Multiple sequence alignment - TraesCS4D01G271300

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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 TraesCS4D01G271300 chr4D 100.000 3199 0 0 1 3199 441899869 441903067 0.000000e+00 5908.0
1 TraesCS4D01G271300 chr4B 92.474 2631 146 17 1 2617 548765783 548768375 0.000000e+00 3714.0
2 TraesCS4D01G271300 chr4B 83.258 890 91 23 1034 1921 659689626 659688793 0.000000e+00 765.0
3 TraesCS4D01G271300 chr4B 94.320 493 28 0 2609 3101 548768606 548769098 0.000000e+00 756.0
4 TraesCS4D01G271300 chr4B 80.560 679 121 5 3 681 94825675 94825008 2.200000e-141 512.0
5 TraesCS4D01G271300 chr4B 82.341 487 70 8 978 1462 660089868 660090340 2.970000e-110 409.0
6 TraesCS4D01G271300 chr4B 87.390 341 32 5 1582 1921 660090486 660090816 6.480000e-102 381.0
7 TraesCS4D01G271300 chr4B 84.566 311 45 3 1915 2222 660092218 660092528 4.010000e-79 305.0
8 TraesCS4D01G271300 chr4B 86.939 245 32 0 1913 2157 659688437 659688193 3.140000e-70 276.0
9 TraesCS4D01G271300 chr4A 91.891 2343 167 12 746 3071 25498061 25495725 0.000000e+00 3253.0
10 TraesCS4D01G271300 chr5A 81.217 953 123 35 986 1921 698888603 698889516 0.000000e+00 717.0
11 TraesCS4D01G271300 chr5A 89.837 246 23 2 1913 2157 698889660 698889904 6.660000e-82 315.0
12 TraesCS4D01G271300 chr5A 88.618 246 23 5 1913 2156 698896135 698896377 8.680000e-76 294.0
13 TraesCS4D01G271300 chr5A 77.694 399 60 19 1293 1665 698820530 698820925 1.930000e-52 217.0
14 TraesCS4D01G271300 chr5A 87.255 102 10 3 1544 1642 698895830 698895931 2.610000e-21 113.0
15 TraesCS4D01G271300 chr5A 92.683 41 3 0 2589 2629 592055991 592056031 3.450000e-05 60.2
16 TraesCS4D01G271300 chr3D 82.690 751 113 12 8 753 68832096 68832834 0.000000e+00 651.0
17 TraesCS4D01G271300 chr3D 96.117 103 4 0 3097 3199 454450493 454450595 5.490000e-38 169.0
18 TraesCS4D01G271300 chr7A 81.818 759 131 5 1 759 566351760 566352511 5.820000e-177 630.0
19 TraesCS4D01G271300 chr7B 81.365 762 132 9 1 757 136291210 136290454 2.110000e-171 612.0
20 TraesCS4D01G271300 chr7D 80.265 755 143 6 2 754 96504303 96505053 5.990000e-157 564.0
21 TraesCS4D01G271300 chr7D 94.495 109 6 0 3091 3199 444355459 444355351 5.490000e-38 169.0
22 TraesCS4D01G271300 chr2D 88.791 455 51 0 1040 1494 479179254 479179708 2.790000e-155 558.0
23 TraesCS4D01G271300 chr2D 80.201 697 127 6 8 701 421127417 421128105 2.200000e-141 512.0
24 TraesCS4D01G271300 chr2D 89.710 379 32 6 1548 1921 479180441 479180817 8.030000e-131 477.0
25 TraesCS4D01G271300 chr2D 90.086 232 23 0 1918 2149 479180980 479181211 5.190000e-78 302.0
26 TraesCS4D01G271300 chr2D 96.154 104 3 1 3097 3199 470027107 470027004 5.490000e-38 169.0
