Multiple sequence alignment - TraesCS6D01G066200

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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 TraesCS6D01G066200 chr6D 100.000 3651 0 0 1 3651 32457798 32461448 0.000000e+00 6743
1 TraesCS6D01G066200 chr6D 80.392 459 58 16 1013 1469 62244501 62244073 1.640000e-83 320
2 TraesCS6D01G066200 chr6A 90.498 1526 81 30 394 1868 36946919 36948431 0.000000e+00 1956
3 TraesCS6D01G066200 chr6A 88.103 933 47 28 1894 2788 36948561 36949467 0.000000e+00 1050
4 TraesCS6D01G066200 chr6A 88.991 763 62 10 2904 3651 36949587 36950342 0.000000e+00 924
5 TraesCS6D01G066200 chr6A 87.097 620 53 16 2 602 36941570 36942181 0.000000e+00 676
6 TraesCS6D01G066200 chr6A 85.920 625 52 25 2 602 36943916 36944528 5.140000e-178 634
7 TraesCS6D01G066200 chr6A 87.421 318 25 5 2 305 36946266 36946582 5.800000e-93 351
8 TraesCS6D01G066200 chr6A 82.176 432 40 10 1152 1573 479105266 479104862 1.620000e-88 337
9 TraesCS6D01G066200 chr6A 84.790 309 29 14 1346 1639 479397770 479398075 9.910000e-76 294
10 TraesCS6D01G066200 chr6A 80.206 389 56 8 1046 1434 577295055 577294688 4.650000e-69 272
11 TraesCS6D01G066200 chr6A 83.630 281 31 6 1196 1476 55365574 55365309 2.180000e-62 250
12 TraesCS6D01G066200 chr6A 75.665 526 95 21 914 1435 577497193 577496697 7.880000e-57 231
13 TraesCS6D01G066200 chr6B 91.200 1000 33 11 916 1868 68292183 68293174 0.000000e+00 1308
14 TraesCS6D01G066200 chr6B 91.531 921 46 19 1895 2795 68293288 68294196 0.000000e+00 1240
15 TraesCS6D01G066200 chr6B 85.077 650 49 16 3016 3643 68294286 68294909 1.440000e-173 619
16 TraesCS6D01G066200 chr6B 79.085 459 55 20 1013 1469 663174051 663173632 9.980000e-71 278
17 TraesCS6D01G066200 chr4B 81.888 519 54 21 917 1428 580959806 580960291 5.680000e-108 401
18 TraesCS6D01G066200 chr7D 82.675 456 40 16 1129 1573 514661909 514661482 5.760000e-98 368
19 TraesCS6D01G066200 chr7D 80.402 199 28 10 3451 3644 617833807 617833999 1.370000e-29 141
20 TraesCS6D01G066200 chr7D 78.218 202 35 7 3453 3651 72176932 72177127 1.780000e-23 121
21 TraesCS6D01G066200 chr1B 82.517 429 38 12 1152 1570 531115926 531116327 3.490000e-90 342
22 TraesCS6D01G066200 chr1B 81.347 193 25 9 3453 3642 365446869 365447053 2.940000e-31 147
23 TraesCS6D01G066200 chr1A 82.517 429 38 10 1152 1570 14356714 14357115 3.490000e-90 342
24 TraesCS6D01G066200 chr2D 79.264 516 62 24 917 1428 245324710 245325184 5.880000e-83 318
25 TraesCS6D01G066200 chr2D 78.613 519 76 24 917 1428 231720905 231721395 9.840000e-81 311
26 TraesCS6D01G066200 chr2D 79.275 193 31 4 3452 3644 628591545 628591362 3.830000e-25 126
27 TraesCS6D01G066200 chr5A 82.493 377 48 7 1093 1469 155216929 155216571 7.610000e-82 315
28 TraesCS6D01G066200 chr3B 82.162 370 42 9 1100 1469 511396807 511396462 2.760000e-76 296
29 TraesCS6D01G066200 chr2A 78.913 460 53 22 1013 1469 735656404 735655986 4.650000e-69 272
30 TraesCS6D01G066200 chr2A 75.444 338 38 18 914 1242 191905876 191906177 4.950000e-24 122
31 TraesCS6D01G066200 chr5B 86.243 189 19 4 1684 1869 166694401 166694217 8.000000e-47 198
32 TraesCS6D01G066200 chr5D 81.463 205 22 10 3452 3651 511950710 511950517 1.760000e-33 154
33 TraesCS6D01G066200 chr5D 78.325 203 33 10 3453 3651 278283938 278283743 1.780000e-23 121
34 TraesCS6D01G066200 chr1D 77.340 203 38 5 3453 3651 270617832 270618030 2.980000e-21 113


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 TraesCS6D01G066200 chr6D 32457798 32461448 3650 False 6743.000000 6743 100.000000 1 3651 1 chr6D.!!$F1 3650
