Multiple sequence alignment - TraesCS7B01G247300

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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 TraesCS7B01G247300 chr7B 100.000 3086 0 0 1 3086 457532247 457529162 0.000000e+00 5699.0
1 TraesCS7B01G247300 chr7B 78.973 837 123 23 927 1742 531816574 531817378 3.530000e-144 521.0
2 TraesCS7B01G247300 chr7B 82.927 369 41 10 2525 2873 614234013 614233647 2.310000e-81 313.0
3 TraesCS7B01G247300 chr7B 79.853 407 55 16 2520 2910 463489672 463489277 3.920000e-69 272.0
4 TraesCS7B01G247300 chr7B 85.356 239 22 7 2524 2755 666556413 666556181 5.140000e-58 235.0
5 TraesCS7B01G247300 chr7A 87.457 2049 148 51 416 2397 491261105 491259099 0.000000e+00 2259.0
6 TraesCS7B01G247300 chr7A 81.679 786 105 15 992 1742 540798186 540798967 4.370000e-173 617.0
7 TraesCS7B01G247300 chr7A 80.689 813 102 29 927 1720 570174516 570175292 5.740000e-162 580.0
8 TraesCS7B01G247300 chr7A 81.267 742 101 17 1022 1732 540871520 540872254 1.610000e-157 566.0
9 TraesCS7B01G247300 chr7A 83.000 300 40 4 2524 2814 18265512 18265809 8.490000e-66 261.0
10 TraesCS7B01G247300 chr7A 76.744 215 33 10 2718 2922 657415820 657415613 1.510000e-18 104.0
11 TraesCS7B01G247300 chr7D 91.195 1590 71 14 921 2499 439868725 439867194 0.000000e+00 2097.0
12 TraesCS7B01G247300 chr7D 86.226 922 82 25 1 902 439869682 439868786 0.000000e+00 957.0
13 TraesCS7B01G247300 chr7D 83.975 649 85 7 988 1617 459427089 459426441 3.400000e-169 604.0
14 TraesCS7B01G247300 chr7D 81.158 812 100 26 927 1720 503291182 503291958 1.220000e-168 603.0
15 TraesCS7B01G247300 chr7D 84.202 595 76 12 927 1516 503738789 503739370 2.080000e-156 562.0
16 TraesCS7B01G247300 chr7D 82.862 601 84 12 927 1523 503337971 503338556 3.530000e-144 521.0
17 TraesCS7B01G247300 chr7D 83.955 536 51 13 2493 3009 439866807 439866288 5.980000e-132 481.0
18 TraesCS7B01G247300 chr7D 78.360 439 56 24 2524 2940 42156840 42156419 6.610000e-62 248.0
19 TraesCS7B01G247300 chr7D 82.707 266 39 1 2551 2809 227286808 227287073 2.390000e-56 230.0
20 TraesCS7B01G247300 chr7D 97.436 78 1 1 3005 3082 439864822 439864746 6.940000e-27 132.0
21 TraesCS7B01G247300 chr7D 86.301 73 9 1 144 216 611834842 611834913 9.170000e-11 78.7
22 TraesCS7B01G247300 chr2B 82.185 421 49 14 2524 2926 6524061 6523649 3.810000e-89 339.0
23 TraesCS7B01G247300 chr2B 79.333 150 14 8 2934 3069 777442064 777442210 4.240000e-14 89.8
24 TraesCS7B01G247300 chr4A 83.202 381 41 12 2524 2886 395026241 395025866 8.250000e-86 327.0
25 TraesCS7B01G247300 chr4A 81.092 238 29 7 2625 2848 680056036 680055801 3.160000e-40 176.0
26 TraesCS7B01G247300 chr5A 83.172 309 39 8 2512 2809 496178181 496178487 1.410000e-68 270.0
27 TraesCS7B01G247300 chr5A 81.699 153 24 3 2664 2814 312261381 312261531 1.160000e-24 124.0
28 TraesCS7B01G247300 chr5A 79.070 129 24 3 144 271 28756657 28756531 5.480000e-13 86.1
29 TraesCS7B01G247300 chr5B 79.215 433 52 21 2524 2926 588157651 588157227 1.820000e-67 267.0
30 TraesCS7B01G247300 chr5B 80.135 297 50 3 2525 2813 673517982 673517687 2.410000e-51 213.0
31 TraesCS7B01G247300 chr5B 77.632 152 17 5 2932 3069 553359505 553359357 3.300000e-10 76.8
32 TraesCS7B01G247300 chr3A 81.788 302 46 5 2524 2817 727681302 727681002 8.550000e-61 244.0
33 TraesCS7B01G247300 chr3B 82.492 297 33 7 2521 2808 674060823 674060537 3.070000e-60 243.0