27 TraesCS4D01G271300 chr2B 88.147 464 46 4 1040 1494 562217399 562217862 7.800000e-151 544.0
28 TraesCS4D01G271300 chr2B 90.667 375 29 5 1551 1921 562218574 562218946 7.970000e-136 494.0
29 TraesCS4D01G271300 chr2B 87.550 249 31 0 1918 2166 562219106 562219354 4.040000e-74 289.0
30 TraesCS4D01G271300 chr2A 88.147 464 46 7 1040 1494 621920625 621921088 7.800000e-151 544.0
31 TraesCS4D01G271300 chr2A 89.840 374 32 5 1552 1921 621921797 621922168 2.890000e-130 475.0
32 TraesCS4D01G271300 chr2A 89.873 237 24 0 1913 2149 621922324 621922560 4.010000e-79 305.0
33 TraesCS4D01G271300 chr5B 79.542 699 127 13 3 697 337031494 337032180 4.800000e-133 484.0
34 TraesCS4D01G271300 chr5B 96.154 104 3 1 3097 3199 135544497 135544394 5.490000e-38 169.0
35 TraesCS4D01G271300 chr6D 79.377 674 128 9 7 679 68542509 68541846 6.250000e-127 464.0
36 TraesCS4D01G271300 chr6D 79.118 340 60 10 1583 1921 302249725 302249396 1.150000e-54 224.0
37 TraesCS4D01G271300 chr6D 96.154 104 3 1 3097 3199 333575303 333575200 5.490000e-38 169.0
38 TraesCS4D01G271300 chr6B 79.412 340 59 10 1583 1921 468010423 468010094 2.480000e-56 230.0
39 TraesCS4D01G271300 chr1A 97.030 101 3 0 3099 3199 556592735 556592635 1.530000e-38 171.0
40 TraesCS4D01G271300 chr3B 94.545 110 5 1 3090 3199 195508368 195508476 5.490000e-38 169.0
41 TraesCS4D01G271300 chr1D 95.192 104 4 1 3097 3199 49343205 49343102 2.550000e-36 163.0
42 TraesCS4D01G271300 chr1D 95.192 104 4 1 3097 3199 52795453 52795350 2.550000e-36 163.0
43 TraesCS4D01G271300 chr5D 92.683 41 3 0 2589 2629 472528026 472528066 3.450000e-05 60.2


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 TraesCS4D01G271300 chr4D 441899869 441903067 3198 False 5908.000000 5908 100.000000 1 3199 1 chr4D.!!$F1 3198
1 TraesCS4D01G271300 chr4B 548765783 548769098 3315 False 2235.000000 3714 93.397000 1 3101 2 chr4B.!!$F1 3100
2 TraesCS4D01G271300 chr4B 659688193 659689626 1433 True 520.500000 765 85.098500 1034 2157 2 chr4B.!!$R2 1123
3 TraesCS4D01G271300 chr4B 94825008 94825675 667 True 512.000000 512 80.560000 3 681 1 chr4B.!!$R1 678
4 TraesCS4D01G271300 chr4B 660089868 660092528 2660 False 365.000000 409 84.765667 978 2222 3 chr4B.!!$F2 1244
5 TraesCS4D01G271300 chr4A 25495725 25498061 2336 True 3253.000000 3253 91.891000 746 3071 1 chr4A.!!$R1 2325
6 TraesCS4D01G271300 chr5A 698888603 698889904 1301 False 516.000000 717 85.527000 986 2157 2 chr5A.!!$F3 1171
7 TraesCS4D01G271300 chr5A 698895830 698896377 547 False 203.500000 294 87.936500 1544 2156 2 chr5A.!!$F4 612
8 TraesCS4D01G271300 chr3D 68832096 68832834 738 False 651.000000 651 82.690000 8 753 1 chr3D.!!$F1 745
