Multiple sequence alignment - TraesCS1D01G222100

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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 TraesCS1D01G222100 chr1D 100.000 3467 0 0 1 3467 309924741 309921275 0.000000e+00 6403.0
1 TraesCS1D01G222100 chr1A 94.294 1998 89 10 798 2777 389806341 389804351 0.000000e+00 3035.0
2 TraesCS1D01G222100 chr1A 93.431 411 23 3 3060 3467 389803219 389802810 1.060000e-169 606.0
3 TraesCS1D01G222100 chr1A 84.703 353 43 9 1 347 389808277 389807930 3.310000e-90 342.0
4 TraesCS1D01G222100 chr1A 90.083 242 14 7 2768 3001 389803458 389803219 4.350000e-79 305.0
5 TraesCS1D01G222100 chr1A 94.000 100 5 1 727 826 389807441 389807343 2.160000e-32 150.0
6 TraesCS1D01G222100 chr1A 89.167 120 10 3 2883 3001 389771562 389771445 2.790000e-31 147.0
7 TraesCS1D01G222100 chr1A 95.000 40 2 0 503 542 520345514 520345475 2.890000e-06 63.9
8 TraesCS1D01G222100 chr3A 95.123 1907 78 7 879 2777 128578327 128580226 0.000000e+00 2992.0
9 TraesCS1D01G222100 chr3A 92.701 411 23 4 3060 3467 128581358 128581764 1.390000e-163 586.0
10 TraesCS1D01G222100 chr3A 87.975 316 28 8 344 651 128569101 128569414 7.070000e-97 364.0
11 TraesCS1D01G222100 chr3A 90.909 242 11 8 2768 3001 128581120 128581358 7.220000e-82 315.0
12 TraesCS1D01G222100 chr3A 89.431 123 10 3 2880 3001 128716266 128716386 5.990000e-33 152.0
13 TraesCS1D01G222100 chr1B 91.937 1265 62 8 728 1983 419953436 419952203 0.000000e+00 1735.0
14 TraesCS1D01G222100 chr1B 96.450 507 17 1 1974 2479 419951956 419951450 0.000000e+00 835.0
15 TraesCS1D01G222100 chr1B 89.167 120 10 3 2883 3001 419780892 419780775 2.790000e-31 147.0
16 TraesCS1D01G222100 chr2D 81.974 1520 236 27 963 2457 426920295 426921801 0.000000e+00 1254.0
17 TraesCS1D01G222100 chr2A 81.484 1523 238 31 963 2457 562106235 562104729 0.000000e+00 1210.0
18 TraesCS1D01G222100 chr7B 91.549 71 5 1 2991 3061 355482985 355483054 2.850000e-16 97.1
19 TraesCS1D01G222100 chr7B 90.141 71 6 1 2991 3061 289577745 289577676 1.330000e-14 91.6
20 TraesCS1D01G222100 chr6B 91.549 71 5 1 2991 3061 273665295 273665364 2.850000e-16 97.1
21 TraesCS1D01G222100 chr6B 88.732 71 7 1 2991 3061 668385985 668385916 6.170000e-13 86.1
22 TraesCS1D01G222100 chr3B 90.141 71 6 1 2991 3061 391081890 391081821 1.330000e-14 91.6
23 TraesCS1D01G222100 chr3B 90.000 70 6 1 2991 3060 86727845 86727913 4.770000e-14 89.8
24 TraesCS1D01G222100 chr3B 94.872 39 2 0 3324 3362 749037995 749038033 1.040000e-05 62.1
25 TraesCS1D01G222100 chr2B 90.141 71 6 1 2991 3061 605032409 605032340 1.330000e-14 91.6
26 TraesCS1D01G222100 chr6D 89.333 75 3 1 2992 3061 178858020 178857946 4.770000e-14 89.8
27 TraesCS1D01G222100 chr6D 100.000 34 0 0 506 539 315629518 315629485 2.890000e-06 63.9
28 TraesCS1D01G222100 chr4B 88.732 71 7 1 2991 3061 167058433 167058364 6.170000e-13 86.1
29 TraesCS1D01G222100 chr7D 73.756 221 45 7 351 559 110219373 110219154 1.330000e-09 75.0
30 TraesCS1D01G222100 chr5A 97.368 38 1 0 3324 3361 290689189 290689226 8.030000e-07 65.8
31 TraesCS1D01G222100 chr5A 92.105 38 3 0 3324 3361 703429676 703429639 2.000000e-03 54.7
32 TraesCS1D01G222100 chr6A 94.737 38 2 0 3324 3361 426636044 426636081 3.740000e-05 60.2


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 TraesCS1D01G222100 chr1D 309921275 309924741 3466 True 6403.000000 6403 100.0000 1 3467 1 chr1D.!!$R1 3466