34 TraesCS7B01G247300 chr3B 77.419 155 26 7 145 297 564312243 564312390 1.970000e-12 84.2
35 TraesCS7B01G247300 chr5D 80.534 262 42 5 2556 2809 424821298 424821038 3.140000e-45 193.0
36 TraesCS7B01G247300 chr5D 92.857 56 3 1 144 199 530372700 530372754 2.550000e-11 80.5
37 TraesCS7B01G247300 chr5D 86.111 72 10 0 145 216 40724301 40724230 9.170000e-11 78.7
38 TraesCS7B01G247300 chr4B 77.926 299 48 15 2524 2817 545148028 545148313 1.470000e-38 171.0
39 TraesCS7B01G247300 chr1D 78.000 150 30 3 146 294 93136159 93136306 1.180000e-14 91.6
40 TraesCS7B01G247300 chr1D 92.857 42 1 2 2886 2926 458884080 458884120 3.320000e-05 60.2
41 TraesCS7B01G247300 chr1D 92.857 42 1 2 2886 2926 458884200 458884240 3.320000e-05 60.2
42 TraesCS7B01G247300 chr6B 84.810 79 11 1 142 220 203896737 203896660 9.170000e-11 78.7
43 TraesCS7B01G247300 chr2D 78.000 150 16 6 2934 3069 634467994 634468140 9.170000e-11 78.7
44 TraesCS7B01G247300 chr2D 100.000 29 0 0 3041 3069 315193436 315193408 2.000000e-03 54.7
45 TraesCS7B01G247300 chr3D 77.333 150 17 8 2934 3069 66565827 66565681 4.270000e-09 73.1
46 TraesCS7B01G247300 chr3D 80.952 84 14 2 147 230 432131727 432131808 7.140000e-07 65.8
47 TraesCS7B01G247300 chr3D 100.000 28 0 0 3041 3068 185338037 185338010 6.000000e-03 52.8
48 TraesCS7B01G247300 chr4D 88.333 60 4 3 2870 2926 12458169 12458110 5.520000e-08 69.4
49 TraesCS7B01G247300 chr1B 100.000 29 0 0 3041 3069 394005615 394005587 2.000000e-03 54.7


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 TraesCS7B01G247300 chr7B 457529162 457532247 3085 True 5699.00 5699 100.000 1 3086 1 chr7B.!!$R1 3085
1 TraesCS7B01G247300 chr7B 531816574 531817378 804 False 521.00 521 78.973 927 1742 1 chr7B.!!$F1 815
2 TraesCS7B01G247300 chr7A 491259099 491261105 2006 True 2259.00 2259 87.457 416 2397 1 chr7A.!!$R1 1981
3 TraesCS7B01G247300 chr7A 540798186 540798967 781 False 617.00 617 81.679 992 1742 1 chr7A.!!$F2 750
4 TraesCS7B01G247300 chr7A 570174516 570175292 776 False 580.00 580 80.689 927 1720 1 chr7A.!!$F4 793
5 TraesCS7B01G247300 chr7A 540871520 540872254 734 False 566.00 566 81.267 1022 1732 1 chr7A.!!$F3 710
6 TraesCS7B01G247300 chr7D 439864746 439869682 4936 True 916.75 2097 89.703 1 3082 4 chr7D.!!$R3 3081
7 TraesCS7B01G247300 chr7D 459426441 459427089 648 True 604.00 604 83.975 988 1617 1 chr7D.!!$R2 629
8 TraesCS7B01G247300 chr7D 503291182 503291958 776 False 603.00 603 81.158 927 1720 1 chr7D.!!$F2 793
9 TraesCS7B01G247300 chr7D 503738789 503739370 581 False 562.00 562 84.202 927 1516 1 chr7D.!!$F4 589
10 TraesCS7B01G247300 chr7D 503337971 503338556 585 False 521.00 521 82.862 927 1523 1 chr7D.!!$F3 596

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
33 34 0.313672 GCTTGTTGCCGGACATGAAA 59.686 50.0 5.05 0.0 35.15 2.69 F
1938 2137 0.039437 TCGCCGACAACTTCACTCTC 60.039 55.0 0.00 0.0 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2223 0.036388 GGGATTCGAACACTGAGGCA 60.036 55.0 0.00 0.0 0.00 4.75 R
2883 3524 0.404040 TCCATGGAGGCCGTTTTTCT 59.596 50.0 11.44 0.0 37.29 2.52 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
31 32 0.955428 GAGCTTGTTGCCGGACATGA 60.955 55.000 5.05 0.00 44.23 3.07
32 33 0.537143 AGCTTGTTGCCGGACATGAA 60.537 50.000 5.05 0.00 44.23 2.57
33 34 0.313672 GCTTGTTGCCGGACATGAAA 59.686 50.000 5.05 0.00 35.15 2.69
58 59 3.606687 ACATGTCATAGGAAACGGGAAC 58.393 45.455 0.00 0.00 0.00 3.62
