Multiple sequence alignment - TraesCS7A01G271400

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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 TraesCS7A01G271400 chr7A 100.000 4794 0 0 826 5619 284726874 284731667 0.000000e+00 8853.0
1 TraesCS7A01G271400 chr7A 100.000 499 0 0 1 499 284726049 284726547 0.000000e+00 922.0
2 TraesCS7A01G271400 chr7B 93.189 1850 64 24 826 2642 242720267 242718447 0.000000e+00 2662.0
3 TraesCS7A01G271400 chr7B 98.336 661 11 0 4959 5619 6987376 6986716 0.000000e+00 1160.0
4 TraesCS7A01G271400 chr7B 98.336 661 11 0 4959 5619 48114851 48115511 0.000000e+00 1160.0
5 TraesCS7A01G271400 chr7B 91.139 869 54 18 3199 4062 242717645 242716795 0.000000e+00 1157.0
6 TraesCS7A01G271400 chr7B 92.214 822 38 12 4161 4960 242716798 242715981 0.000000e+00 1140.0
7 TraesCS7A01G271400 chr7B 92.857 560 29 3 2645 3204 242718370 242717822 0.000000e+00 802.0
8 TraesCS7A01G271400 chr7B 92.200 500 16 7 1 492 242720761 242720277 0.000000e+00 686.0
9 TraesCS7A01G271400 chr7D 95.920 1250 28 9 826 2055 261816627 261817873 0.000000e+00 2004.0
10 TraesCS7A01G271400 chr7D 93.177 894 35 8 4074 4952 261820244 261821126 0.000000e+00 1290.0
11 TraesCS7A01G271400 chr7D 97.631 591 12 1 3197 3785 261819302 261819892 0.000000e+00 1013.0
12 TraesCS7A01G271400 chr7D 94.075 557 30 2 2645 3201 261818640 261819193 0.000000e+00 843.0
13 TraesCS7A01G271400 chr7D 91.122 597 42 7 2053 2642 261817966 261818558 0.000000e+00 798.0
14 TraesCS7A01G271400 chr7D 93.617 470 12 6 1 465 261816150 261816606 0.000000e+00 686.0
15 TraesCS7A01G271400 chr7D 96.183 262 9 1 3814 4075 261819890 261820150 1.450000e-115 427.0
16 TraesCS7A01G271400 chr4A 98.489 662 10 0 4958 5619 301818673 301819334 0.000000e+00 1168.0
17 TraesCS7A01G271400 chr4A 84.906 159 18 3 2903 3055 602376642 602376800 7.540000e-34 156.0
18 TraesCS7A01G271400 chr4A 85.714 84 7 4 2559 2640 602376460 602376540 3.610000e-12 84.2
19 TraesCS7A01G271400 chr6B 98.338 662 11 0 4958 5619 275927398 275928059 0.000000e+00 1162.0
20 TraesCS7A01G271400 chr6B 98.338 662 10 1 4959 5619 584057372 584056711 0.000000e+00 1160.0
21 TraesCS7A01G271400 chr5B 98.042 664 12 1 4957 5619 446984659 446985322 0.000000e+00 1153.0
22 TraesCS7A01G271400 chr5B 90.638 235 17 5 1078 1309 508253915 508254147 1.970000e-79 307.0
23 TraesCS7A01G271400 chr5B 84.956 226 33 1 2902 3127 508255984 508256208 1.570000e-55 228.0
24 TraesCS7A01G271400 chr3B 98.179 659 12 0 4961 5619 567172915 567172257 0.000000e+00 1151.0
25 TraesCS7A01G271400 chr1A 98.179 659 12 0 4961 5619 423902961 423903619 0.000000e+00 1151.0
26 TraesCS7A01G271400 chr3A 97.888 663 14 0 4957 5619 140958005 140958667 0.000000e+00 1147.0
27 TraesCS7A01G271400 chr5D 90.638 235 17 5 1078 1309 421841212 421841444 1.970000e-79 307.0
28 TraesCS7A01G271400 chr5D 84.733 131 20 0 4209 4339 421844393 421844523 1.270000e-26 132.0
29 TraesCS7A01G271400 chr5A 90.129 233 18 5 1078 1307 535354908 535355138 1.180000e-76 298.0
30 TraesCS7A01G271400 chr5A 83.969 131 21 0 4209 4339 535357996 535358126 5.910000e-25 126.0
