Multiple sequence alignment - TraesCS3D01G256200

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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 TraesCS3D01G256200 chr3D 100.000 5340 0 0 1 5340 357805143 357799804 0.000000e+00 9862.0
1 TraesCS3D01G256200 chr3D 79.673 733 100 21 2203 2900 53782901 53782183 2.890000e-132 483.0
2 TraesCS3D01G256200 chr3B 93.313 4696 173 44 736 5340 459449020 459444375 0.000000e+00 6802.0
3 TraesCS3D01G256200 chr3B 86.043 609 54 15 1 591 459450288 459449693 4.540000e-175 625.0
4 TraesCS3D01G256200 chr3B 92.432 185 14 0 1674 1858 609331726 609331542 1.140000e-66 265.0
5 TraesCS3D01G256200 chr3B 91.979 187 15 0 1672 1858 736486164 736486350 4.100000e-66 263.0
6 TraesCS3D01G256200 chr3B 90.909 132 11 1 572 702 459449401 459449270 5.500000e-40 176.0
7 TraesCS3D01G256200 chr3B 84.211 76 10 2 104 178 84816779 84816853 7.420000e-09 73.1
8 TraesCS3D01G256200 chr3A 93.228 4356 188 44 929 5218 477336464 477332150 0.000000e+00 6311.0
9 TraesCS3D01G256200 chr3A 90.441 136 5 3 5213 5340 477332044 477331909 7.110000e-39 172.0
10 TraesCS3D01G256200 chr3A 86.207 116 10 2 761 874 651650794 651650683 2.610000e-23 121.0
11 TraesCS3D01G256200 chr3A 80.952 147 22 4 745 885 696284600 696284454 1.570000e-20 111.0
12 TraesCS3D01G256200 chr3A 82.243 107 13 6 524 625 477336585 477336480 2.650000e-13 87.9
13 TraesCS3D01G256200 chr4A 93.257 1750 73 17 3019 4742 137109813 137108083 0.000000e+00 2536.0
14 TraesCS3D01G256200 chr4A 85.558 547 63 4 1660 2205 595391835 595392366 4.670000e-155 558.0
15 TraesCS3D01G256200 chr4A 79.796 490 61 14 2250 2705 64815144 64815629 6.670000e-84 322.0
16 TraesCS3D01G256200 chr4A 79.513 493 55 19 2250 2705 595392374 595392857 5.190000e-80 309.0
17 TraesCS3D01G256200 chr4A 92.973 185 13 0 1674 1858 701701223 701701039 2.450000e-68 270.0
18 TraesCS3D01G256200 chr2B 87.525 505 47 4 1707 2210 773114487 773113998 2.160000e-158 569.0
19 TraesCS3D01G256200 chr2B 86.090 532 58 4 1678 2208 13325781 13325265 4.670000e-155 558.0
20 TraesCS3D01G256200 chr2B 80.328 488 57 15 2256 2708 13325254 13324771 3.080000e-87 333.0
21 TraesCS3D01G256200 chr2B 91.444 187 16 0 1672 1858 622904874 622905060 1.910000e-64 257.0
22 TraesCS3D01G256200 chr2B 91.005 189 17 0 1670 1858 690777696 690777884 6.860000e-64 255.0
23 TraesCS3D01G256200 chr2B 83.784 222 21 7 2256 2466 773113989 773113772 4.220000e-46 196.0
24 TraesCS3D01G256200 chr2B 81.481 135 23 1 742 874 144022778 144022644 5.650000e-20 110.0
25 TraesCS3D01G256200 chr2B 100.000 30 0 0 63 92 672648829 672648858 7.470000e-04 56.5
26 TraesCS3D01G256200 chr2D 78.954 841 128 28 2092 2897 595031700 595032526 1.320000e-145 527.0
27 TraesCS3D01G256200 chr2D 79.400 733 102 21 2203 2900 74144168 74143450 6.260000e-129 472.0
28 TraesCS3D01G256200 chr2D 79.808 208 36 5 672 874 383336265 383336059 4.310000e-31 147.0
