5270 9.244292 AGGAAAAAGAGAAAATTACCTGATACC 57.756 33.333 0.00 0.00 0.00 2.73
3382 5372 5.657302 ACATACCACAAACCAGGTAAACAAA 59.343 36.000 0.00 0.00 43.14 2.83
3385 5375 4.822896 TCACATACCACAAACCAGGTAAAC 59.177 41.667 0.00 0.00 43.14 2.01
3396 5386 7.390996 ACCAATTACGTTTATCACATACCACAA 59.609 33.333 0.00 0.00 0.00 3.33
3409 5399 3.072944 CCCGACCAACCAATTACGTTTA 58.927 45.455 0.00 0.00 0.00 2.01
3417 5407 0.555769 ATATGCCCCGACCAACCAAT 59.444 50.000 0.00 0.00 0.00 3.16
3431 5421 7.040478 TGGTTCCATAATACTGCTGAAATATGC 60.040 37.037 0.00 0.00 0.00 3.14
3487 5479 0.966179 GGGAGGCCATTTTCACGTTT 59.034 50.000 5.01 0.00 0.00 3.60
3498 5496 2.317371 TTTGCAAATTAGGGAGGCCA 57.683 45.000 8.05 0.00 0.00 5.36
3500 5498 2.169144 AGCATTTGCAAATTAGGGAGGC 59.831 45.455 21.95 18.73 45.16 4.70
3519 5517 2.245159 TGCAGTAGGTGATGCATAGC 57.755 50.000 0.00 0.00 46.97 2.97
3541 5539 0.790814 AAAGCAAGCGCGAGTTAGAC 59.209 50.000 12.10 0.00 45.49 2.59
3592 5590 9.955102 CACTAGGGTAACTAAGGAAATAAAACT 57.045 33.333 0.00 0.00 0.00 2.66
3602 5600 3.129988 CCGTGACACTAGGGTAACTAAGG 59.870 52.174 11.02 1.00 0.00 2.69
3604 5602 3.766545 ACCGTGACACTAGGGTAACTAA 58.233 45.455 11.02 0.00 37.08 2.24
3606 5604 2.299326 ACCGTGACACTAGGGTAACT 57.701 50.000 11.02 0.00 37.08 2.24


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

AutoCloner maintained by Alex Coulton.