1 TraesCS1D01G222100 chr1A 389802810 389808277 5467 True 887.600000 3035 91.3022 1 3467 5 chr1A.!!$R3 3466
2 TraesCS1D01G222100 chr3A 128578327 128581764 3437 False 1297.666667 2992 92.9110 879 3467 3 chr3A.!!$F3 2588
3 TraesCS1D01G222100 chr1B 419951450 419953436 1986 True 1285.000000 1735 94.1935 728 2479 2 chr1B.!!$R2 1751
4 TraesCS1D01G222100 chr2D 426920295 426921801 1506 False 1254.000000 1254 81.9740 963 2457 1 chr2D.!!$F1 1494
5 TraesCS1D01G222100 chr2A 562104729 562106235 1506 True 1210.000000 1210 81.4840 963 2457 1 chr2A.!!$R1 1494

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
404 446 0.107831 TTGGACCACGGTTCAAGAGG 59.892 55.0 5.79 0.0 38.56 3.69 F
1213 2379 0.036306 GTTCCCGCCTTTCTTCCTCA 59.964 55.0 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 2479 0.463295 CCGCAGAAGCTGACCATGAT 60.463 55.0 0.0 0.0 39.1 2.45 R
3044 5397 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.0 0.0 0.0 0.0 4.00 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
47 48 7.974675 GCATATACTTGCTTCTGTGAAAAGTA 58.025 34.615 6.91 6.91 39.57 2.24
57 58 7.095060 TGCTTCTGTGAAAAGTATGCTTCTAAG 60.095 37.037 0.00 0.00 33.01 2.18
60 61 5.253330 TGTGAAAAGTATGCTTCTAAGGGG 58.747 41.667 0.00 0.00 33.01 4.79
64 65 7.007723 TGAAAAGTATGCTTCTAAGGGGAAAA 58.992 34.615 0.00 0.00 33.01 2.29
87 88 2.849880 GTGCTTTCACAAGAAGCACA 57.150 45.000 27.49 1.79 46.41 4.57
92 93 3.732721 GCTTTCACAAGAAGCACATGTTC 59.267 43.478 0.00 0.00 34.71 3.18
105 106 1.873591 ACATGTTCGCTTCTTGTGGAC 59.126 47.619 0.00 0.00 35.29 4.02
109 110 1.495584 TTCGCTTCTTGTGGACGCAC 61.496 55.000 0.00 0.00 38.87 5.34
111 112 1.568612 CGCTTCTTGTGGACGCACAT 61.569 55.000 0.00 0.00 38.87 3.21
149 150 8.898761 TGAGAAGTGTGCTAAGTGAAAATTTTA 58.101 29.630 2.75 0.00 0.00 1.52
150 151 9.170584 GAGAAGTGTGCTAAGTGAAAATTTTAC 57.829 33.333 2.75 3.33 0.00 2.01
159 160 5.508200 AGTGAAAATTTTACGCTTCCACA 57.492 34.783 15.08 0.86 0.00 4.17
162 163 5.974751 GTGAAAATTTTACGCTTCCACAAGA 59.025 36.000 2.75 0.00 0.00 3.02
175 176 2.813754 TCCACAAGAAGCATAGTTGTGC 59.186 45.455 13.01 0.00 46.38 4.57
188 189 6.208644 GCATAGTTGTGCTTCTTGAAAAAGA 58.791 36.000 0.00 0.00 41.82 2.52
189 190 6.697019 GCATAGTTGTGCTTCTTGAAAAAGAA 59.303 34.615 1.32 1.32 41.82 2.52
211 213 0.533308 AAAAGTGAACGCCGCTACCA 60.533 50.000 0.00 0.00 34.67 3.25
213 215 0.321298 AAGTGAACGCCGCTACCATT 60.321 50.000 0.00 0.00 34.67 3.16
214 216 0.321298 AGTGAACGCCGCTACCATTT 60.321 50.000 0.00 0.00 33.01 2.32
367 408 3.308866 GTCTTGACCCGATAAATCCAACG 59.691 47.826 0.00 0.00 0.00 4.10
370 411 2.765135 TGACCCGATAAATCCAACGGTA 59.235 45.455 0.00 0.00 43.22 4.02
374 415 4.395854 ACCCGATAAATCCAACGGTAAAAC 59.604 41.667 0.00 0.00 43.22 2.43
375 416 4.395542 CCCGATAAATCCAACGGTAAAACA 59.604 41.667 0.00 0.00 43.22 2.83
377 418 5.122711 CCGATAAATCCAACGGTAAAACAGT 59.877 40.000 0.00 0.00 40.42 3.55
380 421 7.060174 CGATAAATCCAACGGTAAAACAGTTTG 59.940 37.037 0.00 0.00 34.38 2.93
391 433 4.415881 AAAACAGTTTGGGATTTGGACC 57.584 40.909 0.00 0.00 0.00 4.46
404 446 0.107831 TTGGACCACGGTTCAAGAGG 59.892 55.000 5.79 0.00 38.56 3.69
415 457 4.401202 ACGGTTCAAGAGGTCAAATGTTTT 59.599 37.500 0.00 0.00 0.00 2.43
423 465 9.528018 TCAAGAGGTCAAATGTTTTGAATAAAC 57.472 29.630 4.37 0.00 0.00 2.01
426 468 9.883142 AGAGGTCAAATGTTTTGAATAAACAAA 57.117 25.926 7.11 0.00 42.57 2.83