29 TraesCS3D01G256200 chr7D 84.317 542 58 9 1670 2210 541413525 541413010 6.170000e-139 505.0
30 TraesCS3D01G256200 chr7D 79.564 734 100 22 2203 2900 221986483 221987202 3.740000e-131 479.0
31 TraesCS3D01G256200 chr7D 80.943 488 54 19 2256 2708 541413001 541412518 3.060000e-92 350.0
32 TraesCS3D01G256200 chr7D 86.667 120 12 2 749 864 623508622 623508503 4.340000e-26 130.0
33 TraesCS3D01G256200 chr7D 78.744 207 28 10 104 298 496152988 496153190 2.020000e-24 124.0
34 TraesCS3D01G256200 chr7D 96.970 33 1 0 76 108 28788267 28788235 7.470000e-04 56.5
35 TraesCS3D01G256200 chrUn 80.082 733 96 30 2203 2900 79580892 79580175 2.870000e-137 499.0
36 TraesCS3D01G256200 chr1D 79.536 733 101 21 2203 2900 319561239 319560521 1.350000e-130 477.0
37 TraesCS3D01G256200 chr1D 84.444 135 17 3 742 874 406648413 406648545 4.340000e-26 130.0
38 TraesCS3D01G256200 chr1D 82.927 82 12 2 104 184 85031779 85031699 7.420000e-09 73.1
39 TraesCS3D01G256200 chr2A 77.551 735 101 36 2203 2900 186412670 186413377 8.390000e-103 385.0
40 TraesCS3D01G256200 chr7A 79.918 488 59 22 2256 2708 657007565 657007082 6.670000e-84 322.0
41 TraesCS3D01G256200 chr5A 92.973 185 13 0 1674 1858 544223312 544223496 2.450000e-68 270.0
42 TraesCS3D01G256200 chr6B 91.979 187 15 0 1672 1858 463396215 463396401 4.100000e-66 263.0
43 TraesCS3D01G256200 chr1B 85.294 136 16 3 742 874 278456169 278456303 2.590000e-28 137.0
44 TraesCS3D01G256200 chr1B 82.927 82 12 2 104 184 316152108 316152028 7.420000e-09 73.1
45 TraesCS3D01G256200 chr1B 84.211 76 10 2 104 178 557640423 557640497 7.420000e-09 73.1
46 TraesCS3D01G256200 chr1A 83.803 142 19 2 735 874 586623689 586623828 1.210000e-26 132.0
47 TraesCS3D01G256200 chr1A 83.636 110 11 7 101 206 576884319 576884425 4.400000e-16 97.1
48 TraesCS3D01G256200 chr7B 75.546 229 37 8 113 324 392853186 392852960 1.580000e-15 95.3
49 TraesCS3D01G256200 chr6A 82.927 82 12 2 104 184 130168991 130168911 7.420000e-09 73.1
50 TraesCS3D01G256200 chr6D 90.566 53 3 2 104 155 52234687 52234636 9.600000e-08 69.4


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 TraesCS3D01G256200 chr3D 357799804 357805143 5339 True 9862.000000 9862 100.000000 1 5340 1 chr3D.!!$R2 5339
1 TraesCS3D01G256200 chr3D 53782183 53782901 718 True 483.000000 483 79.673000 2203 2900 1 chr3D.!!$R1 697
2 TraesCS3D01G256200 chr3B 459444375 459450288 5913 True 2534.333333 6802 90.088333 1 5340 3 chr3B.!!$R2 5339
3 TraesCS3D01G256200 chr3A 477331909 477336585 4676 True 2190.300000 6311 88.637333 524 5340 3 chr3A.!!$R3 4816
4 TraesCS3D01G256200 chr4A 137108083 137109813 1730 True 2536.000000 2536 93.257000 3019 4742 1 chr4A.!!$R1 1723
5 TraesCS3D01G256200 chr4A 595391835 595392857 1022 False 433.500000 558 82.535500 1660 2705 2 chr4A.!!$F2 1045
6 TraesCS3D01G256200 chr2B 13324771 13325781 1010 True 445.500000 558 83.209000 1678 2708 2 chr2B.!!$R2 1030