31 TraesCS7A01G271400 chr5A 97.778 45 1 0 2645 2689 76911407 76911451 1.680000e-10 78.7
32 TraesCS7A01G271400 chr4B 77.427 412 70 15 3200 3597 2707839 2708241 2.040000e-54 224.0
33 TraesCS7A01G271400 chr4B 84.277 159 19 3 2903 3055 2696069 2696227 3.510000e-32 150.0
34 TraesCS7A01G271400 chr4B 76.527 311 44 24 2343 2640 2694535 2694829 5.870000e-30 143.0
35 TraesCS7A01G271400 chrUn 84.277 159 19 3 2903 3055 51905104 51905262 3.510000e-32 150.0
36 TraesCS7A01G271400 chrUn 84.277 159 19 3 2903 3055 324645013 324645171 3.510000e-32 150.0
37 TraesCS7A01G271400 chrUn 84.177 158 20 2 2903 3055 51911391 51911548 1.260000e-31 148.0
38 TraesCS7A01G271400 chrUn 84.177 158 20 2 2903 3055 290972577 290972734 1.260000e-31 148.0
39 TraesCS7A01G271400 chrUn 76.531 294 37 23 2343 2618 51910744 51911023 1.270000e-26 132.0
40 TraesCS7A01G271400 chrUn 76.531 294 37 23 2343 2618 290971930 290972209 1.270000e-26 132.0
41 TraesCS7A01G271400 chrUn 94.737 57 3 0 2584 2640 412748144 412748088 7.750000e-14 89.8
42 TraesCS7A01G271400 chrUn 89.394 66 7 0 2261 2326 86462896 86462961 3.610000e-12 84.2
43 TraesCS7A01G271400 chrUn 88.406 69 8 0 2261 2329 222672378 222672310 3.610000e-12 84.2
44 TraesCS7A01G271400 chrUn 88.406 69 8 0 2261 2329 229495706 229495638 3.610000e-12 84.2
45 TraesCS7A01G271400 chrUn 88.406 69 8 0 2261 2329 444796881 444796813 3.610000e-12 84.2
46 TraesCS7A01G271400 chrUn 97.778 45 1 0 2645 2689 296243486 296243442 1.680000e-10 78.7
47 TraesCS7A01G271400 chr4D 76.129 310 47 24 2343 2640 3225921 3225627 2.730000e-28 137.0
48 TraesCS7A01G271400 chr4D 89.394 66 7 0 2261 2326 123438696 123438761 3.610000e-12 84.2
49 TraesCS7A01G271400 chr2D 100.000 46 0 0 2644 2689 565956092 565956137 1.000000e-12 86.1
50 TraesCS7A01G271400 chr2D 95.556 45 2 0 2645 2689 278368867 278368823 7.810000e-09 73.1
51 TraesCS7A01G271400 chr6D 89.394 66 7 0 2261 2326 168783095 168783160 3.610000e-12 84.2
52 TraesCS7A01G271400 chr1B 89.394 66 7 0 2261 2326 491493272 491493337 3.610000e-12 84.2
53 TraesCS7A01G271400 chr1B 95.455 44 2 0 2646 2689 678047887 678047844 2.810000e-08 71.3
54 TraesCS7A01G271400 chr2A 95.556 45 2 0 2645 2689 320189198 320189242 7.810000e-09 73.1
55 TraesCS7A01G271400 chr2B 95.455 44 2 0 2645 2688 313578141 313578098 2.810000e-08 71.3


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 TraesCS7A01G271400 chr7A 284726049 284731667 5618 False 4887.500000 8853 100.000000 1 5619 2 chr7A.!!$F1 5618
1 TraesCS7A01G271400 chr7B 242715981 242720761 4780 True 1289.400000 2662 92.319800 1 4960 5 chr7B.!!$R2 4959
2 TraesCS7A01G271400 chr7B 6986716 6987376 660 True 1160.000000 1160 98.336000 4959 5619 1 chr7B.!!$R1 660
3 TraesCS7A01G271400 chr7B 48114851 48115511 660 False 1160.000000 1160 98.336000 4959 5619 1 chr7B.!!$F1 660
4 TraesCS7A01G271400 chr7D 261816150 261821126 4976 False 1008.714286 2004 94.532143 1 4952 7 chr7D.!!$F1 4951
5 TraesCS7A01G271400 chr4A 301818673 301819334 661 False 1168.000000 1168 98.489000 4958 5619 1 chr4A.!!$F1 661
