Multiple sequence alignment - TraesCS4A01G449600

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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 TraesCS4A01G449600 chr4A 100.000 5079 0 0 1 5079 715642689 715637611 0.000000e+00 9380.0
1 TraesCS4A01G449600 chr4A 91.083 3443 218 53 1699 5079 715913373 715916788 0.000000e+00 4575.0
2 TraesCS4A01G449600 chr4A 91.039 837 40 15 768 1571 715912353 715913187 0.000000e+00 1098.0
3 TraesCS4A01G449600 chr4A 79.233 443 65 23 1034 1455 11678368 11677932 2.990000e-72 283.0
4 TraesCS4A01G449600 chr7A 88.370 2098 176 40 2262 4309 17268735 17266656 0.000000e+00 2460.0
5 TraesCS4A01G449600 chr7A 84.561 1276 132 19 4 1231 17279227 17277969 0.000000e+00 1205.0
6 TraesCS4A01G449600 chr7A 81.787 582 74 17 1698 2270 17271095 17270537 4.630000e-125 459.0
7 TraesCS4A01G449600 chr7A 96.759 216 6 1 1277 1492 17271533 17271319 4.830000e-95 359.0
8 TraesCS4A01G449600 chr7A 80.412 485 50 27 2262 2735 17269922 17269472 1.360000e-85 327.0
9 TraesCS4A01G449600 chr7A 89.216 102 11 0 1112 1213 692617053 692616952 1.480000e-25 128.0
10 TraesCS4A01G449600 chr7D 88.455 1741 121 40 2038 3731 17761473 17759766 0.000000e+00 2028.0
11 TraesCS4A01G449600 chr7D 89.979 948 69 15 3758 4681 17759772 17758827 0.000000e+00 1201.0
12 TraesCS4A01G449600 chr7D 86.065 1141 61 51 644 1703 17763008 17761885 0.000000e+00 1136.0
13 TraesCS4A01G449600 chr7D 80.655 336 49 12 227 548 203024035 203024368 3.930000e-61 246.0
14 TraesCS4A01G449600 chr7D 91.304 115 8 2 1100 1213 600703547 600703434 6.810000e-34 156.0
15 TraesCS4A01G449600 chr7D 100.000 33 0 0 2588 2620 62117096 62117064 1.530000e-05 62.1
16 TraesCS4A01G449600 chr7D 100.000 29 0 0 4978 5006 195821149 195821121 3.000000e-03 54.7
17 TraesCS4A01G449600 chr3D 85.978 542 73 3 3529 4070 12299345 12298807 1.230000e-160 577.0
18 TraesCS4A01G449600 chr3D 86.085 539 72 3 3529 4067 12375490 12376025 1.230000e-160 577.0
19 TraesCS4A01G449600 chr3D 84.854 548 78 5 3510 4055 12385804 12386348 9.610000e-152 547.0
20 TraesCS4A01G449600 chr3D 86.932 176 23 0 1280 1455 12300251 12300076 1.120000e-46 198.0
21 TraesCS4A01G449600 chr3D 86.932 176 23 0 1280 1455 12374584 12374759 1.120000e-46 198.0
22 TraesCS4A01G449600 chr3B 85.055 542 78 3 3529 4070 17989523 17990061 2.670000e-152 549.0
23 TraesCS4A01G449600 chr3B 83.643 538 80 6 3520 4056 17903493 17902963 2.730000e-137 499.0
24 TraesCS4A01G449600 chr3B 83.598 189 29 2 1289 1476 17689071 17688884 5.230000e-40 176.0
25 TraesCS4A01G449600 chr3B 81.218 197 31 5 1018 1208 17689273 17689077 2.450000e-33 154.0
26 TraesCS4A01G449600 chr3B 92.453 53 3 1 762 813 18000250 18000302 1.960000e-09 75.0
27 TraesCS4A01G449600 chr4B 82.792 523 85 5 3531 4052 570139506 570140024 3.580000e-126 462.0
28 TraesCS4A01G449600 chr4B 80.940 383 55 13 1088 1455 570138563 570138942 2.310000e-73 287.0
29 TraesCS4A01G449600 chr4B 80.519 308 48 7 302 606 291811530 291811828 5.120000e-55 226.0
30 TraesCS4A01G449600 chr1D 82.822 489 58 14 340 814 371602865 371603341 1.020000e-111 414.0
31 TraesCS4A01G449600 chr2D 81.568 472 61 15 231 680 516922964 516923431 2.890000e-97 366.0
32 TraesCS4A01G449600 chr2A 79.152 566 84 22 276 814 661150166 661150724 1.340000e-95 361.0
33 TraesCS4A01G449600 chr2A 75.926 216 41 10 4771 4977 67466445 67466232 3.240000e-17 100.0
34 TraesCS4A01G449600 chr1B 80.864 486 70 11 340 813 496078543 496079017 1.340000e-95 361.0
35 TraesCS4A01G449600 chr1B 82.065 184 22 6 4767 4948 487323381 487323555 4.100000e-31 147.0