7 TraesCS3D01G256200 chr2B 773113772 773114487 715 True 382.500000 569 85.654500 1707 2466 2 chr2B.!!$R3 759
8 TraesCS3D01G256200 chr2D 595031700 595032526 826 False 527.000000 527 78.954000 2092 2897 1 chr2D.!!$F1 805
9 TraesCS3D01G256200 chr2D 74143450 74144168 718 True 472.000000 472 79.400000 2203 2900 1 chr2D.!!$R1 697
10 TraesCS3D01G256200 chr7D 221986483 221987202 719 False 479.000000 479 79.564000 2203 2900 1 chr7D.!!$F1 697
11 TraesCS3D01G256200 chr7D 541412518 541413525 1007 True 427.500000 505 82.630000 1670 2708 2 chr7D.!!$R3 1038
12 TraesCS3D01G256200 chrUn 79580175 79580892 717 True 499.000000 499 80.082000 2203 2900 1 chrUn.!!$R1 697
13 TraesCS3D01G256200 chr1D 319560521 319561239 718 True 477.000000 477 79.536000 2203 2900 1 chr1D.!!$R2 697
14 TraesCS3D01G256200 chr2A 186412670 186413377 707 False 385.000000 385 77.551000 2203 2900 1 chr2A.!!$F1 697

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
852 1401 0.249120 TGTGCGGGTGTTCATAGAGG 59.751 55.0 0.00 0.0 0.00 3.69 F
1079 1632 0.692756 CCTTCCTCTTCCTCCCCTCC 60.693 65.0 0.00 0.0 0.00 4.30 F
1273 1829 0.739462 CAATAACTCGAGCCACGGCA 60.739 55.0 13.61 0.0 44.88 5.69 F
2950 3591 0.109723 TCTTAGTGCCGCCCTTTTGT 59.890 50.0 0.00 0.0 0.00 2.83 F
2952 3593 0.671251 TTAGTGCCGCCCTTTTGTTG 59.329 50.0 0.00 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2470 1.079543 CTCTGGTTCCAGCACCTCG 60.080 63.158 13.44 0.0 37.75 4.63 R
2931 3572 0.109723 ACAAAAGGGCGGCACTAAGA 59.890 50.000 4.56 0.0 0.00 2.10 R
2966 3607 5.163416 GCCCAAAATGGTGCTTCTATTGTAT 60.163 40.000 0.00 0.0 35.17 2.29 R
4241 4889 1.319541 CAGACGATACCTCCCGACAT 58.680 55.000 0.00 0.0 0.00 3.06 R
4590 5252 3.895041 CCAGGTGAGCCTTTTTCCTTAAA 59.105 43.478 0.00 0.0 44.18 1.52 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
26 27 7.561722 ACTCATAGACTGACACCAATACTACAT 59.438 37.037 0.00 0.00 0.00 2.29
28 29 8.847196 TCATAGACTGACACCAATACTACATAC 58.153 37.037 0.00 0.00 0.00 2.39
37 38 8.688747 ACACCAATACTACATACTACTACCTC 57.311 38.462 0.00 0.00 0.00 3.85
87 91 9.968870 TCAAATTAAACTACAAAAACGCCTTAT 57.031 25.926 0.00 0.00 0.00 1.73
138 142 5.280654 TGGGTTTATTAGTCCCATCGTAC 57.719 43.478 0.00 0.00 45.19 3.67
303 310 7.012989 AGCATAACCCAAAATACGAGGAATTAC 59.987 37.037 0.00 0.00 0.00 1.89
320 327 6.614496 AGGAATTACTAAATAAGGACGGAGGT 59.386 38.462 0.00 0.00 0.00 3.85
325 332 4.648307 ACTAAATAAGGACGGAGGTGGTAG 59.352 45.833 0.00 0.00 0.00 3.18
326 333 2.842645 ATAAGGACGGAGGTGGTAGT 57.157 50.000 0.00 0.00 0.00 2.73
327 334 3.959495 ATAAGGACGGAGGTGGTAGTA 57.041 47.619 0.00 0.00 0.00 1.82
337 344 5.593502 ACGGAGGTGGTAGTATCTCTTTAAG 59.406 44.000 0.00 0.00 0.00 1.85
362 369 8.382405 AGGATTTTAACCAAACCATATTTGCTT 58.618 29.630 0.00 0.00 0.00 3.91
379 386 2.954989 TGCTTACACCACTGCAAAATCA 59.045 40.909 0.00 0.00 32.12 2.57
406 413 8.965986 AGAAAACTTTCTAACTTGTTTGACAC 57.034 30.769 2.83 0.00 45.17 3.67