6 TraesCS7A01G271400 chr6B 275927398 275928059 661 False 1162.000000 1162 98.338000 4958 5619 1 chr6B.!!$F1 661
7 TraesCS7A01G271400 chr6B 584056711 584057372 661 True 1160.000000 1160 98.338000 4959 5619 1 chr6B.!!$R1 660
8 TraesCS7A01G271400 chr5B 446984659 446985322 663 False 1153.000000 1153 98.042000 4957 5619 1 chr5B.!!$F1 662
9 TraesCS7A01G271400 chr5B 508253915 508256208 2293 False 267.500000 307 87.797000 1078 3127 2 chr5B.!!$F2 2049
10 TraesCS7A01G271400 chr3B 567172257 567172915 658 True 1151.000000 1151 98.179000 4961 5619 1 chr3B.!!$R1 658
11 TraesCS7A01G271400 chr1A 423902961 423903619 658 False 1151.000000 1151 98.179000 4961 5619 1 chr1A.!!$F1 658
12 TraesCS7A01G271400 chr3A 140958005 140958667 662 False 1147.000000 1147 97.888000 4957 5619 1 chr3A.!!$F1 662
13 TraesCS7A01G271400 chr5D 421841212 421844523 3311 False 219.500000 307 87.685500 1078 4339 2 chr5D.!!$F1 3261
14 TraesCS7A01G271400 chr5A 535354908 535358126 3218 False 212.000000 298 87.049000 1078 4339 2 chr5A.!!$F2 3261

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
185 186 0.036732 TTCAGCTCAGCCAATCGGTT 59.963 50.000 0.00 0.0 33.28 4.44 F
964 977 1.303643 CAAAGGCCAGACCCAGACC 60.304 63.158 5.01 0.0 40.58 3.85 F
2178 3350 0.318699 GTGCCCCTTTTGTTCTTCGC 60.319 55.000 0.00 0.0 0.00 4.70 F
3338 5222 1.102978 ATTGCCGCCAATACCAACTC 58.897 50.000 0.00 0.0 39.81 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1048 1061 1.226916 CCGCTGCTCTGCTAGACTG 60.227 63.158 0.00 0.0 0.00 3.51 R
2256 3428 0.588252 GCTTGAGCTGCTTCGTTTCA 59.412 50.000 2.53 0.0 38.21 2.69 R
3951 5853 0.323633 TCAGGCATGAACATGGGTGG 60.324 55.000 15.15 0.0 39.16 4.61 R
4865 6888 0.035152 ATTCAGCAGAATCCACGCCA 60.035 50.000 0.00 0.0 40.39 5.69 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
178 179 1.219124 GGATCGTTCAGCTCAGCCA 59.781 57.895 0.00 0.00 0.00 4.75
185 186 0.036732 TTCAGCTCAGCCAATCGGTT 59.963 50.000 0.00 0.00 33.28 4.44
231 232 1.472662 CCGGCCTACTCCCATCGAAT 61.473 60.000 0.00 0.00 0.00 3.34
235 236 1.336056 GCCTACTCCCATCGAATCGAC 60.336 57.143 7.77 0.00 39.18 4.20
417 426 3.741029 GCTATGAAGCGGTGACTCA 57.259 52.632 0.00 0.00 39.39 3.41
418 427 2.231215 GCTATGAAGCGGTGACTCAT 57.769 50.000 5.67 5.67 39.39 2.90
419 428 2.131183 GCTATGAAGCGGTGACTCATC 58.869 52.381 3.68 0.00 39.39 2.92
420 429 2.481969 GCTATGAAGCGGTGACTCATCA 60.482 50.000 3.68 0.00 39.39 3.07
481 490 3.324846 CCATATACTAGCAACCTGCCTCA 59.675 47.826 0.00 0.00 46.52 3.86
964 977 1.303643 CAAAGGCCAGACCCAGACC 60.304 63.158 5.01 0.00 40.58 3.85
1033 1046 1.388065 CCCTTCTCCGATCGTGCTCT 61.388 60.000 15.09 0.00 0.00 4.09
1047 1060 3.955101 CTCTCTCGCCGCCGGTAG 61.955 72.222 4.45 2.83 34.56 3.18
1056 1069 2.026301 CGCCGGTAGCAGTCTAGC 59.974 66.667 1.90 0.00 44.04 3.42
1332 1350 0.695347 CTTCTCTTCTGTTGCCCCCT 59.305 55.000 0.00 0.00 0.00 4.79
1540 2096 5.086621 GGGGGTGAGGCATATGAAATTATT 58.913 41.667 6.97 0.00 0.00 1.40
1548 2104 9.812347 TGAGGCATATGAAATTATTAATCCACT 57.188 29.630 6.97 0.00 0.00 4.00