87 88 1.407979 CCGGCGACCATTTAGACTAGT 59.592 52.381 9.30 0.00 0.00 2.57
91 92 5.287226 CGGCGACCATTTAGACTAGTTTAT 58.713 41.667 0.00 0.00 0.00 1.40
92 93 5.751990 CGGCGACCATTTAGACTAGTTTATT 59.248 40.000 0.00 0.00 0.00 1.40
93 94 6.292168 CGGCGACCATTTAGACTAGTTTATTG 60.292 42.308 0.00 0.00 0.00 1.90
129 130 9.606631 AGTCAGCTATAATTTAGTTTCCTCAAG 57.393 33.333 0.00 0.00 0.00 3.02
222 223 3.382227 CCATCCAGCTTGCATGTTATTCA 59.618 43.478 1.14 0.00 0.00 2.57
274 276 5.767665 TGTATGCATACATGGTTGGATTACC 59.232 40.000 31.03 4.41 38.28 2.85
280 282 0.916086 ATGGTTGGATTACCGGCTCA 59.084 50.000 0.00 0.00 41.28 4.26
281 283 0.916086 TGGTTGGATTACCGGCTCAT 59.084 50.000 0.00 0.00 41.28 2.90
288 290 3.006859 TGGATTACCGGCTCATGTATCAG 59.993 47.826 0.00 0.00 39.42 2.90
293 295 1.539065 CCGGCTCATGTATCAGTGTCC 60.539 57.143 0.00 0.00 0.00 4.02
302 304 0.455464 TATCAGTGTCCACGAACGCG 60.455 55.000 3.53 3.53 44.79 6.01
328 330 1.070758 ACGCATCCATGGACAGATACC 59.929 52.381 18.99 0.00 0.00 2.73
333 335 2.184533 TCCATGGACAGATACCGTGTT 58.815 47.619 11.44 0.00 41.32 3.32
341 343 4.501921 GGACAGATACCGTGTTCGATTTAC 59.498 45.833 0.00 0.00 39.71 2.01
354 356 4.371855 TCGATTTACGAGTCTGCAAGAT 57.628 40.909 0.00 0.00 46.11 2.40
355 357 4.105486 TCGATTTACGAGTCTGCAAGATG 58.895 43.478 0.00 0.00 46.11 2.90
356 358 3.302092 CGATTTACGAGTCTGCAAGATGC 60.302 47.826 0.00 0.00 45.70 3.91
357 359 6.293725 CGATTTACGAGTCTGCAAGATGCC 62.294 50.000 0.00 0.00 45.70 4.40
386 395 7.175990 GGTGTGTCTGAAATTCACCCTAAATTA 59.824 37.037 0.00 0.00 41.58 1.40
387 396 8.739972 GTGTGTCTGAAATTCACCCTAAATTAT 58.260 33.333 0.00 0.00 0.00 1.28
441 450 3.488048 GCTAGCTGAGCCTGATACG 57.512 57.895 7.70 0.00 46.41 3.06
484 494 4.891260 ACTAAACGGAAACCTACCTCAAG 58.109 43.478 0.00 0.00 0.00 3.02
521 531 2.817844 GTGCCAAGTAGAAACCGGATTT 59.182 45.455 9.46 4.89 0.00 2.17
535 545 7.672660 AGAAACCGGATTTACCTTCCTTTAATT 59.327 33.333 9.46 0.00 36.31 1.40
595 605 3.189495 GCTGAGCTTCACCTTCCTTTAAC 59.811 47.826 0.00 0.00 0.00 2.01
707 725 3.338249 CTGACGTGGGATTCAAGTGAAT 58.662 45.455 6.24 6.24 46.54 2.57
726 744 1.750193 TCTTTTCCGCAGCTAATGGG 58.250 50.000 0.00 0.00 41.42 4.00
796 817 5.744666 TGCAAGATTACGGGCTTAATAAC 57.255 39.130 0.00 0.00 0.00 1.89
874 909 2.978010 CCGGCGCACAGAAACCTT 60.978 61.111 10.83 0.00 0.00 3.50
933 973 3.300667 GAGCTGCAACGAGCCAACG 62.301 63.158 1.02 0.00 44.83 4.10
961 1051 0.395036 TCGGAGGAGCAGAGGAAGAG 60.395 60.000 0.00 0.00 0.00 2.85
962 1052 0.395036 CGGAGGAGCAGAGGAAGAGA 60.395 60.000 0.00 0.00 0.00 3.10
1113 1230 3.068691 AAGGAGCTCGCCACGCTA 61.069 61.111 7.83 0.00 37.96 4.26
1143 1269 4.175489 GTCGCGCTCGTCTGCCTA 62.175 66.667 5.56 0.00 36.96 3.93
1439 1568 3.881926 TGGAGGCCCTGGGCTTACA 62.882 63.158 34.99 32.27 46.62 2.41
1545 1704 1.216178 GCCGTGCATTGGAAGCAAT 59.784 52.632 11.80 0.00 44.64 3.56
1573 1738 1.144057 ATGGATGTCGTCGGCTTCC 59.856 57.895 21.47 21.47 0.00 3.46
1574 1739 1.613317 ATGGATGTCGTCGGCTTCCA 61.613 55.000 29.71 29.71 42.03 3.53
1575 1740 1.810030 GGATGTCGTCGGCTTCCAC 60.810 63.158 22.86 0.02 32.40 4.02
1755 1942 0.900182 ACGACTGGCCTGATCTGACA 60.900 55.000 17.64 0.00 0.00 3.58
1776 1975 2.279851 TGGCACACCGACGAGTTG 60.280 61.111 0.00 0.00 39.70 3.16
1777 1976 2.279918 GGCACACCGACGAGTTGT 60.280 61.111 0.00 0.00 0.00 3.32
1778 1977 2.594962 GGCACACCGACGAGTTGTG 61.595 63.158 15.67 15.67 36.11 3.33