36 TraesCS4A01G449600 chr4D 80.729 384 56 14 1087 1455 456047114 456047494 2.990000e-72 283.0
37 TraesCS4A01G449600 chr6B 81.421 366 48 13 342 697 260120593 260120238 1.080000e-71 281.0
38 TraesCS4A01G449600 chr6B 77.674 215 39 7 4771 4977 76235432 76235645 6.910000e-24 122.0
39 TraesCS4A01G449600 chr6B 78.472 144 21 9 678 814 591256938 591257078 9.060000e-13 86.1
40 TraesCS4A01G449600 chr6B 77.640 161 21 13 2508 2663 205039564 205039714 3.260000e-12 84.2
41 TraesCS4A01G449600 chr7B 78.607 402 57 19 342 727 428474325 428473937 6.570000e-59 239.0
42 TraesCS4A01G449600 chr7B 85.909 220 26 4 329 544 653977270 653977488 3.960000e-56 230.0
43 TraesCS4A01G449600 chr7B 85.882 170 24 0 3094 3263 680096649 680096818 1.120000e-41 182.0
44 TraesCS4A01G449600 chr7B 81.081 185 28 6 4766 4948 745193359 745193180 1.910000e-29 141.0
45 TraesCS4A01G449600 chr7B 79.104 201 39 3 329 526 674575022 674574822 8.870000e-28 135.0
46 TraesCS4A01G449600 chr7B 100.000 29 0 0 4978 5006 159720743 159720715 3.000000e-03 54.7
47 TraesCS4A01G449600 chr2B 78.155 412 55 22 340 739 88247198 88247586 3.960000e-56 230.0
48 TraesCS4A01G449600 chr2B 78.140 215 38 7 4771 4977 77292585 77292798 1.480000e-25 128.0
49 TraesCS4A01G449600 chr2B 94.737 76 4 0 4781 4856 473307325 473307400 8.930000e-23 119.0
50 TraesCS4A01G449600 chr5D 80.714 280 33 8 410 689 310188735 310188993 1.120000e-46 198.0
51 TraesCS4A01G449600 chr5D 84.483 174 16 8 4779 4948 281168276 281168442 1.460000e-35 161.0
52 TraesCS4A01G449600 chr5A 84.118 170 20 4 4766 4933 623563079 623562915 1.890000e-34 158.0
53 TraesCS4A01G449600 chrUn 82.162 185 26 6 4766 4948 88805267 88805088 8.810000e-33 152.0
54 TraesCS4A01G449600 chrUn 88.679 53 6 0 762 814 37210629 37210681 1.180000e-06 65.8
55 TraesCS4A01G449600 chrUn 79.381 97 11 8 2575 2669 99862220 99862131 5.490000e-05 60.2
56 TraesCS4A01G449600 chr5B 83.974 156 17 1 486 641 34259281 34259428 5.300000e-30 143.0
57 TraesCS4A01G449600 chr5B 84.483 58 5 2 759 814 531273198 531273253 3.000000e-03 54.7
58 TraesCS4A01G449600 chr5B 100.000 28 0 0 4979 5006 370003305 370003332 9.000000e-03 52.8
59 TraesCS4A01G449600 chr3A 80.769 130 15 5 227 347 685813036 685812908 5.410000e-15 93.5
60 TraesCS4A01G449600 chr6A 77.778 171 22 13 2502 2667 144053501 144053660 1.950000e-14 91.6
61 TraesCS4A01G449600 chr1A 80.851 94 15 2 2530 2622 547982974 547982883 2.540000e-08 71.3
62 TraesCS4A01G449600 chr1A 79.167 96 14 6 2530 2622 341025535 341025627 1.530000e-05 62.1


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 TraesCS4A01G449600 chr4A 715637611 715642689 5078 True 9380.00 9380 100.000000 1 5079 1 chr4A.!!$R2 5078
1 TraesCS4A01G449600 chr4A 715912353 715916788 4435 False 2836.50 4575 91.061000 768 5079 2 chr4A.!!$F1 4311
2 TraesCS4A01G449600 chr7A 17277969 17279227 1258 True 1205.00 1205 84.561000 4 1231 1 chr7A.!!$R1 1227
3 TraesCS4A01G449600 chr7A 17266656 17271533 4877 True 901.25 2460 86.832000 1277 4309 4 chr7A.!!$R3 3032
4 TraesCS4A01G449600 chr7D 17758827 17763008 4181 True 1455.00 2028 88.166333 644 4681 3 chr7D.!!$R4 4037
5 TraesCS4A01G449600 chr3D 12385804 12386348 544 False 547.00 547 84.854000 3510 4055 1 chr3D.!!$F1 545
6 TraesCS4A01G449600 chr3D 12298807 12300251 1444 True 387.50 577 86.455000 1280 4070 2 chr3D.!!$R1 2790
7 TraesCS4A01G449600 chr3D 12374584 12376025 1441 False 387.50 577 86.508500 1280 4067 2 chr3D.!!$F2 2787
8 TraesCS4A01G449600 chr3B 17989523 17990061 538 False 549.00 549 85.055000 3529 4070 1 chr3B.!!$F1 541
9 TraesCS4A01G449600 chr3B 17902963 17903493 530 True 499.00 499 83.643000 3520 4056 1 chr3B.!!$R1 536