1593 2157 1.324383 TGGACACTGTCTGCGACTTA 58.676 50.000 9.08 0.00 33.15 2.24
1616 2180 2.918345 GCGTGGTGCATTGCAAGGA 61.918 57.895 16.56 0.30 41.47 3.36
1780 2350 3.861840 TGCATCTGTGTACTTTAGAGGC 58.138 45.455 17.85 17.85 45.44 4.70
2071 3243 6.017605 GTGGATGGTACTATTTGCATGAGAAG 60.018 42.308 0.00 0.00 0.00 2.85
2089 3261 5.652014 TGAGAAGAAGAACCAACAAACATGT 59.348 36.000 0.00 0.00 0.00 3.21
2099 3271 6.214191 ACCAACAAACATGTTGTTCATACA 57.786 33.333 12.82 0.00 45.46 2.29
2136 3308 9.480053 CATTCCATTCTTGTAATTTGTGTTTCT 57.520 29.630 0.00 0.00 0.00 2.52
2178 3350 0.318699 GTGCCCCTTTTGTTCTTCGC 60.319 55.000 0.00 0.00 0.00 4.70
2256 3428 6.734137 TGTTTAAGATGCATGTTTTCTTCGT 58.266 32.000 14.96 0.00 32.28 3.85
2304 3476 1.799258 AACGGAAGCCAAAGCAGCAG 61.799 55.000 0.00 0.00 43.56 4.24
2306 3478 2.567497 GGAAGCCAAAGCAGCAGCA 61.567 57.895 3.17 0.00 45.49 4.41
2309 3481 1.885163 AAGCCAAAGCAGCAGCATCC 61.885 55.000 3.17 0.00 45.49 3.51
2415 3591 4.713792 AGAAACATGAACCACTCCTCTT 57.286 40.909 0.00 0.00 0.00 2.85
2416 3592 5.053978 AGAAACATGAACCACTCCTCTTT 57.946 39.130 0.00 0.00 0.00 2.52
2444 3622 4.631377 TCTGCATGTCACTAAAGGATTTCG 59.369 41.667 0.00 0.00 40.09 3.46
2445 3623 3.689161 TGCATGTCACTAAAGGATTTCGG 59.311 43.478 0.00 0.00 40.09 4.30
2507 3689 9.013229 TGTCTTAGCTGTTTGAATGTTATGATT 57.987 29.630 0.00 0.00 0.00 2.57
2570 3753 7.642082 ATTTCTATGCTCAAGCTCTGAAAAT 57.358 32.000 15.08 8.11 42.66 1.82
2581 3764 9.552114 CTCAAGCTCTGAAAATTTTGTATACAG 57.448 33.333 8.47 8.97 32.17 2.74
2593 3776 6.375945 TTTTGTATACAGCTATGCACATGG 57.624 37.500 5.56 0.00 0.00 3.66
2634 3817 5.927689 CAGAATCTGCCTTCTCACATATCTC 59.072 44.000 0.00 0.00 33.18 2.75
2635 3818 5.840149 AGAATCTGCCTTCTCACATATCTCT 59.160 40.000 0.00 0.00 29.38 3.10
2637 3820 3.640498 TCTGCCTTCTCACATATCTCTGG 59.360 47.826 0.00 0.00 0.00 3.86
2638 3821 3.378512 TGCCTTCTCACATATCTCTGGT 58.621 45.455 0.00 0.00 0.00 4.00
2639 3822 4.546674 TGCCTTCTCACATATCTCTGGTA 58.453 43.478 0.00 0.00 0.00 3.25
2640 3823 4.342378 TGCCTTCTCACATATCTCTGGTAC 59.658 45.833 0.00 0.00 0.00 3.34
2641 3824 4.586841 GCCTTCTCACATATCTCTGGTACT 59.413 45.833 0.00 0.00 0.00 2.73
2643 3826 6.407525 GCCTTCTCACATATCTCTGGTACTTT 60.408 42.308 0.00 0.00 0.00 2.66
2658 3919 8.834004 TCTGGTACTTTACATTGTATAGAGGT 57.166 34.615 17.70 4.65 0.00 3.85
2666 3927 5.023533 ACATTGTATAGAGGTTGCGTCAT 57.976 39.130 0.00 0.00 0.00 3.06
2697 3958 5.452917 CGGATCGGAGGGAGTAATAAAGTTT 60.453 44.000 0.00 0.00 0.00 2.66
2702 3963 7.550712 TCGGAGGGAGTAATAAAGTTTCTTAC 58.449 38.462 13.35 13.35 0.00 2.34
2725 3986 7.928307 ACATAATGGAATCTATGTACCATGC 57.072 36.000 0.00 0.00 41.47 4.06
2736 3997 8.978874 ATCTATGTACCATGCTTTCATTAACA 57.021 30.769 0.00 0.00 0.00 2.41
2826 4087 6.683974 AACTGCCATATCAGTGTGATAAAC 57.316 37.500 0.89 0.00 45.77 2.01
2862 4123 4.748102 TCTTTGGTGTAGTTTGATCGTGAC 59.252 41.667 0.00 0.00 0.00 3.67
2909 4178 5.091552 TGCTCTAACTTCCCCTCTTTCTTA 58.908 41.667 0.00 0.00 0.00 2.10
2910 4179 5.546499 TGCTCTAACTTCCCCTCTTTCTTAA 59.454 40.000 0.00 0.00 0.00 1.85