456 498 3.904136 AAAAACTCTCAGGTTGCGATG 57.096 42.857 0.00 0.00 0.00 3.84
457 499 1.813513 AAACTCTCAGGTTGCGATGG 58.186 50.000 0.00 0.00 0.00 3.51
458 500 0.687354 AACTCTCAGGTTGCGATGGT 59.313 50.000 0.00 0.00 0.00 3.55
461 503 0.321564 TCTCAGGTTGCGATGGTTGG 60.322 55.000 0.00 0.00 0.00 3.77
466 508 1.371635 GTTGCGATGGTTGGTGCAC 60.372 57.895 8.80 8.80 37.01 4.57
495 537 2.676463 GCCTCACTTGTCAGCCTAGAAG 60.676 54.545 0.00 0.00 0.00 2.85
498 540 3.764434 CTCACTTGTCAGCCTAGAAGGTA 59.236 47.826 0.00 0.00 37.80 3.08
606 657 2.348998 CAGTGAAGGGCCGCTTCT 59.651 61.111 25.19 10.92 0.00 2.85
628 679 1.062505 ACAAAAGGAAAGGAAGGCCCA 60.063 47.619 0.00 0.00 37.41 5.36
646 697 1.683943 CAAACTGCGGGGATCATCAT 58.316 50.000 0.00 0.00 0.00 2.45
657 708 4.137543 GGGGATCATCATACCTGAACAAC 58.862 47.826 0.00 0.00 32.55 3.32
672 731 1.003839 CAACGACTGCTGGGCCTTA 60.004 57.895 4.53 0.00 0.00 2.69
687 746 2.312390 GCCTTAAACCCACCAAGTTGA 58.688 47.619 3.87 0.00 0.00 3.18
688 747 2.035449 GCCTTAAACCCACCAAGTTGAC 59.965 50.000 3.87 0.00 0.00 3.18
689 748 2.292292 CCTTAAACCCACCAAGTTGACG 59.708 50.000 3.87 0.00 0.00 4.35
710 769 1.597989 GTGGGCCATACGTGTACCA 59.402 57.895 10.70 0.00 0.00 3.25
721 780 5.452776 CCATACGTGTACCAGTCCATACAAT 60.453 44.000 0.00 0.00 33.23 2.71
722 781 6.239092 CCATACGTGTACCAGTCCATACAATA 60.239 42.308 0.00 0.00 33.23 1.90
725 784 4.377897 GTGTACCAGTCCATACAATAGCC 58.622 47.826 0.00 0.00 33.23 3.93
726 785 3.389983 TGTACCAGTCCATACAATAGCCC 59.610 47.826 0.00 0.00 0.00 5.19
727 786 1.774856 ACCAGTCCATACAATAGCCCC 59.225 52.381 0.00 0.00 0.00 5.80
728 787 1.073923 CCAGTCCATACAATAGCCCCC 59.926 57.143 0.00 0.00 0.00 5.40
758 882 1.444553 GCGACTGAACAGGACTCCG 60.445 63.158 6.76 3.50 0.00 4.63
777 901 1.471676 CGATTCCTGGTTCTTCCCGAG 60.472 57.143 0.00 0.00 34.77 4.63
816 1969 6.657117 TGAAGTGTAATACAATAGGCAAGCAA 59.343 34.615 0.00 0.00 0.00 3.91
823 1979 3.262420 ACAATAGGCAAGCAAGTAGTCG 58.738 45.455 0.00 0.00 0.00 4.18
885 2045 2.625737 CATCTGCACTCTTCGTGGAAT 58.374 47.619 0.00 0.00 43.71 3.01
924 2084 2.284684 CGCACAACAGATCGAGAAATCG 60.285 50.000 0.00 0.00 0.00 3.34
931 2091 1.751351 AGATCGAGAAATCGTGAGGCA 59.249 47.619 0.00 0.00 0.00 4.75
1035 2198 1.916651 CGAGTCGTCAAGAGCAATCTG 59.083 52.381 3.82 0.00 0.00 2.90
1213 2379 0.036306 GTTCCCGCCTTTCTTCCTCA 59.964 55.000 0.00 0.00 0.00 3.86
1311 2479 1.473257 GCGATGTGTTAGAGGCCATGA 60.473 52.381 5.01 0.00 0.00 3.07
1447 2616 2.698763 GGGGACGACGAGTGAGGTC 61.699 68.421 0.00 0.00 0.00 3.85
1552 2724 2.444256 GGAGGTCAAGGCGGGCTAT 61.444 63.158 3.84 0.00 0.00 2.97
2070 3504 1.812922 GCATGTCGTCTCTGCTGGG 60.813 63.158 0.00 0.00 33.15 4.45
2072 3506 1.610673 ATGTCGTCTCTGCTGGGGT 60.611 57.895 0.00 0.00 0.00 4.95
2265 3700 2.826128 GGTCTTTTTCCTGATGAACCCC 59.174 50.000 0.00 0.00 31.05 4.95
2406 3841 1.497991 CGCTGACGAGAAAGGACAAA 58.502 50.000 0.00 0.00 43.93 2.83
2486 3921 6.013379 TCTAGGATTGTAGGGATGCTTAGAG 58.987 44.000 0.00 0.00 0.00 2.43
2572 4014 1.955208 GCCGGATTGATGAACTGGGTT 60.955 52.381 5.05 0.00 0.00 4.11
2581 4023 3.383185 TGATGAACTGGGTTTGTTTGGAC 59.617 43.478 0.00 0.00 0.00 4.02
2582 4024 3.094484 TGAACTGGGTTTGTTTGGACT 57.906 42.857 0.00 0.00 0.00 3.85
2583 4025 3.436243 TGAACTGGGTTTGTTTGGACTT 58.564 40.909 0.00 0.00 0.00 3.01
2584 4026 3.835395 TGAACTGGGTTTGTTTGGACTTT 59.165 39.130 0.00 0.00 0.00 2.66