1779 1978 2.928361 CACACCGACGAGTTGTGC 59.072 61.111 10.08 0.00 33.30 4.57
1780 1979 1.880796 CACACCGACGAGTTGTGCA 60.881 57.895 10.08 0.00 33.30 4.57
1781 1980 1.153529 ACACCGACGAGTTGTGCAA 60.154 52.632 0.00 0.00 33.30 4.08
1782 1981 1.275657 CACCGACGAGTTGTGCAAC 59.724 57.895 6.94 6.94 41.45 4.17
1792 1991 0.376852 GTTGTGCAACGCAGTCTTGA 59.623 50.000 0.00 0.00 45.00 3.02
1903 2102 0.819582 ACCAACTGGATACGGGTACG 59.180 55.000 1.86 0.00 45.76 3.67
1938 2137 0.039437 TCGCCGACAACTTCACTCTC 60.039 55.000 0.00 0.00 0.00 3.20
2024 2223 1.374343 CTGCTGTCAGCCGCATCATT 61.374 55.000 21.99 0.00 41.51 2.57
2142 2341 7.018235 CGAAGAGGAAGAAAAGCTTTATGTTC 58.982 38.462 13.10 14.37 36.83 3.18
2144 2343 7.823745 AGAGGAAGAAAAGCTTTATGTTCAA 57.176 32.000 13.10 0.00 36.83 2.69
2158 2357 1.344114 TGTTCAAAGGGGAATTGCAGC 59.656 47.619 0.00 0.00 0.00 5.25
2159 2358 0.975887 TTCAAAGGGGAATTGCAGCC 59.024 50.000 0.00 0.00 0.00 4.85
2160 2359 0.178938 TCAAAGGGGAATTGCAGCCA 60.179 50.000 0.00 0.00 0.00 4.75
2161 2360 0.906775 CAAAGGGGAATTGCAGCCAT 59.093 50.000 0.00 0.00 0.00 4.40
2162 2361 2.109774 CAAAGGGGAATTGCAGCCATA 58.890 47.619 0.00 0.00 0.00 2.74
2163 2362 2.077687 AAGGGGAATTGCAGCCATAG 57.922 50.000 0.00 0.00 0.00 2.23
2164 2363 1.225373 AGGGGAATTGCAGCCATAGA 58.775 50.000 0.00 0.00 0.00 1.98
2165 2364 1.144503 AGGGGAATTGCAGCCATAGAG 59.855 52.381 0.00 0.00 0.00 2.43
2166 2365 1.143684 GGGGAATTGCAGCCATAGAGA 59.856 52.381 0.00 0.00 0.00 3.10
2167 2366 2.225467 GGGAATTGCAGCCATAGAGAC 58.775 52.381 0.00 0.00 0.00 3.36
2168 2367 2.421952 GGGAATTGCAGCCATAGAGACA 60.422 50.000 0.00 0.00 0.00 3.41
2169 2368 3.484407 GGAATTGCAGCCATAGAGACAT 58.516 45.455 0.00 0.00 0.00 3.06
2170 2369 3.252701 GGAATTGCAGCCATAGAGACATG 59.747 47.826 0.00 0.00 0.00 3.21
2171 2370 3.572632 ATTGCAGCCATAGAGACATGT 57.427 42.857 0.00 0.00 0.00 3.21
2172 2371 2.609427 TGCAGCCATAGAGACATGTC 57.391 50.000 18.47 18.47 0.00 3.06
2173 2372 1.202452 TGCAGCCATAGAGACATGTCG 60.202 52.381 19.85 6.03 34.09 4.35
2174 2373 1.202463 GCAGCCATAGAGACATGTCGT 60.202 52.381 19.85 13.74 34.09 4.34
2175 2374 2.739932 GCAGCCATAGAGACATGTCGTT 60.740 50.000 19.85 14.16 34.09 3.85
2176 2375 2.862536 CAGCCATAGAGACATGTCGTTG 59.137 50.000 19.85 14.71 34.09 4.10
2177 2376 2.159043 AGCCATAGAGACATGTCGTTGG 60.159 50.000 23.60 23.60 34.09 3.77
2178 2377 2.418746 GCCATAGAGACATGTCGTTGGT 60.419 50.000 26.03 11.29 34.09 3.67
2179 2378 3.190079 CCATAGAGACATGTCGTTGGTG 58.810 50.000 19.85 14.98 34.09 4.17
2180 2379 3.119137 CCATAGAGACATGTCGTTGGTGA 60.119 47.826 19.85 3.50 34.09 4.02
2181 2380 4.442052 CCATAGAGACATGTCGTTGGTGAT 60.442 45.833 19.85 0.00 34.09 3.06
2266 2502 3.386726 GGGTAATTCCAGTTTTATGCCCC 59.613 47.826 0.00 0.00 38.11 5.80
2281 2517 3.777106 TGCCCCATGTTTTTGCAATTA 57.223 38.095 0.00 0.00 0.00 1.40
2283 2519 4.660168 TGCCCCATGTTTTTGCAATTATT 58.340 34.783 0.00 0.00 0.00 1.40
2355 2591 3.181471 CCATTTGGTGTTAGTTGTGCCAA 60.181 43.478 0.00 0.00 37.42 4.52
2385 2621 7.289587 ACCATTCTTTTTCGTTTTGAACTTG 57.710 32.000 0.00 0.00 35.97 3.16
2393 2629 5.614923 TTCGTTTTGAACTTGTTCTGTCA 57.385 34.783 13.65 0.00 0.00 3.58
2411 2647 3.070878 TGTCATGTTGCTCCTAGTTGTCA 59.929 43.478 0.00 0.00 0.00 3.58
2413 2649 3.324846 TCATGTTGCTCCTAGTTGTCAGT 59.675 43.478 0.00 0.00 0.00 3.41
2449 2685 1.225704 GCTGTGCCCCAAGCTATCT 59.774 57.895 0.00 0.00 44.23 1.98