2911 4180 6.043938 TGCTCTAACTTCCCCTCTTTCTTAAA 59.956 38.462 0.00 0.00 0.00 1.52
2912 4181 7.113437 GCTCTAACTTCCCCTCTTTCTTAAAT 58.887 38.462 0.00 0.00 0.00 1.40
2913 4182 7.612244 GCTCTAACTTCCCCTCTTTCTTAAATT 59.388 37.037 0.00 0.00 0.00 1.82
2914 4183 9.168451 CTCTAACTTCCCCTCTTTCTTAAATTC 57.832 37.037 0.00 0.00 0.00 2.17
2915 4184 8.891501 TCTAACTTCCCCTCTTTCTTAAATTCT 58.108 33.333 0.00 0.00 0.00 2.40
2916 4185 9.168451 CTAACTTCCCCTCTTTCTTAAATTCTC 57.832 37.037 0.00 0.00 0.00 2.87
3137 4482 6.698380 ACTACGTGGTAAGAATTCAACATCT 58.302 36.000 1.30 0.00 0.00 2.90
3338 5222 1.102978 ATTGCCGCCAATACCAACTC 58.897 50.000 0.00 0.00 39.81 3.01
3622 5519 4.381825 GCTCATTATGTGTTTGCATTGGGA 60.382 41.667 0.00 0.00 0.00 4.37
3671 5568 3.323775 TGGGTCCTTCAGGTTCTTTACT 58.676 45.455 0.00 0.00 36.34 2.24
3782 5683 9.581289 TGAAATATTCCAAAAGAGTGGTAGAAA 57.419 29.630 0.00 0.00 39.88 2.52
3880 5782 7.722363 TCTCTCACTGATGTTTACTGTTTACA 58.278 34.615 0.00 0.00 0.00 2.41
3900 5802 7.878477 TTACACCATTAAGTAGAAGTTCACG 57.122 36.000 5.50 0.00 0.00 4.35
3951 5853 3.872511 TCCATTTGTTGCCATCATGAC 57.127 42.857 0.00 0.00 0.00 3.06
4069 5972 4.624024 CACTTGGCTGCATCATTGTTTAAG 59.376 41.667 0.50 0.00 0.00 1.85
4130 6128 7.786943 TGCTTATCCATGGGGTTTGAAAATATA 59.213 33.333 13.02 0.00 34.93 0.86
4351 6349 7.418337 TGTGAAGAGGTACATAATCTTAGCA 57.582 36.000 0.00 0.00 33.53 3.49
4386 6384 2.427453 TGGCAAACCGTTTAACATGTGT 59.573 40.909 0.00 0.00 39.70 3.72
4392 6390 5.831702 AACCGTTTAACATGTGTTAACCA 57.168 34.783 15.72 1.15 46.48 3.67
4397 6395 6.458478 CCGTTTAACATGTGTTAACCAGTGAA 60.458 38.462 15.72 0.24 46.48 3.18
4404 6402 5.906113 TGTGTTAACCAGTGAATTGTTGT 57.094 34.783 2.48 0.00 0.00 3.32
4405 6403 6.274157 TGTGTTAACCAGTGAATTGTTGTT 57.726 33.333 2.48 0.00 0.00 2.83
4469 6467 2.225242 TGGGGTGGTGTAAAATCTGCAT 60.225 45.455 0.00 0.00 0.00 3.96
4470 6468 2.427095 GGGGTGGTGTAAAATCTGCATC 59.573 50.000 0.00 0.00 0.00 3.91
4477 6475 5.068067 TGGTGTAAAATCTGCATCATGATGG 59.932 40.000 31.62 18.89 39.16 3.51
4492 6490 8.268401 GCATCATGATGGACAACTCATTTGTTT 61.268 37.037 31.62 0.00 42.55 2.83
4545 6543 4.697756 TCTGGCGCCCAACCTTCG 62.698 66.667 26.77 1.84 30.80 3.79
4626 6625 5.923733 ACTGTTTGGTGAAAATTGTACCA 57.076 34.783 4.99 4.99 42.40 3.25
4633 6632 5.305585 TGGTGAAAATTGTACCAGAGACTC 58.694 41.667 4.99 0.00 39.43 3.36
4737 6736 2.040813 ACATGCTCAGTCATCCCAGTTT 59.959 45.455 0.00 0.00 0.00 2.66
4745 6744 2.305927 AGTCATCCCAGTTTCGGATTGT 59.694 45.455 0.00 0.00 38.08 2.71
4760 6759 2.373169 GGATTGTGGAGGCCATGAGATA 59.627 50.000 5.01 0.00 35.28 1.98
4764 6763 1.000283 GTGGAGGCCATGAGATACTCG 60.000 57.143 5.01 0.00 35.28 4.18
4765 6764 0.037790 GGAGGCCATGAGATACTCGC 60.038 60.000 5.01 0.00 32.35 5.03
4770 6769 2.945668 GGCCATGAGATACTCGCTTTTT 59.054 45.455 0.00 0.00 32.35 1.94
4804 6804 7.999679 TGTTCTCTTTCATTTGTGTTGATCTT 58.000 30.769 0.00 0.00 0.00 2.40
4812 6812 3.435105 TTGTGTTGATCTTGGTGTTGC 57.565 42.857 0.00 0.00 0.00 4.17
4865 6888 3.806949 TCTCCAGTTTTTGTATGGGCT 57.193 42.857 0.00 0.00 34.71 5.19