407 414 8.573035 AGAAAACTTTCTAACTTGTTTGACACA 58.427 29.630 2.83 0.00 45.17 3.72
408 415 9.187455 GAAAACTTTCTAACTTGTTTGACACAA 57.813 29.630 0.00 0.00 37.34 3.33
409 416 8.515473 AAACTTTCTAACTTGTTTGACACAAC 57.485 30.769 0.00 0.00 40.71 3.32
410 417 6.617879 ACTTTCTAACTTGTTTGACACAACC 58.382 36.000 0.00 0.00 40.71 3.77
415 422 4.122143 ACTTGTTTGACACAACCAATGG 57.878 40.909 0.00 0.00 40.71 3.16
421 428 5.830457 TGTTTGACACAACCAATGGAGAATA 59.170 36.000 6.16 0.00 29.87 1.75
425 432 4.985538 ACACAACCAATGGAGAATACAGT 58.014 39.130 6.16 0.00 0.00 3.55
429 436 4.032960 ACCAATGGAGAATACAGTGCAA 57.967 40.909 6.16 0.00 33.01 4.08
435 442 8.849168 CCAATGGAGAATACAGTGCAAATAATA 58.151 33.333 0.00 0.00 33.01 0.98
642 973 6.208644 CAGATTTTTGACGAACCAATCTGTT 58.791 36.000 15.84 0.00 42.93 3.16
713 1239 5.624344 CACTGATGCTCTCATTTTTCTGT 57.376 39.130 0.00 0.00 32.10 3.41
740 1287 3.303881 TTCAGTCCTCTTCGTGATGTG 57.696 47.619 0.00 0.00 0.00 3.21
747 1294 1.374125 CTTCGTGATGTGCCCGTCA 60.374 57.895 0.00 0.00 34.20 4.35
752 1299 1.739035 CGTGATGTGCCCGTCAACTAT 60.739 52.381 0.00 0.00 38.31 2.12
757 1304 1.621317 TGTGCCCGTCAACTATGAAGA 59.379 47.619 0.00 0.00 37.24 2.87
773 1320 0.318784 AAGACGTCTGTGGCGACTTC 60.319 55.000 20.85 0.00 39.28 3.01
800 1347 2.487762 TCTCAAAATGATGTGCCGGTTC 59.512 45.455 1.90 0.00 0.00 3.62
808 1355 0.687354 ATGTGCCGGTTCAGTCTCTT 59.313 50.000 1.90 0.00 0.00 2.85
814 1363 1.404315 CCGGTTCAGTCTCTTAGGTGC 60.404 57.143 0.00 0.00 0.00 5.01
832 1381 3.326747 GTGCTTATAGGGGTAGAATGCG 58.673 50.000 0.00 0.00 0.00 4.73
836 1385 2.910688 ATAGGGGTAGAATGCGTGTG 57.089 50.000 0.00 0.00 0.00 3.82
850 1399 0.389296 CGTGTGCGGGTGTTCATAGA 60.389 55.000 0.00 0.00 0.00 1.98
852 1401 0.249120 TGTGCGGGTGTTCATAGAGG 59.751 55.000 0.00 0.00 0.00 3.69
865 1414 4.655762 TCATAGAGGTGAGTGTATGTGC 57.344 45.455 0.00 0.00 0.00 4.57
875 1424 4.917998 GTGAGTGTATGTGCCTATGTATCG 59.082 45.833 0.00 0.00 0.00 2.92
878 1427 4.827835 AGTGTATGTGCCTATGTATCGTCT 59.172 41.667 0.00 0.00 0.00 4.18
960 1509 6.674066 TGAGAAACAAACGATACATTTTCCC 58.326 36.000 0.00 0.00 0.00 3.97
964 1513 3.189702 ACAAACGATACATTTTCCCCACG 59.810 43.478 0.00 0.00 0.00 4.94
1079 1632 0.692756 CCTTCCTCTTCCTCCCCTCC 60.693 65.000 0.00 0.00 0.00 4.30
1093 1646 1.541672 CCTCCCTCCTCTCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1273 1829 0.739462 CAATAACTCGAGCCACGGCA 60.739 55.000 13.61 0.00 44.88 5.69
1353 1909 1.950244 CATCTACCCCTCCTCCCCT 59.050 63.158 0.00 0.00 0.00 4.79
1894 2470 2.668550 GTGGTGTCCGAAGCACCC 60.669 66.667 16.43 7.65 35.06 4.61
1993 2569 1.218316 GACGAAGGCCGATGAGGTT 59.782 57.895 0.00 0.00 43.70 3.50
2014 2590 2.125106 GTCAGGGATGCGGACACC 60.125 66.667 3.33 0.00 0.00 4.16
2119 2695 1.601166 ACGTTTCTGCCTGTTTACCC 58.399 50.000 0.00 0.00 0.00 3.69
2127 2703 1.992557 TGCCTGTTTACCCTCCATTCT 59.007 47.619 0.00 0.00 0.00 2.40