1 TraesCS6D01G066200 chr6A 36941570 36950342 8772 False 931.833333 1956 88.005000 2 3651 6 chr6A.!!$F2 3649
2 TraesCS6D01G066200 chr6B 68292183 68294909 2726 False 1055.666667 1308 89.269333 916 3643 3 chr6B.!!$F1 2727

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
197 209 0.038159 AGCAGAGCTTGTACACGTCC 60.038 55.0 0.00 0.0 33.89 4.79 F
325 339 0.105349 TACATTACCCCCTCCCCGAG 60.105 60.0 0.00 0.0 0.00 4.63 F
574 5533 0.179065 CGGAGCTCCATCATGCAAGA 60.179 55.0 31.67 0.0 35.14 3.02 F
1453 6463 1.132588 CGCCTCGATTCCGATTTCTC 58.867 55.0 0.00 0.0 44.62 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 7248 0.037447 GCTTCCATCTATGCCCCTCC 59.963 60.000 0.00 0.00 0.00 4.30 R
2117 7257 1.144716 CTGCGGCAGCTTCCATCTA 59.855 57.895 18.16 0.00 45.42 1.98 R
2430 7578 0.320771 CTACCAGCACGCCTCAAACT 60.321 55.000 0.00 0.00 0.00 2.66 R
2989 8257 0.179089 AAAAATTGCCGCTGTGCACA 60.179 45.000 20.37 20.37 41.88 4.57 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
53 54 2.476619 CGAATTGCTTATAGCTCCACCG 59.523 50.000 0.00 0.00 42.97 4.94
55 56 3.560636 ATTGCTTATAGCTCCACCGTT 57.439 42.857 0.00 0.00 42.97 4.44
78 90 1.465689 CGTCAAAAGGGCATGTTAGCG 60.466 52.381 0.00 0.00 34.64 4.26
80 92 0.887933 CAAAAGGGCATGTTAGCGGT 59.112 50.000 0.00 0.00 34.64 5.68
83 95 0.392998 AAGGGCATGTTAGCGGTCAG 60.393 55.000 0.00 0.00 34.64 3.51
92 104 1.751924 GTTAGCGGTCAGATGAGGAGT 59.248 52.381 0.00 0.00 0.00 3.85
154 166 0.690192 TTTCTCGGATGACCCAAGCA 59.310 50.000 0.00 0.00 34.14 3.91
156 168 0.614697 TCTCGGATGACCCAAGCAGA 60.615 55.000 0.00 0.00 34.14 4.26
185 197 3.123620 CCACCGAAGCAGCAGAGC 61.124 66.667 0.00 0.00 0.00 4.09
195 207 0.946221 GCAGCAGAGCTTGTACACGT 60.946 55.000 0.00 0.00 36.40 4.49
197 209 0.038159 AGCAGAGCTTGTACACGTCC 60.038 55.000 0.00 0.00 33.89 4.79
199 211 0.732880 CAGAGCTTGTACACGTCCGG 60.733 60.000 0.00 0.00 0.00 5.14
210 222 3.656045 CGTCCGGCACAACCCAAC 61.656 66.667 0.00 0.00 33.26 3.77
297 310 3.971971 GGTTAGTATGGAAGGCTAGGGAA 59.028 47.826 0.00 0.00 0.00 3.97
305 318 1.212195 GAAGGCTAGGGAATTTCCGGT 59.788 52.381 9.31 2.11 37.43 5.28
311 324 4.204799 GCTAGGGAATTTCCGGTTACATT 58.795 43.478 9.31 0.00 37.43 2.71
312 325 5.370679 GCTAGGGAATTTCCGGTTACATTA 58.629 41.667 9.31 0.00 37.43 1.90
318 331 1.969713 TTCCGGTTACATTACCCCCT 58.030 50.000 0.00 0.00 34.56 4.79
325 339 0.105349 TACATTACCCCCTCCCCGAG 60.105 60.000 0.00 0.00 0.00 4.63
327 341 1.384082 ATTACCCCCTCCCCGAGTG 60.384 63.158 0.00 0.00 0.00 3.51
359 373 9.199645 AGAGGATATATGTCAACCATCTATCAG 57.800 37.037 1.63 0.00 39.58 2.90
416 5374 9.988350 CAAAATTGCTAACATTAGATTCGTACT 57.012 29.630 2.75 0.00 32.47 2.73
468 5426 9.265938 TGTAATCGTCGACTAAATATTATACGC 57.734 33.333 14.70 0.34 0.00 4.42
534 5493 4.325028 AGCATGCATTTTGTGAGTCAAA 57.675 36.364 21.98 0.00 43.24 2.69
541 5500 2.435372 TTTGTGAGTCAAACTGCCCT 57.565 45.000 0.00 0.00 40.56 5.19
545 5504 2.147150 GTGAGTCAAACTGCCCTCTTC 58.853 52.381 0.00 0.00 0.00 2.87
547 5506 2.439507 TGAGTCAAACTGCCCTCTTCTT 59.560 45.455 0.00 0.00 0.00 2.52
553 5512 5.180304 GTCAAACTGCCCTCTTCTTTTAGAG 59.820 44.000 0.00 0.00 41.10 2.43
554 5513 3.342377 ACTGCCCTCTTCTTTTAGAGC 57.658 47.619 0.00 0.00 40.28 4.09
558 5517 1.831736 CCCTCTTCTTTTAGAGCCGGA 59.168 52.381 5.05 0.00 40.28 5.14
560 5519 2.545731 CTCTTCTTTTAGAGCCGGAGC 58.454 52.381 5.05 0.00 35.64 4.70
572 5531 1.153107 CCGGAGCTCCATCATGCAA 60.153 57.895 31.67 0.00 35.14 4.08
573 5532 1.164662 CCGGAGCTCCATCATGCAAG 61.165 60.000 31.67 12.17 35.14 4.01