9 TraesCS4D01G271300 chr7A 566351760 566352511 751 False 630.000000 630 81.818000 1 759 1 chr7A.!!$F1 758
10 TraesCS4D01G271300 chr7B 136290454 136291210 756 True 612.000000 612 81.365000 1 757 1 chr7B.!!$R1 756
11 TraesCS4D01G271300 chr7D 96504303 96505053 750 False 564.000000 564 80.265000 2 754 1 chr7D.!!$F1 752
12 TraesCS4D01G271300 chr2D 421127417 421128105 688 False 512.000000 512 80.201000 8 701 1 chr2D.!!$F1 693
13 TraesCS4D01G271300 chr2D 479179254 479181211 1957 False 445.666667 558 89.529000 1040 2149 3 chr2D.!!$F2 1109
14 TraesCS4D01G271300 chr2B 562217399 562219354 1955 False 442.333333 544 88.788000 1040 2166 3 chr2B.!!$F1 1126
15 TraesCS4D01G271300 chr2A 621920625 621922560 1935 False 441.333333 544 89.286667 1040 2149 3 chr2A.!!$F1 1109
16 TraesCS4D01G271300 chr5B 337031494 337032180 686 False 484.000000 484 79.542000 3 697 1 chr5B.!!$F1 694
17 TraesCS4D01G271300 chr6D 68541846 68542509 663 True 464.000000 464 79.377000 7 679 1 chr6D.!!$R1 672

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
686 690 0.251877 TGACCTCCCACATCCGTGTA 60.252 55.0 0.0 0.0 41.93 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2684 5418 0.036577 ATGAGTCTGTGGTGAGCAGC 60.037 55.0 0.0 0.0 34.21 5.25 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
42 43 1.663702 CGCTCGTCGAACCCAGTTT 60.664 57.895 0.00 0.00 41.67 2.66
82 83 3.532792 CACACATCGCGACGGACG 61.533 66.667 12.93 6.60 45.66 4.79
83 84 4.034258 ACACATCGCGACGGACGT 62.034 61.111 12.93 7.26 44.60 4.34
122 123 3.461773 CCTGGACCGCTCCGTGAT 61.462 66.667 0.00 0.00 39.88 3.06
127 128 4.796231 ACCGCTCCGTGATGACGC 62.796 66.667 0.00 0.00 44.68 5.19
321 324 0.780637 AGGAGGCGGAGAGGATCATA 59.219 55.000 0.00 0.00 37.82 2.15
387 390 3.901797 CTTTCGCCGCCCCAAGTCT 62.902 63.158 0.00 0.00 0.00 3.24
479 482 2.022129 GCGAGGTCACCGTGAACTG 61.022 63.158 23.89 15.76 45.99 3.16
482 486 1.001048 CGAGGTCACCGTGAACTGTAA 60.001 52.381 23.89 0.00 45.99 2.41
606 610 8.868916 GTTTATATCAAAATTCGCCATGTTTGT 58.131 29.630 4.68 0.00 33.62 2.83
653 657 8.144155 TGAGTTGTTGTGAAAATGTATACGAA 57.856 30.769 0.00 0.00 0.00 3.85
686 690 0.251877 TGACCTCCCACATCCGTGTA 60.252 55.000 0.00 0.00 41.93 2.90
718 724 2.165030 TCCTCCTTATCCACGAACGAAC 59.835 50.000 0.14 0.00 0.00 3.95
798 804 0.755698 TTTGCGGCAGGGGTTTAACA 60.756 50.000 1.67 0.00 0.00 2.41
1172 1206 3.342719 TGCCAATTATCGACTTGAAGCA 58.657 40.909 5.93 5.37 0.00 3.91
1254 1288 1.767692 GGAGTGGGGCTTCTTCCAA 59.232 57.895 0.00 0.00 34.47 3.53
1464 1501 1.617947 GCATCTCCCGGGAAGACTGT 61.618 60.000 26.68 6.68 0.00 3.55
1485 1522 0.679505 ACTACGGAAAGCTCAGCACA 59.320 50.000 0.00 0.00 0.00 4.57