2585 4027 3.885724 ACTGGGTTTGTTTGGACTTTG 57.114 42.857 0.00 0.00 0.00 2.77
2586 4028 2.499693 ACTGGGTTTGTTTGGACTTTGG 59.500 45.455 0.00 0.00 0.00 3.28
2587 4029 2.763448 CTGGGTTTGTTTGGACTTTGGA 59.237 45.455 0.00 0.00 0.00 3.53
2691 4133 5.100259 CGCTAGTCAAATTTCTCCTTCGTA 58.900 41.667 0.00 0.00 0.00 3.43
2709 4151 3.954904 TCGTATAGCTTCTTCCTCTTGCT 59.045 43.478 0.00 0.00 37.72 3.91
2734 4176 2.125106 GACTCCGGCCGAATTGCT 60.125 61.111 30.73 1.48 0.00 3.91
2736 4178 2.125147 CTCCGGCCGAATTGCTGA 60.125 61.111 30.73 12.64 40.15 4.26
2750 4192 1.571955 TGCTGATCTCCTTGCTACCA 58.428 50.000 0.00 0.00 0.00 3.25
2770 4213 4.748144 CCCTCCCCAAGCTGCCAC 62.748 72.222 0.00 0.00 0.00 5.01
2817 5169 2.416638 CCATCCCTCCATCCTCTTCTT 58.583 52.381 0.00 0.00 0.00 2.52
2819 5171 2.948889 TCCCTCCATCCTCTTCTTCA 57.051 50.000 0.00 0.00 0.00 3.02
2820 5172 3.205519 TCCCTCCATCCTCTTCTTCAA 57.794 47.619 0.00 0.00 0.00 2.69
2821 5173 2.840651 TCCCTCCATCCTCTTCTTCAAC 59.159 50.000 0.00 0.00 0.00 3.18
2878 5231 0.248215 GGCTTGGCATCGTCAATTCG 60.248 55.000 0.00 0.00 0.00 3.34
2931 5284 4.507335 CCTCACCATCTTCTCTTCCCAAAA 60.507 45.833 0.00 0.00 0.00 2.44
2997 5350 9.601217 AGAATTTCACGTAAATGCTAATCTACT 57.399 29.630 8.41 0.00 41.06 2.57
3002 5355 7.646314 TCACGTAAATGCTAATCTACTACTCC 58.354 38.462 0.00 0.00 0.00 3.85
3003 5356 6.862090 CACGTAAATGCTAATCTACTACTCCC 59.138 42.308 0.00 0.00 0.00 4.30
3004 5357 6.776603 ACGTAAATGCTAATCTACTACTCCCT 59.223 38.462 0.00 0.00 0.00 4.20
3005 5358 7.040548 ACGTAAATGCTAATCTACTACTCCCTC 60.041 40.741 0.00 0.00 0.00 4.30
3006 5359 6.673839 AAATGCTAATCTACTACTCCCTCC 57.326 41.667 0.00 0.00 0.00 4.30
3007 5360 3.752665 TGCTAATCTACTACTCCCTCCG 58.247 50.000 0.00 0.00 0.00 4.63
3008 5361 3.137913 TGCTAATCTACTACTCCCTCCGT 59.862 47.826 0.00 0.00 0.00 4.69
3009 5362 3.752747 GCTAATCTACTACTCCCTCCGTC 59.247 52.174 0.00 0.00 0.00 4.79
3010 5363 2.955342 ATCTACTACTCCCTCCGTCC 57.045 55.000 0.00 0.00 0.00 4.79
3011 5364 0.842635 TCTACTACTCCCTCCGTCCC 59.157 60.000 0.00 0.00 0.00 4.46
3012 5365 0.549950 CTACTACTCCCTCCGTCCCA 59.450 60.000 0.00 0.00 0.00 4.37
3013 5366 1.145325 CTACTACTCCCTCCGTCCCAT 59.855 57.143 0.00 0.00 0.00 4.00
3014 5367 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
3015 5368 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
3016 5369 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
3017 5370 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
3018 5371 2.606378 ACTCCCTCCGTCCCATAATAC 58.394 52.381 0.00 0.00 0.00 1.89
3019 5372 2.090943 ACTCCCTCCGTCCCATAATACA 60.091 50.000 0.00 0.00 0.00 2.29
3020 5373 2.299297 CTCCCTCCGTCCCATAATACAC 59.701 54.545 0.00 0.00 0.00 2.90
3021 5374 2.043992 CCCTCCGTCCCATAATACACA 58.956 52.381 0.00 0.00 0.00 3.72
3022 5375 2.037251 CCCTCCGTCCCATAATACACAG 59.963 54.545 0.00 0.00 0.00 3.66
3023 5376 2.698797 CCTCCGTCCCATAATACACAGT 59.301 50.000 0.00 0.00 0.00 3.55
3024 5377 3.492656 CCTCCGTCCCATAATACACAGTG 60.493 52.174 0.00 0.00 0.00 3.66
3025 5378 3.101437 TCCGTCCCATAATACACAGTGT 58.899 45.455 11.87 11.87 0.00 3.55
3026 5379 4.279982 TCCGTCCCATAATACACAGTGTA 58.720 43.478 15.90 15.90 37.24 2.90
3027 5380 4.710865 TCCGTCCCATAATACACAGTGTAA 59.289 41.667 17.43 2.47 36.31 2.41
3028 5381 5.187381 TCCGTCCCATAATACACAGTGTAAA 59.813 40.000 17.43 9.25 36.31 2.01