10 TraesCS4A01G449600 chr4B 570138563 570140024 1461 False 374.50 462 81.866000 1088 4052 2 chr4B.!!$F2 2964
11 TraesCS4A01G449600 chr2A 661150166 661150724 558 False 361.00 361 79.152000 276 814 1 chr2A.!!$F1 538

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
506 528 0.107459 AAGAGGCCAGCGAGGAAATC 60.107 55.0 5.01 0.00 41.22 2.17 F
1873 2101 0.878523 CGTGTGCGAGACTTTTGGGA 60.879 55.0 0.00 0.00 41.33 4.37 F
2741 4874 1.032014 AGGAAGCAACAACGCACAAT 58.968 45.0 0.00 0.00 0.00 2.71 F
2793 4926 0.036732 GTGAGGCACCTGGATGTTCA 59.963 55.0 0.00 1.83 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 2171 0.661552 TACGATAGCAGTGGAGCGAC 59.338 55.000 0.00 0.0 40.15 5.19 R
2774 4907 0.036732 TGAACATCCAGGTGCCTCAC 59.963 55.000 0.00 0.0 0.00 3.51 R
4024 6199 2.309528 TGCGCTCTTCCGATAACATT 57.690 45.000 9.73 0.0 0.00 2.71 R
4765 6970 1.515954 CGCGGGACACCATCTAGTT 59.484 57.895 0.00 0.0 36.13 2.24 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
27 28 4.496341 CGTGCCACACAAATATTCTCATCC 60.496 45.833 0.00 0.00 33.40 3.51
33 34 6.127758 CCACACAAATATTCTCATCCGGAAAA 60.128 38.462 9.01 0.75 0.00 2.29
34 35 6.747280 CACACAAATATTCTCATCCGGAAAAC 59.253 38.462 9.01 0.00 0.00 2.43
35 36 6.127730 ACACAAATATTCTCATCCGGAAAACC 60.128 38.462 9.01 0.00 0.00 3.27
36 37 6.095440 CACAAATATTCTCATCCGGAAAACCT 59.905 38.462 9.01 0.00 0.00 3.50
42 43 3.119245 TCTCATCCGGAAAACCTTAGACG 60.119 47.826 9.01 0.00 0.00 4.18
43 44 2.093869 TCATCCGGAAAACCTTAGACGG 60.094 50.000 9.01 0.00 42.45 4.79
44 45 1.341080 TCCGGAAAACCTTAGACGGT 58.659 50.000 0.00 0.00 41.82 4.83
48 49 3.306294 CCGGAAAACCTTAGACGGTAGTT 60.306 47.826 0.00 0.00 35.89 2.24
52 53 7.257722 CGGAAAACCTTAGACGGTAGTTAATA 58.742 38.462 0.00 0.00 35.89 0.98
53 54 7.759433 CGGAAAACCTTAGACGGTAGTTAATAA 59.241 37.037 0.00 0.00 35.89 1.40
70 71 8.084590 AGTTAATAAAAACTCCACTTCAGTCG 57.915 34.615 0.00 0.00 34.60 4.18
77 78 0.251386 TCCACTTCAGTCGCCTCTCT 60.251 55.000 0.00 0.00 0.00 3.10
79 80 0.735632 CACTTCAGTCGCCTCTCTGC 60.736 60.000 0.00 0.00 0.00 4.26
90 91 0.689623 CCTCTCTGCCACTCCACTTT 59.310 55.000 0.00 0.00 0.00 2.66
91 92 1.072965 CCTCTCTGCCACTCCACTTTT 59.927 52.381 0.00 0.00 0.00 2.27
97 98 1.177401 GCCACTCCACTTTTGATCCC 58.823 55.000 0.00 0.00 0.00 3.85
111 112 1.721691 TGATCCCCTCCAAACCCATTT 59.278 47.619 0.00 0.00 0.00 2.32
135 136 3.434319 CGGCGACCAAAGCAGCAT 61.434 61.111 0.00 0.00 36.08 3.79
141 142 0.610232 GACCAAAGCAGCATCCCTGT 60.610 55.000 0.00 0.00 43.71 4.00
150 151 0.546267 AGCATCCCTGTCTCTGGTGT 60.546 55.000 0.00 0.00 0.00 4.16
173 174 2.881539 ATCCGGCTCCTACGACGACA 62.882 60.000 0.00 0.00 0.00 4.35
180 181 1.130749 CTCCTACGACGACAGACCAAG 59.869 57.143 0.00 0.00 0.00 3.61
184 185 0.892358 ACGACGACAGACCAAGCCTA 60.892 55.000 0.00 0.00 0.00 3.93
187 188 0.603569 ACGACAGACCAAGCCTACTG 59.396 55.000 0.00 0.00 36.58 2.74
188 189 0.737715 CGACAGACCAAGCCTACTGC 60.738 60.000 0.00 0.00 41.71 4.40
189 190 0.321671 GACAGACCAAGCCTACTGCA 59.678 55.000 0.00 0.00 44.83 4.41
195 196 1.352352 ACCAAGCCTACTGCATGAAGT 59.648 47.619 12.09 12.09 41.13 3.01
197 198 2.616256 CCAAGCCTACTGCATGAAGTGA 60.616 50.000 17.28 0.00 41.13 3.41
199 200 2.983229 AGCCTACTGCATGAAGTGAAG 58.017 47.619 17.28 6.62 44.83 3.02
212 213 0.881796 AGTGAAGCTCGACGATGTGA 59.118 50.000 0.00 0.00 0.00 3.58
213 214 0.985549 GTGAAGCTCGACGATGTGAC 59.014 55.000 0.00 0.00 0.00 3.67
218 219 1.062685 CTCGACGATGTGACGGAGG 59.937 63.158 0.00 0.00 36.39 4.30
229 230 2.683933 ACGGAGGTCGCCCTTCAT 60.684 61.111 0.00 0.00 42.86 2.57