2164 2741 4.651778 TGTGATTTCTCTTAGGTGGGTTG 58.348 43.478 0.00 0.00 0.00 3.77
2359 2940 5.047802 AGAGTGCCATTCGATCAATTGTTTT 60.048 36.000 5.13 0.00 0.00 2.43
2362 2943 4.685165 TGCCATTCGATCAATTGTTTTGTG 59.315 37.500 5.13 0.00 0.00 3.33
2445 3041 4.655963 TGCAGATTTCTATTCCCTATGCC 58.344 43.478 0.00 0.00 0.00 4.40
2494 3091 2.307496 ACAATTGGATGCAACTGGGA 57.693 45.000 13.04 0.00 0.00 4.37
2629 3252 6.012337 TCTTGATAAATTGGTATGCTCCCA 57.988 37.500 0.00 0.00 0.00 4.37
2640 3263 4.067896 GGTATGCTCCCAGTATTGACATG 58.932 47.826 0.00 0.00 0.00 3.21
2711 3349 6.764308 ATGTAGCAGCACTTGTGATTAAAT 57.236 33.333 4.79 0.00 0.00 1.40
2729 3367 8.407832 TGATTAAATGTATTCACAATGGCTGAG 58.592 33.333 0.00 0.00 38.42 3.35
2804 3442 9.689501 ATTTTAAGGGGTTACGAGAAAATGATA 57.310 29.630 0.00 0.00 0.00 2.15
2809 3447 4.272748 GGGTTACGAGAAAATGATACCAGC 59.727 45.833 0.00 0.00 0.00 4.85
2828 3466 4.033243 CCAGCAAGAAAACTTTGAACAAGC 59.967 41.667 0.00 0.00 0.00 4.01
2931 3572 9.399797 TCTGTATCATGCAAGTATTTCTTCAAT 57.600 29.630 0.00 0.00 33.63 2.57
2940 3581 6.969473 GCAAGTATTTCTTCAATCTTAGTGCC 59.031 38.462 0.00 0.00 33.63 5.01
2950 3591 0.109723 TCTTAGTGCCGCCCTTTTGT 59.890 50.000 0.00 0.00 0.00 2.83
2952 3593 0.671251 TTAGTGCCGCCCTTTTGTTG 59.329 50.000 0.00 0.00 0.00 3.33
2966 3607 5.710099 CCCTTTTGTTGCCAAGAGTTATCTA 59.290 40.000 0.00 0.00 33.45 1.98
3006 3647 5.596836 TTTGGGCATATTAAGCTTTCCAG 57.403 39.130 3.20 0.00 0.00 3.86
3109 3750 7.636150 AATCAAATGCTTAGCACTGAGTTAT 57.364 32.000 20.53 6.57 43.04 1.89
3198 3840 1.493022 TGCATTTATAAGAGGCCGGGT 59.507 47.619 2.18 0.00 0.00 5.28
3217 3859 4.728772 GGGTCCCATGTCAAATCATATGA 58.271 43.478 8.10 8.10 0.00 2.15
3235 3883 8.956446 TCATATGATGTTCCTTATGTCCTAGA 57.044 34.615 0.00 0.00 0.00 2.43
3236 3884 8.807118 TCATATGATGTTCCTTATGTCCTAGAC 58.193 37.037 0.00 0.00 0.00 2.59
3237 3885 5.871396 TGATGTTCCTTATGTCCTAGACC 57.129 43.478 0.00 0.00 0.00 3.85
3238 3886 5.529289 TGATGTTCCTTATGTCCTAGACCT 58.471 41.667 0.00 0.00 0.00 3.85
3239 3887 6.679542 TGATGTTCCTTATGTCCTAGACCTA 58.320 40.000 0.00 0.00 0.00 3.08
3393 4041 8.404889 TGCAATATACATGTACACAAAATTGC 57.595 30.769 23.98 23.98 44.19 3.56
3434 4082 6.877668 TTAGTGGGGAATAGTCATGTTGTA 57.122 37.500 0.00 0.00 0.00 2.41
3489 4137 6.091441 TGTTTTGTTTTATGTGTGTTTGCCTC 59.909 34.615 0.00 0.00 0.00 4.70
3712 4360 6.236409 TGAGAATTCATCTGCAATCTATCCC 58.764 40.000 8.44 0.00 38.96 3.85
3832 4480 9.543783 GTAAAAGATTATAGTGATCCTTCGGTT 57.456 33.333 0.00 0.00 0.00 4.44
3865 4513 7.483059 GCTTGTTCTTCATTCATGCTAAGTTAC 59.517 37.037 0.00 0.00 32.24 2.50
3878 4526 6.978343 TGCTAAGTTACATTTCGTTAGCAT 57.022 33.333 10.27 0.00 46.58 3.79
3883 4531 6.422776 AGTTACATTTCGTTAGCATCCTTG 57.577 37.500 0.00 0.00 0.00 3.61
3891 4539 6.422776 TTCGTTAGCATCCTTGAAGAAATC 57.577 37.500 0.00 0.00 0.00 2.17
4030 4678 6.152323 CACAGATGATGGAGTTGAAGGATTTT 59.848 38.462 0.00 0.00 0.00 1.82