1545 2276 3.970610 CGTATGCATGCTTGATTACTTGC 59.029 43.478 20.33 0.00 37.44 4.01
1618 2387 2.125269 GGTGGCGGACGCTATGTT 60.125 61.111 16.72 0.00 41.60 2.71
1661 2430 3.626924 ACGCTGGCGGAGAACCTT 61.627 61.111 18.99 0.00 44.69 3.50
2096 4570 5.513441 CGGAGAGTATAGGAGGAGTGTACAT 60.513 48.000 0.00 0.00 0.00 2.29
2224 4702 0.959553 GAACTCAGTCTCACCGTCCA 59.040 55.000 0.00 0.00 0.00 4.02
2255 4733 1.447945 TGGCACACCACAATGATACG 58.552 50.000 0.00 0.00 42.67 3.06
2317 4805 4.266976 GTGACATACATGTAGTACAACGGC 59.733 45.833 11.91 0.00 41.95 5.68
2318 4806 3.441163 ACATACATGTAGTACAACGGCG 58.559 45.455 11.91 4.80 39.68 6.46
2344 4832 2.350522 GTCGACTCCAATGAATGTGCT 58.649 47.619 8.70 0.00 0.00 4.40
2439 4928 2.288666 ACGTTCAAGCACAAGTCACAT 58.711 42.857 0.00 0.00 0.00 3.21
2507 5002 5.121380 AGATGGCATCTGTAGGATTTGTT 57.879 39.130 28.33 0.00 38.44 2.83
2571 5066 8.304596 GTTCATACTCATCGTTCAGGGATATAA 58.695 37.037 0.00 0.00 0.00 0.98
2603 5098 5.515548 TTGAATCTCGTCAACAAATCTCG 57.484 39.130 0.00 0.00 32.56 4.04
2629 5363 4.759693 GTCATGTTGTGATTGTTGGTCCTA 59.240 41.667 0.00 0.00 39.48 2.94
2684 5418 0.964358 CAGAAGAGGCCCCTTTGCAG 60.964 60.000 0.00 0.00 0.00 4.41
2687 5421 3.066814 GAGGCCCCTTTGCAGCTG 61.067 66.667 10.11 10.11 0.00 4.24
2720 5454 3.261897 ACTCATAGTGCTTGCTGGTACTT 59.738 43.478 5.74 0.00 34.29 2.24
2835 5569 6.338146 TCCACTATCGAAGAGTTTACAATGG 58.662 40.000 0.77 0.00 43.63 3.16
2896 5630 3.018423 AGCTTTTCACAGAAAGGGTGT 57.982 42.857 5.67 0.00 37.17 4.16
3016 5750 1.604308 CACCATTGCAGCTCACCCA 60.604 57.895 0.00 0.00 0.00 4.51
3017 5751 1.604593 ACCATTGCAGCTCACCCAC 60.605 57.895 0.00 0.00 0.00 4.61
3086 5820 2.546162 GCTAAGGCTCATCCGTTAGGTC 60.546 54.545 0.00 0.00 40.77 3.85
3089 5823 1.437986 GCTCATCCGTTAGGTCGCT 59.562 57.895 0.00 0.00 39.05 4.93
3101 5835 4.357996 GTTAGGTCGCTCATACCTGTTAC 58.642 47.826 5.04 0.00 46.90 2.50
3102 5836 2.736347 AGGTCGCTCATACCTGTTACT 58.264 47.619 0.00 0.00 45.78 2.24
3103 5837 2.688958 AGGTCGCTCATACCTGTTACTC 59.311 50.000 0.00 0.00 45.78 2.59
3104 5838 2.223758 GGTCGCTCATACCTGTTACTCC 60.224 54.545 0.00 0.00 33.97 3.85
3105 5839 2.029623 TCGCTCATACCTGTTACTCCC 58.970 52.381 0.00 0.00 0.00 4.30
3106 5840 2.032620 CGCTCATACCTGTTACTCCCT 58.967 52.381 0.00 0.00 0.00 4.20
3107 5841 2.034812 CGCTCATACCTGTTACTCCCTC 59.965 54.545 0.00 0.00 0.00 4.30
3108 5842 2.365941 GCTCATACCTGTTACTCCCTCC 59.634 54.545 0.00 0.00 0.00 4.30
3109 5843 2.623889 CTCATACCTGTTACTCCCTCCG 59.376 54.545 0.00 0.00 0.00 4.63
3110 5844 2.024655 TCATACCTGTTACTCCCTCCGT 60.025 50.000 0.00 0.00 0.00 4.69
3111 5845 2.610438 TACCTGTTACTCCCTCCGTT 57.390 50.000 0.00 0.00 0.00 4.44