2453 2689 2.105477 CTGTGCCCCAAGCTATCTATGT 59.895 50.000 0.00 0.00 44.23 2.29
2491 2727 9.301606 GCGTAGAAAATGTTTAAAAATGAAAGC 57.698 29.630 0.00 0.00 0.00 3.51
2538 3165 9.965824 AATATAATACCGAAATTGCTTTTGGAG 57.034 29.630 10.86 0.00 45.51 3.86
2539 3166 4.718940 ATACCGAAATTGCTTTTGGAGG 57.281 40.909 10.86 4.95 45.51 4.30
2552 3179 3.785859 GGAGGCCGAGCACCATGA 61.786 66.667 0.00 0.00 0.00 3.07
2566 3193 2.689983 CACCATGAAGGCCTCCAAATAC 59.310 50.000 5.23 0.00 43.14 1.89
2646 3273 8.427902 TGTTACAGAGATAGATGAAGGCATAT 57.572 34.615 0.00 0.00 34.11 1.78
2672 3299 7.892212 TTGCACAAGTGTGTAAAGACCAAATAC 60.892 37.037 11.83 0.00 45.20 1.89
2674 3301 5.144359 CAAGTGTGTAAAGACCAAATACGC 58.856 41.667 0.00 0.00 0.00 4.42
2686 3313 2.343101 CAAATACGCTGAAACGAGGGA 58.657 47.619 0.00 0.00 36.70 4.20
2692 3319 1.970917 GCTGAAACGAGGGATGTGCG 61.971 60.000 0.00 0.00 0.00 5.34
2701 3328 2.427506 GAGGGATGTGCGAAAAAGACT 58.572 47.619 0.00 0.00 0.00 3.24
2707 3334 5.815740 GGGATGTGCGAAAAAGACTAATCTA 59.184 40.000 0.00 0.00 33.57 1.98
2708 3335 6.315393 GGGATGTGCGAAAAAGACTAATCTAA 59.685 38.462 0.00 0.00 33.57 2.10
2712 3339 5.351740 GTGCGAAAAAGACTAATCTAAGGCT 59.648 40.000 0.00 0.00 35.92 4.58
2760 3387 6.151648 TCCTTTCAGACCATGAATTTGTCATC 59.848 38.462 0.00 0.00 44.01 2.92
2767 3394 7.752239 CAGACCATGAATTTGTCATCTTTGTAC 59.248 37.037 0.00 0.00 44.01 2.90
2773 3400 6.770303 TGAATTTGTCATCTTTGTACAGGTCA 59.230 34.615 0.00 0.00 0.00 4.02
2789 3416 6.385649 ACAGGTCACATTTCAACGTATTTT 57.614 33.333 0.00 0.00 0.00 1.82
2795 3422 7.696453 GGTCACATTTCAACGTATTTTATCCTG 59.304 37.037 0.00 0.00 0.00 3.86
2831 3468 4.208873 CGTACGCCTGTTTACTTGTACAAA 59.791 41.667 10.03 0.00 33.56 2.83
2832 3469 5.276773 CGTACGCCTGTTTACTTGTACAAAA 60.277 40.000 10.03 0.00 33.56 2.44
2833 3470 5.564048 ACGCCTGTTTACTTGTACAAAAA 57.436 34.783 10.03 5.59 0.00 1.94
2896 3537 5.788055 TTTTTCAAAAGAAAAACGGCCTC 57.212 34.783 10.96 0.00 38.60 4.70
2926 3569 0.603065 AAGAGCCAAAACGCCATTCC 59.397 50.000 0.00 0.00 0.00 3.01
2927 3570 0.251341 AGAGCCAAAACGCCATTCCT 60.251 50.000 0.00 0.00 0.00 3.36
3025 5141 2.397549 AGGTAACGAACTACGCACAAC 58.602 47.619 0.00 0.00 46.94 3.32
3082 5198 0.389817 TGAACAAGAGCGGTCATCGG 60.390 55.000 18.15 5.40 39.69 4.18
3083 5199 1.079127 AACAAGAGCGGTCATCGGG 60.079 57.895 18.15 3.60 39.69 5.14
3084 5200 1.541310 AACAAGAGCGGTCATCGGGA 61.541 55.000 18.15 0.00 39.69 5.14
3085 5201 1.519455 CAAGAGCGGTCATCGGGAC 60.519 63.158 18.15 0.20 46.20 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.924105 GCAACAAGCTCACTGGCCC 61.924 63.158 0.00 0.00 41.15 5.80
31 32 5.183140 CCCGTTTCCTATGACATGTCTTTTT 59.817 40.000 25.55 11.02 0.00 1.94
32 33 4.700213 CCCGTTTCCTATGACATGTCTTTT 59.300 41.667 25.55 13.30 0.00 2.27
33 34 4.019681 TCCCGTTTCCTATGACATGTCTTT 60.020 41.667 25.55 15.62 0.00 2.52
45 46 1.178534 ACGACCGTTCCCGTTTCCTA 61.179 55.000 0.00 0.00 35.21 2.94
46 47 2.341176 CGACCGTTCCCGTTTCCT 59.659 61.111 0.00 0.00 0.00 3.36
104 105 9.601217 TCTTGAGGAAACTAAATTATAGCTGAC 57.399 33.333 0.00 0.00 44.43 3.51
140 141 9.661563 TTCGGACATATTTCAACTAAACTACAT 57.338 29.630 0.00 0.00 0.00 2.29
205 206 4.751060 ACCAATGAATAACATGCAAGCTG 58.249 39.130 0.00 0.00 39.39 4.24
206 207 5.410355 AACCAATGAATAACATGCAAGCT 57.590 34.783 0.00 0.00 39.39 3.74
257 259 2.441750 AGCCGGTAATCCAACCATGTAT 59.558 45.455 1.90 0.00 39.71 2.29