3029 5382 5.875910 CCGTCCCATAATACACAGTGTAAAA 59.124 40.000 17.43 8.90 36.31 1.52
3030 5383 6.372103 CCGTCCCATAATACACAGTGTAAAAA 59.628 38.462 17.43 6.50 36.31 1.94
3050 5403 6.619801 AAAAACGCTCTTATATCATGGGAC 57.380 37.500 0.00 0.00 0.00 4.46
3051 5404 3.577649 ACGCTCTTATATCATGGGACG 57.422 47.619 0.00 0.00 0.00 4.79
3052 5405 2.231478 ACGCTCTTATATCATGGGACGG 59.769 50.000 0.00 0.00 0.00 4.79
3053 5406 2.492088 CGCTCTTATATCATGGGACGGA 59.508 50.000 0.00 0.00 0.00 4.69
3054 5407 3.428180 CGCTCTTATATCATGGGACGGAG 60.428 52.174 0.00 0.00 0.00 4.63
3055 5408 3.118956 GCTCTTATATCATGGGACGGAGG 60.119 52.174 0.00 0.00 0.00 4.30
3056 5409 3.441101 TCTTATATCATGGGACGGAGGG 58.559 50.000 0.00 0.00 0.00 4.30
3057 5410 3.076937 TCTTATATCATGGGACGGAGGGA 59.923 47.826 0.00 0.00 0.00 4.20
3058 5411 1.944177 ATATCATGGGACGGAGGGAG 58.056 55.000 0.00 0.00 0.00 4.30
3059 5412 0.561184 TATCATGGGACGGAGGGAGT 59.439 55.000 0.00 0.00 0.00 3.85
3060 5413 0.561184 ATCATGGGACGGAGGGAGTA 59.439 55.000 0.00 0.00 0.00 2.59
3061 5414 0.396695 TCATGGGACGGAGGGAGTAC 60.397 60.000 0.00 0.00 0.00 2.73
3062 5415 0.686441 CATGGGACGGAGGGAGTACA 60.686 60.000 0.00 0.00 0.00 2.90
3063 5416 0.264955 ATGGGACGGAGGGAGTACAT 59.735 55.000 0.00 0.00 0.00 2.29
3064 5417 0.396695 TGGGACGGAGGGAGTACATC 60.397 60.000 0.00 0.00 0.00 3.06
3065 5418 0.396695 GGGACGGAGGGAGTACATCA 60.397 60.000 0.00 0.00 0.00 3.07
3066 5419 1.481871 GGACGGAGGGAGTACATCAA 58.518 55.000 0.00 0.00 0.00 2.57
3073 5426 5.186198 CGGAGGGAGTACATCAAAGATTTT 58.814 41.667 0.00 0.00 0.00 1.82
3088 5441 8.166422 TCAAAGATTTTCCTAAACCTCTTCAC 57.834 34.615 0.00 0.00 0.00 3.18
3174 5527 8.378565 CCTATAGGAAAATCTTCATTGGAGCTA 58.621 37.037 14.11 0.00 37.39 3.32
3191 5544 5.180492 TGGAGCTATTTGGTTTGTAAGAACG 59.820 40.000 0.00 0.00 0.00 3.95
3200 5553 4.517453 TGGTTTGTAAGAACGGATTTCCTG 59.483 41.667 0.00 0.00 34.32 3.86
3201 5554 4.517832 GGTTTGTAAGAACGGATTTCCTGT 59.482 41.667 0.00 0.00 34.32 4.00
3263 5616 9.791801 ATTAGCACAAACCTTATGGAAAATTTT 57.208 25.926 2.28 2.28 37.04 1.82
3264 5617 7.495135 AGCACAAACCTTATGGAAAATTTTG 57.505 32.000 8.47 4.25 37.04 2.44
3296 5649 3.973206 TCGAATAGCACCTCTTTTCCA 57.027 42.857 0.00 0.00 31.59 3.53
3298 5651 4.000988 TCGAATAGCACCTCTTTTCCAAC 58.999 43.478 0.00 0.00 31.59 3.77
3300 5653 4.215399 CGAATAGCACCTCTTTTCCAACAA 59.785 41.667 0.00 0.00 31.59 2.83
3304 5657 4.503910 AGCACCTCTTTTCCAACAAAAAC 58.496 39.130 0.00 0.00 0.00 2.43
3312 5665 7.169158 TCTTTTCCAACAAAAACTGAGATGT 57.831 32.000 0.00 0.00 0.00 3.06
3315 5668 8.870160 TTTTCCAACAAAAACTGAGATGTATG 57.130 30.769 0.00 0.00 0.00 2.39
3361 5714 9.713684 ATGATATTCCTATCCTTTGAACCAAAA 57.286 29.630 0.00 0.00 34.03 2.44
3373 5726 2.359531 TGAACCAAAACAGGCCTTAACG 59.640 45.455 0.00 0.00 0.00 3.18
3437 5790 6.613679 TGTGGATAGAACATAGGACATACCAA 59.386 38.462 0.00 0.00 42.04 3.67
3446 5799 9.337396 GAACATAGGACATACCAATCACAAATA 57.663 33.333 0.00 0.00 42.04 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.846350 GCAAGTATATGCTTTCACAAGAAGT 58.154 36.000 2.97 0.00 43.06 3.01
27 28 5.997746 AGCATACTTTTCACAGAAGCAAGTA 59.002 36.000 6.54 6.54 35.09 2.24
34 35 6.655003 CCCTTAGAAGCATACTTTTCACAGAA 59.345 38.462 0.00 0.00 35.82 3.02
37 38 5.013704 TCCCCTTAGAAGCATACTTTTCACA 59.986 40.000 0.00 0.00 35.82 3.58
47 48 5.302823 GCACATATTTTCCCCTTAGAAGCAT 59.697 40.000 0.00 0.00 0.00 3.79