4866 6889 3.420893 TCTCCAGTTTTTGTATGGGCTG 58.579 45.455 0.00 0.00 34.71 4.85
4867 6890 2.493278 CTCCAGTTTTTGTATGGGCTGG 59.507 50.000 0.00 0.00 43.37 4.85
4868 6891 1.066929 CCAGTTTTTGTATGGGCTGGC 60.067 52.381 0.00 0.00 37.32 4.85
4869 6892 0.887933 AGTTTTTGTATGGGCTGGCG 59.112 50.000 0.00 0.00 0.00 5.69
4900 6923 0.447801 GAATTCGCAGTGCCGTCAAT 59.552 50.000 10.11 0.02 0.00 2.57
4948 6981 2.818274 GTTGGTCATCGGCGGGAC 60.818 66.667 19.56 19.56 0.00 4.46
4952 6985 3.823330 GTCATCGGCGGGACTCGT 61.823 66.667 20.17 0.00 41.72 4.18
4999 7032 6.017026 GCCAAGGCCTGACTTTATAGATAAAC 60.017 42.308 5.69 0.00 34.56 2.01
5245 7279 4.162690 GGCGTCCCGATCAGGCTT 62.163 66.667 0.00 0.00 39.21 4.35
5257 7291 3.806521 CGATCAGGCTTCTTAGTCAATGG 59.193 47.826 0.00 0.00 0.00 3.16
5339 7373 9.623000 GGGAAGGTAAGCTCAATAGTAAATTTA 57.377 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 2.267426 GTTGGAATTGTTAATGCGCCC 58.733 47.619 4.18 0.00 0.00 6.13
178 179 2.361438 GACCGATCTACCTGAACCGATT 59.639 50.000 0.00 0.00 0.00 3.34
185 186 2.587522 CCATCTGACCGATCTACCTGA 58.412 52.381 0.00 0.00 0.00 3.86
284 290 7.675062 CATTTGAGGATATGCTTCCTACTAGT 58.325 38.462 0.00 0.00 46.35 2.57
285 291 6.593382 GCATTTGAGGATATGCTTCCTACTAG 59.407 42.308 0.00 0.00 46.35 2.57
286 292 6.043127 TGCATTTGAGGATATGCTTCCTACTA 59.957 38.462 0.00 0.00 46.35 1.82
365 374 7.930325 GGTAGTATTATAACTCGCCTCCTTTTT 59.070 37.037 0.00 0.00 0.00 1.94
407 416 2.476854 GCTTTGATTGATGAGTCACCGC 60.477 50.000 0.00 0.00 33.11 5.68
417 426 6.916387 CGATGCTTATCTTTGCTTTGATTGAT 59.084 34.615 0.00 0.00 0.00 2.57
418 427 6.260377 CGATGCTTATCTTTGCTTTGATTGA 58.740 36.000 0.00 0.00 0.00 2.57
419 428 5.051907 GCGATGCTTATCTTTGCTTTGATTG 60.052 40.000 0.00 0.00 0.00 2.67
420 429 5.039333 GCGATGCTTATCTTTGCTTTGATT 58.961 37.500 0.00 0.00 0.00 2.57
880 889 2.295602 GGTGGAGTAAAGGCCCGGA 61.296 63.158 0.73 0.00 0.00 5.14
883 892 1.001269 GGTGGTGGAGTAAAGGCCC 60.001 63.158 0.00 0.00 0.00 5.80
998 1011 2.837291 GGCTTGTGTTGGGTGCCA 60.837 61.111 0.00 0.00 42.79 4.92
1047 1060 1.877617 CGCTGCTCTGCTAGACTGC 60.878 63.158 0.00 0.00 0.00 4.40
1048 1061 1.226916 CCGCTGCTCTGCTAGACTG 60.227 63.158 0.00 0.00 0.00 3.51
1056 1069 3.847602 CTCCTCCCCGCTGCTCTG 61.848 72.222 0.00 0.00 0.00 3.35
1332 1350 3.456277 GAGAGGATAGCTTTGGGGAAAGA 59.544 47.826 0.00 0.00 31.58 2.52
1540 2096 5.815581 ACCTCATAGCAAAACAGTGGATTA 58.184 37.500 0.00 0.00 0.00 1.75
1548 2104 7.221450 AGTAACAGTTACCTCATAGCAAAACA 58.779 34.615 18.27 0.00 36.81 2.83
1754 2321 5.651530 TCTAAAGTACACAGATGCAGCTAC 58.348 41.667 3.06 0.00 0.00 3.58
1816 2386 4.545208 TGGAACCACATTCATAGAACGA 57.455 40.909 0.00 0.00 39.30 3.85
2089 3261 6.762702 ATGATGCTGATGTTGTATGAACAA 57.237 33.333 0.00 0.00 43.32 2.83
2099 3271 5.421056 ACAAGAATGGAATGATGCTGATGTT 59.579 36.000 0.00 0.00 0.00 2.71
2178 3350 7.569957 GCAAAGAAAACATGCATCTTAAACAGG 60.570 37.037 0.00 0.00 39.81 4.00
2256 3428 0.588252 GCTTGAGCTGCTTCGTTTCA 59.412 50.000 2.53 0.00 38.21 2.69
2272 3444 2.933056 GCTTCCGTTTCTAGCTCTGCTT 60.933 50.000 0.00 0.00 40.44 3.91