258 260 1.841277 AGCCGGTAATCCAACCATGTA 59.159 47.619 1.90 0.00 39.71 2.29
263 265 1.308998 CATGAGCCGGTAATCCAACC 58.691 55.000 1.90 0.00 36.08 3.77
264 266 2.038387 ACATGAGCCGGTAATCCAAC 57.962 50.000 1.90 0.00 0.00 3.77
274 276 1.136891 TGGACACTGATACATGAGCCG 59.863 52.381 0.00 0.00 0.00 5.52
280 282 2.876091 CGTTCGTGGACACTGATACAT 58.124 47.619 0.56 0.00 0.00 2.29
281 283 1.667756 GCGTTCGTGGACACTGATACA 60.668 52.381 0.56 0.00 0.00 2.29
302 304 0.874607 GTCCATGGATGCGTACGGAC 60.875 60.000 19.62 9.19 36.46 4.79
312 314 2.398588 ACACGGTATCTGTCCATGGAT 58.601 47.619 19.62 3.97 0.00 3.41
333 335 3.842732 TCTTGCAGACTCGTAAATCGA 57.157 42.857 0.00 0.00 46.83 3.59
350 352 2.540383 TCAGACACACCTAGGCATCTT 58.460 47.619 9.30 0.00 0.00 2.40
351 353 2.238084 TCAGACACACCTAGGCATCT 57.762 50.000 9.30 3.71 0.00 2.90
352 354 3.334583 TTTCAGACACACCTAGGCATC 57.665 47.619 9.30 1.14 0.00 3.91
354 356 3.072330 TGAATTTCAGACACACCTAGGCA 59.928 43.478 9.30 0.00 0.00 4.75
355 357 3.437049 GTGAATTTCAGACACACCTAGGC 59.563 47.826 9.30 0.00 35.06 3.93
356 358 4.003648 GGTGAATTTCAGACACACCTAGG 58.996 47.826 7.41 7.41 44.91 3.02
357 359 4.003648 GGGTGAATTTCAGACACACCTAG 58.996 47.826 0.00 0.00 46.72 3.02
358 360 3.650942 AGGGTGAATTTCAGACACACCTA 59.349 43.478 0.00 0.00 46.72 3.08
359 361 2.443255 AGGGTGAATTTCAGACACACCT 59.557 45.455 0.00 0.00 46.72 4.00
360 362 2.863809 AGGGTGAATTTCAGACACACC 58.136 47.619 0.00 0.00 46.79 4.16
361 363 6.575162 ATTTAGGGTGAATTTCAGACACAC 57.425 37.500 0.00 0.00 38.10 3.82
397 406 7.121315 CCCGAAGAATTCTTTTCTTTGTAGGAT 59.879 37.037 21.33 0.00 44.75 3.24
398 407 6.430000 CCCGAAGAATTCTTTTCTTTGTAGGA 59.570 38.462 21.33 0.00 44.75 2.94
400 409 6.072452 AGCCCGAAGAATTCTTTTCTTTGTAG 60.072 38.462 21.33 5.42 44.75 2.74
401 410 5.768164 AGCCCGAAGAATTCTTTTCTTTGTA 59.232 36.000 21.33 0.00 44.75 2.41
478 488 2.004583 TTAACGCGACATCCTTGAGG 57.995 50.000 15.93 0.00 0.00 3.86
484 494 1.531058 GGCACAATTAACGCGACATCC 60.531 52.381 15.93 0.00 0.00 3.51
580 590 3.143728 GCTTCGGTTAAAGGAAGGTGAA 58.856 45.455 14.96 0.00 39.96 3.18
595 605 4.547367 GATCCCGGTGGGCTTCGG 62.547 72.222 0.00 6.71 43.94 4.30
641 658 6.033966 CGTGATTAACCAAAATAAGGAAGGC 58.966 40.000 0.00 0.00 0.00 4.35
707 725 1.280710 TCCCATTAGCTGCGGAAAAGA 59.719 47.619 0.00 0.00 0.00 2.52
804 826 0.103937 GAGTGCTAGGCAGTAGGCAG 59.896 60.000 0.00 0.00 42.74 4.85
933 973 2.641277 GCTCCTCCGATCCGATCCC 61.641 68.421 2.69 0.00 0.00 3.85
961 1051 1.874466 GTGCGAGGCTACGAGCTTC 60.874 63.158 9.91 8.31 43.06 3.86
962 1052 2.182030 GTGCGAGGCTACGAGCTT 59.818 61.111 9.91 0.00 41.99 3.74
1164 1293 1.674651 CTCCGACTCCCACACGAGA 60.675 63.158 0.00 0.00 33.83 4.04
1545 1704 4.145436 ACATCCATGTCCACGGGA 57.855 55.556 0.00 0.00 35.87 5.14
1565 1730 4.704833 GCAGCTGGTGGAAGCCGA 62.705 66.667 17.12 0.00 44.68 5.54
1574 1739 2.360852 GCACCATCTGCAGCTGGT 60.361 61.111 31.72 31.72 44.58 4.00
1728 1915 0.811616 CAGGCCAGTCGTAATGAGCC 60.812 60.000 5.01 0.00 40.79 4.70
1755 1942 1.667830 CTCGTCGGTGTGCCACATT 60.668 57.895 0.00 0.00 35.86 2.71
1770 1969 1.083401 GACTGCGTTGCACAACTCG 60.083 57.895 11.44 0.96 39.08 4.18
1771 1970 0.657840 AAGACTGCGTTGCACAACTC 59.342 50.000 11.44 4.37 39.08 3.01
1772 1971 0.378257 CAAGACTGCGTTGCACAACT 59.622 50.000 11.44 0.00 39.08 3.16
1773 1972 0.376852 TCAAGACTGCGTTGCACAAC 59.623 50.000 3.37 3.37 37.92 3.32
1774 1973 0.376852 GTCAAGACTGCGTTGCACAA 59.623 50.000 0.00 0.00 33.79 3.33