574 5533 0.179065 CGGAGCTCCATCATGCAAGA 60.179 55.000 31.67 0.00 35.14 3.02
576 5535 2.584236 GGAGCTCCATCATGCAAGAAT 58.416 47.619 28.43 0.00 35.64 2.40
587 5555 9.722184 TCCATCATGCAAGAATGAAAAATAAAA 57.278 25.926 0.00 0.00 39.90 1.52
622 5590 2.233271 CCTTGAAATGTGCACAGGAGT 58.767 47.619 25.84 9.79 0.00 3.85
664 5639 5.359716 GTGAGACACGTAGAAGAAGAAGA 57.640 43.478 0.00 0.00 0.00 2.87
665 5640 5.387279 GTGAGACACGTAGAAGAAGAAGAG 58.613 45.833 0.00 0.00 0.00 2.85
672 5647 4.019141 ACGTAGAAGAAGAAGAGGAGGAGA 60.019 45.833 0.00 0.00 0.00 3.71
674 5649 5.416326 CGTAGAAGAAGAAGAGGAGGAGAAA 59.584 44.000 0.00 0.00 0.00 2.52
832 5809 3.716195 CACCTGTCATCCGCCCCA 61.716 66.667 0.00 0.00 0.00 4.96
1430 6440 4.241555 CCTCCCTCCGCCAATCCG 62.242 72.222 0.00 0.00 0.00 4.18
1453 6463 1.132588 CGCCTCGATTCCGATTTCTC 58.867 55.000 0.00 0.00 44.62 2.87
1469 6479 1.512310 CTCGCTCCTCGTTGACGTC 60.512 63.158 9.11 9.11 40.80 4.34
1471 6481 1.512310 CGCTCCTCGTTGACGTCTC 60.512 63.158 17.92 9.02 40.80 3.36
1582 6610 2.553247 CGCCTTTTCTTTTCCTCCTCCT 60.553 50.000 0.00 0.00 0.00 3.69
1583 6611 3.501349 GCCTTTTCTTTTCCTCCTCCTT 58.499 45.455 0.00 0.00 0.00 3.36
1584 6612 3.508012 GCCTTTTCTTTTCCTCCTCCTTC 59.492 47.826 0.00 0.00 0.00 3.46
1690 6722 4.142881 GGATTAGCTCCGGCGATTTATTTC 60.143 45.833 9.30 0.00 44.37 2.17
1698 6730 6.548441 TCCGGCGATTTATTTCGAAATAAT 57.452 33.333 32.84 24.69 41.62 1.28
1733 6766 1.277326 CGTCTTGATCGCAAATCGGA 58.723 50.000 0.00 0.00 39.05 4.55
1734 6767 1.658596 CGTCTTGATCGCAAATCGGAA 59.341 47.619 0.00 0.00 39.05 4.30
1761 6794 2.370849 GTTCCTCTAACACTGTTCCCCA 59.629 50.000 0.00 0.00 38.05 4.96
1868 6903 1.356124 ACCAGAGCAAGGTGATGAGT 58.644 50.000 0.00 0.00 38.13 3.41
2024 7164 2.749865 GCTCGCTAACCGCATTGCA 61.750 57.895 9.69 0.00 39.08 4.08
2117 7257 2.288643 GAGGAGGAGGAGGGGCAT 59.711 66.667 0.00 0.00 0.00 4.40
2449 7597 0.320771 AGTTTGAGGCGTGCTGGTAG 60.321 55.000 0.00 0.00 0.00 3.18
2492 7642 1.442017 GTGCGACGCCATTTTGGTC 60.442 57.895 18.69 0.00 40.46 4.02
2495 7646 3.975246 GACGCCATTTTGGTCGGA 58.025 55.556 12.55 0.00 40.46 4.55
2547 7699 4.803426 GCTGCGCGAGGTAGTGCT 62.803 66.667 12.10 0.00 46.78 4.40
2712 7888 4.431416 TGAGTGGGTTAGTGTGTTCATT 57.569 40.909 0.00 0.00 0.00 2.57
2795 7987 2.681848 CTCCATCAGCTTTGGTTAGCAG 59.318 50.000 11.36 0.00 43.68 4.24
2796 7988 2.305635 TCCATCAGCTTTGGTTAGCAGA 59.694 45.455 11.36 0.00 43.68 4.26
2797 7989 3.084039 CCATCAGCTTTGGTTAGCAGAA 58.916 45.455 4.54 0.00 43.68 3.02
2798 7990 3.698040 CCATCAGCTTTGGTTAGCAGAAT 59.302 43.478 4.54 0.00 43.68 2.40
2799 7991 4.201990 CCATCAGCTTTGGTTAGCAGAATC 60.202 45.833 4.54 0.00 43.68 2.52
2800 7992 4.019792 TCAGCTTTGGTTAGCAGAATCA 57.980 40.909 0.00 0.00 43.68 2.57
2801 7993 4.005650 TCAGCTTTGGTTAGCAGAATCAG 58.994 43.478 0.00 0.00 43.68 2.90
2802 7994 2.751806 AGCTTTGGTTAGCAGAATCAGC 59.248 45.455 0.00 0.00 43.68 4.26
2803 7995 2.476854 GCTTTGGTTAGCAGAATCAGCG 60.477 50.000 0.00 0.00 40.89 5.18
2804 7996 2.472695 TTGGTTAGCAGAATCAGCGT 57.527 45.000 0.00 0.00 37.01 5.07
2805 7997 3.603158 TTGGTTAGCAGAATCAGCGTA 57.397 42.857 0.00 0.00 37.01 4.42
2806 7998 2.888594 TGGTTAGCAGAATCAGCGTAC 58.111 47.619 0.00 0.00 37.01 3.67
2807 7999 1.852895 GGTTAGCAGAATCAGCGTACG 59.147 52.381 11.84 11.84 37.01 3.67
2808 8000 2.479049 GGTTAGCAGAATCAGCGTACGA 60.479 50.000 21.65 0.00 37.01 3.43
2809 8001 3.176708 GTTAGCAGAATCAGCGTACGAA 58.823 45.455 21.65 3.41 37.01 3.85
2810 8002 2.363788 AGCAGAATCAGCGTACGAAA 57.636 45.000 21.65 3.00 37.01 3.46
2811 8003 2.893637 AGCAGAATCAGCGTACGAAAT 58.106 42.857 21.65 5.52 37.01 2.17