86 87 1.136252 CGTCCACAAGAAGCGAACATG 60.136 52.381 0.00 0.00 0.00 3.21
87 88 1.148310 CGTCCACAAGAAGCGAACAT 58.852 50.000 0.00 0.00 0.00 2.71
195 196 0.321298 AAATGGTAGCGGCGTTCACT 60.321 50.000 9.37 0.00 0.00 3.41
333 339 4.884744 TCGGGTCAAGACTTTTTCATGAAA 59.115 37.500 16.91 16.91 33.78 2.69
334 340 4.456535 TCGGGTCAAGACTTTTTCATGAA 58.543 39.130 3.38 3.38 33.78 2.57
336 342 6.494893 TTATCGGGTCAAGACTTTTTCATG 57.505 37.500 0.00 0.00 0.00 3.07
337 343 7.148069 GGATTTATCGGGTCAAGACTTTTTCAT 60.148 37.037 0.00 0.00 0.00 2.57
339 345 6.150474 TGGATTTATCGGGTCAAGACTTTTTC 59.850 38.462 0.00 0.00 0.00 2.29
342 348 5.174037 TGGATTTATCGGGTCAAGACTTT 57.826 39.130 0.00 0.00 0.00 2.66
367 408 5.294356 GTCCAAATCCCAAACTGTTTTACC 58.706 41.667 2.41 0.00 0.00 2.85
370 411 3.777522 TGGTCCAAATCCCAAACTGTTTT 59.222 39.130 2.41 0.00 0.00 2.43
374 415 1.269448 CGTGGTCCAAATCCCAAACTG 59.731 52.381 0.00 0.00 31.17 3.16
375 416 1.616159 CGTGGTCCAAATCCCAAACT 58.384 50.000 0.00 0.00 31.17 2.66
377 418 0.186386 ACCGTGGTCCAAATCCCAAA 59.814 50.000 0.00 0.00 31.17 3.28
380 421 0.250989 TGAACCGTGGTCCAAATCCC 60.251 55.000 0.00 0.00 0.00 3.85
391 433 2.878406 ACATTTGACCTCTTGAACCGTG 59.122 45.455 0.00 0.00 0.00 4.94
443 485 0.606401 ACCAACCATCGCAACCTGAG 60.606 55.000 0.00 0.00 0.00 3.35
444 486 0.888736 CACCAACCATCGCAACCTGA 60.889 55.000 0.00 0.00 0.00 3.86
452 494 1.153978 GCATGTGCACCAACCATCG 60.154 57.895 15.69 0.00 41.59 3.84
466 508 0.520404 GACAAGTGAGGCACTGCATG 59.480 55.000 2.82 0.00 44.62 4.06
472 514 0.321671 TAGGCTGACAAGTGAGGCAC 59.678 55.000 14.84 0.00 41.55 5.01
475 517 2.093764 CCTTCTAGGCTGACAAGTGAGG 60.094 54.545 0.00 0.00 0.00 3.86
476 518 2.564947 ACCTTCTAGGCTGACAAGTGAG 59.435 50.000 0.00 0.00 39.63 3.51
480 522 2.432510 CCCTACCTTCTAGGCTGACAAG 59.567 54.545 0.00 0.00 39.63 3.16
495 537 0.111639 TTGCAAAGGTCACCCCTACC 59.888 55.000 0.00 0.00 45.47 3.18
512 554 6.600882 TCACTAGTTAAGAGTTACCCCTTG 57.399 41.667 0.00 0.00 0.00 3.61
514 556 7.809880 AAATCACTAGTTAAGAGTTACCCCT 57.190 36.000 0.00 0.00 0.00 4.79
568 612 6.423905 CACTGCTAACAACAGCTTACTTTCTA 59.576 38.462 0.00 0.00 42.30 2.10
606 657 3.236047 GGGCCTTCCTTTCCTTTTGTTA 58.764 45.455 0.84 0.00 0.00 2.41
628 679 2.487265 GGTATGATGATCCCCGCAGTTT 60.487 50.000 0.00 0.00 0.00 2.66
637 688 4.508124 GTCGTTGTTCAGGTATGATGATCC 59.492 45.833 0.00 0.00 34.73 3.36
646 697 1.270094 CCAGCAGTCGTTGTTCAGGTA 60.270 52.381 0.00 0.00 0.00 3.08
657 708 1.305930 GGTTTAAGGCCCAGCAGTCG 61.306 60.000 0.00 0.00 0.00 4.18
672 731 1.099689 CACGTCAACTTGGTGGGTTT 58.900 50.000 0.00 0.00 0.00 3.27
679 738 2.551912 GCCCACCACGTCAACTTGG 61.552 63.158 4.26 4.26 40.70 3.61
703 762 4.377897 GGCTATTGTATGGACTGGTACAC 58.622 47.826 0.00 0.00 31.05 2.90
705 764 3.244457 GGGGCTATTGTATGGACTGGTAC 60.244 52.174 0.00 0.00 0.00 3.34
729 788 4.742201 CAGTCGCTGTCCCCCGTG 62.742 72.222 0.00 0.00 0.00 4.94
730 789 4.988716 TCAGTCGCTGTCCCCCGT 62.989 66.667 6.72 0.00 32.61 5.28
758 882 1.744114 GCTCGGGAAGAACCAGGAATC 60.744 57.143 0.00 0.00 41.20 2.52
777 901 6.605496 TTACACTTCAAATTTTAATCGCGC 57.395 33.333 0.00 0.00 0.00 6.86
816 1969 5.893897 AACGAAATTCCTACTCGACTACT 57.106 39.130 3.62 0.00 36.45 2.57
885 2045 0.323629 CGGTGCCTTGGAAACTCCTA 59.676 55.000 0.00 0.00 37.46 2.94
924 2084 1.127951 CGTACCGTGATTTTGCCTCAC 59.872 52.381 0.00 0.00 39.69 3.51