1775 1974 0.742635 TGTCAAGACTGCGTTGCACA 60.743 50.000 1.53 0.00 33.79 4.57
1776 1975 0.316196 GTGTCAAGACTGCGTTGCAC 60.316 55.000 1.53 0.00 33.79 4.57
1777 1976 0.461870 AGTGTCAAGACTGCGTTGCA 60.462 50.000 1.53 0.00 36.92 4.08
1778 1977 0.657840 AAGTGTCAAGACTGCGTTGC 59.342 50.000 1.53 0.00 0.00 4.17
1779 1978 1.003545 CCAAGTGTCAAGACTGCGTTG 60.004 52.381 1.53 0.92 0.00 4.10
1780 1979 1.299541 CCAAGTGTCAAGACTGCGTT 58.700 50.000 1.53 0.00 0.00 4.84
1781 1980 0.532862 CCCAAGTGTCAAGACTGCGT 60.533 55.000 1.53 0.00 0.00 5.24
1782 1981 1.845809 GCCCAAGTGTCAAGACTGCG 61.846 60.000 1.53 0.00 0.00 5.18
1827 2026 4.874977 GAGTACTCTGGCGCCGGC 62.875 72.222 31.15 19.07 38.90 6.13
1938 2137 2.726691 CGCCGTGTAGTTGCTTCCG 61.727 63.158 0.00 0.00 0.00 4.30
2024 2223 0.036388 GGGATTCGAACACTGAGGCA 60.036 55.000 0.00 0.00 0.00 4.75
2116 2315 5.412904 ACATAAAGCTTTTCTTCCTCTTCGG 59.587 40.000 18.47 0.00 32.88 4.30
2142 2341 0.906775 ATGGCTGCAATTCCCCTTTG 59.093 50.000 0.50 0.00 0.00 2.77
2144 2343 1.570501 TCTATGGCTGCAATTCCCCTT 59.429 47.619 0.50 0.00 0.00 3.95
2158 2357 3.119137 TCACCAACGACATGTCTCTATGG 60.119 47.826 22.95 23.18 32.32 2.74
2159 2358 4.110036 TCACCAACGACATGTCTCTATG 57.890 45.455 22.95 14.93 0.00 2.23
2160 2359 5.344743 AATCACCAACGACATGTCTCTAT 57.655 39.130 22.95 3.81 0.00 1.98
2161 2360 4.801330 AATCACCAACGACATGTCTCTA 57.199 40.909 22.95 2.81 0.00 2.43
2162 2361 3.685139 AATCACCAACGACATGTCTCT 57.315 42.857 22.95 7.46 0.00 3.10
2163 2362 3.181530 CGAAATCACCAACGACATGTCTC 60.182 47.826 22.95 8.96 0.00 3.36
2164 2363 2.736721 CGAAATCACCAACGACATGTCT 59.263 45.455 22.95 8.01 0.00 3.41
2165 2364 2.478894 ACGAAATCACCAACGACATGTC 59.521 45.455 16.21 16.21 0.00 3.06
2166 2365 2.489971 ACGAAATCACCAACGACATGT 58.510 42.857 0.00 0.00 0.00 3.21
2167 2366 3.483574 GCTACGAAATCACCAACGACATG 60.484 47.826 0.00 0.00 0.00 3.21
2168 2367 2.671396 GCTACGAAATCACCAACGACAT 59.329 45.455 0.00 0.00 0.00 3.06
2169 2368 2.063266 GCTACGAAATCACCAACGACA 58.937 47.619 0.00 0.00 0.00 4.35
2170 2369 2.334838 AGCTACGAAATCACCAACGAC 58.665 47.619 0.00 0.00 0.00 4.34
2171 2370 2.736144 AGCTACGAAATCACCAACGA 57.264 45.000 0.00 0.00 0.00 3.85
2172 2371 6.764877 ATTATAGCTACGAAATCACCAACG 57.235 37.500 0.00 0.00 0.00 4.10
2173 2372 9.640963 AGATATTATAGCTACGAAATCACCAAC 57.359 33.333 0.00 0.00 0.00 3.77
2175 2374 9.639601 CAAGATATTATAGCTACGAAATCACCA 57.360 33.333 0.00 0.00 0.00 4.17
2176 2375 9.856488 TCAAGATATTATAGCTACGAAATCACC 57.144 33.333 0.00 0.00 0.00 4.02
2308 2544 3.755112 TCCCGATGACAAACTGTGTTA 57.245 42.857 0.00 0.00 41.96 2.41
2355 2591 8.989653 TCAAAACGAAAAAGAATGGTAAAACT 57.010 26.923 0.00 0.00 0.00 2.66
2385 2621 3.931578 ACTAGGAGCAACATGACAGAAC 58.068 45.455 0.00 0.00 0.00 3.01
2393 2629 3.580458 AGACTGACAACTAGGAGCAACAT 59.420 43.478 0.00 0.00 0.00 2.71
2435 2671 2.407562 TGACATAGATAGCTTGGGGCA 58.592 47.619 0.00 0.00 44.79 5.36
2436 2672 3.341823 CATGACATAGATAGCTTGGGGC 58.658 50.000 0.00 0.00 42.19 5.80
2439 2675 3.341823 GGCCATGACATAGATAGCTTGG 58.658 50.000 0.00 0.00 0.00 3.61
2449 2685 2.926250 GCCCTGGGCCATGACATA 59.074 61.111 27.77 0.00 44.06 2.29
2538 3165 2.825836 CCTTCATGGTGCTCGGCC 60.826 66.667 0.00 0.00 0.00 6.13
2539 3166 3.512516 GCCTTCATGGTGCTCGGC 61.513 66.667 0.00 0.00 38.35 5.54
2552 3179 6.432403 TTGAATTTTGTATTTGGAGGCCTT 57.568 33.333 6.77 0.00 0.00 4.35