2812 8004 3.262420 AGCAGAATCAGCGTACGAAATT 58.738 40.909 21.65 14.08 37.01 1.82
2813 8005 3.062639 AGCAGAATCAGCGTACGAAATTG 59.937 43.478 21.65 10.97 37.01 2.32
2814 8006 3.345714 CAGAATCAGCGTACGAAATTGC 58.654 45.455 21.65 0.00 0.00 3.56
2815 8007 3.062639 CAGAATCAGCGTACGAAATTGCT 59.937 43.478 21.65 1.55 38.43 3.91
2816 8008 3.684788 AGAATCAGCGTACGAAATTGCTT 59.315 39.130 21.65 8.65 34.99 3.91
2817 8009 3.658351 ATCAGCGTACGAAATTGCTTC 57.342 42.857 21.65 0.00 34.99 3.86
2818 8010 2.409012 TCAGCGTACGAAATTGCTTCA 58.591 42.857 21.65 0.00 34.99 3.02
2819 8011 2.156891 TCAGCGTACGAAATTGCTTCAC 59.843 45.455 21.65 0.00 34.99 3.18
2820 8012 2.096466 CAGCGTACGAAATTGCTTCACA 60.096 45.455 21.65 0.00 34.99 3.58
2821 8013 2.742053 AGCGTACGAAATTGCTTCACAT 59.258 40.909 21.65 0.00 32.89 3.21
2822 8014 3.930229 AGCGTACGAAATTGCTTCACATA 59.070 39.130 21.65 0.00 32.89 2.29
2823 8015 4.019867 GCGTACGAAATTGCTTCACATAC 58.980 43.478 21.65 0.00 33.17 2.39
2824 8016 4.574759 CGTACGAAATTGCTTCACATACC 58.425 43.478 10.44 0.00 33.17 2.73
2825 8017 4.092237 CGTACGAAATTGCTTCACATACCA 59.908 41.667 10.44 0.00 33.17 3.25
2826 8018 5.390040 CGTACGAAATTGCTTCACATACCAA 60.390 40.000 10.44 0.00 33.17 3.67
2827 8019 5.643379 ACGAAATTGCTTCACATACCAAT 57.357 34.783 0.00 0.00 33.17 3.16
2828 8020 5.401550 ACGAAATTGCTTCACATACCAATG 58.598 37.500 0.00 0.00 39.17 2.82
2830 8022 5.863397 CGAAATTGCTTCACATACCAATGTT 59.137 36.000 0.00 0.00 44.07 2.71
2831 8023 6.365789 CGAAATTGCTTCACATACCAATGTTT 59.634 34.615 0.00 0.00 44.07 2.83
2832 8024 7.410728 CGAAATTGCTTCACATACCAATGTTTC 60.411 37.037 0.00 0.00 44.07 2.78
2833 8025 4.782019 TGCTTCACATACCAATGTTTCC 57.218 40.909 0.00 0.00 44.07 3.13
2834 8026 3.509575 TGCTTCACATACCAATGTTTCCC 59.490 43.478 0.00 0.00 44.07 3.97
2835 8027 3.427503 GCTTCACATACCAATGTTTCCCG 60.428 47.826 0.00 0.00 44.07 5.14
2836 8028 3.704800 TCACATACCAATGTTTCCCGA 57.295 42.857 0.00 0.00 44.07 5.14
2837 8029 3.340034 TCACATACCAATGTTTCCCGAC 58.660 45.455 0.00 0.00 44.07 4.79
2838 8030 3.008594 TCACATACCAATGTTTCCCGACT 59.991 43.478 0.00 0.00 44.07 4.18
2839 8031 3.126858 CACATACCAATGTTTCCCGACTG 59.873 47.826 0.00 0.00 44.07 3.51
2840 8032 3.008594 ACATACCAATGTTTCCCGACTGA 59.991 43.478 0.00 0.00 44.07 3.41
2841 8033 2.879103 ACCAATGTTTCCCGACTGAT 57.121 45.000 0.00 0.00 0.00 2.90
2842 8034 3.154827 ACCAATGTTTCCCGACTGATT 57.845 42.857 0.00 0.00 0.00 2.57
2843 8035 3.496331 ACCAATGTTTCCCGACTGATTT 58.504 40.909 0.00 0.00 0.00 2.17
2844 8036 3.506067 ACCAATGTTTCCCGACTGATTTC 59.494 43.478 0.00 0.00 0.00 2.17
2845 8037 3.119495 CCAATGTTTCCCGACTGATTTCC 60.119 47.826 0.00 0.00 0.00 3.13
2846 8038 2.940994 TGTTTCCCGACTGATTTCCA 57.059 45.000 0.00 0.00 0.00 3.53
2848 8040 2.370519 TGTTTCCCGACTGATTTCCAGA 59.629 45.455 0.00 0.00 45.78 3.86
2849 8041 2.742589 GTTTCCCGACTGATTTCCAGAC 59.257 50.000 0.00 0.00 45.78 3.51
2850 8042 1.639722 TCCCGACTGATTTCCAGACA 58.360 50.000 0.00 0.00 45.78 3.41
2851 8043 1.275291 TCCCGACTGATTTCCAGACAC 59.725 52.381 0.00 0.00 45.78 3.67
2852 8044 1.276421 CCCGACTGATTTCCAGACACT 59.724 52.381 0.00 0.00 45.78 3.55
2853 8045 2.496070 CCCGACTGATTTCCAGACACTA 59.504 50.000 0.00 0.00 45.78 2.74
2854 8046 3.056107 CCCGACTGATTTCCAGACACTAA 60.056 47.826 0.00 0.00 45.78 2.24
2855 8047 3.927142 CCGACTGATTTCCAGACACTAAC 59.073 47.826 0.00 0.00 45.78 2.34
2856 8048 4.556233 CGACTGATTTCCAGACACTAACA 58.444 43.478 0.00 0.00 45.78 2.41
2857 8049 5.171476 CGACTGATTTCCAGACACTAACAT 58.829 41.667 0.00 0.00 45.78 2.71