4389 5037 4.524714 AGATCCTGATATGGGTTACACTCG 59.475 45.833 0.00 0.00 0.00 4.18
4584 5246 1.542915 TGAGCTCCATTGCTTGCTTTC 59.457 47.619 12.15 0.00 44.17 2.62
4588 5250 1.619827 CTCCATTGCTTGCTTTCCCAA 59.380 47.619 0.00 0.00 0.00 4.12
4589 5251 1.344114 TCCATTGCTTGCTTTCCCAAC 59.656 47.619 0.00 0.00 0.00 3.77
4590 5252 1.345415 CCATTGCTTGCTTTCCCAACT 59.655 47.619 0.00 0.00 0.00 3.16
4975 5653 1.519455 CTGTCGGCCGTCCAATCTC 60.519 63.158 27.15 7.15 0.00 2.75
4976 5654 2.225791 CTGTCGGCCGTCCAATCTCA 62.226 60.000 27.15 11.07 0.00 3.27
4980 5658 2.189499 GGCCGTCCAATCTCATGGC 61.189 63.158 0.00 0.00 43.13 4.40
5135 5814 2.313317 CTACCTGGACGCCATTACCTA 58.687 52.381 0.00 0.00 30.82 3.08
5180 5872 4.125703 CCAGGAAAGATTCTTCAGATCCG 58.874 47.826 0.00 0.93 0.00 4.18
5215 5907 6.656314 CGATAGTCTGTAGATAGCTGGTAG 57.344 45.833 0.00 0.00 0.00 3.18
5218 5910 7.818446 CGATAGTCTGTAGATAGCTGGTAGTAA 59.182 40.741 0.00 0.00 0.00 2.24
5219 5911 9.504708 GATAGTCTGTAGATAGCTGGTAGTAAA 57.495 37.037 0.00 0.00 0.00 2.01
5262 6073 1.016627 TAATGATCTTGCCAGTGCGC 58.983 50.000 0.00 0.00 41.78 6.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.688747 AGGTAGTAGTATGTAGTATTGGTGTC 57.311 38.462 0.00 0.00 0.00 3.67
12 13 8.501070 AGAGGTAGTAGTATGTAGTATTGGTGT 58.499 37.037 0.00 0.00 0.00 4.16
13 14 8.784994 CAGAGGTAGTAGTATGTAGTATTGGTG 58.215 40.741 0.00 0.00 0.00 4.17
59 61 8.705048 AGGCGTTTTTGTAGTTTAATTTGAAA 57.295 26.923 0.00 0.00 0.00 2.69
110 114 4.476628 GGGACTAATAAACCCAGACGAA 57.523 45.455 0.00 0.00 42.81 3.85
260 266 7.986889 GGGTTATGCTTTGATCATGGTTTTAAT 59.013 33.333 0.00 0.00 0.00 1.40
279 285 8.446599 AGTAATTCCTCGTATTTTGGGTTATG 57.553 34.615 0.00 0.00 0.00 1.90
303 310 4.648307 ACTACCACCTCCGTCCTTATTTAG 59.352 45.833 0.00 0.00 0.00 1.85
309 316 2.244252 AGATACTACCACCTCCGTCCTT 59.756 50.000 0.00 0.00 0.00 3.36
327 334 9.374711 TGGTTTGGTTAAAATCCTTAAAGAGAT 57.625 29.630 0.00 0.00 0.00 2.75
337 344 8.560355 AAGCAAATATGGTTTGGTTAAAATCC 57.440 30.769 16.34 0.00 44.52 3.01
362 369 7.230510 AGTTTTCTATGATTTTGCAGTGGTGTA 59.769 33.333 0.00 0.00 0.00 2.90
398 405 4.647424 TTCTCCATTGGTTGTGTCAAAC 57.353 40.909 1.86 0.00 0.00 2.93
401 408 4.979335 TGTATTCTCCATTGGTTGTGTCA 58.021 39.130 1.86 0.00 0.00 3.58
402 409 5.003804 ACTGTATTCTCCATTGGTTGTGTC 58.996 41.667 1.86 0.00 0.00 3.67
403 410 4.761739 CACTGTATTCTCCATTGGTTGTGT 59.238 41.667 1.86 0.00 0.00 3.72
404 411 4.379813 GCACTGTATTCTCCATTGGTTGTG 60.380 45.833 1.86 3.48 0.00 3.33
405 412 3.758554 GCACTGTATTCTCCATTGGTTGT 59.241 43.478 1.86 0.00 0.00 3.32
406 413 3.758023 TGCACTGTATTCTCCATTGGTTG 59.242 43.478 1.86 0.00 0.00 3.77
407 414 4.032960 TGCACTGTATTCTCCATTGGTT 57.967 40.909 1.86 0.00 0.00 3.67
408 415 3.719268 TGCACTGTATTCTCCATTGGT 57.281 42.857 1.86 0.00 0.00 3.67
409 416 5.587388 ATTTGCACTGTATTCTCCATTGG 57.413 39.130 0.00 0.00 0.00 3.16