2304 3476 3.704061 ACTGTCTAGAAGAAGGAGGATGC 59.296 47.826 0.00 0.00 0.00 3.91
2306 3478 5.199982 TCACTGTCTAGAAGAAGGAGGAT 57.800 43.478 0.00 0.00 0.00 3.24
2309 3481 4.016444 AGCTCACTGTCTAGAAGAAGGAG 58.984 47.826 0.00 0.00 0.00 3.69
2434 3610 7.147966 ACACACTAAGAAAAACCGAAATCCTTT 60.148 33.333 0.00 0.00 0.00 3.11
2444 3622 4.789802 GCAGCAGACACACTAAGAAAAACC 60.790 45.833 0.00 0.00 0.00 3.27
2445 3623 4.035675 AGCAGCAGACACACTAAGAAAAAC 59.964 41.667 0.00 0.00 0.00 2.43
2507 3689 5.560722 TCAGGTGATGAAACAGAAACCTA 57.439 39.130 0.00 0.00 35.87 3.08
2570 3753 6.118852 TCCATGTGCATAGCTGTATACAAAA 58.881 36.000 7.06 0.00 0.00 2.44
2581 3764 7.031372 CCATACAAATTATCCATGTGCATAGC 58.969 38.462 0.00 0.00 0.00 2.97
2593 3776 8.072567 GCAGATTCTGTGACCATACAAATTATC 58.927 37.037 14.90 0.00 33.43 1.75
2634 3817 9.314321 CAACCTCTATACAATGTAAAGTACCAG 57.686 37.037 0.00 0.00 0.00 4.00
2635 3818 7.767198 GCAACCTCTATACAATGTAAAGTACCA 59.233 37.037 0.00 0.00 0.00 3.25
2637 3820 7.490402 ACGCAACCTCTATACAATGTAAAGTAC 59.510 37.037 0.00 0.00 0.00 2.73
2638 3821 7.549839 ACGCAACCTCTATACAATGTAAAGTA 58.450 34.615 0.00 0.00 0.00 2.24
2639 3822 6.403878 ACGCAACCTCTATACAATGTAAAGT 58.596 36.000 0.00 0.00 0.00 2.66
2640 3823 6.533723 TGACGCAACCTCTATACAATGTAAAG 59.466 38.462 0.00 0.00 0.00 1.85
2641 3824 6.399743 TGACGCAACCTCTATACAATGTAAA 58.600 36.000 0.00 0.00 0.00 2.01
2643 3826 5.585820 TGACGCAACCTCTATACAATGTA 57.414 39.130 0.00 0.00 0.00 2.29
2658 3919 3.001838 CCGATCCGAATTAAATGACGCAA 59.998 43.478 0.00 0.00 0.00 4.85
2666 3927 3.036091 ACTCCCTCCGATCCGAATTAAA 58.964 45.455 0.00 0.00 0.00 1.52
2723 3984 5.362430 ACCCAGTTTCTTGTTAATGAAAGCA 59.638 36.000 0.00 0.00 33.54 3.91
2725 3986 7.229506 AGAGACCCAGTTTCTTGTTAATGAAAG 59.770 37.037 0.00 0.00 33.54 2.62
2736 3997 6.153680 CACTATCAGTAGAGACCCAGTTTCTT 59.846 42.308 0.00 0.00 29.81 2.52
2839 4100 4.748102 GTCACGATCAAACTACACCAAAGA 59.252 41.667 0.00 0.00 0.00 2.52
2894 4155 5.065346 GCGAGAATTTAAGAAAGAGGGGAAG 59.935 44.000 0.00 0.00 0.00 3.46
2909 4178 3.744660 AGTGAAAGTCCTGCGAGAATTT 58.255 40.909 1.42 1.42 36.80 1.82
2910 4179 3.244215 TGAGTGAAAGTCCTGCGAGAATT 60.244 43.478 0.00 0.00 34.62 2.17
2911 4180 2.300152 TGAGTGAAAGTCCTGCGAGAAT 59.700 45.455 0.00 0.00 34.62 2.40
2912 4181 1.686587 TGAGTGAAAGTCCTGCGAGAA 59.313 47.619 0.00 0.00 34.62 2.87
2913 4182 1.328279 TGAGTGAAAGTCCTGCGAGA 58.672 50.000 0.00 0.00 34.62 4.04
2914 4183 2.064762 CTTGAGTGAAAGTCCTGCGAG 58.935 52.381 0.00 0.00 34.62 5.03
2915 4184 1.412710 ACTTGAGTGAAAGTCCTGCGA 59.587 47.619 0.00 0.00 35.44 5.10
2916 4185 1.795286 GACTTGAGTGAAAGTCCTGCG 59.205 52.381 5.91 0.00 46.88 5.18
3259 5143 0.618458 TAGCTACCACAAGGGGCAAG 59.382 55.000 0.00 0.00 42.91 4.01
3398 5294 9.833917 ATCCTATTGATCATGATATGTGATGTC 57.166 33.333 8.54 0.00 36.49 3.06
3622 5519 1.068121 AGCTAAGGAACCTTGCCACT 58.932 50.000 15.37 5.34 37.47 4.00
3778 5679 5.825593 TCACCAAAGTATCTGGACTTTCT 57.174 39.130 0.00 0.00 44.52 2.52
3779 5680 5.763204 TGTTCACCAAAGTATCTGGACTTTC 59.237 40.000 0.00 0.00 44.52 2.62