2858 8050 5.639506 CGACTGATTTCCAGACACTAACATT 59.360 40.000 0.00 0.00 45.78 2.71
2859 8051 6.401474 CGACTGATTTCCAGACACTAACATTG 60.401 42.308 0.00 0.00 45.78 2.82
2860 8052 5.182001 ACTGATTTCCAGACACTAACATTGC 59.818 40.000 0.00 0.00 45.78 3.56
2861 8053 5.069318 TGATTTCCAGACACTAACATTGCA 58.931 37.500 0.00 0.00 0.00 4.08
2862 8054 4.829064 TTTCCAGACACTAACATTGCAC 57.171 40.909 0.00 0.00 0.00 4.57
2871 8063 5.726397 ACACTAACATTGCACCGTTAGATA 58.274 37.500 28.57 4.98 44.81 1.98
2876 8068 3.809832 ACATTGCACCGTTAGATATGCTC 59.190 43.478 0.00 0.00 38.90 4.26
2877 8069 3.819564 TTGCACCGTTAGATATGCTCT 57.180 42.857 0.00 0.00 38.90 4.09
2890 8082 2.768253 ATGCTCTCCACGTTTGATCA 57.232 45.000 0.00 0.00 0.00 2.92
2901 8093 1.269448 CGTTTGATCAAAGGGTGGTGG 59.731 52.381 26.05 5.79 33.84 4.61
2902 8094 2.593026 GTTTGATCAAAGGGTGGTGGA 58.407 47.619 21.05 0.00 0.00 4.02
2908 8176 3.238197 AAAGGGTGGTGGATGGCCC 62.238 63.158 0.00 0.00 41.36 5.80
2943 8211 1.510776 CCGTTTTGTTGCCATGCATT 58.489 45.000 0.00 0.00 38.76 3.56
2949 8217 1.806758 GTTGCCATGCATTGACGGC 60.807 57.895 16.80 16.80 45.11 5.68
2951 8219 1.936436 TTGCCATGCATTGACGGCTC 61.936 55.000 22.24 0.59 45.13 4.70
2955 8223 0.659427 CATGCATTGACGGCTCGATT 59.341 50.000 0.00 0.00 0.00 3.34
2963 8231 1.696832 GACGGCTCGATTGGCTTGTC 61.697 60.000 1.50 0.00 0.00 3.18
2965 8233 2.401195 GCTCGATTGGCTTGTCGC 59.599 61.111 0.00 0.00 37.74 5.19
2989 8257 2.377628 AATCGTGTGCAGGGTGTCGT 62.378 55.000 0.00 0.00 0.00 4.34
2994 8262 4.168291 TGCAGGGTGTCGTGTGCA 62.168 61.111 0.00 0.00 43.50 4.57
3037 8319 1.256652 CACACGTCGGACTCATTACG 58.743 55.000 6.57 0.00 40.99 3.18
3049 8331 1.743623 CATTACGCGGGGCTTGTGA 60.744 57.895 12.47 0.00 0.00 3.58
3160 8444 1.207329 GCGGGGAGATACACAAGAACT 59.793 52.381 0.00 0.00 0.00 3.01
3223 8508 6.739112 AGCCAGAGAAACAAAAGTGATAAAC 58.261 36.000 0.00 0.00 0.00 2.01
3252 8546 3.758554 ACAATATCCCAATATGAAGCGCC 59.241 43.478 2.29 0.00 0.00 6.53
3418 8712 0.322997 TTTATGGGAGTTGGGTGCCG 60.323 55.000 0.00 0.00 0.00 5.69
3436 8730 2.272146 CGCACACCATAAGCCCCT 59.728 61.111 0.00 0.00 0.00 4.79
3554 8860 2.666272 TGAAACCTGTGTGCCCAATA 57.334 45.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.615116 GGCCGGCCTAAAAGTTACCTT 60.615 52.381 38.76 0.00 0.00 3.50
4 5 0.699981 AAGGGCCGGCCTAAAAGTTA 59.300 50.000 42.70 0.00 36.10 2.24
38 39 2.202566 GTCAACGGTGGAGCTATAAGC 58.797 52.381 0.00 0.00 42.84 3.09
53 54 1.336755 ACATGCCCTTTTGACGTCAAC 59.663 47.619 29.74 18.17 35.28 3.18
55 56 1.686355 AACATGCCCTTTTGACGTCA 58.314 45.000 15.76 15.76 0.00 4.35
78 90 1.142748 CGGCACTCCTCATCTGACC 59.857 63.158 0.00 0.00 0.00 4.02
80 92 1.323271 GGACGGCACTCCTCATCTGA 61.323 60.000 0.00 0.00 0.00 3.27
83 95 0.036388 TTTGGACGGCACTCCTCATC 60.036 55.000 0.00 0.00 0.00 2.92
125 137 4.756642 GGTCATCCGAGAAATTATGCATGA 59.243 41.667 10.16 0.00 0.00 3.07
154 166 1.145377 GGTGGTGTCGTGGTTGTCT 59.855 57.895 0.00 0.00 0.00 3.41
156 168 2.202960 CGGTGGTGTCGTGGTTGT 60.203 61.111 0.00 0.00 0.00 3.32
185 197 0.876777 TTGTGCCGGACGTGTACAAG 60.877 55.000 5.05 7.29 0.00 3.16
195 207 2.203280 CAGTTGGGTTGTGCCGGA 60.203 61.111 5.05 0.00 38.44 5.14
210 222 2.977772 TTTGGCCTCAAACAAACCAG 57.022 45.000 3.32 0.00 37.89 4.00
247 260 7.707104 GCACCTTGCAAGAAGTATGTAATAAT 58.293 34.615 28.05 0.00 44.26 1.28
297 310 2.854337 AGGGGGTAATGTAACCGGAAAT 59.146 45.455 9.46 0.00 40.73 2.17
305 318 0.342665 TCGGGGAGGGGGTAATGTAA 59.657 55.000 0.00 0.00 0.00 2.41
311 324 4.791069 GCACTCGGGGAGGGGGTA 62.791 72.222 0.00 0.00 32.99 3.69
318 331 0.250727 CCTCTTTTTGCACTCGGGGA 60.251 55.000 0.00 0.00 0.00 4.81