410 417 9.669353 GTATTATTTGCACTGTATTCTCCATTG 57.331 33.333 0.00 0.00 0.00 2.82
572 589 7.872113 ATTGTCATGTTAGAAAGAGGATTCC 57.128 36.000 0.00 0.00 0.00 3.01
640 971 3.048337 TCGTCCTAACCATCCAACAAC 57.952 47.619 0.00 0.00 0.00 3.32
642 973 4.028131 ACTATCGTCCTAACCATCCAACA 58.972 43.478 0.00 0.00 0.00 3.33
647 978 3.383825 ACACCACTATCGTCCTAACCATC 59.616 47.826 0.00 0.00 0.00 3.51
650 981 4.340381 ACATACACCACTATCGTCCTAACC 59.660 45.833 0.00 0.00 0.00 2.85
653 984 5.195185 TGAACATACACCACTATCGTCCTA 58.805 41.667 0.00 0.00 0.00 2.94
713 1239 8.258007 ACATCACGAAGAGGACTGAAATAAATA 58.742 33.333 0.00 0.00 0.00 1.40
725 1251 1.596934 GGGCACATCACGAAGAGGA 59.403 57.895 0.00 0.00 0.00 3.71
731 1257 1.666553 GTTGACGGGCACATCACGA 60.667 57.895 0.00 0.00 0.00 4.35
740 1287 1.278238 CGTCTTCATAGTTGACGGGC 58.722 55.000 6.83 0.00 46.45 6.13
747 1294 2.671351 CGCCACAGACGTCTTCATAGTT 60.671 50.000 17.26 0.00 0.00 2.24
752 1299 1.007734 GTCGCCACAGACGTCTTCA 60.008 57.895 17.26 0.00 0.00 3.02
757 1304 2.050351 CGAAGTCGCCACAGACGT 60.050 61.111 0.00 0.00 45.26 4.34
773 1320 4.100529 GGCACATCATTTTGAGATTGACG 58.899 43.478 0.00 0.00 0.00 4.35
800 1347 4.282195 CCCCTATAAGCACCTAAGAGACTG 59.718 50.000 0.00 0.00 0.00 3.51
808 1355 4.530946 GCATTCTACCCCTATAAGCACCTA 59.469 45.833 0.00 0.00 0.00 3.08
814 1363 4.307432 CACACGCATTCTACCCCTATAAG 58.693 47.826 0.00 0.00 0.00 1.73
832 1381 1.359848 CTCTATGAACACCCGCACAC 58.640 55.000 0.00 0.00 0.00 3.82
836 1385 0.535335 TCACCTCTATGAACACCCGC 59.465 55.000 0.00 0.00 0.00 6.13
839 1388 3.963428 ACACTCACCTCTATGAACACC 57.037 47.619 0.00 0.00 0.00 4.16
850 1399 3.107601 ACATAGGCACATACACTCACCT 58.892 45.455 0.00 0.00 0.00 4.00
852 1401 4.917998 CGATACATAGGCACATACACTCAC 59.082 45.833 0.00 0.00 0.00 3.51
865 1414 2.290916 ACAGACGCAGACGATACATAGG 59.709 50.000 0.00 0.00 43.93 2.57
908 1457 8.768955 GTTACATGTGCAAAATATTTTTGTCCA 58.231 29.630 15.16 9.09 0.00 4.02
909 1458 8.987890 AGTTACATGTGCAAAATATTTTTGTCC 58.012 29.630 15.16 9.65 0.00 4.02
1079 1632 1.541672 GAGGGGAGGAGAGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1093 1646 4.547367 GGCGATGGAACGGGAGGG 62.547 72.222 0.00 0.00 0.00 4.30
1485 2057 3.615509 TAAAGCGGGCGGTGGGAAG 62.616 63.158 0.00 0.00 0.00 3.46
1873 2449 1.374125 TGCTTCGGACACCACGATG 60.374 57.895 0.00 0.00 40.38 3.84
1894 2470 1.079543 CTCTGGTTCCAGCACCTCG 60.080 63.158 13.44 0.00 37.75 4.63
1993 2569 2.606213 TCCGCATCCCTGACCACA 60.606 61.111 0.00 0.00 0.00 4.17
2119 2695 6.320672 ACAGCTTCAAAATATGGAGAATGGAG 59.679 38.462 0.00 0.00 36.68 3.86
2127 2703 7.613022 AGAGAAATCACAGCTTCAAAATATGGA 59.387 33.333 0.00 0.00 0.00 3.41
2164 2741 1.599419 CGTACCACCTGCAACAAAAGC 60.599 52.381 0.00 0.00 0.00 3.51
2359 2940 4.804665 CACAATTTGCACAGAATTCACACA 59.195 37.500 8.44 0.00 0.00 3.72
2362 2943 5.174398 CACTCACAATTTGCACAGAATTCAC 59.826 40.000 8.44 0.00 0.00 3.18