1071 2237 2.742372 GGTGCTGCCATCGTCGTT 60.742 61.111 0.00 0.00 37.17 3.85
1311 2479 0.463295 CCGCAGAAGCTGACCATGAT 60.463 55.000 0.00 0.00 39.10 2.45
1431 2600 2.479650 CGACCTCACTCGTCGTCC 59.520 66.667 2.34 0.00 46.17 4.79
1456 2628 2.432628 GGGAACGACCTGCTCACG 60.433 66.667 0.00 0.00 38.98 4.35
1552 2724 1.184431 TTACACCGGCGAAGTATCCA 58.816 50.000 9.30 0.00 0.00 3.41
2286 3721 3.423154 CGCACGGGCTCCAGAAAC 61.423 66.667 8.62 0.00 38.10 2.78
2512 3953 7.065803 GGTTATGCAGTCAATGTACAGTAACAT 59.934 37.037 0.33 1.89 41.87 2.71
2513 3954 6.370442 GGTTATGCAGTCAATGTACAGTAACA 59.630 38.462 0.33 0.00 0.00 2.41
2515 3956 6.370442 GTGGTTATGCAGTCAATGTACAGTAA 59.630 38.462 0.33 0.00 0.00 2.24
2572 4014 2.096248 AGCGTTCCAAAGTCCAAACAA 58.904 42.857 0.00 0.00 0.00 2.83
2583 4025 9.997482 GAAATATATGAAACTTTAGCGTTCCAA 57.003 29.630 0.00 0.00 0.00 3.53
2584 4026 9.168451 TGAAATATATGAAACTTTAGCGTTCCA 57.832 29.630 0.00 0.00 0.00 3.53
2585 4027 9.434559 GTGAAATATATGAAACTTTAGCGTTCC 57.565 33.333 0.00 0.00 0.00 3.62
2586 4028 9.982291 TGTGAAATATATGAAACTTTAGCGTTC 57.018 29.630 0.00 0.00 0.00 3.95
2635 4077 1.305623 CAGGGAATCCAGGCAGCTT 59.694 57.895 0.09 0.00 34.83 3.74
2691 4133 2.741228 CGCAGCAAGAGGAAGAAGCTAT 60.741 50.000 0.00 0.00 33.59 2.97
2734 4176 1.555075 GGTGTGGTAGCAAGGAGATCA 59.445 52.381 0.00 0.00 0.00 2.92
2736 4178 0.912486 GGGTGTGGTAGCAAGGAGAT 59.088 55.000 0.00 0.00 0.00 2.75
2750 4192 3.971702 GCAGCTTGGGGAGGGTGT 61.972 66.667 0.00 0.00 34.02 4.16
2770 4213 4.767255 GCGGCAGACCAGTGGAGG 62.767 72.222 18.40 5.62 34.57 4.30
2793 5139 1.773391 AGGATGGAGGGATGGCCAG 60.773 63.158 13.05 0.00 37.64 4.85
2800 5146 2.840651 GTTGAAGAAGAGGATGGAGGGA 59.159 50.000 0.00 0.00 0.00 4.20
2977 5330 7.255381 GGGAGTAGTAGATTAGCATTTACGTGA 60.255 40.741 0.00 0.00 0.00 4.35
2997 5350 3.140707 TGTATTATGGGACGGAGGGAGTA 59.859 47.826 0.00 0.00 0.00 2.59
2998 5351 2.090943 TGTATTATGGGACGGAGGGAGT 60.091 50.000 0.00 0.00 0.00 3.85
2999 5352 2.299297 GTGTATTATGGGACGGAGGGAG 59.701 54.545 0.00 0.00 0.00 4.30
3000 5353 2.322658 GTGTATTATGGGACGGAGGGA 58.677 52.381 0.00 0.00 0.00 4.20
3002 5355 2.698797 ACTGTGTATTATGGGACGGAGG 59.301 50.000 0.00 0.00 0.00 4.30
3003 5356 3.132289 ACACTGTGTATTATGGGACGGAG 59.868 47.826 12.53 0.00 0.00 4.63
3004 5357 3.101437 ACACTGTGTATTATGGGACGGA 58.899 45.455 12.53 0.00 0.00 4.69
3005 5358 3.536956 ACACTGTGTATTATGGGACGG 57.463 47.619 12.53 0.00 0.00 4.79
3006 5359 6.971527 TTTTACACTGTGTATTATGGGACG 57.028 37.500 20.31 0.00 32.20 4.79
3027 5380 5.236478 CGTCCCATGATATAAGAGCGTTTTT 59.764 40.000 0.00 0.00 0.00 1.94
3028 5381 4.750098 CGTCCCATGATATAAGAGCGTTTT 59.250 41.667 0.00 0.00 0.00 2.43
3029 5382 4.307432 CGTCCCATGATATAAGAGCGTTT 58.693 43.478 0.00 0.00 0.00 3.60
3030 5383 3.306088 CCGTCCCATGATATAAGAGCGTT 60.306 47.826 0.00 0.00 0.00 4.84
3031 5384 2.231478 CCGTCCCATGATATAAGAGCGT 59.769 50.000 0.00 0.00 0.00 5.07
3032 5385 2.492088 TCCGTCCCATGATATAAGAGCG 59.508 50.000 0.00 0.00 0.00 5.03
3033 5386 3.118956 CCTCCGTCCCATGATATAAGAGC 60.119 52.174 0.00 0.00 0.00 4.09
3034 5387 3.449018 CCCTCCGTCCCATGATATAAGAG 59.551 52.174 0.00 0.00 0.00 2.85
3035 5388 3.076937 TCCCTCCGTCCCATGATATAAGA 59.923 47.826 0.00 0.00 0.00 2.10
3036 5389 3.441101 TCCCTCCGTCCCATGATATAAG 58.559 50.000 0.00 0.00 0.00 1.73
3037 5390 3.181410 ACTCCCTCCGTCCCATGATATAA 60.181 47.826 0.00 0.00 0.00 0.98