3112 5846 1.725803 ACCTGTTACTCCCTCCGTTT 58.274 50.000 0.00 0.00 0.00 3.60
3113 5847 2.052468 ACCTGTTACTCCCTCCGTTTT 58.948 47.619 0.00 0.00 0.00 2.43
3114 5848 2.440627 ACCTGTTACTCCCTCCGTTTTT 59.559 45.455 0.00 0.00 0.00 1.94
3115 5849 3.647590 ACCTGTTACTCCCTCCGTTTTTA 59.352 43.478 0.00 0.00 0.00 1.52
3116 5850 4.102996 ACCTGTTACTCCCTCCGTTTTTAA 59.897 41.667 0.00 0.00 0.00 1.52
3117 5851 5.065235 CCTGTTACTCCCTCCGTTTTTAAA 58.935 41.667 0.00 0.00 0.00 1.52
3118 5852 5.708697 CCTGTTACTCCCTCCGTTTTTAAAT 59.291 40.000 0.00 0.00 0.00 1.40
3119 5853 6.880529 CCTGTTACTCCCTCCGTTTTTAAATA 59.119 38.462 0.00 0.00 0.00 1.40
3120 5854 7.555195 CCTGTTACTCCCTCCGTTTTTAAATAT 59.445 37.037 0.00 0.00 0.00 1.28
3121 5855 8.866970 TGTTACTCCCTCCGTTTTTAAATATT 57.133 30.769 0.00 0.00 0.00 1.28
3122 5856 9.299465 TGTTACTCCCTCCGTTTTTAAATATTT 57.701 29.630 5.89 5.89 0.00 1.40
3123 5857 9.563898 GTTACTCCCTCCGTTTTTAAATATTTG 57.436 33.333 11.05 0.00 0.00 2.32
3124 5858 7.770366 ACTCCCTCCGTTTTTAAATATTTGT 57.230 32.000 11.05 0.00 0.00 2.83
3125 5859 7.823665 ACTCCCTCCGTTTTTAAATATTTGTC 58.176 34.615 11.05 0.00 0.00 3.18
3126 5860 7.668469 ACTCCCTCCGTTTTTAAATATTTGTCT 59.332 33.333 11.05 0.00 0.00 3.41
3127 5861 8.411991 TCCCTCCGTTTTTAAATATTTGTCTT 57.588 30.769 11.05 0.00 0.00 3.01
3128 5862 8.862085 TCCCTCCGTTTTTAAATATTTGTCTTT 58.138 29.630 11.05 0.00 0.00 2.52
3129 5863 9.135843 CCCTCCGTTTTTAAATATTTGTCTTTC 57.864 33.333 11.05 0.00 0.00 2.62
3130 5864 9.908152 CCTCCGTTTTTAAATATTTGTCTTTCT 57.092 29.630 11.05 0.00 0.00 2.52
3145 5879 8.633075 TTTGTCTTTCTAAAGATTGCAACAAG 57.367 30.769 0.00 0.00 45.83 3.16
3146 5880 7.333528 TGTCTTTCTAAAGATTGCAACAAGT 57.666 32.000 0.00 0.00 45.83 3.16
3147 5881 7.195646 TGTCTTTCTAAAGATTGCAACAAGTG 58.804 34.615 0.00 0.00 45.83 3.16
3148 5882 7.066887 TGTCTTTCTAAAGATTGCAACAAGTGA 59.933 33.333 0.00 0.00 45.83 3.41
3149 5883 7.377131 GTCTTTCTAAAGATTGCAACAAGTGAC 59.623 37.037 0.00 0.00 45.83 3.67
3150 5884 6.942532 TTCTAAAGATTGCAACAAGTGACT 57.057 33.333 0.00 0.00 0.00 3.41
3151 5885 8.445275 TTTCTAAAGATTGCAACAAGTGACTA 57.555 30.769 0.00 0.00 0.00 2.59
3152 5886 7.421530 TCTAAAGATTGCAACAAGTGACTAC 57.578 36.000 0.00 0.00 0.00 2.73
3153 5887 6.989759 TCTAAAGATTGCAACAAGTGACTACA 59.010 34.615 0.00 0.00 0.00 2.74
3154 5888 6.639632 AAAGATTGCAACAAGTGACTACAT 57.360 33.333 0.00 0.00 0.00 2.29
3155 5889 7.744087 AAAGATTGCAACAAGTGACTACATA 57.256 32.000 0.00 0.00 0.00 2.29
3156 5890 6.727824 AGATTGCAACAAGTGACTACATAC 57.272 37.500 0.00 0.00 0.00 2.39
3157 5891 4.983215 TTGCAACAAGTGACTACATACG 57.017 40.909 0.00 0.00 0.00 3.06
3158 5892 3.322369 TGCAACAAGTGACTACATACGG 58.678 45.455 0.00 0.00 0.00 4.02