253 254 4.018609 GGAGACGGATGCGTGATG 57.981 61.111 19.71 0.00 0.00 3.07
315 316 2.354902 GCATGAGGCAAACAAGGGT 58.645 52.632 0.00 0.00 43.97 4.34
370 392 2.031012 GGCTGTTGGGCAAAAGGC 59.969 61.111 0.00 0.00 42.77 4.35
378 400 3.042560 GGCAAAAGGCGCAACTCT 58.957 55.556 10.83 0.00 46.16 3.24
379 401 1.372128 GGCAAAAGGCGCAACTCTG 60.372 57.895 10.83 0.00 46.16 3.35
387 409 1.153745 GCGCAACTCTGACTCCGAT 60.154 57.895 0.30 0.00 0.00 4.18
390 412 1.671328 CGCAACTCTGACTCCGATCTA 59.329 52.381 0.00 0.00 0.00 1.98
391 413 2.097629 CGCAACTCTGACTCCGATCTAA 59.902 50.000 0.00 0.00 0.00 2.10
408 430 1.880819 TAACGGACGGCTTCACCTCC 61.881 60.000 0.00 0.00 35.61 4.30
415 437 2.125350 GCTTCACCTCCAGCTCCG 60.125 66.667 0.00 0.00 32.87 4.63
420 442 3.063084 ACCTCCAGCTCCGACGAC 61.063 66.667 0.00 0.00 0.00 4.34
454 476 1.065928 GTCGACGCCTACATGGAGG 59.934 63.158 20.84 20.84 40.14 4.30
457 479 1.742768 GACGCCTACATGGAGGAGG 59.257 63.158 29.37 19.96 40.49 4.30
464 486 0.982852 TACATGGAGGAGGGGCACAG 60.983 60.000 0.00 0.00 0.00 3.66
506 528 0.107459 AAGAGGCCAGCGAGGAAATC 60.107 55.000 5.01 0.00 41.22 2.17
507 529 1.221840 GAGGCCAGCGAGGAAATCA 59.778 57.895 5.01 0.00 41.22 2.57
522 544 1.986882 AATCATGATTTCCTCCGCCC 58.013 50.000 15.36 0.00 0.00 6.13
541 563 4.503643 CGCCCTTCCCCGTTCTATTTATAA 60.504 45.833 0.00 0.00 0.00 0.98
542 564 5.567430 GCCCTTCCCCGTTCTATTTATAAT 58.433 41.667 0.00 0.00 0.00 1.28
543 565 6.008331 GCCCTTCCCCGTTCTATTTATAATT 58.992 40.000 0.00 0.00 0.00 1.40
544 566 6.492429 GCCCTTCCCCGTTCTATTTATAATTT 59.508 38.462 0.00 0.00 0.00 1.82
545 567 7.014905 GCCCTTCCCCGTTCTATTTATAATTTT 59.985 37.037 0.00 0.00 0.00 1.82
546 568 9.577222 CCCTTCCCCGTTCTATTTATAATTTTA 57.423 33.333 0.00 0.00 0.00 1.52
589 611 7.611213 AGTACTTTGTAGTATGGATTTGCAC 57.389 36.000 0.00 0.00 39.01 4.57
595 617 3.719268 AGTATGGATTTGCACTGTCCA 57.281 42.857 14.28 14.28 45.37 4.02
598 620 0.888736 TGGATTTGCACTGTCCACCG 60.889 55.000 9.25 0.00 37.12 4.94
599 621 1.586154 GGATTTGCACTGTCCACCGG 61.586 60.000 0.00 0.00 32.23 5.28
609 631 1.668151 GTCCACCGGTGAACTCTGC 60.668 63.158 36.07 12.76 0.00 4.26
630 652 3.127721 GCTGAACTATGCTCCTTTTGTCC 59.872 47.826 0.00 0.00 0.00 4.02
641 663 1.401018 CCTTTTGTCCGGCGATGAAAC 60.401 52.381 9.30 0.00 0.00 2.78
672 700 6.148270 ACTACGTGTTGATCATGTTTTACG 57.852 37.500 0.00 4.51 42.88 3.18
681 709 4.687018 TGATCATGTTTTACGTAGCGTTGT 59.313 37.500 0.00 0.00 41.54 3.32
703 740 7.681939 TGTATGGTTTTGAGGTTTCAGATAC 57.318 36.000 0.00 0.00 34.15 2.24
706 743 5.556915 TGGTTTTGAGGTTTCAGATACGAT 58.443 37.500 0.00 0.00 34.15 3.73
714 751 2.492019 TTCAGATACGATGGACGCAG 57.508 50.000 0.00 0.00 46.94 5.18
718 755 1.215655 GATACGATGGACGCAGGTGC 61.216 60.000 0.00 0.00 46.94 5.01
739 776 4.014847 CGAAAGCAAAAATATGAGGCGA 57.985 40.909 0.00 0.00 0.00 5.54
740 777 3.786048 CGAAAGCAAAAATATGAGGCGAC 59.214 43.478 0.00 0.00 0.00 5.19
741 778 3.405170 AAGCAAAAATATGAGGCGACG 57.595 42.857 0.00 0.00 0.00 5.12
756 793 4.393155 ACGCCCGAGCAATGCTGA 62.393 61.111 14.48 0.00 39.88 4.26
757 794 2.898840 CGCCCGAGCAATGCTGAT 60.899 61.111 14.48 0.00 39.88 2.90
810 847 3.276857 CCATGTCTTGCTGTAGATGCTT 58.723 45.455 0.00 0.00 0.00 3.91
846 883 6.862711 ACACTTTTGACTTTTCCTAGCTAC 57.137 37.500 0.00 0.00 0.00 3.58
888 946 4.569162 TGGAATGTAAGCCGTTTTAGATCG 59.431 41.667 0.00 0.00 0.00 3.69
890 948 5.064325 GGAATGTAAGCCGTTTTAGATCGTT 59.936 40.000 0.00 0.00 0.00 3.85
891 949 6.256321 GGAATGTAAGCCGTTTTAGATCGTTA 59.744 38.462 0.00 0.00 0.00 3.18
971 1034 4.201980 CCAACTAACTACACCGATCGATCA 60.202 45.833 24.40 4.28 0.00 2.92