325 339 7.148086 TGGTTGACATATATCCTCTTTTTGCAC 60.148 37.037 0.00 0.00 0.00 4.57
327 341 7.333528 TGGTTGACATATATCCTCTTTTTGC 57.666 36.000 0.00 0.00 0.00 3.68
524 5483 1.131638 AGAGGGCAGTTTGACTCACA 58.868 50.000 0.00 0.00 32.52 3.58
534 5493 2.026729 GGCTCTAAAAGAAGAGGGCAGT 60.027 50.000 3.27 0.00 42.79 4.40
541 5500 2.674796 GCTCCGGCTCTAAAAGAAGA 57.325 50.000 0.00 0.00 35.22 2.87
553 5512 2.976903 GCATGATGGAGCTCCGGC 60.977 66.667 27.43 21.07 39.43 6.13
554 5513 1.153107 TTGCATGATGGAGCTCCGG 60.153 57.895 27.43 14.78 39.43 5.14
558 5517 3.292492 TCATTCTTGCATGATGGAGCT 57.708 42.857 2.75 0.00 0.00 4.09
560 5519 8.936070 TTATTTTTCATTCTTGCATGATGGAG 57.064 30.769 2.75 0.00 33.07 3.86
561 5520 9.722184 TTTTATTTTTCATTCTTGCATGATGGA 57.278 25.926 2.75 1.81 33.07 3.41
587 5555 7.275560 CACATTTCAAGGTTTTCTCTCGTTTTT 59.724 33.333 0.00 0.00 0.00 1.94
653 5628 5.650283 TCTTTCTCCTCCTCTTCTTCTTCT 58.350 41.667 0.00 0.00 0.00 2.85
658 5633 4.412060 TCCTCTTTCTCCTCCTCTTCTT 57.588 45.455 0.00 0.00 0.00 2.52
663 5638 3.835395 TGTCTTTCCTCTTTCTCCTCCTC 59.165 47.826 0.00 0.00 0.00 3.71
664 5639 3.837731 CTGTCTTTCCTCTTTCTCCTCCT 59.162 47.826 0.00 0.00 0.00 3.69
665 5640 3.055458 CCTGTCTTTCCTCTTTCTCCTCC 60.055 52.174 0.00 0.00 0.00 4.30
672 5647 1.002544 CTCCGCCTGTCTTTCCTCTTT 59.997 52.381 0.00 0.00 0.00 2.52
674 5649 0.251832 TCTCCGCCTGTCTTTCCTCT 60.252 55.000 0.00 0.00 0.00 3.69
728 5703 1.471851 GGTTTGGTGGGTTTGTTTCCG 60.472 52.381 0.00 0.00 0.00 4.30
731 5706 1.279558 GGTGGTTTGGTGGGTTTGTTT 59.720 47.619 0.00 0.00 0.00 2.83
782 5758 4.807039 GCGGTGCGTATGACGGGT 62.807 66.667 0.70 0.00 42.82 5.28
1690 6722 8.433126 ACGGCTAATAAAATCGAGATTATTTCG 58.567 33.333 18.02 18.80 39.33 3.46
1698 6730 5.898174 TCAAGACGGCTAATAAAATCGAGA 58.102 37.500 0.00 0.00 0.00 4.04
1707 6739 3.446310 TTGCGATCAAGACGGCTAATA 57.554 42.857 0.00 0.00 0.00 0.98
1868 6903 5.451798 GCAAGGAAAACAGGAAATCACTGAA 60.452 40.000 0.00 0.00 39.24 3.02
1933 7073 7.454260 AACAGGAAGTAAATAAAAGCAGGAG 57.546 36.000 0.00 0.00 0.00 3.69
1996 7136 3.678717 TTAGCGAGCGACACGAGGC 62.679 63.158 0.00 0.00 0.00 4.70
2024 7164 0.598065 GCCTCATTTGCCAAGTTCGT 59.402 50.000 0.00 0.00 0.00 3.85
2037 7177 4.891727 CGCCCGCGTTAGCCTCAT 62.892 66.667 4.92 0.00 41.18 2.90
2108 7248 0.037447 GCTTCCATCTATGCCCCTCC 59.963 60.000 0.00 0.00 0.00 4.30
2117 7257 1.144716 CTGCGGCAGCTTCCATCTA 59.855 57.895 18.16 0.00 45.42 1.98
2428 7576 1.597854 CCAGCACGCCTCAAACTGA 60.598 57.895 0.00 0.00 0.00 3.41
2429 7577 0.602638 TACCAGCACGCCTCAAACTG 60.603 55.000 0.00 0.00 0.00 3.16
2430 7578 0.320771 CTACCAGCACGCCTCAAACT 60.321 55.000 0.00 0.00 0.00 2.66
2431 7579 1.912371 GCTACCAGCACGCCTCAAAC 61.912 60.000 0.00 0.00 41.89 2.93
2432 7580 1.671054 GCTACCAGCACGCCTCAAA 60.671 57.895 0.00 0.00 41.89 2.69
2453 7601 2.184020 CTTGATCCAGCACGGGGACA 62.184 60.000 0.00 0.00 37.23 4.02
2455 7603 1.612146 TCTTGATCCAGCACGGGGA 60.612 57.895 0.00 0.00 39.14 4.81
2492 7642 1.472480 ACCTCGCAAAATTCCAATCCG 59.528 47.619 0.00 0.00 0.00 4.18
2495 7646 2.524306 TCCACCTCGCAAAATTCCAAT 58.476 42.857 0.00 0.00 0.00 3.16
2547 7699 8.280258 ACCACTATACTAGTATACTACCACCA 57.720 38.462 17.03 0.00 37.23 4.17
2767 7959 3.084039 CCAAAGCTGATGGAGTGCTAAA 58.916 45.455 12.44 0.00 40.56 1.85
2770 7962 0.403271 ACCAAAGCTGATGGAGTGCT 59.597 50.000 22.17 0.28 40.56 4.40
2795 7987 3.658351 AGCAATTTCGTACGCTGATTC 57.342 42.857 11.24 0.00 32.33 2.52
2796 7988 3.435327 TGAAGCAATTTCGTACGCTGATT 59.565 39.130 11.24 9.75 38.71 2.57