3159 5893 3.006003 TGCAACAAGTGACTACATACGGA 59.994 43.478 0.00 0.00 0.00 4.69
3160 5894 3.612860 GCAACAAGTGACTACATACGGAG 59.387 47.826 0.00 0.00 0.00 4.63
3161 5895 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3162 5896 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
3163 5897 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
3164 5898 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
3165 5899 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3166 5900 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
3167 5901 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
3168 5902 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3169 5903 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3170 5904 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3171 5905 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3172 5906 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3173 5907 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3174 5908 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3175 5909 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3176 5910 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3177 5911 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3178 5912 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3179 5913 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3180 5914 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 2.430367 GGAGTCCGCAAACTGGGT 59.570 61.111 0.00 0.00 0.00 4.51
76 77 2.803155 TACGCCAGGTCTACGTCCGT 62.803 60.000 0.00 0.00 40.99 4.69
127 128 0.443869 CAATGCTTGGACGTCTTCGG 59.556 55.000 16.46 4.90 41.85 4.30
136 137 0.674581 CGGCAGAGACAATGCTTGGA 60.675 55.000 0.00 0.00 43.35 3.53
385 388 2.287103 CGTCGGAGTCGTCATTATCAGA 59.713 50.000 0.00 0.00 37.69 3.27
387 390 1.332686 CCGTCGGAGTCGTCATTATCA 59.667 52.381 4.91 0.00 37.35 2.15
482 486 8.833734 ACCTAAAACTAAAACCCTAAGCTATCT 58.166 33.333 0.00 0.00 0.00 1.98
572 576 4.561735 ATTTTGATATAAACACGGCGGG 57.438 40.909 8.04 8.04 0.00 6.13
653 657 2.420129 GGAGGTCAACATCCAACGCTAT 60.420 50.000 8.88 0.00 45.50 2.97
703 709 2.351823 CGCGTTCGTTCGTGGATAA 58.648 52.632 0.00 0.00 37.62 1.75
798 804 3.836176 GAACCGTCCGTCGCACACT 62.836 63.158 0.00 0.00 38.35 3.55
1191 1225 2.348998 CACGCCTTGCTCTCCCTT 59.651 61.111 0.00 0.00 0.00 3.95
1326 1360 1.079612 GTCCTTGGTACCGAACGGG 60.080 63.158 17.44 3.39 43.62 5.28
1464 1501 0.966179 TGCTGAGCTTTCCGTAGTCA 59.034 50.000 5.83 0.00 0.00 3.41
1485 1522 2.089980 ACGCACGTACTCTACCTCAAT 58.910 47.619 0.00 0.00 0.00 2.57
1545 2276 1.868930 GCTCATCAGCCATCAGACGAG 60.869 57.143 0.00 0.00 40.14 4.18