977 1040 2.498807 ACACCGATCGATCATCAGTG 57.501 50.000 24.40 23.50 43.27 3.66
992 1058 5.128499 ATCATCAGTGACAAAGCTAGTAGCT 59.872 40.000 19.25 19.25 45.56 3.32
1125 1200 2.202703 GCGTACGGGAGCATCGTT 60.203 61.111 18.39 0.00 41.38 3.85
1719 1946 5.240183 GGGTCTAGTTGTCTTGGGTTTTAAC 59.760 44.000 0.00 0.00 0.00 2.01
1734 1961 7.696981 TGGGTTTTAACTATGTTATGGTGGTA 58.303 34.615 0.00 0.00 0.00 3.25
1762 1989 7.730672 TTTCATTCACATATTTTGATGGGGA 57.269 32.000 0.00 0.00 30.63 4.81
1770 1997 1.187974 TTTTGATGGGGATGCTGCTG 58.812 50.000 0.00 0.00 0.00 4.41
1774 2001 1.695239 ATGGGGATGCTGCTGGAGA 60.695 57.895 0.00 0.00 0.00 3.71
1815 2043 1.798813 GAGTAGAGTTGTTTGGTGCGG 59.201 52.381 0.00 0.00 0.00 5.69
1860 2088 1.081892 ATCTTGCTGTGATCGTGTGC 58.918 50.000 0.00 0.00 0.00 4.57
1873 2101 0.878523 CGTGTGCGAGACTTTTGGGA 60.879 55.000 0.00 0.00 41.33 4.37
1900 2132 2.999648 AAGCTCCCGCTCAGCTCA 61.000 61.111 0.00 0.00 46.96 4.26
1907 2139 3.767806 CGCTCAGCTCAGCTCCCA 61.768 66.667 8.35 0.00 36.40 4.37
1908 2140 2.125188 GCTCAGCTCAGCTCCCAC 60.125 66.667 0.67 0.00 36.40 4.61
1923 2155 1.662044 CCACCTCAACTTGCTTGCC 59.338 57.895 0.00 0.00 0.00 4.52
1961 2193 1.598183 CGCTCCACTGCTATCGTACAG 60.598 57.143 0.00 0.00 39.86 2.74
2348 3249 4.942761 AAACAAACATGAGCCATCAACT 57.057 36.364 0.00 0.00 39.39 3.16
2352 3253 4.826733 ACAAACATGAGCCATCAACTAACA 59.173 37.500 0.00 0.00 39.39 2.41
2357 3258 2.805671 TGAGCCATCAACTAACAACACG 59.194 45.455 0.00 0.00 30.61 4.49
2361 3262 3.422603 GCCATCAACTAACAACACGTACG 60.423 47.826 15.01 15.01 0.00 3.67
2368 3269 4.870363 ACTAACAACACGTACGGTTATGT 58.130 39.130 21.06 15.13 0.00 2.29
2389 3290 1.461461 GGGGCCAGCTATCCCACTA 60.461 63.158 20.43 0.00 44.43 2.74
2401 3302 3.327404 CCACTACCACGGCCCCTT 61.327 66.667 0.00 0.00 0.00 3.95
2402 3303 2.046314 CACTACCACGGCCCCTTG 60.046 66.667 0.00 0.00 0.00 3.61
2403 3304 2.203877 ACTACCACGGCCCCTTGA 60.204 61.111 0.00 0.00 0.00 3.02
2405 3306 2.203877 TACCACGGCCCCTTGAGT 60.204 61.111 0.00 0.00 0.00 3.41
2443 3344 9.745880 CCAAATCTAGAGAGCTTAATACGTTAA 57.254 33.333 0.00 0.00 0.00 2.01
2481 3386 7.743520 TGTTCCAAAACAAAAGATCGTTAAC 57.256 32.000 0.00 0.00 42.34 2.01
2483 3388 7.486551 TGTTCCAAAACAAAAGATCGTTAACTG 59.513 33.333 3.71 0.00 42.34 3.16
2735 4868 2.559998 ACAAACAGGAAGCAACAACG 57.440 45.000 0.00 0.00 0.00 4.10
2741 4874 1.032014 AGGAAGCAACAACGCACAAT 58.968 45.000 0.00 0.00 0.00 2.71
2746 4879 4.475944 GAAGCAACAACGCACAATCTTAT 58.524 39.130 0.00 0.00 0.00 1.73
2748 4881 2.342354 GCAACAACGCACAATCTTATGC 59.658 45.455 0.00 0.00 38.52 3.14
2790 4923 1.130054 ACAGTGAGGCACCTGGATGT 61.130 55.000 0.00 0.00 34.49 3.06
2793 4926 0.036732 GTGAGGCACCTGGATGTTCA 59.963 55.000 0.00 1.83 0.00 3.18
2807 4954 9.401058 ACCTGGATGTTCAAAATCTATCTTAAG 57.599 33.333 0.00 0.00 0.00 1.85
2810 4957 9.618890 TGGATGTTCAAAATCTATCTTAAGAGG 57.381 33.333 11.53 6.61 0.00 3.69
2899 5047 2.601666 AGCACCTCCGCTCAGTCA 60.602 61.111 0.00 0.00 37.91 3.41
2908 5056 0.820226 CCGCTCAGTCATCAAGGAGA 59.180 55.000 0.00 0.00 0.00 3.71
2922 5070 2.359169 GGAGATGCTCGGGGACACA 61.359 63.158 0.00 0.00 0.00 3.72
3065 5217 4.273480 GTGTCTCACTCTATCTCTCTCTGC 59.727 50.000 0.00 0.00 0.00 4.26
3066 5218 4.164030 TGTCTCACTCTATCTCTCTCTGCT 59.836 45.833 0.00 0.00 0.00 4.24
3122 5274 4.789807 CCATGAAGGATGTCTCCAAGAAT 58.210 43.478 0.00 0.00 44.79 2.40
3170 5322 1.227263 GTCTGCCGCACCGACATAT 60.227 57.895 7.67 0.00 0.00 1.78
3312 5465 4.669318 GACAATGAATGTGATTGAGGCTG 58.331 43.478 0.00 0.00 44.12 4.85
3364 5521 6.754193 AGGCTTATAAATACTCTGCTCTGTC 58.246 40.000 0.00 0.00 0.00 3.51