2621 3248 6.737720 ATGCCTTCATCTATCTCTGTAACA 57.262 37.500 0.00 0.00 0.00 2.41
2622 3249 9.149225 CAATATGCCTTCATCTATCTCTGTAAC 57.851 37.037 0.00 0.00 34.22 2.50
2623 3250 7.821359 GCAATATGCCTTCATCTATCTCTGTAA 59.179 37.037 0.00 0.00 37.42 2.41
2624 3251 7.038799 TGCAATATGCCTTCATCTATCTCTGTA 60.039 37.037 0.00 0.00 44.23 2.74
2625 3252 6.171921 GCAATATGCCTTCATCTATCTCTGT 58.828 40.000 0.00 0.00 37.42 3.41
2626 3253 6.092396 GTGCAATATGCCTTCATCTATCTCTG 59.908 42.308 0.00 0.00 44.23 3.35
2627 3254 6.171921 GTGCAATATGCCTTCATCTATCTCT 58.828 40.000 0.00 0.00 44.23 3.10
2628 3255 5.936372 TGTGCAATATGCCTTCATCTATCTC 59.064 40.000 0.00 0.00 44.23 2.75
2629 3256 5.872963 TGTGCAATATGCCTTCATCTATCT 58.127 37.500 0.00 0.00 44.23 1.98
2630 3257 6.206243 ACTTGTGCAATATGCCTTCATCTATC 59.794 38.462 0.00 0.00 44.23 2.08
2663 3290 2.093783 CCTCGTTTCAGCGTATTTGGTC 59.906 50.000 0.00 0.00 0.00 4.02
2665 3292 1.396996 CCCTCGTTTCAGCGTATTTGG 59.603 52.381 0.00 0.00 0.00 3.28
2666 3293 2.343101 TCCCTCGTTTCAGCGTATTTG 58.657 47.619 0.00 0.00 0.00 2.32
2672 3299 1.970917 GCACATCCCTCGTTTCAGCG 61.971 60.000 0.00 0.00 0.00 5.18
2674 3301 0.389817 TCGCACATCCCTCGTTTCAG 60.390 55.000 0.00 0.00 0.00 3.02
2686 3313 6.183360 GCCTTAGATTAGTCTTTTTCGCACAT 60.183 38.462 0.00 0.00 35.87 3.21
2728 3355 8.827832 AATTCATGGTCTGAAAGGATGAATAA 57.172 30.769 0.00 0.00 46.62 1.40
2739 3366 7.014518 ACAAAGATGACAAATTCATGGTCTGAA 59.985 33.333 0.00 0.00 45.67 3.02
2740 3367 6.491062 ACAAAGATGACAAATTCATGGTCTGA 59.509 34.615 0.00 0.00 45.67 3.27
2745 3372 7.031372 CCTGTACAAAGATGACAAATTCATGG 58.969 38.462 0.00 0.00 45.67 3.66
2758 3385 6.293407 CGTTGAAATGTGACCTGTACAAAGAT 60.293 38.462 0.00 0.00 0.00 2.40
2760 3387 5.204833 CGTTGAAATGTGACCTGTACAAAG 58.795 41.667 0.00 0.00 0.00 2.77
2767 3394 7.696453 GGATAAAATACGTTGAAATGTGACCTG 59.304 37.037 0.00 0.00 0.00 4.00
2789 3416 7.169645 GGCGTACGTGTATAAAATTTCAGGATA 59.830 37.037 17.90 0.00 0.00 2.59
2795 3422 6.098367 ACAGGCGTACGTGTATAAAATTTC 57.902 37.500 17.90 0.00 42.85 2.17
2799 3427 6.155827 AGTAAACAGGCGTACGTGTATAAAA 58.844 36.000 17.90 0.00 43.83 1.52
2805 3433 2.129607 CAAGTAAACAGGCGTACGTGT 58.870 47.619 17.90 11.43 46.46 4.49
2809 3437 5.655893 TTTGTACAAGTAAACAGGCGTAC 57.344 39.130 8.56 0.00 0.00 3.67
2876 3517 3.195825 TGGAGGCCGTTTTTCTTTTGAAA 59.804 39.130 0.00 0.00 45.65 2.69
2877 3518 2.761208 TGGAGGCCGTTTTTCTTTTGAA 59.239 40.909 0.00 0.00 36.52 2.69
2878 3519 2.379972 TGGAGGCCGTTTTTCTTTTGA 58.620 42.857 0.00 0.00 0.00 2.69
2879 3520 2.880963 TGGAGGCCGTTTTTCTTTTG 57.119 45.000 0.00 0.00 0.00 2.44
2880 3521 2.037121 CCATGGAGGCCGTTTTTCTTTT 59.963 45.455 5.56 0.00 0.00 2.27
2881 3522 1.618343 CCATGGAGGCCGTTTTTCTTT 59.382 47.619 5.56 0.00 0.00 2.52
2882 3523 1.203001 TCCATGGAGGCCGTTTTTCTT 60.203 47.619 11.44 0.00 37.29 2.52
2883 3524 0.404040 TCCATGGAGGCCGTTTTTCT 59.596 50.000 11.44 0.00 37.29 2.52
2884 3525 0.811281 CTCCATGGAGGCCGTTTTTC 59.189 55.000 31.14 0.00 38.51 2.29
2885 3526 2.961424 CTCCATGGAGGCCGTTTTT 58.039 52.632 31.14 0.00 38.51 1.94
2999 3645 3.004629 TGCGTAGTTCGTTACCTTCTTGA 59.995 43.478 0.00 0.00 42.13 3.02
3025 5141 4.870221 TTCATCTTCGCTGATCAATGTG 57.130 40.909 0.00 0.00 0.00 3.21
3064 5180 1.084370 CCCGATGACCGCTCTTGTTC 61.084 60.000 0.00 0.00 36.84 3.18


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

AutoCloner maintained by Alex Coulton.