1613 2382 1.447140 GTCCGCCACTCGCAACATA 60.447 57.895 0.00 0.00 37.30 2.29
1643 2412 3.883744 AAGGTTCTCCGCCAGCGTG 62.884 63.158 11.55 3.73 39.05 5.34
2096 4570 1.405463 CCGGTTCTCTCGACATCATCA 59.595 52.381 0.00 0.00 0.00 3.07
2224 4702 0.951558 GTGTGCCAATTCCGAACTGT 59.048 50.000 0.00 0.00 0.00 3.55
2245 4723 3.001228 CGCACAAGCATACGTATCATTGT 59.999 43.478 21.12 21.12 42.27 2.71
2282 4766 4.206477 TGTATGTCACAAGGTCATCTGG 57.794 45.455 0.00 0.00 32.95 3.86
2287 4775 5.738619 ACTACATGTATGTCACAAGGTCA 57.261 39.130 5.91 0.00 41.55 4.02
2331 4819 4.889409 ACCATACCTTAGCACATTCATTGG 59.111 41.667 0.00 0.00 0.00 3.16
2439 4928 1.779092 ACTACCGGTCTAGCTATCCCA 59.221 52.381 12.40 0.00 0.00 4.37
2552 5047 5.139435 TGCTTATATCCCTGAACGATGAG 57.861 43.478 0.00 0.00 0.00 2.90
2571 5066 5.268118 TGACGAGATTCAACATAGATGCT 57.732 39.130 0.00 0.00 0.00 3.79
2603 5098 3.068024 ACCAACAATCACAACATGACACC 59.932 43.478 0.00 0.00 41.24 4.16
2629 5363 2.030717 TGACGTGCGCATTGGTTTTATT 60.031 40.909 15.91 0.00 0.00 1.40
2639 5373 2.293677 TAGAAATCTGACGTGCGCAT 57.706 45.000 15.91 0.00 0.00 4.73
2642 5376 4.383774 TTTGTTAGAAATCTGACGTGCG 57.616 40.909 0.00 0.00 35.49 5.34
2684 5418 0.036577 ATGAGTCTGTGGTGAGCAGC 60.037 55.000 0.00 0.00 34.21 5.25
2687 5421 2.886081 CACTATGAGTCTGTGGTGAGC 58.114 52.381 6.72 0.00 0.00 4.26
2688 5422 2.495270 AGCACTATGAGTCTGTGGTGAG 59.505 50.000 13.82 0.00 40.29 3.51
2689 5423 2.529632 AGCACTATGAGTCTGTGGTGA 58.470 47.619 13.82 0.00 40.29 4.02
2817 5551 5.547465 TGTGTCCATTGTAAACTCTTCGAT 58.453 37.500 0.00 0.00 0.00 3.59
2835 5569 3.187700 GGACCACTCACGATAATGTGTC 58.812 50.000 0.00 0.00 40.74 3.67
2923 5657 0.325296 AAGCACGAGGACCCATAGGA 60.325 55.000 0.00 0.00 36.73 2.94
3016 5750 1.069823 CAAGTCTGAGGTCTGCACAGT 59.930 52.381 1.67 0.00 33.93 3.55
3017 5751 1.607509 CCAAGTCTGAGGTCTGCACAG 60.608 57.143 0.00 0.00 0.00 3.66
3044 5778 2.102925 CAGCAATGGTTTTGTCCCTTGT 59.897 45.455 0.00 0.00 36.15 3.16
3086 5820 2.032620 AGGGAGTAACAGGTATGAGCG 58.967 52.381 0.00 0.00 0.00 5.03
3089 5823 2.024655 ACGGAGGGAGTAACAGGTATGA 60.025 50.000 0.00 0.00 0.00 2.15
3101 5835 8.051901 AGACAAATATTTAAAAACGGAGGGAG 57.948 34.615 0.00 0.00 0.00 4.30
3102 5836 8.411991 AAGACAAATATTTAAAAACGGAGGGA 57.588 30.769 0.00 0.00 0.00 4.20
3103 5837 9.135843 GAAAGACAAATATTTAAAAACGGAGGG 57.864 33.333 0.00 0.00 0.00 4.30
3104 5838 9.908152 AGAAAGACAAATATTTAAAAACGGAGG 57.092 29.630 0.00 0.00 0.00 4.30
3119 5853 9.252962 CTTGTTGCAATCTTTAGAAAGACAAAT 57.747 29.630 0.59 0.00 46.80 2.32
3120 5854 8.250332 ACTTGTTGCAATCTTTAGAAAGACAAA 58.750 29.630 0.59 0.00 46.80 2.83
3121 5855 7.701924 CACTTGTTGCAATCTTTAGAAAGACAA 59.298 33.333 0.59 4.98 46.80 3.18