3381 5538 8.621532 TGCTCTGTCAAAACTCATTAATTAGT 57.378 30.769 0.00 0.00 0.00 2.24
3451 5616 1.004745 CACCCTACTTGCATCCCAACT 59.995 52.381 0.00 0.00 0.00 3.16
3502 5669 8.573035 TGTTTTGGTATCAAAGTATTGTTCTCC 58.427 33.333 0.66 0.00 42.93 3.71
4024 6199 2.543861 GGAGCTGATCTATTTCGCACGA 60.544 50.000 0.00 0.00 0.00 4.35
4449 6631 4.650972 TGTTGGGATTGGTTACTAGCTT 57.349 40.909 0.00 0.00 0.00 3.74
4450 6632 4.993028 TGTTGGGATTGGTTACTAGCTTT 58.007 39.130 0.00 0.00 0.00 3.51
4451 6633 4.764823 TGTTGGGATTGGTTACTAGCTTTG 59.235 41.667 0.00 0.00 0.00 2.77
4454 6636 6.569127 TGGGATTGGTTACTAGCTTTGATA 57.431 37.500 0.00 0.00 0.00 2.15
4456 6638 8.270137 TGGGATTGGTTACTAGCTTTGATATA 57.730 34.615 0.00 0.00 0.00 0.86
4576 6781 0.323360 TTAAGCTCATGTGCCCCCAC 60.323 55.000 15.81 0.00 42.40 4.61
4951 7156 5.798125 ACAGTCGATCATTCTATCACCAT 57.202 39.130 0.00 0.00 0.00 3.55
5049 7254 1.939934 TCTGTTTCTCCACTGTTTGCG 59.060 47.619 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.127730 GGTTTTCCGGATGAGAATATTTGTGT 60.128 38.462 4.15 0.00 0.00 3.72
27 28 3.582714 ACTACCGTCTAAGGTTTTCCG 57.417 47.619 0.00 0.00 43.00 4.30
34 35 9.091784 GGAGTTTTTATTAACTACCGTCTAAGG 57.908 37.037 0.00 0.00 38.43 2.69
35 36 9.643693 TGGAGTTTTTATTAACTACCGTCTAAG 57.356 33.333 0.00 0.00 38.05 2.18
36 37 9.423061 GTGGAGTTTTTATTAACTACCGTCTAA 57.577 33.333 0.00 0.00 38.05 2.10
42 43 9.281371 ACTGAAGTGGAGTTTTTATTAACTACC 57.719 33.333 0.00 0.00 38.05 3.18
44 45 9.199982 CGACTGAAGTGGAGTTTTTATTAACTA 57.800 33.333 0.00 0.00 38.43 2.24
48 49 5.410439 GGCGACTGAAGTGGAGTTTTTATTA 59.590 40.000 0.00 0.00 0.00 0.98
52 53 1.947456 GGCGACTGAAGTGGAGTTTTT 59.053 47.619 0.00 0.00 0.00 1.94
53 54 1.141053 AGGCGACTGAAGTGGAGTTTT 59.859 47.619 0.00 0.00 41.13 2.43
70 71 1.835927 AAGTGGAGTGGCAGAGAGGC 61.836 60.000 0.00 0.00 44.50 4.70
77 78 1.547675 GGGATCAAAAGTGGAGTGGCA 60.548 52.381 0.00 0.00 0.00 4.92
79 80 1.355720 AGGGGATCAAAAGTGGAGTGG 59.644 52.381 0.00 0.00 0.00 4.00
90 91 1.392407 ATGGGTTTGGAGGGGATCAA 58.608 50.000 0.00 0.00 0.00 2.57
91 92 1.392407 AATGGGTTTGGAGGGGATCA 58.608 50.000 0.00 0.00 0.00 2.92
111 112 4.337177 TTTGGTCGCCGGCCATCA 62.337 61.111 23.46 13.27 35.71 3.07
132 133 0.392193 CACACCAGAGACAGGGATGC 60.392 60.000 0.00 0.00 0.00 3.91
133 134 0.251354 CCACACCAGAGACAGGGATG 59.749 60.000 0.00 0.00 0.00 3.51
134 135 0.117140 TCCACACCAGAGACAGGGAT 59.883 55.000 0.00 0.00 0.00 3.85
135 136 0.105194 TTCCACACCAGAGACAGGGA 60.105 55.000 0.00 0.00 0.00 4.20
141 142 1.899437 GCCGGATTCCACACCAGAGA 61.899 60.000 5.05 0.00 0.00 3.10
150 151 1.076559 TCGTAGGAGCCGGATTCCA 60.077 57.895 22.83 9.76 37.18 3.53
173 174 1.279496 TCATGCAGTAGGCTTGGTCT 58.721 50.000 0.00 0.00 45.17 3.85
180 181 1.399791 GCTTCACTTCATGCAGTAGGC 59.600 52.381 0.00 0.00 45.13 3.93
184 185 1.001293 TCGAGCTTCACTTCATGCAGT 59.999 47.619 0.00 0.00 0.00 4.40
187 188 0.368227 CGTCGAGCTTCACTTCATGC 59.632 55.000 0.00 0.00 0.00 4.06
188 189 1.982612 TCGTCGAGCTTCACTTCATG 58.017 50.000 0.00 0.00 0.00 3.07
189 190 2.094494 ACATCGTCGAGCTTCACTTCAT 60.094 45.455 0.00 0.00 0.00 2.57
195 196 0.454452 CGTCACATCGTCGAGCTTCA 60.454 55.000 0.00 0.00 0.00 3.02
197 198 1.154016 CCGTCACATCGTCGAGCTT 60.154 57.895 0.00 0.00 0.00 3.74
199 200 1.583967 CTCCGTCACATCGTCGAGC 60.584 63.158 0.00 0.00 0.00 5.03
218 219 3.490890 GCTGTCATGAAGGGCGAC 58.509 61.111 0.00 0.00 0.00 5.19
229 230 2.885113 CATCCGTCTCCGCTGTCA 59.115 61.111 0.00 0.00 0.00 3.58
263 264 0.449388 GCCGAGTCCTTGCATTCTTG 59.551 55.000 0.00 0.00 0.00 3.02
299 300 1.331214 CACACCCTTGTTTGCCTCAT 58.669 50.000 0.00 0.00 31.66 2.90