2711 3349 3.008923 TGGTCTCAGCCATTGTGAATACA 59.991 43.478 0.00 0.00 32.81 2.29
2729 3367 2.928334 ACCATGCTCTCAATGATGGTC 58.072 47.619 0.00 0.00 44.30 4.02
2804 3442 4.799564 TGTTCAAAGTTTTCTTGCTGGT 57.200 36.364 0.00 0.00 40.37 4.00
2809 3447 6.095377 AGACAGCTTGTTCAAAGTTTTCTTG 58.905 36.000 0.00 0.00 40.37 3.02
2916 3557 7.182761 CGGCACTAAGATTGAAGAAATACTTG 58.817 38.462 0.00 0.00 39.13 3.16
2931 3572 0.109723 ACAAAAGGGCGGCACTAAGA 59.890 50.000 4.56 0.00 0.00 2.10
2952 3593 9.145865 GCTTCTATTGTATAGATAACTCTTGGC 57.854 37.037 0.00 0.00 32.66 4.52
2966 3607 5.163416 GCCCAAAATGGTGCTTCTATTGTAT 60.163 40.000 0.00 0.00 35.17 2.29
3006 3647 6.204301 GCATGATATGATGCCTCCATACATAC 59.796 42.308 15.48 0.00 42.57 2.39
3109 3750 6.037062 CACATGGCTCGTTGATATCTTACAAA 59.963 38.462 3.98 0.00 0.00 2.83
3198 3840 6.491062 GGAACATCATATGATTTGACATGGGA 59.509 38.462 15.74 0.00 31.21 4.37
3217 3859 6.684538 ACTAGGTCTAGGACATAAGGAACAT 58.315 40.000 9.51 0.00 37.49 2.71
3234 3882 7.272978 TCTGCCAAATAAATGACTACTAGGTC 58.727 38.462 0.00 0.00 36.81 3.85
3235 3883 7.125811 TCTCTGCCAAATAAATGACTACTAGGT 59.874 37.037 0.00 0.00 0.00 3.08
3236 3884 7.500992 TCTCTGCCAAATAAATGACTACTAGG 58.499 38.462 0.00 0.00 0.00 3.02
3237 3885 8.948631 TTCTCTGCCAAATAAATGACTACTAG 57.051 34.615 0.00 0.00 0.00 2.57
3407 4055 9.166222 ACAACATGACTATTCCCCACTAATATA 57.834 33.333 0.00 0.00 0.00 0.86
3489 4137 8.856153 TCCTAGTACTTCTCATATAAGCTCAG 57.144 38.462 0.00 0.00 0.00 3.35
3535 4183 4.830573 GCAGGGAGCAGGTTCTTT 57.169 55.556 0.00 0.00 44.79 2.52
3832 4480 5.833406 TGAATGAAGAACAAGCACAAGAA 57.167 34.783 0.00 0.00 0.00 2.52
3865 4513 5.801350 TCTTCAAGGATGCTAACGAAATG 57.199 39.130 0.00 0.00 0.00 2.32
3878 4526 4.469469 AACAAGGGGATTTCTTCAAGGA 57.531 40.909 0.00 0.00 0.00 3.36
3883 4531 4.949856 TGAGCATAACAAGGGGATTTCTTC 59.050 41.667 0.00 0.00 0.00 2.87
3891 4539 2.238646 TGTACCTGAGCATAACAAGGGG 59.761 50.000 0.00 0.00 0.00 4.79
4241 4889 1.319541 CAGACGATACCTCCCGACAT 58.680 55.000 0.00 0.00 0.00 3.06
4389 5037 6.998968 ATCTGATGGAAGATGAACAGAAAC 57.001 37.500 0.00 0.00 37.79 2.78
4584 5246 4.343814 TGAGCCTTTTTCCTTAAAGTTGGG 59.656 41.667 0.00 0.00 34.11 4.12
4588 5250 4.584743 CAGGTGAGCCTTTTTCCTTAAAGT 59.415 41.667 0.00 0.00 44.18 2.66
4589 5251 4.021981 CCAGGTGAGCCTTTTTCCTTAAAG 60.022 45.833 0.00 0.00 44.18 1.85
4590 5252 3.895041 CCAGGTGAGCCTTTTTCCTTAAA 59.105 43.478 0.00 0.00 44.18 1.52
5000 5678 0.251564 TTGGCCGTCATTTGACCCAT 60.252 50.000 0.00 0.00 41.86 4.00
5100 5779 5.601313 GTCCAGGTAGTTGATAGGTTGGATA 59.399 44.000 0.00 0.00 36.05 2.59
5105 5784 2.167900 GCGTCCAGGTAGTTGATAGGTT 59.832 50.000 0.00 0.00 0.00 3.50
5142 5821 3.267916 TGGTGTCCAGGTAGGGTTT 57.732 52.632 0.00 0.00 38.24 3.27
5180 5872 2.599082 CAGACTATCGTTTTCTGCGGTC 59.401 50.000 0.00 0.00 30.90 4.79
5262 6073 6.801539 TTTTGTCAACTAGCTCATTACTGG 57.198 37.500 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.