3122 5856 7.066887 TCACTTGTTGCAATCTTTAGAAAGACA 59.933 33.333 0.59 0.00 46.80 3.41
3123 5857 7.377131 GTCACTTGTTGCAATCTTTAGAAAGAC 59.623 37.037 0.59 4.61 46.80 3.01
3125 5859 7.420800 AGTCACTTGTTGCAATCTTTAGAAAG 58.579 34.615 0.59 0.00 37.36 2.62
3126 5860 7.333528 AGTCACTTGTTGCAATCTTTAGAAA 57.666 32.000 0.59 0.00 0.00 2.52
3127 5861 6.942532 AGTCACTTGTTGCAATCTTTAGAA 57.057 33.333 0.59 0.00 0.00 2.10
3128 5862 6.989759 TGTAGTCACTTGTTGCAATCTTTAGA 59.010 34.615 0.59 0.00 0.00 2.10
3129 5863 7.189693 TGTAGTCACTTGTTGCAATCTTTAG 57.810 36.000 0.59 0.00 0.00 1.85
3130 5864 7.744087 ATGTAGTCACTTGTTGCAATCTTTA 57.256 32.000 0.59 0.00 0.00 1.85
3131 5865 6.639632 ATGTAGTCACTTGTTGCAATCTTT 57.360 33.333 0.59 0.00 0.00 2.52
3132 5866 6.128553 CGTATGTAGTCACTTGTTGCAATCTT 60.129 38.462 0.59 0.00 0.00 2.40
3133 5867 5.348724 CGTATGTAGTCACTTGTTGCAATCT 59.651 40.000 0.59 0.00 0.00 2.40
3134 5868 5.445939 CCGTATGTAGTCACTTGTTGCAATC 60.446 44.000 0.59 0.00 0.00 2.67
3135 5869 4.391830 CCGTATGTAGTCACTTGTTGCAAT 59.608 41.667 0.59 0.00 0.00 3.56
3136 5870 3.743911 CCGTATGTAGTCACTTGTTGCAA 59.256 43.478 0.00 0.00 0.00 4.08
3137 5871 3.006003 TCCGTATGTAGTCACTTGTTGCA 59.994 43.478 0.00 0.00 0.00 4.08
3138 5872 3.581755 TCCGTATGTAGTCACTTGTTGC 58.418 45.455 0.00 0.00 0.00 4.17
3139 5873 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3140 5874 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3141 5875 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
3142 5876 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3143 5877 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3144 5878 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3145 5879 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3146 5880 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3147 5881 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3148 5882 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3149 5883 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3150 5884 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3151 5885 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3152 5886 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3153 5887 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3154 5888 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3155 5889 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3156 5890 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3157 5891 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3158 5892 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26


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

AutoCloner maintained by Alex Coulton.