2797 7989 3.000041 TGAAGCAATTTCGTACGCTGAT 59.000 40.909 11.24 0.85 38.71 2.90
2798 7990 2.156891 GTGAAGCAATTTCGTACGCTGA 59.843 45.455 11.24 0.00 38.71 4.26
2799 7991 2.096466 TGTGAAGCAATTTCGTACGCTG 60.096 45.455 11.24 6.28 38.71 5.18
2800 7992 2.139917 TGTGAAGCAATTTCGTACGCT 58.860 42.857 11.24 0.00 38.71 5.07
2801 7993 2.587612 TGTGAAGCAATTTCGTACGC 57.412 45.000 11.24 0.00 38.71 4.42
2802 7994 4.092237 TGGTATGTGAAGCAATTTCGTACG 59.908 41.667 9.53 9.53 38.71 3.67
2803 7995 5.539582 TGGTATGTGAAGCAATTTCGTAC 57.460 39.130 0.00 0.00 38.71 3.67
2804 7996 6.150307 ACATTGGTATGTGAAGCAATTTCGTA 59.850 34.615 0.00 0.00 43.18 3.43
2805 7997 5.048083 ACATTGGTATGTGAAGCAATTTCGT 60.048 36.000 0.00 0.00 43.18 3.85
2806 7998 5.401550 ACATTGGTATGTGAAGCAATTTCG 58.598 37.500 0.00 0.00 43.18 3.46
2807 7999 7.148590 GGAAACATTGGTATGTGAAGCAATTTC 60.149 37.037 0.00 3.40 44.14 2.17
2808 8000 6.650390 GGAAACATTGGTATGTGAAGCAATTT 59.350 34.615 0.00 0.00 44.14 1.82
2809 8001 6.165577 GGAAACATTGGTATGTGAAGCAATT 58.834 36.000 0.00 0.00 44.14 2.32
2810 8002 5.337491 GGGAAACATTGGTATGTGAAGCAAT 60.337 40.000 0.00 0.00 44.14 3.56
2811 8003 4.021544 GGGAAACATTGGTATGTGAAGCAA 60.022 41.667 0.00 0.00 44.14 3.91
2812 8004 3.509575 GGGAAACATTGGTATGTGAAGCA 59.490 43.478 0.00 0.00 44.14 3.91
2813 8005 3.427503 CGGGAAACATTGGTATGTGAAGC 60.428 47.826 0.00 0.00 44.14 3.86
2814 8006 4.006989 TCGGGAAACATTGGTATGTGAAG 58.993 43.478 0.00 0.00 44.14 3.02
2815 8007 3.754323 GTCGGGAAACATTGGTATGTGAA 59.246 43.478 0.00 0.00 44.14 3.18
2816 8008 3.008594 AGTCGGGAAACATTGGTATGTGA 59.991 43.478 0.00 0.00 44.14 3.58
2817 8009 3.126858 CAGTCGGGAAACATTGGTATGTG 59.873 47.826 0.00 0.00 44.14 3.21
2818 8010 3.008594 TCAGTCGGGAAACATTGGTATGT 59.991 43.478 0.00 0.00 46.85 2.29
2819 8011 3.605634 TCAGTCGGGAAACATTGGTATG 58.394 45.455 0.00 0.00 37.79 2.39
2820 8012 3.992943 TCAGTCGGGAAACATTGGTAT 57.007 42.857 0.00 0.00 0.00 2.73
2821 8013 3.992943 ATCAGTCGGGAAACATTGGTA 57.007 42.857 0.00 0.00 0.00 3.25
2822 8014 2.879103 ATCAGTCGGGAAACATTGGT 57.121 45.000 0.00 0.00 0.00 3.67
2823 8015 3.119495 GGAAATCAGTCGGGAAACATTGG 60.119 47.826 0.00 0.00 0.00 3.16
2824 8016 3.505680 TGGAAATCAGTCGGGAAACATTG 59.494 43.478 0.00 0.00 0.00 2.82
2825 8017 3.758554 CTGGAAATCAGTCGGGAAACATT 59.241 43.478 0.00 0.00 38.64 2.71
2826 8018 3.009033 TCTGGAAATCAGTCGGGAAACAT 59.991 43.478 0.00 0.00 43.76 2.71
2827 8019 2.370519 TCTGGAAATCAGTCGGGAAACA 59.629 45.455 0.00 0.00 43.76 2.83
2828 8020 2.742589 GTCTGGAAATCAGTCGGGAAAC 59.257 50.000 0.00 0.00 43.76 2.78
2829 8021 2.370519 TGTCTGGAAATCAGTCGGGAAA 59.629 45.455 0.00 0.00 43.76 3.13
2830 8022 1.974957 TGTCTGGAAATCAGTCGGGAA 59.025 47.619 0.00 0.00 43.76 3.97
2831 8023 1.275291 GTGTCTGGAAATCAGTCGGGA 59.725 52.381 0.00 0.00 43.76 5.14
2832 8024 1.276421 AGTGTCTGGAAATCAGTCGGG 59.724 52.381 0.00 0.00 43.76 5.14
2833 8025 2.751166 AGTGTCTGGAAATCAGTCGG 57.249 50.000 0.00 0.00 43.76 4.79
2834 8026 4.556233 TGTTAGTGTCTGGAAATCAGTCG 58.444 43.478 0.00 0.00 43.76 4.18
2835 8027 6.621596 GCAATGTTAGTGTCTGGAAATCAGTC 60.622 42.308 0.00 0.00 43.76 3.51
2836 8028 5.182001 GCAATGTTAGTGTCTGGAAATCAGT 59.818 40.000 0.00 0.00 43.76 3.41
2837 8029 5.181811 TGCAATGTTAGTGTCTGGAAATCAG 59.818 40.000 0.00 0.00 44.68 2.90
2838 8030 5.048782 GTGCAATGTTAGTGTCTGGAAATCA 60.049 40.000 0.00 0.00 0.00 2.57
2839 8031 5.393962 GTGCAATGTTAGTGTCTGGAAATC 58.606 41.667 0.00 0.00 0.00 2.17
2840 8032 4.218417 GGTGCAATGTTAGTGTCTGGAAAT 59.782 41.667 0.00 0.00 0.00 2.17
2841 8033 3.568007 GGTGCAATGTTAGTGTCTGGAAA 59.432 43.478 0.00 0.00 0.00 3.13