3782 5683 4.974645 TGTTCACCAAAGTATCTGGACT 57.025 40.909 0.00 0.00 37.40 3.85
3853 5755 9.856488 GTAAACAGTAAACATCAGTGAGAGATA 57.144 33.333 0.00 0.00 0.00 1.98
3855 5757 7.652105 GTGTAAACAGTAAACATCAGTGAGAGA 59.348 37.037 0.00 0.00 0.00 3.10
3880 5782 8.308931 TGATTACGTGAACTTCTACTTAATGGT 58.691 33.333 0.00 0.00 0.00 3.55
3916 5818 9.213799 GCAACAAATGGAAAATTTACCTCAATA 57.786 29.630 0.00 0.00 0.00 1.90
3951 5853 0.323633 TCAGGCATGAACATGGGTGG 60.324 55.000 15.15 0.00 39.16 4.61
4098 6096 2.651334 ACCCCATGGATAAGCATGCTAT 59.349 45.455 23.00 14.43 34.81 2.97
4130 6128 7.603180 TTCTGCAACATGGATATAGTCTACT 57.397 36.000 0.00 0.00 0.00 2.57
4202 6200 5.581085 CACGAGTATCCAAGACCTAAAAAGG 59.419 44.000 0.00 0.00 0.00 3.11
4351 6349 3.445096 GGTTTGCCAAAGTGATAGCAGAT 59.555 43.478 0.00 0.00 36.44 2.90
4386 6384 5.105752 GCACAACAACAATTCACTGGTTAA 58.894 37.500 0.00 0.00 0.00 2.01
4392 6390 3.696051 AGACTGCACAACAACAATTCACT 59.304 39.130 0.00 0.00 0.00 3.41
4421 6419 0.319555 GTCGCAGCACTAGTTGTCCA 60.320 55.000 0.00 0.00 0.00 4.02
4492 6490 2.169561 TCAACAGTAAGACACAGCACCA 59.830 45.455 0.00 0.00 0.00 4.17
4626 6625 3.322254 ACATTTCACGACCAAGAGTCTCT 59.678 43.478 0.00 0.00 43.91 3.10
4633 6632 2.416547 CAGCCTACATTTCACGACCAAG 59.583 50.000 0.00 0.00 0.00 3.61
4645 6644 7.847711 AGATAGTATTCTCAACAGCCTACAT 57.152 36.000 0.00 0.00 0.00 2.29
4646 6645 8.941995 ATAGATAGTATTCTCAACAGCCTACA 57.058 34.615 0.00 0.00 0.00 2.74
4737 6736 1.224315 CATGGCCTCCACAATCCGA 59.776 57.895 3.32 0.00 35.80 4.55
4745 6744 1.332195 CGAGTATCTCATGGCCTCCA 58.668 55.000 3.32 0.00 38.19 3.86
4760 6759 3.149196 ACATGACCATCAAAAAGCGAGT 58.851 40.909 0.00 0.00 0.00 4.18
4764 6763 5.382618 AGAGAACATGACCATCAAAAAGC 57.617 39.130 0.00 0.00 0.00 3.51
4765 6764 7.428020 TGAAAGAGAACATGACCATCAAAAAG 58.572 34.615 0.00 0.00 0.00 2.27
4770 6769 6.491062 ACAAATGAAAGAGAACATGACCATCA 59.509 34.615 0.00 0.00 0.00 3.07
4804 6804 1.598962 GCTCAGAGCTGCAACACCA 60.599 57.895 15.78 0.00 38.45 4.17
4812 6812 1.093159 GGAACCAATGCTCAGAGCTG 58.907 55.000 23.15 13.67 42.97 4.24
4865 6888 0.035152 ATTCAGCAGAATCCACGCCA 60.035 50.000 0.00 0.00 40.39 5.69
4866 6889 1.064654 GAATTCAGCAGAATCCACGCC 59.935 52.381 4.66 0.00 43.52 5.68
4867 6890 1.267732 CGAATTCAGCAGAATCCACGC 60.268 52.381 4.66 0.00 43.52 5.34
4868 6891 1.267732 GCGAATTCAGCAGAATCCACG 60.268 52.381 4.66 11.75 43.52 4.94
4869 6892 1.739466 TGCGAATTCAGCAGAATCCAC 59.261 47.619 17.16 0.00 43.52 4.02
4900 6923 5.123820 CCTGAACAACAACTCTTCAGTTTCA 59.876 40.000 6.03 0.00 41.24 2.69
5140 7173 0.743688 ATTTGGTGCTGTCGTTTGCA 59.256 45.000 0.00 0.00 36.79 4.08
5186 7219 2.047274 CGGGCTTCGGCTTCTCAA 60.047 61.111 0.00 0.00 41.44 3.02
5245 7279 3.055819 GCAGTGGAGACCATTGACTAAGA 60.056 47.826 15.51 0.00 42.72 2.10
5257 7291 1.818642 ATTCTTGCAGCAGTGGAGAC 58.181 50.000 0.00 0.00 0.00 3.36
5339 7373 6.665248 GCTGGGCCTTATGGAATATTAGAAAT 59.335 38.462 4.53 0.00 34.57 2.17


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

AutoCloner maintained by Alex Coulton.