3038 5391 2.382305 ACTCCCTCCGTCCCATGATATA 59.618 50.000 0.00 0.00 0.00 0.86
3039 5392 1.150135 ACTCCCTCCGTCCCATGATAT 59.850 52.381 0.00 0.00 0.00 1.63
3040 5393 0.561184 ACTCCCTCCGTCCCATGATA 59.439 55.000 0.00 0.00 0.00 2.15
3041 5394 0.561184 TACTCCCTCCGTCCCATGAT 59.439 55.000 0.00 0.00 0.00 2.45
3042 5395 0.396695 GTACTCCCTCCGTCCCATGA 60.397 60.000 0.00 0.00 0.00 3.07
3043 5396 0.686441 TGTACTCCCTCCGTCCCATG 60.686 60.000 0.00 0.00 0.00 3.66
3044 5397 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
3045 5398 0.396695 GATGTACTCCCTCCGTCCCA 60.397 60.000 0.00 0.00 0.00 4.37
3046 5399 0.396695 TGATGTACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
3047 5400 1.481871 TTGATGTACTCCCTCCGTCC 58.518 55.000 0.00 0.00 0.00 4.79
3048 5401 2.758979 TCTTTGATGTACTCCCTCCGTC 59.241 50.000 0.00 0.00 0.00 4.79
3049 5402 2.816411 TCTTTGATGTACTCCCTCCGT 58.184 47.619 0.00 0.00 0.00 4.69
3050 5403 4.408182 AATCTTTGATGTACTCCCTCCG 57.592 45.455 0.00 0.00 0.00 4.63
3051 5404 5.590663 GGAAAATCTTTGATGTACTCCCTCC 59.409 44.000 0.00 0.00 0.00 4.30
3052 5405 6.418946 AGGAAAATCTTTGATGTACTCCCTC 58.581 40.000 0.00 0.00 0.00 4.30
3053 5406 6.394345 AGGAAAATCTTTGATGTACTCCCT 57.606 37.500 0.00 0.00 0.00 4.20
3054 5407 8.459635 GTTTAGGAAAATCTTTGATGTACTCCC 58.540 37.037 0.00 0.00 0.00 4.30
3055 5408 8.459635 GGTTTAGGAAAATCTTTGATGTACTCC 58.540 37.037 0.00 0.00 0.00 3.85
3056 5409 9.232473 AGGTTTAGGAAAATCTTTGATGTACTC 57.768 33.333 0.00 0.00 31.79 2.59
3057 5410 9.232473 GAGGTTTAGGAAAATCTTTGATGTACT 57.768 33.333 0.00 0.00 36.14 2.73
3058 5411 9.232473 AGAGGTTTAGGAAAATCTTTGATGTAC 57.768 33.333 0.00 0.00 36.14 2.90
3059 5412 9.807921 AAGAGGTTTAGGAAAATCTTTGATGTA 57.192 29.630 0.00 0.00 36.14 2.29
3060 5413 8.712228 AAGAGGTTTAGGAAAATCTTTGATGT 57.288 30.769 0.00 0.00 36.14 3.06
3061 5414 8.796475 TGAAGAGGTTTAGGAAAATCTTTGATG 58.204 33.333 0.00 0.00 36.14 3.07
3062 5415 8.797438 GTGAAGAGGTTTAGGAAAATCTTTGAT 58.203 33.333 0.00 0.00 36.14 2.57
3063 5416 7.777910 TGTGAAGAGGTTTAGGAAAATCTTTGA 59.222 33.333 0.00 0.00 36.14 2.69
3064 5417 7.940850 TGTGAAGAGGTTTAGGAAAATCTTTG 58.059 34.615 0.00 0.00 36.14 2.77
3065 5418 8.712228 ATGTGAAGAGGTTTAGGAAAATCTTT 57.288 30.769 0.00 0.00 36.14 2.52
3066 5419 9.454859 CTATGTGAAGAGGTTTAGGAAAATCTT 57.545 33.333 0.00 0.00 36.14 2.40
3073 5426 6.681729 ACAACTATGTGAAGAGGTTTAGGA 57.318 37.500 0.00 0.00 38.69 2.94
3161 5514 6.029346 ACAAACCAAATAGCTCCAATGAAG 57.971 37.500 0.00 0.00 0.00 3.02
3174 5527 6.266786 AGGAAATCCGTTCTTACAAACCAAAT 59.733 34.615 0.00 0.00 42.08 2.32
3200 5553 6.046593 TGAAATGTGACGGATAATCCTACAC 58.953 40.000 0.00 0.00 39.14 2.90
3201 5554 6.228616 TGAAATGTGACGGATAATCCTACA 57.771 37.500 0.00 0.00 33.30 2.74
3243 5596 9.719355 GGATACAAAATTTTCCATAAGGTTTGT 57.281 29.630 0.00 7.53 40.00 2.83
3263 5616 5.335426 GGTGCTATTCGATTCGTAGGATACA 60.335 44.000 5.89 0.00 43.24 2.29
3264 5617 5.094134 GGTGCTATTCGATTCGTAGGATAC 58.906 45.833 5.89 1.16 38.50 2.24
3332 5685 9.392506 TGGTTCAAAGGATAGGAATATCATAGA 57.607 33.333 0.00 0.00 0.00 1.98
3361 5714 2.812011 GTTCATGAACGTTAAGGCCTGT 59.188 45.455 22.09 0.00 0.00 4.00
3373 5726 5.234329 TGTTCTTGACTTCTCGTTCATGAAC 59.766 40.000 25.68 25.68 42.46 3.18
3391 5744 4.221262 ACATTATGCATTGCCTGTGTTCTT 59.779 37.500 3.54 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.