2842 8034 3.146066 GGTGCAATGTTAGTGTCTGGAA 58.854 45.455 0.00 0.00 0.00 3.53
2843 8035 2.778299 GGTGCAATGTTAGTGTCTGGA 58.222 47.619 0.00 0.00 0.00 3.86
2844 8036 1.464608 CGGTGCAATGTTAGTGTCTGG 59.535 52.381 0.00 0.00 0.00 3.86
2845 8037 2.143122 ACGGTGCAATGTTAGTGTCTG 58.857 47.619 0.00 0.00 0.00 3.51
2846 8038 2.543777 ACGGTGCAATGTTAGTGTCT 57.456 45.000 0.00 0.00 0.00 3.41
2847 8039 3.991773 TCTAACGGTGCAATGTTAGTGTC 59.008 43.478 26.25 0.00 44.91 3.67
2848 8040 3.997762 TCTAACGGTGCAATGTTAGTGT 58.002 40.909 26.25 3.57 44.91 3.55
2849 8041 6.649436 CATATCTAACGGTGCAATGTTAGTG 58.351 40.000 26.25 18.57 44.91 2.74
2850 8042 5.236478 GCATATCTAACGGTGCAATGTTAGT 59.764 40.000 26.25 19.54 44.91 2.24
2851 8043 5.466728 AGCATATCTAACGGTGCAATGTTAG 59.533 40.000 23.64 23.64 45.63 2.34
2852 8044 5.364778 AGCATATCTAACGGTGCAATGTTA 58.635 37.500 10.57 10.57 39.94 2.41
2853 8045 4.199310 AGCATATCTAACGGTGCAATGTT 58.801 39.130 9.48 9.48 39.94 2.71
2854 8046 3.808728 AGCATATCTAACGGTGCAATGT 58.191 40.909 0.00 0.00 39.94 2.71
2855 8047 4.060900 AGAGCATATCTAACGGTGCAATG 58.939 43.478 0.00 0.00 39.94 2.82
2856 8048 4.310769 GAGAGCATATCTAACGGTGCAAT 58.689 43.478 0.00 0.00 38.84 3.56
2857 8049 3.492656 GGAGAGCATATCTAACGGTGCAA 60.493 47.826 0.00 0.00 38.84 4.08
2858 8050 2.035961 GGAGAGCATATCTAACGGTGCA 59.964 50.000 0.00 0.00 38.84 4.57
2859 8051 2.035961 TGGAGAGCATATCTAACGGTGC 59.964 50.000 0.00 0.00 38.84 5.01
2860 8052 3.643763 GTGGAGAGCATATCTAACGGTG 58.356 50.000 0.00 0.00 38.84 4.94
2861 8053 2.293677 CGTGGAGAGCATATCTAACGGT 59.706 50.000 5.23 0.00 41.31 4.83
2862 8054 2.293677 ACGTGGAGAGCATATCTAACGG 59.706 50.000 13.72 1.68 45.68 4.44
2871 8063 2.768253 TGATCAAACGTGGAGAGCAT 57.232 45.000 0.00 0.00 0.00 3.79
2876 8068 2.226437 CACCCTTTGATCAAACGTGGAG 59.774 50.000 23.93 16.62 0.00 3.86
2877 8069 2.226330 CACCCTTTGATCAAACGTGGA 58.774 47.619 23.93 5.68 0.00 4.02
2890 8082 2.445155 GGCCATCCACCACCCTTT 59.555 61.111 0.00 0.00 0.00 3.11
2943 8211 1.741401 CAAGCCAATCGAGCCGTCA 60.741 57.895 0.00 0.00 0.00 4.35
2965 8233 1.178534 ACCCTGCACACGATTTTGGG 61.179 55.000 0.54 0.54 39.06 4.12
2989 8257 0.179089 AAAAATTGCCGCTGTGCACA 60.179 45.000 20.37 20.37 41.88 4.57
3014 8295 1.176619 ATGAGTCCGACGTGTGGTCA 61.177 55.000 0.00 0.00 46.42 4.02
3020 8301 1.461317 CGCGTAATGAGTCCGACGTG 61.461 60.000 0.00 8.46 39.15 4.49
3037 8319 4.120331 GTGCATCACAAGCCCCGC 62.120 66.667 0.00 0.00 34.08 6.13
3049 8331 7.425224 AAACTATCTACAGGTCTTAGTGCAT 57.575 36.000 0.00 0.00 0.00 3.96
3183 8467 7.346751 TCTCTGGCTAGTTTTCAAATTTTGT 57.653 32.000 8.89 0.00 0.00 2.83
3196 8481 5.036117 TCACTTTTGTTTCTCTGGCTAGT 57.964 39.130 0.00 0.00 0.00 2.57
3197 8482 7.672983 TTATCACTTTTGTTTCTCTGGCTAG 57.327 36.000 0.00 0.00 0.00 3.42
3202 8487 9.573133 AACAAGTTTATCACTTTTGTTTCTCTG 57.427 29.630 0.00 0.00 43.89 3.35
3223 8508 9.683069 GCTTCATATTGGGATATTGTTAACAAG 57.317 33.333 24.22 8.05 39.47 3.16
3252 8546 6.306356 ACACTAAACAGTACGTAATGTAAGCG 59.694 38.462 26.87 21.35 32.84 4.68
3315 8609 9.209175 GTATCATGTCACAATACTCTAAATCCC 57.791 37.037 0.00 0.00 0.00 3.85
3397 8691 2.422235 CGGCACCCAACTCCCATAAATA 60.422 50.000 0.00 0.00 0.00 1.40
3418 8712 3.518068 GGGGCTTATGGTGTGCGC 61.518 66.667 0.00 0.00 38.63 6.09
3436 8730 1.369692 CCCACCTCTTGCGTGTACA 59.630 57.895 0.00 0.00 0.00 2.90
3517 8823 1.992557 TCATGTCCCAAAACCCTAGCT 59.007 47.619 0.00 0.00 0.00 3.32
3518 8824 2.507407 TCATGTCCCAAAACCCTAGC 57.493 50.000 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.