349 371 2.030490 CTTTTGCCCAACAGCCTGCA 62.030 55.000 0.00 0.00 0.00 4.41
359 381 2.837291 AGTTGCGCCTTTTGCCCA 60.837 55.556 4.18 0.00 36.24 5.36
370 392 0.453793 AGATCGGAGTCAGAGTTGCG 59.546 55.000 0.00 0.00 0.00 4.85
387 409 0.896940 AGGTGAAGCCGTCCGTTAGA 60.897 55.000 0.00 0.00 43.70 2.10
390 412 2.342648 GAGGTGAAGCCGTCCGTT 59.657 61.111 0.00 0.00 43.70 4.44
391 413 3.692406 GGAGGTGAAGCCGTCCGT 61.692 66.667 0.00 0.00 43.70 4.69
401 423 3.062466 CGTCGGAGCTGGAGGTGA 61.062 66.667 0.00 0.00 0.00 4.02
437 459 1.077285 TCCTCCATGTAGGCGTCGA 60.077 57.895 0.00 0.00 36.51 4.20
442 464 2.823758 GCCCCTCCTCCATGTAGGC 61.824 68.421 0.00 0.00 36.51 3.93
470 492 4.666253 TCCCCTTCCGGTCGTCGT 62.666 66.667 0.00 0.00 37.11 4.34
506 528 1.312815 GAAGGGCGGAGGAAATCATG 58.687 55.000 0.00 0.00 0.00 3.07
507 529 0.183731 GGAAGGGCGGAGGAAATCAT 59.816 55.000 0.00 0.00 0.00 2.45
518 540 0.107361 AAATAGAACGGGGAAGGGCG 60.107 55.000 0.00 0.00 0.00 6.13
572 594 4.019771 TGGACAGTGCAAATCCATACTACA 60.020 41.667 10.11 0.00 37.60 2.74
579 601 0.888736 CGGTGGACAGTGCAAATCCA 60.889 55.000 10.11 10.11 40.27 3.41
589 611 0.319900 CAGAGTTCACCGGTGGACAG 60.320 60.000 40.47 27.76 41.55 3.51
595 617 0.249911 GTTCAGCAGAGTTCACCGGT 60.250 55.000 0.00 0.00 0.00 5.28
598 620 2.675348 GCATAGTTCAGCAGAGTTCACC 59.325 50.000 0.00 0.00 0.00 4.02
599 621 3.594134 AGCATAGTTCAGCAGAGTTCAC 58.406 45.455 0.00 0.00 0.00 3.18
609 631 3.372206 CGGACAAAAGGAGCATAGTTCAG 59.628 47.826 0.00 0.00 0.00 3.02
641 663 1.333115 TCAACACGTAGTTCATCGCG 58.667 50.000 0.00 0.00 41.61 5.87
652 680 5.389098 GCTACGTAAAACATGATCAACACGT 60.389 40.000 17.53 17.53 43.11 4.49
672 700 3.749609 ACCTCAAAACCATACAACGCTAC 59.250 43.478 0.00 0.00 0.00 3.58
681 709 6.703319 TCGTATCTGAAACCTCAAAACCATA 58.297 36.000 0.00 0.00 0.00 2.74
718 755 3.786048 GTCGCCTCATATTTTTGCTTTCG 59.214 43.478 0.00 0.00 0.00 3.46
739 776 3.687321 ATCAGCATTGCTCGGGCGT 62.687 57.895 8.54 0.00 42.25 5.68
740 777 2.898840 ATCAGCATTGCTCGGGCG 60.899 61.111 8.54 0.00 42.25 6.13
741 778 2.719979 CATCAGCATTGCTCGGGC 59.280 61.111 8.54 0.00 36.40 6.13
810 847 6.646267 AGTCAAAAGTGTAGTGAGGTGTTAA 58.354 36.000 0.00 0.00 0.00 2.01
846 883 0.178975 ATCCTGGGTCTCTCGCTAGG 60.179 60.000 0.00 0.00 0.00 3.02
888 946 1.062587 GCGCGGATGCATGGATATAAC 59.937 52.381 2.46 0.00 42.97 1.89
890 948 0.805711 CGCGCGGATGCATGGATATA 60.806 55.000 24.84 0.00 42.97 0.86
891 949 2.102438 CGCGCGGATGCATGGATAT 61.102 57.895 24.84 0.00 42.97 1.63
935 997 0.390603 TAGTTGGGTTGGTCGATGCG 60.391 55.000 0.00 0.00 0.00 4.73
992 1058 2.782222 GGCCGTCGCATCCTCACTA 61.782 63.158 0.00 0.00 36.38 2.74
1026 1101 2.935481 TTCTGCAGGGTCAGGGGG 60.935 66.667 15.13 0.00 34.91 5.40
1077 1152 3.376935 CTTGGGAGTGGCGAGCGAT 62.377 63.158 0.00 0.00 0.00 4.58
1125 1200 1.138883 GTCGATGCTCAGCACGGTA 59.861 57.895 17.75 1.62 43.04 4.02
1217 1292 1.451028 GGGTGATGCAGGTCAGAGC 60.451 63.158 0.00 0.00 0.00 4.09
1247 1327 0.103208 GACGGTCCATCAGCAGTAGG 59.897 60.000 0.00 0.00 0.00 3.18
1519 1640 4.342772 CGTGCATACATCTTAGTTTTGCC 58.657 43.478 0.00 0.00 31.99 4.52
1523 1644 4.695455 AGTTGCGTGCATACATCTTAGTTT 59.305 37.500 0.00 0.00 0.00 2.66
1649 1834 6.037281 CGAAGCGCTCATTATCCTCTAGTATA 59.963 42.308 12.06 0.00 0.00 1.47
1747 1974 3.576982 AGCAGCATCCCCATCAAAATATG 59.423 43.478 0.00 0.00 0.00 1.78
1752 1979 0.685131 CCAGCAGCATCCCCATCAAA 60.685 55.000 0.00 0.00 0.00 2.69
1753 1980 1.076559 CCAGCAGCATCCCCATCAA 60.077 57.895 0.00 0.00 0.00 2.57
1840 2068 2.270923 GCACACGATCACAGCAAGATA 58.729 47.619 0.00 0.00 0.00 1.98
1860 2088 2.033194 GGCCGTCCCAAAAGTCTCG 61.033 63.158 0.00 0.00 0.00 4.04
1900 2132 1.073897 GCAAGTTGAGGTGGGAGCT 59.926 57.895 7.16 0.00 0.00 4.09
1907 2139 2.191128 CTAGGCAAGCAAGTTGAGGT 57.809 50.000 7.16 0.00 38.60 3.85
1935 2167 1.135139 GATAGCAGTGGAGCGACAGAA 59.865 52.381 0.00 0.00 40.15 3.02
1939 2171 0.661552 TACGATAGCAGTGGAGCGAC 59.338 55.000 0.00 0.00 40.15 5.19
2106 2371 8.786826 TCGTGAACATATTTTCCAAATCTACT 57.213 30.769 0.00 0.00 0.00 2.57
2348 3249 4.443725 CACACATAACCGTACGTGTTGTTA 59.556 41.667 23.61 19.22 40.49 2.41
2352 3253 2.406130 CCACACATAACCGTACGTGTT 58.594 47.619 20.58 20.58 40.49 3.32
2357 3258 0.745486 GGCCCCACACATAACCGTAC 60.745 60.000 0.00 0.00 0.00 3.67
2361 3262 2.052104 GCTGGCCCCACACATAACC 61.052 63.158 0.00 0.00 0.00 2.85
2368 3269 3.096495 GGGATAGCTGGCCCCACA 61.096 66.667 13.34 0.00 39.89 4.17
2389 3290 3.637273 GACTCAAGGGGCCGTGGT 61.637 66.667 0.00 0.00 0.00 4.16
2400 3301 3.319198 GAGCCCCCGGTGACTCAA 61.319 66.667 0.00 0.00 0.00 3.02
2403 3304 4.974438 TTGGAGCCCCCGGTGACT 62.974 66.667 0.00 0.00 37.93 3.41
2405 3306 2.938798 ATTTGGAGCCCCCGGTGA 60.939 61.111 0.00 0.00 37.93 4.02
2452 3357 8.262715 ACGATCTTTTGTTTTGGAACATTTTT 57.737 26.923 0.00 0.00 44.71 1.94
2472 3377 8.696175 CCCAAAATTTGTTTACAGTTAACGATC 58.304 33.333 4.92 0.00 0.00 3.69
2474 3379 7.769220 TCCCAAAATTTGTTTACAGTTAACGA 58.231 30.769 4.92 0.00 0.00 3.85
2735 4868 0.588252 ATCCGCGCATAAGATTGTGC 59.412 50.000 8.75 4.39 46.94 4.57
2741 4874 0.249447 CACTGGATCCGCGCATAAGA 60.249 55.000 8.75 0.00 0.00 2.10
2746 4879 4.451150 GGTCACTGGATCCGCGCA 62.451 66.667 8.75 0.00 0.00 6.09
2748 4881 4.530857 GGGGTCACTGGATCCGCG 62.531 72.222 7.39 0.00 46.01 6.46
2773 4906 0.326264 GAACATCCAGGTGCCTCACT 59.674 55.000 0.00 0.00 34.40 3.41
2774 4907 0.036732 TGAACATCCAGGTGCCTCAC 59.963 55.000 0.00 0.00 0.00 3.51
2775 4908 0.770499 TTGAACATCCAGGTGCCTCA 59.230 50.000 0.00 0.00 0.00 3.86
2807 4954 4.941263 TGCTACAAACATGGTTGATACCTC 59.059 41.667 29.74 11.97 45.27 3.85
2810 4957 6.092748 CCTTTGCTACAAACATGGTTGATAC 58.907 40.000 29.74 16.99 32.59 2.24
2899 5047 0.399091 TCCCCGAGCATCTCCTTGAT 60.399 55.000 0.00 0.00 35.40 2.57
2908 5056 2.994995 TCGTGTGTCCCCGAGCAT 60.995 61.111 0.00 0.00 0.00 3.79
2922 5070 0.522180 AAAGCGTCTGATCGACTCGT 59.478 50.000 13.30 4.10 40.59 4.18
3065 5217 8.534333 TTTAATGAGGTAATTAGCTATGCGAG 57.466 34.615 16.84 0.00 33.58 5.03
3066 5218 8.896320 TTTTAATGAGGTAATTAGCTATGCGA 57.104 30.769 16.84 1.96 33.58 5.10
3084 5236 6.096705 TCCTTCATGGCCTGTACATTTTAATG 59.903 38.462 3.32 1.03 37.84 1.90
3122 5274 3.703052 TGCAGACATCTGATAGAAGAGCA 59.297 43.478 13.15 0.00 46.59 4.26
3167 5319 0.772124 AATGGTGGCCGGGGAGATAT 60.772 55.000 2.18 0.00 0.00 1.63
3170 5322 2.543797 AAAATGGTGGCCGGGGAGA 61.544 57.895 2.18 0.00 0.00 3.71
3312 5465 3.512033 AGACGTAGCAAAGTCTCATCC 57.488 47.619 0.00 0.00 43.52 3.51
3480 5645 6.469410 ACGGAGAACAATACTTTGATACCAA 58.531 36.000 0.00 0.00 36.64 3.67
3502 5669 8.141268 ACCCATGCCATTTTAAAATATTAGACG 58.859 33.333 12.98 0.00 0.00 4.18
4024 6199 2.309528 TGCGCTCTTCCGATAACATT 57.690 45.000 9.73 0.00 0.00 2.71
4528 6729 2.322355 AATGAACAGAGCCGATCAGG 57.678 50.000 0.00 0.00 44.97 3.86
4533 6738 3.935203 GAGATTCAAATGAACAGAGCCGA 59.065 43.478 0.00 0.00 36.80 5.54
4765 6970 1.515954 CGCGGGACACCATCTAGTT 59.484 57.895 0.00 0.00 36.13 2.24
4937 7142 6.806668 TGGAGTGTAATGGTGATAGAATGA 57.193 37.500 0.00 0.00 0.00 2.57
4951 7156 6.488683 CCTTATTTGTTCCTGTTGGAGTGTAA 59.511 38.462 0.00 0.00 44.24 2.41
5049 7254 1.686052 TGAGTTTGCAATTGACCCACC 59.314 47.619 10.34 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.